From d351612cb7eba51cb1a029aef543addf6a2d552e Mon Sep 17 00:00:00 2001 From: Damien Goutte-Gattat Date: Thu, 12 Dec 2024 14:44:46 +0000 Subject: [PATCH 01/18] Customize OBO artefacts. Use a new command in the Uberon ROBOT plugin to produce "customized" OBO artefacts in which: * all "untranslatable" OWL axioms (owl-axioms tag) are stripped (they were already stripped before, this just changes the way we do it); * all GCI axioms are stripped (#2856); * when a class has several rdfs:comment annotations (which is not allowed in OBO), they are merged into a single annotation (#2847). --- src/ontology/cl-odk.yaml | 2 +- src/ontology/cl.Makefile | 34 ++++++++++++++++++++++++++++++++-- 2 files changed, 33 insertions(+), 3 deletions(-) diff --git a/src/ontology/cl-odk.yaml b/src/ontology/cl-odk.yaml index b29514270..68fbb337c 100644 --- a/src/ontology/cl-odk.yaml +++ b/src/ontology/cl-odk.yaml @@ -34,7 +34,7 @@ robot_plugins: - name: flybase mirror_from: https://github.com/FlyBase/flybase-robot-plugin/releases/download/flybase-robot-plugin-0.2.2/flybase.jar - name: uberon - mirror_from: https://github.com/gouttegd/uberon-robot-plugin/releases/download/uberon-robot-plugin-0.3.1/uberon.jar + mirror_from: https://github.com/gouttegd/uberon-robot-plugin/releases/download/uberon-robot-plugin-0.3.3/uberon.jar subset_group: products: - id: BDS_subset diff --git a/src/ontology/cl.Makefile b/src/ontology/cl.Makefile index 3357090f1..ba05e3b04 100644 --- a/src/ontology/cl.Makefile +++ b/src/ontology/cl.Makefile @@ -175,10 +175,10 @@ test: $(REPORTDIR)/taxon-constraint-check.txt # ---------------------------------------- .PHONY: obocheck -obocheck: $(SRC) +obocheck: $(SRC) | all_robot_plugins $(ROBOT) merge -i $(SRC) \ remove --base-iri $(URIBASE)/CL_ --axioms external --trim false \ - convert -f obo --check false -o $(TMPDIR)/cl-check.obo + uberon:obo-export --merge-comments --obo-output $(TMPDIR)/cl-check.obo fastobo-validator $(TMPDIR)/cl-check.obo test_obsolete: $(ONT).obo @@ -258,6 +258,36 @@ pattern_docs: $(ALL_PATTERN_FILES) -o ../../docs/patterns/ +# ---------------------------------------- +# CUSTOM OBO OUTPUT +# ---------------------------------------- +OBO_EXPORT_OPTIONS = --merge-comments --strip-gci-axioms --strip-owl-axioms + +$(SUBSETDIR)/%.obo: $(SUBSETDIR)/%.owl | all_robot_plugins + $(ROBOT) uberon:obo-export --input $< $(OBO_EXPORT_OPTIONS) --obo-output $@ + +$(ONT).obo: $(ONT).owl | all_robot_plugins + $(ROBOT) uberon:obo-export --input $< $(OBO_EXPORT_OPTIONS) --obo-output $@ + +$(ONT)-base.obo: $(ONT)-base.owl | all_robot_plugins + $(ROBOT) uberon:obo-export --input $< $(OBO_EXPORT_OPTIONS) --obo-output $@ + +$(ONT)-full.obo: $(ONT)-full.owl | all_robot_plugins + $(ROBOT) uberon:obo-export --input $< $(OBO_EXPORT_OPTIONS) --obo-output $@ + +$(ONT)-simple.obo: $(ONT)-simple.owl | all_robot_plugins + $(ROBOT) uberon:obo-export --input $< $(OBO_EXPORT_OPTIONS) --obo-output $@ + +$(ONT)-basic.obo: $(ONT)-basic.owl | all_robot_plugins + $(ROBOT) uberon:obo-export --input $< $(OBO_EXPORT_OPTIONS) --obo-output $@ + +$(ONT)-non-classified.obo: $(ONT)-non-classified.owl | all_robot_plugins + $(ROBOT) uberon:obo-export --input $< $(OBO_EXPORT_OPTIONS) --obo-output $@ + +cl-plus.obo: cl-plus.owl | all_robot_plugins + $(ROBOT) uberon:obo-export --input $< $(OBO_EXPORT_OPTIONS) --obo-output $@ + + # ---------------------------------------- # DIFFS/REPORTS # ---------------------------------------- From 1fec99191a088e72e71150bae75290413902347d Mon Sep 17 00:00:00 2001 From: Damien Goutte-Gattat Date: Thu, 12 Dec 2024 15:18:25 +0000 Subject: [PATCH 02/18] Commit re-generated Makefile. --- src/ontology/Makefile | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/src/ontology/Makefile b/src/ontology/Makefile index 1ddc04e43..4d1a760b0 100644 --- a/src/ontology/Makefile +++ b/src/ontology/Makefile @@ -1,7 +1,7 @@ # ---------------------------------------- # Makefile for cl # Generated using ontology-development-kit -# ODK Version: v1.5.3 +# ODK Version: v1.5.4 # ---------------------------------------- # IMPORTANT: DO NOT EDIT THIS FILE. To override default make goals, use cl.Makefile instead @@ -10,7 +10,7 @@ # More information: https://github.com/INCATools/ontology-development-kit/ # Fingerprint of the configuration file when this Makefile was last generated -CONFIG_HASH= fe26dd231ab531dab5609c794de598d2a28083168916941a3276fe672cfe8be2 +CONFIG_HASH= b8fef012ac2d7e3df8e8871cfa305bf6b9d5b6a56394a042bdf48a83d3d2e019 # ---------------------------------------- @@ -46,7 +46,7 @@ REPORT_PROFILE_OPTS = OBO_FORMAT_OPTIONS = SPARQL_VALIDATION_CHECKS = equivalent-classes owldef-self-reference nolabels pmid-not-dbxref obsolete-replaced_by obsolete-alt-id orcid-contributor illegal-annotation-property label-synonym-polysemy illegal-date def-not-only-xref id-format SPARQL_EXPORTS = cl_terms cl-edges cl-synonyms cl-xrefs cl-def-xrefs -ODK_VERSION_MAKEFILE = v1.5.3 +ODK_VERSION_MAKEFILE = v1.5.4 TODAY ?= $(shell date +%Y-%m-%d) OBODATE ?= $(shell date +'%d:%m:%Y %H:%M') @@ -156,7 +156,7 @@ $(ROBOT_PLUGINS_DIRECTORY)/flybase.jar: curl -L -o $@ https://github.com/FlyBase/flybase-robot-plugin/releases/download/flybase-robot-plugin-0.2.2/flybase.jar $(ROBOT_PLUGINS_DIRECTORY)/uberon.jar: - curl -L -o $@ https://github.com/gouttegd/uberon-robot-plugin/releases/download/uberon-robot-plugin-0.3.1/uberon.jar + curl -L -o $@ https://github.com/gouttegd/uberon-robot-plugin/releases/download/uberon-robot-plugin-0.3.3/uberon.jar # ---------------------------------------- From e9bf7bd9b0d6a069b045df52fedf7f1793b33b13 Mon Sep 17 00:00:00 2001 From: Aleix Puig <94959119+aleixpuigb@users.noreply.github.com> Date: Tue, 17 Dec 2024 12:07:01 +0000 Subject: [PATCH 03/18] Fixes #2855 NTR limbal epithelial stem cell (#2857) * Update cl-edit.owl - Mesothelial cells of gut now part of serosa - tidying up partonomy for intestinal lining - Fixed brush border on enteroycte * Update cl-edit.owl partial fix to missing classifications under intestinal epithelial cell * Update cl-edit.owl * Update cl-edit.owl * Fixes #2674 #2825 * Update cl-edit.owl * Update cl-edit.owl moved colon goblet cell to po colonic epithlium * Fixed 'early colonocyte' Changing the partonomy from colon to colonic epithelium. * Fixes #2855 NTR limbal epithelial stem cell Fixes #2855 NTR limbal epithelial stem cell * Add SubclassOf 'epithelial fate stem cell' --------- Co-authored-by: dosumis Co-authored-by: CEastwood <116108977+Caroline-99@users.noreply.github.com> Co-authored-by: Caroline Eastwood --- src/ontology/cl-edit.owl | 18 ++++++++++++++++++ src/ontology/imports/uberon_terms.txt | 3 ++- 2 files changed, 20 insertions(+), 1 deletion(-) diff --git a/src/ontology/cl-edit.owl b/src/ontology/cl-edit.owl index 390cf6898..fd985cee1 100644 --- a/src/ontology/cl-edit.owl +++ b/src/ontology/cl-edit.owl @@ -3046,6 +3046,7 @@ Declaration(Class(obo:CL_4033088)) Declaration(Class(obo:CL_4033089)) Declaration(Class(obo:CL_4033090)) Declaration(Class(obo:CL_4033091)) +Declaration(Class(obo:CL_4033093)) Declaration(Class(obo:CL_4040000)) Declaration(Class(obo:CL_4040001)) Declaration(Class(obo:CL_4040002)) @@ -3241,6 +3242,7 @@ Declaration(Class(obo:UBERON_0000156)) Declaration(Class(obo:UBERON_0000157)) Declaration(Class(obo:UBERON_0000371)) Declaration(Class(obo:UBERON_0000424)) +Declaration(Class(obo:UBERON_0000482)) Declaration(Class(obo:UBERON_0001004)) Declaration(Class(obo:UBERON_0001335)) Declaration(Class(obo:UBERON_0001786)) @@ -32369,6 +32371,22 @@ AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:37124720") oboInOwl:hasE AnnotationAssertion(rdfs:label obo:CL_4033091 "glycinergic-GABAergic amacrine cell") EquivalentClasses(obo:CL_4033091 ObjectIntersectionOf(obo:CL_0000561 ObjectSomeValuesFrom(obo:RO_0002215 obo:GO_0061534) ObjectSomeValuesFrom(obo:RO_0002215 obo:GO_0061537))) +# Class: obo:CL_4033093 (limbal epithelial stem cell of cornea) + +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:20614614") Annotation(oboInOwl:hasDbXref "PMID:29105366") Annotation(oboInOwl:hasDbXref "PMID:36983561") Annotation(oboInOwl:hasDbXref "PMID:37768272") obo:IAO_0000115 obo:CL_4033093 "A stem cell that is part of the corneo-scleral limbus. This cell type resides at the basal layer of the epithelium and has a small size and high nuclear to cytoplasmatic ratio (Secker and Daniels, 2009). A limbal stem cell is responsible for corneal epithelial renewal and repair (Li et al., 2023), and to help maintain a clear corneal surface by preventing conjunctival epithelial cells from migrating onto the cornea (Wang et al., 2023).") +AnnotationAssertion(terms:contributor obo:CL_4033093 ) +AnnotationAssertion(terms:contributor obo:CL_4033093 ) +AnnotationAssertion(terms:date obo:CL_4033093 "2024-12-11T13:59:19Z"^^xsd:dateTime) +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:20614614") oboInOwl:hasExactSynonym obo:CL_4033093 "limbal epithelial stem cell") +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:17562792") oboInOwl:hasExactSynonym obo:CL_4033093 "limbal stem cell") +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:20614614") Annotation(oboInOwl:hasSynonymType obo:OMO_0003000) oboInOwl:hasRelatedSynonym obo:CL_4033093 "LESC") +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:36983561") Annotation(oboInOwl:hasSynonymType obo:OMO_0003000) oboInOwl:hasRelatedSynonym obo:CL_4033093 "LSC") +AnnotationAssertion(rdfs:label obo:CL_4033093 "limbal epithelial stem cell of cornea") +EquivalentClasses(obo:CL_4033093 ObjectIntersectionOf(obo:CL_0000034 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0006761))) +SubClassOf(obo:CL_4033093 obo:CL_0000036) +SubClassOf(obo:CL_4033093 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0000482)) +SubClassOf(obo:CL_4033093 ObjectSomeValuesFrom(obo:RO_0002203 obo:CL_0000575)) + # Class: obo:CL_4040000 (glial restricted tripotential precursor cell) AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:10719353") obo:IAO_0000115 obo:CL_4040000 "A glial precursor cell that generates oligodendrocytes and type-1 and type-2 astrocytes. It has been shown in some mammals that this cell type may express A2B5, nestin, FGFR-1, FGFR-2, FGFR-3, PLP, and DM-20 antigens. Unlike oligodendrocyte precursor cell, it does not initially express PDGFR-alpha and can differentiate into both type-1 and type-2 astrocytes.") diff --git a/src/ontology/imports/uberon_terms.txt b/src/ontology/imports/uberon_terms.txt index ac467ed38..985ee0a96 100644 --- a/src/ontology/imports/uberon_terms.txt +++ b/src/ontology/imports/uberon_terms.txt @@ -59,4 +59,5 @@ UBERON:0013740 UBERON:0012186 UBERON:0000156 UBERON:0000157 -UBERON:0003884 \ No newline at end of file +UBERON:0003884 +UBERON:0000482 \ No newline at end of file From a0de94a6d9d0d6100bf98dca3163100420392839 Mon Sep 17 00:00:00 2001 From: Alida Avola <81253886+AvolaAmg@users.noreply.github.com> Date: Wed, 18 Dec 2024 09:46:48 +0000 Subject: [PATCH 04/18] Merge cns interneuron interneuron term (#2686) * Merge CNS interneuron with interneuron Fixes #2685 * merge CNS interneuron Fixes #2685 * Update cl-edit.owl * Update cl-edit.owl * Update cl-edit.owl * Fixing QC fail --------- Co-authored-by: CEastwood <116108977+Caroline-99@users.noreply.github.com> --- src/ontology/cl-edit.owl | 18 ++++++------------ src/ontology/components/hra_subset.owl | 9 +++++++++ src/ontology/components/mappings.owl | 18 ++++++++---------- 3 files changed, 23 insertions(+), 22 deletions(-) diff --git a/src/ontology/cl-edit.owl b/src/ontology/cl-edit.owl index fd985cee1..970a222fd 100644 --- a/src/ontology/cl-edit.owl +++ b/src/ontology/cl-edit.owl @@ -449,7 +449,6 @@ Declaration(Class(obo:CL_0000398)) Declaration(Class(obo:CL_0000399)) Declaration(Class(obo:CL_0000400)) Declaration(Class(obo:CL_0000401)) -Declaration(Class(obo:CL_0000402)) Declaration(Class(obo:CL_0000403)) Declaration(Class(obo:CL_0000404)) Declaration(Class(obo:CL_0000405)) @@ -4565,8 +4564,10 @@ AnnotationAssertion(Annotation(oboInOwl:hasDbXref "GOC:tfm") Annotation(oboInOwl AnnotationAssertion(oboInOwl:hasDbXref obo:CL_0000099 "BTO:0003811") AnnotationAssertion(oboInOwl:hasDbXref obo:CL_0000099 "FMA:67313") AnnotationAssertion(oboInOwl:hasDbXref obo:CL_0000099 "WBbt:0005113") +AnnotationAssertion(oboInOwl:hasRelatedSynonym obo:CL_0000099 "CNS interneuron") AnnotationAssertion(rdfs:label obo:CL_0000099 "interneuron") SubClassOf(obo:CL_0000099 obo:CL_0000540) +SubClassOf(obo:CL_0000099 ObjectSomeValuesFrom(obo:RO_0002100 obo:UBERON_0001017)) # Class: obo:CL_0000100 (motor neuron) @@ -7034,13 +7035,6 @@ AnnotationAssertion(rdfs:comment obo:CL_0000401 "Obsoleted as plasmatocytes are AnnotationAssertion(rdfs:label obo:CL_0000401 "obsolete macrophage (sensu Diptera)") AnnotationAssertion(owl:deprecated obo:CL_0000401 "true"^^xsd:boolean) -# Class: obo:CL_0000402 (CNS interneuron) - -AnnotationAssertion(Annotation(oboInOwl:hasDbXref "doi:10.1016/B978-0-12-817424-1.00001-X") obo:IAO_0000115 obo:CL_0000402 "An interneuron that has its cell body in a central nervous system.") -AnnotationAssertion(rdfs:comment obo:CL_0000402 "Interneurons are commonly described as being only found in the central nervous system. However, in CL we define 'interneuron' more broadly as any neuron that is neither a motor neuron nor a sensory neuron, regardless of its location, so we need this term to refer strictly to interneurons of the central nervous system.") -AnnotationAssertion(rdfs:label obo:CL_0000402 "CNS interneuron") -EquivalentClasses(obo:CL_0000402 ObjectIntersectionOf(obo:CL_0000099 ObjectSomeValuesFrom(obo:RO_0002100 obo:UBERON_0001017))) - # Class: obo:CL_0000403 (obo:CL_0000403) AnnotationAssertion(obo:IAO_0000231 obo:CL_0000403 obo:IAO_0000227) @@ -7063,7 +7057,7 @@ AnnotationAssertion(owl:deprecated obo:CL_0000405 "true"^^xsd:boolean) # Class: obo:CL_0000406 (CNS short range interneuron) AnnotationAssertion(rdfs:label obo:CL_0000406 "CNS short range interneuron") -SubClassOf(obo:CL_0000406 obo:CL_0000402) +SubClassOf(obo:CL_0000406 obo:CL_0000099) # Class: obo:CL_0000407 (scolopidial ligament cell) @@ -7091,7 +7085,7 @@ AnnotationAssertion(owl:deprecated obo:CL_0000409 "true"^^xsd:boolean) # Class: obo:CL_0000410 (CNS long range interneuron) AnnotationAssertion(rdfs:label obo:CL_0000410 "CNS long range interneuron") -SubClassOf(obo:CL_0000410 obo:CL_0000402) +SubClassOf(obo:CL_0000410 obo:CL_0000099) # Class: obo:CL_0000411 (Caenorhabditis hypodermal cell) @@ -21366,7 +21360,7 @@ AnnotationAssertion(oboInOwl:hasOBONamespace obo:CL_0004001 "cell") AnnotationAssertion(oboInOwl:id obo:CL_0004001 "CL:0004001") AnnotationAssertion(rdfs:comment obo:CL_0004001 "Local interneurons form the category of interneurons whose axon stays entirely within the gray matter region where the cell body resides (Swanson, 2003, p. 245; Bota and Swanson, 2007, Fig. 3).") AnnotationAssertion(rdfs:label obo:CL_0004001 "local interneuron") -SubClassOf(obo:CL_0004001 obo:CL_0000402) +SubClassOf(obo:CL_0004001 obo:CL_0000099) SubClassOf(obo:CL_0004001 ObjectSomeValuesFrom(obo:RO_0002100 obo:UBERON_0002020)) # Class: obo:CL_0004115 (retinal ganglion cell B) @@ -22036,7 +22030,7 @@ AnnotationAssertion(Annotation(oboInOwl:hasDbXref "CL:CVS") obo:IAO_0000115 obo: AnnotationAssertion(rdfs:comment obo:CL_0005000 "Is_a interneuron, part_of UBERON:0002240.") AnnotationAssertion(rdfs:label obo:CL_0005000 "spinal cord interneuron") EquivalentClasses(obo:CL_0005000 ObjectIntersectionOf(obo:CL_0000099 ObjectSomeValuesFrom(obo:RO_0002100 obo:UBERON_0002240))) -SubClassOf(Annotation(oboInOwl:is_inferred "true") obo:CL_0005000 obo:CL_0000402) +SubClassOf(Annotation(oboInOwl:is_inferred "true") obo:CL_0005000 obo:CL_0000099) # Class: obo:CL_0005001 (iridoblast) diff --git a/src/ontology/components/hra_subset.owl b/src/ontology/components/hra_subset.owl index 9adfdda14..1f692515d 100644 --- a/src/ontology/components/hra_subset.owl +++ b/src/ontology/components/hra_subset.owl @@ -23,6 +23,12 @@ + + + + + + @@ -553,8 +559,11 @@ + + https://github.com/obophenotype/cell-ontology/pull/2686 + true diff --git a/src/ontology/components/mappings.owl b/src/ontology/components/mappings.owl index 38aa1c55c..ba5dc156c 100644 --- a/src/ontology/components/mappings.owl +++ b/src/ontology/components/mappings.owl @@ -645,6 +645,7 @@ FBbt:00005125 ZFA:0009051 + ZFA:0009191 @@ -658,6 +659,12 @@ ZFA:0009051 + + + + ZFA:0009191 + + FBbt:00005123 ZFA:0009052 @@ -2006,15 +2013,6 @@ FBbt:00001687 - - ZFA:0009191 - - - - - ZFA:0009191 - - ZFA:0009193 @@ -4563,5 +4561,5 @@ - + From ef3dee1c74b47a65398f5d15891e0a40fc67d18c Mon Sep 17 00:00:00 2001 From: CEastwood <116108977+Caroline-99@users.noreply.github.com> Date: Thu, 19 Dec 2024 14:54:37 +0000 Subject: [PATCH 05/18] Fixes #2749 NTR- Respiratory airway secretory cell (#2867) * Fixes #2749 Added a new term with textual and logical definitions * fixed synonym --- src/ontology/cl-edit.owl | 13 +++++++++++++ 1 file changed, 13 insertions(+) diff --git a/src/ontology/cl-edit.owl b/src/ontology/cl-edit.owl index 970a222fd..6c48c63fa 100644 --- a/src/ontology/cl-edit.owl +++ b/src/ontology/cl-edit.owl @@ -3138,6 +3138,7 @@ Declaration(Class(obo:CL_4052027)) Declaration(Class(obo:CL_4052028)) Declaration(Class(obo:CL_4052029)) Declaration(Class(obo:CL_4052030)) +Declaration(Class(obo:CL_4052031)) Declaration(Class(obo:CL_4052048)) Declaration(Class(obo:CL_4052049)) Declaration(Class(obo:CP_0000000)) @@ -33406,6 +33407,18 @@ EquivalentClasses(obo:CL_4052030 ObjectIntersectionOf(obo:CL_0000057 ObjectSomeV SubClassOf(obo:CL_4052030 ObjectSomeValuesFrom(obo:RO_0002215 obo:GO_0001816)) SubClassOf(obo:CL_4052030 ObjectSomeValuesFrom(obo:RO_0002215 obo:GO_0070278)) +# Class: obo:CL_4052031 (respiratory airway secretory cell) + +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:35355013") Annotation(oboInOwl:hasDbXref "PMID:36796082") obo:IAO_0000115 obo:CL_4052031 "A secretory epithelial cell of the respiratory and terminal bronchioles.") +AnnotationAssertion(terms:contributor obo:CL_4052031 ) +AnnotationAssertion(terms:date obo:CL_4052031 "2024-11-29T16:14:31Z"^^xsd:dateTime) +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:36796082") Annotation(oboInOwl:hasSynonymType obo:OMO_0003000) oboInOwl:hasRelatedSynonym obo:CL_4052031 "RAS cell") +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:35355018") oboInOwl:hasRelatedSynonym obo:CL_4052031 "terminal and respiratory bronchioles secretory cell") +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:35355013") Annotation(oboInOwl:hasDbXref "PMID:36796082") rdfs:comment obo:CL_4052031 "The respiratory airway secretory cell is cuboidal and has a unique transcriptomic profile compared to other epithelial cells in the same region. In humans, it functions as a multipotent progenitor, capable of regenerating alveolar type 2 (AT2) cells.") +AnnotationAssertion(rdfs:label obo:CL_4052031 "respiratory airway secretory cell") +SubClassOf(obo:CL_4052031 obo:CL_1100001) +SubClassOf(obo:CL_4052031 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0002051)) + # Class: obo:CL_4052048 (intercalated cell of salivary gland) AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:30855909") Annotation(oboInOwl:hasDbXref "PMID:35799078") Annotation(oboInOwl:hasDbXref "PMID:36726292") Annotation(oboInOwl:hasDbXref "PMID:37724716") obo:IAO_0000115 obo:CL_4052048 "A cuboidal epithelial cell that is part of the intercalated duct of salivary gland. This cell expresses proteins commonly associated with acinar cells and displays calcium signaling characteristics similar to secretory cells, indicating an active role in the secretory process rather than ion reabsorption.") From e9b91088b6a07a54c72ccc492f3808ce0773ee32 Mon Sep 17 00:00:00 2001 From: Aleix Puig <94959119+aleixpuigb@users.noreply.github.com> Date: Fri, 20 Dec 2024 16:58:01 +0100 Subject: [PATCH 06/18] Addresses #2786 NTR CD57-positive enterocyte (#2847) * Addresses #2786 NTR CD57-positive enterocyte Fixes #2786 NTR CD57-positive enterocyte * Fixes typo --------- Co-authored-by: CEastwood <116108977+Caroline-99@users.noreply.github.com> --- src/mappings/fbbt.sssom.tsv | 24 +- src/mappings/zfa.sssom.tsv | 14 +- src/ontology/cl-edit.owl | 21 +- src/ontology/components/cellxgene_subset.owl | 640 +++- src/ontology/components/clm-cl.owl | 2734 +++++++++++++++++- src/ontology/imports/merged_import.owl | 323 ++- src/ontology/imports/pr_terms.txt | 3 +- src/templates/cellxgene_subset.tsv | 1404 +++++---- 8 files changed, 4350 insertions(+), 813 deletions(-) diff --git a/src/mappings/fbbt.sssom.tsv b/src/mappings/fbbt.sssom.tsv index ae3ff68eb..f88df7801 100644 --- a/src/mappings/fbbt.sssom.tsv +++ b/src/mappings/fbbt.sssom.tsv @@ -1,17 +1,17 @@ #curie_map: -# CL: "http://purl.obolibrary.org/obo/CL_" -# FBbt: "http://purl.obolibrary.org/obo/FBbt_" -# ORCID: "https://orcid.org/" -# obo: "http://purl.obolibrary.org/obo/" -#mapping_set_id: "http://purl.obolibrary.org/obo/fbbt/fbbt-mappings.sssom.tsv" -#mapping_set_description: "Mappings between the Drosophila Anatomy Ontology and foreign ontologies." +# CL: http://purl.obolibrary.org/obo/CL_ +# FBbt: http://purl.obolibrary.org/obo/FBbt_ +# ORCID: https://orcid.org/ +# obo: http://purl.obolibrary.org/obo/ +#mapping_set_id: http://purl.obolibrary.org/obo/fbbt/fbbt-mappings.sssom.tsv +#mapping_set_description: Mappings between the Drosophila Anatomy Ontology and foreign ontologies. #creator_id: -# - "ORCID:0000-0002-1373-1705" -# - "ORCID:0000-0002-6095-8718" -#license: "https://creativecommons.org/licenses/by/4.0/" -#subject_source: "obo:fbbt.owl" -#object_source: "obo:cl.owl" -#mapping_date: "2024-07-12" +# - ORCID:0000-0002-1373-1705 +# - ORCID:0000-0002-6095-8718 +#license: https://creativecommons.org/licenses/by/4.0/ +#subject_source: obo:fbbt.owl +#object_source: obo:cl.owl +#mapping_date: 2024-07-12 subject_id subject_label predicate_id object_id object_label mapping_justification FBbt:00000092 primordial germ cell semapv:crossSpeciesExactMatch CL:0000301 pole cell semapv:ManualMappingCuration FBbt:00000124 epithelial cell semapv:crossSpeciesExactMatch CL:0000066 epithelial cell semapv:ManualMappingCuration diff --git a/src/mappings/zfa.sssom.tsv b/src/mappings/zfa.sssom.tsv index 4b142d1ee..918df4335 100644 --- a/src/mappings/zfa.sssom.tsv +++ b/src/mappings/zfa.sssom.tsv @@ -1,10 +1,10 @@ #curie_map: -# CL: "http://purl.obolibrary.org/obo/CL_" -# ZFA: "http://purl.obolibrary.org/obo/ZFA_" -#mapping_set_id: "http://purl.obolibrary.org/obo/zfa/zfa.sssom.tsv" -#license: "https://creativecommons.org/licenses/by/3.0/" -#subject_source: "http://purl.obolibrary.org/obo/zfa.owl" -#object_source: "http://purl.obolibrary.org/obo/cl.owl" +# CL: http://purl.obolibrary.org/obo/CL_ +# ZFA: http://purl.obolibrary.org/obo/ZFA_ +#mapping_set_id: http://purl.obolibrary.org/obo/zfa/zfa.sssom.tsv +#license: https://creativecommons.org/licenses/by/3.0/ +#subject_source: http://purl.obolibrary.org/obo/zfa.owl +#object_source: http://purl.obolibrary.org/obo/cl.owl subject_id subject_label predicate_id object_id object_label mapping_justification ZFA:0000003 adaxial cell semapv:crossSpeciesExactMatch CL:0007016 adaxial cell semapv:UnspecifiedMatching ZFA:0000084 yolk semapv:crossSpeciesExactMatch CL:0000428 yolk cell semapv:UnspecifiedMatching @@ -20,7 +20,7 @@ ZFA:0005238 juxtaglomerular cell semapv:crossSpeciesExactMatch CL:0000648 kidney ZFA:0005239 micropylar cell semapv:crossSpeciesExactMatch CL:0007022 micropylar cell semapv:UnspecifiedMatching ZFA:0005240 Kolmer-Agduhr neuron semapv:crossSpeciesExactMatch CL:0005007 Kolmer-Agduhr neuron semapv:UnspecifiedMatching ZFA:0005241 polychromatophilic erythroblast semapv:crossSpeciesExactMatch CL:0000550 polychromatophilic erythroblast semapv:UnspecifiedMatching -ZFA:0005242 multi-ciliated epithelial cell semapv:crossSpeciesExactMatch CL:0005012 multi-ciliated epithelial cell semapv:UnspecifiedMatching +ZFA:0005242 multi-ciliated epithelial cell semapv:crossSpeciesExactMatch CL:0005012 multiciliated epithelial cell semapv:UnspecifiedMatching ZFA:0005243 single ciliated epithelial cell semapv:crossSpeciesExactMatch CL:0005013 single ciliated epithelial cell semapv:UnspecifiedMatching ZFA:0005244 auditory epithelial support cell semapv:crossSpeciesExactMatch CL:0005014 auditory epithelial supporting cell semapv:UnspecifiedMatching ZFA:0005245 xanthoblast semapv:crossSpeciesExactMatch CL:0005002 xanthoblast semapv:UnspecifiedMatching diff --git a/src/ontology/cl-edit.owl b/src/ontology/cl-edit.owl index 6c48c63fa..7ba3fe301 100644 --- a/src/ontology/cl-edit.owl +++ b/src/ontology/cl-edit.owl @@ -3045,6 +3045,7 @@ Declaration(Class(obo:CL_4033088)) Declaration(Class(obo:CL_4033089)) Declaration(Class(obo:CL_4033090)) Declaration(Class(obo:CL_4033091)) +Declaration(Class(obo:CL_4033092)) Declaration(Class(obo:CL_4033093)) Declaration(Class(obo:CL_4040000)) Declaration(Class(obo:CL_4040001)) @@ -3381,7 +3382,7 @@ AnnotationAssertion(rdfs:label obo:IAO_0000115 "definition") AnnotationAssertion(rdfs:label obo:IAO_0000424 "expand expression to") -# Annotation Property: obo:IAO_0000700 (preferred_root) +# Annotation Property: obo:IAO_0000700 (has ontology root term) AnnotationAssertion(rdfs:label obo:IAO_0000700 "preferred_root") @@ -3467,15 +3468,15 @@ AnnotationAssertion(rdfs:label oboInOwl:consider "consider") AnnotationAssertion(rdfs:label oboInOwl:hasBroadSynonym "has_broad_synonym") -# Annotation Property: oboInOwl:hasDbXref (database_cross_reference) +# Annotation Property: oboInOwl:hasDbXref (has cross-reference) AnnotationAssertion(rdfs:label oboInOwl:hasDbXref "database_cross_reference") -# Annotation Property: oboInOwl:hasExactSynonym (has_exact_synonym) +# Annotation Property: oboInOwl:hasExactSynonym (has exact synonym) AnnotationAssertion(rdfs:label oboInOwl:hasExactSynonym "has_exact_synonym") -# Annotation Property: oboInOwl:hasNarrowSynonym (has_narrow_synonym) +# Annotation Property: oboInOwl:hasNarrowSynonym (has narrow synonym) AnnotationAssertion(rdfs:label oboInOwl:hasNarrowSynonym "has_narrow_synonym") @@ -32366,6 +32367,18 @@ AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:37124720") oboInOwl:hasE AnnotationAssertion(rdfs:label obo:CL_4033091 "glycinergic-GABAergic amacrine cell") EquivalentClasses(obo:CL_4033091 ObjectIntersectionOf(obo:CL_0000561 ObjectSomeValuesFrom(obo:RO_0002215 obo:GO_0061534) ObjectSomeValuesFrom(obo:RO_0002215 obo:GO_0061537))) +# Class: obo:CL_4033092 (CD57-positive enterocyte) + +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:37468586") obo:IAO_0000115 obo:CL_4033092 "An enterocyte that is part of a duodenal epithelium and expresses beta-1,3-glucuronyltransferase 1 (B3GAT1), also known as CD57 or HNK-1.") +AnnotationAssertion(terms:contributor obo:CL_4033092 ) +AnnotationAssertion(terms:contributor obo:CL_4033092 ) +AnnotationAssertion(terms:contributor obo:CL_4033092 ) +AnnotationAssertion(terms:date obo:CL_4033092 "2024-12-06T14:32:49Z"^^xsd:dateTime) +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:37468586") oboInOwl:hasExactSynonym obo:CL_4033092 "CD57+ enterocyte") +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:37468586") rdfs:comment obo:CL_4033092 "While CD57 is traditionally associated with immune cells (e.g., NK cells), its expression on enterocytes marks unique epithelial subsets with specific functions or maturation states. These cells are specially enriched in areas of the duodenum within submucosal glands.") +AnnotationAssertion(rdfs:label obo:CL_4033092 "CD57-positive enterocyte") +EquivalentClasses(obo:CL_4033092 ObjectIntersectionOf(obo:CL_0000584 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0008346) ObjectSomeValuesFrom(obo:RO_0002292 obo:PR_000001440))) + # Class: obo:CL_4033093 (limbal epithelial stem cell of cornea) AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:20614614") Annotation(oboInOwl:hasDbXref "PMID:29105366") Annotation(oboInOwl:hasDbXref "PMID:36983561") Annotation(oboInOwl:hasDbXref "PMID:37768272") obo:IAO_0000115 obo:CL_4033093 "A stem cell that is part of the corneo-scleral limbus. This cell type resides at the basal layer of the epithelium and has a small size and high nuclear to cytoplasmatic ratio (Secker and Daniels, 2009). A limbal stem cell is responsible for corneal epithelial renewal and repair (Li et al., 2023), and to help maintain a clear corneal surface by preventing conjunctival epithelial cells from migrating onto the cornea (Wang et al., 2023).") diff --git a/src/ontology/components/cellxgene_subset.owl b/src/ontology/components/cellxgene_subset.owl index 7966e3926..f52bb4fdf 100644 --- a/src/ontology/components/cellxgene_subset.owl +++ b/src/ontology/components/cellxgene_subset.owl @@ -7,12 +7,11 @@ Prefix(rdfs:=) Ontology( - -Annotation(owl:versionInfo "2024-06-13") + +Annotation(owl:versionInfo "2024-12-06") Declaration(Class()) Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -30,6 +29,7 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -44,6 +44,7 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -52,6 +53,7 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -97,32 +99,40 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) +Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -133,7 +143,9 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -141,7 +153,6 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -174,6 +185,7 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -199,6 +211,15 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -255,6 +276,8 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -276,8 +299,10 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -285,6 +310,7 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -339,14 +365,18 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -359,6 +389,7 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -380,8 +411,11 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -403,6 +437,8 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -411,14 +447,17 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) +Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -433,23 +472,29 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -464,18 +509,28 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -488,6 +543,7 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -527,7 +583,11 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -535,14 +595,21 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) +Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -551,6 +618,7 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -578,6 +646,7 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -603,6 +672,7 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -633,8 +703,10 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -644,18 +716,23 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -668,6 +745,8 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -684,9 +763,16 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) +Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -696,6 +782,38 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) Declaration(AnnotationProperty()) @@ -711,10 +829,6 @@ AnnotationAssertion( ) -# Class: () - -AnnotationAssertion( ) - # Class: () AnnotationAssertion( ) @@ -783,6 +897,10 @@ AnnotationAssertion( ) +# Class: () + +AnnotationAssertion( ) + # Class: () AnnotationAssertion( ) @@ -839,6 +957,10 @@ AnnotationAssertion( ) +# Class: () + +AnnotationAssertion( ) + # Class: () AnnotationAssertion( ) @@ -871,6 +993,10 @@ AnnotationAssertion( ) +# Class: () + +AnnotationAssertion( ) + # Class: () AnnotationAssertion( ) @@ -1051,6 +1177,10 @@ AnnotationAssertion( ) +# Class: () + +AnnotationAssertion( ) + # Class: () AnnotationAssertion( ) @@ -1059,10 +1189,22 @@ AnnotationAssertion( ) +# Class: () + +AnnotationAssertion( ) + # Class: () AnnotationAssertion( ) +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + # Class: () AnnotationAssertion( ) @@ -1075,10 +1217,6 @@ AnnotationAssertion( ) -# Class: () - -AnnotationAssertion( ) - # Class: () AnnotationAssertion( ) @@ -1095,10 +1233,6 @@ AnnotationAssertion( ) -# Class: () - -AnnotationAssertion( ) - # Class: () AnnotationAssertion( ) @@ -1111,6 +1245,10 @@ AnnotationAssertion( ) +# Class: () + +AnnotationAssertion( ) + # Class: () AnnotationAssertion( ) @@ -1119,6 +1257,14 @@ AnnotationAssertion( ) +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + # Class: () AnnotationAssertion( ) @@ -1139,6 +1285,10 @@ AnnotationAssertion( ) +# Class: () + +AnnotationAssertion( ) + # Class: () AnnotationAssertion( ) @@ -1147,6 +1297,10 @@ AnnotationAssertion( ) +# Class: () + +AnnotationAssertion( ) + # Class: () AnnotationAssertion( ) @@ -1155,6 +1309,10 @@ AnnotationAssertion( ) +# Class: () + +AnnotationAssertion( ) + # Class: () AnnotationAssertion( ) @@ -1195,10 +1353,18 @@ AnnotationAssertion( ) +# Class: () + +AnnotationAssertion( ) + # Class: () AnnotationAssertion( ) +# Class: () + +AnnotationAssertion( ) + # Class: () AnnotationAssertion( ) @@ -1227,10 +1393,6 @@ AnnotationAssertion( ) -# Class: () - -AnnotationAssertion( ) - # Class: () AnnotationAssertion( ) @@ -1359,6 +1521,10 @@ AnnotationAssertion( ) +# Class: () + +AnnotationAssertion( ) + # Class: () AnnotationAssertion( ) @@ -1459,6 +1625,42 @@ AnnotationAssertion( ) +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + # Class: () AnnotationAssertion( ) @@ -1683,6 +1885,14 @@ AnnotationAssertion( ) +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + # Class: () AnnotationAssertion( ) @@ -1767,6 +1977,10 @@ AnnotationAssertion( ) +# Class: () + +AnnotationAssertion( ) + # Class: () AnnotationAssertion( ) @@ -1775,6 +1989,10 @@ AnnotationAssertion( ) +# Class: () + +AnnotationAssertion( ) + # Class: () AnnotationAssertion( ) @@ -1803,6 +2021,10 @@ AnnotationAssertion( ) +# Class: () + +AnnotationAssertion( ) + # Class: () AnnotationAssertion( ) @@ -2019,6 +2241,10 @@ AnnotationAssertion( ) +# Class: () + +AnnotationAssertion( ) + # Class: () AnnotationAssertion( ) @@ -2027,6 +2253,10 @@ AnnotationAssertion( ) +# Class: () + +AnnotationAssertion( ) + # Class: () AnnotationAssertion( ) @@ -2051,6 +2281,14 @@ AnnotationAssertion( ) +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + # Class: () AnnotationAssertion( ) @@ -2099,6 +2337,10 @@ AnnotationAssertion( ) +# Class: () + +AnnotationAssertion( ) + # Class: () AnnotationAssertion( ) @@ -2183,6 +2425,14 @@ AnnotationAssertion( ) +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + # Class: () AnnotationAssertion( ) @@ -2191,6 +2441,10 @@ AnnotationAssertion( ) +# Class: () + +AnnotationAssertion( ) + # Class: () AnnotationAssertion( ) @@ -2275,6 +2529,14 @@ AnnotationAssertion( ) +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + # Class: () AnnotationAssertion( ) @@ -2307,6 +2569,14 @@ AnnotationAssertion( ) +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + # Class: () AnnotationAssertion( ) @@ -2331,14 +2601,18 @@ AnnotationAssertion( ) -# Class: () +# Class: () -AnnotationAssertion( ) +AnnotationAssertion( ) # Class: () AnnotationAssertion( ) +# Class: () + +AnnotationAssertion( ) + # Class: () AnnotationAssertion( ) @@ -2395,6 +2669,10 @@ AnnotationAssertion( ) +# Class: () + +AnnotationAssertion( ) + # Class: () AnnotationAssertion( ) @@ -2407,6 +2685,10 @@ AnnotationAssertion( ) +# Class: () + +AnnotationAssertion( ) + # Class: () AnnotationAssertion( ) @@ -2431,6 +2713,10 @@ AnnotationAssertion( ) +# Class: () + +AnnotationAssertion( ) + # Class: () AnnotationAssertion( ) @@ -2447,6 +2733,10 @@ AnnotationAssertion( ) +# Class: () + +AnnotationAssertion( ) + # Class: () AnnotationAssertion( ) @@ -2455,6 +2745,10 @@ AnnotationAssertion( ) +# Class: () + +AnnotationAssertion( ) + # Class: () AnnotationAssertion( ) @@ -2463,6 +2757,10 @@ AnnotationAssertion( ) +# Class: () + +AnnotationAssertion( ) + # Class: () AnnotationAssertion( ) @@ -2519,6 +2817,10 @@ AnnotationAssertion( ) +# Class: () + +AnnotationAssertion( ) + # Class: () AnnotationAssertion( ) @@ -2527,6 +2829,10 @@ AnnotationAssertion( ) +# Class: () + +AnnotationAssertion( ) + # Class: () AnnotationAssertion( ) @@ -2551,6 +2857,10 @@ AnnotationAssertion( ) +# Class: () + +AnnotationAssertion( ) + # Class: () AnnotationAssertion( ) @@ -2563,10 +2873,38 @@ AnnotationAssertion( ) +# Class: () + +AnnotationAssertion( ) + # Class: () AnnotationAssertion( ) +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + # Class: () AnnotationAssertion( ) @@ -2615,6 +2953,10 @@ AnnotationAssertion( ) +# Class: () + +AnnotationAssertion( ) + # Class: () AnnotationAssertion( ) @@ -2771,10 +3113,26 @@ AnnotationAssertion( ) +# Class: () + +AnnotationAssertion( ) + # Class: () AnnotationAssertion( ) +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + # Class: () AnnotationAssertion( ) @@ -2803,10 +3161,22 @@ AnnotationAssertion( ) +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + # Class: () AnnotationAssertion( ) +# Class: () + +AnnotationAssertion( ) + # Class: () AnnotationAssertion( ) @@ -2815,6 +3185,10 @@ AnnotationAssertion( ) +# Class: () + +AnnotationAssertion( ) + # Class: () AnnotationAssertion( ) @@ -2823,10 +3197,18 @@ AnnotationAssertion( ) +# Class: () + +AnnotationAssertion( ) + # Class: () AnnotationAssertion( ) +# Class: () + +AnnotationAssertion( ) + # Class: () AnnotationAssertion( ) @@ -2835,6 +3217,10 @@ AnnotationAssertion( ) +# Class: () + +AnnotationAssertion( ) + # Class: () AnnotationAssertion( ) @@ -2867,6 +3253,10 @@ AnnotationAssertion( ) +# Class: () + +AnnotationAssertion( ) + # Class: () AnnotationAssertion( ) @@ -2975,6 +3365,10 @@ AnnotationAssertion( ) +# Class: () + +AnnotationAssertion( ) + # Class: () AnnotationAssertion( ) @@ -3075,6 +3469,10 @@ AnnotationAssertion( ) +# Class: () + +AnnotationAssertion( ) + # Class: () AnnotationAssertion( ) @@ -3195,6 +3593,10 @@ AnnotationAssertion( ) +# Class: () + +AnnotationAssertion( ) + # Class: () AnnotationAssertion( ) @@ -3203,6 +3605,10 @@ AnnotationAssertion( ) +# Class: () + +AnnotationAssertion( ) + # Class: () AnnotationAssertion( ) @@ -3239,6 +3645,10 @@ AnnotationAssertion( ) +# Class: () + +AnnotationAssertion( ) + # Class: () AnnotationAssertion( ) @@ -3251,6 +3661,10 @@ AnnotationAssertion( ) +# Class: () + +AnnotationAssertion( ) + # Class: () AnnotationAssertion( ) @@ -3271,6 +3685,14 @@ AnnotationAssertion( ) +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + # Class: () AnnotationAssertion( ) @@ -3287,6 +3709,10 @@ AnnotationAssertion( ) +# Class: () + +AnnotationAssertion( ) + # Class: () AnnotationAssertion( ) @@ -3335,6 +3761,14 @@ AnnotationAssertion( ) +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + # Class: () AnnotationAssertion( ) @@ -3399,18 +3833,46 @@ AnnotationAssertion( ) +# Class: () + +AnnotationAssertion( ) + # Class: () AnnotationAssertion( ) +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + # Class: () AnnotationAssertion( ) +# Class: () + +AnnotationAssertion( ) + # Class: () AnnotationAssertion( ) +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + # Class: () AnnotationAssertion( ) @@ -3447,5 +3909,133 @@ AnnotationAssertion( ) +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + +# Class: () + +AnnotationAssertion( ) + ) \ No newline at end of file diff --git a/src/ontology/components/clm-cl.owl b/src/ontology/components/clm-cl.owl index 902854fff..45fc34afd 100644 --- a/src/ontology/components/clm-cl.owl +++ b/src/ontology/components/clm-cl.owl @@ -1,14 +1,2732 @@ - - + xmlns:dcterms="http://purl.org/dc/terms/" + xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#"> + + + + None + + Cell Markers Ontology + 2024-12-02 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + description + + + + + + + + license + + + + + + + + title + + + + + + + + + + + + + + + + + + + + + + + + + has characterizing marker set + + + + + + + + + + + + + + TAC1 + + + + + + + + + STAB1 + + + + + + + + + TLL1 + + + + + + + + + MSR1 + + + + + + + + + TNC + + + + + + + + + ROS1 + + + + + + + + + TNIP3 + + + + + + + + + HOMER3 + + + + + + + + + FCGR2B + + + + + + + + + BPIFB2 + + + + + + + + + KCNK2 + + + + + + + + + SEMA5B + + + + + + + + + HMOX1 + + + + + + + + + PVALB + + + + + + + + + CHGA + + + + + + + + + ACTA2 + + + + + + + + + PRR4 + + + + + + + + + ST8SIA4 + + + + + + + + + PLCH1 + + + + + + + + + SMYD1 + + + + + + + + + MYB + + + + + + + + + CCN2 + + + + + + + + + ONECUT2 + + + + + + + + + NPY + + + + + + + + + SFTPA1 + + + + + + + + + CHST8 + + + + + + + + + F13A1 + + + + + + + + + LAMP5 + + + + + + + + + HIGD1B + + + + + + + + + AOC3 + + + + + + + + + TOP2A + + + + + + + + + GRP + + + + + + + + + HCRTR2 + + + + + + + + + SULF1 + + + + + + + + + POU2F3 + + + + + + + + + NUSAP1 + + + + + + + + + LUM + + + + + + + + + RXRG + + + + + + + + + DPT + + + + + + + + + THSD7B + + + + + + + + + VIP + + + + + + + + + TAGLN + + + + + + + + + CHST9 + + + + + + + + + GLYATL2 + + + + + + + + + SST + + + + + + + + + KIT + + + + + + + + + BSND + + + + + + + + + CXCL5 + + + + + + + + + HPGD + + + + + + + + + PCLAF + + + + + + + + + MS4A8 + + + + + + + + + MYO5B + + + + + + + + + SCARA5 + + + + + + + + + FABP4 + + + + + + + + + KCNK3 + + + + + + + + + KRT15 + + + + + + + + + RRM2 + + + + + + + + + THEMIS + + + + + + + + + ANKRD36C + + + + + + + + + CD248 + + + + + + + + + GPR149 + + + + + + + + + UBE2C + + + + + + + + + ASCL3 + + + + + + + + + ADAMTSL1 + + + + + + + + + CA8 + + + + + + + + + C1orf194 + + + + + + + + + ARSJ + + + + + + + + + C6orf58 + + + + + + + + + POU3F1 + + + + + + + + + DMBT1 + + + + + + + + + RELN + + + + + + + + + APOD + + + + + + + + + NPSR1-AS1 + + + + + + + + + LYPD2 + + + + + + + + + PLCG2 + + + + + + + + + PRC1 + + + + + + + + + RORB + + + + + + + + + COL5A2 + + + + + + + + + AGER + + + + + + + + + SERPINB4 + + + + + + + + + MUC5AC + + + + + + + + + LINC00298 + + + + + + + + + PEG10 + + + + + + + + + LINC00507 + + + + + + + + + + + + + + + + + + + + + + + 0.85 + NS forest marker set of alveolar adventitial fibroblast (Human Lung). + + + + + + + + + + + + + + + + + + + + + + + 0.70 + NS forest marker set of alveolar type 1 fibroblast cell (Human Lung). + + + + + + + + + + + + + + + + + + + + + + + 0.80 + NS forest marker set of alveolar macrophage (Human Lung). + + + + + + + + + + + + + + + + + + + + + + + 0.67 + NS forest marker set of CCL3-positive alveolar macrophage (Human Lung). + + + + + + + + + + + + + + + + + + + + + + + 0.41 + NS forest marker set of metallothionein-positive alveolar macrophage (Human Lung). + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 0.26 + NS forest marker set of cycling alveolar macrophage (Human Lung). + + + + + + + + + + + + + + + 0.85 + NS forest marker set of pulmonary alveolar type 1 cell (Human Lung). + + + + + + + + + + + + + + + 0.95 + NS forest marker set of pulmonary alveolar type 2 cell (Human Lung). + + + + + + + + + + + + + + + + + + + + + + + + + + + 0.61 + NS forest marker set of cycling pulmonary alveolar type 2 cell (Human Lung). + + + + + + + + + + + + + + + + + + + + + + + 0.55 + NS forest marker set of bronchial goblet cell (Human Lung). + + + + + + + + + + + + + + + + + + + + + + + 0.81 + NS forest marker set of nasal mucosa goblet cell (Human Lung). + + + + + + + + + + + + + + + + + + + + + + + + + + + 0.46 + NS forest marker set of lung interstitial macrophage (Human Lung). + + + + + + + + + + + + + + + + + + + + + + + 0.82 + NS forest marker set of pulmonary ionocyte (Human Lung). + + + + + + + + + + + + + + + + + + + + + + + 0.86 + NS forest marker set of ciliated columnar cell of tracheobronchial tree (Human Lung). + + + + + + + + + + + + + + + + + + + + + + + 0.94 + NS forest marker set of lung neuroendocrine cell (Human Lung). + + + + + + + + + + + + + + + + + + + + + + + 0.58 + NS forest marker set of pulmonary interstitial fibroblast (Human Lung). + + + + + + + + + + + + + + + + + + + + + + + 0.84 + NS forest marker set of lung pericyte (Human Lung). + + + + + + + + + + + + + + + + + + + + + + + 0.46 + NS forest marker set of airway submucosal gland collecting duct epithelial cell (Human Lung). + + + + + + + + + + + + + + + 0.93 + NS forest marker set of mucus secreting cell of bronchus submucosal gland (Human Lung). + + + + + + + + + + + + + + + + + + + + + + + 0.75 + NS forest marker set of serous secreting cell of bronchus submucosal gland (Human Lung). + + + + + + + + + + + + + + + + + + + + + + + 0.69 + NS forest marker set of tracheobronchial smooth muscle cell (Human Lung). + + + + + + + + + + + + + + + + + + + + + + + + + + + 0.62 + NS forest marker set of respiratory suprabasal cell (Human Lung). + + + + + + + + + + + + + + + + + + + + + + + + + + + 0.56 + NS forest marker set of brush cell of tracheobronchial tree (Human Lung). + + + + + + + + + + + + + + + + + + + + + + + 0.799748111 + NS forest marker set of chandelier pvalb GABAergic cortical interneuron (Human Brain). + + + + + + + + + + + + + + + + + + + + + + + 0.670149932 + NS forest marker set of L2/3 intratelencephalic projecting glutamatergic neuron (Human Brain). + + + + + + + + + + + + + + + + + + + + + + + 0.720108696 + NS forest marker set of L4 intratelencephalic projecting glutamatergic neuron (Human Brain). + + + + + + + + + + + + + + + + + + + + + + + 0.815891473 + NS forest marker set of L5 extratelencephalic projecting glutamatergic cortical neuron (Human Brain). + + + + + + + + + + + + + + + + + + + + + + + + + + + 0.764261336 + NS forest marker set of L5 intratelencephalic projecting glutamatergic neuron (Human Brain). + + + + + + + + + + + + + + + + + + + + + + + 0.899288218 + NS forest marker set of L5/6 near-projecting glutamatergic neuron (Human Brain). + + + + + + + + + + + + + + + + + + + + + + + + + + + 0.631898455 + NS forest marker set of L6 corticothalamic-projecting glutamatergic cortical neuron (Human Brain). + + + + + + + + + + + + + + + + + + + + + + + 0.641695703 + NS forest marker set of L6 intratelencephalic projecting glutamatergic neuron (Human Brain). + + + + + + + + + + + + + + + + + + + + + + + 0.877752028 + NS forest marker set of L6 intratelencephalic projecting Car3 glutamatergic neuron (Human Brain). + + + + + + + + + + + + + + + + + + + + + + + 0.819940964 + NS forest marker set of L6b glutamatergic neuron of the primary motor cortex (Human Brain). + + + + + + + + + + + + + + + + + + + + + + + 0.814687838 + NS forest marker set of lamp5 GABAergic cortical interneuron (Human Brain). + + + + + + + + + + + + + + + + + + + + + + + 0.821678322 + NS forest marker set of Lamp5 Lhx6 neuron (Human Brain). + + + + + + + + + + + + + + + + + + + + + + + 0.724125093 + NS forest marker set of Pax6 (Human Brain). + + + + + + + + + + + + + + + + + + + + + + + + + + + 0.691998764 + NS forest marker set of pvalb GABAergic cortical interneuron (Human Brain). + + + + + + + + + + + + + + + + + + + + + + + 0.628943702 + NS forest marker set of sncg GABAergic cortical interneuron (Human Brain). + + + + + + + + + + + + + + + + + + + + + + + 0.842367005 + NS forest marker set of sst GABAergic cortical interneuron (Human Brain). + + + + + + + + + + + + + + + 0.894026187 + NS forest marker set of sst chodl GABAergic cortical interneuron (Human Brain). + + + + + + + + + + + + + + + 0.855531344 + NS forest marker set of VIP GABAergic cortical interneuron (Human Brain). + + + + + + + + + + + + + + + The marker set MSR1, FABP4 can identify the Human cell type alveolar macrophage in the Lung with a confidence of 0.80 (NS-Forest FBeta value). + + + + + The marker set MSR1, FABP4 can identify the Human cell type alveolar macrophage in the Lung with a confidence of 0.80 (NS-Forest FBeta value). + https://doi.org/10.5281/zenodo.11165918 + + + + + + + + + + + + + + + The marker set AGER can identify the Human cell type pulmonary alveolar type 1 cell in the Lung with a confidence of 0.85 (NS-Forest FBeta value). + + + + + The marker set AGER can identify the Human cell type pulmonary alveolar type 1 cell in the Lung with a confidence of 0.85 (NS-Forest FBeta value). + https://doi.org/10.5281/zenodo.11165918 + + + + + + + + + + + + + + + The marker set SFTPA1 can identify the Human cell type pulmonary alveolar type 2 cell in the Lung with a confidence of 0.95 (NS-Forest FBeta value). + + + + + The marker set SFTPA1 can identify the Human cell type pulmonary alveolar type 2 cell in the Lung with a confidence of 0.95 (NS-Forest FBeta value). + https://doi.org/10.5281/zenodo.11165918 + + + + + + + + + + + + + + + The marker set POU2F3, HOMER3, MYB can identify the Human cell type brush cell of tracheobronchial tree in the Lung with a confidence of 0.56 (NS-Forest FBeta value). + + + + + The marker set POU2F3, HOMER3, MYB can identify the Human cell type brush cell of tracheobronchial tree in the Lung with a confidence of 0.56 (NS-Forest FBeta value). + https://doi.org/10.5281/zenodo.11165918 + + + + + + + + + + + + + + + The marker set C1orf194, MS4A8 can identify the Human cell type ciliated columnar cell of tracheobronchial tree in the Lung with a confidence of 0.86 (NS-Forest FBeta value). + + + + + The marker set C1orf194, MS4A8 can identify the Human cell type ciliated columnar cell of tracheobronchial tree in the Lung with a confidence of 0.86 (NS-Forest FBeta value). + https://doi.org/10.5281/zenodo.11165918 + + + + + + + + + + + + + + + The marker set DPT, APOD can identify the Human cell type pulmonary interstitial fibroblast in the Lung with a confidence of 0.58 (NS-Forest FBeta value). + + + + + The marker set DPT, APOD can identify the Human cell type pulmonary interstitial fibroblast in the Lung with a confidence of 0.58 (NS-Forest FBeta value). + https://doi.org/10.5281/zenodo.11165918 + + + + + + + + + + + + + + + The marker set LYPD2, MUC5AC can identify the Human cell type nasal mucosa goblet cell in the Lung with a confidence of 0.81 (NS-Forest FBeta value). + + + + + The marker set LYPD2, MUC5AC can identify the Human cell type nasal mucosa goblet cell in the Lung with a confidence of 0.81 (NS-Forest FBeta value). + https://doi.org/10.5281/zenodo.11165918 + + + + + + + + + + + + + + + The marker set HIGD1B, KCNK3 can identify the Human cell type lung pericyte in the Lung with a confidence of 0.84 (NS-Forest FBeta value). + + + + + The marker set HIGD1B, KCNK3 can identify the Human cell type lung pericyte in the Lung with a confidence of 0.84 (NS-Forest FBeta value). + https://doi.org/10.5281/zenodo.11165918 + + + + + + + + + + + + + + + The marker set ASCL3, BSND can identify the Human cell type pulmonary ionocyte in the Lung with a confidence of 0.82 (NS-Forest FBeta value). + + + + + The marker set ASCL3, BSND can identify the Human cell type pulmonary ionocyte in the Lung with a confidence of 0.82 (NS-Forest FBeta value). + https://doi.org/10.5281/zenodo.11165918 + + + + + + + + + + + + + + + The marker set ACTA2, TAGLN can identify the Human cell type tracheobronchial smooth muscle cell in the Lung with a confidence of 0.69 (NS-Forest FBeta value). + + + + + The marker set ACTA2, TAGLN can identify the Human cell type tracheobronchial smooth muscle cell in the Lung with a confidence of 0.69 (NS-Forest FBeta value). + https://doi.org/10.5281/zenodo.11165918 + + + + + + + + + + + + + + + The marker set CHGA, GRP can identify the Human cell type lung neuroendocrine cell in the Lung with a confidence of 0.94 (NS-Forest FBeta value). + + + + + The marker set CHGA, GRP can identify the Human cell type lung neuroendocrine cell in the Lung with a confidence of 0.94 (NS-Forest FBeta value). + https://doi.org/10.5281/zenodo.11165918 + + + + + + + + + + + + + + + The marker set PLCG2, ANKRD36C can identify the Human cell type bronchial goblet cell in the Lung with a confidence of 0.55 (NS-Forest FBeta value). + + + + + The marker set PLCG2, ANKRD36C can identify the Human cell type bronchial goblet cell in the Lung with a confidence of 0.55 (NS-Forest FBeta value). + https://doi.org/10.5281/zenodo.11165918 + + + + + + + + + + + + + + + The marker set LINC00298, KIT can identify the Human cell type lamp5 GABAergic cortical interneuron in the Brain with a confidence of 0.814687838 (NS-Forest FBeta value). + + + + + The marker set LINC00298, KIT can identify the Human cell type lamp5 GABAergic cortical interneuron in the Brain with a confidence of 0.814687838 (NS-Forest FBeta value). + https://doi.org/10.5281/zenodo.11165918 + + + + + + + + + + + + + + + The marker set RXRG, THSD7B can identify the Human cell type sncg GABAergic cortical interneuron in the Brain with a confidence of 0.628943702 (NS-Forest FBeta value). + + + + + The marker set RXRG, THSD7B can identify the Human cell type sncg GABAergic cortical interneuron in the Brain with a confidence of 0.628943702 (NS-Forest FBeta value). + https://doi.org/10.5281/zenodo.11165918 + + + + + + + + + + + + + + + The marker set VIP can identify the Human cell type VIP GABAergic cortical interneuron in the Brain with a confidence of 0.855531344 (NS-Forest FBeta value). + + + + + The marker set VIP can identify the Human cell type VIP GABAergic cortical interneuron in the Brain with a confidence of 0.855531344 (NS-Forest FBeta value). + https://doi.org/10.5281/zenodo.11165918 + + + + + + + + + + + + + + + The marker set SST, PLCH1 can identify the Human cell type sst GABAergic cortical interneuron in the Brain with a confidence of 0.842367005 (NS-Forest FBeta value). + + + + + The marker set SST, PLCH1 can identify the Human cell type sst GABAergic cortical interneuron in the Brain with a confidence of 0.842367005 (NS-Forest FBeta value). + https://doi.org/10.5281/zenodo.11165918 + + + + + + + + + + + + + + + The marker set PVALB, TAC1, MYO5B can identify the Human cell type pvalb GABAergic cortical interneuron in the Brain with a confidence of 0.691998764 (NS-Forest FBeta value). + + + + + The marker set PVALB, TAC1, MYO5B can identify the Human cell type pvalb GABAergic cortical interneuron in the Brain with a confidence of 0.691998764 (NS-Forest FBeta value). + https://doi.org/10.5281/zenodo.11165918 + + + + + + + + + + + + + + + The marker set GPR149, CA8 can identify the Human cell type chandelier pvalb GABAergic cortical interneuron in the Brain with a confidence of 0.799748111 (NS-Forest FBeta value). + + + + + The marker set GPR149, CA8 can identify the Human cell type chandelier pvalb GABAergic cortical interneuron in the Brain with a confidence of 0.799748111 (NS-Forest FBeta value). + https://doi.org/10.5281/zenodo.11165918 + + + + + + + + + + + + + + + The marker set CHST8, POU3F1 can identify the Human cell type L5 extratelencephalic projecting glutamatergic cortical neuron in the Brain with a confidence of 0.815891473 (NS-Forest FBeta value). + + + + + The marker set CHST8, POU3F1 can identify the Human cell type L5 extratelencephalic projecting glutamatergic cortical neuron in the Brain with a confidence of 0.815891473 (NS-Forest FBeta value). + https://doi.org/10.5281/zenodo.11165918 + + + + + + + + + + + + + + + The marker set SEMA5B, ADAMTSL1, SULF1 can identify the Human cell type L6 corticothalamic-projecting glutamatergic cortical neuron in the Brain with a confidence of 0.631898455 (NS-Forest FBeta value). + + + + + The marker set SEMA5B, ADAMTSL1, SULF1 can identify the Human cell type L6 corticothalamic-projecting glutamatergic cortical neuron in the Brain with a confidence of 0.631898455 (NS-Forest FBeta value). + https://doi.org/10.5281/zenodo.11165918 + + + + + + + + + + + + + + + The marker set CCN2, ROS1 can identify the Human cell type L6b glutamatergic neuron of the primary motor cortex in the Brain with a confidence of 0.819940964 (NS-Forest FBeta value). + + + + + The marker set CCN2, ROS1 can identify the Human cell type L6b glutamatergic neuron of the primary motor cortex in the Brain with a confidence of 0.819940964 (NS-Forest FBeta value). + https://doi.org/10.5281/zenodo.11165918 + + + + + + + + + + + + + + + The marker set NPY can identify the Human cell type sst chodl GABAergic cortical interneuron in the Brain with a confidence of 0.894026187 (NS-Forest FBeta value). + + + + + The marker set NPY can identify the Human cell type sst chodl GABAergic cortical interneuron in the Brain with a confidence of 0.894026187 (NS-Forest FBeta value). + https://doi.org/10.5281/zenodo.11165918 + + + + + + + + + + + + + + + The marker set AOC3, LUM can identify the Human cell type alveolar type 1 fibroblast cell in the Lung with a confidence of 0.70 (NS-Forest FBeta value). + + + + + The marker set AOC3, LUM can identify the Human cell type alveolar type 1 fibroblast cell in the Lung with a confidence of 0.70 (NS-Forest FBeta value). + https://doi.org/10.5281/zenodo.11165918 + + + + + + + + + + + + + + + The marker set SCARA5, CD248 can identify the Human cell type alveolar adventitial fibroblast in the Lung with a confidence of 0.85 (NS-Forest FBeta value). + + + + + The marker set SCARA5, CD248 can identify the Human cell type alveolar adventitial fibroblast in the Lung with a confidence of 0.85 (NS-Forest FBeta value). + https://doi.org/10.5281/zenodo.11165918 + + + + + + + + + + + + + + + The marker set ONECUT2, COL5A2 can identify the Human cell type L2/3 intratelencephalic projecting glutamatergic neuron in the Brain with a confidence of 0.670149932 (NS-Forest FBeta value). + + + + + The marker set ONECUT2, COL5A2 can identify the Human cell type L2/3 intratelencephalic projecting glutamatergic neuron in the Brain with a confidence of 0.670149932 (NS-Forest FBeta value). + https://doi.org/10.5281/zenodo.11165918 + + + + + + + + + + + + + + + The marker set RORB, ST8SIA4 can identify the Human cell type L4 intratelencephalic projecting glutamatergic neuron in the Brain with a confidence of 0.720108696 (NS-Forest FBeta value). + + + + + The marker set RORB, ST8SIA4 can identify the Human cell type L4 intratelencephalic projecting glutamatergic neuron in the Brain with a confidence of 0.720108696 (NS-Forest FBeta value). + https://doi.org/10.5281/zenodo.11165918 + + + + + + + + + + + + + + + The marker set ARSJ, RORB, KCNK2 can identify the Human cell type L5 intratelencephalic projecting glutamatergic neuron in the Brain with a confidence of 0.764261336 (NS-Forest FBeta value). + + + + + The marker set ARSJ, RORB, KCNK2 can identify the Human cell type L5 intratelencephalic projecting glutamatergic neuron in the Brain with a confidence of 0.764261336 (NS-Forest FBeta value). + https://doi.org/10.5281/zenodo.11165918 + + + + + + + + + + + + + + + The marker set LINC00507, THEMIS can identify the Human cell type L6 intratelencephalic projecting glutamatergic neuron in the Brain with a confidence of 0.641695703 (NS-Forest FBeta value). + + + + + The marker set LINC00507, THEMIS can identify the Human cell type L6 intratelencephalic projecting glutamatergic neuron in the Brain with a confidence of 0.641695703 (NS-Forest FBeta value). + https://doi.org/10.5281/zenodo.11165918 + + + + + + + + + + + + + + + The marker set NPSR1-AS1, TLL1 can identify the Human cell type L5/6 near-projecting glutamatergic neuron in the Brain with a confidence of 0.899288218 (NS-Forest FBeta value). + + + + + The marker set NPSR1-AS1, TLL1 can identify the Human cell type L5/6 near-projecting glutamatergic neuron in the Brain with a confidence of 0.899288218 (NS-Forest FBeta value). + https://doi.org/10.5281/zenodo.11165918 + + + + + + + + + + + + + + + The marker set SMYD1, THEMIS can identify the Human cell type L6 intratelencephalic projecting Car3 glutamatergic neuron in the Brain with a confidence of 0.877752028 (NS-Forest FBeta value). + + + + + The marker set SMYD1, THEMIS can identify the Human cell type L6 intratelencephalic projecting Car3 glutamatergic neuron in the Brain with a confidence of 0.877752028 (NS-Forest FBeta value). + https://doi.org/10.5281/zenodo.11165918 + + + + + + + + + + + + + + + The marker set PRR4, C6orf58 can identify the Human cell type serous secreting cell of bronchus submucosal gland in the Lung with a confidence of 0.75 (NS-Forest FBeta value). + + + + + The marker set PRR4, C6orf58 can identify the Human cell type serous secreting cell of bronchus submucosal gland in the Lung with a confidence of 0.75 (NS-Forest FBeta value). + https://doi.org/10.5281/zenodo.11165918 + + + + + + + + + + + + + + + The marker set BPIFB2 can identify the Human cell type mucus secreting cell of bronchus submucosal gland in the Lung with a confidence of 0.93 (NS-Forest FBeta value). + + + + + The marker set BPIFB2 can identify the Human cell type mucus secreting cell of bronchus submucosal gland in the Lung with a confidence of 0.93 (NS-Forest FBeta value). + https://doi.org/10.5281/zenodo.11165918 + + + + + + + + + + + + + + + The marker set GLYATL2, DMBT1 can identify the Human cell type airway submucosal gland collecting duct epithelial cell in the Lung with a confidence of 0.46 (NS-Forest FBeta value). + + + + + The marker set GLYATL2, DMBT1 can identify the Human cell type airway submucosal gland collecting duct epithelial cell in the Lung with a confidence of 0.46 (NS-Forest FBeta value). + https://doi.org/10.5281/zenodo.11165918 + + + + + + + + + + + + + + + The marker set TNIP3, CXCL5 can identify the Human cell type CCL3-positive alveolar macrophage in the Lung with a confidence of 0.67 (NS-Forest FBeta value). + + + + + The marker set TNIP3, CXCL5 can identify the Human cell type CCL3-positive alveolar macrophage in the Lung with a confidence of 0.67 (NS-Forest FBeta value). + https://doi.org/10.5281/zenodo.11165918 + + + + + + + + + + + + + + + The marker set HMOX1, HPGD can identify the Human cell type metallothionein-positive alveolar macrophage in the Lung with a confidence of 0.41 (NS-Forest FBeta value). + + + + + The marker set HMOX1, HPGD can identify the Human cell type metallothionein-positive alveolar macrophage in the Lung with a confidence of 0.41 (NS-Forest FBeta value). + https://doi.org/10.5281/zenodo.11165918 + + + + + + + + + + + + + + + The marker set F13A1, STAB1, FCGR2B can identify the Human cell type lung interstitial macrophage in the Lung with a confidence of 0.46 (NS-Forest FBeta value). + + + + + The marker set F13A1, STAB1, FCGR2B can identify the Human cell type lung interstitial macrophage in the Lung with a confidence of 0.46 (NS-Forest FBeta value). + https://doi.org/10.5281/zenodo.11165918 + + + + + + + + + + + + + + + The marker set TNC, KRT15, SERPINB4 can identify the Human cell type respiratory suprabasal cell in the Lung with a confidence of 0.62 (NS-Forest FBeta value). + + + + + The marker set TNC, KRT15, SERPINB4 can identify the Human cell type respiratory suprabasal cell in the Lung with a confidence of 0.62 (NS-Forest FBeta value). + https://doi.org/10.5281/zenodo.11165918 + + + + + + + + + + + + + + + The marker set PCLAF, RRM2, UBE2C, NUSAP1 can identify the Human cell type cycling alveolar macrophage in the Lung with a confidence of 0.26 (NS-Forest FBeta value). + + + + + The marker set PCLAF, RRM2, UBE2C, NUSAP1 can identify the Human cell type cycling alveolar macrophage in the Lung with a confidence of 0.26 (NS-Forest FBeta value). + https://doi.org/10.5281/zenodo.11165918 + + + + + + + + + + + + + + + The marker set PEG10, PRC1, TOP2A can identify the Human cell type cycling pulmonary alveolar type 2 cell in the Lung with a confidence of 0.61 (NS-Forest FBeta value). + + + + + The marker set PEG10, PRC1, TOP2A can identify the Human cell type cycling pulmonary alveolar type 2 cell in the Lung with a confidence of 0.61 (NS-Forest FBeta value). + https://doi.org/10.5281/zenodo.11165918 + + + + + + + + + + + + + + + The marker set CHST9, LAMP5 can identify the Human cell type Lamp5 Lhx6 neuron in the Brain with a confidence of 0.821678322 (NS-Forest FBeta value). + + + + + The marker set CHST9, LAMP5 can identify the Human cell type Lamp5 Lhx6 neuron in the Brain with a confidence of 0.821678322 (NS-Forest FBeta value). + https://doi.org/10.5281/zenodo.11165918 + + + + + + + + + + + + + + + The marker set RELN, HCRTR2 can identify the Human cell type http://purl.obolibrary.org/obo/CL_4042032 in the Brain with a confidence of 0.724125093 (NS-Forest FBeta value). + + + + + The marker set RELN, HCRTR2 can identify the Human cell type http://purl.obolibrary.org/obo/CL_4042032 in the Brain with a confidence of 0.724125093 (NS-Forest FBeta value). + https://doi.org/10.5281/zenodo.11165918 + + + + + + + + + + + + + + sequence_collection + + + + + + - - diff --git a/src/ontology/imports/merged_import.owl b/src/ontology/imports/merged_import.owl index cb150f83d..d006760c6 100644 --- a/src/ontology/imports/merged_import.owl +++ b/src/ontology/imports/merged_import.owl @@ -7,8 +7,8 @@ Prefix(rdfs:=) Ontology( - -Annotation(owl:versionInfo "2024-11-21") + +Annotation(owl:versionInfo "2024-12-06") Declaration(Class()) Declaration(Class()) @@ -8422,6 +8422,7 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -8443,6 +8444,7 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -9128,6 +9130,7 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -9144,6 +9147,7 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -13867,6 +13871,7 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -14123,6 +14128,7 @@ Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) +Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) @@ -14267,6 +14273,7 @@ Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) @@ -14323,8 +14330,8 @@ We don't have definitions of 'meaning' or 'expression' or 'property'. For 'refer Personally, I am more comfortable weakening definition to documentation, with instructions as to what is desirable. We also have the outstanding issue of how to aim different definitions to different audiences. A clinical audience reading chebi wants a different sort of definition documentation/definition from a chemistry trained audience, and similarly there is a need for a definition that is adequate for an ontologist to work with."@en) -AnnotationAssertion(rdfs:label "definition") AnnotationAssertion(rdfs:label "definition"@en) +AnnotationAssertion(rdfs:label "definition") # Annotation Property: (editor note) @@ -14345,15 +14352,15 @@ AnnotationAssertion( "true"^^xsd:boolean) AnnotationAssertion( "term_tracker_item") AnnotationAssertion(rdfs:comment "The 'tracker item' can associate a tracker with a specific ontology term."@en) -AnnotationAssertion(rdfs:label "term tracker item") AnnotationAssertion(rdfs:label "term tracker item"@en) +AnnotationAssertion(rdfs:label "term tracker item") # Annotation Property: (expand expression to) AnnotationAssertion( "A macro expansion tag applied to an object property (or possibly a data property) which can be used by a macro-expansion engine to generate more complex expressions from simpler ones"@en) AnnotationAssertion(rdfs:label "expand expression to"@en) -# Annotation Property: (preferred_root) +# Annotation Property: (has ontology root term) AnnotationAssertion( "Ontology annotation property. Relates an ontology to a term that is a designated root term of the ontology. Display tools like OLS can use terms annotated with this property as the starting point for rendering the ontology class hierarchy. There can be more than one root."@en) AnnotationAssertion( "IAO:0000700") @@ -14361,15 +14368,15 @@ AnnotationAssertion( "has_ontology_root_term") AnnotationAssertion( "true"^^xsd:boolean) AnnotationAssertion( "has_ontology_root_term") -AnnotationAssertion(rdfs:label "has ontology root term") AnnotationAssertion(rdfs:label "has ontology root term"@en) +AnnotationAssertion(rdfs:label "has ontology root term") # Annotation Property: (term replaced by) AnnotationAssertion( "Use on obsolete terms, relating the term to another term that can be used as a substitute"@en) AnnotationAssertion(rdfs:comment "Add as annotation triples in the granting ontology"@en) -AnnotationAssertion(rdfs:label "term replaced by") AnnotationAssertion(rdfs:label "term replaced by"@en) +AnnotationAssertion(rdfs:label "term replaced by") # Annotation Property: (defined by construct) @@ -14799,7 +14806,7 @@ AnnotationAssertion(rdfs:label "has_broad_synonym") AnnotationAssertion(rdfs:seeAlso "https://github.com/information-artifact-ontology/ontology-metadata/issues/18") -# Annotation Property: (database_cross_reference) +# Annotation Property: (has cross-reference) AnnotationAssertion( "An annotation property that links an ontology entity or a statement to a prefixed identifier or URI.") AnnotationAssertion( ) @@ -14807,7 +14814,7 @@ AnnotationAssertion( "database_cross_reference") AnnotationAssertion(rdfs:label "has cross-reference") -# Annotation Property: (has_exact_synonym) +# Annotation Property: (has exact synonym) AnnotationAssertion( "An alternative label for a class or property which has the exact same meaning than the preferred name/primary label.") AnnotationAssertion( "https://github.com/information-artifact-ontology/ontology-metadata/issues/20") @@ -14815,7 +14822,7 @@ AnnotationAssertion(rdfs:label "has_exact_synonym") AnnotationAssertion(rdfs:seeAlso "https://github.com/information-artifact-ontology/ontology-metadata/issues/20") -# Annotation Property: (has_narrow_synonym) +# Annotation Property: (has narrow synonym) AnnotationAssertion( "An alternative label for a class or property which has a more specific meaning than the preferred name/primary label.") AnnotationAssertion( "https://github.com/information-artifact-ontology/ontology-metadata/issues/19") @@ -14868,12 +14875,12 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( "part_of") -AnnotationAssertion(rdfs:label "part of") AnnotationAssertion(rdfs:label "part of"@en) +AnnotationAssertion(rdfs:label "part of") AnnotationAssertion(rdfs:seeAlso ) AnnotationAssertion(rdfs:seeAlso ) -AnnotationAssertion(rdfs:seeAlso "http://www.obofoundry.org/ro/#OBO_REL:part_of") AnnotationAssertion(rdfs:seeAlso "https://wiki.geneontology.org/Part_of"^^xsd:anyURI) +AnnotationAssertion(rdfs:seeAlso "http://www.obofoundry.org/ro/#OBO_REL:part_of") SubObjectPropertyOf( ) InverseObjectProperties( ) TransitiveObjectProperty() @@ -14893,8 +14900,8 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( "has_part") -AnnotationAssertion(rdfs:label "has part") AnnotationAssertion(rdfs:label "has part"@en) +AnnotationAssertion(rdfs:label "has part") SubObjectPropertyOf( ) TransitiveObjectProperty() @@ -14907,8 +14914,8 @@ AnnotationAssertion( "preceded_by") AnnotationAssertion( ) AnnotationAssertion( "preceded_by") -AnnotationAssertion(rdfs:label "preceded by") AnnotationAssertion(rdfs:label "preceded by"@en) +AnnotationAssertion(rdfs:label "preceded by") SubObjectPropertyOf( ) InverseObjectProperties( ) TransitiveObjectProperty() @@ -14923,8 +14930,8 @@ AnnotationAssertion( "precedes") AnnotationAssertion( ) AnnotationAssertion( "precedes") -AnnotationAssertion(rdfs:label "precedes") AnnotationAssertion(rdfs:label "precedes"@en) +AnnotationAssertion(rdfs:label "precedes") SubObjectPropertyOf( ) TransitiveObjectProperty() ObjectPropertyDomain( ) @@ -14941,8 +14948,8 @@ AnnotationAssertion( ) AnnotationAssertion( "occurs_in") AnnotationAssertion(rdfs:comment "Paraphrase of definition: a relation between a process and an independent continuant, in which the process takes place entirely within the independent continuant") -AnnotationAssertion(rdfs:label "occurs in") AnnotationAssertion(rdfs:label "occurs in"@en) +AnnotationAssertion(rdfs:label "occurs in") AnnotationAssertion(rdfs:seeAlso "https://wiki.geneontology.org/Occurs_in"^^xsd:anyURI) InverseObjectProperties( ) ObjectPropertyDomain( ) @@ -14990,8 +14997,8 @@ AnnotationAssertion( "external") AnnotationAssertion( "bearer_of") AnnotationAssertion( "bearer_of") -AnnotationAssertion(rdfs:label "bearer of") AnnotationAssertion(rdfs:label "has characteristic"@en) +AnnotationAssertion(rdfs:label "bearer of") InverseFunctionalObjectProperty() ObjectPropertyRange( ) @@ -15002,8 +15009,8 @@ AnnotationAssertion( "external") AnnotationAssertion( "participates_in") AnnotationAssertion( "participates_in") -AnnotationAssertion(rdfs:label "participates in") AnnotationAssertion(rdfs:label "participates in"@en) +AnnotationAssertion(rdfs:label "participates in") InverseObjectProperties( ) ObjectPropertyDomain( ) ObjectPropertyRange( ) @@ -15016,8 +15023,8 @@ AnnotationAssertion( "external") AnnotationAssertion( "has_participant") AnnotationAssertion( "has_participant") -AnnotationAssertion(rdfs:label "has participant") AnnotationAssertion(rdfs:label "has participant"@en) +AnnotationAssertion(rdfs:label "has participant") ObjectPropertyDomain( ) ObjectPropertyRange( ) @@ -15124,8 +15131,8 @@ AnnotationAssertion( ) AnnotationAssertion( "bounding_layer_of") AnnotationAssertion(rdfs:comment "A relationship that applies between a continuant and its outer, bounding layer. Examples include the relationship between a multicellular organism and its integument, between an animal cell and its plasma membrane, and between a membrane bound organelle and its outer/bounding membrane.") -AnnotationAssertion(rdfs:label "bounding layer of") AnnotationAssertion(rdfs:label "bounding layer of"@en) +AnnotationAssertion(rdfs:label "bounding layer of") SubObjectPropertyOf( ) ObjectPropertyDomain( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) ObjectPropertyRange( ) @@ -15170,8 +15177,8 @@ AnnotationAssertion( "immediately_preceded_by") AnnotationAssertion( "immediately_preceded_by") AnnotationAssertion(rdfs:comment "X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y)"@en) -AnnotationAssertion(rdfs:label "immediately preceded by") AnnotationAssertion(rdfs:label "immediately preceded by"@en) +AnnotationAssertion(rdfs:label "immediately preceded by") SubObjectPropertyOf( ) InverseObjectProperties( ) @@ -15183,8 +15190,8 @@ AnnotationAssertion( ) AnnotationAssertion( "immediately_precedes") AnnotationAssertion(rdfs:comment "X immediately_precedes_Y iff: end(X) simultaneous_with start(Y)"@en) -AnnotationAssertion(rdfs:label "immediately precedes") AnnotationAssertion(rdfs:label "immediately precedes"@en) +AnnotationAssertion(rdfs:label "immediately precedes") SubObjectPropertyOf( ) # Object Property: (has soma location) @@ -15290,8 +15297,8 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( "overlaps") -AnnotationAssertion(rdfs:label "overlaps") AnnotationAssertion(rdfs:label "overlaps"@en) +AnnotationAssertion(rdfs:label "overlaps") SubObjectPropertyOf( ) SymmetricObjectProperty() @@ -15412,8 +15419,8 @@ AnnotationAssertion( "has_component") AnnotationAssertion( ) AnnotationAssertion( "has_component") -AnnotationAssertion(rdfs:label "has component") AnnotationAssertion(rdfs:label "has component"@en) +AnnotationAssertion(rdfs:label "has component") AnnotationAssertion(rdfs:seeAlso ) SubObjectPropertyOf( ) @@ -15477,8 +15484,8 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( "regulates") -AnnotationAssertion(rdfs:label "regulates") AnnotationAssertion(rdfs:label "regulates"@en) +AnnotationAssertion(rdfs:label "regulates") SubObjectPropertyOf( ) InverseObjectProperties( ) TransitiveObjectProperty() @@ -15496,8 +15503,8 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( "negatively_regulates") -AnnotationAssertion(rdfs:label "negatively regulates") AnnotationAssertion(rdfs:label "negatively regulates"@en) +AnnotationAssertion(rdfs:label "negatively regulates") SubObjectPropertyOf( ) SubObjectPropertyOf( ) InverseObjectProperties( ) @@ -15512,8 +15519,8 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( "positively_regulates") -AnnotationAssertion(rdfs:label "positively regulates") AnnotationAssertion(rdfs:label "positively regulates"@en) +AnnotationAssertion(rdfs:label "positively regulates") SubObjectPropertyOf( ) SubObjectPropertyOf( ) InverseObjectProperties( ) @@ -15527,8 +15534,8 @@ AnnotationAssertion( "capable_of") AnnotationAssertion( ) AnnotationAssertion( "capable_of") -AnnotationAssertion(rdfs:label "capable of") AnnotationAssertion(rdfs:label "capable of"@en) +AnnotationAssertion(rdfs:label "capable of") SubObjectPropertyOf( ) ObjectPropertyDomain( ) ObjectPropertyRange( ) @@ -15540,8 +15547,8 @@ AnnotationAssertion( "external") AnnotationAssertion( "capable_of_part_of") AnnotationAssertion( "capable_of_part_of") -AnnotationAssertion(rdfs:label "capable of part of") AnnotationAssertion(rdfs:label "capable of part of"@en) +AnnotationAssertion(rdfs:label "capable of part of") AnnotationAssertion(rdfs:seeAlso ) SubObjectPropertyOf( ) SubObjectPropertyOf( ) @@ -15564,8 +15571,8 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( "adjacent_to") -AnnotationAssertion(rdfs:label "adjacent to") AnnotationAssertion(rdfs:label "adjacent to"@en) +AnnotationAssertion(rdfs:label "adjacent to") SubObjectPropertyOf( ) ObjectPropertyDomain( ) ObjectPropertyRange( ) @@ -15602,8 +15609,8 @@ AnnotationAssertion( "starts_with") AnnotationAssertion( ) AnnotationAssertion( "starts_with") -AnnotationAssertion(rdfs:label "starts with") AnnotationAssertion(rdfs:label "starts with"@en) +AnnotationAssertion(rdfs:label "starts with") SubObjectPropertyOf( ) SubObjectPropertyOf( ) TransitiveObjectProperty() @@ -15638,8 +15645,8 @@ AnnotationAssertion( "ends_with") AnnotationAssertion( ) AnnotationAssertion( "ends_with") -AnnotationAssertion(rdfs:label "ends with") AnnotationAssertion(rdfs:label "ends with"@en) +AnnotationAssertion(rdfs:label "ends with") SubObjectPropertyOf( ) SubObjectPropertyOf( ) TransitiveObjectProperty() @@ -15652,8 +15659,8 @@ AnnotationAssertion( "has_start_location") AnnotationAssertion( ) AnnotationAssertion( "has_start_location") -AnnotationAssertion(rdfs:label "has start location") AnnotationAssertion(rdfs:label "has start location"@en) +AnnotationAssertion(rdfs:label "has start location") SubObjectPropertyOf( ) ObjectPropertyDomain( ) ObjectPropertyRange( ) @@ -15666,8 +15673,8 @@ AnnotationAssertion( "has_end_location") AnnotationAssertion( ) AnnotationAssertion( "has_end_location") -AnnotationAssertion(rdfs:label "has end location") AnnotationAssertion(rdfs:label "has end location"@en) +AnnotationAssertion(rdfs:label "has end location") SubObjectPropertyOf( ) ObjectPropertyDomain( ) ObjectPropertyRange( ) @@ -15683,8 +15690,8 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( "has_input") -AnnotationAssertion(rdfs:label "has input") AnnotationAssertion(rdfs:label "has input"@en) +AnnotationAssertion(rdfs:label "has input") AnnotationAssertion(rdfs:seeAlso "https://wiki.geneontology.org/Has_input"^^xsd:anyURI) SubObjectPropertyOf( ) InverseObjectProperties( ) @@ -15701,8 +15708,8 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( "has_output") -AnnotationAssertion(rdfs:label "has output") AnnotationAssertion(rdfs:label "has output"@en) +AnnotationAssertion(rdfs:label "has output") AnnotationAssertion(rdfs:seeAlso "https://wiki.geneontology.org/Has_output"^^xsd:anyURI) SubObjectPropertyOf( ) InverseObjectProperties( ) @@ -15816,8 +15823,8 @@ AnnotationAssertion( "external") AnnotationAssertion( "results_in_developmental_progression_of") AnnotationAssertion( "results_in_developmental_progression_of") -AnnotationAssertion(rdfs:label "results in developmental progression of") AnnotationAssertion(rdfs:label "results in developmental progression of"@en) +AnnotationAssertion(rdfs:label "results in developmental progression of") AnnotationAssertion(rdfs:seeAlso ) SubObjectPropertyOf( ) ObjectPropertyDomain( ) @@ -15833,8 +15840,8 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( "results_in_development_of") -AnnotationAssertion(rdfs:label "results in development of") AnnotationAssertion(rdfs:label "results in development of"@en) +AnnotationAssertion(rdfs:label "results in development of") SubObjectPropertyOf( ) SubObjectPropertyOf( ) @@ -15847,8 +15854,8 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( "results_in_formation_of") -AnnotationAssertion(rdfs:label "results in formation of") AnnotationAssertion(rdfs:label "results in formation of anatomical entity"@en) +AnnotationAssertion(rdfs:label "results in formation of") SubObjectPropertyOf( ) SubObjectPropertyOf( ) InverseObjectProperties( ) @@ -15863,8 +15870,8 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( "results_in_morphogenesis_of") -AnnotationAssertion(rdfs:label "results in morphogenesis of") AnnotationAssertion(rdfs:label "results in morphogenesis of"@en) +AnnotationAssertion(rdfs:label "results in morphogenesis of") SubObjectPropertyOf( ) SubObjectPropertyOf( ) @@ -15878,8 +15885,8 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( "results_in_maturation_of") -AnnotationAssertion(rdfs:label "results in maturation of") AnnotationAssertion(rdfs:label "results in maturation of"@en) +AnnotationAssertion(rdfs:label "results in maturation of") SubObjectPropertyOf( ) SubObjectPropertyOf( ) @@ -15931,8 +15938,8 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( "results_in_acquisition_of_features_of") -AnnotationAssertion(rdfs:label "results in acquisition of features of") AnnotationAssertion(rdfs:label "results in acquisition of features of"@en) +AnnotationAssertion(rdfs:label "results in acquisition of features of") SubObjectPropertyOf( ) SubObjectPropertyOf( ) ObjectPropertyRange( ) @@ -15977,8 +15984,8 @@ AnnotationAssertion( "external") AnnotationAssertion( "regulates_levels_of") AnnotationAssertion( "regulates_levels_of") -AnnotationAssertion(rdfs:label "regulates levels of") AnnotationAssertion(rdfs:label "regulates levels of"@en) +AnnotationAssertion(rdfs:label "regulates levels of") SubObjectPropertyOf( ) ObjectPropertyDomain( ) ObjectPropertyRange( ) @@ -15991,8 +15998,8 @@ AnnotationAssertion( "regulated_by") AnnotationAssertion( ) AnnotationAssertion( "regulated_by") -AnnotationAssertion(rdfs:label "regulated by") AnnotationAssertion(rdfs:label "regulated by"@en) +AnnotationAssertion(rdfs:label "regulated by") SubObjectPropertyOf( ) TransitiveObjectProperty() ObjectPropertyDomain( ) @@ -16006,8 +16013,8 @@ AnnotationAssertion( "negatively_regulated_by") AnnotationAssertion( ) AnnotationAssertion( "negatively_regulated_by") -AnnotationAssertion(rdfs:label "negatively regulated by") AnnotationAssertion(rdfs:label "negatively regulated by"@en) +AnnotationAssertion(rdfs:label "negatively regulated by") SubObjectPropertyOf( ) # Object Property: (positively regulated by) @@ -16018,8 +16025,8 @@ AnnotationAssertion( "positively_regulated_by") AnnotationAssertion( ) AnnotationAssertion( "positively_regulated_by") -AnnotationAssertion(rdfs:label "positively regulated by") AnnotationAssertion(rdfs:label "positively regulated by"@en) +AnnotationAssertion(rdfs:label "positively regulated by") SubObjectPropertyOf( ) # Object Property: (related via localization to) @@ -16039,8 +16046,8 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( "has_target_start_location") -AnnotationAssertion(rdfs:label "has target start location") AnnotationAssertion(rdfs:label "has target start location"@en) +AnnotationAssertion(rdfs:label "has target start location") SubObjectPropertyOf( ) # Object Property: (has target end location) @@ -16053,8 +16060,8 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( "has_target_end_location") -AnnotationAssertion(rdfs:label "has target end location") AnnotationAssertion(rdfs:label "has target end location"@en) +AnnotationAssertion(rdfs:label "has target end location") SubObjectPropertyOf( ) # Object Property: (results in transport along) @@ -16064,8 +16071,8 @@ AnnotationAssertion( "external") AnnotationAssertion( "results_in_transport_along") AnnotationAssertion( "results_in_transport_along") -AnnotationAssertion(rdfs:label "results in transport along") AnnotationAssertion(rdfs:label "results in transport along"@en) +AnnotationAssertion(rdfs:label "results in transport along") SubObjectPropertyOf( ) # Object Property: (results in transport across) @@ -16076,8 +16083,8 @@ AnnotationAssertion( "results_in_transport_across") AnnotationAssertion( ) AnnotationAssertion( "results_in_transport_across") -AnnotationAssertion(rdfs:label "results in transport across") AnnotationAssertion(rdfs:label "results in transport across"@en) +AnnotationAssertion(rdfs:label "results in transport across") SubObjectPropertyOf( ) SubObjectPropertyOf( ) @@ -16087,8 +16094,8 @@ AnnotationAssertion( "external") AnnotationAssertion( "results_in_growth_of") AnnotationAssertion( "results_in_growth_of") -AnnotationAssertion(rdfs:label "results in growth of") AnnotationAssertion(rdfs:label "results in growth of"@en) +AnnotationAssertion(rdfs:label "results in growth of") SubObjectPropertyOf( ) SubObjectPropertyOf( ) @@ -16098,8 +16105,8 @@ AnnotationAssertion( "external") AnnotationAssertion( "results_in_transport_to_from_or_in") AnnotationAssertion( "results_in_transport_to_from_or_in") -AnnotationAssertion(rdfs:label "results in transport to from or in") AnnotationAssertion(rdfs:label "results in transport to from or in"@en) +AnnotationAssertion(rdfs:label "results in transport to from or in") SubObjectPropertyOf( ) # Object Property: (member of) @@ -16133,8 +16140,8 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( "output_of") -AnnotationAssertion(rdfs:label "output of") AnnotationAssertion(rdfs:label "output of"@en) +AnnotationAssertion(rdfs:label "output of") SubObjectPropertyOf( ) SubObjectPropertyOf( ) @@ -16252,8 +16259,8 @@ AnnotationAssertion( "external") AnnotationAssertion( "causally_downstream_of") AnnotationAssertion( "causally_downstream_of") -AnnotationAssertion(rdfs:label "causally downstream of") AnnotationAssertion(rdfs:label "causally downstream of"@en) +AnnotationAssertion(rdfs:label "causally downstream of") SubObjectPropertyOf( ) SubObjectPropertyOf( ) InverseObjectProperties( ) @@ -16287,8 +16294,8 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( "causally_upstream_of") -AnnotationAssertion(rdfs:label "causally upstream of") AnnotationAssertion(rdfs:label "causally upstream of"@en) +AnnotationAssertion(rdfs:label "causally upstream of") SubObjectPropertyOf( ) SubObjectPropertyOf( ) TransitiveObjectProperty() @@ -16642,8 +16649,8 @@ AnnotationAssertion( ) AnnotationAssertion( "produces") AnnotationAssertion(rdfs:comment "Note that this definition doesn't quite distinguish the output of a transformation process from a production process, which is related to the identity/granularity issue.") -AnnotationAssertion(rdfs:label "produces") AnnotationAssertion(rdfs:label "produces"@en) +AnnotationAssertion(rdfs:label "produces") InverseObjectProperties( ) ObjectPropertyDomain( ) ObjectPropertyRange( ) @@ -16656,8 +16663,8 @@ AnnotationAssertion( "produced_by") AnnotationAssertion( ) AnnotationAssertion( "produced_by") -AnnotationAssertion(rdfs:label "produced by") AnnotationAssertion(rdfs:label "produced by"@en) +AnnotationAssertion(rdfs:label "produced by") ObjectPropertyDomain( ) ObjectPropertyRange( ) @@ -16737,8 +16744,8 @@ AnnotationAssertion( "external") AnnotationAssertion( "has_small_molecule_activator") AnnotationAssertion( "has_small_molecule_activator") -AnnotationAssertion(rdfs:label "has small molecule activator") AnnotationAssertion(rdfs:label "has small molecule activator"@en) +AnnotationAssertion(rdfs:label "has small molecule activator") SubObjectPropertyOf( ) InverseObjectProperties( ) @@ -16754,8 +16761,8 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( "acts_on_population_of") -AnnotationAssertion(rdfs:label "acts on population of") AnnotationAssertion(rdfs:label "acts on population of"@en) +AnnotationAssertion(rdfs:label "acts on population of") SubObjectPropertyOf( ) # Object Property: (is small molecule regulator of) @@ -16787,8 +16794,8 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( "results_in_fusion_of") -AnnotationAssertion(rdfs:label "results in fusion of") AnnotationAssertion(rdfs:label "results in fusion of"@en) +AnnotationAssertion(rdfs:label "results in fusion of") SubObjectPropertyOf( ) # Object Property: (has synaptic IO in region) @@ -16812,6 +16819,16 @@ AnnotationAssertion(rdfs:label "has SubObjectPropertyOf( ) ObjectPropertyDomain( ) +# Object Property: (has characterizing marker set) + +AnnotationAssertion( "A relation that applies between a cell type and a set of markers that can be used to uniquely identify that cell type.") +AnnotationAssertion( "C has_characterizing_marker_set y iff: C is a cell type and y is a collection of genes or proteins whose expression is sufficient to distinguish cell type C from most or all other cell types.") +AnnotationAssertion( ) +AnnotationAssertion( "has marker gene combination") +AnnotationAssertion( "has marker signature set") +AnnotationAssertion(rdfs:label "has characterizing marker set") +ObjectPropertyDomain( ) + # Object Property: (different in magnitude relative to) AnnotationAssertion(Annotation( "https://orcid.org/0000-0002-6601-2165") "q1 different_in_magnitude_relative_to q2 if and only if magnitude(q1) NOT =~ magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale.") @@ -17071,7 +17088,7 @@ SubClassOf( ) -# Class: (cell) +# Class: () DisjointClasses( ) DisjointClasses( ) @@ -69077,6 +69094,9 @@ AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0051932") AnnotationAssertion(rdfs:label "synaptic transmission, GABAergic") +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (catecholamine transport) @@ -112266,6 +112286,7 @@ SubClassOf( (Saccharomycotina) AnnotationAssertion( "GC_ID:1") +AnnotationAssertion( "PMID:38895705") AnnotationAssertion(Annotation( ) "true yeasts") AnnotationAssertion( "ncbi_taxonomy") AnnotationAssertion( "NCBITaxon:147537") @@ -112986,6 +113007,7 @@ SubClassOf( (Saccharomycetes) AnnotationAssertion( "GC_ID:1") +AnnotationAssertion( "PMID:38895705") AnnotationAssertion( "ncbi_taxonomy") AnnotationAssertion(Annotation( ) "Hemiascomycetes") AnnotationAssertion( "NCBITaxon:4891") @@ -112995,6 +113017,7 @@ SubClassOf( (Saccharomycetales) AnnotationAssertion( "GC_ID:1") +AnnotationAssertion( "PMID:38895705") AnnotationAssertion( "ncbi_taxonomy") AnnotationAssertion(Annotation( ) "Endomycetales") AnnotationAssertion(Annotation( ) "budding yeasts") @@ -113057,6 +113080,7 @@ AnnotationAssertion( ) "Candida robusta") AnnotationAssertion(Annotation( ) "Mycoderma cerevisiae") AnnotationAssertion(Annotation( ) "Saccharomyces capensis") +AnnotationAssertion(Annotation( ) "Saccharomyces cerevisiae (Desm.) Meyen ex E.C. Hansen, 1883") AnnotationAssertion(Annotation( ) "Saccharomyces diastaticus") AnnotationAssertion(Annotation( ) "Saccharomyces italicus") AnnotationAssertion(Annotation( ) "Saccharomyces oviformis") @@ -116653,6 +116677,16 @@ AnnotationAssertion(rdfs:comment " AnnotationAssertion(rdfs:label "alpha-(1,3)-fucosyltransferase") SubClassOf( ) +# Class: (beta-1,3-glucuronyltransferase) + +AnnotationAssertion(Annotation( "PRO:WCB") "A protein with a core domain structure consisting of a very small cytoplasmic domain followed by a transmembrane domain and a Glycosyltransferase family 43 (Pfam:PF03360) domain.") +AnnotationAssertion( "PIRSF:PIRSF016413") +AnnotationAssertion( "protein") +AnnotationAssertion( "PR:000001325") +AnnotationAssertion(rdfs:comment "Category=family.") +AnnotationAssertion(rdfs:label "beta-1,3-glucuronyltransferase") +SubClassOf( ) + # Class: (bone marrow stromal antigen 2) AnnotationAssertion(Annotation( "PRO:WCB") "A protein that is a translation product of the human BST2 gene or a 1:1 ortholog thereof.") @@ -116973,6 +117007,22 @@ AnnotationAssertion(rdfs:comment " AnnotationAssertion(rdfs:label "CD80 molecule") SubClassOf( ) +# Class: (galactosylgalactosylxylosylprotein 3-beta-glucuronosyltransferase 1) + +AnnotationAssertion(Annotation( "PRO:WCB") "A beta-1,3-glucuronyltransferase that is a translation product of the human B3GAT1 gene or a 1:1 ortholog thereof.") +AnnotationAssertion(Annotation( "PRO:DNx") Annotation( ) "B3GAT1") +AnnotationAssertion( "GlcAT-P") +AnnotationAssertion( "GlcUAT-P") +AnnotationAssertion( "UDP-GlcUA:glycoprotein beta-1,3-glucuronyltransferase") +AnnotationAssertion( "beta-1,3-glucuronyltransferase 1") +AnnotationAssertion( "glucuronosyltransferase P") +AnnotationAssertion( "protein") +AnnotationAssertion(Annotation( ) "GLCATP") +AnnotationAssertion( "PR:000001440") +AnnotationAssertion(rdfs:comment "Category=gene.") +AnnotationAssertion(rdfs:label "galactosylgalactosylxylosylprotein 3-beta-glucuronosyltransferase 1") +SubClassOf( ) + # Class: (cadherin-5) AnnotationAssertion(Annotation( "PRO:WCB") "A cadherin that is a translation product of the human CDH5 gene or a 1:1 ortholog thereof.") @@ -129127,6 +129177,26 @@ SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +# Class: (galactosylgalactosylxylosylprotein 3-beta-glucuronosyltransferase 1 (mouse)) + +AnnotationAssertion(Annotation( "OMA:Q9CW73") Annotation( "PRO:DNx") "A galactosylgalactosylxylosylprotein 3-beta-glucuronosyltransferase 1 that is encoded in the genome of mouse.") +AnnotationAssertion( "UniProtKB:Q9CW73") +AnnotationAssertion(Annotation( "UniProtKB:Q9CW73") "GlcAT-P (mouse)") +AnnotationAssertion(Annotation( "UniProtKB:Q9CW73") "GlcUAT-P (mouse)") +AnnotationAssertion(Annotation( "UniProtKB:Q9CW73") "UDP-GlcUA:glycoprotein beta-1,3-glucuronyltransferase (mouse)") +AnnotationAssertion(Annotation( "UniProtKB:Q9CW73") "beta-1,3-glucuronyltransferase 1 (mouse)") +AnnotationAssertion(Annotation( "UniProtKB:Q9CW73") "glucuronosyltransferase P (mouse)") +AnnotationAssertion(Annotation( "PRO:DNx") Annotation( ) "mB3GAT1") +AnnotationAssertion( "protein") +AnnotationAssertion(Annotation( "UniProtKB:Q9CW73") Annotation( ) "B3gat1") +AnnotationAssertion( "PR:Q9CW73") +AnnotationAssertion(rdfs:comment "Category=organism-gene.") +AnnotationAssertion(rdfs:label "galactosylgalactosylxylosylprotein 3-beta-glucuronosyltransferase 1 (mouse)") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + # Class: (DBH-like monooxygenase protein 1 (mouse)) AnnotationAssertion(Annotation( "OMA:Q9CXI3") Annotation( "PRO:DNx") "A DBH-like monooxygenase protein 1 that is encoded in the genome of mouse.") @@ -129457,6 +129527,28 @@ SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +# Class: (galactosylgalactosylxylosylprotein 3-beta-glucuronosyltransferase 1 (human)) + +AnnotationAssertion(Annotation( "PRO:WCB") Annotation( "UniProtKB:Q9P2W7") "A galactosylgalactosylxylosylprotein 3-beta-glucuronosyltransferase 1 that is encoded in the genome of human.") +AnnotationAssertion(Annotation(rdfs:label "PR:Q9P2W7 located_in GO:0000139") "Reactome:R-HSA-1889953") +AnnotationAssertion( "UniProtKB:Q9P2W7") +AnnotationAssertion( "GlcAT-P (human)") +AnnotationAssertion(Annotation( "UniProtKB:Q9P2W7") "GlcUAT-P (human)") +AnnotationAssertion(Annotation( "UniProtKB:Q9P2W7") "UDP-GlcUA:glycoprotein beta-1,3-glucuronyltransferase (human)") +AnnotationAssertion(Annotation( "UniProtKB:Q9P2W7") "beta-1,3-glucuronyltransferase 1 (human)") +AnnotationAssertion(Annotation( "UniProtKB:Q9P2W7") "glucuronosyltransferase P (human)") +AnnotationAssertion(Annotation( "PRO:DNx") Annotation( ) "hB3GAT1") +AnnotationAssertion( "protein") +AnnotationAssertion(Annotation( "UniProtKB:Q9P2W7") Annotation( ) "B3GAT1") +AnnotationAssertion(Annotation( "UniProtKB:Q9P2W7") Annotation( ) "GLCATP") +AnnotationAssertion( "PR:Q9P2W7") +AnnotationAssertion(rdfs:comment "Category=organism-gene.") +AnnotationAssertion(rdfs:label "galactosylgalactosylxylosylprotein 3-beta-glucuronosyltransferase 1 (human)") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + # Class: (integrin alpha-IIb (mouse)) AnnotationAssertion(Annotation( "OMA:Q9QUM0") Annotation( "PRO:DNx") "An integrin alpha-IIb that is encoded in the genome of mouse.") @@ -130766,7 +130858,6 @@ AnnotationAssertion( "WBbt:0005739") AnnotationAssertion( "Wikipedia:Head") AnnotationAssertion( "XAO:0003024") -AnnotationAssertion( "ZFA:0001114") AnnotationAssertion( "galen:Head") AnnotationAssertion(Annotation( "FMA:7154") "head (volume)") AnnotationAssertion( "adult head") @@ -138025,7 +138116,7 @@ AnnotationAssertion( "ZFA:0000560") AnnotationAssertion(Annotation( "http://orcid.org/0000-0002-6601-2165") "ovarian duct") AnnotationAssertion(Annotation( "http://orcid.org/0000-0002-6601-2165") "ovarian tube") -AnnotationAssertion( "uterine tube") +AnnotationAssertion( "uterine tube") AnnotationAssertion( "uberon") AnnotationAssertion(Annotation( "http://orcid.org/0000-0002-6601-2165") "female reproductive tracts") AnnotationAssertion(Annotation( "ZFA:0000560") Annotation( ) "oviducts") @@ -138527,7 +138618,6 @@ AnnotationAssertion(Annotation( "Wikipedia:Acoelomorpha") ) AnnotationAssertion( ) AnnotationAssertion( ) -AnnotationAssertion( ) AnnotationAssertion( "AAO:0000959") AnnotationAssertion( "CALOHA:TS-2103") AnnotationAssertion( "VHOG:0001248") @@ -138535,7 +138625,6 @@ AnnotationAssertion( "uberon") AnnotationAssertion(Annotation( "Wikipedia:Circulatory_system") Annotation( ) "systema cardiovasculare") AnnotationAssertion( "UBERON:0001009") -AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "circulatory system") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/2/29/Circulatory_System_en.svg"^^xsd:anyURI) @@ -157908,6 +157997,7 @@ SubClassOf( ) SubClassOf( ) SubClassOf(Annotation( "some species only have a single lung") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -162820,7 +162910,6 @@ AnnotationAssertion( "SCTID:361348008") AnnotationAssertion( "TAO:0001438") AnnotationAssertion(Annotation( "ncithesaurus:Cavity") "UMLS:C0333343") -AnnotationAssertion( "ZFA:0001438") AnnotationAssertion( "galen:BodyCavity") AnnotationAssertion(Annotation( "EHDAA2:0000267") "coelomic cavity") AnnotationAssertion(Annotation( "EHDAA2:0000267") "coelomic cavity lumen") @@ -164228,6 +164317,7 @@ SubClassOf( ObjectSomeValuesFrom( # Class: (tonsil) AnnotationAssertion(Annotation( "MGI:cwg") Annotation( "MP:0002380") "Either of the two small almond-shaped masses of lymph tissue found on either side of the oropharynx.") +AnnotationAssertion( ) AnnotationAssertion( "BTO:0001387") AnnotationAssertion( "CALOHA:TS-1053") AnnotationAssertion( "EFO:0001401") @@ -164248,6 +164338,7 @@ AnnotationAssertion( "BTO:0001387") "Mandel") AnnotationAssertion( "UBERON:0002372") AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "tonsil") @@ -166126,6 +166217,7 @@ DisjointClasses( (lymphoid system) AnnotationAssertion(Annotation( "Wikipedia:Lymphoid_system") "The lymphatic system in vertebrates is a network of conduits that carry a clear fluid called lymph. It also includes the lymphoid tissue through which the lymph travels. Lymphoid tissue is found in many organs, particularly the lymph nodes, and in the lymphoid follicles associated with the digestive system such as the tonsils. The system also includes all the structures dedicated to the circulation and production of lymphocytes, which includes the spleen, thymus, bone marrow and the lymphoid tissue associated with the digestive system[WP].") +AnnotationAssertion( ) AnnotationAssertion( "EHDAA2:0001043") AnnotationAssertion( "EHDAA:8677") AnnotationAssertion(Annotation( "MA:th") "EMAPA:37664") @@ -166148,6 +166240,7 @@ AnnotationAssertion(Annotation( "https://orcid.org/0000-0002-6601-2165") "lymphatic drainage system") AnnotationAssertion(Annotation( "Wikipedia:Lymphoid_system") Annotation( ) "systema lymphoideum") AnnotationAssertion( "UBERON:0002465") +AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "lymphoid system") @@ -167160,7 +167253,7 @@ SubClassOf( "EHDAA2") ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf(Annotation( "PMID:16313389") ObjectSomeValuesFrom( )) +SubClassOf(Annotation( "PMID:16313389") ObjectSomeValuesFrom( )) SubClassOf(Annotation( "http://tolweb.org/Chordata/2499") ObjectSomeValuesFrom( )) SubClassOf(Annotation( "PMID:16313389") ObjectSomeValuesFrom( )) @@ -172149,6 +172242,7 @@ SubClassOf( ObjectSomeValuesFrom( # Class: (mucosa of rectum) AnnotationAssertion(Annotation( "OBOL:automatic") "A mucosa that is part of a rectum [Automatically generated definition].") +AnnotationAssertion( ) AnnotationAssertion( "CALOHA:TS-2107") AnnotationAssertion( "EMAPA:27081") AnnotationAssertion( "FMA:15033") @@ -172165,6 +172259,7 @@ AnnotationAssertion(Annotation( "OBOL:automatic") "rectum organ mucosa") AnnotationAssertion( "uberon") AnnotationAssertion( "UBERON:0003346") +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "mucosa of rectum") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) @@ -178396,6 +178491,7 @@ SubClassOf(Annotation( "Wik AnnotationAssertion(Annotation( "MGI:smb") Annotation( "MP:0003574") Annotation( "http://orcid.org/0000-0002-6601-2165") "Initial section of the oviduct through which the ova pass from the ovary to the uterus.") AnnotationAssertion( ) +AnnotationAssertion(Annotation( "https://sourceforge.net/p/geneontology/ontology-requests/8397/") "mammalian oviduct") AnnotationAssertion(Annotation( ) "salpinges") AnnotationAssertion( "salpinx") AnnotationAssertion( "CALOHA:TS-0732") @@ -178411,10 +178507,9 @@ AnnotationAssertion( "ncithesaurus:Fallopian_Tube") "UMLS:C0015560") AnnotationAssertion( "Wikipedia:Fallopian_tube") AnnotationAssertion( "galen:FallopianTube") -AnnotationAssertion(Annotation( "https://sourceforge.net/p/geneontology/ontology-requests/8397/") "mammalian oviduct") AnnotationAssertion( "uterine tube (sensu Mammalia)") AnnotationAssertion( "uberon") -AnnotationAssertion( "fallopian tubes") +AnnotationAssertion(Annotation( ) "fallopian tubes") AnnotationAssertion(Annotation( "EHDAA2:0000504") "female paramesonephric duct") AnnotationAssertion(Annotation( "EMAPA:35660") "paramesonephric duct of female") AnnotationAssertion(Annotation( "Wikipedia:Fallopian_tube") Annotation( ) "tuba uterina") @@ -183154,7 +183249,6 @@ AnnotationAssertion( "pharyngeal arch artery") AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/8/84/Gray473.png"^^xsd:anyURI) SubClassOf( ) -SubClassOf( ) SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) @@ -184782,7 +184876,6 @@ SubClassOf( ObjectSomeValuesFrom( # Class: (arterial system) AnnotationAssertion(Annotation( "https://orcid.org/0000-0002-6601-2165") "The part of the cardiovascular system consisting of all arteries.") -AnnotationAssertion( ) AnnotationAssertion( "BTO:0004690") AnnotationAssertion( "EHDAA2:0000143") AnnotationAssertion( "EHDAA:396") @@ -184793,7 +184886,6 @@ AnnotationAssertion( "VHOG:0000273") AnnotationAssertion( "uberon") AnnotationAssertion( "UBERON:0004572") -AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "arterial system") SubClassOf(Annotation( "MA") ) @@ -184831,7 +184923,6 @@ SubClassOf( ObjectSomeValuesFrom( # Class: (venous system) AnnotationAssertion(Annotation( "https://orcid.org/0000-0002-6601-2165") "The part of the cardiovascular system consisting of all venous vessels. In vertebrates with a double circulation, this can be divided into systemic and pulmonary portions.") -AnnotationAssertion( ) AnnotationAssertion( "BTO:0004692") AnnotationAssertion( "EHDAA2:0002171") AnnotationAssertion( "EHDAA:486") @@ -184844,7 +184935,6 @@ AnnotationAssertion( "vein system") AnnotationAssertion( "uberon") AnnotationAssertion( "UBERON:0004582") -AnnotationAssertion( ) AnnotationAssertion(rdfs:label "venous system") SubClassOf(Annotation( "MA") ) SubClassOf( ObjectSomeValuesFrom( )) @@ -185511,10 +185601,10 @@ SubClassOf( ObjectSomeValuesFrom( # Class: (Peyer's patch epithelium) -AnnotationAssertion(Annotation( "ISBN:0-8153-1691-7") Annotation( "MGI:cwg") Annotation( "MP:0002388") "The specialized epithelium of the Peyer's patch.") +AnnotationAssertion(Annotation( "ISBN:0-8153-1691-7") Annotation( "MGI:cwg") Annotation( "MP:0002388") "The specialized epithelial layer covering the entire Peyer's patch, including both the follicular and interfollicular areas and forming part of the gut-associated lymphoid tissue.") AnnotationAssertion( "EMAPA:36506") AnnotationAssertion( "MA:0000731") -AnnotationAssertion(Annotation( "MA:0000731") "Peyer's patch epithelium") +AnnotationAssertion(Annotation( "MA:0000731") Annotation( "PMID:31813624") "Peyer's patch epithelium") AnnotationAssertion( "uberon") AnnotationAssertion( "UBERON:0004693") AnnotationAssertion( ) @@ -185997,24 +186087,21 @@ SubClassOf( ObjectSomeValuesFrom( # Class: (vasa recta) -AnnotationAssertion(Annotation( "Wikipedia:Vasa_recta") "In the blood supply of the kidney, the vasa recta renis (or straight arteries of kidney, or straight arterioles of kidney) form a series of straight capillaries in the medulla. They lie parallel to the loop of Henle. These vessels branch off the efferent arterioles of juxtamedullary nephrons (those nephrons closest to the medulla), enter the medulla, and surround the loop of Henle.") -AnnotationAssertion( "TODO - is this a vein or set of veins? in MA it is a venous blood vessel") +AnnotationAssertion(Annotation( "PMID:23126245") Annotation( "Wikipedia:Vasa_recta") "A group of microvessels that are part of the kidney. A vasa recta has a hairpin-like shape, entering the renal medulla as the straight arterioles and surrounds the loop of Henle, forming a capillary network. Finally it leaves the renal medulla to ascend to the cortex as the straight venules. The primary function of the vasa recta is to facilitate countercurrent exchange, which is essential for the kidney's ability to concentrate urine") AnnotationAssertion( ) AnnotationAssertion( "EMAPA:30043") AnnotationAssertion( "FMA:72006") AnnotationAssertion( "MA:0002595") AnnotationAssertion( "Wikipedia:Vasa_recta") AnnotationAssertion( "galen:ArteriaeRectae") -AnnotationAssertion(Annotation( "FMA:72006") Annotation( "FMA:TA") Annotation( ) "arteriolae rectae renis") AnnotationAssertion(Annotation( "MP:0011324") "kidney vasa recta") -AnnotationAssertion(Annotation( "EMAPA:30043") "renal medullary capillary") -AnnotationAssertion(Annotation( "FMA:72006") "set of straight arterioles of kidney") -AnnotationAssertion(Annotation( "FMA:72006") "straight arterioles of kidney") AnnotationAssertion(Annotation( "FMA:72006") "vasa recta of kidney") AnnotationAssertion(Annotation( "FMA:72006") Annotation( "FMA:TA") Annotation( ) "vasa recta renis") +AnnotationAssertion(Annotation( "FMA:72006") Annotation( "FMA:TA") Annotation( ) "arteriolae rectae renis") +AnnotationAssertion(Annotation( "EMAPA:30043") "renal medullary capillary") +AnnotationAssertion(Annotation( "FMA:72006") "set of straight arterioles of kidney") +AnnotationAssertion(Annotation( "FMA:72006") "straight arterioles of kidney") AnnotationAssertion( "uberon") -AnnotationAssertion(Annotation( "Wikipedia:Vasa_recta") "arteria recta") -AnnotationAssertion(Annotation( "Wikipedia:Vasa_recta") "arteriae rectae") AnnotationAssertion(Annotation( "Wikipedia:Vasa_recta") Annotation( ) "arteriolae rectae renis") AnnotationAssertion(Annotation( "Wikipedia:Vasa_recta") "arteriolae recti") AnnotationAssertion(Annotation( "Wikipedia:Vasa_recta") "vasa rectae") @@ -186023,7 +186110,7 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "vasa recta") AnnotationAssertion( "https://upload.wikimedia.org/wikipedia/commons/2/21/Kidney_nephron.png"^^xsd:anyURI) -SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (cochlear nerve) @@ -186574,8 +186661,6 @@ AnnotationAssertion( "outer renal medulla vasa recta") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) -SubClassOf( ) -SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -186599,8 +186684,6 @@ AnnotationAssertion( "inner renal medulla vasa recta") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) -SubClassOf( ) -SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -189176,6 +189259,7 @@ SubClassOf( ObjectSomeValuesFrom( # Class: (mucosa of ascending colon) AnnotationAssertion(Annotation( "OBOL:automatic") "A mucosa that is part of an ascending colon [Automatically generated definition].") +AnnotationAssertion( ) AnnotationAssertion( "FMA:15005") AnnotationAssertion(Annotation( "OBOL:automatic") "ascending colon mucosa") AnnotationAssertion(Annotation( "OBOL:automatic") "ascending colon mucosa of organ") @@ -189186,6 +189270,7 @@ AnnotationAssertion(Annotation( "OBOL:automatic") "organ mucosa of ascending colon") AnnotationAssertion( "uberon") AnnotationAssertion( "UBERON:0004990") +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "mucosa of ascending colon") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) @@ -189194,6 +189279,7 @@ SubClassOf( ObjectSomeValuesFrom( # Class: (mucosa of transverse colon) AnnotationAssertion(Annotation( "OBOL:automatic") "A mucosa that is part of a transverse colon [Automatically generated definition].") +AnnotationAssertion( ) AnnotationAssertion( "FMA:15012") AnnotationAssertion(Annotation( "OBOL:automatic") "mucosa of organ of transverse colon") AnnotationAssertion(Annotation( "OBOL:automatic") "mucous membrane of transverse colon") @@ -189204,6 +189290,7 @@ AnnotationAssertion(Annotation( "OBOL:automatic") "transverse colon organ mucosa") AnnotationAssertion( "uberon") AnnotationAssertion( "UBERON:0004991") +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "mucosa of transverse colon") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) @@ -189212,6 +189299,7 @@ SubClassOf( ObjectSomeValuesFrom( # Class: (mucosa of descending colon) AnnotationAssertion(Annotation( "OBOL:automatic") "A mucosa that is part of a descending colon [Automatically generated definition].") +AnnotationAssertion( ) AnnotationAssertion( "FMA:15019") AnnotationAssertion(Annotation( "OBOL:automatic") "descending colon mucosa") AnnotationAssertion(Annotation( "OBOL:automatic") "descending colon mucosa of organ") @@ -189222,6 +189310,7 @@ AnnotationAssertion(Annotation( "OBOL:automatic") "organ mucosa of descending colon") AnnotationAssertion( "uberon") AnnotationAssertion( "UBERON:0004992") +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "mucosa of descending colon") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) @@ -189230,6 +189319,7 @@ SubClassOf( ObjectSomeValuesFrom( # Class: (mucosa of sigmoid colon) AnnotationAssertion(Annotation( "OBOL:automatic") "A mucosa that is part of a sigmoid colon [Automatically generated definition].") +AnnotationAssertion( ) AnnotationAssertion( "FMA:15026") AnnotationAssertion(Annotation( "OBOL:automatic") "mucosa of organ of sigmoid colon") AnnotationAssertion(Annotation( "OBOL:automatic") "mucous membrane of sigmoid colon") @@ -189240,6 +189330,7 @@ AnnotationAssertion(Annotation( "OBOL:automatic") "sigmoid colon organ mucosa") AnnotationAssertion( "uberon") AnnotationAssertion( "UBERON:0004993") +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "mucosa of sigmoid colon") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) @@ -199422,6 +199513,7 @@ SubClassOf( ObjectSomeValuesFrom( AnnotationAssertion(Annotation( "http://orcid.org/0000-0002-6601-2165") "An organ system subdivision that is a network of vessels capable of removing accumulating protein and fluid from the interstitial space and returning it to the vascular space. In some species, this network is connected to the immune system via lymph nodes and lymphocyte-producing organs, with the whole being the lymphoid system.") AnnotationAssertion( "consider merging with lymph vasculature") +AnnotationAssertion( ) AnnotationAssertion( "AAO:0010522") AnnotationAssertion( "CALOHA:TS-2024") AnnotationAssertion( "EFO:0000870") @@ -199438,6 +199530,7 @@ AnnotationAssertion( "VHOG:0001761") "lymporeticular system") AnnotationAssertion( "UBERON:0006558") AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "lymphatic part of lymphoid system") SubClassOf( ) @@ -204152,6 +204245,7 @@ AnnotationAssertion( "SCTID:361355005") AnnotationAssertion(Annotation( "ncithesaurus:Head_and_Neck") "UMLS:C0460004") AnnotationAssertion( "WikipediaCategory:Head_and_neck") +AnnotationAssertion( "ZFA:0001114") AnnotationAssertion( "galen:HeadAndNeck") AnnotationAssertion( "uberon") AnnotationAssertion(Annotation( "https://github.com/obophenotype/uberon/issues/379") "cephalic area") @@ -206371,56 +206465,51 @@ SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) -# Class: (inner medulla vasa recta descending limb) +# Class: (inner medulla descending vasa recta) AnnotationAssertion( "KUPO:0001003") AnnotationAssertion( "uberon") AnnotationAssertion( "UBERON:0009089") -AnnotationAssertion(rdfs:label "inner medulla vasa recta descending limb") +AnnotationAssertion(rdfs:label "inner medulla descending vasa recta") SubClassOf( ) -SubClassOf( ) SubClassOf(Annotation( "KUPO") ObjectSomeValuesFrom( )) -# Class: (outer medulla vasa recta descending limb) +# Class: (outer medulla descending vasa recta) AnnotationAssertion( "KUPO:0001004") AnnotationAssertion( "uberon") AnnotationAssertion( "UBERON:0009090") -AnnotationAssertion(rdfs:label "outer medulla vasa recta descending limb") +AnnotationAssertion(rdfs:label "outer medulla descending vasa recta") SubClassOf( ) -SubClassOf( ) SubClassOf(Annotation( "KUPO") ObjectSomeValuesFrom( )) -# Class: (vasa recta ascending limb) +# Class: (ascending vasa recta) AnnotationAssertion( ) AnnotationAssertion( "KUPO:0001005") AnnotationAssertion( "uberon") AnnotationAssertion( "UBERON:0009091") AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "vasa recta ascending limb") +AnnotationAssertion(rdfs:label "ascending vasa recta") SubClassOf( ) -SubClassOf( ) SubClassOf(Annotation( "KUPO") ObjectSomeValuesFrom( )) -# Class: (inner medulla vasa recta ascending limb) +# Class: (inner medulla ascending vasa recta) AnnotationAssertion( "KUPO:0001006") AnnotationAssertion( "uberon") AnnotationAssertion( "UBERON:0009092") -AnnotationAssertion(rdfs:label "inner medulla vasa recta ascending limb") +AnnotationAssertion(rdfs:label "inner medulla ascending vasa recta") SubClassOf( ) -SubClassOf( ) SubClassOf(Annotation( "KUPO") ObjectSomeValuesFrom( )) -# Class: (outer medulla vasa recta ascending limb) +# Class: (outer medulla ascending vasa recta) AnnotationAssertion( "KUPO:0001007") AnnotationAssertion( "uberon") AnnotationAssertion( "UBERON:0009093") -AnnotationAssertion(rdfs:label "outer medulla vasa recta ascending limb") +AnnotationAssertion(rdfs:label "outer medulla ascending vasa recta") SubClassOf( ) -SubClassOf( ) SubClassOf(Annotation( "KUPO") ObjectSomeValuesFrom( )) # Class: (tip of renal papilla) @@ -206775,16 +206864,15 @@ SubClassOf( ) SubClassOf( ) -# Class: (vasa recta descending limb) +# Class: (descending vasa recta) AnnotationAssertion( ) AnnotationAssertion( "KUPO:0001002") AnnotationAssertion( "uberon") AnnotationAssertion( "UBERON:0009202") AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "vasa recta descending limb") +AnnotationAssertion(rdfs:label "descending vasa recta") SubClassOf( ) -SubClassOf( ) SubClassOf(Annotation( "KUPO") ObjectSomeValuesFrom( )) # Class: (medial nasal process mesenchyme) @@ -207028,7 +207116,7 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "pharyngeal arch mesenchymal region") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) +SubClassOf( ) SubClassOf(Annotation( "EHDAA2") ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -211167,7 +211255,6 @@ AnnotationAssertion( "UBERON:0010341") AnnotationAssertion(rdfs:label "1st arch mesenchyme from head mesenchyme") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) -SubClassOf( ) SubClassOf( ) SubClassOf( ) SubClassOf(Annotation( "EMAPA") ObjectSomeValuesFrom( )) @@ -211186,7 +211273,6 @@ AnnotationAssertion( "2nd arch mesenchyme from head mesenchyme") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) SubClassOf( ) -SubClassOf( ) SubClassOf( ) SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) @@ -211204,7 +211290,6 @@ AnnotationAssertion( "3rd arch mesenchyme from head mesenchyme") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) SubClassOf( ) -SubClassOf( ) SubClassOf( ) SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) @@ -211222,7 +211307,6 @@ AnnotationAssertion( "4th arch mesenchyme from head mesenchyme") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) SubClassOf( ) -SubClassOf( ) SubClassOf( ) SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) @@ -211237,7 +211321,6 @@ AnnotationAssertion( "UBERON:0010347") AnnotationAssertion(rdfs:label "6th arch mesenchyme from head mesenchyme") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) -SubClassOf( ) SubClassOf( ) SubClassOf( ) SubClassOf(Annotation( "EHDAA2") ObjectSomeValuesFrom( )) @@ -215681,6 +215764,7 @@ AnnotationAssertion( "Wikipedia:Acoelomorpha") ) AnnotationAssertion( "EHDAA2:0004731") AnnotationAssertion( "Wikipedia:Coelom") +AnnotationAssertion( "ZFA:0001438") AnnotationAssertion(Annotation( "NCBITaxon:33511") "enterocoelom") AnnotationAssertion( "haemocoelom") AnnotationAssertion( "schizocoelom") @@ -228758,6 +228842,18 @@ EquivalentClasses( ObjectIntersec SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +# Class: (embryonic craniocervical region) + +AnnotationAssertion(Annotation( "https://orcid.org/0000-0002-6095-8718") "A craniocervical region that is part of an embryo.") +AnnotationAssertion( ) +AnnotationAssertion( "2024-09-12T14:40:00Z"^^xsd:dateTime) +AnnotationAssertion( "uberon") +AnnotationAssertion( "UBERON:8450003") +AnnotationAssertion(rdfs:label "embryonic craniocervical region") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + # Class: (placental blood) AnnotationAssertion(Annotation( "http://orcid.org/0000-0001-6595-0902") Annotation( "https://www.ncbi.nlm.nih.gov/books/NBK53254/") "Blood located in the placenta.") @@ -229506,6 +229602,7 @@ SubClassOf(ObjectIntersectionOf( SubClassOf(Annotation( "FMA") ObjectIntersectionOf( ObjectSomeValuesFrom( )) ObjectSomeValuesFrom( )) SubClassOf(ObjectIntersectionOf( ObjectSomeValuesFrom( )) ObjectSomeValuesFrom( )) SubClassOf(Annotation( "EHDAA2") ObjectIntersectionOf( ObjectSomeValuesFrom( )) ObjectSomeValuesFrom( )) +SubClassOf(ObjectIntersectionOf(ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( )) ObjectSomeValuesFrom( )) SubClassOf(ObjectSomeValuesFrom( ) ) SubClassOf(ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( )) SubClassOf(ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( )) diff --git a/src/ontology/imports/pr_terms.txt b/src/ontology/imports/pr_terms.txt index 1aa01315a..697340509 100644 --- a/src/ontology/imports/pr_terms.txt +++ b/src/ontology/imports/pr_terms.txt @@ -49,4 +49,5 @@ PR:000013047 PR:000016626 PR:000003472 PR:000012318 -PR:000064867 \ No newline at end of file +PR:000064867 +PR:000001440 \ No newline at end of file diff --git a/src/templates/cellxgene_subset.tsv b/src/templates/cellxgene_subset.tsv index 0cf80642c..af6b80ddb 100644 --- a/src/templates/cellxgene_subset.tsv +++ b/src/templates/cellxgene_subset.tsv @@ -1,688 +1,806 @@ ID subset ID AI oboInOwl:inSubset -CL:4023015 http://purl.obolibrary.org/obo/cl#cellxgene_subset -CL:0002322 http://purl.obolibrary.org/obo/cl#cellxgene_subset -CL:0002324 http://purl.obolibrary.org/obo/cl#cellxgene_subset -CL:0008001 http://purl.obolibrary.org/obo/cl#cellxgene_subset -CL:4023181 http://purl.obolibrary.org/obo/cl#cellxgene_subset -CL:0008036 http://purl.obolibrary.org/obo/cl#cellxgene_subset -CL:0000878 http://purl.obolibrary.org/obo/cl#cellxgene_subset -CL:0005026 http://purl.obolibrary.org/obo/cl#cellxgene_subset -CL:0013000 http://purl.obolibrary.org/obo/cl#cellxgene_subset -CL:0000897 http://purl.obolibrary.org/obo/cl#cellxgene_subset -CL:0002092 http://purl.obolibrary.org/obo/cl#cellxgene_subset -CL:0000810 http://purl.obolibrary.org/obo/cl#cellxgene_subset -CL:0002544 http://purl.obolibrary.org/obo/cl#cellxgene_subset -CL:0000190 http://purl.obolibrary.org/obo/cl#cellxgene_subset -CL:1001045 http://purl.obolibrary.org/obo/cl#cellxgene_subset -CL:1000326 http://purl.obolibrary.org/obo/cl#cellxgene_subset -CL:0003050 http://purl.obolibrary.org/obo/cl#cellxgene_subset -CL:0009116 http://purl.obolibrary.org/obo/cl#cellxgene_subset -CL:0002366 http://purl.obolibrary.org/obo/cl#cellxgene_subset -CL:0000809 http://purl.obolibrary.org/obo/cl#cellxgene_subset -CL:0001050 http://purl.obolibrary.org/obo/cl#cellxgene_subset -CL:0002193 http://purl.obolibrary.org/obo/cl#cellxgene_subset -CL:0002678 http://purl.obolibrary.org/obo/cl#cellxgene_subset -CL:0000740 http://purl.obolibrary.org/obo/cl#cellxgene_subset -CL:0002377 http://purl.obolibrary.org/obo/cl#cellxgene_subset -CL:0000790 http://purl.obolibrary.org/obo/cl#cellxgene_subset -CL:0000931 http://purl.obolibrary.org/obo/cl#cellxgene_subset -CL:4023056 http://purl.obolibrary.org/obo/cl#cellxgene_subset -CL:0009011 http://purl.obolibrary.org/obo/cl#cellxgene_subset -CL:2000021 http://purl.obolibrary.org/obo/cl#cellxgene_subset +CL:0000604 http://purl.obolibrary.org/obo/cl#cellxgene_subset +CL:2000059 http://purl.obolibrary.org/obo/cl#cellxgene_subset +CL:0002277 http://purl.obolibrary.org/obo/cl#cellxgene_subset CL:0001042 http://purl.obolibrary.org/obo/cl#cellxgene_subset -CL:0000653 http://purl.obolibrary.org/obo/cl#cellxgene_subset -CL:0000136 http://purl.obolibrary.org/obo/cl#cellxgene_subset -CL:0000075 http://purl.obolibrary.org/obo/cl#cellxgene_subset -CL:2000004 http://purl.obolibrary.org/obo/cl#cellxgene_subset -CL:0000595 http://purl.obolibrary.org/obo/cl#cellxgene_subset -CL:0000092 http://purl.obolibrary.org/obo/cl#cellxgene_subset -CL:1000279 http://purl.obolibrary.org/obo/cl#cellxgene_subset -CL:0000068 http://purl.obolibrary.org/obo/cl#cellxgene_subset -CL:0002207 http://purl.obolibrary.org/obo/cl#cellxgene_subset -CL:0000115 http://purl.obolibrary.org/obo/cl#cellxgene_subset -CL:0002591 http://purl.obolibrary.org/obo/cl#cellxgene_subset -CL:1001131 http://purl.obolibrary.org/obo/cl#cellxgene_subset -CL:1001597 http://purl.obolibrary.org/obo/cl#cellxgene_subset -CL:0002538 http://purl.obolibrary.org/obo/cl#cellxgene_subset -CL:0002117 http://purl.obolibrary.org/obo/cl#cellxgene_subset -CL:0000287 http://purl.obolibrary.org/obo/cl#cellxgene_subset -CL:0000912 http://purl.obolibrary.org/obo/cl#cellxgene_subset +CL:0002570 http://purl.obolibrary.org/obo/cl#cellxgene_subset +CL:4023042 http://purl.obolibrary.org/obo/cl#cellxgene_subset +CL:0000677 http://purl.obolibrary.org/obo/cl#cellxgene_subset +CL:0000786 http://purl.obolibrary.org/obo/cl#cellxgene_subset +CL:4023056 http://purl.obolibrary.org/obo/cl#cellxgene_subset +CL:2000047 http://purl.obolibrary.org/obo/cl#cellxgene_subset +CL:0000064 http://purl.obolibrary.org/obo/cl#cellxgene_subset +CL:0002363 http://purl.obolibrary.org/obo/cl#cellxgene_subset +CL:0002410 http://purl.obolibrary.org/obo/cl#cellxgene_subset +CL:4023013 http://purl.obolibrary.org/obo/cl#cellxgene_subset +CL:0000188 http://purl.obolibrary.org/obo/cl#cellxgene_subset +CL:0002521 http://purl.obolibrary.org/obo/cl#cellxgene_subset +CL:0002425 http://purl.obolibrary.org/obo/cl#cellxgene_subset +CL:0000700 http://purl.obolibrary.org/obo/cl#cellxgene_subset +CL:0002457 http://purl.obolibrary.org/obo/cl#cellxgene_subset +CL:0009016 http://purl.obolibrary.org/obo/cl#cellxgene_subset +CL:4023051 http://purl.obolibrary.org/obo/cl#cellxgene_subset +CL:2000030 http://purl.obolibrary.org/obo/cl#cellxgene_subset +CL:0000890 http://purl.obolibrary.org/obo/cl#cellxgene_subset +CL:0002279 http://purl.obolibrary.org/obo/cl#cellxgene_subset +CL:0002139 http://purl.obolibrary.org/obo/cl#cellxgene_subset +CL:1000510 http://purl.obolibrary.org/obo/cl#cellxgene_subset CL:0000646 http://purl.obolibrary.org/obo/cl#cellxgene_subset +CL:0002201 http://purl.obolibrary.org/obo/cl#cellxgene_subset +CL:4033048 http://purl.obolibrary.org/obo/cl#cellxgene_subset +CL:0000928 http://purl.obolibrary.org/obo/cl#cellxgene_subset +CL:0000212 http://purl.obolibrary.org/obo/cl#cellxgene_subset +CL:0002370 http://purl.obolibrary.org/obo/cl#cellxgene_subset +CL:1000331 http://purl.obolibrary.org/obo/cl#cellxgene_subset +CL:0011011 http://purl.obolibrary.org/obo/cl#cellxgene_subset +CL:0002586 http://purl.obolibrary.org/obo/cl#cellxgene_subset +CL:0008002 http://purl.obolibrary.org/obo/cl#cellxgene_subset +CL:0000036 http://purl.obolibrary.org/obo/cl#cellxgene_subset +CL:0000023 http://purl.obolibrary.org/obo/cl#cellxgene_subset +CL:0002399 http://purl.obolibrary.org/obo/cl#cellxgene_subset +CL:0002324 http://purl.obolibrary.org/obo/cl#cellxgene_subset +CL:1000703 http://purl.obolibrary.org/obo/cl#cellxgene_subset +CL:1001602 http://purl.obolibrary.org/obo/cl#cellxgene_subset +CL:4033044 http://purl.obolibrary.org/obo/cl#cellxgene_subset +CL:0002138 http://purl.obolibrary.org/obo/cl#cellxgene_subset +CL:0000903 http://purl.obolibrary.org/obo/cl#cellxgene_subset +CL:0009012 http://purl.obolibrary.org/obo/cl#cellxgene_subset +CL:0002366 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+CL:4030032 http://purl.obolibrary.org/obo/cl#cellxgene_subset +CL:0002605 http://purl.obolibrary.org/obo/cl#cellxgene_subset +CL:0002489 http://purl.obolibrary.org/obo/cl#cellxgene_subset +CL:0002626 http://purl.obolibrary.org/obo/cl#cellxgene_subset +CL:2000032 http://purl.obolibrary.org/obo/cl#cellxgene_subset From 0f8126a1181f667ae434d111c17e11897ecd62a4 Mon Sep 17 00:00:00 2001 From: Aleix Puig <94959119+aleixpuigb@users.noreply.github.com> Date: Tue, 24 Dec 2024 12:54:39 +0100 Subject: [PATCH 07/18] Fixes 2869 wrongly obsoleted 'CNS interneuron' (#2870) * Fixes 2869 wrongly obsoleted 'CNS interneuron' Fixes 2869 wrongly obsoleted 'CNS interneuron' * Mark term as deprecated --- src/ontology/cl-edit.owl | 10 ++ src/ontology/components/hra_subset.owl | 175 +++---------------------- 2 files changed, 30 insertions(+), 155 deletions(-) diff --git a/src/ontology/cl-edit.owl b/src/ontology/cl-edit.owl index 7ba3fe301..aae1f7e3f 100644 --- a/src/ontology/cl-edit.owl +++ b/src/ontology/cl-edit.owl @@ -449,6 +449,7 @@ Declaration(Class(obo:CL_0000398)) Declaration(Class(obo:CL_0000399)) Declaration(Class(obo:CL_0000400)) Declaration(Class(obo:CL_0000401)) +Declaration(Class(obo:CL_0000402)) Declaration(Class(obo:CL_0000403)) Declaration(Class(obo:CL_0000404)) Declaration(Class(obo:CL_0000405)) @@ -7037,6 +7038,15 @@ AnnotationAssertion(rdfs:comment obo:CL_0000401 "Obsoleted as plasmatocytes are AnnotationAssertion(rdfs:label obo:CL_0000401 "obsolete macrophage (sensu Diptera)") AnnotationAssertion(owl:deprecated obo:CL_0000401 "true"^^xsd:boolean) +# Class: obo:CL_0000402 (obsolete CNS interneuron) + +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "doi:10.1016/B978-0-12-817424-1.00001-X") obo:IAO_0000115 obo:CL_0000402 "OBSOLETE. An interneuron that has its cell body in a central nervous system.") +AnnotationAssertion(obo:IAO_0000233 obo:CL_0000402 ) +AnnotationAssertion(obo:IAO_0100001 obo:CL_0000402 obo:CL_0000099) +AnnotationAssertion(rdfs:comment obo:CL_0000402 "Interneurons are commonly described as being only found in the central nervous system. However, in CL we define 'interneuron' more broadly as any neuron that is neither a motor neuron nor a sensory neuron, regardless of its location, so we need this term to refer strictly to interneurons of the central nervous system.") +AnnotationAssertion(rdfs:label obo:CL_0000402 "obsolete CNS interneuron") +AnnotationAssertion(owl:deprecated obo:CL_0000402 "true"^^xsd:boolean) + # Class: obo:CL_0000403 (obo:CL_0000403) AnnotationAssertion(obo:IAO_0000231 obo:CL_0000403 obo:IAO_0000227) diff --git a/src/ontology/components/hra_subset.owl b/src/ontology/components/hra_subset.owl index 1f692515d..bc42baa0d 100644 --- a/src/ontology/components/hra_subset.owl +++ b/src/ontology/components/hra_subset.owl @@ -23,12 +23,6 @@ - - - - - - @@ -559,11 +553,8 @@ - - https://github.com/obophenotype/cell-ontology/pull/2686 - true @@ -1063,15 +1054,6 @@ - - - - - - - - - @@ -2422,42 +2404,6 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - @@ -2872,15 +2818,6 @@ - - - - - - - - - @@ -3703,7 +3640,7 @@ - + @@ -4123,15 +4060,6 @@ - - - - - - - - - @@ -4249,15 +4177,6 @@ - - - - - - - - - @@ -4321,78 +4240,6 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - @@ -4465,6 +4312,15 @@ + + + + + + + + + @@ -4507,9 +4363,18 @@ + + + + + + + + + - + From 389b93e409097d6f1279ab9430f128d72956dc3d Mon Sep 17 00:00:00 2001 From: Damien Goutte-Gattat Date: Sun, 29 Dec 2024 21:00:52 +0000 Subject: [PATCH 08/18] Fix the ID range allocated to Whitney Leach. From the very beginning (commit 50200dd), Whitney Leach has been assigned the bogus ID range (4,018,500..4,018,499] -- note how the upper boundary is _lower_ than the lower boundary. The intention was probably to assign the range (4,018,500..4,018,999], which is what we do here. Given that nobody (not even Whitney Leach) has complained about this invalid range for more than 4 years, it is likely that the range is not actually needed, but even if it is unused, a bogus range will prevent the file from being used by tools that actually _validates_ the contents of an ID range policy file. --- src/ontology/cl-idranges.owl | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/ontology/cl-idranges.owl b/src/ontology/cl-idranges.owl index a666994e5..920470731 100644 --- a/src/ontology/cl-idranges.owl +++ b/src/ontology/cl-idranges.owl @@ -383,7 +383,7 @@ Datatype: idrange:55 Annotations: allocatedto: "Whitney Leach" EquivalentTo: - xsd:integer[>4018500 , <= 4018499] + xsd:integer[>4018500 , <= 4018999] Datatype: idrange:56 Annotations: From 32f1d179b6153ebba966f40d7258a2b941381657 Mon Sep 17 00:00:00 2001 From: Alida Avola <81253886+AvolaAmg@users.noreply.github.com> Date: Thu, 2 Jan 2025 12:10:20 +0100 Subject: [PATCH 09/18] Adjust hierarchy of somatosensory neurons (sensu Teleostei) (#2751) * Adjust hierarchy of somatosensory neurons (sensu Teleostei) Fixes #2727 * Update cl-edit.owl --------- Co-authored-by: CEastwood <116108977+Caroline-99@users.noreply.github.com> --- src/ontology/cl-edit.owl | 30 ++++++++++++++++++++++++++++-- 1 file changed, 28 insertions(+), 2 deletions(-) diff --git a/src/ontology/cl-edit.owl b/src/ontology/cl-edit.owl index aae1f7e3f..00d160a03 100644 --- a/src/ontology/cl-edit.owl +++ b/src/ontology/cl-edit.owl @@ -3092,8 +3092,10 @@ Declaration(Class(obo:CL_4042034)) Declaration(Class(obo:CL_4042035)) Declaration(Class(obo:CL_4042036)) Declaration(Class(obo:CL_4042037)) +Declaration(Class(obo:CL_4042038)) Declaration(Class(obo:CL_4042039)) Declaration(Class(obo:CL_4042040)) +Declaration(Class(obo:CL_4042041)) Declaration(Class(obo:CL_4047006)) Declaration(Class(obo:CL_4047007)) Declaration(Class(obo:CL_4047011)) @@ -8035,7 +8037,7 @@ SubClassOf(obo:CL_0000529 obo:CL_0000710) AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:1842357") Annotation(oboInOwl:hasDbXref "doi:10.1242/dev.108.1.121") obo:IAO_0000115 obo:CL_0000530 "A neuron that develops during the early segmentation stages in teleosts, before the neural tube is formed.") AnnotationAssertion(rdfs:label obo:CL_0000530 "primary neuron (sensu Teleostei)") SubClassOf(obo:CL_0000530 obo:CL_0000540) -SubClassOf(obo:CL_0000530 ObjectSomeValuesFrom(obo:RO_0002100 obo:UBERON_0001017)) +SubClassOf(obo:CL_0000530 ObjectSomeValuesFrom(obo:RO_0002100 obo:UBERON_0002240)) SubClassOf(Annotation(obo:IAO_0000233 "https://github.com/obophenotype/cell-ontology/pull/1950") obo:CL_0000530 ObjectSomeValuesFrom(obo:RO_0002162 obo:NCBITaxon_32443)) # Class: obo:CL_0000531 (primary sensory neuron (sensu Teleostei)) @@ -8046,6 +8048,10 @@ EquivalentClasses(obo:CL_0000531 ObjectIntersectionOf(obo:CL_0000101 obo:CL_0000 # Class: obo:CL_0000532 (CAP motoneuron) +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:17971221") Annotation(oboInOwl:hasDbXref "PMID:35431796") obo:IAO_0000115 obo:CL_0000532 "A primary motor neuron with its soma in the caudal region of a spinal cord. The axon of this motoneuron exit the spinal cord from one single point and innervates the lateral surface of ventral axial muscles") +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:3746410") oboInOwl:hasExactSynonym obo:CL_0000532 "CaP motorneuron") +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:17971221") oboInOwl:hasRelatedSynonym obo:CL_0000532 "cap cell") +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:18077593") oboInOwl:hasRelatedSynonym obo:CL_0000532 "caudal primary motor neuron") AnnotationAssertion(rdfs:label obo:CL_0000532 "CAP motoneuron") SubClassOf(obo:CL_0000532 obo:CL_0000533) @@ -8068,8 +8074,9 @@ SubClassOf(obo:CL_0000534 obo:CL_0000530) AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:1842357") Annotation(oboInOwl:hasDbXref "doi:10.1242/dev.108.1.121") obo:IAO_0000115 obo:CL_0000535 "A neuron of teleosts that develops later than a primary neuron, typically during the larval stages.") AnnotationAssertion(rdfs:label obo:CL_0000535 "secondary neuron (sensu Teleostei)") SubClassOf(obo:CL_0000535 obo:CL_0000540) -SubClassOf(obo:CL_0000535 ObjectSomeValuesFrom(obo:RO_0002100 obo:UBERON_0001017)) +SubClassOf(obo:CL_0000535 ObjectSomeValuesFrom(obo:RO_0002100 obo:UBERON_0002240)) SubClassOf(Annotation(obo:IAO_0000233 "https://github.com/obophenotype/cell-ontology/pull/1950") obo:CL_0000535 ObjectSomeValuesFrom(obo:RO_0002162 obo:NCBITaxon_32443)) +SubClassOf(obo:CL_0000535 ObjectSomeValuesFrom(obo:RO_0002202 obo:UBERON_0002342)) # Class: obo:CL_0000536 (secondary motor neuron (sensu Teleostei)) @@ -32918,6 +32925,15 @@ SubClassOf(obo:CL_4042037 ObjectSomeValuesFrom(obo:RO_0002100 obo:UBERON_0002435 SubClassOf(obo:CL_4042037 ObjectSomeValuesFrom(obo:RO_0002215 obo:GO_0061534)) SubClassOf(obo:CL_4042037 ObjectSomeValuesFrom(obo:RO_0002292 obo:PR_000015665)) +# Class: obo:CL_4042038 (rostral primary motorneuron) + +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:35431796") Annotation(oboInOwl:hasDbXref "PMID:3746410") obo:IAO_0000115 obo:CL_4042038 "A type of primary motor neuron situated in the rostral region of the spinal cord. RoP neurons extend their axons to innervate the ventral trunk musculature.") +AnnotationAssertion(terms:contributor obo:CL_4042038 ) +AnnotationAssertion(terms:date obo:CL_4042038 "2024-11-13T13:42:01Z"^^xsd:dateTime) +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:3746410") Annotation(oboInOwl:hasSynonymType obo:OMO_0003000) oboInOwl:hasRelatedSynonym obo:CL_4042038 "RoP") +AnnotationAssertion(rdfs:label obo:CL_4042038 "rostral primary motorneuron"@en) +SubClassOf(obo:CL_4042038 obo:CL_0000533) + # Class: obo:CL_4042039 (caudal ganglionic eminence derived neuron) AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:12593982") Annotation(oboInOwl:hasDbXref "PMID:12637172") Annotation(oboInOwl:hasDbXref "PMID:20130169") Annotation(oboInOwl:hasDbXref "https://www.ncbi.nlm.nih.gov/books/NBK98190/") obo:IAO_0000115 obo:CL_4042039 "A neuron of the central nervous system that develops from a caudal ganglionic eminence.") @@ -32939,6 +32955,16 @@ SubClassOf(obo:CL_4042040 obo:CL_0000540) SubClassOf(obo:CL_4042040 ObjectSomeValuesFrom(obo:RO_0002100 obo:UBERON_0002420)) SubClassOf(obo:CL_4042040 ObjectSomeValuesFrom(obo:RO_0002215 obo:GO_0061535)) +# Class: obo:CL_4042041 (middle primary motoneuron) + +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:35431796") Annotation(oboInOwl:hasDbXref "PMID:3746410") obo:IAO_0000115 obo:CL_4042041 "A type of primary motor neuron located in the middle region of the spinal cord. This primary motor neuron type is characterized by their distinct axonal pathways that innervate the middle trunk muscles.") +AnnotationAssertion(terms:contributor obo:CL_4042041 ) +AnnotationAssertion(terms:date obo:CL_4042041 "2024-11-13T13:39:28Z"^^xsd:dateTime) +AnnotationAssertion(oboInOwl:hasDbXref obo:CL_4042041 "ZFA:0005179") +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:3746410") Annotation(oboInOwl:hasSynonymType obo:OMO_0003000) oboInOwl:hasRelatedSynonym obo:CL_4042041 "MiP") +AnnotationAssertion(rdfs:label obo:CL_4042041 "middle primary motoneuron"@en) +SubClassOf(obo:CL_4042041 obo:CL_0000533) + # Class: obo:CL_4047006 (fetal artery endothelial cell) AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:34497389") obo:IAO_0000115 obo:CL_4047006 "An endothelial cell that lines an artery in the fetal circulatory system.") From 173fc5092e77adf7413bf6bc32af7f0ffd10faac Mon Sep 17 00:00:00 2001 From: Jasmine Belfiore <166385424+JABelfiore@users.noreply.github.com> Date: Mon, 6 Jan 2025 14:27:59 +0000 Subject: [PATCH 10/18] stomach smooth muscle outer longitudinal layer cell (#2846) def and refs --- src/ontology/cl-edit.owl | 10 ++++++++++ 1 file changed, 10 insertions(+) diff --git a/src/ontology/cl-edit.owl b/src/ontology/cl-edit.owl index 00d160a03..6c65df477 100644 --- a/src/ontology/cl-edit.owl +++ b/src/ontology/cl-edit.owl @@ -3109,6 +3109,7 @@ Declaration(Class(obo:CL_4047029)) Declaration(Class(obo:CL_4047030)) Declaration(Class(obo:CL_4047032)) Declaration(Class(obo:CL_4047034)) +Declaration(Class(obo:CL_4047035)) Declaration(Class(obo:CL_4047051)) Declaration(Class(obo:CL_4047052)) Declaration(Class(obo:CL_4047101)) @@ -33085,8 +33086,17 @@ AnnotationAssertion(terms:contributor obo:CL_4047034 ) +AnnotationAssertion(terms:date obo:CL_4047035 "2024-12-05T16:13:49Z"^^xsd:dateTime) +AnnotationAssertion(rdfs:label obo:CL_4047035 "stomach smooth muscle outer longitudinal layer cell"@en) +SubClassOf(obo:CL_4047035 obo:CL_4047034) + # Class: obo:CL_4047051 (small intestine BEST4+ enterocyte) AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:24223998") Annotation(oboInOwl:hasDbXref "PMID:34497389") obo:IAO_0000115 obo:CL_4047051 "An enterocyte of the human small intestine expressing bestrophin-4 (BEST4) calcium-activated ion channels. These enterocytes have a disinctive transcriptomic profile and are scattered through the small intestine epithelium.") From f9415b6e448b2a6d6011b5eeeb418200eb75a86b Mon Sep 17 00:00:00 2001 From: Aleix Puig <94959119+aleixpuigb@users.noreply.github.com> Date: Tue, 7 Jan 2025 09:59:48 +0000 Subject: [PATCH 11/18] Refresh imports in preparation of release v2024-12-23 (#2868) * Refresh imports in preparation of release v2024-12-23 * Refresh imports --- src/mappings/zfa.sssom.tsv | 1 - src/ontology/components/cellxgene_subset.owl | 4 +- src/ontology/components/mappings.owl | 9 +- src/ontology/imports/merged_import.owl | 3184 +----------------- src/patterns/definitions.owl | 4 +- src/templates/cellxgene_subset.tsv | 1522 ++++----- 6 files changed, 871 insertions(+), 3853 deletions(-) diff --git a/src/mappings/zfa.sssom.tsv b/src/mappings/zfa.sssom.tsv index 918df4335..b7bbfef1e 100644 --- a/src/mappings/zfa.sssom.tsv +++ b/src/mappings/zfa.sssom.tsv @@ -235,7 +235,6 @@ ZFA:0009187 nephrogenic mesenchyme stem cell semapv:crossSpeciesExactMatch CL:00 ZFA:0009188 ligament cell semapv:crossSpeciesExactMatch CL:0000384 ligament cell semapv:UnspecifiedMatching ZFA:0009189 tendon cell semapv:crossSpeciesExactMatch CL:0000388 tendon cell semapv:UnspecifiedMatching ZFA:0009190 electrically responsive cell semapv:crossSpeciesExactMatch CL:0000393 electrically responsive cell semapv:UnspecifiedMatching -ZFA:0009191 CNS interneuron semapv:crossSpeciesExactMatch CL:0000402 CNS interneuron semapv:UnspecifiedMatching ZFA:0009193 electrically signaling cell semapv:crossSpeciesExactMatch CL:0000404 electrically signaling cell semapv:UnspecifiedMatching ZFA:0009194 CNS short range interneuron semapv:crossSpeciesExactMatch CL:0000406 CNS short range interneuron semapv:UnspecifiedMatching ZFA:0009195 CNS long range interneuron semapv:crossSpeciesExactMatch CL:0000410 CNS long range interneuron semapv:UnspecifiedMatching diff --git a/src/ontology/components/cellxgene_subset.owl b/src/ontology/components/cellxgene_subset.owl index f52bb4fdf..ec40c578f 100644 --- a/src/ontology/components/cellxgene_subset.owl +++ b/src/ontology/components/cellxgene_subset.owl @@ -7,8 +7,8 @@ Prefix(rdfs:=) Ontology( - -Annotation(owl:versionInfo "2024-12-06") + +Annotation(owl:versionInfo "2025-01-06") Declaration(Class()) Declaration(Class()) diff --git a/src/ontology/components/mappings.owl b/src/ontology/components/mappings.owl index ba5dc156c..32bf356c8 100644 --- a/src/ontology/components/mappings.owl +++ b/src/ontology/components/mappings.owl @@ -645,7 +645,6 @@ FBbt:00005125 ZFA:0009051 - ZFA:0009191 @@ -659,12 +658,6 @@ ZFA:0009051 - - - - ZFA:0009191 - - FBbt:00005123 ZFA:0009052 @@ -4561,5 +4554,5 @@ - + diff --git a/src/ontology/imports/merged_import.owl b/src/ontology/imports/merged_import.owl index d006760c6..f4adc60c1 100644 --- a/src/ontology/imports/merged_import.owl +++ b/src/ontology/imports/merged_import.owl @@ -7,8 +7,8 @@ Prefix(rdfs:=) Ontology( - -Annotation(owl:versionInfo "2024-12-06") + +Annotation(owl:versionInfo "2025-01-06") Declaration(Class()) Declaration(Class()) @@ -9388,6 +9388,7 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -11287,6 +11288,9 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -14270,7 +14274,6 @@ Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) @@ -14282,7 +14285,6 @@ Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) @@ -14295,7 +14297,6 @@ Declaration(AnnotationProperty( Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty(rdfs:comment)) @@ -14480,7 +14481,6 @@ SubAnnotationPropertyOf( (is negative form of) -AnnotationAssertion( ) AnnotationAssertion( "2018-03-14T00:03:24Z"^^xsd:dateTime) AnnotationAssertion(rdfs:label "is negative form of") @@ -15140,7 +15140,6 @@ ObjectPropertyRange( (occurs across) AnnotationAssertion( "A relationship between a process and a barrier, where the process occurs in a region spanning the barrier. For cellular processes the barrier is typically a membrane. Examples include transport across a membrane and membrane depolarization.") -AnnotationAssertion( ) AnnotationAssertion( "2017-07-20T17:19:37Z"^^xsd:dateTime) AnnotationAssertion(rdfs:label "occurs across") SubObjectPropertyOf( ) @@ -16671,7 +16670,6 @@ ObjectPropertyRange( (has primary input or output) AnnotationAssertion( "p 'has primary input ot output' c iff either (a) p 'has primary input' c or (b) p 'has primary output' c.") -AnnotationAssertion( ) AnnotationAssertion( "2018-12-13T11:26:17Z"^^xsd:dateTime) AnnotationAssertion( "RO:0004007") AnnotationAssertion( "external") @@ -16684,7 +16682,6 @@ SubObjectPropertyOf( (has primary output) AnnotationAssertion(Annotation( ) Annotation( "GOC:dph") Annotation( "GOC:kva") Annotation( "GOC:pt") Annotation(rdfs:comment "PMID:27812932") "p has primary output c if (a) p has output c and (b) the goal of process is to modify, produce, or transform c.") -AnnotationAssertion( ) AnnotationAssertion( "2018-12-13T11:26:32Z"^^xsd:dateTime) AnnotationAssertion( "RO:0004008") AnnotationAssertion( "external") @@ -16698,7 +16695,6 @@ SubObjectPropertyOf( (has primary input) AnnotationAssertion(Annotation( ) Annotation( "GOC:dph") Annotation( "GOC:kva") Annotation( "GOC:pt") Annotation(rdfs:comment "PMID:27812932") "p has primary input c if (a) p has input c and (b) the goal of process is to modify, consume, or transform c.") -AnnotationAssertion( ) AnnotationAssertion( "2018-12-13T11:26:56Z"^^xsd:dateTime) AnnotationAssertion( "RO:0004009") AnnotationAssertion( "external") @@ -16712,7 +16708,6 @@ SubObjectPropertyOf( (causally upstream of or within, negative effect) AnnotationAssertion( ) -AnnotationAssertion( ) AnnotationAssertion( "2018-03-13T23:55:05Z"^^xsd:dateTime) AnnotationAssertion(rdfs:label "causally upstream of or within, negative effect") AnnotationAssertion(rdfs:seeAlso "https://wiki.geneontology.org/Causally_upstream_of_or_within,_negative_effect"^^xsd:anyURI) @@ -16720,7 +16715,6 @@ SubObjectPropertyOf( (causally upstream of or within, positive effect) -AnnotationAssertion( ) AnnotationAssertion( "2018-03-13T23:55:19Z"^^xsd:dateTime) AnnotationAssertion(rdfs:label "causally upstream of or within, positive effect") AnnotationAssertion(rdfs:seeAlso ) @@ -16729,7 +16723,6 @@ SubObjectPropertyOf( (has small molecule regulator) AnnotationAssertion( "a relation between a process and a continuant, in which the process is regulated by the small molecule continuant") -AnnotationAssertion( ) AnnotationAssertion( "2020-04-22T20:27:26Z"^^xsd:dateTime) AnnotationAssertion(rdfs:label "has small molecule regulator"@en) SubObjectPropertyOf( ) @@ -16738,7 +16731,6 @@ InverseObjectProperties( (has small molecule activator) AnnotationAssertion( "a relation between a process and a continuant, in which the process is activated by the small molecule continuant") -AnnotationAssertion( ) AnnotationAssertion( "2020-04-22T20:28:37Z"^^xsd:dateTime) AnnotationAssertion( "RO:0012001") AnnotationAssertion( "external") @@ -16752,7 +16744,6 @@ InverseObjectProperties( (acts on population of) AnnotationAssertion( "p acts on population of c iff c' is a collection, has members of type c, and p has participant c") -AnnotationAssertion( ) AnnotationAssertion( "2020-06-08T17:21:33Z"^^xsd:dateTime) AnnotationAssertion( "RO:0012003") AnnotationAssertion( "external") @@ -16768,7 +16759,6 @@ SubObjectPropertyOf( (is small molecule regulator of) AnnotationAssertion( "a relation between a continuant and a process, in which the continuant is a small molecule that regulates the process") -AnnotationAssertion( ) AnnotationAssertion( "2020-06-24T13:15:17Z"^^xsd:dateTime) AnnotationAssertion(rdfs:label "is small molecule regulator of"@en) SubObjectPropertyOf( ) @@ -16776,7 +16766,6 @@ SubObjectPropertyOf( (is small molecule activator of) AnnotationAssertion( "a relation between a continuant and a process, in which the continuant is a small molecule that activates the process") -AnnotationAssertion( ) AnnotationAssertion( "2020-06-24T13:15:26Z"^^xsd:dateTime) AnnotationAssertion(rdfs:label "is small molecule activator of"@en) AnnotationAssertion(rdfs:seeAlso "https://wiki.geneontology.org/Is_small_molecule_activator_of"^^xsd:anyURI) @@ -16785,7 +16774,6 @@ SubObjectPropertyOf( (results in fusion of) -AnnotationAssertion( ) AnnotationAssertion( "2021-02-26T07:28:29Z"^^xsd:dateTime) AnnotationAssertion( "RO:0012008") AnnotationAssertion( "external") @@ -16801,7 +16789,6 @@ SubObjectPropertyOf( (has synaptic IO in region) AnnotationAssertion( "A relationship between a neuron and a region, where the neuron has a functionally relevant number of input and/or output synapses in that region.") -AnnotationAssertion( ) AnnotationAssertion( "2020-07-17T09:26:52Z"^^xsd:dateTime) AnnotationAssertion( "has synaptic input or output in") AnnotationAssertion(rdfs:label "has synaptic IO in region"@en) @@ -16810,7 +16797,6 @@ SubObjectPropertyOf( (has sensory dendrite in) AnnotationAssertion( "Relation between a sensory neuron and some structure in which it receives sensory input via a sensory dendrite.") -AnnotationAssertion( ) AnnotationAssertion( "2020-07-20T12:10:09Z"^^xsd:dateTime) AnnotationAssertion( "has sensory dendrite location") AnnotationAssertion( "has sensory terminal in") @@ -16894,7 +16880,6 @@ AnnotationAssertion(rdfs:label "devi # Object Property: (results in changes to anatomical or cellular structure) AnnotationAssertion( "p has anatomical participant c iff p has participant c, and c is an anatomical entity") -AnnotationAssertion( ) AnnotationAssertion( "2018-09-26T01:08:58Z"^^xsd:dateTime) AnnotationAssertion( "RO:0040036") AnnotationAssertion( "external") @@ -19385,7 +19370,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of L-glutamate import across plasma membrane) AnnotationAssertion(Annotation( "GOC:TermGenie") "Any process that modulates the frequency, rate or extent of L-glutamate import into a cell.") -AnnotationAssertion( "al") AnnotationAssertion( "2012-06-13T07:34:08Z") AnnotationAssertion( "regulation of L-glutamate import") AnnotationAssertion( "regulation of L-glutamate transport") @@ -19398,7 +19382,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of L-glutamate import across plasma membrane) AnnotationAssertion(Annotation( "GOC:TermGenie") "Any process that stops, prevents or reduces the frequency, rate or extent of L-glutamate import into a cell.") -AnnotationAssertion( "al") AnnotationAssertion( "2012-06-13T07:34:30Z") AnnotationAssertion( "down regulation of L-glutamate transport") AnnotationAssertion( "down-regulation of L-glutamate transport") @@ -19424,7 +19407,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of L-glutamate import across plasma membrane) AnnotationAssertion(Annotation( "GOC:TermGenie") "Any process that activates or increases the frequency, rate or extent of L-glutamate import into a cell.") -AnnotationAssertion( "al") AnnotationAssertion( "2012-06-13T07:34:38Z") AnnotationAssertion( "positive regulation of L-glutamate import") AnnotationAssertion( "positive regulation of L-glutamate transport") @@ -19672,7 +19654,6 @@ SubClassOf( ObjectSomeValuesFrom( (osteoclast proliferation) AnnotationAssertion(Annotation( "CL:0000092") Annotation( "GOC:hjd") "The multiplication or reproduction of osteoclasts, resulting in the expansion of an osteoclast cell population. An osteoclast is a specialized phagocytic cell associated with the absorption and removal of the mineralized matrix of bone tissue, which typically differentiates from monocytes.") -AnnotationAssertion( "hjd") AnnotationAssertion( "2010-02-03T01:50:37Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0002158") @@ -19703,7 +19684,6 @@ SubClassOf( ObjectAllValuesFrom( (male germ cell proliferation) AnnotationAssertion(Annotation( "GOC:hjd") "The multiplication or reproduction of male germ cells, resulting in the expansion of a cell population.") -AnnotationAssertion( "hjd") AnnotationAssertion( "2010-11-18T02:35:14Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0002176") @@ -19714,7 +19694,6 @@ SubClassOf( (cytoplasmic translation) AnnotationAssertion(Annotation( "GOC:hjd") "The chemical reactions and pathways resulting in the formation of a protein in the cytoplasm. This is a ribosome-mediated process in which the information in messenger RNA (mRNA) is used to specify the sequence of amino acids in the protein.") -AnnotationAssertion( "hjd") AnnotationAssertion( "2011-06-09T03:11:53Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0002181") @@ -19729,7 +19708,6 @@ SubClassOf( (cytoplasmic translational elongation) AnnotationAssertion(Annotation( "GOC:hjd") "The successive addition of amino acid residues to a nascent polypeptide chain during protein biosynthesis in the cytoplasm.") -AnnotationAssertion( "hjd") AnnotationAssertion( "2011-06-09T03:14:42Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0002182") @@ -19740,7 +19718,6 @@ SubClassOf( (cytoplasmic translational initiation) AnnotationAssertion(Annotation( "GOC:hjd") "The process preceding formation of the peptide bond between the first two amino acids of a protein in the cytoplasm. This includes the formation of a complex of the ribosome, mRNA or circRNA, and an initiation complex that contains the first aminoacyl-tRNA.") -AnnotationAssertion( "hjd") AnnotationAssertion( "2011-06-09T03:15:48Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0002183") @@ -19751,7 +19728,6 @@ SubClassOf( (cytoplasmic translational termination) AnnotationAssertion(Annotation( "GOC:hjd") "The process resulting in the release of a polypeptide chain from the ribosome in the cytoplasm, usually in response to a termination codon.") -AnnotationAssertion( "hjd") AnnotationAssertion( "2011-06-09T03:17:13Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0002184") @@ -24272,7 +24248,6 @@ EquivalentClasses( ObjectIntersection # Class: (trabecular meshwork development) AnnotationAssertion(Annotation( "PMID:20568247") "The progression of the trabecular meshwork over time, from its formation to the mature structure. The trabecular meshwork is a fenestrated endothelial-like tissue situated at the intersection of the cornea and the iris. The trabecular meshwork provides drainage for the aqueous humor.") -AnnotationAssertion( "hjd") AnnotationAssertion( "2012-04-19T04:50:06Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0002930") @@ -24284,7 +24259,6 @@ SubClassOf( ObjectSomeValuesFrom( (tendon sheath development) AnnotationAssertion(Annotation( "PMID:20696843") "The process whose specific outcome is the progression of a tendon sheath over time, from its formation to the mature structure. A tendon sheath is a layer of membrane around a tendon. It permits the tendon to move.") -AnnotationAssertion( "hjd") AnnotationAssertion( "2012-04-23T02:11:22Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0002932") @@ -24296,7 +24270,6 @@ SubClassOf( ObjectSomeValuesFrom( (synoviocyte proliferation) AnnotationAssertion(Annotation( "PMID:10770586") Annotation( "PMID:9546370") "The multiplication or reproduction of type B synoviocytes by cell division, resulting in the expansion of their population. A type B synoviocyte is a fibroblast-like cell found in synovial tissues.") -AnnotationAssertion( "hjd") AnnotationAssertion( "2012-11-16T14:25:45Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0002941") @@ -24536,7 +24509,6 @@ SubClassOf( (mesodermal-endodermal cell signaling) AnnotationAssertion(Annotation( "GOC:mtg_heart") "Any process that mediates the transfer of information from mesodermal cells to endodermal cells.") -AnnotationAssertion( "tb") AnnotationAssertion( "2009-09-22T03:07:34Z") AnnotationAssertion(Annotation( "GOC:mah") "mesodermal-endodermal cell signalling") AnnotationAssertion( "biological_process") @@ -24547,7 +24519,6 @@ EquivalentClasses( ObjectIntersection # Class: (endodermal-mesodermal cell signaling) AnnotationAssertion(Annotation( "GOC:mtg_heart") "Any process that mediates the transfer of information from endodermal cells to mesodermal cells.") -AnnotationAssertion( "tb") AnnotationAssertion( "2009-09-22T03:10:29Z") AnnotationAssertion(Annotation( "GOC:mah") "endodermal-mesodermal cell signalling") AnnotationAssertion( "biological_process") @@ -24558,7 +24529,6 @@ EquivalentClasses( ObjectIntersection # Class: (cardiogenic plate morphogenesis) AnnotationAssertion(Annotation( "GOC:mtg_heart") "The process in which the anatomical structures of the cardiogenic plate are generated and organized. The cardiogenic plate is the first recognizable structure derived from the heart field.") -AnnotationAssertion( "tb") AnnotationAssertion( "2009-09-22T04:12:18Z") AnnotationAssertion(Annotation( "GOC:mtg_heart") "cardiac crescent morphogenesis") AnnotationAssertion( "biological_process") @@ -24572,7 +24542,6 @@ SubClassOf( ObjectSomeValuesFrom( (embryonic heart tube morphogenesis) AnnotationAssertion(Annotation( "GOC:mtg_heart") "The process in which the anatomical structures of the embryonic heart tube are generated and organized. The embryonic heart tube is an epithelial tube that will give rise to the mature heart.") -AnnotationAssertion( "tb") AnnotationAssertion( "2009-09-22T04:21:17Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0003143") @@ -24587,7 +24556,6 @@ SubClassOf( ObjectSomeValuesFrom( (embryonic heart tube formation) AnnotationAssertion(Annotation( "GOC:mtg_heart") "The process that gives rise to the embryonic heart tube. This process pertains to the initial formation of a structure from unspecified parts. The embryonic heart tube is an epithelial tube that will give rise to the mature heart.") -AnnotationAssertion( "tb") AnnotationAssertion( "2009-09-22T04:22:34Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0003144") @@ -24599,7 +24567,6 @@ SubClassOf( ObjectSomeValuesFrom( (embryonic heart tube formation via epithelial folding) AnnotationAssertion(Annotation( "GOC:mtg_heart") "The process that gives rise to the embryonic heart tube by the cells of the heart field along a linear axis.") -AnnotationAssertion( "tb") AnnotationAssertion( "2009-09-22T04:26:03Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0003145") @@ -24609,7 +24576,6 @@ SubClassOf( (neural crest cell migration involved in heart formation) AnnotationAssertion(Annotation( "GOC:mtg_heart") "The characteristic movement of a cell from the dorsal ridge of the neural tube towards the heart and that contributes to heart formation.") -AnnotationAssertion( "tb") AnnotationAssertion( "2009-09-22T04:29:55Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0003147") @@ -24620,7 +24586,6 @@ SubClassOf( ObjectSomeValuesFrom( (outflow tract septum morphogenesis) AnnotationAssertion(Annotation( "GOC:mtg_heart") "The process in which the anatomical structures of the outflow tract septum are generated and organized. The outflow tract septum is a partition in the outflow tract.") -AnnotationAssertion( "tb") AnnotationAssertion( "2009-09-22T07:51:01Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0003148") @@ -24632,7 +24597,6 @@ SubClassOf( ObjectSomeValuesFrom( (membranous septum morphogenesis) AnnotationAssertion(Annotation( "GOC:mtg_heart") "The process in which the membranous septum is generated and organized. The membranous septum is the upper part of ventricular septum.") -AnnotationAssertion( "tb") AnnotationAssertion( "2009-09-22T07:51:41Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0003149") @@ -24645,7 +24609,6 @@ SubClassOf( ObjectSomeValuesFrom( (muscular septum morphogenesis) AnnotationAssertion(Annotation( "GOC:mtg_heart") "The process in which the muscular septum is generated and organized. The muscular septum is the lower part of the ventricular septum.") -AnnotationAssertion( "tb") AnnotationAssertion( "2009-09-22T07:53:28Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0003150") @@ -24658,7 +24621,6 @@ SubClassOf( ObjectSomeValuesFrom( (outflow tract morphogenesis) AnnotationAssertion(Annotation( "GOC:mtg_heart") Annotation( "UBERON:0004145") "The process in which the anatomical structures of the outflow tract are generated and organized. The outflow tract is the portion of the heart through which blood flows into the arteries.") -AnnotationAssertion( "tb") AnnotationAssertion( "2009-09-22T07:59:24Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0003151") @@ -24671,7 +24633,6 @@ SubClassOf( ObjectSomeValuesFrom( (morphogenesis of an epithelial fold involved in embryonic heart tube formation) AnnotationAssertion(Annotation( "GOC:mtg_heart") "The morphogenetic process in which an epithelial sheet bends along a linear axis, contributing to embryonic heart tube formation.") -AnnotationAssertion( "tb") AnnotationAssertion( "2009-09-23T10:10:24Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0003152") @@ -24683,7 +24644,6 @@ SubClassOf( ObjectSomeValuesFrom( (regulation of animal organ formation) AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:mtg_heart") Annotation( "GOC:tb") "Any process that modulates the rate, frequency or extent of animal organ formation. Organ formation is the process pertaining to the initial formation of an organ from unspecified parts. The process begins with the specific processes that contribute to the appearance of the discrete structure, such as inductive events, and ends when the structural rudiment of the organ is recognizable, such as a condensation of mesenchymal cells into the organ rudiment.") -AnnotationAssertion( "tb") AnnotationAssertion( "2009-09-30T11:21:09Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0003156") @@ -24694,7 +24654,6 @@ SubClassOf( ObjectSomeValuesFrom( (endocardium development) AnnotationAssertion(Annotation( "GOC:mtg_heart") "The process whose specific outcome is the progression of the endocardium over time, from its formation to the mature structure. The endocardium is an anatomical structure comprised of an endothelium and an extracellular matrix that forms the innermost layer of tissue of the heart, and lines the heart chambers.") -AnnotationAssertion( "dph") AnnotationAssertion( "2009-10-01T12:42:27Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0003157") @@ -24707,7 +24666,6 @@ SubClassOf( ObjectSomeValuesFrom( (endothelium development) AnnotationAssertion(Annotation( "GOC:mtg_heart") "The process whose specific outcome is the progression of an endothelium over time, from its formation to the mature structure. Endothelium refers to the layer of cells lining blood vessels, lymphatics, the heart, and serous cavities, and is derived from bone marrow or mesoderm. Corneal endothelium is a special case, derived from neural crest cells.") -AnnotationAssertion( "dph") AnnotationAssertion( "2009-10-01T12:50:57Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0003158") @@ -24718,7 +24676,6 @@ SubClassOf( (morphogenesis of an endothelium) AnnotationAssertion(Annotation( "GOC:mtg_heart") "The process in which the anatomical structure of an endothelium is generated and organized. Endothelium refers to the layer of cells lining blood vessels, lymphatics, the heart, and serous cavities, and is derived from bone marrow or mesoderm. Corneal endothelium is a special case, derived from neural crest cells.") -AnnotationAssertion( "dph") AnnotationAssertion( "2009-10-01T01:34:06Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0003159") @@ -24730,7 +24687,6 @@ SubClassOf( ObjectSomeValuesFrom( (endocardium morphogenesis) AnnotationAssertion(Annotation( "GOC:mtg_heart") "The process in which the anatomical structure of the endocardium is generated and organized. The endocardium is an anatomical structure comprised of an endothelium and an extracellular matrix that forms the innermost layer of tissue of the heart, and lines the heart chambers.") -AnnotationAssertion( "dph") AnnotationAssertion( "2009-10-01T01:37:26Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0003160") @@ -24743,7 +24699,6 @@ SubClassOf( ObjectSomeValuesFrom( (cardiac conduction system development) AnnotationAssertion(Annotation( "GOC:mtg_heart") "The process whose specific outcome is the progression of the cardiac conduction system over time, from its formation to the mature structure. The cardiac conduction system consists of specialized cardiomyocytes that regulate the frequency of heart beat.") -AnnotationAssertion( "dph") AnnotationAssertion( "2009-10-01T01:57:16Z") AnnotationAssertion(Annotation( "GOC:mtg_heart") "cardiac impulse conducting system development") AnnotationAssertion(Annotation( "GOC:mtg_heart") "heart conduction system development") @@ -24756,7 +24711,6 @@ SubClassOf( ObjectSomeValuesFrom( (atrioventricular node development) AnnotationAssertion(Annotation( "GOC:mtg_heart") "The process whose specific outcome is the progression of the atrioventricular (AV) node over time, from its formation to the mature structure. The AV node is part of the cardiac conduction system that controls the timing of ventricle contraction by receiving electrical signals from the sinoatrial (SA) node and relaying them to the His-Purkinje system.") -AnnotationAssertion( "dph") AnnotationAssertion( "2009-10-01T02:05:13Z") AnnotationAssertion(Annotation( "GOC:mtg_heart") "AV node development") AnnotationAssertion( "biological_process") @@ -24768,7 +24722,6 @@ SubClassOf( ObjectSomeValuesFrom( (sinoatrial node development) AnnotationAssertion(Annotation( "GOC:mtg_heart") "The process whose specific outcome is the progression of the sinoatrial (SA) node over time, from its formation to the mature structure. The SA node is part of the cardiac conduction system that controls the timing of heart muscle contraction. It relays electrical signals to the AV node.") -AnnotationAssertion( "dph") AnnotationAssertion( "2009-10-01T02:06:09Z") AnnotationAssertion(Annotation( "GOC:mtg_heart") "SA node development") AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:mtg_cardiac_conduct_nov11") "SAN development") @@ -24782,7 +24735,6 @@ SubClassOf( ObjectSomeValuesFrom( (His-Purkinje system development) AnnotationAssertion(Annotation( "GOC:mtg_heart") "The process whose specific outcome is the progression of the His-Purkinje system over time, from its formation to the mature structure. The His-Purkinje system receives signals from the AV node and is composed of the fibers that regulate cardiac muscle contraction in the ventricles.") -AnnotationAssertion( "dph") AnnotationAssertion( "2009-10-01T02:07:12Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0003164") @@ -24793,7 +24745,6 @@ SubClassOf( ObjectSomeValuesFrom( (Purkinje myocyte development) AnnotationAssertion(Annotation( "GOC:mtg_cardiac_conduct_nov11") Annotation( "GOC:mtg_heart") "The process whose specific outcome is the progression of a Purkinje myocyte over time, from its formation to the mature structure. The Purkinje myocyte (also known as cardiac Purkinje fiber) is part of the cardiac conduction system that receives signals from the bundle of His and innervates the ventricular cardiac muscle.") -AnnotationAssertion( "dph") AnnotationAssertion( "2009-10-01T02:07:50Z") AnnotationAssertion( "cardiac Purkinje fiber development") AnnotationAssertion( "biological_process") @@ -24805,7 +24756,6 @@ SubClassOf( ObjectSomeValuesFrom( (bundle of His development) AnnotationAssertion(Annotation( "GOC:mtg_heart") "The process whose specific outcome is the progression of the bundle of His over time, from its formation to the mature structure. The bundle of His is part of the His-Purkinje system that transmits signals from the AV node to the cardiac Purkinje fibers.") -AnnotationAssertion( "dph") AnnotationAssertion( "2009-10-01T02:08:43Z") AnnotationAssertion(Annotation( "GOC:mtg_heart") "atrioventricular bundle development") AnnotationAssertion( "biological_process") @@ -24817,7 +24767,6 @@ SubClassOf( ObjectSomeValuesFrom( (atrioventricular bundle cell differentiation) AnnotationAssertion(Annotation( "GOC:mtg_heart") "The process in which a relatively unspecialized cell acquires the specialized structural and/or functional features of a cell of the atrioventricular bundle. These cells are specialized cardiomyocytes that transmit signals from the AV node to the cardiac Purkinje fibers.") -AnnotationAssertion( "dph") AnnotationAssertion( "2009-10-01T02:48:23Z") AnnotationAssertion(Annotation( "GOC:mtg_heart") "AV bundle cell differentiation") AnnotationAssertion( "biological_process") @@ -24830,7 +24779,6 @@ SubClassOf( ObjectSomeValuesFrom( (Purkinje myocyte differentiation) AnnotationAssertion(Annotation( "GOC:mtg_cardiac_conduct_nov11") Annotation( "GOC:mtg_heart") "The process in which a relatively unspecialized cell acquires the specialized structural and/or functional features of a Purkinje myocyte (also known as cardiac Purkinje fiber cell). These cells are specialized cardiomyocytes that receive signals from the bundle of His and innervate the ventricular cardiac muscle.") -AnnotationAssertion( "dph") AnnotationAssertion( "2009-10-01T02:49:54Z") AnnotationAssertion( "cardiac Purkinje fiber cell differentiation") AnnotationAssertion( "biological_process") @@ -24843,7 +24791,6 @@ SubClassOf( ObjectSomeValuesFrom( (coronary vein morphogenesis) AnnotationAssertion(Annotation( "GOC:mtg_heart") "The process in which the anatomical structures of veins of the heart are generated and organized.") -AnnotationAssertion( "dph") AnnotationAssertion( "2009-10-08T10:45:41Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0003169") @@ -24855,7 +24802,6 @@ SubClassOf( (heart valve development) AnnotationAssertion(Annotation( "GOC:mtg_heart") "The progression of a heart valve over time, from its formation to the mature structure. A heart valve is a structure that restricts the flow of blood to different regions of the heart and forms from an endocardial cushion.") -AnnotationAssertion( "dph") AnnotationAssertion( "2009-10-08T10:50:09Z") AnnotationAssertion(Annotation( "GOC:mtg_heart") "cardiac valve development") AnnotationAssertion( "biological_process") @@ -24869,7 +24815,6 @@ SubClassOf( ObjectSomeValuesFrom( (heart valve morphogenesis) AnnotationAssertion(Annotation( "GOC:mtg_heart") "The process in which the structure of a heart valve is generated and organized.") -AnnotationAssertion( "dph") AnnotationAssertion( "2009-10-08T11:23:48Z") AnnotationAssertion(Annotation( "GOC:vk") Annotation( "GOC:yaf") "heart valve remodeling") AnnotationAssertion(Annotation( "GOC:vk") Annotation( "GOC:yaf") "heart valve remodelling") @@ -24884,7 +24829,6 @@ SubClassOf( ObjectSomeValuesFrom( (heart valve formation) AnnotationAssertion(Annotation( "GOC:mtg_heart") "The developmental process pertaining to the initial formation of a heart valve from unspecified parts. This process begins with the specific processes that contribute to the appearance of the discrete structure and ends when the structural rudiment is recognizable.") -AnnotationAssertion( "dph") AnnotationAssertion( "2009-10-08T12:20:15Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0003188") @@ -24897,7 +24841,6 @@ SubClassOf( ObjectSomeValuesFrom( (endocardial cushion development) AnnotationAssertion(Annotation( "GOC:mtg_heart") "The progression of a cardiac cushion over time, from its initial formation to the mature structure. The endocardial cushion is a specialized region of mesenchymal cells that will give rise to the heart septa and valves.") -AnnotationAssertion( "dph") AnnotationAssertion( "2009-10-08T01:17:43Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0003197") @@ -24909,7 +24852,6 @@ SubClassOf( ObjectSomeValuesFrom( (endocardial cushion morphogenesis) AnnotationAssertion(Annotation( "GOC:mtg_heart") "The process in which the anatomical structure of the endocardial cushion is generated and organized. The endocardial cushion is a specialized region of mesenchymal cells that will give rise to the heart septa and valves.") -AnnotationAssertion( "dph") AnnotationAssertion( "2009-10-08T01:43:22Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0003203") @@ -24922,7 +24864,6 @@ SubClassOf( ObjectSomeValuesFrom( (cardiac skeleton development) AnnotationAssertion(Annotation( "GOC:mtg_heart") "The progression of the cardiac skeleton over time, from its formation to the mature structure. The cardiac skeleton is a specialized extracellular matrix that separates the atria from the ventricles and provides physical support for the heart.") -AnnotationAssertion( "dph") AnnotationAssertion( "2009-10-13T09:05:04Z") AnnotationAssertion(Annotation( "GOC:mtg_heart") "heart fibrous skeleton development") AnnotationAssertion( "biological_process") @@ -24935,7 +24876,6 @@ SubClassOf( ObjectSomeValuesFrom( (cardiac chamber development) AnnotationAssertion(Annotation( "GOC:mtg_heart") "The progression of a cardiac chamber over time, from its formation to the mature structure. A cardiac chamber is an enclosed cavity within the heart.") -AnnotationAssertion( "dph") AnnotationAssertion( "2009-10-13T09:11:18Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0003205") @@ -24948,7 +24888,6 @@ SubClassOf( ObjectSomeValuesFrom( (cardiac chamber morphogenesis) AnnotationAssertion(Annotation( "GOC:mtg_heart") "The process in which a cardiac chamber is generated and organized. A cardiac chamber is an enclosed cavity within the heart.") -AnnotationAssertion( "dph") AnnotationAssertion( "2009-10-13T09:14:51Z") AnnotationAssertion(Annotation( "GOC:mtg_heart") "heart chamber morphogenesis") AnnotationAssertion( "biological_process") @@ -24963,7 +24902,6 @@ SubClassOf( ObjectSomeValuesFrom( (cardiac chamber formation) AnnotationAssertion(Annotation( "GOC:mtg_heart") "The developmental process pertaining to the initial formation of a cardiac chamber from unspecified parts. A cardiac chamber is an enclosed cavity within the heart.") -AnnotationAssertion( "dph") AnnotationAssertion( "2009-10-13T09:29:13Z") AnnotationAssertion(Annotation( "GOC:mtg_heart") "heart chamber formation") AnnotationAssertion( "biological_process") @@ -24977,7 +24915,6 @@ SubClassOf( ObjectSomeValuesFrom( (cardiac ventricle morphogenesis) AnnotationAssertion(Annotation( "GOC:mtg_heart") "The process in which the cardiac ventricle is generated and organized. A cardiac ventricle receives blood from a cardiac atrium and pumps it out of the heart.") -AnnotationAssertion( "dph") AnnotationAssertion( "2009-10-13T09:38:44Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0003208") @@ -24989,7 +24926,6 @@ SubClassOf( ObjectSomeValuesFrom( (cardiac atrium morphogenesis) AnnotationAssertion(Annotation( "GOC:mtg_heart") "The process in which the cardiac atrium is generated and organized. A cardiac atrium receives blood from a vein and pumps it to a cardiac ventricle.") -AnnotationAssertion( "dph") AnnotationAssertion( "2009-10-13T09:39:44Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0003209") @@ -25001,7 +24937,6 @@ SubClassOf( ObjectSomeValuesFrom( (cardiac atrium formation) AnnotationAssertion(Annotation( "GOC:mtg_heart") "The developmental process pertaining to the initial formation of a cardiac atrium from unspecified parts. A cardiac atrium receives blood from a vein and pumps it to a cardiac ventricle.") -AnnotationAssertion( "dph") AnnotationAssertion( "2009-10-13T09:44:25Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0003210") @@ -25013,7 +24948,6 @@ SubClassOf( ObjectSomeValuesFrom( (cardiac ventricle formation) AnnotationAssertion(Annotation( "GOC:mtg_heart") "The developmental process pertaining to the initial formation of a cardiac ventricle from unspecified parts. A cardiac ventricle receives blood from a cardiac atrium and pumps it out of the heart.") -AnnotationAssertion( "dph") AnnotationAssertion( "2009-10-13T09:46:27Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0003211") @@ -25025,7 +24959,6 @@ SubClassOf( ObjectSomeValuesFrom( (cardiac left atrium morphogenesis) AnnotationAssertion(Annotation( "GOC:mtg_heart") "The process in which the left cardiac atrium is generated and organized.") -AnnotationAssertion( "dph") AnnotationAssertion( "2009-10-13T09:48:16Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0003212") @@ -25036,7 +24969,6 @@ SubClassOf( (cardiac right atrium morphogenesis) AnnotationAssertion(Annotation( "GOC:mtg_heart") "The process in which the right cardiac atrium is generated and organized.") -AnnotationAssertion( "dph") AnnotationAssertion( "2009-10-13T09:49:03Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0003213") @@ -25047,7 +24979,6 @@ SubClassOf( (cardiac left ventricle morphogenesis) AnnotationAssertion(Annotation( "GOC:mtg_heart") "The process in which the left cardiac ventricle is generated and organized.") -AnnotationAssertion( "dph") AnnotationAssertion( "2009-10-13T09:50:08Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0003214") @@ -25058,7 +24989,6 @@ SubClassOf( (cardiac right ventricle morphogenesis) AnnotationAssertion(Annotation( "GOC:mtg_heart") "The process in which the right cardiac ventricle is generated and organized.") -AnnotationAssertion( "dph") AnnotationAssertion( "2009-10-13T09:50:57Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0003215") @@ -25069,7 +24999,6 @@ SubClassOf( (cardiac left atrium formation) AnnotationAssertion(Annotation( "GOC:mtg_heart") "The developmental process pertaining to the initial formation of a left cardiac atrium from unspecified parts.") -AnnotationAssertion( "dph") AnnotationAssertion( "2009-10-13T09:52:31Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0003216") @@ -25081,7 +25010,6 @@ SubClassOf( ObjectSomeValuesFrom( (cardiac right atrium formation) AnnotationAssertion(Annotation( "GOC:mtg_heart") "The developmental process pertaining to the initial formation of a cardiac right atrium from unspecified parts.") -AnnotationAssertion( "dph") AnnotationAssertion( "2009-10-13T09:53:12Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0003217") @@ -25093,7 +25021,6 @@ SubClassOf( ObjectSomeValuesFrom( (cardiac left ventricle formation) AnnotationAssertion(Annotation( "GOC:mtg_heart") "The developmental process pertaining to the initial formation of a left cardiac ventricle from unspecified parts.") -AnnotationAssertion( "dph") AnnotationAssertion( "2009-10-13T09:54:33Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0003218") @@ -25105,7 +25032,6 @@ SubClassOf( ObjectSomeValuesFrom( (cardiac right ventricle formation) AnnotationAssertion(Annotation( "GOC:mtg_heart") "The developmental process pertaining to the initial formation of a right cardiac ventricle from unspecified parts.") -AnnotationAssertion( "dph") AnnotationAssertion( "2009-10-13T09:55:38Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0003219") @@ -25117,7 +25043,6 @@ SubClassOf( ObjectSomeValuesFrom( (left ventricular cardiac muscle tissue morphogenesis) AnnotationAssertion(Annotation( "GOC:mtg_heart") "The process in which the anatomical structures of left cardiac ventricle muscle are generated and organized.") -AnnotationAssertion( "dph") AnnotationAssertion( "2009-10-13T10:18:05Z") AnnotationAssertion(Annotation( "GOC:mtg_heart") "left ventricular myocardium morphogenesis") AnnotationAssertion( "biological_process") @@ -25130,7 +25055,6 @@ SubClassOf( ObjectSomeValuesFrom( (right ventricular cardiac muscle tissue morphogenesis) AnnotationAssertion(Annotation( "GOC:mtg_heart") "The process in which the anatomical structures of the right cardiac ventricle muscle are generated and organized.") -AnnotationAssertion( "dph") AnnotationAssertion( "2009-10-13T10:26:33Z") AnnotationAssertion(Annotation( "GOC:mtg_heart") "right ventricle myocardium morphogenesis") AnnotationAssertion( "biological_process") @@ -25143,7 +25067,6 @@ SubClassOf( ObjectSomeValuesFrom( (ventricular trabecula myocardium morphogenesis) AnnotationAssertion(Annotation( "GOC:mtg_heart") "The process in which the anatomical structures of the trabecular cardiac ventricle muscle are generated and organized.") -AnnotationAssertion( "dph") AnnotationAssertion( "2009-10-13T10:33:00Z") AnnotationAssertion( "biological_process") AnnotationAssertion(Annotation( "GOC:dph") "trabecula carnea morphogenesis") @@ -25156,7 +25079,6 @@ SubClassOf( (left ventricular trabecular myocardium morphogenesis) AnnotationAssertion(Annotation( "GOC:mtg_heart") "The process in which the anatomical structures of cardiac left ventricular trabecular myocardium are generated and organized.") -AnnotationAssertion( "dph") AnnotationAssertion( "2009-10-13T10:45:09Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0003225") @@ -25168,7 +25090,6 @@ SubClassOf( (right ventricular trabecular myocardium morphogenesis) AnnotationAssertion(Annotation( "GOC:mtg_heart") "The process in which the anatomical structures of the right ventricular myocardium are generated and organized.") -AnnotationAssertion( "dph") AnnotationAssertion( "2009-10-13T10:50:59Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0003227") @@ -25181,7 +25102,6 @@ SubClassOf( "GOC:mtg_heart") "The process whose specific outcome is the progression of cardiac muscle of the atrium over time, from its formation to the mature structure.") AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/22614"^^xsd:anyURI) -AnnotationAssertion( "dph") AnnotationAssertion( "2009-10-13T10:53:18Z") AnnotationAssertion(Annotation( "GOC:mtg_heart") "atrial myocardium development") AnnotationAssertion( "biological_process") @@ -25192,7 +25112,6 @@ EquivalentClasses( ObjectIntersection # Class: (ventricular cardiac muscle tissue development) AnnotationAssertion(Annotation( "GOC:mtg_heart") "The process whose specific outcome is the progression of ventricular cardiac muscle over time, from its formation to the mature structure.") -AnnotationAssertion( "dph") AnnotationAssertion( "2009-10-13T10:56:01Z") AnnotationAssertion(Annotation( "GOC:mtg_heart") "ventricular myocardium development") AnnotationAssertion( "biological_process") @@ -25203,7 +25122,6 @@ EquivalentClasses( ObjectIntersection # Class: (cardiac atrium development) AnnotationAssertion(Annotation( "GOC:mtg_heart") "The process whose specific outcome is the progression of a cardiac atrium over time, from its formation to the mature structure. A cardiac atrium receives blood from a vein and pumps it to a cardiac ventricle.") -AnnotationAssertion( "dph") AnnotationAssertion( "2009-10-13T11:02:07Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0003230") @@ -25214,7 +25132,6 @@ SubClassOf( (cardiac ventricle development) AnnotationAssertion(Annotation( "GOC:mtg_heart") "The process whose specific outcome is the progression of a cardiac ventricle over time, from its formation to the mature structure. A cardiac ventricle receives blood from a cardiac atrium and pumps it out of the heart.") -AnnotationAssertion( "dph") AnnotationAssertion( "2009-10-13T11:03:16Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0003231") @@ -25225,7 +25142,6 @@ SubClassOf( (sinus venosus development) AnnotationAssertion(Annotation( "GOC:mtg_heart") "The progression of the sinus venosus over time, from its formation to the mature structure. The sinus venosus is a heart chamber attached to the atrium on the venous side of the embryonic heart.") -AnnotationAssertion( "dph") AnnotationAssertion( "2009-10-13T11:12:34Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0003235") @@ -25236,7 +25152,6 @@ SubClassOf( (sinus venosus morphogenesis) AnnotationAssertion(Annotation( "GOC:mtg_heart") "The process in which the sinus venosus is generated and organized. The sinus venosus is a heart chamber attached to the atrium on the venous side of the embryonic heart.") -AnnotationAssertion( "dph") AnnotationAssertion( "2009-10-13T11:16:52Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0003236") @@ -25248,7 +25163,6 @@ SubClassOf( ObjectSomeValuesFrom( (sinus venosus formation) AnnotationAssertion(Annotation( "GOC:mtg_heart") "The developmental process pertaining to the initial formation of the sinus venosus from unspecified parts. The sinus venosus is a heart chamber attached to the atrium on the venous side of the embryonic heart.") -AnnotationAssertion( "dph") AnnotationAssertion( "2009-10-13T11:18:34Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0003237") @@ -25260,7 +25174,6 @@ SubClassOf( ObjectSomeValuesFrom( (conus arteriosus development) AnnotationAssertion(Annotation( "GOC:mtg_heart") "The progression of the conus arteriosus over time, from its formation to the mature structure. The conus arteriosus is a valved chamber with thick muscular walls stemming from the ventricle and connecting to the pulmonary trunk.") -AnnotationAssertion( "dph") AnnotationAssertion( "2009-10-13T11:20:57Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0003238") @@ -25271,7 +25184,6 @@ SubClassOf( (conus arteriosus morphogenesis) AnnotationAssertion(Annotation( "GOC:mtg_heart") "The process in which the conus arteriosus is generated and organized. The conus arteriosus is a valved chamber with thick muscular walls stemming from the ventricle and connecting to the pulmonary trunk.") -AnnotationAssertion( "dph") AnnotationAssertion( "2009-10-13T11:25:04Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0003239") @@ -25283,7 +25195,6 @@ SubClassOf( ObjectSomeValuesFrom( (conus arteriosus formation) AnnotationAssertion(Annotation( "GOC:mtg_heart") "The developmental process pertaining to the initial formation of the conus arteriosus from unspecified parts. The conus arteriosus is a valved chamber with thick muscular walls stemming from the ventricle and connecting to the pulmonary trunk.") -AnnotationAssertion( "dph") AnnotationAssertion( "2009-10-13T11:25:47Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0003240") @@ -25295,7 +25206,6 @@ SubClassOf( ObjectSomeValuesFrom( (growth involved in heart morphogenesis) AnnotationAssertion(Annotation( "GOC:mtg_heart") "Developmental growth that contributes to the shaping of the heart.") -AnnotationAssertion( "dph") AnnotationAssertion( "2009-10-13T11:28:46Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0003241") @@ -25307,7 +25217,6 @@ SubClassOf( ObjectSomeValuesFrom( (cardiac muscle tissue growth involved in heart morphogenesis) AnnotationAssertion(Annotation( "GOC:mtg_heart") "The developmental growth of cardiac muscle tissue that contributes to the shaping of the heart.") -AnnotationAssertion( "dph") AnnotationAssertion( "2009-10-13T11:44:21Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0003245") @@ -25318,7 +25227,6 @@ SubClassOf( ObjectSomeValuesFrom( (heart capillary growth) AnnotationAssertion(Annotation( "GOC:mtg_heart") "The increase in heart capillaries that accompanies physiological hypertrophy of cardiac muscle.") -AnnotationAssertion( "dph") AnnotationAssertion( "2009-10-13T11:53:12Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0003248") @@ -25331,7 +25239,6 @@ SubClassOf( ObjectSomeValuesFrom( (cell proliferation involved in heart valve morphogenesis) AnnotationAssertion(Annotation( "GOC:mtg_heart") "The multiplication or reproduction of cells that contributes to the shaping of a heart valve.") -AnnotationAssertion( "dph") AnnotationAssertion( "2009-10-13T01:59:19Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0003249") @@ -25342,7 +25249,6 @@ SubClassOf( (regulation of cell proliferation involved in heart valve morphogenesis) AnnotationAssertion(Annotation( "GOC:mtg_heart") "Any process that modulates the rate, frequency or extent of cell proliferation that contributes to the shaping of a heart valve.") -AnnotationAssertion( "dph") AnnotationAssertion( "2009-10-13T02:03:42Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0003250") @@ -25352,7 +25258,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of cell proliferation involved in heart valve morphogenesis) AnnotationAssertion(Annotation( "GOC:mtg_heart") "Any process that increases the rate, frequency or extent of cell proliferation that contributes to the shaping of a heart valve.") -AnnotationAssertion( "dph") AnnotationAssertion( "2009-10-13T02:07:20Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0003251") @@ -25362,7 +25267,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of cell proliferation involved in heart valve morphogenesis) AnnotationAssertion(Annotation( "GOC:mtg_heart") "Any process that decreases the rate, frequency or extent of cell proliferation that contributes to the shaping of a heart valve.") -AnnotationAssertion( "dph") AnnotationAssertion( "2009-10-13T02:10:39Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0003252") @@ -25372,7 +25276,6 @@ EquivalentClasses( ObjectIntersection # Class: (cardiac neural crest cell migration involved in outflow tract morphogenesis) AnnotationAssertion(Annotation( "GOC:mtg_heart") "The orderly movement of a neural crest cell from one site to another that will contribute to the morphogenesis of the outflow tract.") -AnnotationAssertion( "dph") AnnotationAssertion( "2009-10-13T02:14:16Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0003253") @@ -25383,7 +25286,6 @@ SubClassOf( ObjectSomeValuesFrom( (cardioblast migration) AnnotationAssertion(Annotation( "GOC:mtg_heart") "The orderly movement of a cardiac progenitor cell to form the heart field. Cardiac progenitor cells are non-terminally differentiated, mesoderm-derived cells that are committed to differentiate into cells of the heart. A cardioblast is a cardiac precursor cell. It is a cell that has been committed to a cardiac fate, but will undergo more cell division rather than terminally differentiating.") -AnnotationAssertion( "dph") AnnotationAssertion( "2009-10-15T01:52:25Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0003260") @@ -25395,7 +25297,6 @@ SubClassOf( ObjectSomeValuesFrom( (endocardial cushion formation) AnnotationAssertion(Annotation( "GOC:mtg_heart") Annotation( "PMID:15797462") "The developmental process pertaining to the initial formation of an endocardial cushion. The endocardial cushion is a specialized region of mesenchymal cells that will give rise to the heart septa and valves.") -AnnotationAssertion( "dph") AnnotationAssertion( "2009-10-20T08:53:19Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0003272") @@ -25408,7 +25309,6 @@ SubClassOf( ObjectSomeValuesFrom( (cell migration involved in endocardial cushion formation) AnnotationAssertion(Annotation( "GOC:mtg_heart") "The orderly movement of a cell from one site to another that will contribute to the formation of an endocardial cushion. The endocardial cushion is a specialized region of mesenchymal cells that will give rise to the heart septa and valves.") -AnnotationAssertion( "dph") AnnotationAssertion( "2009-10-20T09:08:44Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0003273") @@ -25418,7 +25318,6 @@ EquivalentClasses( ObjectIntersection # Class: (apoptotic process involved in outflow tract morphogenesis) AnnotationAssertion(Annotation( "GOC:mtg_apoptosis") Annotation( "GOC:mtg_heart") "Any apoptotic process that contributes to the shaping of the outflow tract. The outflow tract is the portion of the heart through which blood flows into the arteries.") -AnnotationAssertion( "dph") AnnotationAssertion( "2009-10-20T09:30:01Z") AnnotationAssertion( "apoptosis involved in outflow tract morphogenesis") AnnotationAssertion( "biological_process") @@ -25429,7 +25328,6 @@ EquivalentClasses( ObjectIntersection # Class: (apoptotic process involved in heart valve morphogenesis) AnnotationAssertion(Annotation( "GOC:mtg_apoptosis") Annotation( "GOC:mtg_heart") "Any apoptotic process that contributes to the shaping of a heart valve.") -AnnotationAssertion( "dph") AnnotationAssertion( "2009-10-20T09:34:29Z") AnnotationAssertion( "apoptosis involved in heart valve morphogenesis") AnnotationAssertion( "biological_process") @@ -25441,7 +25339,6 @@ SubClassOf( (apoptotic process involved in endocardial cushion morphogenesis) AnnotationAssertion(Annotation( "GOC:mtg_apoptosis") Annotation( "GOC:mtg_heart") "Any apoptotic process that contributes to the shaping of an endocardial cushion. The endocardial cushion is a specialized region of mesenchymal cells that will give rise to the heart septa and valves.") -AnnotationAssertion( "dph") AnnotationAssertion( "2009-10-20T09:37:03Z") AnnotationAssertion( "apoptosis involved in endocardial cushion morphogenesis") AnnotationAssertion( "biological_process") @@ -25452,7 +25349,6 @@ EquivalentClasses( ObjectIntersection # Class: (apoptotic process involved in heart morphogenesis) AnnotationAssertion(Annotation( "GOC:mtg_apoptosis") Annotation( "GOC:mtg_heart") "Any apoptotic process that contributes to the shaping of the heart.") -AnnotationAssertion( "dph") AnnotationAssertion( "2009-10-20T09:40:22Z") AnnotationAssertion( "apoptosis involved in heart morphogenesis") AnnotationAssertion( "biological_process") @@ -25463,7 +25359,6 @@ EquivalentClasses( ObjectIntersection # Class: (cardiac septum development) AnnotationAssertion(Annotation( "GOC:mtg_heart") "The progression of a cardiac septum over time, from its initial formation to the mature structure.") -AnnotationAssertion( "dph") AnnotationAssertion( "2009-10-20T09:45:13Z") AnnotationAssertion(Annotation( "GOC:mtg_heart") "heart septum development") AnnotationAssertion( "biological_process") @@ -25477,7 +25372,6 @@ SubClassOf( ObjectSomeValuesFrom( (ventricular septum development) AnnotationAssertion(Annotation( "GOC:mtg_heart") "The progression of the ventricular septum over time from its formation to the mature structure.") -AnnotationAssertion( "dph") AnnotationAssertion( "2009-10-20T10:04:51Z") AnnotationAssertion(Annotation( "GOC:mtg_heart") "interventricular septum development") AnnotationAssertion(Annotation( "GOC:mtg_heart") "septum inferius development") @@ -25491,7 +25385,6 @@ SubClassOf( ObjectSomeValuesFrom( (atrial septum development) AnnotationAssertion(Annotation( "GOC:mtg_heart") "The progression of the atrial septum over time, from its initial formation to the mature structure.") -AnnotationAssertion( "dph") AnnotationAssertion( "2009-10-20T10:10:38Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0003283") @@ -25503,7 +25396,6 @@ SubClassOf( ObjectSomeValuesFrom( (cardiac septum cell differentiation) AnnotationAssertion(Annotation( "GOC:mtg_heart") "The process in which an endocardial cushion cell becomes a cell of a cardiac septum.") -AnnotationAssertion( "dph") AnnotationAssertion( "2009-10-20T11:03:46Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0003292") @@ -25515,7 +25407,6 @@ SubClassOf( ObjectSomeValuesFrom( (heart valve cell differentiation) AnnotationAssertion(Annotation( "GOC:mtg_heart") "The process in which an endocardial cushion cell give rise to a cell that is part of a heart valve.") -AnnotationAssertion( "dph") AnnotationAssertion( "2009-10-20T11:06:46Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0003293") @@ -25527,7 +25418,6 @@ SubClassOf( ObjectSomeValuesFrom( (physiological muscle hypertrophy) AnnotationAssertion(Annotation( "GOC:mtg_heart") "The enlargement or overgrowth of all or part of a muscle organ or tissue due to an increase in the size of its muscle cells. Physiological hypertrophy is a normal process during development.") -AnnotationAssertion( "dph") AnnotationAssertion( "2009-10-22T09:24:51Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0003298") @@ -25537,7 +25427,6 @@ SubClassOf( (cardiac muscle hypertrophy) AnnotationAssertion(Annotation( "GOC:mtg_heart") "The enlargement or overgrowth of all or part of the heart muscle due to an increase in size of cardiac muscle cells without cell division.") -AnnotationAssertion( "dph") AnnotationAssertion( "2009-10-22T10:33:56Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0003300") @@ -25547,7 +25436,6 @@ SubClassOf( (physiological cardiac muscle hypertrophy) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:mtg_cardiac_conduct_nov11") Annotation( "GOC:mtg_heart") "The enlargement or overgrowth of all or part of the heart muscle due to an increase in size of cardiac muscle cells without cell division. This process contributes to the developmental growth of the heart.") -AnnotationAssertion( "dph") AnnotationAssertion( "2009-10-22T10:38:10Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0003301") @@ -25559,7 +25447,6 @@ SubClassOf( ObjectSomeValuesFrom( (type B pancreatic cell differentiation) AnnotationAssertion(Annotation( "CL:0000169") Annotation( "GOC:dph") Annotation( "PMID:11076772") "The process in which relatively unspecialized cells acquire specialized structural and/or functional features of a type B pancreatic cell. A type B pancreatic cell is a cell located towards center of the islets of Langerhans that secretes insulin.") -AnnotationAssertion( "dph") AnnotationAssertion( "2009-10-26T09:27:23Z") AnnotationAssertion(Annotation( "GOC:mah") "pancreatic B cell differentiation") AnnotationAssertion(Annotation( "GOC:dph") "pancreatic beta cell differentiation") @@ -25572,7 +25459,6 @@ SubClassOf( ObjectSomeValuesFrom( (pancreatic A cell differentiation) AnnotationAssertion(Annotation( "GOC:dph") Annotation( "PMID:11076772") "The process in which relatively unspecialized cells acquire specialized structural and functional features of a pancreatic A cell. A pancreatic A cell is a cell in the pancreas that secretes glucagon.") -AnnotationAssertion( "dph") AnnotationAssertion( "2009-10-26T09:28:05Z") AnnotationAssertion(Annotation( "GOC:dph") "pancreatic alpha cell differentiation") AnnotationAssertion( "biological_process") @@ -25584,7 +25470,6 @@ SubClassOf( ObjectSomeValuesFrom( (pancreatic D cell differentiation) AnnotationAssertion(Annotation( "GOC:dph") Annotation( "PMID:11076772") "The process in which relatively unspecialized cells acquire specialized structural and functional features that characterize a pancreatic delta cell. A delta cell is a cell of the pancreas that produces somatostatin.") -AnnotationAssertion( "dph") AnnotationAssertion( "2009-10-26T09:30:27Z") AnnotationAssertion(Annotation( "GOC:dph") "pancreatic delta cell differentiation") AnnotationAssertion( "biological_process") @@ -25596,7 +25481,6 @@ SubClassOf( ObjectSomeValuesFrom( (pancreatic PP cell differentiation) AnnotationAssertion(Annotation( "GOC:dph") Annotation( "PMID:11076772") "The process in which relatively unspecialized cells acquire specialized structural and functional features of a pancreatic polypeptide-producing cell. A pancreatic polypeptide-producing cell is a cell in the pancreas that produces pancreatic polypeptide.") -AnnotationAssertion( "dph") AnnotationAssertion( "2009-10-26T09:32:32Z") AnnotationAssertion(Annotation( "GOC:dph") "pancreatic polypeptide-producing cell differentiation") AnnotationAssertion( "biological_process") @@ -25608,7 +25492,6 @@ SubClassOf( ObjectSomeValuesFrom( (heart rudiment development) AnnotationAssertion(Annotation( "GOC:mtg_heart") "The progression of the heart rudiment over time, from its initial formation to the mature structure. The heart rudiment is a cone-like structure that is formed when myocardial progenitor cells of the heart field fuse at the midline. The heart rudiment is the first structure of the heart tube.") -AnnotationAssertion( "dph") AnnotationAssertion( "2009-10-27T08:32:40Z") AnnotationAssertion(Annotation( "GOC:mtg_heart") "heart cone development") AnnotationAssertion( "biological_process") @@ -25622,7 +25505,6 @@ SubClassOf( ObjectSomeValuesFrom( "GOC:mtg_heart") "The process in which the anatomical structures of the heart rudiment are generated and organized.") AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/22938"^^xsd:anyURI) -AnnotationAssertion( "dph") AnnotationAssertion( "2009-10-27T08:38:04Z") AnnotationAssertion(Annotation( "GOC:mtg_heart") "heart cone morphogenesis") AnnotationAssertion( "biological_process") @@ -25637,7 +25519,6 @@ SubClassOf( ObjectSomeValuesFrom( (heart rudiment formation) AnnotationAssertion(Annotation( "GOC:mtg_heart") "The developmental process pertaining to the initial formation of the heart rudiment.") -AnnotationAssertion( "dph") AnnotationAssertion( "2009-10-27T08:43:37Z") AnnotationAssertion(Annotation( "GOC:mtg_heart") "heart cone formation") AnnotationAssertion( "biological_process") @@ -25651,7 +25532,6 @@ SubClassOf( ObjectSomeValuesFrom( (pancreatic A cell development) AnnotationAssertion(Annotation( "GOC:dph") "The process whose specific outcome is the progression of a pancreatic A cell over time, from its formation to the mature structure. A pancreatic A cell is a cell in the pancreas that secretes glucagon.") -AnnotationAssertion( "dph") AnnotationAssertion( "2009-11-02T08:13:55Z") AnnotationAssertion(Annotation( "GOC:dph") "pancreatic alpha cell development") AnnotationAssertion( "biological_process") @@ -25663,7 +25543,6 @@ SubClassOf( ObjectSomeValuesFrom( (type B pancreatic cell development) AnnotationAssertion(Annotation( "CL:0000169") Annotation( "GOC:dph") "The process whose specific outcome is the progression of a type B pancreatic cell over time, from its formation to the mature structure. A type B pancreatic cell is a cell located towards center of the islets of Langerhans that secretes insulin.") -AnnotationAssertion( "dph") AnnotationAssertion( "2009-11-02T08:20:11Z") AnnotationAssertion(Annotation( "GOC:mah") "pancreatic B cell development") AnnotationAssertion(Annotation( "GOC:dph") "pancreatic beta cell development") @@ -25676,7 +25555,6 @@ SubClassOf( ObjectSomeValuesFrom( (pancreatic D cell development) AnnotationAssertion(Annotation( "GOC:dph") "The process whose specific outcome is the progression of a pancreatic delta cell over time, from its formation to the mature structure. A delta cell is a cell of the pancreas that produces somatostatin.") -AnnotationAssertion( "dph") AnnotationAssertion( "2009-11-02T08:23:26Z") AnnotationAssertion(Annotation( "GOC:dph") "pancreatic delta cell development") AnnotationAssertion( "biological_process") @@ -25688,7 +25566,6 @@ SubClassOf( ObjectSomeValuesFrom( (pancreatic PP cell development) AnnotationAssertion(Annotation( "GOC:dph") "The process whose specific outcome is the progression of a pancreatic PP cell over time, from its formation to the mature structure. A pancreatic polypeptide-producing cell is a cell in the pancreas that produces pancreatic polypeptide.") -AnnotationAssertion( "dph") AnnotationAssertion( "2009-11-02T08:25:03Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0003325") @@ -25700,7 +25577,6 @@ SubClassOf( ObjectSomeValuesFrom( (regulation of extracellular matrix constituent secretion) AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:tb") "Any process that modulates the rate, frequency, or extent of the controlled release of molecules that form the extracellular matrix, including carbohydrates and glycoproteins by a cell or a group of cells.") -AnnotationAssertion( "dph") AnnotationAssertion( "2009-11-02T02:07:40Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0003330") @@ -25712,7 +25588,6 @@ SubClassOf( (positive regulation of extracellular matrix constituent secretion) AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:tb") "Any process that increases the rate, frequency, or extent of the controlled release of molecules that form the extracellular matrix, including carbohydrates and glycoproteins by a cell or a group of cells.") -AnnotationAssertion( "dph") AnnotationAssertion( "2009-11-02T02:11:22Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0003331") @@ -25725,7 +25600,6 @@ SubClassOf( (negative regulation of extracellular matrix constituent secretion) AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:tb") "Any process that decreases the rate, frequency, or extent the controlled release of molecules that form the extracellular matrix, including carbohydrates and glycoproteins by a cell or a group of cells.") -AnnotationAssertion( "dph") AnnotationAssertion( "2009-11-02T02:13:49Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0003332") @@ -25738,7 +25612,6 @@ SubClassOf( (amino acid transmembrane transport) AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:tb") "The process in which an amino acid is transported across a membrane.") -AnnotationAssertion( "dph") AnnotationAssertion( "2009-11-02T02:36:11Z") AnnotationAssertion( "amino acid membrane transport") AnnotationAssertion( "biological_process") @@ -25750,7 +25623,6 @@ EquivalentClasses( ObjectIntersection # Class: (keratinocyte development) AnnotationAssertion(Annotation( "GOC:dph") "The process whose specific outcome is the progression of a keratinocyte over time, from its formation to the mature structure.") -AnnotationAssertion( "dph") AnnotationAssertion( "2009-11-24T08:55:57Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0003334") @@ -25762,7 +25634,6 @@ SubClassOf( ObjectSomeValuesFrom( (corneocyte development) AnnotationAssertion(Annotation( "GOC:dph") "The process whose specific outcome is the progression of the corneocyte over time, from its formation to the mature structure. A corneocyte is the last stage of development of a keratinocyte where the keratinocyte flattens, loses its nucleus and eventually delaminates from the epidermis.") -AnnotationAssertion( "dph") AnnotationAssertion( "2009-11-24T09:01:02Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0003335") @@ -25773,7 +25644,6 @@ SubClassOf( ObjectSomeValuesFrom( (mesenchymal to epithelial transition involved in metanephros morphogenesis) AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:yaf") "A transition where a mesenchymal cell establishes apical/basolateral polarity,forms intercellular adhesive junctions, synthesizes basement membrane components and becomes an epithelial cell that will contribute to the shaping of the metanephros.") -AnnotationAssertion( "dph") AnnotationAssertion( "2009-11-24T09:29:49Z") AnnotationAssertion( "biological_process") AnnotationAssertion(Annotation( "GOC:dph") "metanephric mesenchyme to epithelial transition") @@ -25785,7 +25655,6 @@ SubClassOf( ObjectSomeValuesFrom( (metanephros morphogenesis) AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:yaf") "The process in which the anatomical structures of the metanephros are generated and organized.") -AnnotationAssertion( "dph") AnnotationAssertion( "2009-11-24T09:32:09Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0003338") @@ -25797,7 +25666,6 @@ SubClassOf( ObjectSomeValuesFrom( (regulation of mesenchymal to epithelial transition involved in metanephros morphogenesis) AnnotationAssertion(Annotation( "GOC:dph") "Any process that modulates the rate, frequency or extent of the transition where a mesenchymal cell establishes apical/basolateral polarity,forms intercellular adhesive junctions, synthesizes basement membrane components and becomes an epithelial cell that will contribute to the shaping of the metanephros.") -AnnotationAssertion( "dph") AnnotationAssertion( "2009-11-24T09:43:04Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0003339") @@ -25807,7 +25675,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of mesenchymal to epithelial transition involved in metanephros morphogenesis) AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:yaf") "Any process that decreases the rate, frequency or extent of the transition where a mesenchymal cell establishes apical/basolateral polarity,forms intercellular adhesive junctions, synthesizes basement membrane components and becomes an epithelial cell that will contribute to the shaping of the metanephros.") -AnnotationAssertion( "dph") AnnotationAssertion( "2009-11-24T09:46:12Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0003340") @@ -25824,7 +25691,6 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) -AnnotationAssertion( "dph") AnnotationAssertion( "2009-11-24T09:56:26Z") AnnotationAssertion( "microtubule-based flagellum movement") AnnotationAssertion(Annotation( "GOC:bf") "flagellar movement") @@ -25861,7 +25727,6 @@ DisjointClasses( ObjectSomeValuesFrom # Class: (proepicardium development) AnnotationAssertion(Annotation( "GOC:dph") Annotation( "PMID:18722343") "The progression of the proepicardium from its formation to the mature structure. The proepicardium is an outpouching of the septum transversum.") -AnnotationAssertion( "dph") AnnotationAssertion( "2009-12-01T10:30:17Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0003342") @@ -25873,7 +25738,6 @@ SubClassOf( ObjectSomeValuesFrom( (septum transversum development) AnnotationAssertion(Annotation( "GOC:dph") Annotation( "PMID:18722343") "The progression of the septum transversum from its initial formation to the mature structure. The septum transversum is a portion of the trunk mesenchyme.") -AnnotationAssertion( "dph") AnnotationAssertion( "2009-12-01T10:40:17Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0003343") @@ -25884,7 +25748,6 @@ SubClassOf( (pericardium morphogenesis) AnnotationAssertion(Annotation( "GOC:dph") Annotation( "PMID:18722343") "The process in which the anatomical structure of the pericardium is generated and organized.") -AnnotationAssertion( "dph") AnnotationAssertion( "2009-12-01T10:46:34Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0003344") @@ -25897,7 +25760,6 @@ SubClassOf( ObjectSomeValuesFrom( (cardiac endothelial cell differentiation) AnnotationAssertion(Annotation( "GOC:dph") Annotation( "PMID:18722343") "The process in which a relatively unspecialized cell acquires the specialized structural and/or functional features of a cardiac endothelial cell.") -AnnotationAssertion( "dph") AnnotationAssertion( "2009-12-01T11:12:05Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0003348") @@ -25908,7 +25770,6 @@ SubClassOf( (regulation of cilium movement) AnnotationAssertion(Annotation( "GOC:dph") "Any process that modulates the rate, frequency, or extent of cilium movement, the directed, self-propelled movement of a cilium.") -AnnotationAssertion( "dph") AnnotationAssertion( "2009-12-03T10:12:00Z") AnnotationAssertion( "regulation of microtubule-based flagellum movement") AnnotationAssertion( "biological_process") @@ -25922,7 +25783,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of cilium movement) AnnotationAssertion(Annotation( "GOC:dph") "Any process that increases the rate, frequency, or extent of cilium movement, the directed, self-propelled movement of a cilium.") -AnnotationAssertion( "dph") AnnotationAssertion( "2009-12-03T10:16:10Z") AnnotationAssertion( "positive regulation of microtubule-based flagellum movement") AnnotationAssertion( "biological_process") @@ -25936,7 +25796,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of cilium movement) AnnotationAssertion(Annotation( "GOC:dph") "Any process that decreases the rate, frequency, or extent of cilium movement, the directed, self-propelled movement of a cilium.") -AnnotationAssertion( "dph") AnnotationAssertion( "2009-12-03T10:17:47Z") AnnotationAssertion( "negative regulation of microtubule-based flagellum movement") AnnotationAssertion( "biological_process") @@ -25949,7 +25808,6 @@ EquivalentClasses( ObjectIntersection # Class: (noradrenergic neuron differentiation) AnnotationAssertion(Annotation( "GOC:dph") "The process in which a relatively unspecialized cell acquires specialized features of an noradrenergic neuron, a neuron that secretes noradrenaline.") -AnnotationAssertion( "dph") AnnotationAssertion( "2009-12-03T10:34:30Z") AnnotationAssertion(Annotation( "GOC:dph") "norepinephrine secreting neuron differentiation") AnnotationAssertion( "biological_process") @@ -25961,7 +25819,6 @@ SubClassOf( (noradrenergic neuron development) AnnotationAssertion(Annotation( "GOC:dph") "The process whose specific outcome is the progression of a noradrenergic neuron over time, from initial commitment of the cell to a specific fate, to the fully functional differentiated cell.") -AnnotationAssertion( "dph") AnnotationAssertion( "2009-12-03T10:38:37Z") AnnotationAssertion(Annotation( "GOC:dph") "norepinephrine secreting neuron development") AnnotationAssertion( "biological_process") @@ -25974,7 +25831,6 @@ SubClassOf( ObjectSomeValuesFrom( (brainstem development) AnnotationAssertion(Annotation( "GOC:dph") "The progression of the brainstem from its formation to the mature structure. The brainstem is the part of the brain that connects the brain with the spinal cord.") -AnnotationAssertion( "dph") AnnotationAssertion( "2009-12-03T10:47:20Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0003360") @@ -25986,7 +25842,6 @@ SubClassOf( (noradrenergic neuron differentiation involved in brainstem development) AnnotationAssertion(Annotation( "GOC:dph") "The process in which a relatively unspecialized cell acquires specialized features of an noradrenergic neuron that is part of the brainstem.") -AnnotationAssertion( "dph") AnnotationAssertion( "2009-12-03T10:53:30Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0003361") @@ -25997,7 +25852,6 @@ EquivalentClasses( ObjectIntersection AnnotationAssertion(Annotation( "GOC:ascb_2009") Annotation( "GOC:dph") Annotation( "GOC:tb") "The specification and formation of anisotropic intracellular organization that contributes to the self-propelled directed movement of an ameboid cell.") AnnotationAssertion( ) -AnnotationAssertion( "dph") AnnotationAssertion( "2009-12-08T04:50:41Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0003365") @@ -26010,7 +25864,6 @@ DisjointClasses( ObjectSomeValuesFrom # Class: (establishment or maintenance of cytoskeleton polarity involved in ameboidal cell migration) AnnotationAssertion(Annotation( "GOC:ascb_2009") Annotation( "GOC:dph") Annotation( "GOC:tb") "Any cellular process that results in the specification, formation or maintenance of polarized cytoskeletal structures that contribute to the cell polarity of a migrating ameboid cell.") -AnnotationAssertion( "dph") AnnotationAssertion( "2009-12-08T05:42:46Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0003371") @@ -26021,7 +25874,6 @@ SubClassOf( ObjectSomeValuesFrom( (establishment of cell polarity involved in gastrulation cell migration) AnnotationAssertion(Annotation( "GOC:ascb_2009") Annotation( "GOC:dph") Annotation( "GOC:tb") "The specification and formation of anisotropic intracellular organization that contributes to the self-propelled directed movement of an ameboid cell taking part in gastrulation.") -AnnotationAssertion( "dph") AnnotationAssertion( "2009-12-09T06:54:44Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0003379") @@ -26031,7 +25883,6 @@ EquivalentClasses( ObjectIntersection # Class: (establishment or maintenance of cytoskeleton polarity involved in gastrulation) AnnotationAssertion(Annotation( "GOC:ascb_2009") Annotation( "GOC:dph") Annotation( "GOC:tb") "Any cellular process that results in the specification, formation or maintenance of polarized cytoskeletal structures that contribute to the cell polarity of a migrating ameboid cell taking part in gastrulation.") -AnnotationAssertion( "dph") AnnotationAssertion( "2009-12-09T07:10:57Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0003380") @@ -26042,7 +25893,6 @@ SubClassOf( ObjectSomeValuesFrom( (epithelial cell morphogenesis involved in gastrulation) AnnotationAssertion(Annotation( "GOC:ascb_2009") Annotation( "GOC:dph") Annotation( "GOC:tb") "The change in form that occurs when an epithelial cell progresses from it initial formation to its mature state, contributing to the process of gastrulation.") -AnnotationAssertion( "dph") AnnotationAssertion( "2009-12-09T07:18:53Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0003381") @@ -26052,7 +25902,6 @@ EquivalentClasses( ObjectIntersection # Class: (epithelial cell morphogenesis) AnnotationAssertion(Annotation( "GOC:ascb_2009") Annotation( "GOC:dph") Annotation( "GOC:tb") "The change in form that occurs when an epithelial cell progresses from its initial formation to its mature state.") -AnnotationAssertion( "dph") AnnotationAssertion( "2009-12-09T07:21:06Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0003382") @@ -26064,7 +25913,6 @@ SubClassOf( ObjectSomeValuesFrom( (optic vesicle formation) AnnotationAssertion(Annotation( "GOC:ascb_2009") Annotation( "GOC:dph") Annotation( "GOC:tb") "The developmental process pertaining to the initial formation of the optic vesicle from the lateral wall of the forebrain. This process begins with the specific processes that contribute to the appearance of the vesicle and ends when the vesicle has evaginated. The optic vesicle is the evagination of neurectoderm that precedes formation of the optic cup.") -AnnotationAssertion( "dph") AnnotationAssertion( "2009-12-21T01:42:37Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0003403") @@ -26078,7 +25926,6 @@ SubClassOf( ObjectSomeValuesFrom( (optic vesicle morphogenesis) AnnotationAssertion(Annotation( "GOC:ascb_2009") Annotation( "GOC:dph") Annotation( "GOC:tb") "The developmental process pertaining to the formation and shaping of the optic vesicle. This process begins with the specific processes that contribute to the appearance of the vesicle and ends when the vesicle has evaginated. The optic vesicle is the evagination of neurectoderm that precedes formation of the optic cup.") -AnnotationAssertion( "dph") AnnotationAssertion( "2009-12-21T01:54:34Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0003404") @@ -26090,7 +25937,6 @@ SubClassOf( ObjectSomeValuesFrom( (retinal pigment epithelium development) AnnotationAssertion(Annotation( "GOC:ascb_2009") Annotation( "GOC:dph") Annotation( "GOC:tb") "The progression of the retinal pigment epithelium over time, from its initial formation to the mature structure. The retinal pigment epithelium is the melanin-containing layer of cells between the retina and the choroid that absorbs scattered and reflected light and removes waste products produced by the photoreceptor cells.") -AnnotationAssertion( "dph") AnnotationAssertion( "2009-12-21T02:04:27Z") AnnotationAssertion( "biological_process") AnnotationAssertion(Annotation( "GOC:ascb_2009") Annotation( "GOC:dph") Annotation( "GOC:tb") "RPE development") @@ -26103,7 +25949,6 @@ SubClassOf( ObjectSomeValuesFrom( (neural retina development) AnnotationAssertion(Annotation( "GOC:ascb_2009") Annotation( "GOC:dph") Annotation( "GOC:tb") "The progression of the neural retina over time from its initial formation to the mature structure. The neural retina is the part of the retina that contains neurons and photoreceptor cells.") -AnnotationAssertion( "dph") AnnotationAssertion( "2009-12-21T02:15:14Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0003407") @@ -26116,7 +25961,6 @@ SubClassOf( ObjectSomeValuesFrom( (cell motility involved in camera-type eye morphogenesis) AnnotationAssertion(Annotation( "GOC:ascb_2009") Annotation( "GOC:dph") Annotation( "GOC:tb") "Any process involved in the controlled self-propelled movement of a cell that results in translocation of the cell from one place to another and contributes to the physical shaping or formation of the camera-type eye.") -AnnotationAssertion( "dph") AnnotationAssertion( "2009-12-21T03:04:27Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0003411") @@ -26126,7 +25970,6 @@ EquivalentClasses( ObjectIntersection # Class: (chondrocyte differentiation involved in endochondral bone morphogenesis) AnnotationAssertion(Annotation( "GOC:ascb_2009") Annotation( "GOC:dph") Annotation( "GOC:tb") "The process in which a chondroblast acquires specialized structural and/or functional features of a chondrocyte that will contribute to the development of a bone. A chondrocyte is a polymorphic cell that forms cartilage.") -AnnotationAssertion( "dph") AnnotationAssertion( "2009-12-22T08:39:58Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0003413") @@ -26138,7 +25981,6 @@ SubClassOf( ObjectSomeValuesFrom( (chondrocyte morphogenesis involved in endochondral bone morphogenesis) AnnotationAssertion(Annotation( "GOC:ascb_2009") Annotation( "GOC:dph") Annotation( "GOC:tb") "The process in which the structures of a chondrocyte that will contribute to bone development are generated and organized.") -AnnotationAssertion( "dph") AnnotationAssertion( "2009-12-22T08:42:55Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0003414") @@ -26149,7 +25991,6 @@ SubClassOf( ObjectSomeValuesFrom( (chondrocyte hypertrophy) AnnotationAssertion(Annotation( "GOC:ascb_2009") Annotation( "GOC:dph") Annotation( "GOC:tb") "The growth of a chondrocyte, where growth contributes to the progression of the chondrocyte over time.") -AnnotationAssertion( "dph") AnnotationAssertion( "2009-12-22T08:48:44Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0003415") @@ -26160,7 +26001,6 @@ SubClassOf( ObjectSomeValuesFrom( (endochondral bone growth) AnnotationAssertion(Annotation( "GOC:ascb_2009") Annotation( "GOC:dph") Annotation( "GOC:tb") "The increase in size or mass of an endochondral bone that contributes to the shaping of the bone.") -AnnotationAssertion( "dph") AnnotationAssertion( "2009-12-22T08:52:55Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0003416") @@ -26170,7 +26010,6 @@ EquivalentClasses( ObjectIntersection # Class: (growth plate cartilage development) AnnotationAssertion(Annotation( "GOC:ascb_2009") Annotation( "GOC:dph") Annotation( "GOC:tb") "The process whose specific outcome is the progression of the cartilage that will provide a scaffold for mineralization of endochondral bones as they elongate or grow.") -AnnotationAssertion( "dph") AnnotationAssertion( "2009-12-22T08:57:42Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0003417") @@ -26182,7 +26021,6 @@ SubClassOf( ObjectSomeValuesFrom( (growth plate cartilage chondrocyte differentiation) AnnotationAssertion(Annotation( "GOC:ascb_2009") Annotation( "GOC:dph") Annotation( "GOC:tb") "The process in which a chondroblast acquires specialized structural and/or functional features of a chondrocyte that will contribute to the growth of a bone. A chondrocyte is a polymorphic cell that forms cartilage.") -AnnotationAssertion( "dph") AnnotationAssertion( "2009-12-22T09:00:56Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0003418") @@ -26194,7 +26032,6 @@ SubClassOf( ObjectSomeValuesFrom( (growth plate cartilage morphogenesis) AnnotationAssertion(Annotation( "GOC:ascb_2009") Annotation( "GOC:dph") Annotation( "GOC:tb") "The process in which the anatomical structures of growth plate cartilage are generated and organized.") -AnnotationAssertion( "dph") AnnotationAssertion( "2009-12-22T09:21:30Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0003422") @@ -26206,7 +26043,6 @@ SubClassOf( ObjectSomeValuesFrom( (growth plate cartilage chondrocyte morphogenesis) AnnotationAssertion(Annotation( "GOC:ascb_2009") Annotation( "GOC:dph") Annotation( "GOC:tb") "The process in which the structures of a chondrocyte in the growth plate cartilage are generated and organized.") -AnnotationAssertion( "dph") AnnotationAssertion( "2009-12-22T12:22:24Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0003429") @@ -26218,7 +26054,6 @@ SubClassOf( ObjectSomeValuesFrom( (growth plate cartilage chondrocyte growth) AnnotationAssertion(Annotation( "GOC:ascb_2009") Annotation( "GOC:dph") Annotation( "GOC:tb") "The growth of a growth plate cartilage chondrocyte, where growth contributes to the progression of the chondrocyte over time from one condition to another.") -AnnotationAssertion( "dph") AnnotationAssertion( "2009-12-22T12:29:19Z") AnnotationAssertion(Annotation( "GOC:ascb_2009") Annotation( "GOC:dph") Annotation( "GOC:tb") "growth plate cartilage chondrocyte hypertrophy") AnnotationAssertion( "biological_process") @@ -26232,7 +26067,6 @@ SubClassOf( ObjectSomeValuesFrom( (growth plate cartilage chondrocyte development) AnnotationAssertion(Annotation( "GOC:ascb_2009") Annotation( "GOC:dph") Annotation( "GOC:tb") "The progression of a growth plate cartilage chondrocyte over time from after its fate commitment to the mature cell.") -AnnotationAssertion( "dph") AnnotationAssertion( "2009-12-22T12:32:49Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0003431") @@ -26244,7 +26078,6 @@ SubClassOf( ObjectSomeValuesFrom( (cell growth involved in growth plate cartilage chondrocyte morphogenesis) AnnotationAssertion(Annotation( "GOC:ascb_2009") Annotation( "GOC:dph") Annotation( "GOC:tb") "The growth of a growth plate cartilage chondrocyte, where growth contributes to the shaping of the chondrocyte over time.") -AnnotationAssertion( "dph") AnnotationAssertion( "2009-12-22T12:37:48Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0003432") @@ -26255,7 +26088,6 @@ SubClassOf( (chondrocyte development involved in endochondral bone morphogenesis) AnnotationAssertion(Annotation( "GOC:ascb_2009") Annotation( "GOC:dph") Annotation( "GOC:tb") "The progression of a chondrocyte over time from after its commitment to its mature state where the chondrocyte will contribute to the shaping of an endochondral bone.") -AnnotationAssertion( "dph") AnnotationAssertion( "2009-12-22T12:42:44Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0003433") @@ -26267,7 +26099,6 @@ SubClassOf( ObjectSomeValuesFrom( (regulation of cell adhesion involved in growth plate cartilage morphogenesis) AnnotationAssertion(Annotation( "GOC:ascb_2009") Annotation( "GOC:dph") Annotation( "GOC:tb") "Any process that modulates the frequency, rate or extent of attachment of a cell to another cell or to the extracellular matrix and contributes to the shaping of the growth plate cartilage of an endochondral bone.") -AnnotationAssertion( "dph") AnnotationAssertion( "2009-12-22T01:28:15Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0003436") @@ -26277,7 +26108,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of cell communication involved in growth plate cartilage morphogenesis) AnnotationAssertion(Annotation( "GOC:ascb_2009") Annotation( "GOC:dph") Annotation( "GOC:tb") "Any process that modulates the frequency, rate or extent of cell communication that contributes to the shaping of the growth plate cartilage.") -AnnotationAssertion( "dph") AnnotationAssertion( "2009-12-22T01:34:24Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0003437") @@ -26407,7 +26237,6 @@ SubClassOf( "PMID:19686686") Annotation( "PMID:32684327") Annotation( "PMID:32842864") "A motor activity that generates movement along a microtubule, driven by ATP hydrolysis.") AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/18664"^^xsd:anyURI) -AnnotationAssertion( "vw") AnnotationAssertion( "2016-04-04T10:59:42Z") AnnotationAssertion( "dynein") AnnotationAssertion( "kinesin") @@ -28496,7 +28325,6 @@ EquivalentClasses( ObjectIntersection AnnotationAssertion(Annotation( "GOC:mah") Annotation( "ISBN:0198506732") "The chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y.") AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/22880"^^xsd:anyURI) -AnnotationAssertion( "jl") AnnotationAssertion( "2012-10-23T15:40:34Z") AnnotationAssertion( "Wikipedia:Carbohydrate_metabolism") AnnotationAssertion( "carbohydrate metabolism") @@ -28738,7 +28566,6 @@ SubClassOf( (regulation of gluconeogenesis) AnnotationAssertion(Annotation( "GOC:go_curators") "Any process that modulates the frequency, rate or extent of gluconeogenesis, the formation of glucose from noncarbohydrate precursors, such as pyruvate, amino acids and glycerol.") -AnnotationAssertion( "tb") AnnotationAssertion( "2013-01-18T12:47:43Z") AnnotationAssertion( "regulation of glucose biosynthesis") AnnotationAssertion( "regulation of glucose biosynthetic process") @@ -29604,7 +29431,6 @@ SubClassOf( "GOC:dos") Annotation( "GOC:dph") Annotation( "GOC:jl") Annotation( "GOC:mah") "The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter or a transporter complex, a pore or a motor protein.") AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/20292"^^xsd:anyURI) -AnnotationAssertion( "jl") AnnotationAssertion( "2012-12-13T16:25:32Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "single-organism transport") @@ -29648,7 +29474,6 @@ EquivalentClasses( ObjectIntersection # Class: (potassium ion transport) AnnotationAssertion(Annotation( "GOC:ai") "The directed movement of potassium ions (K+) into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-09-03T02:39:22Z") AnnotationAssertion( "sodium/potassium transport") AnnotationAssertion( "cellular potassium ion transport") @@ -29700,7 +29525,6 @@ EquivalentClasses( ObjectIntersection # Class: (iron ion transport) AnnotationAssertion(Annotation( "GOC:ai") "The directed movement of iron (Fe) ions into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.") -AnnotationAssertion( "pr") AnnotationAssertion( "2012-04-18T03:33:45Z") AnnotationAssertion( "iron transport") AnnotationAssertion( "ferric ion import") @@ -29924,7 +29748,6 @@ SubClassOf( ObjectSomeValuesFrom( (vesicle budding from membrane) AnnotationAssertion(Annotation( "GOC:jid") Annotation( "GOC:tb") "The evagination of a membrane, resulting in formation of a vesicle.") -AnnotationAssertion( "jl") AnnotationAssertion( "2013-12-19T15:26:17Z") AnnotationAssertion( "membrane evagination") AnnotationAssertion( "vesicle biosynthesis") @@ -30200,7 +30023,6 @@ SubClassOf( "GOC:mah") "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of an organelle within a cell. An organelle is an organized structure of distinctive morphology and function. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton. Excludes the plasma membrane.") AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/27189"^^xsd:anyURI) -AnnotationAssertion( "jl") AnnotationAssertion( "2013-12-19T15:25:51Z") AnnotationAssertion( "organelle organisation") AnnotationAssertion(Annotation( "GOC:TermGenie") "single organism organelle organization") @@ -30663,7 +30485,6 @@ SubClassOf( (cell adhesion) AnnotationAssertion(Annotation( "GOC:hb") Annotation( "GOC:pf") "The attachment of a cell, either to another cell or to an underlying substrate such as the extracellular matrix, via cell adhesion molecules.") -AnnotationAssertion( "dos") AnnotationAssertion( "2014-04-15T15:59:10Z") AnnotationAssertion( "Wikipedia:Cell_adhesion") AnnotationAssertion( "biological_process") @@ -31931,7 +31752,6 @@ SubClassOf( (behavior) AnnotationAssertion(Annotation( "GOC:ems") Annotation( "GOC:jl") Annotation( "ISBN:0395448956") Annotation( "PMID:20160973") "The internally coordinated responses (actions or inactions) of animals (individuals or groups) to internal or external stimuli, via a mechanism that involves nervous system activity.") -AnnotationAssertion( "jl") AnnotationAssertion( "2012-09-20T14:06:08Z") AnnotationAssertion( "Wikipedia:Behavior") AnnotationAssertion( "behavioral response to stimulus") @@ -32187,7 +32007,6 @@ SubClassOf( "GOC:pdt") "A biological process is the execution of a genetically-encoded biological module or program. It consists of all the steps required to achieve the specific biological objective of the module. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence.") AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/24968"^^xsd:anyURI) -AnnotationAssertion( "jl") AnnotationAssertion( "2012-09-19T15:05:24Z") AnnotationAssertion( "Wikipedia:Biological_process") AnnotationAssertion( "biological process") @@ -32212,7 +32031,6 @@ SubClassOf( "GOC:go_curators") Annotation( "ISBN:0198547684") "A cellular process consisting of the biochemical pathways by which a living organism transforms chemical substances. This includes including anabolism (biosynthetic process) and catabolism (catabolic process). Metabolic processes includes the transformation of small molecules, as well macromolecular processes such as DNA repair and replication, protein synthesis and degradation.") AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/26424"^^xsd:anyURI) AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/28932"^^xsd:anyURI) -AnnotationAssertion( "jl") AnnotationAssertion( "2012-10-17T15:46:40Z") AnnotationAssertion( "Wikipedia:Metabolism") AnnotationAssertion( "metabolism") @@ -32805,7 +32623,6 @@ SubClassOf( (hexose transmembrane transport) AnnotationAssertion(Annotation( "GOC:vw") "The process in which hexose is transported across a membrane. Hexoses are aldoses with a chain of six carbon atoms in the molecule.") -AnnotationAssertion( "bf") AnnotationAssertion( "2010-04-08T10:27:23Z") AnnotationAssertion( "high-affinity hexose transport") AnnotationAssertion( "low-affinity hexose transport") @@ -32838,7 +32655,6 @@ EquivalentClasses( ObjectIntersection AnnotationAssertion(Annotation( "ISBN:0198547684") "A cellular process consisting of the biochemical pathways by which a living organism breaks down substances. This includes the breakdown of carbon compounds with the liberation of energy for use by the cell or organism.") AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/28921"^^xsd:anyURI) AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/28932"^^xsd:anyURI) -AnnotationAssertion( "jl") AnnotationAssertion( "2012-10-17T15:52:35Z") AnnotationAssertion( "Wikipedia:Catabolism") AnnotationAssertion( "breakdown of chemical") @@ -32876,7 +32692,6 @@ EquivalentClasses( ObjectIntersection AnnotationAssertion(Annotation( "GOC:curators") Annotation( "ISBN:0198547684") "A cellular process consisting of the biochemical pathways by which a living organism synthesizes chemical substances. This typically represents the energy-requiring part of metabolism in which simpler substances are transformed into more complex ones.") AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/28932"^^xsd:anyURI) -AnnotationAssertion( "jl") AnnotationAssertion( "2012-10-17T15:52:18Z") AnnotationAssertion( "formation") AnnotationAssertion( "Wikipedia:Anabolism") @@ -33133,7 +32948,6 @@ SubClassOf( (amine metabolic process) AnnotationAssertion(Annotation( "GOC:jl") Annotation( "ISBN:0198506732") "The chemical reactions and pathways involving any organic compound that is weakly basic in character and contains an amino or a substituted amino group. Amines are called primary, secondary, or tertiary according to whether one, two, or three carbon atoms are attached to the nitrogen atom.") -AnnotationAssertion( "jl") AnnotationAssertion( "2009-07-15T11:55:44Z") AnnotationAssertion( "amine metabolism") AnnotationAssertion( "cellular amine metabolic process") @@ -33956,7 +33770,6 @@ EquivalentClasses( ObjectIntersection # Class: (cellular process) AnnotationAssertion(Annotation( "GOC:go_curators") Annotation( "GOC:isa_complete") "Any process that is carried out at the cellular level, but not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level.") -AnnotationAssertion( "jl") AnnotationAssertion( "2012-12-11T16:56:55Z") AnnotationAssertion( "cell physiology") AnnotationAssertion( "cellular physiological process") @@ -34118,7 +33931,6 @@ SubClassOf( (membrane invagination) AnnotationAssertion(Annotation( "GOC:tb") "The infolding of a membrane.") -AnnotationAssertion( "jl") AnnotationAssertion( "2013-12-02T13:58:34Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "single-organism membrane invagination") @@ -34252,7 +34064,6 @@ EquivalentClasses( ObjectIntersection # Class: (intercellular transport) AnnotationAssertion(Annotation( "GOC:dhl") "The movement of substances between cells.") -AnnotationAssertion( "jl") AnnotationAssertion( "2013-12-19T13:24:56Z") AnnotationAssertion( "biological_process") AnnotationAssertion(Annotation( "GOC:TermGenie") "single organism intercellular transport") @@ -35337,7 +35148,6 @@ SubClassOf( (negative regulation of cell cycle process) AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:tb") "Any process that decreases the rate, frequency or extent of a cellular process that is involved in the progression of biochemical and morphological phases and events that occur in a cell during successive cell replication or nuclear replication events.") -AnnotationAssertion( "tb") AnnotationAssertion( "2009-04-27T09:53:22Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0010948") @@ -35348,7 +35158,6 @@ SubClassOf( (positive regulation of protein processing) AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:mah") Annotation( "GOC:tb") "Any process that increases the rate, frequency or extent of protein maturation by peptide bond cleavage.") -AnnotationAssertion( "tb") AnnotationAssertion( "2009-04-27T12:09:13Z") AnnotationAssertion(Annotation( "GOC:bf") "positive regulation of protein maturation by peptide bond cleavage") AnnotationAssertion( "biological_process") @@ -35360,7 +35169,6 @@ SubClassOf( (negative regulation of protein processing) AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:mah") Annotation( "GOC:tb") "Any process that decreases the rate, frequency or extent of protein maturation by peptide bond cleavage.") -AnnotationAssertion( "tb") AnnotationAssertion( "2009-04-27T12:10:19Z") AnnotationAssertion(Annotation( "GOC:bf") "negative regulation of protein maturation by peptide bond cleavage") AnnotationAssertion( "biological_process") @@ -35372,7 +35180,6 @@ SubClassOf( (regulation of amino acid import across plasma membrane) AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:tb") "Any process that modulates the frequency, rate or extent of amino acid import into a cell.") -AnnotationAssertion( "tb") AnnotationAssertion( "2009-05-06T11:33:12Z") AnnotationAssertion( "regulation of amino acid import") AnnotationAssertion( "biological_process") @@ -35383,7 +35190,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of glucan biosynthetic process) AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:tb") "Any process that modulates the rate, frequency, or extent of glucan biosynthesis. Glucan biosynthetic processes are the chemical reactions and pathways resulting in the formation of glucans, polysaccharides consisting only of glucose residues.") -AnnotationAssertion( "tb") AnnotationAssertion( "2009-05-11T12:17:53Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0010962") @@ -35396,7 +35202,6 @@ SubClassOf( (regulation of phosphate transport) AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:tb") "Any process that modulates the frequency, rate or extent of phosphate transport. Phosphate transport is the directed movement of phosphate into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.") -AnnotationAssertion( "tb") AnnotationAssertion( "2009-05-20T11:42:50Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0010966") @@ -35406,7 +35211,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of microtubule nucleation) AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:tb") "Any process that modulates the rate, frequency or extent of microtubule nucleation. Microtubule nucleation is the 'de novo' formation of a microtubule, in which tubulin heterodimers form metastable oligomeric aggregates, some of which go on to support formation of a complete microtubule. Microtubule nucleation usually occurs from a specific site within a cell.") -AnnotationAssertion( "tb") AnnotationAssertion( "2009-05-20T11:51:21Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0010968") @@ -35417,7 +35221,6 @@ SubClassOf( ObjectSomeValuesFrom( (transport along microtubule) AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:mah") Annotation( "GOC:tb") "The movement of organelles or other particles from one location in the cell to another along microtubules, driven by motor activity.") -AnnotationAssertion( "tb") AnnotationAssertion( "2009-05-27T10:56:08Z") AnnotationAssertion( "microtubule-based transport") AnnotationAssertion(Annotation( "GOC:dph") "establishment of localization by movement along microtubule") @@ -35432,7 +35235,6 @@ SubClassOf( (regulation of neuron projection development) AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:tb") "Any process that modulates the rate, frequency or extent of neuron projection development. Neuron projection development is the process whose specific outcome is the progression of a neuron projection over time, from its formation to the mature structure. A neuron projection is any process extending from a neural cell, such as axons or dendrites (collectively called neurites).") -AnnotationAssertion( "tb") AnnotationAssertion( "2009-06-01T10:44:45Z") AnnotationAssertion(Annotation( "GOC:mah") "regulation of neurite biosynthesis") AnnotationAssertion(Annotation( "GOC:mah") "regulation of neurite development") @@ -35446,7 +35248,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of neuron projection development) AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:tb") "Any process that increases the rate, frequency or extent of neuron projection development. Neuron projection development is the process whose specific outcome is the progression of a neuron projection over time, from its formation to the mature structure. A neuron projection is any process extending from a neural cell, such as axons or dendrites (collectively called neurites).") -AnnotationAssertion( "tb") AnnotationAssertion( "2009-06-01T10:46:44Z") AnnotationAssertion(Annotation( "GOC:mah") "positive regulation of neurite biosynthesis") AnnotationAssertion(Annotation( "GOC:mah") "positive regulation of neurite development") @@ -35460,7 +35261,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of neuron projection development) AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:tb") "Any process that decreases the rate, frequency or extent of neuron projection development. Neuron projection development is the process whose specific outcome is the progression of a neuron projection over time, from its formation to the mature structure. A neuron projection is any process extending from a neural cell, such as axons or dendrites (collectively called neurites).") -AnnotationAssertion( "tb") AnnotationAssertion( "2009-06-01T10:47:42Z") AnnotationAssertion(Annotation( "GOC:mah") "negative regulation of neurite biosynthesis") AnnotationAssertion(Annotation( "GOC:mah") "negative regulation of neurite development") @@ -37479,7 +37279,6 @@ EquivalentClasses( ObjectIntersection # Class: (carbohydrate catabolic process) AnnotationAssertion(Annotation( "ISBN:0198506732") "The chemical reactions and pathways resulting in the breakdown of carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y.") -AnnotationAssertion( "jl") AnnotationAssertion( "2012-10-23T16:34:39Z") AnnotationAssertion( "carbohydrate breakdown") AnnotationAssertion( "carbohydrate catabolism") @@ -38226,7 +38025,6 @@ SubClassOf( "GOC:jl") Annotation( "GOC:pr") "The specific behavior of an organism that is associated with reproduction.") AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/23491"^^xsd:anyURI) -AnnotationAssertion( "jl") AnnotationAssertion( "2012-09-19T16:01:37Z") AnnotationAssertion( "reproductive behavior in a multicellular organism") AnnotationAssertion( "reproductive behaviour") @@ -41116,7 +40914,6 @@ SubClassOf( "GOC:dph") Annotation( "GOC:isa_complete") "A biological process that directly contributes to the process of producing new individuals by one or two organisms. The new individuals inherit some proportion of their genetic material from the parent or parents.") AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/27054"^^xsd:anyURI) -AnnotationAssertion( "jl") AnnotationAssertion( "2012-09-19T15:56:06Z") AnnotationAssertion( "Wikipedia:Reproduction") AnnotationAssertion( "biological_process") @@ -41482,7 +41279,6 @@ EquivalentClasses( ObjectIntersection # Class: (signaling) AnnotationAssertion(Annotation( "GOC:mtg_signal") Annotation( "GOC:mtg_signaling_feb11") Annotation( "GOC:signaling") "The entirety of a process in which information is transmitted within a biological system. This process begins with an active signal and ends when a cellular response has been triggered.") -AnnotationAssertion( "jl") AnnotationAssertion( "2010-02-16T09:30:50Z") AnnotationAssertion( "biological signaling") AnnotationAssertion( "signaling process") @@ -45673,7 +45469,6 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) -AnnotationAssertion( "jl") AnnotationAssertion( "2012-09-19T16:07:47Z") AnnotationAssertion( "organismal physiological process") AnnotationAssertion( "biological_process") @@ -45701,7 +45496,6 @@ DisjointClasses( ObjectSomeValuesFrom # Class: (developmental process) AnnotationAssertion(Annotation( "GOC:isa_complete") "A biological process whose specific outcome is the progression of an integrated living unit: an anatomical structure (which may be a subcellular structure, cell, tissue, or organ), or organism over time from an initial condition to a later condition.") -AnnotationAssertion( "jl") AnnotationAssertion( "2012-12-19T12:21:31Z") AnnotationAssertion( "development") AnnotationAssertion( "biological_process") @@ -46003,7 +45797,6 @@ SubClassOf( (tumor necrosis factor production) AnnotationAssertion(Annotation( "GOC:mah") Annotation( "PMID:10891884") Annotation( "PMID:15560120") "The appearance of tumor necrosis factor due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. Tumor necrosis factor is an inflammatory cytokine produced by macrophages/monocytes during acute inflammation and which is responsible for a diverse range of signaling events within cells, leading to necrosis or apoptosis.") -AnnotationAssertion( "sl") AnnotationAssertion( "2015-06-15T22:59:26Z") AnnotationAssertion( "TNF production") AnnotationAssertion( "cachectin production") @@ -46173,7 +45966,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of tumor necrosis factor production) AnnotationAssertion(Annotation( "GOC:mah") Annotation( "PMID:10891884") Annotation( "PMID:15560120") "Any process that modulates the frequency, rate or extent of tumor necrosis factor production.") -AnnotationAssertion( "sl") AnnotationAssertion( "2015-07-09T19:50:02Z") AnnotationAssertion( "regulation of TNF production") AnnotationAssertion( "regulation of TNF-alpha production") @@ -46310,7 +46102,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of interleukin-4 production) AnnotationAssertion(Annotation( "GOC:mah") Annotation( "PMID:29778524") "Any process that stops, prevents, or reduces the frequency, rate, or extent of interleukin-4 production.") -AnnotationAssertion( "bc") AnnotationAssertion( "down regulation of interleukin-4 production") AnnotationAssertion( "down-regulation of interleukin-4 production") AnnotationAssertion( "downregulation of interleukin-4 production") @@ -46385,7 +46176,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of tumor necrosis factor production) AnnotationAssertion(Annotation( "GOC:mah") Annotation( "PMID:10891884") Annotation( "PMID:15560120") "Any process that stops, prevents, or reduces the frequency, rate, or extent of tumor necrosis factor production.") -AnnotationAssertion( "sl") AnnotationAssertion( "2015-07-09T19:50:08Z") AnnotationAssertion( "down regulation of tumor necrosis factor production") AnnotationAssertion( "down-regulation of tumor necrosis factor production") @@ -46618,7 +46408,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of tumor necrosis factor production) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000058") Annotation( "PMID:10891884") Annotation( "PMID:15560120") "Any process that activates or increases the frequency, rate or extent of tumor necrosis factor production.") -AnnotationAssertion( "sl") AnnotationAssertion( "2015-07-09T19:50:14Z") AnnotationAssertion( "positive regulation of TNF production") AnnotationAssertion( "positive regulation of TNF-alpha production") @@ -47218,7 +47007,6 @@ SubClassOf( "GOC:dph") Annotation( "GOC:mah") Annotation( "GOC:tb") "Any process that modulates the frequency, rate or extent of any process in which a protein is transported to, or maintained in, a specific location.") AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/22021"^^xsd:anyURI) -AnnotationAssertion( "jl") AnnotationAssertion( "2015-01-20T14:32:14Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "regulation of cellular protein localisation") AnnotationAssertion( "regulation of cellular protein localization") @@ -47484,7 +47272,6 @@ EquivalentClasses( ObjectIntersection # Class: (amino acid export across plasma membrane) AnnotationAssertion(Annotation( "GOC:jl") "The directed movement of amino acids from inside of a cell, across the plasma membrane and into the extracellular region.") -AnnotationAssertion( "jl") AnnotationAssertion( "2012-11-14T14:27:40Z") AnnotationAssertion( "amino acid export") AnnotationAssertion( "amino acid transmembrane export") @@ -48130,7 +47917,6 @@ EquivalentClasses( ObjectIntersection # Class: (iron import into cell) AnnotationAssertion(Annotation( "PMID:18622392") Annotation( "PMID:23192658") Annotation( "Wikipedia:Human_iron_metabolism") "The directed movement of iron ions from outside of a cell into the cytoplasmic compartment. This may occur via transport across the plasma membrane or via endocytosis.") -AnnotationAssertion( "mah") AnnotationAssertion( "2009-05-01T04:19:14Z") AnnotationAssertion( "ferrous ion import") AnnotationAssertion( "ferrous iron import") @@ -48661,7 +48447,6 @@ EquivalentClasses( ObjectIntersection # Class: (protein localization to Golgi apparatus) AnnotationAssertion(Annotation( "GOC:mah") "A process in which a protein is transported to, or maintained in, a location within the Golgi apparatus.") -AnnotationAssertion( "mah") AnnotationAssertion( "2011-02-14T02:26:36Z") AnnotationAssertion(Annotation( "GOC:mah") "protein localisation in Golgi apparatus") AnnotationAssertion( "protein localization in Golgi apparatus") @@ -49240,7 +49025,6 @@ SubClassOf( (iron ion transmembrane transport) AnnotationAssertion(Annotation( "GOC:mah") Annotation( "PMID:11390404") "A process in which an iron ion is transported from one side of a membrane to the other by means of some agent such as a transporter or pore.") -AnnotationAssertion( "vw") AnnotationAssertion( "2015-02-06T11:29:22Z") AnnotationAssertion( "iron ion membrane transport") AnnotationAssertion( "transmembrane iron transport") @@ -49264,7 +49048,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of iron ion transport) AnnotationAssertion(Annotation( "GOC:mah") "Any process that modulates the frequency, rate or extent of the directed movement of iron ions (Fe) into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.") -AnnotationAssertion( "mah") AnnotationAssertion( "2012-04-18T04:00:14Z") AnnotationAssertion( "regulation of Fe transport") AnnotationAssertion( "regulation of iron transport") @@ -49426,7 +49209,6 @@ EquivalentClasses( ObjectIntersection # Class: (basement membrane disassembly) AnnotationAssertion(Annotation( "GOC:sart") Annotation( "PMID:17301221") "The controlled breakdown of the basement membrane in the context of a normal process such as imaginal disc eversion.") -AnnotationAssertion( "dph") AnnotationAssertion( "2009-08-13T11:27:24Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "basal lamina disassembly") @@ -49995,7 +49777,6 @@ SubClassOf( ObjectAllValuesFrom( (mesenchymal cell migration involved in limb bud formation) AnnotationAssertion(Annotation( "GOC:dgh") "The orderly movement of a mesenchymal cell from one site to another that will contribute to the formation of a limb bud.") -AnnotationAssertion( "bf") AnnotationAssertion( "2010-02-24T02:05:14Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0035322") @@ -50006,7 +49787,6 @@ SubClassOf( ObjectSomeValuesFrom( (pre-B cell receptor complex) AnnotationAssertion(Annotation( "GOC:add") Annotation( "ISBN:0781765196") Annotation( "PMID:16464608") Annotation( "PMID:17306522") "An immunoglobulin-like complex that is present in at least the plasma membrane of pre-B cells, and that is composed of two identical immunoglobulin heavy chains and two surrogate light chains, each composed of the lambda-5 and VpreB proteins, and a signaling subunit, a heterodimer of the Ig-alpha and Ig-beta proteins.") -AnnotationAssertion( "bf") AnnotationAssertion( "2010-03-11T10:46:10Z") AnnotationAssertion( "pre-BCR") AnnotationAssertion( "cellular_component") @@ -50019,7 +49799,6 @@ SubClassOf( ObjectSomeValuesFrom( (protein localization to microtubule) AnnotationAssertion(Annotation( "GOC:bf") Annotation( "GOC:lb") "A process in which a protein is transported to, or maintained at, a microtubule.") -AnnotationAssertion( "bf") AnnotationAssertion( "2010-03-11T11:00:56Z") AnnotationAssertion(Annotation( "GOC:mah") "protein localisation to microtubule") AnnotationAssertion( "biological_process") @@ -50031,7 +49810,6 @@ SubClassOf( (chondroitin sulfate binding) AnnotationAssertion(Annotation( "GOC:kmv") Annotation( "ISBN:0198506732") "Binding to chondroitin sulfate, a glycosaminoglycan made up of two alternating monosaccharides: D-glucuronic acid (GlcA) and N-acetyl-D-galactosamine (GalNAc).") -AnnotationAssertion( "bf") AnnotationAssertion( "2010-03-12T10:25:34Z") AnnotationAssertion( "molecular_function") AnnotationAssertion( "GO:0035374") @@ -50041,7 +49819,6 @@ EquivalentClasses( ObjectIntersection # Class: (transepithelial water transport) AnnotationAssertion(Annotation( "GOC:yaf") "The directed movement of water (H2O) from one side of an epithelium to the other.") -AnnotationAssertion( "bf") AnnotationAssertion( "2010-03-18T10:55:38Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0035377") @@ -50051,7 +49828,6 @@ EquivalentClasses( ObjectIntersection # Class: (protein localization to synapse) AnnotationAssertion(Annotation( "GOC:bf") "Any process in which a protein is transported to, and/or maintained at the synapse, the junction between a nerve fiber of one neuron and another neuron or muscle fiber or glial cell.") -AnnotationAssertion( "bf") AnnotationAssertion( "2010-03-29T10:58:53Z") AnnotationAssertion(Annotation( "GOC:mah") "protein localisation to synapse") AnnotationAssertion( "biological_process") @@ -50062,7 +49838,6 @@ EquivalentClasses( ObjectIntersection # Class: (phosphate ion transmembrane transport) AnnotationAssertion(Annotation( "GOC:vw") "The process in which a phosphate is transported across a membrane.") -AnnotationAssertion( "bf") AnnotationAssertion( "2010-04-08T11:24:06Z") AnnotationAssertion( "phosphate ion membrane transport") AnnotationAssertion( "biological_process") @@ -50074,7 +49849,6 @@ EquivalentClasses( ObjectIntersection # Class: (cell migration involved in vasculogenesis) AnnotationAssertion(Annotation( "GOC:dgh") "The orderly movement of a cell from one site to another that will contribute to the differentiation of an endothelial cell that will form de novo blood vessels and tubes.") -AnnotationAssertion( "bf") AnnotationAssertion( "2010-04-09T03:53:01Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0035441") @@ -50084,7 +49858,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of leukotriene production involved in inflammatory response) AnnotationAssertion(Annotation( "GOC:bf") "Any process that modulates the rate, frequency or extent of the synthesis or release of any leukotriene following a stimulus as part of an inflammatory response.") -AnnotationAssertion( "bf") AnnotationAssertion( "2010-04-26T10:49:22Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0035490") @@ -50094,7 +49867,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of leukotriene production involved in inflammatory response) AnnotationAssertion(Annotation( "GOC:bf") "Any process that increases the rate, frequency or extent of the synthesis or release of any leukotriene following a stimulus as part of an inflammatory response.") -AnnotationAssertion( "bf") AnnotationAssertion( "2010-04-26T10:50:14Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0035491") @@ -50105,7 +49877,6 @@ SubClassOf( (negative regulation of leukotriene production involved in inflammatory response) AnnotationAssertion(Annotation( "GOC:bf") "Any process that decreases the rate, frequency or extent of the synthesis or release of any leukotriene following a stimulus as part of an inflammatory response.") -AnnotationAssertion( "bf") AnnotationAssertion( "2010-04-26T10:50:55Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0035492") @@ -50116,7 +49887,6 @@ SubClassOf( (intracellular signal transduction) AnnotationAssertion(Annotation( "GOC:bf") Annotation( "GOC:jl") Annotation( "GOC:signaling") Annotation( "ISBN:3527303782") "The process in which a signal is passed on to downstream components within the cell, which become activated themselves to further propagate the signal and finally trigger a change in the function or state of the cell.") -AnnotationAssertion( "bf") AnnotationAssertion( "2010-05-14T01:14:37Z") AnnotationAssertion( "intracellular signal transduction pathway") AnnotationAssertion( "signal transmission via intracellular cascade") @@ -50131,7 +49901,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of chromatin binding) AnnotationAssertion(Annotation( "GOC:bf") Annotation( "PMID:20404130") "Any process that modulates the frequency, rate or extent of chromatin binding. Chromatin binding is the selective interaction with chromatin, the network of fibers of DNA, protein, and sometimes RNA, that make up the chromosomes of the eukaryotic nucleus during interphase.") -AnnotationAssertion( "bf") AnnotationAssertion( "2010-05-19T10:28:36Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0035561") @@ -50142,7 +49911,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of chromatin binding) AnnotationAssertion(Annotation( "GOC:bf") Annotation( "PMID:20404130") "Any process that stops or reduces the frequency, rate or extent of chromatin binding. Chromatin binding is the selective interaction with chromatin, the network of fibers of DNA, protein, and sometimes RNA, that make up the chromosomes of the eukaryotic nucleus during interphase.") -AnnotationAssertion( "bf") AnnotationAssertion( "2010-05-19T10:29:06Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0035562") @@ -50153,7 +49921,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of chromatin binding) AnnotationAssertion(Annotation( "GOC:bf") Annotation( "PMID:20404130") "Any process that increases the frequency, rate or extent of chromatin binding. Chromatin binding is the selective interaction with chromatin, the network of fibers of DNA, protein, and sometimes RNA, that make up the chromosomes of the eukaryotic nucleus during interphase.") -AnnotationAssertion( "bf") AnnotationAssertion( "2010-05-19T10:29:41Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0035563") @@ -50164,7 +49931,6 @@ EquivalentClasses( ObjectIntersection # Class: (azurophil granule membrane) AnnotationAssertion(Annotation( "GOC:bf") Annotation( "PMID:17152095") "The lipid bilayer surrounding an azurophil granule, a primary lysosomal granule found in neutrophil granulocytes that contains a wide range of hydrolytic enzymes and is released into the extracellular fluid.") -AnnotationAssertion( "bf") AnnotationAssertion( "2010-10-05T01:29:10Z") AnnotationAssertion( "primary granule membrane") AnnotationAssertion( "cellular_component") @@ -50178,7 +49944,6 @@ SubClassOf( ObjectSomeValuesFrom( (establishment of protein localization to extracellular region) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:bf") "The directed movement of a protein to a specific location within the extracellular region.") -AnnotationAssertion( "bf") AnnotationAssertion( "2010-11-09T10:25:08Z") AnnotationAssertion(Annotation( "GOC:mah") "establishment of protein localisation in extracellular region") AnnotationAssertion( "establishment of protein localization in extracellular region") @@ -50192,7 +49957,6 @@ SubClassOf( (intrahepatic bile duct development) AnnotationAssertion(Annotation( "GOC:bf") Annotation( "PMID:20614624") "The progression of the intrahepatic bile ducts over time, from their formation to the mature structure. Intrahepatic bile ducts (bile ducts within the liver) collect bile from bile canaliculi in the liver, and connect to the extrahepatic bile ducts (bile ducts outside the liver).") -AnnotationAssertion( "bf") AnnotationAssertion( "2010-12-08T04:10:50Z") AnnotationAssertion(Annotation( "PMID:20614624") "IHBD development") AnnotationAssertion(Annotation( "PMID:20614624") "intrahepatic biliary duct development") @@ -50207,7 +49971,6 @@ SubClassOf( ObjectSomeValuesFrom( (cystic duct development) AnnotationAssertion(Annotation( "PMID:20614624") "The progression of the cystic duct over time, from its formation to the mature structure. The cystic duct runs from the gallbladder to the common bile duct.") -AnnotationAssertion( "bf") AnnotationAssertion( "2010-12-10T01:24:28Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0035628") @@ -50220,7 +49983,6 @@ SubClassOf( ObjectSomeValuesFrom( (bone mineralization involved in bone maturation) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:bf") "The deposition of hydroxyapatite, involved in the progression of the skeleton from its formation to its mature state.") -AnnotationAssertion( "bf") AnnotationAssertion( "2010-12-20T01:57:31Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0035630") @@ -50231,7 +49993,6 @@ EquivalentClasses( ObjectIntersection # Class: (enteric smooth muscle cell differentiation) AnnotationAssertion(Annotation( "CL:0002504") Annotation( "GOC:BHF") "The process in which a relatively unspecialized cell acquires specialized features of a smooth muscle cell of the intestine.") -AnnotationAssertion( "bf") AnnotationAssertion( "2011-01-21T02:58:58Z") AnnotationAssertion(Annotation( "CL:0002504") "intestinal smooth muscle cell differentiation") AnnotationAssertion( "biological_process") @@ -50244,7 +50005,6 @@ SubClassOf( ObjectSomeValuesFrom( (neuromast hair cell development) AnnotationAssertion(Annotation( "CL:0000856") "The process whose specific outcome is the progression of a neuromast hair cell over time, from its formation to the mature structure. A neuromast hair cell is a hair cell that acts as a sensory receptor of the neuromast; it is morphologically polarized as a result of the relative position of the single kinocilium and the clusters of stereocilia on its apical surface. Cell development does not include the steps involved in committing a cell to a specific fate.") -AnnotationAssertion( "bf") AnnotationAssertion( "2011-02-14T11:01:42Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0035675") @@ -50256,7 +50016,6 @@ SubClassOf( ObjectSomeValuesFrom( (anterior lateral line neuromast hair cell development) AnnotationAssertion(Annotation( "ISBN:0125296509") Annotation( "ISBN:0387968377") "The process whose specific outcome is the progression of an anterior lateral line neuromast hair cell over time, from its formation to the mature structure. A neuromast hair cell is a hair cell that acts as a sensory receptor of the neuromast; it is morphologically polarized as a result of the relative position of the single kinocilium and the clusters of stereocilia on its apical surface. Cell development does not include the steps involved in committing a cell to a specific fate.") -AnnotationAssertion( "bf") AnnotationAssertion( "2011-02-14T11:03:57Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0035676") @@ -50268,7 +50027,6 @@ SubClassOf( ObjectSomeValuesFrom( (posterior lateral line neuromast hair cell development) AnnotationAssertion(Annotation( "ISBN:0125296509") "The process whose specific outcome is the progression of a posterior lateral line neuromast hair cell over time, from its formation to the mature structure. A neuromast hair cell is a hair cell that acts as a sensory receptor of the neuromast; it is morphologically polarized as a result of the relative position of the single kinocilium and the clusters of stereocilia on its apical surface. Cell development does not include the steps involved in committing a cell to a specific fate.") -AnnotationAssertion( "bf") AnnotationAssertion( "2011-02-14T11:04:57Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0035677") @@ -50280,7 +50038,6 @@ SubClassOf( ObjectSomeValuesFrom( (neuromast hair cell morphogenesis) AnnotationAssertion(Annotation( "CL:0000856") "The change in form (cell shape and size) that occurs when a neuromast hair cell progresses from its initial formation to its mature state. A neuromast hair cell is a hair cell that acts as a sensory receptor of the neuromast; it is morphologically polarized as a result of the relative position of the single kinocilium and the clusters of stereocilia on its apical surface.") -AnnotationAssertion( "bf") AnnotationAssertion( "2011-02-14T11:06:15Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0035678") @@ -50292,7 +50049,6 @@ SubClassOf( ObjectSomeValuesFrom( (astrocyte chemotaxis) AnnotationAssertion(Annotation( "CL:0000127") Annotation( "GOC:BHF") Annotation( "PMID:12271471") "The directed movement of an astrocyte guided by a specific chemical concentration gradient. Movement may be towards a higher concentration (positive chemotaxis) or towards a lower concentration (negative chemotaxis).") -AnnotationAssertion( "bf") AnnotationAssertion( "2011-02-28T03:17:52Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0035700") @@ -50303,7 +50059,6 @@ SubClassOf( (hematopoietic stem cell migration) AnnotationAssertion(Annotation( "CL:0000037") Annotation( "GOC:BHF") Annotation( "PMID:20234092") "The orderly movement of a hematopoietic stem cell from one site to another. A hematopoietic stem cell is a cell from which all cells of the lymphoid and myeloid lineages develop, including blood cells and cells of the immune system.") -AnnotationAssertion( "bf") AnnotationAssertion( "2011-02-28T03:20:36Z") AnnotationAssertion(Annotation( "CL:0000037") "hemopoietic stem cell migration") AnnotationAssertion( "biological_process") @@ -50315,7 +50070,6 @@ SubClassOf( (monocyte homeostasis) AnnotationAssertion(Annotation( "CL:0000576") Annotation( "GOC:BHF") Annotation( "PMID:18832716") "The process of regulating the proliferation and elimination of monocytes such that the total number of monocytes within a whole or part of an organism is stable over time in the absence of an outside stimulus.") -AnnotationAssertion( "bf") AnnotationAssertion( "2011-03-02T11:32:57Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0035702") @@ -50327,7 +50081,6 @@ SubClassOf( (helper T cell chemotaxis) AnnotationAssertion(Annotation( "CL:0000912") Annotation( "GOC:BHF") "The directed movement of a helper T cell in response to an external stimulus.") -AnnotationAssertion( "bf") AnnotationAssertion( "2011-03-02T02:31:48Z") AnnotationAssertion(Annotation( "CL:0000912") "T-helper cell chemotaxis") AnnotationAssertion( "biological_process") @@ -50339,7 +50092,6 @@ SubClassOf( (T-helper 17 cell chemotaxis) AnnotationAssertion(Annotation( "CL:0000899") Annotation( "GOC:BHF") "The directed movement of a T-helper 17 cell in response to an external stimulus.") -AnnotationAssertion( "bf") AnnotationAssertion( "2011-03-02T02:35:16Z") AnnotationAssertion(Annotation( "CL:0000899") "Th17 cell chemotaxis") AnnotationAssertion( "biological_process") @@ -50350,7 +50102,6 @@ EquivalentClasses( ObjectIntersection # Class: (T-helper 1 cell chemotaxis) AnnotationAssertion(Annotation( "CL:0000545") Annotation( "GOC:BHF") "The directed movement of a T-helper 1 cell in response to an external stimulus.") -AnnotationAssertion( "bf") AnnotationAssertion( "2011-03-02T02:36:49Z") AnnotationAssertion(Annotation( "CL:0000545") "Th1 cell chemotaxis") AnnotationAssertion( "biological_process") @@ -50361,7 +50112,6 @@ EquivalentClasses( ObjectIntersection # Class: (T-helper 2 cell chemotaxis) AnnotationAssertion(Annotation( "CL:0000546") Annotation( "GOC:BHF") "The directed movement of a T-helper 2 cell in response to an external stimulus.") -AnnotationAssertion( "bf") AnnotationAssertion( "2011-03-02T02:37:44Z") AnnotationAssertion(Annotation( "CL:0000546") "Th2 cell chemotaxis") AnnotationAssertion( "biological_process") @@ -50372,7 +50122,6 @@ EquivalentClasses( ObjectIntersection # Class: (memory T cell activation) AnnotationAssertion(Annotation( "CL:0000813") Annotation( "GOC:BHF") "The change in morphology and behavior of a memory T cell resulting from exposure to a mitogen, cytokine, chemokine, cellular ligand, or an antigen for which it is specific.") -AnnotationAssertion( "bf") AnnotationAssertion( "2011-03-02T03:03:02Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0035709") @@ -50383,7 +50132,6 @@ SubClassOf( (CD4-positive, alpha-beta T cell activation) AnnotationAssertion(Annotation( "CL:0000624") Annotation( "GOC:BHF") "The change in morphology and behavior of a CD4-positive, alpha-beta T cell resulting from exposure to a mitogen, cytokine, chemokine, cellular ligand, or an antigen for which it is specific.") -AnnotationAssertion( "bf") AnnotationAssertion( "2011-03-02T03:04:11Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0035710") @@ -50394,7 +50142,6 @@ SubClassOf( (T-helper 1 cell activation) AnnotationAssertion(Annotation( "CL:0000545") Annotation( "GOC:BHF") "The change in morphology and behavior of a T-helper 1 cell resulting from exposure to a mitogen, cytokine, chemokine, cellular ligand, or an antigen for which it is specific.") -AnnotationAssertion( "bf") AnnotationAssertion( "2011-03-02T03:05:08Z") AnnotationAssertion(Annotation( "CL:0000545") "Th1 cell activation") AnnotationAssertion( "biological_process") @@ -50406,7 +50153,6 @@ SubClassOf( (T-helper 2 cell activation) AnnotationAssertion(Annotation( "CL:0000546") Annotation( "GOC:BHF") "The change in morphology and behavior of a T helper 2 cell resulting from exposure to a mitogen, cytokine, chemokine, cellular ligand, or an antigen for which it is specific.") -AnnotationAssertion( "bf") AnnotationAssertion( "2011-03-02T03:05:59Z") AnnotationAssertion(Annotation( "CL:0000546") "Th2 cell activation") AnnotationAssertion( "biological_process") @@ -50418,7 +50164,6 @@ SubClassOf( (sodium ion transmembrane transport) AnnotationAssertion(Annotation( "GOC:vw") "A process in which a sodium ion is transported from one side of a membrane to the other by means of some agent such as a transporter or pore.") -AnnotationAssertion( "bf") AnnotationAssertion( "2011-03-10T02:52:36Z") AnnotationAssertion( "sodium ion membrane transport") AnnotationAssertion( "biological_process") @@ -50432,7 +50177,6 @@ SubClassOf( (hepatic stellate cell activation) AnnotationAssertion(Annotation( "CL:0000632") Annotation( "GOC:bf") "A change in the morphology or behavior of a hepatic stellate cell resulting from exposure to a cytokine, chemokine, hormone, cellular ligand or soluble factor.") -AnnotationAssertion( "bf") AnnotationAssertion( "2011-03-11T10:04:12Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0035733") @@ -50443,7 +50187,6 @@ SubClassOf( (intraciliary transport involved in cilium assembly) AnnotationAssertion(Annotation( "GOC:bf") Annotation( "GOC:cilia") "The bidirectional movement of large protein complexes along microtubules within a cilium that contributes to cilium assembly.") -AnnotationAssertion( "bf") AnnotationAssertion( "2011-03-17T10:55:42Z") AnnotationAssertion( "intraflagellar transport") AnnotationAssertion( "biological_process") @@ -50456,7 +50199,6 @@ EquivalentClasses( ObjectIntersection # Class: (cell proliferation involved in compound eye morphogenesis) AnnotationAssertion(Annotation( "GOC:bf") Annotation( "GOC:sart") "The multiplication or reproduction of cells, resulting in the expansion of a cell population that contributes to compound eye morphogenesis.") -AnnotationAssertion( "bf") AnnotationAssertion( "2011-03-17T10:57:03Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0035736") @@ -50466,7 +50208,6 @@ EquivalentClasses( ObjectIntersection # Class: (CD4-positive, alpha-beta T cell proliferation) AnnotationAssertion(Annotation( "CL:0000624") Annotation( "GOC:BHF") "The expansion of a CD4-positive, alpha-beta T cell population by cell division.") -AnnotationAssertion( "bf") AnnotationAssertion( "2011-03-17T02:12:48Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0035739") @@ -50478,7 +50219,6 @@ SubClassOf( (CD8-positive, alpha-beta T cell proliferation) AnnotationAssertion(Annotation( "CL:0000625") Annotation( "GOC:BHF") "The expansion of a CD8-positive, alpha-beta T cell population by cell division.") -AnnotationAssertion( "bf") AnnotationAssertion( "2011-03-17T02:13:54Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0035740") @@ -50490,7 +50230,6 @@ SubClassOf( (activated CD4-positive, alpha-beta T cell proliferation) AnnotationAssertion(Annotation( "CL:0000896") Annotation( "GOC:BHF") "The expansion of an activated CD4-positive, alpha-beta T cell population by cell division.") -AnnotationAssertion( "bf") AnnotationAssertion( "2011-03-17T02:18:39Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0035741") @@ -50501,7 +50240,6 @@ SubClassOf( (activated CD8-positive, alpha-beta T cell proliferation) AnnotationAssertion(Annotation( "CL:0000906") Annotation( "GOC:BHF") "The expansion of an activated CD8-positive, alpha-beta T cell population by cell division.") -AnnotationAssertion( "bf") AnnotationAssertion( "2011-03-17T02:19:58Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0035742") @@ -50512,7 +50250,6 @@ SubClassOf( (CD4-positive, alpha-beta T cell cytokine production) AnnotationAssertion(Annotation( "CL:0000624") Annotation( "GOC:BHF") "Any process that contributes to cytokine production by a CD4-positive, alpha-beta T cell.") -AnnotationAssertion( "bf") AnnotationAssertion( "2011-03-17T02:21:51Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0035743") @@ -50525,7 +50262,6 @@ SubClassOf( (T-helper 1 cell cytokine production) AnnotationAssertion(Annotation( "CL:0000545") Annotation( "GOC:BHF") "Any process that contributes to cytokine production by a T-helper 1 cell.") -AnnotationAssertion( "bf") AnnotationAssertion( "2011-03-17T02:22:54Z") AnnotationAssertion(Annotation( "CL:0000545") "Th1 cell cytokine production") AnnotationAssertion( "biological_process") @@ -50539,7 +50275,6 @@ SubClassOf( ObjectSomeValuesFrom( (T-helper 2 cell cytokine production) AnnotationAssertion(Annotation( "CL:0000546") Annotation( "GOC:BHF") "Any process that contributes to cytokine production by a T-helper 2 cell.") -AnnotationAssertion( "bf") AnnotationAssertion( "2011-03-17T02:23:32Z") AnnotationAssertion(Annotation( "CL:0000546") "Th2 cell cytokine production") AnnotationAssertion( "biological_process") @@ -50553,7 +50288,6 @@ SubClassOf( ObjectSomeValuesFrom( (natural killer cell chemotaxis) AnnotationAssertion(Annotation( "CL:0000623") Annotation( "GOC:BHF") "The directed movement of a natural killer cell guided by a specific chemical concentration gradient. Movement may be towards a higher concentration (positive chemotaxis) or towards a lower concentration (negative chemotaxis).") -AnnotationAssertion( "bf") AnnotationAssertion( "2011-03-17T02:40:10Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0035747") @@ -50564,7 +50298,6 @@ SubClassOf( (B cell chemotaxis) AnnotationAssertion(Annotation( "CL:0000236") Annotation( "GOC:BHF") "The directed movement of a B cell guided by a specific chemical concentration gradient. Movement may be towards a higher concentration (positive chemotaxis) or towards a lower concentration (negative chemotaxis).") -AnnotationAssertion( "bf") AnnotationAssertion( "2011-03-23T10:30:33Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0035754") @@ -50575,7 +50308,6 @@ SubClassOf( (endothelial cell chemotaxis) AnnotationAssertion(Annotation( "CL:0000115") Annotation( "GOC:BHF") "The directed movement of an endothelial cell guided by a specific chemical concentration gradient. Movement may be towards a higher concentration (positive chemotaxis) or towards a lower concentration (negative chemotaxis).") -AnnotationAssertion( "bf") AnnotationAssertion( "2011-03-31T04:31:37Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0035767") @@ -50585,7 +50317,6 @@ EquivalentClasses( ObjectIntersection # Class: (insulin secretion involved in cellular response to glucose stimulus) AnnotationAssertion(Annotation( "GOC:bf") Annotation( "GOC:yaf") Annotation( "PMID:8492079") "The regulated release of proinsulin from secretory granules (B granules) in the B cells of the pancreas; accompanied by cleavage of proinsulin to form mature insulin, in response to a glucose stimulus.") -AnnotationAssertion( "bf") AnnotationAssertion( "2011-04-01T01:14:40Z") AnnotationAssertion(Annotation( "GOC:bf") "insulin secretion involved in cellular response to glucose") AnnotationAssertion( "biological_process") @@ -50596,7 +50327,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of insulin secretion involved in cellular response to glucose stimulus) AnnotationAssertion(Annotation( "GOC:bf") Annotation( "GOC:yaf") "Any process that increases the frequency, rate or extent of the regulated release of insulin that contributes to the response of a cell to glucose.") -AnnotationAssertion( "bf") AnnotationAssertion( "2011-04-01T01:49:09Z") AnnotationAssertion(Annotation( "GOC:bf") "positive regulation of insulin secretion in response to glucose") AnnotationAssertion( "biological_process") @@ -50607,7 +50337,6 @@ EquivalentClasses( ObjectIntersection # Class: (pronephric glomerulus morphogenesis) AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") Annotation( "GOC:yaf") Annotation( "PMID:18787069") "The process in which the anatomical structures of the pronephric glomerulus are generated and organized. The pronephric glomerulus is part of the pronephric nephron and is restricted to one body segment.") -AnnotationAssertion( "bf") AnnotationAssertion( "2011-04-04T10:59:28Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0035775") @@ -50620,7 +50349,6 @@ SubClassOf( ObjectSomeValuesFrom( (pronephric proximal tubule development) AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") Annotation( "GOC:yaf") Annotation( "PMID:18787069") "The progression of the pronephric proximal tubule over time, from its formation to the mature structure. A pronephric nephron tubule is an epithelial tube that is part of the pronephros.") -AnnotationAssertion( "bf") AnnotationAssertion( "2011-04-04T11:02:54Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0035776") @@ -50632,7 +50360,6 @@ SubClassOf( (pronephric distal tubule development) AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") Annotation( "GOC:yaf") Annotation( "PMID:18787069") "The process whose specific outcome is the progression of the pronephric distal tubule over time, from its formation to the mature structure. A pronephric nephron tubule is an epithelial tube that is part of the pronephros.") -AnnotationAssertion( "bf") AnnotationAssertion( "2011-04-04T11:06:01Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0035777") @@ -50644,7 +50371,6 @@ SubClassOf( (pronephric nephron tubule epithelial cell differentiation) AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") Annotation( "GOC:yaf") Annotation( "PMID:18787069") "The process in which relatively unspecialized cells acquire specialized structural and/or functional features that characterize the cells of the pronephric nephron tubule as it progresses from its formation to the mature state.") -AnnotationAssertion( "bf") AnnotationAssertion( "2011-04-04T11:07:47Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0035778") @@ -50657,7 +50383,6 @@ SubClassOf( ObjectSomeValuesFrom( (angioblast cell differentiation) AnnotationAssertion(Annotation( "CL:0000566") Annotation( "GOC:yaf") "The process in which a relatively unspecialized cell acquires the specialized structural and/or functional features of an angioblast cell. Angioblasts are one of the two products formed from hemangioblast cells (the other being pluripotent hemopoietic stem cells).") -AnnotationAssertion( "bf") AnnotationAssertion( "2011-04-04T11:10:38Z") AnnotationAssertion(Annotation( "CL:0000566") "angioblastic mesenchymal cell differentiation") AnnotationAssertion( "biological_process") @@ -50669,7 +50394,6 @@ SubClassOf( ObjectSomeValuesFrom( (cell migration involved in kidney development) AnnotationAssertion(Annotation( "GOC:bf") Annotation( "GOC:mtg_kidney_jan10") Annotation( "GOC:yaf") "The orderly movement of a cell from one site to another that will contribute to the progression of the kidney over time, from its formation to the mature organ.") -AnnotationAssertion( "bf") AnnotationAssertion( "2011-04-06T10:39:52Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0035787") @@ -50679,7 +50403,6 @@ EquivalentClasses( ObjectIntersection # Class: (cell migration involved in metanephros development) AnnotationAssertion(Annotation( "GOC:bf") Annotation( "GOC:mtg_kidney_jan10") Annotation( "GOC:yaf") "The orderly movement of a cell from one site to another that will contribute to the progression of the metanephric kidney over time, from its formation to the mature organ.") -AnnotationAssertion( "bf") AnnotationAssertion( "2011-04-06T10:42:21Z") AnnotationAssertion(Annotation( "GOC:bf") "cell migration involved in metanephric kidney development") AnnotationAssertion( "biological_process") @@ -50690,7 +50413,6 @@ EquivalentClasses( ObjectIntersection # Class: (ureter maturation) AnnotationAssertion(Annotation( "GOC:bf") Annotation( "GOC:mtg_kidney_jan10") Annotation( "GOC:yaf") Annotation( "PMID:17881463") "A developmental process, independent of morphogenetic (shape) change, that is required for the ureter to attain its fully functional state. The ureter is a muscular tube that transports urine from the kidney to the urinary bladder or from the Malpighian tubule to the hindgut.") -AnnotationAssertion( "bf") AnnotationAssertion( "2011-04-14T01:13:39Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0035799") @@ -50702,7 +50424,6 @@ SubClassOf( ObjectSomeValuesFrom( (adrenal cortex development) AnnotationAssertion(Annotation( "PMID:12185666") Annotation( "PMID:21115154") Annotation( "Wikipedia:Adrenal_cortex") "The process whose specific outcome is the progression of the adrenal cortex over time, from its formation to the mature structure. The adrenal cortex is located at the periphery of the adrenal gland and controls glucose and electrolyte metabolism, response to stress and sexual development through the production of different classes of steroid hormones (glucocorticoids, mineralocorticoids and androgens).") -AnnotationAssertion( "bf") AnnotationAssertion( "2011-04-18T10:25:39Z") AnnotationAssertion(Annotation( "MA:0000118") "adrenal gland cortex development") AnnotationAssertion( "biological_process") @@ -50716,7 +50437,6 @@ SubClassOf( ObjectSomeValuesFrom( (adrenal cortex formation) AnnotationAssertion(Annotation( "PMID:12185666") Annotation( "PMID:21115154") "The process that gives rise to the adrenal cortex. This process pertains to the initial formation of a structure from unspecified parts. The adrenogonadal primordium from which the adrenal cortex is formed derives from a condensation of coelomic epithelial cells (the urogenital ridge; the same structure from which gonads and kidney also originate).") -AnnotationAssertion( "bf") AnnotationAssertion( "2011-04-18T10:26:49Z") AnnotationAssertion(Annotation( "MA:0000118") "adrenal gland cortex formation") AnnotationAssertion( "biological_process") @@ -50730,7 +50450,6 @@ SubClassOf( ObjectSomeValuesFrom( (egg coat) AnnotationAssertion(Annotation( "PMID:16944418") Annotation( "PMID:17163408") "A specialized extracellular matrix that surrounds the plasma membrane of the ovum of animals. The egg coat provides structural support and can play an essential role in oogenesis, fertilization and early development.") -AnnotationAssertion( "bf") AnnotationAssertion( "2011-04-19T02:07:23Z") AnnotationAssertion(Annotation( "PMID:16944418") Annotation( "PMID:17163408") "vitelline membrane") AnnotationAssertion(Annotation( "PMID:16944418") Annotation( "PMID:17163408") "zona pellucida") @@ -50744,7 +50463,6 @@ SubClassOf( ObjectAllValuesFrom( (regulation of urine volume) AnnotationAssertion(Annotation( "GOC:mtg_25march11") Annotation( "GOC:yaf") "Any process that modulates the amount of urine excreted from the body over a unit of time.") -AnnotationAssertion( "bf") AnnotationAssertion( "2011-04-20T01:17:38Z") AnnotationAssertion( "regulation of urinary volume") AnnotationAssertion( "regulation of urine flow") @@ -50757,7 +50475,6 @@ SubClassOf( (cloaca development) AnnotationAssertion(Annotation( "GOC:dgh") Annotation( "ISBN:0582227089") "The process whose specific outcome is the progression of the cloaca over time, from it's formation to the mature structure. The cloaca is the common chamber into which intestinal, genital and urinary canals open in vertebrates.") -AnnotationAssertion( "bf") AnnotationAssertion( "2011-05-06T01:54:35Z") AnnotationAssertion(Annotation( "GOC:bf") "cloacal development") AnnotationAssertion( "biological_process") @@ -50772,7 +50489,6 @@ SubClassOf( ObjectSomeValuesFrom( (oviduct epithelium development) AnnotationAssertion(Annotation( "GOC:yaf") Annotation( "PMID:34496237") "The progression of the oviduct epithelium over time from its initial formation to the mature structure. An oviduct is a tube through which an ova passes from the ovary to the uterus, or from the ovary to the outside of the organism. The oviduct epithelium is the specialized epithelium that lines the oviduct.") -AnnotationAssertion( "bf") AnnotationAssertion( "2011-05-10T10:53:05Z") AnnotationAssertion(Annotation( "GOC:yaf") "fallopian tube epithelium development") AnnotationAssertion( "biological_process") @@ -50786,7 +50502,6 @@ SubClassOf( ObjectSomeValuesFrom( (uterine epithelium development) AnnotationAssertion(Annotation( "GOC:bf") Annotation( "GOC:yaf") "The progression of an epithelium of the uterus over time from its initial formation to the mature structure. An epithelium is a tissue that covers the internal or external surfaces of an anatomical structure.") -AnnotationAssertion( "bf") AnnotationAssertion( "2011-05-10T10:57:45Z") AnnotationAssertion(Annotation( "GOC:yaf") "uterus epithelial development") AnnotationAssertion( "biological_process") @@ -50800,7 +50515,6 @@ SubClassOf( ObjectSomeValuesFrom( (oviduct morphogenesis) AnnotationAssertion(Annotation( "GOC:yaf") Annotation( "PMID:22918811") "The process in which anatomical structures of the oviduct are generated and organized. An oviduct is a tube through which an ova passes from the ovary to the uterus, or from the ovary to the outside of the organism.") -AnnotationAssertion( "bf") AnnotationAssertion( "2011-05-10T11:01:20Z") AnnotationAssertion(Annotation( "GOC:yaf") "fallopian tube morphogenesis") AnnotationAssertion( "biological_process") @@ -50814,7 +50528,6 @@ SubClassOf( ObjectSomeValuesFrom( (epithelial cell differentiation involved in kidney development) AnnotationAssertion(Annotation( "GOC:bf") Annotation( "GOC:mtg_kidney_jan10") Annotation( "GOC:yaf") Annotation( "PMID:16216236") "The process in which relatively unspecialized cells acquire specialized structural and/or functional features of an epithelial cell that characterize the cells of the kidney as it progresses from its formation to the mature state.") -AnnotationAssertion( "bf") AnnotationAssertion( "2011-05-11T11:34:21Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0035850") @@ -50824,7 +50537,6 @@ EquivalentClasses( ObjectIntersection # Class: (megakaryocyte development) AnnotationAssertion(Annotation( "CL:0000556") Annotation( "GOC:BHF") Annotation( "GOC:vk") "The process whose specific outcome is the progression of a megakaryocyte cell over time, from its formation to the mature structure. Megakaryocyte development does not include the steps involved in committing a cell to a megakaryocyte fate. A megakaryocyte is a giant cell 50 to 100 micron in diameter, with a greatly lobulated nucleus, found in the bone marrow.") -AnnotationAssertion( "bf") AnnotationAssertion( "2011-05-13T01:28:06Z") AnnotationAssertion(Annotation( "GOC:bf") "megakaryocyte cell development") AnnotationAssertion( "biological_process") @@ -50837,7 +50549,6 @@ SubClassOf( ObjectSomeValuesFrom( (response to potassium ion) AnnotationAssertion(Annotation( "GOC:yaf") "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a potassium ion stimulus.") -AnnotationAssertion( "bf") AnnotationAssertion( "2011-05-25T02:58:45Z") AnnotationAssertion(Annotation( "GOC:bf") "response to K+ ion") AnnotationAssertion(Annotation( "GOC:bf") "response to potassium") @@ -50849,7 +50560,6 @@ EquivalentClasses( ObjectIntersection # Class: (cellular response to potassium ion) AnnotationAssertion(Annotation( "GOC:yaf") "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a potassium ion stimulus.") -AnnotationAssertion( "bf") AnnotationAssertion( "2011-05-25T02:59:11Z") AnnotationAssertion(Annotation( "GOC:bf") "cellular response to K+ ion") AnnotationAssertion(Annotation( "GOC:bf") "cellular response to potassium") @@ -50861,7 +50571,6 @@ EquivalentClasses( ObjectIntersection # Class: (ciliary transition zone) AnnotationAssertion(Annotation( "GOC:cilia") Annotation( "GOC:kmv") Annotation( "PMID:21422230") "A region of the cilium between the basal body and proximal segment that is characterized by Y-shaped assemblages that connect axonemal microtubules to the ciliary membrane. The ciliary transition zone appears to function as a gate that controls ciliary membrane composition and separates the cytosol from the ciliary plasm.") -AnnotationAssertion( "bf") AnnotationAssertion( "2011-05-25T03:09:58Z") AnnotationAssertion( "cilial transition zone") AnnotationAssertion( "cilium transition zone") @@ -50876,7 +50585,6 @@ SubClassOf( ObjectSomeValuesFrom( (nail development) AnnotationAssertion(Annotation( "GOC:bf") Annotation( "ISBN:0323025781") Annotation( "UBERON:0001705") Annotation( "Wikipedia:Nail_(anatomy)") "The process whose specific outcome is the progression of a nail over time, from its formation to the mature structure. A nail is a horn-like envelope covering the outer end of a finger or toe, and consists of the nail plate, the nail matrix and the nail bed below it, and the grooves surrounding it.") -AnnotationAssertion( "bf") AnnotationAssertion( "2011-05-31T02:30:34Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0035878") @@ -50889,7 +50597,6 @@ SubClassOf( ObjectSomeValuesFrom( (amacrine cell differentiation) AnnotationAssertion(Annotation( "CL:0000561") Annotation( "GOC:bf") "The process in which a relatively unspecialized cell acquires specialized features of an amacrine cell, an interneuron generated in the inner nuclear layer (INL) of the vertebrate retina. Amacrine cells integrate, modulate, and interpose a temporal domain in the visual message presented to the retinal ganglion cells, with which they synapse in the inner plexiform layer. Amacrine cells lack large axons.") -AnnotationAssertion( "bf") AnnotationAssertion( "2011-06-06T11:32:50Z") AnnotationAssertion(Annotation( "CL:0000561") "amacrine neuron differentiation") AnnotationAssertion( "biological_process") @@ -50902,7 +50609,6 @@ SubClassOf( ObjectSomeValuesFrom( (enteroendocrine cell differentiation) AnnotationAssertion(Annotation( "CL:0000164") Annotation( "GOC:bf") "The process in which a relatively unspecialized cell acquires specialized structural and/or functional features of an enteroendocrine cell. Enteroendocrine cells are hormonally active epithelial cells in the gut that constitute the diffuse neuroendocrine system.") -AnnotationAssertion( "bf") AnnotationAssertion( "2011-06-06T11:48:51Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0035883") @@ -50912,7 +50618,6 @@ EquivalentClasses( ObjectIntersection # Class: (vascular associated smooth muscle cell differentiation) AnnotationAssertion(Annotation( "GOC:sl") Annotation( "PMID:16151017") Annotation( "PMID:18267954") "The process in which a relatively unspecialized cell acquires specialized features of a vascular smooth muscle cell.") -AnnotationAssertion( "bf") AnnotationAssertion( "2011-06-08T11:23:52Z") AnnotationAssertion(Annotation( "PMID:16151017") "VSMC differentiation") AnnotationAssertion( "vascular smooth muscle cell differentiation") @@ -50926,7 +50631,6 @@ SubClassOf( ObjectSomeValuesFrom( (aortic smooth muscle cell differentiation) AnnotationAssertion(Annotation( "GOC:sl") "The process in which a relatively unspecialized cell acquires specialized features of a smooth muscle cell surrounding the aorta.") -AnnotationAssertion( "bf") AnnotationAssertion( "2011-06-08T11:34:26Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0035887") @@ -50937,7 +50641,6 @@ SubClassOf( (parathyroid hormone secretion) AnnotationAssertion(Annotation( "GOC:cjm") Annotation( "PMID:12171519") Annotation( "PMID:21164021") "The regulated release of parathyroid hormone into the circulatory system.") -AnnotationAssertion( "bf") AnnotationAssertion( "2011-06-22T09:28:54Z") AnnotationAssertion(Annotation( "PMID:12171519") Annotation( "PR:000013429") "PTH secretion") AnnotationAssertion(Annotation( "PR:000013429") "parathormone secretion") @@ -50950,7 +50653,6 @@ SubClassOf( (aorta development) AnnotationAssertion(Annotation( "GOC:bf") Annotation( "GOC:dgh") Annotation( "MA:0000062") Annotation( "UBERON:0000947") Annotation( "Wikipedia:Aorta") "The progression of the aorta over time, from its initial formation to the mature structure. An aorta is an artery that carries blood from the heart to other parts of the body.") -AnnotationAssertion( "bf") AnnotationAssertion( "2011-06-24T11:00:07Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0035904") @@ -50961,7 +50663,6 @@ SubClassOf( (ascending aorta development) AnnotationAssertion(Annotation( "GOC:bf") Annotation( "GOC:dgh") Annotation( "MA:0002570") Annotation( "UBERON:0001496") Annotation( "Wikipedia:Ascending_aorta") "The progression of the ascending aorta over time, from its initial formation to the mature structure. The ascending aorta is the portion of the aorta in a two-pass circulatory system that lies between the heart and the arch of aorta. In a two-pass circulatory system blood passes twice through the heart to supply the body once.") -AnnotationAssertion( "bf") AnnotationAssertion( "2011-06-24T11:02:01Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0035905") @@ -50974,7 +50675,6 @@ SubClassOf( ObjectSomeValuesFrom( (descending aorta development) AnnotationAssertion(Annotation( "GOC:bf") Annotation( "GOC:dgh") Annotation( "MA:0002571") Annotation( "UBERON:0001514") Annotation( "Wikipedia:Descending_aorta") "The progression of the descending aorta over time, from its initial formation to the mature structure. The descending aorta is the portion of the aorta in a two-pass circulatory system from the arch of aorta to the point where it divides into the common iliac arteries. In a two-pass circulatory system blood passes twice through the heart to supply the body once.") -AnnotationAssertion( "bf") AnnotationAssertion( "2011-06-24T11:05:22Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0035906") @@ -50987,7 +50687,6 @@ SubClassOf( ObjectSomeValuesFrom( (dorsal aorta development) AnnotationAssertion(Annotation( "GOC:bf") Annotation( "GOC:dgh") Annotation( "UBERON:0005805") Annotation( "Wikipedia:Aorta") Annotation( "ZFA:0000014") "The progression of the dorsal aorta over time, from its initial formation to the mature structure. The dorsal aorta is a blood vessel in a single-pass circulatory system that carries oxygenated blood from the gills to the rest of the body. In a single-pass circulatory system blood passes once through the heart to supply the body once.") -AnnotationAssertion( "bf") AnnotationAssertion( "2011-06-24T11:07:01Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0035907") @@ -50998,7 +50697,6 @@ SubClassOf( (aorta morphogenesis) AnnotationAssertion(Annotation( "GOC:bf") Annotation( "GOC:dgh") Annotation( "MA:0000062") Annotation( "UBERON:0000947") Annotation( "Wikipedia:Aorta") "The process in which the anatomical structures of an aorta are generated and organized. An aorta is an artery that carries blood from the heart to other parts of the body.") -AnnotationAssertion( "bf") AnnotationAssertion( "2011-06-24T11:11:11Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0035909") @@ -51010,7 +50708,6 @@ SubClassOf( ObjectSomeValuesFrom( (ascending aorta morphogenesis) AnnotationAssertion(Annotation( "GOC:bf") Annotation( "GOC:dgh") Annotation( "MA:0002570") Annotation( "UBERON:0001496") Annotation( "Wikipedia:Ascending_aorta") "The process in which the anatomical structures of the ascending aorta are generated and organized. The ascending aorta is the portion of the aorta in a two-pass circulatory system that lies between the heart and the arch of aorta. In a two-pass circulatory system blood passes twice through the heart to supply the body once.") -AnnotationAssertion( "bf") AnnotationAssertion( "2011-06-24T11:14:52Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0035910") @@ -51024,7 +50721,6 @@ SubClassOf( ObjectSomeValuesFrom( (descending aorta morphogenesis) AnnotationAssertion(Annotation( "GOC:bf") Annotation( "GOC:dgh") Annotation( "MA:0002571") Annotation( "UBERON:0001514") Annotation( "Wikipedia:Descending_aorta") "The process in which the anatomical structures of the descending aorta are generated and organized. The descending aorta is the portion of the aorta in a two-pass circulatory system from the arch of aorta to the point where it divides into the common iliac arteries. In a two-pass circulatory system blood passes twice through the heart to supply the body once.") -AnnotationAssertion( "bf") AnnotationAssertion( "2011-06-24T11:19:24Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0035911") @@ -51038,7 +50734,6 @@ SubClassOf( ObjectSomeValuesFrom( (dorsal aorta morphogenesis) AnnotationAssertion(Annotation( "GOC:bf") Annotation( "GOC:dgh") Annotation( "UBERON:0005805") Annotation( "Wikipedia:Aorta") Annotation( "ZFA:0000014") "The process in which the anatomical structures of the dorsal aorta are generated and organized. The dorsal aorta is a blood vessel in a single-pass circulatory system that carries oxygenated blood from the gills to the rest of the body. In a single-pass circulatory system blood passes once through the heart to supply the body once.") -AnnotationAssertion( "bf") AnnotationAssertion( "2011-06-24T11:22:14Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0035912") @@ -51050,7 +50745,6 @@ SubClassOf( ObjectSomeValuesFrom( (skeletal muscle cell differentiation) AnnotationAssertion(Annotation( "CL:0000188") Annotation( "GOC:BHF") Annotation( "GOC:vk") "The process in which a relatively unspecialized cell acquires specialized features of a skeletal muscle cell, a somatic cell located in skeletal muscle.") -AnnotationAssertion( "bf") AnnotationAssertion( "2011-06-24T02:36:19Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0035914") @@ -51062,7 +50756,6 @@ SubClassOf( ObjectSomeValuesFrom( (steroid hormone secretion) AnnotationAssertion(Annotation( "GOC:sl") "The regulated release of any steroid that acts as a hormone into the circulatory system.") -AnnotationAssertion( "bf") AnnotationAssertion( "2011-07-20T01:01:00Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0035929") @@ -51074,7 +50767,6 @@ SubClassOf( (corticosteroid hormone secretion) AnnotationAssertion(Annotation( "GOC:sl") "The regulated release of any corticosteroid hormone into the circulatory system.") -AnnotationAssertion( "bf") AnnotationAssertion( "2011-07-20T01:03:22Z") AnnotationAssertion(Annotation( "GOC:bf") "corticosteroid secretion") AnnotationAssertion( "biological_process") @@ -51086,7 +50778,6 @@ SubClassOf( (mineralocorticoid secretion) AnnotationAssertion(Annotation( "GOC:sl") "The regulated release of any mineralocorticoid into the circulatory system. Mineralocorticoids are a class of steroid hormones that regulate water and electrolyte metabolism.") -AnnotationAssertion( "bf") AnnotationAssertion( "2011-07-20T01:04:59Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0035931") @@ -51097,7 +50788,6 @@ SubClassOf( (aldosterone secretion) AnnotationAssertion(Annotation( "GOC:sl") "The regulated release of aldosterone into the circulatory system. Aldosterone is a pregnane-based steroid hormone produced by the outer-section (zona glomerulosa) of the adrenal cortex in the adrenal gland, and acts on the distal tubules and collecting ducts of the kidney to cause the conservation of sodium, secretion of potassium, increased water retention, and increased blood pressure. The overall effect of aldosterone is to increase reabsorption of ions and water in the kidney.") -AnnotationAssertion( "bf") AnnotationAssertion( "2011-07-20T01:06:24Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0035932") @@ -51109,7 +50799,6 @@ SubClassOf( (glucocorticoid secretion) AnnotationAssertion(Annotation( "GOC:sl") "The regulated release of any glucocorticoid hormone into the circulatory system. Glucocorticoids are a class of steroid hormones that regulate a variety of physiological processes, in particular control of the concentration of glucose in blood.") -AnnotationAssertion( "bf") AnnotationAssertion( "2011-07-20T01:08:37Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0035933") @@ -51120,7 +50809,6 @@ SubClassOf( (androgen secretion) AnnotationAssertion(Annotation( "GOC:sl") "The regulated release of an androgen into the circulatory system. Androgens are steroid hormones that stimulate or control the development and maintenance of masculine characteristics in vertebrates.") -AnnotationAssertion( "bf") AnnotationAssertion( "2011-07-20T01:11:31Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0035935") @@ -51130,7 +50818,6 @@ SubClassOf( (testosterone secretion) AnnotationAssertion(Annotation( "GOC:sl") Annotation( "PMID:12606499") "The regulated release of testosterone into the circulatory system. Testosterone is an androgen having 17beta-hydroxy and 3-oxo groups, together with unsaturation at C-4-C-5.") -AnnotationAssertion( "bf") AnnotationAssertion( "2011-07-20T01:13:13Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0035936") @@ -51141,7 +50828,6 @@ SubClassOf( (estradiol secretion) AnnotationAssertion(Annotation( "GOC:sl") Annotation( "PMID:21632818") "The regulated release of estradiol into the circulatory system.") -AnnotationAssertion( "bf") AnnotationAssertion( "2011-07-20T01:16:45Z") AnnotationAssertion( "oestradiol secretion") AnnotationAssertion( "biological_process") @@ -51153,7 +50839,6 @@ SubClassOf( (tongue muscle cell differentiation) AnnotationAssertion(Annotation( "CL:0002673") Annotation( "GOC:yaf") Annotation( "PMID:3393851") "The process in which a relatively unspecialized cell acquires specialized features of a tongue muscle cell.") -AnnotationAssertion( "bf") AnnotationAssertion( "2011-08-22T01:35:16Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0035981") @@ -51163,7 +50848,6 @@ EquivalentClasses( ObjectIntersection # Class: (endodermal cell differentiation) AnnotationAssertion(Annotation( "CL:0000223") Annotation( "GOC:yaf") Annotation( "PMID:17624332") "The process in which a relatively unspecialized cell acquires the specialized features of an endoderm cell, a cell of the inner of the three germ layers of the embryo.") -AnnotationAssertion( "bf") AnnotationAssertion( "2011-08-25T04:50:36Z") AnnotationAssertion(Annotation( "CL:0000223") "endoderm cell differentiation") AnnotationAssertion( "biological_process") @@ -51176,7 +50860,6 @@ SubClassOf( ObjectSomeValuesFrom( (tendon development) AnnotationAssertion(Annotation( "GOC:yaf") Annotation( "PMID:21412429") Annotation( "UBERON:0000043") "The process whose specific outcome is the progression of a tendon over time, from its formation to the mature structure. A tendon is a fibrous, strong, connective tissue that connects muscle to bone or integument and is capable of withstanding tension. Tendons and muscles work together to exert a pulling force.") -AnnotationAssertion( "bf") AnnotationAssertion( "2011-08-26T04:14:30Z") AnnotationAssertion( "biological_process") AnnotationAssertion(Annotation( "UBERON:0000043") "sinew development") @@ -51188,7 +50871,6 @@ SubClassOf( (tendon cell differentiation) AnnotationAssertion(Annotation( "CL:0000388") Annotation( "GOC:yaf") Annotation( "PMID:21412429") "The process in which a relatively unspecialized cell acquires the specialized features of a tendon cell. Tendon cell are elongated fibrocytes in which the cytoplasm is stretched between the collagen fibres of the tendon. Tendon cells have a central cell nucleus with a prominent nucleolus, a well-developed rough endoplasmic reticulum, and are responsible for synthesis and turnover of tendon fibres and ground substance.") -AnnotationAssertion( "bf") AnnotationAssertion( "2011-08-26T04:16:06Z") AnnotationAssertion(Annotation( "CL:0000388") "muscle attachment cell differentiation") AnnotationAssertion( "biological_process") @@ -51202,7 +50884,6 @@ SubClassOf( ObjectSomeValuesFrom( (tendon formation) AnnotationAssertion(Annotation( "GOC:yaf") Annotation( "PMID:17567668") Annotation( "UBERON:0000043") "The process that gives rise to a tendon. This process pertains to the initial formation of a tendon from unspecified parts.") -AnnotationAssertion( "bf") AnnotationAssertion( "2011-08-30T01:35:10Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0035992") @@ -51215,7 +50896,6 @@ SubClassOf( ObjectSomeValuesFrom( (deltoid tuberosity development) AnnotationAssertion(Annotation( "GOC:yaf") Annotation( "PMID:17567668") Annotation( "UBERON:0002498") Annotation( "Wikipedia:Deltoid_tuberosity") "The process whose specific outcome is the progression of the deltoid tuberosity over time, from its formation to the mature structure. The deltoid tuberosity is the region on the shaft of the humerus to which the deltoid muscle attaches. The deltoid tuberosity develops through endochondral ossification in a two-phase process; an initiating tendon-dependent phase, and a muscle-dependent growth phase.") -AnnotationAssertion( "bf") AnnotationAssertion( "2011-08-30T01:46:53Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0035993") @@ -51229,7 +50909,6 @@ SubClassOf( ObjectSomeValuesFrom( (limb joint morphogenesis) AnnotationAssertion(Annotation( "GOC:bf") "The process in which the anatomical structures of a limb joint are generated and organized. A limb joint is a flexible region that separates the rigid sections of a limb to allow movement in a controlled manner.") -AnnotationAssertion( "bf") AnnotationAssertion( "2011-10-13T04:52:59Z") AnnotationAssertion(Annotation( "GOC:bf") "knee morphogenesis") AnnotationAssertion(Annotation( "GOC:bf") "leg joint morphogenesis") @@ -51244,7 +50923,6 @@ SubClassOf( ObjectSomeValuesFrom( (osteoclast development) AnnotationAssertion(Annotation( "CL:0000092") Annotation( "GOC:bf") Annotation( "GOC:yaf") "The process whose specific outcome is the progression of a osteoclast from its formation to the mature structure. Cell development does not include the steps involved in committing a cell to a specific fate. An osteoclast is a specialized phagocytic cell associated with the absorption and removal of the mineralized matrix of bone tissue.") -AnnotationAssertion( "bf") AnnotationAssertion( "2011-11-02T05:20:35Z") AnnotationAssertion(Annotation( "GOC:bf") "osteoclast cell development") AnnotationAssertion( "biological_process") @@ -51257,7 +50935,6 @@ SubClassOf( ObjectSomeValuesFrom( (CD8-positive, alpha-beta T cell activation) AnnotationAssertion(Annotation( "CL:0000625") Annotation( "GOC:yaf") "The change in morphology and behavior of a CD8-positive, alpha-beta T cell resulting from exposure to a mitogen, cytokine, chemokine, cellular ligand, or an antigen for which it is specific.") -AnnotationAssertion( "bf") AnnotationAssertion( "2011-11-03T10:34:12Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0036037") @@ -51271,7 +50948,6 @@ AnnotationAssertion(Annotation( ) AnnotationAssertion( ) AnnotationAssertion( ) -AnnotationAssertion( "bf") AnnotationAssertion( "2011-12-12T10:53:24Z") AnnotationAssertion(Annotation( "PMID:19129259") "GEnC fenestration") AnnotationAssertion(Annotation( "PMID:19129259") "glomerular endothelial cell fenestration") @@ -51292,7 +50968,6 @@ DisjointClasses( ObjectSomeValuesFrom # Class: (ciliary basal body) AnnotationAssertion(Annotation( "GOC:cilia") Annotation( "GOC:clt") Annotation( "PMID:21750193") "A membrane-tethered, short cylindrical array of microtubules and associated proteins found at the base of a eukaryotic cilium (also called flagellum) that is similar in structure to a centriole and derives from it. The cilium basal body is the site of assembly and remodeling of the cilium and serves as a nucleation site for axoneme growth. As well as anchoring the cilium, it is thought to provide a selective gateway regulating the entry of ciliary proteins and vesicles by intraflagellar transport.") -AnnotationAssertion( "bf") AnnotationAssertion( "2011-12-15T10:40:20Z") AnnotationAssertion( "basal body") AnnotationAssertion( "NIF_Subcellular:sao11978067") @@ -51311,7 +50986,6 @@ SubClassOf( ObjectSomeValuesFrom( (direct ossification) AnnotationAssertion(Annotation( "GO_REF:0000034") "The formation of bone or of a bony substance, or the conversion of fibrous tissue or of cartilage into bone or a bony substance, that does not require the replacement of preexisting tissues.") -AnnotationAssertion( "bf") AnnotationAssertion( "2011-12-19T01:47:22Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0036072") @@ -51321,7 +50995,6 @@ SubClassOf( (replacement ossification) AnnotationAssertion(Annotation( "GO_REF:0000034") "Ossification that requires the replacement of a preexisting tissue prior to bone tissue formation.") -AnnotationAssertion( "bf") AnnotationAssertion( "2011-12-19T01:53:16Z") AnnotationAssertion(Annotation( "GO_REF:0000034") "indirect ossification") AnnotationAssertion( "biological_process") @@ -51332,7 +51005,6 @@ SubClassOf( (germ cell proliferation) AnnotationAssertion(Annotation( "CL:0000586") Annotation( "GOC:kmv") "The multiplication or reproduction of germ cells, reproductive cells in multicellular organisms, resulting in the expansion of a cell population.") -AnnotationAssertion( "bf") AnnotationAssertion( "2012-01-17T04:06:27Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0036093") @@ -51344,7 +51016,6 @@ SubClassOf( ObjectSomeValuesFrom( (small molecule binding) AnnotationAssertion(Annotation( "GOC:curators") Annotation( "GOC:pde") Annotation( "GOC:pm") "Binding to a small molecule, any low molecular weight, monomeric, non-encoded molecule.") -AnnotationAssertion( "bf") AnnotationAssertion( "2012-01-17T04:20:34Z") AnnotationAssertion( "molecular_function") AnnotationAssertion( "GO:0036094") @@ -51360,7 +51031,6 @@ SubClassOf( (male germ-line stem cell population maintenance) AnnotationAssertion(Annotation( "GOC:sart") Annotation( "PMID:21752937") "The process by which an organism or tissue maintains a population of male germ-line stem cells.") -AnnotationAssertion( "bf") AnnotationAssertion( "2012-01-26T01:58:10Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0036098") @@ -51371,7 +51041,6 @@ SubClassOf( (female germ-line stem cell population maintenance) AnnotationAssertion(Annotation( "GOC:sart") "The process by which an organism or tissue maintains a population of female germ-line stem cells.") -AnnotationAssertion( "bf") AnnotationAssertion( "2012-01-26T01:58:10Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0036099") @@ -51382,7 +51051,6 @@ SubClassOf( (Schwann cell migration) AnnotationAssertion(Annotation( "CL:0002573") Annotation( "PMID:20335460") "The orderly movement of a Schwann cell from one site to another. A Schwann cell is a glial cell that ensheathes axons of neuron in the peripheral nervous system and is necessary for their maintenance and function.") -AnnotationAssertion( "bf") AnnotationAssertion( "2012-03-06T10:44:39Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0036135") @@ -51393,7 +51061,6 @@ SubClassOf( (dendritic cell homeostasis) AnnotationAssertion(Annotation( "CL:0000451") Annotation( "GOC:uh") Annotation( "PMID:12570827") Annotation( "PMID:19176316") "The process of regulating the proliferation and elimination of dendritic cells such that the total number of dendritic cells within a whole or part of an organism is stable over time in the absence of an outside stimulus.") -AnnotationAssertion( "bf") AnnotationAssertion( "2012-03-12T11:05:36Z") AnnotationAssertion( "biological_process") AnnotationAssertion(Annotation( "PMID:19176316") "DC homeostasis") @@ -51405,7 +51072,6 @@ SubClassOf( (inner dynein arm) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:vk") Annotation( "PMID:19347929") Annotation( "PMID:2557057") Annotation( "PMID:7962092") "Inner arm structure present on the outer doublet microtubules of ciliary and flagellar axonemes. The structure of inner dynein arms is complex and may vary within the axoneme. Inner dynein arms are heteromeric, comprising 8 different heavy chains and various subunits. Inner and outer dynein arms have different functions in the generation of microtubule-based motility.") -AnnotationAssertion( "bf") AnnotationAssertion( "2012-03-21T01:24:54Z") AnnotationAssertion( "inner dynein arm complex") AnnotationAssertion( "cellular_component") @@ -51416,7 +51082,6 @@ SubClassOf( (outer dynein arm) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:vk") Annotation( "PMID:2557057") Annotation( "PMID:6218174") "Outer arm structure present on the outer doublet microtubules of ciliary and flagellar axonemes. Outer dynein arms contain 2-3 heavy chains, two or more intermediate chains and a cluster of 4-8 light chains. Inner and outer dynein arms have different functions in the generation of microtubule-based motility.") -AnnotationAssertion( "bf") AnnotationAssertion( "2012-03-21T01:25:03Z") AnnotationAssertion( "outer dynein arm complex") AnnotationAssertion( "cellular_component") @@ -51427,7 +51092,6 @@ SubClassOf( (outer dynein arm assembly) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:vk") Annotation( "PMID:19944400") "The aggregation, arrangement and bonding together of a set of components to form an axonemal dynein outer arm, an outer arm structure present on the outer doublet microtubules of ciliary and flagellar axonemes.") -AnnotationAssertion( "bf") AnnotationAssertion( "2012-03-21T02:25:01Z") AnnotationAssertion(Annotation( "PMID:19944400") "ODA assembly") AnnotationAssertion( "biological_process") @@ -51439,7 +51103,6 @@ SubClassOf( (inner dynein arm assembly) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:vk") Annotation( "PMID:19944400") "The aggregation, arrangement and bonding together of a set of components to form an axonemal dynein inner arm, an inner arm structure present on the outer doublet microtubules of ciliary and flagellar axonemes.") -AnnotationAssertion( "bf") AnnotationAssertion( "2012-03-21T02:25:01Z") AnnotationAssertion(Annotation( "PMID:19944400") "IDA assembly") AnnotationAssertion( "biological_process") @@ -51451,7 +51114,6 @@ SubClassOf( (melanocyte-stimulating hormone secretion) AnnotationAssertion(Annotation( "GOC:cjm") Annotation( "Wikipedia:Melanocyte-stimulating_hormone") "The regulated release of a melanocyte-stimulating hormone, any of a group of peptide hormones that are produced by cells in the intermediate lobe of the pituitary gland, and stimulate the production of melanin to increase pigmentation.") -AnnotationAssertion( "bf") AnnotationAssertion( "2012-03-26T01:16:55Z") AnnotationAssertion(Annotation( "GOC:cjm") "MSH secretion") AnnotationAssertion( "biological_process") @@ -51462,7 +51124,6 @@ SubClassOf( (calcitonin secretion) AnnotationAssertion(Annotation( "GOC:cjm") "The regulated release of calcitonin, a peptide hormone that participates in calcium and phosphorus metabolism, from a cell.") -AnnotationAssertion( "bf") AnnotationAssertion( "2012-03-26T01:30:32Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0036161") @@ -51475,7 +51136,6 @@ SubClassOf( "GOC:cjm") Annotation( "Wikipedia:Oxytocin") "The appearance of oxytocin, a cyclic nonapeptide hormone with amino acid sequence CYIQNCPLG, due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. Oxytocin is the principal uterine-contracting and milk-ejecting hormone of the posterior pituitary, and together with the neuropeptide vasopressin, is believed to influence social cognition and behavior. It also acts as a neurotransmitter in the brain.") AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/21535"^^xsd:anyURI) AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/9542"^^xsd:anyURI) -AnnotationAssertion( "bf") AnnotationAssertion( "2012-03-26T01:43:46Z") AnnotationAssertion( "oxytocin biosynthesis") AnnotationAssertion( "oxytocin secretion") @@ -51489,7 +51149,6 @@ SubClassOf( ObjectSomeValuesFrom( (osteoclast maturation) AnnotationAssertion(Annotation( "CL:0000092") Annotation( "GOC:pg") "A developmental process, independent of morphogenetic (shape) change, that is required for an osteoclast cell to attain its fully functional state. An osteoclast is a specialized phagocytic cell associated with the absorption and removal of the mineralized matrix of bone tissue, and which typically differentiates from monocytes.") -AnnotationAssertion( "bf") AnnotationAssertion( "2012-03-29T02:04:00Z") AnnotationAssertion( "biological_process") AnnotationAssertion(Annotation( "CL:0000092") "chondroclast maturation") @@ -51502,7 +51161,6 @@ SubClassOf( ObjectSomeValuesFrom( (muscle cell projection) AnnotationAssertion(Annotation( "CL:0000187") Annotation( "GOC:kmv") Annotation( "PMID:15930100") Annotation( "PMID:22464329") "A prolongation or process extending from a muscle cell. A muscle cell is a mature contractile cell, commonly known as a myocyte. This cell has as part of its cytoplasm myofibrils organized in various patterns.") -AnnotationAssertion( "bf") AnnotationAssertion( "2012-04-20T10:20:47Z") AnnotationAssertion(Annotation( "CL:0000187") "myocyte projection") AnnotationAssertion(Annotation( "GOC:kmv") "muscle arm") @@ -51515,7 +51173,6 @@ EquivalentClasses( ObjectIntersection # Class: (muscle cell projection membrane) AnnotationAssertion(Annotation( "CL:0000187") Annotation( "GOC:kmv") Annotation( "PMID:15930100") Annotation( "PMID:22464329") "The portion of the plasma membrane surrounding a muscle cell projection.") -AnnotationAssertion( "bf") AnnotationAssertion( "2012-04-20T10:21:51Z") AnnotationAssertion( "cellular_component") AnnotationAssertion( "GO:0036195") @@ -51527,7 +51184,6 @@ SubClassOf( "GOC:bf") Annotation( "GOC:jl") "The covalent alteration of one or more amino acids occurring in proteins, peptides and nascent polypeptides (co-translational, post-translational modifications). Includes the modification of charged tRNAs that are destined to occur in a protein (pre-translation modification).") AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/23112"^^xsd:anyURI) -AnnotationAssertion( "bf") AnnotationAssertion( "2012-04-26T01:47:12Z") AnnotationAssertion( "cellular protein modification process") AnnotationAssertion( "process resulting in protein modification") @@ -51546,7 +51202,6 @@ SubClassOf( (granulocyte activation) AnnotationAssertion(Annotation( "CL:0000094") Annotation( "GOC:nhn") "The change in morphology and behavior of a granulocyte resulting from exposure to a cytokine, chemokine, cellular ligand, or soluble factor.") -AnnotationAssertion( "bf") AnnotationAssertion( "2012-05-11T10:57:48Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0036230") @@ -51557,7 +51212,6 @@ SubClassOf( (response to decreased oxygen levels) AnnotationAssertion(Annotation( "GOC:al") "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus reflecting a decline in the level of oxygen.") -AnnotationAssertion( "bf") AnnotationAssertion( "2012-07-20T01:05:46Z") AnnotationAssertion(Annotation( "GOC:bf") "response to lowered oxygen levels") AnnotationAssertion( "biological_process") @@ -51569,7 +51223,6 @@ SubClassOf( (lymph vessel morphogenesis) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:gr") Annotation( "PMID:18093989") "The process in which the anatomical structures of lymph vessels are generated and organized. The lymph vessel is the vasculature carrying lymph.") -AnnotationAssertion( "bf") AnnotationAssertion( "2012-08-08T10:08:47Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0036303") @@ -51582,7 +51235,6 @@ SubClassOf( ObjectSomeValuesFrom( (umbilical cord morphogenesis) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:gr") Annotation( "PMID:15107403") "The process in which the anatomical structures of the umbilical cord are generated and organized. The umbilical cord is an organ or embryonic origin consisting of the 2 umbilical arteries and the one umbilical vein. The umbilical cord connects the cardiovascular system of the fetus to the mother via the placenta.") -AnnotationAssertion( "bf") AnnotationAssertion( "2012-08-08T10:12:11Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0036304") @@ -51595,7 +51247,6 @@ SubClassOf( ObjectSomeValuesFrom( (ameloblast differentiation) AnnotationAssertion(Annotation( "CL:0000059") "The process in which a relatively unspecialized cell acquires specialized features of an ameloblast, a cylindrical epithelial cell in the innermost layer of the enamel organ.") -AnnotationAssertion( "bf") AnnotationAssertion( "2012-08-08T13:49:15Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0036305") @@ -51605,7 +51256,6 @@ EquivalentClasses( ObjectIntersection # Class: (ghrelin secretion) AnnotationAssertion(Annotation( "GOC:cjm") Annotation( "PMID:14610293") Annotation( "Wikipedia:Ghrelin") "The regulated release of ghrelin from a cell. Ghrelin is a 28 amino acid hunger-stimulating peptide hormone.") -AnnotationAssertion( "bf") AnnotationAssertion( "2012-09-04T14:16:43Z") AnnotationAssertion(Annotation( "GOC:cjm") "pancreatic ghrelin secretion") AnnotationAssertion( "biological_process") @@ -51617,7 +51267,6 @@ SubClassOf( (pancreatic polypeptide secretion) AnnotationAssertion(Annotation( "GOC:cjm") Annotation( "PMID:12730894") Annotation( "Wikipedia:Pancreatic_polypeptide") "The regulated release of pancreatic polypeptide (PP) from a cell. Pancreatic polypeptide is a 36 amino acid polypeptide secreted by islets of Langerhans cells in the pancreas.") -AnnotationAssertion( "bf") AnnotationAssertion( "2012-09-04T14:39:03Z") AnnotationAssertion(Annotation( "GOC:cjm") "PP secretion") AnnotationAssertion( "biological_process") @@ -51628,7 +51277,6 @@ SubClassOf( (hepatocyte homeostasis) AnnotationAssertion(Annotation( "CL:0000182") Annotation( "GOC:nhn") Annotation( "PMID:19878874") "Any biological process involved in the maintenance of the steady-state number of hepatocytes within a population of cells. Hepatocytes are specialized epithelial cells of the liver that are organized into interconnected plates called lobules.") -AnnotationAssertion( "bf") AnnotationAssertion( "2012-09-05T10:17:07Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0036333") @@ -51639,7 +51287,6 @@ SubClassOf( (epidermal stem cell homeostasis) AnnotationAssertion(Annotation( "CL:1000428") Annotation( "GOC:nhn") Annotation( "PMID:17666529") "Any biological process involved in the maintenance of the steady-state number of epidermal stem cells within a population of cells.") -AnnotationAssertion( "bf") AnnotationAssertion( "2012-09-05T10:21:23Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0036334") @@ -51650,7 +51297,6 @@ SubClassOf( (dendritic cell migration) AnnotationAssertion(Annotation( "CL:0000451") Annotation( "GOC:nhn") Annotation( "PMID:19339990") "The movement of a dendritic cell within or between different tissues and organs of the body.") -AnnotationAssertion( "bf") AnnotationAssertion( "2012-09-05T10:24:46Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0036336") @@ -51661,7 +51307,6 @@ SubClassOf( (post-anal tail morphogenesis) AnnotationAssertion(Annotation( "GOC:bf") Annotation( "GOC:kmv") Annotation( "Wikipedia:Chordate") "The process in which a post-anal tail is generated and organized. A post-anal tail is a muscular region of the body that extends posterior to the anus. The post-anal tail may aid locomotion and balance.") -AnnotationAssertion( "bf") AnnotationAssertion( "2012-09-11T13:54:49Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0036342") @@ -51675,7 +51320,6 @@ SubClassOf( ObjectAllValuesFrom( (platelet morphogenesis) AnnotationAssertion(Annotation( "CL:0000233") Annotation( "GOC:BHF") Annotation( "GOC:vk") "Generation and organization of a platelet, a non-nucleated disk-shaped cell formed by extrusion from megakaryocytes, found in the blood of all mammals, and mainly involved in blood coagulation.") -AnnotationAssertion( "bf") AnnotationAssertion( "2012-09-11T15:15:35Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0036344") @@ -51685,7 +51329,6 @@ SubClassOf( (platelet maturation) AnnotationAssertion(Annotation( "CL:0000233") Annotation( "GOC:BHF") Annotation( "GOC:vk") "A developmental process, independent of morphogenetic (shape) change, that is required for a platelet to attain its fully functional state. A platelet is a non-nucleated disk-shaped cell formed by extrusion from megakaryocytes, found in the blood of all mammals, and mainly involved in blood coagulation.") -AnnotationAssertion( "bf") AnnotationAssertion( "2012-09-11T15:23:11Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0036345") @@ -51696,7 +51339,6 @@ SubClassOf( (sodium ion export across plasma membrane) AnnotationAssertion(Annotation( "GOC:vw") Annotation( "PMID:14674689") "The directed movement of sodium ions from inside of a cell, across the plasma membrane and into the extracellular region.") -AnnotationAssertion( "mah") AnnotationAssertion( "2009-12-16T11:13:55Z") AnnotationAssertion( "sodium ion export from cell") AnnotationAssertion( "biological_process") @@ -51709,7 +51351,6 @@ EquivalentClasses( ObjectIntersection # Class: (myofilament) AnnotationAssertion(Annotation( "Wikipedia:Myofilament") "Any of the smallest contractile units of a myofibril (striated muscle fiber).") -AnnotationAssertion( "bf") AnnotationAssertion( "2013-05-22T14:39:06Z") AnnotationAssertion(Annotation( "GOC:bf") "striated muscle filament") AnnotationAssertion( "cellular_component") @@ -51722,7 +51363,6 @@ SubClassOf( ObjectSomeValuesFrom( (myofibroblast differentiation) AnnotationAssertion(Annotation( "CL:0000186") Annotation( "GOC:nhn") "The process in which an undifferentiated cell acquires the features of a myofibroblast cell.") -AnnotationAssertion( "bf") AnnotationAssertion( "2013-10-30T10:06:51Z") AnnotationAssertion(Annotation( "CL:0000186") "myofibroblast cell differentiation") AnnotationAssertion( "biological_process") @@ -51734,7 +51374,6 @@ SubClassOf( (somatodendritic compartment) AnnotationAssertion(Annotation( "GOC:PARL") Annotation( "GOC:pad") "The region of a neuron that includes the cell body (cell soma) and dendrite(s), but excludes the axon.") -AnnotationAssertion( "bf") AnnotationAssertion( "2014-07-24T10:06:19Z") AnnotationAssertion( "cellular_component") AnnotationAssertion( "GO:0036477") @@ -51745,7 +51384,6 @@ SubClassOf( ObjectSomeValuesFrom( (trunk neural crest cell migration) AnnotationAssertion(Annotation( "GOC:PARL") Annotation( "GOC:bf") Annotation( "GOC:mat") Annotation( "PMID:2387238") "The characteristic movement of trunk neural crest cells from the neural tube to other locations in the vertebrate embryo.") -AnnotationAssertion( "bf") AnnotationAssertion( "2014-08-26T15:27:44Z") AnnotationAssertion(Annotation( "PMID:2387238") "trunk NCC migration") AnnotationAssertion( "biological_process") @@ -51758,7 +51396,6 @@ SubClassOf( ObjectSomeValuesFrom( (Golgi membrane fusion) AnnotationAssertion(Annotation( "GOC:PARL") Annotation( "GOC:bf") Annotation( "PMID:12473691") "The joining of two lipid bilayers that surround the Golgi apparatus to form a single Golgi membrane.") -AnnotationAssertion( "bf") AnnotationAssertion( "2015-05-21T10:05:06Z") AnnotationAssertion( "Golgi apparatus membrane fusion") AnnotationAssertion(Annotation( "GOC:bf") "membrane fusion involved in Golgi reassembly") @@ -51773,7 +51410,6 @@ SubClassOf( ObjectSomeValuesFrom( (astrocyte-dopaminergic neuron signaling) AnnotationAssertion(Annotation( "GOC:PARL") Annotation( "GOC:bf") Annotation( "PMID:12794311") Annotation( "PMID:21752258") "Cell-cell signaling that mediates the transfer of information from an astrocyte to a dopaminergic neuron.") -AnnotationAssertion( "bf") AnnotationAssertion( "2016-02-29T14:05:47Z") AnnotationAssertion(Annotation( "GOC:bf") "astrocyte-dopaminergic neuron cell signaling") AnnotationAssertion(Annotation( "PMID:21752258") "mesencephalic dopaminergic neuron-astrocyte crosstalk") @@ -51787,7 +51423,6 @@ EquivalentClasses( ObjectIntersection # Class: (signaling receptor activity) AnnotationAssertion(Annotation( "GOC:bf") Annotation( "GOC:signaling") "Receiving a signal and transmitting it in the cell to initiate a change in cell activity. A signal is a physical entity or change in state that is used to transfer information in order to trigger a response.") -AnnotationAssertion( "bf") AnnotationAssertion( "2011-08-01T02:45:27Z") AnnotationAssertion( "receptor activity") AnnotationAssertion(Annotation( "GOC:bf") "receptor activity involved in signal transduction") @@ -51810,7 +51445,6 @@ SubClassOf( "PMID:15239958") Annotation( "PMID:27903609") "Binding specifically to a substance (cargo) to deliver it to a transport vesicle. Cargo receptors span membranes (for instance the plasma membrane or the endoplasmic reticulum membrane), binding simultaneously to cargo molecules and coat adaptors, to efficiently recruit the cargo molecules to nascent vesicles.") AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/26872"^^xsd:anyURI) -AnnotationAssertion( "bf") AnnotationAssertion( "2011-08-01T02:50:45Z") AnnotationAssertion( "receptor activity") AnnotationAssertion(Annotation( "GOC:signaling") "transport receptor activity") @@ -51838,7 +51472,6 @@ SubClassOf( ObjectSomeValuesFrom( "GOC:nhn") Annotation( "GOC:signaling") Annotation( "PMID:21664429") "The series of molecular signals initiated by the binding of the peptide hormone prolactin to its receptor on the surface of a target cell, and ending with the regulation of a downstream cellular process, e.g. transcription.") AnnotationAssertion( ) -AnnotationAssertion( "bf") AnnotationAssertion( "2012-05-14T01:52:59Z") AnnotationAssertion(Annotation( "PMID:21664429") Annotation( "PR:000013246") "PRL signaling pathway") AnnotationAssertion(Annotation( "GOC:bf") "prolactin-mediated signaling pathway") @@ -51854,7 +51487,6 @@ DisjointClasses( ObjectSomeValuesFrom # Class: (somatostatin receptor signaling pathway) AnnotationAssertion(Annotation( "GOC:jc") Annotation( "PMID:18006219") Annotation( "PMID:8769369") "A G protein-coupled receptor signaling pathway initiated by somatostatin binding to the somatostatin receptor (SSTR) on the surface of a target cell, and ending with the regulation of a downstream cellular process.") -AnnotationAssertion( "bf") AnnotationAssertion( "2012-06-12T10:30:01Z") AnnotationAssertion(Annotation( "GOC:bf") "SST receptor signaling pathway") AnnotationAssertion( "biological_process") @@ -51867,7 +51499,6 @@ SubClassOf( (somatostatin signaling pathway) AnnotationAssertion(Annotation( "GOC:bf") Annotation( "GOC:nhn") Annotation( "GOC:signaling") Annotation( "PMID:18006219") Annotation( "Wikipedia:Somatostatin") "A G protein-coupled receptor signaling pathway initiated by somatostatin binding to a somatostatin receptor (SSTR), and ending with the regulation of a downstream cellular process, e.g. transcription.") -AnnotationAssertion( "bf") AnnotationAssertion( "2012-06-12T10:33:21Z") AnnotationAssertion(Annotation( "Wikipedia:Somatostatin") "SRIF signaling pathway") AnnotationAssertion(Annotation( "Wikipedia:Somatostatin") "SST signaling pathway") @@ -51887,7 +51518,6 @@ SubClassOf( ObjectSomeValuesFrom( "GOC:ar") Annotation( "GOC:bf") "Combining with a pathogen-associated molecular pattern (PAMP), a structure conserved among microbial species to initiate an innate immune response.") AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/17995"^^xsd:anyURI) AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/18588"^^xsd:anyURI) -AnnotationAssertion( "bf") AnnotationAssertion( "2013-05-29T15:24:44Z") AnnotationAssertion( "Wikipedia:Pattern_recognition_receptor") AnnotationAssertion( "PRR") @@ -51906,7 +51536,6 @@ SubClassOf( (cholecystokinin signaling pathway) AnnotationAssertion(Annotation( "GOC:jc") Annotation( "PMID:11181948") "A G protein-coupled receptor signaling pathway initiated by cholecystokinin binding to its receptor on the surface of a target cell, and ending with the regulation of a downstream cellular process, e.g. transcription.") -AnnotationAssertion( "bf") AnnotationAssertion( "2013-07-01T13:05:46Z") AnnotationAssertion( "Wikipedia:Cholecystokinin") AnnotationAssertion(Annotation( "PMID:11181948") Annotation( "Wikipedia:Cholecystokinin") "CCK signaling") @@ -51919,7 +51548,6 @@ SubClassOf( (pronephric nephron tubule formation) AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "The developmental process pertaining to the initial formation of a pronephric nephron tubule from unspecified parts. A pronephric nephron tubule is an epithelial tube that is part of a nephron in the pronephros.") -AnnotationAssertion( "bf") AnnotationAssertion( "2010-07-02T09:37:27Z") AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "pronephric tubule formation") AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "pronephros tubule formation") @@ -51934,7 +51562,6 @@ SubClassOf( ObjectSomeValuesFrom( (pronephric nephron morphogenesis) AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "The process in which the anatomical structures of the pronephric nephron are generated and organized. A pronephric nephron is the functional unit of the pronephros.") -AnnotationAssertion( "bf") AnnotationAssertion( "2010-07-02T09:38:53Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0039007") @@ -51947,7 +51574,6 @@ SubClassOf( ObjectSomeValuesFrom( (pronephric nephron tubule morphogenesis) AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") Annotation( "ZFA:00001558") "The process in which the anatomical structures of a pronephric nephron tubule are generated and organized from an epithelium. A pronephric nephron tubule is an epithelial tube that is part of the pronephric nephron.") -AnnotationAssertion( "bf") AnnotationAssertion( "2010-07-02T09:45:55Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0039008") @@ -51960,7 +51586,6 @@ SubClassOf( ObjectSomeValuesFrom( (pronephric proximal tubule morphogenesis) AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "The process in which the anatomical structures of a pronephric nephron proximal tubule are generated and organized. A pronephric nephron tubule is an epithelial tube that is part of the pronephros.") -AnnotationAssertion( "bf") AnnotationAssertion( "2010-07-02T09:53:12Z") AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "pronephros proximal tubule morphogenesis") AnnotationAssertion( "biological_process") @@ -51974,7 +51599,6 @@ SubClassOf( ObjectSomeValuesFrom( (pronephric distal tubule morphogenesis) AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "The process in which the anatomical structures of a pronephric nephron distal tubule are generated and organized. A pronephric nephron tubule is an epithelial tube that is part of the pronephros.") -AnnotationAssertion( "bf") AnnotationAssertion( "2010-07-02T09:58:03Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0039013") @@ -51987,7 +51611,6 @@ SubClassOf( ObjectSomeValuesFrom( (cell differentiation involved in pronephros development) AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "The process in which relatively unspecialized cells acquire specialized structural and/or functional features that characterize the cells of the pronephros as it progresses from its formation to the mature state.") -AnnotationAssertion( "bf") AnnotationAssertion( "2010-07-02T09:59:25Z") AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "cell differentiation involved in pronephric kidney development") AnnotationAssertion( "biological_process") @@ -51998,7 +51621,6 @@ EquivalentClasses( ObjectIntersection # Class: (cell proliferation involved in pronephros development) AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "The multiplication or reproduction of cells, resulting in the expansion of the population in the pronephros.") -AnnotationAssertion( "bf") AnnotationAssertion( "2010-07-02T10:01:49Z") AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "cell proliferation involved in pronephric kidney development") AnnotationAssertion( "biological_process") @@ -52009,7 +51631,6 @@ EquivalentClasses( ObjectIntersection # Class: (cell-cell signaling involved in pronephros development) AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "Any process that mediates the transfer of information from one cell to another and contributes to the progression of the pronephros over time, from its formation to the mature organ.") -AnnotationAssertion( "bf") AnnotationAssertion( "2010-07-02T10:03:16Z") AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "cell-cell signaling involved in pronephric kidney development") AnnotationAssertion(Annotation( "GOC:mah") "cell-cell signalling involved in pronephros development") @@ -52021,7 +51642,6 @@ EquivalentClasses( ObjectIntersection # Class: (pattern specification involved in pronephros development) AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "Any developmental process that results in the creation of defined areas or spaces within the pronephros to which cells respond and eventually are instructed to differentiate.") -AnnotationAssertion( "bf") AnnotationAssertion( "2010-07-02T10:04:39Z") AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "pattern specification involved in pronephric kidney development") AnnotationAssertion( "biological_process") @@ -52032,7 +51652,6 @@ EquivalentClasses( ObjectIntersection # Class: (pronephric nephron development) AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") Annotation( "XAO:00002785") "The process whose specific outcome is the progression of the pronephric nephron over time, from its formation to the mature structure. A pronephric nephron is the functional unit of the pronephros.") -AnnotationAssertion( "bf") AnnotationAssertion( "2010-07-02T10:10:20Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0039019") @@ -52044,7 +51663,6 @@ SubClassOf( ObjectSomeValuesFrom( (pronephric nephron tubule development) AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") Annotation( "PMID:19909807") Annotation( "PMID:9268568") "The process whose specific outcome is the progression of a pronephric nephron tubule over time, from its formation to the mature structure. The pronephric nephron tubule is an epithelial tube that is part of the pronephric nephron and connects the filtration unit (glomerulus or glomus) of the pronephros to the pronephric duct.") -AnnotationAssertion( "bf") AnnotationAssertion( "2010-07-02T10:11:36Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0039020") @@ -52056,7 +51674,6 @@ SubClassOf( ObjectSomeValuesFrom( (pronephric glomerulus development) AnnotationAssertion(Annotation( "GOC:dgh") Annotation( "GOC:mtg_kidney_jan10") Annotation( "ZFA:00001557") "The progression of the glomerulus of the pronephric kidney over time from its initial formation until its mature state. The pronephric glomerulus is part of the pronephric nephron and is restricted to one body segment.") -AnnotationAssertion( "bf") AnnotationAssertion( "2010-07-02T10:13:38Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0039021") @@ -52069,7 +51686,6 @@ SubClassOf( ObjectSomeValuesFrom( (pronephric duct development) AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") Annotation( "PMID:15647339") Annotation( "XAO:0000063") Annotation( "ZFA:0000150") "The process whose specific outcome is the progression of the pronephric duct over time, from its formation to the mature structure. The pronephric duct collects the filtrate from the pronephric tubules and opens to the exterior of the pronephric kidney.") -AnnotationAssertion( "bf") AnnotationAssertion( "2010-07-02T10:15:03Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0039022") @@ -52081,7 +51697,6 @@ SubClassOf( ObjectSomeValuesFrom( (pronephric duct morphogenesis) AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") Annotation( "XAO:0000063") Annotation( "ZFA:0000150") "The process in which the anatomical structures of the pronephric duct are generated and organized. The pronephric duct collects the filtrate from the pronephric tubules and opens to the exterior of the kidney.") -AnnotationAssertion( "bf") AnnotationAssertion( "2010-07-02T10:18:09Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0039023") @@ -52724,7 +52339,6 @@ SubClassOf( ObjectSomeValuesFrom( "GOC:go_curators") Annotation( "GOC:jl") "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of a protein by the destruction of the native, active configuration, with or without the hydrolysis of peptide bonds.") AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/23112"^^xsd:anyURI) -AnnotationAssertion( "kmv") AnnotationAssertion( "2014-08-21T15:05:45Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "regulation of cellular protein breakdown") AnnotationAssertion( "regulation of cellular protein catabolic process") @@ -56291,7 +55905,6 @@ EquivalentClasses( ObjectIntersection AnnotationAssertion(Annotation( "GOC:mah") "Any process in which macromolecules aggregate, disaggregate, or are modified, resulting in the formation, disassembly, or alteration of a protein complex.") AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/22580"^^xsd:anyURI) -AnnotationAssertion( "mah") AnnotationAssertion( "2010-09-08T10:01:42Z") AnnotationAssertion(Annotation( "GOC:mah") "protein complex subunit organisation") AnnotationAssertion( "protein complex subunit organization") @@ -56493,7 +56106,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of molecular function) AnnotationAssertion(Annotation( "GO:jl") "Any process that stops or reduces the rate or extent of a molecular function, an elemental biological activity occurring at the molecular level, such as catalysis or binding.") -AnnotationAssertion( "jl") AnnotationAssertion( "2009-04-21T04:07:27Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0044092") @@ -56505,7 +56117,6 @@ SubClassOf( (positive regulation of molecular function) AnnotationAssertion(Annotation( "GO:jl") "Any process that activates or increases the rate or extent of a molecular function, an elemental biological activity occurring at the molecular level, such as catalysis or binding.") -AnnotationAssertion( "jl") AnnotationAssertion( "2009-04-21T04:11:06Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0044093") @@ -56517,7 +56128,6 @@ SubClassOf( (translation initiation ternary complex) AnnotationAssertion(Annotation( "GOC:jl") "A ribonucleoprotein complex that contains aminoacylated initiator methionine tRNA, GTP, and initiation factor 2 (either eIF2 in eukaryotes, or IF2 in prokaryotes). In prokaryotes, fMet-tRNA (initiator) is used rather than Met-tRNA (initiator).") -AnnotationAssertion( "jl") AnnotationAssertion( "2009-10-22T02:38:55Z") AnnotationAssertion( "translation initiation (ternary) complex") AnnotationAssertion( "Met-tRNA/eIF2.GTP ternary complex") @@ -56569,7 +56179,6 @@ EquivalentClasses( ObjectIntersection # Class: (small molecule metabolic process) AnnotationAssertion(Annotation( "GOC:curators") Annotation( "GOC:pde") Annotation( "GOC:vw") "The chemical reactions and pathways involving small molecules, any low molecular weight, monomeric, non-encoded molecule.") -AnnotationAssertion( "jl") AnnotationAssertion( "2010-01-26T12:05:20Z") AnnotationAssertion( "small molecule metabolism") AnnotationAssertion( "biological_process") @@ -56584,7 +56193,6 @@ SubClassOf( (small molecule catabolic process) AnnotationAssertion(Annotation( "GOC:curators") Annotation( "GOC:vw") "The chemical reactions and pathways resulting in the breakdown of small molecules, any low molecular weight, monomeric, non-encoded molecule.") -AnnotationAssertion( "jl") AnnotationAssertion( "2010-01-26T12:06:10Z") AnnotationAssertion( "small molecule catabolism") AnnotationAssertion( "biological_process") @@ -56597,7 +56205,6 @@ SubClassOf( (small molecule biosynthetic process) AnnotationAssertion(Annotation( "GOC:curators") Annotation( "GOC:pde") Annotation( "GOC:vw") "The chemical reactions and pathways resulting in the formation of small molecules, any low molecular weight, monomeric, non-encoded molecule.") -AnnotationAssertion( "jl") AnnotationAssertion( "2010-01-26T12:06:49Z") AnnotationAssertion( "small molecule biosynthesis") AnnotationAssertion( "biological_process") @@ -56613,7 +56220,6 @@ SubClassOf( "GOC:go_curators") "The portion of a cell bearing surface projections such as axons, dendrites, cilia, or flagella that includes the nucleus, but excludes all cell projections.") AnnotationAssertion( ) -AnnotationAssertion( "jl") AnnotationAssertion( "2010-02-05T10:37:16Z") AnnotationAssertion( "FBbt:00005107") AnnotationAssertion( "FMA:67301") @@ -56632,7 +56238,6 @@ DisjointClasses( ObjectSomeValuesFrom # Class: (neuron projection terminus) AnnotationAssertion(Annotation( "GOC:jl") "The specialized, terminal region of a neuron projection such as an axon or a dendrite.") -AnnotationAssertion( "jl") AnnotationAssertion( "2010-02-05T02:44:04Z") AnnotationAssertion( "neuron projection terminal") AnnotationAssertion( "neuron terminal specialization") @@ -56647,7 +56252,6 @@ SubClassOf( ObjectSomeValuesFrom( (cone cell pedicle) AnnotationAssertion(Annotation( "PMID:10939333") "A specialized axon terminus which is produced by retinal cone cells. Pedicles are large, conical, flat end-feet (8-10 micrometers diameter) of the retinal cone axon that lie more or less side by side on the same plane at the outer edge of the outer plexiform layer (OPL).") -AnnotationAssertion( "jl") AnnotationAssertion( "2010-07-14T01:30:02Z") AnnotationAssertion( "cone pedicle") AnnotationAssertion( "cellular_component") @@ -56658,7 +56262,6 @@ SubClassOf( (type B pancreatic cell proliferation) AnnotationAssertion(Annotation( "GOC:jl") Annotation( "GOC:yaf") "The multiplication or reproduction of pancreatic B cells, resulting in the expansion of an pancreatic B cell population. Pancreatic B cell are cells of the pancreas that secrete insulin.") -AnnotationAssertion( "jl") AnnotationAssertion( "2010-08-25T01:44:51Z") AnnotationAssertion(Annotation( "GOC:mah") "pancreatic B cell proliferation") AnnotationAssertion( "pancreatic beta cell proliferation") @@ -56671,7 +56274,6 @@ SubClassOf( (fibroblast apoptotic process) AnnotationAssertion(Annotation( "CL:0000057") Annotation( "GOC:jl") Annotation( "GOC:mtg_apoptosis") Annotation( "GOC:yaf") "Any apoptotic process in a fibroblast, a connective tissue cell which secretes an extracellular matrix rich in collagen and other macromolecules.") -AnnotationAssertion( "jl") AnnotationAssertion( "2010-09-23T11:33:38Z") AnnotationAssertion( "fibroblast apoptosis") AnnotationAssertion( "biological_process") @@ -56683,7 +56285,6 @@ SubClassOf( (protein localization to cytoskeleton) AnnotationAssertion(Annotation( "GOC:jl") "A process in which a protein is transported to, or maintained in, a location within the cytoskeleton.") -AnnotationAssertion( "jl") AnnotationAssertion( "2011-12-13T11:43:24Z") AnnotationAssertion(Annotation( "GOC:mah") "protein localisation to cytoskeleton") AnnotationAssertion( "biological_process") @@ -56714,7 +56315,6 @@ DisjointClasses( ObjectSomeValuesFrom # Class: (motile cilium assembly) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:cilia") Annotation( "GOC:krc") Annotation( "GO_REF:0000079") Annotation( "PMID:19776033") Annotation( "PMID:21129373") Annotation( "ZFIN:dsf") "The aggregation, arrangement and bonding together of a set of components to form a motile cilium.") -AnnotationAssertion( "krc") AnnotationAssertion( "2015-02-06T17:23:23Z") AnnotationAssertion( "biological_process") AnnotationAssertion(Annotation( "GOC:TermGenie") "motile primary cilia assembly") @@ -56730,7 +56330,6 @@ EquivalentClasses( ObjectIntersection # Class: (dendritic cell proliferation) AnnotationAssertion(Annotation( "CL:0000451") Annotation( "PMID:18469816") "The expansion of a dendritic cell population by cell division. A dendritic cell is a cell of hematopoietic origin, typically resident in particular tissues, specialized in the uptake, processing, and transport of antigens to lymph nodes for the purpose of stimulating an immune response via T cell activation.") -AnnotationAssertion( "jl") AnnotationAssertion( "2012-04-05T04:31:39Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0044565") @@ -56740,7 +56339,6 @@ EquivalentClasses( ObjectIntersection # Class: (chondrocyte activation) AnnotationAssertion(Annotation( "CL:0000138") Annotation( "GOC:jl") "A change in the morphology or behavior of a chondrocyte resulting from exposure to an activating factor such as a cellular or soluble ligand. A chondrocyte is a polymorphic cell that forms cartilage.") -AnnotationAssertion( "jl") AnnotationAssertion( "2012-04-05T04:45:38Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0044566") @@ -56751,7 +56349,6 @@ SubClassOf( (multi-organism reproductive process) AnnotationAssertion(Annotation( "GOC:jl") "A biological process that directly contributes to the process of producing new individuals, involving another organism.") -AnnotationAssertion( "jl") AnnotationAssertion( "2012-09-19T15:56:30Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0044703") @@ -56763,7 +56360,6 @@ SubClassOf( "GOC:jl") "A multicellular organism process which involves another multicellular organism of the same or different species.") AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/21459"^^xsd:anyURI) -AnnotationAssertion( "jl") AnnotationAssertion( "2012-09-19T16:06:16Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0044706") @@ -56773,7 +56369,6 @@ SubClassOf( (protein transmembrane import into intracellular organelle) AnnotationAssertion(Annotation( "GOC:jl") "The directed movement of proteins into an intracellular organelle, across a membrane.") -AnnotationAssertion( "jl") AnnotationAssertion( "2012-11-07T15:37:36Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0044743") @@ -56783,7 +56378,6 @@ EquivalentClasses( ObjectIntersection # Class: (cilium organization) AnnotationAssertion(Annotation( "GOC:cilia") Annotation( "GOC:jl") "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a cilium, a specialized eukaryotic organelle that consists of a filiform extrusion of the cell surface. Each cilium is bounded by an extrusion of the cytoplasmic membrane, and contains a regular longitudinal array of microtubules, anchored basally in a centriole.") -AnnotationAssertion( "jl") AnnotationAssertion( "2013-03-27T15:09:58Z") AnnotationAssertion( "microtubule-based flagellum organization") AnnotationAssertion( "biological_process") @@ -56800,7 +56394,6 @@ SubClassOf( ObjectAllValuesFrom( (biological phase) AnnotationAssertion(Annotation( "GOC:jl") "A distinct period or stage in a biological process or cycle.") -AnnotationAssertion( "jl") AnnotationAssertion( "2014-07-16T13:12:40Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0044848") @@ -56817,7 +56410,6 @@ DisjointClasses( (lipoprotein localization) AnnotationAssertion(Annotation( "GOC:jl") "Any process in which a lipoprotein is transported to, or maintained in, a specific location.") -AnnotationAssertion( "jl") AnnotationAssertion( "2014-11-25T16:27:06Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0044872") @@ -56828,7 +56420,6 @@ SubClassOf( (lipoprotein localization to membrane) AnnotationAssertion(Annotation( "GOC:jl") "A process in which a lipoprotein is transported to, or maintained in, a specific location in a membrane.") -AnnotationAssertion( "jl") AnnotationAssertion( "2014-11-25T16:28:43Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0044873") @@ -56839,7 +56430,6 @@ SubClassOf( (lipoprotein localization to outer membrane) AnnotationAssertion(Annotation( "GOC:jl") "A process in which a lipoprotein is transported to, or maintained in, a specific location in an outer membrane.") -AnnotationAssertion( "jl") AnnotationAssertion( "2014-11-25T16:30:30Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0044874") @@ -56850,7 +56440,6 @@ SubClassOf( (protein-containing complex binding) AnnotationAssertion(Annotation( "GOC:jl") "Binding to a macromolecular complex.") -AnnotationAssertion( "jl") AnnotationAssertion( "2014-12-16T11:38:58Z") AnnotationAssertion( "protein complex binding") AnnotationAssertion( "molecular_function") @@ -61861,7 +61450,6 @@ SubClassOf( (intracellular transport) AnnotationAssertion(Annotation( "GOC:ai") "The directed movement of substances within a cell.") -AnnotationAssertion( "jl") AnnotationAssertion( "2013-12-18T14:04:50Z") AnnotationAssertion( "biological_process") AnnotationAssertion(Annotation( "GOC:TermGenie") "single organism intracellular transport") @@ -67277,7 +66865,6 @@ EquivalentClasses( ObjectIntersection # Class: (import into nucleus) AnnotationAssertion(Annotation( "GOC:ai") "The directed movement of substances into the nucleus.") -AnnotationAssertion( "jl") AnnotationAssertion( "2013-12-19T15:26:34Z") AnnotationAssertion( "nuclear import") AnnotationAssertion( "nuclear translocation") @@ -67290,7 +66877,6 @@ EquivalentClasses( ObjectIntersection AnnotationAssertion(Annotation( "GOC:ai") Annotation( "GOC:dos") "Any process in which a cell, a substance, or a cellular entity, such as a protein complex or organelle, is transported, tethered to or otherwise maintained in a specific location. In the case of substances, localization may also be achieved via selective degradation.") AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/27052"^^xsd:anyURI) -AnnotationAssertion( "jl") AnnotationAssertion( "2013-12-18T13:51:04Z") AnnotationAssertion( "establishment and maintenance of localization") AnnotationAssertion( "establishment and maintenance of position") @@ -68600,7 +68186,6 @@ SubClassOf( ObjectAllValuesFrom( "GOC:tb") Annotation( "GOC:vw") "A cellular localization process whereby a substance or cellular entity, such as a protein complex or organelle, is transported to, and/or maintained in, a specific location within a cell including the localization of substances or cellular entities to the cell membrane.") AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/27189"^^xsd:anyURI) -AnnotationAssertion( "jl") AnnotationAssertion( "2013-12-18T14:04:32Z") AnnotationAssertion(Annotation( "GOC:mah") "cellular localisation") AnnotationAssertion( "establishment and maintenance of cellular localization") @@ -69782,7 +69367,6 @@ EquivalentClasses( ObjectIntersection # Class: (transmembrane transport) AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:jid") "The process in which a solute is transported across a lipid bilayer, from one side of a membrane to the other.") -AnnotationAssertion( "tb") AnnotationAssertion( "2015-10-21T13:22:47Z") AnnotationAssertion( "membrane transport") AnnotationAssertion( "ATP hydrolysis coupled transmembrane transport") @@ -69875,7 +69459,6 @@ SubClassOf( (vibrational conductance of sound to the inner ear) AnnotationAssertion(Annotation( "GOC:mh") "The transmission of vibrations via ossicles to the inner ear.") -AnnotationAssertion( "jid") AnnotationAssertion( "2009-10-13T10:59:39Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0055127") @@ -72054,7 +71637,6 @@ SubClassOf( (bronchus cartilage development) AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:mtg_lung") "The process whose specific outcome is the progression of lung cartilage over time, from its formation to the mature structure. Cartilage is a connective tissue dominated by extracellular matrix containing collagen type II and large amounts of proteoglycan, particularly chondroitin sulfate.") -AnnotationAssertion( "dph") AnnotationAssertion( "2009-04-10T08:12:06Z") AnnotationAssertion( "pulmonary cartilage development") AnnotationAssertion( "biological_process") @@ -72067,7 +71649,6 @@ SubClassOf( ObjectSomeValuesFrom( (bronchus cartilage morphogenesis) AnnotationAssertion(Annotation( "GOC:dph") "The process in which the bronchus cartilage is generated and organized. The bronchus cartilage is the connective tissue of the portion of the airway that connects to the lungs.") -AnnotationAssertion( "dph") AnnotationAssertion( "2009-04-10T08:47:41Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0060533") @@ -72080,7 +71661,6 @@ SubClassOf( ObjectSomeValuesFrom( (trachea cartilage development) AnnotationAssertion(Annotation( "GOC:dph") "The process whose specific outcome is the progression of the tracheal cartilage over time, from its formation to the mature structure. Cartilage is a connective tissue dominated by extracellular matrix containing collagen type II and large amounts of proteoglycan, particularly chondroitin sulfate.") -AnnotationAssertion( "dph") AnnotationAssertion( "2009-04-10T09:00:18Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0060534") @@ -72092,7 +71672,6 @@ SubClassOf( ObjectSomeValuesFrom( (trachea cartilage morphogenesis) AnnotationAssertion(Annotation( "GOC:dph") "The process in which the anatomical structures of cartilage in the trachea are generated and organized.") -AnnotationAssertion( "dph") AnnotationAssertion( "2009-04-10T09:07:48Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0060535") @@ -72105,7 +71684,6 @@ SubClassOf( ObjectSomeValuesFrom( (cartilage morphogenesis) AnnotationAssertion(Annotation( "GOC:dph") "The process in which the anatomical structures of cartilage are generated and organized.") -AnnotationAssertion( "dph") AnnotationAssertion( "2009-04-10T09:13:27Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0060536") @@ -72117,7 +71695,6 @@ SubClassOf( ObjectSomeValuesFrom( (muscle tissue development) AnnotationAssertion(Annotation( "GOC:dph") "The progression of muscle tissue over time, from its initial formation to its mature state. Muscle tissue is a contractile tissue made up of actin and myosin fibers.") -AnnotationAssertion( "dph") AnnotationAssertion( "2009-04-10T08:05:37Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0060537") @@ -72128,7 +71705,6 @@ SubClassOf( (skeletal muscle organ development) AnnotationAssertion(Annotation( "GOC:dph") "The progression of a skeletal muscle organ over time from its initial formation to its mature state. A skeletal muscle organ includes the skeletal muscle tissue and its associated connective tissue.") -AnnotationAssertion( "dph") AnnotationAssertion( "2009-04-10T08:25:12Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0060538") @@ -72140,7 +71716,6 @@ SubClassOf( "GOC:dph") "The progression of the diaphragm over time from its initial formation to the mature structure. The diaphragm is a skeletal muscle that is responsible for contraction and expansion of the lungs.") AnnotationAssertion( ) -AnnotationAssertion( "dph") AnnotationAssertion( "2009-04-10T08:44:56Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0060539") @@ -72156,7 +71731,6 @@ DisjointClasses( ObjectSomeValuesFrom AnnotationAssertion(Annotation( "GOC:dph") "The process in which the anatomical structures of the diaphragm are generated and organized.") AnnotationAssertion( ) -AnnotationAssertion( "dph") AnnotationAssertion( "2009-04-10T08:47:51Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0060540") @@ -72171,7 +71745,6 @@ DisjointClasses( ObjectSomeValuesFrom # Class: (respiratory system development) AnnotationAssertion(Annotation( "GOC:dph") "The progression of the respiratory system over time from its formation to its mature structure. The respiratory system carries out respiratory gaseous exchange.") -AnnotationAssertion( "dph") AnnotationAssertion( "2009-04-10T08:55:42Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0060541") @@ -72183,7 +71756,6 @@ SubClassOf( (developmental growth involved in morphogenesis) AnnotationAssertion(Annotation( "GOC:dph") "The increase in size or mass of an anatomical structure that contributes to the structure attaining its shape.") -AnnotationAssertion( "dph") AnnotationAssertion( "2009-04-28T08:42:53Z") AnnotationAssertion(Annotation( "GOC:dph") "differential growth") AnnotationAssertion( "biological_process") @@ -72195,7 +71767,6 @@ SubClassOf( (apoptotic process involved in morphogenesis) AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:mtg_apoptosis") "Any apoptotic process that contributes to the shaping of an anatomical structure.") -AnnotationAssertion( "dph") AnnotationAssertion( "2009-04-28T09:17:27Z") AnnotationAssertion( "apoptosis involved in morphogenesis") AnnotationAssertion( "biological_process") @@ -72209,7 +71780,6 @@ SubClassOf( (epithelial tube morphogenesis) AnnotationAssertion(Annotation( "GOC:dph") "The process in which the anatomical structures of a tube are generated and organized from an epithelium. Epithelial tubes transport gases, liquids and cells from one site to another and form the basic structure of many organs and tissues, with tube shape and organization varying from the single-celled excretory organ in Caenorhabditis elegans to the branching trees of the mammalian kidney and insect tracheal system.") -AnnotationAssertion( "dph") AnnotationAssertion( "2009-04-28T09:33:36Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0060562") @@ -72221,7 +71791,6 @@ SubClassOf( (neuroepithelial cell differentiation) AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:tb") "The process in which epiblast cells acquire specialized features of neuroepithelial cells.") -AnnotationAssertion( "dph") AnnotationAssertion( "2009-04-29T01:50:05Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0060563") @@ -72231,7 +71800,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of peptide hormone processing) AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:tb") "Any process that modulates the rate, frequency or extent of peptide hormone processing. Peptide hormone processing is the generation of a mature peptide hormone by posttranslational processing of a prohormone.") -AnnotationAssertion( "dph") AnnotationAssertion( "2009-04-29T03:16:05Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0060568") @@ -72241,7 +71809,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of peptide hormone processing) AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:tb") "Any process that increases the rate, frequency or extent of peptide hormone processing. Peptide hormone processing is the generation of a mature peptide hormone by posttranslational processing of a prohormone.") -AnnotationAssertion( "dph") AnnotationAssertion( "2009-04-29T03:22:05Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0060569") @@ -72251,7 +71818,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of peptide hormone processing) AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:tb") "Any process that decreases the rate, frequency or extent of peptide hormone processing. Peptide hormone processing is the generation of a mature peptide hormone by posttranslational processing of a prohormone.") -AnnotationAssertion( "dph") AnnotationAssertion( "2009-04-29T03:24:55Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0060570") @@ -72261,7 +71827,6 @@ EquivalentClasses( ObjectIntersection # Class: (morphogenesis of an epithelial fold) AnnotationAssertion(Annotation( "GOC:dph") "The morphogenetic process in which an epithelial sheet bends along a linear axis.") -AnnotationAssertion( "dph") AnnotationAssertion( "2009-04-30T09:27:17Z") AnnotationAssertion(Annotation( "GOC:dph") "epithelial folding") AnnotationAssertion( "biological_process") @@ -72274,7 +71839,6 @@ SubClassOf( (morphogenesis of an epithelial bud) AnnotationAssertion(Annotation( "GOC:dph") "The morphogenetic process in which a bud forms from an epithelial sheet. A bud is a protrusion that forms form the sheet by localized folding.") -AnnotationAssertion( "dph") AnnotationAssertion( "2009-04-30T09:38:35Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0060572") @@ -72285,7 +71849,6 @@ SubClassOf( (intestinal epithelial cell maturation) AnnotationAssertion(Annotation( "GOC:dph") Annotation( "PMID:18824147") "The developmental process, independent of morphogenetic (shape) change, that is required for a columna/cuboidal epithelial cell of the intestine to attain its fully functional state. A columnar/cuboidal epithelial cell of the intestine mature as they migrate from the intestinal crypt to the villus.") -AnnotationAssertion( "dph") AnnotationAssertion( "2009-05-06T08:10:41Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0060574") @@ -72297,7 +71860,6 @@ SubClassOf( ObjectSomeValuesFrom( (intestinal epithelial cell differentiation) AnnotationAssertion(Annotation( "GOC:dph") "The process in which a relatively unspecialized cell acquires specialized features of a columnar/cuboidal epithelial cell of the intestine.") -AnnotationAssertion( "dph") AnnotationAssertion( "2009-05-06T08:17:56Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0060575") @@ -72309,7 +71871,6 @@ SubClassOf( ObjectSomeValuesFrom( (intestinal epithelial cell development) AnnotationAssertion(Annotation( "GOC:dph") "The process whose specific outcome is the progression of a columnar/cuboidal epithelial cell of the intestine over time, from its formation to the mature structure.") -AnnotationAssertion( "dph") AnnotationAssertion( "2009-05-06T08:20:24Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0060576") @@ -72321,7 +71882,6 @@ SubClassOf( ObjectSomeValuesFrom( (pulmonary vein morphogenesis) AnnotationAssertion(Annotation( "GOC:dph") "The process in which the anatomical structure of the pulmonary venous blood vessels are generated and organized. Pulmonary veins are blood vessels that transport blood from the lungs to the heart.") -AnnotationAssertion( "dph") AnnotationAssertion( "2009-05-06T08:44:04Z") AnnotationAssertion( "biological_process") AnnotationAssertion(Annotation( "GOC:dph") "pulmonary venous blood vessel morphogenesis") @@ -72333,7 +71893,6 @@ SubClassOf( (superior vena cava morphogenesis) AnnotationAssertion(Annotation( "GOC:dph") "The process in which the anatomical structure of superior vena cava generated and organized. The superior vena cava is a blood vessel that transports blood from the upper body to the heart.") -AnnotationAssertion( "dph") AnnotationAssertion( "2009-05-06T08:47:21Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0060578") @@ -72344,7 +71903,6 @@ SubClassOf( (cell fate commitment involved in pattern specification) AnnotationAssertion(Annotation( "GOC:dph") "The commitment of cells to specific cell fates and their capacity to differentiate into particular kinds of cells within a field of cells that will exhibit a certain pattern of differentiation. Positional information is established through protein signals that emanate from a localized source within a developmental field resulting in specification of a cell type. Those signals are then interpreted in a cell-autonomous manner resulting in the determination of the cell type.") -AnnotationAssertion( "dph") AnnotationAssertion( "2009-05-07T12:40:55Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0060581") @@ -72355,7 +71913,6 @@ EquivalentClasses( ObjectIntersection AnnotationAssertion(Annotation( "PMID:31431773") "A chemical homeostatic process involved in the maintenance of a steady state level of iron within extracellular body fluids, such as blood, xylem or phloem, of a multicellular organism. This is distinct from maintenance of cellular homeostasis, which occurs within a cell.") AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/24554"^^xsd:anyURI) -AnnotationAssertion( "dph") AnnotationAssertion( "2009-05-08T02:18:21Z") AnnotationAssertion( "multicellular organismal iron ion homeostasis") AnnotationAssertion( "biological_process") @@ -72366,7 +71923,6 @@ EquivalentClasses( ObjectIntersection # Class: (chondroblast differentiation) AnnotationAssertion(Annotation( "GOC:dph") "The process in which a mesenchymal cell, acquires specialized structural and/or functional features of a chondroblast. Differentiation includes the processes involved in commitment of a cell to a chondroblast fate. A chondroblast is a precursor cell to chondrocytes.") -AnnotationAssertion( "dph") AnnotationAssertion( "2009-05-11T07:47:36Z") AnnotationAssertion( "biological_process") AnnotationAssertion(Annotation( "GOC:dph") "chondrocyte progenitor cell differentiation") @@ -72379,7 +71935,6 @@ SubClassOf( ObjectSomeValuesFrom( (mammary gland formation) AnnotationAssertion(Annotation( "GOC:dph") Annotation( "PMID:16168142") Annotation( "PMID:17120154") "The process pertaining to the initial formation of the mammary gland from unspecified parts. The process begins with formation of the mammary line and ends when the solid mammary bud invades the primary mammary mesenchyme.") -AnnotationAssertion( "dph") AnnotationAssertion( "2009-05-13T08:47:52Z") AnnotationAssertion(Annotation( "GOC:dph") "mammary line formation") AnnotationAssertion(Annotation( "GOC:dph") "mammary placode formation") @@ -72396,7 +71951,6 @@ SubClassOf( ObjectSomeValuesFrom( (mammary placode formation) AnnotationAssertion(Annotation( "GOC:dph") Annotation( "PMID:16168142") "The developmental process in which the mammary placode forms. The mammary placode is a transient lens shaped structure that will give rise to the mammary bud proper.") -AnnotationAssertion( "dph") AnnotationAssertion( "2009-05-13T11:55:20Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0060596") @@ -72408,7 +71962,6 @@ SubClassOf( ObjectSomeValuesFrom( (lateral sprouting involved in mammary gland duct morphogenesis) AnnotationAssertion(Annotation( "GOC:dph") Annotation( "PMID:17120154") "The process in which a branch forms along the side of a mammary duct.") -AnnotationAssertion( "dph") AnnotationAssertion( "2009-05-13T12:38:06Z") AnnotationAssertion(Annotation( "GOC:dph") "mammary gland duct secondary branching") AnnotationAssertion( "biological_process") @@ -72419,7 +71972,6 @@ EquivalentClasses( ObjectIntersection # Class: (lateral sprouting from an epithelium) AnnotationAssertion(Annotation( "GOC:dph") "The process in which a branch forms along the side of an epithelium.") -AnnotationAssertion( "dph") AnnotationAssertion( "2009-05-14T02:33:01Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0060601") @@ -72430,7 +71982,6 @@ SubClassOf( ObjectSomeValuesFrom( (mammary gland duct morphogenesis) AnnotationAssertion(Annotation( "GOC:dph") Annotation( "PMID:17120154") "The process in which anatomical structures of the mammary ducts are generated and organized. Mammary ducts are epithelial tubes that transport milk.") -AnnotationAssertion( "dph") AnnotationAssertion( "2009-05-15T09:22:25Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0060603") @@ -72443,7 +71994,6 @@ SubClassOf( ObjectSomeValuesFrom( (mesenchymal cell differentiation involved in mammary gland development) AnnotationAssertion(Annotation( "GOC:dph") "The process in which a relatively unspecialized cell acquires specialized features of a mammary gland mesenchymal cell. Mammary gland mesenchymal cells form a loosely connected network of cells that surround the mammary ducts.") -AnnotationAssertion( "dph") AnnotationAssertion( "2009-05-15T12:17:06Z") AnnotationAssertion(Annotation( "GOC:dph") "mammary gland mesenchymal cell differentiation") AnnotationAssertion( "biological_process") @@ -72454,7 +72004,6 @@ EquivalentClasses( ObjectIntersection # Class: (mammary gland fat development) AnnotationAssertion(Annotation( "GOC:dph") "The progression of the mammary gland fat over time, from its formation to the mature structure. The mammary fat is an adipose structure in the gland that is invaded by the mammary ducts.") -AnnotationAssertion( "dph") AnnotationAssertion( "2009-05-15T12:27:57Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0060611") @@ -72466,7 +72015,6 @@ SubClassOf( ObjectSomeValuesFrom( (adipose tissue development) AnnotationAssertion(Annotation( "GOC:dph") "The process whose specific outcome is the progression of adipose tissue over time, from its formation to the mature structure. Adipose tissue is specialized tissue that is used to store fat.") -AnnotationAssertion( "dph") AnnotationAssertion( "2009-05-15T12:36:28Z") AnnotationAssertion( "biological_process") AnnotationAssertion(Annotation( "GOC:mah") Annotation( "GOC:sl") "adipogenesis") @@ -72479,7 +72027,6 @@ SubClassOf( ObjectSomeValuesFrom( (mammary gland bud formation) AnnotationAssertion(Annotation( "GOC:dph") Annotation( "PMID:12558599") "The morphogenetic process in which a bud forms from the mammary placode. A mammary bud is bulb of epithelial cells that is distinct from the surrounding epidermis.") -AnnotationAssertion( "dph") AnnotationAssertion( "2009-05-18T08:43:14Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0060615") @@ -72492,7 +72039,6 @@ SubClassOf( ObjectSomeValuesFrom( (mammary gland cord formation) AnnotationAssertion(Annotation( "GOC:dph") Annotation( "PMID:12558599") "The process in which the mammary gland cord forms by elongation of the mammary bud. The cord is formed once the elongating bud breaks through the mesenchyme and reaches the fat pad.") -AnnotationAssertion( "dph") AnnotationAssertion( "2009-05-18T08:57:58Z") AnnotationAssertion(Annotation( "GOC:dph") "mammary gland sprout formation") AnnotationAssertion( "biological_process") @@ -72506,7 +72052,6 @@ SubClassOf( ObjectSomeValuesFrom( (nipple development) AnnotationAssertion(Annotation( "GOC:dph") "The progression of the nipple over time, from its formation to the mature structure. The nipple is a part of the mammary gland that protrudes from the surface ectoderm.") -AnnotationAssertion( "dph") AnnotationAssertion( "2009-05-18T09:29:38Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0060618") @@ -72519,7 +72064,6 @@ SubClassOf( ObjectSomeValuesFrom( (cell migration involved in mammary placode formation) AnnotationAssertion(Annotation( "GOC:dph") Annotation( "PMID:12558599") "The orderly movement of epithelial cells within the mammary line that contributes to the formation of the mammary placode.") -AnnotationAssertion( "dph") AnnotationAssertion( "2009-05-18T09:41:49Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0060619") @@ -72530,7 +72074,6 @@ SubClassOf( (regulation of chromosome condensation) AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:tb") "Any process that modulates the rate, frequency, or extent of chromosome condensation, the progressive compaction of dispersed interphase chromatin into threadlike chromosomes prior to mitotic or meiotic nuclear division, or during apoptosis, in eukaryotic cells.") -AnnotationAssertion( "dph") AnnotationAssertion( "2009-05-18T02:12:13Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0060623") @@ -72540,7 +72083,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of vesicle-mediated transport) AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:tb") "Any process that modulates the rate, frequency, or extent of vesicle-mediated transport, the directed movement of substances, either within a vesicle or in the vesicle membrane, into, out of or within a cell.") -AnnotationAssertion( "dph") AnnotationAssertion( "2009-05-18T02:29:43Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0060627") @@ -72552,7 +72094,6 @@ SubClassOf( (regulation of microtubule-based movement) AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:tb") "Any process that modulates the rate, frequency, or extent of microtubule-based movement, the movement of organelles, other microtubules and other particles along microtubules, mediated by motor proteins.") -AnnotationAssertion( "dph") AnnotationAssertion( "2009-05-18T03:07:02Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0060632") @@ -72562,7 +72103,6 @@ EquivalentClasses( ObjectIntersection # Class: (mesenchymal-epithelial cell signaling) AnnotationAssertion(Annotation( "GOC:dph") "Any process that mediates the transfer of information from a mesenchymal cell to an epithelial cell where it is received and interpreted.") -AnnotationAssertion( "dph") AnnotationAssertion( "2009-05-19T03:59:05Z") AnnotationAssertion(Annotation( "GOC:mah") "mesenchymal-epithelial cell signalling") AnnotationAssertion( "biological_process") @@ -72573,7 +72113,6 @@ EquivalentClasses( ObjectIntersection # Class: (white fat cell differentiation involved in mammary gland fat development) AnnotationAssertion(Annotation( "GOC:dph") Annotation( "PMID:12558599") "The process in which a preadipocyte acquires specialized features of a white adipocyte of the mammary gland. White adipocytes have cytoplasmic lipids arranged in a unique vacuole.") -AnnotationAssertion( "dph") AnnotationAssertion( "2009-05-27T05:50:56Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0060642") @@ -72583,7 +72122,6 @@ EquivalentClasses( ObjectIntersection # Class: (epithelial cell differentiation involved in mammary gland bud morphogenesis) AnnotationAssertion(Annotation( "GOC:dph") "The process in which a cell of the mammary placode becomes a cell of the mammary gland bud.") -AnnotationAssertion( "dph") AnnotationAssertion( "2009-05-29T07:58:13Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0060643") @@ -72595,7 +72133,6 @@ SubClassOf( ObjectSomeValuesFrom( (mammary gland epithelial cell differentiation) AnnotationAssertion(Annotation( "GOC:dph") "The process in which a relatively unspecialized epithelial cell becomes a more specialized epithelial cell of the mammary gland.") -AnnotationAssertion( "dph") AnnotationAssertion( "2009-05-29T08:03:07Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0060644") @@ -72607,7 +72144,6 @@ SubClassOf( ObjectSomeValuesFrom( (mesenchymal cell condensation involved in mammary fat development) AnnotationAssertion(Annotation( "GOC:dph") Annotation( "PMID:12558599") "The cell adhesion process in which mammary mesenchyme cells adhere to one another in the initial stages of the formation of mammary fat development.") -AnnotationAssertion( "dph") AnnotationAssertion( "2009-05-29T08:33:29Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0060647") @@ -72617,7 +72153,6 @@ EquivalentClasses( ObjectIntersection # Class: (mammary gland bud morphogenesis) AnnotationAssertion(Annotation( "GOC:dph") Annotation( "PMID:12558599") "The process in which anatomical structures of the mammary gland buds are generated and organized. Mammary gland buds form by an outpocketing of the mammary placodes and grow to invade the mammary fat, when they form the mammary cord.") -AnnotationAssertion( "dph") AnnotationAssertion( "2009-05-29T08:42:22Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0060648") @@ -72629,7 +72164,6 @@ SubClassOf( ObjectSomeValuesFrom( (mammary gland cord morphogenesis) AnnotationAssertion(Annotation( "GOC:dph") Annotation( "PMID:12558599") "The process in which anatomical structures of the mammary gland cord are generated and organized. Mammary gland cords form when the mammary gland bud invades the mammary fat.") -AnnotationAssertion( "dph") AnnotationAssertion( "2009-05-29T09:06:56Z") AnnotationAssertion(Annotation( "GOC:dph") "mammary gland sprout morphogenesis") AnnotationAssertion( "biological_process") @@ -72642,7 +72176,6 @@ SubClassOf( ObjectSomeValuesFrom( (epithelial cell differentiation involved in mammary gland cord morphogenesis) AnnotationAssertion(Annotation( "GOC:dph") Annotation( "PMID:12558599") "The process in which a relatively unspecialized epithelial cell becomes a more specialized epithelial cell of the mammary gland cord. Epithelial cells of the mammary cord give it its funnel-like shape and some are cornified.") -AnnotationAssertion( "dph") AnnotationAssertion( "2009-05-29T09:17:16Z") AnnotationAssertion( "biological_process") AnnotationAssertion(Annotation( "GOC:dph") "epithelial cell differentiation involved in mammary gland sprout morphogenesis") @@ -72654,7 +72187,6 @@ SubClassOf( (branching involved in mammary gland cord morphogenesis) AnnotationAssertion(Annotation( "GOC:dph") Annotation( "PMID:12558599") "The process in which the branching structure of the mammary gland cord is generated and organized. The mammary gland cord is a solid epithelial structure that will hollow out, forming the mammary duct.") -AnnotationAssertion( "dph") AnnotationAssertion( "2009-05-29T09:29:32Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0060655") @@ -72664,7 +72196,6 @@ EquivalentClasses( ObjectIntersection # Class: (nipple morphogenesis) AnnotationAssertion(Annotation( "GOC:dph") "The process in which the nipple is generated and organized.") -AnnotationAssertion( "dph") AnnotationAssertion( "2009-05-29T10:45:44Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0060658") @@ -72678,7 +72209,6 @@ SubClassOf( ObjectSomeValuesFrom( (epidermis morphogenesis involved in nipple formation) AnnotationAssertion(Annotation( "GOC:dph") Annotation( "PMID:12558599") "The process in which the epidermis of the nipple sheath is uplifted to form an umbrella-like projection.") -AnnotationAssertion( "dph") AnnotationAssertion( "2009-05-29T11:04:04Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0060660") @@ -72688,7 +72218,6 @@ EquivalentClasses( ObjectIntersection # Class: (epithelial cell proliferation involved in salivary gland morphogenesis) AnnotationAssertion(Annotation( "GOC:dph") Annotation( "PMID:17336109") "The multiplication or reproduction of epithelial cells of the submandibular salivary gland, resulting in the expansion of a cell population and the shaping of the gland.") -AnnotationAssertion( "dph") AnnotationAssertion( "2009-06-01T08:36:13Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0060664") @@ -72698,7 +72227,6 @@ EquivalentClasses( ObjectIntersection # Class: (embryonic placenta morphogenesis) AnnotationAssertion(Annotation( "GOC:dph") "The process in which the embryonic placenta is generated and organized.") -AnnotationAssertion( "dph") AnnotationAssertion( "2009-06-02T09:33:37Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0060669") @@ -72710,7 +72238,6 @@ SubClassOf( ObjectSomeValuesFrom( (branching involved in labyrinthine layer morphogenesis) AnnotationAssertion(Annotation( "GOC:dph") Annotation( "PMID:16916377") "The process in which the branches of the fetal placental villi are generated and organized. The villous part of the placenta is called the labyrinth layer.") -AnnotationAssertion( "dph") AnnotationAssertion( "2009-06-02T10:40:40Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0060670") @@ -72721,7 +72248,6 @@ SubClassOf( (epithelial cell differentiation involved in embryonic placenta development) AnnotationAssertion(Annotation( "GOC:dph") Annotation( "PMID:16916377") "The process in which a trophoblast cell acquires specialized features of an epithelial cell of the placental labyrinthine layer.") -AnnotationAssertion( "dph") AnnotationAssertion( "2009-06-02T11:40:52Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0060671") @@ -72732,7 +72258,6 @@ SubClassOf( ObjectSomeValuesFrom( (cell-cell signaling involved in placenta development) AnnotationAssertion(Annotation( "GOC:dph") Annotation( "PMID:16916377") "Any process that mediates the transfer of information from one cell to another.") -AnnotationAssertion( "dph") AnnotationAssertion( "2009-06-02T12:58:03Z") AnnotationAssertion(Annotation( "GOC:mah") "cell-cell signalling involved in placenta development") AnnotationAssertion( "biological_process") @@ -72744,7 +72269,6 @@ SubClassOf( ObjectSomeValuesFrom( (placenta blood vessel development) AnnotationAssertion(Annotation( "GOC:dph") Annotation( "PMID:16916377") "The process whose specific outcome is the progression of a blood vessel of the placenta over time, from its formation to the mature structure.") -AnnotationAssertion( "dph") AnnotationAssertion( "2009-06-02T01:09:43Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0060674") @@ -72755,7 +72279,6 @@ SubClassOf( ObjectSomeValuesFrom( (ureteric bud morphogenesis) AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:mtg_kidney_jan10") "The process in which the ureteric bud is generated and organized.") -AnnotationAssertion( "dph") AnnotationAssertion( "2009-06-02T01:31:41Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0060675") @@ -72767,7 +72290,6 @@ SubClassOf( ObjectSomeValuesFrom( (ureteric bud formation) AnnotationAssertion(Annotation( "GOC:dph") Annotation( "PMID:16916378") "The developmental process pertaining to the initial formation of the ureteric bud from the Wolffian duct. This process begins when the bud protrudes from the duct and ends when it is a recognizable bud.") -AnnotationAssertion( "dph") AnnotationAssertion( "2009-06-02T01:47:23Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0060676") @@ -72779,7 +72301,6 @@ SubClassOf( ObjectSomeValuesFrom( (lateral sprouting involved in ureteric bud morphogenesis) AnnotationAssertion(Annotation( "GOC:dph") Annotation( "PMID:16916378") "The process in which a branch forms along the side of a ureteric bud.") -AnnotationAssertion( "dph") AnnotationAssertion( "2009-06-02T02:44:27Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0060680") @@ -72789,7 +72310,6 @@ EquivalentClasses( ObjectIntersection # Class: (epithelial-mesenchymal cell signaling) AnnotationAssertion(Annotation( "GOC:dph") "Any process that results in the transfer of information from an epithelial cell to a mesenchymal cell where it is interpreted.") -AnnotationAssertion( "dph") AnnotationAssertion( "2009-06-03T06:36:46Z") AnnotationAssertion(Annotation( "GOC:mah") "epithelial-mesenchymal cell signalling") AnnotationAssertion( "biological_process") @@ -72800,7 +72320,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of prostatic bud formation) AnnotationAssertion(Annotation( "GOC:dph") "Any process that modulates the rate, frequency, or extent of prostatic bud formation, the morphogenetic process in which a region of the fetal urogenital sinus epithelium is specified to become the prostate, resulting in prostate bud outgrowth.") -AnnotationAssertion( "dph") AnnotationAssertion( "2009-06-05T12:29:26Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0060685") @@ -72811,7 +72330,6 @@ SubClassOf( ObjectSomeValuesFrom( (negative regulation of prostatic bud formation) AnnotationAssertion(Annotation( "GOC:dph") "Any process that decreases the rate, frequency, or extent of prostatic bud formation, the morphogenetic process in which a region of the fetal urogenital sinus epithelium is specified to become the prostate, resulting in prostate bud outgrowth.") -AnnotationAssertion( "dph") AnnotationAssertion( "2009-06-05T12:35:25Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0060686") @@ -72821,7 +72339,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of branching involved in prostate gland morphogenesis) AnnotationAssertion(Annotation( "GOC:dph") "Any process that modulates the rate, frequency, or extent of prostate gland branching, the process in which the branching structure of the prostate gland is generated and organized. A branch is a division or offshoot from a main stem.") -AnnotationAssertion( "dph") AnnotationAssertion( "2009-06-05T12:37:14Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0060687") @@ -72831,7 +72348,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of morphogenesis of a branching structure) AnnotationAssertion(Annotation( "GOC:dph") "Any process that modulates the rate, frequency, or extent of branching morphogenesis, the process in which the anatomical structures of branches are generated and organized.") -AnnotationAssertion( "dph") AnnotationAssertion( "2009-06-05T12:41:44Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0060688") @@ -72843,7 +72359,6 @@ SubClassOf( (cell differentiation involved in salivary gland development) AnnotationAssertion(Annotation( "GOC:dph") "The process in which a relatively unspecialized cell acquires specialized structural and/or functional features that characterize the cells of the salivary gland.") -AnnotationAssertion( "dph") AnnotationAssertion( "2009-06-08T01:01:35Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0060689") @@ -72853,7 +72368,6 @@ EquivalentClasses( ObjectIntersection # Class: (epithelial cell differentiation involved in salivary gland development) AnnotationAssertion(Annotation( "GOC:dph") "The process in which a relatively unspecialized cell acquire specialized structural and/or functional features of an epithelial cell of the salivary gland.") -AnnotationAssertion( "dph") AnnotationAssertion( "2009-06-08T01:04:19Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0060690") @@ -72863,7 +72377,6 @@ EquivalentClasses( ObjectIntersection # Class: (epithelial cell maturation involved in salivary gland development) AnnotationAssertion(Annotation( "GOC:dph") "The developmental process, independent of morphogenetic (shape) change, that is required for an epithelial cell of the salivary gland to attain its fully functional state.") -AnnotationAssertion( "dph") AnnotationAssertion( "2009-06-08T01:06:00Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0060691") @@ -72874,7 +72387,6 @@ SubClassOf( ObjectSomeValuesFrom( (mesenchymal cell differentiation involved in salivary gland development) AnnotationAssertion(Annotation( "GOC:dph") "The process in which a relatively unspecialized cell acquires specialized features of a mesenchymal cell of the salivary gland. A mesenchymal cell is a loosely associated cell that is part of the connective tissue in an organism. Mesenchymal cells give rise to more mature connective tissue cell types.") -AnnotationAssertion( "dph") AnnotationAssertion( "2009-06-08T01:08:44Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0060692") @@ -72884,7 +72396,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of branching involved in salivary gland morphogenesis) AnnotationAssertion(Annotation( "GOC:dph") "Any process that modulates the rate, frequency, or extent of branching morphogenesis in the salivary gland epithelium.") -AnnotationAssertion( "dph") AnnotationAssertion( "2009-06-08T01:14:44Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0060693") @@ -72895,7 +72406,6 @@ SubClassOf( (acinar cell differentiation involved in salivary gland development) AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:tb") "The process in which a relatively unspecialized cell acquires specialized structural and/or functional features that characterize an acinar cell of the salivary gland. Acinar cells are protein-secreting cells in the gland.") -AnnotationAssertion( "dph") AnnotationAssertion( "2009-06-09T09:32:46Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0060704") @@ -72905,7 +72415,6 @@ EquivalentClasses( ObjectIntersection # Class: (neuron differentiation involved in salivary gland development) AnnotationAssertion(Annotation( "GOC:dph") "The process in which a relatively unspecialized cell acquires specialized structural and/or functional features that characterize the neurons of the salivary gland.") -AnnotationAssertion( "dph") AnnotationAssertion( "2009-06-09T09:35:52Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0060705") @@ -72915,7 +72424,6 @@ EquivalentClasses( ObjectIntersection # Class: (cell differentiation involved in embryonic placenta development) AnnotationAssertion(Annotation( "GOC:dph") "The process in which a relatively unspecialized cell acquires specialized features of the embryonic placenta.") -AnnotationAssertion( "dph") AnnotationAssertion( "2009-06-09T10:26:42Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0060706") @@ -72926,7 +72434,6 @@ SubClassOf( (trophoblast giant cell differentiation) AnnotationAssertion(Annotation( "GOC:dph") Annotation( "PMID:16269175") "The process in which a relatively unspecialized cell acquires specialized features of a trophoblast giant cell of the placenta. Trophoblast giant cells are the cell of the placenta that line the maternal decidua.") -AnnotationAssertion( "dph") AnnotationAssertion( "2009-06-09T10:32:12Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0060707") @@ -72937,7 +72444,6 @@ SubClassOf( (spongiotrophoblast differentiation) AnnotationAssertion(Annotation( "GOC:dph") Annotation( "PMID:16269175") "The process in which a relatively unspecialized cell of the ectoplacental cone acquires specialized features of a spongiotrophoblast of the placenta. A spongiotrophoblast cell is a basophilic cell.") -AnnotationAssertion( "dph") AnnotationAssertion( "2009-06-09T10:38:10Z") AnnotationAssertion(Annotation( "GOC:cjm") "spongiotrophoblast cell differentiation") AnnotationAssertion( "biological_process") @@ -72950,7 +72456,6 @@ SubClassOf( ObjectSomeValuesFrom( (labyrinthine layer development) AnnotationAssertion(Annotation( "GOC:dph") "The process in which the labyrinthine layer of the placenta progresses, from its formation to its mature state.") -AnnotationAssertion( "dph") AnnotationAssertion( "2009-06-09T03:27:43Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0060711") @@ -72963,7 +72468,6 @@ SubClassOf( ObjectSomeValuesFrom( (spongiotrophoblast layer development) AnnotationAssertion(Annotation( "GOC:dph") "The process in which the spongiotrophoblast layer of the placenta progresses from its formation to its mature state.") -AnnotationAssertion( "dph") AnnotationAssertion( "2009-06-09T03:33:40Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0060712") @@ -72975,7 +72479,6 @@ SubClassOf( ObjectSomeValuesFrom( (labyrinthine layer morphogenesis) AnnotationAssertion(Annotation( "GOC:dph") "The process in which the labyrinthine layer of the placenta is generated and organized.") -AnnotationAssertion( "dph") AnnotationAssertion( "2009-06-10T08:10:19Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0060713") @@ -72988,7 +72491,6 @@ SubClassOf( ObjectSomeValuesFrom( (labyrinthine layer formation) AnnotationAssertion(Annotation( "GOC:dph") "The developmental process pertaining to the initial formation of the labyrinthine layer of the placenta.") -AnnotationAssertion( "dph") AnnotationAssertion( "2009-06-10T08:13:14Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0060714") @@ -73001,7 +72503,6 @@ SubClassOf( ObjectSomeValuesFrom( (labyrinthine layer blood vessel development) AnnotationAssertion(Annotation( "GOC:dph") "The process whose specific outcome is the progression of a blood vessel of the labyrinthine layer of the placenta over time, from its formation to the mature structure. The embryonic vessels grow through the layer to come in close contact with the maternal blood supply.") -AnnotationAssertion( "dph") AnnotationAssertion( "2009-06-11T09:04:38Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0060716") @@ -73014,7 +72515,6 @@ SubClassOf( ObjectSomeValuesFrom( (chorion development) AnnotationAssertion(Annotation( "GOC:dph") "The biological process whose specific outcome is the progression of a chorion from an initial condition to its mature state. This process begins with the formation of the structure and ends with the mature structure. The chorion is an extraembryonic membrane.") -AnnotationAssertion( "dph") AnnotationAssertion( "2009-06-11T02:37:50Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0060717") @@ -73025,7 +72525,6 @@ SubClassOf( (chorionic trophoblast cell differentiation) AnnotationAssertion(Annotation( "CL:0011101") Annotation( "GOC:dph") Annotation( "PMID:16983341") "The process in which relatively unspecialized cells of the ectoplacental cone acquire specialized structural and/or functional features that characterize chorionic trophoblasts. These cells will migrate towards the spongiotrophoblast layer and give rise to syncytiotrophoblasts of the labyrinthine layer.") -AnnotationAssertion( "dph") AnnotationAssertion( "2009-06-11T02:48:27Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0060718") @@ -73037,7 +72536,6 @@ SubClassOf( ObjectSomeValuesFrom( (chorionic trophoblast cell development) AnnotationAssertion(Annotation( "CL:0011101") Annotation( "GOC:16983341") Annotation( "GOC:dph") "The process whose specific outcome is the progression of the chorionic trophoblast over time, from its formation to the mature structure. Cell development does not include the steps involved in committing a cell to a specific fate.") -AnnotationAssertion( "dph") AnnotationAssertion( "2009-06-11T02:58:45Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0060719") @@ -73049,7 +72547,6 @@ SubClassOf( ObjectSomeValuesFrom( (cell proliferation involved in embryonic placenta development) AnnotationAssertion(Annotation( "GOC:dph") "The multiplication or reproduction of cells, resulting in the expansion of the population in the embryonic placenta.") -AnnotationAssertion( "dph") AnnotationAssertion( "2009-06-12T12:46:04Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0060722") @@ -73059,7 +72556,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of cell proliferation involved in embryonic placenta development) AnnotationAssertion(Annotation( "GOC:dph") "Any process that modulates the rate, frequency, or extent of cell proliferation involved in embryonic placenta development.") -AnnotationAssertion( "dph") AnnotationAssertion( "2009-06-12T12:50:23Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0060723") @@ -73069,7 +72565,6 @@ EquivalentClasses( ObjectIntersection # Class: (prostate gland growth) AnnotationAssertion(Annotation( "GOC:dph") "The increase in size or mass of the prostate gland where the increase in size or mass has the specific outcome of the progression of the gland, from its formation to its mature state.") -AnnotationAssertion( "dph") AnnotationAssertion( "2009-06-15T09:21:52Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0060736") @@ -73082,7 +72577,6 @@ SubClassOf( ObjectSomeValuesFrom( (prostate gland morphogenetic growth) AnnotationAssertion(Annotation( "GOC:dph") "The differential increase in size or mass of the prostate gland that contributes to the gland attaining its form.") -AnnotationAssertion( "dph") AnnotationAssertion( "2009-06-15T09:24:40Z") AnnotationAssertion(Annotation( "GOC:dph") "prostate gland growth involved in morphogenesis") AnnotationAssertion( "biological_process") @@ -73094,7 +72588,6 @@ SubClassOf( ObjectSomeValuesFrom( (epithelial-mesenchymal signaling involved in prostate gland development) AnnotationAssertion(Annotation( "GOC:dph") "Any process that results in the transfer of information from an epithelial cell to a mesenchymal cell where it is interpreted and contributes to the progression of the prostate gland over time.") -AnnotationAssertion( "dph") AnnotationAssertion( "2009-06-15T09:31:31Z") AnnotationAssertion(Annotation( "GOC:mah") "epithelial-mesenchymal signalling involved in prostate gland development") AnnotationAssertion( "biological_process") @@ -73105,7 +72598,6 @@ EquivalentClasses( ObjectIntersection # Class: (mesenchymal-epithelial cell signaling involved in prostate gland development) AnnotationAssertion(Annotation( "GOC:dph") "Any process that mediates the transfer of information from a mesenchymal cell to an epithelial cell where it is received and interpreted contributing to the progression of the prostate gland over time.") -AnnotationAssertion( "dph") AnnotationAssertion( "2009-06-15T09:35:08Z") AnnotationAssertion(Annotation( "GOC:mah") "mesenchymal-epithelial cell signalling involved in prostate gland development") AnnotationAssertion( "biological_process") @@ -73116,7 +72608,6 @@ EquivalentClasses( ObjectIntersection # Class: (prostate gland epithelium morphogenesis) AnnotationAssertion(Annotation( "GOC:dph") "The process in which the anatomical structures of epithelia of the prostate gland are generated and organized. An epithelium consists of closely packed cells arranged in one or more layers, that covers the outer surfaces of the body or lines any internal cavity or tube.") -AnnotationAssertion( "dph") AnnotationAssertion( "2009-06-16T09:23:22Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0060740") @@ -73129,7 +72620,6 @@ SubClassOf( ObjectSomeValuesFrom( (prostate gland stromal morphogenesis) AnnotationAssertion(Annotation( "GOC:dph") "The process in which the prostate gland stroma is generated and organized. The prostate gland stroma is made up of the mesenchymal or fibroblast cells of the prostate gland.") -AnnotationAssertion( "dph") AnnotationAssertion( "2009-06-16T09:27:01Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0060741") @@ -73144,7 +72634,6 @@ SubClassOf( ObjectSomeValuesFrom( (epithelial cell differentiation involved in prostate gland development) AnnotationAssertion(Annotation( "GOC:dph") "The process in which a relatively unspecialized cell acquires specialized features of an epithelial cell of the prostate gland.") -AnnotationAssertion( "dph") AnnotationAssertion( "2009-06-16T09:32:34Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0060742") @@ -73155,7 +72644,6 @@ SubClassOf( (epithelial cell maturation involved in prostate gland development) AnnotationAssertion(Annotation( "GOC:dph") "The developmental process, independent of morphogenetic (shape) change, that is required for an epithelial cell of the prostate gland to attain its fully functional state. An epithelial cell is a cell usually found in a two-dimensional sheet with a free surface.") -AnnotationAssertion( "dph") AnnotationAssertion( "2009-06-16T09:34:42Z") AnnotationAssertion(Annotation( "GOC:dph") "prostate gland epithelial cell development") AnnotationAssertion( "biological_process") @@ -73167,7 +72655,6 @@ SubClassOf( ObjectSomeValuesFrom( (mammary gland alveolus development) AnnotationAssertion(Annotation( "GOC:dph") "The progression of the mammary gland alveolus over time, from its formation to its mature state. The mammary gland alveolus is a sac-like structure that is found in the mature gland.") -AnnotationAssertion( "dph") AnnotationAssertion( "2009-06-22T10:52:12Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0060749") @@ -73180,7 +72667,6 @@ SubClassOf( ObjectSomeValuesFrom( (regulation of mast cell chemotaxis) AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:tb") "Any process that modulates the rate, frequency or extent of mast cell chemotaxis. Mast cell chemotaxis is the movement of a mast cell in response to an external stimulus.") -AnnotationAssertion( "dph") AnnotationAssertion( "2009-06-22T02:36:06Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0060753") @@ -73190,7 +72676,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of mast cell chemotaxis) AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:tb") "Any process that increases the rate, frequency or extent of mast cell chemotaxis. Mast cell chemotaxis is the movement of a mast cell in response to an external stimulus.") -AnnotationAssertion( "dph") AnnotationAssertion( "2009-06-22T02:38:19Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0060754") @@ -73200,7 +72685,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of mast cell chemotaxis) AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:tb") "Any process that decreases the rate, frequency or extent of mast cell chemotaxis. Mast cell chemotaxis is the movement of a mast cell in response to an external stimulus.") -AnnotationAssertion( "dph") AnnotationAssertion( "2009-06-22T02:40:58Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0060755") @@ -73210,7 +72694,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of response to cytokine stimulus) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:dph") Annotation( "GOC:tb") "Any process that modulates the rate, frequency, or extent of a response to cytokine stimulus.") -AnnotationAssertion( "dph") AnnotationAssertion( "2009-06-22T02:56:12Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0060759") @@ -73220,7 +72703,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of response to cytokine stimulus) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:dph") Annotation( "GOC:tb") "Any process that increases the rate, frequency, or extent of a response to cytokine stimulus.") -AnnotationAssertion( "dph") AnnotationAssertion( "2009-06-22T02:58:04Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0060760") @@ -73230,7 +72712,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of response to cytokine stimulus) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:dph") Annotation( "GOC:tb") "Any process that decreases the rate, frequency, or extent of a response to cytokine stimulus.") -AnnotationAssertion( "dph") AnnotationAssertion( "2009-06-22T02:59:57Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0060761") @@ -73240,7 +72721,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of branching involved in mammary gland duct morphogenesis) AnnotationAssertion(Annotation( "GOC:dph") "Any process that modulates the rate, frequency, or extent of branching involved in mammary gland duct morphogenesis.") -AnnotationAssertion( "dph") AnnotationAssertion( "2009-06-22T05:20:33Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0060762") @@ -73251,7 +72731,6 @@ SubClassOf( (cell-cell signaling involved in mammary gland development) AnnotationAssertion(Annotation( "GOC:dph") "Any process that mediates the transfer of information from one cell to another and contributes to the progression of the mammary gland, from its initial state to the mature structure.") -AnnotationAssertion( "dph") AnnotationAssertion( "2009-07-06T09:24:53Z") AnnotationAssertion(Annotation( "GOC:mah") "cell-cell signalling involved in mammary gland development") AnnotationAssertion( "biological_process") @@ -73263,7 +72742,6 @@ SubClassOf( (epithelial cell proliferation involved in prostate gland development) AnnotationAssertion(Annotation( "GOC:dph") "The multiplication or reproduction of epithelial cells, resulting in the expansion of a cell population that contributes to the progression of the prostate gland over time.") -AnnotationAssertion( "dph") AnnotationAssertion( "2009-07-08T07:32:34Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0060767") @@ -73273,7 +72751,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of epithelial cell proliferation involved in prostate gland development) AnnotationAssertion(Annotation( "GOC:dph") "Any process that modulates the rate, frequency or extent of epithelial cell proliferation that contributes to the progression of the prostate gland over time.") -AnnotationAssertion( "dph") AnnotationAssertion( "2009-07-08T07:34:56Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0060768") @@ -73283,7 +72760,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of epithelial cell proliferation involved in prostate gland development) AnnotationAssertion(Annotation( "GOC:dph") "Any process that increases the rate, frequency or extent of epithelial cell proliferation that contributes to the progression of the prostate gland over time.") -AnnotationAssertion( "dph") AnnotationAssertion( "2009-07-08T07:38:02Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0060769") @@ -73295,7 +72771,6 @@ SubClassOf( ObjectSomeValuesFrom( (negative regulation of epithelial cell proliferation involved in prostate gland development) AnnotationAssertion(Annotation( "GOC:dph") "Any process that decreases the rate, frequency or extent of epithelial cell proliferation that contributes to the progression of the prostate gland over time.") -AnnotationAssertion( "dph") AnnotationAssertion( "2009-07-08T07:40:27Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0060770") @@ -73308,7 +72783,6 @@ SubClassOf( ObjectSomeValuesFrom( (mesenchymal cell proliferation involved in prostate gland development) AnnotationAssertion(Annotation( "GOC:dph") Annotation( "PMID:12221011") "The multiplication or reproduction of mesenchymal cells, resulting in the expansion of a cell population that contributes to the progression of the prostate gland over time.") -AnnotationAssertion( "dph") AnnotationAssertion( "2009-07-28T11:50:56Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0060781") @@ -73318,7 +72792,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of mesenchymal cell proliferation involved in prostate gland development) AnnotationAssertion(Annotation( "GOC:dph") Annotation( "PMID:12221011") "Any process that modulates the frequency, rate or extent of mesenchymal cell proliferation that contributes to the progression of the prostate gland over time. A mesenchymal cell is a cell that normally gives rise to other cells that are organized as three-dimensional masses, rather than sheets.") -AnnotationAssertion( "dph") AnnotationAssertion( "2009-07-28T11:54:20Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0060782") @@ -73328,7 +72801,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of cell proliferation involved in tissue homeostasis) AnnotationAssertion(Annotation( "GOC:dph") "Any process that modulates the frequency, rate or extent of cell proliferation resulting in the maintenance of a steady-state number of cells within a tissue.") -AnnotationAssertion( "dph") AnnotationAssertion( "2009-07-31T01:46:28Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0060784") @@ -73339,7 +72811,6 @@ SubClassOf( ObjectSomeValuesFrom( (regulation of apoptosis involved in tissue homeostasis) AnnotationAssertion(Annotation( "GOC:dph") "Any process that modulates the occurrence or rate of cell death by apoptosis that results in the maintenance of the steady-state number of cells within a tissue.") -AnnotationAssertion( "dph") AnnotationAssertion( "2009-07-31T01:49:54Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0060785") @@ -73350,7 +72821,6 @@ SubClassOf( ObjectSomeValuesFrom( (regulation of cell differentiation involved in tissue homeostasis) AnnotationAssertion(Annotation( "GOC:dph") "Any process that modulates the frequency, rate or extent of cell differentiation that contributes to the maintenance of a steady state of a cell type within a tissue.") -AnnotationAssertion( "dph") AnnotationAssertion( "2009-07-31T01:55:19Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0060786") @@ -73361,7 +72831,6 @@ SubClassOf( ObjectSomeValuesFrom( (ectodermal placode formation) AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:sdb_2009") Annotation( "GOC:tb") "The developmental process in which an ectodermal placode forms. An ectodermal placode is a thickening of the ectoderm that is the primordium of many structures derived from the ectoderm.") -AnnotationAssertion( "dph") AnnotationAssertion( "2009-08-04T12:15:57Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0060788") @@ -73374,7 +72843,6 @@ SubClassOf( ObjectSomeValuesFrom( (hair follicle placode formation) AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:sdb_2009") Annotation( "GOC:tb") "The developmental process in which a hair placode forms. An hair follicle placode is a thickening of the ectoderm that will give rise to the hair follicle bud.") -AnnotationAssertion( "dph") AnnotationAssertion( "2009-08-04T12:18:26Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0060789") @@ -73386,7 +72854,6 @@ SubClassOf( ObjectSomeValuesFrom( (tooth placode formation) AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:sdb_2009") Annotation( "GOC:tb") "The developmental process in which the tooth placode forms. A tooth placode is a thickening of the ectoderm that will give rise to the tooth bud.") -AnnotationAssertion( "dph") AnnotationAssertion( "2009-08-04T12:21:47Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0060790") @@ -73398,7 +72865,6 @@ SubClassOf( ObjectSomeValuesFrom( (sebaceous gland placode formation) AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:sdb_2009") Annotation( "GOC:tb") "The developmental process in which a sebaceous gland placode forms. A sebaceous gland placode is a thickening of the ectoderm that will give rise to the sebaceous gland bud.") -AnnotationAssertion( "dph") AnnotationAssertion( "2009-08-04T12:23:09Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0060791") @@ -73410,7 +72876,6 @@ SubClassOf( ObjectSomeValuesFrom( (sweat gland development) AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:sdb_2009") Annotation( "GOC:tb") "The progression of the sweat gland over time, from its formation to the mature structure. Sweat glands secrete an aqueous solution that is used in thermoregulation.") -AnnotationAssertion( "dph") AnnotationAssertion( "2009-08-04T12:35:12Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0060792") @@ -73421,7 +72886,6 @@ SubClassOf( (sweat gland placode formation) AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:sdb_2009") Annotation( "GOC:tb") "The developmental process in which the sweat gland placode forms. An sweat gland placode is a thickening of the ectoderm that will give rise to the sweat gland bud.") -AnnotationAssertion( "dph") AnnotationAssertion( "2009-08-04T12:38:10Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0060793") @@ -73433,7 +72897,6 @@ SubClassOf( ObjectSomeValuesFrom( (cell fate commitment involved in formation of primary germ layer) AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:sdb_2009") Annotation( "GOC:tb") "The commitment of cells to specific cell fates of the endoderm, ectoderm, or mesoderm as a part of gastrulation.") -AnnotationAssertion( "dph") AnnotationAssertion( "2009-08-04T03:11:22Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0060795") @@ -73443,7 +72906,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of cell differentiation involved in embryonic placenta development) AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:sdb_2009") Annotation( "GOC:tb") "Any process that modulates the rate, frequency or extent of cell differentiation that contributes to the progression of the placenta over time, from its initial condition to its mature state.") -AnnotationAssertion( "dph") AnnotationAssertion( "2009-08-06T01:20:25Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0060800") @@ -73453,7 +72915,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of cell differentiation involved in embryonic placenta development) AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:sdb_2009") Annotation( "GOC:tb") "Any process that decreases the rate, frequency or extent of cell differentiation that contributes to the progression of the placenta over time, from its initial condition to its mature state.") -AnnotationAssertion( "dph") AnnotationAssertion( "2009-08-06T02:02:18Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0060806") @@ -73463,7 +72924,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of translation involved in anterior/posterior axis specification) AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:sdb_2009") Annotation( "GOC:tb") "Any process that modulates the frequency, rate or extent of translation of mRNAs that contribute to the specification of the anterior/posterior axis.") -AnnotationAssertion( "dph") AnnotationAssertion( "2009-08-07T10:02:31Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0060815") @@ -73473,7 +72933,6 @@ EquivalentClasses( ObjectIntersection # Class: (lymphatic endothelial cell differentiation) AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:sdb_2009") Annotation( "GOC:tb") "The process in which a venous blood vessel endothelial cell acquires specialized features of a lymphatic vessel endothelial cell, a thin flattened cell that lines the inside surfaces of lymph vessels.") -AnnotationAssertion( "dph") AnnotationAssertion( "2009-08-11T03:45:20Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0060836") @@ -73485,7 +72944,6 @@ SubClassOf( ObjectSomeValuesFrom( (blood vessel endothelial cell differentiation) AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:sdb_2009") Annotation( "GOC:tb") "The process in which a relatively unspecialized cell acquires specialized features of a blood vessel endothelial cell, a thin flattened cell that lines the inside surfaces of blood vessels.") -AnnotationAssertion( "dph") AnnotationAssertion( "2009-08-11T03:47:36Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0060837") @@ -73497,7 +72955,6 @@ SubClassOf( ObjectSomeValuesFrom( (artery development) AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:sdb_2009") Annotation( "GOC:tb") "The progression of the artery over time, from its initial formation to the mature structure. An artery is a blood vessel that carries blood away from the heart to a capillary bed.") -AnnotationAssertion( "dph") AnnotationAssertion( "2009-08-12T10:10:51Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0060840") @@ -73508,7 +72965,6 @@ SubClassOf( (venous blood vessel development) AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:sdb_2009") Annotation( "GOC:tb") "The progression of the venous blood vessel over time from its initial formation to the mature structure. Venous blood vessels carry blood back to the heart after the capillary bed.") -AnnotationAssertion( "dph") AnnotationAssertion( "2009-08-12T10:14:07Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0060841") @@ -73519,7 +72975,6 @@ SubClassOf( (arterial endothelial cell differentiation) AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:sdb_2009") Annotation( "GOC:tb") "The process in which a relatively unspecialized endothelial cell acquires specialized features of an arterial endothelial cell, a thin flattened cell that lines the inside surfaces of arteries.") -AnnotationAssertion( "dph") AnnotationAssertion( "2009-08-12T10:41:34Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0060842") @@ -73530,7 +72985,6 @@ SubClassOf( (venous endothelial cell differentiation) AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:sdb_2009") Annotation( "GOC:tb") "The process in which a relatively unspecialized endothelial cell acquires specialized features of a venous endothelial cell, a thin flattened cell that lines the inside surfaces of veins.") -AnnotationAssertion( "dph") AnnotationAssertion( "2009-08-12T10:43:40Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0060843") @@ -73541,7 +72995,6 @@ SubClassOf( (branching involved in lymph vessel morphogenesis) AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:sdb_2009") Annotation( "GOC:tb") "The process of the coordinated growth and sprouting of lymph vessels giving rise to the organized lymphatic system.") -AnnotationAssertion( "dph") AnnotationAssertion( "2009-08-12T12:00:48Z") AnnotationAssertion(Annotation( "GOC:dph") "patterning of lymph vessels") AnnotationAssertion( "biological_process") @@ -73554,7 +73007,6 @@ SubClassOf( ObjectSomeValuesFrom( (semicircular canal development) AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:sdb_2009") Annotation( "GOC:tb") "The progression of the semicircular canal from its initial formation to the mature structure.") -AnnotationAssertion( "dph") AnnotationAssertion( "2009-08-13T09:36:37Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0060872") @@ -73566,7 +73018,6 @@ SubClassOf( ObjectSomeValuesFrom( (semicircular canal formation) AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:sdb_2009") Annotation( "GOC:tb") "The developmental process pertaining to the initial formation of the semicircular canal from the otic vesicle. This process begins with the regionalization of the vesicle that specifies the area where the vesicles will form and continues through the process of fusion which forms the initial tubes.") -AnnotationAssertion( "dph") AnnotationAssertion( "2009-08-13T09:45:07Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0060876") @@ -73579,7 +73030,6 @@ SubClassOf( ObjectSomeValuesFrom( (regionalization involved in semicircular canal formation) AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:sdb_2009") Annotation( "GOC:tb") "The pattern specification process that results in the subdivision of the otic epithelium in space to define an area or volume in which cells will differentiate to give rise to the semicircular canals.") -AnnotationAssertion( "dph") AnnotationAssertion( "2009-08-13T09:56:45Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0060877") @@ -73589,7 +73039,6 @@ EquivalentClasses( ObjectIntersection # Class: (pouch outgrowth involved in semicircular canal formation) AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:sdb_2009") Annotation( "GOC:tb") "The morphogenetic process in which an epithelial sheet bends along a linear axis and gives rise to a pouch that will form a semicircular canal.") -AnnotationAssertion( "dph") AnnotationAssertion( "2009-08-13T10:01:01Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0060878") @@ -73601,7 +73050,6 @@ SubClassOf( (limb epidermis development) AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:sdb_2009") Annotation( "GOC:tb") "The process whose specific outcome is the progression of the epidermis of the limb over time, from its formation to the mature structure. The limb epidermis is the outer epithelial layer of the limb, it is a complex stratified squamous epithelium.") -AnnotationAssertion( "dph") AnnotationAssertion( "2009-08-13T12:39:39Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0060887") @@ -73612,7 +73060,6 @@ SubClassOf( ObjectSomeValuesFrom( (neural plate pattern specification) AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:sdb_2009") Annotation( "GOC:tb") "The developmental process that results in the creation of defined areas or spaces within the neural plate to which cells respond and eventually are instructed to differentiate.") -AnnotationAssertion( "dph") AnnotationAssertion( "2009-08-13T02:06:27Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0060896") @@ -73622,7 +73069,6 @@ SubClassOf( (neural plate regionalization) AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:sdb_2009") Annotation( "GOC:tb") "The pattern specification process that results in the subdivision of an axis or axes of the neural plate in space to define an area or volume in which specific patterns of cell differentiation will take place or in which cells interpret a specific environment.") -AnnotationAssertion( "dph") AnnotationAssertion( "2009-08-13T02:09:04Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0060897") @@ -73633,7 +73079,6 @@ SubClassOf( (embryonic camera-type eye formation) AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:sdb_2009") Annotation( "GOC:tb") "The developmental process pertaining to the initial formation of a camera-type eye from unspecified neurectoderm. This process begins with the differentiation of cells that form the optic field and ends when the optic cup has attained its shape.") -AnnotationAssertion( "dph") AnnotationAssertion( "2009-08-13T02:26:54Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0060900") @@ -73645,7 +73090,6 @@ SubClassOf( ObjectSomeValuesFrom( (positive regulation of macrophage cytokine production) AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:tb") "Any process that increases the rate, frequency or extent of macrophage cytokine production. Macrophage cytokine production is the appearance of a chemokine due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.") -AnnotationAssertion( "dph") AnnotationAssertion( "2009-09-04T02:32:18Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0060907") @@ -73655,7 +73099,6 @@ EquivalentClasses( ObjectIntersection # Class: (heart formation) AnnotationAssertion(Annotation( "GOC:mtg_heart") "The developmental process pertaining to the initial formation of the heart from unspecified parts. This process begins with the specific processes that contribute to the appearance of the heart field and the arrival of cardiac neural crest to the heart region. The process ends when the structural rudiment is recognizable.") -AnnotationAssertion( "dph") AnnotationAssertion( "2009-09-17T09:02:13Z") AnnotationAssertion( "biological_process") AnnotationAssertion(Annotation( "GOC:mtg_heart") "cardiogenesis") @@ -73668,7 +73111,6 @@ SubClassOf( ObjectSomeValuesFrom( (mesenchymal cell differentiation involved in lung development) AnnotationAssertion(Annotation( "GOC:dph") "The process in which a relatively unspecialized cell acquires specialized features of a mesenchymal cell of the lung. A mesenchymal cell is a loosely associated cell that is part of the connective tissue in an organism. Mesenchymal cells give rise to more mature connective tissue cell types.") -AnnotationAssertion( "dph") AnnotationAssertion( "2009-09-18T11:45:33Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0060915") @@ -73678,7 +73120,6 @@ EquivalentClasses( ObjectIntersection # Class: (mesenchymal cell proliferation involved in lung development) AnnotationAssertion(Annotation( "GOC:dph") "The multiplication or reproduction of cells, resulting in the expansion of a mesenchymal cell population that contributes to the progression of the lung over time. A mesenchymal cell is a cell that normally gives rise to other cells that are organized as three-dimensional masses, rather than sheets.") -AnnotationAssertion( "dph") AnnotationAssertion( "2009-09-18T11:50:17Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0060916") @@ -73688,7 +73129,6 @@ EquivalentClasses( ObjectIntersection # Class: (cardiac pacemaker cell differentiation) AnnotationAssertion(Annotation( "GOC:mtg_cardiac_conduct_nov11") Annotation( "GOC:mtg_heart") "The process in which a relatively unspecialized cell acquires specialized features of a pacemaker cell. Pacemaker cells are specialized cardiomyocytes that are responsible for regulating the timing of heart contractions.") -AnnotationAssertion( "dph") AnnotationAssertion( "2009-09-29T11:01:31Z") AnnotationAssertion( "pacemaker cell differentiation") AnnotationAssertion( "biological_process") @@ -73700,7 +73140,6 @@ SubClassOf( (sinoatrial node cell differentiation) AnnotationAssertion(Annotation( "GOC:mtg_heart") "The process in which a relatively unspecialized cell acquires specialized features of a sinoatrial (SA) node cell. SA node cells are pacemaker cells that are found in the sinoatrial node.") -AnnotationAssertion( "dph") AnnotationAssertion( "2009-09-29T11:03:30Z") AnnotationAssertion(Annotation( "GOC:mtg_heart") "SA node cell differentiation") AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:mtg_cardiac_conduct_nov11") "SAN cell differentiation") @@ -73715,7 +73154,6 @@ SubClassOf( ObjectSomeValuesFrom( (atrioventricular node cell differentiation) AnnotationAssertion(Annotation( "GOC:mtg_heart") "The process in which a relatively unspecialized cell acquires specialized features of an atrioventricular (AV) node cell. AV node cells are pacemaker cells that are found in the atrioventricular node.") -AnnotationAssertion( "dph") AnnotationAssertion( "2009-09-29T11:07:06Z") AnnotationAssertion( "biological_process") AnnotationAssertion(Annotation( "GOC:mtg_heart") "AV node cell differentiation") @@ -73728,7 +73166,6 @@ SubClassOf( ObjectSomeValuesFrom( (cardiac pacemaker cell development) AnnotationAssertion(Annotation( "GOC:mtg_cardiac_conduct_nov11") Annotation( "GOC:mtg_heart") "The process whose specific outcome is the progression of a pacemaker cell over time, from its formation to the mature state. Pacemaker cells are specialized cardiomyocytes that are responsible for regulating the timing of heart contractions.") -AnnotationAssertion( "dph") AnnotationAssertion( "2009-09-29T11:51:55Z") AnnotationAssertion( "pacemaker cell development") AnnotationAssertion( "biological_process") @@ -73741,7 +73178,6 @@ SubClassOf( ObjectSomeValuesFrom( (atrioventricular node cell development) AnnotationAssertion(Annotation( "GOC:mtg_heart") "The process whose specific outcome is the progression of an atrioventricular (AV) node cell over time, from its formation to the mature state.") -AnnotationAssertion( "dph") AnnotationAssertion( "2009-09-29T11:59:26Z") AnnotationAssertion(Annotation( "GOC:mtg_heart") "AV node cell development") AnnotationAssertion( "biological_process") @@ -73754,7 +73190,6 @@ SubClassOf( ObjectSomeValuesFrom( (sinoatrial node cell development) AnnotationAssertion(Annotation( "GOC:mtg_heart") "The process whose specific outcome is the progression of a sinoatrial (SA) node cell over time, from its formation to the mature state. SA node cells are pacemaker cells that are found in the sinoatrial node.") -AnnotationAssertion( "dph") AnnotationAssertion( "2009-09-29T12:05:47Z") AnnotationAssertion(Annotation( "GOC:mtg_heart") "SA node cell development") AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:mtg_cardiac_conduct_nov11") "SAN cell development") @@ -73769,7 +73204,6 @@ SubClassOf( ObjectSomeValuesFrom( (His-Purkinje system cell differentiation) AnnotationAssertion(Annotation( "GOC:mtg_heart") "The process in which a relatively unspecialized cell acquires the specialized structural and/or functional features of a cell of the His-Purkinje system. These cells form the fibers regulate cardiac muscle contraction in the ventricles.") -AnnotationAssertion( "dph") AnnotationAssertion( "2009-09-29T01:10:32Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0060932") @@ -73781,7 +73215,6 @@ SubClassOf( ObjectSomeValuesFrom( (His-Purkinje system cell development) AnnotationAssertion(Annotation( "GOC:mtg_heart") "The process whose specific outcome is the progression of a His-Purkinje cell over time, from its formation to the mature state. These cells form the fibers that regulate cardiac muscle contraction in the ventricles.") -AnnotationAssertion( "dph") AnnotationAssertion( "2009-09-29T01:15:02Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0060933") @@ -73793,7 +73226,6 @@ SubClassOf( ObjectSomeValuesFrom( (cardiac fibroblast cell differentiation) AnnotationAssertion(Annotation( "GOC:mtg_heart") "The process in which a relatively unspecialized cell acquires the specialized structural and/or functional features of a cardiac fibroblast. A cardiac fibroblast is a connective tissue cell in the heart which secretes an extracellular matrix rich in collagen and other macromolecules.") -AnnotationAssertion( "dph") AnnotationAssertion( "2009-09-29T01:20:04Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0060935") @@ -73804,7 +73236,6 @@ SubClassOf( (cardiac fibroblast cell development) AnnotationAssertion(Annotation( "GOC:mtg_heart") "The process whose specific outcome is the progression of a cardiac fibroblast over time, from its formation to the mature state. A cardiac fibroblast is a connective tissue cell of the heart which secretes an extracellular matrix rich in collagen and other macromolecules.") -AnnotationAssertion( "dph") AnnotationAssertion( "2009-09-29T01:23:03Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0060936") @@ -73816,7 +73247,6 @@ SubClassOf( ObjectSomeValuesFrom( (cardiac neuron differentiation) AnnotationAssertion(Annotation( "GOC:mtg_heart") "The process in which a relatively unspecialized cell acquires specialized features of a neuron of the heart.") -AnnotationAssertion( "dph") AnnotationAssertion( "2009-09-29T02:45:33Z") AnnotationAssertion(Annotation( "GOC:mtg_heart") "heart neuron differentiation") AnnotationAssertion( "biological_process") @@ -73830,7 +73260,6 @@ SubClassOf( ObjectSomeValuesFrom( (cardiac blood vessel endothelial cell differentiation) AnnotationAssertion(Annotation( "GOC:mtg_heart") "The process in which a relatively unspecialized cell acquires specialized features of a blood vessel endothelial cell of the heart. Blood vessel endothelial cells are thin flattened cells that line the inside surfaces of blood vessels.") -AnnotationAssertion( "dph") AnnotationAssertion( "2009-09-29T02:48:55Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0060946") @@ -73842,7 +73271,6 @@ SubClassOf( (cardiac glial cell differentiation) AnnotationAssertion(Annotation( "GOC:mtg_heart") "The process in which a relatively unspecialized cell acquires the specialized features of a glial cell of the heart.") -AnnotationAssertion( "dph") AnnotationAssertion( "2009-09-29T03:06:37Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0060950") @@ -73854,7 +73282,6 @@ SubClassOf( (cardiac glial cell development) AnnotationAssertion(Annotation( "GOC:mtg_heart") "The process aimed at the progression of a cardiac glial cell over time, from its formation to the fully functional mature cell.") -AnnotationAssertion( "dph") AnnotationAssertion( "2009-09-29T03:09:24Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0060952") @@ -73867,7 +73294,6 @@ SubClassOf( ObjectSomeValuesFrom( (endocardial cell differentiation) AnnotationAssertion(Annotation( "GOC:mtg_heart") "The process in which a relatively unspecialized cell acquires the specialized structural and/or functional features of an endocardial cell. An endocardial cell is a specialized endothelial cell that makes up the endocardium portion of the heart. The endocardium is the innermost layer of tissue of the heart, and lines the heart chambers.") -AnnotationAssertion( "dph") AnnotationAssertion( "2009-09-29T03:20:39Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0060956") @@ -73880,7 +73306,6 @@ SubClassOf( ObjectSomeValuesFrom( (endocardial cell development) AnnotationAssertion(Annotation( "GOC:mtg_heart") "The progression of an endocardial cell over time, from its formation to the mature cell. An endocardial cell is a specialized endothelial cell that makes up the endocardium portion of the heart.") -AnnotationAssertion( "dph") AnnotationAssertion( "2009-09-29T03:26:59Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0060958") @@ -73892,7 +73317,6 @@ SubClassOf( ObjectSomeValuesFrom( (cardiac neuron development) AnnotationAssertion(Annotation( "GOC:mtg_heart") "The process whose specific outcome is the progression of a cardiac neuron over time, from its formation to the mature state.") -AnnotationAssertion( "dph") AnnotationAssertion( "2009-09-30T10:14:56Z") AnnotationAssertion(Annotation( "GOC:mtg_heart") "heart neuron development") AnnotationAssertion( "biological_process") @@ -73906,7 +73330,6 @@ SubClassOf( ObjectSomeValuesFrom( (cell migration involved in heart development) AnnotationAssertion(Annotation( "GOC:mtg_heart") "The orderly movement of a cell from one site to another that will contribute to the progression of the heart over time, from its initial formation, to the mature organ.") -AnnotationAssertion( "dph") AnnotationAssertion( "2009-10-06T10:53:49Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0060973") @@ -73916,7 +73339,6 @@ EquivalentClasses( ObjectIntersection # Class: (cell migration involved in heart formation) AnnotationAssertion(Annotation( "GOC:mtg_heart") "The orderly movement of a cell from one site to another that contribute to the formation of the heart. The initial heart structure is made up of mesoderm-derived heart progenitor cells and neural crest-derived cells.") -AnnotationAssertion( "dph") AnnotationAssertion( "2009-10-06T10:56:33Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0060974") @@ -73926,7 +73348,6 @@ EquivalentClasses( ObjectIntersection # Class: (coronary vasculature development) AnnotationAssertion(Annotation( "GOC:mtg_heart") "The process whose specific outcome is the progression of the blood vessels of the heart over time, from its formation to the mature structure.") -AnnotationAssertion( "dph") AnnotationAssertion( "2009-10-06T12:15:23Z") AnnotationAssertion(Annotation( "GOC:mtg_heart") "cardiac blood vessel development") AnnotationAssertion(Annotation( "GOC:mtg_heart") "cardiac vasculature development") @@ -73943,7 +73364,6 @@ SubClassOf( ObjectSomeValuesFrom( (coronary vasculature morphogenesis) AnnotationAssertion(Annotation( "GOC:mtg_heart") "The process in which the anatomical structures of blood vessels of the heart are generated and organized. The blood vessel is the vasculature carrying blood.") -AnnotationAssertion( "dph") AnnotationAssertion( "2009-10-06T12:28:23Z") AnnotationAssertion(Annotation( "GOC:mtg_heart") "cardiac blood vessel morphogenesis") AnnotationAssertion(Annotation( "GOC:mtg_heart") "cardiac vasculature morphogenesis") @@ -73960,7 +73380,6 @@ SubClassOf( ObjectSomeValuesFrom( (angiogenesis involved in coronary vascular morphogenesis) AnnotationAssertion(Annotation( "GOC:mtg_heart") "Blood vessel formation in the heart when new vessels emerge from the proliferation of pre-existing blood vessels.") -AnnotationAssertion( "dph") AnnotationAssertion( "2009-10-06T02:02:12Z") AnnotationAssertion(Annotation( "GOC:mtg_heart") "angiogenesis involved in cardiac vascular morphogenesis") AnnotationAssertion(Annotation( "GOC:mtg_heart") "angiogenesis involved in heart vascular morphogenesis") @@ -73975,7 +73394,6 @@ SubClassOf( ObjectSomeValuesFrom( (vasculogenesis involved in coronary vascular morphogenesis) AnnotationAssertion(Annotation( "GOC:mtg_heart") "The differentiation of endothelial cells from progenitor cells that contributes to blood vessel development in the heart, and the de novo formation of blood vessels and tubes.") -AnnotationAssertion( "dph") AnnotationAssertion( "2009-10-06T02:19:42Z") AnnotationAssertion(Annotation( "GOC:mtg_heart") "coronary vasculogenesis") AnnotationAssertion(Annotation( "GOC:mtg_heart") "vasculogenesis involved in coronary blood vessel morphogenesis") @@ -73987,7 +73405,6 @@ EquivalentClasses( ObjectIntersection # Class: (cell migration involved in coronary vasculogenesis) AnnotationAssertion(Annotation( "GOC:mtg_heart") "The orderly movement of a cell from one site to another that will contribute to the differentiation of an endothelial cell that will form the blood vessels of the heart.") -AnnotationAssertion( "dph") AnnotationAssertion( "2009-10-06T02:33:06Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0060980") @@ -73997,7 +73414,6 @@ EquivalentClasses( ObjectIntersection # Class: (cell migration involved in coronary angiogenesis) AnnotationAssertion(Annotation( "GOC:mtg_heart") "The orderly movement of a cell from one site to another that will contribute to the formation of new blood vessels in the heart from pre-existing blood vessels.") -AnnotationAssertion( "dph") AnnotationAssertion( "2009-10-06T02:49:12Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0060981") @@ -74007,7 +73423,6 @@ EquivalentClasses( ObjectIntersection # Class: (coronary artery morphogenesis) AnnotationAssertion(Annotation( "GOC:mtg_heart") "The process in which the anatomical structures of coronary arteries are generated and organized. Coronary arteries are blood vessels that transport blood to the heart muscle.") -AnnotationAssertion( "dph") AnnotationAssertion( "2009-10-06T02:58:52Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0060982") @@ -74019,7 +73434,6 @@ SubClassOf( (endocrine hormone secretion) AnnotationAssertion(Annotation( "GOC:dph") "The regulated release of a hormone into the circulatory system.") -AnnotationAssertion( "dph") AnnotationAssertion( "2010-01-11T09:03:48Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0060986") @@ -74030,7 +73444,6 @@ SubClassOf( ObjectSomeValuesFrom( (kidney morphogenesis) AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:mtg_kidney_jan10") "Morphogenesis of a kidney. A kidney is an organ that filters the blood and excretes the end products of body metabolism in the form of urine.") -AnnotationAssertion( "dph") AnnotationAssertion( "2010-01-19T08:16:55Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0060993") @@ -74042,7 +73455,6 @@ SubClassOf( ObjectSomeValuesFrom( (cell-cell signaling involved in kidney development) AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:mtg_kidney_jan10") "Any process that mediates the transfer of information from one cell to another and contributes to the progression of the kidney over time, from its formation to the mature organ.") -AnnotationAssertion( "dph") AnnotationAssertion( "2010-01-19T08:33:40Z") AnnotationAssertion(Annotation( "GOC:mah") "cell-cell signalling involved in kidney development") AnnotationAssertion( "biological_process") @@ -74053,7 +73465,6 @@ EquivalentClasses( ObjectIntersection # Class: (pattern specification involved in kidney development) AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:mtg_kidney_jan10") "Any developmental process that results in the creation of defined areas or spaces within the kidney to which cells respond and eventually are instructed to differentiate.") -AnnotationAssertion( "dph") AnnotationAssertion( "2010-01-21T09:05:54Z") AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "kidney pattern specification") AnnotationAssertion( "biological_process") @@ -74067,7 +73478,6 @@ SubClassOf( ObjectSomeValuesFrom( (cell differentiation involved in kidney development) AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "The process in which relatively unspecialized cells acquire specialized structural and/or functional features that characterize the cells of the kidney as it progresses from its formation to the mature state.") -AnnotationAssertion( "dph") AnnotationAssertion( "2010-01-21T09:13:55Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0061005") @@ -74077,7 +73487,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of cell proliferation involved in kidney morphogenesis) AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:mtg_kidney_jan10") "Any process that modulates the frequency, rate or extent of cell proliferation that contributes to the shaping of the kidney.") -AnnotationAssertion( "dph") AnnotationAssertion( "2010-01-21T11:25:23Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0061006") @@ -74087,7 +73496,6 @@ EquivalentClasses( ObjectIntersection # Class: (hepaticobiliary system process) AnnotationAssertion(Annotation( "GOC:dph") "An system process carried out by any of the organs or tissues of the hepaticobiliary system. The hepaticobiliary system is responsible for metabolic and catabolic processing of small molecules absorbed from the blood or gut, hormones and serum proteins, detoxification, storage of glycogen, triglycerides, metals and lipid soluble vitamins and excretion of bile. Included are the synthesis of albumin, blood coagulation factors, complement, and specific binding proteins.") -AnnotationAssertion( "dph") AnnotationAssertion( "2010-01-22T09:09:10Z") AnnotationAssertion(Annotation( "GOC:dph") "hepatobiliary system process") AnnotationAssertion( "biological_process") @@ -74099,7 +73507,6 @@ SubClassOf( (hepaticobiliary system development) AnnotationAssertion(Annotation( "GOC:dph") "The progression of the hepaticobiliary system over time, from its formation to the mature structure. The hepaticobiliary system is responsible for metabolic and catabolic processing of small molecules absorbed from the blood or gut, hormones and serum proteins, detoxification, storage of glycogen, triglycerides, metals and lipid soluble vitamins and excretion of bile. Included are the synthesis of albumin, blood coagulation factors, complement, and specific binding proteins.") -AnnotationAssertion( "dph") AnnotationAssertion( "2010-01-22T09:11:59Z") AnnotationAssertion(Annotation( "GOC:dph") "hepatobiliary system development") AnnotationAssertion( "biological_process") @@ -74111,7 +73518,6 @@ SubClassOf( (common bile duct development) AnnotationAssertion(Annotation( "PMID:20614624") "The progression of the common bile duct over time, from its formation to the mature structure. The common bile duct is formed from the joining of the common hepatic duct running from the liver, and the cystic duct running from the gallbladder. The common bile duct transports bile from the liver and gallbladder to the intestine.") -AnnotationAssertion( "dph") AnnotationAssertion( "2010-01-22T09:17:13Z") AnnotationAssertion(Annotation( "PMID:20614624") "EHBD development") AnnotationAssertion(Annotation( "PMID:20614624") "extrahepatic bile duct development") @@ -74129,7 +73535,6 @@ SubClassOf( ObjectSomeValuesFrom( (gallbladder development) AnnotationAssertion(Annotation( "GOC:dph") "The progression of the gallbladder over time, from its initial formation to the mature structure. The gallbladder is a cavitated organ that stores bile.") -AnnotationAssertion( "dph") AnnotationAssertion( "2010-01-22T09:38:44Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0061010") @@ -74142,7 +73547,6 @@ SubClassOf( ObjectSomeValuesFrom( (hepatic duct development) AnnotationAssertion(Annotation( "GOC:dph") Annotation( "PMID:20614624") "The progression of the hepatic duct over time, from its formation to the mature structure. The hepatic duct is the duct that leads from the liver to the common bile duct.") -AnnotationAssertion( "dph") AnnotationAssertion( "2010-01-22T09:44:39Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0061011") @@ -74155,7 +73559,6 @@ SubClassOf( ObjectSomeValuesFrom( (hepatoblast differentiation) AnnotationAssertion(Annotation( "GOC:dph") Annotation( "PMID:15226394") "The process in which a relatively unspecialized cell acquires specialized features of a hepatoblast. A hepatoblast is a cell that retains the ability to divide and proliferate throughout life to provide progenitor cells that can differentiate into hepatocytes and cholangiocytes.") -AnnotationAssertion( "dph") AnnotationAssertion( "2010-02-02T09:08:03Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0061017") @@ -74167,7 +73570,6 @@ SubClassOf( ObjectSomeValuesFrom( (membrane organization) AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:tb") "A process which results in the assembly, arrangement of constituent parts, or disassembly of a membrane. A membrane is a double layer of lipid molecules that encloses all cells, and, in eukaryotes, many organelles; may be a single or double lipid bilayer; also includes associated proteins.") -AnnotationAssertion( "jl") AnnotationAssertion( "2010-02-08T02:43:11Z") AnnotationAssertion( "cellular membrane organisation") AnnotationAssertion( "cellular membrane organization") @@ -74189,7 +73591,6 @@ SubClassOf( (membrane fusion) AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:tb") "The membrane organization process that joins two lipid bilayers to form a single membrane.") -AnnotationAssertion( "jl") AnnotationAssertion( "2010-02-08T02:48:06Z") AnnotationAssertion( "Wikipedia:Lipid_bilayer_fusion") AnnotationAssertion( "cellular membrane fusion") @@ -74204,7 +73605,6 @@ SubClassOf( (umbilical cord development) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:dph") "The process whose specific outcome is the development of the umbilical cord, from its formation to the mature structure. The umbilical cord is an organ or embryonic origin consisting of the 2 umbilical arteries and the one umbilical vein. The umbilical cord connects the cardiovascular system of the fetus to the mother via the placenta.") -AnnotationAssertion( "dph") AnnotationAssertion( "2010-02-09T09:09:22Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0061027") @@ -74215,7 +73615,6 @@ SubClassOf( (eyelid development in camera-type eye) AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:yaf") "The progression of the eyelid in a camera-type eye from its formation to the mature state. The eyelid is a membranous cover that helps protect and lubricate the eye.") -AnnotationAssertion( "dph") AnnotationAssertion( "2010-02-09T09:36:11Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0061029") @@ -74228,7 +73627,6 @@ SubClassOf( ObjectSomeValuesFrom( (epithelial cell differentiation involved in mammary gland alveolus development) AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:yaf") "The process in which a relatively unspecialized epithelial cell becomes a more specialized epithelial cell of the mammary gland alveolus.") -AnnotationAssertion( "dph") AnnotationAssertion( "2010-02-09T09:43:00Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0061030") @@ -74239,7 +73637,6 @@ SubClassOf( (visceral serous pericardium development) AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:yaf") "The progression of the visceral serous pericardium from its formation to the mature structure. The visceral serous pericardium is the inner layer of the pericardium.") -AnnotationAssertion( "dph") AnnotationAssertion( "2010-02-09T09:52:49Z") AnnotationAssertion(Annotation( "GOC:dph") "epicardium development") AnnotationAssertion( "biological_process") @@ -74252,7 +73649,6 @@ SubClassOf( ObjectSomeValuesFrom( (olfactory bulb mitral cell layer development) AnnotationAssertion(Annotation( "GOC:dph") "The progression of the olfactory bulb mitral cell layer over time from its initial formation until its mature state. The mitral cell layer is composed of pyramidal neurons whose cell bodies are located between the granule cell layer and the plexiform layer.") -AnnotationAssertion( "dph") AnnotationAssertion( "2010-02-09T03:30:23Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0061034") @@ -74265,7 +73661,6 @@ SubClassOf( ObjectSomeValuesFrom( (regulation of cartilage development) AnnotationAssertion(Annotation( "GOC:dph") "Any process that modulates the rate, frequency, or extent of cartilage development, the process whose specific outcome is the progression of the cartilage over time, from its formation to the mature structure. Cartilage is a connective tissue dominated by extracellular matrix containing collagen type II and large amounts of proteoglycan, particularly chondroitin sulfate.") -AnnotationAssertion( "dph") AnnotationAssertion( "2010-02-09T03:41:35Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0061035") @@ -74276,7 +73671,6 @@ SubClassOf( (positive regulation of cartilage development) AnnotationAssertion(Annotation( "GOC:dph") "Any process that increases the rate, frequency, or extent of cartilage development, the process whose specific outcome is the progression of the cartilage over time, from its formation to the mature structure. Cartilage is a connective tissue dominated by extracellular matrix containing collagen type II and large amounts of proteoglycan, particularly chondroitin sulfate.") -AnnotationAssertion( "dph") AnnotationAssertion( "2010-02-09T03:41:35Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0061036") @@ -74289,7 +73683,6 @@ SubClassOf( (negative regulation of cartilage development) AnnotationAssertion(Annotation( "GOC:dph") "Any process that decreases the rate, frequency, or extent of cartilage development, the process whose specific outcome is the progression of the cartilage over time, from its formation to the mature structure. Cartilage is a connective tissue dominated by extracellular matrix containing collagen type II and large amounts of proteoglycan, particularly chondroitin sulfate.") -AnnotationAssertion( "dph") AnnotationAssertion( "2010-02-09T03:41:35Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0061037") @@ -74302,7 +73695,6 @@ SubClassOf( (uterus morphogenesis) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:dph") "The process in which anatomical structures of the uterus are generated and organized.") -AnnotationAssertion( "dph") AnnotationAssertion( "2010-02-22T11:12:35Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0061038") @@ -74315,7 +73707,6 @@ SubClassOf( ObjectSomeValuesFrom( (female gonad morphogenesis) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:dph") "The process in which a female gonad is generated and organized.") -AnnotationAssertion( "dph") AnnotationAssertion( "2010-02-22T11:29:28Z") AnnotationAssertion( "biological_process") AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:tb") "ovary morphogenesis") @@ -74328,7 +73719,6 @@ SubClassOf( ObjectSomeValuesFrom( (regulation of wound healing) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:dph") "Any process that modulates the rate, frequency, or extent of the series of events that restore integrity to a damaged tissue, following an injury.") -AnnotationAssertion( "dph") AnnotationAssertion( "2010-02-25T10:14:37Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0061041") @@ -74339,7 +73729,6 @@ SubClassOf( (negative regulation of wound healing) AnnotationAssertion(Annotation( "GOC:dph") "Any process that decreases the rate, frequency, or extent of the series of events that restore integrity to a damaged tissue, following an injury.") -AnnotationAssertion( "dph") AnnotationAssertion( "2010-02-25T10:33:30Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0061045") @@ -74352,7 +73741,6 @@ SubClassOf( (regulation of branching involved in lung morphogenesis) AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:yaf") "Any process that modulates the rate, frequency, or extent of the process in which a highly ordered sequence of patterning events generates the branched structures of the lung, consisting of reiterated combinations of bud outgrowth, elongation, and dichotomous subdivision of terminal units.") -AnnotationAssertion( "dph") AnnotationAssertion( "2010-02-25T10:41:38Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0061046") @@ -74362,7 +73750,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of branching involved in lung morphogenesis) AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:yaf") "Any process that increases the rate, frequency, or extent of the process in which a highly ordered sequence of patterning events generates the branched structures of the lung, consisting of reiterated combinations of bud outgrowth, elongation, and dichotomous subdivision of terminal units.") -AnnotationAssertion( "dph") AnnotationAssertion( "2010-02-25T10:50:01Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0061047") @@ -74372,7 +73759,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of branching involved in lung morphogenesis) AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:yaf") "Any process that decreases the rate, frequency, or extent of the process in which a highly ordered sequence of patterning events generates the branched structures of the lung, consisting of reiterated combinations of bud outgrowth, elongation, and dichotomous subdivision of terminal units.") -AnnotationAssertion( "dph") AnnotationAssertion( "2010-02-25T10:51:31Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0061048") @@ -74382,7 +73768,6 @@ EquivalentClasses( ObjectIntersection # Class: (cell growth involved in cardiac muscle cell development) AnnotationAssertion(Annotation( "GOC:dph") "The growth of a cardiac muscle cell, where growth contributes to the progression of the cell over time from its initial formation to its mature state.") -AnnotationAssertion( "dph") AnnotationAssertion( "2010-02-25T12:56:07Z") AnnotationAssertion( "biological_process") AnnotationAssertion(Annotation( "GOC:dph") "cardiac muscle cell hypertrophy") @@ -74398,7 +73783,6 @@ SubClassOf( ObjectSomeValuesFrom( (regulation of cell growth involved in cardiac muscle cell development) AnnotationAssertion(Annotation( "GOC:dph") "Any process that modulates the rate, frequency, or extent of the growth of a cardiac muscle cell, where growth contributes to the progression of the cell over time from its initial formation to its mature state.") -AnnotationAssertion( "dph") AnnotationAssertion( "2010-02-25T01:05:16Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0061050") @@ -74409,7 +73793,6 @@ SubClassOf( ObjectSomeValuesFrom( (positive regulation of cell growth involved in cardiac muscle cell development) AnnotationAssertion(Annotation( "GOC:dph") "Any process that increases the rate, frequency, or extent of the growth of a cardiac muscle cell, where growth contributes to the progression of the cell over time from its initial formation to its mature state.") -AnnotationAssertion( "dph") AnnotationAssertion( "2010-02-25T01:08:08Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0061051") @@ -74422,7 +73805,6 @@ SubClassOf( (negative regulation of cell growth involved in cardiac muscle cell development) AnnotationAssertion(Annotation( "GOC:dph") "Any process that decreases the rate, frequency, or extent of the growth of a cardiac muscle cell, where growth contributes to the progression of the cell over time from its initial formation to its mature state.") -AnnotationAssertion( "dph") AnnotationAssertion( "2010-02-25T01:11:30Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0061052") @@ -74435,7 +73817,6 @@ SubClassOf( (somite development) AnnotationAssertion(Annotation( "GOC:dph") "The progression of a somite from its initial formation to the mature structure. Somites are mesodermal clusters that are arranged segmentally along the anterior posterior axis of an embryo.") -AnnotationAssertion( "dph") AnnotationAssertion( "2010-03-02T12:05:13Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0061053") @@ -74447,7 +73828,6 @@ SubClassOf( ObjectSomeValuesFrom( (dermatome development) AnnotationAssertion(Annotation( "GOC:dph") "The progression of the dermatome over time, from its initial formation to the mature structure. The dermatome is the portion of a somite that will form skin.") -AnnotationAssertion( "dph") AnnotationAssertion( "2010-03-02T12:07:37Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0061054") @@ -74460,7 +73840,6 @@ SubClassOf( ObjectSomeValuesFrom( (myotome development) AnnotationAssertion(Annotation( "GOC:dph") "The progression of the myotome over time, from its formation to the mature structure. The myotome is the portion of the somite that will give rise to muscle.") -AnnotationAssertion( "dph") AnnotationAssertion( "2010-03-02T12:11:01Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0061055") @@ -74473,7 +73852,6 @@ SubClassOf( ObjectSomeValuesFrom( (sclerotome development) AnnotationAssertion(Annotation( "GOC:dph") "The progression of the sclerotome over time, from its initial formation to the mature structure. The sclerotome is the portion of the somite that will give rise to a vertebra.") -AnnotationAssertion( "dph") AnnotationAssertion( "2010-03-02T12:12:40Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0061056") @@ -74485,7 +73863,6 @@ SubClassOf( ObjectSomeValuesFrom( (muscle structure development) AnnotationAssertion(Annotation( "GOC:dph") "The progression of a muscle structure over time, from its formation to its mature state. Muscle structures are contractile cells, tissues or organs that are found in multicellular organisms.") -AnnotationAssertion( "dph") AnnotationAssertion( "2010-03-09T08:55:14Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0061061") @@ -74500,7 +73877,6 @@ SubClassOf( ObjectAllValuesFrom( (urethra development) AnnotationAssertion(Annotation( "GOC:dph") "The progression of the urethra over time from its initial formation to the mature structure. The urethra is a renal system organ that carries urine from the bladder to outside the body.") -AnnotationAssertion( "dph") AnnotationAssertion( "2010-03-12T08:24:52Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0061068") @@ -74513,7 +73889,6 @@ SubClassOf( ObjectSomeValuesFrom( (male urethra development) AnnotationAssertion(Annotation( "GOC:dph") "The progression of the male urethra over time from its initial formation to the mature structure. The male urethra is a renal system organ that carries urine from the bladder through the penis to outside the body.") -AnnotationAssertion( "dph") AnnotationAssertion( "2010-03-12T08:28:19Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0061069") @@ -74524,7 +73899,6 @@ SubClassOf( (female urethra development) AnnotationAssertion(Annotation( "GOC:dph") "The progression of the female urethra over time from its initial formation to the mature structure. The female urethra is a renal system organ that carries urine from the bladder to outside the body, exiting above the vaginal opening.") -AnnotationAssertion( "dph") AnnotationAssertion( "2010-03-12T08:29:43Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0061070") @@ -74535,7 +73909,6 @@ SubClassOf( (urethra epithelium development) AnnotationAssertion(Annotation( "GOC:dph") "The progression of the urethra epithelium over time from its initial formation to the mature structure. The urethra is a renal system organ that carries urine from the bladder to outside the body. The epithelium is the tubular, planar layer of cells through which the urine passes.") -AnnotationAssertion( "dph") AnnotationAssertion( "2010-03-12T08:36:53Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0061071") @@ -74548,7 +73921,6 @@ SubClassOf( ObjectSomeValuesFrom( (iris morphogenesis) AnnotationAssertion(Annotation( "GOC:dph") "The process in which the iris is generated and organized. The iris is an anatomical structure in the eye whose opening forms the pupil. The iris is responsible for controlling the diameter and size of the pupil and the amount of light reaching the retina.") -AnnotationAssertion( "dph") AnnotationAssertion( "2010-03-16T10:48:42Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0061072") @@ -74561,7 +73933,6 @@ SubClassOf( ObjectSomeValuesFrom( (ciliary body morphogenesis) AnnotationAssertion(Annotation( "GOC:dph") "The process in which the ciliary body generated and organized. The ciliary body is the circumferential tissue inside the eye composed of the ciliary muscle and ciliary processes.") -AnnotationAssertion( "dph") AnnotationAssertion( "2010-03-16T10:55:19Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0061073") @@ -74574,7 +73945,6 @@ SubClassOf( ObjectSomeValuesFrom( (regulation of neural retina development) AnnotationAssertion(Annotation( "GOC:dph") "Any process that modulates the rate, frequency, or extent of neural retina development, the progression of the neural retina over time from its initial formation to the mature structure. The neural retina is the part of the retina that contains neurons and photoreceptor cells.") -AnnotationAssertion( "dph") AnnotationAssertion( "2010-03-16T11:47:05Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0061074") @@ -74584,7 +73954,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of neural retina development) AnnotationAssertion(Annotation( "GOC:dph") "Any process that increases the rate, frequency, or extent of neural retina development, the progression of the neural retina over time from its initial formation to the mature structure. The neural retina is the part of the retina that contains neurons and photoreceptor cells.") -AnnotationAssertion( "dph") AnnotationAssertion( "2010-03-16T11:59:48Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0061075") @@ -74595,7 +73964,6 @@ SubClassOf( ObjectSomeValuesFrom( (negative regulation of neural retina development) AnnotationAssertion(Annotation( "GOC:dph") "Any process that decreases the rate, frequency, or extent of neural retina development, the progression of the neural retina over time from its initial formation to the mature structure. The neural retina is the part of the retina that contains neurons and photoreceptor cells.") -AnnotationAssertion( "dph") AnnotationAssertion( "2010-03-16T12:46:11Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0061076") @@ -74606,7 +73974,6 @@ SubClassOf( ObjectSomeValuesFrom( (right horn of sinus venosus development) AnnotationAssertion(Annotation( "GOC:dph") "The progression of the right horn of the sinus venosus from its formation to the mature structure.") -AnnotationAssertion( "dph") AnnotationAssertion( "2010-04-08T02:45:10Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0061080") @@ -74618,7 +73985,6 @@ SubClassOf( ObjectSomeValuesFrom( (positive regulation of myeloid leukocyte cytokine production involved in immune response) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:dph") "Any process that modulates the rate, frequency, or extent of the production of a cytokine that contributes to the immune response.") -AnnotationAssertion( "dph") AnnotationAssertion( "2010-04-13T11:26:41Z") AnnotationAssertion( "biological_process") AnnotationAssertion(Annotation( "GOC:dph") "positive regulation of myeloid cell cytokine production involved in immune response") @@ -74629,7 +73995,6 @@ EquivalentClasses( ObjectIntersection # Class: (myeloid leukocyte cytokine production) AnnotationAssertion(Annotation( "GOC:dph") "Any process that contributes to cytokine production by a myeloid cell.") -AnnotationAssertion( "dph") AnnotationAssertion( "2010-04-13T11:29:42Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0061082") @@ -74641,7 +74006,6 @@ SubClassOf( (regulation of protein tyrosine kinase activity) AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:tb") "Any process that modulates the rate, frequency, or extent of protein tyrosine kinase activity.") -AnnotationAssertion( "dph") AnnotationAssertion( "2010-04-26T02:34:53Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0061097") @@ -74653,7 +74017,6 @@ SubClassOf( ObjectSomeValuesFrom( (positive regulation of protein tyrosine kinase activity) AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:tb") "Any process that increases the rate, frequency, or extent of protein tyrosine kinase activity.") -AnnotationAssertion( "dph") AnnotationAssertion( "2010-04-26T02:34:53Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0061098") @@ -74665,7 +74028,6 @@ SubClassOf( (negative regulation of protein tyrosine kinase activity) AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:tb") "Any process that decreases the rate, frequency, or extent of protein tyrosine kinase activity.") -AnnotationAssertion( "dph") AnnotationAssertion( "2010-04-26T02:34:53Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0061099") @@ -74677,7 +74039,6 @@ SubClassOf( (lung neuroendocrine cell differentiation) AnnotationAssertion(Annotation( "GOC:dph") Annotation( "PMID:9126746") "The process in which a relatively unspecialized cell acquires specialized features of a neuroendocrine cell of the lung epithelium.") -AnnotationAssertion( "dph") AnnotationAssertion( "2010-04-27T03:28:46Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0061100") @@ -74689,7 +74050,6 @@ SubClassOf( (neuroendocrine cell differentiation) AnnotationAssertion(Annotation( "GOC:dph") "The process in which a relatively unspecialized cell acquires specialized structural and/or functional features of a neuroendocrine cell. A neuroendocrine cell is a cell that receives input form a neuron which controls the secretion of an endocrine substance.") -AnnotationAssertion( "dph") AnnotationAssertion( "2010-04-28T09:42:20Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0061101") @@ -74699,7 +74059,6 @@ EquivalentClasses( ObjectIntersection # Class: (stomach neuroendocrine cell differentiation) AnnotationAssertion(Annotation( "GOC:dph") Annotation( "PMID:18173746") "The process in which a relatively unspecialized cell acquires specialized features of a neuroendocrine cell of the stomach epithelium.") -AnnotationAssertion( "dph") AnnotationAssertion( "2010-04-28T09:47:07Z") AnnotationAssertion( "biological_process") AnnotationAssertion(Annotation( "GOC:dph") "gastric neuroendocrine cell differentiation") @@ -74712,7 +74071,6 @@ SubClassOf( ObjectSomeValuesFrom( (adrenal chromaffin cell differentiation) AnnotationAssertion(Annotation( "GOC:dph") "The process in which a relatively unspecialized cell acquires specialized structural and/or functional features of an adrenal chromaffin cell. An adrenal chromaffin cell is a neuroendocrine cell that stores epinephrine secretory vesicles.") -AnnotationAssertion( "dph") AnnotationAssertion( "2010-04-29T08:27:53Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0061104") @@ -74724,7 +74082,6 @@ SubClassOf( ObjectSomeValuesFrom( (regulation of stomach neuroendocrine cell differentiation) AnnotationAssertion(Annotation( "GOC:dph") "Any process that modulates the rate, frequency or extent of the differentiation of a neuroendocrine cell in the stomach.") -AnnotationAssertion( "dph") AnnotationAssertion( "2010-04-29T12:19:37Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0061105") @@ -74734,7 +74091,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of stomach neuroendocrine cell differentiation) AnnotationAssertion(Annotation( "GOC:dph") "Any process that decreases the rate, frequency or extent of the differentiation of a neuroendocrine cell in the stomach.") -AnnotationAssertion( "dph") AnnotationAssertion( "2010-04-29T12:23:05Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0061106") @@ -74744,7 +74100,6 @@ EquivalentClasses( ObjectIntersection # Class: (seminal vesicle development) AnnotationAssertion(Annotation( "GOC:dph") "The progression of the seminal vesicle over time, from its formation to the mature structure. The seminal vesicle is a gland that contributes to the production of semen.") -AnnotationAssertion( "dph") AnnotationAssertion( "2010-04-30T10:17:30Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0061107") @@ -74756,7 +74111,6 @@ SubClassOf( (seminal vesicle epithelium development) AnnotationAssertion(Annotation( "GOC:dph") "The progression of the seminal vesicle epithelium over time, from its formation to the mature structure.") -AnnotationAssertion( "dph") AnnotationAssertion( "2010-04-30T10:19:54Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0061108") @@ -74769,7 +74123,6 @@ SubClassOf( ObjectSomeValuesFrom( (dense core granule organization) AnnotationAssertion(Annotation( "GOC:dph") "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a dense core granule. A dense core granule is a secretory organelle found in endocrine cells.") -AnnotationAssertion( "dph") AnnotationAssertion( "2010-05-01T09:34:37Z") AnnotationAssertion(Annotation( "GOC:mah") "dense core granule organisation") AnnotationAssertion( "biological_process") @@ -74781,7 +74134,6 @@ SubClassOf( (epithelial-mesenchymal cell signaling involved in lung development) AnnotationAssertion(Annotation( "GOC:dph") "Any process that results in the transfer of information from an epithelial cell to a mesenchymal cell and contributes to the progression of the lung over time from its initial formation to the mature organ.") -AnnotationAssertion( "dph") AnnotationAssertion( "2010-05-05T11:14:38Z") AnnotationAssertion(Annotation( "GOC:mah") "epithelial-mesenchymal cell signalling involved in lung development") AnnotationAssertion( "biological_process") @@ -74792,7 +74144,6 @@ EquivalentClasses( ObjectIntersection # Class: (pancreas morphogenesis) AnnotationAssertion(Annotation( "GOC:dph") "Morphogenesis of the pancreas. Morphogenesis is the process in which anatomical structures are generated and organized.") -AnnotationAssertion( "dph") AnnotationAssertion( "2010-05-05T11:55:30Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0061113") @@ -74804,7 +74155,6 @@ SubClassOf( ObjectSomeValuesFrom( (branching involved in pancreas morphogenesis) AnnotationAssertion(Annotation( "GOC:dph") "The process in which the branches of the pancreas are generated and organized.") -AnnotationAssertion( "dph") AnnotationAssertion( "2010-05-05T12:03:04Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0061114") @@ -74814,7 +74164,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of heart growth) AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:hjd") "Any process that decreases the rate or extent of heart growth. Heart growth is the increase in size or mass of the heart.") -AnnotationAssertion( "dph") AnnotationAssertion( "2010-05-17T07:31:28Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0061117") @@ -74825,7 +74174,6 @@ SubClassOf( (pancreatic bud formation) AnnotationAssertion(Annotation( "GOC:dph") "The morphogenetic process in which the foregut region specified to become the pancreas forms a bud.") -AnnotationAssertion( "dph") AnnotationAssertion( "2010-05-17T09:33:40Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0061130") @@ -74837,7 +74185,6 @@ SubClassOf( (morphogenesis of a branching epithelium) AnnotationAssertion(Annotation( "GOC:dph") "The process in which the anatomical structures of a branched epithelium are generated and organized.") -AnnotationAssertion( "dph") AnnotationAssertion( "2010-05-25T09:05:34Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0061138") @@ -74848,7 +74195,6 @@ SubClassOf( (lung secretory cell differentiation) AnnotationAssertion(Annotation( "GOC:dph") "The process in which a relatively unspecialized cell acquires specialized features of a lung secretory cell. A lung secretory cell is a specialized epithelial cell of the lung that contains large secretory granules in its apical part.") -AnnotationAssertion( "dph") AnnotationAssertion( "2010-05-25T09:28:53Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0061140") @@ -74859,7 +74205,6 @@ SubClassOf( (lung ciliated cell differentiation) AnnotationAssertion(Annotation( "GOC:cilia") Annotation( "GOC:dph") Annotation( "GOC:krc") "The process in which a relatively unspecialized cell acquires specialized features of a lung ciliated cell. A lung ciliated cell is a specialized lung epithelial cell that contains cilia for moving substances released from lung secretory cells.") -AnnotationAssertion( "dph") AnnotationAssertion( "2010-05-25T09:31:14Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0061141") @@ -74870,7 +74215,6 @@ SubClassOf( (Peyer's patch morphogenesis) AnnotationAssertion(Annotation( "GOC:dph") "The process in which a Peyer's patch is generated and organized. Peyer's patches are typically found as nodules associated with gut epithelium with distinct internal structures including B- and T-zones for the activation of lymphocytes.") -AnnotationAssertion( "dph") AnnotationAssertion( "2010-05-26T06:46:23Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0061146") @@ -74883,7 +74227,6 @@ SubClassOf( ObjectSomeValuesFrom( (endocardial endothelium development) AnnotationAssertion(Annotation( "GOC:dph") "The progression of the endocardial endothelium over time, from its initial formation to the mature structure. The endocardium is an anatomical structure comprised of an endothelium and an extracellular matrix that forms the innermost layer of tissue of the heart, and lines the heart chambers.") -AnnotationAssertion( "dph") AnnotationAssertion( "2010-06-03T09:15:31Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0061147") @@ -74895,7 +74238,6 @@ SubClassOf( ObjectSomeValuesFrom( (extracellular matrix organization involved in endocardium development) AnnotationAssertion(Annotation( "GOC:dph") "A process which results in the assembly, arrangement of constituent parts, or disassembly of an extracellular matrix of the endocardium. The endocardium is an anatomical structure comprised of an endothelium and an extracellular matrix that forms the innermost layer of tissue of the heart, and lines the heart chambers.") -AnnotationAssertion( "dph") AnnotationAssertion( "2010-06-03T09:18:02Z") AnnotationAssertion(Annotation( "GOC:mah") "extracellular matrix organisation involved in endocardium development") AnnotationAssertion( "biological_process") @@ -74906,7 +74248,6 @@ EquivalentClasses( ObjectIntersection # Class: (trachea submucosa development) AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:yaf") "The progression of the trachea submucosa over time from its formation to the mature structure. The trachea submucosa is made up of the glands and elastic tissue that lie under the mucosa in the trachea.") -AnnotationAssertion( "dph") AnnotationAssertion( "2010-06-07T09:58:40Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0061152") @@ -74918,7 +74259,6 @@ SubClassOf( ObjectSomeValuesFrom( (trachea gland development) AnnotationAssertion(Annotation( "GOC:dph") "The progression of a trachea gland over time, from its formation to the mature structure. Trachea glands are found under the mucus of the trachea and secrete mucus, and agents that help protect the lung from injury and infection.") -AnnotationAssertion( "dph") AnnotationAssertion( "2010-06-07T10:10:51Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0061153") @@ -74930,7 +74270,6 @@ SubClassOf( ObjectSomeValuesFrom( (endothelial tube morphogenesis) AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:yaf") "The process in which the anatomical structures of a tube are generated and organized from an endothelium. Endothelium refers to the layer of cells lining blood vessels, lymphatics, the heart, and serous cavities, and is derived from bone marrow or mesoderm. Corneal endothelium is a special case, derived from neural crest cells.") -AnnotationAssertion( "dph") AnnotationAssertion( "2010-06-15T09:05:00Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0061154") @@ -74942,7 +74281,6 @@ SubClassOf( (pulmonary artery endothelial tube morphogenesis) AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:yaf") "The process in which the anatomical structures of a tube are generated and organized from the pulmonary artery endothelium. An pulmonary artery endothelium is an epithelium that lines the pulmonary artery.") -AnnotationAssertion( "dph") AnnotationAssertion( "2010-06-15T09:09:04Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0061155") @@ -74954,7 +74292,6 @@ SubClassOf( ObjectSomeValuesFrom( (pulmonary artery morphogenesis) AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:yaf") "The process in which the anatomical structures of the pulmonary artery are generated and organized. The pulmonary artery is the artery that carries blood from the heart to the lungs.") -AnnotationAssertion( "dph") AnnotationAssertion( "2010-06-15T09:13:47Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0061156") @@ -74965,7 +74302,6 @@ SubClassOf( (regulation of hair follicle placode formation) AnnotationAssertion(Annotation( "GOC:dph") "Any process that modulates the rate, frequency, or extent of hair follicle placode formation, the developmental process in which a hair placode forms. An hair follicle placode is a thickening of the ectoderm that will give rise to the hair follicle bud.") -AnnotationAssertion( "dph") AnnotationAssertion( "2010-06-25T01:03:29Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0061168") @@ -74976,7 +74312,6 @@ SubClassOf( ObjectSomeValuesFrom( (positive regulation of hair placode formation) AnnotationAssertion(Annotation( "GOC:dph") "Any process that increases the rate, frequency, or extent of hair follicle placode formation, the developmental process in which a hair placode forms. An hair follicle placode is a thickening of the ectoderm that will give rise to the hair follicle bud.") -AnnotationAssertion( "dph") AnnotationAssertion( "2010-06-25T01:08:50Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0061169") @@ -74986,7 +74321,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of hair follicle placode formation) AnnotationAssertion(Annotation( "GOC:dph") "Any process that decreases the rate, frequency, or extent of hair follicle placode formation, the developmental process in which a hair placode forms. An hair follicle placode is a thickening of the ectoderm that will give rise to the hair follicle bud.") -AnnotationAssertion( "dph") AnnotationAssertion( "2010-06-25T01:10:48Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0061170") @@ -74997,7 +74331,6 @@ SubClassOf( ObjectSomeValuesFrom( (regulation of insulin secretion involved in cellular response to glucose stimulus) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:dph") "Any process that modulates the frequency, rate or extent of the regulated release of insulin that contributes to the response of a cell to glucose.") -AnnotationAssertion( "dph") AnnotationAssertion( "2010-07-13T09:38:42Z") AnnotationAssertion(Annotation( "GOC:dph") "regulation of insulin secretion in response to glucose") AnnotationAssertion( "biological_process") @@ -75009,7 +74342,6 @@ SubClassOf( ObjectSomeValuesFrom( (negative regulation of insulin secretion involved in cellular response to glucose stimulus) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:dph") "Any process that decreases the frequency, rate or extent of the regulated release of insulin that contributes to the response of a cell to glucose.") -AnnotationAssertion( "dph") AnnotationAssertion( "2010-07-13T09:41:46Z") AnnotationAssertion(Annotation( "GOC:bf") "negative regulation of insulin secretion involved in cellular response to glucose") AnnotationAssertion( "biological_process") @@ -75022,7 +74354,6 @@ SubClassOf( ObjectSomeValuesFrom( (mammary gland epithelium development) AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:yaf") "The process whose specific outcome is the progression of the mammary gland epithelium over time, from its formation to the mature structure. The mammary gland is a large compound sebaceous gland that in female mammals is modified to secrete milk.") -AnnotationAssertion( "dph") AnnotationAssertion( "2010-07-14T08:18:24Z") AnnotationAssertion(Annotation( "GOC:dph") "breast epithelium development") AnnotationAssertion( "biological_process") @@ -75035,7 +74366,6 @@ SubClassOf( ObjectSomeValuesFrom( (regulation of chondrocyte development) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:dph") "Any process that modulates the rate, frequency, or extent of the process whose specific outcome is the progression of a chondrocyte over time, from its commitment to its mature state. Chondrocyte development does not include the steps involved in committing a chondroblast to a chondrocyte fate.") -AnnotationAssertion( "dph") AnnotationAssertion( "2010-07-14T08:28:52Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0061181") @@ -75047,7 +74377,6 @@ SubClassOf( (negative regulation of chondrocyte development) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:dph") "Any process that decreases the rate, frequency, or extent of the process whose specific outcome is the progression of a chondrocyte over time, from its commitment to its mature state. Chondrocyte development does not include the steps involved in committing a chondroblast to a chondrocyte fate.") -AnnotationAssertion( "dph") AnnotationAssertion( "2010-07-14T08:33:05Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0061182") @@ -75060,7 +74389,6 @@ SubClassOf( (regulation of dermatome development) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:dph") "Any process that modulates the rate, frequency, or extent of the progression of the dermatome over time, from its initial formation to the mature structure. The dermatome is the portion of a somite that will form skin.") -AnnotationAssertion( "dph") AnnotationAssertion( "2010-07-14T08:40:26Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0061183") @@ -75070,7 +74398,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of dermatome development) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:dph") "Any process that increases the rate, frequency, or extent of the progression of the dermatome over time, from its initial formation to the mature structure. The dermatome is the portion of a somite that will form skin.") -AnnotationAssertion( "dph") AnnotationAssertion( "2010-07-14T08:42:03Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0061184") @@ -75081,7 +74408,6 @@ SubClassOf( (negative regulation of dermatome development) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:dph") "Any process that decreases the rate, frequency, or extent of the progression of the dermatome over time, from its initial formation to the mature structure. The dermatome is the portion of a somite that will form skin.") -AnnotationAssertion( "dph") AnnotationAssertion( "2010-07-14T08:43:08Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0061185") @@ -75092,7 +74418,6 @@ SubClassOf( (positive regulation of sclerotome development) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:dph") "Any process that increases the rate, frequency, or extent of the progression of the sclerotome over time, from its initial formation to the mature structure. The sclerotome is the portion of the somite that will give rise to a vertebra.") -AnnotationAssertion( "dph") AnnotationAssertion( "2010-07-14T09:17:23Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0061189") @@ -75102,7 +74427,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of sclerotome development) AnnotationAssertion(Annotation( "GOC:dph") "Any process that modulates the rate, frequency, or extent of the progression of the sclerotome over time, from its initial formation to the mature structure. The sclerotome is the portion of the somite that will give rise to a vertebra.") -AnnotationAssertion( "dph") AnnotationAssertion( "2010-07-14T09:19:47Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0061190") @@ -75112,7 +74436,6 @@ EquivalentClasses( ObjectIntersection # Class: (taste bud development) AnnotationAssertion(Annotation( "GOC:dph") "The progression of the taste bud over time, from its formation to the mature state. The taste bud is a specialized area of the tongue that contains taste receptors.") -AnnotationAssertion( "dph") AnnotationAssertion( "2010-07-27T10:55:08Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0061193") @@ -75124,7 +74447,6 @@ SubClassOf( ObjectSomeValuesFrom( (taste bud morphogenesis) AnnotationAssertion(Annotation( "GOC:dph") "The process in which the anatomical structures of the taste bud are generated and organized. The taste bud is a specialized area of the tongue that contains taste receptors.") -AnnotationAssertion( "dph") AnnotationAssertion( "2010-07-27T11:01:31Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0061194") @@ -75138,7 +74460,6 @@ SubClassOf( ObjectSomeValuesFrom( (taste bud formation) AnnotationAssertion(Annotation( "GOC:dph") "The developmental process pertaining to the initial formation of the taste bud from unspecified parts. The taste bud is a specialized area of the tongue that contains taste receptors.") -AnnotationAssertion( "dph") AnnotationAssertion( "2010-07-27T12:22:26Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0061195") @@ -75151,7 +74472,6 @@ SubClassOf( ObjectSomeValuesFrom( (paramesonephric duct development) AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:yaf") "The process whose specific outcome is the progression of the paramesonephric duct over time, from its formation to the mature structure. Mullerian ducts (or paramesonephric ducts) are paired ducts of the embryo that run down the lateral sides of the urogenital ridge and terminate at the mullerian eminence in the primitive urogenital sinus. In the female, they will develop to form the fallopian tubes, uterus, cervix, and the upper portion of the vagina; in the male, they are lost. These ducts are made of tissue of mesodermal origin.") -AnnotationAssertion( "dph") AnnotationAssertion( "2010-07-30T10:54:47Z") AnnotationAssertion(Annotation( "GOC:dph") "Mullerian duct development") AnnotationAssertion( "biological_process") @@ -75164,7 +74484,6 @@ SubClassOf( (mesonephros morphogenesis) AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "The process in which the anatomical structures of the mesonephros are generated and organized.") -AnnotationAssertion( "dph") AnnotationAssertion( "2010-08-17T03:11:10Z") AnnotationAssertion(Annotation( "GOC:dph") "Wolffian body morphogenesis") AnnotationAssertion( "biological_process") @@ -75177,7 +74496,6 @@ SubClassOf( ObjectSomeValuesFrom( (cell differentiation involved in mesonephros development) AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "The process in which relatively unspecialized cells acquire specialized structural and/or functional features that characterize the cells of the mesonephros as it progresses from its formation to the mature state.") -AnnotationAssertion( "dph") AnnotationAssertion( "2010-08-17T03:21:23Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0061208") @@ -75187,7 +74505,6 @@ EquivalentClasses( ObjectIntersection # Class: (cell proliferation involved in mesonephros development) AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "The multiplication or reproduction of cells, resulting in the expansion of the population in the mesonephros.") -AnnotationAssertion( "dph") AnnotationAssertion( "2010-08-17T03:22:46Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0061209") @@ -75197,7 +74514,6 @@ EquivalentClasses( ObjectIntersection # Class: (cell-cell signaling involved in mesonephros development) AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "Any process that mediates the transfer of information from one cell to another and contributes to the progression of the mesonephros over time, from its formation to the mature organ.") -AnnotationAssertion( "dph") AnnotationAssertion( "2010-08-17T03:24:08Z") AnnotationAssertion(Annotation( "GOC:mah") "cell-cell signalling involved in mesonephros development") AnnotationAssertion( "biological_process") @@ -75208,7 +74524,6 @@ EquivalentClasses( ObjectIntersection # Class: (mesonephric collecting duct development) AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "The process whose specific outcome is the progression of a collecting duct in the mesonephros over time, from its formation to the mature structure. The collecting duct regulates water, electrolyte and acid-base balance. The collecting duct is the final common path through which urine flows before entering the ureter and then emptying into the bladder.") -AnnotationAssertion( "dph") AnnotationAssertion( "2010-08-17T03:25:51Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0061211") @@ -75220,7 +74535,6 @@ SubClassOf( ObjectSomeValuesFrom( (mesonephric juxtaglomerular apparatus development) AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "The process whose specific outcome is the progression of the juxtaglomerular apparatus in the mesonephros over time, from its formation to the mature structure. The juxtaglomerular apparatus is an anatomical structure which consists of juxtaglomerular cells, extraglomerular mesangial cells and the macula densa. The juxtaglomerular apparatus lies adjacent to the glomerulus and regulates kidney function by maintaining the blood flow to the kidney and the filtration rate.") -AnnotationAssertion( "dph") AnnotationAssertion( "2010-08-17T03:27:36Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0061212") @@ -75232,7 +74546,6 @@ SubClassOf( ObjectSomeValuesFrom( (positive regulation of mesonephros development) AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "Any process that increases the rate, frequency or extent of mesonephros development. Mesonephros development is the process whose specific outcome is the progression of the mesonephros over time, from its formation to the mature structure. The mesonephros is an organ that filters the blood and excretes the end products of body metabolism in the form of urine.") -AnnotationAssertion( "dph") AnnotationAssertion( "2010-08-17T03:39:35Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0061213") @@ -75242,7 +74555,6 @@ EquivalentClasses( ObjectIntersection # Class: (mesonephric smooth muscle tissue development) AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "The process whose specific outcome is the progression of smooth muscle in the mesonephros over time, from its formation to the mature structure.") -AnnotationAssertion( "dph") AnnotationAssertion( "2010-08-17T03:29:54Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0061214") @@ -75254,7 +74566,6 @@ SubClassOf( ObjectSomeValuesFrom( (mesonephric nephron development) AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "The process whose specific outcome is the progression of a nephron in the mesonephros over time, from its formation to the mature structure. A nephron is the functional unit of the kidney.") -AnnotationAssertion( "dph") AnnotationAssertion( "2010-08-17T03:31:08Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0061215") @@ -75266,7 +74577,6 @@ SubClassOf( ObjectSomeValuesFrom( (regulation of mesonephros development) AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "Any process that modulates the rate, frequency or extent of mesonephros development. Mesonephros development is the process whose specific outcome is the progression of the mesonephros over time, from its formation to the mature structure. The mesonephros is an endocrine and metabolic organ that filters the blood and excretes the end products of body metabolism in the form of urine.") -AnnotationAssertion( "dph") AnnotationAssertion( "2010-08-17T03:35:31Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0061217") @@ -75276,7 +74586,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of mesonephros development) AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "Any process that decreases the rate, frequency or extent of mesonephros development. Mesonephros development is the process whose specific outcome is the progression of the mesonephros over time, from its formation to the mature structure. The mesonephros is an organ that filters the blood and excretes the end products of body metabolism in the form of urine.") -AnnotationAssertion( "dph") AnnotationAssertion( "2010-08-17T03:43:06Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0061218") @@ -75286,7 +74595,6 @@ EquivalentClasses( ObjectIntersection # Class: (mesonephric mesenchyme development) AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "The biological process whose specific outcome is the progression of a mesonephric mesenchyme from an initial condition to its mature state. This process begins with the formation of mesonephric mesenchyme and ends with the mature structure. Mesonephric mesenchyme is the tissue made up of loosely connected mesenchymal cells in the mesonephros.") -AnnotationAssertion( "dph") AnnotationAssertion( "2010-08-17T03:45:44Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0061219") @@ -75298,7 +74606,6 @@ SubClassOf( ObjectSomeValuesFrom( (mesonephric macula densa development) AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "The process whose specific outcome is the progression of the mesonephric macula densa over time, from its formation to the mature structure. The mesonephric macula densa is an area of specialized cells in the distal tubule of the mesonephros that makes contact with the vascular pole of the glomerulus.") -AnnotationAssertion( "dph") AnnotationAssertion( "2010-08-19T01:11:41Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0061220") @@ -75310,7 +74617,6 @@ SubClassOf( ObjectSomeValuesFrom( (mesonephric mesenchyme morphogenesis) AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "The process in which the anatomical structures of a mesonephric mesenchymal tissue are generated and organized. Mesonephric mesenchyme is the tissue made up of loosely connected mesenchymal cells in the mesonephros.") -AnnotationAssertion( "dph") AnnotationAssertion( "2010-08-19T01:17:38Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0061221") @@ -75322,7 +74628,6 @@ SubClassOf( ObjectSomeValuesFrom( (mesonephric glomerulus development) AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "The progression of the mesonephric glomerulus over time from its initial formation until its mature state. The mesonephric glomerulus is a capillary tuft which forms a close network with the visceral epithelium (podocytes) and the mesangium to form the filtration barrier and is surrounded by Bowman's capsule in nephrons of the mature vertebrate kidney, or mesonephros.") -AnnotationAssertion( "dph") AnnotationAssertion( "2010-08-19T01:26:00Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0061224") @@ -75334,7 +74639,6 @@ SubClassOf( ObjectSomeValuesFrom( (pattern specification involved in mesonephros development) AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "Any developmental process that results in the creation of defined areas or spaces within the mesonephros to which cells respond and eventually are instructed to differentiate.") -AnnotationAssertion( "dph") AnnotationAssertion( "2010-08-19T02:22:22Z") AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "mesonephros pattern specification") AnnotationAssertion( "biological_process") @@ -75346,7 +74650,6 @@ EquivalentClasses( ObjectIntersection # Class: (mesonephric nephron morphogenesis) AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "The process in which the anatomical structures of the mesonephric nephron are generated and organized. A mesonephric nephron is the functional unit of the mesonephros.") -AnnotationAssertion( "dph") AnnotationAssertion( "2010-08-19T02:26:24Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0061228") @@ -75359,7 +74662,6 @@ SubClassOf( ObjectSomeValuesFrom( (mesonephric glomerulus vasculature development) AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "The biological process whose specific outcome is the progression of a mesonephric glomerulus vasculature from an initial condition to its mature state. This process begins with the formation of the mesonephric glomerulus vasculature and ends with the mature structure. The mesonephric glomerulus vasculature is composed of the tubule structures that carry blood or lymph in the mesonephric glomerulus.") -AnnotationAssertion( "dph") AnnotationAssertion( "2010-08-19T02:47:06Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0061231") @@ -75371,7 +74673,6 @@ SubClassOf( ObjectSomeValuesFrom( (mesonephric glomerular epithelium development) AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "The process whose specific outcome is the progression of the mesonephric glomerular epithelium over time, from its formation to the mature structure. The mesonephric glomerular epithelium is an epithelial tissue that covers the outer surfaces of the glomerulus in the mesonephros. The mesonephric glomerular epithelium consists of both parietal and visceral epithelium. Mesonephric glomerular parietal epithelial cells are specialized epithelial cells that form tight junctions as a barrier to protein transport. A mesonephric glomerular visceral epithelial cell is a specialized epithelial cell that contains 'feet' that interdigitate with the 'feet' of other glomerular epithelial cells in the mesonephros.") -AnnotationAssertion( "dph") AnnotationAssertion( "2010-08-19T02:49:46Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0061232") @@ -75384,7 +74685,6 @@ SubClassOf( ObjectSomeValuesFrom( (mesonephric glomerulus morphogenesis) AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "The process in which the anatomical structures of the mesonephric glomerulus are generated and organized. The mesonephric glomerulus is a capillary tuft surrounded by Bowman's capsule in nephrons of the vertebrate mesonephros.") -AnnotationAssertion( "dph") AnnotationAssertion( "2010-08-19T02:53:35Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0061234") @@ -75397,7 +74697,6 @@ SubClassOf( ObjectSomeValuesFrom( (mesenchymal stem cell maintenance involved in mesonephric nephron morphogenesis) AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "The process in which an organism retains a population of mesenchymal stem cells that contributes to the shaping of a nephron in the mesonephros. A mesenchymal stem cell is a cell that retains the ability to divide and proliferate throughout life to provide progenitor cells that can differentiate into specialized mesenchymal cells.") -AnnotationAssertion( "dph") AnnotationAssertion( "2010-08-19T02:57:11Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0061235") @@ -75408,7 +74707,6 @@ SubClassOf( ObjectSomeValuesFrom( (mesonephric comma-shaped body morphogenesis) AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "The process in which the mesonephric comma-shaped body is generated and organized. The mesonephric comma-shaped body is the precursor structure to the mesonephric S-shaped body that contributes to the morphogenesis of a nephron in the mesonephros.") -AnnotationAssertion( "dph") AnnotationAssertion( "2010-08-19T03:00:21Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0061236") @@ -75420,7 +74718,6 @@ SubClassOf( ObjectSomeValuesFrom( (mesonephric nephron tubule morphogenesis) AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "The process in which the anatomical structures of a mesonephric nephron tubule are generated and organized. A mesonephric nephron tubule is an epithelial tube that is part of the mesonephric nephron, the functional part of the mesonephros.") -AnnotationAssertion( "dph") AnnotationAssertion( "2010-08-19T03:09:26Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0061240") @@ -75433,7 +74730,6 @@ SubClassOf( ObjectSomeValuesFrom( (mesonephric nephron epithelium development) AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "The process whose specific outcome is the progression of the mesonephric nephron epithelium over time, from its formation to the mature structure. An epithelium is a tissue that covers the internal or external surfaces of an anatomical structure. The mesonephric nephron epithelium is a tissue that covers the surface of a nephron in the mesonephros.") -AnnotationAssertion( "dph") AnnotationAssertion( "2010-08-19T03:11:59Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0061241") @@ -75446,7 +74742,6 @@ SubClassOf( ObjectSomeValuesFrom( (mesonephric nephron tubule development) AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "The progression of a mesonephric nephron tubule over time, from its initial formation to the mature structure. A mesonephric nephron tubule is an epithelial tube that is part of the mesonephric nephron, the functional part of the mesonephros.") -AnnotationAssertion( "dph") AnnotationAssertion( "2010-08-19T03:17:00Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0061242") @@ -75459,7 +74754,6 @@ SubClassOf( (mesonephric renal vesicle morphogenesis) AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "The process in which the anatomical structures of the mesonephric renal vesicle are generated and organized. The renal vesicle is the primordial structure of the mesonephric nephron epithelium, and is formed by the condensation of mesenchymal cells.") -AnnotationAssertion( "dph") AnnotationAssertion( "2010-08-19T03:20:21Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0061243") @@ -75471,7 +74765,6 @@ SubClassOf( ObjectSomeValuesFrom( (mesonephric S-shaped body morphogenesis) AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "The process in which the mesonephric S-shaped body is generated and organized. The mesonephric S-shaped body is the successor of the mesonephric comma-shaped body that contributes to the morphogenesis of a nephron in the mesonephros.") -AnnotationAssertion( "dph") AnnotationAssertion( "2010-08-19T03:23:55Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0061244") @@ -75483,7 +74776,6 @@ SubClassOf( ObjectSomeValuesFrom( (mesonephric glomerular mesangium development) AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "The process whose specific outcome is the progression of the mesonephric glomerular mesangium over time, from its formation to the mature structure. The mesonephric glomerular mesangium is the thin membrane connective tissue composed of mesangial cells in the mesonephros, which helps to support the capillary loops in a renal glomerulus.") -AnnotationAssertion( "dph") AnnotationAssertion( "2010-08-30T12:59:25Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0061247") @@ -75495,7 +74787,6 @@ SubClassOf( ObjectSomeValuesFrom( (mesonephric glomerulus vasculature morphogenesis) AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "The process in which the anatomical structures of the mesonephric glomerulus vasculature are generated and organized. The mesonephric glomerulus vasculature is composed of the tubule structures that carry blood or lymph in the mesonephric glomerulus.") -AnnotationAssertion( "dph") AnnotationAssertion( "2010-08-30T01:11:34Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0061248") @@ -75508,7 +74799,6 @@ SubClassOf( ObjectSomeValuesFrom( (mesonephric glomerular capillary formation) AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "The process that gives rise to a mesonephric glomerular capillary. This process pertains to the initial formation of a structure from unspecified parts.") -AnnotationAssertion( "dph") AnnotationAssertion( "2010-08-30T01:17:08Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0061249") @@ -75520,7 +74810,6 @@ SubClassOf( ObjectSomeValuesFrom( (mesonephric glomerular epithelial cell differentiation) AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "The process in which a relatively unspecialized cell acquires specialized features of a mesonephric glomerular epithelial cell. Mesonephric glomerular epithelial cells are specialized epithelial cells that form part of the mesonephric glomerulus; there are two types, mesonephric glomerular parietal epithelial cells and mesonephric glomerular visceral epithelial cells.") -AnnotationAssertion( "dph") AnnotationAssertion( "2010-08-30T01:20:03Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0061250") @@ -75532,7 +74821,6 @@ SubClassOf( ObjectSomeValuesFrom( (mesonephric glomerular epithelial cell development) AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "The process whose specific outcome is the progression of a mesonephric glomerular epithelial cell over time, from its formation to the mature structure. Mesonephric glomerular epithelial cells are specialized epithelial cells that form part of the mesonephric glomerulus; there are two types, mesonephric glomerular parietal epithelial cells and mesonephric glomerular visceral epithelial cells.") -AnnotationAssertion( "dph") AnnotationAssertion( "2010-08-30T01:20:45Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0061251") @@ -75544,7 +74832,6 @@ SubClassOf( ObjectSomeValuesFrom( "GOC:mtg_kidney_jan10") "The process in which a relatively unspecialized cell acquires specialized features of a mesonephric glomerular visceral epithelial cell. A mesonephric glomerular visceral epithelial cell is a specialized epithelial cell that contains 'feet' that interdigitate with the 'feet' of other glomerular epithelial cells in the mesonephros.") AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/23000"^^xsd:anyURI) -AnnotationAssertion( "dph") AnnotationAssertion( "2010-08-30T02:03:38Z") AnnotationAssertion( "mesonephric glomerular visceral epithelial cell differentiation") AnnotationAssertion( "biological_process") @@ -75558,7 +74845,6 @@ SubClassOf( "GOC:mtg_kidney_jan10") "The process whose specific outcome is the progression of a mesonephric glomerular visceral epithelial cell over time, from its formation to the mature structure. A mesonephric glomerular visceral epithelial cell is a specialized epithelial cell that contains 'feet' that interdigitate with the 'feet' of other glomerular epithelial cells in the mesonephros.") AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/23000"^^xsd:anyURI) -AnnotationAssertion( "dph") AnnotationAssertion( "2010-08-30T02:10:40Z") AnnotationAssertion( "mesonephric glomerular visceral epithelial cell development") AnnotationAssertion( "biological_process") @@ -75572,7 +74858,6 @@ SubClassOf( ObjectSomeValuesFrom( (mesenchymal to epithelial transition involved in mesonephros morphogenesis) AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "A transition where a mesenchymal cell establishes apical/basolateral polarity, forms intercellular adhesive junctions, synthesizes basement membrane components and becomes an epithelial cell that will contribute to the shaping of the mesonephros.") -AnnotationAssertion( "dph") AnnotationAssertion( "2010-08-30T02:35:15Z") AnnotationAssertion( "biological_process") AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "mesonephric mesenchyme to epithelial transition") @@ -75583,7 +74868,6 @@ EquivalentClasses( ObjectIntersection # Class: (mesonephric renal vesicle formation) AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "The developmental process pertaining to the initial formation of the mesonephros.") -AnnotationAssertion( "dph") AnnotationAssertion( "2010-08-30T02:41:20Z") AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "mesonephros formation") AnnotationAssertion( "biological_process") @@ -75596,7 +74880,6 @@ SubClassOf( ObjectSomeValuesFrom( (mesonephric nephron tubule epithelial cell differentiation) AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "The process in which relatively unspecialized cells acquire specialized structural and/or functional features that characterize the cells of the mesonephric nephron tubule as it progresses from its formation to the mature state.") -AnnotationAssertion( "dph") AnnotationAssertion( "2010-08-30T03:02:09Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0061265") @@ -75609,7 +74892,6 @@ SubClassOf( ObjectSomeValuesFrom( (mesenchymal to epithelial transition involved in mesonephric renal vesicle formation) AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "A transition where a mesenchymal cell establishes apical/basolateral polarity,forms intercellular adhesive junctions, synthesizes basement membrane components and becomes an epithelial cell that will contribute to the shaping of the mesonephric renal vesicle.") -AnnotationAssertion( "dph") AnnotationAssertion( "2010-08-30T03:26:30Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0061271") @@ -75619,7 +74901,6 @@ EquivalentClasses( ObjectIntersection # Class: (mesonephric connecting tubule development) AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "The process whose specific outcome is the progression of the mesonephric connecting tubule over time, from its formation to the mature structure. The mesonephric connecting tubule is a tubular segment of the mesonephric nephron; it connects the distal tubule to the collecting duct in the mesonephros.") -AnnotationAssertion( "dph") AnnotationAssertion( "2010-09-02T12:00:56Z") AnnotationAssertion(Annotation( "GOC:dph") "mesonephric collecting tubule development") AnnotationAssertion( "biological_process") @@ -75633,7 +74914,6 @@ SubClassOf( (mesonephric distal tubule morphogenesis) AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "The process in which the anatomical structures of a mesonephric distal tubule are generated and organized. The mesonephric distal tubule is a mesonephric nephron tubule that begins at the macula densa and extends to the mesonephric connecting tubule.") -AnnotationAssertion( "dph") AnnotationAssertion( "2010-09-02T12:12:00Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0061273") @@ -75646,7 +74926,6 @@ SubClassOf( ObjectSomeValuesFrom( (mesonephric distal tubule development) AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "The process whose specific outcome is the progression of the mesonephric distal tubule over time, from its formation to the mature structure. The mesonephric distal tubule is a mesonephric nephron tubule that begins at the terminal segment of the proximal tubule and ends at the mesonephric connecting tubule.") -AnnotationAssertion( "dph") AnnotationAssertion( "2010-09-02T12:16:25Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0061274") @@ -75658,7 +74937,6 @@ SubClassOf( (mesonephric proximal tubule development) AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "The progression of the mesonephric proximal tubule over time, from its formation to the mature structure. The mesonephric proximal tubule extends from the capsule to the distal tubule.") -AnnotationAssertion( "dph") AnnotationAssertion( "2010-09-02T01:08:05Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0061275") @@ -75670,7 +74948,6 @@ SubClassOf( (mesonephric proximal tubule morphogenesis) AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "The process in which the anatomical structures of a mesonephric proximal tubule are generated and organized. The mesonephric proximal tubule extends from the capsule to the distal tubule.") -AnnotationAssertion( "dph") AnnotationAssertion( "2010-09-02T01:11:02Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0061276") @@ -75683,7 +74960,6 @@ SubClassOf( ObjectSomeValuesFrom( (mesonephric nephron tubule formation) AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "The developmental process pertaining to the initial formation of a mesonephric nephron tubule from unspecified parts. A mesonephric nephron tubule is an epithelial tube that is part of a nephron in the mesonephros.") -AnnotationAssertion( "dph") AnnotationAssertion( "2010-09-02T01:16:21Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0061277") @@ -75695,7 +74971,6 @@ SubClassOf( ObjectSomeValuesFrom( (epithelial cell migration involved in mesonephric nephron tubule morphogenesis) AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "The orderly movement of epithelial cells within a renal tubule that contributes to mesonephric nephron tubule morphogenesis.") -AnnotationAssertion( "dph") AnnotationAssertion( "2010-09-02T01:18:53Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0061278") @@ -75705,7 +74980,6 @@ EquivalentClasses( ObjectIntersection # Class: (epithelial cell migration involved in mesonephric distal tubule morphogenesis) AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "The orderly movement of epithelial cells within a renal tubule that contributes to mesonephric distal tubule morphogenesis.") -AnnotationAssertion( "dph") AnnotationAssertion( "2010-09-02T01:20:56Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0061279") @@ -75715,7 +74989,6 @@ EquivalentClasses( ObjectIntersection # Class: (epithelial cell migration involved in mesonephric proximal tubule morphogenesis) AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "The orderly movement of epithelial cells within a renal tubule that contributes to mesonephric proximal tubule morphogenesis.") -AnnotationAssertion( "dph") AnnotationAssertion( "2010-09-02T01:23:43Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0061280") @@ -75725,7 +74998,6 @@ EquivalentClasses( ObjectIntersection # Class: (mesonephric capsule development) AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "The progression of the mesonephric capsule over time, from its formation to the mature structure. The mesonephric capsule is the tough fibrous layer surrounding the mesonephros, covered in a thick layer of perinephric adipose tissue.") -AnnotationAssertion( "dph") AnnotationAssertion( "2010-09-02T01:50:06Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0061285") @@ -75737,7 +75009,6 @@ SubClassOf( ObjectSomeValuesFrom( (mesonephric capsule morphogenesis) AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "The process in which the anatomical structures of the mesonephric capsule are generated and organized. The mesonephric capsule is the tough fibrous layer surrounding the mesonephros, covered in a thick layer of perinephric adipose tissue. It provides some protection from trauma and damage.") -AnnotationAssertion( "dph") AnnotationAssertion( "2010-09-02T01:53:31Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0061286") @@ -75749,7 +75020,6 @@ SubClassOf( ObjectSomeValuesFrom( (mesonephric capsule formation) AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "The developmental process pertaining to the initial formation of a mesonephric capsule from unspecified parts. The mesonephric capsule is the tough fibrous layer surrounding the mesonephros, covered in a thick layer of perinephric adipose tissue. It provides some protection from trauma and damage.") -AnnotationAssertion( "dph") AnnotationAssertion( "2010-09-02T01:55:03Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0061287") @@ -75761,7 +75031,6 @@ SubClassOf( ObjectSomeValuesFrom( (regulation of mesenchymal cell apoptotic process involved in mesonephric nephron morphogenesis) AnnotationAssertion(Annotation( "GOC:mtg_apoptosis") Annotation( "GOC:mtg_kidney_jan10") "Any process that modulates the occurrence or rate of mesenchymal stem cell death by apoptotic process that contributes to the shaping of the nephron in the mesonephros.") -AnnotationAssertion( "dph") AnnotationAssertion( "2010-09-06T09:48:56Z") AnnotationAssertion( "regulation of mesenchymal stem cell apoptotic process involved in mesonephric nephron morphogenesis") AnnotationAssertion( "regulation of mesenchymal stem cell apoptosis involved in mesonephric nephron morphogenesis") @@ -75774,7 +75043,6 @@ SubClassOf( ObjectSomeValuesFrom( (negative regulation of mesenchymal cell apoptotic process involved in mesonephric nephron morphogenesis) AnnotationAssertion(Annotation( "GOC:mtg_apoptosis") Annotation( "GOC:mtg_kidney_jan10") "Any process that reduces the occurrence or rate of mesenchymal stem cell death by apoptotic process that contributes to the shaping of the nephron in the mesonephros.") -AnnotationAssertion( "dph") AnnotationAssertion( "2010-09-06T09:54:49Z") AnnotationAssertion( "negative regulation of mesenchymal stem cell apoptotic process involved in mesonephric nephron morphogenesis") AnnotationAssertion( "negative regulation of mesenchymal stem cell apoptosis involved in mesonephric nephron morphogenesis") @@ -75788,7 +75056,6 @@ SubClassOf( ObjectSomeValuesFrom( (positive regulation of mesenchymal cell apoptotic process involved in mesonephric nephron morphogenesis) AnnotationAssertion(Annotation( "GOC:mtg_apoptosis") Annotation( "GOC:mtg_kidney_jan10") "Any process that increases the occurrence or rate of mesenchymal stem cell death by apoptotic process that contributes to the shaping of the nephron in the mesonephros.") -AnnotationAssertion( "dph") AnnotationAssertion( "2010-09-06T09:58:59Z") AnnotationAssertion( "positive regulation of mesenchymal stem cell apoptotic process involved in mesonephric nephron morphogenesis") AnnotationAssertion( "positive regulation of mesenchymal stem cell apoptosis involved in mesonephric nephron morphogenesis") @@ -75802,7 +75069,6 @@ SubClassOf( ObjectSomeValuesFrom( (retina vasculature development in camera-type eye) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:dph") "The process whose specific outcome is the progression of the vasculature of the retina over time, from its formation to the mature structure.") -AnnotationAssertion( "dph") AnnotationAssertion( "2010-09-06T03:27:06Z") AnnotationAssertion(Annotation( "GOC:dph") "retinal vasculature development") AnnotationAssertion( "biological_process") @@ -75815,7 +75081,6 @@ SubClassOf( ObjectSomeValuesFrom( (retina vasculature morphogenesis in camera-type eye) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:dph") "The process in which the vasculature of the retina is generated and organized.") -AnnotationAssertion( "dph") AnnotationAssertion( "2010-09-06T03:28:25Z") AnnotationAssertion(Annotation( "GOC:dph") "retinal vasculature morphogenesis") AnnotationAssertion( "biological_process") @@ -75829,7 +75094,6 @@ SubClassOf( ObjectSomeValuesFrom( (cerebellum vasculature development) AnnotationAssertion(Annotation( "GOC:dph") "The process whose specific outcome is the progression of the vasculature of the cerebellum over time, from its formation to the mature structure.") -AnnotationAssertion( "dph") AnnotationAssertion( "2010-09-06T03:36:40Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0061300") @@ -75840,7 +75104,6 @@ SubClassOf( (cerebellum vasculature morphogenesis) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:dph") "The process in which the vasculature of the cerebellum is generated and organized.") -AnnotationAssertion( "dph") AnnotationAssertion( "2010-09-06T03:38:05Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0061301") @@ -75854,7 +75117,6 @@ SubClassOf( ObjectSomeValuesFrom( (cornea development in camera-type eye) AnnotationAssertion(Annotation( "GOC:dph") "The progression of the cornea over time, from its formation to the mature structure. The cornea is the transparent structure that covers the anterior of the eye.") -AnnotationAssertion( "dph") AnnotationAssertion( "2010-09-14T02:09:08Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0061303") @@ -75867,7 +75129,6 @@ SubClassOf( ObjectSomeValuesFrom( (retinal blood vessel morphogenesis) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:dph") "The process whose specific outcome is the progression of a blood vessel of the retina over time, from its formation to the mature structure.") -AnnotationAssertion( "dph") AnnotationAssertion( "2010-09-16T09:02:59Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0061304") @@ -75879,7 +75140,6 @@ SubClassOf( (cardiac neural crest cell differentiation involved in heart development) AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:mtg_heart") Annotation( "PMID:19705442") "The process in which a relatively unspecialized cell acquires specialized features of a cardiac neural crest cell that will migrate to the heart and contribute to its development. Cardiac neural crest cells are specialized cells that migrate toward the heart from the third, fourth and sixth pharyngeal arches.") -AnnotationAssertion( "dph") AnnotationAssertion( "2010-09-23T08:50:56Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0061307") @@ -75890,7 +75150,6 @@ SubClassOf( (cardiac neural crest cell development involved in heart development) AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:mtg_heart") "The process aimed at the progression of a cardiac neural crest cell over time, from initial commitment of the cell to its specific fate, to the fully functional differentiated cell that contributes to the development of the heart.") -AnnotationAssertion( "dph") AnnotationAssertion( "2010-09-23T09:01:49Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0061308") @@ -75901,7 +75160,6 @@ SubClassOf( ObjectSomeValuesFrom( (cardiac neural crest cell development involved in outflow tract morphogenesis) AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:mtg_heart") "The process aimed at the progression of a cardiac neural crest cell over time, from initial commitment of the cell to its specific fate, to the fully functional differentiated cell that contributes to the shaping of the outflow tract.") -AnnotationAssertion( "dph") AnnotationAssertion( "2010-09-23T09:08:37Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0061309") @@ -75911,7 +75169,6 @@ EquivalentClasses( ObjectIntersection # Class: (cell surface receptor signaling pathway involved in heart development) AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:mtg_heart") Annotation( "GOC:signaling") "The series of molecular signals initiated by a ligand the binding to its receptor on the surface of a cell, which contributes to the progression of the heart over time.") -AnnotationAssertion( "dph") AnnotationAssertion( "2010-09-23T09:18:32Z") AnnotationAssertion(Annotation( "GOC:bf") "cell surface receptor linked signaling pathway involved in heart development") AnnotationAssertion(Annotation( "GOC:mah") "cell surface receptor linked signalling pathway involved in heart development") @@ -75923,7 +75180,6 @@ EquivalentClasses( ObjectIntersection # Class: (renal filtration cell differentiation) AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:mtg_kidney_jan10") "The process in which a relatively unspecialized cell acquires specialized structural and/or functional features of a renal filtration cell. Renal filtration cells are specialized cells of the renal system that filter fluids by charge, size or both. Differentiation includes the processes involved in commitment of a cell to a specific fate and its subsequent development to the mature state.") -AnnotationAssertion( "dph") AnnotationAssertion( "2010-09-24T12:18:35Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0061318") @@ -75935,7 +75191,6 @@ SubClassOf( ObjectSomeValuesFrom( (nephrocyte differentiation) AnnotationAssertion(Annotation( "CL:0002520") Annotation( "GOC:dph") Annotation( "GOC:mtg_kidney_jan10") Annotation( "PMID:19783135") "The process in which a relatively unspecialized cell acquires the specialized structural and/or functional features of a nephrocyte. A nephrocyte is an insect renal cell that filters hemolymph. Differentiation includes the processes involved in commitment of a cell to a specific fate and its subsequent development to the mature state.") -AnnotationAssertion( "dph") AnnotationAssertion( "2010-09-24T12:23:29Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0061319") @@ -75948,7 +75203,6 @@ SubClassOf( ObjectAllValuesFrom( (pericardial nephrocyte differentiation) AnnotationAssertion(Annotation( "CL:0000474") Annotation( "GOC:dph") Annotation( "GOC:mtg_kidney_jan10") Annotation( "GOC:sart") Annotation( "PMID:19783135") "The process in which a relatively unspecialized cell acquires the specialized structural and/or functional features of a pericardial nephrocyte. A pericardial nephrocyte is an insect renal cell that filters hemolymph and is found with other pericardial nephrocytes in two rows flanking the dorsal vessel. Differentiation includes the processes involved in commitment of a cell to a specific fate and its subsequent development to the mature state.") -AnnotationAssertion( "dph") AnnotationAssertion( "2010-09-24T12:25:53Z") AnnotationAssertion( "pericardial cell differentiation") AnnotationAssertion( "biological_process") @@ -75960,7 +75214,6 @@ SubClassOf( (garland nephrocyte differentiation) AnnotationAssertion(Annotation( "CL:0000486") Annotation( "GOC:dph") Annotation( "GOC:mtg_kidney_jan10") Annotation( "GOC:sart") Annotation( "PMID:19783135") "The process in which a relatively unspecialized cell acquires the specialized structural and/or functional features of a garland nephrocyte. A garland nephrocyte is an insect renal cell that filters hemolymph and forms a ring with other garland nephrocytes around the esophagus. Differentiation includes the processes involved in commitment of a cell to a specific fate and its subsequent development to the mature state.") -AnnotationAssertion( "dph") AnnotationAssertion( "2010-09-24T12:28:16Z") AnnotationAssertion( "garland cell differentiation") AnnotationAssertion( "biological_process") @@ -75973,7 +75226,6 @@ SubClassOf( ObjectSomeValuesFrom( (disseminated nephrocyte differentiation) AnnotationAssertion(Annotation( "CL:0002524") Annotation( "GOC:19783135") Annotation( "GOC:dph") Annotation( "GOC:mtg_kidney_jan10") "The process in which a relatively unspecialized cell acquires the specialized structural and/or functional features of a disseminated nephrocyte. A disseminated nephrocyte is an insect renal cell that filters hemolymph and is found at scattered locations in the fat body or other tissues. Differentiation includes the processes involved in commitment of a cell to a specific fate and its subsequent development to the mature state.") -AnnotationAssertion( "dph") AnnotationAssertion( "2010-09-24T12:30:46Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0061322") @@ -75984,7 +75236,6 @@ SubClassOf( (cell proliferation involved in heart morphogenesis) AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:mtg_heart") "The multiplication or reproduction of cells, resulting in the expansion of a cell population that contributes to the shaping of the heart.") -AnnotationAssertion( "dph") AnnotationAssertion( "2010-09-28T09:05:26Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0061323") @@ -75994,7 +75245,6 @@ EquivalentClasses( ObjectIntersection # Class: (cell proliferation involved in outflow tract morphogenesis) AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:mtg_heart") "The multiplication or reproduction of cells, resulting in the expansion of a cell population that contributes to the shaping of the outflow tract.") -AnnotationAssertion( "dph") AnnotationAssertion( "2010-09-28T09:29:30Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0061325") @@ -76004,7 +75254,6 @@ EquivalentClasses( ObjectIntersection # Class: (renal tubule development) AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:mtg_kidney_jan10") "The progression of the renal tubule over time from its formation to the mature form. A renal tubule is a tube that filters, re-absorbs and secretes substances to rid an organism of waste and to play a role in fluid homeostasis.") -AnnotationAssertion( "dph") AnnotationAssertion( "2010-09-28T12:50:43Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0061326") @@ -76016,7 +75265,6 @@ SubClassOf( ObjectSomeValuesFrom( (Malpighian tubule stellate cell differentiation) AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:mtg_kidney_jan10") Annotation( "PMID:19783135") "The process in which a relatively unspecialized cell acquires specialized features of a Malpighian tubule stellate cell. A Malpighian tubule stellate cell is a specialized epithelial secretory cell that moves chloride ions and water across the tubule epithelium.") -AnnotationAssertion( "dph") AnnotationAssertion( "2010-09-28T01:32:55Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0061330") @@ -76028,7 +75276,6 @@ SubClassOf( ObjectSomeValuesFrom( (epithelial cell proliferation involved in Malpighian tubule morphogenesis) AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:mtg_kidney_jan10") Annotation( "PMID:19783135") "The multiplication or reproduction of epithelial cells, resulting in the expansion of a cell population and contributing to the shaping of a Malpighian tubule.") -AnnotationAssertion( "dph") AnnotationAssertion( "2010-09-28T02:01:02Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0061331") @@ -76038,7 +75285,6 @@ EquivalentClasses( ObjectIntersection # Class: (Malpighian tubule bud morphogenesis) AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:mtg_kidney_jan10") Annotation( "PMID:19783135") "The morphogenetic process in which a bud forms from the embryonic hindgut tube to form the Malpighian tubule. A bud is a protrusion that forms from the tube by localized changes in cell shape and position.") -AnnotationAssertion( "dph") AnnotationAssertion( "2010-09-28T01:39:32Z") AnnotationAssertion(Annotation( "GOC:dph") "Malpighian tubule formation") AnnotationAssertion( "biological_process") @@ -76051,7 +75297,6 @@ SubClassOf( ObjectSomeValuesFrom( (renal tubule morphogenesis) AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:mtg_kidney_jan10") "The process in which the renal tubule is generated by specification of cell fate, through the maintenance of cell polarity, regulated cell proliferation and morphogenetic cell rearrangements, shape changes and growth. A renal tubule is a tube that filters, re-absorbs and secretes substances to rid an organism of waste and to play a role in fluid homeostasis.") -AnnotationAssertion( "dph") AnnotationAssertion( "2010-09-28T01:43:04Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0061333") @@ -76063,7 +75308,6 @@ SubClassOf( ObjectSomeValuesFrom( (cell rearrangement involved in Malpighian tubule morphogenesis) AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:mtg_kidney_jan10") "The movement of an epithelial cell with respect to other epithelial cells that contributes to the shaping of the Malpighian tubule.") -AnnotationAssertion( "dph") AnnotationAssertion( "2010-09-28T02:04:05Z") AnnotationAssertion( "cell migration involved in Malpighian tubule morphogenesis") AnnotationAssertion( "biological_process") @@ -76074,7 +75318,6 @@ EquivalentClasses( ObjectIntersection # Class: (cell growth involved in Malpighian tubule morphogenesis) AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:mtg_kidney_jan10") Annotation( "PMID:19783135") "The growth of an epithelial cell dependent on cycles of endoreplication, where growth contributes to the shaping of the Malpighian tubule.") -AnnotationAssertion( "dph") AnnotationAssertion( "2010-09-28T02:08:25Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0061335") @@ -76084,7 +75327,6 @@ EquivalentClasses( ObjectIntersection # Class: (cell morphogenesis involved in Malpighian tubule morphogenesis) AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:mtg_kidney_jan10") Annotation( "PMID:19783135") "The shape change of an epithelial cell from a columnar to squamous cell morphology that contributes to the shaping of the Malpighian tubule.") -AnnotationAssertion( "dph") AnnotationAssertion( "2010-09-28T02:11:47Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0061336") @@ -76094,7 +75336,6 @@ EquivalentClasses( ObjectIntersection # Class: (cardiac conduction) AnnotationAssertion(Annotation( "GOC:dph") "Transfer of an organized electrical impulse across the heart to coordinate the contraction of cardiac muscles. The process begins with generation of an action potential (in the sinoatrial node (SA) in humans) and ends with a change in the rate, frequency, or extent of the contraction of the heart muscles.") -AnnotationAssertion( "dph") AnnotationAssertion( "2010-09-29T08:46:05Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0061337") @@ -76104,7 +75345,6 @@ SubClassOf( (cell adhesion involved in heart morphogenesis) AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:mtg_heart") Annotation( "PMID:16860783") "The attachment of a cell, either to another cell or to an underlying substrate such as the extracellular matrix, via cell adhesion molecules that contributes to the shaping of the heart.") -AnnotationAssertion( "dph") AnnotationAssertion( "2010-09-29T11:34:06Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0061343") @@ -76114,7 +75354,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of cell adhesion involved in heart morphogenesis) AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:mtg_heart") Annotation( "PMID:16860783") "Any process that modulates the extent of cell adhesion contributing to the shaping of the heart.") -AnnotationAssertion( "dph") AnnotationAssertion( "2010-09-29T11:35:27Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0061344") @@ -76124,7 +75363,6 @@ EquivalentClasses( ObjectIntersection # Class: (neural precursor cell proliferation) AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:yaf") "The multiplication or reproduction of neural precursor cells, resulting in the expansion of a cell population. A neural precursor cell is either a nervous system stem cell or a nervous system progenitor cell.") -AnnotationAssertion( "dph") AnnotationAssertion( "2010-10-01T11:06:04Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0061351") @@ -76134,7 +75372,6 @@ SubClassOf( (cell chemotaxis involved in Malpighian tubule morphogenesis) AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:mtg_kidney_jan10") "The directed movement of the outgrowing Malpighian tubule guided by specific chemical cues/signals. Movement may be towards a guidance cue (positive chemotaxis) or away from it (negative chemotaxis). Guidance contributes to the final positioning of the tubule.") -AnnotationAssertion( "dph") AnnotationAssertion( "2010-10-01T11:57:28Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0061352") @@ -76144,7 +75381,6 @@ EquivalentClasses( ObjectIntersection # Class: (optic chiasma development) AnnotationAssertion(Annotation( "GOC:dph") "The developmental process pertaining to the progression of the optic chiasm from its initial formation to the mature structure. The process begins when the pathfinding of the axons of the developing optic nerve cause some axons to cross at the midline of the brain and ends when the axons are mature.") -AnnotationAssertion( "dph") AnnotationAssertion( "2010-10-13T08:00:29Z") AnnotationAssertion(Annotation( "GOC:dph") "optic chiasm development") AnnotationAssertion( "biological_process") @@ -76158,7 +75394,6 @@ SubClassOf( ObjectSomeValuesFrom( (testosterone biosynthetic process) AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:yaf") "The chemical reactions and pathways resulting in the formation of testosterone, an androgen having 17beta-hydroxy and 3-oxo groups, together with unsaturation at C-4 C-5.") -AnnotationAssertion( "dph") AnnotationAssertion( "2010-10-27T02:50:48Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0061370") @@ -76168,7 +75403,6 @@ EquivalentClasses( ObjectIntersection # Class: (mammary gland lobule development) AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:yaf") "The progression of the mammary gland lobule over time, from its formation to the mature structure. A mammary gland lobule is a small rounded projection of the mammary gland.") -AnnotationAssertion( "dph") AnnotationAssertion( "2010-11-09T09:36:29Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0061377") @@ -76181,7 +75415,6 @@ SubClassOf( ObjectSomeValuesFrom( (Malpighian tubule tip cell differentiation) AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:mtg_kidney_jan10") Annotation( "PMID:7821213") "The process in which a relatively unspecialized cell acquires specialized features of a Malpighian tubule tip cell. A Malpighian tubule tip cell is a mitogenic signaling cell that controls the proliferation of its neighboring cells.") -AnnotationAssertion( "dph") AnnotationAssertion( "2010-11-23T09:52:44Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0061382") @@ -76193,7 +75426,6 @@ SubClassOf( ObjectSomeValuesFrom( (trabecula morphogenesis) AnnotationAssertion(Annotation( "GOC:dph") "The process of shaping a trabecula in an organ. A trabecula is a small, often microscopic, tissue element in the form of a small beam, strut or rod, which generally has a mechanical function. Trabecula are usually but not necessarily, composed of dense collagenous tissue.") -AnnotationAssertion( "dph") AnnotationAssertion( "2010-12-02T08:51:45Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0061383") @@ -76205,7 +75437,6 @@ SubClassOf( (heart trabecula morphogenesis) AnnotationAssertion(Annotation( "GOC:dph") "The process of shaping a trabecula in the heart. A trabecula is a small, often microscopic, tissue element in the form of a small beam, strut or rod, which generally has a mechanical function. Trabecula are usually but not necessarily, composed of dense collagenous tissue.") -AnnotationAssertion( "dph") AnnotationAssertion( "2010-12-02T08:54:20Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0061384") @@ -76216,7 +75447,6 @@ SubClassOf( (fibroblast proliferation involved in heart morphogenesis) AnnotationAssertion(Annotation( "GOC:dph") "The multiplication or reproduction of fibroblasts, resulting in the expansion of a fibroblast population that contributes to the shaping of the heart.") -AnnotationAssertion( "dph") AnnotationAssertion( "2011-02-10T01:41:59Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0061385") @@ -76226,7 +75456,6 @@ EquivalentClasses( ObjectIntersection # Class: (renal system vasculature development) AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:mtg_kidney_jan10") Annotation( "PMID:11891195") "The process whose specific outcome is the progression of vasculature of the renal system over time, from its formation to the mature structure.") -AnnotationAssertion( "dph") AnnotationAssertion( "2012-03-08T12:16:24Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0061437") @@ -76237,7 +75466,6 @@ SubClassOf( ObjectSomeValuesFrom( (renal system vasculature morphogenesis) AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:mtg_kidney_jan10") Annotation( "PMID:11891195") "The process in which the renal system vasculature is generated and organized. Morphogenesis pertains to the creation of form.") -AnnotationAssertion( "dph") AnnotationAssertion( "2012-03-08T12:21:56Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0061438") @@ -76249,7 +75477,6 @@ SubClassOf( ObjectSomeValuesFrom( (kidney vasculature morphogenesis) AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:mtg_kidney_jan10") "The process in which the kidney vasculature is generated and organized. Morphogenesis pertains to the creation of form.") -AnnotationAssertion( "dph") AnnotationAssertion( "2012-03-08T12:30:11Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0061439") @@ -76263,7 +75490,6 @@ SubClassOf( ObjectSomeValuesFrom( (kidney vasculature development) AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:mtg_kidney_jan10") Annotation( "PMID:11891195") "The process whose specific outcome is the progression of the vasculature of the kidney over time, from its formation to the mature structure.") -AnnotationAssertion( "dph") AnnotationAssertion( "2012-03-08T12:39:09Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0061440") @@ -76275,7 +75501,6 @@ SubClassOf( ObjectSomeValuesFrom( (renal artery morphogenesis) AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") Annotation( "PMID:11891195") "The process in which the anatomical structure of a renal artery is generated and organized. Renal arteries supply the kidneys with blood.") -AnnotationAssertion( "dph") AnnotationAssertion( "2012-03-08T12:42:09Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0061441") @@ -76287,7 +75512,6 @@ SubClassOf( ObjectSomeValuesFrom( (connective tissue development) AnnotationAssertion(Annotation( "GOC:BHF") "The progression of a connective tissue over time, from its formation to the mature structure.") -AnnotationAssertion( "dph") AnnotationAssertion( "2012-03-22T12:53:41Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0061448") @@ -76298,7 +75522,6 @@ SubClassOf( (olfactory bulb tufted cell development) AnnotationAssertion(Annotation( "GOC:dph") "The process whose specific outcome is the progression of an olfactory bulb tufted cell over time, from initial commitment of the cell to a specific fate, to the fully functional differentiated cell.") -AnnotationAssertion( "dph") AnnotationAssertion( "2012-05-15T12:30:21Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0061449") @@ -76310,7 +75533,6 @@ SubClassOf( ObjectSomeValuesFrom( (trophoblast cell migration) AnnotationAssertion(Annotation( "GOC:dph") "Trophoblast cell migration that is accomplished by extension and retraction of a pseudopodium. Trophoblast cells line the outside of the blastocyst.") -AnnotationAssertion( "dph") AnnotationAssertion( "2012-07-10T08:38:37Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0061450") @@ -76322,7 +75544,6 @@ SubClassOf( ObjectSomeValuesFrom( (retrotrapezoid nucleus development) AnnotationAssertion(Annotation( "GOC:dph") "The progression of the retrotrapezoid nucleus (RTN) over time from it's initial formation to its mature state. The retrotrapezoid nucleus is a group of neurons in the rostral medulla, which are responsible regulating respiration.") -AnnotationAssertion( "dph") AnnotationAssertion( "2012-07-19T12:38:30Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0061451") @@ -76334,7 +75555,6 @@ SubClassOf( ObjectSomeValuesFrom( (retrotrapezoid nucleus neuron differentiation) AnnotationAssertion(Annotation( "GOC:dph") "The process in which a relatively unspecialized cell acquires specialized features of a neuron whose cell body resides in the retrotrapezoid nucleus.") -AnnotationAssertion( "dph") AnnotationAssertion( "2012-07-19T12:43:18Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0061452") @@ -76346,7 +75566,6 @@ SubClassOf( ObjectSomeValuesFrom( (interstitial cell of Cajal differentiation) AnnotationAssertion(Annotation( "GOC:dph") "The process in which a relatively unspecialized cell acquires specialized features of an interstitial cell of Cajal. An interstitial cell of Cajal is an intestinal neuroepithelial cell that serves as a pacemaker to trigger gut contraction.") -AnnotationAssertion( "dph") AnnotationAssertion( "2012-07-20T08:20:50Z") AnnotationAssertion( "biological_process") AnnotationAssertion(Annotation( "GOC:dph") "ICC differentiation") @@ -76358,7 +75577,6 @@ SubClassOf( (release of sequestered calcium ion into cytosol by Golgi) AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:tb") "The directed movement of calcium ions (Ca2+) out of the Golgi apparatus into the cytosol.") -AnnotationAssertion( "dph") AnnotationAssertion( "2012-07-27T02:29:43Z") AnnotationAssertion( "Golgi calcium ion export") AnnotationAssertion( "biological_process") @@ -76369,7 +75587,6 @@ EquivalentClasses( ObjectIntersection # Class: (reproductive system development) AnnotationAssertion(Annotation( "GOC:dph") "The progression of the reproductive system over time from its formation to the mature structure. The reproductive system consists of the organs that function in reproduction.") -AnnotationAssertion( "dph") AnnotationAssertion( "2012-08-22T17:47:53Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0061458") @@ -76380,7 +75597,6 @@ SubClassOf( (protein localization to lysosome) AnnotationAssertion(Annotation( "GOC:dph") "A process in which a protein is transported to, or maintained in, a location within a lysosome.") -AnnotationAssertion( "dph") AnnotationAssertion( "2012-10-05T10:50:51Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0061462") @@ -76390,7 +75606,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of type B pancreatic cell proliferation) AnnotationAssertion(Annotation( "GOC:dph") "Any process that modulates the frequency, rate or extent of type B pancreatic cell proliferation.") -AnnotationAssertion( "dph") AnnotationAssertion( "2012-11-01T13:16:23Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0061469") @@ -76400,7 +75615,6 @@ EquivalentClasses( ObjectIntersection # Class: (T follicular helper cell differentiation) AnnotationAssertion(Annotation( "GOC:dph") Annotation( "PMID:21572431") "The process in which a relatively unspecialized T cell acquires specialized features of a mature T follicular helper cell.") -AnnotationAssertion( "dph") AnnotationAssertion( "2012-11-02T09:01:48Z") AnnotationAssertion(Annotation( "GOC:dph") "T-helper follicular cell differentiation") AnnotationAssertion( "biological_process") @@ -76411,7 +75625,6 @@ EquivalentClasses( ObjectIntersection # Class: (hematopoietic stem cell homeostasis) AnnotationAssertion(Annotation( "GOC:dph") Annotation( "PMID:21508411") "Any biological process involved in the maintenance of the steady-state number of hematopoietic stem cells within a population of cells.") -AnnotationAssertion( "dph") AnnotationAssertion( "2012-12-04T09:41:02Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0061484") @@ -76422,7 +75635,6 @@ SubClassOf( (memory T cell proliferation) AnnotationAssertion(Annotation( "GOC:dph") Annotation( "PMID:14647273") "The expansion of a memory T cell population by cell division.") -AnnotationAssertion( "dph") AnnotationAssertion( "2012-12-04T09:52:54Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0061485") @@ -76439,7 +75651,6 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) -AnnotationAssertion( "dph") AnnotationAssertion( "2013-03-22T15:41:44Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0061512") @@ -76470,7 +75681,6 @@ DisjointClasses( ObjectSomeValuesFrom # Class: (myeloid cell development) AnnotationAssertion(Annotation( "GOC:dph") "The process whose specific outcome is the progression of a myeloid cell over time, from its formation to the mature structure.") -AnnotationAssertion( "dph") AnnotationAssertion( "2013-04-18T13:03:16Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0061515") @@ -76482,7 +75692,6 @@ SubClassOf( ObjectSomeValuesFrom( (macrophage homeostasis) AnnotationAssertion(Annotation( "GOC:dph") Annotation( "PMID:21727904") "The process of regulating the proliferation and elimination of macrophage cells such that the total number of myeloid cells within a whole or part of an organism is stable over time in the absence of an outside stimulus.") -AnnotationAssertion( "dph") AnnotationAssertion( "2013-04-18T13:25:33Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0061519") @@ -76493,7 +75702,6 @@ SubClassOf( (Langerhans cell differentiation) AnnotationAssertion(Annotation( "GOC:dph") Annotation( "PMID:22729249") "The process in which a precursor cell type acquires the specialized features of a Langerhans cell.") -AnnotationAssertion( "dph") AnnotationAssertion( "2013-04-18T13:29:07Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0061520") @@ -76504,7 +75712,6 @@ SubClassOf( (hepatic stellate cell differentiation) AnnotationAssertion(Annotation( "GOC:dph") Annotation( "PMID:9407545") "The process in which a relatively unspecialized cell acquires the specialized structural and/or functional features of a hepatic stellate cell.") -AnnotationAssertion( "dph") AnnotationAssertion( "2013-04-18T13:36:08Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0061521") @@ -76515,7 +75722,6 @@ SubClassOf( (cilium disassembly) AnnotationAssertion(Annotation( "GOC:cilia") Annotation( "GOC:dph") Annotation( "PMID:17604723") Annotation( "PMID:27350441") "A cellular process that results in the breakdown of a cilium.") -AnnotationAssertion( "dph") AnnotationAssertion( "2013-04-18T14:59:59Z") AnnotationAssertion(Annotation( "GOC:dph") "cilium resorption") AnnotationAssertion( "biological_process") @@ -76527,7 +75733,6 @@ EquivalentClasses( ObjectIntersection # Class: (central canal development) AnnotationAssertion(Annotation( "GOC:cvs") Annotation( "GOC:dph") Annotation( "PMID:23409159") "The process whose specific outcome is the formation of the central canal of the spinal cord from its formation to the mature structure. The central canal is a spinal cord structure that is part of the ventricular system and is filled with cerebral-spinal fluid and runs the length of the spinal cord.") -AnnotationAssertion( "dph") AnnotationAssertion( "2013-04-20T08:18:31Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0061524") @@ -76539,7 +75744,6 @@ SubClassOf( ObjectSomeValuesFrom( (hindgut development) AnnotationAssertion(Annotation( "GOC:dph") "The process whose specific outcome is the progression of the hindgut over time, from its formation to the mature structure. The hindgut is part of the alimentary canal that lies posterior to the midgut.") -AnnotationAssertion( "dph") AnnotationAssertion( "2013-06-14T11:22:21Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0061525") @@ -76550,7 +75754,6 @@ SubClassOf( (acetylcholine secretion) AnnotationAssertion(Annotation( "GOC:dph") "The regulated release of acetylcholine by a cell.") -AnnotationAssertion( "dph") AnnotationAssertion( "2013-06-21T15:40:39Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0061526") @@ -76562,7 +75765,6 @@ SubClassOf( (dopamine secretion, neurotransmission) AnnotationAssertion(Annotation( "GOC:dph") "The regulated release of dopamine by a cell in which the dopamine acts as a neurotransmitter.") -AnnotationAssertion( "dph") AnnotationAssertion( "2013-06-21T15:43:15Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0061527") @@ -76575,7 +75777,6 @@ SubClassOf( ObjectSomeValuesFrom( (norepinephrine secretion, neurotransmission) AnnotationAssertion(Annotation( "GOC:dph") "The regulated release of norepinephrine by a cell, in which the norepinephrine acts as a neurotransmitter.") -AnnotationAssertion( "dph") AnnotationAssertion( "2013-06-21T16:05:08Z") AnnotationAssertion(Annotation( "GOC:dph") "noradrenaline secretion, neurotransmission") AnnotationAssertion( "biological_process") @@ -76588,7 +75789,6 @@ SubClassOf( (gamma-aminobutyric acid secretion, neurotransmission) AnnotationAssertion(Annotation( "GOC:dph") "The regulated release of gamma-aminobutyric acid by a cell, in which the gamma-aminobutyric acid acts as a neurotransmitter.") -AnnotationAssertion( "dph") AnnotationAssertion( "2013-06-21T16:10:50Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0061534") @@ -76601,7 +75801,6 @@ SubClassOf( ObjectSomeValuesFrom( (glutamate secretion, neurotransmission) AnnotationAssertion(Annotation( "GOC:dph") "The controlled release of glutamate by a cell, in which the glutamate acts as a neurotransmitter.") -AnnotationAssertion( "dph") AnnotationAssertion( "2013-06-21T16:14:47Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0061535") @@ -76614,7 +75813,6 @@ SubClassOf( ObjectSomeValuesFrom( (glycine secretion) AnnotationAssertion(Annotation( "GOC:dph") "The controlled release of glycine by a cell.") -AnnotationAssertion( "dph") AnnotationAssertion( "2013-06-21T16:18:23Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0061536") @@ -76625,7 +75823,6 @@ SubClassOf( (glycine secretion, neurotransmission) AnnotationAssertion(Annotation( "GOC:dph") "The controlled release of glycine by a cell, in which glycine acts as a neurotransmitter.") -AnnotationAssertion( "dph") AnnotationAssertion( "2013-06-21T16:19:02Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0061537") @@ -76638,7 +75835,6 @@ SubClassOf( ObjectSomeValuesFrom( (histamine secretion, neurotransmission) AnnotationAssertion(Annotation( "GOC:dph") "The controlled release of histamine by a cell, in which the histamine acts as a neurotransmitter.") -AnnotationAssertion( "dph") AnnotationAssertion( "2013-06-21T16:21:21Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0061538") @@ -76650,7 +75846,6 @@ SubClassOf( (peptide secretion, neurotransmission) AnnotationAssertion(Annotation( "GOC:dph") "The controlled release of a peptide from a cell in which the peptide acts as a neurotransmitter.") -AnnotationAssertion( "dph") AnnotationAssertion( "2013-06-25T09:10:10Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0061544") @@ -76661,7 +75856,6 @@ SubClassOf( (ganglion development) AnnotationAssertion(Annotation( "GOC:dph") "The process whose specific outcome is the progression of a ganglion over time, from its formation to the mature structure.") -AnnotationAssertion( "dph") AnnotationAssertion( "2013-07-10T08:36:12Z") AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:rl") "gangliogenesis") AnnotationAssertion( "biological_process") @@ -76675,7 +75869,6 @@ SubClassOf( ObjectSomeValuesFrom( (sympathetic ganglion development) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:rl") "The process whose specific outcome is the progression of a sympathetic ganglion over time, from its formation to the mature structure.") -AnnotationAssertion( "dph") AnnotationAssertion( "2013-07-10T08:38:01Z") AnnotationAssertion( "biological_process") AnnotationAssertion(Annotation( "GOC:dph") "sympathetic ganglia development") @@ -76688,7 +75881,6 @@ SubClassOf( ObjectSomeValuesFrom( (cranial ganglion development) AnnotationAssertion(Annotation( "GOC:dph") "The process whose specific outcome is the progression of a cranial ganglion over time, from its formation to the mature structure.") -AnnotationAssertion( "dph") AnnotationAssertion( "2013-07-10T08:40:14Z") AnnotationAssertion( "biological_process") AnnotationAssertion(Annotation( "GOC:dph") "cranial ganglia development") @@ -76701,7 +75893,6 @@ SubClassOf( ObjectSomeValuesFrom( (trigeminal ganglion development) AnnotationAssertion(Annotation( "GOC:dph") "The process whose specific outcome is the progression of a trigeminal ganglion over time, from its formation to the mature structure.") -AnnotationAssertion( "dph") AnnotationAssertion( "2013-07-10T08:42:19Z") AnnotationAssertion( "biological_process") AnnotationAssertion(Annotation( "GOC:dph") "trigeminal ganglia development") @@ -76713,7 +75904,6 @@ SubClassOf( (ganglion morphogenesis) AnnotationAssertion(Annotation( "GOC:dph") "The process in which the anatomical structures of ganglion are generated and organized.") -AnnotationAssertion( "dph") AnnotationAssertion( "2013-07-10T08:44:57Z") AnnotationAssertion( "biological_process") AnnotationAssertion(Annotation( "GOC:dph") "ganglia morphogenesis") @@ -76726,7 +75916,6 @@ SubClassOf( ObjectSomeValuesFrom( (ganglion maturation) AnnotationAssertion(Annotation( "GOC:dph") "A developmental process, independent of morphogenetic (shape) change, that is required for ganglion to attain its fully functional state.") -AnnotationAssertion( "dph") AnnotationAssertion( "2013-07-10T08:45:59Z") AnnotationAssertion( "biological_process") AnnotationAssertion(Annotation( "GOC:dph") "ganglia maturation") @@ -76739,7 +75928,6 @@ SubClassOf( ObjectSomeValuesFrom( (ganglion formation) AnnotationAssertion(Annotation( "GOC:dph") "The process that gives rise to ganglion. This process pertains to the initial formation of a structure from unspecified parts.") -AnnotationAssertion( "dph") AnnotationAssertion( "2013-07-10T08:51:50Z") AnnotationAssertion( "biological_process") AnnotationAssertion(Annotation( "GOC:dph") "ganglia formation") @@ -76752,7 +75940,6 @@ SubClassOf( ObjectSomeValuesFrom( (trigeminal ganglion morphogenesis) AnnotationAssertion(Annotation( "GOC:dph") "The process in which the anatomical structure of a trigeminal ganglion is generated and organized.") -AnnotationAssertion( "dph") AnnotationAssertion( "2013-07-10T08:57:12Z") AnnotationAssertion( "biological_process") AnnotationAssertion(Annotation( "GOC:dph") "trigeminal ganglia morphogenesis") @@ -76766,7 +75953,6 @@ SubClassOf( ObjectSomeValuesFrom( (trigeminal ganglion maturation) AnnotationAssertion(Annotation( "GOC:dph") "A developmental process, independent of morphogenetic (shape) change, that is required for a trigeminal ganglion to attain its fully functional state.") -AnnotationAssertion( "dph") AnnotationAssertion( "2013-07-10T08:58:24Z") AnnotationAssertion( "biological_process") AnnotationAssertion(Annotation( "GOC:dph") "trigeminal ganglia maturation") @@ -76780,7 +75966,6 @@ SubClassOf( ObjectSomeValuesFrom( (cranial ganglion maturation) AnnotationAssertion(Annotation( "GOC:dph") "A developmental process, independent of morphogenetic (shape) change, that is required for a cranial ganglion to attain its fully functional state.") -AnnotationAssertion( "dph") AnnotationAssertion( "2013-07-10T08:59:52Z") AnnotationAssertion( "biological_process") AnnotationAssertion(Annotation( "GOC:dph") "cranial ganglia maturation") @@ -76794,7 +75979,6 @@ SubClassOf( ObjectSomeValuesFrom( (cranial ganglion morphogenesis) AnnotationAssertion(Annotation( "GOC:dph") "The process in which the anatomical structure of a cranial ganglion is generated and organized.") -AnnotationAssertion( "dph") AnnotationAssertion( "2013-07-10T09:02:15Z") AnnotationAssertion( "biological_process") AnnotationAssertion(Annotation( "GOC:dph") "cranial ganglia morphogenesis") @@ -76808,7 +75992,6 @@ SubClassOf( ObjectSomeValuesFrom( (cranial ganglion formation) AnnotationAssertion(Annotation( "GOC:dph") "The process that gives rise to a cranial ganglion. This process pertains to the initial formation of a structure from unspecified parts.") -AnnotationAssertion( "dph") AnnotationAssertion( "2013-07-10T09:07:27Z") AnnotationAssertion( "biological_process") AnnotationAssertion(Annotation( "GOC:dph") "cranial ganglia formation") @@ -76821,7 +76004,6 @@ SubClassOf( ObjectSomeValuesFrom( (trigeminal ganglion formation) AnnotationAssertion(Annotation( "GOC:dph") "The process that gives rise to the trigeminal ganglion. This process pertains to the initial formation of a structure from unspecified parts.") -AnnotationAssertion( "dph") AnnotationAssertion( "2013-07-10T09:08:13Z") AnnotationAssertion( "biological_process") AnnotationAssertion(Annotation( "GOC:dph") "trigeminal ganglia formation") @@ -76834,7 +76016,6 @@ SubClassOf( ObjectSomeValuesFrom( (axon development) AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:pg") Annotation( "GOC:pr") "The progression of an axon over time. Covers axonogenesis (de novo generation of an axon) and axon regeneration (regrowth), as well as processes pertaining to the progression of the axon over time (fasciculation and defasciculation).") -AnnotationAssertion( "dph") AnnotationAssertion( "2013-07-18T14:43:01Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0061564") @@ -76844,7 +76025,6 @@ SubClassOf( (actin filament bundle organization) AnnotationAssertion(Annotation( "GOC:dph") "A process that results in the assembly, arrangement of constituent parts, or disassembly of an actin filament bundle.") -AnnotationAssertion( "dph") AnnotationAssertion( "2013-08-02T11:24:11Z") AnnotationAssertion( "biological_process") AnnotationAssertion(Annotation( "GOC:dph") "actin filament cable organization") @@ -76856,7 +76036,6 @@ SubClassOf( (colon epithelial cell migration) AnnotationAssertion(Annotation( "GOC:dph") "The orderly movement of a colonic epithelial cell from one site to another, often during the development of a multicellular organism.") -AnnotationAssertion( "dph") AnnotationAssertion( "2013-12-23T07:26:54Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0061580") @@ -76867,7 +76046,6 @@ SubClassOf( (corneal epithelial cell migration) AnnotationAssertion(Annotation( "GOC:dph") "The orderly movement of a corneal epithelial cell from one site to another, often during the development of a multicellular organism.") -AnnotationAssertion( "dph") AnnotationAssertion( "2013-12-23T07:28:29Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0061581") @@ -76878,7 +76056,6 @@ SubClassOf( (intestinal epithelial cell migration) AnnotationAssertion(Annotation( "GOC:dph") "The orderly movement of an intestinal epithelial cell from one site to another, often during the development of a multicellular organism.") -AnnotationAssertion( "dph") AnnotationAssertion( "2013-12-23T07:30:55Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0061582") @@ -76890,7 +76067,6 @@ SubClassOf( "GOC:dph") "The controlled release of orexin from a cell or a tissue.") AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/23504"^^xsd:anyURI) -AnnotationAssertion( "dph") AnnotationAssertion( "2013-12-26T10:07:38Z") AnnotationAssertion( "hypocretin secretion") AnnotationAssertion( "biological_process") @@ -76902,7 +76078,6 @@ SubClassOf( "GOC:dph") "The controlled release of orexin from a cell in which orexin acts as a neurotransmitter.") AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/23504"^^xsd:anyURI) -AnnotationAssertion( "dph") AnnotationAssertion( "2013-12-26T10:09:37Z") AnnotationAssertion( "hypocretin secretion, neurotransmission") AnnotationAssertion( "biological_process") @@ -76914,7 +76089,6 @@ SubClassOf( (pharyngeal arch artery morphogenesis) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:dph") Annotation( "PMID:20122914") "The process in which the anatomical structures of a pharyngeal arch artery is generated and organized. The pharyngeal arch arteries are a series of six paired embryological vascular structures, the development of which give rise to several major arteries, such as the stapedial artery, the middle meningeal artery, the internal carotid artery and the pulmonary artery.") -AnnotationAssertion( "dph") AnnotationAssertion( "2014-05-09T15:34:06Z") AnnotationAssertion(Annotation( "GOC:dph") "aortic arch artery morphogenesis") AnnotationAssertion( "biological_process") @@ -76928,7 +76102,6 @@ SubClassOf( ObjectSomeValuesFrom( "GOC:dph") Annotation( "GOC:vw") "Binding to a sequence-specific DNA binding RNA polymerase II transcription factor, any of the factors that interact selectively and non-covalently with a specific DNA sequence in order to modulate transcription.") AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/19354"^^xsd:anyURI) -AnnotationAssertion( "dph") AnnotationAssertion( "2014-05-15T09:12:24Z") AnnotationAssertion( "RNA polymerase II sequence-specific DNA binding transcription factor binding") AnnotationAssertion( "RNA polymerase II sequence-specific DNA-binding transcription factor binding") @@ -76943,7 +76116,6 @@ SubClassOf( (seminal vesicle morphogenesis) AnnotationAssertion(Annotation( "GOC:dph") "The process in which the anatomical structures of a seminal vesicle are generated and organized.") -AnnotationAssertion( "dph") AnnotationAssertion( "2015-03-04T13:33:49Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0061682") @@ -76955,7 +76127,6 @@ SubClassOf( ObjectSomeValuesFrom( (branching involved in seminal vesicle morphogenesis) AnnotationAssertion(Annotation( "GOC:dph") Annotation( "PMID:16916376") "The process in which the branching structure of the seminal vesicle is generated and organized. A branch is a division or offshoot from a main stem.") -AnnotationAssertion( "dph") AnnotationAssertion( "2015-03-04T13:39:47Z") AnnotationAssertion(Annotation( "GOC:dph") "gonecyst branching morphogenesis") AnnotationAssertion(Annotation( "GOC:dph") "seminal gland branching morphogenesis") @@ -76972,7 +76143,6 @@ SubClassOf( ObjectSomeValuesFrom( (transferase complex, transferring phosphorus-containing groups) AnnotationAssertion(Annotation( "GOC:bhm") Annotation( "GOC:dph") "A transferase complex capable of catalysis of the transfer of a phosphorus-containing group from one compound (donor) to another (acceptor).") -AnnotationAssertion( "dph") AnnotationAssertion( "2015-05-06T11:22:38Z") AnnotationAssertion( "cellular_component") AnnotationAssertion( "GO:0061695") @@ -76984,7 +76154,6 @@ SubClassOf( "GOC:autophagy") "The chemical reactions and pathways resulting in the breakdown of lipid droplets and hydrolysis of stored triglycerides occurring through the orchestrated activation of cytosolic lipases.") AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/28908"^^xsd:anyURI) -AnnotationAssertion( "dph") AnnotationAssertion( "2015-07-08T13:42:15Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0061725") @@ -76994,7 +76163,6 @@ EquivalentClasses( ObjectIntersection # Class: (secretory granule maturation) AnnotationAssertion(Annotation( "GOC:PARL") Annotation( "GOC:bf") Annotation( "GOC:dph") Annotation( "PMID:16618809") "Steps required to transform an immature secretory vesicle into a mature secretory vesicle. Typically proceeds through homotypic membrane fusion and membrane remodeling.") -AnnotationAssertion( "dph") AnnotationAssertion( "2016-09-09T13:24:34Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0061792") @@ -77045,7 +76213,6 @@ SubClassOf( (regulation of neuroblast migration) AnnotationAssertion(Annotation( "PMID:23149556") "Any process that modulates the frequency, rate or extent of neuroblast migration.") -AnnotationAssertion( "dph") AnnotationAssertion( "2017-03-08T18:17:07Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0061853") @@ -77055,7 +76222,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of neuroblast migration) AnnotationAssertion(Annotation( "PMID:23149556") "Any process that activates or increases the frequency, rate or extent of neuroblast migration.") -AnnotationAssertion( "dph") AnnotationAssertion( "2017-03-08T18:22:30Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0061854") @@ -77065,7 +76231,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of neuroblast migration) AnnotationAssertion(Annotation( "PMID:23149556") "Any process that stops, prevents, or reduces the frequency, rate or extent of neuroblast migration.") -AnnotationAssertion( "dph") AnnotationAssertion( "2017-03-08T18:26:21Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0061855") @@ -77075,7 +76240,6 @@ EquivalentClasses( ObjectIntersection # Class: (Golgi calcium ion transmembrane transport) AnnotationAssertion(Annotation( "PMID:21811607") "A process in which a calcium ion is transported from one side of a Golgi membrane to the other by means of some agent such as a transporter or pore.") -AnnotationAssertion( "dph") AnnotationAssertion( "2017-03-14T16:08:23Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0061856") @@ -77085,7 +76249,6 @@ EquivalentClasses( ObjectIntersection # Class: (hepatic stellate cell migration) AnnotationAssertion(Annotation( "PMID:24204762") "The orderly movement of a hepatic stellate cell from one site to another.") -AnnotationAssertion( "dph") AnnotationAssertion( "2017-05-01T13:01:40Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0061868") @@ -77095,7 +76258,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of hepatic stellate cell migration) AnnotationAssertion(Annotation( "PMID:24204762") "Any process that modulates the frequency, rate or extent of hepatic stellate cell migration.") -AnnotationAssertion( "dph") AnnotationAssertion( "2017-05-01T13:04:20Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0061869") @@ -77105,7 +76267,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of hepatic stellate cell migration) AnnotationAssertion(Annotation( "PMID:24204762") "Any process that increases the frequency, rate or extent of hepatic stellate cell migration.") -AnnotationAssertion( "dph") AnnotationAssertion( "2017-05-01T13:17:23Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0061870") @@ -77115,7 +76276,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of hepatic stellate cell migration) AnnotationAssertion(Annotation( "PMID:24204762") "Any process that stops, prevents or reduces the frequency, rate or extent of hepatic stellate cell migration.") -AnnotationAssertion( "dph") AnnotationAssertion( "2017-05-01T13:20:51Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0061871") @@ -77125,7 +76285,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of astrocyte activation) AnnotationAssertion(Annotation( "GOC:aruk") Annotation( "GOC:bc") Annotation( "PMID:20005821") "Any process that modulates the frequency, rate or extent of astrocyte activation.") -AnnotationAssertion( "dph") AnnotationAssertion( "2017-06-01T22:26:29Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0061888") @@ -77136,7 +76295,6 @@ SubClassOf( ObjectSomeValuesFrom( (negative regulation of astrocyte activation) AnnotationAssertion(Annotation( "GOC:aruk") Annotation( "GOC:bc") Annotation( "PMID:20005821") "Any process that decreases the frequency, rate or extent of astrocyte activation.") -AnnotationAssertion( "dph") AnnotationAssertion( "2017-06-01T22:29:43Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0061889") @@ -77148,7 +76306,6 @@ SubClassOf( ObjectSomeValuesFrom( (positive regulation of astrocyte activation) AnnotationAssertion(Annotation( "GOC:aruk") Annotation( "GOC:bc") Annotation( "PMID:20005821") "Any process that increases the frequency, rate or extent of astrocyte activation.") -AnnotationAssertion( "dph") AnnotationAssertion( "2017-06-01T22:31:50Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0061890") @@ -77160,7 +76317,6 @@ SubClassOf( ObjectSomeValuesFrom( (glial cell activation) AnnotationAssertion(Annotation( "GOC:aruk") Annotation( "GOC:bc") Annotation( "PMID:18723082") "A change in morphology and behavior of a glial cell resulting from exposure to a cytokine, chemokine, cellular ligand, or soluble factor.") -AnnotationAssertion( "dph") AnnotationAssertion( "2017-06-13T13:06:23Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0061900") @@ -77171,7 +76327,6 @@ SubClassOf( ObjectSomeValuesFrom( (protein localization to somatodendritic compartment) AnnotationAssertion(Annotation( "PMID:18341993") "A process in which a protein is transported to or maintained in a location within the somatodendritic compartment.") -AnnotationAssertion( "dph") AnnotationAssertion( "2017-09-08T13:22:26Z") AnnotationAssertion( "somatodendritic protein localization") AnnotationAssertion( "biological_process") @@ -77182,7 +76337,6 @@ EquivalentClasses( ObjectIntersection # Class: (establishment of protein localization to plasma membrane) AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:vw") "The directed movement of a protein to a specific location in a plasma membrane.") -AnnotationAssertion( "dph") AnnotationAssertion( "2017-10-26T12:55:15Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0061951") @@ -77192,7 +76346,6 @@ EquivalentClasses( ObjectIntersection # Class: (replacement bone morphogenesis) AnnotationAssertion(Annotation( "PMID:29852585") "The process in which bones are generated and organized as a result of the conversion of another structural tissue into bone.") -AnnotationAssertion( "dph") AnnotationAssertion( "2018-02-12T18:10:59Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0061971") @@ -77203,7 +76356,6 @@ SubClassOf( (dermal bone morphogenesis) AnnotationAssertion(Annotation( "PMID:12588850") Annotation( "PMID:15003632") "The process in which bone which forms superficially in the organism are generated and organized.") -AnnotationAssertion( "dph") AnnotationAssertion( "2018-02-12T18:16:21Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0061972") @@ -77213,7 +76365,6 @@ EquivalentClasses( ObjectIntersection # Class: (membrane bone morphogenesis) AnnotationAssertion(Annotation( "PMID:14579374") "The process in which bone which forms deep in the organism are generated and organized.") -AnnotationAssertion( "dph") AnnotationAssertion( "2018-02-12T18:21:09Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0061973") @@ -77223,7 +76374,6 @@ EquivalentClasses( ObjectIntersection # Class: (meiosis II cell cycle process) AnnotationAssertion(Annotation( "PMID:29385397") "A process that coontributes to the second meiotic division. The second meiotic division separates chromatids resulting in a haploid number of chromosomes.") -AnnotationAssertion( "dph") AnnotationAssertion( "2018-02-14T22:37:44Z") AnnotationAssertion(Annotation( "PMID:29385397") "second meiotic division") AnnotationAssertion( "biological_process") @@ -77234,7 +76384,6 @@ SubClassOf( (regulation of small molecule metabolic process) AnnotationAssertion(Annotation( "GOC:vw") "Any process that modulates the rate, frequency or extent of a small molecule metabolic process.") -AnnotationAssertion( "dph") AnnotationAssertion( "2018-03-19T14:11:54Z") AnnotationAssertion( "regulation of small molecule metabolism") AnnotationAssertion( "biological_process") @@ -77245,7 +76394,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of small molecule metabolic process) AnnotationAssertion(Annotation( "GOC:vw") "Any process that activates or increases the frequency, rate or extent of a small molecule metabolic process.") -AnnotationAssertion( "dph") AnnotationAssertion( "2018-03-19T14:25:10Z") AnnotationAssertion( "positive regulation of small molecule metabolism") AnnotationAssertion( "biological_process") @@ -77256,7 +76404,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of small molecule metabolic process) AnnotationAssertion(Annotation( "GOC:vw") "Any process that stops, prevents or reduces the frequency, rate or extent of a small molecule metabolic process.") -AnnotationAssertion( "dph") AnnotationAssertion( "2018-03-19T14:27:23Z") AnnotationAssertion( "negative regulation of small molecule metabolism") AnnotationAssertion( "biological_process") @@ -77267,7 +76414,6 @@ EquivalentClasses( ObjectIntersection # Class: (collagen-containing extracellular matrix) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:rph") Annotation( "PMID:21123617") "An extracellular matrix consisting mainly of proteins (especially collagen) and glycosaminoglycans (mostly as proteoglycans) that provides not only essential physical scaffolding for the cellular constituents but can also initiate crucial biochemical and biomechanical cues required for tissue morphogenesis, differentiation and homeostasis. The components are secreted by cells in the vicinity and form a sheet underlying or overlying cells such as endothelial and epithelial cells.") -AnnotationAssertion( "dph") AnnotationAssertion( "2018-04-13T12:47:21Z") AnnotationAssertion( "cellular_component") AnnotationAssertion( "GO:0062023") @@ -77279,7 +76425,6 @@ SubClassOf( ObjectAllValuesFrom( (positive regulation of mitotic sister chromatid segregation) AnnotationAssertion(Annotation( "PMID:12773390") "Any process that starts or increases the frequency, rate or extent of sister chromatid segregation during mitosis.") -AnnotationAssertion( "dph") AnnotationAssertion( "2018-04-23T14:32:23Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0062033") @@ -77289,7 +76434,6 @@ EquivalentClasses( ObjectIntersection # Class: (compound eye pigment cell differentiation) AnnotationAssertion(Annotation( "GOC:ha") Annotation( "PMID:8929534") "The process in which a relatively unspecialized cell acquires the specialized features of a compound eye pigment cell, a cell of the retina containing screening pigments that functions to screen photoreceptors from light leaking from adjacent ommatidia.") -AnnotationAssertion( "dph") AnnotationAssertion( "2018-08-01T12:59:42Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0062056") @@ -77300,7 +76444,6 @@ SubClassOf( ObjectSomeValuesFrom( (stomach development) AnnotationAssertion(Annotation( "PMID:11967278") "The process whose specific outcome is the progression of the stomach over time, from its formation to the mature structure. The stomach is an expanded region of the vertebrate alimentary tract that serves as a food storage compartment and digestive organ.") -AnnotationAssertion( "dph") AnnotationAssertion( "2018-11-20T18:15:45Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0062094") @@ -77311,7 +76454,6 @@ SubClassOf( ObjectSomeValuesFrom( (cargo receptor complex) AnnotationAssertion(Annotation( "PMID:27903609") "Any protein complex that is part of a membrane and which functions as a cargo receptor.") -AnnotationAssertion( "dph") AnnotationAssertion( "2019-07-08T18:09:01Z") AnnotationAssertion( "cellular_component") AnnotationAssertion( "GO:0062137") @@ -77321,7 +76463,6 @@ EquivalentClasses( ObjectIntersection # Class: (detection of stimulus involved in sensory perception of pain) AnnotationAssertion(Annotation( "PMID:19837031") "The series of events involved in the perception of pain in which a stimulus is received and converted into a molecular signal.") -AnnotationAssertion( "dph") AnnotationAssertion( "2019-09-13T13:48:47Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0062149") @@ -77331,7 +76472,6 @@ EquivalentClasses( ObjectIntersection # Class: (lutein metabolic process) AnnotationAssertion(Annotation( "PMID:24397433") "The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform lutein.") -AnnotationAssertion( "dph") AnnotationAssertion( "2019-11-18T15:56:36Z") AnnotationAssertion( "lutein metabolism") AnnotationAssertion( "biological_process") @@ -77342,7 +76482,6 @@ EquivalentClasses( ObjectIntersection # Class: (lutein biosynthetic process) AnnotationAssertion(Annotation( "PMID:24397433") "The chemical reactions and pathways resulting in the formation of lutein.") -AnnotationAssertion( "dph") AnnotationAssertion( "2019-11-18T16:01:00Z") AnnotationAssertion( "lutein anabolism") AnnotationAssertion( "lutein biosynthesis") @@ -77355,7 +76494,6 @@ EquivalentClasses( ObjectIntersection # Class: (lutein catabolic process) AnnotationAssertion(Annotation( "PMID:24397433") "The chemical reactions and pathways resulting in the breakdown of lutein.") -AnnotationAssertion( "dph") AnnotationAssertion( "2019-11-18T16:06:07Z") AnnotationAssertion( "lutein breakdown") AnnotationAssertion( "lutein catabolism") @@ -77368,7 +76506,6 @@ EquivalentClasses( ObjectIntersection # Class: (radial spoke assembly) AnnotationAssertion(Annotation( "PMID:21613541") Annotation( "PMID:21692193") Annotation( "PMID:24124175") Annotation( "PMID:27940518") Annotation( "PMID:8408197") "The aggregation, arrangement and bonding together of a set of components to form the radial spoke, a protein complex that links the outer microtubule doublet of the ciliary or flagellum axoneme with the sheath that surrounds the central pair of microtubules.") -AnnotationAssertion( "dph") AnnotationAssertion( "2019-11-20T17:50:08Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0062177") @@ -77379,7 +76516,6 @@ SubClassOf( ObjectSomeValuesFrom( (ionocyte differentiation) AnnotationAssertion(Annotation( "PMID:17555741") "The process in which a relatively unspecialized cell acquires specialized structural and/or functional features of an ionocyte. Ionocytes are specialized epithelial cells that contribute to osmotic homeostasis.") -AnnotationAssertion( "dph") AnnotationAssertion( "2020-04-20T12:30:35Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0062236") @@ -77389,7 +76525,6 @@ EquivalentClasses( ObjectIntersection # Class: (protein localization to postsynapse) AnnotationAssertion(Annotation( "PMID:31189538") "Any process in which a protein is transported to, and/or maintained at the postsynapse, the part of a synapse that is part of the post-synaptic cell.") -AnnotationAssertion( "dph") AnnotationAssertion( "2020-04-20T13:58:43Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0062237") @@ -78369,7 +77504,6 @@ SubClassOf( ObjectSomeValuesFrom( (protein secretion by platelet) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:mah") "The regulated release of proteins by a platelet or group of platelets.") -AnnotationAssertion( "mah") AnnotationAssertion( "2009-04-09T02:38:05Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0070560") @@ -78381,7 +77515,6 @@ SubClassOf( ObjectSomeValuesFrom( (calcium ion transmembrane transport) AnnotationAssertion(Annotation( "GOC:mah") "A process in which a calcium ion is transported from one side of a membrane to the other by means of some agent such as a transporter or pore.") -AnnotationAssertion( "mah") AnnotationAssertion( "2009-04-28T10:44:09Z") AnnotationAssertion( "calcium ion membrane transport") AnnotationAssertion(Annotation( "GOC:mah") "transmembrane calcium transport") @@ -78394,7 +77527,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of protein processing) AnnotationAssertion(Annotation( "GOC:mah") "Any process that modulates the frequency, rate or extent of protein processing, a protein maturation process achieved by the cleavage of a peptide bond or bonds within a protein.") -AnnotationAssertion( "mah") AnnotationAssertion( "2009-04-29T02:49:14Z") AnnotationAssertion( "regulation of protein maturation by peptide bond cleavage") AnnotationAssertion( "biological_process") @@ -78406,7 +77538,6 @@ SubClassOf( (transepithelial transport) AnnotationAssertion(Annotation( "GOC:mah") Annotation( "GOC:yaf") Annotation( "ISBN:0716731363") "The directed movement of a substance from one side of an epithelium to the other.") -AnnotationAssertion( "mah") AnnotationAssertion( "2009-05-06T03:31:02Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0070633") @@ -78417,7 +77548,6 @@ SubClassOf( (transepithelial ammonium transport) AnnotationAssertion(Annotation( "GOC:mah") Annotation( "GOC:yaf") "The directed movement of ammonium ions from one side of an epithelium to the other.") -AnnotationAssertion( "mah") AnnotationAssertion( "2009-05-06T03:34:43Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0070634") @@ -78427,7 +77557,6 @@ EquivalentClasses( ObjectIntersection # Class: (leukocyte proliferation) AnnotationAssertion(Annotation( "GOC:add") "The expansion of a leukocyte population by cell division.") -AnnotationAssertion( "mah") AnnotationAssertion( "2009-05-28T05:25:28Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0070661") @@ -78440,7 +77569,6 @@ SubClassOf( ObjectAllValuesFrom( (mast cell proliferation) AnnotationAssertion(Annotation( "GOC:add") "The expansion of a mast cell population by cell division.") -AnnotationAssertion( "mah") AnnotationAssertion( "2009-05-28T05:27:51Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0070662") @@ -78451,7 +77579,6 @@ SubClassOf( (regulation of leukocyte proliferation) AnnotationAssertion(Annotation( "GOC:add") Annotation( "GOC:mah") "Any process that modulates the frequency, rate or extent of leukocyte proliferation.") -AnnotationAssertion( "mah") AnnotationAssertion( "2009-05-28T05:30:39Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0070663") @@ -78462,7 +77589,6 @@ SubClassOf( (negative regulation of leukocyte proliferation) AnnotationAssertion(Annotation( "GOC:add") Annotation( "GOC:mah") "Any process that stops, prevents, or reduces the frequency, rate or extent of leukocyte proliferation.") -AnnotationAssertion( "mah") AnnotationAssertion( "2009-05-28T05:34:50Z") AnnotationAssertion(Annotation( "GOC:mah") "down regulation of leukocyte proliferation") AnnotationAssertion(Annotation( "GOC:mah") "down-regulation of leukocyte proliferation") @@ -78477,7 +77603,6 @@ SubClassOf( (positive regulation of leukocyte proliferation) AnnotationAssertion(Annotation( "GOC:add") Annotation( "GOC:mah") "Any process that activates or increases the frequency, rate or extent of leukocyte proliferation.") -AnnotationAssertion( "mah") AnnotationAssertion( "2009-05-28T05:36:46Z") AnnotationAssertion(Annotation( "GOC:mah") "up regulation of leukocyte proliferation") AnnotationAssertion(Annotation( "GOC:mah") "up-regulation of leukocyte proliferation") @@ -78494,7 +77619,6 @@ SubClassOf( (regulation of mast cell proliferation) AnnotationAssertion(Annotation( "GOC:add") Annotation( "GOC:mah") "Any process that modulates the frequency, rate or extent of mast cell proliferation.") -AnnotationAssertion( "mah") AnnotationAssertion( "2009-05-28T05:40:43Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0070666") @@ -78504,7 +77628,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of mast cell proliferation) AnnotationAssertion(Annotation( "GOC:add") Annotation( "GOC:mah") "Any process that stops, prevents or reduces the rate or extent of mast cell proliferation.") -AnnotationAssertion( "mah") AnnotationAssertion( "2009-05-28T05:45:11Z") AnnotationAssertion(Annotation( "GOC:mah") "down regulation of mast cell proliferation") AnnotationAssertion(Annotation( "GOC:mah") "down-regulation of mast cell proliferation") @@ -78518,7 +77641,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of mast cell proliferation) AnnotationAssertion(Annotation( "GOC:add") Annotation( "GOC:mah") "Any process that activates or increases the rate or extent of mast cell proliferation.") -AnnotationAssertion( "mah") AnnotationAssertion( "2009-05-28T05:48:30Z") AnnotationAssertion(Annotation( "GOC:mah") "up regulation of mast cell proliferation") AnnotationAssertion(Annotation( "GOC:mah") "up-regulation of mast cell proliferation") @@ -78533,7 +77655,6 @@ EquivalentClasses( ObjectIntersection # Class: (cellular macromolecule localization) AnnotationAssertion(Annotation( "GOC:mah") "Any process in which a macromolecule is transported to, and/or maintained in, a specific location at the level of a cell. Localization at the cellular level encompasses movement within the cell, from within the cell to the cell surface, or from one location to another at the surface of a cell.") -AnnotationAssertion( "mah") AnnotationAssertion( "2009-06-16T04:08:29Z") AnnotationAssertion(Annotation( "GOC:mah") "cellular macromolecule localisation") AnnotationAssertion( "biological_process") @@ -78545,7 +77666,6 @@ SubClassOf( (tertiary granule) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:mah") Annotation( "GOC:rl") Annotation( "PMID:12070036") "A secretory granule that contains cathepsin and gelatinase and is readily exocytosed upon cell activation; found primarily in mature neutrophil cells.") -AnnotationAssertion( "mah") AnnotationAssertion( "2009-07-20T03:57:00Z") AnnotationAssertion(Annotation( "PMID:23650620") "gelatinase granule") AnnotationAssertion( "cellular_component") @@ -78556,7 +77676,6 @@ SubClassOf( (tertiary granule membrane) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:mah") Annotation( "GOC:rl") Annotation( "PMID:12070036") "The lipid bilayer surrounding a tertiary granule.") -AnnotationAssertion( "mah") AnnotationAssertion( "2009-07-20T03:59:41Z") AnnotationAssertion( "cellular_component") AnnotationAssertion( "GO:0070821") @@ -78568,7 +77687,6 @@ SubClassOf( ObjectSomeValuesFrom( (bicellular tight junction assembly) AnnotationAssertion(Annotation( "GOC:mah") "The aggregation, arrangement and bonding together of a set of components to form a tight junction, an occluding cell-cell junction that is composed of a branching network of sealing strands that completely encircles the apical end of each cell in an epithelial sheet.") -AnnotationAssertion( "mah") AnnotationAssertion( "2009-07-23T04:32:38Z") AnnotationAssertion(Annotation( "GOC:mah") "tight junction formation") AnnotationAssertion( "biological_process") @@ -78581,7 +77699,6 @@ SubClassOf( ObjectSomeValuesFrom( (basement membrane assembly) AnnotationAssertion(Annotation( "GOC:mah") "The aggregation, arrangement and bonding together of a set of components to form a basement membrane, a part of the extracellular region that consists of a thin layer of dense material found in various animal tissues interposed between the cells and the adjacent connective tissue.") -AnnotationAssertion( "mah") AnnotationAssertion( "2009-07-23T05:01:51Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0070831") @@ -78592,7 +77709,6 @@ EquivalentClasses( ObjectIntersection # Class: (dynein complex binding) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:bf") Annotation( "GOC:mah") "Binding to a dynein complex, a protein complex that contains two or three dynein heavy chains and several light chains, and has microtubule motor activity.") -AnnotationAssertion( "mah") AnnotationAssertion( "2009-07-31T01:22:47Z") AnnotationAssertion( "molecular_function") AnnotationAssertion( "dynein binding") @@ -78603,7 +77719,6 @@ EquivalentClasses( ObjectIntersection # Class: (growth factor receptor binding) AnnotationAssertion(Annotation( "GOC:mah") Annotation( "GOC:vw") "Binding to a growth factor receptor.") -AnnotationAssertion( "mah") AnnotationAssertion( "2009-08-07T11:23:02Z") AnnotationAssertion( "molecular_function") AnnotationAssertion( "GO:0070851") @@ -78613,7 +77728,6 @@ SubClassOf( (regulation of bile acid biosynthetic process) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:mah") "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of bile acids.") -AnnotationAssertion( "mah") AnnotationAssertion( "2009-08-14T03:09:02Z") AnnotationAssertion(Annotation( "GOC:mah") "regulation of bile acid anabolism") AnnotationAssertion(Annotation( "GOC:mah") "regulation of bile acid biosynthesis") @@ -78631,7 +77745,6 @@ SubClassOf( (negative regulation of bile acid biosynthetic process) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:mah") "Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of bile acids.") -AnnotationAssertion( "mah") AnnotationAssertion( "2009-08-14T03:16:40Z") AnnotationAssertion(Annotation( "GOC:mah") "down regulation of bile acid biosynthetic process") AnnotationAssertion(Annotation( "GOC:mah") "down-regulation of bile acid biosynthetic process") @@ -78653,7 +77766,6 @@ SubClassOf( (positive regulation of bile acid biosynthetic process) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:mah") "Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of bile acids.") -AnnotationAssertion( "mah") AnnotationAssertion( "2009-08-14T03:22:58Z") AnnotationAssertion(Annotation( "GOC:mah") "positive regulation of bile acid anabolism") AnnotationAssertion(Annotation( "GOC:mah") "positive regulation of bile acid biosynthesis") @@ -78676,7 +77788,6 @@ SubClassOf( (regulation of glycogen metabolic process) AnnotationAssertion(Annotation( "GOC:mah") "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving glycogen.") -AnnotationAssertion( "mah") AnnotationAssertion( "2009-08-20T02:44:53Z") AnnotationAssertion(Annotation( "GOC:mah") "regulation of glycogen metabolism") AnnotationAssertion( "biological_process") @@ -78689,7 +77800,6 @@ SubClassOf( (negative regulation of glycogen metabolic process) AnnotationAssertion(Annotation( "GOC:mah") "Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving glycogen.") -AnnotationAssertion( "mah") AnnotationAssertion( "2009-08-20T02:50:41Z") AnnotationAssertion(Annotation( "GOC:mah") "negative regulation of glycogen metabolism") AnnotationAssertion( "biological_process") @@ -78703,7 +77813,6 @@ SubClassOf( (positive regulation of glycogen metabolic process) AnnotationAssertion(Annotation( "GOC:mah") "Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving glycogen.") -AnnotationAssertion( "mah") AnnotationAssertion( "2009-08-20T02:53:55Z") AnnotationAssertion(Annotation( "GOC:mah") "positive regulation of glycogen metabolism") AnnotationAssertion( "biological_process") @@ -78717,7 +77826,6 @@ SubClassOf( (cellular response to chemical stimulus) AnnotationAssertion(Annotation( "GOC:mah") "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a chemical stimulus.") -AnnotationAssertion( "mah") AnnotationAssertion( "2009-08-27T04:41:45Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0070887") @@ -78730,7 +77838,6 @@ SubClassOf( (organelle assembly) AnnotationAssertion(Annotation( "GOC:mah") "The aggregation, arrangement and bonding together of a set of components to form an organelle. An organelle is an organized structure of distinctive morphology and function. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton. Excludes the plasma membrane.") -AnnotationAssertion( "mah") AnnotationAssertion( "2009-09-15T03:00:51Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0070925") @@ -78742,7 +77849,6 @@ SubClassOf( (neutrophil mediated cytotoxicity) AnnotationAssertion(Annotation( "GOC:add") Annotation( "ISBN:0781765196") "The directed killing of a target cell by a neutrophil.") -AnnotationAssertion( "mah") AnnotationAssertion( "2009-10-01T01:49:30Z") AnnotationAssertion(Annotation( "GOC:add") "neutrophil mediated cell killing") AnnotationAssertion( "biological_process") @@ -78755,7 +77861,6 @@ SubClassOf( (regulation of neutrophil mediated cytotoxicity) AnnotationAssertion(Annotation( "GOC:add") Annotation( "GOC:mah") "Any process that modulates the rate, frequency or extent of neutrophil mediated killing of a target cell, the directed killing of a target cell by a neutrophil.") -AnnotationAssertion( "mah") AnnotationAssertion( "2009-10-01T02:14:36Z") AnnotationAssertion(Annotation( "GOC:add") "regulation of neutrophil mediated cell killing") AnnotationAssertion( "biological_process") @@ -78766,7 +77871,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of neutrophil mediated cytotoxicity) AnnotationAssertion(Annotation( "GOC:add") Annotation( "GOC:mah") "Any process that decreases the frequency, rate or extent of the directed killing of a target cell by a neutrophil.") -AnnotationAssertion( "mah") AnnotationAssertion( "2009-10-01T02:20:17Z") AnnotationAssertion(Annotation( "GOC:mah") "down regulation of neutrophil mediated cytotoxicity") AnnotationAssertion(Annotation( "GOC:mah") "down-regulation of neutrophil mediated cytotoxicity") @@ -78781,7 +77885,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of neutrophil mediated cytotoxicity) AnnotationAssertion(Annotation( "GOC:add") Annotation( "GOC:mah") "Any process that increases the frequency, rate or extent of the directed killing of a target cell by a neutrophil.") -AnnotationAssertion( "mah") AnnotationAssertion( "2009-10-01T02:28:49Z") AnnotationAssertion(Annotation( "GOC:add") "positive regulation of neutrophil mediated cell killing") AnnotationAssertion(Annotation( "GOC:mah") "up regulation of neutrophil mediated cytotoxicity") @@ -78797,7 +77900,6 @@ EquivalentClasses( ObjectIntersection # Class: (bone maturation) AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:mah") "A developmental process, independent of morphogenetic (shape) change, that is required for bone to attain its fully functional state.") -AnnotationAssertion( "mah") AnnotationAssertion( "2009-10-05T04:35:31Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0070977") @@ -78809,7 +77911,6 @@ SubClassOf( ObjectSomeValuesFrom( (sensory perception of gravity) AnnotationAssertion(Annotation( "GOC:mah") "The series of events required for an organism to receive a gravitational stimulus, convert it to a molecular signal, and recognize and characterize the signal. This is a neurological process.") -AnnotationAssertion( "mah") AnnotationAssertion( "2009-11-03T03:25:12Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0070998") @@ -78819,7 +77920,6 @@ SubClassOf( (detection of mechanical stimulus involved in sensory perception of gravity) AnnotationAssertion(Annotation( "GOC:dos") Annotation( "GOC:mah") "The series of events involved in the perception of gravity in which a sensory mechanical stimulus is received and converted into a molecular signal.") -AnnotationAssertion( "mah") AnnotationAssertion( "2009-11-03T03:27:30Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0070999") @@ -78830,7 +77930,6 @@ SubClassOf( (protein localization to chromatin) AnnotationAssertion(Annotation( "GOC:mah") "Any process in which a protein is transported to, or maintained at, a part of a chromosome that is organized into chromatin.") -AnnotationAssertion( "mah") AnnotationAssertion( "2009-11-20T11:51:20Z") AnnotationAssertion(Annotation( "GOC:mah") "protein localisation to chromatin") AnnotationAssertion( "biological_process") @@ -78842,7 +77941,6 @@ SubClassOf( (establishment of protein localization to chromatin) AnnotationAssertion(Annotation( "GOC:mah") "The directed movement of a protein to a part of a chromosome that is organized into chromatin.") -AnnotationAssertion( "mah") AnnotationAssertion( "2009-11-20T11:52:43Z") AnnotationAssertion(Annotation( "GOC:mah") "establishment of protein localisation to chromatin") AnnotationAssertion( "biological_process") @@ -78854,7 +77952,6 @@ SubClassOf( (cellular response to abiotic stimulus) AnnotationAssertion(Annotation( "GOC:mah") "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an abiotic (non-living) stimulus.") -AnnotationAssertion( "mah") AnnotationAssertion( "2009-12-03T01:02:11Z") AnnotationAssertion(Annotation( "GOC:mah") "cellular response to abiotic stress") AnnotationAssertion( "biological_process") @@ -78868,7 +77965,6 @@ SubClassOf( (cellular response to amino acid stimulus) AnnotationAssertion(Annotation( "GOC:mah") "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an amino acid stimulus. An amino acid is a carboxylic acids containing one or more amino groups.") -AnnotationAssertion( "mah") AnnotationAssertion( "2009-12-03T02:08:11Z") AnnotationAssertion(Annotation( "GOC:mah") "cellular response to amino acid") AnnotationAssertion( "biological_process") @@ -78879,7 +77975,6 @@ EquivalentClasses( ObjectIntersection # Class: (cellular response to ammonium ion) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000071") Annotation( "PMID:23509267") "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an ammonium stimulus.") -AnnotationAssertion( "mah") AnnotationAssertion( "2009-12-03T02:39:40Z") AnnotationAssertion( "cellular response to ammonia") AnnotationAssertion( "biological_process") @@ -78890,7 +77985,6 @@ EquivalentClasses( ObjectIntersection # Class: (cellular response to calcium ion) AnnotationAssertion(Annotation( "GOC:mah") "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a calcium ion stimulus.") -AnnotationAssertion( "mah") AnnotationAssertion( "2009-12-10T03:55:01Z") AnnotationAssertion(Annotation( "GOC:mah") "cellular response to Ca2+ ion") AnnotationAssertion( "biological_process") @@ -78902,7 +77996,6 @@ SubClassOf( (cellular response to iron ion) AnnotationAssertion(Annotation( "GOC:mah") "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an iron ion stimulus.") -AnnotationAssertion( "mah") AnnotationAssertion( "2009-12-10T03:57:22Z") AnnotationAssertion(Annotation( "GOC:mah") "cellular response to iron") AnnotationAssertion( "biological_process") @@ -78913,7 +78006,6 @@ EquivalentClasses( ObjectIntersection # Class: (cellular response to ATP) AnnotationAssertion(Annotation( "GOC:mah") "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an ATP (adenosine 5'-triphosphate) stimulus.") -AnnotationAssertion( "mah") AnnotationAssertion( "2009-12-10T05:09:47Z") AnnotationAssertion(Annotation( "GOC:mah") "cellular response to adenosine 5'-triphosphate") AnnotationAssertion(Annotation( "GOC:mah") "cellular response to adenosine triphosphate") @@ -78925,7 +78017,6 @@ EquivalentClasses( ObjectIntersection # Class: (cellular response to carbohydrate stimulus) AnnotationAssertion(Annotation( "GOC:mah") "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a carbohydrate stimulus.") -AnnotationAssertion( "mah") AnnotationAssertion( "2009-12-10T05:13:33Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0071322") @@ -78935,7 +78026,6 @@ EquivalentClasses( ObjectIntersection # Class: (cellular response to hexose stimulus) AnnotationAssertion(Annotation( "GOC:mah") "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a hexose stimulus.") -AnnotationAssertion( "mah") AnnotationAssertion( "2009-12-10T05:37:00Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0071331") @@ -78945,7 +78035,6 @@ EquivalentClasses( ObjectIntersection # Class: (cellular response to glucose stimulus) AnnotationAssertion(Annotation( "GOC:mah") "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a glucose stimulus.") -AnnotationAssertion( "mah") AnnotationAssertion( "2009-12-10T05:38:03Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0071333") @@ -78956,7 +78045,6 @@ SubClassOf( (cellular response to cytokine stimulus) AnnotationAssertion(Annotation( "GOC:mah") "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a cytokine stimulus.") -AnnotationAssertion( "mah") AnnotationAssertion( "2009-12-11T02:41:12Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0071345") @@ -78966,7 +78054,6 @@ SubClassOf( (cellular response to peptide hormone stimulus) AnnotationAssertion(Annotation( "GOC:mah") "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a peptide hormone stimulus. A peptide hormone is any of a class of peptides that are secreted into the blood stream and have endocrine functions in living animals.") -AnnotationAssertion( "mah") AnnotationAssertion( "2009-12-11T03:24:18Z") AnnotationAssertion(Annotation( "GOC:mah") "cellular response to polypeptide hormone stimulus") AnnotationAssertion( "biological_process") @@ -78977,7 +78064,6 @@ EquivalentClasses( ObjectIntersection # Class: (cellular response to glucagon stimulus) AnnotationAssertion(Annotation( "GOC:mah") "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a glucagon stimulus.") -AnnotationAssertion( "mah") AnnotationAssertion( "2009-12-11T03:25:07Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0071377") @@ -78987,7 +78073,6 @@ EquivalentClasses( ObjectIntersection # Class: (cellular response to steroid hormone stimulus) AnnotationAssertion(Annotation( "GOC:mah") "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a steroid hormone stimulus.") -AnnotationAssertion( "mah") AnnotationAssertion( "2009-12-11T03:49:02Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0071383") @@ -78997,7 +78082,6 @@ EquivalentClasses( ObjectIntersection # Class: (cellular response to corticosteroid stimulus) AnnotationAssertion(Annotation( "GOC:mah") "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a corticosteroid hormone stimulus. A corticosteroid is a steroid hormone that is produced in the adrenal cortex. Corticosteroids are involved in a wide range of physiologic systems such as stress response, immune response and regulation of inflammation, carbohydrate metabolism, protein catabolism, blood electrolyte levels, and behavior. They include glucocorticoids and mineralocorticoids.") -AnnotationAssertion( "mah") AnnotationAssertion( "2009-12-11T03:52:07Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0071384") @@ -79007,7 +78091,6 @@ EquivalentClasses( ObjectIntersection # Class: (cellular response to glucocorticoid stimulus) AnnotationAssertion(Annotation( "GOC:mah") "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a glucocorticoid stimulus. Glucocorticoids are hormonal C21 corticosteroids synthesized from cholesterol with the ability to bind with the cortisol receptor and trigger similar effects. Glucocorticoids act primarily on carbohydrate and protein metabolism, and have anti-inflammatory effects.") -AnnotationAssertion( "mah") AnnotationAssertion( "2009-12-11T03:53:56Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0071385") @@ -79017,7 +78100,6 @@ EquivalentClasses( ObjectIntersection # Class: (cellular response to mineralocorticoid stimulus) AnnotationAssertion(Annotation( "GOC:mah") "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a mineralocorticoid stimulus. Mineralocorticoids are hormonal C21 corticosteroids synthesized from cholesterol and characterized by their similarity to aldosterone. Mineralocorticoids act primarily on water and electrolyte balance.") -AnnotationAssertion( "mah") AnnotationAssertion( "2009-12-11T03:59:02Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0071389") @@ -79027,7 +78109,6 @@ EquivalentClasses( ObjectIntersection # Class: (cellular response to estradiol stimulus) AnnotationAssertion(Annotation( "GOC:mah") "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of stimulus by estradiol, a C18 steroid hormone hydroxylated at C3 and C17 that acts as a potent estrogen.") -AnnotationAssertion( "mah") AnnotationAssertion( "2009-12-11T04:10:31Z") AnnotationAssertion(Annotation( "GOC:mah") "cellular response to E2 stimulus") AnnotationAssertion( "biological_process") @@ -79038,7 +78119,6 @@ EquivalentClasses( ObjectIntersection # Class: (cellular response to progesterone stimulus) AnnotationAssertion(Annotation( "GOC:mah") "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a progesterone stimulus.") -AnnotationAssertion( "mah") AnnotationAssertion( "2009-12-11T04:11:13Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0071393") @@ -79048,7 +78128,6 @@ EquivalentClasses( ObjectIntersection # Class: (cellular response to testosterone stimulus) AnnotationAssertion(Annotation( "GOC:mah") "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a testosterone stimulus.") -AnnotationAssertion( "mah") AnnotationAssertion( "2009-12-11T04:11:29Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0071394") @@ -79058,7 +78137,6 @@ EquivalentClasses( ObjectIntersection # Class: (cellular response to lipid) AnnotationAssertion(Annotation( "GOC:mah") "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a lipid stimulus.") -AnnotationAssertion( "mah") AnnotationAssertion( "2009-12-11T04:37:10Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0071396") @@ -79068,7 +78146,6 @@ EquivalentClasses( ObjectIntersection # Class: (cellular response to lipoprotein particle stimulus) AnnotationAssertion(Annotation( "GOC:mah") "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a lipoprotein particle stimulus.") -AnnotationAssertion( "mah") AnnotationAssertion( "2009-12-14T02:48:51Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0071402") @@ -79078,7 +78155,6 @@ EquivalentClasses( ObjectIntersection # Class: (cellular response to amine stimulus) AnnotationAssertion(Annotation( "GOC:mah") "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an amine stimulus. An amine is a compound formally derived from ammonia by replacing one, two or three hydrogen atoms by hydrocarbyl groups.") -AnnotationAssertion( "mah") AnnotationAssertion( "2009-12-14T04:08:17Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0071418") @@ -79088,7 +78164,6 @@ EquivalentClasses( ObjectIntersection # Class: (cellular response to histamine) AnnotationAssertion(Annotation( "GOC:mah") "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a histamine stimulus. Histamine, the biogenic amine 2-(1H-imidazol-4-yl)ethanamine, is involved in local immune responses as well as regulating physiological function in the gut and acting as a neurotransmitter.") -AnnotationAssertion( "mah") AnnotationAssertion( "2009-12-14T04:09:25Z") AnnotationAssertion(Annotation( "GOC:mah") "cellular response to histamine stimulus") AnnotationAssertion( "biological_process") @@ -79099,7 +78174,6 @@ EquivalentClasses( ObjectIntersection # Class: (hematopoietic stem cell proliferation) AnnotationAssertion(Annotation( "CL:0000037") Annotation( "GOC:BHF") Annotation( "GOC:add") Annotation( "GOC:mah") Annotation( "GOC:rl") "The expansion of a hematopoietic stem cell population by cell division. A hematopoietic stem cell is a stem cell from which all cells of the lymphoid and myeloid lineages develop.") -AnnotationAssertion( "mah") AnnotationAssertion( "2009-12-16T10:22:52Z") AnnotationAssertion( "hemopoietic stem cell proliferation") AnnotationAssertion( "biological_process") @@ -79111,7 +78185,6 @@ SubClassOf( ObjectSomeValuesFrom( (cellular response to superoxide) AnnotationAssertion(Annotation( "GOC:mah") "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a superoxide stimulus. Superoxide is the anion, oxygen-, formed by addition of one electron to dioxygen (O2) or any compound containing the superoxide anion.") -AnnotationAssertion( "mah") AnnotationAssertion( "2009-12-16T04:39:14Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0071451") @@ -79121,7 +78194,6 @@ EquivalentClasses( ObjectIntersection # Class: (cellular response to water stimulus) AnnotationAssertion(Annotation( "GOC:mah") "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus reflecting the presence, absence, or concentration of water.") -AnnotationAssertion( "mah") AnnotationAssertion( "2009-12-18T11:32:44Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0071462") @@ -79132,7 +78204,6 @@ SubClassOf( (cellular response to endogenous stimulus) AnnotationAssertion(Annotation( "GOC:mah") "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus arising within the organism.") -AnnotationAssertion( "mah") AnnotationAssertion( "2009-12-18T02:25:40Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0071495") @@ -79144,7 +78215,6 @@ SubClassOf( (dopaminergic neuron differentiation) AnnotationAssertion(Annotation( "GOC:rph") "The process in which a neuroblast acquires the specialized structural and functional features of a dopaminergic neuron, a neuron that secretes dopamine.") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-01-12T02:28:44Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0071542") @@ -79155,7 +78225,6 @@ SubClassOf( (otic vesicle development) AnnotationAssertion(Annotation( "GOC:mah") "The process whose specific outcome is the progression of the otic vesicle over time, from its formation to the mature structure. The otic vesicle is a transient embryonic structure formed during development of the vertebrate inner ear.") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-02-04T04:07:17Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0071599") @@ -79167,7 +78236,6 @@ SubClassOf( (otic vesicle morphogenesis) AnnotationAssertion(Annotation( "GOC:mah") "The process in which the anatomical structures of the otic vesicle are generated and organized. The otic vesicle is a transient embryonic structure formed during development of the vertebrate inner ear.") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-02-04T04:07:27Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0071600") @@ -79180,7 +78248,6 @@ SubClassOf( ObjectSomeValuesFrom( (granulocyte chemotaxis) AnnotationAssertion(Annotation( "GOC:rph") "The movement of a granulocyte in response to an external stimulus.") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-02-09T04:08:17Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0071621") @@ -79191,7 +78258,6 @@ SubClassOf( (regulation of granulocyte chemotaxis) AnnotationAssertion(Annotation( "GOC:mah") "Any process that modulates the rate, frequency or extent of granulocyte chemotaxis. Granulocyte chemotaxis is the movement of a granulocyte in response to an external stimulus.") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-02-09T04:09:24Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0071622") @@ -79201,7 +78267,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of granulocyte chemotaxis) AnnotationAssertion(Annotation( "GOC:mah") "Any process that decreases the rate, frequency or extent of granulocyte chemotaxis. Granulocyte chemotaxis is the movement of a granulocyte in response to an external stimulus.") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-02-09T04:13:19Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0071623") @@ -79211,7 +78276,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of granulocyte chemotaxis) AnnotationAssertion(Annotation( "GOC:mah") "Any process that increases the rate, frequency or extent of granulocyte chemotaxis. Granulocyte chemotaxis is the movement of a granulocyte in response to an external stimulus.") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-02-09T04:15:36Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0071624") @@ -79221,7 +78285,6 @@ EquivalentClasses( ObjectIntersection # Class: (mastication) AnnotationAssertion(Annotation( "GOC:gvg") "The process of biting and mashing food with the teeth prior to swallowing.") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-02-10T11:19:48Z") AnnotationAssertion(Annotation( "GOC:mah") "chewing") AnnotationAssertion( "biological_process") @@ -79232,7 +78295,6 @@ SubClassOf( (smooth muscle cell chemotaxis) AnnotationAssertion(Annotation( "GOC:mah") "The directed movement of a smooth muscle cell in response to an external stimulus.") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-02-16T01:32:59Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0071670") @@ -79244,7 +78306,6 @@ SubClassOf( (regulation of smooth muscle cell chemotaxis) AnnotationAssertion(Annotation( "GOC:mah") "Any process that modulates the frequency, rate, or extent of smooth muscle cell chemotaxis.") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-02-16T01:42:03Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0071671") @@ -79254,7 +78315,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of smooth muscle cell chemotaxis) AnnotationAssertion(Annotation( "GOC:mah") "Any process that stops, prevents, or reduces the frequency, rate, or extent of smooth muscle cell chemotaxis.") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-02-16T01:44:28Z") AnnotationAssertion(Annotation( "GOC:mah") "down regulation of smooth muscle cell chemotaxis") AnnotationAssertion(Annotation( "GOC:mah") "down-regulation of smooth muscle cell chemotaxis") @@ -79268,7 +78328,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of smooth muscle cell chemotaxis) AnnotationAssertion(Annotation( "GOC:mah") "Any process that activates or increases the frequency, rate, or extent of smooth muscle cell chemotaxis.") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-02-16T01:48:14Z") AnnotationAssertion(Annotation( "GOC:mah") "up regulation of smooth muscle cell chemotaxis") AnnotationAssertion(Annotation( "GOC:mah") "up-regulation of smooth muscle cell chemotaxis") @@ -79283,7 +78342,6 @@ EquivalentClasses( ObjectIntersection # Class: (mononuclear cell migration) AnnotationAssertion(Annotation( "GOC:mah") "The movement of a mononuclear cell within or between different tissues and organs of the body.") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-02-16T02:11:00Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0071674") @@ -79294,7 +78352,6 @@ SubClassOf( (regulation of mononuclear cell migration) AnnotationAssertion(Annotation( "GOC:mah") "Any process that modulates the rate, frequency or extent of mononuclear cell migration. Mononuclear cell migration is the movement of a mononuclear cell within or between different tissues and organs of the body.") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-02-16T02:11:53Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0071675") @@ -79304,7 +78361,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of mononuclear cell migration) AnnotationAssertion(Annotation( "GOC:mah") "Any process that decreases the rate, frequency or extent of mononuclear cell migration. Mononuclear cell migration is the movement of a mononuclear cell within or between different tissues and organs of the body.") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-02-16T02:13:55Z") AnnotationAssertion(Annotation( "GOC:mah") "down regulation of mononuclear cell migration") AnnotationAssertion(Annotation( "GOC:mah") "down-regulation of mononuclear cell migration") @@ -79318,7 +78374,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of mononuclear cell migration) AnnotationAssertion(Annotation( "GOC:mah") "Any process that increases the rate, frequency or extent of mononuclear cell migration. Mononuclear cell migration is the movement of a mononuclear cell within or between different tissues and organs of the body.") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-02-16T02:15:29Z") AnnotationAssertion(Annotation( "GOC:mah") "up regulation of mononuclear cell migration") AnnotationAssertion(Annotation( "GOC:mah") "up-regulation of mononuclear cell migration") @@ -79333,7 +78388,6 @@ EquivalentClasses( ObjectIntersection # Class: (protein localization to extracellular region) AnnotationAssertion(Annotation( "GOC:mah") "Any process in which a protein is transported from one specific location in the extracellular region to another, or maintained in a specific extracellular location.") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-02-25T04:00:13Z") AnnotationAssertion(Annotation( "GOC:mah") "protein localisation in extracellular region") AnnotationAssertion( "protein localization in extracellular region") @@ -79345,7 +78399,6 @@ EquivalentClasses( ObjectIntersection # Class: (anatomical structure maturation) AnnotationAssertion(Annotation( "GOC:mah") "A developmental process, independent of morphogenetic (shape) change, that is required for an anatomical structure to attain its fully functional state.") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-03-02T11:43:38Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0071695") @@ -79357,7 +78410,6 @@ SubClassOf( ObjectSomeValuesFrom( (ectodermal placode development) AnnotationAssertion(Annotation( "GOC:mah") "The progression of an ectodermal placode over time from its initial formation until its mature state. An ectodermal placode is a thickening of the ectoderm that is the primordium of many structures derived from the ectoderm.") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-03-02T11:48:01Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0071696") @@ -79369,7 +78421,6 @@ SubClassOf( (ectodermal placode morphogenesis) AnnotationAssertion(Annotation( "GOC:mah") "The process in which the anatomical structures of an ectodermal placode are generated and organized. An ectodermal placode is a thickening of the ectoderm that is the primordium of many structures derived from the ectoderm.") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-03-02T11:49:51Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0071697") @@ -79382,7 +78433,6 @@ SubClassOf( ObjectSomeValuesFrom( (olfactory placode development) AnnotationAssertion(Annotation( "GOC:mah") "The progression of the olfactory placode over time from its initial formation until its mature state. The olfactory placode is a thickening of the neural ectoderm in the head region of the vertebrate embryo which develops into the olfactory region of the nasal cavity.") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-03-02T12:45:14Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0071698") @@ -79393,7 +78443,6 @@ SubClassOf( (olfactory placode morphogenesis) AnnotationAssertion(Annotation( "GOC:mah") "The process in which the anatomical structures of the olfactory placode are generated and organized. The olfactory placode is a thickening of the neural ectoderm in the head region of the vertebrate embryo which develops into the olfactory region of the nasal cavity.") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-03-02T12:45:45Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0071699") @@ -79406,7 +78455,6 @@ SubClassOf( ObjectSomeValuesFrom( (olfactory placode maturation) AnnotationAssertion(Annotation( "GOC:mah") "A developmental process, independent of morphogenetic (shape) change, that is required for the olfactory placode to attain its fully functional state. The olfactory placode is a thickening of the neural ectoderm in the head region of the vertebrate embryo which develops into the olfactory region of the nasal cavity.") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-03-02T01:10:54Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0071700") @@ -79418,7 +78466,6 @@ SubClassOf( ObjectSomeValuesFrom( (nitrogen compound transport) AnnotationAssertion(Annotation( "GOC:mah") "The directed movement of nitrogen-containing compounds into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-03-08T03:56:28Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0071705") @@ -79430,7 +78477,6 @@ SubClassOf( (tumor necrosis factor superfamily cytokine production) AnnotationAssertion(Annotation( "GOC:add") "The appearance of any member of the TNF superfamily due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-03-09T02:40:35Z") AnnotationAssertion(Annotation( "GOC:add") "TNFSF cytokine production") AnnotationAssertion( "biological_process") @@ -79444,7 +78490,6 @@ SubClassOf( (immunoglobulin heavy chain V-D-J recombination) AnnotationAssertion(Annotation( "GOC:add") Annotation( "ISBN:0781735149") "The process in which immunoglobulin heavy chain V, D, and J gene segments are recombined within a single locus utilizing the conserved heptamer and nonomer recombination signal sequences (RSS).") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-03-09T04:20:31Z") AnnotationAssertion(Annotation( "GOC:add") "immunoglobulin V(D)J joining") AnnotationAssertion(Annotation( "GOC:add") "immunoglobulin V(D)J recombination") @@ -79457,7 +78502,6 @@ SubClassOf( (immunoglobulin light chain V-J recombination) AnnotationAssertion(Annotation( "GOC:add") Annotation( "ISBN:0781735149") "The process in which immunoglobulin light chain V and J gene segments are recombined within a single locus utilizing the conserved heptamer and nonomer recombination signal sequences (RSS).") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-03-09T04:22:29Z") AnnotationAssertion(Annotation( "GOC:add") "immunoglobulin V(D)J joining") AnnotationAssertion(Annotation( "GOC:add") "immunoglobulin V(D)J recombination") @@ -79470,7 +78514,6 @@ SubClassOf( (membrane assembly) AnnotationAssertion(Annotation( "GOC:mah") "The aggregation, arrangement and bonding together of a set of components to form a membrane.") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-03-10T11:19:17Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0071709") @@ -79482,7 +78525,6 @@ SubClassOf( ObjectSomeValuesFrom( (basement membrane organization) AnnotationAssertion(Annotation( "GOC:mah") "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the basement membrane.") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-03-10T11:57:10Z") AnnotationAssertion(Annotation( "GOC:mah") "basement membrane organisation") AnnotationAssertion( "biological_process") @@ -79495,7 +78537,6 @@ SubClassOf( (response to nitric oxide) AnnotationAssertion(Annotation( "GOC:mah") Annotation( "GOC:yaf") "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a nitric oxide stimulus.") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-03-17T04:03:38Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0071731") @@ -79505,7 +78546,6 @@ EquivalentClasses( ObjectIntersection # Class: (cellular response to nitric oxide) AnnotationAssertion(Annotation( "GOC:mah") Annotation( "GOC:yaf") "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a nitric oxide stimulus.") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-03-17T04:12:52Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0071732") @@ -79515,7 +78555,6 @@ EquivalentClasses( ObjectIntersection # Class: (IgG immunoglobulin complex) AnnotationAssertion(Annotation( "GOC:add") Annotation( "ISBN:0781765196") "A protein complex composed of two identical immunoglobulin heavy chains of an IgG isotype and two identical immunoglobulin light chains, held together by disulfide bonds. An IgG immunoglobulin complex may be embedded in the plasma membrane or present in the extracellular space, in mucosal areas or other tissues, or circulating in the blood or lymph.") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-03-24T01:44:53Z") AnnotationAssertion(Annotation( "GOC:add") "IgG1") AnnotationAssertion(Annotation( "GOC:add") "IgG2") @@ -79533,7 +78572,6 @@ SubClassOf( (IgG immunoglobulin complex, circulating) AnnotationAssertion(Annotation( "GOC:add") Annotation( "ISBN:0781765196") "A protein complex composed of two identical immunoglobulin heavy chains of an IgG isotype and two identical immunoglobulin light chains, held together by disulfide bonds, and present in the extracellular space, in mucosal areas or other tissues, or circulating in the blood or lymph.") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-03-24T01:44:53Z") AnnotationAssertion(Annotation( "GOC:add") "IgG antibody") AnnotationAssertion(Annotation( "GOC:add") "IgG1 antibody") @@ -79553,7 +78591,6 @@ SubClassOf( (IgD immunoglobulin complex) AnnotationAssertion(Annotation( "GOC:add") Annotation( "ISBN:0781765196") Annotation( "PMID:11282392") "A protein complex composed of two identical immunoglobulin heavy chains of the IgD isotype and two identical immunoglobulin light chains, held together by disulfide bonds. An IgD immunoglobulin complex may be embedded in the plasma membrane or present in the extracellular space, in mucosal areas or other tissues, or circulating in the blood or lymph.") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-03-24T01:44:53Z") AnnotationAssertion( "cellular_component") AnnotationAssertion( "GO:0071738") @@ -79564,7 +78601,6 @@ SubClassOf( (IgD immunoglobulin complex, circulating) AnnotationAssertion(Annotation( "GOC:add") Annotation( "ISBN:0781765196") Annotation( "PMID:11282392") "A protein complex composed of two identical immunoglobulin heavy chains of the IgD isotype and two identical immunoglobulin light chains, held together by disulfide bonds, and present in the extracellular space, in mucosal areas or other tissues, or circulating in the blood or lymph.") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-03-24T01:44:53Z") AnnotationAssertion(Annotation( "GOC:add") "IgD antibody") AnnotationAssertion( "cellular_component") @@ -79577,7 +78613,6 @@ SubClassOf( (IgE immunoglobulin complex) AnnotationAssertion(Annotation( "GOC:add") Annotation( "ISBN:0781765196") "A protein complex composed of two identical immunoglobulin heavy chains of the IgE isotype and two identical immunoglobulin light chains, held together by disulfide bonds. An IgE immunoglobulin complex may be embedded in the plasma membrane or present in the extracellular space, in mucosal areas or other tissues, or circulating in the blood or lymph.") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-03-24T01:44:53Z") AnnotationAssertion( "cellular_component") AnnotationAssertion( "GO:0071742") @@ -79588,7 +78623,6 @@ SubClassOf( (IgE immunoglobulin complex, circulating) AnnotationAssertion(Annotation( "GOC:add") Annotation( "ISBN:0781765196") "A protein complex composed of two identical immunoglobulin heavy chains of the IgE isotype and two identical immunoglobulin light chains, held together by disulfide bonds, and present in the extracellular space, in mucosal areas or other tissues, or circulating in the blood or lymph.") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-03-24T01:44:53Z") AnnotationAssertion(Annotation( "GOC:add") "IgE antibody") AnnotationAssertion( "cellular_component") @@ -79601,7 +78635,6 @@ SubClassOf( (IgA immunoglobulin complex) AnnotationAssertion(Annotation( "GOC:add") Annotation( "ISBN:0781765196") Annotation( "PMID:16362985") "A protein complex composed of two identical immunoglobulin heavy chains of the IgA isotype and two identical immunoglobulin light chains, held together by disulfide bonds, and sometimes complexed with J chain or J chain and secretory component. An IgA immunoglobulin complex may be embedded in the plasma membrane or present in the extracellular space, in mucosal areas or other tissues, or circulating in the blood or lymph.") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-03-24T01:44:53Z") AnnotationAssertion(Annotation( "GOC:add") "IgA1 antibody") AnnotationAssertion(Annotation( "GOC:add") "IgA2 antibody") @@ -79614,7 +78647,6 @@ SubClassOf( (IgA immunoglobulin complex, circulating) AnnotationAssertion(Annotation( "GOC:add") Annotation( "ISBN:0781765196") Annotation( "PMID:16362985") "A protein complex composed of two identical immunoglobulin heavy chains of an IgA isotype and two identical immunoglobulin light chains, held together by disulfide bonds, sometimes complexed with J chain or J chain and secretory component, and present in the extracellular space, in mucosal areas or other tissues, or circulating in the blood or lymph.") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-03-24T01:44:53Z") AnnotationAssertion(Annotation( "GOC:add") "IgA antibody") AnnotationAssertion(Annotation( "GOC:add") "IgA1 antibody") @@ -79629,7 +78661,6 @@ SubClassOf( (IgM immunoglobulin complex) AnnotationAssertion(Annotation( "GOC:add") Annotation( "ISBN:0781765196") Annotation( "PMID:20176268") "A protein complex composed of two identical immunoglobulin heavy chains of the IgM isotype and two identical immunoglobulin light chains, held together by disulfide bonds, and in its circulating form complexed with J chain in polymeric forms. An IgM immunoglobulin complex may be embedded in the plasma membrane or present in the extracellular space, in mucosal areas or other tissues, or circulating in the blood or lymph.") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-03-24T01:44:53Z") AnnotationAssertion( "cellular_component") AnnotationAssertion( "GO:0071753") @@ -79640,7 +78671,6 @@ SubClassOf( (IgM immunoglobulin complex, circulating) AnnotationAssertion(Annotation( "GOC:add") Annotation( "ISBN:0781765196") Annotation( "PMID:20176268") "A polymer of five or six IgM core units each composed of two identical immunoglobulin heavy chains of the IgM isotype and two identical immunoglobulin light chains, held together by disulfide bonds; the individual IgM core units are held together via disulfide bonds with a single J chain polypeptide acting as a bridge between two of the polymeric units. Circulating IgM is present in the extracellular space, in mucosal areas or other tissues, or in the blood or lymph.") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-03-24T01:44:53Z") AnnotationAssertion(Annotation( "GOC:add") "IgM antibody") AnnotationAssertion( "cellular_component") @@ -79653,7 +78683,6 @@ SubClassOf( (nuclear membrane organization) AnnotationAssertion(Annotation( "GOC:mah") "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the nuclear inner or outer membrane.") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-03-29T03:59:35Z") AnnotationAssertion(Annotation( "GOC:mah") "nuclear membrane organisation") AnnotationAssertion( "biological_process") @@ -79667,7 +78696,6 @@ SubClassOf( ObjectSomeValuesFrom( (nuclear outer membrane organization) AnnotationAssertion(Annotation( "GOC:mah") "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the nuclear outer membrane.") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-03-29T04:03:37Z") AnnotationAssertion(Annotation( "GOC:mah") "nuclear outer membrane organisation") AnnotationAssertion( "biological_process") @@ -79681,7 +78709,6 @@ SubClassOf( ObjectSomeValuesFrom( (potassium ion transmembrane transport) AnnotationAssertion(Annotation( "GOC:mah") "A process in which a potassium ion is transported from one side of a membrane to the other.") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-09-03T02:43:49Z") AnnotationAssertion( "potassium ion membrane transport") AnnotationAssertion( "high affinity potassium ion import") @@ -79699,7 +78726,6 @@ SubClassOf( (protein transmembrane transport) AnnotationAssertion(Annotation( "GOC:mah") Annotation( "GOC:vw") "The process in which a protein is transported across a membrane.") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-09-03T02:54:26Z") AnnotationAssertion( "protein membrane transport") AnnotationAssertion( "biological_process") @@ -79711,7 +78737,6 @@ EquivalentClasses( ObjectIntersection # Class: (lipoprotein particle binding) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:mah") "Binding to a lipoprotein particle. A lipoprotein particle, also known as a lipoprotein, is a clathrate complex consisting of a lipid enwrapped in a protein host without covalent binding in such a way that the complex has a hydrophilic outer surface consisting of all the protein and the polar ends of any phospholipids.") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-09-06T03:16:01Z") AnnotationAssertion(Annotation( "GOC:mah") "plasma lipoprotein particle binding") AnnotationAssertion( "molecular_function") @@ -79725,7 +78750,6 @@ SubClassOf( (protein-lipid complex binding) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:mah") "Binding to a protein-lipid complex, any macromolecular complex that contains both protein and lipid molecules.") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-09-06T04:26:27Z") AnnotationAssertion( "molecular_function") AnnotationAssertion( "GO:0071814") @@ -79736,7 +78760,6 @@ EquivalentClasses( ObjectIntersection AnnotationAssertion(Annotation( "GOC:mah") "Any process in which macromolecules aggregate, disaggregate, or are modified, resulting in the formation, disassembly, or alteration of a protein-lipid complex.") AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/25143"^^xsd:anyURI) -AnnotationAssertion( "mah") AnnotationAssertion( "2010-09-08T10:04:36Z") AnnotationAssertion(Annotation( "GOC:mah") "protein-lipid complex subunit organisation") AnnotationAssertion( "protein-lipid complex subunit organization") @@ -79749,7 +78772,6 @@ EquivalentClasses( ObjectIntersection AnnotationAssertion(Annotation( "GOC:mah") "Any process in which macromolecules aggregate, disaggregate, or are modified, resulting in the formation, disassembly, or alteration of a ribonucleoprotein complex.") AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/25143"^^xsd:anyURI) -AnnotationAssertion( "mah") AnnotationAssertion( "2010-09-08T10:10:35Z") AnnotationAssertion(Annotation( "GOC:mah") "RNA-protein complex subunit organization") AnnotationAssertion(Annotation( "GOC:mah") "protein-RNA complex subunit organization") @@ -79764,7 +78786,6 @@ EquivalentClasses( ObjectIntersection AnnotationAssertion(Annotation( "GOC:mah") "A process that results in the biosynthesis of constituent macromolecules, assembly, arrangement of constituent parts, or disassembly of a cellular component.") AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/27189"^^xsd:anyURI) -AnnotationAssertion( "mah") AnnotationAssertion( "2010-09-10T01:39:16Z") AnnotationAssertion(Annotation( "GOC:mah") "cellular component organisation or biogenesis") AnnotationAssertion(Annotation( "GOC:mah") "cellular component organisation or biogenesis at cellular level") @@ -79781,7 +78802,6 @@ SubClassOf( (response to catecholamine) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:mah") "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a catecholamine stimulus. A catecholamine is any of a group of biogenic amines that includes 4-(2-aminoethyl)pyrocatechol [4-(2-aminoethyl)benzene-1,2-diol] and derivatives formed by substitution.") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-09-13T02:51:13Z") AnnotationAssertion(Annotation( "GOC:dos") "response to catecholamine stimulus") AnnotationAssertion( "biological_process") @@ -79792,7 +78812,6 @@ EquivalentClasses( ObjectIntersection # Class: (cellular response to catecholamine stimulus) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:mah") "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a catecholamine stimulus. A catecholamine is any of a group of biogenic amines that includes 4-(2-aminoethyl)pyrocatechol [4-(2-aminoethyl)benzene-1,2-diol] and derivatives formed by substitution.") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-09-13T02:54:50Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0071870") @@ -79802,7 +78821,6 @@ EquivalentClasses( ObjectIntersection # Class: (response to norepinephrine) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:mah") "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a norepinephrine stimulus. Norepinephrine is a catecholamine that has the formula C8H11NO3; it acts as a hormone, and as a neurotransmitter in most of the sympathetic nervous system.") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-09-13T03:31:53Z") AnnotationAssertion(Annotation( "GOC:mah") "response to noradrenaline stimulus") AnnotationAssertion(Annotation( "GOC:dos") "response to norepinephrine stimulus") @@ -79815,7 +78833,6 @@ EquivalentClasses( ObjectIntersection # Class: (cellular response to norepinephrine stimulus) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:mah") "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a norepinephrine stimulus. Norepinephrine is a catecholamine that has the formula C8H11NO3; it acts as a hormone, and as a neurotransmitter in most of the sympathetic nervous system.") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-09-13T03:33:32Z") AnnotationAssertion(Annotation( "GOC:mah") "cellular response to noradrenaline stimulus") AnnotationAssertion( "biological_process") @@ -79827,7 +78844,6 @@ EquivalentClasses( ObjectIntersection # Class: (leukocyte apoptotic process) AnnotationAssertion(Annotation( "CL:0000738") Annotation( "GOC:BHF") Annotation( "GOC:mah") Annotation( "GOC:mtg_apoptosis") "Any apoptotic process in a leukocyte, an achromatic cell of the myeloid or lymphoid lineages capable of ameboid movement, found in blood or other tissue.") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-09-14T12:44:09Z") AnnotationAssertion( "leukocyte apoptosis") AnnotationAssertion( "biological_process") @@ -79842,7 +78858,6 @@ SubClassOf( ObjectAllValuesFrom( (macrophage apoptotic process) AnnotationAssertion(Annotation( "CL:0000235") Annotation( "GOC:BHF") Annotation( "GOC:mah") Annotation( "GOC:mtg_apoptosis") "Any apoptotic process in a macrophage, a mononuclear phagocyte present in a variety of tissues.") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-09-14T12:50:40Z") AnnotationAssertion( "macrophage apoptosis") AnnotationAssertion( "biological_process") @@ -79858,7 +78873,6 @@ SubClassOf( (bicarbonate binding) AnnotationAssertion(Annotation( "GOC:curators") "Binding to bicarbonate ions (CHO3-).") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-09-14T01:47:43Z") AnnotationAssertion( "CHO3- ion binding binding") AnnotationAssertion(Annotation( "CHEBI:17544") "hydrogencarbonate binding") @@ -79870,7 +78884,6 @@ EquivalentClasses( ObjectIntersection # Class: (odontoblast differentiation) AnnotationAssertion(Annotation( "GOC:sl") Annotation( "PMID:20425127") "The process in which a relatively unspecialized cell of neural crest origin acquires the specialized features of an odontoblast, a cell on the outer surface of the dental pulp whose biological function is the creation of dentin.") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-09-14T04:00:40Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0071895") @@ -79880,7 +78893,6 @@ EquivalentClasses( ObjectIntersection # Class: (DNA biosynthetic process) AnnotationAssertion(Annotation( "GOC:mah") "The biosynthetic process resulting in the formation of DNA.") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-09-15T02:14:33Z") AnnotationAssertion(Annotation( "GOC:mah") "DNA anabolism") AnnotationAssertion(Annotation( "GOC:mah") "DNA biosynthesis") @@ -79894,7 +78906,6 @@ EquivalentClasses( ObjectIntersection # Class: (nitrogen cycle metabolic process) AnnotationAssertion(Annotation( "GOC:mah") Annotation( "PMID:16675690") Annotation( "Wikipedia:Nitrogen_cycle") "A nitrogen compound metabolic process that contributes to the nitrogen cycle. The nitrogen cycle is a series of metabolic pathways by which nitrogen is converted between various forms and redox states; it encompasses pathways in which nitrogen is acted upon directly, such as nitrification, denitrification, nitrogen fixation, and mineralization.") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-09-30T05:21:03Z") AnnotationAssertion( "Wikipedia:Nitrogen_cycle") AnnotationAssertion( "biological_process") @@ -79909,7 +78920,6 @@ SubClassOf( (cell periphery) AnnotationAssertion(Annotation( "GOC:pdt") "The broad region around and including the plasma membrane of a cell, encompassing the cell cortex (inside the cell), the plasma membrane, and any external encapsulating structures.") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-10-04T01:51:47Z") AnnotationAssertion( "cellular_component") AnnotationAssertion( "GO:0071944") @@ -79920,7 +78930,6 @@ SubClassOf( (elastic fiber) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:mah") Annotation( "PMID:20236620") "An supramolecular fiber that consists of an insoluble core of polymerized tropoelastin monomers and a surrounding mantle of microfibrils. Elastic fibers provide elasticity and recoiling to tissues and organs, and maintain structural integrity against mechanical strain.") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-10-11T11:44:57Z") AnnotationAssertion(Annotation( "GOC:mah") "elastic fibre") AnnotationAssertion(Annotation( "GOC:BHF") "elastin fiber") @@ -79933,7 +78942,6 @@ SubClassOf( ObjectSomeValuesFrom( (extracellular exosome assembly) AnnotationAssertion(Annotation( "GOC:mah") Annotation( "GOC:tfm") Annotation( "PMID:19442504") Annotation( "PMID:27462458") "The aggregation, arrangement and bonding together of a set of components to form an extracellular vesicular exosome, a membrane-bounded vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Exosomes are defined by their size, which generally ranges from 30 nm to 100 nm.") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-10-18T03:44:18Z") AnnotationAssertion(Annotation( "GOC:vesicles") "extracellular vesicular exosome assembly") AnnotationAssertion( "biological_process") @@ -79945,7 +78953,6 @@ SubClassOf( ObjectSomeValuesFrom( (renal system development) AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") Annotation( "GOC:yaf") Annotation( "PMID:6996269") "The process whose specific outcome is the progression of the renal system over time, from its formation to the mature structure. The renal system maintains fluid balance and contributes to electrolyte balance, acid/base balance, and disposal of nitrogenous waste products. In humans, the renal system comprises a pair of kidneys, a pair of ureters, urinary bladder, urethra, sphincter muscle and associated blood vessels.") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-01-25T10:31:00Z") AnnotationAssertion(Annotation( "GOC:yaf") "urinary system development") AnnotationAssertion(Annotation( "GOC:yaf") Annotation( "PMID:17881463") "urinary tract development") @@ -79959,7 +78966,6 @@ SubClassOf( (Malpighian tubule development) AnnotationAssertion(Annotation( "FBbt:00005786") Annotation( "GOC:mtg_kidney_jan10") Annotation( "PMID:19783135") "The process whose specific outcome is the progression of the Malpighian tubule over time, from its formation to the mature structure. A Malpighian tubule is a fine, thin-walled excretory tubule in insects which leads into the posterior part of the gut.") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-01-25T10:54:30Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0072002") @@ -79974,7 +78980,6 @@ SubClassOf( ObjectAllValuesFrom( (kidney rudiment formation) AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "The developmental process pertaining to the initial formation of a kidney rudiment from unspecified parts. A kidney is an organ that filters the blood and excretes the end products of body metabolism in the form of urine.") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-01-25T11:18:58Z") AnnotationAssertion( "biological_process") AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "kidney anlage formation") @@ -79988,7 +78993,6 @@ SubClassOf( ObjectSomeValuesFrom( (nephron development) AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "The process whose specific outcome is the progression of the nephron over time, from its formation to the mature structure. A nephron is the functional unit of the kidney.") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-01-25T01:37:16Z") AnnotationAssertion( "biological_process") AnnotationAssertion(Annotation( "GOC:rph") "nephrogenesis") @@ -80002,7 +79006,6 @@ SubClassOf( ObjectSomeValuesFrom( (mesangial cell differentiation) AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "The process in which relatively unspecialized cells acquire specialized structural and/or functional features that characterize the mesangial cells of the kidney as it progresses from its formation to the mature state.") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-01-25T01:59:09Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0072007") @@ -80013,7 +79016,6 @@ SubClassOf( (glomerular mesangial cell differentiation) AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "The process in which relatively unspecialized cells acquire specialized structural and/or functional features that characterize the glomerular mesangial cells of the kidney as it progresses from its formation to the mature state.") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-01-25T01:59:33Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0072008") @@ -80025,7 +79027,6 @@ SubClassOf( ObjectSomeValuesFrom( (nephron epithelium development) AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "The process whose specific outcome is the progression of the nephron epithelium over time, from its formation to the mature structure. An epithelium is a tissue that covers the internal or external surfaces of an anatomical structure. The nephron epithelium is a tissue that covers the surface of a nephron.") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-01-25T02:01:39Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0072009") @@ -80037,7 +79038,6 @@ SubClassOf( ObjectSomeValuesFrom( (glomerular epithelium development) AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "The process whose specific outcome is the progression of the glomerular epithelium over time, from its formation to the mature structure. The glomerular epithelium is an epithelial tissue that covers the outer surfaces of the glomerulus. The glomerular epithelium consists of both parietal and visceral epithelium. Metanephric glomerular parietal epithelial cells are specialized epithelial cells that form tight junctions as a barrier to protein transport. A metanephric glomerular visceral epithelial cell is a specialized epithelial cell that contains 'feet' that interdigitate with the 'feet' of other glomerular epithelial cells in the metanephros.") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-01-25T02:02:14Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0072010") @@ -80049,7 +79049,6 @@ SubClassOf( ObjectSomeValuesFrom( (glomerular endothelium development) AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "The process whose specific outcome is the progression of the glomerular endothelium over time, from its formation to the mature structure. The glomerular endothelium is an epithelial tissue that covers the internal surfaces of the glomerulus.") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-01-25T02:02:57Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0072011") @@ -80061,7 +79060,6 @@ SubClassOf( ObjectSomeValuesFrom( (glomerulus vasculature development) AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "The biological process whose specific outcome is the progression of a glomerulus vasculature from an initial condition to its mature state. This process begins with the formation of the glomerulus vasculature and ends with the mature structure. The glomerulus vasculature is composed of the tubule structures that carry blood or lymph in the glomerulus.") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-01-25T02:05:04Z") AnnotationAssertion( "biological_process") AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "glomerulus capillary development") @@ -80074,7 +79072,6 @@ SubClassOf( ObjectSomeValuesFrom( (proximal tubule development) AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "The process whose specific outcome is the progression of the proximal tubule over time, from its formation to the mature structure. In mammals, the proximal tubule is a nephron tubule that connects Bowman's capsule to the descending thin limb of the loop of Henle. It has a brush border epithelial morphology.") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-01-25T02:33:46Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0072014") @@ -80086,7 +79083,6 @@ SubClassOf( "GOC:mtg_kidney_jan10") "The process whose specific outcome is the progression of a glomerular visceral epithelial cell over time, from its formation to the mature structure. A glomerular visceral epithelial cell is a specialized epithelial cell that contains 'feet' that interdigitate with the 'feet' of other glomerular epithelial cells.") AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/23000"^^xsd:anyURI) -AnnotationAssertion( "mah") AnnotationAssertion( "2010-01-25T02:12:45Z") AnnotationAssertion( "glomerular visceral epithelial cell development") AnnotationAssertion( "biological_process") @@ -80099,7 +79095,6 @@ SubClassOf( ObjectSomeValuesFrom( (glomerular parietal epithelial cell development) AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "The process whose specific outcome is the progression of a glomerular parietal epithelial cell over time, from its formation to the mature structure. Glomerular parietal epithelial cells are specialized epithelial cells that form tight junctions as a barrier to protein transport.") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-01-25T02:13:16Z") AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "Bowman's capsule development") AnnotationAssertion( "biological_process") @@ -80112,7 +79107,6 @@ SubClassOf( ObjectSomeValuesFrom( (distal tubule development) AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "The process whose specific outcome is the progression of the distal tubule over time, from its formation to the mature structure. In mammals, the distal tubule is a nephron tubule that begins at the macula densa and extends to the connecting tubule.") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-01-25T02:34:19Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0072017") @@ -80123,7 +79117,6 @@ SubClassOf( (proximal convoluted tubule development) AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "The process whose specific outcome is the progression of the proximal convoluted tubule over time, from its formation to the mature structure. The proximal convoluted tubule is the most proximal portion of the proximal tubule and extends from the glomerular capsule to the proximal straight tubule.") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-01-25T02:35:35Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0072019") @@ -80135,7 +79128,6 @@ SubClassOf( ObjectSomeValuesFrom( (proximal straight tubule development) AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "The process whose specific outcome is the progression of the proximal straight tubule over time, from its formation to the mature structure. The proximal straight tubule is the part of the descending limb that extends from the proximal convoluted tubule to the descending thin tubule.") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-01-25T02:36:14Z") AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "S3 development") AnnotationAssertion( "biological_process") @@ -80148,7 +79140,6 @@ SubClassOf( ObjectSomeValuesFrom( (ascending thin limb development) AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "The process whose specific outcome is the progression of an ascending thin limb over time, from its formation to the mature structure. The ascending thin limb is a segment of a nephron tubule lying in the inner medulla that is permeable to ions but not to water and has a simple epithelium; active transepithelial solute transport is absent.") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-01-25T02:37:13Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0072021") @@ -80161,7 +79152,6 @@ SubClassOf( ObjectSomeValuesFrom( (descending thin limb development) AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "The process whose specific outcome is the progression of the descending thin limb over time, from its formation to the mature structure. The descending thin limb is a part of the loop of Henle situated just after the proximal straight tubule (S3). It extends to the tip of the loop of Henle.") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-01-25T02:37:47Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0072022") @@ -80174,7 +79164,6 @@ SubClassOf( ObjectSomeValuesFrom( (thick ascending limb development) AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "The process whose specific outcome is the progression of the thick ascending limb over time, from its formation to the mature structure. The thick ascending limb is the last part of the loop of Henle. Its thick, mitochondria-rich epithelium characterizes the outer medulla, and is responsible for very avid active salt transport. At the macula densa, the thick ascending limb connects to the distal convoluted tubule.") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-01-25T02:39:51Z") AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "TAL development") AnnotationAssertion( "biological_process") @@ -80187,7 +79176,6 @@ SubClassOf( ObjectSomeValuesFrom( (macula densa development) AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "The process whose specific outcome is the progression of the macula densa over time, from its formation to the mature structure. The macula densa is an area of specialized cells in the distal tubule that makes contact with the vascular pole of the glomerulus.") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-01-25T02:40:15Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0072024") @@ -80201,7 +79189,6 @@ SubClassOf( ObjectSomeValuesFrom( (distal convoluted tubule development) AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "The process whose specific outcome is the progression of the distal convoluted tubule over time, from its formation to the mature structure. The distal convoluted tubule is the first segment of the nephron lying just downstream from the loop of Henle, immediately after the macula densa. Among other functions, in humans it is responsible for the reabsorption of about 5% of filtered sodium via the thiazide-sensitive Na-Cl symporter.") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-01-25T02:40:45Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0072025") @@ -80214,7 +79201,6 @@ SubClassOf( ObjectSomeValuesFrom( (connecting tubule development) AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "The process whose specific outcome is the progression of the connecting tubule over time, from its formation to the mature structure. The connecting tubule is a tubular segment of the nephron; it connects the distal convoluted tubule to the collecting duct.") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-01-25T02:42:05Z") AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "connecting duct development") AnnotationAssertion( "biological_process") @@ -80226,7 +79212,6 @@ SubClassOf( (nephron morphogenesis) AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "The process in which the anatomical structures of the nephron are generated and organized. A nephron is the functional unit of the kidney.") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-01-25T02:45:52Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0072028") @@ -80240,7 +79225,6 @@ SubClassOf( ObjectSomeValuesFrom( (long nephron development) AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "The process whose specific outcome is the progression of a long nephron over time, from its formation to the mature structure. Long nephrons are associated with juxtamedullary glomeruli and extend into the inner medulla.") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-01-25T02:49:08Z") AnnotationAssertion( "biological_process") AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "juxtamedullary nephron development") @@ -80252,7 +79236,6 @@ SubClassOf( (short nephron development) AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "The process whose specific outcome is the progression of a short nephron over time, from its formation to the mature structure. Short nephrons are associated with mid-cortical and superficial glomeruli, are situated entirely in the outer medulla, and have no thin ascending limb.") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-01-25T02:49:32Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0072030") @@ -80263,7 +79246,6 @@ SubClassOf( (proximal convoluted tubule segment 1 development) AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") Annotation( "MA:0002612") "The process whose specific outcome is the progression of the S1 portion of the proximal convoluted tubule over time, from its formation to the mature structure. The S1 portion is the initial portion of the proximal convoluted tubule and is responsible for avid reabsorption of water and solutes.") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-01-25T02:55:57Z") AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "S1 development") AnnotationAssertion( "biological_process") @@ -80276,7 +79258,6 @@ SubClassOf( ObjectSomeValuesFrom( (proximal convoluted tubule segment 2 development) AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") Annotation( "MA:0002613") "The process whose specific outcome is the progression of the S2 portion of the proximal convoluted tubule over time, from its formation to the mature structure. The S2 portion of the tubule is involved in reabsorption of water and sodium chloride.") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-01-25T02:56:36Z") AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "S2 development") AnnotationAssertion( "biological_process") @@ -80289,7 +79270,6 @@ SubClassOf( ObjectSomeValuesFrom( (renal vesicle formation) AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "The developmental process pertaining to the initial formation of the renal vesicle from condensed mesenchymal cells. The renal vesicle is the primordial structure of the nephron epithelium, and is formed by the condensation of mesenchymal cells.") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-01-25T02:57:03Z") AnnotationAssertion( "biological_process") AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "nephron epithelium formation") @@ -80303,7 +79283,6 @@ SubClassOf( ObjectSomeValuesFrom( (mesenchymal to epithelial transition involved in renal vesicle formation) AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "A transition where a mesenchymal cell establishes apical/basolateral polarity,forms intercellular adhesive junctions, synthesizes basement membrane components and becomes an epithelial cell that will contribute to the shaping of the renal vesicle.") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-01-25T03:04:24Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0072036") @@ -80313,7 +79292,6 @@ EquivalentClasses( ObjectIntersection # Class: (mesenchymal stem cell differentiation involved in nephron morphogenesis) AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "The process in which a relatively unspecialized cell acquires specialized features of a mesenchymal stem cell that contributes to the shaping of a nephron. A mesenchymal stem cell is a cell that retains the ability to divide and proliferate throughout life to provide progenitor cells that can differentiate into specialized mesenchymal cells.") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-01-25T03:07:39Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0072037") @@ -80323,7 +79301,6 @@ EquivalentClasses( ObjectIntersection # Class: (mesenchymal stem cell maintenance involved in nephron morphogenesis) AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "The process in which an organism retains a population of mesenchymal stem cells that contributes to the shaping of a nephron. A mesenchymal stem cell is a cell that retains the ability to divide and proliferate throughout life to provide progenitor cells that can differentiate into specialized mesenchymal cells.") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-01-25T03:08:05Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0072038") @@ -80334,7 +79311,6 @@ SubClassOf( ObjectSomeValuesFrom( (regulation of mesenchymal cell apoptotic process involved in nephron morphogenesis) AnnotationAssertion(Annotation( "GOC:mtg_apoptosis") Annotation( "GOC:mtg_kidney_jan10") "Any process that modulates the occurrence or rate of mesenchymal stem cell death by apoptotic process that contributes to the shaping of the nephron.") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-01-25T03:08:34Z") AnnotationAssertion( "regulation of mesenchymal stem cell apoptotic process involved in nephron morphogenesis") AnnotationAssertion( "regulation of mesenchymal stem cell apoptosis involved in nephron morphogenesis") @@ -80347,7 +79323,6 @@ SubClassOf( ObjectSomeValuesFrom( (negative regulation of mesenchymal cell apoptotic process involved in nephron morphogenesis) AnnotationAssertion(Annotation( "GOC:mtg_apoptosis") Annotation( "GOC:mtg_kidney_jan10") "Any process that reduces the occurrence or rate of mesenchymal stem cell death by apoptotic process that contributes to the shaping of the nephron.") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-01-25T03:09:30Z") AnnotationAssertion( "negative regulation of mesenchymal stem cell apoptotic process involved in nephron morphogenesis") AnnotationAssertion( "negative regulation of mesenchymal stem cell apoptosis involved in nephron morphogenesis") @@ -80360,7 +79335,6 @@ SubClassOf( ObjectSomeValuesFrom( (positive regulation of mesenchymal cell apoptotic process involved in nephron morphogenesis) AnnotationAssertion(Annotation( "GOC:mtg_apoptosis") Annotation( "GOC:mtg_kidney_jan10") "Any process that increases the occurrence or rate of mesenchymal stem cell death by apoptotic process that contributes to the shaping of the nephron.") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-01-25T03:10:32Z") AnnotationAssertion( "positive regulation of mesenchymal stem cell apoptotic process involved in nephron morphogenesis") AnnotationAssertion( "positive regulation of mesenchymal stem cell apoptosis involved in nephron morphogenesis") @@ -80373,7 +79347,6 @@ SubClassOf( ObjectSomeValuesFrom( (collecting duct development) AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "The process whose specific outcome is the progression of a collecting duct over time, from its formation to the mature structure. The collecting duct responds to vasopressin and aldosterone to regulate water, electrolyte and acid-base balance. It is the final common path through which urine flows before entering the ureter and then emptying into the bladder.") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-01-25T03:18:06Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0072044") @@ -80386,7 +79359,6 @@ SubClassOf( ObjectSomeValuesFrom( (renal system pattern specification) AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "Any developmental process that results in the creation of defined areas or spaces within an organism to which cells respond and eventually are instructed to differentiate into the anatomical structures of the renal system.") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-01-25T03:31:51Z") AnnotationAssertion( "biological_process") AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "renal system pattern formation") @@ -80399,7 +79371,6 @@ SubClassOf( ObjectSomeValuesFrom( (comma-shaped body morphogenesis) AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "The process in which the comma-shaped body is generated and organized. The comma-shaped body is the precursor structure to the S-shaped body that contributes to the morphogenesis of the nephron.") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-01-25T03:44:48Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0072049") @@ -80412,7 +79383,6 @@ SubClassOf( ObjectSomeValuesFrom( (S-shaped body morphogenesis) AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "The process in which the S-shaped body is generated and organized. The S-shaped body is the successor of the comma-shaped body that contributes to the morphogenesis of the nephron.") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-01-25T03:45:19Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0072050") @@ -80425,7 +79395,6 @@ SubClassOf( ObjectSomeValuesFrom( (juxtaglomerular apparatus development) AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "The process whose specific outcome is the progression of the juxtaglomerular apparatus over time, from its formation to the mature structure. The juxtaglomerular apparatus is an anatomical structure that lies adjacent to the glomerulus and regulates kidney function.") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-01-25T03:52:23Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0072051") @@ -80438,7 +79407,6 @@ SubClassOf( ObjectSomeValuesFrom( (juxtaglomerulus cell differentiation) AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "The process in which relatively unspecialized cells acquire specialized structural and/or functional features that characterize the juxtaglomerulus cells of the kidney as it progresses from its formation to the mature state.") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-01-25T03:58:01Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0072052") @@ -80450,7 +79418,6 @@ SubClassOf( ObjectSomeValuesFrom( (renal inner medulla development) AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "The process whose specific outcome is the progression of the renal inner medulla over time, from its formation to the mature structure. The renal inner medulla is unique to mammalian kidneys and is the innermost region of the mammalian kidney.") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-01-25T03:59:37Z") AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "inner renal medulla development") AnnotationAssertion( "biological_process") @@ -80463,7 +79430,6 @@ SubClassOf( ObjectSomeValuesFrom( (renal outer medulla development) AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "The process whose specific outcome is the progression of the renal outer medulla over time, from its formation to the mature structure. The renal outer medulla is the region of the kidney that lies between the renal cortex and the renal inner medulla.") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-01-25T04:00:42Z") AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "outer renal medulla development") AnnotationAssertion( "biological_process") @@ -80476,7 +79442,6 @@ SubClassOf( ObjectSomeValuesFrom( (renal cortex development) AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "The process whose specific outcome is the progression of the renal cortex over time, from its formation to the mature structure. The renal cortex is the outer region of the kidney.") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-01-25T04:01:12Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0072055") @@ -80488,7 +79453,6 @@ SubClassOf( ObjectSomeValuesFrom( (pyramid development) AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "The process whose specific outcome is the progression of the kidney pyramids over time, from its formation to the mature structure. Kidney pyramids are the conical masses that constitute the renal medulla in a multi-lobed mammalian kidney; they contain the loops of Henle and the medullary collecting ducts.") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-01-25T04:01:36Z") AnnotationAssertion(Annotation( "GOC:mah") "kidney pyramid development") AnnotationAssertion(Annotation( "GOC:mah") "pyramids development") @@ -80504,7 +79468,6 @@ SubClassOf( ObjectSomeValuesFrom( (inner stripe development) AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "The process whose specific outcome is the progression of the inner stripe over time, from its formation to the mature structure. The inner stripe is a deep, centrally located portion of the renal outer medulla and is traversed by thin descending and thick ascending portions of the loops of Henle.") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-01-25T04:01:58Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0072057") @@ -80517,7 +79480,6 @@ SubClassOf( ObjectSomeValuesFrom( (outer stripe development) AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "The process whose specific outcome is the progression of the outer stripe over time, from its formation to the mature structure. The outer stripe is the region of the kidney outer medulla that lies just below the cortex. The proximal straight tubules (S3) characterize this region.") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-01-25T04:02:56Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0072058") @@ -80530,7 +79492,6 @@ SubClassOf( ObjectSomeValuesFrom( (cortical collecting duct development) AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "The process whose specific outcome is the progression of the cortical collecting duct over time, from its formation to the mature structure. The cortical collecting duct is the portion of the collecting duct that resides in the renal cortex.") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-01-25T04:07:07Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0072059") @@ -80541,7 +79502,6 @@ SubClassOf( (outer medullary collecting duct development) AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "The process whose specific outcome is the progression of the outer medullary collecting duct over time, from its formation to the mature structure. The outer medullary collecting duct is the portion of the collecting duct that lies in the renal outer medulla.") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-01-25T04:08:18Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0072060") @@ -80552,7 +79512,6 @@ SubClassOf( (inner medullary collecting duct development) AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "The process whose specific outcome is the progression of the inner medullary collecting duct over time, from its formation to the mature structure. The inner medullary collecting duct is the portion of the collecting duct that lies in the renal inner medulla.") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-01-25T04:08:45Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0072061") @@ -80563,7 +79522,6 @@ SubClassOf( (short descending thin limb development) AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "The process whose specific outcome is the progression of the short descending thin limb over time, from its formation to the mature structure. The short descending thin limb is the descending thin limb of a short nephron that has a squamous epithelial morphology.") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-01-25T04:12:39Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0072063") @@ -80575,7 +79533,6 @@ SubClassOf( ObjectSomeValuesFrom( (long descending thin limb development) AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "The process whose specific outcome is the progression of the long descending thin limb over time, from its formation to the mature structure. The long descending thin limb is the descending thin limb of a long nephron that has a squamous epithelial morphology. The long descending limb starts in the inner stripe of the outer medulla and extends into the inner medulla.") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-01-25T04:13:17Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0072064") @@ -80587,7 +79544,6 @@ SubClassOf( ObjectSomeValuesFrom( (early distal convoluted tubule development) AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "The process whose specific outcome is the progression of the early distal convoluted tubule over time, from its formation to the mature structure. The early distal convoluted tubule contains DCT cells and is vasopressin-insensitive.") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-01-25T04:15:17Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0072067") @@ -80600,7 +79556,6 @@ SubClassOf( ObjectSomeValuesFrom( (late distal convoluted tubule development) AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "The process whose specific outcome is the progression of the late distal convoluted tubule over time, from its formation to the mature structure. The late distal convoluted tubule contains DCT cells and intercalated (IC) alpha and beta cells and is vasopressin-sensitive.") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-01-25T04:15:50Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0072068") @@ -80613,7 +79568,6 @@ SubClassOf( ObjectSomeValuesFrom( (loop of Henle development) AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "The process whose specific outcome is the progression of the loop of Henle over time, from its formation to the mature structure. The loop of Henle is a nephron tubule that connects the proximal convoluted tubule to the distal convoluted tubule.") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-01-25T04:20:27Z") AnnotationAssertion( "intermediate tubule development") AnnotationAssertion( "biological_process") @@ -80625,7 +79579,6 @@ SubClassOf( (kidney interstitial fibroblast differentiation) AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "The process in which relatively unspecialized cells acquire specialized structural and/or functional features that characterize the interstitial fibroblast of the kidney as it progresses from its formation to the mature state.") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-01-25T04:34:31Z") AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "kidney interstitial cell differentiation") AnnotationAssertion( "biological_process") @@ -80637,7 +79590,6 @@ SubClassOf( (kidney epithelium development) AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "The process whose specific outcome is the progression of an epithelium in the kidney over time, from its formation to the mature structure. An epithelium is a tissue that covers the internal or external surfaces of an anatomical structure.") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-01-25T04:37:42Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0072073") @@ -80649,7 +79601,6 @@ SubClassOf( ObjectSomeValuesFrom( (kidney mesenchyme development) AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "The biological process whose specific outcome is the progression of a kidney mesenchyme from an initial condition to its mature state. This process begins with the formation of kidney mesenchyme and ends with the mature structure. Kidney mesenchyme is the tissue made up of loosely connected mesenchymal cells in the kidney.") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-01-25T04:39:04Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0072074") @@ -80661,7 +79612,6 @@ SubClassOf( ObjectSomeValuesFrom( (metanephric mesenchyme development) AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "The biological process whose specific outcome is the progression of a metanephric mesenchyme from an initial condition to its mature state. This process begins with the formation of metanephric mesenchyme and ends with the mature structure. Metanephric mesenchyme is the tissue made up of loosely connected mesenchymal cells in the metanephros.") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-01-25T04:40:11Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0072075") @@ -80673,7 +79623,6 @@ SubClassOf( ObjectSomeValuesFrom( (nephrogenic mesenchyme development) AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "The biological process whose specific outcome is the progression of a nephrogenic mesenchyme from an initial condition to its mature state. This process begins with the formation of nephrogenic mesenchyme and ends with the mature structure. Nephrogenic mesenchyme is the tissue made up of loosely connected mesenchymal cells in the nephron.") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-01-25T04:40:44Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0072076") @@ -80685,7 +79634,6 @@ SubClassOf( ObjectSomeValuesFrom( (renal vesicle morphogenesis) AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "The process in which the anatomical structures of the renal vesicle are generated and organized. The renal vesicle is the primordial structure of the nephron epithelium, and is formed by the condensation of mesenchymal cells.") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-02-01T02:21:06Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0072077") @@ -80699,7 +79647,6 @@ SubClassOf( ObjectSomeValuesFrom( (nephron tubule morphogenesis) AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "The process in which the anatomical structures of a nephron tubule are generated and organized. A nephron tubule is an epithelial tube that is part of the nephron, the functional part of the kidney.") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-02-01T02:25:14Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0072078") @@ -80712,7 +79659,6 @@ SubClassOf( ObjectSomeValuesFrom( (nephron tubule formation) AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "The developmental process pertaining to the initial formation of a nephron tubule from unspecified parts. A nephron tubule is an epithelial tube that is part of the nephron, the functional part of the kidney.") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-02-01T02:29:26Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0072079") @@ -80724,7 +79670,6 @@ SubClassOf( ObjectSomeValuesFrom( (nephron tubule development) AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "The progression of a nephron tubule over time, from its initial formation to the mature structure. A nephron tubule is an epithelial tube that is part of the nephron, the functional part of the kidney.") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-02-01T02:32:12Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0072080") @@ -80736,7 +79681,6 @@ SubClassOf( (renal vesicle development) AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "The process whose specific outcome is the progression of the renal vesicle over time, from its formation to the mature structure. An epithelium is a tissue that covers the internal or external surfaces of an anatomical structure. The renal vesicle is the primordial structure of the nephron epithelium, and is formed by the condensation of mesenchymal cells.") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-02-08T01:18:31Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0072087") @@ -80748,7 +79692,6 @@ SubClassOf( ObjectSomeValuesFrom( (nephron epithelium morphogenesis) AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "The process in which the anatomical structures of the nephron epithelium are generated and organized. The nephron epithelium is a tissue that covers the surface of a nephron.") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-02-08T01:19:06Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0072088") @@ -80761,7 +79704,6 @@ SubClassOf( ObjectSomeValuesFrom( (stem cell proliferation) AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "The multiplication or reproduction of stem cells, resulting in the expansion of a stem cell population. A stem cell is a cell that retains the ability to divide and proliferate throughout life to provide progenitor cells that can differentiate into specialized cells.") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-02-08T02:03:36Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0072089") @@ -80773,7 +79715,6 @@ SubClassOf( ObjectSomeValuesFrom( (regulation of stem cell proliferation) AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "Any process that modulates the frequency, rate or extent of stem cell proliferation. A stem cell is a cell that retains the ability to divide and proliferate throughout life to provide progenitor cells that can differentiate into specialized cells.") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-02-08T02:09:03Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0072091") @@ -80783,7 +79724,6 @@ EquivalentClasses( ObjectIntersection # Class: (metanephric renal vesicle formation) AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "The developmental process pertaining to the initial formation of the metanephros.") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-02-10T01:17:11Z") AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "metanephros formation") AnnotationAssertion( "biological_process") @@ -80796,7 +79736,6 @@ SubClassOf( ObjectSomeValuesFrom( (anterior/posterior pattern specification involved in kidney development) AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "The developmental process that results in the creation of defined areas or spaces within the kidney along the anterior/posterior axis to which cells respond and eventually are instructed to differentiate.") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-02-10T02:06:24Z") AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "kidney anterior/posterior pattern specification") AnnotationAssertion( "biological_process") @@ -80809,7 +79748,6 @@ EquivalentClasses( ObjectIntersection # Class: (anterior/posterior pattern specification involved in ureteric bud development) AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "The developmental process that results in the creation of defined areas or spaces within the ureteric bud along the anterior/posterior axis to which cells respond and eventually are instructed to differentiate.") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-02-10T02:12:09Z") AnnotationAssertion( "biological_process") AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "ureteric bud anterior/posterior pattern formation") @@ -80821,7 +79759,6 @@ SubClassOf( ObjectSomeValuesFrom( (glomerulus morphogenesis) AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "The process in which the anatomical structures of the glomerulus are generated and organized. The glomerulus is a capillary tuft surrounded by Bowman's capsule in nephrons of the vertebrate kidney.") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-02-10T02:32:09Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0072102") @@ -80834,7 +79771,6 @@ SubClassOf( ObjectSomeValuesFrom( (glomerulus vasculature morphogenesis) AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "The process in which the anatomical structures of the glomerulus vasculature are generated and organized. The glomerulus vasculature is composed of the tubule structures that carry blood or lymph in the glomerulus.") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-02-10T02:34:54Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0072103") @@ -80847,7 +79783,6 @@ SubClassOf( ObjectSomeValuesFrom( (glomerular capillary formation) AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "The process that gives rise to a glomerular capillary. This process pertains to the initial formation of a structure from unspecified parts.") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-02-10T02:40:40Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0072104") @@ -80860,7 +79795,6 @@ SubClassOf( ObjectSomeValuesFrom( (ureteric peristalsis) AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "A wavelike sequence of involuntary muscular contraction and relaxation that passes along the ureter, impelling the contents onwards. The ureter is one of a pair of thick-walled tubes that transports urine from the kidney pelvis to the urinary bladder.") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-02-10T03:07:54Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0072105") @@ -80872,7 +79806,6 @@ SubClassOf( (regulation of ureteric bud formation) AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "Any process that modulates the developmental process pertaining to the initial formation of the ureteric bud from the Wolffian duct.") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-02-12T02:34:40Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0072106") @@ -80885,7 +79818,6 @@ SubClassOf( ObjectSomeValuesFrom( (positive regulation of ureteric bud formation) AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "Any process that increases the rate or extent of the developmental process pertaining to the initial formation of the ureteric bud from the Wolffian duct.") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-02-12T02:37:28Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0072107") @@ -80896,7 +79828,6 @@ SubClassOf( ObjectSomeValuesFrom( (positive regulation of mesenchymal to epithelial transition involved in metanephros morphogenesis) AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "Any process that increases the rate, frequency or extent of the transition where a mesenchymal cell establishes apical/basolateral polarity, forms intercellular adhesive junctions, synthesizes basement membrane components and becomes an epithelial cell that will contribute to the shaping of the metanephros.") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-02-12T02:45:57Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0072108") @@ -80907,7 +79838,6 @@ SubClassOf( ObjectSomeValuesFrom( (glomerular mesangium development) AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "The process whose specific outcome is the progression of the glomerular mesangium over time, from its formation to the mature structure. The glomerular mesangium is the thin membrane connective tissue composed of mesangial cells, which helps to support the capillary loops in a renal glomerulus.") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-02-22T10:35:24Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0072109") @@ -80919,7 +79849,6 @@ SubClassOf( ObjectSomeValuesFrom( (cell proliferation involved in kidney development) AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "The multiplication or reproduction of cells, resulting in the expansion of the population in the kidney.") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-02-22T10:48:45Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0072111") @@ -80930,7 +79859,6 @@ EquivalentClasses( ObjectIntersection AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "The process in which a relatively unspecialized cell acquires specialized features of a glomerular visceral epithelial cell. A glomerular visceral epithelial cell is a specialized epithelial cell that contains 'feet' that interdigitate with the 'feet' of other glomerular epithelial cells.") AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/23000"^^xsd:anyURI) -AnnotationAssertion( "mah") AnnotationAssertion( "2010-02-22T10:52:11Z") AnnotationAssertion( "glomerular visceral epithelial cell differentiation") AnnotationAssertion( "biological_process") @@ -80943,7 +79871,6 @@ SubClassOf( (pronephros morphogenesis) AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "The process in which the anatomical structures of the pronephros are generated and organized. In mammals, the pronephros is the first of the three embryonic kidneys to be established and exists only transiently. In lower vertebrates such as fish and amphibia, the pronephros is the fully functional embryonic kidney and is indispensable for larval life.") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-02-22T11:12:15Z") AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "pronephric kidney morphogenesis") AnnotationAssertion( "biological_process") @@ -80956,7 +79883,6 @@ SubClassOf( ObjectSomeValuesFrom( (pronephros formation) AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "The developmental process pertaining to the initial formation of the pronephros. In mammals, the pronephros is the first of the three embryonic kidneys to be established and exists only transiently. In lower vertebrates such as fish and amphibia, the pronephros is the fully functional embryonic kidney and is indispensable for larval life.") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-02-22T11:16:26Z") AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "pronephric kidney formation") AnnotationAssertion( "biological_process") @@ -80969,7 +79895,6 @@ SubClassOf( ObjectSomeValuesFrom( (pronephros maturation) AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "A developmental process, independent of morphogenetic (shape) change, that is required for the pronephros to attain its fully functional state. In mammals, the pronephros is the first of the three embryonic kidneys to be established and exists only transiently. In lower vertebrates such as fish and amphibia, the pronephros is the fully functional embryonic kidney and is indispensable for larval life.") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-02-22T11:25:48Z") AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "pronephric kidney maturation") AnnotationAssertion( "biological_process") @@ -80982,7 +79907,6 @@ SubClassOf( ObjectSomeValuesFrom( (renal capsule development) AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "The process whose specific outcome is the progression of the renal capsule over time, from its formation to the mature structure. The renal capsule is the tough fibrous layer surrounding the kidney, covered in a thick layer of perinephric adipose tissue. It provides some protection from trauma and damage. During development, it comprises a single layer of flattened cells that lie just above the cortical stroma and the condensed mesenchyme of the nephrogenic zone. It is in this region that the early stages of nephron induction and formation of new generations ureteric bud branches occur, as the kidney expands.") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-02-22T02:02:55Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0072127") @@ -80994,7 +79918,6 @@ SubClassOf( ObjectSomeValuesFrom( (renal capsule morphogenesis) AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "The process in which the anatomical structures of the renal capsule are generated and organized. The renal capsule is the tough fibrous layer surrounding the kidney, covered in a thick layer of perinephric adipose tissue. It provides some protection from trauma and damage. During development, it comprises a single layer of flattened cells that lie just above the cortical stroma and the condensed mesenchyme of the nephrogenic zone. It is in this region that the early stages of nephron induction and formation of new generations ureteric bud branches occur, as the kidney expands.") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-02-22T02:06:19Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0072128") @@ -81007,7 +79930,6 @@ SubClassOf( ObjectSomeValuesFrom( (renal capsule formation) AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "The developmental process pertaining to the initial formation of a renal capsule from unspecified parts. The renal capsule is the tough fibrous layer surrounding the kidney, covered in a thick layer of perinephric adipose tissue. It provides some protection from trauma and damage. During development, it comprises a single layer of flattened cells that lie just above the cortical stroma and the condensed mesenchyme of the nephrogenic zone. It is in this region that the early stages of nephron induction and formation of new generations ureteric bud branches occur, as the kidney expands.") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-02-22T02:08:14Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0072129") @@ -81020,7 +79942,6 @@ SubClassOf( ObjectSomeValuesFrom( (kidney mesenchyme morphogenesis) AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "The process in which the anatomical structures of a kidney mesenchymal tissue are generated and organized. Kidney mesenchyme is the tissue made up of loosely connected mesenchymal cells in the kidney.") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-02-22T02:16:43Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0072131") @@ -81032,7 +79953,6 @@ SubClassOf( ObjectSomeValuesFrom( (mesenchyme morphogenesis) AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "The process in which the anatomical structures of a mesenchymal tissue are generated and organized. A mesenchymal tissue is made up of loosely packed stellate cells.") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-02-22T02:17:15Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0072132") @@ -81045,7 +79965,6 @@ SubClassOf( ObjectSomeValuesFrom( (metanephric mesenchyme morphogenesis) AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "The process in which the anatomical structures of a metanephric mesenchymal tissue are generated and organized. Metanephric mesenchyme is the tissue made up of loosely connected mesenchymal cells in the metanephros.") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-02-22T02:20:14Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0072133") @@ -81057,7 +79976,6 @@ SubClassOf( ObjectSomeValuesFrom( (nephrogenic mesenchyme morphogenesis) AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "The process in which the anatomical structures of a nephrogenic mesenchymal tissue are generated and organized. Nephrogenic mesenchyme is the tissue made up of loosely connected mesenchymal cells in the nephron.") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-02-22T02:21:16Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0072134") @@ -81069,7 +79987,6 @@ SubClassOf( ObjectSomeValuesFrom( (mesenchymal cell proliferation involved in ureteric bud development) AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "The multiplication or reproduction of cells, resulting in the expansion of a mesenchymal cell population of the ureteric bud, that contributes to ureteric bud development.") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-02-22T02:40:38Z") AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "ureteric bud mesenchymal cell proliferation") AnnotationAssertion( "biological_process") @@ -81080,7 +79997,6 @@ EquivalentClasses( ObjectIntersection # Class: (glomerular parietal epithelial cell differentiation) AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "The process in which a relatively unspecialized cell acquires specialized features of a glomerular parietal epithelial cell. Glomerular parietal epithelial cells are specialized epithelial cells that form tight junctions as a barrier to protein transport.") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-02-24T01:33:05Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0072139") @@ -81090,7 +80006,6 @@ SubClassOf( (renal interstitial fibroblast development) AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "The process whose specific outcome is the progression of a renal interstitial fibroblast over time, from its formation to the mature structure.") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-02-24T01:39:05Z") AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "kidney interstitial cell development") AnnotationAssertion( "biological_process") @@ -81103,7 +80018,6 @@ SubClassOf( ObjectSomeValuesFrom( (juxtaglomerulus cell development) AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "The process whose specific outcome is the progression of a juxtaglomerulus cell over time, from its formation to the mature structure.") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-02-24T01:42:53Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0072142") @@ -81115,7 +80029,6 @@ SubClassOf( ObjectSomeValuesFrom( (mesangial cell development) AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "The process whose specific outcome is the progression of a mesangial cell in the kidney over time, from its formation to the mature structure.") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-02-24T01:44:28Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0072143") @@ -81127,7 +80040,6 @@ SubClassOf( ObjectSomeValuesFrom( (glomerular mesangial cell development) AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "The process whose specific outcome is the progression of a glomerular mesangial cell in the kidney over time, from its formation to the mature structure.") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-02-24T01:53:13Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0072144") @@ -81139,7 +80051,6 @@ SubClassOf( ObjectSomeValuesFrom( (epithelial cell migration involved in nephron tubule morphogenesis) AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "The orderly movement of epithelial cells within a renal tubule that contributes to nephron tubule morphogenesis.") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-02-24T02:21:25Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0072155") @@ -81149,7 +80060,6 @@ EquivalentClasses( ObjectIntersection # Class: (distal tubule morphogenesis) AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "The process in which the anatomical structures of a distal tubule are generated and organized. The distal tubule is a nephron tubule that begins at the macula densa and extends to the connecting tubule.") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-02-24T02:32:03Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0072156") @@ -81161,7 +80071,6 @@ SubClassOf( ObjectSomeValuesFrom( (epithelial cell migration involved in distal tubule morphogenesis) AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "The orderly movement of epithelial cells within a renal tubule that contributes to distal tubule morphogenesis.") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-02-24T02:33:33Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0072157") @@ -81171,7 +80080,6 @@ EquivalentClasses( ObjectIntersection # Class: (proximal tubule morphogenesis) AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "The process in which the anatomical structures of a proximal tubule are generated and organized. The proximal tubule is a nephron tubule that connects Bowman's capsule to the descending thin limb of the loop of Henle. It has a brush border epithelial morphology.") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-02-24T02:35:36Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0072158") @@ -81183,7 +80091,6 @@ SubClassOf( ObjectSomeValuesFrom( (epithelial cell migration involved in proximal tubule morphogenesis) AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "The orderly movement of epithelial cells within a renal tubule that contributes to proximal tubule morphogenesis.") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-02-24T02:37:08Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0072159") @@ -81193,7 +80100,6 @@ EquivalentClasses( ObjectIntersection # Class: (nephron tubule epithelial cell differentiation) AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "The process in which relatively unspecialized cells acquire specialized structural and/or functional features that characterize the cells of the nephron tubule as it progresses from its formation to the mature state.") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-02-24T02:40:11Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0072160") @@ -81205,7 +80111,6 @@ SubClassOf( ObjectSomeValuesFrom( (mesenchymal cell differentiation involved in kidney development) AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "The process in which relatively unspecialized cells acquire specialized structural and/or functional features that characterize the mesenchymal cells of the kidney as it progresses from its formation to the mature state.") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-02-26T01:31:49Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0072161") @@ -81216,7 +80121,6 @@ SubClassOf( ObjectSomeValuesFrom( (mesonephric epithelium development) AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "The process whose specific outcome is the progression of an epithelium in the mesonephros over time, from its formation to the mature structure. An epithelium is a tissue that covers the internal or external surfaces of an anatomical structure.") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-02-26T01:40:43Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0072163") @@ -81228,7 +80132,6 @@ SubClassOf( ObjectSomeValuesFrom( (mesonephric tubule development) AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "The progression of a mesonephric tubule over time, from its initial formation to the mature structure. A mesonephric tubule is an epithelial tube that is part of the mesonephros.") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-02-26T01:45:58Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0072164") @@ -81240,7 +80143,6 @@ SubClassOf( (metanephric tubule development) AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "The progression of a metanephric tubule over time, from its initial formation to the mature structure. A metanephric tubule is an epithelial tube that is part of the metanephros.") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-02-26T01:58:18Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0072170") @@ -81252,7 +80154,6 @@ SubClassOf( ObjectSomeValuesFrom( (mesonephric tubule morphogenesis) AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "The process in which the anatomical structures of a mesonephric tubule are generated and organized. A mesonephric tubule is an epithelial tube that is part of the mesonephros.") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-02-26T02:02:13Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0072171") @@ -81264,7 +80165,6 @@ SubClassOf( ObjectSomeValuesFrom( (mesonephric tubule formation) AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "The developmental process pertaining to the initial formation of a mesonephric tubule from unspecified parts. A mesonephric tubule is an epithelial tube that is part of the mesonephros.") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-02-26T02:02:37Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0072172") @@ -81276,7 +80176,6 @@ SubClassOf( ObjectSomeValuesFrom( (metanephric tubule morphogenesis) AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "The process in which the anatomical structures of a metanephric tubule are generated and organized from an epithelium. A metanephric tubule is an epithelial tube that is part of the metanephros.") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-02-26T02:06:42Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0072173") @@ -81288,7 +80187,6 @@ SubClassOf( ObjectSomeValuesFrom( (metanephric tubule formation) AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "The developmental process pertaining to the initial formation of a metanephric tubule.") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-02-26T02:07:41Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0072174") @@ -81301,7 +80199,6 @@ SubClassOf( ObjectSomeValuesFrom( "GOC:mtg_kidney_jan10") "The developmental process pertaining to the initial formation of an epithelial tube.") AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/22302"^^xsd:anyURI) -AnnotationAssertion( "mah") AnnotationAssertion( "2010-02-26T02:15:40Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0072175") @@ -81312,7 +80209,6 @@ SubClassOf( ObjectSomeValuesFrom( (nephric duct development) AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "The process whose specific outcome is the progression of a nephric duct over time, from its initial formation to a mature structure. A nephric duct is a tube that drains a primitive kidney.") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-02-26T02:27:31Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0072176") @@ -81323,7 +80219,6 @@ SubClassOf( (mesonephric duct development) AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "The process whose specific outcome is the progression of a mesonephric duct over time, from its initial formation to a mature structure. A mesonephric duct is a tube drains the mesonephros.") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-02-26T02:32:22Z") AnnotationAssertion(Annotation( "GOC:dph") "Wolffian duct development") AnnotationAssertion( "biological_process") @@ -81336,7 +80231,6 @@ SubClassOf( (nephric duct morphogenesis) AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "The process in which the anatomical structures of the nephric duct are generated and organized. A nephric duct is a tube that drains a primitive kidney.") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-02-26T02:35:29Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0072178") @@ -81349,7 +80243,6 @@ SubClassOf( ObjectSomeValuesFrom( (nephric duct formation) AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "The developmental process pertaining to the initial formation of a nephric duct. A nephric duct is a tube that drains a primitive kidney.") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-02-26T02:35:55Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0072179") @@ -81362,7 +80255,6 @@ SubClassOf( ObjectSomeValuesFrom( (mesonephric duct morphogenesis) AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "The process in which the anatomical structures of the mesonephric duct are generated and organized. A mesonephric duct is a tube drains the mesonephros.") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-02-26T02:37:13Z") AnnotationAssertion( "biological_process") AnnotationAssertion(Annotation( "GOC:dph") "Wolffian duct morphogenesis") @@ -81376,7 +80268,6 @@ SubClassOf( ObjectSomeValuesFrom( (mesonephric duct formation) AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "The developmental process pertaining to the initial formation of a mesonephric duct. A mesonephric duct is a tube that drains the mesonephros.") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-02-26T02:38:03Z") AnnotationAssertion(Annotation( "GOC:dph") "Wolffian duct formation") AnnotationAssertion( "biological_process") @@ -81390,7 +80281,6 @@ SubClassOf( (regulation of nephron tubule epithelial cell differentiation) AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "Any process that modulates the frequency, rate or extent of nephron tubule epithelial cell differentiation.") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-02-26T02:45:09Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0072182") @@ -81400,7 +80290,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of nephron tubule epithelial cell differentiation) AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "Any process that decreases the frequency, rate or extent of nephron tubule epithelial cell differentiation.") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-02-26T02:47:25Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0072183") @@ -81411,7 +80300,6 @@ SubClassOf( (ureter development) AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "The process whose specific outcome is the progression of the ureter over time, from its formation to the mature structure. The ureter is a muscular tube that transports urine from the kidney to the urinary bladder or from the Malpighian tubule to the hindgut.") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-03-01T01:44:14Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0072189") @@ -81424,7 +80312,6 @@ SubClassOf( ObjectSomeValuesFrom( (ureter urothelium development) AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "The process whose specific outcome is the progression of the urothelium of the ureter over time, from its formation to the mature structure. The urothelium is an epithelium that makes up the epithelial tube of the ureter.") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-03-01T01:46:31Z") AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "ureter epithelium development") AnnotationAssertion( "biological_process") @@ -81437,7 +80324,6 @@ SubClassOf( ObjectSomeValuesFrom( (ureter smooth muscle development) AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "The process whose specific outcome is the progression of smooth muscle in the ureter over time, from its formation to the mature structure.") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-03-01T01:48:53Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0072191") @@ -81449,7 +80335,6 @@ SubClassOf( ObjectSomeValuesFrom( (ureter smooth muscle cell differentiation) AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "The process in which a relatively unspecialized cell acquires specialized features of a smooth muscle cell in the ureter.") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-03-01T01:55:01Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0072193") @@ -81461,7 +80346,6 @@ SubClassOf( ObjectSomeValuesFrom( (kidney smooth muscle tissue development) AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "The process whose specific outcome is the progression of smooth muscle in the kidney over time, from its formation to the mature structure.") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-03-01T02:05:30Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0072194") @@ -81472,7 +80356,6 @@ SubClassOf( ObjectSomeValuesFrom( (ureter morphogenesis) AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "The process in which the anatomical structures of the ureter are generated and organized. The ureter is a muscular tube that transports urine from the kidney to the urinary bladder.") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-03-01T02:24:55Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0072197") @@ -81485,7 +80368,6 @@ SubClassOf( ObjectSomeValuesFrom( (mesenchymal cell proliferation involved in ureter development) AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "The multiplication or reproduction of cells, resulting in the expansion of a mesenchymal cell population of the ureter, that contributes to ureter development.") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-03-01T03:24:41Z") AnnotationAssertion( "biological_process") AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "ureter mesenchymal cell proliferation") @@ -81497,7 +80379,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of mesenchymal cell proliferation involved in ureter development) AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "Any process that modulates the frequency, rate or extent of mesenchymal cell proliferation that contributes to the progression of the ureter gland over time. A mesenchymal cell is a cell that normally gives rise to other cells that are organized as three-dimensional masses, rather than sheets.") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-03-01T03:38:13Z") AnnotationAssertion( "biological_process") AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "regulation of ureter mesenchymal cell proliferation") @@ -81509,7 +80390,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of mesenchymal cell proliferation involved in ureter development) AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "Any process that decreases the frequency, rate or extent of mesenchymal cell proliferation that contributes to the progression of the ureter gland over time. A mesenchymal cell is a cell that normally gives rise to other cells that are organized as three-dimensional masses, rather than sheets.") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-03-01T03:42:31Z") AnnotationAssertion( "biological_process") AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "negative regulation of ureter mesenchymal cell proliferation") @@ -81523,7 +80403,6 @@ SubClassOf( ObjectSomeValuesFrom( (negative regulation of mesenchymal cell proliferation) AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "Any process that decreases the frequency, rate or extent of mesenchymal cell proliferation. A mesenchymal cell is a cell that normally gives rise to other cells that are organized as three-dimensional masses, rather than sheets.") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-03-01T03:43:29Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0072201") @@ -81535,7 +80414,6 @@ SubClassOf( (cell differentiation involved in metanephros development) AnnotationAssertion(Annotation( "GOC:mah") Annotation( "GOC:mtg_kidney_jan10") "The process in which relatively unspecialized cells acquire specialized structural and/or functional features that characterize the cells of the metanephros as it progresses from its formation to the mature state.") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-03-18T10:40:14Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0072202") @@ -81545,7 +80423,6 @@ EquivalentClasses( ObjectIntersection # Class: (cell proliferation involved in metanephros development) AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "The multiplication or reproduction of cells, resulting in the expansion of the population in the metanephros.") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-03-18T10:42:27Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0072203") @@ -81555,7 +80432,6 @@ EquivalentClasses( ObjectIntersection # Class: (cell-cell signaling involved in metanephros development) AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "Any process that mediates the transfer of information from one cell to another and contributes to the progression of the metanephros over time, from its formation to the mature organ.") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-03-18T10:54:36Z") AnnotationAssertion(Annotation( "GOC:mah") "cell-cell signalling involved in metanephros development") AnnotationAssertion( "biological_process") @@ -81566,7 +80442,6 @@ EquivalentClasses( ObjectIntersection # Class: (metanephric collecting duct development) AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "The process whose specific outcome is the progression of a collecting duct in the metanephros over time, from its formation to the mature structure. The collecting duct responds to vasopressin and aldosterone to regulate water, electrolyte and acid-base balance. The collecting duct is the final common path through which urine flows before entering the ureter and then emptying into the bladder.") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-03-18T11:15:37Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0072205") @@ -81578,7 +80453,6 @@ SubClassOf( ObjectSomeValuesFrom( (metanephric juxtaglomerular apparatus development) AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "The process whose specific outcome is the progression of the juxtaglomerular apparatus in the metanephros over time, from its formation to the mature structure. The juxtaglomerular apparatus is an anatomical structure which consists of juxtaglomerular cells, extraglomerular mesangial cells and the macula densa. The juxtaglomerular apparatus lies adjacent to the glomerulus and regulates kidney function by maintaining the blood flow to the kidney and the filtration rate.") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-03-18T11:17:47Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0072206") @@ -81590,7 +80464,6 @@ SubClassOf( ObjectSomeValuesFrom( (metanephric epithelium development) AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "The process whose specific outcome is the progression of an epithelium in the metanephros over time, from its formation to the mature structure. An epithelium is a tissue that covers the internal or external surfaces of an anatomical structure.") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-03-18T11:50:37Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0072207") @@ -81602,7 +80475,6 @@ SubClassOf( ObjectSomeValuesFrom( (metanephric smooth muscle tissue development) AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "The process whose specific outcome is the progression of smooth muscle in the metanephros over time, from its formation to the mature structure.") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-03-18T11:51:59Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0072208") @@ -81614,7 +80486,6 @@ SubClassOf( ObjectSomeValuesFrom( (metanephric nephron development) AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "The process whose specific outcome is the progression of a nephron in the metanephros over time, from its formation to the mature structure. A nephron is the functional unit of the kidney.") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-03-18T12:52:57Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0072210") @@ -81626,7 +80497,6 @@ SubClassOf( ObjectSomeValuesFrom( (metanephric pyramids development) AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "The process whose specific outcome is the progression of the metanephric pyramids over time, from their formation to the mature structures. Metanephric pyramids are the conical masses that constitute the renal medulla in a metanephros; they contain the loops of Henle and the medullary collecting ducts.") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-03-18T01:04:51Z") AnnotationAssertion(Annotation( "GOC:mah") "metanephric kidney pyramid development") AnnotationAssertion(Annotation( "GOC:mah") "metanephric pyramid development") @@ -81642,7 +80512,6 @@ SubClassOf( ObjectSomeValuesFrom( (metanephric capsule development) AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "The process whose specific outcome is the progression of the metanephric capsule over time, from its formation to the mature structure. The metanephric capsule is the tough fibrous layer surrounding the metanephros, covered in a thick layer of perinephric adipose tissue. It provides some protection from trauma and damage.") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-03-18T01:25:19Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0072213") @@ -81654,7 +80523,6 @@ SubClassOf( ObjectSomeValuesFrom( (metanephric cortex development) AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "The process whose specific outcome is the progression of the metanephric cortex over time, from its formation to the mature structure. The metanephric cortex is the outer region of the metanephros.") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-03-18T01:29:49Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0072214") @@ -81674,7 +80542,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of metanephros development) AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "Any process that increases the rate, frequency or extent of metanephros development. Metanephros development is the process whose specific outcome is the progression of the metanephros over time, from its formation to the mature structure. The metanephros is an organ that filters the blood and excretes the end products of body metabolism in the form of urine.") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-03-18T01:40:12Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0072216") @@ -81684,7 +80551,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of metanephros development) AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "Any process that decreases the rate, frequency or extent of metanephros development. Metanephros development is the process whose specific outcome is the progression of the metanephros over time, from its formation to the mature structure. The metanephros is an organ that filters the blood and excretes the end products of body metabolism in the form of urine.") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-03-18T01:45:48Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0072217") @@ -81694,7 +80560,6 @@ EquivalentClasses( ObjectIntersection # Class: (metanephric ascending thin limb development) AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "The process whose specific outcome is the progression of a metanephric ascending thin limb over time, from its formation to the mature structure. The metanephric ascending thin limb is a segment of a nephron tubule in the metanephros lying in the inner medulla that is permeable to ions but not to water and has a simple epithelium; active transepithelial solute transport is absent.") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-03-18T03:34:42Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0072218") @@ -81706,7 +80571,6 @@ SubClassOf( ObjectSomeValuesFrom( (metanephric cortical collecting duct development) AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "The process whose specific outcome is the progression of the metanephric cortical collecting duct over time, from its formation to the mature structure. The metanephric cortical collecting duct is the portion of the metanephric collecting duct that resides in the renal cortex.") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-03-18T03:34:52Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0072219") @@ -81717,7 +80581,6 @@ SubClassOf( (metanephric descending thin limb development) AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "The process whose specific outcome is the progression of the metanephric descending thin limb over time, from its formation to the mature structure. The metanephric descending thin limb is a part of the metanephric loop of Henle situated just after the proximal straight tubule (S3). It extends to the tip of the metanephric loop of Henle.") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-03-18T03:35:05Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0072220") @@ -81729,7 +80592,6 @@ SubClassOf( ObjectSomeValuesFrom( (metanephric distal convoluted tubule development) AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "The process whose specific outcome is the progression of the metanephric distal convoluted tubule over time, from its formation to the mature structure. The metanephric distal convoluted tubule is the first segment of the metanephric nephron lying just downstream from the loop of Henle, immediately after the macula densa. Among other functions, in humans it is responsible for the reabsorption of about 5% of filtered sodium via the thiazide-sensitive Na-Cl symporter.") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-03-18T03:35:27Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0072221") @@ -81741,7 +80603,6 @@ SubClassOf( ObjectSomeValuesFrom( (metanephric early distal convoluted tubule development) AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "The process whose specific outcome is the progression of the metanephric early distal convoluted tubule over time, from its formation to the mature structure. The metanephric early distal convoluted tubule contains metanephric DCT cells and is vasopressin-insensitive.") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-03-18T03:35:46Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0072222") @@ -81753,7 +80614,6 @@ SubClassOf( ObjectSomeValuesFrom( (metanephric glomerular mesangium development) AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "The process whose specific outcome is the progression of the metanephric glomerular mesangium over time, from its formation to the mature structure. The metanephric glomerular mesangium is the thin membrane connective tissue composed of mesangial cells in the metanephros, which helps to support the capillary loops in a renal glomerulus.") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-03-18T03:35:56Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0072223") @@ -81765,7 +80625,6 @@ SubClassOf( ObjectSomeValuesFrom( (metanephric glomerulus development) AnnotationAssertion(Annotation( "GOC:mah") "The progression of the metanephric glomerulus over time from its initial formation until its mature state. The metanephric glomerulus is a capillary tuft which forms a close network with the visceral epithelium (podocytes) and the mesangium to form the filtration barrier and is surrounded by Bowman's capsule in nephrons of the mature vertebrate kidney, or metanephros.") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-03-18T03:36:20Z") AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "metanephric glomerular development") AnnotationAssertion( "biological_process") @@ -81778,7 +80637,6 @@ SubClassOf( ObjectSomeValuesFrom( (metanephric late distal convoluted tubule development) AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "The process whose specific outcome is the progression of the metanephric late distal convoluted tubule over time, from its formation to the mature structure. The metanephric late distal convoluted tubule contains metanephric DCT cells and intercalated (IC) alpha and beta cells and is vasopressin-sensitive.") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-03-18T03:37:04Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0072225") @@ -81790,7 +80648,6 @@ SubClassOf( ObjectSomeValuesFrom( (metanephric macula densa development) AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "The process whose specific outcome is the progression of the metanephric macula densa over time, from its formation to the mature structure. The metanephric macula densa is an area of specialized cells in the distal tubule of the metanephros that makes contact with the vascular pole of the glomerulus.") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-03-18T03:37:26Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0072227") @@ -81802,7 +80659,6 @@ SubClassOf( ObjectSomeValuesFrom( (metanephric proximal convoluted tubule development) AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "The process whose specific outcome is the progression of the metanephric proximal convoluted tubule over time, from its formation to the mature structure. The metanephric proximal convoluted tubule is the most proximal portion of the metanephric proximal tubule and extends from the metanephric glomerular capsule to the metanephric proximal straight tubule.") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-03-18T03:37:56Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0072229") @@ -81814,7 +80670,6 @@ SubClassOf( ObjectSomeValuesFrom( (metanephric proximal straight tubule development) AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "The process whose specific outcome is the progression of the metanephric proximal straight tubule over time, from its formation to the mature structure. The metanephric proximal straight tubule is the part of the metanephric descending limb that extends from the metanephric proximal convoluted tubule to the metanephric descending thin tubule.") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-03-18T03:38:53Z") AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "metanephric S3 development") AnnotationAssertion( "biological_process") @@ -81827,7 +80682,6 @@ SubClassOf( ObjectSomeValuesFrom( (metanephric proximal convoluted tubule segment 1 development) AnnotationAssertion(Annotation( "GOC:bf") Annotation( "GOC:mtg_kidney_jan10") "The process whose specific outcome is the progression of the S1 portion of the metanephric proximal convoluted tubule over time, from its formation to the mature structure. The S1 portion is the initial portion of the metanephric proximal convoluted tubule and is responsible for avid reabsorption of water and solutes.") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-03-18T03:39:10Z") AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "metanephric S1 development") AnnotationAssertion( "biological_process") @@ -81840,7 +80694,6 @@ SubClassOf( ObjectSomeValuesFrom( (metanephric thick ascending limb development) AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "The process whose specific outcome is the progression of the metanephric thick ascending limb over time, from its formation to the mature structure. The metanephric thick ascending limb is the last part of the metanephric loop of Henle. Its thick, mitochondria-rich epithelium characterizes the outer medulla, and is responsible for very avid active salt transport. At the macula densa, the thick ascending limb connects to the distal convoluted tubule.") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-03-18T03:39:36Z") AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "metanephric TAL development") AnnotationAssertion( "biological_process") @@ -81853,7 +80706,6 @@ SubClassOf( ObjectSomeValuesFrom( (metanephric nephron tubule development) AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "The progression of a metanephric nephron tubule over time, from its initial formation to the mature structure. A metanephric nephron tubule is an epithelial tube that is part of the metanephric nephron, the functional part of the metanephros.") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-03-18T03:41:23Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0072234") @@ -81866,7 +80718,6 @@ SubClassOf( (metanephric distal tubule development) AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "The process whose specific outcome is the progression of the metanephric distal tubule over time, from its formation to the mature structure. The metanephric distal tubule is a metanephric nephron tubule that begins at the metanephric macula densa and extends to the metanephric connecting tubule.") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-03-18T03:45:37Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0072235") @@ -81877,7 +80728,6 @@ SubClassOf( (metanephric loop of Henle development) AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "The process whose specific outcome is the progression of the metanephric loop of Henle over time, from its formation to the mature structure. The metanephric loop of Henle is a metanephric nephron tubule that connects the proximal convoluted tubule to the distal convoluted tubule in the metanephros.") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-03-18T03:46:18Z") AnnotationAssertion( "metanephric intermediate tubule development") AnnotationAssertion( "biological_process") @@ -81889,7 +80739,6 @@ SubClassOf( (metanephric proximal tubule development) AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "The process whose specific outcome is the progression of the metanephric proximal tubule over time, from its formation to the mature structure. The metanephric proximal tubule is a metanephric nephron tubule that connects Bowman's capsule to the descending thin limb of the loop of Henle in the metanephros. It has a brush border epithelial morphology.") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-03-18T03:46:54Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0072237") @@ -81901,7 +80750,6 @@ SubClassOf( (metanephric long nephron development) AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "The process whose specific outcome is the progression of a metanephric long nephron over time, from its formation to the mature structure. Long nephrons are associated with juxtamedullary glomeruli and extend into the inner medulla in the metanephros.") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-03-18T03:48:23Z") AnnotationAssertion( "biological_process") AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "metanephric juxtamedullary nephron development") @@ -81914,7 +80762,6 @@ SubClassOf( (metanephric glomerulus vasculature development) AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "The biological process whose specific outcome is the progression of a metanephric glomerulus vasculature from an initial condition to its mature state. This process begins with the formation of the metanephric glomerulus vasculature and ends with the mature structure. The metanephric glomerulus vasculature is composed of the tubule structures that carry blood or lymph in the metanephric glomerulus.") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-03-18T03:50:29Z") AnnotationAssertion( "biological_process") AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "glomerulus capillary development") @@ -81927,7 +80774,6 @@ SubClassOf( ObjectSomeValuesFrom( (metanephric nephron epithelium development) AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "The process whose specific outcome is the progression of the metanephric nephron epithelium over time, from its formation to the mature structure. An epithelium is a tissue that covers the internal or external surfaces of an anatomical structure. The metanephric nephron epithelium is a tissue that covers the surface of a nephron in the metanephros.") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-03-19T03:29:49Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0072243") @@ -81939,7 +80785,6 @@ SubClassOf( (metanephric glomerular epithelium development) AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "The process whose specific outcome is the progression of the metanephric glomerular epithelium over time, from its formation to the mature structure. The metanephric glomerular epithelium is an epithelial tissue that covers the outer surfaces of the glomerulus in the metanephros. The metanephric glomerular epithelium consists of both parietal and visceral epithelium. Metanephric glomerular parietal epithelial cells are specialized epithelial cells that form tight junctions as a barrier to protein transport. A metanephric glomerular visceral epithelial cell is a specialized epithelial cell that contains 'feet' that interdigitate with the 'feet' of other glomerular epithelial cells in the metanephros.") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-03-19T03:38:47Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0072244") @@ -81953,7 +80798,6 @@ SubClassOf( ObjectSomeValuesFrom( "GOC:mtg_kidney_jan10") "The process in which a relatively unspecialized cell acquires specialized features of a metanephric glomerular visceral epithelial cell. A metanephric glomerular visceral epithelial cell is a specialized epithelial cell that contains 'feet' that interdigitate with the 'feet' of other glomerular epithelial cells in the metanephros.") AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/23000"^^xsd:anyURI) -AnnotationAssertion( "mah") AnnotationAssertion( "2010-03-19T03:44:57Z") AnnotationAssertion( "metanephric glomerular visceral epithelial cell differentiation") AnnotationAssertion( "biological_process") @@ -81967,7 +80811,6 @@ SubClassOf( "GOC:mtg_kidney_jan10") "The process whose specific outcome is the progression of a metanephric glomerular visceral epithelial cell over time, from its formation to the mature structure. A metanephric glomerular visceral epithelial cell is a specialized epithelial cell that contains 'feet' that interdigitate with the 'feet' of other glomerular epithelial cells in the metanephros.") AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/23000"^^xsd:anyURI) -AnnotationAssertion( "mah") AnnotationAssertion( "2010-03-19T03:46:26Z") AnnotationAssertion( "metanephric glomerular visceral epithelial cell development") AnnotationAssertion( "biological_process") @@ -81981,7 +80824,6 @@ SubClassOf( ObjectSomeValuesFrom( (metanephric nephron tubule epithelial cell differentiation) AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "The process in which relatively unspecialized cells acquire specialized structural and/or functional features that characterize the cells of the metanephric nephron tubule as it progresses from its formation to the mature state.") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-03-19T04:11:02Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0072257") @@ -81994,7 +80836,6 @@ SubClassOf( ObjectSomeValuesFrom( (metanephric glomerular endothelium development) AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "The process whose specific outcome is the progression of the metanephric glomerular endothelium over time, from its formation to the mature structure. The metanephric glomerular endothelium is an epithelial tissue that covers the internal surfaces of the glomerulus of the metanephros.") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-03-30T02:42:26Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0072264") @@ -82006,7 +80847,6 @@ SubClassOf( ObjectSomeValuesFrom( (metanephric capsule morphogenesis) AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "The process in which the anatomical structures of the metanephric capsule are generated and organized. The metanephric capsule is the tough fibrous layer surrounding the metanephros, covered in a thick layer of perinephric adipose tissue. It provides some protection from trauma and damage.") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-03-30T02:54:49Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0072265") @@ -82018,7 +80858,6 @@ SubClassOf( ObjectSomeValuesFrom( (metanephric capsule formation) AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "The developmental process pertaining to the initial formation of a metanephric capsule from unspecified parts. The metanephric capsule is the tough fibrous layer surrounding the metanephros, covered in a thick layer of perinephric adipose tissue. It provides some protection from trauma and damage.") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-03-30T02:56:35Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0072266") @@ -82030,7 +80869,6 @@ SubClassOf( ObjectSomeValuesFrom( (pattern specification involved in metanephros development) AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "Any developmental process that results in the creation of defined areas or spaces within the metanephros to which cells respond and eventually are instructed to differentiate.") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-03-30T03:06:30Z") AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "metanephros pattern specification") AnnotationAssertion( "biological_process") @@ -82043,7 +80881,6 @@ EquivalentClasses( ObjectIntersection # Class: (metanephric long descending thin limb development) AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "The process whose specific outcome is the progression of the metanephric long descending thin limb over time, from its formation to the mature structure. The metanephric long descending thin limb is the descending thin limb of a long nephron in the metanephros that has a squamous epithelial morphology. The long descending limb starts in the inner stripe of the outer medulla and extends into the inner medulla.") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-03-30T03:12:05Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0072269") @@ -82055,7 +80892,6 @@ SubClassOf( ObjectSomeValuesFrom( (metanephric short nephron development) AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "The process whose specific outcome is the progression of a short nephron in the metanephros over time, from its formation to the mature structure. Short nephrons are associated with mid-cortical and superficial glomeruli, are situated entirely in the outer medulla, and have no thin ascending limb.") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-03-30T03:15:18Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0072270") @@ -82067,7 +80903,6 @@ SubClassOf( (metanephric short descending thin limb development) AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "The process whose specific outcome is the progression of the metanephric short descending thin limb over time, from its formation to the mature structure. The metanephric short descending thin limb is the descending thin limb of a short nephron in the metanephros that has a squamous epithelial morphology.") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-03-30T03:16:25Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0072271") @@ -82079,7 +80914,6 @@ SubClassOf( ObjectSomeValuesFrom( (metanephric nephron morphogenesis) AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "The process in which the anatomical structures of the metanephric nephron are generated and organized. A metanephric nephron is the functional unit of the metanephros.") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-03-30T03:33:19Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0072273") @@ -82092,7 +80926,6 @@ SubClassOf( ObjectSomeValuesFrom( (metanephric glomerulus morphogenesis) AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "The process in which the anatomical structures of the metanephric glomerulus are generated and organized. The metanephric glomerulus is a capillary tuft surrounded by Bowman's capsule in nephrons of the vertebrate kidney, or metanephros.") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-04-01T02:46:58Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0072275") @@ -82104,7 +80937,6 @@ SubClassOf( ObjectSomeValuesFrom( (metanephric glomerulus vasculature morphogenesis) AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "The process in which the anatomical structures of the metanephric glomerulus vasculature are generated and organized. The metanephric glomerulus vasculature is composed of the tubule structures that carry blood or lymph in the metanephric glomerulus.") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-04-01T02:47:32Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0072276") @@ -82117,7 +80949,6 @@ SubClassOf( ObjectSomeValuesFrom( (metanephric glomerular capillary formation) AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "The process that gives rise to a metanephric glomerular capillary. This process pertains to the initial formation of a structure from unspecified parts.") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-04-01T02:47:56Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0072277") @@ -82129,7 +80960,6 @@ SubClassOf( ObjectSomeValuesFrom( (metanephric comma-shaped body morphogenesis) AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "The process in which the metanephric comma-shaped body is generated and organized. The metanephric comma-shaped body is the precursor structure to the metanephric S-shaped body that contributes to the morphogenesis of a nephron in the metanephros.") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-04-01T03:14:42Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0072278") @@ -82141,7 +80971,6 @@ SubClassOf( ObjectSomeValuesFrom( (mesenchymal stem cell differentiation involved in metanephric nephron morphogenesis) AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "The process in which a relatively unspecialized cell acquires specialized features of a mesenchymal stem cell that contributes to the shaping of a nephronin the metanephros. A mesenchymal stem cell is a cell that retains the ability to divide and proliferate throughout life to provide progenitor cells that can differentiate into specialized mesenchymal cells.") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-04-01T03:22:06Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0072281") @@ -82152,7 +80981,6 @@ SubClassOf( (metanephric nephron tubule morphogenesis) AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "The process in which the anatomical structures of a metanephric nephron tubule are generated and organized. A metanephric nephron tubule is an epithelial tube that is part of the metanephric nephron, the functional part of the metanephros.") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-04-01T03:25:11Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0072282") @@ -82166,7 +80994,6 @@ SubClassOf( ObjectSomeValuesFrom( (metanephric renal vesicle morphogenesis) AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "The process in which the anatomical structures of the metanephric renal vesicle are generated and organized. The renal vesicle is the primordial structure of the metanephric nephron epithelium, and is formed by the condensation of mesenchymal cells.") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-04-01T03:28:00Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0072283") @@ -82178,7 +81005,6 @@ SubClassOf( ObjectSomeValuesFrom( (metanephric S-shaped body morphogenesis) AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "The process in which the metanephric S-shaped body is generated and organized. The metanephric S-shaped body is the successor of the metanephric comma-shaped body that contributes to the morphogenesis of a nephron in the metanephros.") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-04-01T03:41:36Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0072284") @@ -82190,7 +81016,6 @@ SubClassOf( ObjectSomeValuesFrom( (mesenchymal to epithelial transition involved in metanephric renal vesicle formation) AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "A transition where a mesenchymal cell establishes apical/basolateral polarity,forms intercellular adhesive junctions, synthesizes basement membrane components and becomes an epithelial cell that will contribute to the shaping of the metanephric renal vesicle.") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-04-01T03:43:31Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0072285") @@ -82200,7 +81025,6 @@ EquivalentClasses( ObjectIntersection # Class: (metanephric connecting tubule development) AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "The process whose specific outcome is the progression of the metanephric connecting tubule over time, from its formation to the mature structure. The metanephric connecting tubule is a tubular segment of the metanephric nephron; it connects the distal convoluted tubule to the collecting duct in the metanephros.") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-04-09T03:30:09Z") AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "metanephric connecting duct development") AnnotationAssertion( "biological_process") @@ -82213,7 +81037,6 @@ SubClassOf( (metanephric distal tubule morphogenesis) AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "The process in which the anatomical structures of a metanephric distal tubule are generated and organized. The metanephric distal tubule is a metanephric nephron tubule that begins at the macula densa and extends to the metanephric connecting tubule.") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-04-09T03:41:47Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0072287") @@ -82226,7 +81049,6 @@ SubClassOf( ObjectSomeValuesFrom( (metanephric proximal tubule morphogenesis) AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "The process in which the anatomical structures of a metanephric proximal tubule are generated and organized. The metanephric proximal tubule is a metanephric nephron tubule that connects Bowman's capsule to the descending thin limb of the loop of Henle in the metanephros. It has a brush border epithelial morphology.") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-04-09T03:42:03Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0072288") @@ -82239,7 +81061,6 @@ SubClassOf( ObjectSomeValuesFrom( (metanephric nephron tubule formation) AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "The developmental process pertaining to the initial formation of a metanephric nephron tubule from unspecified parts. A metanephric nephron tubule is an epithelial tube that is part of a nephron in the metanephros.") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-04-09T03:47:44Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0072289") @@ -82251,7 +81072,6 @@ SubClassOf( ObjectSomeValuesFrom( (epithelial cell migration involved in metanephric nephron tubule morphogenesis) AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "The orderly movement of epithelial cells within a renal tubule that contributes to metanephric nephron tubule morphogenesis.") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-04-09T03:52:29Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0072290") @@ -82261,7 +81081,6 @@ EquivalentClasses( ObjectIntersection # Class: (epithelial cell migration involved in metanephric distal tubule morphogenesis) AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "The orderly movement of epithelial cells within a renal tubule that contributes to metanephric distal tubule morphogenesis.") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-04-09T03:53:37Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0072291") @@ -82271,7 +81090,6 @@ EquivalentClasses( ObjectIntersection # Class: (epithelial cell migration involved in metanephric proximal tubule morphogenesis) AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "The orderly movement of epithelial cells within a renal tubule that contributes to metanephric proximal tubule morphogenesis.") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-04-09T03:54:28Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0072292") @@ -82281,7 +81099,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of metanephric glomerulus development) AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "Any process that modulates the rate, frequency or extent of metanephric glomerulus development, the progression of the metanephric glomerulus over time from its initial formation until its mature state. The metanephric glomerulus is a capillary tuft surrounded by Bowman's capsule in nephrons of the vertebrate kidney, or metanephros.") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-04-09T05:03:14Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0072298") @@ -82292,7 +81109,6 @@ SubClassOf( (negative regulation of metanephric glomerulus development) AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "Any process that decreases the rate, frequency or extent of metanephric glomerulus development, the progression of the metanephric glomerulus over time from its initial formation until its mature state. The metanephric glomerulus is a capillary tuft surrounded by Bowman's capsule in nephrons of the vertebrate kidney, or metanephros.") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-04-09T05:03:41Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0072299") @@ -82303,7 +81119,6 @@ SubClassOf( (positive regulation of metanephric glomerulus development) AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "Any process that increases the rate, frequency or extent of metanephric glomerulus development, the progression of the metanephric glomerulus over time from its initial formation until its mature state. The metanephric glomerulus is a capillary tuft surrounded by Bowman's capsule in nephrons of the vertebrate kidney, or metanephros.") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-04-09T05:03:41Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0072300") @@ -82314,7 +81129,6 @@ SubClassOf( (regulation of mesenchymal cell apoptotic process involved in metanephric nephron morphogenesis) AnnotationAssertion(Annotation( "GOC:mtg_apoptosis") Annotation( "GOC:mtg_kidney_jan10") "Any process that modulates the occurrence or rate of mesenchymal stem cell death by apoptotic process that contributes to the shaping of the nephron in the metanephros.") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-04-09T05:03:41Z") AnnotationAssertion( "regulation of mesenchymal stem cell apoptotic process involved in metanephric nephron morphogenesis") AnnotationAssertion( "regulation of mesenchymal stem cell apoptosis involved in metanephric nephron morphogenesis") @@ -82327,7 +81141,6 @@ SubClassOf( ObjectSomeValuesFrom( (negative regulation of mesenchymal cell apoptotic process involved in metanephric nephron morphogenesis) AnnotationAssertion(Annotation( "GOC:mtg_apoptosis") Annotation( "GOC:mtg_kidney_jan10") "Any process that reduces the occurrence or rate of mesenchymal stem cell death by apoptotic process that contributes to the shaping of the nephron in the metanephros.") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-04-09T05:03:41Z") AnnotationAssertion( "negative regulation of mesenchymal stem cell apoptotic process involved in metanephric nephron morphogenesis") AnnotationAssertion( "negative regulation of mesenchymal stem cell apoptosis involved in metanephric nephron morphogenesis") @@ -82340,7 +81153,6 @@ SubClassOf( ObjectSomeValuesFrom( (positive regulation of mesenchymal cell apoptotic process involved in metanephric nephron morphogenesis) AnnotationAssertion(Annotation( "GOC:mtg_apoptosis") Annotation( "GOC:mtg_kidney_jan10") "Any process that increases the occurrence or rate of mesenchymal stem cell death by apoptotic process that contributes to the shaping of the nephron in the metanephros.") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-04-09T05:03:41Z") AnnotationAssertion( "positive regulation of mesenchymal stem cell apoptotic process involved in metanephric nephron morphogenesis") AnnotationAssertion( "positive regulation of mesenchymal stem cell apoptosis involved in metanephric nephron morphogenesis") @@ -82353,7 +81165,6 @@ SubClassOf( ObjectSomeValuesFrom( (regulation of metanephric nephron tubule epithelial cell differentiation) AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "Any process that modulates the frequency, rate or extent of metanephric nephron tubule epithelial cell differentiation.") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-04-09T05:03:41Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0072307") @@ -82363,7 +81174,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of metanephric nephron tubule epithelial cell differentiation) AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "Any process that decreases the frequency, rate or extent of metanephric nephron tubule epithelial cell differentiation.") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-04-09T05:03:41Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0072308") @@ -82373,7 +81183,6 @@ EquivalentClasses( ObjectIntersection # Class: (mesenchymal stem cell maintenance involved in metanephric nephron morphogenesis) AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "The process in which an organism retains a population of mesenchymal stem cells that contributes to the shaping of a nephron in the metanephros. A mesenchymal stem cell is a cell that retains the ability to divide and proliferate throughout life to provide progenitor cells that can differentiate into specialized mesenchymal cells.") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-04-09T05:03:41Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0072309") @@ -82384,7 +81193,6 @@ SubClassOf( ObjectSomeValuesFrom( (glomerular epithelial cell development) AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "The process whose specific outcome is the progression of a glomerular epithelial cell over time, from its formation to the mature structure. Glomerular epithelial cells are specialized epithelial cells that form part of the glomerulus; there are two types, glomerular parietal epithelial cells and glomerular visceral epithelial cells.") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-04-09T06:47:31Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0072310") @@ -82395,7 +81203,6 @@ SubClassOf( ObjectSomeValuesFrom( (glomerular epithelial cell differentiation) AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "The process in which a relatively unspecialized cell acquires specialized features of a glomerular epithelial cell. Glomerular epithelial cells are specialized epithelial cells that form part of the glomerulus; there are two types, glomerular parietal epithelial cells and glomerular visceral epithelial cells.") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-04-09T06:49:21Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0072311") @@ -82406,7 +81213,6 @@ SubClassOf( ObjectSomeValuesFrom( (metanephric glomerular epithelial cell differentiation) AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "The process in which a relatively unspecialized cell acquires specialized features of a metanephric glomerular epithelial cell. Metanephric glomerular epithelial cells are specialized epithelial cells that form part of the metanephric glomerulus; there are two types, metanephric glomerular parietal epithelial cells and metanephric glomerular visceral epithelial cells.") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-04-09T06:54:15Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0072312") @@ -82418,7 +81224,6 @@ SubClassOf( ObjectSomeValuesFrom( (metanephric glomerular epithelial cell development) AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "The process whose specific outcome is the progression of a metanephric glomerular epithelial cell over time, from its formation to the mature structure. Metanephric glomerular epithelial cells are specialized epithelial cells that form part of the metanephric glomerulus; there are two types, metanephric glomerular parietal epithelial cells and metanephric glomerular visceral epithelial cells.") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-04-09T06:57:26Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0072313") @@ -82429,7 +81234,6 @@ SubClassOf( ObjectSomeValuesFrom( (monocarboxylic acid catabolic process) AnnotationAssertion(Annotation( "GOC:mah") "The chemical reactions and pathways resulting in the breakdown of monocarboxylic acids, any organic acid containing one carboxyl (-COOH) group.") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-11-02T04:41:55Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0072329") @@ -82439,7 +81243,6 @@ EquivalentClasses( ObjectIntersection # Class: (monocarboxylic acid biosynthetic process) AnnotationAssertion(Annotation( "GOC:mah") "The chemical reactions and pathways resulting in the formation of monocarboxylic acids, any organic acid containing one carboxyl (-COOH) group.") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-11-02T04:51:32Z") AnnotationAssertion(Annotation( "GOC:mah") "monocarboxylic acid anabolism") AnnotationAssertion(Annotation( "GOC:mah") "monocarboxylic acid biosynthesis") @@ -82455,7 +81258,6 @@ SubClassOf( (modified amino acid transport) AnnotationAssertion(Annotation( "GOC:mah") "The directed movement of modified amino acids into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-11-04T12:18:23Z") AnnotationAssertion( "amino acid derivative transport") AnnotationAssertion( "biological_process") @@ -82467,7 +81269,6 @@ EquivalentClasses( ObjectIntersection # Class: (modified amino acid binding) AnnotationAssertion(Annotation( "GOC:mah") "Binding to a modified amino acid.") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-11-04T05:45:32Z") AnnotationAssertion( "amino acid derivative binding") AnnotationAssertion( "molecular_function") @@ -82479,7 +81280,6 @@ SubClassOf( (pancreatic stellate cell proliferation) AnnotationAssertion(Annotation( "CL:0002410") Annotation( "GOC:mah") Annotation( "PMID:17200706") "The multiplication or reproduction of pancreatic stellate cells, resulting in the expansion of a pancreatic stellate cell population. Pancreatic stellate cells are found in the periacinar space of the exocrine pancreas and in perivascular and periductal regions of the pancreas, and have long cytoplasmic processes that encircle the base of the acinus.") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-11-05T03:04:50Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0072343") @@ -82489,7 +81289,6 @@ EquivalentClasses( ObjectIntersection # Class: (modified amino acid transmembrane transporter activity) AnnotationAssertion(Annotation( "GOC:mah") "Enables the transfer of modified amino acids from one side of a membrane to the other.") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-11-11T11:50:31Z") AnnotationAssertion(Annotation( "GOC:mah") "modified amino acid transporter activity") AnnotationAssertion( "amino acid derivative transmembrane transporter activity") @@ -82502,7 +81301,6 @@ SubClassOf( ObjectSomeValuesFrom( (circulatory system development) AnnotationAssertion(Annotation( "GOC:mah") Annotation( "UBERON:0001009") "The process whose specific outcome is the progression of the circulatory system over time, from its formation to the mature structure. The circulatory system is the organ system that passes nutrients (such as amino acids and electrolytes), gases, hormones, blood cells, etc. to and from cells in the body to help fight diseases and help stabilize body temperature and pH to maintain homeostasis.") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-11-16T11:27:39Z") AnnotationAssertion( "cardiovascular system development") AnnotationAssertion( "biological_process") @@ -82515,7 +81313,6 @@ SubClassOf( (vascular cord development) AnnotationAssertion(Annotation( "GOC:mah") Annotation( "PMID:7084422") Annotation( "ZFA:0005077") "The progression of the vascular cord over time from its initial formation until its mature state. The vascular cord is the primordial vasculature that will develop into blood vessels by the process of tubulogenesis.") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-11-16T11:46:55Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0072360") @@ -82527,7 +81324,6 @@ SubClassOf( ObjectSomeValuesFrom( (organelle transport along microtubule) AnnotationAssertion(Annotation( "GOC:mah") "The directed movement of an organelle along a microtubule, mediated by motor proteins. This process begins with the attachment of an organelle to a microtubule, and ends when the organelle reaches its final destination.") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-12-01T04:59:11Z") AnnotationAssertion(Annotation( "GOC:rl") "microtubule-based organelle localization") AnnotationAssertion( "biological_process") @@ -82540,7 +81336,6 @@ SubClassOf( "GOC:mah") "The process in which ammonium is transported across a membrane. Ammonium is the cation NH4+.") AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/22228"^^xsd:anyURI) -AnnotationAssertion( "mah") AnnotationAssertion( "2010-12-10T10:29:57Z") AnnotationAssertion( "ammonia transport") AnnotationAssertion( "ammonium transport") @@ -82554,7 +81349,6 @@ EquivalentClasses( ObjectIntersection # Class: (mesenchymal stem cell differentiation) AnnotationAssertion(Annotation( "CL:0002452") Annotation( "GOC:BHF") "The process in which a relatively unspecialized cell acquires specialized features of a mesenchymal stem cell. A mesenchymal stem cell is a cell that retains the ability to divide and proliferate throughout life to provide progenitor cells that can differentiate into specialized mesenchymal cells.") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-12-15T12:59:30Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0072497") @@ -82564,7 +81358,6 @@ SubClassOf( (seminiferous tubule development) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:mah") Annotation( "UBERON:0001343") "The reproductive developmental process whose specific outcome is the progression of the seminiferous tubule over time, from its formation to the mature structure. Seminiferous tubules are ducts located in the testicles, and are the specific location of meiosis, and the subsequent creation of gametes, namely spermatozoa.") -AnnotationAssertion( "mah") AnnotationAssertion( "2011-01-04T12:50:36Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0072520") @@ -82577,7 +81370,6 @@ SubClassOf( ObjectSomeValuesFrom( (fibroblast activation) AnnotationAssertion(Annotation( "CL:0000057") Annotation( "GOC:BHF") Annotation( "GOC:mah") "A change in the morphology or behavior of a fibroblast resulting from exposure to an activating factor such as a cellular or soluble ligand.") -AnnotationAssertion( "mah") AnnotationAssertion( "2011-01-14T04:35:08Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0072537") @@ -82588,7 +81380,6 @@ SubClassOf( (T-helper 17 type immune response) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:ebc") "An immune response which is associated with resistance to intracellular bacteria with a key role in inflammation and tissue injury. This immune response is associated with pathological autoimmune conditions such as multiple sclerosis, arthritis and psoriasis which is typically orchestrated by the production of particular cytokines by T-helper 17 cells, most notably interleukin-17, IL-21 and IL-22.") -AnnotationAssertion( "mah") AnnotationAssertion( "2011-01-17T11:13:53Z") AnnotationAssertion(Annotation( "GOC:mah") "Th17 immune response") AnnotationAssertion( "biological_process") @@ -82600,7 +81391,6 @@ SubClassOf( ObjectSomeValuesFrom( (T-helper 17 cell differentiation) AnnotationAssertion(Annotation( "CL:0000899") Annotation( "GOC:BHF") Annotation( "GOC:ebc") "The process in which a relatively unspecialized T cell acquires the specialized features of a T-helper 17 (Th17) cell. A Th17 cell is a CD4-positive, alpha-beta T cell with the phenotype RORgamma-t-positive that produces IL-17.") -AnnotationAssertion( "mah") AnnotationAssertion( "2011-01-17T11:18:47Z") AnnotationAssertion( "biological_process") AnnotationAssertion(Annotation( "GOC:mah") "T-helper 17 cell development") @@ -82614,7 +81404,6 @@ SubClassOf( ObjectSomeValuesFrom( (terminal button organization) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:mah") "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a terminal button. A terminal button is the terminal inflated portion of the axon, containing the specialized apparatus necessary to release neurotransmitters.") -AnnotationAssertion( "mah") AnnotationAssertion( "2011-01-25T04:09:35Z") AnnotationAssertion(Annotation( "GOC:mah") "bouton organization") AnnotationAssertion(Annotation( "GOC:mah") "presynaptic bouton organization") @@ -82632,7 +81421,6 @@ SubClassOf( ObjectSomeValuesFrom( (type B pancreatic cell maturation) AnnotationAssertion(Annotation( "CL:0000169") Annotation( "GOC:BHF") "A developmental process, independent of morphogenetic (shape) change, that is required for a type B pancreatic cell to attain its fully functional state. A type B pancreatic cell is a cell located towards center of the islets of Langerhans that secretes insulin.") -AnnotationAssertion( "mah") AnnotationAssertion( "2011-01-27T01:57:14Z") AnnotationAssertion(Annotation( "CL:0000169") Annotation( "GOC:mah") "pancreatic B cell maturation") AnnotationAssertion(Annotation( "CL:0000169") Annotation( "GOC:mah") "pancreatic beta cell maturation") @@ -82647,7 +81435,6 @@ SubClassOf( ObjectSomeValuesFrom( (epithelial cell proliferation involved in liver morphogenesis) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:mah") "The multiplication or reproduction of epithelial cells, resulting in the expansion of a cell population that contributes to the shaping of the liver.") -AnnotationAssertion( "mah") AnnotationAssertion( "2011-02-02T03:37:50Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0072575") @@ -82657,7 +81444,6 @@ EquivalentClasses( ObjectIntersection # Class: (liver morphogenesis) AnnotationAssertion(Annotation( "GOC:mah") "The process in which the anatomical structures of the liver are generated and organized.") -AnnotationAssertion( "mah") AnnotationAssertion( "2011-02-02T03:41:30Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0072576") @@ -82669,7 +81455,6 @@ SubClassOf( ObjectSomeValuesFrom( (endothelial cell apoptotic process) AnnotationAssertion(Annotation( "CL:0000115") Annotation( "GOC:BHF") Annotation( "GOC:mah") Annotation( "GOC:mtg_apoptosis") "Any apoptotic process in an endothelial cell. An endothelial cell comprises the outermost layer or lining of anatomical structures and can be squamous or cuboidal.") -AnnotationAssertion( "mah") AnnotationAssertion( "2011-02-02T03:56:24Z") AnnotationAssertion(Annotation( "GOC:mah") "apoptosis of endothelial cells") AnnotationAssertion(Annotation( "GOC:mah") "endothelial cell programmed cell death by apoptosis") @@ -82685,7 +81470,6 @@ EquivalentClasses( ObjectIntersection # Class: (oxygen metabolic process) AnnotationAssertion(Annotation( "GOC:mah") "The chemical reactions and pathways involving diatomic oxygen (O2).") -AnnotationAssertion( "mah") AnnotationAssertion( "2011-02-11T10:46:51Z") AnnotationAssertion(Annotation( "CHEBI:33263") "diatomic oxygen metabolic process") AnnotationAssertion(Annotation( "GOC:mah") "oxygen metabolism") @@ -82697,7 +81481,6 @@ EquivalentClasses( ObjectIntersection # Class: (establishment of protein localization to organelle) AnnotationAssertion(Annotation( "GOC:mah") "The directed movement of a protein to a specific location on or in an organelle. Encompasses establishment of localization in the membrane or lumen of a membrane-bounded organelle.") -AnnotationAssertion( "mah") AnnotationAssertion( "2011-02-14T01:56:51Z") AnnotationAssertion(Annotation( "GOC:mah") "establishment of protein localisation to organelle") AnnotationAssertion( "biological_process") @@ -82709,7 +81492,6 @@ SubClassOf( (maintenance of protein localization in organelle) AnnotationAssertion(Annotation( "GOC:mah") "Any process in which a protein is maintained in a specific location a specific location on or in an organelle, and is prevented from moving elsewhere. Encompasses establishment of localization in the membrane or lumen of a membrane-bounded organelle.") -AnnotationAssertion( "mah") AnnotationAssertion( "2011-02-14T02:09:13Z") AnnotationAssertion(Annotation( "GOC:mah") "maintenance of protein localisation to organelle") AnnotationAssertion( "maintenance of protein localization to organelle") @@ -82723,7 +81505,6 @@ SubClassOf( ObjectSomeValuesFrom( (protein localization to membrane) AnnotationAssertion(Annotation( "GOC:mah") "A process in which a protein is transported to, or maintained in, a specific location in a membrane.") -AnnotationAssertion( "mah") AnnotationAssertion( "2011-02-14T02:35:18Z") AnnotationAssertion(Annotation( "GOC:mah") "protein localisation in membrane") AnnotationAssertion( "protein localization in membrane") @@ -82737,7 +81518,6 @@ SubClassOf( (protein localization to plasma membrane) AnnotationAssertion(Annotation( "GOC:mah") "A process in which a protein is transported to, or maintained in, a specific location in the plasma membrane.") -AnnotationAssertion( "tb") AnnotationAssertion( "2009-07-10T10:29:23Z") AnnotationAssertion( "biological_process") AnnotationAssertion(Annotation( "GOC:mah") "protein localisation in plasma membrane") @@ -82753,7 +81533,6 @@ EquivalentClasses( ObjectIntersection # Class: (protein localization to vacuole) AnnotationAssertion(Annotation( "GOC:ecd") "A process in which a protein is transported to, or maintained at, a location in a vacuole.") -AnnotationAssertion( "mah") AnnotationAssertion( "2011-02-14T02:55:35Z") AnnotationAssertion(Annotation( "GOC:mah") "protein localisation to vacuole") AnnotationAssertion( "biological_process") @@ -82764,7 +81543,6 @@ EquivalentClasses( ObjectIntersection # Class: (establishment of protein localization to vacuole) AnnotationAssertion(Annotation( "GOC:mah") "The directed movement of a protein to a specific location in a vacuole.") -AnnotationAssertion( "mah") AnnotationAssertion( "2011-02-14T02:56:29Z") AnnotationAssertion(Annotation( "GOC:mah") "establishment of protein localisation to vacuole") AnnotationAssertion( "biological_process") @@ -82776,7 +81554,6 @@ SubClassOf( (maintenance of protein location in vacuole) AnnotationAssertion(Annotation( "GOC:mah") "Any process in which a protein is maintained in a specific location in a vacuole, and is prevented from moving elsewhere.") -AnnotationAssertion( "mah") AnnotationAssertion( "2011-02-14T02:56:57Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0072667") @@ -82788,7 +81565,6 @@ SubClassOf( ObjectSomeValuesFrom( (multinuclear osteoclast differentiation) AnnotationAssertion(Annotation( "CL:0000779") Annotation( "GOC:mah") Annotation( "PMID:12713016") "The process in which a relatively unspecialized monocyte acquires the specialized features of a multinuclear osteoclast. An osteoclast is a specialized phagocytic cell associated with the absorption and removal of the mineralized matrix of bone tissue.") -AnnotationAssertion( "mah") AnnotationAssertion( "2011-02-22T02:10:38Z") AnnotationAssertion( "biological_process") AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:mah") "multinuclear osteoclast formation") @@ -82801,7 +81577,6 @@ SubClassOf( (lymphocyte migration) AnnotationAssertion(Annotation( "CL:0000542") Annotation( "GOC:BHF") Annotation( "GOC:mah") "The movement of a lymphocyte within or between different tissues and organs of the body.") -AnnotationAssertion( "mah") AnnotationAssertion( "2011-02-22T03:38:12Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0072676") @@ -82812,7 +81587,6 @@ SubClassOf( (eosinophil migration) AnnotationAssertion(Annotation( "CL:0000771") Annotation( "GOC:BHF") Annotation( "GOC:mah") "The movement of an eosinophil within or between different tissues and organs of the body.") -AnnotationAssertion( "mah") AnnotationAssertion( "2011-02-22T03:39:31Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0072677") @@ -82822,7 +81596,6 @@ EquivalentClasses( ObjectIntersection # Class: (T cell migration) AnnotationAssertion(Annotation( "CL:0000084") Annotation( "GOC:BHF") Annotation( "GOC:mah") "The movement of a T cell within or between different tissues and organs of the body.") -AnnotationAssertion( "mah") AnnotationAssertion( "2011-02-22T03:40:40Z") AnnotationAssertion(Annotation( "CL:0000084") "T lymphocyte migration") AnnotationAssertion(Annotation( "CL:0000084") "T-cell migration") @@ -82836,7 +81609,6 @@ SubClassOf( (thymocyte migration) AnnotationAssertion(Annotation( "CL:0000893") Annotation( "GOC:BHF") Annotation( "GOC:mah") "The movement of a thymocyte through distinct intrathymic niches (e.g. medulla, cortex), where it receives a unique set of developmental cues required for T-cell development.") -AnnotationAssertion( "mah") AnnotationAssertion( "2011-02-22T03:47:51Z") AnnotationAssertion(Annotation( "CL:0000893") "thymic lymphocyte migration") AnnotationAssertion( "biological_process") @@ -82852,7 +81624,6 @@ SubClassOf( (protein localization to cell cortex) AnnotationAssertion(Annotation( "GOC:mah") "A process in which a protein is transported to, or maintained in, the cell cortex.") -AnnotationAssertion( "mah") AnnotationAssertion( "2012-04-11T01:16:33Z") AnnotationAssertion(Annotation( "GOC:mah") "protein localisation to cell cortex") AnnotationAssertion( "biological_process") @@ -82864,7 +81635,6 @@ SubClassOf( (protein localization to microtubule cytoskeleton) AnnotationAssertion(Annotation( "GOC:mah") "A cellular protein localization process in which a protein is transported to, or maintained at, a location within the microtubule cytoskeleton.") -AnnotationAssertion( "mah") AnnotationAssertion( "2012-04-11T01:19:35Z") AnnotationAssertion(Annotation( "GOC:mah") "protein localisation to microtubule cytoskeleton") AnnotationAssertion( "biological_process") @@ -82939,7 +81709,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of primary metabolic process) AnnotationAssertion(Annotation( "PMID:19211694") "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways within a cell or an organism involving those compounds formed as a part of the normal anabolic and catabolic processes. These processes take place in most, if not all, cells of the organism.") -AnnotationAssertion( "dhl") AnnotationAssertion( "2009-04-22T04:30:52Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0080090") @@ -82950,7 +81719,6 @@ SubClassOf( (regulation of response to stress) AnnotationAssertion(Annotation( "GOC:dhl") "Any process that modulates the frequency, rate or extent of a response to stress. Response to stress is a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a disturbance in organismal or cellular homeostasis, usually, but not necessarily, exogenous (e.g. temperature, humidity, ionizing radiation).") -AnnotationAssertion( "dhl") AnnotationAssertion( "2009-05-06T04:51:28Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0080134") @@ -82963,7 +81731,6 @@ SubClassOf( (intracellular amino acid homeostasis) AnnotationAssertion(Annotation( "PMID:19955263") "A homeostatic process involved in the maintenance of a steady state level of amino acids within a cell.") -AnnotationAssertion( "dhl") AnnotationAssertion( "2010-01-27T04:47:27Z") AnnotationAssertion( "amino acid homeostasis") AnnotationAssertion( "cellular amino acid homeostasis") @@ -82975,7 +81742,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of fertilization) AnnotationAssertion(Annotation( "GOC:DHL") Annotation( "PMID:20478994") "Any process that modulates the rate, frequency or extent of fertilization. Fertilization is the union of gametes of opposite sexes during the process of sexual reproduction to form a zygote. It involves the fusion of the gametic nuclei (karyogamy) and cytoplasm (plasmogamy).") -AnnotationAssertion( "dhl") AnnotationAssertion( "2010-09-01T03:44:27Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0080154") @@ -82986,7 +81752,6 @@ SubClassOf( (regulation of nitric oxide metabolic process) AnnotationAssertion(Annotation( "GOC:DHL") "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving nitric oxide, nitrogen monoxide (NO), a colorless gas only slightly soluble in water.") -AnnotationAssertion( "dhl") AnnotationAssertion( "2010-09-23T04:02:50Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0080164") @@ -82996,7 +81761,6 @@ EquivalentClasses( ObjectIntersection # Class: (lytic vacuole organization) AnnotationAssertion(Annotation( "PMID:20729380") "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a lytic vacuole.") -AnnotationAssertion( "dhl") AnnotationAssertion( "2011-04-25T04:40:46Z") AnnotationAssertion( "lytic vacuole organisation") AnnotationAssertion( "lytic vacuolar assembly") @@ -83011,7 +81775,6 @@ SubClassOf( (extracellular matrix assembly) AnnotationAssertion(Annotation( "GOC:jl") "The aggregation, arrangement and bonding together of the extracellular matrix.") -AnnotationAssertion( "jl") AnnotationAssertion( "2010-07-14T12:52:49Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0085029") @@ -83023,7 +81786,6 @@ SubClassOf( (cardiac muscle cell action potential) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:mtg_cardiac_conduct_nov11") "An action potential that occurs in a cardiac muscle cell.") -AnnotationAssertion( "tb") AnnotationAssertion( "2011-11-10T07:45:11Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0086001") @@ -83034,7 +81796,6 @@ SubClassOf( (cardiac muscle cell action potential involved in contraction) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:mtg_cardiac_conduct_nov11") "An action potential that occurs in a cardiac muscle cell and is involved in its contraction.") -AnnotationAssertion( "tb") AnnotationAssertion( "2011-11-10T07:45:11Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0086002") @@ -83044,7 +81805,6 @@ EquivalentClasses( ObjectIntersection # Class: (cardiac muscle cell contraction) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:mtg_cardiac_conduct_nov11") "The actin filament-based process in which cytoplasmic actin filaments slide past one another resulting in contraction of a cardiac muscle cell.") -AnnotationAssertion( "tb") AnnotationAssertion( "2011-11-10T07:48:15Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0086003") @@ -83055,7 +81815,6 @@ SubClassOf( ObjectSomeValuesFrom( (regulation of cardiac muscle cell contraction) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:mtg_cardiac_conduct_nov11") "Any process that modulates the frequency, rate or extent of cardiac muscle cell contraction.") -AnnotationAssertion( "tb") AnnotationAssertion( "2011-11-10T07:49:10Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0086004") @@ -83066,7 +81825,6 @@ SubClassOf( ObjectSomeValuesFrom( (ventricular cardiac muscle cell action potential) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:mtg_cardiac_conduct_nov11") "An action potential that occurs in a ventricular cardiac muscle cell.") -AnnotationAssertion( "tb") AnnotationAssertion( "2011-11-10T07:59:36Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0086005") @@ -83077,7 +81835,6 @@ SubClassOf( (atrial cardiac muscle cell action potential) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:mtg_cardiac_conduct_nov11") "An action potential that occurs in an atrial cardiac muscle cell.") -AnnotationAssertion( "tb") AnnotationAssertion( "2011-11-10T08:49:13Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0086014") @@ -83089,7 +81846,6 @@ SubClassOf( ObjectSomeValuesFrom( (SA node cell action potential) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:mtg_cardiac_conduct_nov11") "An action potential that occurs in a sinoatrial node cardiac muscle cell.") -AnnotationAssertion( "tb") AnnotationAssertion( "2011-11-10T08:50:15Z") AnnotationAssertion( "SA node cardiac muscle cell action potential") AnnotationAssertion( "SAN cardiac muscle cell action potential") @@ -83105,7 +81861,6 @@ SubClassOf( ObjectSomeValuesFrom( (AV node cell action potential) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:mtg_cardiac_conduct_nov11") "An action potential that occurs in an atrioventricular node cardiac muscle cell.") -AnnotationAssertion( "tb") AnnotationAssertion( "2011-11-10T08:58:56Z") AnnotationAssertion( "AV node cardiac muscle cell action potential") AnnotationAssertion( "atrioventricular node cardiac muscle cell action potential") @@ -83119,7 +81874,6 @@ SubClassOf( ObjectSomeValuesFrom( (Purkinje myocyte action potential) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:mtg_cardiac_conduct_nov11") "An action potential that occurs in a Purkinje myocyte.") -AnnotationAssertion( "tb") AnnotationAssertion( "2011-11-10T08:58:56Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0086017") @@ -83131,7 +81885,6 @@ SubClassOf( ObjectSomeValuesFrom( (SA node cell to atrial cardiac muscle cell signaling) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:mtg_cardiac_conduct_nov11") "Any process that mediates the transfer of information from an SA node cardiomyocyte to an atrial cardiomyocyte.") -AnnotationAssertion( "tb") AnnotationAssertion( "2011-11-10T09:15:01Z") AnnotationAssertion( "SA node cardiac muscle cell to atrial cardiac muscle cell signalling") AnnotationAssertion( "SA node cardiomyocyte to atrial cardiomyocyte signalling") @@ -83147,7 +81900,6 @@ SubClassOf( (cell-cell signaling involved in cardiac conduction) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:mtg_cardiac_conduct_nov11") "Any process that mediates the transfer of information from one cell to another and contributes to the heart process that regulates cardiac muscle contraction; beginning with the generation of an action potential in the sinoatrial node and ending with regulation of contraction of the myocardium.") -AnnotationAssertion( "dph") AnnotationAssertion( "2011-11-16T03:43:52Z") AnnotationAssertion(Annotation( "GOC:mah") "cell-cell signalling involved in cardiac conduction") AnnotationAssertion( "biological_process") @@ -83158,7 +81910,6 @@ EquivalentClasses( ObjectIntersection # Class: (atrial cardiac muscle cell to AV node cell signaling) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:mtg_cardiac_conduct_nov11") "Any process that mediates the transfer of information from an atrial cardiomyocyte to an AV node cell.") -AnnotationAssertion( "tb") AnnotationAssertion( "2011-11-11T02:02:14Z") AnnotationAssertion( "atrial cardiomyocyte to AV node cell signaling") AnnotationAssertion(Annotation( "GOC:mah") "atrial cardiomyocyte to AV node cell signalling") @@ -83172,7 +81923,6 @@ SubClassOf( (AV node cell to bundle of His cell signaling) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:mtg_cardiac_conduct_nov11") "Any process that mediates the transfer of information from an AV node cardiac muscle cell to a bundle of His cardiomyocyte.") -AnnotationAssertion( "tb") AnnotationAssertion( "2011-11-11T02:02:14Z") AnnotationAssertion(Annotation( "GOC:mah") "AV node cell to bundle of His cell signalling") AnnotationAssertion( "atrioventricular node to bundle of His cell signaling") @@ -83185,7 +81935,6 @@ SubClassOf( (bundle of His cell to Purkinje myocyte signaling) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:mtg_cardiac_conduct_nov11") "Any process that mediates the transfer of information from a bundle of His cardiomyocyte to a Purkinje myocyte.") -AnnotationAssertion( "tb") AnnotationAssertion( "2011-11-11T02:02:14Z") AnnotationAssertion( "bundle of His cardiac muscle cell to Purkinje myocyte signaling") AnnotationAssertion(Annotation( "GOC:mah") "bundle of His cardiac muscle cell to Purkinje myocyte signalling") @@ -83198,7 +81947,6 @@ SubClassOf( (Purkinje myocyte to ventricular cardiac muscle cell signaling) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:mtg_cardiac_conduct_nov11") "Any process that mediates the transfer of information from a Purkinje myocyte to a ventricular cardiac muscle cell.") -AnnotationAssertion( "tb") AnnotationAssertion( "2011-11-11T02:02:14Z") AnnotationAssertion(Annotation( "GOC:mah") "Purkinje myocyte to ventricular cardiac muscle cell signalling") AnnotationAssertion( "biological_process") @@ -83211,7 +81959,6 @@ SubClassOf( (bundle of His cell action potential) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:mtg_cardiac_conduct_nov11") "An action potential that occurs in a bundle of His cell.") -AnnotationAssertion( "dph") AnnotationAssertion( "2011-11-15T12:01:18Z") AnnotationAssertion( "bundle of His cardiac muscle cell action potential") AnnotationAssertion( "biological_process") @@ -83224,7 +81971,6 @@ SubClassOf( ObjectSomeValuesFrom( (cell communication involved in cardiac conduction) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:mtg_cardiac_conduct_nov11") "Any process that mediates interactions between a cell and its surroundings that contributes to the process of cardiac conduction. Encompasses interactions such as signaling or attachment between one cell and another cell, between a cell and an extracellular matrix, or between a cell and any other aspect of its environment.") -AnnotationAssertion( "dph") AnnotationAssertion( "2011-11-22T08:57:02Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0086065") @@ -83234,7 +81980,6 @@ EquivalentClasses( ObjectIntersection # Class: (atrial cardiac muscle cell to AV node cell communication) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:mtg_cardiac_conduct_nov11") "The process that mediates interactions between an atrial cardiomyocyte and its surroundings that contributes to the process of the atrial cardiomyocyte communicating with an AV node cell in cardiac conduction. Encompasses interactions such as signaling or attachment between one cell and another cell, between a cell and an extracellular matrix, or between a cell and any other aspect of its environment.") -AnnotationAssertion( "dph") AnnotationAssertion( "2011-11-22T09:05:09Z") AnnotationAssertion( "atrial cardiomyocyte to AV node cell communication") AnnotationAssertion( "atrial cardiomyocyte to atrioventricular node cell communication") @@ -83246,7 +81991,6 @@ SubClassOf( (AV node cell to bundle of His cell communication) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:mtg_cardiac_conduct_nov11") "The process that mediates interactions between an AV node cell and its surroundings that contributes to the process of the AV node cell communicating with a bundle of His cell in cardiac conduction. Encompasses interactions such as signaling or attachment between one cell and another cell, between a cell and an extracellular matrix, or between a cell and any other aspect of its environment.") -AnnotationAssertion( "dph") AnnotationAssertion( "2011-11-22T09:11:44Z") AnnotationAssertion( "atrioventricular node cell to bundle of His cell communication") AnnotationAssertion( "biological_process") @@ -83257,7 +82001,6 @@ SubClassOf( (Purkinje myocyte to ventricular cardiac muscle cell communication) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:mtg_cardiac_conduct_nov11") "The process that mediates interactions between a Purkinje myocyte and its surroundings that contributes to the process of the Purkinje myocyte communicating with a ventricular cardiac muscle cell in cardiac conduction. Encompasses interactions such as signaling or attachment between one cell and another cell, between a cell and an extracellular matrix, or between a cell and any other aspect of its environment.") -AnnotationAssertion( "dph") AnnotationAssertion( "2011-11-22T09:14:49Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0086068") @@ -83268,7 +82011,6 @@ SubClassOf( "GOC:BHF") Annotation( "GOC:mtg_cardiac_conduct_nov11") "The process that mediates interactions between a bundle of His cell and its surroundings that contributes to the process of the bundle of His cell communicating with a Purkinje myocyte in cardiac conduction. Encompasses interactions such as signaling or attachment between one cell and another cell, between a cell and an extracellular matrix, or between a cell and any other aspect of its environment.") AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/20731"^^xsd:anyURI) -AnnotationAssertion( "dph") AnnotationAssertion( "2011-11-22T09:18:49Z") AnnotationAssertion( "bundle of His cardiac muscle cell to Purkinje myocyte communication") AnnotationAssertion( "ventricular conduction system cell to cell communication") @@ -83283,7 +82025,6 @@ SubClassOf( (SA node cell to atrial cardiac muscle cell communication) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:mtg_cardiac_conduct_nov11") "The process that mediates interactions between an SA node cardiomyocyte and its surroundings that contributes to the process of the SA node cardiomyocyte communicating with an atrial cardiomyocyte in cardiac conduction. Encompasses interactions such as signaling or attachment between one cell and another cell, between a cell and an extracellular matrix, or between a cell and any other aspect of its environment.") -AnnotationAssertion( "dph") AnnotationAssertion( "2011-11-22T09:32:45Z") AnnotationAssertion( "SA node cardiac muscle cell to atrial cardiac muscle cell communication") AnnotationAssertion( "SA node cardiomyocyte to atrial cardiomyocyte communication") @@ -83298,7 +82039,6 @@ SubClassOf( (G protein-coupled acetylcholine receptor signaling pathway involved in heart process) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:mtg_cardiac_conduct_nov11") "A G protein-coupled acetylcholine receptor signaling pathway, which contributes to a circulatory system process carried out by the heart.") -AnnotationAssertion( "bf") AnnotationAssertion( "G-protein coupled acetylcholine receptor signaling pathway involved in heart process") AnnotationAssertion(Annotation( "GOC:bf") "G-protein coupled acetylcholine receptor signalling pathway involved in heart process") AnnotationAssertion(Annotation( "GOC:mtg_cardiac_conduct_nov11") "M2 receptor signaling pathway involved in heart process") @@ -83311,7 +82051,6 @@ EquivalentClasses( ObjectIntersection # Class: (G protein-coupled receptor signaling pathway involved in heart process) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:mtg_cardiac_conduct_nov11") Annotation( "PMID:17376402") "An G protein-coupled receptor signaling pathway which contributes to a circulatory system process carried out by the heart.") -AnnotationAssertion( "bf") AnnotationAssertion( "2012-03-19T01:28:23Z") AnnotationAssertion(Annotation( "GOC:bf") "G-protein coupled receptor signaling pathway involved in heart process") AnnotationAssertion(Annotation( "GOC:bf") "G-protein coupled receptor signalling pathway involved in heart process") @@ -83349,7 +82088,6 @@ EquivalentClasses( ObjectIntersection # Class: (amino acid import across plasma membrane) AnnotationAssertion(Annotation( "GOC:krc") Annotation( "PMID:8195186") "The directed movement of an amino acid from outside of a cell, across the plasma membrane and into the cytosol.") -AnnotationAssertion( "jl") AnnotationAssertion( "2012-11-14T14:21:41Z") AnnotationAssertion( "L-amino acid import") AnnotationAssertion( "amino acid transmembrane import") @@ -83363,7 +82101,6 @@ EquivalentClasses( ObjectIntersection # Class: (primitive streak formation) AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:sdb_2009") Annotation( "GOC:tb") "The developmental process pertaining to the initial formation of the primitive streak from unspecified parts. The primitive streak is a ridge of cells running along the midline of the embryo where the mesoderm ingresses. It defines the anterior-posterior axis.") -AnnotationAssertion( "tb") AnnotationAssertion( "2009-07-29T10:31:31Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0090009") @@ -83377,7 +82114,6 @@ SubClassOf( ObjectSomeValuesFrom( (regulation of neutrophil chemotaxis) AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:tb") "Any process that modulates the frequency, rate, or extent of neutrophil chemotaxis. Neutrophil chemotaxis is the directed movement of a neutrophil cell, the most numerous polymorphonuclear leukocyte found in the blood, in response to an external stimulus, usually an infection or wounding.") -AnnotationAssertion( "tb") AnnotationAssertion( "2009-08-03T10:09:34Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0090022") @@ -83387,7 +82123,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of neutrophil chemotaxis) AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:tb") "Any process that increases the frequency, rate, or extent of neutrophil chemotaxis. Neutrophil chemotaxis is the directed movement of a neutrophil cell, the most numerous polymorphonuclear leukocyte found in the blood, in response to an external stimulus, usually an infection or wounding.") -AnnotationAssertion( "tb") AnnotationAssertion( "2009-08-03T10:12:23Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0090023") @@ -83397,7 +82132,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of neutrophil chemotaxis) AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:tb") "Any process that decreases the frequency, rate, or extent of neutrophil chemotaxis. Neutrophil chemotaxis is the directed movement of a neutrophil cell, the most numerous polymorphonuclear leukocyte found in the blood, in response to an external stimulus, usually an infection or wounding.") -AnnotationAssertion( "tb") AnnotationAssertion( "2009-08-03T10:13:09Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0090024") @@ -83407,7 +82141,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of monocyte chemotaxis) AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:tb") "Any process that modulates the frequency, rate, or extent of monocyte chemotaxis.") -AnnotationAssertion( "tb") AnnotationAssertion( "2009-08-03T10:17:03Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0090025") @@ -83417,7 +82150,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of monocyte chemotaxis) AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:tb") "Any process that increases the frequency, rate, or extent of monocyte chemotaxis.") -AnnotationAssertion( "tb") AnnotationAssertion( "2009-08-03T10:18:54Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0090026") @@ -83427,7 +82159,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of monocyte chemotaxis) AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:tb") "Any process that decreases the frequency, rate, or extent of monocyte chemotaxis.") -AnnotationAssertion( "tb") AnnotationAssertion( "2009-08-03T10:19:40Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0090027") @@ -83437,7 +82168,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of steroid hormone biosynthetic process) AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:tb") "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of steroid hormones,compounds with a 1, 2, cyclopentanoperhydrophenanthrene nucleus that act as hormones.") -AnnotationAssertion( "tb") AnnotationAssertion( "2009-08-03T10:38:27Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0090030") @@ -83448,7 +82178,6 @@ SubClassOf( (positive regulation of steroid hormone biosynthetic process) AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:tb") "Any process that increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of steroid hormones,compounds with a 1, 2, cyclopentanoperhydrophenanthrene nucleus that act as hormones.") -AnnotationAssertion( "tb") AnnotationAssertion( "2009-08-03T10:40:32Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0090031") @@ -83460,7 +82189,6 @@ SubClassOf( (negative regulation of steroid hormone biosynthetic process) AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:tb") "Any process that decreases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of steroid hormones,compounds with a 1, 2, cyclopentanoperhydrophenanthrene nucleus that act as hormones.") -AnnotationAssertion( "tb") AnnotationAssertion( "2009-08-03T10:41:35Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0090032") @@ -83472,7 +82200,6 @@ SubClassOf( (positive regulation of microtubule nucleation) AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:tb") "Any process that increases the rate, frequency or extent of microtubule nucleation. Microtubule nucleation is the 'de novo' formation of a microtubule, in which tubulin heterodimers form metastable oligomeric aggregates, some of which go on to support formation of a complete microtubule. Microtubule nucleation usually occurs from a specific site within a cell.") -AnnotationAssertion( "tb") AnnotationAssertion( "2009-08-12T11:33:09Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0090063") @@ -83483,7 +82210,6 @@ SubClassOf( ObjectSomeValuesFrom( (positive regulation of cell cycle process) AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:tb") "Any process that increases the rate, frequency or extent of a cellular process that is involved in the progression of biochemical and morphological phases and events that occur in a cell during successive cell replication or nuclear replication events.") -AnnotationAssertion( "tb") AnnotationAssertion( "2009-09-09T11:39:52Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0090068") @@ -83494,7 +82220,6 @@ SubClassOf( (regulation of ribosome biogenesis) AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:tb") "Any process that modulates the rate, frequency or extent of ribosome biogenesis. Ribosome biogenesis is the cellular process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of ribosome subunits.") -AnnotationAssertion( "tb") AnnotationAssertion( "2009-09-11T10:32:17Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0090069") @@ -83504,7 +82229,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of ribosome biogenesis) AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:tb") "Any process that increases the rate, frequency or extent of ribosome biogenesis. Ribosome biogenesis is the cellular process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of ribosome subunits.") -AnnotationAssertion( "tb") AnnotationAssertion( "2009-09-11T10:32:17Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0090070") @@ -83514,7 +82238,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of ribosome biogenesis) AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:tb") "Any process that decreases the rate, frequency or extent of ribosome biogenesis. Ribosome biogenesis is the cellular process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of ribosome subunits.") -AnnotationAssertion( "tb") AnnotationAssertion( "2009-09-11T10:32:17Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0090071") @@ -83525,7 +82248,6 @@ SubClassOf( (foam cell differentiation) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:add") Annotation( "GOC:dph") Annotation( "GOC:tb") "The process in which a relatively unspecialized cell acquires the specialized features of a foam cell. A foam cell is a type of cell containing lipids in small vacuoles and typically seen in atherosclerotic lesions, as well as other conditions.") -AnnotationAssertion( "tb") AnnotationAssertion( "2009-09-15T03:46:30Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0090077") @@ -83537,7 +82259,6 @@ SubClassOf( "GOC:BHF") Annotation( "GOC:add") Annotation( "GOC:dph") Annotation( "GOC:tb") "The process in which a smooth muscle cell acquires the specialized features of a foam cell. A foam cell is a type of cell containing lipids in small vacuoles and typically seen in atherosclerotic lesions, as well as other conditions.") AnnotationAssertion( ) -AnnotationAssertion( "tb") AnnotationAssertion( "2009-09-15T03:48:10Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0090078") @@ -83551,7 +82272,6 @@ DisjointClasses( ObjectSomeValuesFrom # Class: (regulation of peptide transport) AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:tb") "Any process that modulates the frequency, rate or extent of the directed movement of peptides, compounds of two or more amino acids where the alpha carboxyl group of one is bound to the alpha amino group of another, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.") -AnnotationAssertion( "tb") AnnotationAssertion( "2009-10-23T11:21:38Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0090087") @@ -83562,7 +82282,6 @@ SubClassOf( (positive regulation of extracellular matrix disassembly) AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:tb") "Any process that increases the rate, frequency or extent of extracellular matrix disassembly. Extracellular matrix disassembly is a process that results in the breakdown of the extracellular matrix.") -AnnotationAssertion( "tb") AnnotationAssertion( "2009-11-04T10:03:25Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0090091") @@ -83572,7 +82291,6 @@ EquivalentClasses( ObjectIntersection # Class: (cochlea development) AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:tb") "The progression of the cochlea over time from its formation to the mature structure. The cochlea is the snail-shaped portion of the inner ear that is responsible for the detection of sound.") -AnnotationAssertion( "tb") AnnotationAssertion( "2009-11-18T11:42:15Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0090102") @@ -83585,7 +82303,6 @@ SubClassOf( ObjectSomeValuesFrom( (cochlea morphogenesis) AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:tb") "The process in which the cochlea is generated and organized.") -AnnotationAssertion( "tb") AnnotationAssertion( "2009-11-18T11:45:11Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0090103") @@ -83598,7 +82315,6 @@ SubClassOf( ObjectSomeValuesFrom( (pancreatic epsilon cell differentiation) AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:tb") "The process in which relatively unspecialized cells acquire specialized structural and functional features of a pancreatic epsilon cell. A pancreatic epsilon cell is a cell in the pancreas that secretes ghrelin.") -AnnotationAssertion( "tb") AnnotationAssertion( "2009-11-18T11:48:52Z") AnnotationAssertion( "pancreatic E cell differentiation") AnnotationAssertion( "biological_process") @@ -83611,7 +82327,6 @@ SubClassOf( ObjectSomeValuesFrom( (pancreatic E cell development) AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:tb") "The process whose specific outcome is the progression of a pancreatic E cell over time, from its formation to the mature structure.") -AnnotationAssertion( "tb") AnnotationAssertion( "2009-11-18T11:51:00Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0090105") @@ -83623,7 +82338,6 @@ SubClassOf( ObjectSomeValuesFrom( (regulation of cell-substrate junction assembly) AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:tb") "Any process that modulates the rate, frequency, or extent of cell-substrate junction assembly. Cell-substrate junction assembly is the aggregation, arrangement and bonding together of a set of components to form a junction between a cell and its substrate.") -AnnotationAssertion( "tb") AnnotationAssertion( "2009-11-25T11:00:58Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0090109") @@ -83633,7 +82347,6 @@ EquivalentClasses( ObjectIntersection # Class: (tissue migration) AnnotationAssertion(Annotation( "GOC:ascb_2009") Annotation( "GOC:dph") Annotation( "GOC:tb") "The process in which the population of cells that make up a tissue undergo directed movement.") -AnnotationAssertion( "tb") AnnotationAssertion( "2009-12-07T03:13:55Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0090130") @@ -83643,7 +82356,6 @@ SubClassOf( (mesenchyme migration) AnnotationAssertion(Annotation( "GOC:ascb_2009") Annotation( "GOC:dph") Annotation( "GOC:tb") "The process in which the population of cells that make up a mesenchyme undergo directed movement.") -AnnotationAssertion( "tb") AnnotationAssertion( "2009-12-07T03:15:17Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0090131") @@ -83654,7 +82366,6 @@ SubClassOf( ObjectSomeValuesFrom( (epithelium migration) AnnotationAssertion(Annotation( "GOC:ascb_2009") Annotation( "GOC:dph") Annotation( "GOC:tb") "The process in which the population of cells that make up an epithelium undergo directed movement.") -AnnotationAssertion( "tb") AnnotationAssertion( "2009-12-07T03:19:34Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0090132") @@ -83664,7 +82375,6 @@ SubClassOf( (regulation of actin cytoskeleton organization by cell-cell adhesion) AnnotationAssertion(Annotation( "GOC:ascb_2009") Annotation( "GOC:dph") Annotation( "GOC:tb") "Any cell-cell adhesion process that modulates the formation, arrangement of constituent parts, or disassembly of cytoskeletal structures comprising actin filaments and their associated proteins.") -AnnotationAssertion( "tb") AnnotationAssertion( "2009-12-08T02:05:00Z") AnnotationAssertion(Annotation( "GOC:mah") "regulation of actin cytoskeleton organisation by cell-cell adhesion") AnnotationAssertion( "biological_process") @@ -83676,7 +82386,6 @@ SubClassOf( (establishment of protein localization to membrane) AnnotationAssertion(Annotation( "GOC:ascb_2009") Annotation( "GOC:dph") Annotation( "GOC:tb") "The directed movement of a protein to a specific location in a membrane.") -AnnotationAssertion( "tb") AnnotationAssertion( "2009-12-08T03:18:51Z") AnnotationAssertion(Annotation( "GOC:mah") "establishment of protein localisation in membrane") AnnotationAssertion( "establishment of protein localization in membrane") @@ -83689,7 +82398,6 @@ SubClassOf( (Golgi to lysosome transport) AnnotationAssertion(Annotation( "GOC:ascb_2009") Annotation( "GOC:dph") Annotation( "GOC:tb") "The directed movement of substances from the Golgi to lysosomes.") -AnnotationAssertion( "tb") AnnotationAssertion( "2009-12-08T08:35:13Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0090160") @@ -83699,7 +82407,6 @@ EquivalentClasses( ObjectIntersection # Class: (establishment of epithelial cell polarity) AnnotationAssertion(Annotation( "GOC:ascb_2009") Annotation( "GOC:dph") Annotation( "GOC:tb") "The specification and formation of anisotropic intracellular organization of an epithelial cell.") -AnnotationAssertion( "tb") AnnotationAssertion( "2009-12-08T08:58:27Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0090162") @@ -83710,7 +82417,6 @@ SubClassOf( (Golgi disassembly) AnnotationAssertion(Annotation( "GOC:ascb_2009") Annotation( "GOC:dph") Annotation( "GOC:tb") "A cellular process that results in the breakdown of a Golgi apparatus that contributes to Golgi inheritance.") -AnnotationAssertion( "tb") AnnotationAssertion( "2009-12-08T09:15:11Z") AnnotationAssertion( "Golgi apparatus disassembly") AnnotationAssertion( "biological_process") @@ -83723,7 +82429,6 @@ SubClassOf( ObjectSomeValuesFrom( (Golgi reassembly) AnnotationAssertion(Annotation( "GOC:ascb_2009") Annotation( "GOC:dph") Annotation( "GOC:tb") "The reformation of the Golgi following its breakdown and partitioning contributing to Golgi inheritance.") -AnnotationAssertion( "tb") AnnotationAssertion( "2009-12-08T09:15:11Z") AnnotationAssertion( "Golgi apparatus reassembly") AnnotationAssertion( "biological_process") @@ -83736,7 +82441,6 @@ SubClassOf( ObjectSomeValuesFrom( (regulation of Golgi inheritance) AnnotationAssertion(Annotation( "GOC:ascb_2009") Annotation( "GOC:dph") Annotation( "GOC:tb") "Any process that modulates the rate, frequency or extent of Golgi inheritance. Golgi inheritance is the partitioning of Golgi apparatus between daughter cells at cell division.") -AnnotationAssertion( "tb") AnnotationAssertion( "2009-12-11T10:21:59Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0090170") @@ -83746,7 +82450,6 @@ EquivalentClasses( ObjectIntersection # Class: (chondrocyte morphogenesis) AnnotationAssertion(Annotation( "GOC:ascb_2009") Annotation( "GOC:dph") Annotation( "GOC:tb") "The process in which the structures of a chondrocyte are generated and organized. This process occurs while the initially relatively unspecialized cell is acquiring the specialized features of a chondrocyte.") -AnnotationAssertion( "tb") AnnotationAssertion( "2009-12-11T10:36:02Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0090171") @@ -83758,7 +82461,6 @@ SubClassOf( ObjectSomeValuesFrom( (organelle membrane fusion) AnnotationAssertion(Annotation( "GOC:ascb_2009") Annotation( "GOC:dph") Annotation( "GOC:tb") "The joining of two lipid bilayers to form a single organelle membrane.") -AnnotationAssertion( "tb") AnnotationAssertion( "2009-12-11T11:44:58Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0090174") @@ -83771,7 +82473,6 @@ SubClassOf( (regulation of kidney development) AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:tb") Annotation( "GOC:yaf") "Any process that modulates the rate, frequency or extent of kidney development. Kidney development is the process whose specific outcome is the progression of the kidney over time, from its formation to the mature structure. The kidney is an organ that filters the blood and excretes the end products of body metabolism in the form of urine.") -AnnotationAssertion( "tb") AnnotationAssertion( "2009-12-18T10:50:56Z") AnnotationAssertion( "biological_process") AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:tb") "regulation of nephrogenesis") @@ -83782,7 +82483,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of kidney development) AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:tb") Annotation( "GOC:yaf") "Any process that increases the rate, frequency or extent of kidney development. Kidney development is the process whose specific outcome is the progression of the kidney over time, from its formation to the mature structure. The kidney is an organ that filters the blood and excretes the end products of body metabolism in the form of urine.") -AnnotationAssertion( "tb") AnnotationAssertion( "2009-12-18T10:52:01Z") AnnotationAssertion( "biological_process") AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:tb") "positive regulation of nephrogenesis") @@ -83794,7 +82494,6 @@ SubClassOf( (negative regulation of kidney development) AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:tb") Annotation( "GOC:yaf") "Any process that decreases the rate, frequency or extent of kidney development. Kidney development is the process whose specific outcome is the progression of the kidney over time, from its formation to the mature structure. The kidney is an organ that filters the blood and excretes the end products of body metabolism in the form of urine.") -AnnotationAssertion( "tb") AnnotationAssertion( "2009-12-18T10:58:45Z") AnnotationAssertion( "biological_process") AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:tb") "negative regulation of nephrogenesis") @@ -83806,7 +82505,6 @@ SubClassOf( (regulation of branching involved in ureteric bud morphogenesis) AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:tb") Annotation( "GOC:yaf") "Any process that modulates the rate, frequency or extent of branching involved in ureteric bud morphogenesis, the process in which the branching structure of the ureteric bud is generated and organized. The ureteric bud is an epithelial tube that grows out from the metanephric duct. The bud elongates and branches to give rise to the ureter and kidney collecting tubules.") -AnnotationAssertion( "tb") AnnotationAssertion( "2009-12-18T11:11:17Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0090189") @@ -83818,7 +82516,6 @@ SubClassOf( (positive regulation of branching involved in ureteric bud morphogenesis) AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:tb") Annotation( "GOC:yaf") "Any process that increases the rate, frequency or extent of branching involved in ureteric bud morphogenesis, the process in which the branching structure of the ureteric bud is generated and organized. The ureteric bud is an epithelial tube that grows out from the metanephric duct. The bud elongates and branches to give rise to the ureter and kidney collecting tubules.") -AnnotationAssertion( "tb") AnnotationAssertion( "2009-12-18T11:11:17Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0090190") @@ -83828,7 +82525,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of branching involved in ureteric bud morphogenesis) AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:tb") Annotation( "GOC:yaf") "Any process that decreases the rate, frequency or extent of branching involved in ureteric bud morphogenesis, the process in which the branching structure of the ureteric bud is generated and organized. The ureteric bud is an epithelial tube that grows out from the metanephric duct. The bud elongates and branches to give rise to the ureter and kidney collecting tubules.") -AnnotationAssertion( "tb") AnnotationAssertion( "2009-12-18T11:11:17Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0090191") @@ -83838,7 +82534,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of glomerulus development) AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:tb") Annotation( "GOC:yaf") "Any process that modulates the rate, frequency or extent of glomerulus development, the progression of the glomerulus over time from its initial formation until its mature state. The glomerulus is a capillary tuft surrounded by Bowman's capsule in nephrons of the vertebrate kidney.") -AnnotationAssertion( "tb") AnnotationAssertion( "2009-12-18T11:17:13Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0090192") @@ -83849,7 +82544,6 @@ SubClassOf( ObjectSomeValuesFrom( (positive regulation of glomerulus development) AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:tb") Annotation( "GOC:yaf") "Any process that increases the rate, frequency or extent of glomerulus development, the progression of the glomerulus over time from its initial formation until its mature state. The glomerulus is a capillary tuft surrounded by Bowman's capsule in nephrons of the vertebrate kidney.") -AnnotationAssertion( "tb") AnnotationAssertion( "2009-12-18T11:17:13Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0090193") @@ -83860,7 +82554,6 @@ SubClassOf( (negative regulation of glomerulus development) AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:tb") Annotation( "GOC:yaf") "Any process that decreases the rate, frequency or extent of glomerulus development, the progression of the glomerulus over time from its initial formation until its mature state. The glomerulus is a capillary tuft surrounded by Bowman's capsule in nephrons of the vertebrate kidney.") -AnnotationAssertion( "tb") AnnotationAssertion( "2009-12-18T11:17:13Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0090194") @@ -83871,7 +82564,6 @@ SubClassOf( (spongiotrophoblast layer developmental growth) AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:tb") "The increase in size or mass of the spongiotrophoblast layer of the placenta where the increase in size or mass contributes to the progression of that layer over time from its formation to its mature state.") -AnnotationAssertion( "tb") AnnotationAssertion( "2010-01-08T12:10:44Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0090214") @@ -83883,7 +82575,6 @@ SubClassOf( ObjectSomeValuesFrom( (regulation of muscle system process) AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:tb") "Any process that modulates the frequency, rate or extent of a muscle system process, a multicellular organismal process carried out by any of the organs or tissues in a muscle system.") -AnnotationAssertion( "tb") AnnotationAssertion( "2010-02-03T11:48:13Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0090257") @@ -83894,7 +82585,6 @@ SubClassOf( (regulation of somatostatin secretion) AnnotationAssertion(Annotation( "GOC:BHF") "Any process that modulates the rate, frequency, extent of the regulated release of somatostatin from secretory granules in the D cells of the pancreas.") -AnnotationAssertion( "tb") AnnotationAssertion( "2010-02-05T02:54:14Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0090273") @@ -83905,7 +82595,6 @@ SubClassOf( (positive regulation of somatostatin secretion) AnnotationAssertion(Annotation( "GOC:BHF") "Any process that increases the rate, frequency, extent of the regulated release of somatostatin from secretory granules in the D cells of the pancreas.") -AnnotationAssertion( "tb") AnnotationAssertion( "2010-02-05T02:54:14Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0090274") @@ -83917,7 +82606,6 @@ SubClassOf( (negative regulation of somatostatin secretion) AnnotationAssertion(Annotation( "GOC:BHF") "Any process that decreases the rate, frequency, extent of the regulated release of somatostatin from secretory granules in the D cells of the pancreas.") -AnnotationAssertion( "tb") AnnotationAssertion( "2010-02-05T02:54:14Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0090275") @@ -83929,7 +82617,6 @@ SubClassOf( (regulation of peptide hormone secretion) AnnotationAssertion(Annotation( "GOC:tb") "Any process that modulates the rate, frequency, or extent of the regulated release of a peptide hormone from secretory granules.") -AnnotationAssertion( "tb") AnnotationAssertion( "2010-02-05T02:56:39Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0090276") @@ -83941,7 +82628,6 @@ SubClassOf( (positive regulation of peptide hormone secretion) AnnotationAssertion(Annotation( "GOC:tb") "Any process that increases the rate, frequency, or extent of the regulated release of a peptide hormone from secretory granules.") -AnnotationAssertion( "tb") AnnotationAssertion( "2010-02-05T02:56:39Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0090277") @@ -83954,7 +82640,6 @@ SubClassOf( (negative regulation of peptide hormone secretion) AnnotationAssertion(Annotation( "GOC:tb") "Any process that decreases the rate, frequency, or extent of the regulated release of a peptide hormone from secretory granules.") -AnnotationAssertion( "tb") AnnotationAssertion( "2010-02-05T02:56:39Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0090278") @@ -83967,7 +82652,6 @@ SubClassOf( (regulation of calcium ion import) AnnotationAssertion(Annotation( "GOC:BHF") "Any process that modulates the rate, frequency, or extent of the directed movement of calcium ions into a cell or organelle.") -AnnotationAssertion( "tb") AnnotationAssertion( "2010-02-08T05:11:20Z") AnnotationAssertion( "biological_process") AnnotationAssertion(Annotation( "GOC:tb") "regulation of transmembrane calcium influx") @@ -83978,7 +82662,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of calcium ion import) AnnotationAssertion(Annotation( "GOC:BHF") "Any process that increases the rate, frequency, or extent of the directed movement of calcium ions into a cell or organelle.") -AnnotationAssertion( "tb") AnnotationAssertion( "2010-02-08T05:11:20Z") AnnotationAssertion( "biological_process") AnnotationAssertion(Annotation( "GOC:tb") "positive regulation of transmembrane calcium influx") @@ -83989,7 +82672,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of calcium ion import) AnnotationAssertion(Annotation( "GOC:BHF") "Any process that decreases the rate, frequency, or extent of the directed movement of calcium ions into a cell or organelle.") -AnnotationAssertion( "tb") AnnotationAssertion( "2010-02-08T05:11:20Z") AnnotationAssertion( "biological_process") AnnotationAssertion(Annotation( "GOC:tb") "negative regulation of transmembrane calcium influx") @@ -84000,7 +82682,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of osteoclast proliferation) AnnotationAssertion(Annotation( "GOC:tb") "Any process that modulates the rate, frequency, or extent of the multiplication or reproduction of osteoclasts, resulting in the expansion of an osteoclast cell population.") -AnnotationAssertion( "tb") AnnotationAssertion( "2010-02-18T03:11:03Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0090289") @@ -84010,7 +82691,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of osteoclast proliferation) AnnotationAssertion(Annotation( "GOC:tb") "Any process that increases the rate, frequency, or extent of the multiplication or reproduction of osteoclasts, resulting in the expansion of an osteoclast cell population.") -AnnotationAssertion( "tb") AnnotationAssertion( "2010-02-18T03:11:03Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0090290") @@ -84020,7 +82700,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of osteoclast proliferation) AnnotationAssertion(Annotation( "GOC:tb") "Any process that decreases the rate, frequency, or extent of the multiplication or reproduction of osteoclasts, resulting in the expansion of an osteoclast cell population.") -AnnotationAssertion( "tb") AnnotationAssertion( "2010-02-18T03:11:03Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0090291") @@ -84030,7 +82709,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of neural crest formation) AnnotationAssertion(Annotation( "GOC:tb") "Any process that modulates the rate, frequency, or extent of neural crest formation. Neural crest formation is the formation of the specialized region of ectoderm between the neural ectoderm (neural plate) and non-neural ectoderm. The neural crest gives rise to the neural crest cells that migrate away from this region as neural tube formation proceeds.") -AnnotationAssertion( "tb") AnnotationAssertion( "2010-03-12T04:08:26Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0090299") @@ -84041,7 +82719,6 @@ SubClassOf( ObjectSomeValuesFrom( (positive regulation of neural crest formation) AnnotationAssertion(Annotation( "GOC:tb") "Any process that increases the rate, frequency, or extent of neural crest formation. Neural crest formation is the formation of the specialized region of ectoderm between the neural ectoderm (neural plate) and non-neural ectoderm. The neural crest gives rise to the neural crest cells that migrate away from this region as neural tube formation proceeds.") -AnnotationAssertion( "tb") AnnotationAssertion( "2010-03-12T04:08:26Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0090300") @@ -84051,7 +82728,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of neural crest formation) AnnotationAssertion(Annotation( "GOC:tb") "Any process that decreases the rate, frequency, or extent of neural crest formation. Neural crest formation is the formation of the specialized region of ectoderm between the neural ectoderm (neural plate) and non-neural ectoderm. The neural crest gives rise to the neural crest cells that migrate away from this region as neural tube formation proceeds.") -AnnotationAssertion( "tb") AnnotationAssertion( "2010-03-12T04:08:26Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0090301") @@ -84061,7 +82737,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of wound healing) AnnotationAssertion(Annotation( "GOC:BHF") "Any process that increases the rate, frequency, or extent of the series of events that restore integrity to a damaged tissue, following an injury.") -AnnotationAssertion( "tb") AnnotationAssertion( "2010-03-22T02:12:03Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0090303") @@ -84075,7 +82750,6 @@ SubClassOf( "GOC:dph") Annotation( "GOC:tb") "Any cellular metabolic process involving nucleic acids.") AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/26133"^^xsd:anyURI) AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/27052"^^xsd:anyURI) -AnnotationAssertion( "tb") AnnotationAssertion( "2010-04-07T10:18:47Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0090304") @@ -84087,7 +82761,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of intracellular protein transport) AnnotationAssertion(Annotation( "GOC:tb") "Any process that activates or increases the frequency, rate or extent of the directed movement of proteins within cells.") -AnnotationAssertion( "tb") AnnotationAssertion( "2010-04-16T03:45:07Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0090316") @@ -84097,7 +82770,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of intracellular protein transport) AnnotationAssertion(Annotation( "GOC:tb") "Any process that decreases the frequency, rate or extent of the directed movement of proteins within cells.") -AnnotationAssertion( "tb") AnnotationAssertion( "2010-04-16T03:45:07Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0090317") @@ -84108,7 +82780,6 @@ SubClassOf( ObjectSomeValuesFrom( (regulation of superoxide metabolic process) AnnotationAssertion(Annotation( "GOC:tb") "Any process that modulates the rate, frequency, or extent of superoxide metabolism, the chemical reactions and pathways involving superoxide, the superoxide anion O2- (superoxide free radical), or any compound containing this species.") -AnnotationAssertion( "tb") AnnotationAssertion( "2010-05-06T02:29:05Z") AnnotationAssertion(Annotation( "GOC:tb") "regulation of superoxide metabolism") AnnotationAssertion( "biological_process") @@ -84119,7 +82790,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of locomotion involved in locomotory behavior) AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:kmv") Annotation( "GOC:tb") "Any process that modulates the frequency, rate, or extent of the self-propelled movement of a cell or organism from one location to another in a behavioral context; the aspect of locomotory behavior having to do with movement.") -AnnotationAssertion( "tb") AnnotationAssertion( "2010-05-14T10:24:29Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0090325") @@ -84131,7 +82801,6 @@ SubClassOf( (positive regulation of locomotion involved in locomotory behavior) AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:kmv") Annotation( "GOC:tb") "Any process that increases the frequency, rate, or extent of the self-propelled movement of a cell or organism from one location to another in a behavioral context; the aspect of locomotory behavior having to do with movement.") -AnnotationAssertion( "tb") AnnotationAssertion( "2010-05-14T10:26:58Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0090326") @@ -84144,7 +82813,6 @@ SubClassOf( (negative regulation of locomotion involved in locomotory behavior) AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:kmv") Annotation( "GOC:tb") "Any process that decreases the frequency, rate, or extent of the self-propelled movement of a cell or organism from one location to another in a behavioral context; the aspect of locomotory behavior having to do with movement.") -AnnotationAssertion( "tb") AnnotationAssertion( "2010-05-14T10:26:58Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0090327") @@ -84157,7 +82825,6 @@ SubClassOf( (regulation of olfactory learning) AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:tb") "Any process that modulates the rate, frequency, or extent of olfactory learning. Olfactory learning is any process in an organism in which a relatively long-lasting adaptive behavioral change occurs in response to (repeated) exposure to an olfactory cue.") -AnnotationAssertion( "tb") AnnotationAssertion( "2010-05-14T10:37:22Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0090328") @@ -84170,7 +82837,6 @@ SubClassOf( (regulation of brown fat cell differentiation) AnnotationAssertion(Annotation( "GOC:tb") "Any process that modulates the rate, frequency, or extent of brown fat cell differentiation. Brown fat cell differentiation is the process in which a relatively unspecialized cell acquires specialized features of a brown adipocyte, an animal connective tissue cell involved in adaptive thermogenesis. Brown adipocytes contain multiple small droplets of triglycerides and a high number of mitochondria.") -AnnotationAssertion( "tb") AnnotationAssertion( "2010-06-01T03:16:57Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0090335") @@ -84180,7 +82846,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of brown fat cell differentiation) AnnotationAssertion(Annotation( "GOC:BHF") "Any process that increases the rate, frequency, or extent of brown fat cell differentiation. Brown fat cell differentiation is the process in which a relatively unspecialized cell acquires specialized features of a brown adipocyte, an animal connective tissue cell involved in adaptive thermogenesis. Brown adipocytes contain multiple small droplets of triglycerides and a high number of mitochondria.") -AnnotationAssertion( "tb") AnnotationAssertion( "2010-06-01T03:19:26Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0090336") @@ -84190,7 +82855,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of excitatory postsynaptic potential) AnnotationAssertion(Annotation( "GOC:BHF") "Any process that prevents the establishment or decreases the extent of the excitatory postsynaptic potential (EPSP) which is a temporary increase in postsynaptic potential due to the flow of positively charged ions into the postsynaptic cell. The flow of ions that causes an EPSP is an excitatory postsynaptic current (EPSC) and makes it easier for the neuron to fire an action potential.") -AnnotationAssertion( "tb") AnnotationAssertion( "2010-12-15T01:43:12Z") AnnotationAssertion( "negative regulation of excitatory post-synaptic membrane potential") AnnotationAssertion(Annotation( "GOC:bf") "reduction of excitatory postsynaptic membrane potential") @@ -84203,7 +82867,6 @@ EquivalentClasses( ObjectIntersection # Class: (acinar cell differentiation) AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:tb") "The epithelial cell differentiation process in which a relatively unspecialized cell acquires specialized features of an acinar cell, a secretory cell that is grouped together with other cells of the same type to form grape-shaped clusters known as acini.") -AnnotationAssertion( "tb") AnnotationAssertion( "2012-05-04T09:24:48Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0090425") @@ -84213,7 +82876,6 @@ EquivalentClasses( ObjectIntersection # Class: (protein localization to nuclear envelope) AnnotationAssertion(Annotation( "GOC:tb") "A process in which a protein is transported to, or maintained at, a location within a nuclear envelope.") -AnnotationAssertion( "tb") AnnotationAssertion( "2012-07-30T01:50:41Z") AnnotationAssertion( "protein localization in nuclear envelope") AnnotationAssertion( "biological_process") @@ -84225,7 +82887,6 @@ SubClassOf( (glutamate transmembrane import into vacuole) AnnotationAssertion(Annotation( "GOC:tb") "The directed movement of glutamate into the vacuole across the vacuolar membrane.") -AnnotationAssertion( "tb") AnnotationAssertion( "2012-09-24T14:12:46Z") AnnotationAssertion( "biological_process") AnnotationAssertion(Annotation( "GOC:tb") "vacuolar glutamate import") @@ -84237,7 +82898,6 @@ EquivalentClasses( ObjectIntersection AnnotationAssertion(Annotation( "GOC:tb") "A homeostatic process involved in the maintenance of a steady state level of glutamate within a cell.") AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/24220"^^xsd:anyURI) -AnnotationAssertion( "tb") AnnotationAssertion( "2012-09-24T14:22:02Z") AnnotationAssertion( "cellular glutamate homeostasis") AnnotationAssertion( "glutamate homeostasis") @@ -84249,7 +82909,6 @@ EquivalentClasses( ObjectIntersection # Class: (catecholamine uptake) AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:tb") "The directed movement of catecholamine into a cell.") -AnnotationAssertion( "tb") AnnotationAssertion( "2012-10-17T11:06:17Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0090493") @@ -84260,7 +82919,6 @@ SubClassOf( (dopamine uptake) AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:tb") "The directed movement of dopamine into a cell.") -AnnotationAssertion( "tb") AnnotationAssertion( "2012-10-17T11:12:09Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0090494") @@ -84271,7 +82929,6 @@ SubClassOf( (mesenchyme migration involved in limb bud formation) AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:tb") "The migration of mesenchymal tissue that contributes to the formation of a limb bud.") -AnnotationAssertion( "tb") AnnotationAssertion( "2012-10-17T12:04:20Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0090496") @@ -84281,7 +82938,6 @@ EquivalentClasses( ObjectIntersection # Class: (mesenchymal cell migration) AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:tb") "The orderly movement of a mesenchymal cell from one site to another, often during the development of a multicellular organism.") -AnnotationAssertion( "tb") AnnotationAssertion( "2012-10-17T12:08:17Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0090497") @@ -84292,7 +82948,6 @@ SubClassOf( (L-histidine transmembrane import into vacuole) AnnotationAssertion(Annotation( "GOC:al") "The directed movement of L-histidine into the vacuole across the vacuolar membrane.") -AnnotationAssertion( "tb") AnnotationAssertion( "2012-12-14T11:25:52Z") AnnotationAssertion( "histidine transmembrane import into vacuole") AnnotationAssertion(Annotation( "GOC:tb") "vacuolar histidine import") @@ -84304,7 +82959,6 @@ EquivalentClasses( ObjectIntersection # Class: (L-glutamate transmembrane import into vacuole) AnnotationAssertion(Annotation( "GOC:al") "The directed movement of L-glutamate into the vacuole across the vacuolar membrane.") -AnnotationAssertion( "tb") AnnotationAssertion( "2012-12-14T11:25:52Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0090515") @@ -84315,7 +82969,6 @@ EquivalentClasses( ObjectIntersection AnnotationAssertion(Annotation( "GOC:pm") Annotation( "PMID:21402783") "The orderly movement of a podocyte from one site to another, often during the development of a multicellular organism or multicellular structure. A podocyte is a specialized kidney epithelial cell.") AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/23000"^^xsd:anyURI) -AnnotationAssertion( "tb") AnnotationAssertion( "2013-01-08T11:08:57Z") AnnotationAssertion( "glomerular visceral epithelial cell migration") AnnotationAssertion( "biological_process") @@ -84326,7 +82979,6 @@ EquivalentClasses( ObjectIntersection # Class: (inflammatory response to wounding) AnnotationAssertion(Annotation( "GOC:add") "The immediate defensive reaction by vertebrate tissue to injury caused by chemical or physical agents.") -AnnotationAssertion( "tb") AnnotationAssertion( "2014-08-12T12:13:53Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0090594") @@ -84337,7 +82989,6 @@ SubClassOf( (sensory organ morphogenesis) AnnotationAssertion(Annotation( "GOC:kmv") Annotation( "ISBN:978-0199210893") "Morphogenesis of a sensory organ. A sensory organ is defined as a tissue or set of tissues that work together to receive and transmit signals from external or internal stimuli. Morphogenesis is the process in which anatomical structures are generated and organized. Organs are commonly observed as visibly distinct structures, but may also exist as loosely associated clusters of cells that work together to perform a specific function or functions.") -AnnotationAssertion( "tb") AnnotationAssertion( "2014-08-22T13:23:20Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0090596") @@ -84349,7 +83000,6 @@ SubClassOf( ObjectSomeValuesFrom( (male anatomical structure morphogenesis) AnnotationAssertion(Annotation( "GOC:kmv") Annotation( "GOC:tb") "The processes by which anatomical structures that are only present in the male organism are generated and organized.") -AnnotationAssertion( "tb") AnnotationAssertion( "2014-08-22T13:29:45Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0090598") @@ -84361,7 +83011,6 @@ SubClassOf( ObjectSomeValuesFrom( (microglial cell mediated cytotoxicity) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:nc") Annotation( "PMID:19100238") "The directed killing of a target cell by a microglial cell.") -AnnotationAssertion( "tb") AnnotationAssertion( "2015-04-14T14:04:54Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0090634") @@ -84372,7 +83021,6 @@ SubClassOf( (RNA localization to nucleus) AnnotationAssertion(Annotation( "GOC:mah") Annotation( "PMID:26305931") "A macromolecular localization process in which RNA is transported to and maintained in a location within the nucleus.") -AnnotationAssertion( "tb") AnnotationAssertion( "2016-07-19T17:00:49Z") AnnotationAssertion(Annotation( "GOC:mah") "RNA localisation to nucleus") AnnotationAssertion( "biological_process") @@ -84384,7 +83032,6 @@ SubClassOf( (immunological memory process) AnnotationAssertion(Annotation( "GOC:add") Annotation( "PMID:26086132") Annotation( "PMID:26831526") "Any process of the immune system that can contribute to the formation of immunological memory or an immune response based upon activation of immunological memory.") -AnnotationAssertion( "tb") AnnotationAssertion( "2016-11-11T12:20:30Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0090713") @@ -84395,7 +83042,6 @@ SubClassOf( ObjectSomeValuesFrom( (immunological memory formation process) AnnotationAssertion(Annotation( "GOC:add") Annotation( "PMID:26086132") Annotation( "PMID:26831526") "Any immunological memory process that can contribute to the formation of immunological memory.") -AnnotationAssertion( "tb") AnnotationAssertion( "2016-11-11T12:25:47Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0090715") @@ -84405,7 +83051,6 @@ SubClassOf( (pigment granule membrane) AnnotationAssertion(Annotation( "PMID:11294610") "Any membrane that is part of a pigment granule.") -AnnotationAssertion( "tb") AnnotationAssertion( "2017-05-16T22:33:39Z") AnnotationAssertion( "cellular_component") AnnotationAssertion( "GO:0090741") @@ -84426,7 +83071,6 @@ SubClassOf( ObjectSomeValuesFrom( (ciliary plasm) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:cilia") Annotation( "GOC:dos") Annotation( "PMID:17895364") "All of the contents of a cilium, excluding the plasma membrane surrounding the cilium.") -AnnotationAssertion( "pr") AnnotationAssertion( "2011-03-23T01:52:31Z") AnnotationAssertion( "cilium plasm") AnnotationAssertion( "microtubule-based flagellar matrix") @@ -84446,7 +83090,6 @@ SubClassOf( ObjectSomeValuesFrom( (dendritic cell dendrite assembly) AnnotationAssertion(Annotation( "CL:0000451") Annotation( "GOC:BHF") Annotation( "PMID:12200351") "Formation of dendrites, branched cellular projections (or cytoplasmic extension) that are extended from the surface of a dendritic immune cell, and which enable the cell to sample luminal pathogens and increase the surface area for antigen presentation to T cells.") -AnnotationAssertion( "pr") AnnotationAssertion( "2011-03-31T04:52:53Z") AnnotationAssertion( "dendritic extension") AnnotationAssertion( "biological_process") @@ -84458,7 +83101,6 @@ EquivalentClasses( ObjectIntersection # Class: (dendritic cell differentiation) AnnotationAssertion(Annotation( "CL:0000451") Annotation( "GOC:pr") "The process in which a precursor cell type acquires the specialized features of a dendritic cell. A dendritic cell is a leukocyte of dendritic lineage specialized in the uptake, processing, and transport of antigens to lymph nodes for the purpose of stimulating an immune response via T cell activation.") -AnnotationAssertion( "pr") AnnotationAssertion( "2011-04-01T10:08:42Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0097028") @@ -84470,7 +83112,6 @@ SubClassOf( (mature conventional dendritic cell differentiation) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "PMID:15845453") "The process in which antigen-activated dendritic cells acquire the specialized features of a mature conventional dendritic cell. Mature conventional dendritic cells upregulate the surface expression of MHC molecules, chemokine receptors and adhesion molecules, and increase the number of dendrites (cytoplasmic protrusions) in preparation for migration to lymphoid organs where they present antigen to T cells.") -AnnotationAssertion( "pr") AnnotationAssertion( "2011-04-01T10:10:22Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0097029") @@ -84482,7 +83123,6 @@ SubClassOf( (dendritic cell apoptotic process) AnnotationAssertion(Annotation( "CL:0000451") Annotation( "GOC:BHF") Annotation( "GOC:mtg_apoptosis") Annotation( "PMID:15059845") "Any apoptotic process in a dendritic cell, a cell of hematopoietic origin, typically resident in particular tissues, specialized in the uptake, processing, and transport of antigens to lymph nodes for the purpose of stimulating an immune response via T cell activation.") -AnnotationAssertion( "pr") AnnotationAssertion( "2011-05-04T02:18:59Z") AnnotationAssertion( "dendritic cell apoptosis") AnnotationAssertion( "biological_process") @@ -84494,7 +83134,6 @@ SubClassOf( (motor neuron apoptotic process) AnnotationAssertion(Annotation( "CL:0000100") Annotation( "GOC:BHF") Annotation( "GOC:mtg_apoptosis") Annotation( "PMID:14523086") "Any apoptotic process in a motor neuron, an efferent neuron that passes from the central nervous system or a ganglion toward or to a muscle and conducts an impulse that causes movement.") -AnnotationAssertion( "pr") AnnotationAssertion( "2011-05-04T02:21:43Z") AnnotationAssertion( "motoneuron apoptosis") AnnotationAssertion( "motor neuron apoptosis") @@ -84506,7 +83145,6 @@ EquivalentClasses( ObjectIntersection # Class: (type B pancreatic cell apoptotic process) AnnotationAssertion(Annotation( "CL:0000169") Annotation( "GOC:BHF") Annotation( "GOC:mtg_apoptosis") Annotation( "PMID:16087305") "Any apoptotic process in a type B pancreatic cell, a cell located towards center of the islets of Langerhans that secretes insulin.") -AnnotationAssertion( "pr") AnnotationAssertion( "2011-05-04T02:24:38Z") AnnotationAssertion( "pancreatic B cell apoptosis") AnnotationAssertion( "pancreatic beta cell apoptosis") @@ -84519,7 +83157,6 @@ EquivalentClasses( ObjectIntersection # Class: (L-glutamate biosynthetic process) AnnotationAssertion(Annotation( "GOC:yaf") "The chemical reactions and pathways resulting in the formation of L-glutamate, the L enantiomer anion of 2-aminopentanedioic acid.") -AnnotationAssertion( "pr") AnnotationAssertion( "2011-05-24T04:30:38Z") AnnotationAssertion( "L-glutamate anabolism") AnnotationAssertion( "L-glutamate biosynthesis") @@ -84534,7 +83171,6 @@ SubClassOf( (synaptic membrane) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "PMID:20410104") "A specialized area of membrane on either the presynaptic or the postsynaptic side of a synapse, the junction between a nerve fiber of one neuron and another neuron or muscle fiber or glial cell.") -AnnotationAssertion( "pr") AnnotationAssertion( "2011-06-07T11:22:09Z") AnnotationAssertion( "cellular_component") AnnotationAssertion( "GO:0097060") @@ -84548,7 +83184,6 @@ SubClassOf( ObjectSomeValuesFrom( (vascular associated smooth muscle cell development) AnnotationAssertion(Annotation( "GOC:BHF") "The process aimed at the progression of a vascular smooth muscle cell over time, from initial commitment of the cell to a specific fate, to the fully functional differentiated cell. A vascular smooth muscle cell is a non-striated, elongated, spindle-shaped cell found lining the blood vessels.") -AnnotationAssertion( "pr") AnnotationAssertion( "2011-06-20T04:03:08Z") AnnotationAssertion( "vascular smooth muscle cell development") AnnotationAssertion( "biological_process") @@ -84560,7 +83195,6 @@ SubClassOf( ObjectSomeValuesFrom( (amniotic stem cell differentiation) AnnotationAssertion(Annotation( "CL:0002639") Annotation( "GOC:yaf") Annotation( "PMID:20942606") Annotation( "Wikipedia:Amniotic_stem_cells") "The process whereby a relatively unspecialized cell acquires specialized features of an amniotic stem cell. An amniotic stem cell is a mesenchymal stem cell extracted from amniotic fluid. Amniotic stem cells are able to differentiate into various tissue types such as skin, cartilage, cardiac tissue, nerves, muscle, and bone.") -AnnotationAssertion( "pr") AnnotationAssertion( "2011-06-22T11:17:52Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0097086") @@ -84571,7 +83205,6 @@ SubClassOf( (craniofacial suture morphogenesis) AnnotationAssertion(Annotation( "GOC:pr") Annotation( "GOC:sl") Annotation( "Wikipedia:Cranial_sutures") Annotation( "Wikipedia:Head_and_neck_anatomy#Musculoskeletal_system") "The process in which any suture between cranial and/or facial bones is generated and organized.") -AnnotationAssertion( "pr") AnnotationAssertion( "2011-07-05T02:51:54Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0097094") @@ -84587,7 +83220,6 @@ SubClassOf( ObjectAllValuesFrom( (facial suture morphogenesis) AnnotationAssertion(Annotation( "GOC:pr") Annotation( "GOC:sl") Annotation( "Wikipedia:Cranial_sutures") Annotation( "Wikipedia:Head_and_neck_anatomy#Musculoskeletal_system") "The process in which any suture between facial bones is generated and organized.") -AnnotationAssertion( "pr") AnnotationAssertion( "2011-07-05T03:06:27Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0097096") @@ -84598,7 +83230,6 @@ SubClassOf( (postsynaptic membrane assembly) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:sjp") Annotation( "PMID:21424692") "The aggregation, arrangement and bonding together of a set of components to form a postsynaptic membrane, a specialized area of membrane facing the presynaptic membrane on the tip of the nerve ending and separated from it by a minute cleft (the synaptic cleft).") -AnnotationAssertion( "pr") AnnotationAssertion( "2011-07-27T01:26:49Z") AnnotationAssertion( "post-synaptic membrane assembly") AnnotationAssertion( "biological_process") @@ -84611,7 +83242,6 @@ SubClassOf( ObjectSomeValuesFrom( (receptor localization to synapse) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:sjp") Annotation( "PMID:21525273") "Any process in which a receptor is transported to, and/or maintained at the synapse, the junction between a nerve fiber of one neuron and another neuron or muscle fiber or glial cell.") -AnnotationAssertion( "pr") AnnotationAssertion( "2011-07-31T09:20:30Z") AnnotationAssertion( "receptor localisation to synapse") AnnotationAssertion( "biological_process") @@ -84622,7 +83252,6 @@ EquivalentClasses( ObjectIntersection # Class: (mesenchymal cell apoptotic process) AnnotationAssertion(Annotation( "CL:0000134") Annotation( "GOC:mtg_apoptosis") Annotation( "GOC:yaf") Annotation( "PMID:18231833") "Any apoptotic process in a mesenchymal cell. A mesenchymal cell is a loosely associated cell that is part of the connective tissue in an organism. Mesenchymal cells give rise to more mature connective tissue cell types.") -AnnotationAssertion( "pr") AnnotationAssertion( "2011-09-06T02:31:59Z") AnnotationAssertion( "mesenchymal cell apoptosis") AnnotationAssertion( "biological_process") @@ -84634,7 +83263,6 @@ SubClassOf( (GABAergic neuron differentiation) AnnotationAssertion(Annotation( "GOC:kmv") Annotation( "PMID:11517269") "The process in which a neuroblast acquires the specialized structural and functional features of a GABAergic neuron.") -AnnotationAssertion( "pr") AnnotationAssertion( "2011-09-14T09:39:11Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0097154") @@ -84645,7 +83273,6 @@ SubClassOf( (ammonium ion metabolic process) AnnotationAssertion(Annotation( "GOC:dhl") Annotation( "GOC:tb") Annotation( "PMID:14671018") "The chemical reactions and pathways involving the ammonium ion.") -AnnotationAssertion( "pr") AnnotationAssertion( "2011-09-28T04:21:30Z") AnnotationAssertion( "ammonium ion metabolism") AnnotationAssertion( "biological_process") @@ -84658,7 +83285,6 @@ SubClassOf( (amelogenesis) AnnotationAssertion(Annotation( "GOC:cjm") Annotation( "GOC:sl") Annotation( "PMID:10206335") Annotation( "PMID:21196346") "The process whose specific outcome is the formation of tooth enamel, occurring in two stages: secretory stage and maturation stage.") -AnnotationAssertion( "pr") AnnotationAssertion( "2011-11-21T09:01:24Z") AnnotationAssertion( "enamel development") AnnotationAssertion( "biological_process") @@ -84670,7 +83296,6 @@ SubClassOf( (dentinogenesis) AnnotationAssertion(Annotation( "GOC:cjm") Annotation( "GOC:sl") Annotation( "PMID:10206335") Annotation( "PMID:21196346") "The process whose specific outcome is the formation of dentin, the mineralized tissue that constitutes the major bulk of teeth. Dentin may be one of three types: primary dentin, secondary dentin, and tertiary dentin.") -AnnotationAssertion( "pr") AnnotationAssertion( "2011-11-21T09:04:17Z") AnnotationAssertion( "dentin development") AnnotationAssertion( "dentine development") @@ -84683,7 +83308,6 @@ SubClassOf( (apoptotic signaling pathway) AnnotationAssertion(Annotation( "GOC:mtg_apoptosis") "The series of molecular signals which triggers the apoptotic death of a cell. The pathway starts with reception of a signal, and ends when the execution phase of apoptosis is triggered.") -AnnotationAssertion( "pr") AnnotationAssertion( "2011-11-23T09:30:23Z") AnnotationAssertion(Annotation( "GOC:mah") "apoptotic signalling pathway") AnnotationAssertion( "induction of apoptosis by extracellular signals") @@ -84697,7 +83321,6 @@ SubClassOf( ObjectSomeValuesFrom( (extrinsic apoptotic signaling pathway) AnnotationAssertion(Annotation( "GOC:mtg_apoptosis") Annotation( "GOC:yaf") Annotation( "PMID:17340152") "The series of molecular signals in which a signal is conveyed from the cell surface to trigger the apoptotic death of a cell. The pathway starts with either a ligand binding to a cell surface receptor, or a ligand being withdrawn from a cell surface receptor (e.g. in the case of signaling by dependence receptors), and ends when the execution phase of apoptosis is triggered.") -AnnotationAssertion( "pr") AnnotationAssertion( "2011-11-23T09:34:28Z") AnnotationAssertion( "extrinsic apoptotic pathway") AnnotationAssertion(Annotation( "GOC:mah") "extrinsic apoptotic signalling pathway") @@ -84714,7 +83337,6 @@ SubClassOf( (execution phase of apoptosis) AnnotationAssertion(Annotation( "GOC:mtg_apoptosis") Annotation( "PMID:21760595") "A stage of the apoptotic process that starts with the controlled breakdown of the cell through the action of effector caspases or other effector molecules (e.g. cathepsins, calpains etc.). Key steps of the execution phase are rounding-up of the cell, retraction of pseudopodes, reduction of cellular volume (pyknosis), chromatin condensation, nuclear fragmentation (karyorrhexis), plasma membrane blebbing and fragmentation of the cell into apoptotic bodies. When the execution phase is completed, the cell has died.") -AnnotationAssertion( "pr") AnnotationAssertion( "2011-11-23T09:45:24Z") AnnotationAssertion( "execution phase of apoptotic process") AnnotationAssertion( "apoptosis") @@ -84728,7 +83350,6 @@ SubClassOf( ObjectSomeValuesFrom( (renal filtration) AnnotationAssertion(Annotation( "GOC:pr") Annotation( "GOC:sart") "A renal system process in which fluid circulating through the body is filtered through a barrier system.") -AnnotationAssertion( "pr") AnnotationAssertion( "2012-01-03T03:10:17Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0097205") @@ -84738,7 +83359,6 @@ SubClassOf( (lysosomal membrane organization) AnnotationAssertion(Annotation( "GOC:yaf") Annotation( "PMID:20544854") "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a lysosomal membrane. A lysosomal membrane is the lipid bilayer surrounding the lysosome and separating its contents from the cell cytoplasm.") -AnnotationAssertion( "pr") AnnotationAssertion( "2012-01-12T10:16:15Z") AnnotationAssertion(Annotation( "GOC:mah") "lysosomal membrane organisation") AnnotationAssertion( "lysosome membrane organization") @@ -84752,7 +83372,6 @@ SubClassOf( ObjectSomeValuesFrom( (lamellar body membrane) AnnotationAssertion(Annotation( "GOC:sl") Annotation( "PMID:11940594") "The lipid bilayer surrounding a lamellar body. A lamellar body is a membrane-bounded organelle, specialized for the storage and secretion of various substances (surfactant phospholipids, glycoproteins and acid phosphates) which are arranged in the form of tightly packed, concentric, membrane sheets or lamellae. Has some similar properties to, but is distinct from, a lysosome.") -AnnotationAssertion( "pr") AnnotationAssertion( "2012-01-26T10:28:42Z") AnnotationAssertion( "cellular_component") AnnotationAssertion( "GO:0097232") @@ -84764,7 +83383,6 @@ SubClassOf( ObjectSomeValuesFrom( (cellular response to toxic substance) AnnotationAssertion(Annotation( "GOC:pr") "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a toxic stimulus.") -AnnotationAssertion( "pr") AnnotationAssertion( "2012-02-02T12:23:31Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0097237") @@ -84773,7 +83391,6 @@ AnnotationAssertion(rdfs:label "cell # Class: (oligodendrocyte apoptotic process) AnnotationAssertion(Annotation( "CL:0000128") Annotation( "GOC:mtg_apoptosis") Annotation( "GOC:yaf") Annotation( "PMID:16723520") "Any apoptotic process in an oligodendrocyte. Oligodendrocytes belong to a class of large neuroglial (macroglial) cells in the central nervous system, where they form the insulating myelin sheath of axons.") -AnnotationAssertion( "pr") AnnotationAssertion( "2012-03-05T10:51:15Z") AnnotationAssertion( "oligodendrocyte apoptosis") AnnotationAssertion( "biological_process") @@ -84786,7 +83403,6 @@ SubClassOf( "GOC:rph") Annotation( "PMID:25287933") Annotation( "Wikipedia:Renal_secretion#Secretion") "The elimination of substances from peritubular capillaries (or surrounding hemolymph in invertebrates) into the renal tubules to be incorporated subsequently into the urine. Substances that are secreted include organic anions, ammonia, potassium and drugs.") AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/22368"^^xsd:anyURI) -AnnotationAssertion( "pr") AnnotationAssertion( "2012-03-05T02:03:58Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0097254") @@ -84797,7 +83413,6 @@ SubClassOf( (ammonium homeostasis) AnnotationAssertion(Annotation( "GOC:yaf") Annotation( "PMID:12695560") "Any biological process involved in the maintenance of an internal steady state of ammonium.") -AnnotationAssertion( "pr") AnnotationAssertion( "2012-03-22T02:51:22Z") AnnotationAssertion( "ammonia homeostasis") AnnotationAssertion( "biological_process") @@ -84808,7 +83423,6 @@ EquivalentClasses( ObjectIntersection # Class: (intracellular ammonium homeostasis) AnnotationAssertion(Annotation( "GOC:yaf") Annotation( "PMID:12695560") "A homeostatic process involved in the maintenance of a steady state level of ammonium within a cell.") -AnnotationAssertion( "pr") AnnotationAssertion( "2012-03-22T02:54:38Z") AnnotationAssertion( "cellular ammonia homeostasis") AnnotationAssertion( "cellular ammonium homeostasis") @@ -84822,7 +83436,6 @@ SubClassOf( "CL:0000312") Annotation( "GOC:jc") Annotation( "GOC:mtg_apoptosis") Annotation( "PMID:10201527") "Any apoptotic process in a keratinocyte. A keratinocyte is an epidermal cell which synthesizes keratin and undergoes a characteristic change as it moves upward from the basal layers of the epidermis to the cornified (horny) layer of the skin.") AnnotationAssertion( ) -AnnotationAssertion( "pr") AnnotationAssertion( "2012-03-29T10:20:51Z") AnnotationAssertion( "keratinocyte apoptosis") AnnotationAssertion( "biological_process") @@ -84836,7 +83449,6 @@ DisjointClasses( ObjectSomeValuesFrom # Class: (hepatocyte apoptotic process) AnnotationAssertion(Annotation( "CL:0000182") Annotation( "GOC:jc") Annotation( "GOC:mtg_apoptosis") Annotation( "PMID:15856020") "Any apoptotic process in a hepatocyte, the main structural component of the liver.") -AnnotationAssertion( "pr") AnnotationAssertion( "2012-03-29T10:23:21Z") AnnotationAssertion( "hepatocyte apoptosis") AnnotationAssertion( "biological_process") @@ -84847,7 +83459,6 @@ EquivalentClasses( ObjectIntersection # Class: (melanocyte migration) AnnotationAssertion(Annotation( "CL:0000148") Annotation( "GOC:uh") Annotation( "PMID:22637532") "The orderly movement of melanocytes from one site to another, often during the development of a multicellular organism. A melanocyte is a pigment cell derived from the neural crest. It contains melanin-filled pigment granules, which give a brown to black appearance.") -AnnotationAssertion( "pr") AnnotationAssertion( "2012-06-08T10:08:18Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0097324") @@ -84858,7 +83469,6 @@ SubClassOf( (protein localization to heterochromatin) AnnotationAssertion(Annotation( "GOC:mah") "Any process in which a protein is transported to, or maintained at, a part of a chromosome that is organized into heterochromatin.") -AnnotationAssertion( "pr") AnnotationAssertion( "2012-07-03T03:19:07Z") AnnotationAssertion(Annotation( "GOC:mah") "protein localisation to heterochromatin") AnnotationAssertion( "biological_process") @@ -84869,7 +83479,6 @@ EquivalentClasses( ObjectIntersection # Class: (chorionic trophoblast cell proliferation) AnnotationAssertion(Annotation( "CL:0011101") Annotation( "GOC:BHF") Annotation( "PMID:15150278") "The multiplication or reproduction of chorionic trophoblast cells, resulting in the expansion of their population.") -AnnotationAssertion( "pr") AnnotationAssertion( "2012-07-19T10:17:37Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0097360") @@ -84879,7 +83488,6 @@ EquivalentClasses( ObjectIntersection # Class: (carbohydrate derivative binding) AnnotationAssertion(Annotation( "GOC:pr") "Binding to a carbohydrate derivative.") -AnnotationAssertion( "pr") AnnotationAssertion( "2012-08-02T13:03:39Z") AnnotationAssertion( "molecular_function") AnnotationAssertion( "GO:0097367") @@ -84892,7 +83500,6 @@ SubClassOf( (glial cell projection) AnnotationAssertion(Annotation( "GOC:mc") "A prolongation or process extending from a glial cell.") -AnnotationAssertion( "pr") AnnotationAssertion( "2012-10-22T13:55:54Z") AnnotationAssertion( "cellular_component") AnnotationAssertion( "glial process") @@ -84904,7 +83511,6 @@ EquivalentClasses( ObjectIntersection # Class: (neuroblast migration) AnnotationAssertion(Annotation( "CL:0000031") Annotation( "GOC:jc") Annotation( "PMID:15543145") "The orderly movement of a neuroblast from one site to another, often during the development of a multicellular organism or multicellular structure. A neuroblast is any cell that will divide and give rise to a neuron.") -AnnotationAssertion( "pr") AnnotationAssertion( "2012-10-29T08:24:37Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0097402") @@ -84915,7 +83521,6 @@ SubClassOf( (hippocampal interneuron differentiation) AnnotationAssertion(Annotation( "CL:1001569") Annotation( "GOC:jc") Annotation( "PMID:19655320") "The process in which a relatively unspecialized cell acquires specialized features of a hippocampal interneuron.") -AnnotationAssertion( "pr") AnnotationAssertion( "2012-11-04T10:58:28Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0097410") @@ -84926,7 +83531,6 @@ SubClassOf( ObjectSomeValuesFrom( (microtubule bundle) AnnotationAssertion(Annotation( "NIF_Subcellular:sao1872343973") "An arrangement of closely apposed microtubules running parallel to each other.") -AnnotationAssertion( "pr") AnnotationAssertion( "2012-11-07T15:01:27Z") AnnotationAssertion( "NIF_Subcellular:sao1872343973") AnnotationAssertion( "microtubule fascicle") @@ -84940,7 +83544,6 @@ SubClassOf( ObjectSomeValuesFrom( (hippocampal pyramidal neuron differentiation) AnnotationAssertion(Annotation( "CL:1001571") Annotation( "GOC:jc") Annotation( "PMID:19342486") "The process in which a relatively unspecialized cell acquires specialized features of a hippocampal pyramidal neuron, a pyramidal cell of the hippocampus.") -AnnotationAssertion( "pr") AnnotationAssertion( "2012-11-22T09:33:31Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0097432") @@ -84951,7 +83554,6 @@ SubClassOf( (supramolecular fiber organization) AnnotationAssertion(Annotation( "GOC:pr") "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a supramolecular fiber, a polymer consisting of an indefinite number of protein or protein complex subunits that have polymerised to form a fiber-shaped structure.") -AnnotationAssertion( "pr") AnnotationAssertion( "2012-11-27T15:46:25Z") AnnotationAssertion( "extracellular fibril organisation") AnnotationAssertion( "extracellular fibril organization") @@ -84968,7 +83570,6 @@ SubClassOf( (dendritic tree) AnnotationAssertion(Annotation( "GOC:aruk") Annotation( "GOC:bc") Annotation( "NIF_Subcellular:sao172297168") "The entire complement of dendrites for a neuron, consisting of each primary dendrite and all its branches.") -AnnotationAssertion( "pr") AnnotationAssertion( "2012-12-17T12:31:49Z") AnnotationAssertion( "NIF_Subcellular:sao172297168") AnnotationAssertion( "cellular_component") @@ -84981,7 +83582,6 @@ SubClassOf( ObjectSomeValuesFrom( (astrocyte projection) AnnotationAssertion(Annotation( "NIF_Subcellular:sao1630537580") "A prolongation or process extending from the soma of an astrocyte and wrapping around neurons.") -AnnotationAssertion( "pr") AnnotationAssertion( "2012-12-17T13:29:55Z") AnnotationAssertion( "NIF_Subcellular:sao1630537580") AnnotationAssertion( "astrocyte process") @@ -84996,7 +83596,6 @@ SubClassOf( (Schwann cell microvillus) AnnotationAssertion(Annotation( "NIF_Subcellular:sao1890444066") Annotation( "PMID:15988042") "Small finger-like extension of a Schwann cell that contacts the nodal membrane.") -AnnotationAssertion( "pr") AnnotationAssertion( "2012-12-19T13:01:02Z") AnnotationAssertion( "NIF_Subcellular:sao1890444066") AnnotationAssertion( "cellular_component") @@ -85009,7 +83608,6 @@ SubClassOf( "NIF_Subcellular:nlx_subcell_100312") Annotation( "PMID:17765709") Annotation( "PMID:20554881") Annotation( "PMID:24336151") "An axon of a hippocampal granule cell, including dentate gyrus granule cell and CA3 granule cell, characterized by expansions (mossy fiber expansions) giving the fibers a mossy appearance. These unmyelinated axons were first described by Ramon y Cajal.") AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/25796"^^xsd:anyURI) -AnnotationAssertion( "pr") AnnotationAssertion( "2012-12-19T16:51:57Z") AnnotationAssertion( "NIF_Subcellular:nlx_subcell_100312") AnnotationAssertion( "cellular_component") @@ -85021,7 +83619,6 @@ SubClassOf( ObjectSomeValuesFrom( (retinal rod cell apoptotic process) AnnotationAssertion(Annotation( "CL:0000604") Annotation( "GOC:jc") Annotation( "PMID:17202487") "Any apoptotic process in a retinal rod cell, one of the two photoreceptor cell types of the vertebrate retina.") -AnnotationAssertion( "pr") AnnotationAssertion( "2013-03-21T09:44:45Z") AnnotationAssertion( "rod photoreceptor apoptotic process") AnnotationAssertion( "biological_process") @@ -85033,7 +83630,6 @@ SubClassOf( (retinal cone cell apoptotic process) AnnotationAssertion(Annotation( "CL:0000573") Annotation( "GOC:jc") "Any apoptotic process in a retinal cone cell, one of the two photoreceptor cell types of the vertebrate retina.") -AnnotationAssertion( "pr") AnnotationAssertion( "2013-03-21T09:46:22Z") AnnotationAssertion( "cone photoreceptor apoptotic process") AnnotationAssertion( "biological_process") @@ -85045,7 +83641,6 @@ SubClassOf( (motor neuron migration) AnnotationAssertion(Annotation( "CL:0000100") Annotation( "GOC:yaf") Annotation( "PMID:20711475") "The orderly movement of a motor neuron from one site to another. A motor neuron is an efferent neuron that passes from the central nervous system or a ganglion toward or to a muscle and conducts an impulse that causes movement.") -AnnotationAssertion( "pr") AnnotationAssertion( "2013-04-23T13:00:46Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0097475") @@ -85056,7 +83651,6 @@ SubClassOf( (spinal cord motor neuron migration) AnnotationAssertion(Annotation( "CL:0011001") Annotation( "GOC:yaf") Annotation( "PMID:20711475") "The orderly movement of a spinal cord motor neuron from one site to another. A spinal cord motor neuron is a motor neuron that passes from the spinal cord toward or to a muscle and conducts an impulse that causes movement.") -AnnotationAssertion( "pr") AnnotationAssertion( "2013-04-23T13:03:46Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0097476") @@ -85067,7 +83661,6 @@ SubClassOf( (lateral motor column neuron migration) AnnotationAssertion(Annotation( "CL:0011002") Annotation( "GOC:yaf") Annotation( "PMID:20711475") "The orderly movement of a lateral motor column neuron from one site to another. A lateral motor column neuron is a motor neuron that is generated only on limb levels and send axons into the limb mesenchyme.") -AnnotationAssertion( "pr") AnnotationAssertion( "2013-04-23T13:05:32Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0097477") @@ -85078,7 +83671,6 @@ SubClassOf( (dendritic cell dendrite) AnnotationAssertion(Annotation( "CL:0000451") Annotation( "GOC:BHF") Annotation( "GOC:cjm") Annotation( "PMID:12200351") "A branched cellular projection (or cytoplasmic extension) that is extended from the surface of a dendritic immune cell, and which enables the cell to sample luminal pathogens and increase the surface area for antigen presentation to T cells.") -AnnotationAssertion( "pr") AnnotationAssertion( "2013-10-16T13:02:25Z") AnnotationAssertion( "cellular_component") AnnotationAssertion( "GO:0097511") @@ -85088,7 +83680,6 @@ EquivalentClasses( ObjectIntersection # Class: (cardiac myofibril) AnnotationAssertion(Annotation( "GOC:cjm") Annotation( "GOC:devbiol") "A cardiac myofibril is a myofibril specific to cardiac muscle cells.") -AnnotationAssertion( "pr") AnnotationAssertion( "2013-10-16T13:04:58Z") AnnotationAssertion( "cellular_component") AnnotationAssertion( "GO:0097512") @@ -85099,7 +83690,6 @@ SubClassOf( (sperm plasma membrane) AnnotationAssertion(Annotation( "GOC:cjm") "A plasma membrane that is part of a sperm cell.") -AnnotationAssertion( "pr") AnnotationAssertion( "2013-10-18T11:31:17Z") AnnotationAssertion( "cellular_component") AnnotationAssertion( "GO:0097524") @@ -85110,7 +83700,6 @@ SubClassOf( (myeloid leukocyte migration) AnnotationAssertion(Annotation( "GOC:cvs") Annotation( "PMID:22342843") Annotation( "PMID:24157461") "The movement of a myeloid leukocyte within or between different tissues and organs of the body.") -AnnotationAssertion( "pr") AnnotationAssertion( "2013-11-11T13:59:43Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0097529") @@ -85121,7 +83710,6 @@ SubClassOf( (granulocyte migration) AnnotationAssertion(Annotation( "GOC:cvs") Annotation( "PMID:24163421") Annotation( "PMID:24193336") "The movement of a granulocyte within or between different tissues and organs of the body.") -AnnotationAssertion( "pr") AnnotationAssertion( "2013-11-11T14:00:44Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0097530") @@ -85132,7 +83720,6 @@ SubClassOf( (mast cell migration) AnnotationAssertion(Annotation( "GOC:cvs") Annotation( "PMID:24152847") "The movement of a mast cell within or between different tissues and organs of the body.") -AnnotationAssertion( "pr") AnnotationAssertion( "2013-11-11T14:01:41Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0097531") @@ -85143,7 +83730,6 @@ SubClassOf( (lymphoid lineage cell migration) AnnotationAssertion(Annotation( "GOC:pr") Annotation( "PMID:22342843") "The orderly movement of a lymphoid lineage cell from one site to another. A lymphoid lineage cell, also called a lymphoid lineage restricted progenitor cell, is a progenitor cell restricted to the lymphoid lineage.") -AnnotationAssertion( "pr") AnnotationAssertion( "2013-11-28T10:47:15Z") AnnotationAssertion( "lymphoid lineage restricted progenitor cell migration") AnnotationAssertion( "biological_process") @@ -85155,7 +83741,6 @@ SubClassOf( (thymus epithelium morphogenesis) AnnotationAssertion(Annotation( "GOC:pr") Annotation( "PMID:22342843") "The process in which the thymus epithelium is generated and organized.") -AnnotationAssertion( "pr") AnnotationAssertion( "2013-11-28T10:51:03Z") AnnotationAssertion( "thymic epithelium morphogenesis") AnnotationAssertion( "biological_process") @@ -85168,7 +83753,6 @@ SubClassOf( ObjectSomeValuesFrom( (axonemal central pair) AnnotationAssertion(Annotation( "GOC:cilia") Annotation( "GOC:krc") Annotation( "PMID:24283352") "Part of the axoneme consisting of the inner two microtubule doublets of the 9+2 axoneme occurring in most motile cilia.") -AnnotationAssertion( "pr") AnnotationAssertion( "2013-12-12T11:07:09Z") AnnotationAssertion( "central pair") AnnotationAssertion( "axonemal microtubule central pair") @@ -85188,7 +83772,6 @@ SubClassOf( ObjectSomeValuesFrom( "GOC:cilia") Annotation( "GOC:krc") Annotation( "GOC:pr") Annotation( "PMID:5044758") Annotation( "PMID:5664206") Annotation( "Wikipedia:Axoneme") Annotation( "https://github.com/geneontology/go-ontology/issues/26128") "A cellular anatomical entity that is part of an axoneme consisting of a doublet microtubule.") AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/26128"^^xsd:anyURI) -AnnotationAssertion( "pr") AnnotationAssertion( "2013-12-12T11:19:29Z") AnnotationAssertion( "outer doublet") AnnotationAssertion( "axonemal outer doublet") @@ -85207,7 +83790,6 @@ SubClassOf( ObjectSomeValuesFrom( "GOC:vw") "A process in which a calcium ion is transported from one side of a membrane to the other into the cytosol by means of some agent such as a transporter or pore.") AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/23015"^^xsd:anyURI) -AnnotationAssertion( "pr") AnnotationAssertion( "2014-01-23T11:05:13Z") AnnotationAssertion( "calcium transmembrane import into cytosol") AnnotationAssertion( "cytosolic calcium ion transport") @@ -85219,7 +83801,6 @@ EquivalentClasses( ObjectIntersection # Class: (vacuole fusion) AnnotationAssertion(Annotation( "GOC:pr") Annotation( "GOC:vw") Annotation( "Wikipedia:Vacuole") "Merging of two or more vacuoles, or of vacuoles and vesicles within a cell to form a single larger vacuole.") -AnnotationAssertion( "pr") AnnotationAssertion( "2014-02-28T09:49:31Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0097576") @@ -85231,7 +83812,6 @@ SubClassOf( "GOC:vw") Annotation( "PMID:11932440") "The directed movement of potassium ions from inside of a cell, across the plasma membrane and into the extracellular region.") AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/14265"^^xsd:anyURI) -AnnotationAssertion( "pr") AnnotationAssertion( "2009-12-16T11:10:45Z") AnnotationAssertion(Annotation( "GOC:mah") "potassium export") AnnotationAssertion( "potassium ion export") @@ -85245,7 +83825,6 @@ EquivalentClasses( ObjectIntersection # Class: (distal tip cell migration) AnnotationAssertion(Annotation( "CL:0000661") Annotation( "GOC:mm2") Annotation( "PMID:24968003") "The orderly movement of a distal tip cell.") -AnnotationAssertion( "pr") AnnotationAssertion( "2014-08-20T16:06:53Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0097628") @@ -85256,7 +83835,6 @@ SubClassOf( (calcitonin family receptor activity) AnnotationAssertion(Annotation( "GOC:bhm") Annotation( "InterPro:IPR003287") Annotation( "PMID:10871296") Annotation( "PMID:12037140") Annotation( "PMID:18687416") "Combining with any member of the calcitonin family (e.g. adrenomedullin, adrenomedullin 2 (intermedin), amylin, calcitonin and calcitonin gene-related peptides (CGRPs)) to initiate a change in cell activity.") -AnnotationAssertion( "pr") AnnotationAssertion( "2014-09-08T15:32:19Z") AnnotationAssertion( "molecular_function") AnnotationAssertion( "GO:0097642") @@ -85266,7 +83844,6 @@ SubClassOf( (calcitonin family binding) AnnotationAssertion(Annotation( "GOC:bhm") Annotation( "InterPro:IPR021116") Annotation( "PMID:10871296") Annotation( "PMID:12037140") Annotation( "PMID:18687416") "Binding to a member of the calcitonin family (e.g. adrenomedullin, adrenomedullin 2 (intermedin), amylin, calcitonin and calcitonin gene-related peptides (CGRPs)).") -AnnotationAssertion( "pr") AnnotationAssertion( "2014-09-08T20:50:52Z") AnnotationAssertion( "molecular_function") AnnotationAssertion( "GO:0097644") @@ -85276,7 +83853,6 @@ SubClassOf( (G protein-coupled receptor complex) AnnotationAssertion(Annotation( "GOC:bhm") "A protein complex that contains G protein-coupled receptors.") -AnnotationAssertion( "pr") AnnotationAssertion( "2014-09-10T09:14:30Z") AnnotationAssertion( "G-protein coupled receptor complex") AnnotationAssertion( "cellular_component") @@ -85288,7 +83864,6 @@ SubClassOf( ObjectSomeValuesFrom( (A axonemal microtubule) AnnotationAssertion(Annotation( "GOC:cilia") Annotation( "ISBN:0716731363") "A complete microtubule with 13 protofilaments that fuses with an incomplete microtubule called B tubule (containing 10 protofilaments only) to form an axonemal outer doublet. Inner and outer dynein arms, as well as the radial spoke, are attached to the A tubule.") -AnnotationAssertion( "pr") AnnotationAssertion( "2014-09-10T20:41:28Z") AnnotationAssertion( "A tubule") AnnotationAssertion( "cellular_component") @@ -85300,7 +83875,6 @@ SubClassOf( ObjectSomeValuesFrom( (B axonemal microtubule) AnnotationAssertion(Annotation( "GOC:cilia") Annotation( "ISBN:0716731363") "An incomplete microtubule containing 10 protofilaments that fuses with a complete microtubule called A tubule (containing 13 protofilaments) to form an axonemal outer doublet.") -AnnotationAssertion( "pr") AnnotationAssertion( "2014-09-10T20:43:18Z") AnnotationAssertion( "B tubule") AnnotationAssertion( "cellular_component") @@ -85312,7 +83886,6 @@ SubClassOf( ObjectSomeValuesFrom( (intracellular vesicle) AnnotationAssertion(Annotation( "GOC:vesicles") "Any vesicle that is part of the intracellular region.") -AnnotationAssertion( "pr") AnnotationAssertion( "2016-03-29T17:39:45Z") AnnotationAssertion( "cellular_component") AnnotationAssertion( "GO:0097708") @@ -85324,7 +83897,6 @@ SubClassOf( ObjectSomeValuesFrom( (ciliary basal body-plasma membrane docking) AnnotationAssertion(Annotation( "GOC:cilia") Annotation( "PMID:13978319") Annotation( "PMID:23348840") Annotation( "PMID:23530209") Annotation( "PMID:25686250") Annotation( "PMID:26981235") "The docking of a cytosolic centriole/basal body to the plasma membrane via the ciliary transition fibers. In some species this may happen via an intermediate step, by first docking to the ciliary vesicle via the ciliary transition fibers. The basal body-ciliary vesicle then relocates to the plasma membrane, followed by the ciliary vesicle fusing with the plasma membrane, effectively attaching the basal body to the plasma membrane.") -AnnotationAssertion( "pr") AnnotationAssertion( "2016-08-05T16:12:33Z") AnnotationAssertion( "ciliary basal body docking") AnnotationAssertion( "biological_process") @@ -85338,7 +83910,6 @@ SubClassOf( ObjectSomeValuesFrom( (vesicle targeting, trans-Golgi to periciliary membrane compartment) AnnotationAssertion(Annotation( "GOC:cilia") Annotation( "PMID:20106869") Annotation( "PMID:23351793") Annotation( "PMID:24814148") Annotation( "PMID:26485645") "The process in which vesicles formed at the trans-Golgi network are directed to the plasma membrane surrounding the base of the cilium, including the ciliary pocket, mediated by molecules at the vesicle membrane and target membrane surfaces.") -AnnotationAssertion( "pr") AnnotationAssertion( "2016-08-05T16:16:28Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0097712") @@ -85349,7 +83920,6 @@ SubClassOf( ObjectSomeValuesFrom( (neural tissue regeneration) AnnotationAssertion(Annotation( "Wikipedia:Neuroregeneration") "The regrowth of neural tissue following its loss or destruction.") -AnnotationAssertion( "pr") AnnotationAssertion( "2016-08-25T13:14:27Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "neuroregeneration") @@ -85361,7 +83931,6 @@ SubClassOf( (sperm motility) AnnotationAssertion(Annotation( "GOC:cilia") Annotation( "GOC:krc") "Any process involved in the controlled movement of a sperm cell.") -AnnotationAssertion( "pr") AnnotationAssertion( "2016-09-01T12:00:45Z") AnnotationAssertion( "sperm movement") AnnotationAssertion( "biological_process") @@ -85375,7 +83944,6 @@ SubClassOf( (9+2 motile cilium) AnnotationAssertion(Annotation( "GOC:cilia") Annotation( "PMID:22118931") "A motile cilium where the axoneme has a ring of nine outer microtubule doublets plus two central microtubules (and is therefore called a 9+2 axoneme).") -AnnotationAssertion( "pr") AnnotationAssertion( "2016-09-27T15:26:34Z") AnnotationAssertion( "motile 9+2 cilium") AnnotationAssertion( "conventional motile cilium") @@ -85394,7 +83962,6 @@ SubClassOf( ObjectSomeValuesFrom( (extracellular exosome biogenesis) AnnotationAssertion(Annotation( "GOC:PARL") Annotation( "GOC:bf") Annotation( "PMID:19442504") Annotation( "PMID:25392495") "The assembly and secretion of an extracellular exosome, a membrane-bounded vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane.") -AnnotationAssertion( "pr") AnnotationAssertion( "2016-10-03T14:35:25Z") AnnotationAssertion( "exosome assembly or secretion") AnnotationAssertion( "exosome biogenesis") @@ -85409,7 +83976,6 @@ SubClassOf( (de novo centriole assembly) AnnotationAssertion(Annotation( "GOC:cilia") Annotation( "PMID:25047614") Annotation( "PMID:25291643") "Centriole assembly in which a centriole arises de novo, rather than by replication from an existing centriole. This process may occur via different mechanisms. Examples include the deuterosome pathway in multicilated epithelial animal cells and formation of centrioles during parthenogenesis in some insects.") -AnnotationAssertion( "pr") AnnotationAssertion( "2016-10-19T15:13:50Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "acentriolar basal body biogenesis") @@ -85428,7 +83994,6 @@ SubClassOf( (excitatory neuromuscular junction) AnnotationAssertion(Annotation( "GOC:dos") "The junction between the axon of a motor neuron and a muscle fiber. In response to the arrival of action potentials, the presynaptic button releases molecules of neurotransmitters into the synaptic cleft. These diffuse across the cleft and transmit the signal to the postsynaptic membrane of the muscle fiber, leading to a post-synaptic potential responsible for muscle contraction.") -AnnotationAssertion( "dos") AnnotationAssertion( "2013-10-14T12:02:51Z") AnnotationAssertion( "cellular_component") AnnotationAssertion( "GO:0098520") @@ -85438,7 +84003,6 @@ EquivalentClasses( ObjectIntersection # Class: (neuromuscular junction of skeletal muscle fiber) AnnotationAssertion(Annotation( "GOC:dos") "A neuromuscular junction in which the target muscle cell is a skeletal muscle fiber.") -AnnotationAssertion( "dos") AnnotationAssertion( "2013-10-14T12:04:32Z") AnnotationAssertion( "cellular_component") AnnotationAssertion( "GO:0098522") @@ -85450,7 +84014,6 @@ SubClassOf( ObjectSomeValuesFrom( (neuromuscular junction of myotube) AnnotationAssertion(Annotation( "GOC:dos") "A neuromuscular junction in which the target muscle cell is a myotube.") -AnnotationAssertion( "dos") AnnotationAssertion( "2013-10-14T12:05:12Z") AnnotationAssertion( "cellular_component") AnnotationAssertion( "GO:0098523") @@ -85461,7 +84024,6 @@ EquivalentClasses( ObjectIntersection # Class: (neuromuscular junction of somatic muscle myotube) AnnotationAssertion(Annotation( "GOC:dos") "A neuromuscular junction in which the target muscle cell is a somatic muscle myotube, such as an arthropod somatic muscle cell.") -AnnotationAssertion( "dos") AnnotationAssertion( "2013-10-14T12:05:43Z") AnnotationAssertion( "cellular_component") AnnotationAssertion( "GO:0098524") @@ -85471,7 +84033,6 @@ EquivalentClasses( ObjectIntersection # Class: (excitatory neuromuscular junction of somatic myotube) AnnotationAssertion(Annotation( "GOC:dos") "A neuromuscular junction that functions in the excitation of somatic muscle myotubes, such as an arthropod somatic muscle cells.") -AnnotationAssertion( "dos") AnnotationAssertion( "2013-10-14T12:06:08Z") AnnotationAssertion( "cellular_component") AnnotationAssertion( "GO:0098525") @@ -85481,7 +84042,6 @@ EquivalentClasses( ObjectIntersection # Class: (neuromuscular junction of somatic muscle) AnnotationAssertion(Annotation( "GOC:dos") "A neuromuscular junction in which the target muscle cell is a somatic muscle cell, such as those found in nematodes and arthropods.") -AnnotationAssertion( "dos") AnnotationAssertion( "2013-10-14T12:07:05Z") AnnotationAssertion( "cellular_component") AnnotationAssertion( "GO:0098527") @@ -85491,7 +84051,6 @@ EquivalentClasses( ObjectIntersection # Class: (skeletal muscle fiber differentiation) AnnotationAssertion(Annotation( "GOC:dos") "The process in which a relatively unspecialized cell acquires specialized features of a skeletal muscle fiber cell. Skeletal muscle fiber differentiation starts with myoblast fusion and the appearance of specific cell markers (this is the cell development step). Then individual skeletal muscle fibers fuse to form bigger myotubes and start to contract.") -AnnotationAssertion( "dos") AnnotationAssertion( "2013-10-15T14:00:34Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0098528") @@ -85512,7 +84071,6 @@ SubClassOf( ObjectSomeValuesFrom( (centriole assembly) AnnotationAssertion(Annotation( "GOC:dos") Annotation( "PMID:24075808") "A cellular process that results in the assembly of one or more centrioles.") -AnnotationAssertion( "dos") AnnotationAssertion( "2013-10-22T15:55:22Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0098534") @@ -85523,7 +84081,6 @@ SubClassOf( (de novo centriole assembly involved in multi-ciliated epithelial cell differentiation) AnnotationAssertion(Annotation( "GOC:cilia") Annotation( "GOC:dos") Annotation( "PMID:24075808") Annotation( "PMID:5111878") Annotation( "PMID:5661997") "Centriole assembly in which a centriole arises de novo by a process involving an electron-dense structure known as a deuterosome, rather than by duplication of an existing centriole, and occurring as part of multi-ciliated epithelial cell differentiation.") -AnnotationAssertion( "dos") AnnotationAssertion( "2013-10-22T16:03:13Z") AnnotationAssertion( "de novo centriole assembly") AnnotationAssertion( "de novo centriole assembly via deuterosome") @@ -85544,7 +84101,6 @@ SubClassOf( ObjectSomeValuesFrom( (deuterosome) AnnotationAssertion(Annotation( "GOC:cilia") Annotation( "GOC:dos") Annotation( "PMID:24075808") Annotation( "PMID:25047614") Annotation( "PMID:5661997") "A spherical, electron dense, cytoplasmic structure that is involved in de novo assembly of centrioles.") -AnnotationAssertion( "dos") AnnotationAssertion( "2013-10-22T16:21:19Z") AnnotationAssertion( "cellular_component") AnnotationAssertion( "GO:0098536") @@ -85557,7 +84113,6 @@ SubClassOf( ObjectAllValuesFrom( "GOC:dos") Annotation( "GOC:tfm") "OBSOLETE. Nucleus with two or more lobes connected by a thin filament that contains no internal chromatin. Examples include the nuclei of mature basophils, eosinophils and neutrophils in mice and humans.") AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/20764"^^xsd:anyURI) -AnnotationAssertion( "dos") AnnotationAssertion( "2013-10-22T18:31:36Z") AnnotationAssertion( "cellular_component") AnnotationAssertion( "GO:0098537") @@ -85569,7 +84124,6 @@ AnnotationAssertion(owl:deprecated " AnnotationAssertion(Annotation( "GOC:dos") "Reactions triggered in response to the presence of another organism that act to protect the cell or organism from damage caused by that organism.") AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/22173"^^xsd:anyURI) -AnnotationAssertion( "dos") AnnotationAssertion( "2013-11-11T12:59:11Z") AnnotationAssertion( "defence response incompatible interaction") AnnotationAssertion( "defence response to pathogen, incompatible interaction") @@ -85585,7 +84139,6 @@ SubClassOf( (maintenance of protein complex location) AnnotationAssertion(Annotation( "GOC:dos") "Any process in which a protein complex is maintained in a location and prevented from moving elsewhere. These include sequestration, stabilization to prevent transport elsewhere and the active retrieval of protein complexes that move away.") -AnnotationAssertion( "dos") AnnotationAssertion( "2013-11-15T18:20:16Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0098544") @@ -85596,7 +84149,6 @@ SubClassOf( (maintenance of protein complex location in cytoplasm) AnnotationAssertion(Annotation( "GOC:dos") "Any process in which a protein complex is maintained in a specific location within the cytoplasm and is prevented from moving elsewhere.") -AnnotationAssertion( "dos") AnnotationAssertion( "2013-11-15T20:49:15Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0098545") @@ -85606,7 +84158,6 @@ EquivalentClasses( ObjectIntersection # Class: (bounding membrane of organelle) AnnotationAssertion(Annotation( "GOC:dos") "The lipid bilayer that forms the outer-most layer of an organelle.") -AnnotationAssertion( "dos") AnnotationAssertion( "2014-02-26T13:41:31Z") AnnotationAssertion( "cellular_component") AnnotationAssertion( "GO:0098588") @@ -85618,7 +84169,6 @@ SubClassOf( (plasma membrane region) AnnotationAssertion(Annotation( "GOC:dos") "A membrane that is a (regional) part of the plasma membrane.") -AnnotationAssertion( "dos") AnnotationAssertion( "2014-03-06T11:55:32Z") AnnotationAssertion( "region of plasma membrane") AnnotationAssertion( "cellular_component") @@ -85631,7 +84181,6 @@ EquivalentClasses( ObjectIntersection # Class: (mucin granule) AnnotationAssertion(Annotation( "PMID:16377632") "A secretory granule that contains mucin.") -AnnotationAssertion( "dos") AnnotationAssertion( "2014-03-11T15:59:11Z") AnnotationAssertion( "cellular_component") AnnotationAssertion( "GO:0098594") @@ -85641,7 +84190,6 @@ SubClassOf( (cell-cell adhesion) AnnotationAssertion(Annotation( "GOC:dos") "The attachment of one cell to another cell via adhesion molecules.") -AnnotationAssertion( "dos") AnnotationAssertion( "2014-04-16T13:40:03Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "single organismal cell-cell adhesion") @@ -85783,7 +84331,6 @@ EquivalentClasses( ObjectIntersection # Class: (G protein-coupled serotonin receptor signaling pathway) AnnotationAssertion(Annotation( "GOC:mah") "The series of molecular signals generated as a consequence of a G protein-coupled serotonin receptor binding to one of its physiological ligands.") -AnnotationAssertion( "dos") AnnotationAssertion( "2016-12-21T12:07:58Z") AnnotationAssertion( "G-protein coupled serotonin receptor signaling pathway") AnnotationAssertion( "biological_process") @@ -85794,7 +84341,6 @@ EquivalentClasses( ObjectIntersection # Class: (serotonin receptor complex) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:bhm") Annotation( "GO_REF:0000088") Annotation( "PMID:16116092") "A protein complex that is capable of serotonin receptor activity.") -AnnotationAssertion( "dos") AnnotationAssertion( "2016-12-21T12:24:56Z") AnnotationAssertion( "5-HT receptor complex") AnnotationAssertion( "5-hydroxytryptamine receptor complex") @@ -85808,7 +84354,6 @@ EquivalentClasses( ObjectIntersection AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:bhm") Annotation( "GO_REF:0000088") "A protein complex that is capable of G protein-coupled serotonin receptor activity.") AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/12942"^^xsd:anyURI) -AnnotationAssertion( "dos") AnnotationAssertion( "2016-12-21T12:28:12Z") AnnotationAssertion( "G-protein coupled serotonin receptor complex") AnnotationAssertion( "cellular_component") @@ -85820,7 +84365,6 @@ SubClassOf( ObjectSomeValuesFrom( (glycinergic synapse) AnnotationAssertion(Annotation( "GOC:dos") "A synapse that uses glycine as a neurotransmitter.") -AnnotationAssertion( "dos") AnnotationAssertion( "2017-03-07T14:50:33Z") AnnotationAssertion( "cellular_component") AnnotationAssertion( "GO:0098690") @@ -85832,7 +84376,6 @@ SubClassOf( (dopaminergic synapse) AnnotationAssertion(Annotation( "GOC:dos") "A synapse that uses dopamine as a neurotransmitter.") -AnnotationAssertion( "dos") AnnotationAssertion( "2017-03-07T14:51:52Z") AnnotationAssertion( "cellular_component") AnnotationAssertion( "GO:0098691") @@ -85844,7 +84387,6 @@ SubClassOf( (regulation of synaptic vesicle cycle) AnnotationAssertion(Annotation( "GOC:dos") "Any process that modulates the frequency, rate or extent of the synaptic vesicle cycle.") -AnnotationAssertion( "dos") AnnotationAssertion( "2017-03-21T16:06:48Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0098693") @@ -85856,7 +84398,6 @@ EquivalentClasses( ObjectIntersection AnnotationAssertion(Annotation( "GOC:dos") "The directed movement of calcium ions from outside of a cell, across the plasma membrane and into the cytosol.") AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/24965"^^xsd:anyURI) -AnnotationAssertion( "mah") AnnotationAssertion( "2013-02-07T13:07:59Z") AnnotationAssertion( "calcium ion import into cell") AnnotationAssertion(Annotation( "GOC:vw") "calcium ion uptake into cell") @@ -85870,7 +84411,6 @@ SubClassOf( (carbohydrate import across plasma membrane) AnnotationAssertion(Annotation( "GOC:dos") "The directed movement of a carbohydrate from outside of a cell, across the plasma membrane and into the cytosol.") -AnnotationAssertion( "pr") AnnotationAssertion( "2012-05-31T02:45:02Z") AnnotationAssertion( "carbohydrate import into cell") AnnotationAssertion( "biological_process") @@ -85881,7 +84421,6 @@ EquivalentClasses( ObjectIntersection # Class: (D-glucose import across plasma membrane) AnnotationAssertion(Annotation( "GOC:dos") "The directed movement of D-glucose from outside of a cell, across the plasma membrane and into the cytosol.") -AnnotationAssertion( "al") AnnotationAssertion( "2012-12-06T14:54:07Z") AnnotationAssertion( "glucose import across plasma membrane") AnnotationAssertion( "glucose import into cell") @@ -85894,7 +84433,6 @@ EquivalentClasses( ObjectIntersection # Class: (iron ion import across plasma membrane) AnnotationAssertion(Annotation( "GOC:mah") Annotation( "PMID:8321236") "The directed movement of iron ions from outside of a cell, across the plasma membrane and into the cytosol.") -AnnotationAssertion( "pr") AnnotationAssertion( "2012-12-20T08:29:00Z") AnnotationAssertion( "iron ion import into cell") AnnotationAssertion( "biological_process") @@ -85909,7 +84447,6 @@ EquivalentClasses( ObjectIntersection # Class: (L-glutamate import across plasma membrane) AnnotationAssertion(Annotation( "GOC:dos") "The directed movement of L-glutamate from outside of a cell, across the plasma membrane and into the cytosol.") -AnnotationAssertion( "mah") AnnotationAssertion( "2013-06-12T12:32:47Z") AnnotationAssertion( "L-glutamate(1-) import across plasma membrane") AnnotationAssertion( "L-glutamate import into cell") @@ -85922,7 +84459,6 @@ EquivalentClasses( ObjectIntersection # Class: (sodium ion import across plasma membrane) AnnotationAssertion(Annotation( "GOC:dos") "The directed movement of sodium ions from outside of a cell, across the plasma membrane and into the cytosol.") -AnnotationAssertion( "pr") AnnotationAssertion( "2012-08-03T16:55:52Z") AnnotationAssertion( "sodium import") AnnotationAssertion( "sodium ion import into cell") @@ -86238,7 +84774,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of AV node cell action potential) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:mtg_cardiac_conduct_nov11") "Any process that modulates the frequency, rate or extent of action potential creation, propagation or termination in an atrioventricular node myocyte. This typically occurs via modulation of the activity or expression of voltage-gated ion channels.") -AnnotationAssertion( "tb") AnnotationAssertion( "2011-11-10T08:58:56Z") AnnotationAssertion( "regulation of AV node cardiac muscle cell action potential") AnnotationAssertion( "regulation of atrioventricular node cardiac muscle cell action potential") @@ -86251,7 +84786,6 @@ SubClassOf( ObjectSomeValuesFrom( (regulation of bundle of His cell action potential) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:mtg_cardiac_conduct_nov11") "Any process that modulates the frequency, rate or extent of action potential creation, propagation or termination in a cardiac muscle cell of the bundle of His. This typically occurs via modulation of the activity or expression of voltage-gated ion channels.") -AnnotationAssertion( "dph") AnnotationAssertion( "2011-11-15T12:01:18Z") AnnotationAssertion( "regulation of bundle of His cardiac muscle cell action potential") AnnotationAssertion( "biological_process") @@ -86262,7 +84796,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of Purkinje myocyte action potential) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:mtg_cardiac_conduct_nov11") "Any process that modulates the frequency, rate or extent of action potential creation, propagation or termination in a Purkinje myocyte. This typically occurs via modulation of the activity or expression of voltage-gated ion channels.") -AnnotationAssertion( "tb") AnnotationAssertion( "2011-11-10T08:58:56Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0098906") @@ -86273,7 +84806,6 @@ SubClassOf( ObjectSomeValuesFrom( (regulation of SA node cell action potential) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:mtg_cardiac_conduct_nov11") "Any process that modulates the frequency, rate or extent of action potential creation, propagation or termination in an SA node cardiac myocyte. This typically occurs via modulation of the activity or expression of voltage-gated ion channels.") -AnnotationAssertion( "tb") AnnotationAssertion( "2011-11-10T08:50:15Z") AnnotationAssertion( "regulation of SA node cardiac muscle cell action potential") AnnotationAssertion( "regulation of SAN cardiac muscle cell action potential") @@ -86298,7 +84830,6 @@ SubClassOf( ObjectSomeValuesFrom( (regulation of cardiac muscle cell action potential involved in regulation of contraction) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:mtg_cardiac_conduct_nov11") "Any process that modulates the frequency, rate or extent of action potential creation, propagation or termination in a cardiac muscle cell contributing to the regulation of its contraction.") -AnnotationAssertion( "tb") AnnotationAssertion( "2011-11-10T07:45:11Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0098909") @@ -86310,7 +84841,6 @@ SubClassOf( ObjectSomeValuesFrom( (regulation of atrial cardiac muscle cell action potential) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:mtg_cardiac_conduct_nov11") "Any process that modulates the frequency, rate or extent of action potential creation, propagation or termination in an atrial cardiac muscle cell contributing to the regulation of its contraction. This typically occurs via modulation of the activity or expression of voltage-gated ion channels.") -AnnotationAssertion( "tb") AnnotationAssertion( "2011-11-10T08:49:13Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0098910") @@ -86322,7 +84852,6 @@ SubClassOf( ObjectSomeValuesFrom( (regulation of ventricular cardiac muscle cell action potential) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:mtg_cardiac_conduct_nov11") "Any process that modulates the frequency, rate or extent of action potential creation, propagation or termination in a ventricular cardiac muscle cell contributing to the regulation of its contraction. This typically occurs via modulation of the activity or expression of voltage-gated ion channels.") -AnnotationAssertion( "tb") AnnotationAssertion( "2011-11-10T07:59:36Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0098911") @@ -86777,7 +85306,6 @@ EquivalentClasses( ObjectIntersection # Class: (presynaptic actin cytoskeleton organization) AnnotationAssertion(Annotation( "GOC:dos") "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of cytoskeletal structures comprising actin filaments and their associated proteins in the presynaptic actin cytoskeleton.") -AnnotationAssertion( "dos") AnnotationAssertion( "2017-06-09T18:34:19Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0099140") @@ -86788,7 +85316,6 @@ EquivalentClasses( ObjectIntersection # Class: (presynaptic actin cytoskeleton) AnnotationAssertion(Annotation( "GOC:dos") "The actin cytoskeleton that is part of a presynapse.") -AnnotationAssertion( "dos") AnnotationAssertion( "2017-06-09T18:36:19Z") AnnotationAssertion( "cellular_component") AnnotationAssertion( "GO:0099143") @@ -86799,7 +85326,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of exocytic insertion of neurotransmitter receptor to postsynaptic membrane) AnnotationAssertion(Annotation( "GOC:dos") "Any process that modulates the frequency, rate or extent of exocytic fusion of neurotransmitter receptor containing vesicles into the postsynaptic membrane.") -AnnotationAssertion( "dos") AnnotationAssertion( "2017-06-09T18:49:26Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0099145") @@ -86814,7 +85340,6 @@ SubClassOf( ObjectSomeValuesFrom( (cell-cell signaling via exosome) AnnotationAssertion(Annotation( "GOC:dos") Annotation( "PMID:19837038") "Cell-cell signaling in which the ligand is carried between cells by an exosome.") -AnnotationAssertion( "dos") AnnotationAssertion( "2017-07-05T16:40:45Z") AnnotationAssertion( "exosome mediated") AnnotationAssertion( "biological_process") @@ -86825,7 +85350,6 @@ EquivalentClasses( ObjectIntersection # Class: (trans-synaptic signaling via exosome) AnnotationAssertion(Annotation( "GOC:dos") Annotation( "PMID:19837038") "Transynaptic signaling in which the ligand is carried across the synapse by an exosome.") -AnnotationAssertion( "dos") AnnotationAssertion( "2017-07-05T16:49:44Z") AnnotationAssertion( "exosome mediated transynaptic signalling") AnnotationAssertion( "trans-synaptic signalling via exosome") @@ -86838,7 +85362,6 @@ EquivalentClasses( ObjectIntersection # Class: (postsynaptic intermediate filament cytoskeleton) AnnotationAssertion(Annotation( "GOC:dos") Annotation( "PMID:25869803") "The intermediate filament cytoskeleton that is part of a postsynapse.") -AnnotationAssertion( "dos") AnnotationAssertion( "2017-08-28T15:26:08Z") AnnotationAssertion( "cellular_component") AnnotationAssertion( "GO:0099160") @@ -86858,7 +85381,6 @@ EquivalentClasses( ObjectIntersection # Class: (postsynaptic modulation of chemical synaptic transmission) AnnotationAssertion(Annotation( "GOC:dos") "Any process, acting in the postsynapse that results in modulation of chemical synaptic transmission.") -AnnotationAssertion( "dos") AnnotationAssertion( "2017-09-11T17:09:17Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0099170") @@ -86869,7 +85391,6 @@ EquivalentClasses( ObjectIntersection # Class: (presynaptic modulation of chemical synaptic transmission) AnnotationAssertion(Annotation( "GOC:dos") "Any process, acting in the presynapse that results in modulation of chemical synaptic transmission.") -AnnotationAssertion( "dos") AnnotationAssertion( "2017-09-11T17:09:31Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0099171") @@ -86944,7 +85465,6 @@ EquivalentClasses( ObjectIntersection # Class: (presynaptic intermediate filament cytoskeleton) AnnotationAssertion(Annotation( "GOC:dos") "The intermediate filament cytoskeleton that is part of a presynapse.") -AnnotationAssertion( "dos") AnnotationAssertion( "2017-12-01T18:10:21Z") AnnotationAssertion( "cellular_component") AnnotationAssertion( "GO:0099182") @@ -86955,7 +85475,6 @@ EquivalentClasses( ObjectIntersection # Class: (postsynaptic intermediate filament cytoskeleton organization) AnnotationAssertion(Annotation( "GOC:dos") "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of cytoskeletal structures comprised of intermediate filament and their associated proteins in the postsynaptic cytoskeleton.") -AnnotationAssertion( "dos") AnnotationAssertion( "2017-12-20T13:47:30Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0099185") @@ -86967,7 +85486,6 @@ SubClassOf( ObjectSomeValuesFrom( (presynaptic cytoskeleton organization) AnnotationAssertion(Annotation( "GOC:dos") "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of cytoskeletal structures and their associated proteins in the presynaptic cytoskeleton.") -AnnotationAssertion( "dos") AnnotationAssertion( "2017-12-20T15:05:34Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0099187") @@ -86978,7 +85496,6 @@ SubClassOf( ObjectSomeValuesFrom( (postsynaptic cytoskeleton organization) AnnotationAssertion(Annotation( "GOC:dos") "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of cytoskeletal structures comprising cytoskeletal filaments and their associated proteins in the postsynaptic cytoskeleton.") -AnnotationAssertion( "dos") AnnotationAssertion( "2017-12-20T15:06:57Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0099188") @@ -87048,7 +85565,6 @@ SubClassOf( ObjectSomeValuesFrom( (actin filament-based transport) AnnotationAssertion(Annotation( "GOC:dos") Annotation( "GOC:dph") Annotation( "GOC:mah") Annotation( "GOC:tb") "The transport of organelles or other particles from one location in the cell to another along actin filaments.") -AnnotationAssertion( "tb") AnnotationAssertion( "2009-05-27T10:56:08Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0099515") @@ -87533,7 +86049,6 @@ SubClassOf( (regulation of skeletal muscle contraction by action potential) AnnotationAssertion(Annotation( "GOC:cjm") Annotation( "GOC:obol") "Any action potential process that regulates skeletal muscle contraction.") -AnnotationAssertion( "cjm") AnnotationAssertion( "2015-04-02T04:13:19Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0100001") @@ -87584,7 +86099,6 @@ SubClassOf( ObjectSomeValuesFrom( (cellular response to environmental stimulus) AnnotationAssertion(Annotation( "GOC:dos") "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an environmental stimulus.") -AnnotationAssertion( "dos") AnnotationAssertion( "2017-02-17T16:02:42Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0104004") @@ -87594,7 +86108,6 @@ SubClassOf( (regulation of inflammatory response to wounding) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:BHF_miRNA") Annotation( "GOC:rph") Annotation( "PMID:26022821") "Any process that modulates the frequency, rate or extent of the inflammatory response to wounding.") -AnnotationAssertion( "hjd") AnnotationAssertion( "2017-04-28T20:03:14Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0106014") @@ -87604,7 +86117,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of inflammatory response to wounding) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:BHF_miRNA") Annotation( "GOC:rph") Annotation( "PMID:26022821") "Any process that stops, prevents, or reduces the frequency, rate or extent of the inflammatory response to wounding.") -AnnotationAssertion( "hjd") AnnotationAssertion( "2017-04-28T20:09:46Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0106015") @@ -87615,7 +86127,6 @@ SubClassOf( (positive regulation of inflammatory response to wounding) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:BHF_miRNA") Annotation( "GOC:rph") Annotation( "PMID:26022821") "Any process that activates or increases the frequency, rate or extent of the inflammatory response to wounding.") -AnnotationAssertion( "hjd") AnnotationAssertion( "2017-04-28T20:16:31Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0106016") @@ -87626,7 +86137,6 @@ SubClassOf( (neuron projection organization) AnnotationAssertion(Annotation( "GOC:aruk") Annotation( "GOC:bc") Annotation( "PMID:11585923") "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a prolongation or process extending from a neuron, e.g. an axon, or a dendrite.") -AnnotationAssertion( "hjd") AnnotationAssertion( "2017-06-23T18:30:18Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0106027") @@ -87636,7 +86146,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of cardiac muscle cell contraction) AnnotationAssertion(Annotation( "PMID:19525381") "Any process that activates or increases the frequency, rate or extent of cardiac muscle cell contraction.") -AnnotationAssertion( "hjd") AnnotationAssertion( "2018-07-26T16:05:16Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0106134") @@ -87646,7 +86155,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of cardiac muscle cell contraction) AnnotationAssertion(Annotation( "PMID:19525381") "Any process that stops, prevents, or reduces the frequency, rate or extent of cardiac muscle cell contraction.") -AnnotationAssertion( "hjd") AnnotationAssertion( "2018-07-26T16:10:17Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0106135") @@ -87657,7 +86165,6 @@ SubClassOf( ObjectSomeValuesFrom( (regulation of vesicle fusion with Golgi apparatus) AnnotationAssertion(Annotation( "GOC:se") Annotation( "PMID:26195667") "Any process that modulates the frequency, rate or extent of vesicle fusion with Golgi apparatus.") -AnnotationAssertion( "hjd") AnnotationAssertion( "2019-06-27T15:12:22Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0106214") @@ -87667,7 +86174,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of vesicle fusion with Golgi apparatus) AnnotationAssertion(Annotation( "GOC:se") Annotation( "PMID:26195667") "Any process that stops, prevents or reduces the frequency, rate or extent of vesicle fustion with Golgi apparatus.") -AnnotationAssertion( "hjd") AnnotationAssertion( "2019-06-27T15:17:17Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0106215") @@ -87677,7 +86183,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of vesicle fusion with Golgi apparatus) AnnotationAssertion(Annotation( "GOC:se") Annotation( "PMID:26195667") "Any process that activates or increases the frequency, rate or extent of vesicle fusion with Golgi apparatus.") -AnnotationAssertion( "hjd") AnnotationAssertion( "2019-06-27T15:20:59Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0106216") @@ -87687,7 +86192,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of kainate selective glutamate receptor signaling pathway) AnnotationAssertion(Annotation( "PMID:12597860") "Any process that modulates the frequency, rate or extent of the kainate selective glutamate receptor signaling pathway.") -AnnotationAssertion( "hjd") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0106426") AnnotationAssertion(rdfs:label "regulation of kainate selective glutamate receptor signaling pathway") @@ -87696,7 +86200,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of kainate selective glutamate receptor signaling pathway) AnnotationAssertion(Annotation( "PMID:12597860") "Any process that stops, prevents or reduces the frequency, rate or extent of the kainate selective glutamate receptor signaling pathway.") -AnnotationAssertion( "hjd") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0106427") AnnotationAssertion(rdfs:label "negative regulation of kainate selective glutamate receptor signaling pathway") @@ -87706,7 +86209,6 @@ EquivalentClasses( ObjectIntersection AnnotationAssertion(Annotation( "PMID:12597860") "Any process that activates or increases the frequency, rate or extent of the kainate selective glutamate receptor signaling pathway.") AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/23558"^^xsd:anyURI) -AnnotationAssertion( "hjd") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0106428") AnnotationAssertion(rdfs:label "positive regulation of kainate selective glutamate receptor signaling pathway") @@ -87715,7 +86217,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of basement membrane organization) AnnotationAssertion(Annotation( "GOC:ha") Annotation( "PMID:27404358") "Any process that modulates the frequency, rate or extent of the assembly, disassembly or arrangement of constituent parts of the basement membrane.") -AnnotationAssertion( "kmv") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0110011") AnnotationAssertion(rdfs:label "regulation of basement membrane organization") @@ -87725,7 +86226,6 @@ SubClassOf( (regulation of actomyosin structure organization) AnnotationAssertion(Annotation( "GOC:lf") Annotation( "PMID:22790195") "Any process that modulates the frequency, rate or extent of the assembly, arrangement of constituent parts, or disassembly of cytoskeletal structures containing both actin and myosin or paramyosin.") -AnnotationAssertion( "kmv") AnnotationAssertion( "2017-06-20T19:28:58Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0110020") @@ -87735,7 +86235,6 @@ EquivalentClasses( ObjectIntersection # Class: (cardiac muscle myoblast proliferation) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:BHF_miRNA") Annotation( "GOC:rph") Annotation( "PMID:26512644") "The multiplication or reproduction of cardiac muscle myoblasts, resulting in the expansion of a cardiac muscle myoblast cell population. A cardiac myoblast is a precursor cell that has been committed to a cardiac muscle cell fate but retains the ability to divide and proliferate throughout life.") -AnnotationAssertion( "kmv") AnnotationAssertion( "2017-06-29T14:35:24Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0110021") @@ -87745,7 +86244,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of cardiac muscle myoblast proliferation) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:BHF_miRNA") Annotation( "GOC:rph") Annotation( "PMID:26512644") "Any process that modulates the frequency, rate or extent of cardiac muscle myoblast proliferation.") -AnnotationAssertion( "kmv") AnnotationAssertion( "2017-06-29T15:11:47Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0110022") @@ -87755,7 +86253,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of cardiac muscle myoblast proliferation) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:BHF_miRNA") Annotation( "GOC:rph") Annotation( "PMID:26512644") "Any process that stops, prevents, or reduces the frequency, rate or extent of cardiac muscle myoblast proliferation.") -AnnotationAssertion( "kmv") AnnotationAssertion( "2017-06-29T15:18:30Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0110023") @@ -87765,7 +86262,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of cardiac muscle myoblast proliferation) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:BHF_miRNA") Annotation( "GOC:rph") Annotation( "PMID:26512644") "Any process that activates or increases the frequency, rate or extent of cardiac muscle myoblast proliferation.") -AnnotationAssertion( "kmv") AnnotationAssertion( "2017-06-29T15:24:16Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0110024") @@ -87775,7 +86271,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of actin filament organization) AnnotationAssertion(Annotation( "GOC:kmv") "Any process that modulates the frequency, rate or extent of actin filament organization.") -AnnotationAssertion( "kmv") AnnotationAssertion( "2017-09-20T19:52:57Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0110053") @@ -87787,7 +86282,6 @@ SubClassOf( ObjectSomeValuesFrom( (regulation of blood vessel endothelial cell differentiation) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:BHF_miRNA") Annotation( "GOC:rph") Annotation( "PMID:23072816") "Any process that modulates the frequency, rate or extent of blood vessel endothelial cell differentiation.") -AnnotationAssertion( "kmv") AnnotationAssertion( "2017-10-23T14:32:09Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0110057") @@ -87798,7 +86292,6 @@ SubClassOf( (positive regulation of blood vessel endothelial cell differentiation) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:BHF_miRNA") Annotation( "GOC:rph") Annotation( "PMID:23072816") "Any process that activates or increases the frequency, rate or extent of blood vessel endothelial cell differentiation.") -AnnotationAssertion( "kmv") AnnotationAssertion( "2017-10-23T14:38:19Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0110058") @@ -87809,7 +86302,6 @@ SubClassOf( (negative regulation of blood vessel endothelial cell differentiation) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:BHF_miRNA") Annotation( "GOC:rph") Annotation( "PMID:23072816") "Any process that stops, prevents, or reduces the frequency, rate or extent of blood vessel endothelial cell differentiation.") -AnnotationAssertion( "kmv") AnnotationAssertion( "2017-10-23T14:47:29Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0110059") @@ -87820,7 +86312,6 @@ SubClassOf( (ammonium transmembrane transporter complex) AnnotationAssertion(Annotation( "GOC:bhm") Annotation( "PMID:17026539") Annotation( "PMID:23463773") "High affinity ammonium transporter complex that enables the transfer of ammonium from one side of a membrane to the other.") -AnnotationAssertion( "kmv") AnnotationAssertion( "2017-11-20T15:21:10Z") AnnotationAssertion(Annotation( "GOC:bhm") "AMT1 complex") AnnotationAssertion( "cellular_component") @@ -87834,7 +86325,6 @@ SubClassOf( ObjectSomeValuesFrom( (vesicle-mediated intercellular transport) AnnotationAssertion(Annotation( "GOC:sp") Annotation( "PMID:29328915") Annotation( "PMID:29328916") "A cellular transport process in which transported substances are moved in extracellular vesicles between cells; transported substances are enclosed in the vesicle lumen or located in the extracellular vesicle membrane.") -AnnotationAssertion( "kmv") AnnotationAssertion( "2018-01-29T14:46:52Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "endosomal trafficking") @@ -87845,7 +86335,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of placenta blood vessel development) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:BHF_miRNA") Annotation( "GOC:rph") Annotation( "PMID:27748453") "Any process that modulates the frequency, rate or extent of placenta blood vessel development.") -AnnotationAssertion( "kmv") AnnotationAssertion( "2018-02-01T14:49:12Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0110079") @@ -87856,7 +86345,6 @@ SubClassOf( ObjectSomeValuesFrom( (positive regulation of placenta blood vessel development) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:BHF_miRNA") Annotation( "GOC:rph") Annotation( "PMID:27748453") "Any process that activates or increases the frequency, rate or extent of placenta blood vessel development.") -AnnotationAssertion( "kmv") AnnotationAssertion( "2018-02-01T14:55:30Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0110080") @@ -87866,7 +86354,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of placenta blood vessel development) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:BHF_miRNA") Annotation( "GOC:rph") Annotation( "PMID:27748453") "Any process that stops, prevents or reduces the frequency, rate or extent of placenta blood vessel development.") -AnnotationAssertion( "kmv") AnnotationAssertion( "2018-02-01T15:01:11Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0110081") @@ -87876,7 +86363,6 @@ EquivalentClasses( ObjectIntersection # Class: (hippocampal neuron apoptotic process) AnnotationAssertion(Annotation( "GOC:sl") Annotation( "PMID:18940801") "Any apoptotic process that occurs in a hippocampal neuron.") -AnnotationAssertion( "kmv") AnnotationAssertion( "2018-02-13T21:06:23Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0110088") @@ -87886,7 +86372,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of hippocampal neuron apoptotic process) AnnotationAssertion(Annotation( "GOC:sl") Annotation( "PMID:18940801") "Any process that modulates the occurrence or rate of cell death by apoptotic process in hippocampal neurons.") -AnnotationAssertion( "kmv") AnnotationAssertion( "2018-02-13T21:18:29Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0110089") @@ -87896,7 +86381,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of hippocampal neuron apoptotic process) AnnotationAssertion(Annotation( "GOC:sl") Annotation( "PMID:18940801") "Any process that activates or increases the frequency, rate or extent of cell death by apoptotic process in hippocampal neurons.") -AnnotationAssertion( "kmv") AnnotationAssertion( "2018-02-13T21:22:18Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0110090") @@ -87906,7 +86390,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of hippocampal neuron apoptotic process) AnnotationAssertion(Annotation( "GOC:sl") Annotation( "PMID:18940801") "Any process that stops, prevents, or reduces the frequency, rate or extent of cell death by apoptotic process in hippocampal neurons.") -AnnotationAssertion( "kmv") AnnotationAssertion( "2018-02-13T21:25:01Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0110091") @@ -87916,7 +86399,6 @@ EquivalentClasses( ObjectIntersection # Class: (cellular detoxification of aldehyde) AnnotationAssertion(Annotation( "GOC:vw") Annotation( "PMID:25656103") "Any process carried out at the cellular level that reduces or removes the toxicity of an aldehyde. These may include transport of aldehydes away from sensitive areas and to compartments or complexes whose purpose is sequestration of the toxic substance.") -AnnotationAssertion( "kmv") AnnotationAssertion( "2018-02-16T21:19:20Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0110095") @@ -87927,7 +86409,6 @@ SubClassOf( ObjectSomeValuesFrom( (cellular response to aldehyde) AnnotationAssertion(Annotation( "GOC:vw") Annotation( "PMID:25656103") "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an aldehyde stimulus.") -AnnotationAssertion( "kmv") AnnotationAssertion( "2018-02-16T21:29:18Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0110096") @@ -87937,7 +86418,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of animal organ morphogenesis) AnnotationAssertion(Annotation( "GOC:kmv") "Any process that activates or increases the frequency, rate or extent of animal organ morphogenesis.") -AnnotationAssertion( "kmv") AnnotationAssertion( "2018-07-05T14:10:14Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0110110") @@ -87948,7 +86428,6 @@ SubClassOf( ObjectSomeValuesFrom( (negative regulation of animal organ morphogenesis) AnnotationAssertion(Annotation( "GOC:kmv") "Any process that stops, prevents, or reduces the frequency, rate or extent of animal organ morphogenesis.") -AnnotationAssertion( "kmv") AnnotationAssertion( "2018-07-05T14:25:21Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0110111") @@ -87959,7 +86438,6 @@ SubClassOf( ObjectSomeValuesFrom( (regulation of lipid transporter activity) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:BHF_miRNA") Annotation( "GOC:rph") Annotation( "PMID:27365390") "Any process that modulates the frequency, rate, or extent of lipid transporter activity.") -AnnotationAssertion( "kmv") AnnotationAssertion( "2018-07-06T18:53:55Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0110112") @@ -87971,7 +86449,6 @@ SubClassOf( ObjectSomeValuesFrom( (positive regulation of lipid transporter activity) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:BHF_miRNA") Annotation( "GOC:rph") Annotation( "PMID:27365390") "Any process that increases the frequency, rate, or extent of lipid transporter activity.") -AnnotationAssertion( "kmv") AnnotationAssertion( "2018-07-06T19:14:13Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0110113") @@ -87983,7 +86460,6 @@ SubClassOf( ObjectSomeValuesFrom( (negative regulation of lipid transporter activity) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:BHF_miRNA") Annotation( "GOC:rph") Annotation( "PMID:27365390") "Any process that decreases the frequency, rate, or extent of lipid transporter activity.") -AnnotationAssertion( "kmv") AnnotationAssertion( "2018-07-06T19:21:44Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0110114") @@ -87995,7 +86471,6 @@ SubClassOf( ObjectSomeValuesFrom( (regulation of compound eye photoreceptor cell differentiation) AnnotationAssertion(Annotation( "GOC:ha") Annotation( "PMID:16377567") "Any process that modulates the frequency, rate or extent of compound eye photoreceptor cell differentiation.") -AnnotationAssertion( "kmv") AnnotationAssertion( "2018-07-16T18:08:49Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0110116") @@ -88005,7 +86480,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of compound eye photoreceptor cell differentiation) AnnotationAssertion(Annotation( "GOC:ha") Annotation( "PMID:16377567") "Any process that activates or increases the frequency, rate or extent of compound eye photoreceptor cell differentiation.") -AnnotationAssertion( "kmv") AnnotationAssertion( "2018-07-16T18:13:28Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0110117") @@ -88015,7 +86489,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of compound eye photoreceptor cell differentiation) AnnotationAssertion(Annotation( "GOC:ha") Annotation( "PMID:16377567") "Any process that stops, prevents, or reduces the frequency, rate or extent of compound eye photoreceptor cell differentiation.") -AnnotationAssertion( "kmv") AnnotationAssertion( "2018-07-16T18:15:52Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0110118") @@ -88025,7 +86498,6 @@ EquivalentClasses( ObjectIntersection # Class: (myotube cell migration) AnnotationAssertion(Annotation( "GOC:ha") Annotation( "PMID:29122742") "The orderly movement of a myotube cell from one site to another, often during the development of a multicellular organism. Myotubes are multinucleated cells that are formed when proliferating myoblasts exit the cell cycle, differentiate, and fuse.") -AnnotationAssertion( "kmv") AnnotationAssertion( "2018-08-22T20:58:09Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0110122") @@ -88035,7 +86507,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of myotube cell migration) AnnotationAssertion(Annotation( "GOC:ha") Annotation( "PMID:29122742") "Any process that modulates the frequency, rate or extent of myotube cell migration.") -AnnotationAssertion( "kmv") AnnotationAssertion( "2018-08-22T21:06:53Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0110123") @@ -88045,7 +86516,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of myotube cell migration) AnnotationAssertion(Annotation( "GOC:ha") Annotation( "PMID:29122742") "Any process that activates, maintains or increases the frequency, rate or extent of myotube cell migration.") -AnnotationAssertion( "kmv") AnnotationAssertion( "2018-08-22T21:09:38Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0110124") @@ -88055,7 +86525,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of myotube cell migration) AnnotationAssertion(Annotation( "GOC:ha") Annotation( "PMID:29122742") "Any process that stops, prevents, or reduces the frequency, rate or extent of myotube cell migration.") -AnnotationAssertion( "kmv") AnnotationAssertion( "2018-08-22T21:12:47Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0110125") @@ -88068,7 +86537,6 @@ AnnotationAssertion(Annotation( "https://github.com/geneontology/go-ontology/issues/24200"^^xsd:anyURI) AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/26424"^^xsd:anyURI) AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/28978"^^xsd:anyURI) -AnnotationAssertion( "kmv") AnnotationAssertion( "2019-08-12T18:01:37Z") AnnotationAssertion( "cellular anatomical entity") AnnotationAssertion( "cellular_component") @@ -88084,7 +86552,6 @@ SubClassOf( "PMID:24030726") "Any process that modulates the frequency, rate or extent of glutamatergic neuron differentiation.") AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/13107"^^xsd:anyURI) -AnnotationAssertion( "krc") AnnotationAssertion( "2017-03-01T16:10:27Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0120006") @@ -88095,7 +86562,6 @@ EquivalentClasses( ObjectIntersection AnnotationAssertion(Annotation( "PMID:24030726") "Any process that stops, prevents or reduces the frequency, rate or extent of glutamatergic neuron differentiation.") AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/13107"^^xsd:anyURI) -AnnotationAssertion( "krc") AnnotationAssertion( "2017-03-01T16:25:50Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0120007") @@ -88106,7 +86572,6 @@ EquivalentClasses( ObjectIntersection AnnotationAssertion(Annotation( "PMID:24030726") "Any process that activates or increases the frequency, rate or extent of glutamatergic neuron differentiation.") AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/13107"^^xsd:anyURI) -AnnotationAssertion( "krc") AnnotationAssertion( "2017-03-01T16:35:45Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0120008") @@ -88117,7 +86582,6 @@ EquivalentClasses( ObjectIntersection AnnotationAssertion(Annotation( "GOC:cvs") Annotation( "PMID:20472043") "Binding to somatostatin, a polypeptide hormone involved in regulating pancreatic alpha and pancreatic beta cells and controlling growth hormone secretion as well as many other functions. Somatostatin is produced by several cell types including pancreatic delta cells. There are several different mature forms of somatostatin.") AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/13143"^^xsd:anyURI) -AnnotationAssertion( "krc") AnnotationAssertion( "2017-03-17T14:54:21Z") AnnotationAssertion( "molecular_function") AnnotationAssertion( "GO:0120023") @@ -88128,7 +86592,6 @@ EquivalentClasses( ObjectIntersection AnnotationAssertion(Annotation( "GOC:krc") "A prolongation or process extending from a cell and that is bounded by plasma membrane, e.g. a cilium, lamellipodium, or axon.") AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/13193"^^xsd:anyURI) -AnnotationAssertion( "krc") AnnotationAssertion( "2017-03-21T17:26:07Z") AnnotationAssertion( "cellular_component") AnnotationAssertion( "GO:0120025") @@ -88139,7 +86602,6 @@ EquivalentClasses( ObjectIntersection AnnotationAssertion(Annotation( "GOC:mah") Annotation( "PMID:9762918") "The directed movement of hydrogen ions (protons) from inside a cell, across the plasma membrane and into the extracellular region.") AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/13271"^^xsd:anyURI) -AnnotationAssertion( "krc") AnnotationAssertion( "2017-03-31T17:39:03Z") AnnotationAssertion( "hydrogen ion export from cell") AnnotationAssertion( "proton export from cell") @@ -88153,7 +86615,6 @@ EquivalentClasses( ObjectIntersection AnnotationAssertion(Annotation( "GOC:krc") "Formation of a prolongation or process extending and that is bounded by plasma membrane, e.g. a cilium, lamellipodium, or axon.") AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/13298"^^xsd:anyURI) -AnnotationAssertion( "krc") AnnotationAssertion( "2017-04-24T23:56:08Z") AnnotationAssertion(Annotation( "GOC:krc") Annotation( "GOC:rjd") Annotation( "PMID:10328951") Annotation( "PMID:9096956") "eupodium") AnnotationAssertion( "biological_process") @@ -88165,7 +86626,6 @@ EquivalentClasses( ObjectIntersection AnnotationAssertion(Annotation( "GOC:krc") "Any process that modulates the rate, frequency, or extent of plasma membrane bounded cell projection assembly.") AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/13298"^^xsd:anyURI) -AnnotationAssertion( "krc") AnnotationAssertion( "2017-04-26T04:27:04Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0120032") @@ -88176,7 +86636,6 @@ EquivalentClasses( ObjectIntersection AnnotationAssertion(Annotation( "GOC:krc") "Any process that stops, prevents or reduces the frequency, rate or extent of plasma membrane bounded cell projection assembly.") AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/13298"^^xsd:anyURI) -AnnotationAssertion( "krc") AnnotationAssertion( "2017-04-26T04:34:31Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0120033") @@ -88187,7 +86646,6 @@ EquivalentClasses( ObjectIntersection AnnotationAssertion(Annotation( "GOC:krc") "Any process that activates or increases the frequency, rate or extent of plasma membrane bounded cell projection assembly.") AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/13298"^^xsd:anyURI) -AnnotationAssertion( "krc") AnnotationAssertion( "2017-04-26T04:34:45Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0120034") @@ -88199,7 +86657,6 @@ SubClassOf( ObjectSomeValuesFrom( "GOC:krc") "Any process that modulates the frequency, rate or extent of a process involved in the formation, arrangement of constituent parts, or disassembly of plasma membrane bounded cell projections.") AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/13298"^^xsd:anyURI) -AnnotationAssertion( "krc") AnnotationAssertion( "2017-04-26T16:02:06Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0120035") @@ -88211,7 +86668,6 @@ SubClassOf( "GOC:krc") "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a plasma membrane bounded prolongation or process extending from a cell, e.g. a cilium or axon.") AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/13298"^^xsd:anyURI) -AnnotationAssertion( "krc") AnnotationAssertion( "2017-04-26T16:07:02Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0120036") @@ -88222,7 +86678,6 @@ EquivalentClasses( ObjectIntersection AnnotationAssertion(Annotation( "GOC:krc") "The process in which the anatomical structures of a plasma membrane bounded cell projection are generated and organized.") AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/13298"^^xsd:anyURI) -AnnotationAssertion( "krc") AnnotationAssertion( "2017-04-28T23:39:37Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0120039") @@ -88234,7 +86689,6 @@ SubClassOf( "GOC:ha") "All of the contents of a plasma membrane bounded neuron projection, excluding the plasma membrane surrounding the projection.") AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/14472"^^xsd:anyURI) -AnnotationAssertion( "krc") AnnotationAssertion( "2017-11-01T18:58:12Z") AnnotationAssertion( "cellular_component") AnnotationAssertion( "GO:0120111") @@ -88245,7 +86699,6 @@ EquivalentClasses( ObjectIntersection AnnotationAssertion(Annotation( "PMID:28719828") "The formation of mature glucagon by proteolysis of the precursor proglucagon.") AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/14505"^^xsd:anyURI) -AnnotationAssertion( "krc") AnnotationAssertion( "2017-11-08T19:31:42Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0120116") @@ -88257,7 +86710,6 @@ SubClassOf( "GOC:dph") Annotation( "GOC:tb") "Any process that activates or increases the frequency, rate or extent of collagen catabolism. Collagen catabolism is the proteolytic chemical reactions and pathways resulting in the breakdown of collagen in the extracellular matrix.") AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/15720"^^xsd:anyURI) -AnnotationAssertion( "krc") AnnotationAssertion( "2018-05-11T16:31:42Z") AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:tb") "positive regulation of collagen breakdown") AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:tb") "positive regulation of collagen catabolism") @@ -88275,7 +86727,6 @@ EquivalentClasses( ObjectIntersection AnnotationAssertion(Annotation( "GOC:krc") Annotation( "GOC:nln") "The chemical reactions and pathways resulting in the formation of any steroid hormone, naturally occurring substances secreted by specialized cells that affects the metabolism or behavior of other cells possessing functional receptors for the hormone.") AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/16000"^^xsd:anyURI) -AnnotationAssertion( "krc") AnnotationAssertion( "2019-05-20T22:34:00Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0120178") @@ -88286,7 +86737,6 @@ EquivalentClasses( ObjectIntersection AnnotationAssertion(Annotation( "GOC:aruk") Annotation( "GOC:bc") Annotation( "PMID:25490267") "The disaggregation of a cell-substrate junction into its constituent components.") AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/15964"^^xsd:anyURI) -AnnotationAssertion( "krc") AnnotationAssertion( "2018-07-12T17:33:35Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0120180") @@ -88297,7 +86747,6 @@ EquivalentClasses( ObjectIntersection AnnotationAssertion(Annotation( "PMID:20889714") Annotation( "PMID:29899453") "Any process that stops, prevents, or reduces the frequency, rate or extent of protein localization to chromatin.") AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/16012"^^xsd:anyURI) -AnnotationAssertion( "krc") AnnotationAssertion( "2018-07-14T00:19:32Z") AnnotationAssertion(Annotation( "GOC:krc") "negative regulation of protein localisation to chromatin") AnnotationAssertion( "biological_process") @@ -88309,7 +86758,6 @@ EquivalentClasses( ObjectIntersection AnnotationAssertion(Annotation( "PMID:20889714") Annotation( "PMID:29899453") "Any process that activates or increases the frequency, rate or extent of protein localization to chromatin.") AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/16012"^^xsd:anyURI) -AnnotationAssertion( "krc") AnnotationAssertion( "2018-07-14T00:21:28Z") AnnotationAssertion(Annotation( "GOC:krc") "positive regulation of protein localisation to chromatin") AnnotationAssertion( "biological_process") @@ -88321,7 +86769,6 @@ EquivalentClasses( ObjectIntersection AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:BHF_miRNA") Annotation( "GOC:rph") Annotation( "PMID:22767443") "Any process that modulates the frequency, rate or extent of the controlled release of bile acid from a cell or a tissue.") AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/16040"^^xsd:anyURI) -AnnotationAssertion( "krc") AnnotationAssertion( "2018-07-16T22:28:58Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0120188") @@ -88332,7 +86779,6 @@ EquivalentClasses( ObjectIntersection AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:BHF_miRNA") Annotation( "GOC:rph") Annotation( "PMID:22767443") "Any process that activates or increases the frequency, rate or extent of the controlled release of bile acid from a cell or a tissue.") AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/16040"^^xsd:anyURI) -AnnotationAssertion( "krc") AnnotationAssertion( "2018-07-16T22:36:17Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0120189") @@ -88343,7 +86789,6 @@ EquivalentClasses( ObjectIntersection AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:BHF_miRNA") Annotation( "GOC:rph") Annotation( "PMID:22767443") "Any process that stops, prevents or reduces the frequency, rate or extent of the controlled release of bile acid from a cell or a tissue.") AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/16040"^^xsd:anyURI) -AnnotationAssertion( "krc") AnnotationAssertion( "2018-07-16T22:38:34Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0120190") @@ -88354,7 +86799,6 @@ EquivalentClasses( ObjectIntersection AnnotationAssertion(Annotation( "GOC:rl") "A cellular process that results in the aggregation, arrangement and bonding together of a set of components to form a tight junction. A tight junction seals cells together in an epithelium in a way that prevents even small molecules from leaking from one side of the sheet to the other.") AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/16187"^^xsd:anyURI) -AnnotationAssertion( "krc") AnnotationAssertion( "2018-08-14T22:48:05Z") AnnotationAssertion(Annotation( "GOC:rl") "occluding cell junction assembly") AnnotationAssertion(Annotation( "GOC:rl") "occluding junction assembly") @@ -88368,7 +86812,6 @@ SubClassOf( "GOC:krc") Annotation( "GOC:rl") "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a tight junction. A tight junction seals cells together in an epithelium in a way that prevents even small molecules from leaking from one side of the sheet to the other.") AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/16187"^^xsd:anyURI) -AnnotationAssertion( "krc") AnnotationAssertion( "2018-08-14T23:05:40Z") AnnotationAssertion(Annotation( "GOC:rl") "occluding cell junction organization") AnnotationAssertion( "occluding junction organization") @@ -88382,7 +86825,6 @@ SubClassOf( "GOC:krc") "Any process that modulates the frequency, rate or extent of histidine biosynthetic process.") AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/17537"^^xsd:anyURI) -AnnotationAssertion( "krc") AnnotationAssertion( "2019-06-27T20:55:42Z") AnnotationAssertion(Annotation( "GOC:krc") "regulation of histidine anabolism") AnnotationAssertion(Annotation( "GOC:krc") "regulation of histidine biosynthesis") @@ -88397,7 +86839,6 @@ EquivalentClasses( ObjectIntersection AnnotationAssertion(Annotation( "GOC:krc") "Any process that stops, prevents or reduces the frequency, rate or extent of histidine biosynthetic process.") AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/17537"^^xsd:anyURI) -AnnotationAssertion( "krc") AnnotationAssertion( "2019-06-27T20:56:35Z") AnnotationAssertion(Annotation( "GOC:krc") "down regulation of histidine anabolism") AnnotationAssertion(Annotation( "GOC:krc") "down regulation of histidine biosynthesis") @@ -88432,7 +86873,6 @@ EquivalentClasses( ObjectIntersection AnnotationAssertion(Annotation( "GOC:krc") "Any process that activates or increases the frequency, rate or extent of histidine biosynthetic process.") AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/17537"^^xsd:anyURI) -AnnotationAssertion( "krc") AnnotationAssertion( "2019-06-27T20:57:28Z") AnnotationAssertion(Annotation( "GOC:krc") "positive regulation of histidine anabolism") AnnotationAssertion(Annotation( "GOC:krc") "positive regulation of histidine biosynthesis") @@ -88467,7 +86907,6 @@ EquivalentClasses( ObjectIntersection AnnotationAssertion(Annotation( "GOC:krc") Annotation( "PMID:29593216") "Any process that modulates the frequency, rate or extent of blastocyst development.") AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/18871"^^xsd:anyURI) -AnnotationAssertion( "krc") AnnotationAssertion( "2020-02-17T19:59:20Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0120222") @@ -88478,7 +86917,6 @@ EquivalentClasses( ObjectIntersection AnnotationAssertion(Annotation( "GOC:krc") Annotation( "PMID:28177282") "The process in which the larynx is generated and organized. The larynx is a continuation of the pharynx that is involved in breathing, sound production, and protecting the trachea against food aspiration.") AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/18924"^^xsd:anyURI) -AnnotationAssertion( "krc") AnnotationAssertion( "2020-02-22T01:42:04Z") AnnotationAssertion(Annotation( "GOC:krc") Annotation( "PMID:28177282") "laryngeal morphogenesis") AnnotationAssertion( "biological_process") @@ -88492,7 +86930,6 @@ SubClassOf( ObjectSomeValuesFrom( "GOC:krc") Annotation( "PMID:28177282") "The biological process whose specific outcome is the progression of a larynx from an initial condition to its mature state. This process begins with the formation of the larynx and ends with the mature structure. A larynx is a continuation of the pharynx that is involved in breathing, sound production, and protecting the trachea against food aspiration.") AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/18924"^^xsd:anyURI) -AnnotationAssertion( "krc") AnnotationAssertion( "2020-02-24T17:13:10Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0120224") @@ -88506,7 +86943,6 @@ SubClassOf( ObjectSomeValuesFrom( "GOC:krc") Annotation( "PMID:27486780") "A process in which a protein is transported to, or maintained in, a location within a motile cilium.") AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/19588"^^xsd:anyURI) -AnnotationAssertion( "krc") AnnotationAssertion( "2020-06-05T23:43:04Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "protein localization to nonmotile primary cilium") @@ -88519,7 +86955,6 @@ SubClassOf( "GOC:krc") Annotation( "PMID:25397684") "The flow of blood through the network of arteries and veins supplying the cerebrum, enabling the transport of nutrients to the tissues and the removal of waste products.") AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/20107"^^xsd:anyURI) -AnnotationAssertion( "krc") AnnotationAssertion( "2020-10-20T19:13:51Z") AnnotationAssertion( "cerebrum blood circulation") AnnotationAssertion( "telencephelon blood circulation") @@ -88533,7 +86968,6 @@ SubClassOf( "GOC:krc") Annotation( "PMID:25397684") "Any process that modulates the frequency, rate or extent of cerebral blood circulation.") AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/20107"^^xsd:anyURI) -AnnotationAssertion( "krc") AnnotationAssertion( "2020-10-21T06:52:22Z") AnnotationAssertion( "regulation of cerebrum blood circulation") AnnotationAssertion( "regulation of telencephalon blood circulation") @@ -88546,7 +86980,6 @@ EquivalentClasses( ObjectIntersection AnnotationAssertion(Annotation( "GOC:krc") Annotation( "PMID:25397684") "Any process that activates or increases the frequency, rate or extent of cerebral blood circulation.") AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/20107"^^xsd:anyURI) -AnnotationAssertion( "krc") AnnotationAssertion( "2020-10-21T06:55:42Z") AnnotationAssertion( "positive regulation of cerebrum blood circulation") AnnotationAssertion( "positive regulation of telencephalon blood circulation") @@ -88563,7 +86996,6 @@ EquivalentClasses( ObjectIntersection AnnotationAssertion(Annotation( "GOC:krc") Annotation( "PMID:25397684") "Any process that stops, prevents or reduces the frequency, rate or extent of cerebral blood circulation.") AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/20107"^^xsd:anyURI) -AnnotationAssertion( "krc") AnnotationAssertion( "2020-10-21T07:02:05Z") AnnotationAssertion( "down regulation of cerebral blood circulation") AnnotationAssertion( "down-regulation of cerebral blood circulation") @@ -88582,7 +87014,6 @@ SubClassOf( "GOC:krc") "Any process that modulates the frequency, rate or extent of the deposition or modulates the distribution of coloring matter in an organism.") AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/20524"^^xsd:anyURI) -AnnotationAssertion( "krc") AnnotationAssertion( "2021-02-09T19:37:35Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0120305") @@ -88593,7 +87024,6 @@ EquivalentClasses( ObjectIntersection AnnotationAssertion(Annotation( "GOC:ach") Annotation( "GOC:krc") Annotation( "PMID:16278296") "The aggregation, arrangement and bonding together of a set of components to form an axonemal outer doublet, a part of an axoneme consisting of a doublet microtubule.") AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/21154"^^xsd:anyURI) -AnnotationAssertion( "krc") AnnotationAssertion( "2021-03-23T16:28:18Z") AnnotationAssertion( "outer doublet assembly") AnnotationAssertion( "outer-doublet microtubule assembly") @@ -88611,7 +87041,6 @@ SubClassOf( ObjectSomeValuesFrom( "GOC:krc") Annotation( "PMID:32791035") "The assembly and organization of the sperm flagellum, the microtubule-based axoneme and associated structures that are part of a sperm flagellum (or cilium).") AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/21361"^^xsd:anyURI) -AnnotationAssertion( "krc") AnnotationAssertion( "2021-04-29T01:27:27Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0120316") @@ -88625,7 +87054,6 @@ SubClassOf( ObjectSomeValuesFrom( "GOC:krc") Annotation( "MESH:D000067617") Annotation( "PMID:20367664") "A telopode is a plasma membrane bounded cell projection that is present on a telocyte and is tens to hundreds of microns long. Telopodes form a labyrinthine system communicating through gap junctions.") AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/21973"^^xsd:anyURI) -AnnotationAssertion( "krc") AnnotationAssertion( "2021-08-16T16:45:21Z") AnnotationAssertion( "cellular_component") AnnotationAssertion( "GO:0120327") @@ -88636,7 +87064,6 @@ SubClassOf( "GOC:sl") Annotation( "PMID:23239824") "The developmental process pertaining to the initial formation of an endothelial tube.") AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/22302"^^xsd:anyURI) -AnnotationAssertion( "krc") AnnotationAssertion( "2022-05-25T16:17:59Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0120331") @@ -88648,7 +87075,6 @@ SubClassOf( ObjectSomeValuesFrom( "PMID:9334324") "One of the two nuclear divisions that occur as part of the meiotic cell cycle.") AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/19910"^^xsd:anyURI) -AnnotationAssertion( "pg") AnnotationAssertion( "2017-03-23T09:40:00Z") AnnotationAssertion( "meiosis") AnnotationAssertion( "biological_process") @@ -88661,7 +87087,6 @@ EquivalentClasses( ObjectIntersection AnnotationAssertion(Annotation( "ISBN:0198547684") "A mitotic cell cycle process comprising the steps by which the nucleus of a eukaryotic cell divides; the process involves condensation of chromosomal DNA into a highly compacted form. Canonically, mitosis produces two daughter nuclei whose chromosome complement is identical to that of the mother cell.") AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/19910"^^xsd:anyURI) -AnnotationAssertion( "pg") AnnotationAssertion( "2017-03-23T14:44:23Z") AnnotationAssertion( "mitosis") AnnotationAssertion( "biological_process") @@ -88674,7 +87099,6 @@ EquivalentClasses( ObjectIntersection # Class: (exocytic process) AnnotationAssertion(Annotation( "Wikipedia:Exocytosis") "The cellular processes that contribute to exocytosis.") -AnnotationAssertion( "pg") AnnotationAssertion( "2017-05-15T13:20:45Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0140029") @@ -88685,7 +87109,6 @@ EquivalentClasses( ObjectIntersection # Class: (cell-cell adhesion in response to extracellular stimulus) AnnotationAssertion(Annotation( "PMID:14996911") "The attachment of one cell to another cell via adhesion molecules as a result of an extracellular stimulus.") -AnnotationAssertion( "pg") AnnotationAssertion( "2017-05-24T11:37:30Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0140039") @@ -88695,7 +87118,6 @@ EquivalentClasses( ObjectIntersection # Class: (organelle localization by membrane tethering) AnnotationAssertion(Annotation( "PMID:27875684") "The process by which an organelle membrane interacts with another membrane via molecular tethers that physically bridge the two membranes and attach them to each other.") -AnnotationAssertion( "pg") AnnotationAssertion( "2017-06-27T09:58:51Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0140056") @@ -88707,7 +87129,6 @@ SubClassOf( (regulation of lipoprotein transport) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:BHF_miRNA") Annotation( "GOC:RPH") Annotation( "PMID:26501192") "Any process that controls lipoprotein transport.") -AnnotationAssertion( "pg") AnnotationAssertion( "2017-07-21T15:35:47Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0140075") @@ -88717,7 +87138,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of lipoprotein transport) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:BHF_miRNA") Annotation( "GOC:RPH") Annotation( "PMID:26501192") "Any process that stops, prevents or reduces the frequency, rate or extent of lipoprotein transport.") -AnnotationAssertion( "pg") AnnotationAssertion( "2017-07-21T15:39:50Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0140076") @@ -88727,7 +87147,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of lipoprotein transport) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:BHF_miRNA") Annotation( "GOC:RPH") Annotation( "PMID:26501192") "Any process that activates or increases the rate or extent of lipoprotein transport.") -AnnotationAssertion( "pg") AnnotationAssertion( "2017-07-21T15:41:54Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0140077") @@ -88738,7 +87157,6 @@ EquivalentClasses( ObjectIntersection AnnotationAssertion(Annotation( "GOC:molecular_function_refactoring") Annotation( "GOC:pdt") "Catalytic activity that acts to modify a protein.") AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/14225"^^xsd:anyURI) -AnnotationAssertion( "pg") AnnotationAssertion( "2017-09-14T10:32:59Z") AnnotationAssertion( "molecular_function") AnnotationAssertion( "GO:0140096") @@ -88751,7 +87169,6 @@ EquivalentClasses( ObjectIntersection AnnotationAssertion(Annotation( "GOC:molecular_function_refactoring") Annotation( "GOC:pdt") "Catalytic activity that acts to modify DNA.") AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/14225"^^xsd:anyURI) -AnnotationAssertion( "pg") AnnotationAssertion( "2017-09-14T12:03:51Z") AnnotationAssertion( "molecular_function") AnnotationAssertion( "GO:0140097") @@ -88765,7 +87182,6 @@ EquivalentClasses( ObjectIntersection AnnotationAssertion(Annotation( "GOC:molecular_function_refactoring") Annotation( "GOC:pdt") "Catalytic activity that acts to modify RNA, driven by ATP hydrolysis.") AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/14225"^^xsd:anyURI) AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/21612"^^xsd:anyURI) -AnnotationAssertion( "pg") AnnotationAssertion( "2017-09-14T12:05:21Z") AnnotationAssertion( "molecular_function") AnnotationAssertion( "GO:0140098") @@ -88778,7 +87194,6 @@ EquivalentClasses( ObjectIntersection AnnotationAssertion(Annotation( "GOC:molecular_function_refactoring") Annotation( "GOC:pdt") "Catalysis of a biochemical reaction at physiological temperatures in which one of the substrates is a glycoprotein.") AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/14225"^^xsd:anyURI) -AnnotationAssertion( "pg") AnnotationAssertion( "2017-09-15T19:27:54Z") AnnotationAssertion( "molecular_function") AnnotationAssertion( "GO:0140103") @@ -88789,7 +87204,6 @@ EquivalentClasses( ObjectIntersection AnnotationAssertion(Annotation( "PMID:28736435") "The assembly and secretion a set of components to form an extracellular vesicule, a membrane-bounded vesicle that is released into the extracellular region. Extracellular vesicles include exosomes, microvesicles and apoptotic bodies, based on the mechanism by which they are released from cells and differentiated based on their size and content.") AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/14256"^^xsd:anyURI) -AnnotationAssertion( "pg") AnnotationAssertion( "2017-10-23T11:53:42Z") AnnotationAssertion( "extracellular vesicle assembly") AnnotationAssertion( "biological_process") @@ -88800,7 +87214,6 @@ SubClassOf( (export across plasma membrane) AnnotationAssertion(Annotation( "GOC:pg") "The directed movement of some substance from inside of a cell, across the plasma membrane and into the extracellular region.") -AnnotationAssertion( "pg") AnnotationAssertion( "2017-10-24T14:38:16Z") AnnotationAssertion( "efflux") AnnotationAssertion( "biological_process") @@ -88811,7 +87224,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of lymphocyte chemotaxis) AnnotationAssertion(Annotation( "PMID:19255442") "Any process that activates or increases the frequency, rate or extent of lymphocyte chemotaxis.") -AnnotationAssertion( "pg") AnnotationAssertion( "2017-11-02T10:26:40Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0140131") @@ -88821,7 +87233,6 @@ EquivalentClasses( ObjectIntersection # Class: (calcium ion import into vacuole) AnnotationAssertion(Annotation( "GOC:vw") Annotation( "PMID:8628289") "The directed movement of calcium cations into the vacuole across the vacuolar membrane.") -AnnotationAssertion( "pg") AnnotationAssertion( "2017-12-13T15:15:29Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0140146") @@ -88831,7 +87242,6 @@ EquivalentClasses( ObjectIntersection # Class: (ammonium import across plasma membrane) AnnotationAssertion(Annotation( "GOC:vw") Annotation( "PMID:16999738") "The directed movement of an ammonium ion from outside of a cell, across the plasma membrane and into the cytosol.") -AnnotationAssertion( "pg") AnnotationAssertion( "2018-01-26T12:39:56Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0140157") @@ -88841,7 +87251,6 @@ EquivalentClasses( ObjectIntersection # Class: (serotonin-gated cation-selective signaling pathway) AnnotationAssertion(Annotation( "GOC:bhm") Annotation( "PMID:25392484") Annotation( "PMID:27764665") "The series of molecular signals initiated by serotonin binding to a seratonin receptor on the surface of the target cell, followed by the movement of ions through a channel in the receptor complex. Ends with regulation of a downstream cellular process, e.g. transcription.") -AnnotationAssertion( "pg") AnnotationAssertion( "2018-06-02T13:34:51Z") AnnotationAssertion( "5-HT-gated cation-selective signaling pathway") AnnotationAssertion( "5-HT-gated cation-selective signalling pathway") @@ -88856,7 +87265,6 @@ EquivalentClasses( ObjectIntersection # Class: (anterograde axonal transport of neurotransmitter receptor complex) AnnotationAssertion(Annotation( "PMID:28680963") "The directed movement of a neurotransmitter receptor complex along microtubules from the cell body toward the cell periphery in nerve cell axons.") -AnnotationAssertion( "pg") AnnotationAssertion( "2018-07-09T09:41:37Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0140231") @@ -88869,7 +87277,6 @@ SubClassOf( "PMID:27321671") "Translation that occurs at the presynapse.") AnnotationAssertion( "https://github.com/geneontology/synapse/issues/216"^^xsd:anyURI) -AnnotationAssertion( "pg") AnnotationAssertion( "2018-07-13T13:00:33Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0140236") @@ -88882,7 +87289,6 @@ EquivalentClasses( ObjectIntersection AnnotationAssertion(Annotation( "PMID:27321671") "Translation that occurs at the presynapse, and that modulates chemical synaptic transmission.") AnnotationAssertion( "https://github.com/geneontology/synapse/issues/216"^^xsd:anyURI) -AnnotationAssertion( "pg") AnnotationAssertion( "2018-07-13T13:07:23Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0140237") @@ -88895,7 +87301,6 @@ EquivalentClasses( ObjectIntersection AnnotationAssertion(Annotation( "PMID:24719103") "A vesicle-mediated transport process in which the presynapse take up external materials or membrane constituents by the invagination of a small region of the plasma membrane to form a new membrane-bounded vesicle.") AnnotationAssertion( "https://github.com/geneontology/synapse/issues/230"^^xsd:anyURI) -AnnotationAssertion( "pg") AnnotationAssertion( "2018-07-15T07:33:55Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0140238") @@ -88908,7 +87313,6 @@ EquivalentClasses( ObjectIntersection AnnotationAssertion(Annotation( "PMID:12839988") "A vesicle-mediated transport process in which the postsynapse take up external materials or membrane constituents by the invagination of a small region of the plasma membrane to form a new membrane-bounded vesicle.") AnnotationAssertion( "https://github.com/geneontology/synapse/issues/230"^^xsd:anyURI) -AnnotationAssertion( "pg") AnnotationAssertion( "2018-07-15T07:38:27Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0140239") @@ -88921,7 +87325,6 @@ EquivalentClasses( ObjectIntersection AnnotationAssertion(Annotation( "PMID:23083742") "Translation that occurs at the synapse.") AnnotationAssertion( "https://github.com/geneontology/synapse/issues/210"^^xsd:anyURI) -AnnotationAssertion( "pg") AnnotationAssertion( "2018-07-15T09:23:12Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0140241") @@ -88936,7 +87339,6 @@ SubClassOf( ObjectAllValuesFrom( "PMID:20427644") "Translation that occurs at the postsynapse.") AnnotationAssertion( "https://github.com/geneontology/synapse/issues/210"^^xsd:anyURI) -AnnotationAssertion( "pg") AnnotationAssertion( "2018-07-15T09:26:27Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0140242") @@ -88949,7 +87351,6 @@ EquivalentClasses( ObjectIntersection AnnotationAssertion(Annotation( "PMID:20427644") "Any process that regulates translation occurring at the synapse.") AnnotationAssertion( "https://github.com/geneontology/synapse/issues/210"^^xsd:anyURI) -AnnotationAssertion( "pg") AnnotationAssertion( "2018-07-15T09:38:26Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0140243") @@ -88964,7 +87365,6 @@ SubClassOf( ObjectAllValuesFrom( "PMID:20427644") "Any process that regulates translation occurring at the presynapse.") AnnotationAssertion( "https://github.com/geneontology/synapse/issues/210"^^xsd:anyURI) -AnnotationAssertion( "pg") AnnotationAssertion( "2018-07-15T09:38:33Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0140244") @@ -88977,7 +87377,6 @@ EquivalentClasses( ObjectIntersection AnnotationAssertion(Annotation( "PMID:20427644") "Any process that regulates translation occurring at the postsynapse.") AnnotationAssertion( "https://github.com/geneontology/synapse/issues/210"^^xsd:anyURI) -AnnotationAssertion( "pg") AnnotationAssertion( "2018-07-15T09:38:54Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0140245") @@ -88990,7 +87389,6 @@ EquivalentClasses( ObjectIntersection AnnotationAssertion(Annotation( "PMID:17062563") "The chemical reactions and pathways resulting in the breakdown of a protein at a synapse.") AnnotationAssertion( "https://github.com/geneontology/synapse/issues/210"^^xsd:anyURI) -AnnotationAssertion( "pg") AnnotationAssertion( "2018-07-15T10:12:51Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0140246") @@ -89005,7 +87403,6 @@ SubClassOf( ObjectAllValuesFrom( "PMID:27764673") "The chemical reactions and pathways resulting in the breakdown of a protein at a presynapse.") AnnotationAssertion( "https://github.com/geneontology/synapse/issues/204"^^xsd:anyURI) -AnnotationAssertion( "pg") AnnotationAssertion( "2018-07-15T10:23:49Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0140247") @@ -89018,7 +87415,6 @@ EquivalentClasses( ObjectIntersection AnnotationAssertion(Annotation( "PMID:17062563") "The chemical reactions and pathways resulting in the breakdown of a protein at a postsynapse.") AnnotationAssertion( "https://github.com/geneontology/synapse/issues/204"^^xsd:anyURI) -AnnotationAssertion( "pg") AnnotationAssertion( "2018-07-15T10:25:04Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0140249") @@ -89031,7 +87427,6 @@ EquivalentClasses( ObjectIntersection AnnotationAssertion(Annotation( "PMID:23083742") "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of a protein at the synapse.") AnnotationAssertion( "https://github.com/geneontology/synapse/issues/204"^^xsd:anyURI) -AnnotationAssertion( "pg") AnnotationAssertion( "2018-07-15T10:34:56Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0140250") @@ -89046,7 +87441,6 @@ SubClassOf( ObjectAllValuesFrom( "PMID:27764673") "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of a protein at the presynapse.") AnnotationAssertion( "https://github.com/geneontology/synapse/issues/204"^^xsd:anyURI) -AnnotationAssertion( "pg") AnnotationAssertion( "2018-07-15T10:35:39Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0140251") @@ -89059,7 +87453,6 @@ EquivalentClasses( ObjectIntersection AnnotationAssertion(Annotation( "PMID:17062563") "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of a protein at the postsynapse.") AnnotationAssertion( "https://github.com/geneontology/synapse/issues/204"^^xsd:anyURI) -AnnotationAssertion( "pg") AnnotationAssertion( "2018-07-15T10:35:56Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0140252") @@ -89072,7 +87465,6 @@ EquivalentClasses( ObjectIntersection AnnotationAssertion(Annotation( "Wikipedia:Cell_fusion") "A cellular process in which two or more cells combine together, their plasma membrane fusing, producing a single cell. In some cases, nuclei fuse, producing a polyploid cell, while in other cases, nuclei remain separate, producing a syncytium.") AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/15939"^^xsd:anyURI) -AnnotationAssertion( "pg") AnnotationAssertion( "2018-08-13T18:38:18Z") AnnotationAssertion( "cell fusion") AnnotationAssertion( "cell cell fusion") @@ -89085,7 +87477,6 @@ SubClassOf( ObjectSomeValuesFrom( (hexose import across plasma membrane) AnnotationAssertion(Annotation( "PMID:10735857") "The directed movement of hexose from outside of a cell, across the plasma membrane and into the cytosol.") -AnnotationAssertion( "pg") AnnotationAssertion( "2018-10-01T08:49:49Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0140271") @@ -89096,7 +87487,6 @@ EquivalentClasses( ObjectIntersection AnnotationAssertion(Annotation( "GOC:txnOH-2018") "Binding to a DNA-binding transcription factor, a protein that interacts with a specific DNA sequence (sometimes referred to as a motif) within the regulatory region of a gene to modulate transcription.") AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/19354"^^xsd:anyURI) -AnnotationAssertion( "pg") AnnotationAssertion( "2018-11-28T12:48:20Z") AnnotationAssertion( "molecular_function") AnnotationAssertion( "activating transcription factor binding") @@ -89110,7 +87500,6 @@ SubClassOf( "PMID:18706423") "Directly binding to a specific protein and delivering it to a specific cellular location.") AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/17073"^^xsd:anyURI) -AnnotationAssertion( "pg") AnnotationAssertion( "2019-04-01T10:41:38Z") AnnotationAssertion(Annotation(rdfs:label "M6PR transports activated ARSA to the lysosome") "Reactome:R-HSA-2248891") AnnotationAssertion(Annotation(rdfs:label "iRHOM2 transports ADAM17 from ER to the Golgi-network") "Reactome:R-HSA-9662747") @@ -89126,7 +87515,6 @@ EquivalentClasses( ObjectIntersection # Class: (export from cell) AnnotationAssertion(Annotation( "GOC:pg") "The directed movement of some substance from a cell, into the extracellular region. This may occur via transport across the plasma membrane or via exocytosis.") -AnnotationAssertion( "pg") AnnotationAssertion( "2019-05-22T11:20:45Z") AnnotationAssertion( "efflux") AnnotationAssertion( "biological_process") @@ -89138,7 +87526,6 @@ SubClassOf( (lipid export from cell) AnnotationAssertion(Annotation( "GOC:pg") "The directed movement of a lipid from a cell, into the extracellular region.") -AnnotationAssertion( "pg") AnnotationAssertion( "2019-05-22T11:33:07Z") AnnotationAssertion( "lipid efflux") AnnotationAssertion( "biological_process") @@ -89149,7 +87536,6 @@ EquivalentClasses( ObjectIntersection # Class: (lipid import into cell) AnnotationAssertion(Annotation( "GOC:pg") "The directed movement of a lipid from outside of a cell into a cell. This may occur via transport across the plasma membrane or via endocytosis.") -AnnotationAssertion( "pg") AnnotationAssertion( "2019-05-22T11:38:15Z") AnnotationAssertion( "lipid uptake") AnnotationAssertion( "biological_process") @@ -89160,7 +87546,6 @@ EquivalentClasses( ObjectIntersection # Class: (immune receptor activity) AnnotationAssertion(Annotation( "PMID:31415752") Annotation( "Wikipedia:Immune_receptor") "Receiving a signal and transmitting it in a cell to initiate an immune response.") -AnnotationAssertion( "pg") AnnotationAssertion( "2019-10-18T14:11:15Z") AnnotationAssertion( "molecular_function") AnnotationAssertion( "GO:0140375") @@ -89171,7 +87556,6 @@ SubClassOf( "PMID:29247995") "The cleavage of a peptide bond in a precursor form of a signaling receptor ligand, resulting in the mature (active) form of the ligand.") AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/19216"^^xsd:anyURI) -AnnotationAssertion( "pg") AnnotationAssertion( "2020-04-03T13:30:04Z") AnnotationAssertion(Annotation( "GOC:bf") "ligand maturation") AnnotationAssertion( "biological_process") @@ -89183,7 +87567,6 @@ SubClassOf( (nuclear protein-containing complex) AnnotationAssertion(Annotation( "GOC:pg") "A stable assembly of two or more macromolecules, i.e. proteins, nucleic acids, carbohydrates or lipids, in which at least one component is a protein and the constituent parts function together in the nucleus.") -AnnotationAssertion( "pg") AnnotationAssertion( "2020-09-09T05:12:38Z") AnnotationAssertion( "nuclear complex") AnnotationAssertion( "cellular_component") @@ -89196,7 +87579,6 @@ EquivalentClasses( ObjectIntersection AnnotationAssertion(Annotation( "GOC:pg") "Reactions triggered in response to the presence of a symbiont that act to protect or prevent damage to the host.") AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/20261"^^xsd:anyURI) -AnnotationAssertion( "pg") AnnotationAssertion( "2020-11-11T17:19:06Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0140546") @@ -89207,7 +87589,6 @@ SubClassOf( "PMID:19643199") "The division of a vacuole within a cell to form two or more separate vacuoles.") AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/20639"^^xsd:anyURI) -AnnotationAssertion( "pg") AnnotationAssertion( "2021-01-04T10:17:58Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0140572") @@ -89219,7 +87600,6 @@ SubClassOf( "GOC:pg") "Catalytic activity that acts to modify a nucleic acid.") AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/21402"^^xsd:anyURI) -AnnotationAssertion( "pg") AnnotationAssertion( "2021-05-11T06:31:07Z") AnnotationAssertion( "molecular_function") AnnotationAssertion( "GO:0140640") @@ -89231,7 +87611,6 @@ SubClassOf( "PMID:3760547") "The radial migration of a pyramidal neuron along radial glial cells.") AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/21476"^^xsd:anyURI) -AnnotationAssertion( "pg") AnnotationAssertion( "2021-05-25T12:48:12Z") AnnotationAssertion( "radial glia-dependent neuronal migration") AnnotationAssertion( "biological_process") @@ -89245,7 +87624,6 @@ SubClassOf( "PMID:24878343") Annotation( "PMID:25750732") Annotation( "PMID:32933017") Annotation( "PMID:33818025") Annotation( "PMID:33873056") Annotation( "PMID:33988324") "A molecular function characterized by the coupling of ATP hydrolysis to other steps of a reaction mechanism to make the reaction energetically favorable, for example to catalyze a reaction or drive transport against a concentration gradient.") AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/21612"^^xsd:anyURI) AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/22371"^^xsd:anyURI) -AnnotationAssertion( "pg") AnnotationAssertion( "2021-06-15T07:35:06Z") AnnotationAssertion( "ATP hydrolysis-dependent activity") AnnotationAssertion( "ATPase activity") @@ -89267,7 +87645,6 @@ EquivalentClasses( ObjectIntersection AnnotationAssertion(Annotation( "PMID:25096581") "Any process that modulates the frequency, rate, or extent of production of oxytocin.") AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/21535"^^xsd:anyURI) -AnnotationAssertion( "pg") AnnotationAssertion( "2021-06-24T11:28:07Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0140667") @@ -89278,7 +87655,6 @@ EquivalentClasses( ObjectIntersection AnnotationAssertion(Annotation( "PMID:25096581") "Any process that activates or increases the frequency, rate or extent of production of oxytocin.") AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/21535"^^xsd:anyURI) -AnnotationAssertion( "pg") AnnotationAssertion( "2021-06-24T11:31:26Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0140668") @@ -89289,7 +87665,6 @@ EquivalentClasses( ObjectIntersection AnnotationAssertion(Annotation( "PMID:25096581") "Any process that stops, prevents, or reduces the rate of production of oxytocin.") AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/21535"^^xsd:anyURI) -AnnotationAssertion( "pg") AnnotationAssertion( "2021-06-24T11:31:45Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0140669") @@ -89301,7 +87676,6 @@ EquivalentClasses( ObjectIntersection AnnotationAssertion(Annotation( "PMID:28225081") "The aggregation, arrangement and bonding together of a set of components to form a non-membrane-bounded organelle.") AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/21939"^^xsd:anyURI) AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/29106"^^xsd:anyURI) -AnnotationAssertion( "pg") AnnotationAssertion( "2021-08-09T15:30:06Z") AnnotationAssertion( "non-membrane-bounded organelle assembly") AnnotationAssertion( "non-membrane-bounded organelle formation") @@ -89316,7 +87690,6 @@ EquivalentClasses( ObjectIntersection AnnotationAssertion(Annotation( "PMID:25740900") "The elimination of ammonium ions from an excretory cell.") AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/22368"^^xsd:anyURI) -AnnotationAssertion( "pg") AnnotationAssertion( "2021-11-24T17:55:51Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "ammonia excretion") @@ -89328,7 +87701,6 @@ EquivalentClasses( ObjectIntersection AnnotationAssertion(Annotation( "PMID:28373556") "The directed movement of substances from the cytosol into the Golgi apparatus of a cell.") AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/21524"^^xsd:anyURI) -AnnotationAssertion( "pg") AnnotationAssertion( "2022-05-16T06:59:22Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0140820") @@ -89339,7 +87711,6 @@ EquivalentClasses( ObjectIntersection AnnotationAssertion(Annotation( "GOC:curators") "A homeostatic process involved in the maintenance of a steady state level of a chemical within extracellular body fluids, such as blood, xylem or phloem, of a multicellular organism. This is distinct from maintenance of cellular homeostasis, which occurs within a cell.") AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/24554"^^xsd:anyURI) -AnnotationAssertion( "pg") AnnotationAssertion( "2022-12-12T09:11:06Z") AnnotationAssertion( "multicellular organism level chemical homeostasis") AnnotationAssertion( "organismal level chemical homeostasis") @@ -89352,7 +87723,6 @@ EquivalentClasses( ObjectIntersection AnnotationAssertion(Annotation( "GOC:ha") Annotation( "GOC:pg") "An intracellular signaling module that is part of larger signaling pathways that can be initiated either intracellularly or by cell surface receptors. Intracellular signaling cassettes are discrete signaling units that are often shared by multiple signaling pathways.") AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/26557"^^xsd:anyURI) -AnnotationAssertion( "pg") AnnotationAssertion( "2023-12-04T14:13:20Z") AnnotationAssertion( "intracellular signaling cascade") AnnotationAssertion( "intracellular signaling module") @@ -89366,7 +87736,6 @@ SubClassOf( "GOC:dph") Annotation( "GOC:tb") "The biosynthetic process resulting in the formation of a nucleic acid.") AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/27408"^^xsd:anyURI) AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/27633"^^xsd:anyURI) -AnnotationAssertion( "pg") AnnotationAssertion( "2024-03-25T07:33:40Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0141187") @@ -89380,7 +87749,6 @@ EquivalentClasses( ObjectIntersection AnnotationAssertion(Annotation( "GOC:curators") "The cellular DNA metabolic process resulting in the breakdown of a nucleic acid.") AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/27408"^^xsd:anyURI) AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/27633"^^xsd:anyURI) -AnnotationAssertion( "pg") AnnotationAssertion( "2024-03-25T07:35:06Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0141188") @@ -89392,7 +87760,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of protein localization to lysosome) AnnotationAssertion(Annotation( "GOC:aruk") Annotation( "GOC:bc") Annotation( "PMID:24305806") "Any process that modulates the frequency, rate or extent of protein localization to lysosome.") -AnnotationAssertion( "bc") AnnotationAssertion( "2018-02-06T17:07:03Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0150031") @@ -89402,7 +87769,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of protein localization to lysosome) AnnotationAssertion(Annotation( "GOC:aruk") Annotation( "GOC:bc") "Any process that activates or increases the frequency, rate or extent of protein localization to lysosome.") -AnnotationAssertion( "bc") AnnotationAssertion( "2018-02-06T17:11:02Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0150032") @@ -89412,7 +87778,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of protein localization to lysosome) AnnotationAssertion(Annotation( "GOC:aruk") Annotation( "GOC:bc") Annotation( "PMID:24305806") "Any process that stops, prevents or reduces the frequency, rate or extent of protein localization to lysosome.") -AnnotationAssertion( "bc") AnnotationAssertion( "2018-02-06T17:14:16Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0150033") @@ -89422,7 +87787,6 @@ EquivalentClasses( ObjectIntersection # Class: (distal axon) AnnotationAssertion(Annotation( "GOC:aruk") Annotation( "GOC:bc") Annotation( "PMID:17202468") "That part of an axon close to and including the growth cone or the axon terminus.") -AnnotationAssertion( "bc") AnnotationAssertion( "2018-02-19T15:04:24Z") AnnotationAssertion( "distal part of axon") AnnotationAssertion(Annotation( "PMID:17202468") "distal part of the axon") @@ -89435,7 +87799,6 @@ SubClassOf( ObjectSomeValuesFrom( (regulation of synaptic signaling by nitric oxide) AnnotationAssertion(Annotation( "GOC:aruk") Annotation( "GOC:bc") Annotation( "PMID:26311509") "Any process that modulates the frequency, rate or extent of synaptic signaling by nitric oxide.") -AnnotationAssertion( "bc") AnnotationAssertion( "2018-04-23T09:42:25Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0150045") @@ -89446,7 +87809,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of postsynapse assembly) AnnotationAssertion(Annotation( "GOC:aruk") Annotation( "GOC:bc") Annotation( "PMID:16394100") Annotation( "PMID:16672654") Annotation( "PMID:28185854") "Any process that modulates the frequency, rate or extent of postsynapse assembly, the aggregation, arrangement and bonding together of a set of components to form a postsynapse.") -AnnotationAssertion( "bc") AnnotationAssertion( "2018-05-08T16:38:55Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0150052") @@ -89458,7 +87820,6 @@ SubClassOf( ObjectSomeValuesFrom( (visual system development) AnnotationAssertion(Annotation( "GOC:aruk") Annotation( "GOC:bc") Annotation( "GOC:krc") Annotation( "PMID:15004427") Annotation( "PMID:20647017") Annotation( "PMID:22632727") "The process whose specific outcome is the progression of the visual system over time, from its formation to the mature structure, including the eye, parts of the central nervous system (CNS) involved in processing of visual inputs, and connecting nerve pathways.") -AnnotationAssertion( "bc") AnnotationAssertion( "2018-07-23T10:31:58Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "optic pathway development") @@ -89470,7 +87831,6 @@ SubClassOf( (neuroinflammatory response) AnnotationAssertion(Annotation( "GOC:aruk") Annotation( "GOC:bc") Annotation( "PMID:10981966") Annotation( "PMID:11099416") Annotation( "PMID:18164423") "The immediate defensive reaction by neural vertebrate tissue to infection or injury caused by chemical or physical agents.") -AnnotationAssertion( "bc") AnnotationAssertion( "2018-07-26T12:25:34Z") AnnotationAssertion( "nerve tissue inflammatory response") AnnotationAssertion( "nervous tissue inflammatory response") @@ -89483,7 +87843,6 @@ SubClassOf( (regulation of neuroinflammatory response) AnnotationAssertion(Annotation( "GOC:aruk") Annotation( "GOC:bc") Annotation( "PMID:10981966") Annotation( "PMID:11099416") Annotation( "PMID:18164423") "Any process that modulates the frequency, rate or extent of neuroinflammatory response.") -AnnotationAssertion( "bc") AnnotationAssertion( "2018-07-26T12:32:18Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0150077") @@ -89495,7 +87854,6 @@ SubClassOf( ObjectAllValuesFrom( (positive regulation of neuroinflammatory response) AnnotationAssertion(Annotation( "GOC:aruk") Annotation( "GOC:bc") "Any process that activates or increases the frequency, rate or extent of neuroinflammatory response.") -AnnotationAssertion( "bc") AnnotationAssertion( "2018-07-26T12:35:50Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0150078") @@ -89505,7 +87863,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of neuroinflammatory response) AnnotationAssertion(Annotation( "GOC:aruk") Annotation( "GOC:bc") Annotation( "PMID:11099416") Annotation( "PMID:18164423") "Any process that stops, prevents or reduces the frequency, rate or extent of neuroinflammatory response.") -AnnotationAssertion( "bc") AnnotationAssertion( "2018-07-26T12:38:08Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0150079") @@ -89515,7 +87872,6 @@ EquivalentClasses( ObjectIntersection # Class: (glial cell-neuron signaling) AnnotationAssertion(Annotation( "GOC:aruk") Annotation( "GOC:bc") Annotation( "PMID:14980203") Annotation( "PMID:16144764") Annotation( "PMID:16547515") Annotation( "PMID:18685038") Annotation( "PMID:27788368") Annotation( "PMID:9459440") "Cell-cell signaling that mediates the transfer of information from a glial cell to a neuron. This signaling has been shown to be mediated by various molecules, depending on which glial cells release them, and in which tissues the signaling occurs, e.g. microglial cell-derived nerve growth factor (NGF) in the retina, or microglial cell-derived superoxide ions in the cerebellum.") -AnnotationAssertion( "bc") AnnotationAssertion( "2018-12-17T12:28:09Z") AnnotationAssertion( "glia-neuron signaling") AnnotationAssertion( "glia-neuron signalling") @@ -89532,7 +87888,6 @@ EquivalentClasses( ObjectIntersection # Class: (neuron-glial cell signaling) AnnotationAssertion(Annotation( "GOC:aruk") Annotation( "GOC:bc") Annotation( "PMID:10195197") Annotation( "PMID:10196584") Annotation( "PMID:10377338") Annotation( "PMID:10493741") Annotation( "PMID:11356870") Annotation( "PMID:11399439") Annotation( "PMID:15252819") Annotation( "PMID:27788368") "Cell-cell signaling that mediates the transfer of information from a neuron to a glial cell. This signaling has been shown to be mediated by various molecules released by different types of neurons, e.g. glutamate, gamma-amino butyric acid (GABA), noradrenaline, acetylcholine, dopamine and adenosine.") -AnnotationAssertion( "bc") AnnotationAssertion( "2018-12-17T12:30:12Z") AnnotationAssertion( "neuron-glia signaling") AnnotationAssertion( "neuron-glia signalling") @@ -89549,7 +87904,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of monocyte activation) AnnotationAssertion(Annotation( "GOC:aruk") Annotation( "PMID:15597323") "Any process that stops, prevents or reduces the frequency, rate or extent of monocyte activation.") -AnnotationAssertion( "bc") AnnotationAssertion( "2019-04-26T20:01:24Z") AnnotationAssertion( "repression of monocyte activation") AnnotationAssertion( "biological_process") @@ -89560,7 +87914,6 @@ EquivalentClasses( ObjectIntersection # Class: (transport across blood-brain barrier) AnnotationAssertion(Annotation( "GOC:aruk") Annotation( "GOC:bc") Annotation( "PMID:29377008") "The directed movement of substances (e.g. macromolecules, small molecules, ions) through the blood-brain barrier.") -AnnotationAssertion( "bc") AnnotationAssertion( "2019-05-27T09:12:03Z") AnnotationAssertion( "transport across BBB") AnnotationAssertion( "transport across blood brain barrier") @@ -89574,7 +87927,6 @@ SubClassOf( ObjectAllValuesFrom( (protein localization to cell-cell junction) AnnotationAssertion(Annotation( "GOC:aruk") Annotation( "GOC:bc") Annotation( "PMID:26706435") "A process in which a protein is transported to, or maintained, in a location within a cell-cell junction.") -AnnotationAssertion( "bc") AnnotationAssertion( "2019-06-11T11:00:18Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0150105") @@ -89584,7 +87936,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of protein localization to cell-cell junction) AnnotationAssertion(Annotation( "GOC:aruk") Annotation( "GOC:bc") Annotation( "PMID:26706435") "Any process that modulates the frequency, rate or extent of protein localization to cell-cell junction.") -AnnotationAssertion( "bc") AnnotationAssertion( "2019-06-11T11:17:15Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0150106") @@ -89594,7 +87945,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of protein localization to cell-cell junction) AnnotationAssertion(Annotation( "GOC:aruk") Annotation( "GOC:bc") Annotation( "PMID:26706435") "Any process that activates or increases the frequency, rate or extent of protein localization to cell-cell junction.") -AnnotationAssertion( "bc") AnnotationAssertion( "2019-06-11T11:23:58Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0150107") @@ -89604,7 +87954,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of transepithelial transport) AnnotationAssertion(Annotation( "GOC:aruk") Annotation( "PMID:27593915") "Any process that modulates the frequency, rate or extent of transepithelial transport.") -AnnotationAssertion( "bc") AnnotationAssertion( "2019-09-15T07:16:49Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0150111") @@ -89614,7 +87963,6 @@ EquivalentClasses( ObjectIntersection # Class: (cell-substrate junction organization) AnnotationAssertion(Annotation( "GOC:aruk") Annotation( "GOC:bc") Annotation( "PMID:10419689") Annotation( "PMID:1643657") Annotation( "PMID:16805308") Annotation( "PMID:26923917") Annotation( "PMID:8314002") "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a cell-substrate junction. A cell-substrate junction is a specialized region of connection between a cell and the extracellular matrix.") -AnnotationAssertion( "bc") AnnotationAssertion( "2019-11-14T11:06:29Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0150115") @@ -89624,7 +87972,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of cell-substrate junction organization) AnnotationAssertion(Annotation( "GOC:aruk") "Any process that modulates the frequency, rate or extent of cell-substrate junction organization.") -AnnotationAssertion( "bc") AnnotationAssertion( "2019-11-14T12:12:27Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0150116") @@ -89634,7 +87981,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of cell-substrate junction organization) AnnotationAssertion(Annotation( "GOC:aruk") "Any process that activates or increases the frequency, rate or extent of cell-substrate junction organization.") -AnnotationAssertion( "bc") AnnotationAssertion( "2019-11-14T12:15:07Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0150117") @@ -89644,7 +87990,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of cell-substrate junction organization) AnnotationAssertion(Annotation( "GOC:aruk") "Any process that stops, prevents or reduces the frequency, rate or extent of cell-substrate junction organization.") -AnnotationAssertion( "bc") AnnotationAssertion( "2019-11-14T12:16:32Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0150118") @@ -89654,7 +87999,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of protein localization to cell-cell junction) AnnotationAssertion(Annotation( "GOC:aruk") Annotation( "GOC:bc") "Any process that stops, prevents or reduces the frequency, rate or extent of protein localization to cell-cell junction.") -AnnotationAssertion( "bc") AnnotationAssertion( "2019-11-21T13:53:34Z") AnnotationAssertion( "negative regulation of protein localisation to cell-cell junction") AnnotationAssertion( "biological_process") @@ -89665,7 +88009,6 @@ EquivalentClasses( ObjectIntersection # Class: (cell junction disassembly) AnnotationAssertion(Annotation( "GOC:aruk") Annotation( "PMID:25490267") "The disaggregation of a cell junction into its constituent components.") -AnnotationAssertion( "bc") AnnotationAssertion( "2019-12-08T11:12:13Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0150146") @@ -89675,7 +88018,6 @@ EquivalentClasses( ObjectIntersection # Class: (cell-cell junction disassembly) AnnotationAssertion(Annotation( "GOC:aruk") Annotation( "PMID:25490267") "The disaggregation of a cell-cell junction into its constituent components.") -AnnotationAssertion( "bc") AnnotationAssertion( "2019-12-08T11:16:14Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0150147") @@ -89685,7 +88027,6 @@ EquivalentClasses( ObjectIntersection # Class: (transport across blood-cerebrospinal fluid barrier) AnnotationAssertion(Annotation( "GOC:aruk") Annotation( "GOC:bc") Annotation( "PMID:21349151") "The directed movement of substances (e.g. macromolecules, small molecules, ions) through the blood-cerebrospinal fluid barrier.") -AnnotationAssertion( "bc") AnnotationAssertion( "2020-03-26T14:43:04Z") AnnotationAssertion( "transport across BCSFB") AnnotationAssertion( "transport across blood-CSF barrier") @@ -89700,7 +88041,6 @@ SubClassOf( (regulation of transport across blood-brain barrier) AnnotationAssertion(Annotation( "GOC:aruk") Annotation( "GOC:bc") Annotation( "PMID:29377008") Annotation( "PMID:30280653") "Any process that modulates the frequency, rate or extent of transport across the blood-brain barrier.") -AnnotationAssertion( "bc") AnnotationAssertion( "2020-03-26T19:22:26Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0150200") @@ -89711,7 +88051,6 @@ SubClassOf( ObjectSomeValuesFrom( (positive regulation of transport across blood-brain barrier) AnnotationAssertion(Annotation( "GOC:aruk") Annotation( "GOC:bc") Annotation( "PMID:29377008") Annotation( "PMID:30280653") "Any process that activates or increases the frequency, rate or extent of transport across blood-brain barrier.") -AnnotationAssertion( "bc") AnnotationAssertion( "2020-03-26T19:26:38Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0150201") @@ -89722,7 +88061,6 @@ SubClassOf( ObjectSomeValuesFrom( (negative regulation of transport across blood-brain barrier) AnnotationAssertion(Annotation( "GOC:aruk") Annotation( "GOC:bc") Annotation( "PMID:29377008") Annotation( "PMID:30280653") "Any process that stops, prevents or reduces the frequency, rate or extent of transport across blood-brain barrier.") -AnnotationAssertion( "bc") AnnotationAssertion( "2020-03-26T19:28:51Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0150202") @@ -89733,7 +88071,6 @@ SubClassOf( ObjectSomeValuesFrom( (Leydig cell proliferation) AnnotationAssertion(Annotation( "PMID:29632025") "The multiplication or reproduction of Leydig cells, resulting in the expansion of a cell population. Leydig cells are interstitial cells located adjacent to the seminiferous tubules in the testis which produce testosterone.") -AnnotationAssertion( "rynl") AnnotationAssertion( "2022-02-08T20:09:53Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0160024") @@ -89743,7 +88080,6 @@ EquivalentClasses( ObjectIntersection # Class: (somatic sensory system development) AnnotationAssertion(Annotation( "PMID:25832476") Annotation( "PMID:31399790") "The process whose specific outcome is the progression of a somatic sensory system over time from its formation to the mature structure. Somatic sensory system is the sensory system for the sense of touch and pain.") -AnnotationAssertion( "rynl") AnnotationAssertion( "2022-07-07T16:49:26Z") AnnotationAssertion( "somatosensory system development") AnnotationAssertion( "biological_process") @@ -89756,7 +88092,6 @@ SubClassOf( "PMID:10191060") "The regulated release of catecholamine by a cell in which the catecholamine acts as a neurotransmitter.") AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/23804"^^xsd:anyURI) -AnnotationAssertion( "rynl") AnnotationAssertion( "2022-08-17T00:36:44Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0160043") @@ -89767,7 +88102,6 @@ EquivalentClasses( ObjectIntersection AnnotationAssertion(Annotation( "PMID:33842480") "The process of fusing together the edges of a craniofacial suture.") AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/23213"^^xsd:anyURI) -AnnotationAssertion( "rynl") AnnotationAssertion( "2022-08-19T23:18:54Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0160048") @@ -89778,7 +88112,6 @@ EquivalentClasses( ObjectIntersection AnnotationAssertion(Annotation( "PMID:21739672") Annotation( "PMID:31570879") "The process in which an activated T cell acquires specialized features of an exhausted T cell.") AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/25698"^^xsd:anyURI) -AnnotationAssertion( "rynl") AnnotationAssertion( "2023-07-14T22:56:05Z") AnnotationAssertion( "T cell exhaustion") AnnotationAssertion( "biological_process") @@ -89791,7 +88124,6 @@ EquivalentClasses( ObjectIntersection AnnotationAssertion(Annotation( "PMID:23020903") "The process whose specific outcome is the progression of cordate pharynx over time, from its formation to the mature structure.") AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/18285"^^xsd:anyURI) -AnnotationAssertion( "rynl") AnnotationAssertion( "2023-08-29T21:05:28Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0160093") @@ -89804,7 +88136,6 @@ AnnotationAssertion(Annotation( "https://github.com/geneontology/go-ontology/issues/26601"^^xsd:anyURI) AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/26780"^^xsd:anyURI) AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/27521"^^xsd:anyURI) -AnnotationAssertion( "rynl") AnnotationAssertion( "2023-12-13T00:09:44Z") AnnotationAssertion(Annotation( "skos:broadMatch") "RHEA:28695") AnnotationAssertion( "hydrogencarbonate channel activity") @@ -89818,7 +88149,6 @@ SubClassOf( ObjectSomeValuesFrom( "PMID:30650357") Annotation( "PMID:33815406") "The process of regulating the proliferation and elimination of CD8-positive alpha-beta T cells such that the total number of CD8-positive alpha-beta T cells within a whole or part of an organism is stable over time in the absence of an outside stimulus.") AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/27184"^^xsd:anyURI) -AnnotationAssertion( "rynl") AnnotationAssertion( "2024-03-04T23:49:25Z") AnnotationAssertion( "CD8+ T cell homeostasis") AnnotationAssertion( "CD8-positive T cell homeostasis") @@ -89831,7 +88161,6 @@ EquivalentClasses( ObjectIntersection AnnotationAssertion(Annotation( "PMID:36288320") "Enables the transfer of histamine from one side of a membrane to the other.") AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/27277"^^xsd:anyURI) -AnnotationAssertion( "rynl") AnnotationAssertion( "2024-03-15T16:40:36Z") AnnotationAssertion( "molecular_function") AnnotationAssertion( "GO:0160173") @@ -89842,7 +88171,6 @@ EquivalentClasses( ObjectIntersection AnnotationAssertion(Annotation( "PMID:11823786") "Enables the transmembrane transfer of a cation by a channel that opens when glycine is bound by the channel complex or one of its constituent parts on the extracellular side of the plasma membrane.") AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/28887"^^xsd:anyURI) -AnnotationAssertion( "rynl") AnnotationAssertion( "2024-09-10T16:55:41Z") AnnotationAssertion( "molecular_function") AnnotationAssertion( "GO:0160212") @@ -89854,7 +88182,6 @@ SubClassOf( "GOC:curators") "Enables the transfer of a lipid from one side of a membrane to the other.") AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/27252"^^xsd:anyURI) -AnnotationAssertion( "ew") AnnotationAssertion( "2024-03-15T18:47:58Z") AnnotationAssertion( "molecular_function") AnnotationAssertion( "GO:0170055") @@ -89865,7 +88192,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of dendrite development) AnnotationAssertion(Annotation( "GOC:TermGenie") "Any process that activates or increases the frequency, rate or extent of dendrite development.") -AnnotationAssertion( "hjd") AnnotationAssertion( "2012-01-09T10:41:31Z") AnnotationAssertion( "biological_process") AnnotationAssertion(Annotation( "GOC:TermGenie") "up regulation of dendrite development") @@ -89876,7 +88202,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of cytokine production involved in inflammatory response) AnnotationAssertion(Annotation( "GOC:TermGenie") "Any process that modulates the frequency, rate or extent of cytokine production involved in inflammatory response.") -AnnotationAssertion( "rph") AnnotationAssertion( "2012-01-11T09:34:27Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "regulation of cytokine production involved in acute inflammatory response") AnnotationAssertion( "biological_process") @@ -89887,7 +88212,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of cytokine production involved in inflammatory response) AnnotationAssertion(Annotation( "GOC:TermGenie") "Any process that stops, prevents or reduces the frequency, rate or extent of cytokine production involved in inflammatory response.") -AnnotationAssertion( "rph") AnnotationAssertion( "2012-01-11T09:34:31Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of cytokine production involved in acute inflammatory response") AnnotationAssertion(Annotation( "GOC:TermGenie") "negative regulation of cytokine production involved in acute inflammatory response") @@ -89900,7 +88224,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of cytokine production involved in inflammatory response) AnnotationAssertion(Annotation( "GOC:TermGenie") "Any process that activates or increases the frequency, rate or extent of cytokine production involved in inflammatory response.") -AnnotationAssertion( "rph") AnnotationAssertion( "2012-01-11T09:34:35Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "up regulation of cytokine production involved in acute inflammatory response") AnnotationAssertion(Annotation( "GOC:TermGenie") "positive regulation of cytokine production involved in acute inflammatory response") @@ -89913,7 +88236,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of hemostasis) AnnotationAssertion(Annotation( "GOC:TermGenie") "Any process that modulates the frequency, rate or extent of hemostasis.") -AnnotationAssertion( "jl") AnnotationAssertion( "2012-01-19T03:23:38Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:1900046") @@ -89925,7 +88247,6 @@ SubClassOf( (negative regulation of hemostasis) AnnotationAssertion(Annotation( "GOC:TermGenie") "Any process that stops, prevents or reduces the frequency, rate or extent of hemostasis.") -AnnotationAssertion( "jl") AnnotationAssertion( "2012-01-19T03:23:42Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of hemostasis") AnnotationAssertion(Annotation( "GOC:TermGenie") "down-regulation of hemostasis") @@ -89941,7 +88262,6 @@ SubClassOf( (positive regulation of hemostasis) AnnotationAssertion(Annotation( "GOC:TermGenie") "Any process that activates or increases the frequency, rate or extent of hemostasis.") -AnnotationAssertion( "jl") AnnotationAssertion( "2012-01-19T03:23:45Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "up regulation of hemostasis") AnnotationAssertion(Annotation( "GOC:TermGenie") "up-regulation of hemostasis") @@ -89957,7 +88277,6 @@ SubClassOf( (regulation of neuromuscular synaptic transmission) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:kmv") "Any process that modulates the frequency, rate or extent of neuromuscular synaptic transmission.") -AnnotationAssertion( "kmv") AnnotationAssertion( "2012-01-26T10:14:10Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:1900073") @@ -89967,7 +88286,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of neuromuscular synaptic transmission) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:kmv") "Any process that stops, prevents or reduces the frequency, rate or extent of neuromuscular synaptic transmission.") -AnnotationAssertion( "kmv") AnnotationAssertion( "2012-01-26T10:14:18Z") AnnotationAssertion( "biological_process") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of neuromuscular synaptic transmission") @@ -89981,7 +88299,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of neuromuscular synaptic transmission) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:kmv") "Any process that activates or increases the frequency, rate or extent of neuromuscular synaptic transmission.") -AnnotationAssertion( "kmv") AnnotationAssertion( "2012-01-26T10:14:22Z") AnnotationAssertion( "biological_process") AnnotationAssertion(Annotation( "GOC:TermGenie") "activation of neuromuscular synaptic transmission") @@ -89995,7 +88312,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of cellular response to insulin stimulus) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:yaf") "Any process that modulates the frequency, rate or extent of cellular response to insulin stimulus.") -AnnotationAssertion( "yaf") AnnotationAssertion( "2012-01-31T11:22:22Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:1900076") @@ -90005,7 +88321,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of cellular response to insulin stimulus) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:yaf") "Any process that stops, prevents or reduces the frequency, rate or extent of cellular response to insulin stimulus.") -AnnotationAssertion( "yaf") AnnotationAssertion( "2012-01-31T11:23:15Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of cellular response to insulin stimulus") AnnotationAssertion(Annotation( "GOC:TermGenie") "down-regulation of cellular response to insulin stimulus") @@ -90019,7 +88334,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of cellular response to insulin stimulus) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:yaf") "Any process that activates or increases the frequency, rate or extent of cellular response to insulin stimulus.") -AnnotationAssertion( "yaf") AnnotationAssertion( "2012-01-31T11:24:30Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "up regulation of cellular response to insulin stimulus") AnnotationAssertion(Annotation( "GOC:TermGenie") "up-regulation of cellular response to insulin stimulus") @@ -90033,7 +88347,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of plasma cell differentiation) AnnotationAssertion(Annotation( "GOC:TermGenie") "Any process that modulates the frequency, rate or extent of plasma cell differentiation.") -AnnotationAssertion( "bf") AnnotationAssertion( "2012-02-15T10:46:00Z") AnnotationAssertion( "biological_process") AnnotationAssertion(Annotation( "GOC:TermGenie") "regulation of plasma cell development") @@ -90047,7 +88360,6 @@ SubClassOf( (negative regulation of plasma cell differentiation) AnnotationAssertion(Annotation( "GOC:TermGenie") "Any process that stops, prevents or reduces the frequency, rate or extent of plasma cell differentiation.") -AnnotationAssertion( "bf") AnnotationAssertion( "2012-02-15T10:46:05Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of plasma cell differentiation") AnnotationAssertion(Annotation( "GOC:TermGenie") "down-regulation of plasma cell differentiation") @@ -90070,7 +88382,6 @@ SubClassOf( (positive regulation of plasma cell differentiation) AnnotationAssertion(Annotation( "GOC:TermGenie") "Any process that activates or increases the frequency, rate or extent of plasma cell differentiation.") -AnnotationAssertion( "bf") AnnotationAssertion( "2012-02-15T10:46:08Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "up regulation of plasma cell differentiation") AnnotationAssertion(Annotation( "GOC:TermGenie") "up-regulation of plasma cell differentiation") @@ -90093,7 +88404,6 @@ SubClassOf( (extracellular regulation of signal transduction) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:signaling") "Any regulation of signal transduction that takes place in the extracellular region.") -AnnotationAssertion( "bf") AnnotationAssertion( "2012-02-22T10:21:48Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "regulation of signaling pathway in extracellular region") AnnotationAssertion(Annotation( "GOC:TermGenie") "regulation of signalling pathway in extracellular region") @@ -90105,7 +88415,6 @@ EquivalentClasses( ObjectIntersection # Class: (extracellular negative regulation of signal transduction) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:signaling") "Any negative regulation of signal transduction that takes place in extracellular region.") -AnnotationAssertion( "bf") AnnotationAssertion( "2012-02-22T10:27:56Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of signal transduction in extracellular region") AnnotationAssertion(Annotation( "GOC:TermGenie") "down-regulation of signal transduction in extracellular region") @@ -90122,7 +88431,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of execution phase of apoptosis) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:mtg_apoptosis") "Any process that modulates the frequency, rate or extent of execution phase of apoptosis.") -AnnotationAssertion( "pr") AnnotationAssertion( "2012-02-22T11:26:20Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:1900117") @@ -90132,7 +88440,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of execution phase of apoptosis) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:mtg_apoptosis") "Any process that stops, prevents or reduces the frequency, rate or extent of execution phase of apoptosis.") -AnnotationAssertion( "pr") AnnotationAssertion( "2012-02-22T11:26:24Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of execution phase of apoptosis") AnnotationAssertion(Annotation( "GOC:TermGenie") "down-regulation of execution phase of apoptosis") @@ -90147,7 +88454,6 @@ SubClassOf( ObjectSomeValuesFrom( (positive regulation of execution phase of apoptosis) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:mtg_apoptosis") "Any process that activates or increases the frequency, rate or extent of execution phase of apoptosis.") -AnnotationAssertion( "pr") AnnotationAssertion( "2012-02-22T11:26:27Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "up regulation of execution phase of apoptosis") AnnotationAssertion(Annotation( "GOC:TermGenie") "up-regulation of execution phase of apoptosis") @@ -90162,7 +88468,6 @@ SubClassOf( ObjectSomeValuesFrom( (regulation of receptor binding) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:signaling") "Any process that modulates the frequency, rate or extent of a protein or other molecule binding to a receptor.") -AnnotationAssertion( "bf") AnnotationAssertion( "2012-02-22T11:40:53Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "regulation of receptor ligand") AnnotationAssertion( "biological_process") @@ -90174,7 +88479,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of receptor binding) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:signaling") "Any process that stops, prevents or reduces the frequency, rate or extent of a protein or other molecule binding to a receptor.") -AnnotationAssertion( "bf") AnnotationAssertion( "2012-02-22T11:40:57Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of receptor binding") AnnotationAssertion(Annotation( "GOC:TermGenie") "down-regulation of receptor binding") @@ -90191,7 +88495,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of receptor binding) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:signaling") "Any process that activates or increases the frequency, rate or extent of a protein or other molecule binding to a receptor.") -AnnotationAssertion( "bf") AnnotationAssertion( "2012-02-22T11:41:00Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "up regulation of receptor binding") AnnotationAssertion(Annotation( "GOC:TermGenie") "upregulation of receptor binding") @@ -90205,7 +88508,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of hyaluronan biosynthetic process) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:yaf") "Any process that modulates the frequency, rate or extent of hyaluronan biosynthetic process.") -AnnotationAssertion( "yaf") AnnotationAssertion( "2012-02-23T01:09:21Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "regulation of hyaluronan anabolism") AnnotationAssertion(Annotation( "GOC:TermGenie") "regulation of hyaluronan biosynthesis") @@ -90220,7 +88522,6 @@ SubClassOf( (negative regulation of hyaluronan biosynthetic process) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:yaf") "Any process that stops, prevents or reduces the frequency, rate or extent of hyaluronan biosynthetic process.") -AnnotationAssertion( "yaf") AnnotationAssertion( "2012-02-23T01:09:29Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of hyaluronan anabolism") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of hyaluronan biosynthesis") @@ -90255,7 +88556,6 @@ SubClassOf( (positive regulation of hyaluronan biosynthetic process) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:yaf") "Any process that activates or increases the frequency, rate or extent of hyaluronan biosynthetic process.") -AnnotationAssertion( "yaf") AnnotationAssertion( "2012-02-23T01:09:33Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "activation of hyaluronan anabolism") AnnotationAssertion(Annotation( "GOC:TermGenie") "activation of hyaluronan biosynthesis") @@ -90290,7 +88590,6 @@ SubClassOf( (regulation of lipid binding) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:pm") "Any process that modulates the frequency, rate or extent of lipid binding.") -AnnotationAssertion( "pm") AnnotationAssertion( "2012-02-23T04:05:03Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:1900130") @@ -90301,7 +88600,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of lipid binding) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:pm") "Any process that stops, prevents or reduces the frequency, rate or extent of lipid binding.") -AnnotationAssertion( "pm") AnnotationAssertion( "2012-02-23T04:05:07Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of lipid binding") AnnotationAssertion(Annotation( "GOC:TermGenie") "down-regulation of lipid binding") @@ -90316,7 +88614,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of lipid binding) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:pm") "Any process that activates or increases the frequency, rate or extent of lipid binding.") -AnnotationAssertion( "pm") AnnotationAssertion( "2012-02-23T04:05:11Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "up regulation of lipid binding") AnnotationAssertion(Annotation( "GOC:TermGenie") "up-regulation of lipid binding") @@ -90331,7 +88628,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of renin secretion into blood stream) AnnotationAssertion(Annotation( "GOC:TermGenie") "Any process that modulates the frequency, rate or extent of renin secretion into blood stream.") -AnnotationAssertion( "rph") AnnotationAssertion( "2012-02-27T10:32:01Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "regulation of renin release into blood stream") AnnotationAssertion( "biological_process") @@ -90344,7 +88640,6 @@ SubClassOf( ObjectSomeValuesFrom( (negative regulation of renin secretion into blood stream) AnnotationAssertion(Annotation( "GOC:TermGenie") "Any process that stops, prevents or reduces the frequency, rate or extent of renin secretion into blood stream.") -AnnotationAssertion( "rph") AnnotationAssertion( "2012-02-27T10:32:05Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of renin release into blood stream") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of renin secretion into blood stream") @@ -90363,7 +88658,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of renin secretion into blood stream) AnnotationAssertion(Annotation( "GOC:TermGenie") "Any process that activates or increases the frequency, rate or extent of renin secretion into blood stream.") -AnnotationAssertion( "rph") AnnotationAssertion( "2012-02-27T10:32:08Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "positive regulation of renin release into blood stream") AnnotationAssertion(Annotation( "GOC:TermGenie") "up regulation of renin release into blood stream") @@ -90382,7 +88676,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of oligodendrocyte apoptotic process) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:yaf") "Any process that modulates the frequency, rate or extent of oligodendrocyte apoptotic process.") -AnnotationAssertion( "yaf") AnnotationAssertion( "2012-03-06T10:22:45Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "regulation of oligodendrocyte apoptosis") AnnotationAssertion( "biological_process") @@ -90393,7 +88686,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of oligodendrocyte apoptotic process) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:yaf") "Any process that stops, prevents or reduces the frequency, rate or extent of oligodendrocyte apoptotic process.") -AnnotationAssertion( "yaf") AnnotationAssertion( "2012-03-06T10:22:50Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of oligodendrocyte apoptotic process") AnnotationAssertion(Annotation( "GOC:TermGenie") "down-regulation of oligodendrocyte apoptotic process") @@ -90412,7 +88704,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of oligodendrocyte apoptotic process) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:yaf") "Any process that activates or increases the frequency, rate or extent of oligodendrocyte apoptotic process.") -AnnotationAssertion( "yaf") AnnotationAssertion( "2012-03-06T10:22:54Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "up regulation of oligodendrocyte apoptotic process") AnnotationAssertion(Annotation( "GOC:TermGenie") "up-regulation of oligodendrocyte apoptotic process") @@ -90431,7 +88722,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of Schwann cell migration) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:sjw") "Any process that modulates the frequency, rate or extent of Schwann cell migration.") -AnnotationAssertion( "bf") AnnotationAssertion( "2012-03-06T04:14:50Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:1900147") @@ -90441,7 +88731,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of Schwann cell migration) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:sjw") "Any process that stops, prevents or reduces the frequency, rate or extent of Schwann cell migration.") -AnnotationAssertion( "bf") AnnotationAssertion( "2012-03-06T04:14:55Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of Schwann cell migration") AnnotationAssertion(Annotation( "GOC:TermGenie") "down-regulation of Schwann cell migration") @@ -90455,7 +88744,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of Schwann cell migration) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:sjw") "Any process that activates or increases the frequency, rate or extent of Schwann cell migration.") -AnnotationAssertion( "bf") AnnotationAssertion( "2012-03-06T04:14:58Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "up regulation of Schwann cell migration") AnnotationAssertion(Annotation( "GOC:TermGenie") "up-regulation of Schwann cell migration") @@ -90469,7 +88757,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of defense response to fungus) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:dhl") Annotation( "PMID:22242006") "Any process that modulates the frequency, rate or extent of defense response to fungus.") -AnnotationAssertion( "dhl") AnnotationAssertion( "2012-03-06T10:00:16Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "regulation of defence response to fungi") AnnotationAssertion(Annotation( "GOC:TermGenie") "regulation of defence response to fungus") @@ -90487,7 +88774,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of bone mineralization involved in bone maturation) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:TermGenie") "Any process that modulates the frequency, rate or extent of bone mineralization involved in bone maturation.") -AnnotationAssertion( "vk") AnnotationAssertion( "2012-03-07T08:55:07Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:1900157") @@ -90497,7 +88783,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of bone mineralization involved in bone maturation) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:TermGenie") "Any process that stops, prevents or reduces the frequency, rate or extent of bone mineralization involved in bone maturation.") -AnnotationAssertion( "vk") AnnotationAssertion( "2012-03-07T08:55:12Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of bone mineralization involved in bone maturation") AnnotationAssertion(Annotation( "GOC:TermGenie") "down-regulation of bone mineralization involved in bone maturation") @@ -90511,7 +88796,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of bone mineralization involved in bone maturation) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:TermGenie") "Any process that activates or increases the frequency, rate or extent of bone mineralization involved in bone maturation.") -AnnotationAssertion( "vk") AnnotationAssertion( "2012-03-07T08:55:16Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "up regulation of bone mineralization involved in bone maturation") AnnotationAssertion(Annotation( "GOC:TermGenie") "up-regulation of bone mineralization involved in bone maturation") @@ -90525,7 +88809,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of protein localization to nucleus) AnnotationAssertion(Annotation( "GOC:TermGenie") "Any process that modulates the frequency, rate or extent of protein localization to nucleus.") -AnnotationAssertion( "bf") AnnotationAssertion( "2012-03-12T01:23:44Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "regulation of protein localisation to nucleus") AnnotationAssertion(Annotation( "GOC:TermGenie") "regulation of protein localization in cell nucleus") @@ -90538,7 +88821,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of protein localization to nucleus) AnnotationAssertion(Annotation( "GOC:TermGenie") "Any process that stops, prevents or reduces the frequency, rate or extent of protein localization to nucleus.") -AnnotationAssertion( "bf") AnnotationAssertion( "2012-03-12T01:23:48Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of protein localisation to nucleus") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of protein localization in cell nucleus") @@ -90567,7 +88849,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of protein localization to nucleus) AnnotationAssertion(Annotation( "GOC:TermGenie") "Any process that activates or increases the frequency, rate or extent of protein localization to nucleus.") -AnnotationAssertion( "bf") AnnotationAssertion( "2012-03-12T01:23:52Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "activation of protein localization in nucleus") AnnotationAssertion(Annotation( "GOC:TermGenie") "positive regulation of protein localisation to nucleus") @@ -90596,7 +88877,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of oocyte maturation) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:kmv") "Any process that modulates the frequency, rate or extent of oocyte maturation.") -AnnotationAssertion( "kmv") AnnotationAssertion( "2012-03-19T09:41:18Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:1900193") @@ -90606,7 +88886,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of oocyte maturation) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:kmv") "Any process that stops, prevents or reduces the frequency, rate or extent of oocyte maturation.") -AnnotationAssertion( "kmv") AnnotationAssertion( "2012-03-19T09:41:27Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of oocyte maturation") AnnotationAssertion(Annotation( "GOC:TermGenie") "down-regulation of oocyte maturation") @@ -90620,7 +88899,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of oocyte maturation) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:kmv") "Any process that activates or increases the frequency, rate or extent of oocyte maturation.") -AnnotationAssertion( "kmv") AnnotationAssertion( "2012-03-19T09:41:35Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "up regulation of oocyte maturation") AnnotationAssertion(Annotation( "GOC:TermGenie") "up-regulation of oocyte maturation") @@ -90634,7 +88912,6 @@ EquivalentClasses( ObjectIntersection # Class: (mesenchymal cell apoptotic process involved in metanephros development) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:mtg_apoptosis") Annotation( "GOC:mtg_kidney_jan10") Annotation( "GOC:yaf") Annotation( "PMID:17314325") "Any mesenchymal cell apoptotic process that is involved in metanephros development.") -AnnotationAssertion( "yaf") AnnotationAssertion( "2012-03-21T11:58:05Z") AnnotationAssertion( "mesenchymal cell apoptosis involved in metanephros development") AnnotationAssertion( "biological_process") @@ -90645,7 +88922,6 @@ EquivalentClasses( ObjectIntersection # Class: (apoptotic process involved in metanephric collecting duct development) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:mtg_kidney_jan10") Annotation( "GOC:yaf") Annotation( "PMID:17314325") "Any apoptotic process that is involved in metanephric collecting duct development.") -AnnotationAssertion( "yaf") AnnotationAssertion( "2012-03-21T01:21:32Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "apoptotic cell death of metanephric collecting duct development") AnnotationAssertion(Annotation( "GOC:TermGenie") "apoptotic process of metanephric collecting duct development") @@ -90664,7 +88940,6 @@ SubClassOf( (apoptotic process involved in metanephric nephron tubule development) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:mtg_kidney_jan10") Annotation( "GOC:yaf") Annotation( "PMID:17314325") "Any apoptotic process that is involved in metanephric nephron tubule development.") -AnnotationAssertion( "yaf") AnnotationAssertion( "2012-03-21T01:21:45Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "apoptotic cell death of metanephric nephron tubule development") AnnotationAssertion(Annotation( "GOC:TermGenie") "apoptotic process of metanephric nephron tubule development") @@ -90683,7 +88958,6 @@ SubClassOf( (regulation of pronephric nephron tubule development) AnnotationAssertion(Annotation( "GOC:TermGenie") "Any process that modulates the frequency, rate or extent of pronephric nephron tubule development.") -AnnotationAssertion( "bf") AnnotationAssertion( "2012-03-22T09:23:13Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:1900206") @@ -90693,7 +88967,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of pronephric nephron tubule development) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:bf") Annotation( "PMID:9758706") "Any process that stops, prevents or reduces the frequency, rate or extent of pronephric nephron tubule development.") -AnnotationAssertion( "bf") AnnotationAssertion( "2012-03-22T09:23:23Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of pronephric nephron tubule development") AnnotationAssertion(Annotation( "GOC:TermGenie") "down-regulation of pronephric nephron tubule development") @@ -90707,7 +88980,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of mesenchymal cell apoptotic process involved in metanephros development) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:mtg_apoptosis") Annotation( "GOC:mtg_kidney_jan10") Annotation( "GOC:yaf") Annotation( "PMID:17314325") "Any process that modulates the frequency, rate or extent of mesenchymal cell apoptotic process involved in metanephros development.") -AnnotationAssertion( "yaf") AnnotationAssertion( "2012-03-22T10:52:50Z") AnnotationAssertion( "regulation of mesenchymal cell apoptosis involved in metanephros development") AnnotationAssertion( "biological_process") @@ -90718,7 +88990,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of mesenchymal cell apoptotic process involved in metanephros development) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:mtg_apoptosis") Annotation( "GOC:mtg_kidney_jan10") Annotation( "GOC:yaf") Annotation( "PMID:17314325") "Any process that stops, prevents or reduces the frequency, rate or extent of mesenchymal cell apoptotic process involved in metanephros development.") -AnnotationAssertion( "yaf") AnnotationAssertion( "2012-03-22T10:53:00Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of mesenchymal cell apoptosis involved in metanephros development") AnnotationAssertion(Annotation( "GOC:TermGenie") "down-regulation of mesenchymal cell apoptosis involved in metanephros development") @@ -90733,7 +89004,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of mesenchymal cell apoptotic process involved in metanephros development) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:mtg_apoptosis") Annotation( "GOC:mtg_kidney_jan10") Annotation( "GOC:yaf") Annotation( "PMID:17314325") "Any process that activates or increases the frequency, rate or extent of mesenchymal cell apoptotic process involved in metanephros development.") -AnnotationAssertion( "yaf") AnnotationAssertion( "2012-03-22T10:53:09Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "up regulation of mesenchymal cell apoptosis involved in metanephros development") AnnotationAssertion(Annotation( "GOC:TermGenie") "up-regulation of mesenchymal cell apoptosis involved in metanephros development") @@ -90748,7 +89018,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of apoptotic process involved in metanephric collecting duct development) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:mtg_kidney_jan10") Annotation( "GOC:yaf") Annotation( "PMID:17314325") "Any process that modulates the frequency, rate or extent of apoptotic process involved in metanephric collecting duct development.") -AnnotationAssertion( "yaf") AnnotationAssertion( "2012-03-22T10:53:21Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "regulation of apoptotic cell death of metanephric collecting duct development") AnnotationAssertion(Annotation( "GOC:TermGenie") "regulation of apoptotic process of metanephric collecting duct development") @@ -90766,7 +89035,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of apoptotic process involved in metanephric collecting duct development) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:mtg_kidney_jan10") Annotation( "GOC:yaf") Annotation( "PMID:17314325") "Any process that stops, prevents or reduces the frequency, rate or extent of apoptotic process involved in metanephric collecting duct development.") -AnnotationAssertion( "yaf") AnnotationAssertion( "2012-03-22T10:53:31Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of apoptotic cell death of metanephric collecting duct development") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of apoptotic process involved in metanephric collecting duct development") @@ -90820,7 +89088,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of apoptotic process involved in metanephric collecting duct development) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:mtg_kidney_jan10") Annotation( "GOC:yaf") Annotation( "PMID:17314325") "Any process that activates or increases the frequency, rate or extent of apoptotic process involved in metanephric collecting duct development.") -AnnotationAssertion( "yaf") AnnotationAssertion( "2012-03-22T10:53:39Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "activation of apoptotic cell death of metanephric collecting duct development") AnnotationAssertion(Annotation( "GOC:TermGenie") "activation of apoptotic process of metanephric collecting duct development") @@ -90874,7 +89141,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of apoptotic process involved in metanephric nephron tubule development) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:mtg_kidney_jan10") Annotation( "GOC:yaf") Annotation( "PMID:17314325") "Any process that modulates the frequency, rate or extent of apoptotic process involved in metanephric nephron tubule development.") -AnnotationAssertion( "yaf") AnnotationAssertion( "2012-03-22T10:53:51Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "regulation of apoptotic cell death of metanephric nephron tubule development") AnnotationAssertion(Annotation( "GOC:TermGenie") "regulation of apoptotic process of metanephric nephron tubule development") @@ -90892,7 +89158,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of apoptotic process involved in metanephric nephron tubule development) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:mtg_kidney_jan10") Annotation( "GOC:yaf") Annotation( "PMID:17314325") "Any process that stops, prevents or reduces the frequency, rate or extent of apoptotic process involved in metanephric nephron tubule development.") -AnnotationAssertion( "yaf") AnnotationAssertion( "2012-03-22T10:54:01Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of apoptotic cell death of metanephric nephron tubule development") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of apoptotic process involved in metanephric nephron tubule development") @@ -90946,7 +89211,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of apoptotic process involved in metanephric nephron tubule development) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:mtg_kidney_jan10") Annotation( "GOC:yaf") Annotation( "PMID:17314325") "Any process that activates or increases the frequency, rate or extent of apoptotic process involved in metanephric nephron tubule development.") -AnnotationAssertion( "yaf") AnnotationAssertion( "2012-03-22T10:54:09Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "activation of apoptotic cell death of metanephric nephron tubule development") AnnotationAssertion(Annotation( "GOC:TermGenie") "activation of apoptotic process of metanephric nephron tubule development") @@ -91000,7 +89264,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of cytoplasmic translational elongation) AnnotationAssertion(Annotation( "GOC:TermGenie") "Any process that modulates the frequency, rate or extent of cytoplasmic translational elongation.") -AnnotationAssertion( "vw") AnnotationAssertion( "2012-04-03T05:07:02Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:1900247") @@ -91010,7 +89273,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of cytoplasmic translational elongation) AnnotationAssertion(Annotation( "GOC:TermGenie") "Any process that stops, prevents or reduces the frequency, rate or extent of cytoplasmic translational elongation.") -AnnotationAssertion( "vw") AnnotationAssertion( "2012-04-03T05:07:14Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of cytoplasmic translational elongation") AnnotationAssertion(Annotation( "GOC:TermGenie") "down-regulation of cytoplasmic translational elongation") @@ -91025,7 +89287,6 @@ SubClassOf( ObjectSomeValuesFrom( (positive regulation of cytoplasmic translational elongation) AnnotationAssertion(Annotation( "GOC:TermGenie") "Any process that activates or increases the frequency, rate or extent of cytoplasmic translational elongation.") -AnnotationAssertion( "vw") AnnotationAssertion( "2012-04-03T05:07:24Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "up regulation of cytoplasmic translational elongation") AnnotationAssertion(Annotation( "GOC:TermGenie") "up-regulation of cytoplasmic translational elongation") @@ -91039,7 +89300,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of defense response to insect) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "PMID:22474183") "Any process that stops, prevents or reduces the frequency, rate or extent of defense response to insect.") -AnnotationAssertion( "dhl") AnnotationAssertion( "2012-04-12T04:44:00Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of defense response to insect") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of physiological defense response to insect") @@ -91059,7 +89319,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of defense response to insect) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "PMID:22474183") "Any process that activates or increases the frequency, rate or extent of defense response to insect.") -AnnotationAssertion( "dhl") AnnotationAssertion( "2012-04-12T04:44:10Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "positive regulation of physiological defense response to insect") AnnotationAssertion(Annotation( "GOC:TermGenie") "up regulation of defense response to insect") @@ -91078,7 +89337,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of defense response to bacterium) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "PMID:22346749") "Any process that modulates the frequency, rate or extent of defense response to bacterium.") -AnnotationAssertion( "dhl") AnnotationAssertion( "2012-04-24T10:12:43Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "regulation of defence response to bacteria") AnnotationAssertion(Annotation( "GOC:TermGenie") "regulation of defence response to bacterium") @@ -91098,7 +89356,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of defense response to bacterium) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "PMID:22346749") "Any process that stops, prevents or reduces the frequency, rate or extent of defense response to bacterium.") -AnnotationAssertion( "dhl") AnnotationAssertion( "2012-04-24T10:12:54Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of defence response to bacteria") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of defence response to bacterium") @@ -91140,7 +89397,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of defense response to bacterium) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "PMID:22346749") "Any process that activates or increases the frequency, rate or extent of defense response to bacterium.") -AnnotationAssertion( "dhl") AnnotationAssertion( "2012-04-24T10:13:13Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "activation of defence response to bacteria") AnnotationAssertion(Annotation( "GOC:TermGenie") "activation of defence response to bacterium") @@ -91177,7 +89433,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of glutamate receptor signaling pathway) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:TermGenie") "Any process that modulates the frequency, rate or extent of glutamate receptor signaling pathway.") -AnnotationAssertion( "rl") AnnotationAssertion( "2012-04-27T03:45:43Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "regulation of glutamate signaling pathway") AnnotationAssertion(Annotation( "GOC:TermGenie") "regulation of glutamate signalling pathway") @@ -91189,7 +89444,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of glutamate receptor signaling pathway) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:TermGenie") "Any process that stops, prevents or reduces the frequency, rate or extent of glutamate receptor signaling pathway.") -AnnotationAssertion( "rl") AnnotationAssertion( "2012-04-27T03:45:53Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of glutamate receptor signaling pathway") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of glutamate signaling pathway") @@ -91213,7 +89467,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of glutamate receptor signaling pathway) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:TermGenie") "Any process that activates or increases the frequency, rate or extent of glutamate receptor signaling pathway.") -AnnotationAssertion( "rl") AnnotationAssertion( "2012-04-27T03:46:03Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "activation of glutamate signaling pathway") AnnotationAssertion(Annotation( "GOC:TermGenie") "activation of glutamate signalling pathway") @@ -91237,7 +89490,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of glycine import across plasma membrane) AnnotationAssertion(Annotation( "GOC:TermGenie") "Any process that modulates the frequency, rate or extent of glycine import into a cell.") -AnnotationAssertion( "al") AnnotationAssertion( "2012-06-13T07:40:11Z") AnnotationAssertion( "regulation of glycine import") AnnotationAssertion( "biological_process") @@ -91248,7 +89500,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of glycine import across plasma membrane) AnnotationAssertion(Annotation( "GOC:TermGenie") "Any process that stops, prevents or reduces the frequency, rate or extent of glycine import into a cell.") -AnnotationAssertion( "al") AnnotationAssertion( "2012-06-13T07:40:32Z") AnnotationAssertion( "negative regulation of glycine import") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of glycine import") @@ -91263,7 +89514,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of glycine import across plasma membrane) AnnotationAssertion(Annotation( "GOC:TermGenie") "Any process that activates or increases the frequency, rate or extent of glycine import.") -AnnotationAssertion( "al") AnnotationAssertion( "2012-06-13T07:40:40Z") AnnotationAssertion( "positive regulation of glycine import") AnnotationAssertion(Annotation( "GOC:TermGenie") "up regulation of glycine import") @@ -91278,7 +89528,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of potassium ion transmembrane transporter activity) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:TermGenie") "Any process that modulates the frequency, rate or extent of potassium ion transmembrane transporter activity.") -AnnotationAssertion( "rl") AnnotationAssertion( "2012-06-15T01:13:49Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "regulation of potassium transporter activity") AnnotationAssertion( "biological_process") @@ -91291,7 +89540,6 @@ SubClassOf( ObjectSomeValuesFrom( (negative regulation of potassium ion transmembrane transporter activity) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:TermGenie") "Any process that stops, prevents or reduces the frequency, rate or extent of potassium ion transmembrane transporter activity.") -AnnotationAssertion( "rl") AnnotationAssertion( "2012-06-15T01:14:10Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of potassium ion transmembrane transporter activity") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of potassium transporter activity") @@ -91312,7 +89560,6 @@ SubClassOf( ObjectSomeValuesFrom( (positive regulation of potassium ion transmembrane transporter activity) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:TermGenie") "Any process that activates or increases the frequency, rate or extent of potassium ion transmembrane transporter activity.") -AnnotationAssertion( "rl") AnnotationAssertion( "2012-06-15T01:14:18Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "activation of potassium transporter activity") AnnotationAssertion(Annotation( "GOC:TermGenie") "positive regulation of potassium transporter activity") @@ -91333,7 +89580,6 @@ SubClassOf( ObjectSomeValuesFrom( (regulation of calcium ion transmembrane transporter activity) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:TermGenie") "Any process that modulates the frequency, rate or extent of calcium ion transmembrane transporter activity.") -AnnotationAssertion( "rl") AnnotationAssertion( "2012-06-15T07:54:12Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:1901019") @@ -91345,7 +89591,6 @@ SubClassOf( ObjectSomeValuesFrom( (negative regulation of calcium ion transmembrane transporter activity) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:TermGenie") "Any process that stops, prevents or reduces the frequency, rate or extent of calcium ion transmembrane transporter activity.") -AnnotationAssertion( "rl") AnnotationAssertion( "2012-06-15T07:54:32Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of calcium ion transmembrane transporter activity") AnnotationAssertion(Annotation( "GOC:TermGenie") "down-regulation of calcium ion transmembrane transporter activity") @@ -91361,7 +89606,6 @@ SubClassOf( ObjectSomeValuesFrom( (positive regulation of calcium ion transmembrane transporter activity) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:TermGenie") "Any process that activates or increases the frequency, rate or extent of calcium ion transmembrane transporter activity.") -AnnotationAssertion( "rl") AnnotationAssertion( "2012-06-15T07:54:40Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "up regulation of calcium ion transmembrane transporter activity") AnnotationAssertion(Annotation( "GOC:TermGenie") "up-regulation of calcium ion transmembrane transporter activity") @@ -91377,7 +89621,6 @@ SubClassOf( ObjectSomeValuesFrom( (carbohydrate derivative metabolic process) AnnotationAssertion(Annotation( "GOC:TermGenie") "The chemical reactions and pathways involving carbohydrate derivative.") -AnnotationAssertion( "bf") AnnotationAssertion( "2012-07-12T04:05:09Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "carbohydrate derivative metabolism") AnnotationAssertion( "biological_process") @@ -91392,7 +89635,6 @@ EquivalentClasses( ObjectIntersection # Class: (carbohydrate derivative catabolic process) AnnotationAssertion(Annotation( "GOC:TermGenie") "The chemical reactions and pathways resulting in the breakdown of carbohydrate derivative.") -AnnotationAssertion( "bf") AnnotationAssertion( "2012-07-12T04:05:31Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "carbohydrate derivative breakdown") AnnotationAssertion(Annotation( "GOC:TermGenie") "carbohydrate derivative catabolism") @@ -91405,7 +89647,6 @@ EquivalentClasses( ObjectIntersection # Class: (carbohydrate derivative biosynthetic process) AnnotationAssertion(Annotation( "GOC:TermGenie") "The chemical reactions and pathways resulting in the formation of carbohydrate derivative.") -AnnotationAssertion( "bf") AnnotationAssertion( "2012-07-12T04:05:39Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "carbohydrate derivative anabolism") AnnotationAssertion(Annotation( "GOC:TermGenie") "carbohydrate derivative biosynthesis") @@ -91423,7 +89664,6 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) -AnnotationAssertion( "pm") AnnotationAssertion( "2012-07-13T12:32:40Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "insulin metabolism") AnnotationAssertion( "biological_process") @@ -91447,7 +89687,6 @@ DisjointClasses( ObjectSomeValuesFrom # Class: (insulin catabolic process) AnnotationAssertion(Annotation( "GOC:TermGenie") "The chemical reactions and pathways resulting in the breakdown of insulin.") -AnnotationAssertion( "pm") AnnotationAssertion( "2012-07-13T12:33:03Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "insulin breakdown") AnnotationAssertion(Annotation( "GOC:TermGenie") "insulin catabolism") @@ -91462,7 +89701,6 @@ SubClassOf( (mesenchymal cell apoptotic process involved in nephron morphogenesis) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:mtg_apoptosis") "Any mesenchymal cell apoptotic process that is involved in nephron morphogenesis.") -AnnotationAssertion( "pr") AnnotationAssertion( "2012-07-13T01:43:51Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:1901145") @@ -91472,7 +89710,6 @@ EquivalentClasses( ObjectIntersection # Class: (mesenchymal cell apoptotic process involved in mesonephric nephron morphogenesis) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:mtg_apoptosis") "Any mesenchymal cell apoptotic process that is involved in mesonephric nephron morphogenesis.") -AnnotationAssertion( "pr") AnnotationAssertion( "2012-07-13T02:40:43Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:1901146") @@ -91482,7 +89719,6 @@ EquivalentClasses( ObjectIntersection # Class: (mesenchymal cell apoptotic process involved in metanephric nephron morphogenesis) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:mtg_apoptosis") "Any mesenchymal cell apoptotic process that is involved in metanephric nephron morphogenesis.") -AnnotationAssertion( "pr") AnnotationAssertion( "2012-07-13T02:41:12Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:1901147") @@ -91492,7 +89728,6 @@ EquivalentClasses( ObjectIntersection # Class: (gene expression involved in extracellular matrix organization) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:pg") Annotation( "PMID:18668558") "Any gene expression that is involved in extracellular matrix organization. Gene expression includes both transcription to produce an RNA transcript, and the translation of that mRNA into protein. Protein maturation is included in gene expression when required to form an active form of a product from an inactive precursor form.") -AnnotationAssertion( "bf") AnnotationAssertion( "2012-07-16T03:29:30Z") AnnotationAssertion(Annotation( "GOC:bf") "expression of extracellular matrix proteins") AnnotationAssertion( "biological_process") @@ -91504,7 +89739,6 @@ EquivalentClasses( ObjectIntersection # Class: (primary amino compound metabolic process) AnnotationAssertion(Annotation( "GOC:TermGenie") "The chemical reactions and pathways involving primary amino compound.") -AnnotationAssertion( "bf") AnnotationAssertion( "2012-07-18T04:44:39Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "primary amino compound metabolism") AnnotationAssertion( "biological_process") @@ -91515,7 +89749,6 @@ EquivalentClasses( ObjectIntersection # Class: (primary amino compound catabolic process) AnnotationAssertion(Annotation( "GOC:TermGenie") "The chemical reactions and pathways resulting in the breakdown of primary amino compound.") -AnnotationAssertion( "bf") AnnotationAssertion( "2012-07-18T04:45:06Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "primary amino compound breakdown") AnnotationAssertion(Annotation( "GOC:TermGenie") "primary amino compound catabolism") @@ -91528,7 +89761,6 @@ EquivalentClasses( ObjectIntersection # Class: (primary amino compound biosynthetic process) AnnotationAssertion(Annotation( "GOC:TermGenie") "The chemical reactions and pathways resulting in the formation of primary amino compound.") -AnnotationAssertion( "bf") AnnotationAssertion( "2012-07-18T04:45:14Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "primary amino compound anabolism") AnnotationAssertion(Annotation( "GOC:TermGenie") "primary amino compound biosynthesis") @@ -91542,7 +89774,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of trophoblast cell migration) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:TermGenie") "Any process that modulates the frequency, rate or extent of trophoblast cell migration.") -AnnotationAssertion( "vk") AnnotationAssertion( "2012-07-19T07:53:06Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:1901163") @@ -91552,7 +89783,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of trophoblast cell migration) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:TermGenie") "Any process that stops, prevents or reduces the frequency, rate or extent of trophoblast cell migration.") -AnnotationAssertion( "vk") AnnotationAssertion( "2012-07-19T07:53:28Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of trophoblast cell migration") AnnotationAssertion(Annotation( "GOC:TermGenie") "down-regulation of trophoblast cell migration") @@ -91568,7 +89798,6 @@ SubClassOf( ObjectSomeValuesFrom( (positive regulation of trophoblast cell migration) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:TermGenie") "Any process that activates or increases the frequency, rate or extent of trophoblast cell migration.") -AnnotationAssertion( "vk") AnnotationAssertion( "2012-07-19T07:53:35Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "up regulation of trophoblast cell migration") AnnotationAssertion(Annotation( "GOC:TermGenie") "up-regulation of trophoblast cell migration") @@ -91585,7 +89814,6 @@ SubClassOf( ObjectSomeValuesFrom( (neural crest cell migration involved in autonomic nervous system development) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:TermGenie") "Any neural crest cell migration that is involved in autonomic nervous system development.") -AnnotationAssertion( "vk") AnnotationAssertion( "2012-07-19T08:39:56Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:1901166") @@ -91595,7 +89823,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of formation of translation initiation ternary complex) AnnotationAssertion(Annotation( "GOC:TermGenie") "Any process that modulates the frequency, rate or extent of formation of translation initiation ternary complex.") -AnnotationAssertion( "ss") AnnotationAssertion( "2012-07-25T02:26:58Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "regulation of translation initiation ternary complex assembly") AnnotationAssertion( "biological_process") @@ -91606,7 +89833,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of formation of translation initiation ternary complex) AnnotationAssertion(Annotation( "GOC:TermGenie") "Any process that stops, prevents or reduces the frequency, rate or extent of formation of translation initiation ternary complex.") -AnnotationAssertion( "ss") AnnotationAssertion( "2012-07-25T02:27:21Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of formation of translation initiation ternary complex") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of translation initiation ternary complex assembly") @@ -91626,7 +89852,6 @@ SubClassOf( ObjectSomeValuesFrom( (positive regulation of formation of translation initiation ternary complex) AnnotationAssertion(Annotation( "GOC:TermGenie") "Any process that activates or increases the frequency, rate or extent of formation of translation initiation ternary complex.") -AnnotationAssertion( "ss") AnnotationAssertion( "2012-07-25T02:27:29Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "activation of translation initiation ternary complex assembly") AnnotationAssertion(Annotation( "GOC:TermGenie") "positive regulation of translation initiation ternary complex assembly") @@ -91645,7 +89870,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of calcium-mediated signaling involved in cellular response to calcium ion) AnnotationAssertion(Annotation( "GOC:TermGenie") "Any positive regulation of calcium-mediated signaling that is involved in cellular response to calcium ion.") -AnnotationAssertion( "al") AnnotationAssertion( "2012-07-27T10:57:56Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "positive regulation of calcium-mediated signaling involved in cellular response to Ca2+ ion") AnnotationAssertion(Annotation( "GOC:TermGenie") "positive regulation of calcium-mediated signalling involved in cellular response to Ca2+ ion") @@ -91668,7 +89892,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of extracellular matrix assembly) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:TermGenie") "Any process that modulates the frequency, rate or extent of extracellular matrix assembly.") -AnnotationAssertion( "rl") AnnotationAssertion( "2012-07-27T04:04:00Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:1901201") @@ -91679,7 +89902,6 @@ SubClassOf( ObjectSomeValuesFrom( (negative regulation of extracellular matrix assembly) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:TermGenie") "Any process that stops, prevents or reduces the frequency, rate or extent of extracellular matrix assembly.") -AnnotationAssertion( "rl") AnnotationAssertion( "2012-07-27T04:04:24Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of extracellular matrix assembly") AnnotationAssertion(Annotation( "GOC:TermGenie") "down-regulation of extracellular matrix assembly") @@ -91693,7 +89915,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of extracellular matrix assembly) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:TermGenie") "Any process that activates or increases the frequency, rate or extent of extracellular matrix assembly.") -AnnotationAssertion( "rl") AnnotationAssertion( "2012-07-27T04:04:32Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "up regulation of extracellular matrix assembly") AnnotationAssertion(Annotation( "GOC:TermGenie") "up-regulation of extracellular matrix assembly") @@ -91708,7 +89929,6 @@ SubClassOf( ObjectSomeValuesFrom( (regulation of cardiac chamber formation) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:TermGenie") "Any process that modulates the frequency, rate or extent of cardiac chamber formation.") -AnnotationAssertion( "rl") AnnotationAssertion( "2012-07-31T07:18:35Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "regulation of heart chamber formation") AnnotationAssertion( "biological_process") @@ -91719,7 +89939,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of cardiac chamber formation) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:TermGenie") "Any process that stops, prevents or reduces the frequency, rate or extent of cardiac chamber formation.") -AnnotationAssertion( "rl") AnnotationAssertion( "2012-07-31T07:18:57Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of cardiac chamber formation") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of heart chamber formation") @@ -91738,7 +89957,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of cardiac chamber formation) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:TermGenie") "Any process that activates or increases the frequency, rate or extent of cardiac chamber formation.") -AnnotationAssertion( "rl") AnnotationAssertion( "2012-07-31T07:19:05Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "activation of heart chamber formation") AnnotationAssertion(Annotation( "GOC:TermGenie") "positive regulation of heart chamber formation") @@ -91758,7 +89976,6 @@ SubClassOf( ObjectSomeValuesFrom( (regulation of cardiac chamber morphogenesis) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:TermGenie") "Any process that modulates the frequency, rate or extent of cardiac chamber morphogenesis.") -AnnotationAssertion( "rl") AnnotationAssertion( "2012-08-06T17:59:11Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "regulation of heart chamber morphogenesis") AnnotationAssertion( "biological_process") @@ -91770,7 +89987,6 @@ SubClassOf( ObjectSomeValuesFrom( (negative regulation of cardiac chamber morphogenesis) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:TermGenie") "Any process that stops, prevents or reduces the frequency, rate or extent of cardiac chamber morphogenesis.") -AnnotationAssertion( "rl") AnnotationAssertion( "2012-08-06T17:59:34Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of cardiac chamber morphogenesis") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of heart chamber morphogenesis") @@ -91789,7 +90005,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of cardiac chamber morphogenesis) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:TermGenie") "Any process that activates or increases the frequency, rate or extent of cardiac chamber morphogenesis.") -AnnotationAssertion( "rl") AnnotationAssertion( "2012-08-06T17:59:42Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "positive regulation of heart chamber morphogenesis") AnnotationAssertion(Annotation( "GOC:TermGenie") "up regulation of cardiac chamber morphogenesis") @@ -91808,7 +90023,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of lung ciliated cell differentiation) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:TermGenie") "Any process that modulates the frequency, rate or extent of lung ciliated cell differentiation.") -AnnotationAssertion( "vk") AnnotationAssertion( "2012-08-08T08:58:34Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:1901246") @@ -91818,7 +90032,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of lung ciliated cell differentiation) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:TermGenie") "Any process that stops, prevents or reduces the frequency, rate or extent of lung ciliated cell differentiation.") -AnnotationAssertion( "vk") AnnotationAssertion( "2012-08-08T08:58:58Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of lung ciliated cell differentiation") AnnotationAssertion(Annotation( "GOC:TermGenie") "down-regulation of lung ciliated cell differentiation") @@ -91833,7 +90046,6 @@ SubClassOf( ObjectSomeValuesFrom( (positive regulation of lung ciliated cell differentiation) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:TermGenie") "Any process that activates or increases the frequency, rate or extent of lung ciliated cell differentiation.") -AnnotationAssertion( "vk") AnnotationAssertion( "2012-08-08T08:59:05Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "up regulation of lung ciliated cell differentiation") AnnotationAssertion(Annotation( "GOC:TermGenie") "up-regulation of lung ciliated cell differentiation") @@ -91848,7 +90060,6 @@ SubClassOf( ObjectSomeValuesFrom( (regulation of lung goblet cell differentiation) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:TermGenie") "Any process that modulates the frequency, rate or extent of lung goblet cell differentiation.") -AnnotationAssertion( "vk") AnnotationAssertion( "2012-08-08T08:59:12Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "regulation of pulmonary goblet cell differentiation") AnnotationAssertion( "biological_process") @@ -91859,7 +90070,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of lung goblet cell differentiation) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:TermGenie") "Any process that stops, prevents or reduces the frequency, rate or extent of lung goblet cell differentiation.") -AnnotationAssertion( "vk") AnnotationAssertion( "2012-08-08T08:59:36Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of lung goblet cell differentiation") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of pulmonary goblet cell differentiation") @@ -91879,7 +90089,6 @@ SubClassOf( ObjectSomeValuesFrom( (positive regulation of lung goblet cell differentiation) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:TermGenie") "Any process that activates or increases the frequency, rate or extent of lung goblet cell differentiation.") -AnnotationAssertion( "vk") AnnotationAssertion( "2012-08-08T08:59:44Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "positive regulation of pulmonary goblet cell differentiation") AnnotationAssertion(Annotation( "GOC:TermGenie") "up regulation of lung goblet cell differentiation") @@ -91899,7 +90108,6 @@ SubClassOf( ObjectSomeValuesFrom( (carbohydrate derivative transport) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:bf") Annotation( "GOC:jl") "The directed movement of a carbohydrate derivative into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.") -AnnotationAssertion( "bf") AnnotationAssertion( "2012-08-16T14:51:22Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:1901264") @@ -91910,7 +90118,6 @@ SubClassOf( (regulation of flagellated sperm motility) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:cilia") Annotation( "GOC:krc") "Any process that modulates the frequency, rate or extent of flagellated sperm motility.") -AnnotationAssertion( "hjd") AnnotationAssertion( "2012-08-22T20:50:14Z") AnnotationAssertion( "regulation of sperm motility") AnnotationAssertion(Annotation( "GOC:TermGenie") "regulation of sperm movement") @@ -91923,7 +90130,6 @@ SubClassOf( (negative regulation of flagellated sperm motility) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:cilia") Annotation( "GOC:krc") "Any process that stops, prevents or reduces the frequency, rate or extent of flagellated sperm motility.") -AnnotationAssertion( "hjd") AnnotationAssertion( "2012-08-22T20:50:35Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of sperm motility") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of sperm movement") @@ -91945,7 +90151,6 @@ SubClassOf( (regulation of odontoblast differentiation) AnnotationAssertion(Annotation( "GOC:TermGenie") "Any process that modulates the frequency, rate or extent of odontoblast differentiation.") -AnnotationAssertion( "hjd") AnnotationAssertion( "2012-08-31T16:50:05Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:1901329") @@ -91955,7 +90160,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of odontoblast differentiation) AnnotationAssertion(Annotation( "GOC:TermGenie") "Any process that stops, prevents or reduces the frequency, rate or extent of odontoblast differentiation.") -AnnotationAssertion( "hjd") AnnotationAssertion( "2012-08-31T16:50:27Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of odontoblast differentiation") AnnotationAssertion(Annotation( "GOC:TermGenie") "down-regulation of odontoblast differentiation") @@ -91969,7 +90173,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of odontoblast differentiation) AnnotationAssertion(Annotation( "GOC:TermGenie") "Any process that activates or increases the frequency, rate or extent of odontoblast differentiation.") -AnnotationAssertion( "hjd") AnnotationAssertion( "2012-08-31T16:50:35Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "up regulation of odontoblast differentiation") AnnotationAssertion(Annotation( "GOC:TermGenie") "up-regulation of odontoblast differentiation") @@ -91983,7 +90186,6 @@ EquivalentClasses( ObjectIntersection # Class: (catecholamine binding) AnnotationAssertion(Annotation( "GOC:TermGenie") "Binding to catecholamine.") -AnnotationAssertion( "bf") AnnotationAssertion( "2012-09-03T14:08:44Z") AnnotationAssertion( "molecular_function") AnnotationAssertion( "GO:1901338") @@ -91993,7 +90195,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of vasculature development) AnnotationAssertion(Annotation( "GOC:TermGenie") "Any process that modulates the frequency, rate or extent of vasculature development.") -AnnotationAssertion( "bf") AnnotationAssertion( "2012-09-06T09:16:15Z") AnnotationAssertion( "biological_process") AnnotationAssertion(Annotation( "GOC:TermGenie") "regulation of vascular system development") @@ -92005,7 +90206,6 @@ SubClassOf( (negative regulation of vasculature development) AnnotationAssertion(Annotation( "GOC:TermGenie") "Any process that stops, prevents or reduces the frequency, rate or extent of vasculature development.") -AnnotationAssertion( "bf") AnnotationAssertion( "2012-09-06T09:17:24Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of vasculature development") AnnotationAssertion(Annotation( "GOC:TermGenie") "down-regulation of vasculature development") @@ -92027,7 +90227,6 @@ SubClassOf( (regulation of potassium ion transmembrane transport) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:TermGenie") "Any process that modulates the frequency, rate or extent of potassium ion transmembrane transport.") -AnnotationAssertion( "rl") AnnotationAssertion( "2012-09-28T15:58:00Z") AnnotationAssertion( "regulation of potassium ion membrane transport") AnnotationAssertion( "biological_process") @@ -92038,7 +90237,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of potassium ion transmembrane transport) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:TermGenie") "Any process that stops, prevents or reduces the frequency, rate or extent of potassium ion transmembrane transport.") -AnnotationAssertion( "rl") AnnotationAssertion( "2012-09-28T15:59:08Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of potassium ion transmembrane transport") AnnotationAssertion(Annotation( "GOC:TermGenie") "down-regulation of potassium ion transmembrane transport") @@ -92053,7 +90251,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of potassium ion transmembrane transport) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:TermGenie") "Any process that activates or increases the frequency, rate or extent of potassium ion transmembrane transport.") -AnnotationAssertion( "rl") AnnotationAssertion( "2012-09-28T15:59:25Z") AnnotationAssertion( "positive regulation of potassium ion membrane transport") AnnotationAssertion(Annotation( "GOC:TermGenie") "up regulation of potassium ion transmembrane transport") @@ -92068,7 +90265,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of chorionic trophoblast cell proliferation) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:TermGenie") "Any process that modulates the frequency, rate or extent of chorionic trophoblast cell proliferation.") -AnnotationAssertion( "vk") AnnotationAssertion( "2012-10-01T10:03:13Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:1901382") @@ -92078,7 +90274,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of chorionic trophoblast cell proliferation) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:TermGenie") "Any process that stops, prevents or reduces the frequency, rate or extent of chorionic trophoblast cell proliferation.") -AnnotationAssertion( "vk") AnnotationAssertion( "2012-10-01T10:04:23Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of chorionic trophoblast cell proliferation") AnnotationAssertion(Annotation( "GOC:TermGenie") "down-regulation of chorionic trophoblast cell proliferation") @@ -92092,7 +90287,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of chorionic trophoblast cell proliferation) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:TermGenie") "Any process that activates or increases the frequency, rate or extent of chorionic trophoblast cell proliferation.") -AnnotationAssertion( "vk") AnnotationAssertion( "2012-10-01T10:04:41Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "up regulation of chorionic trophoblast cell proliferation") AnnotationAssertion(Annotation( "GOC:TermGenie") "up-regulation of chorionic trophoblast cell proliferation") @@ -92106,7 +90300,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of Golgi calcium ion export) AnnotationAssertion(Annotation( "GOC:TermGenie") "Any process that modulates the frequency, rate or extent of Golgi calcium ion export.") -AnnotationAssertion( "al") AnnotationAssertion( "2012-10-03T07:26:03Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:1901472") @@ -92116,7 +90309,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of lymphangiogenesis) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:dph") Annotation( "PMID:20133819") "Any process that modulates the frequency, rate or extent of lymphangiogenesis.") -AnnotationAssertion( "dph") AnnotationAssertion( "2012-10-15T13:08:17Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "regulation of lymph vessel formation") AnnotationAssertion( "biological_process") @@ -92127,7 +90319,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of lymphangiogenesis) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:dph") Annotation( "PMID:20133819") "Any process that stops, prevents or reduces the frequency, rate or extent of lymphangiogenesis.") -AnnotationAssertion( "dph") AnnotationAssertion( "2012-10-15T13:08:21Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of lymph vessel formation") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of lymphangiogenesis") @@ -92146,7 +90337,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of lymphangiogenesis) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:dph") Annotation( "PMID:20133819") "Any process that activates or increases the frequency, rate or extent of lymphangiogenesis.") -AnnotationAssertion( "dph") AnnotationAssertion( "2012-10-15T13:08:25Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "positive regulation of lymph vessel formation") AnnotationAssertion(Annotation( "GOC:TermGenie") "up regulation of lymph vessel formation") @@ -92165,7 +90355,6 @@ EquivalentClasses( ObjectIntersection # Class: (carbohydrate derivative transmembrane transporter activity) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:pr") "Enables the transfer of carbohydrate derivative from one side of a membrane to the other.") -AnnotationAssertion( "pr") AnnotationAssertion( "2012-10-17T10:31:22Z") AnnotationAssertion( "molecular_function") AnnotationAssertion( "carbohydrate derivative transporter activity") @@ -92177,7 +90366,6 @@ SubClassOf(Annotation( "GO_ # Class: (regulation of endothelial tube morphogenesis) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:dph") "Any process that modulates the frequency, rate or extent of endothelial tube morphogenesis.") -AnnotationAssertion( "dph") AnnotationAssertion( "2012-10-17T14:30:40Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:1901509") @@ -92187,7 +90375,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of hematopoietic progenitor cell differentiation) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:TermGenie") Annotation( "GOC:rl") "Any process that modulates the frequency, rate or extent of hematopoietic progenitor cell differentiation.") -AnnotationAssertion( "vk") AnnotationAssertion( "2012-10-24T11:23:01Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "regulation of haematopoietic progenitor cell differentiation") AnnotationAssertion(Annotation( "GOC:TermGenie") "regulation of haemopoietic progenitor cell differentiation") @@ -92200,7 +90387,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of hematopoietic progenitor cell differentiation) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:TermGenie") Annotation( "GOC:rl") "Any process that stops, prevents or reduces the frequency, rate or extent of hematopoietic progenitor cell differentiation.") -AnnotationAssertion( "vk") AnnotationAssertion( "2012-10-24T11:23:06Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of haematopoietic progenitor cell differentiation") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of haemopoietic progenitor cell differentiation") @@ -92229,7 +90415,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of hematopoietic progenitor cell differentiation) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:TermGenie") Annotation( "GOC:rl") "Any process that activates or increases the frequency, rate or extent of hematopoietic progenitor cell differentiation.") -AnnotationAssertion( "vk") AnnotationAssertion( "2012-10-24T11:23:14Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "activation of haematopoietic progenitor cell differentiation") AnnotationAssertion(Annotation( "GOC:TermGenie") "activation of haemopoietic progenitor cell differentiation") @@ -92258,7 +90443,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of endothelial cell development) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:pr") Annotation( "PMID:19470579") "Any process that modulates the frequency, rate or extent of endothelial cell development.") -AnnotationAssertion( "pr") AnnotationAssertion( "2012-10-30T12:59:50Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:1901550") @@ -92269,7 +90453,6 @@ SubClassOf( ObjectSomeValuesFrom( (negative regulation of endothelial cell development) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:pr") Annotation( "PMID:19470579") "Any process that stops, prevents or reduces the frequency, rate or extent of endothelial cell development.") -AnnotationAssertion( "pr") AnnotationAssertion( "2012-10-30T12:59:54Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of endothelial cell development") AnnotationAssertion(Annotation( "GOC:TermGenie") "down-regulation of endothelial cell development") @@ -92284,7 +90467,6 @@ SubClassOf( ObjectSomeValuesFrom( (positive regulation of endothelial cell development) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:pr") Annotation( "PMID:19470579") "Any process that activates or increases the frequency, rate or extent of endothelial cell development.") -AnnotationAssertion( "pr") AnnotationAssertion( "2012-10-30T12:59:58Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "up regulation of endothelial cell development") AnnotationAssertion(Annotation( "GOC:TermGenie") "up-regulation of endothelial cell development") @@ -92298,7 +90480,6 @@ EquivalentClasses( ObjectIntersection # Class: (dendritic microtubule) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "NIF_Subcellular:sao110773650") "Any microtubule in a dendrite, a neuron projection.") -AnnotationAssertion( "pr") AnnotationAssertion( "2012-11-07T14:37:30Z") AnnotationAssertion( "NIF_Subcellular:sao110773650") AnnotationAssertion(Annotation( "GOC:TermGenie") "microtubule of dendrite") @@ -92314,7 +90495,6 @@ SubClassOf( ObjectSomeValuesFrom( (axon microtubule bundle) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "NIF_Subcellular:sao707332678") "An arrangement of closely apposed microtubules running parallel to each other in the axon hillock and initial segment.") -AnnotationAssertion( "pr") AnnotationAssertion( "2012-11-07T15:37:12Z") AnnotationAssertion( "NIF_Subcellular:sao707332678") AnnotationAssertion( "axon microtubule fascicle") @@ -92328,7 +90508,6 @@ EquivalentClasses( ObjectIntersection # Class: (alpha-amino acid metabolic process) AnnotationAssertion(Annotation( "GOC:TermGenie") "The chemical reactions and pathways involving an alpha-amino acid.") -AnnotationAssertion( "tb") AnnotationAssertion( "2012-11-08T17:39:50Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "alpha-amino acid metabolism") AnnotationAssertion( "biological_process") @@ -92339,7 +90518,6 @@ EquivalentClasses( ObjectIntersection # Class: (alpha-amino acid catabolic process) AnnotationAssertion(Annotation( "GOC:TermGenie") "The chemical reactions and pathways resulting in the breakdown of an alpha-amino acid.") -AnnotationAssertion( "tb") AnnotationAssertion( "2012-11-08T17:39:54Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "alpha-amino acid breakdown") AnnotationAssertion(Annotation( "GOC:TermGenie") "alpha-amino acid catabolism") @@ -92352,7 +90530,6 @@ EquivalentClasses( ObjectIntersection # Class: (alpha-amino acid biosynthetic process) AnnotationAssertion(Annotation( "GOC:TermGenie") "The chemical reactions and pathways resulting in the formation of an alpha-amino acid.") -AnnotationAssertion( "tb") AnnotationAssertion( "2012-11-08T17:39:58Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "alpha-amino acid anabolism") AnnotationAssertion(Annotation( "GOC:TermGenie") "alpha-amino acid biosynthesis") @@ -92366,7 +90543,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of vesicle transport along microtubule) AnnotationAssertion(Annotation( "GOC:TermGenie") "Any process that modulates the frequency, rate or extent of vesicle transport along microtubule.") -AnnotationAssertion( "hjd") AnnotationAssertion( "2012-11-08T21:49:44Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "regulation of microtubule-based vesicle localization") AnnotationAssertion( "biological_process") @@ -92377,7 +90553,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of vesicle transport along microtubule) AnnotationAssertion(Annotation( "GOC:TermGenie") "Any process that stops, prevents or reduces the frequency, rate or extent of vesicle transport along microtubule.") -AnnotationAssertion( "hjd") AnnotationAssertion( "2012-11-08T21:49:48Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of microtubule-based vesicle localization") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of vesicle transport along microtubule") @@ -92396,7 +90571,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of vesicle transport along microtubule) AnnotationAssertion(Annotation( "GOC:TermGenie") "Any process that activates or increases the frequency, rate or extent of vesicle transport along microtubule.") -AnnotationAssertion( "hjd") AnnotationAssertion( "2012-11-08T21:49:53Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "activation of microtubule-based vesicle localization") AnnotationAssertion(Annotation( "GOC:TermGenie") "positive regulation of microtubule-based vesicle localization") @@ -92415,7 +90589,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of terminal button organization) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "PMID:22426000") "Any process that stops, prevents or reduces the frequency, rate or extent of terminal button organization.") -AnnotationAssertion( "lb") AnnotationAssertion( "2012-11-13T10:40:51Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of bouton organization") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of presynaptic bouton organization") @@ -92454,7 +90627,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of terminal button organization) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "PMID:22426000") "Any process that activates or increases the frequency, rate or extent of terminal button organization.") -AnnotationAssertion( "lb") AnnotationAssertion( "2012-11-13T10:40:58Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "positive regulation of bouton organization") AnnotationAssertion(Annotation( "GOC:TermGenie") "positive regulation of presynaptic bouton organization") @@ -92493,7 +90665,6 @@ EquivalentClasses( ObjectIntersection # Class: (organic hydroxy compound metabolic process) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:pr") "The chemical reactions and pathways involving organic hydroxy compound.") -AnnotationAssertion( "pr") AnnotationAssertion( "2012-11-13T12:54:27Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "organic hydroxy compound metabolism") AnnotationAssertion( "biological_process") @@ -92504,7 +90675,6 @@ EquivalentClasses( ObjectIntersection # Class: (organic hydroxy compound catabolic process) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:pr") "The chemical reactions and pathways resulting in the breakdown of organic hydroxy compound.") -AnnotationAssertion( "pr") AnnotationAssertion( "2012-11-13T12:54:31Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "organic hydroxy compound breakdown") AnnotationAssertion(Annotation( "GOC:TermGenie") "organic hydroxy compound catabolism") @@ -92517,7 +90687,6 @@ EquivalentClasses( ObjectIntersection # Class: (organic hydroxy compound biosynthetic process) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:pr") "The chemical reactions and pathways resulting in the formation of organic hydroxy compound.") -AnnotationAssertion( "pr") AnnotationAssertion( "2012-11-13T12:54:36Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "organic hydroxy compound anabolism") AnnotationAssertion(Annotation( "GOC:TermGenie") "organic hydroxy compound biosynthesis") @@ -92532,7 +90701,6 @@ SubClassOf( (organic hydroxy compound transmembrane transporter activity) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:pr") "Enables the transfer of organic hydroxy compound from one side of a membrane to the other.") -AnnotationAssertion( "pr") AnnotationAssertion( "2012-11-13T12:59:01Z") AnnotationAssertion( "molecular_function") AnnotationAssertion( "GO:1901618") @@ -92542,7 +90710,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of lymphocyte chemotaxis) AnnotationAssertion(Annotation( "GOC:TermGenie") "Any process that modulates the frequency, rate or extent of lymphocyte chemotaxis.") -AnnotationAssertion( "tb") AnnotationAssertion( "2012-11-13T23:03:23Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:1901623") @@ -92552,7 +90719,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of lymphocyte chemotaxis) AnnotationAssertion(Annotation( "GOC:TermGenie") "Any process that stops, prevents or reduces the frequency, rate or extent of lymphocyte chemotaxis.") -AnnotationAssertion( "tb") AnnotationAssertion( "2012-11-13T23:03:28Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of lymphocyte chemotaxis") AnnotationAssertion(Annotation( "GOC:TermGenie") "down-regulation of lymphocyte chemotaxis") @@ -92566,7 +90732,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of postsynaptic membrane organization) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "PMID:22426000") "Any process that modulates the frequency, rate or extent of postsynaptic membrane organization.") -AnnotationAssertion( "ans") AnnotationAssertion( "2012-11-15T11:40:15Z") AnnotationAssertion( "regulation of post-synaptic membrane organization") AnnotationAssertion(Annotation( "GOC:TermGenie") "regulation of postsynaptic membrane organisation") @@ -92578,7 +90743,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of postsynaptic membrane organization) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "PMID:22426000") "Any process that stops, prevents or reduces the frequency, rate or extent of postsynaptic membrane organization.") -AnnotationAssertion( "ans") AnnotationAssertion( "2012-11-15T11:40:20Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of postsynaptic membrane organisation") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of postsynaptic membrane organization") @@ -92599,7 +90763,6 @@ SubClassOf( ObjectSomeValuesFrom( (positive regulation of postsynaptic membrane organization) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "PMID:22426000") "Any process that activates or increases the frequency, rate or extent of postsynaptic membrane organization.") -AnnotationAssertion( "ans") AnnotationAssertion( "2012-11-15T11:40:24Z") AnnotationAssertion( "positive regulation of post-synaptic membrane organization") AnnotationAssertion(Annotation( "GOC:TermGenie") "positive regulation of postsynaptic membrane organisation") @@ -92619,7 +90782,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of synoviocyte proliferation) AnnotationAssertion(Annotation( "GOC:TermGenie") "Any process that modulates the frequency, rate or extent of synoviocyte proliferation.") -AnnotationAssertion( "hjd") AnnotationAssertion( "2012-11-16T20:16:23Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:1901645") @@ -92629,7 +90791,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of synoviocyte proliferation) AnnotationAssertion(Annotation( "GOC:TermGenie") "Any process that stops, prevents or reduces the frequency, rate or extent of synoviocyte proliferation.") -AnnotationAssertion( "hjd") AnnotationAssertion( "2012-11-16T20:16:27Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of synoviocyte proliferation") AnnotationAssertion(Annotation( "GOC:TermGenie") "down-regulation of synoviocyte proliferation") @@ -92643,7 +90804,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of synoviocyte proliferation) AnnotationAssertion(Annotation( "GOC:TermGenie") "Any process that activates or increases the frequency, rate or extent of synoviocyte proliferation.") -AnnotationAssertion( "hjd") AnnotationAssertion( "2012-11-16T20:16:32Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "up regulation of synoviocyte proliferation") AnnotationAssertion(Annotation( "GOC:TermGenie") "up-regulation of synoviocyte proliferation") @@ -92657,7 +90817,6 @@ EquivalentClasses( ObjectIntersection # Class: (response to peptide) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:pr") "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a peptide stimulus.") -AnnotationAssertion( "pr") AnnotationAssertion( "2012-11-20T09:45:15Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:1901652") @@ -92667,7 +90826,6 @@ EquivalentClasses( ObjectIntersection # Class: (cellular response to peptide) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:pr") "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a peptide stimulus.") -AnnotationAssertion( "pr") AnnotationAssertion( "2012-11-20T09:45:19Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:1901653") @@ -92677,7 +90835,6 @@ EquivalentClasses( ObjectIntersection # Class: (response to ketone) AnnotationAssertion(Annotation( "GOC:mengo_curators") Annotation( "PMID:23356676") "A response that results in a state of tolerance to ketone.") -AnnotationAssertion( "pr") AnnotationAssertion( "2012-11-20T10:55:47Z") AnnotationAssertion( "process resulting in tolerance to ketone") AnnotationAssertion( "biological_process") @@ -92688,7 +90845,6 @@ EquivalentClasses( ObjectIntersection # Class: (cellular response to ketone) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:pr") "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a ketone stimulus.") -AnnotationAssertion( "pr") AnnotationAssertion( "2012-11-20T10:55:51Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:1901655") @@ -92698,7 +90854,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of skeletal muscle satellite cell activation involved in skeletal muscle regeneration) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:dph") Annotation( "PMID:21272575") "Any process that stops, prevents or reduces the frequency, rate or extent of satellite cell activation involved in skeletal muscle regeneration.") -AnnotationAssertion( "dph") AnnotationAssertion( "2012-11-21T16:21:11Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of satellite cell activation involved in skeletal muscle regeneration") AnnotationAssertion(Annotation( "GOC:TermGenie") "down-regulation of satellite cell activation involved in skeletal muscle regeneration") @@ -92713,7 +90868,6 @@ SubClassOf( ObjectSomeValuesFrom( (proton binding) AnnotationAssertion(Annotation( "GOC:TermGenie") "Binding to proton.") -AnnotationAssertion( "al") AnnotationAssertion( "2012-12-07T13:50:53Z") AnnotationAssertion(Annotation( "GOC:bm") "hydrogen ion binding") AnnotationAssertion( "molecular_function") @@ -92724,7 +90878,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of compound eye retinal cell apoptotic process) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:mtg_apoptosis") Annotation( "PMID:12021768") "Any process that modulates the frequency, rate or extent of compound eye retinal cell apoptotic process.") -AnnotationAssertion( "pr") AnnotationAssertion( "2012-12-12T10:28:35Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:1901692") @@ -92734,7 +90887,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of compound eye retinal cell apoptotic process) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:mtg_apoptosis") Annotation( "PMID:12021768") "Any process that stops, prevents or reduces the frequency, rate or extent of compound eye retinal cell apoptotic process.") -AnnotationAssertion( "pr") AnnotationAssertion( "2012-12-12T10:28:40Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of compound eye retinal cell apoptotic process") AnnotationAssertion(Annotation( "GOC:TermGenie") "down-regulation of compound eye retinal cell apoptotic process") @@ -92748,7 +90900,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of compound eye retinal cell apoptotic process) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:mtg_apoptosis") Annotation( "PMID:12021768") "Any process that activates or increases the frequency, rate or extent of compound eye retinal cell apoptotic process.") -AnnotationAssertion( "pr") AnnotationAssertion( "2012-12-12T10:28:45Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "up regulation of compound eye retinal cell apoptotic process") AnnotationAssertion(Annotation( "GOC:TermGenie") "up-regulation of compound eye retinal cell apoptotic process") @@ -92765,7 +90916,6 @@ SubClassOf( "GOC:TermGenie") Annotation( "GOC:pr") "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a nitrogen compound stimulus.") AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/27194"^^xsd:anyURI) -AnnotationAssertion( "pr") AnnotationAssertion( "2012-12-13T15:06:08Z") AnnotationAssertion( "response to nitrogen molecular entity") AnnotationAssertion( "biological_process") @@ -92779,7 +90929,6 @@ EquivalentClasses( ObjectIntersection AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:pr") "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a nitrogen compound stimulus.") AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/27194"^^xsd:anyURI) -AnnotationAssertion( "pr") AnnotationAssertion( "2012-12-13T15:06:13Z") AnnotationAssertion( "cellular response to nitrogen molecular entity") AnnotationAssertion( "biological_process") @@ -92793,7 +90942,6 @@ EquivalentClasses( ObjectIntersection AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:pr") "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an oxygen-containing compound stimulus.") AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/27194"^^xsd:anyURI) -AnnotationAssertion( "pr") AnnotationAssertion( "2012-12-13T15:11:37Z") AnnotationAssertion( "response to oxygen molecular entity") AnnotationAssertion( "biological_process") @@ -92807,7 +90955,6 @@ SubClassOf( (cellular response to oxygen-containing compound) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:pr") "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an oxygen-containing compound stimulus.") -AnnotationAssertion( "pr") AnnotationAssertion( "2012-12-13T15:11:42Z") AnnotationAssertion( "cellular response to oxygen molecular entity") AnnotationAssertion( "biological_process") @@ -92818,7 +90965,6 @@ EquivalentClasses( ObjectIntersection # Class: (mesenchymal cell differentiation involved in bone development) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:hjd") Annotation( "PMID:21571217") "The process in which relatively unspecialized cells acquire specialized structural and/or functional features that characterize the mesenchymal cells of bone as it progresses from its formation to the mature state.") -AnnotationAssertion( "hjd") AnnotationAssertion( "2012-12-14T16:04:16Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:1901706") @@ -92828,7 +90974,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of gamma-aminobutyric acid catabolic process) AnnotationAssertion(Annotation( "GOC:TermGenie") "Any process that modulates the frequency, rate or extent of gamma-aminobutyric acid catabolic process.") -AnnotationAssertion( "mcc") AnnotationAssertion( "2012-12-19T16:13:24Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "regulation of 4-aminobutanoate catabolic process") AnnotationAssertion(Annotation( "GOC:TermGenie") "regulation of 4-aminobutanoate catabolism") @@ -92847,7 +90992,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of gamma-aminobutyric acid catabolic process) AnnotationAssertion(Annotation( "GOC:TermGenie") "Any process that stops, prevents or reduces the frequency, rate or extent of gamma-aminobutyric acid catabolic process.") -AnnotationAssertion( "mcc") AnnotationAssertion( "2012-12-19T16:13:31Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of 4-aminobutanoate catabolic process") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of 4-aminobutanoate catabolism") @@ -92906,7 +91050,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of gamma-aminobutyric acid catabolic process) AnnotationAssertion(Annotation( "GOC:TermGenie") "Any process that activates or increases the frequency, rate or extent of gamma-aminobutyric acid catabolic process.") -AnnotationAssertion( "mcc") AnnotationAssertion( "2012-12-19T16:13:36Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "activation of 4-aminobutanoate catabolic process") AnnotationAssertion(Annotation( "GOC:TermGenie") "activation of 4-aminobutanoate catabolism") @@ -92965,7 +91108,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of cell proliferation involved in kidney development) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "PMID:18182616") "Any process that modulates the frequency, rate or extent of cell proliferation involved in kidney development.") -AnnotationAssertion( "krc") AnnotationAssertion( "2012-12-27T19:30:31Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:1901722") @@ -92975,7 +91117,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of cell proliferation involved in kidney development) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "PMID:18182616") "Any process that stops, prevents or reduces the frequency, rate or extent of cell proliferation involved in kidney development.") -AnnotationAssertion( "krc") AnnotationAssertion( "2012-12-27T19:30:35Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of cell proliferation involved in kidney development") AnnotationAssertion(Annotation( "GOC:TermGenie") "down-regulation of cell proliferation involved in kidney development") @@ -92989,7 +91130,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of cell proliferation involved in kidney development) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "PMID:18182616") "Any process that activates or increases the frequency, rate or extent of cell proliferation involved in kidney development.") -AnnotationAssertion( "krc") AnnotationAssertion( "2012-12-27T19:30:40Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "up regulation of cell proliferation involved in kidney development") AnnotationAssertion(Annotation( "GOC:TermGenie") "up-regulation of cell proliferation involved in kidney development") @@ -93003,7 +91143,6 @@ EquivalentClasses( ObjectIntersection # Class: (zeaxanthin metabolic process) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:yaf") Annotation( "MetaCyc:PWY-5944") Annotation( "UniPathway:UPA00843") "The chemical reactions and pathways involving zeaxanthin.") -AnnotationAssertion( "yaf") AnnotationAssertion( "2013-01-22T11:36:55Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "zeaxanthin metabolism") AnnotationAssertion( "biological_process") @@ -93014,7 +91153,6 @@ EquivalentClasses( ObjectIntersection # Class: (zeaxanthin catabolic process) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:yaf") Annotation( "MetaCyc:PWY-5944") Annotation( "UniPathway:UPA00843") "The chemical reactions and pathways resulting in the breakdown of zeaxanthin.") -AnnotationAssertion( "yaf") AnnotationAssertion( "2013-01-22T11:37:00Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "zeaxanthin breakdown") AnnotationAssertion(Annotation( "GOC:TermGenie") "zeaxanthin catabolism") @@ -93027,7 +91165,6 @@ EquivalentClasses( ObjectIntersection # Class: (zeaxanthin biosynthetic process) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:yaf") Annotation( "MetaCyc:PWY-5944") Annotation( "UniPathway:UPA00843") "The chemical reactions and pathways resulting in the formation of zeaxanthin.") -AnnotationAssertion( "yaf") AnnotationAssertion( "2013-01-22T11:37:07Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "zeaxanthin anabolism") AnnotationAssertion(Annotation( "GOC:TermGenie") "zeaxanthin biosynthesis") @@ -93041,7 +91178,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of muscle tissue development) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:yaf") Annotation( "PMID:23150719") "Any process that modulates the frequency, rate or extent of muscle tissue development.") -AnnotationAssertion( "yaf") AnnotationAssertion( "2013-02-01T10:30:47Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:1901861") @@ -93051,7 +91187,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of muscle tissue development) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:yaf") Annotation( "PMID:23150719") "Any process that stops, prevents or reduces the frequency, rate or extent of muscle tissue development.") -AnnotationAssertion( "yaf") AnnotationAssertion( "2013-02-01T10:30:52Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of muscle tissue development") AnnotationAssertion(Annotation( "GOC:TermGenie") "down-regulation of muscle tissue development") @@ -93065,7 +91200,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of muscle tissue development) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:yaf") Annotation( "PMID:23150719") "Any process that activates or increases the frequency, rate or extent of muscle tissue development.") -AnnotationAssertion( "yaf") AnnotationAssertion( "2013-02-01T10:30:57Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "up regulation of muscle tissue development") AnnotationAssertion(Annotation( "GOC:TermGenie") "up-regulation of muscle tissue development") @@ -93079,7 +91213,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of calcium ion binding) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:TermGenie") Annotation( "GOC:rl") Annotation( "PMID:16432188") "Any process that modulates the frequency, rate or extent of calcium ion binding.") -AnnotationAssertion( "rl") AnnotationAssertion( "2013-02-06T12:38:12Z") AnnotationAssertion( "biological_process") AnnotationAssertion(Annotation( "GOC:TermGenie") "regulation of calcium ion storage activity") @@ -93091,7 +91224,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of calcium ion binding) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:TermGenie") Annotation( "GOC:rl") Annotation( "PMID:16432188") "Any process that stops, prevents or reduces the frequency, rate or extent of calcium ion binding.") -AnnotationAssertion( "rl") AnnotationAssertion( "2013-02-06T12:38:22Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of calcium ion binding") AnnotationAssertion(Annotation( "GOC:TermGenie") "down-regulation of calcium ion binding") @@ -93111,7 +91243,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of calcium ion binding) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:TermGenie") Annotation( "GOC:rl") Annotation( "PMID:16432188") "Any process that activates or increases the frequency, rate or extent of calcium ion binding.") -AnnotationAssertion( "rl") AnnotationAssertion( "2013-02-06T12:38:26Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "up regulation of calcium ion binding") AnnotationAssertion(Annotation( "GOC:TermGenie") "up-regulation of calcium ion binding") @@ -93131,7 +91262,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of protein depolymerization) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:TermGenie") Annotation( "GOC:rl") Annotation( "PMID:12032137") "Any process that modulates the frequency, rate or extent of protein depolymerization.") -AnnotationAssertion( "rl") AnnotationAssertion( "2013-02-06T13:57:23Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "regulation of protein polymer breakdown") AnnotationAssertion(Annotation( "GOC:TermGenie") "regulation of protein polymer catabolic process") @@ -93145,7 +91275,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of protein depolymerization) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:TermGenie") Annotation( "GOC:rl") Annotation( "PMID:12032137") "Any process that stops, prevents or reduces the frequency, rate or extent of protein depolymerization.") -AnnotationAssertion( "rl") AnnotationAssertion( "2013-02-06T13:57:28Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of protein depolymerization") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of protein polymer breakdown") @@ -93179,7 +91308,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of protein depolymerization) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:TermGenie") Annotation( "GOC:rl") Annotation( "PMID:12032137") "Any process that activates or increases the frequency, rate or extent of protein depolymerization.") -AnnotationAssertion( "rl") AnnotationAssertion( "2013-02-06T13:57:32Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "activation of protein polymer breakdown") AnnotationAssertion(Annotation( "GOC:TermGenie") "activation of protein polymer catabolic process") @@ -93213,7 +91341,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of cell junction assembly) AnnotationAssertion(Annotation( "GOC:TermGenie") "Any process that modulates the frequency, rate or extent of cell junction assembly.") -AnnotationAssertion( "tb") AnnotationAssertion( "2013-02-06T19:40:32Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:1901888") @@ -93224,7 +91351,6 @@ SubClassOf( ObjectSomeValuesFrom( (negative regulation of cell junction assembly) AnnotationAssertion(Annotation( "GOC:TermGenie") "Any process that stops, prevents or reduces the frequency, rate or extent of cell junction assembly.") -AnnotationAssertion( "tb") AnnotationAssertion( "2013-02-06T19:40:41Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of cell junction assembly") AnnotationAssertion(Annotation( "GOC:TermGenie") "down-regulation of cell junction assembly") @@ -93238,7 +91364,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of cell junction assembly) AnnotationAssertion(Annotation( "GOC:TermGenie") "Any process that activates or increases the frequency, rate or extent of cell junction assembly.") -AnnotationAssertion( "tb") AnnotationAssertion( "2013-02-06T19:40:46Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "up regulation of cell junction assembly") AnnotationAssertion(Annotation( "GOC:TermGenie") "up-regulation of cell junction assembly") @@ -93253,7 +91378,6 @@ SubClassOf( ObjectSomeValuesFrom( (dense core granule transport) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:kmv") Annotation( "PMID:23358451") "The directed movement a dense core granule within a cell.") -AnnotationAssertion( "pr") AnnotationAssertion( "2013-02-19T13:00:52Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "dense core vesicle transport") AnnotationAssertion( "biological_process") @@ -93266,7 +91390,6 @@ SubClassOf( (regulation of anterograde dense core granule transport) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:kmv") Annotation( "PMID:23358451") "Any process that modulates the frequency, rate or extent of anterograde dense core granule transport.") -AnnotationAssertion( "pr") AnnotationAssertion( "2013-02-19T13:36:21Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:1901951") @@ -93276,7 +91399,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of anterograde dense core granule transport) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:kmv") Annotation( "PMID:23358451") "Any process that stops, prevents or reduces the frequency, rate or extent of anterograde dense core granule transport.") -AnnotationAssertion( "pr") AnnotationAssertion( "2013-02-19T13:36:30Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of anterograde dense core granule transport") AnnotationAssertion(Annotation( "GOC:TermGenie") "down-regulation of anterograde dense core granule transport") @@ -93290,7 +91412,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of anterograde dense core granule transport) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:kmv") Annotation( "PMID:23358451") "Any process that activates or increases the frequency, rate or extent of anterograde dense core granule transport.") -AnnotationAssertion( "pr") AnnotationAssertion( "2013-02-19T13:36:35Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "up regulation of anterograde dense core granule transport") AnnotationAssertion(Annotation( "GOC:TermGenie") "up-regulation of anterograde dense core granule transport") @@ -93304,7 +91425,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of retrograde dense core granule transport) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:kmv") Annotation( "PMID:23358451") "Any process that modulates the frequency, rate or extent of retrograde dense core granule transport.") -AnnotationAssertion( "pr") AnnotationAssertion( "2013-02-19T13:36:43Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:1901954") @@ -93314,7 +91434,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of retrograde dense core granule transport) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:kmv") Annotation( "PMID:23358451") "Any process that stops, prevents or reduces the frequency, rate or extent of retrograde dense core granule transport.") -AnnotationAssertion( "pr") AnnotationAssertion( "2013-02-19T13:36:47Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of retrograde dense core granule transport") AnnotationAssertion(Annotation( "GOC:TermGenie") "down-regulation of retrograde dense core granule transport") @@ -93328,7 +91447,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of retrograde dense core granule transport) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:kmv") Annotation( "PMID:23358451") "Any process that activates or increases the frequency, rate or extent of retrograde dense core granule transport.") -AnnotationAssertion( "pr") AnnotationAssertion( "2013-02-19T13:36:52Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "up regulation of retrograde dense core granule transport") AnnotationAssertion(Annotation( "GOC:TermGenie") "up-regulation of retrograde dense core granule transport") @@ -93342,7 +91460,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of cell proliferation involved in outflow tract morphogenesis) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:dph") Annotation( "GOC:mtg_heart") Annotation( "PMID:21419760") "Any process that modulates the frequency, rate or extent of cell proliferation involved in outflow tract morphogenesis.") -AnnotationAssertion( "dph") AnnotationAssertion( "2013-02-20T20:30:26Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:1901963") @@ -93352,7 +91469,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of cell proliferation involved in outflow tract morphogenesis) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:dph") Annotation( "GOC:mtg_heart") Annotation( "PMID:21419760") "Any process that activates or increases the frequency, rate or extent of cell proliferation involved in outflow tract morphogenesis.") -AnnotationAssertion( "dph") AnnotationAssertion( "2013-02-20T20:30:31Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "up regulation of cell proliferation involved in outflow tract morphogenesis") AnnotationAssertion(Annotation( "GOC:TermGenie") "up-regulation of cell proliferation involved in outflow tract morphogenesis") @@ -93367,7 +91483,6 @@ EquivalentClasses( ObjectIntersection AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:cilia") Annotation( "GOC:dph") Annotation( "PMID:17719545") "Any process that modulates the frequency, rate or extent of cilium assembly.") AnnotationAssertion( ) -AnnotationAssertion( "dph") AnnotationAssertion( "2013-03-26T18:10:51Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "regulation of ciliogenesis") AnnotationAssertion( "biological_process") @@ -93382,7 +91497,6 @@ DisjointClasses( ObjectSomeValuesFrom # Class: (negative regulation of cilium assembly) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:cilia") Annotation( "GOC:dph") Annotation( "PMID:17719545") "Any process that stops, prevents or reduces the frequency, rate or extent of cilium assembly.") -AnnotationAssertion( "dph") AnnotationAssertion( "2013-03-26T18:10:56Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of ciliogenesis") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of cilium assembly") @@ -93406,7 +91520,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of cilium-dependent cell motility) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:cilia") Annotation( "GOC:jl") "Any process that modulates the frequency, rate or extent of cilium-dependent cell motility.") -AnnotationAssertion( "jl") AnnotationAssertion( "2013-03-27T14:42:38Z") AnnotationAssertion( "regulation of cilium cell motility") AnnotationAssertion( "biological_process") @@ -93418,7 +91531,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of cilium-dependent cell motility) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:cilia") Annotation( "GOC:jl") "Any process that stops, prevents or reduces the frequency, rate or extent of cilium-dependent cell motility.") -AnnotationAssertion( "jl") AnnotationAssertion( "2013-03-27T14:42:42Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of ciliary cell motility") AnnotationAssertion(Annotation( "GOC:TermGenie") "down-regulation of ciliary cell motility") @@ -93434,7 +91546,6 @@ EquivalentClasses( ObjectIntersection # Class: (L-histidine transport) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:kmv") Annotation( "PMID:22822152") "The directed movement of a L-histidine into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.") -AnnotationAssertion( "kmv") AnnotationAssertion( "2013-03-27T16:09:15Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:1902024") @@ -93444,7 +91555,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of hematopoietic stem cell proliferation) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "PMID:23403623") "Any process that modulates the frequency, rate or extent of hematopoietic stem cell proliferation.") -AnnotationAssertion( "ss") AnnotationAssertion( "2013-04-02T05:13:19Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "regulation of hemopoietic stem cell proliferation") AnnotationAssertion( "biological_process") @@ -93455,7 +91565,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of hematopoietic stem cell proliferation) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "PMID:23403623") "Any process that stops, prevents or reduces the frequency, rate or extent of hematopoietic stem cell proliferation.") -AnnotationAssertion( "ss") AnnotationAssertion( "2013-04-02T05:13:24Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of hematopoietic stem cell proliferation") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of hemopoietic stem cell proliferation") @@ -93475,7 +91584,6 @@ SubClassOf( ObjectSomeValuesFrom( (positive regulation of hematopoietic stem cell proliferation) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "PMID:23403623") "Any process that activates or increases the frequency, rate or extent of hematopoietic stem cell proliferation.") -AnnotationAssertion( "ss") AnnotationAssertion( "2013-04-02T05:13:31Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "positive regulation of hemopoietic stem cell proliferation") AnnotationAssertion(Annotation( "GOC:TermGenie") "up regulation of hematopoietic stem cell proliferation") @@ -93494,7 +91602,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of hematopoietic stem cell differentiation) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "PMID:23403623") "Any process that modulates the frequency, rate or extent of hematopoietic stem cell differentiation.") -AnnotationAssertion( "ss") AnnotationAssertion( "2013-04-02T05:19:09Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "regulation of haematopoietic stem cell differentiation") AnnotationAssertion(Annotation( "GOC:TermGenie") "regulation of haemopoietic stem cell differentiation") @@ -93507,7 +91614,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of hematopoietic stem cell differentiation) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "PMID:23403623") "Any process that stops, prevents or reduces the frequency, rate or extent of hematopoietic stem cell differentiation.") -AnnotationAssertion( "ss") AnnotationAssertion( "2013-04-02T05:19:14Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of haematopoietic stem cell differentiation") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of haemopoietic stem cell differentiation") @@ -93536,7 +91642,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of hematopoietic stem cell differentiation) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "PMID:23403623") "Any process that activates or increases the frequency, rate or extent of hematopoietic stem cell differentiation.") -AnnotationAssertion( "ss") AnnotationAssertion( "2013-04-02T05:19:19Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "positive regulation of haematopoietic stem cell differentiation") AnnotationAssertion(Annotation( "GOC:TermGenie") "positive regulation of haemopoietic stem cell differentiation") @@ -93565,7 +91670,6 @@ EquivalentClasses( ObjectIntersection # Class: (response to L-glutamate) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "PMID:23574009") "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an L-glutamate stimulus.") -AnnotationAssertion( "tb") AnnotationAssertion( "2013-04-16T21:21:14Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:1902065") @@ -93575,7 +91679,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of lateral motor column neuron migration) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:yaf") Annotation( "PMID:20711475") "Any process that modulates the frequency, rate or extent of lateral motor column neuron migration.") -AnnotationAssertion( "pr") AnnotationAssertion( "2013-04-23T14:42:18Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:1902076") @@ -93585,7 +91688,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of lateral motor column neuron migration) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:yaf") Annotation( "PMID:20711475") "Any process that stops, prevents or reduces the frequency, rate or extent of lateral motor column neuron migration.") -AnnotationAssertion( "pr") AnnotationAssertion( "2013-04-23T14:42:23Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of lateral motor column neuron migration") AnnotationAssertion(Annotation( "GOC:TermGenie") "down-regulation of lateral motor column neuron migration") @@ -93599,7 +91701,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of lateral motor column neuron migration) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:yaf") Annotation( "PMID:20711475") "Any process that activates or increases the frequency, rate or extent of lateral motor column neuron migration.") -AnnotationAssertion( "pr") AnnotationAssertion( "2013-04-23T14:42:28Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "up regulation of lateral motor column neuron migration") AnnotationAssertion(Annotation( "GOC:TermGenie") "up-regulation of lateral motor column neuron migration") @@ -93613,7 +91714,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of flagellated sperm motility) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:cilia") Annotation( "GOC:jh2") Annotation( "GOC:krc") Annotation( "PMID:7513657") "Any process that activates or increases the frequency, rate or extent of flagellated sperm motility.") -AnnotationAssertion( "bf") AnnotationAssertion( "2013-04-29T09:15:25Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "activation of sperm movement") AnnotationAssertion( "positive regulation of sperm motility") @@ -93635,7 +91735,6 @@ SubClassOf( (regulation of leukocyte differentiation) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:add") "Any process that modulates the frequency, rate or extent of leukocyte differentiation.") -AnnotationAssertion( "pr") AnnotationAssertion( "2013-05-02T17:32:42Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "regulation of immune cell differentiation") AnnotationAssertion(Annotation( "GOC:TermGenie") "regulation of leucocyte differentiation") @@ -93649,7 +91748,6 @@ SubClassOf( (negative regulation of leukocyte differentiation) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:add") "Any process that stops, prevents or reduces the frequency, rate or extent of leukocyte differentiation.") -AnnotationAssertion( "pr") AnnotationAssertion( "2013-05-02T17:32:47Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of immune cell differentiation") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of leucocyte differentiation") @@ -93676,7 +91774,6 @@ SubClassOf( (positive regulation of leukocyte differentiation) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:add") "Any process that activates or increases the frequency, rate or extent of leukocyte differentiation.") -AnnotationAssertion( "pr") AnnotationAssertion( "2013-05-02T17:32:52Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "positive regulation of immune cell differentiation") AnnotationAssertion(Annotation( "GOC:TermGenie") "positive regulation of leucocyte differentiation") @@ -93703,7 +91800,6 @@ SubClassOf( (regulation of organelle assembly) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:pr") "Any process that modulates the frequency, rate or extent of organelle assembly.") -AnnotationAssertion( "pr") AnnotationAssertion( "2013-05-14T09:43:21Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:1902115") @@ -93714,7 +91810,6 @@ SubClassOf( ObjectSomeValuesFrom( (negative regulation of organelle assembly) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:pr") "Any process that stops, prevents or reduces the frequency, rate or extent of organelle assembly.") -AnnotationAssertion( "pr") AnnotationAssertion( "2013-05-14T09:43:31Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of organelle assembly") AnnotationAssertion(Annotation( "GOC:TermGenie") "down-regulation of organelle assembly") @@ -93728,7 +91823,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of organelle assembly) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:pr") "Any process that activates or increases the frequency, rate or extent of organelle assembly.") -AnnotationAssertion( "pr") AnnotationAssertion( "2013-05-14T09:43:36Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "up regulation of organelle assembly") AnnotationAssertion(Annotation( "GOC:TermGenie") "up-regulation of organelle assembly") @@ -93743,7 +91837,6 @@ SubClassOf( ObjectSomeValuesFrom( (regulation of keratinocyte apoptotic process) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:TermGenie") Annotation( "GOC:mtg_apoptosis") Annotation( "GOC:rl") Annotation( "PMID:18938133") "Any process that modulates the frequency, rate or extent of keratinocyte apoptotic process.") -AnnotationAssertion( "rl") AnnotationAssertion( "2013-05-29T14:36:11Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "regulation of keratinocyte apoptosis") AnnotationAssertion( "biological_process") @@ -93754,7 +91847,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of keratinocyte apoptotic process) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:TermGenie") Annotation( "GOC:mtg_apoptosis") Annotation( "GOC:rl") Annotation( "PMID:18938133") "Any process that stops, prevents or reduces the frequency, rate or extent of keratinocyte apoptotic process.") -AnnotationAssertion( "rl") AnnotationAssertion( "2013-05-29T14:36:15Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of keratinocyte apoptotic process") AnnotationAssertion(Annotation( "GOC:TermGenie") "down-regulation of keratinocyte apoptotic process") @@ -93773,7 +91865,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of keratinocyte apoptotic process) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:TermGenie") Annotation( "GOC:mtg_apoptosis") Annotation( "GOC:rl") Annotation( "PMID:18938133") "Any process that activates or increases the frequency, rate or extent of keratinocyte apoptotic process.") -AnnotationAssertion( "rl") AnnotationAssertion( "2013-05-29T14:36:21Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "up regulation of keratinocyte apoptotic process") AnnotationAssertion(Annotation( "GOC:TermGenie") "up-regulation of keratinocyte apoptotic process") @@ -93792,7 +91883,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of prolactin signaling pathway) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "PMID:11773439") "Any process that modulates the frequency, rate or extent of prolactin signaling pathway.") -AnnotationAssertion( "lb") AnnotationAssertion( "2013-06-12T10:10:07Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "regulation of PRL signaling pathway") AnnotationAssertion(Annotation( "GOC:TermGenie") "regulation of prolactin-mediated signaling pathway") @@ -93804,7 +91894,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of prolactin signaling pathway) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "PMID:11773439") "Any process that stops, prevents or reduces the frequency, rate or extent of prolactin signaling pathway.") -AnnotationAssertion( "lb") AnnotationAssertion( "2013-06-12T10:10:12Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of PRL signaling pathway") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of prolactin signaling pathway") @@ -93828,7 +91917,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of prolactin signaling pathway) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "PMID:11773439") "Any process that activates or increases the frequency, rate or extent of prolactin signaling pathway.") -AnnotationAssertion( "lb") AnnotationAssertion( "2013-06-12T10:10:18Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "positive regulation of PRL signaling pathway") AnnotationAssertion(Annotation( "GOC:TermGenie") "positive regulation of prolactin-mediated signaling pathway") @@ -93853,7 +91941,6 @@ EquivalentClasses( ObjectIntersection AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:TermGenie") Annotation( "GOC:mtg_apoptosis") Annotation( "GOC:rl") Annotation( "PMID:14569084") "Any apoptotic process in an erythrocyte.") AnnotationAssertion( ) -AnnotationAssertion( "rl") AnnotationAssertion( "2013-06-13T10:02:29Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "RBC apoptotic process") AnnotationAssertion(Annotation( "GOC:TermGenie") "red blood cell apoptotic process") @@ -93871,7 +91958,6 @@ DisjointClasses( ObjectSomeValuesFrom # Class: (regulation of erythrocyte apoptotic process) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:TermGenie") Annotation( "GOC:mtg_apoptosis") Annotation( "GOC:rl") Annotation( "PMID:14569084") "Any process that modulates the frequency, rate or extent of erythrocyte apoptotic process.") -AnnotationAssertion( "rl") AnnotationAssertion( "2013-06-20T19:30:53Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "regulation of RBC apoptotic process") AnnotationAssertion(Annotation( "GOC:TermGenie") "regulation of red blood cell apoptotic process") @@ -93887,7 +91973,6 @@ EquivalentClasses( ObjectIntersection AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:TermGenie") Annotation( "GOC:mtg_apoptosis") Annotation( "GOC:rl") Annotation( "PMID:14569084") "Any process that stops, prevents or reduces the frequency, rate or extent of erythrocyte apoptotic process.") AnnotationAssertion( ) -AnnotationAssertion( "rl") AnnotationAssertion( "2013-06-20T19:30:59Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of RBC apoptotic process") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of erythrocyte apoptotic process") @@ -93930,7 +92015,6 @@ DisjointClasses( ObjectSomeValuesFrom AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:TermGenie") Annotation( "GOC:mtg_apoptosis") Annotation( "GOC:rl") Annotation( "PMID:14569084") "Any process that activates or increases the frequency, rate or extent of erythrocyte apoptotic process.") AnnotationAssertion( ) -AnnotationAssertion( "rl") AnnotationAssertion( "2013-06-20T19:31:04Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "positive regulation of RBC apoptotic process") AnnotationAssertion(Annotation( "GOC:TermGenie") "positive regulation of red blood cell apoptotic process") @@ -93972,7 +92056,6 @@ DisjointClasses( ObjectSomeValuesFrom # Class: (regulation of apoptotic process involved in outflow tract morphogenesis) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:dph") Annotation( "GOC:mtg_apoptosis") Annotation( "PMID:16839542") "Any process that modulates the frequency, rate or extent of apoptotic process involved in outflow tract morphogenesis.") -AnnotationAssertion( "dph") AnnotationAssertion( "2013-06-24T19:12:24Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "regulation of apoptosis involved in outflow tract morphogenesis") AnnotationAssertion( "biological_process") @@ -93983,7 +92066,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of apoptotic process involved in outflow tract morphogenesis) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:dph") Annotation( "GOC:mtg_apoptosis") Annotation( "PMID:16839542") "Any process that stops, prevents or reduces the frequency, rate or extent of apoptotic process involved in outflow tract morphogenesis.") -AnnotationAssertion( "dph") AnnotationAssertion( "2013-06-24T19:12:30Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of apoptotic process involved in outflow tract morphogenesis") AnnotationAssertion(Annotation( "GOC:TermGenie") "down-regulation of apoptotic process involved in outflow tract morphogenesis") @@ -94002,7 +92084,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of apoptotic process involved in outflow tract morphogenesis) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:dph") Annotation( "GOC:mtg_apoptosis") Annotation( "PMID:16839542") "Any process that activates or increases the frequency, rate or extent of apoptotic process involved in outflow tract morphogenesis.") -AnnotationAssertion( "dph") AnnotationAssertion( "2013-06-24T19:12:42Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "up regulation of apoptotic process involved in outflow tract morphogenesis") AnnotationAssertion(Annotation( "GOC:TermGenie") "up-regulation of apoptotic process involved in outflow tract morphogenesis") @@ -94021,7 +92102,6 @@ EquivalentClasses( ObjectIntersection # Class: (apoptotic process involved in blood vessel morphogenesis) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:dph") Annotation( "GOC:mtg_apoptosis") Annotation( "PMID:16163358") "Any apoptotic process that is involved in blood vessel morphogenesis.") -AnnotationAssertion( "dph") AnnotationAssertion( "2013-06-25T16:16:00Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "apoptotic cell death involved in patterning of blood vessels") AnnotationAssertion(Annotation( "GOC:TermGenie") "apoptotic programmed cell death involved in patterning of blood vessels") @@ -94038,7 +92118,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of chromatin organization) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:bf") Annotation( "GOC:vw") Annotation( "GO_REF:0000058") Annotation( "PMID:18314879") "Any process that modulates the frequency, rate or extent of chromatin organization.") -AnnotationAssertion( "bf") AnnotationAssertion( "2013-07-01T13:21:52Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "regulation of chromatin organisation") AnnotationAssertion(Annotation( "GOC:TermGenie") "regulation of establishment or maintenance of chromatin architecture") @@ -94053,7 +92132,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of sodium ion transmembrane transport) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:TermGenie") Annotation( "GOC:mtg_cardiac_conduct_nov11") Annotation( "GOC:rl") Annotation( "PMID:18591664") "Any process that modulates the frequency, rate or extent of sodium ion transmembrane transport.") -AnnotationAssertion( "rl") AnnotationAssertion( "2013-07-18T13:33:53Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "regulation of sodium ion membrane transport") AnnotationAssertion( "biological_process") @@ -94064,7 +92142,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of sodium ion transmembrane transport) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:TermGenie") Annotation( "GOC:mtg_cardiac_conduct_nov11") Annotation( "GOC:rl") Annotation( "PMID:18591664") "Any process that stops, prevents or reduces the frequency, rate or extent of sodium ion transmembrane transport.") -AnnotationAssertion( "rl") AnnotationAssertion( "2013-07-18T13:34:01Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of sodium ion membrane transport") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of sodium ion transmembrane transport") @@ -94083,7 +92160,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of sodium ion transmembrane transport) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:TermGenie") Annotation( "GOC:mtg_cardiac_conduct_nov11") Annotation( "GOC:rl") Annotation( "PMID:18591664") "Any process that activates or increases the frequency, rate or extent of sodium ion transmembrane transport.") -AnnotationAssertion( "rl") AnnotationAssertion( "2013-07-18T13:34:18Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "positive regulation of sodium ion membrane transport") AnnotationAssertion(Annotation( "GOC:TermGenie") "up regulation of sodium ion membrane transport") @@ -94102,7 +92178,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of apoptotic process involved in morphogenesis) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:sart") Annotation( "PMID:12202035") "Any process that modulates the frequency, rate or extent of apoptotic process involved in morphogenesis.") -AnnotationAssertion( "sart") AnnotationAssertion( "2013-07-29T15:03:16Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "regulation of apoptosis involved in morphogenesis") AnnotationAssertion( "biological_process") @@ -94115,7 +92190,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of apoptotic process involved in morphogenesis) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:sart") Annotation( "PMID:12202035") "Any process that stops, prevents or reduces the frequency, rate or extent of apoptotic process involved in morphogenesis.") -AnnotationAssertion( "sart") AnnotationAssertion( "2013-07-29T15:03:25Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of apoptotic process involved in morphogenesis") AnnotationAssertion(Annotation( "GOC:TermGenie") "down-regulation of apoptotic process involved in morphogenesis") @@ -94144,7 +92218,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of apoptotic process involved in morphogenesis) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:sart") Annotation( "PMID:12202035") "Any process that activates or increases the frequency, rate or extent of apoptotic process involved in morphogenesis.") -AnnotationAssertion( "sart") AnnotationAssertion( "2013-07-29T15:03:33Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "up regulation of apoptotic process involved in morphogenesis") AnnotationAssertion(Annotation( "GOC:TermGenie") "up-regulation of apoptotic process involved in morphogenesis") @@ -94173,7 +92246,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of chromosome condensation) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "PMID:23219725") "Any process that stops, prevents or reduces the frequency, rate or extent of chromosome condensation.") -AnnotationAssertion( "dgf") AnnotationAssertion( "2013-07-29T20:54:14Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of chromosome condensation") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of eukaryotic chromosome condensation") @@ -94197,7 +92269,6 @@ EquivalentClasses( ObjectIntersection # Class: (melanocyte apoptotic process) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:ic") Annotation( "PMID:20530876") "Any apoptotic process in a melanocyte, the main structural component of the epidermis.") -AnnotationAssertion( "pr") AnnotationAssertion( "2013-08-15T16:35:45Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "melanocyte apoptosis") AnnotationAssertion(Annotation( "GOC:TermGenie") "melanophore apoptosis") @@ -94211,7 +92282,6 @@ SubClassOf( (negative regulation of RNA catabolic process) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:bf") Annotation( "PMID:16640457") "Any process that stops, prevents or reduces the frequency, rate or extent of RNA catabolic process.") -AnnotationAssertion( "bf") AnnotationAssertion( "2013-08-22T14:59:39Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of RNA breakdown") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of RNA catabolic process") @@ -94240,7 +92310,6 @@ EquivalentClasses( ObjectIntersection # Class: (protein localization to bicellular tight junction) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "PMID:18332111") "A process in which a protein is transported to, or maintained in, a location within a bicellular tight junction.") -AnnotationAssertion( "tb") AnnotationAssertion( "2013-09-11T21:43:13Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "protein localisation in tight junction") AnnotationAssertion(Annotation( "GOC:TermGenie") "protein localisation to tight junction") @@ -94253,7 +92322,6 @@ EquivalentClasses( ObjectIntersection # Class: (protein localization to cell junction) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "PMID:18332111") "A process in which a protein is transported to, or maintained in, a location within a cell junction.") -AnnotationAssertion( "tb") AnnotationAssertion( "2013-09-13T16:55:57Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "protein localisation in cell junction") AnnotationAssertion(Annotation( "GOC:TermGenie") "protein localisation to cell junction") @@ -94266,7 +92334,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of water channel activity) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:nhn") Annotation( "PMID:22095752") "Any process that modulates the frequency, rate or extent of water channel activity.") -AnnotationAssertion( "bf") AnnotationAssertion( "2013-09-23T12:56:31Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "regulation of aquaporin") AnnotationAssertion(Annotation( "PMID:22095752") "regulation of aquaporin permeability") @@ -94279,7 +92346,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of water channel activity) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:nhn") Annotation( "PMID:22095752") "Any process that activates or increases the frequency, rate or extent of water channel activity.") -AnnotationAssertion( "bf") AnnotationAssertion( "2013-09-23T12:56:49Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "up regulation of water channel activity") AnnotationAssertion(Annotation( "GOC:TermGenie") "up-regulation of water channel activity") @@ -94301,7 +92367,6 @@ SubClassOf( ObjectSomeValuesFrom( (negative regulation of stem cell population maintenance) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:hjd") Annotation( "PMID:22969033") "Any process that stops, prevents or reduces the frequency, rate or extent of stem cell population maintenance.") -AnnotationAssertion( "cjm") AnnotationAssertion( "2013-10-16T22:19:17Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of stem cell maintenance") AnnotationAssertion(Annotation( "GOC:TermGenie") "down-regulation of stem cell maintenance") @@ -94320,7 +92385,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of stem cell population maintenance) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:hjd") Annotation( "PMID:22969033") "Any process that activates or increases the frequency, rate or extent of stem cell population maintenance.") -AnnotationAssertion( "cjm") AnnotationAssertion( "2013-10-16T22:27:47Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "up regulation of stem cell maintenance") AnnotationAssertion(Annotation( "GOC:TermGenie") "up-regulation of stem cell maintenance") @@ -94339,7 +92403,6 @@ EquivalentClasses( ObjectIntersection # Class: (protein localization to cell leading edge) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:lb") Annotation( "PMID:21543326") "A process in which a protein is transported to, or maintained in, a location within a cell leading edge.") -AnnotationAssertion( "jl") AnnotationAssertion( "2013-10-22T12:36:07Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "protein localisation in cell leading edge") AnnotationAssertion(Annotation( "GOC:TermGenie") "protein localisation to cell leading edge") @@ -94353,7 +92416,6 @@ SubClassOf( (regulation of protein localization to synapse) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:kmv") Annotation( "PMID:22588719") "Any process that modulates the frequency, rate or extent of protein localization to synapse.") -AnnotationAssertion( "kmv") AnnotationAssertion( "2013-10-25T15:09:09Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "regulation of protein localisation to synapse") AnnotationAssertion( "biological_process") @@ -94364,7 +92426,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of protein localization to synapse) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:kmv") Annotation( "PMID:22588719") "Any process that activates or increases the frequency, rate or extent of protein localization to synapse.") -AnnotationAssertion( "kmv") AnnotationAssertion( "2013-10-25T15:09:18Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "positive regulation of protein localisation to synapse") AnnotationAssertion(Annotation( "GOC:TermGenie") "up regulation of protein localisation to synapse") @@ -94383,7 +92444,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulatory T cell apoptotic process) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:nhn") Annotation( "PMID:20471291") "Any apoptotic process in a regulatory T cell.") -AnnotationAssertion( "nhn") AnnotationAssertion( "2013-11-04T17:18:09Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "regulatory T lymphocyte apoptotic process") AnnotationAssertion(Annotation( "GOC:TermGenie") "regulatory T-cell apoptotic process") @@ -94400,7 +92460,6 @@ EquivalentClasses( ObjectIntersection # Class: (Sertoli cell apoptotic process) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:ic") Annotation( "PMID:17761895") "Any apoptotic process in a Sertoli cell.") -AnnotationAssertion( "pr") AnnotationAssertion( "2013-11-06T11:27:34Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "Sertoli cell apoptosis") AnnotationAssertion( "biological_process") @@ -94411,7 +92470,6 @@ EquivalentClasses( ObjectIntersection # Class: (cholangiocyte apoptotic process) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "PMID:22961800") "Any apoptotic process in a cholangiocyte.") -AnnotationAssertion( "cls") AnnotationAssertion( "2013-11-12T15:30:08Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "epithelial cell of bile duct apoptotic process") AnnotationAssertion(Annotation( "GOC:TermGenie") "cholangiocyte apoptosis") @@ -94424,7 +92482,6 @@ EquivalentClasses( ObjectIntersection # Class: (hepatoblast apoptotic process) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "PMID:22412967") "Any apoptotic process in a hepatoblast.") -AnnotationAssertion( "cls") AnnotationAssertion( "2013-11-12T17:02:52Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "hepatoblast apoptosis") AnnotationAssertion( "biological_process") @@ -94436,7 +92493,6 @@ SubClassOf( (regulation of sperm capacitation) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:hjd") Annotation( "PMID:22539676") "Any process that modulates the frequency, rate or extent of sperm capacitation.") -AnnotationAssertion( "hjd") AnnotationAssertion( "2013-11-12T21:17:03Z") AnnotationAssertion( "biological_process") AnnotationAssertion(Annotation( "GOC:TermGenie") "regulation of sperm activation") @@ -94450,7 +92506,6 @@ SubClassOf( (negative regulation of sperm capacitation) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:hjd") Annotation( "PMID:22539676") "Any process that stops, prevents or reduces the frequency, rate or extent of sperm capacitation.") -AnnotationAssertion( "hjd") AnnotationAssertion( "2013-11-12T21:17:12Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of sperm capacitation") AnnotationAssertion(Annotation( "GOC:TermGenie") "down-regulation of sperm capacitation") @@ -94473,7 +92528,6 @@ SubClassOf( (positive regulation of sperm capacitation) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:hjd") Annotation( "PMID:22539676") "Any process that activates or increases the frequency, rate or extent of sperm capacitation.") -AnnotationAssertion( "hjd") AnnotationAssertion( "2013-11-12T21:17:21Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "up regulation of sperm capacitation") AnnotationAssertion(Annotation( "GOC:TermGenie") "up-regulation of sperm capacitation") @@ -94497,7 +92551,6 @@ SubClassOf( "GOC:TermGenie") Annotation( "GOC:bhm") Annotation( "PMID:8077207") "A protein complex which is capable of catalytic activity.") AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/19980"^^xsd:anyURI) -AnnotationAssertion( "bhm") AnnotationAssertion( "2013-11-13T16:18:47Z") AnnotationAssertion(Annotation( "GOC:bhm") Annotation( "GOC:jl") "enzyme complex") AnnotationAssertion( "cellular_component") @@ -94509,7 +92562,6 @@ EquivalentClasses( ObjectIntersection # Class: (transmembrane transporter complex) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:bhm") Annotation( "PMID:18024586") "A transmembrane protein complex which enables the transfer of a substance from one side of a membrane to the other.") -AnnotationAssertion( "bhm") AnnotationAssertion( "2013-11-13T16:23:04Z") AnnotationAssertion( "cellular_component") AnnotationAssertion( "GO:1902495") @@ -94521,7 +92573,6 @@ SubClassOf( ObjectSomeValuesFrom( (regulation of apoptotic DNA fragmentation) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:hjd") Annotation( "PMID:15572351") Annotation( "PMID:15723341") "Any process that modulates the frequency, rate or extent of apoptotic DNA fragmentation.") -AnnotationAssertion( "hjd") AnnotationAssertion( "2013-11-15T18:28:32Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "regulation of DNA fragmentation") AnnotationAssertion(Annotation( "GOC:TermGenie") "regulation of chromatinolysis") @@ -94538,7 +92589,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of apoptotic DNA fragmentation) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:hjd") Annotation( "PMID:15572351") "Any process that stops, prevents or reduces the frequency, rate or extent of apoptotic DNA fragmentation.") -AnnotationAssertion( "hjd") AnnotationAssertion( "2013-11-15T18:28:41Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of DNA catabolic process during apoptosis") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of DNA catabolism during apoptosis") @@ -94572,7 +92622,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of apoptotic DNA fragmentation) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:hjd") Annotation( "PMID:15572351") "Any process that activates or increases the frequency, rate or extent of apoptotic DNA fragmentation.") -AnnotationAssertion( "hjd") AnnotationAssertion( "2013-11-15T18:28:50Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "positive regulation of DNA catabolic process during apoptosis") AnnotationAssertion(Annotation( "GOC:TermGenie") "positive regulation of DNA catabolism during apoptosis") @@ -94606,7 +92655,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of organelle transport along microtubule) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:dph") Annotation( "PMID:21147087") "Any process that modulates the frequency, rate or extent of organelle transport along microtubule.") -AnnotationAssertion( "dph") AnnotationAssertion( "2013-11-15T20:15:17Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "regulation of microtubule-based organelle localization") AnnotationAssertion( "biological_process") @@ -94617,7 +92665,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of intracellular signal transduction) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:dph") Annotation( "GOC:signaling") Annotation( "GOC:tb") "Any process that modulates the frequency, rate or extent of intracellular signal transduction.") -AnnotationAssertion( "bf") AnnotationAssertion( "2013-12-02T11:32:52Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "regulation of intracellular signaling cascade") AnnotationAssertion(Annotation( "GOC:TermGenie") "regulation of intracellular signaling chain") @@ -94634,7 +92681,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of intracellular signal transduction) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:dph") Annotation( "GOC:signaling") Annotation( "GOC:tb") "Any process that stops, prevents or reduces the frequency, rate or extent of intracellular signal transduction.") -AnnotationAssertion( "bf") AnnotationAssertion( "2013-12-02T11:33:01Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of intracellular signal transduction") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of intracellular signaling chain") @@ -94679,7 +92725,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of intracellular signal transduction) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:TermGenie") Annotation( "GOC:dph") Annotation( "GOC:signaling") Annotation( "GOC:tb") "Any process that activates or increases the frequency, rate or extent of intracellular signal transduction.") -AnnotationAssertion( "bf") AnnotationAssertion( "2013-12-02T11:33:10Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "positive regulation of intracellular signaling chain") AnnotationAssertion(Annotation( "GOC:TermGenie") "up regulation of intracellular signal transduction") @@ -94724,7 +92769,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of neutrophil activation) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "PMID:17588661") "Any process that modulates the frequency, rate or extent of neutrophil activation.") -AnnotationAssertion( "ecu") AnnotationAssertion( "2013-12-10T15:33:08Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:1902563") @@ -94734,7 +92778,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of neutrophil activation) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "PMID:17588661") "Any process that stops, prevents or reduces the frequency, rate or extent of neutrophil activation.") -AnnotationAssertion( "ecu") AnnotationAssertion( "2013-12-10T15:33:16Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of neutrophil activation") AnnotationAssertion(Annotation( "GOC:TermGenie") "down-regulation of neutrophil activation") @@ -94748,7 +92791,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of neutrophil activation) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "PMID:17588661") "Any process that activates or increases the frequency, rate or extent of neutrophil activation.") -AnnotationAssertion( "ecu") AnnotationAssertion( "2013-12-10T15:33:26Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "up regulation of neutrophil activation") AnnotationAssertion(Annotation( "GOC:TermGenie") "up-regulation of neutrophil activation") @@ -94762,7 +92804,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of eosinophil activation) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "PMID:16254138") "Any process that modulates the frequency, rate or extent of eosinophil activation.") -AnnotationAssertion( "ecu") AnnotationAssertion( "2013-12-10T15:54:35Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:1902566") @@ -94772,7 +92813,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of eosinophil activation) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "PMID:16254138") "Any process that stops, prevents or reduces the frequency, rate or extent of eosinophil activation.") -AnnotationAssertion( "ecu") AnnotationAssertion( "2013-12-10T15:54:43Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of eosinophil activation") AnnotationAssertion(Annotation( "GOC:TermGenie") "down-regulation of eosinophil activation") @@ -94786,7 +92826,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of eosinophil activation) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "PMID:16254138") "Any process that activates or increases the frequency, rate or extent of eosinophil activation.") -AnnotationAssertion( "ecu") AnnotationAssertion( "2013-12-10T15:54:52Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "up regulation of eosinophil activation") AnnotationAssertion(Annotation( "GOC:TermGenie") "up-regulation of eosinophil activation") @@ -94800,7 +92839,6 @@ EquivalentClasses( ObjectIntersection # Class: (protein localization to nucleolus) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "PMID:22809626") "A process in which a protein is transported to, or maintained in, a location within a nucleolus.") -AnnotationAssertion( "mah") AnnotationAssertion( "2013-12-10T16:25:28Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "protein localisation in nucleolus") AnnotationAssertion(Annotation( "GOC:TermGenie") "protein localisation to nucleolus") @@ -94813,7 +92851,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of response to water deprivation) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000058") Annotation( "PMID:24198318") "Any process that activates or increases the frequency, rate or extent of response to water deprivation.") -AnnotationAssertion( "tb") AnnotationAssertion( "2013-12-19T00:31:58Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "positive regulation of response to dehydration") AnnotationAssertion(Annotation( "GOC:TermGenie") "positive regulation of response to drought") @@ -94849,7 +92886,6 @@ SubClassOf( (proton transmembrane transport) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:pr") Annotation( "GO_REF:0000069") "The directed movement of a proton across a membrane.") -AnnotationAssertion( "pr") AnnotationAssertion( "2013-12-20T11:08:37Z") AnnotationAssertion( "hydrogen transport") AnnotationAssertion( "proton transport") @@ -94867,7 +92903,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of neutrophil migration) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000058") Annotation( "PMID:1826836") "Any process that modulates the frequency, rate or extent of neutrophil migration.") -AnnotationAssertion( "sl") AnnotationAssertion( "2014-01-15T18:58:39Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:1902622") @@ -94877,7 +92912,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of neutrophil migration) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000058") Annotation( "PMID:1826836") "Any process that stops, prevents or reduces the frequency, rate or extent of neutrophil migration.") -AnnotationAssertion( "sl") AnnotationAssertion( "2014-01-15T18:58:49Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of neutrophil migration") AnnotationAssertion(Annotation( "GOC:TermGenie") "down-regulation of neutrophil migration") @@ -94891,7 +92925,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of neutrophil migration) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000058") Annotation( "PMID:1826836") "Any process that activates or increases the frequency, rate or extent of neutrophil migration.") -AnnotationAssertion( "sl") AnnotationAssertion( "2014-01-15T18:58:58Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "up regulation of neutrophil migration") AnnotationAssertion(Annotation( "GOC:TermGenie") "up-regulation of neutrophil migration") @@ -94905,7 +92938,6 @@ EquivalentClasses( ObjectIntersection # Class: (neural crest cell differentiation involved in thymus development) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:nhn") Annotation( "GO_REF:0000060") Annotation( "PMID:15741317") Annotation( "PMID:18292542") "Any neural crest cell differentiation that is involved in thymus development.") -AnnotationAssertion( "pr") AnnotationAssertion( "2014-01-21T10:03:20Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:1902637") @@ -94915,7 +92947,6 @@ EquivalentClasses( ObjectIntersection # Class: (neural crest cell differentiation involved in parathyroid gland development) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:nhn") Annotation( "GO_REF:0000060") Annotation( "PMID:15741317") "Any neural crest cell differentiation that is involved in parathyroid gland development.") -AnnotationAssertion( "pr") AnnotationAssertion( "2014-01-21T10:03:29Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:1902638") @@ -94925,7 +92956,6 @@ EquivalentClasses( ObjectIntersection # Class: (calcium ion import into cytosol) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:vw") Annotation( "GO_REF:0000075") "The directed movement of calcium ion into a cytosol.") -AnnotationAssertion( "pr") AnnotationAssertion( "2014-01-22T13:41:11Z") AnnotationAssertion( "calcium import into cytosol") AnnotationAssertion( "biological_process") @@ -94938,7 +92968,6 @@ SubClassOf( ObjectSomeValuesFrom( (negative regulation of RNA biosynthetic process) AnnotationAssertion(Annotation( "GO:jl") Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000058") "Any process that stops, prevents or reduces the frequency, rate or extent of RNA biosynthetic process.") -AnnotationAssertion( "jl") AnnotationAssertion( "2014-02-05T16:32:01Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of RNA anabolism") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of RNA biosynthesis") @@ -94972,7 +93001,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of RNA biosynthetic process) AnnotationAssertion(Annotation( "GO:jl") Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000058") "Any process that activates or increases the frequency, rate or extent of RNA biosynthetic process.") -AnnotationAssertion( "jl") AnnotationAssertion( "2014-02-05T16:32:10Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "positive regulation of RNA anabolism") AnnotationAssertion(Annotation( "GOC:TermGenie") "positive regulation of RNA biosynthesis") @@ -95006,7 +93034,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of receptor localization to synapse) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:kmv") Annotation( "GO_REF:0000058") Annotation( "PMID:22252129") "Any process that modulates the frequency, rate or extent of receptor localization to synapse.") -AnnotationAssertion( "kmv") AnnotationAssertion( "2014-02-07T17:38:31Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "regulation of receptor localisation to synapse") AnnotationAssertion( "biological_process") @@ -95017,7 +93044,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of receptor localization to synapse) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:kmv") Annotation( "GO_REF:0000058") Annotation( "PMID:22252129") "Any process that stops, prevents or reduces the frequency, rate or extent of receptor localization to synapse.") -AnnotationAssertion( "kmv") AnnotationAssertion( "2014-02-07T17:38:41Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of receptor localisation to synapse") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of receptor localization to synapse") @@ -95036,7 +93062,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of receptor localization to synapse) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:kmv") Annotation( "GO_REF:0000058") Annotation( "PMID:22252129") "Any process that activates or increases the frequency, rate or extent of receptor localization to synapse.") -AnnotationAssertion( "kmv") AnnotationAssertion( "2014-02-07T17:38:51Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "positive regulation of receptor localisation to synapse") AnnotationAssertion(Annotation( "GOC:TermGenie") "up regulation of receptor localisation to synapse") @@ -95055,7 +93080,6 @@ EquivalentClasses( ObjectIntersection # Class: (respiratory basal cell differentiation) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000086") Annotation( "MP:0011114") Annotation( "PMID:17909629") "The process in which a relatively unspecialized cell acquires the specialized features of a respiratory basal cell.") -AnnotationAssertion( "cjm") AnnotationAssertion( "2014-02-13T23:41:24Z") AnnotationAssertion(Annotation( "MP:0011114") "airway basal cell differentiation") AnnotationAssertion( "biological_process") @@ -95067,7 +93091,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of neuroblast proliferation) AnnotationAssertion(Annotation( "GOC:PARL") Annotation( "GOC:TermGenie") Annotation( "GOC:rl") Annotation( "GO_REF:0000058") Annotation( "PMID:21168496") "Any process that modulates the frequency, rate or extent of neuroblast proliferation.") -AnnotationAssertion( "rl") AnnotationAssertion( "2014-02-18T10:03:31Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:1902692") @@ -95077,7 +93100,6 @@ EquivalentClasses( ObjectIntersection # Class: (GABA receptor complex) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:bhm") Annotation( "GO_REF:0000088") Annotation( "PMID:18790874") "A protein complex which is capable of GABA receptor activity. Upon binding of gamma-aminobutyric acid (GABA) it transmits the signal from one side of the membrane to the other to initiate a change in cell activity. Major inhibitory receptor in vertebrate brain. Also found in other vertebrate tissues, invertebrates and possibly in plants. Effective benzodiazepine receptor.") -AnnotationAssertion( "bhm") AnnotationAssertion( "2014-02-20T16:07:48Z") AnnotationAssertion( "gamma-aminobutyric acid receptor complex") AnnotationAssertion( "cellular_component") @@ -95088,7 +93110,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of prolactin secretion) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000058") Annotation( "PMID:16159377") "Any process that stops, prevents or reduces the frequency, rate or extent of prolactin secretion.") -AnnotationAssertion( "mr") AnnotationAssertion( "2014-02-24T16:09:28Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of prolactin secretion") AnnotationAssertion(Annotation( "GOC:TermGenie") "down-regulation of prolactin secretion") @@ -95102,7 +93123,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of prolactin secretion) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000058") Annotation( "PMID:16159377") "Any process that activates or increases the frequency, rate or extent of prolactin secretion.") -AnnotationAssertion( "mr") AnnotationAssertion( "2014-02-24T16:09:37Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "up regulation of prolactin secretion") AnnotationAssertion(Annotation( "GOC:TermGenie") "up-regulation of prolactin secretion") @@ -95116,7 +93136,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of skeletal muscle satellite cell proliferation) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000058") Annotation( "PMID:23212449") "Any process that stops, prevents or reduces the frequency, rate or extent of satellite cell proliferation.") -AnnotationAssertion( "mr") AnnotationAssertion( "2014-02-24T16:09:46Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of satellite cell proliferation") AnnotationAssertion(Annotation( "GOC:TermGenie") "down-regulation of satellite cell proliferation") @@ -95130,7 +93149,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of skeletal muscle satellite cell proliferation) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000058") Annotation( "PMID:23212449") "Any process that activates or increases the frequency, rate or extent of skeletal muscle satellite cell proliferation.") -AnnotationAssertion( "mr") AnnotationAssertion( "2014-02-24T16:09:56Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "up regulation of satellite cell proliferation") AnnotationAssertion(Annotation( "GOC:TermGenie") "up-regulation of satellite cell proliferation") @@ -95144,7 +93162,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of satellite cell differentiation) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000058") Annotation( "PMID:23212449") "Any process that stops, prevents or reduces the frequency, rate or extent of satellite cell differentiation.") -AnnotationAssertion( "mr") AnnotationAssertion( "2014-02-24T16:10:05Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of satellite cell differentiation") AnnotationAssertion(Annotation( "GOC:TermGenie") "down-regulation of satellite cell differentiation") @@ -95158,7 +93175,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of skeletal muscle satellite cell differentiation) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000058") Annotation( "PMID:23212449") "Any process that activates or increases the frequency, rate or extent of satellite cell differentiation.") -AnnotationAssertion( "mr") AnnotationAssertion( "2014-02-24T16:10:14Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "up regulation of satellite cell differentiation") AnnotationAssertion(Annotation( "GOC:TermGenie") "up-regulation of satellite cell differentiation") @@ -95172,7 +93188,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of proteoglycan biosynthetic process) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000058") Annotation( "PMID:23212449") "Any process that stops, prevents or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of proteoglycans, any glycoprotein in which the carbohydrate units are glycosaminoglycans.") -AnnotationAssertion( "mr") AnnotationAssertion( "2014-02-24T16:10:43Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of proteoglycan anabolism") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of proteoglycan biosynthesis") @@ -95206,7 +93221,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of proteoglycan biosynthetic process) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000058") Annotation( "PMID:23212449") "Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of proteoglycans, any glycoprotein in which the carbohydrate units are glycosaminoglycans.") -AnnotationAssertion( "mr") AnnotationAssertion( "2014-02-24T16:10:52Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "positive regulation of proteoglycan anabolism") AnnotationAssertion(Annotation( "GOC:TermGenie") "positive regulation of proteoglycan biosynthesis") @@ -95240,7 +93254,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of growth plate cartilage chondrocyte differentiation) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000058") Annotation( "PMID:23212449") "Any process that modulates the rate, frequency, or extent of the process in which a chondroblast acquires specialized structural and/or functional features of a chondrocyte that will contribute to the growth of a bone. A chondrocyte is a polymorphic cell that forms cartilage.") -AnnotationAssertion( "mr") AnnotationAssertion( "2014-02-24T16:11:28Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:1902733") @@ -95250,7 +93263,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of chondrocyte differentiation involved in endochondral bone morphogenesis) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000058") Annotation( "PMID:8662546") "Any process that modulates the rate, frequency, or extent of the process in which a chondroblast acquires specialized structural and/or functional features of a chondrocyte that will contribute to the development of a bone. A chondrocyte is a polymorphic cell that forms cartilage.") -AnnotationAssertion( "mr") AnnotationAssertion( "2014-02-26T15:36:15Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:1902738") @@ -95263,7 +93275,6 @@ SubClassOf( (apoptotic process involved in development) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:mtg_apoptosis") Annotation( "GOC:pg") Annotation( "GO_REF:0000060") "Any apoptotic process that is involved in anatomical structure development.") -AnnotationAssertion( "pr") AnnotationAssertion( "2014-02-28T13:09:43Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "apoptotic cell death involved in anatomical structure development") AnnotationAssertion(Annotation( "GOC:TermGenie") "apoptotic cell death involved in development of an anatomical structure") @@ -95301,7 +93312,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of lens fiber cell differentiation) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:mr") Annotation( "GO_REF:0000058") Annotation( "PMID:17592637") "Any process that modulates the frequency, rate or extent of lens fiber cell differentiation.") -AnnotationAssertion( "mr") AnnotationAssertion( "2014-03-03T23:18:50Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "regulation of lens fibre cell differentiation") AnnotationAssertion( "biological_process") @@ -95312,7 +93322,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of lens fiber cell differentiation) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:mr") Annotation( "GO_REF:0000058") Annotation( "PMID:17592637") "Any process that stops, prevents or reduces the frequency, rate or extent of lens fiber cell differentiation.") -AnnotationAssertion( "mr") AnnotationAssertion( "2014-03-03T23:19:32Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of lens fiber cell differentiation") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of lens fibre cell differentiation") @@ -95332,7 +93341,6 @@ SubClassOf( ObjectSomeValuesFrom( (positive regulation of lens fiber cell differentiation) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:mr") Annotation( "GO_REF:0000058") Annotation( "PMID:17592637") "Any process that activates or increases the frequency, rate or extent of lens fiber cell differentiation.") -AnnotationAssertion( "mr") AnnotationAssertion( "2014-03-03T23:20:12Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "positive regulation of lens fibre cell differentiation") AnnotationAssertion(Annotation( "GOC:TermGenie") "up regulation of lens fiber cell differentiation") @@ -95352,7 +93360,6 @@ SubClassOf( ObjectSomeValuesFrom( (positive regulation of chondrocyte development) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:mr") Annotation( "GO_REF:0000058") Annotation( "PMID:16575901") "Any process that activates or increases the frequency, rate or extent of chondrocyte development.") -AnnotationAssertion( "mr") AnnotationAssertion( "2014-03-07T17:45:55Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "up regulation of chondrocyte development") AnnotationAssertion(Annotation( "GOC:TermGenie") "up-regulation of chondrocyte development") @@ -95369,7 +93376,6 @@ SubClassOf( (skeletal muscle satellite cell migration) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:mr") Annotation( "GO_REF:0000091") Annotation( "PMID:17996437") Annotation( "PMID:19609936") "The orderly movement of a skeletal muscle satellite cell from one site to another. Migration of these cells is a key step in the process of growth and repair of skeletal muscle cells.") -AnnotationAssertion( "mr") AnnotationAssertion( "2014-03-10T15:20:28Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:1902766") @@ -95379,7 +93385,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of skeletal muscle fiber differentiation) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:mr") Annotation( "GO_REF:0000058") Annotation( "PMID:17879321") "Any process that modulates the frequency, rate or extent of skeletal muscle fiber differentiation.") -AnnotationAssertion( "mr") AnnotationAssertion( "2014-03-26T21:18:26Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:1902809") @@ -95389,7 +93394,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of skeletal muscle fiber differentiation) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:mr") Annotation( "GO_REF:0000058") Annotation( "PMID:17879321") "Any process that stops, prevents or reduces the frequency, rate or extent of skeletal muscle fiber differentiation.") -AnnotationAssertion( "mr") AnnotationAssertion( "2014-03-26T21:18:32Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of skeletal muscle fiber differentiation") AnnotationAssertion(Annotation( "GOC:TermGenie") "down-regulation of skeletal muscle fiber differentiation") @@ -95403,7 +93407,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of skeletal muscle fiber differentiation) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:mr") Annotation( "GO_REF:0000058") Annotation( "PMID:17879321") "Any process that activates or increases the frequency, rate or extent of skeletal muscle fiber differentiation.") -AnnotationAssertion( "mr") AnnotationAssertion( "2014-03-26T21:18:38Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "up regulation of skeletal muscle fiber differentiation") AnnotationAssertion(Annotation( "GOC:TermGenie") "up-regulation of skeletal muscle fiber differentiation") @@ -95417,7 +93420,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of protein localization to microtubule) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:vw") Annotation( "GO_REF:0000058") Annotation( "PMID:23087209") "Any process that modulates the frequency, rate or extent of protein localization to microtubule.") -AnnotationAssertion( "tb") AnnotationAssertion( "2014-03-27T22:07:12Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "regulation of protein localisation to microtubule") AnnotationAssertion( "biological_process") @@ -95428,7 +93430,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of protein localization to microtubule) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:vw") Annotation( "GO_REF:0000058") Annotation( "PMID:23087209") "Any process that stops, prevents or reduces the frequency, rate or extent of protein localization to microtubule.") -AnnotationAssertion( "tb") AnnotationAssertion( "2014-03-27T22:07:18Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of protein localisation to microtubule") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of protein localization to microtubule") @@ -95447,7 +93448,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of cell proliferation in dorsal spinal cord) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:mr") Annotation( "GO_REF:0000058") Annotation( "PMID:21730158") "Any process that stops, prevents or reduces the frequency, rate or extent of cell proliferation in dorsal spinal cord.") -AnnotationAssertion( "mr") AnnotationAssertion( "2014-03-31T17:42:50Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of cell proliferation in dorsal spinal cord") AnnotationAssertion(Annotation( "GOC:TermGenie") "down-regulation of cell proliferation in dorsal spinal cord") @@ -95461,7 +93461,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of cell proliferation in dorsal spinal cord) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:mr") Annotation( "GO_REF:0000058") Annotation( "PMID:21730158") "Any process that activates or increases the frequency, rate or extent of cell proliferation in dorsal spinal cord.") -AnnotationAssertion( "mr") AnnotationAssertion( "2014-03-31T17:43:33Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "up regulation of cell proliferation in dorsal spinal cord") AnnotationAssertion(Annotation( "GOC:TermGenie") "up-regulation of cell proliferation in dorsal spinal cord") @@ -95475,7 +93474,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of nuclear migration along microtubule) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000058") Annotation( "PMID:23087209") "Any process that modulates the frequency, rate or extent of nuclear migration along microtubule.") -AnnotationAssertion( "vw") AnnotationAssertion( "2014-04-01T13:50:23Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "regulation of nuclear movement, microtubule-mediated") AnnotationAssertion(Annotation( "GOC:TermGenie") "regulation of nucleus migration") @@ -95495,7 +93493,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of nuclear migration along microtubule) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000058") Annotation( "PMID:23087209") "Any process that stops, prevents or reduces the frequency, rate or extent of nuclear migration along microtubule.") -AnnotationAssertion( "vw") AnnotationAssertion( "2014-04-01T13:50:29Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of microtubule cytoskeleton-dependent nuclear positioning") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of microtubule cytoskeleton-dependent nucleus positioning") @@ -95549,7 +93546,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of nuclear migration along microtubule) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000058") Annotation( "PMID:23087209") "Any process that activates or increases the frequency, rate or extent of nuclear migration along microtubule.") -AnnotationAssertion( "vw") AnnotationAssertion( "2014-04-01T13:50:35Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "positive regulation of microtubule cytoskeleton-dependent nuclear positioning") AnnotationAssertion(Annotation( "GOC:TermGenie") "positive regulation of microtubule cytoskeleton-dependent nucleus positioning") @@ -95603,7 +93599,6 @@ EquivalentClasses( ObjectIntersection # Class: (microtubule cytoskeleton organization involved in mitosis) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000060") Annotation( "PMID:18799626") "Any microtubule cytoskeleton organization that is involved in mitosis.") -AnnotationAssertion( "vw") AnnotationAssertion( "2014-04-02T14:19:38Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "microtubule cytoskeleton organisation involved in mitosis") AnnotationAssertion(Annotation( "GOC:TermGenie") "microtubule dynamics involved in mitosis") @@ -95616,7 +93611,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of embryonic camera-type eye development) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:mr") Annotation( "GO_REF:0000058") Annotation( "PMID:16872597") "Any process that modulates the frequency, rate or extent of embryonic camera-type eye development.") -AnnotationAssertion( "mr") AnnotationAssertion( "2014-04-03T15:24:00Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "regulation of embryonic eye development") AnnotationAssertion( "biological_process") @@ -95627,7 +93621,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of embryonic camera-type eye development) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:mr") Annotation( "GO_REF:0000058") Annotation( "PMID:16872597") "Any process that stops, prevents or reduces the frequency, rate or extent of embryonic camera-type eye development.") -AnnotationAssertion( "mr") AnnotationAssertion( "2014-04-03T15:24:06Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of embryonic camera-type eye development") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of embryonic eye development") @@ -95646,7 +93639,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of embryonic camera-type eye development) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:mr") Annotation( "GO_REF:0000058") Annotation( "PMID:16872597") "Any process that activates or increases the frequency, rate or extent of embryonic camera-type eye development.") -AnnotationAssertion( "mr") AnnotationAssertion( "2014-04-03T15:24:12Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "positive regulation of embryonic eye development") AnnotationAssertion(Annotation( "GOC:TermGenie") "up regulation of embryonic camera-type eye development") @@ -95665,7 +93657,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of retina development in camera-type eye) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:mr") Annotation( "GO_REF:0000058") Annotation( "PMID:16872597") "Any process that modulates the frequency, rate or extent of retina development in camera-type eye.") -AnnotationAssertion( "mr") AnnotationAssertion( "2014-04-03T15:24:17Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "regulation of retina development in camera-style eye") AnnotationAssertion( "biological_process") @@ -95677,7 +93668,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of retina development in camera-type eye) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:mr") Annotation( "GO_REF:0000058") Annotation( "PMID:16872597") "Any process that stops, prevents or reduces the frequency, rate or extent of retina development in camera-type eye.") -AnnotationAssertion( "mr") AnnotationAssertion( "2014-04-03T15:24:23Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of retina development in camera-style eye") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of retina development in camera-type eye") @@ -95702,7 +93692,6 @@ SubClassOf( ObjectSomeValuesFrom( (positive regulation of retina development in camera-type eye) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:mr") Annotation( "GO_REF:0000058") Annotation( "PMID:16872597") "Any process that activates or increases the frequency, rate or extent of retina development in camera-type eye.") -AnnotationAssertion( "mr") AnnotationAssertion( "2014-04-03T15:24:29Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "positive regulation of retina development in camera-style eye") AnnotationAssertion(Annotation( "GOC:TermGenie") "up regulation of retina development in camera-style eye") @@ -95727,7 +93716,6 @@ SubClassOf( ObjectSomeValuesFrom( (regulation of amacrine cell differentiation) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:mr") Annotation( "GO_REF:0000058") Annotation( "PMID:16872597") "Any process that modulates the frequency, rate or extent of amacrine cell differentiation.") -AnnotationAssertion( "mr") AnnotationAssertion( "2014-04-03T15:24:35Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "regulation of amacrine neuron differentiation") AnnotationAssertion( "biological_process") @@ -95738,7 +93726,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of amacrine cell differentiation) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:mr") Annotation( "GO_REF:0000058") Annotation( "PMID:16872597") "Any process that stops, prevents or reduces the frequency, rate or extent of amacrine cell differentiation.") -AnnotationAssertion( "mr") AnnotationAssertion( "2014-04-03T15:24:40Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of amacrine cell differentiation") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of amacrine neuron differentiation") @@ -95757,7 +93744,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of amacrine cell differentiation) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:mr") Annotation( "GO_REF:0000058") Annotation( "PMID:16872597") "Any process that activates or increases the frequency, rate or extent of amacrine cell differentiation.") -AnnotationAssertion( "mr") AnnotationAssertion( "2014-04-03T15:24:46Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "positive regulation of amacrine neuron differentiation") AnnotationAssertion(Annotation( "GOC:TermGenie") "up regulation of amacrine cell differentiation") @@ -95776,7 +93762,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of embryonic pattern specification) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:mr") Annotation( "GO_REF:0000058") Annotation( "PMID:16872597") "Any process that modulates the frequency, rate or extent of embryonic pattern specification.") -AnnotationAssertion( "mr") AnnotationAssertion( "2014-04-03T15:25:15Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "regulation of embryonic pattern biosynthesis") AnnotationAssertion(Annotation( "GOC:TermGenie") "regulation of embryonic pattern formation") @@ -95789,7 +93774,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of embryonic pattern specification) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:mr") Annotation( "GO_REF:0000058") Annotation( "PMID:16872597") "Any process that stops, prevents or reduces the frequency, rate or extent of embryonic pattern specification.") -AnnotationAssertion( "mr") AnnotationAssertion( "2014-04-03T15:25:20Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of embryonic pattern specification") AnnotationAssertion(Annotation( "GOC:TermGenie") "down-regulation of embryonic pattern specification") @@ -95808,7 +93792,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of embryonic pattern specification) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:mr") Annotation( "GO_REF:0000058") Annotation( "PMID:16872597") "Any process that activates or increases the frequency, rate or extent of embryonic pattern specification.") -AnnotationAssertion( "mr") AnnotationAssertion( "2014-04-03T15:25:26Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "up regulation of embryonic pattern specification") AnnotationAssertion(Annotation( "GOC:TermGenie") "up-regulation of embryonic pattern specification") @@ -95827,7 +93810,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of supramolecular fiber organization) AnnotationAssertion(Annotation( "GOC:PARL") Annotation( "GOC:TermGenie") Annotation( "GOC:rl") Annotation( "GO_REF:0000058") Annotation( "PMID:23921388") "Any process that modulates the frequency, rate or extent of supramolecular fiber organization.") -AnnotationAssertion( "rl") AnnotationAssertion( "2014-04-15T16:46:36Z") AnnotationAssertion( "biological_process") AnnotationAssertion(Annotation( "GOC:TermGenie") "regulation of fibril organisation") @@ -95839,7 +93821,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of supramolecular fiber organization) AnnotationAssertion(Annotation( "GOC:PARL") Annotation( "GOC:TermGenie") Annotation( "GOC:rl") Annotation( "GO_REF:0000058") Annotation( "PMID:23921388") "Any process that stops, prevents or reduces the frequency, rate or extent of fibril organization.") -AnnotationAssertion( "rl") AnnotationAssertion( "2014-04-15T16:46:42Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "inhibition of fibril organisation") AnnotationAssertion(Annotation( "GOC:TermGenie") "inhibition of fibril organization") @@ -95859,7 +93840,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of supramolecular fiber organization) AnnotationAssertion(Annotation( "GOC:PARL") Annotation( "GOC:TermGenie") Annotation( "GOC:rl") Annotation( "GO_REF:0000058") Annotation( "PMID:23921388") "Any process that activates or increases the frequency, rate or extent of supramolecular fiber organization.") -AnnotationAssertion( "rl") AnnotationAssertion( "2014-04-15T16:46:48Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "activation of fibril organisation") AnnotationAssertion(Annotation( "GOC:TermGenie") "activation of fibril organization") @@ -95879,7 +93859,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of melanosome transport) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:als") Annotation( "GO_REF:0000058") Annotation( "PMID:23334344") "Any process that modulates the frequency, rate or extent of melanosome transport.") -AnnotationAssertion( "als") AnnotationAssertion( "2014-04-17T11:40:16Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:1902908") @@ -95890,7 +93869,6 @@ SubClassOf( ObjectSomeValuesFrom( (negative regulation of melanosome transport) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:als") Annotation( "GO_REF:0000058") Annotation( "PMID:23334344") "Any process that stops, prevents or reduces the frequency, rate or extent of melanosome transport.") -AnnotationAssertion( "als") AnnotationAssertion( "2014-04-17T11:40:28Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of melanosome transport") AnnotationAssertion(Annotation( "GOC:TermGenie") "down-regulation of melanosome transport") @@ -95905,7 +93883,6 @@ SubClassOf( ObjectSomeValuesFrom( (positive regulation of melanosome transport) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:als") Annotation( "GO_REF:0000058") Annotation( "PMID:23334344") "Any process that activates or increases the frequency, rate or extent of melanosome transport.") -AnnotationAssertion( "als") AnnotationAssertion( "2014-04-17T11:40:34Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "up regulation of melanosome transport") AnnotationAssertion(Annotation( "GOC:TermGenie") "up-regulation of melanosome transport") @@ -95920,7 +93897,6 @@ SubClassOf( ObjectSomeValuesFrom( (protein kinase complex) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:bhm") Annotation( "GO_REF:0000088") Annotation( "PMID:24606918") "A protein complex which is capable of protein kinase activity.") -AnnotationAssertion( "bhm") AnnotationAssertion( "2014-04-17T13:52:40Z") AnnotationAssertion( "cellular_component") AnnotationAssertion( "GO:1902911") @@ -95931,7 +93907,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of neuroepithelial cell differentiation) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:mr") Annotation( "GO_REF:0000058") Annotation( "PMID:16916506") "Any process that activates or increases the frequency, rate or extent of neuroepithelial cell differentiation.") -AnnotationAssertion( "mr") AnnotationAssertion( "2014-04-18T21:06:42Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "up regulation of neuroepithelial cell differentiation") AnnotationAssertion(Annotation( "GOC:TermGenie") "up-regulation of neuroepithelial cell differentiation") @@ -95945,7 +93920,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of lipid transport across blood-brain barrier) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:sjp") Annotation( "GO_REF:0000058") Annotation( "PMID:24345162") "Any process that modulates the frequency, rate or extent of lipid transport across blood-brain barrier.") -AnnotationAssertion( "sjp") AnnotationAssertion( "2014-05-09T09:30:04Z") AnnotationAssertion( "regulation of lipid transport across blood brain barrier") AnnotationAssertion( "biological_process") @@ -95958,7 +93932,6 @@ SubClassOf( ObjectAllValuesFrom( (negative regulation of lipid transport across blood-brain barrier) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:sjp") Annotation( "GO_REF:0000058") Annotation( "PMID:24345162") "Any process that stops, prevents or reduces the frequency, rate or extent of lipid transport across blood-brain barrier.") -AnnotationAssertion( "sjp") AnnotationAssertion( "2014-05-09T09:30:10Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of lipid transport across blood brain barrier") AnnotationAssertion(Annotation( "GOC:TermGenie") "down-regulation of lipid transport across blood brain barrier") @@ -95973,7 +93946,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of lipid transport across blood-brain barrier) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:sjp") Annotation( "GO_REF:0000058") Annotation( "PMID:24345162") "Any process that activates or increases the frequency, rate or extent of lipid transport across blood-brain barrier.") -AnnotationAssertion( "sjp") AnnotationAssertion( "2014-05-09T09:30:16Z") AnnotationAssertion( "positive regulation of lipid transport across blood brain barrier") AnnotationAssertion(Annotation( "GOC:TermGenie") "up regulation of lipid transport across blood brain barrier") @@ -95988,7 +93960,6 @@ EquivalentClasses( ObjectIntersection # Class: (organelle disassembly) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000079") "The disaggregation of an organelle into its constituent components.") -AnnotationAssertion( "jl") AnnotationAssertion( "2014-05-13T12:36:03Z") AnnotationAssertion( "organelle degradation") AnnotationAssertion( "biological_process") @@ -95999,7 +93970,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of bone development) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:mr") Annotation( "GO_REF:0000058") Annotation( "PMID:22510437") "Any process that modulates the frequency, rate or extent of bone development.") -AnnotationAssertion( "mr") AnnotationAssertion( "2014-05-13T22:41:53Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:1903010") @@ -96010,7 +93980,6 @@ SubClassOf( (negative regulation of bone development) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:mr") Annotation( "GO_REF:0000058") Annotation( "PMID:22510437") "Any process that stops, prevents or reduces the frequency, rate or extent of bone development.") -AnnotationAssertion( "mr") AnnotationAssertion( "2014-05-13T22:42:00Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of bone development") AnnotationAssertion(Annotation( "GOC:TermGenie") "down-regulation of bone development") @@ -96027,7 +93996,6 @@ SubClassOf( (positive regulation of bone development) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:mr") Annotation( "GO_REF:0000058") Annotation( "PMID:22510437") "Any process that activates or increases the frequency, rate or extent of bone development.") -AnnotationAssertion( "mr") AnnotationAssertion( "2014-05-13T22:42:06Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "up regulation of bone development") AnnotationAssertion(Annotation( "GOC:TermGenie") "up-regulation of bone development") @@ -96044,7 +94012,6 @@ SubClassOf( (regulation of glycoprotein metabolic process) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:TermGenie") Annotation( "GOC:rl") Annotation( "GO_REF:0000058") Annotation( "PMID:23544079") "Any process that modulates the frequency, rate or extent of glycoprotein metabolic process.") -AnnotationAssertion( "rl") AnnotationAssertion( "2014-05-14T18:44:19Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "regulation of glycoprotein metabolism") AnnotationAssertion( "biological_process") @@ -96056,7 +94023,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of glycoprotein metabolic process) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:TermGenie") Annotation( "GOC:rl") Annotation( "GO_REF:0000058") Annotation( "PMID:23544079") "Any process that stops, prevents or reduces the frequency, rate or extent of glycoprotein metabolic process.") -AnnotationAssertion( "rl") AnnotationAssertion( "2014-05-14T18:44:25Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of glycoprotein metabolic process") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of glycoprotein metabolism") @@ -96076,7 +94042,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of glycoprotein metabolic process) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:TermGenie") Annotation( "GOC:rl") Annotation( "GO_REF:0000058") Annotation( "PMID:23544079") "Any process that activates or increases the frequency, rate or extent of glycoprotein metabolic process.") -AnnotationAssertion( "rl") AnnotationAssertion( "2014-05-14T18:44:31Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "positive regulation of glycoprotein metabolism") AnnotationAssertion(Annotation( "GOC:TermGenie") "up regulation of glycoprotein metabolic process") @@ -96096,7 +94061,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of response to wounding) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:kmv") Annotation( "GO_REF:0000058") Annotation( "PMID:19164535") "Any process that modulates the frequency, rate or extent of response to wounding.") -AnnotationAssertion( "kmv") AnnotationAssertion( "2014-05-18T01:28:46Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "regulation of physiological response to wounding") AnnotationAssertion( "biological_process") @@ -96108,7 +94072,6 @@ SubClassOf( (negative regulation of response to wounding) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:kmv") Annotation( "GO_REF:0000058") Annotation( "PMID:19164535") "Any process that stops, prevents or reduces the frequency, rate or extent of response to wounding.") -AnnotationAssertion( "kmv") AnnotationAssertion( "2014-05-18T01:28:52Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of physiological response to wounding") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of response to wounding") @@ -96129,7 +94092,6 @@ SubClassOf( (positive regulation of response to wounding) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:kmv") Annotation( "GO_REF:0000058") Annotation( "PMID:19164535") "Any process that activates or increases the frequency, rate or extent of response to wounding.") -AnnotationAssertion( "kmv") AnnotationAssertion( "2014-05-18T01:28:58Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "positive regulation of physiological response to wounding") AnnotationAssertion(Annotation( "GOC:TermGenie") "up regulation of physiological response to wounding") @@ -96150,7 +94112,6 @@ SubClassOf( (regulation of leukocyte cell-cell adhesion) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:TermGenie") Annotation( "GOC:rl") Annotation( "GO_REF:0000058") Annotation( "PMID:21106532") "Any process that modulates the frequency, rate or extent of leukocyte cell-cell adhesion.") -AnnotationAssertion( "rl") AnnotationAssertion( "2014-05-19T15:29:58Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "regulation of leukocyte adhesion") AnnotationAssertion(Annotation( "GOC:TermGenie") "regulation of leukocyte cell adhesion") @@ -96164,7 +94125,6 @@ SubClassOf( (negative regulation of leukocyte cell-cell adhesion) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:TermGenie") Annotation( "GOC:rl") Annotation( "GO_REF:0000058") Annotation( "PMID:21106532") "Any process that stops, prevents or reduces the frequency, rate or extent of leukocyte cell-cell adhesion.") -AnnotationAssertion( "rl") AnnotationAssertion( "2014-05-19T15:30:05Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of leukocyte adhesion") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of leukocyte cell adhesion") @@ -96191,7 +94151,6 @@ SubClassOf( (positive regulation of leukocyte cell-cell adhesion) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:TermGenie") Annotation( "GOC:rl") Annotation( "GO_REF:0000058") Annotation( "PMID:21106532") "Any process that activates or increases the frequency, rate or extent of leukocyte cell-cell adhesion.") -AnnotationAssertion( "rl") AnnotationAssertion( "2014-05-19T15:30:15Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "positive regulation of leukocyte adhesion") AnnotationAssertion(Annotation( "GOC:TermGenie") "positive regulation of leukocyte cell adhesion") @@ -96218,7 +94177,6 @@ SubClassOf( (regulation of chondrocyte hypertrophy) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:mr") Annotation( "GO_REF:0000058") Annotation( "PMID:23928032") "Any process that modulates the frequency, rate or extent of chondrocyte hypertrophy.") -AnnotationAssertion( "mr") AnnotationAssertion( "2014-05-20T21:23:13Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:1903041") @@ -96231,7 +94189,6 @@ SubClassOf( (negative regulation of chondrocyte hypertrophy) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:mr") Annotation( "GO_REF:0000058") Annotation( "PMID:23928032") "Any process that stops, prevents or reduces the frequency, rate or extent of chondrocyte hypertrophy.") -AnnotationAssertion( "mr") AnnotationAssertion( "2014-05-20T21:23:19Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of chondrocyte hypertrophy") AnnotationAssertion(Annotation( "GOC:TermGenie") "down-regulation of chondrocyte hypertrophy") @@ -96249,7 +94206,6 @@ SubClassOf( (positive regulation of chondrocyte hypertrophy) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:mr") Annotation( "GO_REF:0000058") Annotation( "PMID:23928032") "Any process that activates or increases the frequency, rate or extent of chondrocyte hypertrophy.") -AnnotationAssertion( "mr") AnnotationAssertion( "2014-05-20T21:23:25Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "up regulation of chondrocyte hypertrophy") AnnotationAssertion(Annotation( "GOC:TermGenie") "up-regulation of chondrocyte hypertrophy") @@ -96267,7 +94223,6 @@ SubClassOf( (neural crest cell migration involved in sympathetic nervous system development) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:TermGenie") Annotation( "GOC:rl") Annotation( "GO_REF:0000060") Annotation( "PMID:19325129") "Any neural crest cell migration that is involved in sympathetic nervous system development.") -AnnotationAssertion( "rl") AnnotationAssertion( "2014-05-22T07:06:02Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:1903045") @@ -96278,7 +94233,6 @@ EquivalentClasses( ObjectIntersection # Class: (meiotic cell cycle process) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:mtg_cell_cycle") Annotation( "GO_REF:0000060") "A process that is part of the meiotic cell cycle.") -AnnotationAssertion( "jl") AnnotationAssertion( "2014-05-22T14:22:28Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:1903046") @@ -96294,7 +94248,6 @@ DisjointClasses( (mitotic cell cycle process) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:mtg_cell_cycle") Annotation( "GO_REF:0000060") "A process that is part of the mitotic cell cycle.") -AnnotationAssertion( "jl") AnnotationAssertion( "2014-05-22T14:22:34Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:1903047") @@ -96305,7 +94258,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of acetylcholine-gated cation channel activity) AnnotationAssertion(Annotation( "GOC:PARL") Annotation( "GOC:TermGenie") Annotation( "GOC:bf") Annotation( "GO_REF:0000059") Annotation( "PMID:21718690") "Any process that modulates the frequency, rate or extent of acetylcholine-gated cation channel activity.") -AnnotationAssertion( "bf") AnnotationAssertion( "2014-05-22T14:46:53Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:1903048") @@ -96318,7 +94270,6 @@ SubClassOf( ObjectSomeValuesFrom( "GOC:BHF") Annotation( "GOC:TermGenie") Annotation( "GOC:rl") Annotation( "GO_REF:0000058") Annotation( "PMID:18307834") "Any process that modulates the frequency, rate or extent of proteolysis involved in cellular catabolic process.") AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/23112"^^xsd:anyURI) -AnnotationAssertion( "rl") AnnotationAssertion( "2014-05-22T18:00:45Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "regulation of peptidolysis involved in cellular protein catabolic process") AnnotationAssertion(Annotation( "GOC:TermGenie") "regulation of peptidolysis involved in cellular protein catabolism") @@ -96337,7 +94288,6 @@ EquivalentClasses( ObjectIntersection AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:TermGenie") Annotation( "GOC:rl") Annotation( "GO_REF:0000058") Annotation( "PMID:18307834") "Any process that stops, prevents or reduces the frequency, rate or extent of proteolysis involved in protein catabolic process.") AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/23112"^^xsd:anyURI) -AnnotationAssertion( "rl") AnnotationAssertion( "2014-05-22T18:00:51Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of peptidolysis involved in cellular protein catabolic process") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of peptidolysis involved in cellular protein catabolism") @@ -96384,7 +94334,6 @@ EquivalentClasses( ObjectIntersection AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:TermGenie") Annotation( "GOC:rl") Annotation( "GO_REF:0000058") Annotation( "PMID:18307834") "Any process that activates or increases the frequency, rate or extent of proteolysis involved in protein catabolic process.") AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/23112"^^xsd:anyURI) -AnnotationAssertion( "rl") AnnotationAssertion( "2014-05-22T18:00:57Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "positive regulation of peptidolysis involved in cellular protein catabolic process") AnnotationAssertion(Annotation( "GOC:TermGenie") "positive regulation of peptidolysis involved in cellular protein catabolism") @@ -96430,7 +94379,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of extracellular matrix organization) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:TermGenie") Annotation( "GOC:rl") Annotation( "GO_REF:0000058") Annotation( "PMID:22357537") "Any process that modulates the frequency, rate or extent of extracellular matrix organization.") -AnnotationAssertion( "rl") AnnotationAssertion( "2014-05-23T17:15:41Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "regulation of extracellular matrix organisation") AnnotationAssertion( "biological_process") @@ -96443,7 +94391,6 @@ SubClassOf( (negative regulation of extracellular matrix organization) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:TermGenie") Annotation( "GOC:rl") Annotation( "GO_REF:0000058") Annotation( "PMID:22357537") "Any process that stops, prevents or reduces the frequency, rate or extent of extracellular matrix organization.") -AnnotationAssertion( "rl") AnnotationAssertion( "2014-05-23T17:15:47Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of extracellular matrix organisation") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of extracellular matrix organization") @@ -96469,7 +94416,6 @@ SubClassOf( (positive regulation of extracellular matrix organization) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:TermGenie") Annotation( "GOC:rl") Annotation( "GO_REF:0000058") Annotation( "PMID:22357537") "Any process that activates or increases the frequency, rate or extent of extracellular matrix organization.") -AnnotationAssertion( "rl") AnnotationAssertion( "2014-05-23T17:15:53Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "positive regulation of extracellular matrix organisation") AnnotationAssertion(Annotation( "GOC:TermGenie") "up regulation of extracellular matrix organisation") @@ -96495,7 +94441,6 @@ SubClassOf( (regulation of melanosome organization) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:TermGenie") Annotation( "GOC:rl") Annotation( "GO_REF:0000058") Annotation( "PMID:24769727") "Any process that modulates the frequency, rate or extent of melanosome organization.") -AnnotationAssertion( "rl") AnnotationAssertion( "2014-05-27T13:27:49Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "regulation of melanosome organisation") AnnotationAssertion( "biological_process") @@ -96508,7 +94453,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of melanosome organization) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:TermGenie") Annotation( "GOC:rl") Annotation( "GO_REF:0000058") Annotation( "PMID:24769727") "Any process that stops, prevents or reduces the frequency, rate or extent of melanosome organization.") -AnnotationAssertion( "rl") AnnotationAssertion( "2014-05-27T13:27:55Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of melanosome organisation") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of melanosome organization") @@ -96533,7 +94477,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of melanosome organization) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:TermGenie") Annotation( "GOC:rl") Annotation( "GO_REF:0000058") Annotation( "PMID:24769727") "Any process that activates or increases the frequency, rate or extent of melanosome organization.") -AnnotationAssertion( "rl") AnnotationAssertion( "2014-05-27T13:28:01Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "positive regulation of melanosome organisation") AnnotationAssertion(Annotation( "GOC:TermGenie") "up regulation of melanosome organisation") @@ -96558,7 +94501,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of protein localization to plasma membrane) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:TermGenie") Annotation( "GOC:rl") Annotation( "GO_REF:0000058") Annotation( "PMID:11602640") "Any process that modulates the frequency, rate or extent of protein localization to plasma membrane.") -AnnotationAssertion( "tb") AnnotationAssertion( "2009-07-10T10:32:44Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "regulation of protein localization in plasma membrane") AnnotationAssertion( "biological_process") @@ -96575,7 +94517,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of protein localization to plasma membrane) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:TermGenie") Annotation( "GOC:rl") Annotation( "GO_REF:0000058") Annotation( "PMID:11602640") "Any process that stops, prevents or reduces the frequency, rate or extent of protein localization to plasma membrane.") -AnnotationAssertion( "tb") AnnotationAssertion( "2014-05-29T17:10:16Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of protein localisation in plasma membrane") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of protein localization in plasma membrane") @@ -96612,7 +94553,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of protein localization to plasma membrane) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:TermGenie") Annotation( "GOC:rl") Annotation( "GO_REF:0000058") Annotation( "PMID:11602640") "Any process that activates or increases the frequency, rate or extent of protein localization to plasma membrane.") -AnnotationAssertion( "tb") AnnotationAssertion( "2009-07-10T10:34:17Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "positive regulation of protein localisation in plasma membrane") AnnotationAssertion(Annotation( "GOC:TermGenie") "positive regulation of protein localization in plasma membrane") @@ -96648,7 +94588,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of actin filament-based movement) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000058") Annotation( "PMID:24798735") "Any process that modulates the frequency, rate or extent of actin filament-based movement.") -AnnotationAssertion( "al") AnnotationAssertion( "2014-06-12T16:55:57Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:1903115") @@ -96658,7 +94597,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of actin filament-based movement) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000058") Annotation( "PMID:24798735") "Any process that activates or increases the frequency, rate or extent of actin filament-based movement.") -AnnotationAssertion( "al") AnnotationAssertion( "2014-06-12T16:56:04Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "up regulation of actin filament-based movement") AnnotationAssertion(Annotation( "GOC:TermGenie") "up-regulation of actin filament-based movement") @@ -96672,7 +94610,6 @@ EquivalentClasses( ObjectIntersection # Class: (protein localization to actin cytoskeleton) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000087") Annotation( "PMID:24798735") "A process in which a protein is transported to, or maintained in, the location of an actin cytoskeleton.") -AnnotationAssertion( "mah") AnnotationAssertion( "2014-06-16T11:27:09Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "protein localisation in actin cytoskeleton") AnnotationAssertion(Annotation( "GOC:TermGenie") "protein localisation to actin cytoskeleton") @@ -96685,7 +94622,6 @@ EquivalentClasses( ObjectIntersection # Class: (protein localization to actin filament bundle) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000087") Annotation( "PMID:24798735") "A process in which a protein is transported to, or maintained in, the location of an actin filament bundle.") -AnnotationAssertion( "mah") AnnotationAssertion( "2014-06-16T11:27:16Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "protein localisation in actin filament bundle") AnnotationAssertion(Annotation( "GOC:TermGenie") "protein localisation to actin filament bundle") @@ -96699,7 +94635,6 @@ EquivalentClasses( ObjectIntersection # Class: (mononuclear cell differentiation) AnnotationAssertion(Annotation( "CL:0000842") Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000086") Annotation( "PMID:24759906") "The process in which a relatively unspecialized cell acquires the specialized features of a mononuclear cell.") -AnnotationAssertion( "cls") AnnotationAssertion( "2014-06-25T15:47:09Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:1903131") @@ -96709,7 +94644,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of calcium ion transmembrane transport) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:TermGenie") Annotation( "GOC:rl") Annotation( "GO_REF:0000058") Annotation( "PMID:24125847") "Any process that modulates the frequency, rate or extent of calcium ion transmembrane transport.") -AnnotationAssertion( "rl") AnnotationAssertion( "2014-07-11T17:09:26Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "regulation of calcium ion membrane transport") AnnotationAssertion(Annotation( "GOC:TermGenie") "regulation of transmembrane calcium transport") @@ -96722,7 +94656,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of calcium ion transmembrane transport) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:TermGenie") Annotation( "GOC:rl") Annotation( "GO_REF:0000058") Annotation( "PMID:24125847") "Any process that stops, prevents or reduces the frequency, rate or extent of calcium ion transmembrane transport.") -AnnotationAssertion( "rl") AnnotationAssertion( "2014-07-11T17:09:32Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of calcium ion membrane transport") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of calcium ion transmembrane transport") @@ -96747,7 +94680,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of dopamine biosynthetic process) AnnotationAssertion(Annotation( "GOC:PARL") Annotation( "GOC:TermGenie") Annotation( "GOC:bf") Annotation( "GO_REF:0000058") "Any process that modulates the frequency, rate or extent of dopamine biosynthetic process.") -AnnotationAssertion( "bf") AnnotationAssertion( "2014-07-14T12:17:41Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "regulation of dopamine anabolism") AnnotationAssertion(Annotation( "GOC:TermGenie") "regulation of dopamine biosynthesis") @@ -96761,7 +94693,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of dopamine biosynthetic process) AnnotationAssertion(Annotation( "GOC:PARL") Annotation( "GOC:TermGenie") Annotation( "GOC:bf") Annotation( "GO_REF:0000058") "Any process that stops, prevents or reduces the frequency, rate or extent of dopamine biosynthetic process.") -AnnotationAssertion( "bf") AnnotationAssertion( "2014-07-14T12:17:47Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of dopamine anabolism") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of dopamine biosynthesis") @@ -96795,7 +94726,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of dopamine biosynthetic process) AnnotationAssertion(Annotation( "GOC:PARL") Annotation( "GOC:TermGenie") Annotation( "GOC:bf") Annotation( "GO_REF:0000058") Annotation( "PMID:19703902") "Any process that activates or increases the frequency, rate or extent of dopamine biosynthetic process.") -AnnotationAssertion( "bf") AnnotationAssertion( "2014-07-14T12:17:53Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "positive regulation of dopamine anabolism") AnnotationAssertion(Annotation( "GOC:TermGenie") "positive regulation of dopamine biosynthesis") @@ -96830,7 +94760,6 @@ EquivalentClasses( ObjectIntersection AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000085") Annotation( "PMID:23515840") "Any apoptotic process in a glomerular visceral epithelial cell.") AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/23000"^^xsd:anyURI) -AnnotationAssertion( "sl") AnnotationAssertion( "2014-07-23T17:07:55Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "glomerular podocyte apoptotic process") AnnotationAssertion( "glomerular visceral epithelial cell apoptotic process") @@ -96845,7 +94774,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of endodermal cell differentiation) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:als") Annotation( "GO_REF:0000058") Annotation( "PMID:23154389") "Any process that modulates the frequency, rate or extent of endodermal cell differentiation.") -AnnotationAssertion( "als") AnnotationAssertion( "2014-07-29T13:22:35Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "regulation of endoderm cell differentiation") AnnotationAssertion( "biological_process") @@ -96856,7 +94784,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of endodermal cell differentiation) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:als") Annotation( "GO_REF:0000058") Annotation( "PMID:23154389") "Any process that stops, prevents or reduces the frequency, rate or extent of endodermal cell differentiation.") -AnnotationAssertion( "als") AnnotationAssertion( "2014-07-29T13:22:41Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of endoderm cell differentiation") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of endodermal cell differentiation") @@ -96875,7 +94802,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of endodermal cell differentiation) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:als") Annotation( "GO_REF:0000058") Annotation( "PMID:23154389") "Any process that activates or increases the frequency, rate or extent of endodermal cell differentiation.") -AnnotationAssertion( "als") AnnotationAssertion( "2014-07-29T13:22:47Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "positive regulation of endoderm cell differentiation") AnnotationAssertion(Annotation( "GOC:TermGenie") "up regulation of endoderm cell differentiation") @@ -96894,7 +94820,6 @@ EquivalentClasses( ObjectIntersection # Class: (melanosome assembly) AnnotationAssertion(Annotation( "GOC:PARL") Annotation( "GOC:TermGenie") Annotation( "GOC:bf") Annotation( "GO_REF:0000079") Annotation( "PMID:22511774") "The aggregation, arrangement and bonding together of a set of components to form a melanosome, a tissue-specific, membrane-bounded cytoplasmic organelle within which melanin pigments are synthesized and stored.") -AnnotationAssertion( "bf") AnnotationAssertion( "2014-07-31T10:41:38Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "melanosome formation") AnnotationAssertion( "biological_process") @@ -96905,7 +94830,6 @@ EquivalentClasses( ObjectIntersection # Class: (multi-ciliated epithelial cell differentiation) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:sp") Annotation( "GO_REF:0000086") Annotation( "PMID:22231168") Annotation( "PMID:24934224") "The process in which a relatively unspecialized cell acquires the specialized features of a multi-ciliated epithelial cell.") -AnnotationAssertion( "tb") AnnotationAssertion( "2014-08-05T19:21:21Z") AnnotationAssertion( "multiciliate cell differentiation") AnnotationAssertion( "biological_process") @@ -96916,7 +94840,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of sodium ion export across plasma membrane) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:TermGenie") Annotation( "GOC:rl") Annotation( "GO_REF:0000058") Annotation( "PMID:17095720") "Any process that modulates the frequency, rate or extent of sodium ion export across the plasma membrane.") -AnnotationAssertion( "rl") AnnotationAssertion( "2014-08-08T17:06:46Z") AnnotationAssertion( "regulation of sodium ion export from cell") AnnotationAssertion( "biological_process") @@ -96929,7 +94852,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of sodium ion export across plasma membrane) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:TermGenie") Annotation( "GOC:rl") Annotation( "GO_REF:0000058") Annotation( "PMID:17095720") "Any process that stops, prevents or reduces the frequency, rate or extent of sodium ion export across the plasma membrane.") -AnnotationAssertion( "rl") AnnotationAssertion( "2014-08-08T17:10:22Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of sodium ion export from cell") AnnotationAssertion(Annotation( "GOC:TermGenie") "down-regulation of sodium ion export from cell") @@ -96954,7 +94876,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of sodium ion export across plasma membrane) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:TermGenie") Annotation( "GOC:rl") Annotation( "GO_REF:0000058") Annotation( "PMID:17095720") "Any process that activates or increases the frequency, rate or extent of sodium ion export across the plasma membrane.") -AnnotationAssertion( "rl") AnnotationAssertion( "2014-08-08T17:10:30Z") AnnotationAssertion( "positive regulation of sodium ion export from cell") AnnotationAssertion(Annotation( "GOC:TermGenie") "up regulation of sodium ion export from cell") @@ -96979,7 +94900,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of potassium ion import) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:TermGenie") Annotation( "GOC:mtg_cardiac_conduct_nov11") Annotation( "GOC:rl") Annotation( "GO_REF:0000058") Annotation( "PMID:10636900") "Any process that modulates the frequency, rate or extent of potassium ion import.") -AnnotationAssertion( "rl") AnnotationAssertion( "2014-08-11T14:26:16Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "regulation of potassium import") AnnotationAssertion(Annotation( "GOC:TermGenie") "regulation of potassium ion uptake") @@ -96991,7 +94911,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of potassium ion import across plasma membrane) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:TermGenie") Annotation( "GOC:mtg_cardiac_conduct_nov11") Annotation( "GOC:rl") Annotation( "GO_REF:0000058") Annotation( "PMID:10636900") "Any process that stops, prevents or reduces the frequency, rate or extent of potassium ion import across the plasma membrane.") -AnnotationAssertion( "rl") AnnotationAssertion( "2014-08-11T14:26:24Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of potassium import") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of potassium ion import") @@ -97016,7 +94935,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of potassium ion import across plasma membrane) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:TermGenie") Annotation( "GOC:mtg_cardiac_conduct_nov11") Annotation( "GOC:rl") Annotation( "GO_REF:0000058") Annotation( "PMID:10636900") "Any process that activates or increases the frequency, rate or extent of potassium ion import across the plasma membrane.") -AnnotationAssertion( "rl") AnnotationAssertion( "2014-08-11T14:26:32Z") AnnotationAssertion( "positive regulation of potassium ion import") AnnotationAssertion(Annotation( "GOC:TermGenie") "positive regulation of potassium import") @@ -97041,7 +94959,6 @@ EquivalentClasses( ObjectIntersection # Class: (protein localization to Golgi membrane) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000087") Annotation( "PMID:11378902") "A process in which a protein is transported to, or maintained in, a location within a Golgi membrane.") -AnnotationAssertion( "mah") AnnotationAssertion( "2014-08-12T14:22:31Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "protein localisation in Golgi membrane") AnnotationAssertion(Annotation( "GOC:TermGenie") "protein localisation to Golgi membrane") @@ -97054,7 +94971,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of glutamate secretion, neurotransmission) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000058") Annotation( "PMID:16782817") "Any process that modulates the frequency, rate or extent of glutamate secretion, neurotransmission.") -AnnotationAssertion( "pad") AnnotationAssertion( "2014-08-13T13:54:15Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:1903294") @@ -97066,7 +94982,6 @@ SubClassOf( ObjectSomeValuesFrom( (negative regulation of glutamate secretion, neurotransmission) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000058") Annotation( "PMID:16782817") "Any process that stops, prevents or reduces the frequency, rate or extent of glutamate secretion, neurotransmission.") -AnnotationAssertion( "pad") AnnotationAssertion( "2014-08-13T13:54:23Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of glutamate secretion, neurotransmission") AnnotationAssertion(Annotation( "GOC:TermGenie") "down-regulation of glutamate secretion, neurotransmission") @@ -97082,7 +94997,6 @@ SubClassOf( ObjectSomeValuesFrom( (positive regulation of glutamate secretion, neurotransmission) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000058") Annotation( "PMID:16782817") "Any process that activates or increases the frequency, rate or extent of glutamate secretion, where glutamate acts as a neurotransmitter.") -AnnotationAssertion( "pad") AnnotationAssertion( "2014-08-13T13:54:31Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "up regulation of glutamate secretion, neurotransmission") AnnotationAssertion(Annotation( "GOC:TermGenie") "up-regulation of glutamate secretion, neurotransmission") @@ -97098,7 +95012,6 @@ SubClassOf( ObjectSomeValuesFrom( (regulation of regulated secretory pathway) AnnotationAssertion(Annotation( "GOC:PARL") Annotation( "GOC:TermGenie") Annotation( "GOC:pad") Annotation( "GO_REF:0000058") Annotation( "PMID:12526776") "Any process that modulates the frequency, rate or extent of regulated secretory pathway.") -AnnotationAssertion( "pad") AnnotationAssertion( "2014-08-18T10:04:53Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:1903305") @@ -97109,7 +95022,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of regulated secretory pathway) AnnotationAssertion(Annotation( "GOC:PARL") Annotation( "GOC:TermGenie") Annotation( "GOC:pad") Annotation( "GO_REF:0000058") Annotation( "PMID:12526776") "Any process that stops, prevents or reduces the frequency, rate or extent of regulated secretory pathway.") -AnnotationAssertion( "pad") AnnotationAssertion( "2014-08-18T10:05:02Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of regulated secretory pathway") AnnotationAssertion(Annotation( "GOC:TermGenie") "down-regulation of regulated secretory pathway") @@ -97124,7 +95036,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of regulated secretory pathway) AnnotationAssertion(Annotation( "GOC:PARL") Annotation( "GOC:TermGenie") Annotation( "GOC:pad") Annotation( "GO_REF:0000058") Annotation( "PMID:12526776") "Any process that activates or increases the frequency, rate or extent of regulated secretory pathway.") -AnnotationAssertion( "pad") AnnotationAssertion( "2014-08-18T10:05:10Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "up regulation of regulated secretory pathway") AnnotationAssertion(Annotation( "GOC:TermGenie") "up-regulation of regulated secretory pathway") @@ -97139,7 +95050,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of nitrogen cycle metabolic process) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:vw") Annotation( "GO_REF:0000058") "Any process that modulates the frequency, rate or extent of nitrogen cycle metabolic process.") -AnnotationAssertion( "vw") AnnotationAssertion( "2014-08-18T12:57:34Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:1903314") @@ -97149,7 +95059,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of nitrogen cycle metabolic process) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:vw") Annotation( "GO_REF:0000058") "Any process that stops, prevents or reduces the frequency, rate or extent of nitrogen cycle metabolic process.") -AnnotationAssertion( "vw") AnnotationAssertion( "2014-08-18T12:57:42Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of nitrogen cycle metabolic process") AnnotationAssertion(Annotation( "GOC:TermGenie") "down-regulation of nitrogen cycle metabolic process") @@ -97163,7 +95072,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of nitrogen cycle metabolic process) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:vw") Annotation( "GO_REF:0000058") "Any process that activates or increases the frequency, rate or extent of nitrogen cycle metabolic process.") -AnnotationAssertion( "vw") AnnotationAssertion( "2014-08-18T12:57:50Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "up regulation of nitrogen cycle metabolic process") AnnotationAssertion(Annotation( "GOC:TermGenie") "up-regulation of nitrogen cycle metabolic process") @@ -97177,7 +95085,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of protein maturation) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:vw") Annotation( "GO_REF:0000058") "Any process that modulates the frequency, rate or extent of protein maturation.") -AnnotationAssertion( "vw") AnnotationAssertion( "2014-08-18T12:59:07Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:1903317") @@ -97188,7 +95095,6 @@ SubClassOf( ObjectSomeValuesFrom( (negative regulation of protein maturation) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:vw") Annotation( "GO_REF:0000058") "Any process that stops, prevents or reduces the frequency, rate or extent of protein maturation.") -AnnotationAssertion( "vw") AnnotationAssertion( "2014-08-18T12:59:15Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of protein maturation") AnnotationAssertion(Annotation( "GOC:TermGenie") "down-regulation of protein maturation") @@ -97203,7 +95109,6 @@ SubClassOf( ObjectSomeValuesFrom( (positive regulation of protein maturation) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:vw") Annotation( "GO_REF:0000058") "Any process that activates or increases the frequency, rate or extent of protein maturation.") -AnnotationAssertion( "vw") AnnotationAssertion( "2014-08-18T12:59:23Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "up regulation of protein maturation") AnnotationAssertion(Annotation( "GOC:TermGenie") "up-regulation of protein maturation") @@ -97218,7 +95123,6 @@ SubClassOf( ObjectSomeValuesFrom( (regulation of vacuolar transport) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:vw") Annotation( "GO_REF:0000058") "Any process that modulates the frequency, rate or extent of vacuolar transport.") -AnnotationAssertion( "vw") AnnotationAssertion( "2014-08-18T13:16:04Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:1903335") @@ -97228,7 +95132,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of vacuolar transport) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:vw") Annotation( "GO_REF:0000058") "Any process that stops, prevents or reduces the frequency, rate or extent of vacuolar transport.") -AnnotationAssertion( "vw") AnnotationAssertion( "2014-08-18T13:16:11Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of vacuolar transport") AnnotationAssertion(Annotation( "GOC:TermGenie") "down-regulation of vacuolar transport") @@ -97242,7 +95145,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of vacuolar transport) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:vw") Annotation( "GO_REF:0000058") "Any process that activates or increases the frequency, rate or extent of vacuolar transport.") -AnnotationAssertion( "vw") AnnotationAssertion( "2014-08-18T13:16:19Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "up regulation of vacuolar transport") AnnotationAssertion(Annotation( "GOC:TermGenie") "up-regulation of vacuolar transport") @@ -97256,7 +95158,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of bicellular tight junction assembly) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:jz") Annotation( "GO_REF:0000058") Annotation( "PMID:25050009") "Any process that stops, prevents or reduces the frequency, rate or extent of tight junction assembly.") -AnnotationAssertion( "pr") AnnotationAssertion( "2014-08-19T11:02:14Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of tight junction assembly") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of tight junction formation") @@ -97275,7 +95176,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of bicellular tight junction assembly) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:jz") Annotation( "GO_REF:0000058") Annotation( "PMID:25050009") "Any process that activates or increases the frequency, rate or extent of tight junction assembly.") -AnnotationAssertion( "pr") AnnotationAssertion( "2014-08-19T11:05:06Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "positive regulation of tight junction formation") AnnotationAssertion(Annotation( "GOC:TermGenie") "up regulation of tight junction assembly") @@ -97294,7 +95194,6 @@ EquivalentClasses( ObjectIntersection # Class: (response to dopamine) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:mr") Annotation( "GO_REF:0000071") Annotation( "PMID:11118945") "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a dopamine stimulus.") -AnnotationAssertion( "mr") AnnotationAssertion( "2014-08-19T19:33:26Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:1903350") @@ -97304,7 +95203,6 @@ EquivalentClasses( ObjectIntersection # Class: (cellular response to dopamine) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:mr") Annotation( "GO_REF:0000071") Annotation( "PMID:11118945") "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a dopamine stimulus.") -AnnotationAssertion( "mr") AnnotationAssertion( "2014-08-19T19:33:35Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:1903351") @@ -97314,7 +95212,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of nucleus organization) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000058") Annotation( "PMID:16943282") "Any process that modulates the frequency, rate or extent of nucleus organization.") -AnnotationAssertion( "hjd") AnnotationAssertion( "2014-08-20T19:36:16Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "regulation of nuclear organisation") AnnotationAssertion(Annotation( "GOC:TermGenie") "regulation of nuclear organization") @@ -97329,7 +95226,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of distal tip cell migration) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:mm2") Annotation( "GO_REF:0000058") Annotation( "PMID:24968003") "Any process that modulates the frequency, rate or extent of distal tip cell migration.") -AnnotationAssertion( "pr") AnnotationAssertion( "2014-08-21T10:05:08Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:1903354") @@ -97339,7 +95235,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of distal tip cell migration) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:mm2") Annotation( "GO_REF:0000058") Annotation( "PMID:24968003") "Any process that stops, prevents or reduces the frequency, rate or extent of distal tip cell migration.") -AnnotationAssertion( "pr") AnnotationAssertion( "2014-08-21T10:05:17Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of distal tip cell migration") AnnotationAssertion(Annotation( "GOC:TermGenie") "down-regulation of distal tip cell migration") @@ -97353,7 +95248,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of distal tip cell migration) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:mm2") Annotation( "GO_REF:0000058") Annotation( "PMID:24968003") "Any process that activates or increases the frequency, rate or extent of distal tip cell migration.") -AnnotationAssertion( "pr") AnnotationAssertion( "2014-08-21T10:05:26Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "up regulation of distal tip cell migration") AnnotationAssertion(Annotation( "GOC:TermGenie") "up-regulation of distal tip cell migration") @@ -97367,7 +95261,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of Golgi organization) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:als") Annotation( "GO_REF:0000058") Annotation( "PMID:17562788") "Any process that modulates the frequency, rate or extent of Golgi organization.") -AnnotationAssertion( "als") AnnotationAssertion( "2014-08-21T10:22:22Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "regulation of Golgi organisation") AnnotationAssertion( "biological_process") @@ -97379,7 +95272,6 @@ EquivalentClasses( ObjectIntersection # Class: (facioacoustic ganglion development) AnnotationAssertion(Annotation( "GOC:PARL") Annotation( "GOC:TermGenie") Annotation( "GOC:bf") Annotation( "GOC:mat") Annotation( "GO_REF:0000094") Annotation( "PMID:18356247") "The process whose specific outcome is the progression of an acoustico-facial VII-VIII ganglion complex over time, from its formation to the mature structure.") -AnnotationAssertion( "bf") AnnotationAssertion( "2014-08-26T12:40:36Z") AnnotationAssertion(Annotation( "UBERON:0012175") "acoustico-facial VII-VIII ganglion complex development") AnnotationAssertion(Annotation( "GOC:TermGenie") "acousticofacial ganglion development") @@ -97394,7 +95286,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of mitotic chromosome condensation) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000058") Annotation( "PMID:9490640") "Any process that modulates the frequency, rate or extent of mitotic chromosome condensation.") -AnnotationAssertion( "al") AnnotationAssertion( "2014-08-26T13:57:13Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:1903379") @@ -97404,7 +95295,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of mitotic chromosome condensation) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000058") Annotation( "PMID:9490640") "Any process that activates or increases the frequency, rate or extent of mitotic chromosome condensation.") -AnnotationAssertion( "al") AnnotationAssertion( "2014-08-26T13:57:29Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "up regulation of mitotic chromosome condensation") AnnotationAssertion(Annotation( "GOC:TermGenie") "up-regulation of mitotic chromosome condensation") @@ -97418,7 +95308,6 @@ EquivalentClasses( ObjectIntersection # Class: (response to bile acid) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:TermGenie") Annotation( "GOC:rl") Annotation( "GO_REF:0000071") Annotation( "PMID:21757002") "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a bile acid stimulus.") -AnnotationAssertion( "rl") AnnotationAssertion( "2014-09-03T12:45:43Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:1903412") @@ -97428,7 +95317,6 @@ EquivalentClasses( ObjectIntersection # Class: (cellular response to bile acid) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:TermGenie") Annotation( "GOC:rl") Annotation( "GO_REF:0000071") Annotation( "PMID:21757002") "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a bile acid stimulus.") -AnnotationAssertion( "rl") AnnotationAssertion( "2014-09-03T12:45:51Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:1903413") @@ -97438,7 +95326,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of cell maturation) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000058") Annotation( "PMID:17459944") "Any process that modulates the frequency, rate or extent of cell maturation.") -AnnotationAssertion( "jl") AnnotationAssertion( "2014-09-15T13:31:23Z") AnnotationAssertion( "biological_process") AnnotationAssertion(Annotation( "GOC:TermGenie") "regulation of functional differentiation") @@ -97450,7 +95337,6 @@ SubClassOf( (negative regulation of cell maturation) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000058") Annotation( "PMID:17459944") "Any process that stops, prevents or reduces the frequency, rate or extent of cell maturation.") -AnnotationAssertion( "jl") AnnotationAssertion( "2014-09-15T13:31:32Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of cell maturation") AnnotationAssertion(Annotation( "GOC:TermGenie") "down-regulation of cell maturation") @@ -97471,7 +95357,6 @@ SubClassOf( (positive regulation of cell maturation) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000058") Annotation( "PMID:17459944") "Any process that activates or increases the frequency, rate or extent of cell maturation.") -AnnotationAssertion( "jl") AnnotationAssertion( "2014-09-15T13:31:41Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "up regulation of cell maturation") AnnotationAssertion(Annotation( "GOC:TermGenie") "up-regulation of cell maturation") @@ -97492,7 +95377,6 @@ SubClassOf( (calcitonin family receptor complex) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:bhm") Annotation( "GO_REF:0000088") Annotation( "PMID:10871296") Annotation( "PMID:12037140") Annotation( "PMID:18687416") "A protein complex which is capable of calcitonin family receptor activity. Calcitonin family receptors may form dimers, trimers or tetramers; adrenomedullin and amylin receptors have only been observed as dimers so far.") -AnnotationAssertion( "pr") AnnotationAssertion( "2014-09-16T13:25:11Z") AnnotationAssertion( "cellular_component") AnnotationAssertion( "GO:1903439") @@ -97504,7 +95388,6 @@ SubClassOf( ObjectSomeValuesFrom( (protein localization to ciliary membrane) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:cilia") Annotation( "GOC:krc") Annotation( "GO_REF:0000087") Annotation( "PMID:22139371") "A process in which a protein is transported to, or maintained in, a location within a ciliary membrane.") -AnnotationAssertion( "pr") AnnotationAssertion( "2014-09-16T15:15:39Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "protein localisation in ciliary membrane") AnnotationAssertion(Annotation( "GOC:TermGenie") "protein localisation to ciliary membrane") @@ -97517,7 +95400,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of brown fat cell differentiation) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000058") Annotation( "PMID:23977283") "Any process that stops, prevents or reduces the frequency, rate or extent of brown fat cell differentiation.") -AnnotationAssertion( "hjd") AnnotationAssertion( "2014-09-17T19:15:00Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of brown adipocyte cell differentiation") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of brown adipocyte differentiation") @@ -97541,7 +95423,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of lactation) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:mr") Annotation( "GO_REF:0000058") Annotation( "PMID:19563620") "Any process that modulates the frequency, rate or extent of lactation.") -AnnotationAssertion( "mr") AnnotationAssertion( "2014-09-24T14:44:13Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:1903487") @@ -97554,7 +95435,6 @@ SubClassOf( (negative regulation of lactation) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:mr") Annotation( "GO_REF:0000058") Annotation( "PMID:19563620") "Any process that stops, prevents or reduces the frequency, rate or extent of lactation.") -AnnotationAssertion( "mr") AnnotationAssertion( "2014-09-24T14:44:22Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of lactation") AnnotationAssertion(Annotation( "GOC:TermGenie") "down-regulation of lactation") @@ -97572,7 +95452,6 @@ SubClassOf( (positive regulation of lactation) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:mr") Annotation( "GO_REF:0000058") Annotation( "PMID:19563620") "Any process that activates or increases the frequency, rate or extent of lactation.") -AnnotationAssertion( "mr") AnnotationAssertion( "2014-09-24T14:44:30Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "up regulation of lactation") AnnotationAssertion(Annotation( "GOC:TermGenie") "up-regulation of lactation") @@ -97590,7 +95469,6 @@ SubClassOf( (mucopolysaccharide metabolic process) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:dph") Annotation( "GO_REF:0000068") Annotation( "PMID:4236091") "The chemical reactions and pathways involving mucopolysaccharide.") -AnnotationAssertion( "dph") AnnotationAssertion( "2014-10-01T21:55:47Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "mucopolysaccharide metabolism") AnnotationAssertion( "biological_process") @@ -97601,7 +95479,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of blood circulation) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:mr") Annotation( "GO_REF:0000058") Annotation( "PMID:10659969") "Any process that modulates the frequency, rate or extent of blood circulation.") -AnnotationAssertion( "mr") AnnotationAssertion( "2014-10-06T18:38:56Z") AnnotationAssertion( "biological_process") AnnotationAssertion(Annotation( "GOC:TermGenie") "regulation of hemolymph circulation") @@ -97613,7 +95490,6 @@ SubClassOf( (negative regulation of blood circulation) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:mr") Annotation( "GO_REF:0000058") Annotation( "PMID:10659969") "Any process that stops, prevents or reduces the frequency, rate or extent of blood circulation.") -AnnotationAssertion( "mr") AnnotationAssertion( "2014-10-06T18:39:05Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of blood circulation") AnnotationAssertion(Annotation( "GOC:TermGenie") "down-regulation of blood circulation") @@ -97634,7 +95510,6 @@ SubClassOf( (positive regulation of blood circulation) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:mr") Annotation( "GO_REF:0000058") Annotation( "PMID:10659969") "Any process that activates or increases the frequency, rate or extent of blood circulation.") -AnnotationAssertion( "mr") AnnotationAssertion( "2014-10-06T18:39:13Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "up regulation of blood circulation") AnnotationAssertion(Annotation( "GOC:TermGenie") "up-regulation of blood circulation") @@ -97655,7 +95530,6 @@ SubClassOf( (regulation of secretion by cell) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:pm") Annotation( "GO_REF:0000058") Annotation( "PMID:12130530") "Any process that modulates the frequency, rate or extent of secretion by cell.") -AnnotationAssertion( "pm") AnnotationAssertion( "2014-10-08T13:24:59Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "regulation of cellular secretion") AnnotationAssertion( "biological_process") @@ -97668,7 +95542,6 @@ SubClassOf( (negative regulation of secretion by cell) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:pm") Annotation( "GO_REF:0000058") Annotation( "PMID:12130530") "Any process that stops, prevents or reduces the frequency, rate or extent of secretion by cell.") -AnnotationAssertion( "pm") AnnotationAssertion( "2014-10-08T13:25:08Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of cellular secretion") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of secretion by cell") @@ -97690,7 +95563,6 @@ SubClassOf( (positive regulation of secretion by cell) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:pm") Annotation( "GO_REF:0000058") Annotation( "PMID:12130530") "Any process that activates or increases the frequency, rate or extent of secretion by cell.") -AnnotationAssertion( "pm") AnnotationAssertion( "2014-10-08T13:25:17Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "positive regulation of cellular secretion") AnnotationAssertion(Annotation( "GOC:TermGenie") "up regulation of cellular secretion") @@ -97712,7 +95584,6 @@ SubClassOf( (meiotic cell cycle process involved in oocyte maturation) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:jz") Annotation( "GO_REF:0000060") Annotation( "PMID:25212395") "Any meiotic cell cycle process that is involved in oocyte maturation.") -AnnotationAssertion( "pr") AnnotationAssertion( "2014-10-09T10:46:14Z") AnnotationAssertion( "meiosis involved in oocyte maturation") AnnotationAssertion( "biological_process") @@ -97723,7 +95594,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of meiotic cell cycle process involved in oocyte maturation) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:jz") Annotation( "GO_REF:0000058") Annotation( "PMID:25212395") "Any process that modulates the frequency, rate or extent of meiotic cell cycle process involved in oocyte maturation.") -AnnotationAssertion( "pr") AnnotationAssertion( "2014-10-09T10:52:38Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "regulation of meiosis involved in oocyte maturation") AnnotationAssertion( "biological_process") @@ -97734,7 +95604,6 @@ EquivalentClasses( ObjectIntersection # Class: (protein localization to postsynaptic membrane) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:kmv") Annotation( "GO_REF:0000087") Annotation( "PMID:9753322") "A process in which a protein is transported to, or maintained in, a location within a postsynaptic membrane.") -AnnotationAssertion( "kmv") AnnotationAssertion( "2014-10-10T11:23:53Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "protein localisation in postsynaptic membrane") AnnotationAssertion(Annotation( "GOC:TermGenie") "protein localisation to postsynaptic membrane") @@ -97747,7 +95616,6 @@ EquivalentClasses( ObjectIntersection # Class: (establishment of protein localization to postsynaptic membrane) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:kmv") Annotation( "GO_REF:0000087") Annotation( "PMID:9753322") "The directed movement of a protein to a specific location in a postsynaptic membrane.") -AnnotationAssertion( "kmv") AnnotationAssertion( "2014-10-10T11:24:03Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "establishment of protein localisation in postsynaptic membrane") AnnotationAssertion(Annotation( "GOC:TermGenie") "establishment of protein localisation to postsynaptic membrane") @@ -97760,7 +95628,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of exosomal secretion) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000058") Annotation( "PMID:24105262") "Any process that modulates the frequency, rate or extent of exosomal secretion.") -AnnotationAssertion( "pga") AnnotationAssertion( "2014-10-14T11:38:52Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "regulation of exosomal secretory pathway") AnnotationAssertion(Annotation( "GOC:TermGenie") "regulation of extracellular vesicular exosome secretion") @@ -97774,7 +95641,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of exosomal secretion) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000058") Annotation( "PMID:24105262") "Any process that stops, prevents or reduces the frequency, rate or extent of exosomal secretion.") -AnnotationAssertion( "pga") AnnotationAssertion( "2014-10-14T11:39:02Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of exosomal secretion") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of exosomal secretory pathway") @@ -97808,7 +95674,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of exosomal secretion) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000058") Annotation( "PMID:24105262") "Any process that activates or increases the frequency, rate or extent of exosomal secretion.") -AnnotationAssertion( "pga") AnnotationAssertion( "2014-10-14T11:39:10Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "positive regulation of exosomal secretory pathway") AnnotationAssertion(Annotation( "GOC:TermGenie") "positive regulation of extracellular vesicular exosome secretion") @@ -97843,7 +95708,6 @@ SubClassOf( ObjectSomeValuesFrom( (regulation of extracellular exosome assembly) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000058") Annotation( "PMID:24105262") "Any process that modulates the frequency, rate or extent of extracellular vesicular exosome assembly.") -AnnotationAssertion( "pga") AnnotationAssertion( "2014-10-20T15:37:25Z") AnnotationAssertion(Annotation( "GOC:vesicles") "regulation of extracellular vesicular exosome assembly") AnnotationAssertion( "biological_process") @@ -97854,7 +95718,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of extracellular exosome assembly) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000058") Annotation( "PMID:24105262") "Any process that stops, prevents or reduces the frequency, rate or extent of extracellular vesicular exosome assembly.") -AnnotationAssertion( "pga") AnnotationAssertion( "2014-10-20T15:37:33Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of extracellular vesicular exosome assembly") AnnotationAssertion(Annotation( "GOC:TermGenie") "down-regulation of extracellular vesicular exosome assembly") @@ -97869,7 +95732,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of extracellular exosome assembly) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000058") Annotation( "PMID:24105262") "Any process that activates or increases the frequency, rate or extent of extracellular vesicular exosome assembly.") -AnnotationAssertion( "pga") AnnotationAssertion( "2014-10-20T15:37:42Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "up regulation of extracellular vesicular exosome assembly") AnnotationAssertion(Annotation( "GOC:TermGenie") "up-regulation of extracellular vesicular exosome assembly") @@ -97884,7 +95746,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of tumor necrosis factor superfamily cytokine production) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000058") Annotation( "PMID:24187568") "Any process that modulates the frequency, rate or extent of tumor necrosis factor superfamily cytokine production.") -AnnotationAssertion( "pga") AnnotationAssertion( "2014-10-21T10:26:05Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "regulation of TNFSF cytokine production") AnnotationAssertion( "biological_process") @@ -97896,7 +95757,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of tumor necrosis factor superfamily cytokine production) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000058") Annotation( "PMID:24187568") "Any process that stops, prevents or reduces the frequency, rate or extent of tumor necrosis factor superfamily cytokine production.") -AnnotationAssertion( "pga") AnnotationAssertion( "2014-10-21T10:26:14Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of TNFSF cytokine production") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of tumor necrosis factor superfamily cytokine production") @@ -97920,7 +95780,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of tumor necrosis factor superfamily cytokine production) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000058") Annotation( "PMID:24187568") "Any process that activates or increases the frequency, rate or extent of tumor necrosis factor superfamily cytokine production.") -AnnotationAssertion( "pga") AnnotationAssertion( "2014-10-21T10:26:23Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "positive regulation of TNFSF cytokine production") AnnotationAssertion(Annotation( "GOC:TermGenie") "up regulation of TNFSF cytokine production") @@ -97944,7 +95803,6 @@ EquivalentClasses( ObjectIntersection # Class: (extracellular vesicle) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:pm") Annotation( "GO_REF:0000064") Annotation( "PMID:24769233") "Any vesicle that is part of the extracellular region.") -AnnotationAssertion( "jl") AnnotationAssertion( "2014-10-22T14:26:11Z") AnnotationAssertion( "cellular_component") AnnotationAssertion(Annotation( "GOC:vesicles") "microparticle") @@ -97955,7 +95813,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of protein localization to cilium) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:cilia") Annotation( "GOC:krc") Annotation( "GO_REF:0000058") Annotation( "PMID:22072986") "Any process that modulates the frequency, rate or extent of protein localization to cilium.") -AnnotationAssertion( "krc") AnnotationAssertion( "2014-10-24T20:58:11Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:1903564") @@ -97965,7 +95822,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of protein localization to cilium) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:cilia") Annotation( "GOC:krc") Annotation( "GO_REF:0000058") Annotation( "PMID:22072986") "Any process that stops, prevents or reduces the frequency, rate or extent of protein localization to cilium.") -AnnotationAssertion( "krc") AnnotationAssertion( "2014-10-24T20:58:20Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of protein localization to cilium") AnnotationAssertion(Annotation( "GOC:TermGenie") "down-regulation of protein localization to cilium") @@ -97979,7 +95835,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of protein localization to cilium) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:cilia") Annotation( "GOC:krc") Annotation( "GO_REF:0000058") Annotation( "PMID:22072986") "Any process that activates or increases the frequency, rate or extent of protein localization to cilium.") -AnnotationAssertion( "krc") AnnotationAssertion( "2014-10-24T20:58:28Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "up regulation of protein localization to cilium") AnnotationAssertion(Annotation( "GOC:TermGenie") "up-regulation of protein localization to cilium") @@ -97993,7 +95848,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of protein localization to ciliary membrane) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:cilia") Annotation( "GOC:krc") Annotation( "GO_REF:0000058") Annotation( "PMID:22072986") "Any process that modulates the frequency, rate or extent of protein localization to ciliary membrane.") -AnnotationAssertion( "krc") AnnotationAssertion( "2014-10-24T21:32:51Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "regulation of protein localisation in ciliary membrane") AnnotationAssertion(Annotation( "GOC:TermGenie") "regulation of protein localisation to ciliary membrane") @@ -98006,7 +95860,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of protein localization to ciliary membrane) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:cilia") Annotation( "GOC:krc") Annotation( "GO_REF:0000058") Annotation( "PMID:22072986") "Any process that stops, prevents or reduces the frequency, rate or extent of protein localization to ciliary membrane.") -AnnotationAssertion( "krc") AnnotationAssertion( "2014-10-24T21:32:59Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of protein localisation in ciliary membrane") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of protein localisation to ciliary membrane") @@ -98035,7 +95888,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of protein localization to ciliary membrane) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:cilia") Annotation( "GOC:krc") Annotation( "GO_REF:0000058") Annotation( "PMID:22072986") "Any process that activates or increases the frequency, rate or extent of protein localization to ciliary membrane.") -AnnotationAssertion( "krc") AnnotationAssertion( "2014-10-24T21:33:08Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "positive regulation of protein localisation in ciliary membrane") AnnotationAssertion(Annotation( "GOC:TermGenie") "positive regulation of protein localisation to ciliary membrane") @@ -98064,7 +95916,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of ATP metabolic process) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000058") Annotation( "PMID:20695849") "Any process that modulates the frequency, rate or extent of ATP metabolic process.") -AnnotationAssertion( "sl") AnnotationAssertion( "2014-10-30T19:04:24Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "regulation of ATP metabolism") AnnotationAssertion( "biological_process") @@ -98075,7 +95926,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of ATP metabolic process) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000058") Annotation( "PMID:20695849") "Any process that stops, prevents or reduces the frequency, rate or extent of ATP metabolic process.") -AnnotationAssertion( "sl") AnnotationAssertion( "2014-10-30T19:04:33Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of ATP metabolic process") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of ATP metabolism") @@ -98094,7 +95944,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of ATP metabolic process) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000058") Annotation( "PMID:20695849") "Any process that activates or increases the frequency, rate or extent of ATP metabolic process.") -AnnotationAssertion( "sl") AnnotationAssertion( "2014-10-30T19:04:42Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "positive regulation of ATP metabolism") AnnotationAssertion(Annotation( "GOC:TermGenie") "up regulation of ATP metabolic process") @@ -98113,7 +95962,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of basophil degranulation) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000058") Annotation( "PMID:10880837") "Any process that modulates the frequency, rate or extent of basophil degranulation.") -AnnotationAssertion( "sl") AnnotationAssertion( "2014-10-31T17:37:24Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:1903581") @@ -98125,7 +95973,6 @@ SubClassOf( ObjectSomeValuesFrom( (negative regulation of basophil degranulation) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000058") Annotation( "PMID:10880837") "Any process that stops, prevents or reduces the frequency, rate or extent of basophil degranulation.") -AnnotationAssertion( "sl") AnnotationAssertion( "2014-10-31T17:37:33Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of basophil degranulation") AnnotationAssertion(Annotation( "GOC:TermGenie") "down-regulation of basophil degranulation") @@ -98141,7 +95988,6 @@ SubClassOf( ObjectSomeValuesFrom( (positive regulation of basophil degranulation) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000058") Annotation( "PMID:10880837") "Any process that activates or increases the frequency, rate or extent of basophil degranulation.") -AnnotationAssertion( "sl") AnnotationAssertion( "2014-10-31T17:37:42Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "up regulation of basophil degranulation") AnnotationAssertion(Annotation( "GOC:TermGenie") "up-regulation of basophil degranulation") @@ -98157,7 +96003,6 @@ SubClassOf( ObjectSomeValuesFrom( (regulation of histamine secretion by mast cell) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:als") Annotation( "GO_REF:0000058") Annotation( "PMID:18253931") "Any process that modulates the frequency, rate or extent of histamine secretion by mast cell.") -AnnotationAssertion( "als") AnnotationAssertion( "2014-11-06T13:19:09Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:1903593") @@ -98169,7 +96014,6 @@ SubClassOf( ObjectSomeValuesFrom( (negative regulation of histamine secretion by mast cell) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:als") Annotation( "GO_REF:0000058") Annotation( "PMID:18253931") "Any process that stops, prevents or reduces the frequency, rate or extent of histamine secretion by mast cell.") -AnnotationAssertion( "als") AnnotationAssertion( "2014-11-06T13:19:18Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of histamine secretion by mast cell") AnnotationAssertion(Annotation( "GOC:TermGenie") "down-regulation of histamine secretion by mast cell") @@ -98184,7 +96028,6 @@ SubClassOf( ObjectSomeValuesFrom( (positive regulation of histamine secretion by mast cell) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:als") Annotation( "GO_REF:0000058") Annotation( "PMID:18253931") "Any process that activates or increases the frequency, rate or extent of histamine secretion by mast cell.") -AnnotationAssertion( "als") AnnotationAssertion( "2014-11-06T13:19:26Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "up regulation of histamine secretion by mast cell") AnnotationAssertion(Annotation( "GOC:TermGenie") "up-regulation of histamine secretion by mast cell") @@ -98201,7 +96044,6 @@ SubClassOf( ObjectSomeValuesFrom( (regulation of DNA catabolic process) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000058") Annotation( "PMID:2001740") "Any process that modulates the frequency, rate or extent of DNA catabolic process.") -AnnotationAssertion( "sl") AnnotationAssertion( "2014-11-19T22:36:35Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "regulation of DNA breakdown") AnnotationAssertion(Annotation( "GOC:TermGenie") "regulation of DNA catabolism") @@ -98214,7 +96056,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of DNA catabolic process) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000058") Annotation( "PMID:2001740") "Any process that stops, prevents or reduces the frequency, rate or extent of DNA catabolic process.") -AnnotationAssertion( "sl") AnnotationAssertion( "2014-11-19T22:36:43Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of DNA breakdown") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of DNA catabolic process") @@ -98243,7 +96084,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of DNA catabolic process) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000058") Annotation( "PMID:2001740") "Any process that activates or increases the frequency, rate or extent of DNA catabolic process.") -AnnotationAssertion( "sl") AnnotationAssertion( "2014-11-19T22:36:51Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "positive regulation of DNA breakdown") AnnotationAssertion(Annotation( "GOC:TermGenie") "positive regulation of DNA catabolism") @@ -98272,7 +96112,6 @@ EquivalentClasses( ObjectIntersection # Class: (acinar cell of sebaceous gland differentiation) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000086") Annotation( "PMID:17018284") Annotation( "PMID:18334552") Annotation( "PMID:19944183") "The process in which a relatively unspecialized cell acquires the specialized features of an acinar cell of sebaceous gland.") -AnnotationAssertion( "cls") AnnotationAssertion( "2014-11-30T11:51:57Z") AnnotationAssertion(Annotation( "CL:0002140") "sebocyte differentiation") AnnotationAssertion( "biological_process") @@ -98283,7 +96122,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of border follicle cell migration) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:als") Annotation( "GO_REF:0000058") Annotation( "PMID:18394891") "Any process that modulates the frequency, rate or extent of border follicle cell migration.") -AnnotationAssertion( "als") AnnotationAssertion( "2014-12-01T13:35:39Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "regulation of border cell migration") AnnotationAssertion( "biological_process") @@ -98294,7 +96132,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of border follicle cell migration) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:als") Annotation( "GO_REF:0000058") Annotation( "PMID:18394891") "Any process that stops, prevents or reduces the frequency, rate or extent of border follicle cell migration.") -AnnotationAssertion( "als") AnnotationAssertion( "2014-12-01T13:41:05Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "inhibition of border follicle cell migration") AnnotationAssertion( "biological_process") @@ -98305,7 +96142,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of border follicle cell migration) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:als") Annotation( "GO_REF:0000058") Annotation( "PMID:18394891") "Any process that activates or increases the frequency, rate or extent of border follicle cell migration.") -AnnotationAssertion( "als") AnnotationAssertion( "2014-12-01T13:41:19Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "activation of border follicle cell migration") AnnotationAssertion( "biological_process") @@ -98316,7 +96152,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of microvillus assembly) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:als") Annotation( "GO_REF:0000058") Annotation( "PMID:22797597") "Any process that stops, prevents or reduces the frequency, rate or extent of microvillus assembly.") -AnnotationAssertion( "als") AnnotationAssertion( "2014-12-03T11:45:08Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of microvillus assembly") AnnotationAssertion(Annotation( "GOC:TermGenie") "down-regulation of microvillus assembly") @@ -98335,7 +96170,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of microvillus assembly) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:als") Annotation( "GO_REF:0000058") Annotation( "PMID:22797597") "Any process that activates or increases the frequency, rate or extent of microvillus assembly.") -AnnotationAssertion( "als") AnnotationAssertion( "2014-12-03T11:45:17Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "up regulation of microvillus assembly") AnnotationAssertion(Annotation( "GOC:TermGenie") "up-regulation of microvillus assembly") @@ -98354,7 +96188,6 @@ EquivalentClasses( ObjectIntersection # Class: (caecum development) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000094") Annotation( "ISBN:0-683-40008-8") "The process whose specific outcome is the progression of a caecum over time, from its formation to the mature structure.") -AnnotationAssertion( "cls") AnnotationAssertion( "2014-12-03T12:05:00Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "cecum development") AnnotationAssertion(Annotation( "GOC:TermGenie") "intestinum crassum caecum development") @@ -98372,7 +96205,6 @@ EquivalentClasses( ObjectIntersection # Class: (substantia propria of cornea development) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000094") Annotation( "PMID:12556382") "The process whose specific outcome is the progression of a substantia propria of cornea over time, from its formation to the mature structure.") -AnnotationAssertion( "cls") AnnotationAssertion( "2014-12-03T13:12:09Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "corneal stroma development") AnnotationAssertion(Annotation( "GOC:TermGenie") "stroma of cornea development") @@ -98385,7 +96217,6 @@ EquivalentClasses( ObjectIntersection # Class: (esophagus development) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000094") Annotation( "ISBN:0-683-40008-8") "The process whose specific outcome is the progression of an esophagus over time, from its formation to the mature structure.") -AnnotationAssertion( "cls") AnnotationAssertion( "2014-12-03T14:41:30Z") AnnotationAssertion(Annotation( "MGI:csmith") "esophageal development") AnnotationAssertion(Annotation( "GOC:TermGenie") "gullet development") @@ -98398,7 +96229,6 @@ EquivalentClasses( ObjectIntersection # Class: (enterocyte differentiation) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000086") Annotation( "PMID:16782882") Annotation( "Wikipedia:List_of_intestinal_epithelial_differentiation_genes") "The process in which a relatively unspecialized cell acquires the specialized features of an enterocyte.") -AnnotationAssertion( "cls") AnnotationAssertion( "2014-12-03T15:08:51Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:1903703") @@ -98408,7 +96238,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of hemopoiesis) AnnotationAssertion(Annotation( "GOC:PARL") Annotation( "GOC:TermGenie") Annotation( "GOC:pad") Annotation( "GO_REF:0000058") Annotation( "PMID:20080761") "Any process that modulates the frequency, rate or extent of hemopoiesis.") -AnnotationAssertion( "pad") AnnotationAssertion( "2014-12-04T15:34:13Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "regulation of blood cell biosynthesis") AnnotationAssertion(Annotation( "GOC:TermGenie") "regulation of blood cell formation") @@ -98425,7 +96254,6 @@ SubClassOf( (negative regulation of hemopoiesis) AnnotationAssertion(Annotation( "GOC:PARL") Annotation( "GOC:TermGenie") Annotation( "GOC:pad") Annotation( "GO_REF:0000058") Annotation( "PMID:20080761") "Any process that stops, prevents or reduces the frequency, rate or extent of hemopoiesis.") -AnnotationAssertion( "pad") AnnotationAssertion( "2014-12-04T15:34:21Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of blood cell biosynthesis") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of blood cell formation") @@ -98464,7 +96292,6 @@ SubClassOf( (positive regulation of hemopoiesis) AnnotationAssertion(Annotation( "GOC:PARL") Annotation( "GOC:TermGenie") Annotation( "GOC:pad") Annotation( "GO_REF:0000058") Annotation( "PMID:20080761") "Any process that activates or increases the frequency, rate or extent of hemopoiesis.") -AnnotationAssertion( "pad") AnnotationAssertion( "2014-12-04T15:34:30Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "positive regulation of blood cell biosynthesis") AnnotationAssertion(Annotation( "GOC:TermGenie") "positive regulation of blood cell formation") @@ -98503,7 +96330,6 @@ SubClassOf( (uterine gland development) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000094") Annotation( "PMID:23619340") "The process whose specific outcome is the progression of an uterine gland over time, from its formation to the mature structure.") -AnnotationAssertion( "cls") AnnotationAssertion( "2014-12-04T18:57:21Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "endometrial gland development") AnnotationAssertion(Annotation( "GOC:TermGenie") "endometrium gland development") @@ -98520,7 +96346,6 @@ EquivalentClasses( ObjectIntersection # Class: (luteal cell differentiation) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000086") Annotation( "MP:0001133") "The process in which a relatively unspecialized cell acquires the specialized features of a luteal cell. Large luteal cells develop from granulosa cells. Small luteal cells develop from theca cells.") -AnnotationAssertion( "cjm") AnnotationAssertion( "2014-12-10T01:36:43Z") AnnotationAssertion(Annotation( "CL:0000175") "lutein cell differentiation") AnnotationAssertion( "biological_process") @@ -98531,7 +96356,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of plasma membrane organization) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000058") Annotation( "PMID:24514900") "Any process that modulates the frequency, rate or extent of plasma membrane organization.") -AnnotationAssertion( "al") AnnotationAssertion( "2014-12-10T18:59:44Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "regulation of plasma membrane organisation") AnnotationAssertion( "biological_process") @@ -98543,7 +96367,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of potassium ion export across plasma membrane) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:TermGenie") Annotation( "GOC:mtg_cardiac_conduct_nov11") Annotation( "GOC:rl") Annotation( "GO_REF:0000058") Annotation( "PMID:19646991") "Any process that modulates the frequency, rate or extent of potassium ion export across the plasma membrane.") -AnnotationAssertion( "rl") AnnotationAssertion( "2013-07-17T16:39:53Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "regulation of potassium export") AnnotationAssertion(Annotation( "GOC:TermGenie") "regulation of potassium export across plasma membrane") @@ -98556,7 +96379,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of potassium ion export across plasma membrane) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:TermGenie") Annotation( "GOC:mtg_cardiac_conduct_nov11") Annotation( "GOC:rl") Annotation( "GO_REF:0000058") Annotation( "PMID:19646991") "Any process that stops, prevents or reduces the frequency, rate or extent of potassium ion export across the plasma membrane.") -AnnotationAssertion( "rl") AnnotationAssertion( "2013-07-17T16:40:02Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of potassium export") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of potassium ion export") @@ -98580,7 +96402,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of potassium ion export across plasma membrane) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:TermGenie") Annotation( "GOC:mtg_cardiac_conduct_nov11") Annotation( "GOC:rl") Annotation( "GO_REF:0000058") Annotation( "PMID:19646991") "Any process that activates or increases the frequency, rate or extent of potassium ion export across the plasma membrane.") -AnnotationAssertion( "rl") AnnotationAssertion( "2013-07-17T16:40:10Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "positive regulation of potassium export") AnnotationAssertion( "positive regulation of potassium ion export") @@ -98604,7 +96425,6 @@ EquivalentClasses( ObjectIntersection # Class: (protein localization to vacuolar membrane) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000087") Annotation( "PMID:25378562") "A process in which a protein is transported to, or maintained in, a location within a vacuolar membrane.") -AnnotationAssertion( "mah") AnnotationAssertion( "2015-01-07T13:15:54Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "protein localisation in vacuolar membrane") AnnotationAssertion(Annotation( "GOC:TermGenie") "protein localisation to vacuolar membrane") @@ -98617,7 +96437,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of cardiac conduction) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:TermGenie") Annotation( "GOC:mtg_cardiac_conduct_nov11") Annotation( "GOC:rph") Annotation( "GO_REF:0000058") Annotation( "PMID:12967627") "Any process that modulates the frequency, rate or extent of cardiac conduction.") -AnnotationAssertion( "rph") AnnotationAssertion( "2015-01-07T13:20:11Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:1903779") @@ -98627,7 +96446,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of cardiac conduction) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:TermGenie") Annotation( "GOC:mtg_cardiac_conduct_nov11") Annotation( "GOC:rph") Annotation( "GO_REF:0000058") Annotation( "PMID:12967627") "Any process that stops, prevents or reduces the frequency, rate or extent of cardiac conduction.") -AnnotationAssertion( "rph") AnnotationAssertion( "2015-01-07T13:20:20Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of cardiac conduction") AnnotationAssertion(Annotation( "GOC:TermGenie") "down-regulation of cardiac conduction") @@ -98641,7 +96459,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of cardiac conduction) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:TermGenie") Annotation( "GOC:mtg_cardiac_conduct_nov11") Annotation( "GOC:rph") Annotation( "GO_REF:0000058") Annotation( "PMID:12967627") "Any process that activates or increases the frequency, rate or extent of cardiac conduction.") -AnnotationAssertion( "rph") AnnotationAssertion( "2015-01-07T13:20:28Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "up regulation of cardiac conduction") AnnotationAssertion(Annotation( "GOC:TermGenie") "up-regulation of cardiac conduction") @@ -98655,7 +96472,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of sodium ion import across plasma membrane) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:TermGenie") Annotation( "GOC:mtg_cardiac_conduct_nov11") Annotation( "GOC:nc") Annotation( "GO_REF:0000058") Annotation( "PMID:19376779") "Any process that modulates the frequency, rate or extent of sodium ion import across the plasma membrane.") -AnnotationAssertion( "nc") AnnotationAssertion( "2015-01-07T16:48:43Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:1903782") @@ -98665,7 +96481,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of sodium ion import across plasma membrane) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:TermGenie") Annotation( "GOC:mtg_cardiac_conduct_nov11") Annotation( "GOC:nc") Annotation( "GO_REF:0000058") Annotation( "PMID:19376779") "Any process that stops, prevents or reduces the frequency, rate or extent of sodium ion import across the plasma membrane.") -AnnotationAssertion( "nc") AnnotationAssertion( "2015-01-07T16:48:51Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of sodium ion import across plasma membrane") AnnotationAssertion(Annotation( "GOC:TermGenie") "down-regulation of sodium ion import across plasma membrane") @@ -98679,7 +96494,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of sodium ion import across plasma membrane) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:TermGenie") Annotation( "GOC:mtg_cardiac_conduct_nov11") Annotation( "GOC:nc") Annotation( "GO_REF:0000058") Annotation( "PMID:19376779") "Any process that activates or increases the frequency, rate or extent of sodium ion import across the plasma membrane.") -AnnotationAssertion( "nc") AnnotationAssertion( "2015-01-07T16:49:00Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "up regulation of sodium ion import across plasma membrane") AnnotationAssertion(Annotation( "GOC:TermGenie") "up-regulation of sodium ion import across plasma membrane") @@ -98693,7 +96507,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of amino acid transmembrane transport) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000058") Annotation( "PMID:16115814") "Any process that modulates the frequency, rate or extent of amino acid transmembrane transport.") -AnnotationAssertion( "al") AnnotationAssertion( "2015-01-08T17:42:18Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "regulation of amino acid membrane transport") AnnotationAssertion( "biological_process") @@ -98704,7 +96517,6 @@ EquivalentClasses( ObjectIntersection # Class: (glycine import across plasma membrane) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000075") Annotation( "PMID:23895341") "The directed movement of glycine from outside of a cell, across the plasma membrane and into the cytosol.") -AnnotationAssertion( "bf") AnnotationAssertion( "2012-05-11T01:16:45Z") AnnotationAssertion( "glycine import") AnnotationAssertion( "glycine import into cell") @@ -98716,7 +96528,6 @@ EquivalentClasses( ObjectIntersection # Class: (L-histidine import across plasma membrane) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000075") Annotation( "PMID:23895341") "The directed movement of L-histidine from outside of a cell, across the plasma membrane and into the cytosol.") -AnnotationAssertion( "dph") AnnotationAssertion( "2012-10-05T10:20:50Z") AnnotationAssertion( "L-histidine import") AnnotationAssertion( "histidine import") @@ -98729,7 +96540,6 @@ EquivalentClasses( ObjectIntersection # Class: (organic acid transmembrane transport) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000069") "The process in which an organic acid is transported across a membrane.") -AnnotationAssertion( "vw") AnnotationAssertion( "2015-01-20T10:20:58Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:1903825") @@ -98740,7 +96550,6 @@ EquivalentClasses( ObjectIntersection AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:vw") Annotation( "GO_REF:0000058") "Any process that stops, prevents or reduces the frequency, rate or extent of a protein localization.") AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/22021"^^xsd:anyURI) -AnnotationAssertion( "jl") AnnotationAssertion( "2015-01-20T14:32:24Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of cellular protein localisation") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of cellular protein localization") @@ -98761,7 +96570,6 @@ EquivalentClasses( ObjectIntersection AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:vw") Annotation( "GO_REF:0000058") "Any process that activates or increases the frequency, rate or extent of a protein localization.") AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/22021"^^xsd:anyURI) -AnnotationAssertion( "jl") AnnotationAssertion( "2015-01-20T14:32:33Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "positive regulation of cellular protein localisation") AnnotationAssertion( "positive regulation of cellular protein localization") @@ -98779,7 +96587,6 @@ EquivalentClasses( ObjectIntersection # Class: (signal transduction involved in cellular response to ammonium ion) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000060") Annotation( "PMID:16297994") "Any signal transduction that is involved in cellular response to ammonium ion.") -AnnotationAssertion( "al") AnnotationAssertion( "2015-01-21T17:52:09Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "signaling cascade involved in cellular response to ammonium ion") AnnotationAssertion(Annotation( "GOC:TermGenie") "signalling cascade involved in cellular response to ammonium ion") @@ -98793,7 +96600,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of aorta morphogenesis) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:BHF_miRNA") Annotation( "GOC:TermGenie") Annotation( "GOC:rph") Annotation( "GO_REF:0000058") Annotation( "PMID:22269326") "Any process that modulates the frequency, rate or extent of aorta morphogenesis.") -AnnotationAssertion( "rph") AnnotationAssertion( "2015-01-23T14:00:51Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:1903847") @@ -98803,7 +96609,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of aorta morphogenesis) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:BHF_miRNA") Annotation( "GOC:TermGenie") Annotation( "GOC:rph") Annotation( "GO_REF:0000058") Annotation( "PMID:22269326") "Any process that stops, prevents or reduces the frequency, rate or extent of aorta morphogenesis.") -AnnotationAssertion( "rph") AnnotationAssertion( "2015-01-23T14:01:01Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of aorta morphogenesis") AnnotationAssertion(Annotation( "GOC:TermGenie") "down-regulation of aorta morphogenesis") @@ -98817,7 +96622,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of aorta morphogenesis) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:BHF_miRNA") Annotation( "GOC:TermGenie") Annotation( "GOC:rph") Annotation( "GO_REF:0000058") Annotation( "PMID:22269326") "Any process that activates or increases the frequency, rate or extent of aorta morphogenesis.") -AnnotationAssertion( "rph") AnnotationAssertion( "2015-01-23T14:01:09Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "up regulation of aorta morphogenesis") AnnotationAssertion(Annotation( "GOC:TermGenie") "up-regulation of aorta morphogenesis") @@ -98831,7 +96635,6 @@ EquivalentClasses( ObjectIntersection # Class: (extraembryonic membrane development) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000094") Annotation( "ISBN:0073040584") "The process whose specific outcome is the progression of an extraembryonic membrane over time, from its formation to the mature structure.") -AnnotationAssertion( "cjm") AnnotationAssertion( "2015-02-05T00:42:16Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:1903867") @@ -98841,7 +96644,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of establishment of T cell polarity) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:als") Annotation( "GO_REF:0000058") Annotation( "PMID:23575248") "Any process that modulates the frequency, rate or extent of establishment of T cell polarity.") -AnnotationAssertion( "als") AnnotationAssertion( "2015-02-09T10:50:21Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "regulation of T cell polarization") AnnotationAssertion(Annotation( "GOC:TermGenie") "regulation of T lymphocyte polarization") @@ -98857,7 +96659,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of establishment of T cell polarity) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:als") Annotation( "GO_REF:0000058") Annotation( "PMID:23575248") "Any process that stops, prevents or reduces the frequency, rate or extent of establishment of T cell polarity.") -AnnotationAssertion( "als") AnnotationAssertion( "2015-02-09T10:50:30Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of T cell polarization") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of T lymphocyte polarization") @@ -98902,7 +96703,6 @@ SubClassOf( ObjectSomeValuesFrom( (positive regulation of establishment of T cell polarity) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:als") Annotation( "GO_REF:0000058") Annotation( "PMID:23575248") "Any process that activates or increases the frequency, rate or extent of establishment of T cell polarity.") -AnnotationAssertion( "als") AnnotationAssertion( "2015-02-09T10:50:40Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "positive regulation of T cell polarization") AnnotationAssertion(Annotation( "GOC:TermGenie") "positive regulation of T lymphocyte polarization") @@ -98947,7 +96747,6 @@ SubClassOf( ObjectSomeValuesFrom( (estradiol binding) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000067") Annotation( "PMID:9048584") "Binding to estradiol.") -AnnotationAssertion( "sl") AnnotationAssertion( "2015-02-11T00:11:34Z") AnnotationAssertion( "molecular_function") AnnotationAssertion( "GO:1903924") @@ -98957,7 +96756,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of respiratory gaseous exchange) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000058") Annotation( "PMID:22819705") "Any process that stops, prevents or reduces the frequency, rate or extent of respiratory gaseous exchange.") -AnnotationAssertion( "sl") AnnotationAssertion( "2015-02-17T20:26:24Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of respiratory gaseous exchange") AnnotationAssertion(Annotation( "GOC:TermGenie") "down-regulation of respiratory gaseous exchange") @@ -98973,7 +96771,6 @@ SubClassOf( (positive regulation of respiratory gaseous exchange) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000058") Annotation( "PMID:22819705") "Any process that activates or increases the frequency, rate or extent of respiratory gaseous exchange.") -AnnotationAssertion( "sl") AnnotationAssertion( "2015-02-17T20:26:35Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "up regulation of respiratory gaseous exchange") AnnotationAssertion(Annotation( "GOC:TermGenie") "up-regulation of respiratory gaseous exchange") @@ -98989,7 +96786,6 @@ SubClassOf( (regulation of hepatocyte apoptotic process) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000058") Annotation( "PMID:8649852") "Any process that modulates the frequency, rate or extent of hepatocyte apoptotic process.") -AnnotationAssertion( "sl") AnnotationAssertion( "2015-02-19T12:54:40Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "regulation of hepatocyte apoptosis") AnnotationAssertion( "biological_process") @@ -99000,7 +96796,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of hepatocyte apoptotic process) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000058") Annotation( "PMID:8649852") "Any process that stops, prevents or reduces the frequency, rate or extent of hepatocyte apoptotic process.") -AnnotationAssertion( "sl") AnnotationAssertion( "2015-02-19T12:54:50Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of hepatocyte apoptotic process") AnnotationAssertion(Annotation( "GOC:TermGenie") "down-regulation of hepatocyte apoptotic process") @@ -99019,7 +96814,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of hepatocyte apoptotic process) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000058") Annotation( "PMID:8649852") "Any process that activates or increases the frequency, rate or extent of hepatocyte apoptotic process.") -AnnotationAssertion( "sl") AnnotationAssertion( "2015-02-19T12:54:59Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "up regulation of hepatocyte apoptotic process") AnnotationAssertion(Annotation( "GOC:TermGenie") "up-regulation of hepatocyte apoptotic process") @@ -99038,7 +96832,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of ventricular cardiac muscle cell action potential) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:TermGenie") Annotation( "GOC:mtg_cardiac_conduct_nov11") Annotation( "GOC:nc") Annotation( "GO_REF:0000058") Annotation( "PMID:25281747") "Any process that stops, prevents or reduces the frequency, rate or extent of ventricular cardiac muscle cell action potential.") -AnnotationAssertion( "nc") AnnotationAssertion( "2015-02-20T14:31:55Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of ventricular cardiac muscle cell action potential") AnnotationAssertion(Annotation( "GOC:TermGenie") "down-regulation of ventricular cardiac muscle cell action potential") @@ -99053,7 +96846,6 @@ SubClassOf( ObjectSomeValuesFrom( (positive regulation of ventricular cardiac muscle cell action potential) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:TermGenie") Annotation( "GOC:mtg_cardiac_conduct_nov11") Annotation( "GOC:nc") Annotation( "GO_REF:0000058") Annotation( "PMID:25281747") "Any process that activates or increases the frequency, rate or extent of ventricular cardiac muscle cell action potential.") -AnnotationAssertion( "nc") AnnotationAssertion( "2015-02-20T14:32:04Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "up regulation of ventricular cardiac muscle cell action potential") AnnotationAssertion(Annotation( "GOC:TermGenie") "up-regulation of ventricular cardiac muscle cell action potential") @@ -99068,7 +96860,6 @@ SubClassOf( ObjectSomeValuesFrom( (negative regulation of atrial cardiac muscle cell action potential) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:TermGenie") Annotation( "GOC:mtg_cardiac_conduct_nov11") Annotation( "GOC:nc") Annotation( "GO_REF:0000058") Annotation( "PMID:25281747") "Any process that stops, prevents or reduces the frequency, rate or extent of atrial cardiac muscle cell action potential.") -AnnotationAssertion( "nc") AnnotationAssertion( "2015-02-20T14:36:33Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of atrial cardiac muscle cell action potential") AnnotationAssertion(Annotation( "GOC:TermGenie") "down-regulation of atrial cardiac muscle cell action potential") @@ -99083,7 +96874,6 @@ SubClassOf( ObjectSomeValuesFrom( (positive regulation of atrial cardiac muscle cell action potential) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:TermGenie") Annotation( "GOC:mtg_cardiac_conduct_nov11") Annotation( "GOC:nc") Annotation( "GO_REF:0000058") Annotation( "PMID:25281747") "Any process that activates or increases the frequency, rate or extent of atrial cardiac muscle cell action potential.") -AnnotationAssertion( "nc") AnnotationAssertion( "2015-02-20T14:36:42Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "up regulation of atrial cardiac muscle cell action potential") AnnotationAssertion(Annotation( "GOC:TermGenie") "up-regulation of atrial cardiac muscle cell action potential") @@ -99097,7 +96887,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of AV node cell action potential) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:TermGenie") Annotation( "GOC:mtg_cardiac_conduct_nov11") Annotation( "GOC:nc") Annotation( "GO_REF:0000058") Annotation( "PMID:25281747") "Any process that stops, prevents or reduces the frequency, rate or extent of AV node cell action potential.") -AnnotationAssertion( "nc") AnnotationAssertion( "2015-02-20T14:59:41Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of AV node cardiac muscle cell action potential") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of AV node cell action potential") @@ -99121,7 +96910,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of AV node cell action potential) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:TermGenie") Annotation( "GOC:mtg_cardiac_conduct_nov11") Annotation( "GOC:nc") Annotation( "GO_REF:0000058") Annotation( "PMID:25281747") "Any process that activates or increases the frequency, rate or extent of AV node cell action potential.") -AnnotationAssertion( "nc") AnnotationAssertion( "2015-02-20T14:59:50Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "positive regulation of AV node cardiac muscle cell action potential") AnnotationAssertion(Annotation( "GOC:TermGenie") "positive regulation of atrioventricular node cardiac muscle cell action potential") @@ -99145,7 +96933,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of glial cell migration) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:TermGenie") Annotation( "GOC:nc") Annotation( "GO_REF:0000058") Annotation( "PMID:19100238") "Any process that modulates the frequency, rate or extent of glial cell migration.") -AnnotationAssertion( "nc") AnnotationAssertion( "2015-03-02T15:13:31Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "regulation of glia cell migration") AnnotationAssertion( "biological_process") @@ -99156,7 +96943,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of glial cell migration) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:TermGenie") Annotation( "GOC:nc") Annotation( "GO_REF:0000058") Annotation( "PMID:19100238") "Any process that stops, prevents or reduces the frequency, rate or extent of glial cell migration.") -AnnotationAssertion( "nc") AnnotationAssertion( "2015-03-02T15:13:38Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of glia cell migration") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of glial cell migration") @@ -99175,7 +96961,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of glial cell migration) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:TermGenie") Annotation( "GOC:nc") Annotation( "GO_REF:0000058") Annotation( "PMID:19100238") "Any process that activates or increases the frequency, rate or extent of glial cell migration.") -AnnotationAssertion( "nc") AnnotationAssertion( "2015-03-02T15:13:43Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "positive regulation of glia cell migration") AnnotationAssertion(Annotation( "GOC:TermGenie") "up regulation of glia cell migration") @@ -99194,7 +96979,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of microglial cell activation) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:TermGenie") Annotation( "GOC:nc") Annotation( "GO_REF:0000058") Annotation( "PMID:19100238") "Any process that modulates the frequency, rate or extent of microglial cell activation.") -AnnotationAssertion( "nc") AnnotationAssertion( "2015-03-02T15:17:33Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:1903978") @@ -99205,7 +96989,6 @@ SubClassOf( ObjectSomeValuesFrom( (negative regulation of microglial cell activation) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:TermGenie") Annotation( "GOC:nc") Annotation( "GO_REF:0000058") Annotation( "PMID:19100238") "Any process that stops, prevents or reduces the frequency, rate or extent of microglial cell activation.") -AnnotationAssertion( "nc") AnnotationAssertion( "2015-03-02T15:17:39Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of microglial cell activation") AnnotationAssertion(Annotation( "GOC:TermGenie") "down-regulation of microglial cell activation") @@ -99220,7 +97003,6 @@ SubClassOf( ObjectSomeValuesFrom( (positive regulation of microglial cell activation) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:TermGenie") Annotation( "GOC:nc") Annotation( "GO_REF:0000058") Annotation( "PMID:19100238") "Any process that activates or increases the frequency, rate or extent of microglial cell activation.") -AnnotationAssertion( "nc") AnnotationAssertion( "2015-03-02T15:17:44Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "up regulation of microglial cell activation") AnnotationAssertion(Annotation( "GOC:TermGenie") "up-regulation of microglial cell activation") @@ -99235,7 +97017,6 @@ SubClassOf( ObjectSomeValuesFrom( (iron ion export across plasma membrane) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:TermGenie") Annotation( "GOC:kom") Annotation( "GOC:rl") Annotation( "GO_REF:0000074") Annotation( "PMID:15514116") "The directed movement of iron ions from inside of a cell, across the plasma membrane and into the extracellular region.") -AnnotationAssertion( "rl") AnnotationAssertion( "2014-09-03T13:01:37Z") AnnotationAssertion( "ferrous iron export") AnnotationAssertion( "ferrous iron export across plasma membrane") @@ -99250,7 +97031,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of sebum secreting cell proliferation) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:hjd") Annotation( "GO_REF:0000058") Annotation( "PMID:16901790") "Any process that modulates the frequency, rate or extent of sebum secreting cell proliferation.") -AnnotationAssertion( "hjd") AnnotationAssertion( "2015-03-06T16:19:44Z") AnnotationAssertion( "biological_process") AnnotationAssertion(Annotation( "GOC:TermGenie") "regulation of sebocyte proliferation") @@ -99261,7 +97041,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of sebum secreting cell proliferation) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:hjd") Annotation( "GO_REF:0000058") Annotation( "PMID:16901790") "Any process that stops, prevents or reduces the frequency, rate or extent of sebum secreting cell proliferation.") -AnnotationAssertion( "hjd") AnnotationAssertion( "2015-03-06T16:19:50Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of sebum secreting cell proliferation") AnnotationAssertion(Annotation( "GOC:TermGenie") "down-regulation of sebum secreting cell proliferation") @@ -99280,7 +97059,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of sebum secreting cell proliferation) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:hjd") Annotation( "GO_REF:0000058") Annotation( "PMID:16901790") "Any process that activates or increases the frequency, rate or extent of sebum secreting cell proliferation.") -AnnotationAssertion( "hjd") AnnotationAssertion( "2015-03-06T16:19:56Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "up regulation of sebum secreting cell proliferation") AnnotationAssertion(Annotation( "GOC:TermGenie") "up-regulation of sebum secreting cell proliferation") @@ -99299,7 +97077,6 @@ EquivalentClasses( ObjectIntersection # Class: (response to serotonin) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000071") Annotation( "PMID:1505525") "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a serotonin stimulus.") -AnnotationAssertion( "sl") AnnotationAssertion( "2015-03-06T19:33:54Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:1904014") @@ -99309,7 +97086,6 @@ EquivalentClasses( ObjectIntersection # Class: (cellular response to serotonin) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000071") Annotation( "PMID:1505525") "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a serotonin stimulus.") -AnnotationAssertion( "sl") AnnotationAssertion( "2015-03-06T19:34:00Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:1904015") @@ -99319,7 +97095,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of vasculature development) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000058") Annotation( "PMID:21472453") "Any process that activates or increases the frequency, rate or extent of vasculature development.") -AnnotationAssertion( "sl") AnnotationAssertion( "2015-03-06T22:17:04Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "up regulation of vasculature development") AnnotationAssertion(Annotation( "GOC:TermGenie") "up-regulation of vasculature development") @@ -99345,7 +97120,6 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) -AnnotationAssertion( "sl") AnnotationAssertion( "2015-03-06T22:27:17Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "epitheliocyte apoptotic process") AnnotationAssertion(Annotation( "GOC:TermGenie") "epithelial cell apoptosis") @@ -99371,7 +97145,6 @@ DisjointClasses( ObjectSomeValuesFrom # Class: (regulation of collagen fibril organization) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000058") Annotation( "PMID:25451920") "Any process that modulates the frequency, rate or extent of collagen fibril organization.") -AnnotationAssertion( "ae") AnnotationAssertion( "2015-03-12T12:36:52Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "regulation of collagen fibril organisation") AnnotationAssertion(Annotation( "GOC:TermGenie") "regulation of fibrillar collagen organization") @@ -99384,7 +97157,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of collagen fibril organization) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000058") Annotation( "PMID:25451920") "Any process that stops, prevents or reduces the frequency, rate or extent of collagen fibril organization.") -AnnotationAssertion( "ae") AnnotationAssertion( "2015-03-12T12:36:59Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of collagen fibril organisation") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of collagen fibril organization") @@ -99408,7 +97180,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of collagen fibril organization) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000058") Annotation( "PMID:25451920") "Any process that activates or increases the frequency, rate or extent of collagen fibril organization.") -AnnotationAssertion( "ae") AnnotationAssertion( "2015-03-12T12:37:06Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "positive regulation of collagen fibril organisation") AnnotationAssertion(Annotation( "GOC:TermGenie") "positive regulation of fibrillar collagen organization") @@ -99432,7 +97203,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of epithelial cell apoptotic process) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000058") Annotation( "PMID:19137015") "Any process that modulates the frequency, rate or extent of epithelial cell apoptotic process.") -AnnotationAssertion( "sl") AnnotationAssertion( "2015-03-13T22:05:41Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "regulation of epitheliocyte apoptotic process") AnnotationAssertion(Annotation( "GOC:TermGenie") "regulation of epithelial cell apoptosis") @@ -99445,7 +97215,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of epithelial cell apoptotic process) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000058") Annotation( "PMID:19137015") "Any process that stops, prevents or reduces the frequency, rate or extent of epithelial cell apoptotic process.") -AnnotationAssertion( "sl") AnnotationAssertion( "2015-03-13T22:05:47Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of epithelial cell apoptotic process") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of epitheliocyte apoptotic process") @@ -99474,7 +97243,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of epithelial cell apoptotic process) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000058") Annotation( "PMID:19137015") "Any process that activates or increases the frequency, rate or extent of epithelial cell apoptotic process.") -AnnotationAssertion( "sl") AnnotationAssertion( "2015-03-13T22:05:53Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "positive regulation of epitheliocyte apoptotic process") AnnotationAssertion(Annotation( "GOC:TermGenie") "up regulation of epithelial cell apoptotic process") @@ -99503,7 +97271,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of iron export across plasma membrane) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:TermGenie") Annotation( "GOC:kom") Annotation( "GO_REF:0000058") Annotation( "PMID:15514116") "Any process that modulates the frequency, rate or extent of export of iron ions from inside of a cell, across the plasma membrane and into the extracellular region.") -AnnotationAssertion( "kom") AnnotationAssertion( "2015-03-16T15:36:37Z") AnnotationAssertion( "regulation of ferrous iron export") AnnotationAssertion( "regulation of iron(2+) export") @@ -99515,7 +97282,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of iron export across plasma membrane) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:TermGenie") Annotation( "GOC:kom") Annotation( "GO_REF:0000058") Annotation( "PMID:15514116") "Any process that stops, prevents or reduces the frequency, rate or extent of export of iron ions from inside of a cell, across the plasma membrane and into the extracellular region.") -AnnotationAssertion( "kom") AnnotationAssertion( "2015-03-16T15:36:43Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of ferrous iron export") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of iron(2+) export") @@ -99535,7 +97301,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of iron export across plasma membrane) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:TermGenie") Annotation( "GOC:kom") Annotation( "GO_REF:0000058") Annotation( "PMID:15514116") "Any process that activates or increases the frequency, rate or extent of export of iron ions from inside of a cell, across the plasma membrane and into the extracellular region.") -AnnotationAssertion( "kom") AnnotationAssertion( "2015-03-16T15:36:49Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "activation of ferrous iron export") AnnotationAssertion(Annotation( "GOC:TermGenie") "activation of iron(2+) export") @@ -99555,7 +97320,6 @@ EquivalentClasses( ObjectIntersection # Class: (response to aldosterone) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000071") Annotation( "PMID:17644563") "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an aldosterone stimulus.") -AnnotationAssertion( "sl") AnnotationAssertion( "2015-03-16T23:07:53Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:1904044") @@ -99565,7 +97329,6 @@ EquivalentClasses( ObjectIntersection # Class: (cellular response to aldosterone) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000071") Annotation( "PMID:17644563") "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an aldosterone stimulus.") -AnnotationAssertion( "sl") AnnotationAssertion( "2015-03-16T23:07:59Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:1904045") @@ -99575,7 +97338,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of cholangiocyte proliferation) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000058") Annotation( "PMID:24434010") "Any process that modulates the frequency, rate or extent of cholangiocyte proliferation.") -AnnotationAssertion( "sl") AnnotationAssertion( "2015-03-18T17:56:14Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "regulation of hepatoblast proliferation") AnnotationAssertion( "biological_process") @@ -99586,7 +97348,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of cholangiocyte proliferation) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000058") Annotation( "PMID:24434010") "Any process that stops, prevents or reduces the frequency, rate or extent of cholangiocyte proliferation.") -AnnotationAssertion( "sl") AnnotationAssertion( "2015-03-18T17:56:20Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of cholangiocyte proliferation") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of hepatoblast proliferation") @@ -99605,7 +97366,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of cholangiocyte proliferation) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000058") Annotation( "PMID:24434010") "Any process that activates or increases the frequency, rate or extent of cholangiocyte proliferation.") -AnnotationAssertion( "sl") AnnotationAssertion( "2015-03-18T17:56:26Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "positive regulation of hepatoblast proliferation") AnnotationAssertion(Annotation( "GOC:TermGenie") "up regulation of cholangiocyte proliferation") @@ -99624,7 +97384,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of sensory perception of pain) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000058") Annotation( "PMID:17167094") "Any process that stops, prevents or reduces the frequency, rate or extent of sensory perception of pain.") -AnnotationAssertion( "sl") AnnotationAssertion( "2015-03-18T20:33:57Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of nociception") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of sensory perception of pain") @@ -99650,7 +97409,6 @@ SubClassOf( (positive regulation of sensory perception of pain) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000058") Annotation( "PMID:17167094") "Any process that activates or increases the frequency, rate or extent of sensory perception of pain.") -AnnotationAssertion( "sl") AnnotationAssertion( "2015-03-18T20:34:03Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "positive regulation of nociception") AnnotationAssertion(Annotation( "GOC:TermGenie") "up regulation of nociception") @@ -99676,7 +97434,6 @@ SubClassOf( (regulation of monoatomic cation transmembrane transport) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000058") Annotation( "PMID:15304482") "Any process that modulates the frequency, rate or extent of cation transmembrane transport.") -AnnotationAssertion( "sl") AnnotationAssertion( "2015-03-18T21:11:43Z") AnnotationAssertion( "regulation of cation transmembrane transport") AnnotationAssertion( "biological_process") @@ -99687,7 +97444,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of cation transmembrane transport) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000058") Annotation( "PMID:15304482") "Any process that stops, prevents or reduces the frequency, rate or extent of cation transmembrane transport.") -AnnotationAssertion( "sl") AnnotationAssertion( "2015-03-18T21:11:50Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of cation transmembrane transport") AnnotationAssertion(Annotation( "GOC:TermGenie") "down-regulation of cation transmembrane transport") @@ -99701,7 +97457,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of cation transmembrane transport) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000058") Annotation( "PMID:15304482") "Any process that activates or increases the frequency, rate or extent of cation transmembrane transport.") -AnnotationAssertion( "sl") AnnotationAssertion( "2015-03-18T21:11:55Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "up regulation of cation transmembrane transport") AnnotationAssertion(Annotation( "GOC:TermGenie") "up-regulation of cation transmembrane transport") @@ -99715,7 +97470,6 @@ EquivalentClasses( ObjectIntersection # Class: (G protein-coupled acetylcholine receptor signaling pathway involved in positive regulation of acetylcholine secretion, neurotransmission) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:kmv") Annotation( "GO_REF:0000060") Annotation( "PMID:22588719") "Any G protein-coupled acetylcholine receptor signaling pathway that is involved in positive regulation of acetylcholine secretion, neurotransmission.") -AnnotationAssertion( "kmv") AnnotationAssertion( "2015-03-19T15:28:47Z") AnnotationAssertion( "G-protein coupled acetylcholine receptor signaling pathway involved in positive regulation of acetylcholine secretion, neurotransmission") AnnotationAssertion(Annotation( "GOC:TermGenie") "G-protein coupled acetylcholine receptor signaling pathway involved in up regulation of acetylcholine secretion") @@ -99743,7 +97497,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of trophectodermal cell proliferation) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000058") Annotation( "PMID:24508636") "Any process that modulates the frequency, rate or extent of trophectodermal cell proliferation.") -AnnotationAssertion( "tb") AnnotationAssertion( "2015-03-20T16:55:56Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "regulation of trophectoderm cell proliferation") AnnotationAssertion( "biological_process") @@ -99755,7 +97508,6 @@ SubClassOf( ObjectSomeValuesFrom( (negative regulation of trophectodermal cell proliferation) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000058") Annotation( "PMID:24508636") "Any process that stops, prevents or reduces the frequency, rate or extent of trophectodermal cell proliferation.") -AnnotationAssertion( "tb") AnnotationAssertion( "2015-03-20T16:56:02Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of trophectoderm cell proliferation") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of trophectodermal cell proliferation") @@ -99774,7 +97526,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of trophectodermal cell proliferation) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000058") Annotation( "PMID:24508636") "Any process that activates or increases the frequency, rate or extent of trophectodermal cell proliferation.") -AnnotationAssertion( "tb") AnnotationAssertion( "2015-03-20T16:56:08Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "positive regulation of trophectoderm cell proliferation") AnnotationAssertion(Annotation( "GOC:TermGenie") "up regulation of trophectoderm cell proliferation") @@ -99793,7 +97544,6 @@ EquivalentClasses( ObjectIntersection # Class: (protein localization to microvillus) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:kmv") Annotation( "GO_REF:0000087") Annotation( "PMID:25335890") "A process in which a protein is transported to, or maintained in, a location within a microvillus.") -AnnotationAssertion( "kmv") AnnotationAssertion( "2015-04-01T18:14:41Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "protein localisation in microvillus") AnnotationAssertion(Annotation( "GOC:TermGenie") "protein localisation to microvillus") @@ -99807,7 +97557,6 @@ EquivalentClasses( ObjectIntersection AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000064") Annotation( "PMID:18667152") "Any cytoplasm that is part of a axon.") AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/14472"^^xsd:anyURI) -AnnotationAssertion( "sl") AnnotationAssertion( "2015-04-06T18:13:14Z") AnnotationAssertion( "axoplasm") AnnotationAssertion( "cellular_component") @@ -99819,7 +97568,6 @@ SubClassOf( ObjectSomeValuesFrom( (response to vasopressin) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000071") Annotation( "PMID:22811487") "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a vasopressin stimulus.") -AnnotationAssertion( "sl") AnnotationAssertion( "2015-04-06T19:39:42Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:1904116") @@ -99829,7 +97577,6 @@ EquivalentClasses( ObjectIntersection # Class: (cellular response to vasopressin) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000071") Annotation( "PMID:22811487") "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a vasopressin stimulus.") -AnnotationAssertion( "sl") AnnotationAssertion( "2015-04-06T19:39:48Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:1904117") @@ -99839,7 +97586,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of otic vesicle morphogenesis) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000058") Annotation( "PMID:25677106") "Any process that modulates the frequency, rate or extent of otic vesicle morphogenesis.") -AnnotationAssertion( "pga") AnnotationAssertion( "2015-04-07T14:00:56Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:1904118") @@ -99849,7 +97595,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of otic vesicle morphogenesis) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000058") Annotation( "PMID:25677106") "Any process that stops, prevents or reduces the frequency, rate or extent of otic vesicle morphogenesis.") -AnnotationAssertion( "pga") AnnotationAssertion( "2015-04-07T14:01:02Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of otic vesicle morphogenesis") AnnotationAssertion(Annotation( "GOC:TermGenie") "down-regulation of otic vesicle morphogenesis") @@ -99863,7 +97608,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of otic vesicle morphogenesis) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000058") Annotation( "PMID:25677106") "Any process that activates or increases the frequency, rate or extent of otic vesicle morphogenesis.") -AnnotationAssertion( "pga") AnnotationAssertion( "2015-04-07T14:01:08Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "up regulation of otic vesicle morphogenesis") AnnotationAssertion(Annotation( "GOC:TermGenie") "up-regulation of otic vesicle morphogenesis") @@ -99877,7 +97621,6 @@ EquivalentClasses( ObjectIntersection # Class: (microglial cell migration) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:TermGenie") Annotation( "GOC:nc") Annotation( "GO_REF:0000091") Annotation( "PMID:19100238") "The orderly movement of a microglial cell from one site to another.") -AnnotationAssertion( "nc") AnnotationAssertion( "2015-04-10T16:04:49Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:1904124") @@ -99887,7 +97630,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of microglial cell migration) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:TermGenie") Annotation( "GOC:nc") Annotation( "GO_REF:0000058") Annotation( "PMID:19100238") "Any process that modulates the frequency, rate or extent of microglial cell migration.") -AnnotationAssertion( "nc") AnnotationAssertion( "2015-04-13T09:06:57Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:1904139") @@ -99897,7 +97639,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of microglial cell migration) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:TermGenie") Annotation( "GOC:nc") Annotation( "GO_REF:0000058") Annotation( "PMID:19100238") "Any process that stops, prevents or reduces the frequency, rate or extent of microglial cell migration.") -AnnotationAssertion( "nc") AnnotationAssertion( "2015-04-13T09:07:03Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of microglial cell migration") AnnotationAssertion(Annotation( "GOC:TermGenie") "down-regulation of microglial cell migration") @@ -99911,7 +97652,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of microglial cell migration) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:TermGenie") Annotation( "GOC:nc") Annotation( "GO_REF:0000058") Annotation( "PMID:19100238") "Any process that activates or increases the frequency, rate or extent of microglial cell migration.") -AnnotationAssertion( "nc") AnnotationAssertion( "2015-04-13T09:07:11Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "up regulation of microglial cell migration") AnnotationAssertion(Annotation( "GOC:TermGenie") "up-regulation of microglial cell migration") @@ -99925,7 +97665,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of meiotic cell cycle process involved in oocyte maturation) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000058") Annotation( "PMID:22674394") "Any process that stops, prevents or reduces the frequency, rate or extent of meiotic cell cycle process involved in oocyte maturation.") -AnnotationAssertion( "tb") AnnotationAssertion( "2015-04-14T15:59:22Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of meiotic cell cycle process involved in oocyte maturation") AnnotationAssertion(Annotation( "GOC:TermGenie") "down-regulation of meiotic cell cycle process involved in oocyte maturation") @@ -99941,7 +97680,6 @@ SubClassOf( ObjectSomeValuesFrom( (positive regulation of meiotic cell cycle process involved in oocyte maturation) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000058") Annotation( "PMID:22674394") "Any process that activates or increases the frequency, rate or extent of meiotic cell cycle process involved in oocyte maturation.") -AnnotationAssertion( "tb") AnnotationAssertion( "2015-04-14T15:59:28Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "up regulation of meiotic cell cycle process involved in oocyte maturation") AnnotationAssertion(Annotation( "GOC:TermGenie") "up-regulation of meiotic cell cycle process involved in oocyte maturation") @@ -99956,7 +97694,6 @@ SubClassOf( ObjectSomeValuesFrom( (regulation of microglial cell mediated cytotoxicity) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:TermGenie") Annotation( "GOC:nc") Annotation( "GO_REF:0000058") Annotation( "PMID:19100238") "Any process that modulates the frequency, rate or extent of microglial cell mediated cytotoxicity.") -AnnotationAssertion( "nc") AnnotationAssertion( "2015-04-15T08:05:29Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:1904149") @@ -99966,7 +97703,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of microglial cell mediated cytotoxicity) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:TermGenie") Annotation( "GOC:nc") Annotation( "GO_REF:0000058") Annotation( "PMID:19100238") "Any process that stops, prevents or reduces the frequency, rate or extent of microglial cell mediated cytotoxicity.") -AnnotationAssertion( "nc") AnnotationAssertion( "2015-04-15T08:05:35Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of microglial cell mediated cytotoxicity") AnnotationAssertion(Annotation( "GOC:TermGenie") "down-regulation of microglial cell mediated cytotoxicity") @@ -99980,7 +97716,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of microglial cell mediated cytotoxicity) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:TermGenie") Annotation( "GOC:nc") Annotation( "GO_REF:0000058") Annotation( "PMID:19100238") "Any process that activates or increases the frequency, rate or extent of microglial cell mediated cytotoxicity.") -AnnotationAssertion( "nc") AnnotationAssertion( "2015-04-15T08:05:42Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "up regulation of microglial cell mediated cytotoxicity") AnnotationAssertion(Annotation( "GOC:TermGenie") "up-regulation of microglial cell mediated cytotoxicity") @@ -99994,7 +97729,6 @@ EquivalentClasses( ObjectIntersection # Class: (DN2 thymocyte differentiation) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:dph") Annotation( "GO_REF:0000086") Annotation( "PMID:25398325") "The process in which a relatively unspecialized cell acquires the specialized features of a DN2 thymocyte. A DN2 thymocyte is a CD4-,CD8- thymocyte that is also CD44+,CD25-.") -AnnotationAssertion( "dph") AnnotationAssertion( "2015-04-15T12:52:53Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:1904155") @@ -100004,7 +97738,6 @@ EquivalentClasses( ObjectIntersection # Class: (DN3 thymocyte differentiation) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:dph") Annotation( "GO_REF:0000086") Annotation( "PMID:25398325") "The process in which a relatively unspecialized cell acquires the specialized features of a DN3 thymocyte. A DN3 thymocyte is a CD4-,CD8- thymocyte that is also CD44+,CD25+.") -AnnotationAssertion( "dph") AnnotationAssertion( "2015-04-15T12:53:00Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:1904156") @@ -100014,7 +97747,6 @@ EquivalentClasses( ObjectIntersection # Class: (DN4 thymocyte differentiation) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:dph") Annotation( "GO_REF:0000086") Annotation( "PMID:25398325") "The process in which a relatively unspecialized cell acquires the specialized features of a DN4 thymocyte. A DN4 thymocyte is a CD4-,CD8- thymocyte that is also CD44-,CD25-.") -AnnotationAssertion( "dph") AnnotationAssertion( "2015-04-15T12:53:07Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:1904157") @@ -100024,7 +97756,6 @@ EquivalentClasses( ObjectIntersection # Class: (axonemal central apparatus assembly) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:cilia") Annotation( "GOC:krc") Annotation( "GO_REF:0000079") Annotation( "PMID:9295136") "The aggregation, arrangement and bonding together of a set of components to form an axonemal central apparatus.") -AnnotationAssertion( "krc") AnnotationAssertion( "2015-04-16T18:46:11Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "axonemal central apparatus formation") AnnotationAssertion( "biological_process") @@ -100036,7 +97767,6 @@ SubClassOf( ObjectSomeValuesFrom( (regulation of bleb assembly) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:als") Annotation( "GO_REF:0000058") Annotation( "PMID:25651887") "Any process that modulates the frequency, rate or extent of bleb assembly.") -AnnotationAssertion( "als") AnnotationAssertion( "2015-04-23T09:32:19Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "regulation of cell blebbing") AnnotationAssertion( "biological_process") @@ -100047,7 +97777,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of bleb assembly) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:als") Annotation( "GO_REF:0000058") Annotation( "PMID:25651887") "Any process that stops, prevents or reduces the frequency, rate or extent of bleb assembly.") -AnnotationAssertion( "als") AnnotationAssertion( "2015-04-23T09:32:25Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of bleb assembly") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of cell blebbing") @@ -100066,7 +97795,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of bleb assembly) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:als") Annotation( "GO_REF:0000058") Annotation( "PMID:25651887") "Any process that activates or increases the frequency, rate or extent of bleb assembly.") -AnnotationAssertion( "als") AnnotationAssertion( "2015-04-23T09:32:31Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "positive regulation of cell blebbing") AnnotationAssertion(Annotation( "GOC:TermGenie") "up regulation of bleb assembly") @@ -100085,7 +97813,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of adipose tissue development) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000058") Annotation( "PMID:23081848") "Any process that modulates the frequency, rate or extent of adipose tissue development.") -AnnotationAssertion( "sl") AnnotationAssertion( "2015-04-29T20:01:01Z") AnnotationAssertion( "biological_process") AnnotationAssertion(Annotation( "GOC:TermGenie") "regulation of adipogenesis") @@ -100096,7 +97823,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of adipose tissue development) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000058") Annotation( "PMID:23081848") "Any process that stops, prevents or reduces the frequency, rate or extent of adipose tissue development.") -AnnotationAssertion( "sl") AnnotationAssertion( "2015-04-29T20:01:07Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of adipose tissue development") AnnotationAssertion(Annotation( "GOC:TermGenie") "down-regulation of adipose tissue development") @@ -100116,7 +97842,6 @@ SubClassOf( ObjectSomeValuesFrom( (positive regulation of adipose tissue development) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000058") Annotation( "PMID:23081848") "Any process that activates or increases the frequency, rate or extent of adipose tissue development.") -AnnotationAssertion( "sl") AnnotationAssertion( "2015-04-29T20:01:13Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "up regulation of adipose tissue development") AnnotationAssertion(Annotation( "GOC:TermGenie") "up-regulation of adipose tissue development") @@ -100136,7 +97861,6 @@ SubClassOf( ObjectSomeValuesFrom( (regulation of cholangiocyte apoptotic process) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000058") Annotation( "PMID:24498161") "Any process that modulates the frequency, rate or extent of cholangiocyte apoptotic process.") -AnnotationAssertion( "sl") AnnotationAssertion( "2015-05-06T15:25:48Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "regulation of epithelial cell of bile duct apoptotic process") AnnotationAssertion(Annotation( "GOC:TermGenie") "regulation of cholangiocyte apoptosis") @@ -100149,7 +97873,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of cholangiocyte apoptotic process) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000058") Annotation( "PMID:24498161") "Any process that stops, prevents or reduces the frequency, rate or extent of cholangiocyte apoptotic process.") -AnnotationAssertion( "sl") AnnotationAssertion( "2015-05-06T15:25:55Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of cholangiocyte apoptotic process") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of epithelial cell of bile duct apoptotic process") @@ -100178,7 +97901,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of cholangiocyte apoptotic process) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000058") Annotation( "PMID:24498161") "Any process that activates or increases the frequency, rate or extent of cholangiocyte apoptotic process.") -AnnotationAssertion( "sl") AnnotationAssertion( "2015-05-06T15:26:00Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "positive regulation of epithelial cell of bile duct apoptotic process") AnnotationAssertion(Annotation( "GOC:TermGenie") "up regulation of cholangiocyte apoptotic process") @@ -100207,7 +97929,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of granulosa cell proliferation) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000058") Annotation( "PMID:22383759") "Any process that modulates the frequency, rate or extent of granulosa cell proliferation.") -AnnotationAssertion( "sl") AnnotationAssertion( "2015-05-07T17:02:25Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:1904195") @@ -100217,7 +97938,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of granulosa cell proliferation) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000058") Annotation( "PMID:22383759") "Any process that stops, prevents or reduces the frequency, rate or extent of granulosa cell proliferation.") -AnnotationAssertion( "sl") AnnotationAssertion( "2015-05-07T17:02:34Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of granulosa cell proliferation") AnnotationAssertion(Annotation( "GOC:TermGenie") "down-regulation of granulosa cell proliferation") @@ -100231,7 +97951,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of granulosa cell proliferation) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000058") Annotation( "PMID:22383759") "Any process that activates or increases the frequency, rate or extent of granulosa cell proliferation.") -AnnotationAssertion( "sl") AnnotationAssertion( "2015-05-07T17:02:40Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "up regulation of granulosa cell proliferation") AnnotationAssertion(Annotation( "GOC:TermGenie") "up-regulation of granulosa cell proliferation") @@ -100245,7 +97964,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of skeletal muscle hypertrophy) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000058") Annotation( "PMID:23470307") "Any process that modulates the frequency, rate or extent of skeletal muscle hypertrophy.") -AnnotationAssertion( "sl") AnnotationAssertion( "2015-05-08T17:38:13Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:1904204") @@ -100255,7 +97973,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of skeletal muscle hypertrophy) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000058") Annotation( "PMID:23470307") "Any process that stops, prevents or reduces the frequency, rate or extent of skeletal muscle hypertrophy.") -AnnotationAssertion( "sl") AnnotationAssertion( "2015-05-08T17:38:19Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of skeletal muscle hypertrophy") AnnotationAssertion(Annotation( "GOC:TermGenie") "down-regulation of skeletal muscle hypertrophy") @@ -100269,7 +97986,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of skeletal muscle hypertrophy) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000058") Annotation( "PMID:23470307") "Any process that activates or increases the frequency, rate or extent of skeletal muscle hypertrophy.") -AnnotationAssertion( "sl") AnnotationAssertion( "2015-05-08T17:38:25Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "up regulation of skeletal muscle hypertrophy") AnnotationAssertion(Annotation( "GOC:TermGenie") "up-regulation of skeletal muscle hypertrophy") @@ -100283,7 +97999,6 @@ EquivalentClasses( ObjectIntersection # Class: (pericyte cell differentiation) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:dph") Annotation( "GO_REF:0000086") Annotation( "PMID:23868830") "The process in which a relatively unspecialized cell acquires the specialized features of a pericyte cell.") -AnnotationAssertion( "dph") AnnotationAssertion( "2015-05-15T14:50:13Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:1904238") @@ -100293,7 +98008,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of bile acid metabolic process) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:bf") Annotation( "GO_REF:0000058") "Any process that modulates the frequency, rate or extent of bile acid metabolic process.") -AnnotationAssertion( "bf") AnnotationAssertion( "2015-05-20T11:04:28Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "regulation of bile acid metabolism") AnnotationAssertion( "biological_process") @@ -100306,7 +98020,6 @@ SubClassOf( (negative regulation of bile acid metabolic process) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:bf") Annotation( "GO_REF:0000058") "Any process that stops, prevents or reduces the frequency, rate or extent of bile acid metabolic process.") -AnnotationAssertion( "bf") AnnotationAssertion( "2015-05-20T11:04:35Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of bile acid metabolic process") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of bile acid metabolism") @@ -100328,7 +98041,6 @@ SubClassOf( (positive regulation of bile acid metabolic process) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:bf") Annotation( "GO_REF:0000058") "Any process that activates or increases the frequency, rate or extent of bile acid metabolic process.") -AnnotationAssertion( "bf") AnnotationAssertion( "2015-05-20T11:04:40Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "positive regulation of bile acid metabolism") AnnotationAssertion(Annotation( "GOC:TermGenie") "up regulation of bile acid metabolic process") @@ -100350,7 +98062,6 @@ SubClassOf( (regulation of iron ion transmembrane transporter activity) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:TermGenie") Annotation( "GOC:kom") Annotation( "GO_REF:0000059") Annotation( "PMID:15514116") "Any process that modulates the frequency, rate or extent of an iron transmembrane transporter activity.") -AnnotationAssertion( "kom") AnnotationAssertion( "2015-05-20T14:05:00Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "regulation of iron cation channel activity") AnnotationAssertion( "regulation of iron channel activity") @@ -100365,7 +98076,6 @@ SubClassOf( ObjectSomeValuesFrom( (regulation of Schwann cell chemotaxis) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000058") Annotation( "PMID:16203995") "Any process that modulates the frequency, rate or extent of Schwann cell chemotaxis.") -AnnotationAssertion( "sl") AnnotationAssertion( "2015-05-28T17:47:41Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:1904266") @@ -100375,7 +98085,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of Schwann cell chemotaxis) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000058") Annotation( "PMID:16203995") "Any process that stops, prevents or reduces the frequency, rate or extent of Schwann cell chemotaxis.") -AnnotationAssertion( "sl") AnnotationAssertion( "2015-05-28T17:47:48Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of Schwann cell chemotaxis") AnnotationAssertion(Annotation( "GOC:TermGenie") "down-regulation of Schwann cell chemotaxis") @@ -100389,7 +98098,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of Schwann cell chemotaxis) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000058") Annotation( "PMID:16203995") "Any process that activates or increases the frequency, rate or extent of Schwann cell chemotaxis.") -AnnotationAssertion( "sl") AnnotationAssertion( "2015-05-28T17:47:55Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "up regulation of Schwann cell chemotaxis") AnnotationAssertion(Annotation( "GOC:TermGenie") "up-regulation of Schwann cell chemotaxis") @@ -100403,7 +98111,6 @@ EquivalentClasses( ObjectIntersection # Class: (cell leading edge cell cortex) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:kmv") Annotation( "GO_REF:0000064") Annotation( "PMID:25843030") "The cell cortex of the leading edge of a cell.") -AnnotationAssertion( "kmv") AnnotationAssertion( "2015-05-28T19:16:03Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "cell cortex of cell leading edge") AnnotationAssertion(Annotation( "GOC:TermGenie") "cell cortex of front of cell") @@ -100423,7 +98130,6 @@ SubClassOf( (regulation of gastro-intestinal system smooth muscle contraction) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000058") Annotation( "PMID:10821044") "Any process that modulates the frequency, rate or extent of gastro-intestinal system smooth muscle contraction.") -AnnotationAssertion( "sl") AnnotationAssertion( "2015-06-09T23:18:42Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:1904304") @@ -100433,7 +98139,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of gastro-intestinal system smooth muscle contraction) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000058") Annotation( "PMID:10821044") "Any process that stops, prevents or reduces the frequency, rate or extent of gastro-intestinal system smooth muscle contraction.") -AnnotationAssertion( "sl") AnnotationAssertion( "2015-06-09T23:18:48Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of gastro-intestinal system smooth muscle contraction") AnnotationAssertion(Annotation( "GOC:TermGenie") "down-regulation of gastro-intestinal system smooth muscle contraction") @@ -100447,7 +98152,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of gastro-intestinal system smooth muscle contraction) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000058") Annotation( "PMID:10821044") "Any process that activates or increases the frequency, rate or extent of gastro-intestinal system smooth muscle contraction.") -AnnotationAssertion( "sl") AnnotationAssertion( "2015-06-09T23:18:54Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "up regulation of gastro-intestinal system smooth muscle contraction") AnnotationAssertion(Annotation( "GOC:TermGenie") "up-regulation of gastro-intestinal system smooth muscle contraction") @@ -100461,7 +98165,6 @@ EquivalentClasses( ObjectIntersection # Class: (transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000061") Annotation( "PMID:20200227") "Any transmitter-gated ion channel activity that is involved in regulation of postsynaptic membrane potential.") -AnnotationAssertion( "dos") AnnotationAssertion( "2015-06-10T18:02:07Z") AnnotationAssertion( "transmitter-gated ion channel activity involved in regulation of postsynaptic membrane potential") AnnotationAssertion(Annotation( "GOC:TermGenie") "ionotropic neurotransmitter receptor activity involved in regulation of post-synaptic membrane potential") @@ -100475,7 +98178,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of smooth muscle contraction involved in micturition) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000058") Annotation( "PMID:18562635") "Any process that modulates the frequency, rate or extent of smooth muscle contraction involved in micturition.") -AnnotationAssertion( "sl") AnnotationAssertion( "2015-06-10T18:46:11Z") AnnotationAssertion( "biological_process") AnnotationAssertion(Annotation( "GOC:TermGenie") "regulation of smooth muscle contraction involved in urination") @@ -100490,7 +98192,6 @@ SubClassOf( (negative regulation of smooth muscle contraction involved in micturition) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000058") Annotation( "PMID:18562635") "Any process that stops, prevents or reduces the frequency, rate or extent of smooth muscle contraction involved in micturition.") -AnnotationAssertion( "sl") AnnotationAssertion( "2015-06-10T18:46:17Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of smooth muscle contraction involved in micturition") AnnotationAssertion(Annotation( "GOC:TermGenie") "down-regulation of smooth muscle contraction involved in micturition") @@ -100516,7 +98217,6 @@ SubClassOf( (positive regulation of smooth muscle contraction involved in micturition) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000058") Annotation( "PMID:18562635") "Any process that activates or increases the frequency, rate or extent of smooth muscle contraction involved in micturition.") -AnnotationAssertion( "sl") AnnotationAssertion( "2015-06-10T18:46:23Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "up regulation of smooth muscle contraction involved in micturition") AnnotationAssertion(Annotation( "GOC:TermGenie") "up-regulation of smooth muscle contraction involved in micturition") @@ -100542,7 +98242,6 @@ SubClassOf( (regulation of dopaminergic neuron differentiation) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000058") Annotation( "PMID:15522889") "Any process that modulates the frequency, rate or extent of dopaminergic neuron differentiation.") -AnnotationAssertion( "sl") AnnotationAssertion( "2015-06-11T18:06:19Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:1904338") @@ -100552,7 +98251,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of dopaminergic neuron differentiation) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000058") Annotation( "PMID:15522889") "Any process that stops, prevents or reduces the frequency, rate or extent of dopaminergic neuron differentiation.") -AnnotationAssertion( "sl") AnnotationAssertion( "2015-06-11T18:06:25Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of dopaminergic neuron differentiation") AnnotationAssertion(Annotation( "GOC:TermGenie") "down-regulation of dopaminergic neuron differentiation") @@ -100566,7 +98264,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of dopaminergic neuron differentiation) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000058") Annotation( "PMID:15522889") "Any process that activates or increases the frequency, rate or extent of dopaminergic neuron differentiation.") -AnnotationAssertion( "sl") AnnotationAssertion( "2015-06-11T18:06:32Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "up regulation of dopaminergic neuron differentiation") AnnotationAssertion(Annotation( "GOC:TermGenie") "up-regulation of dopaminergic neuron differentiation") @@ -100580,7 +98277,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of colon smooth muscle contraction) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000058") Annotation( "PMID:24170253") "Any process that modulates the frequency, rate or extent of colon smooth muscle contraction.") -AnnotationAssertion( "sl") AnnotationAssertion( "2015-06-11T21:16:58Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:1904341") @@ -100591,7 +98287,6 @@ SubClassOf( ObjectSomeValuesFrom( (negative regulation of colon smooth muscle contraction) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000058") Annotation( "PMID:24170253") "Any process that stops, prevents or reduces the frequency, rate or extent of colon smooth muscle contraction.") -AnnotationAssertion( "sl") AnnotationAssertion( "2015-06-11T21:17:05Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of colon smooth muscle contraction") AnnotationAssertion(Annotation( "GOC:TermGenie") "down-regulation of colon smooth muscle contraction") @@ -100606,7 +98301,6 @@ SubClassOf( ObjectSomeValuesFrom( (positive regulation of colon smooth muscle contraction) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000058") Annotation( "PMID:24170253") "Any process that activates or increases the frequency, rate or extent of colon smooth muscle contraction.") -AnnotationAssertion( "sl") AnnotationAssertion( "2015-06-11T21:17:11Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "up regulation of colon smooth muscle contraction") AnnotationAssertion(Annotation( "GOC:TermGenie") "up-regulation of colon smooth muscle contraction") @@ -100621,7 +98315,6 @@ SubClassOf( ObjectSomeValuesFrom( (regulation of gastric mucosal blood circulation) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000058") Annotation( "PMID:10807413") "Any process that modulates the frequency, rate or extent of gastric mucosal blood circulation.") -AnnotationAssertion( "sl") AnnotationAssertion( "2015-06-11T21:20:31Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "regulation of stomach mucosal blood circulation") AnnotationAssertion( "biological_process") @@ -100632,7 +98325,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of gastric mucosal blood circulation) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000058") Annotation( "PMID:10807413") "Any process that stops, prevents or reduces the frequency, rate or extent of gastric mucosal blood circulation.") -AnnotationAssertion( "sl") AnnotationAssertion( "2015-06-11T21:20:44Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of gastric mucosal blood circulation") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of stomach mucosal blood circulation") @@ -100651,7 +98343,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of gastric mucosal blood circulation) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000058") Annotation( "PMID:10807413") "Any process that activates or increases the frequency, rate or extent of gastric mucosal blood circulation.") -AnnotationAssertion( "sl") AnnotationAssertion( "2015-06-11T21:20:50Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "positive regulation of stomach mucosal blood circulation") AnnotationAssertion(Annotation( "GOC:TermGenie") "up regulation of gastric mucosal blood circulation") @@ -100670,7 +98361,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of small intestine smooth muscle contraction) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000058") Annotation( "PMID:11991626") "Any process that modulates the frequency, rate or extent of small intestine smooth muscle contraction.") -AnnotationAssertion( "sl") AnnotationAssertion( "2015-06-11T21:37:34Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:1904347") @@ -100681,7 +98371,6 @@ SubClassOf( ObjectSomeValuesFrom( (negative regulation of small intestine smooth muscle contraction) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000058") Annotation( "PMID:11991626") "Any process that stops, prevents or reduces the frequency, rate or extent of small intestine smooth muscle contraction.") -AnnotationAssertion( "sl") AnnotationAssertion( "2015-06-11T21:37:40Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of small intestine smooth muscle contraction") AnnotationAssertion(Annotation( "GOC:TermGenie") "down-regulation of small intestine smooth muscle contraction") @@ -100696,7 +98385,6 @@ SubClassOf( ObjectSomeValuesFrom( (positive regulation of small intestine smooth muscle contraction) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000058") Annotation( "PMID:11991626") "Any process that activates or increases the frequency, rate or extent of small intestine smooth muscle contraction.") -AnnotationAssertion( "sl") AnnotationAssertion( "2015-06-11T21:37:46Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "up regulation of small intestine smooth muscle contraction") AnnotationAssertion(Annotation( "GOC:TermGenie") "up-regulation of small intestine smooth muscle contraction") @@ -100711,7 +98399,6 @@ SubClassOf( ObjectSomeValuesFrom( (regulation of protein catabolic process in the vacuole) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:TermGenie") Annotation( "GOC:rl") Annotation( "GO_REF:0000058") Annotation( "PMID:25635054") "Any process that modulates the frequency, rate or extent of protein catabolic process in the vacuole.") -AnnotationAssertion( "rl") AnnotationAssertion( "2015-06-12T09:10:36Z") AnnotationAssertion( "biological_process") AnnotationAssertion(Annotation( "GOC:TermGenie") "regulation of vacuolar protein breakdown") @@ -100725,7 +98412,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of protein catabolic process in the vacuole) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:TermGenie") Annotation( "GOC:rl") Annotation( "GO_REF:0000058") Annotation( "PMID:25635054") "Any process that stops, prevents or reduces the frequency, rate or extent of protein catabolic process in the vacuole.") -AnnotationAssertion( "rl") AnnotationAssertion( "2015-06-12T09:10:42Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of protein catabolic process in the vacuole") AnnotationAssertion(Annotation( "GOC:TermGenie") "down-regulation of protein catabolic process in the vacuole") @@ -100759,7 +98445,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of protein catabolic process in the vacuole) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:TermGenie") Annotation( "GOC:rl") Annotation( "GO_REF:0000058") Annotation( "PMID:25635054") "Any process that activates or increases the frequency, rate or extent of protein catabolic process in the vacuole.") -AnnotationAssertion( "rl") AnnotationAssertion( "2015-06-12T09:10:49Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "up regulation of protein catabolic process in the vacuole") AnnotationAssertion(Annotation( "GOC:TermGenie") "up-regulation of protein catabolic process in the vacuole") @@ -100793,7 +98478,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of calcitonin secretion) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000058") Annotation( "PMID:11278900") "Any process that modulates the frequency, rate or extent of calcitonin secretion.") -AnnotationAssertion( "sl") AnnotationAssertion( "2015-06-15T17:54:52Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:1904362") @@ -100804,7 +98488,6 @@ SubClassOf( (negative regulation of calcitonin secretion) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000058") Annotation( "PMID:11278900") "Any process that stops, prevents or reduces the frequency, rate or extent of calcitonin secretion.") -AnnotationAssertion( "sl") AnnotationAssertion( "2015-06-15T17:54:58Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of calcitonin secretion") AnnotationAssertion(Annotation( "GOC:TermGenie") "down-regulation of calcitonin secretion") @@ -100820,7 +98503,6 @@ SubClassOf( (positive regulation of calcitonin secretion) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000058") Annotation( "PMID:11278900") "Any process that activates or increases the frequency, rate or extent of calcitonin secretion.") -AnnotationAssertion( "sl") AnnotationAssertion( "2015-06-15T17:55:05Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "up regulation of calcitonin secretion") AnnotationAssertion(Annotation( "GOC:TermGenie") "up-regulation of calcitonin secretion") @@ -100836,7 +98518,6 @@ SubClassOf( (regulation of protein localization to cell periphery) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000058") Annotation( "PMID:18216290") "Any process that modulates the frequency, rate or extent of protein localization to cell periphery.") -AnnotationAssertion( "sl") AnnotationAssertion( "2015-06-22T22:09:25Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:1904375") @@ -100846,7 +98527,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of protein localization to cell periphery) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000058") Annotation( "PMID:18216290") "Any process that stops, prevents or reduces the frequency, rate or extent of protein localization to cell periphery.") -AnnotationAssertion( "sl") AnnotationAssertion( "2015-06-22T22:09:32Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of protein localization to cell periphery") AnnotationAssertion(Annotation( "GOC:TermGenie") "down-regulation of protein localization to cell periphery") @@ -100860,7 +98540,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of protein localization to cell periphery) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000058") Annotation( "PMID:18216290") "Any process that activates or increases the frequency, rate or extent of protein localization to cell periphery.") -AnnotationAssertion( "sl") AnnotationAssertion( "2015-06-22T22:09:37Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "up regulation of protein localization to cell periphery") AnnotationAssertion(Annotation( "GOC:TermGenie") "up-regulation of protein localization to cell periphery") @@ -100874,7 +98553,6 @@ EquivalentClasses( ObjectIntersection # Class: (rod bipolar cell differentiation) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000086") Annotation( "PMID:16914133") "The process in which a relatively unspecialized cell acquires the specialized features of a rod bipolar cell.") -AnnotationAssertion( "sl") AnnotationAssertion( "2015-06-23T19:01:11Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:1904389") @@ -100884,7 +98562,6 @@ EquivalentClasses( ObjectIntersection # Class: (cone retinal bipolar cell differentiation) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000086") Annotation( "PMID:24123365") "The process in which a relatively unspecialized cell acquires the specialized features of a cone retinal bipolar cell.") -AnnotationAssertion( "sl") AnnotationAssertion( "2015-06-23T19:01:16Z") AnnotationAssertion(Annotation( "PMID:14745032") "cone bipolar cell differentiation") AnnotationAssertion( "retinal cone bipolar cell differentiation") @@ -100896,7 +98573,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of neuromuscular junction development) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000058") Annotation( "PMID:7722643") "Any process that modulates the frequency, rate or extent of neuromuscular junction development.") -AnnotationAssertion( "sl") AnnotationAssertion( "2015-06-23T19:23:42Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "regulation of neuromuscular junction organization") AnnotationAssertion( "biological_process") @@ -100909,7 +98585,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of neuromuscular junction development) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000058") Annotation( "PMID:7722643") "Any process that stops, prevents or reduces the frequency, rate or extent of neuromuscular junction development.") -AnnotationAssertion( "sl") AnnotationAssertion( "2015-06-23T19:23:48Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of neuromuscular junction development") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of neuromuscular junction organization") @@ -100938,7 +98613,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of neuromuscular junction development) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000058") Annotation( "PMID:7722643") "Any process that activates or increases the frequency, rate or extent of neuromuscular junction development.") -AnnotationAssertion( "sl") AnnotationAssertion( "2015-06-23T19:23:54Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "positive regulation of neuromuscular junction organization") AnnotationAssertion(Annotation( "GOC:TermGenie") "up regulation of neuromuscular junction development") @@ -100967,7 +98641,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of nitric oxide metabolic process) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000058") Annotation( "PMID:11991626") "Any process that stops, prevents or reduces the frequency, rate or extent of nitric oxide metabolic process.") -AnnotationAssertion( "sl") AnnotationAssertion( "2015-06-24T20:56:41Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of nitric oxide metabolic process") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of nitric oxide metabolism") @@ -100986,7 +98659,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of nitric oxide metabolic process) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000058") Annotation( "PMID:11991626") "Any process that activates or increases the frequency, rate or extent of nitric oxide metabolic process.") -AnnotationAssertion( "sl") AnnotationAssertion( "2015-06-24T20:56:47Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "positive regulation of nitric oxide metabolism") AnnotationAssertion(Annotation( "GOC:TermGenie") "up regulation of nitric oxide metabolic process") @@ -101005,7 +98677,6 @@ EquivalentClasses( ObjectIntersection # Class: (melatonin binding) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:mr") Annotation( "GO_REF:0000067") Annotation( "PMID:10379923") "Binding to melatonin.") -AnnotationAssertion( "mr") AnnotationAssertion( "2015-06-25T19:19:53Z") AnnotationAssertion( "molecular_function") AnnotationAssertion( "GO:1904408") @@ -101015,7 +98686,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of secretory granule organization) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000058") Annotation( "PMID:15039777") "Any process that modulates the frequency, rate or extent of secretory granule organization.") -AnnotationAssertion( "sl") AnnotationAssertion( "2015-06-25T19:40:42Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "regulation of secretory granule organisation") AnnotationAssertion( "biological_process") @@ -101027,7 +98697,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of secretory granule organization) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000058") Annotation( "PMID:15039777") "Any process that stops, prevents or reduces the frequency, rate or extent of secretory granule organization.") -AnnotationAssertion( "sl") AnnotationAssertion( "2015-06-25T19:40:49Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of secretory granule organisation") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of secretory granule organization") @@ -101051,7 +98720,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of secretory granule organization) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000058") Annotation( "PMID:15039777") "Any process that activates or increases the frequency, rate or extent of secretory granule organization.") -AnnotationAssertion( "sl") AnnotationAssertion( "2015-06-25T19:40:55Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "positive regulation of secretory granule organisation") AnnotationAssertion(Annotation( "GOC:TermGenie") "up regulation of secretory granule organisation") @@ -101075,7 +98743,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of cardiac ventricle development) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000058") Annotation( "PMID:19590510") "Any process that modulates the frequency, rate or extent of cardiac ventricle development.") -AnnotationAssertion( "sl") AnnotationAssertion( "2015-06-25T19:52:15Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:1904412") @@ -101085,7 +98752,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of cardiac ventricle development) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000058") Annotation( "PMID:19590510") "Any process that stops, prevents or reduces the frequency, rate or extent of cardiac ventricle development.") -AnnotationAssertion( "sl") AnnotationAssertion( "2015-06-25T19:52:21Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of cardiac ventricle development") AnnotationAssertion(Annotation( "GOC:TermGenie") "down-regulation of cardiac ventricle development") @@ -101100,7 +98766,6 @@ SubClassOf( ObjectSomeValuesFrom( (positive regulation of cardiac ventricle development) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000058") Annotation( "PMID:19590510") "Any process that activates or increases the frequency, rate or extent of cardiac ventricle development.") -AnnotationAssertion( "sl") AnnotationAssertion( "2015-06-25T19:52:27Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "up regulation of cardiac ventricle development") AnnotationAssertion(Annotation( "GOC:TermGenie") "up-regulation of cardiac ventricle development") @@ -101115,7 +98780,6 @@ SubClassOf( ObjectSomeValuesFrom( (positive regulation of calcium ion transmembrane transport) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000058") Annotation( "PMID:22910094") "Any process that activates or increases the frequency, rate or extent of calcium ion transmembrane transport.") -AnnotationAssertion( "sl") AnnotationAssertion( "2015-07-02T20:44:25Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "positive regulation of calcium ion membrane transport") AnnotationAssertion(Annotation( "GOC:TermGenie") "positive regulation of transmembrane calcium transport") @@ -101139,7 +98803,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of iron ion import across plasma membrane) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:TermGenie") Annotation( "GOC:kom") Annotation( "GO_REF:0000058") Annotation( "PMID:18353247") "Any process that modulates the frequency, rate or extent of iron ions import across plasma membrane.") -AnnotationAssertion( "rl") AnnotationAssertion( "2015-03-04T14:37:36Z") AnnotationAssertion( "biological_process") AnnotationAssertion(Annotation( "GOC:TermGenie") "regulation of ferrous ion import into cell") @@ -101153,7 +98816,6 @@ SubClassOf( ObjectSomeValuesFrom( (negative regulation of iron ion import across plasma membrane) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:TermGenie") Annotation( "GOC:kom") Annotation( "GO_REF:0000058") Annotation( "PMID:18353247") "Any process that stops, prevents or reduces the frequency, rate or extent of iron ions import across plasma membrane.") -AnnotationAssertion( "rl") AnnotationAssertion( "2015-07-06T13:49:58Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "inhibition of ferrous ion import into cell") AnnotationAssertion(Annotation( "GOC:TermGenie") "inhibition of ferrous iron import across plasma membrane") @@ -101174,7 +98836,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of iron ion import across plasma membrane) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:TermGenie") Annotation( "GOC:kom") Annotation( "GO_REF:0000058") Annotation( "PMID:18353247") "Any process that activates or increases the frequency, rate or extent of iron ions import across plasma membrane.") -AnnotationAssertion( "rl") AnnotationAssertion( "2015-07-06T13:50:04Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "activation of ferrous ion import into cell") AnnotationAssertion(Annotation( "GOC:TermGenie") "activation of ferrous iron import across plasma membrane") @@ -101195,7 +98856,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of neuronal action potential) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000058") Annotation( "PMID:25126967") "Any process that stops, prevents or reduces the frequency, rate or extent of neuronal action potential.") -AnnotationAssertion( "sl") AnnotationAssertion( "2015-07-09T18:02:40Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of neuronal action potential") AnnotationAssertion(Annotation( "GOC:TermGenie") "down-regulation of neuronal action potential") @@ -101215,7 +98875,6 @@ SubClassOf( ObjectSomeValuesFrom( (positive regulation of neuronal action potential) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000058") Annotation( "PMID:25126967") "Any process that activates or increases the frequency, rate or extent of neuronal action potential.") -AnnotationAssertion( "sl") AnnotationAssertion( "2015-07-09T18:02:46Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "up regulation of neuronal action potential") AnnotationAssertion(Annotation( "GOC:TermGenie") "up-regulation of neuronal action potential") @@ -101235,7 +98894,6 @@ SubClassOf( ObjectSomeValuesFrom( (cloacal gland development) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:mr") Annotation( "GO_REF:0000094") Annotation( "PMID:18805421") "The process whose specific outcome is the progression of a cloacal gland over time, from its formation to the mature structure.") -AnnotationAssertion( "mr") AnnotationAssertion( "2015-07-15T22:14:39Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:1904484") @@ -101245,7 +98903,6 @@ EquivalentClasses( ObjectIntersection # Class: (protein localization to ciliary transition zone) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:kmv") Annotation( "GO_REF:0000087") Annotation( "PMID:21422230") "A process in which a protein is transported to, or maintained in, a location within a ciliary transition zone.") -AnnotationAssertion( "kmv") AnnotationAssertion( "2015-07-17T20:43:21Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "protein localisation in ciliary transition zone") AnnotationAssertion(Annotation( "GOC:TermGenie") "protein localisation to ciliary transition zone") @@ -101258,7 +98915,6 @@ EquivalentClasses( ObjectIntersection # Class: (myofibroblast cell apoptotic process) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000085") Annotation( "PMID:23026405") "Any apoptotic process in a myofibroblast cell.") -AnnotationAssertion( "sl") AnnotationAssertion( "2015-07-28T18:29:08Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "MFB apoptotic process") AnnotationAssertion(Annotation( "GOC:TermGenie") "MFB apoptosis") @@ -101272,7 +98928,6 @@ SubClassOf( (regulation of myofibroblast cell apoptotic process) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000058") Annotation( "PMID:26119034") "Any process that modulates the frequency, rate or extent of myofibroblast cell apoptotic process.") -AnnotationAssertion( "sl") AnnotationAssertion( "2015-07-29T15:52:14Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "regulation of MFB apoptotic process") AnnotationAssertion(Annotation( "GOC:TermGenie") "regulation of MFB apoptosis") @@ -101285,7 +98940,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of myofibroblast cell apoptotic process) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000058") Annotation( "PMID:26119034") "Any process that stops, prevents or reduces the frequency, rate or extent of myofibroblast cell apoptotic process.") -AnnotationAssertion( "sl") AnnotationAssertion( "2015-07-29T15:52:20Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of MFB apoptotic process") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of myofibroblast cell apoptotic process") @@ -101314,7 +98968,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of myofibroblast cell apoptotic process) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000058") Annotation( "PMID:26119034") "Any process that activates or increases the frequency, rate or extent of myofibroblast cell apoptotic process.") -AnnotationAssertion( "sl") AnnotationAssertion( "2015-07-29T15:52:26Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "positive regulation of MFB apoptotic process") AnnotationAssertion(Annotation( "GOC:TermGenie") "up regulation of MFB apoptotic process") @@ -101343,7 +98996,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of microtubule binding) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:als") Annotation( "GO_REF:0000059") Annotation( "PMID:24520051") "Any process that modulates the frequency, rate or extent of microtubule binding.") -AnnotationAssertion( "als") AnnotationAssertion( "2015-07-30T10:32:13Z") AnnotationAssertion( "biological_process") AnnotationAssertion(Annotation( "GOC:TermGenie") "regulation of microtubule severing activity") @@ -101356,7 +99008,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of microtubule binding) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:als") Annotation( "GO_REF:0000059") Annotation( "PMID:24520051") "Any process that stops, prevents or reduces the frequency, rate or extent of microtubule binding.") -AnnotationAssertion( "als") AnnotationAssertion( "2015-07-30T10:32:29Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of microtubule binding") AnnotationAssertion(Annotation( "GOC:TermGenie") "down-regulation of microtubule binding") @@ -101381,7 +99032,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of microtubule binding) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:als") Annotation( "GO_REF:0000059") Annotation( "PMID:24520051") "Any process that activates or increases the frequency, rate or extent of microtubule binding.") -AnnotationAssertion( "als") AnnotationAssertion( "2015-07-30T10:32:36Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "up regulation of microtubule binding") AnnotationAssertion(Annotation( "GOC:TermGenie") "up-regulation of microtubule binding") @@ -101406,7 +99056,6 @@ EquivalentClasses( ObjectIntersection # Class: (response to glycoprotein) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000071") Annotation( "PMID:14597422") "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a glycoprotein stimulus.") -AnnotationAssertion( "sl") AnnotationAssertion( "2015-08-20T16:46:24Z") AnnotationAssertion( "response to glycoproteins") AnnotationAssertion( "biological_process") @@ -101417,7 +99066,6 @@ EquivalentClasses( ObjectIntersection # Class: (cellular response to glycoprotein) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000071") Annotation( "PMID:14597422") "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a glycoprotein stimulus.") -AnnotationAssertion( "sl") AnnotationAssertion( "2015-08-20T16:46:30Z") AnnotationAssertion( "cellular response to glycoproteins") AnnotationAssertion( "biological_process") @@ -101429,7 +99077,6 @@ EquivalentClasses( ObjectIntersection AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:bhm") Annotation( "GO_REF:0000088") Annotation( "PMID:16116092") "A protein complex which is capable of serotonin-activated cation-selective channel activity. Mainly found in pre- and postsynaptic membranes of the brain and gastrointestinal tract. Depending on its location it transports Ca2+, Mg2+, Na+ or K+. It is always a pentamer, containing at least the 5HT3A subunit forming 5HT3A homopentamers or 5HT3A/B heteropentamers. In human, 5HT3A/C, A/D and A/E heteropentamers also exist.") AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/12942"^^xsd:anyURI) -AnnotationAssertion( "bhm") AnnotationAssertion( "2015-08-26T13:19:49Z") AnnotationAssertion( "serotonin receptor complex") AnnotationAssertion( "5-HT-3 receptor complex") @@ -101446,7 +99093,6 @@ SubClassOf( ObjectSomeValuesFrom( (fat cell apoptotic process) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000085") Annotation( "PMID:17024416") "Any apoptotic process in a fat cell.") -AnnotationAssertion( "sl") AnnotationAssertion( "2015-08-27T18:13:06Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "adipocyte apoptotic process") AnnotationAssertion(Annotation( "GOC:TermGenie") "adipose cell apoptotic process") @@ -101462,7 +99108,6 @@ SubClassOf( (regulation of glycine secretion, neurotransmission) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000058") Annotation( "PMID:22988142") "Any process that modulates the frequency, rate or extent of glycine secretion, neurotransmission.") -AnnotationAssertion( "hjd") AnnotationAssertion( "2015-08-27T20:03:38Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:1904624") @@ -101473,7 +99118,6 @@ SubClassOf( ObjectSomeValuesFrom( (negative regulation of glycine secretion, neurotransmission) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000058") Annotation( "PMID:22988142") "Any process that stops, prevents or reduces the frequency, rate or extent of glycine secretion, neurotransmission.") -AnnotationAssertion( "hjd") AnnotationAssertion( "2015-08-27T20:03:44Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of glycine secretion, neurotransmission") AnnotationAssertion(Annotation( "GOC:TermGenie") "down-regulation of glycine secretion, neurotransmission") @@ -101488,7 +99132,6 @@ SubClassOf( ObjectSomeValuesFrom( (positive regulation of glycine secretion, neurotransmission) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000058") Annotation( "PMID:22988142") "Any process that activates or increases the frequency, rate or extent of glycine secretion, neurotransmission.") -AnnotationAssertion( "hjd") AnnotationAssertion( "2015-08-27T20:03:49Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "up regulation of glycine secretion, neurotransmission") AnnotationAssertion(Annotation( "GOC:TermGenie") "up-regulation of glycine secretion, neurotransmission") @@ -101504,7 +99147,6 @@ SubClassOf( ObjectSomeValuesFrom( "GOC:TermGenie") Annotation( "GO_REF:0000058") Annotation( "PMID:23692924") "Any process that modulates the frequency, rate or extent of glomerular visceral epithelial cell apoptotic process.") AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/23000"^^xsd:anyURI) -AnnotationAssertion( "sl") AnnotationAssertion( "2015-08-28T14:14:44Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "regulation of glomerular podocyte apoptotic process") AnnotationAssertion( "regulation of glomerular visceral epithelial cell apoptotic process") @@ -101520,7 +99162,6 @@ EquivalentClasses( ObjectIntersection AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000058") Annotation( "PMID:23692924") "Any process that stops, prevents or reduces the frequency, rate or extent of glomerular visceral epithelial cell apoptotic process.") AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/23000"^^xsd:anyURI) -AnnotationAssertion( "sl") AnnotationAssertion( "2015-08-28T14:14:50Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of glomerular podocyte apoptotic process") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of glomerular visceral epithelial cell apoptotic process") @@ -101560,7 +99201,6 @@ EquivalentClasses( ObjectIntersection AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000058") Annotation( "PMID:23692924") "Any process that activates or increases the frequency, rate or extent of glomerular visceral epithelial cell apoptotic process.") AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/23000"^^xsd:anyURI) -AnnotationAssertion( "sl") AnnotationAssertion( "2015-08-28T14:14:56Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "positive regulation of glomerular podocyte apoptotic process") AnnotationAssertion( "positive regulation of glomerular visceral epithelial cell apoptotic process") @@ -101599,7 +99239,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of fat cell apoptotic process) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000058") Annotation( "PMID:17024416") "Any process that modulates the frequency, rate or extent of fat cell apoptotic process.") -AnnotationAssertion( "sl") AnnotationAssertion( "2015-08-31T20:59:28Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "regulation of adipocyte apoptotic process") AnnotationAssertion(Annotation( "GOC:TermGenie") "regulation of adipose cell apoptotic process") @@ -101614,7 +99253,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of fat cell apoptotic process) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000058") Annotation( "PMID:17024416") "Any process that stops, prevents or reduces the frequency, rate or extent of fat cell apoptotic process.") -AnnotationAssertion( "sl") AnnotationAssertion( "2015-08-31T20:59:34Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of adipocyte apoptotic process") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of adipose cell apoptotic process") @@ -101653,7 +99291,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of fat cell apoptotic process) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000058") Annotation( "PMID:17024416") "Any process that activates or increases the frequency, rate or extent of fat cell apoptotic process.") -AnnotationAssertion( "sl") AnnotationAssertion( "2015-08-31T20:59:40Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "positive regulation of adipocyte apoptotic process") AnnotationAssertion(Annotation( "GOC:TermGenie") "positive regulation of adipose cell apoptotic process") @@ -101692,7 +99329,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of lung alveolus development) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000058") Annotation( "PMID:23962064") "Any process that modulates the frequency, rate or extent of lung alveolus development.") -AnnotationAssertion( "sl") AnnotationAssertion( "2015-09-03T22:44:44Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "regulation of alveolarization") AnnotationAssertion(Annotation( "GOC:TermGenie") "regulation of alveologenesis") @@ -101704,7 +99340,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of lung alveolus development) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000058") Annotation( "PMID:23962064") "Any process that stops, prevents or reduces the frequency, rate or extent of lung alveolus development.") -AnnotationAssertion( "sl") AnnotationAssertion( "2015-09-03T22:44:50Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of alveolarization") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of alveologenesis") @@ -101729,7 +99364,6 @@ SubClassOf( ObjectSomeValuesFrom( (positive regulation of lung alveolus development) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000058") Annotation( "PMID:23962064") "Any process that activates or increases the frequency, rate or extent of lung alveolus development.") -AnnotationAssertion( "sl") AnnotationAssertion( "2015-09-03T22:44:56Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "positive regulation of alveolarization") AnnotationAssertion(Annotation( "GOC:TermGenie") "positive regulation of alveologenesis") @@ -101754,7 +99388,6 @@ SubClassOf( ObjectSomeValuesFrom( (D-glucose transmembrane transport) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000069") Annotation( "PMID:9090050") "The process in which D-glucose is transported across a membrane.") -AnnotationAssertion( "vw") AnnotationAssertion( "2015-09-04T17:20:16Z") AnnotationAssertion( "glucose transmembrane transport") AnnotationAssertion( "biological_process") @@ -101766,7 +99399,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of cell differentiation involved in stem cell population maintenance) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:BHF_miRNA") Annotation( "GOC:TermGenie") Annotation( "GOC:rph") Annotation( "GO_REF:0000060") Annotation( "PMID:19409607") "Any negative regulation of cell differentiation that is involved in stem cell population maintenance.") -AnnotationAssertion( "tb") AnnotationAssertion( "2015-09-12T00:46:08Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of cell differentiation involved in stem cell population maintenance") AnnotationAssertion(Annotation( "GOC:TermGenie") "down-regulation of cell differentiation involved in stem cell population maintenance") @@ -101785,7 +99417,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of somatic stem cell population maintenance) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:BHF_miRNA") Annotation( "GOC:TermGenie") Annotation( "GOC:rph") Annotation( "GO_REF:0000058") Annotation( "PMID:19409607") "Any process that modulates the frequency, rate or extent of somatic stem cell population maintenance.") -AnnotationAssertion( "rph") AnnotationAssertion( "2015-09-14T08:40:19Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:1904672") @@ -101795,7 +99426,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of somatic stem cell population maintenance) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:BHF_miRNA") Annotation( "GOC:TermGenie") Annotation( "GOC:rph") Annotation( "GO_REF:0000058") Annotation( "PMID:19409607") "Any process that stops, prevents or reduces the frequency, rate or extent of somatic stem cell population maintenance.") -AnnotationAssertion( "rph") AnnotationAssertion( "2015-09-14T08:40:25Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of somatic stem cell population maintenance") AnnotationAssertion(Annotation( "GOC:TermGenie") "down-regulation of somatic stem cell population maintenance") @@ -101809,7 +99439,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of somatic stem cell population maintenance) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:BHF_miRNA") Annotation( "GOC:TermGenie") Annotation( "GOC:rph") Annotation( "GO_REF:0000058") Annotation( "PMID:19409607") "Any process that activates or increases the frequency, rate or extent of somatic stem cell population maintenance.") -AnnotationAssertion( "rph") AnnotationAssertion( "2015-09-14T08:40:32Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "up regulation of somatic stem cell population maintenance") AnnotationAssertion(Annotation( "GOC:TermGenie") "up-regulation of somatic stem cell population maintenance") @@ -101823,7 +99452,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of somatic stem cell division) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:BHF_miRNA") Annotation( "GOC:TermGenie") Annotation( "GOC:rph") Annotation( "GO_REF:0000058") Annotation( "PMID:19409607") "Any process that modulates the frequency, rate or extent of somatic stem cell division.") -AnnotationAssertion( "rph") AnnotationAssertion( "2015-09-14T08:47:22Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "regulation of somatic stem cell renewal") AnnotationAssertion( "biological_process") @@ -101834,7 +99462,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of somatic stem cell division) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:BHF_miRNA") Annotation( "GOC:TermGenie") Annotation( "GOC:rph") Annotation( "GO_REF:0000058") Annotation( "PMID:19409607") "Any process that stops, prevents or reduces the frequency, rate or extent of somatic stem cell division.") -AnnotationAssertion( "rph") AnnotationAssertion( "2015-09-14T08:47:28Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of somatic stem cell division") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of somatic stem cell renewal") @@ -101853,7 +99480,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of somatic stem cell division) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:BHF_miRNA") Annotation( "GOC:TermGenie") Annotation( "GOC:rph") Annotation( "GO_REF:0000058") Annotation( "PMID:19409607") "Any process that activates or increases the frequency, rate or extent of somatic stem cell division.") -AnnotationAssertion( "rph") AnnotationAssertion( "2015-09-14T08:47:34Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "positive regulation of somatic stem cell renewal") AnnotationAssertion(Annotation( "GOC:TermGenie") "up regulation of somatic stem cell division") @@ -101872,7 +99498,6 @@ EquivalentClasses( ObjectIntersection # Class: (peptide transmembrane transporter activity) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:vw") Annotation( "GO_REF:0000070") "Enables the transfer of a peptide from one side of a membrane to the other.") -AnnotationAssertion( "tb") AnnotationAssertion( "2015-09-22T18:50:41Z") AnnotationAssertion(Annotation(rdfs:label "Glutathione is taken up by the bacterium") "Reactome:R-HSA-1500817") AnnotationAssertion( "molecular_function") @@ -101886,7 +99511,6 @@ EquivalentClasses( ObjectIntersection AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000058") Annotation( "PMID:12242291") "Any process that modulates the frequency, rate or extent of cytoplasmic translational initiation.") AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/21560"^^xsd:anyURI) -AnnotationAssertion( "dos") AnnotationAssertion( "2015-09-25T14:39:38Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:1904688") @@ -101897,7 +99521,6 @@ SubClassOf( ObjectSomeValuesFrom( (negative regulation of cytoplasmic translational initiation) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000058") Annotation( "PMID:12242291") "Any process that stops, prevents or reduces the frequency, rate or extent of cytoplasmic translational initiation.") -AnnotationAssertion( "dos") AnnotationAssertion( "2015-09-25T14:39:44Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of cytoplasmic translational initiation") AnnotationAssertion(Annotation( "GOC:TermGenie") "down-regulation of cytoplasmic translational initiation") @@ -101911,7 +99534,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of cytoplasmic translational initiation) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000058") Annotation( "PMID:12242291") "Any process that activates or increases the frequency, rate or extent of cytoplasmic translational initiation.") -AnnotationAssertion( "dos") AnnotationAssertion( "2015-09-25T14:39:50Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "up regulation of cytoplasmic translational initiation") AnnotationAssertion(Annotation( "GOC:TermGenie") "up-regulation of cytoplasmic translational initiation") @@ -101925,7 +99547,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of type B pancreatic cell proliferation) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000058") Annotation( "PMID:24055447") "Any process that stops, prevents or reduces the frequency, rate or extent of type B pancreatic cell proliferation.") -AnnotationAssertion( "sl") AnnotationAssertion( "2015-09-25T15:23:38Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of pancreatic B cell proliferation") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of pancreatic beta cell proliferation") @@ -101949,7 +99570,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of type B pancreatic cell proliferation) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000058") Annotation( "PMID:24055447") "Any process that activates or increases the frequency, rate or extent of type B pancreatic cell proliferation.") -AnnotationAssertion( "sl") AnnotationAssertion( "2015-09-25T15:23:44Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "positive regulation of pancreatic B cell proliferation") AnnotationAssertion(Annotation( "GOC:TermGenie") "positive regulation of pancreatic beta cell proliferation") @@ -101973,7 +99593,6 @@ EquivalentClasses( ObjectIntersection # Class: (midbrain morphogenesis) AnnotationAssertion(Annotation( "GOC:PARL") Annotation( "GOC:TermGenie") Annotation( "GOC:bf") Annotation( "GO_REF:0000083") Annotation( "PMID:21347250") "The developmental process by which a midbrain is generated and organized.") -AnnotationAssertion( "bf") AnnotationAssertion( "2015-09-29T09:15:28Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "MB morphogenesis") AnnotationAssertion( "biological_process") @@ -101987,7 +99606,6 @@ SubClassOf( ObjectSomeValuesFrom( (regulation of acinar cell proliferation) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000058") Annotation( "PMID:9788538") "Any process that modulates the frequency, rate or extent of acinar cell proliferation.") -AnnotationAssertion( "sl") AnnotationAssertion( "2015-09-30T15:19:50Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "regulation of acinic cell proliferation") AnnotationAssertion(Annotation( "GOC:TermGenie") "regulation of acinous cell proliferation") @@ -101999,7 +99617,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of acinar cell proliferation) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000058") Annotation( "PMID:9788538") "Any process that stops, prevents or reduces the frequency, rate or extent of acinar cell proliferation.") -AnnotationAssertion( "sl") AnnotationAssertion( "2015-09-30T15:19:57Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of acinar cell proliferation") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of acinic cell proliferation") @@ -102023,7 +99640,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of acinar cell proliferation) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000058") Annotation( "PMID:9788538") "Any process that activates or increases the frequency, rate or extent of acinar cell proliferation.") -AnnotationAssertion( "sl") AnnotationAssertion( "2015-09-30T15:20:03Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "positive regulation of acinic cell proliferation") AnnotationAssertion(Annotation( "GOC:TermGenie") "positive regulation of acinous cell proliferation") @@ -102047,7 +99663,6 @@ EquivalentClasses( ObjectIntersection # Class: (granulosa cell apoptotic process) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000085") Annotation( "PMID:19208546") "Any apoptotic process in a granulosa cell.") -AnnotationAssertion( "sl") AnnotationAssertion( "2015-09-30T21:29:54Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "granulosa cell of ovary apoptotic process") AnnotationAssertion(Annotation( "GOC:TermGenie") "granulosa cell apoptosis") @@ -102060,7 +99675,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of vascular associated smooth muscle cell proliferation) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000058") Annotation( "PMID:23246467") "Any process that modulates the frequency, rate or extent of vascular smooth muscle cell proliferation.") -AnnotationAssertion( "sl") AnnotationAssertion( "2015-10-01T16:05:20Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "regulation of VSMC proliferation") AnnotationAssertion( "regulation of vascular smooth muscle cell proliferation") @@ -102072,7 +99686,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of vascular associated smooth muscle cell proliferation) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000058") Annotation( "PMID:23246467") "Any process that stops, prevents or reduces the frequency, rate or extent of vascular smooth muscle cell proliferation.") -AnnotationAssertion( "sl") AnnotationAssertion( "2015-10-01T16:05:26Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of VSMC proliferation") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of vascular smooth muscle cell proliferation") @@ -102092,7 +99705,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of vascular associated smooth muscle cell proliferation) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000058") Annotation( "PMID:23246467") "Any process that activates or increases the frequency, rate or extent of vascular smooth muscle cell proliferation.") -AnnotationAssertion( "sl") AnnotationAssertion( "2015-10-01T16:05:32Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "positive regulation of VSMC proliferation") AnnotationAssertion( "positive regulation of vascular smooth muscle cell proliferation") @@ -102112,7 +99724,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of granulosa cell apoptotic process) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000058") Annotation( "PMID:19208546") "Any process that modulates the frequency, rate or extent of granulosa cell apoptotic process.") -AnnotationAssertion( "sl") AnnotationAssertion( "2015-10-01T16:09:38Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "regulation of granulosa cell of ovary apoptotic process") AnnotationAssertion(Annotation( "GOC:TermGenie") "regulation of granulosa cell apoptosis") @@ -102125,7 +99736,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of granulosa cell apoptotic process) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000058") Annotation( "PMID:19208546") "Any process that stops, prevents or reduces the frequency, rate or extent of granulosa cell apoptotic process.") -AnnotationAssertion( "sl") AnnotationAssertion( "2015-10-01T16:09:45Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of granulosa cell apoptotic process") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of granulosa cell of ovary apoptotic process") @@ -102154,7 +99764,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of granulosa cell apoptotic process) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000058") Annotation( "PMID:19208546") "Any process that activates or increases the frequency, rate or extent of granulosa cell apoptotic process.") -AnnotationAssertion( "sl") AnnotationAssertion( "2015-10-01T16:09:51Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "positive regulation of granulosa cell of ovary apoptotic process") AnnotationAssertion(Annotation( "GOC:TermGenie") "up regulation of granulosa cell apoptotic process") @@ -102183,7 +99792,6 @@ EquivalentClasses( ObjectIntersection # Class: (tertiary granule lumen) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000064") Annotation( "PMID:23650620") "Any membrane-enclosed lumen that is part of a tertiary granule.") -AnnotationAssertion( "mec") AnnotationAssertion( "2015-10-12T12:53:10Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "membrane-enclosed lumen of gelatinase granule") AnnotationAssertion(Annotation( "GOC:TermGenie") "membrane-enclosed lumen of tertiary granule") @@ -102197,7 +99805,6 @@ EquivalentClasses( ObjectIntersection # Class: (vascular associated smooth muscle cell migration) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:BHF_miRNA") Annotation( "GOC:TermGenie") Annotation( "GOC:rph") Annotation( "GO_REF:0000091") Annotation( "PMID:20693317") "The orderly movement of a vascular associated smooth muscle cell from one site to another.") -AnnotationAssertion( "rph") AnnotationAssertion( "2015-10-15T09:56:00Z") AnnotationAssertion( "vascular smooth muscle cell migration") AnnotationAssertion( "biological_process") @@ -102208,7 +99815,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of apoptotic process involved in development) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000058") Annotation( "PMID:22801495") "Any process that stops, prevents or reduces the frequency, rate or extent of apoptotic process involved in development.") -AnnotationAssertion( "es") AnnotationAssertion( "2015-10-19T14:12:27Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of apoptotic cell death involved in anatomical structure development") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of apoptotic cell death involved in development of an anatomical structure") @@ -102364,7 +99970,6 @@ SubClassOf( ObjectSomeValuesFrom( (positive regulation of apoptotic process involved in development) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000058") Annotation( "PMID:22801495") "Any process that activates or increases the frequency, rate or extent of apoptotic process involved in development.") -AnnotationAssertion( "es") AnnotationAssertion( "2015-10-19T14:12:34Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "positive regulation of apoptotic cell death involved in anatomical structure development") AnnotationAssertion(Annotation( "GOC:TermGenie") "positive regulation of apoptotic cell death involved in development of an anatomical structure") @@ -102520,7 +100125,6 @@ SubClassOf( ObjectSomeValuesFrom( (regulation of apoptotic process involved in development) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000058") Annotation( "PMID:22801495") "Any process that modulates the frequency, rate or extent of apoptotic process involved in development.") -AnnotationAssertion( "es") AnnotationAssertion( "2015-10-19T15:02:28Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "regulation of apoptotic cell death involved in anatomical structure development") AnnotationAssertion(Annotation( "GOC:TermGenie") "regulation of apoptotic cell death involved in development of an anatomical structure") @@ -102560,7 +100164,6 @@ SubClassOf( ObjectSomeValuesFrom( (regulation of protein localization to nucleolus) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:BHF_telomere") Annotation( "GOC:TermGenie") Annotation( "GOC:nc") Annotation( "GO_REF:0000058") Annotation( "PMID:24415760") "Any process that modulates the frequency, rate or extent of protein localization to nucleolus.") -AnnotationAssertion( "nc") AnnotationAssertion( "2015-10-19T15:16:17Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "regulation of protein localisation in nucleolus") AnnotationAssertion(Annotation( "GOC:TermGenie") "regulation of protein localisation to nucleolus") @@ -102573,7 +100176,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of protein localization to nucleolus) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:BHF_telomere") Annotation( "GOC:TermGenie") Annotation( "GOC:nc") Annotation( "GO_REF:0000058") Annotation( "PMID:24415760") "Any process that stops, prevents or reduces the frequency, rate or extent of protein localization to nucleolus.") -AnnotationAssertion( "nc") AnnotationAssertion( "2015-10-19T15:16:24Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of protein localisation in nucleolus") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of protein localisation to nucleolus") @@ -102602,7 +100204,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of protein localization to nucleolus) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:BHF_telomere") Annotation( "GOC:TermGenie") Annotation( "GOC:nc") Annotation( "GO_REF:0000058") Annotation( "PMID:24415760") "Any process that activates or increases the frequency, rate or extent of protein localization to nucleolus.") -AnnotationAssertion( "nc") AnnotationAssertion( "2015-10-19T15:16:30Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "positive regulation of protein localisation in nucleolus") AnnotationAssertion(Annotation( "GOC:TermGenie") "positive regulation of protein localisation to nucleolus") @@ -102631,7 +100232,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of vascular associated smooth muscle cell migration) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:BHF_miRNA") Annotation( "GOC:TermGenie") Annotation( "GOC:rph") Annotation( "GO_REF:0000058") Annotation( "PMID:20693317") "Any process that modulates the frequency, rate or extent of vascular associated smooth muscle cell migration.") -AnnotationAssertion( "rph") AnnotationAssertion( "2015-10-19T15:49:52Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "regulation of vascular smooth muscle cell migration") AnnotationAssertion( "biological_process") @@ -102642,7 +100242,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of vascular associated smooth muscle cell migration) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:BHF_miRNA") Annotation( "GOC:TermGenie") Annotation( "GOC:rph") Annotation( "GO_REF:0000058") Annotation( "PMID:20693317") "Any process that stops, prevents or reduces the frequency, rate or extent of vascular associated smooth muscle cell migration.") -AnnotationAssertion( "rph") AnnotationAssertion( "2015-10-19T15:49:58Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of vascular associated smooth muscle cell migration") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of vascular smooth muscle cell migration") @@ -102661,7 +100260,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of vascular associated smooth muscle cell migration) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:BHF_miRNA") Annotation( "GOC:TermGenie") Annotation( "GOC:rph") Annotation( "GO_REF:0000058") Annotation( "PMID:20693317") "Any process that activates or increases the frequency, rate or extent of vascular associated smooth muscle cell migration.") -AnnotationAssertion( "rph") AnnotationAssertion( "2015-10-19T15:50:05Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "positive regulation of vascular smooth muscle cell migration") AnnotationAssertion(Annotation( "GOC:TermGenie") "up regulation of vascular associated smooth muscle cell migration") @@ -102680,7 +100278,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of myofibroblast differentiation) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:BHF_miRNA") Annotation( "GOC:TermGenie") Annotation( "GOC:rph") Annotation( "GO_REF:0000058") Annotation( "PMID:20533548") "Any process that modulates the frequency, rate or extent of myofibroblast differentiation.") -AnnotationAssertion( "rph") AnnotationAssertion( "2015-10-23T12:15:05Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "regulation of myofibroblast cell differentiation") AnnotationAssertion( "biological_process") @@ -102691,7 +100288,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of myofibroblast differentiation) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:BHF_miRNA") Annotation( "GOC:TermGenie") Annotation( "GOC:rph") Annotation( "GO_REF:0000058") Annotation( "PMID:20533548") "Any process that stops, prevents or reduces the frequency, rate or extent of myofibroblast differentiation.") -AnnotationAssertion( "rph") AnnotationAssertion( "2015-10-23T12:15:11Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of myofibroblast cell differentiation") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of myofibroblast differentiation") @@ -102710,7 +100306,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of myofibroblast differentiation) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:BHF_miRNA") Annotation( "GOC:TermGenie") Annotation( "GOC:rph") Annotation( "GO_REF:0000058") Annotation( "PMID:20533548") "Any process that activates or increases the frequency, rate or extent of myofibroblast differentiation.") -AnnotationAssertion( "rph") AnnotationAssertion( "2015-10-23T12:15:17Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "positive regulation of myofibroblast cell differentiation") AnnotationAssertion(Annotation( "GOC:TermGenie") "up regulation of myofibroblast cell differentiation") @@ -102729,7 +100324,6 @@ EquivalentClasses( ObjectIntersection # Class: (intramembranous bone morphogenesis) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000083") Annotation( "PMID:26399686") "The developmental process by which an intramembranous bone is generated and organized.") -AnnotationAssertion( "dos") AnnotationAssertion( "2015-10-28T11:46:04Z") AnnotationAssertion( "biological_process") AnnotationAssertion(Annotation( "GOC:TermGenie") "intramembranous bones morphogenesis") @@ -102741,7 +100335,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of protein localization to cell cortex) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000058") Annotation( "PMID:17115027") "Any process that modulates the frequency, rate or extent of protein localization to cell cortex.") -AnnotationAssertion( "es") AnnotationAssertion( "2015-10-29T16:55:01Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "regulation of protein localisation to cell cortex") AnnotationAssertion( "biological_process") @@ -102753,7 +100346,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of protein localization to cell cortex) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000058") Annotation( "PMID:17115027") "Any process that stops, prevents or reduces the frequency, rate or extent of protein localization to cell cortex.") -AnnotationAssertion( "es") AnnotationAssertion( "2015-10-29T16:55:08Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of protein localisation to cell cortex") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of protein localization to cell cortex") @@ -102773,7 +100365,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of protein localization to cell cortex) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000058") Annotation( "PMID:17115027") "Any process that activates or increases the frequency, rate or extent of protein localization to cell cortex.") -AnnotationAssertion( "es") AnnotationAssertion( "2015-10-29T16:55:15Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "positive regulation of protein localisation to cell cortex") AnnotationAssertion(Annotation( "GOC:TermGenie") "up regulation of protein localisation to cell cortex") @@ -102793,7 +100384,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of euchromatin binding) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:BHF_telomere") Annotation( "GOC:TermGenie") Annotation( "GOC:nc") Annotation( "GO_REF:0000059") Annotation( "PMID:22723415") "Any process that modulates the frequency, rate or extent of euchromatin binding.") -AnnotationAssertion( "nc") AnnotationAssertion( "2015-11-09T11:43:04Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:1904793") @@ -102804,7 +100394,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of euchromatin binding) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:BHF_telomere") Annotation( "GOC:TermGenie") Annotation( "GOC:nc") Annotation( "GO_REF:0000059") Annotation( "PMID:22723415") "Any process that stops, prevents or reduces the frequency, rate or extent of euchromatin binding.") -AnnotationAssertion( "nc") AnnotationAssertion( "2015-11-09T11:43:12Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of euchromatin binding") AnnotationAssertion(Annotation( "GOC:TermGenie") "down-regulation of euchromatin binding") @@ -102819,7 +100408,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of euchromatin binding) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:BHF_telomere") Annotation( "GOC:TermGenie") Annotation( "GOC:nc") Annotation( "GO_REF:0000059") Annotation( "PMID:22723415") "Any process that activates or increases the frequency, rate or extent of euchromatin binding.") -AnnotationAssertion( "nc") AnnotationAssertion( "2015-11-09T11:43:19Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "up regulation of euchromatin binding") AnnotationAssertion(Annotation( "GOC:TermGenie") "up-regulation of euchromatin binding") @@ -102834,7 +100422,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of dense core granule transport) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000058") Annotation( "PMID:22699897") "Any process that modulates the frequency, rate or extent of dense core granule transport.") -AnnotationAssertion( "es") AnnotationAssertion( "2015-11-11T10:40:10Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "regulation of dense core vesicle transport") AnnotationAssertion( "biological_process") @@ -102846,7 +100433,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of dense core granule transport) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000058") Annotation( "PMID:22699897") "Any process that stops, prevents or reduces the frequency, rate or extent of dense core granule transport.") -AnnotationAssertion( "es") AnnotationAssertion( "2015-11-11T10:40:18Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of dense core granule transport") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of dense core vesicle transport") @@ -102866,7 +100452,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of dense core granule transport) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000058") Annotation( "PMID:22699897") "Any process that activates or increases the frequency, rate or extent of dense core granule transport.") -AnnotationAssertion( "es") AnnotationAssertion( "2015-11-11T10:40:25Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "positive regulation of dense core vesicle transport") AnnotationAssertion(Annotation( "GOC:TermGenie") "up regulation of dense core granule transport") @@ -102886,7 +100471,6 @@ EquivalentClasses( ObjectIntersection # Class: (serous membrane development) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:dph") Annotation( "GO_REF:0000094") Annotation( "PMID:15840053") "The process whose specific outcome is the progression of a serous membrane over time, from its formation to the mature structure.") -AnnotationAssertion( "dph") AnnotationAssertion( "2015-11-17T19:00:01Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "tunica serosa development") AnnotationAssertion(Annotation( "GOC:TermGenie") "wall of serous sac development") @@ -102899,7 +100483,6 @@ EquivalentClasses( ObjectIntersection # Class: (visceral peritoneum development) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:dph") Annotation( "GO_REF:0000094") Annotation( "PMID:15840053") "The process whose specific outcome is the progression of a visceral peritoneum over time, from its formation to the mature structure.") -AnnotationAssertion( "dph") AnnotationAssertion( "2015-11-17T19:00:17Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:1904818") @@ -102910,7 +100493,6 @@ SubClassOf( ObjectSomeValuesFrom( (parietal peritoneum development) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:dph") Annotation( "GO_REF:0000094") Annotation( "PMID:15840053") "The process whose specific outcome is the progression of a parietal peritoneum over time, from its formation to the mature structure.") -AnnotationAssertion( "dph") AnnotationAssertion( "2015-11-17T19:00:24Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "peritoneal cavity lining development") AnnotationAssertion( "biological_process") @@ -102922,7 +100504,6 @@ SubClassOf( ObjectSomeValuesFrom( (peritoneum development) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:dph") Annotation( "GO_REF:0000094") Annotation( "PMID:15840053") "The process whose specific outcome is the progression of a peritoneum over time, from its formation to the mature structure.") -AnnotationAssertion( "dph") AnnotationAssertion( "2015-11-18T17:23:51Z") AnnotationAssertion( "biological_process") AnnotationAssertion(Annotation( "GOC:TermGenie") "peritonaeum development") @@ -102933,7 +100514,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of aortic smooth muscle cell differentiation) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:BHF_miRNA") Annotation( "GOC:TermGenie") Annotation( "GOC:rph") Annotation( "GO_REF:0000058") Annotation( "PMID:22034194") "Any process that modulates the frequency, rate or extent of aortic smooth muscle cell differentiation.") -AnnotationAssertion( "rph") AnnotationAssertion( "2015-11-24T10:20:40Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:1904829") @@ -102943,7 +100523,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of aortic smooth muscle cell differentiation) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:BHF_miRNA") Annotation( "GOC:TermGenie") Annotation( "GOC:rph") Annotation( "GO_REF:0000058") Annotation( "PMID:22034194") "Any process that stops, prevents or reduces the frequency, rate or extent of aortic smooth muscle cell differentiation.") -AnnotationAssertion( "rph") AnnotationAssertion( "2015-11-24T10:20:47Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of aortic smooth muscle cell differentiation") AnnotationAssertion(Annotation( "GOC:TermGenie") "down-regulation of aortic smooth muscle cell differentiation") @@ -102957,7 +100536,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of aortic smooth muscle cell differentiation) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:BHF_miRNA") Annotation( "GOC:TermGenie") Annotation( "GOC:rph") Annotation( "GO_REF:0000058") Annotation( "PMID:22034194") "Any process that activates or increases the frequency, rate or extent of aortic smooth muscle cell differentiation.") -AnnotationAssertion( "rph") AnnotationAssertion( "2015-11-24T10:20:54Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "up regulation of aortic smooth muscle cell differentiation") AnnotationAssertion(Annotation( "GOC:TermGenie") "up-regulation of aortic smooth muscle cell differentiation") @@ -102971,7 +100549,6 @@ EquivalentClasses( ObjectIntersection # Class: (dorsal root ganglion morphogenesis) AnnotationAssertion(Annotation( "GOC:PARL") Annotation( "GOC:TermGenie") Annotation( "GOC:bf") Annotation( "GO_REF:0000083") Annotation( "PMID:18936100") "The developmental process by which a dorsal root ganglion is generated and organized.") -AnnotationAssertion( "bf") AnnotationAssertion( "2015-12-01T16:41:17Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "ganglion of dorsal root morphogenesis") AnnotationAssertion(Annotation( "GOC:TermGenie") "ganglion spinalis morphogenesis") @@ -102991,7 +100568,6 @@ SubClassOf( ObjectSomeValuesFrom( (facioacoustic ganglion morphogenesis) AnnotationAssertion(Annotation( "GOC:PARL") Annotation( "GOC:TermGenie") Annotation( "GOC:bf") Annotation( "GOC:mat") Annotation( "GO_REF:0000083") Annotation( "PMID:18356247") "The developmental process by which an acoustico-facial VII-VIII ganglion complex is generated and organized.") -AnnotationAssertion( "bf") AnnotationAssertion( "2015-12-01T17:02:06Z") AnnotationAssertion(Annotation( "UBERON:0012175") "acoustico-facial VII-VIII ganglion complex morphogenesis") AnnotationAssertion(Annotation( "GOC:TermGenie") "acousticofacial ganglion morphogenesis") @@ -103008,7 +100584,6 @@ SubClassOf( ObjectSomeValuesFrom( (regulation of male germ-line stem cell asymmetric division) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000058") Annotation( "PMID:19339709") "Any process that modulates the frequency, rate or extent of male germ-line stem cell asymmetric division.") -AnnotationAssertion( "sl") AnnotationAssertion( "2015-12-05T00:28:31Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "regulation of male germ-line stem cell renewal") AnnotationAssertion( "biological_process") @@ -103020,7 +100595,6 @@ SubClassOf( ObjectSomeValuesFrom( (negative regulation of male germ-line stem cell asymmetric division) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000058") Annotation( "PMID:19339709") "Any process that stops, prevents or reduces the frequency, rate or extent of male germ-line stem cell asymmetric division.") -AnnotationAssertion( "sl") AnnotationAssertion( "2015-12-05T00:28:39Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of male germ-line stem cell asymmetric division") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of male germ-line stem cell renewal") @@ -103041,7 +100615,6 @@ SubClassOf( ObjectSomeValuesFrom( (positive regulation of male germ-line stem cell asymmetric division) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000058") Annotation( "PMID:19339709") "Any process that activates or increases the frequency, rate or extent of male germ-line stem cell asymmetric division.") -AnnotationAssertion( "sl") AnnotationAssertion( "2015-12-05T00:28:46Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "positive regulation of male germ-line stem cell renewal") AnnotationAssertion(Annotation( "GOC:TermGenie") "up regulation of male germ-line stem cell asymmetric division") @@ -103061,7 +100634,6 @@ SubClassOf( ObjectSomeValuesFrom( (excitatory synapse assembly) AnnotationAssertion(Annotation( "GOC:PARL") Annotation( "GOC:TermGenie") Annotation( "GOC:bf") Annotation( "GO_REF:0000079") Annotation( "PMID:21670302") "The aggregation, arrangement and bonding together of a set of components to form an excitatory synapse.") -AnnotationAssertion( "bf") AnnotationAssertion( "2015-12-17T10:31:26Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "excitatory synapse formation") AnnotationAssertion( "biological_process") @@ -103072,7 +100644,6 @@ EquivalentClasses( ObjectIntersection # Class: (cranial skeletal system development) AnnotationAssertion(Annotation( "GOC:PARL") Annotation( "GOC:TermGenie") Annotation( "GOC:bf") Annotation( "GO_REF:0000094") Annotation( "PMID:11262227") "The process whose specific outcome is the progression of a cranial skeletal system over time, from its formation to the mature structure. The cranial skeletal system is the skeletal subdivision of the head, and includes the skull (cranium plus mandible), pharyngeal and/or hyoid apparatus.") -AnnotationAssertion( "bf") AnnotationAssertion( "2016-01-07T13:45:06Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "cranial skeleton development") AnnotationAssertion(Annotation( "PMID:11262227") "craniofacial development") @@ -103086,7 +100657,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of excitatory synapse assembly) AnnotationAssertion(Annotation( "GOC:PARL") Annotation( "GOC:TermGenie") Annotation( "GOC:bf") Annotation( "GO_REF:0000058") "Any process that modulates the frequency, rate or extent of excitatory synapse assembly.") -AnnotationAssertion( "bf") AnnotationAssertion( "2016-01-07T14:35:53Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "regulation of excitatory synapse formation") AnnotationAssertion( "biological_process") @@ -103097,7 +100667,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of excitatory synapse assembly) AnnotationAssertion(Annotation( "GOC:PARL") Annotation( "GOC:TermGenie") Annotation( "GOC:bf") Annotation( "GO_REF:0000058") "Any process that stops, prevents or reduces the frequency, rate or extent of excitatory synapse assembly.") -AnnotationAssertion( "bf") AnnotationAssertion( "2016-01-07T14:36:00Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of excitatory synapse assembly") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of excitatory synapse formation") @@ -103116,7 +100685,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of excitatory synapse assembly) AnnotationAssertion(Annotation( "GOC:PARL") Annotation( "GOC:TermGenie") Annotation( "GOC:bf") Annotation( "GO_REF:0000058") Annotation( "PMID:21670302") "Any process that activates or increases the frequency, rate or extent of excitatory synapse assembly.") -AnnotationAssertion( "bf") AnnotationAssertion( "2016-01-07T14:36:07Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "positive regulation of excitatory synapse formation") AnnotationAssertion(Annotation( "GOC:TermGenie") "up regulation of excitatory synapse assembly") @@ -103135,7 +100703,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of hepatic stellate cell proliferation) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000058") Annotation( "PMID:15358192") "Any process that modulates the frequency, rate or extent of hepatic stellate cell proliferation.") -AnnotationAssertion( "sl") AnnotationAssertion( "2016-01-14T15:56:59Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "regulation of Ito cell proliferation") AnnotationAssertion(Annotation( "GOC:TermGenie") "regulation of hepatic perisinusoidal cell proliferation") @@ -103148,7 +100715,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of hepatic stellate cell proliferation) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000058") Annotation( "PMID:15358192") "Any process that stops, prevents or reduces the frequency, rate or extent of hepatic stellate cell proliferation.") -AnnotationAssertion( "sl") AnnotationAssertion( "2016-01-14T15:57:06Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of Ito cell proliferation") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of hepatic perisinusoidal cell proliferation") @@ -103177,7 +100743,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of hepatic stellate cell proliferation) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000058") Annotation( "PMID:15358192") "Any process that activates or increases the frequency, rate or extent of hepatic stellate cell proliferation.") -AnnotationAssertion( "sl") AnnotationAssertion( "2016-01-14T15:57:13Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "positive regulation of Ito cell proliferation") AnnotationAssertion(Annotation( "GOC:TermGenie") "positive regulation of hepatic perisinusoidal cell proliferation") @@ -103206,7 +100771,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of cell proliferation in midbrain) AnnotationAssertion(Annotation( "GOC:PARL") Annotation( "GOC:TermGenie") Annotation( "GOC:bf") Annotation( "GO_REF:0000058") Annotation( "PMID:18953410") Annotation( "PMID:24431302") "Any process that modulates the frequency, rate or extent of cell proliferation in midbrain.") -AnnotationAssertion( "bf") AnnotationAssertion( "2016-02-01T13:16:11Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "regulation of cell proliferation in mesencephalon") AnnotationAssertion( "biological_process") @@ -103218,7 +100782,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of cell proliferation in midbrain) AnnotationAssertion(Annotation( "GOC:PARL") Annotation( "GOC:TermGenie") Annotation( "GOC:bf") Annotation( "GO_REF:0000058") Annotation( "PMID:18953410") Annotation( "PMID:24431302") "Any process that stops, prevents or reduces the frequency, rate or extent of cell proliferation in midbrain.") -AnnotationAssertion( "bf") AnnotationAssertion( "2016-02-01T13:16:19Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of cell proliferation in mesencephalon") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of cell proliferation in midbrain") @@ -103242,7 +100805,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of cell proliferation in midbrain) AnnotationAssertion(Annotation( "GOC:PARL") Annotation( "GOC:TermGenie") Annotation( "GOC:bf") Annotation( "GO_REF:0000058") Annotation( "PMID:24431302") "Any process that activates or increases the frequency, rate or extent of cell proliferation in midbrain.") -AnnotationAssertion( "bf") AnnotationAssertion( "2016-02-01T13:16:27Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "positive regulation of cell proliferation in mesencephalon") AnnotationAssertion(Annotation( "GOC:TermGenie") "up regulation of cell proliferation in mesencephalon") @@ -103266,7 +100828,6 @@ EquivalentClasses( ObjectIntersection # Class: (interneuron migration) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:ah") Annotation( "GO_REF:0000091") Annotation( "PMID:18622031") "The orderly movement of an interneuron from one site to another.") -AnnotationAssertion( "ah") AnnotationAssertion( "2016-02-01T14:04:32Z") AnnotationAssertion(Annotation( "GOC:ah") "inter neuron migration") AnnotationAssertion(Annotation( "GOC:ah") "inter-neuron migration") @@ -103278,7 +100839,6 @@ EquivalentClasses( ObjectIntersection # Class: (sensory neuron migration) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:ah") Annotation( "GO_REF:0000091") Annotation( "PMID:18622031") "The orderly movement of a sensory neuron from one site to another.") -AnnotationAssertion( "ah") AnnotationAssertion( "2016-02-01T14:15:50Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:1904937") @@ -103288,7 +100848,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of cardiac ventricle formation) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:BHF_miRNA") Annotation( "GOC:TermGenie") Annotation( "GOC:bc") Annotation( "GO_REF:0000058") Annotation( "PMID:23575307") "Any process that modulates the frequency, rate or extent of cardiac ventricle formation.") -AnnotationAssertion( "bc") AnnotationAssertion( "2016-02-02T16:37:16Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:1904942") @@ -103298,7 +100857,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of cardiac ventricle formation) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:BHF_miRNA") Annotation( "GOC:TermGenie") Annotation( "GOC:bc") Annotation( "GO_REF:0000058") Annotation( "PMID:23575307") "Any process that stops, prevents or reduces the frequency, rate or extent of cardiac ventricle formation.") -AnnotationAssertion( "bc") AnnotationAssertion( "2016-02-02T16:37:24Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of cardiac ventricle formation") AnnotationAssertion(Annotation( "GOC:TermGenie") "down-regulation of cardiac ventricle formation") @@ -103313,7 +100871,6 @@ SubClassOf( ObjectSomeValuesFrom( (positive regulation of cardiac ventricle formation) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:BHF_miRNA") Annotation( "GOC:TermGenie") Annotation( "GOC:bc") Annotation( "GO_REF:0000058") Annotation( "PMID:23575307") "Any process that activates or increases the frequency, rate or extent of cardiac ventricle formation.") -AnnotationAssertion( "bc") AnnotationAssertion( "2016-02-02T16:37:31Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "up regulation of cardiac ventricle formation") AnnotationAssertion(Annotation( "GOC:TermGenie") "up-regulation of cardiac ventricle formation") @@ -103327,7 +100884,6 @@ EquivalentClasses( ObjectIntersection # Class: (midbrain dopaminergic neuron differentiation) AnnotationAssertion(Annotation( "GOC:PARL") Annotation( "GOC:TermGenie") Annotation( "GOC:bf") Annotation( "GO_REF:0000086") Annotation( "PMID:17331494") Annotation( "PMID:19122665") "The process in which a relatively unspecialized cell acquires the specialized features of a midbrain dopaminergic neuron.") -AnnotationAssertion( "bf") AnnotationAssertion( "2016-02-04T14:38:10Z") AnnotationAssertion(Annotation( "PMID:19122665") "DA neurogenesis from midbrain floor plate") AnnotationAssertion(Annotation( "PMID:24287202") "mDA neuron differentiation") @@ -103342,7 +100898,6 @@ SubClassOf( ObjectSomeValuesFrom( (ATPase complex) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:bhm") Annotation( "GO_REF:0000088") Annotation( "PMID:9606181") "A protein complex which is capable of ATPase activity.") -AnnotationAssertion( "bhm") AnnotationAssertion( "2016-02-04T22:13:32Z") AnnotationAssertion( "VPS4 complex") AnnotationAssertion( "cellular_component") @@ -103354,7 +100909,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of establishment of protein localization) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000058") Annotation( "PMID:22761445") "Any process that stops, prevents or reduces the frequency, rate or extent of establishment of protein localization.") -AnnotationAssertion( "mec") AnnotationAssertion( "2016-02-05T09:59:24Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of establishment of protein localisation") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of establishment of protein localization") @@ -103385,7 +100939,6 @@ SubClassOf( (positive regulation of establishment of protein localization) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000058") Annotation( "PMID:22761445") "Any process that activates or increases the frequency, rate or extent of establishment of protein localization.") -AnnotationAssertion( "mec") AnnotationAssertion( "2016-02-05T09:59:32Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "positive regulation of establishment of protein localisation") AnnotationAssertion(Annotation( "GOC:TermGenie") "positive regulation of protein positioning") @@ -103416,7 +100969,6 @@ SubClassOf( (regulation of midbrain dopaminergic neuron differentiation) AnnotationAssertion(Annotation( "GOC:PARL") Annotation( "GOC:TermGenie") Annotation( "GOC:bf") Annotation( "GO_REF:0000058") Annotation( "PMID:21347250") "Any process that modulates the frequency, rate or extent of midbrain dopaminergic neuron differentiation.") -AnnotationAssertion( "bf") AnnotationAssertion( "2016-02-09T12:00:21Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "regulation of DA neurogenesis from midbrain floor plate") AnnotationAssertion(Annotation( "GOC:TermGenie") "regulation of mDA neuron differentiation") @@ -103430,7 +100982,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of midbrain dopaminergic neuron differentiation) AnnotationAssertion(Annotation( "GOC:PARL") Annotation( "GOC:TermGenie") Annotation( "GOC:bf") Annotation( "GO_REF:0000058") "Any process that stops, prevents or reduces the frequency, rate or extent of midbrain dopaminergic neuron differentiation.") -AnnotationAssertion( "bf") AnnotationAssertion( "2016-02-09T12:00:29Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of DA neurogenesis from midbrain floor plate") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of mDA neuron differentiation") @@ -103464,7 +101015,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of midbrain dopaminergic neuron differentiation) AnnotationAssertion(Annotation( "GOC:PARL") Annotation( "GOC:TermGenie") Annotation( "GOC:bf") Annotation( "GO_REF:0000058") Annotation( "PMID:21347250") "Any process that activates or increases the frequency, rate or extent of midbrain dopaminergic neuron differentiation.") -AnnotationAssertion( "bf") AnnotationAssertion( "2016-02-09T12:00:36Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "positive regulation of DA neurogenesis from midbrain floor plate") AnnotationAssertion(Annotation( "GOC:TermGenie") "positive regulation of mDA neuron differentiation") @@ -103498,7 +101048,6 @@ EquivalentClasses( ObjectIntersection # Class: (slow muscle cell migration) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:ymb") Annotation( "GO_REF:0000091") Annotation( "PMID:14667409") Annotation( "PMID:15572133") Annotation( "PMID:25534553") "The orderly movement of a slow muscle cell from one site to another.") -AnnotationAssertion( "ymb") AnnotationAssertion( "2016-02-16T21:20:11Z") AnnotationAssertion(Annotation( "PMID:14667409") "slow-twitch muscle cell migration") AnnotationAssertion( "biological_process") @@ -103511,7 +101060,6 @@ EquivalentClasses( ObjectIntersection AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:lb") Annotation( "GO_REF:0000079") Annotation( "PMID:24725409") "The aggregation, arrangement and bonding together of adjacent microvilli through the formation of Ca(2+)-dependent adhesion links between them, forming a brush border.") AnnotationAssertion( ) -AnnotationAssertion( "tb") AnnotationAssertion( "2016-02-17T00:58:30Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "brush border formation") AnnotationAssertion( "biological_process") @@ -103525,7 +101073,6 @@ DisjointClasses( ObjectSomeValuesFrom # Class: (lymphatic endothelial cell migration) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000091") Annotation( "PMID:25745057") "The orderly movement of a lymphatic endothelial cell from one site to another in the wall of a lymphatic vessel.") -AnnotationAssertion( "dgh") AnnotationAssertion( "2016-02-18T20:49:43Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:1904977") @@ -103536,7 +101083,6 @@ SubClassOf( ObjectSomeValuesFrom( (regulation of endothelial cell activation) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:BHF_miRNA") Annotation( "GOC:TermGenie") Annotation( "GOC:bc") Annotation( "GO_REF:0000058") Annotation( "PMID:24255059") "Any process that modulates the frequency, rate or extent of endothelial cell activation.") -AnnotationAssertion( "bc") AnnotationAssertion( "2016-02-29T16:16:09Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:1904987") @@ -103546,7 +101092,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of endothelial cell activation) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:BHF_miRNA") Annotation( "GOC:TermGenie") Annotation( "GOC:bc") Annotation( "GO_REF:0000058") Annotation( "PMID:24255059") "Any process that stops, prevents or reduces the frequency, rate or extent of endothelial cell activation.") -AnnotationAssertion( "bc") AnnotationAssertion( "2016-02-29T16:16:18Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of endothelial cell activation") AnnotationAssertion(Annotation( "GOC:TermGenie") "down-regulation of endothelial cell activation") @@ -103560,7 +101105,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of endothelial cell activation) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:BHF_miRNA") Annotation( "GOC:TermGenie") Annotation( "GOC:bc") Annotation( "GO_REF:0000058") Annotation( "PMID:24255059") "Any process that activates or increases the frequency, rate or extent of endothelial cell activation.") -AnnotationAssertion( "bc") AnnotationAssertion( "2016-02-29T16:16:25Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "up regulation of endothelial cell activation") AnnotationAssertion(Annotation( "GOC:TermGenie") "up-regulation of endothelial cell activation") @@ -103574,7 +101118,6 @@ EquivalentClasses( ObjectIntersection # Class: (transmembrane phosphate ion transport from cytosol to vacuole) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000078") Annotation( "PMID:26554016") "The directed movement of phosphate ions from the cytosol across the vacuolar membrane and into the vacuolar lumen.") -AnnotationAssertion( "tb") AnnotationAssertion( "2016-03-03T00:34:12Z") AnnotationAssertion( "vacuolar phosphate transport") AnnotationAssertion( "biological_process") @@ -103585,7 +101128,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of membrane lipid metabolic process) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000058") Annotation( "PMID:25954280") "Any process that modulates the frequency, rate or extent of membrane lipid metabolic process.") -AnnotationAssertion( "tb") AnnotationAssertion( "2016-03-08T20:41:32Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "regulation of membrane lipid metabolism") AnnotationAssertion( "biological_process") @@ -103596,7 +101138,6 @@ EquivalentClasses( ObjectIntersection # Class: (carboxylic acid transmembrane transport) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000069") Annotation( "PMID:10869563") "The process in which carboxylic acid is transported across a membrane.") -AnnotationAssertion( "vw") AnnotationAssertion( "2016-03-09T15:33:53Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:1905039") @@ -103606,7 +101147,6 @@ EquivalentClasses( ObjectIntersection # Class: (otic placode development) AnnotationAssertion(Annotation( "GOC:PARL") Annotation( "GOC:TermGenie") Annotation( "GOC:bf") Annotation( "GOC:mat") Annotation( "GO_REF:0000094") Annotation( "PMID:18356247") "The process whose specific outcome is the progression of an otic placode over time, from its formation to the mature structure.") -AnnotationAssertion( "bf") AnnotationAssertion( "2016-03-10T09:30:20Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "placoda otica development") AnnotationAssertion( "biological_process") @@ -103622,7 +101162,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of vascular associated smooth muscle cell differentiation) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:BHF_miRNA") Annotation( "GOC:TermGenie") Annotation( "GOC:rph") Annotation( "GO_REF:0000058") Annotation( "PMID:19088079") "Any process that modulates the frequency, rate or extent of vascular smooth muscle cell differentiation.") -AnnotationAssertion( "rph") AnnotationAssertion( "2016-03-21T11:14:53Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "regulation of VSMC differentiation") AnnotationAssertion(Annotation( "GOC:TermGenie") "regulation of vascular smooth muscle cell differentiation") @@ -103634,7 +101173,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of vascular associated smooth muscle cell differentiation) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:BHF_miRNA") Annotation( "GOC:TermGenie") Annotation( "GOC:rph") Annotation( "GO_REF:0000058") Annotation( "PMID:19088079") "Any process that stops, prevents or reduces the frequency, rate or extent of vascular smooth muscle cell differentiation.") -AnnotationAssertion( "rph") AnnotationAssertion( "2016-03-21T11:15:03Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of VSMC differentiation") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of vascular associated smooth muscle cell differentiation") @@ -103658,7 +101196,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of vascular associated smooth muscle cell differentiation) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:BHF_miRNA") Annotation( "GOC:TermGenie") Annotation( "GOC:rph") Annotation( "GO_REF:0000058") Annotation( "PMID:19088079") "Any process that activates or increases the frequency, rate or extent of vascular smooth muscle cell differentiation.") -AnnotationAssertion( "rph") AnnotationAssertion( "2016-03-21T11:15:13Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "positive regulation of VSMC differentiation") AnnotationAssertion(Annotation( "GOC:TermGenie") "positive regulation of vascular smooth muscle cell differentiation") @@ -103682,7 +101219,6 @@ EquivalentClasses( ObjectIntersection # Class: (allantois development) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000094") Annotation( "PMID:17440924") Annotation( "PMID:21470579") "The process whose specific outcome is the progression of an allantois over time, from its formation to the mature structure.") -AnnotationAssertion( "cls") AnnotationAssertion( "2016-03-21T15:18:21Z") AnnotationAssertion( "biological_process") AnnotationAssertion(Annotation( "GOC:TermGenie") "allantoic bud development") @@ -103693,7 +101229,6 @@ EquivalentClasses( ObjectIntersection # Class: (anterior visceral endoderm cell migration) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000091") Annotation( "PMID:17078044") "The orderly movement of an anterior visceral endoderm cell from one site to another.") -AnnotationAssertion( "cls") AnnotationAssertion( "2016-03-21T15:18:32Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:1905070") @@ -103703,7 +101238,6 @@ EquivalentClasses( ObjectIntersection # Class: (tight junction disassembly) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:TermGenie") Annotation( "GOC:rl") Annotation( "GO_REF:0000079") Annotation( "PMID:18718461") "The disaggregation of an tight junction into its constituent components.") -AnnotationAssertion( "rl") AnnotationAssertion( "2016-03-23T12:35:08Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "occluding cell junction disassembly") AnnotationAssertion( "occluding junction disassembly") @@ -103715,7 +101249,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of tight junction disassembly) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:TermGenie") Annotation( "GOC:rl") Annotation( "GO_REF:0000058") Annotation( "PMID:18718461") "Any process that modulates the frequency, rate or extent of tight junction disassembly.") -AnnotationAssertion( "rl") AnnotationAssertion( "2016-03-23T19:32:51Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "regulation of occluding cell junction disassembly") AnnotationAssertion(Annotation( "GOC:TermGenie") "regulation of occluding junction disassembly") @@ -103727,7 +101260,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of tight junction disassembly) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:TermGenie") Annotation( "GOC:rl") Annotation( "GO_REF:0000058") Annotation( "PMID:18718461") "Any process that stops, prevents or reduces the frequency, rate or extent of tight junction disassembly.") -AnnotationAssertion( "rl") AnnotationAssertion( "2016-03-23T19:33:01Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of occluding cell junction disassembly") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of tight junction disassembly") @@ -103748,7 +101280,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of tight junction disassembly) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:TermGenie") Annotation( "GOC:rl") Annotation( "GO_REF:0000058") Annotation( "PMID:18718461") "Any process that activates or increases the frequency, rate or extent of tight junction disassembly.") -AnnotationAssertion( "rl") AnnotationAssertion( "2016-03-23T19:33:10Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "positive regulation of occluding cell junction disassembly") AnnotationAssertion(Annotation( "GOC:TermGenie") "positive regulation of occluding junction disassembly") @@ -103769,7 +101300,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of cerebellar neuron development) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000058") Annotation( "PMID:26609159") "Any process that modulates the frequency, rate or extent of cerebellar neuron development.") -AnnotationAssertion( "hjd") AnnotationAssertion( "2016-03-24T19:45:17Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:1905079") @@ -103780,7 +101310,6 @@ SubClassOf( ObjectSomeValuesFrom( (negative regulation of cerebellar neuron development) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000058") Annotation( "PMID:26609159") "Any process that stops, prevents or reduces the frequency, rate or extent of cerebellar neuron development.") -AnnotationAssertion( "hjd") AnnotationAssertion( "2016-03-24T19:45:26Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of cerebellar neuron development") AnnotationAssertion(Annotation( "GOC:TermGenie") "down-regulation of cerebellar neuron development") @@ -103795,7 +101324,6 @@ SubClassOf( ObjectSomeValuesFrom( (positive regulation of cerebellar neuron development) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000058") Annotation( "PMID:26609159") "Any process that activates or increases the frequency, rate or extent of cerebellar neuron development.") -AnnotationAssertion( "hjd") AnnotationAssertion( "2016-03-24T19:45:35Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "up regulation of cerebellar neuron development") AnnotationAssertion(Annotation( "GOC:TermGenie") "up-regulation of cerebellar neuron development") @@ -103810,7 +101338,6 @@ SubClassOf( ObjectSomeValuesFrom( (regulation of pulmonary blood vessel remodeling) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:BHF_miRNA") Annotation( "GOC:TermGenie") Annotation( "GOC:bc") Annotation( "GO_REF:0000058") Annotation( "PMID:22161164") "Any process that modulates the frequency, rate or extent of pulmonary blood vessel remodeling.") -AnnotationAssertion( "bc") AnnotationAssertion( "2016-04-06T13:07:24Z") AnnotationAssertion( "regulation of pulmonary blood vessel remodelling") AnnotationAssertion( "biological_process") @@ -103821,7 +101348,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of pulmonary blood vessel remodeling) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:BHF_miRNA") Annotation( "GOC:TermGenie") Annotation( "GOC:bc") Annotation( "GO_REF:0000058") Annotation( "PMID:22161164") "Any process that stops, prevents or reduces the frequency, rate or extent of pulmonary blood vessel remodeling.") -AnnotationAssertion( "bc") AnnotationAssertion( "2016-04-06T13:07:33Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of pulmonary blood vessel remodeling") AnnotationAssertion(Annotation( "GOC:TermGenie") "down-regulation of pulmonary blood vessel remodeling") @@ -103836,7 +101362,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of pulmonary blood vessel remodeling) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:BHF_miRNA") Annotation( "GOC:TermGenie") Annotation( "GOC:bc") Annotation( "GO_REF:0000058") Annotation( "PMID:22161164") "Any process that activates or increases the frequency, rate or extent of pulmonary blood vessel remodeling.") -AnnotationAssertion( "bc") AnnotationAssertion( "2016-04-06T13:07:42Z") AnnotationAssertion( "positive regulation of pulmonary blood vessel remodelling") AnnotationAssertion(Annotation( "GOC:TermGenie") "up regulation of pulmonary blood vessel remodeling") @@ -103851,7 +101376,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of axo-dendritic protein transport) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000058") Annotation( "PMID:20694152") "Any process that modulates the frequency, rate or extent of axo-dendritic protein transport.") -AnnotationAssertion( "sl") AnnotationAssertion( "2016-04-11T20:38:31Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "regulation of axonal protein transport") AnnotationAssertion( "biological_process") @@ -103862,7 +101386,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of axo-dendritic protein transport) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000058") Annotation( "PMID:20694152") "Any process that stops, prevents or reduces the frequency, rate or extent of axo-dendritic protein transport.") -AnnotationAssertion( "sl") AnnotationAssertion( "2016-04-11T20:38:40Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of axo-dendritic protein transport") AnnotationAssertion(Annotation( "GOC:TermGenie") "down-regulation of axo-dendritic protein transport") @@ -103881,7 +101404,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of axo-dendritic protein transport) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000058") Annotation( "PMID:20694152") "Any process that activates or increases the frequency, rate or extent of axo-dendritic protein transport.") -AnnotationAssertion( "sl") AnnotationAssertion( "2016-04-11T20:38:48Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "up regulation of axo-dendritic protein transport") AnnotationAssertion(Annotation( "GOC:TermGenie") "up-regulation of axo-dendritic protein transport") @@ -103900,7 +101422,6 @@ EquivalentClasses( ObjectIntersection # Class: (apical ectodermal ridge formation) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000081") Annotation( "PMID:18359901") Annotation( "PMID:9323126") Annotation( "PMID:9596583") "The process that gives rise to the apical ectodermal ridge. This process pertains to the initial formation of a structure from unspecified parts.") -AnnotationAssertion( "dph") AnnotationAssertion( "2016-04-13T11:46:40Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "apical epidermal ridge formation") AnnotationAssertion( "biological_process") @@ -103914,7 +101435,6 @@ SubClassOf( ObjectSomeValuesFrom( (regulation of apical ectodermal ridge formation) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000058") Annotation( "PMID:18359901") "Any process that modulates the frequency, rate or extent of apical ectodermal ridge formation.") -AnnotationAssertion( "dph") AnnotationAssertion( "2016-04-13T12:16:40Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "regulation of apical epidermal ridge formation") AnnotationAssertion( "biological_process") @@ -103928,7 +101448,6 @@ SubClassOf( ObjectSomeValuesFrom( (negative regulation of apical ectodermal ridge formation) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000058") Annotation( "PMID:18359901") "Any process that stops, prevents or reduces the frequency, rate or extent of apical ectodermal ridge formation.") -AnnotationAssertion( "dph") AnnotationAssertion( "2016-04-13T12:16:48Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of apical ectodermal ridge formation") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of apical epidermal ridge formation") @@ -103958,7 +101477,6 @@ SubClassOf( ObjectSomeValuesFrom( (positive regulation of apical ectodermal ridge formation) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000058") Annotation( "PMID:18359901") "Any process that activates or increases the frequency, rate or extent of apical ectodermal ridge formation.") -AnnotationAssertion( "dph") AnnotationAssertion( "2016-04-13T12:16:57Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "positive regulation of apical epidermal ridge formation") AnnotationAssertion(Annotation( "GOC:TermGenie") "up regulation of apical ectodermal ridge formation") @@ -103985,7 +101503,6 @@ SubClassOf( ObjectSomeValuesFrom( (response to acetylcholine) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000071") Annotation( "PMID:21238497") "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an acetylcholine stimulus.") -AnnotationAssertion( "dos") AnnotationAssertion( "2016-04-14T08:54:49Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:1905144") @@ -103995,7 +101512,6 @@ EquivalentClasses( ObjectIntersection # Class: (cellular response to acetylcholine) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000071") Annotation( "PMID:21238497") "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an acetylcholine stimulus.") -AnnotationAssertion( "dos") AnnotationAssertion( "2016-04-14T08:54:58Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:1905145") @@ -104005,7 +101521,6 @@ EquivalentClasses( ObjectIntersection # Class: (lysosomal protein catabolic process) AnnotationAssertion(Annotation( "GOC:PARL") Annotation( "GOC:TermGenie") Annotation( "GOC:bf") Annotation( "GO_REF:0000062") Annotation( "PMID:24334770") "Any cellular protein catabolic process that takes place in a lysosome.") -AnnotationAssertion( "bf") AnnotationAssertion( "2016-04-14T12:50:34Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "cellular protein breakdown in lysosome") AnnotationAssertion( "cellular protein catabolic process in lysosome") @@ -104024,7 +101539,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of smooth muscle hypertrophy) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:BHF_miRNA") Annotation( "GOC:TermGenie") Annotation( "GOC:bc") Annotation( "GO_REF:0000058") Annotation( "PMID:22161164") "Any process that modulates the frequency, rate or extent of smooth muscle hypertrophy.") -AnnotationAssertion( "bc") AnnotationAssertion( "2016-04-15T12:47:07Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:1905147") @@ -104034,7 +101548,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of smooth muscle hypertrophy) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:BHF_miRNA") Annotation( "GOC:TermGenie") Annotation( "GOC:bc") Annotation( "GO_REF:0000058") Annotation( "PMID:22161164") "Any process that stops, prevents or reduces the frequency, rate or extent of smooth muscle hypertrophy.") -AnnotationAssertion( "bc") AnnotationAssertion( "2016-04-15T12:47:16Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of smooth muscle hypertrophy") AnnotationAssertion(Annotation( "GOC:TermGenie") "down-regulation of smooth muscle hypertrophy") @@ -104048,7 +101561,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of smooth muscle hypertrophy) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:BHF_miRNA") Annotation( "GOC:TermGenie") Annotation( "GOC:bc") Annotation( "GO_REF:0000058") Annotation( "PMID:22161164") "Any process that activates or increases the frequency, rate or extent of smooth muscle hypertrophy.") -AnnotationAssertion( "bc") AnnotationAssertion( "2016-04-15T12:47:24Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "up regulation of smooth muscle hypertrophy") AnnotationAssertion(Annotation( "GOC:TermGenie") "up-regulation of smooth muscle hypertrophy") @@ -104062,7 +101574,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of membrane invagination) AnnotationAssertion(Annotation( "GOC:PARL") Annotation( "GOC:TermGenie") Annotation( "GOC:bf") Annotation( "GO_REF:0000058") Annotation( "PMID:26589353") "Any process that modulates the frequency, rate or extent of membrane invagination.") -AnnotationAssertion( "bf") AnnotationAssertion( "2016-04-18T15:43:54Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:1905153") @@ -104072,7 +101583,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of membrane invagination) AnnotationAssertion(Annotation( "GOC:PARL") Annotation( "GOC:TermGenie") Annotation( "GOC:bf") Annotation( "GO_REF:0000058") Annotation( "PMID:26589353") "Any process that stops, prevents or reduces the frequency, rate or extent of membrane invagination.") -AnnotationAssertion( "bf") AnnotationAssertion( "2016-04-18T15:44:04Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of membrane invagination") AnnotationAssertion(Annotation( "GOC:TermGenie") "down-regulation of membrane invagination") @@ -104086,7 +101596,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of membrane invagination) AnnotationAssertion(Annotation( "GOC:PARL") Annotation( "GOC:TermGenie") Annotation( "GOC:bf") Annotation( "GO_REF:0000058") "Any process that activates or increases the frequency, rate or extent of membrane invagination.") -AnnotationAssertion( "bf") AnnotationAssertion( "2016-04-18T15:44:12Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "up regulation of membrane invagination") AnnotationAssertion(Annotation( "GOC:TermGenie") "up-regulation of membrane invagination") @@ -104100,7 +101609,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of photosynthesis) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000058") Annotation( "PMID:7592491") "Any process that stops, prevents or reduces the frequency, rate or extent of photosynthesis.") -AnnotationAssertion( "tb") AnnotationAssertion( "2016-04-19T16:12:29Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of photosynthesis") AnnotationAssertion(Annotation( "GOC:TermGenie") "down-regulation of photosynthesis") @@ -104114,7 +101622,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of photosynthesis) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000058") Annotation( "PMID:7592491") "Any process that activates or increases the frequency, rate or extent of photosynthesis.") -AnnotationAssertion( "tb") AnnotationAssertion( "2016-04-19T16:12:39Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "up regulation of photosynthesis") AnnotationAssertion(Annotation( "GOC:TermGenie") "up-regulation of photosynthesis") @@ -104128,7 +101635,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of lysosomal protein catabolic process) AnnotationAssertion(Annotation( "GOC:PARL") Annotation( "GOC:TermGenie") Annotation( "GOC:bf") Annotation( "GO_REF:0000058") Annotation( "PMID:23499937") "Any process that modulates the frequency, rate or extent of lysosomal protein catabolic process.") -AnnotationAssertion( "bf") AnnotationAssertion( "2016-04-26T12:10:01Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "regulation of cellular protein breakdown in lysosome") AnnotationAssertion(Annotation( "GOC:TermGenie") "regulation of cellular protein catabolic process in lysosome") @@ -104146,7 +101652,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of lysosomal protein catabolic process) AnnotationAssertion(Annotation( "GOC:PARL") Annotation( "GOC:TermGenie") Annotation( "GOC:bf") Annotation( "GO_REF:0000058") "Any process that stops, prevents or reduces the frequency, rate or extent of lysosomal protein catabolic process.") -AnnotationAssertion( "bf") AnnotationAssertion( "2016-04-26T12:10:10Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of cellular protein breakdown in lysosome") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of cellular protein catabolic process in lysosome") @@ -104200,7 +101705,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of lysosomal protein catabolic process) AnnotationAssertion(Annotation( "GOC:PARL") Annotation( "GOC:TermGenie") Annotation( "GOC:bf") Annotation( "GO_REF:0000058") "Any process that activates or increases the frequency, rate or extent of lysosomal protein catabolic process.") -AnnotationAssertion( "bf") AnnotationAssertion( "2016-04-26T12:10:19Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "positive regulation of cellular protein breakdown in lysosome") AnnotationAssertion(Annotation( "GOC:TermGenie") "positive regulation of cellular protein catabolic process in lysosome") @@ -104254,7 +101758,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of cardiocyte differentiation) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:BHF_miRNA") Annotation( "GOC:TermGenie") Annotation( "GOC:bc") Annotation( "GO_REF:0000058") Annotation( "PMID:23069713") "Any process that modulates the frequency, rate or extent of cardiocyte differentiation.") -AnnotationAssertion( "bc") AnnotationAssertion( "2016-06-02T07:20:01Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "regulation of cardiac cell differentiation") AnnotationAssertion(Annotation( "GOC:TermGenie") "regulation of heart cell differentiation") @@ -104266,7 +101769,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of cardiocyte differentiation) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:BHF_miRNA") Annotation( "GOC:TermGenie") Annotation( "GOC:bc") Annotation( "GO_REF:0000058") Annotation( "PMID:23069713") "Any process that stops, prevents or reduces the frequency, rate or extent of cardiocyte differentiation.") -AnnotationAssertion( "bc") AnnotationAssertion( "2016-06-02T07:20:09Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of cardiac cell differentiation") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of cardiocyte differentiation") @@ -104291,7 +101793,6 @@ SubClassOf( ObjectSomeValuesFrom( (positive regulation of cardiocyte differentiation) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:BHF_miRNA") Annotation( "GOC:TermGenie") Annotation( "GOC:bc") Annotation( "GO_REF:0000058") Annotation( "PMID:23069713") "Any process that activates or increases the frequency, rate or extent of cardiocyte differentiation.") -AnnotationAssertion( "bc") AnnotationAssertion( "2016-06-02T07:20:16Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "positive regulation of cardiac cell differentiation") AnnotationAssertion(Annotation( "GOC:TermGenie") "positive regulation of heart cell differentiation") @@ -104316,7 +101817,6 @@ SubClassOf( ObjectSomeValuesFrom( (negative regulation of mitotic chromosome condensation) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000058") Annotation( "PMID:23219725") "Any process that stops, prevents or reduces the frequency, rate or extent of mitotic chromosome condensation.") -AnnotationAssertion( "vw") AnnotationAssertion( "2016-06-03T08:41:08Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:1905213") @@ -104326,7 +101826,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of RNA binding) AnnotationAssertion(Annotation( "GOC:PARL") Annotation( "GOC:TermGenie") Annotation( "GOC:bf") Annotation( "GO_REF:0000059") "Any process that modulates the frequency, rate or extent of RNA binding.") -AnnotationAssertion( "bf") AnnotationAssertion( "2016-06-06T10:20:56Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:1905214") @@ -104337,7 +101836,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of RNA binding) AnnotationAssertion(Annotation( "GOC:PARL") Annotation( "GOC:TermGenie") Annotation( "GOC:bf") Annotation( "GO_REF:0000059") "Any process that stops, prevents or reduces the frequency, rate or extent of RNA binding.") -AnnotationAssertion( "bf") AnnotationAssertion( "2016-06-06T10:21:04Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of RNA binding") AnnotationAssertion(Annotation( "GOC:TermGenie") "down-regulation of RNA binding") @@ -104352,7 +101850,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of RNA binding) AnnotationAssertion(Annotation( "GOC:PARL") Annotation( "GOC:TermGenie") Annotation( "GOC:bf") Annotation( "GO_REF:0000059") Annotation( "PMID:25116364") "Any process that activates or increases the frequency, rate or extent of RNA binding.") -AnnotationAssertion( "bf") AnnotationAssertion( "2016-06-06T10:21:12Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "up regulation of RNA binding") AnnotationAssertion(Annotation( "GOC:TermGenie") "up-regulation of RNA binding") @@ -104367,7 +101864,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of platelet formation) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000058") Annotation( "PMID:10606160") "Any process that modulates the frequency, rate or extent of platelet formation.") -AnnotationAssertion( "sl") AnnotationAssertion( "2016-06-06T22:15:46Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "regulation of platelet extrusion") AnnotationAssertion( "biological_process") @@ -104379,7 +101875,6 @@ SubClassOf( ObjectSomeValuesFrom( (negative regulation of platelet formation) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000058") Annotation( "PMID:10606160") "Any process that stops, prevents or reduces the frequency, rate or extent of platelet formation.") -AnnotationAssertion( "sl") AnnotationAssertion( "2016-06-06T22:15:54Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of platelet extrusion") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of platelet formation") @@ -104398,7 +101893,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of platelet formation) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000058") Annotation( "PMID:10606160") "Any process that activates or increases the frequency, rate or extent of platelet formation.") -AnnotationAssertion( "sl") AnnotationAssertion( "2016-06-06T22:16:02Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "positive regulation of platelet extrusion") AnnotationAssertion(Annotation( "GOC:TermGenie") "up regulation of platelet extrusion") @@ -104418,7 +101912,6 @@ SubClassOf( ObjectSomeValuesFrom( (epicardium morphogenesis) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:TermGenie") Annotation( "GOC:rl") Annotation( "GO_REF:0000083") Annotation( "PMID:18718461") "The developmental process by which an epicardium is generated and organized.") -AnnotationAssertion( "rl") AnnotationAssertion( "2016-06-07T10:02:32Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "heart epicardium morphogenesis") AnnotationAssertion(Annotation( "GOC:TermGenie") "visceral serous pericardium of heart morphogenesis") @@ -104432,7 +101925,6 @@ EquivalentClasses( ObjectIntersection # Class: (cellular response to L-glutamate) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000071") Annotation( "PMID:25962137") "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a L-glutamate(1-) stimulus.") -AnnotationAssertion( "sl") AnnotationAssertion( "2016-06-07T17:30:08Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "cellular response to L-glutamate(1-)") @@ -104444,7 +101936,6 @@ EquivalentClasses( ObjectIntersection AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:pr") Annotation( "GOC:vw") Annotation( "GO_REF:0000058") Annotation( "PMID:654321") "Any process that stops, prevents or reduces the frequency, rate or extent of chromatin organization.") AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/22766"^^xsd:anyURI) -AnnotationAssertion( "pr") AnnotationAssertion( "2016-06-15T20:14:47Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of chromatin organisation") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of chromatin organization") @@ -104476,7 +101967,6 @@ EquivalentClasses( ObjectIntersection AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:pr") Annotation( "GOC:vw") Annotation( "GO_REF:0000058") Annotation( "PMID:654321") "Any process that activates or increases the frequency, rate or extent of chromatin organization.") AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/22766"^^xsd:anyURI) -AnnotationAssertion( "pr") AnnotationAssertion( "2016-06-15T20:14:56Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "positive regulation of chromatin organisation") AnnotationAssertion(Annotation( "GOC:TermGenie") "positive regulation of establishment or maintenance of chromatin architecture") @@ -104509,7 +101999,6 @@ SubClassOf( ObjectSomeValuesFrom( (Meynert cell differentiation) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000086") Annotation( "PMID:4142639") "The process in which a relatively unspecialized cell acquires the specialized features of a Meynert cell.") -AnnotationAssertion( "cjm") AnnotationAssertion( "2016-06-15T23:44:17Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:1905270") @@ -104519,7 +102008,6 @@ EquivalentClasses( ObjectIntersection # Class: (Rohon-Beard neuron differentiation) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000086") Annotation( "ZFIN:ZDB-PUB-120807-45") "The process in which a relatively unspecialized cell acquires the specialized features of a Rohon-Beard neuron.") -AnnotationAssertion( "cjm") AnnotationAssertion( "2016-06-16T23:17:04Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:1905275") @@ -104529,7 +102017,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of epithelial tube formation) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:bhm") Annotation( "GO_REF:0000058") Annotation( "PMID:25745997") "Any process that modulates the frequency, rate or extent of epithelial tube formation.") -AnnotationAssertion( "bhm") AnnotationAssertion( "2016-06-20T09:35:41Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:1905276") @@ -104542,7 +102029,6 @@ SubClassOf( (negative regulation of epithelial tube formation) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:bhm") Annotation( "GO_REF:0000058") Annotation( "PMID:25745997") "Any process that stops, prevents or reduces the frequency, rate or extent of epithelial tube formation.") -AnnotationAssertion( "bhm") AnnotationAssertion( "2016-06-20T09:35:49Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of epithelial tube formation") AnnotationAssertion(Annotation( "GOC:TermGenie") "down-regulation of epithelial tube formation") @@ -104560,7 +102046,6 @@ SubClassOf( (positive regulation of epithelial tube formation) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:bhm") Annotation( "GO_REF:0000058") Annotation( "PMID:25745997") "Any process that activates or increases the frequency, rate or extent of epithelial tube formation.") -AnnotationAssertion( "bhm") AnnotationAssertion( "2016-06-20T09:35:57Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "up regulation of epithelial tube formation") AnnotationAssertion(Annotation( "GOC:TermGenie") "up-regulation of epithelial tube formation") @@ -104578,7 +102063,6 @@ SubClassOf( (fibrous ring of heart morphogenesis) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:TermGenie") Annotation( "GOC:rl") Annotation( "GO_REF:0000083") Annotation( "PMID:16037571") "The developmental process by which a fibrous ring of heart is generated and organized.") -AnnotationAssertion( "rl") AnnotationAssertion( "2016-06-21T09:46:54Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "anulus fibrosus of heart morphogenesis") AnnotationAssertion( "biological_process") @@ -104595,7 +102079,6 @@ EquivalentClasses( ObjectIntersection # Class: (vascular associated smooth muscle cell apoptotic process) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:BHF_miRNA") Annotation( "GOC:TermGenie") Annotation( "GOC:rph") Annotation( "GO_REF:0000085") Annotation( "PMID:26493107") "Any apoptotic process in a vascular associated smooth muscle cell.") -AnnotationAssertion( "rph") AnnotationAssertion( "2016-06-23T13:24:20Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "VSMC apoptotic process") AnnotationAssertion(Annotation( "GOC:TermGenie") "vascular smooth muscle cell apoptotic process") @@ -104610,7 +102093,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of neural crest cell differentiation) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:TermGenie") Annotation( "GOC:rl") Annotation( "GO_REF:0000058") Annotation( "PMID:15073157") "Any process that modulates the frequency, rate or extent of neural crest cell differentiation.") -AnnotationAssertion( "rl") AnnotationAssertion( "2016-06-28T15:02:01Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:1905292") @@ -104620,7 +102102,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of neural crest cell differentiation) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:TermGenie") Annotation( "GOC:rl") Annotation( "GO_REF:0000058") Annotation( "PMID:15073157") "Any process that stops, prevents or reduces the frequency, rate or extent of neural crest cell differentiation.") -AnnotationAssertion( "rl") AnnotationAssertion( "2016-06-28T15:02:09Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of neural crest cell differentiation") AnnotationAssertion(Annotation( "GOC:TermGenie") "down-regulation of neural crest cell differentiation") @@ -104635,7 +102116,6 @@ SubClassOf( ObjectSomeValuesFrom( (positive regulation of neural crest cell differentiation) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:TermGenie") Annotation( "GOC:rl") Annotation( "GO_REF:0000058") Annotation( "PMID:15073157") "Any process that activates or increases the frequency, rate or extent of neural crest cell differentiation.") -AnnotationAssertion( "rl") AnnotationAssertion( "2016-06-28T15:02:16Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "up regulation of neural crest cell differentiation") AnnotationAssertion(Annotation( "GOC:TermGenie") "up-regulation of neural crest cell differentiation") @@ -104650,7 +102130,6 @@ SubClassOf( ObjectSomeValuesFrom( (regulation of intestinal epithelial cell development) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:BHF_miRNA") Annotation( "GOC:TermGenie") Annotation( "GOC:rph") Annotation( "GO_REF:0000058") Annotation( "PMID:23904268") "Any process that modulates the frequency, rate or extent of intestinal epithelial cell development.") -AnnotationAssertion( "rph") AnnotationAssertion( "2016-06-30T11:40:47Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:1905298") @@ -104661,7 +102140,6 @@ SubClassOf( ObjectSomeValuesFrom( (negative regulation of intestinal epithelial cell development) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:BHF_miRNA") Annotation( "GOC:TermGenie") Annotation( "GOC:rph") Annotation( "GO_REF:0000058") Annotation( "PMID:23904268") "Any process that stops, prevents or reduces the frequency, rate or extent of intestinal epithelial cell development.") -AnnotationAssertion( "rph") AnnotationAssertion( "2016-06-30T11:40:55Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of intestinal epithelial cell development") AnnotationAssertion(Annotation( "GOC:TermGenie") "down-regulation of intestinal epithelial cell development") @@ -104677,7 +102155,6 @@ SubClassOf( ObjectSomeValuesFrom( (positive regulation of intestinal epithelial cell development) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:BHF_miRNA") Annotation( "GOC:TermGenie") Annotation( "GOC:rph") Annotation( "GO_REF:0000058") Annotation( "PMID:23904268") "Any process that activates or increases the frequency, rate or extent of intestinal epithelial cell development.") -AnnotationAssertion( "rph") AnnotationAssertion( "2016-06-30T11:41:02Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "up regulation of intestinal epithelial cell development") AnnotationAssertion(Annotation( "GOC:TermGenie") "up-regulation of intestinal epithelial cell development") @@ -104692,7 +102169,6 @@ SubClassOf( ObjectSomeValuesFrom( (regulation of cardiac myofibril assembly) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:TermGenie") Annotation( "GOC:rl") Annotation( "GO_REF:0000058") Annotation( "PMID:16151019") "Any process that modulates the frequency, rate or extent of cardiac myofibril assembly.") -AnnotationAssertion( "rl") AnnotationAssertion( "2016-07-06T10:01:49Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "regulation of cardiac myofibril development") AnnotationAssertion(Annotation( "GOC:TermGenie") "regulation of cardiac myofibril morphogenesis") @@ -104706,7 +102182,6 @@ SubClassOf( ObjectSomeValuesFrom( (negative regulation of cardiac myofibril assembly) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:TermGenie") Annotation( "GOC:rl") Annotation( "GO_REF:0000058") Annotation( "PMID:16151019") "Any process that stops, prevents or reduces the frequency, rate or extent of cardiac myofibril assembly.") -AnnotationAssertion( "rl") AnnotationAssertion( "2016-07-06T10:01:58Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of cardiac myofibril assembly") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of cardiac myofibril development") @@ -104736,7 +102211,6 @@ SubClassOf( ObjectSomeValuesFrom( (positive regulation of cardiac myofibril assembly) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:TermGenie") Annotation( "GOC:rl") Annotation( "GO_REF:0000058") Annotation( "PMID:16151019") "Any process that activates or increases the frequency, rate or extent of cardiac myofibril assembly.") -AnnotationAssertion( "rl") AnnotationAssertion( "2016-07-06T10:02:07Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "positive regulation of cardiac myofibril development") AnnotationAssertion(Annotation( "GOC:TermGenie") "positive regulation of cardiac myofibril morphogenesis") @@ -104765,7 +102239,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of cardiac neural crest cell migration involved in outflow tract morphogenesis) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:TermGenie") Annotation( "GOC:rl") Annotation( "GO_REF:0000058") Annotation( "PMID:17628518") "Any process that modulates the frequency, rate or extent of cardiac neural crest cell migration involved in outflow tract morphogenesis.") -AnnotationAssertion( "rl") AnnotationAssertion( "2016-07-11T17:34:26Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:1905310") @@ -104775,7 +102248,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of cardiac neural crest cell migration involved in outflow tract morphogenesis) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:TermGenie") Annotation( "GOC:rl") Annotation( "GO_REF:0000058") Annotation( "PMID:17628518") "Any process that stops, prevents or reduces the frequency, rate or extent of cardiac neural crest cell migration involved in outflow tract morphogenesis.") -AnnotationAssertion( "rl") AnnotationAssertion( "2016-07-11T17:34:35Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of cardiac neural crest cell migration involved in outflow tract morphogenesis") AnnotationAssertion(Annotation( "GOC:TermGenie") "down-regulation of cardiac neural crest cell migration involved in outflow tract morphogenesis") @@ -104789,7 +102261,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of cardiac neural crest cell migration involved in outflow tract morphogenesis) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:TermGenie") Annotation( "GOC:rl") Annotation( "GO_REF:0000058") Annotation( "PMID:17628518") "Any process that activates or increases the frequency, rate or extent of cardiac neural crest cell migration involved in outflow tract morphogenesis.") -AnnotationAssertion( "rl") AnnotationAssertion( "2016-07-11T17:34:43Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "up regulation of cardiac neural crest cell migration involved in outflow tract morphogenesis") AnnotationAssertion(Annotation( "GOC:TermGenie") "up-regulation of cardiac neural crest cell migration involved in outflow tract morphogenesis") @@ -104803,7 +102274,6 @@ EquivalentClasses( ObjectIntersection # Class: (cell proliferation involved in endocardial cushion morphogenesis) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:TermGenie") Annotation( "GOC:rl") Annotation( "GO_REF:0000060") Annotation( "PMID:20652948") "Any cell proliferation that is involved in endocardial cushion morphogenesis.") -AnnotationAssertion( "rl") AnnotationAssertion( "2016-07-12T13:56:36Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:1905315") @@ -104813,7 +102283,6 @@ EquivalentClasses( ObjectIntersection # Class: (mesenchymal stem cell migration) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000091") Annotation( "PMID:24924806") Annotation( "PMID:25181476") "The orderly movement of a mesenchymal stem cell from one site to another.") -AnnotationAssertion( "sl") AnnotationAssertion( "2016-07-14T17:13:02Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:1905319") @@ -104823,7 +102292,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of mesenchymal stem cell migration) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000058") Annotation( "PMID:26846297") "Any process that modulates the frequency, rate or extent of mesenchymal stem cell migration.") -AnnotationAssertion( "sl") AnnotationAssertion( "2016-07-15T22:19:14Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:1905320") @@ -104833,7 +102301,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of mesenchymal stem cell migration) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000058") Annotation( "PMID:26846297") "Any process that stops, prevents or reduces the frequency, rate or extent of mesenchymal stem cell migration.") -AnnotationAssertion( "sl") AnnotationAssertion( "2016-07-15T22:19:22Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of mesenchymal stem cell migration") AnnotationAssertion(Annotation( "GOC:TermGenie") "down-regulation of mesenchymal stem cell migration") @@ -104847,7 +102314,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of mesenchymal stem cell migration) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000058") Annotation( "PMID:26846297") "Any process that activates or increases the frequency, rate or extent of mesenchymal stem cell migration.") -AnnotationAssertion( "sl") AnnotationAssertion( "2016-07-15T22:19:29Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "up regulation of mesenchymal stem cell migration") AnnotationAssertion(Annotation( "GOC:TermGenie") "up-regulation of mesenchymal stem cell migration") @@ -104861,7 +102327,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of morphogenesis of an epithelium) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:bhm") Annotation( "GO_REF:0000058") Annotation( "PMID:25745997") "Any process that modulates the frequency, rate or extent of morphogenesis of an epithelium.") -AnnotationAssertion( "bhm") AnnotationAssertion( "2016-07-22T07:13:49Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "regulation of epithelium morphogenesis") AnnotationAssertion( "biological_process") @@ -104874,7 +102339,6 @@ SubClassOf( (negative regulation of morphogenesis of an epithelium) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:bhm") Annotation( "GO_REF:0000058") Annotation( "PMID:25745997") "Any process that stops, prevents or reduces the frequency, rate or extent of morphogenesis of an epithelium.") -AnnotationAssertion( "bhm") AnnotationAssertion( "2016-07-22T07:13:57Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of epithelium morphogenesis") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of morphogenesis of an epithelium") @@ -104896,7 +102360,6 @@ SubClassOf( (positive regulation of morphogenesis of an epithelium) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:bhm") Annotation( "GO_REF:0000058") Annotation( "PMID:25745997") "Any process that activates or increases the frequency, rate or extent of morphogenesis of an epithelium.") -AnnotationAssertion( "bhm") AnnotationAssertion( "2016-07-22T07:14:05Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "positive regulation of epithelium morphogenesis") AnnotationAssertion(Annotation( "GOC:TermGenie") "up regulation of epithelium morphogenesis") @@ -104918,7 +102381,6 @@ SubClassOf( (ciliary transition zone assembly) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:cilia") Annotation( "GO_REF:0000079") Annotation( "PMID:21725307") Annotation( "PMID:23644468") Annotation( "PMID:24448408") Annotation( "PMID:26595381") Annotation( "PMID:26982032") "The aggregation, arrangement and bonding together of a set of components to form a ciliary transition zone.") -AnnotationAssertion( "pr") AnnotationAssertion( "2016-08-04T14:49:43Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "cilial transition zone assembly") AnnotationAssertion(Annotation( "GOC:TermGenie") "cilial transition zone formation") @@ -104934,7 +102396,6 @@ SubClassOf( ObjectSomeValuesFrom( (pericyte cell migration) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:BHF_miRNA") Annotation( "GOC:TermGenie") Annotation( "GOC:rph") Annotation( "GO_REF:0000091") Annotation( "PMID:26268439") "The orderly movement of a pericyte cell from one site to another.") -AnnotationAssertion( "rph") AnnotationAssertion( "2016-08-05T12:01:48Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:1905351") @@ -104944,7 +102405,6 @@ EquivalentClasses( ObjectIntersection # Class: (protein localization to presynapse) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000087") Annotation( "PMID:24449494") "A process in which a protein is transported to, or maintained in, a location within a presynapse.") -AnnotationAssertion( "dos") AnnotationAssertion( "2016-08-18T14:42:59Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "protein localisation in presynapse") AnnotationAssertion(Annotation( "GOC:TermGenie") "protein localisation to presynapse") @@ -104958,7 +102418,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of protein localization to presynapse) AnnotationAssertion(Annotation( "GOC:PARL") Annotation( "GOC:TermGenie") Annotation( "GOC:bf") Annotation( "GO_REF:0000058") Annotation( "PMID:24449494") "Any process that modulates the frequency, rate or extent of protein localization to presynapse.") -AnnotationAssertion( "dos") AnnotationAssertion( "2016-08-18T14:56:00Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "regulation of protein localisation in presynapse") AnnotationAssertion(Annotation( "GOC:TermGenie") "regulation of protein localisation to presynapse") @@ -104972,7 +102431,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of protein localization to presynapse) AnnotationAssertion(Annotation( "GOC:PARL") Annotation( "GOC:TermGenie") Annotation( "GOC:bf") Annotation( "GO_REF:0000058") Annotation( "PMID:24449494") "Any process that stops, prevents or reduces the frequency, rate or extent of protein localization to presynapse.") -AnnotationAssertion( "dos") AnnotationAssertion( "2016-08-18T14:56:08Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of protein localisation in presynapse") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of protein localisation to presynapse") @@ -105006,7 +102464,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of protein localization to presynapse) AnnotationAssertion(Annotation( "GOC:PARL") Annotation( "GOC:TermGenie") Annotation( "GOC:bf") Annotation( "GO_REF:0000058") Annotation( "PMID:24449494") "Any process that activates or increases the frequency, rate or extent of protein localization to presynapse.") -AnnotationAssertion( "dos") AnnotationAssertion( "2016-08-18T14:56:21Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "positive regulation of protein localisation in presynapse") AnnotationAssertion(Annotation( "GOC:TermGenie") "positive regulation of protein localisation to presynapse") @@ -105040,7 +102497,6 @@ EquivalentClasses( ObjectIntersection # Class: (activated CD8-positive, alpha-beta T cell apoptotic process) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000085") Annotation( "PMID:24187568") "Any apoptotic process in an activated CD8-positive, alpha-beta T cell.") -AnnotationAssertion( "pga") AnnotationAssertion( "2016-08-25T08:09:27Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "activated CD8-positive, alpha-beta T lymphocyte apoptotic process") AnnotationAssertion(Annotation( "GOC:TermGenie") "activated CD8-positive, alpha-beta T-cell apoptotic process") @@ -105057,7 +102513,6 @@ EquivalentClasses( ObjectIntersection # Class: (activated CD4-positive, alpha-beta T cell apoptotic process) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000085") Annotation( "PMID:24187568") "Any apoptotic process in an activated CD4-positive, alpha-beta T cell.") -AnnotationAssertion( "pga") AnnotationAssertion( "2016-08-25T08:13:40Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "activated CD4-positive, alpha-beta T lymphocyte apoptotic process") AnnotationAssertion(Annotation( "GOC:TermGenie") "activated CD4-positive, alpha-beta T-cell apoptotic process") @@ -105074,7 +102529,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of activated CD4-positive, alpha-beta T cell apoptotic process) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000058") Annotation( "PMID:24187568") "Any process that modulates the frequency, rate or extent of activated CD4-positive, alpha-beta T cell apoptotic process.") -AnnotationAssertion( "pga") AnnotationAssertion( "2016-08-25T09:09:46Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "regulation of activated CD4-positive, alpha-beta T lymphocyte apoptotic process") AnnotationAssertion(Annotation( "GOC:TermGenie") "regulation of activated CD4-positive, alpha-beta T-cell apoptotic process") @@ -105091,7 +102545,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of activated CD4-positive, alpha-beta T cell apoptotic process) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000058") Annotation( "PMID:24187568") "Any process that stops, prevents or reduces the frequency, rate or extent of activated CD4-positive, alpha-beta T cell apoptotic process.") -AnnotationAssertion( "pga") AnnotationAssertion( "2016-08-25T09:09:53Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of activated CD4-positive, alpha-beta T cell apoptotic process") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of activated CD4-positive, alpha-beta T lymphocyte apoptotic process") @@ -105140,7 +102593,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of activated CD4-positive, alpha-beta T cell apoptotic process) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000058") Annotation( "PMID:24187568") "Any process that activates or increases the frequency, rate or extent of activated CD4-positive, alpha-beta T cell apoptotic process.") -AnnotationAssertion( "pga") AnnotationAssertion( "2016-08-25T09:10:00Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "positive regulation of activated CD4-positive, alpha-beta T lymphocyte apoptotic process") AnnotationAssertion(Annotation( "GOC:TermGenie") "positive regulation of activated CD4-positive, alpha-beta T-cell apoptotic process") @@ -105189,7 +102641,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of activated CD8-positive, alpha-beta T cell apoptotic process) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000058") Annotation( "PMID:24187568") "Any process that modulates the frequency, rate or extent of activated CD8-positive, alpha-beta T cell apoptotic process.") -AnnotationAssertion( "pga") AnnotationAssertion( "2016-08-25T09:13:56Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "regulation of activated CD8-positive, alpha-beta T lymphocyte apoptotic process") AnnotationAssertion(Annotation( "GOC:TermGenie") "regulation of activated CD8-positive, alpha-beta T-cell apoptotic process") @@ -105206,7 +102657,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of activated CD8-positive, alpha-beta T cell apoptotic process) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000058") Annotation( "PMID:24187568") "Any process that stops, prevents or reduces the frequency, rate or extent of activated CD8-positive, alpha-beta T cell apoptotic process.") -AnnotationAssertion( "pga") AnnotationAssertion( "2016-08-25T09:14:03Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of activated CD8-positive, alpha-beta T cell apoptotic process") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of activated CD8-positive, alpha-beta T lymphocyte apoptotic process") @@ -105255,7 +102705,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of activated CD8-positive, alpha-beta T cell apoptotic process) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000058") Annotation( "PMID:24187568") "Any process that activates or increases the frequency, rate or extent of activated CD8-positive, alpha-beta T cell apoptotic process.") -AnnotationAssertion( "pga") AnnotationAssertion( "2016-08-25T09:14:10Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "positive regulation of activated CD8-positive, alpha-beta T lymphocyte apoptotic process") AnnotationAssertion(Annotation( "GOC:TermGenie") "positive regulation of activated CD8-positive, alpha-beta T-cell apoptotic process") @@ -105304,7 +102753,6 @@ EquivalentClasses( ObjectIntersection # Class: (response to glycine) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000071") Annotation( "PMID:18984164") "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a glycine stimulus.") -AnnotationAssertion( "sl") AnnotationAssertion( "2016-09-08T22:09:15Z") AnnotationAssertion( "response to Gly") AnnotationAssertion( "response to aminoacetic acid") @@ -105318,7 +102766,6 @@ EquivalentClasses( ObjectIntersection # Class: (cellular response to glycine) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000071") Annotation( "PMID:18984164") "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a glycine stimulus.") -AnnotationAssertion( "sl") AnnotationAssertion( "2016-09-08T22:09:23Z") AnnotationAssertion( "cellular response to Gly") AnnotationAssertion( "cellular response to aminoacetic acid") @@ -105332,7 +102779,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of retrograde trans-synaptic signaling by neuropeptide) AnnotationAssertion(Annotation( "GOC:PARL") Annotation( "GOC:TermGenie") Annotation( "GOC:bf") Annotation( "GO_REF:0000058") Annotation( "PMID:19448629") "Any process that modulates the frequency, rate or extent of retrograde trans-synaptic signaling by neuropeptide.") -AnnotationAssertion( "bf") AnnotationAssertion( "2016-09-14T10:56:47Z") AnnotationAssertion( "biological_process") AnnotationAssertion(Annotation( "GOC:bf") "regulation of neuropeptide-mediated retrograde trans-synaptic signaling") @@ -105343,7 +102789,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of retrograde trans-synaptic signaling by neuropeptide) AnnotationAssertion(Annotation( "GOC:PARL") Annotation( "GOC:TermGenie") Annotation( "GOC:bf") Annotation( "GO_REF:0000058") Annotation( "PMID:19448629") "Any process that stops, prevents or reduces the frequency, rate or extent of retrograde trans-synaptic signaling by neuropeptide.") -AnnotationAssertion( "bf") AnnotationAssertion( "2016-09-14T10:56:55Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of retrograde trans-synaptic signaling by neuropeptide") AnnotationAssertion(Annotation( "GOC:TermGenie") "down-regulation of retrograde trans-synaptic signaling by neuropeptide") @@ -105359,7 +102804,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of retrograde trans-synaptic signaling by neuropeptide) AnnotationAssertion(Annotation( "GOC:PARL") Annotation( "GOC:TermGenie") Annotation( "GOC:bf") Annotation( "GO_REF:0000058") Annotation( "PMID:19448629") "Any process that activates or increases the frequency, rate or extent of retrograde trans-synaptic signaling by neuropeptide.") -AnnotationAssertion( "bf") AnnotationAssertion( "2016-09-14T10:57:02Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "up regulation of retrograde trans-synaptic signaling by neuropeptide") AnnotationAssertion(Annotation( "GOC:TermGenie") "up-regulation of retrograde trans-synaptic signaling by neuropeptide") @@ -105374,7 +102818,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of myeloid progenitor cell differentiation) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000058") Annotation( "PMID:27010503") "Any process that modulates the frequency, rate or extent of myeloid progenitor cell differentiation.") -AnnotationAssertion( "rz") AnnotationAssertion( "2016-09-16T12:32:18Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:1905453") @@ -105384,7 +102827,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of myeloid progenitor cell differentiation) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000058") Annotation( "PMID:27010503") "Any process that stops, prevents or reduces the frequency, rate or extent of myeloid progenitor cell differentiation.") -AnnotationAssertion( "rz") AnnotationAssertion( "2016-09-16T12:32:26Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of myeloid progenitor cell differentiation") AnnotationAssertion(Annotation( "GOC:TermGenie") "down-regulation of myeloid progenitor cell differentiation") @@ -105398,7 +102840,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of myeloid progenitor cell differentiation) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000058") Annotation( "PMID:27010503") "Any process that activates or increases the frequency, rate or extent of myeloid progenitor cell differentiation.") -AnnotationAssertion( "rz") AnnotationAssertion( "2016-09-16T12:32:33Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "up regulation of myeloid progenitor cell differentiation") AnnotationAssertion(Annotation( "GOC:TermGenie") "up-regulation of myeloid progenitor cell differentiation") @@ -105412,7 +102853,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of lymphoid progenitor cell differentiation) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000058") Annotation( "PMID:27010503") "Any process that modulates the frequency, rate or extent of lymphoid progenitor cell differentiation.") -AnnotationAssertion( "rz") AnnotationAssertion( "2016-09-16T12:32:40Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:1905456") @@ -105422,7 +102862,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of lymphoid progenitor cell differentiation) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000058") Annotation( "PMID:27010503") "Any process that stops, prevents or reduces the frequency, rate or extent of lymphoid progenitor cell differentiation.") -AnnotationAssertion( "rz") AnnotationAssertion( "2016-09-16T12:32:48Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of lymphoid progenitor cell differentiation") AnnotationAssertion(Annotation( "GOC:TermGenie") "down-regulation of lymphoid progenitor cell differentiation") @@ -105436,7 +102875,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of lymphoid progenitor cell differentiation) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000058") Annotation( "PMID:27010503") "Any process that activates or increases the frequency, rate or extent of lymphoid progenitor cell differentiation.") -AnnotationAssertion( "rz") AnnotationAssertion( "2016-09-16T12:32:55Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "up regulation of lymphoid progenitor cell differentiation") AnnotationAssertion(Annotation( "GOC:TermGenie") "up-regulation of lymphoid progenitor cell differentiation") @@ -105450,7 +102888,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of vascular associated smooth muscle cell apoptotic process) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:BHF_miRNA") Annotation( "GOC:TermGenie") Annotation( "GOC:rph") Annotation( "GO_REF:0000058") Annotation( "PMID:26493107") "Any process that modulates the frequency, rate or extent of vascular associated smooth muscle cell apoptotic process.") -AnnotationAssertion( "rph") AnnotationAssertion( "2016-09-19T11:33:54Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "regulation of VSMC apoptotic process") AnnotationAssertion(Annotation( "GOC:TermGenie") "regulation of vascular smooth muscle cell apoptotic process") @@ -105465,7 +102902,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of vascular associated smooth muscle cell apoptotic process) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:BHF_miRNA") Annotation( "GOC:TermGenie") Annotation( "GOC:rph") Annotation( "GO_REF:0000058") Annotation( "PMID:26493107") "Any process that stops, prevents or reduces the frequency, rate or extent of vascular associated smooth muscle cell apoptotic process.") -AnnotationAssertion( "rph") AnnotationAssertion( "2016-09-19T11:34:03Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of VSMC apoptotic process") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of vascular associated smooth muscle cell apoptotic process") @@ -105504,7 +102940,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of vascular associated smooth muscle cell apoptotic process) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:BHF_miRNA") Annotation( "GOC:TermGenie") Annotation( "GOC:rph") Annotation( "GO_REF:0000058") Annotation( "PMID:26493107") "Any process that activates or increases the frequency, rate or extent of vascular associated smooth muscle cell apoptotic process.") -AnnotationAssertion( "rph") AnnotationAssertion( "2016-09-19T11:34:10Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "positive regulation of VSMC apoptotic process") AnnotationAssertion(Annotation( "GOC:TermGenie") "positive regulation of vascular smooth muscle cell apoptotic process") @@ -105543,7 +102978,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of protein localization to membrane) AnnotationAssertion(Annotation( "GOC:PARL") Annotation( "GOC:TermGenie") Annotation( "GOC:bc") Annotation( "GO_REF:0000058") Annotation( "PMID:26911690") "Any process that modulates the frequency, rate or extent of protein localization to membrane.") -AnnotationAssertion( "bc") AnnotationAssertion( "2016-09-21T16:20:03Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "regulation of protein localisation in membrane") AnnotationAssertion(Annotation( "GOC:TermGenie") "regulation of protein localization in membrane") @@ -105555,7 +102989,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of protein localization to membrane) AnnotationAssertion(Annotation( "GOC:PARL") Annotation( "GOC:TermGenie") Annotation( "GOC:bc") Annotation( "GO_REF:0000058") Annotation( "PMID:26911690") "Any process that stops, prevents or reduces the frequency, rate or extent of protein localization to membrane.") -AnnotationAssertion( "bc") AnnotationAssertion( "2016-09-21T16:20:10Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of protein localisation in membrane") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of protein localization in membrane") @@ -105579,7 +103012,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of protein localization to membrane) AnnotationAssertion(Annotation( "GOC:PARL") Annotation( "GOC:TermGenie") Annotation( "GOC:bc") Annotation( "GO_REF:0000058") Annotation( "PMID:26911690") "Any process that activates or increases the frequency, rate or extent of protein localization to membrane.") -AnnotationAssertion( "bc") AnnotationAssertion( "2016-09-21T16:20:18Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "positive regulation of protein localisation in membrane") AnnotationAssertion(Annotation( "GOC:TermGenie") "positive regulation of protein localization in membrane") @@ -105603,7 +103035,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of motor neuron migration) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000058") Annotation( "PMID:16516839") "Any process that modulates the frequency, rate or extent of motor neuron migration.") -AnnotationAssertion( "hbye") AnnotationAssertion( "2016-09-23T12:49:54Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:1905483") @@ -105613,7 +103044,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of motor neuron migration) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000058") Annotation( "PMID:16516839") "Any process that stops, prevents or reduces the frequency, rate or extent of motor neuron migration.") -AnnotationAssertion( "hbye") AnnotationAssertion( "2016-09-23T12:50:11Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of motor neuron migration") AnnotationAssertion(Annotation( "GOC:TermGenie") "down-regulation of motor neuron migration") @@ -105627,7 +103057,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of motor neuron migration) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000058") Annotation( "PMID:16516839") "Any process that activates or increases the frequency, rate or extent of motor neuron migration.") -AnnotationAssertion( "hbye") AnnotationAssertion( "2016-09-23T12:50:19Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "up regulation of motor neuron migration") AnnotationAssertion(Annotation( "GOC:TermGenie") "up-regulation of motor neuron migration") @@ -105641,7 +103070,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of branching morphogenesis of a nerve) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000058") Annotation( "PMID:16516839") "Any process that activates or increases the frequency, rate or extent of branching morphogenesis of a nerve.") -AnnotationAssertion( "hbye") AnnotationAssertion( "2016-09-23T14:11:52Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "up regulation of branching morphogenesis of a nerve") AnnotationAssertion(Annotation( "GOC:TermGenie") "up-regulation of branching morphogenesis of a nerve") @@ -105655,7 +103083,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of motile cilium assembly) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:cilia") Annotation( "GOC:krc") Annotation( "GO_REF:0000058") Annotation( "PMID:25294941") "Any process that modulates the frequency, rate or extent of motile cilium assembly.") -AnnotationAssertion( "krc") AnnotationAssertion( "2016-09-27T18:27:47Z") AnnotationAssertion( "biological_process") AnnotationAssertion(Annotation( "GOC:TermGenie") "regulation of motile primary cilia assembly") @@ -105671,7 +103098,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of motile cilium assembly) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:cilia") Annotation( "GOC:krc") Annotation( "GO_REF:0000058") Annotation( "PMID:25294941") "Any process that stops, prevents or reduces the frequency, rate or extent of motile cilium assembly.") -AnnotationAssertion( "krc") AnnotationAssertion( "2016-09-27T18:27:55Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "inhibition of motile primary cilia assembly") AnnotationAssertion(Annotation( "GOC:TermGenie") "inhibition of motile primary cilia formation") @@ -105711,7 +103137,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of motile cilium assembly) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:cilia") Annotation( "GOC:krc") Annotation( "GO_REF:0000058") Annotation( "PMID:25294941") "Any process that activates or increases the frequency, rate or extent of motile cilium assembly.") -AnnotationAssertion( "krc") AnnotationAssertion( "2016-09-27T18:28:03Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "activation of motile primary cilia assembly") AnnotationAssertion(Annotation( "GOC:TermGenie") "activation of motile primary cilia formation") @@ -105751,7 +103176,6 @@ EquivalentClasses( ObjectIntersection # Class: (protein localization to microtubule organizing center) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000087") Annotation( "PMID:19001497") "A process in which a protein is transported to, or maintained in, a location within a microtubule organizing center.") -AnnotationAssertion( "mah") AnnotationAssertion( "2016-09-28T12:32:16Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "protein localisation in microtubule organizing center") AnnotationAssertion(Annotation( "GOC:TermGenie") "protein localisation to microtubule organizing center") @@ -105764,7 +103188,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of fertilization) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:hbye") Annotation( "GO_REF:0000058") Annotation( "PMID:27564576") "Any process that activates or increases the frequency, rate or extent of fertilization.") -AnnotationAssertion( "pr") AnnotationAssertion( "2016-09-30T14:32:32Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "positive regulation of syngamy") AnnotationAssertion(Annotation( "GOC:TermGenie") "up regulation of fertilization") @@ -105783,7 +103206,6 @@ EquivalentClasses( ObjectIntersection # Class: (macrophage migration) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000091") Annotation( "PMID:25749876") "The orderly movement of a macrophage from one site to another.") -AnnotationAssertion( "sl") AnnotationAssertion( "2016-09-30T22:17:45Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:1905517") @@ -105793,7 +103215,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of macrophage migration) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000058") Annotation( "PMID:25749876") "Any process that modulates the frequency, rate or extent of macrophage migration.") -AnnotationAssertion( "sl") AnnotationAssertion( "2016-10-03T15:29:06Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:1905521") @@ -105803,7 +103224,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of macrophage migration) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000058") Annotation( "PMID:25749876") "Any process that stops, prevents or reduces the frequency, rate or extent of macrophage migration.") -AnnotationAssertion( "sl") AnnotationAssertion( "2016-10-03T15:29:14Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of macrophage migration") AnnotationAssertion(Annotation( "GOC:TermGenie") "down-regulation of macrophage migration") @@ -105817,7 +103237,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of macrophage migration) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000058") Annotation( "PMID:25749876") "Any process that activates or increases the frequency, rate or extent of macrophage migration.") -AnnotationAssertion( "sl") AnnotationAssertion( "2016-10-03T15:29:21Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "up regulation of macrophage migration") AnnotationAssertion(Annotation( "GOC:TermGenie") "up-regulation of macrophage migration") @@ -105831,7 +103250,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of blood vessel branching) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:BHF_telomere") Annotation( "GOC:TermGenie") Annotation( "GOC:nc") Annotation( "GO_REF:0000058") Annotation( "PMID:23201774") "Any process that modulates the frequency, rate or extent of blood vessel branching.") -AnnotationAssertion( "nc") AnnotationAssertion( "2016-10-12T14:19:33Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "regulation of branching involved in blood vessel morphogenesis") AnnotationAssertion( "biological_process") @@ -105845,7 +103263,6 @@ SubClassOf( (negative regulation of vessel branching) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:BHF_telomere") Annotation( "GOC:TermGenie") Annotation( "GOC:nc") Annotation( "GO_REF:0000058") Annotation( "PMID:23201774") "Any process that stops, prevents or reduces the frequency, rate or extent of blood vessel branching.") -AnnotationAssertion( "nc") AnnotationAssertion( "2016-10-12T14:19:41Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of branching involved in blood vessel morphogenesis") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of patterning of blood vessels") @@ -105867,7 +103284,6 @@ SubClassOf( (positive regulation of blood vessel branching) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:BHF_telomere") Annotation( "GOC:TermGenie") Annotation( "GOC:nc") Annotation( "GO_REF:0000058") Annotation( "PMID:23201774") "Any process that activates or increases the frequency, rate or extent of blood vessel branching.") -AnnotationAssertion( "nc") AnnotationAssertion( "2016-10-12T14:19:49Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "positive regulation of branching involved in blood vessel morphogenesis") AnnotationAssertion(Annotation( "GOC:TermGenie") "up regulation of branching involved in blood vessel morphogenesis") @@ -105889,7 +103305,6 @@ SubClassOf( (regulation of mitotic nuclear envelope disassembly) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000058") Annotation( "PMID:18765790") "Any process that modulates the frequency, rate or extent of mitotic nuclear envelope disassembly.") -AnnotationAssertion( "hbye") AnnotationAssertion( "2016-10-14T13:14:57Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "regulation of mitotic nuclear envelope breakdown") AnnotationAssertion(Annotation( "GOC:TermGenie") "regulation of mitotic nuclear envelope catabolism") @@ -105902,7 +103317,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of mitotic nuclear envelope disassembly) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000058") Annotation( "PMID:18765790") "Any process that stops, prevents or reduces the frequency, rate or extent of mitotic nuclear envelope disassembly.") -AnnotationAssertion( "hbye") AnnotationAssertion( "2016-10-14T13:15:08Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of mitotic nuclear envelope breakdown") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of mitotic nuclear envelope catabolism") @@ -105931,7 +103345,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of mitotic nuclear envelope disassembly) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000058") Annotation( "PMID:18765790") "Any process that activates or increases the frequency, rate or extent of mitotic nuclear envelope disassembly.") -AnnotationAssertion( "hbye") AnnotationAssertion( "2016-10-14T13:15:17Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "positive regulation of mitotic nuclear envelope breakdown") AnnotationAssertion(Annotation( "GOC:TermGenie") "positive regulation of mitotic nuclear envelope catabolism") @@ -105960,7 +103373,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of vascular endothelial cell proliferation) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:BHF_telomere") Annotation( "GOC:TermGenie") Annotation( "GOC:nc") Annotation( "GO_REF:0000058") Annotation( "PMID:23201774") "Any process that modulates the frequency, rate or extent of vascular endothelial cell proliferation.") -AnnotationAssertion( "nc") AnnotationAssertion( "2016-10-17T09:24:17Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:1905562") @@ -105970,7 +103382,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of vascular endothelial cell proliferation) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:BHF_telomere") Annotation( "GOC:TermGenie") Annotation( "GOC:nc") Annotation( "GO_REF:0000058") Annotation( "PMID:23201774") "Any process that stops, prevents or reduces the frequency, rate or extent of vascular endothelial cell proliferation.") -AnnotationAssertion( "nc") AnnotationAssertion( "2016-10-17T09:24:26Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of vascular endothelial cell proliferation") AnnotationAssertion(Annotation( "GOC:TermGenie") "down-regulation of vascular endothelial cell proliferation") @@ -105984,7 +103395,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of vascular endothelial cell proliferation) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:BHF_telomere") Annotation( "GOC:TermGenie") Annotation( "GOC:nc") Annotation( "GO_REF:0000058") Annotation( "PMID:23201774") "Any process that activates or increases the frequency, rate or extent of vascular endothelial cell proliferation.") -AnnotationAssertion( "nc") AnnotationAssertion( "2016-10-17T09:24:35Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "up regulation of vascular endothelial cell proliferation") AnnotationAssertion(Annotation( "GOC:TermGenie") "up-regulation of vascular endothelial cell proliferation") @@ -105998,7 +103408,6 @@ EquivalentClasses( ObjectIntersection # Class: (outer hair cell apoptotic process) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000085") Annotation( "PMID:12062759") Annotation( "PMID:24472721") "Any apoptotic process in an outer hair cell.") -AnnotationAssertion( "sl") AnnotationAssertion( "2016-10-21T22:42:13Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "cochlear outer hair cell apoptotic process") AnnotationAssertion(Annotation( "GOC:TermGenie") "cochlear outer hair cell apoptosis") @@ -106011,7 +103420,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of outer hair cell apoptotic process) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000058") Annotation( "PMID:24472721") "Any process that modulates the frequency, rate or extent of outer hair cell apoptotic process.") -AnnotationAssertion( "sl") AnnotationAssertion( "2016-10-24T22:35:34Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "regulation of cochlear outer hair cell apoptotic process") AnnotationAssertion(Annotation( "GOC:TermGenie") "regulation of cochlear outer hair cell apoptosis") @@ -106024,7 +103432,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of outer hair cell apoptotic process) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000058") Annotation( "PMID:24472721") "Any process that stops, prevents or reduces the frequency, rate or extent of outer hair cell apoptotic process.") -AnnotationAssertion( "sl") AnnotationAssertion( "2016-10-24T22:35:43Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of cochlear outer hair cell apoptotic process") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of outer hair cell apoptotic process") @@ -106053,7 +103460,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of outer hair cell apoptotic process) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000058") Annotation( "PMID:24472721") "Any process that activates or increases the frequency, rate or extent of outer hair cell apoptotic process.") -AnnotationAssertion( "sl") AnnotationAssertion( "2016-10-24T22:35:51Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "positive regulation of cochlear outer hair cell apoptotic process") AnnotationAssertion(Annotation( "GOC:TermGenie") "up regulation of cochlear outer hair cell apoptotic process") @@ -106082,7 +103488,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of presynapse assembly) AnnotationAssertion(Annotation( "GOC:PARL") Annotation( "GOC:TermGenie") Annotation( "GOC:bc") Annotation( "GO_REF:0000058") Annotation( "PMID:25533483") "Any process that modulates the frequency, rate or extent of presynapse assembly.") -AnnotationAssertion( "bc") AnnotationAssertion( "2016-10-27T16:08:13Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "regulation of presynapse biogenesis") AnnotationAssertion(Annotation( "GOC:TermGenie") "regulation of presynaptic terminal assembly") @@ -106096,7 +103501,6 @@ SubClassOf( ObjectSomeValuesFrom( (negative regulation of presynapse assembly) AnnotationAssertion(Annotation( "GOC:PARL") Annotation( "GOC:TermGenie") Annotation( "GOC:bc") Annotation( "GO_REF:0000058") Annotation( "PMID:25533483") "Any process that stops, prevents or reduces the frequency, rate or extent of presynapse assembly.") -AnnotationAssertion( "bc") AnnotationAssertion( "2016-10-27T16:08:20Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of presynapse assembly") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of presynapse biogenesis") @@ -106121,7 +103525,6 @@ SubClassOf( ObjectSomeValuesFrom( (positive regulation of presynapse assembly) AnnotationAssertion(Annotation( "GOC:PARL") Annotation( "GOC:TermGenie") Annotation( "GOC:bc") Annotation( "GO_REF:0000058") Annotation( "PMID:25533483") "Any process that activates or increases the frequency, rate or extent of presynapse assembly.") -AnnotationAssertion( "bc") AnnotationAssertion( "2016-10-27T16:08:28Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "positive regulation of presynapse biogenesis") AnnotationAssertion(Annotation( "GOC:TermGenie") "positive regulation of presynaptic terminal assembly") @@ -106145,7 +103548,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of serotonin biosynthetic process) AnnotationAssertion(Annotation( "GOC:PARL") Annotation( "GOC:TermGenie") Annotation( "GOC:pad") Annotation( "GO_REF:0000058") Annotation( "PMID:25642596") "Any process that modulates the frequency, rate or extent of serotonin biosynthetic process.") -AnnotationAssertion( "pad") AnnotationAssertion( "2016-10-31T14:26:20Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "regulation of serotonin anabolism") AnnotationAssertion(Annotation( "GOC:TermGenie") "regulation of serotonin biosynthesis") @@ -106159,7 +103561,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of serotonin biosynthetic process) AnnotationAssertion(Annotation( "GOC:PARL") Annotation( "GOC:TermGenie") Annotation( "GOC:pad") Annotation( "GO_REF:0000058") Annotation( "PMID:25642596") "Any process that stops, prevents or reduces the frequency, rate or extent of serotonin biosynthetic process.") -AnnotationAssertion( "pad") AnnotationAssertion( "2016-10-31T14:26:28Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of serotonin anabolism") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of serotonin biosynthesis") @@ -106193,7 +103594,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of serotonin biosynthetic process) AnnotationAssertion(Annotation( "GOC:PARL") Annotation( "GOC:TermGenie") Annotation( "GOC:pad") Annotation( "GO_REF:0000058") Annotation( "PMID:25642596") "Any process that activates or increases the frequency, rate or extent of serotonin biosynthetic process.") -AnnotationAssertion( "pad") AnnotationAssertion( "2016-10-31T14:26:36Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "positive regulation of serotonin anabolism") AnnotationAssertion(Annotation( "GOC:TermGenie") "positive regulation of serotonin biosynthesis") @@ -106227,7 +103627,6 @@ EquivalentClasses( ObjectIntersection # Class: (protein localization to euchromatin) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000087") Annotation( "PMID:20889714") "A process in which a protein is transported to, or maintained in, a location within an euchromatin.") -AnnotationAssertion( "pga") AnnotationAssertion( "2016-11-01T16:16:14Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "protein localisation in euchromatin") AnnotationAssertion(Annotation( "GOC:TermGenie") "protein localisation to euchromatin") @@ -106240,7 +103639,6 @@ EquivalentClasses( ObjectIntersection # Class: (establishment of protein localization to euchromatin) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000087") Annotation( "PMID:20889714") "The directed movement of a protein to a specific location in an euchromatin.") -AnnotationAssertion( "pga") AnnotationAssertion( "2016-11-01T16:16:22Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "establishment of protein localisation in euchromatin") AnnotationAssertion(Annotation( "GOC:TermGenie") "establishment of protein localisation to euchromatin") @@ -106253,7 +103651,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of protein localization to chromatin) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000058") Annotation( "PMID:20889714") "Any process that modulates the frequency, rate or extent of protein localization to chromatin.") -AnnotationAssertion( "pga") AnnotationAssertion( "2016-11-01T16:33:52Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "regulation of protein localisation to chromatin") AnnotationAssertion( "biological_process") @@ -106264,7 +103661,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of artery morphogenesis) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:BHF_miRNA") Annotation( "GOC:TermGenie") Annotation( "GOC:rph") Annotation( "GO_REF:0000058") Annotation( "PMID:27389411") "Any process that modulates the frequency, rate or extent of artery morphogenesis.") -AnnotationAssertion( "rph") AnnotationAssertion( "2016-11-09T12:19:37Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "regulation of arterial morphogenesis") AnnotationAssertion(Annotation( "GOC:TermGenie") "regulation of arteriogenesis") @@ -106276,7 +103672,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of artery morphogenesis) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:BHF_miRNA") Annotation( "GOC:TermGenie") Annotation( "GOC:rph") Annotation( "GO_REF:0000058") Annotation( "PMID:27389411") "Any process that stops, prevents or reduces the frequency, rate or extent of artery morphogenesis.") -AnnotationAssertion( "rph") AnnotationAssertion( "2016-11-09T12:19:53Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of arterial morphogenesis") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of arteriogenesis") @@ -106300,7 +103695,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of artery morphogenesis) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:BHF_miRNA") Annotation( "GOC:TermGenie") Annotation( "GOC:rph") Annotation( "GO_REF:0000058") Annotation( "PMID:27389411") "Any process that activates or increases the frequency, rate or extent of artery morphogenesis.") -AnnotationAssertion( "rph") AnnotationAssertion( "2016-11-09T12:20:01Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "positive regulation of arterial morphogenesis") AnnotationAssertion(Annotation( "GOC:TermGenie") "positive regulation of arteriogenesis") @@ -106324,7 +103718,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of calcium ion import across plasma membrane) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:bhm") Annotation( "GO_REF:0000058") Annotation( "PMID:17640527") "Any process that modulates the frequency, rate or extent of calcium ion import across plasma membrane.") -AnnotationAssertion( "bhm") AnnotationAssertion( "2016-11-11T09:26:06Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:1905664") @@ -106335,7 +103728,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of calcium ion import across plasma membrane) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:bhm") Annotation( "GO_REF:0000058") Annotation( "PMID:17640527") "Any process that activates or increases the frequency, rate or extent of calcium ion import across plasma membrane.") -AnnotationAssertion( "bhm") AnnotationAssertion( "2016-11-11T09:26:23Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "up regulation of calcium ion import across plasma membrane") AnnotationAssertion(Annotation( "GOC:TermGenie") "up-regulation of calcium ion import across plasma membrane") @@ -106350,7 +103742,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of lysosome organization) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000058") Annotation( "PMID:25561470") "Any process that modulates the frequency, rate or extent of lysosome organization.") -AnnotationAssertion( "sl") AnnotationAssertion( "2016-11-11T22:01:04Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "regulation of lysosome organisation") AnnotationAssertion( "biological_process") @@ -106362,7 +103753,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of lysosome organization) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000058") Annotation( "PMID:25561470") "Any process that stops, prevents or reduces the frequency, rate or extent of lysosome organization.") -AnnotationAssertion( "sl") AnnotationAssertion( "2016-11-11T22:01:12Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of lysosome organisation") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of lysosome organization") @@ -106386,7 +103776,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of lysosome organization) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000058") Annotation( "PMID:25561470") "Any process that activates or increases the frequency, rate or extent of lysosome organization.") -AnnotationAssertion( "sl") AnnotationAssertion( "2016-11-11T22:01:20Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "positive regulation of lysosome organisation") AnnotationAssertion(Annotation( "GOC:TermGenie") "up regulation of lysosome organisation") @@ -106410,7 +103799,6 @@ EquivalentClasses( ObjectIntersection # Class: (nucleus disassembly) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:autophagy") Annotation( "GOC:pr") Annotation( "GO_REF:0000079") "The disaggregation of a nucleus into its constituent components.") -AnnotationAssertion( "pr") AnnotationAssertion( "2016-11-14T13:38:57Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "cell nucleus disassembly") AnnotationAssertion( "biological_process") @@ -106421,7 +103809,6 @@ EquivalentClasses( ObjectIntersection # Class: (cytoplasmic microtubule bundle) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000064") Annotation( "PMID:11007487") Annotation( "PMID:26124291") "Any microtubule bundle that is part of a cytoplasm.") -AnnotationAssertion( "mah") AnnotationAssertion( "2016-11-24T16:52:02Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "microtubule bundle of cytoplasm") AnnotationAssertion(Annotation( "GOC:TermGenie") "microtubule fascicle of cytoplasm") @@ -106433,7 +103820,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of saliva secretion) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000058") Annotation( "PMID:23419067") "Any process that stops, prevents or reduces the frequency, rate or extent of saliva secretion.") -AnnotationAssertion( "pga") AnnotationAssertion( "2016-12-09T10:24:00Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of saliva secretion") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of salivation") @@ -106452,7 +103838,6 @@ EquivalentClasses( ObjectIntersection # Class: (protein localization to cytoplasmic microtubule) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000087") Annotation( "PMID:15177031") "A process in which a protein is transported to, or maintained in, a location within a cytoplasmic microtubule.") -AnnotationAssertion( "mah") AnnotationAssertion( "2016-12-12T15:31:07Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "protein localisation to cytoplasmic microtubule") AnnotationAssertion( "biological_process") @@ -106463,7 +103848,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of mesodermal cell differentiation) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:BHF_miRNA") Annotation( "GOC:TermGenie") Annotation( "GOC:rph") Annotation( "GO_REF:0000058") Annotation( "PMID:23765923") "Any process that modulates the frequency, rate or extent of mesodermal cell differentiation.") -AnnotationAssertion( "rph") AnnotationAssertion( "2016-12-21T12:44:13Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "regulation of mesoderm cell differentiation") AnnotationAssertion( "biological_process") @@ -106474,7 +103858,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of mesodermal cell differentiation) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:BHF_miRNA") Annotation( "GOC:TermGenie") Annotation( "GOC:rph") Annotation( "GO_REF:0000058") Annotation( "PMID:23765923") "Any process that stops, prevents or reduces the frequency, rate or extent of mesodermal cell differentiation.") -AnnotationAssertion( "rph") AnnotationAssertion( "2016-12-21T12:44:23Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of mesoderm cell differentiation") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of mesodermal cell differentiation") @@ -106493,7 +103876,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of mesodermal cell differentiation) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:BHF_miRNA") Annotation( "GOC:TermGenie") Annotation( "GOC:rph") Annotation( "GO_REF:0000058") Annotation( "PMID:23765923") "Any process that activates or increases the frequency, rate or extent of mesodermal cell differentiation.") -AnnotationAssertion( "rph") AnnotationAssertion( "2016-12-21T12:44:32Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "positive regulation of mesoderm cell differentiation") AnnotationAssertion(Annotation( "GOC:TermGenie") "up regulation of mesoderm cell differentiation") @@ -106512,7 +103894,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of detection of mechanical stimulus involved in sensory perception of touch) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000058") Annotation( "PMID:8692859") "Any process that modulates the frequency, rate or extent of detection of mechanical stimulus involved in sensory perception of touch.") -AnnotationAssertion( "hbye") AnnotationAssertion( "2017-01-09T15:11:04Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "regulation of perception of touch, detection of mechanical stimulus") AnnotationAssertion(Annotation( "GOC:TermGenie") "regulation of perception of touch, sensory detection of mechanical stimulus") @@ -106529,7 +103910,6 @@ SubClassOf( ObjectSomeValuesFrom( (negative regulation of detection of mechanical stimulus involved in sensory perception of touch) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000058") Annotation( "PMID:8692859") "Any process that stops, prevents or reduces the frequency, rate or extent of detection of mechanical stimulus involved in sensory perception of touch.") -AnnotationAssertion( "hbye") AnnotationAssertion( "2017-01-09T15:11:14Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of detection of mechanical stimulus involved in sensory perception of touch") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of perception of touch, detection of mechanical stimulus") @@ -106574,7 +103954,6 @@ SubClassOf( ObjectSomeValuesFrom( (positive regulation of detection of mechanical stimulus involved in sensory perception of touch) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000058") Annotation( "PMID:8692859") "Any process that activates or increases the frequency, rate or extent of detection of mechanical stimulus involved in sensory perception of touch.") -AnnotationAssertion( "hbye") AnnotationAssertion( "2017-01-09T15:11:23Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "positive regulation of perception of touch, detection of mechanical stimulus") AnnotationAssertion(Annotation( "GOC:TermGenie") "positive regulation of perception of touch, sensory detection of mechanical stimulus") @@ -106619,7 +103998,6 @@ SubClassOf( ObjectSomeValuesFrom( (excitatory synapse pruning) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000079") Annotation( "PMID:27779093") "The disaggregation of an excitatory synapse into its constituent components.") -AnnotationAssertion( "tb") AnnotationAssertion( "2017-01-11T22:03:06Z") AnnotationAssertion( "synapse clearance") AnnotationAssertion( "synapse disassembly") @@ -106634,7 +104012,6 @@ SubClassOf( (regulation of synapse pruning) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000058") Annotation( "PMID:27779093") "Any process that modulates the frequency, rate or extent of synapse pruning.") -AnnotationAssertion( "tb") AnnotationAssertion( "2017-01-11T22:03:15Z") AnnotationAssertion( "regulation of synapse clearance") AnnotationAssertion(Annotation( ) "regulation of synapse disassembly") @@ -106649,7 +104026,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of synapse pruning) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000058") Annotation( "PMID:27779093") "Any process that stops, prevents or reduces the frequency, rate or extent of synapse pruning.") -AnnotationAssertion( "tb") AnnotationAssertion( "2017-01-11T22:03:24Z") AnnotationAssertion( "regulation of synapse clearance") AnnotationAssertion( "regulation of synapse disassembly") @@ -106667,7 +104043,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of synapse pruning) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000058") Annotation( "PMID:27779093") "Any process that activates or increases the frequency, rate or extent of synapse pruning.") -AnnotationAssertion( "tb") AnnotationAssertion( "2017-01-11T22:03:33Z") AnnotationAssertion( "regulation of synapse clearance") AnnotationAssertion( "regulation of synapse disassembly") @@ -106685,7 +104060,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of synapse organization) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000058") Annotation( "PMID:27779093") "Any process that stops, prevents or reduces the frequency, rate or extent of synapse organization.") -AnnotationAssertion( "tb") AnnotationAssertion( "2017-01-11T22:03:41Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of synapse development") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of synapse organisation") @@ -106719,7 +104093,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of excitatory synapse pruning) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000058") Annotation( "PMID:27779093") "Any process that modulates the frequency, rate or extent of excitatory synapse pruning.") -AnnotationAssertion( "tb") AnnotationAssertion( "2017-01-12T02:38:27Z") AnnotationAssertion( "regulation of synapse clearance") AnnotationAssertion( "regulation of synapse disassembly") @@ -106733,7 +104106,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of excitatory synapse pruning) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000058") Annotation( "PMID:27779093") "Any process that stops, prevents or reduces the frequency, rate or extent of excitatory synapse pruning.") -AnnotationAssertion( "tb") AnnotationAssertion( "2017-01-12T02:38:36Z") AnnotationAssertion( "regulation of synapse clearance") AnnotationAssertion( "regulation of synapse disassembly") @@ -106751,7 +104123,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of chromosome condensation) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:bhm") Annotation( "GO_REF:0000058") Annotation( "PMID:17268547") "Any process that activates or increases the frequency, rate or extent of chromosome condensation.") -AnnotationAssertion( "bhm") AnnotationAssertion( "2017-01-13T14:13:44Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "positive regulation of eukaryotic chromosome condensation") AnnotationAssertion(Annotation( "GOC:TermGenie") "positive regulation of nuclear chromosome condensation") @@ -106775,7 +104146,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of microtubule nucleation) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000058") Annotation( "PMID:27689799") "Any process that stops, prevents or reduces the frequency, rate or extent of microtubule nucleation.") -AnnotationAssertion( "hbye") AnnotationAssertion( "2017-01-17T12:00:56Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of microtubule nucleation") AnnotationAssertion(Annotation( "GOC:TermGenie") "down-regulation of microtubule nucleation") @@ -106790,7 +104160,6 @@ SubClassOf( ObjectSomeValuesFrom( (epididymis development) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000094") Annotation( "PMID:12388089") "The process whose specific outcome is the progression of an epididymis over time, from its formation to the mature structure.") -AnnotationAssertion( "sl") AnnotationAssertion( "2017-01-27T00:00:33Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "epididymus development") AnnotationAssertion( "biological_process") @@ -106801,7 +104170,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of protein localization to cell leading edge) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000058") Annotation( "PMID:26324884") "Any process that modulates the frequency, rate or extent of protein localization to cell leading edge.") -AnnotationAssertion( "sl") AnnotationAssertion( "2017-01-27T19:34:55Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "regulation of protein localisation in cell leading edge") AnnotationAssertion(Annotation( "GOC:TermGenie") "regulation of protein localisation to cell leading edge") @@ -106814,7 +104182,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of protein localization to cell leading edge) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000058") Annotation( "PMID:26324884") "Any process that stops, prevents or reduces the frequency, rate or extent of protein localization to cell leading edge.") -AnnotationAssertion( "sl") AnnotationAssertion( "2017-01-27T19:35:04Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of protein localisation in cell leading edge") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of protein localisation to cell leading edge") @@ -106843,7 +104210,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of protein localization to cell leading edge) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000058") Annotation( "PMID:26324884") "Any process that activates or increases the frequency, rate or extent of protein localization to cell leading edge.") -AnnotationAssertion( "sl") AnnotationAssertion( "2017-01-27T19:35:13Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "positive regulation of protein localisation in cell leading edge") AnnotationAssertion(Annotation( "GOC:TermGenie") "positive regulation of protein localisation to cell leading edge") @@ -106872,7 +104238,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of oogenesis) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000058") Annotation( "PMID:26434723") "Any process that modulates the frequency, rate or extent of oogenesis.") -AnnotationAssertion( "hbye") AnnotationAssertion( "2017-01-31T09:31:05Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "regulation of ovum development") AnnotationAssertion( "biological_process") @@ -106884,7 +104249,6 @@ SubClassOf( ObjectSomeValuesFrom( (negative regulation of oogenesis) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000058") Annotation( "PMID:26434723") "Any process that stops, prevents or reduces the frequency, rate or extent of oogenesis.") -AnnotationAssertion( "hbye") AnnotationAssertion( "2017-01-31T09:31:15Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of oogenesis") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of ovum development") @@ -106904,7 +104268,6 @@ SubClassOf( ObjectSomeValuesFrom( (positive regulation of oogenesis) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000058") Annotation( "PMID:26434723") "Any process that activates or increases the frequency, rate or extent of oogenesis.") -AnnotationAssertion( "hbye") AnnotationAssertion( "2017-01-31T09:31:23Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "positive regulation of ovum development") AnnotationAssertion(Annotation( "GOC:TermGenie") "up regulation of oogenesis") @@ -106924,7 +104287,6 @@ SubClassOf( ObjectSomeValuesFrom( (regulation of smooth muscle tissue development) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:bhm") Annotation( "GO_REF:0000058") Annotation( "PMID:14709716") "Any process that modulates the frequency, rate or extent of smooth muscle tissue development.") -AnnotationAssertion( "bhm") AnnotationAssertion( "2017-02-01T14:31:16Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:1905899") @@ -106934,7 +104296,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of smooth muscle tissue development) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:bhm") Annotation( "GO_REF:0000058") Annotation( "PMID:14709716") "Any process that stops, prevents or reduces the frequency, rate or extent of smooth muscle tissue development.") -AnnotationAssertion( "bhm") AnnotationAssertion( "2017-02-01T14:31:24Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of smooth muscle tissue development") AnnotationAssertion(Annotation( "GOC:TermGenie") "down-regulation of smooth muscle tissue development") @@ -106948,7 +104309,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of smooth muscle tissue development) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:bhm") Annotation( "GO_REF:0000058") Annotation( "PMID:14709716") "Any process that activates or increases the frequency, rate or extent of smooth muscle tissue development.") -AnnotationAssertion( "bhm") AnnotationAssertion( "2017-02-01T14:31:33Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "up regulation of smooth muscle tissue development") AnnotationAssertion(Annotation( "GOC:TermGenie") "up-regulation of smooth muscle tissue development") @@ -106962,7 +104322,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of mesoderm formation) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:BHF_miRNA") Annotation( "GOC:TermGenie") Annotation( "GOC:rph") Annotation( "GO_REF:0000058") Annotation( "PMID:23939491") "Any process that modulates the frequency, rate or extent of mesoderm formation.") -AnnotationAssertion( "rph") AnnotationAssertion( "2017-02-03T12:28:20Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:1905902") @@ -106972,7 +104331,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of mesoderm formation) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:BHF_miRNA") Annotation( "GOC:TermGenie") Annotation( "GOC:rph") Annotation( "GO_REF:0000058") Annotation( "PMID:23939491") "Any process that stops, prevents or reduces the frequency, rate or extent of mesoderm formation.") -AnnotationAssertion( "rph") AnnotationAssertion( "2017-02-03T12:28:29Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of mesoderm formation") AnnotationAssertion(Annotation( "GOC:TermGenie") "down-regulation of mesoderm formation") @@ -106987,7 +104345,6 @@ SubClassOf( ObjectSomeValuesFrom( (positive regulation of mesoderm formation) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:BHF_miRNA") Annotation( "GOC:TermGenie") Annotation( "GOC:rph") Annotation( "GO_REF:0000058") Annotation( "PMID:23939491") "Any process that activates or increases the frequency, rate or extent of mesoderm formation.") -AnnotationAssertion( "rph") AnnotationAssertion( "2017-02-03T12:28:38Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "up regulation of mesoderm formation") AnnotationAssertion(Annotation( "GOC:TermGenie") "up-regulation of mesoderm formation") @@ -107002,7 +104359,6 @@ SubClassOf( ObjectSomeValuesFrom( (regulation of calcium ion export across plasma membrane) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:BHF_miRNA") Annotation( "GOC:TermGenie") Annotation( "GOC:rph") Annotation( "GO_REF:0000058") Annotation( "PMID:22362515") "Any process that modulates the frequency, rate or extent of calcium ion export across the plasma membrane.") -AnnotationAssertion( "rph") AnnotationAssertion( "2017-02-07T13:20:39Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "regulation of calcium ion efflux from cell") AnnotationAssertion( "regulation of calcium ion export from cell") @@ -107014,7 +104370,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of calcium ion export across plasma membrane) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:BHF_miRNA") Annotation( "GOC:TermGenie") Annotation( "GOC:rph") Annotation( "GO_REF:0000058") Annotation( "PMID:22362515") "Any process that stops, prevents or reduces the frequency, rate or extent of calcium ion export across the plasma membrane.") -AnnotationAssertion( "rph") AnnotationAssertion( "2017-02-07T13:20:48Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of calcium ion efflux from cell") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of calcium ion export from cell") @@ -107034,7 +104389,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of calcium ion export across plasma membrane) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:BHF_miRNA") Annotation( "GOC:TermGenie") Annotation( "GOC:rph") Annotation( "GO_REF:0000058") Annotation( "PMID:22362515") "Any process that activates or increases the frequency, rate or extent of calcium ion export across the plasma membrane.") -AnnotationAssertion( "rph") AnnotationAssertion( "2017-02-07T13:20:56Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "positive regulation of calcium ion efflux from cell") AnnotationAssertion( "positive regulation of calcium ion export from cell") @@ -107054,7 +104408,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of acetylcholine biosynthetic process) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:aruk") Annotation( "GOC:bc") Annotation( "GO_REF:0000058") Annotation( "PMID:20164328") "Any process that modulates the frequency, rate or extent of acetylcholine biosynthetic process.") -AnnotationAssertion( "bc") AnnotationAssertion( "2017-02-08T13:08:30Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "regulation of acetylcholine anabolism") AnnotationAssertion(Annotation( "GOC:TermGenie") "regulation of acetylcholine biosynthesis") @@ -107068,7 +104421,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of acetylcholine biosynthetic process) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:aruk") Annotation( "GOC:bc") Annotation( "GO_REF:0000058") Annotation( "PMID:20164328") "Any process that stops, prevents or reduces the frequency, rate or extent of acetylcholine biosynthetic process.") -AnnotationAssertion( "bc") AnnotationAssertion( "2017-02-08T13:08:39Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of acetylcholine anabolism") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of acetylcholine biosynthesis") @@ -107102,7 +104454,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of acetylcholine biosynthetic process) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:aruk") Annotation( "GOC:bc") Annotation( "GO_REF:0000058") Annotation( "PMID:20164328") "Any process that activates or increases the frequency, rate or extent of acetylcholine biosynthetic process.") -AnnotationAssertion( "bc") AnnotationAssertion( "2017-02-08T13:08:48Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "positive regulation of acetylcholine anabolism") AnnotationAssertion(Annotation( "GOC:TermGenie") "positive regulation of acetylcholine biosynthesis") @@ -107136,7 +104487,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of germ cell proliferation) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000058") Annotation( "PMID:15342467") "Any process that modulates the frequency, rate or extent of germ cell proliferation.") -AnnotationAssertion( "hbye") AnnotationAssertion( "2017-02-09T14:51:31Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:1905936") @@ -107147,7 +104497,6 @@ SubClassOf( ObjectSomeValuesFrom( (negative regulation of germ cell proliferation) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000058") Annotation( "PMID:15342467") "Any process that stops, prevents or reduces the frequency, rate or extent of germ cell proliferation.") -AnnotationAssertion( "hbye") AnnotationAssertion( "2017-02-09T14:51:41Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of germ cell proliferation") AnnotationAssertion(Annotation( "GOC:TermGenie") "down-regulation of germ cell proliferation") @@ -107162,7 +104511,6 @@ SubClassOf( ObjectSomeValuesFrom( (positive regulation of germ cell proliferation) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000058") Annotation( "PMID:15342467") "Any process that activates or increases the frequency, rate or extent of germ cell proliferation.") -AnnotationAssertion( "hbye") AnnotationAssertion( "2017-02-09T14:51:51Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "up regulation of germ cell proliferation") AnnotationAssertion(Annotation( "GOC:TermGenie") "up-regulation of germ cell proliferation") @@ -107177,7 +104525,6 @@ SubClassOf( ObjectSomeValuesFrom( (regulation of gonad development) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000058") Annotation( "PMID:15342467") "Any process that modulates the frequency, rate or extent of gonad development.") -AnnotationAssertion( "hbye") AnnotationAssertion( "2017-02-09T17:01:50Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "regulation of gonadogenesis") AnnotationAssertion( "biological_process") @@ -107188,7 +104535,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of gonad development) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000058") Annotation( "PMID:15342467") "Any process that stops, prevents or reduces the frequency, rate or extent of gonad development.") -AnnotationAssertion( "hbye") AnnotationAssertion( "2017-02-09T17:01:59Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of gonad development") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of gonadogenesis") @@ -107208,7 +104554,6 @@ SubClassOf( ObjectSomeValuesFrom( (positive regulation of gonad development) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000058") Annotation( "PMID:15342467") "Any process that activates or increases the frequency, rate or extent of gonad development.") -AnnotationAssertion( "hbye") AnnotationAssertion( "2017-02-09T17:02:08Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "positive regulation of gonadogenesis") AnnotationAssertion(Annotation( "GOC:TermGenie") "up regulation of gonad development") @@ -107228,7 +104573,6 @@ SubClassOf( ObjectSomeValuesFrom( (regulation of response to calcium ion) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:aruk") Annotation( "GOC:bc") Annotation( "GO_REF:0000058") Annotation( "PMID:11404397") "Any process that modulates the frequency, rate or extent of response to calcium ion.") -AnnotationAssertion( "bc") AnnotationAssertion( "2017-02-13T10:56:34Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "regulation of response to Ca2+ ion") AnnotationAssertion( "biological_process") @@ -107239,7 +104583,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of response to calcium ion) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:aruk") Annotation( "GOC:bc") Annotation( "GO_REF:0000058") Annotation( "PMID:11404397") "Any process that stops, prevents or reduces the frequency, rate or extent of response to calcium ion.") -AnnotationAssertion( "bc") AnnotationAssertion( "2017-02-13T10:56:41Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of response to Ca2+ ion") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of response to calcium ion") @@ -107258,7 +104601,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of response to calcium ion) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:aruk") Annotation( "GOC:bc") Annotation( "GO_REF:0000058") Annotation( "PMID:11404397") "Any process that activates or increases the frequency, rate or extent of response to calcium ion.") -AnnotationAssertion( "bc") AnnotationAssertion( "2017-02-13T10:56:49Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "positive regulation of response to Ca2+ ion") AnnotationAssertion(Annotation( "GOC:TermGenie") "up regulation of response to Ca2+ ion") @@ -107277,7 +104619,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of calcium ion import across plasma membrane) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GOC:bhm") Annotation( "GO_REF:0000058") Annotation( "PMID:17640527") "Any process that stops, prevents or reduces the frequency, rate or extent of calcium ion import across plasma membrane.") -AnnotationAssertion( "bhm") AnnotationAssertion( "2017-02-17T09:42:30Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of calcium ion import across plasma membrane") AnnotationAssertion(Annotation( "GOC:TermGenie") "down-regulation of calcium ion import across plasma membrane") @@ -107292,7 +104633,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of lipid localization) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000058") Annotation( "PMID:17564681") "Any process that modulates the frequency, rate or extent of lipid localization.") -AnnotationAssertion( "rz") AnnotationAssertion( "2017-02-21T12:12:22Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "regulation of lipid localisation") AnnotationAssertion( "biological_process") @@ -107303,7 +104643,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of lipid localization) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000058") Annotation( "PMID:17564681") "Any process that stops, prevents or reduces the frequency, rate or extent of lipid localization.") -AnnotationAssertion( "rz") AnnotationAssertion( "2017-02-21T12:12:41Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of lipid localisation") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of lipid localization") @@ -107322,7 +104661,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of lipid localization) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000058") Annotation( "PMID:17564681") "Any process that activates or increases the frequency, rate or extent of lipid localization.") -AnnotationAssertion( "rz") AnnotationAssertion( "2017-02-21T12:12:49Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "positive regulation of lipid localisation") AnnotationAssertion(Annotation( "GOC:TermGenie") "up regulation of lipid localisation") @@ -107341,7 +104679,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of endothelial tube morphogenesis) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:BHF_miRNA") Annotation( "GOC:TermGenie") Annotation( "GOC:rph") Annotation( "GO_REF:0000058") Annotation( "PMID:25961718") "Any process that stops, prevents or reduces the frequency, rate or extent of endothelial tube morphogenesis.") -AnnotationAssertion( "rph") AnnotationAssertion( "2017-02-21T15:17:31Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "down regulation of endothelial tube morphogenesis") AnnotationAssertion(Annotation( "GOC:TermGenie") "down-regulation of endothelial tube morphogenesis") @@ -107356,7 +104693,6 @@ SubClassOf( ObjectSomeValuesFrom( (positive regulation of endothelial tube morphogenesis) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:BHF_miRNA") Annotation( "GOC:TermGenie") Annotation( "GOC:rph") Annotation( "GO_REF:0000058") Annotation( "PMID:25961718") "Any process that activates or increases the frequency, rate or extent of endothelial tube morphogenesis.") -AnnotationAssertion( "rph") AnnotationAssertion( "2017-02-21T15:17:39Z") AnnotationAssertion(Annotation( "GOC:TermGenie") "up regulation of endothelial tube morphogenesis") AnnotationAssertion(Annotation( "GOC:TermGenie") "up-regulation of endothelial tube morphogenesis") @@ -107371,7 +104707,6 @@ SubClassOf( ObjectSomeValuesFrom( (glutamatergic neuron differentiation) AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000086") Annotation( "PMID:24030726") "The process in which a relatively unspecialized cell acquires the specialized features of a glutamatergic neuron.") -AnnotationAssertion( "sl") AnnotationAssertion( "2017-02-23T17:40:43Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:1905962") @@ -107381,7 +104716,6 @@ EquivalentClasses( ObjectIntersection # Class: (retinal cell apoptotic process) AnnotationAssertion(Annotation( "GOC:mtg_apoptosis") Annotation( "PMID:15558487") Annotation( "PMID:24664675") "Any apoptotic process in a retinal cell.") -AnnotationAssertion( "pr") AnnotationAssertion( "2012-12-12T10:15:08Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "induction of retinal programmed cell death") @@ -107393,7 +104727,6 @@ SubClassOf( (compound eye retinal cell apoptotic process) AnnotationAssertion(Annotation( "GOC:mtg_apoptosis") Annotation( "PMID:12021768") "Any apoptotic process in a compound eye retinal cell.") -AnnotationAssertion( "pr") AnnotationAssertion( "2012-12-12T10:21:07Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:1990010") @@ -107404,7 +104737,6 @@ SubClassOf( (calcium ion export across plasma membrane) AnnotationAssertion(Annotation( "GOC:mah") Annotation( "PMID:2145281") "The directed movement of calcium ions from inside of a cell, across the plasma membrane and into the extracellular region.") -AnnotationAssertion( "mah") AnnotationAssertion( "2013-02-07T13:01:29Z") AnnotationAssertion(Annotation( "GOC:vw") Annotation( "PMID:2145281") "calcium ion efflux from cell") AnnotationAssertion( "calcium ion export from cell") @@ -107428,7 +104760,6 @@ SubClassOf( (retrograde neuronal dense core vesicle transport) AnnotationAssertion(Annotation( "GOC:kmv") Annotation( "PMID:23358451") Annotation( "PMID:24762653") "The directed movement of neuronal dense core vesicles along axonal microtubules towards the cell body.") -AnnotationAssertion( "pr") AnnotationAssertion( "2013-02-19T13:31:44Z") AnnotationAssertion( "retrograde dense core granule trafficking") AnnotationAssertion( "retrograde dense core granule transport") @@ -107441,7 +104772,6 @@ EquivalentClasses( ObjectIntersection # Class: (lens fiber cell apoptotic process) AnnotationAssertion(Annotation( "CL:0011004") Annotation( "GOC:hjd") Annotation( "PMID:11095619") "Any apoptotic process in a lens fiber cell. Lens fiber cells are elongated, tightly packed cells that make up the bulk of the mature lens in a camera-type eye.") -AnnotationAssertion( "hjd") AnnotationAssertion( "2013-05-01T19:09:28Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:1990086") @@ -107452,7 +104782,6 @@ EquivalentClasses( ObjectIntersection AnnotationAssertion(Annotation( "GOC:hjd") Annotation( "PMID:10572093") Annotation( "PMID:12154376") Annotation( "PMID:16773132") Annotation( "PMID:18617898") "The process whereby a membrane-bounded vesicle is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane.") AnnotationAssertion( ) -AnnotationAssertion( "hjd") AnnotationAssertion( "2013-09-04T21:08:14Z") AnnotationAssertion(Annotation( "PMID:18617898") "exosomal secretory pathway") AnnotationAssertion(Annotation( "GOC:hjd") "extracellular vesicular exosome secretion") @@ -107472,7 +104801,6 @@ DisjointClasses( ObjectSomeValuesFrom # Class: (euchromatin binding) AnnotationAssertion(Annotation( "GOC:vw") Annotation( "PMID:22431512") "Binding to euchromatin, a dispersed and relatively uncompacted form of chromatin.") -AnnotationAssertion( "tb") AnnotationAssertion( "2013-09-11T19:18:38Z") AnnotationAssertion( "molecular_function") AnnotationAssertion( "GO:1990188") @@ -107483,7 +104811,6 @@ SubClassOf( (transferase complex) AnnotationAssertion(Annotation( "GOC:bhm") Annotation( "PMID:16540464") "A protein complex capable of catalyzing the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor).") -AnnotationAssertion( "bhm") AnnotationAssertion( "2013-11-12T13:20:12Z") AnnotationAssertion( "cellular_component") AnnotationAssertion( "GO:1990234") @@ -107493,7 +104820,6 @@ EquivalentClasses( ObjectIntersection # Class: (steroid hormone binding) AnnotationAssertion(Annotation( "GOC:ln") "Binding to a steroid hormone.") -AnnotationAssertion( "pr") AnnotationAssertion( "2013-11-15T09:26:18Z") AnnotationAssertion( "molecular_function") AnnotationAssertion( "GO:1990239") @@ -107505,7 +104831,6 @@ SubClassOf( (keratin filament binding) AnnotationAssertion(Annotation( "GOC:krc") Annotation( "PMID:6170061") "Binding to a keratin filament, an intermediate filament composed of acidic and basic keratins (types I and II), typically expressed in epithelial cells.") -AnnotationAssertion( "tb") AnnotationAssertion( "2013-12-13T22:05:25Z") AnnotationAssertion( "molecular_function") AnnotationAssertion( "GO:1990254") @@ -107516,7 +104841,6 @@ SubClassOf( (neutrophil migration) AnnotationAssertion(Annotation( "PMID:1826836") "The movement of a neutrophil within or between different tissues and organs of the body.") -AnnotationAssertion( "sl") AnnotationAssertion( "2014-01-10T00:17:47Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:1990266") @@ -107527,7 +104851,6 @@ SubClassOf( (RNA localization to chromatin) AnnotationAssertion(Annotation( "GOC:dos") Annotation( "GOC:mah") Annotation( "PMID:22582262") "A process in which RNA is transported to and maintained in a part of a chromosome that is organized into chromatin.") -AnnotationAssertion( "mah") AnnotationAssertion( "2014-01-30T15:55:34Z") AnnotationAssertion( "RNA localisation to chromatin") AnnotationAssertion( "biological_process") @@ -107539,7 +104862,6 @@ SubClassOf( (transporter complex) AnnotationAssertion(Annotation( "GOC:bhm") Annotation( "PMID:15449578") "A protein complex facilitating transport of molecules (proteins, small molecules, nucleic acids) into, out of or within a cell, or between cells.") -AnnotationAssertion( "bhm") AnnotationAssertion( "2014-03-26T14:23:27Z") AnnotationAssertion( "cellular_component") AnnotationAssertion( "GO:1990351") @@ -107550,7 +104872,6 @@ EquivalentClasses( ObjectIntersection # Class: (baculum development) AnnotationAssertion(Annotation( "GOC:sl") Annotation( "PMID:21471296") "The reproductive developmental process whose specific outcome is the progression of the baculum over time, from its formation to the mature structure.") -AnnotationAssertion( "sl") AnnotationAssertion( "2014-05-01T23:59:13Z") AnnotationAssertion(Annotation( "GOC:sl") "os penis development") AnnotationAssertion(Annotation( "GOC:sl") "penile bone development") @@ -107564,7 +104885,6 @@ SubClassOf( (lipid transport across blood-brain barrier) AnnotationAssertion(Annotation( "GOC:sjp") Annotation( "PMID:24345162") "The directed movement of lipid molecules passing through the blood-brain barrier.") -AnnotationAssertion( "sjp") AnnotationAssertion( "2014-05-08T09:52:28Z") AnnotationAssertion( "lipid transport across blood brain barrier") AnnotationAssertion( "biological_process") @@ -107577,7 +104897,6 @@ SubClassOf( ObjectAllValuesFrom( (detoxification of iron ion) AnnotationAssertion(Annotation( "GOC:sart") Annotation( "PMID:23064556") "Any process that reduces or removes the toxicity of iron ion. These include transport of iron away from sensitive areas and to compartments or complexes whose purpose is sequestration of iron ion.") -AnnotationAssertion( "sart") AnnotationAssertion( "2014-08-19T10:12:46Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:1990461") @@ -107589,7 +104908,6 @@ SubClassOf( ObjectSomeValuesFrom( (dense core granule maturation) AnnotationAssertion(Annotation( "GOC:kmv") Annotation( "PMID:22654674") "Steps required to transform a dense core granule generated at the trans-Golgi network into a fully formed and transmissible dense core granule. Dense core granule maturation proceeds through clathrin-mediated membrane remodeling events and is essential for efficient processing of cargo within dense core granules as well as for removing factors that might otherwise interfere with dense core granule trafficking and exocytosis.") -AnnotationAssertion( "kmv") AnnotationAssertion( "2014-09-30T20:35:11Z") AnnotationAssertion( "dense core vesicle maturation") AnnotationAssertion( "biological_process") @@ -107601,7 +104919,6 @@ SubClassOf( (potassium ion import across plasma membrane) AnnotationAssertion(Annotation( "PMID:9139127") "The directed movement of potassium ions from outside of a cell, across the plasma membrane and into the cytosol.") -AnnotationAssertion( "vw") AnnotationAssertion( "2014-12-04T09:48:12Z") AnnotationAssertion( "potassium import") AnnotationAssertion( "potassium ion import") @@ -107614,7 +104931,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of cytoplasmic translational termination) AnnotationAssertion(Annotation( "PMID:11570975") "Any process that modulates the frequency, rate or extent of cytoplasmic translational termination.") -AnnotationAssertion( "vw") AnnotationAssertion( "2014-12-10T15:48:55Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:1990580") @@ -107626,7 +104942,6 @@ SubClassOf( ObjectSomeValuesFrom( (sebum secreting cell proliferation) AnnotationAssertion(Annotation( "GOC:hjd") Annotation( "PMID:16901790") Annotation( "PMID:18474083") "The multiplication or reproduction of sebocytes by cell division, resulting in the expansion of their population. A sebocyte is an epithelial cell that makes up the sebaceous glands, and secrete sebum.") -AnnotationAssertion( "hjd") AnnotationAssertion( "2015-02-23T19:43:49Z") AnnotationAssertion( "biological_process") AnnotationAssertion(Annotation( "GOC:dph") "sebocyte proliferation") @@ -107649,7 +104964,6 @@ SubClassOf( (axonemal central apparatus) AnnotationAssertion(Annotation( "GOC:cilia") Annotation( "PMID:21586547") Annotation( "PMID:9295136") "Part of the 9+2 axoneme, that occurs in most motile cilia, consisting of the pair of two single central microtubules and their associated structures which include the central pair projections, the central pair bridges linking the two tubules, and the central pair caps which are attached to the distal or plus ends of the microtubules.") -AnnotationAssertion( "krc") AnnotationAssertion( "2015-03-27T22:33:23Z") AnnotationAssertion( "cellular_component") AnnotationAssertion( "GO:1990716") @@ -107660,7 +104974,6 @@ SubClassOf( ObjectSomeValuesFrom( (C1 axonemal microtubule) AnnotationAssertion(Annotation( "GOC:cilia") Annotation( "PMID:21586547") Annotation( "PMID:9295136") "One of two microtubules present in the axonemal central pair. It is distinguishable from the C2 axonemal microtubule (also called C2 tubule) by the presence of differing protein components of the projections.") -AnnotationAssertion( "krc") AnnotationAssertion( "2015-03-27T22:55:12Z") AnnotationAssertion( "C1 tubule") AnnotationAssertion( "cellular_component") @@ -107672,7 +104985,6 @@ SubClassOf( ObjectSomeValuesFrom( (C2 axonemal microtubule) AnnotationAssertion(Annotation( "GOC:cilia") Annotation( "PMID:21586547") Annotation( "PMID:9295136") "One of two microtubules present in the axonemal central pair. It is distinguishable from the C1 axonemal microtubule (also called C1 tubule) by the presence of differing protein components of the projections.") -AnnotationAssertion( "krc") AnnotationAssertion( "2015-03-27T22:58:40Z") AnnotationAssertion( "C2 tubule") AnnotationAssertion( "cellular_component") @@ -107684,7 +104996,6 @@ SubClassOf( ObjectSomeValuesFrom( (granulosa cell proliferation) AnnotationAssertion(Annotation( "PMID:22383759") "The multiplication or reproduction of granulosa cells, resulting in the expansion of the granulosa cells population. A granulosa cell is a supporting cell for the developing female gamete in the ovary of mammals. They develop from the coelomic epithelial cells of the gonadal ridge.") -AnnotationAssertion( "sl") AnnotationAssertion( "2015-05-06T18:56:04Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:1990739") @@ -107695,7 +105006,6 @@ SubClassOf( (cellular detoxification) AnnotationAssertion(Annotation( "GOC:vw") "Any process carried out at the cellular level that reduces or removes the toxicity of a toxic substance. These may include transport of the toxic substance away from sensitive areas and to compartments or complexes whose purpose is sequestration of the toxic substance.") -AnnotationAssertion( "vw") AnnotationAssertion( "2015-05-18T16:17:46Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:1990748") @@ -107707,7 +105017,6 @@ SubClassOf( ObjectSomeValuesFrom( (Schwann cell chemotaxis) AnnotationAssertion(Annotation( "PMID:16203995") "The directed movement of a Schwann cell guided by a specific chemical concentration gradient. Movement may be towards a higher concentration (positive chemotaxis) or towards a lower concentration (negative chemotaxis).") -AnnotationAssertion( "sl") AnnotationAssertion( "2015-05-21T19:19:09Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:1990751") @@ -107719,7 +105028,6 @@ SubClassOf( (colon smooth muscle contraction) AnnotationAssertion(Annotation( "PMID:24170253") "A process in which force is generated within smooth muscle tissue, resulting in a change in muscle geometry of the large intestine, exclusive of the rectum. The colon is that part of the large intestine that connects the small intestine to the rectum.") -AnnotationAssertion( "sl") AnnotationAssertion( "2015-06-10T18:29:21Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:1990765") @@ -107733,7 +105041,6 @@ SubClassOf( ObjectAllValuesFrom( (gastric mucosal blood circulation) AnnotationAssertion(Annotation( "PMID:10807413") "The flow of blood through the gastric mucosa of an animal, enabling the transport of nutrients and the removal of waste products.") -AnnotationAssertion( "sl") AnnotationAssertion( "2015-06-10T20:11:09Z") AnnotationAssertion( "stomach mucosal blood circulation") AnnotationAssertion( "biological_process") @@ -107745,7 +105052,6 @@ SubClassOf( (small intestine smooth muscle contraction) AnnotationAssertion(Annotation( "PMID:11991626") "A process in which force is generated within smooth muscle tissue, resulting in a change in muscle geometry in the intestine between the stomach and the large intestine.") -AnnotationAssertion( "sl") AnnotationAssertion( "2015-06-11T18:02:33Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:1990770") @@ -107759,7 +105065,6 @@ SubClassOf( ObjectAllValuesFrom( (lipoprotein particle) AnnotationAssertion(Annotation( "GOC:vesicles") "A spherical particle containing non-covalently associated proteins and lipids. Examples are plasma lipoprotein particles which transport lipids in the blood or lymph.") -AnnotationAssertion( "pr") AnnotationAssertion( "2015-06-18T08:42:53Z") AnnotationAssertion( "cellular_component") AnnotationAssertion( "GO:1990777") @@ -107779,7 +105084,6 @@ SubClassOf( (dorsal root ganglion development) AnnotationAssertion(Annotation( "PMID:18583150") "The process whose specific outcome is the progression of a dorsal root ganglion over time, from its formation to the mature structure.") -AnnotationAssertion( "sl") AnnotationAssertion( "2015-07-02T22:09:54Z") AnnotationAssertion( "DRG development") AnnotationAssertion( "biological_process") @@ -107791,7 +105095,6 @@ SubClassOf( (ligand-gated ion channel signaling pathway) AnnotationAssertion(Annotation( "GOC:bhm") Annotation( "PMID:25869137") "The series of molecular signals initiated by activation of a ligand-gated ion channel on the surface of a cell. The pathway begins with binding of an extracellular ligand to a ligand-gated ion channel and ends with a molecular function that directly regulates a downstream cellular process, e.g. transcription.") -AnnotationAssertion( "bhm") AnnotationAssertion( "2015-07-20T12:09:56Z") AnnotationAssertion( "ligand-gated ion channel signalling pathway") AnnotationAssertion( "biological_process") @@ -107802,7 +105105,6 @@ EquivalentClasses( ObjectIntersection # Class: (basic amino acid transmembrane transport) AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:vw") "The directed movement of basic amino acids from one side of a membrane to the other.") -AnnotationAssertion( "vw") AnnotationAssertion( "2015-08-19T07:47:00Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:1990822") @@ -107812,7 +105114,6 @@ EquivalentClasses( ObjectIntersection # Class: (adaptive thermogenesis) AnnotationAssertion(Annotation( "PMID:17260010") Annotation( "PMID:20363363") "The regulated production of heat in response to short term environmental changes, such as stress, diet or reduced temperature.") -AnnotationAssertion( "sl") AnnotationAssertion( "2015-08-31T18:19:49Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:1990845") @@ -107823,7 +105124,6 @@ SubClassOf( "PMID:26283797") "Any process in which the vacuole is transported to, and/or maintained in, a specific location within the cell.") AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/22182"^^xsd:anyURI) -AnnotationAssertion( "mcc") AnnotationAssertion( "2015-09-10T08:16:02Z") AnnotationAssertion( "maintenance of vacuolar localization") AnnotationAssertion( "maintenance of vacuole localization") @@ -107837,7 +105137,6 @@ EquivalentClasses( ObjectIntersection # Class: (acinar cell proliferation) AnnotationAssertion(Annotation( "PMID:9788538") "The multiplication or reproduction of acinar cells, resulting in the expansion of a cell population. An acinar cell is a secretory cell that is grouped together with other cells of the same type to form grape-shaped clusters known as acini (singular acinus).") -AnnotationAssertion( "sl") AnnotationAssertion( "2015-09-25T14:26:09Z") AnnotationAssertion( "acinic cell proliferation") AnnotationAssertion( "acinous cell proliferation") @@ -107850,7 +105149,6 @@ SubClassOf( (vascular associated smooth muscle cell proliferation) AnnotationAssertion(Annotation( "PMID:23246467") "The multiplication or reproduction of vascular smooth muscle cells, resulting in the expansion of a cell population. A vascular smooth muscle cell is a non-striated, elongated, spindle-shaped cell found lining the blood vessels.") -AnnotationAssertion( "sl") AnnotationAssertion( "2015-09-29T16:34:59Z") AnnotationAssertion( "VSMC proliferation") AnnotationAssertion( "vascular smooth muscle cell proliferation") @@ -107863,7 +105161,6 @@ SubClassOf( (ribonucleoprotein complex) AnnotationAssertion(Annotation( "GOC:krc") Annotation( "GOC:vesicles") "A macromolecular complex that contains both RNA and protein molecules.") -AnnotationAssertion( "pr") AnnotationAssertion( "2015-11-19T12:26:37Z") AnnotationAssertion( "Wikipedia:Ribonucleoprotein") AnnotationAssertion( "RNA-protein complex") @@ -107883,7 +105180,6 @@ SubClassOf( ObjectSomeValuesFrom( "PMID:19022436") "The cytoplasm of an ovum.") AnnotationAssertion( ) -AnnotationAssertion( "sl") AnnotationAssertion( "2015-12-10T21:40:16Z") AnnotationAssertion( "cellular_component") AnnotationAssertion( "GO:1990917") @@ -107897,7 +105193,6 @@ DisjointClasses( ObjectSomeValuesFrom # Class: (hepatic stellate cell proliferation) AnnotationAssertion(Annotation( "GOC:sl") Annotation( "PMID:15358192") Annotation( "PMID:18466260") "The multiplication or reproduction of hepatic stellate cells, resulting in the expansion of a hepatic stellate cell population. Hepatic stellate cells are found in the perisinusoidal space of the liver, and are capable of multiple roles including storage of retinol, presentation of antigen to T cells (including CD1d-restricted NKT cells), and upon activation, production of extracellular matrix components. This cell type comprises approximately 8-15% of total cells in the liver.") -AnnotationAssertion( "sl") AnnotationAssertion( "2016-01-13T23:12:57Z") AnnotationAssertion( "Ito cell proliferation") AnnotationAssertion( "hepatic perisinusoidal cell proliferation") @@ -107911,7 +105206,6 @@ SubClassOf( (eosinophil homeostasis) AnnotationAssertion(Annotation( "PMID:10606160") "The process of regulating the proliferation and elimination of eosinophils such that the total number of eosinophils within a whole or part of an organism is stable over time in the absence of an outside stimulus.") -AnnotationAssertion( "sl") AnnotationAssertion( "2016-06-06T22:34:31Z") AnnotationAssertion( "eosinocyte homeostasis") AnnotationAssertion( "eosinophilic granulocyte homeostasis") @@ -107927,7 +105221,6 @@ SubClassOf( (basophil homeostasis) AnnotationAssertion(Annotation( "PMID:10606160") "The process of regulating the proliferation and elimination of basophils such that the total number of basophils within a whole or part of an organism is stable over time in the absence of an outside stimulus.") -AnnotationAssertion( "sl") AnnotationAssertion( "2016-06-06T22:38:22Z") AnnotationAssertion( "basophilic leucocyte homeostasis") AnnotationAssertion( "biological_process") @@ -107940,7 +105233,6 @@ SubClassOf( (regulation of metanephric S-shaped body morphogenesis) AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") Annotation( "GOC:obol") Annotation( "GOC:yaf") "Any process that modulates the frequency, rate or extent of metanephric S-shaped body morphogenesis.") -AnnotationAssertion( "jl") AnnotationAssertion( "2010-07-30T02:14:33Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:2000004") @@ -107951,7 +105243,6 @@ SubClassOf( ObjectSomeValuesFrom( (negative regulation of metanephric S-shaped body morphogenesis) AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") Annotation( "GOC:obol") Annotation( "GOC:yaf") "Any process that stops, prevents, or reduces the frequency, rate or extent of metanephric S-shaped body morphogenesis.") -AnnotationAssertion( "jl") AnnotationAssertion( "2010-07-30T02:14:37Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:2000005") @@ -107961,7 +105252,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of metanephric comma-shaped body morphogenesis) AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") Annotation( "GOC:obol") Annotation( "GOC:yaf") "Any process that modulates the frequency, rate or extent of metanephric comma-shaped body morphogenesis.") -AnnotationAssertion( "jl") AnnotationAssertion( "2010-07-30T02:17:12Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:2000006") @@ -107972,7 +105262,6 @@ SubClassOf( ObjectSomeValuesFrom( (negative regulation of metanephric comma-shaped body morphogenesis) AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") Annotation( "GOC:obol") Annotation( "GOC:yaf") "Any process that stops, prevents, or reduces the frequency, rate or extent of metanephric comma-shaped body morphogenesis.") -AnnotationAssertion( "jl") AnnotationAssertion( "2010-07-30T02:17:17Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:2000007") @@ -107982,7 +105271,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of male gonad development) AnnotationAssertion(Annotation( "GOC:obol") Annotation( "GOC:yaf") "Any process that modulates the frequency, rate or extent of male gonad development.") -AnnotationAssertion( "jl") AnnotationAssertion( "2010-07-15T03:29:05Z") AnnotationAssertion(Annotation( "GOC:obol") "regulation of testicular development") AnnotationAssertion(Annotation( "GOC:obol") "regulation of testis development") @@ -107994,7 +105282,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of male gonad development) AnnotationAssertion(Annotation( "GOC:obol") Annotation( "GOC:yaf") "Any process that stops, prevents, or reduces the frequency, rate or extent of male gonad development.") -AnnotationAssertion( "jl") AnnotationAssertion( "2010-07-15T03:29:10Z") AnnotationAssertion(Annotation( "GOC:obol") "negative regulation of testicular development") AnnotationAssertion(Annotation( "GOC:obol") "negative regulation of testis development") @@ -108006,7 +105293,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of male gonad development) AnnotationAssertion(Annotation( "GOC:obol") "Any process that activates or increases the frequency, rate or extent of male gonad development.") -AnnotationAssertion( "jl") AnnotationAssertion( "2010-07-15T03:29:13Z") AnnotationAssertion(Annotation( "GOC:obol") "positive regulation of testicular development") AnnotationAssertion(Annotation( "GOC:obol") "positive regulation of testis development") @@ -108018,7 +105304,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of multicellular organismal development) AnnotationAssertion(Annotation( "GOC:obol") "Any process that modulates the frequency, rate or extent of multicellular organismal development.") -AnnotationAssertion( "tb") AnnotationAssertion( "2010-08-05T11:25:59Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:2000026") @@ -108030,7 +105315,6 @@ SubClassOf( (regulation of animal organ morphogenesis) AnnotationAssertion(Annotation( "GOC:obol") "Any process that modulates the frequency, rate or extent of animal organ morphogenesis.") -AnnotationAssertion( "tb") AnnotationAssertion( "2010-08-05T11:26:27Z") AnnotationAssertion( "biological_process") AnnotationAssertion(Annotation( "GOC:obol") "regulation of histogenesis and organogenesis") @@ -108041,7 +105325,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of stem cell division) AnnotationAssertion(Annotation( "GOC:obol") "Any process that modulates the frequency, rate or extent of stem cell division.") -AnnotationAssertion( "tb") AnnotationAssertion( "2010-08-05T11:34:53Z") AnnotationAssertion(Annotation( "GOC:obol") "regulation of stem cell renewal") AnnotationAssertion( "biological_process") @@ -108054,7 +105337,6 @@ SubClassOf( "GOC:obol") "Any process that modulates the frequency, rate or extent of stem cell population maintenance.") AnnotationAssertion( ) -AnnotationAssertion( "tb") AnnotationAssertion( "2010-08-05T11:35:25Z") AnnotationAssertion( "biological_process") AnnotationAssertion(Annotation( "GOC:obol") "regulation of maintenance of pluripotency") @@ -108068,7 +105350,6 @@ DisjointClasses( ObjectSomeValuesFrom # Class: (regulation of ureter smooth muscle cell differentiation) AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") Annotation( "GOC:obol") Annotation( "GOC:yaf") "Any process that modulates the frequency, rate or extent of ureter smooth muscle cell differentiation.") -AnnotationAssertion( "jl") AnnotationAssertion( "2010-08-20T01:44:16Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:2000061") @@ -108079,7 +105360,6 @@ SubClassOf( (negative regulation of ureter smooth muscle cell differentiation) AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") Annotation( "GOC:obol") Annotation( "GOC:yaf") "Any process that stops, prevents, or reduces the frequency, rate or extent of ureter smooth muscle cell differentiation.") -AnnotationAssertion( "jl") AnnotationAssertion( "2010-08-20T01:44:23Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:2000062") @@ -108090,7 +105370,6 @@ SubClassOf( ObjectSomeValuesFrom( (positive regulation of ureter smooth muscle cell differentiation) AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") Annotation( "GOC:obol") Annotation( "GOC:yaf") "Any process that activates or increases the frequency, rate or extent of ureter smooth muscle cell differentiation.") -AnnotationAssertion( "jl") AnnotationAssertion( "2010-08-20T01:44:28Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:2000063") @@ -108101,7 +105380,6 @@ SubClassOf( ObjectSomeValuesFrom( (regulation of defense response to insect) AnnotationAssertion(Annotation( "GOC:obol") "Any process that modulates the frequency, rate or extent of defense response to insect.") -AnnotationAssertion( "tb") AnnotationAssertion( "2010-08-23T09:30:00Z") AnnotationAssertion(Annotation( "GOC:obol") "regulation of physiological defense response to insect") AnnotationAssertion( "biological_process") @@ -108112,7 +105390,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of response to water deprivation) AnnotationAssertion(Annotation( "GOC:obol") "Any process that modulates the frequency, rate or extent of response to water deprivation.") -AnnotationAssertion( "tb") AnnotationAssertion( "2010-08-23T11:32:32Z") AnnotationAssertion(Annotation( "GOC:obol") "regulation of response to dehydration") AnnotationAssertion(Annotation( "GOC:obol") "regulation of response to drought") @@ -108127,7 +105404,6 @@ SubClassOf( (regulation of type B pancreatic cell development) AnnotationAssertion(Annotation( "GOC:obol") Annotation( "GOC:yaf") "Any process that modulates the frequency, rate or extent of pancreatic B cell development.") -AnnotationAssertion( "tb") AnnotationAssertion( "2010-08-27T11:19:37Z") AnnotationAssertion(Annotation( "GOC:mah") "regulation of pancreatic B cell development") AnnotationAssertion(Annotation( "GOC:obol") "regulation of pancreatic beta cell development") @@ -108139,7 +105415,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of type B pancreatic cell development) AnnotationAssertion(Annotation( "GOC:obol") Annotation( "GOC:yaf") "Any process that stops, prevents, or reduces the frequency, rate or extent of pancreatic B cell development.") -AnnotationAssertion( "tb") AnnotationAssertion( "2010-08-27T11:21:17Z") AnnotationAssertion(Annotation( "GOC:mah") "negative regulation of pancreatic B cell development") AnnotationAssertion(Annotation( "GOC:obol") "negative regulation of pancreatic beta cell development") @@ -108152,7 +105427,6 @@ SubClassOf( ObjectSomeValuesFrom( (positive regulation of type B pancreatic cell development) AnnotationAssertion(Annotation( "GOC:obol") Annotation( "GOC:yaf") "Any process that activates or increases the frequency, rate or extent of pancreatic B cell development.") -AnnotationAssertion( "tb") AnnotationAssertion( "2010-08-27T11:21:19Z") AnnotationAssertion(Annotation( "GOC:mah") "positive regulation of pancreatic B cell development") AnnotationAssertion(Annotation( "GOC:obol") "positive regulation of pancreatic beta cell development") @@ -108166,7 +105440,6 @@ SubClassOf( ObjectSomeValuesFrom( (regulation of mesenchymal to epithelial transition involved in mesonephros morphogenesis) AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "Any process that modulates the frequency, rate or extent of mesenchymal to epithelial transition involved in mesonephros morphogenesis.") -AnnotationAssertion( "dph") AnnotationAssertion( "2010-09-03T06:06:41Z") AnnotationAssertion( "biological_process") AnnotationAssertion(Annotation( "GOC:obol") "regulation of mesonephric mesenchyme to epithelial transition") @@ -108177,7 +105450,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of mesenchymal to epithelial transition involved in mesonephros morphogenesis) AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "Any process that stops, prevents, or reduces the frequency, rate or extent of mesenchymal to epithelial transition involved in mesonephros morphogenesis.") -AnnotationAssertion( "dph") AnnotationAssertion( "2010-09-03T06:08:21Z") AnnotationAssertion( "biological_process") AnnotationAssertion(Annotation( "GOC:obol") "negative regulation of mesonephric mesenchyme to epithelial transition") @@ -108188,7 +105460,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of mesenchymal to epithelial transition involved in mesonephros morphogenesis) AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "Any process that activates or increases the frequency, rate or extent of mesenchymal to epithelial transition involved in mesonephros morphogenesis.") -AnnotationAssertion( "dph") AnnotationAssertion( "2010-09-03T06:08:24Z") AnnotationAssertion( "biological_process") AnnotationAssertion(Annotation( "GOC:obol") "positive regulation of mesonephric mesenchyme to epithelial transition") @@ -108199,7 +105470,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of mesonephric glomerulus development) AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "Any process that modulates the frequency, rate or extent of mesonephric glomerulus development.") -AnnotationAssertion( "dph") AnnotationAssertion( "2010-09-03T06:09:19Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:2000087") @@ -108210,7 +105480,6 @@ SubClassOf( ObjectSomeValuesFrom( (negative regulation of mesonephric glomerulus development) AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "Any process that stops, prevents, or reduces the frequency, rate or extent of mesonephric glomerulus development.") -AnnotationAssertion( "dph") AnnotationAssertion( "2010-09-03T06:09:22Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:2000088") @@ -108220,7 +105489,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of mesonephric glomerulus development) AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "Any process that activates or increases the frequency, rate or extent of mesonephric glomerulus development.") -AnnotationAssertion( "dph") AnnotationAssertion( "2010-09-03T06:09:24Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:2000089") @@ -108230,7 +105498,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of mesonephric nephron tubule epithelial cell differentiation) AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "Any process that modulates the frequency, rate or extent of mesonephric nephron tubule epithelial cell differentiation.") -AnnotationAssertion( "dph") AnnotationAssertion( "2010-09-03T06:12:25Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:2000093") @@ -108240,7 +105507,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of mesonephric nephron tubule epithelial cell differentiation) AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") "Any process that stops, prevents, or reduces the frequency, rate or extent of mesonephric nephron tubule epithelial cell differentiation.") -AnnotationAssertion( "dph") AnnotationAssertion( "2010-09-03T06:12:28Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:2000094") @@ -108250,7 +105516,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of leukocyte apoptotic process) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:mtg_apoptosis") "Any process that modulates the frequency, rate or extent of leukocyte apoptotic process.") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-09-15T01:42:05Z") AnnotationAssertion( "regulation of leukocyte apoptosis") AnnotationAssertion( "biological_process") @@ -108261,7 +105526,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of leukocyte apoptotic process) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:mtg_apoptosis") "Any process that stops, prevents, or reduces the frequency, rate or extent of leukocyte apoptotic process.") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-09-15T01:42:09Z") AnnotationAssertion( "negative regulation of leukocyte apoptosis") AnnotationAssertion( "biological_process") @@ -108272,7 +105536,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of leukocyte apoptotic process) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:mtg_apoptosis") "Any process that activates or increases the frequency, rate or extent of leukocyte apoptotic process.") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-09-15T01:42:12Z") AnnotationAssertion( "positive regulation of leukocyte apoptosis") AnnotationAssertion( "biological_process") @@ -108283,7 +105546,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of macrophage apoptotic process) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:mtg_apoptosis") "Any process that modulates the frequency, rate or extent of macrophage apoptotic process.") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-09-15T01:44:15Z") AnnotationAssertion( "regulation of macrophage apoptosis") AnnotationAssertion( "biological_process") @@ -108296,7 +105558,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of macrophage apoptotic process) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:mtg_apoptosis") "Any process that stops, prevents, or reduces the frequency, rate or extent of macrophage apoptotic process.") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-09-15T01:44:18Z") AnnotationAssertion( "negative regulation of macrophage apoptosis") AnnotationAssertion( "biological_process") @@ -108309,7 +105570,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of macrophage apoptotic process) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:mtg_apoptosis") "Any process that activates or increases the frequency, rate or extent of macrophage apoptotic process.") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-09-15T01:44:21Z") AnnotationAssertion( "positive regulation of macrophage apoptosis") AnnotationAssertion( "biological_process") @@ -108322,7 +105582,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of establishment of cell polarity) AnnotationAssertion(Annotation( "GOC:dph") "Any process that modulates the frequency, rate or extent of establishment of cell polarity.") -AnnotationAssertion( "dph") AnnotationAssertion( "2010-09-16T01:22:36Z") AnnotationAssertion(Annotation( "GOC:obol") "regulation of cell polarization") AnnotationAssertion( "biological_process") @@ -108334,7 +105593,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of cell proliferation involved in heart morphogenesis) AnnotationAssertion(Annotation( "GOC:dph") "Any process that modulates the frequency, rate or extent of cell proliferation involved in heart morphogenesis.") -AnnotationAssertion( "dph") AnnotationAssertion( "2010-09-29T12:43:53Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:2000136") @@ -108344,7 +105602,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of cell proliferation involved in heart morphogenesis) AnnotationAssertion(Annotation( "GOC:dph") "Any process that stops, prevents, or reduces the frequency, rate or extent of cell proliferation involved in heart morphogenesis.") -AnnotationAssertion( "dph") AnnotationAssertion( "2010-09-29T12:43:55Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:2000137") @@ -108354,7 +105611,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of cell proliferation involved in heart morphogenesis) AnnotationAssertion(Annotation( "GOC:dph") "Any process that activates or increases the frequency, rate or extent of cell proliferation involved in heart morphogenesis.") -AnnotationAssertion( "dph") AnnotationAssertion( "2010-09-29T12:43:57Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:2000138") @@ -108364,7 +105620,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of cell motility) AnnotationAssertion(Annotation( "GOC:mah") "Any process that modulates the frequency, rate or extent of cell motility.") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-10-01T09:41:21Z") AnnotationAssertion(Annotation( "GOC:obol") "regulation of cell locomotion") AnnotationAssertion(Annotation( "GOC:obol") "regulation of movement of a cell") @@ -108378,7 +105633,6 @@ SubClassOf( (negative regulation of cell motility) AnnotationAssertion(Annotation( "GOC:mah") "Any process that stops, prevents, or reduces the frequency, rate or extent of cell motility.") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-10-01T09:41:26Z") AnnotationAssertion(Annotation( "GOC:obol") "negative regulation of cell locomotion") AnnotationAssertion(Annotation( "GOC:obol") "negative regulation of movement of a cell") @@ -108392,7 +105646,6 @@ SubClassOf( (positive regulation of cell motility) AnnotationAssertion(Annotation( "GOC:mah") "Any process that activates or increases the frequency, rate or extent of cell motility.") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-10-01T09:41:30Z") AnnotationAssertion(Annotation( "GOC:obol") "positive regulation of cell locomotion") AnnotationAssertion(Annotation( "GOC:obol") "positive regulation of movement of a cell") @@ -108406,7 +105659,6 @@ SubClassOf( (positive regulation of cilium-dependent cell motility) AnnotationAssertion(Annotation( "GOC:cilia") Annotation( "GOC:jl") "Any process that activates or increases the frequency, rate or extent of cilium-dependent cell motility.") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-10-04T12:41:05Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "positive regulation of ciliary cell motility") @@ -108417,7 +105669,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of dendrite development) AnnotationAssertion(Annotation( "GOC:obol") "Any process that stops, prevents, or reduces the frequency, rate or extent of dendrite development.") -AnnotationAssertion( "rl") AnnotationAssertion( "2010-10-07T10:53:15Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:2000171") @@ -108427,7 +105678,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of branching morphogenesis of a nerve) AnnotationAssertion(Annotation( "GOC:BHF") "Any process that modulates the frequency, rate or extent of branching morphogenesis of a nerve.") -AnnotationAssertion( "rl") AnnotationAssertion( "2010-10-07T12:07:54Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:2000172") @@ -108437,7 +105687,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of branching morphogenesis of a nerve) AnnotationAssertion(Annotation( "GOC:BHF") "Any process that stops, prevents, or reduces the frequency, rate or extent of branching morphogenesis of a nerve.") -AnnotationAssertion( "rl") AnnotationAssertion( "2010-10-07T12:07:56Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:2000173") @@ -108447,7 +105696,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of pro-T cell differentiation) AnnotationAssertion(Annotation( "GOC:BHF") "Any process that modulates the frequency, rate or extent of pro-T cell differentiation.") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-10-11T10:24:30Z") AnnotationAssertion(Annotation( "GOC:obol") "regulation of pro-T lymphocyte differentiation") AnnotationAssertion( "biological_process") @@ -108459,7 +105707,6 @@ SubClassOf( ObjectSomeValuesFrom( (negative regulation of pro-T cell differentiation) AnnotationAssertion(Annotation( "GOC:BHF") "Any process that stops, prevents, or reduces the frequency, rate or extent of pro-T cell differentiation.") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-10-11T10:24:33Z") AnnotationAssertion(Annotation( "GOC:obol") "negative regulation of pro-T lymphocyte differentiation") AnnotationAssertion( "biological_process") @@ -108471,7 +105718,6 @@ SubClassOf( ObjectSomeValuesFrom( (positive regulation of pro-T cell differentiation) AnnotationAssertion(Annotation( "GOC:BHF") "Any process that activates or increases the frequency, rate or extent of pro-T cell differentiation.") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-10-11T10:24:35Z") AnnotationAssertion(Annotation( "GOC:obol") "positive regulation of pro-T lymphocyte differentiation") AnnotationAssertion( "biological_process") @@ -108483,7 +105729,6 @@ SubClassOf( ObjectSomeValuesFrom( (regulation of neural precursor cell proliferation) AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:yaf") "Any process that modulates the frequency, rate or extent of neural precursor cell proliferation.") -AnnotationAssertion( "dph") AnnotationAssertion( "2010-10-13T12:40:41Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:2000177") @@ -108493,7 +105738,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of neural precursor cell proliferation) AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:yaf") "Any process that stops, prevents, or reduces the frequency, rate or extent of neural precursor cell proliferation.") -AnnotationAssertion( "dph") AnnotationAssertion( "2010-10-13T12:40:43Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:2000178") @@ -108503,7 +105747,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of neural precursor cell proliferation) AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:yaf") "Any process that activates or increases the frequency, rate or extent of neural precursor cell proliferation.") -AnnotationAssertion( "dph") AnnotationAssertion( "2010-10-13T12:40:45Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:2000179") @@ -108513,7 +105756,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of blood vessel morphogenesis) AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:yaf") "Any process that stops, prevents, or reduces the frequency, rate or extent of blood vessel morphogenesis.") -AnnotationAssertion( "dph") AnnotationAssertion( "2010-10-13T12:46:31Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:2000181") @@ -108525,7 +105767,6 @@ SubClassOf( (regulation of progesterone biosynthetic process) AnnotationAssertion(Annotation( "GOC:dph") "Any process that modulates the frequency, rate or extent of progesterone biosynthetic process.") -AnnotationAssertion( "dph") AnnotationAssertion( "2010-10-14T07:36:06Z") AnnotationAssertion(Annotation( "GOC:obol") "regulation of progesterone anabolism") AnnotationAssertion(Annotation( "GOC:obol") "regulation of progesterone biosynthesis") @@ -108539,7 +105780,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of progesterone biosynthetic process) AnnotationAssertion(Annotation( "GOC:dph") "Any process that stops, prevents, or reduces the frequency, rate or extent of progesterone biosynthetic process.") -AnnotationAssertion( "dph") AnnotationAssertion( "2010-10-14T07:36:10Z") AnnotationAssertion(Annotation( "GOC:obol") "negative regulation of progesterone anabolism") AnnotationAssertion(Annotation( "GOC:obol") "negative regulation of progesterone biosynthesis") @@ -108553,7 +105793,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of progesterone biosynthetic process) AnnotationAssertion(Annotation( "GOC:dph") "Any process that activates or increases the frequency, rate or extent of progesterone biosynthetic process.") -AnnotationAssertion( "dph") AnnotationAssertion( "2010-10-14T07:36:14Z") AnnotationAssertion(Annotation( "GOC:obol") "positive regulation of progesterone anabolism") AnnotationAssertion(Annotation( "GOC:obol") "positive regulation of progesterone biosynthesis") @@ -108567,7 +105806,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of phosphate transmembrane transport) AnnotationAssertion(Annotation( "GOC:obol") "Any process that modulates the frequency, rate or extent of phosphate transmembrane transport.") -AnnotationAssertion( "vw") AnnotationAssertion( "2010-10-15T11:33:04Z") AnnotationAssertion( "regulation of phosphate membrane transport") AnnotationAssertion( "biological_process") @@ -108578,7 +105816,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of phosphate transmembrane transport) AnnotationAssertion(Annotation( "GOC:obol") "Any process that stops, prevents, or reduces the frequency, rate or extent of phosphate transmembrane transport.") -AnnotationAssertion( "vw") AnnotationAssertion( "2010-10-15T11:33:08Z") AnnotationAssertion( "negative regulation of phosphate membrane transport") AnnotationAssertion( "biological_process") @@ -108589,7 +105826,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of phosphate transmembrane transport) AnnotationAssertion(Annotation( "GOC:obol") "Any process that activates or increases the frequency, rate or extent of phosphate transmembrane transport.") -AnnotationAssertion( "vw") AnnotationAssertion( "2010-10-15T11:33:10Z") AnnotationAssertion( "positive regulation of phosphate membrane transport") AnnotationAssertion( "biological_process") @@ -108600,7 +105836,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of female gonad development) AnnotationAssertion(Annotation( "GOC:obol") "Any process that modulates the frequency, rate or extent of female gonad development.") -AnnotationAssertion( "yaf") AnnotationAssertion( "2010-10-19T10:45:34Z") AnnotationAssertion(Annotation( "GOC:obol") "regulation of ovarian development") AnnotationAssertion(Annotation( "GOC:obol") "regulation of ovary development") @@ -108614,7 +105849,6 @@ SubClassOf( (negative regulation of female gonad development) AnnotationAssertion(Annotation( "GOC:obol") "Any process that stops, prevents, or reduces the frequency, rate or extent of female gonad development.") -AnnotationAssertion( "yaf") AnnotationAssertion( "2010-10-19T10:45:38Z") AnnotationAssertion(Annotation( "GOC:obol") "negative regulation of ovarian development") AnnotationAssertion(Annotation( "GOC:obol") "negative regulation of ovary development") @@ -108630,7 +105864,6 @@ SubClassOf( (positive regulation of female gonad development) AnnotationAssertion(Annotation( "GOC:obol") "Any process that activates or increases the frequency, rate or extent of female gonad development.") -AnnotationAssertion( "yaf") AnnotationAssertion( "2010-10-19T10:45:41Z") AnnotationAssertion(Annotation( "GOC:obol") "positive regulation of ovarian development") AnnotationAssertion(Annotation( "GOC:obol") "positive regulation of ovary development") @@ -108646,7 +105879,6 @@ SubClassOf( (regulation of glutamate metabolic process) AnnotationAssertion(Annotation( "GOC:sl") "Any process that modulates the frequency, rate or extent of glutamate metabolic process.") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-11-03T02:43:51Z") AnnotationAssertion(Annotation( "GOC:obol") "regulation of glutamate metabolism") AnnotationAssertion(Annotation( "GOC:obol") "regulation of glutamic acid metabolic process") @@ -108660,7 +105892,6 @@ SubClassOf( (negative regulation of glutamate metabolic process) AnnotationAssertion(Annotation( "GOC:sl") "Any process that stops, prevents, or reduces the frequency, rate or extent of glutamate metabolic process.") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-11-03T02:43:55Z") AnnotationAssertion(Annotation( "GOC:obol") "negative regulation of glutamate metabolism") AnnotationAssertion(Annotation( "GOC:obol") "negative regulation of glutamic acid metabolic process") @@ -108674,7 +105905,6 @@ SubClassOf( (positive regulation of glutamate metabolic process) AnnotationAssertion(Annotation( "GOC:sl") "Any process that activates or increases the frequency, rate or extent of glutamate metabolic process.") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-11-03T02:43:59Z") AnnotationAssertion(Annotation( "GOC:obol") "positive regulation of glutamate metabolism") AnnotationAssertion(Annotation( "GOC:obol") "positive regulation of glutamic acid metabolic process") @@ -108688,7 +105918,6 @@ SubClassOf( (regulation of testosterone biosynthetic process) AnnotationAssertion(Annotation( "GOC:obol") Annotation( "GOC:yaf") "Any process that modulates the frequency, rate or extent of testosterone biosynthetic process.") -AnnotationAssertion( "yaf") AnnotationAssertion( "2010-11-09T10:38:33Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:2000224") @@ -108698,7 +105927,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of testosterone biosynthetic process) AnnotationAssertion(Annotation( "GOC:obol") Annotation( "GOC:yaf") "Any process that stops, prevents, or reduces the frequency, rate or extent of testosterone biosynthetic process.") -AnnotationAssertion( "yaf") AnnotationAssertion( "2010-11-09T10:38:37Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:2000225") @@ -108708,7 +105936,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of pancreatic A cell differentiation) AnnotationAssertion(Annotation( "GOC:mah") "Any process that modulates the frequency, rate or extent of pancreatic A cell differentiation.") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-11-09T03:43:37Z") AnnotationAssertion(Annotation( "GOC:obol") "regulation of pancreatic alpha cell differentiation") AnnotationAssertion( "biological_process") @@ -108719,7 +105946,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of pancreatic A cell differentiation) AnnotationAssertion(Annotation( "GOC:mah") "Any process that stops, prevents, or reduces the frequency, rate or extent of pancreatic A cell differentiation.") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-11-09T03:43:40Z") AnnotationAssertion(Annotation( "GOC:obol") "negative regulation of pancreatic alpha cell differentiation") AnnotationAssertion( "biological_process") @@ -108731,7 +105957,6 @@ SubClassOf( ObjectSomeValuesFrom( (positive regulation of pancreatic A cell differentiation) AnnotationAssertion(Annotation( "GOC:mah") "Any process that activates or increases the frequency, rate or extent of pancreatic A cell differentiation.") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-11-09T03:43:42Z") AnnotationAssertion(Annotation( "GOC:obol") "positive regulation of pancreatic alpha cell differentiation") AnnotationAssertion( "biological_process") @@ -108743,7 +105968,6 @@ SubClassOf( ObjectSomeValuesFrom( (regulation of pancreatic stellate cell proliferation) AnnotationAssertion(Annotation( "GOC:mah") "Any process that modulates the frequency, rate or extent of pancreatic stellate cell proliferation.") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-11-09T03:45:18Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:2000229") @@ -108753,7 +105977,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of pancreatic stellate cell proliferation) AnnotationAssertion(Annotation( "GOC:mah") "Any process that stops, prevents, or reduces the frequency, rate or extent of pancreatic stellate cell proliferation.") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-11-09T03:45:21Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:2000230") @@ -108763,7 +105986,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of pancreatic stellate cell proliferation) AnnotationAssertion(Annotation( "GOC:mah") "Any process that activates or increases the frequency, rate or extent of pancreatic stellate cell proliferation.") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-11-09T03:45:23Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:2000231") @@ -108773,7 +105995,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of reproductive process) AnnotationAssertion(Annotation( "GOC:mah") "Any process that modulates the frequency, rate or extent of reproductive process.") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-11-10T02:44:02Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:2000241") @@ -108784,7 +106005,6 @@ SubClassOf( (negative regulation of reproductive process) AnnotationAssertion(Annotation( "GOC:mah") "Any process that stops, prevents, or reduces the frequency, rate or extent of reproductive process.") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-11-10T02:44:05Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:2000242") @@ -108796,7 +106016,6 @@ SubClassOf( (positive regulation of reproductive process) AnnotationAssertion(Annotation( "GOC:mah") "Any process that activates or increases the frequency, rate or extent of reproductive process.") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-11-10T02:44:08Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:2000243") @@ -108808,7 +106027,6 @@ SubClassOf( (negative regulation of establishment or maintenance of neuroblast polarity) AnnotationAssertion(Annotation( "GOC:obol") "Any process that stops, prevents, or reduces the frequency, rate or extent of establishment or maintenance of neuroblast polarity.") -AnnotationAssertion( "vw") AnnotationAssertion( "2010-11-11T11:40:34Z") AnnotationAssertion(Annotation( "GOC:obol") "negative regulation of establishment and/or maintenance of neuroblast cell polarity") AnnotationAssertion( "biological_process") @@ -108821,7 +106039,6 @@ SubClassOf( ObjectSomeValuesFrom( (regulation of male germ cell proliferation) AnnotationAssertion(Annotation( "GOC:obol") "Any process that modulates the frequency, rate or extent of male germ cell proliferation.") -AnnotationAssertion( "dph") AnnotationAssertion( "2010-11-18T09:29:44Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:2000254") @@ -108831,7 +106048,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of male germ cell proliferation) AnnotationAssertion(Annotation( "GOC:obol") "Any process that stops, prevents or reduces the frequency, rate or extent of male germ cell proliferation.") -AnnotationAssertion( "dph") AnnotationAssertion( "2010-11-18T09:29:47Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:2000255") @@ -108842,7 +106058,6 @@ SubClassOf( (positive regulation of male germ cell proliferation) AnnotationAssertion(Annotation( "GOC:obol") "Any process that activates or increases the frequency, rate or extent of male germ cell proliferation.") -AnnotationAssertion( "dph") AnnotationAssertion( "2010-11-18T09:29:50Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:2000256") @@ -108853,7 +106068,6 @@ SubClassOf( (regulation of fibroblast apoptotic process) AnnotationAssertion(Annotation( "GOC:mtg_apoptosis") Annotation( "GOC:obol") Annotation( "GOC:yaf") "Any process that modulates the frequency, rate or extent of fibroblast apoptotic process.") -AnnotationAssertion( "jl") AnnotationAssertion( "2010-11-23T01:07:23Z") AnnotationAssertion( "regulation of fibroblast apoptosis") AnnotationAssertion( "biological_process") @@ -108864,7 +106078,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of fibroblast apoptotic process) AnnotationAssertion(Annotation( "GOC:mtg_apoptosis") Annotation( "GOC:obol") Annotation( "GOC:yaf") "Any process that stops, prevents or reduces the frequency, rate or extent of fibroblast apoptotic process.") -AnnotationAssertion( "jl") AnnotationAssertion( "2010-11-23T01:07:27Z") AnnotationAssertion( "negative regulation of fibroblast apoptosis") AnnotationAssertion( "biological_process") @@ -108875,7 +106088,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of fibroblast apoptotic process) AnnotationAssertion(Annotation( "GOC:mtg_apoptosis") Annotation( "GOC:obol") Annotation( "GOC:yaf") "Any process that activates or increases the frequency, rate or extent of fibroblast apoptotic process.") -AnnotationAssertion( "jl") AnnotationAssertion( "2010-11-23T01:07:29Z") AnnotationAssertion( "positive regulation of fibroblast apoptosis") AnnotationAssertion( "biological_process") @@ -108886,7 +106098,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of signaling receptor activity) AnnotationAssertion(Annotation( "GOC:obol") "Any process that stops, prevents or reduces the frequency, rate or extent of a signaling receptor activity.") -AnnotationAssertion( "bf") AnnotationAssertion( "2010-12-02T09:28:47Z") AnnotationAssertion( "negative regulation of receptor activity") AnnotationAssertion( "negative regulation of signalling receptor activity") @@ -108901,7 +106112,6 @@ SubClassOf( (positive regulation of signaling receptor activity) AnnotationAssertion(Annotation( "GOC:obol") "Any process that activates or increases the frequency, rate or extent of signaling receptor activity.") -AnnotationAssertion( "bf") AnnotationAssertion( "2010-12-02T09:28:50Z") AnnotationAssertion( "positive regulation of signalling receptor activity") AnnotationAssertion( "biological_process") @@ -108915,7 +106125,6 @@ SubClassOf( (regulation of DNA biosynthetic process) AnnotationAssertion(Annotation( "GOC:obol") "Any process that modulates the frequency, rate or extent of DNA biosynthetic process.") -AnnotationAssertion( "yaf") AnnotationAssertion( "2010-12-08T04:48:15Z") AnnotationAssertion(Annotation( "GOC:obol") "regulation of DNA anabolism") AnnotationAssertion(Annotation( "GOC:obol") "regulation of DNA biosynthesis") @@ -108929,7 +106138,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of DNA biosynthetic process) AnnotationAssertion(Annotation( "GOC:obol") "Any process that stops, prevents or reduces the frequency, rate or extent of DNA biosynthetic process.") -AnnotationAssertion( "yaf") AnnotationAssertion( "2010-12-08T04:48:20Z") AnnotationAssertion(Annotation( "GOC:obol") "negative regulation of DNA anabolism") AnnotationAssertion(Annotation( "GOC:obol") "negative regulation of DNA biosynthesis") @@ -108944,7 +106152,6 @@ EquivalentClasses( ObjectIntersection AnnotationAssertion(Annotation( "GOC:obol") "Any process that modulates the frequency, rate or extent of cellular amino acid biosynthetic process.") AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/28908"^^xsd:anyURI) -AnnotationAssertion( "vw") AnnotationAssertion( "2010-12-10T11:54:19Z") AnnotationAssertion(Annotation( "GOC:obol") "regulation of cellular amino acid anabolism") AnnotationAssertion(Annotation( "GOC:obol") "regulation of cellular amino acid biosynthesis") @@ -108959,7 +106166,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of amino acid biosynthetic process) AnnotationAssertion(Annotation( "GOC:obol") "Any process that stops, prevents or reduces the frequency, rate or extent of an amino acid biosynthetic process.") -AnnotationAssertion( "vw") AnnotationAssertion( "2010-12-10T11:54:23Z") AnnotationAssertion(Annotation( "GOC:obol") "negative regulation of amino acid anabolism") AnnotationAssertion(Annotation( "GOC:obol") "negative regulation of amino acid biosynthesis") @@ -108974,7 +106180,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of amino acid biosynthetic process) AnnotationAssertion(Annotation( "GOC:obol") "Any process that activates or increases the frequency, rate or extent of cellular amino acid biosynthetic process.") -AnnotationAssertion( "vw") AnnotationAssertion( "2010-12-10T11:54:27Z") AnnotationAssertion(Annotation( "GOC:obol") "positive regulation of amino acid anabolism") AnnotationAssertion(Annotation( "GOC:obol") "positive regulation of amino acid biosynthesis") @@ -108989,7 +106194,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of myotome development) AnnotationAssertion(Annotation( "GOC:BHF") "Any process that activates or increases the frequency, rate or extent of myotome development.") -AnnotationAssertion( "rl") AnnotationAssertion( "2010-12-16T05:17:15Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:2000287") @@ -108999,7 +106203,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of myoblast proliferation) AnnotationAssertion(Annotation( "GOC:BHF") "Any process that activates or increases the frequency, rate or extent of myoblast proliferation.") -AnnotationAssertion( "rl") AnnotationAssertion( "2010-12-16T05:20:52Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:2000288") @@ -109009,7 +106212,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of myotome development) AnnotationAssertion(Annotation( "GOC:mah") "Any process that modulates the frequency, rate or extent of myotome development.") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-12-20T10:22:05Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:2000290") @@ -109019,7 +106221,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of myoblast proliferation) AnnotationAssertion(Annotation( "GOC:mah") "Any process that modulates the frequency, rate or extent of myoblast proliferation.") -AnnotationAssertion( "mah") AnnotationAssertion( "2010-12-20T10:34:26Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:2000291") @@ -109029,7 +106230,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of defecation) AnnotationAssertion(Annotation( "GOC:obol") "Any process that modulates the frequency, rate or extent of defecation.") -AnnotationAssertion( "bf") AnnotationAssertion( "2010-12-21T09:23:08Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:2000292") @@ -109040,7 +106240,6 @@ SubClassOf( (negative regulation of defecation) AnnotationAssertion(Annotation( "GOC:obol") "Any process that stops, prevents or reduces the frequency, rate or extent of defecation.") -AnnotationAssertion( "bf") AnnotationAssertion( "2010-12-21T09:23:13Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:2000293") @@ -109053,7 +106252,6 @@ SubClassOf( (positive regulation of defecation) AnnotationAssertion(Annotation( "GOC:obol") "Any process that activates or increases the frequency, rate or extent of defecation.") -AnnotationAssertion( "bf") AnnotationAssertion( "2010-12-21T09:23:16Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:2000294") @@ -109066,7 +106264,6 @@ SubClassOf( (regulation of synaptic vesicle exocytosis) AnnotationAssertion(Annotation( "GOC:obol") "Any process that modulates the frequency, rate or extent of synaptic vesicle exocytosis.") -AnnotationAssertion( "dph") AnnotationAssertion( "2011-01-03T08:20:40Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:2000300") @@ -109078,7 +106275,6 @@ SubClassOf( ObjectSomeValuesFrom( (negative regulation of synaptic vesicle exocytosis) AnnotationAssertion(Annotation( "GOC:obol") "Any process that stops, prevents or reduces the frequency, rate or extent of synaptic vesicle exocytosis.") -AnnotationAssertion( "dph") AnnotationAssertion( "2011-01-03T08:21:00Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:2000301") @@ -109088,7 +106284,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of synaptic vesicle exocytosis) AnnotationAssertion(Annotation( "GOC:obol") "Any process that activates or increases the frequency, rate or extent of synaptic vesicle exocytosis.") -AnnotationAssertion( "dph") AnnotationAssertion( "2011-01-03T08:21:14Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:2000302") @@ -109099,7 +106294,6 @@ SubClassOf( ObjectSomeValuesFrom( (regulation of kainate selective glutamate receptor activity) AnnotationAssertion(Annotation( "GOC:BHF") "Any process that modulates the frequency, rate or extent of kainate selective glutamate receptor activity.") -AnnotationAssertion( "bf") AnnotationAssertion( "2011-01-18T10:14:16Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:2000312") @@ -109110,7 +106304,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of T-helper 17 type immune response) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:mah") "Any process that modulates the frequency, rate or extent of T-helper 17 type immune response.") -AnnotationAssertion( "mah") AnnotationAssertion( "2011-01-18T01:32:26Z") AnnotationAssertion(Annotation( "GOC:obol") "regulation of Th17 immune response") AnnotationAssertion( "biological_process") @@ -109121,7 +106314,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of T-helper 17 type immune response) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:mah") "Any process that stops, prevents or reduces the frequency, rate or extent of T-helper 17 type immune response.") -AnnotationAssertion( "mah") AnnotationAssertion( "2011-01-18T01:33:00Z") AnnotationAssertion(Annotation( "GOC:obol") "negative regulation of Th17 immune response") AnnotationAssertion( "biological_process") @@ -109132,7 +106324,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of T-helper 17 type immune response) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:mah") "Any process that activates or increases the frequency, rate or extent of T-helper 17 type immune response.") -AnnotationAssertion( "mah") AnnotationAssertion( "2011-01-18T01:33:24Z") AnnotationAssertion(Annotation( "GOC:obol") "positive regulation of Th17 immune response") AnnotationAssertion( "biological_process") @@ -109143,7 +106334,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of T-helper 17 cell differentiation) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:mah") "Any process that modulates the frequency, rate or extent of T-helper 17 cell differentiation.") -AnnotationAssertion( "mah") AnnotationAssertion( "2011-01-18T01:43:48Z") AnnotationAssertion( "biological_process") AnnotationAssertion(Annotation( "GOC:obol") "regulation of T-helper 17 cell development") @@ -109155,7 +106345,6 @@ SubClassOf( ObjectSomeValuesFrom( (negative regulation of T-helper 17 cell differentiation) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:mah") "Any process that stops, prevents or reduces the frequency, rate or extent of T-helper 17 cell differentiation.") -AnnotationAssertion( "mah") AnnotationAssertion( "2011-01-18T01:44:31Z") AnnotationAssertion( "biological_process") AnnotationAssertion(Annotation( "GOC:obol") "negative regulation of T-helper 17 cell development") @@ -109167,7 +106356,6 @@ SubClassOf( ObjectSomeValuesFrom( (positive regulation of T-helper 17 cell differentiation) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:mah") "Any process that activates or increases the frequency, rate or extent of T-helper 17 cell differentiation.") -AnnotationAssertion( "mah") AnnotationAssertion( "2011-01-18T01:45:08Z") AnnotationAssertion( "biological_process") AnnotationAssertion(Annotation( "GOC:obol") "positive regulation of T-helper 17 cell development") @@ -109179,7 +106367,6 @@ SubClassOf( ObjectSomeValuesFrom( (regulation of terminal button organization) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:mah") "Any process that modulates the frequency, rate or extent of terminal button organization.") -AnnotationAssertion( "mah") AnnotationAssertion( "2011-01-28T11:29:08Z") AnnotationAssertion(Annotation( "GOC:obol") "regulation of bouton organization") AnnotationAssertion(Annotation( "GOC:obol") "regulation of presynaptic bouton organization") @@ -109194,7 +106381,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of endothelial cell apoptotic process) AnnotationAssertion(Annotation( "GOC:mah") Annotation( "GOC:mtg_apoptosis") "Any process that modulates the frequency, rate or extent of endothelial cell apoptotic process.") -AnnotationAssertion( "mah") AnnotationAssertion( "2011-02-03T10:43:16Z") AnnotationAssertion(Annotation( "GOC:obol") "regulation of apoptosis of endothelial cells") AnnotationAssertion(Annotation( "GOC:obol") "regulation of endothelial cell programmed cell death by apoptosis") @@ -109210,7 +106396,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of endothelial cell apoptotic process) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:mah") Annotation( "GOC:mtg_apoptosis") "Any process that stops, prevents or reduces the frequency, rate or extent of endothelial cell apoptotic process.") -AnnotationAssertion( "mah") AnnotationAssertion( "2011-02-03T10:43:20Z") AnnotationAssertion(Annotation( "GOC:obol") "negative regulation of apoptosis of endothelial cells") AnnotationAssertion(Annotation( "GOC:obol") "negative regulation of endothelial cell programmed cell death by apoptosis") @@ -109226,7 +106411,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of endothelial cell apoptotic process) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:mah") Annotation( "GOC:mtg_apoptosis") "Any process that activates or increases the frequency, rate or extent of endothelial cell apoptotic process.") -AnnotationAssertion( "mah") AnnotationAssertion( "2011-02-03T10:43:23Z") AnnotationAssertion(Annotation( "GOC:obol") "positive regulation of apoptosis of endothelial cells") AnnotationAssertion(Annotation( "GOC:obol") "positive regulation of endothelial cell programmed cell death by apoptosis") @@ -109242,7 +106426,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of ovarian follicle development) AnnotationAssertion(Annotation( "GOC:obol") "Any process that modulates the frequency, rate or extent of ovarian follicle development.") -AnnotationAssertion( "yaf") AnnotationAssertion( "2011-02-03T02:01:28Z") AnnotationAssertion( "biological_process") AnnotationAssertion(Annotation( "GOC:obol") "regulation of follicular phase") @@ -109253,7 +106436,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of ovarian follicle development) AnnotationAssertion(Annotation( "GOC:obol") "Any process that stops, prevents or reduces the frequency, rate or extent of ovarian follicle development.") -AnnotationAssertion( "yaf") AnnotationAssertion( "2011-02-03T02:01:32Z") AnnotationAssertion( "biological_process") AnnotationAssertion(Annotation( "GOC:obol") "negative regulation of follicular phase") @@ -109264,7 +106446,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of oxygen metabolic process) AnnotationAssertion(Annotation( "GOC:mah") "Any process that modulates the frequency, rate or extent of oxygen metabolic process.") -AnnotationAssertion( "mah") AnnotationAssertion( "2011-02-11T02:03:32Z") AnnotationAssertion(Annotation( "GOC:obol") "regulation of diatomic oxygen metabolic process") AnnotationAssertion(Annotation( "GOC:obol") "regulation of oxygen metabolism") @@ -109276,7 +106457,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of oxygen metabolic process) AnnotationAssertion(Annotation( "GOC:mah") "Any process that stops, prevents or reduces the frequency, rate or extent of oxygen metabolic process.") -AnnotationAssertion( "mah") AnnotationAssertion( "2011-02-11T02:03:44Z") AnnotationAssertion(Annotation( "GOC:obol") "negative regulation of diatomic oxygen metabolic process") AnnotationAssertion(Annotation( "GOC:obol") "negative regulation of oxygen metabolism") @@ -109288,7 +106468,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of oxygen metabolic process) AnnotationAssertion(Annotation( "GOC:mah") "Any process that activates or increases the frequency, rate or extent of oxygen metabolic process.") -AnnotationAssertion( "mah") AnnotationAssertion( "2011-02-11T02:03:52Z") AnnotationAssertion(Annotation( "GOC:obol") "positive regulation of diatomic oxygen metabolic process") AnnotationAssertion(Annotation( "GOC:obol") "positive regulation of oxygen metabolism") @@ -109300,7 +106479,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of mesoderm development) AnnotationAssertion(Annotation( "GOC:BHF") "Any process that modulates the frequency, rate or extent of mesoderm development.") -AnnotationAssertion( "vk") AnnotationAssertion( "2011-02-15T03:09:46Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:2000380") @@ -109311,7 +106489,6 @@ SubClassOf( (negative regulation of mesoderm development) AnnotationAssertion(Annotation( "GOC:BHF") "Any process that stops, prevents or reduces the frequency, rate or extent of mesoderm development.") -AnnotationAssertion( "vk") AnnotationAssertion( "2011-02-15T03:10:02Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:2000381") @@ -109323,7 +106500,6 @@ SubClassOf( (positive regulation of mesoderm development) AnnotationAssertion(Annotation( "GOC:BHF") "Any process that activates or increases the frequency, rate or extent of mesoderm development.") -AnnotationAssertion( "vk") AnnotationAssertion( "2011-02-15T03:10:12Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:2000382") @@ -109335,7 +106511,6 @@ SubClassOf( (regulation of ectoderm development) AnnotationAssertion(Annotation( "GOC:BHF") "Any process that modulates the frequency, rate or extent of ectoderm development.") -AnnotationAssertion( "vk") AnnotationAssertion( "2011-02-15T03:17:10Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:2000383") @@ -109346,7 +106521,6 @@ SubClassOf( (negative regulation of ectoderm development) AnnotationAssertion(Annotation( "GOC:BHF") "Any process that stops, prevents or reduces the frequency, rate or extent of ectoderm development.") -AnnotationAssertion( "vk") AnnotationAssertion( "2011-02-15T03:17:27Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:2000384") @@ -109358,7 +106532,6 @@ SubClassOf( (positive regulation of ectoderm development) AnnotationAssertion(Annotation( "GOC:BHF") "Any process that activates or increases the frequency, rate or extent of ectoderm development.") -AnnotationAssertion( "vk") AnnotationAssertion( "2011-02-15T03:17:39Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:2000385") @@ -109370,7 +106543,6 @@ SubClassOf( (positive regulation of ovarian follicle development) AnnotationAssertion(Annotation( "GOC:obol") "Any process that activates or increases the frequency, rate or extent of ovarian follicle development.") -AnnotationAssertion( "yaf") AnnotationAssertion( "2011-02-16T02:21:21Z") AnnotationAssertion( "biological_process") AnnotationAssertion(Annotation( "GOC:obol") "positive regulation of follicular phase") @@ -109381,7 +106553,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of antral ovarian follicle growth) AnnotationAssertion(Annotation( "GOC:obol") "Any process that modulates the frequency, rate or extent of antral ovarian follicle growth.") -AnnotationAssertion( "yaf") AnnotationAssertion( "2011-02-16T04:53:43Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:2000387") @@ -109391,7 +106562,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of antral ovarian follicle growth) AnnotationAssertion(Annotation( "GOC:obol") "Any process that activates or increases the frequency, rate or extent of antral ovarian follicle growth.") -AnnotationAssertion( "yaf") AnnotationAssertion( "2011-02-16T04:54:01Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:2000388") @@ -109401,7 +106571,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of lymphocyte migration) AnnotationAssertion(Annotation( "GOC:mah") "Any process that modulates the frequency, rate or extent of lymphocyte migration.") -AnnotationAssertion( "mah") AnnotationAssertion( "2011-02-23T10:45:19Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:2000401") @@ -109411,7 +106580,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of lymphocyte migration) AnnotationAssertion(Annotation( "GOC:mah") "Any process that stops, prevents or reduces the frequency, rate or extent of lymphocyte migration.") -AnnotationAssertion( "mah") AnnotationAssertion( "2011-02-23T10:45:47Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:2000402") @@ -109421,7 +106589,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of lymphocyte migration) AnnotationAssertion(Annotation( "GOC:mah") "Any process that activates or increases the frequency, rate or extent of lymphocyte migration.") -AnnotationAssertion( "mah") AnnotationAssertion( "2011-02-23T10:46:06Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:2000403") @@ -109431,7 +106598,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of T cell migration) AnnotationAssertion(Annotation( "GOC:mah") "Any process that modulates the frequency, rate or extent of T cell migration.") -AnnotationAssertion( "mah") AnnotationAssertion( "2011-02-23T10:48:24Z") AnnotationAssertion(Annotation( "GOC:obol") "regulation of T lymphocyte migration") AnnotationAssertion(Annotation( "GOC:obol") "regulation of T-cell migration") @@ -109444,7 +106610,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of T cell migration) AnnotationAssertion(Annotation( "GOC:mah") "Any process that stops, prevents or reduces the frequency, rate or extent of T cell migration.") -AnnotationAssertion( "mah") AnnotationAssertion( "2011-02-23T10:48:52Z") AnnotationAssertion(Annotation( "GOC:obol") "negative regulation of T lymphocyte migration") AnnotationAssertion(Annotation( "GOC:obol") "negative regulation of T-cell migration") @@ -109457,7 +106622,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of T cell migration) AnnotationAssertion(Annotation( "GOC:mah") "Any process that activates or increases the frequency, rate or extent of T cell migration.") -AnnotationAssertion( "mah") AnnotationAssertion( "2011-02-23T10:49:12Z") AnnotationAssertion(Annotation( "GOC:obol") "positive regulation of T lymphocyte migration") AnnotationAssertion(Annotation( "GOC:obol") "positive regulation of T-cell migration") @@ -109470,7 +106634,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of thymocyte migration) AnnotationAssertion(Annotation( "GOC:mah") "Any process that modulates the frequency, rate or extent of thymocyte migration.") -AnnotationAssertion( "mah") AnnotationAssertion( "2011-02-23T01:33:32Z") AnnotationAssertion(Annotation( "GOC:obol") "regulation of thymic lymphocyte migration") AnnotationAssertion( "biological_process") @@ -109485,7 +106648,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of thymocyte migration) AnnotationAssertion(Annotation( "GOC:mah") "Any process that stops, prevents or reduces the frequency, rate or extent of thymocyte migration.") -AnnotationAssertion( "mah") AnnotationAssertion( "2011-02-23T01:34:01Z") AnnotationAssertion(Annotation( "GOC:obol") "negative regulation of thymic lymphocyte migration") AnnotationAssertion( "biological_process") @@ -109500,7 +106662,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of thymocyte migration) AnnotationAssertion(Annotation( "GOC:mah") "Any process that activates or increases the frequency, rate or extent of thymocyte migration.") -AnnotationAssertion( "mah") AnnotationAssertion( "2011-02-23T01:34:23Z") AnnotationAssertion(Annotation( "GOC:obol") "positive regulation of thymic lymphocyte migration") AnnotationAssertion( "biological_process") @@ -109515,7 +106676,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of eosinophil migration) AnnotationAssertion(Annotation( "GOC:mah") "Any process that modulates the frequency, rate or extent of eosinophil migration.") -AnnotationAssertion( "mah") AnnotationAssertion( "2011-02-23T01:43:23Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:2000416") @@ -109525,7 +106685,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of eosinophil migration) AnnotationAssertion(Annotation( "GOC:mah") "Any process that stops, prevents or reduces the frequency, rate or extent of eosinophil migration.") -AnnotationAssertion( "mah") AnnotationAssertion( "2011-02-23T01:43:52Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:2000417") @@ -109535,7 +106694,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of eosinophil migration) AnnotationAssertion(Annotation( "GOC:mah") "Any process that activates or increases the frequency, rate or extent of eosinophil migration.") -AnnotationAssertion( "mah") AnnotationAssertion( "2011-02-23T01:44:14Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:2000418") @@ -109545,7 +106703,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of eosinophil chemotaxis) AnnotationAssertion(Annotation( "GOC:obol") "Any process that modulates the frequency, rate or extent of eosinophil chemotaxis.") -AnnotationAssertion( "bf") AnnotationAssertion( "2011-02-24T01:16:44Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:2000422") @@ -109555,7 +106712,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of eosinophil chemotaxis) AnnotationAssertion(Annotation( "GOC:obol") "Any process that stops, prevents or reduces the frequency, rate or extent of eosinophil chemotaxis.") -AnnotationAssertion( "bf") AnnotationAssertion( "2011-02-24T01:17:12Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:2000423") @@ -109565,7 +106721,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of eosinophil chemotaxis) AnnotationAssertion(Annotation( "GOC:obol") "Any process that activates or increases the frequency, rate or extent of eosinophil chemotaxis.") -AnnotationAssertion( "bf") AnnotationAssertion( "2011-02-24T01:17:35Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:2000424") @@ -109575,7 +106730,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of apoptotic cell clearance) AnnotationAssertion(Annotation( "GOC:obol") "Any process that modulates the frequency, rate or extent of apoptotic cell clearance.") -AnnotationAssertion( "bf") AnnotationAssertion( "2011-02-25T11:50:11Z") AnnotationAssertion(Annotation( "GOC:obol") "regulation of apoptotic cell removal") AnnotationAssertion(Annotation( "GOC:obol") "regulation of efferocytosis") @@ -109588,7 +106742,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of apoptotic cell clearance) AnnotationAssertion(Annotation( "GOC:obol") "Any process that stops, prevents or reduces the frequency, rate or extent of apoptotic cell clearance.") -AnnotationAssertion( "bf") AnnotationAssertion( "2011-02-25T11:50:39Z") AnnotationAssertion(Annotation( "GOC:obol") "negative regulation of apoptotic cell removal") AnnotationAssertion(Annotation( "GOC:obol") "negative regulation of efferocytosis") @@ -109601,7 +106754,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of apoptotic cell clearance) AnnotationAssertion(Annotation( "GOC:obol") "Any process that activates or increases the frequency, rate or extent of apoptotic cell clearance.") -AnnotationAssertion( "bf") AnnotationAssertion( "2011-02-25T11:50:59Z") AnnotationAssertion(Annotation( "GOC:obol") "positive regulation of apoptotic cell removal") AnnotationAssertion(Annotation( "GOC:obol") "positive regulation of efferocytosis") @@ -109614,7 +106766,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of astrocyte chemotaxis) AnnotationAssertion(Annotation( "GOC:obol") "Any process that modulates the frequency, rate or extent of astrocyte chemotaxis.") -AnnotationAssertion( "bf") AnnotationAssertion( "2011-03-04T10:53:50Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:2000458") @@ -109624,7 +106775,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of astrocyte chemotaxis) AnnotationAssertion(Annotation( "GOC:obol") "Any process that stops, prevents or reduces the frequency, rate or extent of astrocyte chemotaxis.") -AnnotationAssertion( "bf") AnnotationAssertion( "2011-03-04T10:54:28Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:2000459") @@ -109634,7 +106784,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of excitatory postsynaptic potential) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:bf") "Any process that enhances the establishment or increases the extent of the excitatory postsynaptic potential (EPSP) which is a temporary increase in postsynaptic potential due to the flow of positively charged ions into the postsynaptic cell. The flow of ions that causes an EPSP is an excitatory postsynaptic current (EPSC) and makes it easier for the neuron to fire an action potential.") -AnnotationAssertion( "rl") AnnotationAssertion( "2011-03-04T02:43:32Z") AnnotationAssertion( "positive regulation of excitatory post-synaptic membrane potential") AnnotationAssertion( "biological_process") @@ -109647,7 +106796,6 @@ SubClassOf( ObjectSomeValuesFrom( (positive regulation of astrocyte chemotaxis) AnnotationAssertion(Annotation( "GOC:obol") "Any process that activates or increases the frequency, rate or extent of astrocyte chemotaxis.") -AnnotationAssertion( "bf") AnnotationAssertion( "2011-03-04T04:43:29Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:2000464") @@ -109657,7 +106805,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of hematopoietic stem cell migration) AnnotationAssertion(Annotation( "GOC:obol") "Any process that modulates the frequency, rate or extent of hematopoietic stem cell migration.") -AnnotationAssertion( "bf") AnnotationAssertion( "2011-03-09T09:34:08Z") AnnotationAssertion(Annotation( "GOC:obol") "regulation of hemopoietic stem cell migration") AnnotationAssertion( "biological_process") @@ -109668,7 +106815,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of hematopoietic stem cell migration) AnnotationAssertion(Annotation( "GOC:obol") "Any process that stops, prevents or reduces the frequency, rate or extent of hematopoietic stem cell migration.") -AnnotationAssertion( "bf") AnnotationAssertion( "2011-03-09T09:34:54Z") AnnotationAssertion(Annotation( "GOC:obol") "negative regulation of hemopoietic stem cell migration") AnnotationAssertion( "biological_process") @@ -109679,7 +106825,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of hematopoietic stem cell migration) AnnotationAssertion(Annotation( "GOC:obol") "Any process that activates or increases the frequency, rate or extent of hematopoietic stem cell migration.") -AnnotationAssertion( "bf") AnnotationAssertion( "2011-03-09T09:35:25Z") AnnotationAssertion(Annotation( "GOC:obol") "positive regulation of hemopoietic stem cell migration") AnnotationAssertion( "biological_process") @@ -109691,7 +106836,6 @@ EquivalentClasses( ObjectIntersection AnnotationAssertion(Annotation( "GOC:obol") "Any process that modulates the frequency, rate or extent of metanephric glomerular visceral epithelial cell development.") AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/23000"^^xsd:anyURI) -AnnotationAssertion( "yaf") AnnotationAssertion( "2011-03-09T05:16:40Z") AnnotationAssertion( "regulation of metanephric glomerular visceral epithelial cell development") AnnotationAssertion( "biological_process") @@ -109703,7 +106847,6 @@ EquivalentClasses( ObjectIntersection AnnotationAssertion(Annotation( "GOC:obol") "Any process that activates or increases the frequency, rate or extent of metanephric glomerular visceral epithelial cell development.") AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/23000"^^xsd:anyURI) -AnnotationAssertion( "yaf") AnnotationAssertion( "2011-03-09T05:17:26Z") AnnotationAssertion( "positive regulation of metanephric glomerular visceral epithelial cell development") AnnotationAssertion( "biological_process") @@ -109714,7 +106857,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of hepatic stellate cell activation) AnnotationAssertion(Annotation( "GOC:obol") "Any process that modulates the frequency, rate or extent of hepatic stellate cell activation.") -AnnotationAssertion( "bf") AnnotationAssertion( "2011-03-14T03:48:32Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:2000489") @@ -109724,7 +106866,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of hepatic stellate cell activation) AnnotationAssertion(Annotation( "GOC:obol") "Any process that stops, prevents or reduces the frequency, rate or extent of hepatic stellate cell activation.") -AnnotationAssertion( "bf") AnnotationAssertion( "2011-03-14T03:49:18Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:2000490") @@ -109734,7 +106875,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of hepatic stellate cell activation) AnnotationAssertion(Annotation( "GOC:obol") "Any process that activates or increases the frequency, rate or extent of hepatic stellate cell activation.") -AnnotationAssertion( "bf") AnnotationAssertion( "2011-03-14T03:49:48Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:2000491") @@ -109744,7 +106884,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of cell proliferation involved in compound eye morphogenesis) AnnotationAssertion(Annotation( "GOC:obol") "Any process that modulates the frequency, rate or extent of cell proliferation involved in compound eye morphogenesis.") -AnnotationAssertion( "bf") AnnotationAssertion( "2011-03-18T02:18:34Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:2000495") @@ -109754,7 +106893,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of cell proliferation involved in compound eye morphogenesis) AnnotationAssertion(Annotation( "GOC:obol") "Any process that stops, prevents or reduces the frequency, rate or extent of cell proliferation involved in compound eye morphogenesis.") -AnnotationAssertion( "bf") AnnotationAssertion( "2011-03-18T02:19:22Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:2000496") @@ -109764,7 +106902,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of cell proliferation involved in compound eye morphogenesis) AnnotationAssertion(Annotation( "GOC:obol") "Any process that activates or increases the frequency, rate or extent of cell proliferation involved in compound eye morphogenesis.") -AnnotationAssertion( "bf") AnnotationAssertion( "2011-03-18T02:19:54Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:2000497") @@ -109774,7 +106911,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of natural killer cell chemotaxis) AnnotationAssertion(Annotation( "GOC:BHF") "Any process that modulates the frequency, rate or extent of natural killer cell chemotaxis.") -AnnotationAssertion( "bf") AnnotationAssertion( "2011-03-21T10:09:23Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:2000501") @@ -109784,7 +106920,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of natural killer cell chemotaxis) AnnotationAssertion(Annotation( "GOC:BHF") "Any process that stops, prevents or reduces the frequency, rate or extent of natural killer cell chemotaxis.") -AnnotationAssertion( "bf") AnnotationAssertion( "2011-03-21T10:09:32Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:2000502") @@ -109794,7 +106929,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of natural killer cell chemotaxis) AnnotationAssertion(Annotation( "GOC:BHF") "Any process that activates or increases the frequency, rate or extent of natural killer cell chemotaxis.") -AnnotationAssertion( "bf") AnnotationAssertion( "2011-03-21T10:09:38Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:2000503") @@ -109804,7 +106938,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of blood vessel remodeling) AnnotationAssertion(Annotation( "GOC:obol") "Any process that activates or increases the frequency, rate or extent of blood vessel remodeling.") -AnnotationAssertion( "pr") AnnotationAssertion( "2011-03-21T10:33:20Z") AnnotationAssertion( "positive regulation of blood vessel remodelling") AnnotationAssertion( "biological_process") @@ -109815,7 +106948,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of dendritic cell chemotaxis) AnnotationAssertion(Annotation( "GOC:obol") "Any process that modulates the frequency, rate or extent of dendritic cell chemotaxis.") -AnnotationAssertion( "ebc") AnnotationAssertion( "2011-03-22T10:21:38Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:2000508") @@ -109825,7 +106957,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of dendritic cell chemotaxis) AnnotationAssertion(Annotation( "GOC:obol") "Any process that stops, prevents or reduces the frequency, rate or extent of dendritic cell chemotaxis.") -AnnotationAssertion( "ebc") AnnotationAssertion( "2011-03-22T10:21:45Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:2000509") @@ -109835,7 +106966,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of dendritic cell chemotaxis) AnnotationAssertion(Annotation( "GOC:obol") "Any process that activates or increases the frequency, rate or extent of dendritic cell chemotaxis.") -AnnotationAssertion( "ebc") AnnotationAssertion( "2011-03-22T10:21:49Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:2000510") @@ -109845,7 +106975,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of CD4-positive, alpha-beta T cell activation) AnnotationAssertion(Annotation( "GOC:obol") "Any process that modulates the frequency, rate or extent of CD4-positive, alpha-beta T cell activation.") -AnnotationAssertion( "ebc") AnnotationAssertion( "2011-03-22T10:36:56Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:2000514") @@ -109855,7 +106984,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of CD4-positive, alpha-beta T cell activation) AnnotationAssertion(Annotation( "GOC:obol") "Any process that stops, prevents or reduces the frequency, rate or extent of CD4-positive, alpha-beta T cell activation.") -AnnotationAssertion( "ebc") AnnotationAssertion( "2011-03-22T10:37:02Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:2000515") @@ -109865,7 +106993,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of CD4-positive, alpha-beta T cell activation) AnnotationAssertion(Annotation( "GOC:obol") "Any process that activates or increases the frequency, rate or extent of CD4-positive, alpha-beta T cell activation.") -AnnotationAssertion( "ebc") AnnotationAssertion( "2011-03-22T10:37:06Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:2000516") @@ -109875,7 +107002,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of T-helper 1 cell activation) AnnotationAssertion(Annotation( "GOC:obol") "Any process that modulates the frequency, rate or extent of T-helper 1 cell activation.") -AnnotationAssertion( "ebc") AnnotationAssertion( "2011-03-22T10:40:19Z") AnnotationAssertion(Annotation( "GOC:obol") "regulation of Th1 cell activation") AnnotationAssertion( "biological_process") @@ -109886,7 +107012,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of T-helper 1 cell activation) AnnotationAssertion(Annotation( "GOC:obol") "Any process that stops, prevents or reduces the frequency, rate or extent of T-helper 1 cell activation.") -AnnotationAssertion( "ebc") AnnotationAssertion( "2011-03-22T10:40:26Z") AnnotationAssertion(Annotation( "GOC:obol") "negative regulation of Th1 cell activation") AnnotationAssertion( "biological_process") @@ -109897,7 +107022,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of T-helper 1 cell activation) AnnotationAssertion(Annotation( "GOC:obol") "Any process that activates or increases the frequency, rate or extent of T-helper 1 cell activation.") -AnnotationAssertion( "ebc") AnnotationAssertion( "2011-03-22T10:40:31Z") AnnotationAssertion(Annotation( "GOC:obol") "positive regulation of Th1 cell activation") AnnotationAssertion( "biological_process") @@ -109908,7 +107032,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of T cell costimulation) AnnotationAssertion(Annotation( "GOC:obol") "Any process that modulates the frequency, rate or extent of T cell costimulation.") -AnnotationAssertion( "ebc") AnnotationAssertion( "2011-03-23T10:23:24Z") AnnotationAssertion(Annotation( "GOC:obol") "regulation of T cell co-stimulation") AnnotationAssertion(Annotation( "GOC:obol") "regulation of T lymphocyte costimulation") @@ -109923,7 +107046,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of T cell costimulation) AnnotationAssertion(Annotation( "GOC:obol") "Any process that stops, prevents or reduces the frequency, rate or extent of T cell costimulation.") -AnnotationAssertion( "ebc") AnnotationAssertion( "2011-03-23T10:23:31Z") AnnotationAssertion(Annotation( "GOC:obol") "negative regulation of T cell co-stimulation") AnnotationAssertion(Annotation( "GOC:obol") "negative regulation of T lymphocyte costimulation") @@ -109938,7 +107060,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of T cell costimulation) AnnotationAssertion(Annotation( "GOC:obol") "Any process that activates or increases the frequency, rate or extent of T cell costimulation.") -AnnotationAssertion( "ebc") AnnotationAssertion( "2011-03-23T10:23:36Z") AnnotationAssertion(Annotation( "GOC:obol") "positive regulation of T cell co-stimulation") AnnotationAssertion(Annotation( "GOC:obol") "positive regulation of T lymphocyte costimulation") @@ -109953,7 +107074,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of myeloid dendritic cell chemotaxis) AnnotationAssertion(Annotation( "GOC:obol") "Any process that modulates the frequency, rate or extent of myeloid dendritic cell chemotaxis.") -AnnotationAssertion( "ebc") AnnotationAssertion( "2011-03-23T12:18:32Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:2000527") @@ -109963,7 +107083,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of myeloid dendritic cell chemotaxis) AnnotationAssertion(Annotation( "GOC:obol") "Any process that stops, prevents or reduces the frequency, rate or extent of myeloid dendritic cell chemotaxis.") -AnnotationAssertion( "ebc") AnnotationAssertion( "2011-03-23T12:18:39Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:2000528") @@ -109973,7 +107092,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of myeloid dendritic cell chemotaxis) AnnotationAssertion(Annotation( "GOC:obol") "Any process that activates or increases the frequency, rate or extent of myeloid dendritic cell chemotaxis.") -AnnotationAssertion( "ebc") AnnotationAssertion( "2011-03-23T12:18:45Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:2000529") @@ -109983,7 +107101,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of B cell chemotaxis) AnnotationAssertion(Annotation( "GOC:obol") "Any process that modulates the frequency, rate or extent of B cell chemotaxis.") -AnnotationAssertion( "ebc") AnnotationAssertion( "2011-03-29T09:49:25Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:2000537") @@ -109993,7 +107110,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of B cell chemotaxis) AnnotationAssertion(Annotation( "GOC:obol") "Any process that activates or increases the frequency, rate or extent of B cell chemotaxis.") -AnnotationAssertion( "ebc") AnnotationAssertion( "2011-03-29T09:49:33Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:2000538") @@ -110003,7 +107119,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of gastrulation) AnnotationAssertion(Annotation( "GOC:obol") "Any process that stops, prevents or reduces the frequency, rate or extent of gastrulation.") -AnnotationAssertion( "yaf") AnnotationAssertion( "2011-04-01T04:10:08Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:2000542") @@ -110015,7 +107130,6 @@ SubClassOf( (positive regulation of gastrulation) AnnotationAssertion(Annotation( "GOC:obol") "Any process that activates or increases the frequency, rate or extent of gastrulation.") -AnnotationAssertion( "yaf") AnnotationAssertion( "2011-04-01T04:10:15Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:2000543") @@ -110027,7 +107141,6 @@ SubClassOf( (regulation of dendritic cell dendrite assembly) AnnotationAssertion(Annotation( "GOC:obol") "Any process that modulates the frequency, rate or extent of dendritic cell dendrite assembly.") -AnnotationAssertion( "ebc") AnnotationAssertion( "2011-04-03T07:21:55Z") AnnotationAssertion( "biological_process") AnnotationAssertion(Annotation( "GOC:obol") "regulation of dendritic extension") @@ -110038,7 +107151,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of dendritic cell dendrite assembly) AnnotationAssertion(Annotation( "GOC:obol") "Any process that stops, prevents or reduces the frequency, rate or extent of dendritic cell dendrite assembly.") -AnnotationAssertion( "ebc") AnnotationAssertion( "2011-04-03T07:22:01Z") AnnotationAssertion( "biological_process") AnnotationAssertion(Annotation( "GOC:obol") "negative regulation of dendritic extension") @@ -110049,7 +107161,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of dendritic cell dendrite assembly) AnnotationAssertion(Annotation( "GOC:obol") "Any process that activates or increases the frequency, rate or extent of dendritic cell dendrite assembly.") -AnnotationAssertion( "ebc") AnnotationAssertion( "2011-04-03T07:22:06Z") AnnotationAssertion( "biological_process") AnnotationAssertion(Annotation( "GOC:obol") "positive regulation of dendritic extension") @@ -110060,7 +107171,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of B cell chemotaxis) AnnotationAssertion(Annotation( "GOC:obol") "Any process that stops, prevents or reduces the frequency, rate or extent of B cell chemotaxis.") -AnnotationAssertion( "ebc") AnnotationAssertion( "2011-04-03T07:25:59Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:2000550") @@ -110070,7 +107180,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of T-helper 2 cell cytokine production) AnnotationAssertion(Annotation( "GOC:obol") "Any process that modulates the frequency, rate or extent of T-helper 2 cell cytokine production.") -AnnotationAssertion( "ebc") AnnotationAssertion( "2011-04-03T07:32:47Z") AnnotationAssertion(Annotation( "GOC:obol") "regulation of Th2 cell cytokine production") AnnotationAssertion( "biological_process") @@ -110082,7 +107191,6 @@ SubClassOf( ObjectSomeValuesFrom( (negative regulation of T-helper 2 cell cytokine production) AnnotationAssertion(Annotation( "GOC:obol") "Any process that stops, prevents or reduces the frequency, rate or extent of T-helper 2 cell cytokine production.") -AnnotationAssertion( "ebc") AnnotationAssertion( "2011-04-03T07:32:54Z") AnnotationAssertion(Annotation( "GOC:obol") "negative regulation of Th2 cell cytokine production") AnnotationAssertion( "biological_process") @@ -110094,7 +107202,6 @@ SubClassOf( ObjectSomeValuesFrom( (positive regulation of T-helper 2 cell cytokine production) AnnotationAssertion(Annotation( "GOC:obol") "Any process that activates or increases the frequency, rate or extent of T-helper 2 cell cytokine production.") -AnnotationAssertion( "ebc") AnnotationAssertion( "2011-04-03T07:32:58Z") AnnotationAssertion(Annotation( "GOC:obol") "positive regulation of Th2 cell cytokine production") AnnotationAssertion( "biological_process") @@ -110106,7 +107213,6 @@ SubClassOf( ObjectSomeValuesFrom( (regulation of T-helper 1 cell cytokine production) AnnotationAssertion(Annotation( "GOC:obol") "Any process that modulates the frequency, rate or extent of T-helper 1 cell cytokine production.") -AnnotationAssertion( "ebc") AnnotationAssertion( "2011-04-03T07:35:43Z") AnnotationAssertion(Annotation( "GOC:obol") "regulation of Th1 cell cytokine production") AnnotationAssertion( "biological_process") @@ -110118,7 +107224,6 @@ SubClassOf( ObjectSomeValuesFrom( (negative regulation of T-helper 1 cell cytokine production) AnnotationAssertion(Annotation( "GOC:obol") "Any process that stops, prevents or reduces the frequency, rate or extent of T-helper 1 cell cytokine production.") -AnnotationAssertion( "ebc") AnnotationAssertion( "2011-04-03T07:35:51Z") AnnotationAssertion(Annotation( "GOC:obol") "negative regulation of Th1 cell cytokine production") AnnotationAssertion( "biological_process") @@ -110130,7 +107235,6 @@ SubClassOf( ObjectSomeValuesFrom( (positive regulation of T-helper 1 cell cytokine production) AnnotationAssertion(Annotation( "GOC:obol") "Any process that activates or increases the frequency, rate or extent of T-helper 1 cell cytokine production.") -AnnotationAssertion( "ebc") AnnotationAssertion( "2011-04-03T07:35:56Z") AnnotationAssertion(Annotation( "GOC:obol") "positive regulation of Th1 cell cytokine production") AnnotationAssertion( "biological_process") @@ -110142,7 +107246,6 @@ SubClassOf( ObjectSomeValuesFrom( (regulation of CD4-positive, alpha-beta T cell proliferation) AnnotationAssertion(Annotation( "GOC:obol") "Any process that modulates the frequency, rate or extent of CD4-positive, alpha-beta T cell proliferation.") -AnnotationAssertion( "ebc") AnnotationAssertion( "2011-04-03T09:01:04Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:2000561") @@ -110152,7 +107255,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of CD4-positive, alpha-beta T cell proliferation) AnnotationAssertion(Annotation( "GOC:obol") "Any process that stops, prevents or reduces the frequency, rate or extent of CD4-positive, alpha-beta T cell proliferation.") -AnnotationAssertion( "ebc") AnnotationAssertion( "2011-04-03T09:01:11Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:2000562") @@ -110162,7 +107264,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of CD4-positive, alpha-beta T cell proliferation) AnnotationAssertion(Annotation( "GOC:obol") "Any process that activates or increases the frequency, rate or extent of CD4-positive, alpha-beta T cell proliferation.") -AnnotationAssertion( "ebc") AnnotationAssertion( "2011-04-03T09:01:15Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:2000563") @@ -110172,7 +107273,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of CD8-positive, alpha-beta T cell proliferation) AnnotationAssertion(Annotation( "GOC:obol") "Any process that modulates the frequency, rate or extent of CD8-positive, alpha-beta T cell proliferation.") -AnnotationAssertion( "ebc") AnnotationAssertion( "2011-04-03T09:03:13Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:2000564") @@ -110182,7 +107282,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of CD8-positive, alpha-beta T cell proliferation) AnnotationAssertion(Annotation( "GOC:obol") "Any process that stops, prevents or reduces the frequency, rate or extent of CD8-positive, alpha-beta T cell proliferation.") -AnnotationAssertion( "ebc") AnnotationAssertion( "2011-04-03T09:03:19Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:2000565") @@ -110192,7 +107291,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of CD8-positive, alpha-beta T cell proliferation) AnnotationAssertion(Annotation( "GOC:obol") "Any process that activates or increases the frequency, rate or extent of CD8-positive, alpha-beta T cell proliferation.") -AnnotationAssertion( "ebc") AnnotationAssertion( "2011-04-03T09:03:24Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:2000566") @@ -110202,7 +107300,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of memory T cell activation) AnnotationAssertion(Annotation( "GOC:obol") "Any process that modulates the frequency, rate or extent of memory T cell activation.") -AnnotationAssertion( "ebc") AnnotationAssertion( "2011-04-03T09:10:06Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:2000567") @@ -110212,7 +107309,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of memory T cell activation) AnnotationAssertion(Annotation( "GOC:obol") "Any process that activates or increases the frequency, rate or extent of memory T cell activation.") -AnnotationAssertion( "ebc") AnnotationAssertion( "2011-04-03T09:10:12Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:2000568") @@ -110222,7 +107318,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of T-helper 2 cell activation) AnnotationAssertion(Annotation( "GOC:obol") "Any process that modulates the frequency, rate or extent of T-helper 2 cell activation.") -AnnotationAssertion( "ebc") AnnotationAssertion( "2011-04-03T09:14:53Z") AnnotationAssertion(Annotation( "GOC:obol") "regulation of Th2 cell activation") AnnotationAssertion( "biological_process") @@ -110233,7 +107328,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of T-helper 2 cell activation) AnnotationAssertion(Annotation( "GOC:obol") "Any process that activates or increases the frequency, rate or extent of T-helper 2 cell activation.") -AnnotationAssertion( "ebc") AnnotationAssertion( "2011-04-03T09:14:59Z") AnnotationAssertion(Annotation( "GOC:obol") "positive regulation of Th2 cell activation") AnnotationAssertion( "biological_process") @@ -110244,7 +107338,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of DNA biosynthetic process) AnnotationAssertion(Annotation( "GOC:obol") "Any process that activates or increases the frequency, rate or extent of DNA biosynthetic process.") -AnnotationAssertion( "yaf") AnnotationAssertion( "2011-04-04T10:01:20Z") AnnotationAssertion(Annotation( "GOC:obol") "positive regulation of DNA anabolism") AnnotationAssertion(Annotation( "GOC:obol") "positive regulation of DNA biosynthesis") @@ -110258,7 +107351,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of optic nerve formation) AnnotationAssertion(Annotation( "GOC:obol") "Any process that modulates the frequency, rate or extent of optic nerve formation.") -AnnotationAssertion( "yaf") AnnotationAssertion( "2011-04-11T03:41:30Z") AnnotationAssertion( "biological_process") AnnotationAssertion(Annotation( "GOC:obol") "regulation of CN II biosynthesis") @@ -110271,7 +107363,6 @@ SubClassOf( ObjectSomeValuesFrom( (negative regulation of optic nerve formation) AnnotationAssertion(Annotation( "GOC:obol") "Any process that stops, prevents or reduces the frequency, rate or extent of optic nerve formation.") -AnnotationAssertion( "yaf") AnnotationAssertion( "2011-04-11T03:41:35Z") AnnotationAssertion( "biological_process") AnnotationAssertion(Annotation( "GOC:obol") "negative regulation of CN II biosynthesis") @@ -110283,7 +107374,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of optic nerve formation) AnnotationAssertion(Annotation( "GOC:obol") "Any process that activates or increases the frequency, rate or extent of optic nerve formation.") -AnnotationAssertion( "yaf") AnnotationAssertion( "2011-04-11T03:41:39Z") AnnotationAssertion( "biological_process") AnnotationAssertion(Annotation( "GOC:obol") "positive regulation of CN II biosynthesis") @@ -110295,7 +107385,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of cell proliferation involved in mesonephros development) AnnotationAssertion(Annotation( "GOC:obol") "Any process that modulates the frequency, rate or extent of cell proliferation involved in mesonephros development.") -AnnotationAssertion( "yaf") AnnotationAssertion( "2011-04-18T08:42:19Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:2000606") @@ -110305,7 +107394,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of cell proliferation involved in mesonephros development) AnnotationAssertion(Annotation( "GOC:obol") "Any process that stops, prevents or reduces the frequency, rate or extent of cell proliferation involved in mesonephros development.") -AnnotationAssertion( "yaf") AnnotationAssertion( "2011-04-18T08:42:23Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:2000607") @@ -110315,7 +107403,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of cell proliferation involved in mesonephros development) AnnotationAssertion(Annotation( "GOC:obol") "Any process that activates or increases the frequency, rate or extent of cell proliferation involved in mesonephros development.") -AnnotationAssertion( "yaf") AnnotationAssertion( "2011-04-18T08:42:25Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:2000608") @@ -110325,7 +107412,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of thyroid hormone generation) AnnotationAssertion(Annotation( "GOC:obol") "Any process that modulates the frequency, rate or extent of thyroid hormone generation.") -AnnotationAssertion( "yaf") AnnotationAssertion( "2011-04-18T10:12:14Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:2000609") @@ -110337,7 +107423,6 @@ SubClassOf( (negative regulation of thyroid hormone generation) AnnotationAssertion(Annotation( "GOC:obol") "Any process that stops, prevents or reduces the frequency, rate or extent of thyroid hormone generation.") -AnnotationAssertion( "yaf") AnnotationAssertion( "2011-04-18T10:12:19Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:2000610") @@ -110350,7 +107435,6 @@ SubClassOf( (positive regulation of thyroid hormone generation) AnnotationAssertion(Annotation( "GOC:obol") "Any process that activates or increases the frequency, rate or extent of thyroid hormone generation.") -AnnotationAssertion( "yaf") AnnotationAssertion( "2011-04-18T10:12:22Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:2000611") @@ -110363,7 +107447,6 @@ SubClassOf( (regulation of thyroid-stimulating hormone secretion) AnnotationAssertion(Annotation( "GOC:obol") "Any process that modulates the frequency, rate or extent of thyroid-stimulating hormone secretion.") -AnnotationAssertion( "yaf") AnnotationAssertion( "2011-04-18T12:56:16Z") AnnotationAssertion(Annotation( "GOC:obol") "regulation of TSH secretion") AnnotationAssertion(Annotation( "GOC:obol") "regulation of thyroid stimulating hormone secretion") @@ -110375,7 +107458,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of thyroid-stimulating hormone secretion) AnnotationAssertion(Annotation( "GOC:obol") "Any process that stops, prevents or reduces the frequency, rate or extent of thyroid-stimulating hormone secretion.") -AnnotationAssertion( "yaf") AnnotationAssertion( "2011-04-18T12:56:20Z") AnnotationAssertion(Annotation( "GOC:obol") "negative regulation of TSH secretion") AnnotationAssertion(Annotation( "GOC:obol") "negative regulation of thyroid stimulating hormone secretion") @@ -110387,7 +107469,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of thyroid-stimulating hormone secretion) AnnotationAssertion(Annotation( "GOC:obol") "Any process that activates or increases the frequency, rate or extent of thyroid-stimulating hormone secretion.") -AnnotationAssertion( "yaf") AnnotationAssertion( "2011-04-18T12:56:22Z") AnnotationAssertion(Annotation( "GOC:obol") "positive regulation of TSH secretion") AnnotationAssertion(Annotation( "GOC:obol") "positive regulation of thyroid stimulating hormone secretion") @@ -110399,7 +107480,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of stem cell proliferation) AnnotationAssertion(Annotation( "GOC:dph") "Any process that stops, prevents or reduces the frequency, rate or extent of stem cell proliferation.") -AnnotationAssertion( "dph") AnnotationAssertion( "2011-04-27T01:04:22Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:2000647") @@ -110409,7 +107489,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of stem cell proliferation) AnnotationAssertion(Annotation( "GOC:dph") "Any process that activates or increases the frequency, rate or extent of stem cell proliferation.") -AnnotationAssertion( "dph") AnnotationAssertion( "2011-04-27T01:04:25Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:2000648") @@ -110419,7 +107498,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of sodium ion transmembrane transporter activity) AnnotationAssertion(Annotation( "GOC:obol") "Any process that modulates the frequency, rate or extent of sodium ion transmembrane transporter activity.") -AnnotationAssertion( "yaf") AnnotationAssertion( "2011-04-28T08:42:53Z") AnnotationAssertion(Annotation( "GOC:obol") "regulation of sodium transporter activity") AnnotationAssertion( "biological_process") @@ -110432,7 +107510,6 @@ SubClassOf( ObjectSomeValuesFrom( (negative regulation of sodium ion transmembrane transporter activity) AnnotationAssertion(Annotation( "GOC:obol") "Any process that stops, prevents or reduces the frequency, rate or extent of sodium ion transmembrane transporter activity.") -AnnotationAssertion( "yaf") AnnotationAssertion( "2011-04-28T08:42:57Z") AnnotationAssertion(Annotation( "GOC:obol") "negative regulation of sodium transporter activity") AnnotationAssertion( "biological_process") @@ -110445,7 +107522,6 @@ SubClassOf( ObjectSomeValuesFrom( (positive regulation of sodium ion transmembrane transporter activity) AnnotationAssertion(Annotation( "GOC:obol") "Any process that activates or increases the frequency, rate or extent of sodium ion transmembrane transporter activity.") -AnnotationAssertion( "yaf") AnnotationAssertion( "2011-04-28T08:43:00Z") AnnotationAssertion(Annotation( "GOC:obol") "positive regulation of sodium transporter activity") AnnotationAssertion( "biological_process") @@ -110458,7 +107534,6 @@ SubClassOf( ObjectSomeValuesFrom( (regulation of cellular response to testosterone stimulus) AnnotationAssertion(Annotation( "GOC:BHF") "Any process that modulates the frequency, rate or extent of cellular response to testosterone stimulus.") -AnnotationAssertion( "vk") AnnotationAssertion( "2011-05-02T03:23:56Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:2000654") @@ -110468,7 +107543,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of cellular response to testosterone stimulus) AnnotationAssertion(Annotation( "GOC:BHF") "Any process that stops, prevents or reduces the frequency, rate or extent of cellular response to testosterone stimulus.") -AnnotationAssertion( "vk") AnnotationAssertion( "2011-05-02T03:23:59Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:2000655") @@ -110478,7 +107552,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of dendritic cell apoptotic process) AnnotationAssertion(Annotation( "GOC:mtg_apoptosis") Annotation( "GOC:obol") "Any process that modulates the frequency, rate or extent of dendritic cell apoptotic process.") -AnnotationAssertion( "pr") AnnotationAssertion( "2011-05-09T07:34:16Z") AnnotationAssertion( "regulation of dendritic cell apoptosis") AnnotationAssertion( "biological_process") @@ -110489,7 +107562,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of dendritic cell apoptotic process) AnnotationAssertion(Annotation( "GOC:mtg_apoptosis") Annotation( "GOC:obol") "Any process that stops, prevents or reduces the frequency, rate or extent of dendritic cell apoptotic process.") -AnnotationAssertion( "pr") AnnotationAssertion( "2011-05-09T07:34:21Z") AnnotationAssertion( "negative regulation of dendritic cell apoptosis") AnnotationAssertion( "biological_process") @@ -110500,7 +107572,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of dendritic cell apoptotic process) AnnotationAssertion(Annotation( "GOC:mtg_apoptosis") Annotation( "GOC:obol") "Any process that activates or increases the frequency, rate or extent of dendritic cell apoptotic process.") -AnnotationAssertion( "pr") AnnotationAssertion( "2011-05-09T07:34:26Z") AnnotationAssertion( "positive regulation of dendritic cell apoptosis") AnnotationAssertion( "biological_process") @@ -110511,7 +107582,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of motor neuron apoptotic process) AnnotationAssertion(Annotation( "GOC:mtg_apoptosis") Annotation( "GOC:obol") "Any process that modulates the frequency, rate or extent of motor neuron apoptotic process.") -AnnotationAssertion( "pr") AnnotationAssertion( "2011-05-09T10:56:17Z") AnnotationAssertion(Annotation( "GOC:obol") "regulation of motoneuron apoptosis") AnnotationAssertion( "regulation of motor neuron apoptosis") @@ -110523,7 +107593,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of motor neuron apoptotic process) AnnotationAssertion(Annotation( "GOC:mtg_apoptosis") Annotation( "GOC:obol") "Any process that stops, prevents or reduces the frequency, rate or extent of motor neuron apoptotic process.") -AnnotationAssertion( "pr") AnnotationAssertion( "2011-05-09T10:56:21Z") AnnotationAssertion(Annotation( "GOC:obol") "negative regulation of motoneuron apoptosis") AnnotationAssertion( "negative regulation of motor neuron apoptosis") @@ -110535,7 +107604,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of motor neuron apoptotic process) AnnotationAssertion(Annotation( "GOC:mtg_apoptosis") Annotation( "GOC:obol") "Any process that activates or increases the frequency, rate or extent of motor neuron apoptotic process.") -AnnotationAssertion( "pr") AnnotationAssertion( "2011-05-09T10:56:24Z") AnnotationAssertion(Annotation( "GOC:obol") "positive regulation of motoneuron apoptosis") AnnotationAssertion( "positive regulation of motor neuron apoptosis") @@ -110547,7 +107615,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of type B pancreatic cell apoptotic process) AnnotationAssertion(Annotation( "GOC:mtg_apoptosis") Annotation( "GOC:obol") "Any process that modulates the frequency, rate or extent of type B pancreatic cell apoptotic process.") -AnnotationAssertion( "pr") AnnotationAssertion( "2011-05-09T11:51:09Z") AnnotationAssertion(Annotation( "GOC:obol") "regulation of pancreatic B cell apoptosis") AnnotationAssertion(Annotation( "GOC:obol") "regulation of pancreatic beta cell apoptosis") @@ -110560,7 +107627,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of type B pancreatic cell apoptotic process) AnnotationAssertion(Annotation( "GOC:mtg_apoptosis") Annotation( "GOC:obol") "Any process that stops, prevents or reduces the frequency, rate or extent of type B pancreatic cell apoptotic process.") -AnnotationAssertion( "pr") AnnotationAssertion( "2011-05-09T11:51:12Z") AnnotationAssertion(Annotation( "GOC:obol") "negative regulation of pancreatic B cell apoptosis") AnnotationAssertion(Annotation( "GOC:obol") "negative regulation of pancreatic beta cell apoptosis") @@ -110573,7 +107639,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of type B pancreatic cell apoptotic process) AnnotationAssertion(Annotation( "GOC:mtg_apoptosis") Annotation( "GOC:obol") "Any process that activates or increases the frequency, rate or extent of type B pancreatic cell apoptotic process.") -AnnotationAssertion( "pr") AnnotationAssertion( "2011-05-09T11:51:15Z") AnnotationAssertion(Annotation( "GOC:obol") "positive regulation of pancreatic B cell apoptosis") AnnotationAssertion(Annotation( "GOC:obol") "positive regulation of pancreatic beta cell apoptosis") @@ -110586,7 +107651,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of cardiac muscle cell myoblast differentiation) AnnotationAssertion(Annotation( "GOC:obol") "Any process that modulates the frequency, rate or extent of cardiac muscle cell myoblast differentiation.") -AnnotationAssertion( "yaf") AnnotationAssertion( "2011-05-25T09:08:01Z") AnnotationAssertion(Annotation( "GOC:obol") "regulation of myocardial precursor cell differentiation") AnnotationAssertion( "biological_process") @@ -110598,7 +107662,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of cardiac muscle cell myoblast differentiation) AnnotationAssertion(Annotation( "GOC:obol") "Any process that stops, prevents or reduces the frequency, rate or extent of cardiac muscle cell myoblast differentiation.") -AnnotationAssertion( "yaf") AnnotationAssertion( "2011-05-25T09:08:06Z") AnnotationAssertion(Annotation( "GOC:obol") "negative regulation of myocardial precursor cell differentiation") AnnotationAssertion( "biological_process") @@ -110610,7 +107673,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of epithelial cell differentiation involved in kidney development) AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") Annotation( "GOC:yaf") "Any process that modulates the frequency, rate or extent of epithelial cell differentiation involved in kidney development.") -AnnotationAssertion( "bf") AnnotationAssertion( "2011-05-16T04:23:52Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:2000696") @@ -110620,7 +107682,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of epithelial cell differentiation involved in kidney development) AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") Annotation( "GOC:yaf") "Any process that stops, prevents or reduces the frequency, rate or extent of epithelial cell differentiation involved in kidney development.") -AnnotationAssertion( "bf") AnnotationAssertion( "2011-05-16T04:23:55Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:2000697") @@ -110630,7 +107691,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of epithelial cell differentiation involved in kidney development) AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") Annotation( "GOC:yaf") "Any process that activates or increases the frequency, rate or extent of epithelial cell differentiation involved in kidney development.") -AnnotationAssertion( "bf") AnnotationAssertion( "2011-05-16T04:23:57Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:2000698") @@ -110640,7 +107700,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of cardiac muscle cell myoblast differentiation) AnnotationAssertion(Annotation( "GOC:obol") "Any process that activates or increases the frequency, rate or extent of cardiac muscle cell myoblast differentiation.") -AnnotationAssertion( "yaf") AnnotationAssertion( "2011-05-25T09:08:09Z") AnnotationAssertion(Annotation( "GOC:obol") "positive regulation of myocardial precursor cell differentiation") AnnotationAssertion( "biological_process") @@ -110652,7 +107711,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of cardiac muscle cell differentiation) AnnotationAssertion(Annotation( "GOC:BHF") "Any process that modulates the frequency, rate or extent of cardiac muscle cell differentiation.") -AnnotationAssertion( "vk") AnnotationAssertion( "2011-06-08T10:51:06Z") AnnotationAssertion(Annotation( "GOC:obol") "regulation of cardiomyocyte differentiation") AnnotationAssertion( "biological_process") @@ -110664,7 +107722,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of cardiac muscle cell differentiation) AnnotationAssertion(Annotation( "GOC:BHF") "Any process that stops, prevents or reduces the frequency, rate or extent of cardiac muscle cell differentiation.") -AnnotationAssertion( "vk") AnnotationAssertion( "2011-06-08T10:51:11Z") AnnotationAssertion(Annotation( "GOC:obol") "negative regulation of cardiomyocyte differentiation") AnnotationAssertion( "biological_process") @@ -110676,7 +107733,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of cardiac muscle cell differentiation) AnnotationAssertion(Annotation( "GOC:BHF") "Any process that activates or increases the frequency, rate or extent of cardiac muscle cell differentiation.") -AnnotationAssertion( "vk") AnnotationAssertion( "2011-06-08T10:51:15Z") AnnotationAssertion(Annotation( "GOC:obol") "positive regulation of cardiomyocyte differentiation") AnnotationAssertion( "biological_process") @@ -110688,7 +107744,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of mesenchymal cell proliferation involved in ureter development) AnnotationAssertion(Annotation( "GOC:obol") "Any process that activates or increases the frequency, rate or extent of mesenchymal cell proliferation involved in ureter development.") -AnnotationAssertion( "yaf") AnnotationAssertion( "2011-06-10T02:27:19Z") AnnotationAssertion( "biological_process") AnnotationAssertion(Annotation( "GOC:obol") "positive regulation of ureter mesenchymal cell proliferation") @@ -110701,7 +107756,6 @@ SubClassOf( ObjectSomeValuesFrom( (regulation of stem cell differentiation) AnnotationAssertion(Annotation( "GOC:obol") "Any process that modulates the frequency, rate or extent of stem cell differentiation.") -AnnotationAssertion( "yaf") AnnotationAssertion( "2011-06-14T02:05:16Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:2000736") @@ -110711,7 +107765,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of stem cell differentiation) AnnotationAssertion(Annotation( "GOC:obol") "Any process that stops, prevents or reduces the frequency, rate or extent of stem cell differentiation.") -AnnotationAssertion( "yaf") AnnotationAssertion( "2011-06-14T02:05:20Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:2000737") @@ -110721,7 +107774,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of stem cell differentiation) AnnotationAssertion(Annotation( "GOC:obol") "Any process that activates or increases the frequency, rate or extent of stem cell differentiation.") -AnnotationAssertion( "yaf") AnnotationAssertion( "2011-06-14T02:05:23Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:2000738") @@ -110731,7 +107783,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of mesenchymal stem cell differentiation) AnnotationAssertion(Annotation( "GOC:obol") "Any process that modulates the frequency, rate or extent of mesenchymal stem cell differentiation.") -AnnotationAssertion( "yaf") AnnotationAssertion( "2011-06-14T02:31:27Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:2000739") @@ -110741,7 +107792,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of mesenchymal stem cell differentiation) AnnotationAssertion(Annotation( "GOC:obol") "Any process that stops, prevents or reduces the frequency, rate or extent of mesenchymal stem cell differentiation.") -AnnotationAssertion( "yaf") AnnotationAssertion( "2011-06-14T02:31:31Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:2000740") @@ -110751,7 +107801,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of mesenchymal stem cell differentiation) AnnotationAssertion(Annotation( "GOC:obol") "Any process that activates or increases the frequency, rate or extent of mesenchymal stem cell differentiation.") -AnnotationAssertion( "yaf") AnnotationAssertion( "2011-06-14T02:31:34Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:2000741") @@ -110761,7 +107810,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of cytoplasmic translation) AnnotationAssertion(Annotation( "GOC:obol") "Any process that modulates the frequency, rate or extent of cytoplasmic translation.") -AnnotationAssertion( "vw") AnnotationAssertion( "2011-06-20T10:39:19Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:2000765") @@ -110771,7 +107819,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of cytoplasmic translation) AnnotationAssertion(Annotation( "GOC:obol") "Any process that stops, prevents or reduces the frequency, rate or extent of cytoplasmic translation.") -AnnotationAssertion( "vw") AnnotationAssertion( "2011-06-20T10:39:23Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:2000766") @@ -110781,7 +107828,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of cytoplasmic translation) AnnotationAssertion(Annotation( "GOC:obol") "Any process that activates or increases the frequency, rate or extent of cytoplasmic translation.") -AnnotationAssertion( "vw") AnnotationAssertion( "2011-06-20T10:39:26Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:2000767") @@ -110791,7 +107837,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of nephron tubule epithelial cell differentiation) AnnotationAssertion(Annotation( "GOC:obol") "Any process that activates or increases the frequency, rate or extent of nephron tubule epithelial cell differentiation.") -AnnotationAssertion( "yaf") AnnotationAssertion( "2011-06-22T11:55:06Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:2000768") @@ -110801,7 +107846,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of mesenchymal cell proliferation involved in lung development) AnnotationAssertion(Annotation( "PMID:21513708") "Any process that modulates the frequency, rate or extent of mesenchymal cell proliferation involved in lung development.") -AnnotationAssertion( "pr") AnnotationAssertion( "2011-06-24T01:53:50Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:2000790") @@ -110811,7 +107855,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of mesenchymal cell proliferation involved in lung development) AnnotationAssertion(Annotation( "PMID:21513708") "Any process that stops, prevents or reduces the frequency, rate or extent of mesenchymal cell proliferation involved in lung development.") -AnnotationAssertion( "pr") AnnotationAssertion( "2011-06-24T01:53:53Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:2000791") @@ -110823,7 +107866,6 @@ SubClassOf( ObjectSomeValuesFrom( (positive regulation of mesenchymal cell proliferation involved in lung development) AnnotationAssertion(Annotation( "PMID:21513708") "Any process that activates or increases the frequency, rate or extent of mesenchymal cell proliferation involved in lung development.") -AnnotationAssertion( "pr") AnnotationAssertion( "2011-06-24T01:53:56Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:2000792") @@ -110835,7 +107877,6 @@ SubClassOf( ObjectSomeValuesFrom( (cell proliferation involved in heart valve development) AnnotationAssertion(Annotation( "GOC:BHF") "Any cell proliferation that is involved in heart valve development.") -AnnotationAssertion( "bf") AnnotationAssertion( "2011-06-24T03:12:15Z") AnnotationAssertion(Annotation( "GOC:obol") "cell proliferation of cardiac valve development") AnnotationAssertion(Annotation( "GOC:obol") "cell proliferation of heart valve development") @@ -110847,7 +107888,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of epithelial cell proliferation involved in lung morphogenesis) AnnotationAssertion(Annotation( "PMID:21513708") "Any process that modulates the frequency, rate or extent of epithelial cell proliferation involved in lung morphogenesis.") -AnnotationAssertion( "pr") AnnotationAssertion( "2011-06-25T07:22:38Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:2000794") @@ -110857,7 +107897,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of epithelial cell proliferation involved in lung morphogenesis) AnnotationAssertion(Annotation( "PMID:21513708") "Any process that stops, prevents or reduces the frequency, rate or extent of epithelial cell proliferation involved in lung morphogenesis.") -AnnotationAssertion( "pr") AnnotationAssertion( "2011-06-25T07:22:42Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:2000795") @@ -110867,7 +107906,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of amniotic stem cell differentiation) AnnotationAssertion(Annotation( "GOC:obol") "Any process that modulates the frequency, rate or extent of amniotic stem cell differentiation.") -AnnotationAssertion( "yaf") AnnotationAssertion( "2011-06-29T02:18:59Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:2000797") @@ -110877,7 +107915,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of amniotic stem cell differentiation) AnnotationAssertion(Annotation( "GOC:obol") "Any process that stops, prevents or reduces the frequency, rate or extent of amniotic stem cell differentiation.") -AnnotationAssertion( "yaf") AnnotationAssertion( "2011-06-29T02:19:03Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:2000798") @@ -110887,7 +107924,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of amniotic stem cell differentiation) AnnotationAssertion(Annotation( "GOC:obol") "Any process that activates or increases the frequency, rate or extent of amniotic stem cell differentiation.") -AnnotationAssertion( "yaf") AnnotationAssertion( "2011-06-29T02:19:06Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:2000799") @@ -110897,7 +107933,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of bicellular tight junction assembly) AnnotationAssertion(Annotation( "GOC:BHF") "Any process that modulates the frequency, rate or extent of tight junction assembly.") -AnnotationAssertion( "vk") AnnotationAssertion( "2011-07-06T01:08:28Z") AnnotationAssertion(Annotation( "GOC:obol") "regulation of tight junction formation") AnnotationAssertion( "biological_process") @@ -110908,7 +107943,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of myoblast proliferation) AnnotationAssertion(Annotation( "GOC:obol") "Any process that stops, prevents or reduces the frequency, rate or extent of myoblast proliferation.") -AnnotationAssertion( "pr") AnnotationAssertion( "2011-07-12T03:06:04Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:2000818") @@ -110918,7 +107952,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of heart morphogenesis) AnnotationAssertion(Annotation( "GOC:BHF") "Any process that modulates the frequency, rate or extent of heart morphogenesis.") -AnnotationAssertion( "vk") AnnotationAssertion( "2011-07-19T10:08:58Z") AnnotationAssertion( "biological_process") AnnotationAssertion(Annotation( "GOC:obol") "regulation of cardiac morphogenesis") @@ -110929,7 +107962,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of parathyroid hormone secretion) AnnotationAssertion(Annotation( "GOC:obol") "Any process that modulates the frequency, rate or extent of parathyroid hormone secretion.") -AnnotationAssertion( "bf") AnnotationAssertion( "2011-07-26T08:37:53Z") AnnotationAssertion(Annotation( "GOC:obol") "regulation of PTH secretion") AnnotationAssertion(Annotation( "GOC:obol") "regulation of parathormone secretion") @@ -110944,7 +107976,6 @@ SubClassOf( (negative regulation of parathyroid hormone secretion) AnnotationAssertion(Annotation( "GOC:obol") "Any process that stops, prevents or reduces the frequency, rate or extent of parathyroid hormone secretion.") -AnnotationAssertion( "bf") AnnotationAssertion( "2011-07-26T08:37:57Z") AnnotationAssertion(Annotation( "GOC:obol") "negative regulation of PTH secretion") AnnotationAssertion(Annotation( "GOC:obol") "negative regulation of parathormone secretion") @@ -110960,7 +107991,6 @@ SubClassOf( (positive regulation of parathyroid hormone secretion) AnnotationAssertion(Annotation( "GOC:obol") "Any process that activates or increases the frequency, rate or extent of parathyroid hormone secretion.") -AnnotationAssertion( "bf") AnnotationAssertion( "2011-07-26T08:38:00Z") AnnotationAssertion(Annotation( "GOC:obol") "positive regulation of PTH secretion") AnnotationAssertion(Annotation( "GOC:obol") "positive regulation of parathormone secretion") @@ -110976,7 +108006,6 @@ SubClassOf( (regulation of steroid hormone secretion) AnnotationAssertion(Annotation( "GOC:sl") "Any process that modulates the frequency, rate or extent of steroid hormone secretion.") -AnnotationAssertion( "bf") AnnotationAssertion( "2011-07-26T08:38:46Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:2000831") @@ -110989,7 +108018,6 @@ SubClassOf( (negative regulation of steroid hormone secretion) AnnotationAssertion(Annotation( "GOC:sl") "Any process that stops, prevents or reduces the frequency, rate or extent of steroid hormone secretion.") -AnnotationAssertion( "bf") AnnotationAssertion( "2011-07-26T08:38:50Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:2000832") @@ -111003,7 +108031,6 @@ SubClassOf( (positive regulation of steroid hormone secretion) AnnotationAssertion(Annotation( "GOC:sl") "Any process that activates or increases the frequency, rate or extent of steroid hormone secretion.") -AnnotationAssertion( "bf") AnnotationAssertion( "2011-07-26T08:38:51Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:2000833") @@ -111017,7 +108044,6 @@ SubClassOf( (regulation of androgen secretion) AnnotationAssertion(Annotation( "GOC:sl") "Any process that modulates the frequency, rate or extent of androgen secretion.") -AnnotationAssertion( "bf") AnnotationAssertion( "2011-07-26T08:39:45Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:2000834") @@ -111027,7 +108053,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of androgen secretion) AnnotationAssertion(Annotation( "GOC:sl") "Any process that stops, prevents or reduces the frequency, rate or extent of androgen secretion.") -AnnotationAssertion( "bf") AnnotationAssertion( "2011-07-26T08:39:48Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:2000835") @@ -111037,7 +108062,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of androgen secretion) AnnotationAssertion(Annotation( "GOC:sl") "Any process that activates or increases the frequency, rate or extent of androgen secretion.") -AnnotationAssertion( "bf") AnnotationAssertion( "2011-07-26T08:39:51Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:2000836") @@ -111047,7 +108071,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of testosterone secretion) AnnotationAssertion(Annotation( "GOC:sl") "Any process that modulates the frequency, rate or extent of testosterone secretion.") -AnnotationAssertion( "bf") AnnotationAssertion( "2011-07-26T08:42:29Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:2000843") @@ -111057,7 +108080,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of testosterone secretion) AnnotationAssertion(Annotation( "GOC:sl") "Any process that stops, prevents or reduces the frequency, rate or extent of testosterone secretion.") -AnnotationAssertion( "bf") AnnotationAssertion( "2011-07-26T08:42:33Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:2000844") @@ -111067,7 +108089,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of testosterone secretion) AnnotationAssertion(Annotation( "GOC:sl") "Any process that activates or increases the frequency, rate or extent of testosterone secretion.") -AnnotationAssertion( "bf") AnnotationAssertion( "2011-07-26T08:42:36Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:2000845") @@ -111077,7 +108098,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of corticosteroid hormone secretion) AnnotationAssertion(Annotation( "GOC:sl") "Any process that modulates the frequency, rate or extent of corticosteroid hormone secretion.") -AnnotationAssertion( "bf") AnnotationAssertion( "2011-07-26T08:43:38Z") AnnotationAssertion( "biological_process") AnnotationAssertion(Annotation( "GOC:obol") "regulation of corticosteroid secretion") @@ -111089,7 +108109,6 @@ SubClassOf( (negative regulation of corticosteroid hormone secretion) AnnotationAssertion(Annotation( "GOC:sl") "Any process that stops, prevents or reduces the frequency, rate or extent of corticosteroid hormone secretion.") -AnnotationAssertion( "bf") AnnotationAssertion( "2011-07-26T08:43:42Z") AnnotationAssertion( "biological_process") AnnotationAssertion(Annotation( "GOC:obol") "negative regulation of corticosteroid secretion") @@ -111102,7 +108121,6 @@ SubClassOf( (positive regulation of corticosteroid hormone secretion) AnnotationAssertion(Annotation( "GOC:sl") "Any process that activates or increases the frequency, rate or extent of corticosteroid hormone secretion.") -AnnotationAssertion( "bf") AnnotationAssertion( "2011-07-26T08:43:45Z") AnnotationAssertion( "biological_process") AnnotationAssertion(Annotation( "GOC:obol") "positive regulation of corticosteroid secretion") @@ -111115,7 +108133,6 @@ SubClassOf( (regulation of glucocorticoid secretion) AnnotationAssertion(Annotation( "GOC:sl") "Any process that modulates the frequency, rate or extent of glucocorticoid secretion.") -AnnotationAssertion( "bf") AnnotationAssertion( "2011-07-26T08:44:43Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:2000849") @@ -111125,7 +108142,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of glucocorticoid secretion) AnnotationAssertion(Annotation( "GOC:sl") "Any process that stops, prevents or reduces the frequency, rate or extent of glucocorticoid secretion.") -AnnotationAssertion( "bf") AnnotationAssertion( "2011-07-26T08:44:48Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:2000850") @@ -111135,7 +108151,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of glucocorticoid secretion) AnnotationAssertion(Annotation( "GOC:sl") "Any process that activates or increases the frequency, rate or extent of glucocorticoid secretion.") -AnnotationAssertion( "bf") AnnotationAssertion( "2011-07-26T08:44:51Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:2000851") @@ -111145,7 +108160,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of mineralocorticoid secretion) AnnotationAssertion(Annotation( "GOC:sl") "Any process that modulates the frequency, rate or extent of mineralocorticoid secretion.") -AnnotationAssertion( "bf") AnnotationAssertion( "2011-07-26T08:46:38Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:2000855") @@ -111156,7 +108170,6 @@ SubClassOf( (negative regulation of mineralocorticoid secretion) AnnotationAssertion(Annotation( "GOC:sl") "Any process that stops, prevents or reduces the frequency, rate or extent of mineralocorticoid secretion.") -AnnotationAssertion( "bf") AnnotationAssertion( "2011-07-26T08:46:42Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:2000856") @@ -111168,7 +108181,6 @@ SubClassOf( (positive regulation of mineralocorticoid secretion) AnnotationAssertion(Annotation( "GOC:sl") "Any process that activates or increases the frequency, rate or extent of mineralocorticoid secretion.") -AnnotationAssertion( "bf") AnnotationAssertion( "2011-07-26T08:46:45Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:2000857") @@ -111180,7 +108192,6 @@ SubClassOf( (regulation of aldosterone secretion) AnnotationAssertion(Annotation( "GOC:sl") "Any process that modulates the frequency, rate or extent of aldosterone secretion.") -AnnotationAssertion( "bf") AnnotationAssertion( "2011-07-26T08:47:27Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:2000858") @@ -111191,7 +108202,6 @@ SubClassOf( (negative regulation of aldosterone secretion) AnnotationAssertion(Annotation( "GOC:sl") "Any process that stops, prevents or reduces the frequency, rate or extent of aldosterone secretion.") -AnnotationAssertion( "bf") AnnotationAssertion( "2011-07-26T08:47:31Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:2000859") @@ -111203,7 +108213,6 @@ SubClassOf( (positive regulation of aldosterone secretion) AnnotationAssertion(Annotation( "GOC:sl") "Any process that activates or increases the frequency, rate or extent of aldosterone secretion.") -AnnotationAssertion( "bf") AnnotationAssertion( "2011-07-26T08:47:34Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:2000860") @@ -111215,7 +108224,6 @@ SubClassOf( (regulation of estradiol secretion) AnnotationAssertion(Annotation( "GOC:sl") "Any process that modulates the frequency, rate or extent of estradiol secretion.") -AnnotationAssertion( "bf") AnnotationAssertion( "2011-07-26T08:49:13Z") AnnotationAssertion(Annotation( "GOC:obol") "regulation of oestradiol secretion") AnnotationAssertion( "biological_process") @@ -111226,7 +108234,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of estradiol secretion) AnnotationAssertion(Annotation( "GOC:sl") "Any process that stops, prevents or reduces the frequency, rate or extent of estradiol secretion.") -AnnotationAssertion( "bf") AnnotationAssertion( "2011-07-26T08:49:17Z") AnnotationAssertion(Annotation( "GOC:obol") "negative regulation of oestradiol secretion") AnnotationAssertion( "biological_process") @@ -111237,7 +108244,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of estradiol secretion) AnnotationAssertion(Annotation( "GOC:sl") "Any process that activates or increases the frequency, rate or extent of estradiol secretion.") -AnnotationAssertion( "bf") AnnotationAssertion( "2011-07-26T08:49:20Z") AnnotationAssertion(Annotation( "GOC:obol") "positive regulation of oestradiol secretion") AnnotationAssertion( "biological_process") @@ -111248,7 +108254,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of progesterone secretion) AnnotationAssertion(Annotation( "GOC:sl") "Any process that modulates the frequency, rate or extent of progesterone secretion.") -AnnotationAssertion( "bf") AnnotationAssertion( "2011-07-26T08:51:14Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:2000870") @@ -111260,7 +108265,6 @@ SubClassOf( (negative regulation of progesterone secretion) AnnotationAssertion(Annotation( "GOC:sl") "Any process that stops, prevents or reduces the frequency, rate or extent of progesterone secretion.") -AnnotationAssertion( "bf") AnnotationAssertion( "2011-07-26T08:51:19Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:2000871") @@ -111274,7 +108278,6 @@ SubClassOf( (positive regulation of progesterone secretion) AnnotationAssertion(Annotation( "GOC:sl") "Any process that activates or increases the frequency, rate or extent of progesterone secretion.") -AnnotationAssertion( "bf") AnnotationAssertion( "2011-07-26T08:51:22Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:2000872") @@ -111288,7 +108291,6 @@ SubClassOf( (regulation of pro-B cell differentiation) AnnotationAssertion(Annotation( "GOC:obol") "Any process that modulates the frequency, rate or extent of pro-B cell differentiation.") -AnnotationAssertion( "yaf") AnnotationAssertion( "2011-08-02T03:05:45Z") AnnotationAssertion(Annotation( "GOC:obol") "regulation of pro-B lymphocyte differentiation") AnnotationAssertion( "biological_process") @@ -111300,7 +108302,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of pro-B cell differentiation) AnnotationAssertion(Annotation( "GOC:obol") "Any process that stops, prevents or reduces the frequency, rate or extent of pro-B cell differentiation.") -AnnotationAssertion( "yaf") AnnotationAssertion( "2011-08-02T03:05:50Z") AnnotationAssertion(Annotation( "GOC:obol") "negative regulation of pro-B lymphocyte differentiation") AnnotationAssertion( "biological_process") @@ -111312,7 +108313,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of pro-B cell differentiation) AnnotationAssertion(Annotation( "GOC:obol") "Any process that activates or increases the frequency, rate or extent of pro-B cell differentiation.") -AnnotationAssertion( "yaf") AnnotationAssertion( "2011-08-02T03:05:53Z") AnnotationAssertion(Annotation( "GOC:obol") "positive regulation of pro-B lymphocyte differentiation") AnnotationAssertion( "biological_process") @@ -111324,7 +108324,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of forebrain neuron differentiation) AnnotationAssertion(Annotation( "GOC:obol") "Any process that modulates the frequency, rate or extent of forebrain neuron differentiation.") -AnnotationAssertion( "yaf") AnnotationAssertion( "2011-08-03T12:09:12Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:2000977") @@ -111334,7 +108333,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of forebrain neuron differentiation) AnnotationAssertion(Annotation( "GOC:obol") "Any process that stops, prevents or reduces the frequency, rate or extent of forebrain neuron differentiation.") -AnnotationAssertion( "yaf") AnnotationAssertion( "2011-08-03T12:09:16Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:2000978") @@ -111344,7 +108342,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of forebrain neuron differentiation) AnnotationAssertion(Annotation( "GOC:obol") "Any process that activates or increases the frequency, rate or extent of forebrain neuron differentiation.") -AnnotationAssertion( "yaf") AnnotationAssertion( "2011-08-03T12:09:19Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:2000979") @@ -111354,7 +108351,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of inner ear receptor cell differentiation) AnnotationAssertion(Annotation( "GOC:obol") "Any process that modulates the frequency, rate or extent of inner ear receptor cell differentiation.") -AnnotationAssertion( "yaf") AnnotationAssertion( "2011-08-03T02:38:43Z") AnnotationAssertion(Annotation( "GOC:obol") "regulation of inner ear hair cell differentiation") AnnotationAssertion( "biological_process") @@ -111365,7 +108361,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of inner ear receptor cell differentiation) AnnotationAssertion(Annotation( "GOC:obol") "Any process that stops, prevents or reduces the frequency, rate or extent of inner ear receptor cell differentiation.") -AnnotationAssertion( "yaf") AnnotationAssertion( "2011-08-03T02:38:47Z") AnnotationAssertion(Annotation( "GOC:obol") "negative regulation of inner ear hair cell differentiation") AnnotationAssertion( "biological_process") @@ -111376,7 +108371,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of inner ear receptor cell differentiation) AnnotationAssertion(Annotation( "GOC:obol") "Any process that activates or increases the frequency, rate or extent of inner ear receptor cell differentiation.") -AnnotationAssertion( "yaf") AnnotationAssertion( "2011-08-03T02:38:51Z") AnnotationAssertion(Annotation( "GOC:obol") "positive regulation of inner ear hair cell differentiation") AnnotationAssertion( "biological_process") @@ -111387,7 +108381,6 @@ EquivalentClasses( ObjectIntersection # Class: (mesenchymal cell differentiation involved in renal system development) AnnotationAssertion(Annotation( "GOC:mtg_kidney_jan10") Annotation( "GOC:obol") Annotation( "GOC:yaf") "The process in which relatively unspecialized cells acquire specialized structural and/or functional features that characterize the mesenchymal cells of the renal system as it progresses from its formation to the mature state.") -AnnotationAssertion( "yaf") AnnotationAssertion( "2011-08-09T04:05:14Z") AnnotationAssertion( "biological_process") AnnotationAssertion(Annotation( "GOC:obol") "mesenchymal cell differentiation involved in urinary system development") @@ -111399,7 +108392,6 @@ EquivalentClasses( ObjectIntersection # Class: (epithelial cell proliferation involved in renal tubule morphogenesis) AnnotationAssertion(Annotation( "GOC:obol") "Any epithelial cell proliferation that is involved in renal tubule morphogenesis.") -AnnotationAssertion( "yaf") AnnotationAssertion( "2011-08-12T11:37:29Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:2001013") @@ -111409,7 +108401,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of skeletal muscle cell differentiation) AnnotationAssertion(Annotation( "GOC:obol") "Any process that modulates the frequency, rate or extent of skeletal muscle cell differentiation.") -AnnotationAssertion( "yaf") AnnotationAssertion( "2011-08-11T08:54:37Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:2001014") @@ -111419,7 +108410,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of skeletal muscle cell differentiation) AnnotationAssertion(Annotation( "GOC:obol") "Any process that stops, prevents or reduces the frequency, rate or extent of skeletal muscle cell differentiation.") -AnnotationAssertion( "yaf") AnnotationAssertion( "2011-08-11T08:54:41Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:2001015") @@ -111429,7 +108419,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of skeletal muscle cell differentiation) AnnotationAssertion(Annotation( "GOC:obol") "Any process that activates or increases the frequency, rate or extent of skeletal muscle cell differentiation.") -AnnotationAssertion( "yaf") AnnotationAssertion( "2011-08-11T08:54:44Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:2001016") @@ -111439,7 +108428,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of retrograde axon cargo transport) AnnotationAssertion(Annotation( "GOC:obol") "Any process that modulates the frequency, rate or extent of retrograde axon cargo transport.") -AnnotationAssertion( "kmv") AnnotationAssertion( "2011-08-11T09:44:42Z") AnnotationAssertion(Annotation( "GOC:obol") "regulation of retrograde axonal transport") AnnotationAssertion( "biological_process") @@ -111450,7 +108438,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of retrograde axon cargo transport) AnnotationAssertion(Annotation( "GOC:obol") "Any process that stops, prevents or reduces the frequency, rate or extent of retrograde axon cargo transport.") -AnnotationAssertion( "kmv") AnnotationAssertion( "2011-08-11T09:44:46Z") AnnotationAssertion(Annotation( "GOC:obol") "negative regulation of retrograde axonal transport") AnnotationAssertion( "biological_process") @@ -111461,7 +108448,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of retrograde axon cargo transport) AnnotationAssertion(Annotation( "GOC:obol") "Any process that activates or increases the frequency, rate or extent of retrograde axon cargo transport.") -AnnotationAssertion( "kmv") AnnotationAssertion( "2011-08-11T09:44:49Z") AnnotationAssertion(Annotation( "GOC:obol") "positive regulation of retrograde axonal transport") AnnotationAssertion( "biological_process") @@ -111472,7 +108458,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of endothelial cell chemotaxis) AnnotationAssertion(Annotation( "GOC:BHF") "Any process that modulates the frequency, rate or extent of endothelial cell chemotaxis.") -AnnotationAssertion( "rl") AnnotationAssertion( "2011-08-22T01:07:26Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:2001026") @@ -111482,7 +108467,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of endothelial cell chemotaxis) AnnotationAssertion(Annotation( "GOC:BHF") "Any process that stops, prevents or reduces the frequency, rate or extent of endothelial cell chemotaxis.") -AnnotationAssertion( "rl") AnnotationAssertion( "2011-08-22T01:07:31Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:2001027") @@ -111492,7 +108476,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of endothelial cell chemotaxis) AnnotationAssertion(Annotation( "GOC:BHF") "Any process that activates or increases the frequency, rate or extent of endothelial cell chemotaxis.") -AnnotationAssertion( "rl") AnnotationAssertion( "2011-08-22T01:07:34Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:2001028") @@ -111502,7 +108485,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of tongue muscle cell differentiation) AnnotationAssertion(Annotation( "GOC:obol") "Any process that modulates the frequency, rate or extent of tongue muscle cell differentiation.") -AnnotationAssertion( "yaf") AnnotationAssertion( "2011-08-24T11:10:16Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:2001035") @@ -111512,7 +108494,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of tongue muscle cell differentiation) AnnotationAssertion(Annotation( "GOC:obol") "Any process that stops, prevents or reduces the frequency, rate or extent of tongue muscle cell differentiation.") -AnnotationAssertion( "yaf") AnnotationAssertion( "2011-08-24T11:10:20Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:2001036") @@ -111522,7 +108503,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of tongue muscle cell differentiation) AnnotationAssertion(Annotation( "GOC:obol") "Any process that activates or increases the frequency, rate or extent of tongue muscle cell differentiation.") -AnnotationAssertion( "yaf") AnnotationAssertion( "2011-08-24T11:10:22Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:2001037") @@ -111532,7 +108512,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of tendon cell differentiation) AnnotationAssertion(Annotation( "GOC:obol") "Any process that modulates the frequency, rate or extent of tendon cell differentiation.") -AnnotationAssertion( "yaf") AnnotationAssertion( "2011-09-01T09:20:32Z") AnnotationAssertion(Annotation( "GOC:obol") "regulation of muscle attachment cell differentiation") AnnotationAssertion( "biological_process") @@ -111544,7 +108523,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of tendon cell differentiation) AnnotationAssertion(Annotation( "GOC:obol") "Any process that stops, prevents or reduces the frequency, rate or extent of tendon cell differentiation.") -AnnotationAssertion( "yaf") AnnotationAssertion( "2011-09-01T09:20:38Z") AnnotationAssertion(Annotation( "GOC:obol") "negative regulation of muscle attachment cell differentiation") AnnotationAssertion( "biological_process") @@ -111556,7 +108534,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of tendon cell differentiation) AnnotationAssertion(Annotation( "GOC:obol") "Any process that activates or increases the frequency, rate or extent of tendon cell differentiation.") -AnnotationAssertion( "yaf") AnnotationAssertion( "2011-09-01T09:20:42Z") AnnotationAssertion(Annotation( "GOC:obol") "positive regulation of muscle attachment cell differentiation") AnnotationAssertion( "biological_process") @@ -111568,7 +108545,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of mesenchymal cell apoptotic process) AnnotationAssertion(Annotation( "GOC:mtg_apoptosis") Annotation( "GOC:obol") "Any process that modulates the frequency, rate or extent of mesenchymal cell apoptotic process.") -AnnotationAssertion( "yaf") AnnotationAssertion( "2011-09-08T02:49:59Z") AnnotationAssertion( "regulation of mesenchymal cell apoptosis") AnnotationAssertion( "biological_process") @@ -111579,7 +108555,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of mesenchymal cell apoptotic process) AnnotationAssertion(Annotation( "GOC:mtg_apoptosis") Annotation( "GOC:obol") "Any process that stops, prevents or reduces the frequency, rate or extent of mesenchymal cell apoptotic process.") -AnnotationAssertion( "yaf") AnnotationAssertion( "2011-09-08T02:50:05Z") AnnotationAssertion( "negative regulation of mesenchymal cell apoptosis") AnnotationAssertion( "biological_process") @@ -111590,7 +108565,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of mesenchymal cell apoptotic process) AnnotationAssertion(Annotation( "GOC:mtg_apoptosis") Annotation( "GOC:obol") "Any process that activates or increases the frequency, rate or extent of mesenchymal cell apoptotic process.") -AnnotationAssertion( "yaf") AnnotationAssertion( "2011-09-08T02:50:09Z") AnnotationAssertion( "positive regulation of mesenchymal cell apoptosis") AnnotationAssertion( "biological_process") @@ -111601,7 +108575,6 @@ EquivalentClasses( ObjectIntersection # Class: (glycogen binding) AnnotationAssertion(Annotation( "GOC:mengo_curators") "Binding to glycogen.") -AnnotationAssertion( "jl") AnnotationAssertion( "2011-09-14T12:01:06Z") AnnotationAssertion( "molecular_function") AnnotationAssertion(Annotation( "GOC:obol") "animal starch binding") @@ -111613,7 +108586,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of RNA biosynthetic process) AnnotationAssertion(Annotation( "GOC:dph") "Any process that modulates the frequency, rate or extent of RNA biosynthetic process.") -AnnotationAssertion( "dph") AnnotationAssertion( "2011-10-17T11:36:25Z") AnnotationAssertion(Annotation( "GOC:obol") "regulation of RNA anabolism") AnnotationAssertion(Annotation( "GOC:obol") "regulation of RNA biosynthesis") @@ -111627,7 +108599,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of renal water transport) AnnotationAssertion(Annotation( "GOC:obol") "Any process that modulates the frequency, rate or extent of renal water transport.") -AnnotationAssertion( "yaf") AnnotationAssertion( "2011-10-24T11:37:51Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:2001151") @@ -111640,7 +108611,6 @@ SubClassOf( (negative regulation of renal water transport) AnnotationAssertion(Annotation( "GOC:obol") "Any process that stops, prevents or reduces the frequency, rate or extent of renal water transport.") -AnnotationAssertion( "yaf") AnnotationAssertion( "2011-10-24T11:37:57Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:2001152") @@ -111653,7 +108623,6 @@ SubClassOf( (positive regulation of renal water transport) AnnotationAssertion(Annotation( "GOC:obol") "Any process that activates or increases the frequency, rate or extent of renal water transport.") -AnnotationAssertion( "yaf") AnnotationAssertion( "2011-10-24T11:38:01Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:2001153") @@ -111666,7 +108635,6 @@ SubClassOf( (regulation of ATP biosynthetic process) AnnotationAssertion(Annotation( "GOC:obol") "Any process that modulates the frequency, rate or extent of ATP biosynthetic process.") -AnnotationAssertion( "kmv") AnnotationAssertion( "2011-10-26T03:18:03Z") AnnotationAssertion(Annotation( "GOC:obol") "regulation of ATP anabolism") AnnotationAssertion(Annotation( "GOC:obol") "regulation of ATP biosynthesis") @@ -111681,7 +108649,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of ATP biosynthetic process) AnnotationAssertion(Annotation( "GOC:obol") "Any process that stops, prevents or reduces the frequency, rate or extent of ATP biosynthetic process.") -AnnotationAssertion( "kmv") AnnotationAssertion( "2011-10-26T03:18:13Z") AnnotationAssertion(Annotation( "GOC:obol") "negative regulation of ATP anabolism") AnnotationAssertion(Annotation( "GOC:obol") "negative regulation of ATP biosynthesis") @@ -111696,7 +108663,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of ATP biosynthetic process) AnnotationAssertion(Annotation( "GOC:obol") "Any process that activates or increases the frequency, rate or extent of ATP biosynthetic process.") -AnnotationAssertion( "kmv") AnnotationAssertion( "2011-10-26T03:18:26Z") AnnotationAssertion(Annotation( "GOC:obol") "positive regulation of ATP anabolism") AnnotationAssertion(Annotation( "GOC:obol") "positive regulation of ATP biosynthesis") @@ -111711,7 +108677,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of CD8-positive, alpha-beta T cell activation) AnnotationAssertion(Annotation( "GOC:obol") "Any process that modulates the frequency, rate or extent of CD8-positive, alpha-beta T cell activation.") -AnnotationAssertion( "yaf") AnnotationAssertion( "2011-11-03T01:16:51Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:2001185") @@ -111721,7 +108686,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of CD8-positive, alpha-beta T cell activation) AnnotationAssertion(Annotation( "GOC:obol") "Any process that stops, prevents or reduces the frequency, rate or extent of CD8-positive, alpha-beta T cell activation.") -AnnotationAssertion( "yaf") AnnotationAssertion( "2011-11-03T01:16:57Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:2001186") @@ -111731,7 +108695,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of CD8-positive, alpha-beta T cell activation) AnnotationAssertion(Annotation( "GOC:obol") "Any process that activates or increases the frequency, rate or extent of CD8-positive, alpha-beta T cell activation.") -AnnotationAssertion( "yaf") AnnotationAssertion( "2011-11-03T01:17:02Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:2001187") @@ -111741,7 +108704,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of gamma-delta T cell activation involved in immune response) AnnotationAssertion(Annotation( "GOC:obol") "Any process that modulates the frequency, rate or extent of gamma-delta T cell activation involved in immune response.") -AnnotationAssertion( "yaf") AnnotationAssertion( "2011-11-03T04:28:38Z") AnnotationAssertion( "biological_process") AnnotationAssertion(Annotation( "GOC:obol") "regulation of gamma-delta T cell activation during immune response") @@ -111756,7 +108718,6 @@ SubClassOf( ObjectSomeValuesFrom( (negative regulation of gamma-delta T cell activation involved in immune response) AnnotationAssertion(Annotation( "GOC:obol") "Any process that stops, prevents or reduces the frequency, rate or extent of gamma-delta T cell activation involved in immune response.") -AnnotationAssertion( "yaf") AnnotationAssertion( "2011-11-03T04:28:44Z") AnnotationAssertion( "biological_process") AnnotationAssertion(Annotation( "GOC:obol") "negative regulation of gamma-delta T cell activation during immune response") @@ -111771,7 +108732,6 @@ SubClassOf( ObjectSomeValuesFrom( (positive regulation of gamma-delta T cell activation involved in immune response) AnnotationAssertion(Annotation( "GOC:obol") "Any process that activates or increases the frequency, rate or extent of gamma-delta T cell activation involved in immune response.") -AnnotationAssertion( "yaf") AnnotationAssertion( "2011-11-03T04:28:48Z") AnnotationAssertion( "biological_process") AnnotationAssertion(Annotation( "GOC:obol") "positive regulation of gamma-delta T cell activation during immune response") @@ -111786,7 +108746,6 @@ SubClassOf( ObjectSomeValuesFrom( (regulation of dendritic cell differentiation) AnnotationAssertion(Annotation( "GOC:obol") "Any process that modulates the frequency, rate or extent of dendritic cell differentiation.") -AnnotationAssertion( "yaf") AnnotationAssertion( "2011-11-04T02:01:27Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:2001198") @@ -111796,7 +108755,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of dendritic cell differentiation) AnnotationAssertion(Annotation( "GOC:obol") "Any process that stops, prevents or reduces the frequency, rate or extent of dendritic cell differentiation.") -AnnotationAssertion( "yaf") AnnotationAssertion( "2011-11-04T02:01:33Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:2001199") @@ -111806,7 +108764,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of dendritic cell differentiation) AnnotationAssertion(Annotation( "GOC:obol") "Any process that activates or increases the frequency, rate or extent of dendritic cell differentiation.") -AnnotationAssertion( "yaf") AnnotationAssertion( "2011-11-04T02:01:36Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:2001200") @@ -111816,7 +108773,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of osteoclast development) AnnotationAssertion(Annotation( "GOC:obol") "Any process that modulates the frequency, rate or extent of osteoclast development.") -AnnotationAssertion( "yaf") AnnotationAssertion( "2011-11-10T10:58:59Z") AnnotationAssertion(Annotation( "GOC:obol") "regulation of osteoclast cell development") AnnotationAssertion( "biological_process") @@ -111827,7 +108783,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of osteoclast development) AnnotationAssertion(Annotation( "GOC:obol") "Any process that stops, prevents or reduces the frequency, rate or extent of osteoclast development.") -AnnotationAssertion( "yaf") AnnotationAssertion( "2011-11-10T10:59:06Z") AnnotationAssertion(Annotation( "GOC:obol") "negative regulation of osteoclast cell development") AnnotationAssertion( "biological_process") @@ -111839,7 +108794,6 @@ SubClassOf( ObjectSomeValuesFrom( (positive regulation of osteoclast development) AnnotationAssertion(Annotation( "GOC:obol") "Any process that activates or increases the frequency, rate or extent of osteoclast development.") -AnnotationAssertion( "yaf") AnnotationAssertion( "2011-11-10T10:59:12Z") AnnotationAssertion(Annotation( "GOC:obol") "positive regulation of osteoclast cell development") AnnotationAssertion( "biological_process") @@ -111851,7 +108805,6 @@ SubClassOf( ObjectSomeValuesFrom( (regulation of vasculogenesis) AnnotationAssertion(Annotation( "GOC:obol") "Any process that modulates the frequency, rate or extent of vasculogenesis.") -AnnotationAssertion( "yaf") AnnotationAssertion( "2011-11-15T01:22:31Z") AnnotationAssertion(Annotation( "GOC:obol") "regulation of vascular morphogenesis") AnnotationAssertion( "biological_process") @@ -111862,7 +108815,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of vasculogenesis) AnnotationAssertion(Annotation( "GOC:obol") "Any process that stops, prevents or reduces the frequency, rate or extent of vasculogenesis.") -AnnotationAssertion( "yaf") AnnotationAssertion( "2011-11-15T01:22:36Z") AnnotationAssertion(Annotation( "GOC:obol") "negative regulation of vascular morphogenesis") AnnotationAssertion( "biological_process") @@ -111873,7 +108825,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of vasculogenesis) AnnotationAssertion(Annotation( "GOC:obol") "Any process that activates or increases the frequency, rate or extent of vasculogenesis.") -AnnotationAssertion( "yaf") AnnotationAssertion( "2011-11-15T01:22:39Z") AnnotationAssertion(Annotation( "GOC:obol") "positive regulation of vascular morphogenesis") AnnotationAssertion( "biological_process") @@ -111884,7 +108835,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of neuron migration) AnnotationAssertion(Annotation( "GOC:obol") "Any process that modulates the frequency, rate or extent of neuron migration.") -AnnotationAssertion( "kmv") AnnotationAssertion( "2011-11-17T10:01:38Z") AnnotationAssertion(Annotation( "GOC:obol") "regulation of neuron chemotaxis") AnnotationAssertion(Annotation( "GOC:obol") "regulation of neuronal migration") @@ -111899,7 +108849,6 @@ SubClassOf( ObjectAllValuesFrom( (negative regulation of neuron migration) AnnotationAssertion(Annotation( "GOC:obol") "Any process that stops, prevents or reduces the frequency, rate or extent of neuron migration.") -AnnotationAssertion( "kmv") AnnotationAssertion( "2011-11-17T10:01:45Z") AnnotationAssertion(Annotation( "GOC:obol") "negative regulation of neuron chemotaxis") AnnotationAssertion(Annotation( "GOC:obol") "negative regulation of neuronal migration") @@ -111912,7 +108861,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of neuron migration) AnnotationAssertion(Annotation( "GOC:obol") "Any process that activates or increases the frequency, rate or extent of neuron migration.") -AnnotationAssertion( "kmv") AnnotationAssertion( "2011-11-17T10:01:49Z") AnnotationAssertion(Annotation( "GOC:obol") "positive regulation of neuron chemotaxis") AnnotationAssertion(Annotation( "GOC:obol") "positive regulation of neuronal migration") @@ -111925,7 +108873,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of apoptotic signaling pathway) AnnotationAssertion(Annotation( "GOC:mtg_apoptosis") "Any process that modulates the frequency, rate or extent of apoptotic signaling pathway.") -AnnotationAssertion( "pr") AnnotationAssertion( "2011-11-24T01:20:49Z") AnnotationAssertion(Annotation( "GOC:mah") "regulation of apoptotic signalling pathway") AnnotationAssertion( "biological_process") @@ -111937,7 +108884,6 @@ SubClassOf( ObjectSomeValuesFrom( (negative regulation of apoptotic signaling pathway) AnnotationAssertion(Annotation( "GOC:mtg_apoptosis") "Any process that stops, prevents or reduces the frequency, rate or extent of apoptotic signaling pathway.") -AnnotationAssertion( "pr") AnnotationAssertion( "2011-11-24T01:20:54Z") AnnotationAssertion(Annotation( "GOC:mah") "negative regulation of apoptotic signalling pathway") AnnotationAssertion( "biological_process") @@ -111950,7 +108896,6 @@ SubClassOf( ObjectSomeValuesFrom( "GOC:mtg_apoptosis") "Any process that activates or increases the frequency, rate or extent of apoptotic signaling pathway.") AnnotationAssertion( ) -AnnotationAssertion( "pr") AnnotationAssertion( "2011-11-24T01:20:58Z") AnnotationAssertion(Annotation( "GOC:mah") "positive regulation of apoptotic signalling pathway") AnnotationAssertion( "biological_process") @@ -111965,7 +108910,6 @@ DisjointClasses( ObjectSomeValuesFrom # Class: (regulation of extrinsic apoptotic signaling pathway) AnnotationAssertion(Annotation( "GOC:mtg_apoptosis") "Any process that modulates the frequency, rate or extent of extrinsic apoptotic signaling pathway.") -AnnotationAssertion( "pr") AnnotationAssertion( "2011-11-24T01:30:05Z") AnnotationAssertion(Annotation( "GOC:mah") "regulation of extrinsic apoptotic signalling pathway") AnnotationAssertion( "regulation of extrinsic apoptosis") @@ -111977,7 +108921,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of extrinsic apoptotic signaling pathway) AnnotationAssertion(Annotation( "GOC:mtg_apoptosis") "Any process that stops, prevents or reduces the frequency, rate or extent of extrinsic apoptotic signaling pathway.") -AnnotationAssertion( "pr") AnnotationAssertion( "2011-11-24T01:30:11Z") AnnotationAssertion(Annotation( "GOC:mah") "negative regulation of extrinsic apoptotic signalling pathway") AnnotationAssertion( "negative regulation of extrinsic apoptosis") @@ -111989,7 +108932,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of extrinsic apoptotic signaling pathway) AnnotationAssertion(Annotation( "GOC:mtg_apoptosis") "Any process that activates or increases the frequency, rate or extent of extrinsic apoptotic signaling pathway.") -AnnotationAssertion( "pr") AnnotationAssertion( "2011-11-24T01:30:16Z") AnnotationAssertion(Annotation( "GOC:mah") "positive regulation of extrinsic apoptotic signalling pathway") AnnotationAssertion( "positive regulation of extrinsic apoptosis") @@ -112001,7 +108943,6 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of chromosome organization) AnnotationAssertion(Annotation( "GOC:obol") "Any process that stops, prevents or reduces the frequency, rate or extent of chromosome organization.") -AnnotationAssertion( "yaf") AnnotationAssertion( "2011-12-02T02:01:20Z") AnnotationAssertion(Annotation( "GOC:obol") "negative regulation of chromosome organisation") AnnotationAssertion( "biological_process") @@ -112015,7 +108956,6 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of chromosome organization) AnnotationAssertion(Annotation( "GOC:obol") "Any process that activates or increases the frequency, rate or extent of chromosome organization.") -AnnotationAssertion( "yaf") AnnotationAssertion( "2011-12-02T02:01:26Z") AnnotationAssertion(Annotation( "GOC:obol") "positive regulation of chromosome organisation") AnnotationAssertion( "biological_process") @@ -112029,7 +108969,6 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of cation channel activity) AnnotationAssertion(Annotation( "GOC:BHF") "Any process that modulates the frequency, rate or extent of cation channel activity.") -AnnotationAssertion( "vk") AnnotationAssertion( "2011-12-07T07:14:43Z") AnnotationAssertion(Annotation( "GOC:obol") "regulation of cation diffusion facilitator activity") AnnotationAssertion(Annotation( "GOC:obol") "regulation of nonselective cation channel activity") @@ -112043,7 +108982,6 @@ SubClassOf( ObjectSomeValuesFrom( (negative regulation of cation channel activity) AnnotationAssertion(Annotation( "GOC:BHF") "Any process that stops, prevents or reduces the frequency, rate or extent of cation channel activity.") -AnnotationAssertion( "vk") AnnotationAssertion( "2011-12-07T07:14:51Z") AnnotationAssertion(Annotation( "GOC:obol") "negative regulation of cation diffusion facilitator activity") AnnotationAssertion(Annotation( "GOC:obol") "negative regulation of nonselective cation channel activity") @@ -112057,7 +108995,6 @@ SubClassOf( ObjectSomeValuesFrom( (positive regulation of cation channel activity) AnnotationAssertion(Annotation( "GOC:BHF") "Any process that activates or increases the frequency, rate or extent of cation channel activity.") -AnnotationAssertion( "vk") AnnotationAssertion( "2011-12-07T07:14:57Z") AnnotationAssertion(Annotation( "GOC:obol") "positive regulation of cation diffusion facilitator activity") AnnotationAssertion(Annotation( "GOC:obol") "positive regulation of nonselective cation channel activity") @@ -115160,7 +112097,6 @@ SubClassOf( (high nuclear/cytoplasmic ratio) AnnotationAssertion(Annotation( "Wikipedia:NC_ratio&oldid=931936284") Annotation( "http://lymerick.net/blood-cells.pdf") "A quality inhering in a cell by virtue of the cell having a high nuclear/cytoplasmic ratio.") -AnnotationAssertion( "http://orcid.org/0000-0001-5208-3432") AnnotationAssertion( "high N:C ratio") AnnotationAssertion( "quality") AnnotationAssertion( "PATO:0040072") @@ -115582,7 +112518,6 @@ SubClassOf( (anatomical structure quality) AnnotationAssertion( "A quality of continuant that exist at the anatomical level of organisation and anything under it. This includes, but is not limited to, cells , tissues, and components.") -AnnotationAssertion( "http://orcid.org/0000-0001-7258-9596") AnnotationAssertion( "quality") AnnotationAssertion( "PATO:0070044") AnnotationAssertion(rdfs:label "anatomical structure quality") @@ -115591,7 +112526,6 @@ SubClassOf( (anatomical histological quality) AnnotationAssertion( "A quality inhering in an anotomical structure by virtue of its capacity to be stained by specific histological dyes.") -AnnotationAssertion( "http://orcid.org/0000-0001-7258-9596") AnnotationAssertion( "quality") AnnotationAssertion( "PATO:0070045") AnnotationAssertion(rdfs:label "anatomical histological quality") @@ -115600,7 +112534,6 @@ SubClassOf( (neutrophillic) AnnotationAssertion(Annotation( "GOC:add") "An affinity inhering in an anatomical structure by virtue of the bearer exhibiting a molecular interaction that stains and colors, pale-pink, with Wright-Giemsa stain.") -AnnotationAssertion( "http://orcid.org/0000-0001-7258-9596") AnnotationAssertion( "quality") AnnotationAssertion( "PATO:0070046") AnnotationAssertion(rdfs:label "neutrophillic") @@ -115609,7 +112542,6 @@ SubClassOf( (polychromatophilic) AnnotationAssertion(Annotation( "GOC:add") "An affinity inhering in an anatomical structure by virtue of the bearer exhibiting a molecular interaction for both basic and acid stains under specific pH conditions.") -AnnotationAssertion( "http://orcid.org/0000-0001-7258-9596") AnnotationAssertion( "quality") AnnotationAssertion( "PATO:0070047") AnnotationAssertion(rdfs:label "polychromatophilic") @@ -136010,6 +132942,43 @@ AnnotationAssertion(rdfs:label " SubClassOf(Annotation( "CARO") ) SubClassOf( ObjectSomeValuesFrom( )) +# Class: (basal lamina of epithelium) + +AnnotationAssertion(Annotation( "http://orcid.org/0000-0001-9114-8737") "Acellular anatomical structure that consists of a thin sheet of fibrous proteins that underlie and support the cells of an epithelium. It separates the cells of an epithelium from any underlying tissue.") +AnnotationAssertion( ) +AnnotationAssertion( "AAO:0010269") +AnnotationAssertion( "AEO:0000065") +AnnotationAssertion( "BILA:0000065") +AnnotationAssertion( "CARO:0000065") +AnnotationAssertion( "EHDAA2:0003065") +AnnotationAssertion( "FMA:62918") +AnnotationAssertion( "HAO:0000065") +AnnotationAssertion( "MESH:D001485") +AnnotationAssertion( "NCIT:C32186") +AnnotationAssertion( "NIF_Subcellular:sao1397492660") +AnnotationAssertion( "TAO:0001485") +AnnotationAssertion( "TGMA:0001850") +AnnotationAssertion(Annotation( "ncithesaurus:Basal_Lamina") "UMLS:C0085872") +AnnotationAssertion( "VHOG:0001592") +AnnotationAssertion( "WBbt:0005756") +AnnotationAssertion( "Wikipedia:Basal_lamina") +AnnotationAssertion( "XAO:0003163") +AnnotationAssertion( "ZFA:0001485") +AnnotationAssertion(Annotation( "FMA:62918") "basal lamina of connective tissue") +AnnotationAssertion( "uberon") +AnnotationAssertion(Annotation( "CARO:0000065") "basal lamina") +AnnotationAssertion(Annotation( "VHOG:0001592") Annotation( ) "basal laminae") +AnnotationAssertion(Annotation( "Wikipedia:Basal_lamina") Annotation( ) "lamina basalis") +AnnotationAssertion( "UBERON:0000482") +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "basal lamina of epithelium") +AnnotationAssertion( "https://upload.wikimedia.org/wikipedia/commons/6/65/Basal_lamina.jpg"^^xsd:anyURI) +SubClassOf(Annotation( "FMA") ) +SubClassOf(Annotation( "FMA") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + # Class: (epithelium) AnnotationAssertion(Annotation( "Wikipedia:Epithelium") Annotation( "http://orcid.org/0000-0001-9114-8737") "Portion of tissue, that consists of one or more layers of epithelial cells connected to each other by cell junctions and which is underlain by a basal lamina. Examples: simple squamous epithelium, glandular cuboidal epithelium, transitional epithelium, myoepithelium[CARO].") @@ -157996,7 +154965,7 @@ SubClassOf( ) SubClassOf( ) SubClassOf( ) -SubClassOf(Annotation( "some species only have a single lung") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -159177,7 +156146,7 @@ AnnotationAssertion( "limb") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) -SubClassOf(Annotation( "extends to stem tetrapods such as Eusthenopteron") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -187123,6 +184092,66 @@ SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +# Class: (respiratory system basal lamina) + +AnnotationAssertion(Annotation( "OBOL:automatic") "A basal lamina that is part of a respiratory system [Automatically generated definition].") +AnnotationAssertion(Annotation( "MA:th") "EMAPA:37571") +AnnotationAssertion( "MA:0001816") +AnnotationAssertion(Annotation( "OBOL:automatic") "apparatus respiratorius basal lamina") +AnnotationAssertion(Annotation( "OBOL:automatic") "apparatus respiratorius basal lamina of connective tissue") +AnnotationAssertion(Annotation( "OBOL:automatic") "basal lamina of apparatus respiratorius") +AnnotationAssertion(Annotation( "OBOL:automatic") "basal lamina of connective tissue of apparatus respiratorius") +AnnotationAssertion(Annotation( "OBOL:automatic") "basal lamina of connective tissue of respiratory system") +AnnotationAssertion(Annotation( "OBOL:automatic") "basal lamina of respiratory system") +AnnotationAssertion(Annotation( "OBOL:automatic") "respiratory system basal lamina of connective tissue") +AnnotationAssertion( "uberon") +AnnotationAssertion( "UBERON:0004798") +AnnotationAssertion(rdfs:label "respiratory system basal lamina") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (trachea basal lamina) + +AnnotationAssertion(Annotation( "OBOL:automatic") "A basal lamina that is part of a respiratory airway [Automatically generated definition].") +AnnotationAssertion(Annotation( "MA:th") "EMAPA:37553") +AnnotationAssertion( "MA:0001855") +AnnotationAssertion( "NCIT:C49303") +AnnotationAssertion(Annotation( "ncithesaurus:Trachea_Basal_Lamina") "UMLS:C1710454") +AnnotationAssertion(Annotation( "OBOL:automatic") "basal lamina of connective tissue of respiratory airway") +AnnotationAssertion( "uberon") +AnnotationAssertion( "UBERON:0004799") +AnnotationAssertion(rdfs:label "trachea basal lamina") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (bronchus basal lamina) + +AnnotationAssertion(Annotation( "OBOL:automatic") "A basal lamina that is part of a bronchus [Automatically generated definition].") +AnnotationAssertion(Annotation( "MA:th") "EMAPA:37810") +AnnotationAssertion( "MA:0001833") +AnnotationAssertion( "NCIT:C49207") +AnnotationAssertion(Annotation( "ncithesaurus:Bronchus_Basal_Lamina") "UMLS:C1707050") +AnnotationAssertion(Annotation( "OBOL:automatic") "basal lamina of bronchi") +AnnotationAssertion(Annotation( "OBOL:automatic") "basal lamina of bronchial trunk") +AnnotationAssertion(Annotation( "OBOL:automatic") "basal lamina of bronchus") +AnnotationAssertion(Annotation( "OBOL:automatic") "basal lamina of connective tissue of bronchi") +AnnotationAssertion(Annotation( "OBOL:automatic") "basal lamina of connective tissue of bronchial trunk") +AnnotationAssertion(Annotation( "OBOL:automatic") "basal lamina of connective tissue of bronchus") +AnnotationAssertion(Annotation( "OBOL:automatic") "bronchi basal lamina") +AnnotationAssertion(Annotation( "OBOL:automatic") "bronchi basal lamina of connective tissue") +AnnotationAssertion(Annotation( "OBOL:automatic") "bronchial trunk basal lamina") +AnnotationAssertion(Annotation( "OBOL:automatic") "bronchial trunk basal lamina of connective tissue") +AnnotationAssertion(Annotation( "OBOL:automatic") "bronchus basal lamina of connective tissue") +AnnotationAssertion( "uberon") +AnnotationAssertion( "UBERON:0004800") +AnnotationAssertion(rdfs:label "bronchus basal lamina") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + # Class: (cervix epithelium) AnnotationAssertion(Annotation( "OBOL:automatic") "An epithelium that is part of a uterine cervix [Automatically generated definition].") @@ -228684,7 +225713,6 @@ SubClassOf( ObjectSomeValuesFrom( # Class: (red bone marrow of sternum) AnnotationAssertion(Annotation( "http://orcid.org/0000-0001-7655-4833") "Red bone marrow located in the sternum.") -AnnotationAssertion( "http://orcid.org/0000-0002-2825-0621") AnnotationAssertion( "sternum red bone marrow") AnnotationAssertion( "uberon") AnnotationAssertion( "UBERON:8410080") @@ -228696,7 +225724,6 @@ SubClassOf( ObjectSomeValuesFrom( # Class: (blood microvessel) AnnotationAssertion(Annotation( "Wikipedia:Microcirculation") Annotation( "http://orcid.org/0000-0002-7073-9172") "Any of the smallest blood vessels where blood circulates within organ tissues. Microvessels include terminal arterioles, metarterioles, capillaries, and venules (but exclude lymphatic capillaries). Arterioles carry oxygenated blood to the capillaries, and blood flows out of the capillaries through venules into veins.") -AnnotationAssertion( "http://orcid.org/0000-0002-2825-0621") AnnotationAssertion( "microvasculature") AnnotationAssertion( "microvessel") AnnotationAssertion( "uberon") @@ -228832,7 +225859,6 @@ SubClassOf( ObjectSomeValuesFrom( AnnotationAssertion(Annotation( "GO:0007588") "An anatomical system that eliminates waste products that arise as a result of metabolic activity.") AnnotationAssertion( ) -AnnotationAssertion( "http://orcid.org/0000-0002-6095-8718") AnnotationAssertion( "2022-05-25T18:21:29Z") AnnotationAssertion( "uberon") AnnotationAssertion( "UBERON:8450002") diff --git a/src/patterns/definitions.owl b/src/patterns/definitions.owl index 1b4b15e6e..c94c5e8de 100644 --- a/src/patterns/definitions.owl +++ b/src/patterns/definitions.owl @@ -7,8 +7,8 @@ Prefix(rdfs:=) Ontology( - -Annotation(owl:versionInfo "2024-12-16") + +Annotation(owl:versionInfo "2025-01-06") Declaration(Class()) Declaration(Class()) diff --git a/src/templates/cellxgene_subset.tsv b/src/templates/cellxgene_subset.tsv index af6b80ddb..b5e08b948 100644 --- a/src/templates/cellxgene_subset.tsv +++ b/src/templates/cellxgene_subset.tsv @@ -1,806 +1,806 @@ ID subset ID AI oboInOwl:inSubset -CL:0000604 http://purl.obolibrary.org/obo/cl#cellxgene_subset -CL:2000059 http://purl.obolibrary.org/obo/cl#cellxgene_subset -CL:0002277 http://purl.obolibrary.org/obo/cl#cellxgene_subset -CL:0001042 http://purl.obolibrary.org/obo/cl#cellxgene_subset -CL:0002570 http://purl.obolibrary.org/obo/cl#cellxgene_subset -CL:4023042 http://purl.obolibrary.org/obo/cl#cellxgene_subset -CL:0000677 http://purl.obolibrary.org/obo/cl#cellxgene_subset -CL:0000786 http://purl.obolibrary.org/obo/cl#cellxgene_subset -CL:4023056 http://purl.obolibrary.org/obo/cl#cellxgene_subset -CL:2000047 http://purl.obolibrary.org/obo/cl#cellxgene_subset -CL:0000064 http://purl.obolibrary.org/obo/cl#cellxgene_subset +CL:0000864 http://purl.obolibrary.org/obo/cl#cellxgene_subset +CL:0000525 http://purl.obolibrary.org/obo/cl#cellxgene_subset +CL:0002262 http://purl.obolibrary.org/obo/cl#cellxgene_subset +CL:0000492 http://purl.obolibrary.org/obo/cl#cellxgene_subset +CL:0000129 http://purl.obolibrary.org/obo/cl#cellxgene_subset +CL:4033034 http://purl.obolibrary.org/obo/cl#cellxgene_subset +CL:2000064 http://purl.obolibrary.org/obo/cl#cellxgene_subset +CL:0000776 http://purl.obolibrary.org/obo/cl#cellxgene_subset +CL:0000324 http://purl.obolibrary.org/obo/cl#cellxgene_subset +CL:0002504 http://purl.obolibrary.org/obo/cl#cellxgene_subset +CL:0000160 http://purl.obolibrary.org/obo/cl#cellxgene_subset +CL:0000451 http://purl.obolibrary.org/obo/cl#cellxgene_subset +CL:0002420 http://purl.obolibrary.org/obo/cl#cellxgene_subset +CL:0002586 http://purl.obolibrary.org/obo/cl#cellxgene_subset +CL:0004215 http://purl.obolibrary.org/obo/cl#cellxgene_subset +CL:0002368 http://purl.obolibrary.org/obo/cl#cellxgene_subset +CL:0000644 http://purl.obolibrary.org/obo/cl#cellxgene_subset +CL:0000513 http://purl.obolibrary.org/obo/cl#cellxgene_subset CL:0002363 http://purl.obolibrary.org/obo/cl#cellxgene_subset -CL:0002410 http://purl.obolibrary.org/obo/cl#cellxgene_subset -CL:4023013 http://purl.obolibrary.org/obo/cl#cellxgene_subset -CL:0000188 http://purl.obolibrary.org/obo/cl#cellxgene_subset -CL:0002521 http://purl.obolibrary.org/obo/cl#cellxgene_subset -CL:0002425 http://purl.obolibrary.org/obo/cl#cellxgene_subset -CL:0000700 http://purl.obolibrary.org/obo/cl#cellxgene_subset -CL:0002457 http://purl.obolibrary.org/obo/cl#cellxgene_subset -CL:0009016 http://purl.obolibrary.org/obo/cl#cellxgene_subset -CL:4023051 http://purl.obolibrary.org/obo/cl#cellxgene_subset +CL:0019019 http://purl.obolibrary.org/obo/cl#cellxgene_subset +CL:4023048 http://purl.obolibrary.org/obo/cl#cellxgene_subset +CL:0002326 http://purl.obolibrary.org/obo/cl#cellxgene_subset +CL:4023070 http://purl.obolibrary.org/obo/cl#cellxgene_subset +CL:0000666 http://purl.obolibrary.org/obo/cl#cellxgene_subset +CL:0002488 http://purl.obolibrary.org/obo/cl#cellxgene_subset +CL:0000151 http://purl.obolibrary.org/obo/cl#cellxgene_subset +CL:2000042 http://purl.obolibrary.org/obo/cl#cellxgene_subset +CL:4030018 http://purl.obolibrary.org/obo/cl#cellxgene_subset +CL:1001319 http://purl.obolibrary.org/obo/cl#cellxgene_subset +CL:0000545 http://purl.obolibrary.org/obo/cl#cellxgene_subset +CL:2000084 http://purl.obolibrary.org/obo/cl#cellxgene_subset +CL:0000679 http://purl.obolibrary.org/obo/cl#cellxgene_subset +CL:0000190 http://purl.obolibrary.org/obo/cl#cellxgene_subset +CL:0000682 http://purl.obolibrary.org/obo/cl#cellxgene_subset +CL:0000049 http://purl.obolibrary.org/obo/cl#cellxgene_subset +CL:1000494 http://purl.obolibrary.org/obo/cl#cellxgene_subset +CL:0000253 http://purl.obolibrary.org/obo/cl#cellxgene_subset +CL:0000499 http://purl.obolibrary.org/obo/cl#cellxgene_subset +CL:0000067 http://purl.obolibrary.org/obo/cl#cellxgene_subset +CL:4030028 http://purl.obolibrary.org/obo/cl#cellxgene_subset +CL:0000800 http://purl.obolibrary.org/obo/cl#cellxgene_subset +CL:0002203 http://purl.obolibrary.org/obo/cl#cellxgene_subset CL:2000030 http://purl.obolibrary.org/obo/cl#cellxgene_subset -CL:0000890 http://purl.obolibrary.org/obo/cl#cellxgene_subset -CL:0002279 http://purl.obolibrary.org/obo/cl#cellxgene_subset -CL:0002139 http://purl.obolibrary.org/obo/cl#cellxgene_subset -CL:1000510 http://purl.obolibrary.org/obo/cl#cellxgene_subset -CL:0000646 http://purl.obolibrary.org/obo/cl#cellxgene_subset -CL:0002201 http://purl.obolibrary.org/obo/cl#cellxgene_subset -CL:4033048 http://purl.obolibrary.org/obo/cl#cellxgene_subset -CL:0000928 http://purl.obolibrary.org/obo/cl#cellxgene_subset -CL:0000212 http://purl.obolibrary.org/obo/cl#cellxgene_subset -CL:0002370 http://purl.obolibrary.org/obo/cl#cellxgene_subset -CL:1000331 http://purl.obolibrary.org/obo/cl#cellxgene_subset -CL:0011011 http://purl.obolibrary.org/obo/cl#cellxgene_subset -CL:0002586 http://purl.obolibrary.org/obo/cl#cellxgene_subset -CL:0008002 http://purl.obolibrary.org/obo/cl#cellxgene_subset -CL:0000036 http://purl.obolibrary.org/obo/cl#cellxgene_subset -CL:0000023 http://purl.obolibrary.org/obo/cl#cellxgene_subset -CL:0002399 http://purl.obolibrary.org/obo/cl#cellxgene_subset -CL:0002324 http://purl.obolibrary.org/obo/cl#cellxgene_subset -CL:1000703 http://purl.obolibrary.org/obo/cl#cellxgene_subset -CL:1001602 http://purl.obolibrary.org/obo/cl#cellxgene_subset -CL:4033044 http://purl.obolibrary.org/obo/cl#cellxgene_subset -CL:0002138 http://purl.obolibrary.org/obo/cl#cellxgene_subset -CL:0000903 http://purl.obolibrary.org/obo/cl#cellxgene_subset -CL:0009012 http://purl.obolibrary.org/obo/cl#cellxgene_subset -CL:0002366 http://purl.obolibrary.org/obo/cl#cellxgene_subset +CL:0000810 http://purl.obolibrary.org/obo/cl#cellxgene_subset +CL:1000597 http://purl.obolibrary.org/obo/cl#cellxgene_subset +CL:0000809 http://purl.obolibrary.org/obo/cl#cellxgene_subset +CL:0000123 http://purl.obolibrary.org/obo/cl#cellxgene_subset +CL:1000443 http://purl.obolibrary.org/obo/cl#cellxgene_subset +CL:0002320 http://purl.obolibrary.org/obo/cl#cellxgene_subset +CL:0000510 http://purl.obolibrary.org/obo/cl#cellxgene_subset +CL:0000834 http://purl.obolibrary.org/obo/cl#cellxgene_subset 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+CL:0001082 http://purl.obolibrary.org/obo/cl#cellxgene_subset +CL:4023189 http://purl.obolibrary.org/obo/cl#cellxgene_subset +CL:0009039 http://purl.obolibrary.org/obo/cl#cellxgene_subset +CL:0003001 http://purl.obolibrary.org/obo/cl#cellxgene_subset +CL:0000893 http://purl.obolibrary.org/obo/cl#cellxgene_subset +CL:0000808 http://purl.obolibrary.org/obo/cl#cellxgene_subset +CL:0000990 http://purl.obolibrary.org/obo/cl#cellxgene_subset +CL:0000767 http://purl.obolibrary.org/obo/cl#cellxgene_subset +CL:0002340 http://purl.obolibrary.org/obo/cl#cellxgene_subset +CL:1001451 http://purl.obolibrary.org/obo/cl#cellxgene_subset +CL:0010012 http://purl.obolibrary.org/obo/cl#cellxgene_subset +CL:0000222 http://purl.obolibrary.org/obo/cl#cellxgene_subset From 352278e8743eaa5d7108f6cbb7cc2a91daa74517 Mon Sep 17 00:00:00 2001 From: Aleix Puig <94959119+aleixpuigb@users.noreply.github.com> Date: Wed, 8 Jan 2025 11:10:14 +0000 Subject: [PATCH 12/18] Release v2025-01-08 (#2878) --- cl-base.owl | 8148 ++++++-- cl.obo | 16872 +++++++++------- patterns/definitions.owl | 784 +- src/ontology/components/cellxgene_subset.owl | 4 +- src/ontology/mirror/README.md | 1 - src/ontology/reports/cl-base-diff.md | 12310 ++++++++--- .../reports/cl-edit.owl-obo-report.tsv | 222 +- .../subsets/blood_and_immune_upper_slim.json | 1501 +- .../subsets/blood_and_immune_upper_slim.obo | 780 +- .../subsets/blood_and_immune_upper_slim.owl | 1378 +- .../subsets/blood_and_immune_upper_slim.tsv | 841 +- src/ontology/subsets/eye_upper_slim.json | 1397 +- src/ontology/subsets/eye_upper_slim.obo | 762 +- src/ontology/subsets/eye_upper_slim.owl | 1947 +- src/ontology/subsets/eye_upper_slim.tsv | 705 +- .../general_cell_types_upper_slim.json | 1224 +- .../subsets/general_cell_types_upper_slim.obo | 657 +- .../subsets/general_cell_types_upper_slim.owl | 1202 +- .../subsets/general_cell_types_upper_slim.tsv | 628 +- src/ontology/subsets/kidney_upper_slim.json | 1264 +- src/ontology/subsets/kidney_upper_slim.obo | 675 +- src/ontology/subsets/kidney_upper_slim.owl | 1822 +- src/ontology/subsets/kidney_upper_slim.tsv | 743 +- src/ontology/tmp/README.md | 1 - subsets/blood_and_immune_upper_slim.json | 1501 +- subsets/blood_and_immune_upper_slim.obo | 780 +- subsets/blood_and_immune_upper_slim.owl | 1378 +- subsets/blood_and_immune_upper_slim.tsv | 841 +- subsets/eye_upper_slim.json | 1397 +- subsets/eye_upper_slim.obo | 762 +- subsets/eye_upper_slim.owl | 1947 +- subsets/eye_upper_slim.tsv | 705 +- subsets/general_cell_types_upper_slim.json | 1224 +- subsets/general_cell_types_upper_slim.obo | 657 +- subsets/general_cell_types_upper_slim.owl | 1202 +- subsets/general_cell_types_upper_slim.tsv | 628 +- subsets/kidney_upper_slim.json | 1264 +- subsets/kidney_upper_slim.obo | 675 +- subsets/kidney_upper_slim.owl | 1822 +- subsets/kidney_upper_slim.tsv | 743 +- 40 files changed, 42402 insertions(+), 30992 deletions(-) delete mode 100644 src/ontology/mirror/README.md delete mode 100644 src/ontology/tmp/README.md diff --git a/cl-base.owl b/cl-base.owl index 1dd8717e0..867b47322 100644 --- a/cl-base.owl +++ b/cl-base.owl @@ -22,7 +22,7 @@ xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#" xmlns:ncbitaxon="http://purl.obolibrary.org/obo/ncbitaxon#"> - + An ontology of cell types. Cell Ontology @@ -38,7 +38,7 @@ See PMID:15693950, PMID:12799354, PMID:20123131, PMID:21208450; Contact Alexander Diehl, addiehl@buffalo.edu, university at buffalo. - 2024-09-26 + 2025-01-08 @@ -178,15 +178,15 @@ - + - + - + - + @@ -244,24 +244,12 @@ - - - - - - - - - - - - @@ -322,12 +310,6 @@ - - - - - - @@ -611,6 +593,12 @@ + + + + + + @@ -676,6 +664,252 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + @@ -778,7 +1012,6 @@ Covers cells actively being cultured or stored in a quiescent state for future u CARO:0000013 cell in vivo - obsolete native cell true @@ -1075,9 +1308,15 @@ Covers cells actively being cultured or stored in a quiescent state for future u A germ cell that supports male gamete production. In some species, non-germ cells known as Sertoli cells also play a role in spermatogenesis. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Male germ cells are specialized cells that give rise to the male gametes and are therefore crucial for sexual reproduction in males. Through a complex process called spermatogenesis in the testes male germ cells undergo several stages of development, each with distinctive morphological and physiological characteristics, eventually differentiating into mature spermatozoa (sperm). +Male germ cells are responsible for transferring genetic material from male to offspring as part of sexual reproduction. In the initial stage of their life cycle, they exist as spermatogonial stem cells, which multiply by mitotic division to self-renew and to produce daughter cells. The daughter cells then undergo meiotic division, a process that reduces the number of chromosomes in each cell by half, from diploid to haploid – the formation of spermatids. This is critical for maintaining genetic stability from generation to generation, as it ensures that when an egg and sperm cell unite during fertilization, the resulting offspring will have the correct number of chromosomes. The final phase of spermatogenesis is called spermiogenesis, during which spermatozoa - mature and motile sperm cells – are produced from round spermatids. +The matured male germ cells or sperm cells are highly specialized, having a streamlined shape designed for efficient movement towards the female egg. A sperm cell is divided into three main parts, namely the head, midpiece, and tail. The head contains the genetic material, the midpiece contains mitochondria that provide energy, and the tail, termed as the flagellum, propels the sperm cell forward. Each of these parts play significant roles in fertilization. FMA:72290 MA:0002765 VHOG:0001531 + https://cellxgene.cziscience.com/cellguide/CL_0000015 ncithesaurus:Spermatogenic_Cell male germ cell @@ -1096,6 +1335,19 @@ Covers cells actively being cultured or stored in a quiescent state for future u PMID:29462262 https://orcid.org/0000-0001-5208-3432 + + + + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Male germ cells are specialized cells that give rise to the male gametes and are therefore crucial for sexual reproduction in males. Through a complex process called spermatogenesis in the testes male germ cells undergo several stages of development, each with distinctive morphological and physiological characteristics, eventually differentiating into mature spermatozoa (sperm). +Male germ cells are responsible for transferring genetic material from male to offspring as part of sexual reproduction. In the initial stage of their life cycle, they exist as spermatogonial stem cells, which multiply by mitotic division to self-renew and to produce daughter cells. The daughter cells then undergo meiotic division, a process that reduces the number of chromosomes in each cell by half, from diploid to haploid – the formation of spermatids. This is critical for maintaining genetic stability from generation to generation, as it ensures that when an egg and sperm cell unite during fertilization, the resulting offspring will have the correct number of chromosomes. The final phase of spermatogenesis is called spermiogenesis, during which spermatozoa - mature and motile sperm cells – are produced from round spermatids. +The matured male germ cells or sperm cells are highly specialized, having a streamlined shape designed for efficient movement towards the female egg. A sperm cell is divided into three main parts, namely the head, midpiece, and tail. The head contains the genetic material, the midpiece contains mitochondria that provide energy, and the tail, termed as the flagellum, propels the sperm cell forward. Each of these parts play significant roles in fertilization. + DOI:10.1016/S0092-8674(00)81834-6 + DOI:10.1016/S1534-5807(02)00173-9 + DOI:10.1242/dev.202046 + https://www.ncbi.nlm.nih.gov/books/NBK553142/ + @@ -1282,6 +1534,11 @@ Covers cells actively being cultured or stored in a quiescent state for future u A mature male germ cell that develops from a spermatid. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Sperm cells, also known as spermatozoa or male gametes, are highly specialized cells that are pivotal for sexual reproduction in animals. Produced in the male reproductive organs, specifically the testes, sperm cells play an important role in the process of fertilization, where they fuse with a female gamete or egg cell (ovum) to form a zygote, which marks the beginning of a new organism. +Sperm cells hold several unique traits that set them apart from other body cells. Structurally, a sperm cell possesses two main structures: the head, containing the nucleus carrying the paternal genetic information, and the flagellum, which generates energy and grants the sperm cell mobility +The process of fertilization occurs when one sperm cell successfully penetrates the egg, delivering its genetic information, and ultimately leading to the formation of a new individual combining both paternal and maternal genetic materials. Notably, while hundreds of millions of sperm cells may be released during ejaculation, only one has the opportunity to successfully fertilize the egg, underscoring the highly competitive nature of this biological process. BTO:0001277 BTO:0002046 CALOHA:TS-0949 @@ -1289,6 +1546,7 @@ Covers cells actively being cultured or stored in a quiescent state for future u FMA:67338 WBbt:0006798 ZFA:0009006 + https://cellxgene.cziscience.com/cellguide/CL_0000019 sperm cell spermatozoid spermatozoon @@ -1308,6 +1566,18 @@ Covers cells actively being cultured or stored in a quiescent state for future u GOC:tfm MESH:D013094 + + + + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Sperm cells, also known as spermatozoa or male gametes, are highly specialized cells that are pivotal for sexual reproduction in animals. Produced in the male reproductive organs, specifically the testes, sperm cells play an important role in the process of fertilization, where they fuse with a female gamete or egg cell (ovum) to form a zygote, which marks the beginning of a new organism. +Sperm cells hold several unique traits that set them apart from other body cells. Structurally, a sperm cell possesses two main structures: the head, containing the nucleus carrying the paternal genetic information, and the flagellum, which generates energy and grants the sperm cell mobility +The process of fertilization occurs when one sperm cell successfully penetrates the egg, delivering its genetic information, and ultimately leading to the formation of a new individual combining both paternal and maternal genetic materials. Notably, while hundreds of millions of sperm cells may be released during ejaculation, only one has the opportunity to successfully fertilize the egg, underscoring the highly competitive nature of this biological process. + DOI:10.1080/19420889.2015.1017156 + DOI:10.1152/physrev.00009.2020 + https://www.ncbi.nlm.nih.gov/books/NBK26914/ + @@ -1514,6 +1784,13 @@ Covers cells actively being cultured or stored in a quiescent state for future u oocyte + + + + A female germ cell that has entered meiosis. + GOC:tfm + ISBN:0721662544 + @@ -1532,13 +1809,6 @@ Covers cells actively being cultured or stored in a quiescent state for future u true - - - - A female germ cell that has entered meiosis. - GOC:tfm - ISBN:0721662544 - @@ -1734,7 +2004,7 @@ Covers cells actively being cultured or stored in a quiescent state for future u - + @@ -1812,10 +2082,18 @@ Covers cells actively being cultured or stored in a quiescent state for future u + A non-terminally differentiated cell that develops form the neuroectoderm. Glioblast has the potential to differentiate into various types of glial cells, including astrocytes and oligodendrocytes. ZFA:0009010 glioblast + + + + A non-terminally differentiated cell that develops form the neuroectoderm. Glioblast has the potential to differentiate into various types of glial cells, including astrocytes and oligodendrocytes. + PMID:37824650 + Wikipedia:Glioblast + @@ -2348,7 +2626,6 @@ Covers cells actively being cultured or stored in a quiescent state for future u - @@ -2635,7 +2912,6 @@ Covers cells actively being cultured or stored in a quiescent state for future u - @@ -3291,6 +3567,7 @@ Covers cells actively being cultured or stored in a quiescent state for future u FMA:70335 VHOG:0001529 ZFA:0009025 + myoblast @@ -3319,14 +3596,7 @@ Covers cells actively being cultured or stored in a quiescent state for future u - - - - - - - - + A connective tissue cell which secretes an extracellular matrix rich in collagen and other macromolecules. Flattened and irregular in outline with branching processes; appear fusiform or spindle-shaped. BTO:0000452 @@ -3404,8 +3674,8 @@ Covers cells actively being cultured or stored in a quiescent state for future u - + @@ -3631,7 +3901,6 @@ Covers cells actively being cultured or stored in a quiescent state for future u - @@ -3666,7 +3935,7 @@ Covers cells actively being cultured or stored in a quiescent state for future u - + @@ -4270,6 +4539,7 @@ Covers cells actively being cultured or stored in a quiescent state for future u ZFA:0009045 pancreas epithelial cell pancreatic epithelial cell + epithelial cell of pancreas @@ -4463,7 +4733,6 @@ Covers cells actively being cultured or stored in a quiescent state for future u - @@ -4502,7 +4771,7 @@ Covers cells actively being cultured or stored in a quiescent state for future u A tissue-resident macrophage of the reticuloendothelial system found on the luminal surface of the hepatic sinusoids involved in erythrocyte clearance. Markers include F4/80+, CD11b-low, CD68-positive, sialoadhesin-positive, CD163/SRCR-positive. Irregular, with long processes including lamellipodia extending into the sinusoid lumen, have flattened nucleus with cytoplasm containing characteristic invaginations of the plasma membrane (vermiform bodies); lie within the sinusoid lumen attached to the endothelial surface; derived from the bone marrow, form a major part of the body's mononuclear phagocyte system. - This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. Kupffer cells are tissue-resident macrophages located in the liver. They are an integral part of the mononuclear phagocyte system and are responsible for the phagocytosis of dead or dying cells, microbes, and other foreign substances. Kupffer cells account for approximately 80-90% of tissue-resident macrophages in the body. They are found within the lumen of liver sinusoids and interface with microbial populations and products. The primary role of Kupffer cells is to maintain homeostasis in the liver. They continuously filter and cleanse the blood that flows through the liver, removing pathogens, endotoxins, particulate matter, aged and dysfunctional red blood cells, and miscellaneous waste products. These cells also play an important role in maintaining iron homeostasis. During the process of phagocytosis, Kupffer cells recycle iron from degraded red blood cells, which is then utilized in the formation of new erythrocytes. @@ -4542,7 +4811,7 @@ Kupffer cells also play key roles in various immune responses and inflammatory p - This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. Kupffer cells are tissue-resident macrophages located in the liver. They are an integral part of the mononuclear phagocyte system and are responsible for the phagocytosis of dead or dying cells, microbes, and other foreign substances. Kupffer cells account for approximately 80-90% of tissue-resident macrophages in the body. They are found within the lumen of liver sinusoids and interface with microbial populations and products. The primary role of Kupffer cells is to maintain homeostasis in the liver. They continuously filter and cleanse the blood that flows through the liver, removing pathogens, endotoxins, particulate matter, aged and dysfunctional red blood cells, and miscellaneous waste products. These cells also play an important role in maintaining iron homeostasis. During the process of phagocytosis, Kupffer cells recycle iron from degraded red blood cells, which is then utilized in the formation of new erythrocytes. @@ -4605,7 +4874,6 @@ Kupffer cells also play key roles in various immune responses and inflammatory p - @@ -4661,11 +4929,16 @@ Kupffer cells also play key roles in various immune responses and inflammatory p A specialized phagocytic cell associated with the absorption and removal of the mineralized matrix of bone tissue, which typically differentiates from monocytes. This cell has the following markers: tartrate-resistant acid phosphatase type 5-positive, PU.1-positive, c-fos-positive, nuclear factor NF-kappa-B p100 subunit-positive, tumor necrosis factor receptor superfamily member 11A-positive and macrophage colony-stimulating factor 1 receptor-positive. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Osteoclasts, derived from the monocyte/macrophage lineage, play a crucial role in bone remodeling through bone resorption. They are distinguished from other cells by their large size and their unique ability to secrete enzymes and acids that dissolve the calcium phosphate in bone. The formation of osteoclasts is influenced by two primary factors: macrophage colony-stimulating factor (M-CSF) and the ligand-activated receptor (RANKL) of nuclear factor kappa B (NF-κB). +Osteoclasts also collaborate with osteoblasts, responsible for new bone formation, to maintain bone health and adapt bone structure. Their coordinated actions allow continuous remodeling while preserving overall bone strength and integrity. Imbalances in osteoclast activity can lead to pathological conditions. For example, excessive activity may contribute to diseases like osteoporosis, periprosthetic osteolysis, bone tumors, and Paget's disease. Other the other hand, osteoclast deficiency ca result in conditions like osteopetrosis. BTO:0000968 CALOHA:TS-0721 FMA:66781 MESH:D010010 ZFA:0009047 + https://cellxgene.cziscience.com/cellguide/CL_0000092 chondroclast Morphology: Highly vesicular; markers: Surface: RANK, cFMS (MCSF receptor); Secreted: cathepsin K and TRAP (tartate resistant acid phosphatase); transcription factors: PU.1, cFOS, MITF, NFkB (p52); role or process: tissue remodelling: bone resorption; lineage: hematopoietic, myeloid. @@ -4695,6 +4968,17 @@ Kupffer cells also play key roles in various immune responses and inflammatory p PMID:15055519 PMID:17380158 + + + + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Osteoclasts, derived from the monocyte/macrophage lineage, play a crucial role in bone remodeling through bone resorption. They are distinguished from other cells by their large size and their unique ability to secrete enzymes and acids that dissolve the calcium phosphate in bone. The formation of osteoclasts is influenced by two primary factors: macrophage colony-stimulating factor (M-CSF) and the ligand-activated receptor (RANKL) of nuclear factor kappa B (NF-κB). +Osteoclasts also collaborate with osteoblasts, responsible for new bone formation, to maintain bone health and adapt bone structure. Their coordinated actions allow continuous remodeling while preserving overall bone strength and integrity. Imbalances in osteoclast activity can lead to pathological conditions. For example, excessive activity may contribute to diseases like osteoporosis, periprosthetic osteolysis, bone tumors, and Paget's disease. Other the other hand, osteoclast deficiency ca result in conditions like osteopetrosis. + DOI:10.3389/fmed.2017.00234 + DOI:10.37175/stemedicine.v1i4.57 + https://www.sciencedirect.com/topics/medicine-and-dentistry/osteoclast + @@ -4763,7 +5047,6 @@ Kupffer cells also play key roles in various immune responses and inflammatory p - @@ -5165,7 +5448,6 @@ Kupffer cells also play key roles in various immune responses and inflammatory p - @@ -5346,7 +5628,7 @@ Kupffer cells also play key roles in various immune responses and inflammatory p - + Most generally any neuron which is not motor or sensory. Interneurons may also refer to neurons whose axons remain within a particular brain region as contrasted with projection neurons which have axons projecting to other brain regions. BTO:0003811 @@ -5354,6 +5636,7 @@ Kupffer cells also play key roles in various immune responses and inflammatory p FMA:67313 WBbt:0005113 ZFA:0009051 + CNS interneuron interneuron @@ -5447,6 +5730,7 @@ Kupffer cells also play key roles in various immune responses and inflammatory p MESH:D011984 WBbt:0005759 ZFA:0009053 + sensory neuron @@ -5474,16 +5758,31 @@ Kupffer cells also play key roles in various immune responses and inflammatory p - + + A neuron type that respond to multiple stimuli such as mechanical, thermal and chemical. This neuron type is responsible for integrating different types of sensory inputs, allowing organisms to respond appropriately to diverse environmental challenges. ZFA:0009054 + polymodal sensory neuron polymodal neuron + + + + A neuron type that respond to multiple stimuli such as mechanical, thermal and chemical. This neuron type is responsible for integrating different types of sensory inputs, allowing organisms to respond appropriately to diverse environmental challenges. + PMID:23749412 + PMID:36381588 + ZFA:0009054 + + + + polymodal sensory neuron + PMID:23749412 + @@ -5534,18 +5833,7 @@ Kupffer cells also play key roles in various immune responses and inflammatory p - - - - - - - - - - - - + @@ -5577,7 +5865,7 @@ Kupffer cells also play key roles in various immune responses and inflammatory p - + Neuron with two neurites that are fused grossly when they protrude from the soma and bifurcate a short distance from the soma. FMA:67305 ZFA:0009057 @@ -5602,7 +5890,7 @@ Kupffer cells also play key roles in various immune responses and inflammatory p - + Neuron with one neurite that extends from the cell body. FMA:67278 ZFA:0009058 @@ -5796,10 +6084,35 @@ Kupffer cells also play key roles in various immune responses and inflammatory p - - columnar neuron + + + + + + + + + A neuron of the invertebrate central nervous system. This neuron innervates the central complex (CX) of an invertebrate brain and it forms columnar patterns with its dendrites. It is involved in navigation and spatial processing. + Columnar neurons have been widely studied in Diptera, locusts, honey bees and other insects. In the mammalian brain, a "columnar organisation" is referred to neurons of the neocortex, however these differ from columnar neurons which are found in the insects central nervous system. columnar neuron + + + + A neuron of the invertebrate central nervous system. This neuron innervates the central complex (CX) of an invertebrate brain and it forms columnar patterns with its dendrites. It is involved in navigation and spatial processing. + PMID:34696823 + PMID:37608556 + + + + + Columnar neurons have been widely studied in Diptera, locusts, honey bees and other insects. In the mammalian brain, a "columnar organisation" is referred to neurons of the neocortex, however these differ from columnar neurons which are found in the insects central nervous system. + PMID:18837039 + PMID:32374034 + PMID:34696823 + PMID:37608556 + PMID:9153131 + @@ -5821,7 +6134,7 @@ Kupffer cells also play key roles in various immune responses and inflammatory p A vertebrate phagocyte with a single nucleus. - This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. Mononuclear phagocytes are immune cells that form a critical part of the body's innate immune system, the body's first line of defense against infections. Mononuclear phagocytes are characterized by the presence of a single, large nucleus. The ‘Mononuclear Phagocyte System’ nomenclature was introduced to distinguish mononuclear monocytes and macrophages from other cells with multiple nuclei. However, the cells within the mononuclear phagocyte system represent a highly heterogeneous group, all of which are able to perform highly efficient phagocytosis - engulfing and digesting microbes and cellular debris to fight infections and to maintain normal tissue homeostasis. In addition to phagocytosis, mononuclear phagocytes also secrete chemical compounds to recruit other immune cells to a site of infection. These cells produce different types of signaling molecules, including cytokines, chemokines, and reactive oxygen species, triggering a cascade of responses to ensure rapid and efficient containment and neutralization of invading pathogens. These cells are also involved in antigen presentation, a process essential for stimulating an adaptive immune response. They can process and present antigens to T cells, thereby linking the innate and adaptive immune responses. @@ -5850,7 +6163,7 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf - This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. Mononuclear phagocytes are immune cells that form a critical part of the body's innate immune system, the body's first line of defense against infections. Mononuclear phagocytes are characterized by the presence of a single, large nucleus. The ‘Mononuclear Phagocyte System’ nomenclature was introduced to distinguish mononuclear monocytes and macrophages from other cells with multiple nuclei. However, the cells within the mononuclear phagocyte system represent a highly heterogeneous group, all of which are able to perform highly efficient phagocytosis - engulfing and digesting microbes and cellular debris to fight infections and to maintain normal tissue homeostasis. In addition to phagocytosis, mononuclear phagocytes also secrete chemical compounds to recruit other immune cells to a site of infection. These cells produce different types of signaling molecules, including cytokines, chemokines, and reactive oxygen species, triggering a cascade of responses to ensure rapid and efficient containment and neutralization of invading pathogens. These cells are also involved in antigen presentation, a process essential for stimulating an adaptive immune response. They can process and present antigens to T cells, thereby linking the innate and adaptive immune responses. @@ -5872,12 +6185,28 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Surface ectoderm cells give rise to external structures such as the epidermis, hair, nails, and sweat glands. They are critical during the early stages of embryonic development, where they delineate and create the organism's exterior body plan. Beyond forming the organism's physical exterior, surface ectodermal cells have other significant roles. For instance, these cells lead to the development of the anterior pituitary gland and the enamel of the teeth. They are also integral to the formation of the sensory organs, including the eyes and the ears. In the eyes, they form the cornea and lens epithelium. In the ears, they form the external ear canal and certain parts of the inner ear. Therefore, these cells are instrumental in the development of various sensory systems in an organism. +Certain abnormalities or mutations in surface ectodermal cells could lead to medical conditions known as ectodermal dysplasias. These are a group of inherited disorders affecting the development or function of teeth, hair, nails, and sweat glands. Therefore, understanding the formation and function of surface ectodermal cells is also important in identifying and addressing certain genetic disorders and conditions. In summary, surface ectodermal cells are essential in embryonic development, contributing to the creation of the external physical appearance and the sensory organs of an organism. FMA:72552 + https://cellxgene.cziscience.com/cellguide/CL_0000114 cell of surface ectoderm surface ectoderm cell surface ectodermal cell + + + + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Surface ectoderm cells give rise to external structures such as the epidermis, hair, nails, and sweat glands. They are critical during the early stages of embryonic development, where they delineate and create the organism's exterior body plan. Beyond forming the organism's physical exterior, surface ectodermal cells have other significant roles. For instance, these cells lead to the development of the anterior pituitary gland and the enamel of the teeth. They are also integral to the formation of the sensory organs, including the eyes and the ears. In the eyes, they form the cornea and lens epithelium. In the ears, they form the external ear canal and certain parts of the inner ear. Therefore, these cells are instrumental in the development of various sensory systems in an organism. +Certain abnormalities or mutations in surface ectodermal cells could lead to medical conditions known as ectodermal dysplasias. These are a group of inherited disorders affecting the development or function of teeth, hair, nails, and sweat glands. Therefore, understanding the formation and function of surface ectodermal cells is also important in identifying and addressing certain genetic disorders and conditions. In summary, surface ectodermal cells are essential in embryonic development, contributing to the creation of the external physical appearance and the sensory organs of an organism. + DOI:10.1038/srep32007 + https://www.ncbi.nlm.nih.gov/books/NBK539836/ + https://www.ncbi.nlm.nih.gov/books/NBK563130 + @@ -5958,20 +6287,13 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf - - + - - - - - - ZFA:0009067 CNS neuron (sensu Vertebrata) @@ -6002,7 +6324,6 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf - @@ -6063,7 +6384,7 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf - + A neuron of the vertebrate central nervous system that is small in size. This general class includes small neurons in the granular layer of the cerebellar cortex, cerebral cortex neurons that are not pyramidal cells and small neurons without axons found in the olfactory bulb. BTO:0003393 ZFA:0009070 @@ -6088,8 +6409,6 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf - - @@ -6098,7 +6417,7 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf An inhibitory neuron and the sole output neuron of the cerebellar cortex, the Purkinje cell's soma is located between the granular and molecular layers of the cerebellum. It is one of the largest neural cells in the mammalian brain, ranging from 50 to 80 micrometres in diameter. Purkinje cells have planar, fan-shaped dendrites that branch extensively with little overlap. This cell type receives synaptic input from parallel fibres, which modulate high-frequency spike activity known as "simple spikes," and climbing fibres, which modulate infrequent calcium spike activity known as "complex spikes". Purkinje cells are involved in motor coordination, particularly in correcting movements in progress. - This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. Purkinje cells, named after the Czech anatomist Jan Evangelista Purkyně who discovered them, are unique inhibitory neurons in the cerebellar cortex. They are a critical part of the vertebrate nervous system as they provide the only signal output from the cortex to the cerebellar nuclei. They are one of the few types of neurons that are large enough to be seen with the naked eye. The most distinct hallmark of Purkinje cells is their elaborate dendritic arbor, which forms a broad and intricately branching structure resembling a tree. These numerous branches each receive excitatory synaptic inputs from more than 100,000 parallel fibers; in addition, a single climbing fiber makes hundreds of synapses to the soma and proximal dendrites. A single long axon forms an inhibitory projection to the cerebellar nuclei. Purkinje cells play key roles in the coordination of fine, voluntary motor movements and balance. As the sole output of all motor coordination in the cerebellar cortex, they serve as a central relay in the cerebro-cerebellar loop. Each Purkinje cell receives two types of synaptic input: one from parallel fibers (which are axons of granule cells), and the other from climbing fibers (originating from the inferior olivary nucleus). The Purkinje cells process and integrate these diverse kinds of input signals to generate output that controls timing and coordination of movements. @@ -6131,7 +6450,7 @@ Purkinje cells are also known to be implicated in a variety of diseases. Their p - This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. Purkinje cells, named after the Czech anatomist Jan Evangelista Purkyně who discovered them, are unique inhibitory neurons in the cerebellar cortex. They are a critical part of the vertebrate nervous system as they provide the only signal output from the cortex to the cerebellar nuclei. They are one of the few types of neurons that are large enough to be seen with the naked eye. The most distinct hallmark of Purkinje cells is their elaborate dendritic arbor, which forms a broad and intricately branching structure resembling a tree. These numerous branches each receive excitatory synaptic inputs from more than 100,000 parallel fibers; in addition, a single climbing fiber makes hundreds of synapses to the soma and proximal dendrites. A single long axon forms an inhibitory projection to the cerebellar nuclei. Purkinje cells play key roles in the coordination of fine, voluntary motor movements and balance. As the sole output of all motor coordination in the cerebellar cortex, they serve as a central relay in the cerebro-cerebellar loop. Each Purkinje cell receives two types of synaptic input: one from parallel fibers (which are axons of granule cells), and the other from climbing fibers (originating from the inferior olivary nucleus). The Purkinje cells process and integrate these diverse kinds of input signals to generate output that controls timing and coordination of movements. @@ -6193,7 +6512,7 @@ Purkinje cells are also known to be implicated in a variety of diseases. Their p - + @@ -6201,8 +6520,7 @@ Purkinje cells are also known to be implicated in a variety of diseases. Their p - - + @@ -6270,7 +6588,7 @@ Purkinje cells are also known to be implicated in a variety of diseases. Their p A non-neuronal cell of the nervous system. They not only provide physical support, but also respond to injury, regulate the ionic and chemical composition of the extracellular milieu. Guide neuronal migration during development, and exchange metabolites with neurons. - This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. Glial cells, also known as neuroglia or simply glia, are non-neuronal cells in the central and peripheral nervous systems that provide support and protection for neurons. They constitute approximately half of the total cells in the human brain and more than half in other parts of the nervous system. Glial cells perform several key functions including, but not limited to, maintaining homeostasis, forming the myelin sheath around the neuron axons, and providing support and nutrition to neurons. These different functions are performed by various glial cell types, including astrocytes, oligodendrocytes, microglia and other specialized types. Astrocytes, for example, are the most abundant glial cells and provide metabolic and nutrient support to neurons, help regulate the extracellular ion and neurotransmitter levels, and play a role in the formation and maintenance of the blood-brain barrier, contributing to the overall homeostasis and functioning of the nervous system. Additionally, astrocytes are involved in synaptic communication and participate in processes such as synaptogenesis and synaptic pruning. @@ -6300,7 +6618,7 @@ Despite their overarching function in the support and protection of neurons, gli - This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. Glial cells, also known as neuroglia or simply glia, are non-neuronal cells in the central and peripheral nervous systems that provide support and protection for neurons. They constitute approximately half of the total cells in the human brain and more than half in other parts of the nervous system. Glial cells perform several key functions including, but not limited to, maintaining homeostasis, forming the myelin sheath around the neuron axons, and providing support and nutrition to neurons. These different functions are performed by various glial cell types, including astrocytes, oligodendrocytes, microglia and other specialized types. Astrocytes, for example, are the most abundant glial cells and provide metabolic and nutrient support to neurons, help regulate the extracellular ion and neurotransmitter levels, and play a role in the formation and maintenance of the blood-brain barrier, contributing to the overall homeostasis and functioning of the nervous system. Additionally, astrocytes are involved in synaptic communication and participate in processes such as synaptogenesis and synaptic pruning. @@ -6499,7 +6817,6 @@ Despite their overarching function in the support and protection of neurons, gli - @@ -6548,11 +6865,19 @@ Despite their overarching function in the support and protection of neurons, gli A transcriptomically distinct central nervous system macrophage found in the parenchyma of the central nervous system. Marker include CD11b-positive, F4/80-positive, and CD68-positive. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Microglial cells, sometimes referred to as microglia, are a type of glial cell that primarily exist within the central nervous system (CNS), notably in the brain and the spinal cord. Classified among the resident immune cells, microglial cells represent about 10% of all cells found within the CNS. These cells are derived from progenitor cells in the yolk sac, which differentiates them from other types of glial cells (such as astrocytes and oligodendrocytes) that are derived from neuroectodermal cell lineages. +The primary role of microglial cells is to act as the first and main active form of immune defense in the CNS. They express a vast repertoire of pattern recognition receptors, which allow them to sense and eliminate microbes invading the CNS parenchyma. They represent one of the macrophage populations of the CNS and are responsible for phagocytosis (engulfing and destroying cellular waste or pathogens) in the neural environment. +Microglial cells are particularly responsive to pathogens and injuries and change their morphology in reaction to inflammation or insult: In the normal state they are characterized by a ramified shape with small processes; in response to stimuli, some microglia mature and change to an amoeboid shape. +Beyond their macrophagic activity, they also perform synaptic pruning during brain development, eliminate unnecessarily produced neurons, and facilitate tissue regeneration and repair. they play integral roles in regulating neural development and supporting cell survival and are important for maintaining tissue homeostasis. +While their protective role generally benefits the brain, their over-activation can occasionally lead to neuro-inflammatory diseases, underlining the importance of balanced microglial cell functions. They have been extensively studied for their association with neurodegenerative diseases, such as Alzheimer's disease, Parkinson's disease, and multiple sclerosis. brain macrophage BTO:0000078 BTO:0000962 FMA:54539 ZFA:0009077 + https://cellxgene.cziscience.com/cellguide/CL_0000129 brain-resident macrophage hortega cells microgliocyte @@ -6581,6 +6906,22 @@ Despite their overarching function in the support and protection of neurons, gli PMID:2089275 http://en.wikipedia.org/wiki/Microglia + + + + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Microglial cells, sometimes referred to as microglia, are a type of glial cell that primarily exist within the central nervous system (CNS), notably in the brain and the spinal cord. Classified among the resident immune cells, microglial cells represent about 10% of all cells found within the CNS. These cells are derived from progenitor cells in the yolk sac, which differentiates them from other types of glial cells (such as astrocytes and oligodendrocytes) that are derived from neuroectodermal cell lineages. +The primary role of microglial cells is to act as the first and main active form of immune defense in the CNS. They express a vast repertoire of pattern recognition receptors, which allow them to sense and eliminate microbes invading the CNS parenchyma. They represent one of the macrophage populations of the CNS and are responsible for phagocytosis (engulfing and destroying cellular waste or pathogens) in the neural environment. +Microglial cells are particularly responsive to pathogens and injuries and change their morphology in reaction to inflammation or insult: In the normal state they are characterized by a ramified shape with small processes; in response to stimuli, some microglia mature and change to an amoeboid shape. +Beyond their macrophagic activity, they also perform synaptic pruning during brain development, eliminate unnecessarily produced neurons, and facilitate tissue regeneration and repair. they play integral roles in regulating neural development and supporting cell survival and are important for maintaining tissue homeostasis. +While their protective role generally benefits the brain, their over-activation can occasionally lead to neuro-inflammatory diseases, underlining the importance of balanced microglial cell functions. They have been extensively studied for their association with neurodegenerative diseases, such as Alzheimer's disease, Parkinson's disease, and multiple sclerosis. + DOI:10.1016/j.cell.2019.08.053 + DOI:10.1016/j.conb.2022.102674 + DOI:10.1016/j.tins.2021.11.001 + DOI:10.1038/nri3086 + DOI:10.3389/fnins.2021.742065 + @@ -6640,10 +6981,30 @@ Despite their overarching function in the support and protection of neurons, gli + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Gut endothelial cells are a crucial component of the endothelium, a thin layer of single cells that line the interior surface of blood vessels and lymphatic vessels, including those in the digestive system or "gut". These cells plays an integral role in various physiological and metabolic functions, actively participating in nutrient absorption, host defense, and vascular homeostasis in the gut. +The primary function of gut endothelial cells lies in their ability to control the passage of materials and the transit of white blood cells into and out of the bloodstream. They achieve this through the formation of a semi-permeable barrier, in which permeability is regulated by tight junctions; complex structures that bring the cells together, sealing the space between them. This ensures a controlled, selective passage of nutrients, ions, and water from the bloodstream into the gut and vice versa, helping maintain homeostasis and overall health. +Gut endothelial cells also play a significant role in angiogenesis and serve as a critical regulator of the gut immune responses playing a modulative role in gut immune homeostasis and inflammatory responses. In addition, they generate nitric oxide, a potent vasodilator, which helps in maintaining vascular tonus, preventing platelet and leukocyte adhesion, and decreasing smooth muscle proliferation. These multi-faceted roles make gut endothelial cells indispensable for the normal functioning of the gut and overall health. ZFA:0009078 + https://cellxgene.cziscience.com/cellguide/CL_0000131 gut endothelial cell + + + + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Gut endothelial cells are a crucial component of the endothelium, a thin layer of single cells that line the interior surface of blood vessels and lymphatic vessels, including those in the digestive system or "gut". These cells plays an integral role in various physiological and metabolic functions, actively participating in nutrient absorption, host defense, and vascular homeostasis in the gut. +The primary function of gut endothelial cells lies in their ability to control the passage of materials and the transit of white blood cells into and out of the bloodstream. They achieve this through the formation of a semi-permeable barrier, in which permeability is regulated by tight junctions; complex structures that bring the cells together, sealing the space between them. This ensures a controlled, selective passage of nutrients, ions, and water from the bloodstream into the gut and vice versa, helping maintain homeostasis and overall health. +Gut endothelial cells also play a significant role in angiogenesis and serve as a critical regulator of the gut immune responses playing a modulative role in gut immune homeostasis and inflammatory responses. In addition, they generate nitric oxide, a potent vasodilator, which helps in maintaining vascular tonus, preventing platelet and leukocyte adhesion, and decreasing smooth muscle proliferation. These multi-faceted roles make gut endothelial cells indispensable for the normal functioning of the gut and overall health. + DOI:10.1038/nri2171 + DOI:10.1111/bph.14527 + DOI:10.3390/ijms23073698 + DOI:10.3748/wjg.v17.i5.578 + DOI:full/10.15252/emmm.202114121 + @@ -7286,12 +7647,17 @@ Despite their overarching function in the support and protection of neurons, gli A pigment cell derived from the neural crest. Contains melanin-filled pigment granules, which gives a brown to black appearance. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Melanocytes are specialized cells prevalently found in the skin, but also present in the hair follicles, eyes, inner ear, bones, heart, and brain. Their primary function is the synthesis of melanin, a pigment responsible for coloration of skin, hair, and eyes. The presence and distribution of this pigment play a crucial role in the body's defense mechanism against harmful ultraviolet radiation. +In addition to melanin production, melanocytes also engage in a variety of other biological functions. They play a fundamental role in the immune response, owing to their ability to present antigens to T cells. Furthermore, they contribute to the maintenance of the skin's homeostasis by regulating processes such as extracellular matrix remodeling and cytokine production. A balance in melanocyte function is pivotal, as dysfunctions often result in dermatological disorders. For instance, the loss of melanocytes or reduction in their function may lead to hypopigmentation conditions such as vitiligo, whereas an abnormal increase could result in hyperpigmentation disorders or melanoma, a dangerous type of skin cancer. BTO:0000847 CALOHA:TS-0613 FMA:70545 MESH:D008544 VHOG:0001679 ZFA:0009091 + https://cellxgene.cziscience.com/cellguide/CL_0000148 melanophore @@ -7304,6 +7670,19 @@ Despite their overarching function in the support and protection of neurons, gli A pigment cell derived from the neural crest. Contains melanin-filled pigment granules, which gives a brown to black appearance. SANBI:mhl + + + + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Melanocytes are specialized cells prevalently found in the skin, but also present in the hair follicles, eyes, inner ear, bones, heart, and brain. Their primary function is the synthesis of melanin, a pigment responsible for coloration of skin, hair, and eyes. The presence and distribution of this pigment play a crucial role in the body's defense mechanism against harmful ultraviolet radiation. +In addition to melanin production, melanocytes also engage in a variety of other biological functions. They play a fundamental role in the immune response, owing to their ability to present antigens to T cells. Furthermore, they contribute to the maintenance of the skin's homeostasis by regulating processes such as extracellular matrix remodeling and cytokine production. A balance in melanocyte function is pivotal, as dysfunctions often result in dermatological disorders. For instance, the loss of melanocytes or reduction in their function may lead to hypopigmentation conditions such as vitiligo, whereas an abnormal increase could result in hyperpigmentation disorders or melanoma, a dangerous type of skin cancer. + DOI:10.1002/med.21754 + DOI:10.1038/nrc.2016.37 + DOI:10.1111/j.1751-1097.2007.00226.x + DOI:10.3390/ijms21249769 + https://www.sciencedirect.com/topics/agricultural-and-biological-sciences/melanocyte + @@ -7326,25 +7705,38 @@ Despite their overarching function in the support and protection of neurons, gli - - + + + + + + + + + + + + + - + - A specialized epithelial cell that is capable of synthesizing and secreting certain biomolecules. + An epithelial cell, located in a gland, that is specialised for the synthesis and secretion of specific biomolecules, such as hormones, or mucous. CALOHA:TS-2085 FMA:86494 + glandular epithelial cell - glandular epithelial cell + glandular secretory epithelial cell - A specialized epithelial cell that is capable of synthesizing and secreting certain biomolecules. + An epithelial cell, located in a gland, that is specialised for the synthesis and secretion of specific biomolecules, such as hormones, or mucous. GOC:tfm + ORCID:0000-0002-7073-9172 @@ -7491,9 +7883,16 @@ Despite their overarching function in the support and protection of neurons, gli + - A cell that is usually basal in position, cuboidal with round nucleus, short microvilli, secretes pepsinogen. + + + + + + + An epithelial cell of the stomach that is part of the fundic gastric gland. This cell is characterized by a basally located nucleus, abundant rough endoplasmic reticulum, and large apical secretory granules. It produces and secretes pepsinogen, the inactive precursor of the digestive enzyme pepsin. FMA:62902 chief cell of stomach gastric chief cell @@ -7505,8 +7904,23 @@ Despite their overarching function in the support and protection of neurons, gli - A cell that is usually basal in position, cuboidal with round nucleus, short microvilli, secretes pepsinogen. + An epithelial cell of the stomach that is part of the fundic gastric gland. This cell is characterized by a basally located nucleus, abundant rough endoplasmic reticulum, and large apical secretory granules. It produces and secretes pepsinogen, the inactive precursor of the digestive enzyme pepsin. GOC:tfm + PMID:21907708 + PMID:30571046 + Wikipedia:Gastric_chief_cell + + + + + gastric chief cell + Wikipedia:Chief_cell + + + + + zymogenic cell + Wikipedia:Chief_cell @@ -7568,6 +7982,7 @@ Despite their overarching function in the support and protection of neurons, gli + @@ -7609,7 +8024,8 @@ Despite their overarching function in the support and protection of neurons, gli - + + @@ -7622,14 +8038,8 @@ Despite their overarching function in the support and protection of neurons, gli - - - - - - A specialized, columnar, mucus secreting epithelial cell shaped like a flask or goblet. A narrow basal end contains the nucleus while the apical end is swollen by the accumulation of mucus laden secretory granules. Short microvilli project from the apical plasma membrane. - This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. Goblet cells are specialized, simple columnar, secretory epithelial cells that are mostly found in the respiratory and intestinal tracts. The term "goblet" refers to their shape, which resembles a flask or goblet, specially at their apical end which is swollen due to the accumulation of secretory granules. The primary function of goblet cells is to to protect and lubricate the underlying tissues by secreting large quantities of mucin, a complex glycoprotein, which forms mucus when hydrated. In the respiratory tract, the mucus secreted by these cells traps dust, bacteria, viruses, and other potentially harmful particles in the inhaled air, preventing them from reaching the delicate tissues of the lungs. In the intestines, the goblet cells secrete mucus that acts as a protective barrier shielding the intestinal epithelium from dietary antigens, pathogens and prevents the intestinal epithelium from being eroded by the actions of the digestive enzymes and the abrasive action of passing food material. @@ -7654,7 +8064,7 @@ Goblet cells are capable of rapidly altering their secretory output in response - This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. Goblet cells are specialized, simple columnar, secretory epithelial cells that are mostly found in the respiratory and intestinal tracts. The term "goblet" refers to their shape, which resembles a flask or goblet, specially at their apical end which is swollen due to the accumulation of secretory granules. The primary function of goblet cells is to to protect and lubricate the underlying tissues by secreting large quantities of mucin, a complex glycoprotein, which forms mucus when hydrated. In the respiratory tract, the mucus secreted by these cells traps dust, bacteria, viruses, and other potentially harmful particles in the inhaled air, preventing them from reaching the delicate tissues of the lungs. In the intestines, the goblet cells secrete mucus that acts as a protective barrier shielding the intestinal epithelium from dietary antigens, pathogens and prevents the intestinal epithelium from being eroded by the actions of the digestive enzymes and the abrasive action of passing food material. @@ -7695,26 +8105,62 @@ Goblet cells are capable of rapidly altering their secretory output in response + + + + + + + + + + + + + - + - A large, oval stomach epithelial cell with a central nucleus; source of gastric acid. Secretes HCl. + An epithelial cell of the stomach that is part of the fundic gastric gland. This cell is characterized by its pyramidal shape, abundant mitochondria, and a complex network of secretory canaliculi lined with microvilli. It secretes hydrochloric acid into the stomach lumen and produces intrinsic factor, essential for vitamin B12 absorption. BTO:0001780 FMA:62901 + gastric parietal cell oxyntic cell + Parietal cells have dynamic, actin-supported microvilli that increase in number during active secretion, playing a crucial role in secreting hydrochloric acid and intrinsic factor. The structure and regulation of these microvilli are influenced by proteins such as ASAP3, which modulates Arf6 activity and actin assembly, thereby controlling microvilli formation and parietal cell function. parietal cell - A large, oval stomach epithelial cell with a central nucleus; source of gastric acid. Secretes HCl. + An epithelial cell of the stomach that is part of the fundic gastric gland. This cell is characterized by its pyramidal shape, abundant mitochondria, and a complex network of secretory canaliculi lined with microvilli. It secretes hydrochloric acid into the stomach lumen and produces intrinsic factor, essential for vitamin B12 absorption. GOC:tfm ISBN:0517223651 + PMID:31613538 + PMID:31670611 + + + + + gastric parietal cell + PMID:29263912 + + + + + oxyntic cell + Wikipedia:Parietal_cell + + + + + Parietal cells have dynamic, actin-supported microvilli that increase in number during active secretion, playing a crucial role in secreting hydrochloric acid and intrinsic factor. The structure and regulation of these microvilli are influenced by proteins such as ASAP3, which modulates Arf6 activity and actin assembly, thereby controlling microvilli formation and parietal cell function. + PMID:29263912 + PMID:31613538 @@ -7795,10 +8241,10 @@ Goblet cells are capable of rapidly altering their secretory output in response - + An endocrine cell that is located in the epithelium of the gastrointestinal tract or in the pancreas. - This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. Enteroendocrine cells are a specialized subset of cells located within the epithelial lining of both the small and large intestines, as well as the stomach and pancreas. Constituting less than 1% of the total population of intestinal cells, they are differentiated from a common intestinal cell progenitor, thus sharing lineage with absorptive and goblet cells of the intestines. The distinct characteristic feature of an enteroendocrine cell is its inherent capacity to synthesize and secrete a plethora of gut hormones such as serotonin, somatostatin, neurotensin, cholecystokinin, secretin, gastric inhibitory peptide, motilin, and glucagon-like peptide-1. Integrated within this complex network of signaling agents, these substances control various aspects of the digestive system. Each enteroendocrine cell has its unique combination of hormones to release, determined by its position along the intestinal tract. Intriguingly, these hormones not only modulate local gut function, including motility, absorption and secretion, but also potentiate distant actions on other systems such as endocrine, nervous and immune and play a role in the feeling of satiety. @@ -7821,7 +8267,7 @@ The release of these hormones from enteroendocrine cells is a highly regulated a - This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. Enteroendocrine cells are a specialized subset of cells located within the epithelial lining of both the small and large intestines, as well as the stomach and pancreas. Constituting less than 1% of the total population of intestinal cells, they are differentiated from a common intestinal cell progenitor, thus sharing lineage with absorptive and goblet cells of the intestines. The distinct characteristic feature of an enteroendocrine cell is its inherent capacity to synthesize and secrete a plethora of gut hormones such as serotonin, somatostatin, neurotensin, cholecystokinin, secretin, gastric inhibitory peptide, motilin, and glucagon-like peptide-1. Integrated within this complex network of signaling agents, these substances control various aspects of the digestive system. Each enteroendocrine cell has its unique combination of hormones to release, determined by its position along the intestinal tract. Intriguingly, these hormones not only modulate local gut function, including motility, absorption and secretion, but also potentiate distant actions on other systems such as endocrine, nervous and immune and play a role in the feeling of satiety. @@ -7858,6 +8304,7 @@ The release of these hormones from enteroendocrine cells is a highly regulated a + A neuron that is capable of some hormone secretion in response to neuronal signals. BTO:0002691 @@ -7909,7 +8356,7 @@ The modern definition of neurosecretion has evolved to include the release of an A cell that stores epinephrine secretory vesicles. During times of stress, the nervous system signals the vesicles to secrete their hormonal content. Their name derives from their ability to stain a brownish color with chromic salts. Characteristically, they are located in the adrenal medulla and paraganglia of the sympathetic nervous system. - This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. Chromaffin cells, also known as pheochromocytes, are neuroendocrine cells that are typically located in the adrenal medulla, the innermost part of the adrenal gland, which is situated on top of each kidney. Chromaffin cells are also found in small clusters, known as paraganglia, in various locations throughout the body, including the sympathetic nervous system. They derive their name from their ability to stain a brownish-black color upon exposure to chromic salts, a feature made possible due to their high content of granules rich in catecholamines and catecholamine-related neurotransmitters. The primary function of chromaffin cells is the synthesis and release of catecholamines, specifically epinephrine (adrenaline) and norepinephrine (noradrenaline). These neurotransmitters are vital stress hormones that, when released by the adrenal chromaffing cells into the bloodstream, prepare the body for the 'fight or flight' response. This response can enhance the body's performance in a dangerous situation by increasing heart rate, elevating blood sugar, and increasing blood flow to the muscles. The chromaffin cells in paraganglia are responsible for the local release of catecholamines and play a role in regulating blood pressure and other autonomic functions. @@ -7931,7 +8378,7 @@ In addition to their role in stress response, chromaffin cells also contribute t - This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. Chromaffin cells, also known as pheochromocytes, are neuroendocrine cells that are typically located in the adrenal medulla, the innermost part of the adrenal gland, which is situated on top of each kidney. Chromaffin cells are also found in small clusters, known as paraganglia, in various locations throughout the body, including the sympathetic nervous system. They derive their name from their ability to stain a brownish-black color upon exposure to chromic salts, a feature made possible due to their high content of granules rich in catecholamines and catecholamine-related neurotransmitters. The primary function of chromaffin cells is the synthesis and release of catecholamines, specifically epinephrine (adrenaline) and norepinephrine (noradrenaline). These neurotransmitters are vital stress hormones that, when released by the adrenal chromaffing cells into the bloodstream, prepare the body for the 'fight or flight' response. This response can enhance the body's performance in a dangerous situation by increasing heart rate, elevating blood sugar, and increasing blood flow to the muscles. The chromaffin cells in paraganglia are responsible for the local release of catecholamines and play a role in regulating blood pressure and other autonomic functions. @@ -8530,7 +8977,7 @@ In addition to their role in stress response, chromaffin cells also contribute t A Leydig cell is a testosterone-secreting cell in the interstitial area, between the seminiferous tubules, in the testis. - This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. Leydig cells are a testosterone-secreting cell in the interstitial area in the testes of males. They are named after Franz Leydig, a German anatomist who discovered these cells in 1850. Uniquely situated within the soft connective tissue surrounding the seminiferous tubules, Leydig cells form an integral part of the male reproductive system. They are usually polygonal cells characterized by well developed smooth endoplasmic reticulum, high lipid content and a large round nucleus. They are found across mammalian species, including humans. The primary function of Leydig cells is the production of androgens, the male sex hormones, the most notable of which is testosterone. Leydig cells synthesize testosterone from cholesterol through a series of enzymatic reactions. The production and release of testosterone are mainly regulated by the luteinizing hormone (LH) released by the anterior pituitary gland. In response to LH, Leydig cells convert cholesterol into testosterone, which then plays a crucial role in the development and maintenance of primary and secondary male sexual characteristics. These include the formation and maturation of male reproductive organs, onset of spermatogenesis, and the presentation of male secondary sexual traits such as the deepening of the voice, growth of facial hair, development of muscles, and a broadening of shoulders. @@ -8558,7 +9005,7 @@ Apart from testosterone production, Leydig cells also secrete insulin-like facto - This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. Leydig cells are a testosterone-secreting cell in the interstitial area in the testes of males. They are named after Franz Leydig, a German anatomist who discovered these cells in 1850. Uniquely situated within the soft connective tissue surrounding the seminiferous tubules, Leydig cells form an integral part of the male reproductive system. They are usually polygonal cells characterized by well developed smooth endoplasmic reticulum, high lipid content and a large round nucleus. They are found across mammalian species, including humans. The primary function of Leydig cells is the production of androgens, the male sex hormones, the most notable of which is testosterone. Leydig cells synthesize testosterone from cholesterol through a series of enzymatic reactions. The production and release of testosterone are mainly regulated by the luteinizing hormone (LH) released by the anterior pituitary gland. In response to LH, Leydig cells convert cholesterol into testosterone, which then plays a crucial role in the development and maintenance of primary and secondary male sexual characteristics. These include the formation and maturation of male reproductive organs, onset of spermatogenesis, and the presentation of male secondary sexual traits such as the deepening of the voice, growth of facial hair, development of muscles, and a broadening of shoulders. @@ -8709,7 +9156,7 @@ Apart from testosterone production, Leydig cells also secrete insulin-like facto The main structural component of the liver. They are specialized epithelial cells that are organized into interconnected plates called lobules. Majority of cell population of liver, polygonal in shape, arranged in plates or trabeculae between sinusoids; may have single nucleus or binucleated. - This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. Hepatocytes are the major cell type constituting 70-80% of the liver's cytoplasmic mass, playing crucial roles in maintaining the body's metabolic homeostasis. Dimensions of mature hepatocytes typically range from 20 to 30 μm in humans, but size may vary depending on their location within the liver lobule. Hepatocytes are characterized by high biosynthetic, enzymatic, and endocytic activity. They contain abundant mitochondria, smooth and rough endoplasmic reticulum, peroxisomes, lysosomes, and a large nucleus that is often binucleate. The liver consists of three zones - the periportal Zone 1, midzone 2, and pericentral Zone 3 - which have differential nutrient and oxygen status, and damage susceptibility; hepatocytes in the different zones show signifcant functional heterogeneity ('hepatocyte functional zonation'). Hepatocytes are involved in a multitude of critical functions including the metabolism of lipids, carbohydrates, and proteins, the synthesis of serum proteins (e.g., albumin, transferrin, and lipoproteins), the detoxification and excretion of endogenous and exogenous substances, the storage of vitamins and minerals, and the production and secretion of bile. @@ -8738,7 +9185,7 @@ Alterations in hepatocyte function have significant implications for overall hum - This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. Hepatocytes are the major cell type constituting 70-80% of the liver's cytoplasmic mass, playing crucial roles in maintaining the body's metabolic homeostasis. Dimensions of mature hepatocytes typically range from 20 to 30 μm in humans, but size may vary depending on their location within the liver lobule. Hepatocytes are characterized by high biosynthetic, enzymatic, and endocytic activity. They contain abundant mitochondria, smooth and rough endoplasmic reticulum, peroxisomes, lysosomes, and a large nucleus that is often binucleate. The liver consists of three zones - the periportal Zone 1, midzone 2, and pericentral Zone 3 - which have differential nutrient and oxygen status, and damage susceptibility; hepatocytes in the different zones show signifcant functional heterogeneity ('hepatocyte functional zonation'). Hepatocytes are involved in a multitude of critical functions including the metabolism of lipids, carbohydrates, and proteins, the synthesis of serum proteins (e.g., albumin, transferrin, and lipoproteins), the detoxification and excretion of endogenous and exogenous substances, the storage of vitamins and minerals, and the production and secretion of bile. @@ -8920,10 +9367,16 @@ Alterations in hepatocyte function have significant implications for overall hum A somatic cell located in skeletal muscle. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Skeletal muscle cells, or myocytes, are essential for the musculoskeletal system, featuring a striated appearance from tightly packed sarcomeres. These elongated, multi-nucleated cells convert ATP into mechanical energ and are key for voluntary movement and posture. They also are responsible for maintaining body temperature, storing nutrients, and stabilizing joints. +Skeletal muscle cells organize themselves tightly into bundles to form muscle fibers. Embedded within each of these cells are thousands of myofibrils, which are made up of the contractile proteins, actin (the thin filament), and myosin (the thick filament). Contraction of a skeletal muscle cell occurs when these myofibrils shorten, a process driven by the sliding of actin and myosin filaments over each other in a mechanism famously known as the sliding filament theory. +Additionally, skeletal muscle cells exhibit a high degree of plasticity, which allows for their adaptation in response to alterations in functional demands or damages. They have an innate regenerative capacity due to the presence of satellite cells—quiescent muscle stem cells that reside within the muscle fibers. Upon muscle injury, these satellite cells become activated, proliferate, and differentiate into new muscle cells, thereby contributing to the repair and growth of injured skeletal muscle. With this, skeletal muscle cells serve not only a pivotal biomechanical function but also possess a great capacity for self-healing and regeneration. BTO:0004392 CALOHA:TS-2158 FMA:9727 ZFA:0009115 + https://cellxgene.cziscience.com/cellguide/CL_0000188 skeletal muscle cell @@ -8936,6 +9389,20 @@ Alterations in hepatocyte function have significant implications for overall hum A somatic cell located in skeletal muscle. GOC:tfm + + + + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Skeletal muscle cells, or myocytes, are essential for the musculoskeletal system, featuring a striated appearance from tightly packed sarcomeres. These elongated, multi-nucleated cells convert ATP into mechanical energ and are key for voluntary movement and posture. They also are responsible for maintaining body temperature, storing nutrients, and stabilizing joints. +Skeletal muscle cells organize themselves tightly into bundles to form muscle fibers. Embedded within each of these cells are thousands of myofibrils, which are made up of the contractile proteins, actin (the thin filament), and myosin (the thick filament). Contraction of a skeletal muscle cell occurs when these myofibrils shorten, a process driven by the sliding of actin and myosin filaments over each other in a mechanism famously known as the sliding filament theory. +Additionally, skeletal muscle cells exhibit a high degree of plasticity, which allows for their adaptation in response to alterations in functional demands or damages. They have an innate regenerative capacity due to the presence of satellite cells—quiescent muscle stem cells that reside within the muscle fibers. Upon muscle injury, these satellite cells become activated, proliferate, and differentiate into new muscle cells, thereby contributing to the repair and growth of injured skeletal muscle. With this, skeletal muscle cells serve not only a pivotal biomechanical function but also possess a great capacity for self-healing and regeneration. + DOI:10.1002/cphy.c160033 + DOI:10.3390/biology10101056 + https://www.nature.com/scitable/topicpage/the-sliding-filament-theory-of-muscle-contraction-14567666/ + https://www.ncbi.nlm.nih.gov/books/NBK537139 + https://www.ncbi.nlm.nih.gov/books/NBK9961/ + @@ -8956,7 +9423,13 @@ Alterations in hepatocyte function have significant implications for overall hum A muscle cell that develops tension more slowly than a fast-twitch fiber. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Slow muscle cells, as the name implies, are a type of muscle cell well known for their slow contractile speed. They are also referred to as type I, slow-twitch, or red muscles because of their high myoglobin content which gives them a dark, reddish appearance. These cells are predominantly found in the postural muscles of the body, such as those in the back and lower limbs. +A defining characteristic of slow muscle cells is their significant resistance to fatigue. This is largely due to their efficient oxidative metabolism, which allows them to continuously contract over extended periods without succumbing to fatigue. This extraordinary endurance is facilitated by a high concentration of mitochondria, which enables the efficient use of oxygen for energy production, and capillaries, which supplies the necessary oxygen and nutrients. Additionally, these cells have an abundant supply of myoglobin, a protein that stores and transports oxygen within the muscle cell, further supporting their aerobic metabolism. +The primary role of slow muscle cells in the human body is to provide sustained, low-intensity contractions over a prolonged period. They are responsible for maintaining posture and providing stability, rather than delivering short, powerful bursts of activity. They play a pivotal role in supporting various physical activities such as standing, walking, or any form of exercise that requires endurance over speed. ZFA:0009116 + https://cellxgene.cziscience.com/cellguide/CL_0000189 slow muscle fiber slow muscle cell @@ -8968,6 +9441,19 @@ Alterations in hepatocyte function have significant implications for overall hum GOC:tfm ISBN:0323052908 + + + + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Slow muscle cells, as the name implies, are a type of muscle cell well known for their slow contractile speed. They are also referred to as type I, slow-twitch, or red muscles because of their high myoglobin content which gives them a dark, reddish appearance. These cells are predominantly found in the postural muscles of the body, such as those in the back and lower limbs. +A defining characteristic of slow muscle cells is their significant resistance to fatigue. This is largely due to their efficient oxidative metabolism, which allows them to continuously contract over extended periods without succumbing to fatigue. This extraordinary endurance is facilitated by a high concentration of mitochondria, which enables the efficient use of oxygen for energy production, and capillaries, which supplies the necessary oxygen and nutrients. Additionally, these cells have an abundant supply of myoglobin, a protein that stores and transports oxygen within the muscle cell, further supporting their aerobic metabolism. +The primary role of slow muscle cells in the human body is to provide sustained, low-intensity contractions over a prolonged period. They are responsible for maintaining posture and providing stability, rather than delivering short, powerful bursts of activity. They play a pivotal role in supporting various physical activities such as standing, walking, or any form of exercise that requires endurance over speed. + DOI:10.1093/ptj/81.11.1810 + DOI:10.1186/s13578-015-0054-6 + DOI:10.3389/fphys.2021.747214 + https://www.sciencedirect.com/topics/biochemistry-genetics-and-molecular-biology/slow-muscle-fiber + @@ -8994,7 +9480,13 @@ Alterations in hepatocyte function have significant implications for overall hum A muscle cell that can develop high tension rapidly. It is usually innervated by a single alpha neuron. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Fast muscle cells, also known as type II muscle fibers, are a particular type of muscle cell that specializes in conducting rapid, high-intensity contractions. These cells are primarily found within skeletal muscle groups that are directly involved in gross motor activities, such as running, jumping, or lifting heavy weights. The designation "fast" refers to their speed of contraction in response to neural stimuli, which is significantly quicker when compared to other muscle cell types such as slow-twitch or type I muscle fibers. +The primary function of fast muscle cells revolves around their role in anaerobic metabolism, which provides the energy needed for short, forceful bursts of power. They contain a high concentration of glycolytic enzymes that facilitate this process, leading to a swift break down of glucose to generate ATP (adenosine triphosphate), the primary energy currency in biological systems. On the downside, the byproduct of this very rapid, anaerobic metabolic process is lactic acid, which can build up and cause muscle fatigue. +Fast muscle cells can be further classified into two subtypes based on their metabolic characteristics: type IIa and type IIb/x. Type IIa cells, also known as fast oxidative-glycolytic fibers, possess a good oxygen supply and can function in both anaerobic and aerobic conditions, exhibiting moderate resistance to fatigue. On the other hand, type IIb/x cells, also known as fast glycolytic fibers, primarily rely on anaerobic metabolism and tire out a lot quicker. Both these subtypes can adapt to changing demands due to exercise and conditioning, highlighting the plasticity that is a key characteristic of these versatile muscle cells. ZFA:0009117 + https://cellxgene.cziscience.com/cellguide/CL_0000190 glycolytic muscle fiber fast muscle cell @@ -9006,6 +9498,19 @@ Alterations in hepatocyte function have significant implications for overall hum GOC:tfm ISBN:0323052908 + + + + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Fast muscle cells, also known as type II muscle fibers, are a particular type of muscle cell that specializes in conducting rapid, high-intensity contractions. These cells are primarily found within skeletal muscle groups that are directly involved in gross motor activities, such as running, jumping, or lifting heavy weights. The designation "fast" refers to their speed of contraction in response to neural stimuli, which is significantly quicker when compared to other muscle cell types such as slow-twitch or type I muscle fibers. +The primary function of fast muscle cells revolves around their role in anaerobic metabolism, which provides the energy needed for short, forceful bursts of power. They contain a high concentration of glycolytic enzymes that facilitate this process, leading to a swift break down of glucose to generate ATP (adenosine triphosphate), the primary energy currency in biological systems. On the downside, the byproduct of this very rapid, anaerobic metabolic process is lactic acid, which can build up and cause muscle fatigue. +Fast muscle cells can be further classified into two subtypes based on their metabolic characteristics: type IIa and type IIb/x. Type IIa cells, also known as fast oxidative-glycolytic fibers, possess a good oxygen supply and can function in both anaerobic and aerobic conditions, exhibiting moderate resistance to fatigue. On the other hand, type IIb/x cells, also known as fast glycolytic fibers, primarily rely on anaerobic metabolism and tire out a lot quicker. Both these subtypes can adapt to changing demands due to exercise and conditioning, highlighting the plasticity that is a key characteristic of these versatile muscle cells. + DOI:10.1152/japplphysiol.00636.2019 + DOI:10.3389/fcell.2018.00125 + DOI:10.4161/org.4.3.6312 + https://www.sciencedirect.com/topics/biochemistry-genetics-and-molecular-biology/fast-muscle-fiber + @@ -9038,11 +9543,17 @@ Alterations in hepatocyte function have significant implications for overall hum A non-striated, elongated, spindle-shaped cell found lining the digestive tract, uterus, and blood vessels. They develop from specialized myoblasts (smooth muscle myoblast). + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Smooth muscle cells are a specialized type of muscle cells that are primarily found within the walls of hollow organs such as the intestine, stomach, bladder, uterus, and blood vessels. These cells are an essential component of the autonomic nervous system controling involuntary movements within the body. +Smooth muscle cells play a vital role in many physiological processes due to their unique functionality. They can contract and relax in a slow, sustained, and controlled manner to help modulate the size and shape of the lumens of the organs they surround. For example, in the digestive system, coordinated contraction and relaxation of smooth muscle cells propels food along the gastrointestinal tract - a process known as peristalsis. In the blood vessels, the smooth muscle cells, by contracting or relaxing, either constrict or dilate the vessels, which in turn, help regulate blood flow and pressure. +On a cellular level, smooth muscle cells possess a single, centrally located nucleus and contain an arranged network of actin and myosin filaments, which are the proteins responsible for muscle contraction. Unlike their counterparts in skeletal or cardiac muscles, these cells lack specific contact points for these filaments, hence the lack of visible striations. Furthermore, the contraction of smooth muscle cells is regulated by hormones and neurotransmitters, such as acetylcholine and norepinephrine, adding an additional layer of complex regulation to these highly specialized cells. non-striated muscle cell BTO:0004576 CALOHA:TS-2159 FMA:14072 ZFA:0009118 + https://cellxgene.cziscience.com/cellguide/CL_0000192 SMCs myocytes, smooth muscle smooth muscle fiber @@ -9059,6 +9570,20 @@ Alterations in hepatocyte function have significant implications for overall hum PMID:9315361 http://en.wikipedia.org/wiki/Smooth_muscle_cell + + + + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Smooth muscle cells are a specialized type of muscle cells that are primarily found within the walls of hollow organs such as the intestine, stomach, bladder, uterus, and blood vessels. These cells are an essential component of the autonomic nervous system controling involuntary movements within the body. +Smooth muscle cells play a vital role in many physiological processes due to their unique functionality. They can contract and relax in a slow, sustained, and controlled manner to help modulate the size and shape of the lumens of the organs they surround. For example, in the digestive system, coordinated contraction and relaxation of smooth muscle cells propels food along the gastrointestinal tract - a process known as peristalsis. In the blood vessels, the smooth muscle cells, by contracting or relaxing, either constrict or dilate the vessels, which in turn, help regulate blood flow and pressure. +On a cellular level, smooth muscle cells possess a single, centrally located nucleus and contain an arranged network of actin and myosin filaments, which are the proteins responsible for muscle contraction. Unlike their counterparts in skeletal or cardiac muscles, these cells lack specific contact points for these filaments, hence the lack of visible striations. Furthermore, the contraction of smooth muscle cells is regulated by hormones and neurotransmitters, such as acetylcholine and norepinephrine, adding an additional layer of complex regulation to these highly specialized cells. + DOI:10.1093/ptj/81.11.1810 + https://training.seer.cancer.gov/anatomy/muscular/types.html + https://www.ncbi.nlm.nih.gov/books/NBK10854/ + https://www.ncbi.nlm.nih.gov/books/NBK526125 + https://www.ncbi.nlm.nih.gov/books/NBK556137/ + @@ -9517,6 +10042,7 @@ Alterations in hepatocyte function have significant implications for overall hum odorant receptor cell olfactory receptor neuron olfactory sensory neuron + olfactory receptor cell @@ -9672,6 +10198,7 @@ Alterations in hepatocyte function have significant implications for overall hum A cell that takes up and metabolizes substances. ZFA:0009129 + absorptive cell @@ -9786,6 +10313,7 @@ Alterations in hepatocyte function have significant implications for overall hum + A supporting cell projecting inward from the basement membrane of seminiferous tubules. They surround and nourish the developing male germ cells and secrete androgen binding protein. Their tight junctions with the spermatogonia and spermatocytes provide a blood-testis barrier. BTO:0001238 CALOHA:TS-0922 @@ -9851,6 +10379,7 @@ Alterations in hepatocyte function have significant implications for overall hum FMA:62121 ZFA:0009135 neurilemmal cell + myelinating Schwann cell @@ -9938,6 +10467,7 @@ Alterations in hepatocyte function have significant implications for overall hum FMA:72549 ZFA:0009137 ectoderm cell + ectodermal cell @@ -9967,8 +10497,13 @@ Alterations in hepatocyte function have significant implications for overall hum A cell of the middle germ layer of the embryo. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Mesodermal cells are pluripotent and the most abundant in the human body. They contribute to the development of several structures such as the skeletal muscles, bones, heart and blood vessels, kidneys, gonads, connective tissues, and certain layers of the skin. Hence, the mesoderm is often regarded as an active and diverse layer due to its role in forming many bodily structures. +In embryonic development, these cells are instrumental, contributing to the body's structures through a carefully coordinated sequence of morphogenetic movements. This process forms the complex multicellular architecture of tissues and organs from a simple ball of cells. Without the function of mesodermal cells, the body's integral structures and systems would cease to form correctly, leading to developmental disorders such as axial mesodermal dysplasia complex FMA:72554 ZFA:0009138 + https://cellxgene.cziscience.com/cellguide/CL_0000222 mesoblast mesoderm cell @@ -9980,6 +10515,17 @@ Alterations in hepatocyte function have significant implications for overall hum A cell of the middle germ layer of the embryo. MESH:D008648 + + + + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Mesodermal cells are pluripotent and the most abundant in the human body. They contribute to the development of several structures such as the skeletal muscles, bones, heart and blood vessels, kidneys, gonads, connective tissues, and certain layers of the skin. Hence, the mesoderm is often regarded as an active and diverse layer due to its role in forming many bodily structures. +In embryonic development, these cells are instrumental, contributing to the body's structures through a carefully coordinated sequence of morphogenetic movements. This process forms the complex multicellular architecture of tissues and organs from a simple ball of cells. Without the function of mesodermal cells, the body's integral structures and systems would cease to form correctly, leading to developmental disorders such as axial mesodermal dysplasia complex + DOI:10.1016/j.ceb.2019.07.012 + DOI:10.5535/arm.2016.40.1.162 + https://www.sciencedirect.com/topics/biochemistry-genetics-and-molecular-biology/mesoderm + @@ -10404,7 +10950,6 @@ Alterations in hepatocyte function have significant implications for overall hum FMA:83806 MESH:D010586 ZFA:0009140 - phagocyte @@ -10838,9 +11383,7 @@ Alterations in hepatocyte function have significant implications for overall hum - - Type of neuron that is a primary mechanosensory cell, with peripheral neurites innervating the skin with free nerve endings. AAO:0010316 EFO:0003711 @@ -11022,7 +11565,6 @@ Alterations in hepatocyte function have significant implications for overall hum Any cell that in taxon some Eukaryota. MESH:D005057 - eukaryotic cell @@ -11769,10 +12311,16 @@ Alterations in hepatocyte function have significant implications for overall hum A mature sexual reproductive cell having a single set of unpaired chromosomes. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Gametes are reproductive cells essential for sexual reproduction in eukaryotic organisms, including humans, animals, and many plants. These cells are haploid, containing half the genome or only one set of chromosomes, which is a contrast to the diploid state (two sets of chromosomes) found in most cells in a multicellular organism. This reduction in genetic material is crucial since it allows for the re-establishment of the diploid number of chromosomes when two gametes merge to form a diploid zygote during fertilization. +There are two major types of gametes in animals: sperm cells in males and egg (or ova) in females. These gametes contribute equally to the genetic makeup of the offspring but are morphologically and functionally distinct. Sperm cells (or spermatozoa) are characterized by their motility, small size, and large quantities; they are produced continuously in vast numbers through a process called spermatogenesis in the male gonads or testes. Female gametes are much larger, fewer in numbers, and are not motile; they undergo a development process known as oogenesis, which takes place within the ovaries. The egg also contributes most of the cytoplasm and organelles (including mitochondria) to the zygote that are required for initial cell division stages after fertilization. +Gametes have a primary role in sexual reproduction and genetic variation, which aids in evolution. The formation of gametes involves a special type of cell division called meiosis that introduces genetic diversity via the process of recombination and independent assortment. Following the fusion of male and female gametes, the combination of paternal and maternal genetic material in the zygote allows for genetic recombination, which is a fundamental source of genetic variation and, thus, evolution. Therefore, gametes not only are critical to the inception of new individuals but also contribute to species survival and evolution. CALOHA:TS-0395 FBbt:00005412 FMA:18649 ZFA:0009156 + https://cellxgene.cziscience.com/cellguide/CL_0000300 haploid nucleated cell haploid germ cell gamete @@ -11790,6 +12338,19 @@ Alterations in hepatocyte function have significant implications for overall hum GOC:tfm ISBN:0721662544 + + + + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Gametes are reproductive cells essential for sexual reproduction in eukaryotic organisms, including humans, animals, and many plants. These cells are haploid, containing half the genome or only one set of chromosomes, which is a contrast to the diploid state (two sets of chromosomes) found in most cells in a multicellular organism. This reduction in genetic material is crucial since it allows for the re-establishment of the diploid number of chromosomes when two gametes merge to form a diploid zygote during fertilization. +There are two major types of gametes in animals: sperm cells in males and egg (or ova) in females. These gametes contribute equally to the genetic makeup of the offspring but are morphologically and functionally distinct. Sperm cells (or spermatozoa) are characterized by their motility, small size, and large quantities; they are produced continuously in vast numbers through a process called spermatogenesis in the male gonads or testes. Female gametes are much larger, fewer in numbers, and are not motile; they undergo a development process known as oogenesis, which takes place within the ovaries. The egg also contributes most of the cytoplasm and organelles (including mitochondria) to the zygote that are required for initial cell division stages after fertilization. +Gametes have a primary role in sexual reproduction and genetic variation, which aids in evolution. The formation of gametes involves a special type of cell division called meiosis that introduces genetic diversity via the process of recombination and independent assortment. Following the fusion of male and female gametes, the combination of paternal and maternal genetic material in the zygote allows for genetic recombination, which is a fundamental source of genetic variation and, thus, evolution. Therefore, gametes not only are critical to the inception of new individuals but also contribute to species survival and evolution. + DOI:10.1038/s41586-020-2347-0 + DOI:10.3389/fcell.2022.1040708 + https://www.ncbi.nlm.nih.gov/books/NBK10008/ + https://www.ncbi.nlm.nih.gov/books/NBK553142/ + @@ -12137,7 +12698,7 @@ Alterations in hepatocyte function have significant implications for overall hum - + @@ -12145,19 +12706,24 @@ Alterations in hepatocyte function have significant implications for overall hum + + + - A cell secreting sebun, an oily substance secreted by sebaceous glands, composed of keratin, fat, and cellular debris. + An epithelial cell that is part of a sebaceous gland. This cell produces and secretes sebum, an oily, lipid-rich substance, through holocrine secretion where the entire cell ruptures to release its contents. - sebocyte + sebum secreting cell + - sebum secreting cell + sebocyte - A cell secreting sebun, an oily substance secreted by sebaceous glands, composed of keratin, fat, and cellular debris. + An epithelial cell that is part of a sebaceous gland. This cell produces and secretes sebum, an oily, lipid-rich substance, through holocrine secretion where the entire cell ruptures to release its contents. MESH:D012629 + PMID:19944183 @@ -12184,7 +12750,7 @@ Alterations in hepatocyte function have significant implications for overall hum - + @@ -12199,7 +12765,7 @@ Alterations in hepatocyte function have significant implications for overall hum - Any secretory cell that is capable of some mucus secretion. + Any cell that is capable of some mucus secretion. BTO:0003689 ZFA:0009159 mucous cell @@ -12209,7 +12775,7 @@ Alterations in hepatocyte function have significant implications for overall hum - Any secretory cell that is capable of some mucus secretion. + Any cell that is capable of some mucus secretion. FBC:Autogenerated @@ -12326,6 +12892,7 @@ Alterations in hepatocyte function have significant implications for overall hum + metanephric mesenchyme stem cell @@ -12998,6 +13565,7 @@ Alterations in hepatocyte function have significant implications for overall hum Any cell that is part of some extraembryonic structure. ZFA:0009176 + extraembryonic cell @@ -13061,7 +13629,13 @@ Alterations in hepatocyte function have significant implications for overall hum An extraembryonic cell that develops from a trophectodermal cell. This cell is found in the outer layer of the blastocyst and can invade other structures in the uterus once the blastocyst implants into the uterine wall. A trophoblast cell is involved in the implantation of the embryo into the uterine wall, placental formation, remodelling of maternal vasculature in the uterus, nutrient and gas exchange, hormone production, and immune modulation to support fetal development. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Trophoblast cells, originating from the blastocyst's outer layer, are highly specialized and pivotal for embryo development. Their crucial roles include facilitating implantation and contributing to the formation of the placenta, an essential organ for fetal nutrition, gas exchange, and waste removal during pregnancy. +These cells play a crucial role in implantation by adhering to the uterus lining. Post-implantation, some trophoblast cells differentiate, forming syncytiotrophoblasts. These multi-nucleated cells absorb nutrients, release waste, and secrete hormones, including human chorionic gonadotropin (hCG), sustaining pregnancy. +Trophoblast cells also play a crucial role in immune tolerance, preventing the maternal immune system from treating the fetus as foreign. This balance is vital for a healthy pregnancy. Dysfunctional trophoblast cells may lead to complications like miscarriages or preeclampsia, emphasizing their importance in both embryology and reproductive medicine. FMA:83028 + https://cellxgene.cziscience.com/cellguide/CL_0000351 trophoblastic cell trophoblast cell @@ -13080,6 +13654,18 @@ Alterations in hepatocyte function have significant implications for overall hum PMID:37630754 doi:10.1007/978-3-030-84725-8 + + + + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Trophoblast cells, originating from the blastocyst's outer layer, are highly specialized and pivotal for embryo development. Their crucial roles include facilitating implantation and contributing to the formation of the placenta, an essential organ for fetal nutrition, gas exchange, and waste removal during pregnancy. +These cells play a crucial role in implantation by adhering to the uterus lining. Post-implantation, some trophoblast cells differentiate, forming syncytiotrophoblasts. These multi-nucleated cells absorb nutrients, release waste, and secrete hormones, including human chorionic gonadotropin (hCG), sustaining pregnancy. +Trophoblast cells also play a crucial role in immune tolerance, preventing the maternal immune system from treating the fetus as foreign. This balance is vital for a healthy pregnancy. Dysfunctional trophoblast cells may lead to complications like miscarriages or preeclampsia, emphasizing their importance in both embryology and reproductive medicine. + DOI:10.1016/j.jri.2023.103811 + DOI:10.1530/JOE-17-0402 + https://www.ncbi.nlm.nih.gov/books/NBK53245 + @@ -13240,6 +13826,11 @@ Alterations in hepatocyte function have significant implications for overall hum A smooth muscle cell that is part of a sphincter. A sphincter is a typically circular muscle that normally maintains constriction of a natural body passage or orifice and which relaxes as required by normal physiological functioning. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Smooth muscle cells, as a broader category, are non-striated, involuntary muscle cells that usually exhibit contractions and dilation to facilitate numerous physiological functions. Sphincter associated smooth muscle cells are a specific type of smooth muscle cell that are primarily associated with the functioning of various anatomical sphincters in the human body. +The traits that distinguishes sphincter associated smooth muscle cells from other smooth muscle cells are their location and specialized function in sphincter mechanisms. Sphincter associated smooth muscle cells play a pivotal role in regulating the opening and closure of the bodily sphincters. These sphincters can be found at multiple locations within the body including the gastrointestinal tract (namely the esophagus, stomach, small intestine, and rectum), the urinary tract, and the circulatory system. Upon receiving signals from the autonomous nervous system, these cells contract or relax to modulate the aperture of sphincters, thus controlling the movement of substances through them. Due to their precise and vital functional role, any dysfunction or dysregulation in these cells can lead to serious medical conditions, such as gastroesophageal reflux or urinary incontinence. + https://cellxgene.cziscience.com/cellguide/CL_0000358 sphincter associated smooth muscle cell @@ -13254,6 +13845,17 @@ Alterations in hepatocyte function have significant implications for overall hum A smooth muscle cell that is part of a sphincter. A sphincter is a typically circular muscle that normally maintains constriction of a natural body passage or orifice and which relaxes as required by normal physiological functioning. GOC:cjm + + + + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Smooth muscle cells, as a broader category, are non-striated, involuntary muscle cells that usually exhibit contractions and dilation to facilitate numerous physiological functions. Sphincter associated smooth muscle cells are a specific type of smooth muscle cell that are primarily associated with the functioning of various anatomical sphincters in the human body. +The traits that distinguishes sphincter associated smooth muscle cells from other smooth muscle cells are their location and specialized function in sphincter mechanisms. Sphincter associated smooth muscle cells play a pivotal role in regulating the opening and closure of the bodily sphincters. These sphincters can be found at multiple locations within the body including the gastrointestinal tract (namely the esophagus, stomach, small intestine, and rectum), the urinary tract, and the circulatory system. Upon receiving signals from the autonomous nervous system, these cells contract or relax to modulate the aperture of sphincters, thus controlling the movement of substances through them. Due to their precise and vital functional role, any dysfunction or dysregulation in these cells can lead to serious medical conditions, such as gastroesophageal reflux or urinary incontinence. + https://www.ncbi.nlm.nih.gov/books/NBK482438/ + https://www.ncbi.nlm.nih.gov/books/NBK532857/ + https://www.ncbi.nlm.nih.gov/books/NBK557452/ + @@ -13281,7 +13883,13 @@ Alterations in hepatocyte function have significant implications for overall hum A smooth muscle cell associated with the vasculature. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Vascular associated smooth muscle cells (VSMCs) are specialized cells that constitute a major component of the blood vessel wall in the circulatory system. They derive their name from the predominantly smooth appearance under microscopic examination, as opposed to the striated appearance of cardiac and skeletal muscles. +A principal function of VSMCs is to regulate vascular tone, which directly dictates blood pressure and blood flow distribution across various body parts. This is achieved through coordinated contraction and relaxation of the muscles in response to a variety of extracellular signals. When a blood vessel is exposed to stimuli like pressure or injury, VSMCs contract, resulting in vasoconstriction and ultimately, an increase in blood pressure. Conversely, in response to vasodilators, these cells relax, leading to vasodilation and a consequent decrease in blood pressure. +VSMCs are also involved in vascular remodeling, a process where blood vessels adapt their structure to long-term changes in hemodynamic conditions or disease states. In diseases like atherosclerosis and hypertension, an aberrant proliferative and synthetic phenotype of VSMCs contributes to the formation of plaques, leading to vessel hardening or even occlusion. Recent research has further implicated these cells in immune responses, recognizing their function in leukocyte recruitment and inflammation, factors that are largely instrumental in vascular pathologies. ZFA:0009181 + https://cellxgene.cziscience.com/cellguide/CL_0000359 VSMC vascular smooth muscle cell @@ -13301,6 +13909,20 @@ Alterations in hepatocyte function have significant implications for overall hum GOC:dsd GOC:tfm + + + + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Vascular associated smooth muscle cells (VSMCs) are specialized cells that constitute a major component of the blood vessel wall in the circulatory system. They derive their name from the predominantly smooth appearance under microscopic examination, as opposed to the striated appearance of cardiac and skeletal muscles. +A principal function of VSMCs is to regulate vascular tone, which directly dictates blood pressure and blood flow distribution across various body parts. This is achieved through coordinated contraction and relaxation of the muscles in response to a variety of extracellular signals. When a blood vessel is exposed to stimuli like pressure or injury, VSMCs contract, resulting in vasoconstriction and ultimately, an increase in blood pressure. Conversely, in response to vasodilators, these cells relax, leading to vasodilation and a consequent decrease in blood pressure. +VSMCs are also involved in vascular remodeling, a process where blood vessels adapt their structure to long-term changes in hemodynamic conditions or disease states. In diseases like atherosclerosis and hypertension, an aberrant proliferative and synthetic phenotype of VSMCs contributes to the formation of plaques, leading to vessel hardening or even occlusion. Recent research has further implicated these cells in immune responses, recognizing their function in leukocyte recruitment and inflammation, factors that are largely instrumental in vascular pathologies. + DOI:10.1093/cvr/cvs135 + DOI:10.1093/cvr/cvy023 + DOI:10.1161/ATVBAHA.118.311229 + DOI:10.3389/fimmu.2020.599415 + DOI:10.3390/ijms20225694 + @@ -13713,7 +14335,13 @@ Alterations in hepatocyte function have significant implications for overall hum - + + + + + + + ZFA:0009185 sensory processing neuron @@ -14215,38 +14843,22 @@ Alterations in hepatocyte function have significant implications for overall hum - - - - - - - - - - - - - - An interneuron that has its cell body in a central nervous system. + OBSOLETE. An interneuron that has its cell body in a central nervous system. + + - ZFA:0009191 + Interneurons are commonly described as being only found in the central nervous system. However, in CL we define 'interneuron' more broadly as any neuron that is neither a motor neuron nor a sensory neuron, regardless of its location, so we need this term to refer strictly to interneurons of the central nervous system. - CNS interneuron + obsolete CNS interneuron + true - An interneuron that has its cell body in a central nervous system. + OBSOLETE. An interneuron that has its cell body in a central nervous system. doi:10.1016/B978-0-12-817424-1.00001-X - - - - ZFA:0009191 - - @@ -14297,7 +14909,7 @@ Alterations in hepatocyte function have significant implications for overall hum - + ZFA:0009194 CNS short range interneuron @@ -14362,8 +14974,14 @@ Alterations in hepatocyte function have significant implications for overall hum Any male germ cell that has characteristic some haploid and is capable of some fertilization. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +The male gamete, also known as a sperm cell, is a highly specialized cell type critical to sexual reproduction. Sperm are produced during a process called spermatogenesis within the male reproductive organ, specifically the testes. They are haploid cells, carrying the genetic material from the male parent, and fuse with the ovum, the female gamete, to form a diploid zygote during fertilization, thereby initiating gestation and the development of a new organism. +The male gamete is distinguished by its morphology, notably its elongated shape which is geared towards locomotion. One of the primary characteristics of a male gamete is its flagellum, or tail, which propels the cell towards the female gamete. It additionally contains an elongated head region housing the nucleus, where the genetic material is stored. The anterior section of the head, the acrosome, releases enzymes essential for penetrating the protective layers of the ovum during the fertilization process. +The function of male gametes does not cease upon fertilization. In addition to delivering the paternal set of chromosomes, fusion of the sperm cell with the ovum causes an increase in cytosolic Ca2+ which then activates the female egg cell to undergo the so-called cortical reaction during which the egg’s zona pellucida is changed so fusion with additional sperm is prevented. The Ca2+ signal also initiates the development of the zygote and eventual formation of an embryo. Male gametes also contribute towards forming the placenta, which supplies nutrients and removes waste products during gestation. BTO:0001277 CALOHA:TS-0949 + https://cellxgene.cziscience.com/cellguide/CL_0000408 male gamete @@ -14384,6 +15002,19 @@ Alterations in hepatocyte function have significant implications for overall hum Any male germ cell that has characteristic some haploid and is capable of some fertilization. FBC:Autogenerated + + + + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +The male gamete, also known as a sperm cell, is a highly specialized cell type critical to sexual reproduction. Sperm are produced during a process called spermatogenesis within the male reproductive organ, specifically the testes. They are haploid cells, carrying the genetic material from the male parent, and fuse with the ovum, the female gamete, to form a diploid zygote during fertilization, thereby initiating gestation and the development of a new organism. +The male gamete is distinguished by its morphology, notably its elongated shape which is geared towards locomotion. One of the primary characteristics of a male gamete is its flagellum, or tail, which propels the cell towards the female gamete. It additionally contains an elongated head region housing the nucleus, where the genetic material is stored. The anterior section of the head, the acrosome, releases enzymes essential for penetrating the protective layers of the ovum during the fertilization process. +The function of male gametes does not cease upon fertilization. In addition to delivering the paternal set of chromosomes, fusion of the sperm cell with the ovum causes an increase in cytosolic Ca2+ which then activates the female egg cell to undergo the so-called cortical reaction during which the egg’s zona pellucida is changed so fusion with additional sperm is prevented. The Ca2+ signal also initiates the development of the zygote and eventual formation of an embryo. Male gametes also contribute towards forming the placenta, which supplies nutrients and removes waste products during gestation. + DOI:10.1016/j.semcdb.2016.04.009 + DOI:10.1242/dev.202046 + https://www.ncbi.nlm.nih.gov/books/NBK26843/ + https://www.ncbi.nlm.nih.gov/books/NBK553142/ + @@ -14401,7 +15032,7 @@ Alterations in hepatocyte function have significant implications for overall hum - + ZFA:0009195 CNS long range interneuron @@ -14676,7 +15307,7 @@ Alterations in hepatocyte function have significant implications for overall hum - + A cell involved in the elimination of metabolic and foreign toxins, and in maintaining the ionic, acid-base and water balance of biological fluids. WBbt:0005812 excretory cell @@ -14903,7 +15534,7 @@ Alterations in hepatocyte function have significant implications for overall hum - + A secretory cell that discharges its product without loss of cytoplasm. @@ -15114,20 +15745,20 @@ Alterations in hepatocyte function have significant implications for overall hum - + A stem cell that gives rise to the follicle cells that surround the oocyte in female arthropods. somatic stem cell FBbt:00004903 follicle stem cell (sensu Arthropoda) - + - + https://github.com/obophenotype/cell-ontology/issues/1943 @@ -15267,8 +15898,19 @@ Alterations in hepatocyte function have significant implications for overall hum - - + + + + + + + + + + + + + An epithelial cell of the parathyroid gland that is arranged in wide, irregular interconnecting columns; responsible for the synthesis and secretion of parathyroid hormone. BTO:0004712 CALOHA:TS-2140 @@ -15353,6 +15995,7 @@ Alterations in hepatocyte function have significant implications for overall hum FMA:83435 brown adipose cell brown fat cell + brown adipocyte @@ -15430,7 +16073,6 @@ Alterations in hepatocyte function have significant implications for overall hum - @@ -15781,6 +16423,7 @@ Alterations in hepatocyte function have significant implications for overall hum noradrenaline secreting cell norepinephrin secreting cell norepinephrine secreting cell + noradrenergic cell @@ -16252,7 +16895,7 @@ Alterations in hepatocyte function have significant implications for overall hum - + @@ -16265,14 +16908,14 @@ Alterations in hepatocyte function have significant implications for overall hum FBbt:00004904 follicle cell of egg chamber - + - + @@ -16882,7 +17525,7 @@ Alterations in hepatocyte function have significant implications for overall hum - A connective tissue cell of an organ found in the loose connective tissue. These are most often associated with the uterine mucosa and the ovary as well as the hematopoietic system and elsewhere. + A connective tissue cell of an organ found in the loose connective tissue. BTO:0002064 FMA:83624 @@ -16895,7 +17538,7 @@ Alterations in hepatocyte function have significant implications for overall hum - A connective tissue cell of an organ found in the loose connective tissue. These are most often associated with the uterine mucosa and the ovary as well as the hematopoietic system and elsewhere. + A connective tissue cell of an organ found in the loose connective tissue. GOC:tfm MESH:D017154 @@ -16923,6 +17566,7 @@ Alterations in hepatocyte function have significant implications for overall hum + @@ -16930,7 +17574,7 @@ Alterations in hepatocyte function have significant implications for overall hum A supporting cell for the developing female gamete in the ovary of mammals. They develop from the coelomic epithelial cells of the gonadal ridge. Granulosa cells form a single layer around the mammalian oocyte in the primordial ovarian follicle and advance to form a multilayered cumulus oophorus surrounding the ovum in the Graafian follicle. The major functions of granulosa cells include the production of steroids and LH receptors. - This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. Granulosa cells are a type of somatic cell most commonly known for their crucial role within the ovarian follicles of female mammalian species. Named for their grainy appearance, they are situated in the follicular epithelium, lining the inner part of the follicle and directly surrounding the oocyte. These cells stand as an integral part of the ovarian structure and function. One of the primary roles of granulosa cells is to aid in the production and secretion of sex hormones, particularly estrogen. They achieve this by working in tandem with theca cells, which stay attached to the external layer of the follicle. Theca cells produce androstenedione (a type of androgen) which granulosa cells then convert into estradiol, a form of estrogen, with the help of the enzyme aromatase. Moreover, granulosa cells participate in luteinization, transforming into luteal granulosa cells as a response to the luteinizing hormone during ovulation. This allows the formation of the corpus luteum, responsible for the secretion of progesterone necessary to maintain pregnancy. @@ -16953,7 +17597,7 @@ Granulosa cells also play a significant role in follicular development and oocyt - This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. Granulosa cells are a type of somatic cell most commonly known for their crucial role within the ovarian follicles of female mammalian species. Named for their grainy appearance, they are situated in the follicular epithelium, lining the inner part of the follicle and directly surrounding the oocyte. These cells stand as an integral part of the ovarian structure and function. One of the primary roles of granulosa cells is to aid in the production and secretion of sex hormones, particularly estrogen. They achieve this by working in tandem with theca cells, which stay attached to the external layer of the follicle. Theca cells produce androstenedione (a type of androgen) which granulosa cells then convert into estradiol, a form of estrogen, with the help of the enzyme aromatase. Moreover, granulosa cells participate in luteinization, transforming into luteal granulosa cells as a response to the luteinizing hormone during ovulation. This allows the formation of the corpus luteum, responsible for the secretion of progesterone necessary to maintain pregnancy. @@ -16977,9 +17621,10 @@ Granulosa cells also play a significant role in follicular development and oocyt + A cell found throughout the gastrointestinal tract and in the pancreas. They secrete somatostatin in both an endocrine and paracrine manner. Somatostatin inhibits gastrin, cholecystokinin, insulin, glucagon, pancreatic enzymes, and gastric hydrochloric acid. A variety of substances which inhibit gastric acid secretion (vasoactive intestinal peptide, calcitonin gene-related peptide, cholecystokinin, beta-adrenergic agonists, and gastric inhibitory peptide) are thought to act by releasing somatostatin. - This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. Type D enteroendocrine cells, also known as D or delta cells, are specialized hormone-releasing cells found in the pancreas and also scattered throughout the lining of the gastrointestinal tract in mammals, notably within the stomach and the upper part of the small intestine known as the duodenum. The primary role of D cells is to produce and secrete somatostatin, a potent paracrine inhibitor. In the gastrointestinal tract, somatostatin slows down digestion. It reduces gastric acid secretion and slows down the rate of gastric emptying, thereby prolonging and controling the digestive p. Functionally, these effects are aimed at sustaining nutrient absorption to optimize energy extraction from consumed food. @@ -17000,7 +17645,7 @@ In the pancreas, D cells maintain a vital role in endocrine regulation. D cells - This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. Type D enteroendocrine cells, also known as D or delta cells, are specialized hormone-releasing cells found in the pancreas and also scattered throughout the lining of the gastrointestinal tract in mammals, notably within the stomach and the upper part of the small intestine known as the duodenum. The primary role of D cells is to produce and secrete somatostatin, a potent paracrine inhibitor. In the gastrointestinal tract, somatostatin slows down digestion. It reduces gastric acid secretion and slows down the rate of gastric emptying, thereby prolonging and controling the digestive p. Functionally, these effects are aimed at sustaining nutrient absorption to optimize energy extraction from consumed food. @@ -17022,15 +17667,14 @@ In the pancreas, D cells maintain a vital role in endocrine regulation. D cells - - + - A flattened stroma cell forming a sheath or theca outside the basal lamina lining the mature ovarian follicle. Thecal interstitial or stromal cells are steroidogenic, and produce primarily androgens which serve as precusors of estrogens in the granulosa cells. + A specialized stromal cell that forms the theca layer outside the basal lamina lining the ovarian follicle, appearing during the secondary follicle stage. BTO:0002850 ZFA:0009229 @@ -17041,8 +17685,10 @@ In the pancreas, D cells maintain a vital role in endocrine regulation. D cells - A flattened stroma cell forming a sheath or theca outside the basal lamina lining the mature ovarian follicle. Thecal interstitial or stromal cells are steroidogenic, and produce primarily androgens which serve as precusors of estrogens in the granulosa cells. + A specialized stromal cell that forms the theca layer outside the basal lamina lining the ovarian follicle, appearing during the secondary follicle stage. MESH:D013799 + PMID:15833266 + PMID:36758341 @@ -17147,16 +17793,10 @@ In the pancreas, D cells maintain a vital role in endocrine regulation. D cells + - - - - - - - - An endocrine cell found in the pyloric gland mucosa (antral mucosa) of the stomach of mammals and responsible for the secretion of gastrin and enkephalin. Most abundant in pyloric antrum, pyramidal in form with a narrow apex bearing long microvilli. + An endocrine cell found in the stomach and duodenum and is responsible for the secretion of gastrin and enkephalin. Most abundant in pyloric antrum, pyramidal in form with a narrow apex bearing long microvilli. BTO:0004108 FMA:67609 G cell @@ -17166,10 +17806,13 @@ In the pancreas, D cells maintain a vital role in endocrine regulation. D cells - An endocrine cell found in the pyloric gland mucosa (antral mucosa) of the stomach of mammals and responsible for the secretion of gastrin and enkephalin. Most abundant in pyloric antrum, pyramidal in form with a narrow apex bearing long microvilli. + An endocrine cell found in the stomach and duodenum and is responsible for the secretion of gastrin and enkephalin. Most abundant in pyloric antrum, pyramidal in form with a narrow apex bearing long microvilli. GOC:tfm ISBN:0517223651 MESH:D019863 + PMID:10700044 + PMID:35674015 + PMID:37240181 @@ -17201,11 +17844,29 @@ In the pancreas, D cells maintain a vital role in endocrine regulation. D cells - + + + + + + + + + + + + + + + + + + + An epithelial cell found in the basal part of the intestinal glands (crypts of Lieberkuhn) including the appendix. Paneth cells synthesize and secrete lysozyme and cryptdins. Numerous in the deeper parts of the intestinal crypts, particularly in the duodenum, rich in zinc, contain large acidophilic granules, with irregular apical microvilli and prominent membrane-bound vacuoles containing matrix. - This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. Paneth cells are specialized epithelial cells that are primarily located at the bottom of the crypts of Lieberkühn in the small intestine, where they play a pivotal role in maintaining gut homeostasis. They have also been found in smaller numbers in the colonic crypts and other parts of the gastrointestinal tract. Paneth cells are characterized by large acidophilic granules, which take up most of the cytoplasmic volume, causing the nucleus to be pushed toward the base of the cell. Paneth cells function as a part of the innate immune system. The large granules inside the cells are filled with antimicrobial peptides, such as defensins and lysozymes. Upon bacterial intrusion or cellular signaling indicating a potential infection, Paneth cells release the granules containing the antimicrobial substances into the crypt lumen, effectively serving as the first line of defense against bacterial invasion within the gastrointestinal tract. In essence, Paneth cells serve as guardians, protecting the intestinal stem cells from harmful pathogens that may disturb the gut ecosystem. @@ -17216,12 +17877,6 @@ In addition to their primary role in immunity, Paneth cells are also crucial for paneth cell - - - - - true - @@ -17231,11 +17886,12 @@ In addition to their primary role in immunity, Paneth cells are also crucial for MESH:D019879 PMID:29184701 PMID:32308658 + PMID:33484640 - This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. Paneth cells are specialized epithelial cells that are primarily located at the bottom of the crypts of Lieberkühn in the small intestine, where they play a pivotal role in maintaining gut homeostasis. They have also been found in smaller numbers in the colonic crypts and other parts of the gastrointestinal tract. Paneth cells are characterized by large acidophilic granules, which take up most of the cytoplasmic volume, causing the nucleus to be pushed toward the base of the cell. Paneth cells function as a part of the innate immune system. The large granules inside the cells are filled with antimicrobial peptides, such as defensins and lysozymes. Upon bacterial intrusion or cellular signaling indicating a potential infection, Paneth cells release the granules containing the antimicrobial substances into the crypt lumen, effectively serving as the first line of defense against bacterial invasion within the gastrointestinal tract. In essence, Paneth cells serve as guardians, protecting the intestinal stem cells from harmful pathogens that may disturb the gut ecosystem. @@ -17348,8 +18004,14 @@ In addition to their primary role in immunity, Paneth cells are also crucial for A precursor cell destined to differentiate into smooth muscle myocytes. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +A precursor to the smooth muscle cell, the smooth muscle myoblast, is integral to various body systems, including the cardiovascular, gastrointestinal, and respiratory systems. Smooth muscle myoblasts arise from the differentiation of mesenchymal stem cells, a process tightly regulated by specific genetic factors and environmental signals. Their role extends to myogenesis, particularly in the formation of muscular tissue, especially during embryonic development. +Smooth muscle myoblasts possess distinctive cellular characteristics. In contrast to skeletal muscle myoblasts, they do not fuse to create multinucleated fibers. Instead, they differentiate into individual, uninucleated smooth muscle cells. This differentiation unfolds in two distinct phases: proliferation, marked by rapid division to increase cell numbers, and differentiation, involving structural and functional transformation into mature smooth muscle cells. This intricate process is intricately mediated by various signaling molecules and transcription factors. +Functionally, smooth muscle myoblasts and the mature muscle cells they generate play pivotal roles in various physiological processes. Smooth muscle cells orchestrate involuntary muscle responses and are integral to body systems that regulate blood flow, propel food along the digestive tract, and control airflow in the respiratory tract. These diverse functions underscore the significance of smooth muscle myoblasts in the body's growth, maintenance, and overall function. FMA:84798 ZFA:0009235 + https://cellxgene.cziscience.com/cellguide/CL_0000514 myoblast, smooth muscle satellite cell @@ -17362,6 +18024,18 @@ In addition to their primary role in immunity, Paneth cells are also crucial for GOC:tfm MESH:D032390 + + + + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +A precursor to the smooth muscle cell, the smooth muscle myoblast, is integral to various body systems, including the cardiovascular, gastrointestinal, and respiratory systems. Smooth muscle myoblasts arise from the differentiation of mesenchymal stem cells, a process tightly regulated by specific genetic factors and environmental signals. Their role extends to myogenesis, particularly in the formation of muscular tissue, especially during embryonic development. +Smooth muscle myoblasts possess distinctive cellular characteristics. In contrast to skeletal muscle myoblasts, they do not fuse to create multinucleated fibers. Instead, they differentiate into individual, uninucleated smooth muscle cells. This differentiation unfolds in two distinct phases: proliferation, marked by rapid division to increase cell numbers, and differentiation, involving structural and functional transformation into mature smooth muscle cells. This intricate process is intricately mediated by various signaling molecules and transcription factors. +Functionally, smooth muscle myoblasts and the mature muscle cells they generate play pivotal roles in various physiological processes. Smooth muscle cells orchestrate involuntary muscle responses and are integral to body systems that regulate blood flow, propel food along the digestive tract, and control airflow in the respiratory tract. These diverse functions underscore the significance of smooth muscle myoblasts in the body's growth, maintenance, and overall function. + DOI:10.1074/jbc.RA118.001739 + https://www.ncbi.nlm.nih.gov/books/NBK544225/ + https://www.sciencedirect.com/topics/medicine-and-dentistry/smooth-muscle + @@ -17443,6 +18117,7 @@ In addition to their primary role in immunity, Paneth cells are also crucial for perineural satellite cell perineuronal satellite oligodendroglial cell satellite oligodendrocyte + perineuronal satellite cell @@ -17716,6 +18391,7 @@ In addition to their primary role in immunity, Paneth cells are also crucial for A neuron which sends impulses peripherally to activate muscles or secretory cells. ZFA:0009239 output neuron + efferent neuron @@ -17778,20 +18454,26 @@ In addition to their primary role in immunity, Paneth cells are also crucial for - - + + + + + + + + A neuron that develops during the early segmentation stages in teleosts, before the neural tube is formed. ZFA:0009242 primary neuron (sensu Teleostei) - + - + https://github.com/obophenotype/cell-ontology/pull/1950 @@ -17840,23 +18522,52 @@ In addition to their primary role in immunity, Paneth cells are also crucial for + A primary motor neuron with its soma in the caudal region of a spinal cord. The axon of this motoneuron exit the spinal cord from one single point and innervates the lateral surface of ventral axial muscles ZFA:0009243 + CaP motorneuron + cap cell + caudal primary motor neuron CAP motoneuron + + + + A primary motor neuron with its soma in the caudal region of a spinal cord. The axon of this motoneuron exit the spinal cord from one single point and innervates the lateral surface of ventral axial muscles + PMID:17971221 + PMID:35431796 + ZFA:0009243 + + + + CaP motorneuron + PMID:3746410 + + + + + cap cell + PMID:17971221 + + + + + caudal primary motor neuron + PMID:18077593 + - + A primary neuron (sensu Teleostei) that has a motor function. ZFA:0009244 primary motor neuron (sensu Teleostei) @@ -17879,8 +18590,8 @@ In addition to their primary role in immunity, Paneth cells are also crucial for - + A primary neuron (sensu Teleostei) that is neither a sensory neuron or a motor neuron. ZFA:0009245 primary interneuron (sensu Teleostei) @@ -17903,21 +18614,27 @@ In addition to their primary role in immunity, Paneth cells are also crucial for - - - + + + + + + + + + A neuron of teleosts that develops later than a primary neuron, typically during the larval stages. ZFA:0009246 secondary neuron (sensu Teleostei) - + - + https://github.com/obophenotype/cell-ontology/pull/1950 @@ -17947,8 +18664,8 @@ In addition to their primary role in immunity, Paneth cells are also crucial for - + A secondary neuron (sensu Teleostei) that has a motor function. ZFA:0009247 secondary motor neuron (sensu Teleostei) @@ -18475,7 +19192,6 @@ In addition to their primary role in immunity, Paneth cells are also crucial for - @@ -18609,7 +19325,6 @@ In addition to their primary role in immunity, Paneth cells are also crucial for metazoan cell - obsolete animal cell true @@ -18641,7 +19356,6 @@ In addition to their primary role in immunity, Paneth cells are also crucial for - @@ -18738,7 +19452,6 @@ In addition to their primary role in immunity, Paneth cells are also crucial for - @@ -19165,7 +19878,7 @@ In addition to their primary role in immunity, Paneth cells are also crucial for - + neuronal brush cell @@ -19265,9 +19978,7 @@ In addition to their primary role in immunity, Paneth cells are also crucial for - - @@ -19312,8 +20023,13 @@ In addition to their primary role in immunity, Paneth cells are also crucial for A hematopoietic progenitor cell that is committed to the granulocyte and monocyte lineages. These cells are CD123-positive, and do not express Gata1 or Gata2 but do express C/EBPa, and Pu.1. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Granulocyte monocyte progenitor cells (GMP cells), originating from hematopoietic stem cells in the bone marrow, are a critical intermediate in myeloid cell development. Positioned at a key differentiation juncture, these cells exhibit bidirectional potential, giving rise to both granulocyte and monocyte lineages. +Their primary role is to generate mature granulocytes and monocytes, essential components of the body's innate immunity and inflammatory responses. Granulocytes, such as neutrophils, eosinophils, and basophils, contribute to the first line of defense against infections by migrating to the infection site and phagocytosing pathogens. Monocytes can differentiate into macrophages or dendritic cells, playing diverse roles in immune responses. CFU-C , Colony forming unit in culture ZFA:0009251 + https://cellxgene.cziscience.com/cellguide/CL_0000557 colony forming unit granulocyte macrophage granulocyte-macrophage progenitor granulocyte/monocyte precursor @@ -19342,6 +20058,17 @@ In addition to their primary role in immunity, Paneth cells are also crucial for http://en.wikipedia.org/wiki/CFU-GM http://www.copewithcytokines.de + + + + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Granulocyte monocyte progenitor cells (GMP cells), originating from hematopoietic stem cells in the bone marrow, are a critical intermediate in myeloid cell development. Positioned at a key differentiation juncture, these cells exhibit bidirectional potential, giving rise to both granulocyte and monocyte lineages. +Their primary role is to generate mature granulocytes and monocytes, essential components of the body's innate immunity and inflammatory responses. Granulocytes, such as neutrophils, eosinophils, and basophils, contribute to the first line of defense against infections by migrating to the infection site and phagocytosing pathogens. Monocytes can differentiate into macrophages or dendritic cells, playing diverse roles in immune responses. + DOI:10.1016/j.immuni.2017.10.021 + DOI:10.1146/annurev-immunol-081022113627 + DOI:10.1186/2050-7771-2-1 + @@ -19454,7 +20181,6 @@ In addition to their primary role in immunity, Paneth cells are also crucial for - @@ -19596,7 +20322,6 @@ In addition to their primary role in immunity, Paneth cells are also crucial for - @@ -20088,7 +20813,6 @@ In addition to their primary role in immunity, Paneth cells are also crucial for - @@ -20241,10 +20965,10 @@ In addition to their primary role in immunity, Paneth cells are also crucial for + - @@ -20596,7 +21320,6 @@ In addition to their primary role in immunity, Paneth cells are also crucial for - @@ -20605,7 +21328,7 @@ In addition to their primary role in immunity, Paneth cells are also crucial for A subtype of enteroendocrine cells found in the gastrointestinal mucosa, particularly in the glands of pyloric antrum; duodenum; and ileum. These cell type secretes serotonin and some neurotransmitters including enkephalins and substance P. Their secretory granules stain readily with silver (argentaffin stain). - This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. Type EC enteroendocrine cells, also known as enterochromaffin cells, are a vital hormone-secreting cell type found in the gastrointestinal tract. These cells are named after their location in the intestines (“entero”) and because they are stainable by chromium salts (“chromaffin”). The primary function of type EC enteroendocrine cells is to act as chemosensors and lies in their capacity to produce and secrete serotonin, also known as 5-hydroxytryptamine (5-HT). Serotonin is a neurotransmitter that plays a significant role in modulating motility, secretion, vasodilation, perception of pain, and appetite in the gastrointestinal system. However, its function is not limited to the gastrointestinal tract; once secreted, serotonin is distributed via the bloodstream and contributes to regulating mood, appetite, and sleep in the brain. @@ -20630,7 +21353,7 @@ Via specific chemosensory receptors type EC enteroendocrine cells are able to re - This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. Type EC enteroendocrine cells, also known as enterochromaffin cells, are a vital hormone-secreting cell type found in the gastrointestinal tract. These cells are named after their location in the intestines (“entero”) and because they are stainable by chromium salts (“chromaffin”). The primary function of type EC enteroendocrine cells is to act as chemosensors and lies in their capacity to produce and secrete serotonin, also known as 5-hydroxytryptamine (5-HT). Serotonin is a neurotransmitter that plays a significant role in modulating motility, secretion, vasodilation, perception of pain, and appetite in the gastrointestinal system. However, its function is not limited to the gastrointestinal tract; once secreted, serotonin is distributed via the bloodstream and contributes to regulating mood, appetite, and sleep in the brain. @@ -20923,7 +21646,6 @@ Via specific chemosensory receptors type EC enteroendocrine cells are able to re - @@ -21287,7 +22009,6 @@ Via specific chemosensory receptors type EC enteroendocrine cells are able to re - @@ -21336,6 +22057,12 @@ Via specific chemosensory receptors type EC enteroendocrine cells are able to re + + + + + + @@ -21344,7 +22071,7 @@ Via specific chemosensory receptors type EC enteroendocrine cells are able to re A tissue-resident macrophage found in the alveoli of the lungs. Ingests small inhaled particles resulting in degradation and presentation of the antigen to immunocompetent cells. Markers include F4/80-positive, CD11b-/low, CD11c-positive, CD68-positive, sialoadhesin-positive, dectin-1-positive, MR-positive, CX3CR1-negative. - This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. Alveolar macrophages are unique tissue-resident macrophages found in the lungs, specifically in the air sacs or alveoli where gas exchange occurs. They are characterized by specific surface markers including: F4/80-positive, CD11b-/low, CD11c-positive, CD68-positive, sialoadhesin-positive, dectin-1-positive, MR-positive, CX3CR1-negative. These specialized immune cells form a crucial part of the body's defense mechanism, playing important roles in pulmonary health and homeostasis. They are the first line of defense in the pulmonary immune response, acting as scavengers that patrol the alveoli and engulf foreign particles like bacteria, dust, and other debris that enter the lungs through inhalation. The primary function of these alveolar macrophages is phagocytosis, whereby they consume and digest foreign substances, dead cells, and other particulates. In the lung, alveolar macrophages are also responsible for clearing surfactant. Additionally, alveolar macrophages also play an integral role in initiating the immune response, as they secrete several pro-inflammatory cytokines and chemokines that recruit other immune cells to the site of infection or inflammation. @@ -21358,6 +22085,7 @@ Beyond their role in host defense, alveolar macrophages contribute to tissue rem Markers: Mouse: F4/80mid, CD11b-/low, CD11c+, CD68+, sialoadhesin+, dectin-1+, MR+, CX3CR1-. + The marker set MSR1, FABP4 can identify the Human cell type alveolar macrophage in the Lung with a confidence of 0.80 (NS-Forest FBeta value). alveolar macrophage @@ -21379,7 +22107,7 @@ Beyond their role in host defense, alveolar macrophages contribute to tissue rem - This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. Alveolar macrophages are unique tissue-resident macrophages found in the lungs, specifically in the air sacs or alveoli where gas exchange occurs. They are characterized by specific surface markers including: F4/80-positive, CD11b-/low, CD11c-positive, CD68-positive, sialoadhesin-positive, dectin-1-positive, MR-positive, CX3CR1-negative. These specialized immune cells form a crucial part of the body's defense mechanism, playing important roles in pulmonary health and homeostasis. They are the first line of defense in the pulmonary immune response, acting as scavengers that patrol the alveoli and engulf foreign particles like bacteria, dust, and other debris that enter the lungs through inhalation. The primary function of these alveolar macrophages is phagocytosis, whereby they consume and digest foreign substances, dead cells, and other particulates. In the lung, alveolar macrophages are also responsible for clearing surfactant. Additionally, alveolar macrophages also play an integral role in initiating the immune response, as they secrete several pro-inflammatory cytokines and chemokines that recruit other immune cells to the site of infection or inflammation. @@ -21389,6 +22117,12 @@ Beyond their role in host defense, alveolar macrophages contribute to tissue rem DOI:10.1038/nri3600 DOI:10.14348/molcells.2021.0058 + + + + The marker set MSR1, FABP4 can identify the Human cell type alveolar macrophage in the Lung with a confidence of 0.80 (NS-Forest FBeta value). + https://doi.org/10.5281/zenodo.11165918 + @@ -21398,6 +22132,12 @@ Beyond their role in host defense, alveolar macrophages contribute to tissue rem + + + + + + An epithelial cell that has its apical plasma membrane folded into microvilli to provide ample surface for the absorption of nutrients from the intestinal lumen. BTO:0000398 @@ -21683,7 +22423,13 @@ Beyond their role in host defense, alveolar macrophages contribute to tissue rem An elongated, spindle-shaped, cell that is located between the basal lamina and the plasmalemma of a muscle fiber. These cells are mostly quiescent, but upon activation they divide to produce cells that generate new muscle fibers. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Skeletal muscle satellite cells (SMSCs) are a type of adult stem cell that nestles on the outer surface of the myofiber, positioned between the sarcolemma (plasma membrane of the muscle cell) and peripheral basement membrane. +The primary function of SMSCs lies in their capacity to facilitate the growth and repair of damaged skeletal muscle. Upon muscle injury or trauma, these normally quiescent cells activate, proliferate, and differentiate into myoblasts. These myoblasts subsequently mature and fuse to form myotubes, which ultimately help in the repair and rebuilding of muscle fibers. This response is an integral part of the skeletal muscle's ability to recover from injury and adapt to enhanced or changing physical demands, thereby maintaining and improving muscle function. +Furthermore, SMSCs also contribute to hypertrophic muscle growth due to resistance exercise and endurance training, with the notable feature of their multi-nucleated nature resulting from the fusion of differentiated myoblasts. The additional nuclei support enhanced protein synthesis, thus allowing the muscle fibers to grow and strengthen in response to exercise. In aging and in diseases, the number or functionality of these cells can decrease, leading to impaired muscle regeneration and progressive muscle weakness. ZFA:0009272 + https://cellxgene.cziscience.com/cellguide/CL_0000594 Skeletal muscle satellite cells are not traditionally referred to as myoblasts. They are a heterogeneous population whose division, following activiation, contributes to the formation of skeletal muscle fibers and to maintenance of the skeletal muscle statelite cell population. skeletal muscle satellite cell @@ -21697,6 +22443,20 @@ Beyond their role in host defense, alveolar macrophages contribute to tissue rem PMID:21849021 PMID:23303905 + + + + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Skeletal muscle satellite cells (SMSCs) are a type of adult stem cell that nestles on the outer surface of the myofiber, positioned between the sarcolemma (plasma membrane of the muscle cell) and peripheral basement membrane. +The primary function of SMSCs lies in their capacity to facilitate the growth and repair of damaged skeletal muscle. Upon muscle injury or trauma, these normally quiescent cells activate, proliferate, and differentiate into myoblasts. These myoblasts subsequently mature and fuse to form myotubes, which ultimately help in the repair and rebuilding of muscle fibers. This response is an integral part of the skeletal muscle's ability to recover from injury and adapt to enhanced or changing physical demands, thereby maintaining and improving muscle function. +Furthermore, SMSCs also contribute to hypertrophic muscle growth due to resistance exercise and endurance training, with the notable feature of their multi-nucleated nature resulting from the fusion of differentiated myoblasts. The additional nuclei support enhanced protein synthesis, thus allowing the muscle fibers to grow and strengthen in response to exercise. In aging and in diseases, the number or functionality of these cells can decrease, leading to impaired muscle regeneration and progressive muscle weakness. + DOI:10.1016/s1357-2725(03)00042-6 + DOI:10.1152/physrev.00061.2017 + DOI:10.1186/s13287-022-02706-5 + DOI:10.1369/0022155411426780 + DOI:10.22074/cellj.2016.4714 + @@ -21810,7 +22570,7 @@ Beyond their role in host defense, alveolar macrophages contribute to tissue rem - + @@ -22187,7 +22947,6 @@ Beyond their role in host defense, alveolar macrophages contribute to tissue rem - @@ -22556,7 +23315,6 @@ Beyond their role in host defense, alveolar macrophages contribute to tissue rem - @@ -22967,6 +23725,18 @@ Beyond their role in host defense, alveolar macrophages contribute to tissue rem + + + + + + + + + + + + @@ -22976,7 +23746,7 @@ Beyond their role in host defense, alveolar macrophages contribute to tissue rem A secretory cell that is grouped together with other cells of the same type to form grape shaped clusters known as acini (singular acinus). - This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. Acinar cells are specialized exocrine gland cells that secrete specific enzymes and fluids to aid in digestion. Found primarily in the pancreas and salivary glands, the term acinar is derived from the Latin word 'acinus' which means 'grape'; this is because acinar cells are arranged in a grape-like cluster around small ducts, formulating an acinus structure. In the salivary glands, acinar cells secrete digestive enzymes as well as other substances such as mucus and water. These secretions service the initial stages of the digestive process, preparing the consumed food for onward digestion in the stomach and intestines by lubricating and partially breaking it down. @@ -23001,7 +23771,7 @@ Acinar cells have high protein synthesis rates and are susceptible to accumulati - This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. Acinar cells are specialized exocrine gland cells that secrete specific enzymes and fluids to aid in digestion. Found primarily in the pancreas and salivary glands, the term acinar is derived from the Latin word 'acinus' which means 'grape'; this is because acinar cells are arranged in a grape-like cluster around small ducts, formulating an acinus structure. In the salivary glands, acinar cells secrete digestive enzymes as well as other substances such as mucus and water. These secretions service the initial stages of the digestive process, preparing the consumed food for onward digestion in the stomach and intestines by lubricating and partially breaking it down. @@ -23251,7 +24021,6 @@ Acinar cells have high protein synthesis rates and are susceptible to accumulati - @@ -23441,7 +24210,6 @@ Acinar cells have high protein synthesis rates and are susceptible to accumulati - @@ -24150,6 +24918,7 @@ Acinar cells have high protein synthesis rates and are susceptible to accumulati + @@ -24169,6 +24938,7 @@ Acinar cells have high protein synthesis rates and are susceptible to accumulati BTO:0001068 FMA:83417 ZFA:0009284 + pinealocyte @@ -24213,7 +24983,7 @@ Acinar cells have high protein synthesis rates and are susceptible to accumulati A specialized kidney epithelial cell, contained within a glomerulus, that contains "feet" that interdigitate with the "feet" of other podocytes. - This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. Podocytes are highly specialized, terminally differentiated glomerular visceral epithelial cells that wrap around the capillaries in the kidneys. They play an essential role in kidney function, particularly in the filtration selectivity of the glomerulus. Each podocyte is characterized by a unique architecture with a large cell body, ‘major processes’ extending outwardly from the cell body and ‘foot processes’, also known as pedicels, which surround. the glomerular capillary loops Podocytes represent the last barrier of the glomerular filtration membrane in the kidney. This barrier prevents the leakage of plasma proteins from the blood into the urine, hence maintaining protein homeostasis in the body. The foot processes of the podocytes interdigitate with those from neighboring cells. The cell-cell junctions between the foot processes, the slit-diaphragms, are thought to create a molecular sensor of renal filtration that prevents the passage of macromolecules while allowing water and small solutes to pass. @@ -24243,7 +25013,7 @@ The importance of podocytes is further emphasized by the effects of their damage - This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. Podocytes are highly specialized, terminally differentiated glomerular visceral epithelial cells that wrap around the capillaries in the kidneys. They play an essential role in kidney function, particularly in the filtration selectivity of the glomerulus. Each podocyte is characterized by a unique architecture with a large cell body, ‘major processes’ extending outwardly from the cell body and ‘foot processes’, also known as pedicels, which surround. the glomerular capillary loops Podocytes represent the last barrier of the glomerular filtration membrane in the kidney. This barrier prevents the leakage of plasma proteins from the blood into the urine, hence maintaining protein homeostasis in the body. The foot processes of the podocytes interdigitate with those from neighboring cells. The cell-cell junctions between the foot processes, the slit-diaphragms, are thought to create a molecular sensor of renal filtration that prevents the passage of macromolecules while allowing water and small solutes to pass. @@ -24603,7 +25373,7 @@ The importance of podocytes is further emphasized by the effects of their damage An endothelial cell that has small pores, or fenestrations, which allow for the efficient exchange of substances between the blood and surrounding tissues. - This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. Fenestrated cells are specialized epithelial cells that are characterized by a distinctive structural feature, fenestrations or tiny pores, which allow an exchange of substances such as fluids, nutrients, and waste between blood vessels and the surrounding tissue environments. These cells are present in various types of epithelial tissues in the human body, including the intestinal tract, endocrine glands, and certain parts of the renal system. There are multiple types of endothelial cell fenestrations. The most common type is found in systemic capillaries of the endocrine tissue (e.g., pancreatic islets), gastrointestinal mucosa, and renal peritubular capillaries. Here, the fenestrated cells have fenestrations in their peripheral cytoplasm with a unique thin and permeable diaphragm that provides a high degree of selectivity, blocking the passage of larger molecules while allowing the free movement of smaller ones. In contrast, other types of fenestrations, such as the discontinuous epithelium of the liver sinusoidal endothelial cells, do not have diaphragms. @@ -24625,7 +25395,7 @@ Overall, fenestrated cells contribute immensely to important physiological proce - This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. Fenestrated cells are specialized epithelial cells that are characterized by a distinctive structural feature, fenestrations or tiny pores, which allow an exchange of substances such as fluids, nutrients, and waste between blood vessels and the surrounding tissue environments. These cells are present in various types of epithelial tissues in the human body, including the intestinal tract, endocrine glands, and certain parts of the renal system. There are multiple types of endothelial cell fenestrations. The most common type is found in systemic capillaries of the endocrine tissue (e.g., pancreatic islets), gastrointestinal mucosa, and renal peritubular capillaries. Here, the fenestrated cells have fenestrations in their peripheral cytoplasm with a unique thin and permeable diaphragm that provides a high degree of selectivity, blocking the passage of larger molecules while allowing the free movement of smaller ones. In contrast, other types of fenestrations, such as the discontinuous epithelium of the liver sinusoidal endothelial cells, do not have diaphragms. @@ -24965,9 +25735,27 @@ Overall, fenestrated cells contribute immensely to important physiological proce - + + A neuron with soma location in the central nervous system that project its axon to the contralateral side of a central nervous system. This neuron can have its soma in the spinal cord, in the hemisphere of the brain, in the retina or in the ventral nerve cord of invertebrates. + Historically, commissural neurons, particularly in the spinal cord, have been used as a model to understand axon guidance during development. commissural neuron + + + + A neuron with soma location in the central nervous system that project its axon to the contralateral side of a central nervous system. This neuron can have its soma in the spinal cord, in the hemisphere of the brain, in the retina or in the ventral nerve cord of invertebrates. + PMID:17560562 + PMID:31693445 + + + + + Historically, commissural neurons, particularly in the spinal cord, have been used as a model to understand axon guidance during development. + PMID:25960414 + PMID:27532244 + PMID:31514748 + PMID:33438755 + @@ -25105,15 +25893,9 @@ radial glial cells acting as neural progenitors throughout life. - - - - - - An absorptive cell of the gut epithelium that endocytoses microorganisms and intact macromolecules from the gut lumen and transports them to the subepithelial space where they are presented to antigen-presenting cells and lymphocytes. - This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. M cells, or microfold cells, of the gut are specialized epithelial cells found in the lining of the gut, specifically in the follicle-associated epithelium of mucosa-associated lymphoid tissue, where they function as sentries against toxins and pathogens. M cells are characterized by apical microfolds (hence their alternate name) which express unique adhesion molecules that enable them to sample the luminal macromolecules. Other morphological features that distinguish M cells from other intestinal mucosal cells include sparse microvilli and a reduced thickness of the glycocalyx, which permits adhesion while not hindering the transport of molecules. They also have unique intraepithelial invaginations on the basolateral side which are filled with macrophages and other immune cells that can process the engulfed macromolecules quickly. @@ -25140,7 +25922,7 @@ These morphological characteristics enable M cells to serve a dual role in immun - This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. M cells, or microfold cells, of the gut are specialized epithelial cells found in the lining of the gut, specifically in the follicle-associated epithelium of mucosa-associated lymphoid tissue, where they function as sentries against toxins and pathogens. M cells are characterized by apical microfolds (hence their alternate name) which express unique adhesion molecules that enable them to sample the luminal macromolecules. Other morphological features that distinguish M cells from other intestinal mucosal cells include sparse microvilli and a reduced thickness of the glycocalyx, which permits adhesion while not hindering the transport of molecules. They also have unique intraepithelial invaginations on the basolateral side which are filled with macrophages and other immune cells that can process the engulfed macromolecules quickly. @@ -25232,8 +26014,8 @@ These morphological characteristics enable M cells to serve a dual role in immun - + @@ -25250,12 +26032,6 @@ These morphological characteristics enable M cells to serve a dual role in immun ZFA:0009295 cerebrospinal fluid secreting cell - - - - - true - @@ -25374,13 +26150,7 @@ These morphological characteristics enable M cells to serve a dual role in immun - - - - - - - + Any interneuron that has characteristic some stellate morphology. ZFA:0009297 @@ -25464,7 +26234,6 @@ These morphological characteristics enable M cells to serve a dual role in immun - @@ -25534,7 +26303,6 @@ These morphological characteristics enable M cells to serve a dual role in immun - @@ -25597,7 +26365,7 @@ These morphological characteristics enable M cells to serve a dual role in immun A cell that stores and secretes pancreatic polypeptide hormone. - This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. PP cells, also known as pancreatic polypeptide cells (and previously called F cells or gamma cells), are enteroendocrine cells predominantly found in the islets of Langerhans in the head of the pancreas. They are one of the four main endocrine cell types present in the pancreatic islets, along with type A, B and D cells. PP cells are notable for their production of pancreatic polypeptide, an anorexigenic hormone that modulates food intake and energy homeostasis. By secreting pancreatic polypeptide, PP cells play a significant role in the management of both digestive and appetite regulation. Upon ingestion of food, there is a significant increase in the secretion of pancreatic polypeptide, which then reduces biliary secretion and helps slow down the movement of food through the digestive tract. This allows more time for digestion to take place and nutrients to be absorbed, promoting the efficient use of dietary intake. The pancreatic polypeptide further reduces appetite by interacting with the hypothalamus, the area of the brain responsible for control of hunger. @@ -25620,7 +26388,7 @@ Given their important role in digestion, malfunction or damage to PP cells can l - This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. PP cells, also known as pancreatic polypeptide cells (and previously called F cells or gamma cells), are enteroendocrine cells predominantly found in the islets of Langerhans in the head of the pancreas. They are one of the four main endocrine cell types present in the pancreatic islets, along with type A, B and D cells. PP cells are notable for their production of pancreatic polypeptide, an anorexigenic hormone that modulates food intake and energy homeostasis. By secreting pancreatic polypeptide, PP cells play a significant role in the management of both digestive and appetite regulation. Upon ingestion of food, there is a significant increase in the secretion of pancreatic polypeptide, which then reduces biliary secretion and helps slow down the movement of food through the digestive tract. This allows more time for digestion to take place and nutrients to be absorbed, promoting the efficient use of dietary intake. The pancreatic polypeptide further reduces appetite by interacting with the hypothalamus, the area of the brain responsible for control of hunger. @@ -26449,7 +27217,7 @@ Given their important role in digestion, malfunction or damage to PP cells can l A cell of a layer of transitional epithelium in the wall of the proximal urethra, bladder, ureter or renal pelvis, external to the lamina propria. - This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. Urothelial cells are a unique type of epithelial cell found lining the urinary tract system. They form the urothelium, a specialized, multi-layered epithelium that lines major portions of the urinary tract, including the renal pelvis, ureters, bladder, and the proximal part of the urethra. The distinct characteristic of urothelial cells is their ability to stretch and contract depending on the volume of liquid they contain - a feature that facilitates the essential role they play in maintaining the functionality and integrity of the urinary system. The primary function of urothelial cells is to provide an impermeable barrier to urine, preventing the toxic components present in the urine from seeping back into the body's bloodstream. The urothelium consists of a superficial umbrella cell layer, 1–2 layers of intermediate cells, and a basal cell layer. The umbrella layer is composed of large, mostly binucleated cells that are covered in an asymmetrical unit membrane, the uroplakin plaques. These plaques function to seal the apical membrane of the bladder from the toxic and highly variable contents of urine. The lipid bilayer structure of uroplakin plaques has an exceptionally high concentration of uroplakins that contribute to the barrier function of the urothelium. @@ -26472,7 +27240,7 @@ Beyond their mechanical function, urothelial cells also play a role in sensing a - This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. Urothelial cells are a unique type of epithelial cell found lining the urinary tract system. They form the urothelium, a specialized, multi-layered epithelium that lines major portions of the urinary tract, including the renal pelvis, ureters, bladder, and the proximal part of the urethra. The distinct characteristic of urothelial cells is their ability to stretch and contract depending on the volume of liquid they contain - a feature that facilitates the essential role they play in maintaining the functionality and integrity of the urinary system. The primary function of urothelial cells is to provide an impermeable barrier to urine, preventing the toxic components present in the urine from seeping back into the body's bloodstream. The urothelium consists of a superficial umbrella cell layer, 1–2 layers of intermediate cells, and a basal cell layer. The umbrella layer is composed of large, mostly binucleated cells that are covered in an asymmetrical unit membrane, the uroplakin plaques. These plaques function to seal the apical membrane of the bladder from the toxic and highly variable contents of urine. The lipid bilayer structure of uroplakin plaques has an exceptionally high concentration of uroplakins that contribute to the barrier function of the urothelium. @@ -26710,7 +27478,7 @@ Beyond their mechanical function, urothelial cells also play a role in sensing a - + @@ -26959,13 +27727,18 @@ Beyond their mechanical function, urothelial cells also play a role in sensing a Cardiac muscle cells are striated muscle cells that are responsible for heart contraction. In mammals, the contractile fiber resembles those of skeletal muscle but are only one third as large in diameter, are richer in sarcoplasm, and contain centrally located instead of peripheral nuclei. - FMA:83808 + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Cardiac muscle cells, also known as cardiomyocytes or cardiac myocytes, are specialized cells that form the heart tissue. These cells are elongated, branched, and contain a single centrally located nucleus. Their anatomy is composed primarily of densely packed myofibrils, which are protein structures that consist of sarcomeres - the fundamental units of muscle contraction. Cardiac muscle cells are united at their ends through specialized junctions known as intercalated discs, which allow the heart to contract in a unified, powerful and rhythmic way. +Functionally, cardiac muscle cells are responsible for the heart's consistent pumping action that circulates blood throughout the body. Unlike most cells in the body, cardiac muscle cells spontaneously depolarize and generate action potentials without external stimulation. This unique trait stems from the presence of ion channels in the cells' membrane that allow a cyclic flow of ions across the membrane, which create the electrical impulses necessary for heart contraction. The spread of these electrical signals from one cardiac muscle cell to another - facilitated by the interconnected network made by the intercalated disks - results in a synchronized contraction of the heart muscle. +Unlike skeletal muscle cells which can tire and need rest, cardiac muscle cells have to work ceaselessly throughout the entire lifespan, without the opportunity for rest, to ensure continuous circulation of blood. This is made possible through the high volume of mitochondria and a constant supply of oxygen from coronary circulation. In conclusion, cardiac muscle cells, through their unique structure and vital functionality, play a pivotal role in sustaining life by providing the means for blood to reach every cell in the body. cardiocyte BTO:0001539 CALOHA:TS-0115 FMA:14067 MESH:D032383 ZFA:0009316 + https://cellxgene.cziscience.com/cellguide/CL_0000746 cardiac muscle fiber cardiac myocyte cardiomyocyte @@ -26986,6 +27759,19 @@ Beyond their mechanical function, urothelial cells also play a role in sensing a PMID:22426062 PMID:4711263 + + + + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Cardiac muscle cells, also known as cardiomyocytes or cardiac myocytes, are specialized cells that form the heart tissue. These cells are elongated, branched, and contain a single centrally located nucleus. Their anatomy is composed primarily of densely packed myofibrils, which are protein structures that consist of sarcomeres - the fundamental units of muscle contraction. Cardiac muscle cells are united at their ends through specialized junctions known as intercalated discs, which allow the heart to contract in a unified, powerful and rhythmic way. +Functionally, cardiac muscle cells are responsible for the heart's consistent pumping action that circulates blood throughout the body. Unlike most cells in the body, cardiac muscle cells spontaneously depolarize and generate action potentials without external stimulation. This unique trait stems from the presence of ion channels in the cells' membrane that allow a cyclic flow of ions across the membrane, which create the electrical impulses necessary for heart contraction. The spread of these electrical signals from one cardiac muscle cell to another - facilitated by the interconnected network made by the intercalated disks - results in a synchronized contraction of the heart muscle. +Unlike skeletal muscle cells which can tire and need rest, cardiac muscle cells have to work ceaselessly throughout the entire lifespan, without the opportunity for rest, to ensure continuous circulation of blood. This is made possible through the high volume of mitochondria and a constant supply of oxygen from coronary circulation. In conclusion, cardiac muscle cells, through their unique structure and vital functionality, play a pivotal role in sustaining life by providing the means for blood to reach every cell in the body. + DOI:10.1016/j.ccep.2010.10.012 + DOI:10.1038/nrcardio.2016.203 + https://www.ncbi.nlm.nih.gov/books/NBK572070 + https://www.sciencedirect.com/topics/agricultural-and-biological-sciences/cardiac-muscle + @@ -27039,7 +27825,7 @@ Beyond their mechanical function, urothelial cells also play a role in sensing a - + @@ -27047,7 +27833,6 @@ Beyond their mechanical function, urothelial cells also play a role in sensing a - @@ -27198,11 +27983,9 @@ Beyond their mechanical function, urothelial cells also play a role in sensing a A bipolar neuron found in the retina that is synapsed by rod photoreceptor cells but not by cone photoreceptor cells. These neurons depolarize in response to light. - FMA:67750 ZFA:0009321 - rod bipolar cell @@ -27250,6 +28033,7 @@ Beyond their mechanical function, urothelial cells also play a role in sensing a A bipolar neuron found in the retina and having connections with cone photoreceptor cells and neurons in the inner plexiform layer. ZFA:0009322 + cone retinal bipolar cell @@ -27279,6 +28063,7 @@ Beyond their mechanical function, urothelial cells also play a role in sensing a An OFF-bipolar neuron found in the retina and having connections with cone photoreceptors cells and neurons in the outer half of the inner plexiform layer. The cell body of these cells is in the middle of the inner plexiform layer. The dendritic tree is stout and the axon terminates in sublamina 1. The axonal terminal is wide and has only a few varicosities. DB1 cone bipolar cell + type 1 cone bipolar cell (sensu Mus) @@ -27293,7 +28078,7 @@ Beyond their mechanical function, urothelial cells also play a role in sensing a - + @@ -27322,9 +28107,10 @@ Beyond their mechanical function, urothelial cells also play a role in sensing a An OFF-bipolar neuron found in the retina and having connections with cone photoreceptors cells and neurons in the outer half of the inner plexiform layer. The dendritic tree is not well filled and the dendrites are more delicate than in type 1 cells. The axon terminal is bushier and exhibits a dense plexus of varicosities in the inner part of sublamina 1 (Ghosh et al., 2004). It can be differentiated from other retinal bipolar neurons by its expression of marker genes: Neto1, Lhx3 and Irx-6 (Shekhar, 2016). FMB cone bipolar cell + type 2 cone bipolar cell (sensu Mus) - + @@ -27344,7 +28130,7 @@ Beyond their mechanical function, urothelial cells also play a role in sensing a - + PMID:27565351 @@ -27410,6 +28196,7 @@ Beyond their mechanical function, urothelial cells also play a role in sensing a An OFF-bipolar neuron found in the retina and having connections with cone photoreceptors cells and neurons in the outer half of the inner plexiform layer. The cell has a diffuse axon terminal with varicosities in sublaminae 1 and 2 of the inner plexiform layer. DB3 cone bipolar cell + type 4 cone bipolar cell (sensu Mus) @@ -27433,6 +28220,7 @@ Beyond their mechanical function, urothelial cells also play a role in sensing a An ON-bipolar neuron found in the retina and having connections with cone photoreceptors cells and neurons in the inner half of the inner plexiform layer. The axon terminal is restricted to sublamina 3 of the inner plexiform layer. It is narrowly stratified and branched. The dendritic tree has many delicate branches. DB4 cone bipolar cell + type 5 cone bipolar cell (sensu Mus) @@ -27456,6 +28244,7 @@ Beyond their mechanical function, urothelial cells also play a role in sensing a An ON-bipolar neuron found in the retina and having connections with cone photoreceptors cells and neurons in the inner half of the inner plexiform layer. The cell has a loose, delicate axon terminal that opens in sublamina 3 of the inner plexiform layer and descends into sublamina 4. DB5 cone bipolar cell + type 6 cone bipolar cell (sensu Mus) @@ -27479,6 +28268,7 @@ Beyond their mechanical function, urothelial cells also play a role in sensing a An ON-bipolar neuron found in the retina and having connections with cone photoreceptors cells and neurons in the inner half of the inner plexiform layer. The axon terminal is narrowly stratified and are found just below a calretinin-expressing band in sublamina 4 of the inner plexiform layer. IMB cone bipolar cell + type 7 cone bipolar cell (sensu Mus) @@ -27508,6 +28298,7 @@ Beyond their mechanical function, urothelial cells also play a role in sensing a An ON-bipolar neuron found in the retina and having connections with cone photoreceptors cells and neurons in the inner half of the inner plexiform layer. This cell has the widest dendritic field and the widest axon terminal of all retinal bipolar cells. The axon terminal is delicate and stratified through sublaminae 4 and 5 of the inner plexiform layer. DB6 cone bipolar cell + type 8 cone bipolar cell (sensu Mus) @@ -27531,6 +28322,7 @@ Beyond their mechanical function, urothelial cells also play a role in sensing a An ON-bipolar neuron found in the retina and having connections with cone photoreceptors cells and neurons in the inner half of the inner plexiform layer. The dendritic tree is wide and the dendritic convergence indicates cone selectivity. The axon terminal is sparsely branched and terminates in sublamina 5 of the inner plexiform layer. BB cone bipolar cell + type 9 cone bipolar cell (sensu Mus) @@ -29243,7 +30035,6 @@ Beyond their mechanical function, urothelial cells also play a role in sensing a - @@ -29541,7 +30332,6 @@ Beyond their mechanical function, urothelial cells also play a role in sensing a - @@ -30056,7 +30846,6 @@ Beyond their mechanical function, urothelial cells also play a role in sensing a - @@ -30423,7 +31212,6 @@ Beyond their mechanical function, urothelial cells also play a role in sensing a - @@ -30521,7 +31309,6 @@ Beyond their mechanical function, urothelial cells also play a role in sensing a - @@ -30596,7 +31383,6 @@ Beyond their mechanical function, urothelial cells also play a role in sensing a - @@ -30679,7 +31465,6 @@ Beyond their mechanical function, urothelial cells also play a role in sensing a - @@ -31837,7 +32622,6 @@ Beyond their mechanical function, urothelial cells also play a role in sensing a - @@ -31960,7 +32744,6 @@ Beyond their mechanical function, urothelial cells also play a role in sensing a - @@ -32362,7 +33145,6 @@ Beyond their mechanical function, urothelial cells also play a role in sensing a - @@ -32828,7 +33610,6 @@ Beyond their mechanical function, urothelial cells also play a role in sensing a - @@ -32983,7 +33764,6 @@ Beyond their mechanical function, urothelial cells also play a role in sensing a - @@ -34210,7 +34990,6 @@ Beyond their mechanical function, urothelial cells also play a role in sensing a - @@ -34249,7 +35028,7 @@ Beyond their mechanical function, urothelial cells also play a role in sensing a A monocyte that responds rapidly to microbial stimuli by secreting cytokines and antimicrobial factors and which is characterized by high expression of CCR2 in both rodents and humans, negative for the lineage markers CD3, CD19, and CD20, and of larger size than non-classical monocytes. - This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. Classical monocytes are a subtype of monocytes that are characterized by high CD14 but no CD16 expression. Emerging from the bone marrow and entering the bloodstream, these cells play central roles in immune responses and regulation of inflammation. CD14-positive CD16-negative monocytes form the majority of circulating monocytes in the body, typically contributing to around 80-90% of the total monocyte pool. The primary function of the classical monocytes is to serve in the frontline of host defense against infections. They are primed to migrate to sites of infection, and they express pattern recognition receptors that help them identify and phagocytose pathogens, leading to their destruction. Classical monocytes also contribute to inflammation by producing several pro-inflammatory cytokines including interleukins and tumor necrosis factors. @@ -34281,7 +35060,7 @@ In response to specific signals from tissues under pathological conditions, such - This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. Classical monocytes are a subtype of monocytes that are characterized by high CD14 but no CD16 expression. Emerging from the bone marrow and entering the bloodstream, these cells play central roles in immune responses and regulation of inflammation. CD14-positive CD16-negative monocytes form the majority of circulating monocytes in the body, typically contributing to around 80-90% of the total monocyte pool. The primary function of the classical monocytes is to serve in the frontline of host defense against infections. They are primed to migrate to sites of infection, and they express pattern recognition receptors that help them identify and phagocytose pathogens, leading to their destruction. Classical monocytes also contribute to inflammation by producing several pro-inflammatory cytokines including interleukins and tumor necrosis factors. @@ -34322,7 +35101,6 @@ In response to specific signals from tissues under pathological conditions, such - @@ -34452,7 +35230,7 @@ In response to specific signals from tissues under pathological conditions, such - + @@ -34491,11 +35269,11 @@ In response to specific signals from tissues under pathological conditions, such - + An elicited macrophage that is recruited into the tissues in response to injury and infection as part of an inflammatory response, expresses high levels of pro-inflammatory cytokines, ROS and NO, and shows potent microbicidal activity. - This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. Inflammatory macrophages, also sometimes referred to as M1 or classically activated macrophages, play an important role in the inflammatory response. The M1/M2 classification is based upon macrophage polarization rather than macrophage location and refers to macrophage activation towards either a more inflammatory or more resolving phenotype, respectively, although the functional diversity of macrophages is more nuanced than such a dichotomy suggests. Inflammatory macrophages are derived from monocytes recruited to a site of infection or injury. M1 macrophages are classically activated, typically by IFN-γ or lipopolysaccharide (LPS). Upon sensing signs of inflammation, they quickly respond by increasing their pro-inflammatory activity. They achieve this by producing a range of signaling molecules, such as nitric oxide, reactive oxygen species, and numerous cytokines such as tumor necrosis factor-alpha (TNF-alpha) and interleukin-1, -6 and -12. The release of these potent molecules helps to recruit other immune cells to the site, killing off pathogenic organisms and facilitation inflammation. At the same time, M1 macrophages can also present antigens to T cells, thereby helping to induce an adaptive immune response. Over time, these macrophages may transition in phenotype and function to help resolve the inflammation and promote tissue repair. @@ -34524,7 +35302,7 @@ Despite the beneficial role of inflammatory macrophages in dealing with pathogen - This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. Inflammatory macrophages, also sometimes referred to as M1 or classically activated macrophages, play an important role in the inflammatory response. The M1/M2 classification is based upon macrophage polarization rather than macrophage location and refers to macrophage activation towards either a more inflammatory or more resolving phenotype, respectively, although the functional diversity of macrophages is more nuanced than such a dichotomy suggests. Inflammatory macrophages are derived from monocytes recruited to a site of infection or injury. M1 macrophages are classically activated, typically by IFN-γ or lipopolysaccharide (LPS). Upon sensing signs of inflammation, they quickly respond by increasing their pro-inflammatory activity. They achieve this by producing a range of signaling molecules, such as nitric oxide, reactive oxygen species, and numerous cytokines such as tumor necrosis factor-alpha (TNF-alpha) and interleukin-1, -6 and -12. The release of these potent molecules helps to recruit other immune cells to the site, killing off pathogenic organisms and facilitation inflammation. At the same time, M1 macrophages can also present antigens to T cells, thereby helping to induce an adaptive immune response. Over time, these macrophages may transition in phenotype and function to help resolve the inflammation and promote tissue repair. @@ -34728,7 +35506,6 @@ Despite the beneficial role of inflammatory macrophages in dealing with pathogen - @@ -34945,7 +35722,6 @@ Despite the beneficial role of inflammatory macrophages in dealing with pathogen - @@ -35036,7 +35812,6 @@ Despite the beneficial role of inflammatory macrophages in dealing with pathogen - @@ -35139,7 +35914,6 @@ Despite the beneficial role of inflammatory macrophages in dealing with pathogen - @@ -35256,7 +36030,6 @@ Despite the beneficial role of inflammatory macrophages in dealing with pathogen - @@ -35357,7 +36130,6 @@ Despite the beneficial role of inflammatory macrophages in dealing with pathogen - @@ -35486,6 +36258,13 @@ Despite the beneficial role of inflammatory macrophages in dealing with pathogen A tissue-resident macrophage found in the central nervous system. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Central Nervous System (CNS) macrophages represent an integral part of the brain's innate immune system. These immune cells play crucial roles in maintenance and regulation, homeostasis, and disease response, thereby helping in the overall cognitive functioning of an organism. +There are different macrophage populations in the CNS, often classified into microglial cells, which reside in the parenchyma, and non-parenchymal macrophages at the interface between the brain and the periphery, including the perivascular spaces, the choroid plexus, and the meninges. CNS macrophages are derived from erythromyeloid progenitors in the yolk sac. CNS macrophages have distinct morphologies: Meningeal and perivascular macrophages have a more elongated shape than microglia, which are characterized by a small cell body with fine processes; in contrast, choroid plexus macrophages typically have a stellate shape. +Microglia are the most abundant abundant mononuclear phagocytes and have been shown to play a number of physiological roles, including proinflammatory and anti-inflammatory functions, synaptic pruning and remodeling, and apoptotic cell removal through phagocytosis. Non-parenchymal CAMs primarily support the barrier function against external antigens. Meningeal macrophages have been shown to respond to peripheral microbial challenges and to protect the brain against fatal viral infection. +CNS macrophages are also involved in the initiation and progression of many neurological diseases, such as Alzheimer's disease and Parkinson's disease as well as multiple sclerosis. + https://cellxgene.cziscience.com/cellguide/CL_0000878 CNS macrophage central nervous system macrophage @@ -35503,6 +36282,20 @@ Despite the beneficial role of inflammatory macrophages in dealing with pathogen GO_REF:0000031 PMID:16322748 + + + + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Central Nervous System (CNS) macrophages represent an integral part of the brain's innate immune system. These immune cells play crucial roles in maintenance and regulation, homeostasis, and disease response, thereby helping in the overall cognitive functioning of an organism. +There are different macrophage populations in the CNS, often classified into microglial cells, which reside in the parenchyma, and non-parenchymal macrophages at the interface between the brain and the periphery, including the perivascular spaces, the choroid plexus, and the meninges. CNS macrophages are derived from erythromyeloid progenitors in the yolk sac. CNS macrophages have distinct morphologies: Meningeal and perivascular macrophages have a more elongated shape than microglia, which are characterized by a small cell body with fine processes; in contrast, choroid plexus macrophages typically have a stellate shape. +Microglia are the most abundant abundant mononuclear phagocytes and have been shown to play a number of physiological roles, including proinflammatory and anti-inflammatory functions, synaptic pruning and remodeling, and apoptotic cell removal through phagocytosis. Non-parenchymal CAMs primarily support the barrier function against external antigens. Meningeal macrophages have been shown to respond to peripheral microbial challenges and to protect the brain against fatal viral infection. +CNS macrophages are also involved in the initiation and progression of many neurological diseases, such as Alzheimer's disease and Parkinson's disease as well as multiple sclerosis. + DOI:10.1007/s00281-013-0382-8 + DOI:10.1016/j.immuni.2022.10.005 + DOI:10.1016/j.tins.2021.07.002 + DOI:10.1038/s41583-019-0201-x + @@ -35543,6 +36336,7 @@ Despite the beneficial role of inflammatory macrophages in dealing with pathogen MM MnMΦ sdΜΦ + meningeal macrophage @@ -35673,7 +36467,6 @@ Despite the beneficial role of inflammatory macrophages in dealing with pathogen - @@ -36114,7 +36907,6 @@ Despite the beneficial role of inflammatory macrophages in dealing with pathogen - @@ -36141,6 +36933,7 @@ Despite the beneficial role of inflammatory macrophages in dealing with pathogen An immature myeloid leukocyte of heterogeneous phenotype found particularly in cancer and sepsis patients that is capable of suppressing activity of T cells in ex vivo assays. This cell type is CD45-positive, CD11b-positive. + Markers: Mouse: CD11b+GR1+CD31+; Human: CD34+ CD33+CD15-CD13+. (According to some reports in humans these cells are iNOS+ARG1+IL13+IFNg+); location: In cancerous tissue; in the blood and lymphoid organs in sepsis. myeloid suppressor cell @@ -36196,7 +36989,7 @@ Despite the beneficial role of inflammatory macrophages in dealing with pathogen An elicited macrophage characterized by low production of pro-inflammatory and Th1 polarizing cytokines and high expression of arginase-1, and associated with tissue remodelling. - This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. Alternatively activated macrophages, also referred to as M2 macrophages, are immune cells originating from monocytes. The M1/M2 classification is based upon macrophage polarization rather than macrophage location and refers to macrophage activation towards either a more inflammatory or more resolving phenotype, respectively, although the functional diversity of macrophages is more nuanced than such a dichotomy suggests. M2 macrophages cells are differentiated from their precursors generally in response to Th2 cytokines, such as interleukin-4 (IL-4), interleukin-10 (IL-10), and interleukin-13 (IL-13). Tissue-resident macrophages are also sometimes said to have an “M2-like” phenotype. M2 macrophages play key roles in immunoregulation and disease resolution. @@ -36226,7 +37019,7 @@ However, dysfunction of M2 macrophages can be harmful. Alternatively activated m - This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. Alternatively activated macrophages, also referred to as M2 macrophages, are immune cells originating from monocytes. The M1/M2 classification is based upon macrophage polarization rather than macrophage location and refers to macrophage activation towards either a more inflammatory or more resolving phenotype, respectively, although the functional diversity of macrophages is more nuanced than such a dichotomy suggests. M2 macrophages cells are differentiated from their precursors generally in response to Th2 cytokines, such as interleukin-4 (IL-4), interleukin-10 (IL-10), and interleukin-13 (IL-13). Tissue-resident macrophages are also sometimes said to have an “M2-like” phenotype. M2 macrophages play key roles in immunoregulation and disease resolution. @@ -36378,7 +37171,6 @@ However, dysfunction of M2 macrophages can be harmful. Alternatively activated m - @@ -38099,6 +38891,7 @@ However, dysfunction of M2 macrophages can be harmful. Alternatively activated m Tc1 T-lymphocyte Th1 CD8-positive T cell Th1 non-TFH CD8-positive T cell + This cell type is compatible with the HIPC Lyoplate markers for 'Tc1 CD8+ T cell', but its logical definition includes additional known characteristics of Tc1 T cells. Tc1 cell @@ -38800,6 +39593,7 @@ However, dysfunction of M2 macrophages can be harmful. Alternatively activated m activated CD4-negative, CD8-negative type I NK T-cell activated CD4-negative, CD8-negative type I NK T-lymphocyte activated CD4-negative, CD8-negative type I NKT cell + activated CD4-negative, CD8-negative type I NK T cell @@ -39399,7 +40193,6 @@ However, dysfunction of M2 macrophages can be harmful. Alternatively activated m - @@ -39474,7 +40267,6 @@ However, dysfunction of M2 macrophages can be harmful. Alternatively activated m - @@ -39571,7 +40363,6 @@ However, dysfunction of M2 macrophages can be harmful. Alternatively activated m - @@ -40043,6 +40834,7 @@ However, dysfunction of M2 macrophages can be harmful. Alternatively activated m A lymphocyte of B lineage with the commitment to express an immunoglobulin complex. + Types of B lineage lymphocytes include B cells and antibody secreting cells (plasmablasts and plasma cells). Lymphocytes of B cell lineage can be distinguished from those of T cell lineage by their lack of CD3e (as part of the T cell receptor complex). lymphocyte of B lineage @@ -43239,6 +44031,7 @@ However, dysfunction of M2 macrophages can be harmful. Alternatively activated m + CD71-positive common myeloid precursor OR CD7-negative lymphoid precursor OR CD7-positive lymphoid Originally described in the dendritic cell ontology (DC_CL:1100000)(PMID:19243617). CD34-positive, CD38-positive common myeloid progenitor OR CD34-positive, CD38-positive common lymphoid progenitor @@ -43349,9 +44142,9 @@ However, dysfunction of M2 macrophages can be harmful. Alternatively activated m - Immature CD8_alpha-negative CD11b-positive dendritic cell is a CD8_alpha-negative CD11b-positive dendritic cell that is CD80-low, CD86-low, and MHCII-low. + Immature CD8-alpha-negative CD11b-positive dendritic cell is a CD8-alpha-negative CD11b-positive dendritic cell that is CD80-low, CD86-low, and MHCII-low. Originally described in the dendritic cell ontology (DC_CL:0000010)(PMID:19243617). - immature CD8_alpha-negative CD11b-positive dendritic cell + immature CD8-alpha-negative CD11b-positive dendritic cell @@ -43362,7 +44155,7 @@ However, dysfunction of M2 macrophages can be harmful. Alternatively activated m - Immature CD8_alpha-negative CD11b-positive dendritic cell is a CD8_alpha-negative CD11b-positive dendritic cell that is CD80-low, CD86-low, and MHCII-low. + Immature CD8-alpha-negative CD11b-positive dendritic cell is a CD8-alpha-negative CD11b-positive dendritic cell that is CD80-low, CD86-low, and MHCII-low. GOC:amm GOC:tfm GO_REF:0000031 @@ -43439,11 +44232,11 @@ However, dysfunction of M2 macrophages can be harmful. Alternatively activated m - CD8_alpha-negative CD11b-negative dendritic cell is a conventional dendritic cell that is CD11b-negative, CD4-negative CD8_alpha-negative and is CD205-positive. This cell is able to cross- present antigen to CD8-alpha-positive T cells. + CD8-alpha-negative CD11b-negative dendritic cell is a conventional dendritic cell that is CD11b-negative, CD4-negative CD8-alpha-negative and is CD205-positive. This cell is able to cross- present antigen to CD8-alpha-positive T cells. DC.8-4-11b- triple negative dendritic cell These markers are associated with mouse cells. Originally described in the dendritic cell ontology (DC_CL:0000011)(PMID:19243617). - CD8_alpha-negative CD11b-negative dendritic cell + CD8-alpha-negative CD11b-negative dendritic cell @@ -43454,7 +44247,7 @@ However, dysfunction of M2 macrophages can be harmful. Alternatively activated m - CD8_alpha-negative CD11b-negative dendritic cell is a conventional dendritic cell that is CD11b-negative, CD4-negative CD8_alpha-negative and is CD205-positive. This cell is able to cross- present antigen to CD8-alpha-positive T cells. + CD8-alpha-negative CD11b-negative dendritic cell is a conventional dendritic cell that is CD11b-negative, CD4-negative CD8-alpha-negative and is CD205-positive. This cell is able to cross- present antigen to CD8-alpha-positive T cells. GOC:amm GO_REF:0000031 PMCID:PMC2346585 @@ -43525,7 +44318,7 @@ However, dysfunction of M2 macrophages can be harmful. Alternatively activated m - CD8_alpha-negative CD11b-positive dendritic cell is a conventional dendritic cell that is CD11b-positive, CD4-positive and is CD205-negative and CD8_alpha-negative. + CD8-alpha-negative CD11b-positive dendritic cell is a conventional dendritic cell that is CD11b-positive, CD4-positive and is CD205-negative and CD8-alpha-negative. DC.4+ Defined as having a disposition to secreting anti-inflammatory cytokines. These markers are associated with mouse cells. Originally described in the dendritic cell ontology (DC_CL:0000012)(PMID:19243617). CD4-positive CD11b-positive dendritic cell @@ -43533,7 +44326,7 @@ However, dysfunction of M2 macrophages can be harmful. Alternatively activated m - CD8_alpha-negative CD11b-positive dendritic cell is a conventional dendritic cell that is CD11b-positive, CD4-positive and is CD205-negative and CD8_alpha-negative. + CD8-alpha-negative CD11b-positive dendritic cell is a conventional dendritic cell that is CD11b-positive, CD4-positive and is CD205-negative and CD8-alpha-negative. GOC:amm GOC:tfm GO_REF:0000031 @@ -43624,10 +44417,10 @@ However, dysfunction of M2 macrophages can be harmful. Alternatively activated m - CD8_alpha-positive CD11b-negative dendritic cell is a conventional dendritic cell that is CD11b-negative, CD4-negative and is CD205-positive and CD8_alpha-positive. + CD8-alpha-positive CD11b-negative dendritic cell is a conventional dendritic cell that is CD11b-negative, CD4-negative and is CD205-positive and CD8-alpha-positive. DC.8+ Cells are defined as having a disposition to secreting inflammatory cytokines. Originally described in the dendritic cell ontology (DC_CL:0000013)(PMID:19243617). - CD8_alpha-positive CD11b-negative dendritic cell + CD8-alpha-positive CD11b-negative dendritic cell @@ -43638,7 +44431,7 @@ However, dysfunction of M2 macrophages can be harmful. Alternatively activated m - CD8_alpha-positive CD11b-negative dendritic cell is a conventional dendritic cell that is CD11b-negative, CD4-negative and is CD205-positive and CD8_alpha-positive. + CD8-alpha-positive CD11b-negative dendritic cell is a conventional dendritic cell that is CD11b-negative, CD4-negative and is CD205-positive and CD8-alpha-positive. GOC:amm GOC:tfm GO_REF:0000031 @@ -43671,9 +44464,9 @@ However, dysfunction of M2 macrophages can be harmful. Alternatively activated m - Immature CD8_alpha-negative CD11b-negative dendritic cell is a CD8_alpha-negative CD11b-negative dendritic cell that is CD80-low, CD86-low, and MHCII-low. + Immature CD8-alpha-negative CD11b-negative dendritic cell is a CD8-alpha-negative CD11b-negative dendritic cell that is CD80-low, CD86-low, and MHCII-low. These markers are associated with mouse cells. Originally described in the dendritic cell ontology (DC_CL:0000014)(PMID:19243617). - immature CD8_alpha-negative CD11b-negative dendritic cell + immature CD8-alpha-negative CD11b-negative dendritic cell @@ -43684,7 +44477,7 @@ However, dysfunction of M2 macrophages can be harmful. Alternatively activated m - Immature CD8_alpha-negative CD11b-negative dendritic cell is a CD8_alpha-negative CD11b-negative dendritic cell that is CD80-low, CD86-low, and MHCII-low. + Immature CD8-alpha-negative CD11b-negative dendritic cell is a CD8-alpha-negative CD11b-negative dendritic cell that is CD80-low, CD86-low, and MHCII-low. GOC:amm GO_REF:0000031 PMCID:PMC2346585 @@ -43730,9 +44523,9 @@ However, dysfunction of M2 macrophages can be harmful. Alternatively activated m - Mature CD8_alpha-negative CD11b-negative dendritic cell is a CD8_alpha-negative CD11b-negative dendritic cell that is CD80-high, CD86-high, MHCII-high and is CD83-positive. + Mature CD8-alpha-negative CD11b-negative dendritic cell is a CD8-alpha-negative CD11b-negative dendritic cell that is CD80-high, CD86-high, MHCII-high and is CD83-positive. These markers are associated with mouse cells. Defined as having a disposition to secretion of anti-inflammatory cytokines. Originally described in the dendritic cell ontology (DC_CL:0000015)(PMID:19243617). - mature CD8_alpha-negative CD11b-negative dendritic cell + mature CD8-alpha-negative CD11b-negative dendritic cell @@ -43743,7 +44536,7 @@ However, dysfunction of M2 macrophages can be harmful. Alternatively activated m - Mature CD8_alpha-negative CD11b-negative dendritic cell is a CD8_alpha-negative CD11b-negative dendritic cell that is CD80-high, CD86-high, MHCII-high and is CD83-positive. + Mature CD8-alpha-negative CD11b-negative dendritic cell is a CD8-alpha-negative CD11b-negative dendritic cell that is CD80-high, CD86-high, MHCII-high and is CD83-positive. GOC:amm GOC:tfm GO_REF:0000031 @@ -43786,9 +44579,9 @@ However, dysfunction of M2 macrophages can be harmful. Alternatively activated m - Mature CD8_alpha-negative CD11b-positive dendritic cell is a CD8_alpha-negative CD11b-positive dendritic cell that is CD80-high, CD86-high, MHCII-high and is CD83-positive. + Mature CD8-alpha-negative CD11b-positive dendritic cell is a CD8-alpha-negative CD11b-positive dendritic cell that is CD80-high, CD86-high, MHCII-high and is CD83-positive. Originally described in the dendritic cell ontology (DC_CL:0000016)(PMID:19243617). - mature CD8_alpha-negative CD11b-positive dendritic cell + mature CD8-alpha-negative CD11b-positive dendritic cell @@ -43799,7 +44592,7 @@ However, dysfunction of M2 macrophages can be harmful. Alternatively activated m - Mature CD8_alpha-negative CD11b-positive dendritic cell is a CD8_alpha-negative CD11b-positive dendritic cell that is CD80-high, CD86-high, MHCII-high and is CD83-positive. + Mature CD8-alpha-negative CD11b-positive dendritic cell is a CD8-alpha-negative CD11b-positive dendritic cell that is CD80-high, CD86-high, MHCII-high and is CD83-positive. GOC:amm GOC:tfm GO_REF:0000031 @@ -43832,9 +44625,9 @@ However, dysfunction of M2 macrophages can be harmful. Alternatively activated m - Immature CD8_alpha-positive CD11b-negative dendritic cell is a CD8_alpha-positive CD11b-negative dendritic cell that is CD80-low, CD86-low, and MHCII-low. + Immature CD8-alpha-positive CD11b-negative dendritic cell is a CD8-alpha-positive CD11b-negative dendritic cell that is CD80-low, CD86-low, and MHCII-low. Originally described in the dendritic cell ontology (DC_CL:0000017)(PMID:19243617). - immature CD8_alpha-positive CD11b-negative dendritic cell + immature CD8-alpha-positive CD11b-negative dendritic cell @@ -43845,7 +44638,7 @@ However, dysfunction of M2 macrophages can be harmful. Alternatively activated m - Immature CD8_alpha-positive CD11b-negative dendritic cell is a CD8_alpha-positive CD11b-negative dendritic cell that is CD80-low, CD86-low, and MHCII-low. + Immature CD8-alpha-positive CD11b-negative dendritic cell is a CD8-alpha-positive CD11b-negative dendritic cell that is CD80-low, CD86-low, and MHCII-low. GOC:amm GOC:tfm GO_REF:0000031 @@ -43888,9 +44681,9 @@ However, dysfunction of M2 macrophages can be harmful. Alternatively activated m - Mature CD8_alpha-positive CD11b-negative dendritic cell is a CD8_alpha-positive CD11b-negative dendritic cell that is CD80-high, CD86-high, MHCII-high and is CD83-positive. + Mature CD8-alpha-positive CD11b-negative dendritic cell is a CD8-alpha-positive CD11b-negative dendritic cell that is CD80-high, CD86-high, MHCII-high and is CD83-positive. Originally described in the dendritic cell ontology (DC_CL:0000018)(PMID:19243617). - mature CD8_alpha-positive CD11b-negative dendritic cell + mature CD8-alpha-positive CD11b-negative dendritic cell @@ -43901,7 +44694,7 @@ However, dysfunction of M2 macrophages can be harmful. Alternatively activated m - Mature CD8_alpha-positive CD11b-negative dendritic cell is a CD8_alpha-positive CD11b-negative dendritic cell that is CD80-high, CD86-high, MHCII-high and is CD83-positive. + Mature CD8-alpha-positive CD11b-negative dendritic cell is a CD8-alpha-positive CD11b-negative dendritic cell that is CD80-high, CD86-high, MHCII-high and is CD83-positive. GOC:amm GO_REF:0000031 PMCID:PMC2346585 @@ -44097,7 +44890,6 @@ However, dysfunction of M2 macrophages can be harmful. Alternatively activated m - @@ -44331,6 +45123,7 @@ However, dysfunction of M2 macrophages can be harmful. Alternatively activated m + Originally described in the dendritic cell ontology (DC_CL:1110000)(PMID:19243617). CD7-negative lymphoid progenitor OR granulocyte monocyte progenitor @@ -44477,9 +45270,9 @@ However, dysfunction of M2 macrophages can be harmful. Alternatively activated m - CD8_alpha-low Langerhans cell is a Langerhans cell that is CD205-high and is CD8_alpha-low. + CD8-alpha-low Langerhans cell is a Langerhans cell that is CD205-high and is CD8-alpha-low. These markers are associated with mouse cells. Originally described in the dendritic cell ontology (DC_CL:0000027)(PMID:19243617). They are also CD205-high, CD281-positive (TLR1), CD282-positive (TLR2), CD283-positive (TLR3), CD285-positive (TLR5), CD286-positive (TLR6), and CD289-positive (TLR9). - CD8_alpha-low Langerhans cell + CD8-alpha-low Langerhans cell @@ -44490,7 +45283,7 @@ However, dysfunction of M2 macrophages can be harmful. Alternatively activated m - CD8_alpha-low Langerhans cell is a Langerhans cell that is CD205-high and is CD8_alpha-low. + CD8-alpha-low Langerhans cell is a Langerhans cell that is CD205-high and is CD8-alpha-low. GOC:amm GO_REF:0000031 PMCID:PMC2346585 @@ -44624,9 +45417,9 @@ However, dysfunction of M2 macrophages can be harmful. Alternatively activated m - Immature CD8_alpha-low Langerhans cell is a CD8_alpha-low Langerhans cell that is CD80-low, CD86-low, and MHCII-low. + Immature CD8-alpha-low Langerhans cell is a CD8-alpha-low Langerhans cell that is CD80-low, CD86-low, and MHCII-low. These markers are associated with mouse cells. Originally described in the dendritic cell ontology (DC_CL:0000030)(PMID:19243617). - immature CD8_alpha-low Langerhans cell + immature CD8-alpha-low Langerhans cell @@ -44637,7 +45430,7 @@ However, dysfunction of M2 macrophages can be harmful. Alternatively activated m - Immature CD8_alpha-low Langerhans cell is a CD8_alpha-low Langerhans cell that is CD80-low, CD86-low, and MHCII-low. + Immature CD8-alpha-low Langerhans cell is a CD8-alpha-low Langerhans cell that is CD80-low, CD86-low, and MHCII-low. GOC:amm GOC:tfm GO_REF:0000031 @@ -44657,6 +45450,7 @@ However, dysfunction of M2 macrophages can be harmful. Alternatively activated m + Originally described in the dendritic cell ontology (DC_CL:1111000)(PMID:19243617). CD115-positive monocyte OR common dendritic progenitor @@ -44698,9 +45492,9 @@ However, dysfunction of M2 macrophages can be harmful. Alternatively activated m - Mature CD8_alpha-low Langerhans cell is a CD8_alpha-low Langerhans cell that that is CD80-high, CD86-high, MHCII-high and is CD83-positive. + Mature CD8-alpha-low Langerhans cell is a CD8-alpha-low Langerhans cell that that is CD80-high, CD86-high, MHCII-high and is CD83-positive. These markers are associated with mouse cells. Originally described in the dendritic cell ontology (DC_CL:0000031)(PMID:19243617). - mature CD8_alpha-low Langerhans cell + mature CD8-alpha-low Langerhans cell @@ -44711,7 +45505,7 @@ However, dysfunction of M2 macrophages can be harmful. Alternatively activated m - Mature CD8_alpha-low Langerhans cell is a CD8_alpha-low Langerhans cell that that is CD80-high, CD86-high, MHCII-high and is CD83-positive. + Mature CD8-alpha-low Langerhans cell is a CD8-alpha-low Langerhans cell that that is CD80-high, CD86-high, MHCII-high and is CD83-positive. GOC:amm GO_REF:0000031 PMCID:PMC2346585 @@ -44747,7 +45541,6 @@ However, dysfunction of M2 macrophages can be harmful. Alternatively activated m - @@ -44827,7 +45620,6 @@ However, dysfunction of M2 macrophages can be harmful. Alternatively activated m - @@ -45010,7 +45802,6 @@ However, dysfunction of M2 macrophages can be harmful. Alternatively activated m - @@ -45135,7 +45926,6 @@ However, dysfunction of M2 macrophages can be harmful. Alternatively activated m - @@ -45331,7 +46121,6 @@ However, dysfunction of M2 macrophages can be harmful. Alternatively activated m - @@ -45401,7 +46190,6 @@ However, dysfunction of M2 macrophages can be harmful. Alternatively activated m - @@ -45520,9 +46308,7 @@ However, dysfunction of M2 macrophages can be harmful. Alternatively activated m - - @@ -45665,6 +46451,7 @@ However, dysfunction of M2 macrophages can be harmful. Alternatively activated m + Originally described in the dendritic cell ontology (DC_CL:1111100)(PMID:19243617). CD117-positive common myeloid progenitor OR CD217-positive common lymphoid progenitor @@ -45747,7 +46534,6 @@ However, dysfunction of M2 macrophages can be harmful. Alternatively activated m - Granule cell that is part of the cerebral cortex. cortical granule cell @@ -45831,7 +46617,14 @@ However, dysfunction of M2 macrophages can be harmful. Alternatively activated m A connective tissue cell found in bone. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Bone cells, also known as osteocytes, form the building blocks of the skeletal system. They represent the most common type of bone cell, making up approximately 95% of the total bone cell population in mature adult bone tissue. Osteocytes are a stellate shape with numerous long, slender dendritic processes. +The formation of bone is a complex process involving the action of osteoclasts - cells that break down and reabsorb old bone, followed by osteoblasts that rebuild the bone. Osteocytes serve as coordinators for these two types of bone cells to ensure a balance in the bone remodeling process, contributing to maintaining both bone strength and mineral homeostasis. +The primary functions of osteocytes involve the creation, maintenance, and repair of bone tissue. They ensure that bone remodeling is performed by forming a network within the bone and communicating with other cells to help them respond to mechanical strain and damage. +A remarkable aspect of osteocytes is their ability to perceive mechanical forces, translating them into biochemical signals that regulate bone remodeling and adaptation. Defects in osteocyte function, aside from other bone cells, have been associated with several bone disorders such as osteoporosis, renal osteodystrophy, and skeletal manifestations of diabetes. 2011-11-16T04:28:16Z + https://cellxgene.cziscience.com/cellguide/CL_0001035 bone cell @@ -45843,6 +46636,20 @@ However, dysfunction of M2 macrophages can be harmful. Alternatively activated m GOC:add GO_REF:0000034 + + + + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Bone cells, also known as osteocytes, form the building blocks of the skeletal system. They represent the most common type of bone cell, making up approximately 95% of the total bone cell population in mature adult bone tissue. Osteocytes are a stellate shape with numerous long, slender dendritic processes. +The formation of bone is a complex process involving the action of osteoclasts - cells that break down and reabsorb old bone, followed by osteoblasts that rebuild the bone. Osteocytes serve as coordinators for these two types of bone cells to ensure a balance in the bone remodeling process, contributing to maintaining both bone strength and mineral homeostasis. +The primary functions of osteocytes involve the creation, maintenance, and repair of bone tissue. They ensure that bone remodeling is performed by forming a network within the bone and communicating with other cells to help them respond to mechanical strain and damage. +A remarkable aspect of osteocytes is their ability to perceive mechanical forces, translating them into biochemical signals that regulate bone remodeling and adaptation. Defects in osteocyte function, aside from other bone cells, have been associated with several bone disorders such as osteoporosis, renal osteodystrophy, and skeletal manifestations of diabetes. + DOI:10.1007/s00795-015-0099-y + DOI:10.1007/s11914-012-0105-4 + DOI:10.1016/j.jot.2021.04.005 + DOI:10.1038/s41413-020-0099-y + @@ -46650,7 +47457,6 @@ However, dysfunction of M2 macrophages can be harmful. Alternatively activated m - @@ -46925,7 +47731,6 @@ However, dysfunction of M2 macrophages can be harmful. Alternatively activated m - @@ -47546,7 +48351,6 @@ However, dysfunction of M2 macrophages can be harmful. Alternatively activated m - @@ -47812,7 +48616,6 @@ However, dysfunction of M2 macrophages can be harmful. Alternatively activated m - @@ -47867,7 +48670,6 @@ However, dysfunction of M2 macrophages can be harmful. Alternatively activated m - @@ -47986,7 +48788,6 @@ However, dysfunction of M2 macrophages can be harmful. Alternatively activated m - @@ -48129,7 +48930,6 @@ However, dysfunction of M2 macrophages can be harmful. Alternatively activated m - @@ -48334,7 +49134,6 @@ However, dysfunction of M2 macrophages can be harmful. Alternatively activated m - @@ -48549,7 +49348,6 @@ However, dysfunction of M2 macrophages can be harmful. Alternatively activated m - @@ -49344,7 +50142,6 @@ However, dysfunction of M2 macrophages can be harmful. Alternatively activated m - @@ -49431,7 +50228,6 @@ However, dysfunction of M2 macrophages can be harmful. Alternatively activated m - @@ -49760,7 +50556,6 @@ However, dysfunction of M2 macrophages can be harmful. Alternatively activated m - @@ -49910,7 +50705,6 @@ However, dysfunction of M2 macrophages can be harmful. Alternatively activated m - @@ -50365,7 +51159,6 @@ However, dysfunction of M2 macrophages can be harmful. Alternatively activated m - @@ -50444,7 +51237,6 @@ However, dysfunction of M2 macrophages can be harmful. Alternatively activated m - @@ -50601,7 +51393,6 @@ However, dysfunction of M2 macrophages can be harmful. Alternatively activated m - @@ -50652,7 +51443,6 @@ However, dysfunction of M2 macrophages can be harmful. Alternatively activated m - @@ -50711,7 +51501,6 @@ However, dysfunction of M2 macrophages can be harmful. Alternatively activated m - @@ -50798,7 +51587,6 @@ However, dysfunction of M2 macrophages can be harmful. Alternatively activated m - @@ -50893,7 +51681,6 @@ However, dysfunction of M2 macrophages can be harmful. Alternatively activated m - @@ -50964,7 +51751,6 @@ However, dysfunction of M2 macrophages can be harmful. Alternatively activated m - @@ -51031,7 +51817,6 @@ However, dysfunction of M2 macrophages can be harmful. Alternatively activated m - @@ -51115,7 +51900,6 @@ However, dysfunction of M2 macrophages can be harmful. Alternatively activated m - @@ -53710,14 +54494,14 @@ However, dysfunction of M2 macrophages can be harmful. Alternatively activated m - A conventional thymic dendritic cell that is CD8alpha-positive. + A conventional thymic dendritic cell that is CD8-alpha-positive. 2010-06-07T02:48:36Z CD8alpha-alpha-positive thymic conventional dendritic cell DC.8+.Th - CD8alpha-positive thymic conventional dendritic cell + CD8-alpha-positive thymic conventional dendritic cell @@ -53728,7 +54512,7 @@ However, dysfunction of M2 macrophages can be harmful. Alternatively activated m - A conventional thymic dendritic cell that is CD8alpha-positive. + A conventional thymic dendritic cell that is CD8-alpha-positive. GOC:tfm PMID:19273629 http://www.immgen.org/index_content.html @@ -53862,6 +54646,12 @@ However, dysfunction of M2 macrophages can be harmful. Alternatively activated m + + + + + + A squamous pulmonary alveolar epithelial cell that is flattened and branched. A pulmonary alveolar type 1 cell covers more than 98% of the alveolar surface. This large cell has thin (50-100 nm) cytoplasmic extensions to form the air-blood barrier essential for normal gas exchange. @@ -53883,6 +54673,7 @@ However, dysfunction of M2 macrophages can be harmful. Alternatively activated m ATI + The marker set AGER can identify the Human cell type pulmonary alveolar type 1 cell in the Lung with a confidence of 0.85 (NS-Forest FBeta value). pulmonary alveolar type 1 cell @@ -53913,6 +54704,12 @@ However, dysfunction of M2 macrophages can be harmful. Alternatively activated m ATI + + + + The marker set AGER can identify the Human cell type pulmonary alveolar type 1 cell in the Lung with a confidence of 0.85 (NS-Forest FBeta value). + https://doi.org/10.5281/zenodo.11165918 + @@ -53937,12 +54734,19 @@ However, dysfunction of M2 macrophages can be harmful. Alternatively activated m + + + + + + + A pulmonary alveolar epithelial cell that modulates the fluid surrounding the alveolar epithelium by secreting and recycling surfactants. This cell type also contributes to tissue repair and can differentiate after injury into a pulmonary alveolar type 1 cell. This cuboidal cell is thicker than squamous alveolar cells, have a rounded apical surface that projects above the level of surrounding epithelium. The free surface is covered by short microvilli. @@ -53966,6 +54770,7 @@ However, dysfunction of M2 macrophages can be harmful. Alternatively activated m lung type II cell + The marker set SFTPA1 can identify the Human cell type pulmonary alveolar type 2 cell in the Lung with a confidence of 0.95 (NS-Forest FBeta value). pulmonary alveolar type 2 cell @@ -53997,6 +54802,12 @@ However, dysfunction of M2 macrophages can be harmful. Alternatively activated m ATII + + + + The marker set SFTPA1 can identify the Human cell type pulmonary alveolar type 2 cell in the Lung with a confidence of 0.95 (NS-Forest FBeta value). + https://doi.org/10.5281/zenodo.11165918 + @@ -54031,7 +54842,7 @@ However, dysfunction of M2 macrophages can be harmful. Alternatively activated m A secretory cell found in pancreatic acini that secretes digestive enzymes and mucins. This cell is a typical zymogenic cell, have a basal nucleus and basophilic cytoplasm consisting of regular arrays of granular endoplasmic reticulum with mitochondria and dense secretory granules. - This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. Pancreatic acinar cells are the functional units of the exocrine pancreas. These cells are structurally arranged in small clusters - or acini - with a small central lumen, and their primary function is to produce and secrete enzymes that facilitate digestion of proteins, carbohydrates, and fats within the small intestine. Some of the most important digestive enzymes synthesized by the pancreatic acinar cells include amylase, which digests carbohydrates, lipase, which breaks down fats, and several proteases such as trypsin and chymotrypsin which are vital for the digestion of proteins. Importantly, these enzymes are produced as proenzymes or zymogens to avoid autolysis, or the breakdown of the pancreas itself. @@ -54066,7 +54877,7 @@ Dysregulation in the function of pancreatic acinar cells can lead to severe heal - This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. Pancreatic acinar cells are the functional units of the exocrine pancreas. These cells are structurally arranged in small clusters - or acini - with a small central lumen, and their primary function is to produce and secrete enzymes that facilitate digestion of proteins, carbohydrates, and fats within the small intestine. Some of the most important digestive enzymes synthesized by the pancreatic acinar cells include amylase, which digests carbohydrates, lipase, which breaks down fats, and several proteases such as trypsin and chymotrypsin which are vital for the digestion of proteins. Importantly, these enzymes are produced as proenzymes or zymogens to avoid autolysis, or the breakdown of the pancreas itself. @@ -54145,7 +54956,7 @@ Dysregulation in the function of pancreatic acinar cells can lead to severe heal An enteroendocrine cell that produces glucagon. - This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. Type A enteroendocrine cells, also known as alpha cells or A cells, are a species of endocrine cells primarily located in the pancreatic islets of Langerhans; they have also been identified within the lining of the stomach. Functionally, these cells are pivotal in glucose metabolism and homeostasis, accounting for about 20% of the total population of cells in the pancreatic islets. The primary role of type A enteroendocrine cells involves the synthesis, storage, and secretion of the peptide hormone glucagon, which is critical in energy regulation throughout the body. In response to a decrease in blood glucose levels, the pancreatic A cells are stimulated to secrete glucagon into the bloodstream. Glucagon acts on its target cells, mainly in the liver, to stimulate glycogenolysis and gluconeogenesis processes, thereby increasing blood glucose levels back to normal. In this way, pancreatic A cells play an integral role in maintaining glucose homeostasis and preventing hypoglycemia. @@ -54154,6 +54965,7 @@ Until recently, glucagon has been considered a pancreas-specific hormone; howeve 2010-09-10T10:48:54Z FMA:62939 https://cellxgene.cziscience.com/cellguide/CL_0002067 + type A enteroendocrine cell @@ -54166,7 +54978,7 @@ Until recently, glucagon has been considered a pancreas-specific hormone; howeve - This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. Type A enteroendocrine cells, also known as alpha cells or A cells, are a species of endocrine cells primarily located in the pancreatic islets of Langerhans; they have also been identified within the lining of the stomach. Functionally, these cells are pivotal in glucose metabolism and homeostasis, accounting for about 20% of the total population of cells in the pancreatic islets. The primary role of type A enteroendocrine cells involves the synthesis, storage, and secretion of the peptide hormone glucagon, which is critical in energy regulation throughout the body. In response to a decrease in blood glucose levels, the pancreatic A cells are stimulated to secrete glucagon into the bloodstream. Glucagon acts on its target cells, mainly in the liver, to stimulate glycogenolysis and gluconeogenesis processes, thereby increasing blood glucose levels back to normal. In this way, pancreatic A cells play an integral role in maintaining glucose homeostasis and preventing hypoglycemia. @@ -54270,12 +55082,6 @@ Until recently, glucagon has been considered a pancreas-specific hormone; howeve - - - - - - Columnar cell which populate the epithelium of large intestine and absorb water. This cell is the most numerous of the epithelial cell types in the large intestine; bear apical microvilli, contain secretory granules in their apical cytoplasm; secretion appears to be largely mucins, but is also rich in antibodies of the IgA type. @@ -54392,22 +55198,39 @@ Until recently, glucagon has been considered a pancreas-specific hormone; howeve + - Infrequent type of columnar epithelial cell. This cell is characterized by the presence of a tuft of blunt, squat microvilli (approximately 120-140/cell) on the cell surface. The microvilli contain filaments that stretch into the underlying cytoplasm. They have a distinctive pear shape with a wide base and a narrow microvillous apex. Function not known. + + + + + + + A rare type of columnar epithelial cell that is part of the tracheobronchial epithelium. This cell is characterized by a distinctive tuft of apical microvilli, which extends into the cytoplasm, and a pear-shaped morphology, broad at the base and tapering to a narrow apex. It plays vital roles in chemosensation, producing cytokines like IL-25, and enhancing mucociliary clearance through acetylcholine release to support mucus movement and airway defense. + 2010-06-29T03:22:46Z pulmonary brush cell + The marker set POU2F3, HOMER3, MYB can identify the Human cell type brush cell of tracheobronchial tree in the Lung with a confidence of 0.56 (NS-Forest FBeta value). brush cell of tracheobronchial tree - Infrequent type of columnar epithelial cell. This cell is characterized by the presence of a tuft of blunt, squat microvilli (approximately 120-140/cell) on the cell surface. The microvilli contain filaments that stretch into the underlying cytoplasm. They have a distinctive pear shape with a wide base and a narrow microvillous apex. Function not known. + A rare type of columnar epithelial cell that is part of the tracheobronchial epithelium. This cell is characterized by a distinctive tuft of apical microvilli, which extends into the cytoplasm, and a pear-shaped morphology, broad at the base and tapering to a narrow apex. It plays vital roles in chemosensation, producing cytokines like IL-25, and enhancing mucociliary clearance through acetylcholine release to support mucus movement and airway defense. GOC:tfm ISBN:0517223651 PMID:15817800 + PMID:30291131 + PMID:37925434 + + + + + The marker set POU2F3, HOMER3, MYB can identify the Human cell type brush cell of tracheobronchial tree in the Lung with a confidence of 0.56 (NS-Forest FBeta value). + https://doi.org/10.5281/zenodo.11165918 @@ -54439,6 +55262,7 @@ Until recently, glucagon has been considered a pancreas-specific hormone; howeve 2010-06-29T03:38:14Z FMA:69075 ZFA:0009383 + endo-epithelial cell @@ -55038,7 +55862,6 @@ Until recently, glucagon has been considered a pancreas-specific hormone; howeve - @@ -55427,8 +56250,13 @@ Until recently, glucagon has been considered a pancreas-specific hormone; howeve A cardiac myocyte that is connected to other cardiac myocytes by transverse intercalated discs (GO:0014704) at a regular interval. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Cardiac myocytes, also known as cardiac muscle cells, form the majority of the cardiac tissue and are responsible for the contractile function of the heart. These myocytes are columnar-shaped cells with centrally located nuclei, and they exhibit visibly striated cytoplasm due to the organized array of myofibrils, which are composed of filaments of actin and myosin. Cardiac myocytes connect with each other through specialized structures called intercalated discs, facilitating electrical and mechanical continuity and enabling synchronous contraction of the heart. They also possess a high number of mitochondria to meet their high energy demand for continuous heartbeat action. +Cardiac myocytes are capable of automaticity, meaning they have the unique ability to spontaneously and rhythmically generate their electrical impulses, a characteristic led by pacemaker cells. The electrical signals initiated and propagated in these cells are responsible for heartbeats. They also respond to the electrical signals transmitted by the autonomic nervous system and chemical signals like hormones. Thus, cardiac myocytes not only participate in maintaining the heart’s function but also play a role in modulating heart rate and strength of contraction in response to the body's changing needs. Consequently, malfunction of these cells leads to serious cardiac diseases such as heart failure and arrhythmias. 2010-08-23T11:33:10Z FMA:67967 + https://cellxgene.cziscience.com/cellguide/CL_0002098 regular cardiac muscle cell regular cardiac muscle fiber regular cardiac myocyte @@ -55439,6 +56267,18 @@ Until recently, glucagon has been considered a pancreas-specific hormone; howeve A cardiac myocyte that is connected to other cardiac myocytes by transverse intercalated discs (GO:0014704) at a regular interval. GOC:tfm + + + + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Cardiac myocytes, also known as cardiac muscle cells, form the majority of the cardiac tissue and are responsible for the contractile function of the heart. These myocytes are columnar-shaped cells with centrally located nuclei, and they exhibit visibly striated cytoplasm due to the organized array of myofibrils, which are composed of filaments of actin and myosin. Cardiac myocytes connect with each other through specialized structures called intercalated discs, facilitating electrical and mechanical continuity and enabling synchronous contraction of the heart. They also possess a high number of mitochondria to meet their high energy demand for continuous heartbeat action. +Cardiac myocytes are capable of automaticity, meaning they have the unique ability to spontaneously and rhythmically generate their electrical impulses, a characteristic led by pacemaker cells. The electrical signals initiated and propagated in these cells are responsible for heartbeats. They also respond to the electrical signals transmitted by the autonomic nervous system and chemical signals like hormones. Thus, cardiac myocytes not only participate in maintaining the heart’s function but also play a role in modulating heart rate and strength of contraction in response to the body's changing needs. Consequently, malfunction of these cells leads to serious cardiac diseases such as heart failure and arrhythmias. + DOI:10.3389/fphys.2013.00102 + https://www.ncbi.nlm.nih.gov/books/NBK572070 + https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3164530 + https://www.sciencedirect.com/topics/agricultural-and-biological-sciences/cardiac-muscle + @@ -55469,6 +56309,7 @@ Until recently, glucagon has been considered a pancreas-specific hormone; howeve 2010-08-24T01:42:02Z FMA:69273 epithelial cell of zona glomerulosa of adrenal gland + type I cell of adrenal cortex @@ -55584,6 +56425,7 @@ Until recently, glucagon has been considered a pancreas-specific hormone; howeve CD38-negative naive B lymphocyte CD38-negative naive B-cell CD38-negative naive B-lymphocyte + CD38-negative naive B cell @@ -56932,8 +57774,14 @@ Until recently, glucagon has been considered a pancreas-specific hormone; howeve Regular cardiac myocyte of a cardiac atrium. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Regular atrial cardiac myocytes, also known as atrial myocytes, are specialized muscle cells found in the atria – the upper chambers of the heart. They contract and relax during the heart's cycle, modulating the pumping of blood through the atria and into the ventricles. Additionally, endowed with inherent rhythmic electrical activity, atrial myocytes contribute significantly to the initiation and propagation of the heart’s electrical impulses. +A distinguishing feature that separates atrial myocytes from other cardiac myocytes is their ability to synthesize and secrete atrial natriuretic peptide (ANP) in response to atrial stretch or dilatation. ANP acts as a potent vasodilator and diuretic, helping to maintain blood pressure and volume homeostasis. The phenomena of atrial stretch or distension, which triggers ANP release, is often in response to excess blood volume entering the heart, providing a mechanism at the cellular level which actively regulates systemic cardiovascular balance. +Like all cardiac myocytes, atrial myocytes are embedded in a dense network of connective tissue that provides structural support. These cells are characterized by a single, centrally located nucleus, and overall, have a rod-like appearance with branching ends that connect with adjacent cells to form a continuous, synchronized ensemble. Their cytoplasm is abundant with mitochondria, reflecting the high energy demand associated with constant contraction and relaxation. At the ultrastructural level, atrial myocytes display striations due to the regular arrangement of actin and myosin proteins, which facilitate the contraction process essential for the heart's pump function. 2010-08-23T11:41:03Z FMA:83108 + https://cellxgene.cziscience.com/cellguide/CL_0002129 atrial cardiac muscle cell atrial myocyte regular atrial cardiac muscle fiber @@ -56947,6 +57795,20 @@ Until recently, glucagon has been considered a pancreas-specific hormone; howeve Regular cardiac myocyte of a cardiac atrium. GOC:tfm + + + + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Regular atrial cardiac myocytes, also known as atrial myocytes, are specialized muscle cells found in the atria – the upper chambers of the heart. They contract and relax during the heart's cycle, modulating the pumping of blood through the atria and into the ventricles. Additionally, endowed with inherent rhythmic electrical activity, atrial myocytes contribute significantly to the initiation and propagation of the heart’s electrical impulses. +A distinguishing feature that separates atrial myocytes from other cardiac myocytes is their ability to synthesize and secrete atrial natriuretic peptide (ANP) in response to atrial stretch or dilatation. ANP acts as a potent vasodilator and diuretic, helping to maintain blood pressure and volume homeostasis. The phenomena of atrial stretch or distension, which triggers ANP release, is often in response to excess blood volume entering the heart, providing a mechanism at the cellular level which actively regulates systemic cardiovascular balance. +Like all cardiac myocytes, atrial myocytes are embedded in a dense network of connective tissue that provides structural support. These cells are characterized by a single, centrally located nucleus, and overall, have a rod-like appearance with branching ends that connect with adjacent cells to form a continuous, synchronized ensemble. Their cytoplasm is abundant with mitochondria, reflecting the high energy demand associated with constant contraction and relaxation. At the ultrastructural level, atrial myocytes display striations due to the regular arrangement of actin and myosin proteins, which facilitate the contraction process essential for the heart's pump function. + DOI:10.1016/j.bbamcr.2015.11.025 + DOI:10.1111/pace.14107 + DOI:10.1172/JCI25417 + https://www.sciencedirect.com/topics/agricultural-and-biological-sciences/cardiac-muscle + https://www.sciencedirect.com/topics/neuroscience/cardiac-action-potential + @@ -57209,9 +58071,15 @@ Until recently, glucagon has been considered a pancreas-specific hormone; howeve A endothelial cell of a lymphatic vessel. The border of the oak leaf-shaped endothelial cell of initial lymphatics are joined by specialized buttons. The discontinuous feature of buttons distinguishes them from zippers in collecting lymphatics, but both types of junctions are composed of proteins typical of adherens junctions and tight junctions found in the endothelium of blood vessels. Buttons seal the sides of flaps of the oak leaf-shaped endothelial cell, leaving open the tips of flaps as routes for fluid entry without disassembly and reformation of intercellular junctions. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Endothelial cells of lymphatic vessels are specialized type of cells that form the interior lining of the lymphatic system, which primarily comprises the lymph vessels and nodes. These cells play a critical role in creating a barrier between the lymphatic system and the surrounding tissues. They are structurally different from the endothelial cells of the blood vessels due to the presence of anchoring filaments and lack of a continuous basement membrane, and have a unique phenotype marked by the expression of various cell-specific markers such as Prox-1, VEGFR-3, and LYVE-1. +A significant function of these endothelial cells is to maintain the fluid balance within the body. They facilitate the uptake of excess interstitial fluid that collects in the body tissues, and ensure its transport back into the bloodstream via the lymphatic vessels. These cells also enable the absorption of fats and fat-soluble vitamins from the digestive system, and their subsequent transport in the form of chyle, a milky fluid, to the blood. +Furthermore, endothelial cells of lymphatic vessels play a pivotal role in the body's immune response. They enable the passage of lymphocytes, that are crucial for the body's defense mechanism, from the tissues into the lymph where these cells are activated to fight against foreign bodies and infections. Also, they regulate inflammation reactions by controlling the migration of inflammatory cells, and are thus involved in pathological conditions with an inflammatory component. Lastly, these cells have been noted for their involvement in various disease states related to tissue edema, metastasis, and tumor growth, thus highlighting their importance in both health and disease states. 2010-08-24T02:05:28Z BTO:0004167 FMA:68458 + https://cellxgene.cziscience.com/cellguide/CL_0002138 LEC lymphatic endothelial cell @@ -57231,6 +58099,20 @@ Until recently, glucagon has been considered a pancreas-specific hormone; howeve GOC:tfm PMID:17846148 + + + + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Endothelial cells of lymphatic vessels are specialized type of cells that form the interior lining of the lymphatic system, which primarily comprises the lymph vessels and nodes. These cells play a critical role in creating a barrier between the lymphatic system and the surrounding tissues. They are structurally different from the endothelial cells of the blood vessels due to the presence of anchoring filaments and lack of a continuous basement membrane, and have a unique phenotype marked by the expression of various cell-specific markers such as Prox-1, VEGFR-3, and LYVE-1. +A significant function of these endothelial cells is to maintain the fluid balance within the body. They facilitate the uptake of excess interstitial fluid that collects in the body tissues, and ensure its transport back into the bloodstream via the lymphatic vessels. These cells also enable the absorption of fats and fat-soluble vitamins from the digestive system, and their subsequent transport in the form of chyle, a milky fluid, to the blood. +Furthermore, endothelial cells of lymphatic vessels play a pivotal role in the body's immune response. They enable the passage of lymphocytes, that are crucial for the body's defense mechanism, from the tissues into the lymph where these cells are activated to fight against foreign bodies and infections. Also, they regulate inflammation reactions by controlling the migration of inflammatory cells, and are thus involved in pathological conditions with an inflammatory component. Lastly, these cells have been noted for their involvement in various disease states related to tissue edema, metastasis, and tumor growth, thus highlighting their importance in both health and disease states. + DOI:10.1016/j.it.2022.10.010 + DOI:10.1038/s41577-020-0281-x + DOI:10.3389/fimmu.2019.00036 + DOI:10.3389/fphys.2020.00509/full + DOI:10.3892/mco.2017.1356 + @@ -57240,10 +58122,16 @@ Until recently, glucagon has been considered a pancreas-specific hormone; howeve An endothelial cell of the vascular tree, which includes blood vessels and lymphatic vessels. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Endothelial cells of the vascular tree, commonly referred to as vascular endothelial cells, line the entire circulatory system, from the heart to the smallest capillaries. These cells have a unique, flattened shape, and are tightly bound together, forming a thin layer known as the endothelium. The endothelium is responsible for maintaining the interior surface of blood vessels, and plays a critical role in ensuring the smooth flow of blood. +Vascular endothelial cells act as a semi-permeable membrane, controlling the passage of materials and the transit of white blood cells into and out of the bloodstream. These cells are also involved in blood coagulation. When a blood vessel is damaged, endothelial cells promote clotting to prevent excessive bleeding and facilitate wound healing. Other functions include regulation of blood pressure and blood volume by releasing vasodilators and vasoconstrictors to either widen or constrict blood vessels, accordingly. +Furthermore, the endothelial cells are crucial in the formation of new blood vessels, a process known as angiogenesis. This is particularly important in wound healing and the growth of new tissues during development or after injury. In the context of diseases such as cancer, angiogenesis helps facilitate tumor growth by providing nutrients and oxygen. 2010-08-24T02:06:40Z BTO:0001854 CALOHA:TS-1106 FMA:67755 + https://cellxgene.cziscience.com/cellguide/CL_0002139 vascular endothelial cell cubodial endothelial cell of vascular tree @@ -57258,6 +58146,19 @@ Until recently, glucagon has been considered a pancreas-specific hormone; howeve GOC:tfm PMID:12768659 + + + + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Endothelial cells of the vascular tree, commonly referred to as vascular endothelial cells, line the entire circulatory system, from the heart to the smallest capillaries. These cells have a unique, flattened shape, and are tightly bound together, forming a thin layer known as the endothelium. The endothelium is responsible for maintaining the interior surface of blood vessels, and plays a critical role in ensuring the smooth flow of blood. +Vascular endothelial cells act as a semi-permeable membrane, controlling the passage of materials and the transit of white blood cells into and out of the bloodstream. These cells are also involved in blood coagulation. When a blood vessel is damaged, endothelial cells promote clotting to prevent excessive bleeding and facilitate wound healing. Other functions include regulation of blood pressure and blood volume by releasing vasodilators and vasoconstrictors to either widen or constrict blood vessels, accordingly. +Furthermore, the endothelial cells are crucial in the formation of new blood vessels, a process known as angiogenesis. This is particularly important in wound healing and the growth of new tissues during development or after injury. In the context of diseases such as cancer, angiogenesis helps facilitate tumor growth by providing nutrients and oxygen. + DOI:10.1038/s41569-022-00770-1 + DOI:10.1186/s12872-015-0124-z + DOI:10.3389/fphys.2022.863265/full + https://www.sciencedirect.com/topics/medicine-and-dentistry/vascular-endothelial-cell + @@ -57267,7 +58168,7 @@ Until recently, glucagon has been considered a pancreas-specific hormone; howeve - + @@ -57277,20 +58178,20 @@ Until recently, glucagon has been considered a pancreas-specific hormone; howeve - - A sebum secreting cell of the skin that secretes sebum into the hair follicles. + An acinar cell that is part of a skin sebaceous gland. This cell produces and secretes sebum into hair follicles. 2010-08-24T09:27:52Z - sebocyte + acinar cell of sebaceous gland BTO:0004613 FMA:70953 - acinar cell of sebaceous gland + acinar cell of skin sebaceous gland + skin sebocyte @@ -57301,8 +58202,9 @@ Until recently, glucagon has been considered a pancreas-specific hormone; howeve - A sebum secreting cell of the skin that secretes sebum into the hair follicles. + An acinar cell that is part of a skin sebaceous gland. This cell produces and secretes sebum into hair follicles. GOC:tfm + PMID:37205445 @@ -57420,8 +58322,26 @@ Until recently, glucagon has been considered a pancreas-specific hormone; howeve + + + + + + + + + + + + + + + + + + + - @@ -57429,10 +58349,16 @@ Until recently, glucagon has been considered a pancreas-specific hormone; howeve + + + + + + A multi-ciliated epithelial cell located in the trachea and bronchi, characterized by a columnar shape and motile cilia on its apical surface. These cilia facilitate mucociliary clearance by moving mucus and trapped particles toward the pharynx. - This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. Ciliated columnar cells of the tracheobronchial tree compose the inner lining of the tracheobronchial tree, the system of airways consisting of trachea, bronchi and bronchioles that allow passage of air into the lungs, where gas exchange occurs. A defining feature of these endo-epithelial cells are the tiny hair-like structures covering their surface, known as cilia. The nucleus is located at the base of the cell, and the area above it is rich in mitochondria and well-developed endoplasmic reticulum, both crucial for the energy-intensive process of cilia operation. The primary function of these ciliated cells is to keep the respiratory tract clean via mucociliary clearance or the respiratory escalator. These cells create a two-layered 'coat': The lower "sol" layer is watery where the cilia can beat in coordinated waves, and the upper "gel" layer is thick and sticky, trapping inhaled particles, such as dust, bacteria, viruses, and other potentially harmful substances. This rhythmical beating of the cilia then moves the mucus and trapped particles upwards and out of the respiratory tract, which is then either coughed out or swallowed. @@ -57440,10 +58366,12 @@ Damage or dysfunction of these ciliated cells, as seen in diseases such as prima 2010-08-24T03:38:29Z FMA:70542 https://cellxgene.cziscience.com/cellguide/CL_0002145 + ciliated columnar cell of tracheobronchial tree + The marker set C1orf194, MS4A8 can identify the Human cell type ciliated columnar cell of tracheobronchial tree in the Lung with a confidence of 0.86 (NS-Forest FBeta value). These cells possess numerous cilia on their surface, typically ranging from 200 to 300 per cell. The cilia vary in length, measuring between 6 to 7 μm in the upper airways (trachea) and becoming shorter, around 4 μm, in the smaller airways (terminal bronchioles). These cells form a two-layered 'coat' in the airway: the lower 'sol' layer is watery, allowing the cilia to beat in coordinated waves, while the upper 'gel' layer is thick and sticky, trapping inhaled particles. - ciliated columnar cell of tracheobronchial tree + multiciliated columnar cell of tracheobronchial tree @@ -57455,7 +58383,7 @@ Damage or dysfunction of these ciliated cells, as seen in diseases such as prima - This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. Ciliated columnar cells of the tracheobronchial tree compose the inner lining of the tracheobronchial tree, the system of airways consisting of trachea, bronchi and bronchioles that allow passage of air into the lungs, where gas exchange occurs. A defining feature of these endo-epithelial cells are the tiny hair-like structures covering their surface, known as cilia. The nucleus is located at the base of the cell, and the area above it is rich in mitochondria and well-developed endoplasmic reticulum, both crucial for the energy-intensive process of cilia operation. The primary function of these ciliated cells is to keep the respiratory tract clean via mucociliary clearance or the respiratory escalator. These cells create a two-layered 'coat': The lower "sol" layer is watery where the cilia can beat in coordinated waves, and the upper "gel" layer is thick and sticky, trapping inhaled particles, such as dust, bacteria, viruses, and other potentially harmful substances. This rhythmical beating of the cilia then moves the mucus and trapped particles upwards and out of the respiratory tract, which is then either coughed out or swallowed. @@ -57465,6 +58393,12 @@ Damage or dysfunction of these ciliated cells, as seen in diseases such as prima DOI:10.1152/ajplung.00329.2019 DOI:10.1159/000196486 + + + + The marker set C1orf194, MS4A8 can identify the Human cell type ciliated columnar cell of tracheobronchial tree in the Lung with a confidence of 0.86 (NS-Forest FBeta value). + https://doi.org/10.5281/zenodo.11165918 + @@ -57801,8 +58735,14 @@ Damage or dysfunction of these ciliated cells, as seen in diseases such as prima A cell type that makes up the highly vascular membrane lining the marrow cavity of long bones. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Endosteal cells, also known as osteogenic cells, are a specialized type of cell that resides in the endosteum of the bone marrow cavity. The endosteum is a thin vascular membrane of connective tissue that lines the inner surface of the bony tissue that forms the medullary cavity of long bones. This specific location assigns endosteal cells critical roles in the bone maintenance and regeneration process as they actively participate in bone remodeling, a process that involves both the formation and resorption of bone tissue. +Endosteal cells function by regulating the activity of both osteoblasts and osteoclasts. Osteoblasts are cells that deposit new bone, and osteoclasts are responsible for bone resorption, a process important for the maintenance, repair, and remodelling of bones. When new bone tissue is required, such as in instances of bone fractures or increased mechanical stress, endosteal cells differentiate into osteoblasts to facilitate the bone formation process. Conversely, when bone resorption is necessary, these cells are known to release signals that lead to the recruitment and activation of osteoclasts. +In addition to this, endosteal cells play a significant role in hematopoiesis, which is the formation of blood cellular components. They function in this process by providing a niche for hematopoietic stem cells, serving to support their maintenance and differentiation. Understanding the functionality of endosteal cells is important in the field of regenerative medicine and stem cell therapy, especially in diseases affecting bone remodeling and hematopoiesis. 2010-08-24T03:33:58Z FMA:86495 + https://cellxgene.cziscience.com/cellguide/CL_0002157 endosteal cell @@ -57813,6 +58753,20 @@ Damage or dysfunction of these ciliated cells, as seen in diseases such as prima FMA:0618947256 GOC:tfm + + + + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Endosteal cells, also known as osteogenic cells, are a specialized type of cell that resides in the endosteum of the bone marrow cavity. The endosteum is a thin vascular membrane of connective tissue that lines the inner surface of the bony tissue that forms the medullary cavity of long bones. This specific location assigns endosteal cells critical roles in the bone maintenance and regeneration process as they actively participate in bone remodeling, a process that involves both the formation and resorption of bone tissue. +Endosteal cells function by regulating the activity of both osteoblasts and osteoclasts. Osteoblasts are cells that deposit new bone, and osteoclasts are responsible for bone resorption, a process important for the maintenance, repair, and remodelling of bones. When new bone tissue is required, such as in instances of bone fractures or increased mechanical stress, endosteal cells differentiate into osteoblasts to facilitate the bone formation process. Conversely, when bone resorption is necessary, these cells are known to release signals that lead to the recruitment and activation of osteoclasts. +In addition to this, endosteal cells play a significant role in hematopoiesis, which is the formation of blood cellular components. They function in this process by providing a niche for hematopoietic stem cells, serving to support their maintenance and differentiation. Understanding the functionality of endosteal cells is important in the field of regenerative medicine and stem cell therapy, especially in diseases affecting bone remodeling and hematopoiesis. + DOI:10.1038/leu.2010.214 + DOI:10.1126/science.75570 + DOI:10.1182/blood-2004-06-2480 + DOI:10.1182/blood-2009-08-239194 + https://www.sciencedirect.com/topics/engineering/endosteum + @@ -57981,7 +58935,6 @@ Damage or dysfunction of these ciliated cells, as seen in diseases such as prima - @@ -58040,6 +58993,7 @@ Damage or dysfunction of these ciliated cells, as seen in diseases such as prima 2010-08-26T01:47:13Z FMA:67870 + olfactory epithelial cell @@ -58133,7 +59087,6 @@ Damage or dysfunction of these ciliated cells, as seen in diseases such as prima - @@ -58381,7 +59334,7 @@ Damage or dysfunction of these ciliated cells, as seen in diseases such as prima - + @@ -58390,7 +59343,7 @@ Damage or dysfunction of these ciliated cells, as seen in diseases such as prima - + An epithelial cell found in the lining of the stomach. @@ -58417,20 +59370,24 @@ Damage or dysfunction of these ciliated cells, as seen in diseases such as prima - - An epithelial cell within one of the pits in the embryonic gastric mucosa from which the gastric glands develop . + + + A simple columnar cell that populates the entire luminal surface including the gastric pits. This cell types secrete mucus to form a thick protective, lubricant layer over the gastric wall. 2010-08-25T03:23:22Z + FMA:62949 FMA:86552 + surface mucosal cell of stomach foveolar cell of stomach - An epithelial cell within one of the pits in the embryonic gastric mucosa from which the gastric glands develop . + A simple columnar cell that populates the entire luminal surface including the gastric pits. This cell types secrete mucus to form a thick protective, lubricant layer over the gastric wall. GOC:tfm - http://www.merriam-webster.com/medical/foveolar + ISBN:0517223651 + Wikipedia:Foveolar_cell @@ -58444,7 +59401,7 @@ Damage or dysfunction of these ciliated cells, as seen in diseases such as prima - + @@ -58454,7 +59411,8 @@ Damage or dysfunction of these ciliated cells, as seen in diseases such as prima - + + An epithelial cell of the stomach. This cell produces mucous. 2010-08-25T03:38:51Z @@ -58487,6 +59445,7 @@ Damage or dysfunction of these ciliated cells, as seen in diseases such as prima + @@ -58513,24 +59472,19 @@ Damage or dysfunction of these ciliated cells, as seen in diseases such as prima - - - - - - - - - A simple columnar cell that populates the entire luminal surface including the gastric pits. This cell types secrete mucus to form a thick protective, lubricant layer over the gastric wall. + OBSOLETE. A simple columnar cell that populates the entire luminal surface including the gastric pits. This cell types secrete mucus to form a thick protective, lubricant layer over the gastric wall. + 2010-08-25T03:45:10Z FMA:62949 - surface mucosal cell of stomach + Duplicate with foveolar cell of stomach + obsolete surface mucosal cell of stomach + true - A simple columnar cell that populates the entire luminal surface including the gastric pits. This cell types secrete mucus to form a thick protective, lubricant layer over the gastric wall. + OBSOLETE. A simple columnar cell that populates the entire luminal surface including the gastric pits. This cell types secrete mucus to form a thick protective, lubricant layer over the gastric wall. GOC:tfm ISBN:0517223651 @@ -58680,7 +59634,6 @@ Damage or dysfunction of these ciliated cells, as seen in diseases such as prima - @@ -59239,7 +60192,7 @@ Damage or dysfunction of these ciliated cells, as seen in diseases such as prima A cell type found in the gastrointestinal and respiratory tracts that is characterized by the presence of a tuft of blunt, squat microvilli (120-140 per cell). Function of this cell type is not known. - This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. Brush cells, also referred to as tuft cells or multivesicular cells, are a specialized type of epithelial cell mainly noted for their characteristic 'brush border' composed of microvilli. These cells reside in the epithelial lining of tissue organs such as the respiratory tract, gastrointestinal tract, and the bile ducts. The name derives from their distinct appearance under the microscope, which resembles a brush due to the dense layer of microvilli protruding into the lumen. A key function of brush cells is chemosensation: They express a variety of signaling molecules and receptors that enable them to detect specific chemical stimuli in the environment and act as sensory transducers. Many of these receptors are responsive to luminal content, which makes brush cells vital for regulating and coordinating appropriate physiological responses to changes in these substances. @@ -59265,7 +60218,7 @@ Recent research has also elucidated an important role for these cells in immunit - This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. Brush cells, also referred to as tuft cells or multivesicular cells, are a specialized type of epithelial cell mainly noted for their characteristic 'brush border' composed of microvilli. These cells reside in the epithelial lining of tissue organs such as the respiratory tract, gastrointestinal tract, and the bile ducts. The name derives from their distinct appearance under the microscope, which resembles a brush due to the dense layer of microvilli protruding into the lumen. A key function of brush cells is chemosensation: They express a variety of signaling molecules and receptors that enable them to detect specific chemical stimuli in the environment and act as sensory transducers. Many of these receptors are responsive to luminal content, which makes brush cells vital for regulating and coordinating appropriate physiological responses to changes in these substances. @@ -59780,8 +60733,14 @@ Recent research has also elucidated an important role for these cells in immunit A cell of the transparent layer of simple cuboidal epithelium over the anterior surface of the lens; transform into lens fiber(s). + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +The anterior lens cells, also known as lens epithelial cells, are an integral part of the eye's structure and play a critical role in the organ's physiological functioning. They are situated in the anterior portion of the lens, precisely in the lens capsule, and stretch over the lens' frontal surface. +The primary function of anterior lens cells is to facilitate eye accommodation by controlling the shape and thickness of the eye lens. +The cells are involved in continuous proliferation, migration, and differentiation into lens fiber cells, helping to maintain lens growth and transparency. Anterior lens cells have a prolonged life span and reveal an extraordinary ability to function indefinitely, a characteristic that is critical for maintaining lens transparency. Damage or disturbance to the anterior lens cells can give rise to lens opacity, eventually leading to cataracts, which is a common cause of vision loss. 2010-09-07T10:45:45Z FMA:63181 + https://cellxgene.cziscience.com/cellguide/CL_0002223 anterior lens cell @@ -59792,6 +60751,18 @@ Recent research has also elucidated an important role for these cells in immunit GOC:tfm ISBN:0517223651 + + + + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +The anterior lens cells, also known as lens epithelial cells, are an integral part of the eye's structure and play a critical role in the organ's physiological functioning. They are situated in the anterior portion of the lens, precisely in the lens capsule, and stretch over the lens' frontal surface. +The primary function of anterior lens cells is to facilitate eye accommodation by controlling the shape and thickness of the eye lens. +The cells are involved in continuous proliferation, migration, and differentiation into lens fiber cells, helping to maintain lens growth and transparency. Anterior lens cells have a prolonged life span and reveal an extraordinary ability to function indefinitely, a characteristic that is critical for maintaining lens transparency. Damage or disturbance to the anterior lens cells can give rise to lens opacity, eventually leading to cataracts, which is a common cause of vision loss. + DOI:10.1016/j.biocel.2007.10.034 + DOI:10.1111/aos.14600 + DOI:10.1155/2021/9951032 + @@ -59857,7 +60828,7 @@ Recent research has also elucidated an important role for these cells in immunit A lens fiber cell that develops from primary lens fiber; located towards the center of lens; cell organelles are normally degraded or in the process of being degraded. - This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. Secondary lens fibers are a specialized type of elongated cells located within the structure of the eye's lens. They play an essential role in vision by enabling light transmission and focus on the retina, which allows for clear, distinct vision. These cells are characterized by their lack of nuclei and organelles, their orderly alignment, and their high protein content, particularly crystallins. Lens fibers are differentiated from equatorial epithelial cells of the lens in a process that involves cell elongation, denucleation and tight packing, which serve to reduce light scattering occurrences in the eye. This differentiation accelerates substantially after birth in comparison to during embryogenesis and continues throughout life, contributing to the growth of the eye lens. Secondary lens fibers are specifically those cells that are newly differentiated and cover the old lens fiber core. This process also leads to the removal of light-obstructing cellular components, mainly nuclei and organelles, making these fibers transparent and ideal for their function. @@ -59879,7 +60850,7 @@ The fibers carry out their primary function of light refraction via a high conce - This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. Secondary lens fibers are a specialized type of elongated cells located within the structure of the eye's lens. They play an essential role in vision by enabling light transmission and focus on the retina, which allows for clear, distinct vision. These cells are characterized by their lack of nuclei and organelles, their orderly alignment, and their high protein content, particularly crystallins. Lens fibers are differentiated from equatorial epithelial cells of the lens in a process that involves cell elongation, denucleation and tight packing, which serve to reduce light scattering occurrences in the eye. This differentiation accelerates substantially after birth in comparison to during embryogenesis and continues throughout life, contributing to the growth of the eye lens. Secondary lens fibers are specifically those cells that are newly differentiated and cover the old lens fiber core. This process also leads to the removal of light-obstructing cellular components, mainly nuclei and organelles, making these fibers transparent and ideal for their function. @@ -60384,7 +61355,7 @@ The fibers carry out their primary function of light refraction via a high conce - + A fibroblast in the bone marrow. 2010-09-07T02:25:18Z @@ -60426,13 +61397,21 @@ The fibers carry out their primary function of light refraction via a high conce + + + + + + A fibroblasts found in interstitial spaces in the pulmonary tract. Greater numbers of these cells are found in idiopathic pulmonary fibrosis. + 2010-09-07T02:29:38Z FMA:84467 pulmonary myofibroblast pulmonary septal cell + The marker set DPT, APOD can identify the Human cell type pulmonary interstitial fibroblast in the Lung with a confidence of 0.58 (NS-Forest FBeta value). pulmonary interstitial fibroblast @@ -60447,6 +61426,12 @@ The fibers carry out their primary function of light refraction via a high conce A fibroblasts found in interstitial spaces in the pulmonary tract. Greater numbers of these cells are found in idiopathic pulmonary fibrosis. GOC:tfm + + + + The marker set DPT, APOD can identify the Human cell type pulmonary interstitial fibroblast in the Lung with a confidence of 0.58 (NS-Forest FBeta value). + https://doi.org/10.5281/zenodo.11165918 + @@ -60515,8 +61500,14 @@ The fibers carry out their primary function of light refraction via a high conce A circular smooth muscle cell of the iris, innervated by the ciliary nerves (parasympathetic), and acting to contract the pupil. This muscle cell derives from neuroectoderm. This smooth muscle cell results from transformation of epithelial cells to smooth muscle cells. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +The smooth muscle cell of sphincter of pupil is a specialized cell type typically found within the eye, more specifically within the sphincter muscle of the iris. +These cells can constrict and dilate in response to light signals, tightly regulating the amount of light reaching the retina. Contraction narrows the pupil in bright conditions (pupillary constriction), protecting the retina from excessive light. In low light, relaxation allows dilation (pupillary dilation), enhancing visual perception in dim conditions. +These cells are also innervated by parasympathetic fibers from the oculomotor nerve. Light signals to the Edinger-Westphal nucleus stimulate the release of acetylcholine, contracting the cells. On the contrary, sympathetic stimulation induces relaxation. This precise control plays a crucial role in optimizing visual function, highlighting their essential role in vision biology. 2010-09-08T08:53:42Z FMA:70611 + https://cellxgene.cziscience.com/cellguide/CL_0002243 smooth muscle fiber of sphincter of pupil smooth muscle fibre of sphincter of pupil @@ -60536,6 +61527,19 @@ The fibers carry out their primary function of light refraction via a high conce ISBN:0721662544 ISBN:0721694128 + + + + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +The smooth muscle cell of sphincter of pupil is a specialized cell type typically found within the eye, more specifically within the sphincter muscle of the iris. +These cells can constrict and dilate in response to light signals, tightly regulating the amount of light reaching the retina. Contraction narrows the pupil in bright conditions (pupillary constriction), protecting the retina from excessive light. In low light, relaxation allows dilation (pupillary dilation), enhancing visual perception in dim conditions. +These cells are also innervated by parasympathetic fibers from the oculomotor nerve. Light signals to the Edinger-Westphal nucleus stimulate the release of acetylcholine, contracting the cells. On the contrary, sympathetic stimulation induces relaxation. This precise control plays a crucial role in optimizing visual function, highlighting their essential role in vision biology. + https://www.ncbi.nlm.nih.gov/books/NBK532252/ + https://www.ncbi.nlm.nih.gov/books/NBK537180/ + https://www.sciencedirect.com/topics/neuroscience/iris-dilator-muscle + https://www.sciencedirect.com/topics/neuroscience/iris-sphincter-muscle + @@ -60730,7 +61734,7 @@ The fibers carry out their primary function of light refraction via a high conce A cell that is found in a zone occupying the bottom region of the crypt; provide the source of most of the cell types of the intestinal epithelium; proliferate by mitotic division; differentiates into columnar or goblet cells. - This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. Intestinal crypt stem cells, also known as crypt base columnar cells, are a unique type of cell, characterized by the highly specific marker LGR5, found in the intestinal epithelium. Situated at the bottom of the minute pockets known as crypts of Lieberkühn, these are undifferentiated cells that have the ability to perpetually self-renew, as well as differentiate into various other cell types that constitute the epithelial lining of the intestine. The fundamental role of intestinal crypt stem cells is to provide a constant supply of new cells to maintain the cellular turnover of the intestinal epithelium, a tissue known for rapid self-renewal. These stem cells are nurtured and protected by specialized epithelial and mesenchymal cells, and together constitute the intestinal stem cell niche. @@ -60753,7 +61757,7 @@ Research studies suggest that dysregulation in intestinal crypt stem cell prolif - This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. Intestinal crypt stem cells, also known as crypt base columnar cells, are a unique type of cell, characterized by the highly specific marker LGR5, found in the intestinal epithelium. Situated at the bottom of the minute pockets known as crypts of Lieberkühn, these are undifferentiated cells that have the ability to perpetually self-renew, as well as differentiate into various other cell types that constitute the epithelial lining of the intestine. The fundamental role of intestinal crypt stem cells is to provide a constant supply of new cells to maintain the cellular turnover of the intestinal epithelium, a tissue known for rapid self-renewal. These stem cells are nurtured and protected by specialized epithelial and mesenchymal cells, and together constitute the intestinal stem cell niche. @@ -60777,7 +61781,7 @@ Research studies suggest that dysregulation in intestinal crypt stem cell prolif - + @@ -60786,7 +61790,7 @@ Research studies suggest that dysregulation in intestinal crypt stem cell prolif - + An epithelial cell of the musculomembranous digestive tube extending from the mouth to the anus. @@ -60813,7 +61817,7 @@ Research studies suggest that dysregulation in intestinal crypt stem cell prolif - + @@ -60822,10 +61826,10 @@ Research studies suggest that dysregulation in intestinal crypt stem cell prolif - + - An epithelial cell of the esophagus. + An epithelial cell of the lining of the esophagus. 2010-09-08T09:28:20Z FMA:63071 @@ -60842,7 +61846,7 @@ Research studies suggest that dysregulation in intestinal crypt stem cell prolif - An epithelial cell of the esophagus. + An epithelial cell of the lining of the esophagus. GOC:tfm @@ -60872,10 +61876,10 @@ Research studies suggest that dysregulation in intestinal crypt stem cell prolif - + - An epithelial cell of the large intestine. + An epithelial cell of the lining of the large intestine. 2010-09-08T09:28:22Z BTO:0004297 @@ -60893,7 +61897,7 @@ Research studies suggest that dysregulation in intestinal crypt stem cell prolif - An epithelial cell of the large intestine. + An epithelial cell of the lining of the large intestine. GOC:tfm @@ -60920,7 +61924,7 @@ Research studies suggest that dysregulation in intestinal crypt stem cell prolif - An epithelial cell of the small intestine. + An epithelial cell of the lining of the small intestine. 2010-09-08T09:41:46Z FMA:256159 @@ -60936,7 +61940,7 @@ Research studies suggest that dysregulation in intestinal crypt stem cell prolif - An epithelial cell of the small intestine. + An epithelial cell of the lining of the small intestine. GOC:tfm @@ -60951,7 +61955,7 @@ Research studies suggest that dysregulation in intestinal crypt stem cell prolif - + @@ -60963,37 +61967,40 @@ Research studies suggest that dysregulation in intestinal crypt stem cell prolif + + + + + + - A stromal cell of the endometrium that is fibroblastic in appearance. During decidualization this cell may differentiate into a decidual stromal cell. + A stromal cell of the endometrium, characterized by its fibroblast-like morphology, regenerative capacity, and ability to undergo decidualization. It differentiates into a decidual stromal cell during pregnancy, essential for embryo implantation and maintenance. This cell is involved in tissue proliferation, remodeling, and breakdown, responding to hormonal changes, particularly estrogen and progesterone. 2010-09-08T09:50:04Z + stromal cell of uterus CALOHA:TS-1266 FMA:86490 endometrial stromal cell endometrial stromal fibroblast + stromal cell of endometrium - - - - - true - - A stromal cell of the endometrium that is fibroblastic in appearance. During decidualization this cell may differentiate into a decidual stromal cell. + A stromal cell of the endometrium, characterized by its fibroblast-like morphology, regenerative capacity, and ability to undergo decidualization. It differentiates into a decidual stromal cell during pregnancy, essential for embryo implantation and maintenance. This cell is involved in tissue proliferation, remodeling, and breakdown, responding to hormonal changes, particularly estrogen and progesterone. PMID:11331626 PMID:30013421 PMID:30309298 - Wiki:Decidualization&oldid=908981933#Endometrial_stromal_cells_(ESCs) + PMID:31907034 + Wikipedia:Decidualization https://doi.org/10.1038/s41591-020-1040-z @@ -61055,6 +62062,7 @@ Research studies suggest that dysregulation in intestinal crypt stem cell prolif 2010-09-08T01:46:51Z FMA:256167 MESH:D000072637 + epithelial cell of thyroid gland @@ -61126,7 +62134,7 @@ Research studies suggest that dysregulation in intestinal crypt stem cell prolif - + @@ -61135,19 +62143,19 @@ Research studies suggest that dysregulation in intestinal crypt stem cell prolif - + + + + + + An epithelial cell of the parathyroid gland. 2010-09-08T02:29:38Z FMA:70547 + epithelial cell of parathyroid gland - - - - - true - @@ -61201,8 +62209,14 @@ Research studies suggest that dysregulation in intestinal crypt stem cell prolif An endothelial cell that lines any of the venous cavities through which blood passes in various glands and organs such as the spleen and liver. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Endothelial cells of sinusoids, often referred to as sinusoidal endothelial cells (SECs), are a specialized type of endothelial cell that primarily reside in the capillaries of the liver, spleen, and bone marrow. These cells form the innermost monolayer of the sinusoidal blood vessels, also known as sinusoids, that mediate the exchange of nutrients, metabolites, and waste materials between the blood and the surrounding organ tissue. SECs possess distinctive morphological features including a large, flattened shape, an abundance of fenestrations or pores, and the lack of a continuous basement membrane. These structural characteristics distinguish sinusoidal endothelial cells from other, more regularly structured endothelial cells in the body. +Due to their special fenestrated structure, SECs facilitate the exchange of macromolecules, like lipoproteins and hyaluronan, between plasma and the surrounding organ parenchymal cells. These fenestrations act like sieves, allowing the passage of substances based on their size and charge. It's noteworthy that the permeability characteristics of SECs can be regulated dynamically according to the body's homeostatic needs. +Beyond their key role in exchange mechanisms, endothelial cells of sinusoids are involved in several other functions. In the liver, for example, they help in the removal and endocytic degradation of waste macromolecules, immune response, and regulation of liver regeneration. They also participate in the formation and remodeling of blood vessels, a process known as angiogenesis. Additionally, in recent years, it has been discovered that these cells may have a role in disease conditions like cirrhosis and liver cancer. 2010-09-14T10:57:26Z FMA:63134 + https://cellxgene.cziscience.com/cellguide/CL_0002262 endothelial cell of sinusoid @@ -61214,6 +62228,20 @@ Research studies suggest that dysregulation in intestinal crypt stem cell prolif GOC:tfm ISBN:0618947256 + + + + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Endothelial cells of sinusoids, often referred to as sinusoidal endothelial cells (SECs), are a specialized type of endothelial cell that primarily reside in the capillaries of the liver, spleen, and bone marrow. These cells form the innermost monolayer of the sinusoidal blood vessels, also known as sinusoids, that mediate the exchange of nutrients, metabolites, and waste materials between the blood and the surrounding organ tissue. SECs possess distinctive morphological features including a large, flattened shape, an abundance of fenestrations or pores, and the lack of a continuous basement membrane. These structural characteristics distinguish sinusoidal endothelial cells from other, more regularly structured endothelial cells in the body. +Due to their special fenestrated structure, SECs facilitate the exchange of macromolecules, like lipoproteins and hyaluronan, between plasma and the surrounding organ parenchymal cells. These fenestrations act like sieves, allowing the passage of substances based on their size and charge. It's noteworthy that the permeability characteristics of SECs can be regulated dynamically according to the body's homeostatic needs. +Beyond their key role in exchange mechanisms, endothelial cells of sinusoids are involved in several other functions. In the liver, for example, they help in the removal and endocytic degradation of waste macromolecules, immune response, and regulation of liver regeneration. They also participate in the formation and remodeling of blood vessels, a process known as angiogenesis. Additionally, in recent years, it has been discovered that these cells may have a role in disease conditions like cirrhosis and liver cancer. + DOI:10.1007/s10456-021-09780-y + DOI:10.1016/j.jhep.2016.07.009 + DOI:10.1038/s41575-018-0020-y + DOI:10.1038/s41598-020-57652-0 + DOI:10.1186/1476-5926-1-1 + @@ -61246,13 +62274,13 @@ Research studies suggest that dysregulation in intestinal crypt stem cell prolif - + - + A type of enteroendocrine cell found in the stomach that secretes glucagon. 2010-09-10T10:54:42Z @@ -61284,6 +62312,7 @@ Research studies suggest that dysregulation in intestinal crypt stem cell prolif + A D cell located in the colon. 2010-09-10T11:37:35Z @@ -61345,13 +62374,14 @@ Research studies suggest that dysregulation in intestinal crypt stem cell prolif - + + A type D cell found in the stomach. 2010-09-10T01:36:03Z @@ -61560,7 +62590,7 @@ Research studies suggest that dysregulation in intestinal crypt stem cell prolif A PP cell located in the islets of the pancreas. - This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. Pancreatic polypeptide (PP) cells (also called F or gamma cells) are unique endocrine cells located within the Islets of Langerhans in the pancreas. PP cells are one of the rarer pancreatic cell types and are more prevalent in the head and neck of the pancreas. They are critical in normal pancreatic physiological functions and are involved in the development of pancreatic endocrine disorders. The primary function of PP cells is the production and secretion of the pancreatic polypeptide hormone (PP). This hormone plays a crucial role in several gastrointestinal functions and metabolic responses. The release of the PP hormone is stimulated after eating, especially in protein-rich meals, leading to it being present in large amounts during digestion. The fundamental role of PP is to self-regulate pancreatic secretion activities ensuring its exocrine and endocrine functions are under control. @@ -61588,7 +62618,7 @@ The pancreatic polypeptide hormone from PP cells also aids in adapting to low ph - This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. Pancreatic polypeptide (PP) cells (also called F or gamma cells) are unique endocrine cells located within the Islets of Langerhans in the pancreas. PP cells are one of the rarer pancreatic cell types and are more prevalent in the head and neck of the pancreas. They are critical in normal pancreatic physiological functions and are involved in the development of pancreatic endocrine disorders. The primary function of PP cells is the production and secretion of the pancreatic polypeptide hormone (PP). This hormone plays a crucial role in several gastrointestinal functions and metabolic responses. The release of the PP hormone is stimulated after eating, especially in protein-rich meals, leading to it being present in large amounts during digestion. The fundamental role of PP is to self-regulate pancreatic secretion activities ensuring its exocrine and endocrine functions are under control. @@ -62281,7 +63311,7 @@ The pancreatic polypeptide hormone from PP cells also aids in adapting to low ph - + A synovial cell that is macrophage-like, characterized by surface ruffles or lamellipodia, plasma membrane invaginations and associated micropinocytotic vesicles, Golgi apparatus and little granular endoplasmic reticulum. 2010-09-13T03:39:17Z @@ -62290,14 +63320,14 @@ The pancreatic polypeptide hormone from PP cells also aids in adapting to low ph Type A cells are usually round and located in the upper part of the synovial intima. type A synovial cell - + - + PMID:10770586 @@ -62329,7 +63359,7 @@ The pancreatic polypeptide hormone from PP cells also aids in adapting to low ph A cell that is part of pigmented ciliary epithelium. This cell type uptakes sodium and chloride ions from stromal interstitium and passes the ions to non-pigmented ciliary epithelial cells via gap junctions. - This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. Pigmented ciliary epithelial cells, which are a type of pigment cell, have a crucial function within the eye's ciliary body. The ciliary body, located behind the iris, is one of the eye’s most vital structures and consists of two types of epithelial cells: the pigmented and the non-pigmented ciliary epithelial cells. The pigmented ciliary epithelial cells form the outer layer of the ciliary body and exhibit a black or brown pigmentation due to the melanin they contain. One key function of pigmented ciliary epithelial cells is to aid in the formation of aqueous humor, an intraocular fluid that nourishes the cornea and lens, and maintains intraocular pressure which is essential for the eye’s shape and light refraction. These cells facilitate this function in conjunction with the non-pigmented ciliary epithelial cells. Together, the pigmented and non-pigmented ciliary epithelial cells form a bilayer epithelium that allows the secretion of aqueous humor through a bi-directional fluid transport mechanism. @@ -62353,7 +63383,7 @@ Pigmented ciliary epithelial cells also contribute to the blood-aqueous barrier, - This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. Pigmented ciliary epithelial cells, which are a type of pigment cell, have a crucial function within the eye's ciliary body. The ciliary body, located behind the iris, is one of the eye’s most vital structures and consists of two types of epithelial cells: the pigmented and the non-pigmented ciliary epithelial cells. The pigmented ciliary epithelial cells form the outer layer of the ciliary body and exhibit a black or brown pigmentation due to the melanin they contain. One key function of pigmented ciliary epithelial cells is to aid in the formation of aqueous humor, an intraocular fluid that nourishes the cornea and lens, and maintains intraocular pressure which is essential for the eye’s shape and light refraction. These cells facilitate this function in conjunction with the non-pigmented ciliary epithelial cells. Together, the pigmented and non-pigmented ciliary epithelial cells form a bilayer epithelium that allows the secretion of aqueous humor through a bi-directional fluid transport mechanism. @@ -62972,11 +64002,17 @@ Pigmented ciliary epithelial cells also contribute to the blood-aqueous barrier, A cell of the embryo. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Embryonic cells in metazoans, which include all multicellular animals, are biological units in their earliest developmental stages from conception until the organism is fully formed. +They are derived from a fertilized egg, which undergoes a series of cell divisions to produce a multicellular organism. During the early phases of embryonic development, these cells exhibit pluripotency, meaning they possess the potential to differentiate into a diverse array of specialized cell types that constitute different body tissues and structures. +The balance between cell proliferation and differentiation in embryonic cells is crucial for successful development. When cells continue to divide without differentiating, overgrowth may occur leading to conditions such as teratomas (tumors of embryonic cells). Conversely, if cell differentiation proceeds at the expense of cell proliferation, developmental anomalies could occur regarding size or mass of the organism or its parts. 2010-09-15T03:39:21Z CALOHA:TS-0263 FMA:82840 WBbt:0007028 ZFA:0007089 + https://cellxgene.cziscience.com/cellguide/CL_0002321 embryonic cell (metazoa) @@ -62985,6 +64021,18 @@ Pigmented ciliary epithelial cells also contribute to the blood-aqueous barrier, A cell of the embryo. FMA:0618947256 + + + + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Embryonic cells in metazoans, which include all multicellular animals, are biological units in their earliest developmental stages from conception until the organism is fully formed. +They are derived from a fertilized egg, which undergoes a series of cell divisions to produce a multicellular organism. During the early phases of embryonic development, these cells exhibit pluripotency, meaning they possess the potential to differentiate into a diverse array of specialized cell types that constitute different body tissues and structures. +The balance between cell proliferation and differentiation in embryonic cells is crucial for successful development. When cells continue to divide without differentiating, overgrowth may occur leading to conditions such as teratomas (tumors of embryonic cells). Conversely, if cell differentiation proceeds at the expense of cell proliferation, developmental anomalies could occur regarding size or mass of the organism or its parts. + DOI:10.1002/iub.1404 + DOI:10.1093/molehr/gan048 + https://www.ncbi.nlm.nih.gov/books/NBK9906/ + @@ -63376,7 +64424,7 @@ Pigmented ciliary epithelial cells also contribute to the blood-aqueous barrier, An epithelial cell type that lacks the columnar shape typical for other respiratory epithelial cells. This cell type is able to differentiate into other respiratory epithelial cells in response to injury. - This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. The basal epithelial cells of the tracheobronchial tree are critical components found in the lining of the airway passages, including the trachea and bronchi. They are keratin-5-positive, nonciliated, cuboidal cells and typically tightly attached to the basement membrane. In humans, the proportion of basal cells in the respiratory epithelium gradually decreases going down the tracheobronchial tree: they represent approximately 34% of the cells in the trachea, 27% in the large airways, and 10% in the small airways, although it is worth noting that there are differences in the compositions of the tracheobronchial epithelia between different species. Basal epithelial cells serve as the basal layer of the tracheobronchial epithelium, providing both structural and regenerative support for the epithelial tissue that lines the upper regions of the respiratory tract. They serve as progenitor or stem cells that are capable of differentiating into multiple cell types, such as ciliated and secretory cells. This gives them a central role in homeostatic maintenance of the epithelium, and in repairing damaged epithelium after an injury or during disease. This regenerative capacity is crucial in maintaining the integrity of the tracheobronchial surface, especially given its continual exposure to inhaled irritants and microorganisms. @@ -63396,7 +64444,7 @@ In addition to their primary restorative function, basal epithelial cells are al - This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. The basal epithelial cells of the tracheobronchial tree are critical components found in the lining of the airway passages, including the trachea and bronchi. They are keratin-5-positive, nonciliated, cuboidal cells and typically tightly attached to the basement membrane. In humans, the proportion of basal cells in the respiratory epithelium gradually decreases going down the tracheobronchial tree: they represent approximately 34% of the cells in the trachea, 27% in the large airways, and 10% in the small airways, although it is worth noting that there are differences in the compositions of the tracheobronchial epithelia between different species. Basal epithelial cells serve as the basal layer of the tracheobronchial epithelium, providing both structural and regenerative support for the epithelial tissue that lines the upper regions of the respiratory tract. They serve as progenitor or stem cells that are capable of differentiating into multiple cell types, such as ciliated and secretory cells. This gives them a central role in homeostatic maintenance of the epithelium, and in repairing damaged epithelium after an injury or during disease. This regenerative capacity is crucial in maintaining the integrity of the tracheobronchial surface, especially given its continual exposure to inhaled irritants and microorganisms. @@ -63443,28 +64491,37 @@ In addition to their primary restorative function, basal epithelial cells are al - + + + + + + + + + - A ciliated cell of the bronchus. + A multi-ciliated epithelial cell located in the bronchus epithelium, characterized by a columnar shape and motile cilia on its apical surface. 2010-09-20T02:21:12Z + ciliated epithelial cell of the bronchus - ciliated cell of the bronchus + multiciliated epithelial cell of the bronchus - A ciliated cell of the bronchus. + A multi-ciliated epithelial cell located in the bronchus epithelium, characterized by a columnar shape and motile cilia on its apical surface. GOC:tfm PMID:18757316 @@ -63515,6 +64572,7 @@ In addition to their primary restorative function, basal epithelial cells are al 2010-09-20T02:31:53Z BTO:0001107 + preadipocyte @@ -63534,6 +64592,7 @@ In addition to their primary restorative function, basal epithelial cells are al A preadipocyte that is capable of differentiating into a brown adipocyte. This cell type expresses uncoupling protein-1, PPAR-gamma, PR-domain-containing 16; and PGC-1alpha (peroxisome proliferator-activated receptor-gamma (PPARgamma) coactivator-1alpha). 2010-09-20T02:38:38Z + brown preadipocyte @@ -63624,7 +64683,6 @@ In addition to their primary restorative function, basal epithelial cells are al - @@ -63813,8 +64871,15 @@ In addition to their primary restorative function, basal epithelial cells are al + - + + + + + + + @@ -63894,7 +64959,6 @@ In addition to their primary restorative function, basal epithelial cells are al - @@ -63991,7 +65055,6 @@ In addition to their primary restorative function, basal epithelial cells are al - @@ -64075,7 +65138,6 @@ In addition to their primary restorative function, basal epithelial cells are al - @@ -64136,7 +65198,6 @@ In addition to their primary restorative function, basal epithelial cells are al - @@ -64199,7 +65260,6 @@ In addition to their primary restorative function, basal epithelial cells are al - @@ -64262,7 +65322,6 @@ In addition to their primary restorative function, basal epithelial cells are al - @@ -64326,8 +65385,14 @@ In addition to their primary restorative function, basal epithelial cells are al An endothelial cell that lines the intracavitary lumen of the heart, separating the circulating blood from the underlying myocardium. This cell type releases a number of vasoactive substances including prostacyclin, nitrous oxide and endothelin. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Endocardial cells, often referred to as endothelial cells of the heart, constitute the innermost lining layer of the heart tissues, forming the endocardium. They play a critical role in maintaining heart functionality and homeostasis. These cells, flat and squamous in structure, are adjoined closely to form a tight barrier that separates the heart's muscular layer, the myocardium, from the blood flowing through the heart chambers. +Functionally, endocardial cells are key players in several crucial physiological processes within the heart. Synthesizing matrix molecules that contribute to the structural formation of the heart, these cells actively partake in maintaining its structural integrity. They also exhibit unique metabolic activity, which aids in maintaining optimal cardiac functioning in both healthy and pathological conditions. Importantly, they are known for their involvement in modulating myocardial contraction and relaxation, that is crucial for normal heart rhythm and function. They achieve this by producing factors like nitric oxide (NO) which, amongst other things, aids in the regulation of blood pressure, prevents blood clotting and inhibits the adherence of blood cells to the vessel wall. +In pathological states, endocardial cells can undergo a transformation process known as endothelial-mesenchymal transition (EndMT), which is inherently involved in several cardiac diseases. In this transition, they acquire the ability to migrate and differentiate into several other types of cells contributing to disease progression. Moreover, their dysfunction can lead to endocarditis, an inflammation of the endocardium, as well as increase the risk of other heart diseases. 2010-09-21T04:33:05Z FMA:75621 + https://cellxgene.cziscience.com/cellguide/CL_0002350 endocardial endothelial cell endothelial cell of endocardium @@ -64341,6 +65406,20 @@ In addition to their primary restorative function, basal epithelial cells are al GOC:tfm ISSN:0452-3458 + + + + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Endocardial cells, often referred to as endothelial cells of the heart, constitute the innermost lining layer of the heart tissues, forming the endocardium. They play a critical role in maintaining heart functionality and homeostasis. These cells, flat and squamous in structure, are adjoined closely to form a tight barrier that separates the heart's muscular layer, the myocardium, from the blood flowing through the heart chambers. +Functionally, endocardial cells are key players in several crucial physiological processes within the heart. Synthesizing matrix molecules that contribute to the structural formation of the heart, these cells actively partake in maintaining its structural integrity. They also exhibit unique metabolic activity, which aids in maintaining optimal cardiac functioning in both healthy and pathological conditions. Importantly, they are known for their involvement in modulating myocardial contraction and relaxation, that is crucial for normal heart rhythm and function. They achieve this by producing factors like nitric oxide (NO) which, amongst other things, aids in the regulation of blood pressure, prevents blood clotting and inhibits the adherence of blood cells to the vessel wall. +In pathological states, endocardial cells can undergo a transformation process known as endothelial-mesenchymal transition (EndMT), which is inherently involved in several cardiac diseases. In this transition, they acquire the ability to migrate and differentiate into several other types of cells contributing to disease progression. Moreover, their dysfunction can lead to endocarditis, an inflammation of the endocardium, as well as increase the risk of other heart diseases. + DOI:10.1016/j.medici.2017.08.003 + DOI:10.1016/j.ydbio.2009.06.033 + DOI:10.1101/cshperspect.a036723 + DOI:10.1161/ATVBAHA.121.313788 + DOI:10.1161/CIRCRESAHA.117.312136 + @@ -64453,7 +65532,6 @@ In addition to their primary restorative function, basal epithelial cells are al - @@ -64565,7 +65643,6 @@ In addition to their primary restorative function, basal epithelial cells are al - @@ -64657,7 +65734,6 @@ In addition to their primary restorative function, basal epithelial cells are al - @@ -64787,7 +65863,6 @@ In addition to their primary restorative function, basal epithelial cells are al - @@ -64949,7 +66024,6 @@ In addition to their primary restorative function, basal epithelial cells are al - @@ -64967,6 +66041,7 @@ In addition to their primary restorative function, basal epithelial cells are al 2010-09-22T10:47:28Z EryP-CFC inner blood island hemangioblast + primitive erythroid progenitor @@ -65003,6 +66078,7 @@ In addition to their primary restorative function, basal epithelial cells are al granule cell precursor granule cell progenitor GCP + cerebellar granule cell precursor @@ -65100,8 +66176,14 @@ In addition to their primary restorative function, basal epithelial cells are al An epithelial cell of the cortical portion of the thymus. Epithelial cells in this region are required for positive selection of CD8-positive T cells. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Cortical thymic epithelial cells (cTECs) are a vital cell type located in the thymus, a lymphoid organ that plays a key role in the development of T cells, which are essential for the adaptive immune system. cTECs also have a role in forming barriers and lining surfaces. In the thymus, their presence contributes to the distinctive architecture of both the cortex and medulla. +cTECs also play a significant part in the selection and development of T cells. During T cell maturation, these cells express both self and non-self proteins via the major histocompatibility complex (MHC) to immature T cells. cTECs then stimulate the T cells that can recognize such proteins, an important event known as positive selection. This process aids in the creation of a diverse T cell receptor (TCR) repertoire that can react to a wide range of antigens, therefore ensuring effective immunity. +Apart from aiding in T cells' positive selection, cTECs also contribute to eliminating self-reactive T cells, a role essential in preventing autoimmune diseases. These cells induce an apoptosis-driven process known as "negative selection" which eliminates T cells that are too highly reactive to self-antigens. 2010-09-23T03:17:12Z BTO:0004562 + https://cellxgene.cziscience.com/cellguide/CL_0002364 cTEC @@ -65114,6 +66196,18 @@ In addition to their primary restorative function, basal epithelial cells are al GOC:tfm PMID:18403190 + + + + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Cortical thymic epithelial cells (cTECs) are a vital cell type located in the thymus, a lymphoid organ that plays a key role in the development of T cells, which are essential for the adaptive immune system. cTECs also have a role in forming barriers and lining surfaces. In the thymus, their presence contributes to the distinctive architecture of both the cortex and medulla. +cTECs also play a significant part in the selection and development of T cells. During T cell maturation, these cells express both self and non-self proteins via the major histocompatibility complex (MHC) to immature T cells. cTECs then stimulate the T cells that can recognize such proteins, an important event known as positive selection. This process aids in the creation of a diverse T cell receptor (TCR) repertoire that can react to a wide range of antigens, therefore ensuring effective immunity. +Apart from aiding in T cells' positive selection, cTECs also contribute to eliminating self-reactive T cells, a role essential in preventing autoimmune diseases. These cells induce an apoptosis-driven process known as "negative selection" which eliminates T cells that are too highly reactive to self-antigens. + DOI:10.1016/bs.ai.2014.09.003 + DOI:10.1038/nri3667 + DOI:10.1111/sji.13094 + @@ -65140,8 +66234,14 @@ In addition to their primary restorative function, basal epithelial cells are al An epithelial cell of the medullary thymus. This cell type expresses a diverse range of tissue-specific antigens. This promiscuous gene expression is a cell-autonomous property of medullary epithelial cells and is maintained during the entire period of thymic T cell output. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Medullary thymic epithelial cells (mTECs) are distinct cells situated in the thymic medulla, a vital organ where T cells mature. mTECs are recognized by their unique appearance, characterized by large, plump cells with abundant cytoplasm and irregularly shaped nuclei. They inhabit a microenvironment closely interacting with various thymic cell types, including conventional dendritic cells and thymocytes. +The primary function of mTECs revolves around negative selection of developing T cells, thus preventing autoimmune responses. mTECs allow developing T cells to recognize and be responsive to foreign antigens while remaining tolerant to the body's own tissues. They achieve this through a process called promiscuous gene expression where they express and display a vast array of self-antigens. This process is regulated by a transcriptional regulator called autoimmune regulator (Aire), which contributes to immunological self-tolerance. +mTECs themselves have a self-renewing ability and sustain the continuous export of mature T cells. They also express a number of genes that encode for chemokines and other signaling molecules which draw in and retain developing T cells for the process of negative selection. The three-dimensional network formed by these cells provides a physical platform for such selection. Together, mTECs hold a critical place in the maintenance of immune homeostasis, demonstrating the conceptual links that exist between population of stromal cells, thymocytes development, tissue-restricted antigen expression, and negative selection. 2010-09-23T03:17:14Z BTO:0004563 + https://cellxgene.cziscience.com/cellguide/CL_0002365 mTEC medullary thymic epithelial cell @@ -65153,6 +66253,18 @@ In addition to their primary restorative function, basal epithelial cells are al GOC:tfm PMID:18180458 + + + + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Medullary thymic epithelial cells (mTECs) are distinct cells situated in the thymic medulla, a vital organ where T cells mature. mTECs are recognized by their unique appearance, characterized by large, plump cells with abundant cytoplasm and irregularly shaped nuclei. They inhabit a microenvironment closely interacting with various thymic cell types, including conventional dendritic cells and thymocytes. +The primary function of mTECs revolves around negative selection of developing T cells, thus preventing autoimmune responses. mTECs allow developing T cells to recognize and be responsive to foreign antigens while remaining tolerant to the body's own tissues. They achieve this through a process called promiscuous gene expression where they express and display a vast array of self-antigens. This process is regulated by a transcriptional regulator called autoimmune regulator (Aire), which contributes to immunological self-tolerance. +mTECs themselves have a self-renewing ability and sustain the continuous export of mature T cells. They also express a number of genes that encode for chemokines and other signaling molecules which draw in and retain developing T cells for the process of negative selection. The three-dimensional network formed by these cells provides a physical platform for such selection. Together, mTECs hold a critical place in the maintenance of immune homeostasis, demonstrating the conceptual links that exist between population of stromal cells, thymocytes development, tissue-restricted antigen expression, and negative selection. + DOI:10.1007/s11427-013-4482-4 + DOI:10.4049/jimmunol.2100692 + DOI:10.7554/eLife.60188 + @@ -65179,8 +66291,14 @@ In addition to their primary restorative function, basal epithelial cells are al A smooth muscle cell of the myometrium that enlarges and stretches during pregnancy, and contracts in response to oxytocin. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Myometrial cells are specialized smooth muscle cells located in the myometrium, the middle layer of the uterine wall. Unique to female reproductive physiology, they play a key role in pregnancy and childbirth. +These cells are distinctive in their capability to substantially increase in size and number during pregnancy, preparing the uterus to accommodate the growing fetus. As pregnancy progresses, myometrial cells demonstrate a progressive growth in uterine mass through cellular hypertrophy. They are also responsible for the production of extracellular matrix proteins like collagen, which aids in supporting cell structure and function, further facilitating uterine enlargement. +During childbirth, myometrial cells are responsible for the expansion and contraction of the uterus. They can propagate action potentials and generate considerable force, which is critical to their function in the reproductive system. After pregnancy, these cells can reduce in size, a process known as uterine involution. Given the important role these cells play in female reproductive physiology, dysregulation of the myometrial cell function can contribute to uterine pathologies such as uterine fibroids. 2010-09-23T03:46:34Z BTO:0004519 + https://cellxgene.cziscience.com/cellguide/CL_0002366 myometrium smooth muscle cell myometrial cell @@ -65192,6 +66310,20 @@ In addition to their primary restorative function, basal epithelial cells are al GOC:tfm PMID:11429640 + + + + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Myometrial cells are specialized smooth muscle cells located in the myometrium, the middle layer of the uterine wall. Unique to female reproductive physiology, they play a key role in pregnancy and childbirth. +These cells are distinctive in their capability to substantially increase in size and number during pregnancy, preparing the uterus to accommodate the growing fetus. As pregnancy progresses, myometrial cells demonstrate a progressive growth in uterine mass through cellular hypertrophy. They are also responsible for the production of extracellular matrix proteins like collagen, which aids in supporting cell structure and function, further facilitating uterine enlargement. +During childbirth, myometrial cells are responsible for the expansion and contraction of the uterus. They can propagate action potentials and generate considerable force, which is critical to their function in the reproductive system. After pregnancy, these cells can reduce in size, a process known as uterine involution. Given the important role these cells play in female reproductive physiology, dysregulation of the myometrial cell function can contribute to uterine pathologies such as uterine fibroids. + DOI:10.1073/pnas.070447210 + DOI:10.1093/humupd/dmr031 + DOI:10.1177/1535370220938741 + https://www.sciencedirect.com/topics/medicine-and-dentistry/uterine-contraction + https://www.sciencedirect.com/topics/veterinary-science-and-veterinary-medicine/myometrium + @@ -65259,18 +66391,19 @@ In addition to their primary restorative function, basal epithelial cells are al - An endo-epithelial cell of the respiratory tract. + An epithelial cell of the respiratory tract epithelium. These cells have an endodermal origin. 2010-09-23T04:38:49Z BTO:0004533 airway epithelial cell + respiratory epithelial cell - respiratory epithelial cell + respiratory tract epithelial cell - An endo-epithelial cell of the respiratory tract. + An epithelial cell of the respiratory tract epithelium. These cells have an endodermal origin. GOC:tfm @@ -65314,16 +66447,17 @@ In addition to their primary restorative function, basal epithelial cells are al A simple columnar epithelial cell that secretes mucin. Rough endoplasmic reticulum, mitochondria, the nucleus, and other organelles are concentrated in the basal portion. The apical plasma membrane projects microvilli to increase surface area for secretion. - This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. The respiratory goblet cell is a highly specialized cell type found primarily within the respiratory tract, including the nose, trachea, and lungs. Named because their shape resembles a goblet - a drinking vessel with a wide body and narrow neck - these cells form a vital part of the respiratory system's protective mechanisms. They are found within the columnar epithelium lining these organs, which forms a barrier between the internal body and the exterior environment. A principal function of the respiratory goblet cell is the production and secretion of mucus, a carbohydrate-rich, viscous and gel-like substance that plays a critical role in trapping dust, bacteria, viruses, and other airborne particles that are inhaled. The mucus secreted by the goblet cells covers the lining of the respiratory tract, effectively catching these particles and preventing them from reaching the lungs and causing infection. Mucus also provides hydration and lubrication to the respiratory tract surfaces, which is important in maintaining the tissue's health and functioning. In addition to their mucus-secreting capabilities, respiratory goblet cells also play a significant role in the body's inflammatory responses. When the respiratory system is exposed to irritants or pathogens, the number and activity of goblet cells often increase, leading to a higher production of mucus. This is a protective response designed to trap and neutralize the harmful substances more effectively. However, in conditions like chronic obstructive pulmonary disease (COPD) and asthma, an overproliferation of goblet cells, also known as goblet cell hyperplasia, can lead to excessive mucus production and airway obstruction. 2010-09-23T04:42:27Z https://cellxgene.cziscience.com/cellguide/CL_0002370 + respiratory goblet cell respiratory mucosa goblet cells - respiratory goblet cell + respiratory tract goblet cell @@ -65335,7 +66469,7 @@ In addition to their mucus-secreting capabilities, respiratory goblet cells also - This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. The respiratory goblet cell is a highly specialized cell type found primarily within the respiratory tract, including the nose, trachea, and lungs. Named because their shape resembles a goblet - a drinking vessel with a wide body and narrow neck - these cells form a vital part of the respiratory system's protective mechanisms. They are found within the columnar epithelium lining these organs, which forms a barrier between the internal body and the exterior environment. A principal function of the respiratory goblet cell is the production and secretion of mucus, a carbohydrate-rich, viscous and gel-like substance that plays a critical role in trapping dust, bacteria, viruses, and other airborne particles that are inhaled. The mucus secreted by the goblet cells covers the lining of the respiratory tract, effectively catching these particles and preventing them from reaching the lungs and causing infection. Mucus also provides hydration and lubrication to the respiratory tract surfaces, which is important in maintaining the tissue's health and functioning. @@ -65362,11 +66496,17 @@ In addition to their mucus-secreting capabilities, respiratory goblet cells also + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Somatic cells represent the majority of the cell types in the human body. They are fundamental building blocks of organs, tissues, and other bodily structures, with every organ being composed of distinct subpopulations of these cells. +The primary function of somatic cells is to maintain the function and survival of an organism. They carry significant information in the form of DNA, and through the process of mitosis, contribute to the repair and regeneration of body tissues. +Further, some types of somatic cells work in a collaborative manner to form complex functional structures such as the skin and lining of the gut, demonstrating a higher level of organization. However, it's important to note that somatic cells are distinct from germ cells, which are responsible for sexual reproduction by forming sperm or eggs. Any alterations in the DNA of somatic cells, due to mutations, will not affect the offspring as they aren't involved in transmission of genetic information to the next generation. +While most somatic cells contain two copies of each chromosome (diploid), a certain subset may possess a single set of chromosomes (haploid), specifically found in male ants, bees, and other hymenopterans. Hence, diversity is a defining characteristic of somatic cells, reflecting in their structures, roles, and genetic makeup. 2010-09-24T09:44:42Z BTO:0001268 FMA:72300 WBbt:0008378 - + https://cellxgene.cziscience.com/cellguide/CL_0002371 obsolete somatic cell true @@ -65378,6 +66518,19 @@ In addition to their mucus-secreting capabilities, respiratory goblet cells also GOC:tfm ISBN:0721662544 + + + + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Somatic cells represent the majority of the cell types in the human body. They are fundamental building blocks of organs, tissues, and other bodily structures, with every organ being composed of distinct subpopulations of these cells. +The primary function of somatic cells is to maintain the function and survival of an organism. They carry significant information in the form of DNA, and through the process of mitosis, contribute to the repair and regeneration of body tissues. +Further, some types of somatic cells work in a collaborative manner to form complex functional structures such as the skin and lining of the gut, demonstrating a higher level of organization. However, it's important to note that somatic cells are distinct from germ cells, which are responsible for sexual reproduction by forming sperm or eggs. Any alterations in the DNA of somatic cells, due to mutations, will not affect the offspring as they aren't involved in transmission of genetic information to the next generation. +While most somatic cells contain two copies of each chromosome (diploid), a certain subset may possess a single set of chromosomes (haploid), specifically found in male ants, bees, and other hymenopterans. Hence, diversity is a defining characteristic of somatic cells, reflecting in their structures, roles, and genetic makeup. + DOI:10.1038/nrm3980 + https://www.genome.gov/genetics-glossary/Somatic-Cells + https://www.ncbi.nlm.nih.gov/books/NBK557896/ + @@ -65417,6 +66570,7 @@ In addition to their mucus-secreting capabilities, respiratory goblet cells also FBbt:00005812 myofiber myofibril + myotube @@ -65579,6 +66733,7 @@ In addition to their mucus-secreting capabilities, respiratory goblet cells also 2010-09-24T02:10:26Z Schwann cell + non-myelinating Schwann cell @@ -66058,7 +67213,7 @@ In addition to their mucus-secreting capabilities, respiratory goblet cells also 2010-10-04T02:38:58Z - Markers are found in human cells. Normally they represent 3-5% of peripheral blood mDCs (human). These cells express high levels of CD283 (TLR3), are capable of producing IL-12p70 and IFN-beta upon stimulation, and inducing a TH1 response [PMCID:PMC2882828]. They are also Necl2-positive. May be human equivalent of murine CD8alpha-positive DCs. + Markers are found in human cells. Normally they represent 3-5% of peripheral blood mDCs (human). These cells express high levels of CD283 (TLR3), are capable of producing IL-12p70 and IFN-beta upon stimulation, and inducing a TH1 response [PMCID:PMC2882828]. They are also Necl2-positive. May be human equivalent of murine CD8-alpha-positive DCs. CD141-positive myeloid dendritic cell @@ -66779,12 +67934,7 @@ In addition to their mucus-secreting capabilities, respiratory goblet cells also - - - - - - + A cell that is found in the periacinar space of the exocrine pancreas and in perivascular and periductal regions of the pancreas, and has long cytoplasmic processes that encircle the base of the acinus. Expresses several intermediate filament proteins including vimentin and nestin. Shares many of the characteristics of hepatatic stellate cells, but not stellate cells of the central nervous system. Upon activation, this cell type undergoes morphological and gene expression changes that make the cell suggestive of being a type of myofibroblast. @@ -66992,7 +68142,6 @@ In addition to their mucus-secreting capabilities, respiratory goblet cells also - @@ -67284,7 +68433,6 @@ In addition to their mucus-secreting capabilities, respiratory goblet cells also - @@ -68111,7 +69259,6 @@ In addition to their mucus-secreting capabilities, respiratory goblet cells also - @@ -68672,17 +69819,13 @@ In addition to their mucus-secreting capabilities, respiratory goblet cells also + - - - - - - - - - + + + + @@ -68785,12 +69928,12 @@ In addition to their mucus-secreting capabilities, respiratory goblet cells also - Cd4-negative, CD8_alpha-negative, CD11b-positive dendritic cell is a conventional dendritic cell that is CD11b-positive, CD4-negative, CD8_alpha-negative and is CD205-positive. + CD4-negative, CD8-alpha-negative, CD11b-positive dendritic cell is a conventional dendritic cell that is CD11b-positive, CD4-negative, CD8-alpha-negative and is CD205-positive. 2010-11-22T01:10:28Z DC.8-4-11b+ spleen double-negative dendritic cell - Cd4-negative, CD8_alpha-negative, CD11b-positive dendritic cell + CD4-negative, CD8-alpha-negative, CD11b-positive dendritic cell @@ -68801,7 +69944,7 @@ In addition to their mucus-secreting capabilities, respiratory goblet cells also - Cd4-negative, CD8_alpha-negative, CD11b-positive dendritic cell is a conventional dendritic cell that is CD11b-positive, CD4-negative, CD8_alpha-negative and is CD205-positive. + CD4-negative, CD8-alpha-negative, CD11b-positive dendritic cell is a conventional dendritic cell that is CD11b-positive, CD4-negative, CD8-alpha-negative and is CD205-positive. GOC:tfm http://www.immgen.org/index_content.html @@ -68839,11 +69982,11 @@ In addition to their mucus-secreting capabilities, respiratory goblet cells also - A CD11c-low plasmacytoid dendritic cell that is CD8alpha-negative and CD4-positive. + A CD11c-low plasmacytoid dendritic cell that is CD8-alpha-negative and CD4-positive. 2010-11-22T01:27:37Z DC.pDC.8- - CD8_alpha-negative plasmacytoid dendritic cell + CD8-alpha-negative plasmacytoid dendritic cell @@ -68854,7 +69997,7 @@ In addition to their mucus-secreting capabilities, respiratory goblet cells also - A CD11c-low plasmacytoid dendritic cell that is CD8alpha-negative and CD4-positive. + A CD11c-low plasmacytoid dendritic cell that is CD8-alpha-negative and CD4-positive. GOC:tfm http://www.immgen.org/index_content.html @@ -68892,11 +70035,11 @@ In addition to their mucus-secreting capabilities, respiratory goblet cells also - A CD11c-low plasmacytoid dendritic cell that is CD8alpha-positive and CD4-positive. + A CD11c-low plasmacytoid dendritic cell that is CD8-alpha-positive and CD4-positive. 2010-11-22T01:23:07Z DC.pDC.8+ - CD8_alpha-positive plasmacytoid dendritic cell + CD8-alpha-positive plasmacytoid dendritic cell @@ -68907,7 +70050,7 @@ In addition to their mucus-secreting capabilities, respiratory goblet cells also - A CD11c-low plasmacytoid dendritic cell that is CD8alpha-positive and CD4-positive. + A CD11c-low plasmacytoid dendritic cell that is CD8-alpha-positive and CD4-positive. GOC:tfm http://www.immgen.org/index_content.html @@ -69088,13 +70231,13 @@ In addition to their mucus-secreting capabilities, respiratory goblet cells also - A conventional thymic dendritic cell that is CD8alpha-negative. + A conventional thymic dendritic cell that is CD8-alpha-negative. 2010-11-23T10:58:53Z DC.8-.Th - CD8alpha-negative thymic conventional dendritic cell + CD8-alpha-negative thymic conventional dendritic cell @@ -69105,7 +70248,7 @@ In addition to their mucus-secreting capabilities, respiratory goblet cells also - A conventional thymic dendritic cell that is CD8alpha-negative. + A conventional thymic dendritic cell that is CD8-alpha-negative. GOC:tfm PMID:19273629 http://www.immgen.org/index_content.html @@ -69394,6 +70537,7 @@ In addition to their mucus-secreting capabilities, respiratory goblet cells also 2010-11-23T02:00:21Z DC.11cloSer.SI small intestine serosal dendritic cell + @@ -69408,6 +70552,16 @@ In addition to their mucus-secreting capabilities, respiratory goblet cells also GOC:tfm http://www.immgen.org/index_content.html + + + + + http://creativecommons.org/licenses/by/4.0/ + Figure depicts a cross section of intestinal villi in the small intestine, including the crypts of Lieberkuhn (seen here as ‘crypt’), as well as the layer specific locations of cells that exist within the gastrointestinal tract. Layers depicted here include epithelium (rows of cells bordering villus), submucosa (white space below the epithelium containing networks of neurons and ganglia depicted in pink), muscularis mucosae (blue layer), muscularis propria (referred to here as muscle layer). + +ISC: Intestinal Stem Cell +TA: Transit Amplifying Cells + @@ -69883,7 +71037,6 @@ In addition to their mucus-secreting capabilities, respiratory goblet cells also - @@ -69966,7 +71119,6 @@ In addition to their mucus-secreting capabilities, respiratory goblet cells also - @@ -69988,6 +71140,7 @@ In addition to their mucus-secreting capabilities, respiratory goblet cells also A macrophage located in adipose tissue that is CD45-positive, CD11c-positive, and SIRPa-positive. 2010-11-23T04:31:28Z + adipose macrophage @@ -70133,11 +71286,19 @@ In addition to their mucus-secreting capabilities, respiratory goblet cells also + + + + + + A goblet cell located in the nasal epithelium. + 2010-12-03T03:03:02Z MP:0002262 + The marker set LYPD2, MUC5AC can identify the Human cell type nasal mucosa goblet cell in the Lung with a confidence of 0.81 (NS-Forest FBeta value). nasal mucosa goblet cell @@ -70147,6 +71308,12 @@ In addition to their mucus-secreting capabilities, respiratory goblet cells also GOC:cjm GOC:tfm + + + + The marker set LYPD2, MUC5AC can identify the Human cell type nasal mucosa goblet cell in the Lung with a confidence of 0.81 (NS-Forest FBeta value). + https://doi.org/10.5281/zenodo.11165918 + @@ -70567,6 +71734,7 @@ In addition to their mucus-secreting capabilities, respiratory goblet cells also A specialized cell involved in auditory sensory perception. 2010-12-06T03:18:43Z + auditory epithelial cell @@ -70931,7 +72099,13 @@ In addition to their mucus-secreting capabilities, respiratory goblet cells also A smooth muscle cell of the intestine. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Enteric smooth muscle cells are a specialized type of cell found in the gastrointestinal tract. They are an integral part of the enteric nervous system, which regulates the functions of the gastrointestinal system. These cells have a unique structural organization that enables their primary function: the contraction and relaxation necessary for the propulsion of gastrointestinal contents. +Smooth muscle cells in the enteric system possess unique attributes that distinguish them from other smooth muscle cells in the body. One crucial function is peristalsis, where these cells contract in a coordinated manner, generating a wave of contraction and relaxation. This peristaltic movement facilitates the movement of food particles through the digestive tract, playing a vital role in the digestion and absorption processes in animals. Additionally, these cells are responsible for maintaining the tone of gastrointestinal sphincters, controlling passage and preventing one-sided movement of the contents. +Enteric smooth muscle cells are also involved in local immune responses of the gastrointestinal tract. They can communicate with local immune cells and secrete cytokines or other signaling molecules in response to infectious organisms, which makes them crucial mediocellular players in gastrointestinal homeostasis and response to disease. Their interactions with other cell types, such as neurons, myofibroblasts, and interstitial cells of Cajal, further contribute to these cells' role in maintaining the physiological functions of the gastrointestinal system. Overall, enteric smooth muscle cells provide an indispensable contribution to the complex operations of the digestive tract. 2011-01-17T03:39:38Z + https://cellxgene.cziscience.com/cellguide/CL_0002504 intestinal smooth muscle cell enteric smooth muscle cell @@ -70948,6 +72122,18 @@ In addition to their mucus-secreting capabilities, respiratory goblet cells also A smooth muscle cell of the intestine. GOC:tfm + + + + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Enteric smooth muscle cells are a specialized type of cell found in the gastrointestinal tract. They are an integral part of the enteric nervous system, which regulates the functions of the gastrointestinal system. These cells have a unique structural organization that enables their primary function: the contraction and relaxation necessary for the propulsion of gastrointestinal contents. +Smooth muscle cells in the enteric system possess unique attributes that distinguish them from other smooth muscle cells in the body. One crucial function is peristalsis, where these cells contract in a coordinated manner, generating a wave of contraction and relaxation. This peristaltic movement facilitates the movement of food particles through the digestive tract, playing a vital role in the digestion and absorption processes in animals. Additionally, these cells are responsible for maintaining the tone of gastrointestinal sphincters, controlling passage and preventing one-sided movement of the contents. +Enteric smooth muscle cells are also involved in local immune responses of the gastrointestinal tract. They can communicate with local immune cells and secrete cytokines or other signaling molecules in response to infectious organisms, which makes them crucial mediocellular players in gastrointestinal homeostasis and response to disease. Their interactions with other cell types, such as neurons, myofibroblasts, and interstitial cells of Cajal, further contribute to these cells' role in maintaining the physiological functions of the gastrointestinal system. Overall, enteric smooth muscle cells provide an indispensable contribution to the complex operations of the digestive tract. + DOI:10.1038/nrgastro.2012.168 + DOI:10.1111/j.1365-2982.2012.01986.x + DOI:10.1371/journal.pcbi.1009644 + @@ -71457,16 +72643,16 @@ In addition to their mucus-secreting capabilities, respiratory goblet cells also - A CD8alpha alpha positive gamma-delta intraepithelial T cell that expresses a TCR encoded in part by the Vgamma5 gene segment. + A CD8-alpha alpha positive gamma-delta intraepithelial T cell that expresses a TCR encoded in part by the Vgamma5 gene segment. 2011-01-24T10:22:18Z tgd.vg5+.IEL - Vgamma5-positive CD8alpha alpha positive gamma-delta intraepithelial T cell + Vgamma5-positive CD8-alpha alpha positive gamma-delta intraepithelial T cell - A CD8alpha alpha positive gamma-delta intraepithelial T cell that expresses a TCR encoded in part by the Vgamma5 gene segment. + A CD8-alpha alpha positive gamma-delta intraepithelial T cell that expresses a TCR encoded in part by the Vgamma5 gene segment. GOC:tfm http://www.immgen.org/index_content.html @@ -71477,16 +72663,16 @@ In addition to their mucus-secreting capabilities, respiratory goblet cells also - A CD8alpha alpha positive gamma-delta intraepithelial T cell that does not express a TCR partially encoded by the Vgamma5 gene segment. + A CD8-alpha alpha positive gamma-delta intraepithelial T cell that does not express a TCR partially encoded by the Vgamma5 gene segment. 2011-01-24T10:25:44Z tgd.vg5-.IEL - Vgamma5-negative CD8alpha alpha positive gamma-delta intraepithelial T cell + Vgamma5-negative CD8-alpha alpha positive gamma-delta intraepithelial T cell - A CD8alpha alpha positive gamma-delta intraepithelial T cell that does not express a TCR partially encoded by the Vgamma5 gene segment. + A CD8-alpha alpha positive gamma-delta intraepithelial T cell that does not express a TCR partially encoded by the Vgamma5 gene segment. GOC:tfm http://www.immgen.org/index_content.html @@ -72403,6 +73589,7 @@ In addition to their mucus-secreting capabilities, respiratory goblet cells also 2011-02-28T12:38:01Z amniotic epithelial cell + epithelial cell of amnion @@ -72476,7 +73663,7 @@ In addition to their mucus-secreting capabilities, respiratory goblet cells also An epithelial cell of the intrahepatic portion of the bile duct. These cells are flattened or cuboidal in shape, and have a small nuclear-to-cytoplasmic ratio relative to large/extrahepatic cholangiocytes. - This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. Intrahepatic cholangiocytes represent a subset of the biliary epithelial cells that form a network of tubes in the liver called the biliary tree The intrahepatic cholangiocytes reside specifically in the intrahepatic bile ducts and play a crucial role in liver physiology and bile production and secretion, thereby aiding in the digestion and absorption of fats in the small intestine. These specific cholangiocytes arise from bipotent hepatoblasts, whereas extrahepatic cholangiocytes share an embryologic origin with the ventral pancreas. Recent research suggests that there is also heterogeneity within populations of intrahepatic cholangiocytes with different transcriptional profiles, proliferative capacity, and biological function; for example, subpopulations differ in calcium-mobilizing receptors. @@ -72505,7 +73692,7 @@ Intrahepatic cholangiocytes take part in certain pathological conditions, like p - This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. Intrahepatic cholangiocytes represent a subset of the biliary epithelial cells that form a network of tubes in the liver called the biliary tree The intrahepatic cholangiocytes reside specifically in the intrahepatic bile ducts and play a crucial role in liver physiology and bile production and secretion, thereby aiding in the digestion and absorption of fats in the small intestine. These specific cholangiocytes arise from bipotent hepatoblasts, whereas extrahepatic cholangiocytes share an embryologic origin with the ventral pancreas. Recent research suggests that there is also heterogeneity within populations of intrahepatic cholangiocytes with different transcriptional profiles, proliferative capacity, and biological function; for example, subpopulations differ in calcium-mobilizing receptors. @@ -72554,8 +73741,15 @@ Intrahepatic cholangiocytes take part in certain pathological conditions, like p A smooth muscle cell of the aorta. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Aortic smooth muscle cells are specialized and highly differentiated muscle cells that are located in the tunica media layer of the aorta. They consist of spindle-shaped cells with a centrally located nucleus. These cells are rich in actin and myosin, muscle contractile proteins, that allow them to exert force and change shape. +Aortic smooth muscle cells play a vital role in maintaining blood pressure and circulation, and are essential for vascular integrity and function. The primary function of these cells is contraction and relaxation, which enables the regulation of blood flow and pressure in the aorta, and helps in the distribution of oxygen and nutrients throughout the body. +Additionally, a critical characteristic of smooth muscle cells is their plasticity. They can undergo phenotypic modulation in response to changes in their environment or vascular injury, switching from a contractile to a synthetic phenotype. The contractile phenotype is characterized by high contractility and low proliferation rate, while the synthetic phenotype is marked by increased cell proliferation and matrix synthesis but reduced contractile function. +Aortic smooth muscle cells have a significant role in the physiological and pathological processes of the cardiovascular system. In the normal physiological state, they contribute to the elasticity and flexibility of the aorta. Conversely, in pathological states, changes in the function and structure of aortic smooth muscle cells are connected with various vascular diseases, including atherosclerosis, hypertension, and aneurysm. 2011-02-28T01:42:12Z BTO:0004577 + https://cellxgene.cziscience.com/cellguide/CL_0002539 aortic smooth muscle cell @@ -72565,6 +73759,21 @@ Intrahepatic cholangiocytes take part in certain pathological conditions, like p A smooth muscle cell of the aorta. GOC:tfm + + + + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Aortic smooth muscle cells are specialized and highly differentiated muscle cells that are located in the tunica media layer of the aorta. They consist of spindle-shaped cells with a centrally located nucleus. These cells are rich in actin and myosin, muscle contractile proteins, that allow them to exert force and change shape. +Aortic smooth muscle cells play a vital role in maintaining blood pressure and circulation, and are essential for vascular integrity and function. The primary function of these cells is contraction and relaxation, which enables the regulation of blood flow and pressure in the aorta, and helps in the distribution of oxygen and nutrients throughout the body. +Additionally, a critical characteristic of smooth muscle cells is their plasticity. They can undergo phenotypic modulation in response to changes in their environment or vascular injury, switching from a contractile to a synthetic phenotype. The contractile phenotype is characterized by high contractility and low proliferation rate, while the synthetic phenotype is marked by increased cell proliferation and matrix synthesis but reduced contractile function. +Aortic smooth muscle cells have a significant role in the physiological and pathological processes of the cardiovascular system. In the normal physiological state, they contribute to the elasticity and flexibility of the aorta. Conversely, in pathological states, changes in the function and structure of aortic smooth muscle cells are connected with various vascular diseases, including atherosclerosis, hypertension, and aneurysm. + DOI:10.1016/j.devcel.2005.05.017 + DOI:10.1111/febs.12414 + DOI:10.7150/ijbs.49871 + https://training.seer.cancer.gov/anatomy/cells_tissues_membranes/tissues/muscle.html + https://www.sciencedirect.com/topics/medicine-and-dentistry/aortic-smooth-muscle-cell + @@ -72667,7 +73876,7 @@ Intrahepatic cholangiocytes take part in certain pathological conditions, like p An endothelial cell that is part of the vein. - This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. Vein endothelial cells form a thin layer of squamous cells, the endothelium, lining the interior surface of veins throughout the body. They shape the inner cellular lining of the entire vascular system, including the heart, playing a crucial role in blood circulation. The unique characteristic compact arrangement of these cells enables veins to act as a barrier between the blood (that can contain foreign substances) and the surrounding venous tissue and maintain the integrity of the vascular system. The primary function of vein endothelial cells is to control the exchange of substances between the bloodstream and the surrounding tissues. They facilitate selective transportation of molecules depending on their size and solubility, including gases, nutrients, hormones, and waste products. Vein endothelial cells also play a protective role by inhibiting the translocation of toxins or pathogens from blood to tissues. Additionally, these cells are involved in blood coagulation and inflammation response, primarily by producing substances that inhibit blood clot formation under normal conditions and initiating clotting when necessary. @@ -72697,7 +73906,7 @@ Another significant function of vein endothelial cells is the regulation of bloo - This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. Vein endothelial cells form a thin layer of squamous cells, the endothelium, lining the interior surface of veins throughout the body. They shape the inner cellular lining of the entire vascular system, including the heart, playing a crucial role in blood circulation. The unique characteristic compact arrangement of these cells enables veins to act as a barrier between the blood (that can contain foreign substances) and the surrounding venous tissue and maintain the integrity of the vascular system. The primary function of vein endothelial cells is to control the exchange of substances between the bloodstream and the surrounding tissues. They facilitate selective transportation of molecules depending on their size and solubility, including gases, nutrients, hormones, and waste products. Vein endothelial cells also play a protective role by inhibiting the translocation of toxins or pathogens from blood to tissues. Additionally, these cells are involved in blood coagulation and inflammation response, primarily by producing substances that inhibit blood clot formation under normal conditions and initiating clotting when necessary. @@ -72780,6 +73989,7 @@ Another significant function of vein endothelial cells is the regulation of bloo 2011-02-28T04:20:39Z ZFA:0005773 + See CL:0002619. embryonic blood vessel endothelial progenitor cell @@ -73116,6 +74326,7 @@ Another significant function of vein endothelial cells is the regulation of bloo A fibroblast of the lymphatic system. 2011-02-28T05:16:18Z + fibroblast of lymphatic vessel @@ -73458,7 +74669,7 @@ Another significant function of vein endothelial cells is the regulation of bloo - + @@ -73470,7 +74681,7 @@ Another significant function of vein endothelial cells is the regulation of bloo - An epithelial cell of the intestine. + An epithelial cell of the lining of the intestine. 2011-03-01T05:18:31Z ZFA:0009399 @@ -73480,7 +74691,7 @@ Another significant function of vein endothelial cells is the regulation of bloo - An epithelial cell of the intestine. + An epithelial cell of the lining of the intestine. GOC:tfm @@ -73553,6 +74764,7 @@ Another significant function of vein endothelial cells is the regulation of bloo 2011-03-01T05:28:52Z + iris pigment epithelial cell @@ -73715,7 +74927,7 @@ Another significant function of vein endothelial cells is the regulation of bloo A mesenchymal stem cell of adipose tissue. - This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. Mesenchymal stem cells of adipose tissue, also known commonly as adipose-derived stem cells (ADSCs), are a population of adult stem cells that can be obtained easily from adipose tissues. They have many of the same regenerative properties as other mesenchymal stem cells, but are more easily accessible than bone marrow-derived stem cells. Adipose-derived stem cells show immense promise in the field of regenerative medicine due to their ability to differentiate into adipocytes, chondrocytes, myocytes, osteoblasts, and other cell types. ADSCs also possess immunomodulatory and homeostatic functions: they have the ability to suppress immune responses and provide a therapeutic environment for tissue repair and regeneration, as well as supporting the proliferation of adipocytes and the overall expansion of adipose tissue and contributing to the tissue's ability to react to demands of energy storage and mobilization. Dysfunction of these cells may contribute to metabolic complications observed in obesity and diabetes. @@ -73735,7 +74947,7 @@ ADSCs have been used for therapeutic applications such as pathological wound hea - This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. Mesenchymal stem cells of adipose tissue, also known commonly as adipose-derived stem cells (ADSCs), are a population of adult stem cells that can be obtained easily from adipose tissues. They have many of the same regenerative properties as other mesenchymal stem cells, but are more easily accessible than bone marrow-derived stem cells. Adipose-derived stem cells show immense promise in the field of regenerative medicine due to their ability to differentiate into adipocytes, chondrocytes, myocytes, osteoblasts, and other cell types. ADSCs also possess immunomodulatory and homeostatic functions: they have the ability to suppress immune responses and provide a therapeutic environment for tissue repair and regeneration, as well as supporting the proliferation of adipocytes and the overall expansion of adipose tissue and contributing to the tissue's ability to react to demands of energy storage and mobilization. Dysfunction of these cells may contribute to metabolic complications observed in obesity and diabetes. @@ -73840,7 +75052,7 @@ ADSCs have been used for therapeutic applications such as pathological wound hea A glial cell that myelinates or ensheathes axons in the peripheral nervous system. - This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. Schwann cells, also known as neurolemmocytes, are a type of glial cell located in the peripheral nervous system. These cells play a significant role in the healthy functioning of nerves by producing myelin, a fatty substance that forms a coating around nerve fibers. Myelin serves as an insulator and enhances the speed and efficiency of electrical nerve impulses; a single Schwann cell can myelinate a single axon. Myelination starts by the elongation and envelopment of the Schwann cell around the axon, followed by the synthesis and deposition of myelin layers. Some studies suggest that Schwann cells may regulate neuronal action potential, muscular contraction, and the sensitive response. While Schwann cells are most commonly known for the formation of the myelin sheath, some Schwann cells do not form myelin: Remak Schwann cells, a class of nonmyelinating Schwann cells, ensheath axons with smaller diameter, such as C fiber nociceptors in sciatic nerves and form Remak bundles. @@ -73866,7 +75078,7 @@ Schwann cells are found along both motor and sensory neurons and are crucial for - This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. Schwann cells, also known as neurolemmocytes, are a type of glial cell located in the peripheral nervous system. These cells play a significant role in the healthy functioning of nerves by producing myelin, a fatty substance that forms a coating around nerve fibers. Myelin serves as an insulator and enhances the speed and efficiency of electrical nerve impulses; a single Schwann cell can myelinate a single axon. Myelination starts by the elongation and envelopment of the Schwann cell around the axon, followed by the synthesis and deposition of myelin layers. Some studies suggest that Schwann cells may regulate neuronal action potential, muscular contraction, and the sensitive response. While Schwann cells are most commonly known for the formation of the myelin sheath, some Schwann cells do not form myelin: Remak Schwann cells, a class of nonmyelinating Schwann cells, ensheath axons with smaller diameter, such as C fiber nociceptors in sciatic nerves and form Remak bundles. @@ -74350,7 +75562,7 @@ Schwann cells are found along both motor and sensory neurons and are crucial for A blood vessel endothelial cell that is part of the retina. - This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. Retinal blood vessel endothelial cells constitute the innermost lining of the blood vessels found in the retina, the light-sensitive layer of tissue at the back of the eye. The primary role of these cells revolves around their location within the retinal vascular system, forming the structure of the blood-retinal barrier, a subset of the larger blood-ocular barrier system. The endothelial cells are particularly involved in the growth of new retinal blood vessels from pre-existing ones (angiogenesis); this is critical in managing the amount of oxygen and essential nutrients delivered to the ocular tissues. They are crucial for maintaining homeostasis in the retinal environment by controlling the exchange of molecules between the blood and the retina. Furthermore, they mediate immune cell trafficking, supporting the immune privilege of the eye by preventing the unrestricted infiltration of inflammatory cells into the retina, thus maintaining ocular health and normal vision. @@ -74377,7 +75589,7 @@ The malfunction or dysfunction of retinal blood vessel endothelial cells is impl - This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. Retinal blood vessel endothelial cells constitute the innermost lining of the blood vessels found in the retina, the light-sensitive layer of tissue at the back of the eye. The primary role of these cells revolves around their location within the retinal vascular system, forming the structure of the blood-retinal barrier, a subset of the larger blood-ocular barrier system. The endothelial cells are particularly involved in the growth of new retinal blood vessels from pre-existing ones (angiogenesis); this is critical in managing the amount of oxygen and essential nutrients delivered to the ocular tissues. They are crucial for maintaining homeostasis in the retinal environment by controlling the exchange of molecules between the blood and the retina. Furthermore, they mediate immune cell trafficking, supporting the immune privilege of the eye by preventing the unrestricted infiltration of inflammatory cells into the retina, thus maintaining ocular health and normal vision. @@ -74422,7 +75634,7 @@ The malfunction or dysfunction of retinal blood vessel endothelial cells is impl An epithelial cell of the retinal pigmented epithelium. - This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. Retinal pigment epithelial (RPE) cells form a single layer of cells at the back of the eye sandwiched between the neurosensory retina and the choroid, playing a significant role in maintaining vision health. These pigment-laden cells are highly specialized and perform an array of metabolic and transport functions essential for the maintenance of the photoreceptor cells (rods and cones) in the retina. The pigmentation of RPE cells actively aids in the absorption of excess light and the prevention of light scattering, thus enhancing the eye's optical properties. The retinal pigment epithelium forms a key part of the blood/retina barrier. The cells have long sheet-like microvilli on their apical membrane that project into the light-sensitive outer segments of the photoreceptors, forming a close structural interaction. The basolateral membrane of the RPE interacts with the underlying Bruch’s membrane, which separates the RPE cells from fenestrated endothelium of the choriocapillaris. @@ -74446,7 +75658,7 @@ Beyond this, RPE cells take part in the phagocytosis process, where they digest - This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. Retinal pigment epithelial (RPE) cells form a single layer of cells at the back of the eye sandwiched between the neurosensory retina and the choroid, playing a significant role in maintaining vision health. These pigment-laden cells are highly specialized and perform an array of metabolic and transport functions essential for the maintenance of the photoreceptor cells (rods and cones) in the retina. The pigmentation of RPE cells actively aids in the absorption of excess light and the prevention of light scattering, thus enhancing the eye's optical properties. The retinal pigment epithelium forms a key part of the blood/retina barrier. The cells have long sheet-like microvilli on their apical membrane that project into the light-sensitive outer segments of the photoreceptors, forming a close structural interaction. The basolateral membrane of the RPE interacts with the underlying Bruch’s membrane, which separates the RPE cells from fenestrated endothelium of the choriocapillaris. @@ -74606,8 +75818,14 @@ Beyond this, RPE cells take part in the phagocytosis process, where they digest A smooth muscle of the pulmonary artery. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Smooth muscle cells of the pulmonary artery form a principal component of the pulmonary artery's media layer, the middle section of the artery wall typically found between endothelial inner layer (intima) and the outermost connective tissue layer (adventitia). The unique structure of these cells, defined by fusiform shape and the absence of striations, sets them apart from other muscle cell types, including cardiac and skeletal. +The primary function of smooth muscle cells of the pulmonary artery is to regulate the diameter of the pulmonary artery, which in turn controls the flow of blood into the lungs. They accomplish this task through the contraction and relaxation, indicative of vasoconstriction and vasodilation respectively. When these cells contract, the diameter of the artery narrows, leading to reduced blood flow. Conversely, relaxation of these cells widens the artery, facilitating increased blood flow. Such blood flow modulation is crucial for the maintenance of blood pressure and ensuring that the lungs receive an adequate blood supply for efficient oxygen exchange. +As a result, abnormal function or proliferation of these cells can contribute to conditions such as pulmonary hypertension, a condition characterized by high blood pressure in the arteries leading to the lungs. This can occur due to hypoxia (lack of enough oxygen), leading to excessive constriction or proliferation of the smooth muscle cells. 2011-03-06T05:01:28Z BTO:0003336 + https://cellxgene.cziscience.com/cellguide/CL_0002591 smooth muscle cell of the pulmonary artery @@ -74618,6 +75836,18 @@ Beyond this, RPE cells take part in the phagocytosis process, where they digest A smooth muscle of the pulmonary artery. GOC:tfm + + + + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Smooth muscle cells of the pulmonary artery form a principal component of the pulmonary artery's media layer, the middle section of the artery wall typically found between endothelial inner layer (intima) and the outermost connective tissue layer (adventitia). The unique structure of these cells, defined by fusiform shape and the absence of striations, sets them apart from other muscle cell types, including cardiac and skeletal. +The primary function of smooth muscle cells of the pulmonary artery is to regulate the diameter of the pulmonary artery, which in turn controls the flow of blood into the lungs. They accomplish this task through the contraction and relaxation, indicative of vasoconstriction and vasodilation respectively. When these cells contract, the diameter of the artery narrows, leading to reduced blood flow. Conversely, relaxation of these cells widens the artery, facilitating increased blood flow. Such blood flow modulation is crucial for the maintenance of blood pressure and ensuring that the lungs receive an adequate blood supply for efficient oxygen exchange. +As a result, abnormal function or proliferation of these cells can contribute to conditions such as pulmonary hypertension, a condition characterized by high blood pressure in the arteries leading to the lungs. This can occur due to hypoxia (lack of enough oxygen), leading to excessive constriction or proliferation of the smooth muscle cells. + DOI:10.1016/j.apsb.2012.12.007 + DOI:10.1124/pr.115.010652 + https://www.sciencedirect.com/topics/medicine-and-dentistry/pulmonary-artery-smooth-muscle-cell + @@ -74862,8 +76092,14 @@ Beyond this, RPE cells take part in the phagocytosis process, where they digest Any smooth muscle cell that is part of some bronchus. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Bronchial smooth muscle cells are specialized types of cells found in the bronchi of the respiratory system in mammals. These bronchi are tubular structures that function to carry air from the trachea into the lungs. As part of the smooth muscle tissue, bronchial smooth muscle cells are involuntary cells, meaning they function with minimal direct voluntary control. They are characterized by their elongated spindle-shaped structure, with each cell containing a single central nucleus. +The primary function of bronchial smooth muscle cells is to control airway diameter, which directly influences the flow of air into and out of the lungs. Muscular contractions and relaxations mediated by these cells enable the bronchi to constrict or expand, facilitating the regulation of respiratory airflow. Additionally, these cells play a pivotal role in immune responses as they produce and release various substances that can instigate or lessen inflammation of airway tissue. Furthermore, bronchial smooth muscle cells can proliferate and lay down collagen and other extracellular matrix proteins, contributing to the structural integrity of the bronchial tubes. +In pathological conditions, such as asthma and chronic obstructive pulmonary disease, the function and biology of bronchial smooth muscle cells change. Asthma, for example, is associated with an abnormal increase in the mass of the bronchial smooth muscles, leading to narrowing of the airways and resultant breathing difficulties. These cells also exhibit altered contractile behavior and an augmented immune response during inflammatory lung diseases. 2011-03-06T05:46:39Z BTO:0004402 + https://cellxgene.cziscience.com/cellguide/CL_0002598 bronchial smooth muscle cell @@ -74874,6 +76110,19 @@ Beyond this, RPE cells take part in the phagocytosis process, where they digest Any smooth muscle cell that is part of some bronchus. FBC:Autogenerated + + + + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Bronchial smooth muscle cells are specialized types of cells found in the bronchi of the respiratory system in mammals. These bronchi are tubular structures that function to carry air from the trachea into the lungs. As part of the smooth muscle tissue, bronchial smooth muscle cells are involuntary cells, meaning they function with minimal direct voluntary control. They are characterized by their elongated spindle-shaped structure, with each cell containing a single central nucleus. +The primary function of bronchial smooth muscle cells is to control airway diameter, which directly influences the flow of air into and out of the lungs. Muscular contractions and relaxations mediated by these cells enable the bronchi to constrict or expand, facilitating the regulation of respiratory airflow. Additionally, these cells play a pivotal role in immune responses as they produce and release various substances that can instigate or lessen inflammation of airway tissue. Furthermore, bronchial smooth muscle cells can proliferate and lay down collagen and other extracellular matrix proteins, contributing to the structural integrity of the bronchial tubes. +In pathological conditions, such as asthma and chronic obstructive pulmonary disease, the function and biology of bronchial smooth muscle cells change. Asthma, for example, is associated with an abnormal increase in the mass of the bronchial smooth muscles, leading to narrowing of the airways and resultant breathing difficulties. These cells also exhibit altered contractile behavior and an augmented immune response during inflammatory lung diseases. + DOI:10.1152/japplphysiol.00313.2006 + DOI:10.1183/09031936.00019810 + https://www.ncbi.nlm.nih.gov/books/NBK537353/ + https://www.sciencedirect.com/topics/agricultural-and-biological-sciences/bronchial-muscle + @@ -74941,7 +76190,13 @@ Beyond this, RPE cells take part in the phagocytosis process, where they digest A smooth muscle cell of the trachea. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Smooth muscle cells of the trachea have a characteristic 'smooth' (non-striated) appearance under the microscope, a distinguishing feature that differentiates them from skeletal and cardiac muscle cells. The smooth appearance is due to the organization of actin and myosin filaments in the cell, which allows for a controlled, contractile function. +These cells play a key role in controlling the diameter of the trachea, thus regulating the airflow. They are responsible for the involuntary constriction and relaxation of the trachea influencing the air passage during various physiological behaviors like breathing, coughing, and sneezing. This autonomic control allows for adaptations to specific body requirements without conscious control, such as increasing air flow during exercise or restricting it during rest. +In conditions such as asthma, chronic bronchitis, and emphysema, there are changes in smooth muscle cells. For example, the mass of smooth muscle cells increases in chronic airway diseases, possibly in response to chronic inflammation. This increase may indicate a pathological condition or be a part of the body's response to injury and repair. 2011-03-06T05:50:28Z + https://cellxgene.cziscience.com/cellguide/CL_0002600 smooth muscle cell of trachea @@ -74951,6 +76206,18 @@ Beyond this, RPE cells take part in the phagocytosis process, where they digest A smooth muscle cell of the trachea. GOC:tfm + + + + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Smooth muscle cells of the trachea have a characteristic 'smooth' (non-striated) appearance under the microscope, a distinguishing feature that differentiates them from skeletal and cardiac muscle cells. The smooth appearance is due to the organization of actin and myosin filaments in the cell, which allows for a controlled, contractile function. +These cells play a key role in controlling the diameter of the trachea, thus regulating the airflow. They are responsible for the involuntary constriction and relaxation of the trachea influencing the air passage during various physiological behaviors like breathing, coughing, and sneezing. This autonomic control allows for adaptations to specific body requirements without conscious control, such as increasing air flow during exercise or restricting it during rest. +In conditions such as asthma, chronic bronchitis, and emphysema, there are changes in smooth muscle cells. For example, the mass of smooth muscle cells increases in chronic airway diseases, possibly in response to chronic inflammation. This increase may indicate a pathological condition or be a part of the body's response to injury and repair. + DOI:10.1016/s1357-2725(02)00259-5 + https://www.ncbi.nlm.nih.gov/books/NBK9961 + https://www.sciencedirect.com/topics/agricultural-and-biological-sciences/airway-smooth-muscle + @@ -74977,7 +76244,13 @@ Beyond this, RPE cells take part in the phagocytosis process, where they digest A smooth muscle cell of the uterus. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Uterine smooth muscle cells are specialized cells that make up the majority of the uterus and in particular, the myometrium. The myometrium is a thick, involuntary muscle layer, principally consisting of verticillate cell bundles that sculpt the helical architecture of the uterus. This dense muscular tissue, packed with uterine smooth muscle cells, is responsible for the significant contractile force witnessed during the physical processes of labor and childbirth. +In the non-pregnant uterus, they exist in a quiescent phase. Upon implantation, these cells are primarily responsible for the expansion consequently allowing the uterus to accommodate the growing fetus. Towards the end of pregnancy, under the influence of hormonal and mechanical signals, uterine smooth muscle cells transition from a relaxed phase to an active contractile phase, culminating in the delivery of the fetus. +At the cellular level, these transitions involve significant changes in the electrophysiological properties of uterine smooth muscle cells. Governed by a complex interplay of ion channels, transporters, and signaling proteins, these cells adjust their electrical activity, conduction properties, and contracting mechanisms. Any issues with these processes can result in problems such as preterm birth or labor dysfunction. 2011-03-06T05:53:28Z + https://cellxgene.cziscience.com/cellguide/CL_0002601 uterine smooth muscle cell @@ -74993,6 +76266,19 @@ Beyond this, RPE cells take part in the phagocytosis process, where they digest A smooth muscle cell of the uterus. GOC:tfm + + + + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Uterine smooth muscle cells are specialized cells that make up the majority of the uterus and in particular, the myometrium. The myometrium is a thick, involuntary muscle layer, principally consisting of verticillate cell bundles that sculpt the helical architecture of the uterus. This dense muscular tissue, packed with uterine smooth muscle cells, is responsible for the significant contractile force witnessed during the physical processes of labor and childbirth. +In the non-pregnant uterus, they exist in a quiescent phase. Upon implantation, these cells are primarily responsible for the expansion consequently allowing the uterus to accommodate the growing fetus. Towards the end of pregnancy, under the influence of hormonal and mechanical signals, uterine smooth muscle cells transition from a relaxed phase to an active contractile phase, culminating in the delivery of the fetus. +At the cellular level, these transitions involve significant changes in the electrophysiological properties of uterine smooth muscle cells. Governed by a complex interplay of ion channels, transporters, and signaling proteins, these cells adjust their electrical activity, conduction properties, and contracting mechanisms. Any issues with these processes can result in problems such as preterm birth or labor dysfunction. + DOI:10.1177/0036850419850431 + DOI:10.1203/00006450-199811000-00001 + DOI:10.3791/56639 + https://www.ncbi.nlm.nih.gov/books/NBK532927/ + @@ -75273,7 +76559,7 @@ Beyond this, RPE cells take part in the phagocytosis process, where they digest - + @@ -75281,7 +76567,6 @@ Beyond this, RPE cells take part in the phagocytosis process, where they digest - @@ -75294,12 +76579,6 @@ Beyond this, RPE cells take part in the phagocytosis process, where they digest 2011-03-06T07:42:06Z raphe nuclei neuron - - - - - true - @@ -75315,7 +76594,7 @@ Beyond this, RPE cells take part in the phagocytosis process, where they digest - + @@ -75323,7 +76602,6 @@ Beyond this, RPE cells take part in the phagocytosis process, where they digest - @@ -75336,12 +76614,6 @@ Beyond this, RPE cells take part in the phagocytosis process, where they digest 2011-03-06T07:43:34Z neuron of the dorsal spinal cord - - - - - true - @@ -75357,7 +76629,7 @@ Beyond this, RPE cells take part in the phagocytosis process, where they digest - + @@ -75365,7 +76637,6 @@ Beyond this, RPE cells take part in the phagocytosis process, where they digest - @@ -75378,12 +76649,6 @@ Beyond this, RPE cells take part in the phagocytosis process, where they digest 2011-03-06T07:46:03Z neuron of the ventral spinal cord - - - - - true - @@ -75399,7 +76664,7 @@ Beyond this, RPE cells take part in the phagocytosis process, where they digest - + @@ -75434,7 +76699,7 @@ Beyond this, RPE cells take part in the phagocytosis process, where they digest - + @@ -75442,7 +76707,6 @@ Beyond this, RPE cells take part in the phagocytosis process, where they digest - @@ -75455,12 +76719,6 @@ Beyond this, RPE cells take part in the phagocytosis process, where they digest 2011-03-06T07:48:42Z neuron of the substantia nigra - - - - - true - @@ -75625,7 +76883,7 @@ Beyond this, RPE cells take part in the phagocytosis process, where they digest An endothelial cell of the umbilical vein. - This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. Endothelial cells of the umbilical vein form the inner lining of the veins found in the umbilical cord. They are involved in tube formation and migration which are essential for angiogenesis, the process of generating new blood vessels; this is critical during the fetal stage for the development of the circulatory system. Endothelial cells of the umbilical vein also play a role in controlling the passage of white blood cells into tissues during inflammatory responses. Because human umbilical vein endothelial cells (HUVECs) can easily be derived from the umbilical cord, and because they express common endothelial cell markers, they have been used as an epithelial cell model for studies on cell proliferation, migration, angiogenesis, and inflammation. They have been used as models for vascular diseases like atherosclerosis, for investigating how tumor cells infiltrate blood vessels and form metastases. @@ -75644,7 +76902,7 @@ Thus, while endothelial cells of the umbilical vein play a critical role in vasc - This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. Endothelial cells of the umbilical vein form the inner lining of the veins found in the umbilical cord. They are involved in tube formation and migration which are essential for angiogenesis, the process of generating new blood vessels; this is critical during the fetal stage for the development of the circulatory system. Endothelial cells of the umbilical vein also play a role in controlling the passage of white blood cells into tissues during inflammatory responses. Because human umbilical vein endothelial cells (HUVECs) can easily be derived from the umbilical cord, and because they express common endothelial cell markers, they have been used as an epithelial cell model for studies on cell proliferation, migration, angiogenesis, and inflammation. They have been used as models for vascular diseases like atherosclerosis, for investigating how tumor cells infiltrate blood vessels and form metastases. @@ -75755,6 +77013,7 @@ Thus, while endothelial cells of the umbilical vein play a critical role in vasc Any epithelial cell that is part of some gingival epithelium. 2011-03-14T12:46:28Z + gingival epithelial cell @@ -75930,6 +77189,7 @@ Thus, while endothelial cells of the umbilical vein play a critical role in vasc An immature astrocyte. immature astrocytic glia + immature astrocyte @@ -76047,6 +77307,12 @@ Thus, while endothelial cells of the umbilical vein play a critical role in vasc A mature microglial cell that has changed shape to an amoeboid morphology and is capable of cytokine production and antigen presentation. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Mature microglial cells represented one of the macrophage populations within the central nervous system (CNS). Microglial cells serve as the primary immune defense mechanism within the CNS, playing active roles in maintaining brain homeostasis and responding to pathological processes. In response to pathogens and injuries, microglial cells mature and change their morphology from a ramified shape with small processes (normal state) to an amoeboid shape (mature state). +Mature microglial cells possess multiple functional abilities, thereby enabling them to execute diverse roles in order to maintain the health of surrounding neural cells. They act to clear away cellular debris, dead neurons, or plaque formations through the process of phagocytosis. They are also continuously scanning their environment and are able to detect subtle changes in the neural landscape caused by injury, disease, or infection. Upon detection of such changes, these cells become activated and present antigens and secrete cytokines and chemokines to initiate an inflammation response, which sustains the brain’s defense against injurious agents. +Their role is not solely destructive or defensive: mature microglial cells also contribute to neurodevelopment by guiding the formation of neural circuits, synaptogenesis, and remodeling. Furthermore, they assist in managing synaptic plasticity, a key process in learning and memory functions. While the dysregulation of microglial cells has been implicated in various neurodegenerative diseases, they are also regarded as potential therapeutic targets for such conditions, given their crucial roles in maintaining CNS health. + https://cellxgene.cziscience.com/cellguide/CL_0002629 activated microglia mature microglia reactive microglia @@ -76072,6 +77338,20 @@ Thus, while endothelial cells of the umbilical vein play a critical role in vasc PMID:18396103 PMID:20021364 + + + + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Mature microglial cells represented one of the macrophage populations within the central nervous system (CNS). Microglial cells serve as the primary immune defense mechanism within the CNS, playing active roles in maintaining brain homeostasis and responding to pathological processes. In response to pathogens and injuries, microglial cells mature and change their morphology from a ramified shape with small processes (normal state) to an amoeboid shape (mature state). +Mature microglial cells possess multiple functional abilities, thereby enabling them to execute diverse roles in order to maintain the health of surrounding neural cells. They act to clear away cellular debris, dead neurons, or plaque formations through the process of phagocytosis. They are also continuously scanning their environment and are able to detect subtle changes in the neural landscape caused by injury, disease, or infection. Upon detection of such changes, these cells become activated and present antigens and secrete cytokines and chemokines to initiate an inflammation response, which sustains the brain’s defense against injurious agents. +Their role is not solely destructive or defensive: mature microglial cells also contribute to neurodevelopment by guiding the formation of neural circuits, synaptogenesis, and remodeling. Furthermore, they assist in managing synaptic plasticity, a key process in learning and memory functions. While the dysregulation of microglial cells has been implicated in various neurodegenerative diseases, they are also regarded as potential therapeutic targets for such conditions, given their crucial roles in maintaining CNS health. + DOI:10.1111/j.1745-7254.2007.00625.x + DOI:10.1111/jnc.15689 + DOI:10.3389/fimmu.2022.997786 + DOI:10.4103/1673-5374.226386 + DOI:10.4103/1673-5374.322423 + @@ -76200,7 +77480,7 @@ Thus, while endothelial cells of the umbilical vein play a critical role in vasc A basal cell in the respiratory tract. - This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. Respiratory basal cells are highly specialized cells that serve a crucial role in the human airway epithelium, predominantly found lining the surfaces of the trachea and bronchi. These cells exhibit a distinctive columnar shape and are attached directly to the basal lamina. They are characterized by the presence of high amounts of cytoplasmic keratins, predominantly keratin 5 and 14, and transcription factor tumor protein (tp63), which set them apart from other types of lung epithelial cells such as ciliated cells and secretory cells. Basal cells are essential for maintaining airway integrity. They make up one third of all respiratory epithelial cells and serve as stem cells as they can transform into different cell types, like goblet cells, ciliated cells, and club cells, when needed for homeostatic maintenance of the epithelial barrier or to repair and restore a healthy cellular environment after injury. @@ -76222,7 +77502,7 @@ Their position at the interface between the internal environment and the externa - This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. Respiratory basal cells are highly specialized cells that serve a crucial role in the human airway epithelium, predominantly found lining the surfaces of the trachea and bronchi. These cells exhibit a distinctive columnar shape and are attached directly to the basal lamina. They are characterized by the presence of high amounts of cytoplasmic keratins, predominantly keratin 5 and 14, and transcription factor tumor protein (tp63), which set them apart from other types of lung epithelial cells such as ciliated cells and secretory cells. Basal cells are essential for maintaining airway integrity. They make up one third of all respiratory epithelial cells and serve as stem cells as they can transform into different cell types, like goblet cells, ciliated cells, and club cells, when needed for homeostatic maintenance of the epithelial barrier or to repair and restore a healthy cellular environment after injury. @@ -76324,7 +77604,6 @@ Their position at the interface between the internal environment and the externa - An epithelial cell of the anal canal that is keratinized. This cell type is found towards the lower, rectal end of the anal canal. 2011-07-08T02:08:40Z @@ -76741,33 +78020,41 @@ Their position at the interface between the internal environment and the externa - + - + + + + + - + + + - + - A glandular epithelial cell of the endometrium. + A glandular epithelial cell of the endometrium. Following ovulation, these cells secrete a glycogen-rich substance known as histotroph or uterine milk, which nourishes the embryo if implantation occurs. 2011-07-08T03:54:08Z + glandular cell of endometrium FMA:86489 - glandular cell of endometrium + glandular endometrial unciliated epithelial cell - A glandular epithelial cell of the endometrium. + A glandular epithelial cell of the endometrium. Following ovulation, these cells secrete a glycogen-rich substance known as histotroph or uterine milk, which nourishes the embryo if implantation occurs. GOC:tfm + PMID:25023676 @@ -76781,7 +78068,7 @@ Their position at the interface between the internal environment and the externa - + @@ -76862,7 +78149,7 @@ Their position at the interface between the internal environment and the externa - + @@ -77183,7 +78470,7 @@ Their position at the interface between the internal environment and the externa An endothelial stalk cell is a specialized endothelial cell that follows behind the tip cell of an angiogenic sprout. - This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. Endothelial stalk cells are specialized vascular cells vital in angiogenesis, a process through which new blood vessels are formed from pre-existing ones; specifically, endothelial stalk cells are involved in sprouting angiogenesis, where they help form the body of new blood vessels. Vascular sprouting relies on the coordinated activity of migrating endothelial tip cells at the forefront and proliferating stalk cells that elongate the sprout. The process is tightly controlled by different growths factors: Vascular Endothelial Growth Factor acts on endothelial cells, inducing them to become endothelial tip cells that initiate sprouting. After sprouting initiation, activation of Notch signaling suppresses differentiation toward a tip cell phenotype and some of the endothelial cells differentiate into stalk cells, which follow tip cells, multiply, and elongate to provide a structural backbone to the growing vessel sprout. @@ -77203,7 +78490,7 @@ In contrast to endothelial tip cells, which migrate and lead the angiogenic spro - This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. Endothelial stalk cells are specialized vascular cells vital in angiogenesis, a process through which new blood vessels are formed from pre-existing ones; specifically, endothelial stalk cells are involved in sprouting angiogenesis, where they help form the body of new blood vessels. Vascular sprouting relies on the coordinated activity of migrating endothelial tip cells at the forefront and proliferating stalk cells that elongate the sprout. The process is tightly controlled by different growths factors: Vascular Endothelial Growth Factor acts on endothelial cells, inducing them to become endothelial tip cells that initiate sprouting. After sprouting initiation, activation of Notch signaling suppresses differentiation toward a tip cell phenotype and some of the endothelial cells differentiate into stalk cells, which follow tip cells, multiply, and elongate to provide a structural backbone to the growing vessel sprout. @@ -77230,6 +78517,7 @@ In contrast to endothelial tip cells, which migrate and lead the angiogenic spro A multi-fate stem cell that can give rise to different retinal cell types including rod and cone cells. 2011-08-16T02:38:01Z + retinal progenitor cell @@ -77266,7 +78554,13 @@ In contrast to endothelial tip cells, which migrate and lead the angiogenic spro A skeletal muscle cell that is part of the tongue. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Tongue muscle cells are responsible for essential functions like mastication, deglutition (swallowing), phonation (speech), and taste receptivity. They can be classified into two functional classes - extrinsic and intrinsic muscle cells. +The extrinsic tongue muscle cells originate outside the tongue and are primarily involved in determining the position of the tongue within the mouth. Muscle groups such as the genioglossus, hyoglossus, and styloglossus are composed of these extrinsic muscle cells and grant the tongue its wide range of motion. +The intrinsic tongue muscle cells, on the other hand, originate and function within the tongue itself, influencing the shape of the tongue during speech, eating, and swallowing. These cells can contract to alter the tongue's shape, making it long, short, curled, or flat, as needed. Together, these two types of muscle cells allow the tongue to perform its vital functions effectively. Moreover, they play a critical role in maintaining oral health by facilitating physical cleaning of the oral cavity and assisting in the mechanical breakdown of food. 2011-08-16T03:10:02Z + https://cellxgene.cziscience.com/cellguide/CL_0002673 tongue muscle cell @@ -77277,6 +78571,18 @@ In contrast to endothelial tip cells, which migrate and lead the angiogenic spro GOC:tfm PMID:18816858 + + + + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Tongue muscle cells are responsible for essential functions like mastication, deglutition (swallowing), phonation (speech), and taste receptivity. They can be classified into two functional classes - extrinsic and intrinsic muscle cells. +The extrinsic tongue muscle cells originate outside the tongue and are primarily involved in determining the position of the tongue within the mouth. Muscle groups such as the genioglossus, hyoglossus, and styloglossus are composed of these extrinsic muscle cells and grant the tongue its wide range of motion. +The intrinsic tongue muscle cells, on the other hand, originate and function within the tongue itself, influencing the shape of the tongue during speech, eating, and swallowing. These cells can contract to alter the tongue's shape, making it long, short, curled, or flat, as needed. Together, these two types of muscle cells allow the tongue to perform its vital functions effectively. Moreover, they play a critical role in maintaining oral health by facilitating physical cleaning of the oral cavity and assisting in the mechanical breakdown of food. + DOI:10.1002/ca.21011 + https://www.ncbi.nlm.nih.gov/books/NBK507782/ + https://www.ncbi.nlm.nih.gov/books/NBK554405/ + @@ -77465,7 +78771,6 @@ In contrast to endothelial tip cells, which migrate and lead the angiogenic spro - @@ -77557,7 +78862,7 @@ In contrast to endothelial tip cells, which migrate and lead the angiogenic spro - + @@ -77637,6 +78942,7 @@ In contrast to endothelial tip cells, which migrate and lead the angiogenic spro retinal ganglion D cell cell CL:0003001 + bistratified retinal ganglion cell @@ -78577,6 +79883,7 @@ In contrast to endothelial tip cells, which migrate and lead the angiogenic spro + @@ -78950,7 +80257,6 @@ In contrast to endothelial tip cells, which migrate and lead the angiogenic spro - @@ -79011,7 +80317,6 @@ In contrast to endothelial tip cells, which migrate and lead the angiogenic spro - @@ -79160,7 +80465,7 @@ In contrast to endothelial tip cells, which migrate and lead the angiogenic spro - + @@ -79572,6 +80877,7 @@ In contrast to endothelial tip cells, which migrate and lead the angiogenic spro https://orcid.org/0000-0002-5260-9315 cell CL:0004213 + type 3a cone bipolar cell @@ -79608,6 +80914,7 @@ In contrast to endothelial tip cells, which migrate and lead the angiogenic spro https://orcid.org/0000-0002-5260-9315 cell CL:0004214 + type 3b cone bipolar cell @@ -79628,6 +80935,7 @@ In contrast to endothelial tip cells, which migrate and lead the angiogenic spro https://orcid.org/0000-0002-5260-9315 cell CL:0004215 + type 5a cone bipolar cell @@ -79642,6 +80950,7 @@ In contrast to endothelial tip cells, which migrate and lead the angiogenic spro https://orcid.org/0000-0002-5260-9315 cell CL:0004216 + type 5b cone bipolar cell @@ -79664,6 +80973,7 @@ In contrast to endothelial tip cells, which migrate and lead the angiogenic spro cell H1 CL:0004217 + H1 horizontal cell @@ -79699,6 +81009,7 @@ In contrast to endothelial tip cells, which migrate and lead the angiogenic spro cell H2 CL:0004218 + H2 horizontal cell @@ -79736,13 +81047,11 @@ In contrast to endothelial tip cells, which migrate and lead the angiogenic spro A bistratifed retinal amacrine cell with a small dendritic field, dendrite stratification in S1-S2, and a second dendrite stratification in S5. This cell type releases the neurotransmitter glycine. - https://orcid.org/0000-0001-7258-9596 https://orcid.org/0000-0002-5260-9315 cell CL:0004219 - A2 amacrine cell @@ -79979,13 +81288,8 @@ In contrast to endothelial tip cells, which migrate and lead the angiogenic spro + - - - - - - @@ -80221,13 +81525,11 @@ In contrast to endothelial tip cells, which migrate and lead the angiogenic spro An amacrine cell with a flat dendritic arbor and a medium dendritic field. Starburst amacrine cells have post-synaptic terminals in S2. This cell type releases the neurotransmitters gamma-aminobutyric acid (GABA) and acetylcholine. - https://orcid.org/0000-0001-7258-9596 https://orcid.org/0000-0002-5260-9315 cell CL:0004232 - starburst amacrine cell @@ -80712,7 +82014,7 @@ In contrast to endothelial tip cells, which migrate and lead the angiogenic spro - + @@ -80792,12 +82094,10 @@ In contrast to endothelial tip cells, which migrate and lead the angiogenic spro An amicrine that has a medium dendritic field. - https://orcid.org/0000-0001-7258-9596 https://orcid.org/0000-0002-5260-9315 cell CL:0004252 - medium field retinal amacrine cell @@ -80814,12 +82114,10 @@ In contrast to endothelial tip cells, which migrate and lead the angiogenic spro An amicrine that has a wide dendritic field. - https://orcid.org/0000-0001-7258-9596 https://orcid.org/0000-0002-5260-9315 cell CL:0004253 - wide field retinal amacrine cell @@ -80845,7 +82143,7 @@ In contrast to endothelial tip cells, which migrate and lead the angiogenic spro - + @@ -80860,7 +82158,7 @@ In contrast to endothelial tip cells, which migrate and lead the angiogenic spro - + true @@ -81035,7 +82333,7 @@ In contrast to endothelial tip cells, which migrate and lead the angiogenic spro Specialized epithelial cells involved in the maintenance of osmotic homeostasis. They are characterized by abundant mitochondria and ion transporters. In amniotes, they are present in the renal system. In freshwater fish, ionocytes in the skin and gills help maintain osmotic homeostasis by absorbing salt from the external environment. - This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. Ionocytes are specialized cells predominantly found in the mammalian respiratory and renal systems as well as in the gills, skin, and intestinal tract of fish. These cells play crucial roles in maintaining ion and acid-base homeostasis. Ionocytes demonstrate remarkable plasticity and are able to adapt themselves in response to changes in environmental conditions such as pH, salinity, ion concentration, and temperature. These cells work by selectively absorbing specific ions from the environment, thus maintaining the body's internal ionic balance. The most commonly absorbed ions include sodium (Na+), chloride (Cl-), calcium (Ca2+), and hydrogen (H+). Moreover, ionocytes contribute to acid-base regulation. In response to acidosis or alkalosis, ionocytes can either excrete or retain hydrogen (H+) and bicarbonate (HCO3-) ions to readjust the blood pH. Further, experimental evidence suggests a functional complexity of ionocytes, implying diverse roles beyond ion regulation. Recent research highlights ionocytes' involvement in ammonia excretion and the regulation of extracellular fluid volume, highlighting their contribution to the overall homeostatic process. @@ -81056,7 +82354,7 @@ Malfunctioning ionocytes have been implicated in various diseases, including cys - This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. Ionocytes are specialized cells predominantly found in the mammalian respiratory and renal systems as well as in the gills, skin, and intestinal tract of fish. These cells play crucial roles in maintaining ion and acid-base homeostasis. Ionocytes demonstrate remarkable plasticity and are able to adapt themselves in response to changes in environmental conditions such as pH, salinity, ion concentration, and temperature. These cells work by selectively absorbing specific ions from the environment, thus maintaining the body's internal ionic balance. The most commonly absorbed ions include sodium (Na+), chloride (Cl-), calcium (Ca2+), and hydrogen (H+). Moreover, ionocytes contribute to acid-base regulation. In response to acidosis or alkalosis, ionocytes can either excrete or retain hydrogen (H+) and bicarbonate (HCO3-) ions to readjust the blood pH. Further, experimental evidence suggests a functional complexity of ionocytes, implying diverse roles beyond ion regulation. Recent research highlights ionocytes' involvement in ammonia excretion and the regulation of extracellular fluid volume, highlighting their contribution to the overall homeostatic process. @@ -81156,7 +82454,7 @@ Malfunctioning ionocytes have been implicated in various diseases, including cys A cuboidal epithelial cell of the kidney which regulates sodium and potassium balance. The activity of sodium and potassium channels on the apical membrane of the cell is regulated by aldosterone and vasopressin. In mammals this cell type is located in the renal collecting duct system. - This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. Renal principal cells are the major cell type in the initial collecting tubule and the cortical and outer medullary collecting ducts, as well as the connecting tubule, in the nephrons of the kidneys. A key function of renal principal cells is the regulation of water balance in the body. These cells express aquaporin-2 (AQP2) water channels, which facilitate the reabsorption of water from the fluid within the renal tubule lumen back into the blood. The translocation of AQP2 to the cell membrane is controlled by the hormone vasopressin: In response to high vasopressin levels, AQP2 moves to the cell membrane, allowing water to pass through effectively and be reabsorbed, therefore concentrating the urine. Conversely, in low vasopressin conditions, AQP2 is removed from the membrane, reducing water reabsorption and diluting the urine. @@ -81175,7 +82473,7 @@ Renal principal cells are also involved in the regulation of sodium and potassiu - This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. Renal principal cells are the major cell type in the initial collecting tubule and the cortical and outer medullary collecting ducts, as well as the connecting tubule, in the nephrons of the kidneys. A key function of renal principal cells is the regulation of water balance in the body. These cells express aquaporin-2 (AQP2) water channels, which facilitate the reabsorption of water from the fluid within the renal tubule lumen back into the blood. The translocation of AQP2 to the cell membrane is controlled by the hormone vasopressin: In response to high vasopressin levels, AQP2 moves to the cell membrane, allowing water to pass through effectively and be reabsorbed, therefore concentrating the urine. Conversely, in low vasopressin conditions, AQP2 is removed from the membrane, reducing water reabsorption and diluting the urine. @@ -81200,7 +82498,7 @@ Renal principal cells are also involved in the regulation of sodium and potassiu A cuboidal epithelial cell of the kidney that regulates acid/base balance. - This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. Renal intercalated cells are specialized cells located in the collecting duct system of the kidneys. The primary role of intercalated cells is to reabsorb bicarbonate ions and secrete hydrogen ions, thereby maintaining the acid-base homeostasis in the blood. They comprise two main subtypes primarily distinguished by their functional and morphological attributes: alpha and beta intercalated cells. Alpha intercalated cells are more predominant when the body is in a state of acidosis, a condition characterized by an increased acidity of the blood. These cells are specialized in secreting excessive hydrogen ions into the urine through a mechanism involving vacuolar H+-ATPase and H+/K+-ATPase pumps on their apical membranes. They simultaneously reabsorb bicarbonate ions from the tubular fluid and return them to the bloodstream via mechanisms involving carbonic anhydrase II and bicarbonate/chloride exchangers on the basolateral membrane. This dual process helps to increase blood pH towards normal levels. @@ -81223,7 +82521,7 @@ In summary, renal intercalated cells play a critical role in the delicate balanc - This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. Renal intercalated cells are specialized cells located in the collecting duct system of the kidneys. The primary role of intercalated cells is to reabsorb bicarbonate ions and secrete hydrogen ions, thereby maintaining the acid-base homeostasis in the blood. They comprise two main subtypes primarily distinguished by their functional and morphological attributes: alpha and beta intercalated cells. Alpha intercalated cells are more predominant when the body is in a state of acidosis, a condition characterized by an increased acidity of the blood. These cells are specialized in secreting excessive hydrogen ions into the urine through a mechanism involving vacuolar H+-ATPase and H+/K+-ATPase pumps on their apical membranes. They simultaneously reabsorb bicarbonate ions from the tubular fluid and return them to the bloodstream via mechanisms involving carbonic anhydrase II and bicarbonate/chloride exchangers on the basolateral membrane. This dual process helps to increase blood pH towards normal levels. @@ -81260,7 +82558,7 @@ In summary, renal intercalated cells play a critical role in the delicate balanc A cuboidal epithelial cell of the kidney which secretes acid and reabsorbs base to regulate acid/base balance. - This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. Renal alpha-intercalated cells are located within the connecting tubules and collecting ducts of the kidneys, which are components of the kidney's complex nephron system. Along with beta-intercalated cells, they play a critical role in the body’s acid-base balance. Renal alpha-intercalated cells contain an abundance of proton pumps and enzymes like carbonic anhydrase, which aid in the transport of hydrogen ions for secretion in the urine. The bicarbonate/chloride transporters on their apical membrane meanwhile take up bicarbonate ions from the urine and supply them back into the blood. Through this mechanism, these cells contribute significantly to the neutrality of blood pH, and dysfunction of renal alpha-intercalated cells often leads to distal renal tubular acidosis, a condition resulting in acidic blood and alkaline urine. @@ -81281,7 +82579,7 @@ Renal alpha-intercalated cells contain an abundance of proton pumps and enzymes - This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. Renal alpha-intercalated cells are located within the connecting tubules and collecting ducts of the kidneys, which are components of the kidney's complex nephron system. Along with beta-intercalated cells, they play a critical role in the body’s acid-base balance. Renal alpha-intercalated cells contain an abundance of proton pumps and enzymes like carbonic anhydrase, which aid in the transport of hydrogen ions for secretion in the urine. The bicarbonate/chloride transporters on their apical membrane meanwhile take up bicarbonate ions from the urine and supply them back into the blood. Through this mechanism, these cells contribute significantly to the neutrality of blood pH, and dysfunction of renal alpha-intercalated cells often leads to distal renal tubular acidosis, a condition resulting in acidic blood and alkaline urine. @@ -81350,7 +82648,7 @@ Renal alpha-intercalated cells contain an abundance of proton pumps and enzymes A columnar/cuboidal epithelial cell with multiple motile cilia on its apical surface. These cells facilitate the movement of liquids such as mucus or cerebrospinal fluid across the epithelial surface. - This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. The multi-ciliated epithelial cell are terminally differentiated epithelia that line brain ventricles, the respiratory tract and parts of the female and male reproductive organs in animals, playing critical roles in the maintenance of homeostasis through ciliary motion. They are characterized by the presence of hundreds of motile cilia, hair-like microtubule-based organelles that beat in a coordinated fashion to direct fluid flow over the cell surface. Multi-ciliated epithelial cells have fundamental roles in the proper functioning of many organ systems. In the respiratory system, they line the airways and orchestrate the coordinated movement of mucus, effectively clearing the airways of inhaled particles and pathogens. These cells are also vital in the ventricular system of the brain where they facilitate cerebrospinal fluid circulation, thus contributing to the maintenance of the brain's microenvironment. In the fallopian tube, multi-ciliated epithelial cells aid in the transport of oocytes from the ovary to the uterus, a process crucial to reproduction. @@ -81359,11 +82657,12 @@ The formation and function of multi-ciliated epithelial cells is a highly regula multiciliated cell ZFA:0005242 https://cellxgene.cziscience.com/cellguide/CL_0005012 + multi-ciliated epithelial cell multiciliated epithelial cell MCC While the term 'multi-ciliated epithelial cell' refers to cells with multiple motile cilia, there are exceptions where epithelial cells may have multiple non-motile cilia. Examples include olfactory sensory neurons, which have non-motile cilia for sensory detection, and choroid plexus epithelial cells, which possess multiple non-motile cilia with transient motility during development. Multiciliated cells are essential for human health, and their dysfunction can lead to various diseases known as ciliopathies, such as primary ciliary dyskinesia. This condition affects the respiratory system, brain ventricles, and reproductive system, leading to chronic respiratory infections, hydrocephalus, and infertility - multi-ciliated epithelial cell + multiciliated epithelial cell @@ -81377,7 +82676,7 @@ The formation and function of multi-ciliated epithelial cells is a highly regula - This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. The multi-ciliated epithelial cell are terminally differentiated epithelia that line brain ventricles, the respiratory tract and parts of the female and male reproductive organs in animals, playing critical roles in the maintenance of homeostasis through ciliary motion. They are characterized by the presence of hundreds of motile cilia, hair-like microtubule-based organelles that beat in a coordinated fashion to direct fluid flow over the cell surface. Multi-ciliated epithelial cells have fundamental roles in the proper functioning of many organ systems. In the respiratory system, they line the airways and orchestrate the coordinated movement of mucus, effectively clearing the airways of inhaled particles and pathogens. These cells are also vital in the ventricular system of the brain where they facilitate cerebrospinal fluid circulation, thus contributing to the maintenance of the brain's microenvironment. In the fallopian tube, multi-ciliated epithelial cells aid in the transport of oocytes from the ovary to the uterus, a process crucial to reproduction. @@ -81569,7 +82868,7 @@ The formation and function of multi-ciliated epithelial cells is a highly regula Ghrelin secreting cells found in the endocrine pancreas. - This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. Pancreatic epsilon cells are a specialized type of endocrine cell found in the islets of Langerhans, a region of the pancreas responsible for hormone production. These clusters of cells constitute only about 1% of the pancreatic islet cell population, making them a relatively small yet significant component of the pancreas. Pancreatic epsilon cells have a round or ovoid shape with occasional cytoplasmic extensions and are characterized by small and spherical granules. The principal function of pancreatic epsilon cells involves the synthesis and release of the hormone ghrelin, a peptide hormone predominantly produced in the stomach; pancreatic epsilon cells are one of the few sites outside the gastrointestinal tract known to produce this hormone. Ghrelin has multiple vital roles, playing a significant part in generating hunger sensations, promoting fat storage, and influencing various metabolic processes. It also stimulates the release of Growth Hormone (GH) from the anterior pituitary gland. @@ -81591,7 +82890,7 @@ During fetal development, when they form a layer around the islet, epsilon cells - This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. Pancreatic epsilon cells are a specialized type of endocrine cell found in the islets of Langerhans, a region of the pancreas responsible for hormone production. These clusters of cells constitute only about 1% of the pancreatic islet cell population, making them a relatively small yet significant component of the pancreas. Pancreatic epsilon cells have a round or ovoid shape with occasional cytoplasmic extensions and are characterized by small and spherical granules. The principal function of pancreatic epsilon cells involves the synthesis and release of the hormone ghrelin, a peptide hormone predominantly produced in the stomach; pancreatic epsilon cells are one of the few sites outside the gastrointestinal tract known to produce this hormone. Ghrelin has multiple vital roles, playing a significant part in generating hunger sensations, promoting fat storage, and influencing various metabolic processes. It also stimulates the release of Growth Hormone (GH) from the anterior pituitary gland. @@ -81861,7 +83160,7 @@ During fetal development, when they form a layer around the islet, epsilon cells Multi fate stem cell that gives rise to both hepatocytes and cholangiocytes as descendants. The term often refers to fetal precursors of hepatocytes (differently from 'hepatic stem cell', usually applied to the self-renewing pool of hepatocyte precursors in the adult liver). Hepatoblasts may also be endogenous, as some stem cells found in the liver come from the bone marrow via blood circulation. - This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. Hepatoblasts are immature precursor cells that predominate during the early stages of liver development, specifically in the embryonic phase of life. They first arise from the endoderm, one of the three primary germ layers in the very early embryo, and then differentiate into two distinct mature liver cell types - the hepatocytes and cholangiocytes. During liver organogenesis hepatoblasts proliferate and migrate into the septum transversum to form the liver bud. Proliferation and differentiation of these cells are regulated by several soluble factors, such as hepatocyte growth factor, which is a mitogen of both hepatoblasts and mature hepatocytes. As they start to differentiate into hepatocytes and cholangiocytes, the cells begin to express hepatic markers like albumin and alpha-fetoprotein. @@ -81884,7 +83183,7 @@ Although hepatoblasts are specified embryonic liver cells that are bipotential f - This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. Hepatoblasts are immature precursor cells that predominate during the early stages of liver development, specifically in the embryonic phase of life. They first arise from the endoderm, one of the three primary germ layers in the very early embryo, and then differentiate into two distinct mature liver cell types - the hepatocytes and cholangiocytes. During liver organogenesis hepatoblasts proliferate and migrate into the septum transversum to form the liver bud. Proliferation and differentiation of these cells are regulated by several soluble factors, such as hepatocyte growth factor, which is a mitogen of both hepatoblasts and mature hepatocytes. As they start to differentiate into hepatocytes and cholangiocytes, the cells begin to express hepatic markers like albumin and alpha-fetoprotein. @@ -82078,6 +83377,7 @@ Although hepatoblasts are specified embryonic liver cells that are bipotential f Cell that is part of the notochord. 2012-06-27T08:47:31Z + NOTE: TO DO, notochord development still needs work. notochordal cell @@ -82217,7 +83517,13 @@ Although hepatoblasts are specified embryonic liver cells that are bipotential f Skeletogenic cell that has the potential to transform into an osteoblast, and develops from neural crest or mesodermal cells. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Preosteoblast is a critical cell type involved in bone formation, crucial in a process known as ossification or osteogenesis. They are derived from mesenchymal stem cells and are an intermediate stage marking the transition from an osteoprogenitor cell to a fully differentiated osteoblast. The presence of preosteoblasts signifies the site of new bone deposition, highlighting their crucial role in skeletal development and in response to bone injury repairs. +The primary function of preosteoblasts is to differentiate into osteoblasts, which are responsible for secreting osteoid (the unmineralized portion of bone matrix) and regulating the process of bone mineralization. Preosteoblasts are regulated by various growth factors and hormones, including bone morphogenic proteins (BMPs), fibroblast growth factors (FGFs), parathyroid hormone (PTH) and Vitamin D. +However, the function of preosteoblasts is not limited to bone formation alone. In addition to osteogenesis, preosteoblasts significantly contribute to the maintenance of bone homeostasis through regulating the activity of osteoclasts - the cells responsible for bone resorption. This regulation is mediated through RANK/RANKL/OPG pathway signaling. Osteoprotegerin (OPG) released from the preosteoblasts acts as a decoy receptor for RANKL impairing osteoclast formation, hence preventing excessive bone resorption. This regulatory role indicates the dual functionality of preosteoblasts, which are indispensable for both the formation of new bone and the maintenance of existing bone tissue. 2012-06-27T10:57:21Z + https://cellxgene.cziscience.com/cellguide/CL_0007010 osteoprogenitor cell preosteoblast @@ -82228,6 +83534,19 @@ Although hepatoblasts are specified embryonic liver cells that are bipotential f Skeletogenic cell that has the potential to transform into an osteoblast, and develops from neural crest or mesodermal cells. GO_REF:0000034 + + + + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Preosteoblast is a critical cell type involved in bone formation, crucial in a process known as ossification or osteogenesis. They are derived from mesenchymal stem cells and are an intermediate stage marking the transition from an osteoprogenitor cell to a fully differentiated osteoblast. The presence of preosteoblasts signifies the site of new bone deposition, highlighting their crucial role in skeletal development and in response to bone injury repairs. +The primary function of preosteoblasts is to differentiate into osteoblasts, which are responsible for secreting osteoid (the unmineralized portion of bone matrix) and regulating the process of bone mineralization. Preosteoblasts are regulated by various growth factors and hormones, including bone morphogenic proteins (BMPs), fibroblast growth factors (FGFs), parathyroid hormone (PTH) and Vitamin D. +However, the function of preosteoblasts is not limited to bone formation alone. In addition to osteogenesis, preosteoblasts significantly contribute to the maintenance of bone homeostasis through regulating the activity of osteoclasts - the cells responsible for bone resorption. This regulation is mediated through RANK/RANKL/OPG pathway signaling. Osteoprotegerin (OPG) released from the preosteoblasts acts as a decoy receptor for RANKL impairing osteoclast formation, hence preventing excessive bone resorption. This regulatory role indicates the dual functionality of preosteoblasts, which are indispensable for both the formation of new bone and the maintenance of existing bone tissue. + DOI:10.1038/srep32884 + DOI:10.1096/fba.2020-00058 + DOI:10.1210/endo.141.9.7634 + DOI:10.12659/MSMBR.901142 + @@ -83033,18 +84352,18 @@ Covers cells actively being cultured or stored in a quiescent state for future u - + A skeletal muscle satellite cell that has become mitotically active - typically following muscle damage. activated skeletal muscle satellite cell - + - + More accurately - transformation_of ? @@ -83180,7 +84499,7 @@ Covers cells actively being cultured or stored in a quiescent state for future u - + @@ -83195,13 +84514,13 @@ Covers cells actively being cultured or stored in a quiescent state for future u - Any neuron that has its soma located in some anterior lateral line ganglion. + Any peripheral nervous system neuron that has its soma located in some anterior lateral line ganglion. anterior lateral line ganglion neuron - Any neuron that has its soma located in some anterior lateral line ganglion. + Any peripheral nervous system neuron that has its soma located in some anterior lateral line ganglion. FBC:Autogenerated @@ -83451,7 +84770,7 @@ Covers cells actively being cultured or stored in a quiescent state for future u - + An interneuron that has its soma located in the cerebral cortex. cerebral cortex interneuron @@ -83466,20 +84785,6 @@ Covers cells actively being cultured or stored in a quiescent state for future u - - - - - - - - - - - - - - @@ -83492,6 +84797,18 @@ Covers cells actively being cultured or stored in a quiescent state for future u + + + + + + + + + + + + @@ -83627,7 +84944,13 @@ Covers cells actively being cultured or stored in a quiescent state for future u A trophoblast cell that is not part of a placental villous. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Extravillous trophoblasts (EVTs), a specialized subset of trophoblast cells, play crucial roles in establishing and sustaining pregnancy. +Firstly, they anchor the fetus to the maternal tissue, providing structural stability. Secondly, they are instrumental in modifying the maternal spiral arteries to ensure an adequate supply of maternal blood to the placenta and the developing fetus. EVTs invade maternal decidua and myometrium and replace the endothelial lining of the spiral arteries, transforming these high-resistance, narrow vessels into low-resistance, wide vessels, favouring higher blood flow. Thirdly, these cells also play an immunological role, creating an environment conducive to the acceptance of the semi-allogeneic fetus, by expressing non-classical MHC molecules, thereby averting any potential maternal immune response towards fetal tissues. +While EVTs are commonly associated with healthy pregnancies, abnormalities in their function or development have been connected to problematic pregnancies. Conditions like pre-eclampsia and fetal growth restriction (FGR) may arise if EVT cells do not effectively invade the maternal decidua or adequately remodel. 2020-03-02T08:45:06Z + https://cellxgene.cziscience.com/cellguide/CL_0008036 EVT extravillous cytotrophloblast @@ -83641,6 +84964,20 @@ Covers cells actively being cultured or stored in a quiescent state for future u A trophoblast cell that is not part of a placental villous. PMID:31049600 + + + + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Extravillous trophoblasts (EVTs), a specialized subset of trophoblast cells, play crucial roles in establishing and sustaining pregnancy. +Firstly, they anchor the fetus to the maternal tissue, providing structural stability. Secondly, they are instrumental in modifying the maternal spiral arteries to ensure an adequate supply of maternal blood to the placenta and the developing fetus. EVTs invade maternal decidua and myometrium and replace the endothelial lining of the spiral arteries, transforming these high-resistance, narrow vessels into low-resistance, wide vessels, favouring higher blood flow. Thirdly, these cells also play an immunological role, creating an environment conducive to the acceptance of the semi-allogeneic fetus, by expressing non-classical MHC molecules, thereby averting any potential maternal immune response towards fetal tissues. +While EVTs are commonly associated with healthy pregnancies, abnormalities in their function or development have been connected to problematic pregnancies. Conditions like pre-eclampsia and fetal growth restriction (FGR) may arise if EVT cells do not effectively invade the maternal decidua or adequately remodel. + DOI:10.1007/s12522-011-0102-9 + DOI:10.1016/j.it.2017.01.009 + DOI:10.1016/j.preghy.2010.10.003 + DOI:10.1080/19336918.2015.1089376 + DOI:10.1080/19336918.2015.1120397 + @@ -83741,8 +85078,8 @@ Covers cells actively being cultured or stored in a quiescent state for future u An endothelial cell of the venule that is squamous shaped. This is in contrast to the cubodial shape of high endothelial venule cells. - 2024-07-03T19:52:47Z + 2024-07-03T19:52:47Z squamous endothelial cell of venule @@ -84099,10 +85436,17 @@ Covers cells actively being cultured or stored in a quiescent state for future u An enteroendocrine cell that is located in the small intestine. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +The enteroendocrine cell of the small intestine is a specialized type of cell that forms part of the lining of the intestinal wall. These cells are interspersed among absorptive cells, mucus-secreting goblet cells, and other gut cell types, forming the crypt-villus axis, which is the functional unit of the small intestinal epithelium. +Functionally, enteroendocrine cells play a pivotal role in the gut-endocrine system, which is responsible for the digestive process. These cells translate the luminal nutrient status into hormonal signals thereby acting as chemosensors. They contain secretory granules at their base which release hormones into the bloodstream following chemo-sensation. The hormones they secrete perform diverse functions including regulating gastric secretion, gut motility, insulin release, appetite control and other local and systemic effects. +In addition to their endocrine functions, enteroendocrine cells also play a part in the modulation of the immune response in the gut. They can secrete cytokines and chemokines that have a role in directing the immune response to invading pathogens. Moreover, emerging research suggests that these cells play a role in maintaining the balance between gut resident bacteria, known as the gut microbiota, and the host. As such, a comprehensive understanding of the enteroendocrine cells of the small intestine underpins knowledge in nutrition, endocrinology, and various gastroenterological conditions. + https://cellxgene.cziscience.com/cellguide/CL_0009006 small intestine enteroendocrine cell enteroendocrine cell of small intestine + @@ -84110,6 +85454,30 @@ Covers cells actively being cultured or stored in a quiescent state for future u An enteroendocrine cell that is located in the small intestine. http://orcid.org/0000-0003-3440-1876 + + + + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +The enteroendocrine cell of the small intestine is a specialized type of cell that forms part of the lining of the intestinal wall. These cells are interspersed among absorptive cells, mucus-secreting goblet cells, and other gut cell types, forming the crypt-villus axis, which is the functional unit of the small intestinal epithelium. +Functionally, enteroendocrine cells play a pivotal role in the gut-endocrine system, which is responsible for the digestive process. These cells translate the luminal nutrient status into hormonal signals thereby acting as chemosensors. They contain secretory granules at their base which release hormones into the bloodstream following chemo-sensation. The hormones they secrete perform diverse functions including regulating gastric secretion, gut motility, insulin release, appetite control and other local and systemic effects. +In addition to their endocrine functions, enteroendocrine cells also play a part in the modulation of the immune response in the gut. They can secrete cytokines and chemokines that have a role in directing the immune response to invading pathogens. Moreover, emerging research suggests that these cells play a role in maintaining the balance between gut resident bacteria, known as the gut microbiota, and the host. As such, a comprehensive understanding of the enteroendocrine cells of the small intestine underpins knowledge in nutrition, endocrinology, and various gastroenterological conditions. + DOI:10.1016/j.coph.2013.09.008 + DOI:10.1038/mi.2017.73 + DOI:10.1038/nature24489 + DOI:10.1111/j.1365-2613.2011.00767.x + DOI:10.1146/annurev-physiol-021115-105439 + + + + + + http://creativecommons.org/licenses/by/4.0/ + Figure depicts a cross section of intestinal villi in the small intestine, including the crypts of Lieberkuhn (seen here as ‘crypt’), as well as the layer specific locations of cells that exist within the gastrointestinal tract. Layers depicted here include epithelium (rows of cells bordering villus), submucosa (white space below the epithelium containing networks of neurons and ganglia depicted in pink), muscularis mucosae (blue layer), muscularis propria (referred to here as muscle layer). + +ISC: Intestinal Stem Cell +TA: Transit Amplifying Cells + @@ -84206,7 +85574,14 @@ Covers cells actively being cultured or stored in a quiescent state for future u A paneth cell that is located in the epithelium of the colon. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Paneth cells of the colon are specialized secretory epithelial cells that can be found in the large intestine, albeit in small numbers compared with the small intestine where Paneth cells are more abundant. Under disease conditions such as inflammatory bowel disease, Paneth cells increase in numbers in the colon. They reside in the crypts of Lieberkühn, which are glandular structures embedded within the mucosal layer of the small and large intestine. +Paneth cells play a crucial role in maintaining intestinal homeostasis and acting as a frontline of defense in our bodies against ingested microbes. They achieve this through the secretion of antimicrobial peptides and proteins such as lysozyme and defensins, which can directly kill or inhibit the growth of various bacteria, fungi, and viruses. They degranulate these substances into the intestinal lumen, especially under conditions of pathogenic invasion or damage to the epithelial lining. +Moreover, Paneth cells are essential for the maintenance of intestinal stem cells, which continually replace the epithelium of the intestine. They create a niche for these stem cells at the base of the crypts, secreting various signaling molecules and factors that are essential for the growth and differentiation of intestinal stem cells. In essence, the existence and function of Paneth cells are fundamental to the overall gut health and immune defense system, by providing both antimicrobial functions and a conducive environment for the renewal of the intestinal lining. +The role of Paneth cells specifically in the colon is of interest in the context of inflammatory bowel disease, such as ulcerative colitis and Crohn’s disease: Their presence in the colon is thought to represent Paneth cell metaplasia and indicates a chronic inflammatory state. paneth cell of epithelium of large intestine + https://cellxgene.cziscience.com/cellguide/CL_0009009 paneth cell of epithelium of colon paneth-like cell @@ -84221,6 +85596,21 @@ Covers cells actively being cultured or stored in a quiescent state for future u PMID:31753849 http://orcid.org/0000-0003-4183-8865 + + + + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Paneth cells of the colon are specialized secretory epithelial cells that can be found in the large intestine, albeit in small numbers compared with the small intestine where Paneth cells are more abundant. Under disease conditions such as inflammatory bowel disease, Paneth cells increase in numbers in the colon. They reside in the crypts of Lieberkühn, which are glandular structures embedded within the mucosal layer of the small and large intestine. +Paneth cells play a crucial role in maintaining intestinal homeostasis and acting as a frontline of defense in our bodies against ingested microbes. They achieve this through the secretion of antimicrobial peptides and proteins such as lysozyme and defensins, which can directly kill or inhibit the growth of various bacteria, fungi, and viruses. They degranulate these substances into the intestinal lumen, especially under conditions of pathogenic invasion or damage to the epithelial lining. +Moreover, Paneth cells are essential for the maintenance of intestinal stem cells, which continually replace the epithelium of the intestine. They create a niche for these stem cells at the base of the crypts, secreting various signaling molecules and factors that are essential for the growth and differentiation of intestinal stem cells. In essence, the existence and function of Paneth cells are fundamental to the overall gut health and immune defense system, by providing both antimicrobial functions and a conducive environment for the renewal of the intestinal lining. +The role of Paneth cells specifically in the colon is of interest in the context of inflammatory bowel disease, such as ulcerative colitis and Crohn’s disease: Their presence in the colon is thought to represent Paneth cell metaplasia and indicates a chronic inflammatory state. + DOI:10.1002/ibd.20197 + DOI:10.1038/nature09637 + DOI:10.1038/nrmicro2546 + DOI:10.1093/ecco-jcc/jjac190.0884 + DOI:10.1136/gut.48.2.176 + @@ -84268,7 +85658,7 @@ Covers cells actively being cultured or stored in a quiescent state for future u - + @@ -84276,7 +85666,7 @@ Covers cells actively being cultured or stored in a quiescent state for future u - + @@ -84292,7 +85682,12 @@ Covers cells actively being cultured or stored in a quiescent state for future u A rapidly proliferating population of cells that differentiate from stem cells of the intestinal crypt of the colon. Stem cells located in the crypts of Lieberkühn give rise to proliferating progenitor or transit amplifying cells that differentiate into the four major epithelial cell types. These include columnar absorptive cells or enterocytes, mucous secreting goblet cells, enteroendocrine cells and paneth cells. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Transit amplifying cells (TACs) are an intermediate, undifferentiated population between stem cells and differentiated cells. They can be found in multiple regions such as the small intestine and the colon. TACs of the colon, are integral components of the colonic crypts and vital players in the maintenance of colonic tissue. +These cells serve a critical function in the rapid and constant renewal of the epithelium lining the colon, with the whole epithelial surface renewed approximately every 5-7 days. They divide rapidly and progressively differentiate into mature columnar epithelium cells, including enterocytes, goblet cells, and enteroendocrine cells. The continued proliferation of transit amplifying cells is fundamental to maintain the balance in cell population while preventing tissue degeneration and maintaining a state of homeostasis. However, uncontrolled proliferation and compromised differentiation capacity can contribute to the development of colon cancers. transit amplifying cell of large intestine + https://cellxgene.cziscience.com/cellguide/CL_0009011 colon transit amplifying cell transient amplifying cell of colon transient amplifying cell of crypt of Lieberkuhn of colon @@ -84310,6 +85705,19 @@ Covers cells actively being cultured or stored in a quiescent state for future u PMID:20801415 http://orcid.org/0000-0003-4183-8865 + + + + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Transit amplifying cells (TACs) are an intermediate, undifferentiated population between stem cells and differentiated cells. They can be found in multiple regions such as the small intestine and the colon. TACs of the colon, are integral components of the colonic crypts and vital players in the maintenance of colonic tissue. +These cells serve a critical function in the rapid and constant renewal of the epithelium lining the colon, with the whole epithelial surface renewed approximately every 5-7 days. They divide rapidly and progressively differentiate into mature columnar epithelium cells, including enterocytes, goblet cells, and enteroendocrine cells. The continued proliferation of transit amplifying cells is fundamental to maintain the balance in cell population while preventing tissue degeneration and maintaining a state of homeostasis. However, uncontrolled proliferation and compromised differentiation capacity can contribute to the development of colon cancers. + DOI:10.1016/j.cell.2014.02.057 + DOI:10.1053/j.gastro.2018.08.016 + DOI:10.1172/jci.insight.150894 + DOI:10.3389/fbioe.2023.1189225 + https://www.sciencedirect.com/topics/immunology-and-microbiology/intestinal-stem-cell + @@ -84319,7 +85727,7 @@ Covers cells actively being cultured or stored in a quiescent state for future u - + @@ -84327,7 +85735,7 @@ Covers cells actively being cultured or stored in a quiescent state for future u - + @@ -84342,6 +85750,12 @@ Covers cells actively being cultured or stored in a quiescent state for future u A rapidly proliferating population of cells that differentiate from stem cells of the intestinal crypt of the small intestine. Stem cells located in the crypts of Lieberkühn give rise to proliferating progenitor or transit amplifying cells that differentiate into the four major epithelial cell types. These include columnar absorptive cells or enterocytes, mucous secreting goblet cells, enteroendocrine cells and paneth cells. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Transit amplifying cells (TACs) represent an intermediate population between stem cells and fully differentiated cells, and can be found in multiple regions such as the colon and the small intestine. The small intestine's efficiency in absorbing nutrients, its protective barrier function, and its innate cellular renewal every few days is largely dependent on the role played by these TACs. +TACs of the small intestine are primarily present in the crypt-villus structure of the intestine, more specifically in the crypt region. They originate from Lgr5+ intestinal stem cells that reside at the base of the crypts. Following their derivation from stem cells, TACs undergo up to six rounds of rapid division over a 48-72 hour period, effectively amplifying the cell population, hence their name. During this process, they gradually migrate upward along the walls of the crypt from where they differentiate into diverse mature cell types such as enterocytes, goblet cells, and Paneth cells. +TACs serve as an important element in the homeostasis and regeneration of the intestinal epithelium, amplifying the pool of cells available for differentiation. They also minimize genetic errors during DNA replication by serving as a 'buffer zone' between the long-lived stem cells and the terminal differentiated cells of the gut lining, thus reducing the potential for propagation of mutation-causing defects. Lastly, TACs play an essential part in gastrointestinal tissue repair following injury or inflammation. Their rapid proliferation and subsequent differentiation abilities often help expedite the wound healing process in the intestinal epithelium. + https://cellxgene.cziscience.com/cellguide/CL_0009012 small intestine transit amplifying cell transient amplifying cell of crypt of Lieberkuhn of small intestine transient amplifying cell of small intestine @@ -84350,6 +85764,7 @@ Covers cells actively being cultured or stored in a quiescent state for future u transit amplifying cell of small intestine + @@ -84358,6 +85773,28 @@ Covers cells actively being cultured or stored in a quiescent state for future u PMID:20801415 http://orcid.org/0000-0003-4183-8865 + + + + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Transit amplifying cells (TACs) represent an intermediate population between stem cells and fully differentiated cells, and can be found in multiple regions such as the colon and the small intestine. The small intestine's efficiency in absorbing nutrients, its protective barrier function, and its innate cellular renewal every few days is largely dependent on the role played by these TACs. +TACs of the small intestine are primarily present in the crypt-villus structure of the intestine, more specifically in the crypt region. They originate from Lgr5+ intestinal stem cells that reside at the base of the crypts. Following their derivation from stem cells, TACs undergo up to six rounds of rapid division over a 48-72 hour period, effectively amplifying the cell population, hence their name. During this process, they gradually migrate upward along the walls of the crypt from where they differentiate into diverse mature cell types such as enterocytes, goblet cells, and Paneth cells. +TACs serve as an important element in the homeostasis and regeneration of the intestinal epithelium, amplifying the pool of cells available for differentiation. They also minimize genetic errors during DNA replication by serving as a 'buffer zone' between the long-lived stem cells and the terminal differentiated cells of the gut lining, thus reducing the potential for propagation of mutation-causing defects. Lastly, TACs play an essential part in gastrointestinal tissue repair following injury or inflammation. Their rapid proliferation and subsequent differentiation abilities often help expedite the wound healing process in the intestinal epithelium. + DOI:10.1007/s11894-010-0130-3 + DOI:10.1016/j.cell.2014.02.057 + DOI:10.1101/gad.1674008 + + + + + + http://creativecommons.org/licenses/by/4.0/ + Figure depicts a cross section of intestinal villi in the small intestine , including the crypts of Lieberkhun (seen here as ‘crypt’), as well as the layer specific locations of cells that exist within the gastrointestinal tract. Layers depicted here include epithelium (rows of cells bordering villus), submucosa (white space below the epithelium containing networks of neurons and ganglia depicted in pink), muscularis mucosae (blue layer), muscularis propria (referred to here as muscle layer). + +ISC: Intestinal Stem Cell +TA: Transit Amplifying Cells + @@ -84536,7 +85973,7 @@ Covers cells actively being cultured or stored in a quiescent state for future u An intestinal stem cell that is located in the small intestine crypt of Liberkuhn. These stem cells reside at the bottom of crypts in the small intestine and are highly proliferative. They either differentiate into transit amplifying cells or self-renew to form new stem cells. - This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. Intestinal crypt stem cells of the small intestine are a type of adult stem cell intimately involved in the continuous replenishment of the intestinal epithelium, the innermost layer of the intestine responsible for nutrient absorption. These cells, located within the crypts of Lieberkühn, are the origin of various cell lineages that make up the functional units of the small intestine. They possess self-renewal ability, an essential feature of stem cells, which allows them to maintain a steady population in the small intestine. One of the critical roles of intestinal crypt stem cells is to drive the continual renewal process taking place in the small intestine every 3-5 days. By proliferating intensively, these cells produce transient amplifying (TA) cells that are characterized by quick division and progressive differentiation. These cells eventually differentiate into specialized cell types, encompassing absorptive enterocytes, mucin-secreting goblet cells, hormone-secreting enteroendocrine cells, and Paneth cells, all of which have essential roles in digestion and nutrient absorption in the small intestine. @@ -84547,6 +85984,7 @@ Intestinal crypt stem cells of the small intestine are also play a significant p intestinal crypt stem cell of small intestine + @@ -84558,7 +85996,7 @@ Intestinal crypt stem cells of the small intestine are also play a significant p - This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. Intestinal crypt stem cells of the small intestine are a type of adult stem cell intimately involved in the continuous replenishment of the intestinal epithelium, the innermost layer of the intestine responsible for nutrient absorption. These cells, located within the crypts of Lieberkühn, are the origin of various cell lineages that make up the functional units of the small intestine. They possess self-renewal ability, an essential feature of stem cells, which allows them to maintain a steady population in the small intestine. One of the critical roles of intestinal crypt stem cells is to drive the continual renewal process taking place in the small intestine every 3-5 days. By proliferating intensively, these cells produce transient amplifying (TA) cells that are characterized by quick division and progressive differentiation. These cells eventually differentiate into specialized cell types, encompassing absorptive enterocytes, mucin-secreting goblet cells, hormone-secreting enteroendocrine cells, and Paneth cells, all of which have essential roles in digestion and nutrient absorption in the small intestine. @@ -84567,6 +86005,16 @@ Intestinal crypt stem cells of the small intestine are also play a significant p DOI:10.1038/s41575-018-0081-y DOI:10.1073/pnas.1607327113 + + + + + http://creativecommons.org/licenses/by/4.0/ + Figure depicts a cross section of intestinal villi in the small intestine, including the crypts of Lieberkuhn (seen here as ‘crypt’), as well as the layer specific locations of cells that exist within the gastrointestinal tract. Layers depicted here include epithelium (rows of cells bordering villus), submucosa (white space below the epithelium containing networks of neurons and ganglia depicted in pink), muscularis mucosae (blue layer), muscularis propria (referred to here as muscle layer). + +ISC: Intestinal Stem Cell +TA: Transit Amplifying Cells + @@ -84662,7 +86110,12 @@ Intestinal crypt stem cells of the small intestine are also play a significant p - + + + + + + An intestinal tuft cell that is a part of a vermiform appendix. appendix tuft cell @@ -84798,13 +86251,18 @@ Intestinal crypt stem cells of the small intestine are also play a significant p - + - + + + + + + A mesothelial cell that is part of the small intestine. @@ -84828,13 +86286,18 @@ Intestinal crypt stem cells of the small intestine are also play a significant p - + - + + + + + + A mesothelial cell that is part of the colon. mesothelial cell of large intestine @@ -84865,7 +86328,7 @@ Intestinal crypt stem cells of the small intestine are also play a significant p - + An enterocyte that is a part of a vermiform appendix. @@ -84890,7 +86353,7 @@ Intestinal crypt stem cells of the small intestine are also play a significant p - + @@ -84898,7 +86361,7 @@ Intestinal crypt stem cells of the small intestine are also play a significant p - + @@ -84943,7 +86406,6 @@ Intestinal crypt stem cells of the small intestine are also play a significant p - @@ -84979,13 +86441,18 @@ Intestinal crypt stem cells of the small intestine are also play a significant p - + - + + + + + + A mesothelial cell that is located in a vermiform appendix. appendix mesothelial cell @@ -85017,8 +86484,8 @@ Intestinal crypt stem cells of the small intestine are also play a significant p + - An intestinal enteroendocrine cell that is located in a vermiform appendix. appendix enteroendocrine cell @@ -85335,6 +86802,12 @@ Intestinal crypt stem cells of the small intestine are also play a significant p A macrophage that is located in the colon. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Colon macrophages are a heterogeneous population of macrophages in the gastrointestinal tract. Intestinal macrophages represent the largest group of macrophages in the body and play a key role as sentinels for pathogen recognition and elimination. Because the gastrointestinal tract is continually exposed to a high antigenic load derived from microbes and food intake, macrophages in the intestines are crucial not only for the gut’s immune defense but also for maintaining gastrointestinal homeostasis, avoiding chronic inflammation despite constantly facing foreign antigens. The phenotypic profiles and cytokine production of intestinal macrophages therefore differ from conventional macrophages elsewhere in the body. +Colon macrophages orchestrate a wide variety of immune responses. They interact with the colon’s microflora thanks to their location in the mucosal layer, thus playing an important role in shaping gut immunity. By presenting antigens, they help to activate and steer an appropriate immune response either by triggering inflammation against harmful pathogens or by supporting tolerance for beneficial microbes. Therefore, disturbances in the colon macrophage population is thought to contribute to colon-related diseases such as inflammatory bowel disease and colon cancer. +These immune cells are versatile and multifunctional, not just limited to defensive actions. Colon macrophages interact with the enteric nervous system to regulate gut secretion and motility. They also play a crucial role in maintaining colon tissue health and integrity by contributing to tissue repair processes. This occurs either through phagocytosis of dead cells and remnants, or indirectly through the release of growth factor molecules, which stimulate cellular proliferation and differentiation necessary for tissue regeneration. + https://cellxgene.cziscience.com/cellguide/CL_0009038 macrophage of colon @@ -85347,6 +86820,19 @@ Intestinal crypt stem cells of the small intestine are also play a significant p A macrophage that is located in the colon. http://orcid.org/0000-0003-3440-1876 + + + + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Colon macrophages are a heterogeneous population of macrophages in the gastrointestinal tract. Intestinal macrophages represent the largest group of macrophages in the body and play a key role as sentinels for pathogen recognition and elimination. Because the gastrointestinal tract is continually exposed to a high antigenic load derived from microbes and food intake, macrophages in the intestines are crucial not only for the gut’s immune defense but also for maintaining gastrointestinal homeostasis, avoiding chronic inflammation despite constantly facing foreign antigens. The phenotypic profiles and cytokine production of intestinal macrophages therefore differ from conventional macrophages elsewhere in the body. +Colon macrophages orchestrate a wide variety of immune responses. They interact with the colon’s microflora thanks to their location in the mucosal layer, thus playing an important role in shaping gut immunity. By presenting antigens, they help to activate and steer an appropriate immune response either by triggering inflammation against harmful pathogens or by supporting tolerance for beneficial microbes. Therefore, disturbances in the colon macrophage population is thought to contribute to colon-related diseases such as inflammatory bowel disease and colon cancer. +These immune cells are versatile and multifunctional, not just limited to defensive actions. Colon macrophages interact with the enteric nervous system to regulate gut secretion and motility. They also play a crucial role in maintaining colon tissue health and integrity by contributing to tissue repair processes. This occurs either through phagocytosis of dead cells and remnants, or indirectly through the release of growth factor molecules, which stimulate cellular proliferation and differentiation necessary for tissue regeneration. + DOI:10.1016/j.immuni.2022.08.005 + DOI:10.1016/j.jcmgh.2021.08.021 + DOI:10.1038/s41575-019-0172-4 + DOI:10.1038/s41575-023-00769-0 + @@ -85359,7 +86845,7 @@ Intestinal crypt stem cells of the small intestine are also play a significant p - + @@ -85368,6 +86854,13 @@ Intestinal crypt stem cells of the small intestine are also play a significant p A goblet cell that is located in the colon. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Colon goblet cells are a subset of intestinal goblet cells that are localized in the epithelial lining of the colon. They are specialized secretory epithelial cells that are recognized by their characteristic ‘goblet’ or flask-like shape and typically have a distinctive appearance due to the accumulation of secretory vesicles in their cytoplasm. +The primary function of goblet cells is the secretion of mucus, which is an essential substance for the protection and successful functioning of the intestinal tract. In the colon, goblet cells continuously renew the inner mucus layer, which is attached and impervious to bacteria (the outer layer of the colon is unattached and is the habitat of commensal bacteria) +The mucus secreted by goblet cells is rich in glycoproteins known as mucins, especially MUC2, forming a complex web of molecules that comprises the foundational structure of the mucus layer. It traps and eliminates harmful bacteria, while selectively allowing beneficial microbiota to access the epithelial surface and aid in digestion and nutrient absorption. The mucus layer not only provides a provides a protective barrier against pathogen invasion, as well as mechanical damage, and the erosive effects of digestive enzymes, it also acts as a lubricant to facilitate the passage of food material. +Colon goblet cells are also involved in regulating the local immune response within the gut, maintaining the delicate balance between necessary immune reactions to harmful pathogens and tolerance to beneficial microbiota and dietary substances. Goblet cells can modulate immune responses by presenting antigens to dendritic cells, as well as through the production of immunomodulatory molecules that can alter the behavior of immune cells. When the inner mucus layer of the colon is defective, it might be a pathophysiological mechanism for colitis and infectious diseases. + https://cellxgene.cziscience.com/cellguide/CL_0009039 goblet cell of colon @@ -85379,6 +86872,21 @@ Intestinal crypt stem cells of the small intestine are also play a significant p A goblet cell that is located in the colon. http://orcid.org/0000-0003-3440-1876 + + + + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Colon goblet cells are a subset of intestinal goblet cells that are localized in the epithelial lining of the colon. They are specialized secretory epithelial cells that are recognized by their characteristic ‘goblet’ or flask-like shape and typically have a distinctive appearance due to the accumulation of secretory vesicles in their cytoplasm. +The primary function of goblet cells is the secretion of mucus, which is an essential substance for the protection and successful functioning of the intestinal tract. In the colon, goblet cells continuously renew the inner mucus layer, which is attached and impervious to bacteria (the outer layer of the colon is unattached and is the habitat of commensal bacteria) +The mucus secreted by goblet cells is rich in glycoproteins known as mucins, especially MUC2, forming a complex web of molecules that comprises the foundational structure of the mucus layer. It traps and eliminates harmful bacteria, while selectively allowing beneficial microbiota to access the epithelial surface and aid in digestion and nutrient absorption. The mucus layer not only provides a provides a protective barrier against pathogen invasion, as well as mechanical damage, and the erosive effects of digestive enzymes, it also acts as a lubricant to facilitate the passage of food material. +Colon goblet cells are also involved in regulating the local immune response within the gut, maintaining the delicate balance between necessary immune reactions to harmful pathogens and tolerance to beneficial microbiota and dietary substances. Goblet cells can modulate immune responses by presenting antigens to dendritic cells, as well as through the production of immunomodulatory molecules that can alter the behavior of immune cells. When the inner mucus layer of the colon is defective, it might be a pathophysiological mechanism for colitis and infectious diseases. + DOI:10.1038/mi.2015.32 + DOI:10.1038/mi.2016.132 + DOI:10.1038/nrgastro.2013.35 + DOI:10.1038/s41385-018-0039-y + DOI:10.1073/pnas.1006451107 + @@ -85433,9 +86941,20 @@ Intestinal crypt stem cells of the small intestine are also play a significant p - + + + + + + A tuft cell that is a part of the colon. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Tuft cells, also often referred to as brush cells or caveolated cells, are highly specialized sensory cells found in the colon, among other organs. They were named for their unique appearance under an electron microscope, which presents a distinctive ‘tuft-like’ morphology. They are characterized by apical microvilli, arranged in an irregular tuft that confers a dome-like shape. These cells comprise only a small fraction of the cells in the epithelial layer of the colon, making them among the least populous cell types in this region. +Tuft cells in the colon primarily function as chemosensory cells that can sense and respond to environmental changes. These cells can detect and respond to microbial metabolites, helping initiate immune responses against potential threats. +Recent studies have revealed that tuft cells play a role in responding to intestinal parasitic infections. When a gastrointestinal parasite infects the colon, tuft cells are activated and release the cytokine IL-25. This action increases the production of tuft cells and triggers essential Th2 immune responses to expel the parasites. Also, the removal of tuft cells has been linked to increased susceptibility to these infections. However, overactivity of tuft cells has been associated with inflammatory bowel disease, highlighting the need for a delicate balance of tuft cell function to maintain colon homeostasis. + https://cellxgene.cziscience.com/cellguide/CL_0009041 colon tuft cell @@ -85447,6 +86966,18 @@ Intestinal crypt stem cells of the small intestine are also play a significant p A tuft cell that is a part of the colon. http://orcid.org/0000-0003-3440-1876 + + + + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Tuft cells, also often referred to as brush cells or caveolated cells, are highly specialized sensory cells found in the colon, among other organs. They were named for their unique appearance under an electron microscope, which presents a distinctive ‘tuft-like’ morphology. They are characterized by apical microvilli, arranged in an irregular tuft that confers a dome-like shape. These cells comprise only a small fraction of the cells in the epithelial layer of the colon, making them among the least populous cell types in this region. +Tuft cells in the colon primarily function as chemosensory cells that can sense and respond to environmental changes. These cells can detect and respond to microbial metabolites, helping initiate immune responses against potential threats. +Recent studies have revealed that tuft cells play a role in responding to intestinal parasitic infections. When a gastrointestinal parasite infects the colon, tuft cells are activated and release the cytokine IL-25. This action increases the production of tuft cells and triggers essential Th2 immune responses to expel the parasites. Also, the removal of tuft cells has been linked to increased susceptibility to these infections. However, overactivity of tuft cells has been associated with inflammatory bowel disease, highlighting the need for a delicate balance of tuft cell function to maintain colon homeostasis. + DOI:10.1152/ajpgi.00073.2017 + DOI:10.1371/journal.ppat.1010318 + DOI:10.3389/fimmu.2022.822867 + @@ -85464,8 +86995,8 @@ Intestinal crypt stem cells of the small intestine are also play a significant p + - An enteroendocrine cell that is located in the colon. colon enteroendocrine cell @@ -85491,16 +87022,21 @@ Intestinal crypt stem cells of the small intestine are also play a significant p - + - - - An intestinal crypt stem cell that is located in the colon. + + + + + + + + An intestinal crypt stem cell that is located in the crypt of Lieberkuhn of colon. - This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. Intestinal crypt stem cells of the colon, also known as colon crypt base columnar (CBC) cells, are highly specialized cells primarily responsible for the constant self-renewal of the colonic epithelium. These cells are found in the crypts of Lieberkühn - deeply invaginated sections of the colon's mucosal layer. The prime function of intestinal crypt stem cells of the colon is to serve as the source of constant cell regeneration in the colon. Every few days, these stem cells divide and differentiate into the various other types of intestinal cells, such as enterocytes, goblet cells, and enteroendocrine cells. @@ -85513,13 +87049,14 @@ A constant renewal cycle is necessary due to the harsh environment of the colon - An intestinal crypt stem cell that is located in the colon. + An intestinal crypt stem cell that is located in the crypt of Lieberkuhn of colon. + PMID:10841502 http://orcid.org/0000-0003-3440-1876 - This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. Intestinal crypt stem cells of the colon, also known as colon crypt base columnar (CBC) cells, are highly specialized cells primarily responsible for the constant self-renewal of the colonic epithelium. These cells are found in the crypts of Lieberkühn - deeply invaginated sections of the colon's mucosal layer. The prime function of intestinal crypt stem cells of the colon is to serve as the source of constant cell regeneration in the colon. Every few days, these stem cells divide and differentiate into the various other types of intestinal cells, such as enterocytes, goblet cells, and enteroendocrine cells. @@ -85565,6 +87102,7 @@ A constant renewal cycle is necessary due to the harsh environment of the colon This is a general grouping term created for use in the EMBL-EBI Single Cell Expression Atlas anatomograms. Please use a more specific cell type term for annotation if possible, given the information available to you. lymphocyte of small intestine lamina propria + @@ -85573,6 +87111,16 @@ A constant renewal cycle is necessary due to the harsh environment of the colon PMID:26551552 https://orcid.org/0000-0003-4183-8865 + + + + + http://creativecommons.org/licenses/by/4.0/ + Figure depicts a cross section of intestinal villi in the small intestine, including the crypts of Lieberkuhn (seen here as ‘crypt’), as well as the layer specific locations of cells that exist within the gastrointestinal tract. Layers depicted here include epithelium (rows of cells bordering villus), submucosa (white space below the epithelium containing networks of neurons and ganglia depicted in pink), muscularis mucosae (blue layer), muscularis propria (referred to here as muscle layer). + +ISC: Intestinal Stem Cell +TA: Transit Amplifying Cells + @@ -85988,7 +87536,7 @@ A constant renewal cycle is necessary due to the harsh environment of the colon - + @@ -85996,7 +87544,7 @@ A constant renewal cycle is necessary due to the harsh environment of the colon - + @@ -86024,7 +87572,7 @@ A constant renewal cycle is necessary due to the harsh environment of the colon - + @@ -86068,8 +87616,7 @@ A constant renewal cycle is necessary due to the harsh environment of the colon - - + @@ -86174,7 +87721,7 @@ A constant renewal cycle is necessary due to the harsh environment of the colon - + @@ -86182,8 +87729,7 @@ A constant renewal cycle is necessary due to the harsh environment of the colon - - + @@ -86258,7 +87804,7 @@ A constant renewal cycle is necessary due to the harsh environment of the colon - + @@ -86364,7 +87910,7 @@ A constant renewal cycle is necessary due to the harsh environment of the colon - + @@ -86374,7 +87920,7 @@ A constant renewal cycle is necessary due to the harsh environment of the colon - + A stratified squamous epithelial cell that is part of the anal canal. @@ -86704,6 +88250,7 @@ A constant renewal cycle is necessary due to the harsh environment of the colon + @@ -86730,6 +88277,7 @@ A constant renewal cycle is necessary due to the harsh environment of the colon + @@ -86768,6 +88316,12 @@ A constant renewal cycle is necessary due to the harsh environment of the colon + + + + + + A tuft cell located in the small intestine. @@ -86777,6 +88331,7 @@ A constant renewal cycle is necessary due to the harsh environment of the colon tuft cell of epithelium of small intestine tuft cell of small intestine + @@ -86785,6 +88340,16 @@ A constant renewal cycle is necessary due to the harsh environment of the colon http://orcid.org/0000-0003-3440-1876 http://orcid.org/0000-0003-4183-8865 + + + + + http://creativecommons.org/licenses/by/4.0/ + Figure depicts a cross section of intestinal villi in the small intestine, including the crypts of Lieberkuhn (seen here as ‘crypt’), as well as the layer specific locations of cells that exist within the gastrointestinal tract. Layers depicted here include epithelium (rows of cells bordering villus), submucosa (white space below the epithelium containing networks of neurons and ganglia depicted in pink), muscularis mucosae (blue layer), muscularis propria (referred to here as muscle layer). + +ISC: Intestinal Stem Cell +TA: Transit Amplifying Cells + @@ -86860,7 +88425,7 @@ A constant renewal cycle is necessary due to the harsh environment of the colon - + @@ -86869,7 +88434,7 @@ A constant renewal cycle is necessary due to the harsh environment of the colon - + An epithelial cell that is part of an endometrial gland. @@ -87011,6 +88576,12 @@ A constant renewal cycle is necessary due to the harsh environment of the colon + + + + + + A pericyte cell that is part of a lung. @@ -87021,6 +88592,7 @@ A constant renewal cycle is necessary due to the harsh environment of the colon + The marker set HIGD1B, KCNK3 can identify the Human cell type lung pericyte in the Lung with a confidence of 0.84 (NS-Forest FBeta value). lung pericyte @@ -87030,6 +88602,12 @@ A constant renewal cycle is necessary due to the harsh environment of the colon https://orcid.org/0000-0003-3440-1876 https://orcid.org/0000-0003-4183-8865 + + + + The marker set HIGD1B, KCNK3 can identify the Human cell type lung pericyte in the Lung with a confidence of 0.84 (NS-Forest FBeta value). + https://doi.org/10.5281/zenodo.11165918 + @@ -87230,7 +88808,12 @@ A constant renewal cycle is necessary due to the harsh environment of the colon An endothelial cell that is part of a uterus. 2021-12-13T14:39:25Z + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +The endothelial cell of the uterus is a specialized type of endothelial cell found in the inner lining of blood vessels, specifically those in the uterus. These cells play critical roles in maintaining uterine health, fertilization, and pregnancy processes. They form the interior surface of blood vessels, creating a barrier between the vessel lumen and surrounding tissue. This fluid environment, maintained by these endothelial cells, provides a platform for the material exchange between blood and tissues, thereby modulating blood coagulation, immune responses, and controlling vasodilation and vasoconstriction. +Functionally, the endothelial cells of the uterus are paramount in regulating the uterine blood flow, an important determinant of successful conception and pregnancy outcomes. They support the vascular changes during the reproductive cycle, particularly the spiral arteriolar development and function, essential in endometrial thickening, maturation, and eventual shedding during menstruation periods. The cells also contribute to angiogenesis, a process crucial during implantation and placenta development, whereby new blood vessels form from pre-existing vessels to supply the growing fetus with oxygen and nutrients. Uterine endothelial cells are also implicated in mediating immune responses within the uterus. Changes in these cells can influence various conditions such as reproductive disorders and complications including heavy menstrual bleeding, endometrial hyperplasia, fertility problems, and cancer. EFO:0010711 + https://cellxgene.cziscience.com/cellguide/CL_0009095 uterine endothelial cell @@ -87243,6 +88826,19 @@ A constant renewal cycle is necessary due to the harsh environment of the colon https://orcid.org/0000-0003-3440-1876 https://orcid.org/0000-0003-4183-8865 + + + + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +The endothelial cell of the uterus is a specialized type of endothelial cell found in the inner lining of blood vessels, specifically those in the uterus. These cells play critical roles in maintaining uterine health, fertilization, and pregnancy processes. They form the interior surface of blood vessels, creating a barrier between the vessel lumen and surrounding tissue. This fluid environment, maintained by these endothelial cells, provides a platform for the material exchange between blood and tissues, thereby modulating blood coagulation, immune responses, and controlling vasodilation and vasoconstriction. +Functionally, the endothelial cells of the uterus are paramount in regulating the uterine blood flow, an important determinant of successful conception and pregnancy outcomes. They support the vascular changes during the reproductive cycle, particularly the spiral arteriolar development and function, essential in endometrial thickening, maturation, and eventual shedding during menstruation periods. The cells also contribute to angiogenesis, a process crucial during implantation and placenta development, whereby new blood vessels form from pre-existing vessels to supply the growing fetus with oxygen and nutrients. Uterine endothelial cells are also implicated in mediating immune responses within the uterus. Changes in these cells can influence various conditions such as reproductive disorders and complications including heavy menstrual bleeding, endometrial hyperplasia, fertility problems, and cancer. + DOI:10.1002/cphy.c190015 + DOI:10.1111/aji.12128 + DOI:10.1172/jci.insight.163422 + DOI:10.1530/REP-09-0147 + DOI:10.2174/1570161111311050010 + @@ -88200,6 +89796,12 @@ A constant renewal cycle is necessary due to the harsh environment of the colon Any endothelial cell that is part of some heart. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Cardiac endothelial cells are a specialized subset of endothelial cells, the cell type responsible for forming the inner lining of cardiovascular structures such as the heart, and blood vessels. They are a pivotal component of the heart's microenvironment and play a key role in regulating blood pressure, maintaining cardiac homeostasis, in addition to cooperating with other cardiac cells like cardiomyocytes and fibroblasts in the orchestration of a coordinated heart function. +Cardiac endothelial cells contribute to the each stage of the heart's operation, whether during relaxation or contraction. Cardiac endothelial cells release nitric oxide, a potent vasodilator that regulates blood vessel dilation consequently controlling blood pressure and flow. They also produce a myriad of growth factors that aid in new blood vessel formation, known as angiogenesis, crucially needed for tissue repair and regeneration when the heart undergoes damage, as in cases of myocardial infarction. +Furthermore, cardiac endothelial cells control the passage of nutrients, hormones, and gases between the bloodstream and the heart tissue, ensuring its complex metabolic demands are met adequately. They serve as a selective barrier, regulating the transit of cells and signaling molecules, thereby playing a pivotal role in inflammatory responses and immune cell trafficking. They also contribute to the maintenance of blood fluidity and clotting balance through a complex interplay of anti-thrombic and pro-thrombic factors. + https://cellxgene.cziscience.com/cellguide/CL_0010008 cardiac endothelial cell @@ -88210,6 +89812,20 @@ A constant renewal cycle is necessary due to the harsh environment of the colon Any endothelial cell that is part of some heart. FBC:Autogenerated + + + + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Cardiac endothelial cells are a specialized subset of endothelial cells, the cell type responsible for forming the inner lining of cardiovascular structures such as the heart, and blood vessels. They are a pivotal component of the heart's microenvironment and play a key role in regulating blood pressure, maintaining cardiac homeostasis, in addition to cooperating with other cardiac cells like cardiomyocytes and fibroblasts in the orchestration of a coordinated heart function. +Cardiac endothelial cells contribute to the each stage of the heart's operation, whether during relaxation or contraction. Cardiac endothelial cells release nitric oxide, a potent vasodilator that regulates blood vessel dilation consequently controlling blood pressure and flow. They also produce a myriad of growth factors that aid in new blood vessel formation, known as angiogenesis, crucially needed for tissue repair and regeneration when the heart undergoes damage, as in cases of myocardial infarction. +Furthermore, cardiac endothelial cells control the passage of nutrients, hormones, and gases between the bloodstream and the heart tissue, ensuring its complex metabolic demands are met adequately. They serve as a selective barrier, regulating the transit of cells and signaling molecules, thereby playing a pivotal role in inflammatory responses and immune cell trafficking. They also contribute to the maintenance of blood fluidity and clotting balance through a complex interplay of anti-thrombic and pro-thrombic factors. + DOI:10.1007/s00441-021-03471-2 + DOI:10.1530/VB-20-0006 + DOI:10.3389/fcvm.2018.00101 + DOI:10.3389/fphys.2018.00382 + DOI:10.3390/ijms20184411 + @@ -88230,19 +89846,19 @@ A constant renewal cycle is necessary due to the harsh environment of the colon - + Any photoreceptor cell that is part of some camera-type eye. camera type eye photoreceptor cell camera-type eye photoreceptor cell - + - + https://github.com/obophenotype/cell-ontology/issues/2245 @@ -88325,7 +89941,7 @@ A constant renewal cycle is necessary due to the harsh environment of the colon - + @@ -88493,7 +90109,7 @@ A constant renewal cycle is necessary due to the harsh environment of the colon - + @@ -88501,7 +90117,7 @@ A constant renewal cycle is necessary due to the harsh environment of the colon - + @@ -88538,13 +90154,8 @@ A constant renewal cycle is necessary due to the harsh environment of the colon + - - - - - - A CNS interneuron located in the dorsal horn of the spinal cord. dorsal spinal cord interneuron dorsal horn interneuron @@ -88587,6 +90198,7 @@ A constant renewal cycle is necessary due to the harsh environment of the colon A motor neuron that passes from the spinal cord toward or to a muscle and conducts an impulse that causes movement. + spinal cord motor neuron @@ -88625,7 +90237,7 @@ A constant renewal cycle is necessary due to the harsh environment of the colon - + @@ -88655,7 +90267,13 @@ A constant renewal cycle is necessary due to the harsh environment of the colon A vetebrate lens cell that is any of the elongated, tightly packed cells that make up the bulk of the mature lens in a camera-type eye. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Lens fiber cells are specialized, elongated cells located in the ocular lens, an important part of the eye responsible for focusing light onto the retina to create clear defined images. These cells are unique among body cells, as they are transparent and filled with a clear protein called crystallin to facilitate the passage of light. +The entire life cycle of a lens fiber cell includes differentiation from lens epithelial cells, which are the progenitor cells lying at the anterior surface of the lens. In response to various signals, these cells elongate and migrate towards the posterior pole, while simultaneously undergoing a process of denucleation and degradation of cellular organelles. This unique process ensures that the cells do not scatter light, which is critical for the transparency of the lens. After reaching full maturity, lens fiber cells form tightly packed layers, known as laminae, to make up the distinctive architecture of the ocular lens. +Lens fiber cells play pivotal roles in vision. Their primary function is to transmit and focus the light that enters the eye onto the retina, providing the sharpness and clarity necessary for vision. The precise alignment and organization of these cells allow for optimal light transmittance and minimizes scattering, thereby maintaining the transparency of the lens. As such, disruptions or abnormalities in lens fiber cells can lead to serious vision impairment, including conditions like cataracts, a common condition characterized by the opacification of the lens. ZFA:0009401 + https://cellxgene.cziscience.com/cellguide/CL_0011004 lens fibre cell @@ -88668,6 +90286,20 @@ A constant renewal cycle is necessary due to the harsh environment of the colon GO:0070307 GOC:nv + + + + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Lens fiber cells are specialized, elongated cells located in the ocular lens, an important part of the eye responsible for focusing light onto the retina to create clear defined images. These cells are unique among body cells, as they are transparent and filled with a clear protein called crystallin to facilitate the passage of light. +The entire life cycle of a lens fiber cell includes differentiation from lens epithelial cells, which are the progenitor cells lying at the anterior surface of the lens. In response to various signals, these cells elongate and migrate towards the posterior pole, while simultaneously undergoing a process of denucleation and degradation of cellular organelles. This unique process ensures that the cells do not scatter light, which is critical for the transparency of the lens. After reaching full maturity, lens fiber cells form tightly packed layers, known as laminae, to make up the distinctive architecture of the ocular lens. +Lens fiber cells play pivotal roles in vision. Their primary function is to transmit and focus the light that enters the eye onto the retina, providing the sharpness and clarity necessary for vision. The precise alignment and organization of these cells allow for optimal light transmittance and minimizes scattering, thereby maintaining the transparency of the lens. As such, disruptions or abnormalities in lens fiber cells can lead to serious vision impairment, including conditions like cataracts, a common condition characterized by the opacification of the lens. + DOI:10.1016/j.exer.2016.03.016 + DOI:10.1016/j.pbiomolbio.2003.11.012 + DOI:10.1098/rstb.2010.0300 + DOI:10.1242/dev.107953 + https://www.sciencedirect.com/topics/immunology-and-microbiology/lens-fiber + @@ -88694,9 +90326,8 @@ A constant renewal cycle is necessary due to the harsh environment of the colon An interneuron that uses GABA as a vesicular neurotransmitter. These interneurons are inhibitory - GABAergic inhibitory interneuron - + The formal and textual definitions of this term will need to be altered if evidence for non-inhibitory GABA-ergic neurons emerges. GABAergic interneuron @@ -88716,6 +90347,7 @@ A constant renewal cycle is necessary due to the harsh environment of the colon An inhibitory GABAergic interneuron found in the cerebellar cortex. + globular cell Lugaro cell @@ -88724,6 +90356,12 @@ A constant renewal cycle is necessary due to the harsh environment of the colon An inhibitory GABAergic interneuron found in the cerebellar cortex. GOC:nv + + + + globular cell + PMID:34194302 + @@ -88804,6 +90442,7 @@ A constant renewal cycle is necessary due to the harsh environment of the colon A cell derived from the mesoderm that is found at the periphery of the embryo. + lateral mesodermal cell @@ -88821,6 +90460,7 @@ A constant renewal cycle is necessary due to the harsh environment of the colon A cell derived from the mesoderm that is located between the paraxial mesoderm and the lateral plate. + intermediate mesodermal cell @@ -88839,7 +90479,7 @@ A constant renewal cycle is necessary due to the harsh environment of the colon A cell of the neural crest. Neural crest cells are multipotent. Premigratory neural crest cells are found at the neural plate boarder, some of which will undergo ectomesynchymal transition and delamination to form migratory neural crest cells. - This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. Neural crest cells are a group of transient and highly migratory cells that originate from the neuroectoderm during the early stages of embryonic development. They are multipotent cells with an exceptional degree of plasticity, capable of differentiating into various somatic cell types and therefore play a fundamental role in the formation of various organs and tissues, making them critical contributors to the developing embryo. After the initiation of neurulation (the formation of the neural tube) neural crest cells start to undergo epithelial-to-mesenchymal transition and delaminate and migrate from the dorsal neural tube to several regions throughout the embryo. They differentiate into a range of diverse cell types, such as neurons and glial cells of the peripheral nervous system, including sensory and autonomic neurons. They also contribute to the formation of adrenal glands, pigment cells in the skin (melanocytes), cardiac structures, including parts of the heart septum and major arteries, as well as bones and cartilage of the face and skull. @@ -88858,7 +90498,7 @@ Disorders or aberrations in the development or migration of the neural crest cel - This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. Neural crest cells are a group of transient and highly migratory cells that originate from the neuroectoderm during the early stages of embryonic development. They are multipotent cells with an exceptional degree of plasticity, capable of differentiating into various somatic cell types and therefore play a fundamental role in the formation of various organs and tissues, making them critical contributors to the developing embryo. After the initiation of neurulation (the formation of the neural tube) neural crest cells start to undergo epithelial-to-mesenchymal transition and delaminate and migrate from the dorsal neural tube to several regions throughout the embryo. They differentiate into a range of diverse cell types, such as neurons and glial cells of the peripheral nervous system, including sensory and autonomic neurons. They also contribute to the formation of adrenal glands, pigment cells in the skin (melanocytes), cardiac structures, including parts of the heart septum and major arteries, as well as bones and cartilage of the face and skull. @@ -89145,7 +90785,6 @@ Disorders or aberrations in the development or migration of the neural crest cel - @@ -89280,6 +90919,12 @@ Disorders or aberrations in the development or migration of the neural crest cel Any fibroblast that is part of skeletal muscle tissue. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Skeletal muscle fibroblasts (SMFs), with their spindle-shaped morphology, play a crucial role in maintaining the structure and function of skeletal muscles. They produce connective tissues enveloping muscle fibers, offering vital structural support for optimal muscle contraction. SMFs are integral components of the dynamic and complex microenvironment of muscle tissue, contributing significantly to healthy muscle development and homeostasis. +SMFs primarily synthesize and secrete extracellular matrix (ECM) components, such as collagen, fibronectin, and proteoglycans. The resulting ECM exhibits mechanical properties that resist tensile forces from muscle contractions, ensuring muscle efficiency. It also crucially transmits force during muscle movement, aids muscle attachment to the skeletal structure, and serves as a scaffold for muscle regeneration and repair. +Following injury, they proliferate and transform into myofibroblasts, aiding wound contraction and depositing new ECM for tissue repair. Additionally, these fibroblasts modulate inflammatory responses by secreting cytokines and interact with other cell types, like immune cells and satellite cells, to coordinate muscle healing. In diseases, an imbalance in SMF activity may lead to conditions such as fibrosis, marked by excessive ECM deposition and impaired muscle function. + https://cellxgene.cziscience.com/cellguide/CL_0011027 skeleton muscle fibroblast skeletal muscle fibroblast @@ -89291,6 +90936,18 @@ Disorders or aberrations in the development or migration of the neural crest cel PMID:28369879 https://orcid.org/0000-0001-6164-0667 + + + + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Skeletal muscle fibroblasts (SMFs), with their spindle-shaped morphology, play a crucial role in maintaining the structure and function of skeletal muscles. They produce connective tissues enveloping muscle fibers, offering vital structural support for optimal muscle contraction. SMFs are integral components of the dynamic and complex microenvironment of muscle tissue, contributing significantly to healthy muscle development and homeostasis. +SMFs primarily synthesize and secrete extracellular matrix (ECM) components, such as collagen, fibronectin, and proteoglycans. The resulting ECM exhibits mechanical properties that resist tensile forces from muscle contractions, ensuring muscle efficiency. It also crucially transmits force during muscle movement, aids muscle attachment to the skeletal structure, and serves as a scaffold for muscle regeneration and repair. +Following injury, they proliferate and transform into myofibroblasts, aiding wound contraction and depositing new ECM for tissue repair. Additionally, these fibroblasts modulate inflammatory responses by secreting cytokines and interact with other cell types, like immune cells and satellite cells, to coordinate muscle healing. In diseases, an imbalance in SMF activity may lead to conditions such as fibrosis, marked by excessive ECM deposition and impaired muscle function. + DOI:10.1016/j.diff.2016.05.007 + DOI:10.1186/s13578-021-00579-4 + DOI:10.1186/s13578-022-00856-w + @@ -89302,6 +90959,7 @@ Disorders or aberrations in the development or migration of the neural crest cel BTO:0002771 OEC + olfactory ensheathing cell @@ -89392,6 +91050,7 @@ Disorders or aberrations in the development or migration of the neural crest cel MDDC cell + monocyte-derived dendritic cell @@ -89484,6 +91143,12 @@ Disorders or aberrations in the development or migration of the neural crest cel Cells of the uterine chorion that acquire specialized structural and/or functional features that characterize chorionic trophoblasts. These cells will migrate towards the spongiotrophoblast layer and give rise to syncytiotrophoblasts of the labyrinthine layer. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +The chorionic trophoblast cell, vital for placental development in mammals, originates from the blastocyst's outer layer, the trophectoderm. As a significant component of the placenta, the chorion forms the external fetal-maternal interface and consists primarily of chorionic trophoblast cells. These cells are pivotal in embryogenesis, fetal nutrition, waste removal, and immune response generation, contributing crucially to the success of pregnancy. +Chorionic trophoblast cells undergo trophoblast differentiation, giving rise to specialized sub-types: cytotrophoblasts and syncytiotrophoblasts. Cytotrophoblasts, found in the inner layer, serve as stem cells and contribute to proliferative activities. In contrast, syncytiotrophoblasts, originating from cytotrophoblasts, form the outer layer with a distinctive multinucleated, continuous, and non-proliferative structure. These cells play a key role in maternal-fetal gas and nutrient exchange, producing essential hormones like human chorionic gonadotropin (hCG), progesterone, and estrogen, vital for sustaining pregnancy. +Apart from their physiological roles, chorionic trophoblast cells play a crucial role in shielding the fetus from the maternal immune system. They accomplish this by modifying the expression of major histocompatibility complex (MHC) molecules, which are self-identifying proteins utilized by the immune system to identify foreign cells. Through selective expression of specific types of these molecules, trophoblast cells can evade cytotoxic T cells that might otherwise attack them, while still retaining the ability to attract natural killer cells. These natural killer cells assist in trophoblast invasion and the remodeling of blood vessels in the uterus. + https://cellxgene.cziscience.com/cellguide/CL_0011101 chorionic trophoblast cell @@ -89493,6 +91158,20 @@ Disorders or aberrations in the development or migration of the neural crest cel Cells of the uterine chorion that acquire specialized structural and/or functional features that characterize chorionic trophoblasts. These cells will migrate towards the spongiotrophoblast layer and give rise to syncytiotrophoblasts of the labyrinthine layer. GOC:NV + + + + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +The chorionic trophoblast cell, vital for placental development in mammals, originates from the blastocyst's outer layer, the trophectoderm. As a significant component of the placenta, the chorion forms the external fetal-maternal interface and consists primarily of chorionic trophoblast cells. These cells are pivotal in embryogenesis, fetal nutrition, waste removal, and immune response generation, contributing crucially to the success of pregnancy. +Chorionic trophoblast cells undergo trophoblast differentiation, giving rise to specialized sub-types: cytotrophoblasts and syncytiotrophoblasts. Cytotrophoblasts, found in the inner layer, serve as stem cells and contribute to proliferative activities. In contrast, syncytiotrophoblasts, originating from cytotrophoblasts, form the outer layer with a distinctive multinucleated, continuous, and non-proliferative structure. These cells play a key role in maternal-fetal gas and nutrient exchange, producing essential hormones like human chorionic gonadotropin (hCG), progesterone, and estrogen, vital for sustaining pregnancy. +Apart from their physiological roles, chorionic trophoblast cells play a crucial role in shielding the fetus from the maternal immune system. They accomplish this by modifying the expression of major histocompatibility complex (MHC) molecules, which are self-identifying proteins utilized by the immune system to identify foreign cells. Through selective expression of specific types of these molecules, trophoblast cells can evade cytotoxic T cells that might otherwise attack them, while still retaining the ability to attract natural killer cells. These natural killer cells assist in trophoblast invasion and the remodeling of blood vessels in the uterus. + DOI:10.1007/s00018-019-03104-6 + DOI:10.1093/biolre/ioy070 + DOI:10.1155/2014/579279 + https://www.ncbi.nlm.nih.gov/books/NBK53245/ + https://www.sciencedirect.com/topics/medicine-and-dentistry/placenta-development + @@ -89502,6 +91181,7 @@ Disorders or aberrations in the development or migration of the neural crest cel Parasympathetic neurons are part of the parasympathetic nervous sysem and the cell bodies lie in the brain and sacral region of the spinal cord. The neurons are mainly cholinergic. ZFA:0005776 + parasympathetic neuron @@ -89676,7 +91356,7 @@ plexiform layer using GABA. - + @@ -89837,7 +91517,7 @@ plexiform layer using GABA. - + @@ -89845,7 +91525,7 @@ plexiform layer using GABA. - + @@ -89853,6 +91533,7 @@ plexiform layer using GABA. Neuron found in the spiral ganglion. + spiral ganglion neuron @@ -89961,7 +91642,7 @@ plexiform layer using GABA. - + @@ -89969,7 +91650,6 @@ plexiform layer using GABA. - @@ -89984,12 +91664,6 @@ plexiform layer using GABA. neuron of the forebrain - - - - - true - @@ -90035,6 +91709,7 @@ plexiform layer using GABA. PMID:14699587 ZFA:0005730 cranial motoneuron + cranial motor neuron @@ -90068,10 +91743,16 @@ plexiform layer using GABA. + + + + + + An ionocyte that is part of the lung epithelium. The cells from this type are major sources of the CFTR protein in human and mice. - This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. The pulmonary ionocyte is a relatively newly identified, specific epithelial cell type found primarily in the pulmonary or respiratory system. Discovered through novel mapping techniques in 2018, these cells are surprisingly rare, making up less than 2% of the cells in the lung's airway, yet they play an essential role in the airway surface liquid and mucus regulation, a crucial factor in lung health. The main responsibility of the pulmonary ionocyte pertains to the regulation and mobilization of chloride ions. They express a high level of CFTR (Cystic Fibrosis Transmembrane Conductance Regulator) gene, which encodes a protein channel across the membrane of cells that produce mucus, sweat, saliva, tears, and digestive enzymes. The activity of CFTR regulates the movement of chloride ions and fluids in and out of cells, which helps maintain a balance of fluid in the organs they are expressed in. If CFTR is dysfunctional, it can cause conditions such as cystic fibrosis, characterized by thick, sticky mucus that can clog the lungs and obstruct the pancreas, leading to respiratory and digestive issues. @@ -90079,6 +91760,7 @@ The discovery of this cell type offers new doors to the treatment and further un https://cellxgene.cziscience.com/cellguide/CL_0017000 + The marker set ASCL3, BSND can identify the Human cell type pulmonary ionocyte in the Lung with a confidence of 0.82 (NS-Forest FBeta value). pulmonary ionocyte @@ -90091,7 +91773,7 @@ The discovery of this cell type offers new doors to the treatment and further un - This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. The pulmonary ionocyte is a relatively newly identified, specific epithelial cell type found primarily in the pulmonary or respiratory system. Discovered through novel mapping techniques in 2018, these cells are surprisingly rare, making up less than 2% of the cells in the lung's airway, yet they play an essential role in the airway surface liquid and mucus regulation, a crucial factor in lung health. The main responsibility of the pulmonary ionocyte pertains to the regulation and mobilization of chloride ions. They express a high level of CFTR (Cystic Fibrosis Transmembrane Conductance Regulator) gene, which encodes a protein channel across the membrane of cells that produce mucus, sweat, saliva, tears, and digestive enzymes. The activity of CFTR regulates the movement of chloride ions and fluids in and out of cells, which helps maintain a balance of fluid in the organs they are expressed in. If CFTR is dysfunctional, it can cause conditions such as cystic fibrosis, characterized by thick, sticky mucus that can clog the lungs and obstruct the pancreas, leading to respiratory and digestive issues. @@ -90100,6 +91782,12 @@ The discovery of this cell type offers new doors to the treatment and further un DOI:10.1146/annurev-pathol-042420-094031 DOI:10.1172/JCI171268 + + + + The marker set ASCL3, BSND can identify the Human cell type pulmonary ionocyte in the Lung with a confidence of 0.82 (NS-Forest FBeta value). + https://doi.org/10.5281/zenodo.11165918 + @@ -90115,6 +91803,7 @@ The discovery of this cell type offers new doors to the treatment and further un A mesodermal cell that is part of the splanchnic layer of lateral plate mesoderm. + splanchnic mesodermal cell @@ -90134,6 +91823,7 @@ The discovery of this cell type offers new doors to the treatment and further un + @@ -90143,7 +91833,7 @@ The discovery of this cell type offers new doors to the treatment and further un A neuroendocrine cell that is part of the prostate epithelium. - + neuroendocrine cell of prostate epithelium neuroendocrine cell of the prostate @@ -90181,7 +91871,7 @@ The discovery of this cell type offers new doors to the treatment and further un An epithelial cell that is part of the prostatic urethra. - + epithelial cell of prostatic urethra @@ -90205,7 +91895,7 @@ The discovery of this cell type offers new doors to the treatment and further un A supportive cell with a small, oval-shaped body and one to five telopodes. Telopodes are cytoplasmic protrusions from tens to hundreds of micrometers long and mostly below 0.2 microns of caliber. - + interstitial Cajal cell-like cell interstitial Cajal-like cell ICLC @@ -90268,8 +91958,8 @@ The discovery of this cell type offers new doors to the treatment and further un A lymphocyte that has gotten larger after being stimulated by an antigen. - 2022-08-17T14:20:01Z - + + 2022-08-17T14:20:01Z BTO:0000772 EFO:0000572 FMA:83030 @@ -90292,8 +91982,8 @@ The discovery of this cell type offers new doors to the treatment and further un A lymphocyte of B lineage that has gotten larger after being stimulated by an antigen. - 2022-08-17T14:30:32Z - + + 2022-08-17T14:30:32Z EFO:0005293 FMA:83031 @@ -90326,8 +92016,8 @@ The discovery of this cell type offers new doors to the treatment and further un A human dendritic cell that expresses the AXL and SIGLEC6 genes. - 2022-08-25T14:18:37Z - + + 2022-08-25T14:18:37Z AS DC, human Axl+ dendritic cell, human @@ -90718,11 +92408,28 @@ The discovery of this cell type offers new doors to the treatment and further un Any serous secreting cell that is part of the tracheobronchial epithelium. 2020-05-07T16:03:27Z + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Serous cells of the tracheobronchial are found on the surface epithelium, submucosal glands, or both, depending on species. They appear in tubulo-acinar arrangements in submucosal glands. +Tracheobronchial serous cells play a vital role in maintaining respiratory health by secreting serous fluid, which is rich in enzymes, ions, and antimicrobial proteins. This serous fluid is essential in clearing out debris, trapping and neutralizing inhaled pathogens and particulate matters, thereby helping in preventing infections. Their secretory products also include water and electrolytes that, combined with mucus (from mucous cells), maintain proper humidity within the airway and lubricate its surfaces, facilitating unhindered airflow. Dysfunction of these cells may lead to diseases such as cystic fibrosis. + https://cellxgene.cziscience.com/cellguide/CL_0019001 serous cell of tracheobronchial tree tracheobronchial serous cell + + + + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Serous cells of the tracheobronchial are found on the surface epithelium, submucosal glands, or both, depending on species. They appear in tubulo-acinar arrangements in submucosal glands. +Tracheobronchial serous cells play a vital role in maintaining respiratory health by secreting serous fluid, which is rich in enzymes, ions, and antimicrobial proteins. This serous fluid is essential in clearing out debris, trapping and neutralizing inhaled pathogens and particulate matters, thereby helping in preventing infections. Their secretory products also include water and electrolytes that, combined with mucus (from mucous cells), maintain proper humidity within the airway and lubricate its surfaces, facilitating unhindered airflow. Dysfunction of these cells may lead to diseases such as cystic fibrosis. + DOI:10.1016/j.resp.2007.06.017 + DOI:10.1113/jphysiol.2003.052779 + DOI:10.1146/annurev.ph.52.030190.000525 + DOI:10.1152/ajplung.00068.2019 + @@ -90903,6 +92610,7 @@ The discovery of this cell type offers new doors to the treatment and further un 2020-07-21T12:42:48Z smooth muscle cell of blood vessel + blood vessel smooth muscle cell @@ -90936,13 +92644,26 @@ The discovery of this cell type offers new doors to the treatment and further un + + + + + + A smooth muscle cell that is part of the tracheobronchial tree. 2020-07-21T12:50:22Z + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Tracheobronchial smooth muscle cells are universally located in the tracheobronchial tree and play a critical role in controlling and modulating the size of the airway lumen, thereby contributing significantly to the airflow resistance. +These cells display both phasic and tonic characteristics, which are vital for airway contractility. Phasic activity manifests as cyclic contraction and relaxation, similar to the behavior seen in gastrointestinal smooth muscle cells, whilst tonic activity resembles vascular smooth muscle cells, maintaining a constant degree of tension. These features enable tracheobronchial smooth muscle cells to constrict the airways in response to various mechanical and chemical stimuli, including allergens, parasympathetic nervous stimulation, changes in gas composition, and cold air, thus protecting the delicate alveoli from potential damage. +Tracheobronchial smooth muscle cells, beyond their contractile function, actively contribute to airway remodeling in conditions like asthma. Their proliferative and synthetic capabilities lead to smooth muscle hypertrophy, hyperplasia, and the production of extracellular matrix components, collectively causing abnormal airway narrowing. + https://cellxgene.cziscience.com/cellguide/CL_0019019 smooth muscle cell of tracheobronchial tree + The marker set ACTA2, TAGLN can identify the Human cell type tracheobronchial smooth muscle cell in the Lung with a confidence of 0.69 (NS-Forest FBeta value). tracheobronchial smooth muscle cell @@ -90951,6 +92672,24 @@ The discovery of this cell type offers new doors to the treatment and further un A smooth muscle cell that is part of the tracheobronchial tree. PMID:10853867 + + + + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Tracheobronchial smooth muscle cells are universally located in the tracheobronchial tree and play a critical role in controlling and modulating the size of the airway lumen, thereby contributing significantly to the airflow resistance. +These cells display both phasic and tonic characteristics, which are vital for airway contractility. Phasic activity manifests as cyclic contraction and relaxation, similar to the behavior seen in gastrointestinal smooth muscle cells, whilst tonic activity resembles vascular smooth muscle cells, maintaining a constant degree of tension. These features enable tracheobronchial smooth muscle cells to constrict the airways in response to various mechanical and chemical stimuli, including allergens, parasympathetic nervous stimulation, changes in gas composition, and cold air, thus protecting the delicate alveoli from potential damage. +Tracheobronchial smooth muscle cells, beyond their contractile function, actively contribute to airway remodeling in conditions like asthma. Their proliferative and synthetic capabilities lead to smooth muscle hypertrophy, hyperplasia, and the production of extracellular matrix components, collectively causing abnormal airway narrowing. + DOI:10.1007/978-3-540-79090-7_5 + DOI:10.1152/japplphysiol.00950.2012 + https://www.ncbi.nlm.nih.gov/books/NBK556044/ + + + + + The marker set ACTA2, TAGLN can identify the Human cell type tracheobronchial smooth muscle cell in the Lung with a confidence of 0.69 (NS-Forest FBeta value). + https://doi.org/10.5281/zenodo.11165918 + @@ -91249,6 +92988,12 @@ The discovery of this cell type offers new doors to the treatment and further un + + + + + + Goblet cells reside throughout the length of the small and large intestine and are responsible for the production and maintenance of the protective mucus blanket by synthesizing and secreting high-molecular-weight glycoproteins known as mucins. Human intestinal goblet cells secrete the MUC2 mucin, as well as a number of typical mucus components: CLCA1, FCGBP, AGR2, ZG16, and TFF3. 2020-10-14T14:59:07Z @@ -91262,6 +93007,7 @@ The discovery of this cell type offers new doors to the treatment and further un Goblet cells reside throughout the length of the small and large intestine and are responsible for the production and maintenance of the protective mucus blanket by synthesizing and secreting high-molecular-weight glycoproteins known as mucins. Human intestinal goblet cells secrete the MUC2 mucin, as well as a number of typical mucus components: CLCA1, FCGBP, AGR2, ZG16, and TFF3. PMID:1996606 PMID:24942678 + PMID:33484640 @@ -91288,6 +93034,12 @@ The discovery of this cell type offers new doors to the treatment and further un + + + + + + Any brush cell that is part of the intestinal epithelium. @@ -91302,6 +93054,7 @@ The discovery of this cell type offers new doors to the treatment and further un Any brush cell that is part of the intestinal epithelium. PMID:22527717 + PMID:39358509 @@ -91447,6 +93200,7 @@ The discovery of this cell type offers new doors to the treatment and further un Any neuroblast (sensu Vertebrata) that is part of some forebrain. + forebrain neuroblast @@ -91649,8 +93403,9 @@ The discovery of this cell type offers new doors to the treatment and further un + Any goblet cell that is part of some lung epithelium. - This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. Lung goblet cells are critical components of the respiratory tract, specifically found in the bronchial segments. They are secretory epithelial cells known for their signature "goblet" or cup-like shape. Their primary function is to produce and secrete mucus that aids in trapping airborne particles and pathogens, preventing them from reaching the delicate environment of the lung. As part of the lung's epithelial lining, they act as frontline defenders, maintaining lung health and function. The lung goblet cells are densely packed with granules containing mucin glycoproteins, the primary component of mucus. As mucus is produced and secreted, it moves towards the lumen of the lungs where the cilia, hair-like structures of the neighboring ciliated epithelial cells, help to navigate it upwards and out of the respiratory tract. This coordinated action ensures the expulsion of unwanted particles and pathogens, effectively cleaning the respiratory tract. @@ -91668,7 +93423,7 @@ Dysfunction or abnormal proliferation of lung goblet cells can result in patholo - This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. Lung goblet cells are critical components of the respiratory tract, specifically found in the bronchial segments. They are secretory epithelial cells known for their signature "goblet" or cup-like shape. Their primary function is to produce and secrete mucus that aids in trapping airborne particles and pathogens, preventing them from reaching the delicate environment of the lung. As part of the lung's epithelial lining, they act as frontline defenders, maintaining lung health and function. The lung goblet cells are densely packed with granules containing mucin glycoproteins, the primary component of mucus. As mucus is produced and secreted, it moves towards the lumen of the lungs where the cilia, hair-like structures of the neighboring ciliated epithelial cells, help to navigate it upwards and out of the respiratory tract. This coordinated action ensures the expulsion of unwanted particles and pathogens, effectively cleaning the respiratory tract. @@ -91865,22 +93620,41 @@ Dysfunction or abnormal proliferation of lung goblet cells can result in patholo - + - - - Any neuroendocrine cell that is part of some stomach. + + + + + + + + A specialised neuroendocrine cell located in the gastric mucosa that regulates digestive processes including acid secretion and gut motility. This cell stores hormones in large dense core vesicles and synaptic-like microvesicles. + DES cell + diffuse endocrine system cell stomach neuroendocrine cell - Any neuroendocrine cell that is part of some stomach. - FBC:Autogenerated + A specialised neuroendocrine cell located in the gastric mucosa that regulates digestive processes including acid secretion and gut motility. This cell stores hormones in large dense core vesicles and synaptic-like microvesicles. + PMID:15153415 + + + + + DES cell + PMID:15153415 + + + + + diffuse endocrine system cell + PMID:15153415 @@ -91917,23 +93691,30 @@ Dysfunction or abnormal proliferation of lung goblet cells can result in patholo - A neuroendocrine cell that is part of respiratory epithelium of the lung and is involved in the sensory detection of environmental stimuli, including hypoxia, nicotine and air pressure. Ultrastructurally, this cell type is characterized by the presence of cytoplasmic dense core granules, which are considered the storage sites of amine and peptide hormones. Lung neuroendocrine cells are innervated and appear as solitary cells or as clustered masses, localized at airway bifurcation sites, called neuroepithelial bodies that can release serotonin in response to hypoxia and interact with sensory nerve terminals. Lung neuroendocrine cells also function as reserve stem cells that repair the surrounding epithelium after injury. + + + + + + + A neuroendocrine cell that is part of respiratory epithelium of the lung and is involved in the sensory detection of environmental stimuli, including hypoxia, nicotine and air pressure. Ultrastructurally, this cell type is characterized by the presence of cytoplasmic dense core granules, which are considered the storage sites of amine and peptide hormones. Pulmonary neuroendocrine cells are innervated and appear as solitary cells or as clustered masses, localized at airway bifurcation sites, called neuroepithelial bodies that can release serotonin in response to hypoxia and interact with sensory nerve terminals. Pulmonary neuroendocrine cells also function as reserve stem cells that repair the surrounding epithelium after injury. - This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. Lung neuroendocrine cells, also commonly known as pulmonary neuroendocrine cells (PNECs), are predominantly located in the respiratory epithelium of the bronchial and bronchiolar airways in the lungs. These cells, characterised by their small size and granular appearance, have a distinctive morphology that sets them apart from other lung cells. They are considered part of the diffuse neuroendocrine system due to their scattered distribution through the epithelium and have been classified into solitary cells and clustered forms known as neuroepithelial bodies. The primary function of PNECs is linked to regulation and maintenance of the lung environment. They are sensory in nature and can secrete various bioactive substances such as serotonin, calcitonin, calcitonin gene-related peptides, and bombesin-like peptides which modulate airway smooth muscle tone and influence gut motility. For example, they act as oxygen sensors in response to hypoxia and are responsible for releasing neuropeptides that can induce responses. Moreover, PNECs provide an afferent function as they are equipped with long microvilli that project into the lumen of the bronchus and react to changes in the chemical composition of the luminal content. https://cellxgene.cziscience.com/cellguide/CL_1000223 - pulmonary neuroendocrine cell + lung neuroendocrine cell PNEC - lung neuroendocrine cell + The marker set CHGA, GRP can identify the Human cell type lung neuroendocrine cell in the Lung with a confidence of 0.94 (NS-Forest FBeta value). + pulmonary neuroendocrine cell - A neuroendocrine cell that is part of respiratory epithelium of the lung and is involved in the sensory detection of environmental stimuli, including hypoxia, nicotine and air pressure. Ultrastructurally, this cell type is characterized by the presence of cytoplasmic dense core granules, which are considered the storage sites of amine and peptide hormones. Lung neuroendocrine cells are innervated and appear as solitary cells or as clustered masses, localized at airway bifurcation sites, called neuroepithelial bodies that can release serotonin in response to hypoxia and interact with sensory nerve terminals. Lung neuroendocrine cells also function as reserve stem cells that repair the surrounding epithelium after injury. + A neuroendocrine cell that is part of respiratory epithelium of the lung and is involved in the sensory detection of environmental stimuli, including hypoxia, nicotine and air pressure. Ultrastructurally, this cell type is characterized by the presence of cytoplasmic dense core granules, which are considered the storage sites of amine and peptide hormones. Pulmonary neuroendocrine cells are innervated and appear as solitary cells or as clustered masses, localized at airway bifurcation sites, called neuroepithelial bodies that can release serotonin in response to hypoxia and interact with sensory nerve terminals. Pulmonary neuroendocrine cells also function as reserve stem cells that repair the surrounding epithelium after injury. PMID:33355253 doi:10.3109/01902148209069653 doi:10.7554/eLife.78216 @@ -91941,7 +93722,7 @@ The primary function of PNECs is linked to regulation and maintenance of the lun - This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. Lung neuroendocrine cells, also commonly known as pulmonary neuroendocrine cells (PNECs), are predominantly located in the respiratory epithelium of the bronchial and bronchiolar airways in the lungs. These cells, characterised by their small size and granular appearance, have a distinctive morphology that sets them apart from other lung cells. They are considered part of the diffuse neuroendocrine system due to their scattered distribution through the epithelium and have been classified into solitary cells and clustered forms known as neuroepithelial bodies. The primary function of PNECs is linked to regulation and maintenance of the lung environment. They are sensory in nature and can secrete various bioactive substances such as serotonin, calcitonin, calcitonin gene-related peptides, and bombesin-like peptides which modulate airway smooth muscle tone and influence gut motility. For example, they act as oxygen sensors in response to hypoxia and are responsible for releasing neuropeptides that can induce responses. Moreover, PNECs provide an afferent function as they are equipped with long microvilli that project into the lumen of the bronchus and react to changes in the chemical composition of the luminal content. @@ -91952,8 +93733,8 @@ The primary function of PNECs is linked to regulation and maintenance of the lun - pulmonary neuroendocrine cell - PMID:33355253 + lung neuroendocrine cell + PMID:15018448 @@ -91962,6 +93743,12 @@ The primary function of PNECs is linked to regulation and maintenance of the lun PMID:33355253 + + + + The marker set CHGA, GRP can identify the Human cell type lung neuroendocrine cell in the Lung with a confidence of 0.94 (NS-Forest FBeta value). + https://doi.org/10.5281/zenodo.11165918 + @@ -92037,7 +93824,7 @@ The primary function of PNECs is linked to regulation and maintenance of the lun - + @@ -92052,13 +93839,13 @@ The primary function of PNECs is linked to regulation and maintenance of the lun - Any neuron that has its soma located in some posterior lateral line ganglion. + Any peripheral nervous system neuron that has its soma located in some posterior lateral line ganglion. posterior lateral line ganglion neuron - Any neuron that has its soma located in some posterior lateral line ganglion. + Any peripheral nervous system neuron that has its soma located in some posterior lateral line ganglion. FBC:Autogenerated @@ -92070,22 +93857,30 @@ The primary function of PNECs is linked to regulation and maintenance of the lun - + + + + + + + + + - An epithelial cell that is part of the lung epithelium. This cell is characterised by the presence of cilia on its apical surface. + lung ciliated cell - lung ciliated cell + lung multiciliated epithelial cell @@ -92163,10 +93958,17 @@ The primary function of PNECs is linked to regulation and maintenance of the lun A smooth muscle cell that is part of the small intestine. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Smooth muscle cells of the small intestine form a key component of the enteric system which is imperative for gastrointestinal motility. These cells are a specialized subgroup of smooth muscle cells, specifically found in the layers of the small intestine. The small intestine represents a significant part of the digestive system and plays a crucial role in the absorption of nutrients into the bloodstream. +Smooth muscle cells of the small intestine are predominantly responsible for creating the contractions and relaxations that constitute intestinal motility. They trigger these movements in a coordinated and rhythmic manner known as peristalsis and segmentation. Peristalsis is a form of longitudinal and sequential contraction that pushes food from the upper gastrointestinal tract to the lower parts. Segmentation works by squeezing the intestine randomly, thereby facilitating the mixing of food particles and increasing contact with absorptive surfaces. These two processes are critical for intestinal motility and an effective digestive process. +Apart from facilitating transit of food through contractions, these smooth muscle cells play a role in controlling the diameter of the vessels and the blood flow in the small intestine by their constrictive ability. These smooth muscle cells also contribute to the structural integrity of the small intestine by forming a part of its muscularis externa and muscularis mucosae. Additionally, they interact with other cell types such as enteric neurons and interstitial cells of Cajal (ICC), forming an integrated cellular network that ensures optimal functioning of the intestinal tract. FMA:15050 + https://cellxgene.cziscience.com/cellguide/CL_1000275 non-striated muscle fiber of small intestine smooth muscle cell of small intestine + @@ -92180,12 +93982,36 @@ The primary function of PNECs is linked to regulation and maintenance of the lun A smooth muscle cell that is part of the small intestine. GOC:tfm + + + + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Smooth muscle cells of the small intestine form a key component of the enteric system which is imperative for gastrointestinal motility. These cells are a specialized subgroup of smooth muscle cells, specifically found in the layers of the small intestine. The small intestine represents a significant part of the digestive system and plays a crucial role in the absorption of nutrients into the bloodstream. +Smooth muscle cells of the small intestine are predominantly responsible for creating the contractions and relaxations that constitute intestinal motility. They trigger these movements in a coordinated and rhythmic manner known as peristalsis and segmentation. Peristalsis is a form of longitudinal and sequential contraction that pushes food from the upper gastrointestinal tract to the lower parts. Segmentation works by squeezing the intestine randomly, thereby facilitating the mixing of food particles and increasing contact with absorptive surfaces. These two processes are critical for intestinal motility and an effective digestive process. +Apart from facilitating transit of food through contractions, these smooth muscle cells play a role in controlling the diameter of the vessels and the blood flow in the small intestine by their constrictive ability. These smooth muscle cells also contribute to the structural integrity of the small intestine by forming a part of its muscularis externa and muscularis mucosae. Additionally, they interact with other cell types such as enteric neurons and interstitial cells of Cajal (ICC), forming an integrated cellular network that ensures optimal functioning of the intestinal tract. + DOI:10.1007/978-981-13-5895-1_1 + DOI:10.1038/nrgastro.2012.168 + DOI:10.1038/s41575-020-0271-2 + DOI:10.1053/j.gastro.2016.02.030 + DOI:10.1111/j.1582-4934.2008.00352.x + non-striated muscle fiber of small intestine FMA:15050 + + + + + http://creativecommons.org/licenses/by/4.0/ + Figure depicts a cross section of intestinal villi in the small intestine, including the crypts of Lieberkuhn (seen here as ‘crypt’), as well as the layer specific locations of cells that exist within the gastrointestinal tract. Layers depicted here include epithelium (rows of cells bordering villus), submucosa (white space below the epithelium containing networks of neurons and ganglia depicted in pink), muscularis mucosae (blue layer), muscularis propria (referred to here as muscle layer). + +ISC: Intestinal Stem Cell +TA: Transit Amplifying Cells + @@ -92204,6 +94030,12 @@ The primary function of PNECs is linked to regulation and maintenance of the lun + + + + + + @@ -92298,6 +94130,12 @@ The primary function of PNECs is linked to regulation and maintenance of the lun + + + + + + @@ -92305,7 +94143,13 @@ The primary function of PNECs is linked to regulation and maintenance of the lun A smooth muscle cell that is part of the ileum. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +The smooth muscle fiber of the ileum primarily refers to a specific class of muscle cells present in the ileum, the final segment of the small intestine. Distinguished from skeletal muscle and cardiac muscle, smooth muscle does not possess striations and is under the control of the involuntary nervous system. +These cells primarily facilitate the movement of digested food, a process known as peristalsis. These cells coordinate rhythmic contractions and relaxations, propelling the chyme toward the colon. This process is vital for efficient nutrient absorption in the small intestine and the transfer of undigested material to the large intestine. Moreover, the smooth muscle fibers enhance the ileum's ability to expand and adapt to volume changes without elevating internal pressure, known as compliance. +The smooth muscle fiber of the ileum contributes to reflex responses, enhancing muscle contractions to propel intestinal contents in different physiological conditions. This involves intricate molecular signaling with neurotransmitters, hormones, and local signals. Thus, beyond its structural role, the smooth muscle fiber is crucial for the physiological functions of digestion and absorption in the small intestine. FMA:15066 + https://cellxgene.cziscience.com/cellguide/CL_1000278 non-striated muscle fiber of ileum smooth muscle fiber of ileum @@ -92322,6 +94166,18 @@ The primary function of PNECs is linked to regulation and maintenance of the lun A smooth muscle cell that is part of the ileum. GOC:tfm + + + + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +The smooth muscle fiber of the ileum primarily refers to a specific class of muscle cells present in the ileum, the final segment of the small intestine. Distinguished from skeletal muscle and cardiac muscle, smooth muscle does not possess striations and is under the control of the involuntary nervous system. +These cells primarily facilitate the movement of digested food, a process known as peristalsis. These cells coordinate rhythmic contractions and relaxations, propelling the chyme toward the colon. This process is vital for efficient nutrient absorption in the small intestine and the transfer of undigested material to the large intestine. Moreover, the smooth muscle fibers enhance the ileum's ability to expand and adapt to volume changes without elevating internal pressure, known as compliance. +The smooth muscle fiber of the ileum contributes to reflex responses, enhancing muscle contractions to propel intestinal contents in different physiological conditions. This involves intricate molecular signaling with neurotransmitters, hormones, and local signals. Thus, beyond its structural role, the smooth muscle fiber is crucial for the physiological functions of digestion and absorption in the small intestine. + DOI:10.1152/advan.00025.2003 + https://www.ncbi.nlm.nih.gov/books/NBK532857/ + https://www.ncbi.nlm.nih.gov/books/NBK556137/ + @@ -92402,6 +94258,12 @@ The primary function of PNECs is linked to regulation and maintenance of the lun + + + + + + A smooth muscle cell that is part of the colon. FMA:15663 non-striated muscle fiber of colon @@ -92673,6 +94535,12 @@ The primary function of PNECs is linked to regulation and maintenance of the lun + + + + + + A smooth muscle cell that is part of the rectum. FMA:17522 non-striated muscle fiber of rectum @@ -92836,7 +94704,13 @@ The primary function of PNECs is linked to regulation and maintenance of the lun An epithelial cell that is part of the urethra. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Epithelial cells of the urethra constitute the inner lining of the urethra, forming a mucosal barrier that helps protect the body from external contaminants. The type of epithelial cells found in the urethra can vary along its length. In general, the urethra is lined with stratified squamous epithelium in its distal or external portion, which is closer to the external environment. This type of epithelium provides protection against mechanical stress and pathogens. Closer to the bladder, the urethra transitions to a different type of epithelium. In males, the proximal part of the urethra is lined with pseudostratified columnar epithelium in the region where it passes through the prostate gland. In females, the transitional epithelium may be present in the proximal part of the urethra near the bladder. +Epithelial cells of the urethra are primarily dedicated to the protection of underlying tissues from mechanical stress and pathogens during micturition (urination). They do this by creating a tight, impermeable barrier that prevents the entry and colonization of invading microbes. They produce a variety of antimicrobials and are tightly packed to prevent infiltration between cells, forming an integral part of the body's innate immune system. +In addition to their protective role, these cells are involved in the secretion of mucus. This mucus acts as a lubricant that ensures the smooth and easy passage of urine from the bladder through the urethra and out of the body, reducing any potential damage from the erosive action of urine. Epithelial cells of the urethra are dynamic, constantly renewing their numbers to replace any cells lost through wear and tear. Any disruptions to the function or integrity of these cells may contribute to urinary tract infections and other urological disorders. FMA:256165 + https://cellxgene.cziscience.com/cellguide/CL_1000296 epithelial cell of urethra @@ -92846,6 +94720,20 @@ The primary function of PNECs is linked to regulation and maintenance of the lun An epithelial cell that is part of the urethra. GOC:tfm + + + + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Epithelial cells of the urethra constitute the inner lining of the urethra, forming a mucosal barrier that helps protect the body from external contaminants. The type of epithelial cells found in the urethra can vary along its length. In general, the urethra is lined with stratified squamous epithelium in its distal or external portion, which is closer to the external environment. This type of epithelium provides protection against mechanical stress and pathogens. Closer to the bladder, the urethra transitions to a different type of epithelium. In males, the proximal part of the urethra is lined with pseudostratified columnar epithelium in the region where it passes through the prostate gland. In females, the transitional epithelium may be present in the proximal part of the urethra near the bladder. +Epithelial cells of the urethra are primarily dedicated to the protection of underlying tissues from mechanical stress and pathogens during micturition (urination). They do this by creating a tight, impermeable barrier that prevents the entry and colonization of invading microbes. They produce a variety of antimicrobials and are tightly packed to prevent infiltration between cells, forming an integral part of the body's innate immune system. +In addition to their protective role, these cells are involved in the secretion of mucus. This mucus acts as a lubricant that ensures the smooth and easy passage of urine from the bladder through the urethra and out of the body, reducing any potential damage from the erosive action of urine. Epithelial cells of the urethra are dynamic, constantly renewing their numbers to replace any cells lost through wear and tear. Any disruptions to the function or integrity of these cells may contribute to urinary tract infections and other urological disorders. + DOI:10.1016/j.celrep.2018.11.086 + DOI:10.1038/s41385-022-00565-0 + DOI:10.1089/ten.teb.2016.0352 + DOI:10.1101/2020.02.19.937615v2.full + DOI:10.1152/ajprenal.00327.2009 + @@ -92905,12 +94793,7 @@ The primary function of PNECs is linked to regulation and maintenance of the lun - - - - - - + A fibroblast that is part of the connective tissue of prostate. FMA:261271 @@ -92931,12 +94814,7 @@ The primary function of PNECs is linked to regulation and maintenance of the lun - - - - - - + A fibroblast that is part of the outer membrane of prostatic capsule. FMA:261273 fibroblast of outer membrane of prostatic capsule @@ -92954,12 +94832,7 @@ The primary function of PNECs is linked to regulation and maintenance of the lun - - - - - - + A fibroblast that is part of the subepithelial connective tissue of prostatic gland. FMA:261275 @@ -93059,12 +94932,7 @@ The primary function of PNECs is linked to regulation and maintenance of the lun - - - - - - + A fibroblast that is part of the connective tissue of nonglandular part of prostate. FMA:261281 @@ -93083,12 +94951,7 @@ The primary function of PNECs is linked to regulation and maintenance of the lun - - - - - - + A fibroblast that is part of the connective tissue of glandular part of prostate. FMA:261283 @@ -93112,29 +94975,22 @@ The primary function of PNECs is linked to regulation and maintenance of the lun - + - - + - + A fibroblast that is part of the tunica adventitia of artery. FMA:261285 fibroblast of tunica adventitia of artery - - - - - true - @@ -93375,10 +95231,24 @@ The primary function of PNECs is linked to regulation and maintenance of the lun + + + + + + A goblet cell that is part of the epithelium of bronchus. + + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Bronchial goblet cells are a subset of goblet cells that are predominantly found in the respiratory tract, specifically within the bronchi and bronchioles. Named for their flask-like shape and their apparent similarity to a goblet, these cells contribute significantly to the maintenance of lung health and homeostasis. In humans, goblet cells comprise up to 25% of the bronchial epithelial columnar cells and are an integral part of the mucus-secreting system of the respiratory tract and are primarily responsible for the production and secretion of mucus. +The mucus secreted by bronchial goblet cells serves as a protective layer over the delicate and sensitive structures of the bronchi. The mucus, an amalgamation of glycoproteins, lipids, and other substances, traps any inhaled dust, microorganisms, and pollutants, preventing them from reaching deeper lung tissues and causing potential damage. Additionally, the mucus secretion aids in moistening the airway surface, thereby facilitating effective gas exchange and maintaining the overall health of the respiratory tract. +Bronchial goblet cells have an innate defense mechanism wherein they increase secretion of mucus in response to irritants, infection or inflammation in the airway. This strategy, however, if incessantly stimulated, can lead to airway obstruction and health complications like asthma and chronic obstructive pulmonary disease (COPD). FMA:263032 + https://cellxgene.cziscience.com/cellguide/CL_1000312 goblet cell of epithelium of bronchus + The marker set PLCG2, ANKRD36C can identify the Human cell type bronchial goblet cell in the Lung with a confidence of 0.55 (NS-Forest FBeta value). bronchial goblet cell @@ -93387,12 +95257,31 @@ The primary function of PNECs is linked to regulation and maintenance of the lun A goblet cell that is part of the epithelium of bronchus. GOC:tfm + + + + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Bronchial goblet cells are a subset of goblet cells that are predominantly found in the respiratory tract, specifically within the bronchi and bronchioles. Named for their flask-like shape and their apparent similarity to a goblet, these cells contribute significantly to the maintenance of lung health and homeostasis. In humans, goblet cells comprise up to 25% of the bronchial epithelial columnar cells and are an integral part of the mucus-secreting system of the respiratory tract and are primarily responsible for the production and secretion of mucus. +The mucus secreted by bronchial goblet cells serves as a protective layer over the delicate and sensitive structures of the bronchi. The mucus, an amalgamation of glycoproteins, lipids, and other substances, traps any inhaled dust, microorganisms, and pollutants, preventing them from reaching deeper lung tissues and causing potential damage. Additionally, the mucus secretion aids in moistening the airway surface, thereby facilitating effective gas exchange and maintaining the overall health of the respiratory tract. +Bronchial goblet cells have an innate defense mechanism wherein they increase secretion of mucus in response to irritants, infection or inflammation in the airway. This strategy, however, if incessantly stimulated, can lead to airway obstruction and health complications like asthma and chronic obstructive pulmonary disease (COPD). + DOI:10.1016/S0165-6147(00)01600-X + DOI:10.1016/S1357-2725(02)00083-3 + DOI:10.1080/07853890600585795 + DOI:10.2147/COPD.S38938 + goblet cell of epithelium of bronchus FMA:263032 + + + + The marker set PLCG2, ANKRD36C can identify the Human cell type bronchial goblet cell in the Lung with a confidence of 0.55 (NS-Forest FBeta value). + https://doi.org/10.5281/zenodo.11165918 + @@ -93412,12 +95301,6 @@ The primary function of PNECs is linked to regulation and maintenance of the lun - - - - - - A goblet cell that is part of the epithelium of stomach. FMA:263035 goblet cell of epithelium of stomach @@ -93453,6 +95336,7 @@ The primary function of PNECs is linked to regulation and maintenance of the lun + @@ -93499,6 +95383,7 @@ The primary function of PNECs is linked to regulation and maintenance of the lun + @@ -93547,7 +95432,7 @@ The primary function of PNECs is linked to regulation and maintenance of the lun - + @@ -93616,21 +95501,21 @@ The primary function of PNECs is linked to regulation and maintenance of the lun - + - - - - - - A goblet cell that is part of the epithelium of large intestine. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +The large intestine goblet cell is a highly specialized type of mucosal epithelial cell that is located within the epithelial lining of the large intestine. The key function of goblet cells is the production and secretion of a protective layer of mucus which is essential for maintaining gut homeostasis. Goblet cells have a characteristic 'goblet-like' shape, which adapts them for this specific function: organelles such as the nucleus, mitochondria, ER, and Golgi apparatus are located in the basal portion of the cell; while the vesicles with mucins (required for mucus production) are located apically, close to the apical membrane where their exocytosis takes place. +The goblet cells of the large intestine produce a thick layer of mucus that coats the intestinal lumen. This mucus provides a barrier that prevents the direct contact of intestinal cells with bacteria and other potentially toxic substances present in the digestive tract. It also lubricates the intestine to facilitate the smooth passage of digested food material. It is worth noting that the mucus system differs between the small and large intestine: although in both the mucus is built around MUC2 mucin polymers produced by goblet cells, it is becoming clear that there are several types of goblet cells that function in different ways. +From an immunological perspective, large intestine goblet cells participate in promoting a balanced gut immune response. They contribute to the process known as immune tolerance, where they prevent the body's immune system from overreacting to the trillions of bacteria present in the gut. These cells achieve this by secreting molecules that help maintain a calm environment, limiting inflammatory reactions unless absolutely necessary. Any dysfunction or decrease in the number of goblet cells can result in a compromised intestinal barrier leading to various health issues, including inflammatory bowel disease. FMA:263054 + https://cellxgene.cziscience.com/cellguide/CL_1000320 goblet cell of epithelium of large intestine large intestine goblet cell @@ -93641,6 +95526,20 @@ The primary function of PNECs is linked to regulation and maintenance of the lun A goblet cell that is part of the epithelium of large intestine. GOC:tfm + + + + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +The large intestine goblet cell is a highly specialized type of mucosal epithelial cell that is located within the epithelial lining of the large intestine. The key function of goblet cells is the production and secretion of a protective layer of mucus which is essential for maintaining gut homeostasis. Goblet cells have a characteristic 'goblet-like' shape, which adapts them for this specific function: organelles such as the nucleus, mitochondria, ER, and Golgi apparatus are located in the basal portion of the cell; while the vesicles with mucins (required for mucus production) are located apically, close to the apical membrane where their exocytosis takes place. +The goblet cells of the large intestine produce a thick layer of mucus that coats the intestinal lumen. This mucus provides a barrier that prevents the direct contact of intestinal cells with bacteria and other potentially toxic substances present in the digestive tract. It also lubricates the intestine to facilitate the smooth passage of digested food material. It is worth noting that the mucus system differs between the small and large intestine: although in both the mucus is built around MUC2 mucin polymers produced by goblet cells, it is becoming clear that there are several types of goblet cells that function in different ways. +From an immunological perspective, large intestine goblet cells participate in promoting a balanced gut immune response. They contribute to the process known as immune tolerance, where they prevent the body's immune system from overreacting to the trillions of bacteria present in the gut. These cells achieve this by secreting molecules that help maintain a calm environment, limiting inflammatory reactions unless absolutely necessary. Any dysfunction or decrease in the number of goblet cells can result in a compromised intestinal barrier leading to various health issues, including inflammatory bowel disease. + DOI:10.1038/mi.2015.32 + DOI:10.1042/BSR20201471 + DOI:10.1111/imr.12182 + DOI:10.1146/annurev-physiol-021115-105447 + DOI:full/10.1111/febs.15731 + @@ -93653,46 +95552,17 @@ The primary function of PNECs is linked to regulation and maintenance of the lun - - - - - - - - - - - + + - - - - - - - - - - - - - - - - - - - - - + A goblet cell that is part of the epithelium of crypt of Lieberkuhn of large intestine. @@ -93726,7 +95596,7 @@ The primary function of PNECs is linked to regulation and maintenance of the lun - + @@ -93770,6 +95640,7 @@ The primary function of PNECs is linked to regulation and maintenance of the lun + @@ -93777,7 +95648,7 @@ The primary function of PNECs is linked to regulation and maintenance of the lun - + @@ -93810,18 +95681,13 @@ The primary function of PNECs is linked to regulation and maintenance of the lun - + - - - - - - + A goblet cell that is part of the epithelium proper of duodenum. FMA:263063 @@ -93847,7 +95713,7 @@ The primary function of PNECs is linked to regulation and maintenance of the lun - + @@ -93856,17 +95722,7 @@ The primary function of PNECs is linked to regulation and maintenance of the lun - - - - - - - - - - - + A goblet cell that is part of the epithelium proper of jejunum. @@ -93894,7 +95750,7 @@ The primary function of PNECs is linked to regulation and maintenance of the lun - + @@ -93903,21 +95759,17 @@ The primary function of PNECs is linked to regulation and maintenance of the lun - - - - - - - - - - - + A goblet cell that is part of the epithelium proper of ileum. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +The ileal goblet cell is a subset of intestinal goblet cells that are a key component of the epithelium of the ileum, a portion of the small intestine. Goblet cells are named and characterized by their distinctive 'goblet' shape with a narrow base tapering to a broad apical surface; located between the lumen of the intestine and the internal environment of the body, they serve an integral role in maintaining gut homeostasis. +Like all intestinal goblet cells, the primary function of ileal goblet cells is the production and secretion of mucins, large, heavily glycosylated proteins that combine to form mucus. This mucus lining serves as a protective barrier, shielding the underlying tissue from the potentially damaging effects of digestive enzymes, acids, or pathogenic microbes present in the gut lumen. Their strategic location in the ileal segment of the intestinal tract aids in efficient nutrient absorption while also maintaining an impregnable barrier against potential pathogens, ensuring an intricate balance. +Goblet cells of the ileum also play a significant role in immune modulation. They are thought to promote oral tolerance (the immune unresponsiveness to orally ingested antigens such as food) by delivering luminal antigens to underlying dendritic cells, thereby driving immune education and tolerogenic responses. They also secrete bioactive molecules, such as the trefoil factor peptide TFF3, which aids in repairing damaged epithelium. By performing these crucial functions, ileal goblet cells not only aid in maintaining intestinal health, but also contribute significantly to the overall well-being of the organism. FMA:263067 + https://cellxgene.cziscience.com/cellguide/CL_1000326 goblet cell of epithelium proper of ileum ileal goblet cell @@ -93928,6 +95780,19 @@ The primary function of PNECs is linked to regulation and maintenance of the lun A goblet cell that is part of the epithelium proper of ileum. GOC:tfm + + + + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +The ileal goblet cell is a subset of intestinal goblet cells that are a key component of the epithelium of the ileum, a portion of the small intestine. Goblet cells are named and characterized by their distinctive 'goblet' shape with a narrow base tapering to a broad apical surface; located between the lumen of the intestine and the internal environment of the body, they serve an integral role in maintaining gut homeostasis. +Like all intestinal goblet cells, the primary function of ileal goblet cells is the production and secretion of mucins, large, heavily glycosylated proteins that combine to form mucus. This mucus lining serves as a protective barrier, shielding the underlying tissue from the potentially damaging effects of digestive enzymes, acids, or pathogenic microbes present in the gut lumen. Their strategic location in the ileal segment of the intestinal tract aids in efficient nutrient absorption while also maintaining an impregnable barrier against potential pathogens, ensuring an intricate balance. +Goblet cells of the ileum also play a significant role in immune modulation. They are thought to promote oral tolerance (the immune unresponsiveness to orally ingested antigens such as food) by delivering luminal antigens to underlying dendritic cells, thereby driving immune education and tolerogenic responses. They also secrete bioactive molecules, such as the trefoil factor peptide TFF3, which aids in repairing damaged epithelium. By performing these crucial functions, ileal goblet cells not only aid in maintaining intestinal health, but also contribute significantly to the overall well-being of the organism. + DOI:10.1007/s11894-010-0131-2 + DOI:10.1038/nature10863 + DOI:10.1038/s41575-022-00675-x + DOI:10.1111/imr.12182 + @@ -93940,29 +95805,13 @@ The primary function of PNECs is linked to regulation and maintenance of the lun - + - - - - - - - - - - - - - - - - A goblet cell that is part of the epithelium proper of appendix. FMA:263069 goblet cell of epithelium proper of appendix @@ -94018,7 +95867,13 @@ The primary function of PNECs is linked to regulation and maintenance of the lun A goblet cell that is part of the epithelium of trachea. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Tracheal goblet cells are specialized cells found in the lining of the trachea. They are a key component of the tracheobronchial epithelium, a critical region responsible for maintaining open airways and preventing the ingress of harmful particles or irritants. Goblet cells are filled with membrane-bound secretory granules, which are responsible for their distinctive, goblet-like shape. +Goblet cells specialize in the production and secretion of mucus, a slimy substance composed primarily of glycoproteins (mucins) and water. This sticky mucus serves to trap foreign particles and pollutants, such as dust, bacteria, and viruses that an organism breathes in. After trapping these particles, the cilia on neighboring ciliated epithelial cells beat synchronously, forming a coordinated escalator to push mucus upwards toward the pharynx, where it's either swallowed or expectorated. This system, known as the mucociliary clearance or escalator, forms a crucial barrier in the lungs against respiratory pathogens and external insults. +Changes in the number or function of tracheal goblet cells can engender health complications. For example, goblet cell hyperplasia, or excessive growth of goblet cells, is a common feature of chronic inflammatory lung diseases such as asthma and Chronic Obstructive Pulmonary Disease (COPD). This condition results in mucus hypersecretion, airway blockage, and increased risk of respiratory tract infections. FMA:263075 + https://cellxgene.cziscience.com/cellguide/CL_1000329 goblet cell of epithelium of trachea @@ -94030,6 +95885,20 @@ The primary function of PNECs is linked to regulation and maintenance of the lun A goblet cell that is part of the epithelium of trachea. GOC:tfm + + + + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Tracheal goblet cells are specialized cells found in the lining of the trachea. They are a key component of the tracheobronchial epithelium, a critical region responsible for maintaining open airways and preventing the ingress of harmful particles or irritants. Goblet cells are filled with membrane-bound secretory granules, which are responsible for their distinctive, goblet-like shape. +Goblet cells specialize in the production and secretion of mucus, a slimy substance composed primarily of glycoproteins (mucins) and water. This sticky mucus serves to trap foreign particles and pollutants, such as dust, bacteria, and viruses that an organism breathes in. After trapping these particles, the cilia on neighboring ciliated epithelial cells beat synchronously, forming a coordinated escalator to push mucus upwards toward the pharynx, where it's either swallowed or expectorated. This system, known as the mucociliary clearance or escalator, forms a crucial barrier in the lungs against respiratory pathogens and external insults. +Changes in the number or function of tracheal goblet cells can engender health complications. For example, goblet cell hyperplasia, or excessive growth of goblet cells, is a common feature of chronic inflammatory lung diseases such as asthma and Chronic Obstructive Pulmonary Disease (COPD). This condition results in mucus hypersecretion, airway blockage, and increased risk of respiratory tract infections. + DOI:10.1016/S1357-2725(02)00083-3 + DOI:10.1164/ajrccm.154.6.8970383 + DOI:10.1165/ajrcmb.25.5.f218 + DOI:10.2147/COPD.S38938 + DOI:10.3109/01902148.2013.791733 + @@ -94062,7 +95931,13 @@ The primary function of PNECs is linked to regulation and maintenance of the lun A serous secreting cell that is part of the epithelium of trachea. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Serous cells are specialized epithelial cells and can be found lining the trachea and brochus. They are among the major components of the respiratory epithelium. +These cells are known for their production and release of serous secretions, which form a key component of airway mucus. These secretions primarily comprise of water, proteins, and enzymes, such as lysozyme and peroxidases. Their main purposes are to provide hydration and lubrication to the airway tissue and to act as a defense mechanism against pathogens. While the lysozyme and peroxidases contribute to the destruction of bacteria, the water in the secretions helps to liquefy the mucus, facilitating the effective functioning of the ciliated cells that propel the mucus up the trachea. +The coordinated action between serous cells and other cell types in the tracheal epithelium proves essential for maintaining a healthy respiratory tract. Dysfunction or damage of these cells can lead to various respiratory tract disorders, such as cystic fibrosis and asthma. FMA:263078 + https://cellxgene.cziscience.com/cellguide/CL_1000330 serous cell of epithelium of trachea @@ -94073,6 +95948,19 @@ The primary function of PNECs is linked to regulation and maintenance of the lun A serous secreting cell that is part of the epithelium of trachea. GOC:tfm + + + + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Serous cells are specialized epithelial cells and can be found lining the trachea and brochus. They are among the major components of the respiratory epithelium. +These cells are known for their production and release of serous secretions, which form a key component of airway mucus. These secretions primarily comprise of water, proteins, and enzymes, such as lysozyme and peroxidases. Their main purposes are to provide hydration and lubrication to the airway tissue and to act as a defense mechanism against pathogens. While the lysozyme and peroxidases contribute to the destruction of bacteria, the water in the secretions helps to liquefy the mucus, facilitating the effective functioning of the ciliated cells that propel the mucus up the trachea. +The coordinated action between serous cells and other cell types in the tracheal epithelium proves essential for maintaining a healthy respiratory tract. Dysfunction or damage of these cells can lead to various respiratory tract disorders, such as cystic fibrosis and asthma. + DOI:10.1002/dvdy.24250 + DOI:10.1016/B978-012330215-1/50029-6 + DOI:10.1016/S0034-5687(01)00214- + DOI:10.1074/jbc.M208826200 + @@ -94099,7 +95987,12 @@ The primary function of PNECs is linked to regulation and maintenance of the lun A serous secreting cell that is part of the epithelium of bronchus. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Serous cells of the epithelium of the bronchus, also termed bronchial serous cells, are predominantly found within the seromucous glands located in the bronchial submucosa. Serous cells can also be found in the trachea and are characterized by small, sparse, electron-dense granules. +Serous cells are specialized cells responsible for the production and secretion of serous fluid. Serous fluid, mainly composed of water, proteins, and various types of salts, provides many benefits: it helps moisturize the airways, keep the bronchial tube walls moist, and safeguard the bronchial tubes against various foreign particles and infectious agents such as bacteria and viruses. Moreover, the fluid released by these cells assists in the lubrication and reduced friction in the bronchi, allowing for smoother airflow. FMA:263080 + https://cellxgene.cziscience.com/cellguide/CL_1000331 serous cell of epithelium of bronchus @@ -94110,6 +96003,17 @@ The primary function of PNECs is linked to regulation and maintenance of the lun A serous secreting cell that is part of the epithelium of bronchus. GOC:tfm + + + + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Serous cells of the epithelium of the bronchus, also termed bronchial serous cells, are predominantly found within the seromucous glands located in the bronchial submucosa. Serous cells can also be found in the trachea and are characterized by small, sparse, electron-dense granules. +Serous cells are specialized cells responsible for the production and secretion of serous fluid. Serous fluid, mainly composed of water, proteins, and various types of salts, provides many benefits: it helps moisturize the airways, keep the bronchial tube walls moist, and safeguard the bronchial tubes against various foreign particles and infectious agents such as bacteria and viruses. Moreover, the fluid released by these cells assists in the lubrication and reduced friction in the bronchi, allowing for smoother airflow. + DOI:10.1152/physrev.00039.2014 + https://www.ncbi.nlm.nih.gov/books/NBK534789/ + https://www.sciencedirect.com/topics/neuroscience/secretory-cell + @@ -94206,7 +96110,7 @@ The primary function of PNECs is linked to regulation and maintenance of the lun An enterocyte that is part of the epithelium of small intestine. - This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. Enterocytes of the epithelium of the small intestine are specialized cells that reside in the lining of the small intestine, and are primarily responsible for the essential process of nutrient absorption. These cells are columnar epithelial cells with an apical surface lined with microvilli, a feature referred to as the 'brush border', to maximize the surface area available for absorption. Enterocytes play a critical role in both the digestion and absorption of nutrients from food. Their extensive brush border contains enzymes that further assist in nutrient breakdown and transport proteins that transfer nutrients, such as glucose, amino acids, lipids, and vitamins, across the cell membrane. @@ -94215,6 +96119,7 @@ The enterocytes of the small intestine also participate in the barrier function https://cellxgene.cziscience.com/cellguide/CL_1000334 enterocyte of epithelium of small intestine + @@ -94231,7 +96136,7 @@ The enterocytes of the small intestine also participate in the barrier function - This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. Enterocytes of the epithelium of the small intestine are specialized cells that reside in the lining of the small intestine, and are primarily responsible for the essential process of nutrient absorption. These cells are columnar epithelial cells with an apical surface lined with microvilli, a feature referred to as the 'brush border', to maximize the surface area available for absorption. Enterocytes play a critical role in both the digestion and absorption of nutrients from food. Their extensive brush border contains enzymes that further assist in nutrient breakdown and transport proteins that transfer nutrients, such as glucose, amino acids, lipids, and vitamins, across the cell membrane. @@ -94241,6 +96146,16 @@ The enterocytes of the small intestine also participate in the barrier function DOI:10.1084/jem.20191130 DOI:10.3389/fphys.2021.699152/full + + + + + http://creativecommons.org/licenses/by/4.0/ + Figure depicts a cross section of intestinal villi in the small intestine, including the crypts of Lieberkuhn (seen here as ‘crypt’), as well as the layer specific locations of cells that exist within the gastrointestinal tract. Layers depicted here include epithelium (rows of cells bordering villus), submucosa (white space below the epithelium containing networks of neurons and ganglia depicted in pink), muscularis mucosae (blue layer), muscularis propria (referred to here as muscle layer). + +ISC: Intestinal Stem Cell +TA: Transit Amplifying Cells + @@ -94302,8 +96217,7 @@ The enterocytes of the small intestine also participate in the barrier function - - + @@ -94408,7 +96322,7 @@ The enterocytes of the small intestine also participate in the barrier function An enterocyte that is part of the epithelium proper of ileum. - This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. Enterocytes of the epithelium proper of the ileum, commonly known as ileal enterocytes, are specialized epithelial cells found lining the inner surface of the ileum, the final section of the small intestine in the human body. They play a pivotal role in nutrient absorption, digestive metabolic functions, and the maintenance of the host’s immune response. Like enterocytes in other parts of the intestine, ileal enterocytes exhibit distinct characteristics specific to their function and role. They have microvilli on their apical surfaces to increase absorption and are important in the absorption of vitamins and the reabsorption of bile salts. These cells also produce enzymes that metabolize lipids and xenobiotics. @@ -94426,7 +96340,7 @@ Like enterocytes in other parts of the intestine, ileal enterocytes exhibit dist - This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. Enterocytes of the epithelium proper of the ileum, commonly known as ileal enterocytes, are specialized epithelial cells found lining the inner surface of the ileum, the final section of the small intestine in the human body. They play a pivotal role in nutrient absorption, digestive metabolic functions, and the maintenance of the host’s immune response. Like enterocytes in other parts of the intestine, ileal enterocytes exhibit distinct characteristics specific to their function and role. They have microvilli on their apical surfaces to increase absorption and are important in the absorption of vitamins and the reabsorption of bile salts. These cells also produce enzymes that metabolize lipids and xenobiotics. @@ -94454,9 +96368,16 @@ Like enterocytes in other parts of the intestine, ileal enterocytes exhibit dist A paneth cell that is part of the epithelium of small intestine. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Paneth cells of the epithelium of the small intestine, often referred to simply as Paneth cells, are a type of specialized secretory cell that forms an integral part of the intestinal crypts of Lieberkühn – gland-like invaginations lining the small intestine. Named after the Austrian physician Josef Paneth, who first identified them in the late 19th century, these cells are significant because of their substantial involvement in the mucosal immune system and intestinal stem cell maintenance. +Functionally, Paneth cells play a key role in maintaining gut homeostasis and in the first line of antimicrobial defense, mainly through the secretion of a range of antimicrobial peptides and proteins. These include lysozymes, cryptdins, or alpha-defensins, which have potent activity against various gut pathogens including bacteria, fungi, and parasites. Furthermore, Paneth cells of the small intestine are also known to release secretory phospholipase A2, an enzyme active against gram-positive bacteria. Additionally, they secrete several growth factors like EGF, TGF-alpha, and Wnt3, which are crucial for stem cell support and the overall maintenance of intestinal mucosal integrity. +The unique location of Paneth cells at the base of the crypts positions them in very close proximity to intestinal stem cells. This not only facilitates their role in stem cell maintenance but also involves them in epithelial regeneration and repair following injury. Dysfunctional Paneth cells have been associated with several gut disorders, like Crohn’s disease and necrotizing enterocolitis. FMA:263104 + https://cellxgene.cziscience.com/cellguide/CL_1000343 paneth cell of epithelium of small intestine + @@ -94470,6 +96391,30 @@ Like enterocytes in other parts of the intestine, ileal enterocytes exhibit dist A paneth cell that is part of the epithelium of small intestine. GOC:tfm + + + + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Paneth cells of the epithelium of the small intestine, often referred to simply as Paneth cells, are a type of specialized secretory cell that forms an integral part of the intestinal crypts of Lieberkühn – gland-like invaginations lining the small intestine. Named after the Austrian physician Josef Paneth, who first identified them in the late 19th century, these cells are significant because of their substantial involvement in the mucosal immune system and intestinal stem cell maintenance. +Functionally, Paneth cells play a key role in maintaining gut homeostasis and in the first line of antimicrobial defense, mainly through the secretion of a range of antimicrobial peptides and proteins. These include lysozymes, cryptdins, or alpha-defensins, which have potent activity against various gut pathogens including bacteria, fungi, and parasites. Furthermore, Paneth cells of the small intestine are also known to release secretory phospholipase A2, an enzyme active against gram-positive bacteria. Additionally, they secrete several growth factors like EGF, TGF-alpha, and Wnt3, which are crucial for stem cell support and the overall maintenance of intestinal mucosal integrity. +The unique location of Paneth cells at the base of the crypts positions them in very close proximity to intestinal stem cells. This not only facilitates their role in stem cell maintenance but also involves them in epithelial regeneration and repair following injury. Dysfunctional Paneth cells have been associated with several gut disorders, like Crohn’s disease and necrotizing enterocolitis. + DOI:10.1007/s00018-002-8412-z + DOI:10.1038/nature09637 + DOI:10.1038/nrmicro2546 + DOI:10.1146/annurev-physiol-030212-183744 + DOI:10.3389/fimmu.2020.00587 + + + + + + http://creativecommons.org/licenses/by/4.0/ + Figure depicts a cross section of intestinal villi in the small intestine , including the crypts of Lieberkuhn (seen here as ‘crypt’), as well as the layer specific locations of cells that exist within the gastrointestinal tract. Layers depicted here include epithelium (rows of cells bordering villus), submucosa (white space below the epithelium containing networks of neurons and ganglia depicted in pink), muscularis mucosae (blue layer), muscularis propria (referred to here as muscle layer). + +ISC: Intestinal Stem Cell +TA: Transit Amplifying Cells + @@ -94544,36 +96489,44 @@ Like enterocytes in other parts of the intestine, ileal enterocytes exhibit dist - A columnar cell of the colon that is part of the colonic epithelium. - This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + + + + + + + + + + + + + An enterocyte (absorptive epithelial cell) of the colonic epithelium, characterized by a columnar shape. This cell is responsible for the absorption, transport, and metabolization of short-chain fatty acids (SCFAs) produced by gut bacteria, as well as the transport and absorption of water and electrolytes. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. Enterocytes of the colon are specialized epithelial cells located in the lining of the colon, the largest part of the large intestine. These cells play a critical role in absorbing water, electrolytes, and certain vitamins from the food material passed on from the small intestine. With a unique structure of finger-like protrusions referred to as microvilli, the enterocytes increase their surface area for effective absorption. The colon is the last part of the digestive system, and as such, it is responsible for compacting undigested food materials and forming fecal matter. Enterocytes of the colon facilitate this process effectively through absorption of water. Enterocytes are known for their high regeneration potential, replenishing every 4-5 days, enabling the healthy functioning of the colon. They originate from stem cells located in the crypt of the colon and differentiate into mature enterocytes as they migrate upwards towards the luminal surface. This constant turnover aids in maintaining the intestinal barrier, preventing the entry of detrimental substances into the systemic circulation. Their tight junctions with other epithelial cells provide a robust barrier against invasive pathogens. Enterocytes of the colon are involved in the communication with the gut microbiota. These cells harbor enzymes necessary for the metabolism of short-chain fatty acids, which are the byproducts of the fermentation process by gut bacteria. Short-chain fatty acids serve as a major energy source for colonocytes and are important for maintaining colonic health. The dysfunction of enterocytes, therefore, could lead to disorders such as inflammatory bowel disease or colorectal cancer. FMA:263114 https://cellxgene.cziscience.com/cellguide/CL_1000347 - colonocyte enterocyte of colon vacuolar absorptive cell of epithelium of colon colonocyte - - - - - true - - A columnar cell of the colon that is part of the colonic epithelium. + An enterocyte (absorptive epithelial cell) of the colonic epithelium, characterized by a columnar shape. This cell is responsible for the absorption, transport, and metabolization of short-chain fatty acids (SCFAs) produced by gut bacteria, as well as the transport and absorption of water and electrolytes. GOC:tfm + PMID:16870803 + PMID:23821742 + PMID:34497389 - This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. Enterocytes of the colon are specialized epithelial cells located in the lining of the colon, the largest part of the large intestine. These cells play a critical role in absorbing water, electrolytes, and certain vitamins from the food material passed on from the small intestine. With a unique structure of finger-like protrusions referred to as microvilli, the enterocytes increase their surface area for effective absorption. The colon is the last part of the digestive system, and as such, it is responsible for compacting undigested food materials and forming fecal matter. Enterocytes of the colon facilitate this process effectively through absorption of water. Enterocytes are known for their high regeneration potential, replenishing every 4-5 days, enabling the healthy functioning of the colon. They originate from stem cells located in the crypt of the colon and differentiate into mature enterocytes as they migrate upwards towards the luminal surface. This constant turnover aids in maintaining the intestinal barrier, preventing the entry of detrimental substances into the systemic circulation. Their tight junctions with other epithelial cells provide a robust barrier against invasive pathogens. @@ -94584,12 +96537,6 @@ Enterocytes of the colon are involved in the communication with the gut microbio DOI:10.1084/jem.20191130 DOI:10.3389/fimmu.2019.00277 - - - - colonocyte - PMID:34497389 - @@ -94616,7 +96563,13 @@ Enterocytes of the colon are involved in the communication with the gut microbio A basal cell that is part of the epithelium of trachea. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Basal cells of epithelium of trachea are a vital cell population within the respiratory tract's lining, specifically in the trachea's epithelium. These cells are located at the base of the columnar epithelial cell layer and can be identified by their characteristic cuboidal shape, a large nucleus and few organelles, as well as scattered microvilli. The basal cells are not in direct contact with the lumen, which is covered by a layer of ciliated and non-ciliated columnar cells. Instead, the basal cells are connected to, and line, a thin basement membrane. +The primary function of basal cells involves stem cell activity and epithelial tissue maintenance. Basal cells in the trachea play a crucial role in the regeneration and repair of the tracheal epithelium during damage or injury, acting as progenitor cells for ciliated and secretory cells. They serve as a reserve pool of cells, ready to proliferate and differentiate as needed for homeostatic tissue maintenance or in repair processes when the epithelium has been compromised, whether by injury or disease. +These cells are also implicated in numerous disease pathways. Conditions like chronic obstructive pulmonary disease and lung cancer exhibit unusual behavior and quantities of tracheal basal cells, making these cells a focal point in respiratory disease research. In summary, basal cells in the tracheal epithelium have a multifaceted role in maintaining, repairing, and influencing tracheal health, playing a crucial role in the stability of the respiratory system. FMA:263118 + https://cellxgene.cziscience.com/cellguide/CL_1000348 basal cell of epithelium of trachea @@ -94633,6 +96586,19 @@ Enterocytes of the colon are involved in the communication with the gut microbio A basal cell that is part of the epithelium of trachea. GOC:tfm + + + + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Basal cells of epithelium of trachea are a vital cell population within the respiratory tract's lining, specifically in the trachea's epithelium. These cells are located at the base of the columnar epithelial cell layer and can be identified by their characteristic cuboidal shape, a large nucleus and few organelles, as well as scattered microvilli. The basal cells are not in direct contact with the lumen, which is covered by a layer of ciliated and non-ciliated columnar cells. Instead, the basal cells are connected to, and line, a thin basement membrane. +The primary function of basal cells involves stem cell activity and epithelial tissue maintenance. Basal cells in the trachea play a crucial role in the regeneration and repair of the tracheal epithelium during damage or injury, acting as progenitor cells for ciliated and secretory cells. They serve as a reserve pool of cells, ready to proliferate and differentiate as needed for homeostatic tissue maintenance or in repair processes when the epithelium has been compromised, whether by injury or disease. +These cells are also implicated in numerous disease pathways. Conditions like chronic obstructive pulmonary disease and lung cancer exhibit unusual behavior and quantities of tracheal basal cells, making these cells a focal point in respiratory disease research. In summary, basal cells in the tracheal epithelium have a multifaceted role in maintaining, repairing, and influencing tracheal health, playing a crucial role in the stability of the respiratory system. + DOI:10.1164/rccm.201408-1492PP + DOI:10.1165/rcmb.2021-0150ED + DOI:10.1242/dmm.006031 + DOI:10.3389/falgy.2021.787128 + @@ -94655,7 +96621,13 @@ Enterocytes of the colon are involved in the communication with the gut microbio A basal cell found in the bronchus epithelium. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +The basal cells of the epithelium of the bronchus are a vital component of the cellular linings found within the bronchial tubes of the respiratory system. They are typically nonciliated, cuboidal cells that are tightly attached to the basement membrane, thereby providing structural support for the epithelial tissues. +The function of the basal cell of the bronchial epithelium is multifaceted, underscoring the importance of these cells for respiratory health. One of their primary roles involves regeneration and cellular turnover. They serve as local stem cells, being able to proliferate and differentiate into other cell types such as ciliated and secretory epithelial cells. This regenerative function of basal cells is required for maintaining the integrity of the bronchial epithelium and is especially critical after injury or during disease states when there is an increased need for new cells to repair damaged tissue or replace lost cells. +In addition to these regenerative duties, basal cells of the bronchial epithelium play a crucial role in providing a defensive barrier against inhaled substances. They participate in the coordinated immune response directed against airborne pathogens, foreign particles, and toxins that enter the respiratory tract. Basal cells can respond to inflammation or irritation by altering their activities, which include proliferating, differentiating, or producing bioactive substances. Throughout all these responses, the basal cells help to maintain the homeostasis of the bronchial tubes, allowing for the efficient transport of air to and from the lungs. FMA:263120 + https://cellxgene.cziscience.com/cellguide/CL_1000349 basal cell of bronchus basal cell of epithelium of bronchus @@ -94666,6 +96638,19 @@ Enterocytes of the colon are involved in the communication with the gut microbio A basal cell found in the bronchus epithelium. GOC:tfm + + + + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +The basal cells of the epithelium of the bronchus are a vital component of the cellular linings found within the bronchial tubes of the respiratory system. They are typically nonciliated, cuboidal cells that are tightly attached to the basement membrane, thereby providing structural support for the epithelial tissues. +The function of the basal cell of the bronchial epithelium is multifaceted, underscoring the importance of these cells for respiratory health. One of their primary roles involves regeneration and cellular turnover. They serve as local stem cells, being able to proliferate and differentiate into other cell types such as ciliated and secretory epithelial cells. This regenerative function of basal cells is required for maintaining the integrity of the bronchial epithelium and is especially critical after injury or during disease states when there is an increased need for new cells to repair damaged tissue or replace lost cells. +In addition to these regenerative duties, basal cells of the bronchial epithelium play a crucial role in providing a defensive barrier against inhaled substances. They participate in the coordinated immune response directed against airborne pathogens, foreign particles, and toxins that enter the respiratory tract. Basal cells can respond to inflammation or irritation by altering their activities, which include proliferating, differentiating, or producing bioactive substances. Throughout all these responses, the basal cells help to maintain the homeostasis of the bronchial tubes, allowing for the efficient transport of air to and from the lungs. + DOI:10.1002/ar.1092380310 + DOI:10.1038/labinvest.2015.114 + DOI:10.1136/thx.2004.la0104 + DOI:10.3389/falgy.2021.787128 + @@ -94818,7 +96803,15 @@ Enterocytes of the colon are involved in the communication with the gut microbio A M cell that is part of the epithelium of small intestine. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Microfold cells, also widely known as M cells, are a distinct type of epithelial cell found in the gut, including the small intestine, specifically within the Peyer’s patches, a component of the gut-associated lymphoid tissue (GALT). M cells play a crucial role in the immune response within the intestine environment. +These cells are characterized by microfolds (short microvilli, which give them their name), a reduced, thin glycocalyx, and a deeply invaginated basolateral membrane next to immune cells such as B cells, T cells, and macrophages, and DCs. +These features allow the M cells to form the first point of contact between the gut lumen and the intestinal immune system. They are well-regulated gateways that capture and transport antigens, such as bacteria, viruses, and other foreign substances found in the lumen, to the underlying cells of the immune system. This specialized transport mechanism, called ‘transcytosis’, involves engulfment of these antigens from the apical side, transport across their cytoplasm, and release on the basolateral side of the cells, where immune responses can be initiated. +Furthermore, M cells have complex interactions with members of the gut microbiota and other immune cells, making them essential for maintaining gut homeostasis. This cross-talk shapes the diversity and makeup of the gut microbiota, subsequently having a substantial impact on the host's health. In certain situations, pathogenic organisms can exploit the transcytosis mechanism to infiltrate the host's system, causing various infectious diseases. +The overarching significance of M cells in the small intestine lies in their role of surveillance and protection against a wide range of potentially harmful pathogens, while also facilitating beneficial interactions with commensal microbes. FMA:263128 + https://cellxgene.cziscience.com/cellguide/CL_1000353 microfold cell of epithelium of small intestine @@ -94834,6 +96827,21 @@ Enterocytes of the colon are involved in the communication with the gut microbio A M cell that is part of the epithelium of small intestine. GOC:tfm + + + + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Microfold cells, also widely known as M cells, are a distinct type of epithelial cell found in the gut, including the small intestine, specifically within the Peyer’s patches, a component of the gut-associated lymphoid tissue (GALT). M cells play a crucial role in the immune response within the intestine environment. +These cells are characterized by microfolds (short microvilli, which give them their name), a reduced, thin glycocalyx, and a deeply invaginated basolateral membrane next to immune cells such as B cells, T cells, and macrophages, and DCs. +These features allow the M cells to form the first point of contact between the gut lumen and the intestinal immune system. They are well-regulated gateways that capture and transport antigens, such as bacteria, viruses, and other foreign substances found in the lumen, to the underlying cells of the immune system. This specialized transport mechanism, called ‘transcytosis’, involves engulfment of these antigens from the apical side, transport across their cytoplasm, and release on the basolateral side of the cells, where immune responses can be initiated. +Furthermore, M cells have complex interactions with members of the gut microbiota and other immune cells, making them essential for maintaining gut homeostasis. This cross-talk shapes the diversity and makeup of the gut microbiota, subsequently having a substantial impact on the host's health. In certain situations, pathogenic organisms can exploit the transcytosis mechanism to infiltrate the host's system, causing various infectious diseases. +The overarching significance of M cells in the small intestine lies in their role of surveillance and protection against a wide range of potentially harmful pathogens, while also facilitating beneficial interactions with commensal microbes. + DOI:10.1038/mi.2013.30 + DOI:10.1093/jb/mvv121 + DOI:10.1111/j.1574-695X.2007.00359.x + DOI:10.3389/fimmu.2019.01499 + @@ -95006,12 +97014,6 @@ Enterocytes of the colon are involved in the communication with the gut microbio - - - - - - A M cell that is part of the epithelium proper of appendix. FMA:263140 microfold cell of epithelium proper of appendix @@ -95983,8 +97985,14 @@ Enterocytes of the colon are involved in the communication with the gut microbio An endothelial cell that is part of the hepatic sinusoid. These cells possess flattened areas containing perforations about 0.1 micrometers in diameter, known as fenestrae. The fenestrae are arranged in groups known as sieve plates. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Endothelial cells of hepatic sinusoids, also known as hepatic or liver sinusoidal endothelial cells (HSEC or LSEC), are unique, specialized type of endothelial cells located in the liver. They are the building units of the hepatic sinusoid, which functions as a specialized capillary system that facilitates the exchange of various substances between the blood and hepatocytes. This finely tuned environment, facilitated by HSEC, is primordial for the liver's multiple physiologic functions that include nutrient metabolism, toxin inactivation, and immunomodulation. +The HSEC have a distinctive morphology that sets them apart from the typical endothelial cells found in other organs. These cells are exceptionally thin to allow for efficient transfer of molecules and characterized by fenestrations, which are non-diaphragmatic, sieve-like openings that provide an open filtration pathway from the sinusoidal lumen to the space of Disse, where hepatocytes are exposed. The fenestration is a crucial feature that allows lipoproteins, nutrients, and other plasma components easy access to hepatocytes for essential liver functions, including clearance of waste products and metabolic regulation. +HSECs further play a vital role in immune functionality in the liver. They act as a sentinel, determining the nature of the immune response to encountered particulates. They possess a capacity for antigen presentation and express a series of immune-related surface molecules, which helps in immunosurveillance and immunoregulation. The HSEC also aid in the removal and destruction of virus-infected cells, harmful microorganisms, and circulatory waste products to safeguard liver health and general systemic cleanliness. BTO:000125 FMA:62911 + https://cellxgene.cziscience.com/cellguide/CL_1000398 LSEC endotheliocyte of hepatic sinusoid liver sinusoidal endothelial cell @@ -95999,6 +98007,20 @@ Enterocytes of the colon are involved in the communication with the gut microbio GOC:tfm PMID:3926620 + + + + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Endothelial cells of hepatic sinusoids, also known as hepatic or liver sinusoidal endothelial cells (HSEC or LSEC), are unique, specialized type of endothelial cells located in the liver. They are the building units of the hepatic sinusoid, which functions as a specialized capillary system that facilitates the exchange of various substances between the blood and hepatocytes. This finely tuned environment, facilitated by HSEC, is primordial for the liver's multiple physiologic functions that include nutrient metabolism, toxin inactivation, and immunomodulation. +The HSEC have a distinctive morphology that sets them apart from the typical endothelial cells found in other organs. These cells are exceptionally thin to allow for efficient transfer of molecules and characterized by fenestrations, which are non-diaphragmatic, sieve-like openings that provide an open filtration pathway from the sinusoidal lumen to the space of Disse, where hepatocytes are exposed. The fenestration is a crucial feature that allows lipoproteins, nutrients, and other plasma components easy access to hepatocytes for essential liver functions, including clearance of waste products and metabolic regulation. +HSECs further play a vital role in immune functionality in the liver. They act as a sentinel, determining the nature of the immune response to encountered particulates. They possess a capacity for antigen presentation and express a series of immune-related surface molecules, which helps in immunosurveillance and immunoregulation. The HSEC also aid in the removal and destruction of virus-infected cells, harmful microorganisms, and circulatory waste products to safeguard liver health and general systemic cleanliness. + DOI:10.1016/j.jhep.2016.07.009 + DOI:10.1038/cmi.2016.5 + DOI:10.1038/s41575-018-0020-y + DOI:10.1038/s41575-020-00411-3 + https://www.sciencedirect.com/topics/immunology-and-microbiology/disse-space + @@ -96089,7 +98111,7 @@ Enterocytes of the colon are involved in the communication with the gut microbio - + @@ -96098,7 +98120,7 @@ Enterocytes of the colon are involved in the communication with the gut microbio - + An epithelial cell that is part of the appendix. @@ -96187,6 +98209,7 @@ Enterocytes of the colon are involved in the communication with the gut microbio sinoatrial node cell sinoatrial node myocyte sinuatrial node myocyte + myocyte of sinoatrial node @@ -96401,7 +98424,7 @@ Enterocytes of the colon are involved in the communication with the gut microbio A blood vessel endothelial cell that is part of an arterial endothelium. - This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. Endothelial cells of the artery, also referred to as arterial endothelial cells, form an integral part of the arterial system. They form a single layer, known as the endothelium, lining the interior surface of arteries, and are able to respond to the high-pressure and flow conditions present in arteries. The primary role of these cells is to provide a barrier between the vessel wall and the blood, exhibiting selective permeability to regulate the movement of liquids, gases, and blood-borne substances across the vascular wall. Arterial endothelial cells significantly contribute to maintaining vascular homeostasis. They are at the forefront of sensations and responses to mechanical stimuli, like shear stress and blood pressure changes. An additional key function pertains to the production of nitric oxide, which helps to regulate vascular tone and blood pressure, prevents platelet aggregation, limits leukocyte adhesion to the endothelium, and inhibits smooth muscle cell proliferation. These varied but connected functions help to preclude the development of atherosclerosis, ensuring normal circulation and arterial health. @@ -96424,7 +98447,7 @@ Moreover, these cells play a pivotal role in inflammation and coagulation proces - This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. Endothelial cells of the artery, also referred to as arterial endothelial cells, form an integral part of the arterial system. They form a single layer, known as the endothelium, lining the interior surface of arteries, and are able to respond to the high-pressure and flow conditions present in arteries. The primary role of these cells is to provide a barrier between the vessel wall and the blood, exhibiting selective permeability to regulate the movement of liquids, gases, and blood-borne substances across the vascular wall. Arterial endothelial cells significantly contribute to maintaining vascular homeostasis. They are at the forefront of sensations and responses to mechanical stimuli, like shear stress and blood pressure changes. An additional key function pertains to the production of nitric oxide, which helps to regulate vascular tone and blood pressure, prevents platelet aggregation, limits leukocyte adhesion to the endothelium, and inhibits smooth muscle cell proliferation. These varied but connected functions help to preclude the development of atherosclerosis, ensuring normal circulation and arterial health. @@ -97120,7 +99143,7 @@ Moreover, these cells play a pivotal role in inflammation and coagulation proces An epithelial cell that is part of the lacrimal sac. - This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. Epithelial cells of the lacrimal sac play a significant role in the physiology of tear drainage, acting as an integral part of the lacrimal drainage system. The lacrimal sac is part of the nasolacrimal duct system, a conduit which connects the eye to the nasal cavity, and is lined by multilayered, non-keratinizing, squamous epithelial cells. The epithelial cells of the lacrimal sac are specialized for the purpose of maintaining a moist environment and protecting the surface of the eye. They form a barrier that traps and removes potential contaminants from the tear film during the drainage process. These cells also actively contribute to tear turnover by expediting the drainage of excess tears. Dysfunctional epithelial cells of the lacrimal sac can lead to dacryocystitis, a condition characterized by inflammation of the lacrimal sac. @@ -97139,7 +99162,7 @@ Epithelial cells of the lacrimal sac also perform various other tasks which ensu - This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. Epithelial cells of the lacrimal sac play a significant role in the physiology of tear drainage, acting as an integral part of the lacrimal drainage system. The lacrimal sac is part of the nasolacrimal duct system, a conduit which connects the eye to the nasal cavity, and is lined by multilayered, non-keratinizing, squamous epithelial cells. The epithelial cells of the lacrimal sac are specialized for the purpose of maintaining a moist environment and protecting the surface of the eye. They form a barrier that traps and removes potential contaminants from the tear film during the drainage process. These cells also actively contribute to tear turnover by expediting the drainage of excess tears. Dysfunctional epithelial cells of the lacrimal sac can lead to dacryocystitis, a condition characterized by inflammation of the lacrimal sac. @@ -97324,7 +99347,13 @@ Epithelial cells of the lacrimal sac also perform various other tasks which ensu A smooth muscle cell that is part of the ciliary body. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Ciliary muscle cells are specialized contractile cells that constitute the ciliary muscle, a component of the eye in vertebrates. These cells form a ring around the iris, the eye's colored part. Ciliary muscle cells fall into the category of smooth muscle cells, characterized by their lack of the striations typical of skeletal and cardiac muscle cells. Their shape is elongated and pointed at both ends, and they occur in multi-nucleated syncytia where many cells share the same cytoplasm. +Ciliary muscle cells primarily control the eye's accommodation, adjusting the thickness and curvature of the lens to fine-tune the focus of light on the retina. When ciliary muscle cells contract, tension on the zonular fibers holding the lens in place is reduced, allowing the lens to become thicker and increase its refractive power. Conversely, when the ciliary muscle cells relax, the tension on the zonular fibers increases, causing the lens to become flatter and decrease its refractive power. This adjustment facilitates clear vision at different distances, ranging from near to far objects. +Additionally, ciliary muscle cells play a role in draining the eye's aqueous humor, which is the clear fluid that fills the anterior chamber of the eye between the cornea and the lens. By controlling the shape of the surrounding trabecular meshwork through muscle contractions and relaxations, ciliary muscle cells indirectly regulate intraocular pressure, a factor critical for preventing ocular conditions like glaucoma. FMA:70610 + https://cellxgene.cziscience.com/cellguide/CL_1000443 smooth muscle cell of ciliary body @@ -97342,6 +99371,19 @@ Epithelial cells of the lacrimal sac also perform various other tasks which ensu A smooth muscle cell that is part of the ciliary body. GOC:tfm + + + + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Ciliary muscle cells are specialized contractile cells that constitute the ciliary muscle, a component of the eye in vertebrates. These cells form a ring around the iris, the eye's colored part. Ciliary muscle cells fall into the category of smooth muscle cells, characterized by their lack of the striations typical of skeletal and cardiac muscle cells. Their shape is elongated and pointed at both ends, and they occur in multi-nucleated syncytia where many cells share the same cytoplasm. +Ciliary muscle cells primarily control the eye's accommodation, adjusting the thickness and curvature of the lens to fine-tune the focus of light on the retina. When ciliary muscle cells contract, tension on the zonular fibers holding the lens in place is reduced, allowing the lens to become thicker and increase its refractive power. Conversely, when the ciliary muscle cells relax, the tension on the zonular fibers increases, causing the lens to become flatter and decrease its refractive power. This adjustment facilitates clear vision at different distances, ranging from near to far objects. +Additionally, ciliary muscle cells play a role in draining the eye's aqueous humor, which is the clear fluid that fills the anterior chamber of the eye between the cornea and the lens. By controlling the shape of the surrounding trabecular meshwork through muscle contractions and relaxations, ciliary muscle cells indirectly regulate intraocular pressure, a factor critical for preventing ocular conditions like glaucoma. + DOI:10.1016/S1350-9462(98)00011-1 + DOI:10.1038/srep31171 + DOI:10.1111/j.1444-0938.2008.00260.x + https://www.sciencedirect.com/topics/medicine-and-dentistry/ciliary-muscle + @@ -97541,7 +99583,13 @@ Epithelial cells of the lacrimal sac also perform various other tasks which ensu An epithelial cell that is part of the nephron. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Epithelial cells of the nephron form the epithelial lining of the nephron, the functional unit of the kidney that filters the blood to produce urine. Each kidney holds approximately one million nephrons, each of which is composed of several distinct parts, including the renal corpuscle, the proximal tubule, the loop of Henle, and the distal tubule. All sections are lined with highly specialized epithelial cells adapted to perform different functions within the sections of the nephron. +The different epithelial cells of the nephron play crucial roles in the process of filtration, reabsorption, secretion, and excretion, essential tasks for the regulation of body fluid composition and volume. During filtration, the blood is forced through the walls of glomerular capillaries into the Bowman's capsule, where waste products, electrolytes, and water are separated from the blood cells and proteins. As the filtrate then passes through the nephron, epithelial cells of the tubular portion reabsorb useful substances such as glucose, amino acids, and electrolytes, along with most of the water back into the bloodstream. Waste products like urea and creatinine, as well as excess ions and water, remain in the tubule for elimination. +In addition, epithelial cells of the nephron also play a vital part in maintaining the body's acid-base balance by actively secreting hydrogen ions into the urine while reabsorbing bicarbonate from the urine back into the blood. They are also involved in the regulation of blood pressure through the renin-angiotensin-aldosterone system and contribute to erythrocyte production by releasing the hormone erythropoietin in response to low oxygen levels in the blood. Abnormalities or damage in renal epithelial cells often result in impaired kidney function, leading to various renal diseases. FMA:70965 + https://cellxgene.cziscience.com/cellguide/CL_1000449 epithelial cell of nephron @@ -97551,6 +99599,20 @@ Epithelial cells of the lacrimal sac also perform various other tasks which ensu An epithelial cell that is part of the nephron. GOC:tfm + + + + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Epithelial cells of the nephron form the epithelial lining of the nephron, the functional unit of the kidney that filters the blood to produce urine. Each kidney holds approximately one million nephrons, each of which is composed of several distinct parts, including the renal corpuscle, the proximal tubule, the loop of Henle, and the distal tubule. All sections are lined with highly specialized epithelial cells adapted to perform different functions within the sections of the nephron. +The different epithelial cells of the nephron play crucial roles in the process of filtration, reabsorption, secretion, and excretion, essential tasks for the regulation of body fluid composition and volume. During filtration, the blood is forced through the walls of glomerular capillaries into the Bowman's capsule, where waste products, electrolytes, and water are separated from the blood cells and proteins. As the filtrate then passes through the nephron, epithelial cells of the tubular portion reabsorb useful substances such as glucose, amino acids, and electrolytes, along with most of the water back into the bloodstream. Waste products like urea and creatinine, as well as excess ions and water, remain in the tubule for elimination. +In addition, epithelial cells of the nephron also play a vital part in maintaining the body's acid-base balance by actively secreting hydrogen ions into the urine while reabsorbing bicarbonate from the urine back into the blood. They are also involved in the regulation of blood pressure through the renin-angiotensin-aldosterone system and contribute to erythrocyte production by releasing the hormone erythropoietin in response to low oxygen levels in the blood. Abnormalities or damage in renal epithelial cells often result in impaired kidney function, leading to various renal diseases. + DOI:10.1007/978-94-011-2354-9_6 + DOI:10.1007/s004670050586 + DOI:10.1016/B978-0-323-35775-3.00011-4 + DOI:10.1146/annurev-physiol-052521-121841 + DOI:10.1681/ASN.2012010029 + @@ -97708,7 +99770,7 @@ Epithelial cells of the lacrimal sac also perform various other tasks which ensu An epithelial cell that is part of the collecting duct of renal tubule. - This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. Kidney collecting duct epithelial cells are a specialized type of cells that form an integral part of the renal system. Located in the collecting duct system of the kidneys, these cells are responsible for one of the final steps in the process of urine formation, and they are instrumental in the fine tuning of the volume and composition of urine by reabsorbing water and certain solutes back into the bloodstream. These cells express specific channels and carriers that actively and passively transport ions and water. They also have channels on their membranes, such as sodium channels and potassium channels, involved in reabsorbing or secreting these electrolytes depending upon the body's needs. The function of renal collecting duct epithelial cells can be regulated by a variety of hormones, including vasopressin (antidiuretic hormone), which can modulate the ion channels and carriers and hence indirectly influence body fluid homeostasis. @@ -97743,7 +99805,7 @@ Aside from their function in ion and water balance, kidney collecting duct epith - This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. Kidney collecting duct epithelial cells are a specialized type of cells that form an integral part of the renal system. Located in the collecting duct system of the kidneys, these cells are responsible for one of the final steps in the process of urine formation, and they are instrumental in the fine tuning of the volume and composition of urine by reabsorbing water and certain solutes back into the bloodstream. These cells express specific channels and carriers that actively and passively transport ions and water. They also have channels on their membranes, such as sodium channels and potassium channels, involved in reabsorbing or secreting these electrolytes depending upon the body's needs. The function of renal collecting duct epithelial cells can be regulated by a variety of hormones, including vasopressin (antidiuretic hormone), which can modulate the ion channels and carriers and hence indirectly influence body fluid homeostasis. @@ -97855,8 +99917,13 @@ Aside from their function in ion and water balance, kidney collecting duct epith A melanocyte that is part of the skin of body. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Melanocytes of the skin are specialized pigment cells crucial for producing and distributing melanin, the pigment determining skin, in addition to hair and eye color. Located in the basal layer of the epidermis, melanocytes serve as a natural sunscreen, protecting skin cells from harmful UV radiation. Structurally dendritic, they synthesize melanin through melanogenesis, transferring melanosomes to keratinocytes for UV shielding +Beyond pigmentation and UV protection, melanocytes play roles in immune and inflammatory responses. They respond to environmental changes, communicate with skin cell types, and secrete cytokines and growth factors influencing skin homeostasis. Dysregulation may lead to pigment disorders like vitiligo and melasma or contribute to skin cancer, particularly malignant melanoma. CALOHA:TS-2374 FMA:72144 + https://cellxgene.cziscience.com/cellguide/CL_1000458 skin melanocyte @@ -97874,6 +99941,19 @@ Aside from their function in ion and water balance, kidney collecting duct epith A melanocyte that is part of the skin of body. GOC:tfm + + + + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Melanocytes of the skin are specialized pigment cells crucial for producing and distributing melanin, the pigment determining skin, in addition to hair and eye color. Located in the basal layer of the epidermis, melanocytes serve as a natural sunscreen, protecting skin cells from harmful UV radiation. Structurally dendritic, they synthesize melanin through melanogenesis, transferring melanosomes to keratinocytes for UV shielding +Beyond pigmentation and UV protection, melanocytes play roles in immune and inflammatory responses. They respond to environmental changes, communicate with skin cell types, and secrete cytokines and growth factors influencing skin homeostasis. Dysregulation may lead to pigment disorders like vitiligo and melasma or contribute to skin cancer, particularly malignant melanoma. + DOI:10.1016/j.jinf.2015.06.006 + DOI:10.1111/j.1751-1097.2007.00226.x + DOI:10.1615/CritRevEukaryotGeneExpr.2020028454 + DOI:10.5114/pdia.2013.33376 + https://www.sciencedirect.com/topics/biochemistry-genetics-and-molecular-biology/melanocyte + @@ -98535,7 +100615,12 @@ Aside from their function in ion and water balance, kidney collecting duct epith A smooth muscle cell that is part of the prostate gland. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Smooth muscle cells of the prostate constitute a critical component of the prostatic stroma, enveloping glandular structures to support functions like secretion and fluid expulsion. Like other smooth muscles, smooth muscle cells of the prostate lack the striations characteristic of skeletal and cardiac muscle cell. +Functionally, they play a crucial role in reproductive and urinary functions. Smooth muscle cells of the prostate contribute to the transport and expulsion of prostatic secretions into the urethra and respond dynamically to signaling molecules such as hormones and neurotransmitters. For instance, under sympathetic nervous stimulation, they contract and apply pressure on the gland's ducts, facilitating the secretion process. FMA:84583 + https://cellxgene.cziscience.com/cellguide/CL_1000487 smooth muscle fiber of prostate @@ -98553,6 +100638,17 @@ Aside from their function in ion and water balance, kidney collecting duct epith A smooth muscle cell that is part of the prostate gland. GOC:tfm + + + + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Smooth muscle cells of the prostate constitute a critical component of the prostatic stroma, enveloping glandular structures to support functions like secretion and fluid expulsion. Like other smooth muscles, smooth muscle cells of the prostate lack the striations characteristic of skeletal and cardiac muscle cell. +Functionally, they play a crucial role in reproductive and urinary functions. Smooth muscle cells of the prostate contribute to the transport and expulsion of prostatic secretions into the urethra and respond dynamically to signaling molecules such as hormones and neurotransmitters. For instance, under sympathetic nervous stimulation, they contract and apply pressure on the gland's ducts, facilitating the secretion process. + DOI:10.1101/cshperspect.a030510 + https://www.ncbi.nlm.nih.gov/books/NBK279291 + https://www.sciencedirect.com/topics/immunology-and-microbiology/smooth-muscle-cell + @@ -98611,7 +100707,7 @@ Aside from their function in ion and water balance, kidney collecting duct epith An epithelial cell that is part of the bile duct. Cholangiocytes contribute to bile secretion via net release of bicarbonate and water. They are cuboidal epithelium in the small interlobular bile ducts, but become columnar and mucus secreting in larger bile ducts approaching the porta hepatis and the extrahepatic ducts. - This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. Cholangiocytes, also known as biliary epithelial cells, are specialized epithelial cells that line the biliary tract, which constitutes the gall bladder and bile ducts inside the liver. Crucial to the maintenance of the liver's health and function, cholangiocytes have a key role in the modification and secretion of bile, a fluid produced by hepatocytes that is essential to digestion and the absorption of fats and vitamins. Cholangiocytes accomplish their primary function through the expression of a variety of transport proteins located on their apical and basolateral membranes, which propel bile acids and other contents of the bile into the biliary lumen. The hepatic bile, once secreted by the hepatocytes, is further modified by cholangiocytes via secretion and absorption processes. These processes help in the regulation of bile volume and composition, which is fundamental in ensuring the efficient digestion of dietary fats and fat-soluble vitamins and the excretion of cholesterol. @@ -98640,7 +100736,7 @@ In addition to their role in bile modification, cholangiocytes also perform seve - This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. Cholangiocytes, also known as biliary epithelial cells, are specialized epithelial cells that line the biliary tract, which constitutes the gall bladder and bile ducts inside the liver. Crucial to the maintenance of the liver's health and function, cholangiocytes have a key role in the modification and secretion of bile, a fluid produced by hepatocytes that is essential to digestion and the absorption of fats and vitamins. Cholangiocytes accomplish their primary function through the expression of a variety of transport proteins located on their apical and basolateral membranes, which propel bile acids and other contents of the bile into the biliary lumen. The hepatic bile, once secreted by the hepatocytes, is further modified by cholangiocytes via secretion and absorption processes. These processes help in the regulation of bile volume and composition, which is fundamental in ensuring the efficient digestion of dietary fats and fat-soluble vitamins and the excretion of cholesterol. @@ -98766,7 +100862,7 @@ In addition to their role in bile modification, cholangiocytes also perform seve A mesothelial cell that is part of the pleura. - This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. Mesothelial cells of the pleura form a significant part of the pleural membrane, a thin, double-layered serous membrane that lines the thoracic cavity and encompasses the lungs. These specialized cells contribute to the pleura's key function of producing a lubricating serous fluid, which reduces friction between the lung's outer surface (visceral pleura) and the inner lining of the thoracic cavity (parietal pleura) during respiration. The cellular structure of mesothelial cells, characterized by microvilli on their surface, aids in the secretion and absorption of the pleural fluid, effectively supporting the smooth expansion and contraction of the lungs. Dysregulation in mesothelial cells can lead to pathologies, including pleural effusion and malignant mesothelioma. @@ -98787,7 +100883,7 @@ In the event of pleural injury, these cells are also involved in the mesothelial - This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. Mesothelial cells of the pleura form a significant part of the pleural membrane, a thin, double-layered serous membrane that lines the thoracic cavity and encompasses the lungs. These specialized cells contribute to the pleura's key function of producing a lubricating serous fluid, which reduces friction between the lung's outer surface (visceral pleura) and the inner lining of the thoracic cavity (parietal pleura) during respiration. The cellular structure of mesothelial cells, characterized by microvilli on their surface, aids in the secretion and absorption of the pleural fluid, effectively supporting the smooth expansion and contraction of the lungs. Dysregulation in mesothelial cells can lead to pathologies, including pleural effusion and malignant mesothelioma. @@ -98864,7 +100960,7 @@ In the event of pleural injury, these cells are also involved in the mesothelial A mesothelial cell that is part of the visceral pleura. - This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. Mesothelial cells of visceral pleura are specialized epithelial cells that line the inner layer of the pleura, the membrane that envelops the lungs. Positioned adjacent to the lung tissue, these cells form a protective barrier and contribute to the structure of the visceral pleura. They are characterized by their cuboidal to squamous epithelial shape and the presence of microvilli on their surface, a feature aiding in fluid and solute exchange between the pleura and the lungs. The primary function of mesothelial cells of visceral pleura is to secrete a lubricating serous fluid to facilitate smooth, frictionless lung movement within the thoracic cavity during respiration. This helps in the prevention of trauma or damage stemming from the constant rubbing of the lung tissue against the chest wall, hence playing a pivotal role in maintaining respiratory function. Besides fluid secretion, these cells have an essential role in the transportation of fluids and particles across the pleura, as well as in inflammation, wound healing, and tissue repair processes within the pleura. @@ -98884,7 +100980,7 @@ Mesothelial cells of visceral pleura are notably implicated in the development o - This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. Mesothelial cells of visceral pleura are specialized epithelial cells that line the inner layer of the pleura, the membrane that envelops the lungs. Positioned adjacent to the lung tissue, these cells form a protective barrier and contribute to the structure of the visceral pleura. They are characterized by their cuboidal to squamous epithelial shape and the presence of microvilli on their surface, a feature aiding in fluid and solute exchange between the pleura and the lungs. The primary function of mesothelial cells of visceral pleura is to secrete a lubricating serous fluid to facilitate smooth, frictionless lung movement within the thoracic cavity during respiration. This helps in the prevention of trauma or damage stemming from the constant rubbing of the lung tissue against the chest wall, hence playing a pivotal role in maintaining respiratory function. Besides fluid secretion, these cells have an essential role in the transportation of fluids and particles across the pleura, as well as in inflammation, wound healing, and tissue repair processes within the pleura. @@ -98946,19 +101042,13 @@ Mesothelial cells of visceral pleura are notably implicated in the development o - + - - - - - - - + A goblet cell that is part of the small intestine. FMA:86929 goblet cell of epithelium of small intestine @@ -99870,6 +101960,7 @@ Mesothelial cells of visceral pleura are notably implicated in the development o KUPO:0001106 + kidney interstitial alternatively activated macrophage @@ -99904,10 +101995,31 @@ Mesothelial cells of visceral pleura are notably implicated in the development o A tissue-resident macrophage that is part of some kidney. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Kidney resident macrophages are a heterogeneous population of immune cell found in the cortex and medullary regions of the kidney as well as within and surround the glomeruli. Their primary role involves maintaining homeostasis and immune surveillance in the kidney microenvironment, defending against ascending urinary infections. Beyond traditional macrophage roles such as phagocytosis and antigen presentation, kidney resident macrophages also contribute significantly to the response to kidney injury including tissue repair and angiogenesis. +Under normal physiological conditions, kidney resident macrophages work to maintain the balance of the kidney's microenvironment by removing dead cells, pathogens and cellular debris, to limit inflammation and tissue damage. They are ‘professional’ phagocytes, clearing pathogens and debris by engulfing and digesting these harmful materials. Moreover, they are capable of presenting antigens to other immune cells, which aids in the activation of the adaptive immune response. +Kidney resident macrophages show a high degree of plasticity: in response to environmental stimuli they change their morphology and cell surface markers. For example, in response to acute injury, some macrophages adopt a pro-inflammatory phenotype and augment tissue damage; once the injury stimulus is removed, they may change to mediate tissue repair. +While kidney macrophages contribute to wound healing, tissue repair and regeneration by producing key growth factors and cytokines that stimulate cell proliferation, collagen production, and blood vessel formation, dysregulation in their activity can also lead to progressive inflammation and fibrosis, common features in chronic kidney disease. KUPO:0001109 + https://cellxgene.cziscience.com/cellguide/CL_1000698 kidney resident macrophage + + + + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Kidney resident macrophages are a heterogeneous population of immune cell found in the cortex and medullary regions of the kidney as well as within and surround the glomeruli. Their primary role involves maintaining homeostasis and immune surveillance in the kidney microenvironment, defending against ascending urinary infections. Beyond traditional macrophage roles such as phagocytosis and antigen presentation, kidney resident macrophages also contribute significantly to the response to kidney injury including tissue repair and angiogenesis. +Under normal physiological conditions, kidney resident macrophages work to maintain the balance of the kidney's microenvironment by removing dead cells, pathogens and cellular debris, to limit inflammation and tissue damage. They are ‘professional’ phagocytes, clearing pathogens and debris by engulfing and digesting these harmful materials. Moreover, they are capable of presenting antigens to other immune cells, which aids in the activation of the adaptive immune response. +Kidney resident macrophages show a high degree of plasticity: in response to environmental stimuli they change their morphology and cell surface markers. For example, in response to acute injury, some macrophages adopt a pro-inflammatory phenotype and augment tissue damage; once the injury stimulus is removed, they may change to mediate tissue repair. +While kidney macrophages contribute to wound healing, tissue repair and regeneration by producing key growth factors and cytokines that stimulate cell proliferation, collagen production, and blood vessel formation, dysregulation in their activity can also lead to progressive inflammation and fibrosis, common features in chronic kidney disease. + DOI:10.1016/bs.ircmb.2022.01.005 + DOI:10.1172/jci.insight.161078 + DOI:10.3389/fimmu.2021.681748 + DOI:10.3389/fphys.2017.00837 + @@ -100047,27 +102159,15 @@ Mesothelial cells of visceral pleura are notably implicated in the development o - Any urothelial cell that is part of some urothelium of ureter. + A urothelial cell that is part of the urothelium of ureter. KUPO:0001117 ureter urothelial cell - - - - - true - - - - - - true - - Any urothelial cell that is part of some urothelium of ureter. - FBC:Autogenerated + A urothelial cell that is part of the urothelium of ureter. + PMID:36180582 @@ -100514,7 +102614,14 @@ Mesothelial cells of visceral pleura are notably implicated in the development o Any nephron tubule epithelial cell that is part of some renal connecting tubule. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Kidney connecting tubule epithelial cells are found in collecting duct system of the kidney, specifically in at the interconnection segment between the nephron and the collecting ducts. The epithelial cells lining the connecting tubule are crucial for the journey of filtrate before it empties into urine-collecting ducts and therefore play a critical role in maintaining the body’s fluid and electrolyte balance. +One of the principal functions of connecting tubule epithelial cells involves the selective reabsorption and secretion of various solutes. This reabsorption process includes critical regulatory electrolytes such as sodium ions (Na+), chloride ions (Cl-), and bicarbonate ions (HCO3-), thus playing a role in the regulation of the acid-base homeostasis. Their function also involves the secretion of potassium ions (K+) into the renal tubular fluid. +The connecting tubule epithelial cells are primarily intercalated cells, which can be categorized into two types according to their specific functions: type A intercalated cells, which secrete acid, and the type B intercalated cells, which secrete base (bicarbonate) and reabsorb chloride. By regulating the concentrations of these ions, as well as reabsorption of water, connecting tubule epithelial cells contribute substantively to maintaining the body's electrolyte levels, pH balance, and overall homeostasis. +In addition to intercalating cells, the collecting duct system also has principal cells, which are characterized by the expression of the water channel AQP2. AQP2-expressing cells have also been identified in connecting tubules, but there is some controversy whether these represent a unique cell type as there are some morphologic differences compared with principal cells. KUPO:0001058 + https://cellxgene.cziscience.com/cellguide/CL_1000768 @@ -100532,6 +102639,21 @@ Mesothelial cells of visceral pleura are notably implicated in the development o Any nephron tubule epithelial cell that is part of some renal connecting tubule. FBC:Autogenerated + + + + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Kidney connecting tubule epithelial cells are found in collecting duct system of the kidney, specifically in at the interconnection segment between the nephron and the collecting ducts. The epithelial cells lining the connecting tubule are crucial for the journey of filtrate before it empties into urine-collecting ducts and therefore play a critical role in maintaining the body’s fluid and electrolyte balance. +One of the principal functions of connecting tubule epithelial cells involves the selective reabsorption and secretion of various solutes. This reabsorption process includes critical regulatory electrolytes such as sodium ions (Na+), chloride ions (Cl-), and bicarbonate ions (HCO3-), thus playing a role in the regulation of the acid-base homeostasis. Their function also involves the secretion of potassium ions (K+) into the renal tubular fluid. +The connecting tubule epithelial cells are primarily intercalated cells, which can be categorized into two types according to their specific functions: type A intercalated cells, which secrete acid, and the type B intercalated cells, which secrete base (bicarbonate) and reabsorb chloride. By regulating the concentrations of these ions, as well as reabsorption of water, connecting tubule epithelial cells contribute substantively to maintaining the body's electrolyte levels, pH balance, and overall homeostasis. +In addition to intercalating cells, the collecting duct system also has principal cells, which are characterized by the expression of the water channel AQP2. AQP2-expressing cells have also been identified in connecting tubules, but there is some controversy whether these represent a unique cell type as there are some morphologic differences compared with principal cells. + DOI:10.1002/cphy.c110052 + DOI:10.1007/s00418-021-02033-5 + DOI:10.1097/MNH.0b013e32820ac850 + DOI:10.1681/ASN.2019040415 + DOI:10.23876/j.krcp.2017.36.4.305 + @@ -100655,7 +102777,13 @@ Mesothelial cells of visceral pleura are notably implicated in the development o Any epithelial cell of proximal tubule that is part of some proximal convoluted tubule and has part some brush border. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Kidney proximal convoluted tubule epithelial cells line the most voluminous part of the kidney's nephron, the proximal convoluted tubule, located in the cortex of the kidney. These cells are primarily involved in reabsorption and secretion processes, key functions that facilitate homeostasis within the body. +Proximal convoluted tubule epithelial cells extensively function in the reabsorption process to a greater degree than their counterparts in the proximal straight tubule. Approximately two-thirds of filtrated sodium and water, nearly all nutrient sugars and amino acids, and a significant portion of bicarbonates pass through the proximal convoluted tubule, are effectively absorbed by the epithelial cells, and reenter the bodily circulation. By absorbing bicarbonates and secreting protons into the tubular fluid, proximal convoluted tubule epithelial cells also contribute to the pH regulation in the body . +In addition to reabsorption, proximal convoluted tubule epithelial cells also play a critical role in the excretion of waste metabolites and xenobiotics. These cells possess a range of transporters that secrete metabolic end products and certain drugs, hence aiding in their elimination. This function underlines their importance for body detoxification. KUPO:0001045 + https://cellxgene.cziscience.com/cellguide/CL_1000838 kidney proximal convoluted tubule epithelial cell @@ -100665,6 +102793,19 @@ Mesothelial cells of visceral pleura are notably implicated in the development o Any epithelial cell of proximal tubule that is part of some proximal convoluted tubule and has part some brush border. FBC:Autogenerated + + + + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Kidney proximal convoluted tubule epithelial cells line the most voluminous part of the kidney's nephron, the proximal convoluted tubule, located in the cortex of the kidney. These cells are primarily involved in reabsorption and secretion processes, key functions that facilitate homeostasis within the body. +Proximal convoluted tubule epithelial cells extensively function in the reabsorption process to a greater degree than their counterparts in the proximal straight tubule. Approximately two-thirds of filtrated sodium and water, nearly all nutrient sugars and amino acids, and a significant portion of bicarbonates pass through the proximal convoluted tubule, are effectively absorbed by the epithelial cells, and reenter the bodily circulation. By absorbing bicarbonates and secreting protons into the tubular fluid, proximal convoluted tubule epithelial cells also contribute to the pH regulation in the body . +In addition to reabsorption, proximal convoluted tubule epithelial cells also play a critical role in the excretion of waste metabolites and xenobiotics. These cells possess a range of transporters that secrete metabolic end products and certain drugs, hence aiding in their elimination. This function underlines their importance for body detoxification. + DOI:10.1002/cphy.c110060 + DOI:10.1146/annurev-physiol-052521-121841 + DOI:10.1159/000092212 + DOI:10.1681/ASN.2019040415 + @@ -100692,7 +102833,13 @@ Mesothelial cells of visceral pleura are notably implicated in the development o Any epithelial cell of proximal tubule that is part of some proximal straight tubule. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Kidney proximal straight tubule epithelial cells line the straight portion of the proximal tubule of the nephron, extending from the cortical medullary ray into the outer stripe of the outer medulla. They are characterized by a brush border of dense microvilli on their apical surface, enhancing the cell's surface area and aiding reabsorption, though reabsorption occurs more heavily in the proximal convoluted tubule preceding the straight portion of the tubule. +The primary function of the kidney proximal straight tubule epithelial cells is to reabsorb the filtrate that the kidney produces, which includes glucose, sodium, and water. The reabsorption occurs through both passive and active transport methods. These cells exhibit enzyme-rich microvilli that also absorb small proteins and peptides. Consequently, they are involved in the regulation of plasma levels of various substances, including glucose, amino acids, and electrolytes, and maintain the body's pH homeostasis by secreting H+ ions into the urine and absorbing bicarbonate ions. +These cells are also reported to be involved in drug metabolism. Many drugs are filtered from the blood by the kidneys and subsequently reabsorbed by the kidney proximal tubule epithelial cells back into the bloodstream. Furthermore, these cells play a significant role in the progression of kidney diseases. For example, in diabetic nephropathy and acute kidney injury, kidney proximal straight tubule epithelial cells can undergo cellular changes and result in malfunctions such as reduced reabsorption and increased excretion. KUPO:0001046 + https://cellxgene.cziscience.com/cellguide/CL_1000839 kidney proximal straight tubule epithelial cell @@ -100714,6 +102861,20 @@ Mesothelial cells of visceral pleura are notably implicated in the development o Any epithelial cell of proximal tubule that is part of some proximal straight tubule. FBC:Autogenerated + + + + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Kidney proximal straight tubule epithelial cells line the straight portion of the proximal tubule of the nephron, extending from the cortical medullary ray into the outer stripe of the outer medulla. They are characterized by a brush border of dense microvilli on their apical surface, enhancing the cell's surface area and aiding reabsorption, though reabsorption occurs more heavily in the proximal convoluted tubule preceding the straight portion of the tubule. +The primary function of the kidney proximal straight tubule epithelial cells is to reabsorb the filtrate that the kidney produces, which includes glucose, sodium, and water. The reabsorption occurs through both passive and active transport methods. These cells exhibit enzyme-rich microvilli that also absorb small proteins and peptides. Consequently, they are involved in the regulation of plasma levels of various substances, including glucose, amino acids, and electrolytes, and maintain the body's pH homeostasis by secreting H+ ions into the urine and absorbing bicarbonate ions. +These cells are also reported to be involved in drug metabolism. Many drugs are filtered from the blood by the kidneys and subsequently reabsorbed by the kidney proximal tubule epithelial cells back into the bloodstream. Furthermore, these cells play a significant role in the progression of kidney diseases. For example, in diabetic nephropathy and acute kidney injury, kidney proximal straight tubule epithelial cells can undergo cellular changes and result in malfunctions such as reduced reabsorption and increased excretion. + DOI:10.1002/cphy.c110061 + DOI:10.1038/nrd4461 + DOI:10.1146/annurev-physiol-052521-121841 + DOI:10.1681/ASN.2019040415 + DOI:10.2215/CJN.10391012 + @@ -100740,7 +102901,13 @@ Mesothelial cells of visceral pleura are notably implicated in the development o Any epithelial cell of distal tubule that is part of some distal convoluted tubule. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Kidney distal convoluted tubule epithelial cells, often referred to simply as distal convoluted tubule (DCT) cells, constitute a significant portion of the nephron -- the functional building unit of the kidney involved in filtration and reabsorption of substances from blood. The DCT epithelial cells form lining of the distal convoluted tubule, a segment of the nephron located after the loop of Henle and before the collecting tubule. These cells are characterized by unique morphological features such as small size, low height and fewer microvilli compared to proximal convoluted tubule epithelial cells. +These cells perform a host of vital functions contributing to the regulation of extracellular fluid volume and electrolyte balance, blood pressure and pH. While the DCT is less prominent in water and sodium reabsorption compared to the proximal tubule and the loop of Henle, it plays a crucial role in fine-tuning the process. DCT epithelial cells are responsible for the final adjustments of sodium, potassium and calcium reabsorption, thereby affecting overall fluid and electrolyte balance, blood pressure regulation and bone health. The reabsorption process is regulated by hormones including aldosterone and parathyroid hormone. +The distal convoluted tubule (DCT) also plays a significant role in acid-base homeostasis by secreting protons (H+) into the tubular fluid and reabsorbing bicarbonate ions (HCO3-), thus regulating the pH of the blood. The ability of DCT cells to adjust urine concentration plays a part in maintaining the body’s pH balance and preventing conditions like acidosis or alkalosis. In summary, kidney distal convoluted tubule epithelial cells perform functions that are crucial to maintaining body's homeostasis. KUPO:0001056 + https://cellxgene.cziscience.com/cellguide/CL_1000849 @@ -100758,6 +102925,20 @@ Mesothelial cells of visceral pleura are notably implicated in the development o Any epithelial cell of distal tubule that is part of some distal convoluted tubule. FBC:Autogenerated + + + + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Kidney distal convoluted tubule epithelial cells, often referred to simply as distal convoluted tubule (DCT) cells, constitute a significant portion of the nephron -- the functional building unit of the kidney involved in filtration and reabsorption of substances from blood. The DCT epithelial cells form lining of the distal convoluted tubule, a segment of the nephron located after the loop of Henle and before the collecting tubule. These cells are characterized by unique morphological features such as small size, low height and fewer microvilli compared to proximal convoluted tubule epithelial cells. +These cells perform a host of vital functions contributing to the regulation of extracellular fluid volume and electrolyte balance, blood pressure and pH. While the DCT is less prominent in water and sodium reabsorption compared to the proximal tubule and the loop of Henle, it plays a crucial role in fine-tuning the process. DCT epithelial cells are responsible for the final adjustments of sodium, potassium and calcium reabsorption, thereby affecting overall fluid and electrolyte balance, blood pressure regulation and bone health. The reabsorption process is regulated by hormones including aldosterone and parathyroid hormone. +The distal convoluted tubule (DCT) also plays a significant role in acid-base homeostasis by secreting protons (H+) into the tubular fluid and reabsorbing bicarbonate ions (HCO3-), thus regulating the pH of the blood. The ability of DCT cells to adjust urine concentration plays a part in maintaining the body’s pH balance and preventing conditions like acidosis or alkalosis. In summary, kidney distal convoluted tubule epithelial cells perform functions that are crucial to maintaining body's homeostasis. + DOI:10.1002/cphy.c140002 + DOI:10.1007/s40620-021-01032-y + DOI:10.1152/physrev.2000.80.1.277 + DOI:10.1681/ASN.2019040415 + DOI:10.2215/CJN.05920613 + @@ -100785,7 +102966,13 @@ Mesothelial cells of visceral pleura are notably implicated in the development o Any epithelial cell of distal tubule that is part of some macula densa. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Macula densa epithelial cells, as part of the complex nephron structure, play a crucial role in kidney function. These cells, which make up the macula densa, help regulate blood pressure and the filtration rate of the glomerulus by sensing sodium chloride amounts in the kidney tubules. Found where the thick ascending limb of the Loop of Henle touches the afferent arteriole, macula densa epithelial cells are positioned in an optimal location to monitor and respond to changes in the filtrate composition. +These cells maintain intraglomerular homeostasis. When the sodium chloride concentration is high, macula densa cells respond by secreting adenosine and vasoconstricting the afferent arteriole to decrease the glomerular filtration rate. Conversely, if the sodium chloride concentration in the filtrate is low, the production and release of nitric oxide cause vasodilation to enhance the glomerular filtration rate. +Macula densa epithelial cells also have a role in tubuloglomerular feedback mechanisms, an essential autoregulatory renal response. They send feedback to the glomerular mesangial cells, allowing constriction or relaxation of the afferent arteriole as needed depending on the content of the filtrate. KUPO:0001057 + https://cellxgene.cziscience.com/cellguide/CL_1000850 macula densa epithelial cell @@ -100808,6 +102995,20 @@ Mesothelial cells of visceral pleura are notably implicated in the development o Any epithelial cell of distal tubule that is part of some macula densa. FBC:Autogenerated + + + + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Macula densa epithelial cells, as part of the complex nephron structure, play a crucial role in kidney function. These cells, which make up the macula densa, help regulate blood pressure and the filtration rate of the glomerulus by sensing sodium chloride amounts in the kidney tubules. Found where the thick ascending limb of the Loop of Henle touches the afferent arteriole, macula densa epithelial cells are positioned in an optimal location to monitor and respond to changes in the filtrate composition. +These cells maintain intraglomerular homeostasis. When the sodium chloride concentration is high, macula densa cells respond by secreting adenosine and vasoconstricting the afferent arteriole to decrease the glomerular filtration rate. Conversely, if the sodium chloride concentration in the filtrate is low, the production and release of nitric oxide cause vasodilation to enhance the glomerular filtration rate. +Macula densa epithelial cells also have a role in tubuloglomerular feedback mechanisms, an essential autoregulatory renal response. They send feedback to the glomerular mesangial cells, allowing constriction or relaxation of the afferent arteriole as needed depending on the content of the filtrate. + DOI:10.1073/pnas.0736323100 + DOI:10.1146/annurev-physiol-052521-121841 + DOI:10.1161/HYPERTENSIONAHA.115.04739 + DOI:10.1681/ASN.2009070759 + DOI:10.1681/ASN.2015050515 + @@ -101095,7 +103296,7 @@ Mesothelial cells of visceral pleura are notably implicated in the development o An endothelial cell that is part of the glomerular capillary of the kidney. - This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. The glomerular capillary endothelial cell comprises an intrinsic component of the glomerulus in the kidney. Glomeruli contain a network of capillaries where the first step of blood filtration takes place, with glomerular capillary endothelial cells acting as an integral part of this process. Unlike regular endothelial cells that line the vasculature, unique fenestrations (openings) characterize these cells, allowing for enhanced permeability and filtration efficacy. Together with the glomerular basement membrane and podocytes, the glomerular endothelial cells form the glomerular filtration barrier, which is responsible for blood filtration and therefore critical for removal of waste products, such as urea and creatinine, and excess substances, such as glucose and ions, from the bloodstream. The glomerular capillary endothelial cells' fenestrations permit the free flow of a variety of particles, barring larger, negatively charged proteins like serum albumin, enabling the formation of an ultrafiltrate. This ultrafiltrate is the primitive form of urine, which then passes through the proximal tubule for further processing and ultimately helps maintain systemic fluid and electrolyte balance. @@ -101109,7 +103310,7 @@ Moreover, the glomerular capillary endothelial cells are also believed to play a - This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. The glomerular capillary endothelial cell comprises an intrinsic component of the glomerulus in the kidney. Glomeruli contain a network of capillaries where the first step of blood filtration takes place, with glomerular capillary endothelial cells acting as an integral part of this process. Unlike regular endothelial cells that line the vasculature, unique fenestrations (openings) characterize these cells, allowing for enhanced permeability and filtration efficacy. Together with the glomerular basement membrane and podocytes, the glomerular endothelial cells form the glomerular filtration barrier, which is responsible for blood filtration and therefore critical for removal of waste products, such as urea and creatinine, and excess substances, such as glucose and ions, from the bloodstream. The glomerular capillary endothelial cells' fenestrations permit the free flow of a variety of particles, barring larger, negatively charged proteins like serum albumin, enabling the formation of an ultrafiltrate. This ultrafiltrate is the primitive form of urine, which then passes through the proximal tubule for further processing and ultimately helps maintain systemic fluid and electrolyte balance. @@ -101146,7 +103347,12 @@ Moreover, the glomerular capillary endothelial cells are also believed to play a An endothelial cell which is part of the afferent arteriole in the kidney. This cell is responsible for maintaining renal blood flow and glomerular filtration rate. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Kidney afferent arteriole cells are specialized cell types found in the renal vasculature, specifically in the afferent arterioles which help in maintaining the renal blood flow and glomerular filtration rate. They are essential for the proper functioning of the kidneys, contributing to the regulation of blood pressure and fluid balance within the organism. Located before the glomerulus, a tiny, intricate network of capillaries within the nephron, these cells help control the expansion or contraction of the arteriole, thus regulating the pressure and flow of blood into the glomerulus. +Functionally, kidney afferent arteriole cells are largely involved in responding to changes in blood volume and systemic blood pressure. They achieve this by modulating the diameter of the afferent arteriole through a process known as autoregulation. Autoregulation involves two primary mechanisms: the myogenic response and the tubuloglomerular feedback. The myogenic response is essentially the intrinsic ability of the vascular smooth muscle to respond to pressure changes, while the tubuloglomerular feedback is the process where the macula densa cells located near the glomerulus respond to changes in fluid delivery rates in the tubules, sending signals to afferent arterioles to constrict or dilate accordingly. These cells also have significant interaction with renin-containing juxtaglomerular cells, which are located in the wall of afferent arterioles. Juxtaglomerular cells secrete the enzyme renin in response to low blood pressure or sympathetic nerve activity, initiating the renin-angiotensin-aldosterone system cascade that ultimately helps retain sodium and water to increase blood volume and pressure. KUPO:0001038 + https://cellxgene.cziscience.com/cellguide/CL_1001006 kidney afferent arteriole cell @@ -101164,6 +103370,18 @@ Moreover, the glomerular capillary endothelial cells are also believed to play a PMID:24066938 PMID:25834230 + + + + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Kidney afferent arteriole cells are specialized cell types found in the renal vasculature, specifically in the afferent arterioles which help in maintaining the renal blood flow and glomerular filtration rate. They are essential for the proper functioning of the kidneys, contributing to the regulation of blood pressure and fluid balance within the organism. Located before the glomerulus, a tiny, intricate network of capillaries within the nephron, these cells help control the expansion or contraction of the arteriole, thus regulating the pressure and flow of blood into the glomerulus. +Functionally, kidney afferent arteriole cells are largely involved in responding to changes in blood volume and systemic blood pressure. They achieve this by modulating the diameter of the afferent arteriole through a process known as autoregulation. Autoregulation involves two primary mechanisms: the myogenic response and the tubuloglomerular feedback. The myogenic response is essentially the intrinsic ability of the vascular smooth muscle to respond to pressure changes, while the tubuloglomerular feedback is the process where the macula densa cells located near the glomerulus respond to changes in fluid delivery rates in the tubules, sending signals to afferent arterioles to constrict or dilate accordingly. These cells also have significant interaction with renin-containing juxtaglomerular cells, which are located in the wall of afferent arterioles. Juxtaglomerular cells secrete the enzyme renin in response to low blood pressure or sympathetic nerve activity, initiating the renin-angiotensin-aldosterone system cascade that ultimately helps retain sodium and water to increase blood volume and pressure. + DOI:10.1007/s00424-012-1126-7 + DOI:10.1152/ajpregu.00332.2006 + DOI:10.1152/physrev.00042.2012 + DOI:10.2174/15701611113116660149 + @@ -101190,7 +103408,13 @@ Moreover, the glomerular capillary endothelial cells are also believed to play a Any kidney arterial blood vessel cell that is part of some renal efferent arteriole. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Kidney efferent arteriole cells are highly adaptable vascular cells that make up the efferent arterioles in the kidney. These units are integral components of the renal microcirculation system, conducting blood away from the glomeruli after filtration occurs. Efferent arterioles directly affect glomerular hydrostatic pressure and, subsequently, the rate of glomerular filtration. They are the downstream channels that ensure the effective transportation of blood to the peritubular capillaries and vasa recta, critical for maintaining fluid balance and electrolyte homeostasis. +Kidney efferent arteriole cells are exceptional in their ability to perform autoregulation—a critical dynamic control of intrarenal blood flow ensuring stable glomerular filtration rates. This is primarily achieved via myogenic and tubuloglomerular feedback mechanisms, where the cells respond to changes in pressure and the concentration of sodium chloride in the tubular fluid, and constrict or dilate depending on the detected changes. +Cells associated with the efferent arteriole also respond to several systemic influences. Through complex intracellular signaling pathways, they respond to fluctuations in hormones (like angiotensin II and endothelin) and several other mediators such as nitric oxide and prostaglandins. Their adaptive capability helps maintain homeostasis and ensures the entire system's optimal performance under various physiological conditions. Dysfunctions in kidney efferent arteriole cells can lead to severe pathologies like hypertension and chronic kidney disease. KUPO:0001041 + https://cellxgene.cziscience.com/cellguide/CL_1001009 kidney efferent arteriole cell @@ -101199,6 +103423,20 @@ Moreover, the glomerular capillary endothelial cells are also believed to play a Any kidney arterial blood vessel cell that is part of some renal efferent arteriole. FBC:Autogenerated + + + + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Kidney efferent arteriole cells are highly adaptable vascular cells that make up the efferent arterioles in the kidney. These units are integral components of the renal microcirculation system, conducting blood away from the glomeruli after filtration occurs. Efferent arterioles directly affect glomerular hydrostatic pressure and, subsequently, the rate of glomerular filtration. They are the downstream channels that ensure the effective transportation of blood to the peritubular capillaries and vasa recta, critical for maintaining fluid balance and electrolyte homeostasis. +Kidney efferent arteriole cells are exceptional in their ability to perform autoregulation—a critical dynamic control of intrarenal blood flow ensuring stable glomerular filtration rates. This is primarily achieved via myogenic and tubuloglomerular feedback mechanisms, where the cells respond to changes in pressure and the concentration of sodium chloride in the tubular fluid, and constrict or dilate depending on the detected changes. +Cells associated with the efferent arteriole also respond to several systemic influences. Through complex intracellular signaling pathways, they respond to fluctuations in hormones (like angiotensin II and endothelin) and several other mediators such as nitric oxide and prostaglandins. Their adaptive capability helps maintain homeostasis and ensures the entire system's optimal performance under various physiological conditions. Dysfunctions in kidney efferent arteriole cells can lead to severe pathologies like hypertension and chronic kidney disease. + DOI:10.1152/ajpregu.2000.279.2.R629 + DOI:10.1152/physrev.00042.2012 + DOI:10.1159/000072054 + DOI:10.1161/01.HYP.29.1.222 + DOI:10.3748/wjg.v12.i34.5429 + @@ -101267,7 +103505,13 @@ Moreover, the glomerular capillary endothelial cells are also believed to play a Any kidney loop of Henle epithelial cell that is part of some descending limb of loop of Henle. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +The kidney loop of Henle descending limb epithelial cells are highly specialized cells that play a crucial role in maintaining the body's salt and water balance. These cells line the descending limb of the loop of Henle, which is a portion of the renal tubule located in the kidneys, an organ responsible for filtering waste products, ions and extra water from the blood and converting them into urine. However, the descending limb epithelial cells are specifically involved in the countercurrent multiplication system, a mechanism to concentrate urine that involves both active and passive transport processes. +These cells are notably permeable to water but relatively impermeable to solutes, a characteristic that dramatically influences the osmotic gradient in the renal medulla. As filtrate initially descends down the loop of Henle, water gets drawn out due to the increasing osmotic gradient, thereby concentrating the filtrate. Additionally, these epithelial cells are exceptionally thin walled, allowing water to freely diffuse across the membrane. +Furthermore, the kidney loop of Henle descending limb epithelial cells are inextricably linked to the functioning of numerous diuretic drugs, which work by blocking the reabsorption of water and certain electrolytes in the kidneys, leading to increased urine production to rid the body of excess fluids. KUPO:0001053 + https://cellxgene.cziscience.com/cellguide/CL_1001021 kidney loop of Henle descending limb epithelial cell @@ -101283,6 +103527,18 @@ Moreover, the glomerular capillary endothelial cells are also believed to play a Any kidney loop of Henle epithelial cell that is part of some descending limb of loop of Henle. FBC:Autogenerated + + + + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +The kidney loop of Henle descending limb epithelial cells are highly specialized cells that play a crucial role in maintaining the body's salt and water balance. These cells line the descending limb of the loop of Henle, which is a portion of the renal tubule located in the kidneys, an organ responsible for filtering waste products, ions and extra water from the blood and converting them into urine. However, the descending limb epithelial cells are specifically involved in the countercurrent multiplication system, a mechanism to concentrate urine that involves both active and passive transport processes. +These cells are notably permeable to water but relatively impermeable to solutes, a characteristic that dramatically influences the osmotic gradient in the renal medulla. As filtrate initially descends down the loop of Henle, water gets drawn out due to the increasing osmotic gradient, thereby concentrating the filtrate. Additionally, these epithelial cells are exceptionally thin walled, allowing water to freely diffuse across the membrane. +Furthermore, the kidney loop of Henle descending limb epithelial cells are inextricably linked to the functioning of numerous diuretic drugs, which work by blocking the reabsorption of water and certain electrolytes in the kidneys, leading to increased urine production to rid the body of excess fluids. + DOI:10.1007/s00360-018-1164-3 + DOI:10.1146/annurev-physiol-021113-170350 + DOI:10.1152/advan.00227.2022 + @@ -101345,7 +103601,6 @@ Moreover, the glomerular capillary endothelial cells are also believed to play a - @@ -101506,7 +103761,7 @@ Moreover, the glomerular capillary endothelial cells are also believed to play a An endothelial cell that lines the interior surface of the afferent arteriole and maintains vascular tone. This cell responds to changing ion concentrations and blood pressure by releasing vasoactive substances, in order to regulate blood flow into the glomeruli, which is essential for glomerular filtration. - This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. Kidney afferent arteriole endothelial cells are a specialized type of cell located within the kidneys, forming the inner lining of the afferent arterioles, which are responsible for delivering blood to the glomeruli - capillary networks responsible for filtration - from where the process of urine formation begins in the nephrons. The endothelial cells in the kidney afferent arterioles have a key function in regulating the blood flow and filtration. They have autocrine and paracrine signaling capabilities, meaning they can signal to themselves and other nearby cells. They produce nitric oxide, prostacyclin, and endothelin, which are powerful vasodilators and vasoconstrictors that regulate renal blood flow. These cells also engage in the mitigation of kidney injury and inflammation by promoting repair and regeneration, demonstrating the multifaceted roles these cells play in maintaining renal health. @@ -101528,7 +103783,7 @@ The endothelial cells in the kidney afferent arterioles have a key function in r - This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. Kidney afferent arteriole endothelial cells are a specialized type of cell located within the kidneys, forming the inner lining of the afferent arterioles, which are responsible for delivering blood to the glomeruli - capillary networks responsible for filtration - from where the process of urine formation begins in the nephrons. The endothelial cells in the kidney afferent arterioles have a key function in regulating the blood flow and filtration. They have autocrine and paracrine signaling capabilities, meaning they can signal to themselves and other nearby cells. They produce nitric oxide, prostacyclin, and endothelin, which are powerful vasodilators and vasoconstrictors that regulate renal blood flow. These cells also engage in the mitigation of kidney injury and inflammation by promoting repair and regeneration, demonstrating the multifaceted roles these cells play in maintaining renal health. @@ -101589,7 +103844,7 @@ The endothelial cells in the kidney afferent arterioles have a key function in r Any endothelial cell that is part of some renal efferent arteriole. - This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. Kidney efferent arteriole endothelial cells constitute a vital component of the kidney's microvascular system. They are unique endothelial cells found lining the walls of efferent arterioles, which transport blood away from the glomeruli in the kidney. The primary responsibilities of the kidney efferent arteriole endothelial cells involve controling renal blood flow, regulating glomerular filtration rate (GFR), and managing perfusion pressure. They do this by contracting and relaxing, effectively narrowing and widening the arteriole's lumen thereby controling the volume and rate of blood flow to the peritubular capillaries and creating the pressure gradient necessary for filtration in the glomerulus. @@ -101609,7 +103864,7 @@ Furthermore, kidney efferent arteriole endothelial cells show a high degree of p - This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. Kidney efferent arteriole endothelial cells constitute a vital component of the kidney's microvascular system. They are unique endothelial cells found lining the walls of efferent arterioles, which transport blood away from the glomeruli in the kidney. The primary responsibilities of the kidney efferent arteriole endothelial cells involve controling renal blood flow, regulating glomerular filtration rate (GFR), and managing perfusion pressure. They do this by contracting and relaxing, effectively narrowing and widening the arteriole's lumen thereby controling the volume and rate of blood flow to the peritubular capillaries and creating the pressure gradient necessary for filtration in the glomerulus. @@ -101915,7 +104170,6 @@ Furthermore, kidney efferent arteriole endothelial cells show a high degree of p - @@ -101963,7 +104217,6 @@ Furthermore, kidney efferent arteriole endothelial cells show a high degree of p - @@ -102019,7 +104272,7 @@ Furthermore, kidney efferent arteriole endothelial cells show a high degree of p A cell that is part of some vasa recta ascending limb. - This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. The vasa recta ascending limb cells are specialized epithelial cells that are part of the vasa recta in the kidney, a crucial component of the renal medulla that functions as a counter-current exchanger to maintain the concentration gradient required for water reabsorption. These particular cells are located in the ascending limb of the vasa recta, which takes blood flow from the medulla back to the cortex. The primary function of vasa recta ascending limb cells is to preserve the renal medulla's hypertonicity, necessary for the kidney's urine concentration mechanism. Unlike the vasa recta descending limb cells, the venous-like epithelial cells of the ascending vasa recta are highly fenestrated and lack pericyte coverage, which facilitates water reuptake. @@ -102041,7 +104294,7 @@ In the context of normal physiological processes, the function of the vasa recta - This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. The vasa recta ascending limb cells are specialized epithelial cells that are part of the vasa recta in the kidney, a crucial component of the renal medulla that functions as a counter-current exchanger to maintain the concentration gradient required for water reabsorption. These particular cells are located in the ascending limb of the vasa recta, which takes blood flow from the medulla back to the cortex. The primary function of vasa recta ascending limb cells is to preserve the renal medulla's hypertonicity, necessary for the kidney's urine concentration mechanism. Unlike the vasa recta descending limb cells, the venous-like epithelial cells of the ascending vasa recta are highly fenestrated and lack pericyte coverage, which facilitates water reuptake. @@ -102246,7 +104499,7 @@ In the context of normal physiological processes, the function of the vasa recta - Any vasa recta ascending limb cell that is part of some inner medulla vasa recta ascending limb. + Any vasa recta ascending limb cell that is part of some inner medulla ascending vasa recta. KUPO:0001075 inner medulla vasa recta ascending limb cell @@ -102265,7 +104518,7 @@ In the context of normal physiological processes, the function of the vasa recta - Any vasa recta ascending limb cell that is part of some inner medulla vasa recta ascending limb. + Any vasa recta ascending limb cell that is part of some inner medulla ascending vasa recta. FBC:Autogenerated @@ -102293,7 +104546,7 @@ In the context of normal physiological processes, the function of the vasa recta - Any vasa recta ascending limb cell that is part of some outer medulla vasa recta ascending limb. + Any vasa recta ascending limb cell that is part of some outer medulla ascending vasa recta. KUPO:0001076 outer medulla vasa recta ascending limb cell @@ -102312,7 +104565,7 @@ In the context of normal physiological processes, the function of the vasa recta - Any vasa recta ascending limb cell that is part of some outer medulla vasa recta ascending limb. + Any vasa recta ascending limb cell that is part of some outer medulla ascending vasa recta. FBC:Autogenerated @@ -102603,7 +104856,7 @@ In the context of normal physiological processes, the function of the vasa recta A cell that is part of some vasa recta descending limb. - This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. Vasa recta descending limb cells are specialized epithelial cells found in the vasa recta, a network of blood vessels in the renal medulla. These cells line the interior surface of the descending limb of the vasa recta and play a crucial role in the filtering and regulation of substances within the blood. In contrast to vasa recta ascending limb cells, the arterial-like epithelial cells of the descending vasa recta are non-fenestrated and covered by a pericyte layer that regulates the medullary blood flow. They help keeping the body’s fluid and electrolyte balance in check through a process known as countercurrent exchange system, in which the cells of the descending limb are permeable to water but relatively impermeable to solutes, such as sodium and urea. As the blood descends into the medulla along its descending limb, water passively diffuses out of the vasa recta, concentrating the blood in solutes. @@ -102624,7 +104877,7 @@ In addition to their central role in water and solute exchange, these cells cont - This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. Vasa recta descending limb cells are specialized epithelial cells found in the vasa recta, a network of blood vessels in the renal medulla. These cells line the interior surface of the descending limb of the vasa recta and play a crucial role in the filtering and regulation of substances within the blood. In contrast to vasa recta ascending limb cells, the arterial-like epithelial cells of the descending vasa recta are non-fenestrated and covered by a pericyte layer that regulates the medullary blood flow. They help keeping the body’s fluid and electrolyte balance in check through a process known as countercurrent exchange system, in which the cells of the descending limb are permeable to water but relatively impermeable to solutes, such as sodium and urea. As the blood descends into the medulla along its descending limb, water passively diffuses out of the vasa recta, concentrating the blood in solutes. @@ -102667,7 +104920,7 @@ In addition to their central role in water and solute exchange, these cells cont - Any vasa recta descending limb cell that is part of some inner medulla vasa recta descending limb. + Any vasa recta descending limb cell that is part of some inner medulla descending vasa recta. KUPO:0001072 inner medulla vasa recta descending limb cell @@ -102686,7 +104939,7 @@ In addition to their central role in water and solute exchange, these cells cont - Any vasa recta descending limb cell that is part of some inner medulla vasa recta descending limb. + Any vasa recta descending limb cell that is part of some inner medulla descending vasa recta. FBC:Autogenerated @@ -102714,7 +104967,7 @@ In addition to their central role in water and solute exchange, these cells cont - Any vasa recta descending limb cell that is part of some outer medulla vasa recta descending limb. + Any vasa recta descending limb cell that is part of some outer medulla descending vasa recta. KUPO:0001073 outer medulla vasa recta descending limb cell @@ -102733,7 +104986,7 @@ In addition to their central role in water and solute exchange, these cells cont - Any vasa recta descending limb cell that is part of some outer medulla vasa recta descending limb. + Any vasa recta descending limb cell that is part of some outer medulla descending vasa recta. FBC:Autogenerated @@ -102866,8 +105119,15 @@ In addition to their central role in water and solute exchange, these cells cont A urothelial cell that is part of the urothelium of the urinary bladder. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Bladder urothelial cells form the urothelium in the bladder - a specific type of epithelial tissue that constitutes the inner lining of the bladder and other parts of the urinary tract including the renal pelvis, ureters and urethra. These unique cells are specialized to withstand the highly variable and sometimes harsh conditions present in the urinary system. Their key function is maintaining the barrier integrity of the urinary tract even when exposed to high volumes of urine and its solutes, and they play a crucial role in protecting underlying tissues from damage and infection. +The bladder urothelial cells exhibit a remarkable spectrum of phenotypic versatility and have an extraordinary capacity to stretch and retract based on the degree of bladder filling and emptying. In their relaxed state, these cells appear large and cuboidal, but upon stretching, they become thinner and exhibit a squamous cell-like appearance. This distinctive feature enables them to adjust to the changes in the urinary bladder volume while remaining impermeable to urinary solutes, thereby preventing a potential toxicity to the bladder wall and infiltration into the bloodstream. +Apart from their barrier function, bladder urothelial cells also express a number of sensor molecules or respond to thermal, mechanical and chemical stimuli and can release signaling molecules, thereby playing a key role in sensory mechanisms that communicate vital information about the bladder's mechanical state to the nervous system. This communication helps regulate the micturition cycle and maintain urinary continence. Recent studies have also indicated that these cells may play a role in immune responses, highlighting their importance in bladder physiology. +Altered proliferation and differentiation of bladder urothelial cells are implicated in various diseases and conditions such as bladder cancer, interstitial cystitis, and urinary tract infections. KUPO:0001121 NCIT:C32210 + https://cellxgene.cziscience.com/cellguide/CL_1001428 bladder transitional cell transitional epithelial cell of urinary bladder @@ -102880,6 +105140,21 @@ In addition to their central role in water and solute exchange, these cells cont A urothelial cell that is part of the urothelium of the urinary bladder. doi:10.1038/s41385-022-00565-0 + + + + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Bladder urothelial cells form the urothelium in the bladder - a specific type of epithelial tissue that constitutes the inner lining of the bladder and other parts of the urinary tract including the renal pelvis, ureters and urethra. These unique cells are specialized to withstand the highly variable and sometimes harsh conditions present in the urinary system. Their key function is maintaining the barrier integrity of the urinary tract even when exposed to high volumes of urine and its solutes, and they play a crucial role in protecting underlying tissues from damage and infection. +The bladder urothelial cells exhibit a remarkable spectrum of phenotypic versatility and have an extraordinary capacity to stretch and retract based on the degree of bladder filling and emptying. In their relaxed state, these cells appear large and cuboidal, but upon stretching, they become thinner and exhibit a squamous cell-like appearance. This distinctive feature enables them to adjust to the changes in the urinary bladder volume while remaining impermeable to urinary solutes, thereby preventing a potential toxicity to the bladder wall and infiltration into the bloodstream. +Apart from their barrier function, bladder urothelial cells also express a number of sensor molecules or respond to thermal, mechanical and chemical stimuli and can release signaling molecules, thereby playing a key role in sensory mechanisms that communicate vital information about the bladder's mechanical state to the nervous system. This communication helps regulate the micturition cycle and maintain urinary continence. Recent studies have also indicated that these cells may play a role in immune responses, highlighting their importance in bladder physiology. +Altered proliferation and differentiation of bladder urothelial cells are implicated in various diseases and conditions such as bladder cancer, interstitial cystitis, and urinary tract infections. + DOI:10.1038/nrurol.2011.144 + DOI:10.1038/nrurol.2016.13 + DOI:10.1038/s41579-020-0324-0 + DOI:10.1038/s41585-020-0350-8 + DOI:10.1080/03008880410015165 + @@ -102905,22 +105180,36 @@ In addition to their central role in water and solute exchange, these cells cont - Any urothelial cell that is part of some urethra urothelium. + A urothelial cell that is part of the urethra urothelium. This cell plays a crucial role in maintaining the urethral barrier function, protecting against toxic substances in urine, sensing environmental changes, and defending against pathogen entry. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Urethra urothelial cells are highly specialized epithelial cells in the urethra, which is a tubelike structure that carries urine from the bladder to the external urethral orifice. Urothelial cells form the urothelium – a stratified, transitional epithelium lining the bladder, ureters, renal pelvis and urethra. These cells are highly adapted to their specific environment and maintain the crucial function of sustaining the urinary tract's core roles, primarily to transit and store urine without auto-corrosion or pathogen proliferation. +Within the urethra urothelial cells are primarily found in proximal two-thirds of the urethra, while the distal third is lined by stratified squamous epithelial cells. The urothelial cells are renowned for their remarkable impermeability and ability to stretch and recoil during the various stages of urine filling and emptying. They form a tight barrier that prevents reabsorption of harmful byproducts and toxic substances present in the urine, guarding the deeper tissues and bloodstream against potential damage. This is largely attributed to specialized junctions, namely zonulae occludentes or tight junctions, in the umbrella cell layer (one of three layers of the urothelium) that seal the intercellular space between adjacent cells. Together with the urothelial plaque (an apical membrane plaque comprised of uroplakin proteins covering the umbrella cells at the luminal surface), the junctional complexes form a very effective permeability barrier that regulates the passage of water and ion from urine to the underlying tissue. +A noteworthy feature of urothelial cells is their regulatory and sensory roles involving communication with the underlying layers about the filling and emptying status of the urinary tract. The cells also manage a fine balance between proliferation and differentiation, with the basal cells providing a ready pool of cells to replace the superficial layer when damaged. Their remarkable ability for regeneration and turnover, and their response to signals for repair underpins the durability and functionality of the urothelial tract. KUPO:0001124 + https://cellxgene.cziscience.com/cellguide/CL_1001430 urethra urothelial cell - - - true + + A urothelial cell that is part of the urethra urothelium. This cell plays a crucial role in maintaining the urethral barrier function, protecting against toxic substances in urine, sensing environmental changes, and defending against pathogen entry. + PMID:23589830 + PMID:36180582 - - Any urothelial cell that is part of some urethra urothelium. - FBC:Autogenerated + + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Urethra urothelial cells are highly specialized epithelial cells in the urethra, which is a tubelike structure that carries urine from the bladder to the external urethral orifice. Urothelial cells form the urothelium – a stratified, transitional epithelium lining the bladder, ureters, renal pelvis and urethra. These cells are highly adapted to their specific environment and maintain the crucial function of sustaining the urinary tract's core roles, primarily to transit and store urine without auto-corrosion or pathogen proliferation. +Within the urethra urothelial cells are primarily found in proximal two-thirds of the urethra, while the distal third is lined by stratified squamous epithelial cells. The urothelial cells are renowned for their remarkable impermeability and ability to stretch and recoil during the various stages of urine filling and emptying. They form a tight barrier that prevents reabsorption of harmful byproducts and toxic substances present in the urine, guarding the deeper tissues and bloodstream against potential damage. This is largely attributed to specialized junctions, namely zonulae occludentes or tight junctions, in the umbrella cell layer (one of three layers of the urothelium) that seal the intercellular space between adjacent cells. Together with the urothelial plaque (an apical membrane plaque comprised of uroplakin proteins covering the umbrella cells at the luminal surface), the junctional complexes form a very effective permeability barrier that regulates the passage of water and ion from urine to the underlying tissue. +A noteworthy feature of urothelial cells is their regulatory and sensory roles involving communication with the underlying layers about the filling and emptying status of the urinary tract. The cells also manage a fine balance between proliferation and differentiation, with the basal cells providing a ready pool of cells to replace the superficial layer when damaged. Their remarkable ability for regeneration and turnover, and their response to signals for repair underpins the durability and functionality of the urothelial tract. + DOI:10.1038/nrurol.2016.13 + DOI:10.1038/s41385-022-00565-0 + DOI:10.1152/physrev.00030.2012 + DOI:10.1152/physrev.00041.2019 @@ -102943,7 +105232,7 @@ In addition to their central role in water and solute exchange, these cells cont Any renal principal cell that is part of some collecting duct of renal tubule. - This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. The kidney collecting duct principal cell is a highly specialized type of cell found in the late distal convoluted tubule and collecting duct of the kidney's nephron. Principal cells are located at the final segments of the renal tubules, where they play a pivotal role in key homeostatic processes. One of their fundamental functions of kidney collecting duct principal cells is the regulation of water reabsorption, which is mediated by aquaporins (water channel proteins). Antidiuretic hormones, such as vasopressin, can stimulate the redistribution of these water channels from an intracellular pools to the apical plasma membrane of the principal cell; translocation of aquaporin (specifically, AQP2) is associated with an increase of osmotic water permeability. The water reabsorption affects the concentration of the final urine; these cells are therefore directly involved in the maintenance of the body's fluid balance. @@ -102969,7 +105258,7 @@ Kidney collecting duct principal cells also participate in sodium and potassium - This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. The kidney collecting duct principal cell is a highly specialized type of cell found in the late distal convoluted tubule and collecting duct of the kidney's nephron. Principal cells are located at the final segments of the renal tubules, where they play a pivotal role in key homeostatic processes. One of their fundamental functions of kidney collecting duct principal cells is the regulation of water reabsorption, which is mediated by aquaporins (water channel proteins). Antidiuretic hormones, such as vasopressin, can stimulate the redistribution of these water channels from an intracellular pools to the apical plasma membrane of the principal cell; translocation of aquaporin (specifically, AQP2) is associated with an increase of osmotic water permeability. The water reabsorption affects the concentration of the final urine; these cells are therefore directly involved in the maintenance of the body's fluid balance. @@ -103000,8 +105289,14 @@ Kidney collecting duct principal cells also participate in sodium and potassium Any renal intercalated cell that is part of some collecting duct of renal tubule. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +The kidney collecting duct intercalated cell, otherwise referred to simply as the intercalated cell, is a specialized epithelial cell type primarily found in the kidney's collecting duct system. It is among the main cells that line this final component of the nephron, crucial in the physiological system that maintains acid-base homeostasis. This unique cell type comes in mainly three subtypes as per the localization of their proton pumps: type A, type B, and non-A, non-B cells. Each subtype plays different roles in regulating acid-base balance and electrolyte homeostasis in the body under varying physiological conditions. +Type A intercalated cells reabsorb bicarbonate and secrete protons into urine, leading to the production of acidic urine. These cells are typically prevalent on the renal cortex and function particularly in states of metabolic acidosis or potassium depletion. On the other hand, type B intercalated cells secrete bicarbonate and reabsorb protons; thus, they are crucial in alkaline urine production and potassium conservation. These cells are essential to counter metabolic alkalosis or situations of potassium surplus. The non-A, non-B cells have the characteristic features of both type A and B cells, but play a prominent role under conditions of chronically elevated aldosterone and angiotensin II levels. +Through their differentiated roles, intercalated cells also facilitate the reabsorption of sodium and chloride ions, and water to maintain osmolarity. These cells' activity is finely regulated by hormonal signals like aldosterone, angiotensin II, vasopressin, and the parathyroid hormone. Intercalated cell activity can undergo a significant transformation under pathological conditions, and their dysregulation is associated with diseases such as distal renal tubular acidosis, hypertension, and chronic kidney disease. KUPO:0001129 http://en.wikipedia.org/wiki/Collecting_duct_system#Intercalated_cells + https://cellxgene.cziscience.com/cellguide/CL_1001432 kidney collecting duct intercalated cell @@ -103018,6 +105313,20 @@ Kidney collecting duct principal cells also participate in sodium and potassium Any renal intercalated cell that is part of some collecting duct of renal tubule. FBC:Autogenerated + + + + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +The kidney collecting duct intercalated cell, otherwise referred to simply as the intercalated cell, is a specialized epithelial cell type primarily found in the kidney's collecting duct system. It is among the main cells that line this final component of the nephron, crucial in the physiological system that maintains acid-base homeostasis. This unique cell type comes in mainly three subtypes as per the localization of their proton pumps: type A, type B, and non-A, non-B cells. Each subtype plays different roles in regulating acid-base balance and electrolyte homeostasis in the body under varying physiological conditions. +Type A intercalated cells reabsorb bicarbonate and secrete protons into urine, leading to the production of acidic urine. These cells are typically prevalent on the renal cortex and function particularly in states of metabolic acidosis or potassium depletion. On the other hand, type B intercalated cells secrete bicarbonate and reabsorb protons; thus, they are crucial in alkaline urine production and potassium conservation. These cells are essential to counter metabolic alkalosis or situations of potassium surplus. The non-A, non-B cells have the characteristic features of both type A and B cells, but play a prominent role under conditions of chronically elevated aldosterone and angiotensin II levels. +Through their differentiated roles, intercalated cells also facilitate the reabsorption of sodium and chloride ions, and water to maintain osmolarity. These cells' activity is finely regulated by hormonal signals like aldosterone, angiotensin II, vasopressin, and the parathyroid hormone. Intercalated cell activity can undergo a significant transformation under pathological conditions, and their dysregulation is associated with diseases such as distal renal tubular acidosis, hypertension, and chronic kidney disease. + DOI:10.1007/978-3-211-99390-3_106 + DOI:10.1152/physiol.00008.2011 + DOI:10.1152/physrev.00011.2019 + DOI:10.2215/CJN.08880914 + DOI:10.3390/diseases2020071 + @@ -103073,9 +105382,9 @@ Kidney collecting duct principal cells also participate in sodium and potassium - + - + @@ -103200,6 +105509,7 @@ Kidney collecting duct principal cells also participate in sodium and potassium + @@ -103215,6 +105525,7 @@ Kidney collecting duct principal cells also participate in sodium and potassium A sensory neuron of the dorsal root ganglia that senses body position and sends information about how much the muscle is stretched to the spinal cord. proprioceptive neuron + sensory neuron of dorsal root ganglion @@ -103313,11 +105624,10 @@ Kidney collecting duct principal cells also participate in sodium and potassium - - + - + @@ -103422,14 +105732,26 @@ Kidney collecting duct principal cells also participate in sodium and potassium - + + + + + + + The various hormone- or neurotransmitter-secreting cells present throughout the mucosa of the intestinal tract. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Intestinal enteroendocrine cells are a highly specialized cell type found within the gastrointestinal epithelium. They account for approximately 1% of the intestinal epithelial cells in what is known as the largest endocrine organ in the human body. Intestinal enteroendocrine cells exhibit an exceptional diversity, both in terms of their secretory products and their distribution along the intestines, varying from the small intestine to the colon. +The primary function of intestinal enteroendocrine cells is to maintain gut physiology and homeostasis. They are known for their hormone production and are the source of numerous bioactive molecules including somatostatin, serotonin, cholecystokinin, glucose-dependent insulinotropic peptide, motilin, neurotensin, and others. These hormones and neuropeptides act in autocrine, paracrine, or endocrine signaling, impacting various functions including intestinal motility, secretion, nutrient absorption, and gut barrier functions. +Intestinal enteroendocrine cells also serve as the body's frontline of defense, playing an integral role in surveillance against lumen-occurring hazards including pathogen attack. Enteroendocrine cells are divided into ‘closed type’ and ‘open type’. Closed type cells are located close to the basal membrane and do not reach the lumen of the gut. In contrast, the apical side of the open-type intestinal enteroendocrine cells is directly exposed to luminal contents and thus can recognize bacterial metabolites and dietary nutrients. In response, these cells can modulate the immune system responses and thereby function as a key communicator between the gut microbiota and the host. + https://cellxgene.cziscience.com/cellguide/CL_1001516 intestinal enteroendocrine cell @@ -103439,6 +105761,20 @@ Kidney collecting duct principal cells also participate in sodium and potassium The various hormone- or neurotransmitter-secreting cells present throughout the mucosa of the intestinal tract. MP:0010802 + + + + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Intestinal enteroendocrine cells are a highly specialized cell type found within the gastrointestinal epithelium. They account for approximately 1% of the intestinal epithelial cells in what is known as the largest endocrine organ in the human body. Intestinal enteroendocrine cells exhibit an exceptional diversity, both in terms of their secretory products and their distribution along the intestines, varying from the small intestine to the colon. +The primary function of intestinal enteroendocrine cells is to maintain gut physiology and homeostasis. They are known for their hormone production and are the source of numerous bioactive molecules including somatostatin, serotonin, cholecystokinin, glucose-dependent insulinotropic peptide, motilin, neurotensin, and others. These hormones and neuropeptides act in autocrine, paracrine, or endocrine signaling, impacting various functions including intestinal motility, secretion, nutrient absorption, and gut barrier functions. +Intestinal enteroendocrine cells also serve as the body's frontline of defense, playing an integral role in surveillance against lumen-occurring hazards including pathogen attack. Enteroendocrine cells are divided into ‘closed type’ and ‘open type’. Closed type cells are located close to the basal membrane and do not reach the lumen of the gut. In contrast, the apical side of the open-type intestinal enteroendocrine cells is directly exposed to luminal contents and thus can recognize bacterial metabolites and dietary nutrients. In response, these cells can modulate the immune system responses and thereby function as a key communicator between the gut microbiota and the host. + DOI:10.1016/j.coph.2013.09.008 + DOI:10.1038/mi.2017.73 + DOI:10.1038/s41574-019-0168-8 + DOI:10.1111/j.1365-2613.2011.00767.x + DOI:10.1146/annurev-physiol-021115-105439 + @@ -103451,19 +105787,13 @@ Kidney collecting duct principal cells also participate in sodium and potassium - + - - - - - - - + The various hormone- or neurotransmitter-secreting cells present throughout the mucosa of the stomach. stomach enteroendocrine cell @@ -103562,6 +105892,7 @@ Kidney collecting duct principal cells also participate in sodium and potassium Any endothelial cell of vascular tree that is part of some lung. endothelial cell of lung pulmonary vessel endothelial cell + lung endothelial cell @@ -104202,7 +106533,7 @@ Kidney collecting duct principal cells also participate in sodium and potassium - + @@ -104283,12 +106614,6 @@ Kidney collecting duct principal cells also participate in sodium and potassium - - - - - - Glandular cell of appendix epithelium. Example: Goblet cells; enterocytes or absorptive cells; enteroendocrine and M cells. CALOHA:TS-1271 appendix glandular cells @@ -104394,7 +106719,7 @@ Kidney collecting duct principal cells also participate in sodium and potassium - + @@ -104409,7 +106734,8 @@ Kidney collecting duct principal cells also participate in sodium and potassium cervix glandular cell cervix, uterine glandular cell cervix, uterine glandular cells - uterine cervix glandular cell + uterine cervix glandular cell + uterine cervix secretory cell @@ -104480,7 +106806,7 @@ Kidney collecting duct principal cells also participate in sodium and potassium - + @@ -104497,9 +106823,9 @@ Kidney collecting duct principal cells also participate in sodium and potassium Glandular cell of duodenal epithelium. Example: Enterocytes, Goblet cells, enteroendocrine cells; Paneth cells; M cells; Brunner's gland cell. CALOHA:TS-1275 - duodenum glandular cells + duodenum glandular cells - duodenum glandular cell + duodenum secretory cell @@ -104509,7 +106835,7 @@ Kidney collecting duct principal cells also participate in sodium and potassium - + duodenum glandular cells CALOHA:TS-1275 @@ -104522,7 +106848,7 @@ Kidney collecting duct principal cells also participate in sodium and potassium - + @@ -104531,7 +106857,7 @@ Kidney collecting duct principal cells also participate in sodium and potassium - + @@ -104541,8 +106867,8 @@ Kidney collecting duct principal cells also participate in sodium and potassium Glandular cell of epididymal epithelium. CALOHA:TS-1276 epididymal glandular cell - epididymis glandular cells - epididymis glandular cell + epididymis glandular cell + epididymis secretory cell @@ -104559,7 +106885,7 @@ Kidney collecting duct principal cells also participate in sodium and potassium - epididymis glandular cells + epididymis glandular cell CALOHA:TS-1276 @@ -104571,7 +106897,7 @@ Kidney collecting duct principal cells also participate in sodium and potassium - + @@ -104579,7 +106905,7 @@ Kidney collecting duct principal cells also participate in sodium and potassium - + @@ -104590,8 +106916,9 @@ Kidney collecting duct principal cells also participate in sodium and potassium CALOHA:TS-1277 fallopian tube glandular cell fallopian tube glandular cells + oviduct glandular cell uterine tube glandular cell - oviduct glandular cell + oviduct secretory cell @@ -104692,13 +107019,8 @@ Kidney collecting duct principal cells also participate in sodium and potassium - - - - - - - Glandular cell of parathyroid epithelium. Example: Parathyroid chief cell and parathyroid oxyphil cells. + + Glandular (secretory) cell of parathyroid epithelium. CALOHA:TS-1279 parathyroid gland glandular cell parathyroid gland glandular cells @@ -104707,7 +107029,7 @@ Kidney collecting duct principal cells also participate in sodium and potassium - Glandular cell of parathyroid epithelium. Example: Parathyroid chief cell and parathyroid oxyphil cells. + Glandular (secretory) cell of parathyroid epithelium. HPA:HPA NPX:PDR @@ -104842,7 +107164,7 @@ Kidney collecting duct principal cells also participate in sodium and potassium Glandular cell of seminal vesicle epithelium. - This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. Seminal vesicle glandular cells belong to a specialized group of epithelial cells that form the internal lining of the seminal vesicles, a pair of male reproductive organs. These cells are located within the complex tubuloalveolar glands that make up the seminal vesicles and are known for their unique pseudostratified columnar epithelium structure. The primary function of these cells is the secretion of a variety of substances that ultimately constitute around 70% of the fluid volume of semen. Seminal cells produce a high-fructose fluid that serves as an energy source for the spermatozoa and promotes their motility. They also secrete other essential substances like proteins, enzymes, vitamin C, prostaglandins, and various other compounds. Collectively, these substances help in the nourishment, protection, and transportation of the spermatozoa throughout the male reproductive system and during the ejaculation process. @@ -104862,7 +107184,7 @@ Secondary to the production of seminal fluid, the seminal vesicle glandular cell - This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. Seminal vesicle glandular cells belong to a specialized group of epithelial cells that form the internal lining of the seminal vesicles, a pair of male reproductive organs. These cells are located within the complex tubuloalveolar glands that make up the seminal vesicles and are known for their unique pseudostratified columnar epithelium structure. The primary function of these cells is the secretion of a variety of substances that ultimately constitute around 70% of the fluid volume of semen. Seminal cells produce a high-fructose fluid that serves as an energy source for the spermatozoa and promotes their motility. They also secrete other essential substances like proteins, enzymes, vitamin C, prostaglandins, and various other compounds. Collectively, these substances help in the nourishment, protection, and transportation of the spermatozoa throughout the male reproductive system and during the ejaculation process. @@ -104888,7 +107210,7 @@ Secondary to the production of seminal fluid, the seminal vesicle glandular cell - + @@ -104896,8 +107218,8 @@ Secondary to the production of seminal fluid, the seminal vesicle glandular cell - + @@ -104907,10 +107229,10 @@ Secondary to the production of seminal fluid, the seminal vesicle glandular cell A glandular cell found in the epithelium of the small intestine. Example: Enterocytes, Goblet cells, enteroendocrine cells; Paneth cells; M cells; Somatostatin-secreting Cells (D-cells) . CALOHA:TS-1286 FMA:86928 + small intestinal glandular cell small bowel glandular cell - small intestinal glandular cell small intestine glandular cells - small intestine glandular cell + small intestine secretory cell @@ -104921,14 +107243,14 @@ Secondary to the production of seminal fluid, the seminal vesicle glandular cell - - small bowel glandular cell + + small intestinal glandular cell CALOHA:TS-1286 - small intestinal glandular cell + small bowel glandular cell CALOHA:TS-1286 @@ -105078,7 +107400,13 @@ Secondary to the production of seminal fluid, the seminal vesicle glandular cell A distinct endothelial cell forming the walls of the capillaries within the cerebral cortex. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Cerebral cortex endothelial cells are unique endothelial cells responsible for the formation and regulation of the blood-brain barrier (BBB), a specialized structure that separates the circulating blood from the cerebral neural tissue. These cells line the inner surface of nearly all blood vessels that irrigate the cerebral cortex, the outermost layer of the brain involved with complex cognitive functions such as thought, perception, and memory formation. Cerebral cortex endothelial cells are integral to maintaining brain health and function due to their role in regulating brain microenvironment and controlling the passage of essential molecules and cells. +The endothelial cells in the cerebral cortex are distinctive due to their highly selective permeability, largely attributable to the existence of unique tight junctions which maintain the barrier function of the BBB. The tightly interconnected structures of these cells prevent most substances from freely diffusing into the brain tissue, ensuring that harmful agents such as toxins, pathogens, or peripheral immune cells don't reach the brain and compromise its function. These cells also express multiple transporters and enzymes, allowing the selective entry of necessary nutrients and metabolites while excluding toxic substances. +Cerebral cortex endothelial cells also participate in neurovascular coupling, a process where localized neuronal activity increases cerebral blood flow to satisfy the local metabolic demands. The endothelial cells work in coordination with neurons and other cell types such as astrocytes and pericytes to mediate this process. They have been thought to regulate local blood flow by releasing substances in response to neuronal activity. Additionally, these cells are involved in many pathological conditions. Breakdown or dysfunction of the BBB often marked by altered endothelial cell function is linked to numerous neurological disorders including stroke, multiple sclerosis, Alzheimer’s disease, and brain tumors. CALOHA:TS-2372 + https://cellxgene.cziscience.com/cellguide/CL_1001602 cerebral cortex endothelial cells endothelial cells of cerebral cortex @@ -105090,6 +107418,20 @@ Secondary to the production of seminal fluid, the seminal vesicle glandular cell A distinct endothelial cell forming the walls of the capillaries within the cerebral cortex. NPX:PDR + + + + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Cerebral cortex endothelial cells are unique endothelial cells responsible for the formation and regulation of the blood-brain barrier (BBB), a specialized structure that separates the circulating blood from the cerebral neural tissue. These cells line the inner surface of nearly all blood vessels that irrigate the cerebral cortex, the outermost layer of the brain involved with complex cognitive functions such as thought, perception, and memory formation. Cerebral cortex endothelial cells are integral to maintaining brain health and function due to their role in regulating brain microenvironment and controlling the passage of essential molecules and cells. +The endothelial cells in the cerebral cortex are distinctive due to their highly selective permeability, largely attributable to the existence of unique tight junctions which maintain the barrier function of the BBB. The tightly interconnected structures of these cells prevent most substances from freely diffusing into the brain tissue, ensuring that harmful agents such as toxins, pathogens, or peripheral immune cells don't reach the brain and compromise its function. These cells also express multiple transporters and enzymes, allowing the selective entry of necessary nutrients and metabolites while excluding toxic substances. +Cerebral cortex endothelial cells also participate in neurovascular coupling, a process where localized neuronal activity increases cerebral blood flow to satisfy the local metabolic demands. The endothelial cells work in coordination with neurons and other cell types such as astrocytes and pericytes to mediate this process. They have been thought to regulate local blood flow by releasing substances in response to neuronal activity. Additionally, these cells are involved in many pathological conditions. Breakdown or dysfunction of the BBB often marked by altered endothelial cell function is linked to numerous neurological disorders including stroke, multiple sclerosis, Alzheimer’s disease, and brain tumors. + DOI:10.1038/nbt.2247 + DOI:10.1038/nrn1824 + DOI:10.1177/0271678X156179 + DOI:10.1186/s12987-020-00230-3 + DOI:10.3389/fnins.2023.1047778 + @@ -105127,7 +107469,13 @@ Secondary to the production of seminal fluid, the seminal vesicle glandular cell Circulating macrophages and tissue macrophages (alveolar macrophages) of lung. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Lung macrophages refer to macrophage populations in the lungs, including the tissue-resident alveolar macrophages and interstitial macrophages, located in the air spaces and the connective tissue of the lung, respectively, and recruited macrophages. They are important in maintaining tissue homeostasis and immunity. +The primary function of lung macrophages is to patrol and maintain the pulmonary system, where they serve as the first line of defense against airborne pathogens and inhaled particles. They perform phagocytosis of pathogens, particulate matter, dead cells, and other cellular debris from the lungs to maintain clear air passages and optimize gas exchange. They may also participate in tissue repair and the resolution of inflammation following injury. +Lung macrophages also play a critical role in immune regulation. They help to initiate an immune response by secreting cytokines and other inflammatory mediators and by presenting antigens from the pathogens they have engulfed to induce T cell responses. However, if activated improperly, lung macrophages can contribute to inflammatory diseases of the lung such as chronic obstructive pulmonary disease (COPD) or asthma. CALOHA:TS-0576 + https://cellxgene.cziscience.com/cellguide/CL_1001603 lung macrophages lung macrophage @@ -105139,6 +107487,20 @@ Secondary to the production of seminal fluid, the seminal vesicle glandular cell HPA:HPA NPX:PDR + + + + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Lung macrophages refer to macrophage populations in the lungs, including the tissue-resident alveolar macrophages and interstitial macrophages, located in the air spaces and the connective tissue of the lung, respectively, and recruited macrophages. They are important in maintaining tissue homeostasis and immunity. +The primary function of lung macrophages is to patrol and maintain the pulmonary system, where they serve as the first line of defense against airborne pathogens and inhaled particles. They perform phagocytosis of pathogens, particulate matter, dead cells, and other cellular debris from the lungs to maintain clear air passages and optimize gas exchange. They may also participate in tissue repair and the resolution of inflammation following injury. +Lung macrophages also play a critical role in immune regulation. They help to initiate an immune response by secreting cytokines and other inflammatory mediators and by presenting antigens from the pathogens they have engulfed to induce T cell responses. However, if activated improperly, lung macrophages can contribute to inflammatory diseases of the lung such as chronic obstructive pulmonary disease (COPD) or asthma. + DOI:10.1002/JLB.3RU0720-418R + DOI:10.1016/j.immuni.2022.08.010 + DOI:10.1189/jlb.70.2.163 + DOI:10.3389/fimmu.2021.753940/full + DOI:10.3390/cells10040897 + @@ -105378,6 +107740,33 @@ Secondary to the production of seminal fluid, the seminal vesicle glandular cell + + + + + + + + + + + + + + An epithelial cell that is specialised for the synthesis and secretion of specific biomolecules. + + 2024-07-21T09:24:44Z + secretory epithelial cell + + + + + An epithelial cell that is specialised for the synthesis and secretion of specific biomolecules. + + + + + @@ -105472,12 +107861,18 @@ Secondary to the production of seminal fluid, the seminal vesicle glandular cell A specialized, enlarged, connective tissue cell of the decidua with enlarged nucleus, dense membrane‐bound secretory granules and cytoplasmic accumulation of glycogen and lipid droplets. These cells develop by the transformation of endometrial stromal cells during decidualization. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Decidual cells, originating from the endometrial lining in the uterus, undergo significant transformations during pregnancy and are integral to its preparation and maintenance. Their conversion from endometrial fibroblast to a secretory phenotype, known as decidualization, occurs as a normal process in the menstrual cycle or in response to embryo implantation. +With crucial roles in regulating maternal immune responses and placental development, decidual cells have a twofold function: preventing rejection of the conceptus by the mother's immune system and guiding placental development to avoid excessive trophoblast invasion leading to pre-eclampsia. During decidualization, these cells secrete proteins and growth factors supporting embryo implantation and sustaining early pregnancy. Furthermore, decidual cells modulate the activities of natural killer cells, macrophages, and T cells in the uterus, maintaining a balance of pro-inflammatory and anti-inflammatory conditions during pregnancy. 2014-02-20T23:06:41Z BTO:0002770 BTO:0005756 NCIT:C32429 + https://cellxgene.cziscience.com/cellguide/CL_2000002 decidua cell decidual stromal cell + decidualized endometrial stromal cell CL:2000002 decidual cell @@ -105493,6 +107888,18 @@ Secondary to the production of seminal fluid, the seminal vesicle glandular cell Wiki:Decidual_cells&oldid=937509751 Wiki:Decidualization&oldid=908981933 + + + + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Decidual cells, originating from the endometrial lining in the uterus, undergo significant transformations during pregnancy and are integral to its preparation and maintenance. Their conversion from endometrial fibroblast to a secretory phenotype, known as decidualization, occurs as a normal process in the menstrual cycle or in response to embryo implantation. +With crucial roles in regulating maternal immune responses and placental development, decidual cells have a twofold function: preventing rejection of the conceptus by the mother's immune system and guiding placental development to avoid excessive trophoblast invasion leading to pre-eclampsia. During decidualization, these cells secrete proteins and growth factors supporting embryo implantation and sustaining early pregnancy. Furthermore, decidual cells modulate the activities of natural killer cells, macrophages, and T cells in the uterus, maintaining a balance of pro-inflammatory and anti-inflammatory conditions during pregnancy. + DOI:10.1002/rmb2.12088 + DOI:10.1093/humupd/dmw004 + DOI:10.1111/j.1749-6632.2010.05938.x + DOI:10.3390/ijms21114092 + @@ -105507,6 +107914,12 @@ Secondary to the production of seminal fluid, the seminal vesicle glandular cell BTO:0005756 PMID:11719592 + + + + decidualized endometrial stromal cell + PMID:31907034 + @@ -105681,6 +108094,7 @@ Secondary to the production of seminal fluid, the seminal vesicle glandular cell 2014-06-04T15:07:42Z CL:2000008 + microvascular endothelial cell @@ -105771,7 +108185,12 @@ Secondary to the production of seminal fluid, the seminal vesicle glandular cell Any endothelial cell of lymphatic vessel that is part of a dermis. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +A dermis lymphatic vessel endothelial cell is a specialized type of cell that lines the interior surface of lymphatic vessels present in the dermal layer of the skin. These cells are organized into a single layer, forming an integral part of the lymphatic system which acts as the body's secondary circulatory system. The primary function of dermis lymphatic vessel endothelial cells is to facilitate the transportation and regulation of the lymph fluid within the dermis. They act as a barrier, contributing to fluid homeostasis, lipid transport, and immune cell trafficking. These cells are uniquely equipped to let fluid and larger molecules, including proteins and immune cells, into the lymphatic vessels from the surrounding interstitial space. This is enabled by the specialized junctions between the endothelial cells and the presence of primary lymphatic valves that prevent the backflow of lymph. +Another paramount role of dermis lymphatic vessel endothelial cells is their involvement in immune response. By interacting with white blood cells, especially T-cells and dendritic cells, they can mediate local immune surveillance and contribute to both innate and adaptive immune responses. These cells are also implicated in a variety of pathological conditions, including lymphedema and metastasis in cancer. 2014-06-04T15:15:08Z + https://cellxgene.cziscience.com/cellguide/CL_2000011 CL:2000011 dermis lymphatic vessel endothelial cell @@ -105781,6 +108200,19 @@ Secondary to the production of seminal fluid, the seminal vesicle glandular cell Any endothelial cell of lymphatic vessel that is part of a dermis. GOC:TermGenie + + + + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +A dermis lymphatic vessel endothelial cell is a specialized type of cell that lines the interior surface of lymphatic vessels present in the dermal layer of the skin. These cells are organized into a single layer, forming an integral part of the lymphatic system which acts as the body's secondary circulatory system. The primary function of dermis lymphatic vessel endothelial cells is to facilitate the transportation and regulation of the lymph fluid within the dermis. They act as a barrier, contributing to fluid homeostasis, lipid transport, and immune cell trafficking. These cells are uniquely equipped to let fluid and larger molecules, including proteins and immune cells, into the lymphatic vessels from the surrounding interstitial space. This is enabled by the specialized junctions between the endothelial cells and the presence of primary lymphatic valves that prevent the backflow of lymph. +Another paramount role of dermis lymphatic vessel endothelial cells is their involvement in immune response. By interacting with white blood cells, especially T-cells and dendritic cells, they can mediate local immune surveillance and contribute to both innate and adaptive immune responses. These cells are also implicated in a variety of pathological conditions, including lymphedema and metastasis in cancer. + DOI:10.1038/s41423-023-01042-9 + DOI:10.1038/s41467-019-14127-9 + DOI:10.3389/fimmu.2023.1235812 + DOI:10.3389/fphys.2020.00509 + DOI:10.3389/fphys.2020.577584 + @@ -106136,7 +108568,13 @@ Secondary to the production of seminal fluid, the seminal vesicle glandular cell Any native cell that is part of a sebaceous gland. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Sebaceous gland cells, also known as sebocytes, are small, oil-producing glands present in the skin of mammals. These specialized cells are predominantly located in the dermis, particularly on the face, scalp, and upper body. +The primary function of sebaceous gland cells is the production and secretion of sebum, a complex mixture of lipids including triglycerides, wax esters, squalene, and metabolites of fat-soluble vitamins (such as vitamin E), as well as free fatty acids. The production process involves a unique form of programmed cell death called holocrine secretion. In this process, as sebaceous gland cells mature, they progressively accumulate lipid droplets, before ultimately disintegrating and releasing their lipid-rich contents into the gland's ductal system. +The sebum generated by these cells serves multiple purposes. It acts as a waterproofing agent, preventing excessive wetting or drying of the skin and averaging skin's water-holding capacity. Sebum also has antimicrobial properties, providing a natural defense barrier against certain bacterial and fungal species. Additionally, it contributes to the skin’s suppleness and prevents it from becoming brittle. An overproduction or imbalance of sebaceous gland cells can lead to common skin disorders, such as acne, seborrhea, or rosacea, illustrating their importance in skin health. 2014-06-24T23:17:00Z + https://cellxgene.cziscience.com/cellguide/CL_2000021 CL:2000021 sebaceous gland cell @@ -106147,6 +108585,20 @@ Secondary to the production of seminal fluid, the seminal vesicle glandular cell Any native cell that is part of a sebaceous gland. GOC:TermGenie + + + + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Sebaceous gland cells, also known as sebocytes, are small, oil-producing glands present in the skin of mammals. These specialized cells are predominantly located in the dermis, particularly on the face, scalp, and upper body. +The primary function of sebaceous gland cells is the production and secretion of sebum, a complex mixture of lipids including triglycerides, wax esters, squalene, and metabolites of fat-soluble vitamins (such as vitamin E), as well as free fatty acids. The production process involves a unique form of programmed cell death called holocrine secretion. In this process, as sebaceous gland cells mature, they progressively accumulate lipid droplets, before ultimately disintegrating and releasing their lipid-rich contents into the gland's ductal system. +The sebum generated by these cells serves multiple purposes. It acts as a waterproofing agent, preventing excessive wetting or drying of the skin and averaging skin's water-holding capacity. Sebum also has antimicrobial properties, providing a natural defense barrier against certain bacterial and fungal species. Additionally, it contributes to the skin’s suppleness and prevents it from becoming brittle. An overproduction or imbalance of sebaceous gland cells can lead to common skin disorders, such as acne, seborrhea, or rosacea, illustrating their importance in skin health. + DOI:10.1016/j.jid.2016.10.017 + DOI:10.1080/19381980.2017.1375636 + DOI:10.4161/derm.1.2.8472 + https://doi.org/10.2147/CLEP.S323744 + https://www.sciencedirect.com/topics/agricultural-and-biological-sciences/sebum + @@ -106328,7 +108780,6 @@ Secondary to the production of seminal fluid, the seminal vesicle glandular cell - Any basket cell that is part of a cerebellum. @@ -106437,6 +108888,7 @@ Secondary to the production of seminal fluid, the seminal vesicle glandular cell 2014-06-25T01:17:50Z CL:2000030 + hypothalamus cell @@ -106454,7 +108906,7 @@ Secondary to the production of seminal fluid, the seminal vesicle glandular cell - + @@ -106462,13 +108914,20 @@ Secondary to the production of seminal fluid, the seminal vesicle glandular cell - + + + + + + + + Any neuron that is part of a lateral line ganglion. 2014-06-25T01:17:57Z @@ -107018,7 +109477,13 @@ Secondary to the production of seminal fluid, the seminal vesicle glandular cell Any cardiac muscle cell that is part of a cardiac ventricle. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Ventricular cardiac muscle cells, or cardiomyocytes, are specialized cells found in the ventricular walls of the heart. They exhibit unique features, including centrally located nuclei, robust cytoskeletal structures, high mitochondria content, and intercalated discs, which contribute to their efficient pumping of blood throughout the body. +The main role of ventricular cardiac muscle cells is to coordinate contractions, enabling the heart to pump blood throughout the body. This is achieved through controlled ion movement across cell membranes, generating rhythmic electrical signals called action potentials. Intercalated discs between these cells aid synchronized contractions by allowing efficient signal spread through gap junctions. The high mitochondrial content ensures a constant energy supply for this ongoing contraction cycle. +Ventricular cardiac muscle cells contribute not only mechanically but also biochemically by secreting essential hormones like atrial natriuretic peptide and B-type natriuretic peptide for blood pressure regulation and cardiac remodeling. These cells exhibit low turnover under normal conditions, emphasizing their long-term stability, yet have limited regenerative capacity following cardiac injuries. Dysfunction in these cells can result in significant cardiac issues, including heart failure. 2014-08-12T20:50:28Z + https://cellxgene.cziscience.com/cellguide/CL_2000046 CL:2000046 ventricular cardiac muscle cell @@ -107029,6 +109494,19 @@ Secondary to the production of seminal fluid, the seminal vesicle glandular cell Any cardiac muscle cell that is part of a cardiac ventricle. GOC:TermGenie + + + + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Ventricular cardiac muscle cells, or cardiomyocytes, are specialized cells found in the ventricular walls of the heart. They exhibit unique features, including centrally located nuclei, robust cytoskeletal structures, high mitochondria content, and intercalated discs, which contribute to their efficient pumping of blood throughout the body. +The main role of ventricular cardiac muscle cells is to coordinate contractions, enabling the heart to pump blood throughout the body. This is achieved through controlled ion movement across cell membranes, generating rhythmic electrical signals called action potentials. Intercalated discs between these cells aid synchronized contractions by allowing efficient signal spread through gap junctions. The high mitochondrial content ensures a constant energy supply for this ongoing contraction cycle. +Ventricular cardiac muscle cells contribute not only mechanically but also biochemically by secreting essential hormones like atrial natriuretic peptide and B-type natriuretic peptide for blood pressure regulation and cardiac remodeling. These cells exhibit low turnover under normal conditions, emphasizing their long-term stability, yet have limited regenerative capacity following cardiac injuries. Dysfunction in these cells can result in significant cardiac issues, including heart failure. + DOI:10.1016/j.peptides.2018.05.012 + DOI:10.1126/science.aam5894 + https://www.ncbi.nlm.nih.gov/books/NBK535355 + https://www.ncbi.nlm.nih.gov/books/NBK572070/ + @@ -107058,6 +109536,7 @@ Secondary to the production of seminal fluid, the seminal vesicle glandular cell 2014-10-02T23:52:53Z CL:2000047 + brainstem motor neuron @@ -107072,14 +109551,9 @@ Secondary to the production of seminal fluid, the seminal vesicle glandular cell + - - - - - - A lower motor neuron whose soma is located in the anterior horn. Anterior horn motor neurons project from the anterior portion of the grey matter in the spinal cord to some skeletal muscles. 2014-10-03T00:26:27Z @@ -107272,15 +109746,10 @@ Secondary to the production of seminal fluid, the seminal vesicle glandular cell - - - - - - - + A large, granular, liver specific natural killer cell that adheres to the endothelial cells of the hepatic sinusoid. + Pit cells are named for the presence of large cytoplasmic granules that resemble pits (pips) of fruit. hepatic pit cell @@ -107489,9 +109958,15 @@ Secondary to the production of seminal fluid, the seminal vesicle glandular cell A trophoblast of placental villi. These cells fuse to form synctial trophoplast - the placental side of the interface between the placenta and maternal blood sinusoids in the decidua. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +The placental villous trophoblast, a highly specialized cell type crucial for placental development, plays a key role in facilitating exchanges between the maternal bloodstream and the developing fetus. +Structurally, placental villous trophoblasts are situated on the villous tree structures, forming an outer epithelial layer. Comprising two subtypes—proliferating cytotrophoblasts forming the inner layer and terminally differentiated syncytiotrophoblasts constituting the outer layer in contact with maternal blood—these cells define the placental architecture. +Functionally, placental villous trophoblasts play pivotal roles in forming and maintaining the placenta, ensuring the safe development of the fetus. Their primary function involves managing substance exchange between the mother and fetus, mediating the transfer of gases, nutrients, hormones, and waste materials to support optimal fetal growth. Additionally, these trophoblasts synthesize and release crucial hormones like human chorionic gonadotropin (hCG), which maintains the decidua and signals the mother's body to sustain pregnancy. Acting as a physical and immunological barrier, they protect the fetus from maternal immune cells and prevent the transmission of pathogens, contributing significantly to the success of pregnancy. 2014-10-07T17:48:27Z BTO:0006119 BTO:0006208 + https://cellxgene.cziscience.com/cellguide/CL_2000060 vCTB villous cytotrophoblast CL:2000060 @@ -107506,6 +109981,18 @@ Secondary to the production of seminal fluid, the seminal vesicle glandular cell A trophoblast of placental villi. These cells fuse to form synctial trophoplast - the placental side of the interface between the placenta and maternal blood sinusoids in the decidua. PMID:31049600 + + + + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +The placental villous trophoblast, a highly specialized cell type crucial for placental development, plays a key role in facilitating exchanges between the maternal bloodstream and the developing fetus. +Structurally, placental villous trophoblasts are situated on the villous tree structures, forming an outer epithelial layer. Comprising two subtypes—proliferating cytotrophoblasts forming the inner layer and terminally differentiated syncytiotrophoblasts constituting the outer layer in contact with maternal blood—these cells define the placental architecture. +Functionally, placental villous trophoblasts play pivotal roles in forming and maintaining the placenta, ensuring the safe development of the fetus. Their primary function involves managing substance exchange between the mother and fetus, mediating the transfer of gases, nutrients, hormones, and waste materials to support optimal fetal growth. Additionally, these trophoblasts synthesize and release crucial hormones like human chorionic gonadotropin (hCG), which maintains the decidua and signals the mother's body to sustain pregnancy. Acting as a physical and immunological barrier, they protect the fetus from maternal immune cells and prevent the transmission of pathogens, contributing significantly to the success of pregnancy. + DOI:10.1007/s00018-019-03104-6 + DOI:10.3389/fimmu.2020.00343 + DOI:10.3390/nu15163564 + @@ -107603,12 +110090,7 @@ Secondary to the production of seminal fluid, the seminal vesicle glandular cell - - - - - - + Any fibroblast that is part of a female gonad. 2014-10-07T17:57:42Z @@ -108377,6 +110859,7 @@ Secondary to the production of seminal fluid, the seminal vesicle glandular cell 2014-12-02T19:28:38Z CL:2000084 + conjunctiva goblet cell @@ -108594,7 +111077,6 @@ Secondary to the production of seminal fluid, the seminal vesicle glandular cell - Any stellate cell that is part of a dentate gyrus of hippocampal formation. @@ -108870,25 +111352,7 @@ Secondary to the production of seminal fluid, the seminal vesicle glandular cell - - - - - - - - - - - - - - - - - - A ciliated epithelial cell of the esophagus. 2019-02-09T16:40:30Z @@ -108908,18 +111372,13 @@ Secondary to the production of seminal fluid, the seminal vesicle glandular cell - - - - - - - - A tissue-resident macrophage that is part of the placenta. A Hofbauer cell expresses high levels of growth factors and metalloproteinases that support vasculogenesis, angiogenesis, branching morphogenesis and tissue remodeling. A Hofbauer cell has a fetal origin and is present throughout pregnancy. + + A tissue-resident macrophage that is part of the placenta. A Hofbauer cell expresses high levels of growth factors and metalloproteinases that support vasculogenesis, angiogenesis, branching morphogenesis and tissue remodeling. A Hofbauer cell has a fetal origin, is found in the villous stroma, chorion, and amnion, and is present throughout pregnancy. 2019-02-18T19:41:20Z + fetal Hofbauer cell HBC CL:3000001 @@ -108930,17 +111389,24 @@ Secondary to the production of seminal fluid, the seminal vesicle glandular cell - A tissue-resident macrophage that is part of the placenta. A Hofbauer cell expresses high levels of growth factors and metalloproteinases that support vasculogenesis, angiogenesis, branching morphogenesis and tissue remodeling. A Hofbauer cell has a fetal origin and is present throughout pregnancy. + A tissue-resident macrophage that is part of the placenta. A Hofbauer cell expresses high levels of growth factors and metalloproteinases that support vasculogenesis, angiogenesis, branching morphogenesis and tissue remodeling. A Hofbauer cell has a fetal origin, is found in the villous stroma, chorion, and amnion, and is present throughout pregnancy. GOC:CellBLAST PMID:30429548 PMID:30498493 PMID:34745147 PMID:35438172 + + + + fetal Hofbauer cell + PMID:39007150 + HBC + PMID:39007150 @@ -109034,18 +111500,30 @@ Secondary to the production of seminal fluid, the seminal vesicle glandular cell - Peripheral sensory neuron. + A neuron type that is located in a peripheral nervous system and it transmits sensory information from the peripheral (PNS) to the central nervous system (CNS). A sensory neuron converts physical (light, sound, touch) or chemical (such as taste and smell) stimuli into an electrical signal through a process known as sensory transduction. The function of a sensory neuron is to carry informations from the external environment and internal body conditions to the central nervous system for further processing. 2019-02-25T19:34:33Z CL:3000004 + Typically, a sensory neuron has a pseudounipolar morphology. peripheral sensory neuron - Peripheral sensory neuron. + A neuron type that is located in a peripheral nervous system and it transmits sensory information from the peripheral (PNS) to the central nervous system (CNS). A sensory neuron converts physical (light, sound, touch) or chemical (such as taste and smell) stimuli into an electrical signal through a process known as sensory transduction. The function of a sensory neuron is to carry informations from the external environment and internal body conditions to the central nervous system for further processing. GOC:CellBLAST PMID:30096314 + PMID:31554486 + PMID:35858549 + Wikipedia:Sensory_neuron + https://www.britannica.com/science/sensory-neuron + https://www.ncbi.nlm.nih.gov/books/NBK539846/ + + + + + Typically, a sensory neuron has a pseudounipolar morphology. + Wikipedia:Sensory_neuron @@ -109453,12 +111931,20 @@ Secondary to the production of seminal fluid, the seminal vesicle glandular cell + + + + + + Lamp5 cortical interneuron A transcriptomically distinct GABAergic neuron located in the cerebral cortex that expresses Lamp5. The standard transcriptomic reference data for this cell type can be found on the CellxGene census under the collection: 'Transcriptomic cytoarchitecture reveals principles of human neocortex organization', dataset: 'Supercluster: CGE-derived interneurons', Author Categories: 'CrossArea_subclass', clusters Lamp5. + ILX:0770149 + The marker set LINC00298, KIT can identify the Human cell type lamp5 GABAergic cortical interneuron in the Brain with a confidence of 0.814687838 (NS-Forest FBeta value). lamp5 GABAergic cortical interneuron @@ -109469,6 +111955,12 @@ Secondary to the production of seminal fluid, the seminal vesicle glandular cell PMID:37824655 https://cellxgene.cziscience.com/e/e4ddac12-f48f-4455-8e8d-c2a48a683437.cxg/ + + + + The marker set LINC00298, KIT can identify the Human cell type lamp5 GABAergic cortical interneuron in the Brain with a confidence of 0.814687838 (NS-Forest FBeta value). + https://doi.org/10.5281/zenodo.11165918 + @@ -109631,12 +112123,20 @@ Secondary to the production of seminal fluid, the seminal vesicle glandular cell + + + + + + sncg cortical interneuron A transcriptomically distinct GABAergic neuron located in the cerebral cortex that expresses Gamma-synuclein. The standard transcriptomic reference data for this cell type can be found on the CellxGene census under the collection: 'Transcriptomic cytoarchitecture reveals principles of human neocortex organization', dataset: 'Supercluster: CGE-derived interneurons', Author Categories: 'CrossArea_subclass', clusters Sncg. + ILX:0770150 + The marker set RXRG, THSD7B can identify the Human cell type sncg GABAergic cortical interneuron in the Brain with a confidence of 0.628943702 (NS-Forest FBeta value). sncg GABAergic cortical interneuron @@ -109647,6 +112147,12 @@ Secondary to the production of seminal fluid, the seminal vesicle glandular cell PMID:37824655 https://cellxgene.cziscience.com/e/e4ddac12-f48f-4455-8e8d-c2a48a683437.cxg/ + + + + The marker set RXRG, THSD7B can identify the Human cell type sncg GABAergic cortical interneuron in the Brain with a confidence of 0.628943702 (NS-Forest FBeta value). + https://doi.org/10.5281/zenodo.11165918 + @@ -109679,8 +112185,15 @@ Secondary to the production of seminal fluid, the seminal vesicle glandular cell + + + + + + VIP cortical interneuron A transcriptomically distinct cortical GABAergic neuron that expresses the vasocactive intestinal polypeptide and that has its soma located in the cerebral cortex. The standard transcriptomic reference data for this cell type can be found on the CellxGene census under the collection: 'Transcriptomic cytoarchitecture reveals principles of human neocortex organization', dataset: 'Supercluster: CGE-derived interneurons', Author Categories: 'CrossArea_subclass', cluster Vip. + This neuronal type is distinguished by its heterogeneous morphology and electrophysiological characteristics (Pronneke et al., 2015,2020; Apicella and Marchionni, 2022). Variations in morphology and firing patterns are observed in human cortical VIP interneurons. In a study by Lee et al., 2023, four distinct subtypes of VIP neurons were identified, each exhibiting unique morphologies, soma locations, and electrophysiological properties. These subtypes are defined according to their transcriptomic markers: LBH-VIP and CCD184-VIP, both of which display a bipolar morphology with axons and dendrites extending across cortical layers; and SY16-VIP and ADAMTSL1-VIP, characterized by a dendritic arbor that spreads horizontally within the same layer as the soma (Lee et al., 2023). Disruption or malfunction of VIP cortical interneuron is implicated in neurodevelopmental disorders such as Rett Syndrome and Dravet Syndrome (Goff and Goldberg 2021). VIP interneuron @@ -109694,6 +112207,7 @@ Secondary to the production of seminal fluid, the seminal vesicle glandular cell cortical VIP neuron + The marker set VIP can identify the Human cell type VIP GABAergic cortical interneuron in the Brain with a confidence of 0.855531344 (NS-Forest FBeta value). VIP GABAergic cortical interneuron @@ -109761,6 +112275,12 @@ Secondary to the production of seminal fluid, the seminal vesicle glandular cell cortical VIP neuron PMID:36384143 + + + + The marker set VIP can identify the Human cell type VIP GABAergic cortical interneuron in the Brain with a confidence of 0.855531344 (NS-Forest FBeta value). + https://doi.org/10.5281/zenodo.11165918 + @@ -109793,8 +112313,15 @@ Secondary to the production of seminal fluid, the seminal vesicle glandular cell + + + + + + sst cortical interneuron A transcriptomically distinct GABAergic neuron located in the cerebral cortex that expresses somatostatin (sst). The standard transcriptomic reference data for this cell type can be found on the CellxGene census under the collection: 'Transcriptomic cytoarchitecture reveals principles of human neocortex organization', dataset: 'Supercluster: MGE-derived interneurons', Author Categories: 'CrossArea_subclass', cluster Sst. + ILX:0770152 SOM+ inhibitory interneuron @@ -109803,6 +112330,7 @@ Secondary to the production of seminal fluid, the seminal vesicle glandular cell In the mouse cortex, sst GABAergic cortical interneurons show heterogeneous electrophysiological signatures varying between low-threshold spiking (LTS), regular-spiking and fast-spiking (Song, Y. H., Yoon, J., & Lee, S. H. 2021). Sst GABAergic cortical interneurons have multiple functional roles in the brain. In the mouse, they involved in the generation of slow-waves during the sleep phase of non-rapid eye-movement (NREM) (Funk, C. M. et al., 2017), they maintain synaptic plasticity during motor learning (Adler, A., Zhao, R., et al., 2021), they enhance visual perception in the V1 cortical area by suppressing the activity of pyramidal excitatory neurons (Song, YH. et al., 2020). In humans, malfunctioning of sst GABAergic cortical interneurons is associated with neurodegenerative and psychiatric disorders such as Parkinson's disease, Alzheimer's disease, major depressive disorder, bipolar disorder and schizophrenia as individuals affected by these pathologies show a decrease of expression of SST in the brain (Song YH., Yoon J. et al., 2021). + The marker set SST, PLCH1 can identify the Human cell type sst GABAergic cortical interneuron in the Brain with a confidence of 0.842367005 (NS-Forest FBeta value). sst GABAergic cortical interneuron @@ -109841,6 +112369,12 @@ Secondary to the production of seminal fluid, the seminal vesicle glandular cell PMID:32494634 PMID:33742131 + + + + The marker set SST, PLCH1 can identify the Human cell type sst GABAergic cortical interneuron in the Brain with a confidence of 0.842367005 (NS-Forest FBeta value). + https://doi.org/10.5281/zenodo.11165918 + @@ -109873,12 +112407,20 @@ Secondary to the production of seminal fluid, the seminal vesicle glandular cell + + + + + + pvalb cortical interneuron A transcriptomically distinct GABAergic interneuron with a soma located in a cerebral cortex and it expresses Parvalbumin. The standard transcriptomic reference data for this cell type can be found on the CellxGene census under the collection: 'Transcriptomic cytoarchitecture reveals principles of human neocortex organization', dataset: 'Supercluster: MGE-derived interneurons', Author Categories: 'CrossArea_subclass', cluster Pvalb. + ILX:0770154 + The marker set PVALB, TAC1, MYO5B can identify the Human cell type pvalb GABAergic cortical interneuron in the Brain with a confidence of 0.691998764 (NS-Forest FBeta value). pvalb GABAergic cortical interneuron @@ -109889,6 +112431,12 @@ Secondary to the production of seminal fluid, the seminal vesicle glandular cell PMID:37824655 https://cellxgene.cziscience.com/e/9c63201d-bfd9-41a8-bbbc-18d947556f3d.cxg/ + + + + The marker set PVALB, TAC1, MYO5B can identify the Human cell type pvalb GABAergic cortical interneuron in the Brain with a confidence of 0.691998764 (NS-Forest FBeta value). + https://doi.org/10.5281/zenodo.11165918 + @@ -110123,6 +112671,7 @@ Secondary to the production of seminal fluid, the seminal vesicle glandular cell D1-MSN dSPN dopamine 1 medium spiny neuron + direct pathway medium spiny neuron @@ -110252,6 +112801,7 @@ Secondary to the production of seminal fluid, the seminal vesicle glandular cell D2-MSN dopamine 2 medium spiny neuron iSPN + indirect pathway medium spiny neuron @@ -110440,7 +112990,7 @@ Secondary to the production of seminal fluid, the seminal vesicle glandular cell - + @@ -110473,14 +113023,22 @@ Secondary to the production of seminal fluid, the seminal vesicle glandular cell + + + + + + chandelier PV interneuron A transcriptomically distinct pvalb GABAergic cortical interneuron that is recognizable by the straight terminal axonal 'cartridges' of vertically oriented strings of synaptic boutons. Chandelier PV cells' boutons target exclusively the axon initial segment (AIS) of pyramidal cells, with a single cell innervating hundreds of pyramidal cells in a clustered manner. The standard transcriptomic reference data for this cell type can be found on the CellxGene census under the collection: 'Transcriptomic cytoarchitecture reveals principles of human neocortex organization', dataset: 'Supercluster: CGE-derived interneurons', Author Categories: 'CrossArea_subclass', clusters Chandelier. + ILX:0107356 Chandelier PV In mice, Chandelier PV cells have soma found in in upper L2/3, with some in deep L5 and exhibit fast-spiking but lower firing rate compared to basket cells, and have practically absent hyperpolarization sag. + The marker set GPR149, CA8 can identify the Human cell type chandelier pvalb GABAergic cortical interneuron in the Brain with a confidence of 0.799748111 (NS-Forest FBeta value). chandelier pvalb GABAergic cortical interneuron @@ -110496,6 +113054,12 @@ Secondary to the production of seminal fluid, the seminal vesicle glandular cell In mice, Chandelier PV cells have soma found in in upper L2/3, with some in deep L5 and exhibit fast-spiking but lower firing rate compared to basket cells, and have practically absent hyperpolarization sag. PMID:27477017 + + + + The marker set GPR149, CA8 can identify the Human cell type chandelier pvalb GABAergic cortical interneuron in the Brain with a confidence of 0.799748111 (NS-Forest FBeta value). + https://doi.org/10.5281/zenodo.11165918 + @@ -110562,7 +113126,7 @@ Secondary to the production of seminal fluid, the seminal vesicle glandular cell - + @@ -110635,8 +113199,15 @@ Secondary to the production of seminal fluid, the seminal vesicle glandular cell + + + + + + L5 ET glut A transcriptomically distinct glutamatergic neuron, with a soma found in the deeper portion of L5, that has long-range axonal projections including deep subcortical targets outside of the telencephalon and, in some cases, the spinal cord. While the L5 ET neuron projections are not limited to ET targets, they are clearly differentiated from the neuron subclasses whose projections are constrained to intratelencephalic (IT) targets. L5 ET neurons are generally the largest excitatory cortical neurons, typically having a thick apical dendrite with a prominent dendritic tuft in layer 1 and displaying burst-firing physiological characteristics. The standard transcriptomic reference data for this cell type can be found on the CellxGene census under the collection: 'Transcriptomic cytoarchitecture reveals principles of human neocortex organization', dataset: 'Supercluster: Deep layer (non-IT) excitatory neurons ', Author Categories: 'CrossArea_subclass', clusters L5 ET. + subcerebral projection (SCPN) neuron Pyramidal tract-like (PT-l) @@ -110646,6 +113217,7 @@ Secondary to the production of seminal fluid, the seminal vesicle glandular cell L5b neuron + The marker set CHST8, POU3F1 can identify the Human cell type L5 extratelencephalic projecting glutamatergic cortical neuron in the Brain with a confidence of 0.815891473 (NS-Forest FBeta value). L5 extratelencephalic projecting glutamatergic cortical neuron @@ -110694,6 +113266,12 @@ Secondary to the production of seminal fluid, the seminal vesicle glandular cell DOI:10.1016/j.neuron.2011.07.029 + + + + The marker set CHST8, POU3F1 can identify the Human cell type L5 extratelencephalic projecting glutamatergic cortical neuron in the Brain with a confidence of 0.815891473 (NS-Forest FBeta value). + https://doi.org/10.5281/zenodo.11165918 + @@ -110724,12 +113302,20 @@ Secondary to the production of seminal fluid, the seminal vesicle glandular cell + + + + + + L6 CT glut A transcriptomically distinct corticothalamic-projecting neuron with a soma found in cortical layer 6. The standard transcriptomic reference data for this cell type can be found on the CellxGene census under the collection: 'Transcriptomic cytoarchitecture reveals principles of human neocortex organization', dataset: 'Supercluster: Deep layer (non-IT) excitatory neurons', Author Categories: 'CrossArea_subclass', clusters L6 CT. + L6 CT + The marker set SEMA5B, ADAMTSL1, SULF1 can identify the Human cell type L6 corticothalamic-projecting glutamatergic cortical neuron in the Brain with a confidence of 0.631898455 (NS-Forest FBeta value). L6 corticothalamic-projecting glutamatergic cortical neuron @@ -110747,6 +113333,12 @@ Secondary to the production of seminal fluid, the seminal vesicle glandular cell PMID:28625486 PMID:34616075 + + + + The marker set SEMA5B, ADAMTSL1, SULF1 can identify the Human cell type L6 corticothalamic-projecting glutamatergic cortical neuron in the Brain with a confidence of 0.631898455 (NS-Forest FBeta value). + https://doi.org/10.5281/zenodo.11165918 + @@ -110863,11 +113455,19 @@ Secondary to the production of seminal fluid, the seminal vesicle glandular cell + + + + + + L6b subplate glut An excitatory glutamatergic neuron transcriptomically related to the CT subclass, with a soma preferentially located in the bottom of L6 of the primary motor cortex. + L6b subplate glutamatergic neuron of the primary motor cortex + The marker set CCN2, ROS1 can identify the Human cell type L6b glutamatergic neuron of the primary motor cortex in the Brain with a confidence of 0.819940964 (NS-Forest FBeta value). L6b glutamatergic neuron of the primary motor cortex @@ -110876,6 +113476,12 @@ Secondary to the production of seminal fluid, the seminal vesicle glandular cell An excitatory glutamatergic neuron transcriptomically related to the CT subclass, with a soma preferentially located in the bottom of L6 of the primary motor cortex. PMID:33184512 + + + + The marker set CCN2, ROS1 can identify the Human cell type L6b glutamatergic neuron of the primary motor cortex in the Brain with a confidence of 0.819940964 (NS-Forest FBeta value). + https://doi.org/10.5281/zenodo.11165918 + @@ -111024,13 +113630,8 @@ Secondary to the production of seminal fluid, the seminal vesicle glandular cell + - - - - - - L6 IT glut MOp An intratelencephalic-projecting glutamatergic neuron with a soma found in L6 of the primary motor cortex. These cells are short untufted pyramidal cells, which could be stellate or inverted. @@ -111165,12 +113766,7 @@ Secondary to the production of seminal fluid, the seminal vesicle glandular cell - - - - - - + CT VAL/VM glut MOp A corticothalamic-projecting glutamatergic neuron that is located in L6 and lower L5 of the primary motor cortex, with a pyramidal morphology and mostly untufted apical dendrites terminating in midcortical layers. CT VAL/VM (ventroanterior-ventrolateral complex/ventromedial nucleus) cells have a near tonic firing pattern and are distinguished from L6 IT neurons by a lower inter-spike interval adaptation index. @@ -111200,9 +113796,9 @@ Secondary to the production of seminal fluid, the seminal vesicle glandular cell - - - + + + A type of mouse mesothelial fibroblast that is derived from the neural crest, is localized on blood vessels, and is a key component of the pia and arachnoid membranes surrounding the brain. VLMC (Mus musculus) @@ -111210,34 +113806,34 @@ Secondary to the production of seminal fluid, the seminal vesicle glandular cell vascular leptomeningeal cell (Mmus) - + - + - + - + PMID:30096314 - + PMID:30096314 - + PMID:30096314 @@ -111263,7 +113859,6 @@ Secondary to the production of seminal fluid, the seminal vesicle glandular cell - @@ -111393,7 +113988,7 @@ Secondary to the production of seminal fluid, the seminal vesicle glandular cell - + A neuron that has its soma located in CA4 of the hippocampus. @@ -111492,14 +114087,8 @@ Secondary to the production of seminal fluid, the seminal vesicle glandular cell - - - - - - - + CGE interneuron An interneuron that is derived from the caudal ganglionic eminence. @@ -111600,7 +114189,7 @@ Secondary to the production of seminal fluid, the seminal vesicle glandular cell - + @@ -111608,7 +114197,6 @@ Secondary to the production of seminal fluid, the seminal vesicle glandular cell - @@ -111670,24 +114258,39 @@ Secondary to the production of seminal fluid, the seminal vesicle glandular cell - + - An excitatory neuron that has its soma located in the thalamic complex. + An excitatory neuron that has its soma located in the thalamic complex. This neuron type can be involved in a series of circuits related to sensory integration, motor integration, pain processing, social behaviour and reward response. + + Abnormalities in glutametergic neurons of the thalamic complex are associated with pathologies such as schizophrenia, colorectal visceral pain and Parkinson's disease. thalamic excitatory neuron - An excitatory neuron that has its soma located in the thalamic complex. - DOI:10.1101/2022.10.12.511898 + An excitatory neuron that has its soma located in the thalamic complex. This neuron type can be involved in a series of circuits related to sensory integration, motor integration, pain processing, social behaviour and reward response. + PMID:30083593 + PMID:31196673 + PMID:35278647 + PMID:37163009 + PMID:37824663 + PMID:38739251 + + + + + Abnormalities in glutametergic neurons of the thalamic complex are associated with pathologies such as schizophrenia, colorectal visceral pain and Parkinson's disease. + PMID:11532718 + PMID:30083593 + PMID:38739251 @@ -111821,6 +114424,7 @@ in the label. See comments in issue 2357. A cell that is part of the brain vasculature. + brain vascular cell @@ -111866,7 +114470,7 @@ in the label. See comments in issue 2357. - + @@ -111952,7 +114556,6 @@ in the label. See comments in issue 2357. - @@ -112053,7 +114656,7 @@ in the label. See comments in issue 2357. - + @@ -112080,12 +114683,7 @@ in the label. See comments in issue 2357. - - - - - - + stellate L6 IT glut MOp a L6 intratelencephalic projecting glutamatergic neuron of the primary motor cortex that has stellate pyramidal morphology. @@ -112106,12 +114704,7 @@ in the label. See comments in issue 2357. - - - - - - + inverted L6 IT glut MOp a L6 intratelencephalic projecting glutamatergic neuron of the primary motor cortex that has inverted pyramidal morphology. @@ -112155,6 +114748,7 @@ in the label. See comments in issue 2357. ILX:0777213 ChC + chandelier cell @@ -112403,7 +114997,7 @@ in the label. See comments in issue 2357. - + @@ -112411,7 +115005,6 @@ in the label. See comments in issue 2357. - @@ -112439,7 +115032,7 @@ in the label. See comments in issue 2357. - + @@ -112447,7 +115040,6 @@ in the label. See comments in issue 2357. - @@ -112475,7 +115067,7 @@ in the label. See comments in issue 2357. - + @@ -112483,7 +115075,6 @@ in the label. See comments in issue 2357. - @@ -112511,7 +115102,7 @@ in the label. See comments in issue 2357. - + @@ -112519,7 +115110,6 @@ in the label. See comments in issue 2357. - @@ -112902,7 +115492,7 @@ in the label. See comments in issue 2357. - + @@ -113237,6 +115827,7 @@ in the label. See comments in issue 2357. FMA:62364 cochlear hair cell + cochlea auditory hair cell @@ -113258,11 +115849,19 @@ in the label. See comments in issue 2357. + + + + + + sst chodl cortical interneuron A transcriptomically distinct sst GABAergic cortical interneuron that also expresses Chodl. These neurons are rare and correspond to the only known cortical interneurons with long-range projection. The standard transcriptomic reference data for this cell type can be found on the CellxGene census under the collection: 'Transcriptomic cytoarchitecture reveals principles of human neocortex organization', dataset: 'Supercluster: MGE-derived interneurons', Author Categories: 'CrossArea_subclass', clusters Sst Chodl. + long-range GABAergic interneuron + The marker set NPY can identify the Human cell type sst chodl GABAergic cortical interneuron in the Brain with a confidence of 0.894026187 (NS-Forest FBeta value). sst chodl GABAergic cortical interneuron @@ -113275,6 +115874,12 @@ in the label. See comments in issue 2357. PMID:37824655 https://cellxgene.cziscience.com/e/9c63201d-bfd9-41a8-bbbc-18d947556f3d.cxg/ + + + + The marker set NPY can identify the Human cell type sst chodl GABAergic cortical interneuron in the Brain with a confidence of 0.894026187 (NS-Forest FBeta value). + https://doi.org/10.5281/zenodo.11165918 + @@ -113344,7 +115949,7 @@ in the label. See comments in issue 2357. - + @@ -113575,7 +116180,7 @@ in the label. See comments in issue 2357. - + @@ -113752,7 +116357,7 @@ in the label. See comments in issue 2357. - + @@ -113768,6 +116373,7 @@ in the label. See comments in issue 2357. An excitatory glutamatergic interneuron found in the granular layer of the cerebellar cortex and also in the granule cell domain of the cochlear nucleus. Unipolar brush cells have a round or oval cell body with usually a single short dendrite that ends in a brush-like tuft of short dendrites unique to them known as dendrioles. + unipolar brush cell @@ -113872,10 +116478,14 @@ in the label. See comments in issue 2357. + + + + - + @@ -113898,7 +116508,7 @@ in the label. See comments in issue 2357. - + A neuron that is responsible for sensation in the face or motor functions such as biting and chewing. Trigeminal neurons extend a single axon shaft along the lateral white matter of the hindbrain and spinal cord. The highly branched axons innervate the integument of the head. trigeminal neuron @@ -113928,8 +116538,13 @@ in the label. See comments in issue 2357. - + + + + + + A trigeminal neuron that is responsible for sensation in the face. trigeminal sensory neuron @@ -113988,7 +116603,7 @@ in the label. See comments in issue 2357. A neurecto-epithelial cell that is part of the basal layer of the subcommissural organ and specializes in the secretion of proteins into the subarachnoid space. Hypendymal cells have similar characteristics to ependymal cells and express SCO-spondin. - This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. Hypendymal cells are secretory cells located between the ependymal layer and the posterior commissure, forming the hypendmal layer of the subcommissural organ (SCO), a highly conserved gland that is part of the circumventricular system within the brain. Hypendymal cells are bipolar cells with a thin apical pole and basal process. Most of the ultrastructural characteristics of these cells are similar to those described for the ependymal cells (which are arranged into another layer – the ependyma). However, ependymal cells release their secretion into the ventricular cerebrospinal fluid whereas hypendymal cells project processes to the local blood vessels and to the subarachnoidal space. @@ -114007,7 +116622,7 @@ Hypendymal cells are bipolar cells with a thin apical pole and basal process. Mo - This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. Hypendymal cells are secretory cells located between the ependymal layer and the posterior commissure, forming the hypendmal layer of the subcommissural organ (SCO), a highly conserved gland that is part of the circumventricular system within the brain. Hypendymal cells are bipolar cells with a thin apical pole and basal process. Most of the ultrastructural characteristics of these cells are similar to those described for the ependymal cells (which are arranged into another layer – the ependyma). However, ependymal cells release their secretion into the ventricular cerebrospinal fluid whereas hypendymal cells project processes to the local blood vessels and to the subarachnoidal space. @@ -114032,7 +116647,7 @@ Hypendymal cells are bipolar cells with a thin apical pole and basal process. Mo - + @@ -114081,6 +116696,7 @@ Hypendymal cells are bipolar cells with a thin apical pole and basal process. Mo https://orcid.org/0000-0001-7258-9596 https://orcid.org/0000-0001-7655-4833 + There are midget bipolar cells of retina and midget ganglion cells of retina and they are not the same: Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances from the fovea (retinal eccentricity of 4.5mm as compared to 12 mm). Midget ganglion cells (MGC) have larger dendritic fields (here seen at 8 mm) as they increase in eccentricity. @@ -114112,6 +116728,7 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances https://orcid.org/0000-0001-7655-4833 M cell M ganglion cell + These cells should not be confused with M1-M14 retinal ganglion cells described in PMID:16626866 which refer to a different classification of retinal ganglion cells. parasol ganglion cell of retina @@ -114270,6 +116887,12 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances + + + + + + A pulmonary interstitial fibroblast that is part of the alveolus and contains lipid droplets. @@ -114286,6 +116909,7 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances AF1 + The marker set AOC3, LUM can identify the Human cell type alveolar type 1 fibroblast cell in the Lung with a confidence of 0.70 (NS-Forest FBeta value). alveolar type 1 fibroblast cell @@ -114307,6 +116931,12 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances AF1 + + + + The marker set AOC3, LUM can identify the Human cell type alveolar type 1 fibroblast cell in the Lung with a confidence of 0.70 (NS-Forest FBeta value). + https://doi.org/10.5281/zenodo.11165918 + @@ -114321,6 +116951,12 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances + + + + + + A pulmonary interstitial fibroblast that is part of the alveolus and localizes to vascular adventitia. @@ -114336,6 +116972,7 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances MANC + The marker set SCARA5, CD248 can identify the Human cell type alveolar adventitial fibroblast in the Lung with a confidence of 0.85 (NS-Forest FBeta value). alveolar adventitial fibroblast @@ -114368,6 +117005,12 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances MANC + + + + The marker set SCARA5, CD248 can identify the Human cell type alveolar adventitial fibroblast in the Lung with a confidence of 0.85 (NS-Forest FBeta value). + https://doi.org/10.5281/zenodo.11165918 + @@ -114660,13 +117303,8 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances - - - - - - - An epithelial cell that is part of the fallopian tube epithelium that secretes mucous fluid and oviduct-specific products through the stimulation of estrogen and luteinizing hormone. The fallopian tube secretory cell has approximately the same height as the ciliated cell and is usually a more narrow columnar cell. The nucleus is ovoid and perpendicular to the long axis of the cell. The chromatin is more dense and the nucleolus smaller than that seen in the ciliated cell. + + An epithelial cell that is part of the fallopian tube that secretes mucus and oviduct-specific products in response to hormonal stimulation from estrogen and luteinizing hormone. This fallopian tube secretory cell is similar in height to the ciliated cell, but typically exhibits a more narrow, columnar shape. Its nucleus is ovoid and oriented perpendicular to the cell's long axis, with denser chromatin and a smaller nucleolus compared to the ciliated cell. 2022-03-03T10:39:31Z @@ -114679,7 +117317,7 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances - An epithelial cell that is part of the fallopian tube epithelium that secretes mucous fluid and oviduct-specific products through the stimulation of estrogen and luteinizing hormone. The fallopian tube secretory cell has approximately the same height as the ciliated cell and is usually a more narrow columnar cell. The nucleus is ovoid and perpendicular to the long axis of the cell. The chromatin is more dense and the nucleolus smaller than that seen in the ciliated cell. + An epithelial cell that is part of the fallopian tube that secretes mucus and oviduct-specific products in response to hormonal stimulation from estrogen and luteinizing hormone. This fallopian tube secretory cell is similar in height to the ciliated cell, but typically exhibits a more narrow, columnar shape. Its nucleus is ovoid and oriented perpendicular to the cell's long axis, with denser chromatin and a smaller nucleolus compared to the ciliated cell. https://doi.org/10.1186/1477-7827-7-129 https://doi.org/10.3390/cells8080933 https://www.proteinatlas.org/learn/dictionary/normal/fallopian+tube @@ -114698,32 +117336,29 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances - - - - - - + - An epithelial ciliated cell that is part of the fallopian tube. This cell type is found mainly on the apex of the mucosal folds and contributes, together with peristaltic contractions, to the self-propulsion of spermatozoa, the transport of ovum during ovulation and the transport of the fertilized ovum to the intramural fallopian tube. A fallopian tube ciliated cell has a columnar shape and contains an oval or round nucleus, often located perpendicular or parallel to the long axis of the cell. + A multi-ciliated epithelial cell that is part of the fallopian tube, mainly found on the apex of the mucosal folds. This cell exhibits a columnar shape with an oval nucleus and is characterized by the presence of cilia on its surface. The coordinated beating of these cilia, together with peristaltic contractions, contributes to the self-propulsion of spermatozoa, the transport of ovum during ovulation and the transport of the fertilized ovum to the intramural fallopian tube. 2022-03-08T12:40:19Z oviduct ciliated cell + fallopian tube ciliated cell uterine tube ciliated epithelial cell - fallopian tube ciliated cell + fallopian tube multiciliated cell - An epithelial ciliated cell that is part of the fallopian tube. This cell type is found mainly on the apex of the mucosal folds and contributes, together with peristaltic contractions, to the self-propulsion of spermatozoa, the transport of ovum during ovulation and the transport of the fertilized ovum to the intramural fallopian tube. A fallopian tube ciliated cell has a columnar shape and contains an oval or round nucleus, often located perpendicular or parallel to the long axis of the cell. + A multi-ciliated epithelial cell that is part of the fallopian tube, mainly found on the apex of the mucosal folds. This cell exhibits a columnar shape with an oval nucleus and is characterized by the presence of cilia on its surface. The coordinated beating of these cilia, together with peristaltic contractions, contributes to the self-propulsion of spermatozoa, the transport of ovum during ovulation and the transport of the fertilized ovum to the intramural fallopian tube. PMID:16565155 + https://www.proteinatlas.org/humanproteome/tissue/fallopian+tube @@ -115348,9 +117983,10 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances A hillock cell that is located in respiratory epithelium. In some mammalian species, this cell type has been noted to express KRT13 and KRT4 and is postulated to play a role in squamous barrier function and immunomodulation. 2022-06-06T08:31:09Z - hillock cell of respiratory tract + hillock cell of respiratory tract + respiratory hillock cell - respiratory hillock cell + respiratory tract hillock cell @@ -115448,7 +118084,7 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances An enterocyte of the human intestine expressing bestrophin-4 (BEST4) calcium-activated ion channels. 2022-09-07T12:34:20Z - BEST4+ enteroycte + BEST4+ enterocyte @@ -115509,11 +118145,9 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances An amacrine cell that uses glycine as a neurotransmitter. - 2022-10-17T12:40:06Z amacrine cell, glycinergic - glycinergic amacrine cell @@ -115651,6 +118285,7 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances VIC cardiac valve interstitial cell valvular interstitial cell + Activated valve interstitial cells undergo continual turn over into deactivated fibroblasts and other cell fates (such as apoptosis). valve interstitial cell @@ -115709,6 +118344,7 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances 2022-12-09T11:58:49Z VEC valvular endothelial cell + At least in some mammalian species, a valve endothelial cell expresses CD31. Valve endothelial cells can undergo an endothelial to mesenchymal transition to acquire a fibroblast or myofibroblast phenotype that leads to changes in the microenvironmental signals and facilitates tissue regeneration. valve endothelial cell @@ -115747,32 +118383,46 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances - + + + + + + + + + - + + + - - + + - A ciliated cell of the respiratory system. Ciliated cells are present in airway epithelium. + A multiciliated epithelial cell located in the respiratory tract epithelium, characterized by a columnar shape and motile cilia on its apical surface. This cell develops through a highly orchestrated process, transitioning from a basal progenitor via an intermediate deuterosomal cell stage that generates centrioles essential for ciliogenesis. 2023-01-25T11:06:01Z ciliated cell of the respiratory tract - respiratory ciliated cell + respiratory ciliated cell + respiratory multiciliated cell + respiratory tract multiciliated cell - A ciliated cell of the respiratory system. Ciliated cells are present in airway epithelium. + A multiciliated epithelial cell located in the respiratory tract epithelium, characterized by a columnar shape and motile cilia on its apical surface. This cell develops through a highly orchestrated process, transitioning from a basal progenitor via an intermediate deuterosomal cell stage that generates centrioles essential for ciliogenesis. PMID:18757316 PMID:21364219 + PMID:34044844 + PMID:37834236 @@ -116008,7 +118658,7 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances - + @@ -116017,6 +118667,10 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances + + + + @@ -116039,9 +118693,10 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances ciliated cell of the uterus uterine ciliated cell ciliated cell of the endometrium + endometrial ciliated epithelial cell endometrium ciliated epithelial cell In human samples, the expression of FOXJ1 protein, a regulator for motile cilia with epithelial lineage identity, has been noted. - endometrial ciliated epithelial cell + endometrial multiciliated epithelial cell @@ -116074,7 +118729,8 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances A ciliated cell of the endometrial luminal epithelium. This cell is characterized by the presence of motile cilia on its apical surface. 2023-02-09T11:34:42Z - luminal endometrial ciliated epithelial cell + luminal endometrial ciliated epithelial cell + luminal endometrial multiciliated epithelial cell @@ -116088,16 +118744,12 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances + - - - - - - A ciliated cell of the endometrial glandular epithelium. This cell is characterized by the presence of motile cilia on its apical surface. 2023-02-09T11:37:30Z - glandular endometrial ciliated epithelial cell + glandular endometrial ciliated epithelial cell + glandular endometrial multiciliated epithelial cell @@ -116111,6 +118763,7 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances + @@ -116175,6 +118828,7 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances + @@ -116239,6 +118893,7 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances + @@ -116310,6 +118965,7 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances + @@ -116382,6 +119038,7 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances + @@ -116457,6 +119114,7 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances + @@ -116517,6 +119175,7 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances + @@ -116584,6 +119243,7 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances + @@ -116640,6 +119300,7 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances + @@ -116843,7 +119504,6 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances - @@ -116908,13 +119568,22 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances + + + + + + L2/3 IT A transcriptomically distinct intratelencephalic-projecting glutamatergic neuron with a soma found between cortical layer 2-4. This intratelencephalic-projecting glutamatergic neuron has thin-tufted apical dendrites and extends its axonal projection into L5 in the neocortex. This neuronal type has a hyperpolarised resting membrane potential. The standard transcriptomic reference data for this cell type can be found on the CellxGene census under the collection: 'Transcriptomic cytoarchitecture reveals principles of human neocortex organization', dataset: 'Supercluster: IT-projecting excitatory neurons', Author Categories: 'CrossArea_subclass', clusters L2/3 IT. + 2023-10-10T14:10:21Z ILX:0770156 L2/3 IT + Hystorically, the L2/3 intratelencephalic projectic glutametergic neuron was known to have its soma in cortical layer 2/3. MERFISH data showed that this intratelencephalic-projecting glutametergic neuron can have its soma in layer 2/3, 4B, 4C. The position of the soma in layer 4b and 4C is less frequent for this neuronal type in comparison to cortical layer 2/3. + The marker set ONECUT2, COL5A2 can identify the Human cell type L2/3 intratelencephalic projecting glutamatergic neuron in the Brain with a confidence of 0.670149932 (NS-Forest FBeta value). L2/3 intratelencephalic projecting glutamatergic neuron @@ -116940,6 +119609,12 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances Hystorically, the L2/3 intratelencephalic projectic glutametergic neuron was known to have its soma in cortical layer 2/3. MERFISH data showed that this intratelencephalic-projecting glutametergic neuron can have its soma in layer 2/3, 4B, 4C. The position of the soma in layer 4b and 4C is less frequent for this neuronal type in comparison to cortical layer 2/3. PMID:37824655 + + + + The marker set ONECUT2, COL5A2 can identify the Human cell type L2/3 intratelencephalic projecting glutamatergic neuron in the Brain with a confidence of 0.670149932 (NS-Forest FBeta value). + https://doi.org/10.5281/zenodo.11165918 + @@ -117096,12 +119771,21 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances + + + + + + L4 IT A transcriptomically distinct intratelencephalic-projecting glutamatergic neuron with a soma found in cortical layer 3-4. This neuron type can have a pyramidal, star-pyramidal or spiny stellate morphology and projects its output to L2/3 and L5A/B. The standard transcriptomic reference data for this cell type can be found on the CellxGene census under the collection: 'Transcriptomic cytoarchitecture reveals principles of human neocortex organization', dataset: 'Supercluster: IT-projecting excitatory neurons', Author Categories: 'CrossArea_subclass', L4 IT. + 2023-10-10T14:11:25Z L4 IT + Historically, the L4 intratelencephalic projectic glutametergic neuron was known to have its soma in cortical layer 4. MERFISH data showed that this intratelencephalic-projecting glutametergic neuron can also have its soma in layer 3. + The marker set RORB, ST8SIA4 can identify the Human cell type L4 intratelencephalic projecting glutamatergic neuron in the Brain with a confidence of 0.720108696 (NS-Forest FBeta value). L4 intratelencephalic projecting glutamatergic neuron @@ -117119,6 +119803,12 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances PMID:37292694 + + + + The marker set RORB, ST8SIA4 can identify the Human cell type L4 intratelencephalic projecting glutamatergic neuron in the Brain with a confidence of 0.720108696 (NS-Forest FBeta value). + https://doi.org/10.5281/zenodo.11165918 + @@ -117143,12 +119833,20 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances + + + + + + L5 IT An intratelencephalic-projecting glutamatergic neuron with a soma found in cortical layer 5. The standard transcriptomic reference data for this cell type can be found on the CellxGene census under the collection: 'Transcriptomic cytoarchitecture reveals principles of human neocortex organization', dataset: 'Supercluster: IT-projecting excitatory neurons', Author Categories: 'CrossArea_subclass', L5 IT. + 2023-10-10T14:11:59Z ILX:0770157 L5 IT + The marker set ARSJ, RORB, KCNK2 can identify the Human cell type L5 intratelencephalic projecting glutamatergic neuron in the Brain with a confidence of 0.764261336 (NS-Forest FBeta value). L5 intratelencephalic projecting glutamatergic neuron @@ -117167,6 +119865,12 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances PMID:37292694 + + + + The marker set ARSJ, RORB, KCNK2 can identify the Human cell type L5 intratelencephalic projecting glutamatergic neuron in the Brain with a confidence of 0.764261336 (NS-Forest FBeta value). + https://doi.org/10.5281/zenodo.11165918 + @@ -117191,12 +119895,20 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances + + + + + + L6 IT A transcriptomically distinct intratelencephalic-projecting glutamatergic neuron with a soma found in L6 of the primary motor cortex. These cells are short untufted pyramidal cells, which could be stellate or inverted. The standard transcriptomic reference data for this cell type can be found on the CellxGene census under the collection: 'Transcriptomic cytoarchitecture reveals principles of human neocortex organization', dataset: 'Supercluster: IT-projecting excitatory neurons', Author Categories: 'CrossArea_subclass', L6 IT. + 2023-10-10T14:12:23Z ILX:0770158 L6 IT + The marker set LINC00507, THEMIS can identify the Human cell type L6 intratelencephalic projecting glutamatergic neuron in the Brain with a confidence of 0.641695703 (NS-Forest FBeta value). L6 intratelencephalic projecting glutamatergic neuron @@ -117215,6 +119927,12 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances PMID:37292694 + + + + The marker set LINC00507, THEMIS can identify the Human cell type L6 intratelencephalic projecting glutamatergic neuron in the Brain with a confidence of 0.641695703 (NS-Forest FBeta value). + https://doi.org/10.5281/zenodo.11165918 + @@ -117241,21 +119959,22 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances - + An epithelial cell that is part of a ureteric bud. A ureteric bud cell has the potential to induce metanephric mesenchymal cells to proliferate and convert to epithelia that form renal tubules via: (1) the secretion of multiple diffusible growth factors that rescue renal progenitors from apoptosis and stimulate them to proliferate and (2) contact-dependent mechanisms that induce mesenchymal-epithelial conversion. https://orcid.org/0000-0002-1425-877X 2023-10-13T11:22:42Z UB cell + ureteric bud cell - + - + PMID:9374839 @@ -117297,10 +120016,19 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances + + + + + + A near-projecting glutamatergic neuron with a soma found in cortical layer 5/6. + 2023-11-17T11:35:06Z L5/6 NP + + The marker set NPSR1-AS1, TLL1 can identify the Human cell type L5/6 near-projecting glutamatergic neuron in the Brain with a confidence of 0.899288218 (NS-Forest FBeta value). L5/6 near-projecting glutamatergic neuron @@ -117318,6 +120046,12 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances PMID:34004146 + + + + The marker set NPSR1-AS1, TLL1 can identify the Human cell type L5/6 near-projecting glutamatergic neuron in the Brain with a confidence of 0.899288218 (NS-Forest FBeta value). + https://doi.org/10.5281/zenodo.11165918 + @@ -117347,8 +120081,15 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances + + + + + + L6 IT Car3 A transcriptomically distinct intratelencepalic-projecting glutamatergic neuron that expresses Car3 with a soma found in L6 . The standard transcriptomic reference data for this cell type can be found on the CellxGene census under the collection: 'Transcriptomic cytoarchitecture reveals principles of human neocortex organization', dataset: 'Supercluster: IT-projecting excitatory neurons', Author Categories: 'CrossArea_cluster', L6 IT Car3. + 2023-11-23T09:16:14Z L6 IT Car3 glutamatergic neuron @@ -117356,6 +120097,7 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances L6 IT Car3 neuron L6-IT-Car3 L6-IT-Car3 cell + The marker set SMYD1, THEMIS can identify the Human cell type L6 intratelencephalic projecting Car3 glutamatergic neuron in the Brain with a confidence of 0.877752028 (NS-Forest FBeta value). L6 intratelencephalic projecting Car3 glutamatergic neuron @@ -117402,6 +120144,12 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances PMID:37824655 + + + + The marker set SMYD1, THEMIS can identify the Human cell type L6 intratelencephalic projecting Car3 glutamatergic neuron in the Brain with a confidence of 0.877752028 (NS-Forest FBeta value). + https://doi.org/10.5281/zenodo.11165918 + @@ -117587,6 +120335,7 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances + @@ -117661,6 +120410,12 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances + + + + + + @@ -117703,10 +120458,18 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances + + + + + + A(n) serous secreting cell that is part of a(n) bronchus submucosal gland. + + The marker set PRR4, C6orf58 can identify the Human cell type serous secreting cell of bronchus submucosal gland in the Lung with a confidence of 0.75 (NS-Forest FBeta value). serous secreting cell of bronchus submucosal gland @@ -117716,6 +120479,12 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances PMID:5487122 PMID:9651178 + + + + The marker set PRR4, C6orf58 can identify the Human cell type serous secreting cell of bronchus submucosal gland in the Lung with a confidence of 0.75 (NS-Forest FBeta value). + https://doi.org/10.5281/zenodo.11165918 + @@ -117917,6 +120686,12 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances + + + + + + @@ -117951,6 +120726,12 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances + + + + + + @@ -117994,6 +120775,7 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances A keratinocyte of the epidermis suprabasal layer. This cell may express the differentiation markers keratin 10 and keratin 1. 2023-02-02T11:17:04Z + suprabasal keratinocyte @@ -118010,7 +120792,7 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances - + @@ -118097,6 +120879,7 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances 2023-03-02T14:38:32Z retinal astroglia + In response to elevated intraocular pressure, a retinal astrocyte may modulate extracellular matrix remodeling. In the human retina, a retinal astrocyte is GFAP-positive, SOD3-positive and GYPC-positive. retinal astrocyte @@ -118305,11 +121088,10 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances An ON bipolar cell type with dendrites selectively contacting S-cones. - 2023-04-04T09:48:15Z BB cell - + The axons of a blue cone bipolar cell terminate close to the ganglion cell layer, where they transfer the S-cone ON signal to small bistratified ganglion cells. Other targets of a blue cone bipolar cell include amacrine cells and possibly large bistratified ganglion cells. ON-blue cone bipolar cell @@ -118443,6 +121225,12 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances + + + + + + A mucus secreting cell of a submucosal gland of the bronchus. @@ -118450,6 +121238,7 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances 2023-03-16T15:12:52Z bronchial gland mucous cell + The marker set BPIFB2 can identify the Human cell type mucus secreting cell of bronchus submucosal gland in the Lung with a confidence of 0.93 (NS-Forest FBeta value). mucus secreting cell of bronchus submucosal gland @@ -118464,6 +121253,12 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances bronchial gland mucous cell PMID:5487122 + + + + The marker set BPIFB2 can identify the Human cell type mucus secreting cell of bronchus submucosal gland in the Lung with a confidence of 0.93 (NS-Forest FBeta value). + https://doi.org/10.5281/zenodo.11165918 + @@ -118477,12 +121272,19 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances + + + + + + An epithelial cell that is part of a collecting duct of an airway submucosal gland. 2023-03-16T15:20:28Z + The marker set GLYATL2, DMBT1 can identify the Human cell type airway submucosal gland collecting duct epithelial cell in the Lung with a confidence of 0.46 (NS-Forest FBeta value). airway submucosal gland collecting duct epithelial cell @@ -118492,6 +121294,12 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances PMID:25648514 PMID:29656943 + + + + The marker set GLYATL2, DMBT1 can identify the Human cell type airway submucosal gland collecting duct epithelial cell in the Lung with a confidence of 0.46 (NS-Forest FBeta value). + https://doi.org/10.5281/zenodo.11165918 + @@ -118510,6 +121318,7 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances https://orcid.org/0000-0002-9185-3994 2023-03-16T15:51:39Z + airway submucosal gland duct basal cell @@ -118583,6 +121392,7 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances 2023-03-16T16:15:39Z PC-fibro + lung perichondrial fibroblast @@ -118607,14 +121417,13 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances An OFF diffuse bipolar cell that makes synaptic contact with both L/M and S-cone photoreceptors and only minimal contact with rod photoreceptors. - 2023-04-04T10:48:29Z Diffuse Bipolar Cell Type DB1 DB1 bipolar DB1 bipolar cell DB1 cell - + In primates, a diffuse bipolar 1 cell on average makes 81 ribbon (output) synapses, 13 contacts are with OFF parasol cells and 47 contacts are with OFF midget cells. This cell might make flat contacts at both triad-associated and non-triad-associated positions on the cone pedicle. diffuse bipolar 1 cell @@ -118666,11 +121475,10 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances An OFF diffuse bipolar cell that predominantly connects to ON parasol cells and lateral amacrine cells. This cell contains a large number of synaptic ribbons and a small axon arbor area. - 2023-04-04T10:49:07Z DB2 cell - + In primates, a diffuse bipolar 2 cell makes an average of 133 ribbon synapses, 47 contacts are with OFF parasol cells and 4 contacts are with OFF midget cells. diffuse bipolar 2 cell @@ -118703,12 +121511,11 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances An OFF calbindin-positive bipolar cell that has a large dendritic field and stratifies narrowly close to the middle of the inner plexiform layer. Its axon terminal is characterized by regularly branching and varicose processes resembling beads on a string. Most of DB3a contacts with cones are triad-associated. - 2023-04-04T10:53:33Z DB3 cell DB3a cell - + Originally, DB3a cells were termed diffuse bipolar 3 (DB3) cells. When an additional bipolar type which stratifies slightly more vitread and is calbindin negative was detected, this cell was renamed diffuse bipolar 3a cell. The axons of neighboring DB3a cells make homologous gap junctions. The DB3a cells provide the majority of their output to OFF parasol cells. diffuse bipolar 3a cell @@ -118749,11 +121556,10 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances An OFF calbindin-negative bipolar cell that has a large dendritic field and stratifies narrowly close to the middle of the inner plexiform layer. Its axon terminal is characterized by regularly branching and varicose processes resembling beads on a string. Most of DB3b contacts with cones are non-triad-associated. - 2023-04-04T10:53:42Z DB3b cell - + In humans, a DB3b cell is CD15 positive. A DB3b cell might make sparse contacts to rod photoreceptors. diffuse bipolar 3b cell @@ -118787,11 +121593,10 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances An ON diffuse bipolar cell that predominantly connects to ON parasol cells and lateral amacrine cells. - 2023-04-04T09:51:10Z DB4 cell - + diffuse bipolar 4 cell @@ -118817,11 +121622,10 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances An ON diffuse bipolar cell that has a large dendritic field and large axon terminals, which show little or no overlap. This cell predominantly connects to narrow thorny ganglion cells. - 2023-04-04T09:51:22Z DB6 cell - + diffuse bipolar 6 cell @@ -118846,11 +121650,10 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances An OFF bipolar cell with a small dendritic tree that provides most of the triad-associated basal (flat) contacts at cone pedicles. - 2023-04-04T10:54:00Z FMB cell - + flat midget bipolar cell @@ -118875,11 +121678,10 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances An ON bipolar cell with a small dendritic tree that forms most of the central (invaginating) elements opposite the synaptic ribbon at the cone triad. - 2023-04-04T09:51:44Z IMB cell - + invaginating midget bipolar cell @@ -118907,6 +121709,7 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances 2023-04-04T09:54:15Z GB cell + A giant bipolar cell is usually monostratified, although, very rarely, it can be bistratified. giant bipolar cell @@ -118948,6 +121751,7 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances 2023-04-04T10:54:15Z + OFFx cell @@ -118979,6 +121783,7 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances + @@ -119019,6 +121824,7 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances 2023-04-27T10:15:45Z lung resident memory CD4 T cell lung CD4-positive TRM + lung resident memory CD4-positive, alpha-beta T cell @@ -119061,6 +121867,7 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances 2023-04-27T10:16:07Z lung CD8-positive TRM + In the lung, CXCR6 regulates the localization of lung resident memory CD8-positive, alpha-beta T cells. lung resident memory CD8-positive, alpha-beta T cell @@ -119155,6 +121962,12 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances + + + + + + An alveolar macrophage that expresses CCL3. @@ -119162,6 +121975,7 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances 2023-06-15T12:53:08Z alveolar macrophage CCL3-positive + The marker set TNIP3, CXCL5 can identify the Human cell type CCL3-positive alveolar macrophage in the Lung with a confidence of 0.67 (NS-Forest FBeta value). CCL3-positive alveolar macrophage @@ -119176,6 +121990,12 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances alveolar macrophage CCL3-positive PMID:37291214 + + + + The marker set TNIP3, CXCL5 can identify the Human cell type CCL3-positive alveolar macrophage in the Lung with a confidence of 0.67 (NS-Forest FBeta value). + https://doi.org/10.5281/zenodo.11165918 + @@ -119183,6 +122003,12 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances + + + + + + An alveolar macrophage that expresses metallothionein. @@ -119190,7 +122016,9 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances 2023-06-15T12:55:34Z alveolar macrophage MT-positive alveolar macrophage metallothionein-positive + + The marker set HMOX1, HPGD can identify the Human cell type metallothionein-positive alveolar macrophage in the Lung with a confidence of 0.41 (NS-Forest FBeta value). metallothionein-positive alveolar macrophage @@ -119211,6 +122039,12 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances alveolar macrophage metallothionein-positive PMID:37291214 + + + + The marker set HMOX1, HPGD can identify the Human cell type metallothionein-positive alveolar macrophage in the Lung with a confidence of 0.41 (NS-Forest FBeta value). + https://doi.org/10.5281/zenodo.11165918 + @@ -119226,13 +122060,21 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances + + + + + + A macrophage that is part of the lung connective tissue (pulmonary interstitium). This cell performs tissue remodeling and contributes to barrier immunity through antigen presentation. 2023-06-15T12:58:11Z lung IM + + The marker set F13A1, STAB1, FCGR2B can identify the Human cell type lung interstitial macrophage in the Lung with a confidence of 0.46 (NS-Forest FBeta value). lung interstitial macrophage @@ -119250,6 +122092,12 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances PMID:36211428 + + + + The marker set F13A1, STAB1, FCGR2B can identify the Human cell type lung interstitial macrophage in the Lung with a confidence of 0.46 (NS-Forest FBeta value). + https://doi.org/10.5281/zenodo.11165918 + @@ -119257,11 +122105,18 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances + + + + + + An epithelial cell part of respiratory tract epithelium that is a precursor of a multi-ciliated cell. This cell actively amplifies centrioles, a required step for multiciliogenesis. 2023-06-20T10:27:17Z + In humans, deuterosomal cells have been noted to have enriched expression of the following: PLK4, FOXJ1, DEUP1, FOXN4, YPEL1, HES6 and CDC20B. Deuterosomal cells were termed after deuterosomes, the platforms of active centriole amplification. deuterosomal cell @@ -119431,22 +122286,34 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances - A respiratory epithelial cell with topographic nuclear position in between the basal and luminal cell of the airway epithelium. This non-basal, intermediate cell has limited proliferative capacity, ultrastructural features of basal cells and no defined features of the typically differentiated cellular phenotypes. + + + + + + + A respiratory epithelial cell derived from a basal cell, with a topographic nuclear position between the basal and luminal cells of the airway epithelium. This non-basal, intermediate progenitor cell has limited proliferative capacity and can differentiate into multiciliated, secretory, or rare airway cells (ionocytes, tuft cells, neuroendocrine cells). It shares some ultrastructural features with basal cells but lacks the defined characteristics of fully differentiated cellular phenotypes. 2023-06-20T10:44:30Z respiratory parabasal cell + respiratory suprabasal cell respiratory suprabasal progenitor cell + - In humans, respiratory suprabasal cells have been noted to have enriched expression of the following: CK8, KRT13, IVL, and SERPINB3. - respiratory suprabasal cell + In humans, respiratory tract suprabasal cells have been noted to have enriched expression of the following: CK8, KRT13, IVL, and SERPINB3. Single-cell sequencing indicates that suprabasal cells derived from the nasal epithelium are distinct from those in the tracheobronchial epithelium. + The marker set TNC, KRT15, SERPINB4 can identify the Human cell type respiratory suprabasal cell in the Lung with a confidence of 0.62 (NS-Forest FBeta value). + respiratory tract suprabasal cell - A respiratory epithelial cell with topographic nuclear position in between the basal and luminal cell of the airway epithelium. This non-basal, intermediate cell has limited proliferative capacity, ultrastructural features of basal cells and no defined features of the typically differentiated cellular phenotypes. + A respiratory epithelial cell derived from a basal cell, with a topographic nuclear position between the basal and luminal cells of the airway epithelium. This non-basal, intermediate progenitor cell has limited proliferative capacity and can differentiate into multiciliated, secretory, or rare airway cells (ionocytes, tuft cells, neuroendocrine cells). It shares some ultrastructural features with basal cells but lacks the defined characteristics of fully differentiated cellular phenotypes. PMID:25564622 + PMID:34044844 + PMID:35387001 + PMID:37834236 @@ -119463,10 +122330,17 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances - In humans, respiratory suprabasal cells have been noted to have enriched expression of the following: CK8, KRT13, IVL, and SERPINB3. + In humans, respiratory tract suprabasal cells have been noted to have enriched expression of the following: CK8, KRT13, IVL, and SERPINB3. Single-cell sequencing indicates that suprabasal cells derived from the nasal epithelium are distinct from those in the tracheobronchial epithelium. PMID:25658372 + PMID:32726565 doi:10.1101/2023.04.20.537495 + + + + The marker set TNC, KRT15, SERPINB4 can identify the Human cell type respiratory suprabasal cell in the Lung with a confidence of 0.62 (NS-Forest FBeta value). + https://doi.org/10.5281/zenodo.11165918 + @@ -119485,7 +122359,6 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances - @@ -119540,8 +122413,10 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances A neuron that releases catecholamine as a neurotransmitter. + 2023-05-18T12:07:45Z + Frequently used when describing the developing nervous system in zebrafish. A catecholaminergic neuron expresses tyrosine hydroxylase (TH), tyrosine hydroxylase 2 (TH2), aromatic amino acid decarboxylase (AADC), dopamine b-hydroxylase (DBH), and phenylethanolamine-N-methyl transferase (PEMT), which are enzymes necessary for catecholamine synthesis. catecholaminergic neuron @@ -119678,6 +122553,7 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances Polyak's shrub cell SBS ganglion cell sbRGC + small bistratified retinal ganglion cell @@ -119745,6 +122621,7 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances A cell that is adjacent to a vessel. A perivascular cell plays a crucial role in maintaining vascular function and tissue homeostasis. This cell type regulates vessel integrity and flow dynamics. 2023-08-22T13:40:28Z + perivascular cell @@ -119763,7 +122640,7 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances - + @@ -119772,10 +122649,19 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances + + + + + + + + - + + @@ -119788,18 +122674,19 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances - A ciliated cell that is part of a ciliated duct of an airway submucosal gland. + A multi-ciliated epithelial cell located in ciliated duct of an airway submucosal gland, characterized by a columnar shape and motile cilia on its apical surface. 2023-09-08T10:32:27Z + airway submucosal gland duct ciliated cell - airway submucosal gland duct ciliated cell + airway submucosal gland duct multiciliated cell - A ciliated cell that is part of a ciliated duct of an airway submucosal gland. + A multi-ciliated epithelial cell located in ciliated duct of an airway submucosal gland, characterized by a columnar shape and motile cilia on its apical surface. PMID:17707699 PMID:30864819 @@ -119852,6 +122739,7 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances LASP LP LumSec + luminal adaptive secretory precursor cell of mammary gland @@ -119941,7 +122829,6 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances - @@ -119961,6 +122848,7 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances HS-MEC LHS LumHR + Following lineage specification, a luminal hormone-sensing cell expresses receptors for one or more hormones, such as estrogens, progesterone, androgens, and prolactin. In response to progesterone, luminal hormone-sensing cells express TNFSF11, WNT4, and RSPO1, among other factors, which cause branching, proliferation, and partial differentiation in LASP and B-Myo cells during luteal phases of the estrous/menstrual cycle and during gestation. During ductal elongation, ER activity drives expression of AREG in LHS cells, which is necessary for proliferation of the epithelium to fill the mammary fat pad. luminal hormone-sensing cell of mammary gland @@ -120529,8 +123417,6 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances A(n) B cell that is cycling. - - 2024-07-02T09:14:23Z proliferating B cell cycling B cell @@ -120581,8 +123467,6 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances A(n) T cell that is cycling. - - 2024-07-02T09:14:23Z proliferating T cell cycling T cell @@ -120622,8 +123506,6 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances A(n) dendritic cell that is cycling. - - 2024-07-02T09:14:23Z proliferating dendritic cell cycling dendritic cell @@ -120674,8 +123556,6 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances A(n) natural killer cell that is cycling. - - 2024-07-02T09:14:23Z proliferating natural killer cell cycling natural killer cell @@ -120715,8 +123595,6 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances A(n) gamma-delta T cell that is cycling. - - 2024-07-02T09:14:23Z proliferating gamma-delta T cell cycling gamma-delta T cell @@ -120757,8 +123635,6 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances A(n) monocyte that is cycling. - - 2024-07-02T09:14:23Z proliferating monocyte cycling monocyte @@ -120798,8 +123674,6 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances A(n) CD8-positive, alpha-beta T cell that is cycling. - - 2024-07-02T09:14:23Z proliferating CD8-positive, alpha-beta T cell cycling CD8-positive, alpha-beta T cell @@ -120839,8 +123713,6 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances A(n) CD4-positive, alpha-beta T cell that is cycling. - - 2024-07-02T09:14:23Z proliferating CD4-positive, alpha-beta T cell cycling CD4-positive, alpha-beta T cell @@ -120881,8 +123753,6 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances A(n) macrophage that is cycling. - - 2024-07-02T09:14:23Z proliferating macrophage cycling macrophage @@ -120921,10 +123791,17 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances + + + + + + A(n) alveolar macrophage that is cycling. - - 2024-07-02T09:14:23Z + proliferating alveolar macrophage + + The marker set PCLAF, RRM2, UBE2C, NUSAP1 can identify the Human cell type cycling alveolar macrophage in the Lung with a confidence of 0.26 (NS-Forest FBeta value). cycling alveolar macrophage @@ -120939,6 +123816,12 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances proliferating alveolar macrophage PMID:37291214 + + + + The marker set PCLAF, RRM2, UBE2C, NUSAP1 can identify the Human cell type cycling alveolar macrophage in the Lung with a confidence of 0.26 (NS-Forest FBeta value). + https://doi.org/10.5281/zenodo.11165918 + @@ -120974,8 +123857,6 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances A(n) mononuclear phagocyte that is cycling. - - 2024-07-02T09:14:23Z proliferating mononuclear phagocyte cycling mononuclear phagocyte @@ -121026,8 +123907,6 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances A(n) endothelial cell of lymphatic vessel that is cycling. - - 2024-07-02T09:14:23Z proliferating endothelial cell of lymphatic vessel cycling endothelial cell of lymphatic vessel @@ -121077,10 +123956,16 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances + + + + + + A(n) pulmonary alveolar type 2 cell that is cycling. - - 2024-07-02T09:14:23Z + proliferating pulmonary alveolar type 2 cell + The marker set PEG10, PRC1, TOP2A can identify the Human cell type cycling pulmonary alveolar type 2 cell in the Lung with a confidence of 0.61 (NS-Forest FBeta value). cycling pulmonary alveolar type 2 cell @@ -121095,6 +123980,12 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances proliferating pulmonary alveolar type 2 cell PMID:37291214 + + + + The marker set PEG10, PRC1, TOP2A can identify the Human cell type cycling pulmonary alveolar type 2 cell in the Lung with a confidence of 0.61 (NS-Forest FBeta value). + https://doi.org/10.5281/zenodo.11165918 + @@ -121130,8 +124021,6 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances A(n) myeloid cell that is cycling. - - 2024-07-02T09:14:23Z proliferating myeloid cell cycling myeloid cell @@ -121183,8 +124072,6 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances A(n) basal cell that is cycling. - - 2024-07-02T09:14:23Z proliferating basal cell cycling basal cell @@ -121323,6 +124210,417 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances + + + + + An ON diffuse bipolar cell that stratifies in the stratum 3 of the inner plexiform layer to make synapses with ON parasol ganglion cells. A diffuse bipolar 5 cell has high expression of MYO16 compared with other bipolar cells. + + + 2024-10-16T12:46:53Z + DB5 cell + A diffuse bipolar 5 cell typically contacts 7–8 cone photoreceptors. The number and thickness of its dendritic processes are intermediate between those of a diffuse bipolar 6 cell (less dense and thinner) and a diffuse bipolar 4 cell (denser and thicker). + diffuse bipolar 5 cell + + + + + An ON diffuse bipolar cell that stratifies in the stratum 3 of the inner plexiform layer to make synapses with ON parasol ganglion cells. A diffuse bipolar 5 cell has high expression of MYO16 compared with other bipolar cells. + PMID:27833534 + PMID:32032773 + + + + + DB5 cell + PMID:32032773 + + + + + + A diffuse bipolar 5 cell typically contacts 7–8 cone photoreceptors. The number and thickness of its dendritic processes are intermediate between those of a diffuse bipolar 6 cell (less dense and thinner) and a diffuse bipolar 4 cell (denser and thicker). + PMID:27833534 + + + + + + + + + + + + + + + A tissue-resident macrophage that is associated with lipids. This cell responsible of anti-inflammatory functions, lipid accumulation and enhancing phagocytosis (Wculek et al., 2022, Liu et al., 2022). In mice and humans, a lipid-associated macrophage is characterized by the marker Trem2 (Jaitlin et al., 2019). + + + 2024-10-17T10:20:13Z + LAM + Distinct from “adipose macrophage” in Trem2 expression, and is not limited to adipose tissue. Guilliams et al. describe these cells as being distinct from Kupffer cells. + lipid-associated macrophage + + + + + A tissue-resident macrophage that is associated with lipids. This cell responsible of anti-inflammatory functions, lipid accumulation and enhancing phagocytosis (Wculek et al., 2022, Liu et al., 2022). In mice and humans, a lipid-associated macrophage is characterized by the marker Trem2 (Jaitlin et al., 2019). + PMID:31257031 + PMID:34876704 + PMID:35712121 + + + + + LAM + PMID:31257031 + + + + + + Distinct from “adipose macrophage” in Trem2 expression, and is not limited to adipose tissue. Guilliams et al. describe these cells as being distinct from Kupffer cells. + PMID:35021063 + PMID:37153549 + + + + + + + + + + + + + + + + + + + + + + + + + + A tissue-resident macrophage that is part of the placenta. This cell helps preventing immunological rejection of the fetus by modulating the immune environment. A placental resident macrophage has high plasticity to adapt to the changing needs of each phase of pregnancy. + + + 2024-10-31T10:24:21Z + placental macrophage + placental resident macrophage + + + + + A tissue-resident macrophage that is part of the placenta. This cell helps preventing immunological rejection of the fetus by modulating the immune environment. A placental resident macrophage has high plasticity to adapt to the changing needs of each phase of pregnancy. + PMID:39007150 + + + + + placental macrophage + PMID:39007150 + + + + + + + + + + + + + + + + A resident macrophage that is part of the decidua. Some decidual macrophages are derived from maternal blood monocytes that are recruited to the uterus shortly after conception. The main functions of a decidual macrophage are implantation, placental development, immune regulation and vascular remodeling. + + + 2024-10-31T10:33:04Z + decidual macrophage + maternal decidual macrophage + decidual resident macrophage + + + + + A resident macrophage that is part of the decidua. Some decidual macrophages are derived from maternal blood monocytes that are recruited to the uterus shortly after conception. The main functions of a decidual macrophage are implantation, placental development, immune regulation and vascular remodeling. + PMID:39007150 + + + + + decidual macrophage + PMID:39007150 + + + + + maternal decidual macrophage + PMID:39007150 + + + + + + + + + + + + + + + + + + + + + + + + + + A follicular cell of ovary that has begun to degenerate and undergo atresia, a specialized apoptosis. This cell is found in an atretic follicle, which is an ovarian follicle that started to mature but failed to reach full development and instead regresses. + + 2024-11-05T11:23:25Z + atretic follicular cell of ovary + + + + + A follicular cell of ovary that has begun to degenerate and undergo atresia, a specialized apoptosis. This cell is found in an atretic follicle, which is an ovarian follicle that started to mature but failed to reach full development and instead regresses. + PMID:38069168 + + + + + + + + + + + + + + + A granulosa cell that is undergoing atresia. This cell type displays distinct morphological alterations compared with a healthy granulosa cell, including pyknosis (nuclear condensation) and cellular shrinkage. + + 2024-11-05T11:25:28Z + apoptotic granulosa cell + atretic granulosa cell + + + + + A granulosa cell that is undergoing atresia. This cell type displays distinct morphological alterations compared with a healthy granulosa cell, including pyknosis (nuclear condensation) and cellular shrinkage. + PMID:15353131 + PMID:38069168 + + + + + apoptotic granulosa cell + PMID:15353131 + + + + + + + + + + + + + + + + + + + + + + + + + An amacrine cell that uses both GABA and glycine as neurotransmitters. + + 2024-12-02T13:44:17Z + glycinergic/GABAergic amacrine neuron + glycinergic-GABAergic amacrine cell + + + + + An amacrine cell that uses both GABA and glycine as neurotransmitters. + PMID:37124720 + + + + + glycinergic/GABAergic amacrine neuron + PMID:37124720 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + An enterocyte that is part of a duodenal epithelium and expresses beta-1,3-glucuronyltransferase 1 (B3GAT1), also known as CD57 or HNK-1. + + + + 2024-12-06T14:32:49Z + CD57+ enterocyte + While CD57 is traditionally associated with immune cells (e.g., NK cells), its expression on enterocytes marks unique epithelial subsets with specific functions or maturation states. These cells are specially enriched in areas of the duodenum within submucosal glands. + CD57-positive enterocyte + + + + + An enterocyte that is part of a duodenal epithelium and expresses beta-1,3-glucuronyltransferase 1 (B3GAT1), also known as CD57 or HNK-1. + PMID:37468586 + + + + + CD57+ enterocyte + PMID:37468586 + + + + + While CD57 is traditionally associated with immune cells (e.g., NK cells), its expression on enterocytes marks unique epithelial subsets with specific functions or maturation states. These cells are specially enriched in areas of the duodenum within submucosal glands. + PMID:37468586 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + A stem cell that is part of the corneo-scleral limbus. This cell type resides at the basal layer of the epithelium and has a small size and high nuclear to cytoplasmatic ratio (Secker and Daniels, 2009). A limbal stem cell is responsible for corneal epithelial renewal and repair (Li et al., 2023), and to help maintain a clear corneal surface by preventing conjunctival epithelial cells from migrating onto the cornea (Wang et al., 2023). + + + 2024-12-11T13:59:19Z + limbal epithelial stem cell + limbal stem cell + LESC + LSC + limbal epithelial stem cell of cornea + + + + + A stem cell that is part of the corneo-scleral limbus. This cell type resides at the basal layer of the epithelium and has a small size and high nuclear to cytoplasmatic ratio (Secker and Daniels, 2009). A limbal stem cell is responsible for corneal epithelial renewal and repair (Li et al., 2023), and to help maintain a clear corneal surface by preventing conjunctival epithelial cells from migrating onto the cornea (Wang et al., 2023). + PMID:20614614 + PMID:29105366 + PMID:36983561 + PMID:37768272 + + + + + limbal epithelial stem cell + PMID:20614614 + + + + + limbal stem cell + PMID:17562792 + + + + + LESC + PMID:20614614 + + + + + + LSC + PMID:36983561 + + + + + @@ -121373,7 +124671,7 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances 2023-04-03T15:08:05Z equine chorionic girdle cell - Humans, mice and rats have a highly invasive (hemochorial) placentation. Horses have a non-invasive epitheliochorial placenta, except for the transient endometrial cup. + Humans, mice and rats have a highly invasive (hemochorial) placentation. Horses have a non-invasive epitheliochorial placenta, except for the transient endometrial cup. chorionic girdle cell @@ -121391,7 +124689,7 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances - + Humans, mice and rats have a highly invasive (hemochorial) placentation. Horses have a non-invasive epitheliochorial placenta, except for the transient endometrial cup. PMID:27280409 @@ -121468,7 +124766,7 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances fetal pre-type 2 pneumocyte fetal pre-type II alveolar epithelial cell fetal pre-type II pneumocyte - According to PMID:1316350 this cell type does not yet produce surfactant. According to PMID:9109447 and PMID:12114192 this cell type produces low levels of surfactant that can be increased by administration of very low-density lipoproteins. This cell type is of medical relevance, as a central feature of the fetal respiratory distress syndrome seems to be the presence in the lung of abundant pre-type II alveolar epithelial cells (PMID:1316350). + According to PMID:1316350 this cell type does not yet produce surfactant. According to PMID:9109447 and PMID:12114192 this cell type produces low levels of surfactant that can be increased by administration of very low-density lipoproteins. This cell type is of medical relevance, as a central feature of the fetal respiratory distress syndrome seems to be the presence in the lung of abundant pre-type II alveolar epithelial cells (PMID:1316350). fetal pre-type II pulmonary alveolar epithelial cell @@ -121639,15 +124937,8 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances - + - - - - - - - @@ -121680,7 +124971,6 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances - @@ -122119,38 +125409,26 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances + - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + A transcriptomically distinct lamp5 GABAergic cortical interneuron located in the cerebral cortex that expresses Lamp5 and Lhx6. The standard transcriptomic reference data for this cell type can be found on the CellxGene census under the collection: 'Transcriptomic cytoarchitecture reveals principles of human neocortex organization', dataset: 'Supercluster: CGE-derived interneurons', Author Categories: 'CrossArea_subclass', Lamp5 Lhx6. + 2024-04-23T09:37:55Z Ivy cell Lamp5-Lhx6 type + The marker set CHST9, LAMP5 can identify the Human cell type Lamp5 Lhx6 neuron in the Brain with a confidence of 0.821678322 (NS-Forest FBeta value). Lamp5 Lhx6 neuron @@ -122175,6 +125453,12 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances Lamp5-Lhx6 type PMID:30382198 + + + + The marker set CHST9, LAMP5 can identify the Human cell type Lamp5 Lhx6 neuron in the Brain with a confidence of 0.821678322 (NS-Forest FBeta value). + https://doi.org/10.5281/zenodo.11165918 + @@ -122220,17 +125504,7 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances - - - - - - - - - - - + A VIP GABAergic cortical interneuron expressing vasoactive intestinal polypeptide and choline acetyltransferase in the Mmus neocortex. This interneuron releases both γ-aminobutyric acid and acetylcholine. 2024-07-11T12:22:48Z @@ -122644,14 +125918,8 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances - + - - - - - - @@ -122754,6 +126022,7 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances + @@ -122798,6 +126067,7 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances + @@ -122826,6 +126096,556 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances + + + + + A neuron in the central nervous system that is not committed to a differentiated fate, has not been newly derived from neurogenesis, and does not integrate into any circuit. + + 2024-10-10T09:14:45Z + IN + It is hypothesised that immature neurons can be utilised as a neurogenic reserve and that they can be involved in circuit plasticity. + immature neuron + + + + + A neuron in the central nervous system that is not committed to a differentiated fate, has not been newly derived from neurogenesis, and does not integrate into any circuit. + PMID:31096632 + PMID:32116519 + PMID:37833544 + + + + + IN + PMID:32116519 + + + + + + It is hypothesised that immature neurons can be utilised as a neurogenic reserve and that they can be involved in circuit plasticity. + PMID:32116519 + + + + + + + + + + + + + + + An immature neuron of a cerebral cortex. This neuron develops prenatally and remains in an immature state throughout the lifespan of the organism. + + 2024-10-10T09:14:54Z + cIN + cortical immature neuron + + + + + An immature neuron of a cerebral cortex. This neuron develops prenatally and remains in an immature state throughout the lifespan of the organism. + PMID:37833544 + + + + + cIN + PMID:37833544 + + + + + + + + + + A GABAergic interneuron located in the cerebellar cortex. This GABAergic interneuron type has a distinct morphology, it presents a small cell soma near the Purkinje cell layer (PCL), dendrites that extend to the surface of the molecular layer, and beaded axons that make local synapses contacts within the molecular layer. A candelabrum cell is excited by mossy fibers and granule cells but inhibited by Purkinje cells, and it inhibits molecular layer interneurons, which leads to the disinhibition of Purkinje cells. + + 2024-10-15T11:06:31Z + candelabrum interneuron + CC + Candelabrum cells are the most abundant interneurons in the Purkinje cell layer and are present in all cerebellar lobules. + candelabrum cell + + + + + A GABAergic interneuron located in the cerebellar cortex. This GABAergic interneuron type has a distinct morphology, it presents a small cell soma near the Purkinje cell layer (PCL), dendrites that extend to the surface of the molecular layer, and beaded axons that make local synapses contacts within the molecular layer. A candelabrum cell is excited by mossy fibers and granule cells but inhibited by Purkinje cells, and it inhibits molecular layer interneurons, which leads to the disinhibition of Purkinje cells. + PMID:35578131 + + + + + candelabrum interneuron + PMID:35578131 + + + + + CC + PMID:35578131 + + + + + + Candelabrum cells are the most abundant interneurons in the Purkinje cell layer and are present in all cerebellar lobules. + PMID:35578131 + + + + + + + + + + + + + + + An oligodendrocyte of the central nervous system that exhibits immune properties such as self-presentation and non-self antigen presentation to T cells, phagocytosis of debris, and cytokine and chemokine production. Immune oligodendroglia is immunoreactive during inflammation, neurodegenerative disorders, chronic stress and major depressive disorder. + + 2024-10-11T12:51:17Z + immune oligodendrocyte + Im-OL + ImOL + ImOLG + imOLG + During inflammation, immuno oligodendroglia express MHC II to interact with immune cells in mouse models (Harrington et al., 2023; Madeira et al., 2022). In a mouse model of major depressive disorder and chronic stress, immuno oligodendroglia were associated with prefrontal cortex hypomyelination (Kokkosis et al., 2022). + immune oligodendroglia + + + + + An oligodendrocyte of the central nervous system that exhibits immune properties such as self-presentation and non-self antigen presentation to T cells, phagocytosis of debris, and cytokine and chemokine production. Immune oligodendroglia is immunoreactive during inflammation, neurodegenerative disorders, chronic stress and major depressive disorder. + PMID:30747918 + PMID:35301426 + PMID:35615276 + PMID:35662200 + + + + + immune oligodendrocyte + PMID:35615276 + + + + + Im-OL + PMID:35301426 + + + + + + ImOL + PMID:35615276 + + + + + + ImOLG + PMID:30747918 + + + + + + imOLG + PMID:30747918 + + + + + + During inflammation, immuno oligodendroglia express MHC II to interact with immune cells in mouse models (Harrington et al., 2023; Madeira et al., 2022). In a mouse model of major depressive disorder and chronic stress, immuno oligodendroglia were associated with prefrontal cortex hypomyelination (Kokkosis et al., 2022). + PMID:35301426 + PMID:35615276 + PMID:37057892 + + + + + + + + + + + + + + + + + + + + + A transcriptomically distinct GABAergic neuron located in the cerebral cortex that expresses the transcript PAX6. The standard transcriptomic reference data for this cell type can be found on the CellxGene census under the collection: 'Transcriptomic cytoarchitecture reveals principles of human neocortex organization', dataset: 'Supercluster: CGE-derived interneurons', Author Categories: 'CrossArea_subclass', clusters PAX6. + + + 2024-10-11T13:25:51Z + The marker set RELN, HCRTR2 can identify the Human cell type http://purl.obolibrary.org/obo/CL_4042032 in the Brain with a confidence of 0.724125093 (NS-Forest FBeta value). + PAX6 GABAergic cortical interneuron + + + + + A transcriptomically distinct GABAergic neuron located in the cerebral cortex that expresses the transcript PAX6. The standard transcriptomic reference data for this cell type can be found on the CellxGene census under the collection: 'Transcriptomic cytoarchitecture reveals principles of human neocortex organization', dataset: 'Supercluster: CGE-derived interneurons', Author Categories: 'CrossArea_subclass', clusters PAX6. + PMID:37824655 + https://cellxgene.cziscience.com/e/e4ddac12-f48f-4455-8e8d-c2a48a683437.cxg/ + + + + + The marker set RELN, HCRTR2 can identify the Human cell type http://purl.obolibrary.org/obo/CL_4042032 in the Brain with a confidence of 0.724125093 (NS-Forest FBeta value). + https://doi.org/10.5281/zenodo.11165918 + + + + + + + + + + + + + + + A neuron of the central nervous system that expresses POMC and synthesizes the POMC precursor polypeptide. This neuron type is located in the arcuate nucleus of the hypothalamus and in the nucleus tractus solitarius of the brainstem. The pro-opiomelanocortin neuron is part of the central melanocortin system and it is involved in regulating energy homeostasis, metabolism, and appetite. This neuronal type responds to hormonal signals such as levels of leptin and insulin, and its activation results in the release of α-melanocyte-stimulating hormone (α-MSH), which acts on melanocortin receptors to suppress food intake and increase energy expenditure. + + 2024-10-15T10:17:41Z + POMC neuron + POMC-expressing neuron + Pro-opiomelanocortin neurons have a diverse projection pattern. The neurons in the rostral arcuate nucleus project to autonomic areas, caudal arcuate POMC neurons project mainly to hypothalamic areas (Toda et al., 2017). Dysregulation of pro-opiomelanocortin neurons is associated with obesity and metabolic disorders (Quarta et al., 2020). + pro-opiomelanocortin neuron + + + + + A neuron of the central nervous system that expresses POMC and synthesizes the POMC precursor polypeptide. This neuron type is located in the arcuate nucleus of the hypothalamus and in the nucleus tractus solitarius of the brainstem. The pro-opiomelanocortin neuron is part of the central melanocortin system and it is involved in regulating energy homeostasis, metabolism, and appetite. This neuronal type responds to hormonal signals such as levels of leptin and insulin, and its activation results in the release of α-melanocyte-stimulating hormone (α-MSH), which acts on melanocortin receptors to suppress food intake and increase energy expenditure. + PMID:25870542 + PMID:28192062 + + + + + POMC neuron + PMID:34002087 + + + + + POMC-expressing neuron + PMID:34002087 + + + + + Pro-opiomelanocortin neurons have a diverse projection pattern. The neurons in the rostral arcuate nucleus project to autonomic areas, caudal arcuate POMC neurons project mainly to hypothalamic areas (Toda et al., 2017). Dysregulation of pro-opiomelanocortin neurons is associated with obesity and metabolic disorders (Quarta et al., 2020). + PMID:28192062 + PMID:33633406 + + + + + + + + + + An interneuron neuron characterized by the expression of calcitonin gene-related peptide (CGRP), a 37-amino acid neuropeptide. This neuron type is involved in nociception and pain modulation by facilitating the transmission of nociceptive signals from peripheral sensory nerve endings to central nervous system structures. This neuron type is found in the dorsal root ganglia (DRG) and trigeminal ganglion, and the spinal cord dorsal horn. + + 2024-10-30T15:35:08Z + Calcitonin gene-related peptide neuron + CGRP-expressing interneuron + CGRP-positive neuron + CGRP-expressing neuron + + + + + An interneuron neuron characterized by the expression of calcitonin gene-related peptide (CGRP), a 37-amino acid neuropeptide. This neuron type is involved in nociception and pain modulation by facilitating the transmission of nociceptive signals from peripheral sensory nerve endings to central nervous system structures. This neuron type is found in the dorsal root ganglia (DRG) and trigeminal ganglion, and the spinal cord dorsal horn. + PMID:34061020 + + + + + Calcitonin gene-related peptide neuron + PMID:34061020 + + + + + CGRP-expressing interneuron + PMID:34061020 + + + + + CGRP-positive neuron + PMID:34061020 + + + + + + + + + A type of cerebellar inhibitory GABAergic interneuron that is located in the molecular layer of the cerebellum. This cell type inhibits Purkinje cells and other molecular layer interneurons. This interneuron plays a crucial role in regulating cerebellar output through feedforward inhibition and is characterized by its fast-spiking properties. + + 2024-10-31T15:55:31Z + MLI + molecular layer interneuron + + + + + A type of cerebellar inhibitory GABAergic interneuron that is located in the molecular layer of the cerebellum. This cell type inhibits Purkinje cells and other molecular layer interneurons. This interneuron plays a crucial role in regulating cerebellar output through feedforward inhibition and is characterized by its fast-spiking properties. + PMID:30742002 + PMID:33075461 + PMID:34616064 + PMID:38692278 + + + + + MLI + PMID:33075461 + + + + + + + + + + A neuron of the central nervous system with its soma primarily located in the lateral hypothalamic area and surrounding regions, including the zona incerta. This neuron type expresses melanin-concentrating hormone and is involved in regulating various physiological processes, including sleep, feeding behavior, and energy homeostasis. + + 2024-10-31T16:03:26Z + MCH neuron + Nearly all melanin-concentrating hormone neurons express the glutamate transporter VGlut2, however a small subset of them expresses the machinery for GABA release and neurotransmission. + melanin-concentrating hormone neuron + + + + + A neuron of the central nervous system with its soma primarily located in the lateral hypothalamic area and surrounding regions, including the zona incerta. This neuron type expresses melanin-concentrating hormone and is involved in regulating various physiological processes, including sleep, feeding behavior, and energy homeostasis. + PMID:30284033 + PMID:38020069 + PMID:39035036 + + + + + MCH neuron + PMID:30284033 + + + + + Nearly all melanin-concentrating hormone neurons express the glutamate transporter VGlut2, however a small subset of them expresses the machinery for GABA release and neurotransmission. + PMID:38020069 + + + + + + + + + + + + + + + + + A interneuron of the striatum expressing gamma-aminobutyric acid and somatostatin. This interneuron has a fusiform soma with a diameter between 9 - 25 µm, it has a long axon up to the length of 1mm. This neuron type displays a low threshold Ca2+ spike (LTS), a high input resistance, and the expression of long-lasting plateau potentials following depolarization from rest. + + 2024-11-27T18:33:46Z + SOM cell + striatal SST+ IN + Some striatal SST GABAergic neurons can co-release glutamate and generate excitation-inhibition responses in postsynaptic neurons. This interneuron type has the least dense dendritic branches in the striatum. In the dorsomedial striatum these neurons regulate the activity of striatal projection neurons. + sst GABAergic neuron of the striatum + + + + + A interneuron of the striatum expressing gamma-aminobutyric acid and somatostatin. This interneuron has a fusiform soma with a diameter between 9 - 25 µm, it has a long axon up to the length of 1mm. This neuron type displays a low threshold Ca2+ spike (LTS), a high input resistance, and the expression of long-lasting plateau potentials following depolarization from rest. + PMID:30131490 + PMID:30467465 + PMID:33742131 + + + + + SOM cell + PMID:30131490 + + + + + striatal SST+ IN + PMID:33742131 + + + + + Some striatal SST GABAergic neurons can co-release glutamate and generate excitation-inhibition responses in postsynaptic neurons. This interneuron type has the least dense dendritic branches in the striatum. In the dorsomedial striatum these neurons regulate the activity of striatal projection neurons. + PMID:30467465 + PMID:33742131 + + + + + + + + + A type of primary motor neuron situated in the rostral region of the spinal cord. RoP neurons extend their axons to innervate the ventral trunk musculature. + + 2024-11-13T13:42:01Z + RoP + rostral primary motorneuron + + + + + A type of primary motor neuron situated in the rostral region of the spinal cord. RoP neurons extend their axons to innervate the ventral trunk musculature. + PMID:35431796 + PMID:3746410 + + + + + RoP + PMID:3746410 + + + + + + + + + + + + + + + + + A neuron of the central nervous system that develops from a caudal ganglionic eminence. + + 2024-11-14T11:27:25Z + Neurons derived from the caudal ganglionic eminence consist mostly of neurons populating the cortical layers of the brain and some subcortical areas such as the globus pallidus, the striatus and the hippocampus. Amongst neurons derived from the caudal ganglionic eminence there are cortical GABAergic neurons such as Pax6, Lamp5, VIP, sncg, GABAergic; in the hippocampus, mossy fibers, pyramidal neurons, granule neurons and interneurons; in the striatum and globus pallidus, medium spiny projection neurons. + caudal ganglionic eminence derived neuron + + + + + A neuron of the central nervous system that develops from a caudal ganglionic eminence. + PMID:12593982 + PMID:12637172 + PMID:20130169 + https://www.ncbi.nlm.nih.gov/books/NBK98190/ + + + + + Neurons derived from the caudal ganglionic eminence consist mostly of neurons populating the cortical layers of the brain and some subcortical areas such as the globus pallidus, the striatus and the hippocampus. Amongst neurons derived from the caudal ganglionic eminence there are cortical GABAergic neurons such as Pax6, Lamp5, VIP, sncg, GABAergic; in the hippocampus, mossy fibers, pyramidal neurons, granule neurons and interneurons; in the striatum and globus pallidus, medium spiny projection neurons. + PMID:12593982 + PMID:12637172 + PMID:20130169 + https://www.ncbi.nlm.nih.gov/books/NBK98190/ + + + + + + + + + + + + + + + + A glutametergic neuron with its soma located in a basal ganglia. This neuron type is involved in motor control, decision making and learning. + + 2024-11-18T13:37:58Z + The glutametergic neurons in the basal ganglia are part of a series of different circuits such as the corticolstriatal circuit, which is involved in regulating voluntary movements. The subthalamic nucleus circuit, which is involved in modulating the output of the basal ganglia, particularly in controlling movement initiation and inhibition. The thalamocortical loop, which is involved in refining motor movements and integrating sensory information with motor commanding. + glutamatergic neuron of the basal ganglia + + + + + A glutametergic neuron with its soma located in a basal ganglia. This neuron type is involved in motor control, decision making and learning. + DOI:10.1016/j.jocn.2021.05.056 + PMID:11307040 + PMID:16276355 + + + + + The glutametergic neurons in the basal ganglia are part of a series of different circuits such as the corticolstriatal circuit, which is involved in regulating voluntary movements. The subthalamic nucleus circuit, which is involved in modulating the output of the basal ganglia, particularly in controlling movement initiation and inhibition. The thalamocortical loop, which is involved in refining motor movements and integrating sensory information with motor commanding. + PMID:22498715 + PMID:30498197 + PMID:33785138 + + + + + + + + + A type of primary motor neuron located in the middle region of the spinal cord. This primary motor neuron type is characterized by their distinct axonal pathways that innervate the middle trunk muscles. + + 2024-11-13T13:39:28Z + ZFA:0005179 + MiP + middle primary motoneuron + + + + + A type of primary motor neuron located in the middle region of the spinal cord. This primary motor neuron type is characterized by their distinct axonal pathways that innervate the middle trunk muscles. + PMID:35431796 + PMID:3746410 + + + + + MiP + PMID:3746410 + + + + + @@ -122858,8 +126678,6 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances A(n) stromal cell that is cycling. - - 2024-07-19T09:14:23Z proliferating stromal cell cycling stromal cell @@ -122910,8 +126728,6 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances A(n) glial cell that is cycling. - - 2024-07-19T09:14:23Z proliferating glial cell cycling glial cell @@ -122962,8 +126778,6 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances A(n) plasma cell that is cycling. - - 2024-07-19T09:14:23Z proliferating plasma cell cycling plasma cell @@ -123014,8 +126828,6 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances A(n) type EC enteroendocrine cell that is cycling. - - 2024-07-19T09:14:23Z proliferating type EC enteroendocrine cell cycling type EC enteroendocrine cell @@ -123067,8 +126879,6 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances A(n) neuroblast (sensu Vertebrata) that is cycling. - - 2024-07-19T09:14:23Z proliferating neuroblast (sensu Vertebrata) cycling neuroblast (sensu Vertebrata) @@ -123224,6 +127034,63 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances + + + + + + + + + + + + + + + + + + + + + + + + + + + + A transit amplifying cell of the gut epithelium, located in the wall of the intestinal crypt, just above intestinal stem cells from which they derive. These are rapidly dividing cells, capable of multiple rounds of division before differentiating into the various cell types of the gut epithelium (enterocyte, goblet, eneterodendocrine, paneth cells). + + 2024-09-24T10:48:47Z + transit-amplifying cell + TA cell + transit amplifying cell of gut + + + + + A transit amplifying cell of the gut epithelium, located in the wall of the intestinal crypt, just above intestinal stem cells from which they derive. These are rapidly dividing cells, capable of multiple rounds of division before differentiating into the various cell types of the gut epithelium (enterocyte, goblet, eneterodendocrine, paneth cells). + PMID:20683682 + PMID:33195268 + PMID:34497389 + + + + + transit-amplifying cell + PMID:24813615 + + + + + TA cell + PMID:20683682 + + + + @@ -123233,7 +127100,7 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances - + @@ -123298,6 +127165,210 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + A fibroblast located in the lamina propria of the intestinal mucosa. This cell expresses PDGFRα and CD81 and is negative for α-smooth muscle actin (α-SMA). This cell is predominantly located in the small intestine adjacent to myofibroblasts surrounding the crypts. It is capable of synthesizing extracellular matrix components and structural proteins such as collagen and elastin. + + 2024-09-24T15:45:18Z + S1 fibroblast + intestinal lamina propria fibroblast + + + + + A fibroblast located in the lamina propria of the intestinal mucosa. This cell expresses PDGFRα and CD81 and is negative for α-smooth muscle actin (α-SMA). This cell is predominantly located in the small intestine adjacent to myofibroblasts surrounding the crypts. It is capable of synthesizing extracellular matrix components and structural proteins such as collagen and elastin. + PMID:21252048 + PMID:36032088 + + + + + S1 fibroblast + PMID:30270042 + + + + + + + + + + + + + + + + + + + + + Any type G enteroendocrine cell that is part of some epithelium of stomach. + + 2024-10-24T10:43:22Z + type G cell of stomach + + + + + Any type G enteroendocrine cell that is part of some epithelium of stomach. + FBC:Autogenerated + + + + + + + + + An endothelial cell forming the walls of capillaries immediately downstream from arterioles, facilitating the exchange of substances between blood and interstitial fluid. This cell is characterized by a small diameter and may be continuous, fenestrated, or sinusoidal, depending on their location and function. This cell plays a crucial role in tissue oxygenation, nutrient delivery, and maintaining homeostasis within the microvascular network. + + 2024-11-07T12:50:06Z + post-arteriole capillary cell + + + + + An endothelial cell forming the walls of capillaries immediately downstream from arterioles, facilitating the exchange of substances between blood and interstitial fluid. This cell is characterized by a small diameter and may be continuous, fenestrated, or sinusoidal, depending on their location and function. This cell plays a crucial role in tissue oxygenation, nutrient delivery, and maintaining homeostasis within the microvascular network. + PMID:17893694 + PMID:35406678 + + + + + + + + + A specialized endothelial cell located in the transition zone between capillaries and small venules in the microvascular system. It exhibits characteristics of both capillary and venous cells, expressing markers from both types. This cell plays a role in regulating blood flow and substance exchange between blood and tissues. + + 2024-11-07T13:22:16Z + Cap-Venous endothelial cell + pre-venule capillary cell + + + + + A specialized endothelial cell located in the transition zone between capillaries and small venules in the microvascular system. It exhibits characteristics of both capillary and venous cells, expressing markers from both types. This cell plays a role in regulating blood flow and substance exchange between blood and tissues. + DOI:10.1038/s41467-022-33324-7 + PMID:23620236 + + + + + Cap-Venous endothelial cell + DOI:10.1038/s41467-022-33324-7 + + + + + + + + + + + + + + + + + + + + + + A specialized pericyte located within the basement membrane of a blood capillary. This cell is characterized by its ability to produce and release a variety of bioactive molecules, collectively known as the pericyte secretome, including cytokines and regulators of angiogenesis. + + 2024-11-07T15:36:16Z + secretory pericyte + + + + + A specialized pericyte located within the basement membrane of a blood capillary. This cell is characterized by its ability to produce and release a variety of bioactive molecules, collectively known as the pericyte secretome, including cytokines and regulators of angiogenesis. + DOI:10.3389/fncel.2019.00282 + + + + + + + + + + + + + + + A smooth muscle cell that is part of the muscularis externa of the stomach wall. It is characterized by its fusiform shape, involuntary control, and ability to generate slow, sustained contractions. This cell is organized in distinct layers and is essential for gastric motility and digestion. + + 2024-12-05T11:10:18Z + smooth muscle cell of stomach + + + + + A smooth muscle cell that is part of the muscularis externa of the stomach wall. It is characterized by its fusiform shape, involuntary control, and ability to generate slow, sustained contractions. This cell is organized in distinct layers and is essential for gastric motility and digestion. + PMID:21443757 + PMID:33630273 + + + + + + + + + A specialized smooth muscle cell located in the outermost layer of the muscularis externa of the stomach wall. This cell is arranged longitudinally along the stomach's axis and is responsible for the contractions that facilitate food movement toward the pylorus. + + 2024-12-05T16:13:49Z + stomach smooth muscle outer longitudinal layer cell + + + + + A specialized smooth muscle cell located in the outermost layer of the muscularis externa of the stomach wall. This cell is arranged longitudinally along the stomach's axis and is responsible for the contractions that facilitate food movement toward the pylorus. + PMID:21443757 + PMID:33630273 + + + + @@ -123364,17 +127435,129 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances - + - - - + + + + + + + + + + + + + - - + + + A natural killer cell resident to the liver, located in the hepatic sinusoids. In humans this cell type is distinguished from circulating natural killer cells by CD49a or CD69 gene expression. Liver-resident natural killer cells have also been shown to express CCR5, EOMES, KLRB1, GZMK, and CXCR6 in humans. + + https://orcid.org/0000-0001-8134-3037 + 2024-07-29T13:43:11Z + he-NK + hepatic NK + hepatic natural killer cells + intrahepatic NK + liver NK cell + liver resident natural killer cell + liver-specific natural killer cell + lr-NK + Liver-resident natural killer cells play a crucial role in modulating the immune response during inflammation by balancing cytotoxic activity and cytokine production, thereby contributing to the maintenance of liver homeostasis and protection against excessive tissue damage. + liver-resident natural killer cell + + + + + A natural killer cell resident to the liver, located in the hepatic sinusoids. In humans this cell type is distinguished from circulating natural killer cells by CD49a or CD69 gene expression. Liver-resident natural killer cells have also been shown to express CCR5, EOMES, KLRB1, GZMK, and CXCR6 in humans. + PMID:26330348 + PMID:26639736 + PMID:27798170 + PMID:31114585 + PMID:32351704 + PMID:34230995 + PMID:35865550 + + + + + he-NK + PMID:31114585 + + + + + hepatic NK + doi:10.3389/fimmu.2019.00946 + + + + + hepatic natural killer cells + doi:10.3389/fimmu.2019.00946 + + + + + intrahepatic NK + PMID:33828559 + + + + + liver NK cell + PMID:26639736 + + + + + liver resident natural killer cell + PMID:26330348 + + + + + lr-NK + PMID:35726345 + + + + + Liver-resident natural killer cells play a crucial role in modulating the immune response during inflammation by balancing cytotoxic activity and cytokine production, thereby contributing to the maintenance of liver homeostasis and protection against excessive tissue damage. + PMID:34230995 + + + + + + + + + + + + + + + + + + + + + + + + + + + + An ependymal cell that lines the lateral, third, and fourth ventricles of the brain. The cell is characterized by multiple motile cilia on its apical surface, which beats in a coordinated manner to facilitate the movement of cerebrospinal fluid (CSF), contributing to brain homeostasis. 2024-08-20T10:06:15Z @@ -123898,6 +128081,1009 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + A specialized theca cell that forms the inner, highly vascularized layer of the theca surrounding ovarian follicles. Originating from progenitor theca cells, the theca interna cell is steroidogenic, playing a crucial role in the production of androgens, which serves as a precursor for estrogen synthesis in granulosa cells. This cell expresses luteinizing hormone receptors, enabling it to respond to hormonal signals that regulate steroidogenesis. + + 2024-09-30T11:10:15Z + inTC + interna TC + interna theca cell + + + + + A specialized theca cell that forms the inner, highly vascularized layer of the theca surrounding ovarian follicles. Originating from progenitor theca cells, the theca interna cell is steroidogenic, playing a crucial role in the production of androgens, which serves as a precursor for estrogen synthesis in granulosa cells. This cell expresses luteinizing hormone receptors, enabling it to respond to hormonal signals that regulate steroidogenesis. + PMID:15833266 + PMID:31320652 + PMID:32530882 + Wikipedia:Theca_interna + + + + + inTC + PMID:31320652 + + + + + + interna TC + PMID:31320652 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + A specialized theca cell that forms the outer layer of the theca surrounding the ovarian follicle, appearing at the antral follicle. Originating from progenitor theca cells, theca externa cell is characterized by its fibroblast-like appearance and primarily function to provide structural support to the developing follicle. This cell produces collagen fibers and extracellular matrix components such as Col1a1 and Col1a2. + + 2024-09-30T11:10:15Z + exTC + externa TC + externa theca cell + + + + + A specialized theca cell that forms the outer layer of the theca surrounding the ovarian follicle, appearing at the antral follicle. Originating from progenitor theca cells, theca externa cell is characterized by its fibroblast-like appearance and primarily function to provide structural support to the developing follicle. This cell produces collagen fibers and extracellular matrix components such as Col1a1 and Col1a2. + PMID:31320652 + PMID:32530882 + PMID:36758341 + Wikipedia:Theca_externa + + + + + exTC + PMID:31320652 + + + + + + externa TC + PMID:31320652 + + + + + + + + + + + + + + + + + + + + + + + + + + + + A capillary endothelial cell that is part of islet of Langerhans, characterized by a high density of fenestrations —approximately ten times greater than those in exocrine pancreatic capillaries. These fenestrations facilitate efficient hormone exchange, which is essential for maintaining glucose homeostasis. The cell's structure and function are regulated by the local production of vascular endothelial growth factor-A (VEGF-A), which maintains its fenestrated architecture. + + 2024-09-30T14:36:12Z + islet endothelial cell + pancreatic islet endothelial cell + pancreatic islet capillary endothelial cell + + + + + A capillary endothelial cell that is part of islet of Langerhans, characterized by a high density of fenestrations —approximately ten times greater than those in exocrine pancreatic capillaries. These fenestrations facilitate efficient hormone exchange, which is essential for maintaining glucose homeostasis. The cell's structure and function are regulated by the local production of vascular endothelial growth factor-A (VEGF-A), which maintains its fenestrated architecture. + PMID:16607697 + PMID:27124642 + PMID:28396983 + PMID:33200981 + + + + + islet endothelial cell + PMID:16607697 + PMID:28396983 + + + + + pancreatic islet endothelial cell + PMID:16607697 + + + + + + + + + + + + + + + + + + + + + + + + + + Any capillary endothelial cell that is part of an endocrine gland. + + 2024-09-30T15:27:49Z + endocrine gland capillary endothelial cell + + + + + Any capillary endothelial cell that is part of an endocrine gland. + PMID:18480313 + + + + + + + + + + + + + + + + + + + + + + + A capillary endothelial cell that is part of the pituitary gland. This cell is characterized by its fenestrated structure which facilitates the efficient transport of hormones and other signaling molecules, essential for endocrine signalling. + + 2024-09-30T15:31:45Z + In the anterior pituitary gland of rats, capillary endothelial cells are distinguished by numerous fenestrations, which are covered by a single-layered diaphragm. The diaphragm features a dense ring-like structure. + pituitary gland capillary endothelial cell + + + + + A capillary endothelial cell that is part of the pituitary gland. This cell is characterized by its fenestrated structure which facilitates the efficient transport of hormones and other signaling molecules, essential for endocrine signalling. + PMID:10810312 + PMID:32910242 + + + + + In the anterior pituitary gland of rats, capillary endothelial cells are distinguished by numerous fenestrations, which are covered by a single-layered diaphragm. The diaphragm features a dense ring-like structure. + PMID:4899902 + + + + + + + + + + + + + + + + + + + + + + + + + + + + A capillary endothelial cell that is part of the choroid plexus, characterized by its fenestrated nature with 60 to 80 nm fenestrations and lack of tight junctions. This fenestrated structure allows for the rapid delivery of water and other components, aiding in the production of cerebrospinal fluid (CSF). + + 2024-10-01T11:38:22Z + choroid plexus capillary endothelial cell + + + + + A capillary endothelial cell that is part of the choroid plexus, characterized by its fenestrated nature with 60 to 80 nm fenestrations and lack of tight junctions. This fenestrated structure allows for the rapid delivery of water and other components, aiding in the production of cerebrospinal fluid (CSF). + PMID:18480313 + PMID:32375819 + https://www.ncbi.nlm.nih.gov/books/NBK27998/ + + + + + + + + + + + + + + + + + + + + + + + + + + Any epithelial cell that is part of the fallopian tube. + + 2024-10-01T12:09:12Z + oviduct epithelial cell + uterine tube epithelial cell + fallopian tube epithelial cell + + + + + Any epithelial cell that is part of the fallopian tube. + Wikipedia:Fallopian_tube + + + + + oviduct epithelial cell + Wikipedia:Fallopian_tube + + + + + uterine tube epithelial cell + Wikipedia:Fallopian_tube + + + + + + + + + + + + + + + Any epithelial cell that is part of the fallopian tube and lacks cilia. + + 2024-10-01T12:12:12Z + fallopian tube non-ciliated cell + + + + + + + + + + + + + + + + + + + + + A granzyme K-associated CD8 T cell that resides in the lung, characterized by the expression of granzyme K (GZMK), and tissue residency markers CD103 and CD49a. This cell exhibits cytotoxic potential through its expression of multiple granzymes (GZMA, GZMB, GZMH, GZMM) in addition to GZMK. + + + 2024-10-14T15:42:41Z + lung resident CD8-GZMK + Lung resident granzyme K-associated CD8 T cell represents an intermediate stage of T cell differentiation, with GZMK expression peaking during this phase. + lung resident granzyme K-associated CD8 T cell + + + + + A granzyme K-associated CD8 T cell that resides in the lung, characterized by the expression of granzyme K (GZMK), and tissue residency markers CD103 and CD49a. This cell exhibits cytotoxic potential through its expression of multiple granzymes (GZMA, GZMB, GZMH, GZMM) in addition to GZMK. + doi:/10.1101/2022.06.17.496207 + + + + + lung resident CD8-GZMK + doi:/10.1101/2022.06.17.496207 + + + + + + Lung resident granzyme K-associated CD8 T cell represents an intermediate stage of T cell differentiation, with GZMK expression peaking during this phase. + PMID:28322863 + doi:/10.1101/2022.06.17.496207 + + + + + + + + + + + + + + + + + + + + + + + + + + A CD8 T cell characterized by high expression of Granzyme K (GZMK). This cell is enriched in both inflamed tissues, such as synovial tissue in rheumatoid arthritis and respiratory tissues during COVID-19, as well as non-inflamed tissues like the gut and kidneys. Unlike highly cytotoxic GZMB+ CD8+ T cell, GZMK+ CD8+ T cell exhibits lower direct cytotoxic potential, and is involved in producing pro-inflammatory cytokines such as IFN-γ and TNF-α. + + 2024-10-18T09:51:48Z + granzyme K+ CD8 T cell + tissue-enriched expressing GzmK CD8 cell + GZMK high CD8+ T effector memory cell + CD8-GZMK cell + TteK CD8 cell + granzyme K-associated CD8 T cell + + + + + A CD8 T cell characterized by high expression of Granzyme K (GZMK). This cell is enriched in both inflamed tissues, such as synovial tissue in rheumatoid arthritis and respiratory tissues during COVID-19, as well as non-inflamed tissues like the gut and kidneys. Unlike highly cytotoxic GZMB+ CD8+ T cell, GZMK+ CD8+ T cell exhibits lower direct cytotoxic potential, and is involved in producing pro-inflammatory cytokines such as IFN-γ and TNF-α. + PMID:35704599 + PMID:37449888 + + + + + granzyme K+ CD8 T cell + PMID:35704599 + + + + + tissue-enriched expressing GzmK CD8 cell + PMID:35704599 + + + + + GZMK high CD8+ T effector memory cell + PMID:36347862 + + + + + CD8-GZMK cell + doi:/10.1101/2022.06.17.496207 + + + + + + TteK CD8 cell + PMID:35704599 + + + + + + + + + + + + + + + + + + + + + + + + + + + A smooth muscle cell that is part of the fallopian tube. This cell is responsible for peristaltic contractions that facilitate gamete and embryo transport, fluid mixing, and embryo admission to the uterus. + + 2024-10-21T12:16:54Z + oviduct smooth muscle cell + uterine tube smooth muscle cell + The fallopian tube smooth muscle cell in the human contracts dynamically in response to hormones and signaling molecules. Prostaglandins, particularly PGF2α and PGE2, have been shown to increase muscular contractions, while progesterone, levonorgestrel, mifepristone, oxytocin, and human chorionic gonadotropin (hCG) decrease them. These contractile responses are crucial for regulating gamete and embryo transport through the fallopian tube. + fallopian tube smooth muscle cell + + + + + A smooth muscle cell that is part of the fallopian tube. This cell is responsible for peristaltic contractions that facilitate gamete and embryo transport, fluid mixing, and embryo admission to the uterus. + PMID:31183831 + PMID:31613440 + + + + + oviduct smooth muscle cell + PMID:31613440 + + + + + uterine tube smooth muscle cell + PMID:31613440 + + + + + The fallopian tube smooth muscle cell in the human contracts dynamically in response to hormones and signaling molecules. Prostaglandins, particularly PGF2α and PGE2, have been shown to increase muscular contractions, while progesterone, levonorgestrel, mifepristone, oxytocin, and human chorionic gonadotropin (hCG) decrease them. These contractile responses are crucial for regulating gamete and embryo transport through the fallopian tube. + PMID:18621753 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + An epithelial cell that is part of the endometrial luminal epithelium, forming a continuous layer lining the uterine cavity. This cell undergoes cyclical changes during the menstrual cycle, proliferating under estrogen in the proliferative phase, and differentiating under progesterone in the secretory phase to prepare for potential implantation. During the window of implantation, this cell changes from a tall columnar shape to a shorter columnar or cuboidal form, loses polarity, and becomes receptive to blastocyst implantation. + + 2024-10-22T12:02:23Z + endometrial luminal epithelial cell + luminal cell of endometrium + The luminal endometrial unciliated epithelial cell expresses WNT7A, and LGR5 during the proliferative phase, transitioning to express VTCN1 and SULT1E1 in the early secretory phase, and LEFTY1, IL6, and PTGS1 in the mid- to late-secretory phases. + luminal endometrial unciliated epithelial cell + + + + + An epithelial cell that is part of the endometrial luminal epithelium, forming a continuous layer lining the uterine cavity. This cell undergoes cyclical changes during the menstrual cycle, proliferating under estrogen in the proliferative phase, and differentiating under progesterone in the secretory phase to prepare for potential implantation. During the window of implantation, this cell changes from a tall columnar shape to a shorter columnar or cuboidal form, loses polarity, and becomes receptive to blastocyst implantation. + PMID:32929266 + PMID:36581776 + PMID:38559249 + PMID:39198675 + + + + + endometrial luminal epithelial cell + PMID:31317179 + + + + + The luminal endometrial unciliated epithelial cell expresses WNT7A, and LGR5 during the proliferative phase, transitioning to express VTCN1 and SULT1E1 in the early secretory phase, and LEFTY1, IL6, and PTGS1 in the mid- to late-secretory phases. + PMID:39198675 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + A specialized muscle nucleus that is part of an extrafusal muscle fiber and overlaps the muscle-tendon junction, where muscle fibers connect to tendons. Characterized by a distinct transcriptional profile with the expression of genes like COL22A1, this myonucleus supports the structural integrity and function of the junction, playing a key role in transmitting the force generated by muscle contraction to the tendon. + + + 2024-10-30T13:47:39Z + myotendinous junction myonuclei + myotendinous junction nuclei + MTJ nucleus + myotendinous junction nucleus + + + + + A specialized muscle nucleus that is part of an extrafusal muscle fiber and overlaps the muscle-tendon junction, where muscle fibers connect to tendons. Characterized by a distinct transcriptional profile with the expression of genes like COL22A1, this myonucleus supports the structural integrity and function of the junction, playing a key role in transmitting the force generated by muscle contraction to the tendon. + PMID:33311457 + PMID:33311464 + PMID:38398025 + + + + + myotendinous junction myonuclei + PMID:33311464 + + + + + + myotendinous junction nuclei + PMID:33311457 + + + + + + MTJ nucleus + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + A specialized muscle nucleus that is part of an extrafusal muscle fiber, clustered at the postsynaptic side of the neuromuscular junction. This nucleus exhibits a distinct transcriptional profile, including acetylcholine receptor (AChR) subunit genes. It regulates the production of proteins essential for maintaining the structure and function of the neuromuscular junction, supporting efficient nerve-muscle signaling for muscle contraction. + + + 2024-10-31T11:09:04Z + neuromuscular junction myonuclei + neuromuscular junction nuclei + NMJ nuclues + neuromuscular junction nucleus + + + + + A specialized muscle nucleus that is part of an extrafusal muscle fiber, clustered at the postsynaptic side of the neuromuscular junction. This nucleus exhibits a distinct transcriptional profile, including acetylcholine receptor (AChR) subunit genes. It regulates the production of proteins essential for maintaining the structure and function of the neuromuscular junction, supporting efficient nerve-muscle signaling for muscle contraction. + PMID:33037211 + PMID:33311457 + PMID:33311464 + + + + + neuromuscular junction myonuclei + PMID:33311464 + + + + + + neuromuscular junction nuclei + PMID:33311457 + + + + + + NMJ nuclues + + + + + + + + + + A fast type II muscle cell that is part of the skeletal muscle tissue. This cell is characterized by its intermediate metabolic profile, utilizing both glycolytic and oxidative pathways for energy production. In humans, it is distinguished by the expression of myosin heavy chain 1 (MYH1). + + 2024-11-04T10:26:29Z + type 2x fiber + type 2x muscle cell + type 2x muscle fiber + type IIx muscle fiber + In humans, type IIx fiber contains high levels of MYLK2, enhancing contraction speed and force via myosin phosphorylation, especially under low calcium. This mechanism supports post-activation potentiation, increasing force output in fast-twitch muscles. Additionally, this fiber has abundant ACTN3 (α-actinin-3), linked to muscle power, and exhibits the highest shortening velocity among human muscle fiber types. Notably, type IIx fiber is selectively lost in aging-related sarcopenia, increases in proportion in type 2 diabetes and obesity, and is the first to degenerate in Duchenne Muscular Dystrophy, impacting muscle function across various conditions. + type IIx muscle cell + + + + + A fast type II muscle cell that is part of the skeletal muscle tissue. This cell is characterized by its intermediate metabolic profile, utilizing both glycolytic and oxidative pathways for energy production. In humans, it is distinguished by the expression of myosin heavy chain 1 (MYH1). + PMID:34727990 + PMID:35908794 + PMID:36361732 + doi:10.1101/2024.05.15.594276 + + + + + type 2x fiber + PMID:34727990 + + + + + type 2x muscle cell + PMID:34727990 + + + + + type 2x muscle fiber + PMID:34727990 + + + + + type IIx muscle fiber + doi:10.1101/2024.05.15.594276 + + + + + In humans, type IIx fiber contains high levels of MYLK2, enhancing contraction speed and force via myosin phosphorylation, especially under low calcium. This mechanism supports post-activation potentiation, increasing force output in fast-twitch muscles. Additionally, this fiber has abundant ACTN3 (α-actinin-3), linked to muscle power, and exhibits the highest shortening velocity among human muscle fiber types. Notably, type IIx fiber is selectively lost in aging-related sarcopenia, increases in proportion in type 2 diabetes and obesity, and is the first to degenerate in Duchenne Muscular Dystrophy, impacting muscle function across various conditions. + PMID:27199166 + PMID:34727990 + + + + + + + + + + + + + + + A theca cell undergoing atresia, characterized by distinct morphological changes including hypertrophy, altered cell shape, and disrupted layered organization. This cell exhibits reduced steroidogenic capacity and changes in surrounding vascularization. The onset of theca cell atresia can vary, occurring at different stages of follicle atresia depending on the phase of folliculogenesis. + + 2024-11-06T10:10:51Z + During atresia, theca interna and externa cells undergo distinct morphological and functional changes. Theca interna cells round up, expand in cytoplasmic area, and thicken the internal layer as organization degrades, while showing reduced STAR expression, which lowers androgen production. Theca externa cells display decreased ACTA2 expression, weakening structural integrity. + atretic theca cell + + + + + A theca cell undergoing atresia, characterized by distinct morphological changes including hypertrophy, altered cell shape, and disrupted layered organization. This cell exhibits reduced steroidogenic capacity and changes in surrounding vascularization. The onset of theca cell atresia can vary, occurring at different stages of follicle atresia depending on the phase of folliculogenesis. + PMID:20628033 + PMID:38069168 + + + + + During atresia, theca interna and externa cells undergo distinct morphological and functional changes. Theca interna cells round up, expand in cytoplasmic area, and thicken the internal layer as organization degrades, while showing reduced STAR expression, which lowers androgen production. Theca externa cells display decreased ACTA2 expression, weakening structural integrity. + PMID:38069168 + + + + + + + + + + + + + + + + + + + + + + + + + + A natural killer cell that is part of the uterus, specifically within the endometrium during the non-pregnant state and in the decidua during pregnancy. This cell exhibits dynamic changes in frequency throughout the menstrual cycle, with lower levels during menstruation and a significant increase during the mid-secretory phase and early pregnancy. + + 2024-11-15T10:12:40Z + endometrial natural killer cell + uNK cell + uterine natural killer cell + + + + + A natural killer cell that is part of the uterus, specifically within the endometrium during the non-pregnant state and in the decidua during pregnancy. This cell exhibits dynamic changes in frequency throughout the menstrual cycle, with lower levels during menstruation and a significant increase during the mid-secretory phase and early pregnancy. + PMID:35720413 + PMID:39198675 + Wikipedia:Uterine_natural_killer_cells + + + + + endometrial natural killer cell + PMID:35720413 + + + + + uNK cell + PMID:39198675 + + + + + + + + + + A fibroblast that is located beneath the visceral pleura of the lung. This cell contributes to the development of idiopathic pulmonary fibrosis (IPF) by forming fibrotic lesions that originate subpleurally and extend into lung tissue through activation, proliferation, migration, and differentiation into a myofibroblast. + + 2024-11-29T13:54:15Z + subpleural fibroblast + + + + + A fibroblast that is located beneath the visceral pleura of the lung. This cell contributes to the development of idiopathic pulmonary fibrosis (IPF) by forming fibrotic lesions that originate subpleurally and extend into lung tissue through activation, proliferation, migration, and differentiation into a myofibroblast. + PMID:36543915 + PMID:36769178 + PMID:37291214 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + A fibroblast of the adventitia of a blood vessel. This cell contributes to vascular homeostasis, remodeling, and inflammation by producing extracellular matrix components, cytokines, and growth factors. Adventitial fibroblast can transition into an activated state during injury or disease, marked by increased proliferation, migration, matrix deposition, and contractile protein expression + + 2024-12-05T11:01:15Z + Single-cell transcriptomics of murine aorta identifies two adventitial fibroblast-specific markers, PDGFRA and DPEP1, which were validated at the protein level by immunohistochemistry and flow cytometry across human and murine arteries, highlighting fibroblast heterogeneity in health and cardiovascular disease (CVD) in humans and mice. + adventitial fibroblast + + + + + A fibroblast of the adventitia of a blood vessel. This cell contributes to vascular homeostasis, remodeling, and inflammation by producing extracellular matrix components, cytokines, and growth factors. Adventitial fibroblast can transition into an activated state during injury or disease, marked by increased proliferation, migration, matrix deposition, and contractile protein expression + PMID:28705796 + PMID:36718802 + + + + + Single-cell transcriptomics of murine aorta identifies two adventitial fibroblast-specific markers, PDGFRA and DPEP1, which were validated at the protein level by immunohistochemistry and flow cytometry across human and murine arteries, highlighting fibroblast heterogeneity in health and cardiovascular disease (CVD) in humans and mice. + PMID:36718802 + + + + + + + + + + + + + + + + + + A secretory epithelial cell of the respiratory and terminal bronchioles. + + 2024-11-29T16:14:31Z + RAS cell + terminal and respiratory bronchioles secretory cell + The respiratory airway secretory cell is cuboidal and has a unique transcriptomic profile compared to other epithelial cells in the same region. In humans, it functions as a multipotent progenitor, capable of regenerating alveolar type 2 (AT2) cells. + respiratory airway secretory cell + + + + + A secretory epithelial cell of the respiratory and terminal bronchioles. + PMID:35355013 + PMID:36796082 + + + + + RAS cell + PMID:36796082 + + + + + + terminal and respiratory bronchioles secretory cell + PMID:35355018 + + + + + The respiratory airway secretory cell is cuboidal and has a unique transcriptomic profile compared to other epithelial cells in the same region. In humans, it functions as a multipotent progenitor, capable of regenerating alveolar type 2 (AT2) cells. + PMID:35355013 + PMID:36796082 + + + + @@ -124149,6 +129335,12 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances + + + + + + @@ -124161,6 +129353,12 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances + + + + + + @@ -124461,6 +129659,12 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances + + + + + + @@ -124485,6 +129689,12 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances + + + + + + @@ -124689,6 +129899,12 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances + + + + + + @@ -125085,6 +130301,18 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances + + + + + + + + + + + + @@ -125373,6 +130601,12 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances + + + + + + @@ -125415,6 +130649,12 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances + + + + + + @@ -125439,6 +130679,12 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances + + + + + + @@ -125529,6 +130775,12 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances + + + + + + @@ -125601,12 +130853,6 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances - - - - - - @@ -125835,6 +131081,18 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances + + + + + + + + + + + + @@ -126741,6 +131999,12 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances + + + + + + @@ -127263,6 +132527,12 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances + + + + + + @@ -127533,12 +132803,24 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances + + + + + + + + + + + + @@ -127641,6 +132923,12 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances + + + + + + @@ -127683,12 +132971,6 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances - - - - - - @@ -128037,6 +133319,24 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances + + + + + + + + + + + + + + + + + + @@ -128139,6 +133439,12 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances + + + + + + @@ -128187,6 +133493,12 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances + + + + + + @@ -128511,12 +133823,6 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances - - - - - - @@ -128529,6 +133835,12 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances + + + + + + @@ -128613,12 +133925,6 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances - - - - - - @@ -128769,12 +134075,6 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances - - - - - - @@ -130035,6 +135335,12 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances + + + + + + @@ -130125,6 +135431,12 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances + + + + + + @@ -130191,6 +135503,12 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances + + + + + + @@ -130287,6 +135605,12 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances + + + + + + @@ -130473,6 +135797,12 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances + + + + + + @@ -130851,12 +136181,6 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances - - - - - - @@ -131019,12 +136343,6 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances - - - - - - @@ -131241,9 +136559,9 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances - + - + @@ -131349,6 +136667,12 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances + + + + + + @@ -131391,6 +136715,12 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances + + + + + + @@ -131661,6 +136991,12 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances + + + + + + @@ -131679,6 +137015,12 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances + + + + + + @@ -131829,6 +137171,12 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances + + + + + + @@ -131943,6 +137291,12 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances + + + + + + @@ -131955,6 +137309,12 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances + + + + + + @@ -132261,14 +137621,14 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances - + - + - + diff --git a/cl.obo b/cl.obo index 557afc05e..c3843a129 100644 --- a/cl.obo +++ b/cl.obo @@ -1,5 +1,5 @@ format-version: 1.2 -data-version: releases/2024-09-26 +data-version: releases/2025-01-07 subsetdef: abnormal_slim "" subsetdef: added_for_HCA "" subsetdef: attribute_slim "" @@ -44,10 +44,12 @@ subsetdef: http://purl.obolibrary.org/obo/valid_for_go_gp2term "" subsetdef: http://purl.obolibrary.org/obo/valid_for_go_ontology "" subsetdef: http://purl.obolibrary.org/obo/valid_for_gocam "" subsetdef: human_reference_atlas "" +subsetdef: human_subset "" subsetdef: inconsistent_with_fma "" subsetdef: kidney_upper_slim "a subset of general classes related to specific cell types in the kidney" subsetdef: location_grouping "" subsetdef: major_organ "" +subsetdef: mouse_subset "" subsetdef: mpath_slim "" subsetdef: non_informative "" subsetdef: organ_slim "" @@ -100,7 +102,7 @@ ontology: cl property_value: dc:description "An ontology of cell types." xsd:string property_value: dc:title "Cell Ontology" xsd:string property_value: has_ontology_root_term CL:0000000 -property_value: owl:versionInfo "2024-09-26" xsd:string +property_value: owl:versionInfo "2025-01-07" xsd:string property_value: terms:contributor https://orcid.org/0000-0001-5208-3432 property_value: terms:contributor https://orcid.org/0000-0001-9114-8737 property_value: terms:contributor https://orcid.org/0000-0001-9990-8331 @@ -120,7 +122,7 @@ is_a: BFO:0000040 id: CHEBI:36080 is_a: BFO:0000002 is_a: PR:000018263 ! amino acid chain -is_a: PR:000050567 ! protein-containing material entity +is_a: PR:000064867 ! protein-containing molecular entity equivalent_to: PR:000000001 ! protein [Term] @@ -129,6 +131,8 @@ name: cell def: "A material entity of anatomical origin (part of or deriving from an organism) that has as its parts a maximally connected cell compartment surrounded by a plasma membrane." [CARO:mah] comment: The definition of cell is intended to represent all cells, and thus a cell is defined as a material entity and not an anatomical structure, which implies that it is part of an organism (or the entirety of one). subset: cellxgene_subset +subset: human_subset +subset: mouse_subset subset: ubprop:upper_level xref: CALOHA:TS-2035 xref: FBbt:00007002 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} @@ -144,8 +148,6 @@ is_a: UBERON:0000061 ! anatomical structure disjoint_from: GO:0031012 ! extracellular matrix disjoint_from: GO:0032991 ! protein-containing complex disjoint_from: GO:0043226 ! organelle -relationship: has_part GO:0005634 {gci_filler="PATO:0001407", gci_relation="bearer_of"} ! nucleus -relationship: has_part GO:0005634 {gci_filler="PATO:0001908", gci_relation="bearer_of"} ! nucleus relationship: RO:0002162 NCBITaxon:131567 ! in taxon cellular organisms [Term] @@ -154,6 +156,8 @@ name: primary cultured cell def: "A cultured cell that is freshly isolated from a organismal source, or derives in culture from such a cell prior to the culture being passaged." [ReO:mhb] comment: Covers cells actively being cultured or stored in a quiescent state for future use. subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "primary cell culture cell" EXACT [] synonym: "primary cell line cell" RELATED [] synonym: "unpassaged cultured cell" EXACT [] @@ -174,7 +178,6 @@ replaced_by: CLO:0000019 id: CL:0000003 name: obsolete native cell def: "OBSOLETE. A cell that is found in a natural setting, which includes multicellular organism cells 'in vivo' (i.e. part of an organism), and unicellular organisms 'in environment' (i.e. part of a natural environment)." [CARO:mah] -subset: cellxgene_subset subset: ubprop:upper_level synonym: "cell in vivo" NARROW [] xref: CARO:0000013 @@ -196,6 +199,8 @@ consider: CL:0001034 id: CL:0000005 name: neural crest derived fibroblast def: "Any fibroblast that is derived from the neural crest." [https://orcid.org/0000-0001-5208-3432] +subset: human_subset +subset: mouse_subset synonym: "fibroblast neural crest derived" EXACT [] is_a: CL:0000057 ! fibroblast intersection_of: CL:0000057 ! fibroblast @@ -207,6 +212,8 @@ id: CL:0000006 name: neuronal receptor cell def: "Any sensory receptor cell that is a(n) neuron and is capable of some detection of stimulus involved in sensory perception." [FBC:Autogenerated] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "neuronal receptor cell (sensu Animalia)" EXACT [] xref: ZFA:0009001 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000101 ! sensory neuron @@ -219,6 +226,8 @@ intersection_of: capable_of GO:0050906 ! detection of stimulus involved in senso id: CL:0000007 name: early embryonic cell (metazoa) def: "A cell found in the embryo before the formation of all the gem layers is complete." [GOC:tfm] +subset: human_subset +subset: mouse_subset xref: ZFA:0009002 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0002321 ! embryonic cell (metazoa) @@ -226,6 +235,8 @@ is_a: CL:0002321 ! embryonic cell (metazoa) id: CL:0000008 name: migratory cranial neural crest cell def: "Cell that is part of the migratory cranial neural crest population. Migratory cranial neural crest cells develop from premigratory cranial neural crest cells and have undergone epithelial to mesenchymal transition and delamination." [https://orcid.org/0000-0001-5208-3432, ZFA:0007091] +subset: human_subset +subset: mouse_subset xref: ZFA:0007091 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000333 ! migratory neural crest cell @@ -244,6 +255,8 @@ id: CL:0000010 name: cultured cell def: "A cell in vitro that is or has been maintained or propagated as part of a cell culture." [ReO:mhb] comment: Note that this class was re-labeled to 'cultured cell' instead of 'cell line cell', as it intent was clarified to cover any cultured cells of multicellular and unicellular organisms. This includes cells actively being cultured, or cells that have been cultured but are stored in a quiescent state for future use. In having been cultured, cells must establish homeostasis and often replicate in a foreign environment. Accomodation of this stress initiates a selection of cells fit for such challenges, wherein necessary adaptive biochemical and.or genetic changes can occur. These changes can set them apart from the in vivo cells from which they derive, and such changes will typically accumulate and change over increasing time in culture. +subset: human_subset +subset: mouse_subset xref: MESH:D002478 is_a: CL:0000578 ! experimentally modified cell in vitro @@ -251,6 +264,8 @@ is_a: CL:0000578 ! experimentally modified cell in vitro id: CL:0000011 name: migratory trunk neural crest cell def: "Cell that is part of the migratory trunk neural crest population. Migratory trunk neural crest cells develop from premigratory trunk neural crest cells and have undergone epithelial to mesenchymal transition and delamination." [https://orcid.org/0000-0001-5208-3432, ZFA:0007095] +subset: human_subset +subset: mouse_subset xref: ZFA:0007095 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000333 ! migratory neural crest cell @@ -273,6 +288,8 @@ consider: CL:0000140 id: CL:0000014 name: germ line stem cell def: "A stem cell that is the precursor of gametes." [doi:10.1016/j.stem.2012.05.016] +subset: human_subset +subset: mouse_subset synonym: "germline stem cell" EXACT [] xref: FBbt:00004861 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: ZFA:0005956 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} @@ -286,18 +303,24 @@ id: CL:0000015 name: male germ cell def: "A germ cell that supports male gamete production. In some species, non-germ cells known as Sertoli cells also play a role in spermatogenesis." [https://orcid.org/0000-0001-5208-3432, PMID:29462262] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset xref: FMA:72290 +xref: https://cellxgene.cziscience.com/cellguide/CL_0000015 xref: MA:0002765 xref: ncithesaurus:Spermatogenic_Cell xref: VHOG:0001531 is_a: CL:0000586 {is_inferred="true"} ! germ cell relationship: capable_of_part_of GO:0007283 ! spermatogenesis property_value: seeAlso "https://github.com/obophenotype/cell-ontology/issues/574" xsd:string +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nMale germ cells are specialized cells that give rise to the male gametes and are therefore crucial for sexual reproduction in males. Through a complex process called spermatogenesis in the testes male germ cells undergo several stages of development, each with distinctive morphological and physiological characteristics, eventually differentiating into mature spermatozoa (sperm). \nMale germ cells are responsible for transferring genetic material from male to offspring as part of sexual reproduction. In the initial stage of their life cycle, they exist as spermatogonial stem cells, which multiply by mitotic division to self-renew and to produce daughter cells. The daughter cells then undergo meiotic division, a process that reduces the number of chromosomes in each cell by half, from diploid to haploid – the formation of spermatids. This is critical for maintaining genetic stability from generation to generation, as it ensures that when an egg and sperm cell unite during fertilization, the resulting offspring will have the correct number of chromosomes. The final phase of spermatogenesis is called spermiogenesis, during which spermatozoa - mature and motile sperm cells – are produced from round spermatids. \nThe matured male germ cells or sperm cells are highly specialized, having a streamlined shape designed for efficient movement towards the female egg. A sperm cell is divided into three main parts, namely the head, midpiece, and tail. The head contains the genetic material, the midpiece contains mitochondria that provide energy, and the tail, termed as the flagellum, propels the sperm cell forward. Each of these parts play significant roles in fertilization." xsd:string {xref="DOI:10.1016/S0092-8674(00)81834-6", xref="DOI:10.1016/S1534-5807(02)00173-9", xref="DOI:10.1242/dev.202046", xref="https://www.ncbi.nlm.nih.gov/books/NBK553142/"} [Term] id: CL:0000016 name: male germ line stem cell def: "A stem cell that is the precursor of male gametes." [doi:10.1016/j.stem.2012.05.016] +subset: human_subset +subset: mouse_subset xref: FBbt:00004929 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} is_a: CL:0000014 ! germ line stem cell is_a: CL:0000015 ! male germ cell @@ -306,6 +329,8 @@ is_a: CL:0000015 ! male germ cell id: CL:0000017 name: spermatocyte def: "A male germ cell that develops from spermatogonia. The euploid primary spermatocytes undergo meiosis and give rise to the haploid secondary spermatocytes which in turn give rise to spermatids." [GOC:tfm, MESH:D013090] +subset: human_subset +subset: mouse_subset xref: BTO:0001275 xref: CALOHA:TS-0951 xref: EMAPA:31484 @@ -324,6 +349,8 @@ relationship: RO:0002202 CL:0000020 ! develops from spermatogonium id: CL:0000018 name: spermatid def: "A male germ cell that develops from the haploid secondary spermatocytes. Without further division, spermatids undergo structural changes and give rise to spermatozoa." [MESH:D013087] +subset: human_subset +subset: mouse_subset synonym: "nematoblast" EXACT [] xref: BTO:0001274 xref: CALOHA:TS-0950 @@ -351,6 +378,8 @@ id: CL:0000019 name: sperm def: "A mature male germ cell that develops from a spermatid." [GOC:tfm, MESH:D013094] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "sperm cell" EXACT [] synonym: "spermatozoid" EXACT [] synonym: "spermatozoon" EXACT [] @@ -359,17 +388,21 @@ xref: BTO:0002046 xref: CALOHA:TS-0949 xref: FBbt:00004954 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:67338 +xref: https://cellxgene.cziscience.com/cellguide/CL_0000019 xref: WBbt:0006798 xref: ZFA:0009006 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: BFO:0000002 is_a: CL:0000255 ! eukaryotic cell is_a: CL:0000408 {is_inferred="true"} ! male gamete relationship: RO:0002202 CL:0000018 ! develops from spermatid +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nSperm cells, also known as spermatozoa or male gametes, are highly specialized cells that are pivotal for sexual reproduction in animals. Produced in the male reproductive organs, specifically the testes, sperm cells play an important role in the process of fertilization, where they fuse with a female gamete or egg cell (ovum) to form a zygote, which marks the beginning of a new organism.\nSperm cells hold several unique traits that set them apart from other body cells. Structurally, a sperm cell possesses two main structures: the head, containing the nucleus carrying the paternal genetic information, and the flagellum, which generates energy and grants the sperm cell mobility\nThe process of fertilization occurs when one sperm cell successfully penetrates the egg, delivering its genetic information, and ultimately leading to the formation of a new individual combining both paternal and maternal genetic materials. Notably, while hundreds of millions of sperm cells may be released during ejaculation, only one has the opportunity to successfully fertilize the egg, underscoring the highly competitive nature of this biological process." xsd:string {xref="DOI:10.1080/19420889.2015.1017156", xref="DOI:10.1152/physrev.00009.2020", xref="https://www.ncbi.nlm.nih.gov/books/NBK26914/"} [Term] id: CL:0000020 name: spermatogonium def: "An euploid male germ cell of an early stage of spermatogenesis." [MESH:D013093] +subset: human_subset +subset: mouse_subset synonym: "spermatogonial cell" EXACT [] xref: BTO:0000958 xref: CALOHA:TS-2193 @@ -390,6 +423,8 @@ id: CL:0000021 name: female germ cell def: "Female germ cell is a germ cell that supports female gamete production." [GOC:tfm, PMID:11023867, PMID:20454446] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset xref: MA:0000388 xref: ncithesaurus:Egg xref: VHOG:0001530 @@ -403,6 +438,8 @@ relationship: capable_of GO:0048477 ! oogenesis id: CL:0000022 name: female germ line stem cell def: "A stem cell that is the precursor of female gametes." [doi:10.1016/j.stem.2012.05.016] +subset: human_subset +subset: mouse_subset xref: FBbt:00004873 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} is_a: CL:0000014 {is_inferred="true"} ! germ line stem cell is_a: CL:0000021 {is_inferred="true"} ! female germ cell @@ -414,6 +451,8 @@ id: CL:0000023 name: oocyte def: "A female germ cell that has entered meiosis." [GOC:tfm, ISBN:0721662544] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "oogonium" RELATED [] xref: BTO:0000964 xref: CALOHA:TS-0711 @@ -432,6 +471,8 @@ id: CL:0000024 name: oogonial cell def: "An undifferentiated germ cell that proliferates rapidly and gives rise to oocytes." [GOC:tfm, ISBN:0721662544] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset xref: FMA:83673 xref: ZFA:0005878 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: BFO:0000002 @@ -445,6 +486,8 @@ relationship: RO:0002202 CL:0000670 ! develops from primordial germ cell id: CL:0000025 name: egg cell def: "A female gamete where meiosis has progressed to metaphase II and is able to participate in fertilization." [GOC:tfm, ISBN:0721662544] +subset: human_subset +subset: mouse_subset synonym: "mature oocyte" EXACT [] synonym: "ovum" EXACT [] xref: BTO:0000369 @@ -477,6 +520,8 @@ relationship: RO:0002202 CL:0000722 ! develops from cystoblast id: CL:0000027 name: smooth muscle cell neural crest derived def: "A smooth muscle cell derived from the neural crest." [https://orcid.org/0000-0001-5208-3432] +subset: human_subset +subset: mouse_subset is_a: CL:0000192 {is_inferred="true"} ! smooth muscle cell intersection_of: CL:0000192 ! smooth muscle cell intersection_of: RO:0002202 CL:0000333 ! develops from migratory neural crest cell @@ -486,7 +531,7 @@ relationship: RO:0002202 CL:0000008 ! develops from migratory cranial neural cre id: CL:0000028 name: CNS neuron (sensu Nematoda and Protostomia) is_a: BFO:0000002 -is_a: CL:0000540 ! neuron +is_a: CL:2000029 ! central nervous system neuron relationship: part_of UBERON:0001017 ! central nervous system relationship: RO:0002202 CL:0000338 ! develops from neuroblast (sensu Nematoda and Protostomia) @@ -494,6 +539,8 @@ relationship: RO:0002202 CL:0000338 ! develops from neuroblast (sensu Nematoda a id: CL:0000029 name: neural crest derived neuron def: "Any neuron that develops from some migratory neural crest cell." [FBC:Autogenerated] +subset: human_subset +subset: mouse_subset synonym: "neuron neural crest derived" EXACT [] xref: ZFA:0009009 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: BFO:0000002 @@ -505,7 +552,10 @@ relationship: RO:0002202 CL:0002676 ! develops from neural crest derived neurobl [Term] id: CL:0000030 name: glioblast +def: "A non-terminally differentiated cell that develops form the neuroectoderm. Glioblast has the potential to differentiate into various types of glial cells, including astrocytes and oligodendrocytes." [PMID:37824650, Wikipedia:Glioblast] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset xref: ZFA:0009010 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: BFO:0000002 is_a: CL:0000055 ! non-terminally differentiated cell @@ -518,6 +568,8 @@ name: neuroblast (sensu Vertebrata) alt_id: CL:0000337 def: "A cell that will develop into a neuron often after a migration phase." [GOC:NV, http://en.wikipedia.org/wiki/Neuroblast] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "neuroblast" EXACT [] xref: BTO:0000930 xref: FMA:70563 @@ -530,6 +582,8 @@ relationship: RO:0002162 NCBITaxon:7742 ! in taxon Vertebrata id: CL:0000032 name: neuroplacodal cell def: "A cell of a platelike structure, especially a thickened plate of ectoderm in the early embryo, from which a sense organ develops." [GOC:tfm, ISBN:0618947256] +subset: human_subset +subset: mouse_subset synonym: "neural placode cell" EXACT [] xref: ZFA:0009012 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: BFO:0000002 @@ -542,6 +596,8 @@ id: CL:0000033 name: apocrine cell def: "An exocrine cell characterized by loss of part of the cytoplasm during the process of secretion. The secreted substance is accumulated at the apical end and is either budded off through the plasma membrane producing secreted vesicles or dissolved in the cytoplasm that is lost during secretion." [GOC:tfm, ISBN:0721662544, PMID:25960390] subset: human_reference_atlas +subset: human_subset +subset: mouse_subset is_a: CL:0000152 ! exocrine cell property_value: RO:0002175 NCBITaxon:9606 @@ -553,6 +609,8 @@ comment: This term applies to metazoan. For plant stem cells, consider using PO: subset: cellxgene_subset subset: general_cell_types_upper_slim subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "animal stem cell" EXACT [] xref: CALOHA:TS-2086 xref: FMA:63368 @@ -569,6 +627,8 @@ property_value: RO:0002175 NCBITaxon:9606 id: CL:0000035 name: single fate stem cell def: "A stem cell that self-renews as well as give rise to a single mature cell type." [GOC:tfm] +subset: human_subset +subset: mouse_subset synonym: "unipotent stem cell" EXACT [] synonym: "unipotential stem cell" EXACT [] xref: FMA:70569 @@ -584,6 +644,8 @@ id: CL:0000036 name: epithelial fate stem cell subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "epithelial stem cell" EXACT [] is_a: CL:0000035 ! single fate stem cell property_value: RO:0002175 NCBITaxon:9606 @@ -596,6 +658,8 @@ comment: Markers differ between species, and two sets of markers have been descr subset: blood_and_immune_upper_slim subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "blood forming stem cell" EXACT [] synonym: "colony forming unit hematopoietic" RELATED [] synonym: "hemopoietic stem cell" EXACT [] @@ -646,6 +710,8 @@ name: erythroid progenitor cell def: "A progenitor cell committed to the erythroid lineage." [GOC:add, ISBN:0721601464] subset: blood_and_immune_upper_slim subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "BFU-E" RELATED OMO:0003000 [] synonym: "blast forming unit erythroid" RELATED [] synonym: "burst forming unit erythroid" RELATED [] @@ -664,6 +730,8 @@ name: germ line cell def: "A cell that is within the developmental lineage of gametes and is able to pass along its genetic material to offspring." [GOC:tfm, ISBN:0721662544] comment: Originally this term had some plant germ line cell children. subset: general_cell_types_upper_slim +subset: human_subset +subset: mouse_subset subset: ubprop:upper_level xref: ZFA:0009016 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000000 ! cell @@ -674,6 +742,8 @@ id: CL:0000040 name: monoblast def: "A myeloid progenitor cell committed to the monocyte lineage. This cell is CD11b-positive, has basophilic cytoplasm, euchromatin, and the presence of a nucleolus." [GOC:add, http://en.wikipedia.org/wiki/Monoblast, http://www.copewithcytokines.de, PMID:1104740] comment: Morphology: mononuclear cell, diameter 12-20 _M, non-granular, N/C ratio 3/1 - 4/1; markers: CD11b (shared with many other myeloid cells); location: Adult: bone marrow; fetal: liver, Yolk Sac; role or process: hematopoiesis, monocyte development; lineage: hematopoietic, myeloid. +subset: human_subset +subset: mouse_subset synonym: "CFU-M" RELATED OMO:0003000 [] synonym: "colony forming unit macrophage" RELATED [] synonym: "colony forming unit monocyte" RELATED [] @@ -683,7 +753,6 @@ xref: FMA:83553 xref: ZFA:0009017 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000763 ! myeloid cell is_a: CL:0002194 {is_inferred="true"} ! monopoietic cell -is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0002194 ! monopoietic cell intersection_of: capable_of GO:0030224 ! monocyte differentiation intersection_of: has_part CL:0017503 ! basophilic cytoplasm @@ -702,6 +771,8 @@ name: mature eosinophil def: "A fully differentiated eosinophil, a granular leukocyte with a nucleus that usually has two lobes connected by one or more slender threads, and cytoplasm containing coarse, round granules that are uniform in size and which can be stained by the dye eosin. Cells are also differentiated from other granulocytes by a small nuclear-to-cytoplasm ratio (1:3). This cell type is CD49d-positive." [GOC:add, GOC:dsd, GOC:tfm, http://www.cap.org, ISBN:0721601464] comment: Eosinophils are CD125-positive (IL-5R), GM-CSFR-positive, IL-3R-positive, VLA4-positive. They can also express MHC Class I & II, CD4, CD9, CD11a, CD11b, CD11c, CD13, CD15, CD16, CD17, CD18, CD24, CD25,CD28, CD29, CD32, CD33, CD35, CD37, CD39, CD43, CD44, CD45, CD45RB, CD45RO, CD46, CD47, CD48, CD49d, CD49f, CD50, CD52, CD53, CD54, CD55, CD58, CD59, CD62L, CD63, CD65, CD66, CD69, CD71, CD76, CD80, CD81, CD82, CD86, CD87, CD88, CD89, CD92, CD95, CD97, CD98, CD99, CD100, CD101, CD116, CD117, CD119, CD120, CD123, CD124, CD125, CD131, CD137, CD139, CD148, CD149, CD151, CD153, CD156, CD162, CD161, CD162, CD165, CD174, CD182, CD183, CD191, CD192, CD193, CD196, CD213, IL9R, ad integrin, beta-7 integrin, FceRI, IL13Ra1, TGFbR, PAFR, LTB4R, C3aR, CystLT1R, CystLT2R, fMLPR, CRTH2 (PGD2 receptor), histamine 4R, IDO, KYN, PAR-2, Siglec-8, Siglec-10, LIR1, LIR2, LIR3, LIR7, TLR7, TLR8, and VLA-4. Eosinophils can also secrete CXCL1, eotaxin-1, GM-CSF, IL-2, IL-3, IL-4, IL-5, IL-6, IL-8, IL-10, IL-12, IL-13, IL-16, IL-18, IFN-gamma, LTC4, MIP-1alpha, NGF, PAF, RANTES, substance P, TGF-alpha, TGF-beta, TNF-alpha, and VIP. subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "mature eosinocyte" EXACT [] synonym: "mature eosinophil leucocyte" EXACT [] synonym: "mature eosinophil leukocyte" EXACT [] @@ -728,11 +799,12 @@ id: CL:0000042 name: neutrophilic myeloblast def: "A myeloblast committed to the neutrophil lineage. This cell type is GATA-1 positive, C/EBPa-positive, AML-1-positive, c-myb-positive and has low expression of PU.1 transcription factor." [GOC:add, ISBN:0721601464, PMID:12560239, PMID:15514007] comment: These cells are CD11b-negative, CD15-negative, CD16-negative, CD35-negative, CD49d-positive, CD68-positive, lactotransferrin-negative, and fMLP receptor-negative. They are found in the Band 3 fraction. +subset: human_subset +subset: mouse_subset synonym: "neutrophilic granuloblast" RELATED [] xref: ZFA:0009018 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000834 ! neutrophil progenitor cell is_a: CL:0000835 {is_inferred="true"} ! myeloblast -is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000835 ! myeloblast intersection_of: capable_of GO:0030223 ! neutrophil differentiation intersection_of: has_part PR:000001944 ! transcription factor PU.1 @@ -753,6 +825,8 @@ name: mature basophil alt_id: CL:0000739 def: "A fully differentiated basophil, a granular leukocyte with an irregularly shaped, pale-staining nucleus that is partially constricted into two lobes, and with cytoplasm that contains coarse granules of variable size. Basophils contain vasoactive amines such as histamine and serotonin, which are released on appropriate stimulation." [GOC:add, GOC:dsd, GOC:tfm, http://www.cap.org, ISBN:0721601464, PMID:18466030, PMID:19231594, PMID:20837449] comment: Mature basophils are also capable of producing IL-3, IL-5, IL-6, IL-8, IL-13, IL-25, CCL22, tslp, vegf, and LTC4. +subset: human_subset +subset: mouse_subset synonym: "mature basophil leucocyte" EXACT [] synonym: "mature basophil leukocyte" EXACT [] synonym: "polymorphonuclear leucocyte" BROAD [] @@ -788,6 +862,8 @@ id: CL:0000047 name: neural stem cell def: "An undifferentiated neural cell that originates from the neuroectoderm and has the capacity both to perpetually self-renew without differentiating and to generate multiple central nervous system neuronal and glial cell types." [PMID:30639325] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "neuronal stem cell" EXACT [PMID:16305818] synonym: "NSC" EXACT [] xref: BTO:0002881 @@ -802,6 +878,8 @@ relationship: RO:0002202 CL:0000133 ! develops from neurectodermal cell id: CL:0000048 name: multi fate stem cell def: "A stem cell that can give rise to multiple lineages of cells." [GOC:add] +subset: human_subset +subset: mouse_subset synonym: "multi-fate stem cell" EXACT [] synonym: "multifate stem cell" EXACT [] synonym: "multipotent cell" EXACT [] @@ -821,6 +899,8 @@ def: "A progenitor cell committed to myeloid lineage, including the megakaryocyt comment: This cell type is intended to be compatible with any vertebrate common myeloid progenitor. For mammalian CMP known to be CD34-positive, please use the term 'common myeloid progenitor, CD34-positive' (CL_0001059). subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "CFU-GEMM" RELATED OMO:0003000 [ISBN:0878932437] synonym: "CFU-S" RELATED OMO:0003000 [ISBN:0878932437] synonym: "CMP" RELATED OMO:0003000 [ISBN:0878932437] @@ -844,6 +924,8 @@ def: "A progenitor cell committed to the megakaryocyte and erythroid lineages." comment: MEPs are reportedly CD19-negative, CD34-negative, CD45RA-negative, CD110-positive, CD117-positive, and SCA1-negative and reportedly express the transcription factors GATA-1 and NF-E2. subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "CFU-EM" EXACT [] synonym: "CFU-MegE" EXACT [] synonym: "colony forming unit erythroid megakaryocyte" EXACT [] @@ -872,6 +954,8 @@ def: "A oligopotent progenitor cell committed to the lymphoid lineage." [GOC:add comment: CLP are CD7-positive, CD10-positive, CD19-negative, CD34-positive, CD45RA-positive, CD79a-negative, CD127-positive, AA4.1-positive, RAG-negative, Sca-1-low, sIgM-negative, sIgD-negative, TdT-negative, Vpre-B-negative, and pre-BCR-negative. Expression of transcription factors include E2A-positive, EBF-positive, Ikaros-negative, PU.1-negative, and Pax5-negative. subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "CLP" RELATED OMO:0003000 [] synonym: "committed lymphopoietic stem cell" RELATED [] synonym: "common lymphocyte precursor" EXACT [] @@ -893,6 +977,8 @@ property_value: RO:0002175 NCBITaxon:9606 id: CL:0000052 name: totipotent stem cell def: "A stem cell from which all cells of the body can form." [GOC:add, GOC:tfm] +subset: human_subset +subset: mouse_subset synonym: "totipotential stem cell" EXACT [] xref: FMA:84790 xref: MESH:D039901 @@ -902,6 +988,8 @@ is_a: CL:0000723 ! somatic stem cell [Term] id: CL:0000054 name: bone matrix secreting cell +subset: human_subset +subset: mouse_subset is_a: CL:0000151 ! secretory cell [Term] @@ -910,6 +998,8 @@ name: non-terminally differentiated cell def: "A precursor cell with a limited number of potential fates." [SANBI:mhl] comment: define using PATO mulit-potent or oligopotent? subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "blast cell" EXACT [] xref: BTO:0000125 xref: FMA:84782 @@ -919,6 +1009,9 @@ is_a: CL:0011115 ! precursor cell id: CL:0000056 name: myoblast def: "A cell that is commited to differentiating into a muscle cell. Embryonic myoblasts develop from the mesoderm. They undergo proliferation, migrate to their various sites, and then differentiate into the appropriate form of myocytes. Myoblasts also occur as transient populations of cells in muscles undergoing repair." [GOC:tfm, MESH:D032446, PMID:21849021] +subset: cellxgene_subset +subset: human_subset +subset: mouse_subset xref: BTO:0000222 xref: CALOHA:TS-0650 xref: FBbt:00005083 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} @@ -935,21 +1028,23 @@ comment: These cells may be vimentin-positive, fibronectin-positive, fsp1-positi subset: cellxgene_subset subset: general_cell_types_upper_slim subset: human_reference_atlas +subset: human_subset +subset: mouse_subset xref: BTO:0000452 xref: CALOHA:TS-0362 xref: FMA:63877 xref: NCIT:C12482 xref: VHOG:0001482 xref: ZFA:0009026 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} -is_a: BFO:0000002 -is_a: CL:0002320 ! connective tissue cell -relationship: RO:0002202 CL:0000134 ! develops from mesenchymal stem cell +is_a: CL:0000499 ! stromal cell property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000058 name: chondroblast def: "Skeletogenic cell that is typically non-terminally differentiated, secretes an avascular, GAG rich matrix; is not buried in cartilage tissue matrix, retains the ability to divide, located adjacent to cartilage tissue (including within the perichondrium), and develops from prechondroblast (and thus prechondrogenic) cell." [GO_REF:0000034, GOC:tfm, ISBN:0618947256] +subset: human_subset +subset: mouse_subset synonym: "chrondoplast" EXACT [] xref: BTO:0003607 xref: FMA:66783 @@ -967,13 +1062,15 @@ alt_id: CL:0000053 alt_id: CL:0000139 def: "Skeletogenic cell that produces enamel, overlies the odontogenic papilla, and arises from the differentiation of a preameloblast cell." [GO_REF:0000034, GOC:tfm, MESH:D000565] comment: non-encoded relationship from VSAO produces VSAO:0000066 +subset: human_subset +subset: mouse_subset synonym: "amelocyte" EXACT [] synonym: "enamel secreting cell" EXACT [] xref: BTO:0001663 xref: FMA:70576 is_a: CL:0000146 ! simple columnar epithelial cell -is_a: CL:0000151 ! secretory cell is_a: CL:0002077 ! ecto-epithelial cell +is_a: CL:1100001 ! secretory epithelial cell relationship: adjacent_to UBERON:0001763 ! odontogenic papilla relationship: capable_of GO:0097186 ! amelogenesis relationship: part_of UBERON:0005176 ! tooth enamel organ @@ -985,6 +1082,8 @@ id: CL:0000060 name: odontoblast def: "Skeletogenic cell that secretes dentine matrix, is derived from the odontogenic papilla, and develops from a preodontoblast cell." [GO_REF:0000034, ISBN:0618947256] comment: legacy def: One of the cells forming the outer surface of dental pulp that produces tooth dentin. +subset: human_subset +subset: mouse_subset xref: BTO:0001769 xref: CALOHA:TS-0696 xref: FMA:62999 @@ -1004,6 +1103,8 @@ name: cementoblast alt_id: CL:0000859 def: "Skeletogenic cell that produces cementum (a bony substance that covers the root of a tooth), is part of the odontogenic papilla, and develops from a precementoblast cell." [GO_REF:0000034, ISBN:0781733901] comment: Legacy def: A cell of ectomesenchymal origin that aids in the formation the cementum layer on the roots of teeth. +subset: human_subset +subset: mouse_subset synonym: "cementum secreting cell" EXACT [] xref: CALOHA:TS-1164 xref: FMA:63002 @@ -1020,6 +1121,8 @@ name: osteoblast def: "Skeletogenic cell that secretes osteoid, is capable of producing mineralized (hydroxyapatite) matrix, is located adjacent to or within osteoid tissue, and arises from the transformation of a preosteoblast cell." [GO_REF:0000034, MESH:D010006] comment: non-encoded relationships from VSAO - capable_of_producing VSAO:0000020 subset: cellxgene_subset +subset: human_subset +subset: mouse_subset xref: BTO:0001593 xref: CALOHA:TS-0720 xref: FMA:66780 @@ -1045,11 +1148,12 @@ id: CL:0000064 name: ciliated cell def: "A cell that has a filiform extrusion of the cell surface." [GOC:tfm] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset xref: VHOG:0001532 xref: XAO:0000031 xref: ZFA:0009032 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000255 ! eukaryotic cell -is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000000 ! cell intersection_of: has_part GO:0005929 ! cilium relationship: has_part GO:0005929 ! cilium @@ -1060,6 +1164,8 @@ name: ependymal cell def: "A neuroepithelial glial cell, derived from a radial glial cell originating from the neuroectoderm, lines the ventricles of the brain and the central canal of the spinal cord. This cell is characterized by the presence of cilia on its apical surface, which can be motile or non-motile." [doi:/10.3389/fncel.2021.703951, GOC:tfm, https://www.britannica.com/science/ependymal-cell, JB:jb, PMID:34335193, PMID:37008045, PMID:9550134] subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "ependymocyte" NARROW [doi:10.53347/rID-51713] xref: BTO:0001724 xref: FMA:70550 @@ -1067,7 +1173,7 @@ xref: ZFA:0009033 {sssom:mapping_justification="https://w3id.org/semapv/vocab/Un is_a: CL:0000067 ! ciliated epithelial cell is_a: CL:0000125 ! glial cell is_a: CL:0000710 ! neurecto-epithelial cell -intersection_of: CL:0000710 ! neurecto-epithelial cell +intersection_of: CL:0000066 ! epithelial cell intersection_of: part_of UBERON:0004670 ! ependyma relationship: part_of UBERON:0004670 ! ependyma relationship: RO:0002207 CL:0000681 ! directly develops from radial glial cell @@ -1080,6 +1186,8 @@ def: "A cell that is usually found in a two-dimensional sheet with a free surfac subset: cellxgene_subset subset: general_cell_types_upper_slim subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "epitheliocyte" EXACT [] xref: BTO:0000414 xref: CALOHA:TS-2026 @@ -1099,6 +1207,8 @@ id: CL:0000067 name: ciliated epithelial cell def: "An epithelial cell that has a cilia." [GOC:tfm] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset xref: FMA:70605 xref: ZFA:0009035 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000064 ! ciliated cell @@ -1111,6 +1221,8 @@ id: CL:0000068 name: duct epithelial cell def: "An epithelial cell that is part of a duct." [https://orcid.org/0000-0001-5208-3432] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset xref: ZFA:0009372 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000066 ! epithelial cell intersection_of: CL:0000066 ! epithelial cell @@ -1120,6 +1232,8 @@ relationship: part_of UBERON:0000058 ! duct [Term] id: CL:0000069 name: branched duct epithelial cell +subset: human_subset +subset: mouse_subset is_a: CL:0000068 ! duct epithelial cell [Term] @@ -1133,6 +1247,8 @@ name: blood vessel endothelial cell def: "An endothelial cell that lines the vasculature." [GOC:tfm] subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset xref: ZFA:0009036 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0002139 ! endothelial cell of vascular tree intersection_of: CL:0000115 ! endothelial cell @@ -1143,6 +1259,8 @@ property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000072 name: non-branched duct epithelial cell +subset: human_subset +subset: mouse_subset is_a: CL:0000068 ! duct epithelial cell is_a: CL:0002078 ! meso-epithelial cell @@ -1166,6 +1284,8 @@ name: columnar/cuboidal epithelial cell def: "A columnar/cuboidal epithelial cell is a cell usually found in a two dimensional sheet with a free surface. Columnar/cuboidal epithelial cells take on the shape of a column or cube." [GO:0002065, https://orcid.org/0000-0001-5208-3432] subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset xref: ZFA:0009038 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000066 ! epithelial cell property_value: RO:0002175 NCBITaxon:9606 @@ -1175,6 +1295,8 @@ id: CL:0000076 name: squamous epithelial cell def: "Any epithelial cell that is part of some squamous epithelium." [FBC:Autogenerated] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset xref: CALOHA:TS-1249 xref: ZFA:0009039 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000066 ! epithelial cell @@ -1189,6 +1311,8 @@ def: "A flat, squamous-like epithelial cell of mesodermal origin. It forms the m comment: Mesothelial cells, which morphologically resemble squamous epithelial cells, express both epithelial markers (cytokeratins) and mesenchymal markers (vimentin), reflecting their mesodermal origin. They feature surface microvilli and apical-basal polarity. Under certain conditions, they can undergo mesothelial-to-mesenchymal transition. These cells also produce extracellular matrix proteins, maintain serosal homeostasis, and facilitate fluid transport. {xref="PMID:26106328"} subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "mesotheliocyte" EXACT [] xref: FMA:66773 xref: ZFA:0009040 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} @@ -1201,6 +1325,8 @@ property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000078 name: peridermal cell +subset: human_subset +subset: mouse_subset xref: ZFA:0009041 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000076 ! squamous epithelial cell @@ -1209,6 +1335,8 @@ id: CL:0000079 name: stratified epithelial cell def: "An epithelial cell, organized into multiple layers, with only the basal layer being in contact with the basement membrane." [doi:/10.1016/B978-0-12-410424-2.00003-2, https://www.biologyonline.com/dictionary/stratified-epithelium, Wikipedia:Epithelium] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset xref: ZFA:0009042 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: BFO:0000002 is_a: CL:0000066 ! epithelial cell @@ -1218,6 +1346,8 @@ relationship: RO:0002202 CL:0000357 ! develops from stratified epithelial stem c id: CL:0000080 name: circulating cell def: "A cell which moves among different tissues of the body, via blood, lymph, or other medium." [GOC:add] +subset: human_subset +subset: mouse_subset xref: ZFA:0009043 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000255 ! eukaryotic cell intersection_of: CL:0000000 ! cell @@ -1230,6 +1360,8 @@ name: blood cell def: "A cell found predominately in the blood." [GOC:add, GOC:tfm] subset: cellxgene_subset subset: general_cell_types_upper_slim +subset: human_subset +subset: mouse_subset xref: FMA:62844 xref: MESH:D001773 xref: ZFA:0009044 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} @@ -1243,6 +1375,8 @@ id: CL:0000082 name: epithelial cell of lung def: "An epithelial cell of the lung." [https://orcid.org/0000-0001-5208-3432] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "lung epithelial cell" EXACT [] xref: BTO:0004299 is_a: CL:0002632 ! epithelial cell of lower respiratory tract @@ -1254,6 +1388,9 @@ relationship: part_of UBERON:0000115 ! lung epithelium id: CL:0000083 name: epithelial cell of pancreas def: "An epithelial cell of the pancreas." [GOC:tfm] +subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "pancreas epithelial cell" EXACT [] synonym: "pancreatic epithelial cell" EXACT [] xref: BTO:0000028 @@ -1272,6 +1409,8 @@ def: "A type of lymphocyte whose defining characteristic is the expression of a subset: cellxgene_subset subset: general_cell_types_upper_slim subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "immature T cell" RELATED [] synonym: "mature T cell" RELATED [] synonym: "T lymphocyte" EXACT [] @@ -1346,6 +1485,8 @@ def: "A tissue-resident macrophage of the reticuloendothelial system found on th comment: Markers: Mouse: F4/80+, CD11b-low, CD68+, sialoadhesin+, CD163/SRCR+; role or process: immune, antigen-presentation, clearance of senescent erythrocytes, iron metabolism. Kupffer cells are also reportedly C3aR-positive, CD14-low, CD54-positive, CD88-positive, and CD284-positive. They are also capable of producing IL-1, IL-6, TNF-alpha, nitric oxide, PGD2, PGE2, PGF2alpha, and TXA2. subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "hepatic macrophage" EXACT [] synonym: "littoral cell of hepatic sinusoid" EXACT [] synonym: "liver macrophage" EXACT [] @@ -1356,7 +1497,6 @@ xref: BTO:0000685 xref: FMA:14656 xref: https://cellxgene.cziscience.com/cellguide/CL_0000091 is_a: CL:0000864 {is_inferred="true"} ! tissue-resident macrophage -is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000864 ! tissue-resident macrophage intersection_of: capable_of GO:0034102 ! erythrocyte clearance intersection_of: RO:0001025 UBERON:0001281 ! located in hepatic sinusoid @@ -1371,7 +1511,7 @@ relationship: RO:0002104 PR:000001925 ! has plasma membrane part scavenger recep relationship: RO:0002104 PR:000002064 ! has plasma membrane part macrosialin relationship: RO:0015016 PR:000001012 ! has low plasma membrane amount integrin alpha-M property_value: RO:0002175 NCBITaxon:9606 -property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional.\n\nKupffer cells are tissue-resident macrophages located in the liver. They are an integral part of the mononuclear phagocyte system and are responsible for the phagocytosis of dead or dying cells, microbes, and other foreign substances. Kupffer cells account for approximately 80-90% of tissue-resident macrophages in the body. They are found within the lumen of liver sinusoids and interface with microbial populations and products.\nThe primary role of Kupffer cells is to maintain homeostasis in the liver. They continuously filter and cleanse the blood that flows through the liver, removing pathogens, endotoxins, particulate matter, aged and dysfunctional red blood cells, and miscellaneous waste products. These cells also play an important role in maintaining iron homeostasis. During the process of phagocytosis, Kupffer cells recycle iron from degraded red blood cells, which is then utilized in the formation of new erythrocytes.\nKupffer cells also play key roles in various immune responses and inflammatory processes. They secrete various types of cytokines and chemokines, which contribute to the activation and mobilization of other immune cells. They can also produce reactive oxygen species and nitric oxide, which have microbicidal actions. Although their activity is essential for host defense, excessive or prolonged activation of Kupffer cells may contribute to hepatic injury, inflammation, and fibrosis." xsd:string {xref="DOI:10.1002/cphy.c120026", xref="DOI:10.1007/978-1-4939-1311-4_10", xref="DOI:10.1016/j.immuni.2022.08.002", xref="DOI:10.1038/nri.2017.11", xref="DOI:10.1111/j.1478-3231.2006.01342.x"} +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nKupffer cells are tissue-resident macrophages located in the liver. They are an integral part of the mononuclear phagocyte system and are responsible for the phagocytosis of dead or dying cells, microbes, and other foreign substances. Kupffer cells account for approximately 80-90% of tissue-resident macrophages in the body. They are found within the lumen of liver sinusoids and interface with microbial populations and products.\nThe primary role of Kupffer cells is to maintain homeostasis in the liver. They continuously filter and cleanse the blood that flows through the liver, removing pathogens, endotoxins, particulate matter, aged and dysfunctional red blood cells, and miscellaneous waste products. These cells also play an important role in maintaining iron homeostasis. During the process of phagocytosis, Kupffer cells recycle iron from degraded red blood cells, which is then utilized in the formation of new erythrocytes.\nKupffer cells also play key roles in various immune responses and inflammatory processes. They secrete various types of cytokines and chemokines, which contribute to the activation and mobilization of other immune cells. They can also produce reactive oxygen species and nitric oxide, which have microbicidal actions. Although their activity is essential for host defense, excessive or prolonged activation of Kupffer cells may contribute to hepatic injury, inflammation, and fibrosis." xsd:string {xref="DOI:10.1002/cphy.c120026", xref="DOI:10.1007/978-1-4939-1311-4_10", xref="DOI:10.1016/j.immuni.2022.08.002", xref="DOI:10.1038/nri.2017.11", xref="DOI:10.1111/j.1478-3231.2006.01342.x"} [Term] id: CL:0000092 @@ -1379,16 +1519,18 @@ name: osteoclast def: "A specialized phagocytic cell associated with the absorption and removal of the mineralized matrix of bone tissue, which typically differentiates from monocytes. This cell has the following markers: tartrate-resistant acid phosphatase type 5-positive, PU.1-positive, c-fos-positive, nuclear factor NF-kappa-B p100 subunit-positive, tumor necrosis factor receptor superfamily member 11A-positive and macrophage colony-stimulating factor 1 receptor-positive." [GO_REF:0000031, GOC:add, GOC:tfm, ISBN:0781735149, PMID:10428500, PMID:15055519, PMID:17380158] comment: Morphology: Highly vesicular; markers: Surface: RANK, cFMS (MCSF receptor); Secreted: cathepsin K and TRAP (tartate resistant acid phosphatase); transcription factors: PU.1, cFOS, MITF, NFkB (p52); role or process: tissue remodelling: bone resorption; lineage: hematopoietic, myeloid. subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "chondroclast" RELATED [] xref: BTO:0000968 xref: CALOHA:TS-0721 xref: FMA:66781 +xref: https://cellxgene.cziscience.com/cellguide/CL_0000092 xref: MESH:D010010 xref: ZFA:0009047 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000518 ! phagocyte (sensu Vertebrata) is_a: CL:0000766 {is_inferred="true"} ! myeloid leukocyte is_a: CL:0001035 {is_inferred="true"} ! bone cell -is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000766 ! myeloid leukocyte intersection_of: capable_of GO:0045453 ! bone resorption intersection_of: has_part PR:000001850 ! cathepsin K @@ -1408,6 +1550,7 @@ relationship: has_part PR:000011178 ! nuclear factor NF-kappa-B p100 subunit relationship: RO:0002104 PR:000001954 ! has plasma membrane part tumor necrosis factor receptor superfamily member 11A relationship: RO:0002104 PR:000002062 ! has plasma membrane part macrophage colony-stimulating factor 1 receptor relationship: RO:0002202 CL:0000576 ! develops from monocyte +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nOsteoclasts, derived from the monocyte/macrophage lineage, play a crucial role in bone remodeling through bone resorption. They are distinguished from other cells by their large size and their unique ability to secrete enzymes and acids that dissolve the calcium phosphate in bone. The formation of osteoclasts is influenced by two primary factors: macrophage colony-stimulating factor (M-CSF) and the ligand-activated receptor (RANKL) of nuclear factor kappa B (NF-κB).\nOsteoclasts also collaborate with osteoblasts, responsible for new bone formation, to maintain bone health and adapt bone structure. Their coordinated actions allow continuous remodeling while preserving overall bone strength and integrity. Imbalances in osteoclast activity can lead to pathological conditions. For example, excessive activity may contribute to diseases like osteoporosis, periprosthetic osteolysis, bone tumors, and Paget's disease. Other the other hand, osteoclast deficiency ca result in conditions like osteopetrosis." xsd:string {xref="DOI:10.3389/fmed.2017.00234", xref="DOI:10.37175/stemedicine.v1i4.57", xref="https://www.sciencedirect.com/topics/medicine-and-dentistry/osteoclast"} [Term] id: CL:0000093 @@ -1422,6 +1565,8 @@ name: granulocyte def: "A leukocyte with abundant granules in the cytoplasm." [GOC:amm, GOC:tfm, http://en.wikipedia.org/wiki/Granulocyte, MESH:D006098] subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "granular leucocyte" EXACT [] synonym: "granular leukocyte" EXACT [] synonym: "polymorphonuclear leukocyte" EXACT [] @@ -1432,7 +1577,6 @@ xref: FMA:62854 xref: ZFA:0009048 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000081 ! blood cell is_a: CL:0000766 {is_inferred="true"} ! myeloid leukocyte -is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000766 ! myeloid leukocyte intersection_of: capable_of GO:0008015 ! blood circulation intersection_of: CL:4030046 PR:000001002 ! lacks_plasma_membrane_part CD19 molecule @@ -1457,6 +1601,8 @@ property_value: RO:0002175 NCBITaxon:9606 id: CL:0000095 name: neuron associated cell subset: cellxgene_subset +subset: human_subset +subset: mouse_subset is_a: BFO:0000002 is_a: CL:0002319 ! neural cell relationship: RO:0002202 CL:0000133 ! develops from neurectodermal cell @@ -1467,6 +1613,8 @@ name: mature neutrophil def: "A fully differentiated neutrophil, a granular leukocyte having a nucleus with three to five lobes connected by slender threads, and cytoplasm containing fine inconspicuous granules and stainable by neutral dyes. They are produced in bone marrow at a rate of 5e10-10e10/day and have a half-life of 6-8 hours. Neutrophils are CD15-positive, CD16-positive, CD32-positive, CD43-positive, CD181-positive, and CD182-positive." [GOC:add, GOC:tfm, http://www.cap.org, MESH:D009504, PMID:11138776, PMID:12560239, PMID:15514007, PMID:7880385] comment: Neutrophils are also capable of secreting GRO-alpha, IL-1beta, IL-1ra, IL-3, IL-12, IP-10, MIG, MIP-1alpha, MIP-1beta, TGF-beta, TNF-alpha, VEGF, and anti-microbial peptides. They can positively influence the chemotaxis of basophils, T-cells, monocytes, macrophages, dendritic cells, and other neutrophils. Neutrophils are also CD35-positive, CD64-positive, CD89-positive, CD184-positive, and fMLP receptor-positive Ly-6G-positive (mouse), TLR2-low, TLR4-low, and lineage-negative (CD2, CD3, CD5, CD9, CD19, CD36, CD49d, CD56, CD61, CD235a (glycophorin-A)). subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "mature neutrocyte" EXACT [] synonym: "mature neutrophil leucocyte" EXACT [] synonym: "mature neutrophil leukocyte" EXACT [] @@ -1507,6 +1655,8 @@ comment: Mast cells are generally integrin beta-7-negative and positive for TLR2 subset: blood_and_immune_upper_slim subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "histaminocyte" EXACT [] synonym: "labrocyte" EXACT [ISBN:0721601464] synonym: "mastocyte" EXACT [ISBN:0721601464] @@ -1516,7 +1666,6 @@ xref: CALOHA:TS-0603 xref: FMA:66784 is_a: CL:0000766 {is_inferred="true"} ! myeloid leukocyte is_a: CL:0002274 ! histamine secreting cell -is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000766 ! myeloid leukocyte intersection_of: capable_of GO:0002349 ! histamine production involved in inflammatory response intersection_of: capable_of GO:0002539 ! prostaglandin production involved in inflammatory response @@ -1550,6 +1699,8 @@ id: CL:0000098 name: sensory epithelial cell def: "A specialized epithelial cell involved in sensory perception. Restricted to special sense organs of the olfactory, gustatory, and vestibulocochlear receptor systems; contain sensory cells surrounded by supportive, non-receptive cells." [GOC:tfm, ISBN:0517223651, ISBN:0721662544] comment: The term "neuroepithelial cell" is used to describe both this cell type and neurecto-epithelial cell (CL:0000710). +subset: human_subset +subset: mouse_subset synonym: "neuroepithelial cell" BROAD [] xref: BTO:0004301 xref: ZFA:0009050 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} @@ -1564,12 +1715,15 @@ name: interneuron def: "Most generally any neuron which is not motor or sensory. Interneurons may also refer to neurons whose axons remain within a particular brain region as contrasted with projection neurons which have axons projecting to other brain regions." [GOC:tfm, MESH:D007395] subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset +synonym: "CNS interneuron" RELATED [] xref: BTO:0003811 xref: FBbt:00005125 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:67313 xref: WBbt:0005113 xref: ZFA:0009051 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} -is_a: CL:0000540 ! neuron +is_a: CL:2000029 ! central nervous system neuron property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -1578,6 +1732,8 @@ name: motor neuron def: "An efferent neuron that passes from the central nervous system or a ganglion toward or to a muscle and conducts an impulse that causes or inhibits movement." [MESH:D009046, PMID:16875686] subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "motoneuron" EXACT [] xref: BTO:0000312 xref: FBbt:00005123 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} @@ -1591,7 +1747,10 @@ property_value: RO:0002175 NCBITaxon:9606 id: CL:0000101 name: sensory neuron def: "Any neuron having a sensory function; an afferent neuron conveying sensory impulses." [ISBN:0721662544] +subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset xref: BTO:0001037 xref: FBbt:00005124 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:84649 @@ -1607,8 +1766,12 @@ property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000102 name: polymodal neuron +def: "A neuron type that respond to multiple stimuli such as mechanical, thermal and chemical. This neuron type is responsible for integrating different types of sensory inputs, allowing organisms to respond appropriately to diverse environmental challenges." [PMID:23749412, PMID:36381588] +subset: human_subset +subset: mouse_subset +synonym: "polymodal sensory neuron" RELATED [PMID:23749412] xref: ZFA:0009054 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} -is_a: CL:0000540 ! neuron +is_a: CL:2000032 ! peripheral nervous system neuron [Term] id: CL:0000103 @@ -1616,6 +1779,8 @@ name: bipolar neuron def: "A type of interneuron that has two neurites, usually an axon and a dendrite, extending from opposite poles of an ovoid cell body." [GOC:tfm, ISBN:0444009442] subset: BDS_subset subset: cellxgene_subset +subset: human_subset +subset: mouse_subset xref: FMA:67282 xref: ZFA:0009055 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000099 ! interneuron @@ -1628,34 +1793,40 @@ id: CL:0000104 name: multipolar neuron def: "A neuron with three or more neurites, usually an axon and multiple dendrites." [FMA:67287, GOC:tfm] subset: BDS_subset +subset: human_subset +subset: mouse_subset xref: FMA:67287 xref: ZFA:0009056 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} -is_a: CL:0000540 ! neuron -intersection_of: CL:0000540 ! neuron -intersection_of: bearer_of PATO:0070026 ! multipolar neuron morphology +is_a: CL:2000029 ! central nervous system neuron relationship: bearer_of PATO:0070026 ! multipolar neuron morphology [Term] id: CL:0000105 name: pseudounipolar neuron def: "Neuron with two neurites that are fused grossly when they protrude from the soma and bifurcate a short distance from the soma." [FMA:67305, GOC:tfm] +subset: human_subset +subset: mouse_subset xref: FMA:67305 xref: ZFA:0009057 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} -is_a: CL:0000540 ! neuron +is_a: CL:2000032 ! peripheral nervous system neuron [Term] id: CL:0000106 name: unipolar neuron def: "Neuron with one neurite that extends from the cell body." [FMA:67278, GOC:nv] subset: BDS_subset +subset: human_subset +subset: mouse_subset xref: FMA:67278 xref: ZFA:0009058 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} -is_a: CL:0000540 ! neuron +is_a: CL:2000032 ! peripheral nervous system neuron [Term] id: CL:0000107 name: autonomic neuron def: "A neuron whose cell body is within an autonomic ganglion." [GOC:tfm] +subset: human_subset +subset: mouse_subset xref: FMA:80121 xref: ZFA:0009059 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:2000032 ! peripheral nervous system neuron @@ -1667,6 +1838,8 @@ relationship: RO:0002100 UBERON:0002410 ! has soma location autonomic nervous sy id: CL:0000108 name: cholinergic neuron def: "A neuron that uses acetylcholine as a vesicular neurotransmitter." [GOC:tfm] +subset: human_subset +subset: mouse_subset xref: BTO:0004902 xref: FBbt:00007173 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:84796 @@ -1682,6 +1855,8 @@ relationship: capable_of GO:0014055 ! acetylcholine secretion, neurotransmission [Term] id: CL:0000109 name: adrenergic neuron +subset: human_subset +subset: mouse_subset xref: MESH:D059331 xref: ZFA:0009061 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:4033050 ! catecholaminergic neuron @@ -1690,6 +1865,8 @@ is_a: CL:4033050 ! catecholaminergic neuron id: CL:0000110 name: peptidergic neuron def: "A neuron that uses neuropeptides as transmitters." [doi:10.1016/B978-012589762-4/50021-9, PMID:23040809] +subset: human_subset +subset: mouse_subset xref: FBbt:00004101 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: ZFA:0009062 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000540 ! neuron @@ -1698,8 +1875,11 @@ relationship: capable_of GO:0002790 ! peptide secretion [Term] id: CL:0000112 name: columnar neuron -synonym: "columnar neuron" RELATED [] -is_a: CL:0000540 ! neuron +def: "A neuron of the invertebrate central nervous system. This neuron innervates the central complex (CX) of an invertebrate brain and it forms columnar patterns with its dendrites. It is involved in navigation and spatial processing." [PMID:34696823, PMID:37608556] +comment: Columnar neurons have been widely studied in Diptera, locusts, honey bees and other insects. In the mammalian brain, a "columnar organisation" is referred to neurons of the neocortex, however these differ from columnar neurons which are found in the insects central nervous system. {xref="PMID:37608556", xref="PMID:18837039", xref="PMID:32374034", xref="PMID:9153131", xref="PMID:34696823"} +is_a: CL:0000028 ! CNS neuron (sensu Nematoda and Protostomia) +is_a: CL:0008028 ! visual system neuron +relationship: capable_of GO:0007601 ! visual perception [Term] id: CL:0000113 @@ -1707,6 +1887,8 @@ name: mononuclear phagocyte def: "A vertebrate phagocyte with a single nucleus." [GOC:add, GOC:tfm, ISBN:0781735149] subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset xref: BTO:0001433 xref: https://cellxgene.cziscience.com/cellguide/CL_0000113 xref: ZFA:0009064 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} @@ -1715,16 +1897,20 @@ is_a: CL:0000842 ! mononuclear cell intersection_of: CL:0000518 ! phagocyte (sensu Vertebrata) intersection_of: bearer_of PATO:0001407 ! mononucleate property_value: RO:0002175 NCBITaxon:9606 -property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional.\n\nMononuclear phagocytes are immune cells that form a critical part of the body's innate immune system, the body's first line of defense against infections. Mononuclear phagocytes are characterized by the presence of a single, large nucleus. The ‘Mononuclear Phagocyte System’ nomenclature was introduced to distinguish mononuclear monocytes and macrophages from other cells with multiple nuclei. However, the cells within the mononuclear phagocyte system represent a highly heterogeneous group, all of which are able to perform highly efficient phagocytosis - engulfing and digesting microbes and cellular debris to fight infections and to maintain normal tissue homeostasis. \nIn addition to phagocytosis, mononuclear phagocytes also secrete chemical compounds to recruit other immune cells to a site of infection. These cells produce different types of signaling molecules, including cytokines, chemokines, and reactive oxygen species, triggering a cascade of responses to ensure rapid and efficient containment and neutralization of invading pathogens. These cells are also involved in antigen presentation, a process essential for stimulating an adaptive immune response. They can process and present antigens to T cells, thereby linking the innate and adaptive immune responses.\nMononuclear phagocytes play key roles in tissue repair and remodeling. After infection or injury, these cells help in the clearance of dead cells and debris, a crucial step in the initiation of tissue remodeling and the resolution of inflammation. Overall, mononuclear phagocytes are versatile cells that have tailored their functions to meet the unique challenges of different tissues within the body. They are pivotal in homeostasis, immunity, and inflammation, making them important aspects in a range of human diseases including infection, autoimmunity, and cancer." xsd:string {xref="DOI:10.1016/j.coi.2005.11.008", xref="DOI:10.1038/nri3087", xref="DOI:10.3389/fimmu.2019.01893"} +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nMononuclear phagocytes are immune cells that form a critical part of the body's innate immune system, the body's first line of defense against infections. Mononuclear phagocytes are characterized by the presence of a single, large nucleus. The ‘Mononuclear Phagocyte System’ nomenclature was introduced to distinguish mononuclear monocytes and macrophages from other cells with multiple nuclei. However, the cells within the mononuclear phagocyte system represent a highly heterogeneous group, all of which are able to perform highly efficient phagocytosis - engulfing and digesting microbes and cellular debris to fight infections and to maintain normal tissue homeostasis. \nIn addition to phagocytosis, mononuclear phagocytes also secrete chemical compounds to recruit other immune cells to a site of infection. These cells produce different types of signaling molecules, including cytokines, chemokines, and reactive oxygen species, triggering a cascade of responses to ensure rapid and efficient containment and neutralization of invading pathogens. These cells are also involved in antigen presentation, a process essential for stimulating an adaptive immune response. They can process and present antigens to T cells, thereby linking the innate and adaptive immune responses.\nMononuclear phagocytes play key roles in tissue repair and remodeling. After infection or injury, these cells help in the clearance of dead cells and debris, a crucial step in the initiation of tissue remodeling and the resolution of inflammation. Overall, mononuclear phagocytes are versatile cells that have tailored their functions to meet the unique challenges of different tissues within the body. They are pivotal in homeostasis, immunity, and inflammation, making them important aspects in a range of human diseases including infection, autoimmunity, and cancer." xsd:string {xref="DOI:10.1016/j.coi.2005.11.008", xref="DOI:10.1038/nri3087", xref="DOI:10.3389/fimmu.2019.01893"} [Term] id: CL:0000114 name: surface ectodermal cell subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "cell of surface ectoderm" EXACT [] synonym: "surface ectoderm cell" EXACT [] xref: FMA:72552 +xref: https://cellxgene.cziscience.com/cellguide/CL_0000114 is_a: CL:0000221 ! ectodermal cell +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nSurface ectoderm cells give rise to external structures such as the epidermis, hair, nails, and sweat glands. They are critical during the early stages of embryonic development, where they delineate and create the organism's exterior body plan. Beyond forming the organism's physical exterior, surface ectodermal cells have other significant roles. For instance, these cells lead to the development of the anterior pituitary gland and the enamel of the teeth. They are also integral to the formation of the sensory organs, including the eyes and the ears. In the eyes, they form the cornea and lens epithelium. In the ears, they form the external ear canal and certain parts of the inner ear. Therefore, these cells are instrumental in the development of various sensory systems in an organism.\nCertain abnormalities or mutations in surface ectodermal cells could lead to medical conditions known as ectodermal dysplasias. These are a group of inherited disorders affecting the development or function of teeth, hair, nails, and sweat glands. Therefore, understanding the formation and function of surface ectodermal cells is also important in identifying and addressing certain genetic disorders and conditions. In summary, surface ectodermal cells are essential in embryonic development, contributing to the creation of the external physical appearance and the sensory organs of an organism." xsd:string {xref="DOI:10.1038/srep32007", xref="https://www.ncbi.nlm.nih.gov/books/NBK539836/", xref="https://www.ncbi.nlm.nih.gov/books/NBK563130"} [Term] id: CL:0000115 @@ -1733,6 +1919,8 @@ def: "An endothelial cell comprises the outermost layer or lining of anatomical comment: From FMA: 9.07.2001: Endothelial cell has always been classified as a kind of epithelial cell, specifically a squamous cell but that is not true. First, endothelial cell can either be squamous or cuboidal (e.g. high-endothelial cell) and secondly, it has different embryological derivation (mesodermal) than a true epithelial cell (ectodermal and endodermal). The basis for present classification is the fact that it comprises the outermost layer or lining of anatomical structures (location-based) but a better structural basis for the differentia is the cytoskeleton of the cell. Endothelial cell has vimentin filaments while an epithelial cell has keratin filaments. [Onard]. subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "endotheliocyte" EXACT [] xref: BTO:0001176 xref: CALOHA:TS-0278 @@ -1748,6 +1936,8 @@ property_value: RO:0002175 NCBITaxon:9606 id: CL:0000116 name: pioneer neuron def: "Pioneer neurons establish a pathway in the developing central nervous system and then undergo programmed cell death once the adult axons, which follow them, have made connections with the target site. Thus, they are a transient cell type involved in axon guidance." [GOC:cvs, GOC:tfm] +subset: human_subset +subset: mouse_subset xref: FBbt:00005128 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: ZFA:0009066 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000540 ! neuron @@ -1755,19 +1945,20 @@ is_a: CL:0000540 ! neuron [Term] id: CL:0000117 name: CNS neuron (sensu Vertebrata) +subset: human_subset +subset: mouse_subset xref: ZFA:0009067 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} -is_a: BFO:0000002 -is_a: CL:0000540 ! neuron +is_a: CL:2000029 ! central nervous system neuron relationship: part_of UBERON:0001017 ! central nervous system -relationship: RO:0002202 CL:0000031 ! develops from neuroblast (sensu Vertebrata) [Term] id: CL:0000118 name: basket cell def: "Basket cells are inhibitory GABAergic interneurons of the brain. In general, dendrites of basket cells are free branching and contain smooth spines. Axons are highly branched. The branched axonal arborizations give rise to basket-like structures that surround the soma of the target cell. Basket cells form axo-somatic synapses, meaning their synapses target somas of other cells." [WikipediaVersioned:Basket_cell&oldid=951703880] subset: BDS_subset +subset: human_subset +subset: mouse_subset xref: ZFA:0009068 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} -is_a: CL:0000104 ! multipolar neuron is_a: CL:0011005 ! GABAergic interneuron intersection_of: CL:0000099 ! interneuron intersection_of: bearer_of PATO:0070002 ! basket cell morphology @@ -1780,6 +1971,8 @@ id: CL:0000119 name: cerebellar Golgi cell def: "Large intrinsic neuron located in the granule layer of the cerebellar cortex that extends its dendrites into the molecular layer where they receive contact from parallel fibers. The axon of the Golgi cell ramifies densely in the granule layer and enters into a complex arrangement with mossy fiber terminals and granule cell dendrites to form the cerebellar glomerulus. Llinas, Walton and Lang. In The Synaptic Organization of the Brain. 5th ed. 2004." [NIFSTD:sao1415726815] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "cerebellar Golgi neuron" EXACT [] synonym: "cerebellum Golgi cell" EXACT [] synonym: "Golgi cell" EXACT [] @@ -1793,9 +1986,11 @@ id: CL:0000120 name: granule cell def: "A neuron of the vertebrate central nervous system that is small in size. This general class includes small neurons in the granular layer of the cerebellar cortex, cerebral cortex neurons that are not pyramidal cells and small neurons without axons found in the olfactory bulb." [https://medical-dictionary.thefreedictionary.com/granule+cell] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset xref: BTO:0003393 xref: ZFA:0009070 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} -is_a: CL:0000117 ! CNS neuron (sensu Vertebrata) +is_a: CL:2000029 ! central nervous system neuron [Term] id: CL:0000121 @@ -1803,6 +1998,8 @@ name: Purkinje cell def: "An inhibitory neuron and the sole output neuron of the cerebellar cortex, the Purkinje cell's soma is located between the granular and molecular layers of the cerebellum. It is one of the largest neural cells in the mammalian brain, ranging from 50 to 80 micrometres in diameter. Purkinje cells have planar, fan-shaped dendrites that branch extensively with little overlap. This cell type receives synaptic input from parallel fibres, which modulate high-frequency spike activity known as \"simple spikes,\" and climbing fibres, which modulate infrequent calcium spike activity known as \"complex spikes\". Purkinje cells are involved in motor coordination, particularly in correcting movements in progress." [MESH:D011689, PMID:12907269, PMID:14568361, PMID:31424738, PMID:33288911, PMID:38168772] comment: Neurodegenerative disorders affecting Purkinje cells disrupt motor functions. Some of the neurodegenerative disorders that causes loss and degeration of Purkinje cells are Spinocerebellar ataxias (SCAs) (Josef P Kapfhammer and Etsuko Shimobayashi 2023), Friedreich's ataxia (FRDA) (Kevin C Kemp et al., 2016), Fetal alcohol syndrome (Laurent Servais et al., 2016), Dandy-Walker malformation (Alexander Atamian et al., 2024). {xref="PMID:27215193", xref="PMID:17535929", xref="PMID:37426070", xref="https://doi.org/10.1016/j.stem.2023.11.013"} subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "cerebellar Purkinje cell" EXACT [https://doi.org/10.1016/j.proghi.2004.07.002] synonym: "PC" RELATED OMO:0003000 [PMID:38168772] synonym: "PN" RELATED OMO:0003000 [PMID:28821816] @@ -1812,11 +2009,9 @@ xref: CALOHA:TS-0845 xref: FMA:67969 xref: https://cellxgene.cziscience.com/cellguide/CL_0000121 xref: ZFA:0009071 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} -is_a: CL:0000117 ! CNS neuron (sensu Vertebrata) -is_a: CL:0000527 ! efferent neuron is_a: CL:1001611 ! cerebellar neuron relationship: RO:0002100 UBERON:0002129 ! has soma location cerebellar cortex -property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional.\n\nPurkinje cells, named after the Czech anatomist Jan Evangelista Purkyně who discovered them, are unique inhibitory neurons in the cerebellar cortex. They are a critical part of the vertebrate nervous system as they provide the only signal output from the cortex to the cerebellar nuclei. They are one of the few types of neurons that are large enough to be seen with the naked eye. The most distinct hallmark of Purkinje cells is their elaborate dendritic arbor, which forms a broad and intricately branching structure resembling a tree. These numerous branches each receive excitatory synaptic inputs from more than 100,000 parallel fibers; in addition, a single climbing fiber makes hundreds of synapses to the soma and proximal dendrites. A single long axon forms an inhibitory projection to the cerebellar nuclei.\nPurkinje cells play key roles in the coordination of fine, voluntary motor movements and balance. As the sole output of all motor coordination in the cerebellar cortex, they serve as a central relay in the cerebro-cerebellar loop. Each Purkinje cell receives two types of synaptic input: one from parallel fibers (which are axons of granule cells), and the other from climbing fibers (originating from the inferior olivary nucleus). The Purkinje cells process and integrate these diverse kinds of input signals to generate output that controls timing and coordination of movements.\nPurkinje neurons show considerable synaptic plasticity. Throughout life, these cells continue to undergo long-term potentiation and depression at parallel fiber synapses, which cause long-lasting increase or decrease, respectively, of synaptic transmission and have been proposed as mechanisms for motor learning. \nPurkinje cells are also known to be implicated in a variety of diseases. Their progressive loss is a prime feature in certain types of ataxia, a collective term used to describe conditions characterized by loss of muscular control and coordination. Furthermore, a significant reduction in the density of Purkinje cells has been reported in conditions such as autism and Huntington’s disease." xsd:string {xref="DOI:10.1007/s12311-018-0985-7", xref="DOI:10.1038/nrn3886", xref="DOI:10.7554/eLife.63668", xref="https://www.ncbi.nlm.nih.gov/books/NBK545154/", xref="https://www.sciencedirect.com/topics/agricultural-and-biological-sciences/purkinje-cell"} +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nPurkinje cells, named after the Czech anatomist Jan Evangelista Purkyně who discovered them, are unique inhibitory neurons in the cerebellar cortex. They are a critical part of the vertebrate nervous system as they provide the only signal output from the cortex to the cerebellar nuclei. They are one of the few types of neurons that are large enough to be seen with the naked eye. The most distinct hallmark of Purkinje cells is their elaborate dendritic arbor, which forms a broad and intricately branching structure resembling a tree. These numerous branches each receive excitatory synaptic inputs from more than 100,000 parallel fibers; in addition, a single climbing fiber makes hundreds of synapses to the soma and proximal dendrites. A single long axon forms an inhibitory projection to the cerebellar nuclei.\nPurkinje cells play key roles in the coordination of fine, voluntary motor movements and balance. As the sole output of all motor coordination in the cerebellar cortex, they serve as a central relay in the cerebro-cerebellar loop. Each Purkinje cell receives two types of synaptic input: one from parallel fibers (which are axons of granule cells), and the other from climbing fibers (originating from the inferior olivary nucleus). The Purkinje cells process and integrate these diverse kinds of input signals to generate output that controls timing and coordination of movements.\nPurkinje neurons show considerable synaptic plasticity. Throughout life, these cells continue to undergo long-term potentiation and depression at parallel fiber synapses, which cause long-lasting increase or decrease, respectively, of synaptic transmission and have been proposed as mechanisms for motor learning. \nPurkinje cells are also known to be implicated in a variety of diseases. Their progressive loss is a prime feature in certain types of ataxia, a collective term used to describe conditions characterized by loss of muscular control and coordination. Furthermore, a significant reduction in the density of Purkinje cells has been reported in conditions such as autism and Huntington’s disease." xsd:string {xref="DOI:10.1007/s12311-018-0985-7", xref="DOI:10.1038/nrn3886", xref="DOI:10.7554/eLife.63668", xref="https://www.ncbi.nlm.nih.gov/books/NBK545154/", xref="https://www.sciencedirect.com/topics/agricultural-and-biological-sciences/purkinje-cell"} [Term] id: CL:0000122 @@ -1824,11 +2019,12 @@ name: stellate neuron def: "A neuron that has dendritic processes radiating from the cell body forming a star-like shape." [ISBN:9780123973481] subset: BDS_subset subset: cellxgene_subset +subset: human_subset +subset: mouse_subset xref: BTO:0002316 xref: ZFA:0009072 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} -is_a: CL:0000104 ! multipolar neuron -is_a: CL:0000117 ! CNS neuron (sensu Vertebrata) -intersection_of: CL:0000117 ! CNS neuron (sensu Vertebrata) +is_a: CL:2000029 ! central nervous system neuron +intersection_of: CL:0000540 ! neuron intersection_of: bearer_of PATO:0070010 ! stellate morphology relationship: bearer_of PATO:0070010 ! stellate morphology @@ -1836,6 +2032,8 @@ relationship: bearer_of PATO:0070010 ! stellate morphology id: CL:0000123 name: neuron associated cell (sensu Vertebrata) subset: cellxgene_subset +subset: human_subset +subset: mouse_subset is_a: CL:0000095 ! neuron associated cell relationship: RO:0002162 NCBITaxon:7742 ! in taxon Vertebrata relationship: RO:0002202 CL:0000333 ! develops from migratory neural crest cell @@ -1855,6 +2053,8 @@ comment: Not all glial cells develop from glioblasts, with microglia developing subset: cellxgene_subset subset: general_cell_types_upper_slim subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "neuroglia" RELATED [] synonym: "neuroglial cell" EXACT [] xref: BTO:0002606 @@ -1865,13 +2065,15 @@ xref: https://cellxgene.cziscience.com/cellguide/CL_0000125 xref: ZFA:0009073 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000095 ! neuron associated cell property_value: RO:0002175 NCBITaxon:9606 -property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional.\n\nGlial cells, also known as neuroglia or simply glia, are non-neuronal cells in the central and peripheral nervous systems that provide support and protection for neurons. They constitute approximately half of the total cells in the human brain and more than half in other parts of the nervous system. Glial cells perform several key functions including, but not limited to, maintaining homeostasis, forming the myelin sheath around the neuron axons, and providing support and nutrition to neurons.\nThese different functions are performed by various glial cell types, including astrocytes, oligodendrocytes, microglia and other specialized types. Astrocytes, for example, are the most abundant glial cells and provide metabolic and nutrient support to neurons, help regulate the extracellular ion and neurotransmitter levels, and play a role in the formation and maintenance of the blood-brain barrier, contributing to the overall homeostasis and functioning of the nervous system. Additionally, astrocytes are involved in synaptic communication and participate in processes such as synaptogenesis and synaptic pruning.\nOligodendrocytes in the central nervous system function to insulate neurons by producing a fatty substance known as myelin. The myelin sheath enhances the speed and efficiency of nerve impulse conduction along the axons. \nMicroglia, the immune cells of the central nervous system, protect neurons from pathogens and clear away dead neurons through phagocytosis, a process also known as cellular eating. They also contribute to the regulation of inflammation in response to signals of tissue damage or infection in the central nervous system by releasing cytokines and other signaling molecules that modulate the immune response.\nDespite their overarching function in the support and protection of neurons, glial cells have also been shown to play significant roles in the pathophysiology of many psychiatric and neurodegenerative diseases, such as Alzheimer’s, Parkinson’s Disease and multiple sclerosis." xsd:string {xref="DOI:10.1002/glia.24343", xref="DOI:10.1038/nn1988", xref="DOI:10.1101/cshperspect.a020602", xref="DOI:10.1126/science.aat0473", xref="DOI:10.3389/fncel.2017.00024"} +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nGlial cells, also known as neuroglia or simply glia, are non-neuronal cells in the central and peripheral nervous systems that provide support and protection for neurons. They constitute approximately half of the total cells in the human brain and more than half in other parts of the nervous system. Glial cells perform several key functions including, but not limited to, maintaining homeostasis, forming the myelin sheath around the neuron axons, and providing support and nutrition to neurons.\nThese different functions are performed by various glial cell types, including astrocytes, oligodendrocytes, microglia and other specialized types. Astrocytes, for example, are the most abundant glial cells and provide metabolic and nutrient support to neurons, help regulate the extracellular ion and neurotransmitter levels, and play a role in the formation and maintenance of the blood-brain barrier, contributing to the overall homeostasis and functioning of the nervous system. Additionally, astrocytes are involved in synaptic communication and participate in processes such as synaptogenesis and synaptic pruning.\nOligodendrocytes in the central nervous system function to insulate neurons by producing a fatty substance known as myelin. The myelin sheath enhances the speed and efficiency of nerve impulse conduction along the axons. \nMicroglia, the immune cells of the central nervous system, protect neurons from pathogens and clear away dead neurons through phagocytosis, a process also known as cellular eating. They also contribute to the regulation of inflammation in response to signals of tissue damage or infection in the central nervous system by releasing cytokines and other signaling molecules that modulate the immune response.\nDespite their overarching function in the support and protection of neurons, glial cells have also been shown to play significant roles in the pathophysiology of many psychiatric and neurodegenerative diseases, such as Alzheimer’s, Parkinson’s Disease and multiple sclerosis." xsd:string {xref="DOI:10.1002/glia.24343", xref="DOI:10.1038/nn1988", xref="DOI:10.1101/cshperspect.a020602", xref="DOI:10.1126/science.aat0473", xref="DOI:10.3389/fncel.2017.00024"} [Term] id: CL:0000126 name: macroglial cell def: "A neuroglial cell of ectodermal origin, i.e., the astrocytes and oligodendrocytes considered together." [GOC:tfm, ISBN:0721662544] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "macroglia" RELATED OMO:0003004 [doi:10.1152/physrev.2001.81.2.871] synonym: "macrogliocyte" EXACT [] xref: BTO:0000771 @@ -1888,6 +2090,8 @@ def: "A class of large neuroglial (macroglial) cells in the central nervous syst comment: Astrocytes are reportedly CD68-negative, CD121a-positive, CD184-positive, CD192-positive, CRF-positive, EGFR-positive, GFAP-positive, GLUT1-positive, MBP-negative, and NGFR-positive. subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "astrocytic glia" EXACT [] xref: BTO:0000099 xref: CALOHA:TS-0060 @@ -1903,6 +2107,8 @@ def: "A class of large neuroglial (macroglial) cells in the central nervous syst comment: Oligodendrocytes are reportedly MDP-positive and CD4-negative. subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "oligodendroglia" RELATED [] synonym: "OLs" EXACT [PMID:8734446] xref: BTO:0000962 @@ -1922,6 +2128,8 @@ def: "A transcriptomically distinct central nervous system macrophage found in t comment: Unlike macroglial cells, microglial cells arise from hematopoietic stem cells in the yolk sac during early embryogenesis that populate the central nervous system. They derive from embryonic mesoderm and are not from neuroectoderm where glioblast develops from. Markers: Mouse: CD11b+, F4/80+, CD68+. They represent ~12% of the cells in the CNS, but they are not uniformly distributed within the CNS. A normal adult mouse brain has approximately 3.5x10e6 microglia. Microglia are also reportedly CD3-negative, CD4-positive, CD8-negative, CD11b-positive, CD11c-high, CD14-negative, CD19-negative, CD45-low, CD56-negative, CD163-negative, CD200R-positive, CD281-positive, CD282-positive, CD283-positive, CD284-positive, CD285-positive, CD286-positive, CD287-positive, CD288-positive, CD289-positive, Gr1-negative, nestin-positive, and PU.1-positive. {xref="PMID:23616747"} subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "brain macrophage" BROAD [] synonym: "brain-resident macrophage" EXACT [] synonym: "hortega cells" EXACT [http://www.copewithcytokines.de/] @@ -1931,10 +2139,10 @@ synonym: "microgliocyte" EXACT [http://www.copewithcytokines.de/] xref: BTO:0000078 xref: BTO:0000962 xref: FMA:54539 +xref: https://cellxgene.cziscience.com/cellguide/CL_0000129 xref: ZFA:0009077 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000125 ! glial cell is_a: CL:0000878 ! central nervous system macrophage -is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000125 ! glial cell intersection_of: capable_of GO:0045087 ! innate immune response intersection_of: part_of UBERON:0001017 ! central nervous system @@ -1947,6 +2155,7 @@ relationship: RO:0002104 PR:000001813 ! has plasma membrane part adhesion G prot relationship: RO:0002104 PR:000002064 ! has plasma membrane part macrosialin relationship: RO:0002202 CL:0000222 ! develops from mesodermal cell property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nMicroglial cells, sometimes referred to as microglia, are a type of glial cell that primarily exist within the central nervous system (CNS), notably in the brain and the spinal cord. Classified among the resident immune cells, microglial cells represent about 10% of all cells found within the CNS. These cells are derived from progenitor cells in the yolk sac, which differentiates them from other types of glial cells (such as astrocytes and oligodendrocytes) that are derived from neuroectodermal cell lineages. \nThe primary role of microglial cells is to act as the first and main active form of immune defense in the CNS. They express a vast repertoire of pattern recognition receptors, which allow them to sense and eliminate microbes invading the CNS parenchyma. They represent one of the macrophage populations of the CNS and are responsible for phagocytosis (engulfing and destroying cellular waste or pathogens) in the neural environment. \nMicroglial cells are particularly responsive to pathogens and injuries and change their morphology in reaction to inflammation or insult: In the normal state they are characterized by a ramified shape with small processes; in response to stimuli, some microglia mature and change to an amoeboid shape. \nBeyond their macrophagic activity, they also perform synaptic pruning during brain development, eliminate unnecessarily produced neurons, and facilitate tissue regeneration and repair. they play integral roles in regulating neural development and supporting cell survival and are important for maintaining tissue homeostasis. \nWhile their protective role generally benefits the brain, their over-activation can occasionally lead to neuro-inflammatory diseases, underlining the importance of balanced microglial cell functions. They have been extensively studied for their association with neurodegenerative diseases, such as Alzheimer's disease, Parkinson's disease, and multiple sclerosis." xsd:string {xref="DOI:10.1016/j.cell.2019.08.053", xref="DOI:10.1016/j.conb.2022.102674", xref="DOI:10.1016/j.tins.2021.11.001", xref="DOI:10.1038/nri3086", xref="DOI:10.3389/fnins.2021.742065"} [Term] id: CL:0000130 @@ -1958,9 +2167,13 @@ relationship: RO:0002162 NCBITaxon:33317 ! in taxon Protostomia id: CL:0000131 name: gut endothelial cell subset: cellxgene_subset +subset: human_subset +subset: mouse_subset +xref: https://cellxgene.cziscience.com/cellguide/CL_0000131 xref: ZFA:0009078 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000115 ! endothelial cell relationship: RO:0002202 CL:0000223 ! develops from endodermal cell +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nGut endothelial cells are a crucial component of the endothelium, a thin layer of single cells that line the interior surface of blood vessels and lymphatic vessels, including those in the digestive system or \"gut\". These cells plays an integral role in various physiological and metabolic functions, actively participating in nutrient absorption, host defense, and vascular homeostasis in the gut.\nThe primary function of gut endothelial cells lies in their ability to control the passage of materials and the transit of white blood cells into and out of the bloodstream. They achieve this through the formation of a semi-permeable barrier, in which permeability is regulated by tight junctions; complex structures that bring the cells together, sealing the space between them. This ensures a controlled, selective passage of nutrients, ions, and water from the bloodstream into the gut and vice versa, helping maintain homeostasis and overall health.\nGut endothelial cells also play a significant role in angiogenesis and serve as a critical regulator of the gut immune responses playing a modulative role in gut immune homeostasis and inflammatory responses. In addition, they generate nitric oxide, a potent vasodilator, which helps in maintaining vascular tonus, preventing platelet and leukocyte adhesion, and decreasing smooth muscle proliferation. These multi-faceted roles make gut endothelial cells indispensable for the normal functioning of the gut and overall health." xsd:string {xref="DOI:10.1038/nri2171", xref="DOI:10.1111/bph.14527", xref="DOI:10.3390/ijms23073698", xref="DOI:10.3748/wjg.v17.i5.578", xref="DOI:full/10.15252/emmm.202114121"} [Term] id: CL:0000132 @@ -1969,6 +2182,8 @@ def: "An hexagonal, flattened, mitochondria-rich endothelial cell that forms a m subset: cellxgene_subset subset: eye_upper_slim subset: human_reference_atlas +subset: human_subset +subset: mouse_subset xref: CALOHA:TS-0172 xref: FMA:70614 xref: ZFA:0009079 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} @@ -1981,6 +2196,8 @@ property_value: RO:0002175 NCBITaxon:9606 id: CL:0000133 name: neurectodermal cell def: "Ectoderm destined to be nervous tissue." [GOC:tfm, ISBN:068340007X] +subset: human_subset +subset: mouse_subset synonym: "neurectoderm cell" EXACT [] xref: ZFA:0009080 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000221 ! ectodermal cell @@ -1992,6 +2209,8 @@ alt_id: CL:0002452 def: "A connective tissue cell that normally gives rise to other cells that are organized as three-dimensional masses. In humans, this cell type is CD73-positive, CD90-positive, CD105-positive, CD45-negative, CD34-negative, and MHCII-negative. They may further differentiate into osteoblasts, adipocytes, myocytes, neurons, or chondroblasts in vitro. Originally described as residing in the bone marrow, this cell type is now known to reside in many, if not all, adult organs." [FB:ma, GOC:dsd, http://en.wikipedia.org/wiki/Mesenchymal_stem_cell, http://www.copewithcytokines.de/cope.cgi?key=mesenchymal%20stem%20cells, PMCID:PMC2613570, PMID:10102814, PMID:16923606, PMID:17986482, PMID:19960544] comment: Many but not all mesenchymal cells derive from the mesoderm. MSCs are reportedly CD3-negative, CD4-negative, CD5-negative, CD8-negative, CD11a-negative, CD11b-negative, CD14-negative, CD19-negative, CD29-positive, CD31-negative, CD34-negative, CD38-negative, CD40-negative, CD44-positive, CD45-negative, CD49-positive, CD54-positive, CD66b-negative, CD79a-negative, CD80-negative, CD102-positive, CD106-positive, CD117-positive, CD121a-positive, CD121b-positive, CD123-positive, CD124-positive, CD133-negative, CD146-positive, CD166-positive, CD271-positive, B220-negative, Gr1-negative, MHCI-positive, MHCII-negative, SSEA4-negative, sca1-positive, Ter119-negative, and glycophorin A-negative. Cultured MSCs are capable of producing stem cell factor, IL7, IL8, IL11, TGF-beta, cofilin, galectin-1, laminin-receptor 1, cyclophilin A, and MMP-2. subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "BMSC" RELATED OMO:0003000 [] synonym: "bone marrow stromal cells" NARROW [] synonym: "CFU-F" RELATED OMO:0003000 [] @@ -2018,6 +2237,8 @@ name: fibrocyte def: "An inactive fibroblast; cytoplasm is sparse, endoplasmic reticulum is scanty with flattened nucleus. Term used by some histologists; when fibroblasts become relatively inactive in fiber formation. However, this cell has the potential for fibrogenesis in quiescent connective tissue of the adult, as well as during development, other histologists prefer to use the term fibroblast in all circumstances. These cells represent ~0.5% of peripheral blood leukocytes." [GOC:dsd, GOC:tfm, http://en.wikipedia.org/wiki/Fibrocyte, ISBN:0412046911, ISBN:0517223651, PMID:11641248, PMID:15010326, PMID:17607298, PMID:18222966, PMID:8790603, PMID:9551999] comment: Cultured human fibrocytes are MHCI-positive, MHCII-positive, CD1a-negative, CD3-negative, CD4-negative, CD8-negative, CD10-negative, CD11b-positive, CD13-positive, CD14-negative, CD16-negative, CD18-positive, CD19-negative, CD25-negative, CD29-positive, CD32-positive, CD33-negative, CD34-positive, CD38-negative, CD40-positive, CD44-negative, CD45RO-positive, CD49a-positive, CD49b-positive, CD49c-negative, CD49d-negative, CD49e-positive, CD49f-negative, CD56-negative, CD58-positive, CD61-positive, CD64-positive, CD70-negative, CD71-positive, CD80-positive, CD83-negative, CD86-positive, CD103-negative, CD105-positive, CD181-positive, CD182-negative, CD183-positive, CD184-positive, CD185-negative, CD186-negative, CD191-positive, CD192-negative, CD193-positive, CD194-positive, CD195-positive, CD196-negative, CD197-positive, CD199-positive, desmin-negative, F4/80-positive, Gr1-positive, LSP-1-positive, MHCI-positive, MHCII-positive, alpha-SMA-negative, TCRab-negative, TCRgd-negative, and vimentin-positive. Fibrocytes are also capable of secreting angiogenin, bFGF, CCL2, CCL3, CCL4, CCL8, CXCL1, type I collagen, type III collagen, CTGF, fibronectin, GM-CSF, IL-1a, IL-6, IL-8, IL-10, M-CSF, MMP-9, PDGF-A, TGF-alpha, TGF-beta1, TNF-alpha, and VEGF-A. subset: cellxgene_subset +subset: human_subset +subset: mouse_subset xref: FMA:63879 is_a: CL:0000499 {is_inferred="true"} ! stromal cell intersection_of: CL:0000499 ! stromal cell @@ -2035,6 +2256,8 @@ def: "A fat-storing cell found mostly in the abdominal cavity and subcutaneous t subset: cellxgene_subset subset: general_cell_types_upper_slim subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "adipose cell" EXACT [] synonym: "fat cell" EXACT [] xref: BTO:0000443 @@ -2052,6 +2275,8 @@ id: CL:0000137 name: osteocyte def: "A mature osteoblast that has become embedded in the bone matrix. They occupy a small cavity, called lacuna, in the matrix and are connected to adjacent osteocytes via protoplasmic projections called canaliculi." [GOC:tfm, MESH:D010011] comment: VSAO relationship simplified OBO_REL:integral_part_of VSAO:0000118 +subset: human_subset +subset: mouse_subset synonym: "bone cell" BROAD [] xref: BTO:0002038 xref: CALOHA:TS-1167 @@ -2069,6 +2294,8 @@ id: CL:0000138 name: chondrocyte def: "Skeletogenic cell that is terminally differentiated, secretes an avascular, GAG-rich matrix, is embedded in cartilage tissue matrix, retains the ability to divide, and develops from a chondroblast cell." [GO_REF:0000034, MESH:D019902] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "cartilage cell" EXACT [] xref: BTO:0000249 xref: CALOHA:TS-0138 @@ -2083,6 +2310,8 @@ relationship: RO:0002202 CL:0000058 ! develops from chondroblast id: CL:0000140 name: odontocyte def: "Skeletogenic cell that secretes dentine matrix, is derived from odontogenic papilla. Embedded in dentine tissue, and is the transformation of a non-terminally differentiated odontoblast cell." [GO_REF:0000034] +subset: human_subset +subset: mouse_subset xref: ZFA:0009086 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: BFO:0000002 is_a: CL:0002320 ! connective tissue cell @@ -2095,6 +2324,8 @@ id: CL:0000141 name: cementocyte def: "An osteocytelike cell with numerous processes, trapped in a lacuna in the cement of the tooth." [ISBN:0781733901] comment: CHECK: wikipedia says that cementocytes no longer produce cementum, but the phenoscape def is: Skeletogenic cell that produces cementum, is part of the odontogenic papilla, and is a transformation of a cementoblast cell (no change to existing def). +subset: human_subset +subset: mouse_subset xref: FMA:63003 xref: ZFA:0009087 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000137 ! osteocyte @@ -2105,6 +2336,8 @@ relationship: RO:0002202 CL:0000061 ! develops from cementoblast id: CL:0000142 name: hyalocyte def: "A cell occurring in the peripheral part of the vitreous body of the eye that may be responsible for production of hyaluronic acid and collagen." [GOC:tfm, PMID:19073178] +subset: human_subset +subset: mouse_subset synonym: "vitreous cell" RELATED [] xref: BTO:0004271 xref: FMA:70620 @@ -2132,6 +2365,8 @@ def: "A cell capable of processing and presenting lipid and protein antigens to comment: Note change of name; nearly all somatic cells can present antigens to T cells via MHC Class I complexes leading to effector responses, but professional antigen presenting cells constitutively express MHC Class II as well as costimulatory molecules, and thus can initiate immune responses via T cells. subset: blood_and_immune_upper_slim subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "APC" RELATED OMO:0003000 [] xref: ZFA:0009088 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000738 ! leukocyte @@ -2143,6 +2378,8 @@ relationship: capable_of GO:0002504 ! antigen processing and presentation of pep id: CL:0000146 name: simple columnar epithelial cell subset: human_reference_atlas +subset: human_subset +subset: mouse_subset xref: ZFA:0009089 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000075 ! columnar/cuboidal epithelial cell property_value: RO:0002175 NCBITaxon:9606 @@ -2151,6 +2388,8 @@ property_value: RO:0002175 NCBITaxon:9606 id: CL:0000147 name: pigment cell def: "A pigment cell is a cell that contains pigment granules." [GOC:tfm] +subset: human_subset +subset: mouse_subset synonym: "chromatocyte" EXACT [] synonym: "chromatophore" EXACT [] xref: VHOG:0001678 @@ -2165,10 +2404,13 @@ def: "A pigment cell derived from the neural crest. Contains melanin-filled pigm subset: cellxgene_subset subset: general_cell_types_upper_slim subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "melanophore" NARROW [] xref: BTO:0000847 xref: CALOHA:TS-0613 xref: FMA:70545 +xref: https://cellxgene.cziscience.com/cellguide/CL_0000148 xref: MESH:D008544 xref: VHOG:0001679 xref: ZFA:0009091 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} @@ -2181,29 +2423,39 @@ intersection_of: RO:0002202 CL:0000541 ! develops from melanoblast relationship: has_part GO:0042470 ! melanosome relationship: RO:0002202 CL:0000541 ! develops from melanoblast property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nMelanocytes are specialized cells prevalently found in the skin, but also present in the hair follicles, eyes, inner ear, bones, heart, and brain. Their primary function is the synthesis of melanin, a pigment responsible for coloration of skin, hair, and eyes. The presence and distribution of this pigment play a crucial role in the body's defense mechanism against harmful ultraviolet radiation.\nIn addition to melanin production, melanocytes also engage in a variety of other biological functions. They play a fundamental role in the immune response, owing to their ability to present antigens to T cells. Furthermore, they contribute to the maintenance of the skin's homeostasis by regulating processes such as extracellular matrix remodeling and cytokine production. A balance in melanocyte function is pivotal, as dysfunctions often result in dermatological disorders. For instance, the loss of melanocytes or reduction in their function may lead to hypopigmentation conditions such as vitiligo, whereas an abnormal increase could result in hyperpigmentation disorders or melanoma, a dangerous type of skin cancer." xsd:string {xref="DOI:10.1002/med.21754", xref="DOI:10.1038/nrc.2016.37", xref="DOI:10.1111/j.1751-1097.2007.00226.x", xref="DOI:10.3390/ijms21249769", xref="https://www.sciencedirect.com/topics/agricultural-and-biological-sciences/melanocyte"} [Term] id: CL:0000149 name: visual pigment cell +subset: human_subset +subset: mouse_subset synonym: "pigment cell" BROAD [] is_a: CL:0000147 ! pigment cell [Term] id: CL:0000150 -name: glandular epithelial cell -def: "A specialized epithelial cell that is capable of synthesizing and secreting certain biomolecules." [GOC:tfm] +name: glandular secretory epithelial cell +def: "An epithelial cell, located in a gland, that is specialised for the synthesis and secretion of specific biomolecules, such as hormones, or mucous." [GOC:tfm, ORCID:0000-0002-7073-9172] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset +synonym: "glandular epithelial cell" EXACT [] xref: CALOHA:TS-2085 xref: FMA:86494 -is_a: CL:0000066 ! epithelial cell -is_a: CL:0000151 ! secretory cell -relationship: part_of UBERON:0006799 ! glandular epithelium +is_a: CL:1100001 ! secretory epithelial cell +intersection_of: CL:0000066 ! epithelial cell +intersection_of: CL:0000151 ! secretory cell +intersection_of: part_of UBERON:0002530 ! gland +relationship: part_of UBERON:0002530 ! gland [Term] id: CL:0000151 name: secretory cell def: "A cell that specializes in controlled release of one or more substances." [GOC:tfm, ISBN:0721662544] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset xref: BTO:0003659 xref: FMA:86916 is_a: CL:0000000 ! cell @@ -2216,6 +2468,8 @@ id: CL:0000152 name: exocrine cell def: "A cell of an exocrine gland; i.e. a gland that discharges its secretion via a duct." [ISBN:0198547684] subset: general_cell_types_upper_slim +subset: human_subset +subset: mouse_subset xref: FMA:16014 xref: ZFA:0009092 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000151 ! secretory cell @@ -2228,6 +2482,8 @@ relationship: part_of UBERON:0002365 ! exocrine gland id: CL:0000153 name: glycosaminoglycan secreting cell def: "A cell that secretes glycosaminoglycans." [GOC:tfm] +subset: human_subset +subset: mouse_subset synonym: "GAG secreting cell" EXACT [] synonym: "hyaluronic acid secreting cell" NARROW [] xref: ZFA:0009093 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} @@ -2238,6 +2494,8 @@ is_a: CL:0000447 ! carbohydrate secreting cell id: CL:0000154 name: protein secreting cell def: "Any secretory cell that is capable of some protein secretion." [FBC:Autogenerated] +subset: human_subset +subset: mouse_subset is_a: CL:0000151 ! secretory cell intersection_of: CL:0000151 ! secretory cell intersection_of: capable_of GO:0009306 ! protein secretion @@ -2246,15 +2504,19 @@ relationship: capable_of GO:0009306 ! protein secretion [Term] id: CL:0000155 name: peptic cell -def: "A cell that is usually basal in position, cuboidal with round nucleus, short microvilli, secretes pepsinogen." [GOC:tfm] +def: "An epithelial cell of the stomach that is part of the fundic gastric gland. This cell is characterized by a basally located nucleus, abundant rough endoplasmic reticulum, and large apical secretory granules. It produces and secretes pepsinogen, the inactive precursor of the digestive enzyme pepsin." [GOC:tfm, PMID:21907708, PMID:30571046, Wikipedia:Gastric_chief_cell] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "chief cell of stomach" EXACT [] -synonym: "gastric chief cell" EXACT [] +synonym: "gastric chief cell" EXACT [Wikipedia:Chief_cell] synonym: "pepsinogen secreting cell" EXACT [] -synonym: "zymogenic cell" EXACT [] +synonym: "zymogenic cell" EXACT [Wikipedia:Chief_cell] xref: FMA:62902 +is_a: CL:0000152 ! exocrine cell is_a: CL:0000154 ! protein secreting cell is_a: CL:0002659 ! glandular epithelial cell of stomach +relationship: part_of UBERON:0010038 ! fundic gastric gland [Term] id: CL:0000156 @@ -2267,6 +2529,8 @@ is_obsolete: true id: CL:0000157 name: surfactant secreting cell def: "A cell that specializes in secretion of surfactant in the alveoli of the lung." [GOC:tfm, ISBN:0721662544] +subset: human_subset +subset: mouse_subset is_a: CL:0000151 {is_inferred="true"} ! secretory cell intersection_of: CL:0000151 ! secretory cell intersection_of: capable_of GO:0043129 ! surfactant homeostasis @@ -2278,18 +2542,23 @@ name: club cell def: "A non-mucous, epithelial secretory cell that is part of the tracheobronchial tree. A club cell has short microvilli but no cilia. A club cell is able to multiply and differentiate into ciliated cells to regenerate the bronchiolar epithelium and it also protects the tracheobronchial epithelium." [DOI:10.1183/09031936.00146609, DOI:10.1378/chest.12-2762, GOC:tfm, PMID:28128362, PMID:29874100, PMID:7905712] subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "Clara cell" EXACT [] xref: BTO:0004811 xref: FMA:14119 is_a: CL:0000157 ! surfactant secreting cell is_a: CL:0002202 ! epithelial cell of tracheobronchial tree is_a: CL:0011026 ! progenitor cell +is_a: CL:1100001 ! secretory epithelial cell relationship: RO:0002104 GO:0005902 ! has plasma membrane part microvillus property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000159 name: seromucus secreting cell +subset: human_subset +subset: mouse_subset is_a: CL:0000151 ! secretory cell [Term] @@ -2297,18 +2566,20 @@ id: CL:0000160 name: goblet cell def: "A specialized, columnar, mucus secreting epithelial cell shaped like a flask or goblet. A narrow basal end contains the nucleus while the apical end is swollen by the accumulation of mucus laden secretory granules. Short microvilli project from the apical plasma membrane." [http://en.wikipedia.org/wiki/Goblet_cell, MESH:D020397] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "chalice cell" EXACT [] xref: BTO:0001540 xref: FMA:13148 xref: http://en.wikipedia.org/wiki/Goblet_cell xref: https://cellxgene.cziscience.com/cellguide/CL_0000160 xref: ZFA:0009094 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} -is_a: CL:0000066 ! epithelial cell -relationship: capable_of GO:0070254 ! mucus secretion +is_a: CL:0000319 ! mucus secreting cell +is_a: CL:1100001 ! secretory epithelial cell relationship: has_part GO:0005902 ! microvillus relationship: has_part GO:0098594 ! mucin granule property_value: foaf:depiction "https://upload.wikimedia.org/wikipedia/commons/thumb/c/c4/404_Goblet_Cell_new.jpg/800px-404_Goblet_Cell_new.jpg" xsd:string {xref="http://cnx.org/content/col11496/1.6/", xref="https://commons.wikimedia.org/w/index.php?curid=30131227"} -property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional.\n\nGoblet cells are specialized, simple columnar, secretory epithelial cells that are mostly found in the respiratory and intestinal tracts. The term \"goblet\" refers to their shape, which resembles a flask or goblet, specially at their apical end which is swollen due to the accumulation of secretory granules. \nThe primary function of goblet cells is to to protect and lubricate the underlying tissues by secreting large quantities of mucin, a complex glycoprotein, which forms mucus when hydrated. In the respiratory tract, the mucus secreted by these cells traps dust, bacteria, viruses, and other potentially harmful particles in the inhaled air, preventing them from reaching the delicate tissues of the lungs. In the intestines, the goblet cells secrete mucus that acts as a protective barrier shielding the intestinal epithelium from dietary antigens, pathogens and prevents the intestinal epithelium from being eroded by the actions of the digestive enzymes and the abrasive action of passing food material.\nGoblet cells are capable of rapidly altering their secretory output in response to stimuli. For example, irritants like smoke or dust can trigger an increased rate of mucus production, as the body attempts to flush out the harmful particles. Conversely, in conditions such as chronic bronchitis and cystic fibrosis, overactive goblet cells can create a thick accumulation of mucus that obstructs the airways and fosters bacterial growth. Lastly, goblet cells are not static, rather, they undergo a dynamic process known as goblet cell metaplasia-differentiation, wherein non-goblet cells in response to chronic injury or inflammation, can differentiate into goblet cells leading to an accumulation of these cells in the tissue, known as goblet cell hyperplasia." xsd:string {xref="DOI:10.1016/S1357-2725(02)00083-3", xref="DOI:10.1038/s41575-022-00675-x", xref="DOI:10.1165/ajrcmb.25.5.f218", xref="DOI:10.1242/bio.20121701", xref="https://www.ncbi.nlm.nih.gov/books/NBK553208/"} +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nGoblet cells are specialized, simple columnar, secretory epithelial cells that are mostly found in the respiratory and intestinal tracts. The term \"goblet\" refers to their shape, which resembles a flask or goblet, specially at their apical end which is swollen due to the accumulation of secretory granules. \nThe primary function of goblet cells is to to protect and lubricate the underlying tissues by secreting large quantities of mucin, a complex glycoprotein, which forms mucus when hydrated. In the respiratory tract, the mucus secreted by these cells traps dust, bacteria, viruses, and other potentially harmful particles in the inhaled air, preventing them from reaching the delicate tissues of the lungs. In the intestines, the goblet cells secrete mucus that acts as a protective barrier shielding the intestinal epithelium from dietary antigens, pathogens and prevents the intestinal epithelium from being eroded by the actions of the digestive enzymes and the abrasive action of passing food material.\nGoblet cells are capable of rapidly altering their secretory output in response to stimuli. For example, irritants like smoke or dust can trigger an increased rate of mucus production, as the body attempts to flush out the harmful particles. Conversely, in conditions such as chronic bronchitis and cystic fibrosis, overactive goblet cells can create a thick accumulation of mucus that obstructs the airways and fosters bacterial growth. Lastly, goblet cells are not static, rather, they undergo a dynamic process known as goblet cell metaplasia-differentiation, wherein non-goblet cells in response to chronic injury or inflammation, can differentiate into goblet cells leading to an accumulation of these cells in the tissue, known as goblet cell hyperplasia." xsd:string {xref="DOI:10.1016/S1357-2725(02)00083-3", xref="DOI:10.1038/s41575-022-00675-x", xref="DOI:10.1165/ajrcmb.25.5.f218", xref="DOI:10.1242/bio.20121701", xref="https://www.ncbi.nlm.nih.gov/books/NBK553208/"} [Term] id: CL:0000161 @@ -2320,13 +2591,20 @@ consider: CL:0000162 [Term] id: CL:0000162 name: parietal cell -def: "A large, oval stomach epithelial cell with a central nucleus; source of gastric acid. Secretes HCl." [GOC:tfm, ISBN:0517223651] +def: "An epithelial cell of the stomach that is part of the fundic gastric gland. This cell is characterized by its pyramidal shape, abundant mitochondria, and a complex network of secretory canaliculi lined with microvilli. It secretes hydrochloric acid into the stomach lumen and produces intrinsic factor, essential for vitamin B12 absorption." [GOC:tfm, ISBN:0517223651, PMID:31613538, PMID:31670611] +comment: Parietal cells have dynamic, actin-supported microvilli that increase in number during active secretion, playing a crucial role in secreting hydrochloric acid and intrinsic factor. The structure and regulation of these microvilli are influenced by proteins such as ASAP3, which modulates Arf6 activity and actin assembly, thereby controlling microvilli formation and parietal cell function. {xref="PMID:31613538", xref="PMID:29263912"} subset: cellxgene_subset -synonym: "oxyntic cell" EXACT [] +subset: human_subset +subset: mouse_subset +synonym: "gastric parietal cell" EXACT [PMID:29263912] +synonym: "oxyntic cell" EXACT [Wikipedia:Parietal_cell] xref: BTO:0001780 xref: FMA:62901 +is_a: CL:0000152 ! exocrine cell is_a: CL:0002659 ! glandular epithelial cell of stomach -relationship: capable_of GO:0046717 ! acid secretion +relationship: capable_of GO:0001696 ! gastric acid secretion +relationship: has_part GO:0005902 ! microvillus +relationship: part_of UBERON:0010038 ! fundic gastric gland [Term] id: CL:0000163 @@ -2335,13 +2613,12 @@ def: "A cell of an endocrine gland, ductless glands that secrete substances whic subset: cellxgene_subset subset: general_cell_types_upper_slim subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "endocrinocyte" EXACT [] xref: FMA:83809 xref: ZFA:0009096 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000151 ! secretory cell -is_a: CL:0000164 {gci_relation="part_of", gci_filler="UBERON:0000945"} ! enteroendocrine cell -is_a: CL:0000164 {gci_filler="UBERON:0000160", gci_relation="part_of"} ! enteroendocrine cell -is_a: CL:0000164 {gci_filler="UBERON:0001264", gci_relation="part_of"} ! enteroendocrine cell is_a: CL:0000255 ! eukaryotic cell relationship: part_of UBERON:0000949 ! endocrine system property_value: RO:0002175 NCBITaxon:9606 @@ -2351,14 +2628,16 @@ id: CL:0000164 name: enteroendocrine cell def: "An endocrine cell that is located in the epithelium of the gastrointestinal tract or in the pancreas." [GOC:tfm, SANBI:mhl] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset xref: BTO:0003865 xref: FMA:62930 xref: https://cellxgene.cziscience.com/cellguide/CL_0000164 xref: MESH:D019858 xref: ZFA:0009097 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} -is_a: CL:0000150 ! glandular epithelial cell is_a: CL:0000163 ! endocrine cell -property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional.\n\nEnteroendocrine cells are a specialized subset of cells located within the epithelial lining of both the small and large intestines, as well as the stomach and pancreas. Constituting less than 1% of the total population of intestinal cells, they are differentiated from a common intestinal cell progenitor, thus sharing lineage with absorptive and goblet cells of the intestines.\nThe distinct characteristic feature of an enteroendocrine cell is its inherent capacity to synthesize and secrete a plethora of gut hormones such as serotonin, somatostatin, neurotensin, cholecystokinin, secretin, gastric inhibitory peptide, motilin, and glucagon-like peptide-1. Integrated within this complex network of signaling agents, these substances control various aspects of the digestive system. Each enteroendocrine cell has its unique combination of hormones to release, determined by its position along the intestinal tract. Intriguingly, these hormones not only modulate local gut function, including motility, absorption and secretion, but also potentiate distant actions on other systems such as endocrine, nervous and immune and play a role in the feeling of satiety.\nThe release of these hormones from enteroendocrine cells is a highly regulated and dynamic process. The cells are equipped with sensory receptors localized on its luminal side that respond to various stimuli, including changes in nutrient composition, chemical or mechanical changes in the gut lumen, or even signals arising from commensal microbiota. This sensory input stimulates a signaling cascade within the cell, culminating in the release of specific hormones into the interstitial fluid. These hormones then make their way into the bloodstream, acting on their respective target receptors to mediate their duties. The multifunctional characteristics of enteroendocrine cells make them crucial for maintaining gut homeostasis and the overall physiological well being of the body." xsd:string {xref="DOI:10.1038/s41574-019-0168-8", xref="DOI:10.1111/j.1463-1326.2011.01438.x", xref="DOI:10.1196/annals.1294.001", xref="DOI:10.1210/endrev/bnaa018", xref="DOI:10.7554/elife.78512"} +is_a: CL:1100001 ! secretory epithelial cell +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nEnteroendocrine cells are a specialized subset of cells located within the epithelial lining of both the small and large intestines, as well as the stomach and pancreas. Constituting less than 1% of the total population of intestinal cells, they are differentiated from a common intestinal cell progenitor, thus sharing lineage with absorptive and goblet cells of the intestines.\nThe distinct characteristic feature of an enteroendocrine cell is its inherent capacity to synthesize and secrete a plethora of gut hormones such as serotonin, somatostatin, neurotensin, cholecystokinin, secretin, gastric inhibitory peptide, motilin, and glucagon-like peptide-1. Integrated within this complex network of signaling agents, these substances control various aspects of the digestive system. Each enteroendocrine cell has its unique combination of hormones to release, determined by its position along the intestinal tract. Intriguingly, these hormones not only modulate local gut function, including motility, absorption and secretion, but also potentiate distant actions on other systems such as endocrine, nervous and immune and play a role in the feeling of satiety.\nThe release of these hormones from enteroendocrine cells is a highly regulated and dynamic process. The cells are equipped with sensory receptors localized on its luminal side that respond to various stimuli, including changes in nutrient composition, chemical or mechanical changes in the gut lumen, or even signals arising from commensal microbiota. This sensory input stimulates a signaling cascade within the cell, culminating in the release of specific hormones into the interstitial fluid. These hormones then make their way into the bloodstream, acting on their respective target receptors to mediate their duties. The multifunctional characteristics of enteroendocrine cells make them crucial for maintaining gut homeostasis and the overall physiological well being of the body." xsd:string {xref="DOI:10.1038/s41574-019-0168-8", xref="DOI:10.1111/j.1463-1326.2011.01438.x", xref="DOI:10.1196/annals.1294.001", xref="DOI:10.1210/endrev/bnaa018", xref="DOI:10.7554/elife.78512"} [Term] id: CL:0000165 @@ -2367,6 +2646,8 @@ def: "A neuron that is capable of some hormone secretion in response to neuronal comment: The neurosecretory cell is neither an ordinary neuron nor an endocrine cell, but a combination of both. Its neuronal features resemble those of ordinary neurons concerning both structure and function. The production of a visible secretory material marks the neurosecretory neuron as a gland cell, and the fact that extractable cellular products act in the manner of hormones places it in the realm of endocrine elements. \n\nThe modern definition of neurosecretion has evolved to include the release of any neuronal secretory product from a neuron. {xref="https://www.clinicalkey.com/#!/content/book/3-s2.0-B9780323555968000073", xref="PMID:5342440"} subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "neurosecretory cell" RELATED [] synonym: "neurosecretory neuron" RELATED [] xref: BTO:0002691 @@ -2376,6 +2657,7 @@ xref: ZFA:0009098 {sssom:mapping_justification="https://w3id.org/semapv/vocab/Un is_a: CL:0000163 ! endocrine cell is_a: CL:0000527 ! efferent neuron is_a: CL:0000710 ! neurecto-epithelial cell +is_a: CL:1100001 ! secretory epithelial cell intersection_of: CL:0000540 ! neuron intersection_of: capable_of GO:0046879 ! hormone secretion property_value: RO:0002175 NCBITaxon:9606 @@ -2385,6 +2667,8 @@ id: CL:0000166 name: chromaffin cell def: "A cell that stores epinephrine secretory vesicles. During times of stress, the nervous system signals the vesicles to secrete their hormonal content. Their name derives from their ability to stain a brownish color with chromic salts. Characteristically, they are located in the adrenal medulla and paraganglia of the sympathetic nervous system." [MESH:D019439] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "phaeochromocyte" EXACT [] xref: BTO:0000259 xref: FMA:69263 @@ -2392,12 +2676,14 @@ xref: https://cellxgene.cziscience.com/cellguide/CL_0000166 xref: ZFA:0009099 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000029 ! neural crest derived neuron is_a: CL:0000568 ! amine precursor uptake and decarboxylation cell -property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional.\n\nChromaffin cells, also known as pheochromocytes, are neuroendocrine cells that are typically located in the adrenal medulla, the innermost part of the adrenal gland, which is situated on top of each kidney. Chromaffin cells are also found in small clusters, known as paraganglia, in various locations throughout the body, including the sympathetic nervous system. They derive their name from their ability to stain a brownish-black color upon exposure to chromic salts, a feature made possible due to their high content of granules rich in catecholamines and catecholamine-related neurotransmitters.\nThe primary function of chromaffin cells is the synthesis and release of catecholamines, specifically epinephrine (adrenaline) and norepinephrine (noradrenaline). These neurotransmitters are vital stress hormones that, when released by the adrenal chromaffing cells into the bloodstream, prepare the body for the 'fight or flight' response. This response can enhance the body's performance in a dangerous situation by increasing heart rate, elevating blood sugar, and increasing blood flow to the muscles. The chromaffin cells in paraganglia are responsible for the local release of catecholamines and play a role in regulating blood pressure and other autonomic functions.\nIn addition to their role in stress response, chromaffin cells also contribute to the body's immune response. They secrete several peptides including antimicrobial peptides, and the discovery of LPS and cytokine receptors on chromaffin cells suggests that the adrenal medulla may participate in some aspects of the immune response." xsd:string {xref="DOI:10.1002/cphy.c190003", xref="DOI:10.1016/j.biocel.2016.02.003", xref="DOI:10.3389/fendo.2018.00711", xref="DOI:10.3389/fimmu.2022.977175", xref="DOI:10.3389/fimmu.2022.977175/full"} +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nChromaffin cells, also known as pheochromocytes, are neuroendocrine cells that are typically located in the adrenal medulla, the innermost part of the adrenal gland, which is situated on top of each kidney. Chromaffin cells are also found in small clusters, known as paraganglia, in various locations throughout the body, including the sympathetic nervous system. They derive their name from their ability to stain a brownish-black color upon exposure to chromic salts, a feature made possible due to their high content of granules rich in catecholamines and catecholamine-related neurotransmitters.\nThe primary function of chromaffin cells is the synthesis and release of catecholamines, specifically epinephrine (adrenaline) and norepinephrine (noradrenaline). These neurotransmitters are vital stress hormones that, when released by the adrenal chromaffing cells into the bloodstream, prepare the body for the 'fight or flight' response. This response can enhance the body's performance in a dangerous situation by increasing heart rate, elevating blood sugar, and increasing blood flow to the muscles. The chromaffin cells in paraganglia are responsible for the local release of catecholamines and play a role in regulating blood pressure and other autonomic functions.\nIn addition to their role in stress response, chromaffin cells also contribute to the body's immune response. They secrete several peptides including antimicrobial peptides, and the discovery of LPS and cytokine receptors on chromaffin cells suggests that the adrenal medulla may participate in some aspects of the immune response." xsd:string {xref="DOI:10.1002/cphy.c190003", xref="DOI:10.1016/j.biocel.2016.02.003", xref="DOI:10.3389/fendo.2018.00711", xref="DOI:10.3389/fimmu.2022.977175", xref="DOI:10.3389/fimmu.2022.977175/full"} [Term] id: CL:0000167 name: peptide hormone secreting cell def: "Any secretory cell that is capable of some peptide hormone secretion." [FBC:Autogenerated] +subset: human_subset +subset: mouse_subset xref: ZFA:0009100 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000151 ! secretory cell intersection_of: CL:0000151 ! secretory cell @@ -2408,6 +2694,8 @@ relationship: capable_of GO:0030072 ! peptide hormone secretion id: CL:0000168 name: insulin secreting cell def: "Any secretory cell that is capable of some insulin secretion." [FBC:Autogenerated] +subset: human_subset +subset: mouse_subset xref: BTO:0000783 xref: ZFA:0009101 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000154 ! protein secreting cell @@ -2424,6 +2712,8 @@ def: "A cell that secretes insulin and is located towards the center of the isle comment: Pancreatic beta cells are also reportedly CD284-positive. Upon activation, they upregulate their CD14 expression. subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "B-cell of pancreatic islet" EXACT [FMA:70586] synonym: "beta cell" BROAD [ZFA:0009102] synonym: "beta cell islet" RELATED [MA:0002419] @@ -2453,6 +2743,8 @@ property_value: RO:0002175 NCBITaxon:9606 id: CL:0000170 name: glucagon secreting cell def: "A cell that secretes glucagon." [GOC:tfm] +subset: human_subset +subset: mouse_subset synonym: "glucagon-secreting cell" EXACT [] xref: FMA:84045 xref: ZFA:0009103 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} @@ -2467,6 +2759,8 @@ name: pancreatic A cell def: "A type of enteocrine cell found in the periphery of the islets of Langerhans that secretes glucagon." [GOC:tfm, ISBN:0721662544] subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "alpha cell of islet of Langerhans" EXACT [] synonym: "pancreatic alpha cell" EXACT [] xref: BTO:0000990 @@ -2485,6 +2779,8 @@ property_value: RO:0002175 NCBITaxon:9606 id: CL:0000172 name: somatostatin secreting cell def: "Any secretory cell that is capable of some somatostatin secretion." [FBC:Autogenerated] +subset: human_subset +subset: mouse_subset xref: ZFA:0009105 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000167 ! peptide hormone secreting cell intersection_of: CL:0000151 ! secretory cell @@ -2497,6 +2793,8 @@ name: pancreatic D cell def: "A D cell located in the pancreas. Peripherally placed within the islets like type A cells; contains somatostatin." [FMA:0517223651, GOC:tfm] subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "D-cell of pancreatic islet" EXACT [] synonym: "delta cell of islet" EXACT [] synonym: "delta cell of pancreatic islet" EXACT [] @@ -2518,6 +2816,8 @@ property_value: RO:0002175 NCBITaxon:9606 id: CL:0000174 name: steroid hormone secreting cell def: "Any secretory cell that is capable of some steroid hormone secretion." [FBC:Autogenerated] +subset: human_subset +subset: mouse_subset xref: ZFA:0009106 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000151 ! secretory cell intersection_of: CL:0000151 ! secretory cell @@ -2529,6 +2829,8 @@ id: CL:0000175 name: luteal cell def: "A progesterone secreting cell in the corpus luteum. The large luteal cells develop from the granulosa cells. The small luteal cells develop from the theca cells." [MESH:D008184] subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "corpus luteum cell" EXACT [PMID:16790079] synonym: "lutein cell" EXACT [] xref: BTO:0003939 @@ -2542,6 +2844,8 @@ property_value: RO:0002175 NCBITaxon:9606 id: CL:0000176 name: ecdysteroid secreting cell def: "Any secretory cell that is capable of some ecdysteroid secretion." [FBC:Autogenerated] +subset: human_subset +subset: mouse_subset is_a: CL:0000174 ! steroid hormone secreting cell intersection_of: CL:0000151 ! secretory cell intersection_of: capable_of GO:0045457 ! ecdysteroid secretion @@ -2551,6 +2855,8 @@ relationship: capable_of GO:0045457 ! ecdysteroid secretion id: CL:0000177 name: testosterone secreting cell def: "Any secretory cell that is capable of some testosterone secretion." [FBC:Autogenerated] +subset: human_subset +subset: mouse_subset xref: ZFA:0009107 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000151 ! secretory cell intersection_of: CL:0000151 ! secretory cell @@ -2563,6 +2869,8 @@ name: Leydig cell def: "A Leydig cell is a testosterone-secreting cell in the interstitial area, between the seminiferous tubules, in the testis." [GOC:tfm, PMID:12050120] comment: Note that the Amphibian Anatomy Ontology (AA) has a class 'leydig cells' but this is unrelated subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "interstitial cell" BROAD [] synonym: "interstitial cell of Leydig" EXACT [] xref: BTO:0000755 @@ -2577,12 +2885,14 @@ is_a: CL:0000177 ! testosterone secreting cell is_a: CL:4030031 ! interstitial cell relationship: part_of UBERON:0005212 ! Leydig cell region of testis relationship: RO:0002202 CL:0009091 ! develops from Leydig stem cell -property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional.\n\nLeydig cells are a testosterone-secreting cell in the interstitial area in the testes of males. They are named after Franz Leydig, a German anatomist who discovered these cells in 1850. Uniquely situated within the soft connective tissue surrounding the seminiferous tubules, Leydig cells form an integral part of the male reproductive system. They are usually polygonal cells characterized by well developed smooth endoplasmic reticulum, high lipid content and a large round nucleus. They are found across mammalian species, including humans. \nThe primary function of Leydig cells is the production of androgens, the male sex hormones, the most notable of which is testosterone. Leydig cells synthesize testosterone from cholesterol through a series of enzymatic reactions. The production and release of testosterone are mainly regulated by the luteinizing hormone (LH) released by the anterior pituitary gland. In response to LH, Leydig cells convert cholesterol into testosterone, which then plays a crucial role in the development and maintenance of primary and secondary male sexual characteristics. These include the formation and maturation of male reproductive organs, onset of spermatogenesis, and the presentation of male secondary sexual traits such as the deepening of the voice, growth of facial hair, development of muscles, and a broadening of shoulders.\nApart from testosterone production, Leydig cells also secrete insulin-like factor 3 (INSL3) that is essential for testicular descent during embryonic development in males. Dysregulation or loss of Leydig cells can lead to numerous conditions like testosterone deficiency, infertility, and certain forms of testicular cancer. Although not typical, Leydig cells can regenerate if they are damaged, ensuring the continuous production of testosterone and maintaining male reproductive health. They provide an excellent model to study cell differentiation and hormone regulation, thereby enhancing our understanding of reproductive biology and associated disorders." xsd:string {xref="DOI:10.1016/j.coemr.2019.03.001", xref="DOI:10.1093/biolre/ioy059", xref="DOI:10.1210/clinem/dgaa603", xref="DOI:10.3389/fendo.2014.00006", xref="https://www.ncbi.nlm.nih.gov/books/NBK556007/#:~:text=Leydig%20cells%20are%20the%20primary,secondary%20sexual%20characteristics%20and%20behaviors."} +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nLeydig cells are a testosterone-secreting cell in the interstitial area in the testes of males. They are named after Franz Leydig, a German anatomist who discovered these cells in 1850. Uniquely situated within the soft connective tissue surrounding the seminiferous tubules, Leydig cells form an integral part of the male reproductive system. They are usually polygonal cells characterized by well developed smooth endoplasmic reticulum, high lipid content and a large round nucleus. They are found across mammalian species, including humans. \nThe primary function of Leydig cells is the production of androgens, the male sex hormones, the most notable of which is testosterone. Leydig cells synthesize testosterone from cholesterol through a series of enzymatic reactions. The production and release of testosterone are mainly regulated by the luteinizing hormone (LH) released by the anterior pituitary gland. In response to LH, Leydig cells convert cholesterol into testosterone, which then plays a crucial role in the development and maintenance of primary and secondary male sexual characteristics. These include the formation and maturation of male reproductive organs, onset of spermatogenesis, and the presentation of male secondary sexual traits such as the deepening of the voice, growth of facial hair, development of muscles, and a broadening of shoulders.\nApart from testosterone production, Leydig cells also secrete insulin-like factor 3 (INSL3) that is essential for testicular descent during embryonic development in males. Dysregulation or loss of Leydig cells can lead to numerous conditions like testosterone deficiency, infertility, and certain forms of testicular cancer. Although not typical, Leydig cells can regenerate if they are damaged, ensuring the continuous production of testosterone and maintaining male reproductive health. They provide an excellent model to study cell differentiation and hormone regulation, thereby enhancing our understanding of reproductive biology and associated disorders." xsd:string {xref="DOI:10.1016/j.coemr.2019.03.001", xref="DOI:10.1093/biolre/ioy059", xref="DOI:10.1210/clinem/dgaa603", xref="DOI:10.3389/fendo.2014.00006", xref="https://www.ncbi.nlm.nih.gov/books/NBK556007/#:~:text=Leydig%20cells%20are%20the%20primary,secondary%20sexual%20characteristics%20and%20behaviors."} [Term] id: CL:0000179 name: progesterone secreting cell def: "Any secretory cell that is capable of some progesterone secretion." [FBC:Autogenerated] +subset: human_subset +subset: mouse_subset xref: ZFA:0009109 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000174 ! steroid hormone secreting cell is_a: CL:0000255 ! eukaryotic cell @@ -2594,6 +2904,8 @@ relationship: capable_of GO:0042701 ! progesterone secretion id: CL:0000180 name: estradiol secreting cell def: "A steroid hormone secreting cell that secretes estradiol." [https://orcid.org/0000-0001-5208-3432] +subset: human_subset +subset: mouse_subset xref: ZFA:0009110 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000174 ! steroid hormone secreting cell intersection_of: CL:0000151 ! secretory cell @@ -2615,6 +2927,8 @@ def: "The main structural component of the liver. They are specialized epithelia comment: Hepatocytes are reportedly MHC Class I-positive and MHC Class II-positive. subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset xref: BTO:0000575 xref: CALOHA:TS-0454 xref: FMA:14515 @@ -2628,13 +2942,15 @@ relationship: capable_of GO:0098754 ! detoxification relationship: part_of UBERON:0002107 ! liver relationship: RO:0002202 CL:0005026 ! develops from hepatoblast property_value: RO:0002175 NCBITaxon:9606 -property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional.\n\nHepatocytes are the major cell type constituting 70-80% of the liver's cytoplasmic mass, playing crucial roles in maintaining the body's metabolic homeostasis. Dimensions of mature hepatocytes typically range from 20 to 30 μm in humans, but size may vary depending on their location within the liver lobule. Hepatocytes are characterized by high biosynthetic, enzymatic, and endocytic activity. They contain abundant mitochondria, smooth and rough endoplasmic reticulum, peroxisomes, lysosomes, and a large nucleus that is often binucleate. \nThe liver consists of three zones - the periportal Zone 1, midzone 2, and pericentral Zone 3 - which have differential nutrient and oxygen status, and damage susceptibility; hepatocytes in the different zones show signifcant functional heterogeneity ('hepatocyte functional zonation'). Hepatocytes are involved in a multitude of critical functions including the metabolism of lipids, carbohydrates, and proteins, the synthesis of serum proteins (e.g., albumin, transferrin, and lipoproteins), the detoxification and excretion of endogenous and exogenous substances, the storage of vitamins and minerals, and the production and secretion of bile. \nHeterocytes demonstrate a remarkable regenerative capacity, which enables the liver to recover from injury and loss of tissue mass. Notably, hepatocytes perform biotransformation with both phase I and phase II enzymes, which modify drugs, xenobiotics, and various substances for elimination from the body. Phase I enzymes, such as cytochrome P450, catalyze both oxidative and reductive reactions of many xenobiotics; many of the products of phase I enzymes are substrates for the phase II enzymes, which catalyze conjugation reactions. \nAlterations in hepatocyte function have significant implications for overall human health and disease. Certain conditions, such as hepatitis, cirrhosis, and liver cancer, can profoundly affect hepatocyte structure and function, thereby disrupting the liver's ability to perform its vital roles within the body. As the primary site for drug metabolism, changes in hepatocyte function can also impact the effectiveness and toxicity of pharmaceuticals. The regenerative ability of hepatocytes makes them valuable cells for liver regenerative medicine and bioartificial liver support systems, and their study has provided significant insights into liver biology and disease." xsd:string {xref="DOI:10.1016/j.biocel.2011.11.011", xref="DOI:10.1055/s-2007-1007096", xref="DOI:10.1083/jcb.201903090", xref="DOI:10.1111/j.1439-0396.2007.00752.x"} +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nHepatocytes are the major cell type constituting 70-80% of the liver's cytoplasmic mass, playing crucial roles in maintaining the body's metabolic homeostasis. Dimensions of mature hepatocytes typically range from 20 to 30 μm in humans, but size may vary depending on their location within the liver lobule. Hepatocytes are characterized by high biosynthetic, enzymatic, and endocytic activity. They contain abundant mitochondria, smooth and rough endoplasmic reticulum, peroxisomes, lysosomes, and a large nucleus that is often binucleate. \nThe liver consists of three zones - the periportal Zone 1, midzone 2, and pericentral Zone 3 - which have differential nutrient and oxygen status, and damage susceptibility; hepatocytes in the different zones show signifcant functional heterogeneity ('hepatocyte functional zonation'). Hepatocytes are involved in a multitude of critical functions including the metabolism of lipids, carbohydrates, and proteins, the synthesis of serum proteins (e.g., albumin, transferrin, and lipoproteins), the detoxification and excretion of endogenous and exogenous substances, the storage of vitamins and minerals, and the production and secretion of bile. \nHeterocytes demonstrate a remarkable regenerative capacity, which enables the liver to recover from injury and loss of tissue mass. Notably, hepatocytes perform biotransformation with both phase I and phase II enzymes, which modify drugs, xenobiotics, and various substances for elimination from the body. Phase I enzymes, such as cytochrome P450, catalyze both oxidative and reductive reactions of many xenobiotics; many of the products of phase I enzymes are substrates for the phase II enzymes, which catalyze conjugation reactions. \nAlterations in hepatocyte function have significant implications for overall human health and disease. Certain conditions, such as hepatitis, cirrhosis, and liver cancer, can profoundly affect hepatocyte structure and function, thereby disrupting the liver's ability to perform its vital roles within the body. As the primary site for drug metabolism, changes in hepatocyte function can also impact the effectiveness and toxicity of pharmaceuticals. The regenerative ability of hepatocytes makes them valuable cells for liver regenerative medicine and bioartificial liver support systems, and their study has provided significant insights into liver biology and disease." xsd:string {xref="DOI:10.1016/j.biocel.2011.11.011", xref="DOI:10.1055/s-2007-1007096", xref="DOI:10.1083/jcb.201903090", xref="DOI:10.1111/j.1439-0396.2007.00752.x"} [Term] id: CL:0000183 name: contractile cell def: "A cell whose primary function is to shorten." [FB:ma] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset is_a: CL:0000000 ! cell [Term] @@ -2642,6 +2958,8 @@ id: CL:0000185 name: myoepithelial cell def: "Contractile cells resembling smooth muscle cells that are present in glands, notably the mammary gland, and aid in secretion. This cell has long weaving dendritic processes containing myofilament." [GOC:tfm, ISBN:0721662544] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "basket epithelial cell" EXACT [] synonym: "myoepitheliocyte" EXACT [] xref: BTO:0002309 @@ -2658,6 +2976,8 @@ def: "An animal cell that has characteristics of both a fibroblast cell and a sm comment: Myofibroblasts are alpha-SMA-positive, CD34-negative, CD45-negative. They are reportedly capable of secreting IL-1beta, IL-6, and TNF-alpha. subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "MFB" EXACT [PMID:8731193] is_a: CL:0000183 ! contractile cell is_a: CL:0002320 ! connective tissue cell @@ -2668,6 +2988,8 @@ id: CL:0000187 name: muscle cell def: "A mature contractile cell, commonly known as a myocyte. This cell has as part of its cytoplasm myofibrils organized in various patterns." [MESH:D032342] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "muscle fiber" EXACT [] synonym: "myocyte" EXACT [] xref: BTO:0000888 @@ -2691,36 +3013,48 @@ def: "A somatic cell located in skeletal muscle." [GOC:tfm] subset: cellxgene_subset subset: general_cell_types_upper_slim subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "skeletal muscle cell" EXACT [] xref: BTO:0004392 xref: CALOHA:TS-2158 xref: FMA:9727 +xref: https://cellxgene.cziscience.com/cellguide/CL_0000188 xref: ZFA:0009115 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000255 ! eukaryotic cell intersection_of: CL:0000000 ! cell intersection_of: part_of UBERON:0001134 ! skeletal muscle tissue relationship: part_of UBERON:0001134 ! skeletal muscle tissue property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nSkeletal muscle cells, or myocytes, are essential for the musculoskeletal system, featuring a striated appearance from tightly packed sarcomeres. These elongated, multi-nucleated cells convert ATP into mechanical energ and are key for voluntary movement and posture. They also are responsible for maintaining body temperature, storing nutrients, and stabilizing joints.\nSkeletal muscle cells organize themselves tightly into bundles to form muscle fibers. Embedded within each of these cells are thousands of myofibrils, which are made up of the contractile proteins, actin (the thin filament), and myosin (the thick filament). Contraction of a skeletal muscle cell occurs when these myofibrils shorten, a process driven by the sliding of actin and myosin filaments over each other in a mechanism famously known as the sliding filament theory.\nAdditionally, skeletal muscle cells exhibit a high degree of plasticity, which allows for their adaptation in response to alterations in functional demands or damages. They have an innate regenerative capacity due to the presence of satellite cells—quiescent muscle stem cells that reside within the muscle fibers. Upon muscle injury, these satellite cells become activated, proliferate, and differentiate into new muscle cells, thereby contributing to the repair and growth of injured skeletal muscle. With this, skeletal muscle cells serve not only a pivotal biomechanical function but also possess a great capacity for self-healing and regeneration." xsd:string {xref="DOI:10.1002/cphy.c160033", xref="DOI:10.3390/biology10101056", xref="https://www.nature.com/scitable/topicpage/the-sliding-filament-theory-of-muscle-contraction-14567666/", xref="https://www.ncbi.nlm.nih.gov/books/NBK537139", xref="https://www.ncbi.nlm.nih.gov/books/NBK9961/"} [Term] id: CL:0000189 name: slow muscle cell def: "A muscle cell that develops tension more slowly than a fast-twitch fiber." [GOC:tfm, ISBN:0323052908] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "slow muscle fiber" RELATED [ISBN:0815316208] +xref: https://cellxgene.cziscience.com/cellguide/CL_0000189 xref: ZFA:0009116 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0008046 ! extrafusal muscle fiber relationship: RO:0002202 CL:0000857 ! develops from slow muscle myoblast +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nSlow muscle cells, as the name implies, are a type of muscle cell well known for their slow contractile speed. They are also referred to as type I, slow-twitch, or red muscles because of their high myoglobin content which gives them a dark, reddish appearance. These cells are predominantly found in the postural muscles of the body, such as those in the back and lower limbs. \nA defining characteristic of slow muscle cells is their significant resistance to fatigue. This is largely due to their efficient oxidative metabolism, which allows them to continuously contract over extended periods without succumbing to fatigue. This extraordinary endurance is facilitated by a high concentration of mitochondria, which enables the efficient use of oxygen for energy production, and capillaries, which supplies the necessary oxygen and nutrients. Additionally, these cells have an abundant supply of myoglobin, a protein that stores and transports oxygen within the muscle cell, further supporting their aerobic metabolism.\nThe primary role of slow muscle cells in the human body is to provide sustained, low-intensity contractions over a prolonged period. They are responsible for maintaining posture and providing stability, rather than delivering short, powerful bursts of activity. They play a pivotal role in supporting various physical activities such as standing, walking, or any form of exercise that requires endurance over speed." xsd:string {xref="DOI:10.1093/ptj/81.11.1810", xref="DOI:10.1186/s13578-015-0054-6", xref="DOI:10.3389/fphys.2021.747214", xref="https://www.sciencedirect.com/topics/biochemistry-genetics-and-molecular-biology/slow-muscle-fiber"} [Term] id: CL:0000190 name: fast muscle cell def: "A muscle cell that can develop high tension rapidly. It is usually innervated by a single alpha neuron." [GOC:tfm, ISBN:0323052908] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "glycolytic muscle fiber" EXACT [] +xref: https://cellxgene.cziscience.com/cellguide/CL_0000190 xref: ZFA:0009117 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0008046 ! extrafusal muscle fiber relationship: RO:0002202 CL:0000858 ! develops from fast muscle myoblast +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nFast muscle cells, also known as type II muscle fibers, are a particular type of muscle cell that specializes in conducting rapid, high-intensity contractions. These cells are primarily found within skeletal muscle groups that are directly involved in gross motor activities, such as running, jumping, or lifting heavy weights. The designation \"fast\" refers to their speed of contraction in response to neural stimuli, which is significantly quicker when compared to other muscle cell types such as slow-twitch or type I muscle fibers.\nThe primary function of fast muscle cells revolves around their role in anaerobic metabolism, which provides the energy needed for short, forceful bursts of power. They contain a high concentration of glycolytic enzymes that facilitate this process, leading to a swift break down of glucose to generate ATP (adenosine triphosphate), the primary energy currency in biological systems. On the downside, the byproduct of this very rapid, anaerobic metabolic process is lactic acid, which can build up and cause muscle fatigue. \nFast muscle cells can be further classified into two subtypes based on their metabolic characteristics: type IIa and type IIb/x. Type IIa cells, also known as fast oxidative-glycolytic fibers, possess a good oxygen supply and can function in both anaerobic and aerobic conditions, exhibiting moderate resistance to fatigue. On the other hand, type IIb/x cells, also known as fast glycolytic fibers, primarily rely on anaerobic metabolism and tire out a lot quicker. Both these subtypes can adapt to changing demands due to exercise and conditioning, highlighting the plasticity that is a key characteristic of these versatile muscle cells." xsd:string {xref="DOI:10.1152/japplphysiol.00636.2019", xref="DOI:10.3389/fcell.2018.00125", xref="DOI:10.4161/org.4.3.6312", xref="https://www.sciencedirect.com/topics/biochemistry-genetics-and-molecular-biology/fast-muscle-fiber"} [Term] id: CL:0000192 @@ -2730,6 +3064,8 @@ def: "A non-striated, elongated, spindle-shaped cell found lining the digestive subset: cellxgene_subset subset: general_cell_types_upper_slim subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "myocytes, smooth muscle" EXACT [MESH:D032389] synonym: "non-striated muscle cell" BROAD [] synonym: "SMCs" EXACT [PMID:9315361] @@ -2737,11 +3073,13 @@ synonym: "smooth muscle fiber" EXACT [] xref: BTO:0004576 xref: CALOHA:TS-2159 xref: FMA:14072 +xref: https://cellxgene.cziscience.com/cellguide/CL_0000192 xref: ZFA:0009118 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0008000 ! non-striated muscle cell is_a: CL:0008007 ! visceral muscle cell relationship: RO:0002202 CL:0000514 ! develops from smooth muscle myoblast property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nSmooth muscle cells are a specialized type of muscle cells that are primarily found within the walls of hollow organs such as the intestine, stomach, bladder, uterus, and blood vessels. These cells are an essential component of the autonomic nervous system controling involuntary movements within the body.\nSmooth muscle cells play a vital role in many physiological processes due to their unique functionality. They can contract and relax in a slow, sustained, and controlled manner to help modulate the size and shape of the lumens of the organs they surround. For example, in the digestive system, coordinated contraction and relaxation of smooth muscle cells propels food along the gastrointestinal tract - a process known as peristalsis. In the blood vessels, the smooth muscle cells, by contracting or relaxing, either constrict or dilate the vessels, which in turn, help regulate blood flow and pressure.\nOn a cellular level, smooth muscle cells possess a single, centrally located nucleus and contain an arranged network of actin and myosin filaments, which are the proteins responsible for muscle contraction. Unlike their counterparts in skeletal or cardiac muscles, these cells lack specific contact points for these filaments, hence the lack of visible striations. Furthermore, the contraction of smooth muscle cells is regulated by hormones and neurotransmitters, such as acetylcholine and norepinephrine, adding an additional layer of complex regulation to these highly specialized cells." xsd:string {xref="DOI:10.1093/ptj/81.11.1810", xref="https://training.seer.cancer.gov/anatomy/muscular/types.html", xref="https://www.ncbi.nlm.nih.gov/books/NBK10854/", xref="https://www.ncbi.nlm.nih.gov/books/NBK526125", xref="https://www.ncbi.nlm.nih.gov/books/NBK556137/"} [Term] id: CL:0000193 @@ -2768,6 +3106,8 @@ is_obsolete: true id: CL:0000196 name: insect flight muscle cell def: "A muscle cell that is involved in the mechanism of insect flight. This encompasses both, cells that power flight and cells that control flight." [doi:10.2142/biophysics.7.21] +subset: human_subset +subset: mouse_subset xref: FBbt:00003360 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} is_a: CL:0008003 ! somatic muscle myotube @@ -2775,6 +3115,8 @@ is_a: CL:0008003 ! somatic muscle myotube id: CL:0000197 name: sensory receptor cell def: "A cell that is capable of detection of a stimulus involved in sensory perception." [] +subset: human_subset +subset: mouse_subset synonym: "receptor cell" EXACT [] xref: MESH:D011984 is_a: CL:0000255 ! eukaryotic cell @@ -2789,6 +3131,8 @@ id: CL:0000198 name: pain receptor cell def: "The peripheral receptor for pain. Includes receptors which are sensitive to painful mechanical stimuli, extreme heat or cold, and chemical stimuli. All mammalian nociceptors are free nerve endings." [MESH:D009619] comment: Editor note: request detection of stimulus involved in sensory perception of pain; add develops_from relationship +subset: human_subset +subset: mouse_subset synonym: "nociceptor" EXACT [] {seeAlso="https://meshb.nlm.nih.gov/record/ui?ui=D009619"} synonym: "nocireceptor" EXACT [] {seeAlso="https://www.thefreedictionary.com/nocireceptor"} xref: ZFA:0009119 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} @@ -2798,6 +3142,8 @@ is_a: CL:0000006 ! neuronal receptor cell id: CL:0000199 name: mechanoreceptor cell def: "A cell specialized to transduce mechanical stimuli and relay that information centrally in the nervous system." [MESH:D008465] +subset: human_subset +subset: mouse_subset synonym: "mechanoreceptor" RELATED [MP:0000972] xref: ZFA:0009120 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000101 ! sensory neuron @@ -2809,6 +3155,8 @@ relationship: capable_of GO:0050974 ! detection of mechanical stimulus involved id: CL:0000200 name: touch receptor cell def: "Any neuron that is capable of some detection of mechanical stimulus involved in sensory perception of touch." [FBC:Autogenerated] +subset: human_subset +subset: mouse_subset is_a: CL:0000199 ! mechanoreceptor cell intersection_of: CL:0000540 ! neuron intersection_of: capable_of GO:0050976 ! detection of mechanical stimulus involved in sensory perception of touch @@ -2820,6 +3168,8 @@ name: auditory hair cell alt_id: CL:0000201 def: "A mechanoreceptor cell of the auditory or vestibular system that is sensitive to auditory stimuli. The accessory sensory structures are arranged so that appropriate stimuli cause movement of the hair-like projections (stereocilia and kinocilia) which relay the information centrally in the nervous system." [MESH:D006198, WikipediaVersioned:Hair_cell&oldid=1045345915] comment: In mammals these cells are located in the organ of Corti. +subset: human_subset +subset: mouse_subset synonym: "auditory receptor cell" RELATED [] xref: ZFA:0009121 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000855 ! sensory hair cell @@ -2829,6 +3179,8 @@ relationship: capable_of GO:0050910 ! detection of mechanical stimulus involved id: CL:0000203 name: gravity sensitive cell def: "Any neuronal receptor cell that is capable of some detection of mechanical stimulus involved in sensory perception of gravity." [FBC:Autogenerated] +subset: human_subset +subset: mouse_subset is_a: CL:0000006 ! neuronal receptor cell is_a: CL:0000199 ! mechanoreceptor cell intersection_of: CL:0000006 ! neuronal receptor cell @@ -2838,12 +3190,16 @@ relationship: capable_of GO:0070999 ! detection of mechanical stimulus involved [Term] id: CL:0000204 name: acceleration receptive cell +subset: human_subset +subset: mouse_subset is_a: CL:0000006 ! neuronal receptor cell [Term] id: CL:0000205 name: thermoreceptor cell def: "A cellular receptor which mediates the sense of temperature. Thermoreceptor cells in vertebrates are mostly located under the skin. In mammals there are separate types of thermoreceptors for cold and for warmth and pain receptor cells which detect cold or heat extreme enough to cause pain." [GOC:tfm, MESH:D013823, MP:0000971] +subset: human_subset +subset: mouse_subset xref: ZFA:0009123 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000006 ! neuronal receptor cell intersection_of: CL:0000006 ! neuronal receptor cell @@ -2854,6 +3210,8 @@ relationship: capable_of GO:0050960 ! detection of temperature stimulus involved id: CL:0000206 name: chemoreceptor cell def: "A cell specialized to detect chemical substances and relay that information centrally in the nervous system. Chemoreceptors may monitor external stimuli, as in taste and olfaction, or internal stimuli, such as the concentrations of oxygen and carbon dioxide in the blood." [MESH:D002628] +subset: human_subset +subset: mouse_subset xref: ZFA:0009124 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000197 ! sensory receptor cell intersection_of: CL:0000197 ! sensory receptor cell @@ -2864,6 +3222,9 @@ relationship: capable_of GO:0050907 ! detection of chemical stimulus involved in id: CL:0000207 name: olfactory receptor cell def: "Any neuron that is capable of some detection of chemical stimulus involved in sensory perception of smell." [FBC:Autogenerated] +subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "odorant receptor cell" EXACT [] synonym: "olfactory receptor neuron" EXACT [] synonym: "olfactory sensory neuron" EXACT [] @@ -2883,6 +3244,8 @@ relationship: part_of UBERON:0005725 ! olfactory system [Term] id: CL:0000208 name: pH receptor cell +subset: human_subset +subset: mouse_subset is_a: CL:0000206 ! chemoreceptor cell [Term] @@ -2890,6 +3253,8 @@ id: CL:0000209 name: taste receptor cell def: "A specialized cell involved in gustatory sensory perception." [GOC:tfm, ISBN:0618947256] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "taste bud cell" EXACT [] xref: FMA:67910 xref: ZFA:0009126 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} @@ -2905,6 +3270,8 @@ id: CL:0000210 name: photoreceptor cell def: "A cell specialized in detecting light stimuli that are involved in visual perception." [MESH:D010786] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset xref: BTO:0001060 xref: CALOHA:TS-0868 xref: FBbt:00004211 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} @@ -2921,6 +3288,8 @@ property_value: foaf:depiction "https://www.swissbiopics.org/api/image/Photorece id: CL:0000211 name: electrically active cell def: "A cell whose function is determined by the generation or the reception of an electric signal." [FB:ma] +subset: human_subset +subset: mouse_subset xref: ZFA:0009128 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000000 ! cell @@ -2928,7 +3297,10 @@ is_a: CL:0000000 ! cell id: CL:0000212 name: absorptive cell def: "A cell that takes up and metabolizes substances." [CL:CVS] +subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset xref: ZFA:0009129 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000000 ! cell property_value: RO:0002175 NCBITaxon:9606 @@ -2937,6 +3309,8 @@ property_value: RO:0002175 NCBITaxon:9606 id: CL:0000213 name: lining cell def: "A cell within an epithelial cell sheet whose main function is to act as an internal or external covering for a tissue or an organism." [JB:jb] +subset: human_subset +subset: mouse_subset synonym: "boundary cell" EXACT [] xref: ZFA:0009130 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000215 ! barrier cell @@ -2945,6 +3319,8 @@ is_a: CL:0000215 ! barrier cell id: CL:0000214 name: synovial cell def: "A cell located in the synovial joint." [] +subset: human_subset +subset: mouse_subset synonym: "synoviocyte" EXACT [] xref: CALOHA:TS-0995 xref: ZFA:0009131 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} @@ -2956,6 +3332,8 @@ relationship: part_of UBERON:0002217 ! synovial joint id: CL:0000215 name: barrier cell def: "A cell whose primary function is to prevent the transport of stuff across compartments." [JB:jb] +subset: human_subset +subset: mouse_subset xref: ZFA:0009132 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000000 ! cell @@ -2964,6 +3342,8 @@ id: CL:0000216 name: Sertoli cell def: "A supporting cell projecting inward from the basement membrane of seminiferous tubules. They surround and nourish the developing male germ cells and secrete androgen binding protein. Their tight junctions with the spermatogonia and spermatocytes provide a blood-testis barrier." [MESH:D012708] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset xref: BTO:0001238 xref: CALOHA:TS-0922 xref: FMA:72298 @@ -2972,12 +3352,15 @@ xref: ZFA:0009133 {sssom:mapping_justification="https://w3id.org/semapv/vocab/Un is_a: CL:0000511 ! androgen binding protein secreting cell is_a: CL:0000630 {is_inferred="true"} ! supporting cell is_a: CL:0002625 ! seminiferous tubule epithelial cell +is_a: CL:1100001 ! secretory epithelial cell intersection_of: CL:0000630 ! supporting cell intersection_of: part_of UBERON:0001343 ! seminiferous tubule of testis [Term] id: CL:0000217 name: insulating cell +subset: human_subset +subset: mouse_subset xref: ZFA:0009134 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000215 ! barrier cell @@ -2985,6 +3368,9 @@ is_a: CL:0000215 ! barrier cell id: CL:0000218 name: myelinating Schwann cell def: "A neuroglial cell of the peripheral nervous system which forms the insulating myelin sheaths of peripheral axons." [GOC:cvs, GOC:tfm, MESH:D012583] +subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "neurilemmal cell" EXACT [] synonym: "peripheral neuroglial cell" BROAD [] synonym: "Schwann cell" BROAD [] @@ -3000,6 +3386,8 @@ relationship: RO:0002202 CL:0002377 ! develops from immature Schwann cell id: CL:0000219 name: motile cell def: "A cell that moves by its own activities." [FB:ma] +subset: human_subset +subset: mouse_subset xref: ZFA:0009136 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000000 ! cell intersection_of: CL:0000000 ! cell @@ -3019,6 +3407,9 @@ consider: CL:0001034 id: CL:0000221 name: ectodermal cell def: "A cell of the outer of the three germ layers of the embryo." [MESH:D004475] +subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "ectoderm cell" EXACT [] xref: FMA:72549 xref: ZFA:0009137 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} @@ -3031,18 +3422,24 @@ id: CL:0000222 name: mesodermal cell def: "A cell of the middle germ layer of the embryo." [MESH:D008648] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "mesoblast" EXACT [] synonym: "mesoderm cell" EXACT [] xref: FMA:72554 +xref: https://cellxgene.cziscience.com/cellguide/CL_0000222 xref: ZFA:0009138 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000255 ! eukaryotic cell is_a: CL:0002321 ! embryonic cell (metazoa) relationship: part_of UBERON:0000926 ! mesoderm +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nMesodermal cells are pluripotent and the most abundant in the human body. They contribute to the development of several structures such as the skeletal muscles, bones, heart and blood vessels, kidneys, gonads, connective tissues, and certain layers of the skin. Hence, the mesoderm is often regarded as an active and diverse layer due to its role in forming many bodily structures. \nIn embryonic development, these cells are instrumental, contributing to the body's structures through a carefully coordinated sequence of morphogenetic movements. This process forms the complex multicellular architecture of tissues and organs from a simple ball of cells. Without the function of mesodermal cells, the body's integral structures and systems would cease to form correctly, leading to developmental disorders such as axial mesodermal dysplasia complex" xsd:string {xref="DOI:10.1016/j.ceb.2019.07.012", xref="DOI:10.5535/arm.2016.40.1.162", xref="https://www.sciencedirect.com/topics/biochemistry-genetics-and-molecular-biology/mesoderm"} [Term] id: CL:0000223 name: endodermal cell def: "A cell of the inner of the three germ layers of the embryo." [MESH:D004707] +subset: human_subset +subset: mouse_subset synonym: "endoderm cell" EXACT [] xref: FMA:72555 xref: ZFA:0009139 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} @@ -3064,6 +3461,8 @@ consider: CL:0001034 id: CL:0000225 name: anucleate cell def: "A cell that lacks a nucleus." [FB:ma] +subset: human_subset +subset: mouse_subset synonym: "non-nucleated cell" EXACT [] xref: FMA:68647 is_a: CL:0000000 ! cell @@ -3076,6 +3475,8 @@ relationship: bearer_of PATO:0001405 ! anucleate id: CL:0000226 name: single nucleate cell def: "A cell with a single nucleus." [FB:ma, GOC:tfm] +subset: human_subset +subset: mouse_subset is_a: CL:0000255 ! eukaryotic cell is_a: CL:0002242 ! nucleate cell intersection_of: CL:0000000 ! cell @@ -3086,6 +3487,8 @@ relationship: bearer_of PATO:0001407 ! mononucleate id: CL:0000227 name: binucleate cell def: "Any cell that has characteristic some binucleate." [FBC:Autogenerated] +subset: human_subset +subset: mouse_subset is_a: CL:0000228 ! multinucleate cell intersection_of: CL:0000000 ! cell intersection_of: bearer_of PATO:0001406 ! binucleate @@ -3095,6 +3498,8 @@ relationship: bearer_of PATO:0001406 ! binucleate id: CL:0000228 name: multinucleate cell def: "A cell with more than one nucleus." [FB:ma, Wikipedia:Multinucleate] +subset: human_subset +subset: mouse_subset synonym: "multinucleated cells" EXACT [Wikipedia:Multinucleate] synonym: "polynuclear cells" EXACT [Wikipedia:Multinucleate] is_a: CL:0000255 ! eukaryotic cell @@ -3131,6 +3536,8 @@ def: "A red blood cell. In mammals, mature erythrocytes are biconcave disks cont subset: blood_and_immune_upper_slim subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "RBC" EXACT [] synonym: "red blood cell" EXACT [] xref: BTO:0000424 @@ -3159,6 +3566,8 @@ comment: Platelets are reportedly CCR1-positive, CCR2-negative, CCR3-positive, C subset: blood_and_immune_upper_slim subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "anucleate thrombocyte" EXACT [] synonym: "blood platelet" EXACT [] synonym: "enucleate thrombocyte" EXACT [] @@ -3178,7 +3587,8 @@ property_value: RO:0002175 NCBITaxon:9606 id: CL:0000234 name: phagocyte def: "Any cell capable of ingesting particulate matter via phagocytosis." [GOC:add, ISBN:0721601464] -subset: cellxgene_subset +subset: human_subset +subset: mouse_subset xref: BTO:0001044 xref: FMA:83806 xref: MESH:D010586 @@ -3199,6 +3609,8 @@ subset: blood_and_immune_upper_slim subset: cellxgene_subset subset: general_cell_types_upper_slim subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "histiocyte" EXACT [] xref: BTO:0000801 xref: CALOHA:TS-0587 @@ -3225,6 +3637,8 @@ subset: blood_and_immune_upper_slim subset: cellxgene_subset subset: general_cell_types_upper_slim subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "B lymphocyte" EXACT [] synonym: "B-cell" EXACT [] synonym: "B-lymphocyte" EXACT [] @@ -3243,6 +3657,8 @@ property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000237 name: keratinizing barrier epithelial cell +subset: human_subset +subset: mouse_subset is_a: CL:0000240 ! stratified squamous epithelial cell is_a: CL:0000311 ! keratin accumulating cell is_a: CL:0002077 ! ecto-epithelial cell @@ -3251,6 +3667,8 @@ relationship: RO:0002202 CL:0000114 ! develops from surface ectodermal cell [Term] id: CL:0000238 name: non keratinizing barrier epithelial cell +subset: human_subset +subset: mouse_subset is_a: CL:0000240 ! stratified squamous epithelial cell [Term] @@ -3258,6 +3676,8 @@ id: CL:0000239 name: brush border epithelial cell def: "An epithelial cell characterized by the presence of a brush border on its apical surface, which increases the surface area for absorption." [] comment: All brush border cells are columnar-cuboidal. The formal logical definition of this term asserts this. Brush border epithelial cells are predominantly found lining the small intestine and the proximal tubules of the kidneys. +subset: human_subset +subset: mouse_subset xref: https://doi.org/10.1152/ajpgi.00005.2011 xref: PMID:25422372 xref: ZFA:0009143 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} @@ -3271,6 +3691,8 @@ id: CL:0000240 name: stratified squamous epithelial cell def: "A stratified epithelial cell that is part of squamous epithelium, characterized by multiple layers of cells. The basal layer is directly attached to the basement membrane and the apical layer consists of flattened squamous cells. This provides a protective barrier, commonly found in areas subject to abrasion, such as the skin, oral cavity, and esophagus." [PMID:30422572, Wikipedia:Epithelium, Wikipedia:Stratified_squamous_epithelium] subset: human_reference_atlas +subset: human_subset +subset: mouse_subset xref: ZFA:0009144 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000076 ! squamous epithelial cell is_a: CL:0000079 ! stratified epithelial cell @@ -3284,6 +3706,8 @@ id: CL:0000241 name: stratified cuboidal epithelial cell def: "A stratified epithelial cell that is part of cuboidal epithelium, characterized by multiple layers of cuboidal cells forming the apical layer. This provides a protective lining for ducts in large glands, such as sweat glands." [PMID:30422572, Wikipedia:Stratified_cuboidal_epithelium] subset: human_reference_atlas +subset: human_subset +subset: mouse_subset xref: ZFA:0009145 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000075 ! columnar/cuboidal epithelial cell is_a: CL:0000079 ! stratified epithelial cell @@ -3298,6 +3722,8 @@ name: Merkel cell def: "A modified epidermal cell located in the stratum basale. They are found mostly in areas where sensory perception is acute. Merkel cells are closely associated with an expanded terminal bulb of an afferent myelinated nerve fiber." [MESH:D018862] subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "Merkel's cell" EXACT [] xref: FMA:70548 xref: ZFA:0009146 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} @@ -3320,6 +3746,8 @@ id: CL:0000244 name: transitional epithelial cell def: "A cell characteristically found lining hollow organs that are subject to great mechanical change due to contraction and distention; originally thought to represent a transition between stratified squamous and columnar epithelium." [GOC:tfm, ISBN:0721662544] subset: human_reference_atlas +subset: human_subset +subset: mouse_subset xref: FMA:66778 xref: ZFA:0009148 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000066 ! epithelial cell @@ -3335,6 +3763,8 @@ replaced_by: PO:0000353 [Term] id: CL:0000246 name: Mauthner neuron +subset: human_subset +subset: mouse_subset xref: ZFA:0009149 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000099 ! interneuron @@ -3349,9 +3779,7 @@ xref: AAO:0010316 xref: EFO:0003711 xref: VHOG:0001484 xref: ZFA:0009150 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} -is_a: CL:0000006 ! neuronal receptor cell is_a: CL:0000531 ! primary sensory neuron (sensu Teleostei) -is_a: CL:4023168 ! somatosensory neuron [Term] id: CL:0000248 @@ -3365,6 +3793,8 @@ replaced_by: PO:0020047 [Term] id: CL:0000249 name: hatching gland cell +subset: human_subset +subset: mouse_subset xref: ZFA:0009151 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000151 ! secretory cell @@ -3378,6 +3808,8 @@ replaced_by: PO:0020019 [Term] id: CL:0000251 name: extramedullary cell +subset: human_subset +subset: mouse_subset xref: ZFA:0009152 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000101 ! sensory neuron @@ -3392,6 +3824,8 @@ replaced_by: PO:0020048 id: CL:0000253 name: eurydendroid cell subset: cellxgene_subset +subset: human_subset +subset: mouse_subset xref: ZFA:0009153 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000527 ! efferent neuron @@ -3407,7 +3841,8 @@ replaced_by: PO:0020094 id: CL:0000255 name: eukaryotic cell def: "Any cell that in taxon some Eukaryota." [FBC:Autogenerated] -subset: cellxgene_subset +subset: human_subset +subset: mouse_subset xref: MESH:D005057 is_a: CL:0000000 ! cell intersection_of: CL:0000000 ! cell @@ -3418,6 +3853,8 @@ relationship: RO:0002162 NCBITaxon:2759 ! in taxon Eukaryota [Term] id: CL:0000256 name: uric acid accumulating cell +subset: human_subset +subset: mouse_subset is_a: CL:0000325 ! stuff accumulating cell [Term] @@ -3621,6 +4058,8 @@ def: "Any photoreceptor cell that is part of some eye." [FBC:Autogenerated] subset: cellxgene_subset subset: eye_upper_slim subset: human_reference_atlas +subset: human_subset +subset: mouse_subset xref: ZFA:0009154 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000006 ! neuronal receptor cell is_a: CL:0000210 ! photoreceptor cell @@ -3667,6 +4106,8 @@ replaced_by: PO:0000293 id: CL:0000293 name: structural cell def: "A cell whose primary function is to provide structural support, to provide strength and physical integrity to the organism." [TAIR:sr] +subset: human_subset +subset: mouse_subset xref: ZFA:0005745 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000000 ! cell @@ -3681,6 +4122,8 @@ id: CL:0000295 name: somatotropin secreting cell alt_id: CL:0000471 def: "A peptide hormone secreting cell that produces growth hormone, somatotropin." [GOC:tfm, SANBI:mhl] +subset: human_subset +subset: mouse_subset synonym: "growth hormone secreting cell" EXACT [] synonym: "somatotrophin secreting cell" EXACT [] xref: ZFA:0009155 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} @@ -3721,11 +4164,14 @@ is_obsolete: true id: CL:0000300 name: gamete def: "A mature sexual reproductive cell having a single set of unpaired chromosomes." [GOC:tfm, ISBN:0721662544] +subset: human_subset +subset: mouse_subset synonym: "haploid germ cell" RELATED [] synonym: "haploid nucleated cell" EXACT [] xref: CALOHA:TS-0395 xref: FBbt:00005412 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:18649 +xref: https://cellxgene.cziscience.com/cellguide/CL_0000300 xref: ZFA:0009156 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000413 ! haploid cell is_a: CL:0000586 {is_inferred="true"} ! germ cell @@ -3733,11 +4179,14 @@ intersection_of: CL:0000586 ! germ cell intersection_of: bearer_of PATO:0001375 ! haploid intersection_of: capable_of GO:0009566 ! fertilization relationship: capable_of GO:0009566 ! fertilization +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nGametes are reproductive cells essential for sexual reproduction in eukaryotic organisms, including humans, animals, and many plants. These cells are haploid, containing half the genome or only one set of chromosomes, which is a contrast to the diploid state (two sets of chromosomes) found in most cells in a multicellular organism. This reduction in genetic material is crucial since it allows for the re-establishment of the diploid number of chromosomes when two gametes merge to form a diploid zygote during fertilization.\nThere are two major types of gametes in animals: sperm cells in males and egg (or ova) in females. These gametes contribute equally to the genetic makeup of the offspring but are morphologically and functionally distinct. Sperm cells (or spermatozoa) are characterized by their motility, small size, and large quantities; they are produced continuously in vast numbers through a process called spermatogenesis in the male gonads or testes. Female gametes are much larger, fewer in numbers, and are not motile; they undergo a development process known as oogenesis, which takes place within the ovaries. The egg also contributes most of the cytoplasm and organelles (including mitochondria) to the zygote that are required for initial cell division stages after fertilization.\nGametes have a primary role in sexual reproduction and genetic variation, which aids in evolution. The formation of gametes involves a special type of cell division called meiosis that introduces genetic diversity via the process of recombination and independent assortment. Following the fusion of male and female gametes, the combination of paternal and maternal genetic material in the zygote allows for genetic recombination, which is a fundamental source of genetic variation and, thus, evolution. Therefore, gametes not only are critical to the inception of new individuals but also contribute to species survival and evolution." xsd:string {xref="DOI:10.1038/s41586-020-2347-0", xref="DOI:10.3389/fcell.2022.1040708", xref="https://www.ncbi.nlm.nih.gov/books/NBK10008/", xref="https://www.ncbi.nlm.nih.gov/books/NBK553142/"} [Term] id: CL:0000301 name: pole cell def: "A primordial germ cell of insects. Such cells form at the posterior pole of the early embryo." [doi:10.1017/CBO9780511818202.015] +subset: human_subset +subset: mouse_subset xref: FBbt:00000092 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} is_a: CL:0000670 ! primordial germ cell @@ -3773,6 +4222,8 @@ is_obsolete: true id: CL:0000306 name: crystallin accumulating cell subset: eye_upper_slim +subset: human_subset +subset: mouse_subset synonym: "lens cell" EXACT [] is_a: CL:0000325 ! stuff accumulating cell @@ -3782,6 +4233,8 @@ name: tracheal epithelial cell alt_id: CL:1000474 def: "An epithelial cell found in the trachea." [GOC:tfm] comment: This class is for the vertebrate tracheal structure. For the analagous insect cell type, see 'respiratory tube epithelial cell' +subset: human_subset +subset: mouse_subset synonym: "tracheocyte" EXACT [] xref: FMA:74793 is_a: CL:0002202 {is_inferred="true"} ! epithelial cell of tracheobronchial tree @@ -3793,22 +4246,30 @@ relationship: RO:0002202 CL:0000377 ! develops from tracheoblast [Term] id: CL:0000308 name: metal ion accumulating cell +subset: human_subset +subset: mouse_subset is_a: CL:0000325 ! stuff accumulating cell [Term] id: CL:0000309 name: copper accumulating cell +subset: human_subset +subset: mouse_subset synonym: "cuprophilic cell" EXACT [] is_a: CL:0000308 ! metal ion accumulating cell [Term] id: CL:0000310 name: iron accumulating cell +subset: human_subset +subset: mouse_subset is_a: CL:0000308 ! metal ion accumulating cell [Term] id: CL:0000311 name: keratin accumulating cell +subset: human_subset +subset: mouse_subset xref: ZFA:0009157 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000325 ! stuff accumulating cell @@ -3820,6 +4281,8 @@ def: "An epidermal cell which synthesizes keratin and undergoes a characteristic comment: Keratinocytes are reportedly CDw210a-negative, CDw210b-positive, CD281-positive, CD282-positive, CD285-positive, IL22Ra1-positive, Human keratinocytes are reportedly capable of secreting BD-2, BD-3, hCAP-18, CXCL1, CXCL5, CXCL8, elafin, MMP-3, NGAL, PDGF-A, S100A7, S100A8, and S100A9. Transcription factors: STAT3-positive. subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "keratinized cell of epidermis" EXACT [] synonym: "malpighian cell" EXACT [] xref: BTO:0000667 @@ -3841,6 +4304,8 @@ id: CL:0000313 name: serous secreting cell def: "Columnar glandular cell with irregular nucleus, copious granular endoplasmic reticulum and supranuclear granules. Secretes a watery fluid containing proteins known as serous fluid." [GOC:tfm, ISBN:0517223651, ISBN:0721662544] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "serous cell" EXACT [] xref: BTO:0003687 xref: FMA:62511 @@ -3849,12 +4314,16 @@ is_a: CL:0000159 ! seromucus secreting cell [Term] id: CL:0000314 name: milk secreting cell +subset: human_subset +subset: mouse_subset is_a: CL:0000151 ! secretory cell [Term] id: CL:0000315 name: tear secreting cell def: "A cell secreting tears, the fluid secreted by the lacrimal glands. This fluid moistens the conjunctiva and cornea." [MESH:D013666] +subset: human_subset +subset: mouse_subset synonym: "tears secreting cell" EXACT [] is_a: CL:0000152 ! exocrine cell relationship: part_of UBERON:0001817 ! lacrimal gland @@ -3868,13 +4337,19 @@ replaced_by: PO:0000082 [Term] id: CL:0000317 -name: sebum secreting cell -def: "A cell secreting sebun, an oily substance secreted by sebaceous glands, composed of keratin, fat, and cellular debris." [MESH:D012629] +name: sebocyte +def: "An epithelial cell that is part of a sebaceous gland. This cell produces and secretes sebum, an oily, lipid-rich substance, through holocrine secretion where the entire cell ruptures to release its contents." [MESH:D012629, PMID:19944183] +subset: cellxgene_subset subset: human_reference_atlas -synonym: "sebocyte" EXACT [] +subset: human_subset +subset: mouse_subset +synonym: "sebum secreting cell" EXACT [] +is_a: CL:0000150 ! glandular secretory epithelial cell is_a: CL:0000152 ! exocrine cell +is_a: CL:0000362 ! epidermal cell +is_a: CL:0002308 ! epithelial cell of skin gland is_a: CL:2000021 ! sebaceous gland cell -intersection_of: CL:0000151 ! secretory cell +intersection_of: CL:0000066 ! epithelial cell intersection_of: part_of UBERON:0001821 ! sebaceous gland property_value: RO:0002175 NCBITaxon:9606 @@ -3882,18 +4357,22 @@ property_value: RO:0002175 NCBITaxon:9606 id: CL:0000318 name: sweat secreting cell def: "A cell secreting sweat, the fluid excreted by the sweat glands of mammals. It consists of water containing sodium chloride, phosphate, urea, ammonia, and other waste products." [MESH:D013542] -is_a: CL:0000150 ! glandular epithelial cell +subset: human_subset +subset: mouse_subset +is_a: CL:0000150 ! glandular secretory epithelial cell [Term] id: CL:0000319 name: mucus secreting cell -def: "Any secretory cell that is capable of some mucus secretion." [FBC:Autogenerated] +def: "Any cell that is capable of some mucus secretion." [FBC:Autogenerated] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "mucous cell" EXACT [] xref: BTO:0003689 xref: ZFA:0009159 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000159 ! seromucus secreting cell -intersection_of: CL:0000151 ! secretory cell +intersection_of: CL:0000000 ! cell intersection_of: capable_of GO:0070254 ! mucus secretion relationship: capable_of GO:0070254 ! mucus secretion @@ -3919,6 +4398,8 @@ id: CL:0000322 name: pulmonary alveolar epithelial cell def: "An epithelial cell that lines the peripheral gas exchange region of the lungs of air-breathing vertebrates." [GOC:tfm, PMID:20054144, PMID:29463737] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "alveolar epithelial cell" EXACT [] synonym: "alveolus of lung epithelial cell" EXACT [] synonym: "epithelial cell of alveolus of lung" EXACT [] @@ -3939,11 +4420,16 @@ property_value: terms:date "2024-09-02T08:27:21Z" xsd:dateTime [Term] id: CL:0000323 name: lysozyme secreting cell +subset: human_subset +subset: mouse_subset is_a: CL:0000154 ! protein secreting cell [Term] id: CL:0000324 name: metanephric mesenchyme stem cell +subset: cellxgene_subset +subset: human_subset +subset: mouse_subset is_a: BFO:0000002 is_a: CL:0000134 ! mesenchymal stem cell relationship: RO:0002202 CL:0000222 ! develops from mesodermal cell @@ -3952,17 +4438,23 @@ relationship: RO:0002202 CL:0000222 ! develops from mesodermal cell id: CL:0000325 name: stuff accumulating cell def: "A cell that is specialised to accumulate a particular substance(s)." [FB:ma] +subset: human_subset +subset: mouse_subset subset: ubprop:upper_level is_a: CL:0000000 ! cell [Term] id: CL:0000326 name: glycogen accumulating cell +subset: human_subset +subset: mouse_subset is_a: CL:0000325 ! stuff accumulating cell [Term] id: CL:0000327 name: extracellular matrix secreting cell +subset: human_subset +subset: mouse_subset xref: ZFA:0009162 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000499 ! stromal cell @@ -3970,6 +4462,8 @@ is_a: CL:0000499 ! stromal cell id: CL:0000329 name: oxygen accumulating cell def: "Any cell that is capable of some oxygen transport." [FBC:Autogenerated] +subset: human_subset +subset: mouse_subset xref: ZFA:0009164 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000000 ! cell intersection_of: CL:0000000 ! cell @@ -4002,6 +4496,8 @@ replaced_by: PO:0020090 id: CL:0000333 name: migratory neural crest cell def: "A cell derived from the specialized ectoderm flanking each side of the embryonic neural plate, which after the closure of the neural tube, forms masses of cells that migrate out from the dorsal aspect of the neural tube to spread throughout the body." [doi:10.1016/j.stem.2015.02.017] +subset: human_subset +subset: mouse_subset xref: FMA:86667 xref: ZFA:0007086 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000219 ! motile cell @@ -4021,6 +4517,8 @@ is_a: CL:0000521 ! fungal cell id: CL:0000335 name: mesenchyme condensation cell def: "A mesenchymal cell in embryonic development found in a contracting mass and that gives rise to osteoprogenitors." [GOC:tfm, PMID:5025404] +subset: human_subset +subset: mouse_subset xref: ZFA:0009166 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0008019 ! mesenchymal cell @@ -4029,6 +4527,8 @@ id: CL:0000336 name: adrenal medulla chromaffin cell alt_id: CL:1000422 def: "A cell found within the adrenal medulla that secrete biogenic amine hormones upon stimulation." [GOC:tfm, http://www.britannica.com/EBchecked/topic/6405/adrenal-gland] +subset: human_subset +subset: mouse_subset synonym: "medullary chromaffin cell of adrenal gland" EXACT [FMA:69262] xref: FMA:69262 xref: ZFA:0009167 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} @@ -4052,6 +4552,8 @@ relationship: RO:0002162 NCBITaxon:33317 ! in taxon Protostomia id: CL:0000339 name: glioblast (sensu Vertebrata) def: "An early neural cell developing from the early ependymal cell of the neural tube." [GOC:tfm, ISBN:0618947256] +subset: human_subset +subset: mouse_subset synonym: "spongioblast" EXACT [] xref: FMA:70564 xref: ZFA:0009169 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} @@ -4077,6 +4579,8 @@ property_value: RO:0002161 NCBITaxon:33511 id: CL:0000342 name: pigment cell (sensu Vertebrata) def: "Any animal cell containing pigment granules." [GOC:tfm, ISBN:0721662544] +subset: human_subset +subset: mouse_subset xref: ZFA:0009170 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000147 ! pigment cell is_a: CL:0000255 ! eukaryotic cell @@ -4086,6 +4590,8 @@ relationship: RO:0002162 NCBITaxon:7742 ! in taxon Vertebrata id: CL:0000343 name: visual pigment cell (sensu Vertebrata) def: "A pigment cell that is capable of detecting light stimulus that is involved in visual perception." [GOC:tfm] +subset: human_subset +subset: mouse_subset xref: FMA:63846 xref: ZFA:0009171 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000149 ! visual pigment cell @@ -4104,6 +4610,8 @@ id: CL:0000345 name: dental papilla cell def: "A mesenchymal cell that is part of a small mass of condensed mesenchyme in the enamel organ; it differentiates into the dentin and dental pulp." [GOC:tfm, ISBN:0721662544] comment: Merge with odontoblast? +subset: human_subset +subset: mouse_subset xref: ZFA:0009173 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: BFO:0000002 is_a: CL:0008019 ! mesenchymal cell @@ -4115,6 +4623,8 @@ id: CL:0000346 name: hair follicle dermal papilla cell def: "A specialized mesenchymal cell that resides in the dermal papilla located at the bottom of hair follicles. This cell plays a pivotal roles in hair formation, growth, and cycling." [GOC:tfm, PMID:9893172] comment: Are these really all stem cells? +subset: human_subset +subset: mouse_subset is_a: CL:0000134 {is_inferred="true"} ! mesenchymal stem cell is_a: CL:0011026 ! progenitor cell intersection_of: CL:0000134 ! mesenchymal stem cell @@ -4127,6 +4637,8 @@ id: CL:0000347 name: scleral cell def: "A cell of the sclera of the eye." [GOC:add] subset: eye_upper_slim +subset: human_subset +subset: mouse_subset xref: ZFA:0009174 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: BFO:0000002 is_a: CL:0000255 ! eukaryotic cell @@ -4141,6 +4653,8 @@ id: CL:0000348 name: choroidal cell of the eye def: "A structural cell that is part of optic choroid." [GOC:add] subset: eye_upper_slim +subset: human_subset +subset: mouse_subset xref: ZFA:0009175 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: BFO:0000002 is_a: CL:0000255 ! eukaryotic cell @@ -4154,7 +4668,10 @@ relationship: RO:0002202 CL:0000008 ! develops from migratory cranial neural cre id: CL:0000349 name: extraembryonic cell def: "Any cell that is part of some extraembryonic structure." [FBC:Autogenerated] +subset: cellxgene_subset subset: general_cell_types_upper_slim +subset: human_subset +subset: mouse_subset xref: ZFA:0009176 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000255 ! eukaryotic cell intersection_of: CL:0000000 ! cell @@ -4174,22 +4691,30 @@ relationship: part_of UBERON:0010302 ! amnioserosa id: CL:0000351 name: trophoblast cell def: "An extraembryonic cell that develops from a trophectodermal cell. This cell is found in the outer layer of the blastocyst and can invade other structures in the uterus once the blastocyst implants into the uterine wall. A trophoblast cell is involved in the implantation of the embryo into the uterine wall, placental formation, remodelling of maternal vasculature in the uterus, nutrient and gas exchange, hormone production, and immune modulation to support fetal development." [doi:10.1007/978-3-030-84725-8, GOC:tfm, MESH:D014327, PMID:37630754] +subset: human_subset +subset: mouse_subset synonym: "trophoblastic cell" EXACT [doi:10.1007/978-3-030-84725-8] xref: FMA:83028 +xref: https://cellxgene.cziscience.com/cellguide/CL_0000351 is_a: BFO:0000002 is_a: CL:0000349 {is_inferred="true"} ! extraembryonic cell relationship: RO:0002202 CL:1000274 ! develops from trophectodermal cell +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nTrophoblast cells, originating from the blastocyst's outer layer, are highly specialized and pivotal for embryo development. Their crucial roles include facilitating implantation and contributing to the formation of the placenta, an essential organ for fetal nutrition, gas exchange, and waste removal during pregnancy.\nThese cells play a crucial role in implantation by adhering to the uterus lining. Post-implantation, some trophoblast cells differentiate, forming syncytiotrophoblasts. These multi-nucleated cells absorb nutrients, release waste, and secrete hormones, including human chorionic gonadotropin (hCG), sustaining pregnancy.\nTrophoblast cells also play a crucial role in immune tolerance, preventing the maternal immune system from treating the fetus as foreign. This balance is vital for a healthy pregnancy. Dysfunctional trophoblast cells may lead to complications like miscarriages or preeclampsia, emphasizing their importance in both embryology and reproductive medicine." xsd:string {xref="DOI:10.1016/j.jri.2023.103811", xref="DOI:10.1530/JOE-17-0402", xref="https://www.ncbi.nlm.nih.gov/books/NBK53245"} [Term] id: CL:0000352 name: epiblast cell def: "A cell of the outer layer of a blastula that gives rise to the ectoderm after gastrulation." [GOC:tfm, ISBN:0618947256] +subset: human_subset +subset: mouse_subset is_a: CL:0000052 ! totipotent stem cell [Term] id: CL:0000353 name: blastoderm cell def: "An undifferentiated cell produced by early cleavages of the fertilized egg (zygote)." [MESH:D001756] +subset: human_subset +subset: mouse_subset synonym: "blastomere" EXACT [] xref: BTO:0001473 xref: FMA:72551 @@ -4199,6 +4724,8 @@ is_a: CL:0000007 ! early embryonic cell (metazoa) [Term] id: CL:0000354 name: blastemal cell +subset: human_subset +subset: mouse_subset synonym: "blastema cell" EXACT [] xref: ncithesaurus:Blastemal_Cell xref: ZFA:0009178 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} @@ -4209,6 +4736,8 @@ id: CL:0000355 name: multi-potent skeletal muscle stem cell def: "A multifate stem cell found in skeletal muscle than can differentiate into many different cell types, including muscle. Distinct cell type from satellite cell." [PMID:18282570] comment: Multi-potency demonstrated ex vivo. At the time of writing, it is unclear whether the endogenous population differentiates into multiple cell types in vivo. +subset: human_subset +subset: mouse_subset xref: FMA:86767 xref: ZFA:0009179 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000048 {is_inferred="true"} ! multi fate stem cell @@ -4219,11 +4748,15 @@ intersection_of: part_of UBERON:0001134 ! skeletal muscle tissue [Term] id: CL:0000356 name: hair matrix stem cell +subset: human_subset +subset: mouse_subset is_a: CL:0000035 ! single fate stem cell [Term] id: CL:0000357 name: stratified epithelial stem cell +subset: human_subset +subset: mouse_subset xref: ZFA:0009180 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000036 ! epithelial fate stem cell @@ -4231,10 +4764,14 @@ is_a: CL:0000036 ! epithelial fate stem cell id: CL:0000358 name: sphincter associated smooth muscle cell def: "A smooth muscle cell that is part of a sphincter. A sphincter is a typically circular muscle that normally maintains constriction of a natural body passage or orifice and which relaxes as required by normal physiological functioning." [GOC:cjm] +subset: human_subset +subset: mouse_subset +xref: https://cellxgene.cziscience.com/cellguide/CL_0000358 is_a: CL:0000192 {is_inferred="true"} ! smooth muscle cell intersection_of: CL:0000192 ! smooth muscle cell intersection_of: part_of UBERON:0004590 ! sphincter muscle relationship: part_of UBERON:0004590 ! sphincter muscle +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nSmooth muscle cells, as a broader category, are non-striated, involuntary muscle cells that usually exhibit contractions and dilation to facilitate numerous physiological functions. Sphincter associated smooth muscle cells are a specific type of smooth muscle cell that are primarily associated with the functioning of various anatomical sphincters in the human body.\nThe traits that distinguishes sphincter associated smooth muscle cells from other smooth muscle cells are their location and specialized function in sphincter mechanisms. Sphincter associated smooth muscle cells play a pivotal role in regulating the opening and closure of the bodily sphincters. These sphincters can be found at multiple locations within the body including the gastrointestinal tract (namely the esophagus, stomach, small intestine, and rectum), the urinary tract, and the circulatory system. Upon receiving signals from the autonomous nervous system, these cells contract or relax to modulate the aperture of sphincters, thus controlling the movement of substances through them. Due to their precise and vital functional role, any dysfunction or dysregulation in these cells can lead to serious medical conditions, such as gastroesophageal reflux or urinary incontinence." xsd:string {xref="https://www.ncbi.nlm.nih.gov/books/NBK482438/", xref="https://www.ncbi.nlm.nih.gov/books/NBK532857/", xref="https://www.ncbi.nlm.nih.gov/books/NBK557452/"} [Term] id: CL:0000359 @@ -4242,8 +4779,11 @@ name: vascular associated smooth muscle cell def: "A smooth muscle cell associated with the vasculature." [GOC:dsd, GOC:tfm] subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "vascular smooth muscle cell" EXACT [] synonym: "VSMC" EXACT [] +xref: https://cellxgene.cziscience.com/cellguide/CL_0000359 xref: ZFA:0009181 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000192 {is_inferred="true"} ! smooth muscle cell is_a: CL:4033054 ! perivascular cell @@ -4251,11 +4791,14 @@ intersection_of: CL:0000192 ! smooth muscle cell intersection_of: part_of UBERON:0002049 ! vasculature relationship: part_of UBERON:0002049 ! vasculature property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nVascular associated smooth muscle cells (VSMCs) are specialized cells that constitute a major component of the blood vessel wall in the circulatory system. They derive their name from the predominantly smooth appearance under microscopic examination, as opposed to the striated appearance of cardiac and skeletal muscles. \nA principal function of VSMCs is to regulate vascular tone, which directly dictates blood pressure and blood flow distribution across various body parts. This is achieved through coordinated contraction and relaxation of the muscles in response to a variety of extracellular signals. When a blood vessel is exposed to stimuli like pressure or injury, VSMCs contract, resulting in vasoconstriction and ultimately, an increase in blood pressure. Conversely, in response to vasodilators, these cells relax, leading to vasodilation and a consequent decrease in blood pressure.\nVSMCs are also involved in vascular remodeling, a process where blood vessels adapt their structure to long-term changes in hemodynamic conditions or disease states. In diseases like atherosclerosis and hypertension, an aberrant proliferative and synthetic phenotype of VSMCs contributes to the formation of plaques, leading to vessel hardening or even occlusion. Recent research has further implicated these cells in immune responses, recognizing their function in leukocyte recruitment and inflammation, factors that are largely instrumental in vascular pathologies." xsd:string {xref="DOI:10.1093/cvr/cvs135", xref="DOI:10.1093/cvr/cvy023", xref="DOI:10.1161/ATVBAHA.118.311229", xref="DOI:10.3389/fimmu.2020.599415", xref="DOI:10.3390/ijms20225694"} [Term] id: CL:0000360 name: morula cell def: "A cell of the early embryo at the developmental stage in which the blastomeres, resulting from repeated mitotic divisions of the fertilized ovum (zygote), form a compact cell mass." [MESH:D009028] +subset: human_subset +subset: mouse_subset is_a: CL:0000007 ! early embryonic cell (metazoa) is_a: CL:0000255 ! eukaryotic cell relationship: part_of UBERON:0000085 ! morula @@ -4264,6 +4807,8 @@ relationship: part_of UBERON:0000085 ! morula id: CL:0000361 name: gastrula cell def: "A cell of the embryo in the early stage following the blastula, characterized by morphogenetic cell movements, cell differentiation, and the formation of the three germ layers." [MESH:D005775] +subset: human_subset +subset: mouse_subset xref: ZFA:0009182 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000007 ! early embryonic cell (metazoa) relationship: part_of UBERON:0004734 ! gastrula @@ -4274,6 +4819,8 @@ name: epidermal cell alt_id: CL:1000396 def: "An epithelial cell of the integument (the outer layer of an organism)." [Flybase:dsj, MA:ma] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "cell of epidermis" EXACT [FMA:62411] synonym: "epithelial cell of skin" NARROW [FMA:62411] xref: BTO:0001470 @@ -4303,6 +4850,8 @@ is_obsolete: true id: CL:0000365 name: animal zygote def: "Diploid cell produced by the fusion of sperm cell nucleus and egg cell." [ISBN:0471245208] +subset: human_subset +subset: mouse_subset synonym: "zygote" BROAD [] xref: BTO:0000854 xref: EHDAA2:0004546 @@ -4327,6 +4876,8 @@ replaced_by: PO:0000084 [Term] id: CL:0000367 name: sheath cell (sensu Nematoda) +subset: human_subset +subset: mouse_subset synonym: "glial cell (sensu Nematoda)" RELATED [] is_a: CL:0000619 ! supporting cell (sensu Nematoda) @@ -4388,29 +4939,40 @@ replaced_by: CL:0007010 [Term] id: CL:0000376 name: humidity receptor cell +subset: human_subset +subset: mouse_subset is_a: CL:0000006 ! neuronal receptor cell [Term] id: CL:0000377 name: tracheoblast +subset: human_subset +subset: mouse_subset is_a: CL:0000069 ! branched duct epithelial cell [Term] id: CL:0000378 name: supporting cell (sensu Nematoda and Protostomia) +subset: human_subset +subset: mouse_subset synonym: "support cell (sensu Nematoda and Protostomia)" EXACT [] is_a: CL:0000630 ! supporting cell [Term] id: CL:0000379 name: sensory processing neuron +subset: human_subset +subset: mouse_subset xref: ZFA:0009185 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} -is_a: CL:0000540 ! neuron +is_a: CL:2000029 ! central nervous system neuron +relationship: capable_of GO:0050893 ! sensory processing [Term] id: CL:0000380 name: thecogen cell def: "The support cell that makes the thecogen dendritic cap - a cuticle-like matrix around the tip of the eo-dendrite and which encloses the soma of the eo-neuron." [Fbbt:00005173] +subset: human_subset +subset: mouse_subset synonym: "fly sheath cell" EXACT [] xref: FBbt:00005173 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} is_a: CL:0000378 ! supporting cell (sensu Nematoda and Protostomia) @@ -4436,6 +4998,8 @@ relationship: part_of UBERON:0001038 ! chordotonal organ [Term] id: CL:0000383 name: nephrogenic mesenchyme stem cell +subset: human_subset +subset: mouse_subset xref: ZFA:0009187 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000134 ! mesenchymal stem cell is_a: CL:0011026 ! progenitor cell @@ -4444,6 +5008,8 @@ relationship: RO:0002202 CL:0000134 ! develops from mesenchymal stem cell [Term] id: CL:0000384 name: ligament cell +subset: human_subset +subset: mouse_subset xref: ZFA:0009188 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000630 ! supporting cell @@ -4458,6 +5024,8 @@ property_value: RO:0002161 NCBITaxon:33511 [Term] id: CL:0000386 name: attachment cell +subset: human_subset +subset: mouse_subset is_a: CL:0000630 ! supporting cell [Term] @@ -4476,6 +5044,8 @@ id: CL:0000388 name: tendon cell def: "An elongated fibrocyte that is part of a tendon. The cytoplasm is stretched between the collagen fibres of the tendon. They have a central cell nucleus with a prominent nucleolus. Tendon cells have a well-developed rough endoplasmic reticulum and they are responsible for synthesis and turnover of tendon fibres and ground substance." [GOC:NV, GOC:tfm, PMID:957445] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "muscle attachment cell" EXACT [] synonym: "tenocyte" RELATED [] xref: ZFA:0009189 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} @@ -4488,6 +5058,8 @@ relationship: part_of UBERON:0000043 ! tendon [Term] id: CL:0000389 name: socket cell (sensu Nematoda) +subset: human_subset +subset: mouse_subset is_a: CL:0000619 ! supporting cell (sensu Nematoda) is_a: CL:0000658 ! cuticle secreting cell @@ -4516,6 +5088,8 @@ relationship: RO:0002202 CL:0000395 ! develops from procrystal cell id: CL:0000393 name: electrically responsive cell def: "A cell whose function is determined by its response to an electric signal." [FB:ma] +subset: human_subset +subset: mouse_subset xref: ZFA:0009190 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000211 ! electrically active cell @@ -4548,6 +5122,8 @@ id: CL:0000397 name: ganglion interneuron def: "Any interneuron that has its soma located in some ganglion." [FBC:Autogenerated] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset is_a: CL:0000099 {is_inferred="true"} ! interneuron intersection_of: CL:0000099 ! interneuron intersection_of: RO:0002100 UBERON:0000045 ! has soma location ganglion @@ -4584,21 +5160,22 @@ replaced_by: CL:0000394 [Term] id: CL:0000402 -name: CNS interneuron -def: "An interneuron that has its cell body in a central nervous system." [doi:10.1016/B978-0-12-817424-1.00001-X] +name: obsolete CNS interneuron +def: "OBSOLETE. An interneuron that has its cell body in a central nervous system." [doi:10.1016/B978-0-12-817424-1.00001-X] comment: Interneurons are commonly described as being only found in the central nervous system. However, in CL we define 'interneuron' more broadly as any neuron that is neither a motor neuron nor a sensory neuron, regardless of its location, so we need this term to refer strictly to interneurons of the central nervous system. +subset: cellxgene_subset subset: human_reference_atlas -xref: ZFA:0009191 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} -is_a: CL:0000099 ! interneuron -is_a: CL:2000029 ! central nervous system neuron -intersection_of: CL:0000099 ! interneuron -intersection_of: RO:0002100 UBERON:0001017 ! has soma location central nervous system +relationship: term_tracker_item https://github.com/obophenotype/cell-ontology/issues/2869 property_value: RO:0002175 NCBITaxon:9606 +is_obsolete: true +replaced_by: CL:0000099 [Term] id: CL:0000404 name: electrically signaling cell def: "A cell that initiates an electrical signal and passes that signal to another cell." [FB:ma] +subset: human_subset +subset: mouse_subset xref: ZFA:0009193 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000211 ! electrically active cell @@ -4612,8 +5189,10 @@ is_obsolete: true [Term] id: CL:0000406 name: CNS short range interneuron +subset: human_subset +subset: mouse_subset xref: ZFA:0009194 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} -is_a: CL:0000402 ! CNS interneuron +is_a: CL:0000099 ! interneuron [Term] id: CL:0000407 @@ -4628,13 +5207,17 @@ relationship: part_of UBERON:0001038 ! chordotonal organ id: CL:0000408 name: male gamete def: "Any male germ cell that has characteristic some haploid and is capable of some fertilization." [FBC:Autogenerated] +subset: human_subset +subset: mouse_subset xref: BTO:0001277 xref: CALOHA:TS-0949 +xref: https://cellxgene.cziscience.com/cellguide/CL_0000408 is_a: CL:0000015 {is_inferred="true"} ! male germ cell is_a: CL:0000300 {is_inferred="true"} ! gamete intersection_of: CL:0000015 ! male germ cell intersection_of: bearer_of PATO:0001375 ! haploid intersection_of: capable_of GO:0009566 ! fertilization +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nThe male gamete, also known as a sperm cell, is a highly specialized cell type critical to sexual reproduction. Sperm are produced during a process called spermatogenesis within the male reproductive organ, specifically the testes. They are haploid cells, carrying the genetic material from the male parent, and fuse with the ovum, the female gamete, to form a diploid zygote during fertilization, thereby initiating gestation and the development of a new organism.\nThe male gamete is distinguished by its morphology, notably its elongated shape which is geared towards locomotion. One of the primary characteristics of a male gamete is its flagellum, or tail, which propels the cell towards the female gamete. It additionally contains an elongated head region housing the nucleus, where the genetic material is stored. The anterior section of the head, the acrosome, releases enzymes essential for penetrating the protective layers of the ovum during the fertilization process.\nThe function of male gametes does not cease upon fertilization. In addition to delivering the paternal set of chromosomes, fusion of the sperm cell with the ovum causes an increase in cytosolic Ca2+ which then activates the female egg cell to undergo the so-called cortical reaction during which the egg’s zona pellucida is changed so fusion with additional sperm is prevented. The Ca2+ signal also initiates the development of the zygote and eventual formation of an embryo. Male gametes also contribute towards forming the placenta, which supplies nutrients and removes waste products during gestation." xsd:string {xref="DOI:10.1016/j.semcdb.2016.04.009", xref="DOI:10.1242/dev.202046", xref="https://www.ncbi.nlm.nih.gov/books/NBK26843/", xref="https://www.ncbi.nlm.nih.gov/books/NBK553142/"} [Term] id: CL:0000409 @@ -4646,8 +5229,10 @@ replaced_by: CL:0000382 [Term] id: CL:0000410 name: CNS long range interneuron +subset: human_subset +subset: mouse_subset xref: ZFA:0009195 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} -is_a: CL:0000402 ! CNS interneuron +is_a: CL:0000099 ! interneuron [Term] id: CL:0000411 @@ -4665,6 +5250,8 @@ relationship: RO:0002162 NCBITaxon:6237 ! in taxon Caenorhabditis id: CL:0000412 name: polyploid cell def: "A cell that contains more than two haploid sets of chromosomes." [FB:ma, https://bio.libretexts.org/Bookshelves/Introductory_and_General_Biology/Biology_(Kimball)/07%3A_Cell_Division/7.04%3A_Polyploidy, PMID:32646579] +subset: human_subset +subset: mouse_subset is_a: CL:0000000 ! cell intersection_of: CL:0000000 ! cell intersection_of: bearer_of PATO:0001377 ! polyploid @@ -4674,6 +5261,8 @@ relationship: bearer_of PATO:0001377 ! polyploid id: CL:0000413 name: haploid cell def: "A cell whose nucleus contains a single haploid genome." [FB:ma, GOC:tfm] +subset: human_subset +subset: mouse_subset is_a: CL:0000000 ! cell intersection_of: CL:0000000 ! cell intersection_of: bearer_of PATO:0001375 ! haploid @@ -4694,17 +5283,23 @@ consider: CL:0001034 id: CL:0000415 name: diploid cell def: "A cell whose nucleus has two haploid genomes." [FB:ma] +subset: human_subset +subset: mouse_subset xref: FMA:72300 is_a: CL:0000000 ! cell [Term] id: CL:0000416 name: polytene cell +subset: human_subset +subset: mouse_subset is_a: CL:0000412 ! polyploid cell [Term] id: CL:0000417 name: endopolyploid cell +subset: human_subset +subset: mouse_subset is_a: CL:0000412 ! polyploid cell [Term] @@ -4719,6 +5314,8 @@ relationship: RO:0002162 NCBITaxon:6237 ! in taxon Caenorhabditis id: CL:0000419 name: seam cell def: "An epithelial fate stem cell found in flatworms." [GOC:tfm, http://www.wormatlas.org/hermaphrodite/seam%20cells/mainframe.htm] +subset: human_subset +subset: mouse_subset xref: BTO:0003039 is_a: CL:0000036 ! epithelial fate stem cell @@ -4726,6 +5323,8 @@ is_a: CL:0000036 ! epithelial fate stem cell id: CL:0000420 name: syncytial epithelial cell def: "An epithelial cell that forms a syncytium, which is a multinucleated cell resulting from the fusion of multiple cells." [] +subset: human_subset +subset: mouse_subset xref: Wikipedia:Syncytium is_a: CL:0000066 ! epithelial cell is_a: CL:4052002 ! syncytial cell @@ -4743,24 +5342,32 @@ is_a: CL:0000519 ! phagocyte (sensu Nematoda and Protostomia) id: CL:0000422 name: mitogenic signaling cell def: "A cell whose primary function is to cause growth by stimulating cell division in its immediate cellular environment." [FB:ma] +subset: human_subset +subset: mouse_subset is_a: CL:0000000 ! cell [Term] id: CL:0000423 name: tip cell +subset: human_subset +subset: mouse_subset is_a: CL:0000422 ! mitogenic signaling cell [Term] id: CL:0000424 name: excretory cell def: "A cell involved in the elimination of metabolic and foreign toxins, and in maintaining the ionic, acid-base and water balance of biological fluids." [GOC:tfm, PMID:19783135] +subset: human_subset +subset: mouse_subset xref: WBbt:0005812 -is_a: CL:0000151 ! secretory cell +is_a: CL:0000000 ! cell [Term] id: CL:0000425 name: pore cell def: "Forms the terminal part of the cuticle-lined excretory duct of C. elegans." [JB:jb] +subset: human_subset +subset: mouse_subset is_a: CL:0000658 ! cuticle secreting cell [Term] @@ -4774,11 +5381,15 @@ is_obsolete: true id: CL:0000427 name: GLR cell def: "A scaffolding cell type found in C. elegans, this cell plays a supportive role to the muscle arms. May also have an endocrine role." [GOC:tfm, http://wormatlas.psc.edu/hermaphrodite/muscleGLR/mainframe.htm] +subset: human_subset +subset: mouse_subset is_a: CL:0002320 ! connective tissue cell [Term] id: CL:0000428 name: yolk cell +subset: human_subset +subset: mouse_subset xref: ZFA:0000084 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000325 ! stuff accumulating cell is_a: CL:0000349 ! extraembryonic cell @@ -4797,6 +5408,8 @@ relationship: RO:0002162 NCBITaxon:50557 ! in taxon Insecta id: CL:0000430 name: xanthophore cell def: "A pigment cell derived from the neural crest. Contains cartenoid pigments in structures called pterinosomes or xanthosomes. This gives an appearance ranging from a golden yellow to orange and red." [SANBI:mhl] +subset: human_subset +subset: mouse_subset synonym: "xanthophore" RELATED [] xref: ZFA:0009198 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: BFO:0000002 @@ -4808,6 +5421,8 @@ relationship: RO:0002202 CL:0005002 ! develops from xanthoblast id: CL:0000431 name: iridophore def: "A pigment cell derived from the neural crest. The cell contains flat light-reflecting platelets, probably of guanine, in stacks called reflecting platelets or iridisomes. The color-generating components produce a silver, gold, or iridescent color." [SANBI:mhl] +subset: human_subset +subset: mouse_subset synonym: "guanophore" RELATED [] xref: ZFA:0009199 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: BFO:0000002 @@ -4821,6 +5436,8 @@ name: reticular cell def: "A fibroblast that synthesizes collagen and uses it to produce reticular fibers, thus providing structural support. Reticular cells are found in many organs, including the spleen, lymph nodes and kidneys. Subtypes of reticular cells include epithelial, mesenchymal, and fibroblastic reticular cells. Fibroblastic reticular cells are involved in directing B cells and T cells to specific regions within a tissue, whereas epithelial and mesenchymal reticular cells are associated with certain areas of the brain." [GOC:tfm, http://en.wikipedia.org/wiki/Reticular_cell, ISBN:0517223651] subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "reticulum cell" EXACT [] xref: FMA:62877 xref: ZFA:0009200 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} @@ -4840,18 +5457,24 @@ id: CL:0000434 name: eccrine cell def: "A secretory cell that discharges its product without loss of cytoplasm." [ISBN:0198547684] subset: human_reference_atlas -is_a: CL:0000150 ! glandular epithelial cell +subset: human_subset +subset: mouse_subset +is_a: CL:1100001 ! secretory epithelial cell property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000435 name: alkali secreting cell +subset: human_subset +subset: mouse_subset xref: ZFA:0009201 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000151 ! secretory cell [Term] id: CL:0000436 name: vaginal lubricant secreting cell +subset: human_subset +subset: mouse_subset is_a: CL:0000151 ! secretory cell is_a: CL:0000255 ! eukaryotic cell relationship: part_of UBERON:0000996 ! vagina @@ -4860,6 +5483,8 @@ relationship: part_of UBERON:0000996 ! vagina id: CL:0000437 name: gonadtroph def: "A rounded cell that is usually situated next to sinusoids; secretes follicular stimulating hormone (FSH) and luteinizing hormone (LH)." [GOC:tfm, http://en.wikipedia.org/wiki/Gonadotroph, ISBN:0517223651] +subset: human_subset +subset: mouse_subset synonym: "delta basophil" EXACT [] synonym: "follicle stimulating hormone secreting cell" EXACT [] synonym: "gonadotrope" EXACT [] @@ -4877,6 +5502,8 @@ is_a: CL:0000639 ! basophil cell of pars distalis of adenohypophysis id: CL:0000438 name: luteinizing hormone secreting cell def: "A peptide hormone secreting cell pituitary that produces luteinizing hormone." [GOC:tfm] +subset: human_subset +subset: mouse_subset xref: ZFA:0009203 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000151 ! secretory cell intersection_of: CL:0000151 ! secretory cell @@ -4887,6 +5514,8 @@ relationship: capable_of GO:0032275 ! luteinizing hormone secretion id: CL:0000439 name: prolactin secreting cell def: "A peptide hormone cell that secretes prolactin." [GOC:tfm, SANBI:mhl] +subset: human_subset +subset: mouse_subset xref: ZFA:0009204 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000154 ! protein secreting cell is_a: CL:0000167 ! peptide hormone secreting cell @@ -4898,6 +5527,8 @@ relationship: capable_of GO:0070459 ! prolactin secretion id: CL:0000440 name: melanocyte stimulating hormone secreting cell def: "A cell of the intermediate pituitary that produces melanocyte stimulating hormone." [SANBI:mhl] +subset: human_subset +subset: mouse_subset synonym: "melanotrope" EXACT [] synonym: "melanotroph" EXACT [] xref: BTO:0002277 @@ -4923,6 +5554,8 @@ def: "A cell with extensive dendritic processes found in the B cell areas (prima comment: Due to its unique lineage and distinct function, this is not a type of dendritic cell; CL:0000451. subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset xref: BTO:0004267 xref: FMA:83037 xref: MESH:D020566 @@ -4933,6 +5566,8 @@ property_value: RO:0002175 NCBITaxon:9606 id: CL:0000443 name: calcitonin secreting cell def: "Any secretory cell that is capable of some calcitonin secretion." [FBC:Autogenerated] +subset: human_subset +subset: mouse_subset xref: ZFA:0009206 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000167 ! peptide hormone secreting cell intersection_of: CL:0000151 ! secretory cell @@ -4944,6 +5579,8 @@ id: CL:0000444 name: obliquely striated muscle cell def: "A muscle cell in which the fibers are organised into sarcomeres but in which adjacent myofibrils are offset from each other, producing an oblique banding pattern." [GOC:DOS, PMID:8720463] comment: Examples include the somatic muscles of nemotodes and cephalopods. +subset: human_subset +subset: mouse_subset is_a: CL:0000737 ! striated muscle cell intersection_of: CL:0000187 ! muscle cell intersection_of: bearer_of PATO:0002479 ! obliquely striated @@ -4953,12 +5590,16 @@ relationship: bearer_of PATO:0002479 ! obliquely striated [Term] id: CL:0000445 name: apoptosis fated cell +subset: human_subset +subset: mouse_subset is_a: CL:0000000 ! cell [Term] id: CL:0000446 name: chief cell of parathyroid gland def: "An epithelial cell of the parathyroid gland that is arranged in wide, irregular interconnecting columns; responsible for the synthesis and secretion of parathyroid hormone." [FMA:69078, GOC:tfm, ISBN:0517223651] +subset: human_subset +subset: mouse_subset synonym: "parathyroid chief cell" EXACT [] synonym: "parathyroid gland chief cell" EXACT [] synonym: "parathyroid hormone secreting cell" EXACT [] @@ -4966,18 +5607,23 @@ synonym: "principal cell of parathyroid gland" EXACT [] xref: BTO:0004712 xref: CALOHA:TS-2140 xref: FMA:69078 -is_a: CL:0000167 ! peptide hormone secreting cell -is_a: CL:0002260 ! epithelial cell of parathyroid gland +is_a: CL:1001593 ! parathyroid glandular cell +relationship: capable_of GO:0035898 ! parathyroid hormone secretion +relationship: part_of UBERON:0011197 ! parathyroid epithelium [Term] id: CL:0000447 name: carbohydrate secreting cell +subset: human_subset +subset: mouse_subset is_a: CL:0000151 ! secretory cell [Term] id: CL:0000448 name: white adipocyte def: "An adipocyte with light coloration and few mitochondria. It contains a scant ring of cytoplasm surrounding a single large lipid droplet or vacuole." [GOC:tfm, MESH:D052438] +subset: human_subset +subset: mouse_subset synonym: "white adipose cell" EXACT [] synonym: "white fat cell" RELATED [] xref: CALOHA:TS-1119 @@ -4990,6 +5636,9 @@ relationship: RO:0002202 CL:0002334 ! develops from preadipocyte id: CL:0000449 name: brown adipocyte def: "A cell from the thermogenic form of adipose tissue found in many species, particularly in newborns and hibernating mammals, but also in lesser amounts in adults of other mammals including humans. Brown fat is capable of rapid liberation of energy and seems to be important in the maintenance of body temperature immediately after birth and upon waking from hibernation." [MESH:D002001] +subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "brown adipose cell" EXACT [] synonym: "brown fat cell" EXACT [] xref: CALOHA:TS-0099 @@ -5005,6 +5654,8 @@ def: "A cell of hematopoietic origin, typically resident in particular tissues, subset: cellxgene_subset subset: general_cell_types_upper_slim subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "interdigitating cell" RELATED [] synonym: "veiled cell" RELATED [] xref: BTO:0002042 @@ -5014,7 +5665,6 @@ xref: MESH:D003713 xref: ZFA:0009209 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000113 ! mononuclear phagocyte is_a: CL:0000145 ! professional antigen presenting cell -is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000738 ! leukocyte intersection_of: bearer_of PATO:0001407 ! mononucleate intersection_of: capable_of GO:0001816 ! cytokine production @@ -5041,6 +5691,8 @@ property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000452 name: thyroid hormone secreting cell +subset: human_subset +subset: mouse_subset xref: ZFA:0009210 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000163 ! endocrine cell @@ -5051,6 +5703,8 @@ def: "Langerhans cell is a conventional dendritic cell that has plasma membrane comment: Originally described in the dendritic cell ontology (DC_CL:0000021 )(PMID:19243617). These cells are also CD1a-high, CD14-negative, CD207-positive (langerin), CD324-positive (E-cadherin), and DCIR-positive. They reside in the epidermis. subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "LC" EXACT [] xref: BTO:0000705 xref: CALOHA:TS-2375 @@ -5070,6 +5724,8 @@ property_value: RO:0002175 NCBITaxon:9606 id: CL:0000454 name: epinephrine secreting cell def: "A cell capable of producing epinephrine. Epiniphrine is synthesized from norepiniphrine by the actions of the phenylethanolamine N-methyltransferase enzyme, which is expressed in the adrenal glands, androgenic neurons, and in other cell types." [GOC:tfm, PMID:12438093] +subset: human_subset +subset: mouse_subset synonym: "adrenaline secreting cell" EXACT [GO:0048242] synonym: "epinephrin secreting cell" EXACT [] xref: ZFA:0009211 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} @@ -5089,6 +5745,8 @@ replaced_by: PO:0004531 id: CL:0000456 name: mineralocorticoid secreting cell def: "Any secretory cell that is capable of some mineralocorticoid secretion." [FBC:Autogenerated] +subset: human_subset +subset: mouse_subset is_a: CL:0000174 ! steroid hormone secreting cell intersection_of: CL:0000151 ! secretory cell intersection_of: capable_of GO:0035931 ! mineralocorticoid secretion @@ -5097,6 +5755,8 @@ relationship: capable_of GO:0035931 ! mineralocorticoid secretion [Term] id: CL:0000457 name: biogenic amine secreting cell +subset: human_subset +subset: mouse_subset xref: ZFA:0009212 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000151 ! secretory cell @@ -5104,6 +5764,8 @@ is_a: CL:0000151 ! secretory cell id: CL:0000458 name: serotonin secreting cell def: "A cell type that secretes 5-Hydroxytryptamine (serotonin)." [GOC:tfm, PMID:19630576] +subset: human_subset +subset: mouse_subset synonym: "5-HT secreting cell" EXACT [] synonym: "5-Hydroxytryptamine secreting cell" EXACT [] xref: ZFA:0009213 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} @@ -5116,6 +5778,9 @@ relationship: capable_of GO:0001820 ! serotonin secretion id: CL:0000459 name: noradrenergic cell def: "A cell capable of producting norepiniphrine. Norepiniphrine is a catecholamine with multiple roles including as a hormone and a neurotransmitter. In addition, epiniphrine is synthesized from norepiniphrine by the actions of the phenylethanolamine N-methyltransferase enzyme." [GOC:tfm, ISBN:068340007X] +subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "noradrenaline secreting cell" EXACT [] synonym: "norepinephrin secreting cell" EXACT [] synonym: "norepinephrine secreting cell" EXACT [] @@ -5129,6 +5794,8 @@ relationship: capable_of GO:0048243 ! norepinephrine secretion id: CL:0000460 name: glucocorticoid secreting cell def: "Any secretory cell that is capable of some glucocorticoid secretion." [FBC:Autogenerated] +subset: human_subset +subset: mouse_subset xref: ZFA:0009215 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000174 ! steroid hormone secreting cell intersection_of: CL:0000151 ! secretory cell @@ -5158,6 +5825,8 @@ relationship: RO:0002202 CL:0000464 ! develops from epidermoblast id: CL:0000464 name: epidermoblast def: "An epidermal progenitor cell that arises from neuroectoderm and in turn gives rise to the epidermal sheath of ventral and cephalic regions." [GOC:tfm, PMID:7576311] +subset: human_subset +subset: mouse_subset xref: FBbt:00004994 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} is_a: CL:0000055 ! non-terminally differentiated cell is_a: CL:0000710 ! neurecto-epithelial cell @@ -5176,6 +5845,8 @@ id: CL:0000467 name: adrenocorticotropic hormone secreting cell alt_id: CL:0000640 def: "A peptide hormone secreting cell that produces adrenocorticotropin, or corticotropin." [GOC:tfm, SANBI:mhl] +subset: human_subset +subset: mouse_subset synonym: "ACTH secreting cell" EXACT [GO:0051458] synonym: "adrenocorticotrophic hormone secreting cell" EXACT [] synonym: "corticotrophin hormone secreting cell" EXACT [] @@ -5210,6 +5881,8 @@ relationship: RO:0002202 CL:0000338 ! develops from neuroblast (sensu Nematoda a [Term] id: CL:0000470 name: digestive enzyme secreting cell +subset: human_subset +subset: mouse_subset xref: ZFA:0009217 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000154 ! protein secreting cell @@ -5224,6 +5897,8 @@ replaced_by: PO:0000076 id: CL:0000473 name: defensive cell def: "A cell whose primary function is to protect the organism." [JB:jb] +subset: human_subset +subset: mouse_subset is_a: CL:0000000 ! cell [Term] @@ -5246,6 +5921,8 @@ replaced_by: PO:0000245 id: CL:0000476 name: thyrotroph def: "A basophil cell of the anterior pituitary that produces thyroid stimulating hormone, thyrotrophin. This cell type is elongated, polygonal and lie in clusters towards the adenohypophyseal center." [ISBN:0517223651, SANBI:mhl] +subset: human_subset +subset: mouse_subset synonym: "beta-basophil" EXACT [] synonym: "thyroid stimulating hormone secreting cell" EXACT [] synonym: "thyrotrope" EXACT [] @@ -5272,30 +5949,40 @@ relationship: RO:0002202 CL:0000441 ! develops from follicle stem cell (sensu Ar id: CL:0000478 name: oxytocin stimulating hormone secreting cell def: "A peptide hormone secreting cell that secretes oxytocin stimulating hormone" [GO:tfm] +subset: human_subset +subset: mouse_subset is_a: CL:0000167 ! peptide hormone secreting cell [Term] id: CL:0000479 name: vasopressin stimulating hormone secreting cell def: "A peptide hormone secreting cell that secretes vasopressin stimulating hormone" [GO:tfm] +subset: human_subset +subset: mouse_subset is_a: CL:0000167 ! peptide hormone secreting cell [Term] id: CL:0000480 name: secretin stimulating hormone secreting cell def: "A peptide hormone secreting cell that secretes secretin stimulating hormone" [GO:tfm] +subset: human_subset +subset: mouse_subset is_a: CL:0000167 ! peptide hormone secreting cell [Term] id: CL:0000481 name: cholecystokin stimulating hormone secreting cell def: "A peptide hormone secreting cell that secretes cholecystokin stimulating hormone." [GO:tfm] +subset: human_subset +subset: mouse_subset is_a: CL:0000167 ! peptide hormone secreting cell [Term] id: CL:0000482 name: juvenile hormone secreting cell def: "An endocrine cell that secretes juvenile hormone." [GO:tfm] +subset: human_subset +subset: mouse_subset xref: FBbt:00058020 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} is_a: CL:0000151 ! secretory cell intersection_of: CL:0000151 ! secretory cell @@ -5306,6 +5993,8 @@ relationship: capable_of GO:0045443 ! juvenile hormone secretion id: CL:0000483 name: bombesin stimulating hormone secreting cell def: "A peptide hormone secreting cell that secretes bombesin stimulating hormone." [GO:tfm, https://orcid.org/0000-0001-5208-3432] +subset: human_subset +subset: mouse_subset is_a: CL:0000167 ! peptide hormone secreting cell [Term] @@ -5314,6 +6003,8 @@ name: connective tissue type mast cell def: "Mast cell subtype whose granules contain both the serine proteases tryptase and chymase. These cells are primarily found in connective tissue, such as the peritoneal cavity, skin, and intestinal submucosa. Their development is T-cell independent." [GOC:add, GOC:dsd, GOC:tfm, PMID:19923473, PMID:9354811] comment: They are CD88-positive. The cytoplasmic granules contain high levels of histamine and heparin (mouse) or major neutral proteases, tryptase, chymase, carboxypeptidase A, and cathepsin G (humans). Reportedly, they cannot produce leukotrienes (LTC4) and IL-4. They are reportedly very heterogeneous depending upon location and can convert to the MC(T) phenotype. subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "MC(TC)" EXACT [] synonym: "MCTC" EXACT [] synonym: "TC mast cells" EXACT [] @@ -5329,6 +6020,8 @@ name: mucosal type mast cell def: "Mast cell subtype that contains only the serine protease trypase in its granules. These cells are primarily found in mucosal tissue, such as intestinal mucosa and alveoli. They depend upon T-cells for development of phenotype." [GOC:add, GOC:dsd, PMID:19923473, PMID:9354811] comment: They are CD88-negative. The cytoplasmic granules contain low levels of histamine and high levels of chondroitin sulfate (mouse) or major neutral proteases and tryptase (humans). Additionally, they can produce leukotrienes (LTC4), IL-5, IL-6, and low levels of IL-4. They are reportedly very heterogeneous depending upon location and can convert to the MC(T) phenotype. subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "MC(T)" EXACT [] synonym: "MCT" EXACT [] synonym: "T mast cells" EXACT [] @@ -5365,6 +6058,8 @@ relationship: RO:0002162 NCBITaxon:6656 ! in taxon Arthropoda id: CL:0000488 name: visible light photoreceptor cell def: "A photoreceptor cell that detects visible light." [GOC:tfm] +subset: human_subset +subset: mouse_subset xref: ZFA:0009219 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000210 ! photoreceptor cell intersection_of: CL:0000210 ! photoreceptor cell @@ -5374,11 +6069,15 @@ relationship: capable_of GO:0009584 ! detection of visible light [Term] id: CL:0000489 name: scotopic photoreceptor cell +subset: human_subset +subset: mouse_subset is_a: CL:0000210 ! photoreceptor cell [Term] id: CL:0000490 name: photopic photoreceptor cell +subset: human_subset +subset: mouse_subset xref: ZFA:0009220 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000488 ! visible light photoreceptor cell @@ -5395,6 +6094,8 @@ name: CD4-positive helper T cell def: "A CD4-positive, alpha-beta T cell that cooperates with other lymphocytes via direct contact or cytokine release to initiate a variety of immune functions." [GO_REF:0000031, GOC:add, GOC:pam, GOC:tfm, ISBN:0781735149, MESH:D006377] subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "CD4-positive helper T lymphocyte" EXACT [] synonym: "CD4-positive helper T-cell" EXACT [] synonym: "CD4-positive helper T-lymphocyte" EXACT [] @@ -5420,6 +6121,8 @@ is_obsolete: true id: CL:0000494 name: UV sensitive photoreceptor cell def: "A photoreceptor cell that detects ultraviolet light." [GOC:tfm] +subset: human_subset +subset: mouse_subset xref: ZFA:0009221 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000210 ! photoreceptor cell intersection_of: CL:0000210 ! photoreceptor cell @@ -5430,6 +6133,8 @@ relationship: capable_of GO:0009589 ! detection of UV id: CL:0000495 name: blue sensitive photoreceptor cell def: "A photoreceptor cell that is sensitive to blue light." [GO:tfm] +subset: human_subset +subset: mouse_subset xref: ZFA:0009222 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000490 ! photopic photoreceptor cell @@ -5437,6 +6142,8 @@ is_a: CL:0000490 ! photopic photoreceptor cell id: CL:0000496 name: green sensitive photoreceptor cell def: "A photoreceptor cell that is sensitive to green light." [GO:tfm] +subset: human_subset +subset: mouse_subset xref: ZFA:0009223 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000490 ! photopic photoreceptor cell @@ -5444,6 +6151,8 @@ is_a: CL:0000490 ! photopic photoreceptor cell id: CL:0000497 name: red sensitive photoreceptor cell def: "A photoreceptor cell that is sensitive to red light." [GO:tfm] +subset: human_subset +subset: mouse_subset xref: ZFA:0009224 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000490 ! photopic photoreceptor cell @@ -5452,6 +6161,8 @@ id: CL:0000498 name: inhibitory interneuron def: "An interneuron (also called relay neuron, association neuron or local circuit neuron) is a multipolar neuron which connects afferent neurons and efferent neurons in neural pathways. Like motor neurons, interneuron cell bodies are always located in the central nervous system (CNS)." [GOC:tfm, http://en.wikipedia.org/wiki/Interneuron] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset xref: FMA:84776 xref: ZFA:0009225 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000099 ! interneuron @@ -5459,10 +6170,12 @@ is_a: CL:0000099 ! interneuron [Term] id: CL:0000499 name: stromal cell -def: "A connective tissue cell of an organ found in the loose connective tissue. These are most often associated with the uterine mucosa and the ovary as well as the hematopoietic system and elsewhere." [GOC:tfm, MESH:D017154] +def: "A connective tissue cell of an organ found in the loose connective tissue." [GOC:tfm, MESH:D017154] subset: cellxgene_subset subset: general_cell_types_upper_slim subset: human_reference_atlas +subset: human_subset +subset: mouse_subset xref: BTO:0002064 xref: FMA:83624 xref: ZFA:0009226 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} @@ -5475,6 +6188,8 @@ property_value: RO:0002175 NCBITaxon:9606 id: CL:0000500 name: follicular epithelial cell def: "An epithelial somatic cell associated with a maturing oocyte." [] +subset: human_subset +subset: mouse_subset is_a: CL:0000066 ! epithelial cell [Term] @@ -5482,6 +6197,8 @@ id: CL:0000501 name: granulosa cell def: "A supporting cell for the developing female gamete in the ovary of mammals. They develop from the coelomic epithelial cells of the gonadal ridge. Granulosa cells form a single layer around the mammalian oocyte in the primordial ovarian follicle and advance to form a multilayered cumulus oophorus surrounding the ovum in the Graafian follicle. The major functions of granulosa cells include the production of steroids and LH receptors." [MESH:D006107] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "granulosa cell of ovary" EXACT [] xref: BTO:0000542 xref: CALOHA:TS-0729 @@ -5490,33 +6207,38 @@ xref: https://cellxgene.cziscience.com/cellguide/CL_0000501 xref: ZFA:0009227 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000174 ! steroid hormone secreting cell is_a: CL:0002174 ! follicular cell of ovary +is_a: CL:1100001 ! secretory epithelial cell relationship: RO:0002202 CL:4033066 ! develops from pre-granulosa cell -property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional.\n\nGranulosa cells are a type of somatic cell most commonly known for their crucial role within the ovarian follicles of female mammalian species. Named for their grainy appearance, they are situated in the follicular epithelium, lining the inner part of the follicle and directly surrounding the oocyte. These cells stand as an integral part of the ovarian structure and function.\nOne of the primary roles of granulosa cells is to aid in the production and secretion of sex hormones, particularly estrogen. They achieve this by working in tandem with theca cells, which stay attached to the external layer of the follicle. Theca cells produce androstenedione (a type of androgen) which granulosa cells then convert into estradiol, a form of estrogen, with the help of the enzyme aromatase. Moreover, granulosa cells participate in luteinization, transforming into luteal granulosa cells as a response to the luteinizing hormone during ovulation. This allows the formation of the corpus luteum, responsible for the secretion of progesterone necessary to maintain pregnancy.\nGranulosa cells also play a significant role in follicular development and oocyte maturation, involving close communication with the contained oocyte. They support the oocyte through the provision of nutrients and growth factors, control its meiotic cycle and ensure it is appropriately oriented and instructed for impending ovulation. Furthermore, granulosa cells contribute to the formation of the zona pellucida and the follicular fluid, providing an optimal environment for the oocyte's growth and maturation. These cells, thus, perform multiple vital roles, underscoring their importance in fertility and reproductive health." xsd:string {xref="DOI:10.1016/j.ejogrb.2004.01.010", xref="DOI:10.1093/humrep/del408", xref="DOI:10.1093/humupd/6.3.279", xref="DOI:10.1210/jcem-28-3-355", xref="DOI:10.3389/fendo.2019.00832/full"} +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nGranulosa cells are a type of somatic cell most commonly known for their crucial role within the ovarian follicles of female mammalian species. Named for their grainy appearance, they are situated in the follicular epithelium, lining the inner part of the follicle and directly surrounding the oocyte. These cells stand as an integral part of the ovarian structure and function.\nOne of the primary roles of granulosa cells is to aid in the production and secretion of sex hormones, particularly estrogen. They achieve this by working in tandem with theca cells, which stay attached to the external layer of the follicle. Theca cells produce androstenedione (a type of androgen) which granulosa cells then convert into estradiol, a form of estrogen, with the help of the enzyme aromatase. Moreover, granulosa cells participate in luteinization, transforming into luteal granulosa cells as a response to the luteinizing hormone during ovulation. This allows the formation of the corpus luteum, responsible for the secretion of progesterone necessary to maintain pregnancy.\nGranulosa cells also play a significant role in follicular development and oocyte maturation, involving close communication with the contained oocyte. They support the oocyte through the provision of nutrients and growth factors, control its meiotic cycle and ensure it is appropriately oriented and instructed for impending ovulation. Furthermore, granulosa cells contribute to the formation of the zona pellucida and the follicular fluid, providing an optimal environment for the oocyte's growth and maturation. These cells, thus, perform multiple vital roles, underscoring their importance in fertility and reproductive health." xsd:string {xref="DOI:10.1016/j.ejogrb.2004.01.010", xref="DOI:10.1093/humrep/del408", xref="DOI:10.1093/humupd/6.3.279", xref="DOI:10.1210/jcem-28-3-355", xref="DOI:10.3389/fendo.2019.00832/full"} [Term] id: CL:0000502 name: type D enteroendocrine cell def: "A cell found throughout the gastrointestinal tract and in the pancreas. They secrete somatostatin in both an endocrine and paracrine manner. Somatostatin inhibits gastrin, cholecystokinin, insulin, glucagon, pancreatic enzymes, and gastric hydrochloric acid. A variety of substances which inhibit gastric acid secretion (vasoactive intestinal peptide, calcitonin gene-related peptide, cholecystokinin, beta-adrenergic agonists, and gastric inhibitory peptide) are thought to act by releasing somatostatin." [MESH:D019864] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "D cell" EXACT [] xref: FMA:62935 xref: https://cellxgene.cziscience.com/cellguide/CL_0000502 xref: ZFA:0009228 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000164 ! enteroendocrine cell +is_a: CL:0000165 ! neuroendocrine cell is_a: CL:0000172 ! somatostatin secreting cell -property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional.\n\nType D enteroendocrine cells, also known as D or delta cells, are specialized hormone-releasing cells found in the pancreas and also scattered throughout the lining of the gastrointestinal tract in mammals, notably within the stomach and the upper part of the small intestine known as the duodenum. The primary role of D cells is to produce and secrete somatostatin, a potent paracrine inhibitor. \nIn the gastrointestinal tract, somatostatin slows down digestion. It reduces gastric acid secretion and slows down the rate of gastric emptying, thereby prolonging and controling the digestive p. Functionally, these effects are aimed at sustaining nutrient absorption to optimize energy extraction from consumed food.\nIn the pancreas, D cells maintain a vital role in endocrine regulation. D cells in the pancreatic islands secrete somatostatin to inhibit the release of both insulin and glucagon from type A cells and B cells, glucoregulatory hormones that control blood sugar levels. Hence, D cells contribute considerably to the homeostasis of the body's metabolic processes. It is also noteworthy that dysfunctional D cells or irregular somatostatin signaling has been associated with certain pathologies such as neuroendocrine tumors and gastric ulcers." xsd:string {xref="DOI:10.1016/j.pharmthera.2015.05.007", xref="DOI:10.1038/s41574-018-0020-6", xref="DOI:10.1093/annonc/mdh216", xref="https://www.sciencedirect.com/topics/neuroscience/somatostatin-cell"} +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nType D enteroendocrine cells, also known as D or delta cells, are specialized hormone-releasing cells found in the pancreas and also scattered throughout the lining of the gastrointestinal tract in mammals, notably within the stomach and the upper part of the small intestine known as the duodenum. The primary role of D cells is to produce and secrete somatostatin, a potent paracrine inhibitor. \nIn the gastrointestinal tract, somatostatin slows down digestion. It reduces gastric acid secretion and slows down the rate of gastric emptying, thereby prolonging and controling the digestive p. Functionally, these effects are aimed at sustaining nutrient absorption to optimize energy extraction from consumed food.\nIn the pancreas, D cells maintain a vital role in endocrine regulation. D cells in the pancreatic islands secrete somatostatin to inhibit the release of both insulin and glucagon from type A cells and B cells, glucoregulatory hormones that control blood sugar levels. Hence, D cells contribute considerably to the homeostasis of the body's metabolic processes. It is also noteworthy that dysfunctional D cells or irregular somatostatin signaling has been associated with certain pathologies such as neuroendocrine tumors and gastric ulcers." xsd:string {xref="DOI:10.1016/j.pharmthera.2015.05.007", xref="DOI:10.1038/s41574-018-0020-6", xref="DOI:10.1093/annonc/mdh216", xref="https://www.sciencedirect.com/topics/neuroscience/somatostatin-cell"} [Term] id: CL:0000503 name: theca cell -def: "A flattened stroma cell forming a sheath or theca outside the basal lamina lining the mature ovarian follicle. Thecal interstitial or stromal cells are steroidogenic, and produce primarily androgens which serve as precusors of estrogens in the granulosa cells." [MESH:D013799] +def: "A specialized stromal cell that forms the theca layer outside the basal lamina lining the ovarian follicle, appearing during the secondary follicle stage." [MESH:D013799, PMID:15833266, PMID:36758341] subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset xref: BTO:0002850 xref: ZFA:0009229 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} -is_a: CL:0000593 ! androgen secreting cell is_a: CL:0002132 ! stromal cell of ovary -relationship: part_of UBERON:0001305 ! ovarian follicle +relationship: part_of UBERON:0000155 ! theca cell layer property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -5524,6 +6246,8 @@ id: CL:0000504 name: enterochromaffin-like cell def: "A enteroendocrine cell part of the glands of the gastric mucosa. They produce histamine and peptides such as chromogranins. This cell type respond to gastrin by releasing histamine which acts as a paracrine stimulator of the release of hydrochloric acid from the gastric parietal cells." [GOC:tfm, MESH:D019861] comment: Consider enterochromaffin cell (CL:0002065). For several years this cell type was "enterochromaffin cell" despite a MESH dbxref and a free text definition that clearly meant enterochromaffin-like cell. +subset: human_subset +subset: mouse_subset synonym: "ECL" EXACT [] xref: BTO:0002692 is_a: CL:0000164 ! enteroendocrine cell @@ -5533,6 +6257,8 @@ is_a: CL:0002274 ! histamine secreting cell id: CL:0000505 name: substance P secreting cell def: "A peptide hormone secreting cell that secretes substance P." [GO:tfm] +subset: human_subset +subset: mouse_subset xref: ZFA:0009230 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000167 ! peptide hormone secreting cell @@ -5540,6 +6266,8 @@ is_a: CL:0000167 ! peptide hormone secreting cell id: CL:0000506 name: enkephalin secreting cell def: "An endorphine cell that secretes enkephalin." [GO:tfm] +subset: human_subset +subset: mouse_subset xref: ZFA:0009231 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000507 ! endorphin secreting cell @@ -5547,49 +6275,61 @@ is_a: CL:0000507 ! endorphin secreting cell id: CL:0000507 name: endorphin secreting cell def: "A peptide hormone secreting cell that secretes endorphin." [GO:tfm] +subset: human_subset +subset: mouse_subset xref: ZFA:0009232 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000167 ! peptide hormone secreting cell [Term] id: CL:0000508 name: type G enteroendocrine cell -def: "An endocrine cell found in the pyloric gland mucosa (antral mucosa) of the stomach of mammals and responsible for the secretion of gastrin and enkephalin. Most abundant in pyloric antrum, pyramidal in form with a narrow apex bearing long microvilli." [GOC:tfm, ISBN:0517223651, MESH:D019863] +def: "An endocrine cell found in the stomach and duodenum and is responsible for the secretion of gastrin and enkephalin. Most abundant in pyloric antrum, pyramidal in form with a narrow apex bearing long microvilli." [GOC:tfm, ISBN:0517223651, MESH:D019863, PMID:10700044, PMID:35674015, PMID:37240181] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "G cell" EXACT [] xref: BTO:0004108 xref: FMA:67609 is_a: CL:0000164 ! enteroendocrine cell +is_a: CL:0000165 ! neuroendocrine cell is_a: CL:0000506 ! enkephalin secreting cell is_a: CL:0000509 ! gastrin secreting cell -is_a: CL:0002659 ! glandular epithelial cell of stomach -relationship: part_of UBERON:0004997 ! mucosa of pyloric antrum [Term] id: CL:0000509 name: gastrin secreting cell def: "A peptide hormone secreting cell that secretes gastrin." [GO:tfm] subset: human_reference_atlas +subset: human_subset +subset: mouse_subset is_a: CL:0000167 ! peptide hormone secreting cell property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000510 name: paneth cell -def: "An epithelial cell found in the basal part of the intestinal glands (crypts of Lieberkuhn) including the appendix. Paneth cells synthesize and secrete lysozyme and cryptdins. Numerous in the deeper parts of the intestinal crypts, particularly in the duodenum, rich in zinc, contain large acidophilic granules, with irregular apical microvilli and prominent membrane-bound vacuoles containing matrix." [GOC:tfm, ISBN:0517223651, MESH:D019879, PMID:29184701, PMID:32308658] +def: "An epithelial cell found in the basal part of the intestinal glands (crypts of Lieberkuhn) including the appendix. Paneth cells synthesize and secrete lysozyme and cryptdins. Numerous in the deeper parts of the intestinal crypts, particularly in the duodenum, rich in zinc, contain large acidophilic granules, with irregular apical microvilli and prominent membrane-bound vacuoles containing matrix." [GOC:tfm, ISBN:0517223651, MESH:D019879, PMID:29184701, PMID:32308658, PMID:33484640] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset xref: BTO:0000993 xref: FMA:62897 xref: https://cellxgene.cziscience.com/cellguide/CL_0000510 -is_a: CL:0000150 {is_inferred="true"} ! glandular epithelial cell +is_a: CL:0000150 ! glandular secretory epithelial cell is_a: CL:0000323 ! lysozyme secreting cell is_a: CL:0002563 ! intestinal epithelial cell -relationship: part_of UBERON:0001983 ! crypt of Lieberkuhn -property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional.\n\nPaneth cells are specialized epithelial cells that are primarily located at the bottom of the crypts of Lieberkühn in the small intestine, where they play a pivotal role in maintaining gut homeostasis. They have also been found in smaller numbers in the colonic crypts and other parts of the gastrointestinal tract. Paneth cells are characterized by large acidophilic granules, which take up most of the cytoplasmic volume, causing the nucleus to be pushed toward the base of the cell.\nPaneth cells function as a part of the innate immune system. The large granules inside the cells are filled with antimicrobial peptides, such as defensins and lysozymes. Upon bacterial intrusion or cellular signaling indicating a potential infection, Paneth cells release the granules containing the antimicrobial substances into the crypt lumen, effectively serving as the first line of defense against bacterial invasion within the gastrointestinal tract. In essence, Paneth cells serve as guardians, protecting the intestinal stem cells from harmful pathogens that may disturb the gut ecosystem.\nIn addition to their primary role in immunity, Paneth cells are also crucial for supporting the stem cell niche in the intestinal crypts. They are located adjacent to Lgr5+ stem cells and secrete various growth factors such as EGF, TGF-alpha, Wnt3, and Notch ligand Dll4. These factors regulate the self-renewal and differentiation of these stem cells, which continuously replenish the intestinal epithelium. Consequently, any abnormality or dysfunction in Paneth cells could lead to a disturbance in gut homeostasis, possibly resulting in various illnesses such as inflammatory bowel disease." xsd:string {xref="DOI:10.1007/s00018-002-8412-z", xref="DOI:10.1038/nature09637", xref="DOI:10.1038/nrmicro2546", xref="DOI:10.1146/annurev-physiol-030212-183744", xref="DOI:10.3389/fimmu.2020.00587"} +relationship: has_part GO:0005773 ! vacuole +relationship: has_part GO:0005902 ! microvillus +relationship: part_of UBERON:0011184 ! epithelium of crypt of Lieberkuhn +relationship: RO:0002202 CL:4047017 ! develops from transit amplifying cell of gut +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nPaneth cells are specialized epithelial cells that are primarily located at the bottom of the crypts of Lieberkühn in the small intestine, where they play a pivotal role in maintaining gut homeostasis. They have also been found in smaller numbers in the colonic crypts and other parts of the gastrointestinal tract. Paneth cells are characterized by large acidophilic granules, which take up most of the cytoplasmic volume, causing the nucleus to be pushed toward the base of the cell.\nPaneth cells function as a part of the innate immune system. The large granules inside the cells are filled with antimicrobial peptides, such as defensins and lysozymes. Upon bacterial intrusion or cellular signaling indicating a potential infection, Paneth cells release the granules containing the antimicrobial substances into the crypt lumen, effectively serving as the first line of defense against bacterial invasion within the gastrointestinal tract. In essence, Paneth cells serve as guardians, protecting the intestinal stem cells from harmful pathogens that may disturb the gut ecosystem.\nIn addition to their primary role in immunity, Paneth cells are also crucial for supporting the stem cell niche in the intestinal crypts. They are located adjacent to Lgr5+ stem cells and secrete various growth factors such as EGF, TGF-alpha, Wnt3, and Notch ligand Dll4. These factors regulate the self-renewal and differentiation of these stem cells, which continuously replenish the intestinal epithelium. Consequently, any abnormality or dysfunction in Paneth cells could lead to a disturbance in gut homeostasis, possibly resulting in various illnesses such as inflammatory bowel disease." xsd:string {xref="DOI:10.1007/s00018-002-8412-z", xref="DOI:10.1038/nature09637", xref="DOI:10.1038/nrmicro2546", xref="DOI:10.1146/annurev-physiol-030212-183744", xref="DOI:10.3389/fimmu.2020.00587"} [Term] id: CL:0000511 name: androgen binding protein secreting cell def: "A peptide hormone secreting cell that secretes androgen binding protein." [GO:tfm] +subset: human_subset +subset: mouse_subset is_a: CL:0000154 ! protein secreting cell [Term] @@ -5605,6 +6345,8 @@ name: cardiac muscle myoblast alt_id: CL:0000714 def: "A precursor cell destined to differentiate into cardiac muscle cell." [GOC:tfm, MESH:D032386] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "cardiac muscle progenitor cell" EXACT [] synonym: "cardiomyocyte progenitor cell" EXACT [] xref: FMA:84797 @@ -5621,19 +6363,25 @@ id: CL:0000514 name: smooth muscle myoblast def: "A precursor cell destined to differentiate into smooth muscle myocytes." [GOC:tfm, MESH:D032390] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "myoblast, smooth muscle" EXACT [MESH:D032390] synonym: "satellite cell" RELATED [] xref: FMA:84798 +xref: https://cellxgene.cziscience.com/cellguide/CL_0000514 xref: ZFA:0009235 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000056 ! myoblast intersection_of: CL:0000056 ! myoblast intersection_of: RO:0002203 CL:0000192 ! develops into smooth muscle cell relationship: RO:0002203 CL:0000192 ! develops into smooth muscle cell +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nA precursor to the smooth muscle cell, the smooth muscle myoblast, is integral to various body systems, including the cardiovascular, gastrointestinal, and respiratory systems. Smooth muscle myoblasts arise from the differentiation of mesenchymal stem cells, a process tightly regulated by specific genetic factors and environmental signals. Their role extends to myogenesis, particularly in the formation of muscular tissue, especially during embryonic development.\nSmooth muscle myoblasts possess distinctive cellular characteristics. In contrast to skeletal muscle myoblasts, they do not fuse to create multinucleated fibers. Instead, they differentiate into individual, uninucleated smooth muscle cells. This differentiation unfolds in two distinct phases: proliferation, marked by rapid division to increase cell numbers, and differentiation, involving structural and functional transformation into mature smooth muscle cells. This intricate process is intricately mediated by various signaling molecules and transcription factors.\nFunctionally, smooth muscle myoblasts and the mature muscle cells they generate play pivotal roles in various physiological processes. Smooth muscle cells orchestrate involuntary muscle responses and are integral to body systems that regulate blood flow, propel food along the digestive tract, and control airflow in the respiratory tract. These diverse functions underscore the significance of smooth muscle myoblasts in the body's growth, maintenance, and overall function." xsd:string {xref="DOI:10.1074/jbc.RA118.001739", xref="https://www.ncbi.nlm.nih.gov/books/NBK544225/", xref="https://www.sciencedirect.com/topics/medicine-and-dentistry/smooth-muscle"} [Term] id: CL:0000515 name: skeletal muscle myoblast def: "A myoblast that differentiates into skeletal muscle fibers." [SANBI:mhl] +subset: human_subset +subset: mouse_subset synonym: "skeletal myoblast" EXACT [] xref: FMA:84799 xref: ZFA:0009236 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} @@ -5648,7 +6396,10 @@ relationship: RO:0002203 CL:0008002 ! develops into skeletal muscle fiber id: CL:0000516 name: perineuronal satellite cell def: "A non-neuronal cell that surrounds the neuronal cell bodies of the ganglia." [GOC:tfm, MESH:D027161] +subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "perineural satellite cell" EXACT [] synonym: "perineuronal satellite oligodendroglial cell" EXACT [] synonym: "satellite oligodendrocyte" EXACT [] @@ -5662,6 +6413,8 @@ property_value: RO:0002175 NCBITaxon:9606 id: CL:0000517 name: macrophage derived foam cell def: "A type of foam cell derived from a macrophage containing lipids in small vacuoles and typically seen in atherolosclerotic lesions, as well as other conditions." [GOC:add, PMID:20213546] +subset: human_subset +subset: mouse_subset synonym: "lipophage" EXACT [] is_a: BFO:0000002 is_a: CL:0000255 ! eukaryotic cell @@ -5672,6 +6425,8 @@ relationship: RO:0002202 CL:0000235 ! develops from macrophage id: CL:0000518 name: phagocyte (sensu Vertebrata) def: "A phagocyte in vertebrates that is able to phagocytosis." [GOC:tfm] +subset: human_subset +subset: mouse_subset is_a: CL:0000234 ! phagocyte is_a: CL:0000255 ! eukaryotic cell relationship: RO:0002162 NCBITaxon:7742 ! in taxon Vertebrata @@ -5710,6 +6465,8 @@ id: CL:0000523 name: mononuclear cytotrophoblast cell def: "A cell from the inner layer of the trophoblast of the early mammalian embryo that gives rise to the outer surface and villi of the chorion. Mononuclear crytoblasts fuse to give rise to a multinuclear cytotrophoblast." [GOC:tfm, ISBN:0323052908] subset: human_reference_atlas +subset: human_subset +subset: mouse_subset xref: FMA:83042 is_a: CL:0000351 ! trophoblast cell property_value: RO:0002175 NCBITaxon:9606 @@ -5727,6 +6484,8 @@ name: syncytiotrophoblast cell def: "A cell from the outer syncytial layer of the trophoblast of an early mammalian embryo, directly associated with the maternal blood supply. It secretes hCG in order to maintain progesterone secretion and sustain a pregnancy." [GOC:tfm, ISBN:0323052908] subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "plasmidotrophoblast cell" RELATED [] synonym: "syncytial trophoblast cell" EXACT [PMID:11787150] synonym: "syncytiotrophoblastic cell" EXACT [PMID:21733368] @@ -5745,6 +6504,8 @@ id: CL:0000526 name: afferent neuron def: "A neuron which conveys sensory information centrally from the periphery." [GOC:tfm, MESH:D009475] subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "input neuron" EXACT [] xref: FMA:87653 xref: ZFA:0009238 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} @@ -5755,6 +6516,9 @@ property_value: RO:0002175 NCBITaxon:9606 id: CL:0000527 name: efferent neuron def: "A neuron which sends impulses peripherally to activate muscles or secretory cells." [MESH:D009476] +subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "output neuron" EXACT [] xref: ZFA:0009239 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000540 ! neuron @@ -5763,6 +6527,8 @@ is_a: CL:0000540 ! neuron id: CL:0000528 name: nitrergic neuron def: "A nerve cell where transmission is mediated by nitric oxide." [MESH:D026602] +subset: human_subset +subset: mouse_subset xref: FMA:84792 xref: ZFA:0009240 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000540 ! neuron @@ -5771,6 +6537,8 @@ is_a: CL:0000540 ! neuron id: CL:0000529 name: pigmented epithelial cell subset: cellxgene_subset +subset: human_subset +subset: mouse_subset xref: ZFA:0009241 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000710 ! neurecto-epithelial cell @@ -5780,7 +6548,8 @@ name: primary neuron (sensu Teleostei) def: "A neuron that develops during the early segmentation stages in teleosts, before the neural tube is formed." [doi:10.1242/dev.108.1.121, PMID:1842357] xref: ZFA:0009242 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: BFO:0000002 -is_a: CL:0000540 ! neuron +is_a: CL:2000029 ! central nervous system neuron +relationship: RO:0002100 UBERON:0002240 ! has soma location spinal cord relationship: RO:0002162 NCBITaxon:32443 {IAO:0000233="https://github.com/obophenotype/cell-ontology/pull/1950"} ! in taxon Teleostei [Term] @@ -5796,6 +6565,10 @@ intersection_of: CL:0000530 ! primary neuron (sensu Teleostei) [Term] id: CL:0000532 name: CAP motoneuron +def: "A primary motor neuron with its soma in the caudal region of a spinal cord. The axon of this motoneuron exit the spinal cord from one single point and innervates the lateral surface of ventral axial muscles" [PMID:17971221, PMID:35431796] +synonym: "cap cell" RELATED [PMID:17971221] +synonym: "CaP motorneuron" EXACT [PMID:3746410] +synonym: "caudal primary motor neuron" RELATED [PMID:18077593] xref: ZFA:0009243 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000533 ! primary motor neuron (sensu Teleostei) @@ -5804,24 +6577,25 @@ id: CL:0000533 name: primary motor neuron (sensu Teleostei) def: "A primary neuron (sensu Teleostei) that has a motor function." [PMID:1842357] xref: ZFA:0009244 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} -is_a: CL:0000100 ! motor neuron is_a: CL:0000530 ! primary neuron (sensu Teleostei) +is_a: CL:0011001 ! spinal cord motor neuron [Term] id: CL:0000534 name: primary interneuron (sensu Teleostei) def: "A primary neuron (sensu Teleostei) that is neither a sensory neuron or a motor neuron." [PMID:1842357] xref: ZFA:0009245 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} -is_a: CL:0000099 ! interneuron is_a: CL:0000530 ! primary neuron (sensu Teleostei) +is_a: CL:0005000 ! spinal cord interneuron [Term] id: CL:0000535 name: secondary neuron (sensu Teleostei) def: "A neuron of teleosts that develops later than a primary neuron, typically during the larval stages." [doi:10.1242/dev.108.1.121, PMID:1842357] xref: ZFA:0009246 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} -is_a: BFO:0000002 -is_a: CL:0000540 ! neuron +is_a: CL:2000029 ! central nervous system neuron +is_a: UBERON:0010313 ! neural crest-derived structure +relationship: RO:0002100 UBERON:0002240 ! has soma location spinal cord relationship: RO:0002162 NCBITaxon:32443 {IAO:0000233="https://github.com/obophenotype/cell-ontology/pull/1950"} ! in taxon Teleostei [Term] @@ -5829,8 +6603,8 @@ id: CL:0000536 name: secondary motor neuron (sensu Teleostei) def: "A secondary neuron (sensu Teleostei) that has a motor function." [PMID:1842357] xref: ZFA:0009247 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} -is_a: CL:0000100 ! motor neuron is_a: CL:0000535 ! secondary neuron (sensu Teleostei) +is_a: CL:0011001 ! spinal cord motor neuron intersection_of: CL:0000100 ! motor neuron intersection_of: CL:0000535 ! secondary neuron (sensu Teleostei) @@ -5862,6 +6636,8 @@ comment: These cells are also reportedly CD4-negative and CD200-positive. They a subset: cellxgene_subset subset: general_cell_types_upper_slim subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "nerve cell" EXACT [] xref: BTO:0000938 xref: CALOHA:TS-0683 @@ -5874,7 +6650,6 @@ is_a: CL:0000393 ! electrically responsive cell is_a: CL:0000404 ! electrically signaling cell is_a: CL:0002319 ! neural cell relationship: capable_of GO:0019226 ! transmission of nerve impulse -relationship: RO:0002202 CL:0000031 {gci_filler="NCBITaxon:7742", gci_relation="RO:0002162", xref="https://github.com/obophenotype/cell-ontology/issues/757"} ! develops from neuroblast (sensu Vertebrata) property_value: foaf:depiction "https://www.swissbiopics.org/api/image/Neuron_cells.svg" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 @@ -5883,6 +6658,8 @@ id: CL:0000541 name: melanoblast def: "A cell that originates from the neural crest and differentiates into a pigment cell." [GOC:tfm, SANBI:mhl] comment: Derived from UBERON:0002342 neural crest. +subset: human_subset +subset: mouse_subset xref: BTO:0003217 xref: FMA:83377 xref: ZFA:0009249 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} @@ -5897,6 +6674,8 @@ def: "A lymphocyte is a leukocyte commonly found in the blood and lymph that has comment: Editors note: consider adding taxon constraint to vertebrata (PMID:18025161) subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset xref: BTO:0000775 xref: CALOHA:TS-0583 xref: FMA:62863 @@ -5927,6 +6706,8 @@ replaced_by: PO:0000289 [Term] id: CL:0000544 name: slowly adapting mechanoreceptor cell +subset: human_subset +subset: mouse_subset is_a: CL:0000199 ! mechanoreceptor cell [Term] @@ -5936,6 +6717,8 @@ def: "A CD4-positive, alpha-beta T cell that has the phenotype T-bet-positive, C comment: This cell type is compatible with the HIPC Lyoplate markers for 'Th1 CD4+ T cell', but its logical definition includes additional known characteristics of T-helper 1 T cells. subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "helper T cell type 1" EXACT [] synonym: "T helper cells type 1" EXACT [PMID:9419219] synonym: "T(H)-1 cell" EXACT [] @@ -5966,6 +6749,8 @@ def: "A CD4-positive, alpha-beta T cell that has the phenotype GATA-3-positive, comment: This cell type is compatible with the HIPC Lyoplate markers for 'non-Th1/Th17 CD4+ T cell' (see CL:0001051), but includes the additional necessary and sufficient conditions to allow classification as a T-helper 2 T cell. subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "helper T cell type 2" EXACT [] synonym: "T helper cells type 2" EXACT [PMID:9419219] synonym: "T(H)-2 cell" EXACT [] @@ -5994,12 +6779,13 @@ name: proerythroblast def: "An immature, nucleated erythrocyte occupying the stage of erythropoeisis that follows formation of erythroid progenitor cells. This cell is CD71-positive, has both a nucleus and a nucleolus, and lacks hematopoeitic lineage markers." [ISBN:0721601464, PMID:1638021] subset: blood_and_immune_upper_slim subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "pronormoblast" RELATED [] synonym: "rubriblast" EXACT [ISBN:0721601464] xref: FMA:83518 is_a: CL:0000764 {is_inferred="true"} ! erythroid lineage cell is_a: CL:0002242 ! nucleate cell -is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000764 ! erythroid lineage cell intersection_of: bearer_of PATO:0002505 ! nucleated intersection_of: bearer_of PATO:0040072 ! high nuclear/cytoplasmic ratio @@ -6038,7 +6824,6 @@ relationship: RO:0002202 CL:0000038 ! develops from erythroid progenitor cell id: CL:0000548 name: obsolete animal cell def: "OBSOLETE. A native cell that is part of some Metazoa." [] -subset: cellxgene_subset subset: ubprop:upper_level synonym: "metazoan cell" EXACT [] relationship: term_tracker_item https://github.com/obophenotype/cell-ontology/issues/2124 @@ -6050,6 +6835,8 @@ replaced_by: CL:0000000 id: CL:0000549 name: basophilic erythroblast def: "A nucleated immature erythrocyte, having cytoplasm generally similar to that of the earlier proerythroblast but sometimes even more basophilic, and usually regular in outline. The nucleus is still relatively large, but the chromatin strands are thicker and more deeply staining, giving a coarser appearance; the nucleoli have disappeared. This cell is CD71-positive and lacks hematopoeitic lineage markers." [GOC:tfm, ISBN:0721601464] +subset: human_subset +subset: mouse_subset synonym: "basophilic normoblast" EXACT [ISBN:0721601464] synonym: "early erythroblast" EXACT [ISBN:0721601464] synonym: "early normoblast" EXACT [ISBN:0721601464] @@ -6057,7 +6844,6 @@ synonym: "prorubricyte" EXACT [ISBN:0721601464] xref: FMA:83505 xref: ZFA:0005236 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000765 {is_inferred="true"} ! erythroblast -is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000765 ! erythroblast intersection_of: has_part CL:0017503 ! basophilic cytoplasm intersection_of: has_part GO:0000792 ! heterochromatin @@ -6070,6 +6856,8 @@ relationship: RO:0002104 PR:000001945 ! has plasma membrane part transferrin rec id: CL:0000550 name: polychromatophilic erythroblast def: "A nucleated, immature erythrocyte in which the nucleus occupies a relatively smaller part of the cell than in its precursor, the basophilic erythroblast. The cytoplasm is beginning to acquire hemoglobin and thus is no longer a purely basophilic, but takes on acidophilic aspects, which becomes progressively more marked as the cell matures. The chromatin of the nucleus is arranged in coarse, deeply staining clumps. This cell is CD71-positive and lacks hematopoeitic lineage markers." [ISBN:0721601464] +subset: human_subset +subset: mouse_subset synonym: "intermediate erythroblast" EXACT [ISBN:0721601464] synonym: "intermediate normoblast" EXACT [ISBN:0721601464] synonym: "polychromatic erythroblast" EXACT [ISBN:0721601464] @@ -6079,7 +6867,6 @@ synonym: "rubricyte" EXACT [ISBN:0721601464] xref: FMA:83506 xref: ZFA:0005241 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000765 {is_inferred="true"} ! erythroblast -is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000765 ! erythroblast intersection_of: has_part CL:0017504 ! polychromatophilic cytoplasm intersection_of: has_part GO:0000792 ! heterochromatin @@ -6092,12 +6879,16 @@ relationship: RO:0002202 CL:0000549 ! develops from basophilic erythroblast [Term] id: CL:0000551 name: unimodal nocireceptor +subset: human_subset +subset: mouse_subset is_a: CL:0000198 ! pain receptor cell [Term] id: CL:0000552 name: orthochromatic erythroblast def: "The final stage of the nucleated, immature erythrocyte, before nuclear loss. Typically the cytoplasm is described as acidophilic, but it still shows a faint polychromatic tint. The nucleus is small and initially may still have coarse, clumped chromatin, as in its precursor, the polychromatophilic erythroblast, but ultimately it becomes pyknotic, and appears as a deeply staining, blue-black, homogeneous structureless mass. The nucleus is often eccentric and sometimes lobulated." [ISBN:0721601464] +subset: human_subset +subset: mouse_subset synonym: "acidophilic erythroblast" EXACT [ISBN:0721601464] synonym: "eosinophilic erythroblast" EXACT [ISBN:0721601464] synonym: "late erythoblast" EXACT [] @@ -6119,6 +6910,8 @@ def: "The earliest cytologically identifiable precursor in the thrombocytic seri comment: Lineage negative is described here as CD2-negative, CD3-negative, CD4-negative, CD5-negative, CD8a-negative, CD14-negative, CD19-negative, CD20-negative, CD56-negative, Ly6g-negative, and Ter119-negative. subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "CFU-Meg" EXACT [PMID:11722431, PMID:12482498] synonym: "colony-forming unit-megakaryocyte" EXACT [] synonym: "Meg-CFC" EXACT [PMCID:PMC1794060] @@ -6171,13 +6964,17 @@ property_value: RO:0002175 NCBITaxon:9606 id: CL:0000554 name: gastrin stimulating hormone secreting cell def: "A peptide hormone secreting cell that secretes gastrin stimulating hormone." [GOC:tfm] +subset: human_subset +subset: mouse_subset is_a: CL:0000167 ! peptide hormone secreting cell [Term] id: CL:0000555 name: neuronal brush cell subset: cellxgene_subset -is_a: CL:0000117 ! CNS neuron (sensu Vertebrata) +subset: human_subset +subset: mouse_subset +is_a: CL:2000029 ! central nervous system neuron [Term] id: CL:0000556 @@ -6187,6 +6984,8 @@ comment: Megakaryocytes are reportedly CD181-positive and CD182-positive. subset: blood_and_immune_upper_slim subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "megacaryocyte" EXACT [] synonym: "megalocaryocyte" EXACT [] synonym: "megalokaryocyte" EXACT [] @@ -6206,6 +7005,8 @@ def: "A hematopoietic progenitor cell that is committed to the granulocyte and m comment: Originally described in the dendritic cell ontology (DC_CL:0000042)(PMID:19243617). GMPs are reportedly CD16-positive, CD32-positive, CD34-positive, CD38-positive, CD45RA-positive, CD110-negative, CD117-positive, CD123-positive, and SCA1-negative. subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "CFU-C , Colony forming unit in culture" BROAD [http://www.copewithcytokines.de] synonym: "CFU-GM" RELATED OMO:0003000 [ISBN:0721601464, PMCID:PMC2213186, PMCID:PMC548021] synonym: "colony forming unit granulocyte macrophage" EXACT [ISBN:0721601464, PMCID:PMC2213186, PMCID:PMC548021] @@ -6213,12 +7014,11 @@ synonym: "GMP" RELATED OMO:0003000 [ISBN:0721601464, PMCID:PMC2213186, PMCID:PMC synonym: "granulocyte-macrophage progenitor" EXACT [ISBN:0721601464, PMCID:PMC2213186, PMCID:PMC548021] synonym: "granulocyte/monocyte precursor" EXACT [] synonym: "granulocyte/monocyte progenitor" EXACT [] +xref: https://cellxgene.cziscience.com/cellguide/CL_0000557 xref: ZFA:0009251 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000763 ! myeloid cell is_a: CL:0001012 ! CD7-negative lymphoid progenitor OR granulocyte monocyte progenitor -is_a: CL:0011026 ! progenitor cell is_a: CL:1001610 ! bone marrow hematopoietic cell -is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0002032 ! hematopoietic oligopotent progenitor cell intersection_of: capable_of GO:0030225 ! macrophage differentiation intersection_of: capable_of GO:0030851 ! granulocyte differentiation @@ -6236,6 +7036,7 @@ relationship: has_part PR:000001944 ! transcription factor PU.1 relationship: has_part PR:000005307 ! CCAAT/enhancer-binding protein alpha relationship: RO:0002104 PR:000001865 ! has plasma membrane part interleukin-3 receptor class 2 alpha chain property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nGranulocyte monocyte progenitor cells (GMP cells), originating from hematopoietic stem cells in the bone marrow, are a critical intermediate in myeloid cell development. Positioned at a key differentiation juncture, these cells exhibit bidirectional potential, giving rise to both granulocyte and monocyte lineages.\nTheir primary role is to generate mature granulocytes and monocytes, essential components of the body's innate immunity and inflammatory responses. Granulocytes, such as neutrophils, eosinophils, and basophils, contribute to the first line of defense against infections by migrating to the infection site and phagocytosing pathogens. Monocytes can differentiate into macrophages or dendritic cells, playing diverse roles in immune responses." xsd:string {xref="DOI:10.1016/j.immuni.2017.10.021", xref="DOI:10.1146/annurev-immunol-081022113627", xref="DOI:10.1186/2050-7771-2-1"} [Term] id: CL:0000558 @@ -6243,12 +7044,13 @@ name: reticulocyte def: "An immature erythrocyte that changes the protein composition of its plasma membrane by exosome formation and extrusion. The types of protein removed differ between species though removal of the transferrin receptor is apparent in mammals and birds." [GOC:add, GOC:tfm, PMID:15946868, PMID:2037622] subset: blood_and_immune_upper_slim subset: cellxgene_subset +subset: human_subset +subset: mouse_subset xref: BTO:0001173 xref: CALOHA:TS-0864 xref: MESH:D012156 xref: ZFA:0009252 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000764 {is_inferred="true"} ! erythroid lineage cell -is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000764 ! erythroid lineage cell intersection_of: capable_of GO:0071971 ! extracellular exosome assembly intersection_of: CL:4030046 PR:000001002 ! lacks_plasma_membrane_part CD19 molecule @@ -6285,12 +7087,13 @@ def: "A precursor in the monocytic series, being a cell intermediate in developm comment: Morphology: Mononuclear cell, diameter 14-18 _M, fine azurophilic granules; markers: CD11b (shared with many other myeloid cells); location: Adult: bone marrow; Fetal: Liver, Yolk Sac; role or process: hematopoiesis, monocyte development; lineage: hematopoietic, myeloid. subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset xref: BTO:0004657 xref: FMA:83551 xref: ZFA:0009253 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000763 ! myeloid cell is_a: CL:0002194 {is_inferred="true"} ! monopoietic cell -is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0002194 ! monopoietic cell intersection_of: capable_of GO:0030224 ! monocyte differentiation intersection_of: has_part GO:0042582 ! azurophil granule @@ -6305,6 +7108,8 @@ id: CL:0000560 name: band form neutrophil def: "A late neutrophilic metamyelocyte in which the nucleus is indented to more than half the distance to the farthest nuclear margin but in no area being condensed to a single filament. The nucleus is in the form of a curved or coiled band, not having acquired the typical multilobar shape of the mature neutrophil. These cells are fMLP receptor-positive, CD11b-positive, CD35-negative, and CD49d-negative." [GOC:add, GOC:dsd, GOC:tfm, http://www.cap.org, ISBN:0721601464, PMID:10618520, PMID:12560239, PMID:15514007] comment: Found in the Band 1 fraction. +subset: human_subset +subset: mouse_subset synonym: "band" BROAD [] synonym: "band cell" BROAD [] synonym: "band form" BROAD [] @@ -6341,6 +7146,8 @@ def: "Interneuron of the vertebrate retina. They integrate, modulate, and interp subset: cellxgene_subset subset: eye_upper_slim subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "AC" RELATED OMO:0003000 [doi:10.1038/s41598-020-66092-9] synonym: "ACs" RELATED OMO:0003004 [doi:10.1038/s41598-020-66092-9] synonym: "amacrine neuron" EXACT [] @@ -6359,6 +7166,8 @@ property_value: RO:0002175 NCBITaxon:9606 id: CL:0000562 name: nucleate erythrocyte def: "An erythrocyte having a nucleus." [GOC:add, GOc:tfm] +subset: human_subset +subset: mouse_subset synonym: "RBC" BROAD [] synonym: "red blood cell" BROAD [] xref: ZFA:0009256 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} @@ -6381,6 +7190,8 @@ id: CL:0000564 name: neutrophilic promyelocyte def: "A promyelocyte committed to the neutrophil lineage. This cell type is GATA-1-positive, C/EBPa-positive, AML-1-positive, MPO-positive, has low expression of PU.1 transcription factor and lacks lactotransferrin expression." [GOC:add, GOC:dsd, GOC:tfm, ISBN:0721601464, PMID:12560239, PMID:15514007] comment: These cells are CD11b-negative, CD15-positive, CD16-negative, CD49d-positive, CD68-positive, CD35-negative, and fMLP receptor-negative. They are found in the Band 3 fraction. +subset: human_subset +subset: mouse_subset synonym: "neutrophilic premyelocyte" EXACT [] synonym: "neutrophilic progranulocyte" EXACT [] xref: FMA:84196 @@ -6407,6 +7218,8 @@ relationship: RO:0002202 CL:0000042 ! develops from neutrophilic myeloblast id: CL:0000565 name: fat body cell def: "A cell found in fat bodies whose primary function is intermediary metabolism." [FB:ma] +subset: human_subset +subset: mouse_subset is_a: CL:0000325 ! stuff accumulating cell [Term] @@ -6414,12 +7227,13 @@ id: CL:0000566 name: angioblastic mesenchymal cell def: "A mesenchymal stem cell capable of developing into blood vessel endothelium." [GOC:dsd, GOC:tfm, PMID:12768659] comment: These cells are reportedly CD31-positive, CD34-positive, CD144-positive, CD309-positive, and TAL1-positive. +subset: human_subset +subset: mouse_subset synonym: "angioblast" EXACT [] synonym: "chondroplast" EXACT [] xref: ZFA:0009258 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000134 {is_inferred="true"} ! mesenchymal stem cell is_a: CL:0011026 ! progenitor cell -is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000134 ! mesenchymal stem cell intersection_of: RO:0002104 PR:000001444 ! has plasma membrane part cadherin-5 intersection_of: RO:0002104 PR:000002112 ! has plasma membrane part vascular endothelial growth factor receptor 2 @@ -6432,12 +7246,16 @@ relationship: RO:0002202 CL:0000134 ! develops from mesenchymal stem cell [Term] id: CL:0000567 name: polymodal nocireceptor +subset: human_subset +subset: mouse_subset is_a: CL:0000198 ! pain receptor cell [Term] id: CL:0000568 name: amine precursor uptake and decarboxylation cell def: "A cell that originates in the neural crest, that has certain cytochemical and ultrastructural characteristics and is found scattered throughout the body; types include melanocytes, the cells of the chromaffin system, and cells in the hypothalamus, hypophysis, thyroid, parathyroids, lungs, gastrointestinal tract, and pancreas. This cell type concentrates the amino acid precursors of certain amines and decarboxylate them, forming amines that function as regulators and neurotransmitters. This cell type produces substances such as epinephrine, norepinephrine, dopamine, serotonin, enkephalin, somatostatin, neurotensin, and substance P, the actions of which may affect contiguous cells, nearby groups of cells, or distant cells, thus functioning as local or systemic hormones. The name is an acronym for amine precursor uptake and decarboxylation cell." [GOC:tfm, ISBN:0721662544] +subset: human_subset +subset: mouse_subset synonym: "APUD cell" EXACT [] xref: BTO:0003866 xref: FMA:83114 @@ -6449,6 +7267,8 @@ id: CL:0000569 name: cardiac mesenchymal cell def: "A mesenchymal cell found in the developing heart and that develops into some part of the heart. These cells derive from intra- and extra-cardiac sources, including the endocardium, epicardium, neural crest, and second heart field." [PMID:18816864] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset xref: ZFA:0009259 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0008019 ! mesenchymal cell is_a: CL:2000073 ! migratory cardiac neural crest cell @@ -6460,6 +7280,8 @@ relationship: RO:0002203 CL:0002494 ! develops into cardiocyte id: CL:0000570 name: parafollicular cell def: "A neuroepithelial cells that occurs singly or in small groups, close to the outer follicular borders but within the follicular basement membrane of the thyroid. Expresses a form of the neural cell adhesion molecule (N-CAM) on their surface. Secretes calcitonin, 5-hydroxytryptamine and dopamine." [GOC:tfm, ISBN:0517223651] +subset: human_subset +subset: mouse_subset synonym: "C cell" EXACT [] synonym: "C cell of thyroid gland" EXACT [FMA:68653] synonym: "clear cell of thyroid gland" EXACT [FMA:68653] @@ -6468,10 +7290,10 @@ synonym: "thyroid parafollicular cell" EXACT [FMA:68653] xref: FMA:68653 xref: SCTID:176770005 xref: ZFA:0009260 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +is_a: CL:0000150 ! glandular secretory epithelial cell is_a: CL:0000443 {is_inferred="true"} ! calcitonin secreting cell is_a: CL:0000458 ! serotonin secreting cell is_a: CL:0000710 {is_inferred="true"} ! neurecto-epithelial cell -is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000710 ! neurecto-epithelial cell intersection_of: capable_of GO:0001820 ! serotonin secretion intersection_of: capable_of GO:0014046 ! dopamine secretion @@ -6486,6 +7308,8 @@ relationship: RO:0002202 CL:0000333 ! develops from migratory neural crest cell id: CL:0000571 name: leucophore def: "A pigment cell derived from the neural crest. Contains uric acid or other purine crystals deposited in stacks called leucosomes. The crystals reflect light and this gives a white appearance under white light." [SANBI:mhl] +subset: human_subset +subset: mouse_subset xref: ZFA:0009261 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: BFO:0000002 is_a: CL:0000147 ! pigment cell @@ -6498,6 +7322,8 @@ name: retinal cone cell def: "One of the two photoreceptor cell types in the vertebrate retina. In cones the photopigment is in invaginations of the cell membrane of the outer segment. Cones are less sensitive to light than rods, but they provide vision with higher spatial and temporal acuity, and the combination of signals from cones with different pigments allows color vision." [MESH:D017949] subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "cone" RELATED [doi:10.1038/s41598-020-66092-9] xref: BTO:0001036 xref: CALOHA:TS-0866 @@ -6511,6 +7337,8 @@ property_value: RO:0002175 NCBITaxon:9606 id: CL:0000574 name: erythrophore def: "A pigment cell derived from the neural crest. Contains pteridine and/or carotenoid pigments in structures called pterinosomes or erythrosomes. This gives an orange to red appearance." [SANBI:mhl] +subset: human_subset +subset: mouse_subset xref: ZFA:0009263 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: BFO:0000002 is_a: CL:0000147 ! pigment cell @@ -6525,6 +7353,8 @@ def: "An epithelial cell of the cornea." [GOC:tfm] subset: cellxgene_subset subset: eye_upper_slim subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "epithelial cell of cornea" EXACT [FMA:70551] xref: BTO:0004298 xref: CALOHA:TS-0173 @@ -6546,6 +7376,8 @@ subset: blood_and_immune_upper_slim subset: cellxgene_subset subset: general_cell_types_upper_slim subset: human_reference_atlas +subset: human_subset +subset: mouse_subset xref: BTO:0000876 xref: CALOHA:TS-0638 xref: FMA:62864 @@ -6571,6 +7403,8 @@ alt_id: CL:0002065 def: "A subtype of enteroendocrine cells found in the gastrointestinal mucosa, particularly in the glands of pyloric antrum; duodenum; and ileum. These cell type secretes serotonin and some neurotransmitters including enkephalins and substance P. Their secretory granules stain readily with silver (argentaffin stain)." [PMID:9505449] subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "argentaffin cell" EXACT [] synonym: "enterochromaffin cell" EXACT [] synonym: "Kulchitsky cell" EXACT [] @@ -6582,16 +7416,17 @@ is_a: CL:0000164 ! enteroendocrine cell is_a: CL:0000166 ! chromaffin cell is_a: CL:0000458 ! serotonin secreting cell is_a: CL:0000506 ! enkephalin secreting cell -is_a: CL:0002251 ! epithelial cell of alimentary canal relationship: part_of UBERON:0004786 ! gastrointestinal system mucosa property_value: RO:0002175 NCBITaxon:9606 -property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional.\n\nType EC enteroendocrine cells, also known as enterochromaffin cells, are a vital hormone-secreting cell type found in the gastrointestinal tract. These cells are named after their location in the intestines (“entero”) and because they are stainable by chromium salts (“chromaffin”). \nThe primary function of type EC enteroendocrine cells is to act as chemosensors and lies in their capacity to produce and secrete serotonin, also known as 5-hydroxytryptamine (5-HT). Serotonin is a neurotransmitter that plays a significant role in modulating motility, secretion, vasodilation, perception of pain, and appetite in the gastrointestinal system. However, its function is not limited to the gastrointestinal tract; once secreted, serotonin is distributed via the bloodstream and contributes to regulating mood, appetite, and sleep in the brain. \nVia specific chemosensory receptors type EC enteroendocrine cells are able to respond to various environmental, metabolic, and homeostatic stimuli and transduce information from the gut to the nervous system: Food intake, particularly the ingestion of fats and carbohydrates, prompts these cells to produce and release serotonin; the mechanical stimulus of food in the lumen can also trigger release. The distribution, function, and responsiveness of type EC cells reveal them as a crucial link between the intestinal environment, the nervous system, and the regulation of numerous bodily functions." xsd:string {xref="DOI:10.1016/0166-4328(96)00075-7", xref="DOI:10.1016/j.cell.2017.05.034", xref="DOI:10.1038/s41574-019-0168-8", xref="DOI:10.1073/pnas.1804938115"} +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nType EC enteroendocrine cells, also known as enterochromaffin cells, are a vital hormone-secreting cell type found in the gastrointestinal tract. These cells are named after their location in the intestines (“entero”) and because they are stainable by chromium salts (“chromaffin”). \nThe primary function of type EC enteroendocrine cells is to act as chemosensors and lies in their capacity to produce and secrete serotonin, also known as 5-hydroxytryptamine (5-HT). Serotonin is a neurotransmitter that plays a significant role in modulating motility, secretion, vasodilation, perception of pain, and appetite in the gastrointestinal system. However, its function is not limited to the gastrointestinal tract; once secreted, serotonin is distributed via the bloodstream and contributes to regulating mood, appetite, and sleep in the brain. \nVia specific chemosensory receptors type EC enteroendocrine cells are able to respond to various environmental, metabolic, and homeostatic stimuli and transduce information from the gut to the nervous system: Food intake, particularly the ingestion of fats and carbohydrates, prompts these cells to produce and release serotonin; the mechanical stimulus of food in the lumen can also trigger release. The distribution, function, and responsiveness of type EC cells reveal them as a crucial link between the intestinal environment, the nervous system, and the regulation of numerous bodily functions." xsd:string {xref="DOI:10.1016/0166-4328(96)00075-7", xref="DOI:10.1016/j.cell.2017.05.034", xref="DOI:10.1038/s41574-019-0168-8", xref="DOI:10.1073/pnas.1804938115"} [Term] id: CL:0000578 name: experimentally modified cell in vitro def: "A cell in vitro that has undergone physical changes as a consequence of a deliberate and specific experimental procedure." [FB:ma, ReO:mhb] comment: This class has been re-labeled to imply reference only to in vitro experimentally modified cells, similarly, the definition has been slightly updated to reflect this. 'experimentally modified cell' refers only to cells in vitro, and not modified in vivo/in environment cells. There is currently no class representing unmodified in vitro cells (other than the parent 'cell in vitro'), or a class representing modified native cells. More granular subclassing of experimentally modified cell can be found in ReO. MHB 1.12.12 +subset: human_subset +subset: mouse_subset is_a: CL:0001034 ! cell in vitro [Term] @@ -6606,6 +7441,8 @@ id: CL:0000580 name: neutrophilic myelocyte def: "A neutrophil precursor in the granulocytic series, being a cell intermediate in development between a promyelocyte and a metamyelocyte; in this stage, production of primary granules is complete and neutrophil-specific granules has started. No nucleolus is present. This cell type is CD13-positive, CD16-negative, integrin alpha-M-positive, CD15-positive, CD33-positive, CD24-positive, C/EBP-a-positive, C/EBPe-positive, PU.1-positive, lactotransferrin-positive, myeloperoxidase-positive and NGAL-positive." [GOC:add, GOC:dsd, GOC:tfm, http://www.cap.org, ISBN:0721601464, PMID:10618520, PMID:12560239, PMID:15514007] comment: These cells are also CD15-positive, CD35-negative, CD49d-positive, and fMLP receptor-negative. They are found in the Band 2 fraction. +subset: human_subset +subset: mouse_subset xref: BTO:0003455 xref: FMA:83540 xref: ZFA:0009266 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} @@ -6648,11 +7485,12 @@ id: CL:0000581 name: peritoneal macrophage def: "A macrophage resident in the peritoneum under non-inflammatory conditions. Markers include F4/80-high, CD11b-high, CD68-positive, SIGNR1-positive, CD115-high, MHC-II-negative, and Dectin-1-positive." [MESH:D017737, PMID:15771589, PMID:19201820] comment: Markers: Mouse: F4/80-high, CD11b-high, CD68+, SIGNR1+, Dectin-1+. +subset: human_subset +subset: mouse_subset xref: BTO:0001034 xref: FMA:83025 xref: ZFA:0009267 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000864 {is_inferred="true"} ! tissue-resident macrophage -is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000864 ! tissue-resident macrophage intersection_of: capable_of GO:0042742 ! defense response to bacterium intersection_of: CL:4030046 GO:0042613 ! lacks_plasma_membrane_part MHC class II protein complex @@ -6678,6 +7516,8 @@ id: CL:0000582 name: neutrophilic metamyelocyte def: "A neutrophil precursor in the granulocytic series, being a cell intermediate in development between a myelocyte and the band form neutrophil. The protein synthesis seen in earlier stages decreases or stops; the nucleus becomes indented where the indentation is smaller than half the distance to the farthest nuclear margin; chromatin becomes coarse and clumped; specific granules predominate while primary granules are rare; and the cytoplasm becomes amphophilic like that of a mature granulocyte. This cell type is integrin alpha-M-positive, CD13-negative, CD15-positive, CD16-positive, CD33-positive, CD24-positive, fMLP receptor-negative and has expression of C/EBP-a, C/EBP-e, PU.1 transcription factor, lactotransferrin, myeloperoxidase and neutrophil gelatinase associated lipocalin." [GOC:add, GOC:dsd, GOC:tfm, http://www.cap.org, ISBN:0721601464, PMID:10618520, PMID:12560239, PMID:15514007] comment: These cells are also CD35-negative, CD49d-positive, and fMLP receptor-negative. They are found in the Band 2 fraction. +subset: human_subset +subset: mouse_subset synonym: "juvenile neutrophil" EXACT [] xref: FMA:84197 xref: ZFA:0009268 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} @@ -6725,9 +7565,11 @@ relationship: RO:0002202 CL:0000580 ! develops from neutrophilic myelocyte id: CL:0000583 name: alveolar macrophage def: "A tissue-resident macrophage found in the alveoli of the lungs. Ingests small inhaled particles resulting in degradation and presentation of the antigen to immunocompetent cells. Markers include F4/80-positive, CD11b-/low, CD11c-positive, CD68-positive, sialoadhesin-positive, dectin-1-positive, MR-positive, CX3CR1-negative." [GO_REF:0000031, GOC:ana, GOC:dsd, GOC:tfm, MESH:D016676] -comment: Markers: Mouse: F4/80mid, CD11b-/low, CD11c+, CD68+, sialoadhesin+, dectin-1+, MR+, CX3CR1-. +comment: The marker set MSR1, FABP4 can identify the Human cell type alveolar macrophage in the Lung with a confidence of 0.80 (NS-Forest FBeta value). Markers: Mouse: F4/80mid, CD11b-/low, CD11c+, CD68+, sialoadhesin+, dectin-1+, MR+, CX3CR1-. {xref="https://doi.org/10.5281/zenodo.11165918"} subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "dust cell" EXACT [] synonym: "MF.Lu" RELATED [] xref: BTO:0000802 @@ -6736,7 +7578,6 @@ xref: FMA:83023 xref: https://cellxgene.cziscience.com/cellguide/CL_0000583 is_a: CL:0000864 {is_inferred="true"} ! tissue-resident macrophage is_a: CL:1001603 ! lung macrophage -is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000864 ! tissue-resident macrophage intersection_of: capable_of GO:0019882 ! antigen processing and presentation intersection_of: CL:4030046 PR:000001206 ! lacks_plasma_membrane_part CX3C chemokine receptor 1 @@ -6756,9 +7597,10 @@ relationship: RO:0002104 PR:000001813 ! has plasma membrane part adhesion G prot relationship: RO:0002104 PR:000001931 ! has plasma membrane part sialoadhesin relationship: RO:0002104 PR:000002064 ! has plasma membrane part macrosialin relationship: RO:0002104 PR:000002972 ! has plasma membrane part macrophage mannose receptor 1 +relationship: RO:0015004 CLM:1000003 ! has characterizing marker set NS forest marker set of alveolar macrophage (Human Lung). relationship: RO:0015016 PR:000001012 ! has low plasma membrane amount integrin alpha-M property_value: RO:0002175 NCBITaxon:9606 -property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional.\n\nAlveolar macrophages are unique tissue-resident macrophages found in the lungs, specifically in the air sacs or alveoli where gas exchange occurs. They are characterized by specific surface markers including: F4/80-positive, CD11b-/low, CD11c-positive, CD68-positive, sialoadhesin-positive, dectin-1-positive, MR-positive, CX3CR1-negative. These specialized immune cells form a crucial part of the body's defense mechanism, playing important roles in pulmonary health and homeostasis. They are the first line of defense in the pulmonary immune response, acting as scavengers that patrol the alveoli and engulf foreign particles like bacteria, dust, and other debris that enter the lungs through inhalation.\nThe primary function of these alveolar macrophages is phagocytosis, whereby they consume and digest foreign substances, dead cells, and other particulates. In the lung, alveolar macrophages are also responsible for clearing surfactant. Additionally, alveolar macrophages also play an integral role in initiating the immune response, as they secrete several pro-inflammatory cytokines and chemokines that recruit other immune cells to the site of infection or inflammation.\nBeyond their role in host defense, alveolar macrophages contribute to tissue remodeling and wound repair in the lungs, aiding in maintaining lung integrity. They also regulate local inflammation and control the immune response to prevent excessive inflammation that may be harmful. However, an imbalance in the function of alveolar macrophages can contribute to various lung diseases. Abnormal alveolar macrophage activation has been implicated in chronic inflammatory diseases such as emphysema, asthma, and fibrosis." xsd:string {xref="DOI:10.1007/s00424-017-1965-3", xref="DOI:10.1016/j.cellimm.2018.01.005", xref="DOI:10.1038/nri3600", xref="DOI:10.14348/molcells.2021.0058"} +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nAlveolar macrophages are unique tissue-resident macrophages found in the lungs, specifically in the air sacs or alveoli where gas exchange occurs. They are characterized by specific surface markers including: F4/80-positive, CD11b-/low, CD11c-positive, CD68-positive, sialoadhesin-positive, dectin-1-positive, MR-positive, CX3CR1-negative. These specialized immune cells form a crucial part of the body's defense mechanism, playing important roles in pulmonary health and homeostasis. They are the first line of defense in the pulmonary immune response, acting as scavengers that patrol the alveoli and engulf foreign particles like bacteria, dust, and other debris that enter the lungs through inhalation.\nThe primary function of these alveolar macrophages is phagocytosis, whereby they consume and digest foreign substances, dead cells, and other particulates. In the lung, alveolar macrophages are also responsible for clearing surfactant. Additionally, alveolar macrophages also play an integral role in initiating the immune response, as they secrete several pro-inflammatory cytokines and chemokines that recruit other immune cells to the site of infection or inflammation.\nBeyond their role in host defense, alveolar macrophages contribute to tissue remodeling and wound repair in the lungs, aiding in maintaining lung integrity. They also regulate local inflammation and control the immune response to prevent excessive inflammation that may be harmful. However, an imbalance in the function of alveolar macrophages can contribute to various lung diseases. Abnormal alveolar macrophage activation has been implicated in chronic inflammatory diseases such as emphysema, asthma, and fibrosis." xsd:string {xref="DOI:10.1007/s00424-017-1965-3", xref="DOI:10.1016/j.cellimm.2018.01.005", xref="DOI:10.1038/nri3600", xref="DOI:10.14348/molcells.2021.0058"} [Term] id: CL:0000584 @@ -6766,6 +7608,8 @@ name: enterocyte def: "An epithelial cell that has its apical plasma membrane folded into microvilli to provide ample surface for the absorption of nutrients from the intestinal lumen." [SANBI:mhl] subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "differentiated enterocyte" NARROW [https://orcid.org/0000-0001-9610-7627, PMID:33290721] synonym: "mature enterocyte" NARROW [https://orcid.org/0000-0001-9610-7627, PMID:33290721] xref: BTO:0000398 @@ -6775,6 +7619,7 @@ xref: ZFA:0009269 {sssom:mapping_justification="https://w3id.org/semapv/vocab/Un is_a: CL:0000239 ! brush border epithelial cell is_a: CL:0000677 ! gut absorptive cell is_a: CL:0002563 ! intestinal epithelial cell +relationship: RO:0002202 CL:4047019 ! develops from early enterocyte property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -6789,6 +7634,8 @@ id: CL:0000586 name: germ cell def: "The reproductive cell in multicellular organisms." [MESH:D005854] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset xref: BTO:0000535 xref: NCIT:C12597 xref: VHOG:0001534 @@ -6800,12 +7647,16 @@ relationship: capable_of_part_of GO:0009566 ! fertilization id: CL:0000587 name: cold sensing thermoreceptor cell def: "A thermoreceptor cell that detects reduced temperatures." [GOC:tfm] +subset: human_subset +subset: mouse_subset is_a: CL:0000205 ! thermoreceptor cell [Term] id: CL:0000588 name: odontoclast def: "A specialized osteoclast associated with the absorption and removal of cementum." [GOC:add] +subset: human_subset +subset: mouse_subset xref: BTO:0002516 xref: FMA:83027 xref: ZFA:0009270 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} @@ -6818,6 +7669,8 @@ relationship: capable_of GO:0042483 ! negative regulation of odontogenesis id: CL:0000589 name: cochlear inner hair cell def: "A bulbous cell that is medially placed in one row in the organ of Corti. In contrast to the outer hair cells, the inner hair cells are fewer in number, have fewer sensory hairs, and are less differentiated." [MESH:D006199] +subset: human_subset +subset: mouse_subset synonym: "inner hair cell" BROAD [] xref: BTO:0003667 xref: FMA:62365 @@ -6827,6 +7680,8 @@ is_a: CL:4023120 ! cochlea auditory hair cell id: CL:0000590 name: small luteal cell def: "A progesterone secreting cell in the corpus luteum that develops from theca cells." [GOC:tfm, MESH:D008184] +subset: human_subset +subset: mouse_subset synonym: "small lutein cell" EXACT [] synonym: "theca lutein cell" EXACT [] xref: BTO:0002850 @@ -6838,12 +7693,16 @@ relationship: RO:0002202 CL:0000503 ! develops from theca cell id: CL:0000591 name: warmth sensing thermoreceptor cell def: "A thermoreceptor cell that detects increased temperatures." [GOC:tfm, https://orcid.org/0000-0001-5208-3432] +subset: human_subset +subset: mouse_subset is_a: CL:0000205 ! thermoreceptor cell [Term] id: CL:0000592 name: large luteal cell def: "A large, progesterone secreting cell in the corpus luteum that develops from the granulosa cells." [GOC:tfm, MESH:D008184] +subset: human_subset +subset: mouse_subset synonym: "granulosa lutein cell" EXACT [] synonym: "granulosoluteocytus" RELATED [] xref: FMA:18689 @@ -6855,6 +7714,8 @@ relationship: RO:0002202 CL:0000501 ! develops from granulosa cell id: CL:0000593 name: androgen secreting cell def: "A steroid hormone secreting cell that secretes androgen." [GOC:tfm] +subset: human_subset +subset: mouse_subset xref: ZFA:0009271 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000174 ! steroid hormone secreting cell intersection_of: CL:0000151 ! secretory cell @@ -6867,15 +7728,21 @@ name: skeletal muscle satellite cell def: "An elongated, spindle-shaped, cell that is located between the basal lamina and the plasmalemma of a muscle fiber. These cells are mostly quiescent, but upon activation they divide to produce cells that generate new muscle fibers." [GOC:tfm, MESH:D032496, PMID:21849021, PMID:23303905] comment: Skeletal muscle satellite cells are not traditionally referred to as myoblasts. They are a heterogeneous population whose division, following activiation, contributes to the formation of skeletal muscle fibers and to maintenance of the skeletal muscle statelite cell population. subset: cellxgene_subset +subset: human_subset +subset: mouse_subset +xref: https://cellxgene.cziscience.com/cellguide/CL_0000594 xref: ZFA:0009272 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000188 ! cell of skeletal muscle is_a: CL:0000680 ! muscle precursor cell +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nSkeletal muscle satellite cells (SMSCs) are a type of adult stem cell that nestles on the outer surface of the myofiber, positioned between the sarcolemma (plasma membrane of the muscle cell) and peripheral basement membrane. \nThe primary function of SMSCs lies in their capacity to facilitate the growth and repair of damaged skeletal muscle. Upon muscle injury or trauma, these normally quiescent cells activate, proliferate, and differentiate into myoblasts. These myoblasts subsequently mature and fuse to form myotubes, which ultimately help in the repair and rebuilding of muscle fibers. This response is an integral part of the skeletal muscle's ability to recover from injury and adapt to enhanced or changing physical demands, thereby maintaining and improving muscle function.\nFurthermore, SMSCs also contribute to hypertrophic muscle growth due to resistance exercise and endurance training, with the notable feature of their multi-nucleated nature resulting from the fusion of differentiated myoblasts. The additional nuclei support enhanced protein synthesis, thus allowing the muscle fibers to grow and strengthen in response to exercise. In aging and in diseases, the number or functionality of these cells can decrease, leading to impaired muscle regeneration and progressive muscle weakness." xsd:string {xref="DOI:10.1016/s1357-2725(03)00042-6", xref="DOI:10.1152/physrev.00061.2017", xref="DOI:10.1186/s13287-022-02706-5", xref="DOI:10.1369/0022155411426780", xref="DOI:10.22074/cellj.2016.4714"} [Term] id: CL:0000595 name: enucleate erythrocyte def: "An erythrocyte lacking a nucleus." [GOC:add, GOC:tfm] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "RBC" RELATED OMO:0003000 [] synonym: "red blood cell" BROAD [] is_a: CL:0000225 ! anucleate cell @@ -6905,6 +7772,8 @@ name: pyramidal neuron def: "Pyramidal neurons have a pyramid-shaped soma with a single axon, a large apical dendrite and multiple basal dendrites. The apex and an apical dendrite typically point toward the pial surface and other dendrites and an axon emerging from the base. The axons may have local collaterals but also project outside their region. Pyramidal neurons are found in the cerebral cortex, the hippocampus, and the amygdala." [GOC:tfm, MESH:D017966] subset: BDS_subset subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "projection neuron" EXACT [] synonym: "pyramidal cell" EXACT [] xref: BTO:0003102 @@ -6912,7 +7781,7 @@ xref: FMA:67310 xref: FMA:86775 xref: NIFSTD:sao862606388 xref: ZFA:0009273 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} -is_a: CL:0000104 ! multipolar neuron +is_a: CL:2000029 ! central nervous system neuron intersection_of: CL:0000540 ! neuron intersection_of: bearer_of PATO:0070015 ! pyramidal family morphology relationship: bearer_of PATO:0070015 ! pyramidal family morphology @@ -6936,6 +7805,8 @@ is_a: CL:0000521 ! fungal cell id: CL:0000601 name: cochlear outer hair cell def: "A mechanoreceptor in the organ of Corti. In mammals the outer hair cells are arranged in three rows which are further from the modiolus than the single row of inner hair cells. The motile properties of the outer hair cells may contribute actively to tuning the sensitivity and frequency selectivity of the cochlea." [MESH:D018072] +subset: human_subset +subset: mouse_subset xref: BTO:0003666 xref: FMA:62366 is_a: CL:4023120 ! cochlea auditory hair cell @@ -6944,6 +7815,8 @@ is_a: CL:4023120 ! cochlea auditory hair cell id: CL:0000602 name: pressoreceptor cell def: "A receptor in the vascular system, particularly the aorta and carotid sinus, which is sensitive to stretch of the vessel walls." [MESH:D011311] +subset: human_subset +subset: mouse_subset xref: ZFA:0009274 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:1000082 ! stretch receptor cell @@ -6960,6 +7833,8 @@ name: retinal rod cell def: "One of the two photoreceptor cell types of the vertebrate retina. In rods the photopigment is in stacks of membranous disks separate from the outer cell membrane. Rods are more sensitive to light than cones, but rod mediated vision has less spatial and temporal resolution than cone vision." [MESH:D017948] subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "rod" RELATED [doi:10.1038/s41598-020-66092-9] xref: BTO:0001024 xref: CALOHA:TS-0870 @@ -7002,6 +7877,8 @@ is_a: CL:0000596 ! sexual spore id: CL:0000609 name: vestibular hair cell def: "A mechanoreceptor located in the acoustic maculae and the semicircular canals that mediates the sense of balance, movement, and head position. The vestibular hair cells are connected to accessory structures in such a way that movements of the head displace their stereocilia. This influences the membrane potential of the cells which relay information about movements via the vestibular part of the vestibulocochlear nerve to the brain stem." [GOC:tfm, MESH:D018069] +subset: human_subset +subset: mouse_subset synonym: "vestibular receptor cell" EXACT [] xref: FMA:62351 is_a: CL:0002374 ! ear hair cell @@ -7018,13 +7895,14 @@ id: CL:0000611 name: eosinophil progenitor cell def: "Any granulocytopoietic cell that has part some transcription factor PU.1 and has part some CCAAT/enhancer-binding protein alpha and has part some erythroid transcription factor and lacks plasma membrane part some CD19 molecule and lacks plasma membrane part some CD4 molecule and lacks plasma membrane part some integrin alpha-M and lacks plasma membrane part some CD3 epsilon and lacks plasma membrane part some neural cell adhesion molecule 1 and lacks plasma membrane part some CD2 molecule and lacks plasma membrane part some T-cell surface glycoprotein CD8 alpha chain and lacks plasma membrane part some membrane-spanning 4-domains subfamily A member 1 and lacks plasma membrane part some T-cell surface glycoprotein CD5 and lacks plasma membrane part some CD14 molecule and lacks plasma membrane part some lymphocyte antigen 6G and lacks plasma membrane part some lymphocyte antigen 76 (mouse) and has plasma membrane part some CD34 molecule and has plasma membrane part some ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1 and has plasma membrane part some interleukin-3 receptor class 2 alpha chain and has plasma membrane part some interleukin-5 receptor subunit alpha and has plasma membrane part some mast/stem cell growth factor receptor and is capable of some eosinophil differentiation." [FBC:Autogenerated] comment: These cells are CD34-positive, CD45RA-negative, CD71-negative, and lineage-negative (CD2, CD3 epsilon, CD4, CD5, CD8a, CD14, CD19, CD20, integrin alpha-M, NCAM-1, SCA-1, Ly6G, Ly76). +subset: human_subset +subset: mouse_subset synonym: "CFU-Eo" RELATED OMO:0003000 [] synonym: "colony forming unit eosinophil" RELATED [] synonym: "EoP" RELATED OMO:0003000 [PMCID:PMC2212039, PMCID:PMC2626675] synonym: "eosinophil stem cell" RELATED [] is_a: CL:0000763 ! myeloid cell is_a: CL:0002191 {is_inferred="true"} ! granulocytopoietic cell -is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0002191 ! granulocytopoietic cell intersection_of: capable_of GO:0030222 ! eosinophil differentiation intersection_of: CL:4030046 PR:000001002 ! lacks_plasma_membrane_part CD19 molecule @@ -7074,6 +7952,8 @@ relationship: RO:0002202 CL:0000557 ! develops from granulocyte monocyte progeni id: CL:0000612 name: eosinophilic myelocyte def: "A eosinophil precursor in the granulocytic series, being a cell intermediate in development between a promyelocyte and a metamyelocyte;in this stage, production of primary granules is complete and eosinophil-specific granules has started. No nucleolus is present. These cells are integrin alpha-M-positive, CD13-positive, CD15-positive, CD16-negative, CD24-positive, and CD33-positive." [GOC:add, GOC:dsd, http://www.cap.org, ISBN:0721601464, PMID:19622087] +subset: human_subset +subset: mouse_subset xref: BTO:0003454 xref: FMA:83542 is_a: CL:0000772 {is_inferred="true"} ! immature eosinophil @@ -7101,13 +7981,14 @@ id: CL:0000613 name: basophil progenitor cell def: "A progenitor cell committed to the basophil lineage. This cell lacks hematopoietic lineage markers (lin-negative) and is CD34-positive, T1/ST2-low, CD117-negative, and FceRIa-high. This cell also expresses Gata-1, Gata-2 and C/EBPa." [GOC:add, GOC:dsd, http://www.copewithcytokines.de, PMCID:PMC1312421] comment: BaP are also CD13-low and integrin beta-7-low. They are lin-negative (CD2, CD3e, CD4, CD5, CD8, CD11b, CD14, CD19, CD20, ly6g, ly76, and NCAM-1). They also lack expression of mast cell protease 1 (MCP-1) and microphthalmia-associated transcription factor (mitf). +subset: human_subset +subset: mouse_subset synonym: "BaP" EXACT [] synonym: "basophilic stem cell" RELATED [] synonym: "CFU-Bas" RELATED [] synonym: "colony forming unit basophil" RELATED [] is_a: CL:0000763 ! myeloid cell is_a: CL:0002191 {is_inferred="true"} ! granulocytopoietic cell -is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0002191 ! granulocytopoietic cell intersection_of: capable_of GO:0030221 ! basophil differentiation intersection_of: CL:4030046 PR:000001002 ! lacks_plasma_membrane_part CD19 molecule @@ -7153,6 +8034,8 @@ relationship: RO:0015016 PR:000016401 ! has low plasma membrane amount transmemb id: CL:0000614 name: basophilic myelocyte def: "A basophil precursor in the granulocytic series, being a cell intermediate in development between a promyelocyte and a metamyelocyte; in this stage, production of primary granules is complete and basophil-specific granules has started. No nucleolus is present. Markers are being integrin alpha-M-positive, fucosyltransferase FUT4-positive, CD33-positive, CD24-positive, aminopeptidase N-positive." [GOC:add, GOC:tfm, http://www.cap.org, ISBN:0721601464, PMID:18466030] +subset: human_subset +subset: mouse_subset xref: BTO:0003456 xref: FMA:83543 is_a: CL:0000768 {is_inferred="true"} ! immature basophil @@ -7195,6 +8078,8 @@ id: CL:0000617 name: GABAergic neuron def: "A neuron that uses GABA as a vesicular neurotransmitter" [GOC:tfm] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "GABA-ergic neuron" EXACT [] xref: FBbt:00007228 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:84788 @@ -7210,11 +8095,15 @@ relationship: capable_of GO:0061534 ! gamma-aminobutyric acid secretion, neurotr [Term] id: CL:0000618 name: sheath cell +subset: human_subset +subset: mouse_subset is_a: CL:0000075 ! columnar/cuboidal epithelial cell [Term] id: CL:0000619 name: supporting cell (sensu Nematoda) +subset: human_subset +subset: mouse_subset synonym: "support cell (sensu Nematoda)" EXACT [] is_a: CL:0000378 ! supporting cell (sensu Nematoda and Protostomia) @@ -7229,6 +8118,8 @@ is_obsolete: true id: CL:0000621 name: fusion competent myoblast def: "A myoblast that is committed to a myotube-specific program of differentiation but not yet fused. It undergoes very limited additional proliferation. After fusion, it will take on a muscle identity specified by a `muscle founder cell` (CL:0008006)." [PMID:22274696] +subset: human_subset +subset: mouse_subset is_a: CL:0008018 ! somatic muscle myoblast [Term] @@ -7236,16 +8127,21 @@ id: CL:0000622 name: acinar cell def: "A secretory cell that is grouped together with other cells of the same type to form grape shaped clusters known as acini (singular acinus)." [GOC:tfm, http://www.copewithcytokines.de] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "acinic cell" EXACT [] synonym: "acinous cell" EXACT [] xref: FMA:83625 xref: https://cellxgene.cziscience.com/cellguide/CL_0000622 xref: MESH:D061354 xref: ZFA:0009277 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} -is_a: CL:0000150 ! glandular epithelial cell +is_a: CL:0000150 ! glandular secretory epithelial cell is_a: CL:0000154 ! protein secreting cell +intersection_of: CL:0000150 ! glandular secretory epithelial cell +intersection_of: CL:0000154 ! protein secreting cell +intersection_of: part_of UBERON:0009842 ! glandular acinus relationship: part_of UBERON:0009842 ! glandular acinus -property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional.\n\nAcinar cells are specialized exocrine gland cells that secrete specific enzymes and fluids to aid in digestion. Found primarily in the pancreas and salivary glands, the term acinar is derived from the Latin word 'acinus' which means 'grape'; this is because acinar cells are arranged in a grape-like cluster around small ducts, formulating an acinus structure. \nIn the salivary glands, acinar cells secrete digestive enzymes as well as other substances such as mucus and water. These secretions service the initial stages of the digestive process, preparing the consumed food for onward digestion in the stomach and intestines by lubricating and partially breaking it down. \nIn the pancreas, acinar cells are responsible for synthesizing and secreting a significant amount of digestive enzymes, such as trypsin, chymotrypsin, and amylase. These enzymes are stored in zymogen granules inside the acinar cells until they are dispatched into the small intestine. Once within the small intestine, they break down proteins, carbohydrates, and fats into substances that can be absorbed. This is vital to the effective and efficient digestion and absorption of nutrients from the food we consume. \nAcinar cells have high protein synthesis rates and are susceptible to accumulation of misfolded proteins; the subsequential induction of ER stress is thought to be involved in the development of pancreatitis, a serious inflammatory disease of the exocrine pancreas." xsd:string {xref="DOI:10.1007/BF00710764", xref="DOI:10.1038/nrgastro.2013.36", xref="DOI:10.1097/MOG.0b013e32832ebfac", xref="DOI:10.1111/prd.12116", xref="DOI:10.1152/physrev.00011.2011"} +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nAcinar cells are specialized exocrine gland cells that secrete specific enzymes and fluids to aid in digestion. Found primarily in the pancreas and salivary glands, the term acinar is derived from the Latin word 'acinus' which means 'grape'; this is because acinar cells are arranged in a grape-like cluster around small ducts, formulating an acinus structure. \nIn the salivary glands, acinar cells secrete digestive enzymes as well as other substances such as mucus and water. These secretions service the initial stages of the digestive process, preparing the consumed food for onward digestion in the stomach and intestines by lubricating and partially breaking it down. \nIn the pancreas, acinar cells are responsible for synthesizing and secreting a significant amount of digestive enzymes, such as trypsin, chymotrypsin, and amylase. These enzymes are stored in zymogen granules inside the acinar cells until they are dispatched into the small intestine. Once within the small intestine, they break down proteins, carbohydrates, and fats into substances that can be absorbed. This is vital to the effective and efficient digestion and absorption of nutrients from the food we consume. \nAcinar cells have high protein synthesis rates and are susceptible to accumulation of misfolded proteins; the subsequential induction of ER stress is thought to be involved in the development of pancreatitis, a serious inflammatory disease of the exocrine pancreas." xsd:string {xref="DOI:10.1007/BF00710764", xref="DOI:10.1038/nrgastro.2013.36", xref="DOI:10.1097/MOG.0b013e32832ebfac", xref="DOI:10.1111/prd.12116", xref="DOI:10.1152/physrev.00011.2011"} [Term] id: CL:0000623 @@ -7254,6 +8150,8 @@ def: "A lymphocyte that can spontaneously kill a variety of target cells without subset: cellxgene_subset subset: general_cell_types_upper_slim subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "large granular lymphocyte" BROAD [] synonym: "NK cell" EXACT [] synonym: "null cell" BROAD [] @@ -7286,6 +8184,8 @@ name: CD4-positive, alpha-beta T cell def: "A mature alpha-beta T cell that expresses an alpha-beta T cell receptor and the CD4 coreceptor." [GOC:add, ISBN:0781735149] subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "CD4-positive, alpha-beta T lymphocyte" EXACT [] synonym: "CD4-positive, alpha-beta T-cell" EXACT [] synonym: "CD4-positive, alpha-beta T-lymphocyte" EXACT [] @@ -7304,6 +8204,8 @@ name: CD8-positive, alpha-beta T cell def: "A T cell expressing an alpha-beta T cell receptor and the CD8 coreceptor." [GOC:add, GOC:tfm, ISBN:0781735149] subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "CD8-positive, alpha-beta T lymphocyte" EXACT [] synonym: "CD8-positive, alpha-beta T-cell" EXACT [] synonym: "CD8-positive, alpha-beta T-lymphocyte" EXACT [] @@ -7320,10 +8222,11 @@ id: CL:0000626 name: olfactory granule cell def: "A granule cell that has a soma located in an olfactory bulb granule cell layer. An olfactory granule cell is an interneuron that lacks an axon, makes reciprocal dendro-dendritic synapses with mitral cells and tufted cells and is involved in the fine spatio-temporal tuning of the responses of these principal olfactory bulb neurons to odors." [doi:10.1038/s41598-018-27692-8, GOC:mah] comment: Granule cells are the most abundant neuronal population in the olfactory bulb and are continuously renewed throughout life. {xref="doi:10.1038/s41598-018-27692-8"} +subset: human_subset +subset: mouse_subset synonym: "olfactory bulb granule cell" EXACT [doi:10.1038/s41598-018-27692-8] xref: ZFA:0001694 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000120 ! granule cell -is_a: CL:0012001 ! neuron of the forebrain is_a: CL:1001434 ! olfactory bulb interneuron intersection_of: CL:0000120 ! granule cell intersection_of: RO:0002100 UBERON:0005378 ! has soma location olfactory bulb granule cell layer @@ -7338,6 +8241,8 @@ relationship: RO:0002428 GO:0007608 ! involved in regulation of sensory percepti id: CL:0000627 name: transporting cell def: "A cell involved in transporting nutrients, minerals, water, gases and other chemicals between cells for a variety of purposes including conveying nutrition to other tissues, removing waste products from the tissues, conveying gases for respiration, distributing heat and repelling invasion of foreign substances." [TAIR:sr] +subset: human_subset +subset: mouse_subset is_a: CL:0000000 ! cell [Term] @@ -7352,6 +8257,8 @@ relationship: capable_of GO:0015979 ! photosynthesis id: CL:0000629 name: storage cell def: "A cell that is specialized to store a particular substance(s), which is(are) later released from the store for a particular purpose." [FB:ma] +subset: human_subset +subset: mouse_subset is_a: CL:0000325 ! stuff accumulating cell [Term] @@ -7359,6 +8266,8 @@ id: CL:0000630 name: supporting cell def: "A cell whose primary function is to support other cell types." [FB:ma, GOC:tfm] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "supportive cell" EXACT [] xref: BTO:0002315 xref: ZFA:0009387 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} @@ -7368,6 +8277,8 @@ is_a: CL:0000000 ! cell id: CL:0000631 name: labyrinth supporting cell def: "Cells forming a framework supporting the organ of Corti. Specific cells are those of Claudius, Deiters and Hensen." [MESH:D007760] +subset: human_subset +subset: mouse_subset is_a: CL:0000630 ! supporting cell [Term] @@ -7377,6 +8288,8 @@ def: "A cell that is found in the perisinusoidal space of the liver that is capa comment: Hepatic stellate cells are CD271-positive, desmin-positive, DDR-2-positive, GFAP-positive, synamin-positive, synaptophysin-positive, vimentin-positive, They are capable of producing angiotensin II, fibronectin, laminin, MMP-1, MMP-2, MMP-3, MMP-9, MMP-11, TGF-beta1, TIMP-1, TIMP-2, type I collagen, type III collagen, type IV collagen, and type VI collagen. subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "fat-storing cell" RELATED [] synonym: "hepatic perisinusoidal cell" EXACT [] synonym: "Ito cell" EXACT [] @@ -7389,7 +8302,6 @@ xref: FMA:67763 xref: ZFA:0009279 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000057 ! fibroblast is_a: CL:0000327 ! extracellular matrix secreting cell -is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0002320 ! connective tissue cell intersection_of: part_of UBERON:0002107 ! liver intersection_of: RO:0002104 PR:000007939 ! has plasma membrane part glial fibrillary acidic protein @@ -7401,6 +8313,8 @@ property_value: RO:0002175 NCBITaxon:9606 id: CL:0000633 name: Hensen cell def: "A tall supporting cell that is arranged in rows adjacent to the last row of outer phalangeal cells. This cell type constitutes the outer border of the organ of Corti." [GOC:tfm, ISBN:0721662544] +subset: human_subset +subset: mouse_subset synonym: "cell of Hensen" EXACT [] synonym: "external limiting cell of organ of Corti" EXACT [] synonym: "Hensen's cell" EXACT [] @@ -7411,6 +8325,8 @@ is_a: CL:0002490 ! organ of Corti supporting cell id: CL:0000634 name: Claudius cell def: "A cuboidal cell which along with Boettcher's cells form the floor of the external spiral sulcus, external to the organ of Corti." [GOC:tfm, ISBN:0721662544] +subset: human_subset +subset: mouse_subset synonym: "cell of Claudius" EXACT [] synonym: "external supporting cell of Claudius" RELATED [] xref: FMA:79802 @@ -7420,6 +8336,8 @@ is_a: CL:0002315 ! supporting cell of cochlea id: CL:0000635 name: Deiter's cell def: "The outer phalangeal cells of the organ of Corti. This cell holds the base of the hair cell in a cup-shaped depression." [GOC:tfm, http://www.britannica.com/EBchecked/topic/156177/Deiters-cell, ISBN:0721662544] +subset: human_subset +subset: mouse_subset synonym: "Deiters cell" EXACT [] synonym: "outer phalangeal cell" EXACT [] xref: FMA:75725 @@ -7432,6 +8350,8 @@ def: "Astrocyte-like radial glial cell that extends vertically throughout the re subset: cellxgene_subset subset: eye_upper_slim subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "Muller cell" EXACT MISSPELLING [doi:10.21769/BioProtoc.4179] synonym: "Muller glia" EXACT [] synonym: "Müller cell" EXACT [] @@ -7446,8 +8366,10 @@ property_value: RO:0002175 NCBITaxon:9606 id: CL:0000637 name: chromophil cell of anterior pituitary gland def: "A cell that stains readily in the anterior pituitary gland." [GOC:tfm, ISBN:0618947256] +subset: human_subset +subset: mouse_subset xref: FMA:83089 -is_a: CL:0000150 ! glandular epithelial cell +is_a: CL:0000150 ! glandular secretory epithelial cell is_a: CL:0000166 ! chromaffin cell is_a: CL:0000167 ! peptide hormone secreting cell is_a: CL:2000004 ! pituitary gland cell @@ -7459,6 +8381,8 @@ relationship: part_of UBERON:0002196 ! adenohypophysis id: CL:0000638 name: acidophil cell of pars distalis of adenohypophysis def: "An acidophilic chromophil cell that of the anterior pituitary gland." [GOC:tfm] +subset: human_subset +subset: mouse_subset synonym: "acidophil cell of pars anterior of adenohypophysis" EXACT [] synonym: "acidophil of pars anterior of adenohypophysis" EXACT [] synonym: "acidophil of pars distalis of adenohypophysis" EXACT [] @@ -7471,6 +8395,8 @@ relationship: part_of UBERON:0006964 ! pars distalis of adenohypophysis id: CL:0000639 name: basophil cell of pars distalis of adenohypophysis def: "A basophilic chromophil cell that of the anterior pituitary gland." [GOC:tfm] +subset: human_subset +subset: mouse_subset synonym: "basophil cell of anterior lobe of hypophysis" EXACT [] synonym: "beta cell" RELATED [] synonym: "pituitary beta cell" RELATED [] @@ -7481,6 +8407,8 @@ is_a: CL:0000637 ! chromophil cell of anterior pituitary gland id: CL:0000641 name: chromophobe cell def: "A cell that is resistant to stains." [GOC:tfm] +subset: human_subset +subset: mouse_subset synonym: "chromophobic cell" EXACT [] xref: FMA:83626 is_a: CL:0000163 ! endocrine cell @@ -7490,6 +8418,8 @@ id: CL:0000642 name: folliculostellate cell def: "An agranular supporting cell of the anterior pituitary (adenohypophysis) that is characterized by a star-like morphology and ability to form follicles. Folliculostellate cells communicate with each other and with endocrine cells via gap junctions." [doi:10.23937/2572-407X.1510006, JB:jb, PMID:10495875, PMID:15961560] comment: Folliculostellate cells are a heterogeneous group of cells rather than a single cell type, with different morphology and gene expression profiles. Due to this heterogeneity, it is unclear if different properties that have been attributed to folliculostellate cells (pluripotent, proliferative, phagocytic) are common in all folliculostellate cells or limited to particular subsets. {xref="doi:10.23937/2572-407X.1510006", xref="PMID:34734454", xref="PMID:31620083", xref="PMID:18287078"} +subset: human_subset +subset: mouse_subset synonym: "folliculo-stellate cell" EXACT [doi:10.23937/2572-407X.1510006] synonym: "FS cell" RELATED OMO:0003000 [PMID:34734454] synonym: "FSC" RELATED OMO:0003000 [doi:10.23937/2572-407X.1510006] @@ -7506,6 +8436,8 @@ name: Bergmann glial cell def: "Type of radial astrocyte in the cerebellar cortex that have their cell bodies in the Purkinje cell layer and processes that extend into the molecular layer, terminating with bulbous endfeet at the pial surface. Bergmann glia express high densities of glutamate transporters that limit diffusion of the neurotransmitter glutamate during its release from synaptic terminals. Besides their role in early development of the cerebellum, Bergmann glia are also required for the pruning or addition of synapses." [GOC:tfm, http://www.neurolex.org/wiki/Category\:Bergmann_Glial_Cell] subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "Bergmann astrocyte" EXACT [] synonym: "Bergmann glial cell of cerebellum" EXACT [] xref: FMA:54559 @@ -7517,6 +8449,8 @@ property_value: RO:0002175 NCBITaxon:9606 id: CL:0000645 name: pituicyte def: "A glial cell of astrocytic lineage with long processes running parallel to adjacent axons in the proximal infundibulum of the neurohypophysis. These processes form a three-dimensional network among the axons of the hypothalamic neurosecretory cells and are connected by gap junctions which provide for their metabolic coupling. This cell type constitutes most of the nonexcitable tissue in the neurohypophsis; function may include possibly acting as an intermediate in the modulation of oxytocin and vasopressin release. This cell type is highly variable in size and shape and commonly contain lipid droplets and deposits of lipochrome pigment." [http://en.wikipedia.org/wiki/Pituicyte, ISBN:0412046911, ISBN:0517223651, PMID:31915267] +subset: human_subset +subset: mouse_subset xref: BTO:0003793 xref: FMA:83503 is_a: CL:0012000 ! astrocyte of the forebrain @@ -7529,6 +8463,8 @@ name: basal cell def: "Undifferentiated; mitotic stem cell for other epithelial cell types; rounded or elliptical with little cytoplasm and few organelles; contain cytokeratin intermediate filament." [GOC:tfm, ISBN:0517223651] subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset xref: BTO:0000939 xref: FMA:62516 is_a: CL:0000036 ! epithelial fate stem cell @@ -7540,6 +8476,8 @@ name: multinucleated giant cell def: "A phagocytic syncytial cell formed by the fusion of macrophages, occurs in chronic inflammatory responses to persistent microorganism such as M.tuberculosis, component of granulomas. Sometimes used to refer to megakaryocytes." [GOC:add, GOC:tfm, ISBN:0702022918, ISBN:0702024783, PMID:33348900, Wikipedia:Giant_cell] comment: Role or process: Chronic infection, granulomatous inflammation. Consider also megakaryocyte (CL:0000556) as sometimes multinucleated giant cell is used to refer to this. subset: blood_and_immune_upper_slim +subset: human_subset +subset: mouse_subset synonym: "foreign body giant cell" EXACT [ISBN:0702022918, ISBN:0702024783] synonym: "Langerhans giant cell" EXACT [ISBN:0702022918, ISBN:0702024783] synonym: "macrophage polykaryon" EXACT [ISBN:0702022918, ISBN:0702024783] @@ -7565,6 +8503,8 @@ name: kidney granular cell alt_id: CL:0000461 def: "A smooth muscle cell that synthesizes, stores, and secretes the enzyme renin. This cell type are located in the wall of the afferent arteriole at the entrance to the glomerulus. While having a different origin than other kidney smooth muscle cells, this cell type expresses smooth muscle actin upon maturation." [GOC:cvs, GOC:tfm, PMID:11457727] subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "JG cell" EXACT [] synonym: "juxtaglomerular cell" BROAD [] synonym: "renin secreting cell" EXACT [] @@ -7586,6 +8526,8 @@ alt_id: CL:0002186 def: "A cell with delicate radiating processes known as desmosomes that form intercellular bridges between other cells of this type. This cell type forms the stratum spinosum (prickle cell layer). A function of this cell is to generate keratin." [GOC:tfm, ISBN:0721662544, ISBN:0815332181] subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "prickle cell of epidermis" EXACT [] xref: FMA:69059 is_a: CL:0000312 ! keratinocyte @@ -7598,6 +8540,8 @@ name: mesangial cell def: "A cell type that encapsulates the capillaries and venules in the kidney. This cell secretes mesangial matrix that provides the structural support for the capillaries." [GOC:tfm, http://www.copewithcytokines.de/cope.cgi?key=mesangial%20cells] comment: Do all of these cells really develop from some mesenchymal stem cell? subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "kidney mesangial cell" EXACT [] xref: BTO:0000853 xref: CALOHA:TS-0617 @@ -7613,17 +8557,23 @@ id: CL:0000651 name: mucous neck cell def: "A mucus-secreting cell, with numerous apical secretory vesicles containing mucins; nucleus are basally displaced; numerous at the neck of mucus secreting glands" [GOC:tfm] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "neck cell" BROAD [] -is_a: CL:0000150 ! glandular epithelial cell +is_a: CL:0000150 ! glandular secretory epithelial cell is_a: CL:0000319 ! mucus secreting cell [Term] id: CL:0000652 name: pinealocyte def: "This cell type produces and secretes melatonin and forms the pineal parenchyma. Extending from each cell body, which has a spherical, oval or lobulated mucleus, are one or more tortuous basophilic processes, containing parallel microtubules known as synaptic ribbons. These processes end in expanded terminal buds near capillaries or less, frequently, ependymal cells of the pineal recess. The terminal buds contain granular endoplasmic reticulum, mitochondria and electron-dense cored vesicles, which store monoamines and polypeptide hormones, release of which appears to require sympathetic innervation." [GOC:tfm, http://en.wikipedia.org/wiki/Pinealocyte, ISBN:0517223651, PMID:16687276] +subset: cellxgene_subset +subset: human_subset +subset: mouse_subset xref: BTO:0001068 xref: FMA:83417 xref: ZFA:0009284 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +is_a: CL:0000150 ! glandular secretory epithelial cell is_a: CL:0000163 ! endocrine cell is_a: CL:0000710 ! neurecto-epithelial cell is_a: CL:0002319 ! neural cell @@ -7636,6 +8586,8 @@ name: podocyte def: "A specialized kidney epithelial cell, contained within a glomerulus, that contains \"feet\" that interdigitate with the \"feet\" of other podocytes." [GOC:tfm, https://doi.org/10.1101/2021.10.10.463829] subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "epithelial cell of visceral layer of glomerular capsule" BROAD [FMA:70967] synonym: "glomerular podocyte" EXACT [FMA:70967] synonym: "glomerular visceral epithelial cell" EXACT [] @@ -7652,13 +8604,15 @@ intersection_of: part_of UBERON:0005751 ! glomerular visceral epithelium relationship: part_of UBERON:0005751 ! glomerular visceral epithelium property_value: RO:0002175 NCBITaxon:9606 property_value: seeAlso "https://github.com/obophenotype/cell-ontology/issues/1460" xsd:string -property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional.\n\nPodocytes are highly specialized, terminally differentiated glomerular visceral epithelial cells that wrap around the capillaries in the kidneys. They play an essential role in kidney function, particularly in the filtration selectivity of the glomerulus. Each podocyte is characterized by a unique architecture with a large cell body, ‘major processes’ extending outwardly from the cell body and ‘foot processes’, also known as pedicels, which surround. the glomerular capillary loops\nPodocytes represent the last barrier of the glomerular filtration membrane in the kidney. This barrier prevents the leakage of plasma proteins from the blood into the urine, hence maintaining protein homeostasis in the body. The foot processes of the podocytes interdigitate with those from neighboring cells. The cell-cell junctions between the foot processes, the slit-diaphragms, are thought to create a molecular sensor of renal filtration that prevents the passage of macromolecules while allowing water and small solutes to pass.\nPodocytes also contribute to the glomerular basement membrane by secreting collagen and maintain glomerular endothelial cell fenestration by secreting VEGFA. They have been shown to play a role in inducing cytoskeletal regulation, cell adhesion, and inflammatory response, consistent with their essential function in the kidney. \nThe importance of podocytes is further emphasized by the effects of their damage or loss. Abnormalities in podocytes often result in severe kidney diseases (podocytopathies), including focal segmental glomerulosclerosis (FSGS) and minimal change disease (MCD). Injury to the podocytes can result in \"effacement\" or flattening of foot processes, leading to increased permeability of the filtration barrier and proteinuria (an excess of serum protein in urine) which is a common symptom of kidney diseases." xsd:string {xref="DOI:10.1038/s41467-022-33748-1", xref="DOI:10.1038/s41572-020-0196-7", xref="DOI:10.1146/annurev-physiol-020911-153238", xref="DOI:10.1159/000481633", xref="DOI:10.3389/fcell.2021.771931"} +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nPodocytes are highly specialized, terminally differentiated glomerular visceral epithelial cells that wrap around the capillaries in the kidneys. They play an essential role in kidney function, particularly in the filtration selectivity of the glomerulus. Each podocyte is characterized by a unique architecture with a large cell body, ‘major processes’ extending outwardly from the cell body and ‘foot processes’, also known as pedicels, which surround. the glomerular capillary loops\nPodocytes represent the last barrier of the glomerular filtration membrane in the kidney. This barrier prevents the leakage of plasma proteins from the blood into the urine, hence maintaining protein homeostasis in the body. The foot processes of the podocytes interdigitate with those from neighboring cells. The cell-cell junctions between the foot processes, the slit-diaphragms, are thought to create a molecular sensor of renal filtration that prevents the passage of macromolecules while allowing water and small solutes to pass.\nPodocytes also contribute to the glomerular basement membrane by secreting collagen and maintain glomerular endothelial cell fenestration by secreting VEGFA. They have been shown to play a role in inducing cytoskeletal regulation, cell adhesion, and inflammatory response, consistent with their essential function in the kidney. \nThe importance of podocytes is further emphasized by the effects of their damage or loss. Abnormalities in podocytes often result in severe kidney diseases (podocytopathies), including focal segmental glomerulosclerosis (FSGS) and minimal change disease (MCD). Injury to the podocytes can result in \"effacement\" or flattening of foot processes, leading to increased permeability of the filtration barrier and proteinuria (an excess of serum protein in urine) which is a common symptom of kidney diseases." xsd:string {xref="DOI:10.1038/s41467-022-33748-1", xref="DOI:10.1038/s41572-020-0196-7", xref="DOI:10.1146/annurev-physiol-020911-153238", xref="DOI:10.1159/000481633", xref="DOI:10.3389/fcell.2021.771931"} [Term] id: CL:0000654 name: primary oocyte def: "A primary oocyte is an oocyte that has not completed female meosis I." [GOC:tfm, ISBN:0721662544] subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "primary oogonium" RELATED [] xref: BTO:0000512 xref: FMA:18645 @@ -7673,6 +8627,8 @@ property_value: RO:0002175 NCBITaxon:9606 id: CL:0000655 name: secondary oocyte def: "A secondary oocyte is an oocyte that has not completed meiosis II." [GOC:tfm, ISBN:0721662544] +subset: human_subset +subset: mouse_subset synonym: "primary oogonium" RELATED [] xref: BTO:0003094 xref: FMA:18646 @@ -7686,6 +8642,8 @@ relationship: RO:0002202 CL:0000654 ! develops from primary oocyte id: CL:0000656 name: primary spermatocyte def: "A diploid cell that has derived from a spermatogonium and can subsequently begin meiosis and divide into two haploid secondary spermatocytes." [GOC:tfm, ISBN:0721662544] +subset: human_subset +subset: mouse_subset xref: BTO:0001115 xref: CALOHA:TS-2194 xref: FMA:72292 @@ -7701,6 +8659,8 @@ relationship: capable_of GO:0007140 ! male meiotic nuclear division id: CL:0000657 name: secondary spermatocyte def: "One of the two haploid cells into which a primary spermatocyte divides, and which in turn gives origin to spermatids." [GOC:tfm, ISBN:0721662544] +subset: human_subset +subset: mouse_subset xref: BTO:0000709 xref: CALOHA:TS-2195 xref: FBbt:00004941 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} @@ -7718,6 +8678,8 @@ relationship: RO:0002202 CL:0000656 ! develops from primary spermatocyte id: CL:0000658 name: cuticle secreting cell def: "An epithelial cell that secretes cuticle." [GOC:tfm] +subset: human_subset +subset: mouse_subset is_a: CL:0000066 ! epithelial cell is_a: CL:0000327 ! extracellular matrix secreting cell @@ -7725,6 +8687,8 @@ is_a: CL:0000327 ! extracellular matrix secreting cell id: CL:0000659 name: eggshell secreting cell def: "An extracellular matrix secreting cell that secretes eggshell." [GOC:tfm] +subset: human_subset +subset: mouse_subset is_a: CL:0000327 ! extracellular matrix secreting cell is_a: CL:0000500 ! follicular epithelial cell @@ -7732,11 +8696,15 @@ is_a: CL:0000500 ! follicular epithelial cell id: CL:0000660 name: glycocalyx secreting cell def: "An extracellular matrix secreting cell that secretes glycocalyx." [GOC:tfm] +subset: human_subset +subset: mouse_subset is_a: CL:0000327 ! extracellular matrix secreting cell [Term] id: CL:0000661 name: distal tip cell (sensu Nematoda) +subset: human_subset +subset: mouse_subset is_a: CL:0000422 ! mitogenic signaling cell [Term] @@ -7770,6 +8738,8 @@ id: CL:0000666 name: fenestrated endothelial cell def: "An endothelial cell that has small pores, or fenestrations, which allow for the efficient exchange of substances between the blood and surrounding tissues." [DOI:10.1007/978-3-211-99390-3_133] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "window cell" EXACT [] xref: https://cellxgene.cziscience.com/cellguide/CL_0000666 xref: ZFA:0009286 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} @@ -7777,13 +8747,15 @@ is_a: CL:0000115 ! endothelial cell intersection_of: CL:0000115 ! endothelial cell intersection_of: bearer_of PATO:0002064 ! fenestrated relationship: bearer_of PATO:0002064 ! fenestrated -property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional.\n\nFenestrated cells are specialized epithelial cells that are characterized by a distinctive structural feature, fenestrations or tiny pores, which allow an exchange of substances such as fluids, nutrients, and waste between blood vessels and the surrounding tissue environments. These cells are present in various types of epithelial tissues in the human body, including the intestinal tract, endocrine glands, and certain parts of the renal system. \nThere are multiple types of endothelial cell fenestrations. The most common type is found in systemic capillaries of the endocrine tissue (e.g., pancreatic islets), gastrointestinal mucosa, and renal peritubular capillaries. Here, the fenestrated cells have fenestrations in their peripheral cytoplasm with a unique thin and permeable diaphragm that provides a high degree of selectivity, blocking the passage of larger molecules while allowing the free movement of smaller ones. In contrast, other types of fenestrations, such as the discontinuous epithelium of the liver sinusoidal endothelial cells, do not have diaphragms. \nCharacteristically, fenestrated cells play a vital role in the filtering process of body systems. They are a key part of the glomeruli in the kidneys where blood is filtered under high pressure. The fenestrations present in the endothelial cells lining the capillaries of the glomerulus allow the free passage of water and small solute molecules towards the Bowman's capsule, leaving behind larger proteins and cells in the blood, thereby aiding in the filtration and waste removal process. \nIn the endocrine system, fenestrated cells in glandular capillaries allow the prompt release of hormones into the bloodstream. These cells have tightly clustered fenestrations which increase the surface area available for passive diffusion, improving the efficiency of hormone secretion. In villi of the small intestine, these cells increase absorption efficiency, permitting the exchange of water, electrolytes, and nutrients.\nOverall, fenestrated cells contribute immensely to important physiological processes of filtration, absorption, and secretion, primarily connecting our body's circulation system with the surrounding tissues and organs." xsd:string {xref="DOI:10.1002/ar.1092200109", xref="DOI:10.1016/0306-4522(86)90162-4", xref="DOI:10.1016/j.devcel.2012.11.003", xref="DOI:10.1038/s41467-022-31571-2", xref="DOI:10.1152/ajprenal.90601.2008"} +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nFenestrated cells are specialized epithelial cells that are characterized by a distinctive structural feature, fenestrations or tiny pores, which allow an exchange of substances such as fluids, nutrients, and waste between blood vessels and the surrounding tissue environments. These cells are present in various types of epithelial tissues in the human body, including the intestinal tract, endocrine glands, and certain parts of the renal system. \nThere are multiple types of endothelial cell fenestrations. The most common type is found in systemic capillaries of the endocrine tissue (e.g., pancreatic islets), gastrointestinal mucosa, and renal peritubular capillaries. Here, the fenestrated cells have fenestrations in their peripheral cytoplasm with a unique thin and permeable diaphragm that provides a high degree of selectivity, blocking the passage of larger molecules while allowing the free movement of smaller ones. In contrast, other types of fenestrations, such as the discontinuous epithelium of the liver sinusoidal endothelial cells, do not have diaphragms. \nCharacteristically, fenestrated cells play a vital role in the filtering process of body systems. They are a key part of the glomeruli in the kidneys where blood is filtered under high pressure. The fenestrations present in the endothelial cells lining the capillaries of the glomerulus allow the free passage of water and small solute molecules towards the Bowman's capsule, leaving behind larger proteins and cells in the blood, thereby aiding in the filtration and waste removal process. \nIn the endocrine system, fenestrated cells in glandular capillaries allow the prompt release of hormones into the bloodstream. These cells have tightly clustered fenestrations which increase the surface area available for passive diffusion, improving the efficiency of hormone secretion. In villi of the small intestine, these cells increase absorption efficiency, permitting the exchange of water, electrolytes, and nutrients.\nOverall, fenestrated cells contribute immensely to important physiological processes of filtration, absorption, and secretion, primarily connecting our body's circulation system with the surrounding tissues and organs." xsd:string {xref="DOI:10.1002/ar.1092200109", xref="DOI:10.1016/0306-4522(86)90162-4", xref="DOI:10.1016/j.devcel.2012.11.003", xref="DOI:10.1038/s41467-022-31571-2", xref="DOI:10.1152/ajprenal.90601.2008"} [Term] id: CL:0000667 name: collagen secreting cell def: "An extracellular matrix secreting cell that secretes collagen." [GOC:tfm] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset xref: ZFA:0009287 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000327 ! extracellular matrix secreting cell @@ -7804,6 +8776,8 @@ def: "An elongated, contractile cell found wrapped about precapillary arterioles comment: Pericytes are CD10-positive, CD13-positive, CD31-negative, CD45-negative, CD106-positive, CD117-negative, CD140-positive, CD144-negative, CD146-positive, CD271-positive, CD325-positive, NG2-positive, RGS5-positive, SMA-positive, and desmin-positive. A subpopulation is CD248-positive. They are also capable of producing angiopoietin 1, CXCL12, TGF-beta, and VEGF-A. subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "adventitial cell" RELATED [] synonym: "adventitial reticular cell" EXACT [] synonym: "ARC" EXACT [PMID:17986482] @@ -7824,6 +8798,8 @@ id: CL:0000670 name: primordial germ cell def: "A primordial germ cell is a diploid germ cell precursors that transiently exist in the embryo before they enter into close association with the somatic cells of the gonad and become irreversibly committed as germ cells." [GOC:tfm, PMID:1381289] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "gonocyte" EXACT [] synonym: "primitive germ cell" EXACT [] xref: FMA:70567 @@ -7873,12 +8849,16 @@ is_a: CL:0000477 ! follicle cell of egg chamber id: CL:0000675 name: female gamete def: "A mature sexual reproductive cell of the female germline." [GOC:tfm] +subset: human_subset +subset: mouse_subset is_a: CL:0000021 {is_inferred="true"} ! female germ cell is_a: CL:0000300 ! gamete [Term] id: CL:0000676 name: cap cell +subset: human_subset +subset: mouse_subset xref: BTO:0001033 is_a: CL:0000378 ! supporting cell (sensu Nematoda and Protostomia) @@ -7887,6 +8867,8 @@ id: CL:0000677 name: gut absorptive cell def: "Cell of the intestinal epithelium with a brush border made up of many parallel packed microvilli; associated with absorption, particularly of macromolecules." [JB:jb] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset xref: ZFA:0009289 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000255 ! eukaryotic cell relationship: part_of UBERON:0001277 ! intestinal epithelium @@ -7894,7 +8876,11 @@ relationship: part_of UBERON:0001277 ! intestinal epithelium [Term] id: CL:0000678 name: commissural neuron -is_a: CL:0000540 ! neuron +def: "A neuron with soma location in the central nervous system that project its axon to the contralateral side of a central nervous system. This neuron can have its soma in the spinal cord, in the hemisphere of the brain, in the retina or in the ventral nerve cord of invertebrates." [PMID:17560562, PMID:31693445] +comment: Historically, commissural neurons, particularly in the spinal cord, have been used as a model to understand axon guidance during development. {xref="PMID:33438755", xref="PMID:31514748", xref="PMID:27532244", xref="PMID:25960414"} +subset: human_subset +subset: mouse_subset +is_a: CL:2000029 ! central nervous system neuron [Term] id: CL:0000679 @@ -7902,6 +8888,8 @@ name: glutamatergic neuron def: "A neuron that is capable of some neurotansmission by glutamate secretion." [] subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset xref: FBbt:00100291 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: WBbt:0006829 xref: ZFA:0009290 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} @@ -7917,6 +8905,8 @@ id: CL:0000680 name: muscle precursor cell def: "A non-terminally differentiated cell that is capable of developing into a muscle cell." [GOC:add] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset xref: ZFA:0009291 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: BFO:0000002 is_a: CL:0000055 ! non-terminally differentiated cell @@ -7932,6 +8922,8 @@ name: radial glial cell def: "A cell present in the developing CNS. Functions as both a precursor cell and as a scaffold to support neuronal migration." [GOC:dph] comment: Unlike that of mammals, the brain of adult teleost fish exhibits an intense and widespread neurogenic activity as a result of the persistence of\nradial glial cells acting as neural progenitors throughout life. subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "forebrain radial glial cell" NARROW [] xref: ZFA:0009292 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000125 ! glial cell @@ -7944,6 +8936,8 @@ def: "An absorptive cell of the gut epithelium that endocytoses microorganisms a comment: Should double check and see if M cells are particular to a specific region. subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "M cell" BROAD [] synonym: "M-cell" EXACT [] synonym: "microfold cell" EXACT [] @@ -7954,14 +8948,15 @@ xref: ZFA:0009293 {sssom:mapping_justification="https://w3id.org/semapv/vocab/Un is_a: CL:0000473 ! defensive cell is_a: CL:0000627 ! transporting cell is_a: CL:0002251 ! epithelial cell of alimentary canal -relationship: part_of UBERON:0003929 ! digestive tract epithelium property_value: RO:0002175 NCBITaxon:9606 -property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional.\n\nM cells, or microfold cells, of the gut are specialized epithelial cells found in the lining of the gut, specifically in the follicle-associated epithelium of mucosa-associated lymphoid tissue, where they function as sentries against toxins and pathogens. M cells are characterized by apical microfolds (hence their alternate name) which express unique adhesion molecules that enable them to sample the luminal macromolecules. \nOther morphological features that distinguish M cells from other intestinal mucosal cells include sparse microvilli and a reduced thickness of the glycocalyx, which permits adhesion while not hindering the transport of molecules. They also have unique intraepithelial invaginations on the basolateral side which are filled with macrophages and other immune cells that can process the engulfed macromolecules quickly. \nThese morphological characteristics enable M cells to serve a dual role in immune responses. They initiate the immune response by transporting antigens (such as toxic or pathogenic substances) across the epithelial layer to lymphocytes and antigen-presenting cells in the underlying lymphoid tissue. This specialized transport process is called 'transcytosis.' They also have specialized molecules like glycoprotein-2 for bacterial uptake. Simultaneously, M cells help maintain immune tolerance to food antigens and commensal bacteria, preventing unnecessary reactions to non-pathogenic substances and hypersensitivity conditions. While these functions are crucial for well-being, M cell dysfunction can lead to serious conditions like Crohn's disease and other inflammatory bowel diseases." xsd:string {xref="DOI:10.1038/nature08529", xref="DOI:10.1093/jb/mvv121", xref="DOI:10.1136/gut.47.5.735", xref="https://www.ncbi.nlm.nih.gov/books/NBK534232/", xref="https://www.sciencedirect.com/topics/medicine-and-dentistry/microfold-cell"} +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nM cells, or microfold cells, of the gut are specialized epithelial cells found in the lining of the gut, specifically in the follicle-associated epithelium of mucosa-associated lymphoid tissue, where they function as sentries against toxins and pathogens. M cells are characterized by apical microfolds (hence their alternate name) which express unique adhesion molecules that enable them to sample the luminal macromolecules. \nOther morphological features that distinguish M cells from other intestinal mucosal cells include sparse microvilli and a reduced thickness of the glycocalyx, which permits adhesion while not hindering the transport of molecules. They also have unique intraepithelial invaginations on the basolateral side which are filled with macrophages and other immune cells that can process the engulfed macromolecules quickly. \nThese morphological characteristics enable M cells to serve a dual role in immune responses. They initiate the immune response by transporting antigens (such as toxic or pathogenic substances) across the epithelial layer to lymphocytes and antigen-presenting cells in the underlying lymphoid tissue. This specialized transport process is called 'transcytosis.' They also have specialized molecules like glycoprotein-2 for bacterial uptake. Simultaneously, M cells help maintain immune tolerance to food antigens and commensal bacteria, preventing unnecessary reactions to non-pathogenic substances and hypersensitivity conditions. While these functions are crucial for well-being, M cell dysfunction can lead to serious conditions like Crohn's disease and other inflammatory bowel diseases." xsd:string {xref="DOI:10.1038/nature08529", xref="DOI:10.1093/jb/mvv121", xref="DOI:10.1136/gut.47.5.735", xref="https://www.ncbi.nlm.nih.gov/books/NBK534232/", xref="https://www.sciencedirect.com/topics/medicine-and-dentistry/microfold-cell"} [Term] id: CL:0000683 name: ependymoglial cell def: "A cell that transports hormones from neurosecretory cells. This nerve cell is characterized by bipolar shape and endfeet that contact a basal lamina around blood vessels, and/or the pia mater or vitreous body of the eye and additionally contact the ventricular surface or sub-retinal space." [http://neurolex.org/wiki/Category\:Ependymoglial_Cell, JB:jb] +subset: human_subset +subset: mouse_subset synonym: "ependymal astrocyte" EXACT [] xref: MESH:D063928 xref: ZFA:0009294 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} @@ -7970,6 +8965,8 @@ is_a: CL:0000127 ! astrocyte [Term] id: CL:0000684 name: littoral cell of liver +subset: human_subset +subset: mouse_subset is_a: CL:0000077 ! mesothelial cell relationship: part_of UBERON:0002107 ! liver @@ -7984,9 +8981,11 @@ replaced_by: PO:0004010 id: CL:0000686 name: cerebrospinal fluid secreting cell def: "A columnar/cuboidal epithelial cell that secretes cerebrospinal fluid." [GOC:tfm] +subset: human_subset +subset: mouse_subset xref: ZFA:0009295 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} -is_a: CL:0000151 {is_inferred="true"} ! secretory cell is_a: CL:0000710 ! neurecto-epithelial cell +is_a: CL:1100001 ! secretory epithelial cell intersection_of: CL:0000151 ! secretory cell intersection_of: capable_of GO:0033326 ! cerebrospinal fluid secretion relationship: capable_of GO:0033326 ! cerebrospinal fluid secretion @@ -8005,6 +9004,8 @@ relationship: part_of UBERON:0000971 ! ommatidium id: CL:0000688 name: perijunctional fibroblast def: "A fibroblast-like cell that provides support at neuromuscular junctions in vertebrates and are localized outside the synaptic basal lamina." [JB:jb] +subset: human_subset +subset: mouse_subset xref: ZFA:0009296 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000057 ! fibroblast is_a: CL:0000630 ! supporting cell @@ -8013,6 +9014,8 @@ is_a: CL:0000630 ! supporting cell id: CL:0000689 name: myoendocrine cell def: "A cell with both myofibrils and secretory granules." [JB:jb] +subset: human_subset +subset: mouse_subset is_a: CL:0000163 ! endocrine cell [Term] @@ -8029,17 +9032,20 @@ id: CL:0000691 name: stellate interneuron def: "Any interneuron that has characteristic some stellate morphology." [FBC:Autogenerated] subset: BDS_subset +subset: human_subset +subset: mouse_subset xref: ZFA:0009297 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000099 ! interneuron -is_a: CL:0000104 ! multipolar neuron +is_a: CL:0000122 ! stellate neuron intersection_of: CL:0000099 ! interneuron intersection_of: bearer_of PATO:0070010 ! stellate morphology -relationship: bearer_of PATO:0070010 ! stellate morphology [Term] id: CL:0000692 name: terminal Schwann cell def: "A neuroglial cell of the peripheral nervous system inside the basal lamina of the neuromuscular junction providing chemical and physical support to the synapse." [JB:jb, PMID:16136171] +subset: human_subset +subset: mouse_subset synonym: "perisynaptic Schwann cell" EXACT [PMID:18803315] synonym: "Schwann cell" BROAD [] synonym: "teloglia" EXACT [PMID:18803315] @@ -8053,12 +9059,13 @@ id: CL:0000693 name: neurogliaform cell def: "An interneuron that has spider-like appearance with a small round soma, a large number (7-10) of short, smooth, or slightly beaded primary dendrites that give rise to only a few secondary branches, and a branched axon that establishes a dense axonal mesh with thin shafts." [JB:jb, PMID:17122314] subset: BDS_subset +subset: human_subset +subset: mouse_subset synonym: "neuroglioform cell" EXACT [PMID:3235828] synonym: "NGF cell" EXACT [PMID:18568015] synonym: "spiderweb cell" EXACT [] xref: ZFA:0009299 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000099 ! interneuron -is_a: CL:0000104 ! multipolar neuron intersection_of: CL:0000099 ! interneuron intersection_of: bearer_of PATO:0070001 ! neurogliaform morphology relationship: bearer_of PATO:0070001 ! neurogliaform morphology @@ -8078,10 +9085,11 @@ name: Cajal-Retzius cell def: "A neuron of the human embryonic marginal zone which display, as a salient feature, radial ascending processes that contact the pial surface, and a horizontal axon plexus located in the deep marginal zone. One feature of these cells in mammals is that they express the Reelin gene." [PMID:10600995, PMID:9728912] comment: While previously called 'pioneer neurons' of the marginal zone, Cajal-Retzius cells are differentiated from pioneer neurons (which are Reln-negative) by their Reln-immunoreactivity. {xref="PMID:10600995"} subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "CR cells" EXACT [WikipediaVersioned:Cajal–Retzius_cell&oldid=1032081753] synonym: "Horizontal cells of Cajal" EXACT [WikipediaVersioned:Cajal–Retzius_cell&oldid=1032081753] xref: ZFA:0009300 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} -is_a: CL:0000117 ! CNS neuron (sensu Vertebrata) is_a: CL:2000029 ! central nervous system neuron relationship: bearer_of PATO:0070006 ! cortical bipolar morphology relationship: RO:0002100 UBERON:0010403 ! has soma location brain marginal zone @@ -8092,13 +9100,15 @@ id: CL:0000696 name: PP cell def: "A cell that stores and secretes pancreatic polypeptide hormone." [GOC:tfm, JB:jb, PMID:15153415] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "type F enteroendocrine cell" EXACT [] xref: FMA:62938 xref: FMA:83409 xref: https://cellxgene.cziscience.com/cellguide/CL_0000696 is_a: CL:0000164 ! enteroendocrine cell is_a: CL:0000167 ! peptide hormone secreting cell -property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional.\n\nPP cells, also known as pancreatic polypeptide cells (and previously called F cells or gamma cells), are enteroendocrine cells predominantly found in the islets of Langerhans in the head of the pancreas. They are one of the four main endocrine cell types present in the pancreatic islets, along with type A, B and D cells. PP cells are notable for their production of pancreatic polypeptide, an anorexigenic hormone that modulates food intake and energy homeostasis. \nBy secreting pancreatic polypeptide, PP cells play a significant role in the management of both digestive and appetite regulation. Upon ingestion of food, there is a significant increase in the secretion of pancreatic polypeptide, which then reduces biliary secretion and helps slow down the movement of food through the digestive tract. This allows more time for digestion to take place and nutrients to be absorbed, promoting the efficient use of dietary intake. The pancreatic polypeptide further reduces appetite by interacting with the hypothalamus, the area of the brain responsible for control of hunger.\nGiven their important role in digestion, malfunction or damage to PP cells can lead to a disturbance in the digestive process and contribute to some disease conditions. For example, an overproduction of pancreatic polypeptide can result in conditions such as pancreatic tumors and diabetes. Conversely, an under secretion might contribute to obesity due to impaired dietary control. Furthermore, PP cells may also play a role in the body's energy balance, suggesting their implication in conditions related to energy metabolism." xsd:string {xref="DOI:10.1016/j.febslet.2014.07.005", xref="DOI:10.1016/j.mce.2015.06.028", xref="DOI:10.1038/s41580-020-00317-7", xref="DOI:10.1210/jc.2003-030630", xref="DOI:10.1369/00221554155835"} +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nPP cells, also known as pancreatic polypeptide cells (and previously called F cells or gamma cells), are enteroendocrine cells predominantly found in the islets of Langerhans in the head of the pancreas. They are one of the four main endocrine cell types present in the pancreatic islets, along with type A, B and D cells. PP cells are notable for their production of pancreatic polypeptide, an anorexigenic hormone that modulates food intake and energy homeostasis. \nBy secreting pancreatic polypeptide, PP cells play a significant role in the management of both digestive and appetite regulation. Upon ingestion of food, there is a significant increase in the secretion of pancreatic polypeptide, which then reduces biliary secretion and helps slow down the movement of food through the digestive tract. This allows more time for digestion to take place and nutrients to be absorbed, promoting the efficient use of dietary intake. The pancreatic polypeptide further reduces appetite by interacting with the hypothalamus, the area of the brain responsible for control of hunger.\nGiven their important role in digestion, malfunction or damage to PP cells can lead to a disturbance in the digestive process and contribute to some disease conditions. For example, an overproduction of pancreatic polypeptide can result in conditions such as pancreatic tumors and diabetes. Conversely, an under secretion might contribute to obesity due to impaired dietary control. Furthermore, PP cells may also play a role in the body's energy balance, suggesting their implication in conditions related to energy metabolism." xsd:string {xref="DOI:10.1016/j.febslet.2014.07.005", xref="DOI:10.1016/j.mce.2015.06.028", xref="DOI:10.1038/s41580-020-00317-7", xref="DOI:10.1210/jc.2003-030630", xref="DOI:10.1369/00221554155835"} [Term] id: CL:0000697 @@ -8118,6 +9128,8 @@ is_obsolete: true id: CL:0000699 name: paraganglial type 1 cell def: "A type of glomus or chief cell, is sensitive to hypoxia and produce catecholamines." [GOC:tfm] +subset: human_subset +subset: mouse_subset is_a: CL:0000165 ! neuroendocrine cell [Term] @@ -8125,6 +9137,8 @@ id: CL:0000700 name: dopaminergic neuron def: "A neuron that releases dopamine as a neurotransmitter." [GOC:dhill] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "dopaminergic cell" EXACT [] xref: BTO:0004032 xref: FBbt:00005131 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} @@ -8141,6 +9155,8 @@ relationship: capable_of GO:0061527 ! dopamine secretion, neurotransmission id: CL:0000701 name: paraganglia type 2 cell def: "Supports paraganglial type 1 cell." [JB:jb] +subset: human_subset +subset: mouse_subset is_a: CL:0000630 ! supporting cell [Term] @@ -8156,6 +9172,8 @@ relationship: part_of UBERON:0000971 ! ommatidium id: CL:0000703 name: sustentacular cell def: "Cell that provides some or all mechanical, nutritional and phagocytic support to their neighbors." [JB:jb] +subset: human_subset +subset: mouse_subset xref: BTO:0002315 xref: ZFA:0009302 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000630 ! supporting cell @@ -8165,6 +9183,8 @@ id: CL:0000704 name: endothelial tip cell def: "A specialized endothelial cell that senses extracellular signals and guides the directed growth of blood vessels." [PMID:15376331] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset xref: ZFA:0009303 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000071 ! blood vessel endothelial cell @@ -8185,6 +9205,8 @@ def: "A specialized ependymal cell that is part of the choroid plexus epithelium comment: A choroid plexus epithelial cell possesses non-motile 9+0 cilia. While these cilia can exhibit transient motility during development, they generally do not contribute significantly to the directional flow of cerebrospinal fluid (CSF). Instead, they are primarily involved in sensory functions. {xref="PMID:25729351"} subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "choroid plexus cell" BROAD [DOI:10.1101/2022.10.12.511898] synonym: "epithelial cell of choroid plexus" EXACT [] xref: FMA:70549 @@ -8213,6 +9235,8 @@ id: CL:0000708 name: leptomeningeal cell def: "Stromal cell that forms the internal covering of the vertebrate brain and produces ECM for this and the choroid plexus." [JB:jb] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "leptomemingeal cell" RELATED [] xref: ZFA:0009305 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000327 {is_inferred="true"} ! extracellular matrix secreting cell @@ -8235,6 +9259,8 @@ id: CL:0000710 name: neurecto-epithelial cell def: "Epithelial cells derived from neural plate and neural crest." [GOC:tfm] comment: The term "neuroepithelial cell" is used to describe both this cell type and sensory epithelial cell (CL:0000098). +subset: human_subset +subset: mouse_subset synonym: "neuroepithelial cell" BROAD [] xref: BTO:0004301 xref: FMA:70557 @@ -8249,6 +9275,8 @@ id: CL:0000711 name: cumulus cell def: "Cumulus cell is a specialized granulosa cell that surrounds and nourishes the oocyte. This cell-type surrounds the fully-grown oocyte to form a cumulus-oocyte complex (abbr. COC). The terms cumulus oophorus cells, cumulus granulosa cells, cumulus oophorous granulosa cells, granulosa-cumulus cells are used to make a distinction between this cell and the other functionally different subpopulation of granulosa cells at the wall of the Graafian follicle." [GOC:tfm, http://www.copewithcytokines.org/cope.cgi?key=cumulus%20cells] subset: human_reference_atlas +subset: human_subset +subset: mouse_subset xref: BTO:0002236 xref: MESH:D054885 is_a: CL:0000154 ! protein secreting cell @@ -8261,6 +9289,8 @@ property_value: RO:0002175 NCBITaxon:9606 id: CL:0000712 name: stratum granulosum cell def: "Any epidermal cell that is part of some stratum granulosum of epidermis." [FBC:Autogenerated] +subset: human_subset +subset: mouse_subset is_a: CL:0000362 ! epidermal cell intersection_of: CL:0000362 ! epidermal cell intersection_of: part_of UBERON:0002069 ! stratum granulosum of epidermis @@ -8269,6 +9299,8 @@ relationship: part_of UBERON:0002069 ! stratum granulosum of epidermis [Term] id: CL:0000713 name: corona radiata cell +subset: human_subset +subset: mouse_subset is_a: CL:0000711 ! cumulus cell [Term] @@ -8333,6 +9365,8 @@ relationship: RO:0002162 NCBITaxon:6656 ! in taxon Arthropoda id: CL:0000723 name: somatic stem cell def: "A stem cell that can give rise to cell types of the body other than those of the germ-line." [GO:0048103] +subset: human_subset +subset: mouse_subset xref: CALOHA:TS-2086 xref: MESH:D053687 xref: ZFA:0009307 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} @@ -8353,6 +9387,8 @@ is_a: CL:0000725 ! nitrogen fixing cell id: CL:0000725 name: nitrogen fixing cell def: "Any cell that is capable of some nitrogen fixation." [FBC:Autogenerated] +subset: human_subset +subset: mouse_subset is_a: CL:0000000 ! cell intersection_of: CL:0000000 ! cell intersection_of: capable_of GO:0009399 ! nitrogen fixation @@ -8390,6 +9426,8 @@ is_obsolete: true id: CL:0000730 name: leading edge cell def: "A cell at the front of a migrating epithelial sheet." [MA:ma] +subset: human_subset +subset: mouse_subset is_a: CL:0000066 ! epithelial cell [Term] @@ -8397,6 +9435,8 @@ id: CL:0000731 name: urothelial cell def: "A cell of a layer of transitional epithelium in the wall of the proximal urethra, bladder, ureter or renal pelvis, external to the lamina propria." [doi:10.1038/s41385-022-00565-0, GOC:tfm, MA:ma] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "urinary tract transitional epithelial cell" NARROW [] xref: FMA:84127 xref: https://cellxgene.cziscience.com/cellguide/CL_0000731 @@ -8405,11 +9445,13 @@ is_a: CL:0000244 ! transitional epithelial cell intersection_of: CL:0000244 ! transitional epithelial cell intersection_of: part_of UBERON:0000365 ! urothelium relationship: part_of UBERON:0000365 ! urothelium -property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional.\n\nUrothelial cells are a unique type of epithelial cell found lining the urinary tract system. They form the urothelium, a specialized, multi-layered epithelium that lines major portions of the urinary tract, including the renal pelvis, ureters, bladder, and the proximal part of the urethra. The distinct characteristic of urothelial cells is their ability to stretch and contract depending on the volume of liquid they contain - a feature that facilitates the essential role they play in maintaining the functionality and integrity of the urinary system.\nThe primary function of urothelial cells is to provide an impermeable barrier to urine, preventing the toxic components present in the urine from seeping back into the body's bloodstream. The urothelium consists of a superficial umbrella cell layer, 1–2 layers of intermediate cells, and a basal cell layer. The umbrella layer is composed of large, mostly binucleated cells that are covered in an asymmetrical unit membrane, the uroplakin plaques. These plaques function to seal the apical membrane of the bladder from the toxic and highly variable contents of urine. The lipid bilayer structure of uroplakin plaques has an exceptionally high concentration of uroplakins that contribute to the barrier function of the urothelium.\nBeyond their mechanical function, urothelial cells also play a role in sensing and signaling changes in the urinary system. They express a number of sensor molecules or respond to thermal, mechanical and chemical stimuli and can release chemical mediators. This allows them to act as sensory transducers because they detect changes in the filling state of the bladder and transmit this information to the nervous system. Moreover, these versatile cells contribute to the defense mechanism against urinary tract pathogens. They respond to bacterial infections by releasing chemical messengers, cytokines and chemokines, to attract immune cells, and also can engulf pathogens via endocytosis." xsd:string {xref="DOI:10.1002/nau.22195", xref="DOI:10.1038/ki.2009.73", xref="DOI:10.1038/ncpuro0672", xref="DOI:10.1038/s41579-020-0324-0", xref="DOI:10.1152/physrev.00041.2019"} +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nUrothelial cells are a unique type of epithelial cell found lining the urinary tract system. They form the urothelium, a specialized, multi-layered epithelium that lines major portions of the urinary tract, including the renal pelvis, ureters, bladder, and the proximal part of the urethra. The distinct characteristic of urothelial cells is their ability to stretch and contract depending on the volume of liquid they contain - a feature that facilitates the essential role they play in maintaining the functionality and integrity of the urinary system.\nThe primary function of urothelial cells is to provide an impermeable barrier to urine, preventing the toxic components present in the urine from seeping back into the body's bloodstream. The urothelium consists of a superficial umbrella cell layer, 1–2 layers of intermediate cells, and a basal cell layer. The umbrella layer is composed of large, mostly binucleated cells that are covered in an asymmetrical unit membrane, the uroplakin plaques. These plaques function to seal the apical membrane of the bladder from the toxic and highly variable contents of urine. The lipid bilayer structure of uroplakin plaques has an exceptionally high concentration of uroplakins that contribute to the barrier function of the urothelium.\nBeyond their mechanical function, urothelial cells also play a role in sensing and signaling changes in the urinary system. They express a number of sensor molecules or respond to thermal, mechanical and chemical stimuli and can release chemical mediators. This allows them to act as sensory transducers because they detect changes in the filling state of the bladder and transmit this information to the nervous system. Moreover, these versatile cells contribute to the defense mechanism against urinary tract pathogens. They respond to bacterial infections by releasing chemical messengers, cytokines and chemokines, to attract immune cells, and also can engulf pathogens via endocytosis." xsd:string {xref="DOI:10.1002/nau.22195", xref="DOI:10.1038/ki.2009.73", xref="DOI:10.1038/ncpuro0672", xref="DOI:10.1038/s41579-020-0324-0", xref="DOI:10.1152/physrev.00041.2019"} [Term] id: CL:0000732 name: amoeboid cell +subset: human_subset +subset: mouse_subset is_a: CL:0000219 ! motile cell [Term] @@ -8444,6 +9486,8 @@ replaced_by: CL:0011008 id: CL:0000737 name: striated muscle cell def: "Muscle cell which has as its direct parts myofilaments organized into sarcomeres." [GOC:tfm, ISBN:0721662544] +subset: human_subset +subset: mouse_subset xref: BTO:0002916 xref: CALOHA:TS-2157 xref: FMA:86936 @@ -8462,6 +9506,8 @@ name: leukocyte def: "An achromatic cell of the myeloid or lymphoid lineages capable of ameboid movement, found in blood or other tissue." [GOC:add, GOC:tfm, ISBN:978-0-323-05290-0] subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "immune cell" RELATED [] synonym: "leucocyte" EXACT [] synonym: "white blood cell" EXACT [] @@ -8492,6 +9538,8 @@ def: "The set of neurons that receives neural inputs via bipolar, horizontal and subset: cellxgene_subset subset: eye_upper_slim subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "gangliocyte" EXACT [] synonym: "ganglion cell of retina" EXACT [] synonym: "RGC" RELATED OMO:0003000 [doi:10.1038/s41598-020-66092-9] @@ -8500,7 +9548,7 @@ xref: BTO:0001800 xref: FMA:67765 xref: MESH:D012165 xref: ZFA:0009310 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} -is_a: CL:0000117 ! CNS neuron (sensu Vertebrata) +is_a: CL:0000540 ! neuron relationship: RO:0002100 UBERON:0000966 ! has soma location retina property_value: RO:0002175 NCBITaxon:9606 @@ -8508,6 +9556,8 @@ property_value: RO:0002175 NCBITaxon:9606 id: CL:0000741 name: spinal accessory motor neuron def: "A motor neuron that is located in the cervical region of the spinal cord and selectively innervates the sternocleidmastoid or trapezius muscle. Unlike other motor neurons, they extend axons dorsally along lateral margins of the spinal cord." [PMID:16267219] +subset: human_subset +subset: mouse_subset synonym: "SACMN" EXACT [] xref: ZFA:0009311 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0008039 ! lower motor neuron @@ -8516,6 +9566,8 @@ is_a: CL:0008039 ! lower motor neuron id: CL:0000742 name: periarticular chondrocyte def: "A round chondrocyte that first differentiates in the late embryonic growth plate of bone." [PMID:15951842] +subset: human_subset +subset: mouse_subset xref: ZFA:0009312 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:1001607 ! articular chondrocyte @@ -8525,6 +9577,8 @@ name: hypertrophic chondrocyte def: "Chondrocyte that is terminally differentiated, produces type X collagen, is large in size, and often associated with the replacement of cartilage by bone (endochondral ossification)." [GO_REF:0000034, PMID:15951842] comment: is hypertrophic pathological or normal? and can it be described using a pato term? subset: human_reference_atlas +subset: human_subset +subset: mouse_subset xref: ZFA:0009313 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000138 ! chondrocyte property_value: RO:0002175 NCBITaxon:9606 @@ -8533,6 +9587,8 @@ property_value: RO:0002175 NCBITaxon:9606 id: CL:0000744 name: columnar chondrocyte def: "A columnar chondrocyte that differentiates in the late embryonic growth plate of bone. Columnar chondrocytes vigorously proliferate and form columns in the growth plate." [PMID:15951842] +subset: human_subset +subset: mouse_subset xref: ZFA:0009314 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000138 ! chondrocyte @@ -8543,6 +9599,8 @@ def: "A neuron that laterally connects other neurons in the inner nuclear layer subset: cellxgene_subset subset: eye_upper_slim subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "HC" RELATED OMO:0003000 [doi:10.1038/s41598-020-66092-9] synonym: "HCs" RELATED OMO:0003004 [doi:10.1038/s41598-020-66092-9] synonym: "horizontal cell" EXACT [] @@ -8555,12 +9613,13 @@ property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000746 name: cardiac muscle cell -alt_id: FMA:83808 def: "Cardiac muscle cells are striated muscle cells that are responsible for heart contraction. In mammals, the contractile fiber resembles those of skeletal muscle but are only one third as large in diameter, are richer in sarcoplasm, and contain centrally located instead of peripheral nuclei." [GOC:mtg_cardiacconduct_nov11, GOC:tfm, ISBN:0323052908, PMID:22426062, PMID:4711263] comment: This class encompasses the muscle cells responsible for heart* contraction in both vertebrates and arthropods. The ultrastucture of a wide range of arthropod heart cells has been examined including spiders, horseshoe crabs, crustaceans (see Sherman, 1973 and refs therein) and insects (see Lehmacher et al (2012) and refs therein). According to these refs, the cells participating in heart contraction in all cases are transversely striated. Insects hearts additionally contain ostial cells, also transversely striated muscle cells, but which do not participate in heart contraction. subset: cellxgene_subset subset: general_cell_types_upper_slim subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "cardiac muscle fiber" EXACT [GO:0048739] synonym: "cardiac myocyte" EXACT [] synonym: "cardiocyte" BROAD [] @@ -8569,6 +9628,7 @@ synonym: "heart muscle cell" EXACT [] xref: BTO:0001539 xref: CALOHA:TS-0115 xref: FMA:14067 +xref: https://cellxgene.cziscience.com/cellguide/CL_0000746 xref: MESH:D032383 xref: ZFA:0009316 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000737 ! striated muscle cell @@ -8582,11 +9642,14 @@ relationship: bearer_of PATO:0002478 ! transversely striated relationship: participates_in GO:0060047 ! heart contraction relationship: RO:0002202 CL:0000513 ! develops from cardiac muscle myoblast property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nCardiac muscle cells, also known as cardiomyocytes or cardiac myocytes, are specialized cells that form the heart tissue. These cells are elongated, branched, and contain a single centrally located nucleus. Their anatomy is composed primarily of densely packed myofibrils, which are protein structures that consist of sarcomeres - the fundamental units of muscle contraction. Cardiac muscle cells are united at their ends through specialized junctions known as intercalated discs, which allow the heart to contract in a unified, powerful and rhythmic way.\nFunctionally, cardiac muscle cells are responsible for the heart's consistent pumping action that circulates blood throughout the body. Unlike most cells in the body, cardiac muscle cells spontaneously depolarize and generate action potentials without external stimulation. This unique trait stems from the presence of ion channels in the cells' membrane that allow a cyclic flow of ions across the membrane, which create the electrical impulses necessary for heart contraction. The spread of these electrical signals from one cardiac muscle cell to another - facilitated by the interconnected network made by the intercalated disks - results in a synchronized contraction of the heart muscle.\nUnlike skeletal muscle cells which can tire and need rest, cardiac muscle cells have to work ceaselessly throughout the entire lifespan, without the opportunity for rest, to ensure continuous circulation of blood. This is made possible through the high volume of mitochondria and a constant supply of oxygen from coronary circulation. In conclusion, cardiac muscle cells, through their unique structure and vital functionality, play a pivotal role in sustaining life by providing the means for blood to reach every cell in the body." xsd:string {xref="DOI:10.1016/j.ccep.2010.10.012", xref="DOI:10.1038/nrcardio.2016.203", xref="https://www.ncbi.nlm.nih.gov/books/NBK572070", xref="https://www.sciencedirect.com/topics/agricultural-and-biological-sciences/cardiac-muscle"} [Term] id: CL:0000747 name: cyanophore def: "A pigment cell derived from the neural crest. Contains blue pigment of unknown chemical composition in fibrous organelles termed cyanosomes. This gives a blue appearance." [SANBI:mhl] +subset: human_subset +subset: mouse_subset synonym: "blue chromatophore" RELATED [] xref: ZFA:0009317 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: BFO:0000002 @@ -8601,15 +9664,16 @@ def: "A bipolar neuron found in the retina and having connections with photorece subset: cellxgene_subset subset: eye_upper_slim subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "BC" RELATED OMO:0003000 [doi:10.1038/s41598-020-66092-9] synonym: "BCs" RELATED OMO:0003004 [doi:10.1038/s41598-020-66092-9] synonym: "BPs" RELATED OMO:0003004 [GSE137537] xref: ZFA:0009318 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} -is_a: CL:0000103 ! bipolar neuron is_a: CL:0000679 ! glutamatergic neuron is_a: CL:0008028 ! visual system neuron is_a: CL:0009004 ! retinal cell -intersection_of: CL:0000103 ! bipolar neuron +intersection_of: CL:0000540 ! neuron intersection_of: RO:0002100 UBERON:0001791 ! has soma location inner nuclear layer of retina relationship: RO:0002100 UBERON:0001791 ! has soma location inner nuclear layer of retina property_value: RO:0002175 NCBITaxon:9606 @@ -8620,6 +9684,8 @@ name: ON-bipolar cell def: "A bipolar neuron found in the retina and having connections with photoreceptors cells and neurons in the inner half of the inner plexiform layer. These cells depolarize in response to light stimulation of their corresponding photoreceptors." [PMID:14689473] subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset xref: ZFA:0009319 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000748 ! retinal bipolar neuron property_value: RO:0002175 NCBITaxon:9606 @@ -8630,6 +9696,8 @@ name: OFF-bipolar cell def: "A bipolar neuron found in the retina and having connections with photoreceptors cells and neurons in the outer half of the inner plexiform layer. These cells depolarize in response to light to dark transition." [PMID:14689473] subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset xref: ZFA:0009320 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000748 ! retinal bipolar neuron property_value: RO:0002175 NCBITaxon:9606 @@ -8639,7 +9707,8 @@ id: CL:0000751 name: rod bipolar cell def: "A bipolar neuron found in the retina that is synapsed by rod photoreceptor cells but not by cone photoreceptor cells. These neurons depolarize in response to light." [GOC:tfm, PMID:14689473] subset: cellxgene_subset -subset: human_reference_atlas +subset: human_subset +subset: mouse_subset xref: FMA:67750 xref: ZFA:0009321 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000749 ! ON-bipolar cell @@ -8647,12 +9716,14 @@ relationship: RO:0002102 UBERON:0008925 ! axon synapses in sublaminar layer S4 relationship: RO:0002102 UBERON:0008926 ! axon synapses in sublaminar layer S5 relationship: RO:0002103 CL:0000604 ! synapsed by retinal rod cell property_value: RO:0002175 NCBITaxon:32443 {xref="PMID:38627529"} -property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000752 name: cone retinal bipolar cell def: "A bipolar neuron found in the retina and having connections with cone photoreceptor cells and neurons in the inner plexiform layer." [PMID:14689473] +subset: cellxgene_subset +subset: human_subset +subset: mouse_subset xref: ZFA:0009322 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000748 ! retinal bipolar neuron intersection_of: CL:0000748 ! retinal bipolar neuron @@ -8663,6 +9734,9 @@ relationship: RO:0002103 CL:0000573 ! synapsed by retinal cone cell id: CL:0000753 name: type 1 cone bipolar cell (sensu Mus) def: "An OFF-bipolar neuron found in the retina and having connections with cone photoreceptors cells and neurons in the outer half of the inner plexiform layer. The cell body of these cells is in the middle of the inner plexiform layer. The dendritic tree is stout and the axon terminates in sublamina 1. The axonal terminal is wide and has only a few varicosities." [PMID:14689473] +subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "DB1 cone bipolar cell" EXACT [] is_a: CL:0000752 ! cone retinal bipolar cell relationship: RO:0002102 UBERON:0008922 ! axon synapses in sublaminar layer S1 @@ -8671,6 +9745,9 @@ relationship: RO:0002102 UBERON:0008922 ! axon synapses in sublaminar layer S1 id: CL:0000754 name: type 2 cone bipolar cell (sensu Mus) def: "An OFF-bipolar neuron found in the retina and having connections with cone photoreceptors cells and neurons in the outer half of the inner plexiform layer. The dendritic tree is not well filled and the dendrites are more delicate than in type 1 cells. The axon terminal is bushier and exhibits a dense plexus of varicosities in the inner part of sublamina 1 (Ghosh et al., 2004). It can be differentiated from other retinal bipolar neurons by its expression of marker genes: Neto1, Lhx3 and Irx-6 (Shekhar, 2016)." [PMID:14689473, PMID:27565351] +subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "FMB cone bipolar cell" EXACT [] is_a: BFO:0000002 is_a: CL:0000752 ! cone retinal bipolar cell @@ -8687,6 +9764,8 @@ relationship: RO:0002292 PR:Q9ER75 ! expresses iroquois-class homeodomain protei id: CL:0000755 name: type 3 cone bipolar cell (sensu Mus) def: "An OFF-bipolar neuron found in the retina and having connections with cone photoreceptors cells and neurons in the outer half of the inner plexiform layer. The dendritic tree is delicate and the dendritic tips appear small when compared with type 1 cells. The axon terminal is stratified and restricted to sublamina 2 of the inner plexiform layer." [PMID:14689473] +subset: human_subset +subset: mouse_subset synonym: "DB2 cone bipolar cell" EXACT [] is_a: CL:0000752 ! cone retinal bipolar cell relationship: RO:0002102 UBERON:0008923 ! axon synapses in sublaminar layer S2 @@ -8696,6 +9775,9 @@ relationship: RO:0002103 CL:0000604 ! synapsed by retinal rod cell id: CL:0000756 name: type 4 cone bipolar cell (sensu Mus) def: "An OFF-bipolar neuron found in the retina and having connections with cone photoreceptors cells and neurons in the outer half of the inner plexiform layer. The cell has a diffuse axon terminal with varicosities in sublaminae 1 and 2 of the inner plexiform layer." [PMID:14689473] +subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "DB3 cone bipolar cell" EXACT [] is_a: CL:0000752 ! cone retinal bipolar cell relationship: RO:0002102 UBERON:0008923 ! axon synapses in sublaminar layer S2 @@ -8706,6 +9788,9 @@ relationship: RO:0002103 CL:0000604 ! synapsed by retinal rod cell id: CL:0000757 name: type 5 cone bipolar cell (sensu Mus) def: "An ON-bipolar neuron found in the retina and having connections with cone photoreceptors cells and neurons in the inner half of the inner plexiform layer. The axon terminal is restricted to sublamina 3 of the inner plexiform layer. It is narrowly stratified and branched. The dendritic tree has many delicate branches." [PMID:14689473] +subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "DB4 cone bipolar cell" EXACT [] is_a: CL:0000752 ! cone retinal bipolar cell relationship: RO:0002102 UBERON:0008924 ! axon synapses in sublaminar layer S3 @@ -8714,6 +9799,9 @@ relationship: RO:0002102 UBERON:0008924 ! axon synapses in sublaminar layer S3 id: CL:0000758 name: type 6 cone bipolar cell (sensu Mus) def: "An ON-bipolar neuron found in the retina and having connections with cone photoreceptors cells and neurons in the inner half of the inner plexiform layer. The cell has a loose, delicate axon terminal that opens in sublamina 3 of the inner plexiform layer and descends into sublamina 4." [PMID:14689473] +subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "DB5 cone bipolar cell" EXACT [] is_a: CL:0000752 ! cone retinal bipolar cell relationship: RO:0002102 UBERON:0008925 ! axon synapses in sublaminar layer S4 @@ -8722,6 +9810,9 @@ relationship: RO:0002102 UBERON:0008925 ! axon synapses in sublaminar layer S4 id: CL:0000759 name: type 7 cone bipolar cell (sensu Mus) def: "An ON-bipolar neuron found in the retina and having connections with cone photoreceptors cells and neurons in the inner half of the inner plexiform layer. The axon terminal is narrowly stratified and are found just below a calretinin-expressing band in sublamina 4 of the inner plexiform layer." [PMID:14689473] +subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "IMB cone bipolar cell" EXACT [] is_a: CL:0000752 ! cone retinal bipolar cell relationship: RO:0002102 UBERON:0008925 ! axon synapses in sublaminar layer S4 @@ -8730,6 +9821,9 @@ relationship: RO:0002102 UBERON:0008925 ! axon synapses in sublaminar layer S4 id: CL:0000760 name: type 8 cone bipolar cell (sensu Mus) def: "An ON-bipolar neuron found in the retina and having connections with cone photoreceptors cells and neurons in the inner half of the inner plexiform layer. This cell has the widest dendritic field and the widest axon terminal of all retinal bipolar cells. The axon terminal is delicate and stratified through sublaminae 4 and 5 of the inner plexiform layer." [PMID:14689473] +subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "DB6 cone bipolar cell" EXACT [] is_a: CL:0000752 ! cone retinal bipolar cell relationship: RO:0002102 UBERON:0008925 ! axon synapses in sublaminar layer S4 @@ -8739,6 +9833,9 @@ relationship: RO:0002102 UBERON:0008926 ! axon synapses in sublaminar layer S5 id: CL:0000761 name: type 9 cone bipolar cell (sensu Mus) def: "An ON-bipolar neuron found in the retina and having connections with cone photoreceptors cells and neurons in the inner half of the inner plexiform layer. The dendritic tree is wide and the dendritic convergence indicates cone selectivity. The axon terminal is sparsely branched and terminates in sublamina 5 of the inner plexiform layer." [PMID:14689473] +subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "BB cone bipolar cell" EXACT [] is_a: CL:0000752 ! cone retinal bipolar cell relationship: RO:0002102 UBERON:0008926 ! axon synapses in sublaminar layer S5 @@ -8749,6 +9846,8 @@ name: nucleated thrombocyte def: "A nucleated blood cell involved in coagulation, typically seen in birds and other non-mammalian vertebrates." [GOC:add, GOC:tfm, PMID:16360205] comment: Note that this is a non-mammalian cell type. Use platelet ; CL:0000233 for thrombocytes (platelets) in mammals. subset: blood_and_immune_upper_slim +subset: human_subset +subset: mouse_subset xref: ZFA:0009323 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000226 ! single nucleate cell is_a: CL:0000763 {is_inferred="true"} ! myeloid cell @@ -8763,6 +9862,8 @@ id: CL:0000763 name: myeloid cell def: "A cell of the monocyte, granulocyte, mast cell, megakaryocyte, or erythroid lineage." [GOC:add] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset xref: BTO:0001441 xref: CALOHA:TS-0647 xref: MESH:D022423 @@ -8782,6 +9883,8 @@ def: "A immature or mature cell in the lineage leading to and including erythroc comment: Note that in FMA erythropoietic cells are types of nucleated erythrocytes and thus don't include erythrocytes. subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "erythropoietic cell" EXACT [] xref: CALOHA:TS-0290 xref: FMA:62845 @@ -8796,6 +9899,8 @@ name: erythroblast def: "A nucleated precursor of an erythrocyte that lacks hematopoietic lineage markers." [GOC:add, ISBN:0721601464, PMID:18174176] subset: blood_and_immune_upper_slim subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "normoblast" EXACT [] xref: BTO:0001571 xref: CALOHA:TS-0289 @@ -8840,6 +9945,8 @@ id: CL:0000766 name: myeloid leukocyte def: "A cell of the monocyte, granulocyte, or mast cell lineage." [GOC:add] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset xref: ZFA:0009326 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000738 {is_inferred="true"} ! leukocyte is_a: CL:0000763 ! myeloid cell @@ -8854,6 +9961,8 @@ comment: Matures in the bone marrow and account for <1% of leukocytes in the per subset: blood_and_immune_upper_slim subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "basophilic leucocyte" EXACT [] synonym: "basophilic leukocyte" EXACT [] synonym: "polymorphonuclear leucocyte" BROAD [] @@ -8879,6 +9988,8 @@ property_value: RO:0002175 NCBITaxon:9606 id: CL:0000768 name: immature basophil def: "Any of the immature forms of a basophil, in which basophilic specific granules are present but other phenotypic features of the mature form may be lacking." [GOC:add, ISBN:0721601464] +subset: human_subset +subset: mouse_subset synonym: "immature basophilic leucocyte" EXACT [] synonym: "immature basophilic leukocyte" EXACT [] is_a: CL:0000767 {is_inferred="true"} ! basophil @@ -8891,6 +10002,8 @@ relationship: RO:0002202 CL:0000830 ! develops from basophilic promyelocyte id: CL:0000769 name: basophilic metamyelocyte def: "A basophil precursor in the granulocytic series, being a cell intermediate in development between a basophilic myelocyte and a band form basophil. The nucleus becomes indented where the indentation is smaller than half the distance to the farthest nuclear margin; chromatin becomes coarse and clumped; specific granules predominate while primary granules are rare. Markers are CD11b-positive, CD15-positive, CD16-positive, CD24-positive, CD33-positive, and CD13-positive." [GOC:tfm, ISBN:0721601464, PMID:18466030] +subset: human_subset +subset: mouse_subset xref: FMA:84198 is_a: CL:0000768 {is_inferred="true"} ! immature basophil is_a: CL:0002192 ! metamyelocyte @@ -8920,6 +10033,8 @@ relationship: RO:0002202 CL:0000614 ! develops from basophilic myelocyte id: CL:0000770 name: band form basophil def: "A late basophilic metamyelocyte in which the nucleus is in the form of a curved or coiled band, not having acquired the typical multilobar shape of the mature basophil." [GOC:add, http://www.cap.org, ISBN:0721601464, PMID:18466030] +subset: human_subset +subset: mouse_subset is_a: CL:0000768 {is_inferred="true"} ! immature basophil intersection_of: CL:0000768 ! immature basophil intersection_of: has_part CL:0017506 ! banded nucleus @@ -8934,6 +10049,8 @@ comment: Eosinophils are also CD14-negative, CD32-positive, CD44-positive, CD48- subset: blood_and_immune_upper_slim subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "eosinocyte" EXACT [] synonym: "eosinophilic granulocyte" EXACT [] synonym: "eosinophilic leucocyte" EXACT [] @@ -8962,6 +10079,8 @@ property_value: RO:0002175 NCBITaxon:9606 id: CL:0000772 name: immature eosinophil def: "Any of the immature forms of an eosinophil, in which eosinophilic specific granules are present but other phenotypic features of the mature form may be lacking." [GOC:add, ISBN:0721601464] +subset: human_subset +subset: mouse_subset synonym: "immature eosinocyte" EXACT [] synonym: "immature eosinophilic leucocyte" EXACT [] synonym: "immature eosinophilic leukocyte" EXACT [] @@ -8975,6 +10094,8 @@ relationship: RO:0002202 CL:0000833 ! develops from eosinophilic promyelocyte id: CL:0000773 name: eosinophilic metamyelocyte def: "A eosinophil precursor in the granulocytic series, being a cell intermediate in development between a eosinophilic myelocyte and a band form eosinophil. The nucleus becomes indented where the indentation is smaller than half the distance to the farthest nuclear margin; chromatin becomes coarse and clumped; specific granules predominate while primary granules are rare. Markers are integrin alpha-M-positive, fucosyltransferase FUT4-positive, low affinity immunoglobulin gamma Fc region receptor III-positive, CD33-positive, CD24-positive and aminopeptidase N-negative." [GOC:add, GOC:tfm, ISBN:0721601464, PMID:19622087] +subset: human_subset +subset: mouse_subset is_a: CL:0000772 {is_inferred="true"} ! immature eosinophil is_a: CL:0002192 ! metamyelocyte intersection_of: CL:0000772 ! immature eosinophil @@ -9005,6 +10126,8 @@ relationship: RO:0002202 CL:0000612 ! develops from eosinophilic myelocyte id: CL:0000774 name: band form eosinophil def: "A late eosinophilic metamyelocyte in which the nucleus is in the form of a curved or coiled band, not having acquired the typical multilobar shape of the mature eosinophil." [GOC:add, GOC:tfm, http://www.cap.org, ISBN:0721601464, PMID:19622087] +subset: human_subset +subset: mouse_subset is_a: CL:0000772 {is_inferred="true"} ! immature eosinophil intersection_of: CL:0000772 ! immature eosinophil intersection_of: has_part CL:0017506 ! banded nucleus @@ -9018,6 +10141,8 @@ def: "Any of the immature or mature forms of a granular leukocyte that in its ma subset: blood_and_immune_upper_slim subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "neutrocyte" EXACT [] synonym: "neutrophil leucocyte" EXACT [] synonym: "neutrophil leukocyte" EXACT [] @@ -9048,6 +10173,8 @@ id: CL:0000776 name: immature neutrophil def: "Any of the immature forms of a neutrophil in which neutrophilic specific granules are present but other phenotypic features of the mature form may be lacking." [GOC:add, ISBN:0721601464] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "immatuer neutrophilic leukocyte" EXACT [] synonym: "immature neutrocyte" EXACT [] synonym: "immature neutrophil leucocyte" EXACT [] @@ -9064,6 +10191,8 @@ relationship: RO:0002202 CL:0000564 ! develops from neutrophilic promyelocyte id: CL:0000777 name: mesangial phagocyte def: "A tissue-resident macrophage of the renal glomerular mesangium involved in the disposal and degradation of filtration residues, presentation of antigen to T cells and in tissue remodeling." [GOC:add, GOC:tfm, ISBN:0702022918, ISBN:3540536663, PMID:1600140, PMID:16146841] +subset: human_subset +subset: mouse_subset synonym: "mesangial cell" BROAD [] is_a: CL:0000864 {is_inferred="true"} ! tissue-resident macrophage intersection_of: CL:0000864 ! tissue-resident macrophage @@ -9078,6 +10207,8 @@ id: CL:0000778 name: mononuclear osteoclast def: "A specialized mononuclear osteoclast associated with the absorption and removal of bone, precursor of multinuclear osteoclasts." [GOC:add, GOC:tfm, PMID:12713016, PMID:15055519, PMID:17380158, PMID:9415452] comment: Morphology: mononuclear, highly vesicular. +subset: human_subset +subset: mouse_subset xref: ZFA:0009329 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000092 {is_inferred="true"} ! osteoclast is_a: CL:0000113 ! mononuclear phagocyte @@ -9089,6 +10220,8 @@ id: CL:0000779 name: multinuclear osteoclast def: "A specialized multinuclear osteoclast, forming a syncytium through the fusion of mononuclear precursor cells, associated with the absorption and removal of bone." [GOC:add, PMID:12713016, PMID:29379067, PMID:38903088, PMID:9415452] comment: Morphology: multinucleated, highly vesicular. +subset: human_subset +subset: mouse_subset synonym: "multinucleated osteoclast" EXACT [] is_a: CL:0000092 {is_inferred="true"} ! osteoclast is_a: CL:0000783 ! multinucleated phagocyte @@ -9102,6 +10235,8 @@ id: CL:0000780 name: multinuclear odontoclast def: "A specialized multinuclear osteoclast associated with the absorption and removal of cementum." [GOC:add, PMID:9415452] comment: Morphology: multinucleated, highly vesicular; location: roots of deciduous (milk) teeth. +subset: human_subset +subset: mouse_subset synonym: "multinucleated odontoclast" EXACT [] is_a: CL:0000588 {is_inferred="true"} ! odontoclast is_a: CL:0000779 ! multinuclear osteoclast @@ -9114,6 +10249,8 @@ id: CL:0000781 name: mononuclear odontoclast def: "A specialized mononuclear osteoclast associated with the absorption and removal of cementum." [GOC:add, PMID:9415452] comment: Morphology: Mononuclear, highly vesicular; location: roots of deciduous (milk) teeth. +subset: human_subset +subset: mouse_subset xref: ZFA:0009330 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000588 {is_inferred="true"} ! odontoclast is_a: CL:0000778 {is_inferred="true"} ! mononuclear osteoclast @@ -9126,6 +10263,8 @@ name: myeloid dendritic cell def: "A dendritic cell of the myeloid lineage." [GOC:add, PMID:10449155, PMID:17332250, PMID:9521319] comment: These cells are CD1a-negative, CD1b-positive, CD11a-positive, CD11c-positive, CD13-positive, CD14-negative, CD20-negative, CD21-negative, CD33-positive, CD40-negative, CD50-positive, CD54-positive, CD58-positive, CD68-negative, CD80-negative, CD83-negative, CD85j-positive, CD86-positive, CD89-negative, CD95-positive, CD120a-negative, CD120b-positive, CD123-negative, CD178-negative, CD206-negative, CD207-negative, CD209-negative, and TNF-alpha-negative. Upon TLR stimulation, they are capable of producing high levels of TNF-alpha, IL-6, CXCL8 (IL-8). subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "CD11c+CD123- DC" EXACT [] synonym: "interdigitating cell" BROAD [] synonym: "mDC" EXACT [] @@ -9143,6 +10282,8 @@ relationship: RO:0002202 CL:0000763 ! develops from myeloid cell id: CL:0000783 name: multinucleated phagocyte def: "A phagocyte formed by the fusion of mononuclear phagocytes." [GOC:add, GOC:tfm] +subset: human_subset +subset: mouse_subset is_a: CL:0000228 ! multinucleate cell is_a: CL:0000518 {is_inferred="true"} ! phagocyte (sensu Vertebrata) intersection_of: CL:0000518 ! phagocyte (sensu Vertebrata) @@ -9155,6 +10296,8 @@ def: "A dendritic cell type of distinct morphology, localization, and surface ma subset: blood_and_immune_upper_slim subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "DC2" EXACT [] synonym: "interferon-producing cell" EXACT [] synonym: "IPC" EXACT [] @@ -9177,6 +10320,8 @@ name: mature B cell def: "A B cell that is mature, having left the bone marrow. Initially, these cells are IgM-positive and IgD-positive, and they can be activated by antigen." [GOC:add, GOC:dsd, ISBN:0781735149] comment: Mature B cells are also reportedly CD10-negative, CD19-positive, CD22-positive, CD34-negative, CD48-positive, CD79a-positive, CD84-positive, CD127-negative, CD352-positive, RAG-negative, TdT-negative, Vpre-B-negative, and pre-BCR-negative. Transcription factors expressed: Pax5-positive. subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "mature B lymphocyte" EXACT [] synonym: "mature B-cell" EXACT [] synonym: "mature B-lymphocyte" EXACT [] @@ -9202,6 +10347,8 @@ comment: Plasma cells develop in the spleen and migrate to the bone marrow. Plas subset: blood_and_immune_upper_slim subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "effector B cell" RELATED [] synonym: "effector B-cell" RELATED [] synonym: "plasma B cell" EXACT [] @@ -9213,7 +10360,6 @@ xref: FMA:70574 xref: MESH:D010950 xref: ZFA:0009332 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000946 {is_inferred="true"} ! antibody secreting cell -is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000946 ! antibody secreting cell intersection_of: CL:4030046 GO:0019814 ! lacks_plasma_membrane_part immunoglobulin complex intersection_of: CL:4030046 GO:0042613 ! lacks_plasma_membrane_part MHC class II protein complex @@ -9237,6 +10383,8 @@ def: "A memory B cell is a mature B cell that is long-lived, readily activated u comment: Memory B-cells are also reportedly CD5-negative, CD10-negative, CD21-positive, CD22-positive, CD23-negative, CD24-positive, CD25-positive, CD27-positive, CD34-negative, CD38-negative, CD40-positive, CD43-negative, CD44-positive, CD45-positive, CD53-positive, CD80-negative, CD81-negative, CD86-positive, and CD196/CCR6-positive. subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "memory B lymphocyte" EXACT [] synonym: "memory B-cell" EXACT [] synonym: "memory B-lymphocyte" EXACT [] @@ -9260,6 +10408,8 @@ def: "A naive B cell is a mature B cell that has the phenotype surface IgD-posit comment: This cell type is compatible with the HIPC Lyoplate markers for 'naive B cell'. Per DSD: Naive B cells are also reportedly CD10-negative, CD19-positive, CD20-positive, CD21-positive, CD22-positive, CD25-negative, CD27-negative, CD34-negative, CD40-positive, CD43-negative, CD45-positive, CD48-positive, CD53-positive, CD80-negative, CD81-positive, CD84-positive, CD86-negative, CD95-negative, CD138-negative, CD150-positive, CD184/CXCR4-positive, CD185/CXCR5-positive, CD196/CCR6-positive, CD200-positive, CD229-positive, CD243-positive, CD289-positive, CD290-positive, CD352-positive, MHCII/HLA-DR-positive, cadherin 9-positive, and sIgH-positive, Transcription factors: Pax5-positive, ETS1-positive, FOXO1A-positive, KLF4-positive, KLF9-positive, MiTF-positive, OBF1-positive, PLZF-positive, and SpiB-positive. subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "naive B lymphocyte" EXACT [] synonym: "naive B-cell" EXACT [] synonym: "naive B-lymphocyte" EXACT [] @@ -9284,12 +10434,13 @@ name: alpha-beta T cell def: "A T cell that expresses an alpha-beta T cell receptor complex." [GOC:add, GOC:tfm, ISBN:0781735149] subset: blood_and_immune_upper_slim subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "alpha-beta T lymphocyte" EXACT [] synonym: "alpha-beta T-cell" EXACT [] synonym: "alpha-beta T-lymphocyte" EXACT [] xref: ZFA:0009335 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000084 {is_inferred="true"} ! T cell -is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000084 ! T cell intersection_of: RO:0002104 GO:0042105 ! has plasma membrane part alpha-beta T cell receptor complex disjoint_from: CL:0000798 ! gamma-delta T cell @@ -9300,6 +10451,8 @@ id: CL:0000790 name: immature alpha-beta T cell def: "An alpha-beta T cell that has an immature phenotype and has not completed T cell selection." [GOC:add, GOC:tfm, ISBN:0781735149] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "immature alpha-beta T lymphocyte" EXACT [] synonym: "immature alpha-beta T-cell" EXACT [] synonym: "immature alpha-beta T-lymphocyte" EXACT [] @@ -9313,6 +10466,8 @@ id: CL:0000791 name: mature alpha-beta T cell def: "A alpha-beta T cell that has a mature phenotype." [GOC:add, GOC:tfm, ISBN:0781735149] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "mature alpha-beta T lymphocyte" EXACT [] synonym: "mature alpha-beta T-cell" EXACT [] synonym: "mature alpha-beta T-lymphocyte" EXACT [] @@ -9328,6 +10483,8 @@ name: CD4-positive, CD25-positive, alpha-beta regulatory T cell def: "A CD4-positive, CD25-positive, alpha-beta T cell that regulates overall immune responses as well as the responses of other T cell subsets through direct cell-cell contact and cytokine release." [GOC:add, GOC:tfm, ISBN:0781735149, PMID:19464985, PMID:22343568] comment: This cell type is compatible with the HIPC Lyoplate markers for 'Treg'. The inclusion of CD127lo in the logical definition is compatible with both human and mouse T cells of this subtype. subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "CD4-positive, CD25-positive, alpha-beta regulatory T lymphocyte" EXACT [] synonym: "CD4-positive, CD25-positive, alpha-beta regulatory T-cell" EXACT [] synonym: "CD4-positive, CD25-positive, alpha-beta regulatory T-lymphocyte" EXACT [] @@ -9350,6 +10507,8 @@ id: CL:0000793 name: CD4-positive, alpha-beta intraepithelial T cell def: "A CD4-positive, alpha-beta T cell that is found in the columnar epithelium of the gastrointestinal tract." [GOC:add, GOC:tfm, ISBN:0781735149] subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "CD4-positive, alpha-beta intraepithelial T lymphocyte" EXACT [] synonym: "CD4-positive, alpha-beta intraepithelial T-cell" EXACT [] synonym: "CD4-positive, alpha-beta intraepithelial T-lymphocyte" EXACT [] @@ -9370,6 +10529,8 @@ def: "A CD8-positive, alpha-beta T cell that is capable of killing target cells comment: Note that while T cells of this subset are loosely referred to 'cytotoxic T cells,' as many other T cell types, including CD4-positive, alpha-beta T cells and gamma-delta T cells exhibit cytotoxicity in vitro and in vivo. subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "CD8-positive, alpha-beta cytotoxic T lymphocyte" EXACT [] synonym: "CD8-positive, alpha-beta cytotoxic T-cell" EXACT [] synonym: "CD8-positive, alpha-beta cytotoxic T-lymphocyte" EXACT [] @@ -9401,6 +10562,8 @@ property_value: RO:0002175 NCBITaxon:9606 id: CL:0000795 name: CD8-positive, alpha-beta regulatory T cell def: "A CD8-positive, alpha-beta T cell that regulates overall immune responses as well as the responses of other T cell subsets through direct cell-cell contact and cytokine release." [GOC:add, GOC:tfm, ISBN:0781735149] +subset: human_subset +subset: mouse_subset synonym: "CD8+ regulatory T cell" EXACT [] synonym: "CD8+ T(reg)" EXACT [] synonym: "CD8+ Treg" EXACT [] @@ -9425,6 +10588,8 @@ name: CD8-alpha-beta-positive, alpha-beta intraepithelial T cell def: "A alpha-beta intraepithelial T cell found in the columnar epithelium of the gastrointestinal tract. Intraepithelial T cells often have distinct developmental pathways and activation requirements." [GOC:add, ISBN:0781735149] subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "CD8-positive, alpha-beta intraepithelial T lymphocyte" EXACT [] synonym: "CD8-positive, alpha-beta intraepithelial T-cell" EXACT [] synonym: "CD8-positive, alpha-beta intraepithelial T-lymphocyte" EXACT [] @@ -9440,6 +10605,8 @@ property_value: RO:0002175 NCBITaxon:9606 id: CL:0000797 name: alpha-beta intraepithelial T cell def: "A mature alpha-beta T cell of the columnar epithelium of the gastrointestinal tract. Intraepithelial T cells often have distinct developmental pathways and activation requirements." [GOC:add, GOC:tfm, ISBN:0781735149] +subset: human_subset +subset: mouse_subset synonym: "alpha-beta intraepithelial T lymphocyte" EXACT [] synonym: "alpha-beta intraepithelial T-cell" EXACT [] synonym: "alpha-beta intraepithelial T-lymphocyte" EXACT [] @@ -9459,6 +10626,8 @@ comment: Note that gamma-delta T cells have both thymic and extrathymic differen subset: blood_and_immune_upper_slim subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "gamma-delta T lymphocyte" EXACT [] synonym: "gamma-delta T-cell" EXACT [] synonym: "gamma-delta T-lymphocyte" EXACT [] @@ -9466,7 +10635,6 @@ synonym: "gammadelta T cell" EXACT [] synonym: "gd T cell" RELATED OMO:0003000 [] xref: ZFA:0009336 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000084 {is_inferred="true"} ! T cell -is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000084 ! T cell intersection_of: RO:0002104 GO:0042106 ! has plasma membrane part gamma-delta T cell receptor complex relationship: RO:0002104 GO:0042106 ! has plasma membrane part gamma-delta T cell receptor complex @@ -9477,6 +10645,8 @@ id: CL:0000799 name: immature gamma-delta T cell def: "A gamma-delta T cell that has an immature phenotype." [GOC:add, ISBN:0781735149] comment: Note that gamma-delta T cells have both thymic and extrathymic differentiation pathways. +subset: human_subset +subset: mouse_subset synonym: "immature gamma-delta T lymphocyte" EXACT [] synonym: "immature gamma-delta T-cell" EXACT [] synonym: "immature gamma-delta T-lymphocyte" EXACT [] @@ -9494,6 +10664,8 @@ id: CL:0000800 name: mature gamma-delta T cell def: "A gamma-delta T cell that has a mature phenotype. These cells can be found in tissues and circulation where they express unique TCR repertoire depending on their location." [GOC:add, GOC:tfm, ISBN:0781735149] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "mature gamma-delta T lymphocyte" EXACT [] synonym: "mature gamma-delta T-cell" EXACT [] synonym: "mature gamma-delta T-lymphocyte" EXACT [] @@ -9508,6 +10680,8 @@ relationship: RO:0002202 CL:0000799 ! develops from immature gamma-delta T cell id: CL:0000801 name: gamma-delta intraepithelial T cell def: "A mature gamma-delta T cell that is found in the columnar epithelium of the gastrointestinal tract. These cells participate in mucosal immune responses." [GOC:add, GOC:tfm, ISBN:0781735149] +subset: human_subset +subset: mouse_subset synonym: "gamma-delta intraepithelial T lymphocyte" EXACT [] synonym: "gamma-delta intraepithelial T-cell" EXACT [] synonym: "gamma-delta intraepithelial T-lymphocyte" EXACT [] @@ -9526,6 +10700,8 @@ name: CD8-alpha alpha positive, gamma-delta intraepithelial T cell def: "A gamma-delta intraepithelial T cell that has the phenotype CD8-alpha alpha-positive." [GOC:add, GOC:tfm, ISBN:0781735149] subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "CD8-positive, gamma-delta intraepithelial T lymphocyte" EXACT [] synonym: "CD8-positive, gamma-delta intraepithelial T-cell" EXACT [] synonym: "CD8-positive, gamma-delta intraepithelial T-lymphocyte" EXACT [] @@ -9541,6 +10717,8 @@ property_value: RO:0002175 NCBITaxon:9606 id: CL:0000803 name: CD4-negative CD8-negative gamma-delta intraepithelial T cell def: "A gamma-delta intraepithelial T cell that has the phenotype CD4-negative and CD8-negative." [GOC:add, GOC:tfm, ISBN:0781735149] +subset: human_subset +subset: mouse_subset synonym: "CD4-positive, gamma-delta intraepithelial T lymphocyte" EXACT [] synonym: "CD4-positive, gamma-delta intraepithelial T-cell" EXACT [] synonym: "CD4-positive, gamma-delta intraepithelial T-lymphocyte" EXACT [] @@ -9558,13 +10736,14 @@ id: CL:0000805 name: immature single positive thymocyte def: "A thymocyte that has the phenotype CD4-negative, CD8-positive, CD44-negative, CD25-negative, and pre-TCR-positive." [GO_REF:0000031, GOC:add, GOC:tfm, http://www.immgen.org/index_content.html, ISBN:0781735149] comment: Note that this type of thymocyte has passed the beta-selection checkpoint and is rapidly proliferating and rearranging the T cell receptor alpha chain and expressing the CD8 coreceptor. This stage comes between the DN4 and DP stages. +subset: human_subset +subset: mouse_subset synonym: "immature single positive T cell" EXACT [] synonym: "immature single positive T lymphocyte" EXACT [] synonym: "immature single positive T-lymphocyte" EXACT [] synonym: "ISP" EXACT [] synonym: "T.ISP.th" EXACT [] is_a: CL:0000893 {is_inferred="true"} ! thymocyte -is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000893 ! thymocyte intersection_of: CL:4030046 PR:000001004 ! lacks_plasma_membrane_part CD4 molecule intersection_of: CL:4030046 PR:000001307 ! lacks_plasma_membrane_part CD44 molecule @@ -9585,6 +10764,8 @@ id: CL:0000806 name: DN2 thymocyte def: "A thymocyte that has the phenotype CD4-negative, CD8-negative, CD44-positive, and CD25-positive." [GO_REF:0000031, GOC:add, GOC:tfm, ISBN:0781735149] comment: Note that this type of thymocyte is at the earliest stage of T cell receptor rearrangement of the beta, gamma, and delta T cell receptor chains. Also, there is growing evidence that molecular markers characterizing double negative thymocytes are different across species, especially in mouse versus human thymus. If in doubt, please consider using CL:0002489 'double negative thymocyte'. +subset: human_subset +subset: mouse_subset synonym: "DN2 alpha-beta immature T lymphocyte" EXACT [] synonym: "DN2 alpha-beta immature T-cell" EXACT [] synonym: "DN2 alpha-beta immature T-lymphocyte" EXACT [] @@ -9595,7 +10776,6 @@ synonym: "preT.DN2.Th" EXACT [] synonym: "TN2 cell" EXACT [] synonym: "TN2 thymocyte" EXACT [] is_a: CL:0002489 ! double negative thymocyte -is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000893 ! thymocyte intersection_of: CL:4030046 PR:000001004 ! lacks_plasma_membrane_part CD4 molecule intersection_of: CL:4030046 PR:000025402 ! lacks_plasma_membrane_part T cell receptor co-receptor CD8 @@ -9611,6 +10791,8 @@ name: DN3 thymocyte def: "A thymocyte that has the phenotype CD4-negative, CD8-negative, CD44-negative, and CD25-positive and expressing the T cell receptor beta-chain in complex with the pre-T cell receptor alpha chain." [GO_REF:0000031, GOC:add, GOC:tfm, ISBN:0781735149] comment: There is growing evidence that molecular markers characterizing double negative thymocytes are different across species, especially in mouse versus human thymus. If in doubt, please consider using CL:0002489 'double negative thymocyte'. subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "DN3 alpha-beta immature T lymphocyte" EXACT [] synonym: "DN3 alpha-beta immature T-cell" EXACT [] synonym: "DN3 alpha-beta immature T-lymphocyte" EXACT [] @@ -9622,7 +10804,6 @@ synonym: "preT.DN3.Th" EXACT [] synonym: "TN3 cell" EXACT [] synonym: "TN3 thymocyte" EXACT [] is_a: CL:0002489 ! double negative thymocyte -is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000893 ! thymocyte intersection_of: CL:4030046 PR:000001004 ! lacks_plasma_membrane_part CD4 molecule intersection_of: CL:4030046 PR:000001307 ! lacks_plasma_membrane_part CD44 molecule @@ -9640,6 +10821,8 @@ name: DN4 thymocyte def: "A thymocyte that has the phenotype CD4-negative, CD8-negative, CD44-negative, CD25-negative, and pre-TCR-positive." [GO_REF:0000031, GOC:add, GOC:tfm, ISBN:0781735149] comment: Note that this type of thymocyte has passed the beta-selection checkpoint and is rapidly proliferating and beginning to rearrange the T cell receptor alpha chain. There is growing evidence that molecular markers characterizing double negative thymocytes are different across species, especially in mouse versus human thymus. If in doubt, please consider using CL:0002489 'double negative thymocyte'. subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "DN4 alpha-beta immature T lymphocyte" EXACT [] synonym: "DN4 alpha-beta immature T-lymphocyte" EXACT [] synonym: "DN4 cell" EXACT [] @@ -9649,7 +10832,6 @@ synonym: "double negative 4" EXACT [] synonym: "early cortical thymocyte" BROAD [] synonym: "T.DN4.th" EXACT [] is_a: CL:0002489 ! double negative thymocyte -is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000893 ! thymocyte intersection_of: CL:4030046 PR:000001004 ! lacks_plasma_membrane_part CD4 molecule intersection_of: CL:4030046 PR:000001307 ! lacks_plasma_membrane_part CD44 molecule @@ -9668,6 +10850,8 @@ def: "A thymocyte expressing the alpha-beta T cell receptor complex as well as b comment: Thymocytes of this stage are undergoing positive and negative selection. subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "double-positive, alpha-beta immature T lymphocyte" EXACT [] synonym: "DP cell" EXACT [] synonym: "DP thymocyte" EXACT [] @@ -9688,6 +10872,8 @@ id: CL:0000810 name: CD4-positive, alpha-beta thymocyte def: "An immature alpha-beta T cell that is located in the thymus and is CD4-positive and CD8-negative." [GO_REF:0000031, GOC:add, GOC:tfm, ISBN:0781735149] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "CD4-positive, alpha-beta immature T lymphocyte" EXACT [] synonym: "CD4-positive, alpha-beta immature T-cell" EXACT [] synonym: "CD4-positive, alpha-beta immature T-lymphocyte" EXACT [] @@ -9707,6 +10893,8 @@ id: CL:0000811 name: CD8-positive, alpha-beta thymocyte def: "An immature alpha-beta T cell that is located in the thymus and is CD8-positive and CD4-negative." [GO_REF:0000031, GOC:add, GOC:tfm, ISBN:0781735149] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "CD8-positive, alpha-beta immature T cell" RELATED [] synonym: "CD8-positive, alpha-beta immature T lymphocyte" EXACT [] synonym: "CD8-positive, alpha-beta immature T-cell" EXACT [] @@ -9727,6 +10915,8 @@ id: CL:0000813 name: memory T cell def: "A long-lived, antigen-experienced T cell that has acquired a memory phenotype including distinct surface markers and the ability to differentiate into an effector T cell upon antigen reexposure." [GO_REF:0000031, GOC:add, GOC:pam, GOC:tfm, ISBN:0781735149] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "memory T lymphocyte" EXACT [] synonym: "memory T-cell" EXACT [] synonym: "memory T-lymphocyte" EXACT [] @@ -9747,6 +10937,8 @@ name: mature NK T cell def: "A mature alpha-beta T cell of a distinct lineage that bears natural killer markers and a T cell receptor specific for a limited set of ligands. NK T cells have activation and regulatory roles particularly early in an immune response." [GOC:add, ISBN:0781735149] subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "mature natural killer T cell" EXACT [] synonym: "mature natural killer T lymphocyte" EXACT [] synonym: "mature natural killer T-cell" EXACT [] @@ -9775,6 +10967,8 @@ def: "A T cell which regulates overall immune responses as well as the responses comment: This cell type may express FoxP3 and CD25 and secretes IL-10 and TGF-beta. subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "regulatory T lymphocyte" EXACT [] synonym: "regulatory T-cell" EXACT [] synonym: "regulatory T-lymphocyte" EXACT [] @@ -9800,6 +10994,8 @@ comment: Immature B cells are also reportedly CD5-positive, CD10-positive, CD19- subset: blood_and_immune_upper_slim subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "immature B lymphocyte" EXACT [] synonym: "immature B-cell" EXACT [] synonym: "immature B-lymphocyte" EXACT [] @@ -9824,6 +11020,8 @@ name: precursor B cell def: "A precursor B cell is a B cell with the phenotype CD10-positive." [GO_REF:0000031, GOC:rhs, GOC:tfm] subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "pre-B cell" RELATED [] xref: BTO:0001133 xref: CALOHA:TS-0819 @@ -9844,6 +11042,8 @@ def: "An immature B cell of an intermediate stage between the pre-B cell stage a comment: This cell type is compatible with the HIPC Lyoplate markers for 'transitional B cell'. subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "T1 B cell" NARROW [] synonym: "T2 B cell" NARROW [] synonym: "T3 B cell" NARROW [] @@ -9873,6 +11073,8 @@ name: B-1 B cell def: "A B cell of distinct lineage and surface marker expression. B-1 B cells are thought to be the primary source of natural IgM immunoglobulin, that is, IgM produced in large quantities without prior antigenic stimulation and generally reactive against various microorganisms, as well as the source of T-independent IgA immunoglobulin in the mucosal areas. These cells are CD43-positive." [GO_REF:0000031, GOC:add, GOC:dsd, http://en.wikipedia.org/wiki/B-1_cell, PMID:11861604, PMID:20933013, PMID:21220451] comment: There are small numbers of B-1 cells found in the lymph nodes and spleen, while larger numbers can be found in the peritoneal and pleural cavities. B-1 B cells are reportedly CD11b-positive, CD20-positive, CD21-positive, CD27-positive, CD44-positive, CD45RB-positive, CD48-positive, CD70-negative, CD150-positive, CD244-negative, CD352-positive, sIgM-positive, and sIgD-low. subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "B-1 B lymphocyte" EXACT [] synonym: "B-1 B-cell" EXACT [] synonym: "B-1 B-lymphocyte" EXACT [] @@ -9900,6 +11102,8 @@ id: CL:0000820 name: B-1a B cell def: "A B-1 B cell that has the phenotype CD5-positive." [GOC:add, PMID:11861604] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "B-1a B lymphocyte" EXACT [] synonym: "B-1a B-cell" EXACT [] synonym: "B-1a B-lymphocyte" EXACT [] @@ -9921,6 +11125,8 @@ id: CL:0000821 name: B-1b B cell def: "A B-1 B cell that has the phenotype CD5-negative, but having other phenotypic attributes of a B-1 B cell." [GOC:add, PMID:11861604] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "B-1b B lymphocyte" EXACT [] synonym: "B-1b B-cell" EXACT [] synonym: "B-1b B-lymphocyte" EXACT [] @@ -9940,6 +11146,8 @@ name: B-2 B cell def: "A conventional B cell subject to antigenic stimulation and dependent on T cell help and with a distinct surface marker expression pattern from B-1 B cells. These cells are CD43-negative." [GOC:add, GOC:dsd, GOC:tfm, ISBN:0781735149, PMID:11861604, PMID:20933013] comment: B-2 B cells are reportedly CD48-positive, CD244-negative, and CD352-positive. subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "B-0 B cell" RELATED [] synonym: "B-2 B lymphocyte" EXACT [] synonym: "B-2 B-cell" EXACT [] @@ -9962,6 +11170,8 @@ name: immature natural killer cell def: "A natural killer cell that is developmentally immature and expresses natural killer cell receptors (NKR)." [GO_REF:0000031, GOC:add, ISBN:0781735149, PMID:12457618] comment: In mouse the NKR are Ly49 molecules and in human these cells express KIR molecules. subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "immature NK cell" EXACT [] synonym: "p-NK" RELATED [PMID:12457618] xref: ZFA:0009346 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} @@ -9978,6 +11188,8 @@ id: CL:0000824 name: mature natural killer cell def: "A natural killer cell that is developmentally mature and expresses a variety of inhibitory and activating receptors that recognize MHC class I and other stress related molecules." [GO_REF:0000031, GOC:add, ISBN:0781735149, PMID:14685782] subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "LAK cell" BROAD [PMID:14685782] synonym: "lymphokine activated killer cell" BROAD [PMID:14685782] synonym: "mature NK cell" EXACT [] @@ -9991,6 +11203,8 @@ id: CL:0000825 name: pro-NK cell def: "A lymphoid progenitor cell that is committed to the natural killer cell lineage, expressing CD122 (IL-15) receptor, but lacking many of the phenotypic characteristics of later stages of natural killer cell development such as expression of NK activating and inhibitory molecules. In human this cell has the phenotype CD34-positive, CD45RA-positive, CD10-positive, CD117-negative, and CD161 negative." [GO_REF:0000031, GOC:add, GOC:pam, PMID:11532393, PMID:12457618, PMID:15032583, PMID:15766674] comment: Most markers only described for human pro NK cells. +subset: human_subset +subset: mouse_subset synonym: "natural killer cell progenitor" EXACT [] synonym: "NKP" EXACT [PMID:12457618, PMID:15032583, PMID:15766674] synonym: "null cell" RELATED [PMID:11532393] @@ -9998,7 +11212,6 @@ synonym: "preNK cell" RELATED [PMID:11532393] synonym: "pro-natural killer cell" EXACT [] xref: ZFA:0009348 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000838 {is_inferred="true"} ! lymphoid lineage restricted progenitor cell -is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000838 ! lymphoid lineage restricted progenitor cell intersection_of: CL:4030046 PR:000001874 ! lacks_plasma_membrane_part KLRB1-like protein intersection_of: CL:4030046 PR:000002065 ! lacks_plasma_membrane_part mast/stem cell growth factor receptor @@ -10021,6 +11234,8 @@ def: "A progenitor cell of the B cell lineage, with some lineage specific activi comment: Human pro-B cells are reportedly CD10-positive, CD22-positive, CD34-positive, CD38-positive, CD45-low, CD48-positive, CD79a-positive, CD127-positive, CD184-positive, RAG-positive, TdT-positive, Vpre-B-positive, pre-BCR-negative, IgD-negative, and IgM-negative. Transcription factors expressed: Pax5-positive, EBF-positive, E2A-negative, Ikaros-negative, and PU.1-negative. subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "pre-B cell (Philadelphia nomenclature)" RELATED [PMID:11244048] synonym: "pre-pro B cell" BROAD [PMID:17582343] synonym: "pro-B lymphocyte" EXACT [] @@ -10033,7 +11248,6 @@ synonym: "progenitor B-lymphocyte" EXACT [] xref: BTO:0003104 xref: ZFA:0009349 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000838 {is_inferred="true"} ! lymphoid lineage restricted progenitor cell -is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000838 ! lymphoid lineage restricted progenitor cell intersection_of: has_part PR:000001903 ! paired box protein PAX-5 intersection_of: has_part PR:000006611 ! DNA nucleotidylexotransferase @@ -10049,6 +11263,8 @@ id: CL:0000827 name: pro-T cell def: "A lymphoid progenitor cell of the T cell lineage, with some lineage specific marker expression, but not yet fully committed to the T cell lineage." [GOC:add, ISBN:0781735149] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "DN1 cell" NARROW [] synonym: "DN1 thymocyte" NARROW [] synonym: "pro-T lymphocyte" EXACT [] @@ -10066,6 +11282,8 @@ id: CL:0000828 name: thromboblast def: "A progenitor cell of the thrombocyte, a nucleated blood cell involved in coagulation typically seen in birds and other non-mammalian vertebrates." [GOC:add, GOC:tfm, PMID:7758949] comment: Note that this is a non-mammalian cell type. +subset: human_subset +subset: mouse_subset xref: ZFA:0009351 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000226 ! single nucleate cell is_a: CL:0000763 ! myeloid cell @@ -10080,6 +11298,8 @@ relationship: RO:0002202 CL:0000050 ! develops from megakaryocyte-erythroid prog id: CL:0000829 name: basophilic myeloblast def: "A myeloblast committed to the basophil lineage." [GOC:add, ISBN:0721601464] +subset: human_subset +subset: mouse_subset is_a: CL:0000835 {is_inferred="true"} ! myeloblast intersection_of: CL:0000835 ! myeloblast intersection_of: capable_of GO:0030221 ! basophil differentiation @@ -10090,6 +11310,8 @@ relationship: RO:0002202 CL:0000613 ! develops from basophil progenitor cell id: CL:0000830 name: basophilic promyelocyte def: "A promyelocyte committed to the basophil lineage." [GOC:add, ISBN:0721601464] +subset: human_subset +subset: mouse_subset xref: FMA:84208 is_a: CL:0000836 {is_inferred="true"} ! promyelocyte intersection_of: CL:0000836 ! promyelocyte @@ -10102,13 +11324,14 @@ id: CL:0000831 name: mast cell progenitor def: "A progenitor cell of the mast cell lineage. Markers for this cell are FceRIa-low, CD117-positive, CD9-positive, T1/ST2-positive, SCA1-negative, and lineage-negative." [GOC:add, GOC:dsd, http://www.copewithcytokines.de, PMCID:PMC1183570, PMCID:PMC1312421, PMID:8629001, PMID:9354811] comment: MCP are CD16-positive, CD32-positive, CD34-positive, CD45-positive, integrin beta-7-positive, and lin-negative (CD2, CD3e, CD4, CD5, CD8a, CD14, CD19, CD20, CD27, integrin alpha-M, ly6c, ly6g, NCAM-1, and ter119). These cells also express the transcription factors GATA-1, GATA-2, and MITF, but not C/EBPa. +subset: human_subset +subset: mouse_subset synonym: "CFU-Mast" RELATED [] synonym: "CFU-MC" RELATED [] synonym: "colony forming unit mast cell" RELATED [] synonym: "MCP" EXACT [] is_a: CL:0000763 ! myeloid cell is_a: CL:0000839 {is_inferred="true"} ! myeloid lineage restricted progenitor cell -is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000839 ! myeloid lineage restricted progenitor cell intersection_of: capable_of GO:0060374 ! mast cell differentiation intersection_of: CL:4030045 PR:000005307 ! lacks_part CCAAT/enhancer-binding protein alpha @@ -10164,6 +11387,8 @@ relationship: RO:0015016 PR:000007431 ! has low plasma membrane amount high affi id: CL:0000832 name: eosinophilic myeloblast def: "A myeloblast committed to the eosinophil lineage." [GOC:add, ISBN:0721601464] +subset: human_subset +subset: mouse_subset is_a: CL:0000835 {is_inferred="true"} ! myeloblast intersection_of: CL:0000835 ! myeloblast intersection_of: capable_of GO:0030222 ! eosinophil differentiation @@ -10174,6 +11399,8 @@ relationship: RO:0002202 CL:0000611 ! develops from eosinophil progenitor cell id: CL:0000833 name: eosinophilic promyelocyte def: "A promyelocyte committed to the eosinophil lineage." [GOC:add, ISBN:0721601464] +subset: human_subset +subset: mouse_subset xref: FMA:84199 is_a: CL:0000836 {is_inferred="true"} ! promyelocyte intersection_of: CL:0000836 ! promyelocyte @@ -10186,6 +11413,8 @@ id: CL:0000834 name: neutrophil progenitor cell def: "A progenitor cell of the neutrophil lineage." [GOC:add, GOC:tfm, ISBN:0721601464] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "neutrophil stem cell" RELATED [] xref: ZFA:0009352 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000763 ! myeloid cell @@ -10199,6 +11428,8 @@ relationship: RO:0002202 CL:0000557 ! develops from granulocyte monocyte progeni id: CL:0000835 name: myeloblast def: "The most primitive precursor in the granulocytic series, having fine, evenly distributed chromatin, several nucleoli, a high nuclear-to-cytoplasmic ration (5:1-7:1), and a nongranular basophilic cytoplasm. They reside in the bone marrow." [GOC:add, http://en.wikipedia.org/wiki/Myeloblast, http://www.cap.org, ISBN:0721601464] +subset: human_subset +subset: mouse_subset xref: BTO:0000187 xref: FMA:83524 xref: ZFA:0009353 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} @@ -10221,11 +11452,12 @@ name: promyelocyte def: "A precursor in the granulocytic series, being a cell intermediate in development between a myeloblast and myelocyte, that has distinct nucleoli, a nuclear-to-cytoplasmic ratio of 5:1 to 3:1, and containing a few primary cytoplasmic granules. Markers for this cell are fucosyltransferase FUT4-positive, CD33-positive, integrin alpha-M-negative, low affinity immunoglobulin gamma Fc region receptor III-negative, and CD24-negative." [GOC:add, GOC:amm, GOC:tfm, http://www.cap.org, ISBN:0721601464] subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset xref: CALOHA:TS-0825 xref: FMA:83530 is_a: CL:0000763 ! myeloid cell is_a: CL:0002191 ! granulocytopoietic cell -is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000839 ! myeloid lineage restricted progenitor cell intersection_of: bearer_of PATO:0040072 ! high nuclear/cytoplasmic ratio intersection_of: CL:4030046 PR:000001012 ! lacks_plasma_membrane_part integrin alpha-M @@ -10256,6 +11488,8 @@ comment: Markers differ between mouse and human. subset: blood_and_immune_upper_slim subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "hemopoietic progenitor cell" EXACT [] synonym: "MPP" EXACT [] xref: BTO:0000725 @@ -10264,7 +11498,6 @@ xref: ZFA:0009354 {sssom:mapping_justification="https://w3id.org/semapv/vocab/Un is_a: BFO:0000002 is_a: CL:0000255 ! eukaryotic cell is_a: CL:0008001 ! hematopoietic precursor cell -is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000988 ! hematopoietic cell intersection_of: bearer_of PATO:0001402 ! multipotent intersection_of: CL:4030046 PR:000001002 ! lacks_plasma_membrane_part CD19 molecule @@ -10306,6 +11539,8 @@ name: lymphoid lineage restricted progenitor cell def: "A progenitor cell restricted to the lymphoid lineage." [GOC:add, GOC:tfm] comment: Note that this is a class of cell types, not an identified single cell type. subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "lymphoid progenitor cell" BROAD [] xref: BTO:0004731 xref: CALOHA:TS-2025 @@ -10325,6 +11560,8 @@ def: "A progenitor cell restricted to the myeloid lineage." [GOC:add, GOC:tfm, P comment: Note that this is a class of cell types, not an identified single cell type. subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "myeloid progenitor cell" BROAD [] xref: BTO:0004730 xref: CALOHA:TS-2099 @@ -10342,6 +11579,8 @@ id: CL:0000840 name: immature conventional dendritic cell def: "An immature cell of the conventional dendritic cell lineage, characterized by high levels of antigen uptake via endocytosis, macropinocytosis, and phagocytosis, and typically found resident in the tissues. Markers for this cell are CD80-low, CD86-low, and MHC-II-low." [GOC:add, GOC:tfm, PMID:9521319] subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "immature myeloid dendritic cell" NARROW [] is_a: CL:0000766 ! myeloid leukocyte is_a: CL:0000990 {is_inferred="true"} ! conventional dendritic cell @@ -10360,6 +11599,8 @@ id: CL:0000841 name: mature conventional dendritic cell def: "A mature cell of the conventional dendritic cell lineage, characterized by a high capacity for antigen presentation and typically found in a lymph node." [GOC:add, GOC:tfm, PMID:9521319] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "mature dendritic cell" BROAD [GOC:add] synonym: "mature myeloid dendritic cell" NARROW [] xref: FMA:83038 @@ -10382,6 +11623,8 @@ name: mononuclear cell def: "A leukocyte with a single non-segmented nucleus in the mature form." [GOC:add] subset: blood_and_immune_upper_slim subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "mononuclear leukocyte" EXACT [] synonym: "peripheral blood mononuclear cell" NARROW [] xref: BTO:0000878 @@ -10399,6 +11642,8 @@ name: follicular B cell def: "A resting mature B cell that has the phenotype IgM-positive, IgD-positive, CD23-positive and CD21-positive, and found in the B cell follicles of the white pulp of the spleen or the corticol areas of the peripheral lymph nodes. This cell type is also described as being CD19-positive, B220-positive, AA4-negative, CD43-negative, and CD5-negative." [GOC:add, GOC:dsd, http://en.wikipedia.org/wiki/Follicular_B_Cells, ISBN:0781735149, PMCID:PMC2193793, PMID:20933013] comment: Follicular B cells are also reportedly CD48-positive, CD84-positive, CD229-positive, and CD352-positive. subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "Fo B cell" EXACT [] synonym: "Fo B-cell" EXACT [] synonym: "follicular B lymphocyte" EXACT [] @@ -10428,6 +11673,8 @@ def: "A rapidly cycling mature B cell that has distinct phenotypic characteristi comment: Germinal center B cells are also reportedly CD10-positive, CD19-positive, CD20-positive, CD38-positive, CD44-low, CD45-positive, CD48-positive, CD95-positive, CD352-positive, and HLA-DR-positive. Transcription factors: BCL6-positive, Ets1-positive, IRF8-positive, MTA3-positive, OBF1-positive, PAX5-positive, SpiB-positive, and STAT3-positive. subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "GC B cell" EXACT [] synonym: "GC B lymphocyte" EXACT [] synonym: "GC B-cell" EXACT [] @@ -10450,6 +11697,8 @@ name: marginal zone B cell of spleen def: "A mature B cell that is located in the marginal zone of the spleen with the phenotype CD23-negative and CD21-positive and expressing a B cell receptor usually reactive to bacterial cell wall components or senescent self components such as oxidized-LDL. This cell type is also described as being CD19-positive, B220-positive, IgM-high, AA4-negative, CD35-high." [GOC:add, GOC:dsd, http://en.wikipedia.org/wiki/Marginal-zone_B_cell, ISBN:0781735149, PMID:10933592, PMID:20933013] comment: MZ B cells are reportedly CD1-positive (mice), CD20-positive, CD48-positive, CD84-positive, CD150-positive, CD229-positive, and CD352-positive. subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "B cell of marginal zone of spleen" EXACT [] synonym: "marginal zone B cell" BROAD [] synonym: "marginal zone B lymphocyte" BROAD [] @@ -10483,12 +11732,16 @@ property_value: RO:0002175 NCBITaxon:9606 id: CL:0000846 name: vestibular dark cell def: "An epithelial cell of the vestibular sensory organ that is characterized by intense enzymatic activities and numerous basal membrane infoldings." [PMID:11223304] +subset: human_subset +subset: mouse_subset is_a: CL:0000066 ! epithelial cell [Term] id: CL:0000847 name: ciliated olfactory receptor neuron def: "An olfactory receptor cell in which the apical ending of the dendrite is a pronounced ciliated olfactory knob." [PMID:16841163] +subset: human_subset +subset: mouse_subset synonym: "ciliated olfactory sensory neuron" EXACT [] synonym: "ciliated sensory neuron" EXACT [] xref: ZFA:0009358 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} @@ -10501,6 +11754,8 @@ intersection_of: has_part GO:0005929 ! cilium id: CL:0000848 name: microvillous olfactory receptor neuron def: "An olfactory receptor cell in which the apical ending of the dendrite is a knob that bears numerous microvilli." [PMID:16841163] +subset: human_subset +subset: mouse_subset synonym: "microvillous olfactory sensory neuron" EXACT [] synonym: "microvillous sensory neuron" RELATED [] xref: ZFA:0009359 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} @@ -10510,6 +11765,8 @@ is_a: CL:0000207 ! olfactory receptor cell id: CL:0000849 name: crypt olfactory receptor neuron def: "An olfactory receptor cell with short cilia growing in an invagination bordered by microvilli." [PMID:16841163] +subset: human_subset +subset: mouse_subset synonym: "crypt cell" EXACT [] synonym: "crypt olfactory sensory neuron" EXACT [] synonym: "crypt sensory neuron" EXACT [] @@ -10521,6 +11778,8 @@ id: CL:0000850 name: serotonergic neuron alt_id: CL:0000403 def: "A neuron that releases serotonin as a neurotransmitter." [SANBI:mhl] +subset: human_subset +subset: mouse_subset synonym: "5-HT neuron" EXACT [] synonym: "5-hydroxytryptamine neuron" EXACT [] synonym: "serotinergic neuron" RELATED [] @@ -10559,6 +11818,8 @@ relationship: part_of UBERON:0008904 ! neuromast id: CL:0000853 name: olfactory epithelial supporting cell def: "Olfactory epithelial support cell is a columnar cell that extends from the epithelial free margin to the basement membrane of the olfactory epithelium. This cell type has a large, vertically, elongate, euchromatic nucleus, along with other nuclei, forms a layer superficial to the cell body of the receptor cell; sends long somewhat irregular microvilli into the mucus layer; at the base, with expanded end-feet containing numerous lamellated dense bodies resembling lipofuscin of neurons." [GOC:tfm, ISBN:0517223651, SANBI:mhl] +subset: human_subset +subset: mouse_subset synonym: "olfactory epithelial support cell" EXACT [] synonym: "olfactory sustentacular cell" EXACT [] synonym: "supporting cell of olfactory epithelium" EXACT [] @@ -10574,6 +11835,8 @@ intersection_of: part_of UBERON:0001997 ! olfactory epithelium id: CL:0000854 name: interneuromast cell def: "Interneuromast cell is a neuroectodermal cell deposited by the migrating lateral line primordium between the neuromasts. Interneuromast cells proliferate and migrate to form additional neuromasts." [SANBI:mhl] +subset: human_subset +subset: mouse_subset xref: ZFA:0009365 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: BFO:0000002 is_a: CL:0000133 ! neurectodermal cell @@ -10583,6 +11846,8 @@ relationship: RO:0002202 CL:0000032 ! develops from neuroplacodal cell id: CL:0000855 name: sensory hair cell def: "Hair cell is a mechanoreceptor cell that is sensitive to movement of the hair-like projections (stereocilia and kinocilia) which relay the information centrally in the nervous system." [SANBI:mhl] +subset: human_subset +subset: mouse_subset synonym: "hair cell" BROAD [] xref: BTO:0004744 xref: ZFA:0009366 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} @@ -10604,6 +11869,8 @@ relationship: part_of UBERON:0008904 ! neuromast id: CL:0000857 name: slow muscle myoblast def: "A skeletal muscle myoblast that differentiates into slow muscle fibers." [SANBI:mhl] +subset: human_subset +subset: mouse_subset xref: ZFA:0009368 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000515 ! skeletal muscle myoblast intersection_of: CL:0000056 ! myoblast @@ -10614,6 +11881,8 @@ relationship: RO:0002203 CL:0000189 ! develops into slow muscle cell id: CL:0000858 name: fast muscle myoblast def: "A skeletal muscle myoblast that differentiates into fast muscle fibers." [SANBI:mhl] +subset: human_subset +subset: mouse_subset xref: ZFA:0009369 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000515 ! skeletal muscle myoblast intersection_of: CL:0000056 ! myoblast @@ -10627,10 +11896,11 @@ def: "A monocyte that responds rapidly to microbial stimuli by secreting cytokin comment: Markers: CCR2+CXCCR1 (human, mouse, rat). subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "inflammatory monocyte" EXACT [] xref: https://cellxgene.cziscience.com/cellguide/CL_0000860 is_a: CL:0000576 {is_inferred="true"} ! monocyte -is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000576 ! monocyte intersection_of: capable_of GO:0002548 ! monocyte chemotaxis intersection_of: capable_of GO:0006909 ! phagocytosis @@ -10646,7 +11916,7 @@ relationship: CL:4030046 PR:000001020 ! lacks_plasma_membrane_part CD3 epsilon relationship: CL:4030046 PR:000001289 ! lacks_plasma_membrane_part membrane-spanning 4-domains subfamily A member 1 relationship: RO:0015015 PR:000001199 ! has high plasma membrane amount C-C chemokine receptor type 2 property_value: RO:0002175 NCBITaxon:9606 -property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional.\n\nClassical monocytes are a subtype of monocytes that are characterized by high CD14 but no CD16 expression. Emerging from the bone marrow and entering the bloodstream, these cells play central roles in immune responses and regulation of inflammation. CD14-positive CD16-negative monocytes form the majority of circulating monocytes in the body, typically contributing to around 80-90% of the total monocyte pool. \nThe primary function of the classical monocytes is to serve in the frontline of host defense against infections. They are primed to migrate to sites of infection, and they express pattern recognition receptors that help them identify and phagocytose pathogens, leading to their destruction. Classical monocytes also contribute to inflammation by producing several pro-inflammatory cytokines including interleukins and tumor necrosis factors. \nIn response to specific signals from tissues under pathological conditions, such as infection or injury, classical monocytes can leave the bloodstream and migrate towards the affected sites. Following their arrival, these cells differentiate into diverse cell types including macrophages and dendritic cells to combat specific pathogens or injury. Dysregulated monocyte activity can lead to the development of many human diseases including inflammation, infection, tissue injury, and various autoimmune diseases." xsd:string {xref="DOI:10.1038/nri.2017.28", xref="DOI:10.1111/sji.12883", xref="DOI:10.1182/blood-2009-07-235028", xref="DOI:10.3389/fimmu.2015.00423/full", xref="DOI:10.3389/fimmu.2019.02035"} +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nClassical monocytes are a subtype of monocytes that are characterized by high CD14 but no CD16 expression. Emerging from the bone marrow and entering the bloodstream, these cells play central roles in immune responses and regulation of inflammation. CD14-positive CD16-negative monocytes form the majority of circulating monocytes in the body, typically contributing to around 80-90% of the total monocyte pool. \nThe primary function of the classical monocytes is to serve in the frontline of host defense against infections. They are primed to migrate to sites of infection, and they express pattern recognition receptors that help them identify and phagocytose pathogens, leading to their destruction. Classical monocytes also contribute to inflammation by producing several pro-inflammatory cytokines including interleukins and tumor necrosis factors. \nIn response to specific signals from tissues under pathological conditions, such as infection or injury, classical monocytes can leave the bloodstream and migrate towards the affected sites. Following their arrival, these cells differentiate into diverse cell types including macrophages and dendritic cells to combat specific pathogens or injury. Dysregulated monocyte activity can lead to the development of many human diseases including inflammation, infection, tissue injury, and various autoimmune diseases." xsd:string {xref="DOI:10.1038/nri.2017.28", xref="DOI:10.1111/sji.12883", xref="DOI:10.1182/blood-2009-07-235028", xref="DOI:10.3389/fimmu.2015.00423/full", xref="DOI:10.3389/fimmu.2019.02035"} [Term] id: CL:0000861 @@ -10654,12 +11924,13 @@ name: elicited macrophage def: "A macrophage which develops from an inflammatory monocyte and is recruited into the tissues in response to injury and infection as part of an inflammatory response. Markers include CD11b-positive, CD68-positive, and F4/80-positive." [GO_REF:0000031, GOC:add, GOC:ana, GOC:tfm, PMID:15771589] comment: Markers: CD11b+, CD68+; Mouse: F4/80+; role or process: immune, inflammation (inflammatory response). subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "free macrophage" EXACT [] synonym: "wandering histiocyte" EXACT [] xref: FMA:84643 xref: FMA:84645 is_a: CL:0000235 {is_inferred="true"} ! macrophage -is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000235 ! macrophage intersection_of: participates_in GO:0006954 ! inflammatory response intersection_of: RO:0002104 PR:000001012 ! has plasma membrane part integrin alpha-M @@ -10676,6 +11947,8 @@ id: CL:0000862 name: suppressor macrophage def: "A macrophage that suppresses immune responses." [GOC:add, GOC:tfm, PMID:20402419] comment: Markers: May express: IL10, TGFbeta. +subset: human_subset +subset: mouse_subset is_a: CL:0000861 {is_inferred="true"} ! elicited macrophage intersection_of: CL:0000861 ! elicited macrophage intersection_of: capable_of GO:0050777 ! negative regulation of immune response @@ -10687,6 +11960,8 @@ name: inflammatory macrophage def: "An elicited macrophage that is recruited into the tissues in response to injury and infection as part of an inflammatory response, expresses high levels of pro-inflammatory cytokines, ROS and NO, and shows potent microbicidal activity." [GO_REF:0000031, GOC:ana, PMID:19132917] comment: Markers: Express: TNFa, IL1b, IL6, iNOS, NADPH-oxidase; produce: reactive oxygen species, nitric oxide; role or process: immune, inflammation (inflammatory response). subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "classically activated macrophage" EXACT [] synonym: "M1 macrophage" RELATED [PMID:28923980] xref: https://cellxgene.cziscience.com/cellguide/CL_0000863 @@ -10697,20 +11972,22 @@ intersection_of: capable_of GO:0032635 ! interleukin-6 production intersection_of: capable_of GO:0032640 ! tumor necrosis factor production intersection_of: capable_of GO:0042554 ! superoxide anion generation intersection_of: capable_of GO:0042742 ! defense response to bacterium -intersection_of: capable_of GO:0051767 ! nitric-oxide synthase biosynthetic process +intersection_of: capable_of GO:0045428 ! regulation of nitric oxide biosynthetic process relationship: capable_of GO:0032611 ! interleukin-1 beta production relationship: capable_of GO:0032635 ! interleukin-6 production relationship: capable_of GO:0032640 ! tumor necrosis factor production relationship: capable_of GO:0042554 ! superoxide anion generation relationship: capable_of GO:0042742 ! defense response to bacterium -relationship: capable_of GO:0051767 ! nitric-oxide synthase biosynthetic process -property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional.\n\nInflammatory macrophages, also sometimes referred to as M1 or classically activated macrophages, play an important role in the inflammatory response. The M1/M2 classification is based upon macrophage polarization rather than macrophage location and refers to macrophage activation towards either a more inflammatory or more resolving phenotype, respectively, although the functional diversity of macrophages is more nuanced than such a dichotomy suggests.\nInflammatory macrophages are derived from monocytes recruited to a site of infection or injury. M1 macrophages are classically activated, typically by IFN-γ or lipopolysaccharide (LPS). Upon sensing signs of inflammation, they quickly respond by increasing their pro-inflammatory activity. They achieve this by producing a range of signaling molecules, such as nitric oxide, reactive oxygen species, and numerous cytokines such as tumor necrosis factor-alpha (TNF-alpha) and interleukin-1, -6 and -12. The release of these potent molecules helps to recruit other immune cells to the site, killing off pathogenic organisms and facilitation inflammation. At the same time, M1 macrophages can also present antigens to T cells, thereby helping to induce an adaptive immune response. Over time, these macrophages may transition in phenotype and function to help resolve the inflammation and promote tissue repair.\nDespite the beneficial role of inflammatory macrophages in dealing with pathogens, chronic activation of these cells can lead to harmful effects. Over time, continuous production of pro-inflammatory molecules can cause damage to tissues and organs. This is seen in certain chronic inflammatory diseases, such as atherosclerosis, diabetes, obesity, asthma, and various autoimmune disorders. In such situations, the normally protective function of inflammatory macrophages is not properly controlled, which can contribute to disease pathology." xsd:string {xref="DOI:10.1038/s41392-023-01452-1", xref="DOI:10.1186/s12935-021-02089-2", xref="DOI:10.3389/fimmu.2015.00263", xref="DOI:10.3389/fimmu.2020.583084"} +relationship: capable_of GO:0045428 ! regulation of nitric oxide biosynthetic process +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nInflammatory macrophages, also sometimes referred to as M1 or classically activated macrophages, play an important role in the inflammatory response. The M1/M2 classification is based upon macrophage polarization rather than macrophage location and refers to macrophage activation towards either a more inflammatory or more resolving phenotype, respectively, although the functional diversity of macrophages is more nuanced than such a dichotomy suggests.\nInflammatory macrophages are derived from monocytes recruited to a site of infection or injury. M1 macrophages are classically activated, typically by IFN-γ or lipopolysaccharide (LPS). Upon sensing signs of inflammation, they quickly respond by increasing their pro-inflammatory activity. They achieve this by producing a range of signaling molecules, such as nitric oxide, reactive oxygen species, and numerous cytokines such as tumor necrosis factor-alpha (TNF-alpha) and interleukin-1, -6 and -12. The release of these potent molecules helps to recruit other immune cells to the site, killing off pathogenic organisms and facilitation inflammation. At the same time, M1 macrophages can also present antigens to T cells, thereby helping to induce an adaptive immune response. Over time, these macrophages may transition in phenotype and function to help resolve the inflammation and promote tissue repair.\nDespite the beneficial role of inflammatory macrophages in dealing with pathogens, chronic activation of these cells can lead to harmful effects. Over time, continuous production of pro-inflammatory molecules can cause damage to tissues and organs. This is seen in certain chronic inflammatory diseases, such as atherosclerosis, diabetes, obesity, asthma, and various autoimmune disorders. In such situations, the normally protective function of inflammatory macrophages is not properly controlled, which can contribute to disease pathology." xsd:string {xref="DOI:10.1038/s41392-023-01452-1", xref="DOI:10.1186/s12935-021-02089-2", xref="DOI:10.3389/fimmu.2015.00263", xref="DOI:10.3389/fimmu.2020.583084"} [Term] id: CL:0000864 name: tissue-resident macrophage def: "A macrophage constitutively resident in a particular tissue under non-inflammatory conditions, and capable of phagocytosing a variety of extracellular particulate material, including immune complexes, microorganisms, and dead cells." [GO_REF:0000031, GOC:ana, PMID:19770654] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "fixed macrophage" EXACT [] synonym: "resting histiocyte" EXACT [] xref: FMA:84642 @@ -10724,6 +12001,8 @@ relationship: part_of UBERON:0000479 ! tissue id: CL:0000865 name: gastrointestinal tract (lamina propria) macrophage def: "A gut-associated lymphoid tissue macrophage found in lamina propria of the gut." [GO_REF:0000031, GOC:ana, GOC:tfm, https://orcid.org/0000-0002-2825-0621] +subset: human_subset +subset: mouse_subset synonym: "gastrointestinal system (lamina propria) macrophage" EXACT [] synonym: "macrophage of gastrointestinal system (lamina propria)" EXACT [] synonym: "macrophage of gastrointestinal tract (lamina propria)" EXACT [] @@ -10738,6 +12017,8 @@ name: thymic macrophage def: "A tissue-resident macrophage resident found in the thymus, involved in the clearance of apoptotic thymocytes." [GO_REF:0000031, GOC:ana, GOC:tfm, PMID:9048205] comment: Role or process: immune, clearance of apoptotic thymocytes, antigen-presentation. subset: human_reference_atlas +subset: human_subset +subset: mouse_subset is_a: CL:0000864 {is_inferred="true"} ! tissue-resident macrophage intersection_of: CL:0000864 ! tissue-resident macrophage intersection_of: capable_of GO:0043277 ! apoptotic cell clearance @@ -10750,6 +12031,8 @@ property_value: RO:0002175 NCBITaxon:9606 id: CL:0000867 name: secondary lymphoid organ macrophage def: "A tissue-resident macrophage found in a secondary lymphoid organ." [GO_REF:0000031, GOC:ana, GOC:tfm] +subset: human_subset +subset: mouse_subset is_a: CL:0000864 ! tissue-resident macrophage [Term] @@ -10757,9 +12040,10 @@ id: CL:0000868 name: lymph node macrophage def: "A secondary lymphoid organ macrophage found in a lymph node. This cell is CD169-high." [GO_REF:0000031, GOC:ana, GOC:tfm, PMID:11971865] comment: Marker was observed on rat cells. +subset: human_subset +subset: mouse_subset synonym: "MF.LN" EXACT [] is_a: CL:0000867 {is_inferred="true"} ! secondary lymphoid organ macrophage -is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000867 ! secondary lymphoid organ macrophage intersection_of: part_of UBERON:0000029 ! lymph node intersection_of: RO:0015015 PR:000001931 ! has high plasma membrane amount sialoadhesin @@ -10774,6 +12058,8 @@ relationship: RO:0015016 PR:000001813 ! has low plasma membrane amount adhesion id: CL:0000869 name: tonsillar macrophage def: "A gut-associated lymphoid tissue macrophage found in tonsils." [GO_REF:0000031, GOC:ana, PMID:16048540] +subset: human_subset +subset: mouse_subset is_a: CL:0000885 ! gut-associated lymphoid tissue macrophage intersection_of: CL:0000884 ! mucosa-associated lymphoid tissue macrophage intersection_of: capable_of GO:0002395 ! immune response in nasopharyngeal-associated lymphoid tissue @@ -10785,6 +12071,8 @@ relationship: part_of UBERON:0002372 ! tonsil id: CL:0000870 name: Peyer's patch macrophage def: "A gut-associated lymphoid tissue macrophage found in the Peyer's patches." [GO_REF:0000031, GOC:ana, GOC:tfm] +subset: human_subset +subset: mouse_subset is_a: CL:0000885 {is_inferred="true"} ! gut-associated lymphoid tissue macrophage intersection_of: CL:0000885 ! gut-associated lymphoid tissue macrophage intersection_of: part_of UBERON:0001211 ! Peyer's patch @@ -10795,6 +12083,8 @@ id: CL:0000871 name: splenic macrophage def: "A secondary lymphoid organ macrophage found in the spleen." [GO_REF:0000031, PMID:15771589, PMID:16322748] comment: Role or process: immune, clearance of apoptotic and senescent cells. +subset: human_subset +subset: mouse_subset xref: FMA:83026 is_a: CL:0000867 {is_inferred="true"} ! secondary lymphoid organ macrophage is_a: CL:2000074 ! splenocyte @@ -10809,8 +12099,9 @@ name: splenic marginal zone macrophage def: "A splenic macrophage found in the marginal zone of the spleen, involved in recognition and clearance of particulate material from the splenic circulation. Markers include F4/80-negative, MARCO-positive, SR-A-positive, SIGN-R1-positive, and Dectin2-positive." [GO_REF:0000031, GOC:ana, PMID:16861066] comment: Markers: Mouse: F4/80-, MARCO+, SR-A+, SIGN-R1+, Dectin2+. subset: human_reference_atlas +subset: human_subset +subset: mouse_subset is_a: CL:0000871 {is_inferred="true"} ! splenic macrophage -is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000871 ! splenic macrophage intersection_of: CL:4030046 PR:000001012 ! lacks_plasma_membrane_part integrin alpha-M intersection_of: part_of UBERON:0001251 ! marginal zone of spleen @@ -10831,8 +12122,9 @@ id: CL:0000873 name: splenic metallophillic macrophage def: "A splenic macrophage found in the areas surrounding the white pulp of the spleen, adjacent to the marginal sinus. Markers include F4/80-negative, Dectin2-low, sialoadhesin-positive." [GO_REF:0000031, GOC:ana, PMID:20018690] comment: Markers: Mouse: F4/80-, Dectin2-low, sialoadhesin+. +subset: human_subset +subset: mouse_subset is_a: CL:0000871 {is_inferred="true"} ! splenic macrophage -is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000871 ! splenic macrophage intersection_of: adjacent_to UBERON:0001959 ! white pulp of spleen intersection_of: CL:4030046 PR:000001813 ! lacks_plasma_membrane_part adhesion G protein-coupled receptor E1 @@ -10851,8 +12143,9 @@ name: splenic red pulp macrophage def: "A splenic macrophage found in the red-pulp of the spleen, and involved in immune responses to blood-borne pathogens and in the clearance of senescent erythrocytes. Markers include F4/80-positive, CD68-positive, MR-positive, Dectin2-positive, macrosialin-positive, and sialoadhesin-low." [GO_REF:0000031, GOC:ana, PMID:19644016] comment: Markers: Mouse: F4/80+, CD68+, MR+, Dectin2+, macrosialin+, sialoadhesin-low; role or process: immune, clearance of senescent erythrocytes. subset: human_reference_atlas +subset: human_subset +subset: mouse_subset is_a: CL:0000871 {is_inferred="true"} ! splenic macrophage -is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000871 ! splenic macrophage intersection_of: capable_of GO:0006955 ! immune response intersection_of: capable_of GO:0034102 ! erythrocyte clearance @@ -10882,10 +12175,11 @@ def: "A type of monocyte characterized by low expression of CCR2, low responsive comment: Markers: CCR2-CX3CCR1+ (human, mouse, rat); human: CD16+, CCR5+, CD32/FcgRII-high, MHCII+, CD86+; mouse: CD62L-Ly6C-. subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "patrolling monocyte" EXACT [] synonym: "resident monocyte" EXACT [] is_a: CL:0000576 {is_inferred="true"} ! monocyte -is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000576 ! monocyte intersection_of: bearer_of PATO:0000587 ! decreased size intersection_of: capable_of GO:0031294 ! lymphocyte costimulation @@ -10910,8 +12204,9 @@ name: splenic white pulp macrophage def: "A splenic macrophage found in the white pulp of the spleen. Markers include F4/80-negative, CD68-positive, and macrosialin-positive." [GO_REF:0000031, GOC:ana, PMID:11207597] comment: Markers: Mouse: F4/80-, CD68+, macrosialin+. subset: human_reference_atlas +subset: human_subset +subset: mouse_subset is_a: CL:0000871 {is_inferred="true"} ! splenic macrophage -is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000871 ! splenic macrophage intersection_of: CL:4030046 PR:000001813 ! lacks_plasma_membrane_part adhesion G protein-coupled receptor E1 intersection_of: part_of UBERON:0001959 ! white pulp of spleen @@ -10926,6 +12221,8 @@ id: CL:0000877 name: splenic tingible body macrophage def: "A splenic white pulp macrophage found in and around the germinal centers of the white pulp of the spleen that participates in phagocytosis of apoptotic B cells from the germinal centers. A marker for a cell of this type is Mertk-positive." [GO_REF:0000031, GOC:ana, GOC:tfm, PMID:19631584] subset: human_reference_atlas +subset: human_subset +subset: mouse_subset is_a: CL:0000876 {is_inferred="true"} ! splenic white pulp macrophage intersection_of: CL:0000876 ! splenic white pulp macrophage intersection_of: capable_of GO:0043277 ! apoptotic cell clearance @@ -10941,17 +12238,24 @@ id: CL:0000878 name: central nervous system macrophage def: "A tissue-resident macrophage found in the central nervous system." [GO_REF:0000031, PMID:16322748] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "CNS macrophage" EXACT [] +xref: https://cellxgene.cziscience.com/cellguide/CL_0000878 is_a: CL:0000864 {is_inferred="true"} ! tissue-resident macrophage is_a: CL:0002319 ! neural cell intersection_of: CL:0000864 ! tissue-resident macrophage intersection_of: part_of UBERON:0001017 ! central nervous system relationship: part_of UBERON:0001017 ! central nervous system +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nCentral Nervous System (CNS) macrophages represent an integral part of the brain's innate immune system. These immune cells play crucial roles in maintenance and regulation, homeostasis, and disease response, thereby helping in the overall cognitive functioning of an organism. \nThere are different macrophage populations in the CNS, often classified into microglial cells, which reside in the parenchyma, and non-parenchymal macrophages at the interface between the brain and the periphery, including the perivascular spaces, the choroid plexus, and the meninges. CNS macrophages are derived from erythromyeloid progenitors in the yolk sac. CNS macrophages have distinct morphologies: Meningeal and perivascular macrophages have a more elongated shape than microglia, which are characterized by a small cell body with fine processes; in contrast, choroid plexus macrophages typically have a stellate shape.\nMicroglia are the most abundant abundant mononuclear phagocytes and have been shown to play a number of physiological roles, including proinflammatory and anti-inflammatory functions, synaptic pruning and remodeling, and apoptotic cell removal through phagocytosis. Non-parenchymal CAMs primarily support the barrier function against external antigens. Meningeal macrophages have been shown to respond to peripheral microbial challenges and to protect the brain against fatal viral infection.\nCNS macrophages are also involved in the initiation and progression of many neurological diseases, such as Alzheimer's disease and Parkinson's disease as well as multiple sclerosis." xsd:string {xref="DOI:10.1007/s00281-013-0382-8", xref="DOI:10.1016/j.immuni.2022.10.005", xref="DOI:10.1016/j.tins.2021.07.002", xref="DOI:10.1038/s41583-019-0201-x"} [Term] id: CL:0000879 name: meningeal macrophage def: "A border associated macrophage that is part of a meninx. This macrophage type is elongated and amoeboid spindle-shaped with limited mobility. This macrophage is highly phagocytic, expresses scavenger receptors, has dynamic protrusions and extends its processes during inflammation." [GO_REF:0000031, GOC:ana, PMID:11591794, PMID:24078900, PMID:37232741] +subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "MM" RELATED OMO:0003000 [PMID:33556248] synonym: "MnMΦ" RELATED OMO:0003000 [PMID:38347231] synonym: "sdΜΦ" RELATED OMO:0003000 [PMID:37232741] @@ -10968,6 +12272,8 @@ relationship: part_of UBERON:0002360 ! meninx id: CL:0000880 name: choroid plexus macrophage def: "A border associated macrophage found at the interface between the blood and the cerebrospinal fluid in the brain. This central nervous system macrophage has a star-like shaped body and expresses scavenger receptors." [GO_REF:0000031, GOC:ana, PMID:37232741, PMID:9550136] +subset: human_subset +subset: mouse_subset synonym: "cpMΦ" RELATED OMO:0003000 [PMID:37232741] is_a: CL:4042003 ! border associated macrophage intersection_of: CL:4042003 ! border associated macrophage @@ -10980,10 +12286,11 @@ relationship: part_of UBERON:0001886 ! choroid plexus id: CL:0000881 name: perivascular macrophage def: "A border associated macrophage that is adjacent to a small blood vessel of a brain. A perivascular macrophage expresses the markers CD14, CD16 and CD163. In homeostatic conditions, this central nervous system macrophage has a non-motile cell body with extending and retracting projections through the blood vessel wall." [GO_REF:0000031, GOC:tfm, PMID:16507898, PMID:37232741] +subset: human_subset +subset: mouse_subset synonym: "pvMΦ" RELATED OMO:0003000 [PMID:37232741] is_a: CL:4033054 ! perivascular cell is_a: CL:4042003 {is_inferred="true"} ! border associated macrophage -is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:4042003 ! border associated macrophage intersection_of: part_of UBERON:0001981 ! blood vessel intersection_of: RO:0002104 PR:000001483 ! has plasma membrane part low affinity immunoglobulin gamma Fc region receptor III @@ -10999,6 +12306,8 @@ id: CL:0000882 name: thymic medullary macrophage def: "A thymic macrophage found in the thymic medulla." [GO_REF:0000031, GOC:ana, PMID:9048205] subset: human_reference_atlas +subset: human_subset +subset: mouse_subset is_a: CL:0000866 {is_inferred="true"} ! thymic macrophage intersection_of: CL:0000866 ! thymic macrophage intersection_of: part_of UBERON:0002124 ! medulla of thymus @@ -11010,6 +12319,8 @@ id: CL:0000883 name: thymic cortical macrophage def: "A thymic macrophage found in the thymic cortex." [GO_REF:0000031, GOC:ana, GOC:tfm, PMID:9048205] subset: human_reference_atlas +subset: human_subset +subset: mouse_subset is_a: CL:0000866 {is_inferred="true"} ! thymic macrophage intersection_of: CL:0000866 ! thymic macrophage intersection_of: part_of UBERON:0002123 ! cortex of thymus @@ -11020,6 +12331,8 @@ property_value: RO:0002175 NCBITaxon:9606 id: CL:0000884 name: mucosa-associated lymphoid tissue macrophage def: "A tissue-resident macrophage found in the mucosa associated lymphoid tissue." [GO_REF:0000031, GOC:ana, GOC:tfm, PMID:19906191] +subset: human_subset +subset: mouse_subset is_a: CL:0000867 {is_inferred="true"} ! secondary lymphoid organ macrophage intersection_of: CL:0000867 ! secondary lymphoid organ macrophage intersection_of: part_of UBERON:0001961 ! mucosa-associated lymphoid tissue @@ -11029,6 +12342,8 @@ relationship: part_of UBERON:0001961 ! mucosa-associated lymphoid tissue id: CL:0000885 name: gut-associated lymphoid tissue macrophage def: "A mucosa-associated lymphoid tissue macrophage found in the mucosa-associated lymphoid tissues of the gut." [GO_REF:0000031, GOC:ana, PMID:19906191] +subset: human_subset +subset: mouse_subset is_a: CL:0000884 {is_inferred="true"} ! mucosa-associated lymphoid tissue macrophage intersection_of: CL:0000884 ! mucosa-associated lymphoid tissue macrophage intersection_of: capable_of GO:0002387 ! immune response in gut-associated lymphoid tissue @@ -11040,6 +12355,8 @@ relationship: part_of UBERON:0001962 ! gut-associated lymphoid tissue id: CL:0000886 name: nasal and broncial associated lymphoid tissue macrophage def: "A mucosa-associated lymphoid tissue macrophage found in the nasal and bronchial mucosa-associated lymphoid tissues." [GO_REF:0000031, GOC:ana, PMID:16048540] +subset: human_subset +subset: mouse_subset is_a: CL:0000884 {is_inferred="true"} ! mucosa-associated lymphoid tissue macrophage intersection_of: CL:0000884 ! mucosa-associated lymphoid tissue macrophage intersection_of: capable_of GO:0002395 ! immune response in nasopharyngeal-associated lymphoid tissue @@ -11052,6 +12369,8 @@ id: CL:0000887 name: lymph node subcapsular sinus macrophage def: "A lymph node macrophage found in the subcapsular sinus of lymph nodes that participates in sensing, clearance, and antigen presentation of lymph-borne particulate antigens. This macrophage is capable of activating invaraint NKT cells and is CD169-positive." [GO_REF:0000031, GOC:tfm, PMID:14668803, PMID:17934446, PMID:20228797] subset: human_reference_atlas +subset: human_subset +subset: mouse_subset is_a: CL:0000868 {is_inferred="true"} ! lymph node macrophage intersection_of: CL:0000868 ! lymph node macrophage intersection_of: adjacent_to UBERON:0002194 ! capsule of lymph node @@ -11067,6 +12386,8 @@ id: CL:0000888 name: lymph node tingible body macrophage def: "A lymph node macrophage found in the cortex of lymph nodes, in particular in and around the germinal centers, and that participates in phagocytosis of apoptotic B cells from the germinal centers." [GO_REF:0000031, GOC:ana, GOC:tfm, PMID:19631584] subset: human_reference_atlas +subset: human_subset +subset: mouse_subset is_a: CL:0000868 {is_inferred="true"} ! lymph node macrophage intersection_of: CL:0000868 ! lymph node macrophage intersection_of: capable_of GO:0002905 ! regulation of mature B cell apoptotic process @@ -11083,8 +12404,10 @@ name: myeloid suppressor cell def: "An immature myeloid leukocyte of heterogeneous phenotype found particularly in cancer and sepsis patients that is capable of suppressing activity of T cells in ex vivo assays. This cell type is CD45-positive, CD11b-positive." [GO_REF:0000031, GOC:add, GOC:ana, PMID:16168663, PMID:17016554, PMID:17016559] comment: Markers: Mouse: CD11b+GR1+CD31+; Human: CD34+ CD33+CD15-CD13+. (According to some reports in humans these cells are iNOS+ARG1+IL13+IFNg+); location: In cancerous tissue; in the blood and lymphoid organs in sepsis. subset: blood_and_immune_upper_slim +subset: cellxgene_subset +subset: human_subset +subset: mouse_subset is_a: CL:0000766 {is_inferred="true"} ! myeloid leukocyte -is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000766 ! myeloid leukocyte intersection_of: bearer_of PATO:0001501 ! immature intersection_of: capable_of GO:0050777 ! negative regulation of immune response @@ -11101,6 +12424,8 @@ name: alternatively activated macrophage def: "An elicited macrophage characterized by low production of pro-inflammatory and Th1 polarizing cytokines and high expression of arginase-1, and associated with tissue remodelling." [GO_REF:0000031, GOC:ana, GOC:tfm, PMID:20510870] comment: Role or process: tissue remodeling. subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "M2 macrophage" RELATED [PMID:28923980] xref: https://cellxgene.cziscience.com/cellguide/CL_0000890 is_a: CL:0000861 {is_inferred="true"} ! elicited macrophage @@ -11109,12 +12434,14 @@ intersection_of: capable_of GO:0048771 ! tissue remodeling intersection_of: has_part PR:000001844 ! arginase-1 relationship: capable_of GO:0048771 ! tissue remodeling relationship: has_part PR:000001844 ! arginase-1 -property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional.\n\nAlternatively activated macrophages, also referred to as M2 macrophages, are immune cells originating from monocytes. The M1/M2 classification is based upon macrophage polarization rather than macrophage location and refers to macrophage activation towards either a more inflammatory or more resolving phenotype, respectively, although the functional diversity of macrophages is more nuanced than such a dichotomy suggests.\nM2 macrophages cells are differentiated from their precursors generally in response to Th2 cytokines, such as interleukin-4 (IL-4), interleukin-10 (IL-10), and interleukin-13 (IL-13). Tissue-resident macrophages are also sometimes said to have an “M2-like” phenotype. M2 macrophages play key roles in immunoregulation and disease resolution.\nFunctionally, alternatively activated macrophages are essential in wound healing and tissue repair and remodeling, largely due to their potent anti-inflammatory actions and their ability to promote angiogenesis. They achieve these functions by the production of specific growth factors and signaling proteins including Arg1, Ym1/2, Fizz1, and TGF-β. Additionally, they provide defense against specific categories of pathogens, particularly parasites, through specific communication with Th2 cells. \nHowever, dysfunction of M2 macrophages can be harmful. Alternatively activated macrophages have been associated with several pathological conditions such as asthma, fibrosis, and tumor progression. This is due to their capacity to inhibit inflammatory responses, promote unneeded wound healing processes, and support tumour growth and spreading. Furthermore, complex roles have been observed in metabolic disorders, cardiovascular diseases, and neurodegenerative diseases, showing the diverse functional spectrum of these cells." xsd:string {xref="DOI:10.1038/s41392-023-01452-1", xref="DOI:10.1186/s12935-021-02089-2", xref="DOI:10.3389/fimmu.2015.00263", xref="DOI:10.3389/fimmu.2020.583084"} +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nAlternatively activated macrophages, also referred to as M2 macrophages, are immune cells originating from monocytes. The M1/M2 classification is based upon macrophage polarization rather than macrophage location and refers to macrophage activation towards either a more inflammatory or more resolving phenotype, respectively, although the functional diversity of macrophages is more nuanced than such a dichotomy suggests.\nM2 macrophages cells are differentiated from their precursors generally in response to Th2 cytokines, such as interleukin-4 (IL-4), interleukin-10 (IL-10), and interleukin-13 (IL-13). Tissue-resident macrophages are also sometimes said to have an “M2-like” phenotype. M2 macrophages play key roles in immunoregulation and disease resolution.\nFunctionally, alternatively activated macrophages are essential in wound healing and tissue repair and remodeling, largely due to their potent anti-inflammatory actions and their ability to promote angiogenesis. They achieve these functions by the production of specific growth factors and signaling proteins including Arg1, Ym1/2, Fizz1, and TGF-β. Additionally, they provide defense against specific categories of pathogens, particularly parasites, through specific communication with Th2 cells. \nHowever, dysfunction of M2 macrophages can be harmful. Alternatively activated macrophages have been associated with several pathological conditions such as asthma, fibrosis, and tumor progression. This is due to their capacity to inhibit inflammatory responses, promote unneeded wound healing processes, and support tumour growth and spreading. Furthermore, complex roles have been observed in metabolic disorders, cardiovascular diseases, and neurodegenerative diseases, showing the diverse functional spectrum of these cells." xsd:string {xref="DOI:10.1038/s41392-023-01452-1", xref="DOI:10.1186/s12935-021-02089-2", xref="DOI:10.3389/fimmu.2015.00263", xref="DOI:10.3389/fimmu.2020.583084"} [Term] id: CL:0000891 name: foam cell def: "A type of cell containing lipids in small vacuoles and typically seen in atherolosclerotic lesions, as well as other conditions." [GOC:add] +subset: human_subset +subset: mouse_subset xref: BTO:0003872 xref: FMA:83586 xref: MESH:D005487 @@ -11124,6 +12451,8 @@ is_a: CL:0000000 ! cell id: CL:0000892 name: smooth muscle cell derived foam cell def: "A type of foam cell derived from a smooth muscle cell containing lipids in small vacuoles and typically seen in atherolosclerotic lesions, as well as other conditions." [GOC:add, PMID:30664015] +subset: human_subset +subset: mouse_subset is_a: BFO:0000002 is_a: CL:0000255 ! eukaryotic cell is_a: CL:0000891 ! foam cell @@ -11134,6 +12463,8 @@ id: CL:0000893 name: thymocyte def: "An immature T cell located in the thymus." [GO_REF:0000031, GOC:add, GOC:tfm, PMID:12415312] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "immature T cell" BROAD [] synonym: "immature T lymphocyte" BROAD [] synonym: "immature T-cell" BROAD [] @@ -11155,6 +12486,8 @@ id: CL:0000894 name: DN1 thymic pro-T cell def: "A pro-T cell that has the phenotype CD4-negative, CD8-negative, CD44-positive, and CD25-negative." [GO_REF:0000031, GOC:add, GOC:tfm] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "DN1 thymic pro-T lymphocyte" EXACT [] synonym: "DN1 thymic pro-T-cell" EXACT [] synonym: "DN1 thymic pro-T-lymphocyte" EXACT [] @@ -11163,7 +12496,6 @@ synonym: "DN1 thymocyte" EXACT [] synonym: "double negative 1" EXACT [] synonym: "preT.DN1.Th" EXACT [] is_a: CL:0000827 {is_inferred="true"} ! pro-T cell -is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000827 ! pro-T cell intersection_of: CL:4030046 PR:000001004 ! lacks_plasma_membrane_part CD4 molecule intersection_of: CL:4030046 PR:000001084 ! lacks_plasma_membrane_part T-cell surface glycoprotein CD8 alpha chain @@ -11184,6 +12516,8 @@ def: "An antigen inexperienced CD4-positive, alpha-beta T cell with the phenotyp comment: These cells have not been exposed to antigen following thymic T-cell selection; found in blood and secondary lymphoid organs. This cell type is compatible with the HIPC Lyoplate markers for 'naive CD4+ T cell', but includes additional markers known to be expressed on naive CD4+ T cells. subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "naive CD4+ T cell" BROAD [PMID:22343568] synonym: "naive thymus-derived CD4-positive, alpha-beta T lymphocyte" EXACT [] synonym: "naive thymus-derived CD4-positive, alpha-beta T-cell" EXACT [] @@ -11208,6 +12542,8 @@ id: CL:0000896 name: activated CD4-positive, alpha-beta T cell def: "A recently activated CD4-positive, alpha-beta T cell with the phenotype CD69-positive, CD62L-negative, CD127-negative, and CD25-positive." [GO_REF:0000031, GOC:add, GOC:pam] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "activated CD4-positive, alpha-beta T lymphocyte" EXACT [] synonym: "activated CD4-positive, alpha-beta T-cell" EXACT [] synonym: "activated CD4-positive, alpha-beta T-lymphocyte" EXACT [] @@ -11229,6 +12565,8 @@ name: CD4-positive, alpha-beta memory T cell def: "A CD4-positive, alpha-beta T cell that has differentiated into a memory T cell." [GOC:add, http://www.immgen.org/index_content.html, ISBN:0781735149] subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "CD4-positive, alpha-beta memory T lymphocyte" EXACT [] synonym: "CD4-positive, alpha-beta memory T-cell" EXACT [] synonym: "CD4-positive, alpha-beta memory T-lymphocyte" EXACT [] @@ -11247,6 +12585,8 @@ id: CL:0000898 name: naive T cell def: "Mature T cell not yet exposed to antigen with the phenotype CCR7-positive, CD45RA-positive, and CD127-positive. This cell type is also described as being CD25-negative, CD62L-high and CD44-low." [GO_REF:0000031, GOC:add, GOC:pam, GOC:tfm, PMID:19100699] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "naive T lymphocyte" EXACT [] synonym: "naive T-cell" EXACT [] synonym: "naive T-lymphocyte" EXACT [] @@ -11271,6 +12611,8 @@ def: "CD4-positive, alpha-beta T cell with the phenotype RORgamma-t-positive, CX comment: This cell type is compatible with the HIPC Lyoplate markers for 'Th17 CD4+ T cell', but its logical definition includes additional known characteristics of T-helper 17 T cells. subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "helper T cell type 17" EXACT [] synonym: "IL-17-producing CD4+ T helper" EXACT [] synonym: "T helper cells type 17" EXACT [] @@ -11301,6 +12643,8 @@ def: "A CD8-positive, alpha-beta T cell that has not experienced activation via comment: This cell traffics in secondary lymphoid organs and blood. This cell type is compatible with the HIPC Lyoplate markers for 'naive CD8+ T cell', but includes additional markers known to be expressed on naive CD8+ T cells. subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "naive CD8+ T cell" BROAD [PMID:22343568] synonym: "naive thymus-dervied CD8-positive, alpha-beta T lymphocyte" EXACT [] synonym: "naive thymus-dervied CD8-positive, alpha-beta T-cell" EXACT [] @@ -11324,6 +12668,8 @@ id: CL:0000901 name: Tr1 cell def: "CD4-positive alpha-beta T cell with regulatory function that produces IL-10." [GO_REF:0000031, GOC:add, GOC:pam, PMID:16903904] comment: These cells are reportedly induced by IL-10 and are capable of producing IFN-gamma, IL-5, IL-10, and TGF-beta.) +subset: human_subset +subset: mouse_subset synonym: "T-regulatory T cell type 1" EXACT [] synonym: "Tr1 T cell" EXACT [] synonym: "Tr1 T lymphocyte" EXACT [] @@ -11340,6 +12686,8 @@ relationship: capable_of GO:0032613 ! interleukin-10 production id: CL:0000902 name: induced T-regulatory cell def: "CD4-positive alpha-beta T cell with the phenotype CD25-positive, CTLA-4-positive, and FoxP3-positive with regulatory function." [GO_REF:0000031, GOC:add, GOC:pam, GOC:tfm, PMID:19464985] +subset: human_subset +subset: mouse_subset synonym: "adaptive Treg" RELATED [] synonym: "aTreg" RELATED [] synonym: "induced regulatory T cell" EXACT [] @@ -11362,6 +12710,8 @@ id: CL:0000903 name: natural T-regulatory cell def: "CD4-positive alpha-beta T cell with the phenotype FoxP3-positive, CD25-positive, CD62L-positive, and CTLA-4 positive with regulatory function." [GO_REF:0000031, GOC:add, GOC:pam, GOC:tfm, PMID:19464985] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "natural regulatory T cell" EXACT [] synonym: "natural regulatory T lymphocyte" EXACT [] synonym: "natural regulatory T-cell" EXACT [] @@ -11385,6 +12735,7 @@ name: central memory CD4-positive, alpha-beta T cell def: "CD4-positive, alpha-beta memory T cell with the phenotype CCR7-positive, CD127-positive, CD45RA-negative, CD45RO-positive, and CD25-negative." [GO_REF:0000031, GOC:add, GOC:pam, PMID:22343568] comment: This cell type is compatible with the HIPC Lyoplate markers for 'central memory CD4+ T cell', but includes additional markers known to be expressed on central memory CD4+ T cells. subset: cellxgene_subset +subset: human_subset synonym: "central CD4-positive, alpha-beta memory T cell" EXACT [] synonym: "central CD4-positive, alpha-beta memory T lymphocyte" EXACT [] synonym: "central CD4-positive, alpha-beta memory T-cell" EXACT [] @@ -11408,6 +12759,7 @@ def: "CD4-positive, alpha-beta memory T cell with the phenotype CCR7-negative, C comment: This cell type is compatible with the HIPC Lyoplate markers for 'effector memory CD4+ T cell', but includes additional markers known to be expressed on effector memory CD4+ T cells. subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset synonym: "effector CD4-positive, alpha-beta memory T cell" EXACT [] synonym: "effector CD4-positive, alpha-beta memory T lymphocyte" EXACT [] synonym: "effector CD4-positive, alpha-beta memory T-cell" EXACT [] @@ -11430,6 +12782,8 @@ id: CL:0000906 name: activated CD8-positive, alpha-beta T cell def: "A CD8-positive, alpha-beta T cell with the phenotype CD69-positive, CD62L-negative, CD127-negative, CD25-positive, and CCR7-negative." [GO_REF:0000031, GOC:add, GOC:pam, GOC:tfm] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "activated CD8-positive, alpha-beta T lymphocyte" EXACT [] synonym: "activated CD8-positive, alpha-beta T-cell" EXACT [] synonym: "activated CD8-positive, alpha-beta T-lymphocyte" EXACT [] @@ -11453,6 +12807,7 @@ name: central memory CD8-positive, alpha-beta T cell def: "CD8-positive, alpha-beta memory T cell with the phenotype CCR7-positive, CD127-positive, CD45RA-negative, CD45RO-positive, and CD25-negative." [GO_REF:0000031, GOC:add, GOC:pam, GOC:tfm, PMID:20146720, PMID:22343568] comment: This cell type is compatible with the HIPC Lyoplate markers for 'central memory CD8+ T cell', but includes additional markers known to be expressed on central memory CD8+ T cells. subset: cellxgene_subset +subset: human_subset synonym: "central CD8-positive, alpha-beta memory T cell" EXACT [] synonym: "central CD8-positive, alpha-beta memory T lymphocyte" EXACT [] synonym: "central CD8-positive, alpha-beta memory T-cell" EXACT [] @@ -11474,6 +12829,8 @@ id: CL:0000908 name: CD8-positive, alpha-beta cytokine secreting effector T cell def: "A CD8-positive, alpha-beta T cell with the phenotype CD69-positive, CD62L-negative, CD127-negative, and CD25-positive, that secretes cytokines." [GO_REF:0000031, GOC:add, GOC:pam, GOC:tfm, PMID:20146720] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "CD8-positive, alpha-beta cytokine secreting effector T lymphocyte" EXACT [] synonym: "CD8-positive, alpha-beta cytokine secreting effector T-cell" EXACT [] synonym: "CD8-positive, alpha-beta cytokine secreting effector T-lymphocyte" EXACT [] @@ -11499,6 +12856,8 @@ name: CD8-positive, alpha-beta memory T cell def: "A CD8-positive, alpha-beta T cell that has differentiated into a memory T cell." [GOC:add, PMID:20146720] subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "CD8-positive, alpha-beta memory T lymphocyte" EXACT [] synonym: "CD8-positive, alpha-beta memory T-cell" EXACT [] synonym: "CD8-positive, alpha-beta memory T-lymphocyte" EXACT [] @@ -11518,6 +12877,8 @@ name: cytotoxic T cell def: "A mature T cell that differentiated and acquired cytotoxic function with the phenotype perforin-positive and granzyme-B positive." [GO_REF:0000031, GOC:add, GOC:pam, GOC:tfm, PMID:18395547] subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "cytotoxic T lymphocyte" EXACT [] synonym: "cytotoxic T-cell" EXACT [] synonym: "cytotoxic T-lymphocyte" EXACT [] @@ -11534,6 +12895,8 @@ property_value: RO:0002175 NCBITaxon:9606 id: CL:0000911 name: effector T cell def: "A differentiated T cell with ability to traffic to peripheral tissues and is capable of mounting a specific immune response." [GOC:PAM-ADD, GOC:tfm, ISBN:0877799148, PMID:18395547] +subset: human_subset +subset: mouse_subset synonym: "effector T lymphocyte" EXACT [] synonym: "effector T-cell" EXACT [] synonym: "effector T-lymphocyte" EXACT [] @@ -11550,6 +12913,8 @@ id: CL:0000912 name: helper T cell def: "A effector T cell that provides help in the form of secreted cytokines to other immune cells." [GO_REF:0000031, GOC:add, GOC:pam, GOC:tfm, PMID:18395547] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "helper T lymphocyte" EXACT [] synonym: "helper T-cell" EXACT [] synonym: "helper T-lymphocyte" EXACT [] @@ -11568,6 +12933,7 @@ def: "CD8-positive, alpha-beta memory T cell with the phenotype CCR7-negative, C comment: This cell type is compatible with the HIPC Lyoplate markers for 'effector memory CD8+ T cell', but includes additional markers known to be expressed on effector memory CD8+ T cells. subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset synonym: "effector CD8-positive, alpha-beta memory T cell" EXACT [] synonym: "effector CD8-positive, alpha-beta memory T lymphocyte" EXACT [] synonym: "effector CD8-positive, alpha-beta memory T-cell" EXACT [] @@ -11591,6 +12957,8 @@ name: immature NK T cell def: "An immature alpha-beta T-cell that express Egr2. These cells give rise to T cells expressing NK markers." [GO_REF:0000031, GOC:add, GOC:pam, GOC:tfm, PMID:17589542, PMID:19169262] subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "immature NK T lymphocyte" EXACT [] synonym: "immature NK T-cell" EXACT [] synonym: "immature NK T-lymphocyte" EXACT [] @@ -11608,6 +12976,8 @@ name: CD8-alpha-alpha-positive, alpha-beta intraepithelial T cell def: "An alpha-beta intraepithelial T cell with the phenotype CD8-alpha-alpha-positive located in the columnar epithelium of the gastrointestinal tract. These cells have a memory phenotype of CD2-negative and CD5-negative." [GO_REF:0000031, GOC:add, GOC:pam, PMID:11685222] subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "CD8-alpha-alpha-positive, alpha-beta intraepithelial T lymphocyte" EXACT [] synonym: "CD8-alpha-alpha-positive, alpha-beta intraepithelial T-cell" EXACT [] synonym: "CD8-alpha-alpha-positive, alpha-beta intraepithelial T-lymphocyte" EXACT [] @@ -11627,6 +12997,8 @@ id: CL:0000916 name: dendritic epidermal T cell def: "A mature gamma-delta T cell located in the epidermis that regulates wound healing." [GO_REF:0000031, GOC:add, GOC:pam, GOC:tfm, PMID:11976459] comment: In mice, DETC have an invariant T cell receptor. +subset: human_subset +subset: mouse_subset synonym: "dendritic epidermal T lymphocyte" EXACT [] synonym: "dendritic epidermal T-cell" EXACT [] synonym: "dendritic epidermal T-lymphocyte" EXACT [] @@ -11644,6 +13016,9 @@ id: CL:0000917 name: Tc1 cell def: "A CD8-positive, alpha-beta positive T cell that has the phenotype T-bet-positive, eomesodermin-positive, CXCR3-positive, CCR6-negative, and is capable of producing interferon-gamma." [GO_REF:0000031, GOC:add, GOC:pam, PMID:22343568, PMID:9914231] comment: This cell type is compatible with the HIPC Lyoplate markers for 'Tc1 CD8+ T cell', but its logical definition includes additional known characteristics of Tc1 T cells. +subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "CD8-positive Th1 cell" EXACT [] synonym: "T-cytotoxic T cell type 1" EXACT [] synonym: "Tc1 CD8+ T cell" EXACT [PMID:22343568] @@ -11674,6 +13049,8 @@ id: CL:0000918 name: Tc2 cell def: "A CD8-positive, alpha-beta positive T cell expressing GATA-3 and secreting IL-4." [GO_REF:0000031, GOC:add, GOC:pam, GOC:tfm, PMID:9914231] comment: This cell type is compatible with the HIPC Lyoplate markers for 'non-Tc1/Tc17 CD8+ T cell' (see CL:0001052), but includes the additional necessary and sufficient conditions to allow classification as a Tc2 T cell. +subset: human_subset +subset: mouse_subset synonym: "CD8-positive Th2 cell" EXACT [] synonym: "T-cytotoxic T cell type 2" EXACT [] synonym: "Tc2 T cell" EXACT [] @@ -11698,6 +13075,8 @@ relationship: has_part PR:000001941 ! trans-acting T-cell-specific transcription id: CL:0000919 name: CD8-positive, CD25-positive, alpha-beta regulatory T cell def: "A CD8-positive alpha beta-positive T cell with the phenotype FoxP3-positive and having suppressor function." [GO_REF:0000031, GOC:add, GOC:pam, GOC:tfm, PMID:19118505] +subset: human_subset +subset: mouse_subset synonym: "CD8+CD25+ T cell" EXACT [] synonym: "CD8+CD25+ T lymphocyte" EXACT [] synonym: "CD8+CD25+ T(reg)" EXACT [] @@ -11720,6 +13099,8 @@ relationship: RO:0002202 CL:0000906 ! develops from activated CD8-positive, alph id: CL:0000920 name: CD8-positive, CD28-negative, alpha-beta regulatory T cell def: "CD8-positive, alpha-beta positive regulatory T cell with the phenotype CD28-negative and FoxP3-positive." [GO_REF:0000031, GOC:add, GOC:pam, GOC:tfm, PMID:19118505] +subset: human_subset +subset: mouse_subset synonym: "CD8+CD28- T cell" EXACT [] synonym: "CD8+CD28- T lymphocyte" EXACT [] synonym: "CD8+CD28- T(reg)" EXACT [] @@ -11746,6 +13127,8 @@ def: "An alpha-beta T cell expressing NK cell markers that is CD1d restricted an comment: In mouse the canonical TCR is V-alpha-14, and in humans it is V-alpha 24. subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "classical NK T cell" EXACT [] synonym: "invariant NK T cell" RELATED [] synonym: "type I NK T lymphocyte" EXACT [] @@ -11763,6 +13146,8 @@ id: CL:0000922 name: type II NK T cell def: "An alpha-beta T cell expressing NK call markers that is CD1d restricted and expresses a diverse TCR repertoire. Type II NKT cells do not become activated by alpha-galactosylceramide when presented by CD1d." [GO_REF:0000031, GOC:add, GOC:pam, GOC:tfm, PMID:15039760] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "type II NK T lymphocyte" EXACT [] synonym: "type II NK T-cell" EXACT [] synonym: "type II NK T-lymphocyte" EXACT [] @@ -11776,6 +13161,8 @@ relationship: capable_of GO:0002288 ! NK T cell activation involved in immune re id: CL:0000923 name: CD4-positive type I NK T cell def: "A type I NK T cell that has the phenotype CD4-positive." [GO_REF:0000031, GOC:add, GOC:pam, GOC:tfm, PMID:17303398] +subset: human_subset +subset: mouse_subset synonym: "CD4-positive type I NK T lymphocyte" EXACT [] synonym: "CD4-positive type I NK T-cell" EXACT [] synonym: "CD4-positive type I NK T-lymphocyte" EXACT [] @@ -11790,6 +13177,8 @@ relationship: RO:0002104 PR:000001004 ! has plasma membrane part CD4 molecule id: CL:0000924 name: CD4-negative, CD8-negative type I NK T cell def: "A type I NK T cell that has the phenotype CD4-negative and CD8-negative." [GO_REF:0000031, GOC:add, GOC:pam, GOC:tfm, PMID:18997862] +subset: human_subset +subset: mouse_subset synonym: "CD4-negative, CD8-negative type I NK T lymphocyte" EXACT [] synonym: "CD4-negative, CD8-negative type I NK T-cell" EXACT [] synonym: "CD4-negative, CD8-negative type I NK T-lymphocyte" EXACT [] @@ -11806,6 +13195,8 @@ relationship: CL:4030046 PR:000001084 ! lacks_plasma_membrane_part T-cell surfac id: CL:0000925 name: activated CD4-positive type I NK T cell def: "A type I NK T cell that has been recently activated, secretes interferon-gamma and IL-4, and has the phenotype CD4-positive, CD69-positive, and downregulated NK markers." [GO_REF:0000031, GOC:add, GOC:pam, GOC:tfm, PMID:17303398] +subset: human_subset +subset: mouse_subset synonym: "activated CD4-positive type I NK T lymphocyte" EXACT [] synonym: "activated CD4-positive type I NK T-cell" EXACT [] synonym: "activated CD4-positive type I NK T-lymphocyte" EXACT [] @@ -11825,6 +13216,8 @@ relationship: RO:0002202 CL:0000923 ! develops from CD4-positive type I NK T cel id: CL:0000926 name: CD4-positive type I NK T cell secreting interferon-gamma def: "A mature NK T cell that secretes interferon-gamma and enhances type 1 immune responses." [GO_REF:0000031, GOC:add, GOC:pam, GOC:tfm, PMID:17303398] +subset: human_subset +subset: mouse_subset synonym: "CD4-positive type I NK T cell secreting IFN-gamma" EXACT [] synonym: "CD4-positive type I NK T lymphocyte secreting interferon-gamma" EXACT [] synonym: "CD4-positive type I NK T-cell secreting interferon-gamma" EXACT [] @@ -11843,6 +13236,8 @@ relationship: RO:0002202 CL:0000925 ! develops from activated CD4-positive type id: CL:0000927 name: CD4-positive type I NK T cell secreting interleukin-4 def: "A mature NK T cell that predominantly secretes type 2 cytokines such as interleukin-4 and interleukin-13 and enhances type 2 immune responses." [GO_REF:0000031, GOC:add, GOC:pam, GOC:tfm] +subset: human_subset +subset: mouse_subset synonym: "CD4-positive type I NK T cell secreting IL-4" EXACT [] synonym: "CD4-positive type I NK T lymphocyte secreting interleukin-4" EXACT [] synonym: "CD4-positive type I NK T-cell secreting interleukin-4" EXACT [] @@ -11863,6 +13258,9 @@ relationship: RO:0002202 CL:0000925 ! develops from activated CD4-positive type id: CL:0000928 name: activated CD4-negative, CD8-negative type I NK T cell def: "A type I NK T cell that has been recently activated, secretes interferon-gamma and interleukin-4, and has phenotype CD4-negative, CD8-negative, CD69-positive, and downregulated NK markers." [GO_REF:0000031, GOC:add, GOC:pam, GOC:tfm, PMID:17303398] +subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "activated CD4-negative, CD8-negative type I NK T lymphocyte" EXACT [] synonym: "activated CD4-negative, CD8-negative type I NK T-cell" EXACT [] synonym: "activated CD4-negative, CD8-negative type I NK T-lymphocyte" EXACT [] @@ -11881,6 +13279,8 @@ relationship: RO:0002202 CL:0000924 ! develops from CD4-negative, CD8-negative t id: CL:0000929 name: CD4-negative, CD8-negative type I NK T cell secreting interferon-gamma def: "A mature NK T cell that secretes interferon-gamma and enhances Th1 immune responses." [GO_REF:0000031, GOC:add, GOC:pam, GOC:tfm, PMID:17303398] +subset: human_subset +subset: mouse_subset synonym: "CD4-negative, CD8-negative type I NK T cell secreting IFN-gamma" EXACT [] synonym: "CD4-negative, CD8-negative type I NK T lymphocyte secreting interferon-gamma" EXACT [] synonym: "CD4-negative, CD8-negative type I NK T-cell secreting interferon-gamma" EXACT [] @@ -11900,6 +13300,8 @@ relationship: RO:0002202 CL:0000928 ! develops from activated CD4-negative, CD8- id: CL:0000930 name: CD4-negative, CD8-negative type I NK T cell secreting interleukin-4 def: "A mature NK T cell that secretes interleukin-4 and enhances Th2 immune responses." [GO_REF:0000031, GOC:add, GOC:pam, GOC:tfm, PMID:17303398] +subset: human_subset +subset: mouse_subset synonym: "CD4-negative, CD8-negative type I NK T cell secreting IL-4" EXACT [] synonym: "CD4-negative, CD8-negative type I NK T lymphocyte secreting interleukin-4" EXACT [] synonym: "CD4-negative, CD8-negative type I NK T-cell secreting interleukin-4" EXACT [] @@ -11920,6 +13322,8 @@ id: CL:0000931 name: activated type II NK T cell def: "A type II NK T cell that has been recently activated, secretes interferon-gamma and interleukin-4, and has the phenotype CD69-positive and downregulated NK markers." [GO_REF:0000031, GOC:add, GOC:pam, GOC:tfm, PMID:17964217] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "activated type II NK T lymphocyte" EXACT [] synonym: "activated type II NK T-cell" EXACT [] synonym: "activated type II NK T-lymphocyte" EXACT [] @@ -11935,6 +13339,8 @@ relationship: RO:0002104 PR:000001343 ! has plasma membrane part CD69 molecule id: CL:0000932 name: type II NK T cell secreting interferon-gamma def: "A type II NK T cell that has been recently activated, secretes interferon-gamma, and has the phenotype CD69-positive and downregulated NK markers." [GO_REF:0000031, GOC:add, GOC:pam, PMID:17964217] +subset: human_subset +subset: mouse_subset synonym: "type II NK T cell secreting IFN-gamma" EXACT [] synonym: "type II NK T lymphocyte secreting interferon-gamma" EXACT [] synonym: "type II NK T-cell secreting interferon-gamma" EXACT [] @@ -11952,6 +13358,8 @@ relationship: RO:0002202 CL:0000931 ! develops from activated type II NK T cell id: CL:0000933 name: type II NK T cell secreting interleukin-4 def: "A type II NK T cell that has been recently activated, secretes interleukin-4, and has the phenotype CD69-positive and downregulated NK markers." [GO_REF:0000031, GOC:add, GOC:pam, GOC:tfm, PMID:17964217] +subset: human_subset +subset: mouse_subset synonym: "type II NK T cell secreting IL-4" EXACT [] synonym: "type II NK T lymphocyte secreting interleukin-4" EXACT [] synonym: "type II NK T-cell secreting interleukin-4" EXACT [] @@ -11971,6 +13379,8 @@ name: CD4-positive, alpha-beta cytotoxic T cell def: "A CD4-positive, alpha-beta T cell that has cytotoxic function." [GO_REF:0000031, GOC:add, GOC:pam, GOC:tfm, PMID:18440213] subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "CD4-positive, alpha-beta cytotoxic T lymphocyte" EXACT [] synonym: "CD4-positive, alpha-beta cytotoxic T-cell" EXACT [] synonym: "CD4-positive, alpha-beta cytotoxic T-lymphocyte" EXACT [] @@ -11988,6 +13398,8 @@ id: CL:0000935 name: CD4-negative, CD8-negative, alpha-beta intraepithelial T cell def: "A CD4-negative, CD8-negative, alpha-beta intraepithelial T cell that is found in the columnar epithelium of the gastrointestinal tract." [GO_REF:0000031, GOC:add, GOC:pam, PMID:11685222] subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "CD4-negative, CD8-negative, alpha-beta intraepithelial T lymphocyte" EXACT [] synonym: "CD4-negative, CD8-negative, alpha-beta intraepithelial T-cell" EXACT [] synonym: "CD4-negative, CD8-negative, alpha-beta intraepithelial T-lymphocyte" EXACT [] @@ -12006,6 +13418,8 @@ def: "A lymphoid progenitor cell that is found in bone marrow, gives rise to B c comment: Markers are associated with mouse cells. ELP transcription factors include E2A-positive, Ikaros-positive, EBF-negative, Pax5-negative, PU.1-negative. subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "ELP" RELATED OMO:0003000 [] synonym: "GMLP" RELATED OMO:0003000 [PMID:18371378] synonym: "LMPP" RELATED OMO:0003000 [] @@ -12033,9 +13447,10 @@ name: pre-natural killer cell def: "Cell committed to natural killer cell lineage that has the phenotype CD122-positive, CD34-positive, and CD117-positive. This cell type lacks expression of natural killer receptor proteins." [GO_REF:0000031, GOC:add, GOC:dsd, GOC:pam, GOC:tfm, PMID:16551251, PMID:17100874] comment: These cells are also reportedly CD7-low, CD10-negative, CD45RA-positive, alpha-4-beta-7 integrin-high. subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "pre-NK cell" EXACT [] is_a: CL:0000623 ! natural killer cell -is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000623 ! natural killer cell intersection_of: RO:0002104 PR:000001003 ! has plasma membrane part CD34 molecule intersection_of: RO:0002104 PR:000001381 ! has plasma membrane part interleukin-2 receptor subunit beta @@ -12051,12 +13466,12 @@ def: "NK cell that has the phenotype CD56-bright, CD16-negative, and CD84-positi comment: This cell type is compatible with the HIPC Lyoplate markers for 'CD16-CD56bright NK cell'. Markers are associated with human cell types. subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset synonym: "CD16-CD56bright NK cell" EXACT [PMID:22343568] synonym: "CD16-negative, CD56-bright NK cell" EXACT [] synonym: "CD56-bright cytokine secreting natural killer cell" EXACT [] synonym: "CD56-bright cytokine secreting NK cell" EXACT [] is_a: CL:0000824 ! mature natural killer cell -is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000824 ! mature natural killer cell intersection_of: capable_of GO:0032609 ! type II interferon production intersection_of: CL:4030046 PR:000001483 ! lacks_plasma_membrane_part low affinity immunoglobulin gamma Fc region receptor III @@ -12077,6 +13492,7 @@ name: CD16-positive, CD56-dim natural killer cell, human def: "A mature natural killer cell that has the phenotype CD56-low, CD16-positive and which is capable of cytotoxicity and cytokine production." [GO_REF:0000031, GOC:add, GOC:pam, PMID:19796267, PMID:22343568] comment: This cell type is compatible with the HIPC Lyoplate markers for 'CD16+CD56+ NK cell'. Markers are associated with human cell types. subset: cellxgene_subset +subset: human_subset synonym: "CD16+CD56+ NK cell" EXACT [PMID:22343568] synonym: "CD16-positive, CD56-dim NK cell" EXACT [] synonym: "CD16-positive, CD56-low natural killer cell" EXACT [] @@ -12086,7 +13502,6 @@ synonym: "CD16-positive, CD56-positive NK cell" EXACT [] synonym: "cytotoxic CD56-dim natural killer cell" EXACT [] synonym: "cytotoxic CD56-dim NK cell" EXACT [] is_a: CL:0000824 ! mature natural killer cell -is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000824 ! mature natural killer cell intersection_of: capable_of GO:0001816 ! cytokine production intersection_of: capable_of GO:0042267 ! natural killer cell mediated cytotoxicity @@ -12106,6 +13521,8 @@ name: mucosal invariant T cell def: "An alpha-beta T cell that is found in the lamina propria of mucosal tissues and is restricted by the MR-1 molecule." [GO_REF:0000031, GOC:add, GOC:pam, GOC:tfm, PMID:19416870] subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "mucosal invariant T lymphocyte" EXACT [] synonym: "mucosal invariant T-cell" EXACT [] synonym: "mucosal invariant T-lymphocyte" EXACT [] @@ -12124,6 +13541,8 @@ id: CL:0000941 name: thymic conventional dendritic cell def: "A dendritic cell arising in thymus that has the phenotype CD11c-positive, CD11b-negative, and CD45RA-negative." [GO_REF:0000031, GOC:add, GOC:pam, PMID:19273629] comment: In the mouse this cell expresses CD8-alpha-alpha. +subset: human_subset +subset: mouse_subset is_a: CL:0000990 {is_inferred="true"} ! conventional dendritic cell intersection_of: CL:0000990 ! conventional dendritic cell intersection_of: CL:4030046 PR:000001012 ! lacks_plasma_membrane_part integrin alpha-M @@ -12141,6 +13560,8 @@ id: CL:0000942 name: thymic plasmacytoid dendritic cell def: "A plasmacytoid dendritic cell developing in the thymus with phenotype CD11c-negative or low, CD45RA-positive, CD11b-negative, and CD123-positive." [GO_REF:0000031, GOC:add, GOC:pam, GOC:tfm, PMID:19941119] subset: human_reference_atlas +subset: human_subset +subset: mouse_subset is_a: CL:0000784 {is_inferred="true"} ! plasmacytoid dendritic cell intersection_of: CL:0000784 ! plasmacytoid dendritic cell intersection_of: CL:4030046 PR:000001012 ! lacks_plasma_membrane_part integrin alpha-M @@ -12157,6 +13578,8 @@ id: CL:0000943 name: Be1 Cell def: "A Be cell that facilitates development of T-helper 1 (Th1) phenotype in CD4-positive T cells, and secretes high levels of interleukin-2, tumor necrosis factor-alpha and interferon-gamma." [GO_REF:0000031, GOC:dsd, GOC:msz, GOC:tfm, PMID:11101868, PMID:20224569] comment: Be1 cells are also reportedly capable of secreting IL-6, IL-10, and IL-12. They are also reportedly CD11b-negative and B220-positive. +subset: human_subset +subset: mouse_subset synonym: "B effector 1 cell" EXACT [PMID:11101868, PMID:20224569] synonym: "B effector cell type 1" RELATED [] is_a: CL:0000968 {is_inferred="true"} ! Be cell @@ -12175,6 +13598,8 @@ id: CL:0000944 name: Be2 cell def: "A Be cell that facilitates development of T-helper 2 (Th2) phenotype T cells, and secretes high levels of interleukin-2, interleukin-10, interleukin-4, and interleukin-6." [GO_REF:0000031, GOC:dsd, GOC:msz, GOC:tfm, PMID:11101868, PMID:20224569] comment: Be2 cells are also reportedly capable of secreting IL-13 and TNF. They are also reportedly CD11b-negative and B220-positive. +subset: human_subset +subset: mouse_subset synonym: "B effector 2 cell" EXACT [PMID:11101868, PMID:20224569] synonym: "B effector cell type 2" RELATED [] is_a: CL:0000968 {is_inferred="true"} ! Be cell @@ -12195,7 +13620,10 @@ id: CL:0000945 name: lymphocyte of B lineage def: "A lymphocyte of B lineage with the commitment to express an immunoglobulin complex." [GO_REF:0000031, GOC:add, GOC:rhs, GOC:tfm, ISBN:0781735149] comment: Types of B lineage lymphocytes include B cells and antibody secreting cells (plasmablasts and plasma cells). Lymphocytes of B cell lineage can be distinguished from those of T cell lineage by their lack of CD3e (as part of the T cell receptor complex). +subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset is_a: CL:0000542 {is_inferred="true"} ! lymphocyte relationship: RO:0002202 CL:0000826 ! develops from pro-B cell property_value: RO:0002175 NCBITaxon:9606 @@ -12204,6 +13632,8 @@ property_value: RO:0002175 NCBITaxon:9606 id: CL:0000946 name: antibody secreting cell def: "A lymphocyte of B lineage that is devoted to secreting large amounts of immunoglobulin." [GO_REF:0000031, GOC:add, GOC:tfm, ISBN:0721601464, ISBN:0781735149] +subset: human_subset +subset: mouse_subset is_a: CL:0000945 {is_inferred="true"} ! lymphocyte of B lineage intersection_of: CL:0000945 ! lymphocyte of B lineage intersection_of: produces GO:0042571 ! immunoglobulin complex, circulating @@ -12213,6 +13643,8 @@ relationship: produces GO:0042571 ! immunoglobulin complex, circulating id: CL:0000947 name: IgE plasma cell def: "A long lived plasma cell that secretes IgE." [GO_REF:0000031, GOC:msz, ISBN:781735149] +subset: human_subset +subset: mouse_subset is_a: CL:0000974 {is_inferred="true"} ! long lived plasma cell intersection_of: CL:0000974 ! long lived plasma cell intersection_of: produces GO:0071743 ! IgE immunoglobulin complex, circulating @@ -12222,6 +13654,8 @@ relationship: produces GO:0071743 ! IgE immunoglobulin complex, circulating id: CL:0000948 name: IgE memory B cell def: "A class switched memory B cell that expresses IgE on the cell surface." [GO_REF:0000031, GOC:rhs, ISBN:0781765196] +subset: human_subset +subset: mouse_subset synonym: "IgE memory B lymphocyte" EXACT [] synonym: "IgE memory B-cell" EXACT [] synonym: "IgE memory B-lymphocyte" EXACT [] @@ -12238,6 +13672,8 @@ relationship: RO:0002104 GO:0071742 ! has plasma membrane part IgE immunoglobuli id: CL:0000949 name: IgD plasmablast def: "A plasmablast that secretes IgD, and which occur in a small proportion of B cells in the adult." [GO_REF:0000031, GOC:msz] +subset: human_subset +subset: mouse_subset is_a: CL:0000980 {is_inferred="true"} ! plasmablast intersection_of: CL:0000980 ! plasmablast intersection_of: produces GO:0071739 ! IgD immunoglobulin complex, circulating @@ -12247,6 +13683,8 @@ relationship: produces GO:0071739 ! IgD immunoglobulin complex, circulating id: CL:0000950 name: IgE plasmablast def: "A plasmablast that secretes IgE." [GO_REF:0000031, GOC:msz] +subset: human_subset +subset: mouse_subset is_a: CL:0000980 {is_inferred="true"} ! plasmablast intersection_of: CL:0000980 ! plasmablast intersection_of: produces GO:0071743 ! IgE immunoglobulin complex, circulating @@ -12256,6 +13694,8 @@ relationship: produces GO:0071743 ! IgE immunoglobulin complex, circulating id: CL:0000951 name: IgE short lived plasma cell def: "A short lived plasma cell that secretes IgE." [GO_REF:0000031, GOC:msz, ISBN:781735149] +subset: human_subset +subset: mouse_subset is_a: CL:0000975 {is_inferred="true"} ! short lived plasma cell intersection_of: CL:0000975 ! short lived plasma cell intersection_of: produces GO:0071743 ! IgE immunoglobulin complex, circulating @@ -12265,6 +13705,8 @@ relationship: produces GO:0071743 ! IgE immunoglobulin complex, circulating id: CL:0000952 name: preBCR-positive large pre-B-II cell def: "An preBRC-positive large pre-B-II cell is a large pre-B-II cell that is pre-B cell receptor-positive, composed of surrogate light chain protein (SL), which is composed of VpreB , Lambda 5/14.1, in complex with immunoglobulin mu heavy chain (IgHmu) on the cell surface." [GO_REF:0000031, GOC:rhs, GOC:tfm, PMID:9785673] +subset: human_subset +subset: mouse_subset is_a: CL:0000957 {is_inferred="true"} ! large pre-B-II cell intersection_of: CL:0000957 ! large pre-B-II cell intersection_of: CL:4030044 GO:0071708 ! has_not_completed immunoglobulin light chain V-J recombination @@ -12280,6 +13722,8 @@ relationship: RO:0002104 PR:000001859 ! has plasma membrane part immunoglobulin id: CL:0000953 name: preBCR-negative large pre-B-II cell def: "A pre-BCR-negative large pre-B-II cell is a large pre-B-II cell that is pre-B cell receptor-negative, composed of surrogate light chain protein (SL), which is composed of VpreB and Lambda 5/14.1, in complex with immunoglobulin mu heavy chain (IgHmu), on the cell surface, and lack a DNA rearrangement of immunoglobulin light chain genes." [GO_REF:0000031, GOC:rhs, GOC:tfm, PMID:9785673] +subset: human_subset +subset: mouse_subset is_a: CL:0000957 {is_inferred="true"} ! large pre-B-II cell intersection_of: CL:0000957 ! large pre-B-II cell intersection_of: CL:4030044 GO:0071708 ! has_not_completed immunoglobulin light chain V-J recombination @@ -12297,6 +13741,8 @@ name: small pre-B-II cell def: "A small pre-B-II cell is a pre-B-II cell that is Rag1-positive, Rag2-positive, pre-BCR-negative, and BCR-negative, is not proliferating, and carries a DNA rearrangement of one or more immunoglobulin light chain genes." [GO_REF:0000031, GOC:dsd, GOC:rhs, GOC:tfm, PMID:16551251, PMID:18432934, PMID:9785673] comment: Small pre-B-II cells are also reportedly CD10-positive, CD19-positive, CD34-negative, CD79a-positive, CD127-negative, TdT-negative, Vpre-B-negative, sIgM-negative, and sIgD-negative. Transcription factors: PU.1-positive, Ikaros-positive, E2A-positive, and PAX5-positive. subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "small pre-BII cell" EXACT [] is_a: CL:0000955 {is_inferred="true"} ! pre-B-II cell intersection_of: CL:0000955 ! pre-B-II cell @@ -12316,6 +13762,8 @@ id: CL:0000955 name: pre-B-II cell def: "A pre-B-II cell is a precursor B cell that expresses immunoglobulin mu heavy chain (IgHmu+), and lack expression of CD34, TdT, immunoglobulin kappa light chain and immunoglobulin lambda light chain." [GO_REF:0000031, GOC:dsd, GOC:rhs, GOC:tfm, PMID:9785673] comment: pre-B-II cell are also reportedly CD19-positive, CD22-positive, CD38-positive, CD45-positive, and CD48-positive. +subset: human_subset +subset: mouse_subset synonym: "pre-B-lymphocyte" EXACT [] synonym: "pre-BII cell" EXACT [] xref: BTO:0001133 @@ -12336,6 +13784,8 @@ name: pre-B-I cell def: "A pre-B-I cell is a precursor B cell that expresses CD34 and surrogate immunoglobulin light chain (VpreB , Lambda 5 (mouse)/14.1 (human)) on the cell surface, and TdT, Rag1,and Rag2 intracellularly. Cell type carries a D-JH DNA rearrangement, and lacks expression of immunglobulin heavy chain protein." [GO_REF:0000031, GOC:dsd, GOC:rhs, GOC:tfm, PMID:16551251, PMID:18432934, PMID:20839338, PMID:9785673] comment: Human pre-B-I cells are reportedly CD10-positive, CD19-positive, CD22-positive, CD38-positive, CD45-low, CD79a-positive, CD127-negative, pre-BCR-negative, IgM-negative, IgD-negative, and Tdt-positive. Transcription factors expressed: Pax5-positive. subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "pre-BI cell" EXACT [] synonym: "pro-B cell (Philadelphia nomenclature)" RELATED [PMID:11244048] is_a: CL:0000817 {is_inferred="true"} ! precursor B cell @@ -12361,6 +13811,8 @@ name: large pre-B-II cell def: "A large pre-B-II cell is a pre-B-II cell that is proliferating and is Rag1-negative and Rag2-negative." [GO_REF:0000031, GOC:dsd, GOC:rhs, PMID:16551251, PMID:18432934, PMID:9785673] comment: Large pre-B-II cells are also reportedly CD10-positive, CD19-positive, CD34-negative, CD79a-positive, CD127-negative, TdT-negative, Vpre-B-positive, pre-BCR-positive, sIgM-negative, and sIgD-negative. Transcription factors: PU.1-positive, Ikaros-positive, E2A-positive, and PAX5-positive. subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "large pre-B cell" BROAD [PMID:11244048] synonym: "large pre-BII cell" EXACT [] is_a: CL:0000955 {is_inferred="true"} ! pre-B-II cell @@ -12377,6 +13829,8 @@ id: CL:0000958 name: T1 B cell def: "A transitional stage B cell that migrates from the bone marrow into the peripheral circulation, and finally to the spleen. This cell type has the phenotype surface IgM-positive, surface IgD-negative, CD21-negative, CD23-negative, and CD62L-negative, and CD93-positive. This cell type has also been described as IgM-high, CD19-positive, B220-positive, AA4-positive, and CD23-negative." [GO_REF:0000031, GOC:dsd, GOC:msz, GOC:tfm, PMCID:PMC2193793, PMID:12810111] comment: T1 B cells are also reportedly CD10-negative/positive??, CD20-positive, CD24-positive, CD38-positive, CD48-positive, CD84-positive, CD150-positive, CD244-negative, and CD352-positive. +subset: human_subset +subset: mouse_subset synonym: "T1 B lymphocyte" EXACT [] synonym: "T1 B-cell" EXACT [] synonym: "T1 B-lymphocyte" EXACT [] @@ -12399,6 +13853,8 @@ id: CL:0000959 name: T2 B cell def: "A transitional stage B cell that has the phenotype surface IgM-positive, surface IgD-postive, CD21-positive, CD23-positive, CD62L-negative, CD93-positive and is located in the splenic B follicles. This cell type has also been described as IgM-high, CD19-positive, B220-positive, AA4-positive, and CD23-positive." [GO_REF:0000031, GOC:dsd, GOC:msz, GOC:tfm, PMCID:PMC2193793, PMID:12810111] comment: T2 B cells are also reportedly CD20-positive, CD24-positive, CD38-positive, CD48-positive, CD84-positive, CD150-positive, CD244-negative, and CD352-positive. +subset: human_subset +subset: mouse_subset synonym: "T2 B lymphocyte" EXACT [] synonym: "T2 B-cell" EXACT [] synonym: "T2 B-lymphocyte" EXACT [] @@ -12422,6 +13878,8 @@ relationship: RO:0002202 CL:0000958 ! develops from T1 B cell id: CL:0000960 name: T3 B cell def: "A transitional stage B cell that expresses surface IgM and IgD, and CD62L. This cell type appears to be an anergic B cell that does not proliferate upon BCR signaling, is found in the spleen and lymph nodes, and has the phenotype surface IgM-positive, surface IgD-positive, CD21-positive, CD23-positive, CD62L-positive, and CD93-positive. This cell type has also been described as IgM-low, CD19-positive, B220-positive, AA4-positive, and CD23-positive (i.e. this cell-type is distinguished from T2 cells by surface expression of IgM)." [GO_REF:0000031, GOC:msz, GOC:tfm, http://www.immgen.org/index_content.html, PMID:12810111, PMID:17174121] +subset: human_subset +subset: mouse_subset synonym: "An1 B cell" EXACT [PMID:17174121] synonym: "T3 B lymphocyte" EXACT [] synonym: "T3 B-cell" EXACT [] @@ -12447,6 +13905,8 @@ id: CL:0000961 name: Bm1 B cell def: "A follicular B cell that is IgD-positive, CD23-negative, and CD38-negative. This naive cell type is activated in the extrafollicular areas through interaction with interdigitating dendritic cells and antigen-specific CD4-positive T cells." [GO_REF:0000031, GOC:dsd, GOC:msz, PMID:17992590, PMID:18432934, PMID:8006591] comment: These cells are also reportedly CD10-negative, CD39-positive, CD44-positive, CD71-negative, CD77-negative, IgM-positive, IgG-negative, IgA-negative, and IgE-negative. +subset: human_subset +subset: mouse_subset synonym: "Bm1 B lymphocyte" EXACT [] synonym: "Bm1 B-cell" EXACT [] synonym: "Bm1 B-lymphocyte" EXACT [] @@ -12463,6 +13923,8 @@ id: CL:0000962 name: Bm2 B cell def: "A follicular B cell that is IgD-positive and CD23-positive and CD38-positive. This naive cell type is activated in the extrafollicular areas via interaction with dendritic cells and antigen specific T cells." [GO_REF:0000031, GOC:dsd, GOC:msz, PMID:17992590, PMID:18432934, PMID:8006591] comment: These cells are also CD10-negative, CD39-positive, CD44-positive, CD71-negative, CD77-negative, IgM-positive, IgG-negative, IgA-negative, and IgE-negative. +subset: human_subset +subset: mouse_subset synonym: "Bm2 B lymphocyte" EXACT [] synonym: "Bm2 B-cell" EXACT [] synonym: "Bm2 B-lymphocyte" EXACT [] @@ -12479,6 +13941,8 @@ relationship: RO:0002202 CL:0000961 ! develops from Bm1 B cell id: CL:0000963 name: Bm3-delta B cell def: "A germinal center B cell that develops from a Bm3 B cell. This cell has the phenotype IgM-negative, IgD-positive, and CD38-positive." [GO_REF:0000031, GOC:add, GOC:msz, GOC:tfm, PMID:9280752] +subset: human_subset +subset: mouse_subset synonym: "Bm3-delta B lymphocyte" EXACT [] synonym: "Bm3-delta B-cell" EXACT [] synonym: "Bm3-delta B-lymphocyte" EXACT [] @@ -12497,6 +13961,8 @@ id: CL:0000964 name: Bm2' B cell def: "A germinal center B cell that founds a germinal center, and has the phenotype IgD-positive, CD38-positive, and CD23-negative." [GO_REF:0000031, GOC:dsd, GOC:msz, GOC:tfm, PMID:17992590, PMID:18432934, PMID:8006591] comment: Bm2' B cells are also reportedly CD10-positive, CD39-negative, CD44-negative, CD71-positive, CD77-negative, IgM-positive, IgG-negative, IgA-negative, and IgE-negative. +subset: human_subset +subset: mouse_subset synonym: "Bm2' B lymphocyte" EXACT [] synonym: "Bm2' B-cell" EXACT [] synonym: "Bm2-prime B cell" EXACT [] @@ -12519,6 +13985,8 @@ id: CL:0000965 name: Bm3 B cell def: "A germinal center B cell that is rapidly dividing and has the phenotype IgD-negative, CD38-positive, and CD77-positive. Somatic hypermutation of the immunoglobulin V gene region can occur during proliferation of this cell type." [GO_REF:0000031, GOC:dsd, GOC:msz, PMID:18432934, PMID:8006591] comment: Bm3 B cells are also reportedly CD10-positive, CD23-negative, CD39-negative, CD44-negative, CD71-positive, and CD77-positive. +subset: human_subset +subset: mouse_subset synonym: "Bm3 B lymphocyte" EXACT [] synonym: "Bm3 B-cell" EXACT [] synonym: "Bm3 B-lymphocyte" EXACT [] @@ -12540,6 +14008,8 @@ id: CL:0000966 name: Bm4 B cell def: "A germinal center B cell that has the phenotype CD77-negative, IgD-negative, and CD38-positive. These cells have undergone somatic mutation of the B cell receptor." [GO_REF:0000031, GOC:dsd, GOC:msz, PMID:18432934, PMID:8006591] comment: Bm4 B cells are also reportedly CD10-positive, CD23-negative, CD39-negative, CD44-positive, and CD71-positive. +subset: human_subset +subset: mouse_subset synonym: "Bm4 B lymphocyte" EXACT [] synonym: "Bm4 B-cell" EXACT [] synonym: "Bm4 B-lymphocyte" EXACT [] @@ -12561,6 +14031,8 @@ id: CL:0000967 name: Bm5 B cell def: "A memory B cell arising in the germinal center that is IgD-negative and has undergone somatic mutation of the variable region of the immunoglobulin heavy and light chain genes." [GO_REF:0000031, GOC:dsd, GOC:msz, GOC:tfm, PMID:18432934, PMID:8006591] comment: Bm5 B cells are also reportedly CD10-positive, CD23-negative, CD38-negative, CD39-positive, CD44-positive, CD71-positive, and CD77-negative. +subset: human_subset +subset: mouse_subset synonym: "Bm5 B lymphocyte" EXACT [] synonym: "Bm5 B-cell" EXACT [] synonym: "Bm5 B-lymphocyte" EXACT [] @@ -12577,6 +14049,8 @@ relationship: RO:0002202 CL:0000966 ! develops from Bm4 B cell id: CL:0000968 name: Be cell def: "A mature B cell that produces cytokines that can influence CD4 T cell differentiation." [GO_REF:0000031, GOC:msz, GOC:tfm, PMID:11101868, PMID:20224569] +subset: human_subset +subset: mouse_subset synonym: "B effector cell" EXACT [] synonym: "effector B cell" EXACT [] synonym: "effector B lymphocyte" EXACT [] @@ -12596,6 +14070,8 @@ id: CL:0000969 name: regulatory B cell def: "A mature B cell that has the phenotype CD1d-positive and expresses interleukin-10. This cell type has been associated with suppression of chronic inflammatory responses and T cell responses." [GO_REF:0000031, GOC:dsd, GOC:msz, GOC:tfm, MESH:D060151, PMID:11869683, PMID:18482568, PMID:20224569, PMID:20809522] comment: Regulatory B cells reportedly represent 1-2% of the spleen and 7-8% of the peritoneal B220-positive cells in mice. They are also found in the bone marrow, lymph node, and blood of mice. These cells are also reportedly capable of secreting IL-10 and are reportedly CD5-positive, CD21-positive, CD24-positive, CD93-negative, B220-positive, IgM-positive, and IgD-positive. +subset: human_subset +subset: mouse_subset synonym: "B(reg)" EXACT [] synonym: "B10 cell" EXACT [] synonym: "Breg" EXACT [] @@ -12620,6 +14096,8 @@ def: "An unswitched memory B cell is a memory B cell that has the phenotype IgM- comment: This cell type is compatible with the HIPC Lyoplate markers for 'IgD+ memory B cell'. Per DSD: Unswitched memory B cells are also reportedly CD48-positive, CD84-positive, CD229-positive, and CD352-positive. subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "IgD+ memory B cell" BROAD [PMID:22343568] synonym: "non-class-switched memory B cell" EXACT [HP:0032126] synonym: "unswitched memory B lymphocyte" EXACT [] @@ -12648,6 +14126,8 @@ id: CL:0000971 name: IgM memory B cell def: "An IgM memory B cell is an unswitched memory B cell with the phenotype IgM-positive and IgD-negative." [GO_REF:0000031, GOC:dsd, GOC:rhs, ISBN:0781765196, PMID:19447676] comment: IgM memory B cells are also reportedly CD1c-positive, CD95-positive, CD80-positive, CD84-positive, CD86-positive, CD150-negative, CD229-positive, CD289-positive, and CD290-positive. Transcription factors: Notch2-positive, PAX5-positive, SpiB-positive, Ets1-positive, and OBF1-positive. +subset: human_subset +subset: mouse_subset synonym: "IgM memory B lymphocyte" EXACT [] synonym: "IgM memory B-cell" EXACT [] synonym: "IgM memory B-lymphocyte" EXACT [] @@ -12668,6 +14148,8 @@ def: "A class switched memory B cell is a memory B cell that has undergone Ig cl comment: Per DSD: Class switched memory B cells are also reportedly CD48-positive, CD229-positive, and CD352-positive. subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "class switched memory B lymphocyte" EXACT [] synonym: "class switched memory B-cell" EXACT [] synonym: "class switched memory B-lymphocyte" EXACT [] @@ -12687,6 +14169,8 @@ id: CL:0000973 name: IgA memory B cell def: "A class switched memory B cell that expresses IgA." [GO_REF:0000031, GOC:dsd, GOC:msz, ISBN:0781765196] comment: IgA memory B cell are also reportedly RORalpha-positive. +subset: human_subset +subset: mouse_subset synonym: "IgA memory B lymphocyte" EXACT [] synonym: "IgA memory B-cell" EXACT [] synonym: "IgA memory B-lymphocyte" EXACT [] @@ -12703,6 +14187,8 @@ relationship: RO:0002104 GO:0071745 ! has plasma membrane part IgA immunoglobuli id: CL:0000974 name: long lived plasma cell def: "A fully differentiated plasma cell that lives for years, as opposed to months, secretes immunoglobulin, and has the phenotype weakly CD19-positive, CD20-negative, CD38-negative, strongly CD138-positive, MHC Class II-negative, surface immunoglobulin-negative, IgD-negative, and strongly CXCR4-positive. The majority of these cells of this type reside in the bone marrow." [GO_REF:0000031, GOC:msz, GOC:tfm, ISBN:9780781765190, PMID:16014527] +subset: human_subset +subset: mouse_subset is_a: CL:0000786 {is_inferred="true"} ! plasma cell intersection_of: CL:0000786 ! plasma cell intersection_of: CL:4030046 GO:0019814 ! lacks_plasma_membrane_part immunoglobulin complex @@ -12722,6 +14208,8 @@ relationship: RO:0015016 PR:000001002 ! has low plasma membrane amount CD19 mole id: CL:0000975 name: short lived plasma cell def: "A fully differentiated plasma cell that lives for months." [GO_REF:0000031, GOC:msz, PMID:16014527] +subset: human_subset +subset: mouse_subset is_a: CL:0000786 {is_inferred="true"} ! plasma cell intersection_of: CL:0000786 ! plasma cell intersection_of: bearer_of PATO:0001604 ! decreased life span @@ -12731,6 +14219,8 @@ relationship: bearer_of PATO:0001604 ! decreased life span id: CL:0000976 name: IgA short lived plasma cell def: "A short lived plasma cell that secretes IgA. These cells may be found in the bone marrow as well as in the mucosal immune system." [GO_REF:0000031, GOC:msz, ISBN:781735149] +subset: human_subset +subset: mouse_subset is_a: CL:0000975 {is_inferred="true"} ! short lived plasma cell intersection_of: CL:0000975 ! short lived plasma cell intersection_of: produces GO:0071746 ! IgA immunoglobulin complex, circulating @@ -12740,6 +14230,8 @@ relationship: produces GO:0071746 ! IgA immunoglobulin complex, circulating id: CL:0000977 name: IgG short lived plasma cell def: "A short lived plasma cell that secretes IgG." [GO_REF:0000031, GOC:msz, ISBN:781735149] +subset: human_subset +subset: mouse_subset is_a: CL:0000975 {is_inferred="true"} ! short lived plasma cell intersection_of: CL:0000975 ! short lived plasma cell intersection_of: produces GO:0071736 ! IgG immunoglobulin complex, circulating @@ -12749,6 +14241,8 @@ relationship: produces GO:0071736 ! IgG immunoglobulin complex, circulating id: CL:0000978 name: IgM short lived plasma cell def: "A short lived plasma cell that secretes IgM." [GO_REF:0000031, GOC:msz, ISBN:781735149] +subset: human_subset +subset: mouse_subset is_a: CL:0000975 {is_inferred="true"} ! short lived plasma cell intersection_of: CL:0000975 ! short lived plasma cell intersection_of: produces GO:0071754 ! IgM immunoglobulin complex, circulating @@ -12759,6 +14253,8 @@ id: CL:0000979 name: IgG memory B cell def: "An IgG memory B cell is a class switched memory B cell that is class switched and expresses IgG on the cell surface." [GO_REF:0000031, GOC:rhs, ISBN:0781765196] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "IgG memory B lymphocyte" EXACT [] synonym: "IgG memory B-cell" EXACT [] synonym: "IgG memory B-lymphocyte" EXACT [] @@ -12778,6 +14274,8 @@ def: "An activated mature (naive or memory) B cell that is secreting immunoglobu comment: This cell type is compatible with the HIPC Lyoplate markers for 'plasmablast'. Plasmablasts are also reportedly CD48-positive, CD63-positive, CD229-positive, CD270-positive, CD319-positive, CD352-positive, CD361-positive, and IgD-negative. subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "CD20-negative B cell" BROAD [] synonym: "CD27-positive, CD38-positive, CD20-negative B cell" EXACT [] xref: FMA:84371 @@ -12800,6 +14298,8 @@ property_value: RO:0002175 NCBITaxon:9606 id: CL:0000981 name: double negative memory B cell def: "A memory B cell with the phenotype IgD-negative and CD27-negative." [GO_REF:0000031, GOC:msz, GOC:tfm] +subset: human_subset +subset: mouse_subset synonym: "dn memory B cell" EXACT [] synonym: "dn memory B lymphocyte" EXACT [] synonym: "dn memory B-cell" EXACT [] @@ -12818,6 +14318,8 @@ id: CL:0000982 name: IgG plasmablast def: "A plasmablast that secretes IgG." [GO_REF:0000031, GOC:msz] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset is_a: CL:0000980 {is_inferred="true"} ! plasmablast intersection_of: CL:0000980 ! plasmablast intersection_of: produces GO:0071736 ! IgG immunoglobulin complex, circulating @@ -12827,6 +14329,8 @@ relationship: produces GO:0071736 ! IgG immunoglobulin complex, circulating id: CL:0000983 name: IgM plasmablast def: "A plasmablast that secretes IgM." [GO_REF:0000031, GOC:msz] +subset: human_subset +subset: mouse_subset is_a: CL:0000980 {is_inferred="true"} ! plasmablast intersection_of: CL:0000980 ! plasmablast intersection_of: produces GO:0071754 ! IgM immunoglobulin complex, circulating @@ -12837,6 +14341,8 @@ id: CL:0000984 name: IgA plasmablast def: "A plasmablast that secretes IgA." [GO_REF:0000031, GOC:msz] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset is_a: CL:0000980 {is_inferred="true"} ! plasmablast intersection_of: CL:0000980 ! plasmablast intersection_of: produces GO:0071746 ! IgA immunoglobulin complex, circulating @@ -12847,6 +14353,8 @@ id: CL:0000985 name: IgG plasma cell def: "A fully differentiated plasma cell that secretes IgG." [GO_REF:0000031, GOC:msz, ISBN:781735149] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset is_a: CL:0000974 {is_inferred="true"} ! long lived plasma cell intersection_of: CL:0000974 ! long lived plasma cell intersection_of: produces GO:0071736 ! IgG immunoglobulin complex, circulating @@ -12857,6 +14365,8 @@ id: CL:0000986 name: IgM plasma cell def: "A fully differentiated plasma cell that secretes IgM." [GO_REF:0000031, GOC:msz, ISBN:781735149] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset is_a: CL:0000974 {is_inferred="true"} ! long lived plasma cell intersection_of: CL:0000974 ! long lived plasma cell intersection_of: produces GO:0071754 ! IgM immunoglobulin complex, circulating @@ -12867,6 +14377,8 @@ id: CL:0000987 name: IgA plasma cell def: "A fully differentiated plasma cell that secretes IgA." [GO_REF:0000031, GOC:msz, ISBN:781735149] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset is_a: CL:0000974 {is_inferred="true"} ! long lived plasma cell intersection_of: CL:0000974 ! long lived plasma cell intersection_of: produces GO:0071746 ! IgA immunoglobulin complex, circulating @@ -12877,6 +14389,8 @@ id: CL:0000988 name: hematopoietic cell def: "A cell of a hematopoietic lineage." [GO_REF:0000031, GOC:add] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "haematopoietic cell" EXACT [] synonym: "haemopoietic cell" EXACT [] synonym: "hemopoietic cell" EXACT [] @@ -12892,6 +14406,8 @@ id: CL:0000989 name: CD11c-low plasmacytoid dendritic cell def: "CD11c-low plasmacytoid dendritic cell is a leukocyte that is CD11c-low, CD45R-positive, GR1-positive and CD11b-negative." [GO_REF:0000031, GOC:amm, GOC:dsd, PMID:15771572, PMID:17850486] comment: Originally described in the dendritic cell ontology (DC_CL:0000001)(PMID:19243617). These cells are CD281-positive (TLR1), CD282-positive (TLR2), CD285-positive (TLR5), CD286-positive (TLR6), and CD288-positive (TLR8). +subset: human_subset +subset: mouse_subset is_a: CL:0000784 {is_inferred="true"} ! plasmacytoid dendritic cell intersection_of: CL:0000784 ! plasmacytoid dendritic cell intersection_of: CL:4030046 PR:000001012 ! lacks_plasma_membrane_part integrin alpha-M @@ -12911,6 +14427,8 @@ comment: Originally described in the dendritic cell ontology (DC_CL:0000003)(PMI subset: blood_and_immune_upper_slim subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "cDC" EXACT [] synonym: "DC1" EXACT [] synonym: "dendritic reticular cell" EXACT [] @@ -12929,6 +14447,8 @@ id: CL:0000991 name: CD11c-negative plasmacytoid dendritic cell def: "CD11c-negative plasmacytoid dendritic cell is a leukocyte is CD11c-negative, CD45RA-positive, CD85g-positive(ILT7), CD123-positive, CD303-positive." [GO_REF:0000031, GOC:amm, PMID:15771572, PMID:17850486] comment: Originally described in the dendritic cell ontology (DC_CL:0000004)(PMID:19243617). These cells are CD281-positive (TLR1), CD286-positive (TLR6), and CD290-positive (TLR10). +subset: human_subset +subset: mouse_subset synonym: "CD303-positive dendritic cell" EXACT [] is_a: CL:0000784 {is_inferred="true"} ! plasmacytoid dendritic cell intersection_of: CL:0000784 ! plasmacytoid dendritic cell @@ -12948,6 +14468,8 @@ id: CL:0000992 name: immature CD11c-low plasmacytoid dendritic cell def: "Immature CD11c-low plasmacytoid dendritic cell is a CD11c-low plasmacytoid dendritic cell that is CD80-low and CD86-low." [GO_REF:0000031, GOC:amm, PMID:15771572, PMID:17850486] comment: Originally described in the dendritic cell ontology (DC_CL:0000006)(PMID:19243617). +subset: human_subset +subset: mouse_subset is_a: CL:0000766 ! myeloid leukocyte is_a: CL:0000989 {is_inferred="true"} ! CD11c-low plasmacytoid dendritic cell intersection_of: CL:0000989 ! CD11c-low plasmacytoid dendritic cell @@ -12962,6 +14484,8 @@ id: CL:0000993 name: mature CD11c-low plasmacytoid dendritic cell def: "Mature CD11c-low plasmacytoid dendritic cell is a CD11c-low plasmacytoid dendritic cell that is CD83-high and is CD80-positive, CD86-positive, and MHCII-positive." [GO_REF:0000031, GOC:amm, PMID:15771572, PMID:17850486] comment: Originally described in the dendritic cell ontology (DC_CL:0000007)(PMID:19243617). +subset: human_subset +subset: mouse_subset is_a: CL:0000766 ! myeloid leukocyte is_a: CL:0000989 {is_inferred="true"} ! CD11c-low plasmacytoid dendritic cell intersection_of: CL:0000989 ! CD11c-low plasmacytoid dendritic cell @@ -12980,6 +14504,8 @@ id: CL:0000994 name: immature CD11c-negative plasmacytoid dendritic cell def: "Immature CD11c-negative plasmacytoid dendritic cell is a CD11c-negative plasmacytoid dendritic cell is CD80-negative, CD86-low and MHCII-low." [GO_REF:0000031, GOC:amm, PMID:15771572, PMID:17850486] comment: Originally described in the dendritic cell ontology (DC_CL:0000008)(PMID:19243617). +subset: human_subset +subset: mouse_subset is_a: CL:0000991 {is_inferred="true"} ! CD11c-negative plasmacytoid dendritic cell intersection_of: CL:0000991 ! CD11c-negative plasmacytoid dendritic cell intersection_of: capable_of GO:0019882 ! antigen processing and presentation @@ -12995,8 +14521,11 @@ relationship: RO:0015016 PR:000001412 ! has low plasma membrane amount CD86 mole id: CL:0000995 name: CD34-positive, CD38-positive common myeloid progenitor OR CD34-positive, CD38-positive common lymphoid progenitor comment: Originally described in the dendritic cell ontology (DC_CL:1100000)(PMID:19243617). +subset: human_subset +subset: mouse_subset synonym: "CD71-positive common myeloid precursor OR CD7-negative lymphoid precursor OR CD7-positive lymphoid" BROAD [] is_a: CL:0001060 ! hematopoietic oligopotent progenitor cell, lineage-negative +is_a: CL:0011026 ! progenitor cell union_of: CL:0001021 ! CD34-positive, CD38-positive common lymphoid progenitor union_of: CL:0001026 ! CD34-positive, CD38-positive common myeloid progenitor @@ -13005,6 +14534,8 @@ id: CL:0000996 name: mature CD11c-negative plasmacytoid dendritic cell def: "Mature CD11c-negative plasmacytoid dendritic cell is a CD11c-negative plasmacytoid dendritic cell is CD80-high, CD86-high, MHCII-high and is CD83-positive." [GO_REF:0000031, GOC:amm, PMID:15771572, PMID:17850486] comment: Originally described in the dendritic cell ontology (DC_CL:0000009)(PMID:19243617). +subset: human_subset +subset: mouse_subset is_a: CL:0000991 {is_inferred="true"} ! CD11c-negative plasmacytoid dendritic cell intersection_of: CL:0000991 ! CD11c-negative plasmacytoid dendritic cell intersection_of: RO:0002104 PR:000001310 ! has plasma membrane part CD83 molecule @@ -13019,9 +14550,11 @@ relationship: RO:0015015 PR:000001438 ! has high plasma membrane amount CD80 mol [Term] id: CL:0000997 -name: immature CD8_alpha-negative CD11b-positive dendritic cell -def: "Immature CD8_alpha-negative CD11b-positive dendritic cell is a CD8_alpha-negative CD11b-positive dendritic cell that is CD80-low, CD86-low, and MHCII-low." [GO_REF:0000031, GOC:amm, GOC:tfm, PMCID:PMC2346585] +name: immature CD8-alpha-negative CD11b-positive dendritic cell +def: "Immature CD8-alpha-negative CD11b-positive dendritic cell is a CD8-alpha-negative CD11b-positive dendritic cell that is CD80-low, CD86-low, and MHCII-low." [GO_REF:0000031, GOC:amm, GOC:tfm, PMCID:PMC2346585] comment: Originally described in the dendritic cell ontology (DC_CL:0000010)(PMID:19243617). +subset: human_subset +subset: mouse_subset is_a: CL:0000840 ! immature conventional dendritic cell is_a: CL:0000999 {is_inferred="true"} ! CD4-positive CD11b-positive dendritic cell intersection_of: CL:0000999 ! CD4-positive CD11b-positive dendritic cell @@ -13031,9 +14564,11 @@ intersection_of: RO:0015016 PR:000001438 ! has low plasma membrane amount CD80 m [Term] id: CL:0000998 -name: CD8_alpha-negative CD11b-negative dendritic cell -def: "CD8_alpha-negative CD11b-negative dendritic cell is a conventional dendritic cell that is CD11b-negative, CD4-negative CD8_alpha-negative and is CD205-positive. This cell is able to cross- present antigen to CD8-alpha-positive T cells." [GO_REF:0000031, GOC:amm, http://www.immgen.org/index_content.html, PMCID:PMC2346585] +name: CD8-alpha-negative CD11b-negative dendritic cell +def: "CD8-alpha-negative CD11b-negative dendritic cell is a conventional dendritic cell that is CD11b-negative, CD4-negative CD8-alpha-negative and is CD205-positive. This cell is able to cross- present antigen to CD8-alpha-positive T cells." [GO_REF:0000031, GOC:amm, http://www.immgen.org/index_content.html, PMCID:PMC2346585] comment: These markers are associated with mouse cells. Originally described in the dendritic cell ontology (DC_CL:0000011)(PMID:19243617). +subset: human_subset +subset: mouse_subset synonym: "DC.8-4-11b-" EXACT [] synonym: "triple negative dendritic cell" EXACT [] is_a: CL:0000766 ! myeloid leukocyte @@ -13054,8 +14589,10 @@ relationship: RO:0002202 CL:0002010 ! develops from pre-conventional dendritic c [Term] id: CL:0000999 name: CD4-positive CD11b-positive dendritic cell -def: "CD8_alpha-negative CD11b-positive dendritic cell is a conventional dendritic cell that is CD11b-positive, CD4-positive and is CD205-negative and CD8_alpha-negative." [GO_REF:0000031, GOC:amm, GOC:tfm, PMCID:PMC2346585] +def: "CD8-alpha-negative CD11b-positive dendritic cell is a conventional dendritic cell that is CD11b-positive, CD4-positive and is CD205-negative and CD8-alpha-negative." [GO_REF:0000031, GOC:amm, GOC:tfm, PMCID:PMC2346585] comment: Defined as having a disposition to secreting anti-inflammatory cytokines. These markers are associated with mouse cells. Originally described in the dendritic cell ontology (DC_CL:0000012)(PMID:19243617). +subset: human_subset +subset: mouse_subset synonym: "DC.4+" EXACT [] is_a: CL:0000766 ! myeloid leukocyte is_a: CL:0002465 ! CD11b-positive dendritic cell @@ -13073,9 +14610,11 @@ relationship: RO:0002202 CL:0002010 ! develops from pre-conventional dendritic c [Term] id: CL:0001000 -name: CD8_alpha-positive CD11b-negative dendritic cell -def: "CD8_alpha-positive CD11b-negative dendritic cell is a conventional dendritic cell that is CD11b-negative, CD4-negative and is CD205-positive and CD8_alpha-positive." [GO_REF:0000031, GOC:amm, GOC:tfm, PMCID:PMC2346585] +name: CD8-alpha-positive CD11b-negative dendritic cell +def: "CD8-alpha-positive CD11b-negative dendritic cell is a conventional dendritic cell that is CD11b-negative, CD4-negative and is CD205-positive and CD8-alpha-positive." [GO_REF:0000031, GOC:amm, GOC:tfm, PMCID:PMC2346585] comment: Cells are defined as having a disposition to secreting inflammatory cytokines. Originally described in the dendritic cell ontology (DC_CL:0000013)(PMID:19243617). +subset: human_subset +subset: mouse_subset synonym: "DC.8+" EXACT [] is_a: CL:0000766 ! myeloid leukocyte is_a: CL:0000990 {is_inferred="true"} ! conventional dendritic cell @@ -13097,36 +14636,42 @@ relationship: RO:0002202 CL:0002010 ! develops from pre-conventional dendritic c [Term] id: CL:0001001 -name: immature CD8_alpha-negative CD11b-negative dendritic cell -def: "Immature CD8_alpha-negative CD11b-negative dendritic cell is a CD8_alpha-negative CD11b-negative dendritic cell that is CD80-low, CD86-low, and MHCII-low." [GO_REF:0000031, GOC:amm, PMCID:PMC2346585] +name: immature CD8-alpha-negative CD11b-negative dendritic cell +def: "Immature CD8-alpha-negative CD11b-negative dendritic cell is a CD8-alpha-negative CD11b-negative dendritic cell that is CD80-low, CD86-low, and MHCII-low." [GO_REF:0000031, GOC:amm, PMCID:PMC2346585] comment: These markers are associated with mouse cells. Originally described in the dendritic cell ontology (DC_CL:0000014)(PMID:19243617). +subset: human_subset +subset: mouse_subset is_a: CL:0000840 ! immature conventional dendritic cell -is_a: CL:0000998 {is_inferred="true"} ! CD8_alpha-negative CD11b-negative dendritic cell -intersection_of: CL:0000998 ! CD8_alpha-negative CD11b-negative dendritic cell +is_a: CL:0000998 {is_inferred="true"} ! CD8-alpha-negative CD11b-negative dendritic cell +intersection_of: CL:0000998 ! CD8-alpha-negative CD11b-negative dendritic cell intersection_of: RO:0015016 GO:0042613 ! has low plasma membrane amount MHC class II protein complex intersection_of: RO:0015016 PR:000001412 ! has low plasma membrane amount CD86 molecule intersection_of: RO:0015016 PR:000001438 ! has low plasma membrane amount CD80 molecule [Term] id: CL:0001002 -name: mature CD8_alpha-negative CD11b-negative dendritic cell -def: "Mature CD8_alpha-negative CD11b-negative dendritic cell is a CD8_alpha-negative CD11b-negative dendritic cell that is CD80-high, CD86-high, MHCII-high and is CD83-positive." [GO_REF:0000031, GOC:amm, GOC:tfm, PMCID:PMC2346585] +name: mature CD8-alpha-negative CD11b-negative dendritic cell +def: "Mature CD8-alpha-negative CD11b-negative dendritic cell is a CD8-alpha-negative CD11b-negative dendritic cell that is CD80-high, CD86-high, MHCII-high and is CD83-positive." [GO_REF:0000031, GOC:amm, GOC:tfm, PMCID:PMC2346585] comment: These markers are associated with mouse cells. Defined as having a disposition to secretion of anti-inflammatory cytokines. Originally described in the dendritic cell ontology (DC_CL:0000015)(PMID:19243617). +subset: human_subset +subset: mouse_subset is_a: CL:0000841 ! mature conventional dendritic cell -is_a: CL:0000998 {is_inferred="true"} ! CD8_alpha-negative CD11b-negative dendritic cell -intersection_of: CL:0000998 ! CD8_alpha-negative CD11b-negative dendritic cell +is_a: CL:0000998 {is_inferred="true"} ! CD8-alpha-negative CD11b-negative dendritic cell +intersection_of: CL:0000998 ! CD8-alpha-negative CD11b-negative dendritic cell intersection_of: capable_of GO:0001816 ! cytokine production intersection_of: RO:0002104 PR:000001310 ! has plasma membrane part CD83 molecule intersection_of: RO:0015015 GO:0042613 ! has high plasma membrane amount MHC class II protein complex intersection_of: RO:0015015 PR:000001412 ! has high plasma membrane amount CD86 molecule intersection_of: RO:0015015 PR:000001438 ! has high plasma membrane amount CD80 molecule -relationship: RO:0002202 CL:0001001 ! develops from immature CD8_alpha-negative CD11b-negative dendritic cell +relationship: RO:0002202 CL:0001001 ! develops from immature CD8-alpha-negative CD11b-negative dendritic cell [Term] id: CL:0001003 -name: mature CD8_alpha-negative CD11b-positive dendritic cell -def: "Mature CD8_alpha-negative CD11b-positive dendritic cell is a CD8_alpha-negative CD11b-positive dendritic cell that is CD80-high, CD86-high, MHCII-high and is CD83-positive." [GO_REF:0000031, GOC:amm, GOC:tfm, PMCID:PMC2346585] +name: mature CD8-alpha-negative CD11b-positive dendritic cell +def: "Mature CD8-alpha-negative CD11b-positive dendritic cell is a CD8-alpha-negative CD11b-positive dendritic cell that is CD80-high, CD86-high, MHCII-high and is CD83-positive." [GO_REF:0000031, GOC:amm, GOC:tfm, PMCID:PMC2346585] comment: Originally described in the dendritic cell ontology (DC_CL:0000016)(PMID:19243617). +subset: human_subset +subset: mouse_subset is_a: CL:0000841 ! mature conventional dendritic cell is_a: CL:0000999 {is_inferred="true"} ! CD4-positive CD11b-positive dendritic cell intersection_of: CL:0000999 ! CD4-positive CD11b-positive dendritic cell @@ -13134,33 +14679,37 @@ intersection_of: RO:0002104 PR:000001310 ! has plasma membrane part CD83 molecul intersection_of: RO:0015015 GO:0042613 ! has high plasma membrane amount MHC class II protein complex intersection_of: RO:0015015 PR:000001412 ! has high plasma membrane amount CD86 molecule intersection_of: RO:0015015 PR:000001438 ! has high plasma membrane amount CD80 molecule -relationship: RO:0002202 CL:0000997 ! develops from immature CD8_alpha-negative CD11b-positive dendritic cell +relationship: RO:0002202 CL:0000997 ! develops from immature CD8-alpha-negative CD11b-positive dendritic cell [Term] id: CL:0001004 -name: immature CD8_alpha-positive CD11b-negative dendritic cell -def: "Immature CD8_alpha-positive CD11b-negative dendritic cell is a CD8_alpha-positive CD11b-negative dendritic cell that is CD80-low, CD86-low, and MHCII-low." [GO_REF:0000031, GOC:amm, GOC:tfm, PMCID:PMC2346585] +name: immature CD8-alpha-positive CD11b-negative dendritic cell +def: "Immature CD8-alpha-positive CD11b-negative dendritic cell is a CD8-alpha-positive CD11b-negative dendritic cell that is CD80-low, CD86-low, and MHCII-low." [GO_REF:0000031, GOC:amm, GOC:tfm, PMCID:PMC2346585] comment: Originally described in the dendritic cell ontology (DC_CL:0000017)(PMID:19243617). +subset: human_subset +subset: mouse_subset is_a: CL:0000840 ! immature conventional dendritic cell -is_a: CL:0001000 {is_inferred="true"} ! CD8_alpha-positive CD11b-negative dendritic cell -intersection_of: CL:0001000 ! CD8_alpha-positive CD11b-negative dendritic cell +is_a: CL:0001000 {is_inferred="true"} ! CD8-alpha-positive CD11b-negative dendritic cell +intersection_of: CL:0001000 ! CD8-alpha-positive CD11b-negative dendritic cell intersection_of: RO:0015016 GO:0042613 ! has low plasma membrane amount MHC class II protein complex intersection_of: RO:0015016 PR:000001412 ! has low plasma membrane amount CD86 molecule intersection_of: RO:0015016 PR:000001438 ! has low plasma membrane amount CD80 molecule [Term] id: CL:0001005 -name: mature CD8_alpha-positive CD11b-negative dendritic cell -def: "Mature CD8_alpha-positive CD11b-negative dendritic cell is a CD8_alpha-positive CD11b-negative dendritic cell that is CD80-high, CD86-high, MHCII-high and is CD83-positive." [GO_REF:0000031, GOC:amm, PMCID:PMC2346585] +name: mature CD8-alpha-positive CD11b-negative dendritic cell +def: "Mature CD8-alpha-positive CD11b-negative dendritic cell is a CD8-alpha-positive CD11b-negative dendritic cell that is CD80-high, CD86-high, MHCII-high and is CD83-positive." [GO_REF:0000031, GOC:amm, PMCID:PMC2346585] comment: Originally described in the dendritic cell ontology (DC_CL:0000018)(PMID:19243617). +subset: human_subset +subset: mouse_subset is_a: CL:0000841 ! mature conventional dendritic cell -is_a: CL:0001000 {is_inferred="true"} ! CD8_alpha-positive CD11b-negative dendritic cell -intersection_of: CL:0001000 ! CD8_alpha-positive CD11b-negative dendritic cell +is_a: CL:0001000 {is_inferred="true"} ! CD8-alpha-positive CD11b-negative dendritic cell +intersection_of: CL:0001000 ! CD8-alpha-positive CD11b-negative dendritic cell intersection_of: RO:0002104 PR:000001310 ! has plasma membrane part CD83 molecule intersection_of: RO:0015015 GO:0042613 ! has high plasma membrane amount MHC class II protein complex intersection_of: RO:0015015 PR:000001412 ! has high plasma membrane amount CD86 molecule intersection_of: RO:0015015 PR:000001438 ! has high plasma membrane amount CD80 molecule -relationship: RO:0002202 CL:0001004 ! develops from immature CD8_alpha-positive CD11b-negative dendritic cell +relationship: RO:0002202 CL:0001004 ! develops from immature CD8-alpha-positive CD11b-negative dendritic cell [Term] id: CL:0001006 @@ -13168,6 +14717,8 @@ name: dermal dendritic cell def: "Dermal dendritic cell is a conventional dendritic cell that is CD11b-positive, CD205-positive and CD8 alpha-negative." [GO_REF:0000031, GOC:amm, PMCID:PMC2346585] comment: Originally described in the dendritic cell ontology (DC_CL:0000019)(PMID:19243617). These cells are also CD281-positive (TLR1), CD282-positive (TLR2), CD283-positive (TLR3), CD284-positive (TLR4), CD285-positive (TLR5), CD288-positive (TLR8), and CD289-positive (TLR9). subset: human_reference_atlas +subset: human_subset +subset: mouse_subset xref: BTO:0004812 is_a: CL:0002465 ! CD11b-positive dendritic cell intersection_of: CL:0000990 ! conventional dendritic cell @@ -13185,6 +14736,8 @@ id: CL:0001007 name: interstitial dendritic cell def: "Interstitial dendritic cell is a conventional dendritic cell that is CD11b-positive, CD1a-positive, CD206-positive, CD209-positive, and CD36-positive." [GO_REF:0000031, GOC:amm, PMID:17850486] comment: Originally described in the dendritic cell ontology (DC_CL:0000020)(PMID:19243617). These cells are also CD281-positive (TLR1), CD282-positive (TLR2), CD283-positive (TLR3), CD284-positive (TLR4), CD286-positive (TLR6), CD288-positive (TLR8), and CD290-positive (TLR10). +subset: human_subset +subset: mouse_subset is_a: CL:0002465 ! CD11b-positive dendritic cell intersection_of: CL:0000990 ! conventional dendritic cell intersection_of: RO:0002104 PR:000001012 ! has plasma membrane part integrin alpha-M @@ -13202,10 +14755,11 @@ id: CL:0001008 name: Kit and Sca1-positive hematopoietic stem cell def: "A hematopoietic stem cell that has plasma membrane part Kit-positive, SCA-1-positive, CD150-positive and CD34-negative." [GO_REF:0000031, GOC:add, GOC:amm, GOC:tfm, PMID:17952047, PMID:19022770] comment: Cell markers are associated with mouse hematopoietic stem cell. Originally described in the dendritic cell ontology (DC_CL:0000043)(PMID:19243617). +subset: human_subset +subset: mouse_subset synonym: "LSK stem cell" EXACT [] synonym: "Sca1-positive hematopoietic stem cell" EXACT [] is_a: CL:0000037 {is_inferred="true"} ! hematopoietic stem cell -is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000037 ! hematopoietic stem cell intersection_of: CL:4030046 PR:000001014 ! lacks_plasma_membrane_part receptor-type tyrosine-protein phosphatase C isoform CD45RABC intersection_of: CL:4030046 PR:000001084 ! lacks_plasma_membrane_part T-cell surface glycoprotein CD8 alpha chain @@ -13233,6 +14787,8 @@ id: CL:0001009 name: immature dermal dendritic cell def: "Immature dermal dendritic cell is a dermal dendritic cell that is CD80-low, CD86-low, and MHCII-low." [GO_REF:0000031, GOC:amm, PMCID:PMC2346585] comment: Originally described in the dendritic cell ontology (DC_CL:0000022)(PMID:19243617). +subset: human_subset +subset: mouse_subset is_a: CL:0000840 ! immature conventional dendritic cell is_a: CL:0001006 {is_inferred="true"} ! dermal dendritic cell intersection_of: CL:0001006 ! dermal dendritic cell @@ -13245,6 +14801,8 @@ id: CL:0001010 name: mature dermal dendritic cell def: "Mature dermal dendritic cell is a dermal dendritic cell that is CD80-high, CD86-high, MHCII-high and is CD83-positive." [GO_REF:0000031, GOC:amm, PMCID:PMC2346585] comment: Originally described in the dendritic cell ontology (DC_CL:0000023)(PMID:19243617). +subset: human_subset +subset: mouse_subset is_a: CL:0000841 ! mature conventional dendritic cell is_a: CL:0001006 {is_inferred="true"} ! dermal dendritic cell intersection_of: CL:0001006 ! dermal dendritic cell @@ -13259,6 +14817,8 @@ id: CL:0001011 name: immature interstitial dendritic cell def: "Immature interstitial dendritic cell is a interstitial dendritic cell that is CD80-low, CD86-low, and MHCII-low." [GO_REF:0000031, GOC:amm, GOC:tfm, PMID:17850486] comment: Originally described in the dendritic cell ontology (DC_CL:0000024)(PMID:19243617). +subset: human_subset +subset: mouse_subset is_a: CL:0000840 ! immature conventional dendritic cell is_a: CL:0001007 {is_inferred="true"} ! interstitial dendritic cell intersection_of: CL:0001007 ! interstitial dendritic cell @@ -13270,7 +14830,10 @@ intersection_of: RO:0015016 PR:000001438 ! has low plasma membrane amount CD80 m id: CL:0001012 name: CD7-negative lymphoid progenitor OR granulocyte monocyte progenitor comment: Originally described in the dendritic cell ontology (DC_CL:1110000)(PMID:19243617). +subset: human_subset +subset: mouse_subset is_a: CL:0001060 ! hematopoietic oligopotent progenitor cell, lineage-negative +is_a: CL:0011026 ! progenitor cell union_of: CL:0000557 ! granulocyte monocyte progenitor cell union_of: CL:0001027 ! CD7-negative lymphoid progenitor cell @@ -13279,6 +14842,8 @@ id: CL:0001013 name: mature interstitial dendritic cell def: "Mature interstitial dendritic cell is a interstitial dendritic cell that is CD80-high, CD86-high, MHCII-high and is CD83-positive." [GO_REF:0000031, GOC:amm, GOC:tfm, PMID:17850486] comment: Originally described in the dendritic cell ontology (DC_CL:0000025)(PMID:19243617). +subset: human_subset +subset: mouse_subset is_a: CL:0000841 ! mature conventional dendritic cell is_a: CL:0001007 {is_inferred="true"} ! interstitial dendritic cell intersection_of: CL:0001007 ! interstitial dendritic cell @@ -13293,6 +14858,8 @@ id: CL:0001014 name: CD1a-positive Langerhans cell def: "CD1a-positive Langerhans cell is a Langerhans_cell that is CD1a-positive and CD324-positive." [GO_REF:0000031, GOC:amm, PMID:17850486] comment: These markers are associated with human cells. Originally described in the dendritic cell ontology (DC_CL:0000026)(PMID:19243617). These cells are also CD281-positive (TLR1), CD282-positive (TLR2), CD284-positive (TLR4), CD286-positive (TLR6), CD287-positive (TLR7), and CD290-positive (TLR10). When activated, these cells are capable of producing IL-6, IL-8, and IL-15. +subset: human_subset +subset: mouse_subset synonym: "CD1a-LC" EXACT [] is_a: CL:0000453 {is_inferred="true"} ! Langerhans cell intersection_of: CL:0000453 ! Langerhans cell @@ -13303,9 +14870,11 @@ relationship: RO:0002104 PR:000002025 ! has plasma membrane part T-cell surface [Term] id: CL:0001015 -name: CD8_alpha-low Langerhans cell -def: "CD8_alpha-low Langerhans cell is a Langerhans cell that is CD205-high and is CD8_alpha-low." [GO_REF:0000031, GOC:amm, PMCID:PMC2346585] +name: CD8-alpha-low Langerhans cell +def: "CD8-alpha-low Langerhans cell is a Langerhans cell that is CD205-high and is CD8-alpha-low." [GO_REF:0000031, GOC:amm, PMCID:PMC2346585] comment: These markers are associated with mouse cells. Originally described in the dendritic cell ontology (DC_CL:0000027)(PMID:19243617). They are also CD205-high, CD281-positive (TLR1), CD282-positive (TLR2), CD283-positive (TLR3), CD285-positive (TLR5), CD286-positive (TLR6), and CD289-positive (TLR9). +subset: human_subset +subset: mouse_subset is_a: CL:0000453 {is_inferred="true"} ! Langerhans cell intersection_of: CL:0000453 ! Langerhans cell intersection_of: RO:0015015 PR:000001026 ! has high plasma membrane amount lymphocyte antigen 75 @@ -13318,6 +14887,8 @@ id: CL:0001016 name: immature CD1a-positive Langerhans cell def: "Immature CD1a-positive Langerhans cell is a CD1a-positive Langerhans cell that is CD80-low, CD86-low, and MHCII-low." [GO_REF:0000031, GOC:amm, GOC:tfm, PMID:17850486] comment: Originally described in the dendritic cell ontology (DC_CL:0000028)(PMID:19243617). +subset: human_subset +subset: mouse_subset is_a: CL:0000840 ! immature conventional dendritic cell is_a: CL:0001014 {is_inferred="true"} ! CD1a-positive Langerhans cell intersection_of: CL:0001014 ! CD1a-positive Langerhans cell @@ -13330,6 +14901,8 @@ id: CL:0001017 name: mature CD1a-positive Langerhans cell def: "Mature CD1a-positive Langerhans cell is a CD1a-positive Langerhans cell that is CD80-high, CD86-high, MHCII-high and is CD83-positive." [GO_REF:0000031, GOC:amm, GOC:tfm, PMID:17850486] comment: Originally described in the dendritic cell ontology (DC_CL:0000029)(PMID:19243617). When activated, these cells produce IL-6, IL-8, and IL-15. +subset: human_subset +subset: mouse_subset is_a: CL:0000841 ! mature conventional dendritic cell is_a: CL:0001014 {is_inferred="true"} ! CD1a-positive Langerhans cell intersection_of: CL:0001014 ! CD1a-positive Langerhans cell @@ -13341,12 +14914,14 @@ relationship: RO:0002202 CL:0001016 ! develops from immature CD1a-positive Lange [Term] id: CL:0001018 -name: immature CD8_alpha-low Langerhans cell -def: "Immature CD8_alpha-low Langerhans cell is a CD8_alpha-low Langerhans cell that is CD80-low, CD86-low, and MHCII-low." [GO_REF:0000031, GOC:amm, GOC:tfm, PMCID:PMC2346585] +name: immature CD8-alpha-low Langerhans cell +def: "Immature CD8-alpha-low Langerhans cell is a CD8-alpha-low Langerhans cell that is CD80-low, CD86-low, and MHCII-low." [GO_REF:0000031, GOC:amm, GOC:tfm, PMCID:PMC2346585] comment: These markers are associated with mouse cells. Originally described in the dendritic cell ontology (DC_CL:0000030)(PMID:19243617). +subset: human_subset +subset: mouse_subset is_a: CL:0000840 ! immature conventional dendritic cell -is_a: CL:0001015 {is_inferred="true"} ! CD8_alpha-low Langerhans cell -intersection_of: CL:0001015 ! CD8_alpha-low Langerhans cell +is_a: CL:0001015 {is_inferred="true"} ! CD8-alpha-low Langerhans cell +intersection_of: CL:0001015 ! CD8-alpha-low Langerhans cell intersection_of: RO:0015016 GO:0042613 ! has low plasma membrane amount MHC class II protein complex intersection_of: RO:0015016 PR:000001412 ! has low plasma membrane amount CD86 molecule intersection_of: RO:0015016 PR:000001438 ! has low plasma membrane amount CD80 molecule @@ -13355,35 +14930,41 @@ intersection_of: RO:0015016 PR:000001438 ! has low plasma membrane amount CD80 m id: CL:0001019 name: CD115-positive monocyte OR common dendritic progenitor comment: Originally described in the dendritic cell ontology (DC_CL:1111000)(PMID:19243617). +subset: human_subset +subset: mouse_subset +is_a: CL:0000763 ! myeloid cell is_a: CL:0002031 ! hematopoietic lineage restricted progenitor cell union_of: CL:0001022 ! CD115-positive monocyte union_of: CL:0001029 ! common dendritic progenitor [Term] id: CL:0001020 -name: mature CD8_alpha-low Langerhans cell -def: "Mature CD8_alpha-low Langerhans cell is a CD8_alpha-low Langerhans cell that that is CD80-high, CD86-high, MHCII-high and is CD83-positive." [GO_REF:0000031, GOC:amm, PMCID:PMC2346585] +name: mature CD8-alpha-low Langerhans cell +def: "Mature CD8-alpha-low Langerhans cell is a CD8-alpha-low Langerhans cell that that is CD80-high, CD86-high, MHCII-high and is CD83-positive." [GO_REF:0000031, GOC:amm, PMCID:PMC2346585] comment: These markers are associated with mouse cells. Originally described in the dendritic cell ontology (DC_CL:0000031)(PMID:19243617). +subset: human_subset +subset: mouse_subset is_a: CL:0000841 ! mature conventional dendritic cell -is_a: CL:0001015 {is_inferred="true"} ! CD8_alpha-low Langerhans cell -intersection_of: CL:0001015 ! CD8_alpha-low Langerhans cell +is_a: CL:0001015 {is_inferred="true"} ! CD8-alpha-low Langerhans cell +intersection_of: CL:0001015 ! CD8-alpha-low Langerhans cell intersection_of: RO:0002104 PR:000001310 ! has plasma membrane part CD83 molecule intersection_of: RO:0015015 GO:0042613 ! has high plasma membrane amount MHC class II protein complex intersection_of: RO:0015015 PR:000001412 ! has high plasma membrane amount CD86 molecule intersection_of: RO:0015015 PR:000001438 ! has high plasma membrane amount CD80 molecule -relationship: RO:0002202 CL:0001018 ! develops from immature CD8_alpha-low Langerhans cell +relationship: RO:0002202 CL:0001018 ! develops from immature CD8-alpha-low Langerhans cell [Term] id: CL:0001021 name: CD34-positive, CD38-positive common lymphoid progenitor def: "A common lymphoid progenitor that is CD10-positive, CD45RA-positive, CD34-positive and CD38-positive." [GO_REF:0000031, GOC:add, GOC:amm, GOC:tfm, PMCID:PMC2346585, PMID:19022770] comment: These markers are associated with human common lymphoid progenitors. Originally described in the dendritic cell ontology (DC_CL:0000032)(PMID:19243617). +subset: human_subset +subset: mouse_subset synonym: "CD10-positive common lymphocyte precursor" EXACT [] synonym: "CD10-positive common lymphocyte progenitor" EXACT [] synonym: "CD10-positive common lymphoid precursor" EXACT [] is_a: CL:0000051 {is_inferred="true"} ! common lymphoid progenitor is_a: CL:0000995 ! CD34-positive, CD38-positive common myeloid progenitor OR CD34-positive, CD38-positive common lymphoid progenitor -is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000051 ! common lymphoid progenitor intersection_of: RO:0002104 PR:000001003 ! has plasma membrane part CD34 molecule intersection_of: RO:0002104 PR:000001015 ! has plasma membrane part receptor-type tyrosine-protein phosphatase C isoform CD45RA @@ -13401,10 +14982,11 @@ id: CL:0001022 name: CD115-positive monocyte def: "CD115-positive monocyte is a monocyte that is CD115-positive and CD11b-positive." [GO_REF:0000031, GOC:add, GOC:amm, PMID:17952047] comment: These markers are associated with human cells. Originally described in the dendritic cell ontology (DC_CL:0000033)(PMID:19243617). +subset: human_subset +subset: mouse_subset is_a: CL:0000576 {is_inferred="true"} ! monocyte is_a: CL:0000839 ! myeloid lineage restricted progenitor cell is_a: CL:0001019 ! CD115-positive monocyte OR common dendritic progenitor -is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000576 ! monocyte intersection_of: RO:0002104 PR:000001012 ! has plasma membrane part integrin alpha-M intersection_of: RO:0002104 PR:000002062 ! has plasma membrane part macrophage colony-stimulating factor 1 receptor @@ -13417,6 +14999,8 @@ id: CL:0001023 name: Kit-positive, CD34-positive common myeloid progenitor def: "A common myeloid progenitor that is Kit-positive and CD34-positive, Il7ra-negative, and is SCA1-low and Fcgr2-low and Fcgr3-low." [GO_REF:0000031, GOC:add, GOC:amm, GOC:tfm, http://www.immgen.org/index_content.html, PMID:1261582, PMID:17952047] comment: Markers are associated with mouse cells. Originally described in the dendritic cell ontology (DC_CL:0000034)(PMID:19243617). +subset: human_subset +subset: mouse_subset synonym: "CD117-positive common myeloid precursor" BROAD [] is_a: CL:0001030 ! CD117-positive common myeloid progenitor OR CD217-positive common lymphoid progenitor is_a: CL:0001059 {is_inferred="true"} ! common myeloid progenitor, CD34-positive @@ -13440,10 +15024,11 @@ name: CD34-positive, CD38-negative hematopoietic stem cell def: "CD133-positive hematopoietic stem cell is a hematopoietic stem cell that is CD34-positive, CD90-positive, and CD133-positive." [GO_REF:0000031, GOC:add, GOC:amm, GOC:tfm, PMID:10430905, PMID:11750107, PMID:16551251, PMID:20024907, PMID:9389721] comment: Cell markers are associated with human hematopoietic stem cells. Originally described in the dendritic cell ontology (DC_CL:0000035)(PMID:19243617). subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "CD133-positive hematopoietic stem cell" EXACT [PMID:16140871] xref: CALOHA:TS-0448 is_a: CL:0000037 {is_inferred="true"} ! hematopoietic stem cell -is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000037 ! hematopoietic stem cell intersection_of: CL:4030046 PR:000001024 ! lacks_plasma_membrane_part neural cell adhesion molecule 1 intersection_of: CL:4030046 PR:000001408 ! lacks_plasma_membrane_part ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1 @@ -13468,12 +15053,13 @@ id: CL:0001025 name: Kit-positive, Sca1-positive common lymphoid progenitor def: "A common lymphoid progenitor that is Kit-low, FLT3-positive, IL7ralpha-positive, and SCA1-low." [GO_REF:0000031, GOC:add, GOC:amm, GOC:tfm, http://www.immgen.org/index_content.html, PMID:17952047] comment: Markers are associated with mouse cells. +subset: human_subset +subset: mouse_subset synonym: "CD217-positive common lymphocyte precursor" EXACT [] synonym: "CD217-positive common lymphocyte progenitor" EXACT [] synonym: "CD217-positive common lymphoid precursor" EXACT [] is_a: CL:0000051 {is_inferred="true"} ! common lymphoid progenitor is_a: CL:0001030 ! CD117-positive common myeloid progenitor OR CD217-positive common lymphoid progenitor -is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000051 ! common lymphoid progenitor intersection_of: CL:4030046 PR:000001014 ! lacks_plasma_membrane_part receptor-type tyrosine-protein phosphatase C isoform CD45RABC intersection_of: RO:0002104 PR:000001869 ! has plasma membrane part interleukin-7 receptor subunit alpha @@ -13496,6 +15082,8 @@ id: CL:0001026 name: CD34-positive, CD38-positive common myeloid progenitor def: "A common myeloid progenitor that is CD34-positive, CD38-positive, IL3ra-low, CD10-negative, CD7-negative, CD45RA-negative, and IL-5Ralpha-negative." [GO_REF:0000031, GOC:add, GOC:amm, PMCID:PMC2626675, PMID:16551251] comment: Markers are associated with human cell type. Originally described in the dendritic cell ontology (DC_CL:0000038)(PMID:19243617). +subset: human_subset +subset: mouse_subset synonym: "CD71-positive common myeloid precursor" NARROW [] is_a: CL:0000995 ! CD34-positive, CD38-positive common myeloid progenitor OR CD34-positive, CD38-positive common lymphoid progenitor is_a: CL:0001059 ! common myeloid progenitor, CD34-positive @@ -13519,10 +15107,11 @@ id: CL:0001027 name: CD7-negative lymphoid progenitor cell def: "CD7-negative lymphoid progenitor cell is a lymphoid progenitor cell that is CD34-positive, CD7-negative and CD45RA-negative." [GO_REF:0000031, GOC:amm, PMID:16551251] comment: These markers are associated with human cells. Originally described in the dendritic cell ontology (DC_CL:0000039)(PMID:19243617). +subset: human_subset +subset: mouse_subset synonym: "CD7-negative lymphoid precursor" EXACT [] is_a: CL:0000051 {is_inferred="true"} ! common lymphoid progenitor is_a: CL:0001012 ! CD7-negative lymphoid progenitor OR granulocyte monocyte progenitor -is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000051 ! common lymphoid progenitor intersection_of: CL:4030046 PR:000001015 ! lacks_plasma_membrane_part receptor-type tyrosine-protein phosphatase C isoform CD45RA intersection_of: CL:4030046 PR:000001836 ! lacks_plasma_membrane_part CD7 molecule @@ -13537,9 +15126,10 @@ id: CL:0001028 name: CD7-positive lymphoid progenitor cell def: "CD7-positive lymphoid progenitor cell is a lymphoid progenitor cell that is CD34-positive, CD7-positive and is CD45RA-negative." [GO_REF:0000031, GOC:amm, GOC:tfm, PMID:16551251, PMID:19491395] comment: These markers are associated with human cells. Originally described in the dendritic cell ontology (DC_CL:0000040)(PMID:19243617). +subset: human_subset +subset: mouse_subset synonym: "CD7-positive lymphoid precursor" EXACT [] is_a: CL:0000051 {is_inferred="true"} ! common lymphoid progenitor -is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000051 ! common lymphoid progenitor intersection_of: CL:4030046 PR:000001015 ! lacks_plasma_membrane_part receptor-type tyrosine-protein phosphatase C isoform CD45RA intersection_of: RO:0002104 PR:000001003 ! has plasma membrane part CD34 molecule @@ -13555,12 +15145,12 @@ name: common dendritic progenitor def: "Common dendritic precursor is a hematopoietic progenitor cell that is CD117-low, CD135-positive, CD115-positive and lacks plasma membrane parts for hematopoietic lineage markers." [GO_REF:0000031, GOC:amm, GOC:tfm, PMID:16551251, PMID:17922016, PMID:19286519] comment: Surface markers are for mouse cells. Originally described in the dendritic cell ontology (DC_CL:0000041) CDP are reportedly CD2-negative, CD3-negative, CD4-negative, CD5-negative, CD8a-negative, CD11c-positive, CD14-negative, CD19-negative, CD20-negative, CD56-negative, B220-negative, Ly6g-negative, MHCII-positive, and Ter119-negative. (PMID:19243617). subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "CDP" EXACT [PMID:21219184] synonym: "common dendritic precursor" EXACT [] synonym: "pro-DCs" EXACT [PMID:21219184] -is_a: CL:0000763 ! myeloid cell is_a: CL:0001019 ! CD115-positive monocyte OR common dendritic progenitor -is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0002031 ! hematopoietic lineage restricted progenitor cell intersection_of: CL:4030046 PR:000001002 ! lacks_plasma_membrane_part CD19 molecule intersection_of: CL:4030046 PR:000001004 ! lacks_plasma_membrane_part CD4 molecule @@ -13598,7 +15188,10 @@ relationship: RO:0015016 PR:000002065 ! has low plasma membrane amount mast/stem id: CL:0001030 name: CD117-positive common myeloid progenitor OR CD217-positive common lymphoid progenitor comment: Originally described in the dendritic cell ontology (DC_CL:1111100)(PMID:19243617). +subset: human_subset +subset: mouse_subset is_a: CL:0001060 ! hematopoietic oligopotent progenitor cell, lineage-negative +is_a: CL:0011026 ! progenitor cell union_of: CL:0001023 ! Kit-positive, CD34-positive common myeloid progenitor union_of: CL:0001025 ! Kit-positive, Sca1-positive common lymphoid progenitor @@ -13608,6 +15201,8 @@ name: cerebellar granule cell def: "An excitatory granule cell with a soma located in the granular layer of cerebellar cortex. A mature cerebellar granule cell has short dendrites with a characteristic claw-like appearance and a long axon that ascends to the molecular layer where it bifurcates (except in non-teleost fish, where it does not bifurcate) and extends mediolaterally to form parallel fibers." [doi:10.12688/f1000research.15021.1, doi:10.3389/fncir.2020.611841, GOC:mah] comment: It has been noted in at least some mammalian species that granule cells are the most numerous cell type in the cerebellum and in the brain, with at least 99% of all cerebellar neurons being granule cells. {xref="doi:10.3389/fncir.2020.611841"} subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "granule cell of the cerebellum" EXACT [doi:10.3389/fncir.2020.611841] xref: BTO:0004278 xref: ZFA:0001691 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} @@ -13622,9 +15217,10 @@ relationship: RO:0002207 CL:0002362 ! directly develops from cerebellar granule id: CL:0001032 name: cortical granule cell def: "Granule cell that is part of the cerebral cortex." [GOC:mah] +subset: human_subset +subset: mouse_subset is_a: CL:0000120 ! granule cell is_a: CL:0010012 ! cerebral cortex neuron -is_a: CL:0012001 ! neuron of the forebrain intersection_of: CL:0000120 ! granule cell intersection_of: RO:0002100 UBERON:0000956 ! has soma location cerebral cortex @@ -13632,6 +15228,8 @@ intersection_of: RO:0002100 UBERON:0000956 ! has soma location cerebral cortex id: CL:0001033 name: hippocampal granule cell def: "Granule cell with a soma found in the hippocampus." [GOC:mah] +subset: human_subset +subset: mouse_subset is_a: CL:0001032 ! cortical granule cell is_a: CL:0002608 ! hippocampal neuron intersection_of: CL:0000120 ! granule cell @@ -13642,6 +15240,8 @@ id: CL:0001034 name: cell in vitro def: "A cell that is maintained or propagated in a controlled artificial environment for use in an investigation." [ReO:mhb] comment: 'In vitro', translating literally to 'in glass', typically refers to a controlled, often sterile, laboratory setting where cells or other specimens are placed by some agent for the purpose of studying or manipulating them as part of some research investigation. 'In vitro' is intended to contrast with 'native',which refers to cells or other biological entities that are found in a natural setting. It describes unicellular organisms removed from a natural environement and multicellular organism cells removed from an organism, or cells derived in culture from such displaced cells. +subset: human_subset +subset: mouse_subset is_a: CL:0000000 ! cell property_value: terms:contributor https://orcid.org/0000-0001-9114-8737 creation_date: 2012-01-12T09:58:38Z @@ -13652,18 +15252,24 @@ name: bone cell def: "A connective tissue cell found in bone." [GO_REF:0000034, GOC:add] subset: general_cell_types_upper_slim subset: human_reference_atlas +subset: human_subset +subset: mouse_subset +xref: https://cellxgene.cziscience.com/cellguide/CL_0001035 is_a: CL:0000255 ! eukaryotic cell intersection_of: CL:0000000 ! cell intersection_of: part_of UBERON:0001474 ! bone element relationship: part_of UBERON:0001474 ! bone element property_value: RO:0002175 NCBITaxon:9606 property_value: terms:contributor https://orcid.org/0000-0001-9990-8331 +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nBone cells, also known as osteocytes, form the building blocks of the skeletal system. They represent the most common type of bone cell, making up approximately 95% of the total bone cell population in mature adult bone tissue. Osteocytes are a stellate shape with numerous long, slender dendritic processes.\nThe formation of bone is a complex process involving the action of osteoclasts - cells that break down and reabsorb old bone, followed by osteoblasts that rebuild the bone. Osteocytes serve as coordinators for these two types of bone cells to ensure a balance in the bone remodeling process, contributing to maintaining both bone strength and mineral homeostasis.\nThe primary functions of osteocytes involve the creation, maintenance, and repair of bone tissue. They ensure that bone remodeling is performed by forming a network within the bone and communicating with other cells to help them respond to mechanical strain and damage.\nA remarkable aspect of osteocytes is their ability to perceive mechanical forces, translating them into biochemical signals that regulate bone remodeling and adaptation. Defects in osteocyte function, aside from other bone cells, have been associated with several bone disorders such as osteoporosis, renal osteodystrophy, and skeletal manifestations of diabetes." xsd:string {xref="DOI:10.1007/s00795-015-0099-y", xref="DOI:10.1007/s11914-012-0105-4", xref="DOI:10.1016/j.jot.2021.04.005", xref="DOI:10.1038/s41413-020-0099-y"} creation_date: 2011-11-16T04:28:16Z [Term] id: CL:0001039 name: terminally differentiated osteoblast def: "Osteoblast that is terminally differentiated, located adjacent to acellular or cellular bone tissue within periosteum, and is capable of mineralizing the matrix." [VSAO:curator] +subset: human_subset +subset: mouse_subset xref: VSAO:0000116 is_a: CL:0000062 ! osteoblast @@ -13672,6 +15278,8 @@ id: CL:0001040 name: non-terminally differentiated osteoblast def: "Osteoblast that is non-terminally differentiated and located in cellular bone tissue or under the periosteum in acellular bone." [VSAO:curator] comment: VSAO relationship simplified OBO_REL:integral_part_of VSAO:0000118 +subset: human_subset +subset: mouse_subset xref: VSAO:0000117 is_a: CL:0000062 ! osteoblast is_a: CL:0001035 ! bone cell @@ -13682,6 +15290,8 @@ id: CL:0001041 name: CD8-positive, CXCR3-positive, alpha-beta regulatory T cell def: "A CD8-positive alpha-beta-positive T cell with the phenotype CXCR3-positive and having suppressor function. They are capable of producing IL-10, suppressing proliferation, and suppressing IFN-gamma production." [GOC:dsd, PMID:19609979] comment: These cells may be the human equivalent of murine CD8-positive, CD122-positive alpha-beta regulatory T cell. They are also found in the CD45RA-negative and CD62L-positive fraction. +subset: human_subset +subset: mouse_subset synonym: "CD8+CXCR3+ T cell" EXACT [] synonym: "CD8+CXCR3+ T lymphocyte" EXACT [] synonym: "CD8+CXCR3+ T(reg)" EXACT [] @@ -13709,6 +15319,8 @@ name: T-helper 22 cell def: "CD4-positive, alpha-beta T cell that produces IL-22." [GOC:dsd, PMID:19578368, PMID:19578369] comment: TH22 cells are also reportedly CCR4-positive, CCR6-positive, CCR10-positive, CXCR3-negative. TH22 cells are reportedly capable of secreting IL-13. subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "helper T cell type 22" EXACT [] synonym: "T(H)-22 cell" EXACT [] synonym: "Th22 cell" EXACT [] @@ -13727,6 +15339,8 @@ name: activated CD4-positive, alpha-beta T cell, human def: "A recently activated CD4-positive, alpha-beta T cell with the phenotype HLA-DRA-positive, CD38-positive, CD69-positive, CD62L-negative, CD127-negative, and CD25-positive." [GOC:add, PMID:22343568] comment: This cell type is compatible with the HIPC Lyoplate markers for 'activated CD4+ T cell', but includes via logical inference from its parent additional markers known to be expressed on activated CD4+ T cells. The inclusion of HLA-DRA in the definition restricts this definition to human activated CD4+ T cells, as activated mouse T cells do not express MHC class II. subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "activated CD4+ T cell" BROAD [PMID:22343568] synonym: "activated CD4-positive, alpha-beta T lymphocyte, human" EXACT [] synonym: "activated CD4-positive, alpha-beta T-cell, human" EXACT [] @@ -13744,6 +15358,8 @@ name: effector CD4-positive, alpha-beta T cell def: "A CD4-positive, alpha-beta T cell with the phenotype CCR7-negative, CD45RA-positive." [GOC:add, PMID:22343568] comment: This cell type is compatible with the HIPC Lyoplate markers for 'effector CD4+ T cell'. The functional characteristics of this cell type currently undefined in CL, which affects its proper placement within the hierarchy. subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "effector CD4+ T cell" BROAD [PMID:22343568] synonym: "effector CD4-positive, alpha-beta T lymphocyte" EXACT [] synonym: "effector CD4-positive, alpha-beta T-cell" EXACT [] @@ -13764,6 +15380,8 @@ id: CL:0001045 name: naive CCR4-positive regulatory T cell def: "A naive regulatory T cell with the phenotype CD4-positive, CD25-positive, CD127lo, CCR4-positive, and CD45RO-negative." [GOC:add, PMID:22343568] comment: This cell type is compatible with the HIPC Lyoplate markers for 'naive CCR4+ Treg'. The definition is valid for human; its applicability for mouse and other species is unknown. +subset: human_subset +subset: mouse_subset synonym: "naive CCR4+ Treg" EXACT [PMID:22343568] synonym: "naive CCR4-positive regulatory T lymphocyte" EXACT [] synonym: "naive CCR4-positive regulatory T-cell" EXACT [] @@ -13780,6 +15398,7 @@ id: CL:0001046 name: memory CCR4-positive regulatory T cell def: "A memory regulatory T cell with phenotype CD4-positive, CD25-positive, CD127lo, CCR4-positive, and CD45RO-positive." [GOC:add, PMID:22343568] comment: This cell type is compatible with the HIPC Lyoplate markers for 'memory CCR4+ Treg'. The definition is valid for human; its applicability for mouse and other species is unknown. +subset: human_subset synonym: "memory CCR4+ Treg" EXACT [PMID:22343568] synonym: "memory CCR4-positive regulatory T lymphocyte" EXACT [] synonym: "memory CCR4-positive regulatory T-cell" EXACT [] @@ -13798,6 +15417,8 @@ id: CL:0001047 name: CD4-positive, CD25-positive, CCR4-positive, alpha-beta regulatory T cell def: "A CD4-positive, CD25-positive, alpha-beta regulatory T cell with the additional phenotype CCR4-positive." [GOC:add, PMID:22343568] comment: This cell type is compatible with the HIPC Lyoplate markers for 'CCR4+ Treg'. The definition is valid for human; its applicability for mouse and other species is unknown. +subset: human_subset +subset: mouse_subset synonym: "CCR+ Treg" EXACT [PMID:22343568] synonym: "CD4-positive, CD25-positive, CCR4-positive, alpha-beta regulatory T lymphocyte" EXACT [] synonym: "CD4-positive, CD25-positive, CCR4-positive, alpha-beta regulatory T-cell" EXACT [] @@ -13812,6 +15433,8 @@ id: CL:0001048 name: activated CD4-positive, CD25-positive, CCR4-positive, alpha-beta regulatory T cell, human def: "A CD4-positive, CD25-positive, CCR4-positive, alpha-beta T regulatory cell with the phenotype HLA-DRA-positive, indicating recent activation." [GOC:add, PMID:22343568] comment: This cell type is compatible with the HIPC Lyoplate markers for 'activated CCR4+ Treg'. The inclusion of HLA-DRA in the definition restricts this definition to human activated CD4+ T cells, as activated mouse T cells do not express MHC class II. +subset: human_subset +subset: mouse_subset synonym: "activated CCR4+ Treg" EXACT [PMID:22343568] synonym: "activated CD4-positive, CD25-positive, CCR4-positive, alpha-beta regulatory T lymphocyte" EXACT [] synonym: "activated CD4-positive, CD25-positive, CCR4-positive, alpha-beta regulatory T-cell" EXACT [] @@ -13827,6 +15450,8 @@ name: activated CD8-positive, alpha-beta T cell, human def: "A recently activated CD8-positive, alpha-beta T cell with the phenotype HLA-DRA-positive, CD38-positive, CD69-positive, CD62L-negative, CD127-negative, CCR7-negative, and CD25-positive." [GOC:add, PMID:22343568] comment: This cell type is compatible with the HIPC Lyoplate markers for 'activated CD8+ T cell', but includes via logical inference from its parent additional markers known to be expressed on activated CD8+ T cells. The inclusion of HLA-DRA in the definition restricts this definition to human activated CD8+ T cells, as activated mouse T cells do not express MHC class II. subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "activated CD8+ T cell" BROAD [PMID:22343568] synonym: "activated CD8-positive, alpha-beta T lymphocyte, human" EXACT [] synonym: "activated CD8-positive, alpha-beta T-cell, human" EXACT [] @@ -13845,6 +15470,8 @@ def: "A CD8-positive, alpha-beta T cell with the phenotype CCR7-negative, CD45RA comment: This cell type is compatible with the HIPC Lyoplate markers for 'effector CD8+ T cell'. The functional characteristics of this cell type currently undefined in CL, which affects its proper placement within the hierarchy. subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "effector CD8+ T cell" BROAD [PMID:22343568] synonym: "effector CD8-positive, alpha-beta T lymphocyte" EXACT [] synonym: "effector CD8-positive, alpha-beta T-cell" EXACT [] @@ -13866,6 +15493,8 @@ id: CL:0001051 name: CD4-positive, CXCR3-negative, CCR6-negative, alpha-beta T cell def: "A CD4-positive, alpha-beta T cell that has the phenotype CXCR3-negative, CCR6-negative." [GOC:add, PMID:22343568] comment: This cell type is compatible with the HIPC Lyoplate markers for 'non-Th1/Th17 CD4+ T cell'. Cells of this phenotype may include T-helper 2 T cells and some naive CD4+ T cells. +subset: human_subset +subset: mouse_subset synonym: "CD4-positive, CXCR3-negative, CCR6-negative, alpha-beta T lymphocyte" EXACT [] synonym: "CD4-positive, CXCR3-negative, CCR6-negative, alpha-beta T-cell" EXACT [] synonym: "CD4-positive, CXCR3-negative, CCR6-negative, alpha-beta T-lymphocyte" EXACT [] @@ -13882,6 +15511,8 @@ id: CL:0001052 name: CD8-positive, CXCR3-negative, CCR6-negative, alpha-beta T cell def: "A CD8-positive, alpha-beta T cell that has the phenotype CXCR3-negative, CCR6-negative." [GOC:add, PMID:22343568] comment: This cell type is compatible with the HIPC Lyoplate markers for 'non-Tc1/Tc17 CD8+ T cell'. Cells of this phenotype may include Tc2 T cells and some naive CD8+ T cells. +subset: human_subset +subset: mouse_subset synonym: "CD8-positive, CXCR3-negative, CCR6-negative, alpha-beta T lymphocyte" EXACT [] synonym: "CD8-positive, CXCR3-negative, CCR6-negative, alpha-beta T-cell" EXACT [] synonym: "CD8-positive, CXCR3-negative, CCR6-negative, alpha-beta T-lymphocyte" EXACT [] @@ -13898,6 +15529,8 @@ id: CL:0001053 name: IgD-negative memory B cell def: "A memory B cell that lacks expression of surface IgD." [GOC:add, PMID:22343568] comment: This cell type is compatible with the HIPC Lyoplate markers for 'IgD- memory B cell'. The majority of these cells are class-switched, though some are IgM-positive. +subset: human_subset +subset: mouse_subset synonym: "IgD- memory B cell" EXACT [PMID:22343568] is_a: CL:0000787 ! memory B cell intersection_of: CL:0000787 ! memory B cell @@ -13911,9 +15544,10 @@ def: "A monocyte that expresses CD14 and is negative for the lineage markers CD3 comment: This cell type is compatible with the HIPC Lyoplate markers for 'monocyte'. Note that while CD14 is considered a reliable marker for human monocytes, it is only expressed on approximately 85% of mouse monocytes. subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "monocyte" NARROW [PMID:22343568] is_a: CL:0000576 ! monocyte -is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000576 ! monocyte intersection_of: CL:4030046 PR:000001002 ! lacks_plasma_membrane_part CD19 molecule intersection_of: CL:4030046 PR:000001020 ! lacks_plasma_membrane_part CD3 epsilon @@ -13931,6 +15565,8 @@ name: CD14-positive, CD16-low monocyte def: "An intermediate monocyte that is CD14-positive and with low amounts of CD16." [GOC:add, PMID:20628149] comment: Definition is valid for human intermediate monocytes. subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "intermediate monocyte, human" EXACT [] is_a: CL:0002393 ! intermediate monocyte is_a: CL:0002397 ! CD14-positive, CD16-positive monocyte @@ -13947,6 +15583,8 @@ def: "A dendritic cell with the phenotype HLA-DRA-positive." [GOC:add, PMID:2234 comment: This cell type is compatible with the HIPC Lyoplate markers for 'dendritic cell'. The inclusion of HLA-DRA in the definition restricts this definition to human dendritic cells. subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "dendritic cell" BROAD [PMID:22343568] is_a: CL:0000451 ! dendritic cell intersection_of: CL:0000451 ! dendritic cell @@ -13960,6 +15598,8 @@ name: myeloid dendritic cell, human def: "A myeloid dendritic cell with the phenotype HLA-DRA-positive." [GOC:add, PMID:22343568] comment: This cell type is compatible with the HIPC Lyoplate markers for 'myeloid dendritic cell'. The inclusion of HLA-DRA in the definition restricts this definition to human myeloid dendritic cells. subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "myeloid dendritic cell" BROAD [PMID:22343568] is_a: CL:0000782 ! myeloid dendritic cell is_a: CL:0001056 ! dendritic cell, human @@ -13973,6 +15613,8 @@ def: "A plasmacytoid dendritic cell with the phenotype HLA-DRA-positive, CD123-p comment: This cell type is compatible with the HIPC Lyoplate markers for 'plasmacytoid dendritic cell'. The inclusion of HLA-DRA in the definition restricts this definition to human plasmacytoid dendritic cells. subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "plasmacytoid dendritic cell" BROAD [PMID:22343568] is_a: CL:0000784 ! plasmacytoid dendritic cell is_a: CL:0001056 ! dendritic cell, human @@ -13989,6 +15631,8 @@ id: CL:0001059 name: common myeloid progenitor, CD34-positive def: "A progenitor cell committed to myeloid lineage, including the megakaryocyte and erythroid lineages. These cells are CD34-positive, and express Gata1, Gata2, C/EBPa, and Pu.1." [GOC:add, GOC:dsd, GOC:tfm, ISBN:0878932437, PMCID:PMC2212039, PMID:10724173, PMID:16551251, PMID:16647566] comment: CMP are reportedly CD16-positive, CD32-positive, CD38-positive, CD45RA-negative, CD110-negative, CD117-positive, CD123-positive, and SCA1-negative. +subset: human_subset +subset: mouse_subset synonym: "CFU-GEMM" RELATED OMO:0003000 [ISBN:0878932437] synonym: "CFU-S" RELATED OMO:0003000 [ISBN:0878932437] synonym: "CMP" RELATED OMO:0003000 [ISBN:0878932437] @@ -13999,7 +15643,6 @@ synonym: "myeloid stem cell" RELATED [ISBN:0878932437] synonym: "pluripotent stem cell (bone marrow)" RELATED [ISBN:0878932437] is_a: CL:0000049 ! common myeloid progenitor is_a: CL:0011026 ! progenitor cell -is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000049 ! common myeloid progenitor intersection_of: capable_of GO:0002573 ! myeloid leukocyte differentiation intersection_of: capable_of GO:0043011 ! myeloid dendritic cell differentiation @@ -14019,6 +15662,8 @@ relationship: RO:0002104 PR:000001003 ! has plasma membrane part CD34 molecule id: CL:0001060 name: hematopoietic oligopotent progenitor cell, lineage-negative def: "A hematopoietic oligopotent progenitor cell that has the ability to differentiate into limited cell types but lacks lineage cell markers and self renewal capabilities. Cell lacks hematopoeitic lineage markers." [GOC:tfm, PMID:19022770] +subset: human_subset +subset: mouse_subset is_a: CL:0002032 ! hematopoietic oligopotent progenitor cell intersection_of: CL:0002032 ! hematopoietic oligopotent progenitor cell intersection_of: bearer_of PATO:0001401 ! oligopotent @@ -14055,6 +15700,8 @@ name: abnormal cell def: "A cell found in an organism or derived from an organism exhibiting a phenotype that deviates from the expected phenotype of any native cell type of that organism. Abnormal cells are typically found in disease states or disease models." [GOC:add, GOC:cg, GOC:wdd] comment: https://github.com/obophenotype/cell-ontology/issues/448 subset: cellxgene_subset +subset: human_subset +subset: mouse_subset xref: https://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&code=C12913 is_a: CL:0000000 ! cell intersection_of: CL:0000000 ! cell @@ -14070,6 +15717,7 @@ def: "A CD8-positive, alpha beta memory T cell with the phenotype CD45RA-positiv comment: This cell type is seen in human but not found in the mouse. subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset synonym: "CD8+ TEMRA" EXACT [PMID:15032595] synonym: "CD8-positive TEMRA" EXACT [PMID:15032595] synonym: "TEMRA" BROAD [PMID:15032595] @@ -14094,6 +15742,8 @@ name: neoplastic cell def: "An abnormal cell exhibiting dysregulation of cell proliferation or programmed cell death and capable of forming a neoplasm, an aggregate of cells in the form of a tumor mass or an excess number of abnormal cells (liquid tumor) within an organism." [GOC:add, GOC:cg, GOC:wdd] comment: https://github.com/obophenotype/cell-ontology/issues/448 subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "tumor cell" RELATED [] synonym: "tumour cell" RELATED [] xref: https://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&code=C12922 @@ -14110,6 +15760,8 @@ name: malignant cell def: "A neoplastic cell that is capable of entering a surrounding tissue" [GOC:add, GOC:cg, GOC:wdd] comment: https://github.com/obophenotype/cell-ontology/issues/448 subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "cancer cell" RELATED [] xref: https://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&code=C12917 is_a: CL:0001063 ! neoplastic cell @@ -14126,6 +15778,8 @@ def: "A lymphocyte that lacks characteristic T cell, B cell, myeloid cell, and d subset: blood_and_immune_upper_slim subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset is_a: CL:0000542 ! lymphocyte intersection_of: CL:0000542 ! lymphocyte intersection_of: capable_of GO:0001816 ! cytokine production @@ -14145,6 +15799,8 @@ id: CL:0001066 name: erythroid progenitor cell, mammalian def: "A progenitor cell committed to the erythroid lineage. This cell is ter119-positive but lacks expression of other hematopoietic lineage markers (lin-negative)." [GOC:add, ISBN:0721601464] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "BFU-E" RELATED OMO:0003000 [] synonym: "blast forming unit erythroid" RELATED [] synonym: "burst forming unit erythroid" RELATED [] @@ -14153,7 +15809,6 @@ synonym: "colony forming unit erythroid" RELATED [] synonym: "erythroid stem cell" RELATED [] xref: BTO:0004911 is_a: CL:0000038 ! erythroid progenitor cell -is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000038 ! erythroid progenitor cell intersection_of: capable_of GO:0030218 ! erythrocyte differentiation intersection_of: CL:4030046 PR:000001002 ! lacks_plasma_membrane_part CD19 molecule @@ -14187,6 +15842,8 @@ id: CL:0001067 name: group 1 innate lymphoid cell def: "An innate lymphoid cell that is capable of producing the type 1 cytokine IFN-gamma, but not Th2 or Th17 cell-associated cytokines." [GOC:add, GOC:dsd, PMID:23348417] subset: human_reference_atlas +subset: human_subset +subset: mouse_subset is_a: CL:0001065 ! innate lymphoid cell intersection_of: CL:0001065 ! innate lymphoid cell intersection_of: capable_of GO:0032609 ! type II interferon production @@ -14199,6 +15856,8 @@ property_value: terms:date "2017-01-30T20:42:44Z" xsd:dateTime id: CL:0001068 name: ILC1 def: "A group 1 innate lymphoid cell that is non-cytotoxic." [GOC:add, GOC:dsd, PMID:23292121, PMID:23348417] +subset: human_subset +subset: mouse_subset is_a: CL:0001067 ! group 1 innate lymphoid cell property_value: terms:contributor https://orcid.org/0000-0001-9990-8331 property_value: terms:date "2017-01-30T20:54:12Z" xsd:dateTime @@ -14209,6 +15868,8 @@ name: group 2 innate lymphoid cell def: "An innate lymphoid cell that is capable of producing T-helper 2-cell associated cytokines upon stimulation." [GOC:add, GOC:dsd, PMID:23292121, PMID:23562755] subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "ILC2" EXACT [] synonym: "natural helper cell" EXACT [] synonym: "nuocyte" EXACT [] @@ -14225,6 +15886,8 @@ id: CL:0001070 name: beige adipocyte def: "An adipocyte that is beige in color, thermogenic, and which differentiates in white fat tissue from a Myf5-negative progenitor." [GOC:add, GOC:cvs, GOC:ymb, PMID:22796012, PMID:25851693] subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "beige brown adipocyte" EXACT [] synonym: "beige fat cell" EXACT [] synonym: "beige/brite adipocyte" EXACT [] @@ -14242,9 +15905,10 @@ name: group 3 innate lymphoid cell def: "An innate lymphoid cell that constituitively expresses RORgt and is capable of expressing IL17A and/or IL-22." [GOC:add, GOC:dsd, PMID:23292121, PMID:23348417] subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "ILC3" EXACT [] is_a: CL:0001065 ! innate lymphoid cell -is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0001065 ! innate lymphoid cell intersection_of: has_part PR:000003455 ! nuclear receptor ROR-gamma isoform 2 relationship: has_part PR:000003455 ! nuclear receptor ROR-gamma isoform 2 @@ -14256,11 +15920,11 @@ property_value: terms:date "2017-01-31T20:21:26Z" xsd:dateTime id: CL:0001072 name: CD34-negative, CD117-positive innate lymphoid cell, human def: "An innate lymphoid cell in the human with the phenotype CD34-negative, CD117-positive, and a precusor to NK cells, ILC2 cells, and ILC3 cells." [GOC:add, PMID:30193847, PMID:31201208] +subset: human_subset synonym: "CD34-negative, CD117-positive ILC" EXACT [] synonym: "CD34-negative, CD117-positive ILCP" EXACT [] synonym: "CD34-negative, CD117-positive innate lymphoid cell precusor" EXACT [] is_a: CL:0001082 ! immature innate lymphoid cell -is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0001065 ! innate lymphoid cell intersection_of: bearer_of PATO:0001501 ! immature intersection_of: CL:4030046 PR:P28906 ! lacks_plasma_membrane_part hematopoietic progenitor cell antigen CD34 (human) @@ -14275,6 +15939,7 @@ relationship: RO:0002202 CL:0001074 ! develops from CD34-positive, CD56-positive id: CL:0001073 name: CD34-negative, CD56-positive, CD117-positive innate lymphoid cell, human def: "An innate lymphoid cell in the human with the phenotype CD34-negative, CD56-positive, CD117-positive.Thie cell type may include precusors to NK cells and ILC3 cells." [GOC:add, PMID:30193847, PMID:31201208] +subset: human_subset synonym: "CD34-negative, CD56-positive, CD117-positive ILC" EXACT [] synonym: "CD34-negative, CD56-positive, CD117-positive ILCP" EXACT [] synonym: "CD34-negative, CD56-positive, CD117-positive innate lymphoid cell precursor" EXACT [] @@ -14290,9 +15955,9 @@ id: CL:0001074 name: CD34-positive, CD56-positive, CD117-positive common innate lymphoid precursor, human def: "An innate lymphoid cell precursor in the human with the phenotype CD34-positive, CD56-positive, CD117-positive.Thie cell type may include precusors to NK cells and ILC3 cells." [GOC:add, PMID:30193847] subset: cellxgene_subset +subset: human_subset synonym: "CD34-positive, CD56-positive, CD117-positive CILP" EXACT [] is_a: CL:0001082 ! immature innate lymphoid cell -is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0001065 ! innate lymphoid cell intersection_of: bearer_of PATO:0001501 ! immature intersection_of: RO:0002104 PR:P10721 ! has plasma membrane part mast/stem cell growth factor receptor Kit (human) @@ -14308,6 +15973,7 @@ relationship: RO:0002162 NCBITaxon:9606 ! in taxon Homo sapiens id: CL:0001075 name: KLRG1-positive innate lymphoid cell, human def: "An innate lymphoid cell in the human with the phenotype KLRG1-positive that is a precusor for ILC2 cells." [GOC:add, PMID:31201208] +subset: human_subset synonym: "KLRG1-positive ILC" EXACT [] is_a: CL:0001072 ! CD34-negative, CD117-positive innate lymphoid cell, human intersection_of: CL:0001072 ! CD34-negative, CD117-positive innate lymphoid cell, human @@ -14320,6 +15986,7 @@ id: CL:0001076 name: NKp46-positive innate lymphoid cell, human def: "An innate lymphoid cell in the human with the phenotype NKp46-positive that is a precusor for NK cells and ILC3 cells." [GOC:add, PMID:31201208, PMID:31337734] subset: cellxgene_subset +subset: human_subset synonym: "NKp46-positive ILC" EXACT [] is_a: CL:0001074 ! CD34-positive, CD56-positive, CD117-positive common innate lymphoid precursor, human intersection_of: CL:0001074 ! CD34-positive, CD56-positive, CD117-positive common innate lymphoid precursor, human @@ -14332,9 +15999,9 @@ id: CL:0001077 name: ILC1, human def: "An ILC1 cell in the human with the phenotype CD56-negative, IL-7Ralpha-positive, T-bet-positive." [GOC:add, PMID:31500958] subset: cellxgene_subset +subset: human_subset synonym: "innate lymphoid cell 1, human" EXACT [] is_a: CL:0001068 ! ILC1 -is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0001068 ! ILC1 intersection_of: has_part PR:Q9UL17 ! T-box transcription factor TBX21 (human) intersection_of: RO:0002104 PR:P16871 ! has plasma membrane part interleukin-7 receptor subunit alpha (human) @@ -14349,6 +16016,7 @@ name: group 3 innate lymphoid cell, human def: "A group 3 innate lymphoid cell in the human with the phenotype IL-7Ralpha-positive." [GOC:add, PMID:31500958] subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset synonym: "ILC3, human" EXACT [] is_a: CL:0001071 ! group 3 innate lymphoid cell intersection_of: CL:0001071 ! group 3 innate lymphoid cell @@ -14363,6 +16031,7 @@ id: CL:0001079 name: NKp44-positive group 3 innate lymphoid cell, human def: "A group 3 innate lymphoid cell in the human with the phenotype IL-7Ralpha-positive, and NKp44-positive." [GOC:add, PMID:24778151, PMID:31500958] subset: cellxgene_subset +subset: human_subset is_a: CL:0001078 ! group 3 innate lymphoid cell, human intersection_of: CL:0001071 ! group 3 innate lymphoid cell intersection_of: RO:0002104 PR:O95944 ! has plasma membrane part natural cytotoxicity triggering receptor 2 (human) @@ -14375,6 +16044,7 @@ id: CL:0001080 name: NKp44-negative group 3 innate lymphoid cell, human def: "A group 3 innate lymphoid cell in the human with the phenotype IL-7Ralpha-positive, and NKp44-negative." [GOC:add, PMID:24778151, PMID:31500958] subset: cellxgene_subset +subset: human_subset is_a: CL:0001078 ! group 3 innate lymphoid cell, human intersection_of: CL:0001071 ! group 3 innate lymphoid cell intersection_of: CL:4030046 PR:O95944 ! lacks_plasma_membrane_part natural cytotoxicity triggering receptor 2 (human) @@ -14387,9 +16057,9 @@ id: CL:0001081 name: group 2 innate lymphoid cell, human def: "A group 2 innate lymphoid cell in the human with the phenotype CD25-positive, CD127-positive, CD161-positive, and GATA-3-positive." [GOC:add, PMID:24778151, PMID:26844414] subset: cellxgene_subset +subset: human_subset synonym: "ILC2, human" EXACT [] is_a: CL:0001069 ! group 2 innate lymphoid cell -is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0001069 ! group 2 innate lymphoid cell intersection_of: has_part PR:P23771 ! trans-acting T-cell-specific transcription factor GATA-3 (human) intersection_of: RO:0002104 PR:P01589 ! has plasma membrane part interleukin-2 receptor subunit alpha (human) @@ -14409,6 +16079,8 @@ id: CL:0001082 name: immature innate lymphoid cell def: "An innate lyphoid cell with an immature phenotype." [GOC:add] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "immature ILC" EXACT [] is_a: CL:0001065 ! innate lymphoid cell intersection_of: CL:0001065 ! innate lymphoid cell @@ -14421,6 +16093,7 @@ name: effector memory CD4-positive, alpha-beta T cell, terminally differentiated def: "A CD4-positive, alpha beta memory T cell with the phenotype CD45RA-positive, CD45RO-negative, and CCR7-negative." [GOC:add, PMID:17465678, PMID:26883338, PMID:27997758, PMID:29133794] comment: This cell type is seen in human but not found in the mouse. subset: human_reference_atlas +subset: human_subset synonym: "CD4+ TEMRA" EXACT [PMID:17465678] synonym: "CD4-positive TEMRA" EXACT [PMID:17465678] synonym: "TEMRA" BROAD [PMID:17465678] @@ -14446,8 +16119,9 @@ id: CL:0001200 name: lymphocyte of B lineage, CD19-positive def: "A lymphocyte of B lineage that is CD19-positive." [GOC:add] comment: Types of B lineage lymphocytes include B cells and antibody secreting cells (plasmablasts and plasma cells). Lymphocytes of B cell lineage can be distinguished from those of T cell lineage by their lack of CD3e (as part of the T cell receptor complex). +subset: human_subset +subset: mouse_subset is_a: CL:0000945 ! lymphocyte of B lineage -is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000945 ! lymphocyte of B lineage intersection_of: CL:4030046 PR:000001020 ! lacks_plasma_membrane_part CD3 epsilon intersection_of: RO:0002104 PR:000001002 ! has plasma membrane part CD19 molecule @@ -14461,6 +16135,8 @@ property_value: terms:contributor https://orcid.org/0000-0001-9990-8331 id: CL:0001201 name: B cell, CD19-positive def: "A B cell that is CD19-positive." [GOC:add] +subset: human_subset +subset: mouse_subset synonym: "B lymphocyte, CD19-positive" EXACT [] synonym: "B-cell, CD19-positive" EXACT [] synonym: "B-lymphocyte, CD19-positive" EXACT [] @@ -14477,6 +16153,8 @@ property_value: terms:contributor https://orcid.org/0000-0001-9990-8331 id: CL:0001202 name: CD86-positive plasmablast def: "A plasmablast that is CD86-positive." [GOC:add, PMID:20398308] +subset: human_subset +subset: mouse_subset synonym: "CD86+ plasmablast" EXACT [] synonym: "CD86-positive, CD20-negative plasmablast" BROAD [] is_a: CL:0000980 ! plasmablast @@ -14491,6 +16169,7 @@ name: CD8-positive, alpha-beta memory T cell, CD45RO-positive def: "A CD8-positive, alpha-beta T cell with memory phenotype indicated by being CD45RO and CD127-positive. This cell type is also described as being CD25-negative, CD44-high, and CD122-high." [GO_REF:0000031, GOC:tfm, PMID:20146720] subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset synonym: "CD8-positive, alpha-beta memory T lymphocyte, CD45RO-positive" EXACT [] synonym: "CD8-positive, alpha-beta memory T-cell, CD45RO-positive" EXACT [] synonym: "CD8-positive, alpha-beta memory T-lymphocyte, CD45RO-positive" EXACT [] @@ -14516,6 +16195,7 @@ property_value: RO:0002175 NCBITaxon:9606 id: CL:0001204 name: CD4-positive, alpha-beta memory T cell, CD45RO-positive def: "CD4-positive, alpha-beta long-lived T cell with the phenotype CD45RO-positive and CD127-positive. This cell type is also described as being CD25-negative, CD44-high, and CD122-high." [GO_REF:0000031, GOC:add, GOC:tfm, http://www.immgen.org/index_content.html, ISBN:0781735149] +subset: human_subset synonym: "CD4-positive, alpha-beta memory T lymphocyte, CD45RO-positive" EXACT [] synonym: "CD4-positive, alpha-beta memory T-cell, CD45RO-positive" EXACT [] synonym: "CD4-positive, alpha-beta memory T-lymphocyte, CD45RO-positive" EXACT [] @@ -14548,6 +16228,8 @@ id: CL:0002000 name: Kit-positive erythroid progenitor cell def: "An erythroid progenitor cell is Kit-positive, Ly6A-negative, CD41-negative, CD127-negative, and CD123-negative. This cell type is also described as being lin-negative, Kit-positive, CD150-negative, CD41-negative, CD105-positive, and FcgR-negative." [GOC:ak, GOC:tfm, http://www.immgen.org/index_content.html, PMID:19805084] comment: Markers found on mouse cells. +subset: human_subset +subset: mouse_subset synonym: "c- Kit-positive erythroid progenitor cell" EXACT [] is_a: CL:0001066 {is_inferred="true"} ! erythroid progenitor cell, mammalian intersection_of: CL:0001066 ! erythroid progenitor cell, mammalian @@ -14576,6 +16258,8 @@ id: CL:0002001 name: CD34-positive, CD38-positive granulocyte monocyte progenitor def: "A granulocyte monocyte progenitor is CD34-positive, CD38-positive, IL-3receptor-alpha-positive and is CD45RA-negative." [GOC:tfm, PMID:12615892, PMID:19022770] comment: Markers are for human cells. According to different research groups, CD45RA is present or absent on this cell population. +subset: human_subset +subset: mouse_subset is_a: CL:0000557 {is_inferred="true"} ! granulocyte monocyte progenitor cell intersection_of: CL:0000557 ! granulocyte monocyte progenitor cell intersection_of: RO:0002104 PR:000001003 ! has plasma membrane part CD34 molecule @@ -14592,6 +16276,8 @@ id: CL:0002002 name: Kit-positive granulocyte monocyte progenitor def: "A granulocyte monocyte progenitor that is Kit-positive, CD34-positive, Fc-gamma receptor II/II-positive, and is Sca-1-negative, Il7ra-negative, Cxc3r1-negative, and CD90-negative." [GOC:tfm, http://www.immgen.org/index_content.html, PMID:12615892, PMID:16322423, PMID:19022770, PMID:19273628] comment: Markers are found on mouse cells. +subset: human_subset +subset: mouse_subset is_a: CL:0000557 {is_inferred="true"} ! granulocyte monocyte progenitor cell intersection_of: CL:0000557 ! granulocyte monocyte progenitor cell intersection_of: CL:4030046 PR:000001206 ! lacks_plasma_membrane_part CX3C chemokine receptor 1 @@ -14619,6 +16305,8 @@ id: CL:0002003 name: CD34-positive, GlyA-negative erythroid progenitor cell def: "An erythroid progenitor cell that is CD34-positive and is GlyA-negative." [GOC:ak, GOC:tfm, PMID:19621348] comment: Cell markers associated with human cells. +subset: human_subset +subset: mouse_subset xref: FMA:83517 is_a: CL:0001066 {is_inferred="true"} ! erythroid progenitor cell, mammalian intersection_of: CL:0001066 ! erythroid progenitor cell, mammalian @@ -14635,6 +16323,8 @@ id: CL:0002004 name: CD34-negative, GlyA-negative proerythroblast def: "A proerythoblast that is CD34-negative and GlyA-negative." [GOC:ak, GOC:tfm, PMID:19621348] comment: Cell surface markers are associated with human cells. +subset: human_subset +subset: mouse_subset is_a: CL:0000547 {is_inferred="true"} ! proerythroblast intersection_of: CL:0000547 ! proerythroblast intersection_of: CL:4030046 PR:000001003 ! lacks_plasma_membrane_part CD34 molecule @@ -14650,8 +16340,9 @@ id: CL:0002005 name: CD34-positive, CD38-positive megakaryocyte erythroid progenitor cell def: "A megakaryocyte erythroid progenitor cell is CD34-positive, CD38-positive and is IL3-receptor alpha-negative and CD45RA-negative." [GOC:tfm, PMID:12615892, PMID:190227700] comment: Markers are associated with human cell type. +subset: human_subset +subset: mouse_subset is_a: CL:0000050 {is_inferred="true"} ! megakaryocyte-erythroid progenitor cell -is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000050 ! megakaryocyte-erythroid progenitor cell intersection_of: CL:4030046 PR:000001015 ! lacks_plasma_membrane_part receptor-type tyrosine-protein phosphatase C isoform CD45RA intersection_of: CL:4030046 PR:000001865 ! lacks_plasma_membrane_part interleukin-3 receptor class 2 alpha chain @@ -14669,8 +16360,9 @@ id: CL:0002006 name: Kit-positive, CD34-negative megakaryocyte erythroid progenitor cell def: "A megakaryocyte erythroid progenitor cell that is Kit-positive and is Sca1-negative, CD34-negative, CD90-negative, IL7r-alpha-negative and Fcgr II/III-low." [GOC:tfm, http://www.immgen.org/index_content.html, PMID:12615892, PMID:19022770] comment: Markers are associated with mouse cells. +subset: human_subset +subset: mouse_subset is_a: CL:0000050 {is_inferred="true"} ! megakaryocyte-erythroid progenitor cell -is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000050 ! megakaryocyte-erythroid progenitor cell intersection_of: CL:4030046 PR:000001003 ! lacks_plasma_membrane_part CD34 molecule intersection_of: CL:4030046 PR:000001479 ! lacks_plasma_membrane_part low affinity immunoglobulin gamma Fc region receptor II @@ -14694,6 +16386,8 @@ id: CL:0002007 name: Kit-low, CD34-positive eosinophil progenitor cell def: "A lineage marker-negative, CD34-positive, IL5r-alpha-positive, and Sca1-negative eosinophil progenitor cell." [GOC:tfm, PMID:17582345] comment: Markers are found on mouse cells. +subset: human_subset +subset: mouse_subset is_a: CL:0000611 {is_inferred="true"} ! eosinophil progenitor cell intersection_of: CL:0000611 ! eosinophil progenitor cell intersection_of: CL:4030046 PR:000002979 ! lacks_plasma_membrane_part lymphocyte antigen 6A-2/6E-1 @@ -14711,6 +16405,8 @@ id: CL:0002008 name: CD34-positive, CD38-positive eosinophil progenitor cell def: "A lineage marker-negative, CD34-positive, CD38-positive, IL3r-alpha-positive, IL5r-alpha-positive, and CD45RA-negative eosinophil progenitor cell." [GOC:tfm, PMCID:PMC2626675] comment: Markers are associated with human cells. +subset: human_subset +subset: mouse_subset is_a: CL:0000611 {is_inferred="true"} ! eosinophil progenitor cell intersection_of: CL:0000611 ! eosinophil progenitor cell intersection_of: RO:0002104 PR:000001015 ! has plasma membrane part receptor-type tyrosine-protein phosphatase C isoform CD45RA @@ -14726,6 +16422,8 @@ id: CL:0002009 name: macrophage dendritic cell progenitor def: "A progenitor cell that can give rise to plasmacytoid and myeloid dendritic cells, and to monocytes and macrophages." [GOC:tfm, PMID:19273628] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "MDP" EXACT [] is_a: CL:0000763 ! myeloid cell is_a: CL:0002032 {is_inferred="true"} ! hematopoietic oligopotent progenitor cell @@ -14744,9 +16442,10 @@ id: CL:0002010 name: pre-conventional dendritic cell def: "A lin-negative, MHC-II-negative, CD11c-positive, FLT3-positive cell with intermediate expression of SIRP-alpha." [GOC:tfm] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset is_a: CL:0000763 ! myeloid cell is_a: CL:0002031 {is_inferred="true"} ! hematopoietic lineage restricted progenitor cell -is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0002031 ! hematopoietic lineage restricted progenitor cell intersection_of: CL:4030046 GO:0042613 ! lacks_plasma_membrane_part MHC class II protein complex intersection_of: CL:4030046 PR:000001002 ! lacks_plasma_membrane_part CD19 molecule @@ -14788,9 +16487,10 @@ id: CL:0002011 name: Kit-positive macrophage dendritic cell progenitor def: "A progenitor cell that can give rise to plasmacytoid and myeloid dendritic cells, and to monocytes and macrophages. Marker for this cell is Kit-high, CD115-positive, CD135-positive, Cx3cr1-positive, and is Il7ra-negative." [GOC:tfm, PMID:19273628] comment: Markers are associated with mouse cells. +subset: human_subset +subset: mouse_subset synonym: "murine MDP" EXACT [] is_a: CL:0002009 {is_inferred="true"} ! macrophage dendritic cell progenitor -is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0002009 ! macrophage dendritic cell progenitor intersection_of: RO:0002104 PR:000001206 ! has plasma membrane part CX3C chemokine receptor 1 intersection_of: RO:0002104 PR:000002001 ! has plasma membrane part receptor-type tyrosine-protein kinase FLT3 @@ -14809,6 +16509,7 @@ id: CL:0002012 name: Kit-low proerythroblast def: "A proerythoblast that is Kit-low, Lyg76-positive, and CD71-positive." [GOC:ak, GOC:tfm, PMID:19805084] comment: Markers are associated with mouse cells. +subset: mouse_subset is_a: CL:0000547 {is_inferred="true"} ! proerythroblast intersection_of: CL:0000547 ! proerythroblast intersection_of: CL:4030046 PR:000001869 ! lacks_plasma_membrane_part interleukin-7 receptor subunit alpha @@ -14830,6 +16531,8 @@ id: CL:0002013 name: GlyA-positive basophilic erythroblast def: "A basophilic erythroblast that is GlyA-positive." [GOC:ak, GOC:tfm, PMID:1638021] comment: Markers are associated with human cells. +subset: human_subset +subset: mouse_subset is_a: CL:0000549 {is_inferred="true"} ! basophilic erythroblast intersection_of: CL:0000549 ! basophilic erythroblast intersection_of: CL:4030046 PR:000001003 ! lacks_plasma_membrane_part CD34 molecule @@ -14845,6 +16548,7 @@ id: CL:0002014 name: Kit-negative, Ly-76 high basophilic erythroblast def: "A basophilic erythroblast that is Lyg 76-high and is Kit-negative." [GOC:ak, GOC:tfm, PMID:19805084] comment: Cell surface markers are associated with mouse cells. +subset: mouse_subset is_a: CL:0000549 {is_inferred="true"} ! basophilic erythroblast intersection_of: CL:0000549 ! basophilic erythroblast intersection_of: CL:4030046 PR:000001869 ! lacks_plasma_membrane_part interleukin-7 receptor subunit alpha @@ -14863,6 +16567,7 @@ creation_date: 2010-04-26T10:41:22Z id: CL:0002015 name: Kit-negative, Ly-76 high polychromatophilic erythroblast def: "A polychromatophilic erythroblast that is Lyg 76-high and is Kit-negative." [GOC:ak, GOC:tfm, PMID:19805084] +subset: mouse_subset synonym: "late basophilic and polychromatophilic erythroblast" BROAD [] is_a: CL:0000550 {is_inferred="true"} ! polychromatophilic erythroblast intersection_of: CL:0000550 ! polychromatophilic erythroblast @@ -14883,6 +16588,8 @@ id: CL:0002016 name: CD71-low, GlyA-positive polychromatic erythroblast def: "A polychromatiic erythroblast that is Gly-A-positive and CD71-low." [GOC:ak, GOC:tfm, PMID:1638021] comment: Cell surface markers are associated with human cells. +subset: human_subset +subset: mouse_subset is_a: CL:0000550 {is_inferred="true"} ! polychromatophilic erythroblast intersection_of: CL:0000550 ! polychromatophilic erythroblast intersection_of: RO:0002104 PR:000001460 ! has plasma membrane part glycophorin-A @@ -14898,8 +16605,8 @@ id: CL:0002017 name: Kit-negative, Ly-76 high orthochromatophilic erythroblasts def: "An orthochromatophilic erythroblast that is ter119-high, CD71-low, and Kit-negative." [GOC:ak, GOC:tfm, PMID:19805084] comment: Cell surface markers associated with mouse cells. +subset: mouse_subset is_a: CL:0000552 {is_inferred="true"} ! orthochromatic erythroblast -is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000552 ! orthochromatic erythroblast intersection_of: CL:4030046 PR:000001869 ! lacks_plasma_membrane_part interleukin-7 receptor subunit alpha intersection_of: CL:4030046 PR:000002065 ! lacks_plasma_membrane_part mast/stem cell growth factor receptor @@ -14920,8 +16627,9 @@ id: CL:0002018 name: CD71-negative, GlyA-positive orthochromatic erythroblast def: "An erythroblast that is GlyA-positive and CD71-negative." [GOC:ak, GOC:tfm, PMID:1638021] comment: Markers associated with human cells. +subset: human_subset +subset: mouse_subset is_a: CL:0000552 {is_inferred="true"} ! orthochromatic erythroblast -is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000552 ! orthochromatic erythroblast intersection_of: CL:4030046 PR:000001945 ! lacks_plasma_membrane_part transferrin receptor protein 1 intersection_of: RO:0002104 PR:000001460 ! has plasma membrane part glycophorin-A @@ -14936,6 +16644,7 @@ id: CL:0002019 name: Ly-76 high reticulocyte def: "A reticulocyte that is Ly76-high and is Kit-negative." [GOC:ak, GOC:tfm, PMID:18539294] comment: Marker associated with mouse cells. +subset: mouse_subset is_a: CL:0002422 {is_inferred="true"} ! enucleated reticulocyte intersection_of: CL:0002422 ! enucleated reticulocyte intersection_of: RO:0015015 PR:000002981 ! has high plasma membrane amount lymphocyte antigen 76 (mouse) @@ -14949,6 +16658,8 @@ id: CL:0002020 name: GlyA-positive reticulocytes def: "A reticulocyte that is GlyA-positive." [GOC:ak, GOC:tfm, PMID:1638021] comment: Markers is associated with human cells. +subset: human_subset +subset: mouse_subset is_a: CL:0002422 {is_inferred="true"} ! enucleated reticulocyte intersection_of: CL:0002422 ! enucleated reticulocyte intersection_of: RO:0002104 PR:000001460 ! has plasma membrane part glycophorin-A @@ -14962,8 +16673,9 @@ id: CL:0002021 name: GlyA-positive erythrocyte def: "An enucleate erythrocyte that is GlyA-positive." [GOC:ak, GOC:tfm, PMID:20134094] comment: Marker is associated with human cell types. +subset: human_subset +subset: mouse_subset is_a: CL:0000595 {is_inferred="true"} ! enucleate erythrocyte -is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000595 ! enucleate erythrocyte intersection_of: RO:0002104 PR:000001460 ! has plasma membrane part glycophorin-A relationship: RO:0002104 PR:000001460 ! has plasma membrane part glycophorin-A @@ -14976,8 +16688,8 @@ id: CL:0002022 name: Ly-76 high positive erythrocyte def: "An enucleate erythrocyte that is Lyg-76-high." [GOC:ak, GOC:tfm, PMID:19805084] comment: Marker is associated with mouse cell types. +subset: mouse_subset is_a: CL:0000595 {is_inferred="true"} ! enucleate erythrocyte -is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000595 ! enucleate erythrocyte intersection_of: RO:0015015 PR:000002981 ! has high plasma membrane amount lymphocyte antigen 76 (mouse) relationship: RO:0002202 CL:0002019 ! develops from Ly-76 high reticulocyte @@ -14990,8 +16702,9 @@ id: CL:0002023 name: CD34-positive, CD41-positive, CD42-positive megakaryocyte progenitor cell def: "A megakaroycotye progenitor cell that is CD34-positive, CD41-positive and CD42-positive on the cell surface." [GOC:ak, GOC:tfm, PMID:15232614] comment: Markers are associated with human cell type. +subset: human_subset +subset: mouse_subset is_a: CL:0000553 {is_inferred="true"} ! megakaryocyte progenitor cell -is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000553 ! megakaryocyte progenitor cell intersection_of: RO:0002104 PR:000001003 ! has plasma membrane part CD34 molecule intersection_of: RO:0002104 PR:000001907 ! has plasma membrane part platelet glycoprotein Ib alpha chain @@ -15008,8 +16721,9 @@ id: CL:0002024 name: Kit-positive megakaryocyte progenitor cell def: "A megakaryocyte progenitor cell that is Kit-positive, CD41-positive, CD9-positive, Sca-1-negative, IL7ralpha-negative, CD150-negative, and Fcgamma receptor II/III-low." [GOC:ak, GOC:tfm, PMID:16951553] comment: Markers are associated with mouse cells. +subset: human_subset +subset: mouse_subset is_a: CL:0000553 {is_inferred="true"} ! megakaryocyte progenitor cell -is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000553 ! megakaryocyte progenitor cell intersection_of: CL:4030046 PR:000001833 ! lacks_plasma_membrane_part SLAM family member 1 intersection_of: CL:4030046 PR:000001869 ! lacks_plasma_membrane_part interleukin-7 receptor subunit alpha @@ -15034,8 +16748,9 @@ id: CL:0002025 name: CD34-positive, CD41-positive, CD42-negative megakaryocyte progenitor cell def: "A megakaryocyte progenitor cell that is CD34-positive, CD41-positive, and CD42-negative." [GOC:ak, GOC:tfm, PMID:15232614] comment: Markers are commonly associated with human cells. +subset: human_subset +subset: mouse_subset is_a: CL:0000553 {is_inferred="true"} ! megakaryocyte progenitor cell -is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000553 ! megakaryocyte progenitor cell intersection_of: CL:4030046 PR:000001907 ! lacks_plasma_membrane_part platelet glycoprotein Ib alpha chain intersection_of: RO:0002104 PR:000001003 ! has plasma membrane part CD34 molecule @@ -15052,8 +16767,9 @@ id: CL:0002026 name: CD34-negative, CD41-positive, CD42-positive megakaryocyte cell def: "A megakaryocyte progenitor cell that is CD34-negative, CD41-positive and CD42-positive." [GOC:ak, GOC:tfm, PMID:15232614] comment: Markers are commonly associated with human cells. +subset: human_subset +subset: mouse_subset is_a: CL:0000556 {is_inferred="true"} ! megakaryocyte -is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000556 ! megakaryocyte intersection_of: CL:4030046 PR:000001003 ! lacks_plasma_membrane_part CD34 molecule intersection_of: RO:0002104 PR:000001907 ! has plasma membrane part platelet glycoprotein Ib alpha chain @@ -15070,8 +16786,9 @@ id: CL:0002027 name: CD9-positive, CD41-positive megakaryocyte cell def: "A megakaryocyte cell with is CD9-positive and CD41-positive." [GOC:tfm] comment: Markers are commonly associated with mouse cells. +subset: human_subset +subset: mouse_subset is_a: CL:0000556 {is_inferred="true"} ! megakaryocyte -is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000556 ! megakaryocyte intersection_of: RO:0002104 PR:000005178 ! has plasma membrane part CD9 molecule intersection_of: RO:0002104 PR:000009127 ! has plasma membrane part integrin alpha-IIb @@ -15087,10 +16804,11 @@ name: basophil mast progenitor cell def: "A cell type that can give rise to basophil and mast cells. This cell is CD34-positive, CD117-positive, CD125-positive, FceRIa-negative, and T1/ST2-negative, and expresses Gata-1, Gata-2, C/EBPa" [GOC:ak, GOC:dsd, GOC:tfm, PMCID:PMC1312421] comment: There may be an intermediate cell type. These cells also CD13-positive, CD16-positive, CD32-positive, and integrin beta 7-positive. Transcription factors: GATA1-positive, MCP-1-positive, mitf-positive, PU.1-positive, and CEBP/a-low. subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "BMCP" EXACT [] is_a: CL:0000763 ! myeloid cell is_a: CL:0002191 ! granulocytopoietic cell -is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000839 ! myeloid lineage restricted progenitor cell intersection_of: capable_of GO:0030221 ! basophil differentiation intersection_of: capable_of GO:0060374 ! mast cell differentiation @@ -15116,6 +16834,8 @@ creation_date: 2010-04-27T12:46:33Z id: CL:0002029 name: Fc-epsilon RIalpha-low mast cell progenitor def: "A lineage-negative, Kit-positive, CD45-positive mast cell progenitor that is Fc-epsilon RIalpha-low." [GOC:tfm, PMCID:PMC1312421] +subset: human_subset +subset: mouse_subset is_a: CL:0000831 {is_inferred="true"} ! mast cell progenitor intersection_of: CL:0000831 ! mast cell progenitor intersection_of: CL:4030046 PR:000002979 ! lacks_plasma_membrane_part lymphocyte antigen 6A-2/6E-1 @@ -15135,6 +16855,8 @@ id: CL:0002030 name: Fc-epsilon RIalpha-high basophil progenitor cell def: "A lineage negative, Sca1-negative basophil progenitor cell that is Fc epsilon RIalpha-high." [GOC:tfm, PMCID:PMC1312421] comment: Markers are associated with mouse cells. +subset: human_subset +subset: mouse_subset is_a: CL:0000613 {is_inferred="true"} ! basophil progenitor cell intersection_of: CL:0000613 ! basophil progenitor cell intersection_of: CL:4030046 PR:000002065 ! lacks_plasma_membrane_part mast/stem cell growth factor receptor @@ -15152,6 +16874,8 @@ id: CL:0002031 name: hematopoietic lineage restricted progenitor cell def: "A hematopoietic progenitor cell that is capable of developing into only one lineage of hematopoietic cells." [GOC:tfm, PMID:19022770] subset: blood_and_immune_upper_slim +subset: human_subset +subset: mouse_subset is_a: BFO:0000002 is_a: CL:0000255 ! eukaryotic cell is_a: CL:0008001 ! hematopoietic precursor cell @@ -15169,6 +16893,8 @@ name: hematopoietic oligopotent progenitor cell def: "A hematopoietic oligopotent progenitor cell that has the ability to differentiate into limited cell types but lacks lineage cell markers and self renewal capabilities." [GOC:tfm, https://orcid.org/0000-0001-5208-3432, PMID:19022770] comment: This cell type is intended to be compatible with any vertebrate hematopoietic oligopotent progenitor cell. For mammalian hematopoietic oligopotent progenitor cells known to be lineage-negative, please use the term 'hematopoietic oligopotent progenitor cell' (CL_0001060). subset: blood_and_immune_upper_slim +subset: human_subset +subset: mouse_subset is_a: BFO:0000002 is_a: CL:0000255 ! eukaryotic cell is_a: CL:0008001 ! hematopoietic precursor cell @@ -15184,6 +16910,8 @@ id: CL:0002033 name: short term hematopoietic stem cell def: "A hematopoietic stem cell capable of rapid replenishment of myeloerythroid progenitors and limited self renewal capability. This cell is Kit-positive, Sca1-positive, CD34-positive, CD150-positive, and is Flt3-negative." [GOC:tfm, PMID:15572596, PMID:19022770] comment: Markers are associated with mouse cells. These cells are also reportedly CD11b-low and CD90-low. +subset: human_subset +subset: mouse_subset synonym: "ST stem cell" EXACT [] synonym: "ST-HSC" EXACT [] is_a: CL:0001008 {is_inferred="true"} ! Kit and Sca1-positive hematopoietic stem cell @@ -15202,6 +16930,8 @@ id: CL:0002034 name: long term hematopoietic stem cell def: "A hematopoietic stem cell with long term self renewal capability. This cell is Kit-positive, Sca1-positive, CD150-positive, CD90-low, CD34-negative and Flt3-negative." [GOC:tfm, PMID:15572596, PMID:17582345] comment: Markers are associated with mouse cells. +subset: human_subset +subset: mouse_subset synonym: "LT stem cell" EXACT [] synonym: "LT-HSC" EXACT [] is_a: CL:0001008 {is_inferred="true"} ! Kit and Sca1-positive hematopoietic stem cell @@ -15221,6 +16951,8 @@ id: CL:0002035 name: Slamf1-negative multipotent progenitor cell def: "A hematopoietic progenitor that has restricted self-renewal capability. Cell is Kit-positive, Ly6-positive, CD150-negative and Flt3-negative." [GOC:tfm, PMID:19022770] comment: Markers are associated with mouse cells. +subset: human_subset +subset: mouse_subset is_a: CL:0000837 {is_inferred="true"} ! hematopoietic multipotent progenitor cell intersection_of: CL:0000837 ! hematopoietic multipotent progenitor cell intersection_of: CL:4030046 PR:000001833 ! lacks_plasma_membrane_part SLAM family member 1 @@ -15240,6 +16972,8 @@ id: CL:0002036 name: Slamf1-positive multipotent progenitor cell def: "A hematopoietic progenitor that has some limited self-renewal capability. Cells are lin-negative, Kit-positive, CD34-positive, and Slamf1-positive." [GOC:tfm, PMID:19022770] comment: Markers are associated with mouse cells. +subset: human_subset +subset: mouse_subset synonym: "KSL cell" EXACT [] is_a: CL:0000837 {is_inferred="true"} ! hematopoietic multipotent progenitor cell intersection_of: CL:0000837 ! hematopoietic multipotent progenitor cell @@ -15258,6 +16992,8 @@ creation_date: 2010-01-08T11:16:35Z id: CL:0002037 name: CD2-positive, CD5-positive, CD44-positive alpha-beta intraepithelial T cell def: "Intraepithelial T cells with a memory phenotype of CD2-positive, CD5-positive, and CD44-positive." [GOC:tfm, PMID:16048545] +subset: human_subset +subset: mouse_subset synonym: "memory alpha beta IEL" EXACT [PMID:16048545] is_a: CL:0000793 {is_inferred="true"} ! CD4-positive, alpha-beta intraepithelial T cell intersection_of: CL:0000793 ! CD4-positive, alpha-beta intraepithelial T cell @@ -15276,6 +17012,8 @@ name: T follicular helper cell def: "A CD4-positive, CXCR5-positive, CCR7-negative alpha-beta T cell located in follicles of secondary lymph nodes that is BCL6-high, ICOS-high and PD1-high, and stimulates follicular B cells to undergo class-switching and antibody production." [GOC:tfm, PMID:19855402, PMID:20107805, PMID:22043829] subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "follicular B helper T cell" RELATED [PMID:22043829] synonym: "follicular helper T cell" RELATED [PMID:22649468] synonym: "follicular helper T-cell" RELATED [PMID:22508770] @@ -15308,6 +17046,8 @@ creation_date: 2009-10-29T04:01:27Z id: CL:0002039 name: immature NK T cell stage I def: "A CD24-high, CD4-low, CD8-low, CD44-negative, NK1.1-negative NK T cell." [GOC:tfm, PMID:17589542] +subset: human_subset +subset: mouse_subset is_a: CL:0000914 {is_inferred="true"} ! immature NK T cell intersection_of: CL:0000914 ! immature NK T cell intersection_of: CL:4030046 PR:000001307 ! lacks_plasma_membrane_part CD44 molecule @@ -15328,6 +17068,8 @@ id: CL:0002040 name: immature NK T cell stage II def: "A CD24-low, CD44-negative, NK1.1-negative NK T cell." [GOC:tfm, http://www.immgen.org/index_content.html, PMID:17589542] comment: NKT.44-NK1.1-.Th was assigned as an exact synonym based on sorting strategy displayed at immgene.org. +subset: human_subset +subset: mouse_subset synonym: "NKT.44-NK1.1-.Th" EXACT [] is_a: CL:0000914 {is_inferred="true"} ! immature NK T cell intersection_of: CL:0000914 ! immature NK T cell @@ -15345,6 +17087,8 @@ creation_date: 2009-10-29T04:13:43Z id: CL:0002041 name: immature NK T cell stage III def: "A CD24-low, CD44-positive, DX5-low, NK1.1-negative NK T cell." [PMID:17589542] +subset: human_subset +subset: mouse_subset synonym: "NKT.44+.NK1.1-.Th" BROAD [] is_a: CL:0000914 {is_inferred="true"} ! immature NK T cell intersection_of: CL:0000914 ! immature NK T cell @@ -15365,6 +17109,8 @@ id: CL:0002042 name: immature NK T cell stage IV def: "A CD24-low, CD44-positive, DX5-high, NK1.1-negative NK T cell." [GOC:tfm, http://www.immgen.org/index_content.html, PMID:17589542] subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "NKT.44+.NK1.1-.Th" BROAD [] is_a: CL:0000914 {is_inferred="true"} ! immature NK T cell intersection_of: CL:0000914 ! immature NK T cell @@ -15386,6 +17132,8 @@ id: CL:0002043 name: CD34-positive, CD38-negative multipotent progenitor cell def: "A hematopoietic multipotent progenitor cell that is CD34-positive, CD38-negative, CD45RA-negative, and CD90-negative." [GOC:tfm, PMID:18371405, PMID:19022770] comment: Cell markers are associated with human hematopoietic multipotent progenitor cells. +subset: human_subset +subset: mouse_subset is_a: CL:0000837 {is_inferred="true"} ! hematopoietic multipotent progenitor cell intersection_of: CL:0000837 ! hematopoietic multipotent progenitor cell intersection_of: CL:4030046 PR:000001015 ! lacks_plasma_membrane_part receptor-type tyrosine-protein phosphatase C isoform CD45RA @@ -15404,6 +17152,8 @@ id: CL:0002044 name: Kit-positive, integrin beta7-high basophil mast progenitor cell def: "A basophil mast progenitor cell that is Beta-7 integrin-high, Kit-positive FcRgammaII/III-positive and Sca1-negative." [GOC:ak, GOC:tfm] comment: Markers are associated with mouse cells. +subset: human_subset +subset: mouse_subset is_a: CL:0002028 {is_inferred="true"} ! basophil mast progenitor cell intersection_of: CL:0002028 ! basophil mast progenitor cell intersection_of: CL:4030046 PR:000002065 ! lacks_plasma_membrane_part mast/stem cell growth factor receptor @@ -15425,6 +17175,8 @@ name: fraction A pre-pro B cell def: "A pro-B cell that is CD45R/B220-positive, CD43-positive, HSA-low, BP-1-negative and Ly6c-negative. This cell type is also described as being lin-negative, AA4-positive, Kit-positive, IL7Ra-positive and CD45R-positive." [GOC:ak, GOC:tfm, http://www.immgen.org/index_content.html, PMID:12633665, PMID:17582343] comment: Markers associated with mouse cells. subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "fraction A" BROAD [] synonym: "pre pro B cell" RELATED [] is_a: CL:0000826 {is_inferred="true"} ! pro-B cell @@ -15452,6 +17204,8 @@ name: early pro-B cell def: "A pro-B cell that is CD22-positive, CD34-positive, CD38-positive and TdT-positive (has TdT activity). Pre-BCR is expressed on the cell surface. Cell is CD19-negative, CD20-negative, complement receptor type 2-negative and CD10-low. D-to-J recombination of the heavy chain occurs at this stage." [GOC:dsd, GOC:tfm, PMID:18432934] comment: Markers are commonly associated with human cells. These cells are also reportedly CD21-negative. Transcription factors: PU.1-positive, Ikaros-positive, E2A-positive, and PAX5-positive. subset: cellxgene_subset +subset: human_subset +subset: mouse_subset is_a: CL:0000826 {is_inferred="true"} ! pro-B cell intersection_of: CL:0000826 ! pro-B cell intersection_of: CL:4030046 PR:000001002 ! lacks_plasma_membrane_part CD19 molecule @@ -15480,6 +17234,8 @@ id: CL:0002047 name: fraction B precursor B cell def: "A precursor B cell that is CD45RA-positive, CD43-positive, CD24-positive and BP-1-negative." [GOC:ak, GOC:tfm, PMID:18432934] comment: Markers are commonly associated with mouse cells. These cells are also reportedly RAG1-positive and RAG2-positive. +subset: human_subset +subset: mouse_subset synonym: "Fr. B" BROAD [] synonym: "Fraction B" BROAD [] is_a: CL:0002400 {is_inferred="true"} ! fraction B/C precursor B cell @@ -15499,6 +17255,8 @@ name: late pro-B cell def: "A pre-B cell precursor is CD19-low, CD22-positive , CD34-positive, CD38-positive." [GOC:dsd, GOC:tfm, PMID:18432934] comment: Late pro-B cells are also reportedly CD10-positive, CD20-negative, CD21-negative, and TdT-positive. Transcription factors: PU.1-positive, Ikaros-positive, E2A-positive, and PAX5-positive. subset: cellxgene_subset +subset: human_subset +subset: mouse_subset is_a: CL:0000817 {is_inferred="true"} ! precursor B cell intersection_of: CL:0000817 ! precursor B cell intersection_of: RO:0002104 PR:000001003 ! has plasma membrane part CD34 molecule @@ -15517,6 +17275,8 @@ creation_date: 2010-04-28T12:06:06Z id: CL:0002049 name: fraction C precursor B cell def: "A precursor B cell that is CD45R-positive, CD43-positive, CD24-positive, and BP-positive. Intracellularly expression of surrogate light chain, Rag1 and Rag2, TdT, occurs while there is no expression of mu heavy chain." [GOC:tfm, PMID:17582343] +subset: human_subset +subset: mouse_subset synonym: "Fraction C" RELATED [] is_a: CL:0002400 {is_inferred="true"} ! fraction B/C precursor B cell intersection_of: CL:0002400 ! fraction B/C precursor B cell @@ -15543,6 +17303,8 @@ creation_date: 2010-04-28T02:04:01Z id: CL:0002050 name: fraction C' precursor B cell def: "A pre-BCR-positive precursor B cell that is CD24-high, CD25-positive, CD43-positive, CD45R-positive and BP-positive." [GOC:tfm, PMID:17582343] +subset: human_subset +subset: mouse_subset synonym: "Fr. C'" BROAD [] synonym: "Fraction C-prime" BROAD [] is_a: CL:0000817 {is_inferred="true"} ! precursor B cell @@ -15568,6 +17330,8 @@ id: CL:0002051 name: CD38-high pre-BCR positive cell def: "A pre-BCR positive B cell that is CD38-high." [GOC:tfm, PMID:18432934] comment: Markers are associated with human cells. +subset: human_subset +subset: mouse_subset synonym: "large pre-B cell type I" RELATED [] is_a: CL:0000952 {is_inferred="true"} ! preBCR-positive large pre-B-II cell intersection_of: CL:0000952 ! preBCR-positive large pre-B-II cell @@ -15584,6 +17348,8 @@ id: CL:0002052 name: fraction D precursor B cell def: "A pre-B cell that is pre-BCR-negative, and the kappa- and lambda- light immunoglobulin light chain-negative, CD43-low, and is BP-1-positive, CD45R-positive and CD25-positive. This cell type is also described as being AA4-positive, IgM-negative, CD19-positive, CD43-low/negative, and HSA-positive." [GOC:ak, GOC:dsd, GOC:tfm, http://www.immgen.org/index_content.html, PMID:17582343, PMID:18432934] comment: Fraction D precursor B cells are also reportedly CD24-positive and sIgD-negative. +subset: human_subset +subset: mouse_subset synonym: "Fr. D" BROAD [] synonym: "fraction D pre-B cell" EXACT [GOC:tfm] is_a: CL:0002400 ! fraction B/C precursor B cell @@ -15612,6 +17378,8 @@ id: CL:0002053 name: CD22-positive, CD38-low small pre-B cell def: "A small pre-B cell that is CD22-positive and CD38-low." [GOC:tfm, PMID:18432934] comment: Markers are associated with human cell. RAG expression maybe diminishing. +subset: human_subset +subset: mouse_subset synonym: "small pre-B cell" EXACT [] is_a: CL:0000954 {is_inferred="true"} ! small pre-B-II cell intersection_of: CL:0000954 ! small pre-B-II cell @@ -15628,6 +17396,8 @@ id: CL:0002054 name: fraction E immature B cell def: "An immature B cell that is IgM-positive, CD45R-positive, CD43-low, CD25-negative, and CD127-negative. This cell type has also been described as being AA4-positive, IgM-positive, CD19-positive, CD43-low/negative, and HSA-positive." [GOC:ak, GOC:dsd, GOC:tfm, PMID:17582343, PMID:18432934] comment: Markers associated with mouse cells. These cells are also reportedly sIgD-negative. +subset: human_subset +subset: mouse_subset is_a: CL:0000816 {is_inferred="true"} ! immature B cell intersection_of: CL:0000816 ! immature B cell intersection_of: CL:4030046 PR:000001380 ! lacks_plasma_membrane_part interleukin-2 receptor subunit alpha @@ -15650,6 +17420,8 @@ id: CL:0002055 name: CD38-negative immature B cell def: "An immature B cell that is CD38-negative, CD10-low, CD21-low, and CD22-high." [GOC:tfm, PMID:18432934] comment: Markers are associated with human cell type. +subset: human_subset +subset: mouse_subset is_a: CL:0000816 {is_inferred="true"} ! immature B cell intersection_of: CL:0000816 ! immature B cell intersection_of: CL:4030046 PR:000001408 ! lacks_plasma_membrane_part ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1 @@ -15668,6 +17440,8 @@ creation_date: 2010-04-28T03:19:14Z id: CL:0002056 name: fraction F mature B cell def: "A mature B cell subset originally defined as having being CD45R-positive, IgM-positive, IgD-positive and CD43-negative. Subsequent research demonstrated being CD21-positive and CD23-negative and CD93 negative." [GOC:tfm, PMID:17582343] +subset: human_subset +subset: mouse_subset is_a: CL:0000822 ! B-2 B cell intersection_of: CL:0000785 ! mature B cell intersection_of: CL:4030046 PR:000001879 ! lacks_plasma_membrane_part leukosialin @@ -15694,6 +17468,8 @@ name: CD14-positive, CD16-negative classical monocyte def: "A classical monocyte that is CD14-positive, CD16-negative, CD64-positive, CD163-positive." [GOC:add, GOC:tfm, PMID:15615263, PMID:1706877, PMID:19689341, PMID:22343568] comment: This cell type is compatible with the HIPC Lyoplate markers for 'CD16- monocyte'. The markers used in the definition are associated with human monocytes. subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "CD16- monocyte" EXACT [PMID:22343568] synonym: "CD16-negative monocyte" EXACT [] is_a: CL:0000860 {is_inferred="true"} ! classical monocyte @@ -15714,6 +17490,8 @@ id: CL:0002058 name: Gr1-low non-classical monocyte def: "A resident monocyte that is Gr-1 low, CD43-positive, and CX3CR1-positive." [GOC:tfm, PMID:8890901] comment: Markers are associated with mice. The Gr epitope is used to describe this cell type is found on both Ly6c and Ly6g. However, its the Ly6c that is considered the specific marker, and thus used in the cross-product. Also, this cell-type is sometimes described as being Gr1-negative. +subset: human_subset +subset: mouse_subset is_a: CL:0000875 {is_inferred="true"} ! non-classical monocyte is_a: CL:0002398 ! Gr1-positive, CD43-positive monocyte intersection_of: CL:0000875 ! non-classical monocyte @@ -15734,9 +17512,11 @@ creation_date: 2010-06-05T08:25:44Z [Term] id: CL:0002059 -name: CD8alpha-positive thymic conventional dendritic cell -def: "A conventional thymic dendritic cell that is CD8alpha-positive." [GOC:tfm, http://www.immgen.org/index_content.html, PMID:19273629] +name: CD8-alpha-positive thymic conventional dendritic cell +def: "A conventional thymic dendritic cell that is CD8-alpha-positive." [GOC:tfm, http://www.immgen.org/index_content.html, PMID:19273629] subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "CD8alpha-alpha-positive thymic conventional dendritic cell" EXACT [] synonym: "DC.8+.Th" EXACT [] is_a: CL:0000941 {is_inferred="true"} ! thymic conventional dendritic cell @@ -15751,6 +17531,8 @@ creation_date: 2010-06-07T02:48:36Z id: CL:0002060 name: melanophage def: "A melanin-containing macrophage that obtains the pigment by phagocytosis of melanosomes." [GOC:tfm, PMID:20479296, PMID:2943821] +subset: human_subset +subset: mouse_subset is_a: CL:0000864 {is_inferred="true"} ! tissue-resident macrophage relationship: part_of UBERON:0002097 ! skin of body property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 @@ -15760,6 +17542,8 @@ creation_date: 2010-06-22T10:46:12Z id: CL:0002061 name: T-helper 9 cell def: "A T-helper cell that is characterized by secreting interleukin 9 and responding to helminth infections. This cell-type can derives from Th2 cells in the presence of TGF-beta and IL-4. Th2 cytokine production is surpressed." [GOC:tfm, PMID:18931678, PMID:19604299, PMID:20154671] +subset: human_subset +subset: mouse_subset synonym: "T helper cells type 9" EXACT [] synonym: "T(H)-9 cell" EXACT [] synonym: "Th9" EXACT [PMID:18931678] @@ -15778,8 +17562,11 @@ creation_date: 2010-06-22T11:18:44Z id: CL:0002062 name: pulmonary alveolar type 1 cell def: "A squamous pulmonary alveolar epithelial cell that is flattened and branched. A pulmonary alveolar type 1 cell covers more than 98% of the alveolar surface. This large cell has thin (50-100 nm) cytoplasmic extensions to form the air-blood barrier essential for normal gas exchange." [GOC:tfm, http://www.copewithcytokines.de, PMID:20054144, PMID:29463737] +comment: The marker set AGER can identify the Human cell type pulmonary alveolar type 1 cell in the Lung with a confidence of 0.85 (NS-Forest FBeta value). {xref="https://doi.org/10.5281/zenodo.11165918"} subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "AT1" RELATED OMO:0003000 [PMID:29463737] synonym: "ATI" RELATED OMO:0003000 [] synonym: "lung type 1 cells" EXACT [] @@ -15799,6 +17586,7 @@ is_a: CL:0000322 ! pulmonary alveolar epithelial cell intersection_of: CL:0000322 ! pulmonary alveolar epithelial cell intersection_of: capable_of GO:0007585 ! respiratory gaseous exchange by respiratory system relationship: capable_of GO:0007585 ! respiratory gaseous exchange by respiratory system +relationship: RO:0015004 CLM:1000008 ! has characterizing marker set NS forest marker set of pulmonary alveolar type 1 cell (Human Lung). property_value: RO:0002175 NCBITaxon:9606 property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-06-23T04:37:54Z @@ -15807,8 +17595,11 @@ creation_date: 2010-06-23T04:37:54Z id: CL:0002063 name: pulmonary alveolar type 2 cell def: "A pulmonary alveolar epithelial cell that modulates the fluid surrounding the alveolar epithelium by secreting and recycling surfactants. This cell type also contributes to tissue repair and can differentiate after injury into a pulmonary alveolar type 1 cell. This cuboidal cell is thicker than squamous alveolar cells, have a rounded apical surface that projects above the level of surrounding epithelium. The free surface is covered by short microvilli." [GOC:tfm, http://www.copewithcytokines.de, ISBN:0412046911, PMID:36138472, PMID:8540632] +comment: The marker set SFTPA1 can identify the Human cell type pulmonary alveolar type 2 cell in the Lung with a confidence of 0.95 (NS-Forest FBeta value). {xref="https://doi.org/10.5281/zenodo.11165918"} subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "AT2" RELATED OMO:0003000 [PMID:36138472] synonym: "ATII" RELATED OMO:0003000 [] synonym: "cuboidal type II cell" EXACT [] @@ -15829,10 +17620,12 @@ xref: FMA:62501 is_a: CL:0000157 ! surfactant secreting cell is_a: CL:0000322 ! pulmonary alveolar epithelial cell is_a: CL:1000272 ! lung secretory cell +is_a: CL:1100001 ! secretory epithelial cell intersection_of: CL:0000322 ! pulmonary alveolar epithelial cell intersection_of: capable_of GO:0032940 ! secretion by cell intersection_of: capable_of GO:0043129 ! surfactant homeostasis relationship: RO:0002202 CL:4040003 ! develops from fetal pre-type II pulmonary alveolar epithelial cell +relationship: RO:0015004 CLM:1000009 ! has characterizing marker set NS forest marker set of pulmonary alveolar type 2 cell (Human Lung). property_value: RO:0002175 NCBITaxon:9606 property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-06-24T12:04:13Z @@ -15843,6 +17636,8 @@ name: pancreatic acinar cell def: "A secretory cell found in pancreatic acini that secretes digestive enzymes and mucins. This cell is a typical zymogenic cell, have a basal nucleus and basophilic cytoplasm consisting of regular arrays of granular endoplasmic reticulum with mitochondria and dense secretory granules." [GOC:tfm, http://www.copewithcytokines.de/cope.cgi?key=pancreatic%20acinar%20cells, ISBN:0517223651, PMID:20395539] subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "acinar cell of pancreas" EXACT [] xref: BTO:0000028 xref: CALOHA:TS-0737 @@ -15857,13 +17652,15 @@ relationship: has_part GO:0042589 ! zymogen granule membrane relationship: part_of UBERON:0001263 ! pancreatic acinus property_value: RO:0002175 NCBITaxon:9606 property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 -property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional.\n\nPancreatic acinar cells are the functional units of the exocrine pancreas. These cells are structurally arranged in small clusters - or acini - with a small central lumen, and their primary function is to produce and secrete enzymes that facilitate digestion of proteins, carbohydrates, and fats within the small intestine.\nSome of the most important digestive enzymes synthesized by the pancreatic acinar cells include amylase, which digests carbohydrates, lipase, which breaks down fats, and several proteases such as trypsin and chymotrypsin which are vital for the digestion of proteins. Importantly, these enzymes are produced as proenzymes or zymogens to avoid autolysis, or the breakdown of the pancreas itself.\nThe release of these enzymes by the pancreatic acinar cells is strictly regulated by hormones and neurochemicals. Cholecystokinin (CCK) released from the enteroendocrine cells in the duodenum cause the release of these enzymes. Moreover, acinar cells also respond to another hormone, secretin, by releasing bicarbonate-rich fluid which helps to neutralize the gastric acid in the duodenum. \nDysregulation in the function of pancreatic acinar cells can lead to severe health issues, including pancreatitis, which is characterized by inflammatory damage to the organ due to the premature activation of digestive enzymes." xsd:string {xref="DOI:10.1016/0165-6147(89)90192-2", xref="DOI:10.1038/nrgastro.2013.36", xref="DOI:10.1097/01.mog.0000239863.96833.c0", xref="https://www.ncbi.nlm.nih.gov/books/NBK54134/"} +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nPancreatic acinar cells are the functional units of the exocrine pancreas. These cells are structurally arranged in small clusters - or acini - with a small central lumen, and their primary function is to produce and secrete enzymes that facilitate digestion of proteins, carbohydrates, and fats within the small intestine.\nSome of the most important digestive enzymes synthesized by the pancreatic acinar cells include amylase, which digests carbohydrates, lipase, which breaks down fats, and several proteases such as trypsin and chymotrypsin which are vital for the digestion of proteins. Importantly, these enzymes are produced as proenzymes or zymogens to avoid autolysis, or the breakdown of the pancreas itself.\nThe release of these enzymes by the pancreatic acinar cells is strictly regulated by hormones and neurochemicals. Cholecystokinin (CCK) released from the enteroendocrine cells in the duodenum cause the release of these enzymes. Moreover, acinar cells also respond to another hormone, secretin, by releasing bicarbonate-rich fluid which helps to neutralize the gastric acid in the duodenum. \nDysregulation in the function of pancreatic acinar cells can lead to severe health issues, including pancreatitis, which is characterized by inflammatory damage to the organ due to the premature activation of digestive enzymes." xsd:string {xref="DOI:10.1016/0165-6147(89)90192-2", xref="DOI:10.1038/nrgastro.2013.36", xref="DOI:10.1097/01.mog.0000239863.96833.c0", xref="https://www.ncbi.nlm.nih.gov/books/NBK54134/"} creation_date: 2010-06-24T03:16:29Z [Term] id: CL:0002066 name: Feyrter cell def: "A neuroendocrine cell found in the epithelium of the lungs and respiratory tract. This cell type is rounded or elliptical in shape, situated mainly in the basal part of the epithelium; regulates bronchial secretion, smooth muscle contraction, lobular growth, ciliary activity and chemoreception. Cell has an electron-lucent cytoplasm, contains numerous dense-cored vesicles with a clear halo between the core and the limiting membrane." [GOC:tfm, ISBN:0412046911, ISBN:0517223651] +subset: human_subset +subset: mouse_subset synonym: "bronchiolar Kulchitsky cell" EXACT [] synonym: "Kultschitzky cell of bronchiole" EXACT [] synonym: "P cell" RELATED OMO:0003000 [] @@ -15877,6 +17674,9 @@ creation_date: 2010-06-28T08:24:30Z id: CL:0002067 name: type A enteroendocrine cell def: "An enteroendocrine cell that produces glucagon." [GOC:tfm, ISBN:0412046911] +subset: cellxgene_subset +subset: human_subset +subset: mouse_subset xref: FMA:62939 xref: https://cellxgene.cziscience.com/cellguide/CL_0002067 is_a: CL:0000164 ! enteroendocrine cell @@ -15884,7 +17684,7 @@ is_a: CL:0000170 ! glucagon secreting cell intersection_of: CL:0000164 ! enteroendocrine cell intersection_of: capable_of GO:0070091 ! glucagon secretion property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 -property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional.\n\nType A enteroendocrine cells, also known as alpha cells or A cells, are a species of endocrine cells primarily located in the pancreatic islets of Langerhans; they have also been identified within the lining of the stomach. Functionally, these cells are pivotal in glucose metabolism and homeostasis, accounting for about 20% of the total population of cells in the pancreatic islets. \nThe primary role of type A enteroendocrine cells involves the synthesis, storage, and secretion of the peptide hormone glucagon, which is critical in energy regulation throughout the body. In response to a decrease in blood glucose levels, the pancreatic A cells are stimulated to secrete glucagon into the bloodstream. Glucagon acts on its target cells, mainly in the liver, to stimulate glycogenolysis and gluconeogenesis processes, thereby increasing blood glucose levels back to normal. In this way, pancreatic A cells play an integral role in maintaining glucose homeostasis and preventing hypoglycemia.\nPancreatic A cells also participate in the local regulation of islet activities as glucagon acts through glucagon receptors on A, B and D type cells within the islets. Recent studies have also shown that Pancreatic A cells play a role in the generation and regeneration of B type cells. Following beta cell injuries pancreatic A cells increase in numbers and produce Glucagon-like peptide-1 (GLP-1), which increases the proliferation and cytoprotection of beta cells. In response to extreme injury of B type cells pancreatic A cells can transform (transdifferentiate) into functioning B type cells.\nUntil recently, glucagon has been considered a pancreas-specific hormone; however, extrapancreatic glucagon has been reported in patients who had undergone complete, and glucagon-positive cells been identified in the human stomach, indicating that Type A enteroendocrine cells are not restricted to the pancreas." xsd:string {xref="DOI:10.1016/j.diabres.2018.06.013", xref="DOI:10.1210/en.2016-1748", xref="DOI:10.2337/db15-1541", xref="DOI:10.2337/dbi19-0002", xref="DOI:10.3389/fphys.2012.00349/full"} +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nType A enteroendocrine cells, also known as alpha cells or A cells, are a species of endocrine cells primarily located in the pancreatic islets of Langerhans; they have also been identified within the lining of the stomach. Functionally, these cells are pivotal in glucose metabolism and homeostasis, accounting for about 20% of the total population of cells in the pancreatic islets. \nThe primary role of type A enteroendocrine cells involves the synthesis, storage, and secretion of the peptide hormone glucagon, which is critical in energy regulation throughout the body. In response to a decrease in blood glucose levels, the pancreatic A cells are stimulated to secrete glucagon into the bloodstream. Glucagon acts on its target cells, mainly in the liver, to stimulate glycogenolysis and gluconeogenesis processes, thereby increasing blood glucose levels back to normal. In this way, pancreatic A cells play an integral role in maintaining glucose homeostasis and preventing hypoglycemia.\nPancreatic A cells also participate in the local regulation of islet activities as glucagon acts through glucagon receptors on A, B and D type cells within the islets. Recent studies have also shown that Pancreatic A cells play a role in the generation and regeneration of B type cells. Following beta cell injuries pancreatic A cells increase in numbers and produce Glucagon-like peptide-1 (GLP-1), which increases the proliferation and cytoprotection of beta cells. In response to extreme injury of B type cells pancreatic A cells can transform (transdifferentiate) into functioning B type cells.\nUntil recently, glucagon has been considered a pancreas-specific hormone; however, extrapancreatic glucagon has been reported in patients who had undergone complete, and glucagon-positive cells been identified in the human stomach, indicating that Type A enteroendocrine cells are not restricted to the pancreas." xsd:string {xref="DOI:10.1016/j.diabres.2018.06.013", xref="DOI:10.1210/en.2016-1748", xref="DOI:10.2337/db15-1541", xref="DOI:10.2337/dbi19-0002", xref="DOI:10.3389/fphys.2012.00349/full"} creation_date: 2010-09-10T10:48:54Z [Term] @@ -15892,6 +17692,8 @@ id: CL:0002068 name: Purkinje myocyte def: "Specialized cardiac myocyte that is subendocardially interspersed with the regular cardiac muscle cell. They are uninucleate cylindrical cells, associated end-to-end in long rows, continue from the node to the atrioventricular bundle; relatively short compared to ordinary myocytes but are nearly twice their diameter." [FMA:0412046911, GOC:tfm, PMID:19939742] subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "myocytus conducens cardiacus" EXACT [] synonym: "Purkinje cell fiber" EXACT [] synonym: "Purkinje muscle cell" EXACT [] @@ -15906,6 +17708,8 @@ creation_date: 2010-06-28T08:36:15Z id: CL:0002069 name: type II vestibular sensory cell def: "Mostly cylindrical, resemble Type 1 in their contents and the presence of a kinocilium and stereocilium apically; much greater variation in size, some almost span the entire thickness of the sensory epithelium, while others are smaller than Type 1; receive multiple efferent nerve boutons around their bases as well as afferent endings, which are small expansions rather than chalices." [GOC:tfm, ISBN:0517223651] +subset: human_subset +subset: mouse_subset synonym: "type 2 vestibular hair cell" EXACT [] synonym: "type 2 vestibular sensory cell" EXACT [] synonym: "type II hair cell" EXACT [] @@ -15918,6 +17722,8 @@ creation_date: 2010-06-29T09:58:13Z id: CL:0002070 name: type I vestibular sensory cell def: "Bottle-shaped with narrow neck; broad, rounded basal portion where nucleus is located; stereocilia and a single kinocilium is present apically; receive nerve bouton at their base from an afferent cup-shaped (chalice or calyx) nerve ending." [GOC:tfm, ISBN:0517223651] +subset: human_subset +subset: mouse_subset synonym: "type 1 vestibular hair cell" EXACT [] synonym: "type 1 vestibular sensory cell" EXACT [] synonym: "type I hair cell" EXACT [] @@ -15932,6 +17738,8 @@ name: enterocyte of epithelium of large intestine def: "Columnar cell which populate the epithelium of large intestine and absorb water. This cell is the most numerous of the epithelial cell types in the large intestine; bear apical microvilli, contain secretory granules in their apical cytoplasm; secretion appears to be largely mucins, but is also rich in antibodies of the IgA type." [GOC:tfm, ISBN:0517223651] subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "columnar cell" BROAD [] synonym: "columnar cell of the colon" EXACT [] synonym: "vacuolar absorptive cell" EXACT [] @@ -15942,7 +17750,6 @@ is_a: CL:0000584 ! enterocyte is_a: CL:0002253 {is_inferred="true"} ! epithelial cell of large intestine intersection_of: CL:0000584 ! enterocyte intersection_of: part_of UBERON:0001278 ! epithelium of large intestine -relationship: part_of UBERON:0001278 ! epithelium of large intestine property_value: RO:0002175 NCBITaxon:9606 property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-06-29T11:07:25Z @@ -15951,6 +17758,8 @@ creation_date: 2010-06-29T11:07:25Z id: CL:0002072 name: nodal myocyte def: "A specialized cardiac myocyte in the sinoatrial and atrioventricular nodes. The cell is slender and fusiform confined to the nodal center, circumferentially arranged around the nodal artery." [FMA:67101, GOC:tfm] +subset: human_subset +subset: mouse_subset synonym: "cardiac pacemaker cell" EXACT [GOC:pr] synonym: "myocytus nodalis" EXACT [] synonym: "P cell" EXACT [] @@ -15965,6 +17774,8 @@ creation_date: 2010-06-29T11:41:37Z id: CL:0002073 name: transitional myocyte def: "Specialized cardiac myocyte which is in the internodal tract and atrioventricular node. The cell is more slender than ordinary atrial myocytes and has more myofibrils than nodal myocytes." [FMA:67142, GOC:tfm] +subset: human_subset +subset: mouse_subset xref: FMA:67142 is_a: CL:0002086 ! specialized cardiac myocyte property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 @@ -15974,6 +17785,8 @@ creation_date: 2010-06-29T02:39:32Z id: CL:0002074 name: myocardial endocrine cell def: "The myoendocrine cellis a specialized myocyte localized mainly in the right and left atrial appendages, and also scattered within other areas of the atria and along the conductive system in the ventricular septum. The most conspicuous feature distinguishing myoendocrine cells from other atrial myoctyes is the presence of membane-bounded secretory granules (these granules contain precursor of cardiodilatins or atrial natriuretic polypeptides)." [FMA:67111, GOC:tfm] +subset: human_subset +subset: mouse_subset xref: FMA:67111 is_a: CL:0000163 ! endocrine cell is_a: CL:0002086 ! specialized cardiac myocyte @@ -15983,13 +17796,19 @@ creation_date: 2010-06-29T11:50:47Z [Term] id: CL:0002075 name: brush cell of tracheobronchial tree -def: "Infrequent type of columnar epithelial cell. This cell is characterized by the presence of a tuft of blunt, squat microvilli (approximately 120-140/cell) on the cell surface. The microvilli contain filaments that stretch into the underlying cytoplasm. They have a distinctive pear shape with a wide base and a narrow microvillous apex. Function not known." [GOC:tfm, ISBN:0517223651, PMID:15817800] +def: "A rare type of columnar epithelial cell that is part of the tracheobronchial epithelium. This cell is characterized by a distinctive tuft of apical microvilli, which extends into the cytoplasm, and a pear-shaped morphology, broad at the base and tapering to a narrow apex. It plays vital roles in chemosensation, producing cytokines like IL-25, and enhancing mucociliary clearance through acetylcholine release to support mucus movement and airway defense." [GOC:tfm, ISBN:0517223651, PMID:15817800, PMID:30291131, PMID:37925434] +comment: The marker set POU2F3, HOMER3, MYB can identify the Human cell type brush cell of tracheobronchial tree in the Lung with a confidence of 0.56 (NS-Forest FBeta value). {xref="https://doi.org/10.5281/zenodo.11165918"} subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "pulmonary brush cell" RELATED [] +is_a: CL:0000075 ! columnar/cuboidal epithelial cell is_a: CL:0002202 ! epithelial cell of tracheobronchial tree is_a: CL:0002204 ! brush cell intersection_of: CL:0002204 ! brush cell intersection_of: part_of UBERON:0008397 ! tracheobronchial epithelium +relationship: RO:0015004 CLM:1000061 ! has characterizing marker set NS forest marker set of brush cell of tracheobronchial tree (Human Lung). +property_value: RO:0002175 NCBITaxon:9606 property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-06-29T03:22:46Z @@ -15997,6 +17816,9 @@ creation_date: 2010-06-29T03:22:46Z id: CL:0002076 name: endo-epithelial cell def: "An epithelial cell derived from endoderm." [FMA:69075, GOC:tfm] +subset: cellxgene_subset +subset: human_subset +subset: mouse_subset xref: FMA:69075 xref: ZFA:0009383 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: BFO:0000002 @@ -16011,6 +17833,8 @@ creation_date: 2010-06-29T03:38:14Z id: CL:0002077 name: ecto-epithelial cell def: "An epithelial cell derived from ectoderm." [FMA:69074, GOC:tfm] +subset: human_subset +subset: mouse_subset xref: FMA:69074 xref: ZFA:0009385 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: BFO:0000002 @@ -16025,6 +17849,8 @@ creation_date: 2010-06-29T03:38:22Z id: CL:0002078 name: meso-epithelial cell def: "Epithelial cell derived from mesoderm or mesenchyme." [FMA:69076, GOC:tfm] +subset: human_subset +subset: mouse_subset synonym: "epithelial mesenchymal cell" EXACT [] xref: FMA:69076 xref: ZFA:0009388 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} @@ -16042,6 +17868,8 @@ name: pancreatic ductal cell def: "Epithelial cell found in the ducts of the pancreas. This cell type contributes to the high luminal pH." [FMA:63099, GOC:tfm, PMID:14740223] subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset xref: FMA:63099 xref: ZFA:0009380 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000069 ! branched duct epithelial cell @@ -16060,6 +17888,8 @@ id: CL:0002080 name: pancreatic centro-acinar cell def: "A cubodial epithelial cell that is continuous with the lining of intercalated ducts that drain the acinus. This cell type secretes a high pH solution to aid in activation of zymogens, and can differentiate into endocrine and exocrine pancreatic cell types." [GOC:tfm, PMID:12142741, PMID:20018761, PMID:8185160] subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "centroacinar cell of Langerhans" EXACT [] synonym: "pancreatic centroacinar cell" EXACT [] xref: FMA:62455 @@ -16078,6 +17908,8 @@ creation_date: 2010-06-30T08:49:52Z id: CL:0002081 name: type II cell of carotid body def: "This cell resembles a glia cell, express the glial marker S100 and act as a supporting cell to type I cell. This cell is located in a small cluster of type I and type II cells near the fork of the carotid artery." [GOC:tfm, http://en.wikipedia.org/wiki/Carotid_body, PMID:7938227] +subset: human_subset +subset: mouse_subset synonym: "sheath cell of carotid body" EXACT [] xref: FMA:84187 is_a: CL:0000703 ! sustentacular cell @@ -16089,6 +17921,8 @@ creation_date: 2010-06-30T04:23:42Z id: CL:0002082 name: type II cell of adrenal medulla def: "A chromaffin cell of the adrenal medulla that produces epinephrine." [GOC:tfm] +subset: human_subset +subset: mouse_subset synonym: "adrenal secreting cell of the adrenal medulla" EXACT [] synonym: "adrenergic chromaffin cell" EXACT [] synonym: "epiniphrine secreting cell of the adrenal medulla" EXACT [] @@ -16105,6 +17939,8 @@ creation_date: 2010-07-14T09:41:42Z id: CL:0002083 name: type I cell of adrenal medulla def: "A chromaffin cell of the adrenal medulla that produces norepinephrine." [GOC:tfm, ISBN:068340007X] +subset: human_subset +subset: mouse_subset synonym: "noradrenergic chromaffin cell" EXACT [] xref: FMA:69321 is_a: CL:0000336 {is_inferred="true"} ! adrenal medulla chromaffin cell @@ -16119,6 +17955,8 @@ creation_date: 2010-07-14T10:12:24Z id: CL:0002084 name: Boettcher cell def: "A Boettcher cell is a polyhedral cells on the basilar membrane of the cochlea, and is located beneath Claudius cells. A Boettcher cell is considered a supporting cell for the organ of Corti, and is present only in the lower turn of the cochlea. These cells interweave with each other, and project microvilli into the intercellular space. Because of their structural specialization, a Boettcher cell is believed to play a significant role in the function of the cochlea. They demonstrate high levels of calmodulin, and may be involved in mediating Ca(2+) regulation and ion transport." [GOC:tfm, http://en.wikipedia.org/wiki/Boettcher_cell] +subset: human_subset +subset: mouse_subset synonym: "Boettcher's cell" EXACT [] synonym: "Bottcher cell" EXACT [] synonym: "Bottcher's cell" EXACT [] @@ -16132,6 +17970,8 @@ name: tanycyte alt_id: CL:0000643 def: "A specialized elongated ventricular ependymal cell that has processes that extend to the outer, or pial, surface of the CNS. A tanycyte is found in the adult brain, specifically in the third ventricle, cerebral aqueduct, spinal canal, and floor of the fourth ventricle. This cell type is involved in hormonal regulation, gatekeeping molecules between the bloodstream and cerebrospinal fluid, metabolic sensing, and regulating food intake." [GOC:tfm, http://neurolex.org/wiki/Category\:Tanycyte] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "stretch cell" EXACT [PMID:29351662] xref: BTO:0001953 xref: FMA:54560 @@ -16144,6 +17984,8 @@ creation_date: 2010-07-15T11:21:11Z id: CL:0002086 name: specialized cardiac myocyte def: "A cardiac myocyte that is an excitable cells in the myocardium, specifically in the conducting system of heart." [FMA:67968, GOC:tfm] +subset: human_subset +subset: mouse_subset xref: FMA:67968 is_a: CL:0000746 ! cardiac muscle cell property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 @@ -16154,6 +17996,8 @@ id: CL:0002087 name: nongranular leukocyte def: "A leukocyte that lacks granules." [GOC:tfm] subset: blood_and_immune_upper_slim +subset: human_subset +subset: mouse_subset synonym: "agranular leukocyte" EXACT [] xref: FMA:62855 is_a: CL:0000738 {is_inferred="true"} ! leukocyte @@ -16170,6 +18014,8 @@ def: "This is a cell found in the gastrointestinal tract of mammals and serves a comment: Some argue this cell type is of mesenchymal origin. subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "ICC" EXACT [] synonym: "intestinal pacemaker cell" EXACT [GOC:pr] xref: BTO:0003914 @@ -16186,9 +18032,9 @@ creation_date: 2010-07-22T03:26:00Z id: CL:0002089 name: group 2 innate lymphoid cell, mouse def: "A group 2 innate lymphoid cell in the mouse capable of secreting IL-13 in response to a helminth infection. This cell is lineage-negative, ICOS-positive, IL1RL1-positive, IL7Ralpha-positive, and IL17Br-positive." [GOC:add, GOC:tfm, PMID:20200518] +subset: mouse_subset synonym: "nuocyte" BROAD [] is_a: CL:0001069 ! group 2 innate lymphoid cell -is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0001069 ! group 2 innate lymphoid cell intersection_of: capable_of GO:0002830 ! positive regulation of type 2 immune response intersection_of: capable_of GO:0032616 ! interleukin-13 production @@ -16231,6 +18077,8 @@ creation_date: 2010-08-12T02:22:19Z id: CL:0002090 name: polar body def: "One of two small cells formed by the first and second meiotic division of oocytes." [GOC:tfm, http://en.wikipedia.org/wiki/Polar_body, ISBN:068340007X] +subset: human_subset +subset: mouse_subset xref: EHDAA2:0004716 xref: FMA:85543 xref: MESH:D059705 @@ -16244,6 +18092,8 @@ creation_date: 2010-08-23T09:49:53Z id: CL:0002091 name: primary polar body def: "A small cell formed by the first meiotic division of oocytes." [GOC:tfm, ISBN:068340007X] +subset: human_subset +subset: mouse_subset synonym: "first polar body" EXACT [EHDAA2:0000541] synonym: "polocytus primarius" EXACT [FMA:18650] xref: EHDAA2:0000541 @@ -16260,6 +18110,8 @@ name: bone marrow cell def: "A cell found in the bone marrow. This can include fibroblasts, macrophages, adipocytes, osteoblasts, osteoclasts, endothelial cells and hematopoietic cells." [GOC:tfm, ISBN:0618947256] comment: MH consider whether bone marrow cells are bone cells in the structural sense vs. being part of bone organ sense. subset: cellxgene_subset +subset: human_subset +subset: mouse_subset xref: BTO:0004850 xref: FMA:83621 xref: MESH:D001854 @@ -16274,6 +18126,8 @@ creation_date: 2010-07-22T04:48:15Z id: CL:0002093 name: secondary polar body def: "A small cell formed by the second meiotic division of oocytes. In mammals, the second polar body may fail to form unless the ovum has been penetrated by a sperm cell." [GOC:tfm, ISBN:068340007X] +subset: human_subset +subset: mouse_subset synonym: "polocytus secundarius" EXACT [FMA:18651] synonym: "second polar body" EXACT [EHDAA2:0001820] xref: EHDAA2:0001820 @@ -16289,6 +18143,8 @@ id: CL:0002094 name: interstitial cell of ovary def: "A cell that makes up the loose connective tissue of the ovary." [GOC:tfm] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset xref: FMA:18709 is_a: CL:0002132 ! stromal cell of ovary property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 @@ -16299,6 +18155,8 @@ id: CL:0002095 name: hilus cell of ovary def: "A cell in the hilum of the ovary that produces androgens." [GOC:tfm, ISBN:068340007X] subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "hilar cell of ovary" EXACT [] xref: FMA:18710 is_a: CL:0000593 ! androgen secreting cell @@ -16311,6 +18169,8 @@ creation_date: 2010-08-23T11:18:18Z id: CL:0002096 name: internodal tract myocyte def: "A specialised myocyte that lies between the sinoatrial node and the atrioventricular node and is involved in the conduction of electrical signals." [GOC:tfm, ISBN:0781729300] +subset: human_subset +subset: mouse_subset xref: FMA:223275 is_a: CL:0002086 ! specialized cardiac myocyte is_a: CL:0008009 ! transversely striated visceral muscle cell @@ -16325,6 +18185,8 @@ id: CL:0002097 name: cortical cell of adrenal gland def: "A cell of the adrenal cortex. Cell types include those that synthesize and secrete chemical derivatives (steroids) of cholesterol." [GOC:tfm] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "adrenal cortex cell" EXACT [] synonym: "adrenocortical cell" EXACT [] xref: FMA:69545 @@ -16340,11 +18202,15 @@ creation_date: 2010-08-24T01:37:44Z id: CL:0002098 name: regular cardiac myocyte def: "A cardiac myocyte that is connected to other cardiac myocytes by transverse intercalated discs (GO:0014704) at a regular interval." [GOC:tfm] +subset: human_subset +subset: mouse_subset synonym: "regular cardiac muscle cell" EXACT [] synonym: "regular cardiac muscle fiber" EXACT [] xref: FMA:67967 +xref: https://cellxgene.cziscience.com/cellguide/CL_0002098 is_a: CL:0000746 ! cardiac muscle cell property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nCardiac myocytes, also known as cardiac muscle cells, form the majority of the cardiac tissue and are responsible for the contractile function of the heart. These myocytes are columnar-shaped cells with centrally located nuclei, and they exhibit visibly striated cytoplasm due to the organized array of myofibrils, which are composed of filaments of actin and myosin. Cardiac myocytes connect with each other through specialized structures called intercalated discs, facilitating electrical and mechanical continuity and enabling synchronous contraction of the heart. They also possess a high number of mitochondria to meet their high energy demand for continuous heartbeat action.\nCardiac myocytes are capable of automaticity, meaning they have the unique ability to spontaneously and rhythmically generate their electrical impulses, a characteristic led by pacemaker cells. The electrical signals initiated and propagated in these cells are responsible for heartbeats. They also respond to the electrical signals transmitted by the autonomic nervous system and chemical signals like hormones. Thus, cardiac myocytes not only participate in maintaining the heart’s function but also play a role in modulating heart rate and strength of contraction in response to the body's changing needs. Consequently, malfunction of these cells leads to serious cardiac diseases such as heart failure and arrhythmias." xsd:string {xref="DOI:10.3389/fphys.2013.00102", xref="https://www.ncbi.nlm.nih.gov/books/NBK572070", xref="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3164530", xref="https://www.sciencedirect.com/topics/agricultural-and-biological-sciences/cardiac-muscle"} creation_date: 2010-08-23T11:33:10Z [Term] @@ -16352,6 +18218,9 @@ id: CL:0002099 name: type I cell of adrenal cortex alt_id: CL:1000423 def: "A small, polyhedral, cell found in rounded groups or curved columns with deeply staining nuclei, scanty basophilic cytoplasm and a few lipid droplets. This cell in the zona glomerulosa produces mineralocorticoids." [GOC:tfm, ISBN:0517223651] +subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "epithelial cell of zona glomerulosa of adrenal gland" EXACT [] xref: FMA:69273 is_a: CL:0000456 ! mineralocorticoid secreting cell @@ -16366,6 +18235,8 @@ creation_date: 2010-08-24T01:42:02Z id: CL:0002100 name: regular interventricular cardiac myocyte def: "A regular cardiac myocyte of the interventricular region of the heart." [GOC:tfm] +subset: human_subset +subset: mouse_subset xref: FMA:228792 is_a: CL:0002098 ! regular cardiac myocyte property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 @@ -16375,6 +18246,8 @@ creation_date: 2010-08-23T11:40:52Z id: CL:0002101 name: CD38-positive naive B cell def: "A CD38-positive naive B cell is a mature B cell that has the phenotype CD38-positive, surface IgD-positive, surface IgM-positive, and CD27-negative, and that has not yet been activated by antigen in the periphery." [GOC:dsd, GOC:rhs, GOC:tfm, PMID:20123131] +subset: human_subset +subset: mouse_subset synonym: "CD38+ naive B cell" EXACT [] synonym: "CD38+ naive B lymphocyte" EXACT [] synonym: "CD38+ naive B-cell" EXACT [] @@ -16391,6 +18264,9 @@ relationship: RO:0002104 PR:000001408 ! has plasma membrane part ADP-ribosyl cyc id: CL:0002102 name: CD38-negative naive B cell def: "A CD38-negative naive B cell is a mature B cell that has the phenotype CD38-negative, surface IgD-positive, surface IgM-positive, and CD27-negative, that has not yet been activated by antigen in the periphery." [GOC:dsd, GOC:rhs, GOC:tfm, PMID:20123131] +subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "CD38- naive B cell" EXACT [] synonym: "CD38- naive B lymphocyte" EXACT [] synonym: "CD38- naive B-cell" EXACT [] @@ -16407,6 +18283,8 @@ relationship: CL:4030046 PR:000001408 ! lacks_plasma_membrane_part ADP-ribosyl c id: CL:0002103 name: IgG-positive double negative memory B cell def: "An IgG-positive double negative memory B cell is a double negative memory B cell with the phenotype IgG-positive, IgD-negative, and CD27-negative." [GOC:dsd, GOC:rhs, GOC:tfm, PMID:20123131] +subset: human_subset +subset: mouse_subset synonym: "IgG+ dn memory B cell" EXACT [] synonym: "IgG+ dn memory B lymphocyte" EXACT [] synonym: "IgG+ dn memory B-cell" EXACT [] @@ -16431,6 +18309,8 @@ relationship: RO:0002104 GO:0071735 ! has plasma membrane part IgG immunoglobuli id: CL:0002104 name: IgG-negative double negative memory B cell def: "An IgG-negative double negative memory B cell is a double negative memory B cell with the phenotype IgG-negative, IgD-negative, and CD27-negative." [GOC:dsd, GOC:rhs, GOC:tfm, PMID:20123131] +subset: human_subset +subset: mouse_subset synonym: "IgG- dn memory B cell" EXACT [] synonym: "IgG- dn memory B lymphocyte" EXACT [] synonym: "IgG- dn memory B-cell" EXACT [] @@ -16455,6 +18335,8 @@ relationship: CL:4030046 GO:0071735 ! lacks_plasma_membrane_part IgG immunoglobu id: CL:0002105 name: CD38-positive IgG memory B cell def: "A CD38-positive IgG memory B cell is a class switched memory B cell that expresses IgG on the cell surface with the phenotype CD38-positive and IgG-positive." [GOC:dsd, GOC:rhs, GOC:tfm, PMID:20123131] +subset: human_subset +subset: mouse_subset synonym: "CD38+ IgG memory B cell" EXACT [] synonym: "CD38+ IgG memory B lymphocyte" EXACT [] synonym: "CD38+ IgG memory B-cell" EXACT [] @@ -16471,6 +18353,8 @@ relationship: RO:0002104 PR:000001408 ! has plasma membrane part ADP-ribosyl cyc id: CL:0002106 name: IgD-positive CD38-positive IgG memory B cell def: "An IgD-positive CD38-positive IgG memory B cell is a CD38-positive IgG-positive class switched memory B cell that has class switched and expresses IgD on the cell surface with the phenotype IgD-positive, CD38-positive, and IgG-positive." [GOC:dsd, GOC:rhs, GOC:tfm, PMID:20123131] +subset: human_subset +subset: mouse_subset is_a: CL:0002105 {is_inferred="true"} ! CD38-positive IgG memory B cell intersection_of: CL:0002105 ! CD38-positive IgG memory B cell intersection_of: RO:0002104 GO:0071738 ! has plasma membrane part IgD immunoglobulin complex @@ -16480,6 +18364,8 @@ relationship: RO:0002104 GO:0071738 ! has plasma membrane part IgD immunoglobuli id: CL:0002107 name: IgD-negative CD38-positive IgG memory B cell def: "An IgD-negative CD38-positive IgG memory B cell is a CD38-positive IgG-positive that has class switched and lacks expression of IgD on the cell surface with the phenotype IgD-negative, CD38-positive, and IgG-positive." [GOC:dsd, GOC:rhs, GOC:tfm, PMID:20123131] +subset: human_subset +subset: mouse_subset is_a: CL:0001053 ! IgD-negative memory B cell is_a: CL:0002105 {is_inferred="true"} ! CD38-positive IgG memory B cell intersection_of: CL:0002105 ! CD38-positive IgG memory B cell @@ -16489,6 +18375,8 @@ intersection_of: CL:4030046 GO:0071738 ! lacks_plasma_membrane_part IgD immunogl id: CL:0002108 name: CD38-negative IgG memory B cell def: "A CD38-negative IgG memory B cell is a IgG-positive class switched memory B cell that has class switched and expresses IgG on the cell surface with the phenotype CD38-negative, IgD-negative, and IgG-positive." [GOC:dsd, GOC:rhs, GOC:tfm, PMID:20123131] +subset: human_subset +subset: mouse_subset is_a: CL:0000979 {is_inferred="true"} ! IgG memory B cell is_a: CL:0001053 ! IgD-negative memory B cell intersection_of: CL:0000979 ! IgG memory B cell @@ -16500,6 +18388,8 @@ relationship: CL:4030046 PR:000001408 ! lacks_plasma_membrane_part ADP-ribosyl c id: CL:0002109 name: B220-positive CD38-positive naive B cell def: "A B220-positive CD38-positive naive B cell is a CD38-positive naive B cell that has the phenotype B220-positive, CD38-positive, surface IgD-positive, surface IgM-positive, and CD27-negative, and that has not yet been activated by antigen in the periphery." [GOC:dsd, GOC:rhs, GOC:tfm, PMID:20123131] +subset: human_subset +subset: mouse_subset synonym: "B220+CD38+ naive B cell" EXACT [] synonym: "B220+CD38+ naive B lymphocyte" EXACT [] synonym: "B220+CD38+ naive B-cell" EXACT [] @@ -16520,6 +18410,8 @@ relationship: RO:0002104 PR:000001014 ! has plasma membrane part receptor-type t id: CL:0002110 name: B220-low CD38-positive naive B cell def: "A B220-low CD38-positive naive B cell is a CD38-positive naive B cell that has the phenotype B220-low, CD38-positive, surface IgD-positive, surface IgM-positive, and CD27-negative, that has not yet been activated by antigen in the periphery." [GOC:dsd, GOC:rhs, GOC:tfm, PMID:20123131] +subset: human_subset +subset: mouse_subset is_a: CL:0002109 ! B220-positive CD38-positive naive B cell intersection_of: CL:0002101 ! CD38-positive naive B cell intersection_of: RO:0015016 PR:000001014 ! has low plasma membrane amount receptor-type tyrosine-protein phosphatase C isoform CD45RABC @@ -16529,6 +18421,8 @@ relationship: RO:0015016 PR:000001014 ! has low plasma membrane amount receptor- id: CL:0002111 name: CD38-negative unswitched memory B cell def: "An CD38-negative unswitched memory B cell is an unswitched memory B cell that has the phenotype CD38-negative, IgD-positive, CD138-negative, and IgG-negative." [GOC:dsd, GOC:rhs, GOC:tfm, PMID:20123131] +subset: human_subset +subset: mouse_subset synonym: "CD38- unswitched memory B cell" EXACT [] synonym: "CD38- unswitched memory B lymphocyte" EXACT [] synonym: "CD38- unswitched memory B-cell" EXACT [] @@ -16545,6 +18439,8 @@ relationship: CL:4030046 PR:000001408 ! lacks_plasma_membrane_part ADP-ribosyl c id: CL:0002112 name: B220-positive CD38-negative unswitched memory B cell def: "A B220-positive CD38-negative unswitched memory B cell is a CD38-negative unswitched memory B cell that has the phenotype B220-positive, CD38-negative, IgD-positive, CD138-negative, and IgG-negative." [GOC:dsd, GOC:rhs, GOC:tfm, PMID:20123131] +subset: human_subset +subset: mouse_subset is_a: CL:0002111 {is_inferred="true"} ! CD38-negative unswitched memory B cell intersection_of: CL:0002111 ! CD38-negative unswitched memory B cell intersection_of: RO:0002104 PR:000001014 ! has plasma membrane part receptor-type tyrosine-protein phosphatase C isoform CD45RABC @@ -16554,6 +18450,8 @@ relationship: RO:0002104 PR:000001014 ! has plasma membrane part receptor-type t id: CL:0002113 name: B220-low CD38-negative unswitched memory B cell def: "A B220-low CD38-negative unswitched memory B cell is a CD38-negative unswitched memory B cell that has the phenotype B220-low, CD38-negative, IgD-positive, CD138-negative, and IgG-negative." [GOC:dsd, GOC:rhs, GOC:tfm, PMID:20123131] +subset: human_subset +subset: mouse_subset is_a: CL:0002112 ! B220-positive CD38-negative unswitched memory B cell intersection_of: CL:0002111 ! CD38-negative unswitched memory B cell intersection_of: RO:0015016 PR:000001014 ! has low plasma membrane amount receptor-type tyrosine-protein phosphatase C isoform CD45RABC @@ -16563,6 +18461,8 @@ relationship: RO:0015016 PR:000001014 ! has low plasma membrane amount receptor- id: CL:0002114 name: CD38-positive unswitched memory B cell def: "A CD38-positive unswitched memory B cell is an unswitched memory B cell that has the phenotype CD38-positive, IgD-positive, CD138-negative, and IgG-negative." [GOC:dsd, GOC:rhs, GOC:tfm, PMID:20123131] +subset: human_subset +subset: mouse_subset synonym: "CD38+ unswitched memory B cell" EXACT [] synonym: "CD38+ unswitched memory B lymphocyte" EXACT [] synonym: "CD38+ unswitched memory B-cell" EXACT [] @@ -16579,6 +18479,8 @@ relationship: RO:0002104 PR:000001408 ! has plasma membrane part ADP-ribosyl cyc id: CL:0002115 name: B220-positive CD38-positive unswitched memory B cell def: "A B220-positive CD38-positive unswitched memory B cell is a CD38-positive unswitched memory B cell that has the phenotype B220-positive, CD38-positive, IgD-positive, CD138-negative, and IgG-negative." [GOC:dsd, GOC:rhs, GOC:tfm, PMID:20123131] +subset: human_subset +subset: mouse_subset is_a: CL:0002114 {is_inferred="true"} ! CD38-positive unswitched memory B cell intersection_of: CL:0002114 ! CD38-positive unswitched memory B cell intersection_of: RO:0002104 PR:000001014 ! has plasma membrane part receptor-type tyrosine-protein phosphatase C isoform CD45RABC @@ -16588,6 +18490,8 @@ relationship: RO:0002104 PR:000001014 ! has plasma membrane part receptor-type t id: CL:0002116 name: B220-low CD38-positive unswitched memory B cell def: "A B220-low CD38-positive unswitched memory B cell is a CD38-positive unswitched memory B cell that has the phenotype B220-low, CD38-positive, IgD-positive, CD138-negative, and IgG-negative." [GOC:dsd, GOC:rhs, GOC:tfm, PMID:20123131] +subset: human_subset +subset: mouse_subset is_a: CL:0002115 ! B220-positive CD38-positive unswitched memory B cell intersection_of: CL:0002114 ! CD38-positive unswitched memory B cell intersection_of: RO:0015016 PR:000001014 ! has low plasma membrane amount receptor-type tyrosine-protein phosphatase C isoform CD45RABC @@ -16598,6 +18502,8 @@ id: CL:0002117 name: IgG-negative class switched memory B cell def: "A class switched memory B cell that lacks IgG on the cell surface." [GOC:dsd, GOC:rhs, GOC:tfm, PMID:20123131] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "IgG- class switched memory B cell" EXACT [] synonym: "IgG- class switched memory B lymphocyte" EXACT [] synonym: "IgG- class switched memory B-cell" EXACT [] @@ -16614,6 +18520,8 @@ relationship: CL:4030046 GO:0071735 ! lacks_plasma_membrane_part IgG immunoglobu id: CL:0002118 name: CD38-negative IgG-negative class switched memory B cell def: "A CD38-negative IgG-negative memory B cell is a IgG-negative class switched memory B cell that lacks IgG on the cell surface with the phenotype CD38-negative and IgG-negative." [GOC:dsd, GOC:rhs, GOC:tfm, PMID:20123131] +subset: human_subset +subset: mouse_subset is_a: CL:0002117 {is_inferred="true"} ! IgG-negative class switched memory B cell intersection_of: CL:0002117 ! IgG-negative class switched memory B cell intersection_of: CL:4030046 PR:000001408 ! lacks_plasma_membrane_part ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1 @@ -16623,6 +18531,8 @@ relationship: CL:4030046 PR:000001408 ! lacks_plasma_membrane_part ADP-ribosyl c id: CL:0002119 name: CD38-positive IgG-negative class switched memory B cell def: "A CD38-positive IgG-negative memory B cell is an IgG-negative class switched memory B cell that lacks IgG on the cell surface with the phenotype CD38-positive and IgG-negative." [GOC:dsd, GOC:rhs, GOC:tfm, PMID:20123131] +subset: human_subset +subset: mouse_subset is_a: CL:0002117 {is_inferred="true"} ! IgG-negative class switched memory B cell intersection_of: CL:0002117 ! IgG-negative class switched memory B cell intersection_of: RO:0002104 PR:000001408 ! has plasma membrane part ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1 @@ -16632,6 +18542,8 @@ relationship: RO:0002104 PR:000001408 ! has plasma membrane part ADP-ribosyl cyc id: CL:0002120 name: CD24-positive CD38-negative IgG-negative class switched memory B cell def: "An CD24-positive CD38-negative IgG-negative memory B cell is a CD38-negative IgG-negative class switched memory B cell that lacks IgG on the cell surface with the phenotype CD24-positive, CD38-negative, and IgG-negative." [GOC:dsd, GOC:rhs, GOC:tfm, PMID:20123131] +subset: human_subset +subset: mouse_subset is_a: CL:0002118 {is_inferred="true"} ! CD38-negative IgG-negative class switched memory B cell intersection_of: CL:0002118 ! CD38-negative IgG-negative class switched memory B cell intersection_of: RO:0002104 PR:000001932 ! has plasma membrane part signal transducer CD24 @@ -16641,6 +18553,8 @@ relationship: RO:0002104 PR:000001932 ! has plasma membrane part signal transduc id: CL:0002121 name: CD24-negative CD38-negative IgG-negative class switched memory B cell def: "A CD24-negative CD38-negative IgG-negative memory B cell is a CD38-negative IgG-negative class switched memory B cell that lacks IgG on the cell surface with the phenotype CD24-negative, CD38-negative, and IgG-negative." [GOC:dsd, GOC:rhs, GOC:tfm, PMID:20123131] +subset: human_subset +subset: mouse_subset is_a: CL:0002118 {is_inferred="true"} ! CD38-negative IgG-negative class switched memory B cell intersection_of: CL:0002118 ! CD38-negative IgG-negative class switched memory B cell intersection_of: CL:4030046 PR:000001932 ! lacks_plasma_membrane_part signal transducer CD24 @@ -16650,6 +18564,8 @@ relationship: CL:4030046 PR:000001932 ! lacks_plasma_membrane_part signal transd id: CL:0002122 name: B220-positive CD38-positive IgG-negative class switched memory B cell def: "A B220-positive CD38-positive IgG-negative memory B cell is a CD38-positive IgG-negative class switched memory B cell that lacks IgG on the cell surface with the phenotype B220-positive, CD38-positive, and IgG-negative." [GOC:dsd, GOC:rhs, GOC:tfm, PMID:20123131] +subset: human_subset +subset: mouse_subset is_a: CL:0002119 {is_inferred="true"} ! CD38-positive IgG-negative class switched memory B cell intersection_of: CL:0002119 ! CD38-positive IgG-negative class switched memory B cell intersection_of: RO:0002104 PR:000001014 ! has plasma membrane part receptor-type tyrosine-protein phosphatase C isoform CD45RABC @@ -16659,6 +18575,8 @@ relationship: RO:0002104 PR:000001014 ! has plasma membrane part receptor-type t id: CL:0002123 name: B220-low CD38-positive IgG-negative class switched memory B cell def: "A B220-low CD38-positive IgG-negative memory B cell is a CD38-positive IgG-negative class switched memory B cell that lacks IgG on the cell surface with the phenotype B220-low, CD38-positive, and IgG-positive." [GOC:dsd, GOC:rhs, GOC:tfm, PMID:20123131] +subset: human_subset +subset: mouse_subset is_a: CL:0002122 ! B220-positive CD38-positive IgG-negative class switched memory B cell intersection_of: CL:0002119 ! CD38-positive IgG-negative class switched memory B cell intersection_of: RO:0015016 PR:000001014 ! has low plasma membrane amount receptor-type tyrosine-protein phosphatase C isoform CD45RABC @@ -16668,6 +18586,8 @@ relationship: RO:0015016 PR:000001014 ! has low plasma membrane amount receptor- id: CL:0002124 name: CD27-positive gamma-delta T cell def: "A circulating gamma-delta T cell that is CD27-positive and capable of producing IFN-gamma." [GOC:dsd, GOC:tfm, PMID:19270712] +subset: human_subset +subset: mouse_subset synonym: "gammadelta27-positive" EXACT [] synonym: "gd27-positive" EXACT [] is_a: CL:0000800 {is_inferred="true"} ! mature gamma-delta T cell @@ -16686,6 +18606,8 @@ creation_date: 2010-08-18T09:57:19Z id: CL:0002125 name: CD27-negative gamma-delta T cell def: "A circulating gamma-delta T cell that expresses RORgamma(t), is CD27-negative and is capable of IL-17 secretion." [GOC:dsd, GOC:tfm, PMID:19270712] +subset: human_subset +subset: mouse_subset synonym: "gammadelta-17 cells" EXACT [PMID:21976777] is_a: CL:0000800 {is_inferred="true"} ! mature gamma-delta T cell intersection_of: CL:0000800 ! mature gamma-delta T cell @@ -16705,6 +18627,8 @@ creation_date: 2010-08-18T09:57:29Z id: CL:0002126 name: CD25-positive, CD27-positive immature gamma-delta T cell def: "A CD25-positive, CD27-positive immature gamma-delta T cell found in the thymus that has an immature phenotype (i.e. CD24-high, CD25-high, CD62L-high, CD44-high, CD2-low, CD5-low)." [GOC:tfm, PMID:19270712] +subset: human_subset +subset: mouse_subset is_a: CL:0000799 {is_inferred="true"} ! immature gamma-delta T cell is_a: CL:0000893 ! thymocyte intersection_of: CL:0000799 ! immature gamma-delta T cell @@ -16730,6 +18654,8 @@ creation_date: 2010-08-18T10:35:37Z id: CL:0002127 name: innate effector T cell def: "A T cell with a receptor of limited diversity that is capable of immediate effector functions upon stimulation." [GOC:tfm, PMID:20581831] +subset: human_subset +subset: mouse_subset is_a: CL:0000911 {is_inferred="true"} ! effector T cell intersection_of: CL:0000911 ! effector T cell intersection_of: capable_of GO:0045087 ! innate immune response @@ -16742,6 +18668,8 @@ id: CL:0002128 name: Tc17 cell def: "A CD8-positive, alpha-beta T cell that has the phenotype CXCR3-negative, CCR6-positive, CCR5-high, CD45RA-negative, and capable of producing IL-17 and some IFNg." [GOC:add, GOC:dsd, GOC:tfm, PMID:19201830, PMID:22343568] comment: This cell type is compatible with the HIPC Lyoplate markers for 'Tc17 CD8+ T cell', but its logical definition includes additional known characteristics of Tc17 T cells. Found in the CD27-positive, CD28-positive or CD27-negative, CD28-positive fractions with the phenotype CCR4-negative and CCR7-negative (this sentence not part of definition). +subset: human_subset +subset: mouse_subset synonym: "CD8-positive Th17 cell" EXACT [] synonym: "Tc17 CD8+ T cell" EXACT [PMID:22343568] synonym: "Tc17 T cell" EXACT [] @@ -16766,19 +18694,25 @@ id: CL:0002129 name: regular atrial cardiac myocyte def: "Regular cardiac myocyte of a cardiac atrium." [GOC:tfm] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "atrial cardiac muscle cell" EXACT [GOC:pr] synonym: "atrial myocyte" EXACT [] synonym: "regular atrial cardiac muscle fiber" EXACT [] synonym: "regular cardiac muscle cell of atrium" EXACT [] xref: FMA:83108 +xref: https://cellxgene.cziscience.com/cellguide/CL_0002129 is_a: CL:0002098 ! regular cardiac myocyte property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nRegular atrial cardiac myocytes, also known as atrial myocytes, are specialized muscle cells found in the atria – the upper chambers of the heart. They contract and relax during the heart's cycle, modulating the pumping of blood through the atria and into the ventricles. Additionally, endowed with inherent rhythmic electrical activity, atrial myocytes contribute significantly to the initiation and propagation of the heart’s electrical impulses.\nA distinguishing feature that separates atrial myocytes from other cardiac myocytes is their ability to synthesize and secrete atrial natriuretic peptide (ANP) in response to atrial stretch or dilatation. ANP acts as a potent vasodilator and diuretic, helping to maintain blood pressure and volume homeostasis. The phenomena of atrial stretch or distension, which triggers ANP release, is often in response to excess blood volume entering the heart, providing a mechanism at the cellular level which actively regulates systemic cardiovascular balance.\nLike all cardiac myocytes, atrial myocytes are embedded in a dense network of connective tissue that provides structural support. These cells are characterized by a single, centrally located nucleus, and overall, have a rod-like appearance with branching ends that connect with adjacent cells to form a continuous, synchronized ensemble. Their cytoplasm is abundant with mitochondria, reflecting the high energy demand associated with constant contraction and relaxation. At the ultrastructural level, atrial myocytes display striations due to the regular arrangement of actin and myosin proteins, which facilitate the contraction process essential for the heart's pump function." xsd:string {xref="DOI:10.1016/j.bbamcr.2015.11.025", xref="DOI:10.1111/pace.14107", xref="DOI:10.1172/JCI25417", xref="https://www.sciencedirect.com/topics/agricultural-and-biological-sciences/cardiac-muscle", xref="https://www.sciencedirect.com/topics/neuroscience/cardiac-action-potential"} creation_date: 2010-08-23T11:41:03Z [Term] id: CL:0002130 name: regular interatrial cardiac myocyte def: "A cardiac myocyte of the interatrial region of the heart." [GOC:tfm] +subset: human_subset +subset: mouse_subset xref: FMA:228790 is_a: CL:0002098 ! regular cardiac myocyte property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 @@ -16789,6 +18723,8 @@ id: CL:0002131 name: regular ventricular cardiac myocyte def: "Regular cardiac myocyte of a cardiac ventricle." [GOC:tfm] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "regular cardiac muscle cell of ventricle" EXACT [] synonym: "regular ventricular cardiac muscle fiber" EXACT [] synonym: "ventricular cardiac muscle cell" BROAD [GOC:pr] @@ -16803,6 +18739,8 @@ id: CL:0002132 name: stromal cell of ovary def: "A stomal cell of the ovary" [GOC:tfm] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "ovarian stromal cell" EXACT [GOC:cjm] xref: FMA:72299 is_a: CL:0000499 ! stromal cell @@ -16816,6 +18754,8 @@ creation_date: 2010-08-23T12:10:31Z id: CL:0002133 name: stromal cell of ovarian cortex def: "A stromal cell of the ovarian cortex." [GOC:tfm] +subset: human_subset +subset: mouse_subset xref: FMA:256169 is_a: CL:0002132 ! stromal cell of ovary property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 @@ -16825,6 +18765,8 @@ creation_date: 2010-08-23T12:12:15Z id: CL:0002134 name: stromal cell of ovarian medulla def: "A stromal cell of the ovarian medulla." [GOC:tfm] +subset: human_subset +subset: mouse_subset xref: FMA:256171 is_a: CL:0002132 {is_inferred="true"} ! stromal cell of ovary intersection_of: CL:0000499 ! stromal cell @@ -16837,6 +18779,8 @@ creation_date: 2010-08-23T12:12:17Z id: CL:0002135 name: nonkeratinized cell of epidermis def: "Epidermal cells that do not contain keratin. Cell type is usually associated with moist epidermal tissues." [GO:tfm, PMID:1987287] +subset: human_subset +subset: mouse_subset xref: FMA:62880 is_a: CL:0000362 ! epidermal cell relationship: part_of UBERON:0001003 ! skin epidermis @@ -16847,6 +18791,8 @@ creation_date: 2010-08-24T08:43:27Z id: CL:0002136 name: type II cell of adrenal cortex def: "A cell in the zona fasciculata that produce glucocorticoids, e.g cortisol." [GOC:tfm, ISBN:0517223651] +subset: human_subset +subset: mouse_subset synonym: "type II cortical cell of adrenal gland" EXACT [] xref: FMA:69547 is_a: CL:0000460 ! glucocorticoid secreting cell @@ -16858,6 +18804,8 @@ creation_date: 2010-08-24T01:50:42Z id: CL:0002137 name: type III cell of adrenal cortex def: "A cell in the zona reticularis that produce sex hormones." [GOC:tfm, ISBN:0517223651] +subset: human_subset +subset: mouse_subset xref: FMA:69564 is_a: CL:0000593 ! androgen secreting cell is_a: CL:0002097 ! cortical cell of adrenal gland @@ -16871,10 +18819,13 @@ alt_id: CL:1000421 def: "A endothelial cell of a lymphatic vessel. The border of the oak leaf-shaped endothelial cell of initial lymphatics are joined by specialized buttons. The discontinuous feature of buttons distinguishes them from zippers in collecting lymphatics, but both types of junctions are composed of proteins typical of adherens junctions and tight junctions found in the endothelium of blood vessels. Buttons seal the sides of flaps of the oak leaf-shaped endothelial cell, leaving open the tips of flaps as routes for fluid entry without disassembly and reformation of intercellular junctions." [GOC:tfm, PMID:17846148] subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "LEC" EXACT [] synonym: "lymphatic endothelial cell" EXACT [] xref: BTO:0004167 xref: FMA:68458 +xref: https://cellxgene.cziscience.com/cellguide/CL_0002138 is_a: CL:0002139 {is_inferred="true"} ! endothelial cell of vascular tree intersection_of: CL:0000115 ! endothelial cell intersection_of: part_of UBERON:0001473 ! lymphatic vessel @@ -16882,6 +18833,7 @@ relationship: part_of UBERON:0001473 ! lymphatic vessel relationship: RO:0002202 CL:0005022 ! develops from vascular lymphangioblast property_value: RO:0002175 NCBITaxon:9606 property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nEndothelial cells of lymphatic vessels are specialized type of cells that form the interior lining of the lymphatic system, which primarily comprises the lymph vessels and nodes. These cells play a critical role in creating a barrier between the lymphatic system and the surrounding tissues. They are structurally different from the endothelial cells of the blood vessels due to the presence of anchoring filaments and lack of a continuous basement membrane, and have a unique phenotype marked by the expression of various cell-specific markers such as Prox-1, VEGFR-3, and LYVE-1.\nA significant function of these endothelial cells is to maintain the fluid balance within the body. They facilitate the uptake of excess interstitial fluid that collects in the body tissues, and ensure its transport back into the bloodstream via the lymphatic vessels. These cells also enable the absorption of fats and fat-soluble vitamins from the digestive system, and their subsequent transport in the form of chyle, a milky fluid, to the blood.\nFurthermore, endothelial cells of lymphatic vessels play a pivotal role in the body's immune response. They enable the passage of lymphocytes, that are crucial for the body's defense mechanism, from the tissues into the lymph where these cells are activated to fight against foreign bodies and infections. Also, they regulate inflammation reactions by controlling the migration of inflammatory cells, and are thus involved in pathological conditions with an inflammatory component. Lastly, these cells have been noted for their involvement in various disease states related to tissue edema, metastasis, and tumor growth, thus highlighting their importance in both health and disease states." xsd:string {xref="DOI:10.1016/j.it.2022.10.010", xref="DOI:10.1038/s41577-020-0281-x", xref="DOI:10.3389/fimmu.2019.00036", xref="DOI:10.3389/fphys.2020.00509/full", xref="DOI:10.3892/mco.2017.1356"} creation_date: 2010-08-24T02:05:28Z [Term] @@ -16890,27 +18842,33 @@ name: endothelial cell of vascular tree def: "An endothelial cell of the vascular tree, which includes blood vessels and lymphatic vessels." [GOC:dsd, GOC:tfm, PMID:12768659] comment: These cells are reportedly CD31-positive, CD34-positive, CD144-positive, TAL1-positive. subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "cubodial endothelial cell of vascular tree" NARROW [] synonym: "vascular endothelial cell" EXACT [] xref: BTO:0001854 xref: CALOHA:TS-1106 xref: FMA:67755 +xref: https://cellxgene.cziscience.com/cellguide/CL_0002139 is_a: CL:0000115 ! endothelial cell property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nEndothelial cells of the vascular tree, commonly referred to as vascular endothelial cells, line the entire circulatory system, from the heart to the smallest capillaries. These cells have a unique, flattened shape, and are tightly bound together, forming a thin layer known as the endothelium. The endothelium is responsible for maintaining the interior surface of blood vessels, and plays a critical role in ensuring the smooth flow of blood. \nVascular endothelial cells act as a semi-permeable membrane, controlling the passage of materials and the transit of white blood cells into and out of the bloodstream. These cells are also involved in blood coagulation. When a blood vessel is damaged, endothelial cells promote clotting to prevent excessive bleeding and facilitate wound healing. Other functions include regulation of blood pressure and blood volume by releasing vasodilators and vasoconstrictors to either widen or constrict blood vessels, accordingly.\nFurthermore, the endothelial cells are crucial in the formation of new blood vessels, a process known as angiogenesis. This is particularly important in wound healing and the growth of new tissues during development or after injury. In the context of diseases such as cancer, angiogenesis helps facilitate tumor growth by providing nutrients and oxygen." xsd:string {xref="DOI:10.1038/s41569-022-00770-1", xref="DOI:10.1186/s12872-015-0124-z", xref="DOI:10.3389/fphys.2022.863265/full", xref="https://www.sciencedirect.com/topics/medicine-and-dentistry/vascular-endothelial-cell"} creation_date: 2010-08-24T02:06:40Z [Term] id: CL:0002140 -name: acinar cell of sebaceous gland +name: skin sebocyte alt_id: CL:0002587 -def: "A sebum secreting cell of the skin that secretes sebum into the hair follicles." [GOC:tfm] -synonym: "sebocyte" BROAD [] +def: "An acinar cell that is part of a skin sebaceous gland. This cell produces and secretes sebum into hair follicles." [GOC:tfm, PMID:37205445] +subset: human_subset +subset: mouse_subset +synonym: "acinar cell of sebaceous gland" BROAD [] +synonym: "acinar cell of skin sebaceous gland" EXACT [] xref: BTO:0004613 xref: FMA:70953 -is_a: CL:0000317 {is_inferred="true"} ! sebum secreting cell +is_a: CL:0000317 {is_inferred="true"} ! sebocyte is_a: CL:0000622 ! acinar cell -is_a: CL:1000448 ! epithelial cell of sweat gland -intersection_of: CL:0000317 ! sebum secreting cell +intersection_of: CL:0000622 ! acinar cell intersection_of: part_of UBERON:0003487 ! skin sebaceous gland relationship: part_of UBERON:0003487 ! skin sebaceous gland property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 @@ -16920,6 +18878,8 @@ creation_date: 2010-08-24T09:27:52Z id: CL:0002141 name: active chief cell of parathyroid gland def: "A parathyroid chief cell that is actively secreting hormone. Have large Golgi complexes with numerous vesicles and small membrane-bound granules; secretory granules are rare, cytoplasmic glycogen sparse, much of the cytoplasm being occupied by flat sacs of granular endoplasmic reticulum in parallel arrays; in normal humans, inactive chief cells outnumber active chief cells in a ratio of 3-5:1" [FMA:0517223651, GOC:tfm] +subset: human_subset +subset: mouse_subset xref: FMA:69082 is_a: CL:0000446 ! chief cell of parathyroid gland property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 @@ -16929,6 +18889,8 @@ creation_date: 2010-08-24T09:30:15Z id: CL:0002142 name: dark cell of eccrine sweat gland def: "A cell pyramidal in shape, with their broad ends facing and forming the greater extent of the lining of the main lumen. Secretes glycoproteins associated with mucus." [ISBN:0517223651] +subset: human_subset +subset: mouse_subset xref: FMA:70659 is_a: CL:0000152 ! exocrine cell is_a: CL:0000318 ! sweat secreting cell @@ -16942,6 +18904,8 @@ creation_date: 2010-08-24T02:15:16Z id: CL:0002143 name: dark chief cell of parathyroid gland def: "A chief cell that is smaller than light chief cells and has a smaller and darker nucleus and a finely granular cytoplasm with many granules." [GOC:tfm, ISBN:0721662544] +subset: human_subset +subset: mouse_subset xref: FMA:69080 is_a: CL:0000446 ! chief cell of parathyroid gland property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 @@ -16953,6 +18917,8 @@ name: capillary endothelial cell def: "An endothelial cell found in capillaries." [GOC:tfm] subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset xref: BTO:0004956 xref: CALOHA:TS-0112 xref: FMA:67756 @@ -16967,26 +18933,35 @@ creation_date: 2010-08-24T10:15:00Z [Term] id: CL:0002145 -name: ciliated columnar cell of tracheobronchial tree +name: multiciliated columnar cell of tracheobronchial tree def: "A multi-ciliated epithelial cell located in the trachea and bronchi, characterized by a columnar shape and motile cilia on its apical surface. These cilia facilitate mucociliary clearance by moving mucus and trapped particles toward the pharynx." [GOC:tfm, PMID:28400610] -comment: These cells possess numerous cilia on their surface, typically ranging from 200 to 300 per cell. The cilia vary in length, measuring between 6 to 7 μm in the upper airways (trachea) and becoming shorter, around 4 μm, in the smaller airways (terminal bronchioles). These cells form a two-layered 'coat' in the airway: the lower 'sol' layer is watery, allowing the cilia to beat in coordinated waves, while the upper 'gel' layer is thick and sticky, trapping inhaled particles. {xref="PMID:25386990", xref="https://doi.org/10.1016/B978-032304048-8.50071-2"} +comment: The marker set C1orf194, MS4A8 can identify the Human cell type ciliated columnar cell of tracheobronchial tree in the Lung with a confidence of 0.86 (NS-Forest FBeta value). These cells possess numerous cilia on their surface, typically ranging from 200 to 300 per cell. The cilia vary in length, measuring between 6 to 7 μm in the upper airways (trachea) and becoming shorter, around 4 μm, in the smaller airways (terminal bronchioles). These cells form a two-layered 'coat' in the airway: the lower 'sol' layer is watery, allowing the cilia to beat in coordinated waves, while the upper 'gel' layer is thick and sticky, trapping inhaled particles. {xref="https://doi.org/10.5281/zenodo.11165918", xref="PMID:25386990", xref="https://doi.org/10.1016/B978-032304048-8.50071-2"} subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset +synonym: "ciliated columnar cell of tracheobronchial tree" EXACT [] xref: FMA:70542 xref: https://cellxgene.cziscience.com/cellguide/CL_0002145 is_a: CL:0002202 ! epithelial cell of tracheobronchial tree -is_a: CL:0005012 ! multi-ciliated epithelial cell -is_a: CL:4030034 ! respiratory ciliated cell +is_a: CL:4030034 ! respiratory tract multiciliated cell +intersection_of: CL:0000075 ! columnar/cuboidal epithelial cell +intersection_of: bearer_of PATO:0010007 ! multiciliated +intersection_of: has_part GO:0031514 ! motile cilium +intersection_of: part_of UBERON:0008397 ! tracheobronchial epithelium relationship: RO:0002202 CL:0002209 ! develops from intermediate epitheliocyte +relationship: RO:0015004 CLM:1000041 ! has characterizing marker set NS forest marker set of ciliated columnar cell of tracheobronchial tree (Human Lung). property_value: RO:0002175 NCBITaxon:9606 property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 -property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional.\n\nCiliated columnar cells of the tracheobronchial tree compose the inner lining of the tracheobronchial tree, the system of airways consisting of trachea, bronchi and bronchioles that allow passage of air into the lungs, where gas exchange occurs. A defining feature of these endo-epithelial cells are the tiny hair-like structures covering their surface, known as cilia. The nucleus is located at the base of the cell, and the area above it is rich in mitochondria and well-developed endoplasmic reticulum, both crucial for the energy-intensive process of cilia operation.\nThe primary function of these ciliated cells is to keep the respiratory tract clean via mucociliary clearance or the respiratory escalator. These cells create a two-layered 'coat': The lower \"sol\" layer is watery where the cilia can beat in coordinated waves, and the upper \"gel\" layer is thick and sticky, trapping inhaled particles, such as dust, bacteria, viruses, and other potentially harmful substances. This rhythmical beating of the cilia then moves the mucus and trapped particles upwards and out of the respiratory tract, which is then either coughed out or swallowed.\nDamage or dysfunction of these ciliated cells, as seen in diseases such as primary ciliary dyskinesia, cystic fibrosis, or chronic bronchitis, may lead to reduced or ineffective mucociliary clearance and an increased susceptibility to respiratory infections." xsd:string {xref="DOI:10.1101/cshperspect.a028241", xref="DOI:10.1146/annurev-physiol-021014-071931", xref="DOI:10.1152/ajplung.00329.2019", xref="DOI:10.1159/000196486"} +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nCiliated columnar cells of the tracheobronchial tree compose the inner lining of the tracheobronchial tree, the system of airways consisting of trachea, bronchi and bronchioles that allow passage of air into the lungs, where gas exchange occurs. A defining feature of these endo-epithelial cells are the tiny hair-like structures covering their surface, known as cilia. The nucleus is located at the base of the cell, and the area above it is rich in mitochondria and well-developed endoplasmic reticulum, both crucial for the energy-intensive process of cilia operation.\nThe primary function of these ciliated cells is to keep the respiratory tract clean via mucociliary clearance or the respiratory escalator. These cells create a two-layered 'coat': The lower \"sol\" layer is watery where the cilia can beat in coordinated waves, and the upper \"gel\" layer is thick and sticky, trapping inhaled particles, such as dust, bacteria, viruses, and other potentially harmful substances. This rhythmical beating of the cilia then moves the mucus and trapped particles upwards and out of the respiratory tract, which is then either coughed out or swallowed.\nDamage or dysfunction of these ciliated cells, as seen in diseases such as primary ciliary dyskinesia, cystic fibrosis, or chronic bronchitis, may lead to reduced or ineffective mucociliary clearance and an increased susceptibility to respiratory infections." xsd:string {xref="DOI:10.1101/cshperspect.a028241", xref="DOI:10.1146/annurev-physiol-021014-071931", xref="DOI:10.1152/ajplung.00329.2019", xref="DOI:10.1159/000196486"} creation_date: 2010-08-24T03:38:29Z [Term] id: CL:0002146 name: clear cell of eccrine sweat gland def: "A sweat producing cell of eccrine sweat glands. Pyramidal in shape, with its base resting on the basal lamina or myoepitheliocytes, and its microvillus-covered apical plasma membrane line up the intercellular canaliculi. Cell is not stained by hematoxylin or eosin." [GOC:tfm, ISBN:0517223651] +subset: human_subset +subset: mouse_subset xref: FMA:70658 is_a: CL:0000152 ! exocrine cell is_a: CL:0000318 ! sweat secreting cell @@ -17000,6 +18975,8 @@ creation_date: 2010-08-24T10:33:02Z id: CL:0002147 name: clear chief cell of parathyroid gland def: "A chief cell of parathyroid glands that does not stain with hematoxylin or eosin. This cell is larger, has a larger nucleus and fewer secretory granules than dark chief cells." [GOC:tfm, ISBN:0618947256] +subset: human_subset +subset: mouse_subset synonym: "clear chief cell of parathyroid cell" EXACT [] xref: FMA:69081 is_a: CL:0000446 ! chief cell of parathyroid gland @@ -17010,6 +18987,8 @@ creation_date: 2010-08-24T10:39:42Z id: CL:0002148 name: dental pulp cell def: "A cell found within the dental pulp." [GOC:tfm, PMID:36267574] +subset: human_subset +subset: mouse_subset xref: CALOHA:TS-0195 xref: FMA:87170 is_a: CL:0002159 ! general ecto-epithelial cell @@ -17026,6 +19005,8 @@ name: epithelial cell of uterus alt_id: CL:1000294 def: "An epithelial cell of the uterus. This cell has a mesodermal origin." [GOC:tfm, PMID:11331626, PMID:16960017, PMID:21698266] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset xref: FMA:256161 is_a: CL:0002078 ! meso-epithelial cell intersection_of: CL:0000066 ! epithelial cell @@ -17038,6 +19019,8 @@ creation_date: 2010-08-24T10:45:54Z id: CL:0002150 name: epithelioid macrophage def: "Epithelioid macrophage is an activated macrophage that resembles an epithelial cell with finely granular, pale eosinophilic cytoplasm and central, ovoid nucleus (oval or elongate). This cell type is able to merge into one another to form aggregates. The presence of such aggregates may characterize some pathologic conditions, mainly granulomatous inflammation." [MESH:D015622, PMID:12673090] +subset: human_subset +subset: mouse_subset synonym: "epithelioid cell" BROAD [] synonym: "epithelioid histocyte" EXACT [MESH:D015622, PMID:12673090] synonym: "epitheloid macrophage" EXACT [] @@ -17052,6 +19035,8 @@ id: CL:0002151 name: late promyelocyte def: "A promyelocyte that is considerably smaller, with more condensed chromatin, and nucleoli are no longer conspicuous." [ISBN:0412046911] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset xref: FMA:83534 is_a: CL:0000836 ! promyelocyte property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 @@ -17061,6 +19046,8 @@ creation_date: 2010-08-24T03:07:50Z id: CL:0002152 name: columnar cell of endocervix def: "A simple columnar epithelial cell located in the endocervix." [doi:/10.1016/j.autneu.2015.04.008, GOC:tfm, ISBN:0721662544] +subset: human_subset +subset: mouse_subset xref: FMA:86486 is_a: CL:0000146 ! simple columnar epithelial cell is_a: CL:0002535 ! epithelial cell of cervix @@ -17075,6 +19062,8 @@ id: CL:0002153 name: corneocyte def: "The dead keratin-filled squamous cell of the stratum corneum. This cell type lacks a nucleus." [GOC:tfm, ISBN:068340007X] subset: human_reference_atlas +subset: human_subset +subset: mouse_subset xref: BTO:0001943 xref: FMA:68650 is_a: BFO:0000002 @@ -17092,6 +19081,8 @@ id: CL:0002154 name: early promyelocyte def: "A promyelocyte with a nucleus that is indented and contains more marginated heterochromatin compared to its precursor cell (myeloblast); cytoplasm is deeply basophilic and contains numerous mitochondria and meandering cysternae of endoplasmic reticulum; largest of the granulocyte lineages." [FMA:0412046911, GOC:tfm] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset xref: FMA:83533 is_a: CL:0000836 ! promyelocyte property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 @@ -17101,6 +19092,8 @@ creation_date: 2010-08-24T03:07:53Z id: CL:0002155 name: echinocyte def: "A crenated erythrocyte with 30+ crenations, bumps or spurs that are the result of damage due to age or disease." [GOC:tfm] +subset: human_subset +subset: mouse_subset synonym: "burr cell" EXACT [] xref: FMA:81099 is_a: CL:0000595 ! enucleate erythrocyte @@ -17112,17 +19105,23 @@ id: CL:0002157 name: endosteal cell def: "A cell type that makes up the highly vascular membrane lining the marrow cavity of long bones." [FMA:0618947256, GOC:tfm] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset xref: FMA:86495 +xref: https://cellxgene.cziscience.com/cellguide/CL_0002157 is_a: CL:0001035 ! bone cell is_a: CL:0002078 ! meso-epithelial cell relationship: part_of UBERON:0009859 ! endosteum property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nEndosteal cells, also known as osteogenic cells, are a specialized type of cell that resides in the endosteum of the bone marrow cavity. The endosteum is a thin vascular membrane of connective tissue that lines the inner surface of the bony tissue that forms the medullary cavity of long bones. This specific location assigns endosteal cells critical roles in the bone maintenance and regeneration process as they actively participate in bone remodeling, a process that involves both the formation and resorption of bone tissue.\nEndosteal cells function by regulating the activity of both osteoblasts and osteoclasts. Osteoblasts are cells that deposit new bone, and osteoclasts are responsible for bone resorption, a process important for the maintenance, repair, and remodelling of bones. When new bone tissue is required, such as in instances of bone fractures or increased mechanical stress, endosteal cells differentiate into osteoblasts to facilitate the bone formation process. Conversely, when bone resorption is necessary, these cells are known to release signals that lead to the recruitment and activation of osteoclasts.\nIn addition to this, endosteal cells play a significant role in hematopoiesis, which is the formation of blood cellular components. They function in this process by providing a niche for hematopoietic stem cells, serving to support their maintenance and differentiation. Understanding the functionality of endosteal cells is important in the field of regenerative medicine and stem cell therapy, especially in diseases affecting bone remodeling and hematopoiesis." xsd:string {xref="DOI:10.1038/leu.2010.214", xref="DOI:10.1126/science.75570", xref="DOI:10.1182/blood-2004-06-2480", xref="DOI:10.1182/blood-2009-08-239194", xref="https://www.sciencedirect.com/topics/engineering/endosteum"} creation_date: 2010-08-24T03:33:58Z [Term] id: CL:0002158 name: external epithelial cell of tympanic membrane def: "Epithelial cell found on the external side of the tympanic membrane" [GOC:tfm, PMID:5686391] +subset: human_subset +subset: mouse_subset xref: FMA:70558 is_a: CL:0002159 ! general ecto-epithelial cell property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 @@ -17132,6 +19131,8 @@ creation_date: 2010-08-25T10:25:31Z id: CL:0002159 name: general ecto-epithelial cell def: "Epithelial cells derived from general body ectoderm and ectoderm placodes." [GOC:tfm] +subset: human_subset +subset: mouse_subset xref: FMA:70556 is_a: CL:0002077 ! ecto-epithelial cell property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 @@ -17141,6 +19142,8 @@ creation_date: 2010-08-26T08:31:08Z id: CL:0002160 name: basal external epithelial cell of tympanic membrane def: "A cell type found in the basal epithelial layer on the external side of the tympanic membrane. Cell type is flattened with intracellular spaces of variable dimensions." [PMID:5686391] +subset: human_subset +subset: mouse_subset is_a: CL:0002158 ! external epithelial cell of tympanic membrane property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-08-25T10:28:44Z @@ -17149,6 +19152,8 @@ creation_date: 2010-08-25T10:28:44Z id: CL:0002161 name: superficial external epithelial cell of tympanic membrane def: "A cell type found on the superficial layer of the external side of the tympanic membrane. This cell-type lacks a nucleus." [PMID:5686391] +subset: human_subset +subset: mouse_subset is_a: CL:0002158 ! external epithelial cell of tympanic membrane property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-08-25T10:28:48Z @@ -17157,6 +19162,8 @@ creation_date: 2010-08-25T10:28:48Z id: CL:0002162 name: internal epithelial cell of tympanic membrane def: "An extremely flattened cell type found on the inner side of the tympanic membrane. The surface of this cell type carries sparse pleomorphic microvilli that are more common near the junctional zones." [FMA:5686391, GOC:tfm] +subset: human_subset +subset: mouse_subset xref: FMA:70626 is_a: CL:0002076 ! endo-epithelial cell relationship: part_of UBERON:0002364 ! tympanic membrane @@ -17167,6 +19174,8 @@ creation_date: 2010-08-25T10:49:46Z id: CL:0002163 name: internal pillar cell of cochlea def: "A rod-shpaed cell that forms a single row adjacent to and supporting the inner hair cells." [GOC:tfm, http://www.theodora.com/anatomy/the_internal_ear_or_labyrinth.html] +subset: human_subset +subset: mouse_subset xref: FMA:75726 is_a: CL:1000191 ! pillar cell property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 @@ -17176,6 +19185,8 @@ creation_date: 2010-08-25T11:05:21Z id: CL:0002164 name: external pillar cell of cochlea def: "A rod-shaped cell found in 3 or 4 rows that lie adjacent to and support the outer hair cells." [GOC:tfm, http://www.theodora.com/anatomy/the_internal_ear_or_labyrinth.html] +subset: human_subset +subset: mouse_subset xref: FMA:75727 is_a: CL:1000191 ! pillar cell property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 @@ -17185,6 +19196,8 @@ creation_date: 2010-08-25T11:05:23Z id: CL:0002165 name: phalangeal cell def: "A supporting cell that is attached to the basement membrane and forms rows that support the hair cells." [GOC:tfm, ISBN:0618947256] +subset: human_subset +subset: mouse_subset xref: FMA:79800 is_a: CL:0002490 ! organ of Corti supporting cell property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 @@ -17194,11 +19207,12 @@ creation_date: 2010-08-25T01:29:07Z id: CL:0002166 name: epithelial cell of Malassez def: "An epithelial cell that remains from the disintegration of the epithelial root sheath involved in the development of teeth." [GOC:tfm, ISBN:0517223651, ISBN:0815129521] +subset: human_subset +subset: mouse_subset synonym: "epithelial cell rests of Malassez" EXACT [] synonym: "epithelial debris of Malassez" EXACT [] xref: FMA:62987 is_a: CL:0002159 {is_inferred="true"} ! general ecto-epithelial cell -is_a: CL:0002251 ! epithelial cell of alimentary canal relationship: part_of UBERON:0011595 ! jaw region property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-08-26T08:51:27Z @@ -17207,6 +19221,9 @@ creation_date: 2010-08-26T08:51:27Z id: CL:0002167 name: olfactory epithelial cell def: "A specialized cell involved in sensory perception of smell." [GOC:tfm, PMID:7143026] +subset: cellxgene_subset +subset: human_subset +subset: mouse_subset xref: FMA:67870 is_a: CL:0000098 ! sensory epithelial cell is_a: CL:0000206 ! chemoreceptor cell @@ -17221,6 +19238,8 @@ creation_date: 2010-08-26T01:47:13Z id: CL:0002168 name: border cell of cochlea def: "A border cell is a slender columnar cell on the medial portion of the basilar membrane." [FMA:0412046911, GOC:tfm] +subset: human_subset +subset: mouse_subset xref: FMA:79798 is_a: CL:0002315 ! supporting cell of cochlea property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 @@ -17231,6 +19250,8 @@ id: CL:0002169 name: basal cell of olfactory epithelium alt_id: CL:1000395 def: "An epithelial cell located on the basal lamina of the olfactory epithelium." [GOC:tfm, PMID:7143026] +subset: human_subset +subset: mouse_subset synonym: "horizontal basal cell" BROAD [] xref: FMA:62303 is_a: CL:0002167 {is_inferred="true"} ! olfactory epithelial cell @@ -17246,8 +19267,9 @@ creation_date: 2010-08-26T01:58:54Z id: CL:0002170 name: keratinized cell of the oral mucosa def: "A keratinized cell located in the hard palate or gingiva." [GOC:tfm, PMID:12014572] +subset: human_subset +subset: mouse_subset is_a: CL:0000237 ! keratinizing barrier epithelial cell -is_a: CL:0002251 ! epithelial cell of alimentary canal is_a: CL:0002336 ! buccal mucosa cell intersection_of: CL:0000237 ! keratinizing barrier epithelial cell intersection_of: part_of UBERON:0003729 ! mouth mucosa @@ -17259,6 +19281,8 @@ creation_date: 2010-08-26T02:51:30Z id: CL:0002171 name: globose cell of olfactory epithelium def: "A rounded or elliptical epithelial cell, with pale-staining open face nucleus and pale cytoplasm rich in free ribosomes and clusters of centrioles; form a distinct basal zone spaced slightly from the basal surface of the epithelium." [GOC:tfm, PMID:17468753] +subset: human_subset +subset: mouse_subset synonym: "blastema cell of olfactory epithelium" EXACT [] xref: FMA:67874 is_a: CL:0002169 ! basal cell of olfactory epithelium @@ -17269,6 +19293,8 @@ creation_date: 2010-08-26T01:59:18Z id: CL:0002172 name: interdental cell of cochlea def: "A long, spindle-shaped supporting cells arranged in parallel rows that secretes components of the tectorial membrane and potassium ions into the endolymph." [GOC:tfm, MP:0004482, PMID:2111803] +subset: human_subset +subset: mouse_subset synonym: "interdental cell" EXACT [] xref: FMA:79797 is_a: CL:0002315 ! supporting cell of cochlea @@ -17280,6 +19306,8 @@ creation_date: 2010-08-25T02:02:48Z id: CL:0002173 name: extraglomerular mesangial cell def: "A cell that is a specialized type of pericyte providing structural support for the capillary loops of kidney. A flat, elongated cell with extensive fine cytoplasmic processes found outside the kidney glomerulus near the macula densa and bound laterally by afferent and efferent arterioles. Being phagocytic, this cell participates in the continuous turnover of the basal lamina by removing its outer portion containing residues of filtration, while the lamina is renewed on its inner surface by the endothelial cells." [GOC:tfm, http:/www.copewithcytokines.de/cope.cgi?key=Lacis%20cells, ISBN:0412046911] +subset: human_subset +subset: mouse_subset synonym: "Goormaghtigh cell" EXACT [] synonym: "lacis cell" RELATED [] synonym: "polar cushion cells" EXACT [] @@ -17298,6 +19326,8 @@ creation_date: 2010-08-25T02:20:55Z id: CL:0002174 name: follicular cell of ovary def: "A cell within the follicle of an ovary." [GOC:tfm] +subset: human_subset +subset: mouse_subset xref: EMAPA:31247 xref: FMA:70589 is_a: CL:0000500 ! follicular epithelial cell @@ -17312,6 +19342,8 @@ creation_date: 2010-08-25T03:01:27Z id: CL:0002175 name: primary follicular cell of ovary def: "A cell within the primary follicle of the ovary." [GOC:tfm] +subset: human_subset +subset: mouse_subset xref: FMA:70590 is_a: CL:0002174 ! follicular cell of ovary property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 @@ -17321,6 +19353,8 @@ creation_date: 2010-08-25T03:03:42Z id: CL:0002176 name: secondary follicular cell of ovary def: "A cell of a secondary follicile within the ovary." [GOC:tfm] +subset: human_subset +subset: mouse_subset xref: FMA:70591 is_a: CL:0002174 ! follicular cell of ovary property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 @@ -17330,6 +19364,8 @@ creation_date: 2010-08-25T03:03:48Z id: CL:0002177 name: folliculostellate cell of pars distalis of adenohypophysis def: "A supporting cell of the anterior pituitary gland involved in trophic and catabolic processes; expresses a broad spectrum of cytokeratins indicative of their epithelial nature." [GOC:tfm] +subset: human_subset +subset: mouse_subset synonym: "folliculostellate cell of pars anterior of adenohypophysis" EXACT [] xref: FMA:83102 is_a: CL:0000642 {is_inferred="true"} ! folliculostellate cell @@ -17345,21 +19381,28 @@ id: CL:0002178 name: epithelial cell of stomach alt_id: CL:1000399 def: "An epithelial cell found in the lining of the stomach." [GOC:tfm] +subset: human_subset +subset: mouse_subset xref: FMA:62948 is_a: CL:0002251 {is_inferred="true"} ! epithelial cell of alimentary canal intersection_of: CL:0000066 ! epithelial cell -intersection_of: part_of UBERON:0000945 ! stomach -relationship: part_of UBERON:0000945 ! stomach +intersection_of: part_of UBERON:0001276 ! epithelium of stomach +relationship: part_of UBERON:0001276 ! epithelium of stomach property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-08-25T03:22:08Z [Term] id: CL:0002179 name: foveolar cell of stomach -def: "An epithelial cell within one of the pits in the embryonic gastric mucosa from which the gastric glands develop ." [GOC:tfm, http://www.merriam-webster.com/medical/foveolar] +def: "A simple columnar cell that populates the entire luminal surface including the gastric pits. This cell types secrete mucus to form a thick protective, lubricant layer over the gastric wall." [GOC:tfm, ISBN:0517223651, Wikipedia:Foveolar_cell] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset +synonym: "surface mucosal cell of stomach" EXACT [] +xref: FMA:62949 xref: FMA:86552 -is_a: CL:0002178 ! epithelial cell of stomach +is_a: CL:0000075 ! columnar/cuboidal epithelial cell +is_a: CL:0002180 ! mucous cell of stomach property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-08-25T03:23:22Z @@ -17368,12 +19411,15 @@ id: CL:0002180 name: mucous cell of stomach alt_id: CL:1000404 def: "An epithelial cell of the stomach. This cell produces mucous." [GOC:tfm] +subset: human_subset +subset: mouse_subset xref: FMA:63464 is_a: CL:0000319 ! mucus secreting cell -is_a: CL:0002659 ! glandular epithelial cell of stomach +is_a: CL:0002178 ! epithelial cell of stomach +is_a: CL:1100001 ! secretory epithelial cell intersection_of: CL:0000066 ! epithelial cell intersection_of: capable_of GO:0070254 ! mucus secretion -intersection_of: part_of UBERON:0000945 ! stomach +intersection_of: part_of UBERON:0001276 ! epithelium of stomach property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-08-25T03:38:51Z @@ -17382,11 +19428,14 @@ id: CL:0002181 name: mucous neck cell of gastric gland alt_id: CL:1000401 def: "A neck cell that secretes mucus within the stomach. Its products are distinct histochemically from those of the surface mucous cells of stomach." [GOC:tfm, ISBN:0517223651] +subset: human_subset +subset: mouse_subset synonym: "mucus neck cell of gastric gland" EXACT [] xref: FMA:62954 is_a: CL:0000152 ! exocrine cell is_a: CL:0000651 ! mucous neck cell is_a: CL:0002180 ! mucous cell of stomach +is_a: CL:0002659 ! glandular epithelial cell of stomach intersection_of: CL:0000651 ! mucous neck cell intersection_of: part_of UBERON:0000325 ! gastric gland relationship: part_of UBERON:0000325 ! gastric gland @@ -17395,13 +19444,13 @@ creation_date: 2010-08-25T03:41:30Z [Term] id: CL:0002182 -name: surface mucosal cell of stomach -def: "A simple columnar cell that populates the entire luminal surface including the gastric pits. This cell types secrete mucus to form a thick protective, lubricant layer over the gastric wall." [GOC:tfm, ISBN:0517223651] +name: obsolete surface mucosal cell of stomach +def: "OBSOLETE. A simple columnar cell that populates the entire luminal surface including the gastric pits. This cell types secrete mucus to form a thick protective, lubricant layer over the gastric wall." [GOC:tfm, ISBN:0517223651] +comment: Duplicate with foveolar cell of stomach xref: FMA:62949 -is_a: CL:0000075 ! columnar/cuboidal epithelial cell -is_a: CL:0002180 ! mucous cell of stomach -relationship: part_of UBERON:0001276 ! epithelium of stomach property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 +is_obsolete: true +replaced_by: CL:0002179 creation_date: 2010-08-25T03:45:10Z [Term] @@ -17409,6 +19458,8 @@ id: CL:0002183 name: stem cell of gastric gland alt_id: CL:1000400 def: "A stomach epithelial cell that is olumnar in form with a few short apical microvilli; relatively undifferentiated mitotic cell from which other types of gland are derived; few in number, situated in the isthmus region of the gland and base of the gastric pit." [GOC:tfm, ISBN:0517223651] +subset: human_subset +subset: mouse_subset xref: FMA:62953 is_a: CL:0000048 {is_inferred="true"} ! multi fate stem cell is_a: CL:0002178 ! epithelial cell of stomach @@ -17422,6 +19473,8 @@ creation_date: 2010-08-25T03:57:08Z id: CL:0002184 name: basal proper cell of olfactory epithelium def: "A flat or angular epithelial cell with condensed nuclei and darkly staining cytoplasm containing numerous intermediate filaments inserted into desmosomes contacting surrounding supporting cells; lie in contact with the basal lamina of olfactory epithelium." [GOC:tfm, PMID:0517223651, PMID:11891623] +subset: human_subset +subset: mouse_subset synonym: "horizontal basal cells" EXACT [] xref: FMA:62304 is_a: CL:0002169 ! basal cell of olfactory epithelium @@ -17434,6 +19487,8 @@ name: basal cell of epidermis alt_id: CL:1000439 def: "A basally situated, mitotically active, columnar-shaped keratinocyte attached to the basement membrane." [GOC:tfm, ISBN:0517223651] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset xref: FMA:70571 is_a: CL:0000312 ! keratinocyte is_a: CL:0000646 {is_inferred="true"} ! basal cell @@ -17450,12 +19505,13 @@ name: glomerular endothelial cell def: "An endothelial cell that is part of the glomerulus of the kidney. This cell is flattened, highly fenestrated, and plays a vital role in the formation of glomerular ultrafiltrate." [GOC:tfm, PMID:15840009] comment: Glomerular endothelial cells have 60-80 nm fenestrations typically lacking diaphragms in adults but present during embryonic development. Some studies found diaphragms in 2-6% of mature rat glomerular capillaries. Their presence may depend on fixation techniques, developmental stage, or dynamic cell changes. Additionally, these cells help maintain the structural integrity of glomerular capillaries through interactions with the basement membrane and podocytes. {xref="PMID:33123011", xref="PMID:18480313", xref="PMID:19129259"} subset: cellxgene_subset +subset: human_subset subset: kidney_upper_slim +subset: mouse_subset xref: BTO:0004632 xref: FMA:70970 is_a: CL:0000666 ! fenestrated endothelial cell is_a: CL:0002681 ! kidney cortical cell -is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000115 ! endothelial cell intersection_of: part_of UBERON:0000074 ! renal glomerulus relationship: has_part GO:0036053 ! glomerular endothelium fenestra @@ -17468,6 +19524,8 @@ id: CL:0002189 name: granular cell of epidermis def: "A keratinocyte of the epidermis that is characterized by containing granules of keratohyalin and lamellar granules." [ISBN:1416031855] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset xref: FMA:70543 is_a: CL:0000312 ! keratinocyte property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 @@ -17477,6 +19535,8 @@ creation_date: 2010-08-26T03:19:00Z id: CL:0002190 name: squamous cell of epidermis def: "A flat keratinocyte immediately below the cornified layer." [GOC:tfm, ISBN:0517223651] +subset: human_subset +subset: mouse_subset xref: FMA:86925 is_a: CL:0000312 ! keratinocyte property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 @@ -17487,6 +19547,8 @@ id: CL:0002191 name: granulocytopoietic cell def: "A cell involved in the formation of a granulocyte." [GOC:tfm] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset xref: FMA:83519 is_a: CL:0000839 {is_inferred="true"} ! myeloid lineage restricted progenitor cell intersection_of: CL:0000839 ! myeloid lineage restricted progenitor cell @@ -17499,6 +19561,8 @@ creation_date: 2010-08-30T12:54:27Z id: CL:0002192 name: metamyelocyte def: "A eosinophil precursor in the granulocytic series, being a cell intermediate in development between a myelocyte and a band form cell. The nucleus becomes indented where the indentation is smaller than half the distance to the farthest nuclear margin; chromatin becomes coarse and clumped; specific granules predominate while primary granules are rare." [GOC:tfm, http://en.wikipedia.org/wiki/Metamyelocyte, ISBN:0721601464] +subset: human_subset +subset: mouse_subset xref: FMA:83541 is_a: CL:0000763 ! myeloid cell is_a: CL:0002191 ! granulocytopoietic cell @@ -17512,6 +19576,8 @@ name: myelocyte def: "A cell type that is the first of the maturation stages of the granulocytic leukocytes normally found in the bone marrow. Granules are seen in the cytoplasm. The nuclear material of the myelocyte is denser than that of the myeloblast but lacks a definable membrane. The cell is flat and contains increasing numbers of granules as maturation progresses." [GOC:tfm, http://en.wikipedia.org/wiki/Myelocyte, ISBN:0323052908] subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset xref: BTO:0000734 xref: FMA:83525 is_a: CL:0000763 ! myeloid cell @@ -17525,6 +19591,8 @@ creation_date: 2010-08-30T01:08:19Z id: CL:0002194 name: monopoietic cell def: "A cell involved in the formation of a monocyte (monopoiesis)." [GOC:tfm] +subset: human_subset +subset: mouse_subset xref: FMA:83552 is_a: CL:0000839 {is_inferred="true"} ! myeloid lineage restricted progenitor cell intersection_of: CL:0000839 ! myeloid lineage restricted progenitor cell @@ -17537,6 +19605,8 @@ creation_date: 2010-08-30T01:27:48Z id: CL:0002195 name: hepatic stem cell def: "A stem cell that can give rise to the cells of the liver. The term usually refers to the self-renewing pool of hepatocyte precursors in the adult liver (differently from 'hepatoblast', often used for fetal precursors of hepatocytes)." [GOC:tfm, PMID:26798363] +subset: human_subset +subset: mouse_subset synonym: "HpSC" RELATED OMO:0003000 [PMID:18442648] xref: FMA:86577 is_a: CL:0000048 {is_inferred="true"} ! multi fate stem cell @@ -17553,6 +19623,8 @@ name: hepatic oval stem cell alt_id: CL:1000036 def: "A transient hepatic stem cell observed after liver injury with a high nuclear to cytoplasm ratio that can differentiate into mature hepatocytes and bile duct cells. Arises from more than one tissue." [PMID:17901986] subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "hepatic oval cell" EXACT [] synonym: "hepatic progenitor cell" EXACT [https://doi.org/10.1038/s12276-020-0483-0] {terms:contributor="http://orcid.org/0000-0003-1940-6740"} synonym: "liver progenitor cell" EXACT [https://doi.org/10.1038/s12276-020-0483-0] @@ -17569,6 +19641,8 @@ creation_date: 2010-08-30T02:01:49Z id: CL:0002197 name: inactive chief cell of parathyoid gland def: "A parathyroid chief cell that is not actively secreting hormone. Contains small Golgi complexes with only a few grouped vesicles and membrane-bound secretory granules; glycogen and many lipofuscin granules abound but sacs of granular endoplasmic reticulum are rare and dispersed. In normal humans, inactive chief cells out number active chief cells in a ratio of 3-5:1." [GOC:tfm, ISBN:0517223651] +subset: human_subset +subset: mouse_subset is_a: CL:0000446 ! chief cell of parathyroid gland property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-02T11:14:01Z @@ -17577,6 +19651,8 @@ creation_date: 2010-09-02T11:14:01Z id: CL:0002198 name: oncocyte def: "A large epithelial cell with an extremely acidophilic and granular cytoplasm, containing vast numbers of mitochondria; such cells may undergo neoplastic transformation. From the Greek word onkos meaning swelling, this cell type is found in parathyroid, salivary and thyroid glands." [GOC:tfm, ISBN:0721662544, PMID:20013317] +subset: human_subset +subset: mouse_subset synonym: "oxyphil" EXACT [] xref: FMA:67606 xref: MESH:D024862 @@ -17588,6 +19664,8 @@ creation_date: 2010-09-02T11:26:49Z id: CL:0002199 name: oxyphil cell of parathyroid gland def: "An oncocyte located in the parathyroid gland." [PMID:20013317] +subset: human_subset +subset: mouse_subset xref: FMA:69084 is_a: CL:0002198 ! oncocyte is_a: CL:0002260 ! epithelial cell of parathyroid gland @@ -17598,6 +19676,8 @@ creation_date: 2010-09-02T11:33:23Z id: CL:0002200 name: oxyphil cell of thyroid def: "An oncocyte located in the thyroid." [GOC:tfm, PMID:20013317] +subset: human_subset +subset: mouse_subset synonym: "Askanazy cells" EXACT [] synonym: "Hurthle cells" EXACT [] xref: FMA:87169 @@ -17614,6 +19694,8 @@ name: renal beta-intercalated cell def: "A renal intercalated cell that secretes base and reabsorbs acid in the distal segments of the kidney tubule to maintain acid/base balance." [GOC:tfm, PMID:11781354, PMID:25632105] subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "type B intercalated cell" EXACT [PMID:25632105] synonym: "type B-IC" EXACT [PMID:25632105] is_a: CL:0005010 ! renal intercalated cell @@ -17626,6 +19708,8 @@ id: CL:0002202 name: epithelial cell of tracheobronchial tree alt_id: CL:1000407 def: "An epithelial cell of the tracheobronchial tree." [GOC:tfm] +subset: human_subset +subset: mouse_subset xref: FMA:66816 is_a: CL:0002632 ! epithelial cell of lower respiratory tract intersection_of: CL:0000066 ! epithelial cell @@ -17641,6 +19725,8 @@ alt_id: CL:1000387 def: "Brush cell found in the epithelial layer of the colon." [GOC:tfm] comment: Brush cells are a distinct cell type from brush border cell-types. subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "brush cell of large intestine" EXACT [http://orcid.org/0000-0003-4183-8865] synonym: "tuft cell of epithelium of large intestine" EXACT [http://orcid.org/0000-0003-4183-8865] synonym: "tuft cell of large intestine" EXACT [http://orcid.org/0000-0003-4183-8865] @@ -17657,6 +19743,8 @@ id: CL:0002204 name: brush cell def: "A cell type found in the gastrointestinal and respiratory tracts that is characterized by the presence of a tuft of blunt, squat microvilli (120-140 per cell). Function of this cell type is not known." [GOC:tfm, ISBN:0517223651, PMID:15817800] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "caveolated cell" EXACT [] synonym: "fibrillovesicular cell" EXACT [] synonym: "multivesicular cell" EXACT [] @@ -17665,7 +19753,7 @@ xref: FMA:67978 xref: https://cellxgene.cziscience.com/cellguide/CL_0002204 is_a: CL:0002076 ! endo-epithelial cell property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 -property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional.\n\nBrush cells, also referred to as tuft cells or multivesicular cells, are a specialized type of epithelial cell mainly noted for their characteristic 'brush border' composed of microvilli. These cells reside in the epithelial lining of tissue organs such as the respiratory tract, gastrointestinal tract, and the bile ducts. The name derives from their distinct appearance under the microscope, which resembles a brush due to the dense layer of microvilli protruding into the lumen.\nA key function of brush cells is chemosensation: They express a variety of signaling molecules and receptors that enable them to detect specific chemical stimuli in the environment and act as sensory transducers. Many of these receptors are responsive to luminal content, which makes brush cells vital for regulating and coordinating appropriate physiological responses to changes in these substances. \nRecent research has also elucidated an important role for these cells in immunity. Intestinal brush cells have been found to be the source of a cytokine called interleukin-25, which can initiate type 2 immune responses during parasitic infections. This immune function, along with the chemosensing abilities, signifies that brush cells could serve crucial roles in health and disease, although much research is still required to fully elucidate their myriad roles in physiology and pathology. Overall, brush cells are a versatile cell type, whose distinct morphology and functional capabilities allow them to perform a unique set of functions within the body." xsd:string {xref="DOI:10.1007/978-3-211-99390-3_83", xref="DOI:10.1038/nature16161", xref="DOI:10.1111/j.1469-7580.2005.00403.x", xref="DOI:10.3389/fphys.2015.00087", xref="DOI:10.5114/ceji.2022.124416"} +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nBrush cells, also referred to as tuft cells or multivesicular cells, are a specialized type of epithelial cell mainly noted for their characteristic 'brush border' composed of microvilli. These cells reside in the epithelial lining of tissue organs such as the respiratory tract, gastrointestinal tract, and the bile ducts. The name derives from their distinct appearance under the microscope, which resembles a brush due to the dense layer of microvilli protruding into the lumen.\nA key function of brush cells is chemosensation: They express a variety of signaling molecules and receptors that enable them to detect specific chemical stimuli in the environment and act as sensory transducers. Many of these receptors are responsive to luminal content, which makes brush cells vital for regulating and coordinating appropriate physiological responses to changes in these substances. \nRecent research has also elucidated an important role for these cells in immunity. Intestinal brush cells have been found to be the source of a cytokine called interleukin-25, which can initiate type 2 immune responses during parasitic infections. This immune function, along with the chemosensing abilities, signifies that brush cells could serve crucial roles in health and disease, although much research is still required to fully elucidate their myriad roles in physiology and pathology. Overall, brush cells are a versatile cell type, whose distinct morphology and functional capabilities allow them to perform a unique set of functions within the body." xsd:string {xref="DOI:10.1007/978-3-211-99390-3_83", xref="DOI:10.1038/nature16161", xref="DOI:10.1111/j.1469-7580.2005.00403.x", xref="DOI:10.3389/fphys.2015.00087", xref="DOI:10.5114/ceji.2022.124416"} creation_date: 2010-09-02T02:28:53Z [Term] @@ -17673,6 +19761,8 @@ id: CL:0002205 name: brush cell of lobular bronchiole alt_id: CL:1000386 def: "A brush cell found in the epithelium of lobular bronchiole." [GOC:tfm] +subset: human_subset +subset: mouse_subset xref: FMA:263220 is_a: CL:0000082 ! epithelial cell of lung is_a: CL:0002075 ! brush cell of tracheobronchial tree @@ -17687,6 +19777,8 @@ id: CL:0002206 name: brush cell of terminal bronchiole alt_id: CL:1000390 def: "A brush cell of the epithelium in the terminal bronchiole." [GOC:tfm] +subset: human_subset +subset: mouse_subset xref: FMA:263228 is_a: CL:0000082 ! epithelial cell of lung is_a: CL:0002075 ! brush cell of tracheobronchial tree @@ -17703,6 +19795,8 @@ alt_id: CL:1000388 def: "Brush cell of the epithelium in the trachea." [GOC:tfm] subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset xref: FMA:263224 is_a: CL:0000307 {is_inferred="true"} ! tracheal epithelial cell is_a: CL:0002075 {is_inferred="true"} ! brush cell of tracheobronchial tree @@ -17719,6 +19813,8 @@ name: brush cell of bronchus alt_id: CL:1000389 def: "A brush cell found in the epithelium of bronchus." [GOC:tfm] subset: human_reference_atlas +subset: human_subset +subset: mouse_subset xref: FMA:263226 is_a: CL:0002075 ! brush cell of tracheobronchial tree is_a: CL:0002328 ! bronchial epithelial cell @@ -17732,6 +19828,8 @@ creation_date: 2010-09-02T02:38:42Z id: CL:0002209 name: intermediate epitheliocyte def: "An epithelial cell present in the trachea and bronchi; columnar in shape; generally lack cilia; immature forms of ciliated or secretory cells which have been formed from stem cells." [GOC:tfm, ISBN:0517223651] +subset: human_subset +subset: mouse_subset synonym: "undifferentiated columnar cell of tracheobronchial tree" EXACT [] xref: FMA:69060 is_a: CL:0002202 ! epithelial cell of tracheobronchial tree @@ -17742,6 +19840,8 @@ creation_date: 2010-09-02T02:53:59Z id: CL:0002210 name: red muscle cell def: "A slow muscle cell that contains high levels of myoglobin and oxygen storing proteins giving the cell a red appearance." [GOC:tfm, ISBN:0517223651] +subset: human_subset +subset: mouse_subset synonym: "oxidative muscle fiber" EXACT [] synonym: "red muscle fiber" EXACT [] xref: FMA:84448 @@ -17753,6 +19853,8 @@ creation_date: 2010-09-02T03:20:03Z id: CL:0002211 name: type I muscle cell def: "A slow muscle cell that has large amounts of myoglobin, stores energy as triglycerides, generates ATP by the oxidative method and is resistant to fatigue." [GOC:tfm, ISBN:0517223651] +subset: human_subset +subset: mouse_subset synonym: "intermediate muscle fiber" RELATED [MESH:D018657] synonym: "slow twitch fiber" EXACT [] synonym: "slow twitch muscle cell" EXACT [] @@ -17773,6 +19875,8 @@ creation_date: 2010-09-02T03:24:05Z id: CL:0002212 name: type II muscle cell def: "A fast muscle fiber cell that stores energy in the form of glycogen and creatine phosphate." [GOC:tfm] +subset: human_subset +subset: mouse_subset synonym: "type 2 muscle cell" EXACT [] synonym: "type 2 muscle fiber" EXACT [] synonym: "type II muscle fiber" EXACT [] @@ -17786,6 +19890,8 @@ creation_date: 2010-09-02T03:28:45Z id: CL:0002213 name: white muscle cell def: "A muscle cell with low content of myoglobin and other oxygen storing proteins. This muscle cell has a white appearance." [GOC:tfm, ISBN:0517223651] +subset: human_subset +subset: mouse_subset xref: FMA:84449 is_a: CL:0000190 ! fast muscle cell property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 @@ -17795,6 +19901,8 @@ creation_date: 2010-09-02T03:28:48Z id: CL:0002214 name: type IIa muscle cell def: "A type II muscle cell that contains large amounts of myoglobin, has many mitochondria and very many blood capillaries. Type II A cells are red, have a very high capacity for generating ATP by oxidative metabolic processes, split ATP at a very rapid rate, have a fast contraction velocity and are resistant to fatigue." [GOC:tfm] +subset: human_subset +subset: mouse_subset synonym: "fast twitch A" EXACT [] synonym: "fatigue resistant fast twitch muscle cell" EXACT [] synonym: "type 2a muscle cell" EXACT [] @@ -17811,6 +19919,8 @@ creation_date: 2010-09-02T03:31:38Z id: CL:0002215 name: type IIb muscle cell def: "A type II muscle cell that contains a low content of myoglobin, relatively few mitochondria, relatively few blood capillaries and large amounts of glycogen. Type II B fibres are white, geared to generate ATP by anaerobic metabolic processes, not able to supply skeletal muscle fibres continuously with sufficient ATP, fatigue easily, split ATP at a fast rate and have a fast contraction velocity." [GOC:tfm, http://en.wikipedia.org/wiki/Skeletal_muscle, ISBN:0517223651] +subset: human_subset +subset: mouse_subset synonym: "type 2b muscle cell" EXACT [] synonym: "type 2b muscle fiber" EXACT [] synonym: "type IIb muscle fiber" EXACT [] @@ -17824,6 +19934,8 @@ creation_date: 2010-09-02T03:31:42Z id: CL:0002216 name: intermediate muscle cell def: "An intermediate muscle cell that has characteristics of both fast and slow muscle cells." [GOC:tfm] +subset: human_subset +subset: mouse_subset xref: FMA:84450 is_a: CL:0008046 ! extrafusal muscle fiber property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 @@ -17833,6 +19945,8 @@ creation_date: 2010-09-02T03:51:17Z id: CL:0002217 name: intermediate trophoblast cell def: "A trophoblast that leaves the placenta and invades the endometrium and myometrium. This cell type is crucial in increasing blood flow to the fetus." [GOC:tfm, http://www.med.yale.edu/obgyn/kliman/placenta/articles/EOR_Placenta/Trophtoplacenta.html] +subset: human_subset +subset: mouse_subset xref: BTO:0002366 xref: FMA:86564 is_a: CL:0000351 ! trophoblast cell @@ -17844,6 +19958,8 @@ id: CL:0002218 name: immature dendritic epithelial T cell precursor def: "A double negative thymocyte that has a T cell receptor consisting of a gamma chain that has as part a Vgamma3 segment, and a delta chain. This cell type is CD4-negative, CD8-negative and CD24-positive. This cell-type is found in the fetal thymus with highest numbers occurring at E17-E18." [GOC:tfm, http://www.immgen.org] comment: NOTE: currently variable immune gene segments are not represented in the OBO Foundry. Cross-product definitions were not made as a result. Also, there are three different nomenclatures for the variable gamma segments. +subset: human_subset +subset: mouse_subset synonym: "immature DEC precursor" EXACT [] synonym: "immature DETC precursor" EXACT [] is_a: CL:0002404 ! fetal thymocyte @@ -17854,6 +19970,8 @@ creation_date: 2010-10-07T01:58:00Z id: CL:0002219 name: anchoring trophoblast def: "A trophoblast found at the junction of the placenta. This cell type makes a unique fibronectin-trophouteronectin junction that helps mediate attachment of the placenta to the uterus. This cell type is also found junction of the chorion layer of the external membranes and the decidua." [GOC:tfm, http://www.med.yale.edu/obgyn/kliman/placenta/articles/EOR_Placenta/Trophtoplacenta.html] +subset: human_subset +subset: mouse_subset is_a: CL:0000351 ! trophoblast cell property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-02T04:14:28Z @@ -17862,6 +19980,8 @@ creation_date: 2010-09-02T04:14:28Z id: CL:0002220 name: interstitial cell of pineal gland def: "A cell located between the pinealocytes." [GOC:tfm, ISBN:0517223651] +subset: human_subset +subset: mouse_subset xref: FMA:86575 is_a: CL:0000710 ! neurecto-epithelial cell property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 @@ -17871,6 +19991,8 @@ creation_date: 2010-09-02T04:28:41Z id: CL:0002221 name: keratinized squamous cell of esophagus def: "A squamous cell that has keratin in the esophagus." [GOC:tfm, PMID:11694559] +subset: human_subset +subset: mouse_subset xref: FMA:86549 is_a: CL:0000237 ! keratinizing barrier epithelial cell is_a: CL:0002252 ! epithelial cell of esophagus @@ -17882,6 +20004,8 @@ id: CL:0002222 name: vertebrate lens cell def: "A cell comprising the transparent, biconvex body separating the posterior chamber and vitreous body, and constituting part of the refracting mechanism of the mammalian eye." [GOC:tfm, ISBN:0721662544] subset: eye_upper_slim +subset: human_subset +subset: mouse_subset xref: FMA:70950 is_a: CL:0000066 ! epithelial cell is_a: CL:0000306 ! crystallin accumulating cell @@ -17894,9 +20018,13 @@ id: CL:0002223 name: anterior lens cell def: "A cell of the transparent layer of simple cuboidal epithelium over the anterior surface of the lens; transform into lens fiber(s)." [GOC:tfm, ISBN:0517223651] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset xref: FMA:63181 +xref: https://cellxgene.cziscience.com/cellguide/CL_0002223 is_a: CL:0002224 ! lens epithelial cell property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nThe anterior lens cells, also known as lens epithelial cells, are an integral part of the eye's structure and play a critical role in the organ's physiological functioning. They are situated in the anterior portion of the lens, precisely in the lens capsule, and stretch over the lens' frontal surface.\nThe primary function of anterior lens cells is to facilitate eye accommodation by controlling the shape and thickness of the eye lens.\nThe cells are involved in continuous proliferation, migration, and differentiation into lens fiber cells, helping to maintain lens growth and transparency. Anterior lens cells have a prolonged life span and reveal an extraordinary ability to function indefinitely, a characteristic that is critical for maintaining lens transparency. Damage or disturbance to the anterior lens cells can give rise to lens opacity, eventually leading to cataracts, which is a common cause of vision loss." xsd:string {xref="DOI:10.1016/j.biocel.2007.10.034", xref="DOI:10.1111/aos.14600", xref="DOI:10.1155/2021/9951032"} creation_date: 2010-09-07T10:45:45Z [Term] @@ -17905,6 +20033,8 @@ name: lens epithelial cell def: "A cell of the cuboidal epithelium that covers the lens. The cells of the lens epithelium regulate most of the homeostatic functions of the lens. As ions, nutrients, and liquid enter the lens from the aqueous humor, Na+/K+ ATPase pumps in the lens epithelial cells pump ions out of the lens to maintain appropriate lens osmolarity and volume, with equatorially positioned lens epithelium cells contributing most to this current. The activity of the Na+/K+ ATPases keeps water and current flowing through the lens from the poles and exiting through the equatorial regions. The cells of the lens epithelium also serve as the progenitors for new lens fibers. It constantly lays down fibers in the embryo, fetus, infant, and adult, and continues to lay down fibers for lifelong growth." [GOC:tfm, http://en.wikipedia.org/wiki/Lens_%28anatomy%29#Lens_epithelium, ISBN:0721662544] subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset xref: FMA:67559 is_a: CL:0000075 {is_inferred="true"} ! columnar/cuboidal epithelial cell is_a: CL:0002222 ! vertebrate lens cell @@ -17921,6 +20051,8 @@ name: secondary lens fiber def: "A lens fiber cell that develops from primary lens fiber; located towards the center of lens; cell organelles are normally degraded or in the process of being degraded." [GOC:tfm, ISBN:0517223651] subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "secondary lens fibre" EXACT [] xref: https://cellxgene.cziscience.com/cellguide/CL_0002225 is_a: BFO:0000002 @@ -17928,13 +20060,15 @@ is_a: CL:0011004 ! lens fiber cell relationship: RO:0002202 CL:0002228 ! develops from primary lens fiber property_value: RO:0002175 NCBITaxon:9606 property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 -property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional.\n\nSecondary lens fibers are a specialized type of elongated cells located within the structure of the eye's lens. They play an essential role in vision by enabling light transmission and focus on the retina, which allows for clear, distinct vision. These cells are characterized by their lack of nuclei and organelles, their orderly alignment, and their high protein content, particularly crystallins. \nLens fibers are differentiated from equatorial epithelial cells of the lens in a process that involves cell elongation, denucleation and tight packing, which serve to reduce light scattering occurrences in the eye. This differentiation accelerates substantially after birth in comparison to during embryogenesis and continues throughout life, contributing to the growth of the eye lens. Secondary lens fibers are specifically those cells that are newly differentiated and cover the old lens fiber core. This process also leads to the removal of light-obstructing cellular components, mainly nuclei and organelles, making these fibers transparent and ideal for their function. \nThe fibers carry out their primary function of light refraction via a high concentration of specialized proteins known as crystallins, which form a gradient of refractive index together with the cytoplasm. This index manipulation facilitates precise light focus onto the retina. Secondary lens fibers also contribute to the lens's shape and biomechanical properties through intercellular interactions, particularly at the sutures where the ends of the fibers meet. Any disruption to secondary lens fibers can lead to vision problems, including cataracts, which is the clouding of the lens resulting from the aggregation of crystallin proteins." xsd:string {xref="DOI:10.1016/B978-1-4377-1926-0.10005-0", xref="DOI:10.1016/j.biocel.2007.10.034", xref="DOI:10.1098/rstb.2010.0324", xref="DOI:10.1136/bmjophth-2020-000459", xref="https://www.sciencedirect.com/topics/immunology-and-microbiology/lens-fiber"} +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nSecondary lens fibers are a specialized type of elongated cells located within the structure of the eye's lens. They play an essential role in vision by enabling light transmission and focus on the retina, which allows for clear, distinct vision. These cells are characterized by their lack of nuclei and organelles, their orderly alignment, and their high protein content, particularly crystallins. \nLens fibers are differentiated from equatorial epithelial cells of the lens in a process that involves cell elongation, denucleation and tight packing, which serve to reduce light scattering occurrences in the eye. This differentiation accelerates substantially after birth in comparison to during embryogenesis and continues throughout life, contributing to the growth of the eye lens. Secondary lens fibers are specifically those cells that are newly differentiated and cover the old lens fiber core. This process also leads to the removal of light-obstructing cellular components, mainly nuclei and organelles, making these fibers transparent and ideal for their function. \nThe fibers carry out their primary function of light refraction via a high concentration of specialized proteins known as crystallins, which form a gradient of refractive index together with the cytoplasm. This index manipulation facilitates precise light focus onto the retina. Secondary lens fibers also contribute to the lens's shape and biomechanical properties through intercellular interactions, particularly at the sutures where the ends of the fibers meet. Any disruption to secondary lens fibers can lead to vision problems, including cataracts, which is the clouding of the lens resulting from the aggregation of crystallin proteins." xsd:string {xref="DOI:10.1016/B978-1-4377-1926-0.10005-0", xref="DOI:10.1016/j.biocel.2007.10.034", xref="DOI:10.1098/rstb.2010.0324", xref="DOI:10.1136/bmjophth-2020-000459", xref="https://www.sciencedirect.com/topics/immunology-and-microbiology/lens-fiber"} creation_date: 2010-09-07T10:53:39Z [Term] id: CL:0002226 name: non-nucleated secondary lens fiber def: "A secondary lens fiber cell that lacks a nucleus." [GOC:tfm] +subset: human_subset +subset: mouse_subset synonym: "non-nucleated secondary lens fibre" EXACT [] xref: FMA:67561 is_a: CL:0002225 ! secondary lens fiber @@ -17946,6 +20080,8 @@ creation_date: 2010-09-07T11:15:23Z id: CL:0002227 name: nucleated secondary lens fiber def: "A secondary fiber cell that contains a nucleus." [GOC:tfm] +subset: human_subset +subset: mouse_subset synonym: "nucleated secondary lens fibre" EXACT [] xref: FMA:70949 is_a: CL:0002225 ! secondary lens fiber @@ -17957,6 +20093,8 @@ id: CL:0002228 name: primary lens fiber def: "An elongating cell that rapidly obliterates the lumen of the lens vesicle. Subsequently, differentiation of this cell type at the lens equator leads to the formation of secondary fiber cells that come to overlie the primary fibers." [GOC:tfm, PMID:10711704] subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "primary lens fibre" EXACT [] xref: FMA:70613 is_a: BFO:0000002 @@ -17970,6 +20108,8 @@ creation_date: 2010-09-07T11:19:01Z id: CL:0002229 name: light chief cell of parathyroid gland def: "A chief cell that is bigger than dark chief cells and has a larger and lighter nucleus and a cytoplasm with few granules." [GOC:tfm, ISBN:0721662544] +subset: human_subset +subset: mouse_subset xref: FMA:69079 is_a: CL:0000446 ! chief cell of parathyroid gland property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 @@ -17982,6 +20122,8 @@ alt_id: CL:1000295 alt_id: CL:1000408 def: "An epithelial cell of the prostate." [GOC:tfm] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "prostate epithelial cell" EXACT [] xref: FMA:256163 xref: FMA:66817 @@ -17997,6 +20139,8 @@ id: CL:0002232 name: epithelial cell of prostatic duct alt_id: CL:1000462 def: "An epithelial cell of prostatic duct." [GOC:tfm] +subset: human_subset +subset: mouse_subset synonym: "ductal epithelial cell of prostate" EXACT [FMA:74224] xref: FMA:74224 is_a: CL:0000072 {is_inferred="true"} ! non-branched duct epithelial cell @@ -18012,6 +20156,8 @@ id: CL:0002233 name: epithelial cell of prostatic acinus alt_id: CL:1000461 def: "An epithelial cell of the prostatic acinus." [GOC:tfm, PMCID:PMC2673349] +subset: human_subset +subset: mouse_subset synonym: "acinar epithelial cell of prostate" EXACT [FMA:74223] xref: FMA:74223 is_a: CL:0002231 {is_inferred="true"} ! epithelial cell of prostate @@ -18026,6 +20172,8 @@ id: CL:0002234 name: basal cell of prostatic acinus alt_id: CL:1000464 def: "A cell of the basal layer of the epithelium in the prostatic acinus." [GOC:tfm] +subset: human_subset +subset: mouse_subset synonym: "basal epithelial cell of prostatic acinus" EXACT [FMA:74265] xref: FMA:74265 is_a: CL:0002233 ! epithelial cell of prostatic acinus @@ -18039,6 +20187,8 @@ creation_date: 2010-09-07T01:59:08Z id: CL:0002235 name: luminal cell of prostatic acinus def: "A cell of the luminal layer of the epithelium in the prostatic acinus." [GOC:tfm] +subset: human_subset +subset: mouse_subset xref: FMA:74266 is_a: CL:0002233 ! epithelial cell of prostatic acinus is_a: CL:0002340 ! luminal cell of prostate epithelium @@ -18053,6 +20203,8 @@ name: basal epithelial cell of prostatic duct alt_id: CL:1000463 def: "A cell that constitutes the basal layer of epithelium in the prostatic duct." [GOC:tfm, PMID:15226377] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset xref: FMA:74226 is_a: CL:0000068 ! duct epithelial cell is_a: CL:0002341 ! basal cell of prostate epithelium @@ -18066,6 +20218,8 @@ creation_date: 2010-09-07T01:59:12Z id: CL:0002237 name: luminal epithelial cell of prostatic duct def: "A cell that constitutes the luminal layer of epithelium of prostatic duct." [GOC:tfm] +subset: human_subset +subset: mouse_subset xref: FMA:74225 is_a: CL:0000068 ! duct epithelial cell is_a: CL:0002340 ! luminal cell of prostate epithelium @@ -18079,6 +20233,8 @@ creation_date: 2010-09-07T01:59:16Z id: CL:0002238 name: male gonocyte def: "A primordial germ cell that is destined to become a male germ cell." [GOC:tfm] +subset: human_subset +subset: mouse_subset synonym: "male primordial germ cell" EXACT [] synonym: "testis primordial germ cell" EXACT [VHOG:0000662] xref: EHDAA2:0001053 @@ -18094,6 +20250,8 @@ creation_date: 2010-09-07T02:11:13Z id: CL:0002239 name: ooblast def: "A primordial cell from which an oocyte (ovum) ultimately is developed." [GOC:tfm] +subset: human_subset +subset: mouse_subset synonym: "ovary primordial germ cell" EXACT [VHOG:0000661] synonym: "ovigerm" EXACT [FMA:84772] xref: EHDAA2:0000505 @@ -18111,9 +20269,11 @@ creation_date: 2010-09-07T02:11:16Z id: CL:0002240 name: marrow fibroblast def: "A fibroblast in the bone marrow." [GOC:tfm] +subset: human_subset +subset: mouse_subset xref: FMA:84377 is_a: CL:0000057 ! fibroblast -is_a: CL:0002092 ! bone marrow cell +is_a: CL:0010001 ! stromal cell of bone marrow intersection_of: CL:0000057 ! fibroblast intersection_of: part_of UBERON:0002371 ! bone marrow property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 @@ -18123,7 +20283,10 @@ creation_date: 2010-09-07T02:25:18Z id: CL:0002241 name: pulmonary interstitial fibroblast def: "A fibroblasts found in interstitial spaces in the pulmonary tract. Greater numbers of these cells are found in idiopathic pulmonary fibrosis." [GOC:tfm] +comment: The marker set DPT, APOD can identify the Human cell type pulmonary interstitial fibroblast in the Lung with a confidence of 0.58 (NS-Forest FBeta value). {xref="https://doi.org/10.5281/zenodo.11165918"} subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "pulmonary myofibroblast" EXACT [] synonym: "pulmonary septal cell" EXACT [] xref: FMA:84467 @@ -18133,6 +20296,8 @@ intersection_of: CL:0000057 ! fibroblast intersection_of: part_of UBERON:0001004 ! respiratory system intersection_of: part_of UBERON:0005169 ! interstitial tissue relationship: part_of UBERON:0001004 ! respiratory system +relationship: RO:0015004 CLM:1000046 ! has characterizing marker set NS forest marker set of pulmonary interstitial fibroblast (Human Lung). +property_value: RO:0002175 NCBITaxon:9606 property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-07T02:29:38Z @@ -18140,6 +20305,8 @@ creation_date: 2010-09-07T02:29:38Z id: CL:0002242 name: nucleate cell def: "A cell containing at least one nucleus." [GOC:tfm] +subset: human_subset +subset: mouse_subset xref: FMA:67513 is_a: CL:0000000 ! cell intersection_of: CL:0000000 ! cell @@ -18153,21 +20320,27 @@ id: CL:0002243 name: smooth muscle cell of sphincter of pupil def: "A circular smooth muscle cell of the iris, innervated by the ciliary nerves (parasympathetic), and acting to contract the pupil. This muscle cell derives from neuroectoderm. This smooth muscle cell results from transformation of epithelial cells to smooth muscle cells." [GOC:tfm, ISBN:0721662544, ISBN:0721694128] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "smooth muscle fiber of sphincter of pupil" EXACT [] synonym: "smooth muscle fibre of sphincter of pupil" RELATED [] xref: FMA:70611 +xref: https://cellxgene.cziscience.com/cellguide/CL_0002243 is_a: CL:0000358 {is_inferred="true"} ! sphincter associated smooth muscle cell intersection_of: CL:0000192 ! smooth muscle cell intersection_of: part_of UBERON:0001607 ! sphincter pupillae relationship: part_of UBERON:0001607 ! sphincter pupillae relationship: RO:0002202 CL:0000133 ! develops from neurectodermal cell property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nThe smooth muscle cell of sphincter of pupil is a specialized cell type typically found within the eye, more specifically within the sphincter muscle of the iris. \nThese cells can constrict and dilate in response to light signals, tightly regulating the amount of light reaching the retina. Contraction narrows the pupil in bright conditions (pupillary constriction), protecting the retina from excessive light. In low light, relaxation allows dilation (pupillary dilation), enhancing visual perception in dim conditions.\nThese cells are also innervated by parasympathetic fibers from the oculomotor nerve. Light signals to the Edinger-Westphal nucleus stimulate the release of acetylcholine, contracting the cells. On the contrary, sympathetic stimulation induces relaxation. This precise control plays a crucial role in optimizing visual function, highlighting their essential role in vision biology." xsd:string {xref="https://www.ncbi.nlm.nih.gov/books/NBK532252/", xref="https://www.ncbi.nlm.nih.gov/books/NBK537180/", xref="https://www.sciencedirect.com/topics/neuroscience/iris-dilator-muscle", xref="https://www.sciencedirect.com/topics/neuroscience/iris-sphincter-muscle"} creation_date: 2010-09-08T08:53:42Z [Term] id: CL:0002244 name: squamous cell of ectocervix def: "A stratified squamous epithelial cell located in the ectocervix." [doi:/10.1016/j.autneu.2015.04.008, GOC:tfm, http://www.bu.edu/histology/p/19404loa.htm, PMID:32644501] +subset: human_subset +subset: mouse_subset synonym: "ectocervical squamous cell" EXACT [] xref: FMA:86483 is_a: CL:1001575 ! uterine cervix squamous cell @@ -18190,6 +20363,8 @@ creation_date: 2010-09-07T03:43:42Z id: CL:0002246 name: peripheral blood stem cell def: "A hematopoeitic stem cell found in the blood. Normally found in very limited numbers in the peripheral circulation (less than 0.1% of all nucleated cells)." [GOC:tfm] +subset: human_subset +subset: mouse_subset synonym: "PBSC" EXACT [] xref: BTO:0002669 xref: FMA:86711 @@ -18206,6 +20381,8 @@ creation_date: 2010-09-07T03:57:09Z id: CL:0002247 name: pleural macrophage def: "A tissue macrophage that is in the pleural space." [GOC:tfm] +subset: human_subset +subset: mouse_subset xref: FMA:83024 is_a: CL:0000864 ! tissue-resident macrophage property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 @@ -18215,6 +20392,8 @@ creation_date: 2010-09-07T04:16:43Z id: CL:0002248 name: pluripotent stem cell def: "A pluripotent stem cell has the ability to form cells from all three germ layers (ectoderm, mesoderm, and endoderm). However, unlike totipotent stem cells, they cell can not generate all the cells of the whole organism such as placenta." [GOC:tfm, PMID:19343304] +subset: human_subset +subset: mouse_subset xref: FMA:70570 xref: MESH:D039904 is_a: CL:0000723 ! somatic stem cell @@ -18225,6 +20404,8 @@ creation_date: 2010-09-07T04:26:06Z id: CL:0002249 name: primitive cardiac myocyte def: "A stem cell that can differentiate into a cardiac myocyte." [GOC:tfm, PMID:16938308] +subset: human_subset +subset: mouse_subset xref: FMA:75620 is_a: CL:0000035 ! single fate stem cell is_a: CL:0002078 ! meso-epithelial cell @@ -18236,6 +20417,8 @@ id: CL:0002250 name: intestinal crypt stem cell def: "A cell that is found in a zone occupying the bottom region of the crypt; provide the source of most of the cell types of the intestinal epithelium; proliferate by mitotic division; differentiates into columnar or goblet cells." [GOC:tfm, ISBN:0517223651] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "stem cell of intestinal crypt of Lieberkuhn" EXACT [] xref: FMA:63379 xref: https://cellxgene.cziscience.com/cellguide/CL_0002250 @@ -18245,17 +20428,19 @@ intersection_of: CL:0000034 ! stem cell intersection_of: part_of UBERON:0001983 ! crypt of Lieberkuhn relationship: part_of UBERON:0001983 ! crypt of Lieberkuhn property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 -property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional.\n\nIntestinal crypt stem cells, also known as crypt base columnar cells, are a unique type of cell, characterized by the highly specific marker LGR5, found in the intestinal epithelium. Situated at the bottom of the minute pockets known as crypts of Lieberkühn, these are undifferentiated cells that have the ability to perpetually self-renew, as well as differentiate into various other cell types that constitute the epithelial lining of the intestine. \nThe fundamental role of intestinal crypt stem cells is to provide a constant supply of new cells to maintain the cellular turnover of the intestinal epithelium, a tissue known for rapid self-renewal. These stem cells are nurtured and protected by specialized epithelial and mesenchymal cells, and together constitute the intestinal stem cell niche. \nAn important function of intestinal crypt stem cells is to sustain the balance between cell division and programmed cell death, called apoptosis, to ensure the integrity of the intestinal lining. Given their active proliferation rate, these stem cells initiate the creation of diverse differentiated cell types, including enterocytes (the primary absorptive cells in the intestinal lumen), goblet cells (that produce mucus to protect the epithelial layer), enteroendocrine cells (involved in producing gastrointestinal hormones), and Paneth cells (involved in secreting antimicrobial peptides). This diversity in output regulates the physiological activities of the gut ranging from nutrient absorption, hormone secretion, bacterial balance, to immunity.\nResearch studies suggest that dysregulation in intestinal crypt stem cell proliferation and differentiation is associated with several intestinal disorders including intestinal cancer, and various enteropathies." xsd:string {xref="DOI:10.1016/j.cell.2013.07.004", xref="DOI:10.1038/s41575-018-0081-y", xref="DOI:10.1038/s41580-020-0278-0", xref="DOI:10.1101/gad.1674008", xref="DOI:10.1111/j.1365-2184.2009.00642.x"} +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nIntestinal crypt stem cells, also known as crypt base columnar cells, are a unique type of cell, characterized by the highly specific marker LGR5, found in the intestinal epithelium. Situated at the bottom of the minute pockets known as crypts of Lieberkühn, these are undifferentiated cells that have the ability to perpetually self-renew, as well as differentiate into various other cell types that constitute the epithelial lining of the intestine. \nThe fundamental role of intestinal crypt stem cells is to provide a constant supply of new cells to maintain the cellular turnover of the intestinal epithelium, a tissue known for rapid self-renewal. These stem cells are nurtured and protected by specialized epithelial and mesenchymal cells, and together constitute the intestinal stem cell niche. \nAn important function of intestinal crypt stem cells is to sustain the balance between cell division and programmed cell death, called apoptosis, to ensure the integrity of the intestinal lining. Given their active proliferation rate, these stem cells initiate the creation of diverse differentiated cell types, including enterocytes (the primary absorptive cells in the intestinal lumen), goblet cells (that produce mucus to protect the epithelial layer), enteroendocrine cells (involved in producing gastrointestinal hormones), and Paneth cells (involved in secreting antimicrobial peptides). This diversity in output regulates the physiological activities of the gut ranging from nutrient absorption, hormone secretion, bacterial balance, to immunity.\nResearch studies suggest that dysregulation in intestinal crypt stem cell proliferation and differentiation is associated with several intestinal disorders including intestinal cancer, and various enteropathies." xsd:string {xref="DOI:10.1016/j.cell.2013.07.004", xref="DOI:10.1038/s41575-018-0081-y", xref="DOI:10.1038/s41580-020-0278-0", xref="DOI:10.1101/gad.1674008", xref="DOI:10.1111/j.1365-2184.2009.00642.x"} creation_date: 2010-09-08T09:21:22Z [Term] id: CL:0002251 name: epithelial cell of alimentary canal def: "An epithelial cell of the musculomembranous digestive tube extending from the mouth to the anus." [GOC:tfm, ISBN:0721662544] +subset: human_subset +subset: mouse_subset is_a: CL:0002076 ! endo-epithelial cell intersection_of: CL:0000066 ! epithelial cell -intersection_of: part_of UBERON:0001555 ! digestive tract -relationship: part_of UBERON:0001555 ! digestive tract +intersection_of: part_of UBERON:0003929 ! digestive tract epithelium +relationship: part_of UBERON:0003929 ! digestive tract epithelium property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-08T09:26:53Z @@ -18263,14 +20448,16 @@ creation_date: 2010-09-08T09:26:53Z id: CL:0002252 name: epithelial cell of esophagus alt_id: CL:1000402 -def: "An epithelial cell of the esophagus." [GOC:tfm] +def: "An epithelial cell of the lining of the esophagus." [GOC:tfm] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset xref: FMA:63071 xref: ZFA:0009400 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0002251 {is_inferred="true"} ! epithelial cell of alimentary canal intersection_of: CL:0000066 ! epithelial cell -intersection_of: part_of UBERON:0001043 ! esophagus -relationship: part_of UBERON:0001043 ! esophagus +intersection_of: part_of UBERON:0001976 ! epithelium of esophagus +relationship: part_of UBERON:0001976 ! epithelium of esophagus property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-08T09:28:20Z @@ -18278,15 +20465,17 @@ creation_date: 2010-09-08T09:28:20Z id: CL:0002253 name: epithelial cell of large intestine alt_id: CL:1000292 -def: "An epithelial cell of the large intestine." [GOC:tfm] +def: "An epithelial cell of the lining of the large intestine." [GOC:tfm] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "epithelial cell of colon" RELATED [] xref: BTO:0004297 xref: FMA:256157 is_a: CL:0002563 {is_inferred="true"} ! intestinal epithelial cell intersection_of: CL:0002563 ! intestinal epithelial cell intersection_of: part_of UBERON:0000059 ! large intestine -relationship: part_of UBERON:0000059 ! large intestine +relationship: part_of UBERON:0001278 ! epithelium of large intestine property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-08T09:28:22Z @@ -18294,8 +20483,10 @@ creation_date: 2010-09-08T09:28:22Z id: CL:0002254 name: epithelial cell of small intestine alt_id: CL:1000293 -def: "An epithelial cell of the small intestine." [GOC:tfm] +def: "An epithelial cell of the lining of the small intestine." [GOC:tfm] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset xref: FMA:256159 is_a: CL:0002563 {is_inferred="true"} ! intestinal epithelial cell intersection_of: CL:0002563 ! intestinal epithelial cell @@ -18307,15 +20498,20 @@ creation_date: 2010-09-08T09:41:46Z [Term] id: CL:0002255 name: stromal cell of endometrium -def: "A stromal cell of the endometrium that is fibroblastic in appearance. During decidualization this cell may differentiate into a decidual stromal cell." [https://doi.org/10.1038/s41591-020-1040-z, PMID:11331626, PMID:30013421, PMID:30309298, Wiki:Decidualization&oldid=908981933#Endometrial_stromal_cells_(ESCs)] +def: "A stromal cell of the endometrium, characterized by its fibroblast-like morphology, regenerative capacity, and ability to undergo decidualization. It differentiates into a decidual stromal cell during pregnancy, essential for embryo implantation and maintenance. This cell is involved in tissue proliferation, remodeling, and breakdown, responding to hormonal changes, particularly estrogen and progesterone." [https://doi.org/10.1038/s41591-020-1040-z, PMID:11331626, PMID:30013421, PMID:30309298, PMID:31907034, Wikipedia:Decidualization] +subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "endometrial stromal cell" EXACT [] synonym: "endometrial stromal fibroblast" EXACT [PMID:30309298] +synonym: "stromal cell of uterus" BROAD [] xref: CALOHA:TS-1266 xref: FMA:86490 -is_a: CL:0000499 {is_inferred="true"} ! stromal cell +is_a: CL:0000499 ! stromal cell intersection_of: CL:0000499 ! stromal cell -intersection_of: part_of UBERON:0001295 ! endometrium +intersection_of: part_of UBERON:0002337 ! endometrial stroma +relationship: capable_of GO:0046697 ! decidualization relationship: part_of UBERON:0002337 ! endometrial stroma relationship: RO:0002388 CL:2000002 ! has potential to directly develop into decidual cell property_value: RO:0002175 NCBITaxon:9606 @@ -18326,6 +20522,8 @@ creation_date: 2010-09-08T09:50:04Z id: CL:0002256 name: supporting cell of carotid body def: "A supportive cell that has characteristics of glial cell. Processes of this cell envelope the junctions between glomus cells and nerve endings." [GOC:tfm, http://www.copewithcytokines.de/cope.cgi?key=glomus%20cells, PMID:8985136] +subset: human_subset +subset: mouse_subset synonym: "carotid body sustentacular cell" EXACT [] xref: FMA:84188 is_a: CL:0000630 ! supporting cell @@ -18338,9 +20536,12 @@ id: CL:0002257 name: epithelial cell of thyroid gland alt_id: CL:1000297 def: "An epithelial cell of thyroid gland." [GOC:tfm] +subset: cellxgene_subset +subset: human_subset +subset: mouse_subset xref: FMA:256167 xref: MESH:D000072637 -is_a: CL:0000150 ! glandular epithelial cell +is_a: CL:0000150 ! glandular secretory epithelial cell is_a: CL:0002076 {is_inferred="true"} ! endo-epithelial cell intersection_of: CL:0002076 ! endo-epithelial cell intersection_of: part_of UBERON:0002046 ! thyroid gland @@ -18353,6 +20554,8 @@ id: CL:0002258 name: thyroid follicular cell def: "A cell type that varies from squamous to columnar, depending on their activity with microvillus directed luminally. This cell produces and secretes thyroid hormones." [GOC:tfm, ISBN:0517223651] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "follicular cell of thyroid gland" EXACT [] synonym: "principal cell of thyroid gland" EXACT [] synonym: "thyroid gland follicular cell" EXACT [] @@ -18368,6 +20571,8 @@ id: CL:0002259 name: neuroepithelial stem cell def: "The stem cell from which glial precursor cell arises from." [GOC:tfm, PMID:11687496] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "totipotent neuroepithelial stem cell" NARROW [] xref: FMA:87171 is_a: CL:0000723 ! somatic stem cell @@ -18379,11 +20584,14 @@ id: CL:0002260 name: epithelial cell of parathyroid gland alt_id: CL:1000429 def: "An epithelial cell of the parathyroid gland." [GOC:tfm] +subset: cellxgene_subset +subset: human_subset +subset: mouse_subset xref: FMA:70547 -is_a: CL:0002076 {is_inferred="true"} ! endo-epithelial cell -is_a: CL:1001593 ! parathyroid glandular cell -intersection_of: CL:0002076 ! endo-epithelial cell +is_a: CL:0002076 ! endo-epithelial cell +intersection_of: CL:0000066 ! epithelial cell intersection_of: part_of UBERON:0001132 ! parathyroid gland +relationship: part_of UBERON:0001132 ! parathyroid gland property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-08T02:29:38Z @@ -18392,6 +20600,8 @@ id: CL:0002261 name: endothelial cell of viscerocranial mucosa alt_id: CL:1000446 def: "An endothelial cell found in the mucosa associated with the facial skeleton." [GOC:tfm, ISBN:0618947256] +subset: human_subset +subset: mouse_subset xref: FMA:70627 is_a: CL:0002076 ! endo-epithelial cell property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 @@ -18404,19 +20614,25 @@ alt_id: CL:1000403 def: "An endothelial cell that lines any of the venous cavities through which blood passes in various glands and organs such as the spleen and liver." [GOC:tfm, ISBN:0618947256] subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset xref: FMA:63134 +xref: https://cellxgene.cziscience.com/cellguide/CL_0002262 is_a: CL:0000071 ! blood vessel endothelial cell intersection_of: CL:0000115 ! endothelial cell intersection_of: part_of UBERON:0003909 ! sinusoid relationship: part_of UBERON:0003909 ! sinusoid property_value: RO:0002175 NCBITaxon:9606 property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nEndothelial cells of sinusoids, often referred to as sinusoidal endothelial cells (SECs), are a specialized type of endothelial cell that primarily reside in the capillaries of the liver, spleen, and bone marrow. These cells form the innermost monolayer of the sinusoidal blood vessels, also known as sinusoids, that mediate the exchange of nutrients, metabolites, and waste materials between the blood and the surrounding organ tissue. SECs possess distinctive morphological features including a large, flattened shape, an abundance of fenestrations or pores, and the lack of a continuous basement membrane. These structural characteristics distinguish sinusoidal endothelial cells from other, more regularly structured endothelial cells in the body.\nDue to their special fenestrated structure, SECs facilitate the exchange of macromolecules, like lipoproteins and hyaluronan, between plasma and the surrounding organ parenchymal cells. These fenestrations act like sieves, allowing the passage of substances based on their size and charge. It's noteworthy that the permeability characteristics of SECs can be regulated dynamically according to the body's homeostatic needs. \nBeyond their key role in exchange mechanisms, endothelial cells of sinusoids are involved in several other functions. In the liver, for example, they help in the removal and endocytic degradation of waste macromolecules, immune response, and regulation of liver regeneration. They also participate in the formation and remodeling of blood vessels, a process known as angiogenesis. Additionally, in recent years, it has been discovered that these cells may have a role in disease conditions like cirrhosis and liver cancer." xsd:string {xref="DOI:10.1007/s10456-021-09780-y", xref="DOI:10.1016/j.jhep.2016.07.009", xref="DOI:10.1038/s41575-018-0020-y", xref="DOI:10.1038/s41598-020-57652-0", xref="DOI:10.1186/1476-5926-1-1"} creation_date: 2010-09-14T10:57:26Z [Term] id: CL:0002263 name: transitional cell of parathyroid gland def: "One of three types of epithelial cells that populate the parathyroid gland; cytological characteristics intermediate between those of the chief cell and of the oxyphil cell. Because only one hormone is produced, the three cell forms are widely believed to be different phases in the life cycle of a single cell type, with the chief cell being its physiologically active stage." [GOC:tfm, ISBN:0412046911] +subset: human_subset +subset: mouse_subset xref: FMA:69324 is_a: CL:0002260 ! epithelial cell of parathyroid gland property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 @@ -18426,11 +20642,13 @@ creation_date: 2010-09-08T02:33:50Z id: CL:0002264 name: type A cell of stomach def: "A type of enteroendocrine cell found in the stomach that secretes glucagon." [GOC:tfm] +subset: human_subset +subset: mouse_subset xref: FMA:83411 is_a: CL:0002067 ! type A enteroendocrine cell -is_a: CL:0002659 ! glandular epithelial cell of stomach +is_a: CL:1001517 ! stomach enteroendocrine cell intersection_of: CL:0002067 ! type A enteroendocrine cell -intersection_of: part_of UBERON:0000945 ! stomach +intersection_of: part_of UBERON:0001276 ! epithelium of stomach property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-10T10:54:42Z @@ -18438,12 +20656,15 @@ creation_date: 2010-09-10T10:54:42Z id: CL:0002265 name: type D cell of colon def: "A D cell located in the colon." [GOC:tfm] +subset: human_subset +subset: mouse_subset synonym: "colon D-cell" EXACT [] synonym: "colonic delta cell" EXACT [] synonym: "delta cell of colon" EXACT [] xref: FMA:268744 is_a: CL:0000502 ! type D enteroendocrine cell is_a: CL:0009042 ! enteroendocrine cell of colon +is_a: CL:1001588 ! colon glandular cell intersection_of: CL:0000502 ! type D enteroendocrine cell intersection_of: part_of UBERON:0001155 ! colon property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 @@ -18453,6 +20674,8 @@ creation_date: 2010-09-10T11:37:35Z id: CL:0002266 name: type D cell of small intestine def: "A type D cell of the small intestine." [GOC:tfm] +subset: human_subset +subset: mouse_subset synonym: "delta cell of small intestine" EXACT [] synonym: "small intestine D-cell" EXACT [] synonym: "small intestine delta cell" EXACT [] @@ -18468,14 +20691,17 @@ creation_date: 2010-09-10T01:34:22Z id: CL:0002267 name: type D cell of stomach def: "A type D cell found in the stomach." [GOC:tfm] +subset: human_subset +subset: mouse_subset synonym: "delta cell of stomach" EXACT [] synonym: "stomach D-cell" EXACT [] synonym: "stomach delta cell" EXACT [] xref: FMA:83410 is_a: CL:0000502 ! type D enteroendocrine cell is_a: CL:0002659 ! glandular epithelial cell of stomach +is_a: CL:1000222 ! stomach neuroendocrine cell intersection_of: CL:0000502 ! type D enteroendocrine cell -intersection_of: part_of UBERON:0000945 ! stomach +intersection_of: part_of UBERON:0001276 ! epithelium of stomach property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-10T01:36:03Z @@ -18484,6 +20710,8 @@ id: CL:0002268 name: P/D1 enteroendocrine cell def: "An enteroendocrine cell that stores and secretes Ghrelin." [GOC:tfm, ISBN:0517223651, PMID:15153415] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset xref: FMA:63418 is_a: CL:0000164 ! enteroendocrine cell is_a: CL:0002269 ! vasoactive intestinal peptide secreting cell @@ -18494,6 +20722,8 @@ creation_date: 2010-09-10T01:47:45Z id: CL:0002269 name: vasoactive intestinal peptide secreting cell def: "An endocrine cell that secretes vasoactive intestinal peptide." [GOC:tfm] +subset: human_subset +subset: mouse_subset is_a: CL:0000167 ! peptide hormone secreting cell property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-10T01:52:20Z @@ -18502,6 +20732,8 @@ creation_date: 2010-09-10T01:52:20Z id: CL:0002270 name: type EC2 enteroendocrine cell def: "A type EC enteroendocrine cell in the duodenum and jejunum that stores and secretes motilin and 5-hydroxytryptamine." [GOC:tfm, ISBN:0517223651, PMID:15153415] +subset: human_subset +subset: mouse_subset synonym: "Mo enteroendocrine cell" BROAD [] xref: FMA:62941 is_a: CL:0000577 ! type EC enteroendocrine cell @@ -18513,6 +20745,8 @@ creation_date: 2010-09-10T02:13:47Z id: CL:0002271 name: type EC1 enteroendocrine cell def: "A type EC enteredocrine cell in the intestines that stores and secretes substance P and 5-hydroxytryptamine." [GOC:tfm, ISBN:0517223651] +subset: human_subset +subset: mouse_subset xref: FMA:62940 is_a: CL:0000505 ! substance P secreting cell is_a: CL:0000577 ! type EC enteroendocrine cell @@ -18523,6 +20757,8 @@ creation_date: 2010-09-10T02:13:49Z id: CL:0002272 name: motilin secreting cell def: "A cell that secretes motilin, a gastric hormone that at low pH inhibits gastric motor activity, whereas at high pH has a stimulating effect." [GOC:tfm, MESH:D009037] +subset: human_subset +subset: mouse_subset is_a: CL:0000167 ! peptide hormone secreting cell property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-10T02:31:13Z @@ -18531,6 +20767,8 @@ creation_date: 2010-09-10T02:31:13Z id: CL:0002273 name: type ECL enteroendocrine cell def: "A type EC enteroendocrine cell type that is numerous in the fundus of the stomach; stores 5-hydroxytryptamine and histamine." [GOC:tfm, ISBN:0517223651, PMID:15153415] +subset: human_subset +subset: mouse_subset xref: FMA:63208 is_a: CL:0000577 ! type EC enteroendocrine cell is_a: CL:0002274 ! histamine secreting cell @@ -18541,6 +20779,8 @@ creation_date: 2010-09-10T02:35:17Z id: CL:0002274 name: histamine secreting cell def: "A cell type that secretes histamine." [GOC:tfm] +subset: human_subset +subset: mouse_subset is_a: CL:0000457 ! biogenic amine secreting cell intersection_of: CL:0000151 ! secretory cell intersection_of: capable_of GO:0001821 ! histamine secretion @@ -18555,6 +20795,8 @@ def: "A PP cell located in the islets of the pancreas." [GOC:tfm] comment: The term PP cell of pancreatic acinus was obsoleted due to a lack of evidence, making PP cell of pancreatic islets synonymous with pancreatic PP cell. subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "pancreatic polypeptide-secreting cell" EXACT [] synonym: "PP cell of pancreatic islet" EXACT [] synonym: "PP-cell of pancreatic islet" EXACT [] @@ -18571,7 +20813,7 @@ intersection_of: part_of UBERON:0001264 ! pancreas relationship: part_of UBERON:0000006 ! islet of Langerhans property_value: RO:0002175 NCBITaxon:9606 property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 -property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional.\n\nPancreatic polypeptide (PP) cells (also called F or gamma cells) are unique endocrine cells located within the Islets of Langerhans in the pancreas. PP cells are one of the rarer pancreatic cell types and are more prevalent in the head and neck of the pancreas. They are critical in normal pancreatic physiological functions and are involved in the development of pancreatic endocrine disorders.\nThe primary function of PP cells is the production and secretion of the pancreatic polypeptide hormone (PP). This hormone plays a crucial role in several gastrointestinal functions and metabolic responses. The release of the PP hormone is stimulated after eating, especially in protein-rich meals, leading to it being present in large amounts during digestion. The fundamental role of PP is to self-regulate pancreatic secretion activities ensuring its exocrine and endocrine functions are under control.\nThe pancreatic polypeptide hormone from PP cells also aids in adapting to low physical activity and fasting by reducing the production of insulin and glucagon and inhibiting the hepatic glucose production. Additionally, this hormone influences gut motility by slowing down the gastric emptying and reducing small intestinal transit, thereby controlling the pace at which nutritional substances are absorbed. Because of these functions, any malfunction or irregularity in PP cells can result in various disorders such as diabetes and pancreatic diseases." xsd:string {xref="DOI:10.1016/B978-0-12-819402-7.00001-2", xref="DOI:10.1016/B978-012369442-3/50154-9", xref="DOI:10.1016/j.mce.2015.06.028", xref="DOI:10.1038/s42255-019-0148-2", xref="DOI:10.3389/fendo.2023.1192311"} +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nPancreatic polypeptide (PP) cells (also called F or gamma cells) are unique endocrine cells located within the Islets of Langerhans in the pancreas. PP cells are one of the rarer pancreatic cell types and are more prevalent in the head and neck of the pancreas. They are critical in normal pancreatic physiological functions and are involved in the development of pancreatic endocrine disorders.\nThe primary function of PP cells is the production and secretion of the pancreatic polypeptide hormone (PP). This hormone plays a crucial role in several gastrointestinal functions and metabolic responses. The release of the PP hormone is stimulated after eating, especially in protein-rich meals, leading to it being present in large amounts during digestion. The fundamental role of PP is to self-regulate pancreatic secretion activities ensuring its exocrine and endocrine functions are under control.\nThe pancreatic polypeptide hormone from PP cells also aids in adapting to low physical activity and fasting by reducing the production of insulin and glucagon and inhibiting the hepatic glucose production. Additionally, this hormone influences gut motility by slowing down the gastric emptying and reducing small intestinal transit, thereby controlling the pace at which nutritional substances are absorbed. Because of these functions, any malfunction or irregularity in PP cells can result in various disorders such as diabetes and pancreatic diseases." xsd:string {xref="DOI:10.1016/B978-0-12-819402-7.00001-2", xref="DOI:10.1016/B978-012369442-3/50154-9", xref="DOI:10.1016/j.mce.2015.06.028", xref="DOI:10.1038/s42255-019-0148-2", xref="DOI:10.3389/fendo.2023.1192311"} creation_date: 2010-09-10T03:30:31Z [Term] @@ -18589,6 +20831,8 @@ id: CL:0002277 name: type I enteroendocrine cell def: "An enteroendocrine cell commonest in the duodenum and jejunum, rare in ileum, that secretes cholecystokinin. This cell type is involved in the regulation of digestive enzymes and bile." [GOC:tfm] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "CCK cell" EXACT [] xref: FMA:62937 is_a: CL:0000164 ! enteroendocrine cell @@ -18601,6 +20845,8 @@ id: CL:0002278 name: GIP cell def: "An enteroendocrine cell of duodenum and jejunum that produces gastric inhibitory peptide." [GOC:tfm] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "type K enteroendocrine cell" EXACT [] xref: FMA:62942 is_a: CL:0000167 ! peptide hormone secreting cell @@ -18613,6 +20859,8 @@ id: CL:0002279 name: type L enteroendocrine cell def: "A enteroendocrine cell type that is numerous in ileum, present in jejunum and large intestine, few in duodenum. This cell type produces glucagon-like immunoreactants (glicentin, glucagon-37, glucagon-29, GLP-1 and -2) and PYY." [ISBN:0517223651, PMID:15153415] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset xref: FMA:62944 is_a: CL:0000164 ! enteroendocrine cell is_a: CL:0000167 ! peptide hormone secreting cell @@ -18624,6 +20872,8 @@ id: CL:0002280 name: type N enteroendocrine cell def: "An enteroendocrine cell found in the ileum and jejunum that produces neurotensin." [GOC:tfm] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "N cell" EXACT [] xref: FMA:62943 is_a: CL:0000164 ! enteroendocrine cell @@ -18635,6 +20885,8 @@ creation_date: 2010-09-10T04:08:29Z id: CL:0002281 name: type S enteroendocrine cell def: "Scattered in duodenojejunal mucosa, this enteroendocrine cell secretes secretin and serotonin." [GOC:tfm, PMID:15153415] +subset: human_subset +subset: mouse_subset xref: FMA:62936 is_a: CL:0000164 ! enteroendocrine cell is_a: CL:0000167 ! peptide hormone secreting cell @@ -18646,6 +20898,8 @@ creation_date: 2010-09-10T04:44:46Z id: CL:0002282 name: type TG enteroendocrine cell def: "An enteroendocrine cell which produces a gastrin- and cholecystokinin-like peptide. The apical microvilli-rich plasma membrane is in open contact with the small intestine mucosa. This cell type is devoid of gastrin-17 but contains other fragments of the gastrin polypeptide." [DOI:10.1007/978-3-211-99390-3, GOC:tfm, PMID:7013499] +subset: human_subset +subset: mouse_subset xref: FMA:63421 is_a: CL:0000164 ! enteroendocrine cell is_a: CL:0000509 ! gastrin secreting cell @@ -18657,6 +20911,8 @@ id: CL:0002283 name: ecto-epithelial cell of viscerocranial mucosa alt_id: CL:1000440 def: "An epithelial cell of the mucosa associated with facial skeleton." [GOC:tfm, ISBN:0323052908] +subset: human_subset +subset: mouse_subset xref: FMA:70581 is_a: CL:0002159 ! general ecto-epithelial cell property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 @@ -18666,6 +20922,8 @@ creation_date: 2010-09-14T11:04:02Z id: CL:0002284 name: type X enteroendocrine cell def: "An enteroendocrine cell found in the fundus and pylorus; this cell type has dense round secretory granules that contain ghrelin." [GOC:tfm, PMID:20616512] +subset: human_subset +subset: mouse_subset synonym: "A-like" EXACT [] synonym: "X/A-like" EXACT [] xref: FMA:63209 @@ -18678,6 +20936,8 @@ creation_date: 2010-09-13T10:12:12Z id: CL:0002285 name: type III taste bud cell def: "A taste receptor cell that is characterized by morphologically identifiable synaptic contacts with the gustatory nerve fibers and expression of the synaptic membrane protein-25 (SNAP-25) and NCAM." [GOC:tfm, ISBN:0517223651, PMID:15738192] +subset: human_subset +subset: mouse_subset synonym: "taste bud basal cell" BROAD [] synonym: "type 3 taste cell" EXACT [] xref: FMA:67940 @@ -18690,6 +20950,8 @@ creation_date: 2010-09-13T10:57:21Z id: CL:0002286 name: type II taste cell def: "A taste receptor cell that has a short microvilli, a projecting apical region, a large rounded nucleus, and expresses taste chemoreceptors thus making them the transducing cell for taste qualities." [GOC:tfm, PMID:15738192] +subset: human_subset +subset: mouse_subset synonym: "type 2 taste cell" EXACT [] xref: FMA:62381 is_a: CL:0000209 ! taste receptor cell @@ -18701,6 +20963,8 @@ id: CL:0002287 name: type IV taste receptor cell def: "A rounded, mitotically active stem cell which is the source of new cells of the taste bud; located basally." [GOC:tfm, ISBN:0517223651, PMID:15738192] comment: There is debate about the exact lineage of these cell types from this progenitor. See PMID:15738192. +subset: human_subset +subset: mouse_subset synonym: "taste bud basal cell" BROAD [] synonym: "type 4 taste cell" EXACT [] xref: FMA:62380 @@ -18713,6 +20977,8 @@ creation_date: 2010-09-13T10:57:29Z id: CL:0002288 name: type V taste receptor cell def: "A cell type that forms the boundary with the surrounding epithelium." [GOC:tfm, ISBN:0517223651] +subset: human_subset +subset: mouse_subset xref: FMA:67941 is_a: CL:0000209 ! taste receptor cell property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 @@ -18722,6 +20988,8 @@ creation_date: 2010-09-13T10:57:31Z id: CL:0002289 name: type I taste bud cell def: "A densely staining taste receptor cell that contains many dense vacuoles in their apical regions which project into the apical space and bear microvilli. This cell type serves as a supporting cell by surrounding and isolating the other cell types from each other; secrete a dense amorphous material that surrounds the microvilli in the taste pore. This cell type expresses a glial glutumate transporter, GLAST." [GOC:tfm, ISBN:0412046911, ISBN:0517223651, PMID:15738192] +subset: human_subset +subset: mouse_subset synonym: "dark tongue cell" EXACT [] synonym: "type I taste cell" EXACT [] synonym: "type taste 1 cell" EXACT [] @@ -18735,6 +21003,8 @@ creation_date: 2010-09-13T10:57:35Z id: CL:0002290 name: Y chromosome-bearing sperm cell def: "A sperm bearing a Y chromosome. Chromosomal and genetic sex is established at fertilization in mammals and depends upon whether an X-bearing sperm or a Y-bearing sperm fertilizes the X-bearing ovum." [GOC:tfm, ISBN:0721669743] +subset: human_subset +subset: mouse_subset synonym: "Y bearing sperm" EXACT [] synonym: "Y-bearing sperm" EXACT [] xref: FMA:84058 @@ -18746,6 +21016,8 @@ creation_date: 2010-09-13T11:35:24Z id: CL:0002291 name: X chromosome-bearing sperm cell def: "A sperm bearing an X chromosome. Chromosomal and genetic sex is established at fertilization in mammals and depends upon whether an X-bearing sperm or a Y-bearing sperm fertilizes the X-bearing ovum." [GOC:tfm, ISBN:0721669743] +subset: human_subset +subset: mouse_subset synonym: "X bearing sperm" EXACT [] synonym: "X-bearing sperm" EXACT [] xref: FMA:84057 @@ -18758,6 +21030,8 @@ id: CL:0002292 name: type I cell of carotid body def: "A round or oval neuroepithelial cell that contacts other type I cells or capillaries. They occur in clusters that are surrounded by sheath cells (type-II cells) in the carotid body. This cell type is capable of secreting a number of neurotransmitters." [GOC:tfm, ISBN:0517223651] subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "glomus cell" EXACT [] xref: FMA:84186 is_a: CL:0000710 ! neurecto-epithelial cell @@ -18771,6 +21045,8 @@ name: epithelial cell of thymus alt_id: CL:1000459 def: "An epithelial cell of the thymus. Epithelial reticular cells are pleomorphic, stellate, non-phagocytic cells which seem to be supportive in function and are held together by desmosomes. They replace the fibroblastoid reticular cells found in other lymphoid organs. Other epithelial cells in the medulla have the ultrastructure of secretory cells. Although different epithelial cells throughout the thymus appear alike by light microscopy their ultrastructure and function varies." [FMA:72208, GOC:tfm] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "epithelial cell of thymus gland" EXACT [] synonym: "epithelial reticular cell" EXACT [] synonym: "epithelial reticular cell of thymus" EXACT [] @@ -18788,6 +21064,8 @@ creation_date: 2010-09-13T02:34:22Z id: CL:0002294 name: type-1 epithelial cell of thymus def: "An epithelial cell with a well defined Golgi apparatus that makes up the continuous layer of cells bordering the thymic tissue beneath the capsule." [GOC:tfm, PMID:9264335] +subset: human_subset +subset: mouse_subset synonym: "subcapsular thymic epithelial cell" RELATED [PMID:18194204, PMID:2694455] xref: FMA:72209 is_a: CL:0002364 ! cortical thymic epithelial cell @@ -18798,6 +21076,8 @@ creation_date: 2010-09-13T02:37:23Z id: CL:0002295 name: type-6 epithelial cell of thymus def: "A thymic epithelial cell that has an eccentric, round, or irregularly shaped hetero or euchromatic nucleus. The hallmark of this cell type is the presence of vacuoles, which are clustered in one area of the cytoplasm in the vicinity of the nucleus. The vacuoles are small and acquire a grape-like form, occasionally showing delicate internal microvillous projections." [GOC:tfm, PMID:19721455, PMID:9264335] +subset: human_subset +subset: mouse_subset synonym: "cystic thymic epithelial cells" EXACT [] synonym: "large medullary thymic epithelial cells" EXACT [] synonym: "large mTEC" EXACT [] @@ -18810,6 +21090,8 @@ creation_date: 2010-09-13T02:37:26Z id: CL:0002296 name: type-4 epithelial cell of thymus def: "An epithelial cell with high nuclear and cytoplasmic electron-density. This cell type is found in the deeper portions of the cortex but is more abundant in the medulla of the thymus." [FMA:0412046911, GOC:tfm, PMID:9264335] +subset: human_subset +subset: mouse_subset synonym: "dark thymic epithelial cell" EXACT [] xref: FMA:72212 is_a: CL:0002364 ! cortical thymic epithelial cell @@ -18821,6 +21103,8 @@ creation_date: 2010-09-13T02:37:45Z id: CL:0002297 name: type-3 epithelial cell of thymus def: "A thymic epithelial cell with moderate nuclear and cytoplasmic electron-density. Scattered in the cortex, this cell type is predominant in the mid and deep cortex." [PMID:9264335] +subset: human_subset +subset: mouse_subset synonym: "intermediate thymic epithelial cell" EXACT [] xref: FMA:72211 is_a: CL:0002364 ! cortical thymic epithelial cell @@ -18831,6 +21115,8 @@ creation_date: 2010-09-13T02:37:51Z id: CL:0002298 name: type-5 epithelial cell of thymus def: "A thymic epithelial cell type with low nuclear and cytoplasmic electrondensity; has a round, euchromatic nucleus and occurs in small groups at the corticomedullary junction or scattered singly in the medulla." [GOC:tfm, ISBN:0412046911, PMID:19721455, PMID:9264335] +subset: human_subset +subset: mouse_subset synonym: "undifferentiated medullary thymic epithelial cell" EXACT [] synonym: "undifferentiated mTEC" EXACT [] synonym: "undifferentiated thymic epithelial cell" EXACT [] @@ -18843,6 +21129,8 @@ creation_date: 2010-09-13T02:37:54Z id: CL:0002299 name: type-2 epithelial cell of thymus def: "An epithelial cell scattered in the cortex, predominant in the outer cortex with a large pale nucleus and a prominent nucleolus." [GOC:tfm, ISBN:0412046911, PMID:9264335] +subset: human_subset +subset: mouse_subset synonym: "pale thymic epithelial cell" EXACT [] xref: FMA:72210 is_a: CL:0002364 ! cortical thymic epithelial cell @@ -18853,6 +21141,8 @@ creation_date: 2010-09-13T02:37:58Z id: CL:0002300 name: type-7 epithelial cell of thymus def: "A small medullary thymic epithelial cell with a spindle shape, often arranged in groups and connected to each other by large desmosomes and interdigitations. The cytoplasm is sparse, with scanty organelles and thick bundles of cytokeratin." [GOC:tfm, PMID:19721455] +subset: human_subset +subset: mouse_subset synonym: "spindle shaped medullary thymic epithelial cell" EXACT [] synonym: "spindle shaped mTEC" EXACT [] is_a: CL:0002365 ! medullary thymic epithelial cell @@ -18864,6 +21154,8 @@ id: CL:0002301 name: type B synovial cell def: "A resident stromal cell located in the synovial membrane and responsible for the production of immune-related cytokines and chemokines. This cell type secretes glycoproteins and hyaluronic acid, has abundant granular endoplasmic reticulum, but contains fewer vacuoles and vesicles." [GOC:tfm, ISBN:0517223651, PMID:34433485, PMID:34772990] comment: Type B synovial cells play a key role in the pathogenesis of chronic inflammatory diseases, such as rheumatoid arthritis, and are essential for the maintenance of normal joint functions. Fibroblast-like synoviocytes from different joints have different properties, which may contribute to the characteristic pattern of joint involvement in different types of arthritis. {xref="https://en.wikipedia.org/wiki/Fibroblast-like_synoviocyte", xref="PMID:34433485"} +subset: human_subset +subset: mouse_subset synonym: "fibroblast-like synoviocyte" EXACT [] synonym: "synovial fibroblast" EXACT [PMID:23147896] xref: BTO:0003652 @@ -18885,6 +21177,8 @@ id: CL:0002302 name: type A synovial cell def: "A synovial cell that is macrophage-like, characterized by surface ruffles or lamellipodia, plasma membrane invaginations and associated micropinocytotic vesicles, Golgi apparatus and little granular endoplasmic reticulum." [GOC:tfm, ISBN:0517223651] comment: Type A cells are usually round and located in the upper part of the synovial intima. {xref="PMID:10770586"} +subset: human_subset +subset: mouse_subset synonym: "type A synoviocyte" EXACT [] xref: FMA:66787 is_a: CL:0000076 ! squamous epithelial cell @@ -18903,6 +21197,8 @@ comment: In a consensus model of unidirectional secretion, aqueous humour is for subset: cellxgene_subset subset: eye_upper_slim subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "PE cell" EXACT [https://doi.org/10.1016/j.exer.2003.09.021] xref: FMA:70606 xref: https://cellxgene.cziscience.com/cellguide/CL_0002303 @@ -18910,7 +21206,7 @@ is_a: CL:0000529 ! pigmented epithelial cell relationship: part_of UBERON:0001778 ! ciliary epithelium property_value: RO:0002175 NCBITaxon:9606 property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 -property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional.\n\nPigmented ciliary epithelial cells, which are a type of pigment cell, have a crucial function within the eye's ciliary body. The ciliary body, located behind the iris, is one of the eye’s most vital structures and consists of two types of epithelial cells: the pigmented and the non-pigmented ciliary epithelial cells. The pigmented ciliary epithelial cells form the outer layer of the ciliary body and exhibit a black or brown pigmentation due to the melanin they contain.\nOne key function of pigmented ciliary epithelial cells is to aid in the formation of aqueous humor, an intraocular fluid that nourishes the cornea and lens, and maintains intraocular pressure which is essential for the eye’s shape and light refraction. These cells facilitate this function in conjunction with the non-pigmented ciliary epithelial cells. Together, the pigmented and non-pigmented ciliary epithelial cells form a bilayer epithelium that allows the secretion of aqueous humor through a bi-directional fluid transport mechanism.\nPigmented ciliary epithelial cells also contribute to the blood-aqueous barrier, a physiological frontier that controls the entry and exit of various substances from the blood to the aqueous humor and vice versa. The pigmentation in these cells, intensified by melanin, helps to absorb scattered light coming into the eye, reducing any potential damage and glare." xsd:string {xref="DOI:10.1016/S1569-2590(05)10005-6", xref="DOI:10.1111/j.1444-0938.2002.tb02384.x"} +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nPigmented ciliary epithelial cells, which are a type of pigment cell, have a crucial function within the eye's ciliary body. The ciliary body, located behind the iris, is one of the eye’s most vital structures and consists of two types of epithelial cells: the pigmented and the non-pigmented ciliary epithelial cells. The pigmented ciliary epithelial cells form the outer layer of the ciliary body and exhibit a black or brown pigmentation due to the melanin they contain.\nOne key function of pigmented ciliary epithelial cells is to aid in the formation of aqueous humor, an intraocular fluid that nourishes the cornea and lens, and maintains intraocular pressure which is essential for the eye’s shape and light refraction. These cells facilitate this function in conjunction with the non-pigmented ciliary epithelial cells. Together, the pigmented and non-pigmented ciliary epithelial cells form a bilayer epithelium that allows the secretion of aqueous humor through a bi-directional fluid transport mechanism.\nPigmented ciliary epithelial cells also contribute to the blood-aqueous barrier, a physiological frontier that controls the entry and exit of various substances from the blood to the aqueous humor and vice versa. The pigmentation in these cells, intensified by melanin, helps to absorb scattered light coming into the eye, reducing any potential damage and glare." xsd:string {xref="DOI:10.1016/S1569-2590(05)10005-6", xref="DOI:10.1111/j.1444-0938.2002.tb02384.x"} creation_date: 2010-09-13T04:09:27Z [Term] @@ -18921,6 +21217,8 @@ comment: In a consensus model of unidirectional secretion, aqueous humour is for subset: cellxgene_subset subset: eye_upper_slim subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "nonpigmented ciliary epithelial cell" EXACT [PMID:10913011] synonym: "NPE cell" EXACT [https://doi.org/10.1016/j.exer.2003.09.021] xref: FMA:70607 @@ -18934,7 +21232,9 @@ creation_date: 2010-09-13T04:09:31Z id: CL:0002305 name: epithelial cell of distal tubule def: "An epithelial cell of the distal convoluted tubule of the kidney that helps regulate systemic levels of potassium, sodium, calcium, and pH." [GOC:tfm, ISBN:0517223651] +subset: human_subset subset: kidney_upper_slim +subset: mouse_subset synonym: "kidney distal tubule epithelial cell" EXACT [] xref: FMA:70981 xref: KUPO:0001055 @@ -18952,7 +21252,9 @@ def: "An epithelial cell of the proximal tubule of the kidney." [GOC:tfm, ISBN:1 comment: The vast majority of proximal tubule epithelial cells have a brush border, but there are rare exceptions. subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset subset: kidney_upper_slim +subset: mouse_subset synonym: "kidney proximal tubule epithelial cell" EXACT [] xref: FMA:70973 xref: KUPO:0001044 @@ -18969,6 +21271,8 @@ id: CL:0002307 name: brush border cell of the proximal tubule def: "A brush border epithelial cell located in the proximal tubule of the kidney, essential for reabsorbing substances like glucose and amino acids from the glomerular filtrate. These cells also secrete organic ions, playing a crucial role in maintaining kidney homeostasis, including electrolyte and acid-base balance, and excreting metabolic waste." [GOC:tfm, ISBN:1-4160-2328-3, PMID:23799132] comment: The vast majority of proximal tubule epithelial cells have a brush border, but there are rare exceptions. +subset: human_subset +subset: mouse_subset is_a: CL:0000239 ! brush border epithelial cell is_a: CL:0002306 ! epithelial cell of proximal tubule intersection_of: CL:0002306 ! epithelial cell of proximal tubule @@ -18980,6 +21284,8 @@ creation_date: 2010-09-14T11:29:20Z id: CL:0002308 name: epithelial cell of skin gland def: "An epithelial cell of a skin gland." [GOC:tfm] +subset: human_subset +subset: mouse_subset synonym: "epithelial cell of gland of skin" EXACT [] xref: FMA:70657 is_a: CL:0002159 ! general ecto-epithelial cell @@ -18993,6 +21299,8 @@ creation_date: 2010-09-14T12:00:07Z id: CL:0002309 name: corticotroph def: "A basophil chromphil cell of the anterior pitiutary gland that produce adrenocorticotropic hormone, melanocyte-stimulating hormone and lipotropin. This cell type is irregular in shape and has short dendritic processes which are inserted among other neighboring cells;" [GOC:tfm, ISBN:0517223651] +subset: human_subset +subset: mouse_subset xref: BTO:0002509 xref: FMA:83098 xref: MESH:D052680 @@ -19005,6 +21313,8 @@ creation_date: 2010-09-14T02:08:23Z id: CL:0002310 name: mammosomatotroph def: "An acidophil cell of the anterior pituitary gland that produces both prolactin and growth hormone." [GOC:tfm] +subset: human_subset +subset: mouse_subset xref: FMA:83097 is_a: CL:0000295 ! somatotropin secreting cell is_a: CL:0000439 ! prolactin secreting cell @@ -19016,6 +21326,8 @@ creation_date: 2010-09-14T02:25:34Z id: CL:0002311 name: mammotroph def: "An acidophilic cell of the anterior pituitary that produces prolactin." [SANBI:mhl] +subset: human_subset +subset: mouse_subset synonym: "epsilon-acidophil" EXACT [] synonym: "lactotrope" EXACT [] synonym: "lactotroph" EXACT [] @@ -19033,6 +21345,8 @@ creation_date: 2010-09-14T02:30:57Z id: CL:0002312 name: somatotroph def: "An acidophilic cell of the anterior pituitary that produces growth hormone, somatotropin." [SANBI:mhl] +subset: human_subset +subset: mouse_subset synonym: "somatotrope" EXACT [] synonym: "somatotropic cell" EXACT [] synonym: "somatrophic cell" EXACT [] @@ -19047,12 +21361,14 @@ creation_date: 2010-09-14T02:33:09Z id: CL:0002313 name: endocrine-paracrine cell of prostate gland def: "An ecto-epithelial cell of the prostate gland that secretes hormones." [GOC:tfm] +subset: human_subset +subset: mouse_subset synonym: "glandular cell of prostate" EXACT [] synonym: "neuro-epithelial cell of prostate gland" EXACT [] xref: CALOHA:TS-1280 xref: FMA:74390 xref: FMA:86774 -is_a: CL:0000150 ! glandular epithelial cell +is_a: CL:0000150 ! glandular secretory epithelial cell is_a: CL:0002159 ! general ecto-epithelial cell intersection_of: CL:0002159 ! general ecto-epithelial cell intersection_of: capable_of GO:0046879 ! hormone secretion @@ -19066,6 +21382,8 @@ creation_date: 2010-09-14T03:01:58Z id: CL:0002314 name: external supporting cell of vestibular epithelium def: "An auditory epithelial support cell located in the vestibular epithelium that has many hallmarks of glial cells. This cell type express glial markers such as vimentin, S100, glutamate-aspartate transporter, low affinity neurotrophin receptor p75, glial fibrillary acidic protein, and proteolipid protein." [GOC:tfm, PMID:20837532] +subset: human_subset +subset: mouse_subset xref: FMA:75809 is_a: CL:0002316 ! supporting cell of vestibular epithelium property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 @@ -19075,6 +21393,8 @@ creation_date: 2010-09-14T03:20:01Z id: CL:0002315 name: supporting cell of cochlea def: "An epithelial supporting cell located in the cochlea." [GOC:tfm] +subset: human_subset +subset: mouse_subset xref: FMA:79796 is_a: CL:0001035 ! bone cell is_a: CL:0005014 ! auditory epithelial supporting cell @@ -19088,6 +21408,8 @@ creation_date: 2010-09-14T03:31:38Z id: CL:0002316 name: supporting cell of vestibular epithelium def: "A supporting cell of the vestibular epithelium." [GOC:tfm, PMID:20837532] +subset: human_subset +subset: mouse_subset xref: FMA:75607 is_a: CL:0005014 ! auditory epithelial supporting cell intersection_of: CL:0005014 ! auditory epithelial supporting cell @@ -19100,6 +21422,8 @@ creation_date: 2010-09-14T03:31:44Z id: CL:0002317 name: external limiting cell of vestibular epithelium def: "An external limiting cell found in the vestibular epithelium." [GOC:tfm] +subset: human_subset +subset: mouse_subset xref: FMA:75808 is_a: CL:0002316 ! supporting cell of vestibular epithelium property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 @@ -19109,6 +21433,8 @@ creation_date: 2010-09-14T03:33:50Z id: CL:0002318 name: peripheral blood mesothelial cell def: "A mesothelial cell capable of circulating in the blood by first losing its squamous character. This cell can incorporate into the regenerating mesothelium." [GOC:tfm, PMID:14592528] +subset: human_subset +subset: mouse_subset xref: FMA:86712 is_a: BFO:0000002 is_a: CL:0000081 ! blood cell @@ -19122,6 +21448,8 @@ id: CL:0002319 name: neural cell def: "A cell that is part of the nervous system." [GOC:tfm, ISBN:0618947256] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset xref: CALOHA:TS-2040 xref: FMA:70333 is_a: CL:0000255 ! eukaryotic cell @@ -19137,6 +21465,8 @@ name: connective tissue cell alt_id: CL:1000406 def: "A cell of the supporting or framework tissue of the body, arising chiefly from the embryonic mesoderm and including adipose tissue, cartilage, and bone." [GOC:tfm, ISBN:0618947256] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset xref: CALOHA:TS-2096 xref: FMA:63875 xref: MESH:D003239 @@ -19152,12 +21482,16 @@ creation_date: 2010-09-15T03:01:54Z id: CL:0002321 name: embryonic cell (metazoa) def: "A cell of the embryo." [FMA:0618947256] +subset: human_subset +subset: mouse_subset xref: CALOHA:TS-0263 xref: FMA:82840 +xref: https://cellxgene.cziscience.com/cellguide/CL_0002321 xref: WBbt:0007028 xref: ZFA:0007089 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000000 ! cell property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nEmbryonic cells in metazoans, which include all multicellular animals, are biological units in their earliest developmental stages from conception until the organism is fully formed. \nThey are derived from a fertilized egg, which undergoes a series of cell divisions to produce a multicellular organism. During the early phases of embryonic development, these cells exhibit pluripotency, meaning they possess the potential to differentiate into a diverse array of specialized cell types that constitute different body tissues and structures. \nThe balance between cell proliferation and differentiation in embryonic cells is crucial for successful development. When cells continue to divide without differentiating, overgrowth may occur leading to conditions such as teratomas (tumors of embryonic cells). Conversely, if cell differentiation proceeds at the expense of cell proliferation, developmental anomalies could occur regarding size or mass of the organism or its parts." xsd:string {xref="DOI:10.1002/iub.1404", xref="DOI:10.1093/molehr/gan048", xref="https://www.ncbi.nlm.nih.gov/books/NBK9906/"} creation_date: 2010-09-15T03:39:21Z [Term] @@ -19166,6 +21500,8 @@ name: embryonic stem cell def: "A stem cell of embryonic origin." [GOC:dsd, GOC:tfm, ISBN:068340007X, PMID:18179856] comment: This is an in vitro cell type and may be removed in future releases. These cells are reportedly SSEA-4-positive, CD73-negative, and CD324-positive. subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "ESC" EXACT [] xref: BTO:0001086 xref: CALOHA:TS-0263 @@ -19180,6 +21516,8 @@ creation_date: 2010-09-15T03:44:35Z id: CL:0002323 name: amniocyte def: "A cell of a fetus which is suspended in the amniotic fluid. Amniocytes are considered to arise from several tissues including fetal skin, the fetal urinary tract, umbilical cord, and the inner amniotic surface." [BFO:0000066, GOC:tfm, PMID:3211847] +subset: human_subset +subset: mouse_subset xref: BTO:0000066 is_a: CL:0000349 {is_inferred="true"} ! extraembryonic cell intersection_of: CL:0000349 ! extraembryonic cell @@ -19194,6 +21532,8 @@ name: basal-myoepithelial cell of mammary gland def: "A myoepithelial cell that is part of a mammary gland and is located in the basal layer. During lactation, a basal-myoepithelial cell of mammary gland contracts under the stimulation of oxytocin. In humans, a basal-myoepithelial cell of mammary gland can be identified by high levels of CD49f and low levels of EpCAM." [GOC:tfm, PMID:11250738, PMID:19022771, PMID:38059556] comment: Due inconsistencies in naming this and other mammary gland epithelial cell types, several mammary gland experts gathered for a breast atlas annotation jamboree organized by Chan-Zuckerberg initiative. They agreed to label this cell type as basal-myoepithelial cell (and abbreviated: B-Myo cell). {xref="PMID:38059556"} subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "B-Myo cell" RELATED OMO:0003000 [] synonym: "basal" RELATED OMO:0003000 [PMID:37380767] synonym: "basal cell of lactiferous duct" NARROW [FMA:67800] @@ -19220,6 +21560,8 @@ alt_id: CL:0002230 alt_id: CL:1000476 def: "A milk-producing glandular epithelial cell that is part of a mammary gland alveolus and differentiates from a luminal adaptive secretory precursor cell during secretory differentiation (also termed lactogenesis I). Following secretory activation (also termed lactogenesis II), a lactocyte is involved in the synthesis and/or transport of milk constituents including proteins, oligosaccharides, lactose, micronutrients, fat, hormones, immunoglobulins, and cytokines into the lumen of the lactating mammary gland." [doi:10.1177/156482659601700404, GOC:tfm, PMID:19022771, PMID:28717367, PMID:35091553, PMID:35377806] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "epithelial cell of lactiferous gland" EXACT [] synonym: "lactaction-associated mammary epithelial cell" EXACT [PMID:35091553] synonym: "lactation-derived mammary cell" EXACT [PMID:35091553] @@ -19233,7 +21575,7 @@ xref: FMA:79866 is_a: CL:0000314 ! milk secreting cell is_a: CL:0002159 {is_inferred="true"} ! general ecto-epithelial cell is_a: CL:1001586 ! mammary gland glandular cell -intersection_of: CL:0000150 ! glandular epithelial cell +intersection_of: CL:0000150 ! glandular secretory epithelial cell intersection_of: part_of UBERON:0003214 ! mammary gland alveolus relationship: part_of UBERON:0003214 ! mammary gland alveolus relationship: RO:0002202 CL:4033057 ! develops from luminal adaptive secretory precursor cell of mammary gland @@ -19247,6 +21589,8 @@ id: CL:0002326 name: luminal epithelial cell of mammary gland def: "A mammary epithelial cell that occurs in the lumen of the ductal and alveoli structure in the breast." [GOC:tfm, PMID:19022771] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "mature luminal cell" BROAD [PMID:21930782] xref: FMA:73280 is_a: BFO:0000002 @@ -19261,6 +21605,8 @@ id: CL:0002327 name: mammary gland epithelial cell def: "An epithelial cell of the mammary gland." [GOC:tfm, PMID:19022771] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "breast epithelial cell" EXACT [] synonym: "mammary epithelial cell" EXACT [] xref: BTO:0004300 @@ -19276,6 +21622,8 @@ id: CL:0002328 name: bronchial epithelial cell def: "An epithelial cell of the bronchus." [GOC:tfm] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset xref: BTO:0002922 is_a: CL:0002202 ! epithelial cell of tracheobronchial tree intersection_of: CL:0000066 ! epithelial cell @@ -19290,30 +21638,39 @@ name: basal epithelial cell of tracheobronchial tree def: "An epithelial cell type that lacks the columnar shape typical for other respiratory epithelial cells. This cell type is able to differentiate into other respiratory epithelial cells in response to injury." [GOC:tfm] subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset xref: https://cellxgene.cziscience.com/cellguide/CL_0002329 is_a: CL:0002202 ! epithelial cell of tracheobronchial tree property_value: RO:0002175 NCBITaxon:9606 property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 -property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional.\n\nThe basal epithelial cells of the tracheobronchial tree are critical components found in the lining of the airway passages, including the trachea and bronchi. They are keratin-5-positive, nonciliated, cuboidal cells and typically tightly attached to the basement membrane. In humans, the proportion of basal cells in the respiratory epithelium gradually decreases going down the tracheobronchial tree: they represent approximately 34% of the cells in the trachea, 27% in the large airways, and 10% in the small airways, although it is worth noting that there are differences in the compositions of the tracheobronchial epithelia between different species.\nBasal epithelial cells serve as the basal layer of the tracheobronchial epithelium, providing both structural and regenerative support for the epithelial tissue that lines the upper regions of the respiratory tract. They serve as progenitor or stem cells that are capable of differentiating into multiple cell types, such as ciliated and secretory cells. This gives them a central role in homeostatic maintenance of the epithelium, and in repairing damaged epithelium after an injury or during disease. This regenerative capacity is crucial in maintaining the integrity of the tracheobronchial surface, especially given its continual exposure to inhaled irritants and microorganisms. \nIn addition to their primary restorative function, basal epithelial cells are also involved in the initial immune response within the tracheobronchial tree. Equipped with pattern recognition receptors, these cells can identify and respond to pathogenic organisms, triggering an immune response and producing a range of inflammatory mediators, such as cytokines and chemokines, to help combat infections." xsd:string {xref="DOI:10.1165/rcmb.2013-0049OC", xref="DOI:10.1186/s12931-014-0160-8", xref="DOI:10.2353/ajpath.2010.090870"} +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nThe basal epithelial cells of the tracheobronchial tree are critical components found in the lining of the airway passages, including the trachea and bronchi. They are keratin-5-positive, nonciliated, cuboidal cells and typically tightly attached to the basement membrane. In humans, the proportion of basal cells in the respiratory epithelium gradually decreases going down the tracheobronchial tree: they represent approximately 34% of the cells in the trachea, 27% in the large airways, and 10% in the small airways, although it is worth noting that there are differences in the compositions of the tracheobronchial epithelia between different species.\nBasal epithelial cells serve as the basal layer of the tracheobronchial epithelium, providing both structural and regenerative support for the epithelial tissue that lines the upper regions of the respiratory tract. They serve as progenitor or stem cells that are capable of differentiating into multiple cell types, such as ciliated and secretory cells. This gives them a central role in homeostatic maintenance of the epithelium, and in repairing damaged epithelium after an injury or during disease. This regenerative capacity is crucial in maintaining the integrity of the tracheobronchial surface, especially given its continual exposure to inhaled irritants and microorganisms. \nIn addition to their primary restorative function, basal epithelial cells are also involved in the initial immune response within the tracheobronchial tree. Equipped with pattern recognition receptors, these cells can identify and respond to pathogenic organisms, triggering an immune response and producing a range of inflammatory mediators, such as cytokines and chemokines, to help combat infections." xsd:string {xref="DOI:10.1165/rcmb.2013-0049OC", xref="DOI:10.1186/s12931-014-0160-8", xref="DOI:10.2353/ajpath.2010.090870"} creation_date: 2010-09-20T02:10:36Z [Term] id: CL:0002330 name: undifferentiated cell of bronchus epithelium def: "An undifferentiated columnar cell of the bronchus epithelium" [GOC:tfm, PMID:18757316] +subset: human_subset +subset: mouse_subset is_a: CL:0002328 ! bronchial epithelial cell property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-20T02:17:58Z [Term] id: CL:0002332 -name: ciliated cell of the bronchus -def: "A ciliated cell of the bronchus." [GOC:tfm, PMID:18757316] +name: multiciliated epithelial cell of the bronchus +def: "A multi-ciliated epithelial cell located in the bronchus epithelium, characterized by a columnar shape and motile cilia on its apical surface." [GOC:tfm, PMID:18757316] subset: cellxgene_subset subset: human_reference_atlas -is_a: CL:0002145 ! ciliated columnar cell of tracheobronchial tree +subset: human_subset +subset: mouse_subset +synonym: "ciliated epithelial cell of the bronchus" EXACT [] +is_a: CL:0002145 ! multiciliated columnar cell of tracheobronchial tree is_a: CL:0002328 ! bronchial epithelial cell -intersection_of: CL:0000064 ! ciliated cell +intersection_of: CL:0000075 ! columnar/cuboidal epithelial cell +intersection_of: bearer_of PATO:0010007 ! multiciliated +intersection_of: has_part GO:0031514 ! motile cilium intersection_of: part_of UBERON:0002031 ! epithelium of bronchus property_value: RO:0002175 NCBITaxon:9606 property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 @@ -19323,6 +21680,8 @@ creation_date: 2010-09-20T02:21:12Z id: CL:0002333 name: neural crest derived adipocyte def: "An adipocyte derived from a neural crest cell." [GOC:tfm, PMID:17507398] +subset: human_subset +subset: mouse_subset is_a: CL:0000136 ! adipocyte intersection_of: CL:0000136 ! adipocyte intersection_of: RO:0002202 CL:0000333 ! develops from migratory neural crest cell @@ -19334,6 +21693,9 @@ creation_date: 2010-09-20T02:25:25Z id: CL:0002334 name: preadipocyte def: "An undifferentiated fibroblast that can be stimulated to form a fat cell." [GOC:tfm, PMID:18793119] +subset: cellxgene_subset +subset: human_subset +subset: mouse_subset xref: BTO:0001107 is_a: CL:0000057 ! fibroblast property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 @@ -19343,6 +21705,9 @@ creation_date: 2010-09-20T02:31:53Z id: CL:0002335 name: brown preadipocyte def: "A preadipocyte that is capable of differentiating into a brown adipocyte. This cell type expresses uncoupling protein-1, PPAR-gamma, PR-domain-containing 16; and PGC-1alpha (peroxisome proliferator-activated receptor-gamma (PPARgamma) coactivator-1alpha)." [GOC:tfm, PMID:18719589] +subset: cellxgene_subset +subset: human_subset +subset: mouse_subset is_a: CL:0002334 ! preadipocyte property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-20T02:38:38Z @@ -19351,6 +21716,8 @@ creation_date: 2010-09-20T02:38:38Z id: CL:0002336 name: buccal mucosa cell def: "An endothelial cell that lines the oral cavitiy including the mucosa of the gums, the palate, the lip, and the cheek." [GOC:tfm, MESH:D009061] +subset: human_subset +subset: mouse_subset is_a: CL:0002261 ! endothelial cell of viscerocranial mucosa property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-20T02:52:54Z @@ -19361,6 +21728,8 @@ name: keratinocyte stem cell def: "A stem cell located in the bulge of the hair follicle that can give rise to regenerate the new follicle with each hair cycle and to reepithelialize the epidermis during wound repair." [PMID:15339667] subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "bulge keratinocyte" EXACT [] is_a: CL:0000048 ! multi fate stem cell is_a: CL:0000312 ! keratinocyte @@ -19375,9 +21744,9 @@ name: CD56-positive, CD161-positive immature natural killer cell, human def: "A natural killer cell that is developmentally immature, has the phenotype CD34-negative, CD56-positive, CD117-positive, CD122-positive,and CD161-positive." [GO_REF:0000031, GOC:add, ISBN:0781735149, PMID:12457618] comment: Human markers; killer cell immunoglobulin-like receptor 2DL1 is used as a representative example (PRO at this time lacks a KIR superfamily). subset: cellxgene_subset +subset: human_subset synonym: "p-NK" RELATED [PMID:12457618] is_a: CL:0000823 ! immature natural killer cell -is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000823 ! immature natural killer cell intersection_of: CL:4030046 PR:000001003 ! lacks_plasma_membrane_part CD34 molecule intersection_of: RO:0002104 PR:000001024 ! has plasma membrane part neural cell adhesion molecule 1 @@ -19399,6 +21768,8 @@ creation_date: 2010-09-21T10:06:53Z id: CL:0002339 name: prostate stem cell def: "A prostate epithelial cell that is CD133-positive, CD44-positive, integrin A2beta3-high. This cell is a stem cell for the prostate epithelium." [GOC:tfm, PMID:15226377] +subset: human_subset +subset: mouse_subset synonym: "CD133-positive prostate epithelial cell" EXACT [] is_a: CL:0000048 ! multi fate stem cell is_a: CL:0002341 ! basal cell of prostate epithelium @@ -19413,6 +21784,8 @@ name: luminal cell of prostate epithelium def: "The exocrine cell of the prostate, this epithelial cell secretes prostatic acid phosphotase and PSA, and is dependent on androgen hormones for survival." [GOC:tfm] subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset is_a: CL:0002231 ! epithelial cell of prostate property_value: RO:0002175 NCBITaxon:9606 property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 @@ -19424,6 +21797,8 @@ name: basal cell of prostate epithelium def: "An undifferentiated cell of the prostate epithelium that lacks secretory activity." [GOC:tfm, PMCID:PMC2673349] subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset is_a: CL:0002231 ! epithelial cell of prostate property_value: RO:0002175 NCBITaxon:9606 property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 @@ -19433,6 +21808,8 @@ creation_date: 2010-09-20T03:34:10Z id: CL:0002342 name: circulating endothelial cell def: "A circulating endothelial cell of the phenotype CD146-positive, CD105-positive, CD45-negative. This cell type is indicative of recent vascular damage." [GOC:tfm, PMID:19652886] +subset: human_subset +subset: mouse_subset is_a: CL:0000115 ! endothelial cell property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-20T03:49:58Z @@ -19443,16 +21820,19 @@ name: decidual natural killer cell, human def: "A natural killer cell subset that is found in the decidual of the uterus and is CD56-high, Galectin-1-positive and CD16-negative. This cell type represents the most abundant immune cell type in the decidual during the first trimester of pregnancy." [PMID:14568979, PMID:19800965] subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset synonym: "decidual NK cell" EXACT [] synonym: "dNK cell" EXACT [] +is_a: CL:0000349 ! extraembryonic cell is_a: CL:0000824 ! mature natural killer cell -is_a: PR:000050567 ! protein-containing material entity +is_a: CL:4052028 ! uterine natural killer cell intersection_of: CL:0000824 ! mature natural killer cell intersection_of: CL:4030046 PR:000001483 ! lacks_plasma_membrane_part low affinity immunoglobulin gamma Fc region receptor III intersection_of: RO:0002104 PR:000009766 ! has plasma membrane part galectin-1 intersection_of: RO:0002162 NCBITaxon:9606 ! in taxon Homo sapiens intersection_of: RO:0015015 PR:000001024 ! has high plasma membrane amount neural cell adhesion molecule 1 relationship: CL:4030046 PR:000001483 ! lacks_plasma_membrane_part low affinity immunoglobulin gamma Fc region receptor III +relationship: part_of UBERON:0002450 ! decidua relationship: RO:0002104 PR:000009766 ! has plasma membrane part galectin-1 relationship: RO:0002162 NCBITaxon:9606 ! in taxon Homo sapiens relationship: RO:0015015 PR:000001024 ! has high plasma membrane amount neural cell adhesion molecule 1 @@ -19465,9 +21845,9 @@ id: CL:0002344 name: CD56-negative, CD161-positive immature natural killer cell, human def: "A natural killer cell that is developmentally immature, has the phenotype CD34-negative, CD56-negative, CD117-positive, CD122-positive,and CD161-positive." [GO_REF:0000031, GOC:add, ISBN:0781735149, PMID:12457618] comment: Human markers; killer cell immunoglobulin-like receptor 2DL1 is used as a representative example (PRO at this time lacks a KIR superfamily). +subset: human_subset synonym: "p-NK" RELATED [PMID:12457618] is_a: CL:0000823 ! immature natural killer cell -is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000823 ! immature natural killer cell intersection_of: CL:4030046 PR:000001003 ! lacks_plasma_membrane_part CD34 molecule intersection_of: CL:4030046 PR:000001024 ! lacks_plasma_membrane_part neural cell adhesion molecule 1 @@ -19489,9 +21869,9 @@ id: CL:0002345 name: CD27-low, CD11b-low immature natural killer cell, mouse def: "An immature natural killer cell that is NK1.1-positive, DX5-positive, Ly49-positive, CD27-low and CD11b-low. This cell type is found in high numbers in the liver." [GOC:tfm, http:www.immgen.org/index_content.html, PMID:19949422] comment: Markers are associated with mouse cells. +subset: mouse_subset synonym: "preNK.BM" BROAD [] is_a: CL:0000823 ! immature natural killer cell -is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000823 ! immature natural killer cell intersection_of: RO:0002104 PR:000001008 ! has plasma membrane part integrin alpha-2 intersection_of: RO:0002104 PR:000002977 ! has plasma membrane part killer cell lectin-like receptor subfamily B member 1C @@ -19513,8 +21893,8 @@ creation_date: 2010-09-20T04:41:01Z id: CL:0002346 name: Dx5-negative, NK1.1-positive immature natural killer cell, mouse def: "An immature natural killer cell that is NK1.1-positive and DX-5 negative." [GOC:tfm, PMID:12766763] +subset: mouse_subset is_a: CL:0000823 ! immature natural killer cell -is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000823 ! immature natural killer cell intersection_of: CL:4030046 PR:000001008 ! lacks_plasma_membrane_part integrin alpha-2 intersection_of: RO:0002104 PR:000002977 ! has plasma membrane part killer cell lectin-like receptor subfamily B member 1C @@ -19529,8 +21909,8 @@ creation_date: 2010-09-21T10:11:44Z id: CL:0002347 name: CD27-high, CD11b-high natural killer cell, mouse def: "A mature natural killer cell that is CD27-high and CD11b-high. This cell type is capable of interferon-gamma secretion." [GOC:tfm, PMID:19949422] +subset: mouse_subset is_a: CL:0000824 ! mature natural killer cell -is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000824 ! mature natural killer cell intersection_of: capable_of GO:0032609 ! type II interferon production intersection_of: RO:0002162 NCBITaxon:10090 ! in taxon Mus musculus @@ -19547,8 +21927,8 @@ creation_date: 2010-09-21T10:19:49Z id: CL:0002348 name: CD27-low, CD11b-high natural killer cell, mouse def: "A CD27-low, CD11b-high natural killer cell that has a higher threshold of activation due to higher expression of inhibitory receptors." [GOC:tfm, PMID:1994922] +subset: mouse_subset is_a: CL:0000824 ! mature natural killer cell -is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000824 ! mature natural killer cell intersection_of: RO:0002162 NCBITaxon:10090 ! in taxon Mus musculus intersection_of: RO:0015015 PR:000001012 ! has high plasma membrane amount integrin alpha-M @@ -19564,8 +21944,8 @@ creation_date: 2010-09-21T10:19:54Z id: CL:0002349 name: CD27-high, CD11b-low natural killer cell, mouse def: "A natural killer cell that is CD27-high and CD11b-low." [GOC:tfm, PMID:1994922] +subset: mouse_subset is_a: CL:0000824 ! mature natural killer cell -is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000824 ! mature natural killer cell intersection_of: RO:0002162 NCBITaxon:10090 ! in taxon Mus musculus intersection_of: RO:0015015 PR:000001963 ! has high plasma membrane amount CD27 molecule @@ -19584,15 +21964,19 @@ alt_id: CL:1000475 def: "An endothelial cell that lines the intracavitary lumen of the heart, separating the circulating blood from the underlying myocardium. This cell type releases a number of vasoactive substances including prostacyclin, nitrous oxide and endothelin." [GOC:tfm, ISSN:0452-3458] subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "endocardial endothelial cell" EXACT [] synonym: "endothelial cell of endocardium" EXACT [FMA:75621] xref: FMA:75621 +xref: https://cellxgene.cziscience.com/cellguide/CL_0002350 is_a: CL:0010008 ! cardiac endothelial cell intersection_of: CL:0000115 ! endothelial cell intersection_of: part_of UBERON:0002165 ! endocardium relationship: part_of UBERON:0002165 ! endocardium property_value: RO:0002175 NCBITaxon:9606 property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nEndocardial cells, often referred to as endothelial cells of the heart, constitute the innermost lining layer of the heart tissues, forming the endocardium. They play a critical role in maintaining heart functionality and homeostasis. These cells, flat and squamous in structure, are adjoined closely to form a tight barrier that separates the heart's muscular layer, the myocardium, from the blood flowing through the heart chambers.\nFunctionally, endocardial cells are key players in several crucial physiological processes within the heart. Synthesizing matrix molecules that contribute to the structural formation of the heart, these cells actively partake in maintaining its structural integrity. They also exhibit unique metabolic activity, which aids in maintaining optimal cardiac functioning in both healthy and pathological conditions. Importantly, they are known for their involvement in modulating myocardial contraction and relaxation, that is crucial for normal heart rhythm and function. They achieve this by producing factors like nitric oxide (NO) which, amongst other things, aids in the regulation of blood pressure, prevents blood clotting and inhibits the adherence of blood cells to the vessel wall.\nIn pathological states, endocardial cells can undergo a transformation process known as endothelial-mesenchymal transition (EndMT), which is inherently involved in several cardiac diseases. In this transition, they acquire the ability to migrate and differentiate into several other types of cells contributing to disease progression. Moreover, their dysfunction can lead to endocarditis, an inflammation of the endocardium, as well as increase the risk of other heart diseases." xsd:string {xref="DOI:10.1016/j.medici.2017.08.003", xref="DOI:10.1016/j.ydbio.2009.06.033", xref="DOI:10.1101/cshperspect.a036723", xref="DOI:10.1161/ATVBAHA.121.313788", xref="DOI:10.1161/CIRCRESAHA.117.312136"} creation_date: 2010-09-21T04:33:05Z [Term] @@ -19600,6 +21984,8 @@ id: CL:0002351 name: progenitor cell of endocrine pancreas def: "A progenitor cell that is able to differentiate into the pancreas alpha, beta and delta endocrine cells. This cell type expresses neurogenin-3 and Isl-1." [GOC:tfm, PMID:20025937, PMID:20217494, PMID:22728667] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "pancreatic endocrine progenitor" EXACT [] synonym: "pancreatic islet progenitor cell" EXACT [] is_a: CL:0011026 ! progenitor cell @@ -19610,6 +21996,8 @@ creation_date: 2010-09-21T04:41:06Z id: CL:0002352 name: gestational hematopoietic stem cell def: "A hematopoietic stem cell that exists during embryogenesis." [GOC:tfm, ISBN:978-60327-246-6] +subset: human_subset +subset: mouse_subset is_a: CL:0000037 ! hematopoietic stem cell intersection_of: CL:0000037 ! hematopoietic stem cell intersection_of: part_of UBERON:0000922 ! embryo @@ -19621,8 +22009,9 @@ creation_date: 2010-09-22T09:05:13Z id: CL:0002353 name: fetal liver hematopoietic progenitor cell def: "A hematopoietic stem cell that resides in the fetal liver. In mice, this cell type is first observed at E10.5. This cell type is MHC-positive, HSA-positive, AA4.1-positive, CD45-positive, Sca-1 positive, CD150-positive, CD48-negative and CD244-negative." [GOC:tfm, ISBN:978-1-60327-346-6, PMID:16569764] +subset: human_subset +subset: mouse_subset is_a: CL:0002352 {is_inferred="true"} ! gestational hematopoietic stem cell -is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0002352 ! gestational hematopoietic stem cell intersection_of: CL:4030046 PR:000001308 ! lacks_plasma_membrane_part CD48 molecule intersection_of: CL:4030046 PR:000001896 ! lacks_plasma_membrane_part natural killer cell receptor 2B4 @@ -19648,9 +22037,10 @@ creation_date: 2010-09-22T09:08:32Z id: CL:0002354 name: yolk sac hematopoietic stem cell def: "A hematopoietic stem found in the yolk sac. In mice, this cell type is Sca-1-negative, CD45-negative, MHC-negative, HSA-positive, AA4.1-positive, CD44-positive." [doi:10.1097/MOH.0b013e3282f97ae1, GOC:tfm] +subset: human_subset +subset: mouse_subset synonym: "hemangioblast precursor" EXACT [] is_a: CL:0002352 {is_inferred="true"} ! gestational hematopoietic stem cell -is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0002352 ! gestational hematopoietic stem cell intersection_of: CL:4030046 GO:0042611 ! lacks_plasma_membrane_part MHC protein complex intersection_of: CL:4030046 PR:000001006 ! lacks_plasma_membrane_part receptor-type tyrosine-protein phosphatase C @@ -19673,11 +22063,12 @@ id: CL:0002355 name: primitive red blood cell def: "A large nucleated basophilic erythrocyte found in mammalian embryos. This cell type arises from the blood islands of yolk sacs and expresses different types of hemoglobins (beta-H1, gamma-1 and zeta) than adult erythrocytes. Considered a type of erythroblast as this cell type can enucleate in circulation." [DOI:10.1097/MOH.0b013e3282f97ae1, GOC:tfm, PMID:11495698] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "primitive erythroblast" EXACT [] synonym: "primitive erythrocyte" EXACT [] synonym: "primitive erythroid cell" EXACT [] is_a: CL:0002417 {is_inferred="true"} ! primitive erythroid lineage cell -is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0002417 ! primitive erythroid lineage cell intersection_of: bearer_of PATO:0000586 ! increased size intersection_of: has_part PR:000008467 ! hemoglobin subunit zeta @@ -19695,6 +22086,8 @@ creation_date: 2010-09-22T09:27:05Z id: CL:0002356 name: primitive reticulocyte def: "A primitive erythrocyte that has undergone enucleation. This cell type is 3-6 fold bigger than the fetal derived erythrocytes that they co-circulate with during fetal development. Expresses epsilon-gamma hemoglobin chains." [doi:10.1097/MOH.0b013e3282f97ae1, GOC:tfm, PMID:11495698] +subset: human_subset +subset: mouse_subset synonym: "megalocyte" EXACT [] is_a: CL:0002417 {is_inferred="true"} ! primitive erythroid lineage cell intersection_of: CL:0002417 ! primitive erythroid lineage cell @@ -19709,9 +22102,10 @@ creation_date: 2010-09-22T09:35:16Z id: CL:0002357 name: fetal derived definitive erythrocyte def: "A fetal liver derived enucleated erythrocyte. This erythrocyte resembles adult erythrocytes in that they are small (3- to 6- times smaller than primitive erythrocytes) and produce adult hemaglobins." [GOC:tfm, PMID:11495698] +subset: human_subset +subset: mouse_subset synonym: "macrocyte" EXACT [] is_a: CL:0000595 {is_inferred="true"} ! enucleate erythrocyte -is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000595 ! enucleate erythrocyte intersection_of: has_part PR:000008857 ! hemoglobin subunit beta-1 intersection_of: part_of UBERON:0000922 ! embryo @@ -19725,6 +22119,8 @@ creation_date: 2010-09-22T09:38:32Z id: CL:0002358 name: pyrenocyte def: "Derived from the Greek word pyren (the pit of a stone fruit), this is a transient nucleated cell type that results from exclusion of the nucleus from the primitive erythrocyte." [GOC:tfm] +subset: human_subset +subset: mouse_subset is_a: CL:0002417 {is_inferred="true"} ! primitive erythroid lineage cell intersection_of: CL:0002417 ! primitive erythroid lineage cell intersection_of: bearer_of PATO:0000587 ! decreased size @@ -19738,6 +22134,8 @@ creation_date: 2010-09-22T10:02:37Z id: CL:0002359 name: placental hematopoietic stem cell def: "A hematopoietic stem cell of the placenta. This cell type is first observed E10.5 This cell type may give rise to fetal liver hematopoietic stem cells." [GOC:tfm, ISBN:978-1-60327-346-6] +subset: human_subset +subset: mouse_subset is_a: CL:0002352 ! gestational hematopoietic stem cell intersection_of: CL:0000037 ! hematopoietic stem cell intersection_of: part_of UBERON:0001987 ! placenta @@ -19749,6 +22147,8 @@ creation_date: 2010-09-22T10:30:02Z id: CL:0002360 name: AGM hematopoietic stem cell def: "A hematopoietic stem cell from the aorta-gonad-mesonephros region of the developing embryo. First seen at E10.5 in mouse embryos. May give rise to fetal liver HSC." [GOC:tfm, ISBN:978-1-60327-346-6] +subset: human_subset +subset: mouse_subset is_a: CL:0002352 ! gestational hematopoietic stem cell property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-22T10:31:49Z @@ -19757,10 +22157,12 @@ creation_date: 2010-09-22T10:31:49Z id: CL:0002361 name: primitive erythroid progenitor def: "A progenitor cell that is capable of forming colonies of primitive erythrocytes in the blood island of the yolk sac. First arrive at E7.5 in mouse and expresses CD41." [GOC:tfm, ISBN:0813817986, PMID:20711979] +subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "EryP-CFC" EXACT [] synonym: "inner blood island hemangioblast" EXACT [] is_a: CL:0002417 {is_inferred="true"} ! primitive erythroid lineage cell -is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0002417 ! primitive erythroid lineage cell intersection_of: RO:0002104 PR:000009127 ! has plasma membrane part integrin alpha-IIb relationship: RO:0002104 PR:000009127 ! has plasma membrane part integrin alpha-IIb @@ -19772,6 +22174,9 @@ creation_date: 2010-09-22T10:47:28Z id: CL:0002362 name: cerebellar granule cell precursor def: "A cell located in the outermost proliferative zone of the external germinal layer that can differentiate into astroglial cells and granule cells. This cell type is glial fibrillary acidic protein-positive and HNK1-positive." [GOC:tfm, PMID:14745007] +subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "GCP" RELATED OMO:0003000 [doi:10.3389/fncir.2020.611841] synonym: "granule cell precursor" BROAD [doi:10.3389/fncir.2020.611841] synonym: "granule cell progenitor" BROAD [doi:10.3389/fncir.2020.611841] @@ -19788,6 +22193,8 @@ def: "A keratocyte is a specialized fibroblast residing in the cornea stroma th subset: cellxgene_subset subset: eye_upper_slim subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "corneal fibroblast" EXACT [] synonym: "corneal keratocyte" EXACT [] is_a: CL:0000005 ! neural crest derived fibroblast @@ -19804,14 +22211,18 @@ name: cortical thymic epithelial cell def: "An epithelial cell of the cortical portion of the thymus. Epithelial cells in this region are required for positive selection of CD8-positive T cells." [GOC:tfm, PMID:18403190] subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "cTEC" EXACT [] xref: BTO:0004562 +xref: https://cellxgene.cziscience.com/cellguide/CL_0002364 is_a: CL:0002293 ! epithelial cell of thymus intersection_of: CL:0000066 ! epithelial cell intersection_of: part_of UBERON:0002123 ! cortex of thymus relationship: part_of UBERON:0002123 ! cortex of thymus property_value: RO:0002175 NCBITaxon:9606 property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nCortical thymic epithelial cells (cTECs) are a vital cell type located in the thymus, a lymphoid organ that plays a key role in the development of T cells, which are essential for the adaptive immune system. cTECs also have a role in forming barriers and lining surfaces. In the thymus, their presence contributes to the distinctive architecture of both the cortex and medulla.\ncTECs also play a significant part in the selection and development of T cells. During T cell maturation, these cells express both self and non-self proteins via the major histocompatibility complex (MHC) to immature T cells. cTECs then stimulate the T cells that can recognize such proteins, an important event known as positive selection. This process aids in the creation of a diverse T cell receptor (TCR) repertoire that can react to a wide range of antigens, therefore ensuring effective immunity. \nApart from aiding in T cells' positive selection, cTECs also contribute to eliminating self-reactive T cells, a role essential in preventing autoimmune diseases. These cells induce an apoptosis-driven process known as \"negative selection\" which eliminates T cells that are too highly reactive to self-antigens." xsd:string {xref="DOI:10.1016/bs.ai.2014.09.003", xref="DOI:10.1038/nri3667", xref="DOI:10.1111/sji.13094"} creation_date: 2010-09-23T03:17:12Z [Term] @@ -19819,13 +22230,17 @@ id: CL:0002365 name: medullary thymic epithelial cell def: "An epithelial cell of the medullary thymus. This cell type expresses a diverse range of tissue-specific antigens. This promiscuous gene expression is a cell-autonomous property of medullary epithelial cells and is maintained during the entire period of thymic T cell output." [GOC:tfm, PMID:18180458] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "mTEC" EXACT [] xref: BTO:0004563 +xref: https://cellxgene.cziscience.com/cellguide/CL_0002365 is_a: CL:0002293 ! epithelial cell of thymus intersection_of: CL:0000066 ! epithelial cell intersection_of: part_of UBERON:0002124 ! medulla of thymus relationship: part_of UBERON:0002124 ! medulla of thymus property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nMedullary thymic epithelial cells (mTECs) are distinct cells situated in the thymic medulla, a vital organ where T cells mature. mTECs are recognized by their unique appearance, characterized by large, plump cells with abundant cytoplasm and irregularly shaped nuclei. They inhabit a microenvironment closely interacting with various thymic cell types, including conventional dendritic cells and thymocytes.\nThe primary function of mTECs revolves around negative selection of developing T cells, thus preventing autoimmune responses. mTECs allow developing T cells to recognize and be responsive to foreign antigens while remaining tolerant to the body's own tissues. They achieve this through a process called promiscuous gene expression where they express and display a vast array of self-antigens. This process is regulated by a transcriptional regulator called autoimmune regulator (Aire), which contributes to immunological self-tolerance.\nmTECs themselves have a self-renewing ability and sustain the continuous export of mature T cells. They also express a number of genes that encode for chemokines and other signaling molecules which draw in and retain developing T cells for the process of negative selection. The three-dimensional network formed by these cells provides a physical platform for such selection. Together, mTECs hold a critical place in the maintenance of immune homeostasis, demonstrating the conceptual links that exist between population of stromal cells, thymocytes development, tissue-restricted antigen expression, and negative selection." xsd:string {xref="DOI:10.1007/s11427-013-4482-4", xref="DOI:10.4049/jimmunol.2100692", xref="DOI:10.7554/eLife.60188"} creation_date: 2010-09-23T03:17:14Z [Term] @@ -19833,19 +22248,25 @@ id: CL:0002366 name: myometrial cell def: "A smooth muscle cell of the myometrium that enlarges and stretches during pregnancy, and contracts in response to oxytocin." [GOC:tfm, PMID:11429640] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "myometrium smooth muscle cell" EXACT [] xref: BTO:0004519 +xref: https://cellxgene.cziscience.com/cellguide/CL_0002366 is_a: CL:0002601 ! uterine smooth muscle cell intersection_of: CL:0000192 ! smooth muscle cell intersection_of: part_of UBERON:0001296 ! myometrium relationship: part_of UBERON:0001296 ! myometrium property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nMyometrial cells are specialized smooth muscle cells located in the myometrium, the middle layer of the uterine wall. Unique to female reproductive physiology, they play a key role in pregnancy and childbirth. \nThese cells are distinctive in their capability to substantially increase in size and number during pregnancy, preparing the uterus to accommodate the growing fetus. As pregnancy progresses, myometrial cells demonstrate a progressive growth in uterine mass through cellular hypertrophy. They are also responsible for the production of extracellular matrix proteins like collagen, which aids in supporting cell structure and function, further facilitating uterine enlargement.\nDuring childbirth, myometrial cells are responsible for the expansion and contraction of the uterus. They can propagate action potentials and generate considerable force, which is critical to their function in the reproductive system. After pregnancy, these cells can reduce in size, a process known as uterine involution. Given the important role these cells play in female reproductive physiology, dysregulation of the myometrial cell function can contribute to uterine pathologies such as uterine fibroids." xsd:string {xref="DOI:10.1073/pnas.070447210", xref="DOI:10.1093/humupd/dmr031", xref="DOI:10.1177/1535370220938741", xref="https://www.sciencedirect.com/topics/medicine-and-dentistry/uterine-contraction", xref="https://www.sciencedirect.com/topics/veterinary-science-and-veterinary-medicine/myometrium"} creation_date: 2010-09-23T03:46:34Z [Term] id: CL:0002367 name: trabecular meshwork cell def: "A cell that lines the trabecular meshwork, which is an area of tissue in the eye located around the base of the cornea, near the ciliary body, and is responsible for draining the aqueous humor from the eye via the anterior chamber (the chamber on the front of the eye covered by the cornea). This cell may play a role in regulating intraocular pressure." [GOC:tfm, PMID:14500801] +subset: human_subset +subset: mouse_subset synonym: "trabeculocyte" EXACT [] is_a: CL:0000115 {is_inferred="true"} ! endothelial cell intersection_of: CL:0000115 ! endothelial cell @@ -19856,10 +22277,13 @@ creation_date: 2010-09-23T04:18:50Z [Term] id: CL:0002368 -name: respiratory epithelial cell -def: "An endo-epithelial cell of the respiratory tract." [GOC:tfm] +name: respiratory tract epithelial cell +def: "An epithelial cell of the respiratory tract epithelium. These cells have an endodermal origin." [GOC:tfm] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "airway epithelial cell" EXACT [] +synonym: "respiratory epithelial cell" EXACT [] xref: BTO:0004533 is_a: CL:0002076 ! endo-epithelial cell intersection_of: CL:0000066 ! epithelial cell @@ -19879,30 +22303,34 @@ creation_date: 2010-10-01T09:02:42Z [Term] id: CL:0002370 -name: respiratory goblet cell +name: respiratory tract goblet cell def: "A simple columnar epithelial cell that secretes mucin. Rough endoplasmic reticulum, mitochondria, the nucleus, and other organelles are concentrated in the basal portion. The apical plasma membrane projects microvilli to increase surface area for secretion." [GOC:tfm, ISBN:0721662544] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset +synonym: "respiratory goblet cell" EXACT [] synonym: "respiratory mucosa goblet cells" EXACT [MP:0010863] xref: https://cellxgene.cziscience.com/cellguide/CL_0002370 is_a: CL:0000160 ! goblet cell -is_a: CL:0002368 ! respiratory epithelial cell +is_a: CL:0002368 ! respiratory tract epithelial cell intersection_of: CL:0000160 ! goblet cell intersection_of: part_of UBERON:0004802 ! respiratory tract epithelium property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 -property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional.\n\nThe respiratory goblet cell is a highly specialized cell type found primarily within the respiratory tract, including the nose, trachea, and lungs. Named because their shape resembles a goblet - a drinking vessel with a wide body and narrow neck - these cells form a vital part of the respiratory system's protective mechanisms. They are found within the columnar epithelium lining these organs, which forms a barrier between the internal body and the exterior environment.\nA principal function of the respiratory goblet cell is the production and secretion of mucus, a carbohydrate-rich, viscous and gel-like substance that plays a critical role in trapping dust, bacteria, viruses, and other airborne particles that are inhaled. The mucus secreted by the goblet cells covers the lining of the respiratory tract, effectively catching these particles and preventing them from reaching the lungs and causing infection. Mucus also provides hydration and lubrication to the respiratory tract surfaces, which is important in maintaining the tissue's health and functioning.\nIn addition to their mucus-secreting capabilities, respiratory goblet cells also play a significant role in the body's inflammatory responses. When the respiratory system is exposed to irritants or pathogens, the number and activity of goblet cells often increase, leading to a higher production of mucus. This is a protective response designed to trap and neutralize the harmful substances more effectively. However, in conditions like chronic obstructive pulmonary disease (COPD) and asthma, an overproliferation of goblet cells, also known as goblet cell hyperplasia, can lead to excessive mucus production and airway obstruction." xsd:string {xref="DOI:10.1016/S1357-2725(02)00083-3", xref="DOI:10.1111/febs.15731", xref="DOI:10.1165/ajrcmb.25.5.f218", xref="DOI:10.2147/COPD.S38938", xref="DOI:10.3109/01902148.2013.791733"} +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nThe respiratory goblet cell is a highly specialized cell type found primarily within the respiratory tract, including the nose, trachea, and lungs. Named because their shape resembles a goblet - a drinking vessel with a wide body and narrow neck - these cells form a vital part of the respiratory system's protective mechanisms. They are found within the columnar epithelium lining these organs, which forms a barrier between the internal body and the exterior environment.\nA principal function of the respiratory goblet cell is the production and secretion of mucus, a carbohydrate-rich, viscous and gel-like substance that plays a critical role in trapping dust, bacteria, viruses, and other airborne particles that are inhaled. The mucus secreted by the goblet cells covers the lining of the respiratory tract, effectively catching these particles and preventing them from reaching the lungs and causing infection. Mucus also provides hydration and lubrication to the respiratory tract surfaces, which is important in maintaining the tissue's health and functioning.\nIn addition to their mucus-secreting capabilities, respiratory goblet cells also play a significant role in the body's inflammatory responses. When the respiratory system is exposed to irritants or pathogens, the number and activity of goblet cells often increase, leading to a higher production of mucus. This is a protective response designed to trap and neutralize the harmful substances more effectively. However, in conditions like chronic obstructive pulmonary disease (COPD) and asthma, an overproliferation of goblet cells, also known as goblet cell hyperplasia, can lead to excessive mucus production and airway obstruction." xsd:string {xref="DOI:10.1016/S1357-2725(02)00083-3", xref="DOI:10.1111/febs.15731", xref="DOI:10.1165/ajrcmb.25.5.f218", xref="DOI:10.2147/COPD.S38938", xref="DOI:10.3109/01902148.2013.791733"} creation_date: 2010-09-23T04:42:27Z [Term] id: CL:0002371 name: obsolete somatic cell def: "OBSOLETE. A cell of an organism that does not pass on its genetic material to the organism's offspring (i.e. a non-germ line cell)." [GOC:tfm, ISBN:0721662544] -subset: cellxgene_subset subset: ubprop:upper_level xref: BTO:0001268 xref: FMA:72300 +xref: https://cellxgene.cziscience.com/cellguide/CL_0002371 xref: WBbt:0008378 relationship: term_tracker_item https://github.com/obophenotype/cell-ontology/issues/1150 property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nSomatic cells represent the majority of the cell types in the human body. They are fundamental building blocks of organs, tissues, and other bodily structures, with every organ being composed of distinct subpopulations of these cells. \nThe primary function of somatic cells is to maintain the function and survival of an organism. They carry significant information in the form of DNA, and through the process of mitosis, contribute to the repair and regeneration of body tissues.\nFurther, some types of somatic cells work in a collaborative manner to form complex functional structures such as the skin and lining of the gut, demonstrating a higher level of organization. However, it's important to note that somatic cells are distinct from germ cells, which are responsible for sexual reproduction by forming sperm or eggs. Any alterations in the DNA of somatic cells, due to mutations, will not affect the offspring as they aren't involved in transmission of genetic information to the next generation. \nWhile most somatic cells contain two copies of each chromosome (diploid), a certain subset may possess a single set of chromosomes (haploid), specifically found in male ants, bees, and other hymenopterans. Hence, diversity is a defining characteristic of somatic cells, reflecting in their structures, roles, and genetic makeup." xsd:string {xref="DOI:10.1038/nrm3980", xref="https://www.genome.gov/genetics-glossary/Somatic-Cells", xref="https://www.ncbi.nlm.nih.gov/books/NBK557896/"} is_obsolete: true replaced_by: CL:0000000 creation_date: 2010-09-24T09:44:42Z @@ -19912,6 +22340,9 @@ id: CL:0002372 name: myotube alt_id: CL:0000369 def: "A transversely striated, multinucleated syncytial muscle cell, formed by the fusion of myoblasts during muscle development." [GOC:dos, GOC:tfm, ISBN:0323052908, PMID:22274696] +subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "myofiber" EXACT [FBbt:00005812] synonym: "myofibril" EXACT [FBbt:00005812] xref: FBbt:00005812 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} @@ -19929,6 +22360,8 @@ creation_date: 2010-09-24T01:13:01Z id: CL:0002373 name: growth hormone releasing hormone secreting cell def: "A peptide hormone secreting cell that secretes growth hormone releasing hormone." [GOC:dph, GOC:tfm] +subset: human_subset +subset: mouse_subset synonym: "GHRH secreting cell" EXACT [] synonym: "somatocrinin secreting cell" EXACT [] is_a: CL:0000167 ! peptide hormone secreting cell @@ -19939,6 +22372,8 @@ creation_date: 2010-09-24T01:36:44Z id: CL:0002374 name: ear hair cell def: "A hair cell of the ear that contains the organs of balance and hearing." [GOC:dph, GOC:tfm, ISBN:0192801023] +subset: human_subset +subset: mouse_subset synonym: "ear receptor cell" EXACT [] is_a: CL:0000006 ! neuronal receptor cell is_a: CL:0000855 ! sensory hair cell @@ -19954,6 +22389,8 @@ name: Schwann cell precursor def: "A multipotent progenitor cell that develops from a migratory neural crest cell. The schwann cell precursor is embedded among axons, with minimal extracellular space separating them from nerve cell membranes. This cell lacks a basal lamina, which distinguishes it from more mature Schwann cells. In rodents, cadherin-19 (Cdh19) serves as a specific marker for this developmental stage." [GOC:tfm, PMID:15580626, PMID:30971890, PMID:35815410] comment: Schwann cell precursor are capable of differentiating into Schwann cells and other cell types such as melanocytes, neurons, and mesenchymal cells. {xref="PMID:35815410"} subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "Schwann cell precursor cell" EXACT [] synonym: "SCP" RELATED OMO:0003000 [PMID:35815410] is_a: CL:0011026 ! progenitor cell @@ -19967,6 +22404,9 @@ creation_date: 2010-09-24T02:06:10Z id: CL:0002376 name: non-myelinating Schwann cell def: "A glial cell that ensheaths multiple small diameter axons in the peripheral nervous system. The non-myelinating Schwann cell is embedded among neurons (axons) with minimal extracellular spaces separating them from nerve cell membranes and has a basal lamina. Cells can survive without an axon present. These cells can de-differentiate into immature Schwann cells." [GOC:cvs, GOC:tfm, ISBN:0721662544] +subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "Schwann cell" BROAD [] is_a: CL:0002573 ! Schwann cell relationship: RO:0002202 CL:0002377 ! develops from immature Schwann cell @@ -19978,6 +22418,8 @@ id: CL:0002377 name: immature Schwann cell def: "A glial cell that develops from a Schwann cell precursor. The immature Schwann cell is embedded among neurons (axons) with minimal extracellular spaces separating them from nerve cell membranes and has a basal lamina. Cells can survive without an axon present. Immature Schwann cell can be found communally ensheathing large groups of axons." [GOC:cvs, GOC:tfm, ISBN:0721662544] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "Schwann cell" BROAD [] xref: ZFA:0001725 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0002573 ! Schwann cell @@ -19990,6 +22432,8 @@ id: CL:0002378 name: immature Vgamma2-positive fetal thymocyte def: "A double negative thymocyte that has a T cell receptor consisting of a gamma chain containing a Vgamma2 segment, and a delta chain. This cell type is CD4-negative, CD8-negative and CD24-positive and is found in the fetal thymus." [GOC:tfm, http://www.immgen.org] comment: NOTE: currently variable immune gene segments are not represented in the OBO Foundry. Cross-product definitions were not made as a result. Also, there are three different nomenclatures for the variable gamma segments. +subset: human_subset +subset: mouse_subset synonym: "fetal Vgamma2+ thymocyte" BROAD [] is_a: CL:0002404 ! fetal thymocyte property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 @@ -19999,6 +22443,8 @@ creation_date: 2010-10-07T02:21:07Z id: CL:0002379 name: meningothelial cell def: "A neurecto-epithelial cell found in the arachnoid villi of dura mater. This cell type facilitates flow of cerebrospinal fluid into the blood." [GOC:tfm, http://www.aippg.net/forum/viewtopic.php?t=62590] +subset: human_subset +subset: mouse_subset synonym: "arachnoid cap cell" EXACT [] xref: FMA:86588 is_a: CL:0000710 ! neurecto-epithelial cell @@ -20116,6 +22562,8 @@ id: CL:0002393 name: intermediate monocyte def: "A monocyte that has characteristics of both patrolling and inflammatory monocytes." [GOC:tfm, PMID:20628149, PMID:20870168] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset is_a: CL:0000576 ! monocyte intersection_of: CL:0000576 ! monocyte intersection_of: CL:4030044 GO:0030224 ! has_not_completed monocyte differentiation @@ -20136,9 +22584,11 @@ creation_date: 2010-10-04T10:52:03Z id: CL:0002394 name: CD141-positive myeloid dendritic cell def: "A myeloid dendritic cell found in the blood, lymph nodes, tonsil, bone marrow, and spleen that is CD141-positive (BDCA-3), XCR1-positive, and Clec9A-positive. This cell-type can cross-present antigen to CD8-positive T cells and can produce inteferon-beta." [GOC:dsd, GOC:tfm, PMCID:PMC2882828, PMCID:PMC2882837, PMID:17332250, PMID:20628149] -comment: Markers are found in human cells. Normally they represent 3-5% of peripheral blood mDCs (human). These cells express high levels of CD283 (TLR3), are capable of producing IL-12p70 and IFN-beta upon stimulation, and inducing a TH1 response [PMCID:PMC2882828]. They are also Necl2-positive. May be human equivalent of murine CD8alpha-positive DCs. +comment: Markers are found in human cells. Normally they represent 3-5% of peripheral blood mDCs (human). These cells express high levels of CD283 (TLR3), are capable of producing IL-12p70 and IFN-beta upon stimulation, and inducing a TH1 response [PMCID:PMC2882828]. They are also Necl2-positive. May be human equivalent of murine CD8-alpha-positive DCs. subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset is_a: CL:0000782 {is_inferred="true"} ! myeloid dendritic cell is_a: CL:0000784 ! plasmacytoid dendritic cell intersection_of: CL:0000782 ! myeloid dendritic cell @@ -20158,6 +22608,8 @@ id: CL:0002395 name: Gr1-high classical monocyte def: "A resident monocyte that is Gr-1 high, CD43-negative, CX3CR1-negative, CD115-positive, and B220-negative." [GOC:tfm, http://www.immgen.org/index_content.html, PMID:20628149, PMID:8890901] comment: Markers are associated with mice. The Gr epitope is used to describe this cell type is found on both Ly6c and Ly6g. However, its the Ly6c that is considered the specific marker, and thus used in the cross-product. +subset: human_subset +subset: mouse_subset is_a: CL:0000860 {is_inferred="true"} ! classical monocyte is_a: CL:0001022 ! CD115-positive monocyte intersection_of: CL:0000860 ! classical monocyte @@ -20181,6 +22633,8 @@ def: "A patrolling monocyte that is CD14-low and CD16-positive." [GOC:tfm, PMID: comment: Markers are associated with human monocytes. subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "non-classical monocyte, human" EXACT [] is_a: CL:0000875 {is_inferred="true"} ! non-classical monocyte is_a: CL:0001054 ! CD14-positive monocyte @@ -20200,6 +22654,8 @@ name: CD14-positive, CD16-positive monocyte def: "A CD14-positive monocyte that is also CD16-positive and CCR2-negative." [GOC:tfm, PMID:20628149, PMID:21937707, PMID:22343568] comment: This cell type is compatible with the HIPC Lyoplate markers for 'CD16+ monocyte'. Markers are associated with human cells. Note that this cell type encompasses both human intermediate monocytes (CD14+, CD16-low), and human non-classical monocytes (CD14-low, CD16+). subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "CD16+ monocyte" EXACT [PMID:22343568] is_a: CL:0001054 ! CD14-positive monocyte intersection_of: CL:0001054 ! CD14-positive monocyte @@ -20214,6 +22670,8 @@ creation_date: 2010-10-04T12:49:47Z id: CL:0002398 name: Gr1-positive, CD43-positive monocyte def: "An intermediate monocyte that is Gr1-positive, CD43-positive." [GOC:tfm, PMID:20628149] +subset: human_subset +subset: mouse_subset is_a: CL:0001022 ! CD115-positive monocyte is_a: CL:0002393 ! intermediate monocyte intersection_of: CL:0000576 ! monocyte @@ -20234,6 +22692,8 @@ def: "A myeloid dendritic cell that is CD1c-positive." [GOC:dsd, GOC:tfm, PMID:2 comment: Normally represent 10-20% of peripheral blood mDCs (human). They are also CD281-positive (TLR1), CD282-positive (TLR2), CD283-positive (TLR3), CD284-positive (TLR4), CD285-positive (TLR5), CD286-positive (TLR6), CD288-positive (TLR8), and CD290-positive (TLR10) [PMID:20204387]. Upon TLR stimulation, these cells were potent producers of CXCL8 (IL-8), while producing little TNF-alpha. subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset is_a: CL:0000782 {is_inferred="true"} ! myeloid dendritic cell intersection_of: CL:0000782 ! myeloid dendritic cell intersection_of: capable_of GO:0032637 ! interleukin-8 production @@ -20248,6 +22708,8 @@ creation_date: 2010-10-04T02:39:01Z id: CL:0002400 name: fraction B/C precursor B cell def: "A precursor B cell that is AA4-positive, IgM-negative, CD19-positive, CD43-positive and HSA-positive." [GOC:tfm, http://www.immgen.org/index_content.html] +subset: human_subset +subset: mouse_subset is_a: CL:0000817 {is_inferred="true"} ! precursor B cell intersection_of: CL:0000817 ! precursor B cell intersection_of: CL:4030046 GO:0071753 ! lacks_plasma_membrane_part IgM immunoglobulin complex @@ -20266,6 +22728,8 @@ id: CL:0002401 name: mature dendritic epithelial T cell precursor def: "A thymocyte that has a T cell receptor consisting of a gamma chain that has as part a Vgamma3 segment, and a delta chain. This cell type is CD4-negative, CD8-negative and CD24-negative. This cell-type is found in the fetal thymus with highest numbers occurring at E17-E18." [GOC:tfm, http://www.immgen.org/index_content.html] comment: NOTE: currently variable immune gene segments are not represented in the OBO Foundry. Cross-product definitions were not made as a result. Also, there are three different nomenclatures for the variable gamma segments. +subset: human_subset +subset: mouse_subset synonym: "mature DEC precursor" EXACT [] synonym: "mature DETC precursor" EXACT [] is_a: CL:0002404 ! fetal thymocyte @@ -20277,6 +22741,8 @@ creation_date: 2010-10-07T02:05:46Z id: CL:0002402 name: Peyer's patch B cell def: "A resting mature B cell within the Peyer's patch that is CD19-positive, B220-positive, IgM-positive, AA4-negative, CD23-positive, CD43-negative, and CD5-negative." [GOC:tfm, http://www.immgen.org/index_content.html] +subset: human_subset +subset: mouse_subset synonym: "Peyers patch B cell" EXACT [] is_a: CL:0000822 ! B-2 B cell is_a: CL:0009014 ! Peyer's patch lymphocyte @@ -20302,6 +22768,8 @@ id: CL:0002403 name: mature Vgamma2-positive fetal thymocyte def: "A thymocyte that has a T cell receptor consisting of a gamma chain containing Vgamma2 segment, and a delta chain. This cell type is CD4-negative, CD8-negative and CD24-negative. This cell-type is found in the fetal thymus." [GOC:tfm, http://www.immgen.org/index_content.html] comment: NOTE: currently variable immune gene segments are not represented in the OBO Foundry. Cross-product definitions were not made as a result. Also, there are three different nomenclatures for the variable gamma segments. +subset: human_subset +subset: mouse_subset synonym: "fetal Vgamma2-positive" EXACT [] is_a: CL:0002404 ! fetal thymocyte relationship: RO:0002202 CL:0002378 ! develops from immature Vgamma2-positive fetal thymocyte @@ -20312,6 +22780,8 @@ creation_date: 2010-10-07T02:24:36Z id: CL:0002404 name: fetal thymocyte def: "A thymocyte found in the fetal thymus." [GOC:tfm] +subset: human_subset +subset: mouse_subset is_a: CL:0000893 ! thymocyte property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-10-07T02:28:25Z @@ -20320,6 +22790,8 @@ creation_date: 2010-10-07T02:28:25Z id: CL:0002405 name: gamma-delta thymocyte def: "A post-natal thymocyte expressing components of the gamma-delta T cell receptor. This cell type is always double-negative (i.e. CD4-negative, CD8-negative)." [GOC:tfm, PMID:20725107] +subset: human_subset +subset: mouse_subset synonym: "gammadelta thymocyte" EXACT [] synonym: "gd thymocyte" EXACT [] is_a: CL:0000798 ! gamma-delta T cell @@ -20336,6 +22808,8 @@ id: CL:0002406 name: immature Vgamma2-positive thymocyte def: "A double negative post-natal thymocyte that has a T cell receptor consisting of a gamma chain containing a Vgamma2 segment, and a delta chain. This cell type is CD4-negative, CD8-negative and CD24-positive." [GOC:tfm, http://www.immgen.org] comment: NOTE: currently variable immune gene segments are not represented in the OBO Foundry. Cross-product definitions were not made as a result. Also, there are three different nomenclatures for the variable gamma segments. +subset: human_subset +subset: mouse_subset synonym: "Vgamma2-positive thymocyte" BROAD [] is_a: CL:0002405 ! gamma-delta thymocyte property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 @@ -20346,6 +22820,8 @@ id: CL:0002407 name: mature Vgamma2-positive thymocyte def: "A thymocyte that has a T cell receptor consisting of a gamma chain containing Vgamma2 segment, and a delta chain. This cell type is CD4-negative, CD8-negative and CD24-negative." [GOC:tfm, http://www.immgen.org/index_content.html] comment: NOTE: currently variable immune gene segments are not represented in the OBO Foundry. Cross-product definitions were not made as a result. Also, there are three different nomenclatures for the variable gamma segments. +subset: human_subset +subset: mouse_subset synonym: "Vgamma2-positive" EXACT [] is_a: CL:0002405 ! gamma-delta thymocyte relationship: RO:0002202 CL:0002406 ! develops from immature Vgamma2-positive thymocyte @@ -20357,6 +22833,8 @@ id: CL:0002408 name: immature Vgamma2-negative thymocyte def: "A double negative post-natal thymocyte that has a T cell receptor consisting of a gamma chain that does not contain a Vgamma2 segment, and a delta chain. This cell type is CD4-negative, CD8-negative and CD24-positive." [GOC:tfm, http://www.immgen.org] comment: NOTE: currently variable immune gene segments are not represented in the OBO Foundry. Cross-product definitions were not made as a result. Also, there are three different nomenclatures for the variable gamma segments. +subset: human_subset +subset: mouse_subset synonym: "Vgamma2-negative thymocyte" BROAD [] is_a: CL:0002405 ! gamma-delta thymocyte property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 @@ -20367,6 +22845,8 @@ id: CL:0002409 name: mature Vgamma2-negative thymocyte def: "A thymocyte that has a T cell receptor consisting of a gamma chain that does not contain the Vgamma2 segment, and a delta chain. This cell type is CD4-negative, CD8-negative and CD24-negative." [GOC:tfm, http://www.immgen.org/index_content.html] comment: NOTE: currently variable immune gene segments are not represented in the OBO Foundry. Cross-product definitions were not made as a result. Also, there are three different nomenclatures for the variable gamma segments. +subset: human_subset +subset: mouse_subset synonym: "Vgamma2-negative" EXACT [] is_a: CL:0002405 ! gamma-delta thymocyte relationship: RO:0002202 CL:0002408 ! develops from immature Vgamma2-negative thymocyte @@ -20379,11 +22859,13 @@ name: pancreatic stellate cell def: "A cell that is found in the periacinar space of the exocrine pancreas and in perivascular and periductal regions of the pancreas, and has long cytoplasmic processes that encircle the base of the acinus. Expresses several intermediate filament proteins including vimentin and nestin. Shares many of the characteristics of hepatatic stellate cells, but not stellate cells of the central nervous system. Upon activation, this cell type undergoes morphological and gene expression changes that make the cell suggestive of being a type of myofibroblast." [GOC:mah, GOC:tfm, PMID:17200706] subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "pancreas stellate cell" EXACT [] synonym: "PaSC" EXACT [] xref: MESH:D058954 is_a: CL:0000057 ! fibroblast -relationship: part_of UBERON:0001264 ! pancreas +is_a: CL:0002574 ! stromal cell of pancreas property_value: RO:0002175 NCBITaxon:9606 property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-11-10T09:40:33Z @@ -20392,6 +22874,8 @@ creation_date: 2010-11-10T09:40:33Z id: CL:0002411 name: Vgamma1.1-positive, Vdelta6.3-negative thymocyte def: "A gamma-delta receptor that expresses Vgamma1.1 but does not express Vdelta6.3 chains in the T-cell receptor." [GOC:tfm, http://www.immgen.org/index_content.html] +subset: human_subset +subset: mouse_subset synonym: "Vg1.1-positive, Vd6.3-negative T cell" EXACT [] is_a: CL:0002405 ! gamma-delta thymocyte property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 @@ -20401,6 +22885,8 @@ creation_date: 2010-10-07T03:07:44Z id: CL:0002412 name: Vgamma1.1-positive, Vdelta6.3-positive thymocyte def: "A gamma-delta receptor that expresses Vgamma1.1-Vdelta6.3 chains in the T-cell receptor." [GOC:tfm, http://www.immgen.org/index_content.html] +subset: human_subset +subset: mouse_subset synonym: "Vg1.1+Vd6.3+ T cell" EXACT [] is_a: CL:0002405 ! gamma-delta thymocyte property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 @@ -20410,6 +22896,8 @@ creation_date: 2010-10-07T03:03:00Z id: CL:0002413 name: mature Vgamma1.1-positive, Vdelta6.3-negative thymocyte def: "A Vgamma1.1-positive, Vdelta6.3-negative thymocyte that is CD24-negative." [GOC:tfm, http://www.immgen.org] +subset: human_subset +subset: mouse_subset synonym: "mature Vg1.1-positive, Vd6.3-negative T cell" RELATED [] is_a: CL:0002411 ! Vgamma1.1-positive, Vdelta6.3-negative thymocyte property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 @@ -20419,6 +22907,8 @@ creation_date: 2010-10-07T03:10:32Z id: CL:0002414 name: immature Vgamma1.1-positive, Vdelta6.3-negative thymocyte def: "A Vgamma1.1-positive, Vdelta6.3-negative thymocyte that is CD24-positive." [GOC:tfm, http://www.immgen.org/index_content.html] +subset: human_subset +subset: mouse_subset synonym: "immature Vg1.1-positive, Vd6.3-negative T cell" RELATED [] is_a: CL:0002411 ! Vgamma1.1-positive, Vdelta6.3-negative thymocyte property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 @@ -20428,6 +22918,8 @@ creation_date: 2010-10-07T03:10:35Z id: CL:0002415 name: immature Vgamma1.1-positive, Vdelta6.3-positive thymocyte def: "A Vgamma1.1-positive, Vdelta6.3-positive thymocyte that is CD24-positive." [GOC:tfm, http://www.immgen.org/index_content.html] +subset: human_subset +subset: mouse_subset synonym: "immature Vg1.1+Vd6.3+ T cell" EXACT [] is_a: CL:0002412 ! Vgamma1.1-positive, Vdelta6.3-positive thymocyte property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 @@ -20437,6 +22929,8 @@ creation_date: 2010-10-07T03:10:39Z id: CL:0002416 name: mature Vgamma1.1-positive, Vdelta6.3-positive thymocyte def: "A Vgamma1.1-positive, Vdelta6.3-positive thymocyte that is CD24-negative." [GOC:tfm, http://www.immgen.org/index_content.html] +subset: human_subset +subset: mouse_subset synonym: "mature Vg1.1+Vd6.3+ T cell" EXACT [] is_a: CL:0002412 ! Vgamma1.1-positive, Vdelta6.3-positive thymocyte property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 @@ -20446,6 +22940,8 @@ creation_date: 2010-10-07T03:10:41Z id: CL:0002417 name: primitive erythroid lineage cell def: "An immature or mature cell of the first erythroid lineage to arise during embryonic development." [GOC:tfm] +subset: human_subset +subset: mouse_subset is_a: CL:0000764 ! erythroid lineage cell property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-10-12T11:22:41Z @@ -20454,6 +22950,8 @@ creation_date: 2010-10-12T11:22:41Z id: CL:0002418 name: hemangioblast def: "A pluripotent cell in the yolk sac that can give rise to mesenchymal cells including erythrocytes and endothelial cells." [GOC:tfm, ISBN:0813817986, PMID:11495698] +subset: human_subset +subset: mouse_subset xref: MESH:D055018 is_a: BFO:0000002 is_a: CL:0000222 ! mesodermal cell @@ -20466,11 +22964,12 @@ id: CL:0002419 name: mature T cell def: "A T cell that expresses a T cell receptor complex and has completed T cell selection." [GOC:tfm] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "CD3e-positive T cell" EXACT [] synonym: "CD3epsilon T cell" RELATED [] synonym: "mature T-cell" EXACT [] is_a: CL:0000084 {is_inferred="true"} ! T cell -is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000084 ! T cell intersection_of: output_of GO:0045058 ! T cell selection intersection_of: RO:0002104 GO:0042101 ! has plasma membrane part T cell receptor complex @@ -20485,6 +22984,8 @@ name: immature T cell def: "A T cell that has not completed T cell selection." [GOC:tfm] subset: blood_and_immune_upper_slim subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "immature T-cell" EXACT [] xref: BTO:0001372 xref: CALOHA:TS-1042 @@ -20499,6 +23000,8 @@ creation_date: 2010-10-12T01:56:17Z id: CL:0002421 name: nucleated reticulocyte def: "A reticulocyte that retains the nucleus and other organelles. Found in birds, fish, amphibians and reptiles." [GOC:tfm, PMID:18182572, PMID:9011180, PMID:9046052] +subset: human_subset +subset: mouse_subset is_a: CL:0000558 {is_inferred="true"} ! reticulocyte is_a: CL:0002242 ! nucleate cell intersection_of: CL:0000558 ! reticulocyte @@ -20511,6 +23014,8 @@ id: CL:0002422 name: enucleated reticulocyte def: "A reticulocyte lacking a nucleus and showing a basophilic reticulum under vital staining due to the presence of ribosomes." [GOC:tfm, ISBN:0-12203-052-4, ISBN:0721601464] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset xref: CALOHA:TS-0864 xref: FMA:66785 is_a: CL:0000225 ! anucleate cell @@ -20527,6 +23032,8 @@ id: CL:0002423 name: DN2a thymocyte def: "A DN2 thymocyte that is Kit-hi." [GOC:tfm, PMID:20595614] comment: Observed in mice. There is growing evidence that molecular markers characterizing double negative thymocytes are different across species, especially in mouse versus human thymus. If in doubt, please consider using CL:0002489 'double negative thymocyte'. +subset: human_subset +subset: mouse_subset is_a: CL:0000806 {is_inferred="true"} ! DN2 thymocyte intersection_of: CL:0000806 ! DN2 thymocyte intersection_of: RO:0015015 PR:000002065 ! has high plasma membrane amount mast/stem cell growth factor receptor @@ -20539,6 +23046,8 @@ id: CL:0002424 name: DN2b thymocyte def: "A DN2 thymocyte that is Kit-low." [GOC:tfm, PMID:20595614] comment: Observed in mice. There is growing evidence that molecular markers characterizing double negative thymocytes are different across species, especially in mouse versus human thymus. If in doubt, please consider using CL:0002489 'double negative thymocyte'. +subset: human_subset +subset: mouse_subset is_a: CL:0000806 {is_inferred="true"} ! DN2 thymocyte intersection_of: CL:0000806 ! DN2 thymocyte intersection_of: RO:0015016 PR:000002065 ! has low plasma membrane amount mast/stem cell growth factor receptor @@ -20554,10 +23063,11 @@ def: "A pro-T cell that is lin-negative, CD25-negative, CD127-negative, CD44-pos comment: ETPs are reportedly CD1a-negative, CD4-negative, CD7-positive, CD8a-negative, CD8b-negative, CD33-low, CD34-high, CD38-low, CD45RA-positive, and CD45RO-negative. subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "ETP" EXACT [] synonym: "preT.ETP.Th" EXACT [] is_a: CL:0000827 {is_inferred="true"} ! pro-T cell -is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000827 ! pro-T cell intersection_of: CL:4030046 PR:000001380 ! lacks_plasma_membrane_part interleukin-2 receptor subunit alpha intersection_of: RO:0002104 PR:000001307 ! has plasma membrane part CD44 molecule @@ -20576,6 +23086,7 @@ id: CL:0002426 name: CD11b-positive, CD27-positive natural killer cell, mouse def: "A mature natural killer cell that is CD11b-positive and CD27-positive." [GOC:tfm, http://www.immgen.org/index_content.html] comment: A natural killer cell that is NK1.1-positive, CD11b-positive, and CD27-positive. +subset: mouse_subset is_a: CL:0002438 ! NK1.1-positive natural killer cell, mouse intersection_of: CL:0002438 ! NK1.1-positive natural killer cell, mouse intersection_of: RO:0002104 PR:000001012 ! has plasma membrane part integrin alpha-M @@ -20590,6 +23101,8 @@ creation_date: 2010-10-25T03:07:59Z id: CL:0002427 name: resting double-positive thymocyte def: "A double-positive, alpha-beta thymocyte that is small and not proliferating." [GOC:tfm, http://www.immgen.org/index_content.html] +subset: human_subset +subset: mouse_subset synonym: "T.DP.sm.Th" EXACT [] is_a: CL:0000809 {is_inferred="true"} ! double-positive, alpha-beta thymocyte intersection_of: CL:0000809 ! double-positive, alpha-beta thymocyte @@ -20602,6 +23115,8 @@ creation_date: 2010-10-21T01:59:06Z id: CL:0002428 name: double-positive blast def: "A double-positive thymocyte that is large (i.e. has a high forward scatter signal in flow cytometry) and is actively proliferating." [GOC:tfm, http://www.immgen.org/index_content.html] +subset: human_subset +subset: mouse_subset synonym: "activated double-positive thymocyte" EXACT [] synonym: "T.DPb.Th" EXACT [] is_a: CL:0000809 {is_inferred="true"} ! double-positive, alpha-beta thymocyte @@ -20618,6 +23133,8 @@ creation_date: 2010-10-21T01:59:11Z id: CL:0002429 name: CD69-positive double-positive thymocyte def: "A double-positive thymocyte that is CD69-positive and has begun positive selection." [GOC:tfm, http://www.immgen.org/index_content.html] +subset: human_subset +subset: mouse_subset synonym: "T.DP69+.Th" EXACT [] is_a: CL:0000809 {is_inferred="true"} ! double-positive, alpha-beta thymocyte intersection_of: CL:0000809 ! double-positive, alpha-beta thymocyte @@ -20635,6 +23152,8 @@ creation_date: 2010-10-21T02:11:52Z id: CL:0002430 name: CD4-intermediate, CD8-positive double-positive thymocyte def: "A double-positive thymocyte that is undergoing positive selection, has high expression of the alpha-beta T cell receptor, is CD69-positive, and is in the process of down regulating the CD4 co-receptor." [GOC:tfm, http://www.immgen.org/index_content.html] +subset: human_subset +subset: mouse_subset synonym: "T.4int8+.Th" EXACT [] synonym: "T_4int8+_Th" EXACT [] is_a: CL:0000809 {is_inferred="true"} ! double-positive, alpha-beta thymocyte @@ -20655,6 +23174,8 @@ creation_date: 2010-10-21T02:29:19Z id: CL:0002431 name: CD4-positive, CD8-intermediate double-positive thymocyte def: "A double-positive thymocyte that is undergoing positive selection, has high expression of the alpha-beta T cell receptor, is CD69-positive, and is in the process of down regulating the CD8 co-receptor." [GOC:tfm, http://www.immgen.org/index_content.html] +subset: human_subset +subset: mouse_subset synonym: "T.4+8int.Th" EXACT [] synonym: "T_4+8int_Th" EXACT [] is_a: CL:0000809 {is_inferred="true"} ! double-positive, alpha-beta thymocyte @@ -20676,6 +23197,8 @@ id: CL:0002432 name: CD24-positive, CD4 single-positive thymocyte def: "A CD4-positive, CD8-negative thymocyte that is CD24-positive and expresses high levels of the alpha-beta T cell receptor." [GOC:tfm, http://www.immgen.org/index_content.html] comment: Described in the immgene database as being CD24-intermediate. +subset: human_subset +subset: mouse_subset synonym: "CD24-positive, CD4 single-positive semimature thymocyte" EXACT [] synonym: "T.4SP24int.Th" EXACT [] is_a: CL:0000810 {is_inferred="true"} ! CD4-positive, alpha-beta thymocyte @@ -20692,6 +23215,8 @@ creation_date: 2010-10-21T02:43:52Z id: CL:0002433 name: CD69-positive, CD4-positive single-positive thymocyte def: "A CD4-positive, CD8-negative thymocyte that expresses high levels of the alpha-beta T cell receptor and is CD69-positive." [GOC:tfm, http://www.immgen.org/index_content.html] +subset: human_subset +subset: mouse_subset synonym: "intermediate CD4-single-positive" EXACT [] synonym: "T.4SP69+.Th" EXACT [] is_a: CL:0000810 {is_inferred="true"} ! CD4-positive, alpha-beta thymocyte @@ -20709,6 +23234,8 @@ id: CL:0002434 name: CD24-positive, CD8 single-positive thymocyte def: "A CD8-positive, CD4-negative thymocyte that is CD24-positive and expresses high levels of the alpha-beta T cell receptor." [GOC:tfm, http://www.immgen.org/index_content.html] comment: Described in the immgene database as being CD24-intermediate. +subset: human_subset +subset: mouse_subset synonym: "CD24-positive, CD8 single-positive semimature thymocyte" EXACT [] synonym: "T.8SP24int.Th" EXACT [] is_a: CL:0000811 {is_inferred="true"} ! CD8-positive, alpha-beta thymocyte @@ -20725,6 +23252,8 @@ creation_date: 2010-10-21T02:59:10Z id: CL:0002435 name: CD69-positive, CD8-positive single-positive thymocyte def: "A CD8-positive, CD4-negative thymocyte that expresses high levels of the alpha-beta T cell receptor and is CD69-positive." [GOC:tfm, http://www.immgen.org/index_content.html, https://orcid.org/0000-0001-5208-3432] +subset: human_subset +subset: mouse_subset synonym: "intermediate CD8-single-positive" EXACT [] synonym: "T.8SP69+.Th" EXACT [] is_a: CL:0000811 {is_inferred="true"} ! CD8-positive, alpha-beta thymocyte @@ -20742,6 +23271,8 @@ id: CL:0002436 name: mature CD4 single-positive thymocyte def: "A mature CD4-positive, CD8-negative alpha-beta T cell found in the thymus that is CD24-low and has high expression of the T cell receptor." [GOC:tfm, http://www.immgen.org/index_content.html] subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "T.4SP24-.Th" RELATED OMO:0003000 [] is_a: CL:0000624 {is_inferred="true"} ! CD4-positive, alpha-beta T cell intersection_of: CL:0000624 ! CD4-positive, alpha-beta T cell @@ -20759,6 +23290,8 @@ id: CL:0002437 name: mature CD8 single-positive thymocyte def: "A mature CD8-positive, CD4-negative alpha-beta T cell found in the thymus that is CD24-low and has high expression of the T cell receptor." [GOC:tfm, http://www.immgen.org/index_content.html] subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "T.8SP24-.Th" EXACT [] is_a: CL:0000625 {is_inferred="true"} ! CD8-positive, alpha-beta T cell intersection_of: CL:0000625 ! CD8-positive, alpha-beta T cell @@ -20776,10 +23309,10 @@ id: CL:0002438 name: NK1.1-positive natural killer cell, mouse def: "A mature NK cell that is NK1.1-positive." [GOC:tfm] comment: Note: Nk1.1 expression is restricted to C57BL strains of laboratory mice. +subset: mouse_subset synonym: "NK.sp" EXACT [] synonym: "NK1.1-positive NK cell" EXACT [] is_a: CL:0000824 ! mature natural killer cell -is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000824 ! mature natural killer cell intersection_of: RO:0002104 PR:000002977 ! has plasma membrane part killer cell lectin-like receptor subfamily B member 1C intersection_of: RO:0002162 NCBITaxon:10090 ! in taxon Mus musculus @@ -20792,6 +23325,7 @@ creation_date: 2010-10-25T03:18:04Z id: CL:0002439 name: NKGA2-positive natural killer cell, mouse def: "A NK1.1-positive T cell that is NKGA2-positive." [GOC:tfm, http://www.immgen.org/index_content.html] +subset: mouse_subset synonym: "NK.G2A+.SP" EXACT [] is_a: CL:0002438 ! NK1.1-positive natural killer cell, mouse intersection_of: CL:0002438 ! NK1.1-positive natural killer cell, mouse @@ -20805,6 +23339,7 @@ creation_date: 2010-10-25T03:31:09Z id: CL:0002440 name: Ly49D-positive natural killer cell, mouse def: "A NK1.1-positive T cell that is Ly49D-positive." [GOC:tfm, http://www.immgen.org/index_content.html] +subset: mouse_subset synonym: "NK.49D+.Sp" EXACT [] is_a: CL:0002438 ! NK1.1-positive natural killer cell, mouse intersection_of: CL:0002438 ! NK1.1-positive natural killer cell, mouse @@ -20818,6 +23353,7 @@ creation_date: 2010-10-25T03:36:19Z id: CL:0002441 name: CD94-positive natural killer cell, mouse def: "A NK1.1-positive T cell that is CD94-positive." [GOC:tfm, http://www.immgen.org/index_content.html] +subset: mouse_subset synonym: "NK.94+.Sp" EXACT [] is_a: CL:0002438 ! NK1.1-positive natural killer cell, mouse intersection_of: CL:0002438 ! NK1.1-positive natural killer cell, mouse @@ -20831,6 +23367,7 @@ creation_date: 2010-10-25T03:36:28Z id: CL:0002442 name: CD94-negative, Ly49CI-negative natural killer cell, mouse def: "A NK1.1-positive T cell that is CD94-negative and Ly49Cl-negative." [GOC:tfm, http://www.immgen.org/index_content.html] +subset: mouse_subset synonym: "CD94- Ly49I-negative NK cell" EXACT [] synonym: "NK.49Cl-94-.Sp" EXACT [] is_a: CL:0000623 ! natural killer cell @@ -20848,6 +23385,7 @@ creation_date: 2010-10-25T03:56:21Z id: CL:0002443 name: Ly49CI-positive natural killer cell, mouse def: "A NK1.1-positive T cell that is Ly49Cl-positive." [GOC:tfm, http://www.immgen.org/index_content.html] +subset: mouse_subset synonym: "Ly49I-positive NK cell" EXACT [] synonym: "NK.49Cl+.Sp" EXACT [] is_a: CL:0002438 ! NK1.1-positive natural killer cell, mouse @@ -20862,6 +23400,7 @@ creation_date: 2010-10-25T03:36:38Z id: CL:0002444 name: Ly49H-positive natural killer cell, mouse def: "A NK1.1-positive T cell that is Ly49H-positive." [GOC:tfm, http://www.immgen.org/index_content.html] +subset: mouse_subset synonym: "LyH49H-positive" EXACT [] is_a: CL:0002438 ! NK1.1-positive natural killer cell, mouse intersection_of: CL:0002438 ! NK1.1-positive natural killer cell, mouse @@ -20875,6 +23414,7 @@ creation_date: 2010-10-25T03:36:43Z id: CL:0002445 name: Ly49D-negative natural killer cell, mouse def: "A NK1.1-positive T cell that is Ly49D-negative." [GOC:tfm, http://www.immgen.org/index_content.html] +subset: mouse_subset synonym: "NK.49D-.Sp" EXACT [] is_a: CL:0002438 ! NK1.1-positive natural killer cell, mouse intersection_of: CL:0002438 ! NK1.1-positive natural killer cell, mouse @@ -20888,6 +23428,7 @@ creation_date: 2010-10-25T03:39:02Z id: CL:0002446 name: Ly49CI-negative natural killer cell, mouse def: "A NK1.1-positive T cell that is Ly49Cl-negative." [GOC:tfm, http://www.immgen.org/index_content.html] +subset: mouse_subset synonym: "Ly49I-negative NK cell" EXACT [] synonym: "NK.49Cl-.Sp" EXACT [] is_a: CL:0002438 ! NK1.1-positive natural killer cell, mouse @@ -20902,6 +23443,7 @@ creation_date: 2010-10-25T03:52:04Z id: CL:0002447 name: CD94-negative natural killer cell, mouse def: "A NK1.1-positive T cell that is CD94-negative." [GOC:tfm, http://www.immgen.org/index_content.html] +subset: mouse_subset synonym: "NK.94-.Sp" EXACT [] is_a: CL:0002438 ! NK1.1-positive natural killer cell, mouse intersection_of: CL:0002438 ! NK1.1-positive natural killer cell, mouse @@ -20915,6 +23457,7 @@ creation_date: 2010-10-25T03:54:18Z id: CL:0002448 name: Ly49H-negative natural killer cell, mouse def: "A NK1.1-positive T cell that is Ly49H-negative." [GOC:tfm, http://www.immgen.org/index_content.html] +subset: mouse_subset synonym: "LyH49H-negative" EXACT [] is_a: CL:0002438 ! NK1.1-positive natural killer cell, mouse intersection_of: CL:0002438 ! NK1.1-positive natural killer cell, mouse @@ -20928,6 +23471,7 @@ creation_date: 2010-10-25T03:42:42Z id: CL:0002449 name: CD94-positive Ly49CI-positive natural killer cell, mouse def: "A NK1.1-positive T cell that is CD94-positive and Ly49Cl-positive." [GOC:tfm, http://www.immgen.org/index_content.html] +subset: mouse_subset synonym: "NK.49Cl+94+.Sp" EXACT [] is_a: CL:0002441 ! CD94-positive natural killer cell, mouse is_a: CL:0002443 ! Ly49CI-positive natural killer cell, mouse @@ -20942,6 +23486,8 @@ creation_date: 2010-10-25T03:56:27Z id: CL:0002450 name: tether cell def: "A specialized hair cell that has an elongated kinocilium upon which an otolith accretes. The tether cell then anchors the otolith in place." [GOC:cvs, GOC:tfm, PMID:9398434] +subset: human_subset +subset: mouse_subset xref: ZFA:0005565 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0002374 ! ear hair cell property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 @@ -20951,6 +23497,8 @@ creation_date: 2010-11-10T01:41:00Z id: CL:0002451 name: mammary stem cell def: "A multi-fate stem cell that is the source of cells for growth of the mammary gland during puberty and gestation. This cell type gives rise to both the luminal and myoepithelial cell types of the gland, and have been shown to have the ability to regenerate the entire organ in mice. This cell type also plays an important role in carcinogenesis of the breast. This cell type is Lin-, CD24-positive, CD29-hi." [GOC:hjd, GOC:tfm, PMID:15987436, PMID:16397499, PMID:17851544] +subset: human_subset +subset: mouse_subset is_a: CL:0000048 ! multi fate stem cell property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-11-10T01:46:51Z @@ -20961,12 +23509,16 @@ name: oligodendrocyte precursor cell def: "A progenitor cell of the central nervous system that can differentiate into oligodendrocytes or type-2 astrocytes. This cell originates from multiple structures within the developing brain including the medial ganglion eminence and the lateral ganglionic eminence. These cells migrate throughout the central nervous system and persist into adulthood where they play an important role in remyelination of injured neurons." [GOC:tfm, PMID:10704434, PMID:11756508, PMID:20142420, PMID:2182078, PMID:24133281, PMID:9826671] subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "O-2A/OPC" RELATED OMO:0003000 [PMID:24133281] synonym: "O2A/OPC" RELATED OMO:0003000 [PMID:11756508] synonym: "oligodendrocyte-type 2 astrocyte (O-2A) progenitor cell" BROAD [PMID:2253328] synonym: "oligodendrocyte/type-2 astrocyte progenitor cell" BROAD [PMID:24133281] {terms:contributor="https://orcid.org/0000-0002-0819-0473"} xref: MESH:D000073637 +is_a: CL:0000123 ! neuron associated cell (sensu Vertebrata) is_a: CL:0011026 ! progenitor cell +relationship: part_of UBERON:0001017 ! central nervous system relationship: RO:0002202 CL:0000339 ! develops from glioblast (sensu Vertebrata) property_value: RO:0002175 NCBITaxon:9606 property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 @@ -20975,8 +23527,10 @@ creation_date: 2010-11-10T02:51:34Z [Term] id: CL:0002454 -name: Cd4-negative, CD8_alpha-negative, CD11b-positive dendritic cell -def: "Cd4-negative, CD8_alpha-negative, CD11b-positive dendritic cell is a conventional dendritic cell that is CD11b-positive, CD4-negative, CD8_alpha-negative and is CD205-positive." [GOC:tfm, http://www.immgen.org/index_content.html] +name: CD4-negative, CD8-alpha-negative, CD11b-positive dendritic cell +def: "CD4-negative, CD8-alpha-negative, CD11b-positive dendritic cell is a conventional dendritic cell that is CD11b-positive, CD4-negative, CD8-alpha-negative and is CD205-positive." [GOC:tfm, http://www.immgen.org/index_content.html] +subset: human_subset +subset: mouse_subset synonym: "DC.8-4-11b+" EXACT [] synonym: "spleen double-negative dendritic cell" EXACT [] is_a: CL:0002465 {is_inferred="true"} ! CD11b-positive dendritic cell @@ -20990,8 +23544,10 @@ creation_date: 2010-11-22T01:10:28Z [Term] id: CL:0002455 -name: CD8_alpha-negative plasmacytoid dendritic cell -def: "A CD11c-low plasmacytoid dendritic cell that is CD8alpha-negative and CD4-positive." [GOC:tfm, http://www.immgen.org/index_content.html] +name: CD8-alpha-negative plasmacytoid dendritic cell +def: "A CD11c-low plasmacytoid dendritic cell that is CD8-alpha-negative and CD4-positive." [GOC:tfm, http://www.immgen.org/index_content.html] +subset: human_subset +subset: mouse_subset synonym: "DC.pDC.8-" EXACT [] is_a: CL:0000989 {is_inferred="true"} ! CD11c-low plasmacytoid dendritic cell intersection_of: CL:0000989 ! CD11c-low plasmacytoid dendritic cell @@ -21004,8 +23560,10 @@ creation_date: 2010-11-22T01:27:37Z [Term] id: CL:0002456 -name: CD8_alpha-positive plasmacytoid dendritic cell -def: "A CD11c-low plasmacytoid dendritic cell that is CD8alpha-positive and CD4-positive." [GOC:tfm, http://www.immgen.org/index_content.html] +name: CD8-alpha-positive plasmacytoid dendritic cell +def: "A CD11c-low plasmacytoid dendritic cell that is CD8-alpha-positive and CD4-positive." [GOC:tfm, http://www.immgen.org/index_content.html] +subset: human_subset +subset: mouse_subset synonym: "DC.pDC.8+" EXACT [] is_a: CL:0000989 {is_inferred="true"} ! CD11c-low plasmacytoid dendritic cell intersection_of: CL:0000989 ! CD11c-low plasmacytoid dendritic cell @@ -21022,6 +23580,8 @@ name: epidermal Langerhans cell def: "A Langerhans cell that is in the epidermis and is CD45-positive, MHCII-positive, and CD11b-positive." [GOC:tfm, http://www.immgen.org/index_content.html] subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset is_a: CL:0000453 {is_inferred="true"} ! Langerhans cell is_a: CL:0002465 ! CD11b-positive dendritic cell intersection_of: CL:0000453 ! Langerhans cell @@ -21040,6 +23600,8 @@ creation_date: 2010-11-22T03:57:57Z id: CL:0002458 name: langerin-positive dermal dendritic cell def: "A dermal dendritic cell that is langerin-positive and CD103-positive." [GOC:tfm, http://www.immgen.org/index_content.html] +subset: human_subset +subset: mouse_subset is_a: CL:0001006 {is_inferred="true"} ! dermal dendritic cell is_a: CL:0002461 ! CD103-positive dendritic cell intersection_of: CL:0001006 ! dermal dendritic cell @@ -21051,6 +23613,8 @@ creation_date: 2010-11-22T04:06:22Z id: CL:0002459 name: langerin-negative dermal dendritic cell def: "A dermal dendritic cell that is langerin-negative, CD103-negative, and CD11b-positive." [GOC:tfm, http://www.immgen.org/index_content.html] +subset: human_subset +subset: mouse_subset is_a: CL:0001006 {is_inferred="true"} ! dermal dendritic cell intersection_of: CL:0001006 ! dermal dendritic cell intersection_of: CL:4030046 PR:000001010 ! lacks_plasma_membrane_part integrin alpha-E @@ -21061,9 +23625,11 @@ creation_date: 2010-11-22T04:09:44Z [Term] id: CL:0002460 -name: CD8alpha-negative thymic conventional dendritic cell -def: "A conventional thymic dendritic cell that is CD8alpha-negative." [GOC:tfm, http://www.immgen.org/index_content.html, PMID:19273629] +name: CD8-alpha-negative thymic conventional dendritic cell +def: "A conventional thymic dendritic cell that is CD8-alpha-negative." [GOC:tfm, http://www.immgen.org/index_content.html, PMID:19273629] subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "DC.8-.Th" EXACT [] is_a: CL:0000941 {is_inferred="true"} ! thymic conventional dendritic cell intersection_of: CL:0000941 ! thymic conventional dendritic cell @@ -21077,6 +23643,8 @@ creation_date: 2010-11-23T10:58:53Z id: CL:0002461 name: CD103-positive dendritic cell def: "A conventional dendritic cell that is CD103-positive. This cell type is usually found in non-lymphoid tissue." [GOC:tfm, http://www.immgen.org/index_content.html] +subset: human_subset +subset: mouse_subset is_a: CL:0000766 ! myeloid leukocyte is_a: CL:0000990 {is_inferred="true"} ! conventional dendritic cell intersection_of: CL:0000990 ! conventional dendritic cell @@ -21090,6 +23658,8 @@ creation_date: 2010-11-23T01:32:43Z id: CL:0002462 name: adipose dendritic cell def: "A F4/80-negative dendritic cell located in adipose tissue." [GOC:tfm, http://www.immgen.org/index_content.html] +subset: human_subset +subset: mouse_subset is_a: CL:0000766 ! myeloid leukocyte is_a: CL:0000990 {is_inferred="true"} ! conventional dendritic cell is_a: CL:0002320 ! connective tissue cell @@ -21106,6 +23676,8 @@ creation_date: 2010-11-23T01:38:21Z id: CL:0002463 name: SIRPa-positive adipose dendritic cell def: "An adipose dendritic cell that is SIRPa-positive." [GOC:tfm, http://www.immgen.org/index_content.html] +subset: human_subset +subset: mouse_subset synonym: "DC.SIRPa+.Ad" EXACT [] is_a: CL:0002462 ! adipose dendritic cell intersection_of: CL:0000990 ! conventional dendritic cell @@ -21118,6 +23690,8 @@ creation_date: 2010-11-23T01:40:44Z id: CL:0002464 name: SIRPa-negative adipose dendritic cell def: "An adipose dendritic cell that is SIRPa-negative." [GOC:tfm, http://www.immgen.org/index_content.html] +subset: human_subset +subset: mouse_subset synonym: "DC.SIRPa-.Ad" EXACT [] is_a: CL:0002462 ! adipose dendritic cell intersection_of: CL:0000990 ! conventional dendritic cell @@ -21130,6 +23704,8 @@ creation_date: 2010-11-23T01:40:46Z id: CL:0002465 name: CD11b-positive dendritic cell def: "A conventional dendritic cell that expresses CD11b (ITGAM)." [GOC:tfm, http://www.immgen.org/index_content.html] +subset: human_subset +subset: mouse_subset is_a: CL:0000990 {is_inferred="true"} ! conventional dendritic cell intersection_of: CL:0000990 ! conventional dendritic cell intersection_of: RO:0002104 PR:000001012 ! has plasma membrane part integrin alpha-M @@ -21141,6 +23717,8 @@ creation_date: 2010-11-23T01:50:05Z id: CL:0002466 name: small intestine serosal dendritic cell def: "A CD11b-positive dendritic cell located in the serosal portion of the small intestine epithelium. This cell type is CD45-positive, MHC-II-positive, CD11c-low, CD103-negative." [GOC:tfm, http://www.immgen.org/index_content.html] +subset: human_subset +subset: mouse_subset synonym: "DC.11cloSer.SI" EXACT [] is_a: CL:0002465 {is_inferred="true"} ! CD11b-positive dendritic cell intersection_of: CL:0002465 ! CD11b-positive dendritic cell @@ -21152,6 +23730,7 @@ relationship: CL:4030046 PR:000001010 ! lacks_plasma_membrane_part integrin alph relationship: RO:0002104 GO:0042613 ! has plasma membrane part MHC class II protein complex relationship: RO:0002104 PR:000001006 ! has plasma membrane part receptor-type tyrosine-protein phosphatase C relationship: RO:0015016 PR:000001013 ! has low plasma membrane amount integrin alpha-X +property_value: foaf:depiction http://purl.obolibrary.org/obo/cl/images/Small-intestine-cells.png {dc:license="http://creativecommons.org/licenses/by/4.0/", comment="Figure depicts a cross section of intestinal villi in the small intestine, including the crypts of Lieberkuhn (seen here as ‘crypt’), as well as the layer specific locations of cells that exist within the gastrointestinal tract. Layers depicted here include epithelium (rows of cells bordering villus), submucosa (white space below the epithelium containing networks of neurons and ganglia depicted in pink), muscularis mucosae (blue layer), muscularis propria (referred to here as muscle layer).\n\nISC: Intestinal Stem Cell \nTA: Transit Amplifying Cells"} property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-11-23T02:00:21Z @@ -21159,6 +23738,8 @@ creation_date: 2010-11-23T02:00:21Z id: CL:0002467 name: Gr1-high myeloid suppressor cell def: "A myeloid suppressor cell that is Gr1-high and CD11c-negative." [GOC:tfm, http://www.immgen.org/index_content.html] +subset: human_subset +subset: mouse_subset synonym: "MDS.Gr1hi" EXACT [] is_a: CL:0000889 {is_inferred="true"} ! myeloid suppressor cell intersection_of: CL:0000889 ! myeloid suppressor cell @@ -21173,6 +23754,8 @@ creation_date: 2010-11-23T02:15:12Z id: CL:0002468 name: Gr1-low myeloid suppressor cell def: "A myeloid suppressor cell that is Gr1-low and CD11c-positive." [GOC:tfm, http://www.immgen.org/index_content.html] +subset: human_subset +subset: mouse_subset synonym: "MDS.Gr1lo" EXACT [] is_a: CL:0000889 {is_inferred="true"} ! myeloid suppressor cell intersection_of: CL:0000889 ! myeloid suppressor cell @@ -21187,6 +23770,8 @@ creation_date: 2010-11-23T02:19:43Z id: CL:0002469 name: MHC-II-negative classical monocyte def: "Gr1-high monocyte that lacks MHC-II receptor complex." [GOC:tfm, http://www.immgen.org/index_content.html] +subset: human_subset +subset: mouse_subset synonym: "Mo.6C+II-" EXACT [] is_a: CL:0002395 {is_inferred="true"} ! Gr1-high classical monocyte intersection_of: CL:0002395 ! Gr1-high classical monocyte @@ -21200,6 +23785,8 @@ id: CL:0002470 name: MHC-II-positive classical monocyte def: "Gr1-high monocyte that has a MHC-II receptor complex." [GOC:tfm, http://www.immgen.org/index_content.html] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "Mo.6c+II" EXACT [] is_a: CL:0002395 {is_inferred="true"} ! Gr1-high classical monocyte intersection_of: CL:0002395 ! Gr1-high classical monocyte @@ -21212,6 +23799,8 @@ creation_date: 2010-11-23T03:30:21Z id: CL:0002471 name: MHC-II-negative non-classical monocyte def: "Gr1-low non-classical monocyte that lacks expression of a MHC-II complex." [GOC:tfm, http://www.immgen.org/index_content.html] +subset: human_subset +subset: mouse_subset synonym: "Mo.6C-II-" EXACT [] is_a: CL:0002058 {is_inferred="true"} ! Gr1-low non-classical monocyte intersection_of: CL:0002058 ! Gr1-low non-classical monocyte @@ -21224,6 +23813,8 @@ creation_date: 2010-11-23T03:38:15Z id: CL:0002472 name: MHC-II-low non-classical monocyte def: "Gr1-low non-classical monocyte that has low to intermediate expression of the MHC-II complex." [GOC:tfm, http://www.immgen.org/index_content.html] +subset: human_subset +subset: mouse_subset synonym: "Mo.6C-IIint" EXACT [] is_a: CL:0002058 {is_inferred="true"} ! Gr1-low non-classical monocyte intersection_of: CL:0002058 ! Gr1-low non-classical monocyte @@ -21236,6 +23827,8 @@ creation_date: 2010-11-23T03:47:53Z id: CL:0002473 name: MHC-II-high non-classical monocyte def: "Gr1-low non-classical monocyte that has high surface expression of a MHC-II complex." [GOC:tfm, http://www.immgen.org/index_content.html] +subset: human_subset +subset: mouse_subset synonym: "Mo.6C-II+" EXACT [] is_a: CL:0002058 {is_inferred="true"} ! Gr1-low non-classical monocyte intersection_of: CL:0002058 ! Gr1-low non-classical monocyte @@ -21248,6 +23841,8 @@ creation_date: 2010-11-23T03:47:55Z id: CL:0002474 name: lymphoid MHC-II-negative classical monocyte def: "A MHC-II-negative classical monocyte located in lymphoid tissue that is F4/80-positive, CD11c-negative, and CD11b-high." [GOC:tfm, http://www.immgen.org/index_content.html] +subset: human_subset +subset: mouse_subset is_a: CL:0002469 {is_inferred="true"} ! MHC-II-negative classical monocyte intersection_of: CL:0002469 ! MHC-II-negative classical monocyte intersection_of: CL:4030046 PR:000001013 ! lacks_plasma_membrane_part integrin alpha-X @@ -21263,6 +23858,8 @@ creation_date: 2010-11-23T04:00:52Z id: CL:0002475 name: lymphoid MHC-II-negative non-classical monocyte def: "A MHC-II-negative classical monocyte located in lymphoid tissue that is F4/80-positive, CD11c-intermediate, and CD11b-high." [GOC:tfm, http://www.immgen.org/index_content.html] +subset: human_subset +subset: mouse_subset is_a: CL:0002471 ! MHC-II-negative non-classical monocyte intersection_of: CL:0002471 ! MHC-II-negative non-classical monocyte intersection_of: RO:0002104 PR:000001013 ! has plasma membrane part integrin alpha-X @@ -21278,11 +23875,12 @@ creation_date: 2010-11-23T04:09:09Z id: CL:0002476 name: bone marrow macrophage def: "A tissue-resident macrophage located in the bone marrow. This cell type is B220-negative, CD3e-negative, Ly-6C-negative, CD115-positive, F4/80-positive." [GOC:tfm, http://www.immgen.org/index_content.html] +subset: human_subset +subset: mouse_subset synonym: "MF.BM" RELATED OMO:0003000 [] xref: BTO:0004732 is_a: CL:0000864 {is_inferred="true"} ! tissue-resident macrophage is_a: CL:0010004 ! mononuclear cell of bone marrow -is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000864 ! tissue-resident macrophage intersection_of: CL:4030046 PR:000001014 ! lacks_plasma_membrane_part receptor-type tyrosine-protein phosphatase C isoform CD45RABC intersection_of: CL:4030046 PR:000001020 ! lacks_plasma_membrane_part CD3 epsilon @@ -21301,8 +23899,10 @@ creation_date: 2010-11-23T04:19:25Z id: CL:0002477 name: adipose macrophage def: "A macrophage located in adipose tissue that is CD45-positive, CD11c-positive, and SIRPa-positive." [GOC:tfm] +subset: cellxgene_subset +subset: human_subset +subset: mouse_subset is_a: CL:0000864 {is_inferred="true"} ! tissue-resident macrophage -is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000864 ! tissue-resident macrophage intersection_of: RO:0002104 PR:000001006 ! has plasma membrane part receptor-type tyrosine-protein phosphatase C intersection_of: RO:0002104 PR:000001013 ! has plasma membrane part integrin alpha-X @@ -21317,6 +23917,8 @@ creation_date: 2010-11-23T04:31:28Z id: CL:0002478 name: F4/80-negative adipose macrophage def: "An adipose macrophage that does not express F4/80but is MHC-II-positive. This cell type exhibits autofluorescence under typical flow cyometry conditions." [GOC:tfm, http://www.immgen.org/index_content.html] +subset: human_subset +subset: mouse_subset synonym: "MF.Autofl.Ad" EXACT [] is_a: CL:0002477 {is_inferred="true"} ! adipose macrophage intersection_of: CL:0002477 ! adipose macrophage @@ -21331,6 +23933,8 @@ creation_date: 2010-11-23T04:40:50Z id: CL:0002479 name: F4/80-positive adipose macrophage def: "An adipose macrophage that does not express MHC-II but is F4/80-positive." [GOC:tfm, http://www.immgen.org/index_content.html] +subset: human_subset +subset: mouse_subset synonym: "MF.F480+.Ad" EXACT [] is_a: CL:0002477 {is_inferred="true"} ! adipose macrophage intersection_of: CL:0002477 ! adipose macrophage @@ -21345,13 +23949,18 @@ creation_date: 2010-11-23T04:35:53Z id: CL:0002480 name: nasal mucosa goblet cell def: "A goblet cell located in the nasal epithelium." [GOC:cjm, GOC:tfm] +comment: The marker set LYPD2, MUC5AC can identify the Human cell type nasal mucosa goblet cell in the Lung with a confidence of 0.81 (NS-Forest FBeta value). {xref="https://doi.org/10.5281/zenodo.11165918"} subset: cellxgene_subset +subset: human_subset +subset: mouse_subset xref: MP:0002262 -is_a: CL:0002370 ! respiratory goblet cell +is_a: CL:0002370 ! respiratory tract goblet cell is_a: CL:0002631 ! epithelial cell of upper respiratory tract intersection_of: CL:0000160 ! goblet cell intersection_of: part_of UBERON:0001826 ! nasal cavity mucosa relationship: part_of UBERON:0005384 ! nasal cavity epithelium +relationship: RO:0015004 CLM:1000027 ! has characterizing marker set NS forest marker set of nasal mucosa goblet cell (Human Lung). +property_value: RO:0002175 NCBITaxon:9606 property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-12-03T03:03:02Z @@ -21359,6 +23968,8 @@ creation_date: 2010-12-03T03:03:02Z id: CL:0002481 name: peritubular myoid cell def: "The flattened smooth myoepithelial cells of mesodermal origin that lie just outside the basal lamina of the seminiferous tubule." [GOC:cjm, GOC:tfm, MP:0006420] +subset: human_subset +subset: mouse_subset is_a: CL:0000185 {is_inferred="true"} ! myoepithelial cell is_a: CL:0002625 ! seminiferous tubule epithelial cell intersection_of: CL:0000185 ! myoepithelial cell @@ -21370,6 +23981,8 @@ creation_date: 2010-12-03T03:11:48Z id: CL:0002482 name: dermal melanocyte def: "A melanocyte that produces pigment in the dermis." [GOC:cjm, GOC:tfm, MP:0009386] +subset: human_subset +subset: mouse_subset is_a: CL:1000458 ! melanocyte of skin intersection_of: CL:0000148 ! melanocyte intersection_of: part_of UBERON:0002067 ! dermis @@ -21382,6 +23995,8 @@ id: CL:0002483 name: hair follicle melanocyte def: "A melanocyte that produces pigment within the hair follicle." [GOC:tfm, MP:0004381] subset: human_reference_atlas +subset: human_subset +subset: mouse_subset is_a: CL:0002559 ! hair follicle cell is_a: CL:2000000 ! epidermal melanocyte intersection_of: CL:0000148 ! melanocyte @@ -21395,6 +24010,8 @@ id: CL:0002484 name: epithelial melanocyte def: "A melanocyte that produces pigment in the epithelium." [GOC:tfm, MP:0009388] comment: The text defintion reference to the MP term appears to reference an epidermal melanocyte term. This term represents any melanocyte in any epithelium. +subset: human_subset +subset: mouse_subset is_a: CL:0000148 {is_inferred="true"} ! melanocyte intersection_of: CL:0000148 ! melanocyte intersection_of: part_of UBERON:0000483 ! epithelium @@ -21407,6 +24024,8 @@ id: CL:0002485 name: retinal melanocyte def: "A melanocyte of the retina. This cell type is distinct from pigmented retinal epithelium." [GOC:tfm, MP:0010190] subset: eye_upper_slim +subset: human_subset +subset: mouse_subset is_a: CL:0000148 ! melanocyte is_a: CL:0009004 ! retinal cell intersection_of: CL:0000148 ! melanocyte @@ -21419,6 +24038,8 @@ creation_date: 2010-12-03T03:25:32Z id: CL:0002486 name: strial intermediate cell def: "A melanocyte located between the epithelial marginal cell layer and the mesodermal basal cell layer within the intrastrial space; the predominant cellular component of the electrogenic machinery that generates an endocochlear potential (80-100 mV) ." [GOC:tfm, MP:0000048] +subset: human_subset +subset: mouse_subset is_a: CL:0000710 ! neurecto-epithelial cell is_a: CL:0002484 ! epithelial melanocyte is_a: CL:0002491 ! auditory epithelial cell @@ -21432,6 +24053,8 @@ creation_date: 2010-12-03T03:29:15Z id: CL:0002487 name: cutaneous/subcutaneous mechanoreceptor cell def: "A neuronal receptor that respond to mechanical pressure or distortion in the skin." [GOC:tfm, MP:0000973] +subset: human_subset +subset: mouse_subset is_a: CL:0000199 ! mechanoreceptor cell property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-12-06T02:53:30Z @@ -21441,6 +24064,8 @@ id: CL:0002488 name: trophoblast giant cell def: "A trophoblast cell that has a large volume of cytoplasm, is polyploid and is usually mononuclear but is also occasionally multi-nucleate. This cell type is important in establishing maternal physiology and remodeling of the vasculature of the placenta." [GOC:tfm, MP:0001714, MP:19876834] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "giant trophoblast cell" EXACT [] is_a: CL:0000351 {is_inferred="true"} ! trophoblast cell intersection_of: CL:0000351 ! trophoblast cell @@ -21457,6 +24082,8 @@ name: double negative thymocyte def: "A thymocyte that lacks expression of CD4 and CD8." [GOC:tfm, MP:0002407] comment: These are precursors to mature T cells; normally, they do not circulate, but are found in the thymus and they have not undergone rearrangement of the alpha and beta T cell receptor genes. subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "CD4-CD8- T cell" EXACT [MP:0002407] synonym: "double negative T cell" EXACT [] is_a: CL:0000893 ! thymocyte @@ -21472,6 +24099,8 @@ creation_date: 2010-12-06T03:03:38Z id: CL:0002490 name: organ of Corti supporting cell def: "A supporting cell of the organ of Corti." [GOC:tfm, MP:0004300] +subset: human_subset +subset: mouse_subset is_a: CL:0002315 ! supporting cell of cochlea intersection_of: CL:0005014 ! auditory epithelial supporting cell intersection_of: part_of UBERON:0002227 ! spiral organ of cochlea @@ -21483,6 +24112,9 @@ creation_date: 2010-12-06T03:09:01Z id: CL:0002491 name: auditory epithelial cell def: "A specialized cell involved in auditory sensory perception." [GOC:tfm] +subset: cellxgene_subset +subset: human_subset +subset: mouse_subset is_a: CL:0000098 ! sensory epithelial cell intersection_of: CL:0000066 ! epithelial cell intersection_of: capable_of GO:0050910 ! detection of mechanical stimulus involved in sensory perception of sound @@ -21494,6 +24126,8 @@ creation_date: 2010-12-06T03:18:43Z id: CL:0002492 name: strial marginal cell def: "A polarized columnar cell that covesr the lateral surface of the cochlear duct, secretes potassium ions and forms a continuous sheet in contact with the endolymph; marginal cells form extensive interdigitations with the basal and intermediate cells in the normal adult stria." [GOC:tfm, MP:0004366] +subset: human_subset +subset: mouse_subset is_a: CL:0002491 ! auditory epithelial cell property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-12-06T03:20:41Z @@ -21503,6 +24137,8 @@ id: CL:0002493 name: strial basal cell def: "A polarized cell that is juxtaposed to fibrocytes in the underlying spiral ligament. This cell type secretes potassium ions derived from fibrocytes through gap junctions." [GOC:tfm, MP:0004365] comment: Basal cells form a multi-layered epithelial barrier that separates the extracellular spaces of the stria vascularis and the spiral ligament[PMID:18353863] +subset: human_subset +subset: mouse_subset is_a: CL:0002491 ! auditory epithelial cell relationship: part_of UBERON:0002282 ! stria vascularis of cochlear duct property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 @@ -21513,6 +24149,8 @@ id: CL:0002494 name: cardiocyte def: "A cell located in the heart, including both muscle and non muscle cells." [GOC:tfm] comment: From Onard of the FMA: Cardiac muscle cell or cardiac myocyte is a striated muscle cell. Cardiocyte on the other hand is any cell in the heart which includes cells other than muscle cells (e.g. endothelial cell of endocardium). Unless there is a consensus among anatomists that cardiocytes refer only to muscle cells, we will treat them as a general class of cells in the heart. +subset: human_subset +subset: mouse_subset synonym: "heart cell" EXACT [] xref: BTO:0001539 xref: CALOHA:TS-0115 @@ -21530,6 +24168,8 @@ id: CL:0002495 name: fetal cardiomyocyte def: "A fetal and neonatal heart cell that undergoes proliferation and is not yet terminally differentiated into a binucleate or a multinucleate cardiac myocyte." [GOC:tfm, MP:0008788] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "embryonic cardiomyocyte" EXACT [] synonym: "neonatal cardiomyocyte" EXACT [] is_a: CL:0000746 ! cardiac muscle cell @@ -21541,6 +24181,8 @@ id: CL:0002496 name: intraepithelial lymphocyte def: "A T cell that is located in the intestinal epithelium and is capable of a mucosal immune response." [GOC:tfm, MP:0008894] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "IEL" EXACT [] synonym: "intraepithelial T cell" EXACT [] synonym: "intraepithelial T-cell" EXACT [] @@ -21558,6 +24200,8 @@ creation_date: 2010-12-07T09:54:50Z id: CL:0002497 name: primary trophoblast giant cell def: "A trophoblast giant cell derived from the mural trophectoderm." [GOC:tfm, PMCID:PMC85124] +subset: human_subset +subset: mouse_subset xref: EMAPA:16066 is_a: CL:0002488 ! trophoblast giant cell property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 @@ -21567,6 +24211,8 @@ creation_date: 2010-12-07T10:07:47Z id: CL:0002498 name: secondary trophoblast giant cell def: "A trophoblast giant cell that is derived from ectoplacental cone and, later in gestation, the spongiotrophoblast." [GOC:tfm, PMCID:PMC85124] +subset: human_subset +subset: mouse_subset is_a: CL:0002488 ! trophoblast giant cell property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-12-07T10:07:52Z @@ -21575,6 +24221,7 @@ creation_date: 2010-12-07T10:07:52Z id: CL:0002499 name: spongiotrophoblast cell def: "A trophoblast cell that arises in the junctional zone (basal plate) of the placenta." [GOC:tfm, MP:0008959] +subset: mouse_subset synonym: "spongiotrophoblast" EXACT [] is_a: CL:0000351 ! trophoblast cell relationship: part_of UBERON:0004021 ! spongiotrophoblast layer @@ -21585,6 +24232,8 @@ creation_date: 2010-12-07T12:56:56Z id: CL:0002500 name: P enteroendocrine cell def: "A P/D1 enteroendocrine cell that is Grimelius positive and stores bombesin-like polypeptide." [FMA:63418, GOC:tfm] +subset: human_subset +subset: mouse_subset is_a: CL:0002268 ! P/D1 enteroendocrine cell property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-12-07T03:42:06Z @@ -21593,6 +24242,8 @@ creation_date: 2010-12-07T03:42:06Z id: CL:0002501 name: type D1 enteroendocrine cell def: "A P/D1 enteroendocrine cell that is argyrophilic and stores vasoactive intestinal polypeptide." [FMA:63207, GOC:tfm] +subset: human_subset +subset: mouse_subset xref: FMA:63207 is_a: CL:0002268 ! P/D1 enteroendocrine cell property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 @@ -21602,6 +24253,8 @@ creation_date: 2010-12-07T03:42:09Z id: CL:0002502 name: type M enteroendocrine cell def: "An enteroendocrine cell of the small intestine that secretes motilin." [GOC:tfm, PMID:15153415] +subset: human_subset +subset: mouse_subset synonym: "Mo enteroendocrine cell" BROAD [] xref: FMA:63420 is_a: CL:0002272 ! motilin secreting cell @@ -21614,6 +24267,8 @@ id: CL:0002503 name: adventitial cell def: "A cell of the adventitial layer of ductal structures such as the uterer, defent duct, biliary duct, etc" [GOC:tfm] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset xref: BTO:0002441 xref: FMA:84639 is_a: CL:0000630 ! supporting cell @@ -21629,21 +24284,27 @@ id: CL:0002504 name: enteric smooth muscle cell def: "A smooth muscle cell of the intestine." [GOC:tfm] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "intestinal smooth muscle cell" EXACT [] +xref: https://cellxgene.cziscience.com/cellguide/CL_0002504 is_a: CL:0000192 {is_inferred="true"} ! smooth muscle cell intersection_of: CL:0000192 ! smooth muscle cell intersection_of: part_of UBERON:0000160 ! intestine relationship: part_of UBERON:0000160 ! intestine property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nEnteric smooth muscle cells are a specialized type of cell found in the gastrointestinal tract. They are an integral part of the enteric nervous system, which regulates the functions of the gastrointestinal system. These cells have a unique structural organization that enables their primary function: the contraction and relaxation necessary for the propulsion of gastrointestinal contents.\nSmooth muscle cells in the enteric system possess unique attributes that distinguish them from other smooth muscle cells in the body. One crucial function is peristalsis, where these cells contract in a coordinated manner, generating a wave of contraction and relaxation. This peristaltic movement facilitates the movement of food particles through the digestive tract, playing a vital role in the digestion and absorption processes in animals. Additionally, these cells are responsible for maintaining the tone of gastrointestinal sphincters, controlling passage and preventing one-sided movement of the contents.\nEnteric smooth muscle cells are also involved in local immune responses of the gastrointestinal tract. They can communicate with local immune cells and secrete cytokines or other signaling molecules in response to infectious organisms, which makes them crucial mediocellular players in gastrointestinal homeostasis and response to disease. Their interactions with other cell types, such as neurons, myofibroblasts, and interstitial cells of Cajal, further contribute to these cells' role in maintaining the physiological functions of the gastrointestinal system. Overall, enteric smooth muscle cells provide an indispensable contribution to the complex operations of the digestive tract." xsd:string {xref="DOI:10.1038/nrgastro.2012.168", xref="DOI:10.1111/j.1365-2982.2012.01986.x", xref="DOI:10.1371/journal.pcbi.1009644"} creation_date: 2011-01-17T03:39:38Z [Term] id: CL:0002505 name: liver CD103-negative dendritic cell def: "A CD11b-positive dendritic cell that is CD11b-high, CD45-positive, MHC-II-positive and CD103-negative." [GOC:tfm, http://www.immgen.org/index_content.html] +subset: human_subset +subset: mouse_subset synonym: "DC.103-11b+.Lv" EXACT [] -is_a: CL:0002454 {is_inferred="true"} ! Cd4-negative, CD8_alpha-negative, CD11b-positive dendritic cell -intersection_of: CL:0002454 ! Cd4-negative, CD8_alpha-negative, CD11b-positive dendritic cell +is_a: CL:0002454 {is_inferred="true"} ! CD4-negative, CD8-alpha-negative, CD11b-positive dendritic cell +intersection_of: CL:0002454 ! CD4-negative, CD8-alpha-negative, CD11b-positive dendritic cell intersection_of: CL:4030046 PR:000001010 ! lacks_plasma_membrane_part integrin alpha-E intersection_of: RO:0001025 UBERON:0001281 ! located in hepatic sinusoid intersection_of: RO:0002104 GO:0042613 ! has plasma membrane part MHC class II protein complex @@ -21661,10 +24322,12 @@ creation_date: 2011-01-21T01:27:41Z id: CL:0002506 name: liver CD103-positive dendritic cell def: "A CD11b-positive dendritic cell that is CD11b-low, CD45-positive, MHC-II-high and CD103-positive that is located in the liver." [GOC:tfm, http://www.immgen.org/index_content.html] +subset: human_subset +subset: mouse_subset synonym: "DC.103+11b-.Lv" EXACT [] -is_a: CL:0002454 {is_inferred="true"} ! Cd4-negative, CD8_alpha-negative, CD11b-positive dendritic cell +is_a: CL:0002454 {is_inferred="true"} ! CD4-negative, CD8-alpha-negative, CD11b-positive dendritic cell is_a: CL:0002461 ! CD103-positive dendritic cell -intersection_of: CL:0002454 ! Cd4-negative, CD8_alpha-negative, CD11b-positive dendritic cell +intersection_of: CL:0002454 ! CD4-negative, CD8-alpha-negative, CD11b-positive dendritic cell intersection_of: RO:0001025 UBERON:0001281 ! located in hepatic sinusoid intersection_of: RO:0002104 GO:0042613 ! has plasma membrane part MHC class II protein complex intersection_of: RO:0002104 PR:000001006 ! has plasma membrane part receptor-type tyrosine-protein phosphatase C @@ -21681,6 +24344,8 @@ creation_date: 2011-01-21T01:27:45Z id: CL:0002507 name: langerin-positive lymph node dendritic cell def: "A dermal dendritic cell isolated from skin draining lymph nodes that is langerin-positive, MHC-II-positive, and CD4-negative and CD8a-negative." [GOC:tfm, http://www.immgen.org/index_content.html] +subset: human_subset +subset: mouse_subset is_a: CL:0000990 {is_inferred="true"} ! conventional dendritic cell intersection_of: CL:0000990 ! conventional dendritic cell intersection_of: CL:4030046 PR:000001004 ! lacks_plasma_membrane_part CD4 molecule @@ -21698,6 +24363,8 @@ creation_date: 2011-01-21T01:57:00Z id: CL:0002508 name: langerin-negative, CD103-negative lymph node dendritic cell def: "A dermal dendritic cell isolated from skin draining lymph nodes that is langerin-negative, MHC-II-positive, and CD4-negative and CD8a-negative." [GOC:tfm, http://www.immgen.org/index_content.html] +subset: human_subset +subset: mouse_subset is_a: CL:0000990 {is_inferred="true"} ! conventional dendritic cell intersection_of: CL:0000990 ! conventional dendritic cell intersection_of: CL:4030046 PR:000001004 ! lacks_plasma_membrane_part CD4 molecule @@ -21717,7 +24384,9 @@ creation_date: 2011-01-21T02:13:58Z id: CL:0002509 name: CD103-positive, langerin-positive lymph node dendritic cell def: "A langerin-positive lymph node dendritic cell that is CD103-positive and CD11b-low." [GOC:tfm, http://www.immgen.org/index_content.html] -is_a: CL:0002454 ! Cd4-negative, CD8_alpha-negative, CD11b-positive dendritic cell +subset: human_subset +subset: mouse_subset +is_a: CL:0002454 ! CD4-negative, CD8-alpha-negative, CD11b-positive dendritic cell is_a: CL:0002461 ! CD103-positive dendritic cell is_a: CL:0002507 {is_inferred="true"} ! langerin-positive lymph node dendritic cell intersection_of: CL:0002507 ! langerin-positive lymph node dendritic cell @@ -21731,7 +24400,9 @@ creation_date: 2011-01-21T02:07:54Z id: CL:0002510 name: CD103-negative, langerin-positive lymph node dendritic cell def: "A langerin-positive lymph node dendritic cell that is CD103-negative and CD11b-high." [GOC:tfm, http://www.immgen.org/index_content.html] -is_a: CL:0002454 ! Cd4-negative, CD8_alpha-negative, CD11b-positive dendritic cell +subset: human_subset +subset: mouse_subset +is_a: CL:0002454 ! CD4-negative, CD8-alpha-negative, CD11b-positive dendritic cell is_a: CL:0002507 {is_inferred="true"} ! langerin-positive lymph node dendritic cell intersection_of: CL:0002507 ! langerin-positive lymph node dendritic cell intersection_of: CL:4030046 PR:000001010 ! lacks_plasma_membrane_part integrin alpha-E @@ -21745,7 +24416,9 @@ creation_date: 2011-01-21T02:11:14Z id: CL:0002511 name: CD11b-low, CD103-negative, langerin-negative lymph node dendritic cell def: "A langerin-negative lymph node dendritic cell that is CD103-negative and CD11b-low." [GOC:tfm, http://www.immgen.org/index_content.html] -is_a: CL:0002454 ! Cd4-negative, CD8_alpha-negative, CD11b-positive dendritic cell +subset: human_subset +subset: mouse_subset +is_a: CL:0002454 ! CD4-negative, CD8-alpha-negative, CD11b-positive dendritic cell is_a: CL:0002508 {is_inferred="true"} ! langerin-negative, CD103-negative lymph node dendritic cell intersection_of: CL:0002508 ! langerin-negative, CD103-negative lymph node dendritic cell intersection_of: RO:0015016 PR:000001012 ! has low plasma membrane amount integrin alpha-M @@ -21757,7 +24430,9 @@ creation_date: 2011-01-21T02:22:15Z id: CL:0002512 name: CD11b-high, CD103-negative, langerin-negative lymph node dendritic cell def: "A langerin-negative lymph node dendritic cell that is CD103-negative and CD11b-high." [GOC:tfm, http://www.immgen.org/index_content.html] -is_a: CL:0002454 ! Cd4-negative, CD8_alpha-negative, CD11b-positive dendritic cell +subset: human_subset +subset: mouse_subset +is_a: CL:0002454 ! CD4-negative, CD8-alpha-negative, CD11b-positive dendritic cell is_a: CL:0002508 {is_inferred="true"} ! langerin-negative, CD103-negative lymph node dendritic cell intersection_of: CL:0002508 ! langerin-negative, CD103-negative lymph node dendritic cell intersection_of: RO:0015015 PR:000001012 ! has high plasma membrane amount integrin alpha-M @@ -21767,8 +24442,10 @@ creation_date: 2011-01-21T02:16:21Z [Term] id: CL:0002513 -name: Vgamma5-positive CD8alpha alpha positive gamma-delta intraepithelial T cell -def: "A CD8alpha alpha positive gamma-delta intraepithelial T cell that expresses a TCR encoded in part by the Vgamma5 gene segment." [GOC:tfm, http://www.immgen.org/index_content.html] +name: Vgamma5-positive CD8-alpha alpha positive gamma-delta intraepithelial T cell +def: "A CD8-alpha alpha positive gamma-delta intraepithelial T cell that expresses a TCR encoded in part by the Vgamma5 gene segment." [GOC:tfm, http://www.immgen.org/index_content.html] +subset: human_subset +subset: mouse_subset synonym: "tgd.vg5+.IEL" EXACT [] is_a: CL:0000802 ! CD8-alpha alpha positive, gamma-delta intraepithelial T cell property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 @@ -21776,8 +24453,10 @@ creation_date: 2011-01-24T10:22:18Z [Term] id: CL:0002514 -name: Vgamma5-negative CD8alpha alpha positive gamma-delta intraepithelial T cell -def: "A CD8alpha alpha positive gamma-delta intraepithelial T cell that does not express a TCR partially encoded by the Vgamma5 gene segment." [GOC:tfm, http://www.immgen.org/index_content.html] +name: Vgamma5-negative CD8-alpha alpha positive gamma-delta intraepithelial T cell +def: "A CD8-alpha alpha positive gamma-delta intraepithelial T cell that does not express a TCR partially encoded by the Vgamma5 gene segment." [GOC:tfm, http://www.immgen.org/index_content.html] +subset: human_subset +subset: mouse_subset synonym: "tgd.vg5-.IEL" EXACT [] is_a: CL:0000802 ! CD8-alpha alpha positive, gamma-delta intraepithelial T cell property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 @@ -21787,6 +24466,8 @@ creation_date: 2011-01-24T10:25:44Z id: CL:0002515 name: interrenal norepinephrine type cell def: "An interrenal chromaffin cell found in teleosts that contain heterogeneous vesicles with electron-dense granules located asymmetrically within the vesicular membrane." [GOC:MH, GOC:tfm, PMID:12668625] +subset: human_subset +subset: mouse_subset synonym: "interrenal noradrenaline type cell" EXACT [] synonym: "type n interrenal cell" EXACT [] is_a: CL:0000459 ! noradrenergic cell @@ -21798,6 +24479,8 @@ creation_date: 2011-02-08T10:11:55Z id: CL:0002516 name: interrenal chromaffin cell def: "A chromaffin cell interspersed among the interrenal epithelial layer of the anterior kidney of teloest fish." [GOC:MH, GOC:tfm, PMID:12668625] +subset: human_subset +subset: mouse_subset is_a: CL:0000166 ! chromaffin cell property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-02-08T10:21:35Z @@ -21806,6 +24489,8 @@ creation_date: 2011-02-08T10:21:35Z id: CL:0002517 name: interrenal epinephrin secreting cell def: "An interrenal chromaffin cell found in teleosts that contain small, homogeneous electron-lucent granules that are separated from the vesicular membrane by a visible halo." [GOC:MH, GOC:tfm, PMID:12668625] +subset: human_subset +subset: mouse_subset synonym: "interrenal adrenaline secreting cell" RELATED [] synonym: "type a interrenal cell" EXACT [] is_a: CL:0000454 ! epinephrine secreting cell @@ -21818,6 +24503,8 @@ id: CL:0002518 name: kidney epithelial cell def: "An epithelial cell of the kidney." [GOC:tfm, KUPO:SJ] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset xref: KUPO:0001019 xref: ZFA:0009374 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000066 ! epithelial cell @@ -21831,6 +24518,8 @@ creation_date: 2011-02-08T10:46:34Z id: CL:0002519 name: interrenal epithelial cell def: "An interrenal epithelial kidney cell is an epithelial cell found in the anterior kidney of teleosts fish. This cell type is arranged in layers around the posterior cardinal vein and contains many mitochondria with tubulovesicular cristae. Interrenal chromaffin cells are interspersed among the tissue layer created by this cell type." [GOC:mh, GOC:tfm, PMID:12668625] +subset: human_subset +subset: mouse_subset is_a: CL:0002518 ! kidney epithelial cell property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-02-08T11:03:32Z @@ -21851,6 +24540,8 @@ name: subcutaneous adipocyte def: "An adipocyte that is part of subcutaneous adipose tissue." [GOC:tfm] subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "subcutaneous fat cell" EXACT [] is_a: CL:0000136 {is_inferred="true"} ! adipocyte intersection_of: CL:0000136 ! adipocyte @@ -21864,6 +24555,8 @@ creation_date: 2011-02-21T02:51:22Z id: CL:0002522 name: renal filtration cell def: "A renal filtration cell is a specialized cell of the renal system that filter fluids by charge, size or both." [GOC:tfm] +subset: human_subset +subset: mouse_subset is_a: CL:0000255 ! eukaryotic cell is_a: CL:0000424 ! excretory cell relationship: part_of UBERON:0001008 ! renal system @@ -21874,6 +24567,8 @@ creation_date: 2011-02-08T01:37:59Z id: CL:0002523 name: mesonephric podocyte def: "A specialized epithelial cell that contains \"feet\" that interdigitate with the \"feet\" of other glomerular epithelial cells in the mesonephros." [GOC:tfm] +subset: human_subset +subset: mouse_subset synonym: "mesonephric glomerular visceral epithelial cell" EXACT [ZFA:0001674] is_a: CL:0000653 ! podocyte intersection_of: CL:0000653 ! podocyte @@ -21895,6 +24590,8 @@ creation_date: 2011-02-08T02:07:33Z id: CL:0002525 name: metanephric podocyte def: "A specialized epithelial cell that contains \"feet\" that interdigitate with the \"feet\" of other glomerular epithelial cells in the metanephros." [GOC:tfm] +subset: human_subset +subset: mouse_subset synonym: "metanephric glomerular visceral epithelial cell" EXACT [10.1007/s004180050142] is_a: CL:0000653 ! podocyte intersection_of: CL:0000653 ! podocyte @@ -21908,6 +24605,8 @@ id: CL:0002526 name: CD14-positive dermal dendritic cell def: "A dermal dendritic cell that is CD1a-negative and CD14-positive." [GOC:dsd, PMID:19236899, PMID:20309010] comment: They are also CD11c-positive, CD40-positive, CD85j-positive (ILT-2), CD163-positive, CD205-positive (DEC205), CD207-negative (langerin), CD209-positive (DC-SIGN), CD274-positive (PD-L1), CD324-negative (E-cadherin), Factor XIIIa-positive, LOX-I-positive, CLEC6-positive, Dectin-1-positive, and DCIR-positive. Upon stimulation, these cells are capable of producing IL1-beta, IL6, IL8, IL10, IL12p40, IL19, IL20, IL24, TGF-beta, TNF-alpha, GM-CSF, and MCP1. They reside in the dermis. +subset: human_subset +subset: mouse_subset synonym: "CD14+ dermal DC" EXACT [] is_a: CL:0001006 {is_inferred="true"} ! dermal dendritic cell intersection_of: CL:0001006 ! dermal dendritic cell @@ -21922,6 +24621,8 @@ relationship: RO:0002104 PR:000001889 ! has plasma membrane part CD14 molecule id: CL:0002527 name: immature CD14-positive dermal dendritic cell def: "An immature CD14-positive dermal dendritic cell is CD80-low, CD86-low, and MHCII-low." [GOC:dsd] +subset: human_subset +subset: mouse_subset is_a: CL:0001009 ! immature dermal dendritic cell is_a: CL:0002526 {is_inferred="true"} ! CD14-positive dermal dendritic cell intersection_of: CL:0002526 ! CD14-positive dermal dendritic cell @@ -21933,6 +24634,8 @@ intersection_of: RO:0015016 PR:000001438 ! has low plasma membrane amount CD80 m id: CL:0002528 name: mature CD14-positive dermal dendritic cell def: "A mature CD14-positive dermal dendritic cell is CD80-high, CD86-high, MHCII-high and is CD83-positive." [GOC:dsd] +subset: human_subset +subset: mouse_subset is_a: CL:0001010 ! mature dermal dendritic cell is_a: CL:0002526 {is_inferred="true"} ! CD14-positive dermal dendritic cell intersection_of: CL:0002526 ! CD14-positive dermal dendritic cell @@ -21947,6 +24650,8 @@ id: CL:0002529 name: CD1a-positive dermal dendritic cell def: "A dermal dendritic cell that is CD1a-positive and CD14-negative." [GOC:dsd, PMID:20309010] comment: Reside in the dermis. They are also CD11c-positive, CD40-positive, CD207-negative (langerin), CD209-negative (DC-SIGN), and CD324-negative (E-cadherin). When activated, they are capable of producing CXCL8 (IL-8) and IL-15. Possibly a precursor of Langerhans cells or equivalent of langerin-positive dermal DCs in the mouse. +subset: human_subset +subset: mouse_subset synonym: "CD1a+ dermal DC" EXACT [] is_a: CL:0001006 {is_inferred="true"} ! dermal dendritic cell intersection_of: CL:0001006 ! dermal dendritic cell @@ -21957,6 +24662,8 @@ relationship: RO:0002104 PR:000002025 ! has plasma membrane part T-cell surface id: CL:0002530 name: immature CD1a-positive dermal dendritic cell def: "An immature CD1a-positive dermal dendritic cell is CD80-low, CD86-low, and MHCII-low." [GOC:dsd] +subset: human_subset +subset: mouse_subset is_a: CL:0001009 ! immature dermal dendritic cell is_a: CL:0002529 {is_inferred="true"} ! CD1a-positive dermal dendritic cell intersection_of: CL:0002529 ! CD1a-positive dermal dendritic cell @@ -21968,6 +24675,8 @@ intersection_of: RO:0015016 PR:000001438 ! has low plasma membrane amount CD80 m id: CL:0002531 name: mature CD1a-positive dermal dendritic cell def: "A mature CD1a-positive dermal dendritic cell is CD80-high, CD83-positive, CD86-high, and MHCII-high." [GOC:dsd] +subset: human_subset +subset: mouse_subset is_a: CL:0001010 ! mature dermal dendritic cell is_a: CL:0002529 {is_inferred="true"} ! CD1a-positive dermal dendritic cell intersection_of: CL:0002529 ! CD1a-positive dermal dendritic cell @@ -21982,6 +24691,8 @@ id: CL:0002532 name: CD16-positive myeloid dendritic cell def: "A myeloid dendritic cell found in the blood that is CD16-positive." [GOC:dsd, PMID:17332250] comment: Normally represent 65-75% of peripheral blood mDCs (human). They are also CD281-positive (TLR1), CD282-positive (TLR2), CD284-positive (TLR4), CD285-positive (TLR5), CD286-positive (TLR6), CD288-positive (TLR8), CD289-positive (TLR9), and CD290-positive (TLR10) by RT-PCR [PMID:17332250]. Upon TLR stimulation, these cells are potent producers of TNF-alpha, while producing little CXCL8 (IL8). +subset: human_subset +subset: mouse_subset synonym: "CD16+ mDC" EXACT [] synonym: "CD16-mDC" EXACT [] is_a: CL:0000782 {is_inferred="true"} ! myeloid dendritic cell @@ -21995,6 +24706,8 @@ relationship: RO:0002104 PR:000001483 ! has plasma membrane part low affinity im id: CL:0002533 name: immature CD16-positive myeloid dendritic cell def: "An immature CD16-positive myeloid dendritic cell is CD80-low, CD86-low, and MHCII-low." [GOC:dsd] +subset: human_subset +subset: mouse_subset is_a: CL:0000840 ! immature conventional dendritic cell is_a: CL:0002532 {is_inferred="true"} ! CD16-positive myeloid dendritic cell intersection_of: CL:0002532 ! CD16-positive myeloid dendritic cell @@ -22006,6 +24719,8 @@ intersection_of: RO:0015016 PR:000001438 ! has low plasma membrane amount CD80 m id: CL:0002534 name: mature CD16-positive myeloid dendritic cell def: "A mature CD16-positive myeloid dendritic cell is CD80-high, CD83-positive, CD86-high, and MHCII-high." [GOC:dsd] +subset: human_subset +subset: mouse_subset is_a: CL:0000841 ! mature conventional dendritic cell is_a: CL:0002532 {is_inferred="true"} ! CD16-positive myeloid dendritic cell intersection_of: CL:0002532 ! CD16-positive myeloid dendritic cell @@ -22019,6 +24734,8 @@ relationship: RO:0002202 CL:0002533 ! develops from immature CD16-positive myelo id: CL:0002535 name: epithelial cell of cervix def: "An epithelial cell of the cervix." [GOC:tfm] +subset: human_subset +subset: mouse_subset synonym: "cervical canal epithelial cell" EXACT [GOC:tfm] synonym: "cervical canal of uterus epithelial cell" EXACT [GOC:tfm] synonym: "cervix epithelial cell" EXACT [GOC:tfm] @@ -22041,7 +24758,10 @@ creation_date: 2011-02-24T08:20:08Z id: CL:0002536 name: epithelial cell of amnion def: "An epithelial cell that is part of the amnion." [GOC:tfm] +subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "amniotic epithelial cell" EXACT [] is_a: CL:0000066 ! epithelial cell intersection_of: CL:0000066 ! epithelial cell @@ -22055,6 +24775,8 @@ creation_date: 2011-02-28T12:38:01Z id: CL:0002537 name: amnion mesenchymal stem cell def: "A mesenchymal stem cell of the amnion membrane." [GOC:tfm, PMID:20446274, PMID:21339039] +subset: human_subset +subset: mouse_subset synonym: "amniotic membrane stem cell" EXACT [] is_a: CL:0000134 ! mesenchymal stem cell intersection_of: CL:0000134 ! mesenchymal stem cell @@ -22068,6 +24790,8 @@ id: CL:0002538 name: intrahepatic cholangiocyte def: "An epithelial cell of the intrahepatic portion of the bile duct. These cells are flattened or cuboidal in shape, and have a small nuclear-to-cytoplasmic ratio relative to large/extrahepatic cholangiocytes." [GOC:tfm, PMID:23720296] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "small bile duct cholangiocyte" EXACT [PMID:23720296] xref: https://cellxgene.cziscience.com/cellguide/CL_0002538 xref: ZFA:0009379 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} @@ -22076,7 +24800,7 @@ intersection_of: CL:1000488 ! cholangiocyte intersection_of: part_of UBERON:0004823 ! intrahepatic bile duct epithelium relationship: part_of UBERON:0004823 ! intrahepatic bile duct epithelium property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 -property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional.\n\nIntrahepatic cholangiocytes represent a subset of the biliary epithelial cells that form a network of tubes in the liver called the biliary tree The intrahepatic cholangiocytes reside specifically in the intrahepatic bile ducts and play a crucial role in liver physiology and bile production and secretion, thereby aiding in the digestion and absorption of fats in the small intestine. These specific cholangiocytes arise from bipotent hepatoblasts, whereas extrahepatic cholangiocytes share an embryologic origin with the ventral pancreas.\nRecent research suggests that there is also heterogeneity within populations of intrahepatic cholangiocytes with different transcriptional profiles, proliferative capacity, and biological function; for example, subpopulations differ in calcium-mobilizing receptors.\nThe primary function of intrahepatic cholangiocytes is related to bile formation and maintenance of its flow. In addition to their secretory and absorptive activities, they are involved in the regulation of bile composition, volume, and alkalinization, contributing to the neutralization of the acidic chyme (partly digested food) that enters the intestine from the stomach. Intrahepatic cholangiocytes are also recognized for their role in liver regeneration and repair, often proliferating in response to injury. \nIntrahepatic cholangiocytes take part in certain pathological conditions, like primary biliary cirrhosis and cholangiocarcinoma. Changes in these cells often lead to abnormalities in bile formation and transport, causing cholestatic liver diseases. Overall, the primary and secondary functional activities of intrahepatic cholangiocytes are vital in maintaining liver function, digestive processes, and contributing to the body's response to liver injury." xsd:string {xref="DOI:10.1002/hep.31252", xref="DOI:10.1016/j.ajpath.2023.02.012", xref="DOI:10.1016/j.biocel.2010.06.020", xref="DOI:10.1016/j.gastha.2022.07.015"} +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nIntrahepatic cholangiocytes represent a subset of the biliary epithelial cells that form a network of tubes in the liver called the biliary tree The intrahepatic cholangiocytes reside specifically in the intrahepatic bile ducts and play a crucial role in liver physiology and bile production and secretion, thereby aiding in the digestion and absorption of fats in the small intestine. These specific cholangiocytes arise from bipotent hepatoblasts, whereas extrahepatic cholangiocytes share an embryologic origin with the ventral pancreas.\nRecent research suggests that there is also heterogeneity within populations of intrahepatic cholangiocytes with different transcriptional profiles, proliferative capacity, and biological function; for example, subpopulations differ in calcium-mobilizing receptors.\nThe primary function of intrahepatic cholangiocytes is related to bile formation and maintenance of its flow. In addition to their secretory and absorptive activities, they are involved in the regulation of bile composition, volume, and alkalinization, contributing to the neutralization of the acidic chyme (partly digested food) that enters the intestine from the stomach. Intrahepatic cholangiocytes are also recognized for their role in liver regeneration and repair, often proliferating in response to injury. \nIntrahepatic cholangiocytes take part in certain pathological conditions, like primary biliary cirrhosis and cholangiocarcinoma. Changes in these cells often lead to abnormalities in bile formation and transport, causing cholestatic liver diseases. Overall, the primary and secondary functional activities of intrahepatic cholangiocytes are vital in maintaining liver function, digestive processes, and contributing to the body's response to liver injury." xsd:string {xref="DOI:10.1002/hep.31252", xref="DOI:10.1016/j.ajpath.2023.02.012", xref="DOI:10.1016/j.biocel.2010.06.020", xref="DOI:10.1016/j.gastha.2022.07.015"} creation_date: 2011-02-28T01:20:20Z [Term] @@ -22084,18 +24808,24 @@ id: CL:0002539 name: aortic smooth muscle cell def: "A smooth muscle cell of the aorta." [GOC:tfm] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset xref: BTO:0004577 +xref: https://cellxgene.cziscience.com/cellguide/CL_0002539 is_a: CL:0019018 ! blood vessel smooth muscle cell intersection_of: CL:0000359 ! vascular associated smooth muscle cell intersection_of: part_of UBERON:0004178 ! aorta smooth muscle tissue relationship: part_of UBERON:0004178 ! aorta smooth muscle tissue property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nAortic smooth muscle cells are specialized and highly differentiated muscle cells that are located in the tunica media layer of the aorta. They consist of spindle-shaped cells with a centrally located nucleus. These cells are rich in actin and myosin, muscle contractile proteins, that allow them to exert force and change shape. \nAortic smooth muscle cells play a vital role in maintaining blood pressure and circulation, and are essential for vascular integrity and function. The primary function of these cells is contraction and relaxation, which enables the regulation of blood flow and pressure in the aorta, and helps in the distribution of oxygen and nutrients throughout the body.\nAdditionally, a critical characteristic of smooth muscle cells is their plasticity. They can undergo phenotypic modulation in response to changes in their environment or vascular injury, switching from a contractile to a synthetic phenotype. The contractile phenotype is characterized by high contractility and low proliferation rate, while the synthetic phenotype is marked by increased cell proliferation and matrix synthesis but reduced contractile function.\nAortic smooth muscle cells have a significant role in the physiological and pathological processes of the cardiovascular system. In the normal physiological state, they contribute to the elasticity and flexibility of the aorta. Conversely, in pathological states, changes in the function and structure of aortic smooth muscle cells are connected with various vascular diseases, including atherosclerosis, hypertension, and aneurysm." xsd:string {xref="DOI:10.1016/j.devcel.2005.05.017", xref="DOI:10.1111/febs.12414", xref="DOI:10.7150/ijbs.49871", xref="https://training.seer.cancer.gov/anatomy/cells_tissues_membranes/tissues/muscle.html", xref="https://www.sciencedirect.com/topics/medicine-and-dentistry/aortic-smooth-muscle-cell"} creation_date: 2011-02-28T01:42:12Z [Term] id: CL:0002540 name: mesenchymal stem cell of the bone marrow def: "A mesenchymal stem cell that is part of the bone marrow." [GOC:tfm] +subset: human_subset +subset: mouse_subset is_a: CL:0000134 ! mesenchymal stem cell is_a: CL:0002092 ! bone marrow cell intersection_of: CL:0000134 ! mesenchymal stem cell @@ -22107,6 +24837,8 @@ creation_date: 2011-02-28T01:47:47Z id: CL:0002541 name: chorionic membrane mesenchymal stem cell def: "A mesenchymal stem cell of the chorionic membrane." [GOC:tfm] +subset: human_subset +subset: mouse_subset is_a: CL:0000134 ! mesenchymal stem cell intersection_of: CL:0000134 ! mesenchymal stem cell intersection_of: part_of UBERON:0003124 ! chorion membrane @@ -22121,6 +24853,8 @@ alt_id: CL:1000393 def: "An endothelial cell that is part of the vein." [GOC:tfm] subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "endothelial cell of vein" EXACT [] synonym: "venous endothelial cell" EXACT [] xref: FMA:62104 @@ -22132,7 +24866,7 @@ intersection_of: part_of UBERON:0001638 ! vein relationship: part_of UBERON:0001638 ! vein property_value: RO:0002175 NCBITaxon:9606 property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 -property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional.\n\nVein endothelial cells form a thin layer of squamous cells, the endothelium, lining the interior surface of veins throughout the body. They shape the inner cellular lining of the entire vascular system, including the heart, playing a crucial role in blood circulation. The unique characteristic compact arrangement of these cells enables veins to act as a barrier between the blood (that can contain foreign substances) and the surrounding venous tissue and maintain the integrity of the vascular system.\nThe primary function of vein endothelial cells is to control the exchange of substances between the bloodstream and the surrounding tissues. They facilitate selective transportation of molecules depending on their size and solubility, including gases, nutrients, hormones, and waste products. Vein endothelial cells also play a protective role by inhibiting the translocation of toxins or pathogens from blood to tissues. Additionally, these cells are involved in blood coagulation and inflammation response, primarily by producing substances that inhibit blood clot formation under normal conditions and initiating clotting when necessary.\nAnother significant function of vein endothelial cells is the regulation of blood flow and blood pressure. They produce and release several substances, including nitric oxide and prostacyclin, which help in controlling vasodilation and vasoconstriction, thereby regulating blood pressure. These cells are also responsible for angiogenesis, the formation of new blood vessels, which is crucial during wound healing and in the formation of granulation tissue. Consequently, any dysfunction in vein endothelial cells can lead to severe health problems like atherosclerosis, hypertension, and thrombosis." xsd:string {xref="DOI:10.1007/s00441-008-0706-5", xref="DOI:10.1038/s41569-022-00770-1", xref="DOI:10.1038/s41598-021-01360-w", xref="DOI:10.3390/ijms20184411"} +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nVein endothelial cells form a thin layer of squamous cells, the endothelium, lining the interior surface of veins throughout the body. They shape the inner cellular lining of the entire vascular system, including the heart, playing a crucial role in blood circulation. The unique characteristic compact arrangement of these cells enables veins to act as a barrier between the blood (that can contain foreign substances) and the surrounding venous tissue and maintain the integrity of the vascular system.\nThe primary function of vein endothelial cells is to control the exchange of substances between the bloodstream and the surrounding tissues. They facilitate selective transportation of molecules depending on their size and solubility, including gases, nutrients, hormones, and waste products. Vein endothelial cells also play a protective role by inhibiting the translocation of toxins or pathogens from blood to tissues. Additionally, these cells are involved in blood coagulation and inflammation response, primarily by producing substances that inhibit blood clot formation under normal conditions and initiating clotting when necessary.\nAnother significant function of vein endothelial cells is the regulation of blood flow and blood pressure. They produce and release several substances, including nitric oxide and prostacyclin, which help in controlling vasodilation and vasoconstriction, thereby regulating blood pressure. These cells are also responsible for angiogenesis, the formation of new blood vessels, which is crucial during wound healing and in the formation of granulation tissue. Consequently, any dysfunction in vein endothelial cells can lead to severe health problems like atherosclerosis, hypertension, and thrombosis." xsd:string {xref="DOI:10.1007/s00441-008-0706-5", xref="DOI:10.1038/s41569-022-00770-1", xref="DOI:10.1038/s41598-021-01360-w", xref="DOI:10.3390/ijms20184411"} creation_date: 2011-02-28T03:48:11Z [Term] @@ -22140,6 +24874,8 @@ id: CL:0002544 name: aortic endothelial cell def: "An arterial endothelial cell that is part of the aorta endothelium." [GOC:tfm] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset xref: BTO:0003245 xref: CALOHA:TS-0047 is_a: CL:1000413 ! endothelial cell of artery @@ -22150,6 +24886,8 @@ creation_date: 2011-02-28T03:54:42Z id: CL:0002545 name: thoracic aorta endothelial cell def: "An endothelial cell that is part of the thoracic endothelium." [GOC:tfm] +subset: human_subset +subset: mouse_subset is_a: CL:0002544 {is_inferred="true"} ! aortic endothelial cell intersection_of: CL:0002544 ! aortic endothelial cell intersection_of: part_of UBERON:0001515 ! thoracic aorta @@ -22162,6 +24900,9 @@ id: CL:0002546 name: embryonic blood vessel endothelial progenitor cell def: "An endothelial progenitor cell that participates in angiogenesis during development." [GOC:tfm] comment: See CL:0002619. +subset: cellxgene_subset +subset: human_subset +subset: mouse_subset xref: ZFA:0005773 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000222 ! mesodermal cell property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 @@ -22171,6 +24912,8 @@ creation_date: 2011-02-28T04:20:39Z id: CL:0002547 name: fibroblast of the aortic adventitia def: "A fibroblast of the aortic adventitia." [GOC:tfm] +subset: human_subset +subset: mouse_subset is_a: CL:1000306 {is_inferred="true"} ! fibroblast of tunica adventitia of artery intersection_of: CL:1000306 ! fibroblast of tunica adventitia of artery intersection_of: part_of UBERON:0004664 ! aorta tunica adventitia @@ -22183,6 +24926,8 @@ id: CL:0002548 name: fibroblast of cardiac tissue def: "A fibroblast that is part of the heart." [GOC:tfm] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "cardiac fibroblast" EXACT [] is_a: CL:0000057 {is_inferred="true"} ! fibroblast is_a: CL:0002494 {is_inferred="true"} ! cardiocyte @@ -22196,6 +24941,8 @@ creation_date: 2011-02-28T04:57:44Z id: CL:0002549 name: fibroblast of choroid plexus def: "A fibroblast that is part of the choroid plexus." [GOC:tfm] +subset: human_subset +subset: mouse_subset is_a: CL:0000057 {is_inferred="true"} ! fibroblast is_a: CL:0002319 ! neural cell intersection_of: CL:0000057 ! fibroblast @@ -22208,6 +24955,8 @@ creation_date: 2011-02-28T05:01:39Z id: CL:0002550 name: fibroblast of the conjunctiva def: "A fibroblast that is part of the conjuctiva of the eye." [GOC:tfm] +subset: human_subset +subset: mouse_subset is_a: CL:0000057 ! fibroblast intersection_of: CL:0000057 ! fibroblast intersection_of: part_of UBERON:0001811 ! conjunctiva @@ -22219,6 +24968,8 @@ creation_date: 2011-02-28T05:03:44Z id: CL:0002551 name: fibroblast of dermis def: "Any skin fibroblast that is part of some dermis." [FBC:Autogenerated] +subset: human_subset +subset: mouse_subset is_a: CL:0002620 {is_inferred="true"} ! skin fibroblast intersection_of: CL:0002620 ! skin fibroblast intersection_of: part_of UBERON:0002067 ! dermis @@ -22230,6 +24981,8 @@ creation_date: 2011-02-28T05:05:33Z id: CL:0002552 name: fibroblast of gingiva def: "Any fibroblast that is part of some gingiva." [FBC:Autogenerated] +subset: human_subset +subset: mouse_subset is_a: CL:0000057 {is_inferred="true"} ! fibroblast intersection_of: CL:0000057 ! fibroblast intersection_of: part_of UBERON:0001828 ! gingiva @@ -22242,6 +24995,8 @@ id: CL:0002553 name: fibroblast of lung def: "A fibroblast that is part of lung." [GOC:tfm] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset xref: BTO:0000764 xref: CALOHA:TS-0575 is_a: CL:0000057 {is_inferred="true"} ! fibroblast @@ -22255,6 +25010,9 @@ creation_date: 2011-02-28T05:11:03Z id: CL:0002554 name: fibroblast of lymphatic vessel def: "A fibroblast of the lymphatic system." [GOC:tfm] +subset: cellxgene_subset +subset: human_subset +subset: mouse_subset is_a: CL:0000057 {is_inferred="true"} ! fibroblast intersection_of: CL:0000057 ! fibroblast intersection_of: part_of UBERON:0001473 ! lymphatic vessel @@ -22267,6 +25025,8 @@ id: CL:0002555 name: fibroblast of mammary gland def: "A fibroblast that is part of the mammary gland." [GOC:tfm] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset is_a: CL:0000057 {is_inferred="true"} ! fibroblast intersection_of: CL:0000057 ! fibroblast intersection_of: part_of UBERON:0001911 ! mammary gland @@ -22278,6 +25038,8 @@ creation_date: 2011-02-28T05:18:38Z id: CL:0002556 name: fibroblast of periodontium def: "A fibroblast of the periodontium." [GOC:tfm] +subset: human_subset +subset: mouse_subset is_a: CL:0000057 {is_inferred="true"} ! fibroblast intersection_of: CL:0000057 ! fibroblast intersection_of: part_of UBERON:0001758 ! periodontium @@ -22290,6 +25052,8 @@ id: CL:0002557 name: fibroblast of pulmonary artery def: "A fibroblast of pulmonary artery." [GOC:tfm] subset: human_reference_atlas +subset: human_subset +subset: mouse_subset is_a: CL:0000057 {is_inferred="true"} ! fibroblast intersection_of: CL:0000057 ! fibroblast intersection_of: part_of UBERON:0002012 ! pulmonary artery @@ -22303,6 +25067,8 @@ id: CL:0002558 name: fibroblast of villous mesenchyme def: "A fibroblast that is part of villous mesenchyme." [GOC:tfm] subset: human_reference_atlas +subset: human_subset +subset: mouse_subset is_a: CL:0000057 ! fibroblast relationship: part_of UBERON:0001987 ! placenta property_value: RO:0002175 NCBITaxon:9606 @@ -22313,6 +25079,8 @@ creation_date: 2011-02-28T05:24:28Z id: CL:0002559 name: hair follicle cell def: "An animal cell that is part of a hair follicle." [GOC:tfm] +subset: human_subset +subset: mouse_subset is_a: CL:0000255 ! eukaryotic cell intersection_of: CL:0000000 ! cell intersection_of: part_of UBERON:0002073 ! hair follicle @@ -22324,6 +25092,8 @@ creation_date: 2011-03-01T04:11:01Z id: CL:0002560 name: inner root sheath cell def: "An epithelial cell that resides in the inner root sheath of the hair follicle." [GOC:tfm] +subset: human_subset +subset: mouse_subset is_a: CL:0000362 ! epidermal cell is_a: CL:0002559 {is_inferred="true"} ! hair follicle cell intersection_of: CL:0002559 ! hair follicle cell @@ -22336,6 +25106,8 @@ creation_date: 2011-03-01T04:27:51Z id: CL:0002561 name: outer root sheath cell def: "An epithelial cell that is part of the outer root sheath." [GOC:tfm] +subset: human_subset +subset: mouse_subset is_a: CL:0000362 ! epidermal cell is_a: CL:0002559 {is_inferred="true"} ! hair follicle cell intersection_of: CL:0000066 ! epithelial cell @@ -22349,6 +25121,8 @@ id: CL:0002562 name: hair germinal matrix cell def: "An epidermal cell that is part of the germinal matrix." [GOC:tfm] subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "trichocyte" EXACT [] is_a: CL:0000362 {is_inferred="true"} ! epidermal cell is_a: CL:0002559 ! hair follicle cell @@ -22362,12 +25136,14 @@ creation_date: 2011-03-01T04:31:06Z [Term] id: CL:0002563 name: intestinal epithelial cell -def: "An epithelial cell of the intestine." [GOC:tfm] +def: "An epithelial cell of the lining of the intestine." [GOC:tfm] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset xref: ZFA:0009399 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0002251 ! epithelial cell of alimentary canal intersection_of: CL:0000066 ! epithelial cell -intersection_of: part_of UBERON:0000160 ! intestine +intersection_of: part_of UBERON:0001277 ! intestinal epithelium relationship: part_of UBERON:0001277 ! intestinal epithelium property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-03-01T05:18:31Z @@ -22376,6 +25152,8 @@ creation_date: 2011-03-01T05:18:31Z id: CL:0002564 name: nucleus pulposus cell of intervertebral disc def: "A connective tissue cell of the nucleus pulposus cell of intervertebral disc." [GOC:tfm] +subset: human_subset +subset: mouse_subset is_a: CL:0002320 ! connective tissue cell intersection_of: CL:0002320 ! connective tissue cell intersection_of: part_of UBERON:0002242 ! nucleus pulposus @@ -22387,8 +25165,11 @@ creation_date: 2011-03-02T02:12:23Z id: CL:0002565 name: iris pigment epithelial cell def: "A pigment cell located in the epithelium of the iris." [GOC:tfm] +subset: cellxgene_subset subset: eye_upper_slim subset: human_reference_atlas +subset: human_subset +subset: mouse_subset is_a: CL:0000066 ! epithelial cell is_a: CL:0000342 {is_inferred="true"} ! pigment cell (sensu Vertebrata) intersection_of: CL:0000342 ! pigment cell (sensu Vertebrata) @@ -22402,6 +25183,8 @@ creation_date: 2011-03-01T05:28:52Z id: CL:0002566 name: dark melanocyte def: "A melanocyte that appears darker due to content or amount of melanin granules." [GOC:tfm] +subset: human_subset +subset: mouse_subset synonym: "melanotic melanocyte" EXACT [PMID:10985850] synonym: "melanotic melanophore" EXACT [PMID:10985850] is_a: CL:0000148 ! melanocyte @@ -22412,6 +25195,8 @@ creation_date: 2011-03-01T05:57:11Z id: CL:0002567 name: light melanocyte def: "A melanocyte that appears lighter in color." [GOC:tfm] +subset: human_subset +subset: mouse_subset synonym: "amelanotic melanocyte" EXACT [PMID:10985850] synonym: "amelanotic melanophore" EXACT [PMID:10985850] is_a: CL:0000148 ! melanocyte @@ -22423,6 +25208,8 @@ id: CL:0002568 name: mesenchymal stem cell of Wharton's jelly def: "A mesenchymal stem cell that is part of Wharton's jelly." [GOC:tfm] subset: human_reference_atlas +subset: human_subset +subset: mouse_subset is_a: CL:0002569 ! mesenchymal stem cell of umbilical cord property_value: RO:0002175 NCBITaxon:9606 property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 @@ -22432,6 +25219,8 @@ creation_date: 2011-03-01T09:51:18Z id: CL:0002569 name: mesenchymal stem cell of umbilical cord def: "A mesenchymal stem cell of the umbilical cord." [GOC:tfm] +subset: human_subset +subset: mouse_subset is_a: CL:0000134 ! mesenchymal stem cell is_a: CL:0000349 ! extraembryonic cell intersection_of: CL:0000134 ! mesenchymal stem cell @@ -22445,6 +25234,8 @@ id: CL:0002570 name: mesenchymal stem cell of adipose tissue def: "A mesenchymal stem cell of adipose tissue." [GOC:tfm] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "mesenchymal stem cell of adipose" EXACT [] xref: https://cellxgene.cziscience.com/cellguide/CL_0002570 is_a: CL:0000134 ! mesenchymal stem cell @@ -22452,13 +25243,15 @@ intersection_of: CL:0000134 ! mesenchymal stem cell intersection_of: part_of UBERON:0001013 ! adipose tissue relationship: part_of UBERON:0001013 ! adipose tissue property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 -property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional.\n\nMesenchymal stem cells of adipose tissue, also known commonly as adipose-derived stem cells (ADSCs), are a population of adult stem cells that can be obtained easily from adipose tissues. They have many of the same regenerative properties as other mesenchymal stem cells, but are more easily accessible than bone marrow-derived stem cells.\nAdipose-derived stem cells show immense promise in the field of regenerative medicine due to their ability to differentiate into adipocytes, chondrocytes, myocytes, osteoblasts, and other cell types. ADSCs also possess immunomodulatory and homeostatic functions: they have the ability to suppress immune responses and provide a therapeutic environment for tissue repair and regeneration, as well as supporting the proliferation of adipocytes and the overall expansion of adipose tissue and contributing to the tissue's ability to react to demands of energy storage and mobilization. Dysfunction of these cells may contribute to metabolic complications observed in obesity and diabetes. \nADSCs have been used for therapeutic applications such as pathological wound healing, severe refractory acute graft-versus-host disease, and idiopathic thrombocytopenic purpura." xsd:string {xref="DOI:10.1016/j.biopha.2019.108765", xref="DOI:10.1016/j.tibtech.2006.01.010", xref="DOI:10.1038/s41536-019-0083-6", xref="DOI:10.1096/fj.202100332R", xref="DOI:10.1111/dgd.12049"} +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nMesenchymal stem cells of adipose tissue, also known commonly as adipose-derived stem cells (ADSCs), are a population of adult stem cells that can be obtained easily from adipose tissues. They have many of the same regenerative properties as other mesenchymal stem cells, but are more easily accessible than bone marrow-derived stem cells.\nAdipose-derived stem cells show immense promise in the field of regenerative medicine due to their ability to differentiate into adipocytes, chondrocytes, myocytes, osteoblasts, and other cell types. ADSCs also possess immunomodulatory and homeostatic functions: they have the ability to suppress immune responses and provide a therapeutic environment for tissue repair and regeneration, as well as supporting the proliferation of adipocytes and the overall expansion of adipose tissue and contributing to the tissue's ability to react to demands of energy storage and mobilization. Dysfunction of these cells may contribute to metabolic complications observed in obesity and diabetes. \nADSCs have been used for therapeutic applications such as pathological wound healing, severe refractory acute graft-versus-host disease, and idiopathic thrombocytopenic purpura." xsd:string {xref="DOI:10.1016/j.biopha.2019.108765", xref="DOI:10.1016/j.tibtech.2006.01.010", xref="DOI:10.1038/s41536-019-0083-6", xref="DOI:10.1096/fj.202100332R", xref="DOI:10.1111/dgd.12049"} creation_date: 2011-03-01T09:57:17Z [Term] id: CL:0002571 name: hepatic mesenchymal stem cell def: "A mesenchymal stem cell of liver." [GOC:tfm] +subset: human_subset +subset: mouse_subset is_a: CL:0000134 {is_inferred="true"} ! mesenchymal stem cell is_a: CL:0002195 ! hepatic stem cell intersection_of: CL:0000134 ! mesenchymal stem cell @@ -22470,6 +25263,8 @@ creation_date: 2011-03-01T09:58:51Z id: CL:0002572 name: vertebral mesenchymal stem cell def: "A mesenchymal stem cell of the vertebrae." [GOC:tfm] +subset: human_subset +subset: mouse_subset is_a: CL:0000134 {is_inferred="true"} ! mesenchymal stem cell is_a: CL:0001035 ! bone cell intersection_of: CL:0000134 ! mesenchymal stem cell @@ -22485,6 +25280,8 @@ def: "A glial cell that myelinates or ensheathes axons in the peripheral nervous comment: A myelinating Schwann cell wraps around a single axon. Myelination occurs in larger diameter axons, while a process called ensheathment occurs on smaller diameter axons in which a single cell wraps around multiple small, unmyelinated axons separating them with a thin layer of cytoplasm. The structure formed is called a Remak bundle. {xref="PMID:16807057"} subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "neurolemmocyte" EXACT [PMID:32119275, PMID:38638689] xref: BTO:0001220 xref: CALOHA:TS-0898 @@ -22494,7 +25291,7 @@ is_a: CL:0000125 ! glial cell relationship: part_of UBERON:0000010 ! peripheral nervous system property_value: RO:0002175 NCBITaxon:9606 property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 -property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional.\n\nSchwann cells, also known as neurolemmocytes, are a type of glial cell located in the peripheral nervous system. These cells play a significant role in the healthy functioning of nerves by producing myelin, a fatty substance that forms a coating around nerve fibers. Myelin serves as an insulator and enhances the speed and efficiency of electrical nerve impulses; a single Schwann cell can myelinate a single axon. Myelination starts by the elongation and envelopment of the Schwann cell around the axon, followed by the synthesis and deposition of myelin layers. Some studies suggest that Schwann cells may regulate neuronal action potential, muscular contraction, and the sensitive response. \nWhile Schwann cells are most commonly known for the formation of the myelin sheath, some Schwann cells do not form myelin: Remak Schwann cells, a class of nonmyelinating Schwann cells, ensheath axons with smaller diameter, such as C fiber nociceptors in sciatic nerves and form Remak bundles.\nSchwann cells are found along both motor and sensory neurons and are crucial for the advancement and recovery of peripheral nerve injuries, due to their capacity to support nerve regeneration. In cases of nerve injury, Schwann cells play a vital role in recovery by initiating Wallerian degeneration, a process in which the part of the axon distal to the injury site degrades and is then cleared away. Following this, Schwann cells can guide the regrowth of the nerve, providing a conducive environment for axon regeneration. They remodel themselves into a regenerative phenotype, proliferate, and organize themselves into bands of Büngner that provide physical and chemical guidance for the regrowths of axons. This function of Schwann cells in the repair and regeneration of nervous system highlights their therapeutic potential in peripheral nerve injury treatments." xsd:string {xref="DOI:10.1002/glia.23892", xref="DOI:10.1016/B978-0-444-52902-2.00005-9", xref="DOI:10.1016/j.biocel.2006.05.007", xref="DOI:10.1186/1742-2094-8-110", xref="DOI:10.1186/s13064-020-00140-y"} +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nSchwann cells, also known as neurolemmocytes, are a type of glial cell located in the peripheral nervous system. These cells play a significant role in the healthy functioning of nerves by producing myelin, a fatty substance that forms a coating around nerve fibers. Myelin serves as an insulator and enhances the speed and efficiency of electrical nerve impulses; a single Schwann cell can myelinate a single axon. Myelination starts by the elongation and envelopment of the Schwann cell around the axon, followed by the synthesis and deposition of myelin layers. Some studies suggest that Schwann cells may regulate neuronal action potential, muscular contraction, and the sensitive response. \nWhile Schwann cells are most commonly known for the formation of the myelin sheath, some Schwann cells do not form myelin: Remak Schwann cells, a class of nonmyelinating Schwann cells, ensheath axons with smaller diameter, such as C fiber nociceptors in sciatic nerves and form Remak bundles.\nSchwann cells are found along both motor and sensory neurons and are crucial for the advancement and recovery of peripheral nerve injuries, due to their capacity to support nerve regeneration. In cases of nerve injury, Schwann cells play a vital role in recovery by initiating Wallerian degeneration, a process in which the part of the axon distal to the injury site degrades and is then cleared away. Following this, Schwann cells can guide the regrowth of the nerve, providing a conducive environment for axon regeneration. They remodel themselves into a regenerative phenotype, proliferate, and organize themselves into bands of Büngner that provide physical and chemical guidance for the regrowths of axons. This function of Schwann cells in the repair and regeneration of nervous system highlights their therapeutic potential in peripheral nerve injury treatments." xsd:string {xref="DOI:10.1002/glia.23892", xref="DOI:10.1016/B978-0-444-52902-2.00005-9", xref="DOI:10.1016/j.biocel.2006.05.007", xref="DOI:10.1186/1742-2094-8-110", xref="DOI:10.1186/s13064-020-00140-y"} creation_date: 2011-03-02T01:19:27Z [Term] @@ -22502,6 +25299,8 @@ id: CL:0002574 name: stromal cell of pancreas def: "A stromal cell of the pancreas." [GOC:tfm] subset: human_reference_atlas +subset: human_subset +subset: mouse_subset is_a: CL:0000499 {is_inferred="true"} ! stromal cell intersection_of: CL:0000499 ! stromal cell intersection_of: part_of UBERON:0001264 ! pancreas @@ -22514,6 +25313,8 @@ creation_date: 2011-03-02T02:40:41Z id: CL:0002575 name: central nervous system pericyte def: "A pericyte of the central nervous system." [GOC:tfm] +subset: human_subset +subset: mouse_subset is_a: CL:0000669 {is_inferred="true"} ! pericyte is_a: CL:0002319 ! neural cell intersection_of: CL:0000669 ! pericyte @@ -22528,6 +25329,8 @@ name: perineurial cell def: "A glial cell that is part of the perineurium. This cell type has thin long bipolar cytoplasmic processes, pinocytotic vesicles, fragments of external lamina and/or external lamina-like material, attachment plaques, and desmosome-like junctions. Perineurial cells historically have been referred to as fibroblasts because of shape; however, unlike fibroblasts, a perineurial cell: does not have a compact nucleus and large endoplasmic reticulum; does have a double basement membrane opposed to a single basal lamina; is carefully joined to other perineurial cells by tight junctions into a single sheet as opposed to arranged in a large mass; and finally, can surround a small axon bundle at a nerve terminal whereas a fibroblast cannot." [GO:tfm, http://en.wikipedia.org/wiki/Perineurium, NCIT:C41442, PMID:25818566] comment: There are studies that largely accept the idea that the perineurial cell is a modified fibroblast with myofibroblastic features. {xref="PMID:36244793"} subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "perineurial glial cell" EXACT [PMID:25818566] is_a: CL:0000125 ! glial cell is_a: CL:0002320 ! connective tissue cell @@ -22541,6 +25344,8 @@ creation_date: 2011-03-02T03:03:58Z id: CL:0002577 name: placental epithelial cell def: "An epithelial cell of the placenta." [GOC:tfm] +subset: human_subset +subset: mouse_subset is_a: CL:0000066 ! epithelial cell is_a: CL:0000349 {is_inferred="true"} ! extraembryonic cell intersection_of: CL:0000066 ! epithelial cell @@ -22553,6 +25358,8 @@ creation_date: 2011-03-02T03:21:30Z id: CL:0002578 name: mesenteric preadipocyte def: "A preadipocyte found in mesenteric tissue." [GOC:tfm] +subset: human_subset +subset: mouse_subset is_a: CL:0002334 {is_inferred="true"} ! preadipocyte intersection_of: CL:0002334 ! preadipocyte intersection_of: part_of UBERON:0002095 ! mesentery @@ -22564,6 +25371,8 @@ creation_date: 2011-03-03T04:19:40Z id: CL:0002579 name: omentum preadipocyte def: "A preadipocyte that is part of an omentum." [PMID:21484051] +subset: human_subset +subset: mouse_subset is_a: CL:0002334 {is_inferred="true"} ! preadipocyte intersection_of: CL:0002334 ! preadipocyte intersection_of: part_of UBERON:0003688 ! omentum @@ -22575,6 +25384,8 @@ creation_date: 2011-03-03T04:19:42Z id: CL:0002580 name: preadipocyte of the breast def: "A preadipocyte that is part of the breast." [GOC:tfm] +subset: human_subset +subset: mouse_subset is_a: CL:0002334 {is_inferred="true"} ! preadipocyte is_a: CL:4006000 ! fibroblast of breast intersection_of: CL:0002334 ! preadipocyte @@ -22586,6 +25397,8 @@ creation_date: 2011-03-03T04:19:46Z id: CL:0002581 name: perirenal preadipocyte def: "A preadipocyte that is part of a perirenal fat tissue." [PMID:20106964, PMID:31079959] +subset: human_subset +subset: mouse_subset is_a: CL:0002334 {is_inferred="true"} ! preadipocyte intersection_of: CL:0002334 ! preadipocyte intersection_of: part_of UBERON:0005406 ! perirenal fat @@ -22597,6 +25410,8 @@ creation_date: 2011-03-03T04:20:04Z id: CL:0002582 name: visceral preadipocyte def: "A preadipocyte that is part of visceral tissue." [GOC:tfm] +subset: human_subset +subset: mouse_subset is_a: CL:0002334 ! preadipocyte property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-03-03T04:32:56Z @@ -22605,6 +25420,8 @@ creation_date: 2011-03-03T04:32:56Z id: CL:0002583 name: subcutaneous preadipocyte def: "A preadipocyte that is part of subcutaneous tissue." [GOC:tfm] +subset: human_subset +subset: mouse_subset is_a: CL:0002334 {is_inferred="true"} ! preadipocyte intersection_of: CL:0002334 ! preadipocyte intersection_of: part_of UBERON:0002072 ! hypodermis @@ -22616,6 +25433,8 @@ creation_date: 2011-03-03T04:33:01Z id: CL:0002584 name: renal cortical epithelial cell def: "An epithelial cell of the kidney cortex." [GOC:tfm] +subset: human_subset +subset: mouse_subset xref: KUPO:0001016 is_a: CL:0002518 {is_inferred="true"} ! kidney epithelial cell is_a: CL:0002681 {is_inferred="true"} ! kidney cortical cell @@ -22629,6 +25448,8 @@ def: "A blood vessel endothelial cell that is part of the retina." [GOC:tfm] subset: cellxgene_subset subset: eye_upper_slim subset: human_reference_atlas +subset: human_subset +subset: mouse_subset xref: https://cellxgene.cziscience.com/cellguide/CL_0002585 is_a: CL:0000071 {is_inferred="true"} ! blood vessel endothelial cell is_a: CL:0009004 ! retinal cell @@ -22637,7 +25458,7 @@ intersection_of: part_of UBERON:0000966 ! retina relationship: part_of UBERON:0000966 ! retina property_value: RO:0002175 NCBITaxon:9606 property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 -property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional.\n\nRetinal blood vessel endothelial cells constitute the innermost lining of the blood vessels found in the retina, the light-sensitive layer of tissue at the back of the eye. The primary role of these cells revolves around their location within the retinal vascular system, forming the structure of the blood-retinal barrier, a subset of the larger blood-ocular barrier system. \nThe endothelial cells are particularly involved in the growth of new retinal blood vessels from pre-existing ones (angiogenesis); this is critical in managing the amount of oxygen and essential nutrients delivered to the ocular tissues. They are crucial for maintaining homeostasis in the retinal environment by controlling the exchange of molecules between the blood and the retina. Furthermore, they mediate immune cell trafficking, supporting the immune privilege of the eye by preventing the unrestricted infiltration of inflammatory cells into the retina, thus maintaining ocular health and normal vision.\nThe malfunction or dysfunction of retinal blood vessel endothelial cells is implicated in numerous ocular pathologies, particularly diabetic retinopathy, which is one of the leading causes of blindness worldwide. In such conditions, the compromise in the integrity of the blood-retinal barrier and excess angiogenesis can lead to retinal edema and pathological neovascularization, resulting in vision loss." xsd:string {xref="DOI:0.1016/j.preteyeres.2015.08.001", xref="DOI:10.1016/j.preteyeres.2012.08.004", xref="DOI:10.1038/nature04482", xref="DOI:10.5301/EJO.2010.6049"} +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nRetinal blood vessel endothelial cells constitute the innermost lining of the blood vessels found in the retina, the light-sensitive layer of tissue at the back of the eye. The primary role of these cells revolves around their location within the retinal vascular system, forming the structure of the blood-retinal barrier, a subset of the larger blood-ocular barrier system. \nThe endothelial cells are particularly involved in the growth of new retinal blood vessels from pre-existing ones (angiogenesis); this is critical in managing the amount of oxygen and essential nutrients delivered to the ocular tissues. They are crucial for maintaining homeostasis in the retinal environment by controlling the exchange of molecules between the blood and the retina. Furthermore, they mediate immune cell trafficking, supporting the immune privilege of the eye by preventing the unrestricted infiltration of inflammatory cells into the retina, thus maintaining ocular health and normal vision.\nThe malfunction or dysfunction of retinal blood vessel endothelial cells is implicated in numerous ocular pathologies, particularly diabetic retinopathy, which is one of the leading causes of blindness worldwide. In such conditions, the compromise in the integrity of the blood-retinal barrier and excess angiogenesis can lead to retinal edema and pathological neovascularization, resulting in vision loss." xsd:string {xref="DOI:0.1016/j.preteyeres.2015.08.001", xref="DOI:10.1016/j.preteyeres.2012.08.004", xref="DOI:10.1038/nature04482", xref="DOI:10.5301/EJO.2010.6049"} creation_date: 2011-03-06T03:28:27Z [Term] @@ -22647,6 +25468,8 @@ def: "An epithelial cell of the retinal pigmented epithelium." [GOC:tfm] subset: cellxgene_subset subset: eye_upper_slim subset: human_reference_atlas +subset: human_subset +subset: mouse_subset xref: BTO:0004910 xref: FMA:75802 xref: https://cellxgene.cziscience.com/cellguide/CL_0002586 @@ -22659,13 +25482,15 @@ relationship: has_part GO:0042470 ! melanosome relationship: part_of UBERON:0001782 ! pigmented layer of retina property_value: RO:0002175 NCBITaxon:9606 property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 -property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional.\n\nRetinal pigment epithelial (RPE) cells form a single layer of cells at the back of the eye sandwiched between the neurosensory retina and the choroid, playing a significant role in maintaining vision health. These pigment-laden cells are highly specialized and perform an array of metabolic and transport functions essential for the maintenance of the photoreceptor cells (rods and cones) in the retina. The pigmentation of RPE cells actively aids in the absorption of excess light and the prevention of light scattering, thus enhancing the eye's optical properties.\nThe retinal pigment epithelium forms a key part of the blood/retina barrier. The cells have long sheet-like microvilli on their apical membrane that project into the light-sensitive outer segments of the photoreceptors, forming a close structural interaction. The basolateral membrane of the RPE interacts with the underlying Bruch’s membrane, which separates the RPE cells from fenestrated endothelium of the choriocapillaris. \nRPE cells support the photoreceptor by providing them with oxygen and nutrients (such as glucose, retinol and fatty acids) and removing waste products. They also recycle the visual pigment, in a process called the \"visual cycle\", where the RPE cells play a vital role in the regeneration of visual pigment (11-cis retinol) following the absorption of light. This is essential for the maintenance of photoreceptor excitability.\nBeyond this, RPE cells take part in the phagocytosis process, where they digest the shed ends of photoreceptor outer segments, thus, preventing the build-up of waste residue that could otherwise harm retinal health. They also secrete various factors, including growth factors required to maintain the structural integrity of choriocapillaris endothelium and photoreceptors, as well as immunosuppressive factors that play an important role in establishing the immune privilege of the eye." xsd:string {xref="DOI:10.1111/febs.16018", xref="DOI:10.1152/physrev.00021.2004", xref="DOI:10.3389/fphar.2021.727870/full", xref="https://www.sciencedirect.com/topics/chemistry/retinal-pigment"} +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nRetinal pigment epithelial (RPE) cells form a single layer of cells at the back of the eye sandwiched between the neurosensory retina and the choroid, playing a significant role in maintaining vision health. These pigment-laden cells are highly specialized and perform an array of metabolic and transport functions essential for the maintenance of the photoreceptor cells (rods and cones) in the retina. The pigmentation of RPE cells actively aids in the absorption of excess light and the prevention of light scattering, thus enhancing the eye's optical properties.\nThe retinal pigment epithelium forms a key part of the blood/retina barrier. The cells have long sheet-like microvilli on their apical membrane that project into the light-sensitive outer segments of the photoreceptors, forming a close structural interaction. The basolateral membrane of the RPE interacts with the underlying Bruch’s membrane, which separates the RPE cells from fenestrated endothelium of the choriocapillaris. \nRPE cells support the photoreceptor by providing them with oxygen and nutrients (such as glucose, retinol and fatty acids) and removing waste products. They also recycle the visual pigment, in a process called the \"visual cycle\", where the RPE cells play a vital role in the regeneration of visual pigment (11-cis retinol) following the absorption of light. This is essential for the maintenance of photoreceptor excitability.\nBeyond this, RPE cells take part in the phagocytosis process, where they digest the shed ends of photoreceptor outer segments, thus, preventing the build-up of waste residue that could otherwise harm retinal health. They also secrete various factors, including growth factors required to maintain the structural integrity of choriocapillaris endothelium and photoreceptors, as well as immunosuppressive factors that play an important role in establishing the immune privilege of the eye." xsd:string {xref="DOI:10.1111/febs.16018", xref="DOI:10.1152/physrev.00021.2004", xref="DOI:10.3389/fphar.2021.727870/full", xref="https://www.sciencedirect.com/topics/chemistry/retinal-pigment"} creation_date: 2011-03-06T03:37:09Z [Term] id: CL:0002588 name: smooth muscle cell of the umbilical vein def: "A smooth muscle cell of the umbilical vein." [GOC:tfm] +subset: human_subset +subset: mouse_subset is_a: CL:0019018 ! blood vessel smooth muscle cell intersection_of: CL:0000359 ! vascular associated smooth muscle cell intersection_of: part_of UBERON:0002066 ! umbilical vein @@ -22677,6 +25502,8 @@ creation_date: 2011-03-06T05:00:51Z id: CL:0002589 name: smooth muscle cell of the brachiocephalic vasculature def: "A smooth muscle cell of the bachiocephalic vasculature." [GOC:tfm] +subset: human_subset +subset: mouse_subset is_a: CL:0019018 ! blood vessel smooth muscle cell intersection_of: CL:0000359 ! vascular associated smooth muscle cell intersection_of: part_of UBERON:0001529 ! brachiocephalic artery @@ -22688,6 +25515,8 @@ creation_date: 2011-03-06T05:00:58Z id: CL:0002590 name: smooth muscle cell of the brain vasculature def: "A vascular associated smooth muscle cell of the brain vasculature." [GOC:tfm] +subset: human_subset +subset: mouse_subset is_a: CL:0000359 {is_inferred="true"} ! vascular associated smooth muscle cell is_a: CL:0002319 ! neural cell intersection_of: CL:0000359 ! vascular associated smooth muscle cell @@ -22702,13 +25531,17 @@ name: smooth muscle cell of the pulmonary artery def: "A smooth muscle of the pulmonary artery." [GOC:tfm] subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset xref: BTO:0003336 +xref: https://cellxgene.cziscience.com/cellguide/CL_0002591 is_a: CL:0019018 ! blood vessel smooth muscle cell intersection_of: CL:0000359 ! vascular associated smooth muscle cell intersection_of: part_of UBERON:0002012 ! pulmonary artery relationship: part_of UBERON:0002012 ! pulmonary artery property_value: RO:0002175 NCBITaxon:9606 property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nSmooth muscle cells of the pulmonary artery form a principal component of the pulmonary artery's media layer, the middle section of the artery wall typically found between endothelial inner layer (intima) and the outermost connective tissue layer (adventitia). The unique structure of these cells, defined by fusiform shape and the absence of striations, sets them apart from other muscle cell types, including cardiac and skeletal.\nThe primary function of smooth muscle cells of the pulmonary artery is to regulate the diameter of the pulmonary artery, which in turn controls the flow of blood into the lungs. They accomplish this task through the contraction and relaxation, indicative of vasoconstriction and vasodilation respectively. When these cells contract, the diameter of the artery narrows, leading to reduced blood flow. Conversely, relaxation of these cells widens the artery, facilitating increased blood flow. Such blood flow modulation is crucial for the maintenance of blood pressure and ensuring that the lungs receive an adequate blood supply for efficient oxygen exchange.\nAs a result, abnormal function or proliferation of these cells can contribute to conditions such as pulmonary hypertension, a condition characterized by high blood pressure in the arteries leading to the lungs. This can occur due to hypoxia (lack of enough oxygen), leading to excessive constriction or proliferation of the smooth muscle cells." xsd:string {xref="DOI:10.1016/j.apsb.2012.12.007", xref="DOI:10.1124/pr.115.010652", xref="https://www.sciencedirect.com/topics/medicine-and-dentistry/pulmonary-artery-smooth-muscle-cell"} creation_date: 2011-03-06T05:01:28Z [Term] @@ -22716,6 +25549,8 @@ id: CL:0002592 name: smooth muscle cell of the coronary artery def: "A smooth muscle cell of the coronary artery." [GOC:tfm] subset: human_reference_atlas +subset: human_subset +subset: mouse_subset is_a: CL:0002494 ! cardiocyte is_a: CL:0019018 ! blood vessel smooth muscle cell intersection_of: CL:0000359 ! vascular associated smooth muscle cell @@ -22729,6 +25564,8 @@ creation_date: 2011-03-06T05:01:34Z id: CL:0002593 name: smooth muscle cell of the internal thoracic artery def: "A smooth muscle of the internal thoracic artery." [GOC:tfm] +subset: human_subset +subset: mouse_subset is_a: CL:0002595 ! smooth muscle cell of the subclavian artery intersection_of: CL:0000359 ! vascular associated smooth muscle cell intersection_of: part_of UBERON:0002456 ! internal thoracic artery @@ -22740,6 +25577,8 @@ creation_date: 2011-03-06T05:01:41Z id: CL:0002594 name: smooth muscle cell of the umbilical artery def: "A smooth muscle cell of the umbilical artery." [GOC:tfm] +subset: human_subset +subset: mouse_subset is_a: CL:0019018 ! blood vessel smooth muscle cell intersection_of: CL:0000359 ! vascular associated smooth muscle cell intersection_of: part_of UBERON:0001310 ! umbilical artery @@ -22751,6 +25590,8 @@ creation_date: 2011-03-06T05:01:48Z id: CL:0002595 name: smooth muscle cell of the subclavian artery def: "A smooth muscle cell of the subclavian artery." [GOC:tfm] +subset: human_subset +subset: mouse_subset is_a: CL:0019018 ! blood vessel smooth muscle cell intersection_of: CL:0000359 ! vascular associated smooth muscle cell intersection_of: part_of UBERON:0001533 ! subclavian artery @@ -22762,6 +25603,8 @@ creation_date: 2011-03-06T05:01:52Z id: CL:0002596 name: smooth muscle cell of the carotid artery def: "Smooth muscle cell of the carotid artery." [GOC:tfm] +subset: human_subset +subset: mouse_subset is_a: CL:0019018 ! blood vessel smooth muscle cell intersection_of: CL:0000359 ! vascular associated smooth muscle cell intersection_of: part_of UBERON:0005396 ! carotid artery segment @@ -22774,6 +25617,8 @@ id: CL:0002597 name: smooth muscle cell of bladder def: "A smooth muscle cell of the bladder." [GC:tfm] subset: human_reference_atlas +subset: human_subset +subset: mouse_subset xref: KUPO:0001122 is_a: CL:0000192 {is_inferred="true"} ! smooth muscle cell is_a: CL:1001319 ! bladder cell @@ -22789,19 +25634,25 @@ name: bronchial smooth muscle cell def: "Any smooth muscle cell that is part of some bronchus." [FBC:Autogenerated] subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset xref: BTO:0004402 +xref: https://cellxgene.cziscience.com/cellguide/CL_0002598 is_a: CL:0019019 ! tracheobronchial smooth muscle cell intersection_of: CL:0000192 ! smooth muscle cell intersection_of: part_of UBERON:0002185 ! bronchus relationship: part_of UBERON:0002185 ! bronchus property_value: RO:0002175 NCBITaxon:9606 property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nBronchial smooth muscle cells are specialized types of cells found in the bronchi of the respiratory system in mammals. These bronchi are tubular structures that function to carry air from the trachea into the lungs. As part of the smooth muscle tissue, bronchial smooth muscle cells are involuntary cells, meaning they function with minimal direct voluntary control. They are characterized by their elongated spindle-shaped structure, with each cell containing a single central nucleus.\nThe primary function of bronchial smooth muscle cells is to control airway diameter, which directly influences the flow of air into and out of the lungs. Muscular contractions and relaxations mediated by these cells enable the bronchi to constrict or expand, facilitating the regulation of respiratory airflow. Additionally, these cells play a pivotal role in immune responses as they produce and release various substances that can instigate or lessen inflammation of airway tissue. Furthermore, bronchial smooth muscle cells can proliferate and lay down collagen and other extracellular matrix proteins, contributing to the structural integrity of the bronchial tubes.\nIn pathological conditions, such as asthma and chronic obstructive pulmonary disease, the function and biology of bronchial smooth muscle cells change. Asthma, for example, is associated with an abnormal increase in the mass of the bronchial smooth muscles, leading to narrowing of the airways and resultant breathing difficulties. These cells also exhibit altered contractile behavior and an augmented immune response during inflammatory lung diseases." xsd:string {xref="DOI:10.1152/japplphysiol.00313.2006", xref="DOI:10.1183/09031936.00019810", xref="https://www.ncbi.nlm.nih.gov/books/NBK537353/", xref="https://www.sciencedirect.com/topics/agricultural-and-biological-sciences/bronchial-muscle"} creation_date: 2011-03-06T05:46:39Z [Term] id: CL:0002599 name: smooth muscle cell of the esophagus def: "A smooth muscle cell of the esophagus." [GOC:tfm] +subset: human_subset +subset: mouse_subset is_a: CL:0000192 {is_inferred="true"} ! smooth muscle cell intersection_of: CL:0000192 ! smooth muscle cell intersection_of: part_of UBERON:0001043 ! esophagus @@ -22814,11 +25665,15 @@ id: CL:0002600 name: smooth muscle cell of trachea def: "A smooth muscle cell of the trachea." [GOC:tfm] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset +xref: https://cellxgene.cziscience.com/cellguide/CL_0002600 is_a: CL:0019019 ! tracheobronchial smooth muscle cell intersection_of: CL:0000192 ! smooth muscle cell intersection_of: part_of UBERON:0003126 ! trachea relationship: part_of UBERON:0003126 ! trachea property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nSmooth muscle cells of the trachea have a characteristic 'smooth' (non-striated) appearance under the microscope, a distinguishing feature that differentiates them from skeletal and cardiac muscle cells. The smooth appearance is due to the organization of actin and myosin filaments in the cell, which allows for a controlled, contractile function.\nThese cells play a key role in controlling the diameter of the trachea, thus regulating the airflow. They are responsible for the involuntary constriction and relaxation of the trachea influencing the air passage during various physiological behaviors like breathing, coughing, and sneezing. This autonomic control allows for adaptations to specific body requirements without conscious control, such as increasing air flow during exercise or restricting it during rest.\nIn conditions such as asthma, chronic bronchitis, and emphysema, there are changes in smooth muscle cells. For example, the mass of smooth muscle cells increases in chronic airway diseases, possibly in response to chronic inflammation. This increase may indicate a pathological condition or be a part of the body's response to injury and repair." xsd:string {xref="DOI:10.1016/s1357-2725(02)00259-5", xref="https://www.ncbi.nlm.nih.gov/books/NBK9961", xref="https://www.sciencedirect.com/topics/agricultural-and-biological-sciences/airway-smooth-muscle"} creation_date: 2011-03-06T05:50:28Z [Term] @@ -22826,17 +25681,23 @@ id: CL:0002601 name: uterine smooth muscle cell def: "A smooth muscle cell of the uterus." [GOC:tfm] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset +xref: https://cellxgene.cziscience.com/cellguide/CL_0002601 is_a: CL:0000192 {is_inferred="true"} ! smooth muscle cell intersection_of: CL:0000192 ! smooth muscle cell intersection_of: part_of UBERON:0000995 ! uterus relationship: part_of UBERON:0000995 ! uterus property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nUterine smooth muscle cells are specialized cells that make up the majority of the uterus and in particular, the myometrium. The myometrium is a thick, involuntary muscle layer, principally consisting of verticillate cell bundles that sculpt the helical architecture of the uterus. This dense muscular tissue, packed with uterine smooth muscle cells, is responsible for the significant contractile force witnessed during the physical processes of labor and childbirth.\nIn the non-pregnant uterus, they exist in a quiescent phase. Upon implantation, these cells are primarily responsible for the expansion consequently allowing the uterus to accommodate the growing fetus. Towards the end of pregnancy, under the influence of hormonal and mechanical signals, uterine smooth muscle cells transition from a relaxed phase to an active contractile phase, culminating in the delivery of the fetus.\nAt the cellular level, these transitions involve significant changes in the electrophysiological properties of uterine smooth muscle cells. Governed by a complex interplay of ion channels, transporters, and signaling proteins, these cells adjust their electrical activity, conduction properties, and contracting mechanisms. Any issues with these processes can result in problems such as preterm birth or labor dysfunction." xsd:string {xref="DOI:10.1177/0036850419850431", xref="DOI:10.1203/00006450-199811000-00001", xref="DOI:10.3791/56639", xref="https://www.ncbi.nlm.nih.gov/books/NBK532927/"} creation_date: 2011-03-06T05:53:28Z [Term] id: CL:0002602 name: annulus pulposus cell def: "Any connective tissue cell that is part of some annulus fibrosus disci intervertebralis." [FBC:Autogenerated] +subset: human_subset +subset: mouse_subset synonym: "anulus pulposus cell" EXACT [] is_a: CL:0002320 {is_inferred="true"} ! connective tissue cell intersection_of: CL:0002320 ! connective tissue cell @@ -22850,6 +25711,8 @@ id: CL:0002603 name: astrocyte of the cerebellum def: "An astrocyte of the cerebellum." [GOC:tfm] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset is_a: CL:0000127 {is_inferred="true"} ! astrocyte is_a: CL:2000005 ! brain macroglial cell intersection_of: CL:0000127 ! astrocyte @@ -22863,6 +25726,8 @@ id: CL:0002604 name: hippocampal astrocyte def: "An astrocyte that is part of the hippocampus." [https://orcid.org/0000-0001-7258-9596] subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "astrocyte of the hippocampal formation" EXACT [] synonym: "astrocyte of the hippocampus" EXACT [] is_a: CL:0002605 ! astrocyte of the cerebral cortex @@ -22879,6 +25744,8 @@ name: astrocyte of the cerebral cortex def: "A transcriptomically distinct astrocyte that is found in the cerebral cortex." [GOC:tfm] subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset is_a: CL:0012000 ! astrocyte of the forebrain is_a: CL:1001579 ! cerebral cortex glial cell intersection_of: CL:0000127 ! astrocyte @@ -22891,6 +25758,8 @@ creation_date: 2011-03-06T06:57:36Z id: CL:0002606 name: astrocyte of the spinal cord def: "An astrocyte of the spinal cord." [GOC:tfm] +subset: human_subset +subset: mouse_subset is_a: CL:0000127 {is_inferred="true"} ! astrocyte intersection_of: CL:0000127 ! astrocyte intersection_of: part_of UBERON:0002240 ! spinal cord @@ -22903,6 +25772,8 @@ id: CL:0002607 name: migratory enteric neural crest cell def: "A neural crest cell that gives rise to cells of the enteric nervous system." [GOC:tfm] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset is_a: CL:0000333 ! migratory neural crest cell property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-03-06T07:24:35Z @@ -22912,6 +25783,8 @@ id: CL:0002608 name: hippocampal neuron def: "A neuron with a soma found in the hippocampus." [GOC:tfm] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset is_a: CL:0010012 ! cerebral cortex neuron intersection_of: CL:0000540 ! neuron intersection_of: RO:0002100 UBERON:0002421 ! has soma location hippocampal formation @@ -22923,9 +25796,10 @@ creation_date: 2011-03-06T07:31:49Z id: CL:0002610 name: raphe nuclei neuron def: "A neuron of the raphe nuclei." [GOC:tfm] -is_a: CL:0000117 {is_inferred="true"} ! CNS neuron (sensu Vertebrata) +subset: human_subset +subset: mouse_subset is_a: CL:2000029 ! central nervous system neuron -intersection_of: CL:0000117 ! CNS neuron (sensu Vertebrata) +intersection_of: CL:0000540 ! neuron intersection_of: RO:0002100 UBERON:0004684 ! has soma location raphe nuclei relationship: RO:0002100 UBERON:0004684 ! has soma location raphe nuclei property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 @@ -22935,9 +25809,10 @@ creation_date: 2011-03-06T07:42:06Z id: CL:0002611 name: neuron of the dorsal spinal cord def: "A CNS neuron of the dorsal spinal cord." [GOC:tfm] -is_a: CL:0000117 {is_inferred="true"} ! CNS neuron (sensu Vertebrata) +subset: human_subset +subset: mouse_subset is_a: CL:2000029 ! central nervous system neuron -intersection_of: CL:0000117 ! CNS neuron (sensu Vertebrata) +intersection_of: CL:0000540 ! neuron intersection_of: RO:0002100 UBERON:0002256 ! has soma location dorsal horn of spinal cord relationship: RO:0002100 UBERON:0002256 ! has soma location dorsal horn of spinal cord property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 @@ -22947,9 +25822,10 @@ creation_date: 2011-03-06T07:43:34Z id: CL:0002612 name: neuron of the ventral spinal cord def: "A neuron of the ventral spinal cord." [GOC:tfm] -is_a: CL:0000117 {is_inferred="true"} ! CNS neuron (sensu Vertebrata) +subset: human_subset +subset: mouse_subset is_a: CL:2000029 ! central nervous system neuron -intersection_of: CL:0000117 ! CNS neuron (sensu Vertebrata) +intersection_of: CL:0000540 ! neuron intersection_of: RO:0002100 UBERON:0002257 ! has soma location ventral horn of spinal cord relationship: RO:0002100 UBERON:0002257 ! has soma location ventral horn of spinal cord property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 @@ -22959,8 +25835,10 @@ creation_date: 2011-03-06T07:46:03Z id: CL:0002613 name: striatum neuron def: "A neuron of the striatum." [GOC:tfm] +subset: human_subset +subset: mouse_subset is_a: CL:0012001 ! neuron of the forebrain -intersection_of: CL:0000117 ! CNS neuron (sensu Vertebrata) +intersection_of: CL:0000540 ! neuron intersection_of: RO:0002100 UBERON:0002435 ! has soma location striatum relationship: RO:0002100 UBERON:0002435 ! has soma location striatum property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 @@ -22970,9 +25848,10 @@ creation_date: 2011-03-06T07:47:12Z id: CL:0002614 name: neuron of the substantia nigra def: "A neuron of the substantia nigra." [GOC:tfm] -is_a: CL:0000117 {is_inferred="true"} ! CNS neuron (sensu Vertebrata) +subset: human_subset +subset: mouse_subset is_a: CL:2000029 ! central nervous system neuron -intersection_of: CL:0000117 ! CNS neuron (sensu Vertebrata) +intersection_of: CL:0000540 ! neuron intersection_of: RO:0002100 UBERON:0002038 ! has soma location substantia nigra relationship: RO:0002100 UBERON:0002038 ! has soma location substantia nigra property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 @@ -22982,6 +25861,8 @@ creation_date: 2011-03-06T07:48:42Z id: CL:0002615 name: adipocyte of omentum tissue def: "An adipocyte that is part of omentum tissue." [GOC:tfm] +subset: human_subset +subset: mouse_subset synonym: "omental adipocyte" EXACT [] synonym: "omental fat cell" EXACT [] is_a: CL:0000136 {is_inferred="true"} ! adipocyte @@ -22995,6 +25876,8 @@ creation_date: 2011-03-14T10:17:00Z id: CL:0002616 name: perirenal adipocyte def: "An adipocyte of perirenal fat tissue." [GOC:tfm] +subset: human_subset +subset: mouse_subset synonym: "perirenal adipocyte cell" EXACT [] synonym: "perirenal fat cell" EXACT [] is_a: CL:0000136 {is_inferred="true"} ! adipocyte @@ -23010,6 +25893,8 @@ name: adipocyte of breast def: "An adipocyte that is part of the breast." [GOC:tfm] comment: Adipocytes found in the subcutaneous adipose tissue of breast. The breast consists of three main components, the skin, the subcutaneous adipose tissue and the functional glandular tissue that comprises both parenchyma and stroma.[CALOHA] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "breast adipocyte" EXACT [] synonym: "fat cell of breast" EXACT [] xref: CALOHA:TS-2377 @@ -23024,6 +25909,8 @@ creation_date: 2011-03-14T10:17:07Z id: CL:0002618 name: endothelial cell of umbilical vein def: "An endothelial cell of the umbilical vein." [GOC:tfm] +subset: human_subset +subset: mouse_subset xref: BTO:0004296 xref: https://cellxgene.cziscience.com/cellguide/CL_0002618 is_a: CL:0002543 ! vein endothelial cell @@ -23031,7 +25918,7 @@ intersection_of: CL:0000115 ! endothelial cell intersection_of: part_of UBERON:0002066 ! umbilical vein relationship: part_of UBERON:0002066 ! umbilical vein property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 -property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional.\n\nEndothelial cells of the umbilical vein form the inner lining of the veins found in the umbilical cord. They are involved in tube formation and migration which are essential for angiogenesis, the process of generating new blood vessels; this is critical during the fetal stage for the development of the circulatory system. Endothelial cells of the umbilical vein also play a role in controlling the passage of white blood cells into tissues during inflammatory responses.\nBecause human umbilical vein endothelial cells (HUVECs) can easily be derived from the umbilical cord, and because they express common endothelial cell markers, they have been used as an epithelial cell model for studies on cell proliferation, migration, angiogenesis, and inflammation. They have been used as models for vascular diseases like atherosclerosis, for investigating how tumor cells infiltrate blood vessels and form metastases. \nThus, while endothelial cells of the umbilical vein play a critical role in vascular biology, they also represent a powerful tool in disease studies and potential treatment strategies." xsd:string {xref="DOI:10.1002/cyto.a.20952", xref="DOI:10.1007/s12015-006-0015-x", xref="DOI:10.1172/JCI107470", xref="DOI:10.3390/app10030938", xref="https://www.ncbi.nlm.nih.gov/books/NBK53254/"} +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nEndothelial cells of the umbilical vein form the inner lining of the veins found in the umbilical cord. They are involved in tube formation and migration which are essential for angiogenesis, the process of generating new blood vessels; this is critical during the fetal stage for the development of the circulatory system. Endothelial cells of the umbilical vein also play a role in controlling the passage of white blood cells into tissues during inflammatory responses.\nBecause human umbilical vein endothelial cells (HUVECs) can easily be derived from the umbilical cord, and because they express common endothelial cell markers, they have been used as an epithelial cell model for studies on cell proliferation, migration, angiogenesis, and inflammation. They have been used as models for vascular diseases like atherosclerosis, for investigating how tumor cells infiltrate blood vessels and form metastases. \nThus, while endothelial cells of the umbilical vein play a critical role in vascular biology, they also represent a powerful tool in disease studies and potential treatment strategies." xsd:string {xref="DOI:10.1002/cyto.a.20952", xref="DOI:10.1007/s12015-006-0015-x", xref="DOI:10.1172/JCI107470", xref="DOI:10.3390/app10030938", xref="https://www.ncbi.nlm.nih.gov/books/NBK53254/"} creation_date: 2011-03-14T11:36:51Z [Term] @@ -23040,6 +25927,8 @@ name: adult endothelial progenitor cell def: "An adult angioblastic cell released from the bone marrow, or from the kidney in some teleost species, capable of blood circulation and participation in angiogenesis by differentiating into blood vessel endothelial cells." [GOC:tfm, PMID:20807818, PMID:9020076, WikipediaVersioned:Endothelial_progenitor_cell&oldid=1069930016] comment: The existence of adult endothelial progenitor cells has been controversial in the past. subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "EPC" EXACT [] is_a: CL:0000566 ! angioblastic mesenchymal cell property_value: RO:0002175 NCBITaxon:9606 @@ -23054,6 +25943,8 @@ name: skin fibroblast def: "A fibroblast of skin." [GOC:tfm] subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset xref: BTO:0001255 xref: CALOHA:TS-0935 is_a: CL:0000057 {is_inferred="true"} ! fibroblast @@ -23068,6 +25959,9 @@ creation_date: 2011-03-14T12:31:49Z id: CL:0002621 name: gingival epithelial cell def: "Any epithelial cell that is part of some gingival epithelium." [FBC:Autogenerated] +subset: cellxgene_subset +subset: human_subset +subset: mouse_subset is_a: CL:1001576 ! oral mucosa squamous cell intersection_of: CL:0000066 ! epithelial cell intersection_of: part_of UBERON:0001949 ! gingival epithelium @@ -23080,6 +25974,8 @@ id: CL:0002622 name: prostate stromal cell def: "A stromal cell of the prostate." [GOC:tfm] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset xref: BTO:0003972 is_a: CL:0000499 {is_inferred="true"} ! stromal cell intersection_of: CL:0000499 ! stromal cell @@ -23093,6 +25989,8 @@ id: CL:0002623 name: acinar cell of salivary gland def: "An acinar cell of salivary gland." [GOC:tfm] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset is_a: CL:0000622 {is_inferred="true"} ! acinar cell is_a: CL:1001596 ! salivary gland glandular cell intersection_of: CL:0000622 ! acinar cell @@ -23104,6 +26002,8 @@ creation_date: 2011-03-14T02:22:22Z id: CL:0002624 name: paneth cell of the appendix def: "A paneth cell of the appendix." [GOC:tfm] +subset: human_subset +subset: mouse_subset is_a: CL:0000510 {is_inferred="true"} ! paneth cell is_a: CL:1001585 ! appendix glandular cell intersection_of: CL:0000510 ! paneth cell @@ -23115,6 +26015,8 @@ creation_date: 2011-03-15T09:38:18Z id: CL:0002625 name: seminiferous tubule epithelial cell def: "A cell of the seminiferous tubule epithelium." [GOC:tfm] +subset: human_subset +subset: mouse_subset is_a: CL:0000068 ! duct epithelial cell is_a: CL:0000077 {is_inferred="true"} ! mesothelial cell intersection_of: CL:0000066 ! epithelial cell @@ -23127,6 +26029,9 @@ creation_date: 2011-03-15T11:59:23Z id: CL:0002626 name: immature astrocyte def: "An immature astrocyte." [GOC:dsd] +subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "immature astrocytic glia" EXACT [] is_a: CL:0000127 ! astrocyte @@ -23136,6 +26041,8 @@ name: mature astrocyte def: "A mature astrocyte that is capable of producing cytokines." [GOC:dsd, PMID:12898703, PMID:8734446] comment: Mature astrocytes are reportedly able to produce aspartate, ATP, BDNF, BMP-2a, BMP-3, CCL2, CCL3, CCL4, CCL5, CCL19, CCL20,CD40L, CNTF, CTGF, CXCL1, CXCL2, CXCL8, edn-1, aFGF, bFGF, G-CSF, glutamate, GM-CSF, IFN-alpha, IFN-beta, IFN-gamma, IGF-1, IL-1alpha, IL-1beta, IL-2, Il-4, IL-6, IL-10, IL-12, LIF, MIP-2, NGF, nitric oxide, NT3, taurine, TGF-beta, TNF-alpha, TNF-beta. subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "activated astrocyte" EXACT [] synonym: "mature astrocytic glia" EXACT [] is_a: CL:0000127 ! astrocyte @@ -23145,6 +26052,8 @@ id: CL:0002628 name: immature microglial cell def: "An immature microglial cell with a ramified morphology." [GOC:dsd, PMID:18396103, PMID:19461673] comment: Immature microglia are reportedly CD34-positive, CD163-negative, MHCI-negative, MHCII-negative. +subset: human_subset +subset: mouse_subset synonym: "immature microglia" EXACT [] synonym: "quiescent microglia" EXACT [PMID:18396103] synonym: "resting microglia" EXACT [PMID:18396103] @@ -23156,9 +26065,12 @@ name: mature microglial cell def: "A mature microglial cell that has changed shape to an amoeboid morphology and is capable of cytokine production and antigen presentation." [GOC:dsd, PMID:11517395, PMID:14612429, PMID:15246020, PMID:16177057, PMID:18396103, PMID:20021364] comment: Mature microglia are reportedly CCR2-positive, CD4-positive, CD9-positive, CD11a-positive, CD11b-positive, CD11c-positive, CD13-positive, CD16-positive, CDw17-positive, CD18-positive, CD21-positive, CD26-negative, CD32-positive, CD35-positive, CD36-positive, CD40-positive, CD44-positive, CD45-positive, CD53-positive, CD54-positive, CD56-negative, CD58-positive, CD63-positive, CD64-positive, CD66-positive, CD80-positive, CD86-positive, CD87-positive, CD92-positive, CD106-positive, CD107a-positive, CD147-positive, CD155-positive, CD162-positive, CD163-positive, CD171-negative, CD200R-positive, CXCR3-positive, CX3CR1-positive, fibronectin-positive, GD3-positive, GLUT1-positive, GLUT3-negative, GLUT5-positive, MHCI-positive, MHCII-positive, P2X4-positive, RFD7-negative, RGS5-negative, alpha-SMA-negative, vimentin-positive, and vwf-negative. Mature microglia are capable of producing BDNF, CCL3, CCL5, CCL7, CCL8, CCL9, CCL19, CCL20,CD40L, CSF, CXCL1, CXCL2, CXCL4, CXCL5, CXCL8, CXCL9, CXCL10, glutamate, IL-1beta, IL-1ra, IL-3, IL-6, IL-10, IL-12, LT, MMP-2, MMP-9, NGF, nitric oxide, ROS, TGF-beta, TNF-alpha. subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "activated microglia" EXACT [PMID:18396103] synonym: "mature microglia" EXACT [] synonym: "reactive microglia" EXACT [PMID:18396103] +xref: https://cellxgene.cziscience.com/cellguide/CL_0002629 is_a: CL:0000129 {is_inferred="true"} ! microglial cell intersection_of: CL:0000129 ! microglial cell intersection_of: capable_of GO:0001816 ! cytokine production @@ -23169,6 +26081,7 @@ intersection_of: capable_of GO:0019882 ! antigen processing and presentation relationship: capable_of GO:0001816 ! cytokine production relationship: capable_of GO:0002536 ! respiratory burst involved in inflammatory response relationship: capable_of GO:0002537 ! nitric oxide production involved in inflammatory response +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nMature microglial cells represented one of the macrophage populations within the central nervous system (CNS). Microglial cells serve as the primary immune defense mechanism within the CNS, playing active roles in maintaining brain homeostasis and responding to pathological processes. In response to pathogens and injuries, microglial cells mature and change their morphology from a ramified shape with small processes (normal state) to an amoeboid shape (mature state).\nMature microglial cells possess multiple functional abilities, thereby enabling them to execute diverse roles in order to maintain the health of surrounding neural cells. They act to clear away cellular debris, dead neurons, or plaque formations through the process of phagocytosis. They are also continuously scanning their environment and are able to detect subtle changes in the neural landscape caused by injury, disease, or infection. Upon detection of such changes, these cells become activated and present antigens and secrete cytokines and chemokines to initiate an inflammation response, which sustains the brain’s defense against injurious agents.\nTheir role is not solely destructive or defensive: mature microglial cells also contribute to neurodevelopment by guiding the formation of neural circuits, synaptogenesis, and remodeling. Furthermore, they assist in managing synaptic plasticity, a key process in learning and memory functions. While the dysregulation of microglial cells has been implicated in various neurodegenerative diseases, they are also regarded as potential therapeutic targets for such conditions, given their crucial roles in maintaining CNS health." xsd:string {xref="DOI:10.1111/j.1745-7254.2007.00625.x", xref="DOI:10.1111/jnc.15689", xref="DOI:10.3389/fimmu.2022.997786", xref="DOI:10.4103/1673-5374.226386", xref="DOI:10.4103/1673-5374.322423"} [Term] id: CL:0002630 @@ -23182,7 +26095,9 @@ creation_date: 2011-06-16T01:01:41Z id: CL:0002631 name: epithelial cell of upper respiratory tract def: "Any epithelial cell that is part of some upper respiratory tract epithelium." [FBC:Autogenerated] -is_a: CL:0002368 ! respiratory epithelial cell +subset: human_subset +subset: mouse_subset +is_a: CL:0002368 ! respiratory tract epithelial cell intersection_of: CL:0000066 ! epithelial cell intersection_of: part_of UBERON:0004814 ! upper respiratory tract epithelium relationship: part_of UBERON:0004814 ! upper respiratory tract epithelium @@ -23194,7 +26109,9 @@ id: CL:0002632 name: epithelial cell of lower respiratory tract def: "Any epithelial cell that is part of some lower respiratory tract epithelium." [FBC:Autogenerated] subset: cellxgene_subset -is_a: CL:0002368 ! respiratory epithelial cell +subset: human_subset +subset: mouse_subset +is_a: CL:0002368 ! respiratory tract epithelial cell intersection_of: CL:0000066 ! epithelial cell intersection_of: part_of UBERON:0004815 ! lower respiratory tract epithelium relationship: part_of UBERON:0004815 ! lower respiratory tract epithelium @@ -23206,6 +26123,8 @@ id: CL:0002633 name: respiratory basal cell def: "A basal cell in the respiratory tract." [GOC:tfm, PMID:20699479] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "airway basal cell" EXACT [] synonym: "airway basal stem cell" EXACT [] xref: https://cellxgene.cziscience.com/cellguide/CL_0002633 @@ -23214,13 +26133,15 @@ intersection_of: CL:0000646 ! basal cell intersection_of: part_of UBERON:0004802 ! respiratory tract epithelium relationship: part_of UBERON:0004802 ! respiratory tract epithelium property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 -property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional.\n\nRespiratory basal cells are highly specialized cells that serve a crucial role in the human airway epithelium, predominantly found lining the surfaces of the trachea and bronchi. These cells exhibit a distinctive columnar shape and are attached directly to the basal lamina. They are characterized by the presence of high amounts of cytoplasmic keratins, predominantly keratin 5 and 14, and transcription factor tumor protein (tp63), which set them apart from other types of lung epithelial cells such as ciliated cells and secretory cells. \nBasal cells are essential for maintaining airway integrity. They make up one third of all respiratory epithelial cells and serve as stem cells as they can transform into different cell types, like goblet cells, ciliated cells, and club cells, when needed for homeostatic maintenance of the epithelial barrier or to repair and restore a healthy cellular environment after injury.\nTheir position at the interface between the internal environment and the external atmosphere makes these cells a first line of defense against air-borne irritants, allergens, and pathogens. Their robust, intrinsic reparative properties facilitate effective recovery from such adversities. However, damage to respiratory basal cells or abnormalities in their function are associated with several respiratory pathologies such as asthma, chronic obstructive pulmonary disease, and lung cancer. Therefore, understanding these cells' function, and their role in disease, is crucial for the development of new therapeutic strategies for respiratory disorders." xsd:string {xref="DOI:10.1186/s12931-022-02042-5", xref="DOI:10.3389/falgy.2021.787128", xref="DOI:110.1038/s41385-020-00370-7"} +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nRespiratory basal cells are highly specialized cells that serve a crucial role in the human airway epithelium, predominantly found lining the surfaces of the trachea and bronchi. These cells exhibit a distinctive columnar shape and are attached directly to the basal lamina. They are characterized by the presence of high amounts of cytoplasmic keratins, predominantly keratin 5 and 14, and transcription factor tumor protein (tp63), which set them apart from other types of lung epithelial cells such as ciliated cells and secretory cells. \nBasal cells are essential for maintaining airway integrity. They make up one third of all respiratory epithelial cells and serve as stem cells as they can transform into different cell types, like goblet cells, ciliated cells, and club cells, when needed for homeostatic maintenance of the epithelial barrier or to repair and restore a healthy cellular environment after injury.\nTheir position at the interface between the internal environment and the external atmosphere makes these cells a first line of defense against air-borne irritants, allergens, and pathogens. Their robust, intrinsic reparative properties facilitate effective recovery from such adversities. However, damage to respiratory basal cells or abnormalities in their function are associated with several respiratory pathologies such as asthma, chronic obstructive pulmonary disease, and lung cancer. Therefore, understanding these cells' function, and their role in disease, is crucial for the development of new therapeutic strategies for respiratory disorders." xsd:string {xref="DOI:10.1186/s12931-022-02042-5", xref="DOI:10.3389/falgy.2021.787128", xref="DOI:110.1038/s41385-020-00370-7"} creation_date: 2011-06-21T03:11:10Z [Term] id: CL:0002634 name: epithelial cell of anal column def: "An epithelial cell of the anal column." [GOC:tfm] +subset: human_subset +subset: mouse_subset is_a: CL:0002253 ! epithelial cell of large intestine intersection_of: CL:0000066 ! epithelial cell intersection_of: part_of UBERON:0009882 ! anal column @@ -23232,6 +26153,8 @@ creation_date: 2011-07-08T12:11:38Z id: CL:0002635 name: nonkeratinized epithelial cell of anal column def: "A nonkeratinized epithelial cell of the anal canal." [GOC:tfm] +subset: human_subset +subset: mouse_subset xref: FMA:263146 is_a: CL:0002634 ! epithelial cell of anal column property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 @@ -23241,6 +26164,8 @@ creation_date: 2011-07-08T02:05:33Z id: CL:0002636 name: nonkeratinized epithelial cell of inferior part of anal canal def: "A nonkeratinized cell epithleial cell of the inferior part of the anal canal." [GOC:tfm] +subset: human_subset +subset: mouse_subset xref: FMA:263144 is_a: CL:0002635 ! nonkeratinized epithelial cell of anal column is_a: CL:1000438 ! epithelial cell of wall of inferior part of anal canal @@ -23251,9 +26176,10 @@ creation_date: 2011-07-08T02:06:53Z id: CL:0002637 name: keratinized epithelial cell of the anal canal def: "An epithelial cell of the anal canal that is keratinized. This cell type is found towards the lower, rectal end of the anal canal." [GOC:tfm] +subset: human_subset +subset: mouse_subset is_a: CL:0000237 ! keratinizing barrier epithelial cell is_a: CL:0002634 ! epithelial cell of anal column -is_a: CL:0009066 ! stratified squamous epithelial cell of anal canal intersection_of: CL:0000237 ! keratinizing barrier epithelial cell intersection_of: part_of UBERON:0000159 ! anal canal property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 @@ -23263,6 +26189,8 @@ creation_date: 2011-07-08T02:08:40Z id: CL:0002638 name: bronchioalveolar stem cell def: "A respiratory stem cell found at the junction of the terminal (conductive) bronchiole and the respiratory bronchiole. This cell types gives rise to alveolar cell types and club cells in response to lung injury. This cell type expresses markers Scgb1a1 and Sftpc." [GOC:tfm, MP:0011691, PMID:15960971] +subset: human_subset +subset: mouse_subset synonym: "basal epithelial cell of bronchioalveolar duct junction" EXACT [] synonym: "BASC" EXACT [] is_a: CL:0002633 {is_inferred="true"} ! respiratory basal cell @@ -23277,6 +26205,8 @@ id: CL:0002639 name: amniotic stem cell def: "An amniotic stem cell is a mesenchymalstem cell extracted from amniotic fluid. Amniotic stem cells are able to differentiate into various tissue type such as skin, cartilage, cardiac tissue, nerves, muscle, and bone" [GOC:tfm, PMID:20942606] comment: Not clear to me if amniotic stem cell is a different cell type from amnion mesenchymal stem cells. They are treated as distinct in the literature as isolations methods are different, so I will keep them as separate terms for now. +subset: human_subset +subset: mouse_subset is_a: CL:0000134 ! mesenchymal stem cell is_a: CL:0002323 ! amniocyte property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 @@ -23286,6 +26216,8 @@ creation_date: 2011-06-21T03:55:39Z id: CL:0002640 name: amniotic epithelial stem cell def: "An epithelial fate stem cell derived form the amnion membrane." [GOC:tfm, PMID:20446274] +subset: human_subset +subset: mouse_subset is_a: CL:0000036 ! epithelial fate stem cell property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-06-21T04:06:17Z @@ -23294,6 +26226,8 @@ creation_date: 2011-06-21T04:06:17Z id: CL:0002641 name: epithelial cell of esophageal gland proper def: "An epithelial cell of the esophageal gland proper." [GOC:tfm] +subset: human_subset +subset: mouse_subset xref: FMA:256141 is_a: CL:0002657 ! glandular cell of esophagus property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 @@ -23303,6 +26237,8 @@ creation_date: 2011-07-08T02:16:51Z id: CL:0002642 name: epithelial cell of esophageal cardiac gland def: "An epithelial cell of the esophageal cardiac gland that occurs both in the proximal and distal esophagus, within the lamina propia." [GOC:tfm, http://web.mac.com/wjkrause/iWeb/Histology/Blog/E3FA5916-1AA9-4885-B579-5051838D98CB.html] +subset: human_subset +subset: mouse_subset xref: FMA:256143 is_a: CL:0002657 ! glandular cell of esophagus property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 @@ -23312,6 +26248,8 @@ creation_date: 2011-07-08T02:16:54Z id: CL:0002643 name: nonkeratinized cell of stratum corneum of esophageal epithelium def: "An epithelial cell of stratum corneum of esophageal epithelium that lacks keratin." [GOC:tfm] +subset: human_subset +subset: mouse_subset xref: FMA:263148 is_a: CL:0002654 ! epithelial cell of stratum corneum of esophageal epithelium property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 @@ -23321,6 +26259,8 @@ creation_date: 2011-07-08T02:22:09Z id: CL:0002644 name: endo-epithelial cell of tympanic part of viscerocranial mucosa def: "An endothelial cell of viscerocranial mucosa that is part of the tympanic region of the viscerocranial mucosa." [GOC:tfm] +subset: human_subset +subset: mouse_subset xref: FMA:70628 is_a: CL:0002261 ! endothelial cell of viscerocranial mucosa property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 @@ -23330,6 +26270,8 @@ creation_date: 2011-07-08T02:25:44Z id: CL:0002645 name: endo-epithelial cell of pharyngotympanic part of viscerocranial mucosa def: "An endocranial viscerocranial mucosa cell that is part of viscerocranial mucosa." [GOC:tfm] +subset: human_subset +subset: mouse_subset xref: FMA:70629 is_a: CL:0002261 ! endothelial cell of viscerocranial mucosa property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 @@ -23384,6 +26326,8 @@ creation_date: 2011-07-08T02:38:18Z id: CL:0002651 name: endothelial cell of venous sinus of spleen def: "An endothelial cell that is part of the venous sinus of spleen. This endothelial cell has an elongated, spindle-shaped, flattened morphology that is parallel to long axis of sinus. This cell type rests on a basement membrane interrupted by numerous narrow slits." [GOC:tfm] +subset: human_subset +subset: mouse_subset synonym: "stave cell" EXACT [FMA:62817] xref: FMA:72140 is_a: CL:0002262 ! endothelial cell of sinusoid @@ -23396,6 +26340,8 @@ name: endothelial cell of high endothelial venule def: "A venule endothelial cell that is cubodial, expresses leukocyte-specific receptors, and allows for passage of lymphocytes into bloodstream." [GOC:tfm, PMID:20726857] comment: Markers expressed on HEV include: MAdCAM-1,PNAd (sulfated and glycosylated molecules, i.e. GlyCAM-1, CD34, endomucin, nepmucin), ICAM-1, ICAM-2,Fuc-TVII, beta 3GlcNAcT-3, GlcNAc6ST2,CCL21, CCL19, CXCL13, CXCL12, Autotaxin, DARC, angiomodulin, LRHG. subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "endothelial cell of postcapillary venule of lymph node" BROAD [] synonym: "HEV cell" EXACT [] xref: FMA:67759 @@ -23411,6 +26357,8 @@ creation_date: 2011-07-08T03:14:10Z id: CL:0002653 name: squamous endothelial cell def: "A squamous shaped endothelial cell." [GOC:dos] +subset: human_subset +subset: mouse_subset is_a: CL:0000115 ! endothelial cell property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-07-08T03:31:25Z @@ -23419,6 +26367,8 @@ creation_date: 2011-07-08T03:31:25Z id: CL:0002654 name: epithelial cell of stratum corneum of esophageal epithelium def: "An epithelial cell of stratum corneum of esophageal epithelium." [GOC:tfm] +subset: human_subset +subset: mouse_subset xref: FMA:70733 is_a: CL:0002252 ! epithelial cell of esophagus property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 @@ -23428,6 +26378,8 @@ creation_date: 2011-07-08T03:46:35Z id: CL:0002655 name: epithelial cell of stratum spinosum of esophageal epithelium def: "An epithelial cell of stratum spinosum of esophageal epithelium." [GOC:tfm] +subset: human_subset +subset: mouse_subset xref: FMA:70732 is_a: CL:0002252 ! epithelial cell of esophagus property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 @@ -23435,14 +26387,20 @@ creation_date: 2011-07-08T03:48:26Z [Term] id: CL:0002656 -name: glandular cell of endometrium -def: "A glandular epithelial cell of the endometrium." [GOC:tfm] +name: glandular endometrial unciliated epithelial cell +def: "A glandular epithelial cell of the endometrium. Following ovulation, these cells secrete a glycogen-rich substance known as histotroph or uterine milk, which nourishes the embryo if implantation occurs." [GOC:tfm, PMID:25023676] +subset: human_subset +subset: mouse_subset +synonym: "glandular cell of endometrium" BROAD [] xref: FMA:86489 -is_a: CL:0002149 ! epithelial cell of uterus -is_a: CL:1001591 ! oviduct glandular cell -intersection_of: CL:0000150 ! glandular epithelial cell -intersection_of: part_of UBERON:0004811 ! endometrium epithelium -relationship: part_of UBERON:0004811 ! endometrium epithelium +is_a: CL:0000150 ! glandular secretory epithelial cell +is_a: CL:0000152 ! exocrine cell +is_a: CL:0009084 ! epithelial cell of endometrial gland +is_a: CL:1001591 ! oviduct secretory cell +intersection_of: CL:0000066 ! epithelial cell +intersection_of: capable_of GO:0032940 ! secretion by cell +intersection_of: part_of UBERON:0002451 ! endometrial gland +relationship: part_of UBERON:0002451 ! endometrial gland property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-07-08T03:54:08Z @@ -23451,11 +26409,13 @@ id: CL:0002657 name: glandular cell of esophagus def: "A glandular epithelial cell of the esophagus." [GOC:tfm] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset xref: FMA:86548 -is_a: CL:0000150 {is_inferred="true"} ! glandular epithelial cell +is_a: CL:0000150 {is_inferred="true"} ! glandular secretory epithelial cell is_a: CL:0002252 {is_inferred="true"} ! epithelial cell of esophagus -intersection_of: CL:0000150 ! glandular epithelial cell -intersection_of: part_of UBERON:0001043 ! esophagus +intersection_of: CL:0000150 ! glandular secretory epithelial cell +intersection_of: part_of UBERON:0001976 ! epithelium of esophagus property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-07-08T03:55:57Z @@ -23463,10 +26423,12 @@ creation_date: 2011-07-08T03:55:57Z id: CL:0002658 name: glandular cell of the large intestine def: "A glandular epithelial cell of the large intestine." [GOC:tfm] +subset: human_subset +subset: mouse_subset xref: FMA:87194 -is_a: CL:0000150 {is_inferred="true"} ! glandular epithelial cell +is_a: CL:0000150 {is_inferred="true"} ! glandular secretory epithelial cell is_a: CL:0002253 ! epithelial cell of large intestine -intersection_of: CL:0000150 ! glandular epithelial cell +intersection_of: CL:0000150 ! glandular secretory epithelial cell intersection_of: part_of UBERON:0000059 ! large intestine property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-07-08T04:03:01Z @@ -23475,13 +26437,15 @@ creation_date: 2011-07-08T04:03:01Z id: CL:0002659 name: glandular epithelial cell of stomach def: "A glandular epithelial cell that is part of the stomach." [GOC:tfm] +subset: human_subset +subset: mouse_subset synonym: "glandular cell of stomach" EXACT [] xref: CALOHA:TS-1284 xref: FMA:86554 -is_a: CL:0000150 ! glandular epithelial cell +is_a: CL:0000150 ! glandular secretory epithelial cell is_a: CL:0002178 ! epithelial cell of stomach -intersection_of: CL:0000150 ! glandular epithelial cell -intersection_of: part_of UBERON:0000945 ! stomach +intersection_of: CL:0000150 ! glandular secretory epithelial cell +intersection_of: part_of UBERON:0001276 ! epithelium of stomach property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-07-11T01:20:35Z @@ -23490,6 +26454,8 @@ id: CL:0002660 name: luminal cell of acinus of lactiferous gland def: "A luminal epithelial cell of mammary gland located in acinus of structure." [GOC:tfm] comment: Consider if synonymous with mammary alveolar cell CL:0002325. Some use this term to refer to the non-lactating cell type that gives rise to the lactating cell type. +subset: human_subset +subset: mouse_subset xref: FMA:74505 is_a: CL:0002326 ! luminal epithelial cell of mammary gland property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 @@ -23499,6 +26465,8 @@ creation_date: 2011-07-11T01:44:31Z id: CL:0002661 name: luminal cell of lactiferous terminal ductal lobular unit def: "A luminal cell of terminal ducts, i.e.e the terminal branch of a lactiferous duct which alveolar cells drain into." [GOC:tfm] +subset: human_subset +subset: mouse_subset xref: FMA:87168 is_a: CL:0002662 ! luminal cell of lactiferous duct property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 @@ -23508,6 +26476,8 @@ creation_date: 2011-07-11T01:44:33Z id: CL:0002662 name: luminal cell of lactiferous duct def: "A luminal epithelial cell of the lactiferous duct. This cuboidal epithelial cell expresses keratin-18 and is estrogen-receptor alpha positive." [GOC:tfm, PMID:19022771] +subset: human_subset +subset: mouse_subset xref: FMA:74504 is_a: CL:0002326 ! luminal epithelial cell of mammary gland property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 @@ -23517,6 +26487,8 @@ creation_date: 2011-07-11T01:44:48Z id: CL:0002663 name: myocardial endocrine cell of atrium def: "A myocardial endocrine cell that is part of the atrium." [GOC:tfm] +subset: human_subset +subset: mouse_subset xref: FMA:83389 is_a: CL:0002074 {is_inferred="true"} ! myocardial endocrine cell intersection_of: CL:0002074 ! myocardial endocrine cell @@ -23530,6 +26502,8 @@ id: CL:0002664 name: cardioblast def: "A stem cell that can give rise to multiple cell types (i.e. smooth muscle, endothelial) in the developing heart." [GOC:tfm, PMID:19745164] comment: Discrepancy in develops from origins prevents me from making the assertion that cardioblasts give rise to all instances of cardiocytes as we state cardiac muscle cells develop from cardiac myoblast, which in turn develop from muscle stem cell. +subset: human_subset +subset: mouse_subset synonym: "cardiovascular progenitor cell" EXACT [PMID:17519333, PMID:19745164] synonym: "CPC" RELATED OMO:0003000 [PMID:19745164] is_a: CL:0000048 ! multi fate stem cell @@ -23540,6 +26514,8 @@ creation_date: 2011-07-11T03:15:38Z id: CL:0002665 name: otic fibrocyte def: "A fibrocyte of the cochlea that has specialized structural and molecular adaptions." [GOC:tfm, PMID:18353863] +subset: human_subset +subset: mouse_subset is_a: CL:0000135 ! fibrocyte relationship: part_of UBERON:0006725 ! spiral ligament property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 @@ -23549,6 +26525,8 @@ creation_date: 2011-07-11T03:35:01Z id: CL:0002666 name: type 2 otic fibrocyte def: "An otic fibrocyte that underlies the spiral prominence and is part of a mesenchymal gap junction network that regulates ionic homeostasis of the endolymph." [GOC:tfm, PMID:18353863] +subset: human_subset +subset: mouse_subset synonym: "type II otic fibrocyte" EXACT [] synonym: "type II spiral ligament fibrocyte" EXACT [MP:0004488] is_a: CL:0002665 ! otic fibrocyte @@ -23559,6 +26537,8 @@ creation_date: 2011-07-11T03:40:40Z id: CL:0002667 name: type 5 otic fibrocyte def: "An otic fibrocyte that resides above the stria vasularis and is part of a mesenchymal gap junction network that regulates ionic homeostasis of the endolymph." [GOC:tfm, PMID:18353863] +subset: human_subset +subset: mouse_subset synonym: "type V otic fibrocyte" EXACT [] synonym: "type V spiral ligament fibrocyte" EXACT [] is_a: CL:0002665 ! otic fibrocyte @@ -23569,6 +26549,8 @@ creation_date: 2011-07-11T03:40:42Z id: CL:0002668 name: type 4 otic fibrocyte def: "An otic fibrocyte that is lateral to the basilar membrane and anchoris it to the lateral wall." [GOC:tfm, PMID:18353863] +subset: human_subset +subset: mouse_subset synonym: "type IV otic fibrocyte" EXACT [] synonym: "type IV spiral ligament fibrocyte" EXACT [MP:0004490] is_a: CL:0002665 ! otic fibrocyte @@ -23579,6 +26561,8 @@ creation_date: 2011-07-11T03:40:46Z id: CL:0002669 name: type 3 otic fibrocyte def: "An otic fibrocyte that lines the otic capsule." [GOC:tfm, PMID:18353863] +subset: human_subset +subset: mouse_subset synonym: "type III otic fibrocyte" EXACT [] synonym: "type III spiral ligament fibrocyte" EXACT [MP:0004489] is_a: CL:0002665 ! otic fibrocyte @@ -23589,6 +26573,8 @@ creation_date: 2011-07-11T03:40:50Z id: CL:0002670 name: type 1 otic fibrocyte def: "An otic fibrocyte that underlies the stria vascularis and is part of a mesenchymal gap junction network that regulates ionic homeostasis of the endolymph." [GOC:tfm, PMID:18353863] +subset: human_subset +subset: mouse_subset synonym: "type I otic fibrocyte" EXACT [] synonym: "type I spiral ligament fibrocyte" EXACT [MP:0004487] is_a: CL:0002665 ! otic fibrocyte @@ -23600,16 +26586,21 @@ id: CL:0002671 name: endothelial stalk cell def: "An endothelial stalk cell is a specialized endothelial cell that follows behind the tip cell of an angiogenic sprout." [GOC:tfm, PMID:21521739] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset xref: https://cellxgene.cziscience.com/cellguide/CL_0002671 is_a: CL:0000071 ! blood vessel endothelial cell property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 -property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional.\n\nEndothelial stalk cells are specialized vascular cells vital in angiogenesis, a process through which new blood vessels are formed from pre-existing ones; specifically, endothelial stalk cells are involved in sprouting angiogenesis, where they help form the body of new blood vessels. \nVascular sprouting relies on the coordinated activity of migrating endothelial tip cells at the forefront and proliferating stalk cells that elongate the sprout. The process is tightly controlled by different growths factors: Vascular Endothelial Growth Factor acts on endothelial cells, inducing them to become endothelial tip cells that initiate sprouting. After sprouting initiation, activation of Notch signaling suppresses differentiation toward a tip cell phenotype and some of the endothelial cells differentiate into stalk cells, which follow tip cells, multiply, and elongate to provide a structural backbone to the growing vessel sprout. \nIn contrast to endothelial tip cells, which migrate and lead the angiogenic sprout, endothelial stalk cells behind the sprouts continue forming the tube or lumen for blood flow and facilitate maturation and stability of the new vessel. The delicate balance between the activities of stalk and tip cells during angiogenesis is crucial to build a functional vascular network. Dysfunctions in endothelial stalk cells can lead to pathological conditions such as impaired wound healing, unregulated tumor growth, and metastasis due to abnormal angiogenesis." xsd:string {xref="DOI:10.1007/s12079-019-00511-z", xref="DOI:10.1016/j.cmet.2013.08.001", xref="DOI:10.1101/cshperspect.a006569", xref="DOI:10.3389/fcell.2021.642352"} +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nEndothelial stalk cells are specialized vascular cells vital in angiogenesis, a process through which new blood vessels are formed from pre-existing ones; specifically, endothelial stalk cells are involved in sprouting angiogenesis, where they help form the body of new blood vessels. \nVascular sprouting relies on the coordinated activity of migrating endothelial tip cells at the forefront and proliferating stalk cells that elongate the sprout. The process is tightly controlled by different growths factors: Vascular Endothelial Growth Factor acts on endothelial cells, inducing them to become endothelial tip cells that initiate sprouting. After sprouting initiation, activation of Notch signaling suppresses differentiation toward a tip cell phenotype and some of the endothelial cells differentiate into stalk cells, which follow tip cells, multiply, and elongate to provide a structural backbone to the growing vessel sprout. \nIn contrast to endothelial tip cells, which migrate and lead the angiogenic sprout, endothelial stalk cells behind the sprouts continue forming the tube or lumen for blood flow and facilitate maturation and stability of the new vessel. The delicate balance between the activities of stalk and tip cells during angiogenesis is crucial to build a functional vascular network. Dysfunctions in endothelial stalk cells can lead to pathological conditions such as impaired wound healing, unregulated tumor growth, and metastasis due to abnormal angiogenesis." xsd:string {xref="DOI:10.1007/s12079-019-00511-z", xref="DOI:10.1016/j.cmet.2013.08.001", xref="DOI:10.1101/cshperspect.a006569", xref="DOI:10.3389/fcell.2021.642352"} creation_date: 2011-08-16T01:49:32Z [Term] id: CL:0002672 name: retinal progenitor cell def: "A multi-fate stem cell that can give rise to different retinal cell types including rod and cone cells." [GOC:tfm, PMID:20959166, PMID:21148186] +subset: cellxgene_subset +subset: human_subset +subset: mouse_subset is_a: BFO:0000002 is_a: CL:0000048 ! multi fate stem cell relationship: RO:0002202 CL:0000133 ! develops from neurectodermal cell @@ -23621,11 +26612,15 @@ id: CL:0002673 name: tongue muscle cell def: "A skeletal muscle cell that is part of the tongue." [GOC:tfm, PMID:18816858] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset +xref: https://cellxgene.cziscience.com/cellguide/CL_0002673 is_a: CL:0008002 ! skeletal muscle fiber intersection_of: CL:0008002 ! skeletal muscle fiber intersection_of: part_of UBERON:0000378 ! tongue muscle relationship: part_of UBERON:0000378 ! tongue muscle property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nTongue muscle cells are responsible for essential functions like mastication, deglutition (swallowing), phonation (speech), and taste receptivity. They can be classified into two functional classes - extrinsic and intrinsic muscle cells. \nThe extrinsic tongue muscle cells originate outside the tongue and are primarily involved in determining the position of the tongue within the mouth. Muscle groups such as the genioglossus, hyoglossus, and styloglossus are composed of these extrinsic muscle cells and grant the tongue its wide range of motion.\nThe intrinsic tongue muscle cells, on the other hand, originate and function within the tongue itself, influencing the shape of the tongue during speech, eating, and swallowing. These cells can contract to alter the tongue's shape, making it long, short, curled, or flat, as needed. Together, these two types of muscle cells allow the tongue to perform its vital functions effectively. Moreover, they play a critical role in maintaining oral health by facilitating physical cleaning of the oral cavity and assisting in the mechanical breakdown of food." xsd:string {xref="DOI:10.1002/ca.21011", xref="https://www.ncbi.nlm.nih.gov/books/NBK507782/", xref="https://www.ncbi.nlm.nih.gov/books/NBK554405/"} creation_date: 2011-08-16T03:10:02Z [Term] @@ -23651,6 +26646,8 @@ creation_date: 2011-08-16T03:20:58Z id: CL:0002676 name: neural crest derived neuroblast def: "A neuroblast derived from a neural crest cell." [GOC:tfm, PMID:17407019] +subset: human_subset +subset: mouse_subset is_a: CL:0000031 ! neuroblast (sensu Vertebrata) is_a: CL:0011026 ! progenitor cell relationship: RO:0002202 CL:0000333 ! develops from migratory neural crest cell @@ -23664,6 +26661,8 @@ def: "A regulatory T cell that has not encountered antigen." [GOC:tfm] comment: This cell type has been described as CD45RA-negative, but this doesn't fit with our current definition of naive T cell. subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "naive regulatory T lymphocyte" EXACT [] synonym: "naive regulatory T-cell" EXACT [] synonym: "naive regulatory T-lymphocyte" EXACT [] @@ -23679,6 +26678,8 @@ name: memory regulatory T cell def: "A CD4-positive, CD25-positive alpha-beta regulatory T cell that has encountered antigen." [GOC:tfm, PMID:21739668] comment: Cell has been described as being CD45RA-positive in human, but this doesn't fit with our current definition memory T cell. subset: cellxgene_subset +subset: human_subset +subset: mouse_subset is_a: CL:0000792 ! CD4-positive, CD25-positive, alpha-beta regulatory T cell is_a: CL:0000897 ! CD4-positive, alpha-beta memory T cell intersection_of: CL:0000792 ! CD4-positive, CD25-positive, alpha-beta regulatory T cell @@ -23691,8 +26692,9 @@ id: CL:0002679 name: natural helper lymphocyte def: "A lymphocyte found in adipose tissue that lacks lineage markers of other lymphocytes but is capable of mediating TH2 cytokine responses. This cell type is found in fat associated lymphoid clusters, proliferates in response to IL2 and produce large amounts of TH2 cytokines such as IL5, IL6 and IL13" [GOC:tfm, PMID:20023630] subset: blood_and_immune_upper_slim +subset: human_subset +subset: mouse_subset is_a: CL:0000542 {is_inferred="true"} ! lymphocyte -is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000542 ! lymphocyte intersection_of: CL:4030046 GO:0042105 ! lacks_plasma_membrane_part alpha-beta T cell receptor complex intersection_of: CL:4030046 PR:000001002 ! lacks_plasma_membrane_part CD19 molecule @@ -23721,10 +26723,12 @@ creation_date: 2011-08-29T10:08:02Z id: CL:0002680 name: PP cell of intestine def: "A PP cell found in intestine." [GOC:tfm, PMID:2420136, PMID:728970] +subset: human_subset +subset: mouse_subset is_a: CL:0000696 {is_inferred="true"} ! PP cell is_a: CL:1001516 ! intestinal enteroendocrine cell intersection_of: CL:0000696 ! PP cell -intersection_of: part_of UBERON:0000160 ! intestine +intersection_of: part_of UBERON:0001277 ! intestinal epithelium property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-09-27T11:59:01Z @@ -23732,6 +26736,8 @@ creation_date: 2011-09-27T11:59:01Z id: CL:0002681 name: kidney cortical cell def: "A cell that is part of a cortex of kidney." [] +subset: human_subset +subset: mouse_subset is_a: CL:1000497 ! kidney cell intersection_of: CL:1000497 ! kidney cell intersection_of: part_of UBERON:0001225 ! cortex of kidney @@ -23744,6 +26750,9 @@ id: CL:0003001 name: bistratified retinal ganglion cell namespace: cell def: "A retinal ganglion cell that has dendrites stratified in two layers of the inner-plexiform layer." [] +subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "retinal ganglion D cell" EXACT [] is_a: CL:0000740 ! retinal ganglion cell is_a: CL:0004247 ! bistratified cell @@ -23757,6 +26766,8 @@ id: CL:0003002 name: G1 retinal ganglion cell namespace: cell def: "A retinal ganglion cell that has a small dendritic field and a medium dendritic arbor with post sympatic terminals in sublaminar layer S3." [PMID:11978858] +subset: human_subset +subset: mouse_subset is_a: CL:0000740 ! retinal ganglion cell relationship: RO:0013001 UBERON:0008924 ! has synaptic IO in region sublaminar layer S3 property_value: terms:contributor "https://orcid.org/0000-0001-7258-9596" xsd:string @@ -23767,6 +26778,8 @@ id: CL:0003003 name: G2 retinal ganglion cell namespace: cell def: "A mono-stratified retinal ganglion cell that has a small dendritic field and a sparse dendritic arbor with post sympatic terminals in sublaminar layer S3." [PMID:11978858] +subset: human_subset +subset: mouse_subset is_a: CL:0000740 ! retinal ganglion cell relationship: bearer_of PATO:0070063 ! monostratified dendrite cell morphology relationship: RO:0013001 UBERON:0008924 ! has synaptic IO in region sublaminar layer S3 @@ -23779,6 +26792,8 @@ name: G3 retinal ganglion cell namespace: cell def: "A bistratified retinal ganglion cell that has a small dendritic field with sparse density that terminates at the intersection of the S4-S5 sublaminar level, and a second dendrite field that is medium in size and degree of arborization that terminates in sublaminar layer S2." [PMID:11978858] comment: is_a bistratified retinal ganglion cell S4-S5 dendrite field having (small dendritic field, sparse density) and second dendrite field having (medium, meduim) +subset: human_subset +subset: mouse_subset is_a: CL:0003001 ! bistratified retinal ganglion cell relationship: RO:0013001 UBERON:0008923 ! has synaptic IO in region sublaminar layer S2 relationship: RO:0013001 UBERON:0008925 ! has synaptic IO in region sublaminar layer S4 @@ -23792,6 +26807,8 @@ name: G4 retinal ganglion cell namespace: cell def: "A mono-stratified retinal ganglion cell that has a small dendritic field and dense dendritic arbor." [] comment: Masland nomenclature PMID:11978858 +subset: human_subset +subset: mouse_subset is_a: CL:0000740 ! retinal ganglion cell relationship: bearer_of PATO:0070063 ! monostratified dendrite cell morphology property_value: terms:contributor "https://orcid.org/0000-0001-7258-9596" xsd:string @@ -23802,6 +26819,8 @@ id: CL:0003006 name: G4-ON retinal ganglion cell namespace: cell def: "A G4 retinal ganglion cell that has post sympatic terminals in sublaminar layers S3 and S4 and is depolarized by illumination of its receptive field center." [PMID:11978858] +subset: human_subset +subset: mouse_subset is_a: CL:0003005 ! G4 retinal ganglion cell is_a: CL:4023032 ! ON retinal ganglion cell relationship: RO:0013001 UBERON:0008924 ! has synaptic IO in region sublaminar layer S3 @@ -23815,6 +26834,8 @@ name: G4-OFF retinal ganglion cell namespace: cell def: "A G4 retinal ganglion cell that has post sympatic terminals in sublaminar layers S2 and S3 and is depolarized by decreased illumination of their receptive field center" [] comment: Masland nomenclature PMID:11978858 +subset: human_subset +subset: mouse_subset is_a: CL:0003005 ! G4 retinal ganglion cell is_a: CL:4023033 ! OFF retinal ganglion cell relationship: RO:0013001 UBERON:0008923 ! has synaptic IO in region sublaminar layer S2 @@ -23827,6 +26848,8 @@ id: CL:0003008 name: G5 retinal ganglion cell namespace: cell def: "A mono-stratified retinal ganglion cell that has a medium dendritic field and a medium dendritic arbor with post sympatic terminals in sublaminar layer S2." [PMID:11978858] +subset: human_subset +subset: mouse_subset is_a: CL:0000740 ! retinal ganglion cell relationship: bearer_of PATO:0070063 ! monostratified dendrite cell morphology relationship: RO:0013001 UBERON:0008923 ! has synaptic IO in region sublaminar layer S2 @@ -23838,6 +26861,8 @@ id: CL:0003009 name: G6 retinal ganglion cell namespace: cell def: "A mono-stratified retinal ganglion cell that has a medium dendritic field and a sparse dendritic arbor with post sympatic terminals in sublaminar layer S4 and S5." [PMID:11978858] +subset: human_subset +subset: mouse_subset is_a: CL:0000740 ! retinal ganglion cell relationship: bearer_of PATO:0070063 ! monostratified dendrite cell morphology relationship: RO:0013001 UBERON:0008925 ! has synaptic IO in region sublaminar layer S4 @@ -23850,6 +26875,8 @@ id: CL:0003010 name: G7 retinal ganglion cell namespace: cell def: "A bistratified retinal ganglion cell that has a dendrite field that terminates in sublaminar layer S2 and a second dendrite field that terminates in sublaminar layer S4." [PMID:11978858] +subset: human_subset +subset: mouse_subset synonym: "ON-OFF DS" EXACT [] is_a: CL:0003001 ! bistratified retinal ganglion cell relationship: RO:0013001 UBERON:0008923 ! has synaptic IO in region sublaminar layer S2 @@ -23862,6 +26889,8 @@ id: CL:0003011 name: G8 retinal ganglion cell namespace: cell def: "A mono-stratified retinal ganglion cell that has a large dendritic field and a sparse dendritic arbor with post synaptic terminals in sublaminar layer S4." [PMID:11978858] +subset: human_subset +subset: mouse_subset is_a: CL:0000740 ! retinal ganglion cell relationship: bearer_of PATO:0070063 ! monostratified dendrite cell morphology relationship: RO:0013001 UBERON:0008925 ! has synaptic IO in region sublaminar layer S4 @@ -23873,6 +26902,8 @@ id: CL:0003012 name: G9 retinal ganglion cell namespace: cell def: "A mono-stratified retinal ganglion cell that has a large dendritic field and a medium dendritic arbor with post synaptic terminals in sublaminar layer S1 and S2." [PMID:11978858] +subset: human_subset +subset: mouse_subset is_a: CL:0000740 ! retinal ganglion cell relationship: bearer_of PATO:0070063 ! monostratified dendrite cell morphology relationship: RO:0013001 UBERON:0008922 ! has synaptic IO in region sublaminar layer S1 @@ -23886,6 +26917,8 @@ name: G10 retinal ganglion cell namespace: cell def: "A mono-stratified retinal ganglion cell that has a large dendritic field, a medium dendritic arbor, and a long secondary dendrite shaft with post synaptic terminals in sublaminar layer S4." [PMID:11978858] comment: Capable of ON directional sensitivity. +subset: human_subset +subset: mouse_subset xref: https://orcid.org/0000-0001-7258-9596 xref: https://orcid.org/0000-0002-5260-9315 is_a: CL:0000740 ! retinal ganglion cell @@ -23898,6 +26931,8 @@ name: G11 retinal ganglion cell namespace: cell def: "A mono-stratified retinal ganglion cell that has a large dendritic field, a medium dendritic arbor, and a medium length secondary dendrite shaft." [PMID:11978858] comment: Is capable of brisk transient currents. +subset: human_subset +subset: mouse_subset xref: https://orcid.org/0000-0001-7258-9596 xref: https://orcid.org/0000-0002-5260-9315 is_a: CL:0000740 ! retinal ganglion cell @@ -23908,6 +26943,8 @@ id: CL:0003015 name: G11-ON retinal ganglion cell namespace: cell def: "A G11 retinal ganglion cell that has post synaptic terminals in sublaminar layer S4 and is depolarized by illumination of its receptive field center." [PMID:11978858] +subset: human_subset +subset: mouse_subset xref: https://orcid.org/0000-0001-7258-9596 xref: https://orcid.org/0000-0002-5260-9315 is_a: CL:0003014 ! G11 retinal ganglion cell @@ -23919,6 +26956,8 @@ id: CL:0003016 name: G11-OFF retinal ganglion cell namespace: cell def: "A G11 retinal ganglion cell that has post synaptic terminals in sublaminar layer S2 and is depolarized by decreased illumination of their receptive field center" [PMID:11978858] +subset: human_subset +subset: mouse_subset xref: https://orcid.org/0000-0001-7258-9596 xref: https://orcid.org/0000-0002-5260-9315 is_a: CL:0003014 ! G11 retinal ganglion cell @@ -23930,6 +26969,8 @@ id: CL:0003017 name: retinal ganglion cell B3 outer namespace: cell def: "A retinal ganglion B cell that has post synaptic terminals in S2." [PMID:12209831] +subset: human_subset +subset: mouse_subset is_a: CL:0004183 ! retinal ganglion cell B3 relationship: RO:0013001 UBERON:0008923 ! has synaptic IO in region sublaminar layer S2 property_value: terms:contributor "https://orcid.org/0000-0001-7258-9596" xsd:string @@ -23940,6 +26981,8 @@ id: CL:0003018 name: retinal ganglion cell B3 inner namespace: cell def: "A retinal ganglion B3 cell with dentrites terminating in S4." [PMID:12209831] +subset: human_subset +subset: mouse_subset xref: BAMS:1010 is_a: CL:0004183 ! retinal ganglion cell B3 relationship: RO:0013001 UBERON:0008925 ! has synaptic IO in region sublaminar layer S4 @@ -23951,6 +26994,8 @@ id: CL:0003020 name: retinal ganglion cell C outer namespace: cell def: "A retinal ganglion cell C that has post-synaptic terminals in S2." [PMID:12209831] +subset: human_subset +subset: mouse_subset is_a: CL:0004116 ! retinal ganglion cell C relationship: RO:0013001 UBERON:0008923 ! has synaptic IO in region sublaminar layer S2 property_value: terms:contributor "https://orcid.org/0000-0001-7258-9596" xsd:string @@ -23961,6 +27006,8 @@ id: CL:0003021 name: retinal ganglion cell C4 namespace: cell def: "A retinal ganglion cell C outer that has a medium dendritic field and a dense dendritic arbor." [PMID:12209831] +subset: human_subset +subset: mouse_subset is_a: CL:0003020 ! retinal ganglion cell C outer property_value: terms:contributor "https://orcid.org/0000-0001-7258-9596" xsd:string property_value: terms:contributor "https://orcid.org/0000-0002-5260-9315" xsd:string @@ -23970,6 +27017,8 @@ id: CL:0003022 name: retinal ganglion cell C5 namespace: cell def: "A retinal ganglion cell C outer that has medium dendritic density and field size." [PMID:12209831] +subset: human_subset +subset: mouse_subset is_a: CL:0003020 ! retinal ganglion cell C outer property_value: terms:contributor "https://orcid.org/0000-0001-7258-9596" xsd:string property_value: terms:contributor "https://orcid.org/0000-0002-5260-9315" xsd:string @@ -23979,6 +27028,8 @@ id: CL:0003023 name: retinal ganglion cell C6 namespace: cell def: "A retinal ganglion cell C outer that has dense dendritic diversity." [PMID:12209831] +subset: human_subset +subset: mouse_subset is_a: CL:0003020 ! retinal ganglion cell C outer property_value: terms:contributor "https://orcid.org/0000-0001-7258-9596" xsd:string property_value: terms:contributor "https://orcid.org/0000-0002-5260-9315" xsd:string @@ -23988,6 +27039,8 @@ id: CL:0003024 name: retinal ganglion cell C inner namespace: cell def: "A retinal ganglion cell C with medium cell bodies and large dendritic field." [PMID:12209831] +subset: human_subset +subset: mouse_subset is_a: CL:0004116 ! retinal ganglion cell C relationship: RO:0013001 UBERON:0008925 ! has synaptic IO in region sublaminar layer S4 property_value: terms:contributor "https://orcid.org/0000-0001-7258-9596" xsd:string @@ -23998,6 +27051,8 @@ id: CL:0003025 name: retinal ganglion cell C3 namespace: cell def: "A retinal ganglion cell C inner that has sparse dendritic density, and large dendritic field." [PMID:12209831] +subset: human_subset +subset: mouse_subset synonym: "epsilon" RELATED [] is_a: CL:0003024 ! retinal ganglion cell C inner property_value: terms:contributor "https://orcid.org/0000-0001-7258-9596" xsd:string @@ -24008,6 +27063,8 @@ id: CL:0003026 name: retinal ganglion cell D1 namespace: cell def: "A bistratified retinal ganglion cell that has a small dendrite fields with a sparse dendrite arbor terminating in S2 and S3." [PMID:12209831] +subset: human_subset +subset: mouse_subset is_a: CL:0003001 ! bistratified retinal ganglion cell relationship: RO:0013001 UBERON:0008923 ! has synaptic IO in region sublaminar layer S2 relationship: RO:0013001 UBERON:0008924 ! has synaptic IO in region sublaminar layer S3 @@ -24019,6 +27076,8 @@ id: CL:0003027 name: retinal ganglion cell D2 namespace: cell def: "A bistratified retinal ganglion cell D cell that has medium dendritic arbor and a large dendritic field that terminates in S2 and S4." [PMID:12209831] +subset: human_subset +subset: mouse_subset synonym: "iota cell" RELATED [] synonym: "ON-OFF direction selective" RELATED [] is_a: CL:0003001 ! bistratified retinal ganglion cell @@ -24032,6 +27091,8 @@ id: CL:0003028 name: M1 retinal ganglion cell namespace: cell def: "A monostratified retinal ganglion cell that has a small dendrite field with a dense dendrite arbor with post synaptic terminals in sublaminer layer S4." [PMID:16626866] +subset: human_subset +subset: mouse_subset is_a: CL:0000740 ! retinal ganglion cell relationship: bearer_of PATO:0070063 ! monostratified dendrite cell morphology relationship: RO:0013001 UBERON:0008925 ! has synaptic IO in region sublaminar layer S4 @@ -24043,6 +27104,8 @@ id: CL:0003029 name: M2 retinal ganglion cell namespace: cell def: "A monostratified retinal ganglion cell that has a small soma, a small dendrite field with a dense dendrite arbor, and post synaptic terminals in sublaminer layer S2 and S3." [PMID:16626866] +subset: human_subset +subset: mouse_subset is_a: CL:0000740 ! retinal ganglion cell relationship: bearer_of PATO:0070063 ! monostratified dendrite cell morphology relationship: RO:0013001 UBERON:0008923 ! has synaptic IO in region sublaminar layer S2 @@ -24055,6 +27118,8 @@ id: CL:0003030 name: M3 retinal ganglion cell namespace: cell def: "A monostratified retinal ganglion cell that has a medium soma and a small dendrite field." [PMID:16626866] +subset: human_subset +subset: mouse_subset is_a: CL:0000740 ! retinal ganglion cell relationship: bearer_of PATO:0070063 ! monostratified dendrite cell morphology property_value: terms:contributor "https://orcid.org/0000-0001-7258-9596" xsd:string @@ -24065,6 +27130,8 @@ id: CL:0003031 name: M3-ON retinal ganglion cell namespace: cell def: "A monostratified retinal ganglion cell that has post synaptic terminals in sublaminar layer S4 and is depolarized by illumination of its receptive field center." [PMID:16626866] +subset: human_subset +subset: mouse_subset is_a: CL:0003030 ! M3 retinal ganglion cell is_a: CL:4023032 ! ON retinal ganglion cell relationship: RO:0013001 UBERON:0008925 ! has synaptic IO in region sublaminar layer S4 @@ -24076,6 +27143,8 @@ id: CL:0003032 name: M3-OFF retinal ganglion cell namespace: cell def: "A monostratified retinal ganglion cell that has post synaptic terminals in sublaminar layer S2 and is depolarized by decreased illumination of their receptive field center" [PMID:16626866] +subset: human_subset +subset: mouse_subset is_a: CL:0003030 ! M3 retinal ganglion cell is_a: CL:4023033 ! OFF retinal ganglion cell relationship: RO:0013001 UBERON:0008923 ! has synaptic IO in region sublaminar layer S2 @@ -24087,6 +27156,8 @@ id: CL:0003033 name: M4 retinal ganglion cell namespace: cell def: "A monostratified retinal ganglion cell that has a large soma, a medium dendritic field with post synaptic terminals in sublaminar layer S3." [PMID:16626866] +subset: human_subset +subset: mouse_subset is_a: CL:0000740 ! retinal ganglion cell relationship: bearer_of PATO:0070063 ! monostratified dendrite cell morphology relationship: RO:0013001 UBERON:0008924 ! has synaptic IO in region sublaminar layer S3 @@ -24098,6 +27169,8 @@ id: CL:0003034 name: M5 retinal ganglion cell namespace: cell def: "A monostratified retinal ganglion cell that has a small soma, an assymetric dendritic field with post synaptic terminals in sublaminar layer S3." [PMID:16626866] +subset: human_subset +subset: mouse_subset is_a: CL:0000740 ! retinal ganglion cell relationship: bearer_of PATO:0070063 ! monostratified dendrite cell morphology relationship: RO:0013001 UBERON:0008924 ! has synaptic IO in region sublaminar layer S3 @@ -24109,6 +27182,9 @@ id: CL:0003035 name: M6 retinal ganglion cell namespace: cell def: "A monostratified retinal ganglion cell that contains opsin." [PMID:16626866] +subset: human_subset +subset: mouse_subset +is_a: BFO:0000002 is_a: CL:0000740 ! retinal ganglion cell relationship: bearer_of PATO:0070063 ! monostratified dendrite cell morphology relationship: RO:0002292 PR:000001243 ! expresses melanopsin @@ -24120,6 +27196,8 @@ id: CL:0003036 name: M7 retinal ganglion cell namespace: cell def: "A monostratified retinal ganglion cell with large soma and large dendritic field, with medium dendritic arbor, and has dendrites in layers 2 and 5." [PMID:16626866] +subset: human_subset +subset: mouse_subset is_a: CL:0000740 ! retinal ganglion cell relationship: bearer_of PATO:0070063 ! monostratified dendrite cell morphology property_value: terms:contributor "https://orcid.org/0000-0001-7258-9596" xsd:string @@ -24130,6 +27208,8 @@ id: CL:0003037 name: M7-ON retinal ganglion cell namespace: cell def: "An M7 retinal ganglion cells with synaptic terminals in S4 and is depolarized by illumination of its receptive field center." [PMID:16626866] +subset: human_subset +subset: mouse_subset is_a: CL:0003036 ! M7 retinal ganglion cell is_a: CL:4023032 ! ON retinal ganglion cell relationship: RO:0013001 UBERON:0008925 ! has synaptic IO in region sublaminar layer S4 @@ -24141,6 +27221,8 @@ id: CL:0003038 name: M7-OFF retinal ganglion cell namespace: cell def: "An M7 retinal ganglion cells with synaptic terminals in S2 and is depolarized by decreased illumination of their receptive field center" [PMID:16626866] +subset: human_subset +subset: mouse_subset is_a: CL:0003036 ! M7 retinal ganglion cell is_a: CL:4023033 ! OFF retinal ganglion cell relationship: RO:0013001 UBERON:0008923 ! has synaptic IO in region sublaminar layer S2 @@ -24152,6 +27234,8 @@ id: CL:0003039 name: M8 retinal ganglion cell namespace: cell def: "A monostratified retinal ganglion cell with large soma and medium dendritic field, with dense dendritic arbor." [PMID:16626866] +subset: human_subset +subset: mouse_subset is_a: CL:0000740 ! retinal ganglion cell relationship: bearer_of PATO:0070063 ! monostratified dendrite cell morphology property_value: terms:contributor "https://orcid.org/0000-0001-7258-9596" xsd:string @@ -24162,6 +27246,8 @@ id: CL:0003040 name: M9 retinal ganglion cell namespace: cell def: "A monostratified retinal ganglion cell with large soma and large dendritic field, with medium dendritic arbor, and has dendrites in layers 1 and 5." [PMID:16626866] +subset: human_subset +subset: mouse_subset is_a: CL:0000740 ! retinal ganglion cell relationship: bearer_of PATO:0070063 ! monostratified dendrite cell morphology property_value: terms:contributor "https://orcid.org/0000-0001-7258-9596" xsd:string @@ -24172,6 +27258,8 @@ id: CL:0003041 name: M9-ON retinal ganglion cell namespace: cell def: "An M9 retinal ganglion cells with synaptic terminals in S2 and is depolarized by illumination of its receptive field center." [PMID:16626866] +subset: human_subset +subset: mouse_subset is_a: CL:0003040 ! M9 retinal ganglion cell is_a: CL:4023032 ! ON retinal ganglion cell relationship: RO:0013001 UBERON:0008923 ! has synaptic IO in region sublaminar layer S2 @@ -24183,6 +27271,8 @@ id: CL:0003042 name: M9-OFF retinal ganglion cell namespace: cell def: "An M9 retinal ganglion cell with synaptic terminals in S4 that is depolarized by decreased illumination of their receptive field center" [PMID:16626866] +subset: human_subset +subset: mouse_subset is_a: CL:0003040 ! M9 retinal ganglion cell is_a: CL:4023033 ! OFF retinal ganglion cell relationship: RO:0013001 UBERON:0008925 ! has synaptic IO in region sublaminar layer S4 @@ -24194,6 +27284,8 @@ id: CL:0003043 name: M10 retinal ganglion cell namespace: cell def: "A monostratified retinal ganglion cell with large soma and large dendritic field, with dense dendritic arbor." [PMID:16626866] +subset: human_subset +subset: mouse_subset is_a: CL:0000740 ! retinal ganglion cell relationship: bearer_of PATO:0070063 ! monostratified dendrite cell morphology property_value: terms:contributor "https://orcid.org/0000-0001-7258-9596" xsd:string @@ -24204,6 +27296,8 @@ id: CL:0003044 name: M11 retinal ganglion cell namespace: cell def: "A bistratified ganglion cell with small, dense dendritic fields that terminate in S1 and S3." [PMID:16626866] +subset: human_subset +subset: mouse_subset is_a: CL:0003001 ! bistratified retinal ganglion cell relationship: RO:0013001 UBERON:0008922 ! has synaptic IO in region sublaminar layer S1 relationship: RO:0013001 UBERON:0008924 ! has synaptic IO in region sublaminar layer S3 @@ -24215,6 +27309,8 @@ id: CL:0003045 name: M12 retinal ganglion cell namespace: cell def: "A bistratified ganglion cell with larger, asymetric dendritic fields that terminate in S2 and S4." [PMID:16626866] +subset: human_subset +subset: mouse_subset is_a: CL:0003001 ! bistratified retinal ganglion cell relationship: RO:0013001 UBERON:0008923 ! has synaptic IO in region sublaminar layer S2 relationship: RO:0013001 UBERON:0008925 ! has synaptic IO in region sublaminar layer S4 @@ -24226,6 +27322,8 @@ id: CL:0003046 name: M13 retinal ganglion cell namespace: cell def: "A bistratifed retinal ganglion cell that has small, symmetric dendritic fields that terminate in S2 and S4." [PMID:16626866] +subset: human_subset +subset: mouse_subset is_a: CL:0003001 ! bistratified retinal ganglion cell relationship: RO:0013001 UBERON:0008923 ! has synaptic IO in region sublaminar layer S2 relationship: RO:0013001 UBERON:0008925 ! has synaptic IO in region sublaminar layer S4 @@ -24237,6 +27335,8 @@ id: CL:0003047 name: M14 retinal ganglion cell namespace: cell def: "A bistratifed retinal ganglion cell that has small, symmetric dendritic fields that terminate in S1 and S4-S5." [PMID:16626866] +subset: human_subset +subset: mouse_subset is_a: CL:0003001 ! bistratified retinal ganglion cell relationship: RO:0013001 UBERON:0008922 ! has synaptic IO in region sublaminar layer S1 relationship: RO:0013001 UBERON:0008929 ! has synaptic IO in region sublaminar layers S4 or S5 @@ -24248,13 +27348,14 @@ id: CL:0003048 name: L cone cell namespace: cell def: "A cone cell that detects long wavelength light. Exact peak of spectra detected differs between species. In humans, spectra peaks at 564-580 nm." [WikipediaVersioned:Cone_cell&oldid=1111888680] +subset: human_subset +subset: mouse_subset synonym: "L cone" EXACT [PMID:32555229] synonym: "L-cone" EXACT [PMID:29603924] synonym: "long wavelength sensitive cone" EXACT [PMID:31117170] synonym: "long- (L) wavelength-sensitive cone" EXACT [https://doi.org/10.7554/eLife.39166] synonym: "long-wavelength cone" EXACT [https://doi.org/10.1038/323623a0] is_a: CL:0000573 ! retinal cone cell -is_a: PR:000050567 ! protein-containing material entity relationship: has_part PR:000001244 ! long-wave-sensitive opsin 1 property_value: terms:contributor "https://orcid.org/0000-0002-5260-9315" xsd:string @@ -24263,13 +27364,14 @@ id: CL:0003049 name: M cone cell namespace: cell def: "A cone cell that detects medium wavelength light. Exact peak of spectra detected differs between species. In humans, spectra peaks at 534-545 nm." [WikipediaVersioned:Cone_cell&oldid=1111888680] +subset: human_subset +subset: mouse_subset synonym: "M cone" EXACT [PMID:32555229] synonym: "M-cone" EXACT [PMID:29603924] synonym: "middle wavelength sensitive cone" EXACT [PMID:31117170] synonym: "middle- (M) wavelength-sensitive cone" EXACT [https://doi.org/10.7554/eLife.39166] synonym: "middle-wavelength-sensitive (M) cone" EXACT [https://opg.optica.org/josaa/abstract.cfm?URI=josaa-6-1-153] is_a: CL:0000573 ! retinal cone cell -is_a: PR:000050567 ! protein-containing material entity relationship: has_part PR:000001224 ! medium-wave-sensitive opsin property_value: terms:contributor "https://orcid.org/0000-0002-5260-9315" xsd:string @@ -24279,6 +27381,8 @@ name: S cone cell namespace: cell def: "A cone cell that detects short wavelength light. Exact peak of spectra detected differs between species. In humans, spectra peaks at 420-440 nm." [WikipediaVersioned:Cone_cell&oldid=1111888680] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "S cone" EXACT [PMID:32555229] synonym: "S-(short-wavelength sensitive) cone" EXACT [PMID:31117170] synonym: "S-cone" EXACT [PMID:32555229] @@ -24295,6 +27399,8 @@ id: CL:0003051 name: UV cone cell namespace: cell def: "A cone cell that detects ultraviolet (UV) wavelength light." [] +subset: human_subset +subset: mouse_subset is_a: CL:0000573 ! retinal cone cell property_value: terms:contributor "https://orcid.org/0000-0002-5260-9315" xsd:string @@ -24304,8 +27410,10 @@ name: local interneuron namespace: cell def: "An interneuron whose axon stays entirely within the gray matter region where the cell body resides." [] comment: Local interneurons form the category of interneurons whose axon stays entirely within the gray matter region where the cell body resides (Swanson, 2003, p. 245; Bota and Swanson, 2007, Fig. 3). +subset: human_subset +subset: mouse_subset xref: BAMS:1002 -is_a: CL:0000402 ! CNS interneuron +is_a: CL:0000099 ! interneuron relationship: RO:0002100 UBERON:0002020 ! has soma location gray matter [Term] @@ -24313,6 +27421,8 @@ id: CL:0004115 name: retinal ganglion cell B namespace: cell def: "A monostratified retinal ganglion cell with small to medium soma and small to medium dendritic field." [PMID:12209831] +subset: human_subset +subset: mouse_subset is_a: CL:0000740 ! retinal ganglion cell relationship: bearer_of PATO:0070063 ! monostratified dendrite cell morphology property_value: terms:contributor "https://orcid.org/0000-0001-7258-9596" xsd:string @@ -24324,6 +27434,8 @@ name: retinal ganglion cell C namespace: cell def: "A retinal ganglion with cell medium cell bodies and medium to large dendritic fields." [PMID:12209831] comment: Group RGC cells are defined as having small to medium cell bodies and medium to large dendritic fields. Their morphology was more heterogeneous than that of Groups RGA and RGB. We classified cells with a large soma and a large dendritic field as RGA, cells with a small to medium to sized soma and a small to medium to sized dendritic field as RGB, and cells with a small to medium to sized soma but a medium to large dendritic field RGC. +subset: human_subset +subset: mouse_subset is_a: CL:0000740 ! retinal ganglion cell property_value: terms:contributor "https://orcid.org/0000-0001-7258-9596" xsd:string property_value: terms:contributor "https://orcid.org/0000-0002-5260-9315" xsd:string @@ -24334,6 +27446,8 @@ name: retinal ganglion cell A namespace: cell def: "A monostratified retinal ganglion cell with large soma and large dendritic field." [PMID:12209831] comment: This group includes all of the large bodied/large field RGCs in the rat. Group RGA cells have large somata (15 to 39 micrometers in diameter) and large, radially branching dendritic fields (235 to 748 micrometers in diameter), and many exhibit tracer coupling. +subset: human_subset +subset: mouse_subset synonym: "alpha cell" EXACT [] xref: BAMS:1009 is_a: CL:0000740 ! retinal ganglion cell @@ -24347,6 +27461,8 @@ name: retinal ganglion cell B1 namespace: cell def: "A retinal ganglion cell B that has medium body size, medium dendritic field and dense dendritic arbor, and has post synaptic terminals in S2." [PMID:12209831] comment: Could not distingush between B1 and B4 from paper. {xref="PMID:12209831"} +subset: human_subset +subset: mouse_subset synonym: "retinal ganglion cell B4" EXACT [] xref: BAMS:1047 is_a: CL:0004115 ! retinal ganglion cell B @@ -24359,6 +27475,8 @@ id: CL:0004120 name: retinal ganglion cell A1 namespace: cell def: "A retinal ganglion A cell found in the retina with large somata, often polygonal in shape. The dendritic fields consist of three to seven stout dendrites that are sparce near soma. Dendrites terminate in S4." [PMID:12209831] +subset: human_subset +subset: mouse_subset synonym: "I-2" RELATED [] synonym: "inner alpha retinal ganglion cell" EXACT [] synonym: "type I" BROAD [] @@ -24373,6 +27491,8 @@ id: CL:0004121 name: retinal ganglion cell B2 namespace: cell def: "A retinal ganglion cell B that has a very small but very dense dendritic field, and has post synaptic terminals in S2." [PMID:12209831] +subset: human_subset +subset: mouse_subset xref: BAMS:1048 is_a: CL:0004115 ! retinal ganglion cell B relationship: RO:0013001 UBERON:0008923 ! has synaptic IO in region sublaminar layer S2 @@ -24384,6 +27504,8 @@ id: CL:0004124 name: retinal ganglion cell C1 namespace: cell def: "A retinal ganglion cell C inner that has medium dendritic diversity." [PMID:12209831] +subset: human_subset +subset: mouse_subset synonym: "delta" RELATED [] synonym: "MTN projecting" RELATED [] synonym: "ON-direction-selective" RELATED [] @@ -24397,6 +27519,8 @@ id: CL:0004125 name: retinal ganglion cell C2 inner namespace: cell def: "A retinal ganglion cell C inner that has dense dendritic diversity." [PMID:12209831] +subset: human_subset +subset: mouse_subset xref: BAMS:1067 is_a: CL:0003024 ! retinal ganglion cell C inner property_value: terms:contributor "https://orcid.org/0000-0001-7258-9596" xsd:string @@ -24407,6 +27531,8 @@ id: CL:0004126 name: retinal ganglion cell C2 outer namespace: cell def: "A retinal ganglion cell C outer that has symmetrical and dense dendritic dendritic tree with a large dendritic field." [PMID:12209831] +subset: human_subset +subset: mouse_subset xref: BAMS:1066 is_a: CL:0003020 ! retinal ganglion cell C outer property_value: terms:contributor "https://orcid.org/0000-0001-7258-9596" xsd:string @@ -24417,6 +27543,8 @@ id: CL:0004137 name: retinal ganglion cell A2 inner namespace: cell def: "A retinal ganglion A2 cell with dendrites terminating in S4." [PMID:12209831] +subset: human_subset +subset: mouse_subset xref: BAMS:1061 is_a: CL:0004138 ! retinal ganglion cell A2 relationship: RO:0013001 UBERON:0008925 ! has synaptic IO in region sublaminar layer S4 @@ -24428,6 +27556,8 @@ id: CL:0004138 name: retinal ganglion cell A2 namespace: cell def: "A retinal ganglion A cell with dense arbor near soma." [PMID:12209831] +subset: human_subset +subset: mouse_subset synonym: "I-1" RELATED [] synonym: "outer alpha retinal ganglion cell" EXACT [] synonym: "type I" RELATED [] @@ -24440,6 +27570,8 @@ id: CL:0004139 name: retinal ganglion cell A2 outer namespace: cell def: "A retinal ganglion A2 cell with dendrites terminating in S2." [PMID:12209831] +subset: human_subset +subset: mouse_subset xref: BAMS:1065 is_a: CL:0004138 ! retinal ganglion cell A2 relationship: RO:0013001 UBERON:0008923 ! has synaptic IO in region sublaminar layer S2 @@ -24451,6 +27583,8 @@ id: CL:0004161 name: 510 nm-cone namespace: cell def: "A cone whose sensitivity measurements have an average spectral peak of 510 nm. These cones are described in rat." [] +subset: human_subset +subset: mouse_subset xref: BAMS:1028 "MB" is_a: CL:0003049 ! M cone cell property_value: RO:0002175 NCBITaxon:9989 @@ -24462,6 +27596,8 @@ name: 360 nm-cone namespace: cell def: "A cone whose sensitivity measurements have an average spectral peak of 358.2 nm. These cones are described in rat." [] comment: The photopigment curves that provide best fits to...sensitivity measurements have an average spectral peak of 358.2 nm. +subset: human_subset +subset: mouse_subset xref: BAMS:1029 "MB" is_a: CL:0003051 ! UV cone cell property_value: RO:0002175 NCBITaxon:9989 @@ -24473,6 +27609,8 @@ name: retinal ganglion cell B3 namespace: cell def: "A monostratified retinal ganglion cell with medium soma, sparse dendritic tree, and medium dendritic field." [] comment: Sixty to eighty neurons with small somata (12 to 24 micrometers in diameter), small dendritic fields (99 to 289 micrometers in diameter), and small axonal diameters (04. to 07. micrometers in diameter) make up Group RGB. We classified cells with a large soma and a large dendritic field as RGA, cells with a small to medium to sized soma and a small to medium to sized dendritic field as RGB, and cells with a small to medium to sized soma but a medium to large dendritic field RGC. +subset: human_subset +subset: mouse_subset xref: BAMS:1049 is_a: CL:0004115 ! retinal ganglion cell B property_value: terms:contributor "https://orcid.org/0000-0001-7258-9596" xsd:string @@ -24483,6 +27621,9 @@ id: CL:0004213 name: type 3a cone bipolar cell namespace: cell def: "A type of type 3 cone bipolar cell with distinctive curly dendrites." [PMID:19129389] +subset: cellxgene_subset +subset: human_subset +subset: mouse_subset is_a: CL:0000755 ! type 3 cone bipolar cell (sensu Mus) property_value: terms:contributor "https://orcid.org/0000-0001-7258-9596" xsd:string property_value: terms:contributor "https://orcid.org/0000-0002-5260-9315" xsd:string @@ -24492,6 +27633,9 @@ id: CL:0004214 name: type 3b cone bipolar cell namespace: cell def: "A type of type 3 cone bipolar cell with distinctive crescent-shaped dendrites." [PMID:19129389] +subset: cellxgene_subset +subset: human_subset +subset: mouse_subset is_a: CL:0000755 ! type 3 cone bipolar cell (sensu Mus) property_value: terms:contributor "https://orcid.org/0000-0001-7258-9596" xsd:string property_value: terms:contributor "https://orcid.org/0000-0002-5260-9315" xsd:string @@ -24501,6 +27645,9 @@ id: CL:0004215 name: type 5a cone bipolar cell namespace: cell def: "A type 5 cone bipolar cell with narrowly stratified post synaptic terminals." [] +subset: cellxgene_subset +subset: human_subset +subset: mouse_subset is_a: CL:0000757 ! type 5 cone bipolar cell (sensu Mus) property_value: terms:contributor "https://orcid.org/0000-0001-7258-9596" xsd:string property_value: terms:contributor "https://orcid.org/0000-0002-5260-9315" xsd:string @@ -24510,6 +27657,9 @@ id: CL:0004216 name: type 5b cone bipolar cell namespace: cell def: "A type 5 cone bipolar cell with diffuse axonal branches." [] +subset: cellxgene_subset +subset: human_subset +subset: mouse_subset is_a: CL:0000757 ! type 5 cone bipolar cell (sensu Mus) property_value: terms:contributor "https://orcid.org/0000-0001-7258-9596" xsd:string property_value: terms:contributor "https://orcid.org/0000-0002-5260-9315" xsd:string @@ -24519,6 +27669,9 @@ id: CL:0004217 name: H1 horizontal cell namespace: cell def: "A horizontal cell with a large cell body, thick dendrites, and a large dendritic arbor." [PMID:8571130] +subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "A Horizontal Cell" EXACT [] synonym: "H1" RELATED OMO:0003000 [doi:10.1038/s41598-020-66092-9] is_a: CL:0000745 ! retina horizontal cell @@ -24531,6 +27684,9 @@ id: CL:0004218 name: H2 horizontal cell namespace: cell def: "A horizontal cell with a small cell body, thin dendrites, and small dendritic arbor." [PMID:8571130] +subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "B Horizontal Cell" EXACT [] synonym: "H2" RELATED OMO:0003000 [doi:10.1038/s41598-020-66092-9] is_a: CL:0000745 ! retina horizontal cell @@ -24544,13 +27700,13 @@ name: A2 amacrine cell namespace: cell def: "A bistratifed retinal amacrine cell with a small dendritic field, dendrite stratification in S1-S2, and a second dendrite stratification in S5. This cell type releases the neurotransmitter glycine." [PMID:24246263, PMID:9620701] subset: cellxgene_subset -subset: human_reference_atlas +subset: human_subset +subset: mouse_subset is_a: CL:0004250 ! bistratified retinal amacrine cell is_a: CL:0004251 ! narrow field retinal amacrine cell is_a: CL:4030028 ! glycinergic amacrine cell relationship: RO:0013001 UBERON:0008926 ! has synaptic IO in region sublaminar layer S5 relationship: RO:0013001 UBERON:0008927 ! has synaptic IO in region sublaminar layers S1 or S2 -property_value: RO:0002175 NCBITaxon:9606 property_value: terms:contributor "https://orcid.org/0000-0001-7258-9596" xsd:string property_value: terms:contributor "https://orcid.org/0000-0002-5260-9315" xsd:string @@ -24559,6 +27715,8 @@ id: CL:0004220 name: flag amacrine cell namespace: cell def: "An amacrine cell with a small, asymteric dendritic field." [PMID:9620701] +subset: human_subset +subset: mouse_subset is_a: CL:0004251 ! narrow field retinal amacrine cell property_value: terms:contributor "https://orcid.org/0000-0001-7258-9596" xsd:string property_value: terms:contributor "https://orcid.org/0000-0002-5260-9315" xsd:string @@ -24568,6 +27726,8 @@ id: CL:0004221 name: flag A amacrine cell namespace: cell def: "A flag amacrine cell with post-synaptic terminals in S2 and S3. This cell type releases the neurotransmitter glycine." [PMID:24246263, PMID:9620701] +subset: human_subset +subset: mouse_subset is_a: CL:0004220 ! flag amacrine cell is_a: CL:4030028 ! glycinergic amacrine cell relationship: RO:0013001 UBERON:0008923 ! has synaptic IO in region sublaminar layer S2 @@ -24580,6 +27740,8 @@ id: CL:0004222 name: flag B amacrine cell namespace: cell def: "A flag amacrine cell with post-synaptic terminals in S3, S4, and S5. This cell type releases the neurotransmitter glycine." [PMID:24246263, PMID:9620701] +subset: human_subset +subset: mouse_subset is_a: CL:0004220 ! flag amacrine cell is_a: CL:4030028 ! glycinergic amacrine cell relationship: RO:0013001 UBERON:0008924 ! has synaptic IO in region sublaminar layer S3 @@ -24593,6 +27755,8 @@ id: CL:0004223 name: AB diffuse-1 amacrine cell namespace: cell def: "A amacrine cell with a small dendritic field and post-synaptic terminals in S1, S2, S3, and S4. AB diffuse-1 amacrine cells have a tent-shaped dendritic arbor and undulate dendrites." [PMID:9620701] +subset: human_subset +subset: mouse_subset is_a: CL:0004251 ! narrow field retinal amacrine cell relationship: RO:0013001 UBERON:0008922 ! has synaptic IO in region sublaminar layer S1 relationship: RO:0013001 UBERON:0008923 ! has synaptic IO in region sublaminar layer S2 @@ -24606,6 +27770,8 @@ id: CL:0004224 name: AB diffuse-2 amacrine cell namespace: cell def: "A broadly stratifying amacrine cell that has a small dendritic field and post-synaptic terminals in S2 and S3. This cell type releases the neurotransmitter glycine." [PMID:32032773, PMID:9620701] +subset: human_subset +subset: mouse_subset is_a: CL:0004251 ! narrow field retinal amacrine cell is_a: CL:4030028 ! glycinergic amacrine cell relationship: RO:0013001 UBERON:0008923 ! has synaptic IO in region sublaminar layer S2 @@ -24618,6 +27784,8 @@ id: CL:0004225 name: spider amacrine cell namespace: cell def: "A broadly stratifying amacrine cell with a small dendritic field, straight dendrites and post-synaptic terminals in S1, S2, and S3." [PMID:9620701] +subset: human_subset +subset: mouse_subset is_a: CL:0004251 ! narrow field retinal amacrine cell relationship: RO:0013001 UBERON:0008922 ! has synaptic IO in region sublaminar layer S1 relationship: RO:0013001 UBERON:0008923 ! has synaptic IO in region sublaminar layer S2 @@ -24630,10 +27798,12 @@ id: CL:0004226 name: monostratified amacrine cell namespace: cell def: "An amacrine cell with a small dendritic field with post-synaptic terminals in S3 and S4." [PMID:9620701] +subset: human_subset +subset: mouse_subset +is_a: CL:0004246 ! monostratified cell is_a: CL:0004251 ! narrow field retinal amacrine cell intersection_of: CL:0004251 ! narrow field retinal amacrine cell intersection_of: bearer_of PATO:0070063 ! monostratified dendrite cell morphology -relationship: bearer_of PATO:0070063 ! monostratified dendrite cell morphology relationship: RO:0013001 UBERON:0008924 ! has synaptic IO in region sublaminar layer S3 relationship: RO:0013001 UBERON:0008925 ! has synaptic IO in region sublaminar layer S4 property_value: terms:contributor "https://orcid.org/0000-0001-7258-9596" xsd:string @@ -24644,6 +27814,8 @@ id: CL:0004227 name: flat bistratified amacrine cell namespace: cell def: "A bistratified amacrine cell with a small dendritic field. Flat bistratified amacrine cells have post-synaptic terminals both on the border of S1 and S2, and on the border of S3 and S4. This cell type releases the neurotransmitter glycine." [PMID:25630271, PMID:9620701] +subset: human_subset +subset: mouse_subset is_a: CL:0004250 ! bistratified retinal amacrine cell is_a: CL:0004251 ! narrow field retinal amacrine cell is_a: CL:4030028 ! glycinergic amacrine cell @@ -24657,6 +27829,8 @@ id: CL:0004228 name: broad diffuse amacrine cell namespace: cell def: "An amacrine cell with a small dendritic field that has post-synaptic terminals in S1, S2, S3, and S4." [PMID:9620701] +subset: human_subset +subset: mouse_subset is_a: CL:0004251 ! narrow field retinal amacrine cell relationship: RO:0013001 UBERON:0008922 ! has synaptic IO in region sublaminar layer S1 relationship: RO:0013001 UBERON:0008923 ! has synaptic IO in region sublaminar layer S2 @@ -24670,6 +27844,8 @@ id: CL:0004229 name: A2-like amacrine cell namespace: cell def: "A bistratified amacrine cell with a small dendritic field that has dendrite stratification in S2, and in S3 and S4." [PMID:9620701] +subset: human_subset +subset: mouse_subset is_a: CL:0004250 ! bistratified retinal amacrine cell is_a: CL:0004251 ! narrow field retinal amacrine cell relationship: RO:0013001 UBERON:0008923 ! has synaptic IO in region sublaminar layer S2 @@ -24682,6 +27858,8 @@ id: CL:0004230 name: diffuse bistratified amacrine cell namespace: cell def: "A bistratified amacrine cell with a small dendritic field that has post-synaptic terminals in S1 and the border of S1-S2, and termination of a second arbor within the border of S2-S3 and S3." [PMID:9620701] +subset: human_subset +subset: mouse_subset is_a: CL:0004250 ! bistratified retinal amacrine cell is_a: CL:0004251 ! narrow field retinal amacrine cell relationship: RO:0013001 UBERON:0008922 ! has synaptic IO in region sublaminar layer S1 @@ -24696,6 +27874,8 @@ id: CL:0004231 name: recurving diffuse amacrine cell namespace: cell def: "A broadly stratifying amacrine cell with a small dendritic field and a complex dendritic arbor. Recurving diffuse amacrine cells have post-synaptic terminals in S2, S3, and S4." [PMID:9620701] +subset: human_subset +subset: mouse_subset is_a: CL:0004251 ! narrow field retinal amacrine cell relationship: RO:0013001 UBERON:0008923 ! has synaptic IO in region sublaminar layer S2 relationship: RO:0013001 UBERON:0008924 ! has synaptic IO in region sublaminar layer S3 @@ -24709,11 +27889,11 @@ name: starburst amacrine cell namespace: cell def: "An amacrine cell with a flat dendritic arbor and a medium dendritic field. Starburst amacrine cells have post-synaptic terminals in S2. This cell type releases the neurotransmitters gamma-aminobutyric acid (GABA) and acetylcholine." [PMID:32032773, PMID:9620701] subset: cellxgene_subset -subset: human_reference_atlas +subset: human_subset +subset: mouse_subset is_a: CL:0000108 ! cholinergic neuron is_a: CL:4030027 ! GABAergic amacrine cell relationship: RO:0013001 UBERON:0008923 ! has synaptic IO in region sublaminar layer S2 -property_value: RO:0002175 NCBITaxon:9606 property_value: terms:contributor "https://orcid.org/0000-0001-7258-9596" xsd:string property_value: terms:contributor "https://orcid.org/0000-0002-5260-9315" xsd:string @@ -24722,6 +27902,8 @@ id: CL:0004233 name: DAPI-3 amacrine cell namespace: cell def: "An amacrine cell with a medium dendritic field and post-synaptic terminals that stratify at S2, with a second stratification that occurs in S3 and S4. This cell type releases the neurotransmitter glycine." [PMID:9194315] +subset: human_subset +subset: mouse_subset is_a: CL:0004250 ! bistratified retinal amacrine cell is_a: CL:0004252 ! medium field retinal amacrine cell is_a: CL:4030028 ! glycinergic amacrine cell @@ -24735,6 +27917,8 @@ id: CL:0004234 name: diffuse multistratified amacrine cell namespace: cell def: "An amacrine cell with a medium dendritic field and post-synaptic terminals in S2, and in S3-S4." [PMID:9620701] +subset: human_subset +subset: mouse_subset is_a: CL:0004252 ! medium field retinal amacrine cell relationship: RO:0013001 UBERON:0008923 ! has synaptic IO in region sublaminar layer S2 relationship: RO:0013001 UBERON:0009731 ! has synaptic IO in region sublaminar layers S3 or S4 @@ -24746,6 +27930,8 @@ id: CL:0004235 name: AB broad diffuse-1 amacrine cell namespace: cell def: "An amacrine cell with a medium dendritic field and post-synaptic terminals in S2 and S3. This cell type releases the neurotransmitter gamma-aminobutyric acid (GABA)." [PMID:32032773, PMID:9620701] +subset: human_subset +subset: mouse_subset is_a: CL:0004252 ! medium field retinal amacrine cell is_a: CL:4030027 ! GABAergic amacrine cell relationship: RO:0013001 UBERON:0008923 ! has synaptic IO in region sublaminar layer S2 @@ -24758,6 +27944,8 @@ id: CL:0004236 name: AB broad diffuse-2 amacrine cell namespace: cell def: "An amacrine cell with a medium dendritic field and post-synaptic terminals in S2, S3, and S4. This cell type releases the neurotransmitter gamma-aminobutyric acid (GABA)." [PMID:32032773, PMID:9620701] +subset: human_subset +subset: mouse_subset is_a: CL:0004252 ! medium field retinal amacrine cell is_a: CL:4030027 ! GABAergic amacrine cell relationship: RO:0013001 UBERON:0008923 ! has synaptic IO in region sublaminar layer S2 @@ -24771,6 +27959,8 @@ id: CL:0004237 name: fountain amacrine cell namespace: cell def: "A retinal amacrine cell with a medium dendritic field and post-synaptic terminals in S1, S2, S3, and S4. This cell type releases the neurotransmitter gamma-aminobutyric acid (GABA)." [PMID:10614594, PMID:9620701] +subset: human_subset +subset: mouse_subset is_a: CL:0004252 ! medium field retinal amacrine cell is_a: CL:4030027 ! GABAergic amacrine cell relationship: RO:0013001 UBERON:0008922 ! has synaptic IO in region sublaminar layer S1 @@ -24785,6 +27975,8 @@ id: CL:0004238 name: asymmetric bistratified amacrine cell namespace: cell def: "A bistratified amacrine cell with a medium dendritic field, a flat and sparse dendritic arbor, and post-synaptic terminals at the intersections of S1 and S2, and S3 and S4." [PMID:9620701] +subset: human_subset +subset: mouse_subset is_a: CL:0004250 ! bistratified retinal amacrine cell is_a: CL:0004252 ! medium field retinal amacrine cell relationship: RO:0013001 UBERON:0009738 ! has synaptic IO in region border of sublaminar layers S1 and S2 @@ -24797,6 +27989,8 @@ id: CL:0004239 name: wavy bistratified amacrine cell namespace: cell def: "A bistratified amacrine cell with a medium dendritic field and post-synaptic terminals in S1-S2, and S4." [PMID:9620701] +subset: human_subset +subset: mouse_subset is_a: CL:0004250 ! bistratified retinal amacrine cell is_a: CL:0004252 ! medium field retinal amacrine cell relationship: RO:0013001 UBERON:0008922 ! has synaptic IO in region sublaminar layer S1 @@ -24810,6 +28004,8 @@ id: CL:0004240 name: WF1 amacrine cell namespace: cell def: "An amacrine cell with a wide dendritic field, dendrites in S1, and post-synaptic terminals in S1." [PMID:9620701] +subset: human_subset +subset: mouse_subset is_a: CL:0004253 ! wide field retinal amacrine cell relationship: RO:0013001 UBERON:0008922 ! has synaptic IO in region sublaminar layer S1 property_value: terms:contributor "https://orcid.org/0000-0001-7258-9596" xsd:string @@ -24820,6 +28016,8 @@ id: CL:0004241 name: WF2 amacrine cell namespace: cell def: "An amacrine cell with a wide dendritic field, dendrites in S2, and post-synaptic terminals in S1." [PMID:9620701] +subset: human_subset +subset: mouse_subset is_a: CL:0004253 ! wide field retinal amacrine cell relationship: RO:0013001 UBERON:0008922 ! has synaptic IO in region sublaminar layer S1 property_value: terms:contributor "https://orcid.org/0000-0001-7258-9596" xsd:string @@ -24830,6 +28028,8 @@ id: CL:0004242 name: WF3-1 amacrine cell namespace: cell def: "An amacrine cell with a wide dendritic field, dendrites in S3, and post-synaptic terminals in S3. Dendrites of this cell type are straight and minimally branched." [PMID:9620701] +subset: human_subset +subset: mouse_subset is_a: CL:0004253 ! wide field retinal amacrine cell relationship: RO:0013001 UBERON:0008924 ! has synaptic IO in region sublaminar layer S3 property_value: terms:contributor "https://orcid.org/0000-0001-7258-9596" xsd:string @@ -24840,6 +28040,8 @@ id: CL:0004243 name: WF3-2 amacrine cell namespace: cell def: "An amacrine cell with a wild dendritic field, dendrites in S3, and post-synaptic terminals in S3. Dendrites have spikes, cross over each other, and cover a larger volume than dendrties of W3-1 retinal amacrine cells." [PMID:9620701] +subset: human_subset +subset: mouse_subset is_a: CL:0004253 ! wide field retinal amacrine cell relationship: RO:0013001 UBERON:0008924 ! has synaptic IO in region sublaminar layer S3 property_value: terms:contributor "https://orcid.org/0000-0001-7258-9596" xsd:string @@ -24850,6 +28052,8 @@ id: CL:0004244 name: WF4 amacrine cell namespace: cell def: "An amacrine cell with a wide dendritic field, dendrites in S4, and post-synaptic terminals in S4." [PMID:9620701] +subset: human_subset +subset: mouse_subset is_a: CL:0004253 ! wide field retinal amacrine cell relationship: RO:0013001 UBERON:0008925 ! has synaptic IO in region sublaminar layer S4 property_value: terms:contributor "https://orcid.org/0000-0001-7258-9596" xsd:string @@ -24860,6 +28064,8 @@ id: CL:0004245 name: indoleamine-accumulating amacrine cell namespace: cell def: "An amacrine cell with a wide dendritic field and post-synaptic terminals in S5. This cell type releases the neurotransmitters gamma-aminobutyric acid (GABA) and serotonin." [PMID:12486181, PMID:9620701] +subset: human_subset +subset: mouse_subset is_a: CL:0000850 ! serotonergic neuron is_a: CL:0004253 ! wide field retinal amacrine cell is_a: CL:4030027 ! GABAergic amacrine cell @@ -24872,6 +28078,8 @@ id: CL:0004246 name: monostratified cell namespace: cell def: "A central nervous system neuron that stratifies at one and only one location." [PMID:9620701] +subset: human_subset +subset: mouse_subset is_a: CL:2000029 ! central nervous system neuron intersection_of: CL:0000540 ! neuron intersection_of: bearer_of PATO:0070063 ! monostratified dendrite cell morphology @@ -24885,7 +28093,9 @@ id: CL:0004247 name: bistratified cell namespace: cell def: "A neuron that stratifies dendrites at two and only two locations." [https://orcid.org/0000-0002-5260-9315, PMID:9620701] -is_a: CL:0000540 ! neuron +subset: human_subset +subset: mouse_subset +is_a: CL:2000029 ! central nervous system neuron intersection_of: CL:0000540 ! neuron intersection_of: bearer_of PATO:0070062 ! bistratified dendrite cell morphology relationship: bearer_of PATO:0070062 ! bistratified dendrite cell morphology @@ -24896,6 +28106,8 @@ id: CL:0004250 name: bistratified retinal amacrine cell namespace: cell def: "An amicrine that stratifies dendrites at two and only two locations." [PMID:9620701] +subset: human_subset +subset: mouse_subset is_a: CL:0000561 ! amacrine cell is_a: CL:0004247 ! bistratified cell intersection_of: CL:0000561 ! amacrine cell @@ -24908,6 +28120,8 @@ id: CL:0004251 name: narrow field retinal amacrine cell namespace: cell def: "An amicrine that has a narrow dendritic field." [PMID:9620701] +subset: human_subset +subset: mouse_subset is_a: CL:0000561 ! amacrine cell property_value: terms:contributor "https://orcid.org/0000-0001-7258-9596" xsd:string property_value: terms:contributor "https://orcid.org/0000-0002-5260-9315" xsd:string @@ -24917,9 +28131,9 @@ id: CL:0004252 name: medium field retinal amacrine cell namespace: cell def: "An amicrine that has a medium dendritic field." [PMID:9620701] -subset: human_reference_atlas +subset: human_subset +subset: mouse_subset is_a: CL:0000561 ! amacrine cell -property_value: RO:0002175 NCBITaxon:9606 property_value: terms:contributor "https://orcid.org/0000-0001-7258-9596" xsd:string property_value: terms:contributor "https://orcid.org/0000-0002-5260-9315" xsd:string @@ -24928,9 +28142,9 @@ id: CL:0004253 name: wide field retinal amacrine cell namespace: cell def: "An amicrine that has a wide dendritic field." [PMID:9620701] -subset: human_reference_atlas +subset: human_subset +subset: mouse_subset is_a: CL:0000561 ! amacrine cell -property_value: RO:0002175 NCBITaxon:9606 property_value: terms:contributor "https://orcid.org/0000-0001-7258-9596" xsd:string property_value: terms:contributor "https://orcid.org/0000-0002-5260-9315" xsd:string @@ -24939,8 +28153,10 @@ id: CL:0005000 name: spinal cord interneuron def: "A CNS interneuron located in the spinal cord." [CL:CVS] comment: Is_a interneuron, part_of UBERON:0002240. +subset: human_subset +subset: mouse_subset xref: ZFA:0000778 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} -is_a: CL:0000402 {is_inferred="true"} ! CNS interneuron +is_a: CL:0000099 {is_inferred="true"} ! interneuron intersection_of: CL:0000099 ! interneuron intersection_of: RO:0002100 UBERON:0002240 ! has soma location spinal cord relationship: RO:0002100 UBERON:0002240 ! has soma location spinal cord @@ -24950,6 +28166,8 @@ id: CL:0005001 name: iridoblast def: "A non-terminally differentiated cell that originates from the neural crest and differentiates into an iridophore." [CL:CVS] comment: Derived from UBERON:0002342 neural crest. +subset: human_subset +subset: mouse_subset xref: ZFA:0005328 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000055 ! non-terminally differentiated cell is_a: CL:0011026 ! progenitor cell @@ -24959,6 +28177,8 @@ relationship: RO:0002202 CL:0000333 ! develops from migratory neural crest cell id: CL:0005002 name: xanthoblast def: "A non-terminally differentiated cell that differentiates into a xanthophore." [CL:CVS] +subset: human_subset +subset: mouse_subset xref: ZFA:0005245 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000055 ! non-terminally differentiated cell is_a: CL:0011026 ! progenitor cell @@ -24968,6 +28188,8 @@ relationship: RO:0002202 CL:0000333 ! develops from migratory neural crest cell id: CL:0005003 name: leucoblast def: "A non-terminally differentiated cell that originates from the neural crest and differentiates into a leucophore." [CL:CVS] +subset: human_subset +subset: mouse_subset xref: ZFA:0005329 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000055 ! non-terminally differentiated cell is_a: CL:0011026 ! progenitor cell @@ -24977,6 +28199,8 @@ relationship: RO:0002202 CL:0000333 ! develops from migratory neural crest cell id: CL:0005004 name: pigment erythroblast def: "A non-terminally differentiated cell that originates from the neural crest and differentiates into an erythrophore." [CL:CVS] +subset: human_subset +subset: mouse_subset xref: ZFA:0005331 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000055 ! non-terminally differentiated cell is_a: CL:0011026 ! progenitor cell @@ -24986,6 +28210,8 @@ relationship: RO:0002202 CL:0000333 ! develops from migratory neural crest cell id: CL:0005005 name: cyanoblast def: "A non-terminally differentiated cell that originates from the neural crest and differentiates into a cyanophore." [CL:CVS] +subset: human_subset +subset: mouse_subset xref: ZFA:0005332 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000055 ! non-terminally differentiated cell is_a: CL:0011026 ! progenitor cell @@ -24997,16 +28223,20 @@ name: ionocyte def: "Specialized epithelial cells involved in the maintenance of osmotic homeostasis. They are characterized by abundant mitochondria and ion transporters. In amniotes, they are present in the renal system. In freshwater fish, ionocytes in the skin and gills help maintain osmotic homeostasis by absorbing salt from the external environment." [PMID:17555741, PMID:19268451] subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset xref: https://cellxgene.cziscience.com/cellguide/CL_0005006 xref: ZFA:0005323 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000066 ! epithelial cell property_value: RO:0002175 NCBITaxon:9606 -property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional.\n\nIonocytes are specialized cells predominantly found in the mammalian respiratory and renal systems as well as in the gills, skin, and intestinal tract of fish. These cells play crucial roles in maintaining ion and acid-base homeostasis. Ionocytes demonstrate remarkable plasticity and are able to adapt themselves in response to changes in environmental conditions such as pH, salinity, ion concentration, and temperature.\nThese cells work by selectively absorbing specific ions from the environment, thus maintaining the body's internal ionic balance. The most commonly absorbed ions include sodium (Na+), chloride (Cl-), calcium (Ca2+), and hydrogen (H+). Moreover, ionocytes contribute to acid-base regulation. In response to acidosis or alkalosis, ionocytes can either excrete or retain hydrogen (H+) and bicarbonate (HCO3-) ions to readjust the blood pH. Further, experimental evidence suggests a functional complexity of ionocytes, implying diverse roles beyond ion regulation. Recent research highlights ionocytes' involvement in ammonia excretion and the regulation of extracellular fluid volume, highlighting their contribution to the overall homeostatic process.\nMalfunctioning ionocytes have been implicated in various diseases, including cystic fibrosis which is caused by mutations in the chloride channel CFTR, an ionocyte marker." xsd:string {xref="DOI:10.1016/j.jcf.2019.09.010", xref="DOI:10.1038/s41586-018-0393-7", xref="DOI:10.1038/s41598-023-30603-1", xref="DOI:10.1146/annurev-pathol-042420-094031", xref="DOI:10.3389/fmars.2020.00709"} +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nIonocytes are specialized cells predominantly found in the mammalian respiratory and renal systems as well as in the gills, skin, and intestinal tract of fish. These cells play crucial roles in maintaining ion and acid-base homeostasis. Ionocytes demonstrate remarkable plasticity and are able to adapt themselves in response to changes in environmental conditions such as pH, salinity, ion concentration, and temperature.\nThese cells work by selectively absorbing specific ions from the environment, thus maintaining the body's internal ionic balance. The most commonly absorbed ions include sodium (Na+), chloride (Cl-), calcium (Ca2+), and hydrogen (H+). Moreover, ionocytes contribute to acid-base regulation. In response to acidosis or alkalosis, ionocytes can either excrete or retain hydrogen (H+) and bicarbonate (HCO3-) ions to readjust the blood pH. Further, experimental evidence suggests a functional complexity of ionocytes, implying diverse roles beyond ion regulation. Recent research highlights ionocytes' involvement in ammonia excretion and the regulation of extracellular fluid volume, highlighting their contribution to the overall homeostatic process.\nMalfunctioning ionocytes have been implicated in various diseases, including cystic fibrosis which is caused by mutations in the chloride channel CFTR, an ionocyte marker." xsd:string {xref="DOI:10.1016/j.jcf.2019.09.010", xref="DOI:10.1038/s41586-018-0393-7", xref="DOI:10.1038/s41598-023-30603-1", xref="DOI:10.1146/annurev-pathol-042420-094031", xref="DOI:10.3389/fmars.2020.00709"} [Term] id: CL:0005007 name: Kolmer-Agduhr neuron def: "Kolmer-Agduhr neurons are ciliated GABAergic neurons that contact the central canal of the spinal cord and have ipsilateral ascending axons." [PMID:18680739] +subset: human_subset +subset: mouse_subset synonym: "KA cell" EXACT [] synonym: "KA interneuron" EXACT [PMID:15539490] synonym: "KA neuron" EXACT [PMID:9634146] @@ -25019,6 +28249,8 @@ is_a: CL:0011005 ! GABAergic interneuron id: CL:0005008 name: macular hair cell def: "An auditory hair cell located in the macula that is sensitive to auditory stimuli." [GO:cvs] +subset: human_subset +subset: mouse_subset is_a: CL:0000202 ! auditory hair cell is_a: CL:0002374 ! ear hair cell intersection_of: CL:0000202 ! auditory hair cell @@ -25030,11 +28262,13 @@ id: CL:0005009 name: renal principal cell def: "A cuboidal epithelial cell of the kidney which regulates sodium and potassium balance. The activity of sodium and potassium channels on the apical membrane of the cell is regulated by aldosterone and vasopressin. In mammals this cell type is located in the renal collecting duct system." [CL:CVS] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset xref: https://cellxgene.cziscience.com/cellguide/CL_0005009 xref: ZFA:0005322 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000075 ! columnar/cuboidal epithelial cell is_a: CL:0002518 ! kidney epithelial cell -property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional.\n\nRenal principal cells are the major cell type in the initial collecting tubule and the cortical and outer medullary collecting ducts, as well as the connecting tubule, in the nephrons of the kidneys.\nA key function of renal principal cells is the regulation of water balance in the body. These cells express aquaporin-2 (AQP2) water channels, which facilitate the reabsorption of water from the fluid within the renal tubule lumen back into the blood. The translocation of AQP2 to the cell membrane is controlled by the hormone vasopressin: In response to high vasopressin levels, AQP2 moves to the cell membrane, allowing water to pass through effectively and be reabsorbed, therefore concentrating the urine. Conversely, in low vasopressin conditions, AQP2 is removed from the membrane, reducing water reabsorption and diluting the urine. \nRenal principal cells are also involved in the regulation of sodium and potassium levels in the body. They have sodium channels (ENaC) in their luminal membranes which permit the reabsorption of sodium ions from the tubule fluid back into the blood, resulting in a net reabsorption of sodium ions into the systemic circulation. This process is controlled, in part, by the hormone aldosterone. Additionally, renal principal cells contain potassium channels that facilitate the secretion of potassium ions into the urine. The activities of these channels, in coordination with other cell types in the nephron, are critical for maintaining electrolyte balance and overall body homeostasis." xsd:string {xref="DOI:10.1016/j.krcp.2013.07.005", xref="DOI:10.2215/CJN.05760513", xref="DOI:10.2215/CJN.08580813"} +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nRenal principal cells are the major cell type in the initial collecting tubule and the cortical and outer medullary collecting ducts, as well as the connecting tubule, in the nephrons of the kidneys.\nA key function of renal principal cells is the regulation of water balance in the body. These cells express aquaporin-2 (AQP2) water channels, which facilitate the reabsorption of water from the fluid within the renal tubule lumen back into the blood. The translocation of AQP2 to the cell membrane is controlled by the hormone vasopressin: In response to high vasopressin levels, AQP2 moves to the cell membrane, allowing water to pass through effectively and be reabsorbed, therefore concentrating the urine. Conversely, in low vasopressin conditions, AQP2 is removed from the membrane, reducing water reabsorption and diluting the urine. \nRenal principal cells are also involved in the regulation of sodium and potassium levels in the body. They have sodium channels (ENaC) in their luminal membranes which permit the reabsorption of sodium ions from the tubule fluid back into the blood, resulting in a net reabsorption of sodium ions into the systemic circulation. This process is controlled, in part, by the hormone aldosterone. Additionally, renal principal cells contain potassium channels that facilitate the secretion of potassium ions into the urine. The activities of these channels, in coordination with other cell types in the nephron, are critical for maintaining electrolyte balance and overall body homeostasis." xsd:string {xref="DOI:10.1016/j.krcp.2013.07.005", xref="DOI:10.2215/CJN.05760513", xref="DOI:10.2215/CJN.08580813"} [Term] id: CL:0005010 @@ -25042,6 +28276,8 @@ name: renal intercalated cell def: "A cuboidal epithelial cell of the kidney that regulates acid/base balance." [CL:CVS] comment: Intercalated cells are also called “mitochondria-rich cells”, reflecting the high levels of round mitochondria at their apical pole, or in their cytoplasm, a distribution that is quite different from that of other kidney tubule cells, which accumulated mitochondria around the basolateral membrane. These cells also have numerous irregular apical microvilli compared with the surrounding segment-specific cells. Intercalated cells lack a central cilium, at least in the cortex, which also differentiates them from the adjacent principal cells. {xref="PMID:25632105"} subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "intercalated cell" EXACT [] xref: FMA:86560 xref: https://cellxgene.cziscience.com/cellguide/CL_0005010 @@ -25049,7 +28285,7 @@ xref: ZFA:0009375 {sssom:mapping_justification="https://w3id.org/semapv/vocab/Un is_a: CL:0000075 ! columnar/cuboidal epithelial cell is_a: CL:0002078 ! meso-epithelial cell is_a: CL:1000449 ! epithelial cell of nephron -property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional.\n\nRenal intercalated cells are specialized cells located in the collecting duct system of the kidneys. The primary role of intercalated cells is to reabsorb bicarbonate ions and secrete hydrogen ions, thereby maintaining the acid-base homeostasis in the blood. They comprise two main subtypes primarily distinguished by their functional and morphological attributes: alpha and beta intercalated cells.\nAlpha intercalated cells are more predominant when the body is in a state of acidosis, a condition characterized by an increased acidity of the blood. These cells are specialized in secreting excessive hydrogen ions into the urine through a mechanism involving vacuolar H+-ATPase and H+/K+-ATPase pumps on their apical membranes. They simultaneously reabsorb bicarbonate ions from the tubular fluid and return them to the bloodstream via mechanisms involving carbonic anhydrase II and bicarbonate/chloride exchangers on the basolateral membrane. This dual process helps to increase blood pH towards normal levels.\nWhen the body is in a state of alkalosis, a condition characterized by lowered levels of hydrogen ions in the blood, beta intercalated cells are more predominant. They primarily reabsorb hydrogen ions from the tubular fluid through vacuolar H+-ATPase and H+/K+-ATPase pumps on their basolateral membranes, while secreting bicarbonate ions into the urine via pendrin, a bicarbonate/chloride exchanger in the apical membrane. These mechanisms work together to decrease blood pH towards normal levels. \nIn summary, renal intercalated cells play a critical role in the delicate balance of the body’s pH, safeguarding the body from potential harm caused by acidemia or alkalemia." xsd:string {xref="DOI:10.1152/ajprenal.2000.279.1.F195", xref="DOI:10.1161/HYPERTENSIONAHA.121.16492", xref="DOI:10.1681/ASN.V1011", xref="DOI:10.2215/CJN.08880914"} +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nRenal intercalated cells are specialized cells located in the collecting duct system of the kidneys. The primary role of intercalated cells is to reabsorb bicarbonate ions and secrete hydrogen ions, thereby maintaining the acid-base homeostasis in the blood. They comprise two main subtypes primarily distinguished by their functional and morphological attributes: alpha and beta intercalated cells.\nAlpha intercalated cells are more predominant when the body is in a state of acidosis, a condition characterized by an increased acidity of the blood. These cells are specialized in secreting excessive hydrogen ions into the urine through a mechanism involving vacuolar H+-ATPase and H+/K+-ATPase pumps on their apical membranes. They simultaneously reabsorb bicarbonate ions from the tubular fluid and return them to the bloodstream via mechanisms involving carbonic anhydrase II and bicarbonate/chloride exchangers on the basolateral membrane. This dual process helps to increase blood pH towards normal levels.\nWhen the body is in a state of alkalosis, a condition characterized by lowered levels of hydrogen ions in the blood, beta intercalated cells are more predominant. They primarily reabsorb hydrogen ions from the tubular fluid through vacuolar H+-ATPase and H+/K+-ATPase pumps on their basolateral membranes, while secreting bicarbonate ions into the urine via pendrin, a bicarbonate/chloride exchanger in the apical membrane. These mechanisms work together to decrease blood pH towards normal levels. \nIn summary, renal intercalated cells play a critical role in the delicate balance of the body’s pH, safeguarding the body from potential harm caused by acidemia or alkalemia." xsd:string {xref="DOI:10.1152/ajprenal.2000.279.1.F195", xref="DOI:10.1161/HYPERTENSIONAHA.121.16492", xref="DOI:10.1681/ASN.V1011", xref="DOI:10.2215/CJN.08880914"} [Term] id: CL:0005011 @@ -25057,22 +28293,27 @@ name: renal alpha-intercalated cell def: "A cuboidal epithelial cell of the kidney which secretes acid and reabsorbs base to regulate acid/base balance." [CL:CVS] comment: Type A intercalated cells are the more abundant type of intercalated cell in the outer stripe of the outer medulla in most mammalian species. {xref="PMID:25632105"} subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "type A intercalated cell" EXACT [PMID:25632105] synonym: "type A-IC" EXACT [PMID:25632105] xref: https://cellxgene.cziscience.com/cellguide/CL_0005011 xref: ZFA:0009376 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0005010 ! renal intercalated cell relationship: capable_of GO:0046717 ! acid secretion -property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional.\n\nRenal alpha-intercalated cells are located within the connecting tubules and collecting ducts of the kidneys, which are components of the kidney's complex nephron system. Along with beta-intercalated cells, they play a critical role in the body’s acid-base balance. \nRenal alpha-intercalated cells contain an abundance of proton pumps and enzymes like carbonic anhydrase, which aid in the transport of hydrogen ions for secretion in the urine. The bicarbonate/chloride transporters on their apical membrane meanwhile take up bicarbonate ions from the urine and supply them back into the blood. Through this mechanism, these cells contribute significantly to the neutrality of blood pH, and dysfunction of renal alpha-intercalated cells often leads to distal renal tubular acidosis, a condition resulting in acidic blood and alkaline urine." xsd:string {xref="DOI:10.1016/j.semnephrol.2019.04.005", xref="DOI:10.1152/physiol.00008.2011", xref="DOI:10.1172/JCI63492", xref="DOI:10.3390/diseases2020071"} +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nRenal alpha-intercalated cells are located within the connecting tubules and collecting ducts of the kidneys, which are components of the kidney's complex nephron system. Along with beta-intercalated cells, they play a critical role in the body’s acid-base balance. \nRenal alpha-intercalated cells contain an abundance of proton pumps and enzymes like carbonic anhydrase, which aid in the transport of hydrogen ions for secretion in the urine. The bicarbonate/chloride transporters on their apical membrane meanwhile take up bicarbonate ions from the urine and supply them back into the blood. Through this mechanism, these cells contribute significantly to the neutrality of blood pH, and dysfunction of renal alpha-intercalated cells often leads to distal renal tubular acidosis, a condition resulting in acidic blood and alkaline urine." xsd:string {xref="DOI:10.1016/j.semnephrol.2019.04.005", xref="DOI:10.1152/physiol.00008.2011", xref="DOI:10.1172/JCI63492", xref="DOI:10.3390/diseases2020071"} [Term] id: CL:0005012 -name: multi-ciliated epithelial cell +name: multiciliated epithelial cell def: "A columnar/cuboidal epithelial cell with multiple motile cilia on its apical surface. These cells facilitate the movement of liquids such as mucus or cerebrospinal fluid across the epithelial surface." [CL:CVS, PMID:28400610, PMID:30422572, PMID:38032388] comment: While the term 'multi-ciliated epithelial cell' refers to cells with multiple motile cilia, there are exceptions where epithelial cells may have multiple non-motile cilia. Examples include olfactory sensory neurons, which have non-motile cilia for sensory detection, and choroid plexus epithelial cells, which possess multiple non-motile cilia with transient motility during development. Multiciliated cells are essential for human health, and their dysfunction can lead to various diseases known as ciliopathies, such as primary ciliary dyskinesia. This condition affects the respiratory system, brain ventricles, and reproductive system, leading to chronic respiratory infections, hydrocephalus, and infertility {xref="PMID:22118931", xref="PMID:23959957", xref="PMID:26378583", xref="PMID:25729351"} subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "MCC" RELATED OMO:0003000 [] synonym: "multi-ciliated cell" BROAD [] +synonym: "multi-ciliated epithelial cell" EXACT [] synonym: "multiciliated cell" BROAD [] synonym: "multiciliated epithelial cell" EXACT [] xref: https://cellxgene.cziscience.com/cellguide/CL_0005012 @@ -25084,12 +28325,14 @@ intersection_of: bearer_of PATO:0010007 ! multiciliated intersection_of: has_part GO:0031514 ! motile cilium relationship: bearer_of PATO:0010007 ! multiciliated relationship: has_part GO:0031514 ! motile cilium -property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional.\n\nThe multi-ciliated epithelial cell are terminally differentiated epithelia that line brain ventricles, the respiratory tract and parts of the female and male reproductive organs in animals, playing critical roles in the maintenance of homeostasis through ciliary motion. They are characterized by the presence of hundreds of motile cilia, hair-like microtubule-based organelles that beat in a coordinated fashion to direct fluid flow over the cell surface.\nMulti-ciliated epithelial cells have fundamental roles in the proper functioning of many organ systems. In the respiratory system, they line the airways and orchestrate the coordinated movement of mucus, effectively clearing the airways of inhaled particles and pathogens. These cells are also vital in the ventricular system of the brain where they facilitate cerebrospinal fluid circulation, thus contributing to the maintenance of the brain's microenvironment. In the fallopian tube, multi-ciliated epithelial cells aid in the transport of oocytes from the ovary to the uterus, a process crucial to reproduction.\nThe formation and function of multi-ciliated epithelial cells is a highly regulated process that involves several stages of development including cell specification, centriole multiplication, and ciliogenesis. Any disruption in these processes can result in dysfunctional or decreased numbers of cilia, which can lead to a myriad of health issues, ranging from chronic respiratory infections to infertility." xsd:string {xref="DOI:10.1016/j.cub.2014.08.047", xref="DOI:10.1038/nrm.2017.21", xref="DOI:10.1101/cshperspect.a028233"} +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nThe multi-ciliated epithelial cell are terminally differentiated epithelia that line brain ventricles, the respiratory tract and parts of the female and male reproductive organs in animals, playing critical roles in the maintenance of homeostasis through ciliary motion. They are characterized by the presence of hundreds of motile cilia, hair-like microtubule-based organelles that beat in a coordinated fashion to direct fluid flow over the cell surface.\nMulti-ciliated epithelial cells have fundamental roles in the proper functioning of many organ systems. In the respiratory system, they line the airways and orchestrate the coordinated movement of mucus, effectively clearing the airways of inhaled particles and pathogens. These cells are also vital in the ventricular system of the brain where they facilitate cerebrospinal fluid circulation, thus contributing to the maintenance of the brain's microenvironment. In the fallopian tube, multi-ciliated epithelial cells aid in the transport of oocytes from the ovary to the uterus, a process crucial to reproduction.\nThe formation and function of multi-ciliated epithelial cells is a highly regulated process that involves several stages of development including cell specification, centriole multiplication, and ciliogenesis. Any disruption in these processes can result in dysfunctional or decreased numbers of cilia, which can lead to a myriad of health issues, ranging from chronic respiratory infections to infertility." xsd:string {xref="DOI:10.1016/j.cub.2014.08.047", xref="DOI:10.1038/nrm.2017.21", xref="DOI:10.1101/cshperspect.a028233"} [Term] id: CL:0005013 name: single ciliated epithelial cell def: "A ciliated epithelial cell with a single cilium." [CL:CVS] +subset: human_subset +subset: mouse_subset xref: ZFA:0005243 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000067 ! ciliated epithelial cell @@ -25097,6 +28340,8 @@ is_a: CL:0000067 ! ciliated epithelial cell id: CL:0005014 name: auditory epithelial supporting cell def: "A non-sensory cell that extends from the basement membrane to the apical surface of the auditory epithelium and provides support for auditory hair cells." [CL:CVS, GOC:tfm] +subset: human_subset +subset: mouse_subset synonym: "auditory epithelial support cell" EXACT [] xref: ZFA:0005244 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000630 ! supporting cell @@ -25107,6 +28352,8 @@ is_a: CL:0002491 ! auditory epithelial cell id: CL:0005015 name: inner phalangeal cell def: "An auditory epithelial support cell that surrounds the nerve fibers and synapses of the auditory inner hair cells." [CL:CVS] +subset: human_subset +subset: mouse_subset xref: FMA:79801 is_a: CL:0002165 ! phalangeal cell @@ -25128,6 +28375,8 @@ replaced_by: PO:0002002 id: CL:0005018 name: ghrelin secreting cell def: "A cell that secretes ghrelin, the peptide hormone that stimulates hunger." [CL:curator] +subset: human_subset +subset: mouse_subset xref: ZFA:0005599 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000167 ! peptide hormone secreting cell intersection_of: CL:0000151 ! secretory cell @@ -25141,6 +28390,8 @@ def: "Ghrelin secreting cells found in the endocrine pancreas." [PMID:14970313] comment: In mammals the endocrine pancreas is called the Islets of Langerhans. subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "pancreatic E cell" EXACT [] xref: https://cellxgene.cziscience.com/cellguide/CL_0005019 xref: ZFA:0005598 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} @@ -25149,13 +28400,15 @@ is_a: CL:0008024 ! pancreatic endocrine cell intersection_of: CL:0008024 ! pancreatic endocrine cell intersection_of: capable_of GO:0036321 ! ghrelin secretion property_value: RO:0002175 NCBITaxon:9606 -property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional.\n\nPancreatic epsilon cells are a specialized type of endocrine cell found in the islets of Langerhans, a region of the pancreas responsible for hormone production. These clusters of cells constitute only about 1% of the pancreatic islet cell population, making them a relatively small yet significant component of the pancreas. Pancreatic epsilon cells have a round or ovoid shape with occasional cytoplasmic extensions and are characterized by small and spherical granules. \nThe principal function of pancreatic epsilon cells involves the synthesis and release of the hormone ghrelin, a peptide hormone predominantly produced in the stomach; pancreatic epsilon cells are one of the few sites outside the gastrointestinal tract known to produce this hormone. Ghrelin has multiple vital roles, playing a significant part in generating hunger sensations, promoting fat storage, and influencing various metabolic processes. It also stimulates the release of Growth Hormone (GH) from the anterior pituitary gland.\nDuring fetal development, when they form a layer around the islet, epsilon cells are an important source of ghrelin, likely secreting the hormone into the circulation; their numbers decrease in adults. While research on pancreatic epsilon cells is still ongoing, these cells have been implicated in several disease states, most notably Type 2 diabetes and metabolic syndrome. The dysfunction or reduction in the number of pancreatic epsilon cells can lead to anomalies in ghrelin production, impacting overall metabolic homeostasis and glucose regulation." xsd:string {xref="DOI:10.1007/s00125-008-1238-y", xref="DOI:10.1152/physrev.00012.2004", xref="DOI:10.1210/en.2018-00833", xref="DOI:10.3389/fendo.2022.904004", xref="DOI:10.3390/ijms20081867"} +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nPancreatic epsilon cells are a specialized type of endocrine cell found in the islets of Langerhans, a region of the pancreas responsible for hormone production. These clusters of cells constitute only about 1% of the pancreatic islet cell population, making them a relatively small yet significant component of the pancreas. Pancreatic epsilon cells have a round or ovoid shape with occasional cytoplasmic extensions and are characterized by small and spherical granules. \nThe principal function of pancreatic epsilon cells involves the synthesis and release of the hormone ghrelin, a peptide hormone predominantly produced in the stomach; pancreatic epsilon cells are one of the few sites outside the gastrointestinal tract known to produce this hormone. Ghrelin has multiple vital roles, playing a significant part in generating hunger sensations, promoting fat storage, and influencing various metabolic processes. It also stimulates the release of Growth Hormone (GH) from the anterior pituitary gland.\nDuring fetal development, when they form a layer around the islet, epsilon cells are an important source of ghrelin, likely secreting the hormone into the circulation; their numbers decrease in adults. While research on pancreatic epsilon cells is still ongoing, these cells have been implicated in several disease states, most notably Type 2 diabetes and metabolic syndrome. The dysfunction or reduction in the number of pancreatic epsilon cells can lead to anomalies in ghrelin production, impacting overall metabolic homeostasis and glucose regulation." xsd:string {xref="DOI:10.1007/s00125-008-1238-y", xref="DOI:10.1152/physrev.00012.2004", xref="DOI:10.1210/en.2018-00833", xref="DOI:10.3389/fendo.2022.904004", xref="DOI:10.3390/ijms20081867"} [Term] id: CL:0005020 name: lymphangioblast def: "Lymphatic progenitor cells." [CL:CVS] comment: Usually express Prox1, or prox1b. +subset: human_subset +subset: mouse_subset xref: ZFA:0009393 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000048 {is_inferred="true"} ! multi fate stem cell is_a: CL:4033054 ! perivascular cell @@ -25170,6 +28423,8 @@ id: CL:0005021 name: mesenchymal lymphangioblast def: "Mesenchymal derived lymphatic progenitor cells that give rise to the superficial lymphatics." [PMID:15624319, PMID:18430230] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset xref: ZFA:0009394 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000134 ! mesenchymal stem cell is_a: CL:0005020 ! lymphangioblast @@ -25181,6 +28436,8 @@ id: CL:0005022 name: vascular lymphangioblast def: "Lymphatic progenitor cells, derived from the veins, that give rise to lymphatic endothelial cells." [CL:CVS] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "parachordal lymphangioblast" NARROW [] xref: ZFA:0009395 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0005020 {is_inferred="true"} ! lymphangioblast @@ -25194,6 +28451,8 @@ creation_date: 2012-01-12T05:21:09Z id: CL:0005023 name: branchiomotor neuron def: "Cranial motor neuron which innervates muscles derived from the branchial (pharyngeal) arches." [ZFIN:CVS] +subset: human_subset +subset: mouse_subset synonym: "branchi motor neuron" EXACT [] synonym: "special visceral motor neuron" EXACT [] xref: PMID:14699587 @@ -25207,6 +28466,8 @@ relationship: RO:0002130 UBERON:0004164 ! has synaptic terminal in branchiomeric id: CL:0005024 name: somatomotor neuron def: "A motor neuron that innervates a skeletal muscle. These motor neurons are all excitatory and cholinergic." [ZFIN:CVS] +subset: human_subset +subset: mouse_subset synonym: "somatic motor neuron" EXACT [] xref: ZFA:0005733 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000100 ! motor neuron @@ -25221,6 +28482,8 @@ name: visceromotor neuron def: "A motor neuron that synapses to parasympathetic neurons that innervate tear glands, sweat glands, and the smooth muscles and glands of the pulmonary, cardiovascular, and gastrointestinal systems." [ZFIN:CVS] comment: Note that these neurons do not synapse directly onto muscles subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "general visceral motor neuron" EXACT [] xref: ZFA:0005732 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000100 ! motor neuron @@ -25231,16 +28494,20 @@ id: CL:0005026 name: hepatoblast def: "Multi fate stem cell that gives rise to both hepatocytes and cholangiocytes as descendants. The term often refers to fetal precursors of hepatocytes (differently from 'hepatic stem cell', usually applied to the self-renewing pool of hepatocyte precursors in the adult liver). Hepatoblasts may also be endogenous, as some stem cells found in the liver come from the bone marrow via blood circulation." [GOC:CVS, https://orcid.org/0000-0003-1940-6740, PMID:18356246, PMID:20483998, PMID:26798363] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset xref: https://cellxgene.cziscience.com/cellguide/CL_0005026 is_a: CL:0000048 ! multi fate stem cell property_value: seeAlso "https://github.com/obophenotype/cell-ontology/issues/800" xsd:string -property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional.\n\nHepatoblasts are immature precursor cells that predominate during the early stages of liver development, specifically in the embryonic phase of life. They first arise from the endoderm, one of the three primary germ layers in the very early embryo, and then differentiate into two distinct mature liver cell types - the hepatocytes and cholangiocytes. \nDuring liver organogenesis hepatoblasts proliferate and migrate into the septum transversum to form the liver bud. Proliferation and differentiation of these cells are regulated by several soluble factors, such as hepatocyte growth factor, which is a mitogen of both hepatoblasts and mature hepatocytes. As they start to differentiate into hepatocytes and cholangiocytes, the cells begin to express hepatic markers like albumin and alpha-fetoprotein. \nAlthough hepatoblasts are specified embryonic liver cells that are bipotential for hepatocytes and cholangiocytes, a subset of liver cells (called oval cells) has been identified in adults that express stem cell markers, such as CD133 and cKIT, and has been suggested to have the same potential as hepatoblasts to differentiate into hepatocytes and cholangiocytes." xsd:string {xref="DOI:10.1016/j.stem.2014.04.010", xref="DOI:10.1093/jb/mvr001", xref="DOI:10.1242/dev.031369", xref="DOI:10.1242/dev.114215", xref="DOI:10.5966/sctm.2015-0051"} +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nHepatoblasts are immature precursor cells that predominate during the early stages of liver development, specifically in the embryonic phase of life. They first arise from the endoderm, one of the three primary germ layers in the very early embryo, and then differentiate into two distinct mature liver cell types - the hepatocytes and cholangiocytes. \nDuring liver organogenesis hepatoblasts proliferate and migrate into the septum transversum to form the liver bud. Proliferation and differentiation of these cells are regulated by several soluble factors, such as hepatocyte growth factor, which is a mitogen of both hepatoblasts and mature hepatocytes. As they start to differentiate into hepatocytes and cholangiocytes, the cells begin to express hepatic markers like albumin and alpha-fetoprotein. \nAlthough hepatoblasts are specified embryonic liver cells that are bipotential for hepatocytes and cholangiocytes, a subset of liver cells (called oval cells) has been identified in adults that express stem cell markers, such as CD133 and cKIT, and has been suggested to have the same potential as hepatoblasts to differentiate into hepatocytes and cholangiocytes." xsd:string {xref="DOI:10.1016/j.stem.2014.04.010", xref="DOI:10.1093/jb/mvr001", xref="DOI:10.1242/dev.031369", xref="DOI:10.1242/dev.114215", xref="DOI:10.5966/sctm.2015-0051"} [Term] id: CL:0007000 name: preameloblast def: "Skeletogenic cell that has the potential to develop into an ameloblast. Located in the inner enamel epithelium, these cells elongate, their nuclei shift distally (away from the dental papilla), and their cytoplasm becomes filled with organelles needed for synthesis and secretion of enamel proteins." [GO_REF:0000034, PMCID:PMC2737325] comment: unsure of neural crest contribution. In VSAO we have develops_from CL:0000008 +subset: human_subset +subset: mouse_subset is_a: BFO:0000002 is_a: CL:0000055 ! non-terminally differentiated cell is_a: CL:0000255 ! eukaryotic cell @@ -25255,6 +28522,8 @@ id: CL:0007001 name: skeletogenic cell def: "Cell that has the potential to form a skeletal cell type (e.g. cells in periosteum, cells in marrow) and produce extracellular matrix (often mineralized) and skeletal tissue (often mineralized)." [GO_REF:0000034] comment: Needs logical definition. Should be capable_of skeletal system morphogenesis? or skeletal tissue development? needs to be added to GO. NOTES:a cell type of the early embryo (see also: mesenchymal cells) that will give rise to mineralized connective tissue. Scleroblasts can differentiate into osteoblasts (bone-forming cells), chondroblasts (cartilage-forming cells), odontoblasts (dentin-forming cells), ameloblasts (enamel-forming cells). The mesenchymal cells developing into osteoblasts and chondroblasts are derived from the mesoderm. Those developing into odontoblasts are neural crest cells. Those developing into ameloblasts are derived from the ectoderm. (http://www.copewithcytokines.de/cope.cgi?key=scleroblasts) +subset: human_subset +subset: mouse_subset synonym: "scleroblast" EXACT [GO_REF:0000034] is_a: CL:0000000 ! cell property_value: terms:contributor https://orcid.org/0000-0001-9114-8737 @@ -25264,6 +28533,8 @@ creation_date: 2012-06-15T02:51:27Z id: CL:0007002 name: precementoblast def: "Skeletogenic cell that has the potential to develop into a cementoblast." [GO_REF:0000034] +subset: human_subset +subset: mouse_subset is_a: CL:0000055 ! non-terminally differentiated cell is_a: CL:0000255 ! eukaryotic cell relationship: part_of UBERON:0005176 ! tooth enamel organ @@ -25274,6 +28545,8 @@ creation_date: 2012-06-15T04:37:13Z id: CL:0007003 name: preodontoblast def: "Skeletogenic cell that has the potential to form an odontoblast, deposits predentine, and arises from a cranial neural crest cell." [GO_REF:0000034] +subset: human_subset +subset: mouse_subset is_a: CL:0000055 ! non-terminally differentiated cell is_a: CL:0011026 ! progenitor cell relationship: part_of UBERON:0005176 ! tooth enamel organ @@ -25285,6 +28558,8 @@ creation_date: 2012-06-15T05:15:11Z id: CL:0007004 name: premigratory neural crest cell def: "Cell that is part of the neural crest region of the neuroepithelium, prior to migration. Note that not all premigratory neural crest cells may become migratory neural crest cells." [UBERONREF:0000002] +subset: human_subset +subset: mouse_subset xref: ZFA:0007084 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: BFO:0000002 is_a: CL:0011012 ! neural crest cell @@ -25298,6 +28573,9 @@ id: CL:0007005 name: notochordal cell def: "Cell that is part of the notochord." [GO_REF:0000034] comment: NOTE: TO DO, notochord development still needs work. +subset: cellxgene_subset +subset: human_subset +subset: mouse_subset is_a: BFO:0000002 is_a: CL:0000255 ! eukaryotic cell relationship: part_of UBERON:0002328 ! notochord @@ -25309,6 +28587,8 @@ creation_date: 2012-06-27T08:47:31Z id: CL:0007006 name: chordamesodermal cell def: "Mesodermal cell that is axially located and gives rise to the cells of the notochord." [GO_REF:0000034] +subset: human_subset +subset: mouse_subset synonym: "axial mesodermal cell" EXACT [] is_a: CL:0000222 ! mesodermal cell relationship: part_of UBERON:0004880 ! chordamesoderm @@ -25319,6 +28599,8 @@ creation_date: 2012-06-27T08:52:41Z id: CL:0007007 name: notochordal sheath cell def: "Notochordal cell that is part of the outer epithelium of the notochord and surrounds the vacuolated notochord cells." [CL:MAH] +subset: human_subset +subset: mouse_subset xref: ZFA:0005744 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0007005 ! notochordal cell property_value: terms:contributor https://orcid.org/0000-0001-9114-8737 @@ -25328,6 +28610,8 @@ creation_date: 2012-06-27T09:26:37Z id: CL:0007008 name: notochordal vacuole cell def: "Notochordal cell that is inner portion of the notochord and becomes vacuolated as development proceeds." [CL:MAH] +subset: human_subset +subset: mouse_subset synonym: "chordablast" EXACT [GO_REF:0000034] synonym: "chordoblast" EXACT [PMID:14574572] is_a: CL:0007005 ! notochordal cell @@ -25338,6 +28622,8 @@ creation_date: 2012-06-27T09:29:30Z id: CL:0007009 name: prechondroblast def: "Skeletogenic cell that has the potential to develop into a chondroblast; and arises from neural crest, meseosdermal and notochordal and connective tissue cells." [GO_REF:0000034] +subset: human_subset +subset: mouse_subset is_a: CL:0000055 ! non-terminally differentiated cell property_value: terms:contributor https://orcid.org/0000-0001-9114-8737 creation_date: 2012-06-27T10:44:01Z @@ -25347,7 +28633,10 @@ id: CL:0007010 name: preosteoblast def: "Skeletogenic cell that has the potential to transform into an osteoblast, and develops from neural crest or mesodermal cells." [GO_REF:0000034] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "osteoprogenitor cell" EXACT [] +xref: https://cellxgene.cziscience.com/cellguide/CL_0007010 is_a: CL:0000055 ! non-terminally differentiated cell is_a: CL:0001035 ! bone cell is_a: CL:0002320 ! connective tissue cell @@ -25356,6 +28645,7 @@ relationship: part_of UBERON:0008883 ! osteoid relationship: RO:0002202 CL:0000222 ! develops from mesodermal cell relationship: RO:0002202 CL:0000333 ! develops from migratory neural crest cell property_value: terms:contributor https://orcid.org/0000-0001-9114-8737 +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nPreosteoblast is a critical cell type involved in bone formation, crucial in a process known as ossification or osteogenesis. They are derived from mesenchymal stem cells and are an intermediate stage marking the transition from an osteoprogenitor cell to a fully differentiated osteoblast. The presence of preosteoblasts signifies the site of new bone deposition, highlighting their crucial role in skeletal development and in response to bone injury repairs.\nThe primary function of preosteoblasts is to differentiate into osteoblasts, which are responsible for secreting osteoid (the unmineralized portion of bone matrix) and regulating the process of bone mineralization. Preosteoblasts are regulated by various growth factors and hormones, including bone morphogenic proteins (BMPs), fibroblast growth factors (FGFs), parathyroid hormone (PTH) and Vitamin D.\nHowever, the function of preosteoblasts is not limited to bone formation alone. In addition to osteogenesis, preosteoblasts significantly contribute to the maintenance of bone homeostasis through regulating the activity of osteoclasts - the cells responsible for bone resorption. This regulation is mediated through RANK/RANKL/OPG pathway signaling. Osteoprotegerin (OPG) released from the preosteoblasts acts as a decoy receptor for RANKL impairing osteoclast formation, hence preventing excessive bone resorption. This regulatory role indicates the dual functionality of preosteoblasts, which are indispensable for both the formation of new bone and the maintenance of existing bone tissue." xsd:string {xref="DOI:10.1038/srep32884", xref="DOI:10.1096/fba.2020-00058", xref="DOI:10.1210/endo.141.9.7634", xref="DOI:10.12659/MSMBR.901142"} creation_date: 2012-06-27T10:57:21Z [Term] @@ -25363,6 +28653,8 @@ id: CL:0007011 name: enteric neuron def: "Neuron that is part of the enteric nervous system." [CL:MAH] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset xref: ZFA:0005775 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000029 ! neural crest derived neuron is_a: CL:0000107 ! autonomic neuron @@ -25378,12 +28670,16 @@ creation_date: 2012-06-28T08:20:31Z id: CL:0007012 name: non-terminally differentiated odontoblast def: "Odontoblast that non-terminally differentiated, located in the odontogenic papilla and dentine tissue, and transforms from a odontoblast cell." [GO_REF:0000034, PSPUB:0000170] +subset: human_subset +subset: mouse_subset is_a: CL:0000060 ! odontoblast [Term] id: CL:0007013 name: terminally differentiated odontoblast def: "Odontoblast that is terminally differentiated and derived from an odontogenic papilla and associated with dentine." [GO_REF:0000034] +subset: human_subset +subset: mouse_subset is_a: CL:0000060 ! odontoblast [Term] @@ -25414,6 +28710,8 @@ id: CL:0007016 name: adaxial cell def: "Muscle precursor cell that is adjacent to the notochord and part of the presomitic mesoderm." [PMID:8951054] comment: In teleosts, adaxial cells give rise to slow muscle myoblasts. +subset: human_subset +subset: mouse_subset xref: ZFA:0000003 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000680 ! muscle precursor cell relationship: part_of UBERON:0003059 ! presomitic mesoderm @@ -25425,6 +28723,8 @@ id: CL:0007017 name: Stiftchenzellen def: "An epidermal cell with apical microvilli or a single apical projection have synaptic associations with nerve fibres in the epidermis." [PMID:1087183] comment: Taxon specificity not yet fully known, but are known in anuran larvae but not in adults. +subset: human_subset +subset: mouse_subset is_a: CL:0000206 ! chemoreceptor cell relationship: has_part GO:0005902 ! microvillus relationship: part_of UBERON:0001003 ! skin epidermis @@ -25435,6 +28735,8 @@ id: CL:0007018 name: epidermal ciliary cell def: "Ciliated cell of the embryonic epidermis and functions in embryonic movements." [PMCID:PMC3046089] comment: Taxon specificity not clear -present in embryonic anurans. +subset: human_subset +subset: mouse_subset is_a: CL:0000064 ! ciliated cell is_a: CL:0002321 ! embryonic cell (metazoa) relationship: part_of UBERON:0001003 ! skin epidermis @@ -25444,6 +28746,8 @@ property_value: terms:contributor https://orcid.org/0000-0001-9114-8737 id: CL:0007019 name: epidermal mucus secreting cell comment: taxon specificity not clear. Appears in early larval stages of anurans and persists after metamorphosis. +subset: human_subset +subset: mouse_subset is_a: CL:0000319 ! mucus secreting cell property_value: terms:contributor https://orcid.org/0000-0001-9114-8737 @@ -25451,6 +28755,8 @@ property_value: terms:contributor https://orcid.org/0000-0001-9114-8737 id: CL:0007020 name: bottle cell def: "Characteristic early embryonic cell with a bottle or flask shape that is first to migrate inwards at the blastopore during gastrulation in amphibians." [PMID:3197630] +subset: human_subset +subset: mouse_subset is_a: CL:0000007 ! early embryonic cell (metazoa) property_value: terms:contributor https://orcid.org/0000-0001-9114-8737 @@ -25458,6 +28764,8 @@ property_value: terms:contributor https://orcid.org/0000-0001-9114-8737 id: CL:0007021 name: alarm substance cell def: "Secretory cell that produces a chemical mixture that triggers antipredator behavior. The substance is released only upon disruption of the epidermis. [Behavior of teleost fishes, second edition, edited by Pitcher, 1992]" [ISBN-10:0412429403] +subset: human_subset +subset: mouse_subset synonym: "alarm substance secreting cell" EXACT [] synonym: "club cell" RELATED [https://github.com/obophenotype/cell-ontology/issues/583, ISBN-10:0412429403] synonym: "club cell (zebrafish)" EXACT [https://github.com/obophenotype/cell-ontology/issues/583] @@ -25471,6 +28779,8 @@ property_value: terms:contributor https://orcid.org/0000-0001-9114-8737 id: CL:0007022 name: micropylar cell def: "A specialized pore forming cell of the follicle, located adjacent to the animal pole of the oocyte. The micropylar cell makes the single micropyle (pore) through the chorion through which the sperm fertilizes the egg." [PMID:18582455, ZFA:0005239] +subset: human_subset +subset: mouse_subset synonym: "plug cell" EXACT [] xref: ZFA:0005239 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000255 ! eukaryotic cell @@ -25481,6 +28791,8 @@ property_value: terms:contributor https://orcid.org/0000-0001-9114-8737 id: CL:0007023 name: flask cell def: "Epidermal cell rich in mitochondria. In amphibians, appears during metamorphosis." [DOI:10.1007/BF00717048] +subset: human_subset +subset: mouse_subset is_a: CL:0000255 ! eukaryotic cell relationship: part_of UBERON:0001003 ! skin epidermis property_value: terms:contributor https://orcid.org/0000-0001-9114-8737 @@ -25489,6 +28801,8 @@ property_value: terms:contributor https://orcid.org/0000-0001-9114-8737 id: CL:0008000 name: non-striated muscle cell def: "Any muscle cell in which the fibers are not organised into sarcomeres." [GOC:DOS] +subset: human_subset +subset: mouse_subset is_a: CL:0000187 ! muscle cell [Term] @@ -25496,6 +28810,8 @@ id: CL:0008001 name: hematopoietic precursor cell def: "Any hematopoietic cell that is a precursor of some other hematopoietic cell type." [GOC:dos] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset is_a: CL:0000988 ! hematopoietic cell [Term] @@ -25503,6 +28819,8 @@ id: CL:0008002 name: skeletal muscle fiber def: "A transversely striated, synctial cell of skeletal muscle. It is formed when proliferating myoblasts exit the cell cycle, differentiate and fuse." [GOC:tfm, ISBN:0323052908] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset xref: MESH:D018485 is_a: CL:0000188 ! cell of skeletal muscle is_a: CL:0002372 ! myotube @@ -25517,6 +28835,8 @@ relationship: RO:0002202 CL:0000515 ! develops from skeletal muscle myoblast id: CL:0008003 name: somatic muscle myotube def: "A myotube that is part of some somatic muscle. Examples include arthropod somatic muscle cells." [PMID:22274696, PMID:8720463] +subset: human_subset +subset: mouse_subset is_a: CL:0002372 ! myotube is_a: CL:0008004 ! somatic muscle cell intersection_of: CL:0008004 ! somatic muscle cell @@ -25528,6 +28848,8 @@ intersection_of: has_part GO:0030017 ! sarcomere id: CL:0008004 name: somatic muscle cell def: "A muscle cell that is part of some somatic muscle." [GOC:dos] +subset: human_subset +subset: mouse_subset xref: FBbt:00005073 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} is_a: CL:0000187 ! muscle cell @@ -25535,6 +28857,8 @@ is_a: CL:0000187 ! muscle cell id: CL:0008005 name: obliquely striated somatic muscle cell def: "A somatic muscle cell that is obliquely striated and mononucleated. Examples include the somatic muscles of nematodes." [doi:10.3908/wormatlas.1.7, PMID:8720463] +subset: human_subset +subset: mouse_subset is_a: CL:0000226 ! single nucleate cell is_a: CL:0000444 ! obliquely striated muscle cell is_a: CL:0008004 ! somatic muscle cell @@ -25547,12 +28871,16 @@ intersection_of: has_part GO:0030017 ! sarcomere id: CL:0008006 name: muscle founder cell def: "A myoblast that detemines the properties (size, shape and attachment to the epidermis) of a `somatic muscle myotube` (CL:0008003) . It develops into a somatic muscle myotube via fusion with `fusion component myoblasts` (CL:0000621)." [PMID:22274696] +subset: human_subset +subset: mouse_subset is_a: CL:0008018 ! somatic muscle myoblast [Term] id: CL:0008007 name: visceral muscle cell def: "A muscle cell that is part of some visceral muscle." [GOC:dos] +subset: human_subset +subset: mouse_subset xref: FBbt:00005070 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} is_a: CL:0000187 ! muscle cell intersection_of: CL:0000187 ! muscle cell @@ -25563,6 +28891,8 @@ relationship: part_of UBERON:8600004 ! visceral muscle tissue id: CL:0008008 name: striated visceral muscle cell def: "A visceral muscle cell that is striated. Examples include the visceral muscle cells of arhtropods." [GOC:dos] +subset: human_subset +subset: mouse_subset is_a: CL:0000737 ! striated muscle cell is_a: CL:0008007 ! visceral muscle cell intersection_of: CL:0008007 ! visceral muscle cell @@ -25572,6 +28902,8 @@ intersection_of: bearer_of PATO:0001410 {all_some="true"} ! striated id: CL:0008009 name: transversely striated visceral muscle cell def: "A visceral muscle that is transversely striated. Examples include the visceral muscle cells of arthropods." [GOC:dos] +subset: human_subset +subset: mouse_subset is_a: CL:0008008 ! striated visceral muscle cell intersection_of: CL:0008007 ! visceral muscle cell intersection_of: bearer_of PATO:0002478 {all_some="true"} ! transversely striated @@ -25581,6 +28913,8 @@ relationship: bearer_of PATO:0002478 ! transversely striated id: CL:0008010 name: cranial somatomotor neuron def: "A cranial motor neuron whose soma is located in the midbrain andor hindbrain and which innervates the skeletal muscles of the eye or tongue." [PMID:14699587] +subset: human_subset +subset: mouse_subset is_a: CL:0005024 ! somatomotor neuron is_a: CL:0015000 ! cranial motor neuron intersection_of: CL:0015000 ! cranial motor neuron @@ -25591,6 +28925,8 @@ id: CL:0008011 name: skeletal muscle satellite stem cell def: "A skeletal muscle satellite cell that divides by stem cell division. A proportion of this population undergoes symmetric stem cell division, producing two skeletal muscle satellite stem cells. The rest undergo asymmetric stem cell division - retaining their identity while budding off a daughter cell that differentiates into an adult skeletal muscle myoblast." [PMID:23303905] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset is_a: CL:0000035 ! single fate stem cell is_a: CL:0000594 ! skeletal muscle satellite cell intersection_of: CL:0000594 ! skeletal muscle satellite cell @@ -25602,12 +28938,16 @@ disjoint_from: CL:0008020 ! skeletal muscle satellite myogenic cell id: CL:0008012 name: quiescent skeletal muscle satellite cell def: "A skeletal muscle satellite cell that is mitotically quiescent. These cells are wedge shaped and have a large nuclear to cytoplasmic ratio with few organelles, a small nucleus and condensed interphase chromatin. Satellite cells typically remain in this state until activated following muscle damage." [PMID:21849021, PMID:23303905] +subset: human_subset +subset: mouse_subset is_a: CL:0000594 ! skeletal muscle satellite cell [Term] id: CL:0008013 name: cranial visceromotor neuron def: "A visceromotor motor neuron whose soma is located in the hindbrain, and which synapses to parasympathetic neurons that innervate tear glands, sweat glands, and the smooth muscles of the head." [PMID:14699587] +subset: human_subset +subset: mouse_subset is_a: CL:0005025 ! visceromotor neuron is_a: CL:0015000 ! cranial motor neuron is_a: CL:2000029 ! central nervous system neuron @@ -25635,6 +28975,8 @@ property_value: RO:0002161 NCBITaxon:7742 id: CL:0008016 name: activated skeletal muscle satellite cell def: "A skeletal muscle satellite cell that has become mitotically active - typically following muscle damage." [PMID:21849021, PMID:23303905] +subset: human_subset +subset: mouse_subset is_a: CL:0000594 ! skeletal muscle satellite cell relationship: RO:0002202 CL:0008012 {comment="More accurately - transformation_of ?"} ! develops from quiescent skeletal muscle satellite cell @@ -25643,6 +28985,8 @@ id: CL:0008017 name: adult skeletal muscle myoblast def: "A skeletal muscle myoblast that is part of a skeletal mucle. These cells are formed following acivation and division of skeletal muscle satellite cells. They form a transient population that is lost when they fuse to form skeletal muscle fibers." [PMID:23303905] comment: The vast majority of these cells develop from skeletal muscle satellite cells, although there are some reports of other origins. +subset: human_subset +subset: mouse_subset synonym: "myogenic precursor cell" BROAD [PMID:23303905] is_a: CL:0000188 ! cell of skeletal muscle is_a: CL:0000515 ! skeletal muscle myoblast @@ -25654,6 +28998,8 @@ intersection_of: RO:0002203 CL:0008002 ! develops into skeletal muscle fiber id: CL:0008018 name: somatic muscle myoblast def: "A myoblast that is commited to developing into a somatic muscle." [] +subset: human_subset +subset: mouse_subset is_a: CL:0000056 ! myoblast intersection_of: CL:0000056 ! myoblast intersection_of: RO:0002203 CL:0008003 ! develops into somatic muscle myotube @@ -25665,6 +29011,8 @@ name: mesenchymal cell def: "A non-polarised cell precursor cell that is part of some mesenchyme, is associated with the cell matrix but is not connected to other cells and is capable of migration." [] subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "mesenchyme cell" EXACT [] is_a: CL:0000219 ! motile cell is_a: CL:0000255 ! eukaryotic cell @@ -25676,15 +29024,17 @@ property_value: RO:0002175 NCBITaxon:9606 id: CL:0008020 name: skeletal muscle satellite myogenic cell def: "A skeletal muscle satellite cell that undergoes symmetric division to produce two adult skeleltal muscle myoblasts." [GOC:dos, PMID:23303905] +subset: human_subset +subset: mouse_subset is_a: CL:0000594 ! skeletal muscle satellite cell relationship: RO:0002203 CL:0008017 ! develops into adult skeletal muscle myoblast [Term] id: CL:0008021 name: anterior lateral line ganglion neuron -def: "Any neuron that has its soma located in some anterior lateral line ganglion." [FBC:Autogenerated] +def: "Any peripheral nervous system neuron that has its soma located in some anterior lateral line ganglion." [FBC:Autogenerated] is_a: CL:2000031 ! lateral line ganglion neuron -intersection_of: CL:0000540 ! neuron +intersection_of: CL:2000032 ! peripheral nervous system neuron intersection_of: RO:0002100 UBERON:2001391 ! has soma location anterior lateral line ganglion relationship: RO:0002100 UBERON:2001391 ! has soma location anterior lateral line ganglion @@ -25692,6 +29042,8 @@ relationship: RO:0002100 UBERON:2001391 ! has soma location anterior lateral lin id: CL:0008022 name: endocardial cushion cell def: "A mesenchymal cell of the endocardial cushion. These cells develop via an epithelial to mesenchymal transition when endocardial cells break cell-to-cell contacts and migrate into the cardiac jelly. Cells from this population form the heart septa and valves." [PMID:18816864] +subset: human_subset +subset: mouse_subset is_a: CL:0000569 ! cardiac mesenchymal cell is_a: CL:0002494 ! cardiocyte intersection_of: CL:0000569 ! cardiac mesenchymal cell @@ -25711,6 +29063,8 @@ name: pancreatic endocrine cell def: "An endocrine cell that is part of the pancreas." [GOC:dos] subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset is_a: CL:0000083 ! epithelial cell of pancreas is_a: CL:0000164 ! enteroendocrine cell intersection_of: CL:0000163 ! endocrine cell @@ -25721,6 +29075,8 @@ property_value: RO:0002175 NCBITaxon:9606 id: CL:0008025 name: noradrenergic neuron def: "A neuron that release noradrenaline (noriphinephrine) as a neurotransmitter." [GOC:dos] +subset: human_subset +subset: mouse_subset xref: ZFA:0005873 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000459 ! noradrenergic cell is_a: CL:4033050 ! catecholaminergic neuron @@ -25742,6 +29098,8 @@ relationship: part_of UBERON:0003127 ! open tracheal system trachea id: CL:0008027 name: rod bipolar cell (sensu Mus) def: "A bipolar neuron found in the retina that is synapsed by rod photoreceptor cells. These neurons have axons that arborize and synapse to targets in inner plexiform layers 4 and 5 and depolarize in response to light." [] +subset: human_subset +subset: mouse_subset is_a: CL:0000751 ! rod bipolar cell property_value: terms:contributor https://orcid.org/0000-0002-7073-9172 creation_date: 2017-06-29T11:05:22Z @@ -25750,6 +29108,8 @@ creation_date: 2017-06-29T11:05:22Z id: CL:0008028 name: visual system neuron def: "Any neuron that is capable of part of some visual perception." [FBC:Autogenerated] +subset: human_subset +subset: mouse_subset is_a: CL:0000540 ! neuron intersection_of: CL:0000540 ! neuron intersection_of: capable_of_part_of GO:0007601 ! visual perception @@ -25780,8 +29140,10 @@ id: CL:0008031 name: cortical interneuron def: "An interneuron that has its soma located in the cerebral cortex." [] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "cerebral cortex interneuron" EXACT [] -is_a: CL:0000402 ! CNS interneuron +is_a: CL:0000099 ! interneuron is_a: CL:0010012 ! cerebral cortex neuron intersection_of: CL:0000099 ! interneuron intersection_of: RO:0002100 UBERON:0000956 ! has soma location cerebral cortex @@ -25791,6 +29153,7 @@ id: CL:0008032 name: rosehip neuron def: "A GABAergic interneuron in human cortical layer 1 that has large rosehip-shaped axonal boutons and compact arborization." [doi:10.1038/s41593-018-0205-2] comment: A rosehip cell has been shown to have an immunohistochemical profile GAD1+CCK+, CNR1–SST–CALB2–PVALB– that matches a single transcriptomically defined cell type whose specific molecular marker signature is not seen in mouse cortex. {xref="doi:10.1038/s41593-018-0205-2"} +subset: human_subset is_a: BFO:0000002 is_a: CL:0010011 ! cerebral cortex GABAergic interneuron relationship: RO:0002100 UBERON:0005390 ! has soma location cortical layer I @@ -25804,6 +29167,8 @@ id: CL:0008033 name: decidual pericyte def: "A pericyte of the decidual vasculature." [PMID:30429548] subset: added_for_HCA +subset: human_subset +subset: mouse_subset synonym: "decidual perivascular cell" EXACT [] is_a: CL:0000349 ! extraembryonic cell is_a: CL:2000078 ! placental pericyte @@ -25820,6 +29185,8 @@ def: "Mural cells are pericytes and the vascular smooth muscle cells (vSMCs) of subset: added_for_HCA subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset xref: ZFA:0005944 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:4033054 ! perivascular cell property_value: RO:0002175 NCBITaxon:9606 @@ -25830,6 +29197,8 @@ creation_date: 2020-02-29T17:33:55Z id: CL:0008035 name: microcirculation associated smooth muscle cell def: "Any vascular associated smooth muscle cell that is part of some microcirculatory vessel." [FBC:Autogenerated] +subset: human_subset +subset: mouse_subset is_a: CL:0000359 ! vascular associated smooth muscle cell is_a: CL:0008034 ! mural cell intersection_of: CL:0000359 ! vascular associated smooth muscle cell @@ -25845,17 +29214,23 @@ def: "A trophoblast cell that is not part of a placental villous." [PMID:3104960 subset: added_for_HCA subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "EVT" EXACT [PMID:31049600] synonym: "extravillous cytotrophloblast" EXACT [] +xref: https://cellxgene.cziscience.com/cellguide/CL_0008036 is_a: CL:0000351 ! trophoblast cell property_value: RO:0002175 NCBITaxon:9606 property_value: terms:contributor https://orcid.org/0000-0002-7073-9172 +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nExtravillous trophoblasts (EVTs), a specialized subset of trophoblast cells, play crucial roles in establishing and sustaining pregnancy. \nFirstly, they anchor the fetus to the maternal tissue, providing structural stability. Secondly, they are instrumental in modifying the maternal spiral arteries to ensure an adequate supply of maternal blood to the placenta and the developing fetus. EVTs invade maternal decidua and myometrium and replace the endothelial lining of the spiral arteries, transforming these high-resistance, narrow vessels into low-resistance, wide vessels, favouring higher blood flow. Thirdly, these cells also play an immunological role, creating an environment conducive to the acceptance of the semi-allogeneic fetus, by expressing non-classical MHC molecules, thereby averting any potential maternal immune response towards fetal tissues.\nWhile EVTs are commonly associated with healthy pregnancies, abnormalities in their function or development have been connected to problematic pregnancies. Conditions like pre-eclampsia and fetal growth restriction (FGR) may arise if EVT cells do not effectively invade the maternal decidua or adequately remodel." xsd:string {xref="DOI:10.1007/s12522-011-0102-9", xref="DOI:10.1016/j.it.2017.01.009", xref="DOI:10.1016/j.preghy.2010.10.003", xref="DOI:10.1080/19336918.2015.1089376", xref="DOI:10.1080/19336918.2015.1120397"} creation_date: 2020-03-02T08:45:06Z [Term] id: CL:0008037 name: gamma motor neuron def: "A lower motor neuron that innervates only intrafusal muscle fibers. Unlike the alpha motor neurons, gamma motor neurons do not directly adjust the lengthening or shortening of muscles but function in adjusting the sensitivity of muscle spindles and in keeping muscle spindles taut, thereby allowing the continued firing of alpha neurons." [DOI:10.1093/acprof\:oso/9780195159561.001.1, WikipediaVersion:Gamma_motor_neuron&oldid=906640465] +subset: human_subset +subset: mouse_subset synonym: "fusimotor neuron" EXACT [WikipediaVersioned:Gamma_motor_neuron&oldid=1037462173] xref: FMA:83660 xref: MESH:D009047 @@ -25867,6 +29242,8 @@ relationship: RO:0002120 CL:0008047 ! synapsed to intrafusal muscle fiber id: CL:0008038 name: alpha motor neuron def: "A large, multipolar lower motor neuron of the brainstem and spinal cord that innervates the extrafusal muscle fibers of skeletal muscle and are directly responsible for initiating their contraction. While their cell bodies are in the CNS (in the anterior gray horn of the spinal cord), they are part of the somatic nervous system - a branch of the PNS." [DOI:10.1016/B978-0-12-801238-3.05364-2, Wikipedia:Alpha_motor_neuron&oldid=957148643] +subset: human_subset +subset: mouse_subset synonym: "alpha motoneuron" EXACT [] is_a: CL:0008039 ! lower motor neuron relationship: RO:0002120 CL:0008046 ! synapsed to extrafusal muscle fiber @@ -25877,6 +29254,8 @@ creation_date: 2020-09-23T20:16:26Z id: CL:0008039 name: lower motor neuron def: "The motor neurons of vertebrates that directly innervate skeletal muscles. They receive input from upper motor neurons." [Wikipedia:Lower_motor_neuron&oldid=952547294] +subset: human_subset +subset: mouse_subset xref: FMA:84632 is_a: BFO:0000002 is_a: CL:0005024 ! somatomotor neuron @@ -25888,15 +29267,19 @@ creation_date: 2020-09-23T20:22:07Z id: CL:0008040 name: squamous endothelial cell of venule def: "An endothelial cell of the venule that is squamous shaped. This is in contrast to the cubodial shape of high endothelial venule cells." [GOC:tfm] +subset: human_subset +subset: mouse_subset is_a: CL:0002653 ! squamous endothelial cell is_a: CL:1000414 ! endothelial cell of venule -property_value: dc:date "2024-07-03T19:52:47Z" xsd:string property_value: terms:contributor https://orcid.org/0000-0002-7073-9172 +property_value: terms:date "2024-07-03T19:52:47Z" xsd:dateTime [Term] id: CL:0008046 name: extrafusal muscle fiber def: "A skeletal muscle fiber that is innervated by alpha motor neuron and generates tension by contracting, thereby allowing for skeletal movement. These fibers make up the large mass of skeletal muscle tissue and are attached to bones by tendons." [DOI:10.1016/B978-0-443-10321-6.00004-7, Wikipedia:Extrafusal_muscle_fiber&oldid=978415293] +subset: human_subset +subset: mouse_subset synonym: "myofibra extrafusalis" EXACT [] xref: TH:H3.03.00.0.00007 is_a: CL:0008002 ! skeletal muscle fiber @@ -25909,6 +29292,8 @@ creation_date: 2020-09-26T21:06:15Z id: CL:0008047 name: intrafusal muscle fiber def: "A skeletal muscle fiber that is part of a muscle spindle. These are specialized muscle fibers that serve as proprioceptors, detecting the amount and rate of change in length of a muscle. They are innervated by both sensory neurons and motor neurons (gamma and beta motorneurons, collectively referred to as fusimotor neurons)." [DOI:10.1016/B978-0-443-10321-6.00004-7, Wikipedia:Intrafusal_muscle_fiber&oldid=937508784] +subset: human_subset +subset: mouse_subset synonym: "myofibra intrafusalis" EXACT [] xref: TH:H3.03.00.0.00012 is_a: CL:0002319 ! neural cell @@ -25923,6 +29308,8 @@ creation_date: 2020-09-26T21:07:01Z id: CL:0008048 name: upper motor neuron def: "A glutamatergic motor neuron with a soma in the brainstem or cerebral cortex. They do not synapse directly to muscles but rather to lower motor neurons, which do. They are the main controllers of voluntary movement." [Wikipedia:Upper_motor_neuron&oldid=943248837] +subset: human_subset +subset: mouse_subset is_a: CL:0000100 ! motor neuron is_a: CL:0000679 ! glutamatergic neuron relationship: RO:0002120 CL:0008039 ! synapsed to lower motor neuron @@ -25934,6 +29321,8 @@ creation_date: 2020-09-28T09:41:48Z id: CL:0008049 name: Betz cell def: "A giant pyramidal neuron with a soma in layer Vb of the primary motor cortex that sends its axons down the spinal cord via the corticospinal tract, either synapsing directly with alpha motor neurons, or targeting interneurons in the spinal cord. In humans, Betz cells are the largest known in the central nervous system." [DOI:10.1101/2020.03.31.016972, Wikipedia:Betz_cell&oldid=977472330] +subset: human_subset +subset: mouse_subset synonym: "pyramidal cell of Betz" EXACT [] is_a: CL:2000049 ! primary motor cortex pyramidal cell is_a: CL:4023041 ! L5 extratelencephalic projecting glutamatergic cortical neuron @@ -25949,6 +29338,8 @@ creation_date: 2020-09-28T09:52:58Z id: CL:0009000 name: sensory neuron of spinal nerve def: "A sensory neuron of the spinal nerve that senses body position and sends information about how much the muscle is stretched to the spinal cord." [GOC:nv, GOC:pr] +subset: human_subset +subset: mouse_subset synonym: "spinal sensory neuron" EXACT [] is_a: CL:3000004 ! peripheral sensory neuron intersection_of: CL:0000101 ! sensory neuron @@ -25968,6 +29359,8 @@ id: CL:0009002 name: inflammatory cell def: "Any cell participating in the inflammatory response to a foreign substance, e.g. neutrophil, macrophage." [] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset xref: GOC:pr xref: http://en.wikipedia.org/wiki/Inflammatory_response is_a: CL:0000000 ! cell @@ -25990,6 +29383,8 @@ id: CL:0009004 name: retinal cell def: "Any cell in the retina, the innermost layer or coating at the back of the eyeball, which is sensitive to light and in which the optic nerve terminates." [GOC:pr] subset: general_cell_types_upper_slim +subset: human_subset +subset: mouse_subset xref: PMID:10702418 is_a: CL:0002319 ! neural cell intersection_of: CL:0002319 ! neural cell @@ -26001,6 +29396,8 @@ id: CL:0009005 name: salivary gland cell def: "Any cell in a salivary gland." [] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset xref: GOC:pr xref: http://en.wikipedia.org/wiki/Salivary_gland is_a: CL:0000255 ! eukaryotic cell @@ -26011,19 +29408,26 @@ id: CL:0009006 name: enteroendocrine cell of small intestine def: "An enteroendocrine cell that is located in the small intestine." [http://orcid.org/0000-0003-3440-1876] subset: cellxgene_subset +subset: human_subset subset: location_grouping +subset: mouse_subset synonym: "small intestine enteroendocrine cell" EXACT [] +xref: https://cellxgene.cziscience.com/cellguide/CL_0009006 is_a: CL:1001516 ! intestinal enteroendocrine cell -is_a: CL:1001598 ! small intestine glandular cell +is_a: CL:1001598 ! small intestine secretory cell intersection_of: CL:0000164 ! enteroendocrine cell intersection_of: part_of UBERON:0002108 ! small intestine +property_value: foaf:depiction http://purl.obolibrary.org/obo/cl/images/Small-intestine-cells.png {dc:license="http://creativecommons.org/licenses/by/4.0/", comment="Figure depicts a cross section of intestinal villi in the small intestine, including the crypts of Lieberkuhn (seen here as ‘crypt’), as well as the layer specific locations of cells that exist within the gastrointestinal tract. Layers depicted here include epithelium (rows of cells bordering villus), submucosa (white space below the epithelium containing networks of neurons and ganglia depicted in pink), muscularis mucosae (blue layer), muscularis propria (referred to here as muscle layer).\n\nISC: Intestinal Stem Cell \nTA: Transit Amplifying Cells"} property_value: terms:contributor https://orcid.org/0000-0002-2825-0621 +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nThe enteroendocrine cell of the small intestine is a specialized type of cell that forms part of the lining of the intestinal wall. These cells are interspersed among absorptive cells, mucus-secreting goblet cells, and other gut cell types, forming the crypt-villus axis, which is the functional unit of the small intestinal epithelium. \nFunctionally, enteroendocrine cells play a pivotal role in the gut-endocrine system, which is responsible for the digestive process. These cells translate the luminal nutrient status into hormonal signals thereby acting as chemosensors. They contain secretory granules at their base which release hormones into the bloodstream following chemo-sensation. The hormones they secrete perform diverse functions including regulating gastric secretion, gut motility, insulin release, appetite control and other local and systemic effects. \nIn addition to their endocrine functions, enteroendocrine cells also play a part in the modulation of the immune response in the gut. They can secrete cytokines and chemokines that have a role in directing the immune response to invading pathogens. Moreover, emerging research suggests that these cells play a role in maintaining the balance between gut resident bacteria, known as the gut microbiota, and the host. As such, a comprehensive understanding of the enteroendocrine cells of the small intestine underpins knowledge in nutrition, endocrinology, and various gastroenterological conditions." xsd:string {xref="DOI:10.1016/j.coph.2013.09.008", xref="DOI:10.1038/mi.2017.73", xref="DOI:10.1038/nature24489", xref="DOI:10.1111/j.1365-2613.2011.00767.x", xref="DOI:10.1146/annurev-physiol-021115-105439"} [Term] id: CL:0009007 name: gastrointestinal tract (lamina propria) macrophage of small intestine def: "A macrophage which is resident in the lamina propria of the small intestine." [https://orcid.org/0000-0003-4183-8865] +subset: human_subset subset: location_grouping +subset: mouse_subset synonym: "macrophage of small intestine" BROAD [] synonym: "small intestine lamina propria resident macrophage" EXACT [] is_a: CL:0000865 ! gastrointestinal tract (lamina propria) macrophage @@ -26036,7 +29440,9 @@ property_value: terms:contributor https://orcid.org/0000-0002-2825-0621 id: CL:0009008 name: gastrointestinal tract (lamina propria) macrophage of large intestine def: "A macrophage which is resident in the lamina propria of the large intestine." [https://orcid.org/0000-0003-4183-8865] +subset: human_subset subset: location_grouping +subset: mouse_subset synonym: "large intestine lamina propria resident macrophage" EXACT [] synonym: "macrophage of large intestine" BROAD [] is_a: CL:0000865 ! gastrointestinal tract (lamina propria) macrophage @@ -26051,22 +29457,28 @@ name: paneth cell of colon def: "A paneth cell that is located in the epithelium of the colon." [http://orcid.org/0000-0003-4183-8865, PMID:31753849] subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset subset: location_grouping +subset: mouse_subset synonym: "paneth cell of epithelium of colon" EXACT [] synonym: "paneth cell of epithelium of large intestine" BROAD [] synonym: "paneth-like cell" EXACT [] +xref: https://cellxgene.cziscience.com/cellguide/CL_0009009 is_a: CL:0000510 ! paneth cell is_a: CL:1001588 ! colon glandular cell intersection_of: CL:0000510 ! paneth cell intersection_of: part_of UBERON:0000397 ! colonic epithelium property_value: RO:0002175 NCBITaxon:9606 property_value: terms:contributor https://orcid.org/0000-0002-2825-0621 +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nPaneth cells of the colon are specialized secretory epithelial cells that can be found in the large intestine, albeit in small numbers compared with the small intestine where Paneth cells are more abundant. Under disease conditions such as inflammatory bowel disease, Paneth cells increase in numbers in the colon. They reside in the crypts of Lieberkühn, which are glandular structures embedded within the mucosal layer of the small and large intestine. \nPaneth cells play a crucial role in maintaining intestinal homeostasis and acting as a frontline of defense in our bodies against ingested microbes. They achieve this through the secretion of antimicrobial peptides and proteins such as lysozyme and defensins, which can directly kill or inhibit the growth of various bacteria, fungi, and viruses. They degranulate these substances into the intestinal lumen, especially under conditions of pathogenic invasion or damage to the epithelial lining. \nMoreover, Paneth cells are essential for the maintenance of intestinal stem cells, which continually replace the epithelium of the intestine. They create a niche for these stem cells at the base of the crypts, secreting various signaling molecules and factors that are essential for the growth and differentiation of intestinal stem cells. In essence, the existence and function of Paneth cells are fundamental to the overall gut health and immune defense system, by providing both antimicrobial functions and a conducive environment for the renewal of the intestinal lining. \nThe role of Paneth cells specifically in the colon is of interest in the context of inflammatory bowel disease, such as ulcerative colitis and Crohn’s disease: Their presence in the colon is thought to represent Paneth cell metaplasia and indicates a chronic inflammatory state." xsd:string {xref="DOI:10.1002/ibd.20197", xref="DOI:10.1038/nature09637", xref="DOI:10.1038/nrmicro2546", xref="DOI:10.1093/ecco-jcc/jjac190.0884", xref="DOI:10.1136/gut.48.2.176"} [Term] id: CL:0009010 name: transit amplifying cell def: "Transit-amplifying cells (TACs) are an undifferentiated population in transition between stem cells and differentiated cells." [http://orcid.org/0000-0003-4183-8865, PMID:24813615, PMID:28835754] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "TAC" RELATED [] synonym: "TACs" RELATED [] synonym: "transient amplifying cell" EXACT [] @@ -26083,44 +29495,55 @@ name: transit amplifying cell of colon def: "A rapidly proliferating population of cells that differentiate from stem cells of the intestinal crypt of the colon. Stem cells located in the crypts of Lieberkühn give rise to proliferating progenitor or transit amplifying cells that differentiate into the four major epithelial cell types. These include columnar absorptive cells or enterocytes, mucous secreting goblet cells, enteroendocrine cells and paneth cells." [http://orcid.org/0000-0003-4183-8865, PMID:20801415] subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset subset: location_grouping +subset: mouse_subset synonym: "colon transit amplifying cell" EXACT [] synonym: "transient amplifying cell of colon" EXACT [] synonym: "transient amplifying cell of crypt of Lieberkuhn of colon" EXACT [] synonym: "transit amplifying cell of crypt of Lieberkuhn of colon" EXACT [] synonym: "transit amplifying cell of large intestine" BROAD [] synonym: "transit-amplifying cell of colon" EXACT [] -is_a: CL:0009010 ! transit amplifying cell -intersection_of: CL:0009010 ! transit amplifying cell +xref: https://cellxgene.cziscience.com/cellguide/CL_0009011 +is_a: CL:4047017 ! transit amplifying cell of gut +intersection_of: CL:4047017 ! transit amplifying cell of gut intersection_of: part_of UBERON:0013485 ! crypt of Lieberkuhn of colon relationship: part_of UBERON:0013485 ! crypt of Lieberkuhn of colon relationship: RO:0002202 CL:0002250 ! develops from intestinal crypt stem cell property_value: RO:0002175 NCBITaxon:9606 property_value: terms:contributor https://orcid.org/0000-0002-2825-0621 +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nTransit amplifying cells (TACs) are an intermediate, undifferentiated population between stem cells and differentiated cells. They can be found in multiple regions such as the small intestine and the colon. TACs of the colon, are integral components of the colonic crypts and vital players in the maintenance of colonic tissue. \nThese cells serve a critical function in the rapid and constant renewal of the epithelium lining the colon, with the whole epithelial surface renewed approximately every 5-7 days. They divide rapidly and progressively differentiate into mature columnar epithelium cells, including enterocytes, goblet cells, and enteroendocrine cells. The continued proliferation of transit amplifying cells is fundamental to maintain the balance in cell population while preventing tissue degeneration and maintaining a state of homeostasis. However, uncontrolled proliferation and compromised differentiation capacity can contribute to the development of colon cancers." xsd:string {xref="DOI:10.1016/j.cell.2014.02.057", xref="DOI:10.1053/j.gastro.2018.08.016", xref="DOI:10.1172/jci.insight.150894", xref="DOI:10.3389/fbioe.2023.1189225", xref="https://www.sciencedirect.com/topics/immunology-and-microbiology/intestinal-stem-cell"} [Term] id: CL:0009012 name: transit amplifying cell of small intestine def: "A rapidly proliferating population of cells that differentiate from stem cells of the intestinal crypt of the small intestine. Stem cells located in the crypts of Lieberkühn give rise to proliferating progenitor or transit amplifying cells that differentiate into the four major epithelial cell types. These include columnar absorptive cells or enterocytes, mucous secreting goblet cells, enteroendocrine cells and paneth cells." [http://orcid.org/0000-0003-4183-8865, PMID:20801415] subset: cellxgene_subset +subset: human_subset subset: location_grouping +subset: mouse_subset synonym: "small intestine transit amplifying cell" EXACT [] synonym: "transient amplifying cell of crypt of Lieberkuhn of small intestine" EXACT [] synonym: "transient amplifying cell of small intestine" EXACT [] synonym: "transit amplifying cell of crypt of Lieberkuhn of small intestine" EXACT [] synonym: "transit-amplifying cell of small intestine" EXACT [] -is_a: CL:0009010 ! transit amplifying cell -intersection_of: CL:0009010 ! transit amplifying cell +xref: https://cellxgene.cziscience.com/cellguide/CL_0009012 +is_a: CL:4047017 ! transit amplifying cell of gut +intersection_of: CL:4047017 ! transit amplifying cell of gut intersection_of: part_of UBERON:0001241 ! crypt of Lieberkuhn of small intestine relationship: part_of UBERON:0001241 ! crypt of Lieberkuhn of small intestine relationship: RO:0002202 CL:0002250 ! develops from intestinal crypt stem cell +property_value: foaf:depiction http://purl.obolibrary.org/obo/cl/images/Small-intestine-cells.png {dc:license="http://creativecommons.org/licenses/by/4.0/", comment="Figure depicts a cross section of intestinal villi in the small intestine , including the crypts of Lieberkhun (seen here as ‘crypt’), as well as the layer specific locations of cells that exist within the gastrointestinal tract. Layers depicted here include epithelium (rows of cells bordering villus), submucosa (white space below the epithelium containing networks of neurons and ganglia depicted in pink), muscularis mucosae (blue layer), muscularis propria (referred to here as muscle layer).\n\nISC: Intestinal Stem Cell \nTA: Transit Amplifying Cells"} property_value: terms:contributor https://orcid.org/0000-0002-2825-0621 +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nTransit amplifying cells (TACs) represent an intermediate population between stem cells and fully differentiated cells, and can be found in multiple regions such as the colon and the small intestine. The small intestine's efficiency in absorbing nutrients, its protective barrier function, and its innate cellular renewal every few days is largely dependent on the role played by these TACs.\nTACs of the small intestine are primarily present in the crypt-villus structure of the intestine, more specifically in the crypt region. They originate from Lgr5+ intestinal stem cells that reside at the base of the crypts. Following their derivation from stem cells, TACs undergo up to six rounds of rapid division over a 48-72 hour period, effectively amplifying the cell population, hence their name. During this process, they gradually migrate upward along the walls of the crypt from where they differentiate into diverse mature cell types such as enterocytes, goblet cells, and Paneth cells. \nTACs serve as an important element in the homeostasis and regeneration of the intestinal epithelium, amplifying the pool of cells available for differentiation. They also minimize genetic errors during DNA replication by serving as a 'buffer zone' between the long-lived stem cells and the terminal differentiated cells of the gut lining, thus reducing the potential for propagation of mutation-causing defects. Lastly, TACs play an essential part in gastrointestinal tissue repair following injury or inflammation. Their rapid proliferation and subsequent differentiation abilities often help expedite the wound healing process in the intestinal epithelium." xsd:string {xref="DOI:10.1007/s11894-010-0130-3", xref="DOI:10.1016/j.cell.2014.02.057", xref="DOI:10.1101/gad.1674008"} [Term] id: CL:0009013 name: fetal hepatobiliary progenitor cell def: "A progenitor cell with hepatic and biliary lineage potential, identified in mouse and human, and anatomically restricted to the ductal plate of fetal liver." [https://orcid.org/0000-0002-3163-0115, PMID:31350390] subset: added_for_HCA +subset: human_subset +subset: mouse_subset synonym: "fetal hepatobiliary hybrid progenitor cell" EXACT [] synonym: "HHyP cell" EXACT [] is_a: CL:0011026 ! progenitor cell @@ -26132,7 +29555,9 @@ property_value: terms:contributor https://orcid.org/0000-0002-2825-0621 id: CL:0009014 name: Peyer's patch lymphocyte def: "A lymphocyte that is part of a Peyer's patch. These cells have a major role in driving the immune response to antigens sampled from the intestinal lumen, and in regulating the formation of follicle-associated epithelium and M cells in Peyer's patches by converting intestitial enterocytes into M cells." [https://orcid.org/0000-0003-4183-8865, PMID:23525039, PMID:9252325] +subset: human_subset subset: location_grouping +subset: mouse_subset synonym: "Peyer's patch resident lymphocyte" EXACT [] synonym: "small intestine Peyer's patch lymphocyte" NARROW [] is_a: CL:0000542 ! lymphocyte @@ -26145,7 +29570,9 @@ property_value: terms:contributor https://orcid.org/0000-0002-2825-0621 id: CL:0009015 name: Peyer's patch follicular dendritic cell def: "A follicular dendritic cell located in the Peyer's patch. These cells from a meshwork in which Peyer's patch B cells reside." [https://orcid.org/0000-0003-4183-8865, PMID:24437401] +subset: human_subset subset: location_grouping +subset: mouse_subset is_a: CL:0000255 ! eukaryotic cell is_a: CL:0000442 ! follicular dendritic cell intersection_of: CL:0000442 ! follicular dendritic cell @@ -26159,7 +29586,9 @@ name: intestinal crypt stem cell of large intestine def: "An intestinal stem cell that is located in the large intestine crypt of Liberkuhn. These stem cells reside at the bottom of crypts in the large intestine and are highly proliferative. They either differentiate into transit amplifying cells or self-renew to form new stem cells." [https://orcid.org/0000-0003-4183-8865, PMID:20683682] subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset subset: location_grouping +subset: mouse_subset synonym: "crypt stem cell of large intestine" BROAD [] synonym: "stem cell of large intestine crypt of Lieberkuhn" EXACT [] is_a: CL:0002250 ! intestinal crypt stem cell @@ -26175,7 +29604,9 @@ id: CL:0009017 name: intestinal crypt stem cell of small intestine def: "An intestinal stem cell that is located in the small intestine crypt of Liberkuhn. These stem cells reside at the bottom of crypts in the small intestine and are highly proliferative. They either differentiate into transit amplifying cells or self-renew to form new stem cells." [https://orcid.org/0000-0003-4183-8865, PMID:20683682] subset: cellxgene_subset +subset: human_subset subset: location_grouping +subset: mouse_subset synonym: "crypt stem cell of small intestine" BROAD [] synonym: "stem cell of small intestine crypt of Lieberkuhn" EXACT [] xref: https://cellxgene.cziscience.com/cellguide/CL_0009017 @@ -26184,8 +29615,9 @@ is_a: CL:0002254 ! epithelial cell of small intestine intersection_of: CL:0002250 ! intestinal crypt stem cell intersection_of: part_of UBERON:0001241 ! crypt of Lieberkuhn of small intestine relationship: part_of UBERON:0001241 ! crypt of Lieberkuhn of small intestine +property_value: foaf:depiction http://purl.obolibrary.org/obo/cl/images/Small-intestine-cells.png {dc:license="http://creativecommons.org/licenses/by/4.0/", comment="Figure depicts a cross section of intestinal villi in the small intestine, including the crypts of Lieberkuhn (seen here as ‘crypt’), as well as the layer specific locations of cells that exist within the gastrointestinal tract. Layers depicted here include epithelium (rows of cells bordering villus), submucosa (white space below the epithelium containing networks of neurons and ganglia depicted in pink), muscularis mucosae (blue layer), muscularis propria (referred to here as muscle layer).\n\nISC: Intestinal Stem Cell \nTA: Transit Amplifying Cells"} property_value: terms:contributor https://orcid.org/0000-0002-2825-0621 -property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional.\n\nIntestinal crypt stem cells of the small intestine are a type of adult stem cell intimately involved in the continuous replenishment of the intestinal epithelium, the innermost layer of the intestine responsible for nutrient absorption. These cells, located within the crypts of Lieberkühn, are the origin of various cell lineages that make up the functional units of the small intestine. They possess self-renewal ability, an essential feature of stem cells, which allows them to maintain a steady population in the small intestine.\nOne of the critical roles of intestinal crypt stem cells is to drive the continual renewal process taking place in the small intestine every 3-5 days. By proliferating intensively, these cells produce transient amplifying (TA) cells that are characterized by quick division and progressive differentiation. These cells eventually differentiate into specialized cell types, encompassing absorptive enterocytes, mucin-secreting goblet cells, hormone-secreting enteroendocrine cells, and Paneth cells, all of which have essential roles in digestion and nutrient absorption in the small intestine.\nIntestinal crypt stem cells of the small intestine are also play a significant part in injury recovery. Under regular conditions, these cells primarily exist in an active state, facilitating the constant renovation of the gut lining. However, upon injury or loss of regular intestinal crypt stem cells reserve intestinal stem cells, a slow-cycling and radio-resistant population, can be stimulated to take over the duties of active crypt stem cells. Such plasticity provides a powerful regenerative mechanism that ensures the intestinal epithelium's function and structural integrity amidst diverse conditions." xsd:string {xref="DOI:10.1016/j.celrep.2020.107952", xref="DOI:10.1038/s41575-018-0081-y", xref="DOI:10.1073/pnas.1607327113"} +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nIntestinal crypt stem cells of the small intestine are a type of adult stem cell intimately involved in the continuous replenishment of the intestinal epithelium, the innermost layer of the intestine responsible for nutrient absorption. These cells, located within the crypts of Lieberkühn, are the origin of various cell lineages that make up the functional units of the small intestine. They possess self-renewal ability, an essential feature of stem cells, which allows them to maintain a steady population in the small intestine.\nOne of the critical roles of intestinal crypt stem cells is to drive the continual renewal process taking place in the small intestine every 3-5 days. By proliferating intensively, these cells produce transient amplifying (TA) cells that are characterized by quick division and progressive differentiation. These cells eventually differentiate into specialized cell types, encompassing absorptive enterocytes, mucin-secreting goblet cells, hormone-secreting enteroendocrine cells, and Paneth cells, all of which have essential roles in digestion and nutrient absorption in the small intestine.\nIntestinal crypt stem cells of the small intestine are also play a significant part in injury recovery. Under regular conditions, these cells primarily exist in an active state, facilitating the constant renovation of the gut lining. However, upon injury or loss of regular intestinal crypt stem cells reserve intestinal stem cells, a slow-cycling and radio-resistant population, can be stimulated to take over the duties of active crypt stem cells. Such plasticity provides a powerful regenerative mechanism that ensures the intestinal epithelium's function and structural integrity amidst diverse conditions." xsd:string {xref="DOI:10.1016/j.celrep.2020.107952", xref="DOI:10.1038/s41575-018-0081-y", xref="DOI:10.1073/pnas.1607327113"} [Term] id: CL:0009018 @@ -26193,7 +29625,9 @@ name: lymphocyte of large intestine lamina propria def: "A lymphocyte that resides in the lamina propria of the large intestine." [https://orcid.org/0000-0003-4183-8865] comment: This is a general grouping term created for use in the EMBL-EBI Single Cell Expression Atlas anatomograms. Please use a more specific cell type term for annotation if possible, given the information available to you. subset: human_reference_atlas +subset: human_subset subset: location_grouping +subset: mouse_subset synonym: "lamina propria lymphocyte of large intestine" EXACT [] is_a: CL:0000542 ! lymphocyte intersection_of: CL:0000542 ! lymphocyte @@ -26207,6 +29641,8 @@ id: CL:0009019 name: nephrogenic zone cell def: "A kidney cortical cell that is part of the nephrogenic zone." [https://orcid.org/0000-0002-3163-0115, PMID:29449449] subset: added_for_HCA +subset: human_subset +subset: mouse_subset synonym: "cortical nephrogenic niche cell" EXACT [] synonym: "cortical nephrogenic zone cell" EXACT [] is_a: CL:0002681 ! kidney cortical cell @@ -26219,21 +29655,25 @@ property_value: terms:contributor https://orcid.org/0000-0002-2825-0621 id: CL:0009020 name: tuft cell of appendix def: "An intestinal tuft cell that is a part of a vermiform appendix." [http://orcid.org/0000-0003-3440-1876] +subset: human_subset subset: location_grouping +subset: mouse_subset synonym: "appendix tuft cell" EXACT [] synonym: "tuft cell of appendix vermiformis" EXACT [] synonym: "tuft cell of vermiform appendix" EXACT [] is_a: CL:0002203 ! brush cell of epithelium proper of large intestine -is_a: CL:1000405 ! epithelial cell of appendix intersection_of: CL:0019032 ! intestinal tuft cell intersection_of: part_of UBERON:0001154 ! vermiform appendix +relationship: part_of UBERON:0001154 ! vermiform appendix property_value: terms:contributor https://orcid.org/0000-0002-2825-0621 [Term] id: CL:0009021 name: stromal cell of lamina propria of large intestine def: "A stromal cell found in the lamina propria of the large intestine." [http://orcid.org/0000-0003-4183-8865] +subset: human_subset subset: location_grouping +subset: mouse_subset is_a: CL:0000499 ! stromal cell intersection_of: CL:0000499 ! stromal cell intersection_of: part_of UBERON:0011189 ! lamina propria of large intestine @@ -26245,7 +29685,9 @@ id: CL:0009022 name: stromal cell of lamina propria of small intestine def: "A stromal cell found in the lamina propria of the small intestine." [http://orcid.org/0000-0003-4183-8865] subset: cellxgene_subset +subset: human_subset subset: location_grouping +subset: mouse_subset is_a: CL:0000499 ! stromal cell intersection_of: CL:0000499 ! stromal cell intersection_of: part_of UBERON:0001238 ! lamina propria of small intestine @@ -26256,7 +29698,9 @@ property_value: terms:contributor https://orcid.org/0000-0002-2825-0621 id: CL:0009023 name: small intestine Peyer's patch T cell def: "A T cell which resides in the Peyer's patch of the small intestine." [http://orcid.org/0000-0003-4183-8865] +subset: human_subset subset: location_grouping +subset: mouse_subset synonym: "T cell of Peyer's patch of small intestine" EXACT [] synonym: "T cell of small intestine Peyer's patch" EXACT [] is_a: CL:0002419 ! mature T cell @@ -26270,34 +29714,40 @@ property_value: terms:contributor https://orcid.org/0000-0002-2825-0621 id: CL:0009024 name: mesothelial cell of small intestine def: "A mesothelial cell that is part of the small intestine." [http://orcid.org/0000-0003-4183-8865] +subset: human_subset subset: location_grouping +subset: mouse_subset is_a: CL:0000077 ! mesothelial cell -is_a: CL:0002254 ! epithelial cell of small intestine intersection_of: CL:0000077 ! mesothelial cell -intersection_of: part_of UBERON:0002108 ! small intestine +intersection_of: part_of UBERON:0001206 ! serosa of small intestine +relationship: part_of UBERON:0001206 ! serosa of small intestine property_value: terms:contributor https://orcid.org/0000-0002-2825-0621 [Term] id: CL:0009025 name: mesothelial cell of colon def: "A mesothelial cell that is part of the colon." [http://orcid.org/0000-0003-3440-1876, http://orcid.org/0000-0003-4183-8865] +subset: human_subset subset: location_grouping +subset: mouse_subset synonym: "mesothelial cell of large intestine" BROAD [] is_a: CL:0000077 ! mesothelial cell -is_a: CL:0011108 ! colon epithelial cell intersection_of: CL:0000077 ! mesothelial cell -intersection_of: part_of UBERON:0001155 ! colon +intersection_of: part_of UBERON:0003335 ! serosa of colon +relationship: part_of UBERON:0003335 ! serosa of colon property_value: terms:contributor https://orcid.org/0000-0002-2825-0621 [Term] id: CL:0009026 name: enterocyte of appendix def: "An enterocyte that is a part of a vermiform appendix." [http://orcid.org/0000-0003-3440-1876] +subset: human_subset subset: location_grouping +subset: mouse_subset synonym: "appendix enterocyte" EXACT [] synonym: "enterocyte of appendix vermiformis" EXACT [] synonym: "enterocyte of vermiform appendix" EXACT [] -is_a: CL:0000584 ! enterocyte +is_a: CL:0002071 ! enterocyte of epithelium of large intestine is_a: CL:1000405 ! epithelial cell of appendix intersection_of: CL:0000584 ! enterocyte intersection_of: part_of UBERON:0001154 ! vermiform appendix @@ -26307,12 +29757,14 @@ property_value: terms:contributor https://orcid.org/0000-0002-2825-0621 id: CL:0009027 name: transit amplifying cell of appendix def: "A transit amplifying cell that is part of a crypt of Lieberkuhn of large intestine." [http://orcid.org/0000-0003-3440-1876] +subset: human_subset subset: location_grouping +subset: mouse_subset synonym: "appendix transit amplifying cell" EXACT [] synonym: "transit amplifying cell of appendix vermiformis" EXACT [] synonym: "transit amplifying cell of vermiform appendix" EXACT [] -is_a: CL:0009010 ! transit amplifying cell -intersection_of: CL:0009010 ! transit amplifying cell +is_a: CL:4047017 ! transit amplifying cell of gut +intersection_of: CL:4047017 ! transit amplifying cell of gut intersection_of: part_of UBERON:0013486 ! crypt of Lieberkuhn of appendix relationship: part_of UBERON:0013486 ! crypt of Lieberkuhn of appendix relationship: RO:0002202 CL:0009028 ! develops from intestinal crypt stem cell of appendix @@ -26322,14 +29774,15 @@ property_value: terms:contributor https://orcid.org/0000-0002-2825-0621 id: CL:0009028 name: intestinal crypt stem cell of appendix def: "An intestinal crypt stem cell that is located in the vermiform appendix. These stem cells reside at the bottom of crypts in the appendix and are highly proliferative. They either differentiate into transit amplifying cells or self-renew to form new stem cells." [http://orcid.org/0000-0003-3440-1876, PMID:20683682] +subset: human_subset subset: location_grouping +subset: mouse_subset synonym: "appendix intestinal crypt stem cell" EXACT [] synonym: "intestinal crypt stem cell of appendix vermiformis" EXACT [] synonym: "intestinal crypt stem cell of vermiform appendix" EXACT [] synonym: "stem cell of intestinal crypt of Lieberkuhn of appendix" EXACT [] synonym: "stem cell of intestinal crypt of Lieberkuhn of appendix vermiformis" EXACT [] is_a: CL:0009016 ! intestinal crypt stem cell of large intestine -is_a: CL:1000405 ! epithelial cell of appendix intersection_of: CL:0002250 ! intestinal crypt stem cell intersection_of: part_of UBERON:0013486 ! crypt of Lieberkuhn of appendix relationship: part_of UBERON:0013486 ! crypt of Lieberkuhn of appendix @@ -26339,26 +29792,30 @@ property_value: terms:contributor https://orcid.org/0000-0002-2825-0621 id: CL:0009029 name: mesothelial cell of appendix def: "A mesothelial cell that is located in a vermiform appendix." [http://orcid.org/0000-0003-3440-1876] +subset: human_subset subset: location_grouping +subset: mouse_subset synonym: "appendix mesothelial cell" EXACT [] synonym: "mesothelial cell of appendix vermiformis" EXACT [] synonym: "mesothelial cell of vermiform appendix" EXACT [] is_a: CL:0000077 ! mesothelial cell -is_a: CL:1000405 ! epithelial cell of appendix intersection_of: CL:0000077 ! mesothelial cell -intersection_of: part_of UBERON:0001154 ! vermiform appendix +intersection_of: part_of UBERON:0012498 ! serosa of appendix +relationship: part_of UBERON:0012498 ! serosa of appendix property_value: terms:contributor https://orcid.org/0000-0002-2825-0621 [Term] id: CL:0009030 name: enteroendocrine cell of appendix def: "An intestinal enteroendocrine cell that is located in a vermiform appendix." [http://orcid.org/0000-0003-3440-1876] +subset: human_subset subset: location_grouping +subset: mouse_subset synonym: "appendix enteroendocrine cell" EXACT [] synonym: "enteroendocrine cell of appendix vermiformis" EXACT [] synonym: "enteroendocrine cell of vermiform appendix" EXACT [] +is_a: CL:1000405 ! epithelial cell of appendix is_a: CL:1001516 ! intestinal enteroendocrine cell -is_a: CL:1001585 ! appendix glandular cell intersection_of: CL:1001516 ! intestinal enteroendocrine cell intersection_of: part_of UBERON:0001154 ! vermiform appendix property_value: terms:contributor https://orcid.org/0000-0002-2825-0621 @@ -26368,7 +29825,9 @@ id: CL:0009031 name: T cell of appendix def: "A T cell that is located in a vermiform appendix." [http://orcid.org/0000-0003-3440-1876] comment: This is a general grouping term created for use in the EMBL-EBI Single Cell Expression Atlas anatomograms. Please use a more specific cell type term for annotation if possible, given the information available to you. +subset: human_subset subset: location_grouping +subset: mouse_subset synonym: "appendix T cell" EXACT [] synonym: "T cell of appendix vermiformis" EXACT [] synonym: "T cell of vermiform appendix" EXACT [] @@ -26383,7 +29842,9 @@ id: CL:0009032 name: B cell of appendix def: "A B cell that is located in a vermiform appendix." [http://orcid.org/0000-0003-3440-1876] comment: This is a general grouping term created for use in the EMBL-EBI Single Cell Expression Atlas anatomograms. Please use a more specific cell type term for annotation if possible, given the information available to you. +subset: human_subset subset: location_grouping +subset: mouse_subset synonym: "appendix B cell" EXACT [] synonym: "B cell of appendix vermiformis" EXACT [] synonym: "B cell of vermiform appendix" EXACT [] @@ -26398,7 +29859,9 @@ id: CL:0009033 name: plasma cell of appendix def: "A plasma cell that is located in a vermiform appendix." [http://orcid.org/0000-0003-3440-1876] comment: This is a general grouping term created for use in the EMBL-EBI Single Cell Expression Atlas anatomograms. Please use a more specific cell type term for annotation if possible, given the information available to you. +subset: human_subset subset: location_grouping +subset: mouse_subset synonym: "appendix plasma cell" EXACT [] synonym: "plasma cell of appendix vermiformis" EXACT [] synonym: "plasma cell of vermiform appendix" EXACT [] @@ -26413,7 +29876,9 @@ id: CL:0009034 name: dendritic cell of appendix def: "A dendritic cell that is located in a vermiform appendix." [http://orcid.org/0000-0003-3440-1876] comment: This is a general grouping term created for use in the EMBL-EBI Single Cell Expression Atlas anatomograms. Please use a more specific cell type term for annotation if possible, given the information available to you. +subset: human_subset subset: location_grouping +subset: mouse_subset synonym: "appendix dendritic cell" EXACT [] synonym: "dendritic cell of appendix vermiformis" EXACT [] synonym: "dendritic cell of vermiform appendix" EXACT [] @@ -26427,7 +29892,9 @@ property_value: terms:contributor https://orcid.org/0000-0002-2825-0621 id: CL:0009035 name: stromal cell of lamina propria of vermiform appendix def: "A stromal cell found in the lamina propria of the vermiform appendix." [http://orcid.org/0000-0003-3440-1876] +subset: human_subset subset: location_grouping +subset: mouse_subset synonym: "stromal cell of appendix lamina propria" EXACT [] synonym: "stromal cell of lamina propria of appendix vermiformis" EXACT [] is_a: CL:0009021 ! stromal cell of lamina propria of large intestine @@ -26442,7 +29909,9 @@ id: CL:0009036 name: appendix macrophage def: "A macrophage located in the vermiform appendix." [http://orcid.org/0000-0003-3440-1876] comment: This is a general grouping term created for use in the EMBL-EBI Single Cell Expression Atlas anatomograms. Please use a more specific cell type term for annotation if possible, given the information available to you. +subset: human_subset subset: location_grouping +subset: mouse_subset synonym: "macrophage of appendix" EXACT [] synonym: "macrophage of appendix vermiformis" EXACT [] synonym: "macrophage of vermiform appendix" EXACT [] @@ -26457,7 +29926,9 @@ id: CL:0009037 name: lymph node mantle zone B cell def: "A B lymphocyte that resides in the mantle zone of the lymph node germinal center. These are generally IgM and IgD positive activated B cells that form a 'corona' around the germinal center and are part of the establishment of a secondary lymphatic follicule." [http://orcid.org/0000-0003-4183-8865/, https://www.arppress.org/v/vspfiles/assets/images/Chapter1T25LymphNodes.pdf, PMID:8011279] comment: This is a general grouping term created for use in the EMBL-EBI Single Cell Expression Atlas anatomograms. Please use a more specific cell type term for annotation if possible, given the information available to you. +subset: human_subset subset: location_grouping +subset: mouse_subset synonym: "mantle zone B cell" BROAD [] synonym: "mantle zone B cell of lymph node" EXACT [] is_a: CL:0000236 ! B cell @@ -26472,32 +29943,42 @@ name: colon macrophage def: "A macrophage that is located in the colon." [http://orcid.org/0000-0003-3440-1876] comment: This is a general grouping term created for use in the EMBL-EBI Single Cell Expression Atlas anatomograms. Please use a more specific cell type term for annotation if possible, given the information available to you. subset: cellxgene_subset +subset: human_subset subset: location_grouping +subset: mouse_subset synonym: "macrophage of colon" EXACT [] +xref: https://cellxgene.cziscience.com/cellguide/CL_0009038 is_a: CL:0000235 ! macrophage intersection_of: CL:0000235 ! macrophage intersection_of: part_of UBERON:0001155 ! colon relationship: part_of UBERON:0001155 ! colon property_value: terms:contributor https://orcid.org/0000-0002-2825-0621 +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nColon macrophages are a heterogeneous population of macrophages in the gastrointestinal tract. Intestinal macrophages represent the largest group of macrophages in the body and play a key role as sentinels for pathogen recognition and elimination. Because the gastrointestinal tract is continually exposed to a high antigenic load derived from microbes and food intake, macrophages in the intestines are crucial not only for the gut’s immune defense but also for maintaining gastrointestinal homeostasis, avoiding chronic inflammation despite constantly facing foreign antigens. The phenotypic profiles and cytokine production of intestinal macrophages therefore differ from conventional macrophages elsewhere in the body. \nColon macrophages orchestrate a wide variety of immune responses. They interact with the colon’s microflora thanks to their location in the mucosal layer, thus playing an important role in shaping gut immunity. By presenting antigens, they help to activate and steer an appropriate immune response either by triggering inflammation against harmful pathogens or by supporting tolerance for beneficial microbes. Therefore, disturbances in the colon macrophage population is thought to contribute to colon-related diseases such as inflammatory bowel disease and colon cancer. \nThese immune cells are versatile and multifunctional, not just limited to defensive actions. Colon macrophages interact with the enteric nervous system to regulate gut secretion and motility. They also play a crucial role in maintaining colon tissue health and integrity by contributing to tissue repair processes. This occurs either through phagocytosis of dead cells and remnants, or indirectly through the release of growth factor molecules, which stimulate cellular proliferation and differentiation necessary for tissue regeneration." xsd:string {xref="DOI:10.1016/j.immuni.2022.08.005", xref="DOI:10.1016/j.jcmgh.2021.08.021", xref="DOI:10.1038/s41575-019-0172-4", xref="DOI:10.1038/s41575-023-00769-0"} [Term] id: CL:0009039 name: colon goblet cell def: "A goblet cell that is located in the colon." [http://orcid.org/0000-0003-3440-1876] subset: cellxgene_subset +subset: human_subset subset: location_grouping +subset: mouse_subset synonym: "goblet cell of colon" EXACT [] +xref: https://cellxgene.cziscience.com/cellguide/CL_0009039 is_a: CL:0011108 ! colon epithelial cell is_a: CL:1000320 ! large intestine goblet cell intersection_of: CL:0000160 ! goblet cell -intersection_of: part_of UBERON:0001155 ! colon +intersection_of: part_of UBERON:0000397 ! colonic epithelium property_value: terms:contributor https://orcid.org/0000-0002-2825-0621 +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nColon goblet cells are a subset of intestinal goblet cells that are localized in the epithelial lining of the colon. They are specialized secretory epithelial cells that are recognized by their characteristic ‘goblet’ or flask-like shape and typically have a distinctive appearance due to the accumulation of secretory vesicles in their cytoplasm.\nThe primary function of goblet cells is the secretion of mucus, which is an essential substance for the protection and successful functioning of the intestinal tract. In the colon, goblet cells continuously renew the inner mucus layer, which is attached and impervious to bacteria (the outer layer of the colon is unattached and is the habitat of commensal bacteria)\nThe mucus secreted by goblet cells is rich in glycoproteins known as mucins, especially MUC2, forming a complex web of molecules that comprises the foundational structure of the mucus layer. It traps and eliminates harmful bacteria, while selectively allowing beneficial microbiota to access the epithelial surface and aid in digestion and nutrient absorption. The mucus layer not only provides a provides a protective barrier against pathogen invasion, as well as mechanical damage, and the erosive effects of digestive enzymes, it also acts as a lubricant to facilitate the passage of food material.\nColon goblet cells are also involved in regulating the local immune response within the gut, maintaining the delicate balance between necessary immune reactions to harmful pathogens and tolerance to beneficial microbiota and dietary substances. Goblet cells can modulate immune responses by presenting antigens to dendritic cells, as well as through the production of immunomodulatory molecules that can alter the behavior of immune cells. When the inner mucus layer of the colon is defective, it might be a pathophysiological mechanism for colitis and infectious diseases." xsd:string {xref="DOI:10.1038/mi.2015.32", xref="DOI:10.1038/mi.2016.132", xref="DOI:10.1038/nrgastro.2013.35", xref="DOI:10.1038/s41385-018-0039-y", xref="DOI:10.1073/pnas.1006451107"} [Term] id: CL:0009040 name: stromal cell of lamina propria of colon def: "A stromal cell found in the lamina propria of the colon." [http://orcid.org/0000-0003-3440-1876] +subset: human_subset subset: location_grouping +subset: mouse_subset synonym: "stromal cell of colon lamina propria" EXACT [] is_a: CL:0009021 ! stromal cell of lamina propria of large intestine intersection_of: CL:0000499 ! stromal cell @@ -26510,23 +29991,29 @@ id: CL:0009041 name: tuft cell of colon def: "A tuft cell that is a part of the colon." [http://orcid.org/0000-0003-3440-1876] subset: cellxgene_subset +subset: human_subset subset: location_grouping +subset: mouse_subset synonym: "colon tuft cell" EXACT [] +xref: https://cellxgene.cziscience.com/cellguide/CL_0009041 is_a: CL:0002203 ! brush cell of epithelium proper of large intestine -is_a: CL:0011108 ! colon epithelial cell intersection_of: CL:0019032 ! intestinal tuft cell intersection_of: part_of UBERON:0001155 ! colon +relationship: part_of UBERON:0001155 ! colon property_value: terms:contributor https://orcid.org/0000-0002-2825-0621 +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nTuft cells, also often referred to as brush cells or caveolated cells, are highly specialized sensory cells found in the colon, among other organs. They were named for their unique appearance under an electron microscope, which presents a distinctive ‘tuft-like’ morphology. They are characterized by apical microvilli, arranged in an irregular tuft that confers a dome-like shape. These cells comprise only a small fraction of the cells in the epithelial layer of the colon, making them among the least populous cell types in this region.\nTuft cells in the colon primarily function as chemosensory cells that can sense and respond to environmental changes. These cells can detect and respond to microbial metabolites, helping initiate immune responses against potential threats. \nRecent studies have revealed that tuft cells play a role in responding to intestinal parasitic infections. When a gastrointestinal parasite infects the colon, tuft cells are activated and release the cytokine IL-25. This action increases the production of tuft cells and triggers essential Th2 immune responses to expel the parasites. Also, the removal of tuft cells has been linked to increased susceptibility to these infections. However, overactivity of tuft cells has been associated with inflammatory bowel disease, highlighting the need for a delicate balance of tuft cell function to maintain colon homeostasis." xsd:string {xref="DOI:10.1152/ajpgi.00073.2017", xref="DOI:10.1371/journal.ppat.1010318", xref="DOI:10.3389/fimmu.2022.822867"} [Term] id: CL:0009042 name: enteroendocrine cell of colon def: "An enteroendocrine cell that is located in the colon." [http://orcid.org/0000-0003-3440-1876] subset: cellxgene_subset +subset: human_subset subset: location_grouping +subset: mouse_subset synonym: "colon enteroendocrine cell" EXACT [] +is_a: CL:0011108 ! colon epithelial cell is_a: CL:1001516 ! intestinal enteroendocrine cell -is_a: CL:1001588 ! colon glandular cell intersection_of: CL:0000164 ! enteroendocrine cell intersection_of: part_of UBERON:0001155 ! colon property_value: terms:contributor https://orcid.org/0000-0002-2825-0621 @@ -26534,23 +30021,27 @@ property_value: terms:contributor https://orcid.org/0000-0002-2825-0621 [Term] id: CL:0009043 name: intestinal crypt stem cell of colon -def: "An intestinal crypt stem cell that is located in the colon." [http://orcid.org/0000-0003-3440-1876] +def: "An intestinal crypt stem cell that is located in the crypt of Lieberkuhn of colon." [http://orcid.org/0000-0003-3440-1876, PMID:10841502] subset: cellxgene_subset +subset: human_subset subset: location_grouping +subset: mouse_subset xref: https://cellxgene.cziscience.com/cellguide/CL_0009043 -is_a: CL:0002250 ! intestinal crypt stem cell -is_a: CL:0011108 ! colon epithelial cell +is_a: CL:0009016 ! intestinal crypt stem cell of large intestine intersection_of: CL:0002250 ! intestinal crypt stem cell -intersection_of: part_of UBERON:0001155 ! colon +intersection_of: part_of UBERON:0013485 ! crypt of Lieberkuhn of colon +relationship: part_of UBERON:0013485 ! crypt of Lieberkuhn of colon property_value: terms:contributor https://orcid.org/0000-0002-2825-0621 -property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional.\n\nIntestinal crypt stem cells of the colon, also known as colon crypt base columnar (CBC) cells, are highly specialized cells primarily responsible for the constant self-renewal of the colonic epithelium. These cells are found in the crypts of Lieberkühn - deeply invaginated sections of the colon's mucosal layer. \nThe prime function of intestinal crypt stem cells of the colon is to serve as the source of constant cell regeneration in the colon. Every few days, these stem cells divide and differentiate into the various other types of intestinal cells, such as enterocytes, goblet cells, and enteroendocrine cells. \nA constant renewal cycle is necessary due to the harsh environment of the colon where cells continuously encounter abrasive food matter and potential pathogens, leading to a high turnover rate. When the colon's mucosal layer suffers damage, a rapid response is triggered whereby colon crypt stem cells divide faster and are directed to injured sites to repair the epithelial layer. Dysregulation of these cells' function or proliferation can contribute to disorders such as colorectal cancer." xsd:string {xref="DOI:10.1016/j.cell.2013.07.004", xref="DOI:10.1038/s41575-018-0081-y", xref="DOI:10.1073/pnas.1607327113", xref="DOI:10.1111/j.1365-2184.2009.00642.x", xref="DOI:10.1186/s12943-019-0962-x"} +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nIntestinal crypt stem cells of the colon, also known as colon crypt base columnar (CBC) cells, are highly specialized cells primarily responsible for the constant self-renewal of the colonic epithelium. These cells are found in the crypts of Lieberkühn - deeply invaginated sections of the colon's mucosal layer. \nThe prime function of intestinal crypt stem cells of the colon is to serve as the source of constant cell regeneration in the colon. Every few days, these stem cells divide and differentiate into the various other types of intestinal cells, such as enterocytes, goblet cells, and enteroendocrine cells. \nA constant renewal cycle is necessary due to the harsh environment of the colon where cells continuously encounter abrasive food matter and potential pathogens, leading to a high turnover rate. When the colon's mucosal layer suffers damage, a rapid response is triggered whereby colon crypt stem cells divide faster and are directed to injured sites to repair the epithelial layer. Dysregulation of these cells' function or proliferation can contribute to disorders such as colorectal cancer." xsd:string {xref="DOI:10.1016/j.cell.2013.07.004", xref="DOI:10.1038/s41575-018-0081-y", xref="DOI:10.1073/pnas.1607327113", xref="DOI:10.1111/j.1365-2184.2009.00642.x", xref="DOI:10.1186/s12943-019-0962-x"} [Term] id: CL:0009044 name: lymphocyte of small intestine lamina propria def: "A lymphocyte that resides in the lamina propria of the small intestine. Lamina propria leukocytes and intraepithelial lymphocytes are the effector compartments of the gut mucosal immune system. Lymphocytes circulate through gut associated lymphoid tissues until recruitment by intestinal antigens. They are involved in the gut immune response." [https://orcid.org/0000-0003-4183-8865, PMID:26551552] comment: This is a general grouping term created for use in the EMBL-EBI Single Cell Expression Atlas anatomograms. Please use a more specific cell type term for annotation if possible, given the information available to you. +subset: human_subset subset: location_grouping +subset: mouse_subset synonym: "gastrointestinal tract (lamina propria) lymphocyte of small intestine" EXACT [] synonym: "gastrointestinal tract small intestine (lamina propria) leukocyte" BROAD [] synonym: "lamina propria lymphocyte of small intestine" EXACT [] @@ -26561,6 +30052,7 @@ is_a: CL:0000542 ! lymphocyte intersection_of: CL:0000542 ! lymphocyte intersection_of: part_of UBERON:0001238 ! lamina propria of small intestine relationship: part_of UBERON:0001238 ! lamina propria of small intestine +property_value: foaf:depiction http://purl.obolibrary.org/obo/cl/images/Small-intestine-cells.png {dc:license="http://creativecommons.org/licenses/by/4.0/", comment="Figure depicts a cross section of intestinal villi in the small intestine, including the crypts of Lieberkuhn (seen here as ‘crypt’), as well as the layer specific locations of cells that exist within the gastrointestinal tract. Layers depicted here include epithelium (rows of cells bordering villus), submucosa (white space below the epithelium containing networks of neurons and ganglia depicted in pink), muscularis mucosae (blue layer), muscularis propria (referred to here as muscle layer).\n\nISC: Intestinal Stem Cell \nTA: Transit Amplifying Cells"} property_value: terms:contributor https://orcid.org/0000-0002-2825-0621 [Term] @@ -26568,7 +30060,9 @@ id: CL:0009045 name: B cell of medullary sinus of lymph node def: "A B cell found in the lymph node medullary sinus." [http://orcid.org/0000-0003-4183-8865] comment: This is a general grouping term created for use in the EMBL-EBI Single Cell Expression Atlas anatomograms. Please use a more specific cell type term for annotation if possible, given the information available to you. +subset: human_subset subset: location_grouping +subset: mouse_subset is_a: CL:0000236 ! B cell intersection_of: CL:0000236 ! B cell intersection_of: part_of UBERON:0009744 ! lymph node medullary sinus @@ -26580,7 +30074,9 @@ id: CL:0009046 name: T cell of medullary sinus of lymph node def: "A T cell found in the lymph node medullary sinus." [http://orcid.org/0000-0003-4183-8865] comment: This is a general grouping term created for use in the EMBL-EBI Single Cell Expression Atlas anatomograms. Please use a more specific cell type term for annotation if possible, given the information available to you. +subset: human_subset subset: location_grouping +subset: mouse_subset is_a: CL:0000084 ! T cell intersection_of: CL:0000084 ! T cell intersection_of: part_of UBERON:0009744 ! lymph node medullary sinus @@ -26592,7 +30088,9 @@ id: CL:0009047 name: macrophage of medullary sinus of lymph node def: "A macrophage found in the medullary sinus of the lymph node." [http://orcid.org/0000-0003-4183-8865] comment: This is a general grouping term created for use in the EMBL-EBI Single Cell Expression Atlas anatomograms. Please use a more specific cell type term for annotation if possible, given the information available to you. +subset: human_subset subset: location_grouping +subset: mouse_subset synonym: "lymph node medullary sinus macrophage" EXACT [] synonym: "medullary sinus macrophage" BROAD [] is_a: CL:0000235 ! macrophage @@ -26606,7 +30104,9 @@ id: CL:0009048 name: anorectum macrophage def: "A macrophage that is located in the anorectum." [http://orcid.org/0000-0003-3440-1876] comment: This is a general grouping term created for use in the EMBL-EBI Single Cell Expression Atlas anatomograms. Please use a more specific cell type term for annotation if possible, given the information available to you. +subset: human_subset subset: location_grouping +subset: mouse_subset synonym: "macrophage of anorectum" EXACT [] is_a: CL:0000235 ! macrophage intersection_of: CL:0000235 ! macrophage @@ -26618,7 +30118,9 @@ property_value: terms:contributor https://orcid.org/0000-0002-2825-0621 id: CL:0009049 name: smooth muscle cell of high endothelial venule of lymph node def: "A layer of smooth muscle cells that forms the outer layer of the high endothelial venule of lymph node and pumps to allow flow of lymph fluid carrying lymphocytes." [http://orcid.org/0000-0003-4183-8865, PMID:27881983] +subset: human_subset subset: location_grouping +subset: mouse_subset synonym: "high endothelial venule of lymph node smooth muscle cell" EXACT [] synonym: "high endothelial venule smooth muscle cell" BROAD [] is_a: CL:0008035 ! microcirculation associated smooth muscle cell @@ -26633,7 +30135,9 @@ id: CL:0009050 name: B cell of anorectum def: "A B cell that is located in the anorectum." [http://orcid.org/0000-0003-3440-1876] comment: This is a general grouping term created for use in the EMBL-EBI Single Cell Expression Atlas anatomograms. Please use a more specific cell type term for annotation if possible, given the information available to you. +subset: human_subset subset: location_grouping +subset: mouse_subset is_a: CL:0000236 ! B cell intersection_of: CL:0000236 ! B cell intersection_of: part_of UBERON:8410050 ! anorectum @@ -26645,7 +30149,9 @@ id: CL:0009051 name: T cell of anorectum def: "A T cell that is located in the anorectum." [http://orcid.org/0000-0003-3440-1876] comment: This is a general grouping term created for use in the EMBL-EBI Single Cell Expression Atlas anatomograms. Please use a more specific cell type term for annotation if possible, given the information available to you. +subset: human_subset subset: location_grouping +subset: mouse_subset is_a: CL:0000084 ! T cell intersection_of: CL:0000084 ! T cell intersection_of: part_of UBERON:8410050 ! anorectum @@ -26656,7 +30162,9 @@ property_value: terms:contributor https://orcid.org/0000-0002-2825-0621 id: CL:0009052 name: smooth muscle cell of anorectum def: "A smooth muscle cell that is located in the anorectum." [http://orcid.org/0000-0003-3440-1876] +subset: human_subset subset: location_grouping +subset: mouse_subset synonym: "anorectum smooth muscle cell" EXACT [] is_a: CL:1000279 ! smooth muscle cell of large intestine intersection_of: CL:0000192 ! smooth muscle cell @@ -26668,7 +30176,9 @@ property_value: terms:contributor https://orcid.org/0000-0002-2825-0621 id: CL:0009053 name: stromal cell of anorectum lamina propria def: "A stromal cell found in the lamina propria of the anorectum." [http://orcid.org/0000-0003-3440-1876] +subset: human_subset subset: location_grouping +subset: mouse_subset is_a: CL:0009021 ! stromal cell of lamina propria of large intestine intersection_of: CL:0000499 ! stromal cell intersection_of: part_of UBERON:0011189 ! lamina propria of large intestine @@ -26680,7 +30190,9 @@ property_value: terms:contributor https://orcid.org/0000-0002-2825-0621 id: CL:0009054 name: microfold cell of epithelium proper of anorectum def: "A microfold cell (M cell) that is part of the anorectum." [http://orcid.org/0000-0003-3440-1876] +subset: human_subset subset: location_grouping +subset: mouse_subset synonym: "M cell of anorectum" EXACT [] is_a: CL:1000360 ! microfold cell of epithelium proper of large intestine intersection_of: CL:0000682 ! M cell of gut @@ -26692,7 +30204,9 @@ property_value: terms:contributor https://orcid.org/0000-0002-2825-0621 id: CL:0009055 name: paneth cell of anorectum def: "A paneth cell that is located in the anorectum." [http://orcid.org/0000-0003-3440-1876] +subset: human_subset subset: location_grouping +subset: mouse_subset synonym: "anorectum paneth cell" EXACT [] is_a: CL:0000510 ! paneth cell is_a: CL:0002658 ! glandular cell of the large intestine @@ -26705,10 +30219,12 @@ property_value: terms:contributor https://orcid.org/0000-0002-2825-0621 id: CL:0009056 name: transit amplifying cell of anorectum def: "A transit amplifying cell that is located in the anorectum." [http://orcid.org/0000-0003-3440-1876] +subset: human_subset subset: location_grouping +subset: mouse_subset synonym: "anorectum transit amplifying cell" EXACT [] -is_a: CL:0009010 ! transit amplifying cell -intersection_of: CL:0009010 ! transit amplifying cell +is_a: CL:4047017 ! transit amplifying cell of gut +intersection_of: CL:4047017 ! transit amplifying cell of gut intersection_of: part_of UBERON:8410050 ! anorectum relationship: part_of UBERON:8410050 ! anorectum property_value: terms:contributor https://orcid.org/0000-0002-2825-0621 @@ -26717,10 +30233,12 @@ property_value: terms:contributor https://orcid.org/0000-0002-2825-0621 id: CL:0009057 name: anorectum goblet cell def: "A goblet cell that is located in the anorectum." [http://orcid.org/0000-0003-3440-1876] +subset: human_subset subset: location_grouping +subset: mouse_subset synonym: "goblet cell of anorectum" EXACT [] is_a: CL:1000320 ! large intestine goblet cell -intersection_of: CL:0000160 ! goblet cell +intersection_of: CL:1000320 ! large intestine goblet cell intersection_of: part_of UBERON:8410050 ! anorectum relationship: part_of UBERON:8410050 ! anorectum property_value: terms:contributor https://orcid.org/0000-0002-2825-0621 @@ -26729,10 +30247,11 @@ property_value: terms:contributor https://orcid.org/0000-0002-2825-0621 id: CL:0009058 name: enterocyte of anorectum def: "An enterocyte that is located in the anorectum." [http://orcid.org/0000-0003-3440-1876] +subset: human_subset subset: location_grouping +subset: mouse_subset synonym: "anorectum enterocyte" EXACT [] -is_a: CL:0000584 ! enterocyte -is_a: CL:0002253 ! epithelial cell of large intestine +is_a: CL:0002071 ! enterocyte of epithelium of large intestine intersection_of: CL:0000584 ! enterocyte intersection_of: part_of UBERON:8410050 ! anorectum relationship: part_of UBERON:8410050 ! anorectum @@ -26743,7 +30262,9 @@ id: CL:0009059 name: plasma cell of medullary sinus of lymph node def: "A plasma cell that is located in the medullary sinus of the lymph node." [http://orcid.org/0000-0003-4183-8865] comment: This is a general grouping term created for use in the EMBL-EBI Single Cell Expression Atlas anatomograms. Please use a more specific cell type term for annotation if possible, given the information available to you. +subset: human_subset subset: location_grouping +subset: mouse_subset synonym: "medullary plasma cell" BROAD [] synonym: "medullary sinus plasma cell" BROAD [] synonym: "plasma cell of medullary sinus" BROAD [] @@ -26757,7 +30278,9 @@ property_value: terms:contributor https://orcid.org/0000-0002-2825-0621 id: CL:0009060 name: marginal zone B cell of lymph node def: "A mature B cell located in the marginal zone of the lymph node." [http://orcid.org/0000-0003-4183-8865, WikipediaVersioned:Marginal_zone_B-cell&oldid=1032071222] +subset: human_subset subset: location_grouping +subset: mouse_subset synonym: "lymph node marginal zone B cell" EXACT [] synonym: "marginal zone B cell" BROAD [] is_a: CL:0000785 ! mature B cell @@ -26770,11 +30293,12 @@ property_value: terms:contributor https://orcid.org/0000-0002-2825-0621 id: CL:0009061 name: intestinal crypt stem cell of anorectum def: "An intestinal crypt stem cell that is located in the anorectum." [http://orcid.org/0000-0003-3440-1876] +subset: human_subset subset: location_grouping +subset: mouse_subset synonym: "anorectum intestinal crypt stem cell" EXACT [] -is_a: CL:0002250 ! intestinal crypt stem cell -is_a: CL:0002253 ! epithelial cell of large intestine -intersection_of: CL:0002250 ! intestinal crypt stem cell +is_a: CL:0009016 ! intestinal crypt stem cell of large intestine +intersection_of: CL:0009016 ! intestinal crypt stem cell of large intestine intersection_of: part_of UBERON:8410050 ! anorectum relationship: part_of UBERON:8410050 ! anorectum property_value: terms:contributor https://orcid.org/0000-0002-2825-0621 @@ -26783,7 +30307,9 @@ property_value: terms:contributor https://orcid.org/0000-0002-2825-0621 id: CL:0009062 name: germinal center T cell def: "A specialized type of CD4 positive T cell, the follicular helper T cell (TFH cell), that upregulates CXCR5 expression to enable its follicular localization. These specialised T cells reside in the germinal center of the lymph node." [http://orcid.org/0000-0003-4183-8865, PMID:21739669] +subset: human_subset subset: location_grouping +subset: mouse_subset synonym: "lymph node germinal center T follicular helper cell" EXACT [] synonym: "T follicular helper cell of germinal center of lymph node" EXACT [] synonym: "T follicular helper cell of lymph node germinal center" EXACT [] @@ -26797,9 +30323,11 @@ property_value: terms:contributor https://orcid.org/0000-0002-2825-0621 id: CL:0009063 name: enteroendocrine cell of anorectum def: "An enteroendocrine cell that is located in the anorectum." [http://orcid.org/0000-0003-3440-1876] +subset: human_subset subset: location_grouping +subset: mouse_subset synonym: "anorectum enteroendocrine cell" EXACT [] -is_a: CL:0002658 ! glandular cell of the large intestine +is_a: CL:0002253 ! epithelial cell of large intestine is_a: CL:1001516 ! intestinal enteroendocrine cell intersection_of: CL:0000164 ! enteroendocrine cell intersection_of: part_of UBERON:8410050 ! anorectum @@ -26810,7 +30338,9 @@ property_value: terms:contributor https://orcid.org/0000-0002-2825-0621 id: CL:0009064 name: lymph node paracortex T cell def: "A T cell located in the lymph node paracortex, where macrophages and dendritic cells present antigenic peptides to these naïve T cells, stimulating them to become activated helper T cells or cytotoxic T lymphocytes." [http://orcid.org/0000-0003-4183-8865] +subset: human_subset subset: location_grouping +subset: mouse_subset synonym: "paracortex T cell" BROAD [] synonym: "paracortical T cell" BROAD [] synonym: "T cell of lymph node paracortex" EXACT [] @@ -26824,7 +30354,9 @@ property_value: terms:contributor https://orcid.org/0000-0002-2825-0621 id: CL:0009065 name: tuft cell of anorectum def: "An intestinal tuft cell that is located in the anorectum." [http://orcid.org/0000-0003-3440-1876] +subset: human_subset subset: location_grouping +subset: mouse_subset synonym: "anorectum tuft cell" EXACT [] is_a: CL:0002203 ! brush cell of epithelium proper of large intestine intersection_of: CL:0019032 ! intestinal tuft cell @@ -26837,19 +30369,23 @@ id: CL:0009066 name: stratified squamous epithelial cell of anal canal def: "A stratified squamous epithelial cell that is part of the anal canal." [http://orcid.org/0000-0003-3440-1876] comment: This is a general grouping term created for use in the EMBL-EBI Single Cell Expression Atlas anatomograms. Please use a more specific cell type term for annotation if possible, given the information available to you. +subset: human_subset subset: location_grouping +subset: mouse_subset synonym: "anal canal stratified squamous epithelial cell" EXACT [] is_a: CL:0000240 ! stratified squamous epithelial cell is_a: CL:0002253 ! epithelial cell of large intestine intersection_of: CL:0000240 ! stratified squamous epithelial cell -intersection_of: part_of UBERON:0000159 ! anal canal -relationship: part_of UBERON:0000159 ! anal canal +intersection_of: part_of UBERON:0015716 ! anal canal epithelium +relationship: part_of UBERON:0015716 ! anal canal epithelium property_value: terms:contributor https://orcid.org/0000-0002-2825-0621 [Term] id: CL:0009067 name: vacuolated fetal-type enterocyte def: "An enterocyte found in the small intestine of newborn mammals and characterized by the presence of an apical canalicular system (ACS) leading to production of large vacuoles, important for colostral macromolecule uptake. After birth, the vacuolated fetal-type enterocytes are replaced with enterocytes lacking an ACS." [http://orcid.org/0000-0002-7073-9172, PMID:17901585] +subset: human_subset +subset: mouse_subset synonym: "early enterocyte" RELATED [https://orcid.org/0000-0001-9610-7627, PMID:33290721] synonym: "immature enterocyte" RELATED [https://orcid.org/0000-0001-9610-7627, PMID:33290721] synonym: "vacuolated enterocyte" BROAD [] @@ -26863,6 +30399,8 @@ id: CL:0009068 name: CD8aa(I) thymocyte def: "An unconventional T lymphocyte population within the thymic medulla that is potentially a thymic resident population." [PMID:32079746] subset: human_reference_atlas +subset: human_subset +subset: mouse_subset is_a: CL:0000893 ! thymocyte relationship: part_of UBERON:0002124 ! medulla of thymus property_value: RO:0002175 NCBITaxon:9606 @@ -26873,6 +30411,8 @@ id: CL:0009069 name: CD8aa(II) thymocyte def: "An unconventional T lymphocyte population within the thymic medulla that expresses both alpha/beta and gamma/delta T cell signatures." [PMID:32079746] subset: human_reference_atlas +subset: human_subset +subset: mouse_subset is_a: CL:0000893 ! thymocyte relationship: part_of UBERON:0002124 ! medulla of thymus property_value: RO:0002175 NCBITaxon:9606 @@ -26883,6 +30423,8 @@ id: CL:0009070 name: corticomedullary thymic epithelial cell def: "A thymic epithelial cell located at the corticomedullary junction." [PMID:32079746, PMID:33597545] subset: human_reference_atlas +subset: human_subset +subset: mouse_subset is_a: CL:0002293 ! epithelial cell of thymus relationship: part_of UBERON:0003988 ! thymus corticomedullary boundary property_value: RO:0002175 NCBITaxon:9606 @@ -26893,6 +30435,8 @@ id: CL:0009071 name: medullary thymic epithelial cell type 1 def: "A thymic medullary epithelial cell considered to be a pre-AIRE mTEC population." [PMID:24084687, PMID:32079746, PMID:33597545] subset: human_reference_atlas +subset: human_subset +subset: mouse_subset is_a: CL:0002365 ! medullary thymic epithelial cell relationship: part_of UBERON:0003846 ! thymus epithelium property_value: RO:0002175 NCBITaxon:9606 @@ -26903,6 +30447,8 @@ id: CL:0009072 name: medullary thymic epithelial cell type 2 def: "A thymic medullary epithelial cell that expresses AIRE or other canonical markers of mature mTECs like Fezf2." [PMID:17067941, PMID:24084687, PMID:32079746, PMID:33597545] subset: human_reference_atlas +subset: human_subset +subset: mouse_subset is_a: CL:0002365 ! medullary thymic epithelial cell relationship: part_of UBERON:0003846 ! thymus epithelium property_value: RO:0002175 NCBITaxon:9606 @@ -26913,6 +30459,8 @@ id: CL:0009073 name: medullary thymic epithelial cell type 3 def: "A thymic medullary epithelial cell considered to be a post-AIRE cell. This group of AIRE-mTECs is heterogeneous and also includes mTECs within Hassall's Corpuscles." [PMID:16121185, PMID:17067941, PMID:20861360, PMID:24084687, PMID:32079746, PMID:33597545] subset: human_reference_atlas +subset: human_subset +subset: mouse_subset is_a: CL:0002365 ! medullary thymic epithelial cell relationship: part_of UBERON:0003846 ! thymus epithelium property_value: RO:0002175 NCBITaxon:9606 @@ -26923,6 +30471,8 @@ id: CL:0009074 name: medullary thymic epithelial cell type 4 def: "A thymic medullary epithelial cell that expresses typical tuft cell markers instead of classical mTEC or cTEC markers. This population has a bulbous-like structure." [PMID:30022164, PMID:32079746] subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "thymic tuft cell" BROAD [] is_a: CL:0002365 ! medullary thymic epithelial cell relationship: part_of UBERON:0003846 ! thymus epithelium @@ -26934,6 +30484,8 @@ id: CL:0009075 name: myo-medullary thymic epithelial cell def: "A thymic medullary epithelial cell that expresses muscle-specific biomarkers." [PMID:32079746, PMID:33597545] subset: human_reference_atlas +subset: human_subset +subset: mouse_subset is_a: CL:0002365 ! medullary thymic epithelial cell relationship: part_of UBERON:0003846 ! thymus epithelium property_value: RO:0002175 NCBITaxon:9606 @@ -26944,6 +30496,8 @@ id: CL:0009076 name: neuro-medullary thymic epithelial cell def: "A thymic medullary epithelial cell that expresses neuroendocrine biomarkers." [PMID:32079746, PMID:33597545] subset: human_reference_atlas +subset: human_subset +subset: mouse_subset is_a: CL:0002365 ! medullary thymic epithelial cell relationship: part_of UBERON:0003846 ! thymus epithelium property_value: RO:0002175 NCBITaxon:9606 @@ -26954,6 +30508,8 @@ id: CL:0009077 name: subcapsular thymic epithelial cell def: "A thymic epithelial cell located within the subcapsular region of the thymus." [PMID:6209968] subset: human_reference_atlas +subset: human_subset +subset: mouse_subset is_a: CL:0002364 ! cortical thymic epithelial cell relationship: part_of UBERON:0006936 ! thymus subcapsular epithelium property_value: RO:0002175 NCBITaxon:9606 @@ -26964,8 +30520,11 @@ id: CL:0009078 name: thymic fibroblast type 1 def: "A fibroblast located in the thymic capsule." [PMID:32079746] subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "thymic capsular fibroblast" EXACT [] is_a: CL:0000057 ! fibroblast +is_a: CL:4030001 ! stromal cell of thymus relationship: part_of UBERON:0002122 ! capsule of thymus property_value: RO:0002175 NCBITaxon:9606 property_value: terms:contributor https://orcid.org/0000-0002-2825-0621 @@ -26975,8 +30534,11 @@ id: CL:0009079 name: thymic fibroblast type 2 def: "A fibroblast located between thymic lobules." [PMID:32079746] subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "thymic interlobular fibroblast" EXACT [] is_a: CL:0000057 ! fibroblast +is_a: CL:4030001 ! stromal cell of thymus relationship: part_of UBERON:0004791 ! thymus trabecula property_value: RO:0002175 NCBITaxon:9606 property_value: terms:contributor https://orcid.org/0000-0002-2825-0621 @@ -26986,6 +30548,8 @@ id: CL:0009080 name: tuft cell of small intestine def: "A tuft cell located in the small intestine." [http://orcid.org/0000-0003-3440-1876, http://orcid.org/0000-0003-4183-8865] subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "brush cell of epithelium of small intestine" EXACT [] synonym: "brush cell of epithelium proper of small intestine" EXACT [] synonym: "brush cell of small intestine" EXACT [] @@ -26994,6 +30558,8 @@ is_a: CL:0002254 ! epithelial cell of small intestine is_a: CL:0019032 ! intestinal tuft cell intersection_of: CL:0019032 ! intestinal tuft cell intersection_of: part_of UBERON:0002108 ! small intestine +relationship: part_of UBERON:0001902 ! epithelium of small intestine +property_value: foaf:depiction http://purl.obolibrary.org/obo/cl/images/Small-intestine-cells.png {terms:license="http://creativecommons.org/licenses/by/4.0/", comment="Figure depicts a cross section of intestinal villi in the small intestine, including the crypts of Lieberkuhn (seen here as ‘crypt’), as well as the layer specific locations of cells that exist within the gastrointestinal tract. Layers depicted here include epithelium (rows of cells bordering villus), submucosa (white space below the epithelium containing networks of neurons and ganglia depicted in pink), muscularis mucosae (blue layer), muscularis propria (referred to here as muscle layer).\n\nISC: Intestinal Stem Cell \nTA: Transit Amplifying Cells"} property_value: RO:0002175 NCBITaxon:9606 property_value: terms:contributor https://orcid.org/0000-0002-2825-0621 @@ -27003,6 +30569,8 @@ name: specified double negative thymocyte (Homo sapiens) def: "The human equivalent of a DN2 thymocyte; typically contains two phases, in the latter of which these thymocytes begin the process of beta selection." [PMID:32304633] comment: There is growing evidence that molecular markers characterizing double negative thymocytes are different across species, especially in human versus mouse thymus. This term is restricted for use with human data. subset: human_reference_atlas +subset: human_subset +subset: mouse_subset is_a: CL:0002489 ! double negative thymocyte property_value: RO:0002175 NCBITaxon:9606 property_value: terms:contributor https://orcid.org/0000-0002-2825-0621 @@ -27014,6 +30582,8 @@ name: committed double negative thymocyte (Homo sapiens) def: "The human equivalent of a DN3 thymocyte; these thymocytes finish the process of beta selection." [PMID:32304633] comment: There is growing evidence that molecular markers characterizing double negative thymocytes are different across species, especially in human versus mouse thymus. This term is restricted for use with human data. subset: human_reference_atlas +subset: human_subset +subset: mouse_subset is_a: CL:0002489 ! double negative thymocyte property_value: RO:0002175 NCBITaxon:9606 property_value: terms:contributor https://orcid.org/0000-0002-2825-0621 @@ -27025,6 +30595,8 @@ name: rearranging double negative thymocyte (Homo sapiens) def: "The human equivalent of a DN4 thymocyte." [PMID:32304633] comment: There is growing evidence that molecular markers characterizing double negative thymocytes are different across species, especially in human versus mouse thymus. This term is restricted for use with human data. subset: human_reference_atlas +subset: human_subset +subset: mouse_subset is_a: CL:0002489 ! double negative thymocyte property_value: RO:0002175 NCBITaxon:9606 property_value: terms:contributor https://orcid.org/0000-0002-2825-0621 @@ -27035,13 +30607,15 @@ id: CL:0009084 name: epithelial cell of endometrial gland def: "An epithelial cell that is part of an endometrial gland." [https://orcid.org/0000-0003-3440-1876, https://orcid.org/0000-0003-4183-8865] subset: human_reference_atlas +subset: human_subset subset: location_grouping +subset: mouse_subset synonym: "endometrial glandular epithelial cell" EXACT [] xref: EFO:0010710 is_a: CL:0002149 ! epithelial cell of uterus intersection_of: CL:0000066 ! epithelial cell -intersection_of: part_of UBERON:0002451 ! endometrial gland -relationship: part_of UBERON:0002451 ! endometrial gland +intersection_of: part_of UBERON:0012276 ! endometrium glandular epithelium +relationship: part_of UBERON:0012276 ! endometrium glandular epithelium property_value: RO:0002175 NCBITaxon:9606 property_value: terms:contributor https://orcid.org/0000-0002-2825-0621 property_value: terms:date "2021-11-30T16:13:30Z" xsd:dateTime @@ -27050,6 +30624,8 @@ property_value: terms:date "2021-11-30T16:13:30Z" xsd:dateTime id: CL:0009085 name: colony forming unit – Hill cell def: "An adult endothelial progenitor cell characterised in vivo by homing to ischemic sites and paracrine support of angiogenesis. They may form discrete colonies." [WikipediaVersioned:Endothelial_progenitor_cell&oldid=1069930016#Colony_forming_unit_–_Hill] +subset: human_subset +subset: mouse_subset synonym: "CFU-Hill" EXACT [] is_a: CL:0002619 ! adult endothelial progenitor cell property_value: terms:contributor https://orcid.org/0000-0002-2825-0621 @@ -27060,7 +30636,9 @@ id: CL:0009086 name: endothelial cell of respiratory system lymphatic vessel def: "An endothelial cell that is part of a respiratory system lymphatic vessel." [https://orcid.org/0000-0003-3440-1876, https://orcid.org/0000-0003-4183-8865] subset: human_reference_atlas +subset: human_subset subset: location_grouping +subset: mouse_subset xref: EFO:0010667 is_a: CL:0002138 ! endothelial cell of lymphatic vessel intersection_of: CL:0000115 ! endothelial cell @@ -27074,6 +30652,8 @@ property_value: terms:date "2021-12-03T14:00:44Z" xsd:dateTime id: CL:0009087 name: fused extravillous trophoblast def: "An extravillous trophoblast that is polynuclear." [https://orcid.org/0000-0003-3440-1876, https://orcid.org/0000-0003-4183-8865] +subset: human_subset +subset: mouse_subset synonym: "fused EVT" EXACT [] xref: EFO:0010712 is_a: CL:0008036 ! extravillous trophoblast @@ -27084,6 +30664,8 @@ property_value: terms:date "2021-12-03T14:37:32Z" xsd:dateTime id: CL:0009088 name: circulating angiogenic cell def: "An adult endothelial progenitor cell characterised in vivo by homing to ischemic sites and paracrine support of angiogenesis. These cells do not form colonies." [WikipediaVersioned:Endothelial_progenitor_cell&oldid=1069930016#Circulating_angiogenic_cell] +subset: human_subset +subset: mouse_subset is_a: CL:0002619 ! adult endothelial progenitor cell property_value: terms:contributor https://orcid.org/0000-0002-2825-0621 property_value: terms:date "2022-02-18T10:12:57Z" xsd:dateTime @@ -27092,9 +30674,12 @@ property_value: terms:date "2022-02-18T10:12:57Z" xsd:dateTime id: CL:0009089 name: lung pericyte def: "A pericyte cell that is part of a lung." [https://orcid.org/0000-0003-3440-1876, https://orcid.org/0000-0003-4183-8865] +comment: The marker set HIGD1B, KCNK3 can identify the Human cell type lung pericyte in the Lung with a confidence of 0.84 (NS-Forest FBeta value). {xref="https://doi.org/10.5281/zenodo.11165918"} subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset subset: location_grouping +subset: mouse_subset synonym: "lung pericyte cell" EXACT [] synonym: "pulmonary pericyte" EXACT [] xref: EFO:0010669 @@ -27102,6 +30687,7 @@ is_a: CL:0000669 ! pericyte intersection_of: CL:0000669 ! pericyte intersection_of: part_of UBERON:0002048 ! lung relationship: part_of UBERON:0002048 ! lung +relationship: RO:0015004 CLM:1000047 ! has characterizing marker set NS forest marker set of lung pericyte (Human Lung). property_value: RO:0002175 NCBITaxon:9606 property_value: terms:contributor https://orcid.org/0000-0002-2825-0621 property_value: terms:date "2021-12-03T17:13:33Z" xsd:dateTime @@ -27110,6 +30696,8 @@ property_value: terms:date "2021-12-03T17:13:33Z" xsd:dateTime id: CL:0009090 name: endothelial colony forming cell def: "An adult endothelial progenitor cell that is resident of adult vasculature and capable of differentiating to regenerate endothelial cell populations. Endothelial colony forming cells are characterised in vivo by clonal proliferative status, de novo vessel formation, homing to ischemic sites and paracrine support of angiogenesis. These cells are phenotypically similar to endothelial cells." [http://orcid.org/0000-0002-0819-0473, PMID:33419165, WikipediaVersioned:Endothelial_colony_forming_cell&oldid=1068242094] +subset: human_subset +subset: mouse_subset synonym: "ECFC" EXACT [] is_a: CL:0002619 ! adult endothelial progenitor cell relationship: part_of UBERON:0004537 ! blood vasculature @@ -27120,6 +30708,8 @@ property_value: terms:date "2022-02-18T10:15:32Z" xsd:dateTime id: CL:0009091 name: Leydig stem cell def: "A stem cell found in the interstitial compartment of the neonatal testis; it is capable of self-renewal as well as differentiation into steroidogenic cells (adult Leydig cells). Intermediate stages of development include progenitor Leydig cells and immature Leydig cells." [http://orcid.org/0000-0002-0819-0473, PMID:21181888] +subset: human_subset +subset: mouse_subset synonym: "stem Leydig cell" EXACT [] is_a: CL:0000034 ! stem cell is_a: CL:4030031 ! interstitial cell @@ -27132,7 +30722,9 @@ id: CL:0009092 name: endothelial cell of placenta def: "An endothelial cell that is part of a placenta." [https://orcid.org/0000-0003-3440-1876, https://orcid.org/0000-0003-4183-8865] subset: cellxgene_subset +subset: human_subset subset: location_grouping +subset: mouse_subset synonym: "placental endothelial cell" EXACT [] xref: EFO:0010708 is_a: CL:0000115 ! endothelial cell @@ -27146,7 +30738,9 @@ property_value: terms:date "2021-12-13T13:53:01Z" xsd:dateTime id: CL:0009093 name: smooth muscle cell of placenta def: "A smooth muscle cell that is part of a placenta." [https://orcid.org/0000-0003-3440-1876, https://orcid.org/0000-0003-4183-8865] +subset: human_subset subset: location_grouping +subset: mouse_subset synonym: "placental smooth muscle cell" EXACT [] xref: EFO:0010709 is_a: CL:0000192 ! smooth muscle cell @@ -27160,7 +30754,9 @@ property_value: terms:date "2021-12-13T13:56:42Z" xsd:dateTime id: CL:0009094 name: endothelial cell of hepatic portal vein def: "An endothelial cell that is part of a hepatic portal vein." [https://orcid.org/0000-0003-3440-1876, https://orcid.org/0000-0003-4183-8865, PMID:30348985] +subset: human_subset subset: location_grouping +subset: mouse_subset synonym: "portal endothelial cell" BROAD [] xref: EFO:0010704 is_a: CL:0002543 ! vein endothelial cell @@ -27175,20 +30771,26 @@ id: CL:0009095 name: endothelial cell of uterus def: "An endothelial cell that is part of a uterus." [https://orcid.org/0000-0003-3440-1876, https://orcid.org/0000-0003-4183-8865] subset: cellxgene_subset +subset: human_subset subset: location_grouping +subset: mouse_subset synonym: "uterine endothelial cell" EXACT [] xref: EFO:0010711 +xref: https://cellxgene.cziscience.com/cellguide/CL_0009095 is_a: CL:0000115 ! endothelial cell intersection_of: CL:0000115 ! endothelial cell intersection_of: part_of UBERON:0000995 ! uterus relationship: part_of UBERON:0000995 ! uterus property_value: terms:contributor https://orcid.org/0000-0002-2825-0621 property_value: terms:date "2021-12-13T14:39:25Z" xsd:dateTime +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nThe endothelial cell of the uterus is a specialized type of endothelial cell found in the inner lining of blood vessels, specifically those in the uterus. These cells play critical roles in maintaining uterine health, fertilization, and pregnancy processes. They form the interior surface of blood vessels, creating a barrier between the vessel lumen and surrounding tissue. This fluid environment, maintained by these endothelial cells, provides a platform for the material exchange between blood and tissues, thereby modulating blood coagulation, immune responses, and controlling vasodilation and vasoconstriction. \nFunctionally, the endothelial cells of the uterus are paramount in regulating the uterine blood flow, an important determinant of successful conception and pregnancy outcomes. They support the vascular changes during the reproductive cycle, particularly the spiral arteriolar development and function, essential in endometrial thickening, maturation, and eventual shedding during menstruation periods. The cells also contribute to angiogenesis, a process crucial during implantation and placenta development, whereby new blood vessels form from pre-existing vessels to supply the growing fetus with oxygen and nutrients. Uterine endothelial cells are also implicated in mediating immune responses within the uterus. Changes in these cells can influence various conditions such as reproductive disorders and complications including heavy menstrual bleeding, endometrial hyperplasia, fertility problems, and cancer." xsd:string {xref="DOI:10.1002/cphy.c190015", xref="DOI:10.1111/aji.12128", xref="DOI:10.1172/jci.insight.163422", xref="DOI:10.1530/REP-09-0147", xref="DOI:10.2174/1570161111311050010"} [Term] id: CL:0009096 name: esophagus non-keratinized squamous epithelial cell def: "Any cell that is part of the esophageal non-keratinized stratified squamous epithelium. In humans, the esophagus, which requires flexibility to accommodate swallowing of a bolus, is covered with a non-keratinized epithelium." [http://orcid.org/0000-0003-2034-601X, PMID:11694559] +subset: human_subset +subset: mouse_subset synonym: "esophageal non-keratinized squamous epithelial cell" EXACT [] synonym: "esophageal nonkeratinized squamous epithelial cell" EXACT [] synonym: "esophagus non-keratinizing squamous epithelial cell" EXACT [] @@ -27210,6 +30812,8 @@ property_value: terms:date "2022-02-21T15:00:13Z" xsd:dateTime id: CL:0009097 name: embryonic skeletal muscle fiber def: "A skeletal muscle fiber found in an embryo. In mammalian embryos, skeletal muscle expresses myosin heavy chain-embryonic (MyHC-emb, encoded by the MYH3 gene), which regulates skeletal muscle development." [http://orcid.org/0000-0003-2034-601X, PMID:32094117, PMID:7196501] +subset: human_subset +subset: mouse_subset is_a: CL:0008002 ! skeletal muscle fiber intersection_of: CL:0008002 ! skeletal muscle fiber intersection_of: RO:0002491 UBERON:0000068 ! existence starts and ends during embryo stage @@ -27221,6 +30825,8 @@ property_value: terms:date "2022-02-21T15:39:10Z" xsd:dateTime id: CL:0009098 name: fetal and neonatal skeletal muscle fiber def: "A skeletal muscle fiber found at the fetal and neonatal stages. In mammalian fetuses and neonates, skeletal muscle expresses myosin heavy chain-neonatal (MyHC-neo, encoded by the MYH8 gene). This expression disappears shortly after birth and is replaced by expression of adult heavy chain myosins." [http://orcid.org/0000-0003-2034-601X, PMID:26180627, PMID:7196501] +subset: human_subset +subset: mouse_subset is_a: CL:0008002 ! skeletal muscle fiber intersection_of: CL:0008002 ! skeletal muscle fiber intersection_of: RO:0002488 UBERON:0000092 ! existence starts during post-embryonic stage @@ -27235,6 +30841,8 @@ id: CL:0009099 name: fibro/adipogenic progenitor cell def: "A progenitor cell that is a tissue-resident mesenchymal cell, important for skeletal muscle regeneration, and able to differentiate into both adipocytes or fibroblasts." [PMID:20081841, PMID:22045730, PMID:24605102] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "fibro/adipogenic progenitor" EXACT [] is_a: CL:0008019 ! mesenchymal cell is_a: CL:0011026 ! progenitor cell @@ -27246,6 +30854,8 @@ id: CL:0009100 name: hepatic portal fibroblast def: "A fibroblast located in the portal triad. Hepatic portal fibroblast are a non-parenchymal cell population located adjacent to bile duct epithelia in liver and are distinct from stellate cells. They differentiate into fibrogenic myofibroblasts during chronic injury states producing high levels of collagen." [https://orcid.org/0000-0001-7655-4833, PMID:20209607, PMID:24814904] subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "portal fibroblast" BROAD [] is_a: CL:0000057 ! fibroblast intersection_of: CL:0000057 ! fibroblast @@ -27259,6 +30869,8 @@ property_value: terms:date "2022-03-17T12:00:44Z" xsd:dateTime id: CL:0009101 name: fibroblastic reticular cell def: "A reticular cell involved in directing B cells and T cells to specific regions within a tissue." [] +subset: human_subset +subset: mouse_subset synonym: "FRC" RELATED OMO:0003000 [PMID:35440118] is_a: CL:0000186 ! myofibroblast cell is_a: CL:0000432 ! reticular cell @@ -27270,6 +30882,8 @@ property_value: terms:date "2022-03-21T15:20:33Z" xsd:dateTime id: CL:0009102 name: lymph node fibroblastic reticular cell def: "A specialized, fibroblastic reticular cell of mesenchymal origin found in lymph nodes. In human, it expresses several markers common to myofibroblasts (desmin, vimentin, CD73, CD90, α-smooth muscle actin (αSMA)), and can be differentiated from endothelial cells by its lack of CD31 expression. These cells are critical for the overall organization and function of the lymph node. Lymph node fibroblastic reticular cells (FRCs) can be further classified based on their location, function, and unique marker expression." [https://orcid.org/0000-0001-7655-4833, PMID:21435450, PMID:22566825, PMID:25998961, PMID:28262465, PMID:29752062, PMID:34256989] +subset: human_subset +subset: mouse_subset synonym: "fibroblastic reticular cell" BROAD [] is_a: CL:0009101 ! fibroblastic reticular cell intersection_of: CL:0009101 ! fibroblastic reticular cell @@ -27285,6 +30899,8 @@ id: CL:0009103 name: lymph node marginal reticular cell def: "A fibroblastic reticular cell found in the lymph node subcapsular sinus." [https://orcid.org/0000-0001-7655-4833, PMID:21435450, PMID:22566825, PMID:25998961, PMID:28262465, PMID:29752062, PMID:34256989] subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "marginal reticular cell" BROAD [] is_a: CL:0009102 ! lymph node fibroblastic reticular cell relationship: RO:0001025 UBERON:0005463 ! located in subcapsular sinus of lymph node @@ -27299,6 +30915,8 @@ name: B cell zone reticular cell def: "A fibroblastic reticular cell found in the lymph node germinal center dark zone (B cell zone)." [https://orcid.org/0000-0001-7655-4833, PMID:21435450, PMID:22566825, PMID:25998961, PMID:28262465, PMID:29752062, PMID:34256989] comment: B cell zone reticular cells share similarities with Ch25h-expresssing Ccl19lo T reticular cells found at the B cell follicle T zone interface of mouse lymph nodes. subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "lymph node germinal center dark zone fibroblastic reticular cell" EXACT [] synonym: "T-B boundary reticular cell" RELATED [] is_a: CL:0009102 ! lymph node fibroblastic reticular cell @@ -27313,6 +30931,8 @@ id: CL:0009105 name: T cell zone reticular cell def: "A fibroblastic reticular cell found in the lymph node T cell domain." [https://orcid.org/0000-0001-7655-4833, PMID:21435450, PMID:22566825, PMID:25998961, PMID:28262465, PMID:29752062, PMID:34256989] subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "interfollicular reticular cell" RELATED [PMID:34256989] synonym: "lymph node T cell domain fibroblastic reticular cell" EXACT [] is_a: CL:0009102 ! lymph node fibroblastic reticular cell @@ -27328,6 +30948,8 @@ name: medullary reticular cell def: "A specialized fibroblast found in the medulla of lymph node." [https://orcid.org/0000-0001-7655-4833, PMID:21435450, PMID:22566825, PMID:25998961, PMID:28262465, PMID:29752062, PMID:33981032, PMID:34256989] comment: Origin and phenotype of medullary reticular cells are less well understood in humans than in mice. subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "lymph node medullary reticular cell" EXACT [] synonym: "MedRC" RELATED OMO:0003000 [] synonym: "medullary reticular cell of lymph node" EXACT [] @@ -27343,6 +30965,8 @@ id: CL:0009107 name: lymphatic endothelial cell of subcapsular sinus ceiling def: "A lymphatic endothelial cell located in the subcapsular sinus ceiling of a lymph node. In human, it's characterized by a unique marker expression (NT5e+ and Caveolin-1+)." [https://orcid.org/0000-0001-7655-4833, PMID:31402260, PMID:32426372] subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "lymphatic endothelial cell of subcapsular sinus ceiling of lymph node" EXACT [] is_a: CL:0009115 ! lymph node lymphatic vessel endothelial cell relationship: part_of UBERON:8410071 ! subcapsular sinus ceiling @@ -27355,6 +30979,8 @@ id: CL:0009108 name: lymphatic endothelial cell of subcapsular sinus floor def: "A lymphatic endothelial cell located in the subcapsular sinus floor of a lymph node. In human, it's characterized by a unique marker expression (TNFRSF9+)." [https://orcid.org/0000-0001-7655-4833, PMID:31402260, PMID:32426372] subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "lymphatic endothelial cell of subcapsular sinus floor of lymph node" EXACT [] is_a: CL:0009115 ! lymph node lymphatic vessel endothelial cell relationship: part_of UBERON:8410072 ! subcapsular sinus floor @@ -27367,6 +30993,8 @@ id: CL:0009109 name: lymphatic endothelial cell of trabecula def: "A lymphatic endothelial cell located in a lymph node trabecula." [https://orcid.org/0000-0001-7655-4833, PMID:31402260, PMID:32426372] subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "lymphatic endothelial cell of lymph node trabecula" EXACT [] synonym: "lymphatic endothelial cell of trabeculae" EXACT [] is_a: CL:0009115 ! lymph node lymphatic vessel endothelial cell @@ -27380,6 +31008,8 @@ id: CL:0009110 name: lymphatic endothelial cell of medulla ceiling def: "A lymphatic endothelial cell located in the ceiling part of a lymph node medulla." [https://orcid.org/0000-0001-7655-4833, PMID:31402260, PMID:32426372] subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "lymphatic endothelial cell of lymph node medulla ceiling" EXACT [] is_a: CL:0009115 ! lymph node lymphatic vessel endothelial cell relationship: part_of UBERON:0002007 ! medulla of lymph node @@ -27393,6 +31023,8 @@ name: centrocyte def: "A germinal center B cell found in a lymph node germinal center light zone." [https://orcid.org/0000-0001-7655-4833, PMID:17067937] subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "lymph node centrocyte" EXACT [] is_a: CL:0000844 ! germinal center B cell relationship: part_of UBERON:8410052 ! lymph node germinal center light zone @@ -27406,6 +31038,8 @@ name: centroblast def: "A germinal center B cell found in a lymph node germinal center dark zone." [https://orcid.org/0000-0001-7655-4833, PMID:17067937] subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "lymph node centroblast" EXACT [] is_a: CL:0000844 ! germinal center B cell relationship: part_of UBERON:8410053 ! lymph node germinal center dark zone @@ -27419,6 +31053,8 @@ name: T follicular regulatory cell def: "A regulatory T cell present in the B cell follicles and germinal centers of lymphoid tissues. In humans, it is CXCR5+." [https://orcid.org/0000-0001-7655-4833, PMID:15578096, PMID:26501424, PMID:29769249] subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "follicular regulatory T cell" EXACT [] is_a: CL:0000815 ! regulatory T cell relationship: part_of UBERON:0001744 ! lymphoid tissue @@ -27431,6 +31067,8 @@ id: CL:0009114 name: monocytoid B cell def: "A B cell found in the perisinusoidal area of a lymph node. In humans, monocytoid B cells are a morphologically distinct B cell population\n(oval nuclei, abundant cytoplasm, monocyte-like appearance), share many similarities with marginal zone B cells including marker expression, and are increased in disease settings." [https://orcid.org/0000-0001-7655-4833, PMID:33324003] subset: human_reference_atlas +subset: human_subset +subset: mouse_subset is_a: CL:0000236 ! B cell relationship: part_of UBERON:8410066 ! lymph node paracortex property_value: RO:0002175 NCBITaxon:9606 @@ -27442,6 +31080,8 @@ id: CL:0009115 name: lymph node lymphatic vessel endothelial cell def: "An endothelial cell located in a lymph node lymphatic vessel." [https://orcid.org/0000-0001-7655-4833] subset: human_reference_atlas +subset: human_subset +subset: mouse_subset is_a: CL:0002138 ! endothelial cell of lymphatic vessel intersection_of: CL:0000115 ! endothelial cell intersection_of: part_of UBERON:0000029 ! lymph node @@ -27456,6 +31096,8 @@ id: CL:0009116 name: progenitor cell of mammary luminal epithelium def: "A progenitor cell with the potential to differentiate into luminal epithelial cells of mammary glands. In mouse, CD61 and c-kit were found to be coexpressed by the majority of, but not all, committed luminal progenitor cells." [https://orcid.org/0000-0003-4412-7970, PMID:19063729, PMID:20346151, PMID:21930782] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "luminal progenitor cell" BROAD [] synonym: "progenitor cell of luminal mammary epithelium" EXACT [] is_a: CL:0011026 ! progenitor cell @@ -27466,6 +31108,8 @@ property_value: terms:contributor https://orcid.org/0000-0002-2825-0621 id: CL:0010000 name: keratinized cell of hair follicle def: "A hair follicle matrix region cell which synthesizes keratin and undergoes a characteristic change as it moves upward from the hair bulb to become the hair medulla cortex and hair root sheath." [https://github.com/obophenotype/cell-ontology/issues/417] +subset: human_subset +subset: mouse_subset is_a: CL:2000092 ! hair follicular keratinocyte relationship: part_of UBERON:0005933 ! hair root sheath @@ -27473,6 +31117,8 @@ relationship: part_of UBERON:0005933 ! hair root sheath id: CL:0010001 name: stromal cell of bone marrow def: "A stromal cell that is part_of a bone marrow." [] +subset: human_subset +subset: mouse_subset synonym: "bone marrow stromal cell" EXACT [] is_a: CL:0000499 ! stromal cell is_a: CL:0002092 ! bone marrow cell @@ -27484,6 +31130,8 @@ property_value: terms:contributor https://orcid.org/0000-0002-6601-2165 id: CL:0010002 name: epithelial cell of umbilical artery def: "An epithelial cell that is part_of a umbilical artery." [] +subset: human_subset +subset: mouse_subset synonym: "umbilical artery epithelial cell" EXACT [] is_a: CL:0000066 ! epithelial cell intersection_of: CL:0000066 ! epithelial cell @@ -27508,6 +31156,8 @@ replaced_by: CL:0000322 id: CL:0010004 name: mononuclear cell of bone marrow def: "A mononuclear cell that is part_of a bone marrow." [] +subset: human_subset +subset: mouse_subset synonym: "bone marrow mononuclear cell" EXACT [] is_a: CL:0000842 ! mononuclear cell is_a: CL:1001610 ! bone marrow hematopoietic cell @@ -27519,6 +31169,8 @@ property_value: terms:contributor https://orcid.org/0000-0002-6601-2165 id: CL:0010005 name: atrioventricular bundle cell def: "A specialized cardiomyocyte that transmit signals from the AV node to the cardiac Purkinje fibers." [GOC:mtg_heart] +subset: human_subset +subset: mouse_subset synonym: "AV bundle cell" EXACT [] is_a: CL:0010007 ! His-Purkinje system cell intersection_of: CL:0000000 ! cell @@ -27529,6 +31181,8 @@ relationship: part_of UBERON:0002353 ! bundle of His id: CL:0010006 name: cardiac blood vessel endothelial cell def: "Any blood vessel endothelial cell that is part of some heart." [FBC:Autogenerated] +subset: human_subset +subset: mouse_subset is_a: CL:0000071 ! blood vessel endothelial cell is_a: CL:0010008 ! cardiac endothelial cell intersection_of: CL:0000071 ! blood vessel endothelial cell @@ -27538,6 +31192,8 @@ intersection_of: part_of UBERON:0000948 ! heart id: CL:0010007 name: His-Purkinje system cell def: "Any cell that is part of some His-Purkinje system." [FBC:Autogenerated] +subset: human_subset +subset: mouse_subset is_a: CL:0002494 ! cardiocyte intersection_of: CL:0000000 ! cell intersection_of: part_of UBERON:0004146 ! His-Purkinje system @@ -27549,17 +31205,23 @@ name: cardiac endothelial cell def: "Any endothelial cell that is part of some heart." [FBC:Autogenerated] subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset +xref: https://cellxgene.cziscience.com/cellguide/CL_0010008 is_a: CL:0000115 ! endothelial cell is_a: CL:0002494 ! cardiocyte intersection_of: CL:0000115 ! endothelial cell intersection_of: part_of UBERON:0000948 ! heart relationship: part_of UBERON:0000948 ! heart property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nCardiac endothelial cells are a specialized subset of endothelial cells, the cell type responsible for forming the inner lining of cardiovascular structures such as the heart, and blood vessels. They are a pivotal component of the heart's microenvironment and play a key role in regulating blood pressure, maintaining cardiac homeostasis, in addition to cooperating with other cardiac cells like cardiomyocytes and fibroblasts in the orchestration of a coordinated heart function.\nCardiac endothelial cells contribute to the each stage of the heart's operation, whether during relaxation or contraction. Cardiac endothelial cells release nitric oxide, a potent vasodilator that regulates blood vessel dilation consequently controlling blood pressure and flow. They also produce a myriad of growth factors that aid in new blood vessel formation, known as angiogenesis, crucially needed for tissue repair and regeneration when the heart undergoes damage, as in cases of myocardial infarction.\nFurthermore, cardiac endothelial cells control the passage of nutrients, hormones, and gases between the bloodstream and the heart tissue, ensuring its complex metabolic demands are met adequately. They serve as a selective barrier, regulating the transit of cells and signaling molecules, thereby playing a pivotal role in inflammatory responses and immune cell trafficking. They also contribute to the maintenance of blood fluidity and clotting balance through a complex interplay of anti-thrombic and pro-thrombic factors." xsd:string {xref="DOI:10.1007/s00441-021-03471-2", xref="DOI:10.1530/VB-20-0006", xref="DOI:10.3389/fcvm.2018.00101", xref="DOI:10.3389/fphys.2018.00382", xref="DOI:10.3390/ijms20184411"} [Term] id: CL:0010009 name: camera-type eye photoreceptor cell def: "Any photoreceptor cell that is part of some camera-type eye." [FBC:Autogenerated] +subset: human_subset +subset: mouse_subset synonym: "camera type eye photoreceptor cell" EXACT [] is_a: BFO:0000002 is_a: CL:0000287 ! eye photoreceptor cell @@ -27572,6 +31234,8 @@ relationship: part_of UBERON:0000966 {seeAlso="https://github.com/obophenotype/c id: CL:0010010 name: cerebellar stellate cell def: "Any stellate neuron that has its soma located in some cerebellum." [FBC:Autogenerated] +subset: human_subset +subset: mouse_subset is_a: CL:0000122 ! stellate neuron is_a: CL:1001611 ! cerebellar neuron intersection_of: CL:0000122 ! stellate neuron @@ -27582,6 +31246,8 @@ id: CL:0010011 name: cerebral cortex GABAergic interneuron def: "A GABAergic interneuron whose soma is located in the cerebral cortex." [GOC:dos] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset is_a: CL:0008031 ! cortical interneuron is_a: CL:0011005 ! GABAergic interneuron intersection_of: CL:0011005 ! GABAergic interneuron @@ -27594,11 +31260,13 @@ alt_id: CL:0002609 def: "A CNS neuron of the cerebral cortex." [GOC:tfm] subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "cortical neuron" EXACT [] synonym: "neuron of cerebral cortex" EXACT [] xref: BTO:0004102 xref: FMA:84104 -is_a: CL:2000029 ! central nervous system neuron +is_a: CL:0012001 ! neuron of the forebrain intersection_of: CL:0000540 ! neuron intersection_of: RO:0002100 UBERON:0000956 ! has soma location cerebral cortex relationship: RO:0002100 UBERON:0000956 ! has soma location cerebral cortex @@ -27609,12 +31277,16 @@ property_value: terms:contributor https://orcid.org/0000-0001-7258-9596 [Term] id: CL:0010013 name: type I pinealocyte +subset: human_subset +subset: mouse_subset synonym: "light pinealocyte" EXACT [] is_a: CL:0000652 ! pinealocyte [Term] id: CL:0010014 name: type II pinealocyte +subset: human_subset +subset: mouse_subset synonym: "dark pinealocyte" EXACT [] is_a: CL:0000652 ! pinealocyte @@ -27623,18 +31295,24 @@ id: CL:0010015 name: coronet cell def: "A highly specialized cell type exclusive to and forming neuroepithelium of the Saccus vasculosus, covering the caudal diverticulum of the infundibular recess." [GOC:mr, PMID:17595538] comment: Editor note: remember to link to Saccus vasculosus in next uberon release +subset: human_subset +subset: mouse_subset is_a: CL:0000066 ! epithelial cell [Term] id: CL:0010016 name: collar cell def: "A cell with a flagellum surrounded by a collar of microvilli. The motion of the flagellum draws water past the microvilli, serving either a feeding or sensory function. Collar cells are found in multiple animals, including sponges, echinoderms, and cnidarians. They are also found outside animals in the choanoflagellates. Although collar cells are superficially similar, their cytoskeletal structure and functional biology are different in different groups of organisms." [PMID:25840473] +subset: human_subset +subset: mouse_subset is_a: CL:0000064 ! ciliated cell [Term] id: CL:0010017 name: zygote def: "A zygote in a plant or an animal." [] +subset: human_subset +subset: mouse_subset xref: MESH:D015053 is_a: CL:0000000 ! cell property_value: seeAlso https://github.com/obophenotype/cell-ontology/issues/786 @@ -27643,6 +31321,8 @@ property_value: seeAlso https://github.com/obophenotype/cell-ontology/issues/786 id: CL:0010020 name: cardiac glial cell def: "Any glial cell that is part of some heart." [FBC:Autogenerated] +subset: human_subset +subset: mouse_subset is_a: CL:0000125 ! glial cell is_a: CL:0002494 ! cardiocyte intersection_of: CL:0000125 ! glial cell @@ -27653,6 +31333,8 @@ relationship: part_of UBERON:0000948 ! heart id: CL:0010021 name: cardiac myoblast def: "Any myoblast that develops into some cardiac muscle cell." [FBC:Autogenerated] +subset: human_subset +subset: mouse_subset xref: MESH:D032386 is_a: CL:0000056 ! myoblast intersection_of: CL:0000056 ! myoblast @@ -27665,8 +31347,10 @@ name: cardiac neuron def: "A neuron that has its soma in the heart." [PMID:12486170, PMID:29265764] comment: This term is used in 3 GO terms that were created as part of the heart development focus project. subset: cellxgene_subset -is_a: CL:0000540 ! neuron -intersection_of: CL:0000540 ! neuron +subset: human_subset +subset: mouse_subset +is_a: CL:2000032 ! peripheral nervous system neuron +intersection_of: CL:2000032 ! peripheral nervous system neuron intersection_of: RO:0002100 UBERON:0000948 ! has soma location heart relationship: RO:0002100 UBERON:0000948 ! has soma location heart property_value: seeAlso "https://github.com/obophenotype/cell-ontology/pull/1488" xsd:string @@ -27675,16 +31359,21 @@ property_value: seeAlso "https://github.com/obophenotype/cell-ontology/pull/1488 id: CL:0011000 name: dorsal horn interneuron def: "A CNS interneuron located in the dorsal horn of the spinal cord." [GOC:nv] +subset: human_subset +subset: mouse_subset synonym: "dorsal spinal cord interneuron" RELATED [] +is_a: CL:0002611 ! neuron of the dorsal spinal cord is_a: CL:0005000 {is_inferred="true"} ! spinal cord interneuron intersection_of: CL:0000099 ! interneuron intersection_of: RO:0002100 UBERON:0002256 ! has soma location dorsal horn of spinal cord -relationship: RO:0002100 UBERON:0002256 ! has soma location dorsal horn of spinal cord [Term] id: CL:0011001 name: spinal cord motor neuron def: "A motor neuron that passes from the spinal cord toward or to a muscle and conducts an impulse that causes movement." [GOC:nv] +subset: cellxgene_subset +subset: human_subset +subset: mouse_subset is_a: CL:0000100 {is_inferred="true"} ! motor neuron is_a: CL:2000029 ! central nervous system neuron intersection_of: CL:0000100 ! motor neuron @@ -27696,16 +31385,20 @@ id: CL:0011002 name: lateral motor column neuron def: "A motor neuron that is generated only on limb levels and send axons into the limb mesenchyme." [GOC:nv] comment: Need to MIREOT in 'spinal cord lateral column' from Uberon +subset: human_subset +subset: mouse_subset is_a: CL:0011001 ! spinal cord motor neuron [Term] id: CL:0011003 name: magnocellular neurosecretory cell def: "A neurosecretory neuron residing mainly in the hypothalamic supraoptic and paraventricular nuclei and in a number of smaller accessory cell groups between these two nuclei, that is capable of secreting the hormones oxytocin or vasopressin, and sometimes both, into the systemic circulation." [GOC:nv, MP:0009467, PMID:10711808] +subset: human_subset +subset: mouse_subset synonym: "magnocellular neuron" EXACT [] xref: ILX:0107463 is_a: CL:0000165 ! neuroendocrine cell -is_a: CL:2000029 ! central nervous system neuron +is_a: CL:0012001 ! neuron of the forebrain relationship: RO:0002100 UBERON:0001898 ! has soma location hypothalamus property_value: terms:contributor https://orcid.org/0000-0001-7258-9596 @@ -27715,34 +31408,44 @@ name: lens fiber cell def: "A vetebrate lens cell that is any of the elongated, tightly packed cells that make up the bulk of the mature lens in a camera-type eye." [GO:0070307, GOC:nv] subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "lens fibre cell" EXACT [] +xref: https://cellxgene.cziscience.com/cellguide/CL_0011004 xref: ZFA:0009401 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0002222 ! vertebrate lens cell property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nLens fiber cells are specialized, elongated cells located in the ocular lens, an important part of the eye responsible for focusing light onto the retina to create clear defined images. These cells are unique among body cells, as they are transparent and filled with a clear protein called crystallin to facilitate the passage of light.\nThe entire life cycle of a lens fiber cell includes differentiation from lens epithelial cells, which are the progenitor cells lying at the anterior surface of the lens. In response to various signals, these cells elongate and migrate towards the posterior pole, while simultaneously undergoing a process of denucleation and degradation of cellular organelles. This unique process ensures that the cells do not scatter light, which is critical for the transparency of the lens. After reaching full maturity, lens fiber cells form tightly packed layers, known as laminae, to make up the distinctive architecture of the ocular lens. \nLens fiber cells play pivotal roles in vision. Their primary function is to transmit and focus the light that enters the eye onto the retina, providing the sharpness and clarity necessary for vision. The precise alignment and organization of these cells allow for optimal light transmittance and minimizes scattering, thereby maintaining the transparency of the lens. As such, disruptions or abnormalities in lens fiber cells can lead to serious vision impairment, including conditions like cataracts, a common condition characterized by the opacification of the lens." xsd:string {xref="DOI:10.1016/j.exer.2016.03.016", xref="DOI:10.1016/j.pbiomolbio.2003.11.012", xref="DOI:10.1098/rstb.2010.0300", xref="DOI:10.1242/dev.107953", xref="https://www.sciencedirect.com/topics/immunology-and-microbiology/lens-fiber"} [Term] id: CL:0011005 name: GABAergic interneuron def: "An interneuron that uses GABA as a vesicular neurotransmitter. These interneurons are inhibitory" [GOC:CellBLAST, GOC:nv, PMID:29724907] comment: The formal and textual definitions of this term will need to be altered if evidence for non-inhibitory GABA-ergic neurons emerges. -subset: human_reference_atlas +subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "GABAergic inhibitory interneuron" EXACT [] is_a: CL:0000498 ! inhibitory interneuron is_a: CL:0000617 ! GABAergic neuron intersection_of: CL:0000099 ! interneuron intersection_of: capable_of GO:0061534 ! gamma-aminobutyric acid secretion, neurotransmission -property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0011006 name: Lugaro cell def: "An inhibitory GABAergic interneuron found in the cerebellar cortex." [GOC:nv] +subset: human_subset +subset: mouse_subset +synonym: "globular cell" RELATED [PMID:34194302] is_a: CL:4023057 ! cerebellar inhibitory GABAergic interneuron [Term] id: CL:0011007 name: paraxial cell def: "A cell in the area of mesoderm in the neurulating embryo that flanks and forms simultaneously with the neural tube. The cells of this region give rise to somites." [GOC:NV, PMID:11687492] +subset: human_subset +subset: mouse_subset synonym: "paraxial mesoderm cell" EXACT [] synonym: "presomitic mesoderm cell" NARROW [] synonym: "somitic mesoderm cell" EXACT [] @@ -27768,12 +31471,18 @@ is_a: CL:0011008 ! embryonic hemocyte id: CL:0011010 name: lateral mesodermal cell def: "A cell derived from the mesoderm that is found at the periphery of the embryo." [GOC:NV, PMID:9169844] +subset: cellxgene_subset +subset: human_subset +subset: mouse_subset is_a: CL:0000222 ! mesodermal cell [Term] id: CL:0011011 name: intermediate mesodermal cell def: "A cell derived from the mesoderm that is located between the paraxial mesoderm and the lateral plate." [GOC:NV, ISBN:978-0-87969-707-5] +subset: cellxgene_subset +subset: human_subset +subset: mouse_subset is_a: CL:0000222 ! mesodermal cell [Term] @@ -27781,15 +31490,19 @@ id: CL:0011012 name: neural crest cell def: "A cell of the neural crest. Neural crest cells are multipotent. Premigratory neural crest cells are found at the neural plate boarder, some of which will undergo ectomesynchymal transition and delamination to form migratory neural crest cells." [https://orcid.org/0000-0001-5208-3432, https://orcid.org/0000-0002-9900-7880] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset xref: https://cellxgene.cziscience.com/cellguide/CL_0011012 is_a: CL:0000048 ! multi fate stem cell is_a: CL:0002321 ! embryonic cell (metazoa) -property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional.\n\nNeural crest cells are a group of transient and highly migratory cells that originate from the neuroectoderm during the early stages of embryonic development. They are multipotent cells with an exceptional degree of plasticity, capable of differentiating into various somatic cell types and therefore play a fundamental role in the formation of various organs and tissues, making them critical contributors to the developing embryo. \nAfter the initiation of neurulation (the formation of the neural tube) neural crest cells start to undergo epithelial-to-mesenchymal transition and delaminate and migrate from the dorsal neural tube to several regions throughout the embryo. They differentiate into a range of diverse cell types, such as neurons and glial cells of the peripheral nervous system, including sensory and autonomic neurons. They also contribute to the formation of adrenal glands, pigment cells in the skin (melanocytes), cardiac structures, including parts of the heart septum and major arteries, as well as bones and cartilage of the face and skull.\nDisorders or aberrations in the development or migration of the neural crest cells can lead to serious congenital malformations, such as neurocristopathies, including Hirschsprung disease, neuroblastoma, and neurofibromatosis." xsd:string {xref="DOI:10.1002/dvg.23276", xref="DOI:10.1242/dev.193193", xref="DOI:10.3389/fcell.2020.00635/full", xref="https://doi.org/10.1016/j.ydbio.2011.12.042"} +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nNeural crest cells are a group of transient and highly migratory cells that originate from the neuroectoderm during the early stages of embryonic development. They are multipotent cells with an exceptional degree of plasticity, capable of differentiating into various somatic cell types and therefore play a fundamental role in the formation of various organs and tissues, making them critical contributors to the developing embryo. \nAfter the initiation of neurulation (the formation of the neural tube) neural crest cells start to undergo epithelial-to-mesenchymal transition and delaminate and migrate from the dorsal neural tube to several regions throughout the embryo. They differentiate into a range of diverse cell types, such as neurons and glial cells of the peripheral nervous system, including sensory and autonomic neurons. They also contribute to the formation of adrenal glands, pigment cells in the skin (melanocytes), cardiac structures, including parts of the heart septum and major arteries, as well as bones and cartilage of the face and skull.\nDisorders or aberrations in the development or migration of the neural crest cells can lead to serious congenital malformations, such as neurocristopathies, including Hirschsprung disease, neuroblastoma, and neurofibromatosis." xsd:string {xref="DOI:10.1002/dvg.23276", xref="DOI:10.1242/dev.193193", xref="DOI:10.3389/fcell.2020.00635/full", xref="https://doi.org/10.1016/j.ydbio.2011.12.042"} [Term] id: CL:0011013 name: motile sperm cell def: "A sperm cell that is cabaple of motion (motility)." [PMID:30612620] +subset: human_subset +subset: mouse_subset is_a: CL:0000019 ! sperm is_a: CL:0000219 ! motile cell intersection_of: CL:0000019 ! sperm @@ -27801,6 +31514,8 @@ property_value: terms:contributor https://orcid.org/0000-0001-5208-3432 id: CL:0011014 name: non-motile sperm cell def: "A sperm cell that is not cabaple of motion (motility)." [PMID:30612620] +subset: human_subset +subset: mouse_subset is_a: CL:0000019 ! sperm property_value: terms:contributor https://orcid.org/0000-0001-5208-3432 @@ -27808,6 +31523,8 @@ property_value: terms:contributor https://orcid.org/0000-0001-5208-3432 id: CL:0011015 name: amoeboid sperm cell def: "A motile sperm cell that contain no F-actin, and their motility is powered by a dynamic filament system." [PMID:17708982] +subset: human_subset +subset: mouse_subset is_a: CL:0011013 ! motile sperm cell property_value: terms:contributor https://orcid.org/0000-0001-5208-3432 @@ -27815,6 +31532,8 @@ property_value: terms:contributor https://orcid.org/0000-0001-5208-3432 id: CL:0011016 name: flagellated sperm cell def: "A motile sperm cell that contains a slender threadlike microscopic appendage that enables motion." [https://www.lexico.com/en/definition/flagellum, PMID:30612620] +subset: human_subset +subset: mouse_subset is_a: CL:0011013 ! motile sperm cell intersection_of: CL:0011013 ! motile sperm cell intersection_of: capable_of GO:0030317 ! flagellated sperm motility @@ -27825,6 +31544,8 @@ property_value: terms:contributor https://orcid.org/0000-0001-5208-3432 id: CL:0011017 name: vagal neural crest cell def: "Cell that is part of the vagal neural crest population. The vagal neural crest arises from the axial level of somites 1-7 and has been described as a hybrid between the head and the trunk populations." [PMID:22016183] +subset: human_subset +subset: mouse_subset is_a: CL:0011012 ! neural crest cell property_value: terms:contributor https://orcid.org/0000-0001-5208-3432 @@ -27832,6 +31553,8 @@ property_value: terms:contributor https://orcid.org/0000-0001-5208-3432 id: CL:0011018 name: lymphoid tissue–inducer cell def: "A group 3 innate lymphoid cell that express ROR gamma t and IL-7R alpha in the absence of lineage markers (e.g. CD3, CD19, B220, CD11c, Gr-1), with the functional ability to interact with mesenchymal cells through lymphotoxin and tumor necrosis factor. Lymphoid tissue-inducer cells are key to the development of lymph nodes and Peyer’s patches." [GOC:add, PMID:19029905, PMID:21601793, PMID:27935637, PMID:29454785, PMID:9354470] +subset: human_subset +subset: mouse_subset synonym: "LTi" EXACT [] synonym: "lymphoid tissue inducer cell" EXACT [] is_a: CL:0001071 ! group 3 innate lymphoid cell @@ -27843,6 +31566,8 @@ id: CL:0011019 name: mesothelial cell of epicardium def: "A mesothelial cell that is part of the epicardium." [] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset is_a: CL:0000077 ! mesothelial cell is_a: CL:0002494 ! cardiocyte intersection_of: CL:0000077 ! mesothelial cell @@ -27855,6 +31580,8 @@ id: CL:0011020 name: neural progenitor cell def: "An undifferentiated cell that originates from a neural stem cell and has the capacity to generate multiple types of lineage-restricted progenitors but not to self-renew." [PMID:30574073] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset is_a: CL:0000055 ! non-terminally differentiated cell property_value: terms:contributor https://orcid.org/0000-0001-5208-3432 @@ -27862,6 +31589,8 @@ property_value: terms:contributor https://orcid.org/0000-0001-5208-3432 id: CL:0011021 name: fibroblast of upper back skin def: "A fibroblast that is part of upper back skin." [] +subset: human_subset +subset: mouse_subset is_a: CL:0011022 ! fibroblast of skin of back intersection_of: CL:0000057 ! fibroblast intersection_of: part_of UBERON:0009015 ! upper back skin @@ -27872,6 +31601,8 @@ property_value: terms:contributor https://orcid.org/0000-0001-5208-3432 id: CL:0011022 name: fibroblast of skin of back def: "A fibroblast that is part of skin of back." [] +subset: human_subset +subset: mouse_subset is_a: CL:0002620 ! skin fibroblast intersection_of: CL:0000057 ! fibroblast intersection_of: part_of UBERON:0001068 ! skin of back @@ -27883,9 +31614,10 @@ id: CL:0011023 name: CD25+ mast cell def: "A mast cell that is CD25+." [] comment: Mast cells do not normally express CD25, but neoplastic mast cells may be CD25-positive. +subset: human_subset +subset: mouse_subset synonym: "CD25+ neoplastic mast cell" EXACT [] is_a: CL:0001063 ! neoplastic cell -is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0001063 ! neoplastic cell intersection_of: RO:0001000 CL:0000097 ! derives from mast cell intersection_of: RO:0002104 PR:000001380 ! has plasma membrane part interleukin-2 receptor subunit alpha @@ -27898,6 +31630,8 @@ id: CL:0011024 name: double negative T regulatory cell def: "A double negative thymocyte that is CD3-positive, CD4-negative, CD8-negative, that that are present in the periphery in very low numbers and predominantly produce INF-gamma, TNF-alpha, and a low amount of TGF-beta, but not IL-2, IL-4, IL-10 or IL-13 upon activation." [PMID:16285891] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "CD4-negative, CD8-negative, alpha-beta regulatory T cells" EXACT [] synonym: "DN Treg" EXACT [] synonym: "double-negative alpha-beta regulatory T cell" EXACT [] @@ -27912,6 +31646,8 @@ id: CL:0011025 name: exhausted T cell def: "An effector T cell that displays impaired effector functions (e.g., rapid production of effector cytokines, cytotoxicity) and has limited proliferative potential." [PMID:26544946] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "Tex cell" EXACT [] is_a: CL:0000911 ! effector T cell property_value: terms:contributor https://orcid.org/0000-0001-5208-3432 @@ -27921,6 +31657,8 @@ id: CL:0011026 name: progenitor cell def: "A precursor cell that has a tendency to differentiate into a specific type of cell. They are descendants of stem cells, only they are more constrained in their differentiation potential or capacity for self-renewal, and are often more limited in both senses." [https://doi.org/10.1016/B978-0-12-409503-8.00002-0, ISBN:978-1-62808-994-3] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset is_a: BFO:0000002 is_a: CL:0000255 ! eukaryotic cell is_a: CL:0011115 ! precursor cell @@ -27934,17 +31672,24 @@ id: CL:0011027 name: skeletal muscle fibroblast def: "Any fibroblast that is part of skeletal muscle tissue." [https://orcid.org/0000-0001-6164-0667, PMID:28369879] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "skeleton muscle fibroblast" EXACT [] +xref: https://cellxgene.cziscience.com/cellguide/CL_0011027 is_a: CL:0000188 ! cell of skeletal muscle is_a: CL:1001609 ! muscle fibroblast intersection_of: CL:0000057 ! fibroblast intersection_of: part_of UBERON:0001134 ! skeletal muscle tissue property_value: terms:contributor https://orcid.org/0000-0001-5208-3432 +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nSkeletal muscle fibroblasts (SMFs), with their spindle-shaped morphology, play a crucial role in maintaining the structure and function of skeletal muscles. They produce connective tissues enveloping muscle fibers, offering vital structural support for optimal muscle contraction. SMFs are integral components of the dynamic and complex microenvironment of muscle tissue, contributing significantly to healthy muscle development and homeostasis.\nSMFs primarily synthesize and secrete extracellular matrix (ECM) components, such as collagen, fibronectin, and proteoglycans. The resulting ECM exhibits mechanical properties that resist tensile forces from muscle contractions, ensuring muscle efficiency. It also crucially transmits force during muscle movement, aids muscle attachment to the skeletal structure, and serves as a scaffold for muscle regeneration and repair. \nFollowing injury, they proliferate and transform into myofibroblasts, aiding wound contraction and depositing new ECM for tissue repair. Additionally, these fibroblasts modulate inflammatory responses by secreting cytokines and interact with other cell types, like immune cells and satellite cells, to coordinate muscle healing. In diseases, an imbalance in SMF activity may lead to conditions such as fibrosis, marked by excessive ECM deposition and impaired muscle function." xsd:string {xref="DOI:10.1016/j.diff.2016.05.007", xref="DOI:10.1186/s13578-021-00579-4", xref="DOI:10.1186/s13578-022-00856-w"} [Term] id: CL:0011028 name: olfactory ensheathing cell def: "A neural-crest derived glial cell that supports the growth and survival of primary olfactory neuroons from the neuroepithelium in the nasal cavity to the brain by encasing large bundles of numerous unmyelinated axons." [PMID:22456085] +subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "OEC" EXACT [] xref: BTO:0002771 is_a: CL:0000125 ! glial cell @@ -27966,6 +31711,8 @@ property_value: terms:contributor https://orcid.org/0000-0001-5208-3432 id: CL:0011030 name: dermal microvascular endothelial cell def: "Any microvascular endothelial cell that is part of the dermis." [BTO:0004574, CL:patterns/cellPartOfAnatomicalEntity] +subset: human_subset +subset: mouse_subset synonym: "dermal microvascular endothelium cell" EXACT [] synonym: "DMEC cell" EXACT [] is_a: CL:2000008 ! microvascular endothelial cell @@ -27978,7 +31725,10 @@ property_value: terms:contributor https://orcid.org/0000-0001-5208-3432 id: CL:0011031 name: monocyte-derived dendritic cell def: "A dendritic cell that develops from a monocyte." [BTO:0002900, PMID:30719026, PMID:32733468] +subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "MDDC cell" EXACT [] is_a: CL:0000782 ! myeloid dendritic cell relationship: RO:0002202 CL:0000576 ! develops from monocyte @@ -27989,6 +31739,8 @@ property_value: terms:contributor https://orcid.org/0000-0001-5208-3432 id: CL:0011032 name: lysosome-rich enterocyte def: "An enterocyte that possesses a large supranuclear vacuolar system that preferentially internalizes dietary protein via receptor-mediated and fluid-phase endocytosis for intracellular digestion and trans-cellular transport. In zebrafish these cells are located in the posterior region of the mid intestine throughout life. In mammals they are found in the ileum pre-weaning and later are replaced by mature enterocytes." [https://orcid.org/0000-0002-1009-339X, https://orcid.org/0000-0002-2244-7917, PMID:31474562] +subset: human_subset +subset: mouse_subset synonym: "early enterocyte" RELATED [https://orcid.org/0000-0001-9610-7627, PMID:33290721] synonym: "immature enterocyte" RELATED [https://orcid.org/0000-0001-9610-7627, PMID:33290721] synonym: "LRE" EXACT [] @@ -28000,6 +31752,8 @@ property_value: terms:contributor https://orcid.org/0000-0001-5208-3432 id: CL:0011100 name: galanergic neuron def: "Neuron that secretes the neurotransmitter galanin." [GOC:NV, PMID:23159249, ZFIN:CVS, ZFIN:YB] +subset: human_subset +subset: mouse_subset is_a: CL:0000540 ! neuron [Term] @@ -28007,15 +31761,22 @@ id: CL:0011101 name: chorionic trophoblast cell def: "Cells of the uterine chorion that acquire specialized structural and/or functional features that characterize chorionic trophoblasts. These cells will migrate towards the spongiotrophoblast layer and give rise to syncytiotrophoblasts of the labyrinthine layer." [GOC:NV] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset +xref: https://cellxgene.cziscience.com/cellguide/CL_0011101 is_a: CL:0000351 ! trophoblast cell intersection_of: CL:0000351 ! trophoblast cell intersection_of: part_of UBERON:0003124 ! chorion membrane relationship: part_of UBERON:0003124 ! chorion membrane +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nThe chorionic trophoblast cell, vital for placental development in mammals, originates from the blastocyst's outer layer, the trophectoderm. As a significant component of the placenta, the chorion forms the external fetal-maternal interface and consists primarily of chorionic trophoblast cells. These cells are pivotal in embryogenesis, fetal nutrition, waste removal, and immune response generation, contributing crucially to the success of pregnancy.\nChorionic trophoblast cells undergo trophoblast differentiation, giving rise to specialized sub-types: cytotrophoblasts and syncytiotrophoblasts. Cytotrophoblasts, found in the inner layer, serve as stem cells and contribute to proliferative activities. In contrast, syncytiotrophoblasts, originating from cytotrophoblasts, form the outer layer with a distinctive multinucleated, continuous, and non-proliferative structure. These cells play a key role in maternal-fetal gas and nutrient exchange, producing essential hormones like human chorionic gonadotropin (hCG), progesterone, and estrogen, vital for sustaining pregnancy.\nApart from their physiological roles, chorionic trophoblast cells play a crucial role in shielding the fetus from the maternal immune system. They accomplish this by modifying the expression of major histocompatibility complex (MHC) molecules, which are self-identifying proteins utilized by the immune system to identify foreign cells. Through selective expression of specific types of these molecules, trophoblast cells can evade cytotoxic T cells that might otherwise attack them, while still retaining the ability to attract natural killer cells. These natural killer cells assist in trophoblast invasion and the remodeling of blood vessels in the uterus." xsd:string {xref="DOI:10.1007/s00018-019-03104-6", xref="DOI:10.1093/biolre/ioy070", xref="DOI:10.1155/2014/579279", xref="https://www.ncbi.nlm.nih.gov/books/NBK53245/", xref="https://www.sciencedirect.com/topics/medicine-and-dentistry/placenta-development"} [Term] id: CL:0011102 name: parasympathetic neuron def: "Parasympathetic neurons are part of the parasympathetic nervous sysem and the cell bodies lie in the brain and sacral region of the spinal cord. The neurons are mainly cholinergic." [GOC:NV, isbn:0080923437] +subset: cellxgene_subset +subset: human_subset +subset: mouse_subset xref: ZFA:0005776 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000107 ! autonomic neuron @@ -28025,6 +31786,8 @@ name: sympathetic neuron def: "Sympathetic neurons are part of the sympathetic nervous system and are primarily adrenergic producing the neurotransmitter noradrenalin along with other neuropeptides." [GOC:NV, isbn:0080923437] subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset xref: ZFA:0005777 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000107 ! autonomic neuron property_value: RO:0002175 NCBITaxon:9606 @@ -28035,6 +31798,8 @@ name: interplexiform cell def: "A type of interneuron in the retinal inner nuclear layer which\ncarries information from the inner plexiform layer and the outer\nplexiform layer." [GOC:NV, PMID:12771169] comment: Need to MIREOT retinal inner nuclear layer (part of) subset: eye_upper_slim +subset: human_subset +subset: mouse_subset is_a: BFO:0000002 is_a: CL:0000099 ! interneuron is_a: CL:0009004 ! retinal cell @@ -28045,6 +31810,8 @@ id: CL:0011105 name: dopamanergic interplexiform cell def: "A type of interneuron in the retinal inner nuclear layer which\ncarries information from the inner plexiform layer and the outer\nplexiform layer, using dopamine." [GOC:NV, PMID:12771169] comment: This type of cell is found in Danio rerio. +subset: human_subset +subset: mouse_subset is_a: CL:0000700 ! dopaminergic neuron is_a: CL:0011104 ! interplexiform cell intersection_of: CL:0011104 ! interplexiform cell @@ -28055,6 +31822,8 @@ id: CL:0011106 name: GABAnergic interplexiform cell def: "A type of interneuron in the retinal inner nuclear layer which\ncarries information from the inner plexiform layer and the outer\nplexiform layer using GABA." [GOC:NV, PMID:12771169] comment: This type of cell is found in many mammals. +subset: human_subset +subset: mouse_subset is_a: CL:0011005 ! GABAergic interneuron is_a: CL:0011104 ! interplexiform cell intersection_of: CL:0011104 ! interplexiform cell @@ -28075,16 +31844,20 @@ id: CL:0011108 name: colon epithelial cell def: "Epithelial cell that is part of the colon epithelium." [GOC:NV] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "colonic epithelial cell" EXACT [] is_a: CL:0002253 ! epithelial cell of large intestine intersection_of: CL:0000066 ! epithelial cell -intersection_of: part_of UBERON:0001155 ! colon +intersection_of: part_of UBERON:0000397 ! colonic epithelium relationship: part_of UBERON:0000397 ! colonic epithelium [Term] id: CL:0011109 name: hypocretin-secreting neuron def: "A neuron that releases hypocretin as a neurotransmitter." [GOC:NV, PMID:23848055] +subset: human_subset +subset: mouse_subset synonym: "orexin" EXACT [] xref: ZFA:0005778 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000151 ! secretory cell @@ -28097,6 +31870,8 @@ relationship: capable_of GO:0061585 ! orexin secretion, neurotransmission id: CL:0011110 name: histaminergic neuron def: "Neuron that secretes histamine." [GOC:NV, PMID:22677810] +subset: human_subset +subset: mouse_subset xref: FBbt:00007367 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} is_a: CL:0000540 ! neuron is_a: CL:0002274 ! histamine secreting cell @@ -28108,6 +31883,8 @@ relationship: capable_of GO:0061538 ! histamine secretion, neurotransmission id: CL:0011111 name: gonadotropin-releasing hormone neuron def: "A neuroendocrine cell that secretes gonadotropin-releasing hormone (GnRH). A GnRH neuron is born in the nasal placode during embryonic development and migrates through the nose and forebrain to the hypothalamus. This cell regulates reproduction by secreting GnRH into the pituitary portal vessels to induce the release of gonadotropins into the general circulation." [GOC:NV, PMID:21828096] +subset: human_subset +subset: mouse_subset synonym: "GnRH neuron" EXACT [] synonym: "GnRH-secreting neuron" EXACT [] is_a: CL:0000165 ! neuroendocrine cell @@ -28125,8 +31902,11 @@ replaced_by: CL:0011003 id: CL:0011113 name: spiral ganglion neuron def: "Neuron found in the spiral ganglion." [GOC:NV] -is_a: CL:0000540 ! neuron -intersection_of: CL:0000540 ! neuron +subset: cellxgene_subset +subset: human_subset +subset: mouse_subset +is_a: CL:2000032 ! peripheral nervous system neuron +intersection_of: CL:2000032 ! peripheral nervous system neuron intersection_of: RO:0002100 UBERON:0000395 ! has soma location cochlear ganglion relationship: RO:0002100 UBERON:0000395 ! has soma location cochlear ganglion @@ -28134,6 +31914,8 @@ relationship: RO:0002100 UBERON:0000395 ! has soma location cochlear ganglion id: CL:0011114 name: segmented neutrophil of bone marrow def: "A segmented neutrophilic cell of the bone marrow reserve pool that expresses CD11b (integrin alpha-M) and high levels of CD16 (low affinity immunoglobulin gamma Fc region receptor III) on its cell surface." [PMID:11138622, PMID:15514007] +subset: human_subset +subset: mouse_subset is_a: CL:0000096 ! mature neutrophil is_a: CL:1001610 ! bone marrow hematopoietic cell @@ -28143,6 +31925,8 @@ name: precursor cell def: "A cell that, by division or terminal differentiation, can give rise to other cell types." [GOC:dos] comment: Work is needed on GO 'cell differentiation' before it is clear whether the equivalent class definition 'native cell' that capable_of some 'cell differentiation' works. Also, may want to consider merging this with non-terminally differentiated cell. subset: cellxgene_subset +subset: human_subset +subset: mouse_subset is_a: CL:0000000 ! cell intersection_of: CL:0000000 ! cell intersection_of: capable_of GO:0030154 ! cell differentiation @@ -28153,6 +31937,8 @@ id: CL:0012000 name: astrocyte of the forebrain def: "An astrocyte of the forebrain." [] subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "forebrain astrocyte" EXACT [] is_a: CL:0000127 {is_inferred="true"} ! astrocyte is_a: CL:2000005 ! brain macroglial cell @@ -28167,10 +31953,11 @@ id: CL:0012001 name: neuron of the forebrain def: "A CNS neuron of the forebrain." [] subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "forebrain neuron" EXACT [] -is_a: CL:0000117 {is_inferred="true"} ! CNS neuron (sensu Vertebrata) is_a: CL:2000029 ! central nervous system neuron -intersection_of: CL:0000117 ! CNS neuron (sensu Vertebrata) +intersection_of: CL:0000540 ! neuron intersection_of: RO:0002100 UBERON:0001890 ! has soma location forebrain relationship: RO:0002100 UBERON:0001890 ! has soma location forebrain property_value: RO:0002175 NCBITaxon:9606 @@ -28181,6 +31968,8 @@ id: CL:0013000 name: forebrain radial glial cell def: "Any radial glial cell that is part of some forebrain." [FBC:Autogenerated] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset is_a: CL:0000681 ! radial glial cell intersection_of: CL:0000681 ! radial glial cell intersection_of: part_of UBERON:0001890 ! forebrain @@ -28190,6 +31979,9 @@ relationship: part_of UBERON:0001890 ! forebrain id: CL:0015000 name: cranial motor neuron def: "Motor neuron that innervate muscles that control eye, jaw, and facial movements of the vertebrate head and parasympathetic neurons that innervate certain glands and organs." [ZFIN:CVS] +subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "cranial motoneuron" EXACT [] xref: PMID:14699587 xref: ZFA:0005730 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} @@ -28199,21 +31991,28 @@ is_a: CL:0000100 ! motor neuron id: CL:0017000 name: pulmonary ionocyte def: "An ionocyte that is part of the lung epithelium. The cells from this type are major sources of the CFTR protein in human and mice." [PMID:30069044, PMID:30069046] +comment: The marker set ASCL3, BSND can identify the Human cell type pulmonary ionocyte in the Lung with a confidence of 0.82 (NS-Forest FBeta value). {xref="https://doi.org/10.5281/zenodo.11165918"} subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset xref: https://cellxgene.cziscience.com/cellguide/CL_0017000 is_a: CL:0000082 ! epithelial cell of lung is_a: CL:0005006 ! ionocyte intersection_of: CL:0005006 ! ionocyte intersection_of: part_of UBERON:0000115 ! lung epithelium +relationship: RO:0015004 CLM:1000032 ! has characterizing marker set NS forest marker set of pulmonary ionocyte (Human Lung). property_value: RO:0002175 NCBITaxon:9606 property_value: terms:contributor https://orcid.org/0000-0003-2473-2313 -property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional.\n\nThe pulmonary ionocyte is a relatively newly identified, specific epithelial cell type found primarily in the pulmonary or respiratory system. Discovered through novel mapping techniques in 2018, these cells are surprisingly rare, making up less than 2% of the cells in the lung's airway, yet they play an essential role in the airway surface liquid and mucus regulation, a crucial factor in lung health.\nThe main responsibility of the pulmonary ionocyte pertains to the regulation and mobilization of chloride ions. They express a high level of CFTR (Cystic Fibrosis Transmembrane Conductance Regulator) gene, which encodes a protein channel across the membrane of cells that produce mucus, sweat, saliva, tears, and digestive enzymes. The activity of CFTR regulates the movement of chloride ions and fluids in and out of cells, which helps maintain a balance of fluid in the organs they are expressed in. If CFTR is dysfunctional, it can cause conditions such as cystic fibrosis, characterized by thick, sticky mucus that can clog the lungs and obstruct the pancreas, leading to respiratory and digestive issues.\nThe discovery of this cell type offers new doors to the treatment and further understanding of diseases like cystic fibrosis. Increased understanding of pulmonary ionocytes could contribute to the development of novel therapeutic approaches to manipulate the function of CFTR in the lungs and other organs affected by dysfunctional CFTR." xsd:string {xref="DOI:10.1038/s41586-018-0393-7", xref="DOI:10.1146/annurev-pathol-042420-094031", xref="DOI:10.1172/JCI171268"} +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nThe pulmonary ionocyte is a relatively newly identified, specific epithelial cell type found primarily in the pulmonary or respiratory system. Discovered through novel mapping techniques in 2018, these cells are surprisingly rare, making up less than 2% of the cells in the lung's airway, yet they play an essential role in the airway surface liquid and mucus regulation, a crucial factor in lung health.\nThe main responsibility of the pulmonary ionocyte pertains to the regulation and mobilization of chloride ions. They express a high level of CFTR (Cystic Fibrosis Transmembrane Conductance Regulator) gene, which encodes a protein channel across the membrane of cells that produce mucus, sweat, saliva, tears, and digestive enzymes. The activity of CFTR regulates the movement of chloride ions and fluids in and out of cells, which helps maintain a balance of fluid in the organs they are expressed in. If CFTR is dysfunctional, it can cause conditions such as cystic fibrosis, characterized by thick, sticky mucus that can clog the lungs and obstruct the pancreas, leading to respiratory and digestive issues.\nThe discovery of this cell type offers new doors to the treatment and further understanding of diseases like cystic fibrosis. Increased understanding of pulmonary ionocytes could contribute to the development of novel therapeutic approaches to manipulate the function of CFTR in the lungs and other organs affected by dysfunctional CFTR." xsd:string {xref="DOI:10.1038/s41586-018-0393-7", xref="DOI:10.1146/annurev-pathol-042420-094031", xref="DOI:10.1172/JCI171268"} [Term] id: CL:0017001 name: splanchnic mesodermal cell def: "A mesodermal cell that is part of the splanchnic layer of lateral plate mesoderm." [] +subset: cellxgene_subset +subset: human_subset +subset: mouse_subset is_a: CL:0011010 ! lateral mesodermal cell relationship: part_of UBERON:0004872 ! splanchnic layer of lateral plate mesoderm property_value: terms:contributor https://orcid.org/0000-0003-2473-2313 @@ -28223,24 +32022,29 @@ id: CL:0017002 name: prostate neuroendocrine cell def: "A neuroendocrine cell that is part of the prostate epithelium." [http://orcid.org/0000-0001-7772-9578, PMID:33842835] subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "neuroendocrine cell of prostate epithelium" EXACT [] synonym: "neuroendocrine cell of the prostate" EXACT [] +is_a: CL:0000150 ! glandular secretory epithelial cell is_a: CL:0000165 ! neuroendocrine cell intersection_of: CL:0000165 ! neuroendocrine cell intersection_of: part_of UBERON:0000428 ! prostate epithelium relationship: part_of UBERON:0000428 ! prostate epithelium property_value: RO:0002175 NCBITaxon:9606 -created_by: http://orcid.org/0000-0003-2473-2313 +property_value: terms:contributor http://orcid.org/0000-0003-2473-2313 [Term] id: CL:0017003 name: epithelial cell of prostatic urethra def: "An epithelial cell that is part of the prostatic urethra." [PMID:30566875] +subset: human_subset +subset: mouse_subset is_a: CL:1000296 ! epithelial cell of urethra intersection_of: CL:0000066 ! epithelial cell intersection_of: part_of UBERON:0001335 ! prostatic urethra relationship: part_of UBERON:0001335 ! prostatic urethra -created_by: http://orcid.org/0000-0003-2473-2313 +property_value: terms:contributor http://orcid.org/0000-0003-2473-2313 [Term] id: CL:0017004 @@ -28248,6 +32052,8 @@ name: telocyte def: "A supportive cell with a small, oval-shaped body and one to five telopodes. Telopodes are cytoplasmic protrusions from tens to hundreds of micrometers long and mostly below 0.2 microns of caliber." [https://en.wikipedia.org/wiki/Telocyte, MESH:D000067170, PMID:20367664, PMID:28714595, PMID:31311805] comment: Telocytes manage to develop complex networks in almost all organs of the human body. Although staining positively for vimentin antibody, some uncertainty still persists over the mesenchymal origin of these cells. {xref="https://doi.org/10.1016/B978-0-12-818561-2.00001-1"} subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "ICLC" RELATED [PMID:20367664] synonym: "interstitial Cajal cell-like cell" NARROW [PMID:20367664] synonym: "interstitial Cajal-like cell" NARROW [PMID:20367664] @@ -28255,48 +32061,56 @@ synonym: "interstitial neuron" RELATED [PMID:31311805] is_a: CL:0002320 ! connective tissue cell relationship: has_part GO:0120327 ! telopode property_value: RO:0002175 NCBITaxon:9606 -created_by: http://orcid.org/0000-0003-2473-2313 +property_value: terms:contributor http://orcid.org/0000-0003-2473-2313 [Term] id: CL:0017005 name: lymphoblast def: "A lymphocyte that has gotten larger after being stimulated by an antigen." [http://orcid.org/0000-0001-9990-8331, NCIT:C13013] subset: blood_and_immune_upper_slim +subset: human_subset +subset: mouse_subset xref: BTO:0000772 xref: EFO:0000572 xref: FMA:83030 is_a: CL:0000542 ! lymphocyte relationship: output_of GO:0046649 ! lymphocyte activation -property_value: dc:date "2022-08-17T14:20:01Z" xsd:string -created_by: http://orcid.org/0000-0003-2473-2313 +property_value: terms:contributor http://orcid.org/0000-0003-2473-2313 +property_value: terms:date "2022-08-17T14:20:01Z" xsd:dateTime [Term] id: CL:0017006 name: B-lymphoblast def: "A lymphocyte of B lineage that has gotten larger after being stimulated by an antigen." [EFO:0005293, https://orcid.org/0000-0002-2825-0621] subset: blood_and_immune_upper_slim +subset: human_subset +subset: mouse_subset xref: EFO:0005293 xref: FMA:83031 is_a: CL:0000945 ! lymphocyte of B lineage is_a: CL:0017005 ! lymphoblast -property_value: dc:date "2022-08-17T14:30:32Z" xsd:string -created_by: http://orcid.org/0000-0003-2473-2313 +property_value: terms:contributor http://orcid.org/0000-0003-2473-2313 +property_value: terms:date "2022-08-17T14:30:32Z" xsd:dateTime [Term] id: CL:0017009 name: Axl+ dendritic cell, human def: "A human dendritic cell that expresses the AXL and SIGLEC6 genes." [PMID:28428369, PMID:29221729, PMID:31156637] +subset: human_subset +subset: mouse_subset synonym: "AS DC, human" EXACT [] is_a: CL:0001056 ! dendritic cell, human relationship: RO:0002292 PR:O43699 ! expresses sialic acid-binding Ig-like lectin 6 (human) relationship: RO:0002292 PR:P30530 ! expresses tyrosine-protein kinase receptor UFO (human) -property_value: dc:date "2022-08-25T14:18:37Z" xsd:dateTime -created_by: http://orcid.org/0000-0003-2473-2313 +property_value: terms:contributor http://orcid.org/0000-0003-2473-2313 +property_value: terms:date "2022-08-25T14:18:37Z" xsd:dateTime [Term] id: CL:0017010 name: hillock cell of urethral epithelium def: "A hillock cell that is part of the urethra." [http://orcid.org/0000-0001-7772-9578, PMID:30566875] +subset: human_subset +subset: mouse_subset synonym: "hillock cell of urethra" EXACT [] is_a: CL:1000296 ! epithelial cell of urethra is_a: CL:4030024 ! hillock cell @@ -28309,6 +32123,8 @@ property_value: terms:date "2022-10-13T13:51:35Z" xsd:dateTime id: CL:0017011 name: hillock cell of prostatic urethral epithelium def: "A hillock cell that is part of the prostatic urethra." [http://orcid.org/0000-0001-7772-9578, PMID:30566875] +subset: human_subset +subset: mouse_subset synonym: "hillock cell of prostatic urethra" EXACT [] is_a: CL:0017003 ! epithelial cell of prostatic urethra is_a: CL:0017010 ! hillock cell of urethral epithelium @@ -28426,7 +32242,10 @@ name: tracheobronchial serous cell def: "Any serous secreting cell that is part of the tracheobronchial epithelium." [] subset: added_for_HCA subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "serous cell of tracheobronchial tree" EXACT [] +xref: https://cellxgene.cziscience.com/cellguide/CL_0019001 is_a: CL:0000255 ! eukaryotic cell is_a: CL:0000313 ! serous secreting cell intersection_of: CL:0000313 ! serous secreting cell @@ -28434,6 +32253,7 @@ intersection_of: part_of UBERON:0007196 ! tracheobronchial tree relationship: part_of UBERON:0007196 ! tracheobronchial tree property_value: terms:contributor https://orcid.org/0000-0003-2034-601X property_value: terms:date "2020-05-07T16:03:27Z" xsd:dateTime +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nSerous cells of the tracheobronchial are found on the surface epithelium, submucosal glands, or both, depending on species. They appear in tubulo-acinar arrangements in submucosal glands.\nTracheobronchial serous cells play a vital role in maintaining respiratory health by secreting serous fluid, which is rich in enzymes, ions, and antimicrobial proteins. This serous fluid is essential in clearing out debris, trapping and neutralizing inhaled pathogens and particulate matters, thereby helping in preventing infections. Their secretory products also include water and electrolytes that, combined with mucus (from mucous cells), maintain proper humidity within the airway and lubricate its surfaces, facilitating unhindered airflow. Dysfunction of these cells may lead to diseases such as cystic fibrosis." xsd:string {xref="DOI:10.1016/j.resp.2007.06.017", xref="DOI:10.1113/jphysiol.2003.052779", xref="DOI:10.1146/annurev.ph.52.030190.000525", xref="DOI:10.1152/ajplung.00068.2019"} [Term] id: CL:0019002 @@ -28441,6 +32261,8 @@ name: tracheobronchial chondrocyte def: "Any chondrocyte that is part of the tracheobronchial tree." [] subset: added_for_HCA subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "chondrocyte of tracheobronchial tree" EXACT [] is_a: CL:0000138 ! chondrocyte intersection_of: CL:0000138 ! chondrocyte @@ -28457,9 +32279,11 @@ def: "Any goblet cell that is part of the tracheobronchial epithelium." [] subset: added_for_HCA subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "goblet cell of tracheobronchial tree" EXACT [] is_a: CL:0002202 ! epithelial cell of tracheobronchial tree -is_a: CL:0002370 ! respiratory goblet cell +is_a: CL:0002370 ! respiratory tract goblet cell intersection_of: CL:0000160 ! goblet cell intersection_of: part_of UBERON:0008397 ! tracheobronchial epithelium property_value: RO:0002175 NCBITaxon:9606 @@ -28471,6 +32295,8 @@ id: CL:0019015 name: lung parenchyma resident eosinophil def: "An eosinophil with a ring-shaped nucleus that is resident in the lung parenchyma. In mouse, lung parenchyma resident eosinophils are IL-5-independent Siglec-F(intermediate) CD62L+ CD101(low). In human, they are Siglec-8+ CD62L+ IL-3R(low)." [PMID:27548519] subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "lung-resident eosinophil" EXACT [PMID:27548519] synonym: "rEos" EXACT [PMID:27548519] is_a: CL:0000774 ! band form eosinophil @@ -28486,6 +32312,8 @@ id: CL:0019017 name: lymphatic vessel smooth muscle cell def: "A smooth muscle cell that is part of any lymphatic vessel." [PMID:15109561] subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "smooth muscle cell of lymphatic vessel" EXACT [] is_a: CL:0000359 ! vascular associated smooth muscle cell intersection_of: CL:0000192 ! smooth muscle cell @@ -28499,7 +32327,10 @@ property_value: terms:date "2020-07-21T12:29:51Z" xsd:dateTime id: CL:0019018 name: blood vessel smooth muscle cell def: "A smooth muscle cell that is part of any blood vessel." [PMID:9108778] +subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "smooth muscle cell of blood vessel" EXACT [] is_a: CL:0000359 ! vascular associated smooth muscle cell intersection_of: CL:0000192 ! smooth muscle cell @@ -28513,21 +32344,29 @@ property_value: terms:date "2020-07-21T12:42:48Z" xsd:dateTime id: CL:0019019 name: tracheobronchial smooth muscle cell def: "A smooth muscle cell that is part of the tracheobronchial tree." [PMID:10853867] +comment: The marker set ACTA2, TAGLN can identify the Human cell type tracheobronchial smooth muscle cell in the Lung with a confidence of 0.69 (NS-Forest FBeta value). {xref="https://doi.org/10.5281/zenodo.11165918"} subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "smooth muscle cell of tracheobronchial tree" EXACT [] +xref: https://cellxgene.cziscience.com/cellguide/CL_0019019 is_a: CL:0000192 ! smooth muscle cell intersection_of: CL:0000192 ! smooth muscle cell intersection_of: part_of UBERON:0007196 ! tracheobronchial tree relationship: part_of UBERON:0007196 ! tracheobronchial tree +relationship: RO:0015004 CLM:1000056 ! has characterizing marker set NS forest marker set of tracheobronchial smooth muscle cell (Human Lung). property_value: RO:0002175 NCBITaxon:9606 property_value: terms:contributor https://orcid.org/0000-0003-2034-601X property_value: terms:date "2020-07-21T12:50:22Z" xsd:dateTime +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nTracheobronchial smooth muscle cells are universally located in the tracheobronchial tree and play a critical role in controlling and modulating the size of the airway lumen, thereby contributing significantly to the airflow resistance. \nThese cells display both phasic and tonic characteristics, which are vital for airway contractility. Phasic activity manifests as cyclic contraction and relaxation, similar to the behavior seen in gastrointestinal smooth muscle cells, whilst tonic activity resembles vascular smooth muscle cells, maintaining a constant degree of tension. These features enable tracheobronchial smooth muscle cells to constrict the airways in response to various mechanical and chemical stimuli, including allergens, parasympathetic nervous stimulation, changes in gas composition, and cold air, thus protecting the delicate alveoli from potential damage.\nTracheobronchial smooth muscle cells, beyond their contractile function, actively contribute to airway remodeling in conditions like asthma. Their proliferative and synthetic capabilities lead to smooth muscle hypertrophy, hyperplasia, and the production of extracellular matrix components, collectively causing abnormal airway narrowing." xsd:string {xref="DOI:10.1007/978-3-540-79090-7_5", xref="DOI:10.1152/japplphysiol.00950.2012", xref="https://www.ncbi.nlm.nih.gov/books/NBK556044/"} [Term] id: CL:0019020 name: extrahepatic cholangiocyte def: "An epithelial cell of the extrahepatic bile ducts, including the left and right hepatic duct, common hepatic duct, and common bile duct. They are columnar in shape, and have a large nuclear-to-cytoplasmic ratio relative to small/intrahepatic cholangiocytes." [PMID:23720296] +subset: human_subset +subset: mouse_subset synonym: "large bile duct cholangiocyte" EXACT [PMID:23720296] is_a: CL:1000488 ! cholangiocyte intersection_of: CL:1000488 ! cholangiocyte @@ -28541,6 +32380,8 @@ id: CL:0019021 name: endothelial cell of periportal hepatic sinusoid def: "An endothelial cell found in the periportal region hepatic sinusoid, near the portal triad. The fenestrae of these cells are larger but fewer in number compared with those of endothelial cells near the centrilobular region of the hepatic sinusoid." [PMID:27423426] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "periportal hepatic sinusoidal endothelial cell" EXACT [PMID:30348985] synonym: "periportal LSEC" EXACT [PMID:28287163] xref: EFO:0010705 @@ -28556,6 +32397,8 @@ id: CL:0019022 name: endothelial cell of pericentral hepatic sinusoid def: "An endothelial cell found in the centrilobular region hepatic sinusoid, near the central vein. The fenestrae of these cells are smaller but more numerous compared with those of endothelial cells near the periportal region of the hepatic sinusoid." [PMID:27423426] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "central venous hepatic sinusoidal endothelial cell" EXACT [PMID:30348985] synonym: "pericentral LSEC" EXACT [PMID:28287163] xref: EFO:0010706 @@ -28572,6 +32415,8 @@ name: periportal region hepatocyte def: "Any hepatocyte that is part of the liver lobule periportal region. These cells are primarily involved in oxidative energy metabolism." [PMID:29763190] subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "periportal hepatocyte" EXACT [PMID:29763190] is_a: CL:0000182 ! hepatocyte intersection_of: CL:0000182 ! hepatocyte @@ -28587,6 +32432,8 @@ name: midzonal region hepatocyte def: "Any hepatocyte that is part of the liver lobule midzonal region. These cells have mixed functionality in comparison with those in the other two regions of the liver lobule." [PMID:29763190] subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "midzonal hepatocyte" EXACT [PMID:29763190] is_a: CL:0000182 ! hepatocyte intersection_of: CL:0000182 ! hepatocyte @@ -28602,6 +32449,8 @@ name: centrilobular region hepatocyte def: "Any hepatocyte that is part of the liver lobule centrilobular region. These cells are the primary location for the biotransformation of drugs." [PMID:29763190] subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "centrilobular hepatocyte" EXACT [PMID:29763190] is_a: CL:0000182 ! hepatocyte intersection_of: CL:0000182 ! hepatocyte @@ -28614,27 +32463,33 @@ property_value: terms:date "2020-10-12T11:03:51Z" xsd:dateTime [Term] id: CL:0019031 name: intestine goblet cell -def: "Goblet cells reside throughout the length of the small and large intestine and are responsible for the production and maintenance of the protective mucus blanket by synthesizing and secreting high-molecular-weight glycoproteins known as mucins. Human intestinal goblet cells secrete the MUC2 mucin, as well as a number of typical mucus components: CLCA1, FCGBP, AGR2, ZG16, and TFF3." [PMID:1996606, PMID:24942678] +def: "Goblet cells reside throughout the length of the small and large intestine and are responsible for the production and maintenance of the protective mucus blanket by synthesizing and secreting high-molecular-weight glycoproteins known as mucins. Human intestinal goblet cells secrete the MUC2 mucin, as well as a number of typical mucus components: CLCA1, FCGBP, AGR2, ZG16, and TFF3." [PMID:1996606, PMID:24942678, PMID:33484640] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "intestinal goblet cell" EXACT [PMID:1996606] is_a: CL:0000160 ! goblet cell is_a: CL:0002563 ! intestinal epithelial cell intersection_of: CL:0000160 ! goblet cell intersection_of: part_of UBERON:0001277 ! intestinal epithelium +relationship: RO:0002202 CL:4047017 ! develops from transit amplifying cell of gut property_value: terms:contributor https://orcid.org/0000-0003-2034-601X property_value: terms:date "2020-10-14T14:59:07Z" xsd:dateTime [Term] id: CL:0019032 name: intestinal tuft cell -def: "Any brush cell that is part of the intestinal epithelium." [PMID:22527717] +def: "Any brush cell that is part of the intestinal epithelium." [PMID:22527717, PMID:39358509] subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "intestinal brush cell" EXACT [PMID:22527717] is_a: CL:0002204 ! brush cell is_a: CL:0002563 ! intestinal epithelial cell intersection_of: CL:0002204 ! brush cell intersection_of: part_of UBERON:0001277 ! intestinal epithelium +relationship: RO:0002202 CL:0002250 ! develops from intestinal crypt stem cell property_value: RO:0002175 NCBITaxon:9606 property_value: terms:contributor https://orcid.org/0000-0003-2034-601X property_value: terms:date "2020-10-15T12:47:46Z" xsd:dateTime @@ -28654,6 +32509,8 @@ replaced_by: CL:4030005 id: CL:1000001 name: retrotrapezoid nucleus neuron def: "Any neuron that has its soma located in some retrotrapezoid nucleus." [FBC:Autogenerated] +subset: human_subset +subset: mouse_subset is_a: CL:2000029 ! central nervous system neuron intersection_of: CL:0000540 ! neuron intersection_of: RO:0002100 UBERON:0009918 ! has soma location retrotrapezoid nucleus @@ -28663,6 +32520,8 @@ relationship: RO:0002100 UBERON:0009918 ! has soma location retrotrapezoid nucle id: CL:1000022 name: mesonephric nephron tubule epithelial cell def: "Any epithelial cell that is part of some mesonephric nephron tubule." [FBC:Autogenerated] +subset: human_subset +subset: mouse_subset is_a: CL:1000449 ! epithelial cell of nephron is_a: CL:1000507 ! kidney tubule cell intersection_of: CL:0000066 ! epithelial cell @@ -28673,6 +32532,9 @@ relationship: part_of UBERON:0005329 ! mesonephric nephron tubule id: CL:1000042 name: forebrain neuroblast def: "Any neuroblast (sensu Vertebrata) that is part of some forebrain." [FBC:Autogenerated] +subset: cellxgene_subset +subset: human_subset +subset: mouse_subset is_a: CL:0000031 ! neuroblast (sensu Vertebrata) is_a: CL:0002319 ! neural cell intersection_of: CL:0000031 ! neuroblast (sensu Vertebrata) @@ -28692,6 +32554,8 @@ relationship: part_of UBERON:0008906 ! lateral line nerve id: CL:1000073 name: spinal cord radial glial cell def: "Any radial glial cell that is part of some spinal cord." [FBC:Autogenerated] +subset: human_subset +subset: mouse_subset is_a: CL:0000681 ! radial glial cell intersection_of: CL:0000681 ! radial glial cell intersection_of: part_of UBERON:0002240 ! spinal cord @@ -28700,24 +32564,32 @@ relationship: part_of UBERON:0002240 ! spinal cord [Term] id: CL:1000082 name: stretch receptor cell +subset: human_subset +subset: mouse_subset xref: ZFA:0009370 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000006 ! neuronal receptor cell [Term] id: CL:1000083 name: stratified keratinized epithelial stem cell +subset: human_subset +subset: mouse_subset xref: ZFA:0009371 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000357 ! stratified epithelial stem cell [Term] id: CL:1000085 name: stratified non keratinized epithelial stem cell +subset: human_subset +subset: mouse_subset is_a: CL:0000357 ! stratified epithelial stem cell [Term] id: CL:1000090 name: pronephric nephron tubule epithelial cell def: "Any epithelial cell that is part of some pronephric nephron tubule." [FBC:Autogenerated] +subset: human_subset +subset: mouse_subset is_a: CL:1000449 ! epithelial cell of nephron is_a: CL:1000507 ! kidney tubule cell intersection_of: CL:0000066 ! epithelial cell @@ -28728,6 +32600,8 @@ relationship: part_of UBERON:0005310 ! pronephric nephron tubule id: CL:1000123 name: metanephric nephron tubule epithelial cell def: "Any epithelial cell that is part of some metanephric nephron tubule." [FBC:Autogenerated] +subset: human_subset +subset: mouse_subset is_a: CL:1000449 ! epithelial cell of nephron is_a: CL:1000507 ! kidney tubule cell intersection_of: CL:0000066 ! epithelial cell @@ -28739,18 +32613,23 @@ id: CL:1000143 name: lung goblet cell def: "Any goblet cell that is part of some lung epithelium." [FBC:Autogenerated] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset xref: https://cellxgene.cziscience.com/cellguide/CL_1000143 is_a: CL:0000082 ! epithelial cell of lung -is_a: CL:0002370 ! respiratory goblet cell +is_a: CL:0002370 ! respiratory tract goblet cell +is_a: CL:1000272 ! lung secretory cell intersection_of: CL:0000160 ! goblet cell intersection_of: part_of UBERON:0000115 ! lung epithelium -property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional.\n\nLung goblet cells are critical components of the respiratory tract, specifically found in the bronchial segments. They are secretory epithelial cells known for their signature \"goblet\" or cup-like shape. Their primary function is to produce and secrete mucus that aids in trapping airborne particles and pathogens, preventing them from reaching the delicate environment of the lung. As part of the lung's epithelial lining, they act as frontline defenders, maintaining lung health and function.\nThe lung goblet cells are densely packed with granules containing mucin glycoproteins, the primary component of mucus. As mucus is produced and secreted, it moves towards the lumen of the lungs where the cilia, hair-like structures of the neighboring ciliated epithelial cells, help to navigate it upwards and out of the respiratory tract. This coordinated action ensures the expulsion of unwanted particles and pathogens, effectively cleaning the respiratory tract.\nDysfunction or abnormal proliferation of lung goblet cells can result in pathological conditions such as chronic obstructive pulmonary disorder (COPD) and asthma, where excessive mucus production leads to airway obstruction. Furthermore, lung goblet cells respond to a variety of stimuli, including toxins, allergens, irritants, and infections, adjusting their mucus production accordingly." xsd:string {xref="DOI:10.1038/s41385-018-0039-y", xref="DOI:10.1038/s41385-020-00370-7", xref="DOI:10.1159/000512268", xref="DOI:10.1513/AnnalsATS.201802-128AW", xref="https://www.ncbi.nlm.nih.gov/books/NBK553208/"} +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nLung goblet cells are critical components of the respiratory tract, specifically found in the bronchial segments. They are secretory epithelial cells known for their signature \"goblet\" or cup-like shape. Their primary function is to produce and secrete mucus that aids in trapping airborne particles and pathogens, preventing them from reaching the delicate environment of the lung. As part of the lung's epithelial lining, they act as frontline defenders, maintaining lung health and function.\nThe lung goblet cells are densely packed with granules containing mucin glycoproteins, the primary component of mucus. As mucus is produced and secreted, it moves towards the lumen of the lungs where the cilia, hair-like structures of the neighboring ciliated epithelial cells, help to navigate it upwards and out of the respiratory tract. This coordinated action ensures the expulsion of unwanted particles and pathogens, effectively cleaning the respiratory tract.\nDysfunction or abnormal proliferation of lung goblet cells can result in pathological conditions such as chronic obstructive pulmonary disorder (COPD) and asthma, where excessive mucus production leads to airway obstruction. Furthermore, lung goblet cells respond to a variety of stimuli, including toxins, allergens, irritants, and infections, adjusting their mucus production accordingly." xsd:string {xref="DOI:10.1038/s41385-018-0039-y", xref="DOI:10.1038/s41385-020-00370-7", xref="DOI:10.1159/000512268", xref="DOI:10.1513/AnnalsATS.201802-128AW", xref="https://www.ncbi.nlm.nih.gov/books/NBK553208/"} [Term] id: CL:1000147 name: cardiac valve cell def: "A cell that is part of a cardiac valve." [PMID:25311230] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "heart valve cell" EXACT [PMID:30796046] xref: ZFA:0009402 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0002494 ! cardiocyte @@ -28782,6 +32661,8 @@ relationship: part_of UBERON:0001054 ! Malpighian tubule id: CL:1000191 name: pillar cell def: "A rod-like cell in the inner ear, having their heads joined and their bases on the basilar membrane widely separated so as to form a spiral tunnel known as the tunnel of Corti." [GOC:tfm, PMID:12417662] +subset: human_subset +subset: mouse_subset synonym: "cochlear pillar cell" RELATED [] synonym: "pillar cell of cochlea" EXACT [] synonym: "pillar cell of corti" EXACT [] @@ -28793,6 +32674,8 @@ is_a: CL:0002490 ! organ of Corti supporting cell id: CL:1000217 name: growth plate cartilage chondrocyte def: "Any chondrocyte that is part of some growth plate cartilage." [FBC:Autogenerated] +subset: human_subset +subset: mouse_subset is_a: CL:0000138 ! chondrocyte intersection_of: CL:0000138 ! chondrocyte intersection_of: part_of UBERON:0004129 ! growth plate cartilage @@ -28801,21 +32684,28 @@ relationship: part_of UBERON:0004129 ! growth plate cartilage [Term] id: CL:1000222 name: stomach neuroendocrine cell -def: "Any neuroendocrine cell that is part of some stomach." [FBC:Autogenerated] -is_a: CL:0000164 ! enteroendocrine cell +def: "A specialised neuroendocrine cell located in the gastric mucosa that regulates digestive processes including acid secretion and gut motility. This cell stores hormones in large dense core vesicles and synaptic-like microvesicles." [PMID:15153415] +subset: human_subset +subset: mouse_subset +synonym: "DES cell" BROAD [PMID:15153415] +synonym: "diffuse endocrine system cell" BROAD [PMID:15153415] is_a: CL:0000165 ! neuroendocrine cell -is_a: CL:0002659 ! glandular epithelial cell of stomach +is_a: CL:1001517 ! stomach enteroendocrine cell intersection_of: CL:0000165 ! neuroendocrine cell -intersection_of: part_of UBERON:0000945 ! stomach +intersection_of: part_of UBERON:0001276 ! epithelium of stomach +relationship: capable_of GO:0046717 ! acid secretion [Term] id: CL:1000223 -name: lung neuroendocrine cell -def: "A neuroendocrine cell that is part of respiratory epithelium of the lung and is involved in the sensory detection of environmental stimuli, including hypoxia, nicotine and air pressure. Ultrastructurally, this cell type is characterized by the presence of cytoplasmic dense core granules, which are considered the storage sites of amine and peptide hormones. Lung neuroendocrine cells are innervated and appear as solitary cells or as clustered masses, localized at airway bifurcation sites, called neuroepithelial bodies that can release serotonin in response to hypoxia and interact with sensory nerve terminals. Lung neuroendocrine cells also function as reserve stem cells that repair the surrounding epithelium after injury." [doi:10.3109/01902148209069653, doi:10.7554/eLife.78216, PMID:33355253] +name: pulmonary neuroendocrine cell +def: "A neuroendocrine cell that is part of respiratory epithelium of the lung and is involved in the sensory detection of environmental stimuli, including hypoxia, nicotine and air pressure. Ultrastructurally, this cell type is characterized by the presence of cytoplasmic dense core granules, which are considered the storage sites of amine and peptide hormones. Pulmonary neuroendocrine cells are innervated and appear as solitary cells or as clustered masses, localized at airway bifurcation sites, called neuroepithelial bodies that can release serotonin in response to hypoxia and interact with sensory nerve terminals. Pulmonary neuroendocrine cells also function as reserve stem cells that repair the surrounding epithelium after injury." [doi:10.3109/01902148209069653, doi:10.7554/eLife.78216, PMID:33355253] +comment: The marker set CHGA, GRP can identify the Human cell type lung neuroendocrine cell in the Lung with a confidence of 0.94 (NS-Forest FBeta value). {xref="https://doi.org/10.5281/zenodo.11165918"} subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset +synonym: "lung neuroendocrine cell" EXACT [PMID:15018448] synonym: "PNEC" RELATED OMO:0003000 [PMID:33355253] -synonym: "pulmonary neuroendocrine cell" EXACT [PMID:33355253] xref: https://cellxgene.cziscience.com/cellguide/CL_1000223 is_a: CL:0000006 ! neuronal receptor cell is_a: CL:0000098 ! sensory epithelial cell @@ -28827,8 +32717,9 @@ intersection_of: CL:0000165 ! neuroendocrine cell intersection_of: part_of UBERON:0002048 ! lung relationship: capable_of GO:0070483 ! detection of hypoxia relationship: has_part GO:0031045 ! dense core granule +relationship: RO:0015004 CLM:1000043 ! has characterizing marker set NS forest marker set of lung neuroendocrine cell (Human Lung). property_value: RO:0002175 NCBITaxon:9606 -property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional.\n\nLung neuroendocrine cells, also commonly known as pulmonary neuroendocrine cells (PNECs), are predominantly located in the respiratory epithelium of the bronchial and bronchiolar airways in the lungs. These cells, characterised by their small size and granular appearance, have a distinctive morphology that sets them apart from other lung cells. They are considered part of the diffuse neuroendocrine system due to their scattered distribution through the epithelium and have been classified into solitary cells and clustered forms known as neuroepithelial bodies.\nThe primary function of PNECs is linked to regulation and maintenance of the lung environment. They are sensory in nature and can secrete various bioactive substances such as serotonin, calcitonin, calcitonin gene-related peptides, and bombesin-like peptides which modulate airway smooth muscle tone and influence gut motility. For example, they act as oxygen sensors in response to hypoxia and are responsible for releasing neuropeptides that can induce responses. Moreover, PNECs provide an afferent function as they are equipped with long microvilli that project into the lumen of the bronchus and react to changes in the chemical composition of the luminal content." xsd:string {xref="DOI:10.1016/bs.ctdb.2018.12.002", xref="DOI:10.1016/j.devcel.2020.09.024", xref="DOI:10.1242/dmm.046920"} +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nLung neuroendocrine cells, also commonly known as pulmonary neuroendocrine cells (PNECs), are predominantly located in the respiratory epithelium of the bronchial and bronchiolar airways in the lungs. These cells, characterised by their small size and granular appearance, have a distinctive morphology that sets them apart from other lung cells. They are considered part of the diffuse neuroendocrine system due to their scattered distribution through the epithelium and have been classified into solitary cells and clustered forms known as neuroepithelial bodies.\nThe primary function of PNECs is linked to regulation and maintenance of the lung environment. They are sensory in nature and can secrete various bioactive substances such as serotonin, calcitonin, calcitonin gene-related peptides, and bombesin-like peptides which modulate airway smooth muscle tone and influence gut motility. For example, they act as oxygen sensors in response to hypoxia and are responsible for releasing neuropeptides that can induce responses. Moreover, PNECs provide an afferent function as they are equipped with long microvilli that project into the lumen of the bronchus and react to changes in the chemical composition of the luminal content." xsd:string {xref="DOI:10.1016/bs.ctdb.2018.12.002", xref="DOI:10.1016/j.devcel.2020.09.024", xref="DOI:10.1242/dmm.046920"} [Term] id: CL:1000236 @@ -28851,22 +32742,26 @@ relationship: part_of UBERON:2000425 ! anterior lateral line nerve [Term] id: CL:1000245 name: posterior lateral line ganglion neuron -def: "Any neuron that has its soma located in some posterior lateral line ganglion." [FBC:Autogenerated] +def: "Any peripheral nervous system neuron that has its soma located in some posterior lateral line ganglion." [FBC:Autogenerated] is_a: CL:2000031 ! lateral line ganglion neuron -intersection_of: CL:0000540 ! neuron +intersection_of: CL:2000032 ! peripheral nervous system neuron intersection_of: RO:0002100 UBERON:2001314 ! has soma location posterior lateral line ganglion relationship: RO:0002100 UBERON:2001314 ! has soma location posterior lateral line ganglion [Term] id: CL:1000271 -name: lung ciliated cell +name: lung multiciliated epithelial cell def: "An epithelial cell that is part of the lung epithelium. This cell is characterised by the presence of cilia on its apical surface." [PMID:27864314] subset: cellxgene_subset subset: human_reference_atlas -is_a: CL:0000067 ! ciliated epithelial cell +subset: human_subset +subset: mouse_subset +synonym: "lung ciliated cell" EXACT [] is_a: CL:0000082 ! epithelial cell of lung -is_a: CL:4030034 ! respiratory ciliated cell -intersection_of: CL:0000067 ! ciliated epithelial cell +is_a: CL:4030034 ! respiratory tract multiciliated cell +intersection_of: CL:0000075 ! columnar/cuboidal epithelial cell +intersection_of: bearer_of PATO:0010007 ! multiciliated +intersection_of: has_part GO:0031514 ! motile cilium intersection_of: part_of UBERON:0000115 ! lung epithelium property_value: RO:0002175 NCBITaxon:9606 @@ -28875,6 +32770,8 @@ id: CL:1000272 name: lung secretory cell def: "Any secretory cell that is part of some lung." [FBC:Autogenerated] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset is_a: CL:0000151 ! secretory cell is_a: CL:0000255 ! eukaryotic cell intersection_of: CL:0000151 ! secretory cell @@ -28884,6 +32781,8 @@ relationship: part_of UBERON:0002048 ! lung [Term] id: CL:1000274 name: trophectodermal cell +subset: human_subset +subset: mouse_subset synonym: "trophectoderm cell" EXACT [] is_a: CL:0000349 ! extraembryonic cell @@ -28892,28 +32791,38 @@ id: CL:1000275 name: smooth muscle cell of small intestine def: "A smooth muscle cell that is part of the small intestine." [GOC:tfm] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "non-striated muscle fiber of small intestine" EXACT [FMA:15050] xref: FMA:15050 +xref: https://cellxgene.cziscience.com/cellguide/CL_1000275 is_a: CL:0002504 {is_inferred="true"} ! enteric smooth muscle cell intersection_of: CL:0002504 ! enteric smooth muscle cell intersection_of: part_of UBERON:0002108 ! small intestine relationship: part_of UBERON:0002108 ! small intestine +property_value: foaf:depiction http://purl.obolibrary.org/obo/cl/images/Small-intestine-cells.png {dc:license="http://creativecommons.org/licenses/by/4.0/", comment="Figure depicts a cross section of intestinal villi in the small intestine, including the crypts of Lieberkuhn (seen here as ‘crypt’), as well as the layer specific locations of cells that exist within the gastrointestinal tract. Layers depicted here include epithelium (rows of cells bordering villus), submucosa (white space below the epithelium containing networks of neurons and ganglia depicted in pink), muscularis mucosae (blue layer), muscularis propria (referred to here as muscle layer).\n\nISC: Intestinal Stem Cell \nTA: Transit Amplifying Cells"} +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nSmooth muscle cells of the small intestine form a key component of the enteric system which is imperative for gastrointestinal motility. These cells are a specialized subgroup of smooth muscle cells, specifically found in the layers of the small intestine. The small intestine represents a significant part of the digestive system and plays a crucial role in the absorption of nutrients into the bloodstream.\nSmooth muscle cells of the small intestine are predominantly responsible for creating the contractions and relaxations that constitute intestinal motility. They trigger these movements in a coordinated and rhythmic manner known as peristalsis and segmentation. Peristalsis is a form of longitudinal and sequential contraction that pushes food from the upper gastrointestinal tract to the lower parts. Segmentation works by squeezing the intestine randomly, thereby facilitating the mixing of food particles and increasing contact with absorptive surfaces. These two processes are critical for intestinal motility and an effective digestive process.\nApart from facilitating transit of food through contractions, these smooth muscle cells play a role in controlling the diameter of the vessels and the blood flow in the small intestine by their constrictive ability. These smooth muscle cells also contribute to the structural integrity of the small intestine by forming a part of its muscularis externa and muscularis mucosae. Additionally, they interact with other cell types such as enteric neurons and interstitial cells of Cajal (ICC), forming an integrated cellular network that ensures optimal functioning of the intestinal tract." xsd:string {xref="DOI:10.1007/978-981-13-5895-1_1", xref="DOI:10.1038/nrgastro.2012.168", xref="DOI:10.1038/s41575-020-0271-2", xref="DOI:10.1053/j.gastro.2016.02.030", xref="DOI:10.1111/j.1582-4934.2008.00352.x"} [Term] id: CL:1000276 name: smooth muscle fiber of duodenum def: "A smooth muscle cell that is part of the duodenum." [GOC:tfm] +subset: human_subset +subset: mouse_subset synonym: "non-striated muscle fiber of duodenum" EXACT [FMA:15058] xref: FMA:15058 is_a: CL:1000275 {is_inferred="true"} ! smooth muscle cell of small intestine intersection_of: CL:1000275 ! smooth muscle cell of small intestine intersection_of: part_of UBERON:0002114 ! duodenum +relationship: part_of UBERON:0001902 ! epithelium of small intestine relationship: part_of UBERON:0002114 ! duodenum [Term] id: CL:1000277 name: smooth muscle fiber of jejunum def: "A smooth muscle cell that is part of the jejunum." [GOC:tfm] +subset: human_subset +subset: mouse_subset synonym: "non-striated muscle fiber of jejunum" EXACT [FMA:15062] xref: FMA:15062 is_a: CL:1000275 {is_inferred="true"} ! smooth muscle cell of small intestine @@ -28926,12 +32835,17 @@ id: CL:1000278 name: smooth muscle fiber of ileum def: "A smooth muscle cell that is part of the ileum." [GOC:tfm] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "non-striated muscle fiber of ileum" EXACT [FMA:15066] xref: FMA:15066 +xref: https://cellxgene.cziscience.com/cellguide/CL_1000278 is_a: CL:1000275 {is_inferred="true"} ! smooth muscle cell of small intestine intersection_of: CL:1000275 ! smooth muscle cell of small intestine intersection_of: part_of UBERON:0002116 ! ileum +relationship: part_of UBERON:0001902 ! epithelium of small intestine relationship: part_of UBERON:0002116 ! ileum +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nThe smooth muscle fiber of the ileum primarily refers to a specific class of muscle cells present in the ileum, the final segment of the small intestine. Distinguished from skeletal muscle and cardiac muscle, smooth muscle does not possess striations and is under the control of the involuntary nervous system. \nThese cells primarily facilitate the movement of digested food, a process known as peristalsis. These cells coordinate rhythmic contractions and relaxations, propelling the chyme toward the colon. This process is vital for efficient nutrient absorption in the small intestine and the transfer of undigested material to the large intestine. Moreover, the smooth muscle fibers enhance the ileum's ability to expand and adapt to volume changes without elevating internal pressure, known as compliance.\nThe smooth muscle fiber of the ileum contributes to reflex responses, enhancing muscle contractions to propel intestinal contents in different physiological conditions. This involves intricate molecular signaling with neurotransmitters, hormones, and local signals. Thus, beyond its structural role, the smooth muscle fiber is crucial for the physiological functions of digestion and absorption in the small intestine." xsd:string {xref="DOI:10.1152/advan.00025.2003", xref="https://www.ncbi.nlm.nih.gov/books/NBK532857/", xref="https://www.ncbi.nlm.nih.gov/books/NBK556137/"} [Term] id: CL:1000279 @@ -28939,6 +32853,8 @@ name: smooth muscle cell of large intestine def: "A smooth muscle cell that is part of the large intestine." [GOC:tfm] subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "non-striated muscle fiber of large intestine" EXACT [FMA:15653] xref: FMA:15653 is_a: CL:0002504 {is_inferred="true"} ! enteric smooth muscle cell @@ -28951,17 +32867,22 @@ property_value: RO:0002175 NCBITaxon:9606 id: CL:1000280 name: smooth muscle cell of colon def: "A smooth muscle cell that is part of the colon." [GOC:tfm] +subset: human_subset +subset: mouse_subset synonym: "non-striated muscle fiber of colon" EXACT [FMA:15663] xref: FMA:15663 is_a: CL:1000279 ! smooth muscle cell of large intestine intersection_of: CL:0002504 ! enteric smooth muscle cell intersection_of: part_of UBERON:0001155 ! colon relationship: part_of UBERON:0001155 ! colon +relationship: part_of UBERON:0001278 ! epithelium of large intestine [Term] id: CL:1000281 name: smooth muscle cell of cecum def: "A smooth muscle cell that is part of the cecum." [GOC:tfm] +subset: human_subset +subset: mouse_subset synonym: "non-striated muscle fiber of cecum" EXACT [FMA:15681] synonym: "smooth muscle fiber of cecum" EXACT [] xref: FMA:15681 @@ -28974,6 +32895,8 @@ relationship: part_of UBERON:0001153 ! caecum id: CL:1000282 name: smooth muscle fiber of ascending colon def: "A smooth muscle cell that is part of the ascending colon." [GOC:tfm] +subset: human_subset +subset: mouse_subset synonym: "non-striated muscle fiber of ascending colon" EXACT [FMA:17518] xref: FMA:17518 is_a: CL:1000280 {is_inferred="true"} ! smooth muscle cell of colon @@ -28985,6 +32908,8 @@ relationship: part_of UBERON:0001156 ! ascending colon id: CL:1000283 name: smooth muscle fiber of transverse colon def: "A smooth muscle cell that is part of the transverse colon." [GOC:tfm] +subset: human_subset +subset: mouse_subset synonym: "non-striated muscle fiber of transverse colon" EXACT [FMA:17519] xref: FMA:17519 is_a: CL:1000280 {is_inferred="true"} ! smooth muscle cell of colon @@ -28996,6 +32921,8 @@ relationship: part_of UBERON:0001157 ! transverse colon id: CL:1000284 name: smooth muscle fiber of descending colon def: "A smooth muscle cell that is part of the descending colon." [GOC:tfm] +subset: human_subset +subset: mouse_subset synonym: "non-striated muscle fiber of descending colon" EXACT [FMA:17520] xref: FMA:17520 is_a: CL:1000280 {is_inferred="true"} ! smooth muscle cell of colon @@ -29007,6 +32934,8 @@ relationship: part_of UBERON:0001158 ! descending colon id: CL:1000285 name: smooth muscle cell of sigmoid colon def: "A smooth muscle cell that is part of the sigmoid colon." [GOC:tfm] +subset: human_subset +subset: mouse_subset synonym: "non-striated muscle fiber of sigmoid colon" EXACT [FMA:17521] xref: FMA:17521 is_a: CL:1000280 {is_inferred="true"} ! smooth muscle cell of colon @@ -29018,6 +32947,8 @@ relationship: part_of UBERON:0001159 ! sigmoid colon id: CL:1000286 name: smooth muscle cell of rectum def: "A smooth muscle cell that is part of the rectum." [GOC:tfm] +subset: human_subset +subset: mouse_subset synonym: "non-striated muscle fiber of rectum" EXACT [FMA:17522] synonym: "smooth muscle fiber of rectum" EXACT [] xref: FMA:17522 @@ -29025,11 +32956,14 @@ is_a: CL:1000279 ! smooth muscle cell of large intestine intersection_of: CL:0000192 ! smooth muscle cell intersection_of: part_of UBERON:0001052 ! rectum relationship: part_of UBERON:0001052 ! rectum +relationship: part_of UBERON:0001278 ! epithelium of large intestine [Term] id: CL:1000287 name: myocyte of anterior internodal tract def: "A muscle cell that is part of the anterior internodal tract." [GOC:tfm] +subset: human_subset +subset: mouse_subset xref: FMA:223276 is_a: CL:0002096 ! internodal tract myocyte @@ -29037,6 +32971,8 @@ is_a: CL:0002096 ! internodal tract myocyte id: CL:1000288 name: myocyte of atrial branch of anterior internodal tract def: "A muscle cell that is part of the atrial branch of anterior internodal tract." [GOC:tfm] +subset: human_subset +subset: mouse_subset xref: FMA:223277 is_a: CL:0002096 ! internodal tract myocyte @@ -29044,6 +32980,8 @@ is_a: CL:0002096 ! internodal tract myocyte id: CL:1000289 name: myocyte of atrial septal branch of anterior internodal tract def: "A muscle cell that is part of the atrial septal branch of anterior internodal tract." [GOC:tfm] +subset: human_subset +subset: mouse_subset xref: FMA:223278 is_a: CL:0002096 ! internodal tract myocyte @@ -29051,6 +32989,8 @@ is_a: CL:0002096 ! internodal tract myocyte id: CL:1000290 name: myocyte of middle internodal tract def: "A muscle cell that is part of the middle internodal tract." [GOC:tfm] +subset: human_subset +subset: mouse_subset xref: FMA:223279 is_a: CL:0002096 ! internodal tract myocyte @@ -29058,6 +32998,8 @@ is_a: CL:0002096 ! internodal tract myocyte id: CL:1000291 name: myocyte of posterior internodal tract def: "A muscle cell that is part of the posterior internodal tract." [GOC:tfm] +subset: human_subset +subset: mouse_subset xref: FMA:223280 is_a: CL:0002096 ! internodal tract myocyte @@ -29066,16 +33008,22 @@ id: CL:1000296 name: epithelial cell of urethra def: "An epithelial cell that is part of the urethra." [GOC:tfm] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset xref: FMA:256165 +xref: https://cellxgene.cziscience.com/cellguide/CL_1000296 is_a: CL:0000066 ! epithelial cell is_a: CL:1001320 ! urethra cell intersection_of: CL:0000066 ! epithelial cell intersection_of: part_of UBERON:0000057 ! urethra +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nEpithelial cells of the urethra constitute the inner lining of the urethra, forming a mucosal barrier that helps protect the body from external contaminants. The type of epithelial cells found in the urethra can vary along its length. In general, the urethra is lined with stratified squamous epithelium in its distal or external portion, which is closer to the external environment. This type of epithelium provides protection against mechanical stress and pathogens. Closer to the bladder, the urethra transitions to a different type of epithelium. In males, the proximal part of the urethra is lined with pseudostratified columnar epithelium in the region where it passes through the prostate gland. In females, the transitional epithelium may be present in the proximal part of the urethra near the bladder.\nEpithelial cells of the urethra are primarily dedicated to the protection of underlying tissues from mechanical stress and pathogens during micturition (urination). They do this by creating a tight, impermeable barrier that prevents the entry and colonization of invading microbes. They produce a variety of antimicrobials and are tightly packed to prevent infiltration between cells, forming an integral part of the body's innate immune system.\nIn addition to their protective role, these cells are involved in the secretion of mucus. This mucus acts as a lubricant that ensures the smooth and easy passage of urine from the bladder through the urethra and out of the body, reducing any potential damage from the erosive action of urine. Epithelial cells of the urethra are dynamic, constantly renewing their numbers to replace any cells lost through wear and tear. Any disruptions to the function or integrity of these cells may contribute to urinary tract infections and other urological disorders." xsd:string {xref="DOI:10.1016/j.celrep.2018.11.086", xref="DOI:10.1038/s41385-022-00565-0", xref="DOI:10.1089/ten.teb.2016.0352", xref="DOI:10.1101/2020.02.19.937615v2.full", xref="DOI:10.1152/ajprenal.00327.2009"} [Term] id: CL:1000298 name: mesothelial cell of dura mater def: "A mesothelial cell that is part of the dura mater." [GOC:tfm] +subset: human_subset +subset: mouse_subset synonym: "squamous mesothelial cell of dura mater" EXACT [FMA:256516] xref: FMA:256516 is_a: CL:0000077 ! mesothelial cell @@ -29090,33 +33038,41 @@ name: fibroblast of connective tissue of prostate def: "A fibroblast that is part of the connective tissue of prostate." [GOC:tfm] subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset xref: FMA:261271 is_a: CL:0000057 ! fibroblast -relationship: part_of UBERON:0002367 ! prostate gland +is_a: CL:0002622 ! prostate stromal cell property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:1000300 name: fibroblast of outer membrane of prostatic capsule def: "A fibroblast that is part of the outer membrane of prostatic capsule." [GOC:tfm] +subset: human_subset +subset: mouse_subset xref: FMA:261273 is_a: CL:0000057 ! fibroblast -relationship: part_of UBERON:0002367 ! prostate gland +is_a: CL:0002622 ! prostate stromal cell [Term] id: CL:1000301 name: fibroblast of subepithelial connective tissue of prostatic gland def: "A fibroblast that is part of the subepithelial connective tissue of prostatic gland." [GOC:tfm] subset: human_reference_atlas +subset: human_subset +subset: mouse_subset xref: FMA:261275 is_a: CL:0000057 ! fibroblast -relationship: part_of UBERON:0002367 ! prostate gland +is_a: CL:0002622 ! prostate stromal cell property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:1000302 name: fibroblast of papillary layer of dermis def: "A fibroblast that is part of the papillary layer of dermis." [GOC:tfm] +subset: human_subset +subset: mouse_subset xref: FMA:261277 is_a: CL:0002551 {is_inferred="true"} ! fibroblast of dermis intersection_of: CL:0002551 ! fibroblast of dermis @@ -29127,6 +33083,8 @@ relationship: part_of UBERON:0001992 ! papillary layer of dermis id: CL:1000303 name: fibroblast of areolar connective tissue def: "A fibroblast that is part of the areolar connective tissue." [GOC:tfm] +subset: human_subset +subset: mouse_subset xref: FMA:261279 is_a: CL:0000057 {is_inferred="true"} ! fibroblast intersection_of: CL:0000057 ! fibroblast @@ -29138,34 +33096,41 @@ id: CL:1000304 name: fibroblast of connective tissue of nonglandular part of prostate def: "A fibroblast that is part of the connective tissue of nonglandular part of prostate." [GOC:tfm] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset xref: FMA:261281 is_a: CL:0000057 ! fibroblast -relationship: part_of UBERON:0002367 ! prostate gland +is_a: CL:0002622 ! prostate stromal cell [Term] id: CL:1000305 name: fibroblast of connective tissue of glandular part of prostate def: "A fibroblast that is part of the connective tissue of glandular part of prostate." [GOC:tfm] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset xref: FMA:261283 is_a: CL:0000057 ! fibroblast -relationship: part_of UBERON:0002367 ! prostate gland +is_a: CL:0002622 ! prostate stromal cell [Term] id: CL:1000306 name: fibroblast of tunica adventitia of artery def: "A fibroblast that is part of the tunica adventitia of artery." [GOC:tfm] +subset: human_subset +subset: mouse_subset xref: FMA:261285 -is_a: CL:0000057 {is_inferred="true"} ! fibroblast -is_a: CL:0002503 ! adventitial cell +is_a: CL:4052030 ! adventitial fibroblast intersection_of: CL:0000057 ! fibroblast -intersection_of: part_of UBERON:0005734 ! tunica adventitia of blood vessel -relationship: part_of UBERON:0005734 ! tunica adventitia of blood vessel +intersection_of: part_of UBERON:0007240 ! tunica adventitia of artery +relationship: part_of UBERON:0007240 ! tunica adventitia of artery [Term] id: CL:1000307 name: fibroblast of dense regular elastic tissue def: "A fibroblast that is part of the dense regular elastic tissue." [GOC:tfm] +subset: human_subset +subset: mouse_subset xref: FMA:261287 is_a: CL:0000057 ! fibroblast intersection_of: CL:0000057 ! fibroblast @@ -29178,6 +33143,8 @@ id: CL:1000308 name: fibrocyte of adventitia of ureter def: "A fibrocyte that is part of the adventitia of ureter." [GOC:tfm] subset: human_reference_atlas +subset: human_subset +subset: mouse_subset xref: FMA:261289 is_a: CL:0000135 {is_inferred="true"} ! fibrocyte is_a: CL:1000708 ! ureter adventitial cell @@ -29191,6 +33158,8 @@ name: epicardial adipocyte def: "An adipocyte that is part of the epicardial fat." [GOC:tfm] subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "adipocyte of epicardial fat" EXACT [FMA:261293] synonym: "epicardial fat cell" EXACT [FMA:261293] xref: FMA:261293 @@ -29203,6 +33172,8 @@ property_value: RO:0002175 NCBITaxon:9606 id: CL:1000310 name: adipocyte of epicardial fat of right ventricle def: "An adipocyte that is part of the epicardial fat of right ventricle." [GOC:tfm] +subset: human_subset +subset: mouse_subset synonym: "epicardial adipocyte of right ventricle" EXACT [FMA:261297] synonym: "epicardial fat cell of right ventricle" EXACT [FMA:261297] xref: FMA:261297 @@ -29216,6 +33187,8 @@ id: CL:1000311 name: adipocyte of epicardial fat of left ventricle def: "An adipocyte that is part of the epicardial fat of left ventricle." [GOC:tfm] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "epicardial adipocyte of left ventricle" EXACT [FMA:261300] synonym: "epicardial fat cell of left ventricle" EXACT [FMA:261300] xref: FMA:261300 @@ -29228,33 +33201,44 @@ relationship: part_of UBERON:0002084 ! heart left ventricle id: CL:1000312 name: bronchial goblet cell def: "A goblet cell that is part of the epithelium of bronchus." [GOC:tfm] +comment: The marker set PLCG2, ANKRD36C can identify the Human cell type bronchial goblet cell in the Lung with a confidence of 0.55 (NS-Forest FBeta value). {xref="https://doi.org/10.5281/zenodo.11165918"} subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "goblet cell of epithelium of bronchus" EXACT [FMA:263032] xref: FMA:263032 +xref: https://cellxgene.cziscience.com/cellguide/CL_1000312 is_a: CL:0002328 ! bronchial epithelial cell is_a: CL:0019003 ! tracheobronchial goblet cell intersection_of: CL:0000160 ! goblet cell intersection_of: part_of UBERON:0002185 ! bronchus +relationship: RO:0015004 CLM:1000026 ! has characterizing marker set NS forest marker set of bronchial goblet cell (Human Lung). +property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nBronchial goblet cells are a subset of goblet cells that are predominantly found in the respiratory tract, specifically within the bronchi and bronchioles. Named for their flask-like shape and their apparent similarity to a goblet, these cells contribute significantly to the maintenance of lung health and homeostasis. In humans, goblet cells comprise up to 25% of the bronchial epithelial columnar cells and are an integral part of the mucus-secreting system of the respiratory tract and are primarily responsible for the production and secretion of mucus.\nThe mucus secreted by bronchial goblet cells serves as a protective layer over the delicate and sensitive structures of the bronchi. The mucus, an amalgamation of glycoproteins, lipids, and other substances, traps any inhaled dust, microorganisms, and pollutants, preventing them from reaching deeper lung tissues and causing potential damage. Additionally, the mucus secretion aids in moistening the airway surface, thereby facilitating effective gas exchange and maintaining the overall health of the respiratory tract.\nBronchial goblet cells have an innate defense mechanism wherein they increase secretion of mucus in response to irritants, infection or inflammation in the airway. This strategy, however, if incessantly stimulated, can lead to airway obstruction and health complications like asthma and chronic obstructive pulmonary disease (COPD)." xsd:string {xref="DOI:10.1016/S0165-6147(00)01600-X", xref="DOI:10.1016/S1357-2725(02)00083-3", xref="DOI:10.1080/07853890600585795", xref="DOI:10.2147/COPD.S38938"} [Term] id: CL:1000313 name: gastric goblet cell def: "A goblet cell that is part of the epithelium of stomach." [GOC:tfm] +subset: human_subset +subset: mouse_subset synonym: "goblet cell of epithelium of stomach" EXACT [FMA:263035] xref: FMA:263035 is_a: CL:0000160 ! goblet cell is_a: CL:0002180 ! mucous cell of stomach intersection_of: CL:0000160 ! goblet cell intersection_of: part_of UBERON:0000945 ! stomach -relationship: part_of UBERON:0001276 ! epithelium of stomach [Term] id: CL:1000314 name: gastric cardiac gland goblet cell def: "A goblet cell that is part of the epithelium of gastric cardiac gland." [GOC:tfm] +subset: human_subset +subset: mouse_subset synonym: "goblet cell of epithelium of gastric cardiac gland" EXACT [] xref: FMA:263038 is_a: CL:0000152 ! exocrine cell +is_a: CL:0002659 ! glandular epithelial cell of stomach is_a: CL:1000313 ! gastric goblet cell intersection_of: CL:0000160 ! goblet cell intersection_of: part_of UBERON:0008859 ! cardiac gastric gland @@ -29263,9 +33247,12 @@ intersection_of: part_of UBERON:0008859 ! cardiac gastric gland id: CL:1000315 name: principal gastric gland goblet cell def: "A goblet cell that is part of the epithelium of principal gastric gland." [GOC:tfm] +subset: human_subset +subset: mouse_subset synonym: "goblet cell of epithelium of principal gastric gland" EXACT [] xref: FMA:263040 is_a: CL:0000152 ! exocrine cell +is_a: CL:0002659 ! glandular epithelial cell of stomach is_a: CL:1000313 ! gastric goblet cell intersection_of: CL:0000160 ! goblet cell intersection_of: part_of UBERON:0009971 ! principal gastric gland @@ -29283,11 +33270,13 @@ replaced_by: CL:1000495 id: CL:1000317 name: intestinal villus goblet cell def: "A goblet cell that is part of the epithelium of intestinal villus." [GOC:tfm] +subset: human_subset +subset: mouse_subset synonym: "goblet cell of epithelium of intestinal villus" EXACT [] xref: FMA:263046 is_a: CL:1000495 ! small intestine goblet cell intersection_of: CL:0000160 ! goblet cell -intersection_of: part_of UBERON:0001213 ! intestinal villus +intersection_of: part_of UBERON:0013636 ! epithelium of intestinal villus relationship: part_of UBERON:0013636 ! epithelium of intestinal villus [Term] @@ -29309,21 +33298,30 @@ id: CL:1000320 name: large intestine goblet cell def: "A goblet cell that is part of the epithelium of large intestine." [GOC:tfm] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "goblet cell of epithelium of large intestine" EXACT [] xref: FMA:263054 +xref: https://cellxgene.cziscience.com/cellguide/CL_1000320 is_a: CL:0002253 ! epithelial cell of large intestine is_a: CL:0019031 ! intestine goblet cell intersection_of: CL:0000160 ! goblet cell -intersection_of: part_of UBERON:0000059 ! large intestine -relationship: part_of UBERON:0001278 ! epithelium of large intestine +intersection_of: part_of UBERON:0001278 ! epithelium of large intestine +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nThe large intestine goblet cell is a highly specialized type of mucosal epithelial cell that is located within the epithelial lining of the large intestine. The key function of goblet cells is the production and secretion of a protective layer of mucus which is essential for maintaining gut homeostasis. Goblet cells have a characteristic 'goblet-like' shape, which adapts them for this specific function: organelles such as the nucleus, mitochondria, ER, and Golgi apparatus are located in the basal portion of the cell; while the vesicles with mucins (required for mucus production) are located apically, close to the apical membrane where their exocytosis takes place.\nThe goblet cells of the large intestine produce a thick layer of mucus that coats the intestinal lumen. This mucus provides a barrier that prevents the direct contact of intestinal cells with bacteria and other potentially toxic substances present in the digestive tract. It also lubricates the intestine to facilitate the smooth passage of digested food material. It is worth noting that the mucus system differs between the small and large intestine: although in both the mucus is built around MUC2 mucin polymers produced by goblet cells, it is becoming clear that there are several types of goblet cells that function in different ways. \nFrom an immunological perspective, large intestine goblet cells participate in promoting a balanced gut immune response. They contribute to the process known as immune tolerance, where they prevent the body's immune system from overreacting to the trillions of bacteria present in the gut. These cells achieve this by secreting molecules that help maintain a calm environment, limiting inflammatory reactions unless absolutely necessary. Any dysfunction or decrease in the number of goblet cells can result in a compromised intestinal barrier leading to various health issues, including inflammatory bowel disease." xsd:string {xref="DOI:10.1038/mi.2015.32", xref="DOI:10.1042/BSR20201471", xref="DOI:10.1111/imr.12182", xref="DOI:10.1146/annurev-physiol-021115-105447", xref="DOI:full/10.1111/febs.15731"} [Term] id: CL:1000321 name: large intestine crypt goblet cell def: "A goblet cell that is part of the epithelium of crypt of Lieberkuhn of large intestine." [GOC:tfm] subset: human_reference_atlas +subset: human_subset +subset: mouse_subset xref: FMA:263056 +is_a: CL:0002658 ! glandular cell of the large intestine is_a: CL:1000320 ! large intestine goblet cell +intersection_of: CL:0000160 ! goblet cell +intersection_of: part_of UBERON:0022281 ! epithelium of crypt of Lieberkuhn of large intestine +relationship: part_of UBERON:0022281 ! epithelium of crypt of Lieberkuhn of large intestine property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -29331,11 +33329,13 @@ id: CL:1000322 name: pancreatic goblet cell def: "A goblet cell that is part of the epithelium of pancreatic duct." [GOC:tfm] subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "goblet cell of epithelium of pancreatic duct" EXACT [FMA:263058] xref: FMA:263058 is_a: CL:0000069 ! branched duct epithelial cell is_a: CL:0000160 ! goblet cell -is_a: CL:1001433 ! epithelial cell of exocrine pancreas +is_a: CL:1001599 ! pancreas exocrine glandular cell intersection_of: CL:0000160 ! goblet cell intersection_of: part_of UBERON:0001264 ! pancreas relationship: part_of UBERON:0009970 ! epithelium of pancreatic duct @@ -29345,9 +33345,12 @@ property_value: RO:0002175 NCBITaxon:9606 id: CL:1000323 name: pyloric gastric gland goblet cell def: "A goblet cell that is part of the epithelium of pyloric gland." [GOC:tfm] +subset: human_subset +subset: mouse_subset synonym: "goblet cell of epithelium of pyloric gland" EXACT [] xref: FMA:263061 is_a: CL:0000152 ! exocrine cell +is_a: CL:0002659 ! glandular epithelial cell of stomach is_a: CL:1000313 ! gastric goblet cell intersection_of: CL:0000160 ! goblet cell intersection_of: part_of UBERON:0008861 ! pyloric gastric gland @@ -29357,12 +33360,14 @@ id: CL:1000324 name: duodenal goblet cell def: "A goblet cell that is part of the epithelium proper of duodenum." [GOC:tfm] subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "goblet cell of epithelium proper of duodenum" EXACT [] xref: FMA:263063 is_a: CL:1000317 ! intestinal villus goblet cell +is_a: CL:1001589 ! duodenum secretory cell intersection_of: CL:0000160 ! goblet cell -intersection_of: part_of UBERON:0002114 ! duodenum -relationship: part_of UBERON:0008346 ! duodenal epithelium +intersection_of: part_of UBERON:0008346 ! duodenal epithelium property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -29370,11 +33375,14 @@ id: CL:1000325 name: jejunal goblet cell def: "A goblet cell that is part of the epithelium proper of jejunum." [GOC:tfm] subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "goblet cell of epithelium proper of jejunum" EXACT [] xref: FMA:263065 is_a: CL:1000317 ! intestinal villus goblet cell intersection_of: CL:0000160 ! goblet cell -intersection_of: part_of UBERON:0002115 ! jejunum +intersection_of: part_of UBERON:0000400 ! jejunal epithelium +relationship: part_of UBERON:0000400 ! jejunal epithelium property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -29382,22 +33390,29 @@ id: CL:1000326 name: ileal goblet cell def: "A goblet cell that is part of the epithelium proper of ileum." [GOC:tfm] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "goblet cell of epithelium proper of ileum" EXACT [] xref: FMA:263067 +xref: https://cellxgene.cziscience.com/cellguide/CL_1000326 is_a: CL:1000317 ! intestinal villus goblet cell intersection_of: CL:0000160 ! goblet cell -intersection_of: part_of UBERON:0002116 ! ileum +intersection_of: part_of UBERON:0008345 ! ileal epithelium +relationship: part_of UBERON:0008345 ! ileal epithelium +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nThe ileal goblet cell is a subset of intestinal goblet cells that are a key component of the epithelium of the ileum, a portion of the small intestine. Goblet cells are named and characterized by their distinctive 'goblet' shape with a narrow base tapering to a broad apical surface; located between the lumen of the intestine and the internal environment of the body, they serve an integral role in maintaining gut homeostasis.\nLike all intestinal goblet cells, the primary function of ileal goblet cells is the production and secretion of mucins, large, heavily glycosylated proteins that combine to form mucus. This mucus lining serves as a protective barrier, shielding the underlying tissue from the potentially damaging effects of digestive enzymes, acids, or pathogenic microbes present in the gut lumen. Their strategic location in the ileal segment of the intestinal tract aids in efficient nutrient absorption while also maintaining an impregnable barrier against potential pathogens, ensuring an intricate balance.\nGoblet cells of the ileum also play a significant role in immune modulation. They are thought to promote oral tolerance (the immune unresponsiveness to orally ingested antigens such as food) by delivering luminal antigens to underlying dendritic cells, thereby driving immune education and tolerogenic responses. They also secrete bioactive molecules, such as the trefoil factor peptide TFF3, which aids in repairing damaged epithelium. By performing these crucial functions, ileal goblet cells not only aid in maintaining intestinal health, but also contribute significantly to the overall well-being of the organism." xsd:string {xref="DOI:10.1007/s11894-010-0131-2", xref="DOI:10.1038/nature10863", xref="DOI:10.1038/s41575-022-00675-x", xref="DOI:10.1111/imr.12182"} [Term] id: CL:1000327 name: appendix goblet cell def: "A goblet cell that is part of the epithelium proper of appendix." [GOC:tfm] +subset: human_subset +subset: mouse_subset synonym: "goblet cell of epithelium proper of appendix" EXACT [] xref: FMA:263069 is_a: CL:1000320 ! large intestine goblet cell is_a: CL:1000405 ! epithelial cell of appendix intersection_of: CL:0000160 ! goblet cell -intersection_of: part_of UBERON:0001154 ! vermiform appendix +intersection_of: part_of UBERON:0009697 ! epithelium of appendix [Term] id: CL:1000328 @@ -29412,14 +33427,18 @@ name: tracheal goblet cell def: "A goblet cell that is part of the epithelium of trachea." [GOC:tfm] subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "goblet cell of epithelium of trachea" EXACT [FMA:263075] xref: FMA:263075 +xref: https://cellxgene.cziscience.com/cellguide/CL_1000329 is_a: CL:0000307 ! tracheal epithelial cell is_a: CL:0019003 ! tracheobronchial goblet cell intersection_of: CL:0000160 ! goblet cell intersection_of: part_of UBERON:0003126 ! trachea relationship: part_of UBERON:0001901 ! epithelium of trachea property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nTracheal goblet cells are specialized cells found in the lining of the trachea. They are a key component of the tracheobronchial epithelium, a critical region responsible for maintaining open airways and preventing the ingress of harmful particles or irritants. Goblet cells are filled with membrane-bound secretory granules, which are responsible for their distinctive, goblet-like shape.\nGoblet cells specialize in the production and secretion of mucus, a slimy substance composed primarily of glycoproteins (mucins) and water. This sticky mucus serves to trap foreign particles and pollutants, such as dust, bacteria, and viruses that an organism breathes in. After trapping these particles, the cilia on neighboring ciliated epithelial cells beat synchronously, forming a coordinated escalator to push mucus upwards toward the pharynx, where it's either swallowed or expectorated. This system, known as the mucociliary clearance or escalator, forms a crucial barrier in the lungs against respiratory pathogens and external insults.\nChanges in the number or function of tracheal goblet cells can engender health complications. For example, goblet cell hyperplasia, or excessive growth of goblet cells, is a common feature of chronic inflammatory lung diseases such as asthma and Chronic Obstructive Pulmonary Disease (COPD). This condition results in mucus hypersecretion, airway blockage, and increased risk of respiratory tract infections." xsd:string {xref="DOI:10.1016/S1357-2725(02)00083-3", xref="DOI:10.1164/ajrccm.154.6.8970383", xref="DOI:10.1165/ajrcmb.25.5.f218", xref="DOI:10.2147/COPD.S38938", xref="DOI:10.3109/01902148.2013.791733"} [Term] id: CL:1000330 @@ -29427,12 +33446,16 @@ name: serous cell of epithelium of trachea def: "A serous secreting cell that is part of the epithelium of trachea." [GOC:tfm] subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset xref: FMA:263078 +xref: https://cellxgene.cziscience.com/cellguide/CL_1000330 is_a: CL:0019001 ! tracheobronchial serous cell intersection_of: CL:0000313 ! serous secreting cell intersection_of: part_of UBERON:0001901 ! epithelium of trachea relationship: part_of UBERON:0001901 ! epithelium of trachea property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nSerous cells are specialized epithelial cells and can be found lining the trachea and brochus. They are among the major components of the respiratory epithelium. \nThese cells are known for their production and release of serous secretions, which form a key component of airway mucus. These secretions primarily comprise of water, proteins, and enzymes, such as lysozyme and peroxidases. Their main purposes are to provide hydration and lubrication to the airway tissue and to act as a defense mechanism against pathogens. While the lysozyme and peroxidases contribute to the destruction of bacteria, the water in the secretions helps to liquefy the mucus, facilitating the effective functioning of the ciliated cells that propel the mucus up the trachea.\nThe coordinated action between serous cells and other cell types in the tracheal epithelium proves essential for maintaining a healthy respiratory tract. Dysfunction or damage of these cells can lead to various respiratory tract disorders, such as cystic fibrosis and asthma." xsd:string {xref="DOI:10.1002/dvdy.24250", xref="DOI:10.1016/B978-012330215-1/50029-6", xref="DOI:10.1016/S0034-5687(01)00214-", xref="DOI:10.1074/jbc.M208826200"} [Term] id: CL:1000331 @@ -29440,17 +33463,23 @@ name: serous cell of epithelium of bronchus def: "A serous secreting cell that is part of the epithelium of bronchus." [GOC:tfm] subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset xref: FMA:263080 +xref: https://cellxgene.cziscience.com/cellguide/CL_1000331 is_a: CL:0019001 ! tracheobronchial serous cell intersection_of: CL:0000313 ! serous secreting cell intersection_of: part_of UBERON:0002031 ! epithelium of bronchus relationship: part_of UBERON:0002031 ! epithelium of bronchus property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nSerous cells of the epithelium of the bronchus, also termed bronchial serous cells, are predominantly found within the seromucous glands located in the bronchial submucosa. Serous cells can also be found in the trachea and are characterized by small, sparse, electron-dense granules.\nSerous cells are specialized cells responsible for the production and secretion of serous fluid. Serous fluid, mainly composed of water, proteins, and various types of salts, provides many benefits: it helps moisturize the airways, keep the bronchial tube walls moist, and safeguard the bronchial tubes against various foreign particles and infectious agents such as bacteria and viruses. Moreover, the fluid released by these cells assists in the lubrication and reduced friction in the bronchi, allowing for smoother airflow." xsd:string {xref="DOI:10.1152/physrev.00039.2014", xref="https://www.ncbi.nlm.nih.gov/books/NBK534789/", xref="https://www.sciencedirect.com/topics/neuroscience/secretory-cell"} [Term] id: CL:1000332 name: serous cell of epithelium of terminal bronchiole def: "A serous secreting cell that is part of the epithelium of terminal bronchiole." [GOC:tfm] +subset: human_subset +subset: mouse_subset xref: FMA:263082 is_a: CL:0019001 ! tracheobronchial serous cell is_a: CL:1000272 ! lung secretory cell @@ -29462,6 +33491,8 @@ relationship: part_of UBERON:0001958 ! terminal bronchiole epithelium id: CL:1000333 name: serous cell of epithelium of lobular bronchiole def: "A serous secreting cell that is part of the epithelium of bronchiole." [GOC:tfm] +subset: human_subset +subset: mouse_subset xref: FMA:263084 is_a: CL:0019001 ! tracheobronchial serous cell is_a: CL:1000272 ! lung secretory cell @@ -29474,6 +33505,8 @@ id: CL:1000334 name: enterocyte of epithelium of small intestine def: "An enterocyte that is part of the epithelium of small intestine." [GOC:tfm] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset xref: FMA:263086 xref: https://cellxgene.cziscience.com/cellguide/CL_1000334 is_a: CL:0000584 {is_inferred="true"} ! enterocyte @@ -29481,12 +33514,15 @@ is_a: CL:0002254 ! epithelial cell of small intestine intersection_of: CL:0000584 ! enterocyte intersection_of: part_of UBERON:0001902 ! epithelium of small intestine relationship: part_of UBERON:0001902 ! epithelium of small intestine -property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional.\n\nEnterocytes of the epithelium of the small intestine are specialized cells that reside in the lining of the small intestine, and are primarily responsible for the essential process of nutrient absorption. These cells are columnar epithelial cells with an apical surface lined with microvilli, a feature referred to as the 'brush border', to maximize the surface area available for absorption.\nEnterocytes play a critical role in both the digestion and absorption of nutrients from food. Their extensive brush border contains enzymes that further assist in nutrient breakdown and transport proteins that transfer nutrients, such as glucose, amino acids, lipids, and vitamins, across the cell membrane. \nThe enterocytes of the small intestine also participate in the barrier function of the gut lining. Enterocytes are connected by tight junctions, which act as a primary defense line against pathogenic invasion by maintaining intestinal barrier integrity. Additionally, their cell surface is coated in glycocalyx and mucus which forms a defensive barrier preventing the penetration of harmful bacteria into the systemic circulation." xsd:string {xref="DOI:10.1038/nrgastro.2013.35", xref="DOI:10.1038/nri3738", xref="DOI:10.1084/jem.20191130", xref="DOI:10.3389/fphys.2021.699152/full"} +property_value: foaf:depiction http://purl.obolibrary.org/obo/cl/images/Small-intestine-cells.png {dc:license="http://creativecommons.org/licenses/by/4.0/", comment="Figure depicts a cross section of intestinal villi in the small intestine, including the crypts of Lieberkuhn (seen here as ‘crypt’), as well as the layer specific locations of cells that exist within the gastrointestinal tract. Layers depicted here include epithelium (rows of cells bordering villus), submucosa (white space below the epithelium containing networks of neurons and ganglia depicted in pink), muscularis mucosae (blue layer), muscularis propria (referred to here as muscle layer).\n\nISC: Intestinal Stem Cell \nTA: Transit Amplifying Cells"} +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nEnterocytes of the epithelium of the small intestine are specialized cells that reside in the lining of the small intestine, and are primarily responsible for the essential process of nutrient absorption. These cells are columnar epithelial cells with an apical surface lined with microvilli, a feature referred to as the 'brush border', to maximize the surface area available for absorption.\nEnterocytes play a critical role in both the digestion and absorption of nutrients from food. Their extensive brush border contains enzymes that further assist in nutrient breakdown and transport proteins that transfer nutrients, such as glucose, amino acids, lipids, and vitamins, across the cell membrane. \nThe enterocytes of the small intestine also participate in the barrier function of the gut lining. Enterocytes are connected by tight junctions, which act as a primary defense line against pathogenic invasion by maintaining intestinal barrier integrity. Additionally, their cell surface is coated in glycocalyx and mucus which forms a defensive barrier preventing the penetration of harmful bacteria into the systemic circulation." xsd:string {xref="DOI:10.1038/nrgastro.2013.35", xref="DOI:10.1038/nri3738", xref="DOI:10.1084/jem.20191130", xref="DOI:10.3389/fphys.2021.699152/full"} [Term] id: CL:1000335 name: enterocyte of epithelium of intestinal villus def: "An enterocyte that is part of the epithelium of intestinal villus." [GOC:tfm] +subset: human_subset +subset: mouse_subset xref: FMA:263088 is_a: CL:1000334 ! enterocyte of epithelium of small intestine intersection_of: CL:0000584 ! enterocyte @@ -29497,9 +33533,10 @@ relationship: part_of UBERON:0013636 ! epithelium of intestinal villus id: CL:1000337 name: enterocyte of epithelium of duodenal gland def: "An enterocyte that is part of the epithelium of duodenal gland." [GOC:tfm] +subset: human_subset +subset: mouse_subset xref: FMA:263092 -is_a: CL:0000584 ! enterocyte -is_a: CL:0002254 ! epithelial cell of small intestine +is_a: CL:1000334 ! enterocyte of epithelium of small intestine intersection_of: CL:0000584 ! enterocyte intersection_of: part_of UBERON:0001212 ! duodenal gland relationship: part_of UBERON:0001212 ! duodenal gland @@ -29508,6 +33545,8 @@ relationship: part_of UBERON:0001212 ! duodenal gland id: CL:1000338 name: enterocyte of epithelium of crypt of Lieberkuhn of small intestine def: "An enterocyte that is part of the epithelium of crypt of Lieberkuhn of small intestine." [GOC:tfm] +subset: human_subset +subset: mouse_subset xref: FMA:263094 is_a: CL:1000334 ! enterocyte of epithelium of small intestine relationship: part_of UBERON:0001983 ! crypt of Lieberkuhn @@ -29516,6 +33555,8 @@ relationship: part_of UBERON:0001983 ! crypt of Lieberkuhn id: CL:1000339 name: enterocyte of epithelium proper of small intestine def: "An enterocyte that is part of the epithelium proper of small intestine." [GOC:tfm] +subset: human_subset +subset: mouse_subset xref: FMA:263096 is_a: CL:1000334 ! enterocyte of epithelium of small intestine @@ -29523,6 +33564,8 @@ is_a: CL:1000334 ! enterocyte of epithelium of small intestine id: CL:1000340 name: enterocyte of epithelium proper of duodenum def: "An enterocyte that is part of the epithelium proper of duodenum." [GOC:tfm] +subset: human_subset +subset: mouse_subset xref: FMA:263098 is_a: CL:1000339 ! enterocyte of epithelium proper of small intestine relationship: part_of UBERON:0002114 ! duodenum @@ -29531,6 +33574,8 @@ relationship: part_of UBERON:0002114 ! duodenum id: CL:1000341 name: enterocyte of epithelium proper of jejunum def: "An enterocyte that is part of the epithelium proper of jejunum." [GOC:tfm] +subset: human_subset +subset: mouse_subset xref: FMA:263100 is_a: CL:1000339 ! enterocyte of epithelium proper of small intestine @@ -29539,27 +33584,36 @@ id: CL:1000342 name: enterocyte of epithelium proper of ileum def: "An enterocyte that is part of the epithelium proper of ileum." [GOC:tfm] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset xref: FMA:263102 xref: https://cellxgene.cziscience.com/cellguide/CL_1000342 is_a: CL:1000339 ! enterocyte of epithelium proper of small intestine -property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional.\n\nEnterocytes of the epithelium proper of the ileum, commonly known as ileal enterocytes, are specialized epithelial cells found lining the inner surface of the ileum, the final section of the small intestine in the human body. They play a pivotal role in nutrient absorption, digestive metabolic functions, and the maintenance of the host’s immune response. \nLike enterocytes in other parts of the intestine, ileal enterocytes exhibit distinct characteristics specific to their function and role. They have microvilli on their apical surfaces to increase absorption and are important in the absorption of vitamins and the reabsorption of bile salts. These cells also produce enzymes that metabolize lipids and xenobiotics." xsd:string {xref="DOI:10.1038/nri3738", xref="DOI:10.1084/jem.20191130", xref="DOI:10.1111/j.1365-2249.2011.04523.x"} +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nEnterocytes of the epithelium proper of the ileum, commonly known as ileal enterocytes, are specialized epithelial cells found lining the inner surface of the ileum, the final section of the small intestine in the human body. They play a pivotal role in nutrient absorption, digestive metabolic functions, and the maintenance of the host’s immune response. \nLike enterocytes in other parts of the intestine, ileal enterocytes exhibit distinct characteristics specific to their function and role. They have microvilli on their apical surfaces to increase absorption and are important in the absorption of vitamins and the reabsorption of bile salts. These cells also produce enzymes that metabolize lipids and xenobiotics." xsd:string {xref="DOI:10.1038/nri3738", xref="DOI:10.1084/jem.20191130", xref="DOI:10.1111/j.1365-2249.2011.04523.x"} [Term] id: CL:1000343 name: paneth cell of epithelium of small intestine def: "A paneth cell that is part of the epithelium of small intestine." [GOC:tfm] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset xref: FMA:263104 +xref: https://cellxgene.cziscience.com/cellguide/CL_1000343 is_a: CL:0000510 {is_inferred="true"} ! paneth cell -is_a: CL:1001598 ! small intestine glandular cell +is_a: CL:1001598 ! small intestine secretory cell intersection_of: CL:0000510 ! paneth cell intersection_of: part_of UBERON:0001902 ! epithelium of small intestine +property_value: foaf:depiction http://purl.obolibrary.org/obo/cl/images/Small-intestine-cells.png {dc:license="http://creativecommons.org/licenses/by/4.0/", comment="Figure depicts a cross section of intestinal villi in the small intestine , including the crypts of Lieberkuhn (seen here as ‘crypt’), as well as the layer specific locations of cells that exist within the gastrointestinal tract. Layers depicted here include epithelium (rows of cells bordering villus), submucosa (white space below the epithelium containing networks of neurons and ganglia depicted in pink), muscularis mucosae (blue layer), muscularis propria (referred to here as muscle layer).\n\nISC: Intestinal Stem Cell \nTA: Transit Amplifying Cells"} +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nPaneth cells of the epithelium of the small intestine, often referred to simply as Paneth cells, are a type of specialized secretory cell that forms an integral part of the intestinal crypts of Lieberkühn – gland-like invaginations lining the small intestine. Named after the Austrian physician Josef Paneth, who first identified them in the late 19th century, these cells are significant because of their substantial involvement in the mucosal immune system and intestinal stem cell maintenance.\nFunctionally, Paneth cells play a key role in maintaining gut homeostasis and in the first line of antimicrobial defense, mainly through the secretion of a range of antimicrobial peptides and proteins. These include lysozymes, cryptdins, or alpha-defensins, which have potent activity against various gut pathogens including bacteria, fungi, and parasites. Furthermore, Paneth cells of the small intestine are also known to release secretory phospholipase A2, an enzyme active against gram-positive bacteria. Additionally, they secrete several growth factors like EGF, TGF-alpha, and Wnt3, which are crucial for stem cell support and the overall maintenance of intestinal mucosal integrity.\nThe unique location of Paneth cells at the base of the crypts positions them in very close proximity to intestinal stem cells. This not only facilitates their role in stem cell maintenance but also involves them in epithelial regeneration and repair following injury. Dysfunctional Paneth cells have been associated with several gut disorders, like Crohn’s disease and necrotizing enterocolitis." xsd:string {xref="DOI:10.1007/s00018-002-8412-z", xref="DOI:10.1038/nature09637", xref="DOI:10.1038/nrmicro2546", xref="DOI:10.1146/annurev-physiol-030212-183744", xref="DOI:10.3389/fimmu.2020.00587"} [Term] id: CL:1000344 name: paneth cell of epithelium proper of small intestine def: "A Paneth cell that is part of the epithelium proper of small intestine." [GOC:tfm] subset: human_reference_atlas +subset: human_subset +subset: mouse_subset xref: FMA:263106 is_a: CL:1000343 ! paneth cell of epithelium of small intestine property_value: RO:0002175 NCBITaxon:9606 @@ -29568,6 +33622,8 @@ property_value: RO:0002175 NCBITaxon:9606 id: CL:1000345 name: paneth cell of epithelium of crypt of Lieberkuhn of small intestine def: "A paneth cell that is part of the epithelium of crypt of Lieberkuhn of small intestine." [GOC:tfm] +subset: human_subset +subset: mouse_subset xref: FMA:263108 is_a: CL:1000343 ! paneth cell of epithelium of small intestine @@ -29576,6 +33632,8 @@ id: CL:1000346 name: enterocyte of epithelium proper of large intestine alt_id: CL:1000336 def: "An enterocyte that is part of the epithelium proper of large intestine." [GOC:tfm] +subset: human_subset +subset: mouse_subset synonym: "vacuolar absorptive cell of epithelium proper of large intestine" NARROW [] xref: FMA:263090 xref: FMA:263112 @@ -29584,18 +33642,21 @@ is_a: CL:0002071 ! enterocyte of epithelium of large intestine [Term] id: CL:1000347 name: colonocyte -def: "A columnar cell of the colon that is part of the colonic epithelium." [GOC:tfm] +def: "An enterocyte (absorptive epithelial cell) of the colonic epithelium, characterized by a columnar shape. This cell is responsible for the absorption, transport, and metabolization of short-chain fatty acids (SCFAs) produced by gut bacteria, as well as the transport and absorption of water and electrolytes." [GOC:tfm, PMID:16870803, PMID:23821742, PMID:34497389] subset: cellxgene_subset -synonym: "colonocyte" EXACT [PMID:34497389] +subset: human_subset +subset: mouse_subset synonym: "enterocyte of colon" EXACT [] synonym: "vacuolar absorptive cell of epithelium of colon" NARROW [] xref: FMA:263114 xref: https://cellxgene.cziscience.com/cellguide/CL_1000347 -is_a: CL:0002071 {is_inferred="true"} ! enterocyte of epithelium of large intestine +is_a: CL:0002071 ! enterocyte of epithelium of large intestine is_a: CL:0011108 ! colon epithelial cell intersection_of: CL:0002071 ! enterocyte of epithelium of large intestine intersection_of: part_of UBERON:0000397 ! colonic epithelium -property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional.\n\nEnterocytes of the colon are specialized epithelial cells located in the lining of the colon, the largest part of the large intestine. These cells play a critical role in absorbing water, electrolytes, and certain vitamins from the food material passed on from the small intestine. With a unique structure of finger-like protrusions referred to as microvilli, the enterocytes increase their surface area for effective absorption. The colon is the last part of the digestive system, and as such, it is responsible for compacting undigested food materials and forming fecal matter. Enterocytes of the colon facilitate this process effectively through absorption of water.\nEnterocytes are known for their high regeneration potential, replenishing every 4-5 days, enabling the healthy functioning of the colon. They originate from stem cells located in the crypt of the colon and differentiate into mature enterocytes as they migrate upwards towards the luminal surface. This constant turnover aids in maintaining the intestinal barrier, preventing the entry of detrimental substances into the systemic circulation. Their tight junctions with other epithelial cells provide a robust barrier against invasive pathogens.\nEnterocytes of the colon are involved in the communication with the gut microbiota. These cells harbor enzymes necessary for the metabolism of short-chain fatty acids, which are the byproducts of the fermentation process by gut bacteria. Short-chain fatty acids serve as a major energy source for colonocytes and are important for maintaining colonic health. The dysfunction of enterocytes, therefore, could lead to disorders such as inflammatory bowel disease or colorectal cancer." xsd:string {xref="DOI:10.1007/s11894-010-0130-3", xref="DOI:10.1038/nrgastro.2013.35", xref="DOI:10.1038/nri3738", xref="DOI:10.1084/jem.20191130", xref="DOI:10.3389/fimmu.2019.00277"} +relationship: capable_of GO:0019626 ! short-chain fatty acid catabolic process +relationship: capable_of GO:0035377 ! transepithelial water transport +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nEnterocytes of the colon are specialized epithelial cells located in the lining of the colon, the largest part of the large intestine. These cells play a critical role in absorbing water, electrolytes, and certain vitamins from the food material passed on from the small intestine. With a unique structure of finger-like protrusions referred to as microvilli, the enterocytes increase their surface area for effective absorption. The colon is the last part of the digestive system, and as such, it is responsible for compacting undigested food materials and forming fecal matter. Enterocytes of the colon facilitate this process effectively through absorption of water.\nEnterocytes are known for their high regeneration potential, replenishing every 4-5 days, enabling the healthy functioning of the colon. They originate from stem cells located in the crypt of the colon and differentiate into mature enterocytes as they migrate upwards towards the luminal surface. This constant turnover aids in maintaining the intestinal barrier, preventing the entry of detrimental substances into the systemic circulation. Their tight junctions with other epithelial cells provide a robust barrier against invasive pathogens.\nEnterocytes of the colon are involved in the communication with the gut microbiota. These cells harbor enzymes necessary for the metabolism of short-chain fatty acids, which are the byproducts of the fermentation process by gut bacteria. Short-chain fatty acids serve as a major energy source for colonocytes and are important for maintaining colonic health. The dysfunction of enterocytes, therefore, could lead to disorders such as inflammatory bowel disease or colorectal cancer." xsd:string {xref="DOI:10.1007/s11894-010-0130-3", xref="DOI:10.1038/nrgastro.2013.35", xref="DOI:10.1038/nri3738", xref="DOI:10.1084/jem.20191130", xref="DOI:10.3389/fimmu.2019.00277"} [Term] id: CL:1000348 @@ -29603,12 +33664,16 @@ name: basal cell of epithelium of trachea def: "A basal cell that is part of the epithelium of trachea." [GOC:tfm] subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset xref: FMA:263118 +xref: https://cellxgene.cziscience.com/cellguide/CL_1000348 is_a: CL:0002633 {is_inferred="true"} ! respiratory basal cell intersection_of: CL:0002633 ! respiratory basal cell intersection_of: part_of UBERON:0001901 ! epithelium of trachea relationship: part_of UBERON:0001901 ! epithelium of trachea property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nBasal cells of epithelium of trachea are a vital cell population within the respiratory tract's lining, specifically in the trachea's epithelium. These cells are located at the base of the columnar epithelial cell layer and can be identified by their characteristic cuboidal shape, a large nucleus and few organelles, as well as scattered microvilli. The basal cells are not in direct contact with the lumen, which is covered by a layer of ciliated and non-ciliated columnar cells. Instead, the basal cells are connected to, and line, a thin basement membrane.\nThe primary function of basal cells involves stem cell activity and epithelial tissue maintenance. Basal cells in the trachea play a crucial role in the regeneration and repair of the tracheal epithelium during damage or injury, acting as progenitor cells for ciliated and secretory cells. They serve as a reserve pool of cells, ready to proliferate and differentiate as needed for homeostatic tissue maintenance or in repair processes when the epithelium has been compromised, whether by injury or disease.\nThese cells are also implicated in numerous disease pathways. Conditions like chronic obstructive pulmonary disease and lung cancer exhibit unusual behavior and quantities of tracheal basal cells, making these cells a focal point in respiratory disease research. In summary, basal cells in the tracheal epithelium have a multifaceted role in maintaining, repairing, and influencing tracheal health, playing a crucial role in the stability of the respiratory system." xsd:string {xref="DOI:10.1164/rccm.201408-1492PP", xref="DOI:10.1165/rcmb.2021-0150ED", xref="DOI:10.1242/dmm.006031", xref="DOI:10.3389/falgy.2021.787128"} [Term] id: CL:1000349 @@ -29616,20 +33681,26 @@ name: basal cell of epithelium of bronchus alt_id: CL:0002331 def: "A basal cell found in the bronchus epithelium." [GOC:tfm] subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "basal cell of bronchus" EXACT [] xref: FMA:263120 +xref: https://cellxgene.cziscience.com/cellguide/CL_1000349 is_a: CL:0002328 ! bronchial epithelial cell is_a: CL:0002329 ! basal epithelial cell of tracheobronchial tree is_a: CL:0002633 ! respiratory basal cell intersection_of: CL:0002633 ! respiratory basal cell intersection_of: part_of UBERON:0002031 ! epithelium of bronchus property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nThe basal cells of the epithelium of the bronchus are a vital component of the cellular linings found within the bronchial tubes of the respiratory system. They are typically nonciliated, cuboidal cells that are tightly attached to the basement membrane, thereby providing structural support for the epithelial tissues. \nThe function of the basal cell of the bronchial epithelium is multifaceted, underscoring the importance of these cells for respiratory health. One of their primary roles involves regeneration and cellular turnover. They serve as local stem cells, being able to proliferate and differentiate into other cell types such as ciliated and secretory epithelial cells. This regenerative function of basal cells is required for maintaining the integrity of the bronchial epithelium and is especially critical after injury or during disease states when there is an increased need for new cells to repair damaged tissue or replace lost cells. \nIn addition to these regenerative duties, basal cells of the bronchial epithelium play a crucial role in providing a defensive barrier against inhaled substances. They participate in the coordinated immune response directed against airborne pathogens, foreign particles, and toxins that enter the respiratory tract. Basal cells can respond to inflammation or irritation by altering their activities, which include proliferating, differentiating, or producing bioactive substances. Throughout all these responses, the basal cells help to maintain the homeostasis of the bronchial tubes, allowing for the efficient transport of air to and from the lungs." xsd:string {xref="DOI:10.1002/ar.1092380310", xref="DOI:10.1038/labinvest.2015.114", xref="DOI:10.1136/thx.2004.la0104", xref="DOI:10.3389/falgy.2021.787128"} [Term] id: CL:1000350 name: basal cell of epithelium of terminal bronchiole def: "A basal cell that is part of the epithelium of terminal bronchiole." [GOC:tfm] subset: human_reference_atlas +subset: human_subset +subset: mouse_subset xref: FMA:263122 is_a: CL:0002633 {is_inferred="true"} ! respiratory basal cell intersection_of: CL:0002633 ! respiratory basal cell @@ -29642,6 +33713,8 @@ id: CL:1000351 name: basal cell of epithelium of respiratory bronchiole def: "A basal cell that is part of the epithelium of respiratory bronchiole." [GOC:tfm] subset: human_reference_atlas +subset: human_subset +subset: mouse_subset xref: FMA:263124 is_a: CL:0002633 {is_inferred="true"} ! respiratory basal cell intersection_of: CL:0002633 ! respiratory basal cell @@ -29654,6 +33727,8 @@ id: CL:1000352 name: basal cell of epithelium of lobular bronchiole def: "A basal cell that is part of the epithelium of bronchiole." [GOC:tfm] subset: human_reference_atlas +subset: human_subset +subset: mouse_subset xref: FMA:263126 is_a: CL:0002633 {is_inferred="true"} ! respiratory basal cell intersection_of: CL:0002633 ! respiratory basal cell @@ -29666,17 +33741,23 @@ id: CL:1000353 name: microfold cell of epithelium of small intestine def: "A M cell that is part of the epithelium of small intestine." [GOC:tfm] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset xref: FMA:263128 +xref: https://cellxgene.cziscience.com/cellguide/CL_1000353 is_a: CL:0000682 {is_inferred="true"} ! M cell of gut is_a: CL:0002254 ! epithelial cell of small intestine intersection_of: CL:0000682 ! M cell of gut intersection_of: part_of UBERON:0002108 ! small intestine relationship: part_of UBERON:0001902 ! epithelium of small intestine +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nMicrofold cells, also widely known as M cells, are a distinct type of epithelial cell found in the gut, including the small intestine, specifically within the Peyer’s patches, a component of the gut-associated lymphoid tissue (GALT). M cells play a crucial role in the immune response within the intestine environment. \nThese cells are characterized by microfolds (short microvilli, which give them their name), a reduced, thin glycocalyx, and a deeply invaginated basolateral membrane next to immune cells such as B cells, T cells, and macrophages, and DCs. \nThese features allow the M cells to form the first point of contact between the gut lumen and the intestinal immune system. They are well-regulated gateways that capture and transport antigens, such as bacteria, viruses, and other foreign substances found in the lumen, to the underlying cells of the immune system. This specialized transport mechanism, called ‘transcytosis’, involves engulfment of these antigens from the apical side, transport across their cytoplasm, and release on the basolateral side of the cells, where immune responses can be initiated. \nFurthermore, M cells have complex interactions with members of the gut microbiota and other immune cells, making them essential for maintaining gut homeostasis. This cross-talk shapes the diversity and makeup of the gut microbiota, subsequently having a substantial impact on the host's health. In certain situations, pathogenic organisms can exploit the transcytosis mechanism to infiltrate the host's system, causing various infectious diseases.\nThe overarching significance of M cells in the small intestine lies in their role of surveillance and protection against a wide range of potentially harmful pathogens, while also facilitating beneficial interactions with commensal microbes." xsd:string {xref="DOI:10.1038/mi.2013.30", xref="DOI:10.1093/jb/mvv121", xref="DOI:10.1111/j.1574-695X.2007.00359.x", xref="DOI:10.3389/fimmu.2019.01499"} [Term] id: CL:1000354 name: microfold cell of epithelium of intestinal villus def: "A M cell that is part of the epithelium of intestinal villus." [GOC:tfm] +subset: human_subset +subset: mouse_subset xref: FMA:263130 is_a: CL:1000353 ! microfold cell of epithelium of small intestine intersection_of: CL:0000682 ! M cell of gut @@ -29687,6 +33768,8 @@ relationship: part_of UBERON:0013636 ! epithelium of intestinal villus id: CL:1000355 name: microfold cell of epithelium proper of small intestine def: "A M cell that is part of the epithelium proper of small intestine." [GOC:tfm] +subset: human_subset +subset: mouse_subset xref: FMA:263132 is_a: CL:1000353 ! microfold cell of epithelium of small intestine @@ -29694,6 +33777,8 @@ is_a: CL:1000353 ! microfold cell of epithelium of small intestine id: CL:1000356 name: microfold cell of epithelium proper of duodenum def: "A M cell that is part of the epithelium proper of duodenum." [GOC:tfm] +subset: human_subset +subset: mouse_subset xref: FMA:263134 is_a: CL:1000354 ! microfold cell of epithelium of intestinal villus intersection_of: CL:0000682 ! M cell of gut @@ -29704,6 +33789,8 @@ relationship: part_of UBERON:0008346 ! duodenal epithelium id: CL:1000357 name: microfold cell of epithelium proper of jejunum def: "A M cell that is part of the epithelium proper of jejunum." [GOC:tfm] +subset: human_subset +subset: mouse_subset xref: FMA:263136 is_a: CL:1000353 ! microfold cell of epithelium of small intestine intersection_of: CL:0000682 ! M cell of gut @@ -29714,6 +33801,8 @@ relationship: part_of UBERON:0002115 ! jejunum id: CL:1000358 name: microfold cell of epithelium proper of ileum def: "A M cell that is part of the epithelium proper of ileum." [GOC:tfm] +subset: human_subset +subset: mouse_subset xref: FMA:263138 is_a: CL:1000353 ! microfold cell of epithelium of small intestine intersection_of: CL:0000682 ! M cell of gut @@ -29724,17 +33813,20 @@ relationship: part_of UBERON:0002116 ! ileum id: CL:1000359 name: microfold cell of epithelium proper of appendix def: "A M cell that is part of the epithelium proper of appendix." [GOC:tfm] +subset: human_subset +subset: mouse_subset xref: FMA:263140 is_a: CL:1000360 ! microfold cell of epithelium proper of large intestine is_a: CL:1000405 ! epithelial cell of appendix intersection_of: CL:0000682 ! M cell of gut intersection_of: part_of UBERON:0001154 ! vermiform appendix -relationship: part_of UBERON:0009697 ! epithelium of appendix [Term] id: CL:1000360 name: microfold cell of epithelium proper of large intestine def: "A M cell that is part of the epithelium proper of large intestine." [GOC:tfm] +subset: human_subset +subset: mouse_subset xref: FMA:263142 is_a: CL:0000682 ! M cell of gut is_a: CL:0002253 ! epithelial cell of large intestine @@ -29745,6 +33837,8 @@ intersection_of: part_of UBERON:0000059 ! large intestine id: CL:1000361 name: transitional myocyte of interatrial septum def: "A transitional myocyte that is part of the interatrial septum." [GOC:tfm] +subset: human_subset +subset: mouse_subset xref: FMA:263152 is_a: CL:0002073 {is_inferred="true"} ! transitional myocyte is_a: CL:2000022 ! cardiac septum cell @@ -29756,6 +33850,8 @@ relationship: part_of UBERON:0002085 ! interatrial septum id: CL:1000362 name: transitional myocyte of interventricular septum def: "A transitional myocyte that is part of the interventricular septum." [GOC:tfm] +subset: human_subset +subset: mouse_subset xref: FMA:263154 is_a: CL:0002073 {is_inferred="true"} ! transitional myocyte is_a: CL:2000022 ! cardiac septum cell @@ -29767,6 +33863,8 @@ relationship: part_of UBERON:0002094 ! interventricular septum id: CL:1000363 name: transitional myocyte of atrial branch of anterior internodal tract def: "A transitional myocyte that is part of the atrial branch of anterior internodal tract." [GOC:tfm] +subset: human_subset +subset: mouse_subset xref: FMA:263156 is_a: CL:1000480 ! transitional myocyte of internodal tract @@ -29774,6 +33872,8 @@ is_a: CL:1000480 ! transitional myocyte of internodal tract id: CL:1000364 name: transitional myocyte of anterior internodal tract def: "A transitional myocyte that is part of the anterior internodal tract." [GOC:tfm] +subset: human_subset +subset: mouse_subset xref: FMA:263158 is_a: CL:1000480 ! transitional myocyte of internodal tract @@ -29781,6 +33881,8 @@ is_a: CL:1000480 ! transitional myocyte of internodal tract id: CL:1000365 name: transitional myocyte of atrial septal branch of anterior internodal tract def: "A transitional myocyte that is part of the atrial septal branch of anterior internodal tract." [GOC:tfm] +subset: human_subset +subset: mouse_subset xref: FMA:263160 is_a: CL:1000480 ! transitional myocyte of internodal tract @@ -29788,6 +33890,8 @@ is_a: CL:1000480 ! transitional myocyte of internodal tract id: CL:1000366 name: transitional myocyte of middle internodal tract def: "A transitional myocyte that is part of the middle internodal tract." [GOC:tfm] +subset: human_subset +subset: mouse_subset xref: FMA:263162 is_a: CL:1000480 ! transitional myocyte of internodal tract @@ -29795,6 +33899,8 @@ is_a: CL:1000480 ! transitional myocyte of internodal tract id: CL:1000367 name: transitional myocyte of posterior internodal tract def: "A transitional myocyte that is part of the posterior internodal tract." [GOC:tfm] +subset: human_subset +subset: mouse_subset xref: FMA:263164 is_a: CL:1000480 ! transitional myocyte of internodal tract @@ -29802,6 +33908,8 @@ is_a: CL:1000480 ! transitional myocyte of internodal tract id: CL:1000368 name: transitional myocyte of anterior division of left branch of atrioventricular bundle def: "A transitional myocyte that is part of the anterior division of left branch of atrioventricular bundle." [GOC:tfm] +subset: human_subset +subset: mouse_subset xref: FMA:263166 is_a: CL:1000370 ! transitional myocyte of left branch of atrioventricular bundle @@ -29809,6 +33917,8 @@ is_a: CL:1000370 ! transitional myocyte of left branch of atrioventricular bundl id: CL:1000369 name: transitional myocyte of septal division of left branch of atrioventricular bundle def: "A transitional myocyte that is part of the septal division of left branch of atrioventricular bundle." [GOC:tfm] +subset: human_subset +subset: mouse_subset xref: FMA:263168 is_a: CL:1000370 ! transitional myocyte of left branch of atrioventricular bundle @@ -29816,6 +33926,8 @@ is_a: CL:1000370 ! transitional myocyte of left branch of atrioventricular bundl id: CL:1000370 name: transitional myocyte of left branch of atrioventricular bundle def: "A transitional myocyte that is part of the left branch of atrioventricular bundle." [GOC:tfm] +subset: human_subset +subset: mouse_subset xref: FMA:263170 is_a: CL:1000481 ! transitional myocyte of atrioventricular bundle intersection_of: CL:0002073 ! transitional myocyte @@ -29826,6 +33938,8 @@ relationship: part_of UBERON:0005986 ! left bundle branch id: CL:1000371 name: transitional myocyte of right branch of atrioventricular bundle def: "A transitional myocyte that is part of the right branch of atrioventricular bundle." [GOC:tfm] +subset: human_subset +subset: mouse_subset xref: FMA:263172 is_a: CL:1000481 ! transitional myocyte of atrioventricular bundle intersection_of: CL:0002073 ! transitional myocyte @@ -29836,6 +33950,8 @@ relationship: part_of UBERON:0005987 ! right bundle branch id: CL:1000372 name: transitional myocyte of atrial part of atrioventricular bundle def: "A transitional myocyte that is part of the atrial part of atrioventricular bundle." [GOC:tfm] +subset: human_subset +subset: mouse_subset xref: FMA:263174 is_a: CL:1000481 ! transitional myocyte of atrioventricular bundle @@ -29843,6 +33959,8 @@ is_a: CL:1000481 ! transitional myocyte of atrioventricular bundle id: CL:1000373 name: transitional myocyte of ventricular part of atrioventricular bundle def: "A transitional myocyte that is part of the ventricular part of atrioventricular bundle." [GOC:tfm] +subset: human_subset +subset: mouse_subset xref: FMA:263176 is_a: CL:1000481 ! transitional myocyte of atrioventricular bundle @@ -29850,6 +33968,8 @@ is_a: CL:1000481 ! transitional myocyte of atrioventricular bundle id: CL:1000374 name: transitional myocyte of posterior division of left branch of atrioventricular bundle def: "A transitional myocyte that is part of the posterior division of left branch of atrioventricular bundle." [GOC:tfm] +subset: human_subset +subset: mouse_subset xref: FMA:263178 is_a: CL:1000370 ! transitional myocyte of left branch of atrioventricular bundle @@ -29857,6 +33977,8 @@ is_a: CL:1000370 ! transitional myocyte of left branch of atrioventricular bundl id: CL:1000375 name: myocardial endocrine cell of septal division of left branch of atrioventricular bundle def: "A myocardial endocrine cell that is part of the septal division of left branch of atrioventricular bundle." [GOC:tfm] +subset: human_subset +subset: mouse_subset xref: FMA:263180 is_a: CL:0002074 ! myocardial endocrine cell is_a: CL:0008009 ! transversely striated visceral muscle cell @@ -29868,6 +33990,8 @@ relationship: part_of UBERON:0005986 ! left bundle branch id: CL:1000376 name: Purkinje myocyte of interventricular septum def: "A Purkinje myocyte that is part of the interventricular septum." [GOC:tfm] +subset: human_subset +subset: mouse_subset xref: FMA:263182 is_a: CL:0002068 {is_inferred="true"} ! Purkinje myocyte is_a: CL:2000022 ! cardiac septum cell @@ -29879,6 +34003,8 @@ relationship: part_of UBERON:0002094 ! interventricular septum id: CL:1000377 name: dense-core granulated cell of epithelium of trachea def: "A Feyrter cell that is part of the epithelium of trachea." [GOC:tfm] +subset: human_subset +subset: mouse_subset xref: FMA:263184 is_a: CL:0000307 {is_inferred="true"} ! tracheal epithelial cell is_a: CL:0002066 {is_inferred="true"} ! Feyrter cell @@ -29890,6 +34016,8 @@ relationship: part_of UBERON:0001901 ! epithelium of trachea id: CL:1000378 name: type 1 vestibular sensory cell of stato-acoustic epithelium def: "A type I vestibular sensory cell that is part of the stato-acoustic epithelium." [GOC:tfm] +subset: human_subset +subset: mouse_subset xref: FMA:263186 is_a: CL:0002070 ! type I vestibular sensory cell intersection_of: CL:0002070 ! type I vestibular sensory cell @@ -29900,6 +34028,8 @@ relationship: part_of UBERON:0009969 ! statoacoustic epithelium id: CL:1000379 name: type 1 vestibular sensory cell of epithelium of macula of utricle of membranous labyrinth def: "A type I vestibular sensory cell that is part of the epithelium of macula of utricle of membranous labyrinth." [GOC:tfm] +subset: human_subset +subset: mouse_subset xref: FMA:263188 is_a: CL:0002070 ! type I vestibular sensory cell intersection_of: CL:0002070 ! type I vestibular sensory cell @@ -29910,6 +34040,8 @@ relationship: part_of UBERON:0003241 ! epithelium of utricle id: CL:1000380 name: type 1 vestibular sensory cell of epithelium of macula of saccule of membranous labyrinth def: "A type I vestibular sensory cell that is part of the epithelium of macula of saccule of membranous labyrinth." [GOC:tfm] +subset: human_subset +subset: mouse_subset xref: FMA:263190 is_a: CL:0002070 ! type I vestibular sensory cell intersection_of: CL:0002070 ! type I vestibular sensory cell @@ -29921,6 +34053,8 @@ relationship: part_of UBERON:0003242 ! epithelium of saccule id: CL:1000381 name: type 1 vestibular sensory cell of epithelium of crista of ampulla of semicircular duct of membranous labyrinth def: "A type I vestibular sensory cell that is part of the epithelium of crista of ampulla of semicircular duct of membranous labyrinth." [GOC:tfm] +subset: human_subset +subset: mouse_subset xref: FMA:263192 is_a: CL:0002070 ! type I vestibular sensory cell intersection_of: CL:0002070 ! type I vestibular sensory cell @@ -29931,6 +34065,8 @@ relationship: part_of UBERON:0006935 ! crista ampullaris neuroepithelium id: CL:1000382 name: type 2 vestibular sensory cell of stato-acoustic epithelium def: "A type II vestibular sensory cell that is part of the stato-acoustic epithelium." [GOC:tfm] +subset: human_subset +subset: mouse_subset xref: FMA:263194 is_a: CL:0002069 ! type II vestibular sensory cell intersection_of: CL:0002069 ! type II vestibular sensory cell @@ -29941,6 +34077,8 @@ relationship: part_of UBERON:0009969 ! statoacoustic epithelium id: CL:1000383 name: type 2 vestibular sensory cell of epithelium of macula of utricle of membranous labyrinth def: "A type II vestibular sensory cell that is part of the epithelium of macula of utricle of membranous labyrinth." [GOC:tfm] +subset: human_subset +subset: mouse_subset xref: FMA:263196 is_a: CL:0002069 ! type II vestibular sensory cell intersection_of: CL:0002069 ! type II vestibular sensory cell @@ -29951,6 +34089,8 @@ relationship: part_of UBERON:0003241 ! epithelium of utricle id: CL:1000384 name: type 2 vestibular sensory cell of epithelium of macula of saccule of membranous labyrinth def: "A type II vestibular sensory cell that is part of the epithelium of macula of saccule of membranous labyrinth." [GOC:tfm] +subset: human_subset +subset: mouse_subset xref: FMA:263198 is_a: CL:0002069 ! type II vestibular sensory cell intersection_of: CL:0002069 ! type II vestibular sensory cell @@ -29962,6 +34102,8 @@ relationship: part_of UBERON:0003242 ! epithelium of saccule id: CL:1000385 name: type 2 vestibular sensory cell of epithelium of crista of ampulla of semicircular duct of membranous labyrinth def: "A type II vestibular sensory cell that is part of the epithelium of crista of ampulla of semicircular duct of membranous labyrinth." [GOC:tfm] +subset: human_subset +subset: mouse_subset xref: FMA:263200 is_a: CL:0002069 ! type II vestibular sensory cell intersection_of: CL:0002069 ! type II vestibular sensory cell @@ -29972,6 +34114,8 @@ relationship: part_of UBERON:0006935 ! crista ampullaris neuroepithelium id: CL:1000391 name: melanocyte of eyelid def: "A melanocyte that is part of the eyelid." [GOC:tfm] +subset: human_subset +subset: mouse_subset synonym: "eyelid melanocyte" EXACT [FMA:59175] synonym: "sebaceous gland of wolff" EXACT [FMA:59175] xref: FMA:59175 @@ -29984,6 +34128,8 @@ relationship: part_of UBERON:0001711 ! eyelid id: CL:1000394 name: myoepithelial cell of intralobular lactiferous duct def: "A myoepithelial cell that is part of the intralobular part of terminal lactiferous duct." [GOC:tfm] +subset: human_subset +subset: mouse_subset xref: FMA:62158 is_a: CL:0000185 ! myoepithelial cell @@ -29992,6 +34138,8 @@ id: CL:1000397 name: endothelial cell of venous sinus of red pulp of spleen def: "An endothelial cell that is part of the venous sinus of red pulp of spleen." [GOC:tfm] comment: todo - add logical definition to UBERON:0009967 +subset: human_subset +subset: mouse_subset xref: FMA:62817 is_a: CL:0002651 ! endothelial cell of venous sinus of spleen is_a: CL:2000053 ! splenic endothelial cell @@ -30005,34 +34153,43 @@ name: endothelial cell of hepatic sinusoid def: "An endothelial cell that is part of the hepatic sinusoid. These cells possess flattened areas containing perforations about 0.1 micrometers in diameter, known as fenestrae. The fenestrae are arranged in groups known as sieve plates." [GOC:tfm, PMID:3926620] subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "endotheliocyte of hepatic sinusoid" EXACT [FMA:62911] synonym: "liver sinusoidal endothelial cell" EXACT [PMID:30348985] synonym: "LSEC" EXACT [PMID:30348985] xref: BTO:000125 xref: FMA:62911 +xref: https://cellxgene.cziscience.com/cellguide/CL_1000398 is_a: CL:0000666 ! fenestrated endothelial cell is_a: CL:0002262 ! endothelial cell of sinusoid intersection_of: CL:0000115 ! endothelial cell intersection_of: part_of UBERON:0001281 ! hepatic sinusoid relationship: part_of UBERON:0001281 ! hepatic sinusoid property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nEndothelial cells of hepatic sinusoids, also known as hepatic or liver sinusoidal endothelial cells (HSEC or LSEC), are unique, specialized type of endothelial cells located in the liver. They are the building units of the hepatic sinusoid, which functions as a specialized capillary system that facilitates the exchange of various substances between the blood and hepatocytes. This finely tuned environment, facilitated by HSEC, is primordial for the liver's multiple physiologic functions that include nutrient metabolism, toxin inactivation, and immunomodulation.\nThe HSEC have a distinctive morphology that sets them apart from the typical endothelial cells found in other organs. These cells are exceptionally thin to allow for efficient transfer of molecules and characterized by fenestrations, which are non-diaphragmatic, sieve-like openings that provide an open filtration pathway from the sinusoidal lumen to the space of Disse, where hepatocytes are exposed. The fenestration is a crucial feature that allows lipoproteins, nutrients, and other plasma components easy access to hepatocytes for essential liver functions, including clearance of waste products and metabolic regulation.\nHSECs further play a vital role in immune functionality in the liver. They act as a sentinel, determining the nature of the immune response to encountered particulates. They possess a capacity for antigen presentation and express a series of immune-related surface molecules, which helps in immunosurveillance and immunoregulation. The HSEC also aid in the removal and destruction of virus-infected cells, harmful microorganisms, and circulatory waste products to safeguard liver health and general systemic cleanliness." xsd:string {xref="DOI:10.1016/j.jhep.2016.07.009", xref="DOI:10.1038/cmi.2016.5", xref="DOI:10.1038/s41575-018-0020-y", xref="DOI:10.1038/s41575-020-00411-3", xref="https://www.sciencedirect.com/topics/immunology-and-microbiology/disse-space"} [Term] id: CL:1000405 name: epithelial cell of appendix def: "An epithelial cell that is part of the appendix." [GOC:tfm] +subset: human_subset +subset: mouse_subset synonym: "columnar epitheliocyte of appendix" EXACT [FMA:63602] synonym: "epithelial cell of vermiform appendix" EXACT [FMA:63602] xref: FMA:63602 is_a: CL:0002253 ! epithelial cell of large intestine intersection_of: CL:0000066 ! epithelial cell -intersection_of: part_of UBERON:0001154 ! vermiform appendix -relationship: part_of UBERON:0001154 ! vermiform appendix +intersection_of: part_of UBERON:0009697 ! epithelium of appendix +relationship: part_of UBERON:0009697 ! epithelium of appendix [Term] id: CL:1000409 name: myocyte of sinoatrial node def: "A muscle cell that is part of the sinoatrial node." [FMA:67102, GOC:tfm] +subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "SA nodal myocyte" EXACT [FMA:67102] synonym: "SA node cardiac muscle cell" EXACT [GOC:pr] synonym: "sinoatrial node cell" EXACT [GOC:pr] @@ -30049,6 +34206,8 @@ relationship: part_of UBERON:0002351 ! sinoatrial node id: CL:1000410 name: myocyte of atrioventricular node def: "A muscle cell that is part of the atrioventricular node." [FMA:67106, GOC:tfm] +subset: human_subset +subset: mouse_subset synonym: "atrioventricular node cell" EXACT [GOC:pr] synonym: "atrioventricular node myocyte" EXACT [FMA:67106] synonym: "AV nodal myocyte" EXACT [FMA:67106] @@ -30066,6 +34225,8 @@ relationship: part_of UBERON:0002352 ! atrioventricular node id: CL:1000411 name: endothelial cell of Peyer's patch def: "An endothelial cell that is part of the small intestine Peyer's patch." [GOC:tfm] +subset: human_subset +subset: mouse_subset xref: FMA:67757 is_a: CL:0000115 {is_inferred="true"} ! endothelial cell intersection_of: CL:0000115 ! endothelial cell @@ -30077,6 +34238,8 @@ id: CL:1000412 name: endothelial cell of arteriole def: "An endothelial cell that is part of the arteriole." [GOC:tfm] subset: human_reference_atlas +subset: human_subset +subset: mouse_subset xref: FMA:67760 xref: KUPO:0001097 is_a: CL:0000071 {is_inferred="true"} ! blood vessel endothelial cell @@ -30092,6 +34255,8 @@ alt_id: CL:0002542 def: "A blood vessel endothelial cell that is part of an arterial endothelium." [GOC:tfm] subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "arterial endothelial cell" EXACT [] xref: BTO:0004758 xref: FMA:67761 @@ -30102,7 +34267,7 @@ intersection_of: CL:0000115 ! endothelial cell intersection_of: part_of UBERON:0001637 ! artery relationship: part_of UBERON:0001917 ! endothelium of artery property_value: RO:0002175 NCBITaxon:9606 -property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional.\n\nEndothelial cells of the artery, also referred to as arterial endothelial cells, form an integral part of the arterial system. They form a single layer, known as the endothelium, lining the interior surface of arteries, and are able to respond to the high-pressure and flow conditions present in arteries. The primary role of these cells is to provide a barrier between the vessel wall and the blood, exhibiting selective permeability to regulate the movement of liquids, gases, and blood-borne substances across the vascular wall.\nArterial endothelial cells significantly contribute to maintaining vascular homeostasis. They are at the forefront of sensations and responses to mechanical stimuli, like shear stress and blood pressure changes. An additional key function pertains to the production of nitric oxide, which helps to regulate vascular tone and blood pressure, prevents platelet aggregation, limits leukocyte adhesion to the endothelium, and inhibits smooth muscle cell proliferation. These varied but connected functions help to preclude the development of atherosclerosis, ensuring normal circulation and arterial health.\nMoreover, these cells play a pivotal role in inflammation and coagulation processes. During inflammatory events, they express various adhesion molecules, aiding in leukocyte recruitment and rolling onto the vessel walls for immune response. They also produce anticoagulant and procoagulant substances, involved in blood clotting and clot dissolution, respectively. Dysregulation of the usual functions of arterial endothelial cells can result in serious pathophysiological conditions, such as atherosclerosis, hypertension, and other cardiovascular diseases." xsd:string {xref="DOI:10.1007/s00441-008-0706-5", xref="DOI:10.1007/s10456-021-09785-7", xref="DOI:10.1016/j.ccm.2021.08.005", xref="DOI:10.1016/j.jvs.2004.03.043", xref="DOI:10.1177/153857440303700107"} +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nEndothelial cells of the artery, also referred to as arterial endothelial cells, form an integral part of the arterial system. They form a single layer, known as the endothelium, lining the interior surface of arteries, and are able to respond to the high-pressure and flow conditions present in arteries. The primary role of these cells is to provide a barrier between the vessel wall and the blood, exhibiting selective permeability to regulate the movement of liquids, gases, and blood-borne substances across the vascular wall.\nArterial endothelial cells significantly contribute to maintaining vascular homeostasis. They are at the forefront of sensations and responses to mechanical stimuli, like shear stress and blood pressure changes. An additional key function pertains to the production of nitric oxide, which helps to regulate vascular tone and blood pressure, prevents platelet aggregation, limits leukocyte adhesion to the endothelium, and inhibits smooth muscle cell proliferation. These varied but connected functions help to preclude the development of atherosclerosis, ensuring normal circulation and arterial health.\nMoreover, these cells play a pivotal role in inflammation and coagulation processes. During inflammatory events, they express various adhesion molecules, aiding in leukocyte recruitment and rolling onto the vessel walls for immune response. They also produce anticoagulant and procoagulant substances, involved in blood clotting and clot dissolution, respectively. Dysregulation of the usual functions of arterial endothelial cells can result in serious pathophysiological conditions, such as atherosclerosis, hypertension, and other cardiovascular diseases." xsd:string {xref="DOI:10.1007/s00441-008-0706-5", xref="DOI:10.1007/s10456-021-09785-7", xref="DOI:10.1016/j.ccm.2021.08.005", xref="DOI:10.1016/j.jvs.2004.03.043", xref="DOI:10.1177/153857440303700107"} [Term] id: CL:1000414 @@ -30110,6 +34275,8 @@ name: endothelial cell of venule def: "An endothelial cell that is part of the venule." [GOC:tfm] subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset xref: FMA:67762 is_a: CL:0000071 ! blood vessel endothelial cell intersection_of: CL:0002139 ! endothelial cell of vascular tree @@ -30121,6 +34288,8 @@ property_value: RO:0002175 NCBITaxon:9606 id: CL:1000415 name: epithelial cell of gallbladder def: "An epithelial cell that is part of the gallbladder." [GOC:tfm] +subset: human_subset +subset: mouse_subset xref: FMA:67780 is_a: CL:0000066 ! epithelial cell intersection_of: CL:0000066 ! epithelial cell @@ -30140,6 +34309,8 @@ id: CL:1000417 name: myoepithelial cell of sweat gland def: "A myoepithelial cell that is part of the sweat gland." [GOC:tfm] subset: human_reference_atlas +subset: human_subset +subset: mouse_subset xref: FMA:67801 is_a: CL:0000185 {is_inferred="true"} ! myoepithelial cell is_a: CL:1000448 ! epithelial cell of sweat gland @@ -30151,6 +34322,8 @@ property_value: RO:0002175 NCBITaxon:9606 id: CL:1000418 name: myoepithelial cell of lactiferous alveolus def: "A myoepithelial cell that is part of the mammary gland alveolus." [GOC:tfm] +subset: human_subset +subset: mouse_subset synonym: "basal cell of alveolus of lactiferous gland" EXACT [FMA:67802] synonym: "myoepithelial cell of mammary alveolus" EXACT [FMA:67802] xref: FMA:67802 @@ -30163,6 +34336,8 @@ relationship: part_of UBERON:0003214 ! mammary gland alveolus id: CL:1000419 name: myoepithelial cell of lactiferous duct def: "A myoepithelial cell that is part of the lactiferous duct." [GOC:tfm] +subset: human_subset +subset: mouse_subset xref: FMA:67803 is_a: CL:0000068 ! duct epithelial cell is_a: CL:0002324 ! basal-myoepithelial cell of mammary gland @@ -30174,6 +34349,8 @@ relationship: part_of UBERON:0001765 ! mammary duct id: CL:1000420 name: myoepithelial cell of terminal lactiferous duct def: "A myoepithelial cell that is part of the terminal lactiferous duct." [GOC:tfm] +subset: human_subset +subset: mouse_subset xref: FMA:67804 is_a: CL:0000185 ! myoepithelial cell @@ -30181,6 +34358,8 @@ is_a: CL:0000185 ! myoepithelial cell id: CL:1000424 name: chromaffin cell of paraaortic body def: "A chromaffin cell that is part of the paraaortic body." [GOC:tfm] +subset: human_subset +subset: mouse_subset synonym: "chromaffin cell of para-aortic body" EXACT [FMA:69328] xref: FMA:69328 is_a: CL:1000425 ! chromaffin cell of paraganglion @@ -30192,6 +34371,8 @@ relationship: part_of UBERON:0001237 ! paraaortic body id: CL:1000425 name: chromaffin cell of paraganglion def: "A chromaffin cell that is part of the paraganglion." [GOC:tfm] +subset: human_subset +subset: mouse_subset xref: FMA:69335 is_a: CL:0000166 {is_inferred="true"} ! chromaffin cell intersection_of: CL:0000166 ! chromaffin cell @@ -30202,9 +34383,11 @@ relationship: part_of UBERON:0012279 ! chromaffin paraganglion id: CL:1000426 name: chromaffin cell of adrenal gland def: "A chromaffin cell that is part of the adrenal gland." [GOC:tfm] +subset: human_subset +subset: mouse_subset synonym: "adrenal chromaffin cell" EXACT [GO:0061104] xref: FMA:69794 -is_a: CL:0000150 ! glandular epithelial cell +is_a: CL:0000150 ! glandular secretory epithelial cell is_a: CL:0000166 {is_inferred="true"} ! chromaffin cell intersection_of: CL:0000166 ! chromaffin cell intersection_of: part_of UBERON:0002369 ! adrenal gland @@ -30215,6 +34398,8 @@ id: CL:1000427 name: adrenal cortex chromaffin cell def: "A chromaffin cell that is part of the adrenal cortex." [GOC:tfm] comment: Not clear this cell type exists. Can't call it a cortical adrenal cell because of different germ layer origin. +subset: human_subset +subset: mouse_subset synonym: "chromaffin cell of adrenal cortex" EXACT [] xref: FMA:69795 is_a: CL:1000426 ! chromaffin cell of adrenal gland @@ -30227,6 +34412,8 @@ id: CL:1000428 name: stem cell of epidermis def: "A somatic stem cell that is part of the epidermis." [GOC:tfm] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "epidermal stem cell" EXACT [FMA:70541] xref: FMA:70541 xref: ZFA:0007122 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} @@ -30241,6 +34428,8 @@ name: conjunctival epithelial cell def: "An epithelial cell that is part of the conjunctiva." [GOC:tfm] subset: cellxgene_subset subset: eye_upper_slim +subset: human_subset +subset: mouse_subset synonym: "epithelial cell of conjunctiva" EXACT [FMA:70552] xref: FMA:70552 is_a: CL:0000066 {is_inferred="true"} ! epithelial cell @@ -30252,6 +34441,8 @@ relationship: part_of UBERON:0001811 ! conjunctiva id: CL:1000433 name: epithelial cell of lacrimal canaliculus def: "An epithelial cell that is part of the lacrimal canaliculus." [GOC:tfm] +subset: human_subset +subset: mouse_subset xref: FMA:70553 is_a: CL:0000066 ! epithelial cell intersection_of: CL:0000066 ! epithelial cell @@ -30262,6 +34453,8 @@ relationship: part_of UBERON:0001770 ! lacrimal canaliculus id: CL:1000434 name: epithelial cell of external acoustic meatus def: "An epithelial cell that is part of the external acoustic meatus." [GOC:tfm] +subset: human_subset +subset: mouse_subset xref: FMA:70555 is_a: CL:0000066 ! epithelial cell intersection_of: CL:0000066 ! epithelial cell @@ -30272,6 +34465,8 @@ relationship: part_of UBERON:0001352 ! external acoustic meatus id: CL:1000435 name: epithelial cell of lacrimal drainage system def: "An epithelial cell that is part of the lacrimal drainage system." [GOC:tfm, PMID:22594785] +subset: human_subset +subset: mouse_subset synonym: "epithelial cell of lacrimal duct" RELATED [] xref: FMA:70559 is_a: CL:0000072 {is_inferred="true"} ! non-branched duct epithelial cell @@ -30284,18 +34479,22 @@ id: CL:1000436 name: epithelial cell of lacrimal sac def: "An epithelial cell that is part of the lacrimal sac." [GOC:tfm] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset xref: FMA:70560 xref: https://cellxgene.cziscience.com/cellguide/CL_1000436 is_a: CL:1000437 ! epithelial cell of nasolacrimal duct intersection_of: CL:0000066 ! epithelial cell intersection_of: part_of UBERON:0001351 ! lacrimal sac relationship: part_of UBERON:0001351 ! lacrimal sac -property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional.\n\nEpithelial cells of the lacrimal sac play a significant role in the physiology of tear drainage, acting as an integral part of the lacrimal drainage system. The lacrimal sac is part of the nasolacrimal duct system, a conduit which connects the eye to the nasal cavity, and is lined by multilayered, non-keratinizing, squamous epithelial cells. \nThe epithelial cells of the lacrimal sac are specialized for the purpose of maintaining a moist environment and protecting the surface of the eye. They form a barrier that traps and removes potential contaminants from the tear film during the drainage process. These cells also actively contribute to tear turnover by expediting the drainage of excess tears. Dysfunctional epithelial cells of the lacrimal sac can lead to dacryocystitis, a condition characterized by inflammation of the lacrimal sac.\nEpithelial cells of the lacrimal sac also perform various other tasks which ensure the overall health of the eye. They are involved in the regulation of immune responses within the lacrimal apparatus and may have a possible role in host-microbiome interactions. Thus, epithelial cells of the lacrimal sac play a multifaceted role in tear drainage and ocular surface defence, directly translating to eye health and vision quality." xsd:string {xref="DOI:10.1007/s004290050160", xref="DOI:10.1111/j.1442-9071.2012.02818.x", xref="DOI:10.1167/tvst.8.4.32", xref="DOI:10.2147/OPTH.S26048", xref="DOI:10.3389/fimmu.2022.918619"} +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nEpithelial cells of the lacrimal sac play a significant role in the physiology of tear drainage, acting as an integral part of the lacrimal drainage system. The lacrimal sac is part of the nasolacrimal duct system, a conduit which connects the eye to the nasal cavity, and is lined by multilayered, non-keratinizing, squamous epithelial cells. \nThe epithelial cells of the lacrimal sac are specialized for the purpose of maintaining a moist environment and protecting the surface of the eye. They form a barrier that traps and removes potential contaminants from the tear film during the drainage process. These cells also actively contribute to tear turnover by expediting the drainage of excess tears. Dysfunctional epithelial cells of the lacrimal sac can lead to dacryocystitis, a condition characterized by inflammation of the lacrimal sac.\nEpithelial cells of the lacrimal sac also perform various other tasks which ensure the overall health of the eye. They are involved in the regulation of immune responses within the lacrimal apparatus and may have a possible role in host-microbiome interactions. Thus, epithelial cells of the lacrimal sac play a multifaceted role in tear drainage and ocular surface defence, directly translating to eye health and vision quality." xsd:string {xref="DOI:10.1007/s004290050160", xref="DOI:10.1111/j.1442-9071.2012.02818.x", xref="DOI:10.1167/tvst.8.4.32", xref="DOI:10.2147/OPTH.S26048", xref="DOI:10.3389/fimmu.2022.918619"} [Term] id: CL:1000437 name: epithelial cell of nasolacrimal duct def: "An epithelial cell that is part of the nasolacrimal duct." [GOC:tfm] +subset: human_subset +subset: mouse_subset xref: FMA:70561 is_a: CL:1000435 ! epithelial cell of lacrimal drainage system intersection_of: CL:0000072 ! non-branched duct epithelial cell @@ -30306,6 +34505,8 @@ relationship: part_of UBERON:0002392 ! nasolacrimal duct id: CL:1000438 name: epithelial cell of wall of inferior part of anal canal def: "An epithelial cell that is part of the wall of inferior part of anal canal." [GOC:tfm] +subset: human_subset +subset: mouse_subset xref: FMA:70562 is_a: CL:0002634 ! epithelial cell of anal column @@ -30313,6 +34514,8 @@ is_a: CL:0002634 ! epithelial cell of anal column id: CL:1000441 name: epithelial cell of viscerocranial mucosa def: "An epithelial cell that is part of the viscerocranial mucosa." [GOC:tfm] +subset: human_subset +subset: mouse_subset xref: FMA:70583 is_a: CL:0000066 ! epithelial cell @@ -30320,6 +34523,8 @@ is_a: CL:0000066 ! epithelial cell id: CL:1000442 name: urothelial cell of trigone of urinary bladder def: "An urothelial cell that is part of the trigone of urinary bladder." [GOC:tfm] +subset: human_subset +subset: mouse_subset synonym: "epithelial cell of vesical trigone" EXACT [FMA:70598] xref: FMA:70598 is_a: CL:1001428 ! bladder urothelial cell @@ -30330,17 +34535,23 @@ name: ciliary muscle cell def: "A smooth muscle cell that is part of the ciliary body." [GOC:tfm] subset: cellxgene_subset subset: eye_upper_slim +subset: human_subset +subset: mouse_subset synonym: "smooth muscle cell of ciliary body" EXACT [FMA:70610] xref: FMA:70610 +xref: https://cellxgene.cziscience.com/cellguide/CL_1000443 is_a: CL:0000192 {is_inferred="true"} ! smooth muscle cell intersection_of: CL:0000192 ! smooth muscle cell intersection_of: part_of UBERON:0001775 ! ciliary body relationship: part_of UBERON:0001775 ! ciliary body +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nCiliary muscle cells are specialized contractile cells that constitute the ciliary muscle, a component of the eye in vertebrates. These cells form a ring around the iris, the eye's colored part. Ciliary muscle cells fall into the category of smooth muscle cells, characterized by their lack of the striations typical of skeletal and cardiac muscle cells. Their shape is elongated and pointed at both ends, and they occur in multi-nucleated syncytia where many cells share the same cytoplasm.\nCiliary muscle cells primarily control the eye's accommodation, adjusting the thickness and curvature of the lens to fine-tune the focus of light on the retina. When ciliary muscle cells contract, tension on the zonular fibers holding the lens in place is reduced, allowing the lens to become thicker and increase its refractive power. Conversely, when the ciliary muscle cells relax, the tension on the zonular fibers increases, causing the lens to become flatter and decrease its refractive power. This adjustment facilitates clear vision at different distances, ranging from near to far objects.\nAdditionally, ciliary muscle cells play a role in draining the eye's aqueous humor, which is the clear fluid that fills the anterior chamber of the eye between the cornea and the lens. By controlling the shape of the surrounding trabecular meshwork through muscle contractions and relaxations, ciliary muscle cells indirectly regulate intraocular pressure, a factor critical for preventing ocular conditions like glaucoma." xsd:string {xref="DOI:10.1016/S1350-9462(98)00011-1", xref="DOI:10.1038/srep31171", xref="DOI:10.1111/j.1444-0938.2008.00260.x", xref="https://www.sciencedirect.com/topics/medicine-and-dentistry/ciliary-muscle"} [Term] id: CL:1000444 name: mesothelial cell of anterior chamber of eye def: "A mesothelial cell that is part of the anterior chamber of eyeball." [GOC:tfm] +subset: human_subset +subset: mouse_subset xref: FMA:70615 is_a: CL:0000077 ! mesothelial cell intersection_of: CL:0000077 ! mesothelial cell @@ -30351,6 +34562,8 @@ relationship: part_of UBERON:0001766 ! anterior chamber of eyeball id: CL:1000445 name: myoepithelial cell of dilator pupillae def: "A myoepithelial cell that is part of the dilatator pupillae." [GOC:tfm] +subset: human_subset +subset: mouse_subset xref: FMA:70619 is_a: CL:0000185 {is_inferred="true"} ! myoepithelial cell intersection_of: CL:0000185 ! myoepithelial cell @@ -30362,6 +34575,8 @@ id: CL:1000447 name: epithelial cell of stratum germinativum of esophagus def: "A basal cell that is part of the epithelium of esophagus." [GOC:tfm] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "basal cell of esophageal epithelium" EXACT [FMA:70731] xref: FMA:70731 is_a: CL:0000646 {is_inferred="true"} ! basal cell @@ -30374,6 +34589,8 @@ id: CL:1000448 name: epithelial cell of sweat gland def: "An epithelial cell that is part of the sweat gland." [GOC:tfm] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset xref: FMA:70952 is_a: CL:0000362 ! epidermal cell is_a: CL:0002308 ! epithelial cell of skin gland @@ -30386,18 +34603,24 @@ id: CL:1000449 name: epithelial cell of nephron def: "An epithelial cell that is part of the nephron." [GOC:tfm] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset xref: FMA:70965 +xref: https://cellxgene.cziscience.com/cellguide/CL_1000449 is_a: CL:0002518 ! kidney epithelial cell intersection_of: CL:0000066 ! epithelial cell intersection_of: part_of UBERON:0001285 ! nephron relationship: part_of UBERON:0001285 ! nephron +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nEpithelial cells of the nephron form the epithelial lining of the nephron, the functional unit of the kidney that filters the blood to produce urine. Each kidney holds approximately one million nephrons, each of which is composed of several distinct parts, including the renal corpuscle, the proximal tubule, the loop of Henle, and the distal tubule. All sections are lined with highly specialized epithelial cells adapted to perform different functions within the sections of the nephron. \nThe different epithelial cells of the nephron play crucial roles in the process of filtration, reabsorption, secretion, and excretion, essential tasks for the regulation of body fluid composition and volume. During filtration, the blood is forced through the walls of glomerular capillaries into the Bowman's capsule, where waste products, electrolytes, and water are separated from the blood cells and proteins. As the filtrate then passes through the nephron, epithelial cells of the tubular portion reabsorb useful substances such as glucose, amino acids, and electrolytes, along with most of the water back into the bloodstream. Waste products like urea and creatinine, as well as excess ions and water, remain in the tubule for elimination.\nIn addition, epithelial cells of the nephron also play a vital part in maintaining the body's acid-base balance by actively secreting hydrogen ions into the urine while reabsorbing bicarbonate from the urine back into the blood. They are also involved in the regulation of blood pressure through the renin-angiotensin-aldosterone system and contribute to erythrocyte production by releasing the hormone erythropoietin in response to low oxygen levels in the blood. Abnormalities or damage in renal epithelial cells often result in impaired kidney function, leading to various renal diseases." xsd:string {xref="DOI:10.1007/978-94-011-2354-9_6", xref="DOI:10.1007/s004670050586", xref="DOI:10.1016/B978-0-323-35775-3.00011-4", xref="DOI:10.1146/annurev-physiol-052521-121841", xref="DOI:10.1681/ASN.2012010029"} [Term] id: CL:1000450 name: epithelial cell of glomerular capsule def: "An epithelial cell that is part of the glomerular capsule." [GOC:tfm] subset: cellxgene_subset +subset: human_subset subset: kidney_upper_slim +subset: mouse_subset synonym: "Bowmans capsule epithelial cell" EXACT [] synonym: "epithelial cell of Bowman's capsule" EXACT [FMA:70966] xref: FMA:70966 @@ -30420,6 +34643,8 @@ alt_id: CL:1000897 def: "An epithelial cell that is part of the glomerular parietal epithelium." [GOC:tfm] subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "epithelial cell of parietal layer of glomerular capsule" EXACT [FMA:70968] xref: FMA:70968 xref: KUPO:0001035 @@ -30434,6 +34659,8 @@ property_value: RO:0002175 NCBITaxon:9606 id: CL:1000453 name: epithelial cell of intermediate tubule def: "An epithelial cell that is part of the intermediate tubule." [GOC:tfm] +subset: human_subset +subset: mouse_subset xref: FMA:70980 is_a: CL:1000909 ! kidney loop of Henle epithelial cell intersection_of: CL:1000494 ! nephron tubule epithelial cell @@ -30446,7 +34673,9 @@ name: kidney collecting duct epithelial cell def: "An epithelial cell that is part of the collecting duct of renal tubule." [GOC:tfm] subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset subset: kidney_upper_slim +subset: mouse_subset synonym: "epithelial cell of renal collecting tubule" EXACT [FMA:70982] xref: FMA:70982 xref: https://cellxgene.cziscience.com/cellguide/CL_1000454 @@ -30457,12 +34686,14 @@ is_a: CL:1001225 {is_inferred="true"} ! kidney collecting duct cell intersection_of: CL:0000066 ! epithelial cell intersection_of: part_of UBERON:0001232 ! collecting duct of renal tubule property_value: RO:0002175 NCBITaxon:9606 -property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional.\n\nKidney collecting duct epithelial cells are a specialized type of cells that form an integral part of the renal system. Located in the collecting duct system of the kidneys, these cells are responsible for one of the final steps in the process of urine formation, and they are instrumental in the fine tuning of the volume and composition of urine by reabsorbing water and certain solutes back into the bloodstream.\nThese cells express specific channels and carriers that actively and passively transport ions and water. They also have channels on their membranes, such as sodium channels and potassium channels, involved in reabsorbing or secreting these electrolytes depending upon the body's needs. The function of renal collecting duct epithelial cells can be regulated by a variety of hormones, including vasopressin (antidiuretic hormone), which can modulate the ion channels and carriers and hence indirectly influence body fluid homeostasis.\nAside from their function in ion and water balance, kidney collecting duct epithelial cells also aid in maintaining the body's acid-base balance. They have specialized functionality to secret hydrogen ions into the tubular lumen, which contributes to acid excretion. Any dysfunction may have serious implications and lead to various renal or systemic diseases, exemplifying the importance of these cells in maintaining overall body homeostasis." xsd:string {xref="DOI:10.1016/j.ajpath.2014.01.014", xref="DOI:10.1016/j.semnephrol.2019.04.005", xref="DOI:10.2215/CJN.05760513", xref="DOI:10.2215/CJN.08880914"} +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nKidney collecting duct epithelial cells are a specialized type of cells that form an integral part of the renal system. Located in the collecting duct system of the kidneys, these cells are responsible for one of the final steps in the process of urine formation, and they are instrumental in the fine tuning of the volume and composition of urine by reabsorbing water and certain solutes back into the bloodstream.\nThese cells express specific channels and carriers that actively and passively transport ions and water. They also have channels on their membranes, such as sodium channels and potassium channels, involved in reabsorbing or secreting these electrolytes depending upon the body's needs. The function of renal collecting duct epithelial cells can be regulated by a variety of hormones, including vasopressin (antidiuretic hormone), which can modulate the ion channels and carriers and hence indirectly influence body fluid homeostasis.\nAside from their function in ion and water balance, kidney collecting duct epithelial cells also aid in maintaining the body's acid-base balance. They have specialized functionality to secret hydrogen ions into the tubular lumen, which contributes to acid excretion. Any dysfunction may have serious implications and lead to various renal or systemic diseases, exemplifying the importance of these cells in maintaining overall body homeostasis." xsd:string {xref="DOI:10.1016/j.ajpath.2014.01.014", xref="DOI:10.1016/j.semnephrol.2019.04.005", xref="DOI:10.2215/CJN.05760513", xref="DOI:10.2215/CJN.08880914"} [Term] id: CL:1000456 name: mesothelial cell of parietal peritoneum def: "A mesothelial cell that is part of the parietal peritoneum." [GOC:tfm] +subset: human_subset +subset: mouse_subset xref: FMA:72142 is_a: CL:1000490 ! mesothelial cell of peritoneum intersection_of: CL:0000077 ! mesothelial cell @@ -30474,6 +34705,8 @@ id: CL:1000457 name: mesothelial cell of visceral peritoneum def: "A mesothelial cell that is part of the visceral peritoneum." [GOC:tfm] subset: human_reference_atlas +subset: human_subset +subset: mouse_subset xref: FMA:72143 is_a: CL:1000490 ! mesothelial cell of peritoneum intersection_of: CL:0000077 ! mesothelial cell @@ -30487,19 +34720,25 @@ name: melanocyte of skin def: "A melanocyte that is part of the skin of body." [GOC:tfm] subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "skin melanocyte" EXACT [FMA:72144] xref: CALOHA:TS-2374 xref: FMA:72144 +xref: https://cellxgene.cziscience.com/cellguide/CL_1000458 is_a: CL:0000148 {is_inferred="true"} ! melanocyte intersection_of: CL:0000148 ! melanocyte intersection_of: part_of UBERON:0002097 ! skin of body relationship: part_of UBERON:0002097 ! skin of body property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nMelanocytes of the skin are specialized pigment cells crucial for producing and distributing melanin, the pigment determining skin, in addition to hair and eye color. Located in the basal layer of the epidermis, melanocytes serve as a natural sunscreen, protecting skin cells from harmful UV radiation. Structurally dendritic, they synthesize melanin through melanogenesis, transferring melanosomes to keratinocytes for UV shielding\nBeyond pigmentation and UV protection, melanocytes play roles in immune and inflammatory responses. They respond to environmental changes, communicate with skin cell types, and secrete cytokines and growth factors influencing skin homeostasis. Dysregulation may lead to pigment disorders like vitiligo and melasma or contribute to skin cancer, particularly malignant melanoma." xsd:string {xref="DOI:10.1016/j.jinf.2015.06.006", xref="DOI:10.1111/j.1751-1097.2007.00226.x", xref="DOI:10.1615/CritRevEukaryotGeneExpr.2020028454", xref="DOI:10.5114/pdia.2013.33376", xref="https://www.sciencedirect.com/topics/biochemistry-genetics-and-molecular-biology/melanocyte"} [Term] id: CL:1000465 name: chromaffin cell of ovary def: "A chromaffin cell that is part of the ovary." [GOC:tfm] +subset: human_subset +subset: mouse_subset xref: FMA:74319 is_a: CL:0000166 {is_inferred="true"} ! chromaffin cell is_a: CL:2000064 ! ovarian surface epithelial cell @@ -30510,6 +34749,8 @@ intersection_of: part_of UBERON:0000992 ! ovary id: CL:1000466 name: chromaffin cell of right ovary def: "A chromaffin cell that is part of the right ovary." [GOC:tfm] +subset: human_subset +subset: mouse_subset xref: FMA:74320 is_a: CL:1000465 ! chromaffin cell of ovary intersection_of: CL:0000166 ! chromaffin cell @@ -30520,6 +34761,8 @@ relationship: part_of UBERON:0002118 ! right ovary id: CL:1000467 name: chromaffin cell of left ovary def: "A chromaffin cell that is part of the left ovary." [GOC:tfm] +subset: human_subset +subset: mouse_subset xref: FMA:74321 is_a: CL:1000465 ! chromaffin cell of ovary intersection_of: CL:0000166 ! chromaffin cell @@ -30530,6 +34773,8 @@ relationship: part_of UBERON:0002119 ! left ovary id: CL:1000468 name: myoepithelial cell of acinus of lactiferous gland def: "A myoepithelial cell that is part of the acinus of lactiferous gland." [GOC:tfm] +subset: human_subset +subset: mouse_subset synonym: "basal cell of acinus of lactiferous gland" EXACT [FMA:74469] xref: FMA:74469 is_a: CL:0002324 ! basal-myoepithelial cell of mammary gland @@ -30539,6 +34784,8 @@ relationship: part_of UBERON:0001912 ! lobule of mammary gland id: CL:1000469 name: myoepithelial cell of main lactiferous duct def: "A myoepithelial cell that is part of the main lactiferous duct." [GOC:tfm] +subset: human_subset +subset: mouse_subset xref: FMA:74499 is_a: CL:0000185 ! myoepithelial cell @@ -30546,6 +34793,8 @@ is_a: CL:0000185 ! myoepithelial cell id: CL:1000470 name: myoepithelial cell of primary lactiferous duct def: "A myoepithelial cell that is part of the primary lactiferous duct." [GOC:tfm] +subset: human_subset +subset: mouse_subset xref: FMA:74500 is_a: CL:0000185 ! myoepithelial cell @@ -30553,6 +34802,8 @@ is_a: CL:0000185 ! myoepithelial cell id: CL:1000471 name: myoepithelial cell of secondary lactiferous duct def: "A myoepithelial cell that is part of the secondary lactiferous duct." [GOC:tfm] +subset: human_subset +subset: mouse_subset xref: FMA:74501 is_a: CL:0000185 ! myoepithelial cell @@ -30560,6 +34811,8 @@ is_a: CL:0000185 ! myoepithelial cell id: CL:1000472 name: myoepithelial cell of tertiary lactiferous duct def: "A myoepithelial cell that is part of the tertiary lactiferous duct." [GOC:tfm] +subset: human_subset +subset: mouse_subset xref: FMA:74502 is_a: CL:0000185 ! myoepithelial cell @@ -30567,6 +34820,8 @@ is_a: CL:0000185 ! myoepithelial cell id: CL:1000473 name: myoepithelial cell of quarternary lactiferous duct def: "A myoepithelial cell that is part of the quarternary lactiferous duct." [GOC:tfm] +subset: human_subset +subset: mouse_subset xref: FMA:74503 is_a: CL:0000185 ! myoepithelial cell @@ -30575,6 +34830,8 @@ id: CL:1000477 name: cardiac pacemaker cell of sinoatrial node def: "A nodal myocyte that is part of the sinoatrial node." [GOC:tfm] subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "cardiac pacemaker cell of sinuatrial node" EXACT [] synonym: "pacemaker cell of sinoatrial node" EXACT [] synonym: "pacemaker cell of sinuatrial node" EXACT [] @@ -30586,6 +34843,8 @@ property_value: RO:0002175 NCBITaxon:9606 id: CL:1000478 name: transitional myocyte of sinoatrial node def: "A transitional myocyte that is part of the sinoatrial node." [GOC:tfm] +subset: human_subset +subset: mouse_subset synonym: "transitinal myocyte of sinuatrial node" EXACT [] xref: FMA:83384 is_a: CL:0002073 {is_inferred="true"} ! transitional myocyte @@ -30597,6 +34856,8 @@ intersection_of: part_of UBERON:0002351 ! sinoatrial node id: CL:1000479 name: Purkinje myocyte of atrioventricular node def: "A Purkinje myocyte that is part of the atrioventricular node." [GOC:tfm] +subset: human_subset +subset: mouse_subset xref: FMA:83386 is_a: CL:0002068 {is_inferred="true"} ! Purkinje myocyte is_a: CL:1000410 ! myocyte of atrioventricular node @@ -30607,6 +34868,8 @@ intersection_of: part_of UBERON:0002352 ! atrioventricular node id: CL:1000480 name: transitional myocyte of internodal tract def: "A transitional myocyte that is part of the internodal tract." [GOC:tfm] +subset: human_subset +subset: mouse_subset xref: FMA:83387 is_a: CL:0002073 {is_inferred="true"} ! transitional myocyte is_a: CL:0002096 ! internodal tract myocyte @@ -30617,6 +34880,8 @@ intersection_of: part_of UBERON:0009966 ! internodal tract id: CL:1000481 name: transitional myocyte of atrioventricular bundle def: "A transitional myocyte that is part of the atrioventricular bundle." [GOC:tfm] +subset: human_subset +subset: mouse_subset xref: FMA:83388 is_a: CL:0002073 {is_inferred="true"} ! transitional myocyte is_a: CL:0008009 ! transversely striated visceral muscle cell @@ -30629,6 +34894,8 @@ intersection_of: part_of UBERON:0002353 ! bundle of His id: CL:1000482 name: myocardial endocrine cell of interventricular septum def: "A myocardial endocrine cell that is part of the interventricular septum." [GOC:tfm] +subset: human_subset +subset: mouse_subset xref: FMA:83390 is_a: CL:0002074 {is_inferred="true"} ! myocardial endocrine cell is_a: CL:2000022 ! cardiac septum cell @@ -30640,6 +34907,8 @@ relationship: part_of UBERON:0002094 ! interventricular septum id: CL:1000483 name: Purkinje myocyte of internodal tract def: "A Purkinje myocyte that is part of the internodal tract." [GOC:tfm] +subset: human_subset +subset: mouse_subset xref: FMA:83392 is_a: CL:0002068 {is_inferred="true"} ! Purkinje myocyte is_a: CL:0002096 ! internodal tract myocyte @@ -30650,6 +34919,8 @@ intersection_of: part_of UBERON:0009966 ! internodal tract id: CL:1000484 name: Purkinje myocyte of atrioventricular bundle def: "A Purkinje myocyte that is part of the atrioventricular bundle." [GOC:tfm] +subset: human_subset +subset: mouse_subset xref: FMA:83393 is_a: CL:0002068 {is_inferred="true"} ! Purkinje myocyte is_a: CL:0008009 ! transversely striated visceral muscle cell @@ -30664,6 +34935,8 @@ name: basal cell of urothelium def: "A basal cell that is part of the urothelium. Compared to other urothelial cell types, a basal cell of the urothelium is positioned along the basement membrane, is the most undifferentiated and serves a progenitor role." [doi:10.1038/s41385-022-00565-0, GOC:tfm] comment: It has been noted in at least some mammalian species that the urothelial basal cell type is distinguished by expression of high levels of cytokeratin-5 (CK5), p63 and the signalling molecule Sonic hedgehog (Shh). Similar to intermediate cells, the urothelial basal cell type expresses CK17 but is negative for uroplakins (UPK) and CK20. Urothelial basal cells have also been noted to be smaller in diameter than urothelial intermediate cells. {xref="doi:10.1038/s41385-022-00565-0"} subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "urothelial basal cell" EXACT [doi:10.1007/978-3-030-14366-4_8, doi:10.1111/cpr.13170] xref: FMA:84150 is_a: CL:0000646 {is_inferred="true"} ! basal cell @@ -30678,19 +34951,25 @@ name: smooth muscle cell of prostate def: "A smooth muscle cell that is part of the prostate gland." [GOC:tfm] subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "smooth muscle fiber of prostate" EXACT [FMA:84583] xref: FMA:84583 +xref: https://cellxgene.cziscience.com/cellguide/CL_1000487 is_a: CL:0000192 {is_inferred="true"} ! smooth muscle cell intersection_of: CL:0000192 ! smooth muscle cell intersection_of: part_of UBERON:0002367 ! prostate gland relationship: part_of UBERON:0002367 ! prostate gland property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nSmooth muscle cells of the prostate constitute a critical component of the prostatic stroma, enveloping glandular structures to support functions like secretion and fluid expulsion. Like other smooth muscles, smooth muscle cells of the prostate lack the striations characteristic of skeletal and cardiac muscle cell.\nFunctionally, they play a crucial role in reproductive and urinary functions. Smooth muscle cells of the prostate contribute to the transport and expulsion of prostatic secretions into the urethra and respond dynamically to signaling molecules such as hormones and neurotransmitters. For instance, under sympathetic nervous stimulation, they contract and apply pressure on the gland's ducts, facilitating the secretion process." xsd:string {xref="DOI:10.1101/cshperspect.a030510", xref="https://www.ncbi.nlm.nih.gov/books/NBK279291", xref="https://www.sciencedirect.com/topics/immunology-and-microbiology/smooth-muscle-cell"} [Term] id: CL:1000488 name: cholangiocyte def: "An epithelial cell that is part of the bile duct. Cholangiocytes contribute to bile secretion via net release of bicarbonate and water. They are cuboidal epithelium in the small interlobular bile ducts, but become columnar and mucus secreting in larger bile ducts approaching the porta hepatis and the extrahepatic ducts." [GOC:tfm, PMID:16550043, PMID:18356246] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "epithelial cell of bile duct" EXACT [] xref: FMA:86481 xref: https://cellxgene.cziscience.com/cellguide/CL_1000488 @@ -30702,13 +34981,15 @@ intersection_of: capable_of GO:0015106 ! bicarbonate transmembrane transporter a intersection_of: part_of UBERON:0002394 ! bile duct relationship: part_of UBERON:0002394 ! bile duct relationship: RO:0002202 CL:0005026 ! develops from hepatoblast -property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional.\n\nCholangiocytes, also known as biliary epithelial cells, are specialized epithelial cells that line the biliary tract, which constitutes the gall bladder and bile ducts inside the liver. Crucial to the maintenance of the liver's health and function, cholangiocytes have a key role in the modification and secretion of bile, a fluid produced by hepatocytes that is essential to digestion and the absorption of fats and vitamins.\nCholangiocytes accomplish their primary function through the expression of a variety of transport proteins located on their apical and basolateral membranes, which propel bile acids and other contents of the bile into the biliary lumen. The hepatic bile, once secreted by the hepatocytes, is further modified by cholangiocytes via secretion and absorption processes. These processes help in the regulation of bile volume and composition, which is fundamental in ensuring the efficient digestion of dietary fats and fat-soluble vitamins and the excretion of cholesterol.\nIn addition to their role in bile modification, cholangiocytes also perform several other integral functions. For instance, these cells express Toll-like receptors (TLRs) which allow cholangiocytes to initiate an immune response against pathogens in the biliary lumen. When functioning normally, these cells contribute to biliary integrity, hepatic architecture, and overall hepatic physiology. However, when they become pathological, they are involved in the progression of liver diseases, such as primary biliary cirrhosis and cholangiocarcinoma – the malignancy of the biliary tract." xsd:string {xref="DOI:10.1016/j.jcmgh.2015.05.005", xref="DOI:10.1016/j.jhep.2012.10.011", xref="DOI:10.1038/s41575-019-0125-y", xref="DOI:10.1152/ajpgi.00227.2012", xref="DOI:10.5009/gnl16033"} +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nCholangiocytes, also known as biliary epithelial cells, are specialized epithelial cells that line the biliary tract, which constitutes the gall bladder and bile ducts inside the liver. Crucial to the maintenance of the liver's health and function, cholangiocytes have a key role in the modification and secretion of bile, a fluid produced by hepatocytes that is essential to digestion and the absorption of fats and vitamins.\nCholangiocytes accomplish their primary function through the expression of a variety of transport proteins located on their apical and basolateral membranes, which propel bile acids and other contents of the bile into the biliary lumen. The hepatic bile, once secreted by the hepatocytes, is further modified by cholangiocytes via secretion and absorption processes. These processes help in the regulation of bile volume and composition, which is fundamental in ensuring the efficient digestion of dietary fats and fat-soluble vitamins and the excretion of cholesterol.\nIn addition to their role in bile modification, cholangiocytes also perform several other integral functions. For instance, these cells express Toll-like receptors (TLRs) which allow cholangiocytes to initiate an immune response against pathogens in the biliary lumen. When functioning normally, these cells contribute to biliary integrity, hepatic architecture, and overall hepatic physiology. However, when they become pathological, they are involved in the progression of liver diseases, such as primary biliary cirrhosis and cholangiocarcinoma – the malignancy of the biliary tract." xsd:string {xref="DOI:10.1016/j.jcmgh.2015.05.005", xref="DOI:10.1016/j.jhep.2012.10.011", xref="DOI:10.1038/s41575-019-0125-y", xref="DOI:10.1152/ajpgi.00227.2012", xref="DOI:10.5009/gnl16033"} [Term] id: CL:1000489 name: reticular cell of splenic cord def: "A reticular cell that is part of the splenic cord." [GOC:tfm] subset: human_reference_atlas +subset: human_subset +subset: mouse_subset xref: FMA:86497 is_a: CL:0000432 {is_inferred="true"} ! reticular cell is_a: CL:2000051 ! splenic fibroblast @@ -30721,6 +35002,8 @@ property_value: RO:0002175 NCBITaxon:9606 id: CL:1000490 name: mesothelial cell of peritoneum def: "A mesothelial cell that is part of the peritoneum." [GOC:tfm] +subset: human_subset +subset: mouse_subset synonym: "peritoneal mesothelial cell" EXACT [FMA:86736] xref: FMA:86736 is_a: CL:0000077 ! mesothelial cell @@ -30733,6 +35016,8 @@ id: CL:1000491 name: mesothelial cell of pleura def: "A mesothelial cell that is part of the pleura." [GOC:tfm] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "pleural mesothelial cell" EXACT [FMA:86737] xref: FMA:86737 xref: https://cellxgene.cziscience.com/cellguide/CL_1000491 @@ -30740,12 +35025,14 @@ is_a: CL:0000077 ! mesothelial cell intersection_of: CL:0000077 ! mesothelial cell intersection_of: part_of UBERON:0000977 ! pleura relationship: part_of UBERON:0000977 ! pleura -property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional.\n\nMesothelial cells of the pleura form a significant part of the pleural membrane, a thin, double-layered serous membrane that lines the thoracic cavity and encompasses the lungs. These specialized cells contribute to the pleura's key function of producing a lubricating serous fluid, which reduces friction between the lung's outer surface (visceral pleura) and the inner lining of the thoracic cavity (parietal pleura) during respiration. \nThe cellular structure of mesothelial cells, characterized by microvilli on their surface, aids in the secretion and absorption of the pleural fluid, effectively supporting the smooth expansion and contraction of the lungs. Dysregulation in mesothelial cells can lead to pathologies, including pleural effusion and malignant mesothelioma.\nMesothelial cells of the pleura display unique immunologic properties. They act as a first line of defense against infection because they are able to recognize pathogens and respond by secreting various cytokines and chemokines. Additionally, these cells are directly involved in the translocation of immune cells into the pleural cavity during inflammatory response, thereby playing an active role in the immune response within the pleural environment. \nIn the event of pleural injury, these cells are also involved in the mesothelial-mesenchymal transition, a process that allows mesothelial cells to transdifferentiate into myofibroblasts and promote tissue repair." xsd:string {xref="DOI:10.1016/j.ccm.2021.08.005", xref="DOI:10.1016/j.coi.2020.04.005", xref="DOI:10.1152/ajplung.90587.2008", xref="DOI:10.3389/fphys.2014.00284"} +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nMesothelial cells of the pleura form a significant part of the pleural membrane, a thin, double-layered serous membrane that lines the thoracic cavity and encompasses the lungs. These specialized cells contribute to the pleura's key function of producing a lubricating serous fluid, which reduces friction between the lung's outer surface (visceral pleura) and the inner lining of the thoracic cavity (parietal pleura) during respiration. \nThe cellular structure of mesothelial cells, characterized by microvilli on their surface, aids in the secretion and absorption of the pleural fluid, effectively supporting the smooth expansion and contraction of the lungs. Dysregulation in mesothelial cells can lead to pathologies, including pleural effusion and malignant mesothelioma.\nMesothelial cells of the pleura display unique immunologic properties. They act as a first line of defense against infection because they are able to recognize pathogens and respond by secreting various cytokines and chemokines. Additionally, these cells are directly involved in the translocation of immune cells into the pleural cavity during inflammatory response, thereby playing an active role in the immune response within the pleural environment. \nIn the event of pleural injury, these cells are also involved in the mesothelial-mesenchymal transition, a process that allows mesothelial cells to transdifferentiate into myofibroblasts and promote tissue repair." xsd:string {xref="DOI:10.1016/j.ccm.2021.08.005", xref="DOI:10.1016/j.coi.2020.04.005", xref="DOI:10.1152/ajplung.90587.2008", xref="DOI:10.3389/fphys.2014.00284"} [Term] id: CL:1000492 name: mesothelial cell of parietal pleura def: "A mesothelial cell that is part of the parietal pleura." [GOC:tfm] +subset: human_subset +subset: mouse_subset xref: FMA:86738 is_a: CL:1000491 ! mesothelial cell of pleura intersection_of: CL:0000077 ! mesothelial cell @@ -30758,6 +35045,8 @@ name: mesothelial cell of visceral pleura def: "A mesothelial cell that is part of the visceral pleura." [GOC:tfm] subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset xref: FMA:86739 xref: https://cellxgene.cziscience.com/cellguide/CL_1000493 is_a: CL:1000491 ! mesothelial cell of pleura @@ -30765,7 +35054,7 @@ intersection_of: CL:0000077 ! mesothelial cell intersection_of: part_of UBERON:0002401 ! visceral pleura relationship: part_of UBERON:0002401 ! visceral pleura property_value: RO:0002175 NCBITaxon:9606 -property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional.\n\nMesothelial cells of visceral pleura are specialized epithelial cells that line the inner layer of the pleura, the membrane that envelops the lungs. Positioned adjacent to the lung tissue, these cells form a protective barrier and contribute to the structure of the visceral pleura. They are characterized by their cuboidal to squamous epithelial shape and the presence of microvilli on their surface, a feature aiding in fluid and solute exchange between the pleura and the lungs.\nThe primary function of mesothelial cells of visceral pleura is to secrete a lubricating serous fluid to facilitate smooth, frictionless lung movement within the thoracic cavity during respiration. This helps in the prevention of trauma or damage stemming from the constant rubbing of the lung tissue against the chest wall, hence playing a pivotal role in maintaining respiratory function. Besides fluid secretion, these cells have an essential role in the transportation of fluids and particles across the pleura, as well as in inflammation, wound healing, and tissue repair processes within the pleura.\nMesothelial cells of visceral pleura are notably implicated in the development of pleural diseases such as pleural effusion and pleural mesothelioma, a rare and aggressive form of cancer primarily linked with exposure to asbestos. Alterations, such as hyperplasia or metaplasia, may occur in these mesothelial cells under pathological conditions." xsd:string {xref="DOI:10.1016/S1357-2725(03)00242-5", xref="DOI:10.1152/physrev.00026.2003", xref="DOI:10.1371/journal.pone.0276978", xref="DOI:10.3389/fphys.2014.00221", xref="DOI:10.3390/jdb7020007"} +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nMesothelial cells of visceral pleura are specialized epithelial cells that line the inner layer of the pleura, the membrane that envelops the lungs. Positioned adjacent to the lung tissue, these cells form a protective barrier and contribute to the structure of the visceral pleura. They are characterized by their cuboidal to squamous epithelial shape and the presence of microvilli on their surface, a feature aiding in fluid and solute exchange between the pleura and the lungs.\nThe primary function of mesothelial cells of visceral pleura is to secrete a lubricating serous fluid to facilitate smooth, frictionless lung movement within the thoracic cavity during respiration. This helps in the prevention of trauma or damage stemming from the constant rubbing of the lung tissue against the chest wall, hence playing a pivotal role in maintaining respiratory function. Besides fluid secretion, these cells have an essential role in the transportation of fluids and particles across the pleura, as well as in inflammation, wound healing, and tissue repair processes within the pleura.\nMesothelial cells of visceral pleura are notably implicated in the development of pleural diseases such as pleural effusion and pleural mesothelioma, a rare and aggressive form of cancer primarily linked with exposure to asbestos. Alterations, such as hyperplasia or metaplasia, may occur in these mesothelial cells under pathological conditions." xsd:string {xref="DOI:10.1016/S1357-2725(03)00242-5", xref="DOI:10.1152/physrev.00026.2003", xref="DOI:10.1371/journal.pone.0276978", xref="DOI:10.3389/fphys.2014.00221", xref="DOI:10.3390/jdb7020007"} [Term] id: CL:1000494 @@ -30773,6 +35062,8 @@ name: nephron tubule epithelial cell def: "An epithelial cell that is part of a nephron tubule." [GOC:tfm] comment: This needs to be further defined as a juxtamedullary nephron. Will request the juxtamedullary nephron tubule class from UBERON. subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "kidney tubule epithelial cell" EXACT [] xref: FMA:86785 xref: KUPO:0001022 @@ -30787,21 +35078,24 @@ id: CL:1000495 name: small intestine goblet cell def: "A goblet cell that is part of the small intestine." [GOC:tfm] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "goblet cell of epithelium of small intestine" EXACT [] synonym: "goblet cell of small intestine" EXACT [] synonym: "small intestinal goblet cell" EXACT [FMA:86929] xref: FMA:86929 -is_a: CL:0002254 ! epithelial cell of small intestine is_a: CL:0019031 ! intestine goblet cell +is_a: CL:1001598 ! small intestine secretory cell intersection_of: CL:0000160 ! goblet cell -intersection_of: part_of UBERON:0002108 ! small intestine -relationship: part_of UBERON:0001902 ! epithelium of small intestine +intersection_of: part_of UBERON:0001902 ! epithelium of small intestine [Term] id: CL:1000497 name: kidney cell def: "A cell that is part of a kidney." [] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset xref: KUPO:0001010 xref: ZFA:0009389 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000255 ! eukaryotic cell @@ -30814,7 +35108,9 @@ id: CL:1000500 name: kidney interstitial cell def: "A cell that is part of kidney interstitium." [] subset: cellxgene_subset +subset: human_subset subset: kidney_upper_slim +subset: mouse_subset xref: KUPO:0001013 xref: ZFA:0009390 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:1000497 ! kidney cell @@ -30827,6 +35123,8 @@ relationship: part_of UBERON:0005215 ! kidney interstitium id: CL:1000504 name: kidney medulla cell def: "A cell that is part of a renal medulla." [PMID:22343825] +subset: human_subset +subset: mouse_subset xref: KUPO:0001017 xref: ZFA:0009391 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:1000497 ! kidney cell @@ -30838,7 +35136,9 @@ relationship: part_of UBERON:0000362 ! renal medulla id: CL:1000505 name: kidney pelvis cell def: "A cell that is part of a renal pelvis." [] +subset: human_subset subset: kidney_upper_slim +subset: mouse_subset xref: KUPO:0001018 is_a: CL:1000497 ! kidney cell intersection_of: CL:1000497 ! kidney cell @@ -30849,7 +35149,9 @@ relationship: part_of UBERON:0001224 ! renal pelvis id: CL:1000507 name: kidney tubule cell def: "A cell that is part of a nephron tubule." [] +subset: human_subset subset: kidney_upper_slim +subset: mouse_subset xref: KUPO:0001020 is_a: CL:1000497 ! kidney cell intersection_of: CL:1000497 ! kidney cell @@ -30861,6 +35163,8 @@ id: CL:1000510 name: kidney glomerular epithelial cell def: "Any kidney epithelial cell that is part of some glomerular epithelium." [FBC:Autogenerated] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset xref: KUPO:0001023 is_a: CL:1000746 ! glomerular cell intersection_of: CL:0002518 ! kidney epithelial cell @@ -30871,7 +35175,9 @@ relationship: part_of UBERON:0004188 ! glomerular epithelium id: CL:1000546 name: kidney medulla collecting duct epithelial cell def: "An epithelial cell that is part of a renal medulla collecting duct." [] +subset: human_subset subset: kidney_upper_slim +subset: mouse_subset xref: KUPO:0001060 is_a: CL:1000454 ! kidney collecting duct epithelial cell is_a: CL:1000504 ! kidney medulla cell @@ -30883,6 +35189,8 @@ relationship: part_of UBERON:0005185 ! renal medulla collecting duct id: CL:1000547 name: kidney inner medulla collecting duct epithelial cell def: "An epithelial cell that is part of some inner medullary collecting duct." [] +subset: human_subset +subset: mouse_subset xref: KUPO:0001061 is_a: CL:1000546 ! kidney medulla collecting duct epithelial cell is_a: CL:1000617 ! kidney inner medulla cell @@ -30894,6 +35202,8 @@ relationship: part_of UBERON:0004205 ! inner medullary collecting duct id: CL:1000548 name: kidney outer medulla collecting duct epithelial cell def: "An epithelial cell that is part of an outer medullary collecting duct." [] +subset: human_subset +subset: mouse_subset xref: KUPO:0001062 is_a: CL:1000546 ! kidney medulla collecting duct epithelial cell is_a: CL:1000616 ! kidney outer medulla cell @@ -30905,6 +35215,8 @@ relationship: part_of UBERON:0004204 ! outer medullary collecting duct id: CL:1000549 name: kidney cortex collecting duct epithelial cell def: "An epithelial cell that is part of a cortical collecting duct." [] +subset: human_subset +subset: mouse_subset xref: KUPO:0001063 is_a: CL:0002584 ! renal cortical epithelial cell is_a: CL:1000454 ! kidney collecting duct epithelial cell @@ -30916,7 +35228,9 @@ relationship: part_of UBERON:0004203 ! cortical collecting duct id: CL:1000550 name: kidney papillary duct principal epithelial cell def: "Any kidney cell that is part of some papillary duct." [FBC:Autogenerated] +subset: human_subset subset: kidney_upper_slim +subset: mouse_subset xref: KUPO:0001064 is_a: CL:1001225 ! kidney collecting duct cell intersection_of: CL:1000497 ! kidney cell @@ -30927,6 +35241,8 @@ relationship: part_of UBERON:0005167 ! papillary duct id: CL:1000596 name: inner renal cortex cell def: "Any kidney cell that is part of some juxtamedullary cortex." [FBC:Autogenerated] +subset: human_subset +subset: mouse_subset xref: KUPO:0001111 is_a: CL:0002681 ! kidney cortical cell intersection_of: CL:1000497 ! kidney cell @@ -30939,6 +35255,8 @@ name: papillary tips cell def: "A cell that is part of a tip of a renal papilla." [] subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset xref: KUPO:0001112 is_a: CL:1000505 ! kidney pelvis cell is_a: CL:1000617 ! kidney inner medulla cell @@ -30951,6 +35269,8 @@ property_value: RO:0002175 NCBITaxon:9606 id: CL:1000600 name: lower urinary tract cell def: "Any cell that is part of some lower urinary tract." [FBC:Autogenerated] +subset: human_subset +subset: mouse_subset xref: KUPO:0001115 is_a: CL:0000255 ! eukaryotic cell intersection_of: CL:0000000 ! cell @@ -30961,6 +35281,8 @@ relationship: part_of UBERON:0001556 ! lower urinary tract id: CL:1000601 name: ureteral cell def: "Any cell that is part of some ureter." [FBC:Autogenerated] +subset: human_subset +subset: mouse_subset xref: KUPO:0001116 is_a: CL:0000255 ! eukaryotic cell intersection_of: CL:0000000 ! cell @@ -30971,6 +35293,8 @@ relationship: part_of UBERON:0000056 ! ureter id: CL:1000606 name: kidney nerve cell def: "Any neuron that has its soma located in some kidney." [FBC:Autogenerated] +subset: human_subset +subset: mouse_subset xref: KUPO:0001015 is_a: BFO:0000002 is_a: CL:1000500 ! kidney interstitial cell @@ -30983,7 +35307,9 @@ relationship: RO:0002100 UBERON:0002113 ! has soma location kidney id: CL:1000612 name: kidney corpuscule cell def: "Any renal cortical epithelial cell that is part of some renal corpuscle." [FBC:Autogenerated] +subset: human_subset subset: kidney_upper_slim +subset: mouse_subset xref: KUPO:0001021 is_a: CL:0002584 ! renal cortical epithelial cell is_a: CL:1000449 ! epithelial cell of nephron @@ -30996,6 +35322,8 @@ id: CL:1000615 name: kidney cortex tubule cell def: "Any kidney tubule cell that is part of some renal cortex tubule." [FBC:Autogenerated] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset xref: KUPO:0001024 is_a: CL:0002584 ! renal cortical epithelial cell is_a: CL:1000449 ! epithelial cell of nephron @@ -31008,6 +35336,8 @@ relationship: part_of UBERON:0006853 ! renal cortex tubule id: CL:1000616 name: kidney outer medulla cell def: "Any kidney medulla cell that is part of some outer medulla of kidney." [FBC:Autogenerated] +subset: human_subset +subset: mouse_subset xref: KUPO:0001025 is_a: CL:1000504 {is_inferred="true"} ! kidney medulla cell intersection_of: CL:1000504 ! kidney medulla cell @@ -31018,6 +35348,8 @@ relationship: part_of UBERON:0001293 ! outer medulla of kidney id: CL:1000617 name: kidney inner medulla cell def: "Any kidney medulla cell that is part of some inner medulla of kidney." [FBC:Autogenerated] +subset: human_subset +subset: mouse_subset xref: KUPO:0001026 is_a: CL:1000504 {is_inferred="true"} ! kidney medulla cell intersection_of: CL:1000504 ! kidney medulla cell @@ -31028,7 +35360,9 @@ relationship: part_of UBERON:0001294 ! inner medulla of kidney id: CL:1000618 name: juxtaglomerular complex cell def: "Any kidney cortical cell that is part of some juxtaglomerular apparatus." [FBC:Autogenerated] +subset: human_subset subset: kidney_upper_slim +subset: mouse_subset synonym: "juxtaglomerulus cell" EXACT [GO:0072052] xref: KUPO:0001028 is_a: CL:0002681 {is_inferred="true"} ! kidney cortical cell @@ -31040,6 +35374,8 @@ relationship: part_of UBERON:0002303 ! juxtaglomerular apparatus id: CL:1000681 name: kidney cortex interstitial cell def: "A cell that is part of an interstitial compartment of a renal cortex." [PMID:18575881] +subset: human_subset +subset: mouse_subset xref: KUPO:0001091 is_a: CL:0002584 ! renal cortical epithelial cell is_a: CL:1000500 {is_inferred="true"} ! kidney interstitial cell @@ -31051,6 +35387,8 @@ relationship: part_of UBERON:0005270 ! renal cortex interstitium id: CL:1000682 name: kidney medulla interstitial cell def: "A cell that is part of an interstitum of a renal medulla." [PMID:21359760] +subset: human_subset +subset: mouse_subset xref: KUPO:0001092 is_a: CL:1000500 {is_inferred="true"} ! kidney interstitial cell is_a: CL:1000504 {is_inferred="true"} ! kidney medulla cell @@ -31062,6 +35400,8 @@ relationship: part_of UBERON:0005211 ! renal medulla interstitium id: CL:1000691 name: kidney interstitial myofibroblast subset: human_reference_atlas +subset: human_subset +subset: mouse_subset xref: KUPO:0001101 is_a: CL:0000186 ! myofibroblast cell is_a: CL:1000500 ! kidney interstitial cell @@ -31073,6 +35413,8 @@ name: kidney interstitial fibroblast def: "A fibroblast that is part of an interstitial compartment of a kidney." [PMID:10559635] subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset xref: KUPO:0001102 is_a: CL:0000057 ! fibroblast is_a: CL:1000500 ! kidney interstitial cell @@ -31083,6 +35425,8 @@ property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:1000693 name: kidney interstitial fibrocyte +subset: human_subset +subset: mouse_subset xref: KUPO:0001103 is_a: CL:0000135 ! fibrocyte is_a: CL:1000500 ! kidney interstitial cell @@ -31090,7 +35434,10 @@ is_a: CL:1000500 ! kidney interstitial cell [Term] id: CL:1000695 name: kidney interstitial alternatively activated macrophage +subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset xref: KUPO:0001106 is_a: CL:0000890 ! alternatively activated macrophage is_a: CL:1000500 ! kidney interstitial cell @@ -31099,6 +35446,8 @@ property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:1000696 name: kidney interstitial inflammatory macrophage +subset: human_subset +subset: mouse_subset xref: KUPO:0001107 is_a: CL:0000863 ! inflammatory macrophage is_a: CL:1000500 ! kidney interstitial cell @@ -31106,6 +35455,8 @@ is_a: CL:1000500 ! kidney interstitial cell [Term] id: CL:1000697 name: kidney interstitial suppressor macrophage +subset: human_subset +subset: mouse_subset xref: KUPO:0001108 is_a: CL:0000862 ! suppressor macrophage is_a: CL:1000500 ! kidney interstitial cell @@ -31115,14 +35466,20 @@ id: CL:1000698 name: kidney resident macrophage def: "A tissue-resident macrophage that is part of some kidney." [] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset +xref: https://cellxgene.cziscience.com/cellguide/CL_1000698 xref: KUPO:0001109 is_a: CL:0000864 ! tissue-resident macrophage is_a: CL:1000500 ! kidney interstitial cell +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nKidney resident macrophages are a heterogeneous population of immune cell found in the cortex and medullary regions of the kidney as well as within and surround the glomeruli. Their primary role involves maintaining homeostasis and immune surveillance in the kidney microenvironment, defending against ascending urinary infections. Beyond traditional macrophage roles such as phagocytosis and antigen presentation, kidney resident macrophages also contribute significantly to the response to kidney injury including tissue repair and angiogenesis.\nUnder normal physiological conditions, kidney resident macrophages work to maintain the balance of the kidney's microenvironment by removing dead cells, pathogens and cellular debris, to limit inflammation and tissue damage. They are ‘professional’ phagocytes, clearing pathogens and debris by engulfing and digesting these harmful materials. Moreover, they are capable of presenting antigens to other immune cells, which aids in the activation of the adaptive immune response. \nKidney resident macrophages show a high degree of plasticity: in response to environmental stimuli they change their morphology and cell surface markers. For example, in response to acute injury, some macrophages adopt a pro-inflammatory phenotype and augment tissue damage; once the injury stimulus is removed, they may change to mediate tissue repair. \nWhile kidney macrophages contribute to wound healing, tissue repair and regeneration by producing key growth factors and cytokines that stimulate cell proliferation, collagen production, and blood vessel formation, dysregulation in their activity can also lead to progressive inflammation and fibrosis, common features in chronic kidney disease." xsd:string {xref="DOI:10.1016/bs.ircmb.2022.01.005", xref="DOI:10.1172/jci.insight.161078", xref="DOI:10.3389/fimmu.2021.681748", xref="DOI:10.3389/fphys.2017.00837"} [Term] id: CL:1000699 name: kidney resident dendritic cell def: "A resident-dendritic cell that is part of a kidney." [PMID:25266210] +subset: human_subset +subset: mouse_subset xref: KUPO:0001110 is_a: CL:0001007 ! interstitial dendritic cell is_a: CL:1000500 ! kidney interstitial cell @@ -31131,6 +35488,8 @@ is_a: CL:1000500 ! kidney interstitial cell id: CL:1000702 name: kidney pelvis smooth muscle cell def: "Any smooth muscle cell that is part of some kidney pelvis smooth muscle." [FBC:Autogenerated] +subset: human_subset +subset: mouse_subset xref: KUPO:0001113 is_a: CL:0000192 {is_inferred="true"} ! smooth muscle cell is_a: CL:1000505 {is_inferred="true"} ! kidney pelvis cell @@ -31143,6 +35502,8 @@ id: CL:1000703 name: kidney pelvis urothelial cell def: "Any kidney epithelial cell that is part of some kidney pelvis urothelium." [FBC:Autogenerated] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset xref: KUPO:0001114 is_a: CL:0000731 ! urothelial cell is_a: CL:0002518 {is_inferred="true"} ! kidney epithelial cell @@ -31154,10 +35515,12 @@ relationship: part_of UBERON:0004788 ! kidney pelvis urothelium [Term] id: CL:1000706 name: ureter urothelial cell -def: "Any urothelial cell that is part of some urothelium of ureter." [FBC:Autogenerated] +def: "A urothelial cell that is part of the urothelium of ureter." [PMID:36180582] +subset: human_subset +subset: mouse_subset xref: KUPO:0001117 -is_a: CL:0000731 {is_inferred="true"} ! urothelial cell -is_a: CL:1000601 {is_inferred="true"} ! ureteral cell +is_a: CL:0000731 ! urothelial cell +is_a: CL:1000601 ! ureteral cell intersection_of: CL:0000731 ! urothelial cell intersection_of: part_of UBERON:0001254 ! urothelium of ureter relationship: part_of UBERON:0001254 ! urothelium of ureter @@ -31167,6 +35530,8 @@ id: CL:1000708 name: ureter adventitial cell def: "Any ureteral cell that is part of some adventitia of ureter." [FBC:Autogenerated] subset: human_reference_atlas +subset: human_subset +subset: mouse_subset xref: KUPO:0001119 is_a: CL:0000115 ! endothelial cell is_a: CL:0002503 ! adventitial cell @@ -31181,6 +35546,8 @@ id: CL:1000714 name: kidney cortex collecting duct principal cell def: "Any renal principal cell that is part of some cortical collecting duct." [FBC:Autogenerated] subset: human_reference_atlas +subset: human_subset +subset: mouse_subset xref: KUPO:0001130 is_a: CL:1000549 {is_inferred="true"} ! kidney cortex collecting duct epithelial cell is_a: CL:1001431 ! kidney collecting duct principal cell @@ -31193,6 +35560,8 @@ id: CL:1000715 name: kidney cortex collecting duct intercalated cell def: "Any renal intercalated cell that is part of some cortical collecting duct." [FBC:Autogenerated] subset: human_reference_atlas +subset: human_subset +subset: mouse_subset xref: KUPO:0001131 is_a: CL:1000549 {is_inferred="true"} ! kidney cortex collecting duct epithelial cell is_a: CL:1001432 ! kidney collecting duct intercalated cell @@ -31205,6 +35574,8 @@ id: CL:1000716 name: kidney outer medulla collecting duct principal cell def: "Principal cell that is part of some outer medullary collecting duct. It is known in some mammalian species that this cell may express the epithelial sodium channel (ENaC)." [PMID:25632105] subset: human_reference_atlas +subset: human_subset +subset: mouse_subset xref: KUPO:0001132 is_a: CL:1000548 {is_inferred="true"} ! kidney outer medulla collecting duct epithelial cell is_a: CL:1001431 ! kidney collecting duct principal cell @@ -31217,6 +35588,8 @@ id: CL:1000717 name: kidney outer medulla collecting duct intercalated cell def: "Intercalated cell that is part of some outer medullary collecting duct. It is known in some mammalian species that this cell may contribute in the maintenance of acid/base homeostasis." [PMID:25632105] subset: human_reference_atlas +subset: human_subset +subset: mouse_subset xref: KUPO:0001133 is_a: CL:1000548 {is_inferred="true"} ! kidney outer medulla collecting duct epithelial cell is_a: CL:1001432 ! kidney collecting duct intercalated cell @@ -31229,6 +35602,8 @@ id: CL:1000718 name: kidney inner medulla collecting duct principal cell def: "Any renal principal cell that is part of some inner medullary collecting duct." [FBC:Autogenerated] subset: human_reference_atlas +subset: human_subset +subset: mouse_subset xref: KUPO:0001134 is_a: CL:1000547 {is_inferred="true"} ! kidney inner medulla collecting duct epithelial cell is_a: CL:1001431 ! kidney collecting duct principal cell @@ -31240,6 +35615,8 @@ property_value: RO:0002175 NCBITaxon:9606 id: CL:1000719 name: kidney inner medulla collecting duct intercalated cell def: "Any renal intercalated cell that is part of some inner medullary collecting duct." [FBC:Autogenerated] +subset: human_subset +subset: mouse_subset xref: KUPO:0001135 is_a: CL:1000547 {is_inferred="true"} ! kidney inner medulla collecting duct epithelial cell is_a: CL:1001432 ! kidney collecting duct intercalated cell @@ -31250,6 +35627,8 @@ intersection_of: part_of UBERON:0004205 ! inner medullary collecting duct id: CL:1000720 name: kidney papillary duct intercalated cell def: "Any renal intercalated cell that is part of some papillary duct." [FBC:Autogenerated] +subset: human_subset +subset: mouse_subset xref: KUPO:0001136 is_a: CL:1000550 {is_inferred="true"} ! kidney papillary duct principal epithelial cell is_a: CL:1001432 ! kidney collecting duct intercalated cell @@ -31260,6 +35639,8 @@ intersection_of: part_of UBERON:0005167 ! papillary duct id: CL:1000721 name: kidney papillary duct principal cell def: "Any renal principal cell that is part of some papillary duct." [FBC:Autogenerated] +subset: human_subset +subset: mouse_subset xref: KUPO:0001137 is_a: CL:1000550 {is_inferred="true"} ! kidney papillary duct principal epithelial cell is_a: CL:1001431 ! kidney collecting duct principal cell @@ -31272,6 +35653,8 @@ name: glomerular mesangial cell def: "A mesangial cell located among the glomerular capillaries in a renal corpuscle." [https://doi.org/10.1152/physrev.1998.78.3.723, Wikipedia:Intraglomerular_mesangial_cell] comment: Like smooth muscle, a glomerular mesangial cell is contractile and possesses the filaments actin and myosin. The contractile mechanism is also similar to that of smooth muscle, with Ca2+/calmodulin-activated myosin light-chain kinase instigating myosin-actin cross-bridge cycling. Mesangial cell phagocytosis of apoptotic neutrophils involves a novel CD36-independent, alpha(v)beta3/TSP-mediated mechanism that is uncoupled from chemokine secretion, emphasizing the injury-limiting potential of mesangial cell phagocytosis of apoptotic cells. {xref="https://doi.org/10.1152/physrev.1998.78.3.723", xref="PMID:9127003"} subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "intraglomerular mesangial cell" EXACT [CL:cjm] xref: KUPO:0001032 is_a: CL:0000234 ! phagocyte @@ -31286,6 +35669,8 @@ property_value: RO:0002175 NCBITaxon:9606 id: CL:1000746 name: glomerular cell def: "Any kidney corpuscule cell that is part of some renal glomerulus." [FBC:Autogenerated] +subset: human_subset +subset: mouse_subset xref: KUPO:0001036 is_a: CL:1000612 ! kidney corpuscule cell intersection_of: CL:1000612 ! kidney corpuscule cell @@ -31298,7 +35683,10 @@ name: kidney connecting tubule epithelial cell def: "Any nephron tubule epithelial cell that is part of some renal connecting tubule." [FBC:Autogenerated] subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset subset: kidney_upper_slim +subset: mouse_subset +xref: https://cellxgene.cziscience.com/cellguide/CL_1000768 xref: KUPO:0001058 is_a: CL:1000494 {is_inferred="true"} ! nephron tubule epithelial cell is_a: CL:1000615 ! kidney cortex tubule cell @@ -31306,11 +35694,14 @@ intersection_of: CL:1000494 ! nephron tubule epithelial cell intersection_of: part_of UBERON:0005097 ! renal connecting tubule relationship: part_of UBERON:0005097 ! renal connecting tubule property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nKidney connecting tubule epithelial cells are found in collecting duct system of the kidney, specifically in at the interconnection segment between the nephron and the collecting ducts. The epithelial cells lining the connecting tubule are crucial for the journey of filtrate before it empties into urine-collecting ducts and therefore play a critical role in maintaining the body’s fluid and electrolyte balance.\nOne of the principal functions of connecting tubule epithelial cells involves the selective reabsorption and secretion of various solutes. This reabsorption process includes critical regulatory electrolytes such as sodium ions (Na+), chloride ions (Cl-), and bicarbonate ions (HCO3-), thus playing a role in the regulation of the acid-base homeostasis. Their function also involves the secretion of potassium ions (K+) into the renal tubular fluid.\nThe connecting tubule epithelial cells are primarily intercalated cells, which can be categorized into two types according to their specific functions: type A intercalated cells, which secrete acid, and the type B intercalated cells, which secrete base (bicarbonate) and reabsorb chloride. By regulating the concentrations of these ions, as well as reabsorption of water, connecting tubule epithelial cells contribute substantively to maintaining the body's electrolyte levels, pH balance, and overall homeostasis.\nIn addition to intercalating cells, the collecting duct system also has principal cells, which are characterized by the expression of the water channel AQP2. AQP2-expressing cells have also been identified in connecting tubules, but there is some controversy whether these represent a unique cell type as there are some morphologic differences compared with principal cells." xsd:string {xref="DOI:10.1002/cphy.c110052", xref="DOI:10.1007/s00418-021-02033-5", xref="DOI:10.1097/MNH.0b013e32820ac850", xref="DOI:10.1681/ASN.2019040415", xref="DOI:10.23876/j.krcp.2017.36.4.305"} [Term] id: CL:1000803 name: kidney inner medulla interstitial cell def: "A cell that is part of an interstitial compartment of an inner renal medulla." [PMID:21359760] +subset: human_subset +subset: mouse_subset xref: KUPO:0001093 is_a: CL:1000617 {is_inferred="true"} ! kidney inner medulla cell is_a: CL:1000682 {is_inferred="true"} ! kidney medulla interstitial cell @@ -31322,6 +35713,8 @@ relationship: part_of UBERON:0005214 ! inner renal medulla interstitium id: CL:1000804 name: kidney outer medulla interstitial cell def: "A kidney cell that is part of an interstitial compartment of an outer renal medulla." [PMID:8694267] +subset: human_subset +subset: mouse_subset xref: KUPO:0001094 is_a: CL:1000616 {is_inferred="true"} ! kidney outer medulla cell is_a: CL:1000682 {is_inferred="true"} ! kidney medulla interstitial cell @@ -31334,18 +35727,25 @@ id: CL:1000838 name: kidney proximal convoluted tubule epithelial cell def: "Any epithelial cell of proximal tubule that is part of some proximal convoluted tubule and has part some brush border." [FBC:Autogenerated] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset +xref: https://cellxgene.cziscience.com/cellguide/CL_1000838 xref: KUPO:0001045 is_a: CL:0002307 ! brush border cell of the proximal tubule intersection_of: CL:0002306 ! epithelial cell of proximal tubule intersection_of: has_part GO:0005903 ! brush border intersection_of: part_of UBERON:0001287 ! proximal convoluted tubule relationship: part_of UBERON:0001287 ! proximal convoluted tubule +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nKidney proximal convoluted tubule epithelial cells line the most voluminous part of the kidney's nephron, the proximal convoluted tubule, located in the cortex of the kidney. These cells are primarily involved in reabsorption and secretion processes, key functions that facilitate homeostasis within the body.\nProximal convoluted tubule epithelial cells extensively function in the reabsorption process to a greater degree than their counterparts in the proximal straight tubule. Approximately two-thirds of filtrated sodium and water, nearly all nutrient sugars and amino acids, and a significant portion of bicarbonates pass through the proximal convoluted tubule, are effectively absorbed by the epithelial cells, and reenter the bodily circulation. By absorbing bicarbonates and secreting protons into the tubular fluid, proximal convoluted tubule epithelial cells also contribute to the pH regulation in the body .\nIn addition to reabsorption, proximal convoluted tubule epithelial cells also play a critical role in the excretion of waste metabolites and xenobiotics. These cells possess a range of transporters that secrete metabolic end products and certain drugs, hence aiding in their elimination. This function underlines their importance for body detoxification." xsd:string {xref="DOI:10.1002/cphy.c110060", xref="DOI:10.1146/annurev-physiol-052521-121841", xref="DOI:10.1159/000092212", xref="DOI:10.1681/ASN.2019040415"} [Term] id: CL:1000839 name: kidney proximal straight tubule epithelial cell def: "Any epithelial cell of proximal tubule that is part of some proximal straight tubule." [FBC:Autogenerated] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset +xref: https://cellxgene.cziscience.com/cellguide/CL_1000839 xref: KUPO:0001046 is_a: CL:0002306 {is_inferred="true"} ! epithelial cell of proximal tubule is_a: CL:1000616 {is_inferred="true"} ! kidney outer medulla cell @@ -31353,6 +35753,7 @@ is_a: CL:1001021 ! kidney loop of Henle descending limb epithelial cell intersection_of: CL:0002306 ! epithelial cell of proximal tubule intersection_of: part_of UBERON:0001290 ! proximal straight tubule relationship: part_of UBERON:0001290 ! proximal straight tubule +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nKidney proximal straight tubule epithelial cells line the straight portion of the proximal tubule of the nephron, extending from the cortical medullary ray into the outer stripe of the outer medulla. They are characterized by a brush border of dense microvilli on their apical surface, enhancing the cell's surface area and aiding reabsorption, though reabsorption occurs more heavily in the proximal convoluted tubule preceding the straight portion of the tubule.\nThe primary function of the kidney proximal straight tubule epithelial cells is to reabsorb the filtrate that the kidney produces, which includes glucose, sodium, and water. The reabsorption occurs through both passive and active transport methods. These cells exhibit enzyme-rich microvilli that also absorb small proteins and peptides. Consequently, they are involved in the regulation of plasma levels of various substances, including glucose, amino acids, and electrolytes, and maintain the body's pH homeostasis by secreting H+ ions into the urine and absorbing bicarbonate ions.\nThese cells are also reported to be involved in drug metabolism. Many drugs are filtered from the blood by the kidneys and subsequently reabsorbed by the kidney proximal tubule epithelial cells back into the bloodstream. Furthermore, these cells play a significant role in the progression of kidney diseases. For example, in diabetic nephropathy and acute kidney injury, kidney proximal straight tubule epithelial cells can undergo cellular changes and result in malfunctions such as reduced reabsorption and increased excretion." xsd:string {xref="DOI:10.1002/cphy.c110061", xref="DOI:10.1038/nrd4461", xref="DOI:10.1146/annurev-physiol-052521-121841", xref="DOI:10.1681/ASN.2019040415", xref="DOI:10.2215/CJN.10391012"} [Term] id: CL:1000849 @@ -31360,13 +35761,17 @@ name: kidney distal convoluted tubule epithelial cell def: "Any epithelial cell of distal tubule that is part of some distal convoluted tubule." [FBC:Autogenerated] subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset subset: kidney_upper_slim +subset: mouse_subset +xref: https://cellxgene.cziscience.com/cellguide/CL_1000849 xref: KUPO:0001056 is_a: CL:0002305 {is_inferred="true"} ! epithelial cell of distal tubule intersection_of: CL:0002305 ! epithelial cell of distal tubule intersection_of: part_of UBERON:0001292 ! distal convoluted tubule relationship: part_of UBERON:0001292 ! distal convoluted tubule property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nKidney distal convoluted tubule epithelial cells, often referred to simply as distal convoluted tubule (DCT) cells, constitute a significant portion of the nephron -- the functional building unit of the kidney involved in filtration and reabsorption of substances from blood. The DCT epithelial cells form lining of the distal convoluted tubule, a segment of the nephron located after the loop of Henle and before the collecting tubule. These cells are characterized by unique morphological features such as small size, low height and fewer microvilli compared to proximal convoluted tubule epithelial cells. \nThese cells perform a host of vital functions contributing to the regulation of extracellular fluid volume and electrolyte balance, blood pressure and pH. While the DCT is less prominent in water and sodium reabsorption compared to the proximal tubule and the loop of Henle, it plays a crucial role in fine-tuning the process. DCT epithelial cells are responsible for the final adjustments of sodium, potassium and calcium reabsorption, thereby affecting overall fluid and electrolyte balance, blood pressure regulation and bone health. The reabsorption process is regulated by hormones including aldosterone and parathyroid hormone.\nThe distal convoluted tubule (DCT) also plays a significant role in acid-base homeostasis by secreting protons (H+) into the tubular fluid and reabsorbing bicarbonate ions (HCO3-), thus regulating the pH of the blood. The ability of DCT cells to adjust urine concentration plays a part in maintaining the body’s pH balance and preventing conditions like acidosis or alkalosis. In summary, kidney distal convoluted tubule epithelial cells perform functions that are crucial to maintaining body's homeostasis." xsd:string {xref="DOI:10.1002/cphy.c140002", xref="DOI:10.1007/s40620-021-01032-y", xref="DOI:10.1152/physrev.2000.80.1.277", xref="DOI:10.1681/ASN.2019040415", xref="DOI:10.2215/CJN.05920613"} [Term] id: CL:1000850 @@ -31374,6 +35779,9 @@ name: macula densa epithelial cell def: "Any epithelial cell of distal tubule that is part of some macula densa." [FBC:Autogenerated] subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset +xref: https://cellxgene.cziscience.com/cellguide/CL_1000850 xref: KUPO:0001057 is_a: CL:0002305 {is_inferred="true"} ! epithelial cell of distal tubule is_a: CL:1000618 {is_inferred="true"} ! juxtaglomerular complex cell @@ -31381,11 +35789,14 @@ intersection_of: CL:0002305 ! epithelial cell of distal tubule intersection_of: part_of UBERON:0002335 ! macula densa relationship: part_of UBERON:0002335 ! macula densa property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nMacula densa epithelial cells, as part of the complex nephron structure, play a crucial role in kidney function. These cells, which make up the macula densa, help regulate blood pressure and the filtration rate of the glomerulus by sensing sodium chloride amounts in the kidney tubules. Found where the thick ascending limb of the Loop of Henle touches the afferent arteriole, macula densa epithelial cells are positioned in an optimal location to monitor and respond to changes in the filtrate composition.\nThese cells maintain intraglomerular homeostasis. When the sodium chloride concentration is high, macula densa cells respond by secreting adenosine and vasoconstricting the afferent arteriole to decrease the glomerular filtration rate. Conversely, if the sodium chloride concentration in the filtrate is low, the production and release of nitric oxide cause vasodilation to enhance the glomerular filtration rate. \nMacula densa epithelial cells also have a role in tubuloglomerular feedback mechanisms, an essential autoregulatory renal response. They send feedback to the glomerular mesangial cells, allowing constriction or relaxation of the afferent arteriole as needed depending on the content of the filtrate." xsd:string {xref="DOI:10.1073/pnas.0736323100", xref="DOI:10.1146/annurev-physiol-052521-121841", xref="DOI:10.1161/HYPERTENSIONAHA.115.04739", xref="DOI:10.1681/ASN.2009070759", xref="DOI:10.1681/ASN.2015050515"} [Term] id: CL:1000854 name: kidney blood vessel cell def: "A blood vessel cell that is part of a kidney." [PMID:34843404] +subset: human_subset +subset: mouse_subset xref: KUPO:0001014 is_a: BFO:0000002 is_a: CL:1000504 {is_inferred="true"} ! kidney medulla cell @@ -31398,7 +35809,9 @@ relationship: participates_in GO:0008015 ! blood circulation id: CL:1000891 name: kidney arterial blood vessel cell def: "Any kidney blood vessel cell that is part of some kidney arterial blood vessel." [FBC:Autogenerated] +subset: human_subset subset: kidney_upper_slim +subset: mouse_subset xref: KUPO:0001029 is_a: CL:1000854 {is_inferred="true"} ! kidney blood vessel cell intersection_of: CL:1000854 ! kidney blood vessel cell @@ -31410,7 +35823,9 @@ id: CL:1000892 name: kidney capillary endothelial cell def: "An endothelial cell that is part of the capillary of the kidney." [] subset: cellxgene_subset +subset: human_subset subset: kidney_upper_slim +subset: mouse_subset xref: KUPO:0001030 is_a: CL:0002144 ! capillary endothelial cell is_a: CL:1000854 ! kidney blood vessel cell @@ -31422,7 +35837,9 @@ relationship: part_of UBERON:0003527 ! kidney capillary id: CL:1000893 name: kidney venous blood vessel cell def: "Any kidney blood vessel cell that is part of some renal vein." [FBC:Autogenerated] +subset: human_subset subset: kidney_upper_slim +subset: mouse_subset xref: KUPO:0001031 is_a: CL:1000854 {is_inferred="true"} ! kidney blood vessel cell intersection_of: CL:1000854 ! kidney blood vessel cell @@ -31434,6 +35851,8 @@ id: CL:1000909 name: kidney loop of Henle epithelial cell def: "Any nephron tubule epithelial cell that is part of some loop of Henle." [FBC:Autogenerated] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset xref: KUPO:0001047 is_a: CL:1000494 {is_inferred="true"} ! nephron tubule epithelial cell intersection_of: CL:1000494 ! nephron tubule epithelial cell @@ -31445,6 +35864,8 @@ id: CL:1000979 name: ureter smooth muscle cell def: "Any smooth muscle cell that is part of some muscular coat of ureter." [FBC:Autogenerated] subset: human_reference_atlas +subset: human_subset +subset: mouse_subset xref: KUPO:0001118 is_a: CL:0000192 {is_inferred="true"} ! smooth muscle cell is_a: CL:1000601 {is_inferred="true"} ! ureteral cell @@ -31459,6 +35880,8 @@ name: glomerular capillary endothelial cell def: "An endothelial cell that is part of the glomerular capillary of the kidney." [] subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset xref: https://cellxgene.cziscience.com/cellguide/CL_1001005 xref: KUPO:0001037 is_a: CL:0002188 ! glomerular endothelial cell @@ -31467,36 +35890,46 @@ intersection_of: CL:1000892 ! kidney capillary endothelial cell intersection_of: part_of UBERON:0004294 ! glomerular capillary endothelium relationship: part_of UBERON:0004294 ! glomerular capillary endothelium property_value: RO:0002175 NCBITaxon:9606 -property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional.\n\nThe glomerular capillary endothelial cell comprises an intrinsic component of the glomerulus in the kidney. Glomeruli contain a network of capillaries where the first step of blood filtration takes place, with glomerular capillary endothelial cells acting as an integral part of this process. Unlike regular endothelial cells that line the vasculature, unique fenestrations (openings) characterize these cells, allowing for enhanced permeability and filtration efficacy.\nTogether with the glomerular basement membrane and podocytes, the glomerular endothelial cells form the glomerular filtration barrier, which is responsible for blood filtration and therefore critical for removal of waste products, such as urea and creatinine, and excess substances, such as glucose and ions, from the bloodstream. The glomerular capillary endothelial cells' fenestrations permit the free flow of a variety of particles, barring larger, negatively charged proteins like serum albumin, enabling the formation of an ultrafiltrate. This ultrafiltrate is the primitive form of urine, which then passes through the proximal tubule for further processing and ultimately helps maintain systemic fluid and electrolyte balance.\nMoreover, the glomerular capillary endothelial cells are also believed to play a crucial role in renal pathologies. Any compromise to their structural integrity or functional performance can lead to kidney diseases, including but not limited to, diabetic nephropathy and glomerulonephritis. For instance, in diabetes, persistent hyperglycemia can injure these cells, leading to a compromised glomerular filtration barrier and proteinuria, indicating the loss of proteins in the urine." xsd:string {xref="DOI:10.1016/j.biocel.2010.05.015", xref="DOI:10.1016/j.yexcr.2012.02.032", xref="DOI:10.1111/j.1523-1755.2005.00260.x", xref="DOI:10.2337/diacare.28.1.164", xref="DOI:10.3389/fphys.2021.689083"} +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nThe glomerular capillary endothelial cell comprises an intrinsic component of the glomerulus in the kidney. Glomeruli contain a network of capillaries where the first step of blood filtration takes place, with glomerular capillary endothelial cells acting as an integral part of this process. Unlike regular endothelial cells that line the vasculature, unique fenestrations (openings) characterize these cells, allowing for enhanced permeability and filtration efficacy.\nTogether with the glomerular basement membrane and podocytes, the glomerular endothelial cells form the glomerular filtration barrier, which is responsible for blood filtration and therefore critical for removal of waste products, such as urea and creatinine, and excess substances, such as glucose and ions, from the bloodstream. The glomerular capillary endothelial cells' fenestrations permit the free flow of a variety of particles, barring larger, negatively charged proteins like serum albumin, enabling the formation of an ultrafiltrate. This ultrafiltrate is the primitive form of urine, which then passes through the proximal tubule for further processing and ultimately helps maintain systemic fluid and electrolyte balance.\nMoreover, the glomerular capillary endothelial cells are also believed to play a crucial role in renal pathologies. Any compromise to their structural integrity or functional performance can lead to kidney diseases, including but not limited to, diabetic nephropathy and glomerulonephritis. For instance, in diabetes, persistent hyperglycemia can injure these cells, leading to a compromised glomerular filtration barrier and proteinuria, indicating the loss of proteins in the urine." xsd:string {xref="DOI:10.1016/j.biocel.2010.05.015", xref="DOI:10.1016/j.yexcr.2012.02.032", xref="DOI:10.1111/j.1523-1755.2005.00260.x", xref="DOI:10.2337/diacare.28.1.164", xref="DOI:10.3389/fphys.2021.689083"} [Term] id: CL:1001006 name: kidney afferent arteriole cell def: "An endothelial cell which is part of the afferent arteriole in the kidney. This cell is responsible for maintaining renal blood flow and glomerular filtration rate." [PMID:16990493, PMID:22733355, PMID:24066938, PMID:25834230] +subset: human_subset +subset: mouse_subset +xref: https://cellxgene.cziscience.com/cellguide/CL_1001006 xref: KUPO:0001038 is_a: CL:0002681 ! kidney cortical cell is_a: CL:1000891 {is_inferred="true"} ! kidney arterial blood vessel cell intersection_of: CL:1000891 ! kidney arterial blood vessel cell intersection_of: part_of UBERON:0004639 ! renal afferent arteriole relationship: part_of UBERON:0004639 ! renal afferent arteriole +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nKidney afferent arteriole cells are specialized cell types found in the renal vasculature, specifically in the afferent arterioles which help in maintaining the renal blood flow and glomerular filtration rate. They are essential for the proper functioning of the kidneys, contributing to the regulation of blood pressure and fluid balance within the organism. Located before the glomerulus, a tiny, intricate network of capillaries within the nephron, these cells help control the expansion or contraction of the arteriole, thus regulating the pressure and flow of blood into the glomerulus.\nFunctionally, kidney afferent arteriole cells are largely involved in responding to changes in blood volume and systemic blood pressure. They achieve this by modulating the diameter of the afferent arteriole through a process known as autoregulation. Autoregulation involves two primary mechanisms: the myogenic response and the tubuloglomerular feedback. The myogenic response is essentially the intrinsic ability of the vascular smooth muscle to respond to pressure changes, while the tubuloglomerular feedback is the process where the macula densa cells located near the glomerulus respond to changes in fluid delivery rates in the tubules, sending signals to afferent arterioles to constrict or dilate accordingly. These cells also have significant interaction with renin-containing juxtaglomerular cells, which are located in the wall of afferent arterioles. Juxtaglomerular cells secrete the enzyme renin in response to low blood pressure or sympathetic nerve activity, initiating the renin-angiotensin-aldosterone system cascade that ultimately helps retain sodium and water to increase blood volume and pressure." xsd:string {xref="DOI:10.1007/s00424-012-1126-7", xref="DOI:10.1152/ajpregu.00332.2006", xref="DOI:10.1152/physrev.00042.2012", xref="DOI:10.2174/15701611113116660149"} [Term] id: CL:1001009 name: kidney efferent arteriole cell def: "Any kidney arterial blood vessel cell that is part of some renal efferent arteriole." [FBC:Autogenerated] +subset: human_subset +subset: mouse_subset +xref: https://cellxgene.cziscience.com/cellguide/CL_1001009 xref: KUPO:0001041 is_a: CL:0002681 ! kidney cortical cell is_a: CL:1000891 ! kidney arterial blood vessel cell intersection_of: CL:1000891 ! kidney arterial blood vessel cell intersection_of: part_of UBERON:0004640 ! renal efferent arteriole relationship: part_of UBERON:0004640 ! renal efferent arteriole +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nKidney efferent arteriole cells are highly adaptable vascular cells that make up the efferent arterioles in the kidney. These units are integral components of the renal microcirculation system, conducting blood away from the glomeruli after filtration occurs. Efferent arterioles directly affect glomerular hydrostatic pressure and, subsequently, the rate of glomerular filtration. They are the downstream channels that ensure the effective transportation of blood to the peritubular capillaries and vasa recta, critical for maintaining fluid balance and electrolyte homeostasis.\nKidney efferent arteriole cells are exceptional in their ability to perform autoregulation—a critical dynamic control of intrarenal blood flow ensuring stable glomerular filtration rates. This is primarily achieved via myogenic and tubuloglomerular feedback mechanisms, where the cells respond to changes in pressure and the concentration of sodium chloride in the tubular fluid, and constrict or dilate depending on the detected changes.\nCells associated with the efferent arteriole also respond to several systemic influences. Through complex intracellular signaling pathways, they respond to fluctuations in hormones (like angiotensin II and endothelin) and several other mediators such as nitric oxide and prostaglandins. Their adaptive capability helps maintain homeostasis and ensures the entire system's optimal performance under various physiological conditions. Dysfunctions in kidney efferent arteriole cells can lead to severe pathologies like hypertension and chronic kidney disease." xsd:string {xref="DOI:10.1152/ajpregu.2000.279.2.R629", xref="DOI:10.1152/physrev.00042.2012", xref="DOI:10.1159/000072054", xref="DOI:10.1161/01.HYP.29.1.222", xref="DOI:10.3748/wjg.v12.i34.5429"} [Term] id: CL:1001016 name: kidney loop of Henle ascending limb epithelial cell def: "Any kidney loop of Henle epithelial cell that is part of some ascending limb of loop of Henle." [FBC:Autogenerated] subset: cellxgene_subset +subset: human_subset subset: kidney_upper_slim +subset: mouse_subset xref: KUPO:0001048 is_a: CL:0002305 ! epithelial cell of distal tubule is_a: CL:1000909 {is_inferred="true"} ! kidney loop of Henle epithelial cell @@ -31508,12 +35941,16 @@ relationship: part_of UBERON:0005164 ! ascending limb of loop of Henle id: CL:1001021 name: kidney loop of Henle descending limb epithelial cell def: "Any kidney loop of Henle epithelial cell that is part of some descending limb of loop of Henle." [FBC:Autogenerated] +subset: human_subset subset: kidney_upper_slim +subset: mouse_subset +xref: https://cellxgene.cziscience.com/cellguide/CL_1001021 xref: KUPO:0001053 is_a: CL:1000909 {is_inferred="true"} ! kidney loop of Henle epithelial cell intersection_of: CL:1000909 ! kidney loop of Henle epithelial cell intersection_of: part_of UBERON:0001289 ! descending limb of loop of Henle relationship: part_of UBERON:0001289 ! descending limb of loop of Henle +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nThe kidney loop of Henle descending limb epithelial cells are highly specialized cells that play a crucial role in maintaining the body's salt and water balance. These cells line the descending limb of the loop of Henle, which is a portion of the renal tubule located in the kidneys, an organ responsible for filtering waste products, ions and extra water from the blood and converting them into urine. However, the descending limb epithelial cells are specifically involved in the countercurrent multiplication system, a mechanism to concentrate urine that involves both active and passive transport processes. \nThese cells are notably permeable to water but relatively impermeable to solutes, a characteristic that dramatically influences the osmotic gradient in the renal medulla. As filtrate initially descends down the loop of Henle, water gets drawn out due to the increasing osmotic gradient, thereby concentrating the filtrate. Additionally, these epithelial cells are exceptionally thin walled, allowing water to freely diffuse across the membrane.\nFurthermore, the kidney loop of Henle descending limb epithelial cells are inextricably linked to the functioning of numerous diuretic drugs, which work by blocking the reabsorption of water and certain electrolytes in the kidneys, leading to increased urine production to rid the body of excess fluids." xsd:string {xref="DOI:10.1007/s00360-018-1164-3", xref="DOI:10.1146/annurev-physiol-021113-170350", xref="DOI:10.1152/advan.00227.2022"} [Term] id: CL:1001033 @@ -31522,6 +35959,8 @@ def: "An endothelial cell that is part of the peritubular capillary of the kidne comment: Peritubular capillary endothelial cells feature fenestrations measuring 60-70 nm in diameter, each traversed by a thin diaphragm. {xref="PMID:19129259"} subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset xref: KUPO:0001065 is_a: CL:0000666 ! fenestrated endothelial cell is_a: CL:1000892 ! kidney capillary endothelial cell @@ -31534,8 +35973,9 @@ property_value: RO:0002175 NCBITaxon:9606 id: CL:1001036 name: vasa recta cell def: "A cell that is part of a vasa recta." [PMID:12529271, PMID:24381184] +subset: human_subset +subset: mouse_subset xref: KUPO:0001068 -is_a: CL:0002543 ! vein endothelial cell is_a: CL:1000504 {is_inferred="true"} ! kidney medulla cell is_a: CL:2000008 ! microvascular endothelial cell intersection_of: CL:2000008 ! microvascular endothelial cell @@ -31547,6 +35987,8 @@ id: CL:1001045 name: kidney cortex artery cell def: "Any kidney arterial blood vessel cell that is part of some renal cortex artery." [FBC:Autogenerated] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset xref: KUPO:0001077 is_a: CL:0002681 ! kidney cortical cell is_a: CL:1000891 ! kidney arterial blood vessel cell @@ -31558,6 +36000,8 @@ relationship: part_of UBERON:0005268 ! renal cortex artery id: CL:1001052 name: kidney cortex vein cell def: "Any kidney venous blood vessel cell that is part of some renal cortex vein." [FBC:Autogenerated] +subset: human_subset +subset: mouse_subset xref: KUPO:0001084 is_a: CL:0002681 ! kidney cortical cell is_a: CL:1000893 {is_inferred="true"} ! kidney venous blood vessel cell @@ -31569,6 +36013,8 @@ relationship: part_of UBERON:0005269 ! renal cortex vein id: CL:1001064 name: kidney artery smooth muscle cell comment: Note that the source of this term is KUPO:0001096 (artery smooth muscle cell), which we believe actually denotes the kidney specific structure. +subset: human_subset +subset: mouse_subset xref: KUPO:0001096 is_a: CL:0019018 ! blood vessel smooth muscle cell is_a: CL:1000891 ! kidney arterial blood vessel cell @@ -31577,6 +36023,8 @@ is_a: CL:1000891 ! kidney arterial blood vessel cell id: CL:1001066 name: kidney arteriole smooth muscle cell comment: Note that the source of this term is KUPO:0001098 (arteriole smooth muscle cell), which we believe actually denotes the kidney specific structure. +subset: human_subset +subset: mouse_subset xref: KUPO:0001098 is_a: CL:0019018 ! blood vessel smooth muscle cell is_a: CL:1000891 ! kidney arterial blood vessel cell @@ -31585,6 +36033,8 @@ is_a: CL:1000891 ! kidney arterial blood vessel cell id: CL:1001068 name: kidney venous system smooth muscle cell comment: Note that the source of this term is KUPO:0001068 (venous system smooth muscle cell), which we believe actually denotes the kidney specific structure. +subset: human_subset +subset: mouse_subset xref: KUPO:0001100 is_a: CL:0019018 ! blood vessel smooth muscle cell is_a: CL:1000893 ! kidney venous blood vessel cell @@ -31595,6 +36045,8 @@ name: kidney afferent arteriole endothelial cell def: "An endothelial cell that lines the interior surface of the afferent arteriole and maintains vascular tone. This cell responds to changing ion concentrations and blood pressure by releasing vasoactive substances, in order to regulate blood flow into the glomeruli, which is essential for glomerular filtration." [PMID:16990493, PMID:22733355, PMID:24066938, PMID:25834230] subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset xref: https://cellxgene.cziscience.com/cellguide/CL_1001096 xref: KUPO:0001039 is_a: CL:1000412 ! endothelial cell of arteriole @@ -31603,12 +36055,14 @@ is_a: CL:1001006 ! kidney afferent arteriole cell intersection_of: CL:0000115 ! endothelial cell intersection_of: part_of UBERON:0004639 ! renal afferent arteriole property_value: RO:0002175 NCBITaxon:9606 -property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional.\n\nKidney afferent arteriole endothelial cells are a specialized type of cell located within the kidneys, forming the inner lining of the afferent arterioles, which are responsible for delivering blood to the glomeruli - capillary networks responsible for filtration - from where the process of urine formation begins in the nephrons.\nThe endothelial cells in the kidney afferent arterioles have a key function in regulating the blood flow and filtration. They have autocrine and paracrine signaling capabilities, meaning they can signal to themselves and other nearby cells. They produce nitric oxide, prostacyclin, and endothelin, which are powerful vasodilators and vasoconstrictors that regulate renal blood flow. These cells also engage in the mitigation of kidney injury and inflammation by promoting repair and regeneration, demonstrating the multifaceted roles these cells play in maintaining renal health." xsd:string {xref="DOI:10.1046/j.0001-6772.2003.01205.x", xref="DOI:10.1093/ndt/gfl308"} +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nKidney afferent arteriole endothelial cells are a specialized type of cell located within the kidneys, forming the inner lining of the afferent arterioles, which are responsible for delivering blood to the glomeruli - capillary networks responsible for filtration - from where the process of urine formation begins in the nephrons.\nThe endothelial cells in the kidney afferent arterioles have a key function in regulating the blood flow and filtration. They have autocrine and paracrine signaling capabilities, meaning they can signal to themselves and other nearby cells. They produce nitric oxide, prostacyclin, and endothelin, which are powerful vasodilators and vasoconstrictors that regulate renal blood flow. These cells also engage in the mitigation of kidney injury and inflammation by promoting repair and regeneration, demonstrating the multifaceted roles these cells play in maintaining renal health." xsd:string {xref="DOI:10.1046/j.0001-6772.2003.01205.x", xref="DOI:10.1093/ndt/gfl308"} [Term] id: CL:1001097 name: kidney afferent arteriole smooth muscle cell def: "A smooth muscle cell found in the wall of the afferent arteriole. This cell contracts and relaxes in response to changes in blood pressure, a process known as a myogenic response, to alter artery diameter and regulate blood flow into the glomeruli." [PMID:16990493, PMID:22733355, PMID:24066938, PMID:25834230] +subset: human_subset +subset: mouse_subset xref: KUPO:0001040 is_a: CL:0008035 ! microcirculation associated smooth muscle cell is_a: CL:1001006 ! kidney afferent arteriole cell @@ -31622,6 +36076,8 @@ name: kidney efferent arteriole endothelial cell def: "Any endothelial cell that is part of some renal efferent arteriole." [FBC:Autogenerated] subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset xref: https://cellxgene.cziscience.com/cellguide/CL_1001099 xref: KUPO:0001042 is_a: CL:1000412 ! endothelial cell of arteriole @@ -31629,12 +36085,14 @@ is_a: CL:1001009 ! kidney efferent arteriole cell intersection_of: CL:0000115 ! endothelial cell intersection_of: part_of UBERON:0004640 ! renal efferent arteriole property_value: RO:0002175 NCBITaxon:9606 -property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional.\n\nKidney efferent arteriole endothelial cells constitute a vital component of the kidney's microvascular system. They are unique endothelial cells found lining the walls of efferent arterioles, which transport blood away from the glomeruli in the kidney.\nThe primary responsibilities of the kidney efferent arteriole endothelial cells involve controling renal blood flow, regulating glomerular filtration rate (GFR), and managing perfusion pressure. They do this by contracting and relaxing, effectively narrowing and widening the arteriole's lumen thereby controling the volume and rate of blood flow to the peritubular capillaries and creating the pressure gradient necessary for filtration in the glomerulus. \nFurthermore, kidney efferent arteriole endothelial cells show a high degree of plasticity in response to pathophysiological stimuli and can undergo structural and functional changes based on local needs. In conditions like hypertension and diabetes, these cells can experience hypertrophy and endothelial dysfunction, contributing to the progression of renal disease." xsd:string {xref="DOI:10.1016/j.semcdb.2014.08.002", xref="DOI:10.1016/j.semnephrol.2015.01.010", xref="DOI:10.1038/s41581-021-00411-9", xref="DOI:10.1681/ASN.2019111179"} +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nKidney efferent arteriole endothelial cells constitute a vital component of the kidney's microvascular system. They are unique endothelial cells found lining the walls of efferent arterioles, which transport blood away from the glomeruli in the kidney.\nThe primary responsibilities of the kidney efferent arteriole endothelial cells involve controling renal blood flow, regulating glomerular filtration rate (GFR), and managing perfusion pressure. They do this by contracting and relaxing, effectively narrowing and widening the arteriole's lumen thereby controling the volume and rate of blood flow to the peritubular capillaries and creating the pressure gradient necessary for filtration in the glomerulus. \nFurthermore, kidney efferent arteriole endothelial cells show a high degree of plasticity in response to pathophysiological stimuli and can undergo structural and functional changes based on local needs. In conditions like hypertension and diabetes, these cells can experience hypertrophy and endothelial dysfunction, contributing to the progression of renal disease." xsd:string {xref="DOI:10.1016/j.semcdb.2014.08.002", xref="DOI:10.1016/j.semnephrol.2015.01.010", xref="DOI:10.1038/s41581-021-00411-9", xref="DOI:10.1681/ASN.2019111179"} [Term] id: CL:1001100 name: kidney efferent arteriole smooth muscle cell def: "Any smooth muscle cell that is part of some renal efferent arteriole." [FBC:Autogenerated] +subset: human_subset +subset: mouse_subset xref: KUPO:0001043 is_a: CL:0008035 ! microcirculation associated smooth muscle cell is_a: CL:1001009 ! kidney efferent arteriole cell @@ -31648,6 +36106,8 @@ name: kidney loop of Henle thick ascending limb epithelial cell def: "An epithelial cell that is part of some loop of Henle thick ascending limb. It is known in some mammalian species that this cell may express the Na+-K+-2Cl− cotransporter (NKCC2) apically." [PMID:25318757] subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset xref: KUPO:0001049 is_a: CL:1000504 ! kidney medulla cell is_a: CL:1001016 {is_inferred="true"} ! kidney loop of Henle ascending limb epithelial cell @@ -31662,6 +36122,8 @@ name: kidney loop of Henle thin ascending limb epithelial cell def: "An epithelial cell that is part of some loop of Henle thin ascending limb." [] subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset xref: KUPO:0001050 is_a: CL:1000617 ! kidney inner medulla cell is_a: CL:1001016 {is_inferred="true"} ! kidney loop of Henle ascending limb epithelial cell @@ -31676,6 +36138,8 @@ name: kidney loop of Henle medullary thick ascending limb epithelial cell def: "An epithelial cell that is part of some loop of Henle thick ascending limb segment located in the renal medulla." [] subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset xref: KUPO:0001051 is_a: CL:1000616 {is_inferred="true"} ! kidney outer medulla cell is_a: CL:1001106 ! kidney loop of Henle thick ascending limb epithelial cell @@ -31690,6 +36154,8 @@ name: kidney loop of Henle cortical thick ascending limb epithelial cell def: "An epithelial cell that is part of some loop of Henle thick ascending limb segment located in the renal cortex." [] subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset xref: KUPO:0001052 is_a: CL:1001106 ! kidney loop of Henle thick ascending limb epithelial cell intersection_of: CL:1001016 ! kidney loop of Henle ascending limb epithelial cell @@ -31703,6 +36169,8 @@ name: kidney loop of Henle thin descending limb epithelial cell def: "An epithelial cell that is part of some loop of Henle thin descending limb." [] subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset xref: KUPO:0001054 is_a: CL:1000453 ! epithelial cell of intermediate tubule is_a: CL:1000616 ! kidney outer medulla cell @@ -31716,6 +36184,8 @@ property_value: RO:0002175 NCBITaxon:9606 id: CL:1001123 name: kidney outer medulla peritubular capillary cell def: "An endothelial cell that is part of the peritubular capillary of the outer renal medulla." [] +subset: human_subset +subset: mouse_subset xref: KUPO:0001066 is_a: CL:1000616 ! kidney outer medulla cell is_a: CL:1001033 ! peritubular capillary endothelial cell @@ -31727,6 +36197,8 @@ relationship: part_of UBERON:0006341 ! outer renal medulla peritubular capillary id: CL:1001124 name: kidney cortex peritubular capillary cell def: "An endothelial cell that is part of the peritubular capillary of the renal cortex." [] +subset: human_subset +subset: mouse_subset xref: KUPO:0001067 is_a: CL:0002681 ! kidney cortical cell is_a: CL:1001033 ! peritubular capillary endothelial cell @@ -31738,9 +36210,10 @@ relationship: part_of UBERON:0006851 ! renal cortex peritubular capillary id: CL:1001126 name: inner renal medulla vasa recta cell def: "Any vasa recta cell that is part of some inner renal medulla vasa recta." [FBC:Autogenerated] +subset: human_subset +subset: mouse_subset xref: KUPO:0001069 is_a: CL:1000617 {is_inferred="true"} ! kidney inner medulla cell -is_a: CL:1000893 ! kidney venous blood vessel cell is_a: CL:1001036 {is_inferred="true"} ! vasa recta cell intersection_of: CL:1001036 ! vasa recta cell intersection_of: part_of UBERON:0004776 ! inner renal medulla vasa recta @@ -31750,9 +36223,10 @@ relationship: part_of UBERON:0004776 ! inner renal medulla vasa recta id: CL:1001127 name: outer renal medulla vasa recta cell def: "Any vasa recta cell that is part of some outer renal medulla vasa recta." [FBC:Autogenerated] +subset: human_subset +subset: mouse_subset xref: KUPO:0001070 is_a: CL:1000616 {is_inferred="true"} ! kidney outer medulla cell -is_a: CL:1000893 ! kidney venous blood vessel cell is_a: CL:1001036 {is_inferred="true"} ! vasa recta cell intersection_of: CL:1001036 ! vasa recta cell intersection_of: part_of UBERON:0004775 ! outer renal medulla vasa recta @@ -31765,19 +36239,23 @@ def: "A cell that is part of some vasa recta ascending limb." [] comment: It is known in some mammalian species that this cell may express PV-1, a component of the fenestral diaphragm. {xref="PMID:20392799", xref="PMID:20392798", xref="PMID:26062876"} subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset xref: https://cellxgene.cziscience.com/cellguide/CL_1001131 xref: KUPO:0001074 is_a: CL:1001036 {is_inferred="true"} ! vasa recta cell intersection_of: CL:1001036 ! vasa recta cell -intersection_of: part_of UBERON:0009091 ! vasa recta ascending limb -relationship: part_of UBERON:0009091 ! vasa recta ascending limb +intersection_of: part_of UBERON:0009091 ! ascending vasa recta +relationship: part_of UBERON:0009091 ! ascending vasa recta property_value: RO:0002175 NCBITaxon:9606 -property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional.\n\nThe vasa recta ascending limb cells are specialized epithelial cells that are part of the vasa recta in the kidney, a crucial component of the renal medulla that functions as a counter-current exchanger to maintain the concentration gradient required for water reabsorption. These particular cells are located in the ascending limb of the vasa recta, which takes blood flow from the medulla back to the cortex. \nThe primary function of vasa recta ascending limb cells is to preserve the renal medulla's hypertonicity, necessary for the kidney's urine concentration mechanism. Unlike the vasa recta descending limb cells, the venous-like epithelial cells of the ascending vasa recta are highly fenestrated and lack pericyte coverage, which facilitates water reuptake. \nAs the blood flows through the ascending limb, it loses solutes and gains water, which is driven by the high solute concentration in the surrounding interstitium. This process acts in concert with cellular action in the descending limb and contributions from the so-called Loop of Henle, which helps with water and sodium chloride retrieval from the urine.\nIn the context of normal physiological processes, the function of the vasa recta ascending limb cells is essential in maintaining the body's overall fluid balance, electrolyte concentration, and systemic blood pressure. Any dysfunction in these cells may lead to impaired urine concentration or dilution capability of the kidney, potentially resulting in conditions like diabetes insipidus or hyponatremia." xsd:string {xref="DOI:10.1016/B978-0-323-35515-5.00009-9", xref="DOI:10.1053/j.ajkd.2005.01.008", xref="DOI:10.1081/jdi-100101958", xref="DOI:10.1111/apha.12026", xref="DOI:10.1152/ajpregu.00657.2002"} +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nThe vasa recta ascending limb cells are specialized epithelial cells that are part of the vasa recta in the kidney, a crucial component of the renal medulla that functions as a counter-current exchanger to maintain the concentration gradient required for water reabsorption. These particular cells are located in the ascending limb of the vasa recta, which takes blood flow from the medulla back to the cortex. \nThe primary function of vasa recta ascending limb cells is to preserve the renal medulla's hypertonicity, necessary for the kidney's urine concentration mechanism. Unlike the vasa recta descending limb cells, the venous-like epithelial cells of the ascending vasa recta are highly fenestrated and lack pericyte coverage, which facilitates water reuptake. \nAs the blood flows through the ascending limb, it loses solutes and gains water, which is driven by the high solute concentration in the surrounding interstitium. This process acts in concert with cellular action in the descending limb and contributions from the so-called Loop of Henle, which helps with water and sodium chloride retrieval from the urine.\nIn the context of normal physiological processes, the function of the vasa recta ascending limb cells is essential in maintaining the body's overall fluid balance, electrolyte concentration, and systemic blood pressure. Any dysfunction in these cells may lead to impaired urine concentration or dilution capability of the kidney, potentially resulting in conditions like diabetes insipidus or hyponatremia." xsd:string {xref="DOI:10.1016/B978-0-323-35515-5.00009-9", xref="DOI:10.1053/j.ajkd.2005.01.008", xref="DOI:10.1081/jdi-100101958", xref="DOI:10.1111/apha.12026", xref="DOI:10.1152/ajpregu.00657.2002"} [Term] id: CL:1001135 name: arcuate artery cell def: "Any kidney cortex artery cell that is part of some kidney arcuate artery." [FBC:Autogenerated] +subset: human_subset +subset: mouse_subset xref: KUPO:0001078 is_a: CL:1001045 {is_inferred="true"} ! kidney cortex artery cell intersection_of: CL:1001045 ! kidney cortex artery cell @@ -31788,6 +36266,8 @@ relationship: part_of UBERON:0001552 ! kidney arcuate artery id: CL:1001138 name: interlobular artery cell def: "Any kidney cortex artery cell that is part of some interlobular artery." [FBC:Autogenerated] +subset: human_subset +subset: mouse_subset xref: KUPO:0001081 is_a: CL:1001045 {is_inferred="true"} ! kidney cortex artery cell intersection_of: CL:1001045 ! kidney cortex artery cell @@ -31798,6 +36278,8 @@ relationship: part_of UBERON:0004723 ! interlobular artery id: CL:1001142 name: arcuate vein cell def: "Any kidney cortex vein cell that is part of some kidney arcuate vein." [FBC:Autogenerated] +subset: human_subset +subset: mouse_subset xref: KUPO:0001085 is_a: CL:1001052 {is_inferred="true"} ! kidney cortex vein cell intersection_of: CL:1001052 ! kidney cortex vein cell @@ -31808,6 +36290,8 @@ relationship: part_of UBERON:0004719 ! kidney arcuate vein id: CL:1001145 name: interlobular vein cell def: "Any kidney cortex vein cell that is part of some renal interlobular vein." [FBC:Autogenerated] +subset: human_subset +subset: mouse_subset xref: KUPO:0001088 is_a: CL:1001052 {is_inferred="true"} ! kidney cortex vein cell intersection_of: CL:1001052 ! kidney cortex vein cell @@ -31817,29 +36301,35 @@ relationship: part_of UBERON:0005168 ! renal interlobular vein [Term] id: CL:1001209 name: inner medulla vasa recta ascending limb cell -def: "Any vasa recta ascending limb cell that is part of some inner medulla vasa recta ascending limb." [FBC:Autogenerated] +def: "Any vasa recta ascending limb cell that is part of some inner medulla ascending vasa recta." [FBC:Autogenerated] +subset: human_subset +subset: mouse_subset xref: KUPO:0001075 is_a: CL:1001126 {is_inferred="true"} ! inner renal medulla vasa recta cell is_a: CL:1001131 {is_inferred="true"} ! vasa recta ascending limb cell intersection_of: CL:1001131 ! vasa recta ascending limb cell -intersection_of: part_of UBERON:0009092 ! inner medulla vasa recta ascending limb -relationship: part_of UBERON:0009092 ! inner medulla vasa recta ascending limb +intersection_of: part_of UBERON:0009092 ! inner medulla ascending vasa recta +relationship: part_of UBERON:0009092 ! inner medulla ascending vasa recta [Term] id: CL:1001210 name: outer medulla vasa recta ascending limb cell -def: "Any vasa recta ascending limb cell that is part of some outer medulla vasa recta ascending limb." [FBC:Autogenerated] +def: "Any vasa recta ascending limb cell that is part of some outer medulla ascending vasa recta." [FBC:Autogenerated] +subset: human_subset +subset: mouse_subset xref: KUPO:0001076 is_a: CL:1001127 {is_inferred="true"} ! outer renal medulla vasa recta cell is_a: CL:1001131 {is_inferred="true"} ! vasa recta ascending limb cell intersection_of: CL:1001131 ! vasa recta ascending limb cell -intersection_of: part_of UBERON:0009093 ! outer medulla vasa recta ascending limb -relationship: part_of UBERON:0009093 ! outer medulla vasa recta ascending limb +intersection_of: part_of UBERON:0009093 ! outer medulla ascending vasa recta +relationship: part_of UBERON:0009093 ! outer medulla ascending vasa recta [Term] id: CL:1001213 name: arcuate artery endothelial cell def: "Any endothelial cell that is part of some kidney arcuate artery." [FBC:Autogenerated] +subset: human_subset +subset: mouse_subset xref: KUPO:0001079 is_a: CL:1000413 ! endothelial cell of artery is_a: CL:1001135 ! arcuate artery cell @@ -31850,6 +36340,8 @@ intersection_of: part_of UBERON:0001552 ! kidney arcuate artery id: CL:1001214 name: arcuate artery smooth muscle cell def: "Any smooth muscle cell that is part of some kidney arcuate artery." [FBC:Autogenerated] +subset: human_subset +subset: mouse_subset xref: KUPO:0001080 is_a: CL:1001064 ! kidney artery smooth muscle cell is_a: CL:1001135 ! arcuate artery cell @@ -31860,6 +36352,8 @@ intersection_of: part_of UBERON:0001552 ! kidney arcuate artery id: CL:1001216 name: interlobulary artery endothelial cell def: "Any endothelial cell that is part of some interlobular artery." [FBC:Autogenerated] +subset: human_subset +subset: mouse_subset xref: KUPO:0001082 is_a: CL:1000413 ! endothelial cell of artery is_a: CL:1001138 ! interlobular artery cell @@ -31870,6 +36364,8 @@ intersection_of: part_of UBERON:0004723 ! interlobular artery id: CL:1001217 name: interlobulary artery smooth muscle cell def: "Any smooth muscle cell that is part of some interlobular artery." [FBC:Autogenerated] +subset: human_subset +subset: mouse_subset xref: KUPO:0001083 is_a: CL:1001064 ! kidney artery smooth muscle cell is_a: CL:1001138 ! interlobular artery cell @@ -31880,6 +36376,8 @@ intersection_of: part_of UBERON:0004723 ! interlobular artery id: CL:1001220 name: arcuate vein endothelial cell def: "Any endothelial cell that is part of some kidney arcuate vein." [FBC:Autogenerated] +subset: human_subset +subset: mouse_subset xref: KUPO:0001086 is_a: CL:0002543 ! vein endothelial cell is_a: CL:1001142 ! arcuate vein cell @@ -31890,6 +36388,8 @@ intersection_of: part_of UBERON:0004719 ! kidney arcuate vein id: CL:1001221 name: arcuate vein smooth muscle cell def: "Any smooth muscle cell that is part of some kidney arcuate vein." [FBC:Autogenerated] +subset: human_subset +subset: mouse_subset xref: KUPO:0001087 is_a: CL:1001068 ! kidney venous system smooth muscle cell is_a: CL:1001142 ! arcuate vein cell @@ -31900,6 +36400,8 @@ intersection_of: part_of UBERON:0004719 ! kidney arcuate vein id: CL:1001223 name: interlobulary vein endothelial cell def: "Any endothelial cell that is part of some renal interlobular vein." [FBC:Autogenerated] +subset: human_subset +subset: mouse_subset xref: KUPO:0001089 is_a: CL:0002543 ! vein endothelial cell is_a: CL:1001145 ! interlobular vein cell @@ -31910,6 +36412,8 @@ intersection_of: part_of UBERON:0005168 ! renal interlobular vein id: CL:1001224 name: interlobulary vein smooth muscle cell def: "Any smooth muscle cell that is part of some renal interlobular vein." [FBC:Autogenerated] +subset: human_subset +subset: mouse_subset xref: KUPO:0001090 is_a: CL:1001068 ! kidney venous system smooth muscle cell is_a: CL:1001145 ! interlobular vein cell @@ -31921,6 +36425,8 @@ id: CL:1001225 name: kidney collecting duct cell def: "A cell that is part of a collecting duct of renal tubule." [] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset xref: KUPO:0001012 xref: Wikipedia:Kidney_collecting_duct_cell is_a: CL:1000497 ! kidney cell @@ -31935,36 +36441,42 @@ def: "A cell that is part of some vasa recta descending limb." [] comment: It is known in some mammalian species that this cell may express the urea transporter B. {xref="PMID:20392799", xref="PMID:20392798", xref="PMID:26062876"} subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset xref: https://cellxgene.cziscience.com/cellguide/CL_1001285 xref: KUPO:0001071 is_a: CL:1001036 {is_inferred="true"} ! vasa recta cell intersection_of: CL:1001036 ! vasa recta cell -intersection_of: part_of UBERON:0009202 ! vasa recta descending limb -relationship: part_of UBERON:0009202 ! vasa recta descending limb +intersection_of: part_of UBERON:0009202 ! descending vasa recta +relationship: part_of UBERON:0009202 ! descending vasa recta property_value: RO:0002175 NCBITaxon:9606 -property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional.\n\nVasa recta descending limb cells are specialized epithelial cells found in the vasa recta, a network of blood vessels in the renal medulla. These cells line the interior surface of the descending limb of the vasa recta and play a crucial role in the filtering and regulation of substances within the blood.\nIn contrast to vasa recta ascending limb cells, the arterial-like epithelial cells of the descending vasa recta are non-fenestrated and covered by a pericyte layer that regulates the medullary blood flow. They help keeping the body’s fluid and electrolyte balance in check through a process known as countercurrent exchange system, in which the cells of the descending limb are permeable to water but relatively impermeable to solutes, such as sodium and urea. As the blood descends into the medulla along its descending limb, water passively diffuses out of the vasa recta, concentrating the blood in solutes.\nIn addition to their central role in water and solute exchange, these cells contribute to maintaining the medullary osmotic gradient, a critical function to concentrate urine. The osmotic gradient is created by the counterflow of water and solutes between the descending and ascending limbs of the vasa recta and the adjacent Loop of Henle. The selective permeability of the descending limb cells allows them to maintain this gradient, which in turn helps to conserve water, a vital role in the overall function of the renal system. Thus, vasa recta descending limb cells have a significant function in renal physiology, particularly in osmoregulation and fluid balance." xsd:string {xref="DOI:10.1053/j.ajkd.2005.01.008", xref="DOI:10.1081/jdi-100101958", xref="DOI:10.1111/apha.12026#apha12026-bib-0039", xref="DOI:10.1152/ajpregu.00657.2002"} +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nVasa recta descending limb cells are specialized epithelial cells found in the vasa recta, a network of blood vessels in the renal medulla. These cells line the interior surface of the descending limb of the vasa recta and play a crucial role in the filtering and regulation of substances within the blood.\nIn contrast to vasa recta ascending limb cells, the arterial-like epithelial cells of the descending vasa recta are non-fenestrated and covered by a pericyte layer that regulates the medullary blood flow. They help keeping the body’s fluid and electrolyte balance in check through a process known as countercurrent exchange system, in which the cells of the descending limb are permeable to water but relatively impermeable to solutes, such as sodium and urea. As the blood descends into the medulla along its descending limb, water passively diffuses out of the vasa recta, concentrating the blood in solutes.\nIn addition to their central role in water and solute exchange, these cells contribute to maintaining the medullary osmotic gradient, a critical function to concentrate urine. The osmotic gradient is created by the counterflow of water and solutes between the descending and ascending limbs of the vasa recta and the adjacent Loop of Henle. The selective permeability of the descending limb cells allows them to maintain this gradient, which in turn helps to conserve water, a vital role in the overall function of the renal system. Thus, vasa recta descending limb cells have a significant function in renal physiology, particularly in osmoregulation and fluid balance." xsd:string {xref="DOI:10.1053/j.ajkd.2005.01.008", xref="DOI:10.1081/jdi-100101958", xref="DOI:10.1111/apha.12026#apha12026-bib-0039", xref="DOI:10.1152/ajpregu.00657.2002"} [Term] id: CL:1001286 name: inner medulla vasa recta descending limb cell -def: "Any vasa recta descending limb cell that is part of some inner medulla vasa recta descending limb." [FBC:Autogenerated] +def: "Any vasa recta descending limb cell that is part of some inner medulla descending vasa recta." [FBC:Autogenerated] +subset: human_subset +subset: mouse_subset xref: KUPO:0001072 is_a: CL:1001126 {is_inferred="true"} ! inner renal medulla vasa recta cell is_a: CL:1001285 {is_inferred="true"} ! vasa recta descending limb cell intersection_of: CL:1001285 ! vasa recta descending limb cell -intersection_of: part_of UBERON:0009089 ! inner medulla vasa recta descending limb -relationship: part_of UBERON:0009089 ! inner medulla vasa recta descending limb +intersection_of: part_of UBERON:0009089 ! inner medulla descending vasa recta +relationship: part_of UBERON:0009089 ! inner medulla descending vasa recta [Term] id: CL:1001287 name: outer medulla vasa recta descending limb cell -def: "Any vasa recta descending limb cell that is part of some outer medulla vasa recta descending limb." [FBC:Autogenerated] +def: "Any vasa recta descending limb cell that is part of some outer medulla descending vasa recta." [FBC:Autogenerated] +subset: human_subset +subset: mouse_subset xref: KUPO:0001073 is_a: CL:1001127 {is_inferred="true"} ! outer renal medulla vasa recta cell is_a: CL:1001285 {is_inferred="true"} ! vasa recta descending limb cell intersection_of: CL:1001285 ! vasa recta descending limb cell -intersection_of: part_of UBERON:0009090 ! outer medulla vasa recta descending limb -relationship: part_of UBERON:0009090 ! outer medulla vasa recta descending limb +intersection_of: part_of UBERON:0009090 ! outer medulla descending vasa recta +relationship: part_of UBERON:0009090 ! outer medulla descending vasa recta [Term] id: CL:1001318 @@ -31972,6 +36484,8 @@ name: renal interstitial pericyte def: "A pericyte cell located in the kidney interstitium." [] subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset xref: KUPO:0001104 is_a: CL:0000669 {is_inferred="true"} ! pericyte is_a: CL:1000500 ! kidney interstitial cell @@ -31985,6 +36499,8 @@ name: bladder cell def: "Any cell that is part of some urinary bladder." [FBC:Autogenerated] subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset xref: KUPO:0001120 is_a: CL:1000600 ! lower urinary tract cell intersection_of: CL:0000000 ! cell @@ -31996,6 +36512,8 @@ property_value: RO:0002175 NCBITaxon:9606 id: CL:1001320 name: urethra cell def: "Any cell that is part of some urethra." [FBC:Autogenerated] +subset: human_subset +subset: mouse_subset xref: KUPO:0001123 is_a: CL:1000600 ! lower urinary tract cell intersection_of: CL:0000000 ! cell @@ -32008,8 +36526,11 @@ name: bladder urothelial cell def: "A urothelial cell that is part of the urothelium of the urinary bladder." [doi:10.1038/s41385-022-00565-0] subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "bladder transitional cell" NARROW [] synonym: "transitional epithelial cell of urinary bladder" NARROW [] +xref: https://cellxgene.cziscience.com/cellguide/CL_1001428 xref: KUPO:0001121 xref: NCIT:C32210 is_a: CL:0000731 ! urothelial cell @@ -32018,18 +36539,23 @@ intersection_of: CL:0000731 ! urothelial cell intersection_of: part_of UBERON:0004645 ! urinary bladder urothelium relationship: part_of UBERON:0004645 ! urinary bladder urothelium property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nBladder urothelial cells form the urothelium in the bladder - a specific type of epithelial tissue that constitutes the inner lining of the bladder and other parts of the urinary tract including the renal pelvis, ureters and urethra. These unique cells are specialized to withstand the highly variable and sometimes harsh conditions present in the urinary system. Their key function is maintaining the barrier integrity of the urinary tract even when exposed to high volumes of urine and its solutes, and they play a crucial role in protecting underlying tissues from damage and infection.\nThe bladder urothelial cells exhibit a remarkable spectrum of phenotypic versatility and have an extraordinary capacity to stretch and retract based on the degree of bladder filling and emptying. In their relaxed state, these cells appear large and cuboidal, but upon stretching, they become thinner and exhibit a squamous cell-like appearance. This distinctive feature enables them to adjust to the changes in the urinary bladder volume while remaining impermeable to urinary solutes, thereby preventing a potential toxicity to the bladder wall and infiltration into the bloodstream.\nApart from their barrier function, bladder urothelial cells also express a number of sensor molecules or respond to thermal, mechanical and chemical stimuli and can release signaling molecules, thereby playing a key role in sensory mechanisms that communicate vital information about the bladder's mechanical state to the nervous system. This communication helps regulate the micturition cycle and maintain urinary continence. Recent studies have also indicated that these cells may play a role in immune responses, highlighting their importance in bladder physiology. \nAltered proliferation and differentiation of bladder urothelial cells are implicated in various diseases and conditions such as bladder cancer, interstitial cystitis, and urinary tract infections." xsd:string {xref="DOI:10.1038/nrurol.2011.144", xref="DOI:10.1038/nrurol.2016.13", xref="DOI:10.1038/s41579-020-0324-0", xref="DOI:10.1038/s41585-020-0350-8", xref="DOI:10.1080/03008880410015165"} [Term] id: CL:1001430 name: urethra urothelial cell -def: "Any urothelial cell that is part of some urethra urothelium." [FBC:Autogenerated] +def: "A urothelial cell that is part of the urethra urothelium. This cell plays a crucial role in maintaining the urethral barrier function, protecting against toxic substances in urine, sensing environmental changes, and defending against pathogen entry." [PMID:23589830, PMID:36180582] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset +xref: https://cellxgene.cziscience.com/cellguide/CL_1001430 xref: KUPO:0001124 -is_a: CL:0000731 {is_inferred="true"} ! urothelial cell +is_a: CL:0000731 ! urothelial cell is_a: CL:1000296 ! epithelial cell of urethra intersection_of: CL:0000731 ! urothelial cell intersection_of: part_of UBERON:0004787 ! urethra urothelium relationship: part_of UBERON:0004787 ! urethra urothelium +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nUrethra urothelial cells are highly specialized epithelial cells in the urethra, which is a tubelike structure that carries urine from the bladder to the external urethral orifice. Urothelial cells form the urothelium – a stratified, transitional epithelium lining the bladder, ureters, renal pelvis and urethra. These cells are highly adapted to their specific environment and maintain the crucial function of sustaining the urinary tract's core roles, primarily to transit and store urine without auto-corrosion or pathogen proliferation.\nWithin the urethra urothelial cells are primarily found in proximal two-thirds of the urethra, while the distal third is lined by stratified squamous epithelial cells. The urothelial cells are renowned for their remarkable impermeability and ability to stretch and recoil during the various stages of urine filling and emptying. They form a tight barrier that prevents reabsorption of harmful byproducts and toxic substances present in the urine, guarding the deeper tissues and bloodstream against potential damage. This is largely attributed to specialized junctions, namely zonulae occludentes or tight junctions, in the umbrella cell layer (one of three layers of the urothelium) that seal the intercellular space between adjacent cells. Together with the urothelial plaque (an apical membrane plaque comprised of uroplakin proteins covering the umbrella cells at the luminal surface), the junctional complexes form a very effective permeability barrier that regulates the passage of water and ion from urine to the underlying tissue. \nA noteworthy feature of urothelial cells is their regulatory and sensory roles involving communication with the underlying layers about the filling and emptying status of the urinary tract. The cells also manage a fine balance between proliferation and differentiation, with the basal cells providing a ready pool of cells to replace the superficial layer when damaged. Their remarkable ability for regeneration and turnover, and their response to signals for repair underpins the durability and functionality of the urothelial tract." xsd:string {xref="DOI:10.1038/nrurol.2016.13", xref="DOI:10.1038/s41385-022-00565-0", xref="DOI:10.1152/physrev.00030.2012", xref="DOI:10.1152/physrev.00041.2019"} [Term] id: CL:1001431 @@ -32037,6 +36563,8 @@ name: kidney collecting duct principal cell def: "Any renal principal cell that is part of some collecting duct of renal tubule." [FBC:Autogenerated] subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset xref: https://cellxgene.cziscience.com/cellguide/CL_1001431 xref: KUPO:0001128 is_a: CL:0005009 {is_inferred="true"} ! renal principal cell @@ -32044,7 +36572,7 @@ is_a: CL:1000454 ! kidney collecting duct epithelial cell intersection_of: CL:0005009 ! renal principal cell intersection_of: part_of UBERON:0001232 ! collecting duct of renal tubule property_value: RO:0002175 NCBITaxon:9606 -property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional.\n\nThe kidney collecting duct principal cell is a highly specialized type of cell found in the late distal convoluted tubule and collecting duct of the kidney's nephron. Principal cells are located at the final segments of the renal tubules, where they play a pivotal role in key homeostatic processes.\nOne of their fundamental functions of kidney collecting duct principal cells is the regulation of water reabsorption, which is mediated by aquaporins (water channel proteins). Antidiuretic hormones, such as vasopressin, can stimulate the redistribution of these water channels from an intracellular pools to the apical plasma membrane of the principal cell; translocation of aquaporin (specifically, AQP2) is associated with an increase of osmotic water permeability. The water reabsorption affects the concentration of the final urine; these cells are therefore directly involved in the maintenance of the body's fluid balance.\nKidney collecting duct principal cells also participate in sodium and potassium ions regulation. They reabsorb sodium ions from the tubular fluid back into the bloodstream, a process facilitated by the action of aldosterone, a hormone released by the adrenal glands. Similarly, the principal cells secrete potassium ions into the tubular fluid in response to aldosterone, contributing to the regulation of potassium levels in the body. Impaired function of cells can lead to various renal diseases and disorders, highlighting the vital role of kidney collecting duct principal cells in the body's homeostatic processes." xsd:string {xref="DOI:10.1007/s11906-015-0538-0", xref="DOI:10.1016/B978-0-12-386456-7.05402-2", xref="DOI:10.1016/j.biocel.2022.106261", xref="DOI:10.1073/pnas.1710964114"} +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nThe kidney collecting duct principal cell is a highly specialized type of cell found in the late distal convoluted tubule and collecting duct of the kidney's nephron. Principal cells are located at the final segments of the renal tubules, where they play a pivotal role in key homeostatic processes.\nOne of their fundamental functions of kidney collecting duct principal cells is the regulation of water reabsorption, which is mediated by aquaporins (water channel proteins). Antidiuretic hormones, such as vasopressin, can stimulate the redistribution of these water channels from an intracellular pools to the apical plasma membrane of the principal cell; translocation of aquaporin (specifically, AQP2) is associated with an increase of osmotic water permeability. The water reabsorption affects the concentration of the final urine; these cells are therefore directly involved in the maintenance of the body's fluid balance.\nKidney collecting duct principal cells also participate in sodium and potassium ions regulation. They reabsorb sodium ions from the tubular fluid back into the bloodstream, a process facilitated by the action of aldosterone, a hormone released by the adrenal glands. Similarly, the principal cells secrete potassium ions into the tubular fluid in response to aldosterone, contributing to the regulation of potassium levels in the body. Impaired function of cells can lead to various renal diseases and disorders, highlighting the vital role of kidney collecting duct principal cells in the body's homeostatic processes." xsd:string {xref="DOI:10.1007/s11906-015-0538-0", xref="DOI:10.1016/B978-0-12-386456-7.05402-2", xref="DOI:10.1016/j.biocel.2022.106261", xref="DOI:10.1073/pnas.1710964114"} [Term] id: CL:1001432 @@ -32052,13 +36580,17 @@ name: kidney collecting duct intercalated cell def: "Any renal intercalated cell that is part of some collecting duct of renal tubule." [FBC:Autogenerated] subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset xref: http://en.wikipedia.org/wiki/Collecting_duct_system#Intercalated_cells +xref: https://cellxgene.cziscience.com/cellguide/CL_1001432 xref: KUPO:0001129 is_a: CL:0005010 {is_inferred="true"} ! renal intercalated cell is_a: CL:1000454 ! kidney collecting duct epithelial cell intersection_of: CL:0005010 ! renal intercalated cell intersection_of: part_of UBERON:0001232 ! collecting duct of renal tubule property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nThe kidney collecting duct intercalated cell, otherwise referred to simply as the intercalated cell, is a specialized epithelial cell type primarily found in the kidney's collecting duct system. It is among the main cells that line this final component of the nephron, crucial in the physiological system that maintains acid-base homeostasis. This unique cell type comes in mainly three subtypes as per the localization of their proton pumps: type A, type B, and non-A, non-B cells. Each subtype plays different roles in regulating acid-base balance and electrolyte homeostasis in the body under varying physiological conditions. \nType A intercalated cells reabsorb bicarbonate and secrete protons into urine, leading to the production of acidic urine. These cells are typically prevalent on the renal cortex and function particularly in states of metabolic acidosis or potassium depletion. On the other hand, type B intercalated cells secrete bicarbonate and reabsorb protons; thus, they are crucial in alkaline urine production and potassium conservation. These cells are essential to counter metabolic alkalosis or situations of potassium surplus. The non-A, non-B cells have the characteristic features of both type A and B cells, but play a prominent role under conditions of chronically elevated aldosterone and angiotensin II levels. \nThrough their differentiated roles, intercalated cells also facilitate the reabsorption of sodium and chloride ions, and water to maintain osmolarity. These cells' activity is finely regulated by hormonal signals like aldosterone, angiotensin II, vasopressin, and the parathyroid hormone. Intercalated cell activity can undergo a significant transformation under pathological conditions, and their dysregulation is associated with diseases such as distal renal tubular acidosis, hypertension, and chronic kidney disease." xsd:string {xref="DOI:10.1007/978-3-211-99390-3_106", xref="DOI:10.1152/physiol.00008.2011", xref="DOI:10.1152/physrev.00011.2019", xref="DOI:10.2215/CJN.08880914", xref="DOI:10.3390/diseases2020071"} [Term] id: CL:1001433 @@ -32066,6 +36598,8 @@ name: epithelial cell of exocrine pancreas def: "An epithelial cell of the exocrine pancreas." [GOC:tfm] subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "exocrine pancreas cell" EXACT [] xref: FMA:70986 is_a: CL:0000083 ! epithelial cell of pancreas @@ -32078,9 +36612,11 @@ property_value: RO:0002175 NCBITaxon:9606 id: CL:1001434 name: olfactory bulb interneuron def: "A neuron residing in the olfactory bulb that serve to process and refine signals arising from olfactory sensory neurons" [PMID:18603310] -is_a: BFO:0000002 +subset: human_subset +subset: mouse_subset +is_a: CL:0000099 ! interneuron is_a: CL:0000101 ! sensory neuron -is_a: CL:0000402 ! CNS interneuron +is_a: CL:0012001 ! neuron of the forebrain intersection_of: CL:0000099 ! interneuron intersection_of: RO:0002100 UBERON:0002264 ! has soma location olfactory bulb relationship: part_of UBERON:0002264 ! olfactory bulb @@ -32090,6 +36626,8 @@ relationship: RO:0002100 UBERON:0002264 ! has soma location olfactory bulb id: CL:1001435 name: periglomerular cell def: "The small neuron in the glomerular layer of the olfactory bulb whose dendrites arborize within a glomerulus, where it receives synaptic input from olfactory receptor cell axon terminals, and also engages in dendrodendritic interactions with mitral and tufted cell dendrites; uses both GABA and dopamine as a neurotransmitter." [MP:0009943] +subset: human_subset +subset: mouse_subset synonym: "glomerular layer cell" EXACT [NIFEXT:122] synonym: "olfactory bulb (accessory) glomerular layer cell" EXACT [NIFEXT:122] synonym: "olfactory bulb glomerular layer cell" EXACT [NIFEXT:122] @@ -32104,20 +36642,28 @@ relationship: RO:0002100 UBERON:0005377 ! has soma location olfactory bulb glome id: CL:1001436 name: hair-tylotrich neuron def: "The subcutaneous mechanoreceptors that innervate tylotrich hair follicles." [MP:0000977] +subset: human_subset +subset: mouse_subset is_a: CL:0002487 ! cutaneous/subcutaneous mechanoreceptor cell [Term] id: CL:1001437 name: hair-down neuron def: "The subcutaneous mechanoreceptors that innervate vellus hairs." [MP:0000979] +subset: human_subset +subset: mouse_subset is_a: CL:0002487 ! cutaneous/subcutaneous mechanoreceptor cell [Term] id: CL:1001451 name: sensory neuron of dorsal root ganglion def: "A sensory neuron of the dorsal root ganglia that senses body position and sends information about how much the muscle is stretched to the spinal cord." [MP:0004297] +subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "proprioceptive neuron" EXACT [MP:0004297] is_a: CL:0000006 ! neuronal receptor cell +is_a: CL:3000004 ! peripheral sensory neuron is_a: CL:4023168 ! somatosensory neuron intersection_of: CL:0000101 ! sensory neuron intersection_of: RO:0002100 UBERON:0000044 ! has soma location dorsal root ganglion @@ -32130,6 +36676,8 @@ name: medium spiny neuron def: "An inhibitory, GABAergic projection neuron in the striatum that integrates glutamatergic signals arising from the cerebral cortex and thalamus." [doi:10.1073/pnas.242428599, MP:0008462] subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "gamma-aminobutyric acid (GABA)ergic spiny projection neuron" EXACT [doi:10.1073/pnas.242428599] synonym: "gamma-aminobutyric acid ergic spiny projection neuron" EXACT [doi:10.1073/pnas.242428599] synonym: "medium-sized densely spiny neuron" RELATED [BTO:0004778] @@ -32144,6 +36692,8 @@ property_value: RO:0002175 NCBITaxon:9606 id: CL:1001502 name: mitral cell def: "The large glutaminergic nerve cells whose dendrites synapse with axons of the olfactory receptor neurons in the glomerular layer of the olfactory bulb, and whose axons pass centrally in the olfactory tract to the olfactory cortex." [MP:0009954] +subset: human_subset +subset: mouse_subset is_a: CL:1001434 ! olfactory bulb interneuron relationship: RO:0002100 UBERON:0004186 ! has soma location olfactory bulb mitral cell layer @@ -32151,14 +36701,17 @@ relationship: RO:0002100 UBERON:0004186 ! has soma location olfactory bulb mitra id: CL:1001503 name: olfactory bulb tufted cell def: "The principal glutaminergic neuron located in the outer third of the external plexiform layer of the olfactory bulb; a single short primary dendrite traverses the outer external plexiform layer and terminates within an olfactory glomerulus in a tuft of branches, where it receives the input from olfactory receptor neuron axon terminals; axons of the tufted cells transfer information to a number of areas in the brain, including the piriform cortex, entorhinal cortex, olfactory tubercle, and amygdala." [MP:0009955] -is_a: BFO:0000002 -is_a: CL:0000540 ! neuron -relationship: part_of UBERON:0005376 ! olfactory bulb external plexiform layer +subset: human_subset +subset: mouse_subset +is_a: CL:0012001 ! neuron of the forebrain +relationship: RO:0002100 UBERON:0005376 ! has soma location olfactory bulb external plexiform layer [Term] id: CL:1001505 name: parvocellular neurosecretory cell def: "The secretory neurons of the paraventricular nucleus that synthesize and secrete vasopressin, corticotropin-releasing factor (CRF) and thyrotropin-releasing hormone (TRH) into blood vessels in the hypothalamo-pituitary portal system." [MP:0010125] +subset: human_subset +subset: mouse_subset synonym: "parvocellular neuron" EXACT [] synonym: "parvocellular neurosecretory neuron" EXACT [] is_a: CL:0000165 ! neuroendocrine cell @@ -32171,6 +36724,8 @@ relationship: part_of UBERON:0001930 ! paraventricular nucleus of hypothalamus id: CL:1001509 name: glycinergic neuron def: "The neurons that utilize glycine as a neurotransmitter." [MP:0010385] +subset: human_subset +subset: mouse_subset xref: FBbt:00048032 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: ZFA:0009396 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000151 ! secretory cell @@ -32184,25 +36739,33 @@ id: CL:1001516 name: intestinal enteroendocrine cell def: "The various hormone- or neurotransmitter-secreting cells present throughout the mucosa of the intestinal tract." [MP:0010802] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset +xref: https://cellxgene.cziscience.com/cellguide/CL_1001516 is_a: CL:0000164 ! enteroendocrine cell is_a: CL:0002563 ! intestinal epithelial cell intersection_of: CL:0000164 ! enteroendocrine cell -intersection_of: part_of UBERON:0001242 ! intestinal mucosa +intersection_of: part_of UBERON:0001277 ! intestinal epithelium +relationship: RO:0002207 CL:4052006 ! directly develops from intestinal enteroendocrine progenitor +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nIntestinal enteroendocrine cells are a highly specialized cell type found within the gastrointestinal epithelium. They account for approximately 1% of the intestinal epithelial cells in what is known as the largest endocrine organ in the human body. Intestinal enteroendocrine cells exhibit an exceptional diversity, both in terms of their secretory products and their distribution along the intestines, varying from the small intestine to the colon. \nThe primary function of intestinal enteroendocrine cells is to maintain gut physiology and homeostasis. They are known for their hormone production and are the source of numerous bioactive molecules including somatostatin, serotonin, cholecystokinin, glucose-dependent insulinotropic peptide, motilin, neurotensin, and others. These hormones and neuropeptides act in autocrine, paracrine, or endocrine signaling, impacting various functions including intestinal motility, secretion, nutrient absorption, and gut barrier functions.\nIntestinal enteroendocrine cells also serve as the body's frontline of defense, playing an integral role in surveillance against lumen-occurring hazards including pathogen attack. Enteroendocrine cells are divided into ‘closed type’ and ‘open type’. Closed type cells are located close to the basal membrane and do not reach the lumen of the gut. In contrast, the apical side of the open-type intestinal enteroendocrine cells is directly exposed to luminal contents and thus can recognize bacterial metabolites and dietary nutrients. In response, these cells can modulate the immune system responses and thereby function as a key communicator between the gut microbiota and the host." xsd:string {xref="DOI:10.1016/j.coph.2013.09.008", xref="DOI:10.1038/mi.2017.73", xref="DOI:10.1038/s41574-019-0168-8", xref="DOI:10.1111/j.1365-2613.2011.00767.x", xref="DOI:10.1146/annurev-physiol-021115-105439"} [Term] id: CL:1001517 name: stomach enteroendocrine cell def: "The various hormone- or neurotransmitter-secreting cells present throughout the mucosa of the stomach." [MP:0010803] +subset: human_subset +subset: mouse_subset is_a: CL:0000164 ! enteroendocrine cell -is_a: CL:0002659 ! glandular epithelial cell of stomach +is_a: CL:0002178 ! epithelial cell of stomach intersection_of: CL:0000164 ! enteroendocrine cell -intersection_of: part_of UBERON:0001160 ! fundus of stomach -relationship: part_of UBERON:0001160 ! fundus of stomach +intersection_of: part_of UBERON:0000945 ! stomach [Term] id: CL:1001561 name: vomeronasal sensory neuron def: "Chemosensitive cells that innervate the vomernasal organ epithelium and are responsible for receiving and transmitting pheromone signals." [MP:0011679] +subset: human_subset +subset: mouse_subset is_a: CL:0000101 ! sensory neuron intersection_of: CL:0000101 ! sensory neuron intersection_of: RO:0002100 UBERON:0002255 ! has soma location vomeronasal organ @@ -32223,6 +36786,9 @@ replaced_by: CL:0002638 id: CL:1001567 name: lung endothelial cell def: "Any endothelial cell of vascular tree that is part of some lung." [FBC:Autogenerated] +subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "endothelial cell of lung" RELATED [] synonym: "pulmonary vessel endothelial cell" RELATED [] is_a: CL:0002139 ! endothelial cell of vascular tree @@ -32236,6 +36802,8 @@ name: pulmonary artery endothelial cell def: "Any endothelial cell of vascular tree that is part of some pulmonary artery." [FBC:Autogenerated] subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "PAEC cell" RELATED [BTO:0001141] xref: BTO:0001141 is_a: CL:1000413 ! endothelial cell of artery @@ -32248,6 +36816,8 @@ property_value: RO:0002175 NCBITaxon:9606 id: CL:1001569 name: hippocampal interneuron def: "An interneuron with a soma found in the hippocampus." [GOC:pr] +subset: human_subset +subset: mouse_subset xref: FMA:84777 is_a: CL:0002608 ! hippocampal neuron is_a: CL:0008031 ! cortical interneuron @@ -32258,6 +36828,8 @@ intersection_of: RO:0002100 UBERON:0002421 ! has soma location hippocampal forma id: CL:1001571 name: hippocampal pyramidal neuron def: "A pyramidal neuron with a soma found in the hippocampus." [GOC:pr, PMID:19342486] +subset: human_subset +subset: mouse_subset synonym: "hippocampus (CA) pyramidal cell" NARROW [NIFSTD:sao131261273] synonym: "hippocampus (CA) pyramidal neuron" NARROW [NIFSTD:sao131261273] xref: NIFSTD:sao131261273 @@ -32273,6 +36845,8 @@ relationship: part_of UBERON:0002313 ! hippocampus pyramidal layer id: CL:1001572 name: colon endothelial cell def: "A vascular endothelial cell found in colon blood vessels." [https://orcid.org/0000-0001-5208-3432, NPX:PDR] +subset: human_subset +subset: mouse_subset synonym: "colon endothelial cells" RELATED OMO:0003004 [CALOHA:TS-2397] synonym: "colonic endothelial cell" RELATED [CALOHA:TS-2397] xref: CALOHA:TS-2397 @@ -32285,6 +36859,8 @@ relationship: part_of UBERON:0013695 ! colon endothelium id: CL:1001573 name: nasopharyngeal epithelial cell def: "Cell of the nasopharyngeal epithelium." [NPX:PDR] +subset: human_subset +subset: mouse_subset synonym: "nasopharynx respiratory epithelial cells" RELATED [CALOHA:TS-2398] xref: CALOHA:TS-2398 is_a: CL:0002251 ! epithelial cell of alimentary canal @@ -32297,6 +36873,8 @@ relationship: part_of UBERON:0001951 ! epithelium of nasopharynx id: CL:1001575 name: uterine cervix squamous cell def: "Squamous cell of uterine cervix epithelium." [NPX:PDR] +subset: human_subset +subset: mouse_subset synonym: "cervix squamous cell" RELATED [CALOHA:TS-1251] synonym: "cervix squamous epithelial cell" RELATED [CALOHA:TS-1251] synonym: "cervix, uterine squamous epithelial cells" RELATED [CALOHA:TS-1251] @@ -32312,6 +36890,8 @@ intersection_of: part_of UBERON:0000002 ! uterine cervix id: CL:1001576 name: oral mucosa squamous cell def: "Squamous cell of oral epithelium." [NPX:PDR] +subset: human_subset +subset: mouse_subset synonym: "oral cavity mucosa squamous cell" RELATED [CALOHA:TS-1252] synonym: "oral cavity mucosa squamous epithelial cell" RELATED [CALOHA:TS-1252] synonym: "oral mucosa squamous epithelial cell" RELATED [CALOHA:TS-1252] @@ -32328,6 +36908,8 @@ id: CL:1001577 name: tonsil squamous cell def: "Squamous cell of tonsil epithelium." [NPX:PDR] subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "tonsil squamous epithelial cell" RELATED [CALOHA:TS-1253] synonym: "tonsil squamous epithelial cells" RELATED [CALOHA:TS-1253] synonym: "tonsillar squamous cell" RELATED [CALOHA:TS-1253] @@ -32344,6 +36926,8 @@ property_value: RO:0002175 NCBITaxon:9606 id: CL:1001578 name: vagina squamous cell def: "Squamous cell of vaginal epithelium." [NPX:PDR] +subset: human_subset +subset: mouse_subset synonym: "vagina squamous epithelial cell" RELATED [CALOHA:TS-1254] synonym: "vagina squamous epithelial cells" RELATED [CALOHA:TS-1254] synonym: "vaginal squamous cell" RELATED [CALOHA:TS-1254] @@ -32358,6 +36942,8 @@ relationship: part_of UBERON:0001344 ! epithelium of vagina id: CL:1001579 name: cerebral cortex glial cell def: "Glial cell of cerebral cortex." [NPX:PDR] +subset: human_subset +subset: mouse_subset synonym: "brain cortex glial cell" RELATED [CALOHA:TS-1256] synonym: "cerebral cortex glial cells" RELATED [CALOHA:TS-1256] synonym: "cerebrum cortex glial cell" RELATED [CALOHA:TS-1256] @@ -32371,6 +36957,8 @@ relationship: part_of UBERON:0000956 ! cerebral cortex id: CL:1001580 name: hippocampal glial cell def: "A glial cell that is part of the hippocampus." [NPX:PDR] +subset: human_subset +subset: mouse_subset synonym: "hippocampus glial cell" EXACT [CALOHA:TS-1257] synonym: "hippocampus neuroglial cell" EXACT [CALOHA:TS-1257] xref: CALOHA:TS-1257 @@ -32383,6 +36971,8 @@ relationship: part_of UBERON:0002421 ! hippocampal formation id: CL:1001581 name: lateral ventricle glial cell def: "Glial cell of lateral ventricle." [NPX:PDR] +subset: human_subset +subset: mouse_subset synonym: "lateral ventricle glial cells" RELATED [CALOHA:TS-1258] xref: CALOHA:TS-1258 is_a: CL:0000125 ! glial cell @@ -32394,11 +36984,13 @@ relationship: part_of UBERON:0002285 ! telencephalic ventricle id: CL:1001582 name: lateral ventricle neuron def: "Neuron of lateral ventricle." [NPX:PDR] +subset: human_subset +subset: mouse_subset synonym: "lateral ventricle neural cell" RELATED [CALOHA:TS-1261] synonym: "lateral ventricle neuronal cell" RELATED [CALOHA:TS-1261] synonym: "lateral ventricle neuronal cells" RELATED [CALOHA:TS-1261] xref: CALOHA:TS-1261 -is_a: CL:2000029 ! central nervous system neuron +is_a: CL:0012001 ! neuron of the forebrain intersection_of: CL:0000540 ! neuron intersection_of: RO:0002100 UBERON:0002285 ! has soma location telencephalic ventricle relationship: RO:0002100 UBERON:0002285 ! has soma location telencephalic ventricle @@ -32415,6 +37007,8 @@ replaced_by: CL:0002617 id: CL:1001585 name: appendix glandular cell def: "Glandular cell of appendix epithelium. Example: Goblet cells; enterocytes or absorptive cells; enteroendocrine and M cells." [NPX:PDR] +subset: human_subset +subset: mouse_subset synonym: "appendix glandular cells" RELATED [CALOHA:TS-1271] synonym: "caecal appendix glandular cell" RELATED [CALOHA:TS-1271] synonym: "cecal appendix glandular cell" RELATED [CALOHA:TS-1271] @@ -32422,84 +37016,97 @@ synonym: "vermiform appendix glandular cell" RELATED [CALOHA:TS-1271] xref: CALOHA:TS-1271 is_a: CL:0002658 ! glandular cell of the large intestine is_a: CL:1000405 ! epithelial cell of appendix -intersection_of: CL:0000150 ! glandular epithelial cell +intersection_of: CL:0000150 ! glandular secretory epithelial cell intersection_of: part_of UBERON:0001154 ! vermiform appendix -relationship: part_of UBERON:0009697 ! epithelium of appendix [Term] id: CL:1001586 name: mammary gland glandular cell def: "Glandular cell of mammary epithelium. Example: glandular cells of large and intermediate ducts, glandular cells in terminal ducts." [HPA:HPA, NPX:PDR] +subset: human_subset +subset: mouse_subset synonym: "breast glandular cell" RELATED [CALOHA:TS-1272] synonym: "breast glandular cells" RELATED [CALOHA:TS-1272] synonym: "mammary glandular cell" RELATED [CALOHA:TS-1272] xref: CALOHA:TS-1272 -is_a: CL:0000150 ! glandular epithelial cell +is_a: CL:0000150 ! glandular secretory epithelial cell is_a: CL:0000152 ! exocrine cell is_a: CL:0002327 ! mammary gland epithelial cell -intersection_of: CL:0000150 ! glandular epithelial cell +intersection_of: CL:0000150 ! glandular secretory epithelial cell intersection_of: part_of UBERON:0001911 ! mammary gland relationship: part_of UBERON:0003244 ! epithelium of mammary gland [Term] id: CL:1001587 -name: uterine cervix glandular cell +name: uterine cervix secretory cell def: "Glandular cell of uterine cervix epithelium." [NPX:PDR] +subset: human_subset +subset: mouse_subset synonym: "cervix glandular cell" RELATED [CALOHA:TS-1273] synonym: "cervix, uterine glandular cell" RELATED [CALOHA:TS-1273] synonym: "cervix, uterine glandular cells" RELATED [CALOHA:TS-1273] +synonym: "uterine cervix glandular cell" RELATED [] xref: CALOHA:TS-1273 is_a: CL:0002535 ! epithelial cell of cervix -is_a: CL:1001591 ! oviduct glandular cell -intersection_of: CL:0000150 ! glandular epithelial cell +is_a: CL:1001591 ! oviduct secretory cell +intersection_of: CL:1100001 ! secretory epithelial cell intersection_of: part_of UBERON:0000002 ! uterine cervix [Term] id: CL:1001588 name: colon glandular cell def: "Glandular cell of colon epithelium. Example: Goblet cells; enterocytes or absorptive cells; enteroendocrine and M cells." [NPX:PDR] +subset: human_subset +subset: mouse_subset synonym: "colon glandular cells" RELATED [CALOHA:TS-1274] xref: CALOHA:TS-1274 is_a: CL:0002658 ! glandular cell of the large intestine is_a: CL:0011108 ! colon epithelial cell -intersection_of: CL:0000150 ! glandular epithelial cell +intersection_of: CL:0000150 ! glandular secretory epithelial cell intersection_of: part_of UBERON:0001155 ! colon [Term] id: CL:1001589 -name: duodenum glandular cell +name: duodenum secretory cell def: "Glandular cell of duodenal epithelium. Example: Enterocytes, Goblet cells, enteroendocrine cells; Paneth cells; M cells; Brunner's gland cell." [NPX:PDR] subset: cellxgene_subset -synonym: "duodenum glandular cells" RELATED [CALOHA:TS-1275] +subset: human_subset +subset: mouse_subset +synonym: "duodenum glandular cells" NARROW [CALOHA:TS-1275] xref: CALOHA:TS-1275 -is_a: CL:1001598 ! small intestine glandular cell -intersection_of: CL:0000150 ! glandular epithelial cell +is_a: CL:1001598 ! small intestine secretory cell +intersection_of: CL:1100001 ! secretory epithelial cell intersection_of: part_of UBERON:0002114 ! duodenum relationship: part_of UBERON:0008346 ! duodenal epithelium [Term] id: CL:1001590 -name: epididymis glandular cell +name: epididymis secretory cell def: "Glandular cell of epididymal epithelium." [NPX:PDR] +subset: human_subset +subset: mouse_subset synonym: "epididymal glandular cell" RELATED [CALOHA:TS-1276] -synonym: "epididymis glandular cells" RELATED [CALOHA:TS-1276] +synonym: "epididymis glandular cell" RELATED [CALOHA:TS-1276] xref: CALOHA:TS-1276 is_a: CL:0000068 ! duct epithelial cell -is_a: CL:0000150 ! glandular epithelial cell -intersection_of: CL:0000150 ! glandular epithelial cell +is_a: CL:1100001 ! secretory epithelial cell +intersection_of: CL:1100001 ! secretory epithelial cell intersection_of: part_of UBERON:0001301 ! epididymis relationship: part_of UBERON:0004544 ! epididymis epithelium [Term] id: CL:1001591 -name: oviduct glandular cell +name: oviduct secretory cell def: "Glandular cell of oviduct epithelium. Example: peg cells, ciliated cells." [HPA:HPA, NPX:PDR] +subset: human_subset +subset: mouse_subset synonym: "fallopian tube glandular cell" RELATED [CALOHA:TS-1277] synonym: "fallopian tube glandular cells" RELATED [CALOHA:TS-1277] +synonym: "oviduct glandular cell" RELATED [] synonym: "uterine tube glandular cell" RELATED [CALOHA:TS-1277] xref: CALOHA:TS-1277 -is_a: CL:0000150 ! glandular epithelial cell -intersection_of: CL:0000150 ! glandular epithelial cell +is_a: CL:1100001 ! secretory epithelial cell +intersection_of: CL:1100001 ! secretory epithelial cell intersection_of: part_of UBERON:0000993 ! oviduct relationship: part_of UBERON:0004804 ! oviduct epithelium @@ -32507,37 +37114,43 @@ relationship: part_of UBERON:0004804 ! oviduct epithelium id: CL:1001592 name: gallbladder glandular cell def: "Glandular cell of gallbladder epithelium." [NPX:PDR] +subset: human_subset +subset: mouse_subset synonym: "gall bladder glandular cell" EXACT [FMA:7202] synonym: "gall bladder glandular cells" RELATED [CALOHA:TS-1278] synonym: "gallbladder glandular cells" RELATED [CALOHA:TS-1278] xref: CALOHA:TS-1278 -is_a: CL:0000150 ! glandular epithelial cell +is_a: CL:0000150 ! glandular secretory epithelial cell is_a: CL:1000415 ! epithelial cell of gallbladder -intersection_of: CL:0000150 ! glandular epithelial cell +intersection_of: CL:0000150 ! glandular secretory epithelial cell intersection_of: part_of UBERON:0002110 ! gallbladder relationship: part_of UBERON:0002029 ! epithelium of gall bladder [Term] id: CL:1001593 name: parathyroid glandular cell -def: "Glandular cell of parathyroid epithelium. Example: Parathyroid chief cell and parathyroid oxyphil cells." [HPA:HPA, NPX:PDR] +def: "Glandular (secretory) cell of parathyroid epithelium." [HPA:HPA, NPX:PDR] +subset: human_subset +subset: mouse_subset synonym: "parathyroid gland glandular cell" RELATED [CALOHA:TS-1279] synonym: "parathyroid gland glandular cells" RELATED [CALOHA:TS-1279] xref: CALOHA:TS-1279 -is_a: CL:0000150 ! glandular epithelial cell -intersection_of: CL:0000150 ! glandular epithelial cell +is_a: CL:0000150 ! glandular secretory epithelial cell +is_a: CL:0002260 ! epithelial cell of parathyroid gland +intersection_of: CL:0000150 ! glandular secretory epithelial cell intersection_of: part_of UBERON:0001132 ! parathyroid gland -relationship: part_of UBERON:0011197 ! parathyroid epithelium [Term] id: CL:1001595 name: rectum glandular cell def: "Glandular cell of rectal epithelium. Example: Goblet cell; enterocytes or absorptive cells; enteroendocrine and M cells." [NPX:PDR] +subset: human_subset +subset: mouse_subset synonym: "rectal glandular cell" RELATED [CALOHA:TS-1281] synonym: "rectum glandular cells" RELATED [CALOHA:TS-1281] xref: CALOHA:TS-1281 is_a: CL:0002658 ! glandular cell of the large intestine -intersection_of: CL:0000150 ! glandular epithelial cell +intersection_of: CL:0000150 ! glandular secretory epithelial cell intersection_of: part_of UBERON:0001052 ! rectum relationship: part_of UBERON:0003354 ! epithelium of rectum @@ -32545,13 +37158,15 @@ relationship: part_of UBERON:0003354 ! epithelium of rectum id: CL:1001596 name: salivary gland glandular cell def: "Glandular cell of salivary gland. Example: Serous cells, mucous cells, cuboidal epithelial cells of the intercalated ducts, simple cuboidal epithelium of the striated ducts, epithelial cells of excretory ducts." [HPA:HPA, NPX:PDR] +subset: human_subset +subset: mouse_subset synonym: "salivary gland glandular cells" RELATED [CALOHA:TS-1282] xref: CALOHA:TS-1282 -is_a: CL:0000150 ! glandular epithelial cell +is_a: CL:0000150 ! glandular secretory epithelial cell is_a: CL:0000152 ! exocrine cell is_a: CL:0002251 ! epithelial cell of alimentary canal is_a: CL:0009005 ! salivary gland cell -intersection_of: CL:0000150 ! glandular epithelial cell +intersection_of: CL:0000150 ! glandular secretory epithelial cell intersection_of: part_of UBERON:0001044 ! saliva-secreting gland relationship: part_of UBERON:0004809 ! salivary gland epithelium @@ -32560,28 +37175,32 @@ id: CL:1001597 name: seminal vesicle glandular cell def: "Glandular cell of seminal vesicle epithelium." [NPX:PDR] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "seminal vesicle glandular cells" RELATED [CALOHA:TS-1283] xref: CALOHA:TS-1283 xref: https://cellxgene.cziscience.com/cellguide/CL_1001597 is_a: CL:0000068 ! duct epithelial cell -is_a: CL:0000150 ! glandular epithelial cell -intersection_of: CL:0000150 ! glandular epithelial cell +is_a: CL:0000150 ! glandular secretory epithelial cell +intersection_of: CL:0000150 ! glandular secretory epithelial cell intersection_of: part_of UBERON:0000998 ! seminal vesicle relationship: part_of UBERON:0004805 ! seminal vesicle epithelium -property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional.\n\nSeminal vesicle glandular cells belong to a specialized group of epithelial cells that form the internal lining of the seminal vesicles, a pair of male reproductive organs. These cells are located within the complex tubuloalveolar glands that make up the seminal vesicles and are known for their unique pseudostratified columnar epithelium structure. \nThe primary function of these cells is the secretion of a variety of substances that ultimately constitute around 70% of the fluid volume of semen. Seminal cells produce a high-fructose fluid that serves as an energy source for the spermatozoa and promotes their motility. They also secrete other essential substances like proteins, enzymes, vitamin C, prostaglandins, and various other compounds. Collectively, these substances help in the nourishment, protection, and transportation of the spermatozoa throughout the male reproductive system and during the ejaculation process.\nSecondary to the production of seminal fluid, the seminal vesicle glandular cells also play a role in the contraction of the seminal vesicles during ejaculation. The contraction of these glands, induced by sympathetic nerves, ensures the efficient propulsion of the seminal fluid mixed with spermatozoa into the ejaculatory ducts and subsequently to the urethra. Notably, any malfunction or pathological condition affecting these cells can impact male fertility, emphasizing the importance of understanding the intricate functions of seminal vesicle glandular cells in maintaining the healthy physiological function of male reproduction." xsd:string {xref="DOI:10.1007/978-3-030-32300-4_26", xref="DOI:10.1007/s00265-006-0178-0", xref="DOI:10.1111/j.1439-0272.1992.tb02636.x", xref="https://www.ncbi.nlm.nih.gov/books/NBK499854/", xref="https://www.sciencedirect.com/topics/veterinary-science-and-veterinary-medicine/seminal-vesicle"} +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nSeminal vesicle glandular cells belong to a specialized group of epithelial cells that form the internal lining of the seminal vesicles, a pair of male reproductive organs. These cells are located within the complex tubuloalveolar glands that make up the seminal vesicles and are known for their unique pseudostratified columnar epithelium structure. \nThe primary function of these cells is the secretion of a variety of substances that ultimately constitute around 70% of the fluid volume of semen. Seminal cells produce a high-fructose fluid that serves as an energy source for the spermatozoa and promotes their motility. They also secrete other essential substances like proteins, enzymes, vitamin C, prostaglandins, and various other compounds. Collectively, these substances help in the nourishment, protection, and transportation of the spermatozoa throughout the male reproductive system and during the ejaculation process.\nSecondary to the production of seminal fluid, the seminal vesicle glandular cells also play a role in the contraction of the seminal vesicles during ejaculation. The contraction of these glands, induced by sympathetic nerves, ensures the efficient propulsion of the seminal fluid mixed with spermatozoa into the ejaculatory ducts and subsequently to the urethra. Notably, any malfunction or pathological condition affecting these cells can impact male fertility, emphasizing the importance of understanding the intricate functions of seminal vesicle glandular cells in maintaining the healthy physiological function of male reproduction." xsd:string {xref="DOI:10.1007/978-3-030-32300-4_26", xref="DOI:10.1007/s00265-006-0178-0", xref="DOI:10.1111/j.1439-0272.1992.tb02636.x", xref="https://www.ncbi.nlm.nih.gov/books/NBK499854/", xref="https://www.sciencedirect.com/topics/veterinary-science-and-veterinary-medicine/seminal-vesicle"} [Term] id: CL:1001598 -name: small intestine glandular cell +name: small intestine secretory cell def: "A glandular cell found in the epithelium of the small intestine. Example: Enterocytes, Goblet cells, enteroendocrine cells; Paneth cells; M cells; Somatostatin-secreting Cells (D-cells) ." [NCI_Thesaurus:Small_Intestinal_Glandular_Cell, NPX:PDR] +subset: human_subset +subset: mouse_subset synonym: "small bowel glandular cell" RELATED [CALOHA:TS-1286] -synonym: "small intestinal glandular cell" RELATED [CALOHA:TS-1286] +synonym: "small intestinal glandular cell" NARROW [CALOHA:TS-1286] synonym: "small intestine glandular cells" RELATED [CALOHA:TS-1286] xref: CALOHA:TS-1286 xref: FMA:86928 -is_a: CL:0000150 ! glandular epithelial cell is_a: CL:0002254 ! epithelial cell of small intestine -intersection_of: CL:0000150 ! glandular epithelial cell +is_a: CL:1100001 ! secretory epithelial cell +intersection_of: CL:1100001 ! secretory epithelial cell intersection_of: part_of UBERON:0002108 ! small intestine relationship: part_of UBERON:0001902 ! epithelium of small intestine @@ -32590,14 +37209,16 @@ id: CL:1001599 name: pancreas exocrine glandular cell def: "Glandular cell of exocrine pancreas epithelium. Example: pancreatic acinar cell, glandular cells in pancreatic canaliculi, glandular cells in pancreatic ducts." [HPA:HPA, NPX:PDR] subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "exocrine pancreas glandular cell" RELATED [CALOHA:TS-1242] synonym: "pancreas exocrine glandular cells" RELATED [CALOHA:TS-1242] xref: BTO:0000028 xref: CALOHA:TS-1242 -is_a: CL:0000150 ! glandular epithelial cell +is_a: CL:0000150 ! glandular secretory epithelial cell is_a: CL:0000152 ! exocrine cell is_a: CL:1001433 ! epithelial cell of exocrine pancreas -intersection_of: CL:0000150 ! glandular epithelial cell +intersection_of: CL:0000150 ! glandular secretory epithelial cell intersection_of: part_of UBERON:0000017 ! exocrine pancreas relationship: part_of UBERON:0013697 ! exocrine pancreas epithelium property_value: RO:0002175 NCBITaxon:9606 @@ -32606,12 +37227,14 @@ property_value: RO:0002175 NCBITaxon:9606 id: CL:1001601 name: adrenal gland glandular cell def: "Hormone secreting cell located in the cortex of adrenal gland. Glandular cells in the adrenal cortex secrete mineralocorticoids, glucocorticoids and androgens." [NPX:PDR] +subset: human_subset +subset: mouse_subset synonym: "adrenal gland glandular cells" RELATED [CALOHA:TS-2177] synonym: "adrenal glandular cell" RELATED [CALOHA:TS-2177] synonym: "suprarenal gland glandular cell" RELATED [CALOHA:TS-2177] xref: CALOHA:TS-2177 -is_a: CL:0000150 ! glandular epithelial cell -intersection_of: CL:0000150 ! glandular epithelial cell +is_a: CL:0000150 ! glandular secretory epithelial cell +intersection_of: CL:0000150 ! glandular secretory epithelial cell intersection_of: part_of UBERON:0001235 ! adrenal cortex relationship: part_of UBERON:0001235 ! adrenal cortex @@ -32620,32 +37243,42 @@ id: CL:1001602 name: cerebral cortex endothelial cell def: "A distinct endothelial cell forming the walls of the capillaries within the cerebral cortex." [NPX:PDR] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "cerebral cortex endothelial cells" RELATED [CALOHA:TS-2372] synonym: "endothelial cells of cerebral cortex" RELATED [CALOHA:TS-2372] xref: CALOHA:TS-2372 +xref: https://cellxgene.cziscience.com/cellguide/CL_1001602 is_a: CL:0000115 ! endothelial cell is_a: CL:0002319 ! neural cell intersection_of: CL:0000115 ! endothelial cell intersection_of: part_of UBERON:0000956 ! cerebral cortex relationship: part_of UBERON:0000956 ! cerebral cortex relationship: part_of UBERON:0013694 ! brain endothelium +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nCerebral cortex endothelial cells are unique endothelial cells responsible for the formation and regulation of the blood-brain barrier (BBB), a specialized structure that separates the circulating blood from the cerebral neural tissue. These cells line the inner surface of nearly all blood vessels that irrigate the cerebral cortex, the outermost layer of the brain involved with complex cognitive functions such as thought, perception, and memory formation. Cerebral cortex endothelial cells are integral to maintaining brain health and function due to their role in regulating brain microenvironment and controlling the passage of essential molecules and cells.\nThe endothelial cells in the cerebral cortex are distinctive due to their highly selective permeability, largely attributable to the existence of unique tight junctions which maintain the barrier function of the BBB. The tightly interconnected structures of these cells prevent most substances from freely diffusing into the brain tissue, ensuring that harmful agents such as toxins, pathogens, or peripheral immune cells don't reach the brain and compromise its function. These cells also express multiple transporters and enzymes, allowing the selective entry of necessary nutrients and metabolites while excluding toxic substances.\nCerebral cortex endothelial cells also participate in neurovascular coupling, a process where localized neuronal activity increases cerebral blood flow to satisfy the local metabolic demands. The endothelial cells work in coordination with neurons and other cell types such as astrocytes and pericytes to mediate this process. They have been thought to regulate local blood flow by releasing substances in response to neuronal activity. Additionally, these cells are involved in many pathological conditions. Breakdown or dysfunction of the BBB often marked by altered endothelial cell function is linked to numerous neurological disorders including stroke, multiple sclerosis, Alzheimer’s disease, and brain tumors." xsd:string {xref="DOI:10.1038/nbt.2247", xref="DOI:10.1038/nrn1824", xref="DOI:10.1177/0271678X156179", xref="DOI:10.1186/s12987-020-00230-3", xref="DOI:10.3389/fnins.2023.1047778"} [Term] id: CL:1001603 name: lung macrophage def: "Circulating macrophages and tissue macrophages (alveolar macrophages) of lung." [HPA:HPA, NPX:PDR] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "lung macrophages" RELATED [CALOHA:TS-0576] xref: CALOHA:TS-0576 +xref: https://cellxgene.cziscience.com/cellguide/CL_1001603 is_a: CL:0000235 ! macrophage intersection_of: CL:0000235 ! macrophage intersection_of: part_of UBERON:0002048 ! lung relationship: part_of UBERON:0002048 ! lung +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nLung macrophages refer to macrophage populations in the lungs, including the tissue-resident alveolar macrophages and interstitial macrophages, located in the air spaces and the connective tissue of the lung, respectively, and recruited macrophages. They are important in maintaining tissue homeostasis and immunity.\nThe primary function of lung macrophages is to patrol and maintain the pulmonary system, where they serve as the first line of defense against airborne pathogens and inhaled particles. They perform phagocytosis of pathogens, particulate matter, dead cells, and other cellular debris from the lungs to maintain clear air passages and optimize gas exchange. They may also participate in tissue repair and the resolution of inflammation following injury.\nLung macrophages also play a critical role in immune regulation. They help to initiate an immune response by secreting cytokines and other inflammatory mediators and by presenting antigens from the pathogens they have engulfed to induce T cell responses. However, if activated improperly, lung macrophages can contribute to inflammatory diseases of the lung such as chronic obstructive pulmonary disease (COPD) or asthma." xsd:string {xref="DOI:10.1002/JLB.3RU0720-418R", xref="DOI:10.1016/j.immuni.2022.08.010", xref="DOI:10.1189/jlb.70.2.163", xref="DOI:10.3389/fimmu.2021.753940/full", xref="DOI:10.3390/cells10040897"} [Term] id: CL:1001606 name: foreskin keratinocyte def: "Keratinocyte from foreskin." [NPX:PDR] +subset: human_subset +subset: mouse_subset xref: CALOHA:TS-0385 is_a: CL:0000312 ! keratinocyte intersection_of: CL:0000312 ! keratinocyte @@ -32657,6 +37290,8 @@ id: CL:1001607 name: articular chondrocyte def: "Chondrocyte forming the hyaline cartilage found in joints." [NPX:PDR] subset: human_reference_atlas +subset: human_subset +subset: mouse_subset xref: CALOHA:TS-0056 is_a: CL:0000138 ! chondrocyte intersection_of: CL:0000138 ! chondrocyte @@ -32668,6 +37303,8 @@ property_value: RO:0002175 NCBITaxon:9606 id: CL:1001608 name: foreskin fibroblast def: "Fibroblast from foreskin." [NPX:PDR] +subset: human_subset +subset: mouse_subset synonym: "BJ fibroblast" EXACT [] xref: CALOHA:TS-0384 is_a: CL:0002620 ! skin fibroblast @@ -32679,6 +37316,8 @@ relationship: part_of UBERON:0001332 ! prepuce of penis id: CL:1001609 name: muscle fibroblast def: "Fibroblast from muscle organ." [NPX:PDR] +subset: human_subset +subset: mouse_subset xref: CALOHA:TS-0643 is_a: CL:0000057 ! fibroblast intersection_of: CL:0000057 ! fibroblast @@ -32689,6 +37328,8 @@ relationship: part_of UBERON:0001630 ! muscle organ id: CL:1001610 name: bone marrow hematopoietic cell def: "Hematopoietic cells resident in the bone marrow. Include: hematopoietic stem cells (lymphoid stem cells and myeloid stem cells) and the precursor cells for thrombocytes, erythrocytes, basophils, neutrophils, eosinophils, monocytes and lymphocytes." [NPX:PDR] +subset: human_subset +subset: mouse_subset synonym: "bone marrow hematopoietic cells" RELATED [CALOHA:TS-2109] synonym: "bone marrow poietic cells" RELATED [CALOHA:TS-2109] xref: CALOHA:TS-2109 @@ -32702,6 +37343,8 @@ relationship: part_of UBERON:0012429 ! hematopoietic tissue id: CL:1001611 name: cerebellar neuron def: "Neuron of the cerebellum." [NPX:PDR] +subset: human_subset +subset: mouse_subset synonym: "cerebellum neuron" RELATED [CALOHA:TS-2359] xref: CALOHA:TS-2359 xref: FMA:84665 @@ -32710,11 +37353,26 @@ intersection_of: CL:0000540 ! neuron intersection_of: RO:0002100 UBERON:0002037 ! has soma location cerebellum relationship: RO:0002100 UBERON:0002037 ! has soma location cerebellum +[Term] +id: CL:1100001 +name: secretory epithelial cell +def: "An epithelial cell that is specialised for the synthesis and secretion of specific biomolecules." [https://orcid.org/0000-0002-7073-9172] +subset: human_subset +subset: mouse_subset +is_a: CL:0000066 ! epithelial cell +is_a: CL:0000151 ! secretory cell +intersection_of: CL:0000066 ! epithelial cell +intersection_of: CL:0000151 ! secretory cell +property_value: terms:contributor https://orcid.org/0000-0002-7073-9172 +property_value: terms:date "2024-07-21T09:24:44Z" xsd:dateTime + [Term] id: CL:2000000 name: epidermal melanocyte def: "Any melanocyte that is part of a epidermis." [GOC:TermGenie] comment: These cells are found primarily, but not exclusively, in primates including humans +subset: human_subset +subset: mouse_subset is_a: CL:0002484 ! epithelial melanocyte is_a: CL:1000458 ! melanocyte of skin intersection_of: CL:0000148 ! melanocyte @@ -32728,6 +37386,8 @@ id: CL:2000001 name: peripheral blood mononuclear cell def: "A leukocyte with a single non-segmented nucleus in the mature form found in the circulatory pool of blood." [GOC:TermGenie] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset is_a: CL:0000080 ! circulating cell is_a: CL:0000842 ! mononuclear cell intersection_of: CL:0000842 ! mononuclear cell @@ -32741,15 +37401,20 @@ id: CL:2000002 name: decidual cell def: "A specialized, enlarged, connective tissue cell of the decidua with enlarged nucleus, dense membrane‐bound secretory granules and cytoplasmic accumulation of glycogen and lipid droplets. These cells develop by the transformation of endometrial stromal cells during decidualization." [BTO:0002770, NCIT:C32429, PMID:30013421, PMID:30429548, Wiki:Decidual_cells&oldid=937509751, Wiki:Decidualization&oldid=908981933] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "decidua cell" EXACT [BTO:0002770, NCIT:C32429] synonym: "decidual stromal cell" EXACT [BTO:0005756, PMID:11719592] +synonym: "decidualized endometrial stromal cell" EXACT [PMID:31907034] xref: BTO:0002770 xref: BTO:0005756 +xref: https://cellxgene.cziscience.com/cellguide/CL_2000002 xref: NCIT:C32429 is_a: CL:0000349 ! extraembryonic cell is_a: CL:0000499 ! stromal cell relationship: part_of UBERON:0002450 ! decidua relationship: RO:0002202 CL:0002255 ! develops from stromal cell of endometrium +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nDecidual cells, originating from the endometrial lining in the uterus, undergo significant transformations during pregnancy and are integral to its preparation and maintenance. Their conversion from endometrial fibroblast to a secretory phenotype, known as decidualization, occurs as a normal process in the menstrual cycle or in response to embryo implantation.\nWith crucial roles in regulating maternal immune responses and placental development, decidual cells have a twofold function: preventing rejection of the conceptus by the mother's immune system and guiding placental development to avoid excessive trophoblast invasion leading to pre-eclampsia. During decidualization, these cells secrete proteins and growth factors supporting embryo implantation and sustaining early pregnancy. Furthermore, decidual cells modulate the activities of natural killer cells, macrophages, and T cells in the uterus, maintaining a balance of pro-inflammatory and anti-inflammatory conditions during pregnancy." xsd:string {xref="DOI:10.1002/rmb2.12088", xref="DOI:10.1093/humupd/dmw004", xref="DOI:10.1111/j.1749-6632.2010.05938.x", xref="DOI:10.3390/ijms21114092"} creation_date: 2014-02-20T23:06:41Z [Term] @@ -32757,6 +37422,8 @@ id: CL:2000004 name: pituitary gland cell def: "Any cell that is part of a pituitary gland." [GOC:TermGenie] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset is_a: CL:0002319 ! neural cell intersection_of: CL:0000000 ! cell intersection_of: part_of UBERON:0000007 ! pituitary gland @@ -32768,6 +37435,8 @@ creation_date: 2014-03-26T22:14:56Z id: CL:2000005 name: brain macroglial cell def: "Any macroglial cell that is part of a brain." [GOC:TermGenie] +subset: human_subset +subset: mouse_subset is_a: CL:0000126 ! macroglial cell intersection_of: CL:0000126 ! macroglial cell intersection_of: part_of UBERON:0000955 ! brain @@ -32780,6 +37449,8 @@ id: CL:2000006 name: tonsil germinal center B cell def: "Any germinal center B cell that is part of a tonsil." [GOC:TermGenie] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset is_a: CL:0000844 ! germinal center B cell intersection_of: CL:0000844 ! germinal center B cell intersection_of: part_of UBERON:0002372 ! tonsil @@ -32791,6 +37462,8 @@ creation_date: 2014-03-28T21:35:33Z id: CL:2000007 name: articular chondrocyte of knee joint def: "Chondrocyte forming the hyaline cartilage found in the knee joint." [GOC:TermGenie] +subset: human_subset +subset: mouse_subset is_a: CL:1001607 ! articular chondrocyte intersection_of: CL:1001607 ! articular chondrocyte intersection_of: part_of UBERON:0001485 ! knee joint @@ -32802,6 +37475,9 @@ creation_date: 2014-06-04T14:40:11Z id: CL:2000008 name: microvascular endothelial cell def: "Any blood vessel endothelial cell that is part of a microvascular endothelium." [GOC:TermGenie] +subset: cellxgene_subset +subset: human_subset +subset: mouse_subset is_a: CL:0000071 ! blood vessel endothelial cell intersection_of: CL:0000071 ! blood vessel endothelial cell intersection_of: part_of UBERON:0008339 ! microvascular endothelium @@ -32822,6 +37498,8 @@ creation_date: 2014-06-04T15:09:18Z id: CL:2000010 name: dermis blood vessel endothelial cell def: "Any blood vessel endothelial cell that is part of a dermis." [GOC:TermGenie] +subset: human_subset +subset: mouse_subset is_a: CL:0000071 ! blood vessel endothelial cell intersection_of: CL:0000071 ! blood vessel endothelial cell intersection_of: part_of UBERON:0002067 ! dermis @@ -32833,17 +37511,23 @@ creation_date: 2014-06-04T15:12:06Z id: CL:2000011 name: dermis lymphatic vessel endothelial cell def: "Any endothelial cell of lymphatic vessel that is part of a dermis." [GOC:TermGenie] +subset: human_subset +subset: mouse_subset +xref: https://cellxgene.cziscience.com/cellguide/CL_2000011 is_a: CL:0002138 ! endothelial cell of lymphatic vessel intersection_of: CL:0002138 ! endothelial cell of lymphatic vessel intersection_of: part_of UBERON:0002067 ! dermis relationship: part_of UBERON:0002067 ! dermis property_value: terms:contributor http://www.wikidata.org/entity/Q35563349 +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nA dermis lymphatic vessel endothelial cell is a specialized type of cell that lines the interior surface of lymphatic vessels present in the dermal layer of the skin. These cells are organized into a single layer, forming an integral part of the lymphatic system which acts as the body's secondary circulatory system. The primary function of dermis lymphatic vessel endothelial cells is to facilitate the transportation and regulation of the lymph fluid within the dermis. They act as a barrier, contributing to fluid homeostasis, lipid transport, and immune cell trafficking. These cells are uniquely equipped to let fluid and larger molecules, including proteins and immune cells, into the lymphatic vessels from the surrounding interstitial space. This is enabled by the specialized junctions between the endothelial cells and the presence of primary lymphatic valves that prevent the backflow of lymph.\nAnother paramount role of dermis lymphatic vessel endothelial cells is their involvement in immune response. By interacting with white blood cells, especially T-cells and dendritic cells, they can mediate local immune surveillance and contribute to both innate and adaptive immune responses. These cells are also implicated in a variety of pathological conditions, including lymphedema and metastasis in cancer." xsd:string {xref="DOI:10.1038/s41423-023-01042-9", xref="DOI:10.1038/s41467-019-14127-9", xref="DOI:10.3389/fimmu.2023.1235812", xref="DOI:10.3389/fphys.2020.00509", xref="DOI:10.3389/fphys.2020.577584"} creation_date: 2014-06-04T15:15:08Z [Term] id: CL:2000012 name: fibroblast of pedal digit skin def: "Any skin fibroblast that is part of a pedal digit skin." [GOC:TermGenie] +subset: human_subset +subset: mouse_subset is_a: CL:0002620 ! skin fibroblast intersection_of: CL:0002620 ! skin fibroblast intersection_of: part_of UBERON:0003530 ! pedal digit skin @@ -32855,6 +37539,8 @@ creation_date: 2014-06-04T15:16:44Z id: CL:2000013 name: fibroblast of skin of abdomen def: "Any skin fibroblast that is part of a skin of abdomen." [GOC:TermGenie] +subset: human_subset +subset: mouse_subset is_a: CL:0002620 ! skin fibroblast intersection_of: CL:0002620 ! skin fibroblast intersection_of: part_of UBERON:0001416 ! skin of abdomen @@ -32866,6 +37552,8 @@ creation_date: 2014-06-04T15:18:16Z id: CL:2000014 name: fibroblast of upper leg skin def: "Any skin fibroblast that is part of a upper leg skin." [GOC:TermGenie] +subset: human_subset +subset: mouse_subset is_a: CL:0002620 ! skin fibroblast intersection_of: CL:0002620 ! skin fibroblast intersection_of: part_of UBERON:0004262 ! upper leg skin @@ -32877,6 +37565,8 @@ creation_date: 2014-06-04T15:19:44Z id: CL:2000015 name: fibroblast of arm def: "Any skin fibroblast that is part of a arm." [GOC:TermGenie] +subset: human_subset +subset: mouse_subset is_a: CL:0002620 ! skin fibroblast intersection_of: CL:0002620 ! skin fibroblast intersection_of: part_of UBERON:0001460 ! arm @@ -32889,6 +37579,8 @@ id: CL:2000016 name: lung microvascular endothelial cell def: "Any lung endothelial cell that is part of a microvascular endothelium." [GOC:TermGenie] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset is_a: CL:1001567 ! lung endothelial cell is_a: CL:2000008 ! microvascular endothelial cell intersection_of: CL:1001567 ! lung endothelial cell @@ -32900,6 +37592,8 @@ creation_date: 2014-06-04T16:00:56Z id: CL:2000017 name: fibroblast of peridontal ligament def: "Any fibroblast that is part of a periodontal ligament." [GOC:TermGenie] +subset: human_subset +subset: mouse_subset is_a: CL:0002556 ! fibroblast of periodontium intersection_of: CL:0000057 ! fibroblast intersection_of: part_of UBERON:0008266 ! periodontal ligament @@ -32912,6 +37606,8 @@ id: CL:2000018 name: endothelial cell of coronary artery def: "Any endothelial cell of artery that is part of a coronary artery." [GOC:TermGenie] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset is_a: CL:0010006 ! cardiac blood vessel endothelial cell is_a: CL:1000413 ! endothelial cell of artery intersection_of: CL:1000413 ! endothelial cell of artery @@ -32936,6 +37632,8 @@ creation_date: 2014-06-24T23:16:45Z id: CL:2000020 name: inner cell mass cell def: "Any native cell that is part of a inner cell mass." [GOC:TermGenie] +subset: human_subset +subset: mouse_subset is_a: CL:0000255 ! eukaryotic cell intersection_of: CL:0000000 ! cell intersection_of: part_of UBERON:0000087 ! inner cell mass @@ -32948,17 +37646,23 @@ id: CL:2000021 name: sebaceous gland cell def: "Any native cell that is part of a sebaceous gland." [GOC:TermGenie] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset +xref: https://cellxgene.cziscience.com/cellguide/CL_2000021 is_a: CL:0000255 ! eukaryotic cell intersection_of: CL:0000000 ! cell intersection_of: part_of UBERON:0001821 ! sebaceous gland relationship: part_of UBERON:0001821 ! sebaceous gland property_value: terms:contributor http://www.wikidata.org/entity/Q35563349 +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nSebaceous gland cells, also known as sebocytes, are small, oil-producing glands present in the skin of mammals. These specialized cells are predominantly located in the dermis, particularly on the face, scalp, and upper body. \nThe primary function of sebaceous gland cells is the production and secretion of sebum, a complex mixture of lipids including triglycerides, wax esters, squalene, and metabolites of fat-soluble vitamins (such as vitamin E), as well as free fatty acids. The production process involves a unique form of programmed cell death called holocrine secretion. In this process, as sebaceous gland cells mature, they progressively accumulate lipid droplets, before ultimately disintegrating and releasing their lipid-rich contents into the gland's ductal system. \nThe sebum generated by these cells serves multiple purposes. It acts as a waterproofing agent, preventing excessive wetting or drying of the skin and averaging skin's water-holding capacity. Sebum also has antimicrobial properties, providing a natural defense barrier against certain bacterial and fungal species. Additionally, it contributes to the skin’s suppleness and prevents it from becoming brittle. An overproduction or imbalance of sebaceous gland cells can lead to common skin disorders, such as acne, seborrhea, or rosacea, illustrating their importance in skin health." xsd:string {xref="DOI:10.1016/j.jid.2016.10.017", xref="DOI:10.1080/19381980.2017.1375636", xref="DOI:10.4161/derm.1.2.8472", xref="https://doi.org/10.2147/CLEP.S323744", xref="https://www.sciencedirect.com/topics/agricultural-and-biological-sciences/sebum"} creation_date: 2014-06-24T23:17:00Z [Term] id: CL:2000022 name: cardiac septum cell def: "Any native cell that is part of a cardiac septum." [GOC:TermGenie] +subset: human_subset +subset: mouse_subset is_a: CL:0002494 ! cardiocyte intersection_of: CL:0000000 ! cell intersection_of: part_of UBERON:0002099 ! cardiac septum @@ -32970,6 +37674,8 @@ creation_date: 2014-06-24T23:17:07Z id: CL:2000023 name: spinal cord ventral column interneuron def: "Any interneuron that is part of a spinal cord ventral column." [GOC:TermGenie] +subset: human_subset +subset: mouse_subset is_a: CL:0005000 ! spinal cord interneuron intersection_of: CL:0000099 ! interneuron intersection_of: RO:0002100 UBERON:0005375 ! has soma location spinal cord ventral column @@ -32981,6 +37687,8 @@ creation_date: 2014-06-25T00:23:36Z id: CL:2000024 name: spinal cord medial motor column neuron def: "Any neuron that is part of a spinal cord medial motor column." [GOC:TermGenie] +subset: human_subset +subset: mouse_subset is_a: CL:2000029 ! central nervous system neuron intersection_of: CL:0000540 ! neuron intersection_of: RO:0002100 UBERON:0004059 ! has soma location spinal cord medial motor column @@ -32992,6 +37700,8 @@ creation_date: 2014-06-25T00:23:43Z id: CL:2000025 name: spinal cord oligodendrocyte def: "Any oligodendrocyte that is part of a spinal cord." [GOC:TermGenie] +subset: human_subset +subset: mouse_subset is_a: CL:0000128 ! oligodendrocyte intersection_of: CL:0000128 ! oligodendrocyte intersection_of: part_of UBERON:0002240 ! spinal cord @@ -33011,8 +37721,9 @@ creation_date: 2014-06-25T00:23:57Z id: CL:2000027 name: cerebellum basket cell def: "Any basket cell that is part of a cerebellum." [GOC:TermGenie] +subset: human_subset +subset: mouse_subset is_a: CL:0000118 ! basket cell -is_a: CL:0000402 ! CNS interneuron is_a: CL:1001611 ! cerebellar neuron intersection_of: CL:0000118 ! basket cell intersection_of: RO:0002100 UBERON:0002037 ! has soma location cerebellum @@ -33023,6 +37734,8 @@ creation_date: 2014-06-25T00:24:03Z id: CL:2000028 name: cerebellum glutamatergic neuron def: "Any glutamatergic neuron that is part of a cerebellum." [GOC:TermGenie] +subset: human_subset +subset: mouse_subset is_a: CL:0000679 ! glutamatergic neuron is_a: CL:1001611 ! cerebellar neuron intersection_of: CL:0000679 ! glutamatergic neuron @@ -33034,6 +37747,8 @@ creation_date: 2014-06-25T00:24:10Z id: CL:2000029 name: central nervous system neuron def: "Any neuron that is part of a central nervous system." [GOC:TermGenie] +subset: human_subset +subset: mouse_subset is_a: CL:0000540 ! neuron intersection_of: CL:0000540 ! neuron intersection_of: RO:0002100 UBERON:0001017 ! has soma location central nervous system @@ -33045,6 +37760,9 @@ creation_date: 2014-06-25T01:17:43Z id: CL:2000030 name: hypothalamus cell def: "Any native cell that is part of a hypothalamus." [GOC:TermGenie] +subset: cellxgene_subset +subset: human_subset +subset: mouse_subset is_a: CL:0002319 ! neural cell intersection_of: CL:0000000 ! cell intersection_of: part_of UBERON:0001898 ! hypothalamus @@ -33056,10 +37774,12 @@ creation_date: 2014-06-25T01:17:50Z id: CL:2000031 name: lateral line ganglion neuron def: "Any neuron that is part of a lateral line ganglion." [GOC:TermGenie] -is_a: CL:0000540 ! neuron -intersection_of: CL:0000540 ! neuron +is_a: BFO:0000002 +is_a: CL:2000032 ! peripheral nervous system neuron +intersection_of: CL:2000032 ! peripheral nervous system neuron intersection_of: RO:0002100 UBERON:2000120 ! has soma location lateral line ganglion relationship: RO:0002100 UBERON:2000120 ! has soma location lateral line ganglion +relationship: RO:0002162 NCBITaxon:32443 ! in taxon Teleostei property_value: terms:contributor http://www.wikidata.org/entity/Q35563349 creation_date: 2014-06-25T01:17:57Z @@ -33070,6 +37790,8 @@ alt_id: CL:0000111 def: "A neuron that is part of a peripheral nervous system." [GOC:TermGenie, ISBN:0721662544] subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "peripheral neuron" EXACT [] synonym: "PNS neuron" EXACT [] xref: FMA:84664 @@ -33085,6 +37807,8 @@ creation_date: 2014-06-25T02:28:17Z id: CL:2000033 name: limb basal cell of epidermis def: "Any basal cell of epidermis that is part of a limb." [GOC:TermGenie] +subset: human_subset +subset: mouse_subset is_a: CL:0002187 ! basal cell of epidermis intersection_of: CL:0002187 ! basal cell of epidermis intersection_of: part_of UBERON:0002101 ! limb @@ -33165,6 +37889,8 @@ id: CL:2000040 name: bladder microvascular endothelial cell def: "Any microvascular endothelial cell that is part of a urinary bladder." [GOC:TermGenie] subset: human_reference_atlas +subset: human_subset +subset: mouse_subset is_a: CL:1001319 ! bladder cell is_a: CL:2000008 ! microvascular endothelial cell intersection_of: CL:2000008 ! microvascular endothelial cell @@ -33178,6 +37904,8 @@ id: CL:2000041 name: dermis microvascular lymphatic vessel endothelial cell def: "Any dermis lymphatic vessel endothelial cell that is part of a microvascular endothelium." [GOC:TermGenie] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset is_a: CL:0011030 ! dermal microvascular endothelial cell is_a: CL:2000011 ! dermis lymphatic vessel endothelial cell intersection_of: CL:2000011 ! dermis lymphatic vessel endothelial cell @@ -33190,6 +37918,8 @@ id: CL:2000042 name: embryonic fibroblast def: "Any fibroblast that is part of a embryo." [GOC:TermGenie] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset is_a: CL:0000057 ! fibroblast intersection_of: CL:0000057 ! fibroblast intersection_of: part_of UBERON:0000922 ! embryo @@ -33202,6 +37932,8 @@ id: CL:2000043 name: brain pericyte def: "Any pericyte cell that is part of a brain." [GOC:TermGenie] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset is_a: CL:0002575 ! central nervous system pericyte intersection_of: CL:0000669 ! pericyte intersection_of: part_of UBERON:0000955 ! brain @@ -33213,6 +37945,8 @@ creation_date: 2014-07-09T00:18:22Z id: CL:2000044 name: brain microvascular endothelial cell def: "Any microvascular endothelial cell that is part of a brain." [GOC:TermGenie] +subset: human_subset +subset: mouse_subset is_a: CL:0002319 ! neural cell is_a: CL:2000008 ! microvascular endothelial cell intersection_of: CL:2000008 ! microvascular endothelial cell @@ -33225,6 +37959,8 @@ creation_date: 2014-07-09T00:24:53Z id: CL:2000045 name: foreskin melanocyte def: "Any melanocyte of skin that is part of a skin of prepuce of penis." [GOC:TermGenie] +subset: human_subset +subset: mouse_subset synonym: "melanocyte of foreskin" EXACT [] is_a: CL:1000458 ! melanocyte of skin intersection_of: CL:1000458 ! melanocyte of skin @@ -33239,17 +37975,24 @@ id: CL:2000046 name: ventricular cardiac muscle cell def: "Any cardiac muscle cell that is part of a cardiac ventricle." [GOC:TermGenie] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset +xref: https://cellxgene.cziscience.com/cellguide/CL_2000046 is_a: CL:0000746 ! cardiac muscle cell intersection_of: CL:0000746 ! cardiac muscle cell intersection_of: part_of UBERON:0002082 ! cardiac ventricle relationship: part_of UBERON:0002082 ! cardiac ventricle property_value: terms:contributor http://www.wikidata.org/entity/Q35563349 +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nVentricular cardiac muscle cells, or cardiomyocytes, are specialized cells found in the ventricular walls of the heart. They exhibit unique features, including centrally located nuclei, robust cytoskeletal structures, high mitochondria content, and intercalated discs, which contribute to their efficient pumping of blood throughout the body. \nThe main role of ventricular cardiac muscle cells is to coordinate contractions, enabling the heart to pump blood throughout the body. This is achieved through controlled ion movement across cell membranes, generating rhythmic electrical signals called action potentials. Intercalated discs between these cells aid synchronized contractions by allowing efficient signal spread through gap junctions. The high mitochondrial content ensures a constant energy supply for this ongoing contraction cycle.\nVentricular cardiac muscle cells contribute not only mechanically but also biochemically by secreting essential hormones like atrial natriuretic peptide and B-type natriuretic peptide for blood pressure regulation and cardiac remodeling. These cells exhibit low turnover under normal conditions, emphasizing their long-term stability, yet have limited regenerative capacity following cardiac injuries. Dysfunction in these cells can result in significant cardiac issues, including heart failure." xsd:string {xref="DOI:10.1016/j.peptides.2018.05.012", xref="DOI:10.1126/science.aam5894", xref="https://www.ncbi.nlm.nih.gov/books/NBK535355", xref="https://www.ncbi.nlm.nih.gov/books/NBK572070/"} creation_date: 2014-08-12T20:50:28Z [Term] id: CL:2000047 name: brainstem motor neuron def: "Any motor neuron that is part of a brainstem." [GOC:TermGenie] +subset: cellxgene_subset +subset: human_subset +subset: mouse_subset is_a: CL:0000100 ! motor neuron is_a: CL:2000029 ! central nervous system neuron intersection_of: CL:0000100 ! motor neuron @@ -33263,12 +38006,14 @@ id: CL:2000048 name: anterior horn motor neuron def: "A lower motor neuron whose soma is located in the anterior horn. Anterior horn motor neurons project from the anterior portion of the grey matter in the spinal cord to some skeletal muscles." [DOI:10.1016/B978-0-12-817962-8.00025-1] comment: Yang & Connolly (DOI:10.1016/B978-0-323-37101-8.00140-5) classify these as alpha motor neurons. Consider reflecting this if more references support this. +subset: human_subset +subset: mouse_subset synonym: "anterior horn cell" EXACT [] synonym: "ventral horn of spinal cord spinal cord motor neuron" EXACT [] xref: NCIT:C12645 +is_a: CL:0002612 ! neuron of the ventral spinal cord is_a: CL:0008039 ! lower motor neuron is_a: CL:0011001 ! spinal cord motor neuron -relationship: RO:0002100 UBERON:0002257 ! has soma location ventral horn of spinal cord property_value: terms:contributor http://www.wikidata.org/entity/Q35563349 creation_date: 2014-10-03T00:26:27Z @@ -33277,6 +38022,8 @@ id: CL:2000049 name: primary motor cortex pyramidal cell def: "Any pyramidal cell that is part of a primary motor cortex." [GOC:TermGenie] comment: http://www.ncbi.nlm.nih.gov/pubmed/12524689 +subset: human_subset +subset: mouse_subset is_a: CL:4023111 ! cerebral cortex pyramidal neuron intersection_of: CL:0000598 ! pyramidal neuron intersection_of: RO:0002100 UBERON:0001384 ! has soma location primary motor cortex @@ -33297,6 +38044,8 @@ creation_date: 2014-10-06T17:43:59Z id: CL:2000051 name: splenic fibroblast def: "Any fibroblast that is part of a spleen." [GOC:TermGenie] +subset: human_subset +subset: mouse_subset is_a: CL:0000057 ! fibroblast intersection_of: CL:0000057 ! fibroblast intersection_of: part_of UBERON:0002106 ! spleen @@ -33309,6 +38058,8 @@ id: CL:2000052 name: umbilical artery endothelial cell def: "Any endothelial cell of artery that is part of a umbilical cord." [GOC:TermGenie] comment: http://www.sciencellonline.com/site/productInformation.php?keyword=8010 +subset: human_subset +subset: mouse_subset is_a: CL:0000349 ! extraembryonic cell is_a: CL:1000413 ! endothelial cell of artery intersection_of: CL:1000413 ! endothelial cell of artery @@ -33323,6 +38074,8 @@ name: splenic endothelial cell def: "Any endothelial cell that is part of a spleen." [GOC:TermGenie] comment: http://www.sciencellonline.com/site/productInformation.php?keyword=5500 subset: human_reference_atlas +subset: human_subset +subset: mouse_subset is_a: CL:0000115 ! endothelial cell intersection_of: CL:0000115 ! endothelial cell intersection_of: part_of UBERON:0002106 ! spleen @@ -33336,9 +38089,11 @@ id: CL:2000054 name: hepatic pit cell def: "A large, granular, liver specific natural killer cell that adheres to the endothelial cells of the hepatic sinusoid." [GOC:dos, PMID:9408963] comment: Pit cells are named for the presence of large cytoplasmic granules that resemble pits (pips) of fruit. +subset: cellxgene_subset subset: human_reference_atlas -is_a: CL:0000623 ! natural killer cell -relationship: RO:0001025 UBERON:0001281 ! located in hepatic sinusoid +subset: human_subset +subset: mouse_subset +is_a: CL:4047101 ! liver-resident natural killer cell property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -33347,6 +38102,8 @@ name: liver dendritic cell def: "Any dendritic cell that is part of a liver." [GOC:TermGenie] comment: http://www.jleukbio.org/content/66/2/322.abstract subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "hepatic dendritic cell" EXACT [] is_a: CL:0000451 ! dendritic cell intersection_of: CL:0000451 ! dendritic cell @@ -33359,6 +38116,8 @@ creation_date: 2014-10-06T19:16:11Z id: CL:2000056 name: Meynert cell def: "Any pyramidal cell that is part of a regional part of cerebral cortex." [GOC:TermGenie] +subset: human_subset +subset: mouse_subset is_a: CL:2000049 ! primary motor cortex pyramidal cell property_value: terms:contributor http://www.wikidata.org/entity/Q35563349 creation_date: 2014-10-06T19:20:41Z @@ -33368,6 +38127,8 @@ id: CL:2000057 name: femural osteoblast def: "Any osteoblast that is part of a femur." [GOC:TermGenie] comment: http://www.sciencellonline.com/site/productInformation.php?keyword=4610 +subset: human_subset +subset: mouse_subset is_a: CL:0000062 ! osteoblast is_a: CL:0001035 ! bone cell intersection_of: CL:0000062 ! osteoblast @@ -33381,6 +38142,8 @@ id: CL:2000058 name: calvarial osteoblast def: "Any osteoblast that is part of a skull." [GOC:TermGenie] comment: http://www.sciencellonline.com/site/productInformation.php?keyword=4600 +subset: human_subset +subset: mouse_subset is_a: CL:0000062 ! osteoblast intersection_of: CL:0000062 ! osteoblast intersection_of: part_of UBERON:0003129 ! skull @@ -33394,6 +38157,8 @@ name: prostate gland microvascular endothelial cell def: "Any microvascular endothelial cell that is part of a prostate gland." [GOC:TermGenie] comment: http://www.sciencellonline.com/site/productInformation.php?keyword=4400 subset: cellxgene_subset +subset: human_subset +subset: mouse_subset is_a: CL:2000008 ! microvascular endothelial cell intersection_of: CL:2000008 ! microvascular endothelial cell intersection_of: part_of UBERON:0002367 ! prostate gland @@ -33407,16 +38172,19 @@ name: placental villous trophoblast def: "A trophoblast of placental villi. These cells fuse to form synctial trophoplast - the placental side of the interface between the placenta and maternal blood sinusoids in the decidua." [PMID:31049600] comment: Same as synctial trophoblast? subset: cellxgene_subset +subset: mouse_subset synonym: "vCTB" EXACT [PMID:31049600] synonym: "villous cytotrophoblast" EXACT [] xref: BTO:0006119 xref: BTO:0006208 +xref: https://cellxgene.cziscience.com/cellguide/CL_2000060 is_a: CL:0000351 ! trophoblast cell intersection_of: CL:0000351 ! trophoblast cell intersection_of: part_of UBERON:0010005 ! placental labyrinth villous relationship: part_of UBERON:0010005 ! placental labyrinth villous property_value: seeAlso "http://www.sciencellonline.com/site/productInformation.php?keyword=7120" xsd:string property_value: terms:contributor http://www.wikidata.org/entity/Q35563349 +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nThe placental villous trophoblast, a highly specialized cell type crucial for placental development, plays a key role in facilitating exchanges between the maternal bloodstream and the developing fetus.\nStructurally, placental villous trophoblasts are situated on the villous tree structures, forming an outer epithelial layer. Comprising two subtypes—proliferating cytotrophoblasts forming the inner layer and terminally differentiated syncytiotrophoblasts constituting the outer layer in contact with maternal blood—these cells define the placental architecture.\nFunctionally, placental villous trophoblasts play pivotal roles in forming and maintaining the placenta, ensuring the safe development of the fetus. Their primary function involves managing substance exchange between the mother and fetus, mediating the transfer of gases, nutrients, hormones, and waste materials to support optimal fetal growth. Additionally, these trophoblasts synthesize and release crucial hormones like human chorionic gonadotropin (hCG), which maintains the decidua and signals the mother's body to sustain pregnancy. Acting as a physical and immunological barrier, they protect the fetus from maternal immune cells and prevent the transmission of pathogens, contributing significantly to the success of pregnancy." xsd:string {xref="DOI:10.1007/s00018-019-03104-6", xref="DOI:10.3389/fimmu.2020.00343", xref="DOI:10.3390/nu15163564"} creation_date: 2014-10-07T17:48:27Z [Term] @@ -33425,6 +38193,8 @@ name: placental amniotic mesenchymal stromal cell def: "Any mesenchymal stem cell that is part of a placenta." [GOC:TermGenie] comment: http://www.sciencellonline.com/site/productInformation.php?keyword=7140 subset: human_reference_atlas +subset: human_subset +subset: mouse_subset is_a: CL:0000134 ! mesenchymal stem cell intersection_of: CL:0000134 ! mesenchymal stem cell intersection_of: part_of UBERON:0001987 ! placenta @@ -33439,6 +38209,8 @@ name: placental villus capillary endothelial cell def: "Any capillary endothelial cell that is part of a placenta." [GOC:TermGenie] comment: http://www.ncbi.nlm.nih.gov/books/NBK53245/ subset: human_reference_atlas +subset: human_subset +subset: mouse_subset is_a: CL:0002144 ! capillary endothelial cell is_a: CL:0009092 ! endothelial cell of placenta intersection_of: CL:0002144 ! capillary endothelial cell @@ -33452,10 +38224,12 @@ id: CL:2000063 name: ovarian fibroblast def: "Any fibroblast that is part of a female gonad." [GOC:TermGenie] comment: http://www.sciencellonline.com/site/productInformation.php?keyword=7330 +subset: human_subset +subset: mouse_subset is_a: CL:0000057 ! fibroblast +is_a: CL:0002132 ! stromal cell of ovary intersection_of: CL:0000057 ! fibroblast intersection_of: part_of UBERON:0000992 ! ovary -relationship: part_of UBERON:0000992 ! ovary property_value: terms:contributor http://www.wikidata.org/entity/Q35563349 creation_date: 2014-10-07T17:57:42Z @@ -33465,6 +38239,8 @@ name: ovarian surface epithelial cell def: "Any epithelial cell that is part of a female gonad." [GOC:TermGenie] comment: http://www.sciencellonline.com/site/productInformation.php?keyword=7310 subset: cellxgene_subset +subset: human_subset +subset: mouse_subset is_a: CL:0000066 ! epithelial cell intersection_of: CL:0000066 ! epithelial cell intersection_of: part_of UBERON:0000992 ! ovary @@ -33477,6 +38253,8 @@ id: CL:2000065 name: ovarian microvascular endothelial cell def: "Any microvascular endothelial cell that is part of a female urethra." [GOC:TermGenie] comment: http://www.sciencellonline.com/site/productInformation.php?keyword=7300 +subset: human_subset +subset: mouse_subset is_a: CL:1001320 ! urethra cell is_a: CL:2000008 ! microvascular endothelial cell intersection_of: CL:2000008 ! microvascular endothelial cell @@ -33491,6 +38269,8 @@ name: cardiac ventricle fibroblast def: "Any fibroblast that is part of a cardiac ventricle." [GOC:TermGenie] comment: http://www.sciencellonline.com/site/productInformation.php?keyword=6310 subset: human_reference_atlas +subset: human_subset +subset: mouse_subset is_a: CL:0002548 ! fibroblast of cardiac tissue intersection_of: CL:0000057 ! fibroblast intersection_of: part_of UBERON:0002082 ! cardiac ventricle @@ -33505,6 +38285,8 @@ name: cardiac atrium fibroblast def: "Any fibroblast that is part of a cardiac atrium." [GOC:TermGenie] comment: http://www.sciencellonline.com/site/productInformation.php?keyword=6320 subset: human_reference_atlas +subset: human_subset +subset: mouse_subset is_a: CL:0002548 ! fibroblast of cardiac tissue intersection_of: CL:0000057 ! fibroblast intersection_of: part_of UBERON:0002081 ! cardiac atrium @@ -33518,6 +38300,8 @@ id: CL:2000068 name: pericardium fibroblast def: "Any fibroblast that is part of a pericardium." [GOC:TermGenie] comment: http://www.sciencellonline.com/site/productInformation.php?keyword=6430 +subset: human_subset +subset: mouse_subset is_a: CL:0000057 ! fibroblast intersection_of: CL:0000057 ! fibroblast intersection_of: part_of UBERON:0002407 ! pericardium @@ -33530,6 +38314,8 @@ id: CL:2000069 name: gallbladder fibroblast def: "Any fibroblast that is part of a gallbladder." [GOC:TermGenie] comment: http://www.sciencellonline.com/site/productInformation.php?keyword=5430 +subset: human_subset +subset: mouse_subset is_a: CL:0000057 ! fibroblast intersection_of: CL:0000057 ! fibroblast intersection_of: part_of UBERON:0002110 ! gallbladder @@ -33542,6 +38328,8 @@ id: CL:2000070 name: optic choroid fibroblast def: "Any fibroblast that is part of a optic choroid." [GOC:TermGenie] comment: http://www.sciencellonline.com/site/productInformation.php?keyword=6620 +subset: human_subset +subset: mouse_subset is_a: CL:0000057 ! fibroblast intersection_of: CL:0000057 ! fibroblast intersection_of: part_of UBERON:0001776 ! optic choroid @@ -33554,6 +38342,8 @@ id: CL:2000071 name: mammary microvascular endothelial cell def: "Any microvascular endothelial cell that is part of a breast." [GOC:TermGenie] comment: http://www.sciencellonline.com/site/productInformation.php?keyword=7600 +subset: human_subset +subset: mouse_subset is_a: CL:2000008 ! microvascular endothelial cell intersection_of: CL:2000008 ! microvascular endothelial cell intersection_of: part_of UBERON:0000310 ! breast @@ -33566,6 +38356,8 @@ id: CL:2000072 name: adipose microvascular endothelial cell def: "Any microvascular endothelial cell that is part of a adipose tissue." [GOC:TermGenie] comment: http://www.sciencellonline.com/site/productInformation.php?keyword=7200 +subset: human_subset +subset: mouse_subset is_a: CL:0002320 ! connective tissue cell is_a: CL:2000008 ! microvascular endothelial cell intersection_of: CL:2000008 ! microvascular endothelial cell @@ -33578,6 +38370,8 @@ creation_date: 2014-10-07T22:13:45Z id: CL:2000073 name: migratory cardiac neural crest cell def: "Any migratory neural crest cell that is part of a cardiac neural crest." [GOC:TermGenie] +subset: human_subset +subset: mouse_subset synonym: "cardiac neural crest cell" EXACT [PMID:33060096] is_a: CL:0000333 ! migratory neural crest cell intersection_of: CL:0000333 ! migratory neural crest cell @@ -33591,6 +38385,8 @@ id: CL:2000074 name: splenocyte def: "Any leukocyte that is part of a spleen." [GOC:TermGenie] comment: Splenocytes is a vague term that refers to any one of the different white blood cell types in the spleen. This name is seen many references as such and is not explained further, necessitating a need for this terminology. +subset: human_subset +subset: mouse_subset is_a: CL:0000738 ! leukocyte intersection_of: CL:0000738 ! leukocyte intersection_of: part_of UBERON:0002106 ! spleen @@ -33602,6 +38398,8 @@ creation_date: 2014-11-05T01:26:50Z id: CL:2000075 name: anterior visceral endoderm cell def: "Any endodermal cell that is part of a anterior visceral endoderm." [GOC:TermGenie] +subset: human_subset +subset: mouse_subset is_a: CL:0000223 ! endodermal cell intersection_of: CL:0000223 ! endodermal cell intersection_of: part_of UBERON:0004044 ! anterior visceral endoderm @@ -33613,6 +38411,8 @@ creation_date: 2014-11-05T01:34:13Z id: CL:2000076 name: hindlimb stylopod vein endothelial cell def: "Any vein endothelial cell that is part of a hindlimb stylopod." [GOC:TermGenie] +subset: human_subset +subset: mouse_subset is_a: CL:0002543 ! vein endothelial cell intersection_of: CL:0002543 ! vein endothelial cell intersection_of: part_of UBERON:0000376 ! hindlimb stylopod @@ -33624,6 +38424,8 @@ creation_date: 2014-12-02T18:40:47Z id: CL:2000077 name: skeletal muscle tissue of pectoralis major striated muscle cell def: "Any striated muscle cell that is part of a skeletal muscle tissue of pectoralis major." [GOC:TermGenie] +subset: human_subset +subset: mouse_subset is_a: CL:0000188 ! cell of skeletal muscle is_a: CL:0000737 ! striated muscle cell intersection_of: CL:0000737 ! striated muscle cell @@ -33636,6 +38438,8 @@ creation_date: 2014-12-02T18:48:17Z id: CL:2000078 name: placental pericyte def: "Any pericyte cell that is part of a placenta." [GOC:TermGenie] +subset: human_subset +subset: mouse_subset is_a: CL:0000669 ! pericyte intersection_of: CL:0000669 ! pericyte intersection_of: part_of UBERON:0001987 ! placenta @@ -33647,6 +38451,8 @@ creation_date: 2014-12-02T18:51:03Z id: CL:2000079 name: mesenchymal stem cell of femoral bone marrow def: "Any mesenchymal stem cell of the bone marrow that is part of a femur." [GOC:TermGenie] +subset: human_subset +subset: mouse_subset is_a: CL:0002540 ! mesenchymal stem cell of the bone marrow intersection_of: CL:0002540 ! mesenchymal stem cell of the bone marrow intersection_of: part_of UBERON:0000981 ! femur @@ -33658,6 +38464,8 @@ creation_date: 2014-12-02T19:07:31Z id: CL:2000080 name: mesenchymal stem cell of abdominal adipose tissue def: "Any mesenchymal stem cell of adipose tissue that is part of an abdomen." [GOC:TermGenie] +subset: human_subset +subset: mouse_subset synonym: "mesenchymal stem cell of abdominal adipose" EXACT [] is_a: CL:0002570 ! mesenchymal stem cell of adipose tissue intersection_of: CL:0002570 ! mesenchymal stem cell of adipose tissue @@ -33670,6 +38478,8 @@ creation_date: 2014-12-02T19:10:34Z id: CL:2000081 name: melanocyte of skin of face def: "Any melanocyte of skin that is part of a skin of face." [GOC:TermGenie] +subset: human_subset +subset: mouse_subset is_a: CL:1000458 ! melanocyte of skin intersection_of: CL:1000458 ! melanocyte of skin intersection_of: part_of UBERON:1000021 ! skin of face @@ -33692,6 +38502,8 @@ creation_date: 2014-12-02T19:10:45Z id: CL:2000083 name: hair follicle dermal papilla cell of scalp def: "Any hair follicle dermal papilla cell that is part of a scalp." [GOC:TermGenie] +subset: human_subset +subset: mouse_subset is_a: CL:0000346 ! hair follicle dermal papilla cell intersection_of: CL:0000346 ! hair follicle dermal papilla cell intersection_of: part_of UBERON:0000403 ! scalp @@ -33703,6 +38515,9 @@ creation_date: 2014-12-02T19:10:50Z id: CL:2000084 name: conjunctiva goblet cell def: "Any goblet cell that is part of a conjunctiva." [GOC:TermGenie] +subset: cellxgene_subset +subset: human_subset +subset: mouse_subset is_a: CL:0000160 ! goblet cell is_a: CL:1000432 ! conjunctival epithelial cell intersection_of: CL:0000160 ! goblet cell @@ -33714,6 +38529,8 @@ creation_date: 2014-12-02T19:28:38Z id: CL:2000085 name: mononuclear cell of umbilical cord def: "Any mononuclear cell that is part of a umbilical cord." [GOC:TermGenie] +subset: human_subset +subset: mouse_subset is_a: CL:0000349 ! extraembryonic cell is_a: CL:0000842 ! mononuclear cell intersection_of: CL:0000842 ! mononuclear cell @@ -33726,6 +38543,8 @@ creation_date: 2014-12-02T20:14:16Z id: CL:2000086 name: neocortex basket cell def: "Any basket cell that is part of a neocortex." [GOC:TermGenie] +subset: human_subset +subset: mouse_subset is_a: CL:0000118 ! basket cell is_a: CL:0010011 ! cerebral cortex GABAergic interneuron intersection_of: CL:0000118 ! basket cell @@ -33738,6 +38557,8 @@ creation_date: 2014-12-24T00:37:19Z id: CL:2000087 name: dentate gyrus of hippocampal formation basket cell def: "Any basket cell that is part of a dentate gyrus of hippocampal formation." [GOC:TermGenie] +subset: human_subset +subset: mouse_subset is_a: CL:0000118 ! basket cell is_a: CL:0010011 ! cerebral cortex GABAergic interneuron is_a: CL:1001569 ! hippocampal interneuron @@ -33751,6 +38572,8 @@ creation_date: 2014-12-24T00:37:24Z id: CL:2000088 name: Ammon's horn basket cell def: "Any basket cell that is part of a Ammon's horn." [GOC:TermGenie] +subset: human_subset +subset: mouse_subset is_a: CL:0000118 ! basket cell is_a: CL:0010011 ! cerebral cortex GABAergic interneuron is_a: CL:1001569 ! hippocampal interneuron @@ -33765,6 +38588,8 @@ id: CL:2000089 name: dentate gyrus granule cell def: "A granule cell that has soma location in the dentate gyrus cell layer of the hippocampal formation and has an elliptical cell body and characteristic cone-shaped tree of spiny apical dendrites. The branches extend throughout the molecular layer and the distal tips of the dendritic tree end just at the hippocampal fissure or at the ventricular surface. The dentate gyrus granule cell is the principal cell type of the dentate gyrus." [GOC:TermGenie, PMID:17765709] comment: As far as can be determined, all dentate granule cells appear to project to CA3 and the axon trajectory is partially correlated with the position of the parent cell body. {xref="PMID:17765709"} +subset: human_subset +subset: mouse_subset synonym: "dentate gyrus of hippocampal formation granule cell" EXACT [] is_a: CL:0001033 ! hippocampal granule cell is_a: CL:4023062 ! dentate gyrus neuron @@ -33778,8 +38603,9 @@ creation_date: 2015-02-23T05:48:23Z id: CL:2000090 name: dentate gyrus of hippocampal formation stellate cell def: "Any stellate cell that is part of a dentate gyrus of hippocampal formation." [GOC:TermGenie] +subset: human_subset +subset: mouse_subset is_a: CL:0000122 ! stellate neuron -is_a: CL:0012001 ! neuron of the forebrain is_a: CL:4023062 ! dentate gyrus neuron intersection_of: CL:0000122 ! stellate neuron intersection_of: RO:0002100 UBERON:0001885 ! has soma location dentate gyrus of hippocampal formation @@ -33791,6 +38617,8 @@ id: CL:2000091 name: endometrial microvascular endothelial cell def: "Any microvascular endothelial cell that is part of a endometrial blood vessel." [GOC:TermGenie] subset: human_reference_atlas +subset: human_subset +subset: mouse_subset is_a: CL:0009095 ! endothelial cell of uterus is_a: CL:2000008 ! microvascular endothelial cell intersection_of: CL:2000008 ! microvascular endothelial cell @@ -33805,6 +38633,8 @@ id: CL:2000092 name: hair follicular keratinocyte def: "Any keratinocyte that is part of a hair follicle." [GOC:TermGenie] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset is_a: CL:0000312 ! keratinocyte is_a: CL:0002559 ! hair follicle cell intersection_of: CL:0000312 ! keratinocyte @@ -33817,6 +38647,8 @@ id: CL:2000093 name: bronchus fibroblast of lung def: "Any fibroblast of lung that is part of a bronchus." [GOC:TermGenie] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset is_a: CL:0002553 ! fibroblast of lung intersection_of: CL:0002553 ! fibroblast of lung intersection_of: part_of UBERON:0002185 ! bronchus @@ -33828,6 +38660,8 @@ creation_date: 2015-03-31T21:16:22Z id: CL:2000094 name: nasal cavity respiratory epithelium epithelial cell of viscerocranial mucosa def: "Any epithelial cell of viscerocranial mucosa that is part of a nasal cavity respiratory epithelium." [GOC:TermGenie] +subset: human_subset +subset: mouse_subset is_a: CL:0002631 ! epithelial cell of upper respiratory tract is_a: CL:1000441 ! epithelial cell of viscerocranial mucosa intersection_of: CL:1000441 ! epithelial cell of viscerocranial mucosa @@ -33841,6 +38675,8 @@ id: CL:2000095 name: cord blood hematopoietic stem cell def: "Any hematopoietic stem cell that is part of a umbilical cord blood." [GOC:TermGenie] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset is_a: CL:0002246 ! peripheral blood stem cell is_a: CL:0002352 ! gestational hematopoietic stem cell intersection_of: CL:0000037 ! hematopoietic stem cell @@ -33853,6 +38689,8 @@ creation_date: 2015-05-26T18:58:34Z id: CL:2000096 name: fibroblast of the reticular layer of dermis def: "Any fibroblast that is part of a reticular layer of dermis." [GOC:TermGenie] +subset: human_subset +subset: mouse_subset is_a: CL:0002551 ! fibroblast of dermis intersection_of: CL:0000057 ! fibroblast intersection_of: part_of UBERON:0001993 ! reticular layer of dermis @@ -33864,6 +38702,8 @@ creation_date: 2015-08-11T16:28:16Z id: CL:2000097 name: midbrain dopaminergic neuron def: "Any dopaminergic neuron that is part of a midbrain." [GOC:TermGenie] +subset: human_subset +subset: mouse_subset is_a: CL:0000700 ! dopaminergic neuron is_a: CL:2000029 ! central nervous system neuron intersection_of: CL:0000700 ! dopaminergic neuron @@ -33876,24 +38716,24 @@ creation_date: 2015-12-03T16:42:40Z id: CL:3000000 name: ciliated epithelial cell of esophagus def: "A ciliated epithelial cell of the esophagus." [GOC:CellBLAST, PMID:29802404] -is_a: CL:0000067 ! ciliated epithelial cell +subset: human_subset +subset: mouse_subset is_a: CL:0002252 ! epithelial cell of esophagus -intersection_of: CL:0000067 ! ciliated epithelial cell -intersection_of: part_of UBERON:0001976 ! epithelium of esophagus -relationship: part_of UBERON:0001976 ! epithelium of esophagus property_value: terms:contributor http://www.wikidata.org/entity/Q97529981 creation_date: 2019-02-09T16:40:30Z [Term] id: CL:3000001 name: Hofbauer cell -def: "A tissue-resident macrophage that is part of the placenta. A Hofbauer cell expresses high levels of growth factors and metalloproteinases that support vasculogenesis, angiogenesis, branching morphogenesis and tissue remodeling. A Hofbauer cell has a fetal origin and is present throughout pregnancy." [GOC:CellBLAST, PMID:30429548, PMID:30498493, PMID:34745147, PMID:35438172] +def: "A tissue-resident macrophage that is part of the placenta. A Hofbauer cell expresses high levels of growth factors and metalloproteinases that support vasculogenesis, angiogenesis, branching morphogenesis and tissue remodeling. A Hofbauer cell has a fetal origin, is found in the villous stroma, chorion, and amnion, and is present throughout pregnancy." [GOC:CellBLAST, PMID:30429548, PMID:30498493, PMID:34745147, PMID:35438172] comment: Hofbauer cells are a heterogenic group of macrophages that resemble M2-like cells. Initially described in chorionic villi in humans, a Hofbauer cell is now often used to describe any fetal-derived placental macrophage that resides within the placental villous core, amnion, and chorion laeve. {xref="PMID:30498493"} subset: cellxgene_subset subset: human_reference_atlas -synonym: "HBC" RELATED OMO:0003000 [] -is_a: CL:0000864 ! tissue-resident macrophage -relationship: part_of UBERON:0001987 ! placenta +subset: human_subset +subset: mouse_subset +synonym: "fetal Hofbauer cell" EXACT [PMID:39007150] +synonym: "HBC" RELATED OMO:0003000 [PMID:39007150] +is_a: CL:4033087 ! placental resident macrophage property_value: RO:0002175 NCBITaxon:9606 property_value: terms:contributor http://www.wikidata.org/entity/Q97529981 property_value: terms:contributor https://orcid.org/0000-0001-6677-8489 @@ -33904,6 +38744,8 @@ id: CL:3000002 name: sympathetic noradrenergic neuron def: "Sympathetic noradrenergic neuron." [GOC:CellBLAST, PMID:30096314] subset: human_reference_atlas +subset: human_subset +subset: mouse_subset is_a: CL:0008025 ! noradrenergic neuron is_a: CL:0011103 ! sympathetic neuron intersection_of: CL:0011103 ! sympathetic neuron @@ -33916,6 +38758,8 @@ creation_date: 2019-02-25T19:30:14Z id: CL:3000003 name: sympathetic cholinergic neuron def: "Sympathetic cholinergic neuron." [GOC:CellBLAST, PMID:30096314] +subset: human_subset +subset: mouse_subset is_a: CL:0000108 ! cholinergic neuron is_a: CL:0011103 ! sympathetic neuron intersection_of: CL:0011103 ! sympathetic neuron @@ -33926,7 +38770,10 @@ creation_date: 2019-02-25T19:32:20Z [Term] id: CL:3000004 name: peripheral sensory neuron -def: "Peripheral sensory neuron." [GOC:CellBLAST, PMID:30096314] +def: "A neuron type that is located in a peripheral nervous system and it transmits sensory information from the peripheral (PNS) to the central nervous system (CNS). A sensory neuron converts physical (light, sound, touch) or chemical (such as taste and smell) stimuli into an electrical signal through a process known as sensory transduction. The function of a sensory neuron is to carry informations from the external environment and internal body conditions to the central nervous system for further processing." [GOC:CellBLAST, https://www.britannica.com/science/sensory-neuron, https://www.ncbi.nlm.nih.gov/books/NBK539846/, PMID:30096314, PMID:31554486, PMID:35858549, Wikipedia:Sensory_neuron] +comment: Typically, a sensory neuron has a pseudounipolar morphology. {xref="Wikipedia:Sensory_neuron"} +subset: human_subset +subset: mouse_subset is_a: CL:0000101 ! sensory neuron is_a: CL:2000032 ! peripheral nervous system neuron intersection_of: CL:2000032 ! peripheral nervous system neuron @@ -33939,6 +38786,8 @@ id: CL:4006000 name: fibroblast of breast def: "A fibroblast that is part of the breast." [] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "breast fibroblast" EXACT [] is_a: CL:0000057 ! fibroblast intersection_of: CL:0000057 ! fibroblast @@ -33950,6 +38799,8 @@ property_value: terms:contributor https://orcid.org/0000-0001-9897-3238 id: CL:4006001 name: fibroblast of skin of scalp def: "A fibroblast that is part of the skin of scalp." [] +subset: human_subset +subset: mouse_subset synonym: "skin of scalp fibroblast" EXACT [] is_a: CL:0002620 ! skin fibroblast intersection_of: CL:0000057 ! fibroblast @@ -33961,6 +38812,8 @@ property_value: terms:contributor https://orcid.org/0000-0001-9897-3238 id: CL:4023000 name: beta motor neuron def: "A motor neuron that innervates both intrafusal and extrafusal muscle fibers. Low abundancy. They control both muscle contraction and responsiveness of the sensory feedback from muscle spindles." [PMID:25346659] +subset: human_subset +subset: mouse_subset is_a: CL:0008039 ! lower motor neuron relationship: RO:0002120 CL:0008046 ! synapsed to extrafusal muscle fiber relationship: RO:0002120 CL:0008047 ! synapsed to intrafusal muscle fiber @@ -33970,6 +38823,8 @@ property_value: terms:contributor https://orcid.org/0000-0001-7258-9596 id: CL:4023001 name: static beta motor neuron def: "A beta motor neuron that innervates nuclear chain fibers." [PMID:25346659] +subset: human_subset +subset: mouse_subset is_a: CL:4023000 ! beta motor neuron property_value: terms:contributor https://orcid.org/0000-0001-7258-9596 @@ -33977,6 +38832,8 @@ property_value: terms:contributor https://orcid.org/0000-0001-7258-9596 id: CL:4023002 name: dynamic beta motor neuron def: "A beta motor neuron that innervates the nuclear bag fibers of muscle spindles." [PMID:25346659] +subset: human_subset +subset: mouse_subset is_a: CL:4023000 ! beta motor neuron property_value: terms:contributor https://orcid.org/0000-0001-7258-9596 @@ -33984,6 +38841,8 @@ property_value: terms:contributor https://orcid.org/0000-0001-7258-9596 id: CL:4023003 name: nuclear chain fiber def: "A type of intrafusal muscle fiber that has nuclei arranged in a linear row. Unlike nuclear bag fibers, the equatorial region of these fibers (in the centre of the spindle) is not expanded. These fibers are responsible for the detection of changes in muscle length. They are innervated by static gamma motor neurons and are principally associated with type II sensory fibers." [DOI:10.1016/B978-0-323-39632-5.00024-4, PMID:139469] +subset: human_subset +subset: mouse_subset is_a: CL:0008047 ! intrafusal muscle fiber property_value: terms:contributor https://orcid.org/0000-0001-7258-9596 @@ -33991,6 +38850,8 @@ property_value: terms:contributor https://orcid.org/0000-0001-7258-9596 id: CL:4023004 name: nuclear bag fiber def: "A type of intrafusal muscle fiber that lies in the center of a muscle spindle. Nuclei are clustered centrally and give the equatorial region a swollen appearance. They are associated with associated with dynamic gamma motor neurons, and the stretching of the equatorial region of the nuclear bag fibers results in an increase in the firing rate of type Ia sensory fibers." [DOI:10.1016/B978-0-323-39632-5.00024-4, PMID:139469] +subset: human_subset +subset: mouse_subset is_a: CL:0008047 ! intrafusal muscle fiber property_value: terms:contributor https://orcid.org/0000-0001-7258-9596 @@ -33998,6 +38859,8 @@ property_value: terms:contributor https://orcid.org/0000-0001-7258-9596 id: CL:4023005 name: dynamic nuclear bag fiber def: "A nuclear bag fiber that is sensitive mainly to the rate of change in muscle length." [DOI:10.1016/B978-0-323-39632-5.00024-4] +subset: human_subset +subset: mouse_subset synonym: "bag1 fiber" EXACT [] synonym: "nuclear bag1 intrafusal fiber" EXACT [] is_a: CL:4023004 ! nuclear bag fiber @@ -34007,6 +38870,8 @@ property_value: terms:contributor https://orcid.org/0000-0001-7258-9596 id: CL:4023006 name: static nuclear bag fiber def: "A nuclear bag fiber that is sensitive only changes in muscle length but not the rate of that change." [DOI:10.1016/B978-0-323-39632-5.00024-4] +subset: human_subset +subset: mouse_subset synonym: "bag2 fiber" EXACT [] synonym: "nuclear bag2 intrafusal fiber" EXACT [] is_a: CL:4023004 ! nuclear bag fiber @@ -34017,6 +38882,7 @@ id: CL:4023007 name: L2/3 bipolar VIP GABAergic interneuron (Mmus) def: "A VIP GABAergic cortical interneuron with bipolar morphology, with a soma found in L2/3. L2/3 bipolar VIP cells have extending axons across all layers (with preferences for layers II/III and Va) and a dendritic tree that is vertically more restricted than deeper layer VIP cells and extend fewer dendrites into the layers outside their home layer (location of soma). L2/3 bipolar VIP cells have great variability in firing patterns, though most are continuous adapting. L2/3 bipolar VIP cells are more depolarized in their resting state, had less fast rectification, and had smaller after hyperpolarization than deeper VIP cells." [PMID:26420784] subset: BDS_subset +subset: mouse_subset synonym: "L2/3 bipolar Vip (Mus musculus)" EXACT [] is_a: CL:0000103 ! bipolar neuron is_a: CL:4023016 ! VIP GABAergic cortical interneuron @@ -34032,6 +38898,8 @@ name: intratelencephalic-projecting glutamatergic cortical neuron def: "A glutamatergic neuron located in the cerebral cortex that projects to structures of telencephalic origins." [PMID:34616075] subset: BDS_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "IT neuron" EXACT [doi:10.1038/s41467-021-24565-z] xref: ILX:0770100 is_a: CL:0000679 ! glutamatergic neuron @@ -34050,6 +38918,8 @@ name: extratelencephalic-projecting glutamatergic cortical neuron def: "A glutamatergic neuron located in the cerebral cortex that projects to structures not derived from telencephalon." [DOI:10.1101/2020.10.19.343129] subset: BDS_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "ET projecting neuron" EXACT [] xref: ILX:0770101 is_a: CL:0000679 ! glutamatergic neuron @@ -34068,6 +38938,7 @@ name: alpha7 GABAergic cortical interneuron (Mmus) def: "A GABAergic cortical interneuron that is strongly labelled for α7 nAChRs. These cells have soma found in L1 and have multipolar dendrites with vertically descending axonal collaterals that project deep into the column, usually branching and terminating in L5A." [PMID:30413647, PMID:33184512] comment: Unlike typical Lamp5 electrophysiology, A7 cells have Vip- and Sst-like firing properties, with active depolarizing hump at near-threshold membrane potentials, and larger hyperpolarization sag, stronger burst, and rebound firing. A7 cells have a transcriptomics signature that looks like Lamp5 GABAergic interneuron. {xref="PMID:33184512", xref="PMID:30413647", xref="DOI:10.1101/2020.10.19.343129"} subset: BDS_subset +subset: mouse_subset synonym: "A7 cell (Mus musculus)" EXACT [] is_a: BFO:0000002 is_a: CL:0010011 ! cerebral cortex GABAergic interneuron @@ -34080,8 +38951,11 @@ property_value: terms:contributor https://orcid.org/0000-0001-7258-9596 id: CL:4023011 name: lamp5 GABAergic cortical interneuron def: "A transcriptomically distinct GABAergic neuron located in the cerebral cortex that expresses Lamp5. The standard transcriptomic reference data for this cell type can be found on the CellxGene census under the collection: 'Transcriptomic cytoarchitecture reveals principles of human neocortex organization', dataset: 'Supercluster: CGE-derived interneurons', Author Categories: 'CrossArea_subclass', clusters Lamp5." [https://cellxgene.cziscience.com/e/e4ddac12-f48f-4455-8e8d-c2a48a683437.cxg/, PMID:30382198, PMID:37824655] +comment: The marker set LINC00298, KIT can identify the Human cell type lamp5 GABAergic cortical interneuron in the Brain with a confidence of 0.814687838 (NS-Forest FBeta value). {xref="https://doi.org/10.5281/zenodo.11165918"} subset: BDS_subset subset: cellxgene_subset +subset: human_subset +subset: mouse_subset xref: ILX:0770149 is_a: CL:4023064 ! caudal ganglionic eminence derived cortical interneuron intersection_of: CL:0000099 ! interneuron @@ -34089,7 +38963,9 @@ intersection_of: capable_of GO:0061534 ! gamma-aminobutyric acid secretion, neur intersection_of: RO:0002100 UBERON:0000956 ! has soma location cerebral cortex intersection_of: RO:0002292 PR:000032148 ! expresses lysosome-associated membrane glycoprotein 5 relationship: RO:0002292 PR:000032148 ! expresses lysosome-associated membrane glycoprotein 5 +relationship: RO:0015004 CLM:1000074 ! has characterizing marker set NS forest marker set of lamp5 GABAergic cortical interneuron (Human Brain). property_value: IAO:0000028 "Lamp5 cortical interneuron" xsd:string +property_value: RO:0002175 NCBITaxon:9606 property_value: terms:contributor https://orcid.org/0000-0001-7258-9596 [Term] @@ -34099,6 +38975,8 @@ def: "A glutamatergic neuron located in the cerebral cortex that projects axons subset: BDS_subset subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "NP neuron" EXACT [] xref: ILX:0770103 is_a: CL:0000679 ! glutamatergic neuron @@ -34118,6 +38996,8 @@ def: "A glutamatergic neuron located in the cerebral cortex that projects to the subset: BDS_subset subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "CT projecting neuron" EXACT [] is_a: CL:0000679 ! glutamatergic neuron is_a: CL:0010012 ! cerebral cortex neuron @@ -34134,6 +39014,7 @@ id: CL:4023014 name: L5 VIP GABAergic interneuron (Mmus) def: "A VIP GABAergic cortical interneuron with a soma found in L5. L5 VIP cells have mostly local morphology with some deep-projecting axons. They show only moderate resistance, comparable to that of sst subclass and unlike typical VIP subclass cells that tend to show high input resistance. L5 VIP cells show particularly low resting membrane potential." [PMID:26420784, PMID:26612957] subset: BDS_subset +subset: mouse_subset synonym: "L5 VIP (Mus musculus)" EXACT [] is_a: CL:4023016 ! VIP GABAergic cortical interneuron relationship: RO:0002100 UBERON:0005394 ! has soma location cortical layer V @@ -34146,8 +39027,11 @@ property_value: terms:contributor https://orcid.org/0000-0001-7258-9596 id: CL:4023015 name: sncg GABAergic cortical interneuron def: "A transcriptomically distinct GABAergic neuron located in the cerebral cortex that expresses Gamma-synuclein. The standard transcriptomic reference data for this cell type can be found on the CellxGene census under the collection: 'Transcriptomic cytoarchitecture reveals principles of human neocortex organization', dataset: 'Supercluster: CGE-derived interneurons', Author Categories: 'CrossArea_subclass', clusters Sncg." [https://cellxgene.cziscience.com/e/e4ddac12-f48f-4455-8e8d-c2a48a683437.cxg/, PMID:33186530, PMID:37824655] +comment: The marker set RXRG, THSD7B can identify the Human cell type sncg GABAergic cortical interneuron in the Brain with a confidence of 0.628943702 (NS-Forest FBeta value). {xref="https://doi.org/10.5281/zenodo.11165918"} subset: BDS_subset subset: cellxgene_subset +subset: human_subset +subset: mouse_subset xref: ILX:0770150 is_a: CL:4023064 ! caudal ganglionic eminence derived cortical interneuron intersection_of: CL:0000099 ! interneuron @@ -34155,15 +39039,20 @@ intersection_of: capable_of GO:0061534 ! gamma-aminobutyric acid secretion, neur intersection_of: RO:0002100 UBERON:0000956 ! has soma location cerebral cortex intersection_of: RO:0002292 PR:000015325 ! expresses gamma-synuclein relationship: RO:0002292 PR:000015325 ! expresses gamma-synuclein +relationship: RO:0015004 CLM:1000081 ! has characterizing marker set NS forest marker set of sncg GABAergic cortical interneuron (Human Brain). property_value: IAO:0000028 "sncg cortical interneuron" xsd:string +property_value: RO:0002175 NCBITaxon:9606 property_value: terms:contributor https://orcid.org/0000-0001-7258-9596 [Term] id: CL:4023016 name: VIP GABAergic cortical interneuron def: "A transcriptomically distinct cortical GABAergic neuron that expresses the vasocactive intestinal polypeptide and that has its soma located in the cerebral cortex. The standard transcriptomic reference data for this cell type can be found on the CellxGene census under the collection: 'Transcriptomic cytoarchitecture reveals principles of human neocortex organization', dataset: 'Supercluster: CGE-derived interneurons', Author Categories: 'CrossArea_subclass', cluster Vip." [https://cellxgene.cziscience.com/e/e4ddac12-f48f-4455-8e8d-c2a48a683437.cxg/, PMID:33186530, PMID:37824655] +comment: The marker set VIP can identify the Human cell type VIP GABAergic cortical interneuron in the Brain with a confidence of 0.855531344 (NS-Forest FBeta value). {xref="https://doi.org/10.5281/zenodo.11165918"} subset: BDS_subset subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "cortical VIP neuron" RELATED [PMID:36384143] synonym: "Vip" RELATED [ILX:0770151] synonym: "Vip GABAergic neuron" BROAD [ILX:0770151] @@ -34179,7 +39068,9 @@ intersection_of: capable_of GO:0061534 ! gamma-aminobutyric acid secretion, neur intersection_of: RO:0002100 UBERON:0000956 ! has soma location cerebral cortex intersection_of: RO:0002292 PR:000017299 ! expresses VIP peptides relationship: RO:0002292 PR:000017299 ! expresses VIP peptides +relationship: RO:0015004 CLM:1000085 ! has characterizing marker set NS forest marker set of VIP GABAergic cortical interneuron (Human Brain). property_value: IAO:0000028 "VIP cortical interneuron" xsd:string +property_value: RO:0002175 NCBITaxon:9606 property_value: terms:contributor https://orcid.org/0000-0001-7258-9596 property_value: terms:description "This neuronal type is distinguished by its heterogeneous morphology and electrophysiological characteristics (Pronneke et al., 2015,2020; Apicella and Marchionni, 2022). Variations in morphology and firing patterns are observed in human cortical VIP interneurons. In a study by Lee et al., 2023, four distinct subtypes of VIP neurons were identified, each exhibiting unique morphologies, soma locations, and electrophysiological properties. These subtypes are defined according to their transcriptomic markers: LBH-VIP and CCD184-VIP, both of which display a bipolar morphology with axons and dendrites extending across cortical layers; and SY16-VIP and ADAMTSL1-VIP, characterized by a dendritic arbor that spreads horizontally within the same layer as the soma (Lee et al., 2023). Disruption or malfunction of VIP cortical interneuron is implicated in neurodevelopmental disorders such as Rett Syndrome and Dravet Syndrome (Goff and Goldberg 2021)." xsd:string {xref="PMID:26420784", xref="PMID:31210267", xref="PMID:33794534", xref="PMID:35221922"} @@ -34187,9 +39078,11 @@ property_value: terms:description "This neuronal type is distinguished by its he id: CL:4023017 name: sst GABAergic cortical interneuron def: "A transcriptomically distinct GABAergic neuron located in the cerebral cortex that expresses somatostatin (sst). The standard transcriptomic reference data for this cell type can be found on the CellxGene census under the collection: 'Transcriptomic cytoarchitecture reveals principles of human neocortex organization', dataset: 'Supercluster: MGE-derived interneurons', Author Categories: 'CrossArea_subclass', cluster Sst." [https://cellxgene.cziscience.com/e/9c63201d-bfd9-41a8-bbbc-18d947556f3d.cxg/, PMID:27477017, PMID:33742131, PMID:37824655] -comment: In the mouse cortex, sst GABAergic cortical interneurons show heterogeneous electrophysiological signatures varying between low-threshold spiking (LTS), regular-spiking and fast-spiking (Song, Y. H., Yoon, J., & Lee, S. H. 2021). Sst GABAergic cortical interneurons have multiple functional roles in the brain. In the mouse, they involved in the generation of slow-waves during the sleep phase of non-rapid eye-movement (NREM) (Funk, C. M. et al., 2017), they maintain synaptic plasticity during motor learning (Adler, A., Zhao, R., et al., 2021), they enhance visual perception in the V1 cortical area by suppressing the activity of pyramidal excitatory neurons (Song, YH. et al., 2020). In humans, malfunctioning of sst GABAergic cortical interneurons is associated with neurodegenerative and psychiatric disorders such as Parkinson's disease, Alzheimer's disease, major depressive disorder, bipolar disorder and schizophrenia as individuals affected by these pathologies show a decrease of expression of SST in the brain (Song YH., Yoon J. et al., 2021). {xref="PMID:30792151", xref="PMID:33742131", xref="PMID:28821651", xref="PMID:32494634"} +comment: In the mouse cortex, sst GABAergic cortical interneurons show heterogeneous electrophysiological signatures varying between low-threshold spiking (LTS), regular-spiking and fast-spiking (Song, Y. H., Yoon, J., & Lee, S. H. 2021). Sst GABAergic cortical interneurons have multiple functional roles in the brain. In the mouse, they involved in the generation of slow-waves during the sleep phase of non-rapid eye-movement (NREM) (Funk, C. M. et al., 2017), they maintain synaptic plasticity during motor learning (Adler, A., Zhao, R., et al., 2021), they enhance visual perception in the V1 cortical area by suppressing the activity of pyramidal excitatory neurons (Song, YH. et al., 2020). In humans, malfunctioning of sst GABAergic cortical interneurons is associated with neurodegenerative and psychiatric disorders such as Parkinson's disease, Alzheimer's disease, major depressive disorder, bipolar disorder and schizophrenia as individuals affected by these pathologies show a decrease of expression of SST in the brain (Song YH., Yoon J. et al., 2021). The marker set SST, PLCH1 can identify the Human cell type sst GABAergic cortical interneuron in the Brain with a confidence of 0.842367005 (NS-Forest FBeta value). {xref="PMID:30792151", xref="PMID:33742131", xref="PMID:28821651", xref="https://doi.org/10.5281/zenodo.11165918", xref="PMID:32494634"} subset: BDS_subset subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "SOM+ inhibitory interneuron" RELATED [PMID:30001424] synonym: "somatostatin-expressing inhibitory interneuron" RELATED [PMID:30001424] synonym: "SST+ IN" RELATED [PMID:33742131] @@ -34200,15 +39093,20 @@ intersection_of: capable_of GO:0061534 ! gamma-aminobutyric acid secretion, neur intersection_of: RO:0002100 UBERON:0000956 ! has soma location cerebral cortex intersection_of: RO:0002292 PR:000015665 ! expresses somatostatin relationship: RO:0002292 PR:000015665 ! expresses somatostatin +relationship: RO:0015004 CLM:1000082 ! has characterizing marker set NS forest marker set of sst GABAergic cortical interneuron (Human Brain). property_value: IAO:0000028 "sst cortical interneuron" xsd:string +property_value: RO:0002175 NCBITaxon:9606 property_value: terms:contributor https://orcid.org/0000-0001-7258-9596 [Term] id: CL:4023018 name: pvalb GABAergic cortical interneuron def: "A transcriptomically distinct GABAergic interneuron with a soma located in a cerebral cortex and it expresses Parvalbumin. The standard transcriptomic reference data for this cell type can be found on the CellxGene census under the collection: 'Transcriptomic cytoarchitecture reveals principles of human neocortex organization', dataset: 'Supercluster: MGE-derived interneurons', Author Categories: 'CrossArea_subclass', cluster Pvalb." [https://cellxgene.cziscience.com/e/9c63201d-bfd9-41a8-bbbc-18d947556f3d.cxg/, PMID:27477017, PMID:37824655] +comment: The marker set PVALB, TAC1, MYO5B can identify the Human cell type pvalb GABAergic cortical interneuron in the Brain with a confidence of 0.691998764 (NS-Forest FBeta value). {xref="https://doi.org/10.5281/zenodo.11165918"} subset: BDS_subset subset: cellxgene_subset +subset: human_subset +subset: mouse_subset xref: ILX:0770154 is_a: CL:4023069 ! medial ganglionic eminence derived GABAergic cortical interneuron intersection_of: CL:4023069 ! medial ganglionic eminence derived GABAergic cortical interneuron @@ -34216,7 +39114,9 @@ intersection_of: capable_of GO:0061534 ! gamma-aminobutyric acid secretion, neur intersection_of: RO:0002100 UBERON:0000956 ! has soma location cerebral cortex intersection_of: RO:0002292 PR:000013502 ! expresses parvalbumin alpha relationship: RO:0002292 PR:000013502 ! expresses parvalbumin alpha +relationship: RO:0015004 CLM:1000080 ! has characterizing marker set NS forest marker set of pvalb GABAergic cortical interneuron (Human Brain). property_value: IAO:0000028 "pvalb cortical interneuron" xsd:string +property_value: RO:0002175 NCBITaxon:9606 property_value: terms:contributor https://orcid.org/0000-0001-7258-9596 [Term] @@ -34224,6 +39124,7 @@ id: CL:4023019 name: L5/6 cck, VIP GABAergic interneuron (Mmus) def: "A VIP GABAergic cortical interneuron that expresses cck. L5/6 cck cells have soma found mainly in L5 and L6 and have large axonal arborization." [PMID:33184512] subset: BDS_subset +subset: mouse_subset synonym: "L5/6 CCK Vip (Mus musculus)" EXACT [] is_a: CL:4023016 ! VIP GABAergic cortical interneuron is_a: CL:4023071 ! L5/6 cck GABAergic interneuron (Mmus) @@ -34236,6 +39137,8 @@ property_value: terms:contributor https://orcid.org/0000-0001-7258-9596 id: CL:4023020 name: dynamic gamma motor neuron def: "A gamma motor neuron that innervates dynamic nuclear bag fibers (bag1 fibers) and enhances the sensitivities of Ia sensory neurons. They alter muscle spindle sensitivity and increases its discharge in response to velocity of muscle length (rather than just magnitude)." [PMID:13933877, PMID:139469, WikipediaVersion:Gamma_motor_neuron&oldid=906640465] +subset: human_subset +subset: mouse_subset is_a: CL:0008037 ! gamma motor neuron relationship: RO:0002120 CL:4023005 ! synapsed to dynamic nuclear bag fiber property_value: terms:contributor https://orcid.org/0000-0001-7258-9596 @@ -34244,6 +39147,8 @@ property_value: terms:contributor https://orcid.org/0000-0001-7258-9596 id: CL:4023021 name: static gamma motor neuron def: "A gamma motor neuron that innervates static nuclear bag fibers (bag2 fibers) and increases their firing, in response to an increase in the magnitude of change in length, and controls the static sensitivity of the stretch reflex." [PMID:13933877, PMID:139469, WikipediaVersion:Gamma_motor_neuron&oldid=906640465] +subset: human_subset +subset: mouse_subset is_a: CL:0008037 ! gamma motor neuron relationship: RO:0002120 CL:4023006 ! synapsed to static nuclear bag fiber property_value: terms:contributor https://orcid.org/0000-0001-7258-9596 @@ -34253,6 +39158,7 @@ id: CL:4023022 name: canopy lamp5 GABAergic cortical interneuron (Mmus) def: "A Lamp5 GABAergic cortical interneuron that has extended axons in the surface of L1. Canopy Lamp5 cells resemble neurogliaform cells in having elongated horizontal axonal arbors largely confined to L1; but the dendritic arbors are wider and have fewer branches, while the axon is less tortuous and extends further from the soma" [PMID:30413647] subset: BDS_subset +subset: mouse_subset is_a: CL:4023011 ! lamp5 GABAergic cortical interneuron relationship: RO:0002162 NCBITaxon:10090 ! in taxon Mus musculus relationship: RO:0002292 PR:Q9D387 ! expresses lysosome-associated membrane glycoprotein 5 (mouse) @@ -34264,6 +39170,7 @@ id: CL:4023023 name: L5,6 neurogliaform lamp5 GABAergic interneuron (Mmus) def: "A lamp 5 GABAergic cortical interneuron with neurogliaform morphology with a soma found in L5,6. L5,6 NGC lamp5 have deep afterhyperpolarization (AHP) but narrow action potentials (APs). Unlike other deep neurogliaform cells (which are caudal ganglionic eminence (CGE) derived), L5,6 NGC lamp5 cells are medial ganglionic eminence (MGE)-derived" [PMID:26727548] subset: BDS_subset +subset: mouse_subset synonym: "L5,6 NGC Lamp5 (Mus musculus)" EXACT [] is_a: CL:0000693 ! neurogliaform cell is_a: CL:4023011 ! lamp5 GABAergic cortical interneuron @@ -34277,6 +39184,7 @@ id: CL:4023024 name: neurogliaform lamp5 GABAergic cortical interneuron (Mmus) def: "A lamp5 GABAergic cortical interneuron with layer-adapting morphology. NGC lamp5 cells have a small round soma, short dendrites, and a wide dense axonal arbor that tends to establish a dense axonal mesh with high connection probability both to themselves and L2 pyramidal cells. NGC lamp5 cells have unique synaptic properties that distinguish them from other GABAergic interneurons, including the release of GABA to the extracellular space via volume transmission, and the ability to produce GABA-B responses in connected postsynaptic targets." [PMID:27477017] subset: BDS_subset +subset: mouse_subset synonym: "NGC Lamp5 (Mus musculus)" EXACT [] is_a: CL:0000693 ! neurogliaform cell is_a: CL:4023011 ! lamp5 GABAergic cortical interneuron @@ -34290,6 +39198,7 @@ id: CL:4023025 name: long-range projecting sst GABAergic cortical interneuron (Mmus) def: "A sst GABAergic cortical interneuron that is both an interneuron and a projecting neuron. They are found in all layers from upper L2/3 down to the bottom of L6. They have long-range projections, some with axons fading into white matter. These cells have low rebound potential, low hyperpolarization sag, and high variability in membrane time constant." [PMID:26727548] subset: BDS_subset +subset: mouse_subset synonym: "LP SST (Mus musculus)" EXACT [] is_a: CL:4023121 ! sst chodl GABAergic cortical interneuron relationship: RO:0002162 NCBITaxon:10090 ! in taxon Mus musculus @@ -34300,6 +39209,9 @@ property_value: terms:contributor https://orcid.org/0000-0001-7258-9596 id: CL:4023026 name: direct pathway medium spiny neuron def: "A medium spiny neuron that expresses dopamine type 1 receptors and projects to the globus pallidus internus or the substantia nigra pars reticulata." [PMID:34727523, WikipediaVersioned:Medium_spiny_neuron&oldid=1109726850] +subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "D1-MSN" EXACT OMO:0003000 [PMID:34727523] synonym: "dopamine 1 medium spiny neuron" EXACT [https://orcid.org/0000-0001-7258-9596] synonym: "dSPN" EXACT OMO:0003000 [PMID:30096299] @@ -34313,6 +39225,7 @@ id: CL:4023027 name: L5 sst T-Martinotti interneuron (Mmus) def: "A sst GABAergic cortical interneuron with a soma found in L5 and possesses 'T-shaped' Martinotti morphologies with local axonal plexus in L5a and translaminar axons restricted to the uppermost part of L1. They show low-threshold spiking patterns with strong rebound firing, and inhibit the L1 apical tuft of nearby pyramidal cells." [PMID:28254942, PMID:29326172] subset: BDS_subset +subset: mouse_subset synonym: "L5 T Martinotti SST (Mus musculus)" EXACT [] is_a: BFO:0000002 is_a: CL:0010011 ! cerebral cortex GABAergic interneuron @@ -34328,6 +39241,7 @@ id: CL:4023028 name: L5 non-Martinotti sst GABAergic interneuron (Mmus) def: "A sst GABAergic cortical interneuron with a soma found in lower L5 with mostly local axonal arborization but with some sparse ascending axons. L5 non-Martinotti sst cells show somatic localization and local axon plexus in L5b and L5b/6 and substantial innervation of L3 and L4, and receive thalamic input from the ventral posteromedial nucleus and specifically target L4 neurons, avoiding L5 pyramidal cells. L5 non-Martinotti sst cells tend to show a higher input resistance and seem to be less stuttering." [PMID:28254942, PMID:29326172] subset: BDS_subset +subset: mouse_subset synonym: "L5 non-Martinotti SST (Mus musculus)" EXACT [] is_a: BFO:0000002 is_a: CL:0010011 ! cerebral cortex GABAergic interneuron @@ -34341,6 +39255,9 @@ property_value: terms:contributor https://orcid.org/0000-0001-7258-9596 id: CL:4023029 name: indirect pathway medium spiny neuron def: "A medium spiny neuron that expresses dopamine type 2 receptors and projects to the external globus pallidus." [PMID:34727523, WikipediaVersioned:Medium_spiny_neuron&oldid=1109726850] +subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "D2-MSN" EXACT OMO:0003000 [PMID:34727523] synonym: "dopamine 2 medium spiny neuron" EXACT [https://orcid.org/0000-0001-7258-9596] synonym: "iSPN" EXACT OMO:0003000 [PMID:30096299] @@ -34355,6 +39272,7 @@ name: L2/3/5 fan Martinotti sst GABAergic interneuron (Mmus) def: "A sst GABAergic cortical interneuron that has \"fanning-out' Martinotti morphology that is found in layer 2/3/5 of the cerebral cortex. They have local axon arbor and long ascending axons that spreads horizontally and arborizes significantly in L1." [PMID:27225074, PMID:27477017, PMID:28254942, PMID:29326172] comment: L2/3/5 fan Martionotti SST cells have an adapting firing pattern and non-zero afterdepolarization (ADP). {xref="PMID:33184512"} subset: BDS_subset +subset: mouse_subset synonym: "L2/3/5 fan Martinotti SST (Mus musculus)" EXACT [] is_a: BFO:0000002 is_a: CL:0010011 ! cerebral cortex GABAergic interneuron @@ -34369,6 +39287,7 @@ id: CL:4023031 name: L4 sst Martinotti interneuron (Mmus) def: "A sst GABAergic cortical interneuron with a soma found in lower L2/3 and upper 5, L4 Sst cells have Martinotti morphology with ascending axons but denser local axons and sparser ‘fanning-out’ projections to L1. L4 sst cells have smaller membrane time constant to calb2 (L2/3/5 fan Martinotti Cell) and non-zero afterdepolarization (ADP)." [PMID:33184512] subset: BDS_subset +subset: mouse_subset synonym: "L4 SST (Mus musculus)" EXACT [] is_a: BFO:0000002 is_a: CL:0010011 ! cerebral cortex GABAergic interneuron @@ -34384,6 +39303,8 @@ id: CL:4023032 name: ON retinal ganglion cell comment: A retinal ganglion cell that is depolarized by illumination of its receptive field center. {xref="PMID:19602302"} subset: cellxgene_subset +subset: human_subset +subset: mouse_subset is_a: CL:0000740 ! retinal ganglion cell property_value: terms:contributor http://orcid.org/0000-0001-7258-9596 @@ -34392,6 +39313,8 @@ id: CL:4023033 name: OFF retinal ganglion cell def: "A retinal ganglion cell that is depolarized by decreased illumination of their receptive field center." [PMID:19602302] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset is_a: CL:0000740 ! retinal ganglion cell property_value: terms:contributor http://orcid.org/0000-0001-7258-9596 @@ -34410,9 +39333,11 @@ replaced_by: PCL:1000002 id: CL:4023035 name: lateral ganglionic eminence derived neuron def: "A neuron that is derived from a precursor cell in the lateral ganglion eminence." [wikipediaversioned:Ganglionic_eminence&oldid=1186824360] +subset: human_subset +subset: mouse_subset synonym: "LGE-derived neuron" EXACT [PMID:10377350] is_a: BFO:0000002 -is_a: CL:0000540 ! neuron +is_a: CL:2000029 ! central nervous system neuron intersection_of: CL:0000540 ! neuron intersection_of: RO:0002202 UBERON:0004025 ! develops from lateral ganglionic eminence relationship: RO:0002202 UBERON:0004025 ! develops from lateral ganglionic eminence @@ -34423,14 +39348,18 @@ property_value: terms:contributor "https://orcid.org/0000-0002-7073-9172" xsd:st id: CL:4023036 name: chandelier pvalb GABAergic cortical interneuron def: "A transcriptomically distinct pvalb GABAergic cortical interneuron that is recognizable by the straight terminal axonal 'cartridges' of vertically oriented strings of synaptic boutons. Chandelier PV cells' boutons target exclusively the axon initial segment (AIS) of pyramidal cells, with a single cell innervating hundreds of pyramidal cells in a clustered manner. The standard transcriptomic reference data for this cell type can be found on the CellxGene census under the collection: 'Transcriptomic cytoarchitecture reveals principles of human neocortex organization', dataset: 'Supercluster: CGE-derived interneurons', Author Categories: 'CrossArea_subclass', clusters Chandelier." [https://cellxgene.cziscience.com/e/9c63201d-bfd9-41a8-bbbc-18d947556f3d.cxg/, PMID:27477017] -comment: In mice, Chandelier PV cells have soma found in in upper L2/3, with some in deep L5 and exhibit fast-spiking but lower firing rate compared to basket cells, and have practically absent hyperpolarization sag. {xref="PMID:27477017"} +comment: The marker set GPR149, CA8 can identify the Human cell type chandelier pvalb GABAergic cortical interneuron in the Brain with a confidence of 0.799748111 (NS-Forest FBeta value). In mice, Chandelier PV cells have soma found in in upper L2/3, with some in deep L5 and exhibit fast-spiking but lower firing rate compared to basket cells, and have practically absent hyperpolarization sag. {xref="https://doi.org/10.5281/zenodo.11165918", xref="PMID:27477017"} subset: BDS_subset subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "Chandelier PV" EXACT [] xref: ILX:0107356 is_a: CL:4023018 ! pvalb GABAergic cortical interneuron is_a: CL:4023083 ! chandelier cell +relationship: RO:0015004 CLM:1000063 ! has characterizing marker set NS forest marker set of chandelier pvalb GABAergic cortical interneuron (Human Brain). property_value: IAO:0000028 "chandelier PV interneuron" xsd:string +property_value: RO:0002175 NCBITaxon:9606 property_value: terms:contributor https://orcid.org/0000-0001-7258-9596 [Term] @@ -34440,6 +39369,8 @@ def: "A glutamatergic neuron with a soma found in cortical layer 6b. They are tr subset: BDS_subset subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset xref: ILX:0770163 is_a: CL:0000679 ! glutamatergic neuron is_a: CL:0010012 ! cerebral cortex neuron @@ -34456,8 +39387,10 @@ name: amygdala excitatory neuron def: "Any neuron that has its soma located in some amygdala and is capable of some glutamate secretion, neurotransmission." [FBC:Autogenerated] comment: An excitatory neuron that is located in the amygdala. {xref="DOI:10.1101/2022.10.12.511898"} subset: human_reference_atlas +subset: human_subset +subset: mouse_subset is_a: CL:0000679 ! glutamatergic neuron -is_a: CL:2000029 ! central nervous system neuron +is_a: CL:0012001 ! neuron of the forebrain intersection_of: CL:0000540 ! neuron intersection_of: capable_of GO:0061535 ! glutamate secretion, neurotransmission intersection_of: RO:0002100 UBERON:0001876 ! has soma location amygdala @@ -34471,6 +39404,8 @@ name: L2/3-6 intratelencephalic projecting glutamatergic neuron def: "An intratelencephalic-projecting glutamatergic neuron with a soma found in cortical layers L2/3-6." [https://cellxgene.cziscience.com/e/c3aa4f95-7a18-4a7d-8dd8-ca324d714363.cxg/, PMID:34616075] subset: BDS_subset subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "L2/3-6 IT projecting neuron" EXACT [] is_a: CL:4023008 ! intratelencephalic-projecting glutamatergic cortical neuron property_value: IAO:0000028 "L2/3-6 IT glut" xsd:string @@ -34480,8 +39415,11 @@ property_value: terms:contributor https://orcid.org/0000-0001-7258-9596 id: CL:4023041 name: L5 extratelencephalic projecting glutamatergic cortical neuron def: "A transcriptomically distinct glutamatergic neuron, with a soma found in the deeper portion of L5, that has long-range axonal projections including deep subcortical targets outside of the telencephalon and, in some cases, the spinal cord. While the L5 ET neuron projections are not limited to ET targets, they are clearly differentiated from the neuron subclasses whose projections are constrained to intratelencephalic (IT) targets. L5 ET neurons are generally the largest excitatory cortical neurons, typically having a thick apical dendrite with a prominent dendritic tuft in layer 1 and displaying burst-firing physiological characteristics. The standard transcriptomic reference data for this cell type can be found on the CellxGene census under the collection: 'Transcriptomic cytoarchitecture reveals principles of human neocortex organization', dataset: 'Supercluster: Deep layer (non-IT) excitatory neurons ', Author Categories: 'CrossArea_subclass', clusters L5 ET." [https://cellxgene.cziscience.com/e/d01c9dff-abd1-4825-bf30-2eb2ba74597e.cxg/, PMID:34616075, PMID:37824655] +comment: The marker set CHST8, POU3F1 can identify the Human cell type L5 extratelencephalic projecting glutamatergic cortical neuron in the Brain with a confidence of 0.815891473 (NS-Forest FBeta value). {xref="https://doi.org/10.5281/zenodo.11165918"} subset: BDS_subset subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "burst-firing layer 5 neuron" EXACT [DOI:10.3389/fncel.2011.00001] synonym: "L5b neuron" RELATED OMO:0003000 [DOI:10.1016/j.neuron.2011.07.029] synonym: "pyramidal tract (PT) neuron" NARROW [DOI:10.1038/nrn3469] @@ -34493,22 +39431,29 @@ is_a: CL:4023111 ! cerebral cortex pyramidal neuron intersection_of: CL:4023009 ! extratelencephalic-projecting glutamatergic cortical neuron intersection_of: RO:0002100 UBERON:0005394 ! has soma location cortical layer V relationship: RO:0002100 UBERON:0005394 ! has soma location cortical layer V +relationship: RO:0015004 CLM:1000067 ! has characterizing marker set NS forest marker set of L5 extratelencephalic projecting glutamatergic cortical neuron (Human Brain). property_value: IAO:0000028 "L5 ET glut" xsd:string +property_value: RO:0002175 NCBITaxon:9606 property_value: terms:contributor https://orcid.org/0000-0001-7258-9596 [Term] id: CL:4023042 name: L6 corticothalamic-projecting glutamatergic cortical neuron def: "A transcriptomically distinct corticothalamic-projecting neuron with a soma found in cortical layer 6. The standard transcriptomic reference data for this cell type can be found on the CellxGene census under the collection: 'Transcriptomic cytoarchitecture reveals principles of human neocortex organization', dataset: 'Supercluster: Deep layer (non-IT) excitatory neurons', Author Categories: 'CrossArea_subclass', clusters L6 CT." [https://cellxgene.cziscience.com/e/d01c9dff-abd1-4825-bf30-2eb2ba74597e.cxg/, PMID:34616075, PMID:37824655] +comment: The marker set SEMA5B, ADAMTSL1, SULF1 can identify the Human cell type L6 corticothalamic-projecting glutamatergic cortical neuron in the Brain with a confidence of 0.631898455 (NS-Forest FBeta value). {xref="https://doi.org/10.5281/zenodo.11165918"} subset: BDS_subset subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "L6 CT" EXACT [PMID:28625486, PMID:34616075] is_a: CL:4023013 ! corticothalamic-projecting glutamatergic cortical neuron intersection_of: CL:4023013 ! corticothalamic-projecting glutamatergic cortical neuron intersection_of: RO:0002100 UBERON:0005395 ! has soma location cortical layer VI relationship: RO:0002100 UBERON:0005395 ! has soma location cortical layer VI relationship: RO:0013001 UBERON:0010225 ! has synaptic IO in region thalamic complex +relationship: RO:0015004 CLM:1000070 ! has characterizing marker set NS forest marker set of L6 corticothalamic-projecting glutamatergic cortical neuron (Human Brain). property_value: IAO:0000028 "L6 CT glut" xsd:string +property_value: RO:0002175 NCBITaxon:9606 property_value: terms:contributor https://orcid.org/0000-0001-7258-9596 [Term] @@ -34517,6 +39462,8 @@ name: L5/6 near-projecting glutamatergic neuron of the primary motor cortex def: "A transcriptomically distinct near-projecting glutamatergic neuron with a soma found in layer 5/6 of the primary motor cortex. The standard transcriptomic reference data for this cell type can be found on the CellxGene census under the collection: 'Transcriptomic cytoarchitecture reveals principles of human neocortex organization', dataset: 'Supercluster: Deep layer (non-IT) excitatory neurons', Author Categories: 'CrossArea_subclass', cluster L5/6 NP." [https://cellxgene.cziscience.com/e/d01c9dff-abd1-4825-bf30-2eb2ba74597e.cxg/, PMID:31209381, PMID:34616075] subset: BDS_subset subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "L5/6 NP M1" EXACT [] synonym: "L5/6 NP MOp" EXACT [] xref: ILX:0770161 @@ -34532,6 +39479,8 @@ id: CL:4023044 name: non-medulla, extratelencephalic-projecting glutamatergic neuron of the primary motor cortex def: "An extratelencephalic-projecting glutamatergic neuron located in layer 5b of the primary motor cortex that does not project to the medulla. Non-MY ET cells are large, big-tufted cells with the apical dendrite often bifurcating close to the soma, suggesting they are corticospinal cells. Non-MY ET cells have bigger hyperpolarization sag, lower input resistance, and smaller AP width, compared to L5 IT neurons." [DOI:10.1101/2020.10.19.343129, PMID:24137110, PMID:9236245] subset: BDS_subset +subset: human_subset +subset: mouse_subset synonym: "non-MY ET M1" EXACT [] synonym: "non-MY ET MOp (Mus)" EXACT [] is_a: CL:2000049 ! primary motor cortex pyramidal cell @@ -34544,6 +39493,8 @@ id: CL:4023045 name: medulla-projecting glutamatergic neuron of the primary motor cortex def: "An extratelencephalic-projecting glutamatergic neuron located in layer 5b of the primary motor cortex that projects to the medulla. MY ET cells are large, big-tufted cells with the apical dendrite often bifurcating close to the soma, suggesting they are corticospinal cells. MY ET cells have bigger hyperpolarization sag, lower input resistance, and smaller AP width, compared to L5 IT neurons." [DOI:10.1101/2020.10.19.343129, PMID:24137110, PMID:9236245] subset: BDS_subset +subset: human_subset +subset: mouse_subset synonym: "medulla-projecting extratelencephalic-projecting glutamatergic neuron of the primary motor cortex" EXACT [] synonym: "MY ET M1" EXACT [] synonym: "MY ET MOp" EXACT [] @@ -34558,11 +39509,16 @@ property_value: terms:contributor https://orcid.org/0000-0001-7258-9596 id: CL:4023046 name: L6b glutamatergic neuron of the primary motor cortex def: "An excitatory glutamatergic neuron transcriptomically related to the CT subclass, with a soma preferentially located in the bottom of L6 of the primary motor cortex." [PMID:33184512] +comment: The marker set CCN2, ROS1 can identify the Human cell type L6b glutamatergic neuron of the primary motor cortex in the Brain with a confidence of 0.819940964 (NS-Forest FBeta value). {xref="https://doi.org/10.5281/zenodo.11165918"} subset: BDS_subset +subset: human_subset +subset: mouse_subset synonym: "L6b subplate glutamatergic neuron of the primary motor cortex" EXACT [] is_a: CL:4023038 ! L6b glutamatergic cortical neuron relationship: RO:0002100 UBERON:0001384 ! has soma location primary motor cortex +relationship: RO:0015004 CLM:1000073 ! has characterizing marker set NS forest marker set of L6b glutamatergic neuron of the primary motor cortex (Human Brain). property_value: IAO:0000028 "L6b subplate glut" xsd:string +property_value: RO:0002175 NCBITaxon:9606 property_value: terms:contributor https://orcid.org/0000-0001-7258-9596 [Term] @@ -34571,6 +39527,8 @@ name: L2/3 intratelencephalic projecting glutamatergic neuron of the primary mot def: "An intratelencephalic-projecting glutamatergic neuron with a soma found in cortical layer 2/3 of the primary motor cortex." [PMID:34616075] subset: BDS_subset subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "L2/3 IT M1" EXACT [PMID:34616075] synonym: "L2/3 IT MOp" EXACT [PMID:34616075] is_a: CL:4030059 ! L2/3 intratelencephalic projecting glutamatergic neuron @@ -34586,6 +39544,8 @@ name: L4/5 intratelencephalic projecting glutamatergic neuron of the primary mot def: "An intratelencephalic-projecting glutamatergic with a soma located in upper L5 of the primary motor cortex. These cells have thin untufted apical dendrites." [PMID:33184512] subset: BDS_subset subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "L4/5 IT M1" EXACT [] synonym: "L4/5 IT MOp" EXACT [] xref: ILX:0770174 @@ -34601,6 +39561,8 @@ id: CL:4023049 name: L5 intratelencephalic projecting glutamatergic neuron of the primary motor cortex def: "An intratelencephalic-projecting glutamatergic neuron with a soma found in L5 of the primary motor cortex." [PMID:33184512] subset: BDS_subset +subset: human_subset +subset: mouse_subset synonym: "L5 IT M1" EXACT [] synonym: "L5 IT MOp" EXACT [] xref: ILX:0770157 @@ -34617,14 +39579,16 @@ name: L6 intratelencephalic projecting glutamatergic neuron of the primary motor def: "An intratelencephalic-projecting glutamatergic neuron with a soma found in L6 of the primary motor cortex. These cells are short untufted pyramidal cells, which could be stellate or inverted." [PMID:33184512, PMID:34616063, PMID:34616075, PMID:9236245] subset: BDS_subset subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "L6 IT M1" EXACT [] synonym: "L6 IT MOp" EXACT [] xref: ILX:0770158 is_a: CL:2000049 ! primary motor cortex pyramidal cell +is_a: CL:4023095 ! untufted pyramidal neuron is_a: CL:4030065 ! L6 intratelencephalic projecting glutamatergic neuron intersection_of: CL:4030065 ! L6 intratelencephalic projecting glutamatergic neuron intersection_of: RO:0002100 UBERON:0001384 ! has soma location primary motor cortex -relationship: bearer_of PATO:0070019 ! untufted pyramidal morphology property_value: IAO:0000028 "L6 IT glut MOp" xsd:string property_value: terms:contributor https://orcid.org/0000-0001-7258-9596 @@ -34634,6 +39598,8 @@ name: vascular leptomeningeal cell def: "A transcriptomically distinct type of mesothelial fibroblast that is derived from the neural crest, is localized on blood vessels, and is a key component of the pia and arachnoid membranes surrounding the brain. The standard transcriptomic reference data for this cell type can be found on the CellxGene census under the collection: 'Transcriptomic cytoarchitecture reveals principles of human neocortex organization', dataset: 'Supercluster: Non-neuronal cells', Author Categories: 'CrossArea_subclass', clusters VLMC." [https://cellxgene.cziscience.com/e/5346f9c6-755e-4336-94cc-38706ec00c2f.cxg/, PMID:27284195, PMID:29443965, PMID:30096314, PMID:37824655] subset: BDS_subset subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "VLMC" EXACT [] xref: ILX:0770143 is_a: CL:4023058 ! mesothelial fibroblast of the leptomeninx @@ -34644,6 +39610,8 @@ property_value: terms:contributor https://orcid.org/0000-0001-7258-9596 id: CL:4023052 name: Betz upper motor neuron def: "A Betz cell that synapses with lower motor neurons directly." [DOI:10.1101/2020.03.31.016972, PMID:18558853, PMID:28751609] +subset: human_subset +subset: mouse_subset is_a: CL:0008049 ! Betz cell relationship: RO:0002120 CL:0008039 ! synapsed to lower motor neuron property_value: RO:0002175 NCBITaxon:9606 @@ -34653,6 +39621,8 @@ property_value: terms:contributor https://orcid.org/0000-0001-7258-9596 id: CL:4023053 name: spinal interneuron synapsing Betz cell def: "A Betz cell that syanpses with spinal interneurons." [DOI:10.1101/2020.03.31.016972, PMID:18558853] +subset: human_subset +subset: mouse_subset is_a: CL:0008049 ! Betz cell relationship: RO:0002120 CL:0005000 ! synapsed to spinal cord interneuron property_value: RO:0002175 NCBITaxon:9685 @@ -34664,6 +39634,8 @@ id: CL:4023054 name: mesothelial fibroblast def: "A mesothelial cell that has undergone mesothelial-to-mesenchymal transition (MMT) to become a fibroblast cell." [PMID:26106328] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset is_a: CL:0000057 ! fibroblast relationship: RO:0002202 CL:0000077 ! develops from mesothelial cell property_value: terms:contributor https://orcid.org/0000-0001-7258-9596 @@ -34674,11 +39646,13 @@ name: corticothalamic VAL/VM projecting glutamatergic neuron of the primary moto def: "A corticothalamic-projecting glutamatergic neuron that is located in L6 and lower L5 of the primary motor cortex, with a pyramidal morphology and mostly untufted apical dendrites terminating in midcortical layers. CT VAL/VM (ventroanterior-ventrolateral complex/ventromedial nucleus) cells have a near tonic firing pattern and are distinguished from L6 IT neurons by a lower inter-spike interval adaptation index." [PMID:20556241, PMID:9236245] comment: The assertion of this cell type under L6 CT is due to the ambiguity of lower L5 and L6. subset: BDS_subset +subset: human_subset +subset: mouse_subset synonym: "CT VAL/VM M1" EXACT [] synonym: "CT VAL/VM MOp" EXACT [] is_a: CL:2000049 ! primary motor cortex pyramidal cell is_a: CL:4023042 ! L6 corticothalamic-projecting glutamatergic cortical neuron -relationship: bearer_of PATO:0070019 ! untufted pyramidal morphology +is_a: CL:4023095 ! untufted pyramidal neuron property_value: IAO:0000028 "CT VAL/VM glut MOp" xsd:string property_value: terms:contributor https://orcid.org/0000-0001-7258-9596 @@ -34688,6 +39662,7 @@ name: vascular leptomeningeal cell (Mmus) def: "A type of mouse mesothelial fibroblast that is derived from the neural crest, is localized on blood vessels, and is a key component of the pia and arachnoid membranes surrounding the brain." [PMID:30096314] subset: BDS_subset subset: cellxgene_subset +subset: mouse_subset synonym: "VLMC (Mus musculus)" EXACT [] is_a: CL:4023051 ! vascular leptomeningeal cell relationship: RO:0002162 NCBITaxon:10090 ! in taxon Mus musculus @@ -34702,7 +39677,8 @@ name: cerebellar inhibitory GABAergic interneuron def: "Any GABAergic interneuron that has its soma located in some cerebellar cortex." [FBC:Autogenerated] comment: A GABAergic interneuron whose soma is located in the cerebellar cortex. {xref="DOI:10.1101/2022.10.12.511898"} subset: human_reference_atlas -is_a: CL:0000402 ! CNS interneuron +subset: human_subset +subset: mouse_subset is_a: CL:0011005 ! GABAergic interneuron is_a: CL:1001611 ! cerebellar neuron intersection_of: CL:0011005 ! GABAergic interneuron @@ -34715,6 +39691,8 @@ property_value: terms:contributor http://orcid.org/0000-0001-7258-9596 id: CL:4023058 name: mesothelial fibroblast of the leptomeninx def: "A mesothelial fibroblast found in the leptomeninx." [] +subset: human_subset +subset: mouse_subset is_a: CL:0002319 ! neural cell is_a: CL:4023054 ! mesothelial fibroblast intersection_of: CL:4023054 ! mesothelial fibroblast @@ -34729,6 +39707,8 @@ def: "An oligodendrocyte precursor cell that is committed to differentiate." [PM comment: COPs are distinct from OPCs in that the lack expression of Pdgfra and Cspg4 and come out as distinct clusters in transcriptomic profiling. This is the reason that this term is not modelled as a subclassOf OPC but instead linked using develops_from. {xref="PMID:27284195"} subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "committed oligodendrocyte precursor" EXACT [] synonym: "COP" EXACT OMO:0003000 [] is_a: CL:0000123 ! neuron associated cell (sensu Vertebrata) @@ -34741,6 +39721,8 @@ id: CL:4023060 name: hippocampal CA1-3 neuron def: "A neuron that has its soma located in CA1-3 of the hippocampus." [DOI:10.1101/2022.10.12.511898] subset: human_reference_atlas +subset: human_subset +subset: mouse_subset is_a: CL:0002608 ! hippocampal neuron relationship: RO:0002100 UBERON:0001954 ! has soma location Ammon's horn property_value: IAO:0000116 "It is unclear as to if the modelling of Ammon's horn includes CA4 (which could be considered part of the dentate gyrus) in Uberon, hence no equivalent class axiom was made." xsd:string @@ -34752,7 +39734,9 @@ id: CL:4023061 name: hippocampal CA4 neuron def: "A neuron that has its soma located in CA4 of the hippocampus." [DOI:10.1101/2022.10.12.511898] subset: human_reference_atlas -is_a: CL:0000540 ! neuron +subset: human_subset +subset: mouse_subset +is_a: CL:2000029 ! central nervous system neuron property_value: RO:0002175 NCBITaxon:9606 property_value: terms:contributor http://orcid.org/0000-0001-7258-9596 @@ -34761,6 +39745,8 @@ id: CL:4023062 name: dentate gyrus neuron def: "A neuron with its soma located in the dentate gyrus of the hippocampus." [] subset: human_reference_atlas +subset: human_subset +subset: mouse_subset is_a: CL:0002608 ! hippocampal neuron intersection_of: CL:0000540 ! neuron intersection_of: RO:0002100 UBERON:0001885 ! has soma location dentate gyrus of hippocampal formation @@ -34773,6 +39759,8 @@ id: CL:4023063 name: medial ganglionic eminence derived interneuron def: "An interneuron that is derived from the medial ganglionic eminence." [DOI:10.1101/2022.10.12.511898] subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "MGE interneuron" EXACT [] is_a: BFO:0000002 is_a: CL:0000099 ! interneuron @@ -34788,17 +39776,18 @@ id: CL:4023064 name: caudal ganglionic eminence derived cortical interneuron def: "An interneuron that is derived from the caudal ganglionic eminence." [PMID:20130169, PMID:37824655, PMID:37824663] subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "caudal ganglionic eminence derived GABAergic cortical interneuron" EXACT [PMID:20130169] synonym: "CGE cortical interneuron" RELATED OMO:0003000 [PMID:20130169] synonym: "CGE interneuron" RELATED OMO:0003000 [PMID:37824663] synonym: "CGE-derived cell" RELATED OMO:0003000 [PMID:27034423] synonym: "CGE-derived GABAergic IN" RELATED OMO:0003000 [PMID:27034423] synonym: "CGE-derived interneuron" RELATED OMO:0003000 [PMID:20130169, PMID:37824655] -is_a: BFO:0000002 is_a: CL:0010011 ! cerebral cortex GABAergic interneuron +is_a: CL:4042039 ! caudal ganglionic eminence derived neuron intersection_of: CL:0000099 ! interneuron intersection_of: RO:0002202 UBERON:0004026 ! develops from caudal ganglionic eminence -relationship: RO:0002202 UBERON:0004026 ! develops from caudal ganglionic eminence property_value: IAO:0000028 "CGE interneuron" xsd:string property_value: RO:0002175 NCBITaxon:9606 property_value: terms:contributor http://orcid.org/0000-0001-7258-9596 @@ -34809,6 +39798,8 @@ name: meis2 expressing cortical GABAergic cell def: "A GABAergic cell located in the cerebral cortex that expresses meis2." [PMID:33372656] subset: BDS_subset subset: cellxgene_subset +subset: human_subset +subset: mouse_subset is_a: BFO:0000002 is_a: CL:0000617 ! GABAergic neuron is_a: CL:0010012 ! cerebral cortex neuron @@ -34821,9 +39812,10 @@ id: CL:4023066 name: horizontal pyramidal neuron def: "A pyramidal neuron which has an apical tree which is oriented parallel to the pia. This is unlike typical pyramidal neurons which have its apical dendrite aligned vertically." [PMID:30715238] subset: BDS_subset -is_a: CL:0000117 ! CNS neuron (sensu Vertebrata) +subset: human_subset +subset: mouse_subset is_a: CL:0000598 ! pyramidal neuron -intersection_of: CL:0000117 ! CNS neuron (sensu Vertebrata) +intersection_of: CL:0000540 ! neuron intersection_of: bearer_of PATO:0070016 ! horizontal pyramidal morphology relationship: bearer_of PATO:0070016 ! horizontal pyramidal morphology property_value: terms:contributor https://orcid.org/0000-0001-7258-9596 @@ -34842,10 +39834,14 @@ replaced_by: PCL:1000004 [Term] id: CL:4023068 name: thalamic excitatory neuron -def: "An excitatory neuron that has its soma located in the thalamic complex." [DOI:10.1101/2022.10.12.511898] +def: "An excitatory neuron that has its soma located in the thalamic complex. This neuron type can be involved in a series of circuits related to sensory integration, motor integration, pain processing, social behaviour and reward response." [PMID:30083593, PMID:31196673, PMID:35278647, PMID:37163009, PMID:37824663, PMID:38739251] +comment: Abnormalities in glutametergic neurons of the thalamic complex are associated with pathologies such as schizophrenia, colorectal visceral pain and Parkinson's disease. {xref="PMID:11532718", xref="PMID:30083593", xref="PMID:38739251"} +subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset is_a: CL:0000679 ! glutamatergic neuron -is_a: CL:2000029 ! central nervous system neuron +is_a: CL:0012001 ! neuron of the forebrain intersection_of: CL:0000540 ! neuron intersection_of: capable_of GO:0061535 ! glutamate secretion, neurotransmission intersection_of: RO:0002100 UBERON:0010225 ! has soma location thalamic complex @@ -34857,6 +39853,8 @@ property_value: terms:contributor http://orcid.org/0000-0001-7258-9596 id: CL:4023069 name: medial ganglionic eminence derived GABAergic cortical interneuron def: "A GABAergic cortical interneuron that develops from the medial ganglionic eminence and has migrated to the cerebral cortex." [PMID:12637172] +subset: human_subset +subset: mouse_subset synonym: "MGE cortical interneuron" EXACT [] is_a: CL:0010011 ! cerebral cortex GABAergic interneuron is_a: CL:4023063 ! medial ganglionic eminence derived interneuron @@ -34885,6 +39883,7 @@ id: CL:4023071 name: L5/6 cck GABAergic interneuron (Mmus) def: "A GABAergic cortical interneuron that expresses cck. L5/6 cck cells have soma found mainly in L5 and L6 and have large axonal arborization." [PMID:33184512] subset: BDS_subset +subset: mouse_subset synonym: "L5/6 CCK (Mus musculus)" EXACT [] is_a: BFO:0000002 is_a: CL:0010011 ! cerebral cortex GABAergic interneuron @@ -34898,7 +39897,10 @@ property_value: terms:contributor https://orcid.org/0000-0001-7258-9596 id: CL:4023072 name: brain vascular cell def: "A cell that is part of the brain vasculature." [DOI:10.1101/2022.10.12.511898] +subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset is_a: CL:0002319 ! neural cell intersection_of: CL:0000000 ! cell intersection_of: part_of UBERON:0008998 ! vasculature of brain @@ -34920,7 +39922,9 @@ id: CL:4023074 name: mammillary body neuron def: "A neuron that has its soma located in the mammillary body." [DOI:10.1101/2022.10.12.511898] subset: human_reference_atlas -is_a: CL:2000029 ! central nervous system neuron +subset: human_subset +subset: mouse_subset +is_a: CL:0012001 ! neuron of the forebrain intersection_of: CL:0000540 ! neuron intersection_of: RO:0002100 UBERON:0002206 ! has soma location mammillary body relationship: RO:0002100 UBERON:0002206 ! has soma location mammillary body @@ -34932,6 +39936,7 @@ id: CL:4023075 name: L6 th sst GABAergic interneuron (Mmus) def: "A sst GABAergic cortical interneuron found in L6 that expresses tyrosine hydroxylase. L6 Th+ SST cells have mostly local axonal arborization within L6." [PMID:22357664] subset: BDS_subset +subset: mouse_subset synonym: "L6 Th+ SST (Mus musculus)" EXACT [] synonym: "L6 tyrosine hydroxylase positive sst expressing GABAergic cortical interneuron (Mus musculus)" EXACT [] is_a: BFO:0000002 @@ -34948,9 +39953,10 @@ id: CL:4023076 name: Martinotti neuron def: "An interneuron that has Martinotti morphology. These interneurons are scattered throughout various layers of the cerebral cortex, sending their axons up to the cortical layer I where they form axonal arborization." [WikipediaVersioned:Martinotti_cell&oldid=9947732] subset: BDS_subset +subset: human_subset +subset: mouse_subset xref: ILX:0107375 xref: NIFEXT:55 -is_a: CL:0000104 ! multipolar neuron is_a: CL:0011005 ! GABAergic interneuron intersection_of: CL:0000099 ! interneuron intersection_of: bearer_of PATO:0070007 ! Martinotti morphology @@ -34963,6 +39969,8 @@ id: CL:4023077 name: bitufted neuron def: "A type of interneuron that has two clusters of dendritic branches that originate directly from the soma and extend in opposite directions and axons that form a plexus which spreads widely. Compared to bipolar neurons, bitufted neurons have branching that occur close to the soma." [PMID:18568015] subset: BDS_subset +subset: human_subset +subset: mouse_subset xref: ILX:0777212 {IAO:0000116="Interlex cross reference refers specifically to Markram 2015 rat bitufted cell."} is_a: CL:0000099 ! interneuron intersection_of: CL:0000099 ! interneuron @@ -34986,7 +39994,9 @@ id: CL:4023079 name: midbrain-derived inhibitory neuron def: "A GABAergic inhibitory neuron that is derived from the midbrain." [DOI:10.1101/2022.10.12.511898] subset: human_reference_atlas -is_a: CL:0000540 ! neuron +subset: human_subset +subset: mouse_subset +is_a: CL:2000029 ! central nervous system neuron is_a: UBERON:0004121 ! ectoderm-derived structure intersection_of: CL:0000540 ! neuron intersection_of: RO:0002202 UBERON:0001891 ! develops from midbrain @@ -34999,9 +40009,11 @@ id: CL:4023080 name: stellate L6 intratelencephalic projecting glutamatergic neuron of the primary motor cortex (Mmus) def: "a L6 intratelencephalic projecting glutamatergic neuron of the primary motor cortex that has stellate pyramidal morphology." [PMID:9236245] subset: BDS_subset +subset: human_subset +subset: mouse_subset synonym: "stellate L6 IT MOp (Mus musculus)" EXACT [] is_a: CL:4023050 ! L6 intratelencephalic projecting glutamatergic neuron of the primary motor cortex -relationship: bearer_of PATO:0070020 ! stellate pyramidal morphology +is_a: CL:4023093 ! stellate pyramidal neuron property_value: IAO:0000028 "stellate L6 IT glut MOp" xsd:string property_value: terms:contributor https://orcid.org/0000-0001-7258-9596 @@ -35010,9 +40022,11 @@ id: CL:4023081 name: inverted L6 intratelencephalic projecting glutamatergic neuron of the primary motor cortex (Mmus) def: "a L6 intratelencephalic projecting glutamatergic neuron of the primary motor cortex that has inverted pyramidal morphology." [PMID:9236245] subset: BDS_subset +subset: human_subset +subset: mouse_subset synonym: "inverted L6 IT MOp (Mus musculus)" EXACT [] is_a: CL:4023050 ! L6 intratelencephalic projecting glutamatergic neuron of the primary motor cortex -relationship: bearer_of PATO:0070021 ! inverted pyramidal morphology +is_a: CL:4023092 ! inverted pyramidal neuron property_value: IAO:0000028 "inverted L6 IT glut MOp" xsd:string property_value: terms:contributor https://orcid.org/0000-0001-7258-9596 @@ -35021,6 +40035,9 @@ id: CL:4023083 name: chandelier cell def: "A GABAergic interneuron that selectively innervates the axon initial segment of pyramidal cells. Their local axonal clusters are formed by high-frequency branching at shallow angles, often ramifying around, above or below their somata with a high bouton density. The characteristic terminal portions of the axon form short vertical rows of boutons, resembling the candlesticks and candles of a chandelier. Chandelier cells can be multipolar or bitufted." [PMID:15378039, PMID:27199673, PMID:37824655] subset: BDS_subset +subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "axo-axonic cell" BROAD [PMID:27199673, PMID:33862423] synonym: "ChC" RELATED OMO:0003000 [PMID:15378039] xref: ILX:0777213 {IAO:0000116="Interlex cross reference refers specifically to Markram 2015 rat chandelier cell."} @@ -35035,6 +40052,8 @@ id: CL:4023086 name: T Martinotti neuron def: "A Martinotti neuron that has axons that form a horizontal ramification, making it T-shaped." [doi:10.1016/b978-0-12-369497-3.10004-4] subset: BDS_subset +subset: human_subset +subset: mouse_subset synonym: "T-shaped Martinotti neuron" EXACT [] is_a: CL:4023076 ! Martinotti neuron intersection_of: CL:0000099 ! interneuron @@ -35048,6 +40067,8 @@ id: CL:4023087 name: fan Martinotti neuron def: "A Martinotti neuron that has axons that form a fan-like plexus." [doi:10.1016/b978-0-12-369497-3.10004-4] subset: BDS_subset +subset: human_subset +subset: mouse_subset synonym: "fanning-out Martinotti neuron" EXACT [] is_a: CL:4023076 ! Martinotti neuron intersection_of: CL:0000099 ! interneuron @@ -35061,6 +40082,8 @@ id: CL:4023088 name: large basket cell def: "A basket cell that is large, and typically ascends to give rise to many long horizontally and vertically projecting axon collaterals that traverse neighboring columns and can extend through all cortical layers." [PMID:11884355] subset: BDS_subset +subset: human_subset +subset: mouse_subset is_a: CL:2000086 ! neocortex basket cell intersection_of: CL:0000099 ! interneuron intersection_of: bearer_of PATO:0070004 ! large basket cell morphology @@ -35074,6 +40097,8 @@ id: CL:4023089 name: nest basket cell def: "A basket cell which has simpler dendritic arbors (compared to small or large basket cells), and an axonal plexus of intermediate density, composed of a few long, smooth axonal branches." [PMID:11884355] subset: BDS_subset +subset: human_subset +subset: mouse_subset is_a: CL:2000086 ! neocortex basket cell intersection_of: CL:0000099 ! interneuron intersection_of: bearer_of PATO:0070005 ! nest basket cell morphology @@ -35087,6 +40112,8 @@ id: CL:4023090 name: small basket cell def: "A basket cell with axonal arbors composed of frequent, short, curvy axonal branches that tend to be near their somata and within the same layer." [PMID:11884355] subset: BDS_subset +subset: human_subset +subset: mouse_subset is_a: CL:2000086 ! neocortex basket cell intersection_of: CL:0000099 ! interneuron intersection_of: bearer_of PATO:0070003 ! small basket cell morphology @@ -35100,9 +40127,10 @@ id: CL:4023092 name: inverted pyramidal neuron def: "A pyramidal neuron which has an apical tree which is oriented towards the white matter." [PMID:30715238] subset: BDS_subset -is_a: CL:0000117 ! CNS neuron (sensu Vertebrata) +subset: human_subset +subset: mouse_subset is_a: CL:0000598 ! pyramidal neuron -intersection_of: CL:0000117 ! CNS neuron (sensu Vertebrata) +intersection_of: CL:0000540 ! neuron intersection_of: bearer_of PATO:0070021 ! inverted pyramidal morphology relationship: bearer_of PATO:0070021 ! inverted pyramidal morphology property_value: terms:contributor https://orcid.org/0000-0001-7258-9596 @@ -35112,9 +40140,10 @@ id: CL:4023093 name: stellate pyramidal neuron def: "A pyramidal neuron which lacks a tuft formation but extends small radial distances forming a star-like shape." [PMID:30715238] subset: BDS_subset -is_a: CL:0000117 ! CNS neuron (sensu Vertebrata) +subset: human_subset +subset: mouse_subset is_a: CL:0000598 ! pyramidal neuron -intersection_of: CL:0000117 ! CNS neuron (sensu Vertebrata) +intersection_of: CL:0000540 ! neuron intersection_of: bearer_of PATO:0070020 ! stellate pyramidal morphology relationship: bearer_of PATO:0070020 ! stellate pyramidal morphology property_value: terms:contributor https://orcid.org/0000-0001-7258-9596 @@ -35124,9 +40153,10 @@ id: CL:4023094 name: tufted pyramidal neuron def: "A pyramidal neuron which has a distinctive tuft formation, distal from the soma." [PMID:30715238] subset: BDS_subset -is_a: CL:0000117 ! CNS neuron (sensu Vertebrata) +subset: human_subset +subset: mouse_subset is_a: CL:0000598 ! pyramidal neuron -intersection_of: CL:0000117 ! CNS neuron (sensu Vertebrata) +intersection_of: CL:0000540 ! neuron intersection_of: bearer_of PATO:0070018 ! tufted pyramidal morphology relationship: bearer_of PATO:0070018 ! tufted pyramidal morphology property_value: terms:contributor https://orcid.org/0000-0001-7258-9596 @@ -35136,9 +40166,10 @@ id: CL:4023095 name: untufted pyramidal neuron def: "A pyramidal neuron which lacks a clear tuft formation but extends to large radial distances." [PMID:30715238] subset: BDS_subset -is_a: CL:0000117 ! CNS neuron (sensu Vertebrata) +subset: human_subset +subset: mouse_subset is_a: CL:0000598 ! pyramidal neuron -intersection_of: CL:0000117 ! CNS neuron (sensu Vertebrata) +intersection_of: CL:0000540 ! neuron intersection_of: bearer_of PATO:0070019 ! untufted pyramidal morphology relationship: bearer_of PATO:0070019 ! untufted pyramidal morphology property_value: terms:contributor https://orcid.org/0000-0001-7258-9596 @@ -35147,6 +40178,8 @@ property_value: terms:contributor https://orcid.org/0000-0001-7258-9596 id: CL:4023097 name: arachnoid barrier cell def: "A mesothelial fibroblast of the arachnoid barrier layer. Arachnoid barrier cells make up the tight-junctioned layer in the leptomeninx that functions as the physiologic barrier between the cerebrospinal fluid in the subarachnoid space and the fenestrated capillaries in the dura." [PMID:23298861] +subset: human_subset +subset: mouse_subset synonym: "AB cell" RELATED OMO:0003000 [PMID:23298861] synonym: "ABC" RELATED OMO:0003000 [PMID:30096314] is_a: CL:4023058 ! mesothelial fibroblast of the leptomeninx @@ -35254,6 +40287,8 @@ replaced_by: CL:4023065 id: CL:4023107 name: reticulospinal neuron def: "A neuron with soma location in the reticular formation with axons that extend into the spinal cord such. Reticulospinal neuron activity can lead to a variety of motor behaviors." [PMID:29720934] +subset: human_subset +subset: mouse_subset synonym: "RSN" EXACT [PMID:29720934] is_a: CL:2000029 ! central nervous system neuron intersection_of: CL:0000540 ! neuron @@ -35267,6 +40302,8 @@ property_value: terms:contributor https://orcid.org/0000-0001-7258-9596 id: CL:4023108 name: oxytocin-secreting magnocellular cell def: "A magnocellular neurosecretory cell that is capable of producing and secreting oxytocin." [WikipediaVersioned:Magnocellular_neurosecretory_cell&oldid=1021059931] +subset: human_subset +subset: mouse_subset is_a: CL:0011003 ! magnocellular neurosecretory cell intersection_of: CL:0011003 ! magnocellular neurosecretory cell intersection_of: capable_of GO:0036162 ! oxytocin production @@ -35277,6 +40314,8 @@ property_value: terms:contributor https://orcid.org/0000-0001-7258-9596 id: CL:4023109 name: vasopressin-secreting magnocellular cell def: "A magnocellular neurosecretory cell that is capable of producing and secreting vasopressin." [WikipediaVersioned:Magnocellular_neurosecretory_cell&oldid=1021059931] +subset: human_subset +subset: mouse_subset is_a: CL:0000167 ! peptide hormone secreting cell is_a: CL:0011003 ! magnocellular neurosecretory cell intersection_of: CL:0011003 ! magnocellular neurosecretory cell @@ -35288,8 +40327,10 @@ property_value: terms:contributor https://orcid.org/0000-0001-7258-9596 id: CL:4023110 name: amygdala pyramidal neuron def: "A pyramidal neuron with soma located in the amygdala." [PMID:1375860] +subset: human_subset +subset: mouse_subset is_a: CL:0000598 ! pyramidal neuron -is_a: CL:2000029 ! central nervous system neuron +is_a: CL:0012001 ! neuron of the forebrain intersection_of: CL:0000598 ! pyramidal neuron intersection_of: RO:0002100 UBERON:0001876 ! has soma location amygdala relationship: RO:0002100 UBERON:0001876 ! has soma location amygdala @@ -35299,6 +40340,8 @@ property_value: terms:contributor https://orcid.org/0000-0001-7258-9596 id: CL:4023111 name: cerebral cortex pyramidal neuron def: "A pyramidal neuron with soma located in the cerebral cortex." [PMID:30715238] +subset: human_subset +subset: mouse_subset is_a: CL:0000598 ! pyramidal neuron is_a: CL:0010012 ! cerebral cortex neuron intersection_of: CL:0000598 ! pyramidal neuron @@ -35309,6 +40352,8 @@ property_value: terms:contributor https://orcid.org/0000-0001-7258-9596 id: CL:4023112 name: vestibular afferent neuron def: "An afferent neuron of the vestibular system that innervate the base of the hair cell and increase or decrease their neural firing rate as the receptor cell is excited or inhibited." [PMID:2585041] +subset: human_subset +subset: mouse_subset is_a: CL:0000101 ! sensory neuron relationship: RO:0002120 CL:0000609 ! synapsed to vestibular hair cell property_value: terms:contributor https://orcid.org/0000-0001-7258-9596 @@ -35317,6 +40362,8 @@ property_value: terms:contributor https://orcid.org/0000-0001-7258-9596 id: CL:4023113 name: bouton vestibular afferent neuron def: "A vestibular afferent neuron that makes bouton synapses to type II hair cells." [PMID:10706428] +subset: human_subset +subset: mouse_subset is_a: CL:4023112 ! vestibular afferent neuron relationship: has_part GO:0043195 ! terminal bouton relationship: RO:0002130 CL:0002069 ! has synaptic terminal in type II vestibular sensory cell @@ -35326,6 +40373,8 @@ property_value: terms:contributor https://orcid.org/0000-0001-7258-9596 id: CL:4023114 name: calyx vestibular afferent neuron def: "A vestibular afferent neuron which posseses a unique postsynaptic terminal, the calyx, which completely covers the basolateral walls of type I hair cells and receives input from multiple ribbon synapses." [PMID:25355208] +subset: human_subset +subset: mouse_subset is_a: CL:4023112 ! vestibular afferent neuron relationship: has_part GO:0099096 ! vestibular calyx terminal relationship: RO:0002130 CL:0002070 ! has synaptic terminal in type I vestibular sensory cell @@ -35336,6 +40385,8 @@ id: CL:4023115 name: type 1 spiral ganglion neuron def: "A spiral ganglion neuron that innervates inner hair cells. Type 1 spiral ganglion neurons are myelinated and bipolar." [WikipediaVersioned:Spiral_ganglion&oldid=994446209] comment: Type 1 spiral ganglion neurons comprise the vast majority of spiral ganglion cells. {xref="WikipediaVersioned:Spiral_ganglion&oldid=994446209"} +subset: human_subset +subset: mouse_subset synonym: "type I spiral ganglion cell" EXACT [] is_a: CL:0011113 ! spiral ganglion neuron is_a: UBERON:0000122 ! neuron projection bundle @@ -35350,6 +40401,8 @@ id: CL:4023116 name: type 2 spiral ganglion neuron def: "A spiral ganglion neuron that innervates outer hair cells. Type 1 spiral ganglion neurons are unmyelinated and unipolar." [WikipediaVersioned:Spiral_ganglion&oldid=994446209] comment: Outer hair cells form reciprocal synapses onto type 2 spiral ganglion cells, suggesting that the type 2 cells have both afferent and efferent roles. {xref="WikipediaVersioned:Spiral_ganglion&oldid=994446209"} +subset: human_subset +subset: mouse_subset synonym: "type II spiral ganglion cell" EXACT [] is_a: CL:0011113 ! spiral ganglion neuron is_a: UBERON:0000122 ! neuron projection bundle @@ -35365,6 +40418,7 @@ name: L5/6 non-Martinotti sst GABAergic interneuron (Mmus) def: "A sst GABAergic interneuron does not have Martinotti morphology with a soma found in L5/6 of the cerebral cortex." [PMID:27477017] comment: L5/6 non-Martinotti SST cells have strongly facilitating excitatory inputs and moderately depressing outputs. They have faster action potential than Martinotti morphology SST cells and slightly slower than PV basket cells. {xref="PMID:27477017"} subset: BDS_subset +subset: mouse_subset synonym: "L5/6 non-Martinotti morphology sst expressing GABAergic cortical interneuron (Mus musculus)" EXACT [] synonym: "L5/6 non-Martinotti SST (Mus musculus)" EXACT [] is_a: BFO:0000002 @@ -35380,6 +40434,8 @@ id: CL:4023119 name: displaced amacrine cell def: "A subpopulation of amacrine cell that migrate further than other amacrine cells, and come to lie basal to the inner plexiform layer (IPL) in the ganglion cell layer. Displaced amacrine cells still have their neurites extending apically into the IPL, and therefore exhibit an inverted polarity with respect to the other amacrine cells." [PMID:21557506, PMID:67960] comment: Displaced amacrine cells are a subset of Sox2 expressing amacrine cells. {xref="PMID:18719084"} +subset: human_subset +subset: mouse_subset synonym: "dACs" EXACT [] synonym: "inverted amacrine cell" EXACT [] is_a: CL:0000561 ! amacrine cell @@ -35390,6 +40446,9 @@ property_value: terms:contributor https://orcid.org/0000-0001-7258-9596 id: CL:4023120 name: cochlea auditory hair cell def: "An auditory hair cell found in the cochlea." [Wikipedia:Hair_cell] +subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "cochlear hair cell" EXACT [] xref: FMA:62364 is_a: BFO:0000002 @@ -35404,11 +40463,16 @@ property_value: terms:contributor https://orcid.org/0000-0001-7258-9596 id: CL:4023121 name: sst chodl GABAergic cortical interneuron def: "A transcriptomically distinct sst GABAergic cortical interneuron that also expresses Chodl. These neurons are rare and correspond to the only known cortical interneurons with long-range projection. The standard transcriptomic reference data for this cell type can be found on the CellxGene census under the collection: 'Transcriptomic cytoarchitecture reveals principles of human neocortex organization', dataset: 'Supercluster: MGE-derived interneurons', Author Categories: 'CrossArea_subclass', clusters Sst Chodl." [https://cellxgene.cziscience.com/e/9c63201d-bfd9-41a8-bbbc-18d947556f3d.cxg/, PMID:15845086, PMID:31209381, PMID:33372656, PMID:37824655] +comment: The marker set NPY can identify the Human cell type sst chodl GABAergic cortical interneuron in the Brain with a confidence of 0.894026187 (NS-Forest FBeta value). {xref="https://doi.org/10.5281/zenodo.11165918"} subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "long-range GABAergic interneuron" BROAD [] is_a: CL:4023017 ! sst GABAergic cortical interneuron relationship: RO:0002292 PR:000005444 ! expresses chondrolectin +relationship: RO:0015004 CLM:1000083 ! has characterizing marker set NS forest marker set of sst chodl GABAergic cortical interneuron (Human Brain). property_value: IAO:0000028 "sst chodl cortical interneuron" xsd:string +property_value: RO:0002175 NCBITaxon:9606 property_value: terms:contributor https://orcid.org/0000-0001-7258-9596 [Term] @@ -35416,6 +40480,8 @@ id: CL:4023122 name: oxytocin receptor sst GABAergic cortical interneuron def: "An interneuron located in the cerebral cortex that expresses the oxytocin receptor. These interneurons also express somatostatin." [PMID:25303526] comment: These cells were first identified in mouse. {xref="PMID:25303526"} +subset: human_subset +subset: mouse_subset synonym: "OxtrINs" RELATED OMO:0003000 [PMID:25303526] is_a: BFO:0000002 is_a: CL:0010011 ! cerebral cortex GABAergic interneuron @@ -35428,7 +40494,9 @@ property_value: terms:contributor https://orcid.org/0000-0001-7258-9596 id: CL:4023123 name: hypothalamus kisspeptin neuron def: "A kisspeptin neuron that is located in the hypothalamus. These neurons project to and activate gonadotrophin-releasing hormone neurons (acting via the kisspeptin receptor) in the hypothalamus and stimulate the secretion of gonadotrophin-releasing hormone." [PMID:30042117] -is_a: CL:2000029 ! central nervous system neuron +subset: human_subset +subset: mouse_subset +is_a: CL:0012001 ! neuron of the forebrain is_a: CL:4023130 ! kisspeptin neuron intersection_of: CL:4023130 ! kisspeptin neuron intersection_of: RO:0002100 UBERON:0001898 ! has soma location hypothalamus @@ -35440,6 +40508,8 @@ property_value: terms:contributor https://orcid.org/0000-0002-0819-0473 id: CL:4023124 name: dentate gyrus kisspeptin neuron def: "A kisspeptin neuron that is located in the dentate gyrus of the hippocampus." [WikipediaVersioned:Kisspeptin&oldid=1042853037] +subset: human_subset +subset: mouse_subset is_a: CL:4023062 ! dentate gyrus neuron is_a: CL:4023130 ! kisspeptin neuron intersection_of: CL:4023130 ! kisspeptin neuron @@ -35452,6 +40522,8 @@ id: CL:4023125 name: KNDy neuron def: "A hypothalamus kisspeptin neuron that coexpresses kisspeptin, neurokinin B and dynorphin." [WikipediaVersioned:KNDy_neuron&oldid=964682278] comment: KNDy neurons are involved in the negative feedback of gonadotropin-releasing hormone release in the hypothalamic–pituitary–gonadal axis. Sex steroids released from the gonads act on KNDy neurons as inhibitors of kisspeptin release. This inhibition provides negative feedback control on the hypothalamic–pituitary–gonadal axis. Other roles of KNDy neurons include influences on prolactin production; puberty; stress' effects on reproduction; and the control of thermoregulation. {xref="WikipediaVersioned:KNDy_neuron&oldid=964682278"} +subset: human_subset +subset: mouse_subset synonym: "kisspeptin, neurokinin B and dynorphin expressing neuron" EXACT [] is_a: CL:4023123 ! hypothalamus kisspeptin neuron intersection_of: CL:4023123 ! hypothalamus kisspeptin neuron @@ -35466,6 +40538,8 @@ property_value: terms:contributor https://orcid.org/0000-0002-0819-0473 id: CL:4023127 name: arcuate nucleus of hypothalamus KNDy neuron def: "a KNDy neuron that is located in the arcuate nucleus of the hypothalamus." [PMID:30042117] +subset: human_subset +subset: mouse_subset is_a: CL:4023125 ! KNDy neuron intersection_of: CL:4023125 ! KNDy neuron intersection_of: RO:0002100 UBERON:0001932 ! has soma location arcuate nucleus of hypothalamus @@ -35477,6 +40551,8 @@ property_value: terms:contributor https://orcid.org/0000-0002-0819-0473 id: CL:4023128 name: rostral periventricular region of the third ventricle KNDy neuron def: "a KNDy neuron that is located in the rostral periventricular region of the third ventricle." [PMID:30042117, WikipediaVersioned:KNDy_neuron&oldid=964682278] +subset: human_subset +subset: mouse_subset synonym: "RP3V KNDy neuron" EXACT [] is_a: CL:4023125 ! KNDy neuron intersection_of: CL:4023125 ! KNDy neuron @@ -35491,6 +40567,8 @@ id: CL:4023129 name: retinoblast def: "A retinal cell that is immature or undifferentiated." [PMID:17565741] subset: eye_upper_slim +subset: human_subset +subset: mouse_subset synonym: "retinal stem cell" EXACT [PMID:17565741] is_a: CL:0009004 ! retinal cell relationship: part_of UBERON:0000966 ! retina @@ -35502,8 +40580,10 @@ id: CL:4023130 name: kisspeptin neuron def: "A neuron that expresses kisspeptin. These neurons are predominantly located in the hypothalamus, but also found in other parts of the brain including the hippocampal dentate gyrus." [PMID:30042117] comment: Gonadal sex steroids stimulate kisspeptin neurons in the RP3V, but inhibit kisspeptin neurons in the ARC. {xref="PMID:30042117"} +subset: human_subset +subset: mouse_subset is_a: BFO:0000002 -is_a: CL:0000540 ! neuron +is_a: CL:2000029 ! central nervous system neuron intersection_of: CL:0000540 ! neuron intersection_of: RO:0002292 PR:000009344 ! expresses metastasis-suppressor KiSS-1 relationship: RO:0002292 PR:000009344 ! expresses metastasis-suppressor KiSS-1 @@ -35515,6 +40595,8 @@ id: CL:4023154 name: myelinating glial cell alt_id: CL:0000328 def: "A glial cell that myelinates axonal processes." [DOI:10.1007/3-540-29623-9_3240] +subset: human_subset +subset: mouse_subset is_a: CL:0000125 ! glial cell intersection_of: CL:0000125 ! glial cell intersection_of: has_part GO:0043209 ! myelin sheath @@ -35526,6 +40608,8 @@ id: CL:4023158 name: octopus cell of the mammalian cochlear nucleus def: "A neuron in the posterior ventral cochlear nucleus that is distinguished by their long, thick and tentacle-shaped dendrites that typically emanate from one side of the cell body." [WikipediaVersioned:title=Cochlear_nucleus&oldid=1090176664] comment: Octopus cells respond only at the onset of a broad-band simple tonal stimulus and form a pathway to the superior paraolivary nucleus and to the ventral nucleus of the lateral lemniscus. {xref="WikipediaVersioned:title=Cochlear_nucleus&oldid=1090176664", xref="PMID:11976365"} +subset: human_subset +subset: mouse_subset is_a: CL:2000029 ! central nervous system neuron relationship: RO:0002100 UBERON:0002831 ! has soma location posteroventral cochlear nucleus relationship: RO:0013001 UBERON:8440043 ! has synaptic IO in region superior paraolivary nucleus @@ -35536,6 +40620,8 @@ property_value: terms:contributor http://orcid.org/0000-0001-7258-9596 id: CL:4023159 name: double bouquet cell def: "An interneuron that has double bouquet morphology." [PMID:15378039] +subset: human_subset +subset: mouse_subset is_a: CL:0000099 ! interneuron intersection_of: CL:0000099 ! interneuron intersection_of: bearer_of PATO:0070061 ! double bouquet morphology @@ -35547,6 +40633,8 @@ id: CL:4023160 name: cartwheel cell def: "A neuron of the dorsal cochlear nucleus with spiny dendrites that receive input from the axons of granule cells and with axons that release GABA and glycine onto cartwheel, pyramidal and giant cell targets." [ILX:0102311, WikipediaVersioned:Cartwheel_cell&oldid=1040398094] comment: Cartwheel cells share many of the features, molecular and electrophysiological, of cerebellar Purkinje neurons. {xref="ILX:0102311"} +subset: human_subset +subset: mouse_subset xref: ILX:0102311 is_a: CL:0000617 ! GABAergic neuron is_a: CL:1001509 ! glycinergic neuron @@ -35559,7 +40647,10 @@ property_value: terms:contributor http://orcid.org/0000-0001-7258-9596 id: CL:4023161 name: unipolar brush cell def: "An excitatory glutamatergic interneuron found in the granular layer of the cerebellar cortex and also in the granule cell domain of the cochlear nucleus. Unipolar brush cells have a round or oval cell body with usually a single short dendrite that ends in a brush-like tuft of short dendrites unique to them known as dendrioles." [PMID:9193142, WikipediaVersioned:Unipolar_brush_cell&oldid=1045937026] -is_a: CL:0000402 ! CNS interneuron +subset: cellxgene_subset +subset: human_subset +subset: mouse_subset +is_a: CL:0000099 ! interneuron is_a: CL:0000679 ! glutamatergic neuron relationship: bearer_of PATO:0070025 ! unipolar neuron morphology relationship: RO:0002100 UBERON:0002028 ! has soma location hindbrain @@ -35569,6 +40660,8 @@ property_value: terms:contributor http://orcid.org/0000-0001-7258-9596 id: CL:4023162 name: bushy cell def: "A neuron found in the anterior part of the ventral cochlear nucleus that has the appearance of bushes, having short dendrites. Bushy cells give outputs to different parts of the superior olivary complex." [WikipediaVersioned:Bushy_cell&oldid=879061753] +subset: human_subset +subset: mouse_subset is_a: CL:2000029 ! central nervous system neuron relationship: RO:0002100 UBERON:0002830 ! has soma location anteroventral cochlear nucleus relationship: RO:0013001 UBERON:0002128 ! has synaptic IO in region superior olivary complex @@ -35578,6 +40671,8 @@ property_value: terms:contributor http://orcid.org/0000-0001-7258-9596 id: CL:4023163 name: spherical bushy cell def: "A bushy cell that receives only few large excitatory endbulb synapses from auditory nerves. Spherical bush cells give excitatory input to the lateral and medial parts of the superior olive." [PMID:31881018, WikipediaVersioned:Bushy_cell&oldid=879061753] +subset: human_subset +subset: mouse_subset synonym: "SBC" RELATED OMO:0003000 [PMID:31881018] is_a: CL:4023162 ! bushy cell property_value: terms:contributor http://orcid.org/0000-0001-7258-9596 @@ -35586,6 +40681,8 @@ property_value: terms:contributor http://orcid.org/0000-0001-7258-9596 id: CL:4023164 name: globular bushy cell def: "A bushy cell that receives a large number of medium-sized synapses, called modified endbulbs. Globular bushy cells extend to the superior olive on both sides of the brainstem where they give input to the bipolar neurons." [PMID:31881018, WikipediaVersioned:Bushy_cell&oldid=879061753] +subset: human_subset +subset: mouse_subset synonym: "GBC" EXACT OMO:0003000 [PMID:31881018] is_a: CL:4023162 ! bushy cell property_value: terms:contributor http://orcid.org/0000-0001-7258-9596 @@ -35594,9 +40691,12 @@ property_value: terms:contributor http://orcid.org/0000-0001-7258-9596 id: CL:4023168 name: somatosensory neuron def: "A neuron that is part of the somatic sensory system. Somatosensory neurons innervate the skin or integument to detect different types of thermal, chemical, and mechanical touch stimuli." [PMID:22865660] -is_a: CL:0000540 ! neuron +subset: human_subset +subset: mouse_subset +is_a: CL:2000032 ! peripheral nervous system neuron intersection_of: CL:0000540 ! neuron intersection_of: part_of UBERON:0003942 ! somatosensory system +intersection_of: RO:0002100 UBERON:0000010 ! has soma location peripheral nervous system relationship: part_of UBERON:0003942 ! somatosensory system property_value: terms:contributor http://orcid.org/0000-0001-7258-9596 @@ -35604,24 +40704,30 @@ property_value: terms:contributor http://orcid.org/0000-0001-7258-9596 id: CL:4023169 name: trigeminal neuron def: "A neuron that is responsible for sensation in the face or motor functions such as biting and chewing. Trigeminal neurons extend a single axon shaft along the lateral white matter of the hindbrain and spinal cord. The highly branched axons innervate the integument of the head." [PMID:22190641, WikipediaVersioned:Trigeminal_nerve&oldid=1099897926] -is_a: CL:0000540 ! neuron +subset: human_subset +subset: mouse_subset +is_a: CL:2000029 ! central nervous system neuron property_value: terms:contributor http://orcid.org/0000-0001-7258-9596 [Term] id: CL:4023170 name: trigeminal sensory neuron def: "A trigeminal neuron that is responsible for sensation in the face." [https://www.ncbi.nlm.nih.gov/books/NBK539823/] +subset: human_subset +subset: mouse_subset is_a: CL:0000006 ! neuronal receptor cell -is_a: CL:4023168 ! somatosensory neuron is_a: CL:4023169 ! trigeminal neuron intersection_of: CL:4023169 ! trigeminal neuron intersection_of: capable_of GO:0050906 ! detection of stimulus involved in sensory perception +relationship: part_of UBERON:0003942 ! somatosensory system property_value: terms:contributor http://orcid.org/0000-0001-7258-9596 [Term] id: CL:4023171 name: trigeminal motor neuron def: "A trigeminal neuron that is responsible for motor functions such as biting and chewing." [https://www.ncbi.nlm.nih.gov/books/NBK539823/] +subset: human_subset +subset: mouse_subset is_a: CL:0000100 ! motor neuron is_a: CL:4023169 ! trigeminal neuron intersection_of: CL:0000100 ! motor neuron @@ -35633,22 +40739,26 @@ id: CL:4023181 name: hypendymal cell def: "A neurecto-epithelial cell that is part of the basal layer of the subcommissural organ and specializes in the secretion of proteins into the subarachnoid space. Hypendymal cells have similar characteristics to ependymal cells and express SCO-spondin." [https://orcid.org/0000-0001-7258-9596, PMID:26778959, PMID:9579598] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset xref: https://cellxgene.cziscience.com/cellguide/CL_4023181 is_a: CL:0000710 ! neurecto-epithelial cell is_a: CL:0002319 ! neural cell relationship: part_of UBERON:0002139 ! subcommissural organ relationship: RO:0002292 PR:000015658 ! expresses SCO-spondin property_value: terms:contributor http://orcid.org/0000-0002-2105-0715 -property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional.\n\nHypendymal cells are secretory cells located between the ependymal layer and the posterior commissure, forming the hypendmal layer of the subcommissural organ (SCO), a highly conserved gland that is part of the circumventricular system within the brain. \nHypendymal cells are bipolar cells with a thin apical pole and basal process. Most of the ultrastructural characteristics of these cells are similar to those described for the ependymal cells (which are arranged into another layer – the ependyma). However, ependymal cells release their secretion into the ventricular cerebrospinal fluid whereas hypendymal cells project processes to the local blood vessels and to the subarachnoidal space." xsd:string {xref="DOI:10.1002/(SICI)1097-0029(19980415)41:2<98::AID-JEMT2>3.0.CO;2-M", xref="DOI:10.1111/joa.13709", xref="DOI:10.3389/fncel.2015.00480"} +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nHypendymal cells are secretory cells located between the ependymal layer and the posterior commissure, forming the hypendmal layer of the subcommissural organ (SCO), a highly conserved gland that is part of the circumventricular system within the brain. \nHypendymal cells are bipolar cells with a thin apical pole and basal process. Most of the ultrastructural characteristics of these cells are similar to those described for the ependymal cells (which are arranged into another layer – the ependyma). However, ependymal cells release their secretion into the ventricular cerebrospinal fluid whereas hypendymal cells project processes to the local blood vessels and to the subarachnoidal space." xsd:string {xref="DOI:10.1002/(SICI)1097-0029(19980415)41:2<98::AID-JEMT2>3.0.CO;2-M", xref="DOI:10.1111/joa.13709", xref="DOI:10.3389/fncel.2015.00480"} [Term] id: CL:4023187 name: koniocellular cell def: "A neuron with a small cell body that is located in a koniocellular layer of the lateral geniculate nucleus (LGN)." [WikipediaVersioned:Lateral_geniculate_nucleus&oldid=1098375993] comment: In adult monkeys, koniocellular cells can be distinguished from parvocellular and magnocellular of the LGN by their expression of calbindin, the alpha subunit of type II calmodulin-dependent protein kinase, and the gamma subunit of protein kinase C. {xref="PMID:10845061"} +subset: human_subset +subset: mouse_subset synonym: "K cell" EXACT [PMID:10845061] xref: NIFEXT:44 -is_a: CL:2000029 ! central nervous system neuron +is_a: CL:0012001 ! neuron of the forebrain intersection_of: CL:0000540 ! neuron intersection_of: RO:0002100 UBERON:0013615 ! has soma location koniocellular layer of dorsal nucleus of lateral geniculate body relationship: RO:0002100 UBERON:0013615 ! has soma location koniocellular layer of dorsal nucleus of lateral geniculate body @@ -35659,7 +40769,10 @@ id: CL:4023188 name: midget ganglion cell of retina def: "A retinal ganglion cell that originate in the ganglion cell layer of the retina, and project to the parvocellular layers of the lateral geniculate nucleus (LGN). These cells are known as midget retinal ganglion cells due to the small sizes of their dendritic trees and cell bodies." [PMID:32533915, WikipediaVersioned:Midget_cell&oldid=982299713] comment: There are midget bipolar cells of retina and midget ganglion cells of retina and they are not the same:\nMidget bipolar cells (imb, fmb) have larger axon terminals at greater distances from the fovea (retinal eccentricity of 4.5mm as compared to 12 mm). Midget ganglion cells (MGC) have larger dendritic fields (here seen at 8 mm) as they increase in eccentricity. +subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset is_a: CL:0000740 ! retinal ganglion cell relationship: RO:0013001 UBERON:0013607 ! has synaptic IO in region parvocellular layer of dorsal nucleus of lateral geniculate body property_value: RO:0002175 NCBITaxon:9606 @@ -35671,7 +40784,10 @@ id: CL:4023189 name: parasol ganglion cell of retina def: "A retinal ganglion cell located in the ganglion cell layer of the retina. This cell projects to magnocellular cells in the lateral geniculate nucleus (LGN). They have large cell bodies and extensive, branching dendritic networks that contribute to their large receptive fields." [PMID:32533915, WikipediaVersioned:Parasol_cell&oldid=1032171532] comment: These cells should not be confused with M1-M14 retinal ganglion cells described in PMID:16626866 which refer to a different classification of retinal ganglion cells. +subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "M cell" RELATED [] synonym: "M ganglion cell" RELATED [] is_a: CL:0000740 ! retinal ganglion cell @@ -35684,6 +40800,8 @@ property_value: terms:contributor "https://orcid.org/0000-0001-7655-4833" xsd:st id: CL:4028001 name: pulmonary capillary endothelial cell def: "Any capillary endothelial cell that is part of a lung." [] +subset: human_subset +subset: mouse_subset synonym: "lung capillary endothelial cell" EXACT [] is_a: CL:0002144 ! capillary endothelial cell is_a: CL:2000016 ! lung microvascular endothelial cell @@ -35698,6 +40816,8 @@ id: CL:4028002 name: alveolar capillary type 1 endothelial cell def: "An alveolar capillary endothelial cell that is located distally to alveolar capillary type 2 endothelial cells." [PMID:31233341, PMID:32059772, PMID:32059779, PMID:32091393, PMID:33057196, PMID:33705684] subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "CAP1" RELATED OMO:0003000 [] synonym: "capillary 1 cell" BROAD [] synonym: "gCAP" RELATED OMO:0003000 [PMID:33057196] @@ -35713,6 +40833,8 @@ id: CL:4028003 name: alveolar capillary type 2 endothelial cell def: "An alveolar capillary endothelial cell that is located proximally to alveolar capillary type 1 endothelial cells and in close apposition to alveolar type 1 epithelial cells (also known as type I pneumocytes)." [PMID:31233341, PMID:32059772, PMID:32059779, PMID:32091393, PMID:33057196] subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "aCAP" RELATED OMO:0003000 [] synonym: "aerocyte" BROAD [PMID:33057196] synonym: "alveolar capillary cell" BROAD [] @@ -35729,8 +40851,11 @@ creation_date: 2021-11-23T03:23:53Z id: CL:4028004 name: alveolar type 1 fibroblast cell def: "A pulmonary interstitial fibroblast that is part of the alveolus and contains lipid droplets." [PMID:22268140, PMID:26706109, PMID:28886382, PMID:29489752, PMID:30675802, PMID:33624948, PMID:33707239, PMID:9074756] +comment: The marker set AOC3, LUM can identify the Human cell type alveolar type 1 fibroblast cell in the Lung with a confidence of 0.70 (NS-Forest FBeta value). {xref="https://doi.org/10.5281/zenodo.11165918"} subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "AF1" RELATED OMO:0003000 [] synonym: "alveolar fibroblast" BROAD [] synonym: "alveolar fibroblast 1" BROAD [] @@ -35741,6 +40866,7 @@ synonym: "pulmonary lipofibroblast" BROAD [] is_a: CL:0002241 ! pulmonary interstitial fibroblast is_a: CL:0002553 ! fibroblast of lung relationship: part_of UBERON:0002299 ! alveolus of lung +relationship: RO:0015004 CLM:1000002 ! has characterizing marker set NS forest marker set of alveolar type 1 fibroblast cell (Human Lung). property_value: RO:0002175 NCBITaxon:9606 property_value: terms:contributor https://orcid.org/0000-0001-9610-7627 property_value: terms:contributor https://orcid.org/0000-0002-1425-877X @@ -35752,8 +40878,11 @@ creation_date: 2021-12-09T15:34:13Z id: CL:4028006 name: alveolar adventitial fibroblast def: "A pulmonary interstitial fibroblast that is part of the alveolus and localizes to vascular adventitia." [PMID:26706109, PMID:28886382, PMID:29752282, PMID:30675802, PMID:33208946, PMID:33624948] +comment: The marker set SCARA5, CD248 can identify the Human cell type alveolar adventitial fibroblast in the Lung with a confidence of 0.85 (NS-Forest FBeta value). {xref="https://doi.org/10.5281/zenodo.11165918"} subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "adventitial fibroblast" BROAD [] synonym: "AdvF" RELATED OMO:0003000 [PMID:33208946] synonym: "AF2" RELATED OMO:0003000 [] @@ -35766,6 +40895,7 @@ synonym: "type-2 associated stromal cell" BROAD [] is_a: CL:0002241 ! pulmonary interstitial fibroblast is_a: CL:0002553 ! fibroblast of lung relationship: part_of UBERON:0002299 ! alveolus of lung +relationship: RO:0015004 CLM:1000001 ! has characterizing marker set NS forest marker set of alveolar adventitial fibroblast (Human Lung). property_value: RO:0002175 NCBITaxon:9606 property_value: terms:contributor https://orcid.org/0000-0002-3293-5463 creation_date: 2021-12-09T15:53:21Z @@ -35775,6 +40905,8 @@ id: CL:4029001 name: gamete-nursing cell namespace: cell def: "A cell that supports the development of a gamete by providing it cytoplasmic material (including entire organelles) by direct cross-membrane channels (del Pino, 2021)." [doi:10.1016/bs.ctdb.2020.10.008] +subset: human_subset +subset: mouse_subset xref: BTO:0000953 is_a: CL:0000000 ! cell property_value: terms:contributor http://orcid.org/0000-0002-6095-8718 @@ -35786,6 +40918,8 @@ name: germline-derived nurse cell namespace: cell def: "A gamete-nursing cell that derives from a germline cell (del Pino, 2021)." [doi:10.1016/bs.ctdb.2020.10.008] comment: Nurse cells were first described in insects, but recent works suggest they also exist in some mammals (Lei and Spradling, 2016). {xref="doi:10.1126/science.aad2156"} +subset: human_subset +subset: mouse_subset is_a: CL:0000039 ! germ line cell is_a: CL:4029001 ! gamete-nursing cell property_value: terms:contributor http://orcid.org/0000-0002-6095-8718 @@ -35797,6 +40931,8 @@ name: somatic nurse-like cell namespace: cell def: "A gamete-nursing cell that derives from the somatic tissues of the gonad (del Pino, 2021)." [doi:10.1016/bs.ctdb.2020.10.008] comment: We follow what seems to be a common usage in the literature, which is to reserve the term “nurse cell” proper to cells from the germ line, hence the label “nurse-like”. This term encompasses pyriform cells described in reptiles, bird, and amphibians (del Pino, 2021); it does not encompass mammalian Sertoli cells, which do not appear to transfer cytoplasmic material to spermatogonia (França et al., 2016). {xref="doi:10.1111/andr.12165"} +subset: human_subset +subset: mouse_subset is_a: CL:4029001 ! gamete-nursing cell property_value: terms:contributor http://orcid.org/0000-0002-6095-8718 property_value: terms:date "2022-06-08T15:38:03Z" xsd:dateTime @@ -35806,6 +40942,8 @@ id: CL:4030000 name: choroidal melanocyte def: "A melanocyte located in the vascular uvea and involved in photoprotection, regulation of oxidative damage and immune responses." [http://orcid.org/0000-0002-0819-0473, PMID:31819095] comment: Cellular functions and extracellular interactions of choroidal melanocytes are distinct to skin melanocytes. They might have both neuroectodermal as well as mesectodermal origins. {xref="PMID:34082079", xref="PMID:31819095"} +subset: human_subset +subset: mouse_subset synonym: "uveal melanocyte" EXACT [] is_a: CL:0000148 ! melanocyte intersection_of: CL:0000148 ! melanocyte @@ -35817,6 +40955,8 @@ creation_date: 2022-01-20T12:59:06Z id: CL:4030001 name: stromal cell of thymus def: "A stromal cell that is part of the thymus." [doi:10.1038/s41467-020-20082-7] +subset: human_subset +subset: mouse_subset synonym: "thymic stromal cell" EXACT [] is_a: CL:0000499 ! stromal cell intersection_of: CL:0000499 ! stromal cell @@ -35828,6 +40968,8 @@ property_value: terms:date "2022-07-08T11:39:38Z" xsd:dateTime id: CL:4030002 name: effector memory CD45RA-positive, alpha-beta T cell, terminally differentiated def: "An alpha-beta memory T cell with the phenotype CD45RA-positive." [https://orcid.org/0000-0002-2825-0621] +subset: human_subset +subset: mouse_subset synonym: "effector memory RA T cell" BROAD [PMID:16237082] synonym: "TEMRA" BROAD [PMID:16237082] synonym: "TEMRA cell" EXACT [PMID:25104859] @@ -35840,6 +40982,8 @@ creation_date: 2022-02-01T13:04:46Z id: CL:4030003 name: interstitial cell of thymus def: "A cell that makes up the loose connective tissue of the thymus." [doi:10.1038/s41467-020-20082-7] +subset: human_subset +subset: mouse_subset synonym: "thymic interstitial cell" EXACT [] is_a: CL:4030001 ! stromal cell of thymus property_value: terms:date "2022-07-08T11:48:36Z" xsd:dateTime @@ -35848,6 +40992,8 @@ property_value: terms:date "2022-07-08T11:48:36Z" xsd:dateTime id: CL:4030004 name: thymic nurse cell def: "A large epithelial cell found in the thymus. This cell type may internalize thymocytes through extensions of plasma membrane. The cell surface and cytoplasmic vacuoles of a thymic nurse cell express MHC Class I and MHC Class II antigens. The interaction of these antigens with a developing thymocyte determines whether the thymocyte undergoes positive or negative selection." [https://en.wikipedia.org/wiki/Thymic_nurse_cell] +subset: human_subset +subset: mouse_subset is_a: CL:0002293 ! epithelial cell of thymus property_value: terms:contributor https://orcid.org/0000-0002-0819-0473 property_value: terms:date "2022-02-18T12:43:20Z" xsd:dateTime @@ -35856,6 +41002,8 @@ property_value: terms:date "2022-02-18T12:43:20Z" xsd:dateTime id: CL:4030005 name: kidney collecting duct beta-intercalated cell def: "A renal beta-intercalated cell that is part of the cortical collecting duct. The medullary collecting duct does not contain the renal beta-intercalated cell type." [PMID:24051376, PMID:31300091, PMID:32016094] +subset: human_subset +subset: mouse_subset synonym: "B-IC" EXACT [PMID:32016094] synonym: "kidney collecting duct intercalated cell type B" EXACT [PMID:31300091] is_a: CL:0002201 ! renal beta-intercalated cell @@ -35867,26 +41015,31 @@ property_value: terms:date "2022-09-14T16:19:11Z" xsd:dateTime [Term] id: CL:4030006 name: fallopian tube secretory epithelial cell -def: "An epithelial cell that is part of the fallopian tube epithelium that secretes mucous fluid and oviduct-specific products through the stimulation of estrogen and luteinizing hormone. The fallopian tube secretory cell has approximately the same height as the ciliated cell and is usually a more narrow columnar cell. The nucleus is ovoid and perpendicular to the long axis of the cell. The chromatin is more dense and the nucleolus smaller than that seen in the ciliated cell." [https://doi.org/10.1186/1477-7827-7-129, https://doi.org/10.3390/cells8080933, https://www.proteinatlas.org/learn/dictionary/normal/fallopian+tube] +def: "An epithelial cell that is part of the fallopian tube that secretes mucus and oviduct-specific products in response to hormonal stimulation from estrogen and luteinizing hormone. This fallopian tube secretory cell is similar in height to the ciliated cell, but typically exhibits a more narrow, columnar shape. Its nucleus is ovoid and oriented perpendicular to the cell's long axis, with denser chromatin and a smaller nucleolus compared to the ciliated cell." [https://doi.org/10.1186/1477-7827-7-129, https://doi.org/10.3390/cells8080933, https://www.proteinatlas.org/learn/dictionary/normal/fallopian+tube] comment: The other cell types of the fallopian tube epithelium include the ciliated cell and the intercalary cell, or peg cell. The fallopian tube secretory epithelial cell type has been implicated as a source of high-grade serous ovarian carcinoma. {xref="https://doi.org/10.1016/j.ccr.2013.10.013", xref="https://www.proteinatlas.org/learn/dictionary/normal/fallopian+tube"} subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "oviduct secretory epithelial cell" BROAD [] synonym: "uterine tube secretory epithelial cell" EXACT [] -is_a: CL:1001591 ! oviduct glandular cell -relationship: part_of UBERON:0003889 ! fallopian tube +is_a: CL:1001591 ! oviduct secretory cell +is_a: CL:4052019 ! fallopian tube non-ciliated cell property_value: RO:0002175 NCBITaxon:9606 property_value: terms:contributor https://orcid.org/0000-0002-0819-0473 property_value: terms:date "2022-03-03T10:39:31Z" xsd:dateTime [Term] id: CL:4030007 -name: fallopian tube ciliated cell -def: "An epithelial ciliated cell that is part of the fallopian tube. This cell type is found mainly on the apex of the mucosal folds and contributes, together with peristaltic contractions, to the self-propulsion of spermatozoa, the transport of ovum during ovulation and the transport of the fertilized ovum to the intramural fallopian tube. A fallopian tube ciliated cell has a columnar shape and contains an oval or round nucleus, often located perpendicular or parallel to the long axis of the cell." [PMID:16565155] +name: fallopian tube multiciliated cell +def: "A multi-ciliated epithelial cell that is part of the fallopian tube, mainly found on the apex of the mucosal folds. This cell exhibits a columnar shape with an oval nucleus and is characterized by the presence of cilia on its surface. The coordinated beating of these cilia, together with peristaltic contractions, contributes to the self-propulsion of spermatozoa, the transport of ovum during ovulation and the transport of the fertilized ovum to the intramural fallopian tube." [https://www.proteinatlas.org/humanproteome/tissue/fallopian+tube, PMID:16565155] subset: human_reference_atlas +subset: human_subset +subset: mouse_subset +synonym: "fallopian tube ciliated cell" EXACT [] synonym: "oviduct ciliated cell" BROAD [] synonym: "uterine tube ciliated epithelial cell" EXACT [] -is_a: CL:0005012 ! multi-ciliated epithelial cell -relationship: part_of UBERON:0003889 ! fallopian tube +is_a: CL:0005012 ! multiciliated epithelial cell +is_a: CL:4052018 ! fallopian tube epithelial cell relationship: part_of UBERON:0007589 ! ciliated columnar oviduct epithelium property_value: RO:0002175 NCBITaxon:9606 property_value: terms:contributor https://orcid.org/0000-0002-0819-0473 @@ -35896,6 +41049,8 @@ property_value: terms:date "2022-03-08T12:40:19Z" xsd:dateTime id: CL:4030008 name: pronephric podocyte def: "A specialized epithelial cell that contains \"feet\" that interdigitate with the \"feet\" of other glomerular epithelial cells in the pronephros." [PMID:10322630] +subset: human_subset +subset: mouse_subset synonym: "pronephric glomerular visceral epithelial cell" EXACT [ZFA:0001673] is_a: CL:0000653 ! podocyte intersection_of: CL:0000653 ! podocyte @@ -35910,6 +41065,8 @@ name: epithelial cell of proximal tubule segment 1 def: "A brush border cell that is part of segment 1 (S1) of the proximal tubule epithelium, located in the renal cortex." [PMID:23799132, PMID:23897681, PMID:31249312] subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "epithelial cell of segment 1 of proximal tubule" EXACT [] is_a: CL:1000838 ! kidney proximal convoluted tubule epithelial cell intersection_of: CL:0000066 ! epithelial cell @@ -35924,6 +41081,8 @@ id: CL:4030010 name: epithelial cell of proximal tubule segment 2 def: "A brush border cell that is part of segment 2 (S2) of the proximal tubule epithelium, located in the renal cortex. In addition to its reabsorptive functions, it is also specialized in the secretion of organic anions and cations, including para-aminohippurate." [PMID:23799132, PMID:23897681, PMID:31249312, PMID:31253652] subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "epithelial cell of segment 2 of proximal tubule" EXACT [] is_a: CL:1000838 ! kidney proximal convoluted tubule epithelial cell intersection_of: CL:0000066 ! epithelial cell @@ -35940,6 +41099,8 @@ def: "A brush border cell that is part of segment 3 (S3) of the proximal tubule comment: The epithelial cell of proximal tubule segment 3 operates under relatively hypoxic conditions and is particularly susceptible to ischemic injury. {xref="PMID:31249312"} subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "epithelial cell of segment 3 of proximal tubule" EXACT [] is_a: CL:0002307 ! brush border cell of the proximal tubule is_a: CL:1000839 ! kidney proximal straight tubule epithelial cell @@ -35954,6 +41115,8 @@ id: CL:4030012 name: kidney loop of Henle short descending thin limb epithelial cell def: "Epithelial cell of the descending thin limb of the short loop (cortical) nephron limited to the outer medulla (mainly inner strip). It is known in some mammalian species that the short descending limb of the loop of Henle selectively expresses the serine protease Corin, the homeobox TF Uncx, and the urea channel Slc14a2." [PMID:33769951] subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "epithelial cell of the descending thin limb of the short loop of Henle" EXACT [] is_a: CL:0000076 ! squamous epithelial cell is_a: CL:1001111 ! kidney loop of Henle thin descending limb epithelial cell @@ -35969,6 +41132,8 @@ id: CL:4030013 name: kidney loop of Henle long descending thin limb outer medulla epithelial cell def: "Epithelial cell of the descending thin limb of the long loop (juxtamedullary) nephron that spans the outer medulla (inner stripe). It is known in some mammalian species that the long descending limb of the loop of Henle in the outer medulla selectively expresses the secreted activin-antagonist protein follistatin (Fst), the GPI-linked adhesion protein Cdh13, and the protein kinase Stk32a." [http://orcid.org/0000-0003-2804-127X, PMID:33769951] subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "epithelial cell of the outer medulla of the long descending limb of the loop of Henle" EXACT [] is_a: CL:1001111 ! kidney loop of Henle thin descending limb epithelial cell relationship: part_of UBERON:0005100 ! long descending thin limb @@ -35980,6 +41145,8 @@ id: CL:4030014 name: kidney loop of Henle long descending thin limb inner medulla epithelial cell def: "Epithelial cell of the descending thin limb of the long loop (juxtamedullary) nephron that spans the inner medulla. It is known in some mammalian species that the long descending limb of the loop of Henle in the inner medulla selectively expresses the nuclear receptor Nr2e3, the Ig kappa chain Igkc, and the secreted protein dermokine (Dmkn). SLC14A2, which expresses a urea transporter, is also expressed in the inner medulla." [http://orcid.org/0000-0003-2804-127X, https://www.ncbi.nlm.nih.gov/gene/8170, PMID:33769951] subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "epithelial cell of the inner medulla of the long descending limb of the loop of Henle" EXACT [] is_a: CL:1001111 ! kidney loop of Henle thin descending limb epithelial cell relationship: part_of UBERON:0005100 ! long descending thin limb @@ -35991,6 +41158,8 @@ id: CL:4030015 name: kidney collecting duct alpha-intercalated cell def: "A renal alpha-intercalated cell that is part of the collecting duct of the renal tubule." [PMID:31249312, PMID:9890303] subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "kidney collecting duct intercalated cell type A" EXACT [PMID:9890303] is_a: CL:0005011 ! renal alpha-intercalated cell is_a: CL:1001432 ! kidney collecting duct intercalated cell @@ -36005,6 +41174,8 @@ id: CL:4030016 name: epithelial cell of early distal convoluted tubule def: "An epithelial cell located in the early distal convoluted tubule." [http://orcid.org/0000-0003-2804-127X, PMID:24855283] subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "DCT1 cell" BROAD [PMID:24855283] is_a: CL:1000849 ! kidney distal convoluted tubule epithelial cell intersection_of: CL:0000066 ! epithelial cell @@ -36019,6 +41190,8 @@ name: epithelial cell of late distal convoluted tubule def: "An epithelial cell located in the late distal convoluted tubule." [http://orcid.org/0000-0003-2804-127X, PMID:24855283] comment: Although mineralocorticoid receptors are expressed throughout the entire [distal convoluted tubule], the DCT2 is sensitive to the actions of aldosterone, because it expresses an enzyme called 11-β hydroxysteroid dehydrogenase 2 (11-βHSD2) {xref="PMID:24855283"} subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "DCT2 cell" BROAD [PMID:24855283] is_a: CL:1000849 ! kidney distal convoluted tubule epithelial cell intersection_of: CL:0000066 ! epithelial cell @@ -36033,6 +41206,8 @@ name: kidney connecting tubule principal cell def: "A renal principal cell located in the connecting tubule." [http://orcid.org/0000-0003-2804-127X, PMID:27582101, PMID:31249312] subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset is_a: CL:0005009 ! renal principal cell is_a: CL:1000768 ! kidney connecting tubule epithelial cell intersection_of: CL:0005009 ! renal principal cell @@ -36045,6 +41220,8 @@ id: CL:4030019 name: kidney connecting tubule intercalated cell def: "A renal intercalated cell that is part of the renal connecting tubule." [PMID:9890303] subset: human_reference_atlas +subset: human_subset +subset: mouse_subset is_a: CL:0005010 ! renal intercalated cell is_a: CL:1000768 ! kidney connecting tubule epithelial cell intersection_of: CL:0005010 ! renal intercalated cell @@ -36057,6 +41234,8 @@ id: CL:4030020 name: kidney connecting tubule alpha-intercalated cell def: "A renal alpha-intercalated cell that is part of the renal connecting tubule." [PMID:2254448, PMID:24937428, PMID:9890303] subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "connecting tubule A-IC" EXACT [PMID:24937428] synonym: "kidney connecting tubule intercalated cell type A" EXACT [PMID:9890303] is_a: CL:0005011 ! renal alpha-intercalated cell @@ -36071,6 +41250,8 @@ id: CL:4030021 name: kidney connecting tubule beta-intercalated cell def: "A renal beta-intercalated cell that is part of the renal connecting tubule." [PMID:2254448, PMID:9890303] subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "connecting tubule B-IC" EXACT [PMID:32065116] synonym: "kidney connecting tubule intercalated cell type B" EXACT [PMID:9890303] is_a: CL:0002201 ! renal beta-intercalated cell @@ -36086,6 +41267,8 @@ name: renal medullary fibroblast def: "A fibroblast that is located in the renal medulla interstitium." [https://doi.org/10.1101/2021.07.28.454201, PMID:10559635] comment: It has been noted that inner medullary fibroblasts are involved in the regulation of water and electrolyte homeostasis. {xref="PMID:10559635"} subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "kidney medullary fibroblast" EXACT [] is_a: CL:1000682 ! kidney medulla interstitial cell is_a: CL:1000692 ! kidney interstitial fibroblast @@ -36096,11 +41279,14 @@ property_value: terms:date "2022-07-05T12:13:40Z" xsd:dateTime [Term] id: CL:4030023 -name: respiratory hillock cell +name: respiratory tract hillock cell def: "A hillock cell that is located in respiratory epithelium. In some mammalian species, this cell type has been noted to express KRT13 and KRT4 and is postulated to play a role in squamous barrier function and immunomodulation." [https://orcid.org/0000-0001-7772-9578, PMID:30069044, PMID:32726565, PMID:33442032] subset: cellxgene_subset -synonym: "hillock cell of respiratory tract" NARROW [] -is_a: CL:0002368 ! respiratory epithelial cell +subset: human_subset +subset: mouse_subset +synonym: "hillock cell of respiratory tract" EXACT [] +synonym: "respiratory hillock cell" EXACT [] +is_a: CL:0002368 ! respiratory tract epithelial cell is_a: CL:4030024 ! hillock cell intersection_of: CL:4030024 ! hillock cell intersection_of: part_of UBERON:0004802 ! respiratory tract epithelium @@ -36110,6 +41296,8 @@ property_value: terms:date "2022-06-06T08:31:09Z" xsd:dateTime id: CL:4030024 name: hillock cell def: "An epithelial, transitional cell type between basal and secretory; located in stratified, non-ciliated structures (called hillocks) with high cell turnover in epithelium. In some mammalian species, this cell type has been noted to express KRT13 and is postulated to play a role in squamous barrier function and immunomodulation." [PMID:30069044] +subset: human_subset +subset: mouse_subset is_a: CL:0000066 ! epithelial cell property_value: terms:date "2022-06-24T14:52:24Z" xsd:dateTime @@ -36118,6 +41306,8 @@ id: CL:4030025 name: renal cortical fibroblast def: "A fibroblast that is located in the renal cortical interstitium." [PMID:10559635] comment: Renal cortical fibroblasts have key roles in mediating intercellular communication with neighboring/infiltrating cells and extracellular matrix and maintenance of renal tissue architecture. They additionally have an endocrine function in the production of epoetin. {xref="PMID:16230044"} +subset: human_subset +subset: mouse_subset synonym: "kidney cortical fibroblast" EXACT [] is_a: CL:1000681 ! kidney cortex interstitial cell is_a: CL:1000692 ! kidney interstitial fibroblast @@ -36127,9 +41317,10 @@ property_value: terms:date "2022-07-05T15:50:17Z" xsd:dateTime [Term] id: CL:4030026 -name: BEST4+ enteroycte +name: BEST4+ enterocyte def: "An enterocyte of the human intestine expressing bestrophin-4 (BEST4) calcium-activated ion channels." [https://orcid.org/0000-0002-7431-4139, PMID:24223998, PMID:35176508] subset: cellxgene_subset +subset: human_subset is_a: CL:0000584 ! enterocyte intersection_of: CL:0000584 ! enterocyte intersection_of: RO:0002292 PR:Q8NFU0 ! expresses bestrophin-4 (human) @@ -36142,6 +41333,8 @@ id: CL:4030027 name: GABAergic amacrine cell def: "An amacrine cell that uses GABA as a neurotransmitter." [https://doi.org/10.1016/j.cell.2020.08.013] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "amacrine cell, GABAergic" EXACT [] is_a: CL:0000561 ! amacrine cell is_a: CL:0011005 ! GABAergic interneuron @@ -36154,13 +41347,13 @@ id: CL:4030028 name: glycinergic amacrine cell def: "An amacrine cell that uses glycine as a neurotransmitter." [https://doi.org/10.1016/j.cell.2020.08.013] subset: cellxgene_subset -subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "amacrine cell, glycinergic" EXACT [] is_a: CL:0000561 ! amacrine cell is_a: CL:1001509 ! glycinergic neuron intersection_of: CL:0000561 ! amacrine cell intersection_of: capable_of GO:0061537 ! glycine secretion, neurotransmission -property_value: RO:0002175 NCBITaxon:9606 property_value: terms:date "2022-10-17T12:40:06Z" xsd:dateTime [Term] @@ -36168,6 +41361,8 @@ id: CL:4030029 name: blood lymphocyte def: "A lymphocyte located in blood." [https://orcid.org/0000-0001-9990-8331] subset: blood_and_immune_upper_slim +subset: human_subset +subset: mouse_subset is_a: CL:0000542 ! lymphocyte is_a: CL:2000001 ! peripheral blood mononuclear cell intersection_of: CL:0000542 ! lymphocyte @@ -36178,6 +41373,8 @@ property_value: terms:date "2022-11-04T14:40:00Z" xsd:dateTime id: CL:4030030 name: peripheral blood lymphocyte def: "A blood lymphocyte located in the flowing, circulating blood of the body." [https://orcid.org/0000-0001-9990-8331, https://orcid.org/0000-0003-2534-198X, https://sciencing.com/what-peripheral-blood-4672930.html, PMID:31092833] +subset: human_subset +subset: mouse_subset is_a: CL:4030029 ! blood lymphocyte relationship: RO:0001025 UBERON:0013755 ! located in arterial blood relationship: RO:0001025 UBERON:0013756 ! located in venous blood @@ -36188,6 +41385,8 @@ property_value: terms:date "2022-11-14T10:08:14Z" xsd:dateTime id: CL:4030031 name: interstitial cell def: "Any cell that is located within the interstitium between the cells most prominent in defining a given tissue. \"Interstitial cell\" is a morphological term and refers to a variety of cells with differing origins and phenotypes." [PMID:24987007] +subset: human_subset +subset: mouse_subset is_a: CL:0000255 ! eukaryotic cell intersection_of: CL:0000000 ! cell intersection_of: part_of UBERON:0005169 ! interstitial tissue @@ -36199,7 +41398,10 @@ id: CL:4030032 name: valve interstitial cell def: "An interstitial cell that is part of a cardiac valve leaflet. Along with valve endothelial cells, a valve interstitial cell maintains tissue homeostasis for the function of cardiac valves through secreting biochemical signals, matrix proteins and matrix remodeling enzymes." [https://doi.org/10.1098/rsif.2017.0580, https://doi.org/10.1161/ATVBAHA.120.314789, https://doi.org/10.1161/JAHA.117.006339, https://doi.org/10.2353/ajpath.2007.070251, https://orcid.org/0000-0001-7655-4833, PMID:25311230] comment: Activated valve interstitial cells undergo continual turn over into deactivated fibroblasts and other cell fates (such as apoptosis). {xref="PMID:25311230"} +subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "cardiac valve interstitial cell" EXACT [] synonym: "valvular interstitial cell" EXACT [PMID:25311230] synonym: "VIC" EXACT OMO:0003000 [PMID:25311230, PMID:30796046] @@ -36217,6 +41419,9 @@ id: CL:4030033 name: valve endothelial cell def: "An endothelial cell that lines a surface of a cardiac valve leaflet. Along with valve interstitial cells, a valve endothelial cell maintains tissue homeostasis for the function of cardiac valves through secreting biochemical signals, matrix proteins and matrix remodeling enzymes." [PMID:25311230] comment: At least in some mammalian species, a valve endothelial cell expresses CD31. Valve endothelial cells can undergo an endothelial to mesenchymal transition to acquire a fibroblast or myofibroblast phenotype that leads to changes in the microenvironmental signals and facilitates tissue regeneration. {xref="PMID:25311230"} +subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "valvular endothelial cell" EXACT [PMID:25311230] synonym: "VEC" EXACT OMO:0003000 [PMID:25311230, PMID:30796046] is_a: CL:0010008 ! cardiac endothelial cell @@ -36227,19 +41432,29 @@ property_value: terms:date "2022-12-09T11:58:49Z" xsd:dateTime [Term] id: CL:4030034 -name: respiratory ciliated cell -def: "A ciliated cell of the respiratory system. Ciliated cells are present in airway epithelium." [PMID:18757316, PMID:21364219] +name: respiratory tract multiciliated cell +def: "A multiciliated epithelial cell located in the respiratory tract epithelium, characterized by a columnar shape and motile cilia on its apical surface. This cell develops through a highly orchestrated process, transitioning from a basal progenitor via an intermediate deuterosomal cell stage that generates centrioles essential for ciliogenesis." [PMID:18757316, PMID:21364219, PMID:34044844, PMID:37834236] +subset: human_subset +subset: mouse_subset synonym: "ciliated cell of the respiratory tract" EXACT [] -is_a: CL:0000064 ! ciliated cell -intersection_of: CL:0000064 ! ciliated cell +synonym: "respiratory ciliated cell" EXACT [] +synonym: "respiratory multiciliated cell" EXACT [] +is_a: CL:0002368 ! respiratory tract epithelial cell +is_a: CL:0005012 ! multiciliated epithelial cell +is_a: UBERON:0004119 ! endoderm-derived structure +intersection_of: CL:0000075 ! columnar/cuboidal epithelial cell +intersection_of: bearer_of PATO:0010007 ! multiciliated +intersection_of: has_part GO:0031514 ! motile cilium intersection_of: part_of UBERON:0004802 ! respiratory tract epithelium -relationship: part_of UBERON:0004802 ! respiratory tract epithelium +relationship: RO:0002207 CL:4033044 ! directly develops from deuterosomal cell property_value: terms:date "2023-01-25T11:06:01Z" xsd:dateTime [Term] id: CL:4030035 name: dental pulp stem cell def: "A dental pulp cell that possesses stem-cell-like qualities, including self-renewal capability and multi-lineage differentiation." [DOI:10.1177/154405910208100806, https://orcid.org/0000-0002-2825-0621] +subset: human_subset +subset: mouse_subset synonym: "DPSC" EXACT OMO:0003000 [] is_a: CL:0000034 ! stem cell is_a: CL:0002148 ! dental pulp cell @@ -36251,6 +41466,8 @@ property_value: terms:date "2023-01-10T14:02:02Z" xsd:dateTime id: CL:4030036 name: early spermatid def: "A spermatid in an early stage of maturation that has a round morphology and is transcriptionally active." [https://www.proteinatlas.org/humanproteome/single+cell+type/Germ+cells#earlyspermatids] +subset: human_subset +subset: mouse_subset synonym: "round spermatid" EXACT [https://doi.org/10.1016/B978-0-323-01970-5.50014-2] is_a: CL:0000018 ! spermatid relationship: capable_of GO:0007286 ! spermatid development @@ -36261,6 +41478,8 @@ property_value: terms:date "2023-02-01T13:56:00Z" xsd:dateTime id: CL:4030037 name: late spermatid def: "A spermatid in a late stage of maturation that has an elongated morphology and is transcriptionally inert when the acrosome is fully developed." [https://www.proteinatlas.org/humanproteome/single+cell+type/Germ+cells#latespermatids] +subset: human_subset +subset: mouse_subset synonym: "elongated spermatid" EXACT [https://doi.org/10.1016/B978-0-323-01970-5.50014-2] is_a: CL:0000018 ! spermatid relationship: capable_of GO:0007286 ! spermatid development @@ -36273,6 +41492,8 @@ id: CL:4030038 name: CD24-positive, CD-133-positive, vimentin-positive proximal tubular cell def: "A CD24-positive, CD-133-positive, vimentin-positive cell found scattered throughout a renal proximal tubule and that may participate in tubular regeneration. Compared to other proximal tubular cell types, this cell contains less cytoplasm, fewer mitochondria and no brush border." [PMID:21281815, PMID:23124355] comment: After acute tubular injury, this cell type becomes more numerous. In healthy rat kidneys, this cell is not detectable, whereas after unilateral ureteral obstruction (renal injury), it may appear de novo, arguing against the notion that this cell type represents a pre-existing progenitor cell population. In at least one study, data indicate that this cell type represents transiently dedifferentiated tubular cells involved in regeneration. {xref="PMID:23124355"} +subset: human_subset +subset: mouse_subset synonym: "CD133+CD24+CD106- tubular cell" BROAD [https://doi.org/10.1002/stem.1130] synonym: "CD24+CD133+ tubular cell" BROAD [PMID:23124355] synonym: "CD24-positive tubular cell" BROAD [PMID:23124355] @@ -36288,6 +41509,8 @@ id: CL:4030039 name: von Economo neuron def: "An extratelencephalic-projecting glutamatergic cortical neuron that is morphologically-defined with a large, spindle-shaped cell body, thick bipolar dendrites with limited branching and a moderate density of spines, and often an axon initial segment that emanates from the side of the cell body. This cell type is associated with markers POU3F, BMP3 and ITGA4." [DOI:10.1007/BF02970950, DOI:10.1101/2022.10.12.511898, PMID:32127543] comment: In humans, a von Economo neuron is restricted to layer 5 of the anterior cingulate, frontoinsular, and medial frontopolar regions of cerebral cortex, while in some other species it is also found in the frontal and occipital poles and may not be restricted to layer 5. {xref="PMID:32127543"} +subset: human_subset +subset: mouse_subset synonym: "VEN" RELATED OMO:0003000 [PMID:32127543] is_a: CL:4023009 ! extratelencephalic-projecting glutamatergic cortical neuron relationship: bearer_of PATO:0070006 ! cortical bipolar morphology @@ -36295,16 +41518,20 @@ property_value: terms:date "2023-05-25T07:29:21Z" xsd:dateTime [Term] id: CL:4030040 -name: endometrial ciliated epithelial cell +name: endometrial multiciliated epithelial cell def: "A multi-ciliated cell of the endometrial epithelium. This cell is characterized by the presence of 9+2 motile cilia on its apical surface, which facilitates the movement of mucus across the endometrial surface." [doi:10.1016/j.coemr.2024.100503, doi:10.1038/s41591-020-1040-z, https://www.proteinatlas.org/humanproteome/single+cell+type/Glandular+epithelial+cells#endometrialciliatedcells, PMID:31290979, PMID:37999981] comment: In human samples, the expression of FOXJ1 protein, a regulator for motile cilia with epithelial lineage identity, has been noted. {xref="ttps://www.nature.com/articles/s41591-020-1040-z"} +subset: human_subset +subset: mouse_subset synonym: "ciliated cell of the endometrium" EXACT [] synonym: "ciliated cell of the uterus" BROAD [] +synonym: "endometrial ciliated epithelial cell" EXACT [] synonym: "endometrium ciliated epithelial cell" EXACT [] synonym: "uterine ciliated cell" BROAD [] is_a: CL:0002149 ! epithelial cell of uterus -is_a: CL:0005012 ! multi-ciliated epithelial cell -intersection_of: CL:0005012 ! multi-ciliated epithelial cell +is_a: CL:0005012 ! multiciliated epithelial cell +intersection_of: CL:0000075 ! columnar/cuboidal epithelial cell +intersection_of: bearer_of PATO:0010007 ! multiciliated intersection_of: has_part GO:0097729 ! 9+2 motile cilium intersection_of: part_of UBERON:0004811 ! endometrium epithelium relationship: has_part GO:0097729 ! 9+2 motile cilium @@ -36313,18 +41540,24 @@ property_value: terms:date "2023-02-09T11:25:14Z" xsd:dateTime [Term] id: CL:4030041 -name: luminal endometrial ciliated epithelial cell +name: luminal endometrial multiciliated epithelial cell def: "A ciliated cell of the endometrial luminal epithelium. This cell is characterized by the presence of motile cilia on its apical surface." [doi:10.1038/s41591-020-1040-z] -is_a: CL:4030040 ! endometrial ciliated epithelial cell +subset: human_subset +subset: mouse_subset +synonym: "luminal endometrial ciliated epithelial cell" EXACT [] +is_a: CL:4030040 ! endometrial multiciliated epithelial cell relationship: part_of UBERON:0011949 ! endometrium luminal epithelium property_value: terms:date "2023-02-09T11:34:42Z" xsd:dateTime [Term] id: CL:4030042 -name: glandular endometrial ciliated epithelial cell +name: glandular endometrial multiciliated epithelial cell def: "A ciliated cell of the endometrial glandular epithelium. This cell is characterized by the presence of motile cilia on its apical surface." [doi:10.1038/s41591-020-1040-z] -is_a: CL:4030040 ! endometrial ciliated epithelial cell -relationship: part_of UBERON:0012276 ! endometrium glandular epithelium +subset: human_subset +subset: mouse_subset +synonym: "glandular endometrial ciliated epithelial cell" EXACT [] +is_a: CL:0009084 ! epithelial cell of endometrial gland +is_a: CL:4030040 ! endometrial multiciliated epithelial cell property_value: terms:date "2023-02-09T11:37:30Z" xsd:dateTime [Term] @@ -36332,9 +41565,12 @@ id: CL:4030043 name: matrix D1 medium spiny neuron def: "A DRD1-expressing medium spiny neuron that is part of a matrix compartment of dorsal striatum." [doi:10.1016/j.cub.2021.10.015] comment: In Rhesus macaques, both matrix D1 and D2 medium spiny neuron cell types have been noted to have enriched gene expression of the following: EPHA4, GDA, STXBP6, and SEMA3E. Broadly understood, matrix MSNs receive neocortical inputs from the associative and sensorimotor cortex and give rise to the direct and indirect pathways. {xref="doi:10.1016/j.cub.2021.10.015"} +subset: human_subset +subset: mouse_subset synonym: "D1-matrix" RELATED OMO:0003000 [doi:10.1016/j.cub.2021.10.015] synonym: "D1M" RELATED OMO:0003000 [doi:10.1016/j.cub.2021.10.015] synonym: "matrix D1-MSN" RELATED OMO:0003000 [doi:10.1016/j.cub.2021.10.015] +is_a: CL:0002613 ! striatum neuron is_a: CL:4023026 ! direct pathway medium spiny neuron property_value: terms:date "2023-06-02T14:05:03Z" xsd:dateTime @@ -36343,9 +41579,12 @@ id: CL:4030047 name: matrix D2 medium spiny neuron def: "A DRD2-expressing medium spiny neuron that is part of a matrix compartment of dorsal striatum." [doi:10.1016/j.cub.2021.10.015] comment: In Rhesus macaques, both matrix D1 and D2 medium spiny neuron cell types have been noted to have enriched gene expression of the following: EPHA4, GDA, STXBP6, and SEMA3E. Broadly understood, matrix MSNs receive neocortical inputs from the associative and sensorimotor cortex and give rise to the direct and indirect pathways. {xref="doi:10.1016/j.cub.2021.10.015"} +subset: human_subset +subset: mouse_subset synonym: "D2-matrix" RELATED OMO:0003000 [doi:10.1016/j.cub.2021.10.015] synonym: "D2M" RELATED OMO:0003000 [doi:10.1016/j.cub.2021.10.015] synonym: "matrix D2-MSN" RELATED OMO:0003000 [doi:10.1016/j.cub.2021.10.015] +is_a: CL:0002613 ! striatum neuron is_a: CL:4023029 ! indirect pathway medium spiny neuron property_value: terms:date "2023-06-02T14:40:25Z" xsd:dateTime @@ -36354,10 +41593,13 @@ id: CL:4030048 name: striosomal D1 medium spiny neuron def: "A DRD1-expressing medium spiny neuron that is part of a striosome of dorsal striatum." [doi:10.1016/j.cub.2021.10.015] comment: In Rhesus macaques, both striosomal D1 and D2 medium spiny neuron (MSN) cell types have been noted to have enriched gene expression of the following: KCNT1, KHDRBS3, FAM163A, BACH2, and KCNIP1. Striosomal MSN activations have been noted to influence cognitive and emotional decision making and value-based learning. In contrast to matrix MSNs, striosomal MSNs receive input from limbic territories, including the anterior cingulate cortex, orbitofrontal cortex, and anterior insular cortex, and project directly to midbrain dopamine neurons. {xref="doi:10.1016/j.cub.2021.10.015"} +subset: human_subset +subset: mouse_subset synonym: "D1-striosome" RELATED OMO:0003000 [DOI:10.1016/j.cub.2021.10.015] synonym: "D1S" RELATED OMO:0003000 [doi:10.1016/j.cub.2021.10.015] synonym: "striosome D1 medium spiny neuron" EXACT [doi:10.1016/j.cub.2021.10.015] synonym: "striosome D1-MSN" RELATED OMO:0003000 [doi:10.1016/j.cub.2021.10.015] +is_a: CL:0002613 ! striatum neuron is_a: CL:4023026 ! direct pathway medium spiny neuron property_value: terms:date "2023-06-02T14:50:43Z" xsd:dateTime @@ -36366,10 +41608,13 @@ id: CL:4030049 name: striosomal D2 medium spiny neuron def: "A DRD2-expressing medium spiny neuron that is part of a striosome of dorsal striatum." [doi:10.1016/j.cub.2021.10.015] comment: In Rhesus macaques, both striosomal D1 and D2 medium spiny neuron (MSN) cell types have been noted to have enriched gene expression of the following: KCNT1, KHDRBS3, FAM163A, BACH2, and KCNIP1. Striosomal MSN activations have been noted to influence cognitive and emotional decision making and value-based learning. In contrast to matrix MSNs, striosomal MSNs receive input from limbic territories, including the anterior cingulate cortex, orbitofrontal cortex, and anterior insular cortex, and project directly to midbrain dopamine neurons. {xref="doi:10.1016/j.cub.2021.10.015"} +subset: human_subset +subset: mouse_subset synonym: "D2-striosome" RELATED OMO:0003000 [doi:10.1016/j.cub.2021.10.015] synonym: "D2S" RELATED OMO:0003000 [doi:10.1016/j.cub.2021.10.015] synonym: "striosome D2 medium spiny neuron" EXACT [doi:10.1016/j.cub.2021.10.015] synonym: "striosome D2-MSN" RELATED OMO:0003000 [doi:10.1016/j.cub.2021.10.015] +is_a: CL:0002613 ! striatum neuron is_a: CL:4023029 ! indirect pathway medium spiny neuron property_value: terms:date "2023-06-02T15:03:08Z" xsd:dateTime @@ -36378,11 +41623,14 @@ id: CL:4030050 name: D1/D2-hybrid medium spiny neuron def: "A medium spiny neuron that expresses both DRD1 and DRD2 and is part of an extra-striosomal part of dorsal striatum." [doi:10.1016/j.cub.2021.10.015] comment: It has been noted in non-human primate species that the D1/D2-hybrid medium spiny neuron (D1/2) cell type shows the same amount of DRD1 expression as nearby D1 medium spiny neurons but far less DRD2 expression compared to nearby D2 medium spiny neurons. In Rhesus macaques, RXFP1 has been noted as a highly specific marker gene for the D1/2 cell type. The D1/2 cell type has also been described as having characteristics similar to a novel medium spiny neuron described in rodents (D1H or eccentric spiny projection neuron). Although an extrastriosomal cell type, the D1/2 cell type had been noted to express many of the genes associated with striosome, suggesting a possible homology to ‘‘exo-patch’’ cells. {xref="doi:10.1016/j.cub.2021.10.015"} +subset: human_subset +subset: mouse_subset synonym: "D1/2" RELATED OMO:0003000 [doi:10.1016/j.cub.2021.10.015] synonym: "D1/D2 hybrid" RELATED OMO:0003000 [doi:10.1016/j.cub.2021.10.015] synonym: "D1/D2-hybrid MSN" RELATED OMO:0003000 [doi:10.1016/j.cub.2021.10.015] synonym: "hybrid D1/2 cell type" RELATED OMO:0003000 [doi:10.1016/j.cub.2021.10.015] is_a: BFO:0000002 +is_a: CL:0002613 ! striatum neuron is_a: CL:1001474 ! medium spiny neuron relationship: RO:0002100 UBERON:0005382 ! has soma location dorsal striatum relationship: RO:0002292 PR:000001175 ! expresses D(1A) dopamine receptor @@ -36394,10 +41642,13 @@ id: CL:4030051 name: nucleus accumbens shell and olfactory tubercle D1 medium spiny neuron def: "A DRD1-expressing medium spiny neuron that is part of a nucleus accumbens shell or olfactory tubercle." [doi:10.1016/j.cub.2021.10.015] comment: In Rhesus macaques, both nucleus accumbens shell and olfactory tubercle D1 and D2 medium spiny neuron cell types have been noted to have enriched gene expression of the following: GREB1L, ARHGAP6, and GRIA4. {xref="doi:10.1016/j.cub.2021.10.015"} +subset: human_subset +subset: mouse_subset synonym: "D1Sh" RELATED OMO:0003000 [doi:10.1016/j.cub.2021.10.015] synonym: "NAc shell and OT D1 medium spiny neuron" EXACT [doi:10.1016/j.cub.2021.10.015] synonym: "NAc shell and OT D1-MSN" RELATED OMO:0003000 [doi:10.1016/j.cub.2021.10.015] is_a: BFO:0000002 +is_a: CL:0002613 ! striatum neuron is_a: CL:1001474 ! medium spiny neuron relationship: RO:0002100 UBERON:0005403 ! has soma location ventral striatum relationship: RO:0002292 PR:000001175 ! expresses D(1A) dopamine receptor @@ -36408,11 +41659,14 @@ id: CL:4030052 name: nucleus accumbens shell and olfactory tubercle D2 medium spiny neuron def: "A DRD2-expressing medium spiny neuron that is part of a nucleus accumbens shell or olfactory tubercle." [doi:10.1016/j.cub.2021.10.015] comment: In Rhesus macaques, both nucleus accumbens shell and olfactory tubercle D1 and D2 medium spiny neuron cell types have been noted to have enriched gene expression of the following: GREB1L, ARHGAP6, and GRIA4. {xref="doi:10.1016/j.cub.2021.10.015"} +subset: human_subset +subset: mouse_subset synonym: "D2Sh" RELATED OMO:0003000 [doi:10.1016/j.cub.2021.10.015] synonym: "NAc shell and OT D2 medium spiny neuron" EXACT [doi:10.1016/j.cub.2021.10.015] synonym: "NAc shell and OT D2-MSN" RELATED OMO:0003000 [doi:10.1016/j.cub.2021.10.015] synonym: "nucleus accumbens shell and olfactory tubercle D2-MSN" RELATED OMO:0003000 [doi:10.1016/j.cub.2021.10.015] is_a: BFO:0000002 +is_a: CL:0002613 ! striatum neuron is_a: CL:1001474 ! medium spiny neuron relationship: RO:0002100 UBERON:0005403 ! has soma location ventral striatum relationship: RO:0002292 PR:000001177 ! expresses D(2) dopamine receptor @@ -36423,7 +41677,10 @@ id: CL:4030053 name: Island of Calleja granule cell def: "A DRD1-expressing, medium spiny neuron-like granule cell that is part of an Island of Calleja." [doi:10.1016/j.cub.2021.10.015] comment: In Rhesus macaques, the Island of Calleja granule cell type has been noted to have enriched gene expression of CPNE4. {xref="doi:10.1016/j.cub.2021.10.015"} +subset: human_subset +subset: mouse_subset synonym: "D1-ICj" RELATED OMO:0003000 [doi:10.1016/j.cub.2021.10.015] +is_a: BFO:0000002 is_a: CL:0000120 ! granule cell is_a: CL:0002613 ! striatum neuron relationship: RO:0002292 PR:000001175 ! expresses D(1A) dopamine receptor @@ -36434,9 +41691,12 @@ id: CL:4030054 name: RXFP1-positive interface island D1-medium spiny neuron def: "A DRD1-expressing medium spiny neuron that is part of dense, RXFP1-positive cell islands throughout the nucleus accumbens, putamen, and near the adjacent septal nuclei." [doi:10.1016/j.cub.2021.10.015] comment: Regarding the abbreviation D1-NUDAP, NUDAP stands for "neurochemically unique domains in the accumbens and putamen". In Rhesus macaques, the RXFP1-positive interface island D1-medium spiny neuron (D1-NUDAP) has been noted to have upregulation of OPRM1 compared to DRD1-expressing medium spiny neurons located outside of the D1-exclusive island and in Islands of Calleja. Kappa-opioid receptor gene (OPRK1) has been noted to be absent from D1-NUDAP cells. Many striosome-specific markers have been noted to be upregulated in D1-NUDAP cells, including KCNIP1, KCNT1, KHDRBS3, and BACH2. PDYN, an acknowledged D1-striosome marker gene, has also been noted to be expressed in D1-NUDAPs. D1-NUDAPs also express some genes found to be selectively expressed in the matrix, including STXBP6, GDA, and SEMA3E. Gene enrichment analysis has revealed that D1-NUDAP neurons express genes that have been implicated in drug addiction and many other functions. {xref="doi:10.1016/j.cub.2021.10.015"} +subset: human_subset +subset: mouse_subset synonym: "D1-NUDAP" RELATED OMO:0003000 [doi:10.1016/j.cub.2021.10.015] synonym: "RXFP1-positive island D1-medium spiny neuron" EXACT [doi:10.1016/j.cub.2021.10.015] is_a: BFO:0000002 +is_a: CL:0002613 ! striatum neuron is_a: CL:1001474 ! medium spiny neuron relationship: RO:0002100 UBERON:0005403 ! has soma location ventral striatum relationship: RO:0002292 PR:000001175 ! expresses D(1A) dopamine receptor @@ -36449,6 +41709,8 @@ name: intermediate cell of urothelium def: "A urothelial cell that is part of the regenerative layer(s) of cells directly superficial to basal cells in urothelium. The layer of intermediate cells in the urothelium ranges from one to several layers thick depending on the species with intermediate cells attached to adjacent cell layers and one another via desmosomes." [doi:10.1038/s41385-022-00565-0] comment: It has been noted in at least some mammalian species that the urothelial intermediate cell type is similar to basal cells by expressing CK17 and (unlike umbrella cells) p63 but is positive for uroplakins (UPK) and negative for CK5. Urothelial intermediate cells have also been noted to be larger in diameter than urothelial basal cells. {xref="doi:10.1038/s41385-022-00565-0"} subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "urothelial intermediate cell" EXACT [doi:10.1007/978-3-030-14366-4_8] xref: FMA:84155 is_a: CL:0000731 ! urothelial cell @@ -36462,6 +41724,8 @@ name: umbrella cell of urothelium def: "A urothelial cell that is terminally differentiated and part of the urothelial apical surface that forms the high-resistance barrier of urothelium. Umbrella cells have been described as the largest of urothelial cell types, highly polarized, and, in some species, multinucleated. In the relaxed state, these cells form a dome-shaped structure at the apical pole and can also cover multiple underlying intermediate cells, leading to the name umbrella cells. In contrast, these cells flatten when the bladder is filled." [doi:10.1038/s41385-022-00565-0] comment: Umbrella cells are attached to sub-superficial cell layers via desmosomes, while tight junctions localized between superficial cells aid in forming a high-resistance barrier function. Another distinguishing feature of an umbrella cell type is the presence of subapical discoidal/fusiform-shaped vesicles contributing to the plasticity in urothelial cell surface area through a regulated process of endocytosis/exocytosis. It has been noted in at least some mammalian species that the urothelial umbrella cell type expresses UPK1A, UPK1B, UPK2 and UPK3A. Unlike intermediate and basal cells of the urothelium, CK17 is reported to be completely absent and p63 not expressed in umbrella cells. {xref="doi:10.1038/s41385-022-00565-0"} subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "facet cell of urothelium" EXACT [doi:10.1038/s41385-022-00565-0] synonym: "superficial cell of urothelium" EXACT [doi:10.1038/s41385-022-00565-0] xref: FMA:84149 @@ -36475,6 +41739,8 @@ id: CL:4030057 name: eccentric medium spiny neuron def: "A medium spiny neuron that exhibits transcriptional divergence from direct and indirect spiny projection neurons, for example, enrichment in Casz1, Otof, Cacng5 and Pcdh8 noted in mice. Whilst in general medium spiny neurons have been found to be differentially distributed across the basal ganglia, the eccentric medium spiny neuron cell type has been found to be more evenly distributed throughout cerebral nuclei." [doi:10.1016/j.cell.2018.07.028, doi:10.1101/2022.10.12.511898] comment: The term “eccentric” is used in the name eccentric medium spiny neuron (MSN) due to the exhibited transcriptional divergence from canonical spiny projection neurons. It has been noted in at least one study that an eccentric MSN differs in expression from direct and indirect MSNs by 110 genes (more than the 68 that distinguished direct and indirect spiny projection neurons from each other) and expresses many genes that have little expression in the rest of the striatum. It also has been noted in at least one human study that most eccentric MSNs expressed only DRD1, but many in the basal ganglia co-expressed DRD1 and DRD2, suggesting regional specialization of a more broadly distributed cell type. {xref="doi:10.1101/2022.10.12.511898", xref="doi:10.1016/j.cell.2018.07.028"} +subset: human_subset +subset: mouse_subset synonym: "eccentric MSN" RELATED OMO:0003000 [doi:10.1101/2022.10.12.511898] synonym: "eccentric spiny projection neuron" EXACT [doi:10.1016/j.cell.2018.07.028] synonym: "eccentric SPN" RELATED OMO:0003000 [doi:10.1016/j.cell.2018.07.028] @@ -36486,11 +41752,12 @@ property_value: terms:date "2023-06-23T14:59:36Z" xsd:dateTime id: CL:4030058 name: TCR-positive macrophage def: "A macrophage that expresses the T cell receptor complex at the cell surface." [https://orcid.org/0000-0001-9990-8331, PMID:26074923] +subset: human_subset +subset: mouse_subset synonym: "T cell receptor positive macrophage" EXACT [PMID:26074923] synonym: "TCR+ macrophage" EXACT [PMID:26074923] synonym: "TCR.macs" RELATED [PMID:37500727] {synonymtypedef="OMO:0003000"} is_a: CL:0000235 ! macrophage -is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000235 ! macrophage intersection_of: RO:0002104 GO:0042101 ! has plasma membrane part T cell receptor complex relationship: RO:0002104 GO:0042101 ! has plasma membrane part T cell receptor complex @@ -36501,14 +41768,19 @@ property_value: terms:date "2023-09-26T12:27:14Z" xsd:dateTime id: CL:4030059 name: L2/3 intratelencephalic projecting glutamatergic neuron def: "A transcriptomically distinct intratelencephalic-projecting glutamatergic neuron with a soma found between cortical layer 2-4. This intratelencephalic-projecting glutamatergic neuron has thin-tufted apical dendrites and extends its axonal projection into L5 in the neocortex. This neuronal type has a hyperpolarised resting membrane potential. The standard transcriptomic reference data for this cell type can be found on the CellxGene census under the collection: 'Transcriptomic cytoarchitecture reveals principles of human neocortex organization', dataset: 'Supercluster: IT-projecting excitatory neurons', Author Categories: 'CrossArea_subclass', clusters L2/3 IT." [https://cellxgene.cziscience.com/e/c3aa4f95-7a18-4a7d-8dd8-ca324d714363.cxg/, PMID:25622573, PMID:34004146, PMID:37292694, PMID:37824655] -comment: Hystorically, the L2/3 intratelencephalic projectic glutametergic neuron was known to have its soma in cortical layer 2/3. MERFISH data showed that this intratelencephalic-projecting glutametergic neuron can have its soma in layer 2/3, 4B, 4C. The position of the soma in layer 4b and 4C is less frequent for this neuronal type in comparison to cortical layer 2/3. {xref="PMID:37824655"} +comment: Hystorically, the L2/3 intratelencephalic projectic glutametergic neuron was known to have its soma in cortical layer 2/3. MERFISH data showed that this intratelencephalic-projecting glutametergic neuron can have its soma in layer 2/3, 4B, 4C. The position of the soma in layer 4b and 4C is less frequent for this neuronal type in comparison to cortical layer 2/3. The marker set ONECUT2, COL5A2 can identify the Human cell type L2/3 intratelencephalic projecting glutamatergic neuron in the Brain with a confidence of 0.670149932 (NS-Forest FBeta value). {xref="https://doi.org/10.5281/zenodo.11165918", xref="PMID:37824655"} +subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "L2/3 IT" RELATED OMO:0003000 [PMID:34004146] xref: ILX:0770156 is_a: CL:4023040 ! L2/3-6 intratelencephalic projecting glutamatergic neuron intersection_of: CL:4023040 ! L2/3-6 intratelencephalic projecting glutamatergic neuron intersection_of: RO:0002100 UBERON:8440000 ! has soma location cortical layer II/III relationship: RO:0002100 UBERON:8440000 ! has soma location cortical layer II/III +relationship: RO:0015004 CLM:1000065 ! has characterizing marker set NS forest marker set of L2/3 intratelencephalic projecting glutamatergic neuron (Human Brain). property_value: IAO:0000028 "L2/3 IT" xsd:string +property_value: RO:0002175 NCBITaxon:9606 property_value: terms:contributor https://orcid.org/0000-0003-4389-9821 property_value: terms:date "2023-10-10T14:10:21Z" xsd:dateTime @@ -36516,6 +41788,8 @@ property_value: terms:date "2023-10-10T14:10:21Z" xsd:dateTime id: CL:4030060 name: L2 intratelencephalic projecting glutamatergic neuron def: "An intratelencephalic-projecting glutamatergic neuron with a soma found in cortical layer 2." [PMID:34004146] +subset: human_subset +subset: mouse_subset synonym: "L2 IT" RELATED OMO:0003000 [PMID:34004146] is_a: CL:4023040 ! L2/3-6 intratelencephalic projecting glutamatergic neuron intersection_of: CL:4023040 ! L2/3-6 intratelencephalic projecting glutamatergic neuron @@ -36529,6 +41803,8 @@ property_value: terms:date "2023-10-10T14:10:36Z" xsd:dateTime id: CL:4030061 name: L3 intratelencephalic projecting glutamatergic neuron def: "An intratelencephalic-projecting glutamatergic neuron with a soma found in cortical layer 3." [PMID:34004146] +subset: human_subset +subset: mouse_subset synonym: "L3 IT" RELATED OMO:0003000 [PMID:34004146] is_a: CL:4023040 ! L2/3-6 intratelencephalic projecting glutamatergic neuron intersection_of: CL:4023040 ! L2/3-6 intratelencephalic projecting glutamatergic neuron @@ -36542,6 +41818,8 @@ property_value: terms:date "2023-10-10T14:10:47Z" xsd:dateTime id: CL:4030062 name: L4/5 intratelencephalic projecting glutamatergic neuron def: "An intratelencephalic-projecting glutamatergic with a soma located in cortical layer 4/5." [PMID:34004146] +subset: human_subset +subset: mouse_subset synonym: "L4/5 IT" RELATED OMO:0003000 [PMID:34004146] is_a: CL:4023040 ! L2/3-6 intratelencephalic projecting glutamatergic neuron intersection_of: CL:4023040 ! L2/3-6 intratelencephalic projecting glutamatergic neuron @@ -36555,13 +41833,18 @@ property_value: terms:date "2023-10-10T14:11:04Z" xsd:dateTime id: CL:4030063 name: L4 intratelencephalic projecting glutamatergic neuron def: "A transcriptomically distinct intratelencephalic-projecting glutamatergic neuron with a soma found in cortical layer 3-4. This neuron type can have a pyramidal, star-pyramidal or spiny stellate morphology and projects its output to L2/3 and L5A/B. The standard transcriptomic reference data for this cell type can be found on the CellxGene census under the collection: 'Transcriptomic cytoarchitecture reveals principles of human neocortex organization', dataset: 'Supercluster: IT-projecting excitatory neurons', Author Categories: 'CrossArea_subclass', L4 IT." [https://cellxgene.cziscience.com/e/c3aa4f95-7a18-4a7d-8dd8-ca324d714363.cxg/, PMID:37292694, PMID:37824655] -comment: Historically, the L4 intratelencephalic projectic glutametergic neuron was known to have its soma in cortical layer 4. MERFISH data showed that this intratelencephalic-projecting glutametergic neuron can also have its soma in layer 3. +comment: The marker set RORB, ST8SIA4 can identify the Human cell type L4 intratelencephalic projecting glutamatergic neuron in the Brain with a confidence of 0.720108696 (NS-Forest FBeta value). Historically, the L4 intratelencephalic projectic glutametergic neuron was known to have its soma in cortical layer 4. MERFISH data showed that this intratelencephalic-projecting glutametergic neuron can also have its soma in layer 3. {xref="https://doi.org/10.5281/zenodo.11165918"} +subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "L4 IT" RELATED OMO:0003000 [PMID:37292694] is_a: CL:4023040 ! L2/3-6 intratelencephalic projecting glutamatergic neuron intersection_of: CL:4023040 ! L2/3-6 intratelencephalic projecting glutamatergic neuron intersection_of: RO:0002100 UBERON:0005393 ! has soma location cortical layer IV relationship: RO:0002100 UBERON:0005393 ! has soma location cortical layer IV +relationship: RO:0015004 CLM:1000066 ! has characterizing marker set NS forest marker set of L4 intratelencephalic projecting glutamatergic neuron (Human Brain). property_value: IAO:0000028 "L4 IT" xsd:string +property_value: RO:0002175 NCBITaxon:9606 property_value: terms:contributor https://orcid.org/0000-0003-4389-9821 property_value: terms:date "2023-10-10T14:11:25Z" xsd:dateTime @@ -36569,13 +41852,18 @@ property_value: terms:date "2023-10-10T14:11:25Z" xsd:dateTime id: CL:4030064 name: L5 intratelencephalic projecting glutamatergic neuron def: "An intratelencephalic-projecting glutamatergic neuron with a soma found in cortical layer 5. The standard transcriptomic reference data for this cell type can be found on the CellxGene census under the collection: 'Transcriptomic cytoarchitecture reveals principles of human neocortex organization', dataset: 'Supercluster: IT-projecting excitatory neurons', Author Categories: 'CrossArea_subclass', L5 IT." [https://cellxgene.cziscience.com/e/c3aa4f95-7a18-4a7d-8dd8-ca324d714363.cxg/, PMID:37292694, PMID:37609206, PMID:37824655] +comment: The marker set ARSJ, RORB, KCNK2 can identify the Human cell type L5 intratelencephalic projecting glutamatergic neuron in the Brain with a confidence of 0.764261336 (NS-Forest FBeta value). {xref="https://doi.org/10.5281/zenodo.11165918"} +subset: human_subset +subset: mouse_subset synonym: "L5 IT" RELATED [PMID:37292694] {synonymtypedef="OMO:0003000"} xref: ILX:0770157 is_a: CL:4023040 ! L2/3-6 intratelencephalic projecting glutamatergic neuron intersection_of: CL:4023040 ! L2/3-6 intratelencephalic projecting glutamatergic neuron intersection_of: RO:0002100 UBERON:0005394 ! has soma location cortical layer V relationship: RO:0002100 UBERON:0005394 ! has soma location cortical layer V +relationship: RO:0015004 CLM:1000068 ! has characterizing marker set NS forest marker set of L5 intratelencephalic projecting glutamatergic neuron (Human Brain). property_value: IAO:0000028 "L5 IT" xsd:string +property_value: RO:0002175 NCBITaxon:9606 property_value: terms:contributor https://orcid.org/0000-0003-4389-9821 property_value: terms:date "2023-10-10T14:11:59Z" xsd:dateTime @@ -36583,13 +41871,18 @@ property_value: terms:date "2023-10-10T14:11:59Z" xsd:dateTime id: CL:4030065 name: L6 intratelencephalic projecting glutamatergic neuron def: "A transcriptomically distinct intratelencephalic-projecting glutamatergic neuron with a soma found in L6 of the primary motor cortex. These cells are short untufted pyramidal cells, which could be stellate or inverted. The standard transcriptomic reference data for this cell type can be found on the CellxGene census under the collection: 'Transcriptomic cytoarchitecture reveals principles of human neocortex organization', dataset: 'Supercluster: IT-projecting excitatory neurons', Author Categories: 'CrossArea_subclass', L6 IT." [https://cellxgene.cziscience.com/e/c3aa4f95-7a18-4a7d-8dd8-ca324d714363.cxg/, PMID:37292694, PMID:37609206, PMID:37824655] +comment: The marker set LINC00507, THEMIS can identify the Human cell type L6 intratelencephalic projecting glutamatergic neuron in the Brain with a confidence of 0.641695703 (NS-Forest FBeta value). {xref="https://doi.org/10.5281/zenodo.11165918"} +subset: human_subset +subset: mouse_subset synonym: "L6 IT" RELATED OMO:0003000 [PMID:37292694] xref: ILX:0770158 is_a: CL:4023040 ! L2/3-6 intratelencephalic projecting glutamatergic neuron intersection_of: CL:4023040 ! L2/3-6 intratelencephalic projecting glutamatergic neuron intersection_of: RO:0002100 UBERON:0005395 ! has soma location cortical layer VI relationship: RO:0002100 UBERON:0005395 ! has soma location cortical layer VI +relationship: RO:0015004 CLM:1000071 ! has characterizing marker set NS forest marker set of L6 intratelencephalic projecting glutamatergic neuron (Human Brain). property_value: IAO:0000028 "L6 IT" xsd:string +property_value: RO:0002175 NCBITaxon:9606 property_value: terms:contributor https://orcid.org/0000-0003-4389-9821 property_value: terms:date "2023-10-10T14:12:23Z" xsd:dateTime @@ -36597,6 +41890,9 @@ property_value: terms:date "2023-10-10T14:12:23Z" xsd:dateTime id: CL:4030066 name: ureteric bud cell def: "An epithelial cell that is part of a ureteric bud. A ureteric bud cell has the potential to induce metanephric mesenchymal cells to proliferate and convert to epithelia that form renal tubules via: (1) the secretion of multiple diffusible growth factors that rescue renal progenitors from apoptosis and stimulate them to proliferate and (2) contact-dependent mechanisms that induce mesenchymal-epithelial conversion." [PMID:17133361, PMID:24183650, PMID:9374839] +subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "UB cell" RELATED OMO:0003000 [PMID:24183650] is_a: BFO:0000002 is_a: CL:0000068 ! duct epithelial cell @@ -36612,11 +41908,17 @@ property_value: terms:date "2023-10-13T11:22:42Z" xsd:dateTime id: CL:4030067 name: L5/6 near-projecting glutamatergic neuron def: "A near-projecting glutamatergic neuron with a soma found in cortical layer 5/6." [PMID:34004146, PMID:37292694, PMID:37824655] +comment: The marker set NPSR1-AS1, TLL1 can identify the Human cell type L5/6 near-projecting glutamatergic neuron in the Brain with a confidence of 0.899288218 (NS-Forest FBeta value). {xref="https://doi.org/10.5281/zenodo.11165918"} +subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "L5/6 NP" RELATED OMO:0003000 [PMID:34004146] is_a: CL:4023012 ! near-projecting glutamatergic cortical neuron intersection_of: CL:4023012 ! near-projecting glutamatergic cortical neuron intersection_of: RO:0002100 UBERON:8440002 ! has soma location cortical layer V/VI relationship: RO:0002100 UBERON:8440002 ! has soma location cortical layer V/VI +relationship: RO:0015004 CLM:1000069 ! has characterizing marker set NS forest marker set of L5/6 near-projecting glutamatergic neuron (Human Brain). +property_value: RO:0002175 NCBITaxon:9606 property_value: terms:contributor https://orcid.org/0000-0003-4389-9821 property_value: terms:date "2023-11-17T11:35:06Z" xsd:dateTime @@ -36624,6 +41926,9 @@ property_value: terms:date "2023-11-17T11:35:06Z" xsd:dateTime id: CL:4030068 name: L6 intratelencephalic projecting Car3 glutamatergic neuron def: "A transcriptomically distinct intratelencepalic-projecting glutamatergic neuron that expresses Car3 with a soma found in L6 . The standard transcriptomic reference data for this cell type can be found on the CellxGene census under the collection: 'Transcriptomic cytoarchitecture reveals principles of human neocortex organization', dataset: 'Supercluster: IT-projecting excitatory neurons', Author Categories: 'CrossArea_cluster', L6 IT Car3." [doi:10.1007/s00424-024-02923-2, doi:10.1101/2022.11.30.518285, PMID:34004146, PMID:37824655] +comment: The marker set SMYD1, THEMIS can identify the Human cell type L6 intratelencephalic projecting Car3 glutamatergic neuron in the Brain with a confidence of 0.877752028 (NS-Forest FBeta value). {xref="https://doi.org/10.5281/zenodo.11165918"} +subset: human_subset +subset: mouse_subset synonym: "L6 IT Car3" RELATED OMO:0003000 [doi:10.1101/2022.11.06.515349] synonym: "L6 IT Car3 glutamatergic neuron" EXACT OMO:0003000 [https://orcid.org/0000-0003-4389-9821] synonym: "L6 IT Car3 neuron" RELATED OMO:0003000 [PMID:37824655] @@ -36633,9 +41938,11 @@ is_a: BFO:0000002 is_a: CL:4030065 ! L6 intratelencephalic projecting glutamatergic neuron intersection_of: CL:4030065 ! L6 intratelencephalic projecting glutamatergic neuron intersection_of: RO:0002100 UBERON:0005395 ! has soma location cortical layer VI -intersection_of: RO:0002292 PR:000004919 ! expresses -relationship: RO:0002292 PR:000004919 ! expresses +intersection_of: RO:0002292 PR:000004919 ! expresses carbonic anhydrase 3 +relationship: RO:0002292 PR:000004919 ! expresses carbonic anhydrase 3 +relationship: RO:0015004 CLM:1000072 ! has characterizing marker set NS forest marker set of L6 intratelencephalic projecting Car3 glutamatergic neuron (Human Brain). property_value: IAO:0000028 "L6 IT Car3" xsd:string +property_value: RO:0002175 NCBITaxon:9606 property_value: terms:contributor https://orcid.org/0000-0003-4389-9821 property_value: terms:date "2023-11-23T09:16:14Z" xsd:dateTime @@ -36644,6 +41951,8 @@ id: CL:4032000 name: club-like cell of the urethral epithelium def: "An epithelial cell of the urethra that has an expression profile similar to lung club cells. Club-like cells of the urethra epithelium are similar to lung club cells in their expression of SCGB1A1 and in their enrichment of immunomodulatory programs." [PMID:30566875, PMID:32497356] comment: Club cells typically refer to bronchiolar exocrine cells found in the lungs. This cell type is given the name club cell due to their similarity to club cells in the lungs. {xref="PMID:30566875"} +subset: human_subset +subset: mouse_subset synonym: "club cell of the urethra epithelium" EXACT [] synonym: "club-like cell of the prostatic urethra epithelium" EXACT [https://orcid.org/0000-0001-7258-9596] synonym: "prostate club cell" EXACT [PMID:30566875] @@ -36657,6 +41966,8 @@ property_value: terms:contributor http://orcid.org/0000-0001-6757-4744 id: CL:4032001 name: reelin GABAergic cortical interneuron def: "A GABAergic interneuron located in the cerebral cortex that expresses reelin (rln)." [PMID:23803971] +subset: human_subset +subset: mouse_subset synonym: "rln GABAergic cortical interneuron" EXACT [PMID:29904965] is_a: BFO:0000002 is_a: CL:0010011 ! cerebral cortex GABAergic interneuron @@ -36673,6 +41984,8 @@ property_value: terms:contributor "http://orcid.org/0000-0001-7476-6306" xsd:str id: CL:4033000 name: endothelial cell of venule of lymph node def: "A(n) endothelial cell that is part of a(n) venule of lymph node." [PMID:28217126] +subset: human_subset +subset: mouse_subset is_a: CL:1000414 ! endothelial cell of venule intersection_of: CL:0000115 ! endothelial cell intersection_of: part_of UBERON:8410041 ! venule of lymph node @@ -36683,6 +41996,8 @@ property_value: terms:contributor https://orcid.org/0000-0001-6677-8489 id: CL:4033001 name: endothelial cell of arteriole of lymph node def: "A(n) endothelial cell that is part of a(n) arteriole of lymph node." [PMID:28217126] +subset: human_subset +subset: mouse_subset is_a: CL:1000412 ! endothelial cell of arteriole intersection_of: CL:0000115 ! endothelial cell intersection_of: part_of UBERON:8410042 ! arteriole of lymph node @@ -36693,6 +42008,9 @@ property_value: terms:contributor https://orcid.org/0000-0001-6677-8489 id: CL:4033002 name: neuroendocrine cell of epithelium of crypt of Lieberkuhn def: "A(n) neuroendocrine cell that is part of a(n) epithelium of crypt of Lieberkuhn." [PMID:31390635] +subset: human_subset +subset: mouse_subset +is_a: CL:0000150 ! glandular secretory epithelial cell is_a: CL:0000165 ! neuroendocrine cell is_a: CL:1001516 ! intestinal enteroendocrine cell intersection_of: CL:0000165 ! neuroendocrine cell @@ -36705,6 +42023,8 @@ id: CL:4033003 name: myoepithelial cell of bronchus submucosal gland def: "A(n) myoepithelial cell that is part of a(n) bronchus submucosal gland." [PMID:19996346, PMID:5487122] subset: human_reference_atlas +subset: human_subset +subset: mouse_subset is_a: CL:0000185 ! myoepithelial cell is_a: CL:0002328 ! bronchial epithelial cell intersection_of: CL:0000185 ! myoepithelial cell @@ -36717,9 +42037,12 @@ property_value: terms:contributor https://orcid.org/0000-0001-6677-8489 id: CL:4033004 name: smooth muscle cell of taenia coli def: "A(n) smooth muscle cell that is part of a(n) taenia coli." [PMID:10715339, PMID:22320805] +subset: human_subset +subset: mouse_subset is_a: CL:1000279 ! smooth muscle cell of large intestine intersection_of: CL:0000192 ! smooth muscle cell intersection_of: part_of UBERON:0012419 ! taenia coli +relationship: part_of UBERON:0001278 ! epithelium of large intestine relationship: part_of UBERON:0012419 ! taenia coli property_value: terms:contributor https://orcid.org/0000-0001-6677-8489 @@ -36727,12 +42050,17 @@ property_value: terms:contributor https://orcid.org/0000-0001-6677-8489 id: CL:4033005 name: serous secreting cell of bronchus submucosal gland def: "A(n) serous secreting cell that is part of a(n) bronchus submucosal gland." [PMID:5487122, PMID:9651178] +comment: The marker set PRR4, C6orf58 can identify the Human cell type serous secreting cell of bronchus submucosal gland in the Lung with a confidence of 0.75 (NS-Forest FBeta value). {xref="https://doi.org/10.5281/zenodo.11165918"} +subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset is_a: CL:0000152 ! exocrine cell is_a: CL:0019001 ! tracheobronchial serous cell intersection_of: CL:0000313 ! serous secreting cell intersection_of: part_of UBERON:8410043 ! bronchus submucosal gland relationship: part_of UBERON:8410043 ! bronchus submucosal gland +relationship: RO:0015004 CLM:1000054 ! has characterizing marker set NS forest marker set of serous secreting cell of bronchus submucosal gland (Human Lung). property_value: RO:0002175 NCBITaxon:9606 property_value: terms:contributor https://orcid.org/0000-0001-6677-8489 @@ -36740,6 +42068,8 @@ property_value: terms:contributor https://orcid.org/0000-0001-6677-8489 id: CL:4033006 name: endothelial cell of efferent lymphatic vessel def: "A(n) endothelial cell that is part of a(n) efferent lymphatic vessel." [PMID:32094869] +subset: human_subset +subset: mouse_subset is_a: CL:0002138 ! endothelial cell of lymphatic vessel intersection_of: CL:0000115 ! endothelial cell intersection_of: part_of UBERON:0010397 ! efferent lymphatic vessel @@ -36751,6 +42081,8 @@ id: CL:4033007 name: brush cell of epithelium of lobar bronchus def: "A(n) brush cell that is part of a(n) epithelium of lobar bronchus." [PMID:15817800] subset: human_reference_atlas +subset: human_subset +subset: mouse_subset is_a: CL:0000082 ! epithelial cell of lung is_a: CL:0002208 ! brush cell of bronchus intersection_of: CL:0002204 ! brush cell @@ -36764,6 +42096,8 @@ id: CL:4033008 name: vein endothelial cell of respiratory system def: "A(n) vein endothelial cell that is part of a(n) respiratory system." [PMID:34030460] subset: human_reference_atlas +subset: human_subset +subset: mouse_subset is_a: CL:0002543 ! vein endothelial cell intersection_of: CL:0002543 ! vein endothelial cell intersection_of: part_of UBERON:0001004 ! respiratory system @@ -36776,6 +42110,8 @@ id: CL:4033009 name: goblet cell of epithelium of lobar bronchus def: "A(n) goblet cell that is part of a(n) epithelium of lobar bronchus." [PMID:18757316] subset: human_reference_atlas +subset: human_subset +subset: mouse_subset is_a: CL:1000143 ! lung goblet cell is_a: CL:1000312 ! bronchial goblet cell intersection_of: CL:0000160 ! goblet cell @@ -36789,9 +42125,11 @@ id: CL:4033010 name: neuroendocrine cell of epithelium of lobar bronchus def: "A(n) neuroendocrine cell that is part of a(n) epithelium of lobar bronchus." [PMID:26711336, PMID:33355253] subset: human_reference_atlas +subset: human_subset +subset: mouse_subset is_a: CL:0000082 ! epithelial cell of lung is_a: CL:0002328 ! bronchial epithelial cell -is_a: CL:1000223 ! lung neuroendocrine cell +is_a: CL:1000223 ! pulmonary neuroendocrine cell intersection_of: CL:0000165 ! neuroendocrine cell intersection_of: part_of UBERON:0002339 ! epithelium of lobar bronchus relationship: part_of UBERON:0002339 ! epithelium of lobar bronchus @@ -36802,9 +42140,12 @@ property_value: terms:contributor https://orcid.org/0000-0001-6677-8489 id: CL:4033011 name: smooth muscle cell of large intestine smooth muscle circular layer def: "A(n) smooth muscle cell that is part of a(n) large intestine smooth muscle circular layer." [PMID:24997029] +subset: human_subset +subset: mouse_subset is_a: CL:1000279 ! smooth muscle cell of large intestine intersection_of: CL:0000192 ! smooth muscle cell intersection_of: part_of UBERON:0012398 ! large intestine smooth muscle circular layer +relationship: part_of UBERON:0001278 ! epithelium of large intestine relationship: part_of UBERON:0012398 ! large intestine smooth muscle circular layer property_value: terms:contributor https://orcid.org/0000-0001-6677-8489 @@ -36812,9 +42153,12 @@ property_value: terms:contributor https://orcid.org/0000-0001-6677-8489 id: CL:4033012 name: smooth muscle cell of large intestine smooth muscle longitudinal layer def: "A(n) smooth muscle cell that is part of a(n) large intestine smooth muscle longitudinal layer." [PMID:24997029] +subset: human_subset +subset: mouse_subset is_a: CL:1000279 ! smooth muscle cell of large intestine intersection_of: CL:0000192 ! smooth muscle cell intersection_of: part_of UBERON:0012399 ! large intestine smooth muscle longitudinal layer +relationship: part_of UBERON:0001278 ! epithelium of large intestine relationship: part_of UBERON:0012399 ! large intestine smooth muscle longitudinal layer property_value: terms:contributor https://orcid.org/0000-0001-6677-8489 @@ -36822,6 +42166,9 @@ property_value: terms:contributor https://orcid.org/0000-0001-6677-8489 id: CL:4033013 name: suprabasal keratinocyte def: "A keratinocyte of the epidermis suprabasal layer. This cell may express the differentiation markers keratin 10 and keratin 1." [https://www.proteinatlas.org/humanproteome/single+cell+type/squamous+epithelial+cells#suprabasalkeratinocytes, PMID:35883599, PMID:9520465] +subset: cellxgene_subset +subset: human_subset +subset: mouse_subset is_a: CL:0000312 ! keratinocyte intersection_of: CL:0000312 ! keratinocyte intersection_of: part_of UBERON:0010402 ! epidermis suprabasal layer @@ -36835,11 +42182,13 @@ name: peg cell def: "A small, narrow, peg-shaped epithelial cell with little cytoplasm that is part of oviduct epithelium. This cell is rarer than the ciliated and secretory epithelial cells of the fallopian tube epithelium and is often found intercalated between them. Peg cells are generally distributed basally along the epithelium and have been found in high concentrations at the fimbriated, distal end of the fallopian tube in humans. It may have a regenerative/stem-cell function. In humans, markers include EPCAM, CD44, and ITGA6." [PMID:2210508, PMID:22911892, PMID:30023181] comment: In vitro evidence supports a stem-cell/regenerative function for these cells {xref="PMID:22911892"} subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "fallopian tube epithelial stem-like cell" EXACT [PMID:22911892] synonym: "FTE stem-like cell" EXACT [PMID:22911892] synonym: "FTESC" EXACT OMO:0003000 [PMID:22911892] synonym: "intercalary cell" EXACT [PMID:22911892] -is_a: CL:0000066 ! epithelial cell +is_a: CL:4052019 ! fallopian tube non-ciliated cell relationship: part_of UBERON:0004804 ! oviduct epithelium property_value: RO:0002175 NCBITaxon:9606 property_value: terms:contributor https://orcid.org/0000-0001-6677-8489 @@ -36850,7 +42199,10 @@ id: CL:4033015 name: retinal astrocyte def: "A star-shaped glial cell that is part of some retina. This cell links neurons to blood vessels and may provide structural and physiological support to optic nerve head axons." [PMID:25236977, PMID:33796062] comment: In response to elevated intraocular pressure, a retinal astrocyte may modulate extracellular matrix remodeling. In the human retina, a retinal astrocyte is GFAP-positive, SOD3-positive and GYPC-positive. {xref="PMID:33796062", xref="PMID:32555229"} +subset: cellxgene_subset subset: eye_upper_slim +subset: human_subset +subset: mouse_subset synonym: "retinal astroglia" RELATED OMO:0003004 [PMID:33796062] is_a: CL:0000127 ! astrocyte is_a: CL:0009004 ! retinal cell @@ -36865,6 +42217,8 @@ id: CL:4033016 name: secondary crest myofibroblast def: "A myofibroblast that is part of an alveoli during alveolarization. The contractile force of this cell elongates the secondary crest, while producing a framework of elastin and tenascin. During the maturation of the septa, secondary crest myofibroblasts, together with matrix fibroblasts, secrete metalloproteinases and other ECM‐remodeling proteins to thin the septal tip ECM. The secondary crest myofibroblast continues producing elastin, eventually undergoing apoptosis during adulthood." [PMID:31331942, PMID:33624948] subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "alveolar myofibroblast" RELATED [PMID:31331942] synonym: "SCMF" RELATED OMO:0003000 [PMID:33624948] synonym: "SCMFs" RELATED OMO:0003004 [PMID:25448080] @@ -36883,6 +42237,8 @@ id: CL:4033017 name: bronchiolar smooth muscle cell def: "A smooth muscle cell that is part of a bronchiole." [ISBN:9781260462982, PMID:15347627] subset: human_reference_atlas +subset: human_subset +subset: mouse_subset is_a: CL:0019019 ! tracheobronchial smooth muscle cell intersection_of: CL:0000192 ! smooth muscle cell intersection_of: part_of UBERON:0002186 ! bronchiole @@ -36897,6 +42253,8 @@ id: CL:4033018 name: lung megakaryocyte def: "A megakaryocyte that is resident in the lung connective tissue." [PMID:33351116] subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "lung MKs" RELATED OMO:0003004 [PMID:33351116] synonym: "lung resident megakaryocyte" EXACT [PMID:36524131] synonym: "lung-resident megakaryocyte" EXACT [PMID:36524131] @@ -36916,10 +42274,11 @@ id: CL:4033019 name: ON-blue cone bipolar cell def: "An ON bipolar cell type with dendrites selectively contacting S-cones." [PMID:32032773] comment: The axons of a blue cone bipolar cell terminate close to the ganglion cell layer, where they transfer the S-cone ON signal to small bistratified ganglion cells. Other targets of a blue cone bipolar cell include amacrine cells and possibly large bistratified ganglion cells. {xref="PMID:32032773"} -subset: human_reference_atlas +subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "BB cell" RELATED OMO:0003000 [PMID:32032773] is_a: CL:0000749 ! ON-bipolar cell -property_value: RO:0002175 NCBITaxon:9606 property_value: terms:contributor https://orcid.org/0000-0001-6677-8489 property_value: terms:date "2023-04-04T09:48:15Z" xsd:dateTime @@ -36928,6 +42287,8 @@ id: CL:4033020 name: mucus secreting cell of trachea gland def: "A mucus secreting cell that is part of a submucosal gland of the trachea." [PMID:18931053, PMID:29656943] subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "tracheal submucosal gland mucous cell" EXACT [PMID:18931053] is_a: CL:0000307 ! tracheal epithelial cell is_a: CL:4033037 ! mucus secreting cell of tracheobronchial tree submucosal gland @@ -36944,6 +42305,8 @@ id: CL:4033021 name: myoepithelial cell of trachea gland def: "A myoepithelial cell that is part of a submucosal gland of the trachea." [PMID:29656943] subset: human_reference_atlas +subset: human_subset +subset: mouse_subset is_a: CL:0000185 ! myoepithelial cell is_a: CL:0000307 ! tracheal epithelial cell intersection_of: CL:0000185 ! myoepithelial cell @@ -36958,13 +42321,17 @@ property_value: terms:date "2023-03-16T13:36:43Z" xsd:dateTime id: CL:4033022 name: mucus secreting cell of bronchus submucosal gland def: "A mucus secreting cell of a submucosal gland of the bronchus." [PMID:19965983] +comment: The marker set BPIFB2 can identify the Human cell type mucus secreting cell of bronchus submucosal gland in the Lung with a confidence of 0.93 (NS-Forest FBeta value). {xref="https://doi.org/10.5281/zenodo.11165918"} subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "bronchial gland mucous cell" EXACT [PMID:5487122] is_a: CL:0002328 ! bronchial epithelial cell is_a: CL:4033037 ! mucus secreting cell of tracheobronchial tree submucosal gland intersection_of: CL:0000319 ! mucus secreting cell intersection_of: part_of UBERON:8410043 ! bronchus submucosal gland relationship: part_of UBERON:8410043 ! bronchus submucosal gland +relationship: RO:0015004 CLM:1000053 ! has characterizing marker set NS forest marker set of mucus secreting cell of bronchus submucosal gland (Human Lung). property_value: RO:0002175 NCBITaxon:9606 property_value: terms:contributor https://orcid.org/0000-0001-6677-8489 property_value: terms:contributor https://orcid.org/0000-0002-9185-3994 @@ -36974,9 +42341,13 @@ property_value: terms:date "2023-03-16T15:12:52Z" xsd:dateTime id: CL:4033023 name: airway submucosal gland collecting duct epithelial cell def: "An epithelial cell that is part of a collecting duct of an airway submucosal gland." [PMID:25648514, PMID:29656943] +comment: The marker set GLYATL2, DMBT1 can identify the Human cell type airway submucosal gland collecting duct epithelial cell in the Lung with a confidence of 0.46 (NS-Forest FBeta value). {xref="https://doi.org/10.5281/zenodo.11165918"} subset: human_reference_atlas +subset: human_subset +subset: mouse_subset is_a: CL:0000066 ! epithelial cell relationship: part_of UBERON:8410077 ! airway submucosal gland +relationship: RO:0015004 CLM:1000052 ! has characterizing marker set NS forest marker set of airway submucosal gland collecting duct epithelial cell (Human Lung). property_value: RO:0002175 NCBITaxon:9606 property_value: terms:contributor https://orcid.org/0000-0001-6677-8489 property_value: terms:contributor https://orcid.org/0000-0002-9185-3994 @@ -36986,7 +42357,10 @@ property_value: terms:date "2023-03-16T15:20:28Z" xsd:dateTime id: CL:4033024 name: airway submucosal gland duct basal cell def: "A basal cell that is part of a duct of an airway submucosal gland." [PMID:29656943, PMID:35046051] +subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset is_a: CL:0000646 ! basal cell relationship: part_of UBERON:8410077 ! airway submucosal gland property_value: RO:0002175 NCBITaxon:9606 @@ -36999,6 +42373,8 @@ id: CL:4033025 name: perichondrial fibroblast def: "A fibroblast that is part of the fibrous layer of the perichondrium. This cell is responsible for collagen fiber production." [wikipedia:Perichondrium] subset: human_reference_atlas +subset: human_subset +subset: mouse_subset is_a: CL:0000057 ! fibroblast intersection_of: CL:0000057 ! fibroblast intersection_of: part_of UBERON:0008305 ! outer fibrous layer of perichondrium @@ -37012,7 +42388,10 @@ property_value: terms:date "2023-03-16T16:12:50Z" xsd:dateTime id: CL:4033026 name: lung perichondrial fibroblast def: "A perichondrial fibroblast that is part of the lung." [PMID:36543915] +subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "PC-fibro" RELATED OMO:0003000 [PMID:36543915] is_a: CL:0002553 ! fibroblast of lung is_a: CL:4033025 ! perichondrial fibroblast @@ -37028,13 +42407,14 @@ id: CL:4033027 name: diffuse bipolar 1 cell def: "An OFF diffuse bipolar cell that makes synaptic contact with both L/M and S-cone photoreceptors and only minimal contact with rod photoreceptors." [PMID:22006647] comment: In primates, a diffuse bipolar 1 cell on average makes 81 ribbon (output) synapses, 13 contacts are with OFF parasol cells and 47 contacts are with OFF midget cells. This cell might make flat contacts at both triad-associated and non-triad-associated positions on the cone pedicle. {xref="PMID:22006647", xref="PMID:32032773"} -subset: human_reference_atlas +subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "DB1 bipolar" RELATED OMO:0003000 [PMID:22006647] synonym: "DB1 bipolar cell" RELATED OMO:0003000 [PMID:22006647] synonym: "DB1 cell" RELATED OMO:0003000 [PMID:32032773] synonym: "Diffuse Bipolar Cell Type DB1" EXACT [PMID:22006647] is_a: CL:0000750 ! OFF-bipolar cell -property_value: RO:0002175 NCBITaxon:9606 property_value: terms:contributor https://orcid.org/0000-0001-6677-8489 property_value: terms:date "2023-04-04T10:48:29Z" xsd:dateTime @@ -37043,10 +42423,11 @@ id: CL:4033028 name: diffuse bipolar 2 cell def: "An OFF diffuse bipolar cell that predominantly connects to ON parasol cells and lateral amacrine cells. This cell contains a large number of synaptic ribbons and a small axon arbor area." [PMID:25309346, PMID:26500507, PMID:27833534] comment: In primates, a diffuse bipolar 2 cell makes an average of 133 ribbon synapses, 47 contacts are with OFF parasol cells and 4 contacts are with OFF midget cells. {xref="PMID:32032773"} -subset: human_reference_atlas +subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "DB2 cell" RELATED OMO:0003000 [PMID:32032773] is_a: CL:0000750 ! OFF-bipolar cell -property_value: RO:0002175 NCBITaxon:9606 property_value: terms:contributor https://orcid.org/0000-0001-6677-8489 property_value: terms:date "2023-04-04T10:49:07Z" xsd:dateTime @@ -37055,11 +42436,12 @@ id: CL:4033029 name: diffuse bipolar 3a cell def: "An OFF calbindin-positive bipolar cell that has a large dendritic field and stratifies narrowly close to the middle of the inner plexiform layer. Its axon terminal is characterized by regularly branching and varicose processes resembling beads on a string. Most of DB3a contacts with cones are triad-associated." [PMID:32032773, PMID:32555229, PMID:33009001] comment: Originally, DB3a cells were termed diffuse bipolar 3 (DB3) cells. When an additional bipolar type which stratifies slightly more vitread and is calbindin negative was detected, this cell was renamed diffuse bipolar 3a cell. The axons of neighboring DB3a cells make homologous gap junctions. The DB3a cells provide the majority of their output to OFF parasol cells. {xref="DOI:10.3389/fnana.2015.00122", xref="PMID:32032773"} -subset: human_reference_atlas +subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "DB3 cell" RELATED OMO:0003000 [DOI:10.3389/fnana.2015.00122] synonym: "DB3a cell" RELATED OMO:0003000 [PMID:32032773] is_a: CL:0000750 ! OFF-bipolar cell -property_value: RO:0002175 NCBITaxon:9606 property_value: terms:contributor https://orcid.org/0000-0001-6677-8489 property_value: terms:date "2023-04-04T10:53:33Z" xsd:dateTime @@ -37068,10 +42450,11 @@ id: CL:4033030 name: diffuse bipolar 3b cell def: "An OFF calbindin-negative bipolar cell that has a large dendritic field and stratifies narrowly close to the middle of the inner plexiform layer. Its axon terminal is characterized by regularly branching and varicose processes resembling beads on a string. Most of DB3b contacts with cones are non-triad-associated." [PMID:32032773, PMID:32555229] comment: In humans, a DB3b cell is CD15 positive. A DB3b cell might make sparse contacts to rod photoreceptors. {xref="PMID:24107939", xref="PMID:33009001", xref="PMID:32032773"} -subset: human_reference_atlas +subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "DB3b cell" RELATED OMO:0003000 [PMID:32032773] is_a: CL:0000750 ! OFF-bipolar cell -property_value: RO:0002175 NCBITaxon:9606 property_value: terms:contributor https://orcid.org/0000-0001-6677-8489 property_value: terms:date "2023-04-04T10:53:42Z" xsd:dateTime @@ -37079,10 +42462,11 @@ property_value: terms:date "2023-04-04T10:53:42Z" xsd:dateTime id: CL:4033031 name: diffuse bipolar 4 cell def: "An ON diffuse bipolar cell that predominantly connects to ON parasol cells and lateral amacrine cells." [PMID:27833534, PMID:32032773, PMID:32555229] -subset: human_reference_atlas +subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "DB4 cell" RELATED OMO:0003000 [PMID:32032773] is_a: CL:0000749 ! ON-bipolar cell -property_value: RO:0002175 NCBITaxon:9606 property_value: terms:contributor https://orcid.org/0000-0001-6677-8489 property_value: terms:date "2023-04-04T09:51:10Z" xsd:dateTime @@ -37090,10 +42474,11 @@ property_value: terms:date "2023-04-04T09:51:10Z" xsd:dateTime id: CL:4033032 name: diffuse bipolar 6 cell def: "An ON diffuse bipolar cell that has a large dendritic field and large axon terminals, which show little or no overlap. This cell predominantly connects to narrow thorny ganglion cells." [PMID:32032773, PMID:32555229] -subset: human_reference_atlas +subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "DB6 cell" RELATED OMO:0003000 [PMID:32032773] is_a: CL:0000749 ! ON-bipolar cell -property_value: RO:0002175 NCBITaxon:9606 property_value: terms:contributor https://orcid.org/0000-0001-6677-8489 property_value: terms:date "2023-04-04T09:51:22Z" xsd:dateTime @@ -37101,10 +42486,11 @@ property_value: terms:date "2023-04-04T09:51:22Z" xsd:dateTime id: CL:4033033 name: flat midget bipolar cell def: "An OFF bipolar cell with a small dendritic tree that provides most of the triad-associated basal (flat) contacts at cone pedicles." [PMID:32032773, PMID:32555229] -subset: human_reference_atlas +subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "FMB cell" RELATED OMO:0003000 [PMID:32032773] is_a: CL:0000750 ! OFF-bipolar cell -property_value: RO:0002175 NCBITaxon:9606 property_value: terms:contributor https://orcid.org/0000-0001-6677-8489 property_value: terms:date "2023-04-04T10:54:00Z" xsd:dateTime @@ -37112,10 +42498,11 @@ property_value: terms:date "2023-04-04T10:54:00Z" xsd:dateTime id: CL:4033034 name: invaginating midget bipolar cell def: "An ON bipolar cell with a small dendritic tree that forms most of the central (invaginating) elements opposite the synaptic ribbon at the cone triad." [PMID:32032773, PMID:32555229] -subset: human_reference_atlas +subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "IMB cell" RELATED OMO:0003000 [PMID:32032773] is_a: CL:0000749 ! ON-bipolar cell -property_value: RO:0002175 NCBITaxon:9606 property_value: terms:contributor https://orcid.org/0000-0001-6677-8489 property_value: terms:date "2023-04-04T09:51:44Z" xsd:dateTime @@ -37124,6 +42511,9 @@ id: CL:4033035 name: giant bipolar cell def: "An ON bipolar cell that has large dendritic and axonal fields." [PMID:32032773, PMID:32555229] comment: A giant bipolar cell is usually monostratified, although, very rarely, it can be bistratified. {xref="PMID:32032773"} +subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "GB cell" RELATED OMO:0003000 [PMID:32032773] is_a: CL:0000749 ! ON-bipolar cell property_value: terms:contributor https://orcid.org/0000-0001-6677-8489 @@ -37133,6 +42523,9 @@ property_value: terms:date "2023-04-04T09:54:15Z" xsd:dateTime id: CL:4033036 name: OFFx cell def: "An OFF bipolar cell that is fovea-specific and expresses FEZF1, NXPH1 and NXPH2." [PMID:30712875, PMID:31995762, PMID:32555229] +subset: cellxgene_subset +subset: human_subset +subset: mouse_subset is_a: BFO:0000002 is_a: CL:0000750 ! OFF-bipolar cell relationship: part_of UBERON:0001786 ! fovea centralis @@ -37144,6 +42537,9 @@ property_value: terms:date "2023-04-04T10:54:15Z" xsd:dateTime id: CL:4033037 name: mucus secreting cell of tracheobronchial tree submucosal gland def: "A mucus secreting cell of a submucosal gland of the tracheobronchial tree." [PMID:30864819] +subset: human_subset +subset: mouse_subset +is_a: CL:0000150 ! glandular secretory epithelial cell is_a: CL:0000152 ! exocrine cell is_a: CL:0000319 ! mucus secreting cell is_a: CL:0002202 ! epithelial cell of tracheobronchial tree @@ -37158,7 +42554,10 @@ property_value: terms:date "2023-04-20T10:55:50Z" xsd:dateTime id: CL:4033038 name: lung resident memory CD4-positive, alpha-beta T cell def: "An alpha-beta CD4 T cell that resides in the lung." [PMID:24064670, PMID:31265968] +subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "lung CD4-positive TRM" RELATED OMO:0003000 [PMID:31265968] synonym: "lung resident memory CD4 T cell" EXACT [PMID:24064670] is_a: CL:0000897 ! CD4-positive, alpha-beta memory T cell @@ -37173,7 +42572,10 @@ id: CL:4033039 name: lung resident memory CD8-positive, alpha-beta T cell def: "An alpha-beta CD8 T cell that resides in the lung." [PMID:28418771, PMID:31265968] comment: In the lung, CXCR6 regulates the localization of lung resident memory CD8-positive, alpha-beta T cells. {xref="PMID:31558615"} +subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "lung CD8-positive TRM" RELATED OMO:0003000 [PMID:31265968] is_a: CL:0000909 ! CD8-positive, alpha-beta memory T cell relationship: part_of UBERON:0002048 ! lung @@ -37186,6 +42588,8 @@ property_value: terms:date "2023-04-27T10:16:07Z" xsd:dateTime id: CL:4033040 name: lung resident memory CD8-positive, CD103-positive, alpha-beta T cell def: "A lung resident memory CD8-positive, alpha-beta T cell that is CD103-positive." [PMID:27776108] +subset: human_subset +subset: mouse_subset synonym: "lung resident memory CD8-positive CD103-positive, alpha-beta T cell" EXACT [PMID:27776108] synonym: "lung TRM CD8-positive, CD103-positive cell" EXACT [PMID:27776108] synonym: "lung TRM CD8-positive, integrin alpha E-positive cell" EXACT [PMID:27776108] @@ -37201,10 +42605,14 @@ property_value: terms:date "2023-05-24T12:23:35Z" xsd:dateTime id: CL:4033041 name: CCL3-positive alveolar macrophage def: "An alveolar macrophage that expresses CCL3." [PMID:37291214] +comment: The marker set TNIP3, CXCL5 can identify the Human cell type CCL3-positive alveolar macrophage in the Lung with a confidence of 0.67 (NS-Forest FBeta value). {xref="https://doi.org/10.5281/zenodo.11165918"} subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "alveolar macrophage CCL3-positive" EXACT [PMID:37291214] is_a: CL:0000583 ! alveolar macrophage relationship: RO:0002292 PR:000002123 ! expresses C-C motif chemokine 3 +relationship: RO:0015004 CLM:1000004 ! has characterizing marker set NS forest marker set of CCL3-positive alveolar macrophage (Human Lung). property_value: RO:0002175 NCBITaxon:9606 property_value: terms:contributor https://orcid.org/0000-0001-6677-8489 property_value: terms:contributor https://orcid.org/0000-0002-9185-3994 @@ -37214,10 +42622,15 @@ property_value: terms:date "2023-06-15T12:53:08Z" xsd:dateTime id: CL:4033042 name: metallothionein-positive alveolar macrophage def: "An alveolar macrophage that expresses metallothionein." [PMID:37291214] +comment: The marker set HMOX1, HPGD can identify the Human cell type metallothionein-positive alveolar macrophage in the Lung with a confidence of 0.41 (NS-Forest FBeta value). {xref="https://doi.org/10.5281/zenodo.11165918"} +subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "alveolar macrophage metallothionein-positive" EXACT [PMID:37291214] synonym: "alveolar macrophage MT-positive" EXACT [PMID:37291214] is_a: CL:0000583 ! alveolar macrophage +relationship: RO:0015004 CLM:1000005 ! has characterizing marker set NS forest marker set of metallothionein-positive alveolar macrophage (Human Lung). property_value: RO:0002175 NCBITaxon:9606 property_value: terms:contributor https://orcid.org/0000-0001-6677-8489 property_value: terms:contributor https://orcid.org/0000-0002-9185-3994 @@ -37227,12 +42640,17 @@ property_value: terms:date "2023-06-15T12:55:34Z" xsd:dateTime id: CL:4033043 name: lung interstitial macrophage def: "A macrophage that is part of the lung connective tissue (pulmonary interstitium). This cell performs tissue remodeling and contributes to barrier immunity through antigen presentation." [PMID:33382972, PMID:35017701, PMID:36211428] +comment: The marker set F13A1, STAB1, FCGR2B can identify the Human cell type lung interstitial macrophage in the Lung with a confidence of 0.46 (NS-Forest FBeta value). {xref="https://doi.org/10.5281/zenodo.11165918"} +subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "lung IM" RELATED OMO:0003000 [PMID:36211428] is_a: CL:0000864 ! tissue-resident macrophage is_a: CL:0002320 ! connective tissue cell is_a: CL:1001603 ! lung macrophage relationship: part_of UBERON:0000114 ! lung connective tissue +relationship: RO:0015004 CLM:1000031 ! has characterizing marker set NS forest marker set of lung interstitial macrophage (Human Lung). property_value: RO:0002175 NCBITaxon:9606 property_value: terms:contributor https://orcid.org/0000-0001-6677-8489 property_value: terms:contributor https://orcid.org/0000-0002-9185-3994 @@ -37243,8 +42661,12 @@ id: CL:4033044 name: deuterosomal cell def: "An epithelial cell part of respiratory tract epithelium that is a precursor of a multi-ciliated cell. This cell actively amplifies centrioles, a required step for multiciliogenesis." [PMID:31558434, PMID:331922198, PMID:36883528, PMID:37291214] comment: In humans, deuterosomal cells have been noted to have enriched expression of the following: PLK4, FOXJ1, DEUP1, FOXN4, YPEL1, HES6 and CDC20B. Deuterosomal cells were termed after deuterosomes, the platforms of active centriole amplification. {xref="PMID:31558434", xref="PMID:36883528", xref="PMID:331922198"} +subset: cellxgene_subset subset: human_reference_atlas -is_a: CL:0002368 ! respiratory epithelial cell +subset: human_subset +subset: mouse_subset +is_a: CL:0002368 ! respiratory tract epithelial cell +relationship: capable_of GO:0098535 ! de novo centriole assembly involved in multi-ciliated epithelial cell differentiation property_value: RO:0002175 NCBITaxon:9606 property_value: terms:contributor https://orcid.org/0000-0001-6677-8489 property_value: terms:contributor https://orcid.org/0000-0002-9185-3994 @@ -37255,6 +42677,8 @@ id: CL:4033045 name: lung migratory dendritic cell def: "A dendritic cell that captures antigens in a lung and migrates to a lymph node or to the spleen to activate T cells." [PMID:34516781] subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "lung mDC" RELATED OMO:0003000 [PMID:34516781] synonym: "lung mDCs" RELATED OMO:0003004 [PMID:34516781] is_a: CL:0000451 ! dendritic cell @@ -37267,6 +42691,8 @@ property_value: terms:date "2023-06-21T10:04:46Z" xsd:dateTime id: CL:4033046 name: ON midget ganglion cell def: "A midget ganglion cell that depolarizes in response to increased light intensity in the center of its receptive field. The majority of input that this cell receives comes from invaginating midget bipolar cells." [PMID:32032773] +subset: human_subset +subset: mouse_subset synonym: "inner stratifying midget cell" EXACT [PMID:32032773] synonym: "ON-midget cell" EXACT [PMID:34093409] synonym: "ON-midget RGC" EXACT [PMID:34093409] @@ -37281,6 +42707,8 @@ property_value: terms:date "2023-08-08T09:40:08Z" xsd:dateTime id: CL:4033047 name: OFF midget ganglion cell def: "A midget ganglion cell that depolarizes in response to decreased light intensity in the center of its receptive field. The majority of input that this cell receives comes from flat midget bipolar cells." [PMID:32032773] +subset: human_subset +subset: mouse_subset synonym: "OFF-midget cell" EXACT [PMID:34093409] synonym: "OFF-midget RGC" EXACT [PMID:34093409] synonym: "outer stratifying midget cell" EXACT [PMID:32032773] @@ -37293,15 +42721,20 @@ property_value: terms:date "2023-08-08T11:05:37Z" xsd:dateTime [Term] id: CL:4033048 -name: respiratory suprabasal cell -def: "A respiratory epithelial cell with topographic nuclear position in between the basal and luminal cell of the airway epithelium. This non-basal, intermediate cell has limited proliferative capacity, ultrastructural features of basal cells and no defined features of the typically differentiated cellular phenotypes." [PMID:25564622] -comment: In humans, respiratory suprabasal cells have been noted to have enriched expression of the following: CK8, KRT13, IVL, and SERPINB3. {xref="PMID:25658372", xref="doi:10.1101/2023.04.20.537495"} +name: respiratory tract suprabasal cell +def: "A respiratory epithelial cell derived from a basal cell, with a topographic nuclear position between the basal and luminal cells of the airway epithelium. This non-basal, intermediate progenitor cell has limited proliferative capacity and can differentiate into multiciliated, secretory, or rare airway cells (ionocytes, tuft cells, neuroendocrine cells). It shares some ultrastructural features with basal cells but lacks the defined characteristics of fully differentiated cellular phenotypes." [PMID:25564622, PMID:34044844, PMID:35387001, PMID:37834236] +comment: The marker set TNC, KRT15, SERPINB4 can identify the Human cell type respiratory suprabasal cell in the Lung with a confidence of 0.62 (NS-Forest FBeta value). In humans, respiratory tract suprabasal cells have been noted to have enriched expression of the following: CK8, KRT13, IVL, and SERPINB3. Single-cell sequencing indicates that suprabasal cells derived from the nasal epithelium are distinct from those in the tracheobronchial epithelium. {xref="PMID:25658372", xref="PMID:32726565", xref="doi:10.1101/2023.04.20.537495", xref="https://doi.org/10.5281/zenodo.11165918"} +subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "respiratory parabasal cell" EXACT [PMID:25564622] +synonym: "respiratory suprabasal cell" EXACT [] synonym: "respiratory suprabasal progenitor cell" EXACT [PMID:25658372] -is_a: CL:0002368 ! respiratory epithelial cell +is_a: CL:0002368 ! respiratory tract epithelial cell is_a: CL:0011026 ! progenitor cell relationship: RO:0002202 CL:0002633 ! develops from respiratory basal cell +relationship: RO:0015004 CLM:1000059 ! has characterizing marker set NS forest marker set of respiratory suprabasal cell (Human Lung). property_value: RO:0002175 NCBITaxon:9606 property_value: terms:contributor https://orcid.org/0000-0001-6677-8489 property_value: terms:contributor https://orcid.org/0000-0002-9185-3994 @@ -37311,9 +42744,10 @@ property_value: terms:date "2023-06-20T10:44:30Z" xsd:dateTime id: CL:4033049 name: taste receptor cell of tongue def: "A taste receptor cell that is part of a taste bud of a tongue." [DOI:10.1111/j.1096-3642.1981.tb01137.x, http://www.nejohnston.org/Birds/documents/AvianTongues_Johnston.pdf, PMID:10052456, PMID:28655883] +subset: human_subset +subset: mouse_subset synonym: "gustatory cell of tongue" RELATED [DOI:10.1016/s0022-5320(69)80043-2] is_a: CL:0000209 ! taste receptor cell -is_a: CL:0002251 ! epithelial cell of alimentary canal is_a: CL:0002319 ! neural cell intersection_of: CL:0000209 ! taste receptor cell intersection_of: part_of UBERON:0014451 ! tongue taste bud @@ -37326,11 +42760,15 @@ id: CL:4033050 name: catecholaminergic neuron def: "A neuron that releases catecholamine as a neurotransmitter." [ISBN:0521442516, PMID:12094209] comment: Frequently used when describing the developing nervous system in zebrafish. A catecholaminergic neuron expresses tyrosine hydroxylase (TH), tyrosine hydroxylase 2 (TH2), aromatic amino acid decarboxylase (AADC), dopamine b-hydroxylase (DBH), and phenylethanolamine-N-methyl transferase (PEMT), which are enzymes necessary for catecholamine synthesis. {xref="https://orcid.org/0000-0002-2244-7917", xref="PMID:12128258", xref="PMID:10191060", xref="PMID:34880760"} +subset: human_reference_atlas +subset: human_subset +subset: mouse_subset is_a: CL:0000151 ! secretory cell is_a: CL:0000540 ! neuron intersection_of: CL:0000540 ! neuron intersection_of: capable_of GO:0160043 ! catecholamine secretion, neurotransmission relationship: capable_of GO:0160043 ! catecholamine secretion, neurotransmission +property_value: RO:0002175 NCBITaxon:9606 property_value: terms:contributor https://orcid.org/0000-0001-6677-8489 property_value: terms:date "2023-05-18T12:07:45Z" xsd:dateTime @@ -37338,6 +42776,8 @@ property_value: terms:date "2023-05-18T12:07:45Z" xsd:dateTime id: CL:4033051 name: OFF parasol ganglion cell def: "A parasol ganglion cell that depolarizes in response to decreased light intensity in the center of its receptive field. The majority of input that this cell receives comes from DB3a bipolar cells." [PMID:32032773] +subset: human_subset +subset: mouse_subset synonym: "OFF-parasol retinal ganglion cell" EXACT [PMID:34093409] synonym: "OFF-parasol RGC" EXACT [PMID:34093409] synonym: "outer parasol cell" EXACT [PMID:32032773] @@ -37352,6 +42792,8 @@ property_value: terms:date "2023-08-08T12:34:57Z" xsd:dateTime id: CL:4033052 name: ON parasol ganglion cell def: "A parasol ganglion cell that depolarizes in response to increased light intensity in the center of its receptive field. The majority of input that this cell receives comes from DB4 bipolar cells." [PMID:32032773] +subset: human_subset +subset: mouse_subset synonym: "inner parasol cell" EXACT [PMID:32032773] synonym: "ON-parasol retinal ganglion cell" EXACT [PMID:34093409] synonym: "ON-parasol RGC" EXACT [PMID:34093409] @@ -37366,6 +42808,9 @@ property_value: terms:date "2023-08-08T12:39:35Z" xsd:dateTime id: CL:4033053 name: small bistratified retinal ganglion cell def: "A bistratfied retinal ganglion cell with a small dendritic field that has dendrites in the ON and OFF sublamina of the retinal inner plexiform layer and carries blue-ON/yellow-OFF signals. This cell receives bipolar and amacrine input to both the OFF and ON dendritic tree." [PMID:32032773] +subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "Polyak's shrub cell" RELATED [PMID:32032773] synonym: "sbRGC" RELATED OMO:0003000 [PMID:34093409] synonym: "SBS ganglion cell" RELATED OMO:0003000 [PMID:32032773] @@ -37380,6 +42825,9 @@ property_value: terms:date "2023-08-08T12:43:56Z" xsd:dateTime id: CL:4033054 name: perivascular cell def: "A cell that is adjacent to a vessel. A perivascular cell plays a crucial role in maintaining vascular function and tissue homeostasis. This cell type regulates vessel integrity and flow dynamics." [PMID:24928499, PMID:27889329] +subset: cellxgene_subset +subset: human_subset +subset: mouse_subset is_a: CL:0000000 ! cell intersection_of: CL:0000000 ! cell intersection_of: adjacent_to UBERON:0002049 ! vasculature @@ -37389,11 +42837,17 @@ property_value: terms:date "2023-08-22T13:40:28Z" xsd:dateTime [Term] id: CL:4033055 -name: airway submucosal gland duct ciliated cell -def: "A ciliated cell that is part of a ciliated duct of an airway submucosal gland." [PMID:17707699, PMID:30864819] +name: airway submucosal gland duct multiciliated cell +def: "A multi-ciliated epithelial cell located in ciliated duct of an airway submucosal gland, characterized by a columnar shape and motile cilia on its apical surface." [PMID:17707699, PMID:30864819] subset: human_reference_atlas -is_a: CL:0000064 ! ciliated cell -intersection_of: CL:0000064 ! ciliated cell +subset: human_subset +subset: mouse_subset +synonym: "airway submucosal gland duct ciliated cell" EXACT [] +is_a: CL:0000068 ! duct epithelial cell +is_a: CL:0005012 ! multiciliated epithelial cell +intersection_of: CL:0000075 ! columnar/cuboidal epithelial cell +intersection_of: bearer_of PATO:0010007 ! multiciliated +intersection_of: has_part GO:0031514 ! motile cilium intersection_of: part_of UBERON:8410077 ! airway submucosal gland intersection_of: part_of UBERON:8600014 ! submucosal gland ciliated duct relationship: part_of UBERON:8410077 ! airway submucosal gland @@ -37408,6 +42862,8 @@ id: CL:4033056 name: onychocyte def: "A differentiated flat keratinocyte that is part of a nail plate. An onychocyte is firmly adherent and does not desquamate." [PMID:24079581] subset: human_reference_atlas +subset: human_subset +subset: mouse_subset is_a: CL:0000312 ! keratinocyte relationship: part_of UBERON:0008198 ! nail plate property_value: RO:0002175 NCBITaxon:9606 @@ -37418,6 +42874,9 @@ property_value: terms:date "2023-10-03T12:49:46Z" xsd:dateTime id: CL:4033057 name: luminal adaptive secretory precursor cell of mammary gland def: "A luminal epithelial cell of the mammary gland that can proliferate and has the potential to differentiate into a lactocyte during pregnancy. In humans, a luminal adaptive secretory precursor cell can be identified by high levels of the markers EpCAM and CD49f, and in mice it can be identified by low levels of CD29 and high levels of CD14, Kit, CD61, and Tspan8." [https://nrs.harvard.edu/URN-3\:HUL.INSTREPOS\:37368328, https://orcid.org/0000-0001-6677-8489, PMID:19648928, PMID:35617956] +subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "alveolar cell" BROAD [PMID:35617956] synonym: "alveolar progenitor" BROAD [PMID:26390871] synonym: "AP" RELATED OMO:0003000 [https://nrs.harvard.edu/URN-3\:HUL.INSTREPOS\:37368328] @@ -37440,6 +42899,9 @@ id: CL:4033058 name: luminal hormone-sensing cell of mammary gland def: "A luminal epithelial cell of the mammary gland that transduces endocrine cues to orchestrate proliferation, architectural remodeling, and differentiation of other cells in the mammary gland via paracrine signaling. This cell expresses high levels of estrogen receptors. In humans, a luminal hormone-sensing cell can be identified by high levels of EpCAM and low levels of CD49f, and in mice it can be identified by low levels of CD29 and high levels of Foxa1, CD133, and Sca1 (Ly6a)." [https://nrs.harvard.edu/URN-3\:HUL.INSTREPOS\:37368328, https://orcid.org/0000-0001-6677-8489, PMID:19648928, PMID:26390871, PMID:34156490] comment: Following lineage specification, a luminal hormone-sensing cell expresses receptors for one or more hormones, such as estrogens, progesterone, androgens, and prolactin. In response to progesterone, luminal hormone-sensing cells express TNFSF11, WNT4, and RSPO1, among other factors, which cause branching, proliferation, and partial differentiation in LASP and B-Myo cells during luteal phases of the estrous/menstrual cycle and during gestation. During ductal elongation, ER activity drives expression of AREG in LHS cells, which is necessary for proliferation of the epithelium to fill the mammary fat pad. {xref="PMID:34156490", xref="PMID:26390871", xref="https://orcid.org/0000-0003-4969-670X"} +subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "ER-positive luminal hormone-sensor cell" EXACT [https://nrs.harvard.edu/URN-3\:HUL.INSTREPOS\:37368328] synonym: "hormone sensing cell" BROAD [doi:10.1101/2023.04.21.537845] synonym: "hormone-sensing mammary epithelial cell" BROAD [PMID:26390871] @@ -37450,7 +42912,6 @@ synonym: "LumHR" RELATED OMO:0003000 [PMID:37380767] synonym: "luminal hormone-responsive cell" BROAD [PMID:37380767] synonym: "luminal mature cell" BROAD [PMID:20346151] is_a: CL:0002326 ! luminal epithelial cell of mammary gland -is_a: PR:000050567 ! protein-containing material entity relationship: RO:0002104 PR:000007204 ! has plasma membrane part estrogen receptor property_value: terms:contributor https://orcid.org/0000-0001-6677-8489 property_value: terms:contributor https://orcid.org/0000-0003-4969-670X @@ -37460,6 +42921,8 @@ property_value: terms:date "2023-10-16T08:30:25Z" xsd:dateTime id: CL:4033059 name: lactocyte type 1 def: "A lactocyte that highly expresses genes associated with transcription, immune cell function, and cellular stress. A lactocyte type 1 also expresses genes involved in milk component biosynthesis (e.g., LALBA and CSNs), albeit at lower levels than a lactocyte type 2." [PMID:35091553, PMID:35377806] +subset: human_subset +subset: mouse_subset synonym: "LC1" RELATED OMO:0003000 [PMID:35091553] synonym: "LMC major luminal cluster 1" RELATED [PMID:35091553] synonym: "luminal cluster 1 cell" BROAD [PMID:34097179] @@ -37473,6 +42936,8 @@ property_value: terms:date "2023-10-16T13:15:36Z" xsd:dateTime id: CL:4033060 name: lactocyte type 2 def: "A lactocyte that highly expresses genes associated with lipid production and milk component biosynthesis." [PMID:35091553, PMID:35377806] +subset: human_subset +subset: mouse_subset synonym: "LC2" RELATED OMO:0003000 [PMID:35091553] synonym: "LMC major luminal cluster 2" RELATED [PMID:35091553] synonym: "luminal cluster 2 cell" BROAD [PMID:35377806] @@ -37485,6 +42950,8 @@ property_value: terms:date "2023-10-16T13:15:55Z" xsd:dateTime id: CL:4033061 name: endothelial cell of central vein of liver def: "An endothelial cell that is part of a central vein of liver." [PMID:28287163] +subset: human_subset +subset: mouse_subset synonym: "endothelial cell of central vein" BROAD [PMID:28287163] is_a: CL:0002543 ! vein endothelial cell intersection_of: CL:0000115 ! endothelial cell @@ -37497,6 +42964,8 @@ id: CL:4033062 name: interstitial extravillous trophoblast cell def: "A trophoblast cell that invades the uterine wall to anchor the placenta to the uterus. An interstitial extravillous trophoblast cell differentiates from an extravillous trophoblast cell, becoming hyperchromatic and changing its morphology to a fibroblast-like spindle-shaped cell. In humans, this cell can be distinguished by the expression of placental-specific protein 8, which stimulates migration." [doi:10.1007/978-3-030-84725-8, PMID:37630754] subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "iEVT" RELATED OMO:0003000 [PMID:37630754] synonym: "interstitial extravillous trophoblast" RELATED [PMID:37630754] synonym: "interstitial trophoblast" RELATED [PMID:11337369] @@ -37513,6 +42982,8 @@ name: endovascular extravillous trophoblast cell def: "A trophoblast cell that invades the maternal spiral arteries and replace the endothelial lining, remodeling the vessels and allowing for adequate blood transport into the placenta. An endovascular extravillous trophoblast cell differentiates from an extravillous trophoblast cell. In humans, this cell can be distinguished by the expression of CD56." [doi:10.1007/978-3-030-84725-8, PMID:37630754] comment: Shortly after implantation, the endovascular extravillous trophoblast cells occlude the maternal spiral arteries, preventing premature oxygen delivery to the placental villi and reducing fetal oxidative stress. {xref="PMID:37630754"} subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "eEVT" RELATED OMO:0003000 [PMID:37630754] synonym: "endovascular extravillous trophoblast" RELATED [PMID:37630754] synonym: "endovascular trophoblast" RELATED [PMID:11337369] @@ -37528,6 +42999,8 @@ name: uterine resident macrophage def: "A tissue-resident macrophage that is part of the uterus." [PMID:36113384] comment: Uterine macrophages are reported to be evenly distributed throughout the endometrial stroma but with aggregations observed close to the lumen of superficial secretory glands. {xref="PMID:36113384"} subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "uterine macrophage" BROAD [PMID:36113384] is_a: CL:0000864 ! tissue-resident macrophage intersection_of: CL:0000864 ! tissue-resident macrophage @@ -37541,6 +43014,8 @@ property_value: terms:date "2024-01-08T16:05:09Z" xsd:dateTime id: CL:4033065 name: preplasmablast def: "A mature B cell that serves as an intermediate stage in the differentiation of naive B cells into a plasmablast. A preplasmablast expresses CD30 and IL-6R and lacks expression of CD20, CD23, CD38 and CD138." [PMID:21918187, PMID:30755708, PMID:33150420] +subset: human_subset +subset: mouse_subset synonym: "pre-plasmablast" EXACT [PMID:23613519] synonym: "prePB" RELATED OMO:0003000 [PMID:21918187] synonym: "preplasmablastic cell" EXACT [PMID:33661294] @@ -37555,6 +43030,8 @@ property_value: terms:date "2024-04-25T09:14:58Z" xsd:dateTime id: CL:4033066 name: pre-granulosa cell def: "A supporting cell that is part of the ovary and differentiates into a granulosa cell. A pre-granulosa cell develops from an early supporting gonadal cell by repressing testis determination, which can then proliferate to form primordial follicles." [PMID:17639032, PMID:32759216, PMID:33970370, PMID:38178246] +subset: human_subset +subset: mouse_subset synonym: "ovarian pregranulosa cell" EXACT [PMID:32759216] synonym: "PG cell" RELATED OMO:0003000 [PMID:32759216] synonym: "pregranulosa cell" EXACT [PMID:17639032, PMID:32759216] @@ -37570,6 +43047,8 @@ property_value: terms:date "2024-06-07T12:04:57Z" xsd:dateTime id: CL:4033067 name: mural granulosa cell def: "A follicular cell of ovary that differentiates from a cuboidal granulosa cell during the secondary follicle stage. Mural granulosa cells line the inner surface of the follicle wall, surrounding the fluid-filled antral cavity. These cells produce oestrogen during the follicular phase in response to follicle-stimulating hormone (FSH), and progesterone after ovulation in response to luteinizing hormone (LH)." [PMID:27815559, PMID:33970370, PMID:34198768] +subset: human_subset +subset: mouse_subset synonym: "MGC" RELATED OMO:0003000 [doi:10.1530/REP-16-0500] synonym: "mural GC" RELATED OMO:0003000 [PMID:34198768] xref: EFO:0005289 @@ -37584,6 +43063,8 @@ property_value: terms:date "2024-06-07T12:15:13Z" xsd:dateTime id: CL:4033068 name: cycling B cell def: "A(n) B cell that is cycling." [PMID:31348891] +subset: human_subset +subset: mouse_subset synonym: "proliferating B cell" EXACT [PMID:31348891] is_a: CL:0000236 ! B cell intersection_of: CL:0000236 ! B cell @@ -37591,13 +43072,13 @@ intersection_of: participates_in GO:0022402 ! cell cycle process intersection_of: RO:0000086 PATO:0002354 ! has quality active relationship: participates_in GO:0022402 ! cell cycle process relationship: RO:0000086 PATO:0002354 ! has quality active -property_value: terms:contributor https://orcid.org/0000-0001-6677-8489 -property_value: terms:date "2024-07-02T09:14:23Z" xsd:string [Term] id: CL:4033069 name: cycling T cell def: "A(n) T cell that is cycling." [PMID:37291214] +subset: human_subset +subset: mouse_subset synonym: "proliferating T cell" EXACT [PMID:37291214] is_a: CL:0000084 ! T cell intersection_of: CL:0000084 ! T cell @@ -37605,26 +43086,26 @@ intersection_of: participates_in GO:0022402 ! cell cycle process intersection_of: RO:0000086 PATO:0002354 ! has quality active relationship: participates_in GO:0022402 ! cell cycle process relationship: RO:0000086 PATO:0002354 ! has quality active -property_value: terms:contributor https://orcid.org/0000-0001-6677-8489 -property_value: terms:date "2024-07-02T09:14:23Z" xsd:string [Term] id: CL:4033070 name: cycling dendritic cell def: "A(n) dendritic cell that is cycling." [PMID:32066951] +subset: human_subset +subset: mouse_subset synonym: "proliferating dendritic cell" EXACT [PMID:32066951] is_a: CL:0000451 ! dendritic cell is_a: CL:4033078 ! cycling mononuclear phagocyte intersection_of: CL:0000451 ! dendritic cell intersection_of: participates_in GO:0022402 ! cell cycle process intersection_of: RO:0000086 PATO:0002354 ! has quality active -property_value: terms:contributor https://orcid.org/0000-0001-6677-8489 -property_value: terms:date "2024-07-02T09:14:23Z" xsd:string [Term] id: CL:4033071 name: cycling natural killer cell def: "A(n) natural killer cell that is cycling." [PMID:34062119] +subset: human_subset +subset: mouse_subset synonym: "proliferating natural killer cell" EXACT [PMID:34062119] is_a: CL:0000623 ! natural killer cell intersection_of: CL:0000623 ! natural killer cell @@ -37632,26 +43113,26 @@ intersection_of: participates_in GO:0022402 ! cell cycle process intersection_of: RO:0000086 PATO:0002354 ! has quality active relationship: participates_in GO:0022402 ! cell cycle process relationship: RO:0000086 PATO:0002354 ! has quality active -property_value: terms:contributor https://orcid.org/0000-0001-6677-8489 -property_value: terms:date "2024-07-02T09:14:23Z" xsd:string [Term] id: CL:4033072 name: cycling gamma-delta T cell def: "A(n) gamma-delta T cell that is cycling." [PMID:32066951] +subset: human_subset +subset: mouse_subset synonym: "proliferating gamma-delta T cell" EXACT [PMID:32066951] is_a: CL:0000798 ! gamma-delta T cell is_a: CL:4033069 ! cycling T cell intersection_of: CL:0000798 ! gamma-delta T cell intersection_of: participates_in GO:0022402 ! cell cycle process intersection_of: RO:0000086 PATO:0002354 ! has quality active -property_value: terms:contributor https://orcid.org/0000-0001-6677-8489 -property_value: terms:date "2024-07-02T09:14:23Z" xsd:string [Term] id: CL:4033073 name: cycling monocyte def: "A(n) monocyte that is cycling." [PMID:31348891] +subset: human_subset +subset: mouse_subset synonym: "proliferating monocyte" EXACT [PMID:31348891] is_a: CL:0000576 ! monocyte is_a: CL:4033078 ! cycling mononuclear phagocyte @@ -37659,39 +43140,39 @@ is_a: CL:4033081 ! cycling myeloid cell intersection_of: CL:0000576 ! monocyte intersection_of: participates_in GO:0022402 ! cell cycle process intersection_of: RO:0000086 PATO:0002354 ! has quality active -property_value: terms:contributor https://orcid.org/0000-0001-6677-8489 -property_value: terms:date "2024-07-02T09:14:23Z" xsd:string [Term] id: CL:4033074 name: cycling CD8-positive, alpha-beta T cell def: "A(n) CD8-positive, alpha-beta T cell that is cycling." [PMID:34062119] +subset: human_subset +subset: mouse_subset synonym: "proliferating CD8-positive, alpha-beta T cell" EXACT [PMID:34062119] is_a: CL:0000625 ! CD8-positive, alpha-beta T cell is_a: CL:4033069 ! cycling T cell intersection_of: CL:0000625 ! CD8-positive, alpha-beta T cell intersection_of: participates_in GO:0022402 ! cell cycle process intersection_of: RO:0000086 PATO:0002354 ! has quality active -property_value: terms:contributor https://orcid.org/0000-0001-6677-8489 -property_value: terms:date "2024-07-02T09:14:23Z" xsd:string [Term] id: CL:4033075 name: cycling CD4-positive, alpha-beta T cell def: "A(n) CD4-positive, alpha-beta T cell that is cycling." [PMID:34062119] +subset: human_subset +subset: mouse_subset synonym: "proliferating CD4-positive, alpha-beta T cell" EXACT [PMID:34062119] is_a: CL:0000624 ! CD4-positive, alpha-beta T cell is_a: CL:4033069 ! cycling T cell intersection_of: CL:0000624 ! CD4-positive, alpha-beta T cell intersection_of: participates_in GO:0022402 ! cell cycle process intersection_of: RO:0000086 PATO:0002354 ! has quality active -property_value: terms:contributor https://orcid.org/0000-0001-6677-8489 -property_value: terms:date "2024-07-02T09:14:23Z" xsd:string [Term] id: CL:4033076 name: cycling macrophage def: "A(n) macrophage that is cycling." [PMID:33208946] +subset: human_subset +subset: mouse_subset synonym: "proliferating macrophage" EXACT [PMID:33208946] is_a: CL:0000235 ! macrophage is_a: CL:4033078 ! cycling mononuclear phagocyte @@ -37699,26 +43180,30 @@ is_a: CL:4033081 ! cycling myeloid cell intersection_of: CL:0000235 ! macrophage intersection_of: participates_in GO:0022402 ! cell cycle process intersection_of: RO:0000086 PATO:0002354 ! has quality active -property_value: terms:contributor https://orcid.org/0000-0001-6677-8489 -property_value: terms:date "2024-07-02T09:14:23Z" xsd:string [Term] id: CL:4033077 name: cycling alveolar macrophage def: "A(n) alveolar macrophage that is cycling." [PMID:37291214] +comment: The marker set PCLAF, RRM2, UBE2C, NUSAP1 can identify the Human cell type cycling alveolar macrophage in the Lung with a confidence of 0.26 (NS-Forest FBeta value). {xref="https://doi.org/10.5281/zenodo.11165918"} +subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "proliferating alveolar macrophage" EXACT [PMID:37291214] is_a: CL:0000583 ! alveolar macrophage is_a: CL:4033076 ! cycling macrophage intersection_of: CL:0000583 ! alveolar macrophage intersection_of: participates_in GO:0022402 ! cell cycle process intersection_of: RO:0000086 PATO:0002354 ! has quality active -property_value: terms:contributor https://orcid.org/0000-0001-6677-8489 -property_value: terms:date "2024-07-02T09:14:23Z" xsd:string +relationship: RO:0015004 CLM:1000006 ! has characterizing marker set NS forest marker set of cycling alveolar macrophage (Human Lung). +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:4033078 name: cycling mononuclear phagocyte def: "A(n) mononuclear phagocyte that is cycling." [PMID:37468583] +subset: human_subset +subset: mouse_subset synonym: "proliferating mononuclear phagocyte" EXACT [PMID:37468583] is_a: CL:0000113 ! mononuclear phagocyte intersection_of: CL:0000113 ! mononuclear phagocyte @@ -37726,13 +43211,13 @@ intersection_of: participates_in GO:0022402 ! cell cycle process intersection_of: RO:0000086 PATO:0002354 ! has quality active relationship: participates_in GO:0022402 ! cell cycle process relationship: RO:0000086 PATO:0002354 ! has quality active -property_value: terms:contributor https://orcid.org/0000-0001-6677-8489 -property_value: terms:date "2024-07-02T09:14:23Z" xsd:string [Term] id: CL:4033079 name: cycling endothelial cell of lymphatic vessel def: "A(n) endothelial cell of lymphatic vessel that is cycling." [PMID:37291214] +subset: human_subset +subset: mouse_subset synonym: "proliferating endothelial cell of lymphatic vessel" EXACT [PMID:37291214] is_a: CL:0002138 ! endothelial cell of lymphatic vessel intersection_of: CL:0002138 ! endothelial cell of lymphatic vessel @@ -37740,13 +43225,14 @@ intersection_of: participates_in GO:0022402 ! cell cycle process intersection_of: RO:0000086 PATO:0002354 ! has quality active relationship: participates_in GO:0022402 ! cell cycle process relationship: RO:0000086 PATO:0002354 ! has quality active -property_value: terms:contributor https://orcid.org/0000-0001-6677-8489 -property_value: terms:date "2024-07-02T09:14:23Z" xsd:string [Term] id: CL:4033080 name: cycling pulmonary alveolar type 2 cell def: "A(n) pulmonary alveolar type 2 cell that is cycling." [PMID:37291214] +comment: The marker set PEG10, PRC1, TOP2A can identify the Human cell type cycling pulmonary alveolar type 2 cell in the Lung with a confidence of 0.61 (NS-Forest FBeta value). {xref="https://doi.org/10.5281/zenodo.11165918"} +subset: human_subset +subset: mouse_subset synonym: "proliferating pulmonary alveolar type 2 cell" EXACT [PMID:37291214] is_a: CL:0002063 ! pulmonary alveolar type 2 cell intersection_of: CL:0002063 ! pulmonary alveolar type 2 cell @@ -37754,13 +43240,15 @@ intersection_of: participates_in GO:0022402 ! cell cycle process intersection_of: RO:0000086 PATO:0002354 ! has quality active relationship: participates_in GO:0022402 ! cell cycle process relationship: RO:0000086 PATO:0002354 ! has quality active -property_value: terms:contributor https://orcid.org/0000-0001-6677-8489 -property_value: terms:date "2024-07-02T09:14:23Z" xsd:string +relationship: RO:0015004 CLM:1000010 ! has characterizing marker set NS forest marker set of cycling pulmonary alveolar type 2 cell (Human Lung). +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:4033081 name: cycling myeloid cell def: "A(n) myeloid cell that is cycling." [PMID:38301653] +subset: human_subset +subset: mouse_subset synonym: "proliferating myeloid cell" EXACT [PMID:38301653] is_a: CL:0000763 ! myeloid cell intersection_of: CL:0000763 ! myeloid cell @@ -37768,13 +43256,13 @@ intersection_of: participates_in GO:0022402 ! cell cycle process intersection_of: RO:0000086 PATO:0002354 ! has quality active relationship: participates_in GO:0022402 ! cell cycle process relationship: RO:0000086 PATO:0002354 ! has quality active -property_value: terms:contributor https://orcid.org/0000-0001-6677-8489 -property_value: terms:date "2024-07-02T09:14:23Z" xsd:string [Term] id: CL:4033082 name: cycling basal cell def: "A(n) basal cell that is cycling." [PMID:33208946] +subset: human_subset +subset: mouse_subset synonym: "proliferating basal cell" EXACT [PMID:33208946] is_a: BFO:0000002 is_a: CL:0000646 ! basal cell @@ -37783,14 +43271,14 @@ intersection_of: participates_in GO:0022402 ! cell cycle process intersection_of: RO:0000086 PATO:0002354 ! has quality active relationship: participates_in GO:0022402 ! cell cycle process relationship: RO:0000086 PATO:0002354 ! has quality active -property_value: terms:contributor https://orcid.org/0000-0001-6677-8489 -property_value: terms:date "2024-07-02T09:14:23Z" xsd:string [Term] id: CL:4033083 name: squamous granulosa cell def: "A granulosa cell that has a squamous morphology and form a single layer around the oocyte in primordial follicles. This cell develops directly into a cuboidal granulosa cell during the primordial-to-primary follicle transition." [PMID:28892263] comment: Often in literature squamous granulosa cell and pre-granulosa cell are used as synonyms. However, this term only makes reference to the quiescent granulosa cells that surround the primordial ovarian follicle, while a pre-granulosa cell proliferates to form the primordial follicle (and thus cells become the squamous granulosa cells). {xref="https://orcid.org/0000-0001-6677-8489"} +subset: human_subset +subset: mouse_subset synonym: "flattened granulosa cell" EXACT [PMID:22402964] synonym: "pre-granulosa cell" RELATED [PMID:33914868] synonym: "squamous GC" RELATED OMO:0003000 [PMID:33914868] @@ -37805,6 +43293,8 @@ property_value: terms:date "2024-09-24T13:13:24Z" xsd:dateTime id: CL:4033084 name: cuboidal granulosa cell def: "A granulosa cell that has a cuboidal morphology and develops from squamous granulosa cell during the transition between primordial follicle to primary follicle. Cuboidal granulosa cells proliferate to form a second layer within secondary follicles." [PMID:28892263] +subset: human_subset +subset: mouse_subset synonym: "columnar GC" RELATED OMO:0003000 [PMID:19001500] synonym: "columnar granulosa cell" EXACT [PMID:19001500] synonym: "cuboidal epithelial granulosa cell" EXACT [PMID:31849844] @@ -37815,10 +43305,148 @@ relationship: RO:0002207 CL:4033083 ! directly develops from squamous granulosa property_value: terms:contributor https://orcid.org/0000-0001-6677-8489 property_value: terms:date "2024-09-24T13:14:57Z" xsd:dateTime +[Term] +id: CL:4033085 +name: diffuse bipolar 5 cell +def: "An ON diffuse bipolar cell that stratifies in the stratum 3 of the inner plexiform layer to make synapses with ON parasol ganglion cells. A diffuse bipolar 5 cell has high expression of MYO16 compared with other bipolar cells." [PMID:27833534, PMID:32032773] +comment: A diffuse bipolar 5 cell typically contacts 7–8 cone photoreceptors. The number and thickness of its dendritic processes are intermediate between those of a diffuse bipolar 6 cell (less dense and thinner) and a diffuse bipolar 4 cell (denser and thicker). {xref="PMID:27833534"} +subset: human_subset +subset: mouse_subset +synonym: "DB5 cell" RELATED OMO:0003000 [PMID:32032773] +is_a: CL:0000749 ! ON-bipolar cell +property_value: RO:0002175 NCBITaxon:9443 +property_value: terms:contributor https://orcid.org/0000-0001-6677-8489 +property_value: terms:date "2024-10-16T12:46:53Z" xsd:dateTime + +[Term] +id: CL:4033086 +name: lipid-associated macrophage +def: "A tissue-resident macrophage that is associated with lipids. This cell responsible of anti-inflammatory functions, lipid accumulation and enhancing phagocytosis (Wculek et al., 2022, Liu et al., 2022). In mice and humans, a lipid-associated macrophage is characterized by the marker Trem2 (Jaitlin et al., 2019)." [PMID:31257031, PMID:34876704, PMID:35712121] +comment: Distinct from “adipose macrophage” in Trem2 expression, and is not limited to adipose tissue. Guilliams et al. describe these cells as being distinct from Kupffer cells. {xref="PMID:37153549", xref="PMID:35021063"} +subset: human_subset +subset: mouse_subset +synonym: "LAM" RELATED OMO:0003000 [PMID:31257031] +is_a: CL:0000235 ! macrophage +relationship: RO:0002292 PR:000016626 ! expresses triggering receptor expressed on myeloid cells 2 +property_value: terms:contributor https://orcid.org/0000-0001-6677-8489 +property_value: terms:contributor https://orcid.org/0000-0001-8134-3037 +property_value: terms:date "2024-10-17T10:20:13Z" xsd:dateTime + +[Term] +id: CL:4033087 +name: placental resident macrophage +def: "A tissue-resident macrophage that is part of the placenta. This cell helps preventing immunological rejection of the fetus by modulating the immune environment. A placental resident macrophage has high plasticity to adapt to the changing needs of each phase of pregnancy." [PMID:39007150] +subset: human_subset +subset: mouse_subset +synonym: "placental macrophage" BROAD [PMID:39007150] +is_a: CL:0000864 ! tissue-resident macrophage +intersection_of: CL:0000864 ! tissue-resident macrophage +intersection_of: part_of UBERON:0001987 ! placenta +relationship: part_of UBERON:0001987 ! placenta +property_value: terms:contributor https://orcid.org/0000-0001-6677-8489 +property_value: terms:contributor https://orcid.org/0000-0001-7655-4833 +property_value: terms:date "2024-10-31T10:24:21Z" xsd:dateTime + +[Term] +id: CL:4033088 +name: decidual resident macrophage +def: "A resident macrophage that is part of the decidua. Some decidual macrophages are derived from maternal blood monocytes that are recruited to the uterus shortly after conception. The main functions of a decidual macrophage are implantation, placental development, immune regulation and vascular remodeling." [PMID:39007150] +subset: human_subset +subset: mouse_subset +synonym: "decidual macrophage" BROAD [PMID:39007150] +synonym: "maternal decidual macrophage" BROAD [PMID:39007150] +is_a: CL:0000349 ! extraembryonic cell +is_a: CL:4033087 ! placental resident macrophage +relationship: part_of UBERON:0002450 ! decidua +property_value: terms:contributor https://orcid.org/0000-0001-6677-8489 +property_value: terms:contributor https://orcid.org/0000-0001-7655-4833 +property_value: terms:date "2024-10-31T10:33:04Z" xsd:dateTime + +[Term] +id: CL:4033089 +name: atretic follicular cell of ovary +def: "A follicular cell of ovary that has begun to degenerate and undergo atresia, a specialized apoptosis. This cell is found in an atretic follicle, which is an ovarian follicle that started to mature but failed to reach full development and instead regresses." [PMID:38069168] +subset: human_subset +subset: mouse_subset +is_a: CL:0002174 ! follicular cell of ovary +intersection_of: CL:0002174 ! follicular cell of ovary +intersection_of: participates_in GO:0001552 ! ovarian follicle atresia +relationship: participates_in GO:0001552 ! ovarian follicle atresia +property_value: terms:contributor https://orcid.org/0000-0001-6677-8489 +property_value: terms:date "2024-11-05T11:23:25Z" xsd:dateTime + +[Term] +id: CL:4033090 +name: atretic granulosa cell +def: "A granulosa cell that is undergoing atresia. This cell type displays distinct morphological alterations compared with a healthy granulosa cell, including pyknosis (nuclear condensation) and cellular shrinkage." [PMID:15353131, PMID:38069168] +subset: human_subset +subset: mouse_subset +synonym: "apoptotic granulosa cell" RELATED [PMID:15353131] +is_a: CL:4033089 ! atretic follicular cell of ovary +relationship: RO:0002202 CL:0000501 ! develops from granulosa cell +property_value: terms:contributor https://orcid.org/0000-0001-6677-8489 +property_value: terms:date "2024-11-05T11:25:28Z" xsd:dateTime + +[Term] +id: CL:4033091 +name: glycinergic-GABAergic amacrine cell +def: "An amacrine cell that uses both GABA and glycine as neurotransmitters." [PMID:37124720] +subset: human_subset +subset: mouse_subset +synonym: "glycinergic/GABAergic amacrine neuron" EXACT [PMID:37124720] +is_a: CL:4030027 ! GABAergic amacrine cell +is_a: CL:4030028 ! glycinergic amacrine cell +intersection_of: CL:0000561 ! amacrine cell +intersection_of: capable_of GO:0061534 ! gamma-aminobutyric acid secretion, neurotransmission +intersection_of: capable_of GO:0061537 ! glycine secretion, neurotransmission +property_value: terms:contributor https://orcid.org/0000-0001-6677-8489 +property_value: terms:date "2024-12-02T13:44:17Z" xsd:dateTime + +[Term] +id: CL:4033092 +name: CD57-positive enterocyte +def: "An enterocyte that is part of a duodenal epithelium and expresses beta-1,3-glucuronyltransferase 1 (B3GAT1), also known as CD57 or HNK-1." [PMID:37468586] +comment: While CD57 is traditionally associated with immune cells (e.g., NK cells), its expression on enterocytes marks unique epithelial subsets with specific functions or maturation states. These cells are specially enriched in areas of the duodenum within submucosal glands. {xref="PMID:37468586"} +subset: human_subset +subset: mouse_subset +synonym: "CD57+ enterocyte" EXACT [PMID:37468586] +is_a: CL:1000335 ! enterocyte of epithelium of intestinal villus +intersection_of: CL:0000584 ! enterocyte +intersection_of: part_of UBERON:0008346 ! duodenal epithelium +intersection_of: RO:0002292 PR:000001440 ! expresses galactosylgalactosylxylosylprotein 3-beta-glucuronosyltransferase 1 +relationship: part_of UBERON:0008346 ! duodenal epithelium +relationship: RO:0002292 PR:000001440 ! expresses galactosylgalactosylxylosylprotein 3-beta-glucuronosyltransferase 1 +property_value: terms:contributor https://orcid.org/0000-0001-6677-8489 +property_value: terms:contributor https://orcid.org/0000-0001-7655-4833 +property_value: terms:contributor https://orcid.org/0000-0001-9961-7673 +property_value: terms:date "2024-12-06T14:32:49Z" xsd:dateTime + +[Term] +id: CL:4033093 +name: limbal epithelial stem cell of cornea +def: "A stem cell that is part of the corneo-scleral limbus. This cell type resides at the basal layer of the epithelium and has a small size and high nuclear to cytoplasmatic ratio (Secker and Daniels, 2009). A limbal stem cell is responsible for corneal epithelial renewal and repair (Li et al., 2023), and to help maintain a clear corneal surface by preventing conjunctival epithelial cells from migrating onto the cornea (Wang et al., 2023)." [PMID:20614614, PMID:29105366, PMID:36983561, PMID:37768272] +subset: human_subset +subset: mouse_subset +synonym: "LESC" RELATED OMO:0003000 [PMID:20614614] +synonym: "limbal epithelial stem cell" EXACT [PMID:20614614] +synonym: "limbal stem cell" EXACT [PMID:17562792] +synonym: "LSC" RELATED OMO:0003000 [PMID:36983561] +is_a: CL:0000036 ! epithelial fate stem cell +intersection_of: CL:0000034 ! stem cell +intersection_of: part_of UBERON:0006761 ! corneo-scleral junction +relationship: part_of UBERON:0000482 ! basal lamina of epithelium +relationship: part_of UBERON:0006761 ! corneo-scleral junction +relationship: RO:0002203 CL:0000575 ! develops into corneal epithelial cell +property_value: terms:contributor https://orcid.org/0000-0001-6677-8489 +property_value: terms:contributor https://orcid.org/0000-0001-7655-4833 +property_value: terms:date "2024-12-11T13:59:19Z" xsd:dateTime + [Term] id: CL:4040000 name: glial restricted tripotential precursor cell def: "A glial precursor cell that generates oligodendrocytes and type-1 and type-2 astrocytes. It has been shown in some mammals that this cell type may express A2B5, nestin, FGFR-1, FGFR-2, FGFR-3, PLP, and DM-20 antigens. Unlike oligodendrocyte precursor cell, it does not initially express PDGFR-alpha and can differentiate into both type-1 and type-2 astrocytes." [PMID:10719353] +subset: human_subset +subset: mouse_subset synonym: "glial restricted precursor" BROAD [PMID:10719353] synonym: "GRP cell" RELATED OMO:0003000 [PMID:11756508] synonym: "tripotential glial-restricted precursor cell" EXACT [PMID:11921204] @@ -37831,9 +43459,11 @@ property_value: terms:date "2023-04-03T14:54:32Z" xsd:dateTime id: CL:4040001 name: chorionic girdle cell def: "A horse-specific, highly invasive trophoblast cell that invades the endometrium where it forms endometrial cups." [PMID:27280409, PMID:35328607] +comment: Humans, mice and rats have a highly invasive (hemochorial) placentation. Horses have a non-invasive epitheliochorial placenta, except for the transient endometrial cup. {xref="PMID:27280409"} +subset: human_subset +subset: mouse_subset synonym: "equine chorionic girdle cell" EXACT [PMID:35328607] is_a: CL:0011101 ! chorionic trophoblast cell -property_value: oboInOwl:note "Humans, mice and rats have a highly invasive (hemochorial) placentation. Horses have a non-invasive epitheliochorial placenta, except for the transient endometrial cup." xsd:string {xref="PMID:27280409"} property_value: RO:0002175 NCBITaxon:9789 property_value: terms:contributor https://orcid.org/0000-0002-0819-0473 property_value: terms:date "2023-04-03T15:08:05Z" xsd:dateTime @@ -37842,6 +43472,8 @@ property_value: terms:date "2023-04-03T15:08:05Z" xsd:dateTime id: CL:4040002 name: enteroglial cell def: "Glial cell that provides support to the enteric nervous system. It is involved in enteric neurotransmission, in maintaining the integrity of the mucosal barrier of the gut and serves as a link between the nervous and immune systems of the gut. In enteric nerve strands, glial processes ensheath multiaxonal bundles which distinguishes enteric glia from all other peripheral glia. Ultrastructurally, the most conspicuous trait of an enteroglial cell is the presence of 10 nm filaments, which criss-cross the cell body, form axial bundles in the processes and appear to firmly anchor the cells to the ganglionic surfaces. Similar to astrocytes, their main constituent is glial fibrillary acidic protein (GFAP)." [PMID:16336493, PMID:17483847, PMID:25975510] +subset: human_subset +subset: mouse_subset synonym: "enteric glia" RELATED OMO:0003004 [PMID:11169131] synonym: "enteric glial cell" EXACT [PMID:11169131, PMID:25170211] is_a: CL:0000125 ! glial cell @@ -37856,12 +43488,14 @@ property_value: terms:date "2023-04-03T15:15:40Z" xsd:dateTime id: CL:4040003 name: fetal pre-type II pulmonary alveolar epithelial cell def: "Precursor of type II pneumocyte. These cells do not have lamellar bodies, which are a marker of type II pneumocyte maturity." [PMID:1316350] +comment: According to PMID:1316350 this cell type does not yet produce surfactant. According to PMID:9109447 and PMID:12114192 this cell type produces low levels of surfactant that can be increased by administration of very low-density lipoproteins. This cell type is of medical relevance, as a central feature of the fetal respiratory distress syndrome seems to be the presence in the lung of abundant pre-type II alveolar epithelial cells (PMID:1316350). +subset: human_subset +subset: mouse_subset synonym: "fetal alveolar pre-type II epithelial cell" EXACT [PMID:9624168] synonym: "fetal pre-type 2 pneumocyte" EXACT [https://orcid.org/0000-0002-0819-0473] synonym: "fetal pre-type II alveolar epithelial cell" EXACT [PMID:12114192] synonym: "fetal pre-type II pneumocyte" EXACT [] is_a: CL:0000322 ! pulmonary alveolar epithelial cell -property_value: oboInOwl:note "According to PMID:1316350 this cell type does not yet produce surfactant. According to PMID:9109447 and PMID:12114192 this cell type produces low levels of surfactant that can be increased by administration of very low-density lipoproteins. This cell type is of medical relevance, as a central feature of the fetal respiratory distress syndrome seems to be the presence in the lung of abundant pre-type II alveolar epithelial cells (PMID:1316350)." xsd:string property_value: terms:contributor https://orcid.org/0000-0002-0819-0473 property_value: terms:date "2023-06-02T09:19:31Z" xsd:dateTime @@ -37869,6 +43503,8 @@ property_value: terms:date "2023-06-02T09:19:31Z" xsd:dateTime id: CL:4040004 name: mesenchymal stem cell of orbital adipose tissue def: "Any mesenchymal stem cell of adipose tissue that is part of an orbital region." [https://orcid.org/0000-0002-0819-0473] +subset: human_subset +subset: mouse_subset synonym: "OAMSC" EXACT [PMID:31377878] synonym: "orbital adipose-derived mesenchymal stem cell" EXACT [PMID:31377878] synonym: "Orbital ASCs" EXACT [PMID:30210548] @@ -37884,6 +43520,8 @@ id: CL:4040005 name: mesenchymal stem cell of apical papilla def: "A mesenchymal stem cell that is part of the apical papilla tooth root." [PMID:30834270, PMID:34026757] comment: The mesenchymal stem cells of the apical papilla have high capacity for osteogenic, adipogenic, and chondrogenic differentiation. {xref="PMID:34026757"} +subset: human_subset +subset: mouse_subset synonym: "SCAP" RELATED OMO:0003000 [PMID:37887345] synonym: "SCAPs" RELATED OMO:0003004 [PMID:30834270] synonym: "stem cells from the apical papilla" BROAD OMO:0003004 [PMID:30834270] @@ -37896,6 +43534,8 @@ property_value: terms:date "2023-11-02T09:44:47Z" xsd:dateTime id: CL:4040006 name: dermal chromatophore def: "A chromatophore that is part of the dermis." [PMID:28553007] +subset: human_subset +subset: mouse_subset is_a: CL:0000147 ! pigment cell is_a: CL:0000255 ! eukaryotic cell relationship: part_of UBERON:0002067 ! dermis @@ -37906,11 +43546,11 @@ property_value: terms:date "2024-03-07T09:37:14Z" xsd:dateTime id: CL:4042001 name: TAC3-positive striatal interneuron def: "A GABAergic interneuron that has its soma located in the striatum and that has an enriched expression of the genes TAC3 and LHX6." [PMID:32999462, PMID:34727523] +subset: human_subset +subset: mouse_subset synonym: "TAC3 interneuron" EXACT [PMID:34727523] -is_a: CL:0000402 ! CNS interneuron +is_a: CL:0002613 ! striatum neuron is_a: CL:0011005 ! GABAergic interneuron -is_a: PR:000050567 ! protein-containing material entity -relationship: RO:0002100 UBERON:0002435 ! has soma location striatum relationship: RO:0002104 PR:000016004 ! has plasma membrane part tachykinin-3 property_value: terms:contributor https://orcid.org/0000-0002-0098-8958 property_value: terms:date "2024-03-05T14:29:32Z" xsd:dateTime @@ -37920,11 +43560,12 @@ id: CL:4042002 name: TAC3-positive medium spiny neuron def: "A nucleus accumbens shell and olfactory tubercle D1 medium spiny neuron that co-expresses TAC3 and the DRD1 receptor." [PMID:34727523] comment: A TAC3-positive medium spiny neuron has its soma in a cluster in the medial shell region of the nucleus accumbens. In Rhesus Macaque, this medium spiny neuron has an enriched expression of the genes MPPED1, HPCAL1, MEIS3. {xref="PMID:34727523"} +subset: human_subset +subset: mouse_subset synonym: "D1Sh TAC3 archetype" RELATED OMO:0003000 [PMID:34727523] synonym: "TAC3-positive D1Sh-MSN" RELATED OMO:0003000 [PMID:34727523] synonym: "TAC3-positive MSN" RELATED OMO:0003000 [PMID:34727523] is_a: CL:4030051 ! nucleus accumbens shell and olfactory tubercle D1 medium spiny neuron -is_a: PR:000050567 ! protein-containing material entity relationship: RO:0002104 PR:000016004 ! has plasma membrane part tachykinin-3 property_value: terms:contributor https://orcid.org/0000-0002-0098-8958 property_value: terms:date "2024-03-05T13:36:54Z" xsd:dateTime @@ -37934,6 +43575,8 @@ id: CL:4042003 name: border associated macrophage def: "A central nervous system macrophage that is part of a choroid plexus, a meninx and a perivascular space. A border associated macrophage interacts with various components of the CNS vasculature and meninges, it participates in immune surveillance and in the regulation of the blood brain barrier." [PMID:37232741, PMID:37626977] comment: In humans, a border associate macrophage expresses CD45 and CD11B. This cell is also known to have the following molecular signature: CD206, CD38, LYVE1, CD163, CD169. {xref="PMID:29426702", xref="PMID:37232741"} +subset: human_subset +subset: mouse_subset synonym: "BAM" RELATED OMO:0003000 [PMID:36945367] synonym: "CAM" RELATED OMO:0003000 [PMID:33556248] synonym: "CNS-associated macrophage" RELATED [PMID:37232741] @@ -37945,6 +43588,8 @@ property_value: terms:date "2024-03-26T16:39:56Z" xsd:dateTime id: CL:4042004 name: choroid epiplexus macrophage def: "A choroid plexus macrophage that is part of the apical surface of some choroid plexus epithelium. This macrophage has a star-like shaped body." [PMID:31061494, PMID:37232741] +subset: human_subset +subset: mouse_subset synonym: "cpepiMΦ" RELATED OMO:0003000 [PMID:38347231] synonym: "epiplexus cpMΦ" RELATED OMO:0003000 [PMID:38347231] synonym: "Kolmer’s cell" EXACT [PMID:31433571] @@ -37957,6 +43602,8 @@ property_value: terms:date "2024-03-26T19:14:58Z" xsd:dateTime id: CL:4042005 name: stromal choroid plexus macrophage def: "A choroid plexus macrophage that is part of a choroid plexus stroma." [PMID:38347231] +subset: human_subset +subset: mouse_subset synonym: "cpstMΦ" RELATED OMO:0003000 [PMID:37626977] synonym: "stromal cpMΦ" RELATED OMO:0003000 [PMID:37232741, PMID:38347231] is_a: CL:0000880 ! choroid plexus macrophage @@ -37968,6 +43615,8 @@ property_value: terms:date "2024-03-26T19:21:51Z" xsd:dateTime id: CL:4042006 name: dural macrophage def: "A border associated macrophage which is part of a dura matter. This macrophage phagocytoses intruding pathogens and foreign molecules detected in the bloodstream or in the cerebrospinal fluid. This cell has an amoeboid body with dynamic protrusions in homeostasis." [PMID:31061494] +subset: human_subset +subset: mouse_subset synonym: "dmMΦ" RELATED OMO:0003000 [PMID:37232741] is_a: CL:4042003 ! border associated macrophage relationship: part_of UBERON:0002092 ! brain dura mater @@ -37979,6 +43628,8 @@ id: CL:4042007 name: protoplasmic astrocyte def: "An astrocyte with highly branched protrusions, found in neocortex layers 2-6. It is involved with the formation and elimination of synapses, glutamate clearance, modulation of synaptic functions and regulation of blood flow in response to synaptic activity." [PMID:19279265, PMID:25904839, PMID:34616062, PMID:37139179, PMID:37824655] comment: This astrocyte extends its branches to several hundred of dendrites to multiple neurons to envelope 100,000 or more synapses. In humans, a protoplasmic astrocyte has an average diameter of 142 µm, and its diameter ranges between 100 and 400 µm. In rodents the average diameter of a protoplasmic astrocites is 56 µm. {xref="PMID:20012068", xref="PMID:19279265"} +subset: human_subset +subset: mouse_subset is_a: CL:0000029 ! neural crest derived neuron is_a: CL:0002605 ! astrocyte of the cerebral cortex is_a: CL:0010012 ! cerebral cortex neuron @@ -37992,6 +43643,8 @@ id: CL:4042008 name: fibrous astrocyte def: "A cell type located in the first layer of the neocortex with radial protrusions extending transversely into the deeper cortex layers, herby facilitating communication across neurons, astrocytes, capillaries, meninges and cerebrospinal fluid through contact with neurons, pia mater and capillaries." [PMID:19279265, PMID:22144298, PMID:28280934, PMID:31435019, PMID:34616062, PMID:37824655] comment: In humans, a fibrous astrocyte diameter is circa 182 µm. In rodents, a fibrous astrocyte diameter is circa 85 µm. {xref="PMID:28280934"} +subset: human_subset +subset: mouse_subset is_a: CL:0000029 ! neural crest derived neuron is_a: CL:0000127 ! astrocyte is_a: CL:2000029 ! central nervous system neuron @@ -38004,6 +43657,8 @@ property_value: terms:date "2024-04-08T16:29:28Z" xsd:dateTime id: CL:4042009 name: interlaminar astrocyte def: "An astrocyte type that presents radial protrusions across the layers of a cortex. The soma of this astrocyte is part of the first layer of a neocortex. This astrocyte extents its protrusions transversally to the deeper layers of a cortex and it creates contact with neurons, the pia matter and capillaries. This astrocyte is involved in facilitating the communication across neurons, astrocytes, capillaries, meninges and the cerebrospinal fluid." [PMID:19279265, PMID:30552685, PMID:31435019, PMID:32930323, PMID:34616062, PMID:37824655] +subset: human_subset +subset: mouse_subset synonym: "ILA" RELATED OMO:0003000 [PMID:30552685] is_a: CL:0000029 ! neural crest derived neuron is_a: CL:0002605 ! astrocyte of the cerebral cortex @@ -38017,6 +43672,8 @@ property_value: terms:date "2024-04-08T16:33:45Z" xsd:dateTime id: CL:4042010 name: pial interlaminar astrocyte def: "An interlaminar astrocyte whose soma is part of the first layer of a neocortex and is in contact with a pia surface." [PMID:32930323, PMID:37139179] +subset: human_subset +subset: mouse_subset is_a: CL:4042009 ! interlaminar astrocyte property_value: terms:contributor https://orcid.org/0000-0002-0098-8958 property_value: terms:date "2024-04-08T16:37:57Z" xsd:dateTime @@ -38025,6 +43682,8 @@ property_value: terms:date "2024-04-08T16:37:57Z" xsd:dateTime id: CL:4042011 name: subpial interlaminar astrocyte def: "An interlaminar astrocyte type whose soma is part of the upper first layer of the neocortex and its processes extend to a pia surface." [PMID:32930323, PMID:37139179] +subset: human_subset +subset: mouse_subset is_a: CL:4042009 ! interlaminar astrocyte relationship: RO:0002170 UBERON:0002361 ! connected to pia mater property_value: terms:contributor https://orcid.org/0000-0002-0098-8958 @@ -38034,6 +43693,8 @@ property_value: terms:date "2024-04-08T16:39:09Z" xsd:dateTime id: CL:4042012 name: L2 marginal neuron def: "An L2 intratelencephalic projecting glutamatergic neuron with a soma on the L1-L2 border. This neuron type has small apical dendrites projecting to L1." [PMID:29311847, PMID:32108571] +subset: human_subset +subset: mouse_subset synonym: "L2MN" RELATED OMO:0003000 [PMID:29311847, PMID:32108571] synonym: "layer 2 marginal neuron" EXACT [PMID:32108571] is_a: CL:4030060 ! L2 intratelencephalic projecting glutamatergic neuron @@ -38045,8 +43706,15 @@ property_value: terms:date "2024-04-23T09:31:39Z" xsd:dateTime id: CL:4042013 name: Lamp5 Lhx6 neuron def: "A transcriptomically distinct lamp5 GABAergic cortical interneuron located in the cerebral cortex that expresses Lamp5 and Lhx6. The standard transcriptomic reference data for this cell type can be found on the CellxGene census under the collection: 'Transcriptomic cytoarchitecture reveals principles of human neocortex organization', dataset: 'Supercluster: CGE-derived interneurons', Author Categories: 'CrossArea_subclass', Lamp5 Lhx6." [https://cellxgene.cziscience.com/e/e4ddac12-f48f-4455-8e8d-c2a48a683437.cxg/, PMID:34004146, PMID:36007006, PMID:37824655, PMID:37824669] +comment: The marker set CHST9, LAMP5 can identify the Human cell type Lamp5 Lhx6 neuron in the Brain with a confidence of 0.821678322 (NS-Forest FBeta value). {xref="https://doi.org/10.5281/zenodo.11165918"} +subset: human_subset +subset: mouse_subset synonym: "Ivy cell" EXACT [PMID:36007006] synonym: "Lamp5-Lhx6 type" EXACT [PMID:30382198] +is_a: CL:4023011 ! lamp5 GABAergic cortical interneuron +relationship: RO:0002292 PR:000032533 ! expresses LIM/homeobox protein Lhx6 +relationship: RO:0015004 CLM:1000075 ! has characterizing marker set NS forest marker set of Lamp5 Lhx6 neuron (Human Brain). +property_value: RO:0002175 NCBITaxon:9606 property_value: terms:contributor https://orcid.org/0000-0002-0098-8958 property_value: terms:date "2024-04-23T09:37:55Z" xsd:dateTime @@ -38054,6 +43722,8 @@ property_value: terms:date "2024-04-23T09:37:55Z" xsd:dateTime id: CL:4042014 name: spiny VIP neuron def: "A VIP GABAergic cortical interneuron with a soma located in L1-3 of some neocortex in Mmus. This neuron has a multipolar morphology with spiny dendrites concentrating on L1 of the cortex, and has a burst firing electrophysiological signature with highly dynamic dendritic spines." [PMID:35418660] +subset: human_subset +subset: mouse_subset synonym: "multipolar VIP neuron" RELATED [PMID:35418660] synonym: "superficial VIP-positive spiny neuron" EXACT [PMID:35418660] is_a: CL:4023016 ! VIP GABAergic cortical interneuron @@ -38066,11 +43736,14 @@ id: CL:4042015 name: VIP-ChAT interneuron def: "A VIP GABAergic cortical interneuron expressing vasoactive intestinal polypeptide and choline acetyltransferase in the Mmus neocortex. This interneuron releases both γ-aminobutyric acid and acetylcholine." [PMID:30382198, PMID:31754098, PMID:32027647, PMID:33301603] comment: Work in the mouse barrel cortex and somatosensory cortex shows that a VIP-ChAT interneuron is predominantely located in L2/3 and more rarely in the deeper layers of the cortex (Dudai et al., 2021; Dudai et al., 2020). This neuronal type could be transcriptomically distinct as transcriptomic studies have identified VIP neurons expressing ChAT in a whole brain mouse transcriptomic study (Tasic et al., 2018). {xref="PMID:30382198", xref="PMID:32027647", xref="PMID:33301603"} +subset: human_subset +subset: mouse_subset synonym: "VChI" RELATED OMO:0003000 [PMID:32027647] synonym: "VIP+/ChAT+ cell" RELATED [PMID:33301603] synonym: "VIP+/ChAT+ interneuron" EXACT [PMID:33301603] synonym: "VIP/ChAT interneuron" EXACT [PMID:32027647] is_a: CL:0000108 ! cholinergic neuron +is_a: CL:4023016 ! VIP GABAergic cortical interneuron property_value: terms:contributor https://orcid.org/0000-0002-0098-8958 property_value: terms:date "2024-07-11T12:22:48Z" xsd:dateTime @@ -38078,6 +43751,8 @@ property_value: terms:date "2024-07-11T12:22:48Z" xsd:dateTime id: CL:4042016 name: nasal serous secreting cell def: "A serous secreting cell that is part of a submucosal gland in the nasal cavity respiratory epithelium." [PMID:37291214] +subset: human_subset +subset: mouse_subset synonym: "nasal mucous secretory cell" RELATED [PMID:11005715] xref: https://cellxgene.cziscience.com/e/9f222629-9e39-47d0-b83f-e08d610c7479.cxg/ is_a: CL:0000152 ! exocrine cell @@ -38092,12 +43767,14 @@ id: CL:4042017 name: alpha1-tanycyte def: "A tanycyte cell found in the ventromedial and dorsomedial nuclei of the hypothalamus. This type of tanycyte extends its protrusions close to parenchymal neurons without contacting blood vessels. It expresses the glial marker S-100β." [PMID:16344112, PMID:26578855, wikipedia:Tanycyte] comment: In rodents, a1 tanycytes are known to express DARPP-32, GPR50, NA Vimentin, Connexin 43, GLT-1, GLUT1(+) (Goodman and Hajihosseini 2015; Prevot et al., 2018). {xref="PMID:26578855"} +subset: human_subset +subset: mouse_subset synonym: "DMH tanycyte" RELATED [PMID:29351662] synonym: "VMH tanycyte" RELATED [PMID:29351662] is_a: CL:0002085 ! tanycyte is_a: CL:0012000 ! astrocyte of the forebrain relationship: part_of UBERON:0004642 ! third ventricle ependyma -relationship: RO:0002292 PR:000014419 ! expresses +relationship: RO:0002292 PR:000014419 ! expresses protein S100-B property_value: terms:contributor https://orcid.org/0000-0002-0098-8958 property_value: terms:date "2024-08-19T13:06:16Z" xsd:dateTime @@ -38106,10 +43783,12 @@ id: CL:4042018 name: alpha2-tanycyte def: "A type of tanycyte found in the dorsomedial arcuate nucleus of the hypothalamus. This mono-ciliated tanycyte extends its protrusion to the arcuate nucleus and expresses the glial marker S-100β." [PMID:16344112, PMID:26578855, PMID:29351662, wikipedia:Tanycyte] comment: In rodents, this type of tanycyte is more developmentally advanced than alpha1 tanycytes, shows a high neurogenic competence and expresses the following markers DARPP-32, Vimentin, GPR50, Connexin-43, GLT-1, GLUT1(+) (Goodman and Hajihosseini 2015; Prevot et al., 2018) {xref="PMID:26578855"} +subset: human_subset +subset: mouse_subset synonym: "dmARH tanycyte" RELATED [PMID:29351662] is_a: CL:0002085 ! tanycyte relationship: overlaps UBERON:0001932 ! arcuate nucleus of hypothalamus -relationship: RO:0002292 PR:000014419 ! expresses +relationship: RO:0002292 PR:000014419 ! expresses protein S100-B property_value: terms:contributor https://orcid.org/0000-0002-0098-8958 property_value: terms:date "2024-08-19T13:13:20Z" xsd:dateTime @@ -38117,6 +43796,8 @@ property_value: terms:date "2024-08-19T13:13:20Z" xsd:dateTime id: CL:4042019 name: beta1-tanycyte def: "A type of tanycyte found in the lateral infundibular recess of the brain. This tanycyte has an elongated morphology with multiple microvilli extending to the third ventricle in the lateral zones of the median eminence. This type of tanycyte expresses FGF receptors 1 and 2, is in contact with GnRH neurons, and is involved in the release of gonadotropin-releasing hormone (GnRH)." [PMID:16344112, PMID:26578855, PMID:29351662, Wikipedia:Tanycyte] +subset: human_subset +subset: mouse_subset synonym: "vmARH tanycyte" RELATED [PMID:29351662] is_a: CL:0000151 ! secretory cell is_a: CL:0002085 ! tanycyte @@ -38133,6 +43814,8 @@ property_value: terms:date "2024-08-19T13:17:32Z" xsd:dateTime id: CL:4042020 name: beta2-tanycyte def: "A type of tanycyte found in the floor of the infundibular recess in the brain. This tanycyte has an elongated morphology with multiple microvilli extending medially and ventrally to the median eminence, contacting the pial surface and blood vessels. This type of tanycyte expresses FGF receptors 1 and 2, is in contact with GnRH neurons, and is involved in the release of gonadotropin-releasing hormone (GnRH)." [PMID:16344112, PMID:26578855, PMID:29351662, wikipedia:Tanycyte] +subset: human_subset +subset: mouse_subset synonym: "ME tanycyte" RELATED [PMID:29351662] is_a: CL:0002085 ! tanycyte is_a: CL:0012000 ! astrocyte of the forebrain @@ -38148,6 +43831,8 @@ id: CL:4042021 name: neuronal-restricted precursor def: "A progenitor cell of the central nervous system that differentiates exclusively onto neurons. This progenitor cell is found in a hippocampus subventricular zone, developing cortex and spinal cord of the central nervous system." [PMID:10467245] comment: In vitro cultures of embryonic mouse neural tubes show that neuronal-restricted precursors (NRPs) are derived from multipotent neuroepithelial cells to give rise to neurons. This progression suggests a linear relationship between multipotent progenitors and neuronal-restricted differentiation. (Mayer-Proschel et al., 1997). In the spinal cord of rats, neural-restricted precursor cells give rise cholinergic, GABAergic, glutametergic neurons (Cao and Howard et al., 2002). {xref="PMID:9354325", xref="PMID:12429182"} +subset: human_subset +subset: mouse_subset synonym: "NRP" RELATED [PMID:12429182] {synonymtypedef="OMO:0003000"} is_a: CL:0000123 ! neuron associated cell (sensu Vertebrata) is_a: CL:0011026 ! progenitor cell @@ -38160,6 +43845,8 @@ id: CL:4042022 name: astrocyte-restricted precursor def: "A progenitor cell of the central nervous system that differentiates exclusively onto astrocytes. This progenitor cell expresses CD44 and S100 calcium-binding protein B." [PMID:15531362, PMID:33052610] comment: In vitro, this progenitor cell can differentiate from glial-restricted precursor cells. {xref="PMID:33052610"} +subset: human_subset +subset: mouse_subset synonym: "ARP" RELATED [PMID:33052610] {synonymtypedef="OMO:0003000"} synonym: "astrocyte precursor cell" RELATED [PMID:33052610] is_a: CL:0000123 ! neuron associated cell (sensu Vertebrata) @@ -38175,12 +43862,13 @@ id: CL:4042023 name: striatal pthlh-expressing interneuron def: "A GABAergic interneuron expressing PTHLH and PVALB that has its soma in a striatum. This GABAergic interneuron type presents a spatial expression gradient of PVALB in the mouse striatum." [PMID:30134177, PMID:37292997] comment: According to spatial transcriptomic data in the human striatum, pthlh-expressing interneurons are one of the most abundant population of interneurons in the striatum (Leonardo D. Garma, et al., 2024). {xref="PMID:37292997"} +subset: human_subset +subset: mouse_subset synonym: "PTHLH/PVALB cell" RELATED [PMID:37292997] synonym: "PTHLH +/PVALB+ interneuron" RELATED [PMID:37292997] is_a: BFO:0000002 -is_a: CL:0000402 ! CNS interneuron +is_a: CL:0002613 ! striatum neuron is_a: CL:0011005 ! GABAergic interneuron -relationship: RO:0002100 UBERON:0002435 ! has soma location striatum relationship: RO:0002292 PR:000013433 ! expresses parathyroid hormone-related protein relationship: RO:0002292 PR:000013502 ! expresses parvalbumin alpha property_value: terms:contributor https://orcid.org/0000-0002-0098-8958 @@ -38190,8 +43878,10 @@ property_value: terms:date "2024-09-17T10:20:15Z" xsd:dateTime id: CL:4042024 name: striatal PTHLH MOXD1 expressing interneuron def: "A pthlh-expressing interneuron that expresses MOXD1 and has its soma in a striatum." [PMID:30134177] +subset: human_subset +subset: mouse_subset is_a: CL:4042023 ! striatal pthlh-expressing interneuron -relationship: RO:0002292 PR:000010529 ! expresses +relationship: RO:0002292 PR:000010529 ! expresses DBH-like monooxygenase protein 1 property_value: terms:contributor https://orcid.org/0000-0002-0098-8958 property_value: terms:date "2024-09-17T10:26:57Z" xsd:dateTime @@ -38199,6 +43889,8 @@ property_value: terms:date "2024-09-17T10:26:57Z" xsd:dateTime id: CL:4042025 name: substantia nigra dopaminergic neuron def: "A midbrain dopaminergic neuron that has its soma located in a substantia nigra. This dopaminergic neuron type is highly metabolically active and it is involved in the regulation of movement, cognition, motivation and reward. Neurodegeneration of this dopaminergic neuronal type causes loss in fine motor control in Parkinson's Disease." [PMID:32826893, PMID:35308118] +subset: human_subset +subset: mouse_subset synonym: "SNpc dopaminergic neuron" NARROW [PMID:35308118] is_a: CL:0002614 ! neuron of the substantia nigra is_a: CL:2000097 ! midbrain dopaminergic neuron @@ -38209,7 +43901,10 @@ property_value: terms:date "2024-09-16T13:09:29Z" xsd:dateTime id: CL:4042026 name: GABAergic interneuron of the anterior substantia nigra pars reticulata def: "A GABAergic interneuron that has its soma in the anterior section of the substantia nigra pars reticulata. This GABAergic interneuron is characterized by the expression of Six3 and Foxp1 and it develops from Nkx6-2 expressing neuronal progenitors in the ventrolateral midbrain-diencephalon region." [PMID:36148148] +subset: human_subset +subset: mouse_subset synonym: "aSNpr" RELATED OMO:0003000 [PMID:36148148] +is_a: BFO:0000002 is_a: CL:0002614 ! neuron of the substantia nigra relationship: RO:0002292 PR:000007643 ! expresses forkhead box protein P1 relationship: RO:0002292 PR:000013047 ! expresses POU domain, class 6, transcription factor 2 @@ -38221,16 +43916,201 @@ property_value: terms:date "2024-09-23T13:56:01Z" xsd:dateTime id: CL:4042027 name: GABAergic interneuron of the posterior substantia nigra pars reticulata def: "A GABAergic interneuron that has its soma in the posterior section of the substantia nigra pars reticulata. This GABAergic interneuron is characterised by the expression of the transcription factors Pax5, Ctip2 and Pou6f2 and it develops from the ventrolateral r1 neuroepithelium expresing NKX61." [PMID:36148148] +subset: human_subset +subset: mouse_subset synonym: "pSNpr" RELATED [PMID:36148148] +is_a: BFO:0000002 is_a: CL:0002614 ! neuron of the substantia nigra relationship: RO:0002292 PR:000001903 ! expresses paired box protein PAX-5 property_value: terms:contributor https://orcid.org/0000-0002-0098-8958 property_value: terms:date "2024-09-23T14:49:11Z" xsd:dateTime +[Term] +id: CL:4042028 +name: immature neuron +def: "A neuron in the central nervous system that is not committed to a differentiated fate, has not been newly derived from neurogenesis, and does not integrate into any circuit." [PMID:31096632, PMID:32116519, PMID:37833544] +comment: It is hypothesised that immature neurons can be utilised as a neurogenic reserve and that they can be involved in circuit plasticity. {xref="PMID:32116519"} +subset: human_subset +subset: mouse_subset +synonym: "IN" RELATED OMO:0003000 [PMID:32116519] +is_a: CL:2000029 ! central nervous system neuron +property_value: terms:contributor https://orcid.org/0000-0002-0098-8958 +property_value: terms:date "2024-10-10T09:14:45Z" xsd:dateTime + +[Term] +id: CL:4042029 +name: cortical immature neuron +def: "An immature neuron of a cerebral cortex. This neuron develops prenatally and remains in an immature state throughout the lifespan of the organism." [PMID:37833544] +subset: human_subset +subset: mouse_subset +synonym: "cIN" RELATED OMO:0003000 [PMID:37833544] +is_a: CL:4042028 ! immature neuron +relationship: part_of UBERON:0000956 ! cerebral cortex +property_value: terms:contributor https://orcid.org/0000-0002-0098-8958 +property_value: terms:date "2024-10-10T09:14:54Z" xsd:dateTime + +[Term] +id: CL:4042030 +name: candelabrum cell +def: "A GABAergic interneuron located in the cerebellar cortex. This GABAergic interneuron type has a distinct morphology, it presents a small cell soma near the Purkinje cell layer (PCL), dendrites that extend to the surface of the molecular layer, and beaded axons that make local synapses contacts within the molecular layer. A candelabrum cell is excited by mossy fibers and granule cells but inhibited by Purkinje cells, and it inhibits molecular layer interneurons, which leads to the disinhibition of Purkinje cells." [PMID:35578131] +comment: Candelabrum cells are the most abundant interneurons in the Purkinje cell layer and are present in all cerebellar lobules. {xref="PMID:35578131"} +subset: human_subset +subset: mouse_subset +synonym: "candelabrum interneuron" EXACT [PMID:35578131] +synonym: "CC" RELATED OMO:0003000 [PMID:35578131] +is_a: CL:1001611 ! cerebellar neuron +property_value: terms:contributor https://orcid.org/0000-0002-0098-8958 +property_value: terms:date "2024-10-15T11:06:31Z" xsd:dateTime + +[Term] +id: CL:4042031 +name: immune oligodendroglia +def: "An oligodendrocyte of the central nervous system that exhibits immune properties such as self-presentation and non-self antigen presentation to T cells, phagocytosis of debris, and cytokine and chemokine production. Immune oligodendroglia is immunoreactive during inflammation, neurodegenerative disorders, chronic stress and major depressive disorder." [PMID:30747918, PMID:35301426, PMID:35615276, PMID:35662200] +comment: During inflammation, immuno oligodendroglia express MHC II to interact with immune cells in mouse models (Harrington et al., 2023; Madeira et al., 2022). In a mouse model of major depressive disorder and chronic stress, immuno oligodendroglia were associated with prefrontal cortex hypomyelination (Kokkosis et al., 2022). {xref="PMID:35615276", xref="PMID:37057892", xref="PMID:35301426"} +subset: human_subset +subset: mouse_subset +synonym: "Im-OL" RELATED OMO:0003000 [PMID:35301426] +synonym: "immune oligodendrocyte" EXACT [PMID:35615276] +synonym: "ImOL" RELATED OMO:0003000 [PMID:35615276] +synonym: "ImOLG" RELATED OMO:0003000 [PMID:30747918] +synonym: "imOLG" RELATED OMO:0003000 [PMID:30747918] +is_a: CL:0000128 ! oligodendrocyte +relationship: capable_of GO:0002504 ! antigen processing and presentation of peptide or polysaccharide antigen via MHC class II +property_value: terms:contributor https://orcid.org/0000-0002-0098-8958 +property_value: terms:date "2024-10-11T12:51:17Z" xsd:dateTime + +[Term] +id: CL:4042032 +name: PAX6 GABAergic cortical interneuron +def: "A transcriptomically distinct GABAergic neuron located in the cerebral cortex that expresses the transcript PAX6. The standard transcriptomic reference data for this cell type can be found on the CellxGene census under the collection: 'Transcriptomic cytoarchitecture reveals principles of human neocortex organization', dataset: 'Supercluster: CGE-derived interneurons', Author Categories: 'CrossArea_subclass', clusters PAX6." [https://cellxgene.cziscience.com/e/e4ddac12-f48f-4455-8e8d-c2a48a683437.cxg/, PMID:37824655] +comment: The marker set RELN, HCRTR2 can identify the Human cell type http://purl.obolibrary.org/obo/CL_4042032 in the Brain with a confidence of 0.724125093 (NS-Forest FBeta value). {xref="https://doi.org/10.5281/zenodo.11165918"} +subset: human_subset +subset: mouse_subset +is_a: CL:4023064 ! caudal ganglionic eminence derived cortical interneuron +relationship: RO:0002292 PR:000012318 ! expresses paired box protein Pax-6 +relationship: RO:0015004 CLM:1000079 ! has characterizing marker set NS forest marker set of Pax6 (Human Brain). +property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:contributor https://orcid.org/0000-0002-0098-8958 +property_value: terms:date "2024-10-11T13:25:51Z" xsd:dateTime + +[Term] +id: CL:4042033 +name: pro-opiomelanocortin neuron +def: "A neuron of the central nervous system that expresses POMC and synthesizes the POMC precursor polypeptide. This neuron type is located in the arcuate nucleus of the hypothalamus and in the nucleus tractus solitarius of the brainstem. The pro-opiomelanocortin neuron is part of the central melanocortin system and it is involved in regulating energy homeostasis, metabolism, and appetite. This neuronal type responds to hormonal signals such as levels of leptin and insulin, and its activation results in the release of α-melanocyte-stimulating hormone (α-MSH), which acts on melanocortin receptors to suppress food intake and increase energy expenditure." [PMID:25870542, PMID:28192062] +comment: Pro-opiomelanocortin neurons have a diverse projection pattern. The neurons in the rostral arcuate nucleus project to autonomic areas, caudal arcuate POMC neurons project mainly to hypothalamic areas (Toda et al., 2017). Dysregulation of pro-opiomelanocortin neurons is associated with obesity and metabolic disorders (Quarta et al., 2020). {xref="PMID:28192062", xref="PMID:33633406"} +subset: human_subset +subset: mouse_subset +synonym: "POMC neuron" RELATED [PMID:34002087] +synonym: "POMC-expressing neuron" RELATED [PMID:34002087] +is_a: CL:0000165 ! neuroendocrine cell +relationship: RO:0002292 PR:000013015 ! expresses pro-opiomelanocortin +property_value: terms:contributor https://orcid.org/0000-0002-0098-8958 +property_value: terms:date "2024-10-15T10:17:41Z" xsd:dateTime + +[Term] +id: CL:4042034 +name: CGRP-expressing neuron +def: "An interneuron neuron characterized by the expression of calcitonin gene-related peptide (CGRP), a 37-amino acid neuropeptide. This neuron type is involved in nociception and pain modulation by facilitating the transmission of nociceptive signals from peripheral sensory nerve endings to central nervous system structures. This neuron type is found in the dorsal root ganglia (DRG) and trigeminal ganglion, and the spinal cord dorsal horn." [PMID:34061020] +subset: human_subset +subset: mouse_subset +synonym: "Calcitonin gene-related peptide neuron" EXACT [PMID:34061020] +synonym: "CGRP-expressing interneuron" RELATED [PMID:34061020] +synonym: "CGRP-positive neuron" RELATED [PMID:34061020] +is_a: CL:0000526 ! afferent neuron +is_a: CL:2000029 ! central nervous system neuron +property_value: terms:contributor https://orcid.org/0000-0002-0098-8958 +property_value: terms:date "2024-10-30T15:35:08Z" xsd:dateTime + +[Term] +id: CL:4042035 +name: molecular layer interneuron +def: "A type of cerebellar inhibitory GABAergic interneuron that is located in the molecular layer of the cerebellum. This cell type inhibits Purkinje cells and other molecular layer interneurons. This interneuron plays a crucial role in regulating cerebellar output through feedforward inhibition and is characterized by its fast-spiking properties." [PMID:30742002, PMID:33075461, PMID:34616064, PMID:38692278] +subset: human_subset +subset: mouse_subset +synonym: "MLI" RELATED [PMID:33075461] {RELATED="OMO:0003000"} +is_a: CL:1001611 ! cerebellar neuron +property_value: terms:contributor https://orcid.org/0000-0002-0098-8958 +property_value: terms:date "2024-10-31T15:55:31Z" xsd:dateTime + +[Term] +id: CL:4042036 +name: melanin-concentrating hormone neuron +def: "A neuron of the central nervous system with its soma primarily located in the lateral hypothalamic area and surrounding regions, including the zona incerta. This neuron type expresses melanin-concentrating hormone and is involved in regulating various physiological processes, including sleep, feeding behavior, and energy homeostasis." [PMID:30284033, PMID:38020069, PMID:39035036] +comment: Nearly all melanin-concentrating hormone neurons express the glutamate transporter VGlut2, however a small subset of them expresses the machinery for GABA release and neurotransmission. {xref="PMID:38020069"} +subset: human_subset +subset: mouse_subset +synonym: "MCH neuron" RELATED [PMID:30284033] +is_a: CL:2000029 ! central nervous system neuron +property_value: terms:contributor https://orcid.org/0000-0002-0098-8958 +property_value: terms:date "2024-10-31T16:03:26Z" xsd:dateTime + +[Term] +id: CL:4042037 +name: sst GABAergic neuron of the striatum +def: "A interneuron of the striatum expressing gamma-aminobutyric acid and somatostatin. This interneuron has a fusiform soma with a diameter between 9 - 25 µm, it has a long axon up to the length of 1mm. This neuron type displays a low threshold Ca2+ spike (LTS), a high input resistance, and the expression of long-lasting plateau potentials following depolarization from rest." [PMID:30131490, PMID:30467465, PMID:33742131] +comment: Some striatal SST GABAergic neurons can co-release glutamate and generate excitation-inhibition responses in postsynaptic neurons. This interneuron type has the least dense dendritic branches in the striatum. In the dorsomedial striatum these neurons regulate the activity of striatal projection neurons. {xref="PMID:30467465", xref="PMID:33742131"} +subset: human_subset +subset: mouse_subset +synonym: "SOM cell" BROAD [PMID:30131490] +synonym: "striatal SST+ IN" RELATED [PMID:33742131] +is_a: BFO:0000002 +is_a: CL:0000617 ! GABAergic neuron +is_a: CL:0002613 ! striatum neuron +relationship: RO:0002292 PR:000015665 ! expresses somatostatin +property_value: terms:contributor https://orcid.org/0000-0002-0098-8958 +property_value: terms:date "2024-11-27T18:33:46Z" xsd:dateTime + +[Term] +id: CL:4042038 +name: rostral primary motorneuron +def: "A type of primary motor neuron situated in the rostral region of the spinal cord. RoP neurons extend their axons to innervate the ventral trunk musculature." [PMID:35431796, PMID:3746410] +synonym: "RoP" RELATED OMO:0003000 [PMID:3746410] +is_a: CL:0000533 ! primary motor neuron (sensu Teleostei) +property_value: terms:contributor https://orcid.org/0000-0002-0098-8958 +property_value: terms:date "2024-11-13T13:42:01Z" xsd:dateTime + +[Term] +id: CL:4042039 +name: caudal ganglionic eminence derived neuron +def: "A neuron of the central nervous system that develops from a caudal ganglionic eminence." [https://www.ncbi.nlm.nih.gov/books/NBK98190/, PMID:12593982, PMID:12637172, PMID:20130169] +comment: Neurons derived from the caudal ganglionic eminence consist mostly of neurons populating the cortical layers of the brain and some subcortical areas such as the globus pallidus, the striatus and the hippocampus. Amongst neurons derived from the caudal ganglionic eminence there are cortical GABAergic neurons such as Pax6, Lamp5, VIP, sncg, GABAergic; in the hippocampus, mossy fibers, pyramidal neurons, granule neurons and interneurons; in the striatum and globus pallidus, medium spiny projection neurons. {xref="https://www.ncbi.nlm.nih.gov/books/NBK98190/", xref="PMID:12637172", xref="PMID:12593982", xref="PMID:20130169"} +subset: human_subset +subset: mouse_subset +is_a: BFO:0000002 +is_a: CL:2000029 ! central nervous system neuron +relationship: RO:0002202 UBERON:0004026 ! develops from caudal ganglionic eminence +property_value: terms:contributor https://orcid.org/0000-0002-0098-8958 +property_value: terms:date "2024-11-14T11:27:25Z" xsd:dateTime + +[Term] +id: CL:4042040 +name: glutamatergic neuron of the basal ganglia +def: "A glutametergic neuron with its soma located in a basal ganglia. This neuron type is involved in motor control, decision making and learning." [DOI:10.1016/j.jocn.2021.05.056, PMID:11307040, PMID:16276355] +comment: The glutametergic neurons in the basal ganglia are part of a series of different circuits such as the corticolstriatal circuit, which is involved in regulating voluntary movements. The subthalamic nucleus circuit, which is involved in modulating the output of the basal ganglia, particularly in controlling movement initiation and inhibition. The thalamocortical loop, which is involved in refining motor movements and integrating sensory information with motor commanding. {xref="PMID:30498197", xref="PMID:22498715", xref="PMID:33785138"} +subset: human_subset +subset: mouse_subset +is_a: CL:0000679 ! glutamatergic neuron +is_a: CL:2000029 ! central nervous system neuron +relationship: RO:0002100 UBERON:0002420 ! has soma location basal ganglion +property_value: terms:contributor https://orcid.org/0000-0002-0098-8958 +property_value: terms:date "2024-11-18T13:37:58Z" xsd:dateTime + +[Term] +id: CL:4042041 +name: middle primary motoneuron +def: "A type of primary motor neuron located in the middle region of the spinal cord. This primary motor neuron type is characterized by their distinct axonal pathways that innervate the middle trunk muscles." [PMID:35431796, PMID:3746410] +synonym: "MiP" RELATED OMO:0003000 [PMID:3746410] +xref: ZFA:0005179 +is_a: CL:0000533 ! primary motor neuron (sensu Teleostei) +property_value: terms:contributor https://orcid.org/0000-0002-0098-8958 +property_value: terms:date "2024-11-13T13:39:28Z" xsd:dateTime + [Term] id: CL:4047001 name: cycling stromal cell def: "A(n) stromal cell that is cycling." [PMID:34497389] +subset: human_subset +subset: mouse_subset synonym: "proliferating stromal cell" EXACT [PMID:34497389] is_a: CL:0000499 ! stromal cell intersection_of: CL:0000499 ! stromal cell @@ -38238,13 +44118,13 @@ intersection_of: participates_in GO:0022402 ! cell cycle process intersection_of: RO:0000086 PATO:0002354 ! has quality active relationship: participates_in GO:0022402 ! cell cycle process relationship: RO:0000086 PATO:0002354 ! has quality active -property_value: terms:contributor https://orcid.org/0009-0005-7919-4905 -property_value: terms:date "2024-07-19T09:14:23Z" xsd:string [Term] id: CL:4047002 name: cycling glial cell def: "A(n) glial cell that is cycling." [PMID:34497389] +subset: human_subset +subset: mouse_subset synonym: "proliferating glial cell" EXACT [PMID:34497389] is_a: CL:0000125 ! glial cell intersection_of: CL:0000125 ! glial cell @@ -38252,13 +44132,13 @@ intersection_of: participates_in GO:0022402 ! cell cycle process intersection_of: RO:0000086 PATO:0002354 ! has quality active relationship: participates_in GO:0022402 ! cell cycle process relationship: RO:0000086 PATO:0002354 ! has quality active -property_value: terms:contributor https://orcid.org/0009-0005-7919-4905 -property_value: terms:date "2024-07-19T09:14:23Z" xsd:string [Term] id: CL:4047003 name: cycling plasma cell def: "A(n) plasma cell that is cycling." [PMID:34497389] +subset: human_subset +subset: mouse_subset synonym: "proliferating plasma cell" EXACT [PMID:34497389] is_a: CL:0000786 ! plasma cell intersection_of: CL:0000786 ! plasma cell @@ -38266,13 +44146,13 @@ intersection_of: participates_in GO:0022402 ! cell cycle process intersection_of: RO:0000086 PATO:0002354 ! has quality active relationship: participates_in GO:0022402 ! cell cycle process relationship: RO:0000086 PATO:0002354 ! has quality active -property_value: terms:contributor https://orcid.org/0009-0005-7919-4905 -property_value: terms:date "2024-07-19T09:14:23Z" xsd:string [Term] id: CL:4047004 name: cycling type EC enteroendocrine cell def: "A(n) type EC enteroendocrine cell that is cycling." [PMID:34497389] +subset: human_subset +subset: mouse_subset synonym: "proliferating type EC enteroendocrine cell" EXACT [PMID:34497389] is_a: CL:0000577 ! type EC enteroendocrine cell intersection_of: CL:0000577 ! type EC enteroendocrine cell @@ -38280,13 +44160,13 @@ intersection_of: participates_in GO:0022402 ! cell cycle process intersection_of: RO:0000086 PATO:0002354 ! has quality active relationship: participates_in GO:0022402 ! cell cycle process relationship: RO:0000086 PATO:0002354 ! has quality active -property_value: terms:contributor https://orcid.org/0009-0005-7919-4905 -property_value: terms:date "2024-07-19T09:14:23Z" xsd:string [Term] id: CL:4047005 name: cycling neuroblast (sensu Vertebrata) def: "A(n) neuroblast (sensu Vertebrata) that is cycling." [PMID:34497389] +subset: human_subset +subset: mouse_subset synonym: "proliferating neuroblast (sensu Vertebrata)" EXACT [PMID:34497389] is_a: BFO:0000002 is_a: CL:0000031 ! neuroblast (sensu Vertebrata) @@ -38295,13 +44175,13 @@ intersection_of: participates_in GO:0022402 ! cell cycle process intersection_of: RO:0000086 PATO:0002354 ! has quality active relationship: participates_in GO:0022402 ! cell cycle process relationship: RO:0000086 PATO:0002354 ! has quality active -property_value: terms:contributor https://orcid.org/0009-0005-7919-4905 -property_value: terms:date "2024-07-19T09:14:23Z" xsd:string [Term] id: CL:4047006 name: fetal artery endothelial cell def: "An endothelial cell that lines an artery in the fetal circulatory system." [PMID:34497389] +subset: human_subset +subset: mouse_subset synonym: "endothelial cell of fetal artery" EXACT [PMID:34497389] synonym: "fetal arterial EC" EXACT [PMID:34497389] synonym: "fetal artery EC" EXACT [PMID:34497389] @@ -38313,6 +44193,8 @@ property_value: terms:date "2024-08-16T13:52:25Z" xsd:dateTime id: CL:4047007 name: immature pericyte def: "A pericyte that is in an early stage of development, found in newly forming or remodeling blood vessels. An immature pericyte is characterized by it's mesenchymal stem cell-like properties and high proliferative capacity, which allows it to differentiate into various types of pericytes and contribute to the structural and functional maturation of the vasculature. Immature pericytes are stellate in new vessels and elongated with less protrusions in remodeling vessels." [PMID:21839917, PMID:28564607, PMID:32466671, PMID:34497389, PMID:36685855] +subset: human_subset +subset: mouse_subset synonym: "immature PCs" RELATED OMO:0003000 [PMID:28564607] synonym: "imPCs" RELATED OMO:0003000 [PMID:28564607] is_a: CL:0000669 ! pericyte @@ -38323,6 +44205,8 @@ property_value: terms:date "2024-08-19T11:32:32Z" xsd:dateTime id: CL:4047011 name: fetal vein endothelial cell def: "An endothelial cell that lines the veins in the fetal circulatory system." [doi:10.1101/2021.04.07.438755] +subset: human_subset +subset: mouse_subset synonym: "fetal vein EC" RELATED OMO:0003000 [doi:10.1101/2021.04.07.438755] synonym: "fetal venous EC" RELATED OMO:0003000 [doi:10.1101/2021.04.07.438755] synonym: "fetal venous endothelial cell" EXACT [doi:10.1101/2021.04.07.438755] @@ -38334,19 +44218,39 @@ property_value: terms:date "2024-09-05T15:45:32Z" xsd:dateTime id: CL:4047012 name: angiogenic pericyte def: "A specialized pericyte that actively participates in the formation of new blood vessels during angiogenesis by undergoing phenotypic changes, increasing proliferation, and interacting closely with endothelial cells." [PMID:24853910, PMID:34497389] +subset: human_subset +subset: mouse_subset is_a: CL:0000669 ! pericyte property_value: terms:contributor https://orcid.org/0009-0005-7919-4905 property_value: terms:date "2024-09-06T08:41:39Z" xsd:dateTime +[Term] +id: CL:4047017 +name: transit amplifying cell of gut +def: "A transit amplifying cell of the gut epithelium, located in the wall of the intestinal crypt, just above intestinal stem cells from which they derive. These are rapidly dividing cells, capable of multiple rounds of division before differentiating into the various cell types of the gut epithelium (enterocyte, goblet, eneterodendocrine, paneth cells)." [PMID:20683682, PMID:33195268, PMID:34497389] +subset: human_subset +subset: mouse_subset +synonym: "TA cell" RELATED [PMID:20683682] +synonym: "transit-amplifying cell" BROAD [PMID:24813615] +is_a: CL:0009010 ! transit amplifying cell +intersection_of: CL:0009010 ! transit amplifying cell +intersection_of: part_of UBERON:0013740 ! wall of crypt of Lieberkuhn +relationship: part_of UBERON:0013740 ! wall of crypt of Lieberkuhn +relationship: RO:0002207 CL:0002250 ! directly develops from intestinal crypt stem cell +property_value: terms:contributor https://orcid.org/0009-0005-7919-4905 +property_value: terms:date "2024-09-24T10:48:47Z" xsd:dateTime + [Term] id: CL:4047018 name: early colonocyte def: "An enterocyte that is part of the colon, in the early stages of differentiation, located in the intestinal crypt-villus axis." [PMID:28049136, PMID:36060223] +subset: human_subset +subset: mouse_subset synonym: "early enterocyte of colon" EXACT [doi:10.1101/2021.01.13.426602] is_a: CL:1000347 ! colonocyte is_a: CL:4047019 ! early enterocyte intersection_of: CL:4047019 ! early enterocyte -intersection_of: part_of UBERON:0001155 ! colon +intersection_of: part_of UBERON:0000397 ! colonic epithelium property_value: terms:contributor https://orcid.org/0009-0005-7919-4905 property_value: terms:date "2024-09-24T11:50:13Z" xsd:dateTime @@ -38354,6 +44258,8 @@ property_value: terms:date "2024-09-24T11:50:13Z" xsd:dateTime id: CL:4047019 name: early enterocyte def: "An enterocyte in the early stages of development, located above the transit-amplifying cell zone in the intestinal crypt-villus axis." [PMID:20683682, PMID:35235783] +subset: human_subset +subset: mouse_subset is_a: CL:0000584 ! enterocyte intersection_of: CL:0000584 ! enterocyte intersection_of: part_of UBERON:0013740 ! wall of crypt of Lieberkuhn @@ -38361,12 +44267,98 @@ relationship: part_of UBERON:0013740 ! wall of crypt of Lieberkuhn property_value: terms:contributor https://orcid.org/0009-0005-7919-4905 property_value: terms:date "2024-09-24T12:11:09Z" xsd:dateTime +[Term] +id: CL:4047023 +name: intestinal lamina propria fibroblast +def: "A fibroblast located in the lamina propria of the intestinal mucosa. This cell expresses PDGFRα and CD81 and is negative for α-smooth muscle actin (α-SMA). This cell is predominantly located in the small intestine adjacent to myofibroblasts surrounding the crypts. It is capable of synthesizing extracellular matrix components and structural proteins such as collagen and elastin." [PMID:21252048, PMID:36032088] +subset: human_subset +subset: mouse_subset +synonym: "S1 fibroblast" RELATED [PMID:30270042] +is_a: CL:0000057 ! fibroblast +is_a: CL:0000151 ! secretory cell +intersection_of: CL:0000057 ! fibroblast +intersection_of: capable_of GO:0070278 ! extracellular matrix constituent secretion +intersection_of: part_of UBERON:0004780 ! gastrointestinal system lamina propria +relationship: capable_of GO:0070278 ! extracellular matrix constituent secretion +relationship: part_of UBERON:0004780 ! gastrointestinal system lamina propria +property_value: terms:contributor https://orcid.org/0009-0005-7919-4905 +property_value: terms:date "2024-09-24T15:45:18Z" xsd:dateTime + +[Term] +id: CL:4047025 +name: type G cell of stomach +def: "Any type G enteroendocrine cell that is part of some epithelium of stomach." [FBC:Autogenerated] +subset: human_subset +subset: mouse_subset +is_a: CL:0000508 ! type G enteroendocrine cell +is_a: CL:1000222 ! stomach neuroendocrine cell +intersection_of: CL:0000508 ! type G enteroendocrine cell +intersection_of: part_of UBERON:0001276 ! epithelium of stomach +property_value: terms:contributor https://orcid.org/0009-0005-7919-4905 +property_value: terms:date "2024-10-24T10:43:22Z" xsd:dateTime + +[Term] +id: CL:4047029 +name: post-arteriole capillary cell +def: "An endothelial cell forming the walls of capillaries immediately downstream from arterioles, facilitating the exchange of substances between blood and interstitial fluid. This cell is characterized by a small diameter and may be continuous, fenestrated, or sinusoidal, depending on their location and function. This cell plays a crucial role in tissue oxygenation, nutrient delivery, and maintaining homeostasis within the microvascular network." [PMID:17893694, PMID:35406678] +subset: human_subset +subset: mouse_subset +is_a: CL:0002144 ! capillary endothelial cell +property_value: terms:contributor https://orcid.org/0009-0005-7919-4905 +property_value: terms:date "2024-11-07T12:50:06Z" xsd:dateTime + +[Term] +id: CL:4047030 +name: pre-venule capillary cell +def: "A specialized endothelial cell located in the transition zone between capillaries and small venules in the microvascular system. It exhibits characteristics of both capillary and venous cells, expressing markers from both types. This cell plays a role in regulating blood flow and substance exchange between blood and tissues." [DOI:10.1038/s41467-022-33324-7, PMID:23620236] +subset: human_subset +subset: mouse_subset +synonym: "Cap-Venous endothelial cell" EXACT [DOI:10.1038/s41467-022-33324-7] +is_a: CL:0002144 ! capillary endothelial cell +property_value: terms:contributor https://orcid.org/0009-0005-7919-4905 +property_value: terms:date "2024-11-07T13:22:16Z" xsd:dateTime + +[Term] +id: CL:4047032 +name: secretory pericyte +def: "A specialized pericyte located within the basement membrane of a blood capillary. This cell is characterized by its ability to produce and release a variety of bioactive molecules, collectively known as the pericyte secretome, including cytokines and regulators of angiogenesis." [DOI:10.3389/fncel.2019.00282] +subset: human_subset +subset: mouse_subset +is_a: CL:0000151 ! secretory cell +is_a: CL:0000669 ! pericyte +relationship: capable_of GO:0001816 ! cytokine production +relationship: capable_of GO:0045765 ! regulation of angiogenesis +property_value: terms:contributor https://orcid.org/0009-0005-7919-4905 +property_value: terms:date "2024-11-07T15:36:16Z" xsd:dateTime + +[Term] +id: CL:4047034 +name: smooth muscle cell of stomach +def: "A smooth muscle cell that is part of the muscularis externa of the stomach wall. It is characterized by its fusiform shape, involuntary control, and ability to generate slow, sustained contractions. This cell is organized in distinct layers and is essential for gastric motility and digestion." [PMID:21443757, PMID:33630273] +subset: human_subset +subset: mouse_subset +is_a: CL:0000192 ! smooth muscle cell +relationship: part_of CL:4047034 ! smooth muscle cell of stomach +property_value: terms:contributor https://orcid.org/0009-0005-7919-4905 +property_value: terms:date "2024-12-05T11:10:18Z" xsd:dateTime + +[Term] +id: CL:4047035 +name: stomach smooth muscle outer longitudinal layer cell +def: "A specialized smooth muscle cell located in the outermost layer of the muscularis externa of the stomach wall. This cell is arranged longitudinally along the stomach's axis and is responsible for the contractions that facilitate food movement toward the pylorus." [PMID:21443757, PMID:33630273] +subset: human_subset +subset: mouse_subset +is_a: CL:4047034 ! smooth muscle cell of stomach +property_value: terms:contributor https://orcid.org/0009-0005-7919-4905 +property_value: terms:date "2024-12-05T16:13:49Z" xsd:dateTime + [Term] id: CL:4047051 name: small intestine BEST4+ enterocyte def: "An enterocyte of the human small intestine expressing bestrophin-4 (BEST4) calcium-activated ion channels. These enterocytes have a disinctive transcriptomic profile and are scattered through the small intestine epithelium." [PMID:24223998, PMID:34497389] +subset: human_subset is_a: CL:1000334 ! enterocyte of epithelium of small intestine -is_a: CL:4030026 ! BEST4+ enteroycte +is_a: CL:4030026 ! BEST4+ enterocyte intersection_of: CL:0000584 ! enterocyte intersection_of: part_of UBERON:0001902 ! epithelium of small intestine intersection_of: RO:0002292 PR:Q8NFU0 ! expresses bestrophin-4 (human) @@ -38377,23 +44369,52 @@ property_value: terms:date "2024-07-25T13:05:50Z" xsd:dateTime id: CL:4047052 name: BEST4+ colonocyte def: "An enterocyte of the human colon expressing bestrophin-4 (BEST4) calcium-activated ion channels. These cells have a distinct transcriptomic profile compared to other enterocytes and are scattered through the colon epithelium." [PMID:24223998, PMID:34497389] +subset: human_subset is_a: CL:1000347 ! colonocyte -is_a: CL:4030026 ! BEST4+ enteroycte +is_a: CL:4030026 ! BEST4+ enterocyte intersection_of: CL:1000347 ! colonocyte intersection_of: RO:0002292 PR:Q8NFU0 ! expresses bestrophin-4 (human) property_value: terms:contributor https://orcid.org/0009-0005-7919-4905 property_value: terms:date "2024-07-25T13:21:19Z" xsd:dateTime +[Term] +id: CL:4047101 +name: liver-resident natural killer cell +def: "A natural killer cell resident to the liver, located in the hepatic sinusoids. In humans this cell type is distinguished from circulating natural killer cells by CD49a or CD69 gene expression. Liver-resident natural killer cells have also been shown to express CCR5, EOMES, KLRB1, GZMK, and CXCR6 in humans." [PMID:26330348, PMID:26639736, PMID:27798170, PMID:31114585, PMID:32351704, PMID:34230995, PMID:35865550] +comment: Liver-resident natural killer cells play a crucial role in modulating the immune response during inflammation by balancing cytotoxic activity and cytokine production, thereby contributing to the maintenance of liver homeostasis and protection against excessive tissue damage. {xref="PMID:34230995"} +subset: human_subset +subset: mouse_subset +synonym: "he-NK" EXACT [PMID:31114585] +synonym: "hepatic natural killer cells" EXACT [doi:10.3389/fimmu.2019.00946] +synonym: "hepatic NK" EXACT [doi:10.3389/fimmu.2019.00946] +synonym: "intrahepatic NK" EXACT [PMID:33828559] +synonym: "liver NK cell" EXACT [PMID:26639736] +synonym: "liver resident natural killer cell" EXACT [PMID:26330348] +synonym: "liver-specific natural killer cell" EXACT [] +synonym: "lr-NK" EXACT [PMID:35726345] +is_a: CL:0000623 ! natural killer cell +intersection_of: CL:0000623 ! natural killer cell +intersection_of: RO:0001025 UBERON:0001281 ! located in hepatic sinusoid +relationship: RO:0001025 UBERON:0001281 ! located in hepatic sinusoid +property_value: terms:contributor "https://orcid.org/0000-0001-8134-3037" xsd:string +property_value: terms:contributor https://orcid.org/0009-0005-7919-4905 +property_value: terms:date "2024-07-29T13:43:11Z" xsd:dateTime + [Term] id: CL:4052001 name: multiciliated ependymal cell def: "An ependymal cell that lines the lateral, third, and fourth ventricles of the brain. The cell is characterized by multiple motile cilia on its apical surface, which beats in a coordinated manner to facilitate the movement of cerebrospinal fluid (CSF), contributing to brain homeostasis." [PMID:25045600, PMID:28067220, PMID:37008045] comment: multiciliated ependymal cell, with an average of 16 motile cilia per cell, exhibits two types of planar cell polarity (PCP): rotational polarity, with unidirectional cilia orientation, and translational polarity, with asymmetric cilia positioning in the apical area. This location-specific PCP varies across the ventricular wall, aligning with the direction of CSF flow. These cells are interconnected by adherens and gap junctions, which support intercellular communication and maintain the structural integrity of the ependymal layer. Unlike some other cell types, these cells lack tight junctions. {xref="PMID:25045600", xref="PMID:27311928"} +subset: human_subset +subset: mouse_subset synonym: "E1" RELATED OMO:0003000 [PMID:28067220, PMID:37008045] synonym: "multiciliated ependymal cells" BROAD [PMID:25045600] is_a: CL:0000065 ! ependymal cell -is_a: CL:0005012 ! multi-ciliated epithelial cell -relationship: part_of UBERON:0005357 ! brain ependyma +is_a: CL:0005012 ! multiciliated epithelial cell +intersection_of: CL:0000075 ! columnar/cuboidal epithelial cell +intersection_of: bearer_of PATO:0010007 ! multiciliated +intersection_of: has_part GO:0031514 ! motile cilium +intersection_of: part_of UBERON:0004670 ! ependyma property_value: terms:contributor https://orcid.org/0009-0000-8480-9277 property_value: terms:date "2024-08-20T10:06:15Z" xsd:dateTime @@ -38401,6 +44422,8 @@ property_value: terms:date "2024-08-20T10:06:15Z" xsd:dateTime id: CL:4052002 name: syncytial cell def: "A multinucleate cell formed by the fusion of multiple uninuclear cells through plasma membrane fusion. This process leads to a single large cell containing multiple nuclei within a shared cytoplasm." [PMID:20851884, Wikipedia:Syncytium] +subset: human_subset +subset: mouse_subset synonym: "SC" RELATED OMO:0003000 [PMID:9067520] synonym: "syncytium" EXACT [WBbt:0008074] is_a: BFO:0000002 @@ -38416,6 +44439,8 @@ property_value: terms:date "2024-08-15T10:38:46Z" xsd:dateTime id: CL:4052003 name: intestinal villus capillary endothelial cell def: "A capillary endothelial cell that is part of the intestinal villus. This cell is highly fenestrated, with fenestrations most numerous at the villus tips, and plays a vital role in nutrient absorption and maintaining the selective permeability of the intestinal barrier." [PMID:18480313, PMID:35810168, PMID:38051275] +subset: human_subset +subset: mouse_subset synonym: "villus blood capillary endothelial cells" BROAD [PMID:35810168] synonym: "villus tip endothelial cell" RELATED [PMID:38051275] is_a: CL:0000666 ! fenestrated endothelial cell @@ -38430,6 +44455,8 @@ property_value: terms:date "2024-09-17T10:03:25Z" xsd:dateTime id: CL:4052004 name: intestinal fibroblastic reticular cell def: "A specialized fibroblastic reticular cell that is part of gut-associated lymphoid tissue (GALT), responsible for forming a structural network that facilitates immune cell interactions. This cell is found in Peyer's patches, cryptopatches, and isolated lymphoid follicles. It plays crucial roles in maintaining intestinal immunity by controlling innate lymphoid cell homeostasis and function, organizing lymphoid structures, and contributing to intestinal microbiome balance." [PMID:33707780, PMID:35440118] +subset: human_subset +subset: mouse_subset synonym: "Ccl19-expressing fibroblastic reticular cell" NARROW [PMID:35440118] synonym: "gut-associated secondary lymphoid organs fibroblastic reticular cell" RELATED [PMID:35440118] synonym: "solitary intestinal lymphoid tissue fibroblastic reticular cell" NARROW [PMID:35440118] @@ -38443,6 +44470,8 @@ property_value: terms:description "Intestinal fibroblastic reticular cells devel id: CL:4052005 name: intestinal subserosal fibroblast def: "A fibroblast that is part of the subserosa of intestine. This cell interacts with immune cells and play roles in inflammation and fibrosis. In certain conditions, such as Crohn's disease, subserosal fibroblast may differentiate into myofibroblasts." [PMID:23143399, PMID:26694715, PMID:38877292] +subset: human_subset +subset: mouse_subset is_a: CL:0000057 ! fibroblast relationship: part_of UBERON:0001243 ! serosa of intestine relationship: part_of UBERON:0012375 ! subserosa @@ -38454,6 +44483,8 @@ id: CL:4052006 name: intestinal enteroendocrine progenitor def: "An epithelial cell that is part of the crypt of Lieberkuhn, originating from intestinal stem cells and giving rise to enteroendocrine cells (EECs). In mouse and human, this cell can be characterized by the expression of Neurog3, and has the ability to proliferate and differentiate into multiple EEC subtypes. Its proliferative potential contributes to crypt growth, distinguishing it from fully differentiated EECs." [doi:/10.1038/s41467-021-27901-5, PMID:31756561, PMID:32531023, PMID:35913117, PMID:38260422] comment: The EEC progenitor is also present in other organisms; for example, flies have EEC progenitors but lack intestinal crypts and do not express the same markers. Instead, they are Dl+ and Pros+. {xref="PMID:25670791"} +subset: human_subset +subset: mouse_subset synonym: "EEC Progenitor" RELATED OMO:0003000 [PMID:31756561] is_a: CL:0002563 ! intestinal epithelial cell is_a: CL:0011026 ! progenitor cell @@ -38467,6 +44498,8 @@ id: CL:4052007 name: subepithelial intestinal fibroblast def: "A fibroblast located adjacent to the intestinal epithelium in both the small intestine and colon, specifically around the crypts. This cell is characterized by the expression of PDGFRα and various collagen isoforms, including COL4A5 and COL4A6. It secretes signalling molecules like TGF-β, Wnt ligands, and BMPs, which are crucial for epithelial homeostasis, intestinal stem cell support, and basement membrane formation." [PMID:30270042, PMID:33430285, PMID:33916891, PMID:37080817] comment: The S2 fibroblast population has been identified as a subset of intestinal fibroblasts located near the epithelial lining. This population is divided into two subtypes: S2a and S2b. S2a is involved in epithelial differentiation, while S2b, located at the top of the crypt, regulates intestinal stem cell proliferation, niche formation, and wound healing. {xref="PMID:30270042", xref="PMID:33916891", xref="PMID:37495570"} +subset: human_subset +subset: mouse_subset synonym: "S2 fibroblast" RELATED [PMID:30270042, PMID:33916891] synonym: "S2 mesenchymal cells" RELATED [PMID:33916891] is_a: CL:0000057 ! fibroblast @@ -38478,6 +44511,8 @@ property_value: terms:date "2024-09-23T09:59:27Z" xsd:dateTime id: CL:4052008 name: crypt-bottom fibroblast def: "A subepithelial intestinal fibroblast that is located adjacent to the base of the crypt of Lieberkühn, near the intestinal stem cells. Characterized by low PDGFRα expression, this cell is crucial for maintaining the intestinal stem cell niche. Crypt-bottom fibroblast secretes key signaling molecules including canonical Wnt ligands (Wnt2, Wnt2b), Wnt potentiators (Rspo3), and BMP inhibitors (Grem1), which collectively regulate intestinal stem cell function and epithelial homeostasis." [doi:/10.1371/journal.pbio.3001032, PMID:33916891] +subset: human_subset +subset: mouse_subset synonym: "bottom pericryptic-associated fibroblasts" RELATED [PMID:33916891] synonym: "CBFs" RELATED OMO:0003000 [doi:/10.1371/journal.pbio.3001032] is_a: CL:4052007 ! subepithelial intestinal fibroblast @@ -38491,6 +44526,8 @@ id: CL:4052009 name: crypt-top fibroblast def: "A subepithelial intestinal fibroblast that is located adjacent to the top of the crypt of Lieberkuhn. Characterized by high experession of PDGFRα, this cell secretes a range of signaling factors, including WNTs and BMPs, that drive epithelial differentiation, creating a gradient that regulates the balance between stem cell maintenance and differentiation." [doi:/10.1371/journal.pbio.3001032, PMID:33916891] comment: S2b fibroblasts are located at the top of the crypt and express NRG1 and NPY. {xref="PMID:37495570"} +subset: human_subset +subset: mouse_subset synonym: "CTFs" RELATED OMO:0003000 [doi:/10.1371/journal.pbio.3001032] synonym: "S2b fibroblast" RELATED [PMID:37495570] synonym: "top pericryptic fibroblast" RELATED [PMID:33916891] @@ -38503,6 +44540,8 @@ property_value: terms:date "2024-09-23T11:14:04Z" xsd:dateTime id: CL:4052010 name: pre-theca cell def: "A stromal cell that serves as a precursor to the theca cell layers in the ovary growing follicles. This cell is present in the early stages of follicular growth, particularly in smaller follicles. Unlike mature theca cell, a pre-theca cell is initially non-steroidogenic and lacks luteinizing hormone receptors." [PMID:20628033, PMID:31320652, PMID:36205477] +subset: human_subset +subset: mouse_subset synonym: "early theca cell" EXACT [PMID:36205477] synonym: "progenitor theca cell" EXACT [PMID:31320652] is_a: CL:0002132 ! stromal cell of ovary @@ -38515,6 +44554,8 @@ property_value: terms:date "2024-09-25T11:15:57Z" xsd:dateTime id: CL:4052011 name: follicle associated enterocyte def: "An enterocyte found in the follicle-associated epithelium (FAE) that covers Peyer's patches and other mucosa-associated lymphoid tissues. This cell has reduced absorptive capacity and expresses higher levels of chemokines CCL20 and CXCL16, compared to regular villus enterocytes. It contributes to antigen sampling and immune interactions, supporting the specialized function of the FAE in mucosal immunity." [PMID:29339448, PMID:34634036, PMID:7107724] +subset: human_subset +subset: mouse_subset synonym: "FAE enterocyte" RELATED OMO:0003000 [PMID:7107724] synonym: "follicle-associated epithelium enterocyte" EXACT [PMID:7107724] synonym: "follicular enterocyte" RELATED [PMID:7107724] @@ -38522,10 +44563,321 @@ is_a: CL:0000584 ! enterocyte property_value: terms:contributor https://orcid.org/0009-0000-8480-9277 property_value: terms:date "2024-09-25T15:28:25Z" xsd:dateTime +[Term] +id: CL:4052012 +name: interna theca cell +def: "A specialized theca cell that forms the inner, highly vascularized layer of the theca surrounding ovarian follicles. Originating from progenitor theca cells, the theca interna cell is steroidogenic, playing a crucial role in the production of androgens, which serves as a precursor for estrogen synthesis in granulosa cells. This cell expresses luteinizing hormone receptors, enabling it to respond to hormonal signals that regulate steroidogenesis." [PMID:15833266, PMID:31320652, PMID:32530882, Wikipedia:Theca_interna] +subset: human_subset +subset: mouse_subset +synonym: "inTC" RELATED OMO:0003000 [PMID:31320652] +synonym: "interna TC" RELATED OMO:0003000 [PMID:31320652] +is_a: CL:0000503 ! theca cell +is_a: CL:0000593 ! androgen secreting cell +intersection_of: CL:0000503 ! theca cell +intersection_of: part_of UBERON:0000157 ! theca interna +disjoint_from: CL:4052013 ! externa theca cell +relationship: part_of UBERON:0000157 ! theca interna +relationship: RO:0002202 CL:4052010 ! develops from pre-theca cell +property_value: terms:contributor https://orcid.org/0009-0000-8480-9277 +property_value: terms:date "2024-09-30T11:10:15Z" xsd:dateTime + +[Term] +id: CL:4052013 +name: externa theca cell +def: "A specialized theca cell that forms the outer layer of the theca surrounding the ovarian follicle, appearing at the antral follicle. Originating from progenitor theca cells, theca externa cell is characterized by its fibroblast-like appearance and primarily function to provide structural support to the developing follicle. This cell produces collagen fibers and extracellular matrix components such as Col1a1 and Col1a2." [PMID:31320652, PMID:32530882, PMID:36758341, Wikipedia:Theca_externa] +subset: human_subset +subset: mouse_subset +synonym: "exTC" RELATED OMO:0003000 [PMID:31320652] +synonym: "externa TC" RELATED OMO:0003000 [PMID:31320652] +is_a: CL:0000503 ! theca cell +intersection_of: CL:0000503 ! theca cell +intersection_of: part_of UBERON:0000156 ! theca externa +relationship: part_of UBERON:0000156 ! theca externa +relationship: RO:0002202 CL:4052010 ! develops from pre-theca cell +property_value: terms:contributor https://orcid.org/0009-0000-8480-9277 +property_value: terms:date "2024-09-30T11:10:15Z" xsd:dateTime + +[Term] +id: CL:4052014 +name: pancreatic islet capillary endothelial cell +def: "A capillary endothelial cell that is part of islet of Langerhans, characterized by a high density of fenestrations —approximately ten times greater than those in exocrine pancreatic capillaries. These fenestrations facilitate efficient hormone exchange, which is essential for maintaining glucose homeostasis. The cell's structure and function are regulated by the local production of vascular endothelial growth factor-A (VEGF-A), which maintains its fenestrated architecture." [PMID:16607697, PMID:27124642, PMID:28396983, PMID:33200981] +subset: human_subset +subset: mouse_subset +synonym: "islet endothelial cell" BROAD [PMID:16607697, PMID:28396983] +synonym: "pancreatic islet endothelial cell" BROAD [PMID:16607697] +is_a: CL:0000666 ! fenestrated endothelial cell +is_a: CL:0002144 ! capillary endothelial cell +intersection_of: CL:0002144 ! capillary endothelial cell +intersection_of: part_of UBERON:0000006 ! islet of Langerhans +relationship: part_of UBERON:0000006 ! islet of Langerhans +property_value: terms:contributor https://orcid.org/0009-0000-8480-9277 +property_value: terms:date "2024-09-30T14:36:12Z" xsd:dateTime + +[Term] +id: CL:4052015 +name: endocrine gland capillary endothelial cell +def: "Any capillary endothelial cell that is part of an endocrine gland." [PMID:18480313] +subset: human_subset +subset: mouse_subset +is_a: CL:0002144 ! capillary endothelial cell +intersection_of: CL:0002144 ! capillary endothelial cell +intersection_of: part_of UBERON:0002368 ! endocrine gland +relationship: part_of UBERON:0002368 ! endocrine gland +property_value: terms:contributor https://orcid.org/0009-0000-8480-9277 +property_value: terms:date "2024-09-30T15:27:49Z" xsd:dateTime + +[Term] +id: CL:4052016 +name: pituitary gland capillary endothelial cell +def: "A capillary endothelial cell that is part of the pituitary gland. This cell is characterized by its fenestrated structure which facilitates the efficient transport of hormones and other signaling molecules, essential for endocrine signalling." [PMID:10810312, PMID:32910242] +comment: In the anterior pituitary gland of rats, capillary endothelial cells are distinguished by numerous fenestrations, which are covered by a single-layered diaphragm. The diaphragm features a dense ring-like structure. {xref="PMID:4899902"} +subset: human_subset +subset: mouse_subset +is_a: CL:0000666 ! fenestrated endothelial cell +is_a: CL:2000004 ! pituitary gland cell +is_a: CL:2000044 ! brain microvascular endothelial cell +is_a: CL:4052015 ! endocrine gland capillary endothelial cell +intersection_of: CL:0002144 ! capillary endothelial cell +intersection_of: part_of UBERON:0000007 ! pituitary gland +property_value: terms:contributor https://orcid.org/0009-0000-8480-9277 +property_value: terms:date "2024-09-30T15:31:45Z" xsd:dateTime + +[Term] +id: CL:4052017 +name: choroid plexus capillary endothelial cell +def: "A capillary endothelial cell that is part of the choroid plexus, characterized by its fenestrated nature with 60 to 80 nm fenestrations and lack of tight junctions. This fenestrated structure allows for the rapid delivery of water and other components, aiding in the production of cerebrospinal fluid (CSF)." [https://www.ncbi.nlm.nih.gov/books/NBK27998/, PMID:18480313, PMID:32375819] +subset: human_subset +subset: mouse_subset +is_a: CL:0000666 ! fenestrated endothelial cell +is_a: CL:0002144 ! capillary endothelial cell +is_a: CL:2000044 ! brain microvascular endothelial cell +intersection_of: CL:0002144 ! capillary endothelial cell +intersection_of: part_of UBERON:0001886 ! choroid plexus +relationship: part_of UBERON:0001886 ! choroid plexus +property_value: terms:contributor https://orcid.org/0009-0000-8480-9277 +property_value: terms:date "2024-10-01T11:38:22Z" xsd:dateTime + +[Term] +id: CL:4052018 +name: fallopian tube epithelial cell +def: "Any epithelial cell that is part of the fallopian tube." [Wikipedia:Fallopian_tube] +subset: human_subset +subset: mouse_subset +synonym: "oviduct epithelial cell" BROAD [Wikipedia:Fallopian_tube] +synonym: "uterine tube epithelial cell" EXACT [Wikipedia:Fallopian_tube] +is_a: CL:0000066 ! epithelial cell +intersection_of: CL:0000066 ! epithelial cell +intersection_of: part_of UBERON:0003889 ! fallopian tube +relationship: part_of UBERON:0003889 ! fallopian tube +property_value: terms:contributor https://orcid.org/0009-0000-8480-9277 +property_value: terms:date "2024-10-01T12:09:12Z" xsd:dateTime + +[Term] +id: CL:4052019 +name: fallopian tube non-ciliated cell +def: "Any epithelial cell that is part of the fallopian tube and lacks cilia." [] +subset: human_subset +subset: mouse_subset +is_a: CL:4052018 ! fallopian tube epithelial cell +relationship: CL:4030045 GO:0005929 ! lacks_part cilium +property_value: terms:contributor https://orcid.org/0009-0000-8480-9277 +property_value: terms:date "2024-10-01T12:12:12Z" xsd:dateTime + +[Term] +id: CL:4052020 +name: lung resident granzyme K-associated CD8 T cell +def: "A granzyme K-associated CD8 T cell that resides in the lung, characterized by the expression of granzyme K (GZMK), and tissue residency markers CD103 and CD49a. This cell exhibits cytotoxic potential through its expression of multiple granzymes (GZMA, GZMB, GZMH, GZMM) in addition to GZMK." [doi:/10.1101/2022.06.17.496207] +comment: Lung resident granzyme K-associated CD8 T cell represents an intermediate stage of T cell differentiation, with GZMK expression peaking during this phase. {xref="PMID:28322863", xref="doi:/10.1101/2022.06.17.496207"} +subset: human_subset +subset: mouse_subset +synonym: "lung resident CD8-GZMK" RELATED OMO:0003000 [doi:/10.1101/2022.06.17.496207] +is_a: CL:4033040 ! lung resident memory CD8-positive, CD103-positive, alpha-beta T cell +is_a: CL:4052021 ! granzyme K-associated CD8 T cell +intersection_of: CL:4033040 ! lung resident memory CD8-positive, CD103-positive, alpha-beta T cell +intersection_of: RO:0002292 PR:000003472 ! expresses granzyme K +property_value: terms:contributor https://orcid.org/0000-0002-2336-2552 +property_value: terms:contributor https://orcid.org/0009-0000-8480-9277 +property_value: terms:date "2024-10-14T15:42:41Z" xsd:dateTime + +[Term] +id: CL:4052021 +name: granzyme K-associated CD8 T cell +def: "A CD8 T cell characterized by high expression of Granzyme K (GZMK). This cell is enriched in both inflamed tissues, such as synovial tissue in rheumatoid arthritis and respiratory tissues during COVID-19, as well as non-inflamed tissues like the gut and kidneys. Unlike highly cytotoxic GZMB+ CD8+ T cell, GZMK+ CD8+ T cell exhibits lower direct cytotoxic potential, and is involved in producing pro-inflammatory cytokines such as IFN-γ and TNF-α." [PMID:35704599, PMID:37449888] +subset: human_subset +subset: mouse_subset +synonym: "CD8-GZMK cell" RELATED OMO:0003000 [doi:/10.1101/2022.06.17.496207] +synonym: "granzyme K+ CD8 T cell" EXACT [PMID:35704599] +synonym: "GZMK high CD8+ T effector memory cell" NARROW [PMID:36347862] +synonym: "tissue-enriched expressing GzmK CD8 cell" EXACT [PMID:35704599] +synonym: "TteK CD8 cell" RELATED OMO:0003000 [PMID:35704599] +is_a: CL:0000909 ! CD8-positive, alpha-beta memory T cell +intersection_of: CL:0000909 ! CD8-positive, alpha-beta memory T cell +intersection_of: RO:0002292 PR:000003472 ! expresses granzyme K +relationship: RO:0002292 PR:000003472 ! expresses granzyme K +property_value: terms:contributor https://orcid.org/0009-0000-8480-9277 +property_value: terms:date "2024-10-18T09:51:48Z" xsd:dateTime + +[Term] +id: CL:4052022 +name: fallopian tube smooth muscle cell +def: "A smooth muscle cell that is part of the fallopian tube. This cell is responsible for peristaltic contractions that facilitate gamete and embryo transport, fluid mixing, and embryo admission to the uterus." [PMID:31183831, PMID:31613440] +comment: The fallopian tube smooth muscle cell in the human contracts dynamically in response to hormones and signaling molecules. Prostaglandins, particularly PGF2α and PGE2, have been shown to increase muscular contractions, while progesterone, levonorgestrel, mifepristone, oxytocin, and human chorionic gonadotropin (hCG) decrease them. These contractile responses are crucial for regulating gamete and embryo transport through the fallopian tube. {xref="PMID:18621753"} +subset: human_subset +subset: mouse_subset +synonym: "oviduct smooth muscle cell" BROAD [PMID:31613440] +synonym: "uterine tube smooth muscle cell" EXACT [PMID:31613440] +is_a: CL:0000192 ! smooth muscle cell +intersection_of: CL:0000192 ! smooth muscle cell +intersection_of: part_of UBERON:0003889 ! fallopian tube +relationship: part_of UBERON:0003889 ! fallopian tube +property_value: terms:contributor https://orcid.org/0009-0000-8480-9277 +property_value: terms:date "2024-10-21T12:16:54Z" xsd:dateTime + +[Term] +id: CL:4052023 +name: luminal endometrial unciliated epithelial cell +def: "An epithelial cell that is part of the endometrial luminal epithelium, forming a continuous layer lining the uterine cavity. This cell undergoes cyclical changes during the menstrual cycle, proliferating under estrogen in the proliferative phase, and differentiating under progesterone in the secretory phase to prepare for potential implantation. During the window of implantation, this cell changes from a tall columnar shape to a shorter columnar or cuboidal form, loses polarity, and becomes receptive to blastocyst implantation." [PMID:32929266, PMID:36581776, PMID:38559249, PMID:39198675] +comment: The luminal endometrial unciliated epithelial cell expresses WNT7A, and LGR5 during the proliferative phase, transitioning to express VTCN1 and SULT1E1 in the early secretory phase, and LEFTY1, IL6, and PTGS1 in the mid- to late-secretory phases. {xref="PMID:39198675"} +subset: human_subset +subset: mouse_subset +synonym: "endometrial luminal epithelial cell" BROAD [PMID:31317179] +synonym: "luminal cell of endometrium" BROAD [] +is_a: CL:0002149 ! epithelial cell of uterus +is_a: CL:1001591 ! oviduct secretory cell +intersection_of: CL:0000066 ! epithelial cell +intersection_of: capable_of GO:0032940 ! secretion by cell +intersection_of: part_of UBERON:0011949 ! endometrium luminal epithelium +relationship: part_of UBERON:0011949 ! endometrium luminal epithelium +property_value: terms:contributor https://orcid.org/0009-0000-8480-9277 +property_value: terms:date "2024-10-22T12:02:23Z" xsd:dateTime + +[Term] +id: CL:4052024 +name: myotendinous junction nucleus +def: "A specialized muscle nucleus that is part of an extrafusal muscle fiber and overlaps the muscle-tendon junction, where muscle fibers connect to tendons. Characterized by a distinct transcriptional profile with the expression of genes like COL22A1, this myonucleus supports the structural integrity and function of the junction, playing a key role in transmitting the force generated by muscle contraction to the tendon." [PMID:33311457, PMID:33311464, PMID:38398025] +synonym: "MTJ nucleus" RELATED OMO:0003000 [] +synonym: "myotendinous junction myonuclei" EXACT OMO:0003004 [PMID:33311464] +synonym: "myotendinous junction nuclei" EXACT OMO:0003004 [PMID:33311457] +is_a: GO:0005634 ! nucleus +intersection_of: GO:0005634 ! nucleus +intersection_of: overlaps GO:0005927 ! muscle tendon junction +intersection_of: part_of CL:0008046 ! extrafusal muscle fiber +relationship: overlaps GO:0005927 ! muscle tendon junction +relationship: part_of CL:0008046 ! extrafusal muscle fiber +property_value: terms:contributor https://orcid.org/0009-0000-8480-9277 +property_value: terms:contributor https://orcid.org/0009-0001-6947-615X +property_value: terms:date "2024-10-30T13:47:39Z" xsd:dateTime + +[Term] +id: CL:4052025 +name: neuromuscular junction nucleus +def: "A specialized muscle nucleus that is part of an extrafusal muscle fiber, clustered at the postsynaptic side of the neuromuscular junction. This nucleus exhibits a distinct transcriptional profile, including acetylcholine receptor (AChR) subunit genes. It regulates the production of proteins essential for maintaining the structure and function of the neuromuscular junction, supporting efficient nerve-muscle signaling for muscle contraction." [PMID:33037211, PMID:33311457, PMID:33311464] +synonym: "neuromuscular junction myonuclei" EXACT OMO:0003004 [PMID:33311464] +synonym: "neuromuscular junction nuclei" EXACT OMO:0003004 [PMID:33311457] +synonym: "NMJ nuclues" RELATED OMO:0003000 [] +is_a: GO:0005634 ! nucleus +intersection_of: GO:0005634 ! nucleus +intersection_of: overlaps GO:0098522 ! neuromuscular junction of skeletal muscle fiber +intersection_of: part_of CL:0008046 ! extrafusal muscle fiber +relationship: overlaps GO:0098522 ! neuromuscular junction of skeletal muscle fiber +relationship: part_of CL:0008046 ! extrafusal muscle fiber +property_value: terms:contributor https://orcid.org/0009-0000-8480-9277 +property_value: terms:contributor https://orcid.org/0009-0001-6947-615X +property_value: terms:date "2024-10-31T11:09:04Z" xsd:dateTime + +[Term] +id: CL:4052026 +name: type IIx muscle cell +def: "A fast type II muscle cell that is part of the skeletal muscle tissue. This cell is characterized by its intermediate metabolic profile, utilizing both glycolytic and oxidative pathways for energy production. In humans, it is distinguished by the expression of myosin heavy chain 1 (MYH1)." [doi:10.1101/2024.05.15.594276, PMID:34727990, PMID:35908794, PMID:36361732] +comment: In humans, type IIx fiber contains high levels of MYLK2, enhancing contraction speed and force via myosin phosphorylation, especially under low calcium. This mechanism supports post-activation potentiation, increasing force output in fast-twitch muscles. Additionally, this fiber has abundant ACTN3 (α-actinin-3), linked to muscle power, and exhibits the highest shortening velocity among human muscle fiber types. Notably, type IIx fiber is selectively lost in aging-related sarcopenia, increases in proportion in type 2 diabetes and obesity, and is the first to degenerate in Duchenne Muscular Dystrophy, impacting muscle function across various conditions. {xref="PMID:27199166", xref="PMID:34727990"} +subset: human_subset +subset: mouse_subset +synonym: "type 2x fiber" EXACT [PMID:34727990] +synonym: "type 2x muscle cell" EXACT [PMID:34727990] +synonym: "type 2x muscle fiber" EXACT [PMID:34727990] +synonym: "type IIx muscle fiber" EXACT [doi:10.1101/2024.05.15.594276] +is_a: CL:0002212 ! type II muscle cell +property_value: terms:contributor https://orcid.org/0009-0000-8480-9277 +property_value: terms:date "2024-11-04T10:26:29Z" xsd:dateTime + +[Term] +id: CL:4052027 +name: atretic theca cell +def: "A theca cell undergoing atresia, characterized by distinct morphological changes including hypertrophy, altered cell shape, and disrupted layered organization. This cell exhibits reduced steroidogenic capacity and changes in surrounding vascularization. The onset of theca cell atresia can vary, occurring at different stages of follicle atresia depending on the phase of folliculogenesis." [PMID:20628033, PMID:38069168] +comment: During atresia, theca interna and externa cells undergo distinct morphological and functional changes. Theca interna cells round up, expand in cytoplasmic area, and thicken the internal layer as organization degrades, while showing reduced STAR expression, which lowers androgen production. Theca externa cells display decreased ACTA2 expression, weakening structural integrity. {xref="PMID:38069168"} +subset: human_subset +subset: mouse_subset +is_a: CL:4033089 ! atretic follicular cell of ovary +relationship: RO:0002202 CL:0000503 ! develops from theca cell +property_value: terms:contributor https://orcid.org/0009-0000-8480-9277 +property_value: terms:date "2024-11-06T10:10:51Z" xsd:dateTime + +[Term] +id: CL:4052028 +name: uterine natural killer cell +def: "A natural killer cell that is part of the uterus, specifically within the endometrium during the non-pregnant state and in the decidua during pregnancy. This cell exhibits dynamic changes in frequency throughout the menstrual cycle, with lower levels during menstruation and a significant increase during the mid-secretory phase and early pregnancy." [PMID:35720413, PMID:39198675, Wikipedia:Uterine_natural_killer_cells] +subset: human_subset +subset: mouse_subset +synonym: "endometrial natural killer cell" NARROW [PMID:35720413] +synonym: "uNK cell" RELATED OMO:0003000 [PMID:39198675] +is_a: CL:0000623 ! natural killer cell +intersection_of: CL:0000623 ! natural killer cell +intersection_of: part_of UBERON:0000995 ! uterus +relationship: part_of UBERON:0000995 ! uterus +property_value: terms:contributor https://orcid.org/0009-0000-8480-9277 +property_value: terms:date "2024-11-15T10:12:40Z" xsd:dateTime + +[Term] +id: CL:4052029 +name: subpleural fibroblast +def: "A fibroblast that is located beneath the visceral pleura of the lung. This cell contributes to the development of idiopathic pulmonary fibrosis (IPF) by forming fibrotic lesions that originate subpleurally and extend into lung tissue through activation, proliferation, migration, and differentiation into a myofibroblast." [PMID:36543915, PMID:36769178, PMID:37291214] +subset: human_subset +subset: mouse_subset +is_a: CL:0002553 ! fibroblast of lung +property_value: terms:contributor https://orcid.org/0009-0000-8480-9277 +property_value: terms:date "2024-11-29T13:54:15Z" xsd:dateTime + +[Term] +id: CL:4052030 +name: adventitial fibroblast +def: "A fibroblast of the adventitia of a blood vessel. This cell contributes to vascular homeostasis, remodeling, and inflammation by producing extracellular matrix components, cytokines, and growth factors. Adventitial fibroblast can transition into an activated state during injury or disease, marked by increased proliferation, migration, matrix deposition, and contractile protein expression" [PMID:28705796, PMID:36718802] +comment: Single-cell transcriptomics of murine aorta identifies two adventitial fibroblast-specific markers, PDGFRA and DPEP1, which were validated at the protein level by immunohistochemistry and flow cytometry across human and murine arteries, highlighting fibroblast heterogeneity in health and cardiovascular disease (CVD) in humans and mice. {xref="PMID:36718802"} +subset: human_subset +subset: mouse_subset +is_a: CL:0000057 ! fibroblast +is_a: CL:0000151 ! secretory cell +is_a: CL:0002503 ! adventitial cell +intersection_of: CL:0000057 ! fibroblast +intersection_of: part_of UBERON:0005734 ! tunica adventitia of blood vessel +relationship: capable_of GO:0001816 ! cytokine production +relationship: capable_of GO:0070278 ! extracellular matrix constituent secretion +relationship: part_of UBERON:0005734 ! tunica adventitia of blood vessel +property_value: terms:contributor https://orcid.org/0009-0000-8480-9277 +property_value: terms:date "2024-12-05T11:01:15Z" xsd:dateTime + +[Term] +id: CL:4052031 +name: respiratory airway secretory cell +def: "A secretory epithelial cell of the respiratory and terminal bronchioles." [PMID:35355013, PMID:36796082] +comment: The respiratory airway secretory cell is cuboidal and has a unique transcriptomic profile compared to other epithelial cells in the same region. In humans, it functions as a multipotent progenitor, capable of regenerating alveolar type 2 (AT2) cells. {xref="PMID:36796082", xref="PMID:35355013"} +subset: human_subset +subset: mouse_subset +synonym: "RAS cell" RELATED OMO:0003000 [PMID:36796082] +synonym: "terminal and respiratory bronchioles secretory cell" RELATED [PMID:35355018] +is_a: CL:0000082 ! epithelial cell of lung +is_a: CL:0002202 ! epithelial cell of tracheobronchial tree +is_a: CL:1000272 ! lung secretory cell +is_a: CL:1100001 ! secretory epithelial cell +relationship: part_of UBERON:0002051 ! epithelium of bronchiole +property_value: terms:contributor https://orcid.org/0009-0000-8480-9277 +property_value: terms:date "2024-11-29T16:14:31Z" xsd:dateTime + [Term] id: CL:4052048 name: intercalated cell of salivary gland def: "A cuboidal epithelial cell that is part of the intercalated duct of salivary gland. This cell expresses proteins commonly associated with acinar cells and displays calcium signaling characteristics similar to secretory cells, indicating an active role in the secretory process rather than ion reabsorption." [PMID:30855909, PMID:35799078, PMID:36726292, PMID:37724716] +subset: human_subset +subset: mouse_subset synonym: "Id cell" RELATED [PMID:35799078] synonym: "intercalated duct cell" BROAD [PMID:37724716] synonym: "salivary intercalated duct cells" EXACT [PMID:37724716] @@ -38541,6 +44893,8 @@ property_value: terms:date "2024-09-11T09:55:55Z" xsd:dateTime id: CL:4052049 name: striated cell of salivary gland def: "An columnar/cuboidal epithelial cell that is part of the striated duct of salivary gland, characterized by basal striations formed by infoldings of the plasma membrane. This cell play a crucial role in modifying the electrolyte composition and concentration of saliva through active ion transport, particularly the absorption of sodium and secretion of potassium." [PMID:30855909, PMID:34147989, PMID:36726292] +subset: human_subset +subset: mouse_subset synonym: "SD cells" BROAD [PMID:11590591] synonym: "striated duct cells" BROAD [PMID:11590591] is_a: CL:0000068 ! duct epithelial cell @@ -38556,6 +44910,338 @@ property_value: terms:contributor https://orcid.org/0000-0003-4389-9821 property_value: terms:contributor https://orcid.org/0009-0000-8480-9277 property_value: terms:date "2024-09-11T10:00:25Z" xsd:dateTime +[Term] +id: CLM:1000001 +name: NS forest marker set of alveolar adventitial fibroblast (Human Lung). +is_a: SO:0001260 ! sequence_collection +relationship: has_part http://identifiers.org/ensembl/ENSG00000168079 ! SCARA5 +relationship: has_part http://identifiers.org/ensembl/ENSG00000174807 ! CD248 +property_value: STATO:0000663 "0.85" xsd:string + +[Term] +id: CLM:1000002 +name: NS forest marker set of alveolar type 1 fibroblast cell (Human Lung). +is_a: SO:0001260 ! sequence_collection +relationship: has_part http://identifiers.org/ensembl/ENSG00000131471 ! AOC3 +relationship: has_part http://identifiers.org/ensembl/ENSG00000139329 ! LUM +property_value: STATO:0000663 "0.70" xsd:string + +[Term] +id: CLM:1000003 +name: NS forest marker set of alveolar macrophage (Human Lung). +is_a: SO:0001260 ! sequence_collection +relationship: has_part http://identifiers.org/ensembl/ENSG00000038945 ! MSR1 +relationship: has_part http://identifiers.org/ensembl/ENSG00000170323 ! FABP4 +property_value: STATO:0000663 "0.80" xsd:string + +[Term] +id: CLM:1000004 +name: NS forest marker set of CCL3-positive alveolar macrophage (Human Lung). +is_a: SO:0001260 ! sequence_collection +relationship: has_part http://identifiers.org/ensembl/ENSG00000050730 ! TNIP3 +relationship: has_part http://identifiers.org/ensembl/ENSG00000163735 ! CXCL5 +property_value: STATO:0000663 "0.67" xsd:string + +[Term] +id: CLM:1000005 +name: NS forest marker set of metallothionein-positive alveolar macrophage (Human Lung). +is_a: SO:0001260 ! sequence_collection +relationship: has_part http://identifiers.org/ensembl/ENSG00000100292 ! HMOX1 +relationship: has_part http://identifiers.org/ensembl/ENSG00000164120 ! HPGD +property_value: STATO:0000663 "0.41" xsd:string + +[Term] +id: CLM:1000006 +name: NS forest marker set of cycling alveolar macrophage (Human Lung). +is_a: SO:0001260 ! sequence_collection +relationship: has_part http://identifiers.org/ensembl/ENSG00000137804 ! NUSAP1 +relationship: has_part http://identifiers.org/ensembl/ENSG00000166803 ! PCLAF +relationship: has_part http://identifiers.org/ensembl/ENSG00000171848 ! RRM2 +relationship: has_part http://identifiers.org/ensembl/ENSG00000175063 ! UBE2C +property_value: STATO:0000663 "0.26" xsd:string + +[Term] +id: CLM:1000008 +name: NS forest marker set of pulmonary alveolar type 1 cell (Human Lung). +is_a: SO:0001260 ! sequence_collection +relationship: has_part http://identifiers.org/ensembl/ENSG00000204305 ! AGER +property_value: STATO:0000663 "0.85" xsd:string + +[Term] +id: CLM:1000009 +name: NS forest marker set of pulmonary alveolar type 2 cell (Human Lung). +is_a: SO:0001260 ! sequence_collection +relationship: has_part http://identifiers.org/ensembl/ENSG00000122852 ! SFTPA1 +property_value: STATO:0000663 "0.95" xsd:string + +[Term] +id: CLM:1000010 +name: NS forest marker set of cycling pulmonary alveolar type 2 cell (Human Lung). +is_a: SO:0001260 ! sequence_collection +relationship: has_part http://identifiers.org/ensembl/ENSG00000131747 ! TOP2A +relationship: has_part http://identifiers.org/ensembl/ENSG00000198901 ! PRC1 +relationship: has_part http://identifiers.org/ensembl/ENSG00000242265 ! PEG10 +property_value: STATO:0000663 "0.61" xsd:string + +[Term] +id: CLM:1000026 +name: NS forest marker set of bronchial goblet cell (Human Lung). +is_a: SO:0001260 ! sequence_collection +relationship: has_part http://identifiers.org/ensembl/ENSG00000174501 ! ANKRD36C +relationship: has_part http://identifiers.org/ensembl/ENSG00000197943 ! PLCG2 +property_value: STATO:0000663 "0.55" xsd:string + +[Term] +id: CLM:1000027 +name: NS forest marker set of nasal mucosa goblet cell (Human Lung). +is_a: SO:0001260 ! sequence_collection +relationship: has_part http://identifiers.org/ensembl/ENSG00000197353 ! LYPD2 +relationship: has_part http://identifiers.org/ensembl/ENSG00000215182 ! MUC5AC +property_value: STATO:0000663 "0.81" xsd:string + +[Term] +id: CLM:1000031 +name: NS forest marker set of lung interstitial macrophage (Human Lung). +is_a: SO:0001260 ! sequence_collection +relationship: has_part http://identifiers.org/ensembl/ENSG00000010327 ! STAB1 +relationship: has_part http://identifiers.org/ensembl/ENSG00000072694 ! FCGR2B +relationship: has_part http://identifiers.org/ensembl/ENSG00000124491 ! F13A1 +property_value: STATO:0000663 "0.46" xsd:string + +[Term] +id: CLM:1000032 +name: NS forest marker set of pulmonary ionocyte (Human Lung). +is_a: SO:0001260 ! sequence_collection +relationship: has_part http://identifiers.org/ensembl/ENSG00000162399 ! BSND +relationship: has_part http://identifiers.org/ensembl/ENSG00000176009 ! ASCL3 +property_value: STATO:0000663 "0.82" xsd:string + +[Term] +id: CLM:1000041 +name: NS forest marker set of ciliated columnar cell of tracheobronchial tree (Human Lung). +is_a: SO:0001260 ! sequence_collection +relationship: has_part http://identifiers.org/ensembl/ENSG00000166959 ! MS4A8 +relationship: has_part http://identifiers.org/ensembl/ENSG00000179902 ! C1orf194 +property_value: STATO:0000663 "0.86" xsd:string + +[Term] +id: CLM:1000043 +name: NS forest marker set of lung neuroendocrine cell (Human Lung). +is_a: SO:0001260 ! sequence_collection +relationship: has_part http://identifiers.org/ensembl/ENSG00000100604 ! CHGA +relationship: has_part http://identifiers.org/ensembl/ENSG00000134443 ! GRP +property_value: STATO:0000663 "0.94" xsd:string + +[Term] +id: CLM:1000046 +name: NS forest marker set of pulmonary interstitial fibroblast (Human Lung). +is_a: SO:0001260 ! sequence_collection +relationship: has_part http://identifiers.org/ensembl/ENSG00000143196 ! DPT +relationship: has_part http://identifiers.org/ensembl/ENSG00000189058 ! APOD +property_value: STATO:0000663 "0.58" xsd:string + +[Term] +id: CLM:1000047 +name: NS forest marker set of lung pericyte (Human Lung). +is_a: SO:0001260 ! sequence_collection +relationship: has_part http://identifiers.org/ensembl/ENSG00000131097 ! HIGD1B +relationship: has_part http://identifiers.org/ensembl/ENSG00000171303 ! KCNK3 +property_value: STATO:0000663 "0.84" xsd:string + +[Term] +id: CLM:1000052 +name: NS forest marker set of airway submucosal gland collecting duct epithelial cell (Human Lung). +is_a: SO:0001260 ! sequence_collection +relationship: has_part http://identifiers.org/ensembl/ENSG00000156689 ! GLYATL2 +relationship: has_part http://identifiers.org/ensembl/ENSG00000187908 ! DMBT1 +property_value: STATO:0000663 "0.46" xsd:string + +[Term] +id: CLM:1000053 +name: NS forest marker set of mucus secreting cell of bronchus submucosal gland (Human Lung). +is_a: SO:0001260 ! sequence_collection +relationship: has_part http://identifiers.org/ensembl/ENSG00000078898 ! BPIFB2 +property_value: STATO:0000663 "0.93" xsd:string + +[Term] +id: CLM:1000054 +name: NS forest marker set of serous secreting cell of bronchus submucosal gland (Human Lung). +is_a: SO:0001260 ! sequence_collection +relationship: has_part http://identifiers.org/ensembl/ENSG00000111215 ! PRR4 +relationship: has_part http://identifiers.org/ensembl/ENSG00000184530 ! C6orf58 +property_value: STATO:0000663 "0.75" xsd:string + +[Term] +id: CLM:1000056 +name: NS forest marker set of tracheobronchial smooth muscle cell (Human Lung). +is_a: SO:0001260 ! sequence_collection +relationship: has_part http://identifiers.org/ensembl/ENSG00000107796 ! ACTA2 +relationship: has_part http://identifiers.org/ensembl/ENSG00000149591 ! TAGLN +property_value: STATO:0000663 "0.69" xsd:string + +[Term] +id: CLM:1000059 +name: NS forest marker set of respiratory suprabasal cell (Human Lung). +is_a: SO:0001260 ! sequence_collection +relationship: has_part http://identifiers.org/ensembl/ENSG00000041982 ! TNC +relationship: has_part http://identifiers.org/ensembl/ENSG00000171346 ! KRT15 +relationship: has_part http://identifiers.org/ensembl/ENSG00000206073 ! SERPINB4 +property_value: STATO:0000663 "0.62" xsd:string + +[Term] +id: CLM:1000061 +name: NS forest marker set of brush cell of tracheobronchial tree (Human Lung). +is_a: SO:0001260 ! sequence_collection +relationship: has_part http://identifiers.org/ensembl/ENSG00000051128 ! HOMER3 +relationship: has_part http://identifiers.org/ensembl/ENSG00000118513 ! MYB +relationship: has_part http://identifiers.org/ensembl/ENSG00000137709 ! POU2F3 +property_value: STATO:0000663 "0.56" xsd:string + +[Term] +id: CLM:1000063 +name: NS forest marker set of chandelier pvalb GABAergic cortical interneuron (Human Brain). +is_a: SO:0001260 ! sequence_collection +relationship: has_part http://identifiers.org/ensembl/ENSG00000174948 ! GPR149 +relationship: has_part http://identifiers.org/ensembl/ENSG00000178538 ! CA8 +property_value: STATO:0000663 "0.799748111" xsd:string + +[Term] +id: CLM:1000065 +name: NS forest marker set of L2/3 intratelencephalic projecting glutamatergic neuron (Human Brain). +is_a: SO:0001260 ! sequence_collection +relationship: has_part http://identifiers.org/ensembl/ENSG00000119547 ! ONECUT2 +relationship: has_part http://identifiers.org/ensembl/ENSG00000204262 ! COL5A2 +property_value: STATO:0000663 "0.670149932" xsd:string + +[Term] +id: CLM:1000066 +name: NS forest marker set of L4 intratelencephalic projecting glutamatergic neuron (Human Brain). +is_a: SO:0001260 ! sequence_collection +relationship: has_part http://identifiers.org/ensembl/ENSG00000113532 ! ST8SIA4 +relationship: has_part http://identifiers.org/ensembl/ENSG00000198963 ! RORB +property_value: STATO:0000663 "0.720108696" xsd:string + +[Term] +id: CLM:1000067 +name: NS forest marker set of L5 extratelencephalic projecting glutamatergic cortical neuron (Human Brain). +is_a: SO:0001260 ! sequence_collection +relationship: has_part http://identifiers.org/ensembl/ENSG00000124302 ! CHST8 +relationship: has_part http://identifiers.org/ensembl/ENSG00000185668 ! POU3F1 +property_value: STATO:0000663 "0.815891473" xsd:string + +[Term] +id: CLM:1000068 +name: NS forest marker set of L5 intratelencephalic projecting glutamatergic neuron (Human Brain). +is_a: SO:0001260 ! sequence_collection +relationship: has_part http://identifiers.org/ensembl/ENSG00000082482 ! KCNK2 +relationship: has_part http://identifiers.org/ensembl/ENSG00000180801 ! ARSJ +relationship: has_part http://identifiers.org/ensembl/ENSG00000198963 ! RORB +property_value: STATO:0000663 "0.764261336" xsd:string + +[Term] +id: CLM:1000069 +name: NS forest marker set of L5/6 near-projecting glutamatergic neuron (Human Brain). +is_a: SO:0001260 ! sequence_collection +relationship: has_part http://identifiers.org/ensembl/ENSG00000038295 ! TLL1 +relationship: has_part http://identifiers.org/ensembl/ENSG00000197085 ! NPSR1-AS1 +property_value: STATO:0000663 "0.899288218" xsd:string + +[Term] +id: CLM:1000070 +name: NS forest marker set of L6 corticothalamic-projecting glutamatergic cortical neuron (Human Brain). +is_a: SO:0001260 ! sequence_collection +relationship: has_part http://identifiers.org/ensembl/ENSG00000082684 ! SEMA5B +relationship: has_part http://identifiers.org/ensembl/ENSG00000137573 ! SULF1 +relationship: has_part http://identifiers.org/ensembl/ENSG00000178031 ! ADAMTSL1 +property_value: STATO:0000663 "0.631898455" xsd:string + +[Term] +id: CLM:1000071 +name: NS forest marker set of L6 intratelencephalic projecting glutamatergic neuron (Human Brain). +is_a: SO:0001260 ! sequence_collection +relationship: has_part http://identifiers.org/ensembl/ENSG00000172673 ! THEMIS +relationship: has_part http://identifiers.org/ensembl/ENSG00000256193 ! LINC00507 +property_value: STATO:0000663 "0.641695703" xsd:string + +[Term] +id: CLM:1000072 +name: NS forest marker set of L6 intratelencephalic projecting Car3 glutamatergic neuron (Human Brain). +is_a: SO:0001260 ! sequence_collection +relationship: has_part http://identifiers.org/ensembl/ENSG00000115593 ! SMYD1 +relationship: has_part http://identifiers.org/ensembl/ENSG00000172673 ! THEMIS +property_value: STATO:0000663 "0.877752028" xsd:string + +[Term] +id: CLM:1000073 +name: NS forest marker set of L6b glutamatergic neuron of the primary motor cortex (Human Brain). +is_a: SO:0001260 ! sequence_collection +relationship: has_part http://identifiers.org/ensembl/ENSG00000047936 ! ROS1 +relationship: has_part http://identifiers.org/ensembl/ENSG00000118523 ! CCN2 +property_value: STATO:0000663 "0.819940964" xsd:string + +[Term] +id: CLM:1000074 +name: NS forest marker set of lamp5 GABAergic cortical interneuron (Human Brain). +is_a: SO:0001260 ! sequence_collection +relationship: has_part http://identifiers.org/ensembl/ENSG00000157404 ! KIT +relationship: has_part http://identifiers.org/ensembl/ENSG00000235665 ! LINC00298 +property_value: STATO:0000663 "0.814687838" xsd:string + +[Term] +id: CLM:1000075 +name: NS forest marker set of Lamp5 Lhx6 neuron (Human Brain). +is_a: SO:0001260 ! sequence_collection +relationship: has_part http://identifiers.org/ensembl/ENSG00000125869 ! LAMP5 +relationship: has_part http://identifiers.org/ensembl/ENSG00000154080 ! CHST9 +property_value: STATO:0000663 "0.821678322" xsd:string + +[Term] +id: CLM:1000079 +name: NS forest marker set of Pax6 (Human Brain). +is_a: SO:0001260 ! sequence_collection +relationship: has_part http://identifiers.org/ensembl/ENSG00000137252 ! HCRTR2 +relationship: has_part http://identifiers.org/ensembl/ENSG00000189056 ! RELN +property_value: STATO:0000663 "0.724125093" xsd:string + +[Term] +id: CLM:1000080 +name: NS forest marker set of pvalb GABAergic cortical interneuron (Human Brain). +is_a: SO:0001260 ! sequence_collection +relationship: has_part http://identifiers.org/ensembl/ENSG00000006128 ! TAC1 +relationship: has_part http://identifiers.org/ensembl/ENSG00000100362 ! PVALB +relationship: has_part http://identifiers.org/ensembl/ENSG00000167306 ! MYO5B +property_value: STATO:0000663 "0.691998764" xsd:string + +[Term] +id: CLM:1000081 +name: NS forest marker set of sncg GABAergic cortical interneuron (Human Brain). +is_a: SO:0001260 ! sequence_collection +relationship: has_part http://identifiers.org/ensembl/ENSG00000143171 ! RXRG +relationship: has_part http://identifiers.org/ensembl/ENSG00000144229 ! THSD7B +property_value: STATO:0000663 "0.628943702" xsd:string + +[Term] +id: CLM:1000082 +name: NS forest marker set of sst GABAergic cortical interneuron (Human Brain). +is_a: SO:0001260 ! sequence_collection +relationship: has_part http://identifiers.org/ensembl/ENSG00000114805 ! PLCH1 +relationship: has_part http://identifiers.org/ensembl/ENSG00000157005 ! SST +property_value: STATO:0000663 "0.842367005" xsd:string + +[Term] +id: CLM:1000083 +name: NS forest marker set of sst chodl GABAergic cortical interneuron (Human Brain). +is_a: SO:0001260 ! sequence_collection +relationship: has_part http://identifiers.org/ensembl/ENSG00000122585 ! NPY +property_value: STATO:0000663 "0.894026187" xsd:string + +[Term] +id: CLM:1000085 +name: NS forest marker set of VIP GABAergic cortical interneuron (Human Brain). +is_a: SO:0001260 ! sequence_collection +relationship: has_part http://identifiers.org/ensembl/ENSG00000146469 ! VIP +property_value: STATO:0000663 "0.855531344" xsd:string + [Term] id: CP:0000000 name: obsolete CP:0000000 @@ -38645,7 +45331,6 @@ relationship: regulates GO:0006310 ! DNA recombination id: GO:0000070 name: mitotic sister chromatid segregation namespace: biological_process -alt_id: GO:0016359 def: "The cell cycle process in which replicated homologous chromosomes are organized and then physically separated and apportioned to two sets during the mitotic cell cycle. Each replicated chromosome, composed of two sister chromatids, aligns at the cell equator, paired with its homologous partner. One homolog of each morphologic type goes into each of the resulting chromosome sets." [GOC:ai, GOC:jl] subset: goslim_pombe synonym: "mitotic chromosome segregation" EXACT [] @@ -38673,32 +45358,6 @@ intersection_of: GO:0009058 ! biosynthetic process intersection_of: has_primary_output CHEBI:57595 relationship: has_primary_output CHEBI:57595 -[Term] -id: GO:0000122 -name: negative regulation of transcription by RNA polymerase II -namespace: biological_process -alt_id: GO:0010553 -alt_id: GO:0045816 -def: "Any process that stops, prevents, or reduces the frequency, rate or extent of transcription mediated by RNA polymerase II." [GOC:go_curators, GOC:txnOH] -synonym: "down regulation of global transcription from RNA polymerase II promoter" RELATED [] -synonym: "down regulation of transcription from RNA polymerase II promoter" EXACT [] -synonym: "down-regulation of global transcription from RNA polymerase II promoter" RELATED [] -synonym: "down-regulation of transcription from RNA polymerase II promoter" EXACT [] -synonym: "downregulation of global transcription from RNA polymerase II promoter" RELATED [] -synonym: "downregulation of transcription from RNA polymerase II promoter" EXACT [] -synonym: "inhibition of global transcription from RNA polymerase II promoter" RELATED [] -synonym: "inhibition of transcription from RNA polymerase II promoter" EXACT [] -synonym: "negative regulation of gene-specific transcription from RNA polymerase II promoter" RELATED [] -synonym: "negative regulation of global transcription from Pol II promoter" RELATED [] -synonym: "negative regulation of transcription from Pol II promoter" EXACT [] -synonym: "negative regulation of transcription from RNA polymerase II promoter" EXACT [] -synonym: "negative regulation of transcription from RNA polymerase II promoter, global" RELATED [] -is_a: GO:0006357 ! regulation of transcription by RNA polymerase II -is_a: GO:0045892 ! negative regulation of DNA-templated transcription -intersection_of: GO:0065007 ! biological regulation -intersection_of: negatively_regulates GO:0006366 ! transcription by RNA polymerase II -relationship: negatively_regulates GO:0006366 ! transcription by RNA polymerase II - [Term] id: GO:0000139 name: Golgi membrane @@ -38714,7 +45373,6 @@ relationship: bounding_layer_of GO:0005794 ! Golgi apparatus id: GO:0000146 name: microfilament motor activity namespace: molecular_function -alt_id: GO:0030898 def: "A motor activity that generates movement along a microfilament, driven by ATP hydrolysis." [PMID:29716949] synonym: "actin filament motor activity" EXACT [GOC:dph] synonym: "actin-activated ATPase activity" EXACT [] @@ -38783,7 +45441,6 @@ relationship: has_primary_output CHEBI:18154 id: GO:0000272 name: polysaccharide catabolic process namespace: biological_process -alt_id: GO:0044244 def: "The chemical reactions and pathways resulting in the breakdown of a polysaccharide, a polymer of many (typically more than 10) monosaccharide residues linked glycosidically." [PMID:33139480] synonym: "multicellular organismal polysaccharide catabolic process" NARROW [] synonym: "polysaccharide breakdown" EXACT [] @@ -38799,7 +45456,6 @@ relationship: has_primary_input CHEBI:18154 id: GO:0000278 name: mitotic cell cycle namespace: biological_process -alt_id: GO:0007067 def: "Progression through the phases of the mitotic cell cycle, the most common eukaryotic cell cycle, which canonically comprises four successive phases called G1, S, G2, and M and includes replication of the genome and the subsequent segregation of chromosomes into daughter cells. In some variant cell cycles nuclear replication or nuclear division may not be followed by cell division, or G1 and G2 phases may be absent." [GOC:mah, ISBN:0815316194] comment: Note that this term should not be confused with 'GO:0140014 ; mitotic nuclear division'. 'GO:0000278 ; mitotic cell cycle represents the entire mitotic cell cycle, while 'GO:0140014 ; mitotic nuclear division' specifically represents the actual nuclear division step of the mitotic cell cycle. subset: goslim_chembl @@ -38891,7 +45547,6 @@ relationship: results_in_fusion_of GO:0031965 ! nuclear membrane id: GO:0000741 name: karyogamy namespace: biological_process -alt_id: GO:0007335 def: "The creation of a single nucleus from multiple nuclei as a result of fusing the lipid bilayers that surround each nuclei." [GOC:elh] synonym: "nuclear fusion" EXACT [] synonym: "nuclear fusion during karyogamy" EXACT [] @@ -38918,16 +45573,13 @@ intersection_of: has_part GO:0045026 ! plasma membrane fusion id: GO:0000785 name: chromatin namespace: cellular_component -alt_id: GO:0000789 -alt_id: GO:0000790 -alt_id: GO:0005717 def: "The ordered and organized complex of DNA, protein, and sometimes RNA, that forms the chromosome." [GOC:elh, PMID:20404130] comment: Chromosomes include parts that are not part of the chromatin. Examples include the kinetochore. synonym: "chromosome scaffold" RELATED [] synonym: "cytoplasmic chromatin" NARROW [] synonym: "nuclear chromatin" NARROW [] xref: NIF_Subcellular:sao1615953555 -is_a: GO:0110165 ! cellular anatomical entity +is_a: GO:0110165 ! cellular anatomical structure relationship: part_of GO:0005694 ! chromosome property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28301" xsd:anyURI @@ -38935,8 +45587,6 @@ property_value: term_tracker_item "https://github.com/geneontology/go-ontology/i id: GO:0000791 name: euchromatin namespace: cellular_component -alt_id: GO:0005719 -alt_id: GO:0035327 def: "A dispersed and relatively uncompacted form of chromatin that is in a transcription-competent conformation." [PMID:32017156] synonym: "nuclear euchromatin" RELATED [] synonym: "transcriptionally active chromatin" EXACT [] @@ -38949,8 +45599,6 @@ property_value: term_tracker_item "https://github.com/geneontology/go-ontology/i id: GO:0000792 name: heterochromatin namespace: cellular_component -alt_id: GO:0005720 -alt_id: GO:0035328 def: "A compact and highly condensed form of chromatin that is refractory to transcription." [PMID:32017156] synonym: "nuclear heterochromatin" NARROW [] synonym: "transcriptionally inactive chromatin" EXACT [] @@ -38974,7 +45622,7 @@ name: regulation of glutamine family amino acid metabolic process namespace: biological_process def: "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving amino acids of the glutamine family, comprising arginine, glutamate, glutamine and proline." [GOC:go_curators] synonym: "regulation of glutamine family amino acid metabolism" EXACT [] -is_a: GO:0006521 ! regulation of cellular amino acid metabolic process +is_a: GO:0006521 ! regulation of amino acid metabolic process intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0009064 ! glutamine family amino acid metabolic process relationship: regulates GO:0009064 ! glutamine family amino acid metabolic process @@ -38983,9 +45631,6 @@ relationship: regulates GO:0009064 ! glutamine family amino acid metabolic proce id: GO:0000902 name: cell morphogenesis namespace: biological_process -alt_id: GO:0007148 -alt_id: GO:0045790 -alt_id: GO:0045791 def: "The developmental process in which the size or shape of a cell is generated and organized." [GOC:clt, GOC:dph, GOC:go_curators, GOC:tb] subset: goslim_chembl subset: goslim_drosophila @@ -38997,102 +45642,6 @@ intersection_of: GO:0009653 ! anatomical structure morphogenesis intersection_of: results_in_morphogenesis_of CL:0000000 ! cell relationship: results_in_morphogenesis_of CL:0000000 ! cell -[Term] -id: GO:0000976 -name: transcription cis-regulatory region binding -namespace: molecular_function -alt_id: GO:0000975 -alt_id: GO:0000984 -alt_id: GO:0001017 -alt_id: GO:0044212 -def: "Binding to a specific sequence of DNA that is part of a regulatory region that controls transcription of that section of the DNA. The transcribed region might be described as a gene, cistron, or operon." [GOC:txnOH] -comment: Note that this term is meant to also capture non-specific binding to regulatory regions. Also, to minimize ambiguity in the use of the word "promoter" in GO, we have chosen the phrase "transcription regulatory region" to refer to all of the regulatory regions. Regulatory regions in the DNA which control initiation may include the "core promoter" where the basal transcription machinery binds, the "core promoter proximal region" where regulatory factors other than the basal machinery bind. There are also additional regulatory regions, in both the DNA and the RNA transcript, which regulate elongation or termination of transcription. -synonym: "bacterial-type RNA polymerase regulatory region DNA binding" NARROW [] -synonym: "bacterial-type RNA polymerase transcription regulatory region sequence-specific DNA binding" NARROW [] -synonym: "eubacterial-type RNA polymerase regulatory region DNA binding" NARROW [] -synonym: "eubacterial-type RNA polymerase regulatory region sequence-specific DNA binding" NARROW [] -synonym: "regulatory region DNA binding" BROAD [] -synonym: "transcription regulatory region DNA binding" RELATED [] -synonym: "transcription regulatory region sequence-specific DNA binding" EXACT [] -is_a: GO:0001067 ! transcription regulatory region nucleic acid binding -is_a: GO:1990837 ! sequence-specific double-stranded DNA binding -property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/19312" xsd:anyURI -property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/20791" xsd:anyURI -created_by: krc -creation_date: 2010-08-10T02:58:18Z - -[Term] -id: GO:0000977 -name: RNA polymerase II transcription regulatory region sequence-specific DNA binding -namespace: molecular_function -alt_id: GO:0001012 -def: "Binding to a specific sequence of DNA that is part of a regulatory region that controls the transcription of a gene or cistron by RNA polymerase II." [GOC:txnOH] -comment: To minimize ambiguity in the use of the word "promoter" in GO, we have chosen the phrase "transcription regulatory region" to refer to all of the regulatory regions. Regulatory regions in the DNA which control initiation may include the "core promoter" where the basal transcription machinery binds, the "core promoter proximal region" where regulatory factors other than the basal machinery bind. There are also additional regulatory regions, in both the DNA and the RNA transcript, which regulate elongation or termination of transcription. -synonym: "RNA polymerase II regulatory region DNA binding" RELATED [] -is_a: GO:0000976 ! transcription cis-regulatory region binding -property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/19312" xsd:anyURI -created_by: krc -creation_date: 2010-08-10T11:05:36Z - -[Term] -id: GO:0000981 -name: DNA-binding transcription factor activity, RNA polymerase II-specific -namespace: molecular_function -alt_id: GO:0000982 -alt_id: GO:0001133 -alt_id: GO:0001200 -alt_id: GO:0001201 -alt_id: GO:0001202 -alt_id: GO:0001203 -alt_id: GO:0003705 -def: "A DNA-binding transcription factor activity that modulates the transcription of specific gene sets transcribed by RNA polymerase II." [GOC:txnOH-2018] -comment: For usage guidance, see comment in GO:0003700 ; DNA-binding transcription factor activity. -synonym: "copper ion regulated core promoter proximal region sequence-specific DNA binding RNA polymerase II transcription factor activity" NARROW [] -synonym: "metal ion regulated core promoter proximal region sequence-specific DNA binding RNA polymerase II transcription factor activity" NARROW [] -synonym: "metal ion regulated sequence-specific DNA binding RNA polymerase II transcription factor activity" NARROW [] -synonym: "RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity" NARROW [] -synonym: "RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity" NARROW [] -synonym: "RNA polymerase II transcription factor activity, copper ion regulated core promoter proximal region sequence-specific binding" NARROW [] -synonym: "RNA polymerase II transcription factor activity, copper ion regulated proximal promoter sequence-specific DNA binding" NARROW [] -synonym: "RNA polymerase II transcription factor activity, metal ion regulated core promoter proximal region sequence-specific binding" NARROW [] -synonym: "RNA polymerase II transcription factor activity, metal ion regulated proximal promoter sequence-specific DNA binding" NARROW [] -synonym: "RNA polymerase II transcription factor activity, metal ion regulated sequence-specific DNA binding" NARROW [] -synonym: "RNA polymerase II transcription factor activity, sequence-specific DNA binding" EXACT [] -synonym: "RNA polymerase II transcription factor activity, sequence-specific transcription regulatory region DNA binding" EXACT [] -synonym: "RNA polymerase II transcription factor activity, zinc ion regulated core promoter proximal region sequence-specific DNA binding" NARROW [] -synonym: "RNA polymerase II transcription factor activity, zinc ion regulated proximal promoter sequence-specific DNA binding" NARROW [] -synonym: "sequence-specific distal enhancer binding RNA polymerase II transcription factor activity" NARROW [] -synonym: "sequence-specific DNA binding RNA polymerase II transcription factor activity" EXACT [] -synonym: "sequence-specific transcription regulatory region DNA binding RNA polymerase II transcription factor recruiting transcription factor activity" RELATED [] -synonym: "transcription factor" BROAD [GOC:vw] -synonym: "transcription factor activity, RNA polymerase II core promoter proximal region sequence-specific binding" NARROW [] -synonym: "transcription factor activity, RNA polymerase II distal enhancer sequence-specific binding" NARROW [] -synonym: "transcription factor activity, RNA polymerase II proximal promoter sequence-specific DNA binding" NARROW [] -synonym: "zinc ion regulated core promoter proximal region sequence-specific DNA binding RNA polymerase II transcription factor activity" NARROW [] -is_a: GO:0003700 ! DNA-binding transcription factor activity -intersection_of: GO:0140110 ! transcription regulator activity -intersection_of: has_part GO:0000977 ! RNA polymerase II transcription regulatory region sequence-specific DNA binding -intersection_of: part_of GO:0006357 ! regulation of transcription by RNA polymerase II -relationship: has_part GO:0000977 ! RNA polymerase II transcription regulatory region sequence-specific DNA binding -relationship: occurs_in GO:0000785 ! chromatin -relationship: part_of GO:0006357 ! regulation of transcription by RNA polymerase II -property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/15530" xsd:anyURI -property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/16131" xsd:anyURI -property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/16152" xsd:anyURI -created_by: krc -creation_date: 2010-08-10T02:37:21Z - -[Term] -id: GO:0001067 -name: transcription regulatory region nucleic acid binding -namespace: molecular_function -def: "Binding to a nucleic acid region that regulates a nucleic acid-based process. Such processes include transcription, DNA replication, and DNA repair." [GOC:txnOH] -synonym: "regulatory region nucleic acid binding" RELATED [] -is_a: GO:0003676 ! nucleic acid binding -property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/20791" xsd:anyURI -created_by: krc -creation_date: 2010-10-21T04:08:56Z - [Term] id: GO:0001101 name: response to acid chemical @@ -39105,145 +45654,6 @@ synonym: "response to acid anion" RELATED [] synonym: "response to oxoanion" RELATED [] is_a: GO:0042221 ! response to chemical -[Term] -id: GO:0001216 -name: DNA-binding transcription activator activity -namespace: molecular_function -alt_id: GO:0001140 -alt_id: GO:0001215 -def: "A DNA-binding transcription factor activity that activates or increases transcription of specific gene sets." [GOC:txnOH-2018] -comment: For usage guidance, see comment in GO:0003700 ; DNA-binding transcription factor activity. -synonym: "bacterial-type RNA polymerase core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription" RELATED [] -synonym: "bacterial-type RNA polymerase transcriptional activator activity, metal ion regulated sequence-specific DNA binding" NARROW [] -synonym: "bacterial-type RNA polymerase transcriptional activator activity, sequence-specific DNA binding" NARROW [] -synonym: "metal ion regulated sequence-specific DNA binding bacterial-type RNA polymerase transcription factor activity involved in positive regulation of transcription" NARROW [] -synonym: "sequence-specific DNA binding bacterial-type RNA polymerase transcription factor activity involved in positive regulation of transcription" NARROW [] -synonym: "transcriptional activator activity, bacterial-type RNA polymerase core promoter proximal region sequence-specific binding" NARROW [] -synonym: "transcriptional activator activity, bacterial-type RNA polymerase proximal promoter sequence-specific DNA binding" RELATED [] -is_a: GO:0003700 ! DNA-binding transcription factor activity -intersection_of: GO:0140110 ! transcription regulator activity -intersection_of: has_part GO:0000976 ! transcription cis-regulatory region binding -intersection_of: part_of GO:0045893 ! positive regulation of DNA-templated transcription -relationship: part_of GO:0045893 ! positive regulation of DNA-templated transcription -property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/16534" xsd:anyURI -property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/16736" xsd:anyURI -created_by: krc -creation_date: 2011-01-26T03:09:27Z - -[Term] -id: GO:0001217 -name: DNA-binding transcription repressor activity -namespace: molecular_function -alt_id: GO:0001141 -alt_id: GO:0001218 -alt_id: GO:0001219 -alt_id: GO:0001220 -def: "A DNA-binding transcription factor activity that represses or decreases the transcription of specific gene sets." [GOC:txnOH-2018] -comment: For usage guidance, see comment in GO:0003700 ; DNA-binding transcription factor activity. -synonym: "bacterial-type DNA binding transcription repressor activity" NARROW [] -synonym: "bacterial-type RNA polymerase core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription" NARROW [] -synonym: "bacterial-type RNA polymerase transcriptional repressor activity, cadmium ion regulated sequence-specific DNA binding" NARROW [] -synonym: "bacterial-type RNA polymerase transcriptional repressor activity, copper ion regulated sequence-specific DNA binding" NARROW [] -synonym: "bacterial-type RNA polymerase transcriptional repressor activity, metal ion regulated sequence-specific DNA binding" NARROW [] -synonym: "bacterial-type RNA polymerase transcriptional repressor activity, sequence-specific DNA binding" NARROW [] -synonym: "cadmium ion regulated sequence-specific DNA binding bacterial-type RNA polymerase transcription factor activity involved in negative regulation of transcription" NARROW [] -synonym: "copper ion regulated sequence-specific DNA binding bacterial-type RNA polymerase transcription factor activity involved in negative regulation of transcription" NARROW [] -synonym: "metal ion regulated sequence-specific DNA binding bacterial-type RNA polymerase transcription factor activity involved in negative regulation of transcription" NARROW [] -synonym: "sequence-specific DNA binding bacterial-type RNA polymerase transcription factor activity involved in negative regulation of transcription" NARROW [] -synonym: "transcriptional repressor activity, bacterial-type RNA polymerase core promoter proximal region sequence-specific binding" NARROW [] -synonym: "transcriptional repressor activity, bacterial-type RNA polymerase proximal promoter sequence-specific DNA binding" NARROW [] -is_a: GO:0003700 ! DNA-binding transcription factor activity -intersection_of: GO:0140110 ! transcription regulator activity -intersection_of: has_part GO:0000976 ! transcription cis-regulatory region binding -intersection_of: part_of GO:0045892 ! negative regulation of DNA-templated transcription -relationship: part_of GO:0045892 ! negative regulation of DNA-templated transcription -property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/16736" xsd:anyURI -property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/20253" xsd:anyURI -created_by: krc -creation_date: 2011-01-26T03:15:45Z - -[Term] -id: GO:0001227 -name: DNA-binding transcription repressor activity, RNA polymerase II-specific -namespace: molecular_function -alt_id: GO:0001078 -alt_id: GO:0001206 -alt_id: GO:0001210 -alt_id: GO:0001214 -def: "A DNA-binding transcription factor activity that represses or decreases the transcription of specific gene sets transcribed by RNA polymerase II." [GOC:txnOH-2018] -comment: For usage guidance, see comment in GO:0003700 ; DNA-binding transcription factor activity. -synonym: "distal enhancer DNA-binding transcription repressor activity, RNA polymerase II-specific" NARROW [] -synonym: "metal ion regulated core promoter proximal region sequence-specific DNA binding RNA polymerase II transcription factor activity involved in negative regulation of transcription" NARROW [] -synonym: "metal ion regulated sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription" NARROW [] -synonym: "proximal promoter DNA-binding transcription repressor activity, RNA polymerase II-specific" NARROW [] -synonym: "RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription" NARROW [] -synonym: "RNA polymerase II distal enhancer sequence-specific DNA-binding transcription factor activity involved in negative regulation of transcription" NARROW [] -synonym: "RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription" EXACT [] -synonym: "RNA polymerase II transcriptional repressor activity, metal ion regulated core promoter proximal region sequence-specific binding" NARROW [] -synonym: "RNA polymerase II transcriptional repressor activity, metal ion regulated proximal promoter sequence-specific DNA binding" NARROW [] -synonym: "sequence-specific distal enhancer binding RNA polymerase II transcription factor activity involved in negative regulation of transcription" NARROW [] -synonym: "transcriptional repressor activity, metal ion regulated sequence-specific DNA binding" NARROW [] -synonym: "transcriptional repressor activity, RNA polymerase II distal enhancer sequence-specific binding" NARROW [] -synonym: "transcriptional repressor activity, RNA polymerase II proximal promoter sequence-specific DNA binding" NARROW [] -synonym: "transcriptional repressor activity, RNA polymerase II transcription regulatory region sequence-specific DNA binding" EXACT [] -is_a: GO:0000981 ! DNA-binding transcription factor activity, RNA polymerase II-specific -is_a: GO:0001217 ! DNA-binding transcription repressor activity -intersection_of: GO:0140110 ! transcription regulator activity -intersection_of: has_part GO:0000977 ! RNA polymerase II transcription regulatory region sequence-specific DNA binding -intersection_of: part_of GO:0000122 ! negative regulation of transcription by RNA polymerase II -relationship: part_of GO:0000122 ! negative regulation of transcription by RNA polymerase II -property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/16131" xsd:anyURI -property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/16152" xsd:anyURI -property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/16534" xsd:anyURI -property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/20253" xsd:anyURI -created_by: krc -creation_date: 2010-10-26T03:56:48Z - -[Term] -id: GO:0001228 -name: DNA-binding transcription activator activity, RNA polymerase II-specific -namespace: molecular_function -alt_id: GO:0001077 -alt_id: GO:0001205 -alt_id: GO:0001209 -alt_id: GO:0001211 -alt_id: GO:0001212 -alt_id: GO:0001213 -def: "A DNA-binding transcription factor activity that activates or increases transcription of specific gene sets transcribed by RNA polymerase II." [GOC:aruk, GOC:txnOH-2018, PMID:20737563, PMID:27145859] -comment: For usage guidance, see comment in GO:0003700 ; DNA-binding transcription factor activity. -synonym: "copper ion regulated core promoter proximal region sequence-specific DNA binding RNA polymerase II transcription factor activity involved in positive regulation of transcription" NARROW [] -synonym: "distal enhancer DNA-binding transcription activator activity, RNA polymerase II-specific" NARROW [] -synonym: "metal ion regulated core promoter proximal region sequence-specific DNA binding RNA polymerase II transcription factor activity involved in positive regulation of transcription" NARROW [] -synonym: "metal ion regulated sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription" NARROW [] -synonym: "proximal promoter DNA-binding transcription activator activity, RNA polymerase II-specific" NARROW [] -synonym: "RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription" NARROW [] -synonym: "RNA polymerase II distal enhancer sequence-specific DNA-binding transcription factor activity involved in positive regulation of transcription" NARROW [] -synonym: "RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription" EXACT [] -synonym: "RNA polymerase II transcriptional activator activity, copper ion regulated proximal promoter sequence-specific DNA binding" NARROW [] -synonym: "RNA polymerase II transcriptional activator activity, metal ion regulated core promoter proximal region sequence-specific binding" NARROW [] -synonym: "RNA polymerase II transcriptional activator activity, metal ion regulated proximal promoter sequence-specific DNA binding" NARROW [] -synonym: "RNA polymerase II transcriptional activator activity, zinc ion regulated core promoter proximal region sequence-specific binding" NARROW [] -synonym: "RNA polymerase II transcriptional activator activity, zinc ion regulated proximal promoter sequence-specific DNA binding" NARROW [] -synonym: "sequence-specific distal enhancer binding RNA polymerase II transcription factor activity involved in positive regulation of transcription" NARROW [] -synonym: "transcriptional activator activity, metal ion regulated sequence-specific DNA binding" NARROW [] -synonym: "transcriptional activator activity, RNA polymerase II core promoter proximal region sequence-specific binding" NARROW [] -synonym: "transcriptional activator activity, RNA polymerase II distal enhancer sequence-specific DNA binding" NARROW [] -synonym: "transcriptional activator activity, RNA polymerase II proximal promoter sequence-specific DNA binding" NARROW [] -synonym: "transcriptional activator activity, RNA polymerase II transcription regulatory region sequence-specific DNA binding" EXACT [] -synonym: "zinc ion regulated core promoter proximal region sequence-specific DNA binding RNA polymerase II transcription factor activity involved in positive regulation of transcription" NARROW [] -is_a: GO:0000981 ! DNA-binding transcription factor activity, RNA polymerase II-specific -is_a: GO:0001216 ! DNA-binding transcription activator activity -intersection_of: GO:0140110 ! transcription regulator activity -intersection_of: has_part GO:0000977 ! RNA polymerase II transcription regulatory region sequence-specific DNA binding -intersection_of: part_of GO:0045944 ! positive regulation of transcription by RNA polymerase II -relationship: part_of GO:0045944 ! positive regulation of transcription by RNA polymerase II -property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/16131" xsd:anyURI -property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/16152" xsd:anyURI -property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/16534" xsd:anyURI -property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/20253" xsd:anyURI -created_by: krc -creation_date: 2012-01-26T03:10:20Z - [Term] id: GO:0001501 name: skeletal system development @@ -39397,6 +45807,17 @@ relationship: part_of GO:0001547 ! antral ovarian follicle growth relationship: part_of GO:0048165 ! fused antrum stage relationship: results_in_acquisition_of_features_of CL:0000711 ! cumulus cell +[Term] +id: GO:0001552 +name: ovarian follicle atresia +namespace: biological_process +def: "A periodic process in which immature ovarian follicles degenerate and are subsequently re-absorbed." [GOC:mtg_apoptosis, PMID:18638134] +is_a: BFO:0000003 +is_a: GO:0003006 ! developmental process involved in reproduction +relationship: has_part GO:0097191 ! extrinsic apoptotic signaling pathway +relationship: has_participant UBERON:0001305 ! ovarian follicle +relationship: part_of GO:0008585 ! female gonad development + [Term] id: GO:0001553 name: luteinization @@ -39516,7 +45937,6 @@ relationship: results_in_formation_of GO:0097427 ! microtubule bundle id: GO:0001621 name: G protein-coupled ADP receptor activity namespace: molecular_function -alt_id: GO:0045032 def: "Combining with ADP and transmitting the signal across the membrane by activating an associated G-protein; promotes the exchange of GDP for GTP on the alpha subunit of a heterotrimeric G-protein complex." [GOC:mah, GOC:signaling, PMID:11196645] synonym: "ADP receptor activity" BROAD [] synonym: "ADP-activated adenosine receptor activity" RELATED [] @@ -39559,7 +45979,6 @@ relationship: has_primary_input CHEBI:60466 id: GO:0001654 name: eye development namespace: biological_process -alt_id: GO:0042460 def: "The process whose specific outcome is the progression of the eye over time, from its formation to the mature structure. The eye is the organ of sight." [GOC:jid, GOC:jl] xref: Wikipedia:Eye_development is_a: GO:0007423 ! sensory organ development @@ -39671,27 +46090,23 @@ relationship: part_of CL:0000019 ! sperm id: GO:0001673 name: male germ cell nucleus namespace: cellular_component -alt_id: GO:0043081 def: "The nucleus of a male germ cell, a reproductive cell in males." [CL:0000015, GOC:hjd, GOC:mtg_sensu] synonym: "male germ-cell nucleus" EXACT [] is_a: GO:0043073 ! germ cell nucleus intersection_of: GO:0005634 ! nucleus intersection_of: part_of CL:0000015 ! male germ cell relationship: part_of CL:0000015 ! male germ cell -relationship: RO:0002162 NCBITaxon:2759 {all_only="true"} ! in taxon Eukaryota [Term] id: GO:0001674 name: female germ cell nucleus namespace: cellular_component -alt_id: GO:0043080 def: "The nucleus of the female germ cell, a reproductive cell in females." [CL:0000021, GOC:hjd] synonym: "female germ-cell nucleus" EXACT [] is_a: GO:0043073 ! germ cell nucleus intersection_of: GO:0005634 ! nucleus intersection_of: part_of CL:0000021 ! female germ cell relationship: part_of CL:0000021 ! female germ cell -relationship: RO:0002162 NCBITaxon:2759 {all_only="true"} ! in taxon Eukaryota [Term] id: GO:0001675 @@ -39750,7 +46165,6 @@ relationship: has_primary_input_or_output CHEBI:58432 id: GO:0001694 name: histamine biosynthetic process namespace: biological_process -alt_id: GO:0001693 def: "The chemical reactions and pathways resulting in the formation of histamine, a physiologically active amine, found in plant and animal tissue and released from mast cells as part of an allergic reaction in humans." [GOC:jl, ISBN:0395825172] synonym: "histamine anabolism" EXACT [] synonym: "histamine biosynthesis" EXACT [] @@ -39771,7 +46185,7 @@ synonym: "histamine breakdown" EXACT [] synonym: "histamine catabolism" EXACT [] synonym: "histamine degradation" EXACT [] is_a: GO:0001692 ! histamine metabolic process -is_a: GO:0042402 ! cellular biogenic amine catabolic process +is_a: GO:0042402 ! biogenic amine catabolic process intersection_of: GO:0009056 ! catabolic process intersection_of: has_primary_input CHEBI:58432 relationship: has_primary_input CHEBI:58432 @@ -39807,8 +46221,6 @@ relationship: RO:0002162 NCBITaxon:32525 {all_only="true"} ! in taxon Theria [Term] id: GO:0001910 @@ -41066,7 +47466,6 @@ relationship: results_in_organization_of GO:0045211 ! postsynaptic membrane id: GO:0001942 name: hair follicle development namespace: biological_process -alt_id: GO:0001943 def: "The process whose specific outcome is the progression of the hair follicle over time, from its formation to the mature structure. A hair follicle is a tube-like opening in the epidermis where the hair shaft develops and into which the sebaceous glands open." [GOC:dph, UBERON:0002073] is_a: GO:0022405 ! hair cycle process is_a: GO:0048856 ! anatomical structure development @@ -41372,7 +47771,6 @@ relationship: regulates GO:0006814 ! sodium ion transport id: GO:0002036 name: regulation of L-glutamate import across plasma membrane namespace: biological_process -alt_id: GO:1900920 def: "Any process that modulates the frequency, rate or extent of L-glutamate import into a cell." [GOC:TermGenie] synonym: "regulation of L-glutamate import" BROAD [] synonym: "regulation of L-glutamate transport" BROAD [] @@ -41381,14 +47779,12 @@ is_a: GO:0010958 ! regulation of amino acid import across plasma membrane intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0098712 ! L-glutamate import across plasma membrane relationship: regulates GO:0098712 ! L-glutamate import across plasma membrane -created_by: al creation_date: 2012-06-13T07:34:08Z [Term] id: GO:0002037 name: negative regulation of L-glutamate import across plasma membrane namespace: biological_process -alt_id: GO:1900921 def: "Any process that stops, prevents or reduces the frequency, rate or extent of L-glutamate import into a cell." [GOC:TermGenie] synonym: "down regulation of L-glutamate import" EXACT [GOC:TermGenie] synonym: "down regulation of L-glutamate transport" BROAD [] @@ -41412,14 +47808,12 @@ is_a: GO:0051956 ! negative regulation of amino acid transport intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0098712 ! L-glutamate import across plasma membrane relationship: negatively_regulates GO:0098712 ! L-glutamate import across plasma membrane -created_by: al creation_date: 2012-06-13T07:34:30Z [Term] id: GO:0002038 name: positive regulation of L-glutamate import across plasma membrane namespace: biological_process -alt_id: GO:1900922 def: "Any process that activates or increases the frequency, rate or extent of L-glutamate import into a cell." [GOC:TermGenie] synonym: "activation of L-glutamate import" NARROW [GOC:TermGenie] synonym: "activation of L-glutamate transport" NARROW [] @@ -41443,7 +47837,6 @@ is_a: GO:0051957 ! positive regulation of amino acid transport intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0098712 ! L-glutamate import across plasma membrane relationship: positively_regulates GO:0098712 ! L-glutamate import across plasma membrane -created_by: al creation_date: 2012-06-13T07:34:38Z [Term] @@ -41540,8 +47933,8 @@ namespace: biological_process def: "The process in which a relatively unspecialized cell acquires specialized features of a glandular epithelial cell. A glandular epithelial cell is a columnar/cuboidal epithelial cell found in a two dimensional sheet with a free surface exposed to the lumen of a gland." [GOC:dph] is_a: GO:0002065 ! columnar/cuboidal epithelial cell differentiation intersection_of: GO:0030154 ! cell differentiation -intersection_of: results_in_acquisition_of_features_of CL:0000150 ! glandular epithelial cell -relationship: results_in_acquisition_of_features_of CL:0000150 ! glandular epithelial cell +intersection_of: results_in_acquisition_of_features_of CL:0000150 ! glandular secretory epithelial cell +relationship: results_in_acquisition_of_features_of CL:0000150 ! glandular secretory epithelial cell [Term] id: GO:0002068 @@ -41550,9 +47943,9 @@ namespace: biological_process def: "The process whose specific outcome is the progression of a glandular epithelial cell over time, from its formation to the mature structure. A glandular epithelial cell is a columnar/cuboidal epithelial cell is a cell found in a two dimensional sheet with a free surface exposed to the lumen of a gland." [GOC:dph] is_a: GO:0002066 ! columnar/cuboidal epithelial cell development intersection_of: GO:0032502 ! developmental process -intersection_of: results_in_development_of CL:0000150 ! glandular epithelial cell +intersection_of: results_in_development_of CL:0000150 ! glandular secretory epithelial cell relationship: part_of GO:0002067 ! glandular epithelial cell differentiation -relationship: results_in_development_of CL:0000150 ! glandular epithelial cell +relationship: results_in_development_of CL:0000150 ! glandular secretory epithelial cell [Term] id: GO:0002069 @@ -41583,9 +47976,9 @@ namespace: biological_process def: "The developmental process, independent of morphogenetic (shape) change, that is required for a glandular epithelial cell to attain its fully functional state. A glandular epithelial cell is a columnar/cuboidal epithelial cell is a cell found in a two dimensional sheet with a free surface exposed to the lumen of a gland." [GOC:dph] is_a: GO:0002069 ! columnar/cuboidal epithelial cell maturation intersection_of: GO:0021700 ! developmental maturation -intersection_of: results_in_maturation_of CL:0000150 ! glandular epithelial cell +intersection_of: results_in_maturation_of CL:0000150 ! glandular secretory epithelial cell relationship: part_of GO:0002068 ! glandular epithelial cell development -relationship: results_in_maturation_of CL:0000150 ! glandular epithelial cell +relationship: results_in_maturation_of CL:0000150 ! glandular secretory epithelial cell [Term] id: GO:0002072 @@ -41699,7 +48092,6 @@ is_a: GO:0070661 ! leukocyte proliferation intersection_of: GO:0008283 ! cell population proliferation intersection_of: acts_on_population_of CL:0000092 ! osteoclast relationship: acts_on_population_of CL:0000092 ! osteoclast -created_by: hjd creation_date: 2010-02-03T01:50:37Z [Term] @@ -41729,7 +48121,6 @@ is_a: GO:0036093 ! germ cell proliferation intersection_of: GO:0008283 ! cell population proliferation intersection_of: acts_on_population_of CL:0000015 ! male germ cell relationship: acts_on_population_of CL:0000015 ! male germ cell -created_by: hjd creation_date: 2010-11-18T02:35:14Z [Term] @@ -41745,7 +48136,6 @@ is_a: GO:0006412 ! translation intersection_of: GO:0006412 ! translation intersection_of: process_has_causal_agent GO:0022626 ! cytosolic ribosome relationship: process_has_causal_agent GO:0022626 ! cytosolic ribosome -created_by: hjd creation_date: 2011-06-09T03:11:53Z [Term] @@ -41757,7 +48147,6 @@ is_a: GO:0006414 ! translational elongation intersection_of: GO:0006414 ! translational elongation intersection_of: part_of GO:0002181 ! cytoplasmic translation relationship: part_of GO:0002181 ! cytoplasmic translation -created_by: hjd creation_date: 2011-06-09T03:14:42Z [Term] @@ -41769,7 +48158,6 @@ is_a: GO:0006413 ! translational initiation intersection_of: GO:0006413 ! translational initiation intersection_of: part_of GO:0002181 ! cytoplasmic translation relationship: part_of GO:0002181 ! cytoplasmic translation -created_by: hjd creation_date: 2011-06-09T03:15:48Z [Term] @@ -41782,7 +48170,6 @@ intersection_of: GO:0006415 ! translational termination intersection_of: occurs_in GO:0005829 ! cytosol relationship: occurs_in GO:0005829 ! cytosol relationship: part_of GO:0002181 ! cytoplasmic translation -created_by: hjd creation_date: 2011-06-09T03:17:13Z [Term] @@ -41818,7 +48205,6 @@ relationship: part_of GO:0002381 ! immunoglobulin production involved in immunog id: GO:0002213 name: defense response to insect namespace: biological_process -alt_id: GO:0002214 def: "A response to protect an organism from a directly detected or perceived external threat from an insect or insects to that organism." [GOC:add] synonym: "physiological defense response to insect" EXACT [] is_a: BFO:0000003 @@ -41831,7 +48217,6 @@ relationship: has_primary_input NCBITaxon:50557 ! Insecta id: GO:0002215 name: defense response to nematode namespace: biological_process -alt_id: GO:0002216 def: "A response to protect an organism from a directly detected or perceived external threat from a nematode or nematodes, which results in restriction of damage to the organism attacked or prevention/recovery from the infection caused by the attack." [GOC:add, PMID:11516579, PMID:14506883] synonym: "physiological defense response to nematode" EXACT [] is_a: BFO:0000003 @@ -42987,8 +49372,6 @@ intersection_of: part_of GO:0006955 ! immune response id: GO:0002367 name: cytokine production involved in immune response namespace: biological_process -alt_id: GO:0002374 -alt_id: GO:0002375 def: "The appearance of a cytokine due to biosynthesis or secretion following a cellular stimulus contributing to an immune response, resulting in an increase in its intracellular or extracellular levels." [GO_REF:0000022, GOC:add, ISBN:0781735149] comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select one of the 'regulation' children terms. subset: gocheck_do_not_annotate @@ -43105,8 +49488,6 @@ property_value: RO:0002161 NCBITaxon:4895 id: GO:0002377 name: immunoglobulin production namespace: biological_process -alt_id: GO:0002378 -alt_id: GO:0048305 def: "The appearance of immunoglobulin due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels." [GOC:add, ISBN:0781735149] comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select one of the 'regulation' children terms. subset: gocheck_do_not_annotate @@ -43119,8 +49500,6 @@ is_a: GO:0002440 ! production of molecular mediator of immune response id: GO:0002381 name: immunoglobulin production involved in immunoglobulin-mediated immune response namespace: biological_process -alt_id: GO:0002379 -alt_id: GO:0002380 def: "The appearance of immunoglobulin due to biosynthesis or secretion following a cellular stimulus during an immune response, resulting in an increase in its intracellular or extracellular levels." [GOC:add, ISBN:0781735149, PMID:9185563] comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select one of the 'regulation' children terms. subset: gocheck_do_not_annotate @@ -43153,8 +49532,6 @@ relationship: RO:0002162 NCBITaxon:7742 {all_only="true"} ! in taxon Vertebrata id: GO:0002385 name: mucosal immune response namespace: biological_process -alt_id: GO:0002386 -alt_id: GO:0002422 def: "An immune response taking place in mucosal tissues, including those of the intestinal tract, nasal and upper respiratory tract, and genital tract." [GO_REF:0000022, GOC:jal, ISBN:0781735149] synonym: "immune response in MALT" NARROW [] synonym: "immune response in mucosal-associated lymphoid tissue" NARROW [] @@ -43194,7 +49571,6 @@ is_a: GO:0002388 ! immune response in Peyer's patch is_a: GO:0002394 ! tolerance induction in gut-associated lymphoid tissue intersection_of: GO:0002507 ! tolerance induction intersection_of: occurs_in UBERON:0001211 ! Peyer's patch -relationship: RO:0002162 NCBITaxon:32524 {all_only="true"} ! in taxon Amniota [Term] id: GO:0002394 @@ -43381,8 +49757,6 @@ relationship: part_of GO:0002351 ! serotonin production involved in inflammatory id: GO:0002443 name: leukocyte mediated immunity namespace: biological_process -alt_id: GO:0019723 -alt_id: GO:0042087 def: "Any process involved in the carrying out of an immune response by a leukocyte." [GO_REF:0000022, GOC:add, ISBN:0781735149] synonym: "cell-mediated immune response" RELATED [] synonym: "cellular immune response" RELATED [] @@ -44652,12 +51026,12 @@ synonym: "downregulation of proteolysis associated with antigen processing and p synonym: "inhibition of proteolysis associated with antigen processing and presentation" NARROW [] is_a: GO:0002584 ! negative regulation of antigen processing and presentation of peptide antigen is_a: GO:0002628 ! regulation of proteolysis associated with antigen processing and presentation -is_a: GO:0031330 ! negative regulation of cellular catabolic process is_a: GO:0042177 ! negative regulation of protein catabolic process is_a: GO:1903051 ! negative regulation of proteolysis involved in protein catabolic process intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0002496 ! proteolysis associated with antigen processing and presentation relationship: negatively_regulates GO:0002496 ! proteolysis associated with antigen processing and presentation +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29024" xsd:anyURI [Term] id: GO:0002630 @@ -44671,7 +51045,6 @@ synonym: "up-regulation of proteolysis associated with antigen processing and pr synonym: "upregulation of proteolysis associated with antigen processing and presentation" EXACT [] is_a: GO:0002585 ! positive regulation of antigen processing and presentation of peptide antigen is_a: GO:0002628 ! regulation of proteolysis associated with antigen processing and presentation -is_a: GO:0031331 ! positive regulation of cellular catabolic process is_a: GO:0045732 ! positive regulation of protein catabolic process is_a: GO:1903052 ! positive regulation of proteolysis involved in protein catabolic process intersection_of: GO:0065007 ! biological regulation @@ -44770,8 +51143,6 @@ relationship: positively_regulates GO:0002467 ! germinal center formation id: GO:0002637 name: regulation of immunoglobulin production namespace: biological_process -alt_id: GO:0002640 -alt_id: GO:0051023 def: "Any process that modulates the frequency, rate, or extent of immunoglobulin production." [GOC:add] synonym: "regulation of antibody production" EXACT [] synonym: "regulation of immunoglobulin biosynthetic process" NARROW [] @@ -44785,8 +51156,6 @@ relationship: regulates GO:0002377 ! immunoglobulin production id: GO:0002638 name: negative regulation of immunoglobulin production namespace: biological_process -alt_id: GO:0002641 -alt_id: GO:0051025 def: "Any process that stops, prevents, or reduces the frequency, rate, or extent of immunoglobulin production." [GOC:add] synonym: "down regulation of immunoglobulin production" EXACT [] synonym: "down-regulation of immunoglobulin production" EXACT [] @@ -44804,7 +51173,6 @@ relationship: negatively_regulates GO:0002377 ! immunoglobulin production id: GO:0002639 name: positive regulation of immunoglobulin production namespace: biological_process -alt_id: GO:0002642 alt_id: GO:0051024 def: "Any process that activates or increases the frequency, rate, or extent of immunoglobulin production." [GOC:add] synonym: "activation of immunoglobulin production" NARROW [] @@ -45766,7 +52134,6 @@ relationship: positively_regulates GO:0019724 ! B cell mediated immunity id: GO:0002715 name: regulation of natural killer cell mediated immunity namespace: biological_process -alt_id: GO:0045845 def: "Any process that modulates the frequency, rate, or extent of natural killer cell mediated immunity." [GOC:add] synonym: "regulation of natural killer cell activity" RELATED [] synonym: "regulation of NK cell mediated immunity" EXACT [] @@ -45780,7 +52147,6 @@ relationship: regulates GO:0002228 ! natural killer cell mediated immunity id: GO:0002716 name: negative regulation of natural killer cell mediated immunity namespace: biological_process -alt_id: GO:0030102 def: "Any process that stops, prevents, or reduces the frequency, rate, or extent of natural killer cell mediated immunity." [GOC:add] synonym: "down regulation of natural killer cell mediated immunity" EXACT [] synonym: "down-regulation of natural killer cell mediated immunity" EXACT [] @@ -45800,7 +52166,6 @@ relationship: negatively_regulates GO:0002228 ! natural killer cell mediated imm id: GO:0002717 name: positive regulation of natural killer cell mediated immunity namespace: biological_process -alt_id: GO:0045846 def: "Any process that activates or increases the frequency, rate, or extent of natural killer cell mediated immunity." [GOC:add] synonym: "activation of natural killer cell mediated immunity" NARROW [] synonym: "positive regulation of natural killer cell activity" RELATED [] @@ -45821,8 +52186,6 @@ relationship: positively_regulates GO:0002228 ! natural killer cell mediated imm id: GO:0002718 name: regulation of cytokine production involved in immune response namespace: biological_process -alt_id: GO:0002739 -alt_id: GO:0002742 def: "Any process that modulates the frequency, rate, or extent of cytokine production that contributes to an immune response." [GOC:add] synonym: "regulation of cytokine biosynthetic process involved in immune response" NARROW [] synonym: "regulation of cytokine production during immune response" RELATED [GOC:dph] @@ -45837,8 +52200,6 @@ relationship: regulates GO:0002367 ! cytokine production involved in immune resp id: GO:0002719 name: negative regulation of cytokine production involved in immune response namespace: biological_process -alt_id: GO:0002740 -alt_id: GO:0002743 def: "Any process that stops, prevents, or reduces the frequency, rate, or extent of cytokine production contributing to an immune response." [GOC:add] synonym: "down regulation of cytokine production during immune response" RELATED [] synonym: "down-regulation of cytokine production during immune response" EXACT [] @@ -45858,8 +52219,6 @@ relationship: negatively_regulates GO:0002367 ! cytokine production involved in id: GO:0002720 name: positive regulation of cytokine production involved in immune response namespace: biological_process -alt_id: GO:0002741 -alt_id: GO:0002744 def: "Any process that activates or increases the frequency, rate, or extent of cytokine production that contributes to an immune response." [GOC:add] synonym: "activation of cytokine production during immune response" NARROW [] synonym: "positive regulation of cytokine biosynthetic process involved in immune response" NARROW [] @@ -47044,7 +53403,6 @@ intersection_of: GO:0048856 ! anatomical structure development intersection_of: results_in_development_of UBERON:0005969 ! eye trabecular meshwork relationship: part_of GO:0043010 ! camera-type eye development relationship: results_in_development_of UBERON:0005969 ! eye trabecular meshwork -created_by: hjd creation_date: 2012-04-19T04:50:06Z [Term] @@ -47057,7 +53415,6 @@ intersection_of: GO:0048856 ! anatomical structure development intersection_of: results_in_development_of UBERON:0000304 ! tendon sheath relationship: part_of GO:0035989 ! tendon development relationship: results_in_development_of UBERON:0000304 ! tendon sheath -created_by: hjd creation_date: 2012-04-23T02:11:22Z [Term] @@ -47069,7 +53426,6 @@ is_a: GO:0050673 ! epithelial cell proliferation intersection_of: GO:0008283 ! cell population proliferation intersection_of: acts_on_population_of CL:0002301 ! type B synovial cell relationship: acts_on_population_of CL:0002301 ! type B synovial cell -created_by: hjd creation_date: 2012-11-16T14:25:45Z [Term] @@ -47165,7 +53521,6 @@ is_a: GO:0003013 ! circulatory system process id: GO:0003016 name: respiratory system process namespace: biological_process -alt_id: GO:0010802 def: "A process carried out by the organs or tissues of the respiratory system. The respiratory system is an organ system responsible for respiratory gaseous exchange." [GOC:dph, GOC:mtg_cardio, GOC:tb] subset: goslim_generic synonym: "respiratory gaseous exchange" EXACT [] @@ -47311,7 +53666,6 @@ intersection_of: has_end_location CL:0000223 ! endodermal cell intersection_of: has_start_location CL:0000222 ! mesodermal cell relationship: has_end_location CL:0000223 ! endodermal cell relationship: has_start_location CL:0000222 ! mesodermal cell -created_by: tb creation_date: 2009-09-22T03:07:34Z [Term] @@ -47326,7 +53680,6 @@ intersection_of: has_end_location CL:0000222 ! mesodermal cell intersection_of: has_start_location CL:0000223 ! endodermal cell relationship: has_end_location CL:0000222 ! mesodermal cell relationship: has_start_location CL:0000223 ! endodermal cell -created_by: tb creation_date: 2009-09-22T03:10:29Z [Term] @@ -47341,7 +53694,6 @@ intersection_of: GO:0009653 ! anatomical structure morphogenesis intersection_of: results_in_morphogenesis_of UBERON:0004139 ! cardiogenic plate relationship: part_of GO:0003007 ! heart morphogenesis relationship: results_in_morphogenesis_of UBERON:0004139 ! cardiogenic plate -created_by: tb creation_date: 2009-09-22T04:12:18Z [Term] @@ -47357,7 +53709,6 @@ relationship: part_of GO:0003007 ! heart morphogenesis relationship: part_of GO:0035050 ! embryonic heart tube development relationship: part_of GO:0048562 ! embryonic organ morphogenesis relationship: results_in_morphogenesis_of UBERON:0004141 ! heart tube -created_by: tb creation_date: 2009-09-22T04:21:17Z [Term] @@ -47370,7 +53721,6 @@ intersection_of: GO:0048646 ! anatomical structure formation involved in morphog intersection_of: results_in_formation_of UBERON:0004141 ! heart tube relationship: part_of GO:0003143 ! embryonic heart tube morphogenesis relationship: results_in_formation_of UBERON:0004141 ! heart tube -created_by: tb creation_date: 2009-09-22T04:22:34Z [Term] @@ -47379,7 +53729,6 @@ name: embryonic heart tube formation via epithelial folding namespace: biological_process def: "The process that gives rise to the embryonic heart tube by the cells of the heart field along a linear axis." [GOC:mtg_heart] is_a: GO:0003144 ! embryonic heart tube formation -created_by: tb creation_date: 2009-09-22T04:26:03Z [Term] @@ -47392,7 +53741,6 @@ is_a: GO:0060974 ! cell migration involved in heart formation intersection_of: GO:0001755 ! neural crest cell migration intersection_of: part_of GO:0060914 ! heart formation relationship: part_of GO:0061308 ! cardiac neural crest cell development involved in heart development -created_by: tb creation_date: 2009-09-22T04:29:55Z [Term] @@ -47405,7 +53753,6 @@ intersection_of: GO:0009653 ! anatomical structure morphogenesis intersection_of: results_in_morphogenesis_of UBERON:0004142 ! outflow tract septum relationship: part_of GO:0003151 ! outflow tract morphogenesis relationship: results_in_morphogenesis_of UBERON:0004142 ! outflow tract septum -created_by: tb creation_date: 2009-09-22T07:51:01Z [Term] @@ -47419,7 +53766,6 @@ intersection_of: GO:0009653 ! anatomical structure morphogenesis intersection_of: results_in_morphogenesis_of UBERON:0004666 ! interventricular septum membranous part relationship: part_of GO:0060412 ! ventricular septum morphogenesis relationship: results_in_morphogenesis_of UBERON:0004666 ! interventricular septum membranous part -created_by: tb creation_date: 2009-09-22T07:51:41Z [Term] @@ -47432,7 +53778,6 @@ intersection_of: GO:0009653 ! anatomical structure morphogenesis intersection_of: results_in_morphogenesis_of UBERON:0004667 ! interventricular septum muscular part relationship: part_of GO:0060412 ! ventricular septum morphogenesis relationship: results_in_morphogenesis_of UBERON:0004667 ! interventricular septum muscular part -created_by: tb creation_date: 2009-09-22T07:53:28Z [Term] @@ -47446,7 +53791,6 @@ intersection_of: GO:0009653 ! anatomical structure morphogenesis intersection_of: results_in_morphogenesis_of UBERON:0004145 ! outflow tract relationship: part_of GO:0003007 ! heart morphogenesis relationship: results_in_morphogenesis_of UBERON:0004145 ! outflow tract -created_by: tb creation_date: 2009-09-22T07:59:24Z [Term] @@ -47459,7 +53803,6 @@ is_a: GO:0060571 ! morphogenesis of an epithelial fold intersection_of: GO:0060571 ! morphogenesis of an epithelial fold intersection_of: part_of GO:0003144 ! embryonic heart tube formation relationship: part_of GO:0003145 ! embryonic heart tube formation via epithelial folding -created_by: tb creation_date: 2009-09-23T10:10:24Z [Term] @@ -47471,7 +53814,6 @@ is_a: GO:2000027 ! regulation of animal organ morphogenesis intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0048645 ! animal organ formation relationship: regulates GO:0048645 ! animal organ formation -created_by: tb creation_date: 2009-09-30T11:21:09Z [Term] @@ -47484,7 +53826,6 @@ intersection_of: GO:0048856 ! anatomical structure development intersection_of: results_in_development_of UBERON:0002165 ! endocardium relationship: part_of GO:0007507 ! heart development relationship: results_in_development_of UBERON:0002165 ! endocardium -created_by: dph creation_date: 2009-10-01T12:42:27Z [Term] @@ -47496,7 +53837,6 @@ is_a: GO:0060429 ! epithelium development intersection_of: GO:0048856 ! anatomical structure development intersection_of: results_in_development_of UBERON:0001986 ! endothelium relationship: results_in_development_of UBERON:0001986 ! endothelium -created_by: dph creation_date: 2009-10-01T12:50:57Z [Term] @@ -47509,7 +53849,6 @@ intersection_of: GO:0009653 ! anatomical structure morphogenesis intersection_of: results_in_morphogenesis_of UBERON:0001986 ! endothelium relationship: part_of GO:0003158 ! endothelium development relationship: results_in_morphogenesis_of UBERON:0001986 ! endothelium -created_by: dph creation_date: 2009-10-01T01:34:06Z [Term] @@ -47523,7 +53862,6 @@ intersection_of: GO:0009653 ! anatomical structure morphogenesis intersection_of: results_in_morphogenesis_of UBERON:0002165 ! endocardium relationship: part_of GO:0003157 ! endocardium development relationship: results_in_morphogenesis_of UBERON:0002165 ! endocardium -created_by: dph creation_date: 2009-10-01T01:37:26Z [Term] @@ -47537,7 +53875,6 @@ is_a: GO:0048738 ! cardiac muscle tissue development intersection_of: GO:0048856 ! anatomical structure development intersection_of: results_in_development_of UBERON:0002350 ! conducting system of heart relationship: results_in_development_of UBERON:0002350 ! conducting system of heart -created_by: dph creation_date: 2009-10-01T01:57:16Z [Term] @@ -47551,7 +53888,6 @@ intersection_of: GO:0048856 ! anatomical structure development intersection_of: results_in_development_of UBERON:0002352 ! atrioventricular node relationship: part_of GO:0003161 ! cardiac conduction system development relationship: results_in_development_of UBERON:0002352 ! atrioventricular node -created_by: dph creation_date: 2009-10-01T02:05:13Z [Term] @@ -47567,7 +53903,6 @@ intersection_of: GO:0048856 ! anatomical structure development intersection_of: results_in_development_of UBERON:0002351 ! sinoatrial node relationship: part_of GO:0003161 ! cardiac conduction system development relationship: results_in_development_of UBERON:0002351 ! sinoatrial node -created_by: dph creation_date: 2009-10-01T02:06:09Z [Term] @@ -47580,7 +53915,6 @@ intersection_of: GO:0048856 ! anatomical structure development intersection_of: results_in_development_of UBERON:0004146 ! His-Purkinje system relationship: part_of GO:0003161 ! cardiac conduction system development relationship: results_in_development_of UBERON:0004146 ! His-Purkinje system -created_by: dph creation_date: 2009-10-01T02:07:12Z [Term] @@ -47594,7 +53928,6 @@ intersection_of: GO:0048856 ! anatomical structure development intersection_of: results_in_development_of UBERON:0002354 ! cardiac Purkinje fiber relationship: part_of GO:0003164 ! His-Purkinje system development relationship: results_in_development_of UBERON:0002354 ! cardiac Purkinje fiber -created_by: dph creation_date: 2009-10-01T02:07:50Z [Term] @@ -47608,7 +53941,6 @@ intersection_of: GO:0048856 ! anatomical structure development intersection_of: results_in_development_of UBERON:0002353 ! bundle of His relationship: part_of GO:0003164 ! His-Purkinje system development relationship: results_in_development_of UBERON:0002353 ! bundle of His -created_by: dph creation_date: 2009-10-01T02:08:43Z [Term] @@ -47622,7 +53954,6 @@ intersection_of: GO:0030154 ! cell differentiation intersection_of: results_in_acquisition_of_features_of CL:0010005 ! atrioventricular bundle cell relationship: part_of GO:0003166 ! bundle of His development relationship: results_in_acquisition_of_features_of CL:0010005 ! atrioventricular bundle cell -created_by: dph creation_date: 2009-10-01T02:48:23Z [Term] @@ -47636,7 +53967,6 @@ intersection_of: GO:0030154 ! cell differentiation intersection_of: results_in_acquisition_of_features_of CL:0002068 ! Purkinje myocyte relationship: part_of GO:0003165 ! Purkinje myocyte development relationship: results_in_acquisition_of_features_of CL:0002068 ! Purkinje myocyte -created_by: dph creation_date: 2009-10-01T02:49:54Z [Term] @@ -47649,7 +53979,6 @@ is_a: GO:0060977 ! coronary vasculature morphogenesis intersection_of: GO:0009653 ! anatomical structure morphogenesis intersection_of: results_in_morphogenesis_of UBERON:0004148 ! cardiac vein relationship: results_in_morphogenesis_of UBERON:0004148 ! cardiac vein -created_by: dph creation_date: 2009-10-08T10:45:41Z [Term] @@ -47663,7 +53992,6 @@ intersection_of: GO:0048856 ! anatomical structure development intersection_of: results_in_development_of UBERON:0000946 ! cardiac valve relationship: part_of GO:0007507 ! heart development relationship: results_in_development_of UBERON:0000946 ! cardiac valve -created_by: dph creation_date: 2009-10-08T10:50:09Z [Term] @@ -47679,7 +54007,6 @@ intersection_of: GO:0009653 ! anatomical structure morphogenesis intersection_of: results_in_morphogenesis_of UBERON:0000946 ! cardiac valve relationship: part_of GO:0003170 ! heart valve development relationship: results_in_morphogenesis_of UBERON:0000946 ! cardiac valve -created_by: dph creation_date: 2009-10-08T11:23:48Z [Term] @@ -47693,7 +54020,6 @@ intersection_of: GO:0048646 ! anatomical structure formation involved in morphog intersection_of: results_in_formation_of UBERON:0000946 ! cardiac valve relationship: part_of GO:0003179 ! heart valve morphogenesis relationship: results_in_formation_of UBERON:0000946 ! cardiac valve -created_by: dph creation_date: 2009-10-08T12:20:15Z [Term] @@ -47706,7 +54032,6 @@ intersection_of: GO:0048856 ! anatomical structure development intersection_of: results_in_development_of UBERON:0002062 ! endocardial cushion relationship: part_of GO:0007507 ! heart development relationship: results_in_development_of UBERON:0002062 ! endocardial cushion -created_by: dph creation_date: 2009-10-08T01:17:43Z [Term] @@ -47720,7 +54045,6 @@ intersection_of: results_in_morphogenesis_of UBERON:0002062 ! endocardial cushio relationship: part_of GO:0003007 ! heart morphogenesis relationship: part_of GO:0003197 ! endocardial cushion development relationship: results_in_morphogenesis_of UBERON:0002062 ! endocardial cushion -created_by: dph creation_date: 2009-10-08T01:43:22Z [Term] @@ -47734,7 +54058,6 @@ intersection_of: GO:0048856 ! anatomical structure development intersection_of: results_in_development_of UBERON:0004292 ! cardiac skeleton relationship: part_of GO:0007507 ! heart development relationship: results_in_development_of UBERON:0004292 ! cardiac skeleton -created_by: dph creation_date: 2009-10-13T09:05:04Z [Term] @@ -47747,7 +54070,6 @@ intersection_of: GO:0048856 ! anatomical structure development intersection_of: results_in_development_of UBERON:0004151 ! cardiac chamber relationship: part_of GO:0007507 ! heart development relationship: results_in_development_of UBERON:0004151 ! cardiac chamber -created_by: dph creation_date: 2009-10-13T09:11:18Z [Term] @@ -47763,7 +54085,6 @@ intersection_of: results_in_morphogenesis_of UBERON:0004151 ! cardiac chamber relationship: part_of GO:0003007 ! heart morphogenesis relationship: part_of GO:0003205 ! cardiac chamber development relationship: results_in_morphogenesis_of UBERON:0004151 ! cardiac chamber -created_by: dph creation_date: 2009-10-13T09:14:51Z [Term] @@ -47778,7 +54099,6 @@ intersection_of: GO:0048646 ! anatomical structure formation involved in morphog intersection_of: results_in_formation_of UBERON:0004151 ! cardiac chamber relationship: part_of GO:0003206 ! cardiac chamber morphogenesis relationship: results_in_formation_of UBERON:0004151 ! cardiac chamber -created_by: dph creation_date: 2009-10-13T09:29:13Z [Term] @@ -47791,7 +54111,6 @@ intersection_of: GO:0009653 ! anatomical structure morphogenesis intersection_of: results_in_morphogenesis_of UBERON:0002082 ! cardiac ventricle relationship: part_of GO:0003231 ! cardiac ventricle development relationship: results_in_morphogenesis_of UBERON:0002082 ! cardiac ventricle -created_by: dph creation_date: 2009-10-13T09:38:44Z [Term] @@ -47804,7 +54123,6 @@ intersection_of: GO:0009653 ! anatomical structure morphogenesis intersection_of: results_in_morphogenesis_of UBERON:0002081 ! cardiac atrium relationship: part_of GO:0003230 ! cardiac atrium development relationship: results_in_morphogenesis_of UBERON:0002081 ! cardiac atrium -created_by: dph creation_date: 2009-10-13T09:39:44Z [Term] @@ -47817,7 +54135,6 @@ intersection_of: GO:0048646 ! anatomical structure formation involved in morphog intersection_of: results_in_formation_of UBERON:0002081 ! cardiac atrium relationship: part_of GO:0003209 ! cardiac atrium morphogenesis relationship: results_in_formation_of UBERON:0002081 ! cardiac atrium -created_by: dph creation_date: 2009-10-13T09:44:25Z [Term] @@ -47830,7 +54147,6 @@ intersection_of: GO:0048646 ! anatomical structure formation involved in morphog intersection_of: results_in_formation_of UBERON:0002082 ! cardiac ventricle relationship: part_of GO:0003208 ! cardiac ventricle morphogenesis relationship: results_in_formation_of UBERON:0002082 ! cardiac ventricle -created_by: dph creation_date: 2009-10-13T09:46:27Z [Term] @@ -47842,7 +54158,6 @@ is_a: GO:0003209 ! cardiac atrium morphogenesis intersection_of: GO:0009653 ! anatomical structure morphogenesis intersection_of: results_in_morphogenesis_of UBERON:0002079 ! left cardiac atrium relationship: results_in_morphogenesis_of UBERON:0002079 ! left cardiac atrium -created_by: dph creation_date: 2009-10-13T09:48:16Z [Term] @@ -47854,7 +54169,6 @@ is_a: GO:0003209 ! cardiac atrium morphogenesis intersection_of: GO:0009653 ! anatomical structure morphogenesis intersection_of: results_in_morphogenesis_of UBERON:0002078 ! right cardiac atrium relationship: results_in_morphogenesis_of UBERON:0002078 ! right cardiac atrium -created_by: dph creation_date: 2009-10-13T09:49:03Z [Term] @@ -47866,7 +54180,6 @@ is_a: GO:0003208 ! cardiac ventricle morphogenesis intersection_of: GO:0009653 ! anatomical structure morphogenesis intersection_of: results_in_morphogenesis_of UBERON:0002084 ! heart left ventricle relationship: results_in_morphogenesis_of UBERON:0002084 ! heart left ventricle -created_by: dph creation_date: 2009-10-13T09:50:08Z [Term] @@ -47878,7 +54191,6 @@ is_a: GO:0003208 ! cardiac ventricle morphogenesis intersection_of: GO:0009653 ! anatomical structure morphogenesis intersection_of: results_in_morphogenesis_of UBERON:0002080 ! heart right ventricle relationship: results_in_morphogenesis_of UBERON:0002080 ! heart right ventricle -created_by: dph creation_date: 2009-10-13T09:50:57Z [Term] @@ -47891,7 +54203,6 @@ intersection_of: GO:0048646 ! anatomical structure formation involved in morphog intersection_of: results_in_formation_of UBERON:0002079 ! left cardiac atrium relationship: part_of GO:0003212 ! cardiac left atrium morphogenesis relationship: results_in_formation_of UBERON:0002079 ! left cardiac atrium -created_by: dph creation_date: 2009-10-13T09:52:31Z [Term] @@ -47904,7 +54215,6 @@ intersection_of: GO:0048646 ! anatomical structure formation involved in morphog intersection_of: results_in_formation_of UBERON:0002078 ! right cardiac atrium relationship: part_of GO:0003213 ! cardiac right atrium morphogenesis relationship: results_in_formation_of UBERON:0002078 ! right cardiac atrium -created_by: dph creation_date: 2009-10-13T09:53:12Z [Term] @@ -47917,7 +54227,6 @@ intersection_of: GO:0048646 ! anatomical structure formation involved in morphog intersection_of: results_in_formation_of UBERON:0002084 ! heart left ventricle relationship: part_of GO:0003214 ! cardiac left ventricle morphogenesis relationship: results_in_formation_of UBERON:0002084 ! heart left ventricle -created_by: dph creation_date: 2009-10-13T09:54:33Z [Term] @@ -47930,7 +54239,6 @@ intersection_of: GO:0048646 ! anatomical structure formation involved in morphog intersection_of: results_in_formation_of UBERON:0002080 ! heart right ventricle relationship: part_of GO:0003215 ! cardiac right ventricle morphogenesis relationship: results_in_formation_of UBERON:0002080 ! heart right ventricle -created_by: dph creation_date: 2009-10-13T09:55:38Z [Term] @@ -47944,7 +54252,6 @@ intersection_of: GO:0009653 ! anatomical structure morphogenesis intersection_of: results_in_morphogenesis_of UBERON:0003382 ! cardiac muscle of left ventricle relationship: part_of GO:0003214 ! cardiac left ventricle morphogenesis relationship: results_in_morphogenesis_of UBERON:0003382 ! cardiac muscle of left ventricle -created_by: dph creation_date: 2009-10-13T10:18:05Z [Term] @@ -47958,7 +54265,6 @@ intersection_of: GO:0009653 ! anatomical structure morphogenesis intersection_of: results_in_morphogenesis_of UBERON:0003381 ! cardiac muscle of right ventricle relationship: part_of GO:0003215 ! cardiac right ventricle morphogenesis relationship: results_in_morphogenesis_of UBERON:0003381 ! cardiac muscle of right ventricle -created_by: dph creation_date: 2009-10-13T10:26:33Z [Term] @@ -47972,7 +54278,6 @@ is_a: GO:0061384 ! heart trabecula morphogenesis intersection_of: GO:0009653 ! anatomical structure morphogenesis intersection_of: results_in_morphogenesis_of UBERON:0004126 ! trabecular layer of ventricle relationship: results_in_morphogenesis_of UBERON:0004126 ! trabecular layer of ventricle -created_by: dph creation_date: 2009-10-13T10:33:00Z [Term] @@ -47985,7 +54290,6 @@ is_a: GO:0003222 ! ventricular trabecula myocardium morphogenesis intersection_of: GO:0009653 ! anatomical structure morphogenesis intersection_of: results_in_morphogenesis_of UBERON:0005064 ! left ventricular trabecular myocardium relationship: results_in_morphogenesis_of UBERON:0005064 ! left ventricular trabecular myocardium -created_by: dph creation_date: 2009-10-13T10:45:09Z [Term] @@ -47998,7 +54302,6 @@ is_a: GO:0003222 ! ventricular trabecula myocardium morphogenesis intersection_of: GO:0009653 ! anatomical structure morphogenesis intersection_of: results_in_morphogenesis_of UBERON:0005066 ! right ventricular trabecular myocardium relationship: results_in_morphogenesis_of UBERON:0005066 ! right ventricular trabecular myocardium -created_by: dph creation_date: 2009-10-13T10:50:59Z [Term] @@ -48012,7 +54315,6 @@ intersection_of: GO:0048856 ! anatomical structure development intersection_of: results_in_development_of UBERON:0004490 ! cardiac muscle tissue of atrium relationship: results_in_development_of UBERON:0004490 ! cardiac muscle tissue of atrium property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/22614" xsd:anyURI -created_by: dph creation_date: 2009-10-13T10:53:18Z [Term] @@ -48025,7 +54327,6 @@ is_a: GO:0048738 ! cardiac muscle tissue development intersection_of: GO:0048856 ! anatomical structure development intersection_of: results_in_development_of UBERON:0018649 ! cardiac muscle tissue of ventricle relationship: results_in_development_of UBERON:0018649 ! cardiac muscle tissue of ventricle -created_by: dph creation_date: 2009-10-13T10:56:01Z [Term] @@ -48037,7 +54338,6 @@ is_a: GO:0003205 ! cardiac chamber development intersection_of: GO:0048856 ! anatomical structure development intersection_of: results_in_development_of UBERON:0002081 ! cardiac atrium relationship: results_in_development_of UBERON:0002081 ! cardiac atrium -created_by: dph creation_date: 2009-10-13T11:02:07Z [Term] @@ -48049,7 +54349,6 @@ is_a: GO:0003205 ! cardiac chamber development intersection_of: GO:0048856 ! anatomical structure development intersection_of: results_in_development_of UBERON:0002082 ! cardiac ventricle relationship: results_in_development_of UBERON:0002082 ! cardiac ventricle -created_by: dph creation_date: 2009-10-13T11:03:16Z [Term] @@ -48061,7 +54360,6 @@ is_a: GO:0003205 ! cardiac chamber development intersection_of: GO:0048856 ! anatomical structure development intersection_of: results_in_development_of UBERON:0002063 ! sinus venosus relationship: results_in_development_of UBERON:0002063 ! sinus venosus -created_by: dph creation_date: 2009-10-13T11:12:34Z [Term] @@ -48074,7 +54372,6 @@ intersection_of: GO:0009653 ! anatomical structure morphogenesis intersection_of: results_in_morphogenesis_of UBERON:0002063 ! sinus venosus relationship: part_of GO:0003235 ! sinus venosus development relationship: results_in_morphogenesis_of UBERON:0002063 ! sinus venosus -created_by: dph creation_date: 2009-10-13T11:16:52Z [Term] @@ -48087,7 +54384,6 @@ intersection_of: GO:0048646 ! anatomical structure formation involved in morphog intersection_of: results_in_formation_of UBERON:0002063 ! sinus venosus relationship: part_of GO:0003236 ! sinus venosus morphogenesis relationship: results_in_formation_of UBERON:0002063 ! sinus venosus -created_by: dph creation_date: 2009-10-13T11:18:34Z [Term] @@ -48099,7 +54395,6 @@ is_a: GO:0003205 ! cardiac chamber development intersection_of: GO:0048856 ! anatomical structure development intersection_of: results_in_development_of UBERON:0003983 ! conus arteriosus relationship: results_in_development_of UBERON:0003983 ! conus arteriosus -created_by: dph creation_date: 2009-10-13T11:20:57Z [Term] @@ -48112,7 +54407,6 @@ intersection_of: GO:0009653 ! anatomical structure morphogenesis intersection_of: results_in_morphogenesis_of UBERON:0003983 ! conus arteriosus relationship: part_of GO:0003238 ! conus arteriosus development relationship: results_in_morphogenesis_of UBERON:0003983 ! conus arteriosus -created_by: dph creation_date: 2009-10-13T11:25:04Z [Term] @@ -48125,7 +54419,6 @@ intersection_of: GO:0048646 ! anatomical structure formation involved in morphog intersection_of: results_in_formation_of UBERON:0003983 ! conus arteriosus relationship: part_of GO:0003239 ! conus arteriosus morphogenesis relationship: results_in_formation_of UBERON:0003983 ! conus arteriosus -created_by: dph creation_date: 2009-10-13T11:25:47Z [Term] @@ -48138,7 +54431,6 @@ intersection_of: GO:0040007 ! growth intersection_of: part_of GO:0003007 ! heart morphogenesis relationship: part_of GO:0003007 ! heart morphogenesis relationship: part_of GO:0060419 ! heart growth -created_by: dph creation_date: 2009-10-13T11:28:46Z [Term] @@ -48151,7 +54443,6 @@ is_a: GO:0055017 ! cardiac muscle tissue growth intersection_of: GO:0055017 ! cardiac muscle tissue growth intersection_of: part_of GO:0003007 ! heart morphogenesis relationship: part_of GO:0055008 ! cardiac muscle tissue morphogenesis -created_by: dph creation_date: 2009-10-13T11:44:21Z [Term] @@ -48166,7 +54457,6 @@ intersection_of: results_in_growth_of UBERON:0006966 ! coronary capillary relationship: part_of GO:0060419 ! heart growth relationship: part_of GO:0060976 ! coronary vasculature development relationship: results_in_growth_of UBERON:0006966 ! coronary capillary -created_by: dph creation_date: 2009-10-13T11:53:12Z [Term] @@ -48179,7 +54469,6 @@ is_a: GO:2000793 ! cell proliferation involved in heart valve development intersection_of: GO:0008283 ! cell population proliferation intersection_of: part_of GO:0003179 ! heart valve morphogenesis relationship: part_of GO:0003179 ! heart valve morphogenesis -created_by: dph creation_date: 2009-10-13T01:59:19Z [Term] @@ -48191,7 +54480,6 @@ is_a: GO:2000136 ! regulation of cell proliferation involved in heart morphogene intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0003249 ! cell proliferation involved in heart valve morphogenesis relationship: regulates GO:0003249 ! cell proliferation involved in heart valve morphogenesis -created_by: dph creation_date: 2009-10-13T02:03:42Z [Term] @@ -48204,7 +54492,6 @@ is_a: GO:2000138 ! positive regulation of cell proliferation involved in heart m intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0003249 ! cell proliferation involved in heart valve morphogenesis relationship: positively_regulates GO:0003249 ! cell proliferation involved in heart valve morphogenesis -created_by: dph creation_date: 2009-10-13T02:07:20Z [Term] @@ -48217,7 +54504,6 @@ is_a: GO:2000137 ! negative regulation of cell proliferation involved in heart m intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0003249 ! cell proliferation involved in heart valve morphogenesis relationship: negatively_regulates GO:0003249 ! cell proliferation involved in heart valve morphogenesis -created_by: dph creation_date: 2009-10-13T02:10:39Z [Term] @@ -48230,7 +54516,6 @@ is_a: GO:0060973 ! cell migration involved in heart development intersection_of: GO:0001755 ! neural crest cell migration intersection_of: part_of GO:0003151 ! outflow tract morphogenesis relationship: part_of GO:0061309 ! cardiac neural crest cell development involved in outflow tract morphogenesis -created_by: dph creation_date: 2009-10-13T02:14:16Z [Term] @@ -48243,7 +54528,6 @@ is_a: GO:0060974 ! cell migration involved in heart formation intersection_of: GO:0016477 ! cell migration intersection_of: results_in_movement_of CL:0002664 ! cardioblast relationship: results_in_movement_of CL:0002664 ! cardioblast -created_by: dph creation_date: 2009-10-15T01:52:25Z [Term] @@ -48257,7 +54541,6 @@ intersection_of: GO:0048646 ! anatomical structure formation involved in morphog intersection_of: results_in_formation_of UBERON:0002062 ! endocardial cushion relationship: part_of GO:0003203 ! endocardial cushion morphogenesis relationship: results_in_formation_of UBERON:0002062 ! endocardial cushion -created_by: dph creation_date: 2009-10-20T08:53:19Z [Term] @@ -48269,7 +54552,6 @@ is_a: GO:0060973 ! cell migration involved in heart development intersection_of: GO:0016477 ! cell migration intersection_of: part_of GO:0003272 ! endocardial cushion formation relationship: part_of GO:0003272 ! endocardial cushion formation -created_by: dph creation_date: 2009-10-20T09:08:44Z [Term] @@ -48282,7 +54564,6 @@ is_a: GO:0003278 ! apoptotic process involved in heart morphogenesis intersection_of: GO:0006915 ! apoptotic process intersection_of: part_of GO:0003151 ! outflow tract morphogenesis relationship: part_of GO:0003151 ! outflow tract morphogenesis -created_by: dph creation_date: 2009-10-20T09:30:01Z [Term] @@ -48295,7 +54576,6 @@ is_a: GO:0003278 ! apoptotic process involved in heart morphogenesis intersection_of: GO:0006915 ! apoptotic process intersection_of: part_of GO:0003179 ! heart valve morphogenesis relationship: part_of GO:0003179 ! heart valve morphogenesis -created_by: dph creation_date: 2009-10-20T09:34:29Z [Term] @@ -48308,7 +54588,6 @@ is_a: GO:0003278 ! apoptotic process involved in heart morphogenesis intersection_of: GO:0006915 ! apoptotic process intersection_of: part_of GO:0003203 ! endocardial cushion morphogenesis relationship: part_of GO:0003203 ! endocardial cushion morphogenesis -created_by: dph creation_date: 2009-10-20T09:37:03Z [Term] @@ -48321,7 +54600,6 @@ is_a: GO:0060561 ! apoptotic process involved in morphogenesis intersection_of: GO:0006915 ! apoptotic process intersection_of: part_of GO:0003007 ! heart morphogenesis relationship: part_of GO:0003007 ! heart morphogenesis -created_by: dph creation_date: 2009-10-20T09:40:22Z [Term] @@ -48335,7 +54613,6 @@ intersection_of: GO:0048856 ! anatomical structure development intersection_of: results_in_development_of UBERON:0002099 ! cardiac septum relationship: part_of GO:0003205 ! cardiac chamber development relationship: results_in_development_of UBERON:0002099 ! cardiac septum -created_by: dph creation_date: 2009-10-20T09:45:13Z [Term] @@ -48350,7 +54627,6 @@ intersection_of: GO:0048856 ! anatomical structure development intersection_of: results_in_development_of UBERON:0002094 ! interventricular septum relationship: part_of GO:0003231 ! cardiac ventricle development relationship: results_in_development_of UBERON:0002094 ! interventricular septum -created_by: dph creation_date: 2009-10-20T10:04:51Z [Term] @@ -48363,7 +54639,6 @@ intersection_of: GO:0048856 ! anatomical structure development intersection_of: results_in_development_of UBERON:0002085 ! interatrial septum relationship: part_of GO:0003230 ! cardiac atrium development relationship: results_in_development_of UBERON:0002085 ! interatrial septum -created_by: dph creation_date: 2009-10-20T10:10:38Z [Term] @@ -48376,7 +54651,6 @@ intersection_of: GO:0030154 ! cell differentiation intersection_of: results_in_acquisition_of_features_of CL:2000022 ! cardiac septum cell relationship: part_of GO:0003279 ! cardiac septum development relationship: results_in_acquisition_of_features_of CL:2000022 ! cardiac septum cell -created_by: dph creation_date: 2009-10-20T11:03:46Z [Term] @@ -48389,7 +54663,6 @@ intersection_of: GO:0030154 ! cell differentiation intersection_of: results_in_acquisition_of_features_of CL:1000147 ! cardiac valve cell relationship: part_of GO:0003170 ! heart valve development relationship: results_in_acquisition_of_features_of CL:1000147 ! cardiac valve cell -created_by: dph creation_date: 2009-10-20T11:06:46Z [Term] @@ -48398,7 +54671,6 @@ name: physiological muscle hypertrophy namespace: biological_process def: "The enlargement or overgrowth of all or part of a muscle organ or tissue due to an increase in the size of its muscle cells. Physiological hypertrophy is a normal process during development." [GOC:mtg_heart] is_a: GO:0014896 ! muscle hypertrophy -created_by: dph creation_date: 2009-10-22T09:24:51Z [Term] @@ -48407,7 +54679,6 @@ name: cardiac muscle hypertrophy namespace: biological_process def: "The enlargement or overgrowth of all or part of the heart muscle due to an increase in size of cardiac muscle cells without cell division." [GOC:mtg_heart] is_a: GO:0014897 ! striated muscle hypertrophy -created_by: dph creation_date: 2009-10-22T10:33:56Z [Term] @@ -48418,7 +54689,6 @@ def: "The enlargement or overgrowth of all or part of the heart muscle due to an is_a: GO:0003298 ! physiological muscle hypertrophy is_a: GO:0003300 ! cardiac muscle hypertrophy relationship: part_of GO:0055017 ! cardiac muscle tissue growth -created_by: dph creation_date: 2009-10-22T10:38:10Z [Term] @@ -48433,7 +54703,6 @@ intersection_of: GO:0030154 ! cell differentiation intersection_of: results_in_acquisition_of_features_of CL:0000169 ! type B pancreatic cell relationship: part_of GO:0031018 ! endocrine pancreas development relationship: results_in_acquisition_of_features_of CL:0000169 ! type B pancreatic cell -created_by: dph creation_date: 2009-10-26T09:27:23Z [Term] @@ -48447,7 +54716,6 @@ intersection_of: GO:0030154 ! cell differentiation intersection_of: results_in_acquisition_of_features_of CL:0000171 ! pancreatic A cell relationship: part_of GO:0031018 ! endocrine pancreas development relationship: results_in_acquisition_of_features_of CL:0000171 ! pancreatic A cell -created_by: dph creation_date: 2009-10-26T09:28:05Z [Term] @@ -48457,11 +54725,11 @@ namespace: biological_process def: "The process in which relatively unspecialized cells acquire specialized structural and functional features that characterize a pancreatic delta cell. A delta cell is a cell of the pancreas that produces somatostatin." [GOC:dph, PMID:11076772] synonym: "pancreatic delta cell differentiation" EXACT [GOC:dph] is_a: GO:0035883 ! enteroendocrine cell differentiation +is_a: GO:0061101 ! neuroendocrine cell differentiation intersection_of: GO:0030154 ! cell differentiation intersection_of: results_in_acquisition_of_features_of CL:0000173 ! pancreatic D cell relationship: part_of GO:0031018 ! endocrine pancreas development relationship: results_in_acquisition_of_features_of CL:0000173 ! pancreatic D cell -created_by: dph creation_date: 2009-10-26T09:30:27Z [Term] @@ -48475,7 +54743,6 @@ intersection_of: GO:0030154 ! cell differentiation intersection_of: results_in_acquisition_of_features_of CL:0002275 ! pancreatic PP cell relationship: part_of GO:0031018 ! endocrine pancreas development relationship: results_in_acquisition_of_features_of CL:0002275 ! pancreatic PP cell -created_by: dph creation_date: 2009-10-26T09:32:32Z [Term] @@ -48489,7 +54756,6 @@ intersection_of: GO:0048856 ! anatomical structure development intersection_of: results_in_development_of UBERON:0004291 ! heart rudiment relationship: part_of GO:0035050 ! embryonic heart tube development relationship: results_in_development_of UBERON:0004291 ! heart rudiment -created_by: dph creation_date: 2009-10-27T08:32:40Z [Term] @@ -48502,9 +54768,10 @@ is_a: GO:0002009 ! morphogenesis of an epithelium is_a: GO:0048598 ! embryonic morphogenesis intersection_of: GO:0009653 ! anatomical structure morphogenesis intersection_of: results_in_morphogenesis_of UBERON:0004291 ! heart rudiment +relationship: part_of GO:0003007 ! heart morphogenesis relationship: part_of GO:0003313 ! heart rudiment development relationship: results_in_morphogenesis_of UBERON:0004291 ! heart rudiment -created_by: dph +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/22938" xsd:anyURI creation_date: 2009-10-27T08:38:04Z [Term] @@ -48519,7 +54786,6 @@ intersection_of: GO:0048646 ! anatomical structure formation involved in morphog intersection_of: results_in_formation_of UBERON:0004291 ! heart rudiment relationship: part_of GO:0003314 ! heart rudiment morphogenesis relationship: results_in_formation_of UBERON:0004291 ! heart rudiment -created_by: dph creation_date: 2009-10-27T08:43:37Z [Term] @@ -48528,12 +54794,11 @@ name: pancreatic A cell development namespace: biological_process def: "The process whose specific outcome is the progression of a pancreatic A cell over time, from its formation to the mature structure. A pancreatic A cell is a cell in the pancreas that secretes glucagon." [GOC:dph] synonym: "pancreatic alpha cell development" EXACT [GOC:dph] -is_a: GO:0002068 ! glandular epithelial cell development +is_a: GO:0002064 ! epithelial cell development intersection_of: GO:0032502 ! developmental process intersection_of: results_in_development_of CL:0000171 ! pancreatic A cell relationship: part_of GO:0003310 ! pancreatic A cell differentiation relationship: results_in_development_of CL:0000171 ! pancreatic A cell -created_by: dph creation_date: 2009-11-02T08:13:55Z [Term] @@ -48543,12 +54808,11 @@ namespace: biological_process def: "The process whose specific outcome is the progression of a type B pancreatic cell over time, from its formation to the mature structure. A type B pancreatic cell is a cell located towards center of the islets of Langerhans that secretes insulin." [CL:0000169, GOC:dph] synonym: "pancreatic B cell development" EXACT [GOC:mah] synonym: "pancreatic beta cell development" EXACT [GOC:dph] -is_a: GO:0002068 ! glandular epithelial cell development +is_a: GO:0002064 ! epithelial cell development intersection_of: GO:0032502 ! developmental process intersection_of: results_in_development_of CL:0000169 ! type B pancreatic cell relationship: part_of GO:0003309 ! type B pancreatic cell differentiation relationship: results_in_development_of CL:0000169 ! type B pancreatic cell -created_by: dph creation_date: 2009-11-02T08:20:11Z [Term] @@ -48557,12 +54821,12 @@ name: pancreatic D cell development namespace: biological_process def: "The process whose specific outcome is the progression of a pancreatic delta cell over time, from its formation to the mature structure. A delta cell is a cell of the pancreas that produces somatostatin." [GOC:dph] synonym: "pancreatic delta cell development" EXACT [GOC:dph] -is_a: GO:0002068 ! glandular epithelial cell development +is_a: GO:0002066 ! columnar/cuboidal epithelial cell development +is_a: GO:0048666 ! neuron development intersection_of: GO:0032502 ! developmental process intersection_of: results_in_development_of CL:0000173 ! pancreatic D cell relationship: part_of GO:0003311 ! pancreatic D cell differentiation relationship: results_in_development_of CL:0000173 ! pancreatic D cell -created_by: dph creation_date: 2009-11-02T08:23:26Z [Term] @@ -48570,12 +54834,11 @@ id: GO:0003325 name: pancreatic PP cell development namespace: biological_process def: "The process whose specific outcome is the progression of a pancreatic PP cell over time, from its formation to the mature structure. A pancreatic polypeptide-producing cell is a cell in the pancreas that produces pancreatic polypeptide." [GOC:dph] -is_a: GO:0002068 ! glandular epithelial cell development +is_a: GO:0002064 ! epithelial cell development intersection_of: GO:0048468 ! cell development intersection_of: results_in_development_of CL:0002275 ! pancreatic PP cell relationship: part_of GO:0003312 ! pancreatic PP cell differentiation relationship: results_in_development_of CL:0002275 ! pancreatic PP cell -created_by: dph creation_date: 2009-11-02T08:25:03Z [Term] @@ -48588,7 +54851,6 @@ is_a: GO:1903530 ! regulation of secretion by cell intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0070278 ! extracellular matrix constituent secretion relationship: regulates GO:0070278 ! extracellular matrix constituent secretion -created_by: dph creation_date: 2009-11-02T02:07:40Z [Term] @@ -48602,7 +54864,6 @@ is_a: GO:1903532 ! positive regulation of secretion by cell intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0070278 ! extracellular matrix constituent secretion relationship: positively_regulates GO:0070278 ! extracellular matrix constituent secretion -created_by: dph creation_date: 2009-11-02T02:11:22Z [Term] @@ -48616,7 +54877,6 @@ is_a: GO:1903531 ! negative regulation of secretion by cell intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0070278 ! extracellular matrix constituent secretion relationship: negatively_regulates GO:0070278 ! extracellular matrix constituent secretion -created_by: dph creation_date: 2009-11-02T02:13:49Z [Term] @@ -48631,7 +54891,6 @@ is_a: GO:0055085 ! transmembrane transport intersection_of: GO:0006810 ! transport intersection_of: has_primary_input CHEBI:35238 intersection_of: results_in_transport_across GO:0016020 ! membrane -created_by: dph creation_date: 2009-11-02T02:36:11Z [Term] @@ -48644,7 +54903,6 @@ intersection_of: GO:0032502 ! developmental process intersection_of: results_in_development_of CL:0000312 ! keratinocyte relationship: part_of GO:0030216 ! keratinocyte differentiation relationship: results_in_development_of CL:0000312 ! keratinocyte -created_by: dph creation_date: 2009-11-24T08:55:57Z [Term] @@ -48657,7 +54915,6 @@ intersection_of: GO:0048856 ! anatomical structure development intersection_of: results_in_development_of CL:0002153 ! corneocyte relationship: part_of GO:0003334 ! keratinocyte development relationship: results_in_development_of CL:0002153 ! corneocyte -created_by: dph creation_date: 2009-11-24T09:01:02Z [Term] @@ -48672,7 +54929,6 @@ is_a: GO:0072202 ! cell differentiation involved in metanephros development intersection_of: GO:0060231 ! mesenchymal to epithelial transition intersection_of: part_of GO:0003338 ! metanephros morphogenesis relationship: part_of GO:0072283 ! metanephric renal vesicle morphogenesis -created_by: dph creation_date: 2009-11-24T09:29:49Z [Term] @@ -48685,7 +54941,6 @@ intersection_of: GO:0009653 ! anatomical structure morphogenesis intersection_of: results_in_morphogenesis_of UBERON:0000081 ! metanephros relationship: part_of GO:0001656 ! metanephros development relationship: results_in_morphogenesis_of UBERON:0000081 ! metanephros -created_by: dph creation_date: 2009-11-24T09:32:09Z [Term] @@ -48697,7 +54952,6 @@ is_a: GO:2000696 ! regulation of epithelial cell differentiation involved in kid intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0003337 ! mesenchymal to epithelial transition involved in metanephros morphogenesis relationship: regulates GO:0003337 ! mesenchymal to epithelial transition involved in metanephros morphogenesis -created_by: dph creation_date: 2009-11-24T09:43:04Z [Term] @@ -48710,14 +54964,12 @@ is_a: GO:2000697 ! negative regulation of epithelial cell differentiation involv intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0003337 ! mesenchymal to epithelial transition involved in metanephros morphogenesis relationship: negatively_regulates GO:0003337 ! mesenchymal to epithelial transition involved in metanephros morphogenesis -created_by: dph creation_date: 2009-11-24T09:46:12Z [Term] id: GO:0003341 name: cilium movement namespace: biological_process -alt_id: GO:0036142 def: "The directed, self-propelled movement of a cilium." [GOC:dph, GOC:jl] comment: Note that we deem cilium and microtubule-based flagellum to be equivalent. synonym: "ciliary motility" RELATED [] @@ -48741,7 +54993,6 @@ property_value: RO:0002161 NCBITaxon:3398 property_value: RO:0002161 NCBITaxon:4890 property_value: RO:0002161 NCBITaxon:5782 property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/19809" xsd:anyURI -created_by: dph creation_date: 2009-11-24T09:56:26Z [Term] @@ -48754,7 +55005,6 @@ intersection_of: GO:0048856 ! anatomical structure development intersection_of: results_in_development_of UBERON:0004160 ! proepicardium relationship: part_of GO:0003343 ! septum transversum development relationship: results_in_development_of UBERON:0004160 ! proepicardium -created_by: dph creation_date: 2009-12-01T10:30:17Z [Term] @@ -48766,7 +55016,6 @@ is_a: GO:0060485 ! mesenchyme development intersection_of: GO:0048856 ! anatomical structure development intersection_of: results_in_development_of UBERON:0004161 ! septum transversum relationship: results_in_development_of UBERON:0004161 ! septum transversum -created_by: dph creation_date: 2009-12-01T10:40:17Z [Term] @@ -48780,7 +55029,6 @@ intersection_of: GO:0009653 ! anatomical structure morphogenesis intersection_of: results_in_morphogenesis_of UBERON:0002407 ! pericardium relationship: part_of GO:0060039 ! pericardium development relationship: results_in_morphogenesis_of UBERON:0002407 ! pericardium -created_by: dph creation_date: 2009-12-01T10:46:34Z [Term] @@ -48793,14 +55041,12 @@ is_a: GO:0045446 ! endothelial cell differentiation intersection_of: GO:0030154 ! cell differentiation intersection_of: results_in_acquisition_of_features_of CL:0010008 ! cardiac endothelial cell relationship: results_in_acquisition_of_features_of CL:0010008 ! cardiac endothelial cell -created_by: dph creation_date: 2009-12-01T11:12:05Z [Term] id: GO:0003352 name: regulation of cilium movement namespace: biological_process -alt_id: GO:1900172 def: "Any process that modulates the rate, frequency, or extent of cilium movement, the directed, self-propelled movement of a cilium." [GOC:dph] comment: Note that we deem cilium and microtubule-based flagellum to be equivalent. synonym: "regulation of flagellar movement" RELATED [GOC:TermGenie] @@ -48810,14 +55056,12 @@ is_a: GO:0060632 ! regulation of microtubule-based movement intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0003341 ! cilium movement relationship: regulates GO:0003341 ! cilium movement -created_by: dph creation_date: 2009-12-03T10:12:00Z [Term] id: GO:0003353 name: positive regulation of cilium movement namespace: biological_process -alt_id: GO:1900174 def: "Any process that increases the rate, frequency, or extent of cilium movement, the directed, self-propelled movement of a cilium." [GOC:dph] comment: Note that we deem cilium and microtubule-based flagellum to be equivalent. synonym: "positive regulation of flagellar movement" RELATED [GOC:TermGenie] @@ -48828,14 +55072,12 @@ is_a: GO:0048522 ! positive regulation of cellular process intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0003341 ! cilium movement relationship: positively_regulates GO:0003341 ! cilium movement -created_by: dph creation_date: 2009-12-03T10:16:10Z [Term] id: GO:0003354 name: negative regulation of cilium movement namespace: biological_process -alt_id: GO:1900173 def: "Any process that decreases the rate, frequency, or extent of cilium movement, the directed, self-propelled movement of a cilium." [GOC:dph] comment: Note that we deem cilium and microtubule-based flagellum to be equivalent. synonym: "negative regulation of flagellum movement" RELATED [] @@ -48845,7 +55087,6 @@ is_a: GO:0048523 ! negative regulation of cellular process intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0003341 ! cilium movement relationship: negatively_regulates GO:0003341 ! cilium movement -created_by: dph creation_date: 2009-12-03T10:17:47Z [Term] @@ -48858,7 +55099,6 @@ is_a: GO:0030182 ! neuron differentiation intersection_of: GO:0030154 ! cell differentiation intersection_of: results_in_acquisition_of_features_of CL:0008025 ! noradrenergic neuron relationship: results_in_acquisition_of_features_of CL:0008025 ! noradrenergic neuron -created_by: dph creation_date: 2009-12-03T10:34:30Z [Term] @@ -48872,7 +55112,6 @@ intersection_of: GO:0032502 ! developmental process intersection_of: results_in_development_of CL:0008025 ! noradrenergic neuron relationship: part_of GO:0003357 ! noradrenergic neuron differentiation relationship: results_in_development_of CL:0008025 ! noradrenergic neuron -created_by: dph creation_date: 2009-12-03T10:38:37Z [Term] @@ -48884,7 +55123,6 @@ is_a: GO:0048856 ! anatomical structure development intersection_of: GO:0048856 ! anatomical structure development intersection_of: results_in_development_of UBERON:0002298 ! brainstem relationship: results_in_development_of UBERON:0002298 ! brainstem -created_by: dph creation_date: 2009-12-03T10:47:20Z [Term] @@ -48896,7 +55134,6 @@ is_a: GO:0003357 ! noradrenergic neuron differentiation intersection_of: GO:0003357 ! noradrenergic neuron differentiation intersection_of: part_of GO:0003360 ! brainstem development relationship: part_of GO:0003360 ! brainstem development -created_by: dph creation_date: 2009-12-03T10:53:30Z [Term] @@ -48909,7 +55146,6 @@ intersection_of: GO:0030010 ! establishment of cell polarity intersection_of: part_of GO:0001667 ! ameboidal-type cell migration relationship: part_of GO:0001667 ! ameboidal-type cell migration property_value: RO:0002161 NCBITaxon:4751 -created_by: dph creation_date: 2009-12-08T04:50:41Z [Term] @@ -48921,7 +55157,6 @@ is_a: GO:0030952 ! establishment or maintenance of cytoskeleton polarity intersection_of: GO:0030952 ! establishment or maintenance of cytoskeleton polarity intersection_of: part_of GO:0001667 ! ameboidal-type cell migration relationship: part_of GO:0003365 ! establishment of cell polarity involved in ameboidal cell migration -created_by: dph creation_date: 2009-12-08T05:42:46Z [Term] @@ -48933,7 +55168,6 @@ is_a: GO:0003365 ! establishment of cell polarity involved in ameboidal cell mig intersection_of: GO:0030010 ! establishment of cell polarity intersection_of: part_of GO:0042074 ! cell migration involved in gastrulation relationship: part_of GO:0042074 ! cell migration involved in gastrulation -created_by: dph creation_date: 2009-12-09T06:54:44Z [Term] @@ -48945,7 +55179,6 @@ is_a: GO:0003371 ! establishment or maintenance of cytoskeleton polarity involve intersection_of: GO:0030952 ! establishment or maintenance of cytoskeleton polarity intersection_of: part_of GO:0007369 ! gastrulation relationship: part_of GO:0003379 ! establishment of cell polarity involved in gastrulation cell migration -created_by: dph creation_date: 2009-12-09T07:10:57Z [Term] @@ -48957,7 +55190,6 @@ is_a: GO:0003382 ! epithelial cell morphogenesis intersection_of: GO:0003382 ! epithelial cell morphogenesis intersection_of: part_of GO:0007369 ! gastrulation relationship: part_of GO:0007369 ! gastrulation -created_by: dph creation_date: 2009-12-09T07:18:53Z [Term] @@ -48970,7 +55202,6 @@ intersection_of: GO:0009653 ! anatomical structure morphogenesis intersection_of: results_in_maturation_of CL:0000066 ! epithelial cell relationship: part_of GO:0002064 ! epithelial cell development relationship: results_in_maturation_of CL:0000066 ! epithelial cell -created_by: dph creation_date: 2009-12-09T07:21:06Z [Term] @@ -48985,7 +55216,6 @@ intersection_of: results_in_formation_of UBERON:0004128 ! optic vesicle relationship: part_of GO:0003404 ! optic vesicle morphogenesis relationship: part_of GO:0060900 ! embryonic camera-type eye formation relationship: results_in_formation_of UBERON:0004128 ! optic vesicle -created_by: dph creation_date: 2009-12-21T01:42:37Z [Term] @@ -48999,7 +55229,6 @@ intersection_of: GO:0009653 ! anatomical structure morphogenesis intersection_of: results_in_morphogenesis_of UBERON:0004128 ! optic vesicle relationship: part_of GO:0048596 ! embryonic camera-type eye morphogenesis relationship: results_in_morphogenesis_of UBERON:0004128 ! optic vesicle -created_by: dph creation_date: 2009-12-21T01:54:34Z [Term] @@ -49013,7 +55242,6 @@ intersection_of: GO:0048856 ! anatomical structure development intersection_of: results_in_development_of UBERON:0001782 ! pigmented layer of retina relationship: part_of GO:0060041 ! retina development in camera-type eye relationship: results_in_development_of UBERON:0001782 ! pigmented layer of retina -created_by: dph creation_date: 2009-12-21T02:04:27Z [Term] @@ -49026,7 +55254,6 @@ intersection_of: GO:0048856 ! anatomical structure development intersection_of: results_in_development_of UBERON:0003902 ! retinal neural layer relationship: part_of GO:0060041 ! retina development in camera-type eye relationship: results_in_development_of UBERON:0003902 ! retinal neural layer -created_by: dph creation_date: 2009-12-21T02:15:14Z [Term] @@ -49038,7 +55265,6 @@ is_a: GO:0048870 ! cell motility intersection_of: GO:0048870 ! cell motility intersection_of: part_of GO:0048593 ! camera-type eye morphogenesis relationship: part_of GO:0048593 ! camera-type eye morphogenesis -created_by: dph creation_date: 2009-12-21T03:04:27Z [Term] @@ -49050,7 +55276,6 @@ is_a: GO:0002062 ! chondrocyte differentiation intersection_of: GO:0002062 ! chondrocyte differentiation intersection_of: part_of GO:0060350 ! endochondral bone morphogenesis relationship: part_of GO:0060351 ! cartilage development involved in endochondral bone morphogenesis -created_by: dph creation_date: 2009-12-22T08:39:58Z [Term] @@ -49062,7 +55287,6 @@ is_a: GO:0090171 ! chondrocyte morphogenesis intersection_of: GO:0090171 ! chondrocyte morphogenesis intersection_of: part_of GO:0060350 ! endochondral bone morphogenesis relationship: part_of GO:0003433 ! chondrocyte development involved in endochondral bone morphogenesis -created_by: dph creation_date: 2009-12-22T08:42:55Z [Term] @@ -49072,7 +55296,6 @@ namespace: biological_process def: "The growth of a chondrocyte, where growth contributes to the progression of the chondrocyte over time." [GOC:ascb_2009, GOC:dph, GOC:tb] is_a: GO:0048588 ! developmental cell growth relationship: part_of GO:0002063 ! chondrocyte development -created_by: dph creation_date: 2009-12-22T08:48:44Z [Term] @@ -49084,7 +55307,6 @@ is_a: GO:0098868 ! bone growth intersection_of: GO:0048589 ! developmental growth intersection_of: results_in_growth_of UBERON:0002513 ! endochondral bone relationship: results_in_growth_of UBERON:0002513 ! endochondral bone -created_by: dph creation_date: 2009-12-22T08:52:55Z [Term] @@ -49098,7 +55320,6 @@ intersection_of: GO:0048856 ! anatomical structure development intersection_of: results_in_development_of UBERON:0004129 ! growth plate cartilage relationship: part_of GO:0003416 ! endochondral bone growth relationship: results_in_development_of UBERON:0004129 ! growth plate cartilage -created_by: dph creation_date: 2009-12-22T08:57:42Z [Term] @@ -49111,7 +55332,6 @@ intersection_of: GO:0030154 ! cell differentiation intersection_of: results_in_acquisition_of_features_of CL:1000217 ! growth plate cartilage chondrocyte relationship: part_of GO:0003417 ! growth plate cartilage development relationship: results_in_acquisition_of_features_of CL:1000217 ! growth plate cartilage chondrocyte -created_by: dph creation_date: 2009-12-22T09:00:56Z [Term] @@ -49124,7 +55344,6 @@ intersection_of: GO:0009653 ! anatomical structure morphogenesis intersection_of: results_in_morphogenesis_of UBERON:0004129 ! growth plate cartilage relationship: part_of GO:0003417 ! growth plate cartilage development relationship: results_in_morphogenesis_of UBERON:0004129 ! growth plate cartilage -created_by: dph creation_date: 2009-12-22T09:21:30Z [Term] @@ -49137,7 +55356,6 @@ is_a: GO:0003422 ! growth plate cartilage morphogenesis intersection_of: GO:0090171 ! chondrocyte morphogenesis intersection_of: results_in_morphogenesis_of UBERON:0004129 ! growth plate cartilage relationship: part_of GO:0003418 ! growth plate cartilage chondrocyte differentiation -created_by: dph creation_date: 2009-12-22T12:22:24Z [Term] @@ -49152,7 +55370,6 @@ intersection_of: GO:0040007 ! growth intersection_of: results_in_growth_of CL:1000217 ! growth plate cartilage chondrocyte relationship: part_of GO:0003431 ! growth plate cartilage chondrocyte development relationship: results_in_growth_of CL:1000217 ! growth plate cartilage chondrocyte -created_by: dph creation_date: 2009-12-22T12:29:19Z [Term] @@ -49165,7 +55382,6 @@ intersection_of: GO:0048468 ! cell development intersection_of: results_in_development_of CL:1000217 ! growth plate cartilage chondrocyte relationship: part_of GO:0003418 ! growth plate cartilage chondrocyte differentiation relationship: results_in_development_of CL:1000217 ! growth plate cartilage chondrocyte -created_by: dph creation_date: 2009-12-22T12:32:49Z [Term] @@ -49177,7 +55393,6 @@ is_a: GO:0003430 ! growth plate cartilage chondrocyte growth intersection_of: GO:0048588 ! developmental cell growth intersection_of: part_of GO:0003429 ! growth plate cartilage chondrocyte morphogenesis relationship: part_of GO:0003429 ! growth plate cartilage chondrocyte morphogenesis -created_by: dph creation_date: 2009-12-22T12:37:48Z [Term] @@ -49189,7 +55404,6 @@ is_a: GO:0002063 ! chondrocyte development intersection_of: GO:0002063 ! chondrocyte development intersection_of: part_of GO:0060350 ! endochondral bone morphogenesis relationship: part_of GO:0003413 ! chondrocyte differentiation involved in endochondral bone morphogenesis -created_by: dph creation_date: 2009-12-22T12:42:44Z [Term] @@ -49201,7 +55415,6 @@ is_a: GO:0030155 ! regulation of cell adhesion intersection_of: GO:0030155 ! regulation of cell adhesion intersection_of: part_of GO:0003422 ! growth plate cartilage morphogenesis relationship: part_of GO:0003422 ! growth plate cartilage morphogenesis -created_by: dph creation_date: 2009-12-22T01:28:15Z [Term] @@ -49213,14 +55426,12 @@ is_a: GO:0010646 ! regulation of cell communication intersection_of: GO:0010646 ! regulation of cell communication intersection_of: part_of GO:0003422 ! growth plate cartilage morphogenesis relationship: part_of GO:0003422 ! growth plate cartilage morphogenesis -created_by: dph creation_date: 2009-12-22T01:34:24Z [Term] id: GO:0003674 name: molecular_function namespace: molecular_function -alt_id: GO:0005554 def: "A molecular process that can be carried out by the action of a single macromolecular machine, usually via direct physical interactions with other molecular entities. Function in this sense denotes an action, or activity, that a gene product (or a complex) performs." [GOC:pdt] comment: Note that, in addition to forming the root of the molecular function ontology, this term is recommended for the annotation of gene products whose molecular function is unknown. When this term is used for annotation, it indicates that no information was available about the molecular function of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this. Despite its name, this is not a type of 'function' in the sense typically defined by upper ontologies such as Basic Formal Ontology (BFO). It is instead a BFO:process carried out by a single gene product or complex. subset: goslim_candida @@ -49238,7 +55449,6 @@ disjoint_from: GO:0008150 ! biological_process id: GO:0003676 name: nucleic acid binding namespace: molecular_function -alt_id: GO:0000496 def: "Binding to a nucleic acid." [GOC:jl] subset: goslim_chembl subset: goslim_metagenomics @@ -49255,7 +55465,6 @@ relationship: has_primary_input CHEBI:33696 id: GO:0003677 name: DNA binding namespace: molecular_function -alt_id: GO:0043566 def: "Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid)." [GOC:dph, GOC:jl, GOC:tb, GOC:vw] subset: goslim_agr subset: goslim_candida @@ -49299,85 +55508,10 @@ intersection_of: GO:0005488 ! binding intersection_of: has_primary_input GO:0000785 ! chromatin relationship: has_primary_input GO:0000785 ! chromatin -[Term] -id: GO:0003690 -name: double-stranded DNA binding -namespace: molecular_function -def: "Binding to double-stranded DNA." [GOC:elh, GOC:vw] -synonym: "dsDNA binding" EXACT [GOC:elh] -is_a: GO:0003677 ! DNA binding -intersection_of: GO:0005488 ! binding -intersection_of: has_primary_input CHEBI:4705 -relationship: has_primary_input CHEBI:4705 - -[Term] -id: GO:0003700 -name: DNA-binding transcription factor activity -namespace: molecular_function -alt_id: GO:0000130 -alt_id: GO:0001071 -alt_id: GO:0001130 -alt_id: GO:0001131 -alt_id: GO:0001151 -alt_id: GO:0001199 -alt_id: GO:0001204 -def: "A transcription regulator activity that modulates transcription of gene sets via selective and non-covalent binding to a specific double-stranded genomic DNA sequence (sometimes referred to as a motif) within a cis-regulatory region. Regulatory regions include promoters (proximal and distal) and enhancers. Genes are transcriptional units, and include bacterial operons." [GOC:txnOH-2018] -comment: Usage guidance: Most DNA-binding transcription factors do not have enzymatic activity. The presence of specific DNA-binding domains known to be present in DNA-binding transcription factors (HOX, GATA etc) should be used to help decide whether a protein is a DNA binding transcription factor or a coregulator. If a protein has an enzymatic activity (for example, ubiquitin ligase, histone acetyl transferase) and no known DNA binding domain, consider annotating to GO:0003712 transcription coregulator activity. Special care should be taken with proteins containing zinc fingers, Myb/SANT and ARID domains, since only a subset of proteins containing these domains directly and selectively bind to regulatory DNA motifs in cis-regulatory regions. -subset: goslim_agr -subset: goslim_candida -subset: goslim_chembl -subset: goslim_drosophila -subset: goslim_metagenomics -subset: goslim_mouse -subset: goslim_plant -subset: goslim_yeast -synonym: "bacterial-type DNA binding transcription factor activity" NARROW [] -synonym: "bacterial-type RNA polymerase core promoter proximal region sequence-specific DNA binding transcription factor activity" NARROW [] -synonym: "bacterial-type RNA polymerase transcription enhancer sequence-specific DNA binding transcription factor activity" NARROW [] -synonym: "bacterial-type RNA polymerase transcription factor activity, metal ion regulated sequence-specific DNA binding" NARROW [] -synonym: "bacterial-type RNA polymerase transcription factor activity, sequence-specific DNA binding" NARROW [] -synonym: "DNA binding transcription factor activity" EXACT [] -synonym: "gene-specific transcription factor activity" EXACT [] -synonym: "metal ion regulated sequence-specific DNA binding bacterial-type RNA polymerase transcription factor activity" NARROW [] -synonym: "metal ion regulated sequence-specific DNA binding transcription factor activity" NARROW [] -synonym: "nucleic acid binding transcription factor activity" BROAD [] -synonym: "sequence-specific DNA binding bacterial-type RNA polymerase transcription factor activity" NARROW [] -synonym: "sequence-specific DNA binding transcription factor activity" EXACT [] -synonym: "transcription factor activity" BROAD [] -synonym: "transcription factor activity, bacterial-type RNA polymerase core promoter proximal region sequence-specific binding" NARROW [] -synonym: "transcription factor activity, bacterial-type RNA polymerase proximal promoter sequence-specific DNA binding" NARROW [] -synonym: "transcription factor activity, bacterial-type RNA polymerase transcription enhancer sequence-specific binding" NARROW [] -synonym: "transcription factor activity, metal ion regulated sequence-specific DNA binding" NARROW [] -is_a: BFO:0000003 -is_a: GO:0140110 ! transcription regulator activity -intersection_of: GO:0140110 ! transcription regulator activity -intersection_of: has_part GO:0000976 ! transcription cis-regulatory region binding -intersection_of: part_of GO:0006355 ! regulation of DNA-templated transcription -relationship: has_part GO:0000976 ! transcription cis-regulatory region binding -relationship: part_of GO:0006355 ! regulation of DNA-templated transcription -property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/15704" xsd:anyURI -property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/16534" xsd:anyURI -property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/20253" xsd:anyURI -created_by: krc -creation_date: 2010-10-21T04:37:54Z - -[Term] -id: GO:0003707 -name: nuclear steroid receptor activity -namespace: molecular_function -def: "Combining with a steroid hormone and transmitting the signal within the cell to initiate a change in cell activity or function." [GOC:signaling, PMID:14708019] -synonym: "steroid hormone receptor activity" BROAD [] -is_a: GO:0004879 ! nuclear receptor activity -relationship: part_of GO:0043401 ! steroid hormone receptor signaling pathway -property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/16717" xsd:anyURI -property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/26957" xsd:anyURI - [Term] id: GO:0003723 name: RNA binding namespace: molecular_function -alt_id: GO:0000498 -alt_id: GO:0044822 def: "Binding to an RNA molecule or a portion thereof." [GOC:jl, GOC:mah] subset: goslim_agr subset: goslim_candida @@ -49425,7 +55559,6 @@ property_value: term_tracker_item "https://github.com/geneontology/go-ontology/i id: GO:0003777 name: microtubule motor activity namespace: molecular_function -alt_id: GO:1990939 def: "A motor activity that generates movement along a microtubule, driven by ATP hydrolysis." [PMID:19686686, PMID:32684327, PMID:32842864] comment: Consider also annotating to the molecular function term 'microtubule binding ; GO:0008017'. synonym: "ATP-dependent microtubule motor activity" EXACT [] @@ -49444,7 +55577,6 @@ intersection_of: GO:0003774 ! cytoskeletal motor activity intersection_of: has_participant GO:0005874 ! microtubule relationship: has_participant GO:0005874 ! microtubule property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/18664" xsd:anyURI -created_by: vw creation_date: 2016-04-04T10:59:42Z [Term] @@ -49482,7 +55614,6 @@ is_a: GO:0016788 ! hydrolase activity, acting on ester bonds id: GO:0004536 name: DNA nuclease activity namespace: molecular_function -alt_id: GO:0004537 def: "Catalysis of the hydrolysis of ester linkages within deoxyribonucleic acid." [GOC:mah, ISBN:0198547684] synonym: "caspase-activated deoxyribonuclease activity" NARROW [] synonym: "deoxyribonuclease activity" EXACT [] @@ -49497,7 +55628,6 @@ relationship: part_of GO:0006259 ! DNA metabolic process id: GO:0004672 name: protein kinase activity namespace: molecular_function -alt_id: GO:0050222 def: "Catalysis of the phosphorylation of an amino acid residue in a protein, usually according to the reaction: a protein + ATP = a phosphoprotein + ADP." [PMID:25399640] comment: Note that triphosphate is used as a phosphate donor by at least one kinase. subset: goslim_candida @@ -49529,7 +55659,6 @@ is_a: GO:0140096 ! catalytic activity, acting on a protein id: GO:0004713 name: protein tyrosine kinase activity namespace: molecular_function -alt_id: GO:0004718 def: "Catalysis of the reaction: ATP + a protein tyrosine = ADP + protein tyrosine phosphate." [RHEA:10596] synonym: "protein-tyrosine kinase activity" EXACT [] xref: EC:2.7.10.- {source="skos:exactMatch"} @@ -49910,6 +56039,15 @@ xref: Reactome:R-HSA-9831136 "SH pentamer is phosphorylated" xref: Reactome:R-HSA-983703 "p-6Y-SYK phosphorylates BLNK (SLP65)" xref: Reactome:R-HSA-983707 "SYK autophosphorylates at the activated BCR" xref: Reactome:R-HSA-983709 "LYN, FYN, BLK phosphorylate ITAMs of Ig-alpha (CD79A) and Ig-beta (CD79B)" +xref: Reactome:R-HSA-9841924 "ABL1 phosphorylates PPARG2" +xref: Reactome:R-HSA-9842648 "Autophosphorylation of LTK dimer:ALKAL1,2" +xref: Reactome:R-HSA-9842651 "Active LTK receptor phosphorylates SHC1" +xref: Reactome:R-HSA-9842666 "Active LTK phosphorylates IRS1" +xref: Reactome:R-HSA-9842667 "CLIP1-LTK fusion autophosphorylates" +xref: Reactome:R-HSA-9860500 "Phosphorylation of KDR (VEGFR2) and FLT4 (VEGFR3) and PECAM1 in PECAM1:CDH5:KDR:FLT4:CTNNB1" +xref: Reactome:R-HSA-9860759 "p-T816-PKN2 phosphorylates AKT1 on serine-308" +xref: Reactome:R-HSA-9861469 "p-Y397-PTK2 (FAK) phosphorylates CHUK (IKKA)" +xref: Reactome:R-HSA-9865196 "p-Y393-ABL1 phosphorylates tyrosine-407 of YAP1" xref: RHEA:10596 {source="skos:exactMatch"} is_a: GO:0004672 ! protein kinase activity relationship: has_participant CHEBI:15378 @@ -49973,71 +56111,10 @@ is_a: GO:0004713 ! protein tyrosine kinase activity is_a: GO:0019199 ! transmembrane receptor protein kinase activity property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28176" xsd:anyURI -[Term] -id: GO:0004879 -name: nuclear receptor activity -namespace: molecular_function -alt_id: GO:0003708 -alt_id: GO:0004880 -alt_id: GO:0004882 -alt_id: GO:0004884 -alt_id: GO:0004886 -alt_id: GO:0004887 -alt_id: GO:0008434 -alt_id: GO:0038050 -alt_id: GO:0038051 -alt_id: GO:0038052 -def: "A DNA-binding transcription factor activity regulated by binding to a ligand that modulates the transcription of specific gene sets transcribed by RNA polymerase II. Nuclear receptor ligands are usually lipid-based (such as a steroid hormone) and the binding of the ligand to its receptor often occurs in the cytosol, which leads to its translocation to the nucleus." [GOC:txnOH-2018, PMID:23457262] -comment: Usage guidance: Nuclear receptors are a protein family defined by the presence of a C4-type zinc finger DNA-binding domain and a ligand binding domain. For nuclear receptors, the DNA binding motif is most often referred to as a response element. GO:0004879 is intended for annotation of nuclear receptors that regulate transcription by binding directly to DNA. When the nuclear receptor functions by binding to other transcription factors or transcription factor complexes, consider instead annotating to 'GO:0030374 ; nuclear receptor transcription coactivator activity' or GO:0140536 ; nuclear corepressor activity. -synonym: "1,25-(OH)2D3 receptor activity" NARROW [Wikipedia:Calcitriol] -synonym: "9-cis retinoic acid receptor activity" NARROW [] -synonym: "androgen receptor activity" NARROW [] -synonym: "calcitriol receptor activity" NARROW [] -synonym: "ecdysteroid hormone receptor activity" NARROW [] -synonym: "estrogen nuclear receptor activity" NARROW [GOC:bf] -synonym: "glucocorticoid receptor activity" NARROW [GOC:bf] -synonym: "juvenile hormone receptor activity" NARROW [] -synonym: "ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity" EXACT [] -synonym: "ligand-dependent nuclear receptor activity" RELATED [GOC:bf] -synonym: "ligand-dependent transcription factor activity" RELATED [GOC:bf] -synonym: "nuclear hormone receptor" NARROW [] -synonym: "retinoic acid receptor activity" NARROW [] -synonym: "retinoid-X receptor activity" NARROW [GOC:bf] -synonym: "RNA polymerase II transcription factor activity, estrogen-activated sequence-specific DNA binding" NARROW [] -synonym: "RNA polymerase II transcription factor activity, glucocorticoid-activated sequence-specific DNA binding" NARROW [] -synonym: "RNA polymerase II transcription factor activity, ligand-activated sequence-specific DNA binding" EXACT [] -synonym: "RXR" NARROW [] -synonym: "thyroid hormone receptor activity" NARROW [] -synonym: "vitamin A receptor activity" NARROW [] -synonym: "vitamin D receptor activity" NARROW [] -synonym: "vitamin D3 receptor activity" NARROW [GOC:bf, Wikipedia:Calcitriol_receptor] -is_a: GO:0000981 ! DNA-binding transcription factor activity, RNA polymerase II-specific -is_a: GO:0038023 ! signaling receptor activity -is_a: GO:0098531 ! ligand-activated transcription factor activity -relationship: part_of GO:0030522 ! intracellular receptor signaling pathway -property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/19518" xsd:anyURI -property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/20253" xsd:anyURI - -[Term] -id: GO:0004883 -name: nuclear glucocorticoid receptor activity -namespace: molecular_function -def: "Combining with a glucocorticoid and transmitting the signal within the cell trigger a change in cell activity or function." [GOC:signaling, PMID:17689856, PMID:20920967] -synonym: "glucocorticoid receptor activity" BROAD [] -is_a: GO:0003707 ! nuclear steroid receptor activity -intersection_of: GO:0038023 ! signaling receptor activity -intersection_of: has_primary_input CHEBI:24261 -relationship: has_primary_input CHEBI:24261 -relationship: part_of GO:0042921 ! nuclear receptor-mediated glucocorticoid signaling pathway -relationship: part_of GO:0043402 ! glucocorticoid mediated signaling pathway -property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/16717" xsd:anyURI - [Term] id: GO:0004888 name: transmembrane signaling receptor activity namespace: molecular_function -alt_id: GO:0004926 -alt_id: GO:0099600 def: "Combining with an extracellular or intracellular signal and transmitting the signal from one side of the membrane to the other to initiate a change in cell activity or state as part of signal transduction." [GOC:go_curators, Wikipedia:Transmembrane_receptor] comment: This term includes intracellular membrane receptors, e.g. IP3 triggered release of Ca2+ from intracellular stores. synonym: "transmembrane receptor activity" BROAD [GOC:bf, GOC:signaling] @@ -50049,7 +56126,6 @@ is_a: GO:0038023 ! signaling receptor activity id: GO:0004896 name: cytokine receptor activity namespace: molecular_function -alt_id: GO:0004907 def: "Combining with a cytokine and transmitting the signal from one side of the membrane to the other to initiate a change in cell activity." [GOC:add, GOC:mah] synonym: "hematopoietin/interferon-class (D200-domain) cytokine receptor activity" RELATED [] synonym: "IL receptor" NARROW [] @@ -50076,11 +56152,6 @@ property_value: RO:0002161 NCBITaxon:4751 id: GO:0004930 name: G protein-coupled receptor activity namespace: molecular_function -alt_id: GO:0001622 -alt_id: GO:0001623 -alt_id: GO:0001624 -alt_id: GO:0001625 -alt_id: GO:0016526 def: "Combining with an extracellular signal and transmitting the signal across the membrane by activating an associated G-protein; promotes the exchange of GDP for GTP on the alpha subunit of a heterotrimeric G-protein complex." [GOC:bf, Wikipedia:GPCR] subset: goslim_chembl synonym: "EBV-induced receptor" NARROW [] @@ -50103,6 +56174,7 @@ synonym: "super conserved receptor expressed in brain receptor activity" NARROW xref: Reactome:R-HSA-114552 "Thrombin-activated PARs activate G12/13" xref: Reactome:R-HSA-114558 "Thrombin-activated PARs activate Gq" xref: Reactome:R-HSA-167408 "The high affinity receptor complex binds to G-protein" +xref: Reactome:R-HSA-381706 "GLP1R:GLP1 activates G(s)" xref: Wikipedia:GPCR is_a: BFO:0000003 is_a: GO:0004888 ! transmembrane signaling receptor activity @@ -50204,8 +56276,6 @@ relationship: has_primary_input CHEBI:7872 id: GO:0004993 name: G protein-coupled serotonin receptor activity namespace: molecular_function -alt_id: GO:0001585 -alt_id: GO:0016609 def: "Combining with the biogenic amine serotonin and transmitting the signal across the membrane by activating an associated G-protein. Serotonin (5-hydroxytryptamine) is a neurotransmitter and hormone found in vertebrates and invertebrates." [GOC:ai] synonym: "5-HT receptor" EXACT [] synonym: "5-hydroxytryptamine receptor" EXACT [] @@ -50240,7 +56310,6 @@ relationship: part_of GO:0038170 ! somatostatin signaling pathway id: GO:0005000 name: vasopressin receptor activity namespace: molecular_function -alt_id: GO:0016931 def: "Combining with vasopressin to initiate a change in cell activity." [GOC:ai] synonym: "vasopressin activated calcium mobilizing receptor activity" NARROW [] is_a: GO:0008528 ! G protein-coupled peptide receptor activity @@ -50351,7 +56420,6 @@ relationship: has_primary_input PR:000002065 ! mast/stem cell growth factor rece id: GO:0005215 name: transporter activity namespace: molecular_function -alt_id: GO:0005478 def: "Enables the directed movement of substances (such as macromolecules, small molecules, ions) into, out of or within a cell, accross or in between cells." [GOC:ai, GOC:dgf] comment: Some transporters, such as certain members of the SLC family, are referred to as 'carriers'; however GO uses carrier with a different meaning: a carrier binds to and transports the substance (see GO:0140104 molecular carrier activity), whereas a transporter forms some pore that allows the passing of molecules. subset: gocheck_do_not_annotate @@ -50388,7 +56456,7 @@ property_value: term_tracker_item "https://github.com/geneontology/go-ontology/i id: GO:0005227 name: calcium-activated cation channel activity namespace: molecular_function -def: "Enables the calcium concentration-regulatable energy-independent passage of cations across a lipid bilayer down a concentration gradient." [GOC:dph, GOC:mtg_transport] +def: "Enables the transmembrane transfer of an inorganic cation by a channel that opens when a calcium cation has been bound by the channel complex or one of its constituent parts." [GOC:dph, GOC:mtg_transport] synonym: "calcium activated cation channel activity" EXACT [] synonym: "intracellular calcium-activated potassium channel" NARROW [] synonym: "polycystin" NARROW [] @@ -50400,6 +56468,7 @@ intersection_of: has_primary_input CHEBI:23906 intersection_of: has_small_molecule_activator CHEBI:29108 relationship: has_small_molecule_activator CHEBI:29108 property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/24605" xsd:anyURI +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28979" xsd:anyURI [Term] id: GO:0005230 @@ -50428,8 +56497,6 @@ relationship: part_of GO:0060079 ! excitatory postsynaptic potential id: GO:0005261 name: monoatomic cation channel activity namespace: molecular_function -alt_id: GO:0015281 -alt_id: GO:0015338 def: "Enables the energy-independent facilitated diffusion of a monoatomic cation through a transmembrane aqueous pore or channel." [GOC:def, GOC:dph, GOC:mtg_transport, GOC:pr, ISBN:0815340729] synonym: "cation channel activity" BROAD [] synonym: "cation diffusion facilitator activity" EXACT [] @@ -50462,10 +56529,14 @@ xref: Reactome:R-HSA-3295579 "TRPs transport extracellular Ca2+ to cytosol" xref: Reactome:R-HSA-8949145 "VDAC1,2,3 translocate calcium from the cytosol to the mitochondrial intermembrane space" xref: Reactome:R-HSA-8949178 "MCU translocates calcium from the mitochondrial intermembrane space to the mitochondrial matrix" xref: Reactome:R-HSA-9663785 "CHRNA9:CHRNA10:AcCho transports Ca2+ from the extracellular region to the cytosol" +xref: Reactome:R-HSA-9858800 "TRPV4 tetramer:CALM1:Ca2+ transports calcium ions (Ca2+) from the extracellular region to the cytosol" +xref: RHEA:29671 {source="skos:broadMatch"} is_a: GO:0015085 ! calcium ion transmembrane transporter activity is_a: GO:0015267 ! channel activity intersection_of: GO:0015267 ! channel activity intersection_of: has_primary_input CHEBI:29108 +relationship: has_participant CHEBI:29108 +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27521" xsd:anyURI [Term] id: GO:0005267 @@ -50484,10 +56555,13 @@ xref: Reactome:R-HSA-1299338 "Activation of TRESK" xref: Reactome:R-HSA-1299359 "Activation of TALK" xref: Reactome:R-HSA-2534365 "Slo3 Potassium Transport" xref: Reactome:R-HSA-5578910 "KCNK dimers transport K+ from cytosol to extracellular region" +xref: RHEA:29463 {source="skos:broadMatch"} is_a: GO:0005261 ! monoatomic cation channel activity is_a: GO:0015079 ! potassium ion transmembrane transporter activity intersection_of: GO:0015267 ! channel activity intersection_of: has_primary_input CHEBI:29103 +relationship: has_participant CHEBI:29103 +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27521" xsd:anyURI [Term] id: GO:0005272 @@ -50500,16 +56574,18 @@ xref: Reactome:R-HSA-9717374 "SCN3A:SCN2B,4B transports Na+ from the extracellul xref: Reactome:R-HSA-9717382 "SCN9A:SCN1B,2B,4B transports Na+ from the extracellular region to the cytosol" xref: Reactome:R-HSA-9717395 "TRPM5 transports Na+ from the extracellular region to the cytosol" xref: Reactome:R-HSA-9717396 "SCN2A:SCN1B,2B,4B transports Na+ from the extracellular region to the cytosol" +xref: RHEA:34963 {source="skos:broadMatch"} is_a: GO:0015081 ! sodium ion transmembrane transporter activity is_a: GO:0015267 ! channel activity intersection_of: GO:0015267 ! channel activity intersection_of: has_primary_input CHEBI:29101 +relationship: has_participant CHEBI:29101 +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27521" xsd:anyURI [Term] id: GO:0005275 name: amine transmembrane transporter activity namespace: molecular_function -alt_id: GO:0005279 def: "Enables the transfer of amines, including polyamines, from one side of a membrane to the other. Amines are organic compounds that are weakly basic in character and contain an amino (-NH2) or substituted amino group." [GOC:mtg_transport, ISBN:0198506732, ISBN:0815340729] synonym: "amine/amide/polyamine channel activity" BROAD [] synonym: "amine/polyamine transmembrane transporter activity" EXACT [] @@ -50557,29 +56633,25 @@ synonym: "L-glutamate transporter activity" BROAD [] xref: Reactome:R-HSA-210444 "L-Glutamate loading of synaptic vesicle" xref: Reactome:R-HSA-428052 "SLC17A6,7,8 exchange cytosolic L-Glu for synaptic vesicle H+" xref: Reactome:R-HSA-5624256 "Defective SLC17A8 does not exchange cytosolic L-Glu for synaptic vesicle H+" -xref: RHEA:66336 {source="skos:broadMatch"} is_a: GO:0015172 ! acidic amino acid transmembrane transporter activity intersection_of: GO:0022857 ! transmembrane transporter activity intersection_of: has_primary_input CHEBI:29985 -relationship: has_participant CHEBI:29985 relationship: has_primary_input CHEBI:29985 relationship: part_of GO:0015813 ! L-glutamate transmembrane transport +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27521" xsd:anyURI [Term] id: GO:0005315 name: phosphate transmembrane transporter activity namespace: molecular_function -alt_id: GO:0005317 -alt_id: GO:1901677 def: "Enables the transfer of phosphate ions from one side of a membrane to the other, up its concentration gradient. The transporter binds the solute and undergoes a series of conformational changes. Transport works equally well in either direction and is driven by a chemiosmotic source of energy. Secondary active transporters include symporters and antiporters." [GOC:mtg_transport] synonym: "inorganic phosphate transmembrane transporter activity" EXACT [] -xref: RHEA:32823 is_a: GO:0015291 ! secondary active transmembrane transporter activity intersection_of: GO:0022857 ! transmembrane transporter activity intersection_of: has_primary_input CHEBI:43474 -relationship: has_participant CHEBI:43474 relationship: has_primary_input CHEBI:43474 property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27121" xsd:anyURI +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27521" xsd:anyURI [Term] id: GO:0005319 @@ -50633,7 +56705,6 @@ relationship: part_of GO:1903825 ! organic acid transmembrane transport id: GO:0005347 name: ATP transmembrane transporter activity namespace: molecular_function -alt_id: GO:0005348 def: "Enables the transfer of ATP, adenosine triphosphate, from one side of a membrane to the other." [GOC:ai] xref: Reactome:R-HSA-9717392 "CALHM1:CALHM3 transports ATP from the cytosol to the extracellular region" is_a: GO:0022857 ! transmembrane transporter activity @@ -50657,9 +56728,6 @@ relationship: part_of GO:0006833 ! water transport id: GO:0005381 name: iron ion transmembrane transporter activity namespace: molecular_function -alt_id: GO:0005382 -alt_id: GO:0016033 -alt_id: GO:0097689 def: "Enables the transfer of iron (Fe) ions from one side of a membrane to the other." [GOC:ai] comment: An example of this is mouse ferroportin (UniProtKB:Q9JHI9), which transports iron out of the cell. synonym: "iron cation channel activity" EXACT [] @@ -50743,8 +56811,6 @@ relationship: has_primary_input CHEBI:29108 id: GO:0005515 name: protein binding namespace: molecular_function -alt_id: GO:0001948 -alt_id: GO:0045308 def: "Binding to a protein." [GOC:go_curators] subset: goslim_candida subset: goslim_chembl @@ -50756,6 +56822,7 @@ subset: goslim_plant_ribbon subset: goslim_prokaryote_ribbon synonym: "glycoprotein binding" NARROW [] synonym: "protein amino acid binding" EXACT [] +xref: Reactome:R-HSA-9866132 "Intermediate II binds CYC1, UQCRC1, UQCRC2, UQCRH" is_a: BFO:0000003 is_a: GO:0005488 ! binding intersection_of: GO:0005488 ! binding @@ -50825,7 +56892,6 @@ relationship: has_primary_input CHEBI:16336 id: GO:0005575 name: cellular_component namespace: cellular_component -alt_id: GO:0008372 def: "A location, relative to cellular compartments and structures, occupied by a macromolecular machine. There are three types of cellular components described in the gene ontology: (1) the cellular anatomical entity where a gene product carries out a molecular function (e.g., plasma membrane, cytoskeleton) or membrane-enclosed compartments (e.g., mitochondrion); (2) virion components, where viral proteins act, and (3) the stable macromolecular complexes of which gene product are parts (e.g., the clathrin complex)." [GOC:pdt] comment: Note that, in addition to forming the root of the cellular component ontology, this term is recommended for the annotation of gene products whose cellular component is unknown. When this term is used for annotation, it indicates that no information was available about the cellular component of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this. subset: goslim_candida @@ -50864,7 +56930,7 @@ subset: goslim_prokaryote_ribbon subset: goslim_yeast synonym: "extracellular" EXACT [] xref: Wikipedia:Extracellular -is_a: GO:0110165 ! cellular anatomical entity +is_a: GO:0110165 ! cellular anatomical structure [Term] id: GO:0005577 @@ -50930,8 +56996,6 @@ is_a: GO:0098651 ! basement membrane collagen trimer id: GO:0005604 name: basement membrane namespace: cellular_component -alt_id: GO:0005605 -alt_id: GO:0008003 def: "A collagen-containing extracellular matrix consisting of a thin layer of dense material found in various animal tissues interposed between the cells and the adjacent connective tissue. It consists of the basal lamina plus an associated layer of reticulin fibers." [ISBN:0198547684, PMID:22505934] comment: Note that this term has no relationship to 'membrane ; GO:0016020' because the basement membrane is not a lipid bilayer. synonym: "basal lamina" RELATED [] @@ -50951,7 +57015,7 @@ subset: goslim_drosophila subset: goslim_generic synonym: "intercellular space" RELATED [] xref: NIF_Subcellular:sao1425028079 -is_a: GO:0110165 ! cellular anatomical entity +is_a: GO:0110165 ! cellular anatomical structure relationship: part_of GO:0005576 ! extracellular region [Term] @@ -50969,7 +57033,7 @@ synonym: "nucleocytoplasm" RELATED [GOC:mah] synonym: "protoplasm" EXACT [] synonym: "protoplast" RELATED [GOC:mah] xref: Wikipedia:Intracellular -is_a: GO:0110165 ! cellular anatomical entity +is_a: GO:0110165 ! cellular anatomical structure relationship: part_of CL:0000000 ! cell property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/17776" xsd:anyURI @@ -51005,7 +57069,6 @@ relationship: RO:0002162 NCBITaxon:2759 {all_only="true"} ! in taxon Eukaryota id: GO:0005635 name: nuclear envelope namespace: cellular_component -alt_id: GO:0005636 def: "The double lipid bilayer enclosing the nucleus and separating its contents from the rest of the cytoplasm; includes the intermembrane space, a gap of width 20-40 nm (also called the perinuclear space)." [ISBN:0198547684] subset: goslim_chembl subset: goslim_generic @@ -51030,25 +57093,6 @@ intersection_of: bounding_layer_of GO:0005634 ! nucleus relationship: bounding_layer_of GO:0005634 ! nucleus relationship: part_of GO:0042175 ! nuclear outer membrane-endoplasmic reticulum membrane network -[Term] -id: GO:0005667 -name: transcription regulator complex -namespace: cellular_component -alt_id: GO:0044797 -alt_id: GO:0044798 -def: "A protein complex that is capable of associating with DNA by direct binding, or via other DNA-binding proteins or complexes, and regulating transcription." [GOC:jl] -subset: goslim_pir -synonym: "cytoplasmic transcription factor complex" RELATED [] -synonym: "nuclear transcription factor complex" RELATED [] -synonym: "transcription factor complex" RELATED [] -is_a: BFO:0000004 -is_a: GO:0032991 ! protein-containing complex -intersection_of: GO:0032991 ! protein-containing complex -intersection_of: capable_of GO:0140110 ! transcription regulator activity -relationship: capable_of GO:0140110 ! transcription regulator activity -created_by: jl -creation_date: 2013-08-28T12:11:37Z - [Term] id: GO:0005694 name: chromosome @@ -51070,7 +57114,7 @@ synonym: "chromatid" RELATED [] synonym: "interphase chromosome" NARROW [] synonym: "prophase chromosome" NARROW [] xref: Wikipedia:Chromosome -is_a: GO:0043232 ! intracellular non-membrane-bounded organelle +is_a: GO:0043232 ! intracellular membraneless organelle [Term] id: GO:0005730 @@ -51086,7 +57130,7 @@ subset: goslim_plant subset: goslim_yeast xref: NIF_Subcellular:sao1820400233 xref: Wikipedia:Nucleolus -is_a: GO:0043232 ! intracellular non-membrane-bounded organelle +is_a: GO:0043232 ! intracellular membraneless organelle relationship: part_of GO:0031981 ! nuclear lumen [Term] @@ -51104,7 +57148,7 @@ subset: goslim_prokaryote subset: goslim_prokaryote_ribbon subset: goslim_yeast xref: Wikipedia:Cytoplasm -is_a: GO:0110165 ! cellular anatomical entity +is_a: GO:0110165 ! cellular anatomical structure relationship: part_of GO:0005622 ! intracellular anatomical structure property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/23023" xsd:anyURI @@ -51224,6 +57268,35 @@ synonym: "vesicular component" RELATED [NIF_Subcellular:sao138219748] xref: NIF_Subcellular:sao819927218 is_a: GO:0031410 ! cytoplasmic vesicle +[Term] +id: GO:0005814 +name: centriole +namespace: cellular_component +def: "A cellular organelle, found close to the nucleus in many eukaryotic cells, consisting of a small cylinder with microtubular walls, 300-500 nm long and 150-250 nm in diameter. It contains nine short, parallel, peripheral microtubular fibrils, each fibril consisting of one complete microtubule fused to two incomplete microtubules. Cells usually have two centrioles, lying at right angles to each other. At division, each pair of centrioles generates another pair and the twin pairs form the pole of the mitotic spindle." [ISBN:0198547684] +comment: In most eukaryotic cells, 'ciliary basal body' (GO:0036064) and 'centriole' (GO:0005814) represent a common entity that cycles through its function in cell division, then ciliogenesis, then cell division again. However, these structures are modified extensively as they transition into each other, and may contain different proteins, specific to each component. +synonym: "daughter centriole" NARROW [GOC:cilia] +synonym: "mother centriole" NARROW [GOC:cilia] +xref: NIF_Subcellular:sao95019936 +xref: Wikipedia:Centriole +is_a: GO:0043232 ! intracellular membraneless organelle +relationship: part_of GO:0005815 ! microtubule organizing center + +[Term] +id: GO:0005815 +name: microtubule organizing center +namespace: cellular_component +def: "An intracellular structure that can catalyze gamma-tubulin-dependent microtubule nucleation and that can anchor microtubules by interacting with their minus ends, plus ends or sides." [GOC:vw, ISBN:0815316194, PMID:17072892, PMID:17245416, Wikipedia:Microtubule_organizing_center] +subset: goslim_candida +subset: goslim_chembl +subset: goslim_euk_cellular_processes_ribbon +subset: goslim_generic +subset: goslim_yeast +synonym: "microtubule organising centre" EXACT [] +synonym: "MTOC" EXACT [] +xref: Wikipedia:Microtubule_organizing_center +is_a: GO:0110165 ! cellular anatomical structure +relationship: part_of GO:0015630 ! microtubule cytoskeleton + [Term] id: GO:0005829 name: cytosol @@ -51239,14 +57312,13 @@ subset: goslim_mouse subset: goslim_plant xref: NIF_Subcellular:sao101633890 xref: Wikipedia:Cytosol -is_a: GO:0110165 ! cellular anatomical entity +is_a: GO:0110165 ! cellular anatomical structure relationship: part_of GO:0005737 ! cytoplasm [Term] id: GO:0005840 name: ribosome namespace: cellular_component -alt_id: GO:0033279 def: "An intracellular organelle, about 200 A in diameter, consisting of RNA and protein. It is the site of protein biosynthesis resulting from translation of messenger RNA (mRNA). It consists of two subunits, one large and one small, each containing only protein and RNA. Both the ribosome and its subunits are characterized by their sedimentation coefficients, expressed in Svedberg units (symbol: S). Hence, the prokaryotic ribosome (70S) comprises a large (50S) subunit and a small (30S) subunit, while the eukaryotic ribosome (80S) comprises a large (60S) subunit and a small (40S) subunit. Two sites on the ribosomal large subunit are involved in translation, namely the aminoacyl site (A site) and peptidyl site (P site). Ribosomes from prokaryotes, eukaryotes, mitochondria, and chloroplasts have characteristically distinct ribosomal proteins." [ISBN:0198506732] subset: goslim_candida subset: goslim_chembl @@ -51264,10 +57336,10 @@ synonym: "membrane bound ribosome" NARROW [NIF_Subcellular:sao1291545653] synonym: "ribosomal RNA" RELATED [] xref: NIF_Subcellular:sao1429207766 xref: Wikipedia:Ribosome -is_a: GO:0043232 ! intracellular non-membrane-bounded organelle -is_a: PR:000050567 ! protein-containing material entity +is_a: GO:0043232 ! intracellular membraneless organelle relationship: capable_of_part_of GO:0006412 ! translation relationship: has_part CHEBI:33697 +relationship: has_part PR:000000001 ! protein [Term] id: GO:0005856 @@ -51288,7 +57360,7 @@ subset: goslim_plant_ribbon subset: goslim_prokaryote subset: goslim_yeast xref: Wikipedia:Cytoskeleton -is_a: GO:0043232 ! intracellular non-membrane-bounded organelle +is_a: GO:0043232 ! intracellular membraneless organelle [Term] id: GO:0005858 @@ -51388,8 +57460,6 @@ relationship: part_of GO:0015629 ! actin cytoskeleton id: GO:0005886 name: plasma membrane namespace: cellular_component -alt_id: GO:0005887 -alt_id: GO:0005904 def: "The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins." [ISBN:0716731363] subset: goslim_agr subset: goslim_candida @@ -51482,11 +57552,18 @@ xref: Wikipedia:Tight_junction is_a: GO:0070160 ! tight junction relationship: part_of GO:0043296 ! apical junction complex +[Term] +id: GO:0005927 +name: muscle tendon junction +namespace: cellular_component +def: "A cell-substrate junction found at the terminal anchorage site of skeletal muscle cells to tendons." [GOC:mtg_muscle, PMID:12842007] +synonym: "myotendinous junction" EXACT [] +is_a: GO:0030055 ! cell-substrate junction + [Term] id: GO:0005929 name: cilium namespace: cellular_component -alt_id: GO:0072372 def: "A specialized eukaryotic organelle that consists of a filiform extrusion of the cell surface and of some cytoplasmic parts. Each cilium is largely bounded by an extrusion of the cytoplasmic (plasma) membrane, and contains a regular longitudinal array of microtubules, anchored to a basal body." [GOC:cilia, GOC:curators, GOC:kmv, GOC:vw, ISBN:0198547684, PMID:16824949, PMID:17009929, PMID:20144998] comment: Note that we deem cilium and microtubule-based flagellum to be equivalent. In most eukaryotic species, intracellular sub-components of the cilium, such as the ciliary base and rootlet, are located near the plasma membrane. In Diplomonads such as Giardia, instead, the same ciliary parts are located further intracellularly. Also, 'cilium' may be used when axonemal structure and/or motility are unknown, or when axonemal structure is unusual. For all other cases, please refer to children of 'cilium'. Finally, note that any role of ciliary proteins in sensory events should be captured by annotating to relevant biological process terms. subset: goslim_chembl @@ -51502,7 +57579,6 @@ xref: NIF_Subcellular:sao787716553 xref: Wikipedia:Cilium is_a: GO:0043227 ! membrane-bounded organelle is_a: GO:0120025 ! plasma membrane bounded cell projection -is_a: PR:000050567 ! protein-containing material entity relationship: has_part GO:0030990 ! intraciliary transport particle relationship: RO:0002160 NCBITaxon:2759 ! only in taxon Eukaryota relationship: RO:0002162 NCBITaxon:2759 {all_only="true"} ! in taxon Eukaryota @@ -51517,8 +57593,6 @@ property_value: RO:0002161 NCBITaxon:5782 id: GO:0005930 name: axoneme namespace: cellular_component -alt_id: GO:0035085 -alt_id: GO:0035086 def: "The bundle of microtubules and associated proteins that forms the core of cilia (also called flagella) in eukaryotic cells and is responsible for their movements." [GOC:bf, GOC:cilia, ISBN:0198547684] comment: Note that cilia and eukaryotic flagella are deemed to be equivalent. In diplomonad species, such as Giardia, the axoneme may extend intracellularly up to 5um away from the plane of the plasma membrane. subset: goslim_pir @@ -51527,7 +57601,7 @@ synonym: "cilium axoneme" EXACT [] synonym: "flagellar axoneme" EXACT [] synonym: "flagellum axoneme" EXACT [] xref: Wikipedia:Axoneme -is_a: GO:0110165 ! cellular anatomical entity +is_a: GO:0110165 ! cellular anatomical structure relationship: has_part GO:0005874 ! microtubule relationship: part_of GO:0005856 ! cytoskeleton relationship: part_of GO:0097014 ! ciliary plasm @@ -51553,8 +57627,6 @@ property_value: term_tracker_item "https://github.com/geneontology/go-ontology/i id: GO:0005975 name: carbohydrate metabolic process namespace: biological_process -alt_id: GO:0044261 -alt_id: GO:0044723 def: "The chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y." [GOC:mah, ISBN:0198506732] subset: goslim_agr subset: goslim_candida @@ -51576,14 +57648,12 @@ intersection_of: GO:0008152 ! metabolic process intersection_of: has_primary_input_or_output CHEBI:16646 relationship: has_primary_input_or_output CHEBI:16646 property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/22880" xsd:anyURI -created_by: jl creation_date: 2012-10-23T15:40:34Z [Term] id: GO:0005976 name: polysaccharide metabolic process namespace: biological_process -alt_id: GO:0044263 def: "The chemical reactions and pathways involving a polysaccharide, a polymer of many (typically more than 10) monosaccharide residues linked glycosidically." [ISBN:0198547684] subset: goslim_pir synonym: "glycan metabolic process" NARROW [] @@ -51622,12 +57692,13 @@ xref: MetaCyc:GLYCOGENSYNTH-PWY {source="skos:narrowMatch"} xref: MetaCyc:PWY-5067 {source="skos:narrowMatch"} xref: MetaCyc:PWY-7900 {source="skos:narrowMatch"} is_a: GO:0005977 ! glycogen metabolic process -is_a: GO:0009250 ! glucan biosynthetic process +is_a: GO:0009058 ! biosynthetic process intersection_of: GO:0009058 ! biosynthetic process intersection_of: has_primary_output CHEBI:28087 relationship: has_primary_output CHEBI:28087 property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27107" xsd:anyURI property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28527" xsd:anyURI +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28968" xsd:anyURI [Term] id: GO:0005979 @@ -51749,7 +57820,7 @@ relationship: has_primary_input_or_output CHEBI:37396 [Term] id: GO:0006081 -name: cellular aldehyde metabolic process +name: aldehyde metabolic process namespace: biological_process def: "The chemical reactions and pathways involving aldehydes, any organic compound with the formula R-CH=O, as carried out by individual cells." [GOC:go_curators, ISBN:0198506732] subset: goslim_pir @@ -51757,10 +57828,11 @@ synonym: "aldehyde metabolism" EXACT [] synonym: "alkanal metabolic process" EXACT [] synonym: "alkanal metabolism" EXACT [] is_a: BFO:0000003 -is_a: GO:0044237 ! cellular metabolic process +is_a: GO:0008152 ! metabolic process intersection_of: GO:0008152 ! metabolic process intersection_of: has_primary_input_or_output CHEBI:17478 relationship: has_primary_input_or_output CHEBI:17478 +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28908" xsd:anyURI [Term] id: GO:0006082 @@ -51770,7 +57842,6 @@ def: "The chemical reactions and pathways involving organic acids, any acidic co subset: goslim_pir synonym: "organic acid metabolism" EXACT [] is_a: BFO:0000003 -is_a: GO:0044237 ! cellular metabolic process is_a: GO:0044281 ! small molecule metabolic process intersection_of: GO:0008152 ! metabolic process intersection_of: has_primary_input_or_output CHEBI:64709 @@ -51797,7 +57868,7 @@ subset: goslim_yeast synonym: "energy pathways" BROAD [] synonym: "intermediary metabolism" RELATED [GOC:mah] synonym: "metabolic energy generation" RELATED [] -is_a: GO:0044237 ! cellular metabolic process +is_a: GO:0008152 ! metabolic process [Term] id: GO:0006094 @@ -51806,13 +57877,16 @@ namespace: biological_process def: "The formation of glucose from noncarbohydrate precursors, such as pyruvate, amino acids and glycerol." [MetaCyc:GLUCONEO-PWY] synonym: "glucose biosynthesis" EXACT [] synonym: "glucose biosynthetic process" EXACT [] -xref: MetaCyc:GLUCONEO-PWY +xref: MetaCyc:GLUCONEO-PWY {source="skos:narrowMatch"} +xref: MetaCyc:PWY-6142 {source="skos:narrowMatch"} +xref: MetaCyc:PWY66-399 {source="skos:narrowMatch"} xref: Wikipedia:Gluconeogenesis is_a: GO:0006006 ! glucose metabolic process is_a: GO:0009058 ! biosynthetic process intersection_of: GO:0009058 ! biosynthetic process intersection_of: has_primary_output CHEBI:4167 relationship: has_primary_output CHEBI:4167 +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28953" xsd:anyURI [Term] id: GO:0006109 @@ -51829,7 +57903,6 @@ relationship: regulates GO:0005975 ! carbohydrate metabolic process id: GO:0006111 name: regulation of gluconeogenesis namespace: biological_process -alt_id: GO:0090526 def: "Any process that modulates the frequency, rate or extent of gluconeogenesis, the formation of glucose from noncarbohydrate precursors, such as pyruvate, amino acids and glycerol." [GOC:go_curators] synonym: "regulation of gluconeogenesis involved in cellular glucose homeostasis" RELATED [] synonym: "regulation of glucose biosynthesis" BROAD [] @@ -51839,7 +57912,6 @@ is_a: GO:0010906 ! regulation of glucose metabolic process intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0006094 ! gluconeogenesis relationship: regulates GO:0006094 ! gluconeogenesis -created_by: tb creation_date: 2013-01-18T12:47:43Z [Term] @@ -51855,7 +57927,6 @@ is_a: GO:0015980 ! energy derivation by oxidation of organic compounds id: GO:0006139 name: nucleobase-containing compound metabolic process namespace: biological_process -alt_id: GO:0055134 def: "Any cellular metabolic process involving nucleobases, nucleosides, nucleotides and nucleic acids." [GOC:ai] subset: goslim_pir subset: goslim_plant @@ -51889,7 +57960,6 @@ relationship: has_primary_output CHEBI:456216 id: GO:0006259 name: DNA metabolic process namespace: biological_process -alt_id: GO:0055132 def: "Any cellular metabolic process involving deoxyribonucleic acid. This is one of the two main types of nucleic acid, consisting of a long, unbranched macromolecule formed from one, or more commonly, two, strands of linked deoxyribonucleotides." [ISBN:0198506732] subset: goslim_agr subset: goslim_candida @@ -51927,7 +57997,6 @@ relationship: has_primary_input CHEBI:16991 id: GO:0006309 name: apoptotic DNA fragmentation namespace: biological_process -alt_id: GO:0008178 def: "The cleavage of DNA during apoptosis, which usually occurs in two stages: cleavage into fragments of about 50 kbp followed by cleavage between nucleosomes to yield 200 bp fragments." [GOC:dph, GOC:mah, GOC:mtg_apoptosis, GOC:tb, ISBN:0721639976, PMID:15723341, PMID:23379520] comment: DNA fragmentation in response to apoptotic signals is achieved through the activity of apoptotic nucleases. In human, these include DNA fragmentation factor (DFF) or caspase-activated DNase (CAD) and endonuclease G (Endo G) (reviewed in PMID:15723341). Caution is needed when apoptotic DNA laddering assays show presence of fragmented DNA. A positive assay may simply reflect the end point of a whole apoptotic process. Unless clear experimental evidence is available to show that a gene product is directly involved in fragmenting DNA, please do not annotate to GO:0006309 'apoptotic DNA fragmentation' and consider annotating instead to a more upstream process such as, e.g., GO:0042981 'regulation of apoptotic process', GO:0006915 'apoptotic process', GO:0097190 'apoptotic signaling pathway'. Also, note that gene products involved in compartmentalization of apoptotic nucleases and in activation or repression of their enzymatic activity should be annotated to the regulation term GO:1902510 'regulation of apoptotic DNA fragmentation' or to one of its children (see PMID:15723341). synonym: "chromatinolysis" BROAD [GOC:mtg_apoptosis] @@ -51959,11 +58028,6 @@ is_a: GO:0006259 ! DNA metabolic process id: GO:0006325 name: chromatin organization namespace: biological_process -alt_id: GO:0006333 -alt_id: GO:0006336 -alt_id: GO:0016568 -alt_id: GO:0031497 -alt_id: GO:0034724 def: "The assembly or remodeling of chromatin composed of DNA complexed with histones, other associated proteins, and sometimes RNA." [PMID:20404130] subset: goslim_generic subset: goslim_pombe @@ -51988,96 +58052,6 @@ relationship: results_in_organization_of GO:0000785 ! chromatin property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/22130" xsd:anyURI property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/23549" xsd:anyURI -[Term] -id: GO:0006351 -name: DNA-templated transcription -namespace: biological_process -alt_id: GO:0001121 -alt_id: GO:0006350 -alt_id: GO:0061018 -alt_id: GO:0061022 -def: "The synthesis of an RNA transcript from a DNA template." [GOC:jl, GOC:txnOH] -subset: goslim_drosophila -subset: goslim_euk_cellular_processes_ribbon -subset: goslim_generic -subset: goslim_metagenomics -subset: goslim_mouse -subset: goslim_pir -subset: goslim_pombe -subset: goslim_prokaryote -subset: goslim_prokaryote_ribbon -synonym: "bacterial transcription" NARROW [] -synonym: "cellular transcription" BROAD [] -synonym: "DNA-dependent transcription" EXACT [] -synonym: "transcription" BROAD [] -synonym: "transcription from bacterial-type RNA polymerase promoter" NARROW [] -synonym: "transcription, DNA-dependent" EXACT [GOC:txnOH] -synonym: "transcription, DNA-templated" EXACT [] -xref: Wikipedia:Transcription_(genetics) -relationship: part_of GO:0010467 ! gene expression -property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/14854" xsd:anyURI -property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/16737" xsd:anyURI -property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/22258" xsd:anyURI -property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/22555" xsd:anyURI - -[Term] -id: GO:0006355 -name: regulation of DNA-templated transcription -namespace: biological_process -alt_id: GO:0032583 -alt_id: GO:0045449 -alt_id: GO:0061019 -def: "Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription." [GOC:go_curators, GOC:txnOH] -subset: goslim_drosophila -subset: goslim_generic -subset: goslim_prokaryote -subset: goslim_prokaryote_ribbon -synonym: "regulation of cellular transcription, DNA-dependent" EXACT [] -synonym: "regulation of gene-specific transcription" RELATED [] -synonym: "regulation of transcription, DNA-dependent" EXACT [GOC:txnOH] -synonym: "regulation of transcription, DNA-templated" EXACT [] -synonym: "transcriptional control" BROAD [] -is_a: GO:0010468 ! regulation of gene expression -intersection_of: GO:0065007 ! biological regulation -intersection_of: regulates GO:0006351 ! DNA-templated transcription -relationship: regulates GO:0006351 ! DNA-templated transcription -property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/25256" xsd:anyURI - -[Term] -id: GO:0006357 -name: regulation of transcription by RNA polymerase II -namespace: biological_process -alt_id: GO:0006358 -alt_id: GO:0010551 -def: "Any process that modulates the frequency, rate or extent of transcription mediated by RNA polymerase II." [GOC:go_curators, GOC:txnOH] -synonym: "global transcription regulation from Pol II promoter" RELATED [] -synonym: "regulation of gene-specific transcription from RNA polymerase II promoter" RELATED [] -synonym: "regulation of global transcription from Pol II promoter" RELATED [] -synonym: "regulation of transcription from Pol II promoter" EXACT [] -synonym: "regulation of transcription from RNA polymerase II promoter" EXACT [] -synonym: "regulation of transcription from RNA polymerase II promoter, global" RELATED [] -is_a: GO:0006355 ! regulation of DNA-templated transcription -intersection_of: GO:0065007 ! biological regulation -intersection_of: regulates GO:0006366 ! transcription by RNA polymerase II -relationship: regulates GO:0006366 ! transcription by RNA polymerase II - -[Term] -id: GO:0006366 -name: transcription by RNA polymerase II -namespace: biological_process -alt_id: GO:0032568 -alt_id: GO:0032569 -def: "The synthesis of RNA from a DNA template by RNA polymerase II (RNAP II), originating at an RNA polymerase II promoter. Includes transcription of messenger RNA (mRNA) and certain small nuclear RNAs (snRNAs)." [GOC:jl, GOC:txnOH, ISBN:0321000382] -subset: goslim_yeast -synonym: "gene-specific transcription from RNA polymerase II promoter" RELATED [] -synonym: "general transcription from RNA polymerase II promoter" RELATED [] -synonym: "RNA polymerase II transcription factor activity" RELATED [] -synonym: "specific transcription from RNA polymerase II promoter" RELATED [GOC:mah] -synonym: "transcription from Pol II promoter" EXACT [] -synonym: "transcription from RNA polymerase II promoter" EXACT [] -is_a: GO:0006351 ! DNA-templated transcription -property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/14854" xsd:anyURI - [Term] id: GO:0006401 name: RNA catabolic process @@ -52140,9 +58114,6 @@ intersection_of: results_in_transport_across GO:0005635 ! nuclear envelope id: GO:0006412 name: translation namespace: biological_process -alt_id: GO:0006416 -alt_id: GO:0006453 -alt_id: GO:0043037 def: "The cellular metabolic process in which a protein is formed, using the sequence of a mature mRNA or circRNA molecule to specify the sequence of amino acids in a polypeptide chain. Translation is mediated by the ribosome, and begins with the formation of a ternary complex between aminoacylated initiator methionine tRNA, GTP, and initiation factor 2, which subsequently associates with the small subunit of the ribosome and an mRNA or circRNA. Translation ends with the release of a polypeptide chain from the ribosome." [GOC:go_curators] subset: goslim_candida subset: goslim_chembl @@ -52175,8 +58146,6 @@ relationship: starts_with GO:0006413 ! translational initiation id: GO:0006413 name: translational initiation namespace: biological_process -alt_id: GO:0006440 -alt_id: GO:0006454 def: "The process preceding formation of the peptide bond between the first two amino acids of a protein. This includes the formation of a complex of the ribosome, mRNA or circRNA, and an initiation complex that contains the first aminoacyl-tRNA." [ISBN:019879276X] subset: goslim_yeast synonym: "biopolymerisation" BROAD [] @@ -52184,7 +58153,7 @@ synonym: "biopolymerization" BROAD [] synonym: "protein synthesis initiation" BROAD [] synonym: "translation initiation" EXACT [] is_a: BFO:0000003 -is_a: GO:0044237 ! cellular metabolic process +is_a: GO:0008152 ! metabolic process relationship: part_of GO:0006412 ! translation relationship: starts_with GO:0001677 ! formation of translation initiation ternary complex @@ -52192,8 +58161,6 @@ relationship: starts_with GO:0001677 ! formation of translation initiation terna id: GO:0006414 name: translational elongation namespace: biological_process -alt_id: GO:0006442 -alt_id: GO:0006455 def: "The successive addition of amino acid residues to a nascent polypeptide chain during protein biosynthesis." [GOC:ems] subset: goslim_yeast synonym: "protein synthesis elongation" BROAD [] @@ -52205,8 +58172,6 @@ relationship: part_of GO:0006412 ! translation id: GO:0006415 name: translational termination namespace: biological_process -alt_id: GO:0006443 -alt_id: GO:0006456 def: "The process resulting in the release of a polypeptide chain from the ribosome, usually in response to a termination codon (UAA, UAG, or UGA in the universal genetic code)." [GOC:hjd, ISBN:019879276X] synonym: "protein synthesis termination" BROAD [] synonym: "translation termination" EXACT [] @@ -52218,7 +58183,6 @@ relationship: part_of GO:0006412 ! translation id: GO:0006417 name: regulation of translation namespace: biological_process -alt_id: GO:0006445 def: "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of proteins by the translation of mRNA or circRNA." [GOC:isa_complete] subset: goslim_yeast synonym: "regulation of protein anabolism" EXACT [] @@ -52335,7 +58299,6 @@ relationship: has_primary_input_or_output CHEBI:60466 id: GO:0006520 name: amino acid metabolic process namespace: biological_process -alt_id: GO:0006519 def: "The chemical reactions and pathways involving amino acids, carboxylic acids containing one or more amino groups." [ISBN:0198506732] subset: goslim_chembl subset: goslim_drosophila @@ -52358,16 +58321,15 @@ property_value: term_tracker_item "https://github.com/geneontology/go-ontology/i [Term] id: GO:0006521 -name: regulation of cellular amino acid metabolic process +name: regulation of amino acid metabolic process namespace: biological_process def: "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving amino acids." [GOC:go_curators] synonym: "regulation of amino acid metabolism" EXACT [] -is_a: GO:0010565 ! regulation of cellular ketone metabolic process -is_a: GO:0033238 ! regulation of amine metabolic process is_a: GO:0080090 ! regulation of primary metabolic process intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0006520 ! amino acid metabolic process relationship: regulates GO:0006520 ! amino acid metabolic process +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28908" xsd:anyURI [Term] id: GO:0006536 @@ -52409,7 +58371,6 @@ relationship: has_primary_output CHEBI:14321 id: GO:0006538 name: glutamate catabolic process namespace: biological_process -alt_id: GO:0019459 def: "The chemical reactions and pathways resulting in the breakdown of glutamate, the anion of 2-aminopentanedioic acid." [GOC:go_curators] synonym: "glutamate breakdown" EXACT [] synonym: "glutamate catabolism" EXACT [] @@ -52495,7 +58456,7 @@ relationship: has_primary_input CHEBI:57595 [Term] id: GO:0006575 -name: cellular modified amino acid metabolic process +name: modified amino acid metabolic process namespace: biological_process def: "The chemical reactions and pathways involving compounds derived from amino acids, organic acids containing one or more amino substituents." [GOC:ai] subset: goslim_drosophila @@ -52504,14 +58465,15 @@ subset: goslim_prokaryote synonym: "amino acid derivative metabolic process" EXACT [] synonym: "cellular amino acid derivative metabolic process" EXACT [] synonym: "cellular amino acid derivative metabolism" EXACT [] +synonym: "cellular modified amino acid metabolic process" EXACT [GOC:mah] synonym: "cellular modified amino acid metabolism" EXACT [GOC:mah] -synonym: "modified amino acid metabolic process" EXACT [GOC:mah] synonym: "modified amino acid metabolism" EXACT [GOC:mah] is_a: BFO:0000003 -is_a: GO:0044237 ! cellular metabolic process +is_a: GO:0008152 ! metabolic process intersection_of: GO:0008152 ! metabolic process intersection_of: has_primary_input_or_output CHEBI:83821 relationship: has_primary_input_or_output CHEBI:83821 +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28908" xsd:anyURI [Term] id: GO:0006576 @@ -52579,7 +58541,6 @@ intersection_of: results_in_transport_across GO:0005635 ! nuclear envelope id: GO:0006611 name: protein export from nucleus namespace: biological_process -alt_id: GO:0097349 def: "The directed movement of a protein from the nucleus into the cytoplasm." [GOC:jl] synonym: "copper-induced protein export from nucleus" RELATED [GOC:al] synonym: "protein export from cell nucleus" EXACT [] @@ -52634,6 +58595,19 @@ intersection_of: GO:0008152 ! metabolic process intersection_of: has_primary_input_or_output CHEBI:18059 relationship: has_primary_input_or_output CHEBI:18059 +[Term] +id: GO:0006643 +name: membrane lipid metabolic process +namespace: biological_process +def: "The chemical reactions and pathways involving membrane lipids, any lipid found in or associated with a biological membrane." [GOC:ai] +synonym: "membrane lipid metabolism" EXACT [] +is_a: GO:0006629 ! lipid metabolic process +intersection_of: GO:0008152 ! metabolic process +intersection_of: has_primary_input_or_output CHEBI:18059 +intersection_of: occurs_in GO:0016020 ! membrane +relationship: occurs_in GO:0016020 ! membrane +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28908" xsd:anyURI + [Term] id: GO:0006687 name: glycosphingolipid metabolic process @@ -52709,7 +58683,6 @@ synonym: "C21-steroid hormone synthesis" EXACT [] is_a: GO:0006694 ! steroid biosynthetic process is_a: GO:0008207 ! C21-steroid hormone metabolic process is_a: GO:0042446 ! hormone biosynthetic process -is_a: GO:0044249 ! cellular biosynthetic process intersection_of: GO:0009058 ! biosynthetic process intersection_of: has_primary_output CHEBI:64600 relationship: has_primary_output CHEBI:64600 @@ -52863,8 +58836,6 @@ relationship: has_primary_input CHEBI:24943 id: GO:0006754 name: ATP biosynthetic process namespace: biological_process -alt_id: GO:0006758 -alt_id: GO:0006759 def: "The chemical reactions and pathways resulting in the formation of ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator." [GOC:go_curators, ISBN:0198506732] synonym: "ATP anabolism" EXACT [] synonym: "ATP biosynthesis" EXACT [] @@ -52906,13 +58877,25 @@ intersection_of: GO:0008152 ! metabolic process intersection_of: has_primary_input_or_output CHEBI:18421 relationship: has_primary_input_or_output CHEBI:18421 +[Term] +id: GO:0006809 +name: nitric oxide biosynthetic process +namespace: biological_process +def: "The chemical reactions and pathways resulting in the formation of nitric oxide, nitrogen monoxide (NO), a colorless gas only slightly soluble in water." [GOC:ai] +synonym: "nitric oxide anabolism" EXACT [] +synonym: "nitric oxide biosynthesis" EXACT [] +synonym: "nitric oxide formation" EXACT [] +synonym: "nitric oxide synthesis" EXACT [] +is_a: GO:0009058 ! biosynthetic process +is_a: GO:0046209 ! nitric oxide metabolic process +intersection_of: GO:0009058 ! biosynthetic process +intersection_of: has_primary_output CHEBI:16480 +relationship: has_primary_output CHEBI:16480 + [Term] id: GO:0006810 name: transport namespace: biological_process -alt_id: GO:0015457 -alt_id: GO:0015460 -alt_id: GO:0044765 def: "The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter or a transporter complex, a pore or a motor protein." [GOC:dos, GOC:dph, GOC:jl, GOC:mah] comment: Note that this term should not be used for direct annotation. It should be possible to make a more specific annotation to one of the children of this term, for e.g. to transmembrane transport, to microtubule-based transport or to vesicle-mediated transport. subset: gocheck_do_not_annotate @@ -52927,7 +58910,6 @@ subset: goslim_prokaryote_ribbon synonym: "single-organism transport" RELATED [] is_a: GO:0051234 ! establishment of localization property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/20292" xsd:anyURI -created_by: jl creation_date: 2012-12-13T16:25:32Z [Term] @@ -52949,9 +58931,6 @@ relationship: has_primary_input CHEBI:24867 id: GO:0006812 name: monoatomic cation transport namespace: biological_process -alt_id: GO:0006819 -alt_id: GO:0015674 -alt_id: GO:0072512 def: "The directed movement of a monoatomic cation, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Monatomic cations (also called simple cations) are positively charged ions consisting of exactly one atom." [GOC:ai] synonym: "cation transport" BROAD [] synonym: "di-, tri-valent inorganic cation transport" NARROW [GOC:mah] @@ -52966,8 +58945,6 @@ relationship: has_primary_input CHEBI:23906 id: GO:0006813 name: potassium ion transport namespace: biological_process -alt_id: GO:0015458 -alt_id: GO:0071804 def: "The directed movement of potassium ions (K+) into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:ai] synonym: "cellular potassium ion transport" EXACT [] synonym: "K+ conductance" RELATED [] @@ -52982,15 +58959,12 @@ is_a: GO:0006810 ! transport intersection_of: GO:0006810 ! transport intersection_of: has_primary_input CHEBI:29103 relationship: has_primary_input CHEBI:29103 -created_by: mah creation_date: 2010-09-03T02:39:22Z [Term] id: GO:0006814 name: sodium ion transport namespace: biological_process -alt_id: GO:0006834 -alt_id: GO:0016974 def: "The directed movement of sodium ions (Na+) into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:ai] synonym: "mitochondrial sodium/calcium ion exchange" NARROW [] synonym: "sodium channel auxiliary protein activity" RELATED [GOC:mah] @@ -53034,11 +59008,6 @@ relationship: has_primary_input CHEBI:43474 id: GO:0006826 name: iron ion transport namespace: biological_process -alt_id: GO:0015681 -alt_id: GO:0015682 -alt_id: GO:0015684 -alt_id: GO:0033216 -alt_id: GO:0097286 def: "The directed movement of iron (Fe) ions into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:ai] synonym: "ferric ion import" NARROW [] synonym: "ferric ion transport" NARROW [] @@ -53054,7 +59023,6 @@ is_a: GO:0006810 ! transport intersection_of: GO:0006810 ! transport intersection_of: has_primary_input CHEBI:24875 relationship: has_primary_input CHEBI:24875 -created_by: pr creation_date: 2012-04-18T03:33:45Z [Term] @@ -53072,7 +59040,6 @@ relationship: has_primary_input CHEBI:15377 id: GO:0006835 name: dicarboxylic acid transport namespace: biological_process -alt_id: GO:0006841 def: "The directed movement of dicarboxylic acids into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:krc] synonym: "sodium:dicarboxylate transport" RELATED [] is_a: BFO:0000003 @@ -53128,7 +59095,6 @@ intersection_of: occurs_in GO:0005576 ! extracellular region id: GO:0006865 name: amino acid transport namespace: biological_process -alt_id: GO:0006866 def: "The directed movement of amino acids, organic acids containing one or more amino substituents, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:ai] subset: goslim_pir subset: goslim_yeast @@ -53216,7 +59182,6 @@ is_a: GO:0019725 ! cellular homeostasis id: GO:0006886 name: intracellular protein transport namespace: biological_process -alt_id: GO:0032779 def: "The directed movement of proteins in a cell, including the movement of proteins between specific compartments or structures within a cell, such as organelles of a eukaryotic cell." [GOC:mah] subset: goslim_generic subset: goslim_prokaryote @@ -53232,8 +59197,6 @@ relationship: part_of GO:0008104 ! protein localization id: GO:0006887 name: exocytosis namespace: biological_process -alt_id: GO:0016194 -alt_id: GO:0016195 def: "A process of secretion by a cell that results in the release of intracellular molecules (e.g. hormones, matrix proteins) contained within a membrane-bounded vesicle. Exocytosis can occur either by full fusion, when the vesicle collapses into the plasma membrane, or by a kiss-and-run mechanism that involves the formation of a transient contact, a pore, between a granule (for example of chromaffin cells) and the plasma membrane. The latter process most of the time leads to only partial secretion of the granule content. Exocytosis begins with steps that prepare vesicles for fusion with the membrane (tethering and docking) and ends when molecules are secreted from the cell." [GOC:mah, ISBN:0716731363, PMID:22323285] subset: goslim_yeast synonym: "nonselective vesicle exocytosis" RELATED [] @@ -53287,9 +59250,6 @@ relationship: has_target_start_location GO:0005794 ! Golgi apparatus id: GO:0006897 name: endocytosis namespace: biological_process -alt_id: GO:0016193 -alt_id: GO:0016196 -alt_id: GO:0098701 def: "A vesicle-mediated transport process in which cells take up external materials or membrane constituents by the invagination of a part of the plasma membrane to form a new membrane-bounded vesicle." [GOC:mah, ISBN:0198506732, ISBN:0716731363, Wikipedia:Endocytosis] subset: goslim_yeast synonym: "endocytic import into cell" EXACT [] @@ -53309,8 +59269,6 @@ property_value: term_tracker_item "https://github.com/geneontology/go-ontology/i id: GO:0006900 name: vesicle budding from membrane namespace: biological_process -alt_id: GO:0006902 -alt_id: GO:1902591 def: "The evagination of a membrane, resulting in formation of a vesicle." [GOC:jid, GOC:tb] synonym: "membrane evagination" EXACT [] synonym: "nonselective vesicle assembly" RELATED [] @@ -53322,7 +59280,6 @@ synonym: "vesicle formation" EXACT [] is_a: GO:0016050 ! vesicle organization is_a: GO:0061024 ! membrane organization relationship: part_of GO:0016192 ! vesicle-mediated transport -created_by: jl creation_date: 2013-12-19T15:26:17Z [Term] @@ -53361,7 +59318,6 @@ property_value: term_tracker_item "https://github.com/geneontology/go-ontology/i id: GO:0006913 name: nucleocytoplasmic transport namespace: biological_process -alt_id: GO:0000063 def: "The directed movement of molecules between the nucleus and the cytoplasm." [GOC:go_curators] comment: Note that transport through the nuclear pore complex is not transmembrane because the nuclear membrane is a double membrane, and is not traversed. subset: goslim_chembl @@ -53382,8 +59338,6 @@ relationship: results_in_transport_to_from_or_in GO:0031981 ! nuclear lumen id: GO:0006915 name: apoptotic process namespace: biological_process -alt_id: GO:0006917 -alt_id: GO:0008632 def: "A programmed cell death process which begins when a cell receives an internal (e.g. DNA damage) or external signal (e.g. an extracellular death ligand), and proceeds through a series of biochemical events (signaling pathway phase) which trigger an execution phase. The execution phase is the last step of an apoptotic process, and is typically characterized by rounding-up of the cell, retraction of pseudopodes, reduction of cellular volume (pyknosis), chromatin condensation, nuclear fragmentation (karyorrhexis), plasma membrane blebbing and fragmentation of the cell into apoptotic bodies. When the execution phase is completed, the cell has died." [GOC:cjm, GOC:dhl, GOC:ecd, GOC:go_curators, GOC:mtg_apoptosis, GOC:tb, ISBN:0198506732, PMID:18846107, PMID:21494263] synonym: "activation of apoptosis" NARROW [] synonym: "apoptosis" NARROW [] @@ -53540,8 +59494,6 @@ property_value: term_tracker_item "https://github.com/geneontology/go-ontology/i id: GO:0006952 name: defense response namespace: biological_process -alt_id: GO:0002217 -alt_id: GO:0042829 def: "Reactions, triggered in response to the presence of a foreign body or the occurrence of an injury, which result in restriction of damage to the organism attacked or prevention/recovery from the infection caused by the attack." [GOC:go_curators] synonym: "antimicrobial peptide activity" RELATED [] synonym: "defence response" EXACT [] @@ -53582,7 +59534,6 @@ is_a: GO:0006955 ! immune response id: GO:0006996 name: organelle organization namespace: biological_process -alt_id: GO:1902589 def: "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of an organelle within a cell. An organelle is an organized structure of distinctive morphology and function. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton. Excludes the plasma membrane." [GOC:mah] comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. subset: gocheck_do_not_annotate @@ -53597,14 +59548,12 @@ intersection_of: GO:0016043 ! cellular component organization intersection_of: results_in_organization_of GO:0043226 ! organelle relationship: results_in_organization_of GO:0043226 ! organelle property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27189" xsd:anyURI -created_by: jl creation_date: 2013-12-19T15:25:51Z [Term] id: GO:0006997 name: nucleus organization namespace: biological_process -alt_id: GO:0048287 def: "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the nucleus." [GOC:dph, GOC:ems, GOC:jl, GOC:mah] subset: goslim_candida subset: goslim_drosophila @@ -53807,7 +59756,6 @@ relationship: results_in_organization_of GO:0005794 ! Golgi apparatus id: GO:0007033 name: vacuole organization namespace: biological_process -alt_id: GO:0044086 def: "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a vacuole." [GOC:mah] subset: goslim_drosophila subset: goslim_pir @@ -53895,6 +59843,19 @@ intersection_of: GO:0034329 ! cell junction assembly intersection_of: results_in_assembly_of GO:0005911 ! cell-cell junction relationship: results_in_assembly_of GO:0005911 ! cell-cell junction +[Term] +id: GO:0007044 +name: cell-substrate junction assembly +namespace: biological_process +def: "The aggregation, arrangement and bonding together of a set of components to form a junction between a cell and its substrate." [GOC:mah] +comment: The primary label for merged term was 'cell-substrate adherens junction assembly' GO:0007045. The term was merged into the parent 'cell-substrate junction assembly', because, based on the most recent litarature, 'adherens junction' is always a 'cell-cell junction' (PMID:20571587, PMID:17854762, PMID:21422226, PMID:28096264, PMID:28401269, PMID:26923917). +synonym: "cell-substrate adherens junction assembly" RELATED [] +is_a: GO:0034329 ! cell junction assembly +is_a: GO:0150115 ! cell-substrate junction organization +intersection_of: GO:0034329 ! cell junction assembly +intersection_of: results_in_assembly_of GO:0030055 ! cell-substrate junction +relationship: results_in_assembly_of GO:0030055 ! cell-substrate junction + [Term] id: GO:0007049 name: cell cycle @@ -53973,7 +59934,6 @@ relationship: regulates GO:0140014 ! mitotic nuclear division id: GO:0007097 name: nuclear migration namespace: biological_process -alt_id: GO:0040023 def: "The directed movement of the nucleus to a specific location within a cell." [GOC:ai] synonym: "establishment of cell nucleus localization" RELATED [] synonym: "establishment of localization of nucleus" RELATED [] @@ -54078,7 +60038,6 @@ is_a: GO:0009987 ! cellular process id: GO:0007155 name: cell adhesion namespace: biological_process -alt_id: GO:0098602 def: "The attachment of a cell, either to another cell or to an underlying substrate such as the extracellular matrix, via cell adhesion molecules." [GOC:hb, GOC:pf] subset: goslim_candida subset: goslim_chembl @@ -54093,7 +60052,6 @@ synonym: "cell adhesion molecule activity" RELATED [] synonym: "single organism cell adhesion" RELATED [] xref: Wikipedia:Cell_adhesion is_a: GO:0009987 ! cellular process -created_by: dos creation_date: 2014-04-15T15:59:10Z [Term] @@ -54132,8 +60090,6 @@ relationship: negatively_regulates GO:0007155 ! cell adhesion id: GO:0007163 name: establishment or maintenance of cell polarity namespace: biological_process -alt_id: GO:0030012 -alt_id: GO:0030467 def: "Any cellular process that results in the specification, formation or maintenance of anisotropic intracellular organization or cell growth patterns." [GOC:mah] subset: goslim_drosophila subset: goslim_generic @@ -54148,11 +60104,6 @@ is_a: GO:0009987 ! cellular process id: GO:0007165 name: signal transduction namespace: biological_process -alt_id: GO:0023014 -alt_id: GO:0023015 -alt_id: GO:0023016 -alt_id: GO:0023033 -alt_id: GO:0023045 def: "The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell." [GOC:go_curators, GOC:mtg_signaling_feb11] comment: Note that signal transduction is defined broadly to include a ligand interacting with a receptor, downstream signaling steps and a response being triggered. A change in form of the signal in every step is not necessary. Note that in many cases the end of this process is regulation of the initiation of transcription. Note that specific transcription factors may be annotated to this term, but core/general transcription machinery such as RNA polymerase should not. subset: goslim_candida @@ -54205,7 +60156,6 @@ property_value: term_tracker_item "https://github.com/geneontology/go-ontology/i id: GO:0007186 name: G protein-coupled receptor signaling pathway namespace: biological_process -alt_id: GO:0038042 def: "The series of molecular signals initiated by a ligand binding to its receptor, in which the activated receptor promotes the exchange of GDP for GTP on the alpha-subunit of an associated heterotrimeric G-protein complex. The GTP-bound activated alpha-G-protein then dissociates from the beta- and gamma-subunits to further transmit the signal within the cell. The pathway begins with receptor-ligand interaction, and ends with regulation of a downstream cellular process. The pathway can start from the plasma membrane, Golgi or nuclear membrane." [GOC:bf, GOC:mah, PMID:16902576, PMID:24568158, Wikipedia:G_protein-coupled_receptor] subset: goslim_drosophila synonym: "dimeric G-protein coupled receptor signaling pathway" NARROW [] @@ -54330,7 +60280,6 @@ relationship: has_participant GO:0045202 ! synapse id: GO:0007269 name: neurotransmitter secretion namespace: biological_process -alt_id: GO:0010554 def: "The regulated release of neurotransmitter from the presynapse into the synaptic cleft via calcium-regulated exocytosis during synaptic transmission." [GOC:dph] comment: A neurotransmitter is any of a group of substances that are released on excitation from the axon terminal of a presynaptic neuron of the central or peripheral nervous system and travel across the synaptic cleft to either excite or inhibit the target cell. Among the many substances that have the properties of a neurotransmitter are acetylcholine, noradrenaline, adrenaline, dopamine, glycine, gamma-aminobutyrate, glutamic acid, substance P, enkephalins, endorphins and serotonin. subset: goslim_synapse @@ -54389,7 +60338,6 @@ property_value: term_tracker_item "https://github.com/geneontology/go-ontology/i id: GO:0007276 name: gamete generation namespace: biological_process -alt_id: GO:0009552 def: "The generation and maintenance of gametes in a multicellular organism. A gamete is a haploid reproductive cell." [GOC:ems, GOC:mtg_sensu] synonym: "gametogenesis" RELATED [] is_a: GO:0048609 ! multicellular organismal reproductive process @@ -54574,7 +60522,6 @@ relationship: results_in_movement_of CL:0000579 ! border follicle cell id: GO:0007308 name: oocyte construction namespace: biological_process -alt_id: GO:0048110 def: "The synthesis, deposition, and organization of the materials in a cell of an ovary; where the cell can then undergo meiosis and form an ovum. An example of this is found in Drosophila melanogaster." [GOC:dph, GOC:ems, GOC:mtg_sensu, GOC:tb, ISBN:0198506732] synonym: "oocyte arrangement" EXACT [GOC:dph, GOC:tb] is_a: GO:0003006 ! developmental process involved in reproduction @@ -54588,7 +60535,6 @@ relationship: results_in_formation_of CL:0000023 ! oocyte id: GO:0007309 name: oocyte axis specification namespace: biological_process -alt_id: GO:0048111 def: "The establishment, maintenance and elaboration of an axis in the oocyte. An example of this is found in Drosophila melanogaster." [GOC:mtg_sensu, ISBN:0879694238] synonym: "oocyte axis determination" RELATED [] is_a: BFO:0000003 @@ -54603,7 +60549,6 @@ relationship: part_of GO:0007308 ! oocyte construction id: GO:0007314 name: oocyte anterior/posterior axis specification namespace: biological_process -alt_id: GO:0048112 def: "Polarization of the oocyte along its anterior-posterior axis. An example of this is found in Drosophila melanogaster." [GOC:dph, GOC:mtg_sensu, GOC:tb, ISBN:0879694238] synonym: "oocyte anterior/posterior axis determination" EXACT [GOC:dph, GOC:tb] is_a: GO:0007309 ! oocyte axis specification @@ -54668,7 +60613,6 @@ relationship: regulates GO:0000278 ! mitotic cell cycle id: GO:0007349 name: cellularization namespace: biological_process -alt_id: GO:0009796 def: "The separation of a multi-nucleate cell or syncytium into individual cells. An example of this is found in Drosophila melanogaster embryo development." [GOC:go_curators, GOC:mtg_sensu, ISBN:0716731363] is_a: GO:0048646 ! anatomical structure formation involved in morphogenesis relationship: part_of GO:0007275 ! multicellular organism development @@ -54762,8 +60706,6 @@ relationship: results_in_development_of UBERON:0001016 ! nervous system id: GO:0007405 name: neuroblast proliferation namespace: biological_process -alt_id: GO:0043349 -alt_id: GO:0043350 def: "The expansion of a neuroblast population by cell division. A neuroblast is any cell that will divide and give rise to a neuron." [GOC:ai, GOC:mtg_sensu, GOC:sart] is_a: BFO:0000003 is_a: GO:0061351 ! neural precursor cell proliferation @@ -54795,8 +60737,6 @@ relationship: negatively_regulates GO:0007405 ! neuroblast proliferation id: GO:0007407 name: neuroblast activation namespace: biological_process -alt_id: GO:0043351 -alt_id: GO:0043352 def: "A change in the morphology or behavior of a neuroblast resulting from exposure to an activating factor such as a cellular or soluble ligand." [GOC:go_curators, GOC:mtg_sensu] is_a: BFO:0000003 is_a: GO:0001775 ! cell activation @@ -54804,13 +60744,11 @@ intersection_of: GO:0001775 ! cell activation intersection_of: has_primary_input CL:0000031 ! neuroblast (sensu Vertebrata) relationship: has_primary_input CL:0000031 ! neuroblast (sensu Vertebrata) relationship: part_of GO:0048699 ! generation of neurons -relationship: RO:0002162 NCBITaxon:33208 {all_only="true"} ! in taxon Metazoa [Term] id: GO:0007409 name: axonogenesis namespace: biological_process -alt_id: GO:0007410 def: "De novo generation of a long process of a neuron, including the terminal branched region. Refers to the morphogenesis or creation of shape or form of the developing axon, which carries efferent (outgoing) action potentials from the cell body towards target cells." [GOC:dph, GOC:jid, GOC:pg, GOC:pr, ISBN:0198506732] comment: Note that 'axonogenesis' differs from 'axon development' in that the latter also covers other processes, such as axon regeneration (regrowth after loss or damage, not necessarily of the whole axon). synonym: "axon growth" NARROW [] @@ -55080,7 +61018,6 @@ relationship: results_in_development_of UBERON:0003855 ! gonad mesenchyme id: GO:0007507 name: heart development namespace: biological_process -alt_id: GO:0007511 def: "The process whose specific outcome is the progression of the heart over time, from its formation to the mature structure. The heart is a hollow, muscular organ, which, by contracting rhythmically, keeps up the circulation of the blood." [GOC:jid, UBERON:0000948] synonym: "cardiac development" RELATED [] synonym: "dorsal vessel development" NARROW [] @@ -55121,7 +61058,6 @@ relationship: results_in_development_of UBERON:0001630 ! muscle organ id: GO:0007519 name: skeletal muscle tissue development namespace: biological_process -alt_id: GO:0048637 def: "The developmental sequence of events leading to the formation of adult skeletal muscle tissue. The main events are: the fusion of myoblasts to form myotubes that increase in size by further fusion to them of myoblasts, the formation of myofibrils within their cytoplasm and the establishment of functional neuromuscular junctions with motor neurons. At this stage they can be regarded as mature muscle fibers." [GOC:mtg_muscle] synonym: "myogenesis" RELATED [] is_a: GO:0014706 ! striated muscle tissue development @@ -55155,8 +61091,6 @@ is_a: GO:0003006 ! developmental process involved in reproduction id: GO:0007552 name: metamorphosis namespace: biological_process -alt_id: GO:0046698 -alt_id: GO:0046699 def: "A biological process in which an animal physically develops after birth or hatching, involving a conspicuous and relatively abrupt change in the animal's form or structure. Examples include the change from tadpole to frog, and the change from larva to adult. An example of this is found in Drosophila melanogaster." [GOC:sensu, ISBN:0198506732, ISBN:0721662544] xref: Wikipedia:Metamorphosis is_a: GO:0007275 ! multicellular organism development @@ -55167,7 +61101,7 @@ name: regulation of ecdysteroid metabolic process namespace: biological_process def: "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving ecdysteroids, a group of polyhydroxylated ketosteroids which initiate post-embryonic development, including the metamorphosis of immature forms and the development of the reproductive system and the maturation of oocytes in adult females." [ISBN:0198506732] synonym: "regulation of ecdysteroid metabolism" EXACT [] -is_a: GO:0010565 ! regulation of cellular ketone metabolic process +is_a: GO:0010565 ! regulation of ketone metabolic process is_a: GO:0032350 ! regulation of hormone metabolic process intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0045455 ! ecdysteroid metabolic process @@ -55242,7 +61176,6 @@ relationship: regulates GO:0045443 ! juvenile hormone secretion id: GO:0007560 name: imaginal disc morphogenesis namespace: biological_process -alt_id: GO:0007452 def: "The process in which the anatomical structures derived from an imaginal disc are generated and organized. The imaginal discs are epithelial infoldings in the larvae of holometabolous insects that develop into adult appendages (legs, antennae, wings, etc.) during metamorphosis from larval to adult form." [GOC:jid] synonym: "imaginal disc metamorphosis" EXACT [] is_a: GO:0009887 ! animal organ morphogenesis @@ -55406,9 +61339,6 @@ is_a: GO:0007606 ! sensory perception of chemical stimulus id: GO:0007610 name: behavior namespace: biological_process -alt_id: GO:0023032 -alt_id: GO:0044708 -alt_id: GO:0044709 def: "The internally coordinated responses (actions or inactions) of animals (individuals or groups) to internal or external stimuli, via a mechanism that involves nervous system activity." [GOC:ems, GOC:jl, ISBN:0395448956, PMID:20160973] comment: 1. Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation reviews.\n2. While a broader definition of behavior encompassing plants and single cell organisms would be justified on the basis of some usage (see PMID:20160973 for discussion), GO uses a tight definition that limits behavior to animals and to responses involving the nervous system, excluding plant responses that GO classifies under development, and responses of unicellular organisms that has general classifications for covering the responses of cells in multicellular organisms (e.g. cell chemotaxis). subset: gocheck_do_not_annotate @@ -55424,7 +61354,6 @@ disjoint_from: GO:0032502 ! developmental process relationship: process_has_causal_agent UBERON:0001016 ! nervous system relationship: RO:0002160 NCBITaxon:33208 ! only in taxon Metazoa relationship: RO:0002162 NCBITaxon:33208 {all_only="true"} ! in taxon Metazoa -created_by: jl creation_date: 2012-09-20T14:06:08Z [Term] @@ -55495,7 +61424,6 @@ relationship: part_of GO:0042221 ! response to chemical id: GO:0008015 name: blood circulation namespace: biological_process -alt_id: GO:0070261 def: "The flow of blood through the body of an animal, enabling the transport of nutrients to the tissues and the removal of waste products." [GOC:mtg_heart, ISBN:0192800825] subset: goslim_pir synonym: "hemolymph circulation" RELATED [] @@ -55616,7 +61544,6 @@ is_a: GO:0005515 ! protein binding id: GO:0008094 name: ATP-dependent activity, acting on DNA namespace: molecular_function -alt_id: GO:0004011 def: "Catalytic activity that acts to modify DNA, driven by ATP hydrolysis." [GOC:pdt] synonym: "adenosinetriphosphatase (DNA-dependent)" EXACT [] synonym: "ATPase activity, acting on DNA" EXACT [] @@ -55636,9 +61563,6 @@ property_value: term_tracker_item "https://github.com/geneontology/go-ontology/i id: GO:0008104 name: protein localization namespace: biological_process -alt_id: GO:0008105 -alt_id: GO:0016249 -alt_id: GO:0034613 def: "Any process in which a protein is transported to, or maintained in, a specific location." [GOC:ai] subset: goslim_drosophila synonym: "asymmetric protein localisation" RELATED [GOC:mah] @@ -55677,9 +61601,6 @@ property_value: term_tracker_item "https://github.com/geneontology/go-ontology/i id: GO:0008150 name: biological_process namespace: biological_process -alt_id: GO:0000004 -alt_id: GO:0007582 -alt_id: GO:0044699 def: "A biological process is the execution of a genetically-encoded biological module or program. It consists of all the steps required to achieve the specific biological objective of the module. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence." [GOC:pdt] comment: Note that, in addition to forming the root of the biological process ontology, this term is recommended for the annotation of gene products whose biological process is unknown. When this term is used for annotation, it indicates that no information was available about the biological process of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this. subset: goslim_candida @@ -55696,16 +61617,13 @@ synonym: "single-organism process" RELATED [] xref: Wikipedia:Biological_process is_a: BFO:0000015 property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/24968" xsd:anyURI -created_by: jl creation_date: 2012-09-19T15:05:24Z [Term] id: GO:0008152 name: metabolic process namespace: biological_process -alt_id: GO:0044236 -alt_id: GO:0044710 -def: "The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation." [GOC:go_curators, ISBN:0198547684] +def: "A cellular process consisting of the biochemical pathways by which a living organism transforms chemical substances. This includes including anabolism (biosynthetic process) and catabolism (catabolic process). Metabolic processes includes the transformation of small molecules, as well macromolecular processes such as DNA repair and replication, protein synthesis and degradation." [GOC:go_curators, ISBN:0198547684] comment: Note that metabolic processes do not include single functions or processes such as protein-protein interactions, protein-nucleic acids, nor receptor-ligand interactions. subset: gocheck_do_not_annotate subset: goslim_chembl @@ -55714,24 +61632,19 @@ subset: goslim_metagenomics subset: goslim_pir subset: goslim_plant subset: goslim_prokaryote_ribbon -synonym: "metabolic process resulting in cell growth" NARROW [] synonym: "metabolism" EXACT [] -synonym: "metabolism resulting in cell growth" NARROW [] -synonym: "multicellular organism metabolic process" NARROW [] -synonym: "single-organism metabolic process" RELATED [] xref: Wikipedia:Metabolism -is_a: GO:0008150 ! biological_process +is_a: GO:0009987 ! cellular process disjoint_from: GO:0044848 ! biological phase disjoint_from: GO:0051179 ! localization property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/26424" xsd:anyURI -created_by: jl +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28932" xsd:anyURI creation_date: 2012-10-17T15:46:40Z [Term] id: GO:0008186 name: ATP-dependent activity, acting on RNA namespace: molecular_function -alt_id: GO:0004010 def: "Catalysis of the reaction: ATP + H2O = ADP + phosphate; this reaction requires the presence of RNA, and it drives another reaction." [GOC:jl] synonym: "ATPase activity, acting on RNA" EXACT [] synonym: "ATPase, acting on RNA" EXACT [] @@ -55800,7 +61713,6 @@ namespace: biological_process def: "The chemical reactions and pathways involving C21-steroid hormones, steroid compounds containing 21 carbons which function as hormones." [GOC:ai] synonym: "C21-steroid hormone metabolism" EXACT [] is_a: GO:0008202 ! steroid metabolic process -is_a: GO:0009987 ! cellular process is_a: GO:0042445 ! hormone metabolic process intersection_of: GO:0008152 ! metabolic process intersection_of: has_primary_input_or_output CHEBI:64600 @@ -55840,7 +61752,6 @@ namespace: biological_process def: "The chemical reactions and pathways involving mineralocorticoids, hormonal C21 corticosteroids synthesized from cholesterol. Mineralocorticoids act primarily on water and electrolyte balance." [ISBN:0198506732] synonym: "mineralocorticoid metabolism" EXACT [] is_a: GO:0008202 ! steroid metabolic process -is_a: GO:0009987 ! cellular process is_a: GO:0042445 ! hormone metabolic process intersection_of: GO:0008152 ! metabolic process intersection_of: has_primary_input_or_output CHEBI:25354 @@ -56031,8 +61942,6 @@ is_a: GO:0007612 ! learning id: GO:0008320 name: protein transmembrane transporter activity namespace: molecular_function -alt_id: GO:0015266 -alt_id: GO:0015463 def: "Enables the transfer of a protein from one side of a membrane to the other." [GOC:jl] synonym: "protein channel activity" RELATED [] xref: Reactome:R-HSA-1268022 "TOMM40 complex translocates proteins from the cytosol to the mitochondrial intermembrane space" @@ -56091,7 +62000,6 @@ relationship: capable_of GO:0004970 ! glutamate-gated receptor activity id: GO:0008347 name: glial cell migration namespace: biological_process -alt_id: GO:0043359 def: "The orderly movement of a glial cell, non-neuronal cells that provide support and nutrition, maintain homeostasis, form myelin, and participate in signal transmission in the nervous system." [GOC:jl, GOC:mtg_sensu] synonym: "glia cell migration" EXACT [] is_a: BFO:0000003 @@ -56107,8 +62015,6 @@ relationship: RO:0002162 NCBITaxon:33208 {all_only="true"} ! in taxon Metazoa id: GO:0008348 name: negative regulation of antimicrobial humoral response namespace: biological_process -alt_id: GO:0042154 -alt_id: GO:0042155 def: "Any process that stops, prevents, or reduces the frequency, rate, or extent of an antimicrobial humoral response." [GOC:go_curators] synonym: "attenuation of antimicrobial humoral response" EXACT [] synonym: "down regulation of antimicrobial humoral response" EXACT [] @@ -56168,7 +62074,6 @@ is_a: GO:0008595 ! anterior/posterior axis specification, embryo id: GO:0008366 name: axon ensheathment namespace: biological_process -alt_id: GO:0042553 def: "Any process in which the axon of a neuron is insulated, and that insulation maintained, thereby preventing dispersion of the electrical signal." [GOC:jl, ISBN:0878932437] synonym: "cellular axon ensheathment" EXACT [] synonym: "cellular nerve ensheathment" RELATED [] @@ -56203,8 +62108,6 @@ relationship: has_primary_input CHEBI:16796 id: GO:0008519 name: ammonium channel activity namespace: molecular_function -alt_id: GO:0015251 -alt_id: GO:0051739 def: "Enables the energy-independent facilitated diffusion of ammonium through a transmembrane aqueous pore or channel." [PMID:17710640] synonym: "ammonia transmembrane transporter activity" BROAD [] synonym: "ammonium transmembrane transporter activity" BROAD [] @@ -56215,18 +62118,17 @@ xref: Reactome:R-HSA-444419 "RhBG mediates ammonium effflux out of kidney collec xref: Reactome:R-HSA-446277 "RhCG mediates ammonium efflux out of kidney collecting duct cells" xref: Reactome:R-HSA-446278 "RhBG mediates ammonium influx into kidney collecting duct cells" xref: Reactome:R-HSA-5623051 "Defective RHAG does not transport NH4+ from cytosol to extracellular region (rbc)" -xref: RHEA:28747 xref: TC:1.A.11 is_a: GO:0015267 ! channel activity intersection_of: GO:0015267 ! channel activity intersection_of: GO:0022857 ! transmembrane transporter activity intersection_of: has_primary_input CHEBI:28938 -relationship: has_participant CHEBI:28938 relationship: has_primary_input CHEBI:28938 relationship: part_of GO:0072488 {source="GO_REF:0000090"} ! ammonium transmembrane transport property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/22368" xsd:anyURI property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/23129" xsd:anyURI property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/26941" xsd:anyURI +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27521" xsd:anyURI [Term] id: GO:0008528 @@ -56266,7 +62168,6 @@ relationship: results_in_development_of UBERON:0000473 ! testis id: GO:0008585 name: female gonad development namespace: biological_process -alt_id: GO:0061039 def: "The process whose specific outcome is the progression of the female gonad over time, from its formation to the mature structure." [GOC:dph, GOC:jid, GOC:tb] synonym: "ovarian development" RELATED [GOC:sl] synonym: "ovary development" RELATED [GOC:sl] @@ -56319,8 +62220,6 @@ relationship: has_primary_output CHEBI:18059 id: GO:0008643 name: carbohydrate transport namespace: biological_process -alt_id: GO:0006861 -alt_id: GO:0008644 def: "The directed movement of carbohydrate into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Carbohydrates are a group of organic compounds based of the general formula Cx(H2O)y." [GOC:ai] subset: goslim_pir subset: goslim_yeast @@ -56335,9 +62234,6 @@ relationship: has_primary_input CHEBI:16646 id: GO:0008645 name: hexose transmembrane transport namespace: biological_process -alt_id: GO:0008646 -alt_id: GO:0008647 -alt_id: GO:0035428 def: "The process in which hexose is transported across a membrane. Hexoses are aldoses with a chain of six carbon atoms in the molecule." [GOC:vw] comment: Note that this term is not intended for use in annotating lateral movement within membranes. synonym: "hexose membrane transport" RELATED [] @@ -56349,7 +62245,6 @@ intersection_of: GO:0006810 ! transport intersection_of: has_primary_input CHEBI:18133 intersection_of: results_in_transport_across GO:0016020 ! membrane relationship: has_primary_input CHEBI:18133 -created_by: bf creation_date: 2010-04-08T10:27:23Z [Term] @@ -56375,29 +62270,26 @@ property_value: term_tracker_item "https://github.com/geneontology/go-ontology/i id: GO:0009056 name: catabolic process namespace: biological_process -alt_id: GO:0044243 -alt_id: GO:0044712 -def: "The chemical reactions and pathways resulting in the breakdown of substances, including the breakdown of carbon compounds with the liberation of energy for use by the cell or organism." [ISBN:0198547684] +def: "A cellular process consisting of the biochemical pathways by which a living organism breaks down substances. This includes the breakdown of carbon compounds with the liberation of energy for use by the cell or organism." [ISBN:0198547684] subset: goslim_agr subset: goslim_chembl subset: goslim_plant subset: goslim_plant_ribbon -synonym: "breakdown" EXACT [] +synonym: "breakdown of chemical" EXACT [] +synonym: "breakdown of molecule" EXACT [] +synonym: "breakdown of substance" EXACT [] synonym: "catabolism" EXACT [] synonym: "degradation" EXACT [] -synonym: "multicellular organismal catabolic process" NARROW [] -synonym: "single-organism catabolic process" RELATED [] xref: Wikipedia:Catabolism is_a: GO:0008152 ! metabolic process -created_by: jl +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28921" xsd:anyURI +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28932" xsd:anyURI creation_date: 2012-10-17T15:52:35Z [Term] id: GO:0009057 name: macromolecule catabolic process namespace: biological_process -alt_id: GO:0043285 -alt_id: GO:0044266 def: "The chemical reactions and pathways resulting in the breakdown of a macromolecule, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass." [GOC:mah] subset: goslim_pir synonym: "biopolymer catabolic process" EXACT [GOC:mtg_chebi_dec09] @@ -56418,9 +62310,7 @@ relationship: has_primary_input CHEBI:33694 id: GO:0009058 name: biosynthetic process namespace: biological_process -alt_id: GO:0044274 -alt_id: GO:0044711 -def: "The chemical reactions and pathways resulting in the formation of substances; typically the energy-requiring part of metabolism in which simpler substances are transformed into more complex ones." [GOC:curators, ISBN:0198547684] +def: "A cellular process consisting of the biochemical pathways by which a living organism synthesizes chemical substances. This typically represents the energy-requiring part of metabolism in which simpler substances are transformed into more complex ones." [GOC:curators, ISBN:0198547684] subset: goslim_chembl subset: goslim_metagenomics subset: goslim_plant @@ -56433,14 +62323,13 @@ synonym: "single-organism biosynthetic process" RELATED [] synonym: "synthesis" EXACT [] xref: Wikipedia:Anabolism is_a: GO:0008152 ! metabolic process -created_by: jl +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28932" xsd:anyURI creation_date: 2012-10-17T15:52:18Z [Term] id: GO:0009059 name: macromolecule biosynthetic process namespace: biological_process -alt_id: GO:0043284 def: "The chemical reactions and pathways resulting in the formation of a macromolecule, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass." [GOC:mah] comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. subset: gocheck_do_not_annotate @@ -56450,8 +62339,8 @@ synonym: "macromolecule anabolism" EXACT [] synonym: "macromolecule biosynthesis" EXACT [] synonym: "macromolecule formation" EXACT [] synonym: "macromolecule synthesis" EXACT [] +is_a: GO:0009058 ! biosynthetic process is_a: GO:0043170 ! macromolecule metabolic process -is_a: GO:0044249 ! cellular biosynthetic process intersection_of: GO:0009058 ! biosynthetic process intersection_of: has_primary_output CHEBI:33694 relationship: has_primary_output CHEBI:33694 @@ -56707,8 +62596,6 @@ is_a: GO:0009628 ! response to abiotic stimulus id: GO:0009306 name: protein secretion namespace: biological_process -alt_id: GO:0045166 -alt_id: GO:0045731 def: "The controlled release of proteins from a cell." [GOC:ai] synonym: "glycoprotein secretion" NARROW [] synonym: "protein secretion during cell fate commitment" NARROW [] @@ -56723,7 +62610,6 @@ intersection_of: has_primary_input PR:000000001 ! protein id: GO:0009308 name: amine metabolic process namespace: biological_process -alt_id: GO:0044106 def: "The chemical reactions and pathways involving any organic compound that is weakly basic in character and contains an amino or a substituted amino group. Amines are called primary, secondary, or tertiary according to whether one, two, or three carbon atoms are attached to the nitrogen atom." [GOC:jl, ISBN:0198506732] subset: goslim_chembl subset: goslim_pir @@ -56734,7 +62620,6 @@ is_a: GO:0008152 ! metabolic process intersection_of: GO:0008152 ! metabolic process intersection_of: has_primary_input_or_output CHEBI:32952 relationship: has_primary_input_or_output CHEBI:32952 -created_by: jl creation_date: 2009-07-15T11:55:44Z [Term] @@ -57014,7 +62899,6 @@ is_a: GO:0050896 ! response to stimulus id: GO:0009611 name: response to wounding namespace: biological_process -alt_id: GO:0002245 def: "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to the organism." [GOC:go_curators] synonym: "physiological response to wounding" EXACT [] is_a: GO:0006950 ! response to stress @@ -57033,8 +62917,6 @@ is_a: GO:0009628 ! response to abiotic stimulus id: GO:0009617 name: response to bacterium namespace: biological_process -alt_id: GO:0009618 -alt_id: GO:0009680 def: "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus from a bacterium." [GOC:hb] synonym: "response to bacteria" EXACT [] is_a: BFO:0000003 @@ -57047,7 +62929,6 @@ relationship: has_primary_input NCBITaxon:2 ! Bacteria id: GO:0009620 name: response to fungus namespace: biological_process -alt_id: GO:0009621 def: "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus from a fungus." [GOC:hb] synonym: "response to fungi" EXACT [] is_a: BFO:0000003 @@ -57211,7 +63092,6 @@ relationship: regulates GO:0008356 ! asymmetric cell division id: GO:0009790 name: embryo development namespace: biological_process -alt_id: GO:0009795 def: "The process whose specific outcome is the progression of an embryo from its formation until the end of its embryonic life stage. The end of the embryonic stage is organism-specific. For example, for mammals, the process would begin with zygote formation and end with birth. For insects, the process would begin at zygote formation and end with larval hatching. For plant zygotic embryos, this would be from zygote formation to the end of seed dormancy. For plant vegetative embryos, this would be from the initial determination of the cell or group of cells to form an embryo until the point when the embryo becomes independent of the parent plant." [GOC:go_curators, GOC:isa_complete, GOC:mtg_sensu] subset: gocheck_do_not_annotate subset: goslim_chembl @@ -57364,7 +63244,6 @@ relationship: positively_regulates GO:0009058 ! biosynthetic process id: GO:0009892 name: negative regulation of metabolic process namespace: biological_process -alt_id: GO:0044252 def: "Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways within a cell or an organism." [GOC:go_curators] synonym: "down regulation of metabolic process" EXACT [] synonym: "down-regulation of metabolic process" EXACT [] @@ -57375,7 +63254,7 @@ synonym: "negative regulation of metabolism" EXACT [] synonym: "negative regulation of multicellular organismal metabolic process" NARROW [] synonym: "negative regulation of organismal metabolism" EXACT [] is_a: GO:0019222 ! regulation of metabolic process -is_a: GO:0048519 ! negative regulation of biological process +is_a: GO:0048523 ! negative regulation of cellular process intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0008152 ! metabolic process relationship: negatively_regulates GO:0008152 ! metabolic process @@ -57384,7 +63263,6 @@ relationship: negatively_regulates GO:0008152 ! metabolic process id: GO:0009893 name: positive regulation of metabolic process namespace: biological_process -alt_id: GO:0044253 def: "Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways within a cell or an organism." [GOC:go_curators] synonym: "activation of metabolic process" NARROW [] synonym: "positive regulation of metabolism" EXACT [] @@ -57397,7 +63275,7 @@ synonym: "up-regulation of metabolic process" EXACT [] synonym: "up-regulation of organismal metabolic process" NARROW [] synonym: "upregulation of metabolic process" EXACT [] is_a: GO:0019222 ! regulation of metabolic process -is_a: GO:0048518 ! positive regulation of biological process +is_a: GO:0048522 ! positive regulation of cellular process intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0008152 ! metabolic process relationship: positively_regulates GO:0008152 ! metabolic process @@ -57456,7 +63334,6 @@ relationship: positively_regulates GO:0009056 ! catabolic process id: GO:0009913 name: epidermal cell differentiation namespace: biological_process -alt_id: GO:0043355 def: "The process in which a relatively unspecialized cell acquires specialized features of an epidermal cell, any of the cells making up the epidermis." [GOC:dph, GOC:go_curators, GOC:mtg_sensu, GOC:sdb_2009, GOC:tb] synonym: "hypodermal cell differentiation" RELATED [GOC:kmv, GOC:rk] is_a: GO:0030855 ! epithelial cell differentiation @@ -57495,7 +63372,6 @@ is_a: GO:0003002 ! regionalization id: GO:0009966 name: regulation of signal transduction namespace: biological_process -alt_id: GO:0035466 def: "Any process that modulates the frequency, rate or extent of signal transduction." [GOC:sm] synonym: "regulation of signaling pathway" RELATED [] synonym: "regulation of signalling pathway" RELATED [GOC:mah] @@ -57510,7 +63386,6 @@ relationship: regulates GO:0007165 ! signal transduction id: GO:0009967 name: positive regulation of signal transduction namespace: biological_process -alt_id: GO:0035468 def: "Any process that activates or increases the frequency, rate or extent of signal transduction." [GOC:sm] synonym: "activation of signal transduction" NARROW [] synonym: "positive regulation of signaling pathway" RELATED [] @@ -57531,7 +63406,6 @@ relationship: positively_regulates GO:0007165 ! signal transduction id: GO:0009968 name: negative regulation of signal transduction namespace: biological_process -alt_id: GO:0035467 def: "Any process that stops, prevents, or reduces the frequency, rate or extent of signal transduction." [GOC:sm] synonym: "down regulation of signal transduction" EXACT [] synonym: "down-regulation of signal transduction" EXACT [] @@ -57551,7 +63425,6 @@ relationship: negatively_regulates GO:0007165 ! signal transduction id: GO:0009977 name: proton motive force dependent protein transmembrane transporter activity namespace: molecular_function -alt_id: GO:0015557 def: "Catalysis of the transfer of proteins from one side of a membrane to the other. Transportation is dependent on pH gradient across the membrane." [PMID:11526245, PMID:25494301] synonym: "arginine targeting transmembrane transporter activity" EXACT [] synonym: "delta-pH-dependent protein transporter activity" EXACT [] @@ -57567,9 +63440,6 @@ intersection_of: results_in_transport_across GO:0016020 ! membrane id: GO:0009987 name: cellular process namespace: biological_process -alt_id: GO:0008151 -alt_id: GO:0044763 -alt_id: GO:0050875 def: "Any process that is carried out at the cellular level, but not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level." [GOC:go_curators, GOC:isa_complete] comment: This term should not be used for direct annotation. It should be possible to make a more specific annotation to one of the children of this term. subset: gocheck_do_not_annotate @@ -57580,7 +63450,6 @@ synonym: "cellular physiological process" EXACT [] synonym: "single-organism cellular process" RELATED [] is_a: GO:0008150 ! biological_process disjoint_from: GO:0044848 ! biological phase -created_by: jl creation_date: 2012-12-11T16:56:55Z [Term] @@ -57612,8 +63481,6 @@ relationship: results_in_acquisition_of_features_of CL:0000023 ! oocyte id: GO:0010001 name: glial cell differentiation namespace: biological_process -alt_id: GO:0007404 -alt_id: GO:0043360 def: "The process in which a relatively unspecialized cell acquires the specialized features of a glial cell." [GOC:go_curators, GOC:mtg_sensu] synonym: "glia cell differentiation" EXACT [] synonym: "neuroglia differentiation" EXACT [] @@ -57686,7 +63553,7 @@ id: GO:0010109 name: regulation of photosynthesis namespace: biological_process def: "Any process that modulates the frequency, rate or extent of photosynthesis." [GOC:sm] -is_a: GO:0031323 ! regulation of cellular metabolic process +is_a: GO:0019222 ! regulation of metabolic process intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0015979 ! photosynthesis relationship: regulates GO:0015979 ! photosynthesis @@ -57705,7 +63572,6 @@ relationship: regulates GO:1902600 ! proton transmembrane transport id: GO:0010160 name: formation of animal organ boundary namespace: biological_process -alt_id: GO:0048862 def: "The regionalization process that specifies animal organ primordium boundaries resulting in a restriction of organogenesis to a limited spatial domain and keeping the organ separate from surrounding tissues." [GOC:dph, GOC:isa_complete, PMID:9611175] synonym: "organ boundary specification" EXACT [] is_a: GO:0003002 ! regionalization @@ -57751,12 +63617,10 @@ relationship: results_in_organization_of GO:0012505 ! endomembrane system id: GO:0010324 name: membrane invagination namespace: biological_process -alt_id: GO:1902534 def: "The infolding of a membrane." [GOC:tb] subset: goslim_yeast synonym: "single-organism membrane invagination" RELATED [] is_a: GO:0061024 ! membrane organization -created_by: jl creation_date: 2013-12-02T13:58:34Z [Term] @@ -57905,7 +63769,6 @@ relationship: regulates GO:0010481 ! epidermal cell division id: GO:0010496 name: intercellular transport namespace: biological_process -alt_id: GO:1902585 def: "The movement of substances between cells." [GOC:dhl] synonym: "single organism intercellular transport" RELATED [GOC:TermGenie] synonym: "single-organism intercellular transport" RELATED [] @@ -57919,7 +63782,6 @@ intersection_of: results_in_transport_across GO:0005615 ! extracellular space relationship: has_target_end_location CL:0000000 ! cell relationship: has_target_start_location CL:0000000 ! cell relationship: results_in_transport_across GO:0005615 ! extracellular space -created_by: jl creation_date: 2013-12-19T13:24:56Z [Term] @@ -57959,7 +63821,7 @@ id: GO:0010556 name: regulation of macromolecule biosynthetic process namespace: biological_process def: "Any process that modulates the rate, frequency or extent of the chemical reactions and pathways resulting in the formation of a macromolecule, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass." [GOC:dph, GOC:tb] -is_a: GO:0031326 ! regulation of cellular biosynthetic process +is_a: GO:0009889 ! regulation of biosynthetic process is_a: GO:0060255 ! regulation of macromolecule metabolic process intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0009059 ! macromolecule biosynthetic process @@ -57970,9 +63832,9 @@ id: GO:0010557 name: positive regulation of macromolecule biosynthetic process namespace: biological_process def: "Any process that increases the rate, frequency or extent of the chemical reactions and pathways resulting in the formation of a macromolecule, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass." [GOC:dph, GOC:tb] +is_a: GO:0009891 ! positive regulation of biosynthetic process is_a: GO:0010556 ! regulation of macromolecule biosynthetic process is_a: GO:0010604 ! positive regulation of macromolecule metabolic process -is_a: GO:0031328 ! positive regulation of cellular biosynthetic process intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0009059 ! macromolecule biosynthetic process relationship: positively_regulates GO:0009059 ! macromolecule biosynthetic process @@ -57982,9 +63844,9 @@ id: GO:0010558 name: negative regulation of macromolecule biosynthetic process namespace: biological_process def: "Any process that decreases the rate, frequency or extent of the chemical reactions and pathways resulting in the formation of a macromolecule, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass." [GOC:dph, GOC:tb] +is_a: GO:0009890 ! negative regulation of biosynthetic process is_a: GO:0010556 ! regulation of macromolecule biosynthetic process is_a: GO:0010605 ! negative regulation of macromolecule metabolic process -is_a: GO:0031327 ! negative regulation of cellular biosynthetic process intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0009059 ! macromolecule biosynthetic process relationship: negatively_regulates GO:0009059 ! macromolecule biosynthetic process @@ -58036,22 +63898,23 @@ relationship: regulates GO:0022402 ! cell cycle process [Term] id: GO:0010565 -name: regulation of cellular ketone metabolic process +name: regulation of ketone metabolic process namespace: biological_process def: "Any process that modulates the chemical reactions and pathways involving any of a class of organic compounds that contain the carbonyl group, CO, and in which the carbonyl group is bonded only to carbon atoms. The general formula for a ketone is RCOR, where R and R are alkyl or aryl groups." [GOC:dph, GOC:tb] -is_a: GO:0031323 ! regulation of cellular metabolic process -is_a: GO:0062012 ! regulation of small molecule metabolic process +is_a: GO:0019222 ! regulation of metabolic process intersection_of: GO:0065007 ! biological regulation -intersection_of: regulates GO:0042180 ! cellular ketone metabolic process -relationship: regulates GO:0042180 ! cellular ketone metabolic process +intersection_of: regulates GO:0042180 ! ketone metabolic process +relationship: regulates GO:0042180 ! ketone metabolic process +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28908" xsd:anyURI [Term] id: GO:0010566 name: regulation of ketone biosynthetic process namespace: biological_process def: "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of a ketone, carried out by individual cells." [GOC:dph, GOC:tb] -is_a: GO:0010565 ! regulation of cellular ketone metabolic process -is_a: GO:0031326 ! regulation of cellular biosynthetic process +is_a: GO:0009889 ! regulation of biosynthetic process +is_a: GO:0010565 ! regulation of ketone metabolic process +is_a: GO:0062012 ! regulation of small molecule metabolic process intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0042181 ! ketone biosynthetic process relationship: regulates GO:0042181 ! ketone biosynthetic process @@ -58061,8 +63924,9 @@ id: GO:0010567 name: regulation of ketone catabolic process namespace: biological_process def: "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of a ketone, carried out by individual cells." [GOC:dph, GOC:tb] -is_a: GO:0010565 ! regulation of cellular ketone metabolic process -is_a: GO:0031329 ! regulation of cellular catabolic process +is_a: GO:0009894 ! regulation of catabolic process +is_a: GO:0010565 ! regulation of ketone metabolic process +is_a: GO:0062012 ! regulation of small molecule metabolic process intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0042182 ! ketone catabolic process relationship: regulates GO:0042182 ! ketone catabolic process @@ -59243,7 +65107,6 @@ is_a: GO:0045786 ! negative regulation of cell cycle intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0022402 ! cell cycle process relationship: negatively_regulates GO:0022402 ! cell cycle process -created_by: tb creation_date: 2009-04-27T09:53:22Z [Term] @@ -59258,7 +65121,6 @@ is_a: GO:1903319 ! positive regulation of protein maturation intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0016485 ! protein processing relationship: positively_regulates GO:0016485 ! protein processing -created_by: tb creation_date: 2009-04-27T12:09:13Z [Term] @@ -59273,7 +65135,6 @@ is_a: GO:1903318 ! negative regulation of protein maturation intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0016485 ! protein processing relationship: negatively_regulates GO:0016485 ! protein processing -created_by: tb creation_date: 2009-04-27T12:10:19Z [Term] @@ -59286,7 +65147,6 @@ is_a: GO:1903789 ! regulation of amino acid transmembrane transport intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0089718 ! amino acid import across plasma membrane relationship: regulates GO:0089718 ! amino acid import across plasma membrane -created_by: tb creation_date: 2009-05-06T11:33:12Z [Term] @@ -59298,7 +65158,6 @@ is_a: GO:0032885 ! regulation of polysaccharide biosynthetic process intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0009250 ! glucan biosynthetic process relationship: regulates GO:0009250 ! glucan biosynthetic process -created_by: tb creation_date: 2009-05-11T12:17:53Z [Term] @@ -59310,7 +65169,6 @@ is_a: GO:0051049 ! regulation of transport intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0006817 ! phosphate ion transport relationship: regulates GO:0006817 ! phosphate ion transport -created_by: tb creation_date: 2009-05-20T11:42:50Z [Term] @@ -59322,7 +65180,6 @@ is_a: GO:0031113 ! regulation of microtubule polymerization intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0007020 ! microtubule nucleation relationship: regulates GO:0007020 ! microtubule nucleation -created_by: tb creation_date: 2009-05-20T11:51:21Z [Term] @@ -59339,7 +65196,6 @@ is_a: GO:0099111 ! microtubule-based transport intersection_of: GO:0006810 ! transport intersection_of: results_in_transport_along GO:0005874 ! microtubule relationship: results_in_transport_along GO:0005874 ! microtubule -created_by: tb creation_date: 2009-05-27T10:56:08Z [Term] @@ -59355,7 +65211,6 @@ is_a: GO:0120035 ! regulation of plasma membrane bounded cell projection organiz intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0031175 ! neuron projection development relationship: regulates GO:0031175 ! neuron projection development -created_by: tb creation_date: 2009-06-01T10:44:45Z [Term] @@ -59372,7 +65227,6 @@ is_a: GO:0031346 ! positive regulation of cell projection organization intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0031175 ! neuron projection development relationship: positively_regulates GO:0031175 ! neuron projection development -created_by: tb creation_date: 2009-06-01T10:46:44Z [Term] @@ -59390,14 +65244,12 @@ is_a: GO:0031345 ! negative regulation of cell projection organization intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0031175 ! neuron projection development relationship: negatively_regulates GO:0031175 ! neuron projection development -created_by: tb creation_date: 2009-06-01T10:47:42Z [Term] id: GO:0012501 name: programmed cell death namespace: biological_process -alt_id: GO:0016244 def: "A process which begins when a cell receives an internal or external signal and activates a series of biochemical events (signaling pathway). The process ends with the death of the cell." [GOC:lr, GOC:mtg_apoptosis] comment: Note that this term should be used to annotate gene products in the organism undergoing the programmed cell death. To annotate genes in another organism whose products modulate programmed cell death in a host organism, consider the term 'modulation by symbiont of host programmed cell death ; GO:0052040'. Also, note that 'programmed cell death ; GO:0012501' should be used to refer to instances of caspase-independent cell death mechanisms, in the absence of further indications on the process taking place. At present, caspase-independent cell death is not yet represented in GO due to the lack of consensus and in-depth research on the topic. 'programmed cell death ; GO:0012501' may also be used to annotate gene products in taxa where apoptosis as defined in GO:0006915 does not occur, such as plants. You may also consider these specific children: GO:0097468 'programmed cell death in response to reactive oxygen species' (with descendants GO:0010421 'hydrogen peroxide-mediated programmed cell death' and GO:0010343 'singlet oxygen-mediated programmed cell death'), and GO:0009626 'plant-type hypersensitive response' and its children. subset: goslim_agr @@ -59433,7 +65285,7 @@ subset: goslim_candida subset: goslim_flybase_ribbon subset: goslim_yeast xref: Wikipedia:Endomembrane_system -is_a: GO:0110165 ! cellular anatomical entity +is_a: GO:0110165 ! cellular anatomical structure relationship: has_part GO:0005773 ! vacuole relationship: has_part GO:0005886 ! plasma membrane relationship: part_of CL:0000000 ! cell @@ -59636,7 +65488,6 @@ relationship: results_in_development_of CL:0000031 ! neuroblast (sensu Vertebrat id: GO:0014020 name: primary neural tube formation namespace: biological_process -alt_id: GO:0014024 def: "The formation of the neural tube from an epithelial cell sheet (the neuroepithelium or neural plate). In primary neurulation, the cells surrounding the neural plate direct the neural plate cells to proliferate, invaginate, and pinch off from the surface to form a hollow epithelial tube. Primary neurulation is the typical mechanism of formation of the anterior neural tube." [GOC:ef, ISBN:0878932585, PMID:15327780] synonym: "neural rod cavitation" RELATED [] synonym: "primary neural tube morphogenesis" EXACT [GOC:dph] @@ -60759,7 +66610,6 @@ relationship: negatively_regulates GO:0014909 ! smooth muscle cell migration id: GO:0015031 name: protein transport namespace: biological_process -alt_id: GO:0015831 def: "The directed movement of proteins into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:ai] subset: goslim_chembl subset: goslim_pir @@ -60794,9 +66644,10 @@ synonym: "proton transporter activity" EXACT [] xref: Reactome:R-HSA-1222516 "Intraphagosomal pH is lowered to 5 by V-ATPase" xref: Reactome:R-HSA-164834 "Enzyme-bound ATP is released" xref: Reactome:R-HSA-168313 "Virion-associated M2 protein mediated ion infusion" -xref: Reactome:R-HSA-170026 "Protons are translocated from the intermembrane space to the matrix" +xref: Reactome:R-HSA-170026 "UCP1 imports a proton" xref: Reactome:R-HSA-74723 "Endosome acidification" xref: Reactome:R-HSA-917841 "Acidification of Tf:TfR1 containing endosome" +xref: Reactome:R-HSA-9864415 "AAC1 imports a proton" is_a: GO:0022857 ! transmembrane transporter activity intersection_of: GO:0005215 ! transporter activity intersection_of: has_primary_input CHEBI:15378 @@ -60808,51 +66659,45 @@ relationship: part_of GO:1902600 {source="GO_REF:0000090"} ! proton transmembran id: GO:0015079 name: potassium ion transmembrane transporter activity namespace: molecular_function -alt_id: GO:0015388 -alt_id: GO:0022817 def: "Enables the transfer of potassium ions (K+) from one side of a membrane to the other." [GOC:ai] synonym: "potassium transporter activity" EXACT [] synonym: "potassium uptake permease activity" RELATED [] synonym: "potassium uptake transmembrane transporter activity" RELATED [] -xref: RHEA:29463 is_a: GO:0022857 ! transmembrane transporter activity intersection_of: GO:0022857 ! transmembrane transporter activity intersection_of: has_primary_input CHEBI:29103 -relationship: has_participant CHEBI:29103 relationship: has_primary_input CHEBI:29103 relationship: part_of GO:0071805 {source="GO_REF:0000090"} ! potassium ion transmembrane transport +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27521" xsd:anyURI [Term] id: GO:0015081 name: sodium ion transmembrane transporter activity namespace: molecular_function -alt_id: GO:0022816 -def: "Enables the transfer of sodium ions (Na+) from one side of a membrane to the other." [GOC:ai, GOC:BHF, RHEA:34963] +def: "Enables the transfer of sodium ions (Na+) from one side of a membrane to the other." [GOC:ai, GOC:BHF] synonym: "sodium transporter activity" EXACT [] -xref: RHEA:34963 is_a: GO:0022857 ! transmembrane transporter activity intersection_of: GO:0022857 ! transmembrane transporter activity intersection_of: has_primary_input CHEBI:29101 -relationship: has_participant CHEBI:29101 relationship: has_primary_input CHEBI:29101 relationship: part_of GO:0035725 ! sodium ion transmembrane transport property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/24076" xsd:anyURI +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27521" xsd:anyURI [Term] id: GO:0015085 name: calcium ion transmembrane transporter activity namespace: molecular_function -def: "Enables the transfer of calcium (Ca) ions from one side of a membrane to the other." [GOC:dgf, RHEA:29671] +def: "Enables the transfer of calcium (Ca) ions from one side of a membrane to the other." [GOC:dgf] xref: MetaCyc:TRANS-RXN-144 xref: Reactome:R-HSA-2534359 "CatSper Channel Mediated Calcium Transport" -xref: RHEA:29671 is_a: GO:0022857 ! transmembrane transporter activity intersection_of: GO:0022857 ! transmembrane transporter activity intersection_of: has_primary_input CHEBI:29108 -relationship: has_participant CHEBI:29108 relationship: has_primary_input CHEBI:29108 relationship: part_of GO:0070588 ! calcium ion transmembrane transport property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/26941" xsd:anyURI +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27521" xsd:anyURI [Term] id: GO:0015106 @@ -60861,14 +66706,13 @@ namespace: molecular_function def: "Enables the transfer of bicarbonate from one side of a membrane to the other. Bicarbonate is the hydrogencarbonate ion, HCO3-." [GOC:ai] synonym: "hydrogencarbonate transmembrane transporter activity" EXACT [] xref: Reactome:R-HSA-2752067 "BESTs transport cytosolic HCO3- to extracellular region" -xref: RHEA:28695 is_a: GO:0022857 ! transmembrane transporter activity intersection_of: GO:0022857 ! transmembrane transporter activity intersection_of: has_primary_input CHEBI:17544 -relationship: has_participant CHEBI:17544 relationship: has_primary_input CHEBI:17544 relationship: part_of GO:0015701 ! bicarbonate transport property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/26780" xsd:anyURI +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27521" xsd:anyURI [Term] id: GO:0015125 @@ -60891,7 +66735,6 @@ relationship: part_of GO:0015721 ! bile acid and bile salt transport id: GO:0015144 name: carbohydrate transmembrane transporter activity namespace: molecular_function -alt_id: GO:1901476 def: "Enables the transfer of carbohydrate from one side of a membrane to the other." [GOC:jl, GOC:mtg_transport, ISBN:0815340729] synonym: "carbohydrate transporter activity" RELATED [] synonym: "sugar transporter" NARROW [] @@ -60929,7 +66772,6 @@ relationship: part_of GO:0015774 ! polysaccharide transport id: GO:0015171 name: amino acid transmembrane transporter activity namespace: molecular_function -alt_id: GO:0015359 def: "Enables the transfer of amino acids from one side of a membrane to the other. Amino acids are organic molecules that contain an amino group and a carboxyl group." [GOC:ai, GOC:mtg_transport, ISBN:0815340729] synonym: "amino acid permease activity" EXACT [] synonym: "amino acid transporter activity" BROAD [] @@ -60994,7 +66836,7 @@ name: acidic amino acid transmembrane transporter activity namespace: molecular_function def: "Enables the transfer of acidic amino acids from one side of a membrane to the other. Acidic amino acids have side chains with a negative charge at pH 7.3." [GOC:ai, GOC:mtg_transport, ISBN:0815340729] synonym: "acidic amino acid transporter activity" BROAD [] -xref: Reactome:R-HSA-372448 "SLC25A12,13 exchange cytosolic L-Glu for mitochondrial matrix L-Asp" +xref: Reactome:R-HSA-372448 "SLC25A12,13 exchange L-Glu and L-Asp" is_a: GO:0015171 ! amino acid transmembrane transporter activity relationship: part_of GO:0015800 ! acidic amino acid transport @@ -61002,8 +66844,6 @@ relationship: part_of GO:0015800 ! acidic amino acid transport id: GO:0015174 name: basic amino acid transmembrane transporter activity namespace: molecular_function -alt_id: GO:0005286 -alt_id: GO:0015326 def: "Enables the transfer of basic amino acids from one side of a membrane to the other. Basic amino acids have side chains with a positive charge at pH 7.3." [GOC:ai, GOC:mtg_transport, ISBN:0815340729] synonym: "basic amino acid permease activity" EXACT [] synonym: "basic amino acid transporter activity" BROAD [] @@ -61077,13 +66917,14 @@ xref: Reactome:R-HSA-432067 "Aquaporin-4 passively transports water out of cell" xref: Reactome:R-HSA-445714 "Aquaporin-3 passively transports water out of cell" xref: Reactome:R-HSA-507868 "Aquaporins passively transport water into cells" xref: Reactome:R-HSA-507870 "Aquaporins passively transport water out of cells" -xref: RHEA:29667 +xref: RHEA:29667 {source="skos:broadMatch"} is_a: GO:0005372 ! water transmembrane transporter activity is_a: GO:0015267 ! channel activity intersection_of: GO:0015267 ! channel activity intersection_of: has_primary_input CHEBI:15377 relationship: has_participant CHEBI:15377 property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/26941" xsd:anyURI +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27521" xsd:anyURI [Term] id: GO:0015252 @@ -61104,9 +66945,6 @@ property_value: term_tracker_item "https://github.com/geneontology/go-ontology/i id: GO:0015267 name: channel activity namespace: molecular_function -alt_id: GO:0015249 -alt_id: GO:0015268 -alt_id: GO:0022838 def: "Enables the energy-independent facilitated diffusion of a solute through a transmembrane aqueous pore or channel. Stereospecificity is not exhibited but this transport may be specific for a particular molecular species or class of molecules." [GOC:mtg_transport, ISBN:0815340729] synonym: "alpha-type channel activity" RELATED [] synonym: "channel-forming toxin activity" RELATED [] @@ -61124,7 +66962,7 @@ is_a: GO:0022803 ! passive transmembrane transporter activity id: GO:0015269 name: calcium-activated potassium channel activity namespace: molecular_function -def: "Enables the calcium concentration-regulatable energy-independent passage of potassium ions across a lipid bilayer down a concentration gradient." [GOC:dph, GOC:mtg_transport] +def: "Enables the transmembrane transfer of a potassium cation by a channel that opens when a calcium cation has been bound by the channel complex or one of its constituent parts." [GOC:dph, GOC:mtg_transport] xref: Reactome:R-HSA-9663752 "KCNN2 transports K+ from the cytosol to the extracellular region" xref: Reactome:R-HSA-9667809 "KCNMA1:KCNMB1 transports potassium ions from the cytosol to the extracellular region" is_a: GO:0005227 ! calcium-activated cation channel activity @@ -61187,10 +67025,6 @@ intersection_of: has_small_molecule_activator CHEBI:24431 id: GO:0015291 name: secondary active transmembrane transporter activity namespace: molecular_function -alt_id: GO:0015290 -alt_id: GO:0015353 -alt_id: GO:0015404 -alt_id: GO:0015570 def: "Enables the transfer of a solute from one side of a membrane to the other, up its concentration gradient. The transporter binds the solute and undergoes a series of conformational changes. Transport works equally well in either direction and is driven by a chemiosmotic source of energy, not direct ATP coupling. Secondary active transporters include symporters and antiporters." [GOC:mtg_transport, ISBN:0198506732, ISBN:0815340729, PMID:10839820] synonym: "active transporter" BROAD [] synonym: "coupled carrier" EXACT [] @@ -61242,6 +67076,22 @@ namespace: molecular_function def: "Binding to monomeric or multimeric forms of tubulin, including microtubules." [GOC:clt] is_a: GO:0008092 ! cytoskeletal protein binding +[Term] +id: GO:0015636 +name: short-chain fatty acid transmembrane transporter activity +namespace: molecular_function +def: "Enables the transfer of short-chain fatty acids from one side of a membrane to the other. A short-chain fatty acid has an aliphatic tail containing fewer than 6 carbons." [GOC:mah] +comment: While there is not universal consensus on the lengths of short-, medium-, long- and very-long-chain fatty acids, the GO uses the definitions in ChEBI (see CHEBI:26666, CHEBI:59554, CHEBI:15904 and CHEBI:27283). +synonym: "short-chain fatty acid transporter activity" RELATED [] +synonym: "short-chain fatty acid uptake transporter activity" RELATED [] +is_a: GO:0022857 ! transmembrane transporter activity +intersection_of: GO:0005215 ! transporter activity +intersection_of: has_primary_input CHEBI:58951 +intersection_of: results_in_transport_across GO:0016020 ! membrane +relationship: has_primary_input CHEBI:58951 +relationship: part_of GO:0015912 ! short-chain fatty acid transport +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/26445" xsd:anyURI + [Term] id: GO:0015669 name: gas transport @@ -61350,7 +67200,6 @@ relationship: has_primary_input CHEBI:59888 id: GO:0015813 name: L-glutamate transmembrane transport namespace: biological_process -alt_id: GO:0089711 def: "The directed movement of L-glutamate across a membrane by means of some agent such as a transporter or a pore." [PMID:21307582] synonym: "L-glutamate transport" BROAD [] synonym: "mitochondrial aspartate/glutamate transport" RELATED [] @@ -61474,6 +67323,34 @@ intersection_of: GO:0006810 ! transport intersection_of: has_primary_input CHEBI:72587 relationship: has_primary_input CHEBI:72587 +[Term] +id: GO:0015912 +name: short-chain fatty acid transport +namespace: biological_process +def: "The directed movement of short-chain fatty acids into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. A short-chain fatty acid has an aliphatic tail containing fewer than 6 carbons." [GOC:ai] +comment: While there is not universal consensus on the lengths of short-, medium-, long- and very-long-chain fatty acids, the GO uses the definitions in ChEBI (see CHEBI:26666, CHEBI:59554, CHEBI:15904 and CHEBI:27283). +is_a: BFO:0000003 +is_a: GO:0006810 ! transport +intersection_of: GO:0006810 ! transport +intersection_of: has_primary_input CHEBI:58951 +relationship: has_primary_input CHEBI:58951 +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/26445" xsd:anyURI + +[Term] +id: GO:0015913 +name: short-chain fatty acid transmembrane transport +namespace: biological_process +def: "The directed movement of short-chain fatty acids into a cell or organelle. A short-chain fatty acid has an aliphatic tail containing fewer than 6 carbons." [GOC:ai] +comment: While there is not universal consensus on the lengths of short-, medium-, long- and very-long-chain fatty acids, the GO uses the definitions in ChEBI (see CHEBI:26666, CHEBI:59554, CHEBI:15904 and CHEBI:27283). +synonym: "short-chain fatty acid import" RELATED [] +synonym: "short-chain fatty acid uptake" EXACT [] +is_a: GO:0015912 ! short-chain fatty acid transport +is_a: GO:0055085 ! transmembrane transport +intersection_of: GO:0055085 ! transmembrane transport +intersection_of: has_primary_input CHEBI:58951 +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/24587" xsd:anyURI +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/26445" xsd:anyURI + [Term] id: GO:0015931 name: nucleobase-containing compound transport @@ -61514,7 +67391,7 @@ subset: goslim_plant_ribbon subset: goslim_prokaryote subset: goslim_prokaryote_ribbon xref: Wikipedia:Photosynthesis -is_a: GO:0044237 ! cellular metabolic process +is_a: GO:0008152 ! metabolic process property_value: RO:0002161 NCBITaxon:33208 property_value: RO:0002161 NCBITaxon:4895 @@ -61530,9 +67407,6 @@ is_a: GO:0006091 ! generation of precursor metabolites and energy id: GO:0016020 name: membrane namespace: cellular_component -alt_id: GO:0016021 -alt_id: GO:0098589 -alt_id: GO:0098805 def: "A lipid bilayer along with all the proteins and protein complexes embedded in it and attached to it." [GOC:dos, GOC:mah, ISBN:0815316194] subset: goslim_candida subset: goslim_chembl @@ -61549,7 +67423,7 @@ synonym: "transmembrane" RELATED [GOC:mah] synonym: "whole membrane" NARROW [] xref: Wikipedia:Biological_membrane xref: Wikipedia:Transmembrane_protein -is_a: GO:0110165 ! cellular anatomical entity +is_a: GO:0110165 ! cellular anatomical structure disjoint_from: GO:0031012 ! extracellular matrix creation_date: 2014-03-06T11:37:54Z @@ -61557,8 +67431,6 @@ creation_date: 2014-03-06T11:37:54Z id: GO:0016042 name: lipid catabolic process namespace: biological_process -alt_id: GO:0006724 -alt_id: GO:0044240 def: "The chemical reactions and pathways resulting in the breakdown of lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent." [GOC:go_curators] synonym: "lipid breakdown" EXACT [] synonym: "lipid catabolism" EXACT [] @@ -61577,8 +67449,6 @@ relationship: has_primary_input CHEBI:18059 id: GO:0016043 name: cellular component organization namespace: biological_process -alt_id: GO:0044235 -alt_id: GO:0071842 def: "A process that results in the assembly, arrangement of constituent parts, or disassembly of a cellular component." [GOC:ai, GOC:jl, GOC:mah] subset: gocheck_do_not_annotate subset: goslim_agr @@ -61614,7 +67484,6 @@ is_a: GO:0009582 ! detection of abiotic stimulus id: GO:0016049 name: cell growth namespace: biological_process -alt_id: GO:0048591 def: "The process in which a cell irreversibly increases in size over time by accretion and biosynthetic production of matter similar to that already present." [GOC:ai] subset: gocheck_do_not_annotate subset: goslim_drosophila @@ -61652,7 +67521,6 @@ relationship: results_in_organization_of GO:0031982 ! vesicle id: GO:0016051 name: carbohydrate biosynthetic process namespace: biological_process -alt_id: GO:0006093 def: "The chemical reactions and pathways resulting in the formation of carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y." [ISBN:0198506732] synonym: "anabolic carbohydrate metabolic process" EXACT [] synonym: "anabolic carbohydrate metabolism" EXACT [] @@ -61670,9 +67538,6 @@ relationship: has_primary_output CHEBI:16646 id: GO:0016052 name: carbohydrate catabolic process namespace: biological_process -alt_id: GO:0006095 -alt_id: GO:0044276 -alt_id: GO:0044724 def: "The chemical reactions and pathways resulting in the breakdown of carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y." [ISBN:0198506732] synonym: "carbohydrate breakdown" EXACT [] synonym: "carbohydrate catabolism" EXACT [] @@ -61686,7 +67551,6 @@ is_a: GO:0009056 ! catabolic process intersection_of: GO:0009056 ! catabolic process intersection_of: has_primary_input CHEBI:16646 relationship: has_primary_input CHEBI:16646 -created_by: jl creation_date: 2012-10-23T16:34:39Z [Term] @@ -61699,7 +67563,6 @@ synonym: "organic acid biosynthesis" EXACT [] synonym: "organic acid formation" EXACT [] synonym: "organic acid synthesis" EXACT [] is_a: GO:0006082 ! organic acid metabolic process -is_a: GO:0044249 ! cellular biosynthetic process is_a: GO:0044283 ! small molecule biosynthetic process intersection_of: GO:0009058 ! biosynthetic process intersection_of: has_primary_output CHEBI:64709 @@ -61777,7 +67640,6 @@ relationship: part_of GO:0099504 ! synaptic vesicle cycle id: GO:0016192 name: vesicle-mediated transport namespace: biological_process -alt_id: GO:0006899 def: "A cellular transport process in which transported substances are moved in membrane-bounded vesicles; transported substances are enclosed in the vesicle lumen or located in the vesicle membrane. The process begins with a step that directs a substance to the forming vesicle, and includes vesicle budding and coating. Vesicles are then targeted to, and fuse with, an acceptor membrane." [GOC:ai, GOC:mah, ISBN:08789310662000] subset: goslim_candida subset: goslim_chembl @@ -61863,7 +67725,6 @@ relationship: part_of GO:0007143 ! female meiotic nuclear division id: GO:0016325 name: oocyte microtubule cytoskeleton organization namespace: biological_process -alt_id: GO:0048130 def: "Formation and maintenance of a polarized microtubule array originating from a microtubule-organizing center (MTOC) in the oocyte. An example of this is found in Drosophila melanogaster." [GOC:mtg_sensu, PMID:11231123] synonym: "oocyte microtubule cytoskeleton organisation" EXACT [] is_a: GO:0030951 ! establishment or maintenance of microtubule cytoskeleton polarity @@ -61960,7 +67821,6 @@ property_value: term_tracker_item "https://github.com/geneontology/go-ontology/i id: GO:0016485 name: protein processing namespace: biological_process -alt_id: GO:0051605 def: "Any protein maturation process achieved by the cleavage of a peptide bond or bonds within a protein. Protein maturation is the process leading to the attainment of the full functional capacity of a protein." [GOC:curators, GOC:jl, GOC:jsg] subset: goslim_chembl synonym: "peptidolysis during protein maturation" RELATED [GOC:mah] @@ -62160,8 +68020,6 @@ is_a: GO:0016817 ! hydrolase activity, acting on acid anhydrides id: GO:0016887 name: ATP hydrolysis activity namespace: molecular_function -alt_id: GO:0004002 -alt_id: GO:0042623 def: "Catalysis of the reaction: ATP + H2O = ADP + H+ phosphate. ATP hydrolysis is used in some reactions as an energy source, for example to catalyze a reaction or drive transport against a concentration gradient." [RHEA:13065] comment: Note that this term is meant to specifically represent the ATPase activity of proteins using ATP as a source of energy to drive a reaction. If possible, gene products should also be annotated to a child of 'ATP-dependent activity ; GO:0140657', to capture their overall function. synonym: "adenosine 5'-triphosphatase activity" EXACT [] @@ -62204,13 +68062,13 @@ property_value: term_tracker_item "https://github.com/geneontology/go-ontology/i id: GO:0016907 name: G protein-coupled acetylcholine receptor activity namespace: molecular_function -alt_id: GO:0004981 def: "Combining with acetylcholine and transmitting the signal across the membrane by activating an associated G-protein; promotes the exchange of GDP for GTP on the alpha subunit of a heterotrimeric G-protein complex." [GOC:bf, GOC:fj, GOC:mah] synonym: "acetylcholine receptor activity, G-protein coupled" EXACT [GOC:bf] synonym: "G protein coupled acetylcholine receptor activity" EXACT [] synonym: "G-protein coupled acetylcholine receptor activity" EXACT [] synonym: "metabotropic acetylcholine receptor activity" EXACT [] synonym: "muscarinic acetylcholine receptor activity" EXACT [] +xref: Reactome:R-HSA-400012 "Acetylcholine binds Muscarinic Acetylcholine Receptor M3" is_a: GO:0008227 ! G protein-coupled amine receptor activity is_a: GO:0015464 ! acetylcholine receptor activity is_a: GO:0099528 ! G protein-coupled neurotransmitter receptor activity @@ -62240,8 +68098,6 @@ relationship: has_primary_input CHEBI:59888 id: GO:0016922 name: nuclear receptor binding namespace: molecular_function -alt_id: GO:0035257 -alt_id: GO:0035258 def: "Binding to a nuclear receptor protein. Nuclear receptor proteins are DNA-binding transcription factors which are regulated by binding to a ligand." [PMID:7776974] synonym: "ligand-dependent nuclear receptor binding" EXACT [] synonym: "ligand-dependent nuclear receptor interactor activity" RELATED [] @@ -62264,25 +68120,6 @@ intersection_of: GO:0005488 ! binding intersection_of: has_primary_input CHEBI:25905 relationship: has_primary_input CHEBI:25905 -[Term] -id: GO:0017053 -name: transcription repressor complex -namespace: cellular_component -alt_id: GO:0090568 -alt_id: GO:0090569 -def: "A protein complex that possesses activity that prevents or downregulates transcription." [GOC:mah] -subset: goslim_pir -synonym: "cytoplasmic transcriptional repressor complex" RELATED [] -synonym: "nuclear transcriptional repressor complex" RELATED [] -synonym: "transcription factor inhibitor complex" EXACT [GOC:bhm] -synonym: "transcriptional repressor complex" EXACT [] -is_a: GO:0005667 ! transcription regulator complex -intersection_of: GO:0032991 ! protein-containing complex -intersection_of: capable_of GO:0001217 ! DNA-binding transcription repressor activity -relationship: capable_of GO:0001217 ! DNA-binding transcription repressor activity -created_by: tb -creation_date: 2014-05-09T13:23:51Z - [Term] id: GO:0017111 name: ribonucleoside triphosphate phosphatase activity @@ -62350,7 +68187,6 @@ property_value: RO:0002161 NCBITaxon:4751 id: GO:0017148 name: negative regulation of translation namespace: biological_process -alt_id: GO:0016478 def: "Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of proteins by the translation of mRNA or circRNA." [GOC:isa_complete] synonym: "down regulation of protein biosynthetic process" EXACT [] synonym: "down-regulation of protein biosynthetic process" EXACT [] @@ -62448,9 +68284,6 @@ relationship: has_primary_input_or_output CHEBI:33853 id: GO:0019098 name: reproductive behavior namespace: biological_process -alt_id: GO:0033057 -alt_id: GO:0044704 -alt_id: GO:0044705 def: "The specific behavior of an organism that is associated with reproduction." [GOC:jl, GOC:pr] synonym: "multi-organism reproductive behavior" NARROW [] synonym: "multicellular organism reproductive behavior" NARROW [] @@ -62462,7 +68295,6 @@ is_a: GO:0048609 ! multicellular organismal reproductive process intersection_of: GO:0007610 ! behavior intersection_of: GO:0048609 ! multicellular organismal reproductive process property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/23491" xsd:anyURI -created_by: jl creation_date: 2012-09-19T16:01:37Z [Term] @@ -62545,13 +68377,12 @@ relationship: part_of GO:0071345 ! cellular response to cytokine stimulus id: GO:0019222 name: regulation of metabolic process namespace: biological_process -alt_id: GO:0044246 def: "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways within a cell or an organism." [GOC:go_curators] subset: goslim_metagenomics synonym: "regulation of metabolism" EXACT [] synonym: "regulation of multicellular organismal metabolic process" NARROW [] synonym: "regulation of organismal metabolic process" NARROW [GOC:tb] -is_a: GO:0050789 ! regulation of biological process +is_a: GO:0050794 ! regulation of cellular process intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0008152 ! metabolic process relationship: regulates GO:0008152 ! metabolic process @@ -62666,9 +68497,6 @@ relationship: has_primary_input CHEBI:33853 id: GO:0019538 name: protein metabolic process namespace: biological_process -alt_id: GO:0006411 -alt_id: GO:0044267 -alt_id: GO:0044268 def: "The chemical reactions and pathways involving a protein. Includes protein modification." [GOC:ma] comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. subset: gocheck_do_not_annotate @@ -62708,6 +68536,23 @@ intersection_of: GO:0009056 ! catabolic process intersection_of: has_primary_input CHEBI:33566 relationship: has_primary_input CHEBI:33566 +[Term] +id: GO:0019626 +name: short-chain fatty acid catabolic process +namespace: biological_process +def: "The chemical reactions and pathways resulting in the breakdown of a short-chain fatty acid. A short-chain fatty acid has an aliphatic tail containing fewer than 6 carbons." [ISBN:0198506732] +comment: While there is not universal consensus on the lengths of short-, medium-, long- and very-long-chain fatty acids, the GO uses the definitions in ChEBI (see CHEBI:26666, CHEBI:59554, CHEBI:15904 and CHEBI:27283). +synonym: "short-chain fatty acid breakdown" EXACT [] +synonym: "short-chain fatty acid catabolism" EXACT [] +synonym: "short-chain fatty acid degradation" EXACT [] +xref: MetaCyc:ACETOACETATE-DEG-PWY +is_a: GO:0009056 ! catabolic process +is_a: GO:0046459 ! short-chain fatty acid metabolic process +intersection_of: GO:0009056 ! catabolic process +intersection_of: has_primary_input CHEBI:58951 +relationship: has_primary_input CHEBI:58951 +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/26445" xsd:anyURI + [Term] id: GO:0019722 name: calcium-mediated signaling @@ -62758,8 +68603,6 @@ relationship: RO:0002162 NCBITaxon:131567 {all_only="true"} ! in taxon cellular id: GO:0019730 name: antimicrobial humoral response namespace: biological_process -alt_id: GO:0006960 -alt_id: GO:0019735 def: "An immune response against microbes mediated through a body fluid. Examples of this process are seen in the antimicrobial humoral response of Drosophila melanogaster and Mus musculus." [GOC:go_curators, GOC:mtg_sensu] is_a: GO:0006959 ! humoral immune response is_a: GO:0140546 ! defense response to symbiont @@ -62806,7 +68649,6 @@ is_a: GO:0032991 ! protein-containing complex id: GO:0019815 name: B cell receptor complex namespace: cellular_component -alt_id: GO:0042570 def: "An immunoglobulin complex that is present in the plasma membrane of B cells and that in its canonical form is composed of two identical immunoglobulin heavy chains and two identical immunoglobulin light chains and a signaling subunit, a heterodimer of the Ig-alpha and Ig-beta proteins." [GOC:add, ISBN:0781735149] comment: Note that an immunoglobulin complex has the function of antigen binding if a suitable antigen is available. synonym: "antibody" RELATED [GOC:mah] @@ -62869,7 +68711,6 @@ is_a: GO:0016020 ! membrane id: GO:0019882 name: antigen processing and presentation namespace: biological_process -alt_id: GO:0030333 def: "The process in which an antigen-presenting cell expresses antigen (peptide or lipid) on its cell surface in association with an MHC protein complex." [GO_REF:0000022, GOC:add, ISBN:0781735149, PMID:15771591, PMID:15928678] synonym: "antigen presentation" EXACT [] synonym: "antigen processing" EXACT [] @@ -62898,7 +68739,6 @@ property_value: term_tracker_item "https://github.com/geneontology/go-ontology/i id: GO:0019955 name: cytokine binding namespace: molecular_function -alt_id: GO:0019965 def: "Binding to a cytokine, any of a group of proteins that function to control the survival, growth and differentiation of tissues and cells, and which have autocrine and paracrine activity." [GOC:ai, GOC:bf, ISBN:0198599471] synonym: "IL binding" NARROW [] synonym: "interleukin binding" NARROW [] @@ -64881,7 +70721,7 @@ name: pyramidal neuron differentiation namespace: biological_process def: "The process in which a neuroblast or one of its progeny commits to a pyramidal neuron fate, migrates from the ventricular zone to the appropriate layer in the cortex and develops into a mature neuron." [GO_REF:0000021, GOC:cls, GOC:dgh, GOC:dph, GOC:jid] synonym: "projection neuron differentiation" BROAD [PMID:16226447] -is_a: GO:0030182 ! neuron differentiation +is_a: GO:0021953 ! central nervous system neuron differentiation intersection_of: GO:0030154 ! cell differentiation intersection_of: results_in_acquisition_of_features_of CL:0000598 ! pyramidal neuron relationship: results_in_acquisition_of_features_of CL:0000598 ! pyramidal neuron @@ -64978,7 +70818,7 @@ id: GO:0021889 name: olfactory bulb interneuron differentiation namespace: biological_process def: "The process in which a neuroblast acquires specialized features of an interneuron residing in the olfactory bulb." [GO_REF:0000021, GOC:cls, GOC:dgh, GOC:dph, GOC:jid, PMID:12626695] -is_a: GO:0021953 ! central nervous system neuron differentiation +is_a: GO:0021879 ! forebrain neuron differentiation intersection_of: GO:0030154 ! cell differentiation intersection_of: results_in_acquisition_of_features_of CL:1001434 ! olfactory bulb interneuron relationship: part_of GO:0021772 ! olfactory bulb development @@ -64989,7 +70829,7 @@ id: GO:0021891 name: olfactory bulb interneuron development namespace: biological_process def: "The process whose specific outcome is the progression of an interneuron residing in the olfactory bulb, from its initial commitment, to the fully functional differentiated cell." [GO_REF:0000021, GOC:cls, GOC:dgh, GOC:dph, GOC:jid, PMID:12626695] -is_a: GO:0021954 ! central nervous system neuron development +is_a: GO:0021884 ! forebrain neuron development intersection_of: GO:0048468 ! cell development intersection_of: results_in_development_of CL:1001434 ! olfactory bulb interneuron relationship: part_of GO:0021889 ! olfactory bulb interneuron differentiation @@ -65011,7 +70851,7 @@ id: GO:0021894 name: cerebral cortex GABAergic interneuron development namespace: biological_process def: "The process whose specific outcome is the progression of a cerebral cortex GABAergic interneuron over time, from initial commitment to its fate, to the fully functional differentiated cell." [GO_REF:0000021, GOC:cls, GOC:dgh, GOC:dph, GOC:jid, PMID:12626695] -is_a: GO:0021954 ! central nervous system neuron development +is_a: GO:0021884 ! forebrain neuron development intersection_of: GO:0032502 ! developmental process intersection_of: results_in_development_of CL:0010011 ! cerebral cortex GABAergic interneuron relationship: part_of GO:0021892 ! cerebral cortex GABAergic interneuron differentiation @@ -65022,10 +70862,9 @@ id: GO:0021895 name: cerebral cortex neuron differentiation namespace: biological_process def: "The process in which a relatively unspecialized cell acquires specialized features of a neuron residing in the cerebral cortex." [GO_REF:0000021, GOC:cls, GOC:dgh, GOC:dph, GOC:jid] -is_a: GO:0021953 ! central nervous system neuron differentiation +is_a: GO:0021879 ! forebrain neuron differentiation intersection_of: GO:0030154 ! cell differentiation intersection_of: results_in_acquisition_of_features_of CL:0010012 ! cerebral cortex neuron -relationship: part_of GO:0030900 ! forebrain development relationship: results_in_acquisition_of_features_of CL:0010012 ! cerebral cortex neuron [Term] @@ -65299,7 +71138,6 @@ is_a: GO:0042552 ! myelination intersection_of: GO:0042552 ! myelination intersection_of: occurs_in UBERON:0001017 ! central nervous system relationship: part_of GO:0014003 ! oligodendrocyte development -relationship: RO:0002162 NCBITaxon:33213 {all_only="true"} ! in taxon Bilateria [Term] id: GO:0022011 @@ -65486,7 +71324,6 @@ relationship: positively_regulates GO:0098609 ! cell-cell adhesion id: GO:0022411 name: cellular component disassembly namespace: biological_process -alt_id: GO:0071845 def: "A cellular process that results in the breakdown of a cellular component." [GOC:isa_complete] comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. subset: gocheck_do_not_annotate @@ -65524,7 +71361,6 @@ property_value: term_tracker_item "https://github.com/geneontology/go-ontology/i id: GO:0022414 name: reproductive process namespace: biological_process -alt_id: GO:0044702 def: "A biological process that directly contributes to the process of producing new individuals by one or two organisms. The new individuals inherit some proportion of their genetic material from the parent or parents." [GOC:dph, GOC:isa_complete] subset: gocheck_do_not_annotate subset: goslim_agr @@ -65539,7 +71375,6 @@ xref: Wikipedia:Reproduction is_a: GO:0008150 ! biological_process disjoint_from: GO:0044848 ! biological phase property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27054" xsd:anyURI -created_by: jl creation_date: 2012-09-19T15:56:06Z [Term] @@ -65603,7 +71438,6 @@ relationship: part_of GO:0048477 ! oogenesis id: GO:0022607 name: cellular component assembly namespace: biological_process -alt_id: GO:0071844 def: "The aggregation, arrangement and bonding together of a cellular component." [GOC:isa_complete] subset: goslim_chembl subset: goslim_euk_cellular_processes_ribbon @@ -65667,9 +71501,6 @@ relationship: results_in_assembly_of GO:1990904 ! ribonucleoprotein complex id: GO:0022626 name: cytosolic ribosome namespace: cellular_component -alt_id: GO:0005830 -alt_id: GO:0009281 -alt_id: GO:0030871 def: "A ribosome located in the cytosol." [GOC:mtg_sensu] synonym: "70S ribosome" NARROW [] synonym: "80S ribosome" NARROW [] @@ -65684,12 +71515,10 @@ relationship: RO:0002162 NCBITaxon:131567 {all_only="true"} ! in taxon cellular id: GO:0022803 name: passive transmembrane transporter activity namespace: molecular_function -alt_id: GO:0022814 def: "Enables the transfer of a single solute from one side of a membrane to the other by a mechanism involving conformational change, either by facilitated diffusion or in a membrane potential dependent process if the solute is charged." [GOC:mtg_transport, ISBN:0815340729] synonym: "facilitated diffusion" RELATED [] synonym: "porters" BROAD [] synonym: "uniporter activity z" NARROW [] -xref: Reactome:R-HSA-429767 "Passive I- efflux mediated by SMCT1" xref: Wikipedia:Facilitated_diffusion is_a: GO:0022857 ! transmembrane transporter activity @@ -65757,8 +71586,6 @@ relationship: has_small_molecule_activator CHEBI:24867 id: GO:0022848 name: acetylcholine-gated monoatomic cation-selective channel activity namespace: molecular_function -alt_id: GO:0004889 -alt_id: GO:0016904 def: "Selectively enables the transmembrane transfer of a cation by a channel that opens upon binding acetylcholine." [GOC:mah, PMID:2466967] synonym: "acetylcholine-activated cation-selective channel activity" EXACT [] synonym: "acetylcholine-gated cation channel activity" EXACT [] @@ -65790,7 +71617,6 @@ intersection_of: has_small_molecule_activator CHEBI:14321 id: GO:0022850 name: serotonin-gated monoatomic cation channel activity namespace: molecular_function -alt_id: GO:0005232 def: "Enables the transmembrane transfer of a cation by a channel that opens when serotonin has been bound by the channel complex or one of its constituent parts." [GOC:mtg_transport, PMID:12867984] comment: Note that this term represents an activity and not a gene product. Consider also annotating to the molecular function term 'G protein-coupled serotonin receptor activity ; GO:0004993'. synonym: "5-hydroxytryptamine-gated receptor-channel" NARROW [] @@ -65824,11 +71650,6 @@ property_value: term_tracker_item "https://github.com/geneontology/go-ontology/i id: GO:0022857 name: transmembrane transporter activity namespace: molecular_function -alt_id: GO:0005386 -alt_id: GO:0015563 -alt_id: GO:0015646 -alt_id: GO:0022891 -alt_id: GO:0022892 def: "Enables the transfer of a substance, usually a specific substance or a group of related substances, from one side of a membrane to the other." [GOC:jid, GOC:mtg_transport, ISBN:0815340729] subset: goslim_chembl subset: goslim_drosophila @@ -65932,8 +71753,6 @@ creation_date: 2010-02-16T09:30:50Z id: GO:0023052 name: signaling namespace: biological_process -alt_id: GO:0023046 -alt_id: GO:0044700 def: "The entirety of a process in which information is transmitted within a biological system. This process begins with an active signal and ends when a cellular response has been triggered." [GOC:mtg_signal, GOC:mtg_signaling_feb11, GOC:signaling] comment: Note that a signal is any variable property or parameter that serves to convey information, and may be a physical entity such as a gene product or small molecule, a photon, or a change in state such as movement or voltage change. subset: goslim_agr @@ -65952,7 +71771,6 @@ synonym: "signalling process" RELATED [GOC:mah] synonym: "single organism signaling" RELATED [] is_a: GO:0050789 ! regulation of biological process disjoint_from: GO:0044848 ! biological phase -created_by: jl creation_date: 2010-02-16T09:30:50Z [Term] @@ -66013,7 +71831,6 @@ property_value: term_tracker_item "https://github.com/geneontology/go-ontology/i id: GO:0030007 name: intracellular potassium ion homeostasis namespace: biological_process -alt_id: GO:0017079 def: "A homeostatic process involved in the maintenance of a steady state level of potassium ions within a cell." [GOC:mah] synonym: "cellular potassium ion homeostasis" EXACT [] is_a: GO:0030003 ! intracellular monoatomic cation homeostasis @@ -66027,8 +71844,6 @@ intersection_of: regulates_levels_of CHEBI:29103 id: GO:0030010 name: establishment of cell polarity namespace: biological_process -alt_id: GO:0000283 -alt_id: GO:0030468 def: "The specification and formation of anisotropic intracellular organization or cell growth patterns." [GOC:mah] synonym: "bud site selection/establishment of cell polarity" NARROW [] synonym: "cell polarization" EXACT [] @@ -66051,7 +71866,7 @@ name: sarcomere namespace: cellular_component def: "The repeating unit of a myofibril in a muscle cell, composed of an array of overlapping thick and thin filaments between two adjacent Z discs." [ISBN:0815316194] xref: Wikipedia:Sarcomere -is_a: GO:0110165 ! cellular anatomical entity +is_a: GO:0110165 ! cellular anatomical structure relationship: part_of GO:0030016 ! myofibril [Term] @@ -66150,9 +71965,17 @@ subset: goslim_agr subset: goslim_drosophila subset: goslim_flybase_ribbon xref: Wikipedia:Cell_junction -is_a: GO:0110165 ! cellular anatomical entity +is_a: GO:0110165 ! cellular anatomical structure property_value: RO:0002161 NCBITaxon:4751 +[Term] +id: GO:0030055 +name: cell-substrate junction +namespace: cellular_component +def: "A cell junction that forms a connection between a cell and the extracellular matrix." [GOC:aruk, GOC:bc, GOC:hb, GOC:mah, PMID:10419689, PMID:1643657, PMID:16805308, PMID:26923917, PMID:8314002] +synonym: "cell-matrix junction" EXACT [] +is_a: GO:0070161 ! anchoring junction + [Term] id: GO:0030070 name: insulin processing @@ -66210,7 +72033,6 @@ property_value: term_tracker_item "https://github.com/geneontology/go-ontology/i id: GO:0030098 name: lymphocyte differentiation namespace: biological_process -alt_id: GO:0046650 def: "The process in which a relatively unspecialized precursor cell acquires specialized features of a lymphocyte. A lymphocyte is a leukocyte commonly found in the blood and lymph that has the characteristics of a large nucleus, a neutral staining cytoplasm, and prominent heterochromatin." [CL:0000542, GOC:go_curators] comment: Note that immunologists typically use the word 'development' to refer to cells of B or T cell lineages undergoing the process that GO describes as 'cell differentiation'. synonym: "lymphocyte cell differentiation" EXACT [] @@ -66336,8 +72158,6 @@ relationship: regulates GO:0006508 ! proteolysis id: GO:0030163 name: protein catabolic process namespace: biological_process -alt_id: GO:0044254 -alt_id: GO:0044257 def: "The chemical reactions and pathways resulting in the breakdown of a protein by the destruction of the native, active configuration, with or without the hydrolysis of peptide bonds." [GOC:mah] comment: This term refers to the breakdown of mature proteins. For cleavage events involved in generating a mature protein from a precursor, consider instead the term 'protein maturation ; GO:0051604' and its children. subset: goslim_candida @@ -66420,7 +72240,6 @@ relationship: results_in_acquisition_of_features_of CL:0000540 ! neuron id: GO:0030183 name: B cell differentiation namespace: biological_process -alt_id: GO:0042115 def: "The process in which a precursor cell type acquires the specialized features of a B cell. A B cell is a lymphocyte of B lineage with the phenotype CD19-positive and capable of B cell mediated immunity." [GO_REF:0000022, GOC:mah] comment: Note that immunologists typically use the word 'development' to refer to cells of B or T cell lineages undergoing the process that GO describes as 'cell differentiation'. synonym: "B cell development" RELATED [GOC:add] @@ -66433,6 +72252,28 @@ intersection_of: GO:0030154 ! cell differentiation intersection_of: results_in_acquisition_of_features_of CL:0000236 ! B cell relationship: results_in_acquisition_of_features_of CL:0000236 ! B cell +[Term] +id: GO:0030184 +name: nitric oxide transmembrane transporter activity +namespace: molecular_function +def: "Enables the transfer of nitric oxide, nitrogen monoxide, from one side of a membrane to the other." [GOC:mah] +is_a: GO:0022857 ! transmembrane transporter activity +intersection_of: GO:0022857 ! transmembrane transporter activity +intersection_of: has_primary_input CHEBI:16480 +relationship: has_primary_input CHEBI:16480 +relationship: part_of GO:0030185 ! nitric oxide transport + +[Term] +id: GO:0030185 +name: nitric oxide transport +namespace: biological_process +def: "The directed movement of nitric oxide, nitrogen monoxide, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:mah] +is_a: BFO:0000003 +is_a: GO:0006810 ! transport +intersection_of: GO:0006810 ! transport +intersection_of: has_primary_input CHEBI:16480 +relationship: has_primary_input CHEBI:16480 + [Term] id: GO:0030186 name: melatonin metabolic process @@ -66711,8 +72552,6 @@ relationship: results_in_acquisition_of_features_of CL:0000312 ! keratinocyte id: GO:0030217 name: T cell differentiation namespace: biological_process -alt_id: GO:0042112 -alt_id: GO:0046652 def: "The process in which a precursor cell type acquires characteristics of a more mature T-cell. A T cell is a type of lymphocyte whose definin characteristic is the expression of a T cell receptor complex." [GO_REF:0000022, GOC:jid, GOC:mah] comment: Note that the term 'thymocyte differentiation' was merged into this term because thymocytes are T cells, and thus the term was essentially redundant. Note that immunologists typically use the word 'development' to refer to cells of B or T cell lineages undergoing the process that GO describes as 'cell differentiation'. synonym: "T cell development" RELATED [GOC:add] @@ -66780,7 +72619,6 @@ relationship: results_in_acquisition_of_features_of CL:0000767 ! basophil id: GO:0030222 name: eosinophil differentiation namespace: biological_process -alt_id: GO:0035856 def: "The process in which a relatively unspecialized myeloid precursor cell acquires the specializes features of an eosinophil." [GOC:add, GOC:mah] synonym: "eosinophil cell development" RELATED [GOC:bf] synonym: "eosinophil cell differentiation" EXACT [] @@ -66851,7 +72689,7 @@ def: "Formation of myofibrils, the repeating units of striated muscle." [GOC:mah is_a: GO:0010927 ! cellular component assembly involved in morphogenesis is_a: GO:0031032 ! actomyosin structure organization is_a: GO:0097435 ! supramolecular fiber organization -is_a: GO:0140694 ! non-membrane-bounded organelle assembly +is_a: GO:0140694 ! membraneless organelle assembly intersection_of: GO:0022607 ! cellular component assembly intersection_of: results_in_assembly_of GO:0030016 ! myofibril relationship: part_of GO:0055002 ! striated muscle cell development @@ -66861,7 +72699,6 @@ relationship: results_in_assembly_of GO:0030016 ! myofibril id: GO:0030246 name: carbohydrate binding namespace: molecular_function -alt_id: GO:0005529 def: "Binding to a carbohydrate, which includes monosaccharides, oligosaccharides and polysaccharides as well as substances derived from monosaccharides by reduction of the carbonyl group (alditols), by oxidation of one or more hydroxy groups to afford the corresponding aldehydes, ketones, or carboxylic acids, or by replacement of one or more hydroxy group(s) by a hydrogen atom. Cyclitols are generally not regarded as carbohydrates." [GOC:mah] subset: goslim_agr subset: goslim_chembl @@ -66883,7 +72720,6 @@ relationship: has_primary_input CHEBI:16646 id: GO:0030247 name: polysaccharide binding namespace: molecular_function -alt_id: GO:0002506 def: "Binding to a polysaccharide, a polymer of many (typically more than 10) monosaccharide residues linked glycosidically." [GOC:mah] synonym: "polysaccharide assembly with MHC class II protein complex" NARROW [] is_a: BFO:0000003 @@ -66904,7 +72740,6 @@ is_a: GO:0030072 ! peptide hormone secretion id: GO:0030261 name: chromosome condensation namespace: biological_process -alt_id: GO:0000068 def: "The progressive compaction of dispersed interphase chromatin into threadlike chromosomes prior to mitotic or meiotic nuclear division, or during apoptosis, in eukaryotic cells." [GOC:mah, ISBN:0815316194] synonym: "DNA condensation" BROAD [Wikipedia:DNA_condensation] synonym: "eukaryotic chromosome condensation" EXACT [GOC:bf] @@ -67036,7 +72871,7 @@ subset: goslim_drosophila subset: goslim_generic subset: goslim_pir subset: goslim_plant -is_a: GO:0110165 ! cellular anatomical entity +is_a: GO:0110165 ! cellular anatomical structure relationship: part_of CL:0000000 ! cell relationship: part_of GO:0071944 ! cell periphery @@ -67055,8 +72890,6 @@ relationship: results_in_acquisition_of_features_of CL:0000092 ! osteoclast id: GO:0030317 name: flagellated sperm motility namespace: biological_process -alt_id: GO:0097724 -alt_id: GO:1905419 def: "The directed, self-propelled movement of a cilium (aka flagellum) that contributes to the movement of a flagellated sperm." [GO_REF:0000060, GOC:cilia, GOC:krc, GOC:TermGenie, PMID:26680031] synonym: "flagellated sperm movement" EXACT [] synonym: "sperm flagellum movement" EXACT [GOC:cilia, GOC:krc] @@ -67241,7 +73074,6 @@ property_value: term_tracker_item "https://github.com/geneontology/go-ontology/i id: GO:0030437 name: ascospore formation namespace: biological_process -alt_id: GO:0007151 def: "The process in which cells that are products of meiosis acquire the specialized features of ascospores. Ascospores are generally found in clusters of four or eight spores within a single mother cell, the ascus, and are characteristic of the ascomycete fungi (phylum Ascomycota)." [GOC:di, GOC:mah, GOC:mcc, PMID:16339736] comment: Note that ascospores and asci are separate biological structures. The ascus is the structure that contain the ascospores, but the development of the ascus is a different process than the formation of the ascospores themselves; for instance, some mutations affect sporulation without affecting ascus development. For this reason, GO:0030437 ascospore formation and GO:0075317 ascus development are different terms and are not linked. subset: goslim_pombe @@ -67262,7 +73094,6 @@ relationship: RO:0002162 NCBITaxon:4890 {all_only="true"} ! in taxon Ascomycota id: GO:0030473 name: nuclear migration along microtubule namespace: biological_process -alt_id: GO:0000065 def: "The directed movement of the nucleus along microtubules within the cell, mediated by motor proteins." [GOC:mah, GOC:sgd_curators] synonym: "microtubule cytoskeleton-dependent nuclear positioning" EXACT [] synonym: "microtubule cytoskeleton-dependent nucleus positioning" EXACT [] @@ -67334,27 +73165,6 @@ intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0030282 ! bone mineralization relationship: negatively_regulates GO:0030282 ! bone mineralization -[Term] -id: GO:0030518 -name: nuclear receptor-mediated steroid hormone signaling pathway -namespace: biological_process -def: "A nuclear receptor-mediated signaling pathway initiated by a steroid binding to an intracellular receptor of the nuclear receptor protein family, and ending with regulation of a downstream cellular process, e.g. transcription." [GOC:mah, GOC:signaling] -synonym: "intracellular steroid hormone receptor signaling pathway" EXACT [] -synonym: "steroid hormone receptor signaling pathway" BROAD [GOC:bf] -synonym: "steroid hormone receptor signalling pathway" BROAD [GOC:bf] -is_a: GO:0043401 ! steroid hormone receptor signaling pathway -is_a: GO:0141193 ! nuclear receptor-mediated signaling pathway - -[Term] -id: GO:0030522 -name: intracellular receptor signaling pathway -namespace: biological_process -def: "The series of molecular signals initiated by a ligand binding to a receptor located within a cell." [GOC:bf, GOC:mah] -synonym: "intracellular receptor mediated signaling pathway" EXACT [] -synonym: "intracellular receptor-mediated signaling pathway" EXACT [] -synonym: "intracellular receptor-mediated signalling pathway" EXACT [] -is_a: GO:0035556 ! intracellular signal transduction - [Term] id: GO:0030539 name: male genitalia development @@ -67381,7 +73191,6 @@ relationship: part_of GO:0046660 ! female sex differentiation id: GO:0030573 name: bile acid catabolic process namespace: biological_process -alt_id: GO:0019613 def: "The chemical reactions and pathways resulting in the breakdown of bile acids, any of a group of steroid carboxylic acids occurring in bile." [GOC:go_curators] synonym: "bile acid 7alpha-dehydroxylation pathway" NARROW [] synonym: "bile acid breakdown" EXACT [] @@ -67955,7 +73764,6 @@ relationship: capable_of_part_of GO:0035735 ! intraciliary transport involved in id: GO:0031012 name: extracellular matrix namespace: cellular_component -alt_id: GO:0005578 def: "A structure lying external to one or more cells, which provides structural support, biochemical or biomechanical cues for cells or tissues." [GOC:BHF, GOC:mah, GOC:rph, NIF_Subcellular:nlx_subcell_20090513, PMID:21123617, PMID:28089324] subset: goslim_chembl subset: goslim_drosophila @@ -68020,6 +73828,21 @@ is_a: GO:0099515 ! actin filament-based transport intersection_of: GO:0007097 ! nuclear migration intersection_of: results_in_transport_along GO:0005884 ! actin filament +[Term] +id: GO:0031023 +name: microtubule organizing center organization +namespace: biological_process +def: "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a microtubule organizing center, a structure from which microtubules grow." [GOC:dph, GOC:jl, GOC:mah] +subset: goslim_pir +synonym: "microtubule organising center organisation" EXACT [] +synonym: "microtubule organizing center organization and biogenesis" RELATED [GOC:mah] +is_a: GO:0007017 ! microtubule-based process +is_a: GO:0016043 ! cellular component organization +intersection_of: GO:0016043 ! cellular component organization +intersection_of: results_in_organization_of GO:0005815 ! microtubule organizing center +relationship: part_of GO:0000226 ! microtubule cytoskeleton organization +relationship: results_in_organization_of GO:0005815 ! microtubule organizing center + [Term] id: GO:0031032 name: actomyosin structure organization @@ -68300,7 +74123,7 @@ def: "The area of a motile cell closest to the direction of movement." [GOC:pg] subset: goslim_pir synonym: "front of cell" EXACT [] synonym: "leading edge of cell" EXACT [] -is_a: GO:0110165 ! cellular anatomical entity +is_a: GO:0110165 ! cellular anatomical structure relationship: part_of CL:0000000 ! cell [Term] @@ -68321,7 +74144,7 @@ id: GO:0031256 name: leading edge membrane namespace: cellular_component def: "The portion of the plasma membrane surrounding the leading edge of a motile cell." [GOC:mah] -is_a: GO:0110165 ! cellular anatomical entity +is_a: GO:0110165 ! cellular anatomical structure relationship: part_of GO:0005886 ! plasma membrane relationship: part_of GO:0031252 ! cell leading edge @@ -68448,189 +74271,6 @@ intersection_of: GO:0031294 ! lymphocyte costimulation intersection_of: has_primary_input CL:0000236 ! B cell relationship: has_primary_input CL:0000236 ! B cell -[Term] -id: GO:0031323 -name: regulation of cellular metabolic process -namespace: biological_process -def: "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways by which individual cells transform chemical substances." [GOC:mah] -comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. -subset: gocheck_do_not_annotate -synonym: "regulation of cellular metabolism" EXACT [] -is_a: GO:0019222 ! regulation of metabolic process -is_a: GO:0050794 ! regulation of cellular process -intersection_of: GO:0065007 ! biological regulation -intersection_of: regulates GO:0044237 ! cellular metabolic process -relationship: regulates GO:0044237 ! cellular metabolic process -property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27189" xsd:anyURI - -[Term] -id: GO:0031324 -name: negative regulation of cellular metabolic process -namespace: biological_process -def: "Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways by which individual cells transform chemical substances." [GOC:mah] -comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. -subset: gocheck_do_not_annotate -synonym: "down regulation of cellular metabolic process" EXACT [] -synonym: "down-regulation of cellular metabolic process" EXACT [] -synonym: "downregulation of cellular metabolic process" EXACT [] -synonym: "inhibition of cellular metabolic process" NARROW [] -synonym: "negative regulation of cellular metabolism" EXACT [] -is_a: GO:0009892 ! negative regulation of metabolic process -is_a: GO:0031323 ! regulation of cellular metabolic process -is_a: GO:0048523 ! negative regulation of cellular process -intersection_of: GO:0065007 ! biological regulation -intersection_of: negatively_regulates GO:0044237 ! cellular metabolic process -relationship: negatively_regulates GO:0044237 ! cellular metabolic process -property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27189" xsd:anyURI - -[Term] -id: GO:0031325 -name: positive regulation of cellular metabolic process -namespace: biological_process -def: "Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways by which individual cells transform chemical substances." [GOC:mah] -comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. -subset: gocheck_do_not_annotate -synonym: "activation of cellular metabolic process" NARROW [] -synonym: "positive regulation of cellular metabolism" EXACT [] -synonym: "stimulation of cellular metabolic process" NARROW [] -synonym: "up regulation of cellular metabolic process" EXACT [] -synonym: "up-regulation of cellular metabolic process" EXACT [] -synonym: "upregulation of cellular metabolic process" EXACT [] -is_a: GO:0009893 ! positive regulation of metabolic process -is_a: GO:0031323 ! regulation of cellular metabolic process -is_a: GO:0048522 ! positive regulation of cellular process -intersection_of: GO:0065007 ! biological regulation -intersection_of: positively_regulates GO:0044237 ! cellular metabolic process -relationship: positively_regulates GO:0044237 ! cellular metabolic process -property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27189" xsd:anyURI - -[Term] -id: GO:0031326 -name: regulation of cellular biosynthetic process -namespace: biological_process -def: "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of substances, carried out by individual cells." [GOC:mah] -comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. -subset: gocheck_do_not_annotate -synonym: "regulation of cellular anabolism" EXACT [] -synonym: "regulation of cellular biosynthesis" EXACT [] -synonym: "regulation of cellular formation" EXACT [] -synonym: "regulation of cellular synthesis" EXACT [] -is_a: GO:0009889 ! regulation of biosynthetic process -is_a: GO:0031323 ! regulation of cellular metabolic process -intersection_of: GO:0065007 ! biological regulation -intersection_of: regulates GO:0044249 ! cellular biosynthetic process -relationship: regulates GO:0044249 ! cellular biosynthetic process -property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27189" xsd:anyURI - -[Term] -id: GO:0031327 -name: negative regulation of cellular biosynthetic process -namespace: biological_process -def: "Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of substances, carried out by individual cells." [GOC:mah] -comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. -subset: gocheck_do_not_annotate -synonym: "down regulation of cellular biosynthetic process" EXACT [] -synonym: "down-regulation of cellular biosynthetic process" EXACT [] -synonym: "downregulation of cellular biosynthetic process" EXACT [] -synonym: "inhibition of cellular biosynthetic process" NARROW [] -synonym: "negative regulation of cellular anabolism" EXACT [] -synonym: "negative regulation of cellular biosynthesis" EXACT [] -synonym: "negative regulation of cellular formation" EXACT [] -synonym: "negative regulation of cellular synthesis" EXACT [] -is_a: GO:0009890 ! negative regulation of biosynthetic process -is_a: GO:0031324 ! negative regulation of cellular metabolic process -is_a: GO:0031326 ! regulation of cellular biosynthetic process -intersection_of: GO:0065007 ! biological regulation -intersection_of: negatively_regulates GO:0044249 ! cellular biosynthetic process -relationship: negatively_regulates GO:0044249 ! cellular biosynthetic process -property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27189" xsd:anyURI - -[Term] -id: GO:0031328 -name: positive regulation of cellular biosynthetic process -namespace: biological_process -def: "Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of substances, carried out by individual cells." [GOC:mah] -comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. -subset: gocheck_do_not_annotate -synonym: "activation of cellular biosynthetic process" NARROW [] -synonym: "positive regulation of cellular anabolism" EXACT [] -synonym: "positive regulation of cellular biosynthesis" EXACT [] -synonym: "positive regulation of cellular formation" EXACT [] -synonym: "positive regulation of cellular synthesis" EXACT [] -synonym: "stimulation of cellular biosynthetic process" NARROW [] -synonym: "up regulation of cellular biosynthetic process" EXACT [] -synonym: "up-regulation of cellular biosynthetic process" EXACT [] -synonym: "upregulation of cellular biosynthetic process" EXACT [] -is_a: GO:0009891 ! positive regulation of biosynthetic process -is_a: GO:0031325 ! positive regulation of cellular metabolic process -is_a: GO:0031326 ! regulation of cellular biosynthetic process -intersection_of: GO:0065007 ! biological regulation -intersection_of: positively_regulates GO:0044249 ! cellular biosynthetic process -relationship: positively_regulates GO:0044249 ! cellular biosynthetic process -property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27189" xsd:anyURI - -[Term] -id: GO:0031329 -name: regulation of cellular catabolic process -namespace: biological_process -def: "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of substances, carried out by individual cells." [GOC:mah] -comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. -subset: gocheck_do_not_annotate -synonym: "regulation of cellular breakdown" EXACT [] -synonym: "regulation of cellular catabolism" EXACT [] -synonym: "regulation of cellular degradation" EXACT [] -is_a: GO:0009894 ! regulation of catabolic process -is_a: GO:0031323 ! regulation of cellular metabolic process -intersection_of: GO:0065007 ! biological regulation -intersection_of: regulates GO:0044248 ! cellular catabolic process -relationship: regulates GO:0044248 ! cellular catabolic process -property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27189" xsd:anyURI - -[Term] -id: GO:0031330 -name: negative regulation of cellular catabolic process -namespace: biological_process -def: "Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of substances, carried out by individual cells." [GOC:mah] -comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. -subset: gocheck_do_not_annotate -synonym: "down regulation of cellular catabolic process" EXACT [] -synonym: "down-regulation of cellular catabolic process" EXACT [] -synonym: "downregulation of cellular catabolic process" EXACT [] -synonym: "inhibition of cellular catabolic process" NARROW [] -synonym: "negative regulation of cellular breakdown" EXACT [] -synonym: "negative regulation of cellular catabolism" EXACT [] -synonym: "negative regulation of cellular degradation" EXACT [] -is_a: GO:0009895 ! negative regulation of catabolic process -is_a: GO:0031324 ! negative regulation of cellular metabolic process -is_a: GO:0031329 ! regulation of cellular catabolic process -intersection_of: GO:0065007 ! biological regulation -intersection_of: negatively_regulates GO:0044248 ! cellular catabolic process -relationship: negatively_regulates GO:0044248 ! cellular catabolic process -property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27189" xsd:anyURI - -[Term] -id: GO:0031331 -name: positive regulation of cellular catabolic process -namespace: biological_process -def: "Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of substances, carried out by individual cells." [GOC:mah] -comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. -subset: gocheck_do_not_annotate -synonym: "activation of cellular catabolic process" NARROW [] -synonym: "positive regulation of cellular breakdown" EXACT [] -synonym: "positive regulation of cellular catabolism" EXACT [] -synonym: "positive regulation of cellular degradation" EXACT [] -synonym: "stimulation of cellular catabolic process" NARROW [] -synonym: "up regulation of cellular catabolic process" EXACT [] -synonym: "up-regulation of cellular catabolic process" EXACT [] -synonym: "upregulation of cellular catabolic process" EXACT [] -is_a: GO:0009896 ! positive regulation of catabolic process -is_a: GO:0031325 ! positive regulation of cellular metabolic process -is_a: GO:0031329 ! regulation of cellular catabolic process -intersection_of: GO:0065007 ! biological regulation -intersection_of: positively_regulates GO:0044248 ! cellular catabolic process -relationship: positively_regulates GO:0044248 ! cellular catabolic process -property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27189" xsd:anyURI - [Term] id: GO:0031333 name: negative regulation of protein-containing complex assembly @@ -68855,6 +74495,7 @@ id: GO:0031400 name: negative regulation of protein modification process namespace: biological_process def: "Any process that stops, prevents, or reduces the frequency, rate or extent of the covalent alteration of one or more amino acid residues within a protein." [GOC:mah, GOC:tb] +subset: gocheck_obsoletion_candidate synonym: "down regulation of protein modification" EXACT [] synonym: "down-regulation of protein modification" EXACT [] synonym: "downregulation of protein modification" EXACT [] @@ -68871,6 +74512,7 @@ id: GO:0031401 name: positive regulation of protein modification process namespace: biological_process def: "Any process that activates or increases the frequency, rate or extent of the covalent alteration of one or more amino acid residues within a protein." [GOC:mah, GOC:tb] +subset: gocheck_obsoletion_candidate synonym: "activation of protein modification" NARROW [] synonym: "stimulation of protein modification" NARROW [] synonym: "up regulation of protein modification" EXACT [] @@ -68911,7 +74553,6 @@ relationship: has_primary_input CHEBI:29067 id: GO:0031410 name: cytoplasmic vesicle namespace: cellular_component -alt_id: GO:0016023 def: "A vesicle found in the cytoplasm of a cell." [GOC:ai, GOC:mah, GOC:vesicles] subset: goslim_agr subset: goslim_candida @@ -68942,7 +74583,6 @@ relationship: part_of GO:0030216 ! keratinocyte differentiation id: GO:0031503 name: protein-containing complex localization namespace: biological_process -alt_id: GO:0034629 def: "A localization process that acts on a protein complex; the complex is transported to, or maintained in, a specific location." [GOC:mah] synonym: "cellular protein complex localisation" RELATED [GOC:mah] synonym: "cellular protein complex localization" RELATED [] @@ -68962,8 +74602,6 @@ property_value: term_tracker_item "https://github.com/geneontology/go-ontology/i id: GO:0031514 name: motile cilium namespace: cellular_component -alt_id: GO:0009434 -alt_id: GO:0031512 def: "A cilium which may have a variable arrangement of axonemal microtubules and also contains molecular motors. It may beat with a whip-like pattern that promotes cell motility or transport of fluids and other cells across a cell surface, such as on epithelial cells that line the lumenal ducts of various tissues; or they may display a distinct twirling motion that directs fluid flow asymmetrically across the cellular surface to affect asymmetric body plan organization. Motile cilia can be found in single as well as multiple copies per cell." [GOC:cilia, GOC:dgh, GOC:kmv, PMID:17009929, PMID:20144998, PMID:22118931] synonym: "microtubule-based flagellum" RELATED [] synonym: "motile cilia" EXACT [] @@ -69036,7 +74674,6 @@ is_a: GO:0048522 ! positive regulation of cellular process intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0042552 ! myelination relationship: positively_regulates GO:0042552 ! myelination -relationship: RO:0002162 NCBITaxon:6072 {all_only="true"} ! in taxon Eumetazoa [Term] id: GO:0031644 @@ -69202,7 +74839,6 @@ namespace: biological_process def: "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving glucocorticoids." [GOC:mah] synonym: "regulation of glucocorticoid metabolism" EXACT [] is_a: GO:0019218 ! regulation of steroid metabolic process -is_a: GO:0031323 ! regulation of cellular metabolic process is_a: GO:0032350 ! regulation of hormone metabolic process intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0008211 ! glucocorticoid metabolic process @@ -69218,7 +74854,6 @@ synonym: "down-regulation of glucocorticoid metabolic process" EXACT [] synonym: "downregulation of glucocorticoid metabolic process" EXACT [] synonym: "inhibition of glucocorticoid metabolic process" NARROW [] synonym: "negative regulation of glucocorticoid metabolism" EXACT [] -is_a: GO:0031324 ! negative regulation of cellular metabolic process is_a: GO:0031943 ! regulation of glucocorticoid metabolic process is_a: GO:0032351 ! negative regulation of hormone metabolic process is_a: GO:0045939 ! negative regulation of steroid metabolic process @@ -69237,7 +74872,6 @@ synonym: "stimulation of glucocorticoid metabolic process" NARROW [] synonym: "up regulation of glucocorticoid metabolic process" EXACT [] synonym: "up-regulation of glucocorticoid metabolic process" EXACT [] synonym: "upregulation of glucocorticoid metabolic process" EXACT [] -is_a: GO:0031325 ! positive regulation of cellular metabolic process is_a: GO:0031943 ! regulation of glucocorticoid metabolic process is_a: GO:0032352 ! positive regulation of hormone metabolic process is_a: GO:0045940 ! positive regulation of steroid metabolic process @@ -69294,11 +74928,12 @@ id: GO:0031949 name: regulation of glucocorticoid catabolic process namespace: biological_process def: "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of glucocorticoids." [GOC:mah] -is_a: GO:0031329 ! regulation of cellular catabolic process +is_a: GO:0009894 ! regulation of catabolic process is_a: GO:0031943 ! regulation of glucocorticoid metabolic process intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0006713 ! glucocorticoid catabolic process relationship: regulates GO:0006713 ! glucocorticoid catabolic process +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29024" xsd:anyURI [Term] id: GO:0031950 @@ -69309,12 +74944,13 @@ synonym: "down regulation of glucocorticoid catabolic process" EXACT [] synonym: "down-regulation of glucocorticoid catabolic process" EXACT [] synonym: "downregulation of glucocorticoid catabolic process" EXACT [] synonym: "inhibition of glucocorticoid catabolic process" NARROW [] -is_a: GO:0031330 ! negative regulation of cellular catabolic process +is_a: GO:0009895 ! negative regulation of catabolic process is_a: GO:0031944 ! negative regulation of glucocorticoid metabolic process is_a: GO:0031949 ! regulation of glucocorticoid catabolic process intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0006713 ! glucocorticoid catabolic process relationship: negatively_regulates GO:0006713 ! glucocorticoid catabolic process +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29024" xsd:anyURI [Term] id: GO:0031951 @@ -69326,22 +74962,13 @@ synonym: "stimulation of glucocorticoid catabolic process" NARROW [] synonym: "up regulation of glucocorticoid catabolic process" EXACT [] synonym: "up-regulation of glucocorticoid catabolic process" EXACT [] synonym: "upregulation of glucocorticoid catabolic process" EXACT [] -is_a: GO:0031331 ! positive regulation of cellular catabolic process +is_a: GO:0009896 ! positive regulation of catabolic process is_a: GO:0031945 ! positive regulation of glucocorticoid metabolic process is_a: GO:0031949 ! regulation of glucocorticoid catabolic process intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0006713 ! glucocorticoid catabolic process relationship: positively_regulates GO:0006713 ! glucocorticoid catabolic process -[Term] -id: GO:0031958 -name: nuclear receptor-mediated corticosteroid signaling pathway -namespace: biological_process -def: "A nuclear receptor-mediated signaling pathway initiated by a corticosteroid binding to an intracellular receptor of the nuclear receptor protein family, and ending with regulation of a downstream cellular process, e.g. transcription." [PMID:11027914, PMID:12606724] -synonym: "corticosteroid receptor signalling pathway" BROAD [] -synonym: "intracellular corticosteroid receptor signaling pathway" EXACT [] -is_a: GO:0030518 ! nuclear receptor-mediated steroid hormone signaling pathway - [Term] id: GO:0031965 name: nuclear membrane @@ -69359,7 +74986,7 @@ name: organelle envelope namespace: cellular_component def: "A double membrane structure enclosing an organelle, including two lipid bilayers and the region between them. In some cases, an organelle envelope may have more than two membranes." [GOC:mah, GOC:pz] subset: goslim_mouse -is_a: GO:0110165 ! cellular anatomical entity +is_a: GO:0110165 ! cellular anatomical structure relationship: part_of GO:0043227 ! membrane-bounded organelle relationship: part_of GO:0043229 ! intracellular organelle @@ -69380,7 +75007,7 @@ id: GO:0031974 name: membrane-enclosed lumen namespace: cellular_component def: "The enclosed volume within a sealed membrane or between two sealed membranes. Encompasses the volume enclosed by the membranes of a particular organelle, e.g. endoplasmic reticulum lumen, or the space between the two lipid bilayers of a double membrane surrounding an organelle, e.g. nuclear envelope lumen." [GOC:add, GOC:mah] -is_a: GO:0110165 ! cellular anatomical entity +is_a: GO:0110165 ! cellular anatomical structure disjoint_from: GO:0045202 ! synapse [Term] @@ -69395,7 +75022,6 @@ relationship: part_of GO:0005634 ! nucleus id: GO:0031982 name: vesicle namespace: cellular_component -alt_id: GO:0031988 def: "Any small, fluid-filled, spherical organelle enclosed by membrane." [GOC:mah, GOC:pz, GOC:vesicles] subset: goslim_pir synonym: "membrane-bounded vesicle" RELATED [] @@ -69443,6 +75069,20 @@ intersection_of: GO:0005488 ! binding intersection_of: has_primary_input CHEBI:36235 relationship: has_primary_input CHEBI:36235 +[Term] +id: GO:0032053 +name: ciliary basal body organization +namespace: biological_process +def: "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a ciliary basal body, a short cylindrical array of microtubules and associated proteins found at the base of a eukaryotic cilium (also called flagellum)." [GOC:cilia, GOC:dph, GOC:jl, GOC:krc, GOC:mah, PMID:9889124] +synonym: "microtubule basal body organisation" BROAD [GOC:mah] +synonym: "microtubule basal body organization" BROAD [] +synonym: "microtubule basal body organization and biogenesis" RELATED [GOC:mah] +is_a: GO:0031023 ! microtubule organizing center organization +is_a: GO:0044782 ! cilium organization +intersection_of: GO:0016043 ! cellular component organization +intersection_of: results_in_organization_of GO:0036064 ! ciliary basal body +relationship: results_in_organization_of GO:0036064 ! ciliary basal body + [Term] id: GO:0032057 name: negative regulation of translational initiation in response to stress @@ -70164,10 +75804,10 @@ name: aldosterone metabolic process namespace: biological_process def: "The chemical reactions and pathways involving aldosterone, a corticosteroid hormone that is produced by the zona glomerulosa of the adrenal cortex and regulates salt (sodium and potassium) and water balance." [PMID:16527843] synonym: "aldosterone metabolism" EXACT [] -is_a: GO:0006081 ! cellular aldehyde metabolic process +is_a: GO:0006081 ! aldehyde metabolic process is_a: GO:0008207 ! C21-steroid hormone metabolic process is_a: GO:0008212 ! mineralocorticoid metabolic process -is_a: GO:0042180 ! cellular ketone metabolic process +is_a: GO:0042180 ! ketone metabolic process is_a: GO:1901615 ! organic hydroxy compound metabolic process intersection_of: GO:0008152 ! metabolic process intersection_of: has_primary_input_or_output CHEBI:27584 @@ -70205,7 +75845,7 @@ name: regulation of aldosterone metabolic process namespace: biological_process def: "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving aldosterone." [GOC:mah] synonym: "regulation of aldosterone metabolism" EXACT [] -is_a: GO:0010565 ! regulation of cellular ketone metabolic process +is_a: GO:0010565 ! regulation of ketone metabolic process is_a: GO:0019218 ! regulation of steroid metabolic process is_a: GO:0032350 ! regulation of hormone metabolic process intersection_of: GO:0065007 ! biological regulation @@ -70222,11 +75862,9 @@ synonym: "down-regulation of aldosterone metabolic process" EXACT [] synonym: "downregulation of aldosterone metabolic process" EXACT [] synonym: "inhibition of aldosterone metabolic process" NARROW [] synonym: "negative regulation of aldosterone metabolism" EXACT [] -is_a: GO:0031324 ! negative regulation of cellular metabolic process is_a: GO:0032344 ! regulation of aldosterone metabolic process is_a: GO:0032351 ! negative regulation of hormone metabolic process is_a: GO:0045939 ! negative regulation of steroid metabolic process -is_a: GO:0062014 ! negative regulation of small molecule metabolic process intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0032341 ! aldosterone metabolic process relationship: negatively_regulates GO:0032341 ! aldosterone metabolic process @@ -70242,11 +75880,9 @@ synonym: "stimulation of aldosterone metabolic process" NARROW [] synonym: "up regulation of aldosterone metabolic process" EXACT [] synonym: "up-regulation of aldosterone metabolic process" EXACT [] synonym: "upregulation of aldosterone metabolic process" EXACT [] -is_a: GO:0031325 ! positive regulation of cellular metabolic process is_a: GO:0032344 ! regulation of aldosterone metabolic process is_a: GO:0032352 ! positive regulation of hormone metabolic process is_a: GO:0045940 ! positive regulation of steroid metabolic process -is_a: GO:0062013 ! positive regulation of small molecule metabolic process intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0032341 ! aldosterone metabolic process relationship: positively_regulates GO:0032341 ! aldosterone metabolic process @@ -70274,6 +75910,7 @@ synonym: "downregulation of aldosterone biosynthetic process" EXACT [] synonym: "inhibition of aldosterone biosynthetic process" NARROW [] is_a: GO:0032345 ! negative regulation of aldosterone metabolic process is_a: GO:0032347 ! regulation of aldosterone biosynthetic process +is_a: GO:0062014 ! negative regulation of small molecule metabolic process is_a: GO:0090032 ! negative regulation of steroid hormone biosynthetic process intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0032342 ! aldosterone biosynthetic process @@ -70291,6 +75928,7 @@ synonym: "up-regulation of aldosterone biosynthetic process" EXACT [] synonym: "upregulation of aldosterone biosynthetic process" EXACT [] is_a: GO:0032346 ! positive regulation of aldosterone metabolic process is_a: GO:0032347 ! regulation of aldosterone biosynthetic process +is_a: GO:0062013 ! positive regulation of small molecule metabolic process is_a: GO:0090031 ! positive regulation of steroid hormone biosynthetic process intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0032342 ! aldosterone biosynthetic process @@ -70350,7 +75988,7 @@ synonym: "down regulation of hormone biosynthetic process" EXACT [] synonym: "down-regulation of hormone biosynthetic process" EXACT [] synonym: "downregulation of hormone biosynthetic process" EXACT [] synonym: "inhibition of hormone biosynthetic process" NARROW [] -is_a: GO:0031327 ! negative regulation of cellular biosynthetic process +is_a: GO:0009890 ! negative regulation of biosynthetic process is_a: GO:0032351 ! negative regulation of hormone metabolic process is_a: GO:0046885 ! regulation of hormone biosynthetic process intersection_of: GO:0065007 ! biological regulation @@ -70682,11 +76320,9 @@ relationship: has_primary_input GO:0005764 ! lysosome id: GO:0032432 name: actin filament bundle namespace: cellular_component -alt_id: GO:0000141 -alt_id: GO:0030482 def: "An assembly of actin filaments that are on the same axis but may be oriented with the same or opposite polarities and may be packed with different levels of tightness." [GOC:mah] synonym: "actin cable" RELATED [GOC:mah] -is_a: GO:0110165 ! cellular anatomical entity +is_a: GO:0110165 ! cellular anatomical structure relationship: has_part GO:0005884 ! actin filament relationship: part_of GO:0015629 ! actin cytoskeleton @@ -70780,8 +76416,6 @@ relationship: positively_regulates GO:0032606 ! type I interferon production id: GO:0032501 name: multicellular organismal process namespace: biological_process -alt_id: GO:0044707 -alt_id: GO:0050874 def: "Any biological process, occurring at the level of a multicellular organism, pertinent to its function." [GOC:curators, GOC:dph, GOC:isa_complete, GOC:tb] comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. subset: gocheck_do_not_annotate @@ -70795,14 +76429,12 @@ property_value: RO:0002161 NCBITaxon:2157 property_value: RO:0002161 NCBITaxon:4896 property_value: RO:0002161 NCBITaxon:4932 property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27189" xsd:anyURI -created_by: jl creation_date: 2012-09-19T16:07:47Z [Term] id: GO:0032502 name: developmental process namespace: biological_process -alt_id: GO:0044767 def: "A biological process whose specific outcome is the progression of an integrated living unit: an anatomical structure (which may be a subcellular structure, cell, tissue, or organ), or organism over time from an initial condition to a later condition." [GOC:isa_complete] subset: goslim_agr subset: goslim_flybase_ribbon @@ -70811,7 +76443,6 @@ synonym: "development" NARROW [] synonym: "single-organism developmental process" RELATED [] is_a: GO:0008150 ! biological_process disjoint_from: GO:0044848 ! biological phase -created_by: jl creation_date: 2012-12-19T12:21:31Z [Term] @@ -70940,8 +76571,6 @@ relationship: occurs_in GO:0016020 ! membrane id: GO:0032606 name: type I interferon production namespace: biological_process -alt_id: GO:0045351 -alt_id: GO:0072641 def: "The appearance of type I interferon due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. Type I interferons include the interferon-alpha, beta, delta, episilon, zeta, kappa, tau, and omega gene families." [GOC:add, ISBN:0126896631, PMID:15546383, PMID:16681834] comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select one of the 'regulation' children terms. subset: gocheck_do_not_annotate @@ -70955,8 +76584,6 @@ is_a: GO:0001816 ! cytokine production id: GO:0032609 name: type II interferon production namespace: biological_process -alt_id: GO:0042095 -alt_id: GO:0072643 def: "The appearance of interferon-gamma due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. Interferon-gamma is also known as type II interferon." [GOC:add, GOC:mah, PMID:15546383] subset: gocheck_do_not_annotate synonym: "IFNG production" EXACT [GOC:mah] @@ -70970,8 +76597,6 @@ is_a: GO:0001816 ! cytokine production id: GO:0032611 name: interleukin-1 beta production namespace: biological_process -alt_id: GO:0050702 -alt_id: GO:0050720 def: "The appearance of interleukin-1 beta due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels." [GOC:mah] subset: gocheck_do_not_annotate synonym: "IL-1 beta production" EXACT [] @@ -70983,8 +76608,6 @@ is_a: GO:0032612 ! interleukin-1 production id: GO:0032612 name: interleukin-1 production namespace: biological_process -alt_id: GO:0042222 -alt_id: GO:0050701 def: "The appearance of interleukin-1 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels." [GOC:mah] subset: gocheck_do_not_annotate synonym: "IL-1 production" EXACT [] @@ -70996,8 +76619,6 @@ is_a: GO:0001816 ! cytokine production id: GO:0032613 name: interleukin-10 production namespace: biological_process -alt_id: GO:0042091 -alt_id: GO:0072608 def: "The appearance of interleukin-10 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels." [GOC:mah] subset: gocheck_do_not_annotate synonym: "IL-10 production" EXACT [] @@ -71009,8 +76630,6 @@ is_a: GO:0001816 ! cytokine production id: GO:0032616 name: interleukin-13 production namespace: biological_process -alt_id: GO:0042231 -alt_id: GO:0072611 def: "The appearance of interleukin-13 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels." [GOC:mah] subset: gocheck_do_not_annotate synonym: "IL-13 production" EXACT [] @@ -71022,8 +76641,6 @@ is_a: GO:0001816 ! cytokine production id: GO:0032620 name: interleukin-17 production namespace: biological_process -alt_id: GO:0042235 -alt_id: GO:0072615 def: "The appearance of any member of the interleukin-17 family of cytokines due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels." [GOC:mah, GOC:rv, Wikipedia:Interleukin_17] subset: gocheck_do_not_annotate synonym: "CTLA-8 production" EXACT [GOC:BHF] @@ -71037,8 +76654,6 @@ is_a: GO:0001816 ! cytokine production id: GO:0032623 name: interleukin-2 production namespace: biological_process -alt_id: GO:0042094 -alt_id: GO:0070970 def: "The appearance of interleukin-2 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels." [GOC:mah] subset: gocheck_do_not_annotate synonym: "IL-2 production" EXACT [] @@ -71050,8 +76665,6 @@ is_a: GO:0001816 ! cytokine production id: GO:0032626 name: interleukin-22 production namespace: biological_process -alt_id: GO:0042239 -alt_id: GO:0072620 def: "The appearance of interleukin-22 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels." [GOC:mah] subset: gocheck_do_not_annotate synonym: "IL-22 production" EXACT [] @@ -71066,9 +76679,6 @@ is_a: GO:0001816 ! cytokine production id: GO:0032633 name: interleukin-4 production namespace: biological_process -alt_id: GO:0042097 -alt_id: GO:0042224 -alt_id: GO:0072602 def: "The appearance of interleukin-4 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels." [GOC:mah] subset: gocheck_do_not_annotate synonym: "IL-4 production" EXACT [] @@ -71080,8 +76690,6 @@ is_a: GO:0001816 ! cytokine production id: GO:0032634 name: interleukin-5 production namespace: biological_process -alt_id: GO:0042225 -alt_id: GO:0072603 def: "The appearance of interleukin-5 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels." [GOC:mah] subset: gocheck_do_not_annotate synonym: "IL-5 production" EXACT [] @@ -71093,8 +76701,6 @@ is_a: GO:0001816 ! cytokine production id: GO:0032635 name: interleukin-6 production namespace: biological_process -alt_id: GO:0042226 -alt_id: GO:0072604 def: "The appearance of interleukin-6 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels." [GOC:mah] subset: gocheck_do_not_annotate synonym: "IL-6 production" EXACT [] @@ -71106,8 +76712,6 @@ is_a: GO:0001816 ! cytokine production id: GO:0032637 name: interleukin-8 production namespace: biological_process -alt_id: GO:0042228 -alt_id: GO:0072606 def: "The appearance of interleukin-8 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels." [GOC:mah] subset: gocheck_do_not_annotate synonym: "IL-8 production" EXACT [] @@ -71119,8 +76723,6 @@ is_a: GO:0001816 ! cytokine production id: GO:0032638 name: interleukin-9 production namespace: biological_process -alt_id: GO:0042229 -alt_id: GO:0072607 def: "The appearance of interleukin-9 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels." [GOC:mah] subset: gocheck_do_not_annotate synonym: "IL-9 production" EXACT [] @@ -71132,8 +76734,6 @@ is_a: GO:0001816 ! cytokine production id: GO:0032640 name: tumor necrosis factor production namespace: biological_process -alt_id: GO:0042533 -alt_id: GO:1990774 def: "The appearance of tumor necrosis factor due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. Tumor necrosis factor is an inflammatory cytokine produced by macrophages/monocytes during acute inflammation and which is responsible for a diverse range of signaling events within cells, leading to necrosis or apoptosis." [GOC:mah, PMID:10891884, PMID:15560120] comment: Note that this term refers only to the specific, original 'tumor necrosis factor' protein (TNF) and not other members of the tumor necrosis factor superfamily (those with the gene symbol root 'TNFSF'). That this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select one of the 'regulation' children terms. subset: gocheck_do_not_annotate @@ -71154,15 +76754,12 @@ synonym: "tumor necrosis factor secretion" NARROW [] synonym: "tumor necrosis factor synthesis" NARROW [] synonym: "tumor necrosis factor-alpha production" RELATED [] is_a: GO:0071706 ! tumor necrosis factor superfamily cytokine production -created_by: sl creation_date: 2015-06-15T22:59:26Z [Term] id: GO:0032649 name: regulation of type II interferon production namespace: biological_process -alt_id: GO:0045072 -alt_id: GO:1902713 def: "Any process that modulates the frequency, rate, or extent of interferon-gamma production. Interferon-gamma is also known as type II interferon." [GOC:add, GOC:mah, PMID:15546383] synonym: "regulation of interferon-gamma biosynthetic process" NARROW [] synonym: "regulation of interferon-gamma production" EXACT [] @@ -71176,8 +76773,6 @@ relationship: regulates GO:0032609 ! type II interferon production id: GO:0032651 name: regulation of interleukin-1 beta production namespace: biological_process -alt_id: GO:0050706 -alt_id: GO:0050722 def: "Any process that modulates the frequency, rate, or extent of interleukin-1 beta production." [GOC:mah] synonym: "regulation of IL-1 beta production" EXACT [] synonym: "regulation of interleukin-1 beta biosynthetic process" NARROW [] @@ -71191,8 +76786,6 @@ relationship: regulates GO:0032611 ! interleukin-1 beta production id: GO:0032652 name: regulation of interleukin-1 production namespace: biological_process -alt_id: GO:0045360 -alt_id: GO:0050704 def: "Any process that modulates the frequency, rate, or extent of interleukin-1 production." [GOC:mah] synonym: "regulation of IL-1 production" EXACT [] synonym: "regulation of interleukin-1 biosynthetic process" NARROW [] @@ -71206,8 +76799,6 @@ relationship: regulates GO:0032612 ! interleukin-1 production id: GO:0032653 name: regulation of interleukin-10 production namespace: biological_process -alt_id: GO:0045074 -alt_id: GO:2001179 def: "Any process that modulates the frequency, rate, or extent of interleukin-10 production." [GOC:mah] synonym: "regulation of IL-10 production" EXACT [] synonym: "regulation of interleukin-10 biosynthetic process" NARROW [] @@ -71221,8 +76812,6 @@ relationship: regulates GO:0032613 ! interleukin-10 production id: GO:0032656 name: regulation of interleukin-13 production namespace: biological_process -alt_id: GO:0045366 -alt_id: GO:2000665 def: "Any process that modulates the frequency, rate, or extent of interleukin-13 production." [GOC:mah] synonym: "regulation of IL-13 production" EXACT [] synonym: "regulation of interleukin-13 biosynthetic process" NARROW [] @@ -71236,8 +76825,6 @@ relationship: regulates GO:0032616 ! interleukin-13 production id: GO:0032660 name: regulation of interleukin-17 production namespace: biological_process -alt_id: GO:0045378 -alt_id: GO:1905076 def: "Any process that modulates the frequency, rate, or extent of production of any member of the interleukin-17 family of cytokines." [GOC:add, GOC:mah, PMID:16482511] synonym: "regulation of CTLA-8 production" EXACT [GOC:TermGenie] synonym: "regulation of Cytotoxic T-lymphocyte-associated antigen 8 secretion" EXACT [] @@ -71253,8 +76840,6 @@ relationship: regulates GO:0032620 ! interleukin-17 production id: GO:0032663 name: regulation of interleukin-2 production namespace: biological_process -alt_id: GO:0045076 -alt_id: GO:1900040 def: "Any process that modulates the frequency, rate, or extent of interleukin-2 production." [GOC:mah] synonym: "regulation of IL-2 production" EXACT [] synonym: "regulation of interleukin-2 biosynthetic process" NARROW [] @@ -71268,7 +76853,6 @@ relationship: regulates GO:0032623 ! interleukin-2 production id: GO:0032666 name: regulation of interleukin-22 production namespace: biological_process -alt_id: GO:0045393 def: "Any process that modulates the frequency, rate, or extent of interleukin-22 production." [GOC:mah] synonym: "regulation of IL-22 production" EXACT [] synonym: "regulation of interleukin-22 biosynthetic process" NARROW [] @@ -71281,8 +76865,6 @@ relationship: regulates GO:0032626 ! interleukin-22 production id: GO:0032673 name: regulation of interleukin-4 production namespace: biological_process -alt_id: GO:0045402 -alt_id: GO:0150133 def: "Any process that modulates the frequency, rate, or extent of interleukin-4 production." [GOC:mah, PMID:29778524] synonym: "regulation of IL-4 production" EXACT [] synonym: "regulation of interleukin-4 biosynthetic process" NARROW [] @@ -71296,8 +76878,6 @@ relationship: regulates GO:0032633 ! interleukin-4 production id: GO:0032674 name: regulation of interleukin-5 production namespace: biological_process -alt_id: GO:0045405 -alt_id: GO:2000662 def: "Any process that modulates the frequency, rate, or extent of interleukin-5 production." [GOC:mah] synonym: "regulation of IL-5 production" EXACT [] synonym: "regulation of interleukin-5 biosynthetic process" NARROW [] @@ -71311,7 +76891,6 @@ relationship: regulates GO:0032634 ! interleukin-5 production id: GO:0032675 name: regulation of interleukin-6 production namespace: biological_process -alt_id: GO:0045408 def: "Any process that modulates the frequency, rate, or extent of interleukin-6 production." [GOC:mah] synonym: "regulation of IL-6 production" EXACT [] synonym: "regulation of interleukin-6 biosynthetic process" NARROW [] @@ -71324,8 +76903,6 @@ relationship: regulates GO:0032635 ! interleukin-6 production id: GO:0032677 name: regulation of interleukin-8 production namespace: biological_process -alt_id: GO:0045414 -alt_id: GO:2000482 def: "Any process that modulates the frequency, rate, or extent of interleukin-8 production." [GOC:mah] synonym: "regulation of IL-8 production" EXACT [] synonym: "regulation of interleukin-8 biosynthetic process" NARROW [] @@ -71339,7 +76916,6 @@ relationship: regulates GO:0032637 ! interleukin-8 production id: GO:0032678 name: regulation of interleukin-9 production namespace: biological_process -alt_id: GO:0045417 def: "Any process that modulates the frequency, rate, or extent of interleukin-9 production." [GOC:mah] synonym: "regulation of IL-9 production" EXACT [] synonym: "regulation of interleukin-9 biosynthetic process" NARROW [] @@ -71352,8 +76928,6 @@ relationship: regulates GO:0032638 ! interleukin-9 production id: GO:0032680 name: regulation of tumor necrosis factor production namespace: biological_process -alt_id: GO:0042534 -alt_id: GO:1904467 def: "Any process that modulates the frequency, rate or extent of tumor necrosis factor production." [GOC:mah, PMID:10891884, PMID:15560120] comment: Note that this term refers only to the specific, original 'tumor necrosis factor' protein (TNF) and not other members of the tumor necrosis factor superfamily (those with the gene symbol root 'TNFSF'). synonym: "regulation of cachectin production" EXACT [GOC:TermGenie] @@ -71366,15 +76940,12 @@ is_a: GO:1903555 ! regulation of tumor necrosis factor superfamily cytokine prod intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0032640 ! tumor necrosis factor production relationship: regulates GO:0032640 ! tumor necrosis factor production -created_by: sl creation_date: 2015-07-09T19:50:02Z [Term] id: GO:0032689 name: negative regulation of type II interferon production namespace: biological_process -alt_id: GO:0045077 -alt_id: GO:1902714 def: "Any process that stops, prevents, or reduces the frequency, rate, or extent of interferon-gamma production. Interferon-gamma is also known as type II interferon." [GOC:add, GOC:mah, PMID:15546383] synonym: "down regulation of interferon-gamma production" EXACT [] synonym: "down-regulation of interferon-gamma production" EXACT [] @@ -71393,8 +76964,6 @@ relationship: negatively_regulates GO:0032609 ! type II interferon production id: GO:0032691 name: negative regulation of interleukin-1 beta production namespace: biological_process -alt_id: GO:0050713 -alt_id: GO:0050724 def: "Any process that stops, prevents, or reduces the frequency, rate, or extent of interleukin-1 beta production." [GOC:mah] synonym: "down regulation of interleukin-1 beta production" EXACT [] synonym: "down-regulation of interleukin-1 beta production" EXACT [] @@ -71413,8 +76982,6 @@ relationship: negatively_regulates GO:0032611 ! interleukin-1 beta production id: GO:0032692 name: negative regulation of interleukin-1 production namespace: biological_process -alt_id: GO:0045361 -alt_id: GO:0050711 def: "Any process that stops, prevents, or reduces the frequency, rate, or extent of interleukin-1 production." [GOC:mah] synonym: "down regulation of interleukin-1 production" EXACT [] synonym: "down-regulation of interleukin-1 production" EXACT [] @@ -71433,8 +77000,6 @@ relationship: negatively_regulates GO:0032612 ! interleukin-1 production id: GO:0032693 name: negative regulation of interleukin-10 production namespace: biological_process -alt_id: GO:0045081 -alt_id: GO:2001180 def: "Any process that stops, prevents, or reduces the frequency, rate, or extent of interleukin-10 production." [GOC:mah] synonym: "down regulation of interleukin-10 production" EXACT [] synonym: "down-regulation of interleukin-10 production" EXACT [] @@ -71453,8 +77018,6 @@ relationship: negatively_regulates GO:0032613 ! interleukin-10 production id: GO:0032696 name: negative regulation of interleukin-13 production namespace: biological_process -alt_id: GO:0045367 -alt_id: GO:2000666 def: "Any process that stops, prevents, or reduces the frequency, rate, or extent of interleukin-13 production." [GOC:mah] synonym: "down regulation of interleukin-13 production" EXACT [] synonym: "down-regulation of interleukin-13 production" EXACT [] @@ -71473,8 +77036,6 @@ relationship: negatively_regulates GO:0032616 ! interleukin-13 production id: GO:0032700 name: negative regulation of interleukin-17 production namespace: biological_process -alt_id: GO:0045379 -alt_id: GO:1905077 def: "Any process that stops, prevents, or reduces the frequency, rate, or extent of production of any member of the interleukin-17 family of cytokines." [GOC:add, GOC:mah, PMID:16482511] synonym: "down regulation of interleukin-17 production" EXACT [] synonym: "downregulation of interleukin-17 production" EXACT [] @@ -71494,8 +77055,6 @@ relationship: negatively_regulates GO:0032620 ! interleukin-17 production id: GO:0032703 name: negative regulation of interleukin-2 production namespace: biological_process -alt_id: GO:0045085 -alt_id: GO:1900041 def: "Any process that stops, prevents, or reduces the frequency, rate, or extent of interleukin-2 production." [GOC:mah] synonym: "down regulation of interleukin-2 production" EXACT [] synonym: "down-regulation of interleukin-2 production" EXACT [] @@ -71514,7 +77073,6 @@ relationship: negatively_regulates GO:0032623 ! interleukin-2 production id: GO:0032706 name: negative regulation of interleukin-22 production namespace: biological_process -alt_id: GO:0045394 def: "Any process that stops, prevents, or reduces the frequency, rate, or extent of interleukin-22 production." [GOC:mah] synonym: "down regulation of interleukin-22 production" EXACT [] synonym: "down-regulation of interleukin-22 production" EXACT [] @@ -71532,8 +77090,6 @@ relationship: negatively_regulates GO:0032626 ! interleukin-22 production id: GO:0032713 name: negative regulation of interleukin-4 production namespace: biological_process -alt_id: GO:0045403 -alt_id: GO:0150134 def: "Any process that stops, prevents, or reduces the frequency, rate, or extent of interleukin-4 production." [GOC:mah, PMID:29778524] synonym: "down regulation of interleukin-4 production" EXACT [] synonym: "down-regulation of interleukin-4 production" EXACT [] @@ -71547,14 +77103,11 @@ is_a: GO:0032673 ! regulation of interleukin-4 production intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0032633 ! interleukin-4 production relationship: negatively_regulates GO:0032633 ! interleukin-4 production -created_by: bc [Term] id: GO:0032714 name: negative regulation of interleukin-5 production namespace: biological_process -alt_id: GO:0045406 -alt_id: GO:2000663 def: "Any process that stops, prevents, or reduces the frequency, rate, or extent of interleukin-5 production." [GOC:mah] synonym: "down regulation of interleukin-5 production" EXACT [] synonym: "down-regulation of interleukin-5 production" EXACT [] @@ -71573,8 +77126,6 @@ relationship: negatively_regulates GO:0032634 ! interleukin-5 production id: GO:0032715 name: negative regulation of interleukin-6 production namespace: biological_process -alt_id: GO:0045409 -alt_id: GO:1900165 def: "Any process that stops, prevents, or reduces the frequency, rate, or extent of interleukin-6 production." [GOC:mah] synonym: "down regulation of interleukin-6 production" EXACT [] synonym: "down-regulation of interleukin-6 production" EXACT [] @@ -71593,8 +77144,6 @@ relationship: negatively_regulates GO:0032635 ! interleukin-6 production id: GO:0032717 name: negative regulation of interleukin-8 production namespace: biological_process -alt_id: GO:0045415 -alt_id: GO:2000483 def: "Any process that stops, prevents, or reduces the frequency, rate, or extent of interleukin-8 production." [GOC:mah] synonym: "down regulation of interleukin-8 production" EXACT [] synonym: "down-regulation of interleukin-8 production" EXACT [] @@ -71613,7 +77162,6 @@ relationship: negatively_regulates GO:0032637 ! interleukin-8 production id: GO:0032718 name: negative regulation of interleukin-9 production namespace: biological_process -alt_id: GO:0045418 def: "Any process that stops, prevents, or reduces the frequency, rate, or extent of interleukin-9 production." [GOC:mah] synonym: "down regulation of interleukin-9 production" EXACT [] synonym: "down-regulation of interleukin-9 production" EXACT [] @@ -71631,8 +77179,6 @@ relationship: negatively_regulates GO:0032638 ! interleukin-9 production id: GO:0032720 name: negative regulation of tumor necrosis factor production namespace: biological_process -alt_id: GO:0042536 -alt_id: GO:1904468 def: "Any process that stops, prevents, or reduces the frequency, rate, or extent of tumor necrosis factor production." [GOC:mah, PMID:10891884, PMID:15560120] comment: Note that this term refers only to the specific, original 'tumor necrosis factor' protein (TNF) and not other members of the tumor necrosis factor superfamily (those with the gene symbol root 'TNFSF'). synonym: "down regulation of tumor necrosis factor production" EXACT [] @@ -71650,15 +77196,12 @@ is_a: GO:1903556 ! negative regulation of tumor necrosis factor superfamily cyto intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0032640 ! tumor necrosis factor production relationship: negatively_regulates GO:0032640 ! tumor necrosis factor production -created_by: sl creation_date: 2015-07-09T19:50:08Z [Term] id: GO:0032729 name: positive regulation of type II interferon production namespace: biological_process -alt_id: GO:0045078 -alt_id: GO:1902715 def: "Any process that activates or increases the frequency, rate, or extent of interferon-gamma production. Interferon-gamma is also known as type II interferon." [GOC:add, GOC:mah, PMID:15546383] synonym: "activation of interferon-gamma production" NARROW [] synonym: "positive regulation of interferon-gamma biosynthetic process" NARROW [] @@ -71680,8 +77223,6 @@ relationship: RO:0002162 NCBITaxon:6072 {all_only="true"} ! in taxon Eumetazoa id: GO:0032731 name: positive regulation of interleukin-1 beta production namespace: biological_process -alt_id: GO:0050718 -alt_id: GO:0050725 def: "Any process that activates or increases the frequency, rate, or extent of interleukin-1 beta production." [GOC:mah] synonym: "activation of interleukin-1 beta production" NARROW [] synonym: "positive regulation of IL-1 beta production" EXACT [] @@ -71701,8 +77242,6 @@ relationship: positively_regulates GO:0032611 ! interleukin-1 beta production id: GO:0032732 name: positive regulation of interleukin-1 production namespace: biological_process -alt_id: GO:0045362 -alt_id: GO:0050716 def: "Any process that activates or increases the frequency, rate, or extent of interleukin-1 production." [GOC:mah] synonym: "activation of interleukin-1 production" NARROW [] synonym: "positive regulation of IL-1 production" EXACT [] @@ -71722,8 +77261,6 @@ relationship: positively_regulates GO:0032612 ! interleukin-1 production id: GO:0032733 name: positive regulation of interleukin-10 production namespace: biological_process -alt_id: GO:0045082 -alt_id: GO:2001181 def: "Any process that activates or increases the frequency, rate, or extent of interleukin-10 production." [GOC:mah] synonym: "activation of interleukin-10 production" NARROW [] synonym: "positive regulation of IL-10 production" EXACT [] @@ -71743,8 +77280,6 @@ relationship: positively_regulates GO:0032613 ! interleukin-10 production id: GO:0032736 name: positive regulation of interleukin-13 production namespace: biological_process -alt_id: GO:0045368 -alt_id: GO:2000667 def: "Any process that activates or increases the frequency, rate, or extent of interleukin-13 production." [GOC:mah] synonym: "activation of interleukin-13 production" NARROW [] synonym: "positive regulation of IL-13 production" EXACT [] @@ -71764,8 +77299,6 @@ relationship: positively_regulates GO:0032616 ! interleukin-13 production id: GO:0032740 name: positive regulation of interleukin-17 production namespace: biological_process -alt_id: GO:0045380 -alt_id: GO:1905078 def: "Any process that activates or increases the frequency, rate, or extent of production of any member of the interleukin-17 family of cytokines." [GOC:add, GOC:mah, PMID:16482511] synonym: "activation of interleukin-17 production" NARROW [] synonym: "positive regulation of CTLA-8 production" EXACT [GOC:TermGenie] @@ -71787,8 +77320,6 @@ relationship: positively_regulates GO:0032620 ! interleukin-17 production id: GO:0032743 name: positive regulation of interleukin-2 production namespace: biological_process -alt_id: GO:0045086 -alt_id: GO:1900042 def: "Any process that activates or increases the frequency, rate, or extent of interleukin-2 production." [GOC:mah] synonym: "activation of interleukin-2 production" NARROW [] synonym: "positive regulation of IL-2 production" EXACT [] @@ -71808,7 +77339,6 @@ relationship: positively_regulates GO:0032623 ! interleukin-2 production id: GO:0032746 name: positive regulation of interleukin-22 production namespace: biological_process -alt_id: GO:0045395 def: "Any process that activates or increases the frequency, rate, or extent of interleukin-22 production." [GOC:mah] synonym: "activation of interleukin-22 production" NARROW [] synonym: "positive regulation of IL-22 production" EXACT [] @@ -71827,8 +77357,6 @@ relationship: positively_regulates GO:0032626 ! interleukin-22 production id: GO:0032753 name: positive regulation of interleukin-4 production namespace: biological_process -alt_id: GO:0045404 -alt_id: GO:0150135 def: "Any process that activates or increases the frequency, rate, or extent of interleukin-4 production." [GOC:mah] synonym: "activation of interleukin-4 production" NARROW [] synonym: "positive regulation of IL-4 production" EXACT [] @@ -71848,8 +77376,6 @@ relationship: positively_regulates GO:0032633 ! interleukin-4 production id: GO:0032754 name: positive regulation of interleukin-5 production namespace: biological_process -alt_id: GO:0045407 -alt_id: GO:2000664 def: "Any process that activates or increases the frequency, rate, or extent of interleukin-5 production." [GOC:mah] synonym: "activation of interleukin-5 production" NARROW [] synonym: "positive regulation of IL-5 production" EXACT [] @@ -71869,8 +77395,6 @@ relationship: positively_regulates GO:0032634 ! interleukin-5 production id: GO:0032755 name: positive regulation of interleukin-6 production namespace: biological_process -alt_id: GO:0045410 -alt_id: GO:2000778 def: "Any process that activates or increases the frequency, rate, or extent of interleukin-6 production." [GOC:mah] synonym: "activation of interleukin-6 production" NARROW [] synonym: "positive regulation of IL-6 production" EXACT [] @@ -71892,8 +77416,6 @@ relationship: RO:0002162 NCBITaxon:6072 {all_only="true"} ! in taxon Eumetazoa id: GO:0032757 name: positive regulation of interleukin-8 production namespace: biological_process -alt_id: GO:0045416 -alt_id: GO:2000484 def: "Any process that activates or increases the frequency, rate, or extent of interleukin-8 production." [GOC:mah] synonym: "activation of interleukin-8 production" NARROW [] synonym: "positive regulation of IL-8 production" EXACT [] @@ -71913,7 +77435,6 @@ relationship: positively_regulates GO:0032637 ! interleukin-8 production id: GO:0032758 name: positive regulation of interleukin-9 production namespace: biological_process -alt_id: GO:0045419 def: "Any process that activates or increases the frequency, rate, or extent of interleukin-9 production." [GOC:mah] synonym: "activation of interleukin-9 production" NARROW [] synonym: "positive regulation of IL-9 production" EXACT [] @@ -71932,8 +77453,6 @@ relationship: positively_regulates GO:0032638 ! interleukin-9 production id: GO:0032760 name: positive regulation of tumor necrosis factor production namespace: biological_process -alt_id: GO:0042535 -alt_id: GO:1904469 def: "Any process that activates or increases the frequency, rate or extent of tumor necrosis factor production." [GO_REF:0000058, GOC:TermGenie, PMID:10891884, PMID:15560120] comment: Note that this term refers only to the specific, original 'tumor necrosis factor' protein (TNF) and not other members of the tumor necrosis factor superfamily (those with the gene symbol root 'TNFSF'). synonym: "activation of tumor necrosis factor production" NARROW [] @@ -71955,7 +77474,6 @@ is_a: GO:1903557 ! positive regulation of tumor necrosis factor superfamily cyto intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0032640 ! tumor necrosis factor production relationship: positively_regulates GO:0032640 ! tumor necrosis factor production -created_by: sl creation_date: 2015-07-09T19:50:14Z [Term] @@ -72015,7 +77533,6 @@ relationship: positively_regulates GO:0032762 ! mast cell cytokine production id: GO:0032774 name: RNA biosynthetic process namespace: biological_process -alt_id: GO:0062103 def: "The chemical reactions and pathways resulting in the formation of RNA, ribonucleic acid, one of the two main type of nucleic acid, consisting of a long, unbranched macromolecule formed from ribonucleotides joined in 3',5'-phosphodiester linkage. Includes polymerization of ribonucleotide monomers. Refers not only to transcription but also to e.g. viral RNA replication." [GOC:mah, GOC:txnOH] comment: Note that, in some cases, viral RNA replication and viral transcription from RNA actually refer to the same process, but may be called differently depending on the focus of a specific research study. subset: gocheck_do_not_annotate @@ -72652,7 +78169,6 @@ property_value: term_tracker_item "https://github.com/geneontology/go-ontology/i id: GO:0032880 name: regulation of protein localization namespace: biological_process -alt_id: GO:1903827 def: "Any process that modulates the frequency, rate or extent of any process in which a protein is transported to, or maintained in, a specific location." [GOC:dph, GOC:mah, GOC:tb] subset: goslim_chembl synonym: "regulation of cellular protein localisation" EXACT [GOC:TermGenie] @@ -72663,7 +78179,6 @@ intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0008104 ! protein localization relationship: regulates GO:0008104 ! protein localization property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/22021" xsd:anyURI -created_by: jl creation_date: 2015-01-20T14:32:14Z [Term] @@ -72960,7 +78475,6 @@ relationship: regulates GO:0030029 ! actin filament-based process id: GO:0032973 name: amino acid export across plasma membrane namespace: biological_process -alt_id: GO:0044746 def: "The directed movement of amino acids from inside of a cell, across the plasma membrane and into the extracellular region." [GOC:jl] synonym: "amino acid efflux" EXACT [] synonym: "amino acid export" BROAD [] @@ -72972,7 +78486,6 @@ intersection_of: has_primary_input CHEBI:35238 intersection_of: has_target_end_location GO:0005576 ! extracellular region intersection_of: has_target_start_location GO:0005829 ! cytosol intersection_of: results_in_transport_across GO:0005886 ! plasma membrane -created_by: jl creation_date: 2012-11-14T14:27:40Z [Term] @@ -73036,9 +78549,6 @@ relationship: capable_of GO:0015277 ! kainate selective glutamate receptor activ id: GO:0032984 name: protein-containing complex disassembly namespace: biological_process -alt_id: GO:0034623 -alt_id: GO:0043241 -alt_id: GO:0043624 def: "The disaggregation of a protein-containing macromolecular complex into its constituent components." [GOC:mah] synonym: "cellular macromolecule complex disassembly" RELATED [] synonym: "cellular protein complex disassembly" RELATED [] @@ -73093,7 +78603,6 @@ property_value: term_tracker_item "https://github.com/geneontology/go-ontology/i id: GO:0032991 name: protein-containing complex namespace: cellular_component -alt_id: GO:0043234 def: "A stable assembly of two or more macromolecules, i.e. proteins, nucleic acids, carbohydrates or lipids, in which at least one component is a protein and the constituent parts function together." [GOC:dos, GOC:mah] comment: A protein complex in this context is meant as a stable set of interacting proteins which can be co-purified by an acceptable method, and where the complex has been shown to exist as an isolated, functional unit in vivo. Acceptable experimental methods include stringent protein purification followed by detection of protein interaction. The following methods should be considered non-acceptable: simple immunoprecipitation, pull-down experiments from cell extracts without further purification, colocalization and 2-hybrid screening. Interactions that should not be captured as protein complexes include: 1) enzyme/substrate, receptor/ligand or any similar transient interactions, unless these are a critical part of the complex assembly or are required e.g. for the receptor to be functional; 2) proteins associated in a pull-down/co-immunoprecipitation assay with no functional link or any evidence that this is a defined biological entity rather than a loose-affinity complex; 3) any complex where the only evidence is based on genetic interaction data; 4) partial complexes, where some subunits (e.g. transmembrane ones) cannot be expressed as recombinant proteins and are excluded from experiments (in this case, independent evidence is necessary to find out the composition of the full complex, if known). Interactions that may be captured as protein complexes include: 1) enzyme/substrate or receptor/ligand if the complex can only assemble and become functional in the presence of both classes of subunits; 2) complexes where one of the members has not been shown to be physically linked to the other(s), but is a homologue of, and has the same functionality as, a protein that has been experimentally demonstrated to form a complex with the other member(s); 3) complexes whose existence is accepted based on localization and pharmacological studies, but for which experimental evidence is not yet available for the complex as a whole. subset: goslim_agr @@ -73108,8 +78617,8 @@ synonym: "protein complex" NARROW [] synonym: "protein containing complex" EXACT [] synonym: "protein-protein complex" NARROW [] is_a: GO:0005575 ! cellular_component -is_a: PR:000050567 ! protein-containing material entity -disjoint_from: GO:0110165 ! cellular anatomical entity +disjoint_from: GO:0110165 ! cellular anatomical structure +relationship: has_part PR:000000001 ! protein [Term] id: GO:0032994 @@ -73665,44 +79174,6 @@ intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0033080 ! immature T cell proliferation in thymus relationship: positively_regulates GO:0033080 ! immature T cell proliferation in thymus -[Term] -id: GO:0033143 -name: regulation of intracellular steroid hormone receptor signaling pathway -namespace: biological_process -def: "Any process that modulates the frequency, rate or extent of the activity of any intracellular steroid hormone receptor signaling pathway." [GOC:mah] -synonym: "regulation of steroid hormone receptor signaling pathway" BROAD [GOC:bf] -synonym: "regulation of steroid hormone receptor signalling pathway" BROAD [] -is_a: GO:1902531 ! regulation of intracellular signal transduction -intersection_of: GO:0065007 ! biological regulation -intersection_of: regulates GO:0030518 ! nuclear receptor-mediated steroid hormone signaling pathway -relationship: regulates GO:0030518 ! nuclear receptor-mediated steroid hormone signaling pathway - -[Term] -id: GO:0033144 -name: negative regulation of intracellular steroid hormone receptor signaling pathway -namespace: biological_process -def: "Any process that stops, prevents, or reduces the frequency, rate or extent of the activity of any intracellular steroid hormone receptor signaling pathway." [GOC:mah] -synonym: "negative regulation of steroid hormone receptor signaling pathway" BROAD [GOC:bf] -synonym: "negative regulation of steroid hormone receptor signalling pathway" BROAD [GOC:bf] -is_a: GO:0033143 ! regulation of intracellular steroid hormone receptor signaling pathway -is_a: GO:1902532 ! negative regulation of intracellular signal transduction -intersection_of: GO:0065007 ! biological regulation -intersection_of: negatively_regulates GO:0030518 ! nuclear receptor-mediated steroid hormone signaling pathway -relationship: negatively_regulates GO:0030518 ! nuclear receptor-mediated steroid hormone signaling pathway - -[Term] -id: GO:0033145 -name: positive regulation of intracellular steroid hormone receptor signaling pathway -namespace: biological_process -def: "Any process that activates or increases the frequency, rate or extent of the activity of any intracellular steroid hormone receptor signaling pathway." [GOC:mah] -synonym: "positive regulation of steroid hormone receptor signaling pathway" BROAD [GOC:bf] -synonym: "positive regulation of steroid hormone receptor signalling pathway" BROAD [] -is_a: GO:0033143 ! regulation of intracellular steroid hormone receptor signaling pathway -is_a: GO:1902533 ! positive regulation of intracellular signal transduction -intersection_of: GO:0065007 ! biological regulation -intersection_of: positively_regulates GO:0030518 ! nuclear receptor-mediated steroid hormone signaling pathway -relationship: positively_regulates GO:0030518 ! nuclear receptor-mediated steroid hormone signaling pathway - [Term] id: GO:0033151 name: V(D)J recombination @@ -73769,7 +79240,6 @@ relationship: has_primary_input CHEBI:30616 id: GO:0033212 name: iron import into cell namespace: biological_process -alt_id: GO:0070627 def: "The directed movement of iron ions from outside of a cell into the cytoplasmic compartment. This may occur via transport across the plasma membrane or via endocytosis." [PMID:18622392, PMID:23192658, Wikipedia:Human_iron_metabolism] synonym: "ferrous ion import" NARROW [] synonym: "ferrous iron import" NARROW [] @@ -73784,7 +79254,6 @@ intersection_of: has_target_end_location GO:0005622 ! intracellular anatomical s intersection_of: has_target_start_location GO:0005576 ! extracellular region relationship: has_target_end_location GO:0005622 ! intracellular anatomical structure relationship: has_target_start_location GO:0005576 ! extracellular region -created_by: mah creation_date: 2009-05-01T04:19:14Z [Term] @@ -74078,6 +79547,20 @@ synonym: "granzyme B localization in T-cell secretory granule" EXACT [] synonym: "granzyme B localization in T-lymphocyte secretory granule" EXACT [] is_a: GO:0033375 ! protease localization to T cell secretory granule +[Term] +id: GO:0033484 +name: intracellular nitric oxide homeostasis +namespace: biological_process +def: "A homeostatic process involved in the maintenance of a steady state level of nitric oxide within a cell." [GOC:mah] +synonym: "cellular nitric oxide homeostasis" EXACT [] +synonym: "nitric oxide homeostasis" BROAD [] +synonym: "NO homeostasis" BROAD [] +is_a: GO:0055082 ! intracellular chemical homeostasis +intersection_of: GO:0055082 ! intracellular chemical homeostasis +intersection_of: regulates_levels_of CHEBI:16480 +relationship: regulates_levels_of CHEBI:16480 +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/24224" xsd:anyURI + [Term] id: GO:0033500 name: carbohydrate homeostasis @@ -74353,7 +79836,6 @@ relationship: positively_regulates GO:0033687 ! osteoblast proliferation id: GO:0033750 name: ribosome localization namespace: biological_process -alt_id: GO:0033753 def: "A process in which a ribosome is transported to, and/or maintained in, a specific location." [GOC:mah] synonym: "establishment of ribosome localisation" RELATED [] synonym: "establishment of ribosome localization" RELATED [] @@ -74390,8 +79872,6 @@ relationship: has_primary_input CHEBI:18059 id: GO:0034067 name: protein localization to Golgi apparatus namespace: biological_process -alt_id: GO:0000042 -alt_id: GO:0072600 def: "A process in which a protein is transported to, or maintained in, a location within the Golgi apparatus." [GOC:mah] synonym: "establishment of protein localisation to Golgi" NARROW [GOC:mah] synonym: "establishment of protein localization in Golgi" NARROW [] @@ -74405,7 +79885,6 @@ is_a: GO:0033365 ! protein localization to organelle intersection_of: GO:0008104 ! protein localization intersection_of: has_target_end_location GO:0005794 ! Golgi apparatus relationship: has_target_end_location GO:0005794 ! Golgi apparatus -created_by: mah creation_date: 2011-02-14T02:26:36Z [Term] @@ -74536,7 +80015,6 @@ intersection_of: results_in_transport_across GO:0016020 ! membrane id: GO:0034220 name: monoatomic ion transmembrane transport namespace: biological_process -alt_id: GO:0099131 def: "A process in which a monoatomic ion is transported across a membrane. Monatomic ions (also called simple ions) are ions consisting of exactly one atom." [GOC:mah] comment: Note that this term is not intended for use in annotating lateral movement within membranes. synonym: "ATP hydrolysis coupled ion transmembrane transport" NARROW [] @@ -74972,7 +80450,6 @@ relationship: has_target_end_location GO:0005694 ! chromosome id: GO:0034504 name: protein localization to nucleus namespace: biological_process -alt_id: GO:0044744 def: "A process in which a protein transports or maintains the localization of another protein to the nucleus." [GOC:ecd] synonym: "protein localisation to nucleus" EXACT [GOC:mah] synonym: "protein localization in cell nucleus" EXACT [] @@ -75093,10 +80570,6 @@ relationship: capable_of GO:0005272 ! sodium channel activity id: GO:0034755 name: iron ion transmembrane transport namespace: biological_process -alt_id: GO:0000040 -alt_id: GO:0006827 -alt_id: GO:0061839 -alt_id: GO:1903874 def: "A process in which an iron ion is transported from one side of a membrane to the other by means of some agent such as a transporter or pore." [GOC:mah, PMID:11390404] comment: Note that this term is not intended for use in annotating lateral movement within membranes. synonym: "ferrous ion transmembrane transport" NARROW [] @@ -75116,14 +80589,12 @@ is_a: GO:0006826 ! iron ion transport is_a: GO:0055085 ! transmembrane transport intersection_of: GO:0006826 ! iron ion transport intersection_of: results_in_transport_across GO:0016020 ! membrane -created_by: vw creation_date: 2015-02-06T11:29:22Z [Term] id: GO:0034756 name: regulation of iron ion transport namespace: biological_process -alt_id: GO:1900390 def: "Any process that modulates the frequency, rate or extent of the directed movement of iron ions (Fe) into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:mah] synonym: "regulation of Fe transport" EXACT [] synonym: "regulation of iron import" NARROW [GOC:TermGenie] @@ -75133,7 +80604,6 @@ is_a: GO:0051049 ! regulation of transport intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0006826 ! iron ion transport relationship: regulates GO:0006826 ! iron ion transport -created_by: mah creation_date: 2012-04-18T04:00:14Z [Term] @@ -75327,7 +80797,6 @@ relationship: positively_regulates GO:0034220 ! monoatomic ion transmembrane tra id: GO:0034769 name: basement membrane disassembly namespace: biological_process -alt_id: GO:0060881 def: "The controlled breakdown of the basement membrane in the context of a normal process such as imaginal disc eversion." [GOC:sart, PMID:17301221] comment: Note that this term has no relationship to 'membrane disassembly ; GO:0030397' because the basement membrane is not a lipid bilayer. synonym: "basal lamina disassembly" RELATED [] @@ -75336,7 +80805,6 @@ is_a: GO:0071711 ! basement membrane organization intersection_of: GO:0022411 ! cellular component disassembly intersection_of: results_in_disassembly_of GO:0005604 ! basement membrane relationship: results_in_disassembly_of GO:0005604 ! basement membrane -created_by: dph creation_date: 2009-08-13T11:27:24Z [Term] @@ -75448,8 +80916,6 @@ relationship: results_in_acquisition_of_features_of CL:0002494 ! cardiocyte id: GO:0035082 name: axoneme assembly namespace: biological_process -alt_id: GO:0035083 -alt_id: GO:0035084 def: "The assembly and organization of an axoneme, the bundle of microtubules and associated proteins that forms the core of cilia (also called flagella) in eukaryotic cells and is responsible for their movements." [GOC:bf, GOC:cilia, GOC:jl, ISBN:0815316194] comment: Note that cilia and eukaryotic flagella are deemed to be equivalent. synonym: "axoneme biogenesis" RELATED [GOC:mah] @@ -75522,7 +80988,6 @@ relationship: results_in_morphogenesis_of UBERON:0000990 ! reproductive system id: GO:0035136 name: forelimb morphogenesis namespace: biological_process -alt_id: GO:0035140 def: "The process in which the anatomical structures of the forelimb are generated and organized. The forelimbs are the front limbs of an animal, e.g. the arms of a human." [GOC:go_curators] synonym: "arm morphogenesis" NARROW [GOC:bf, GOC:cjm] is_a: GO:0035108 ! limb morphogenesis @@ -75969,7 +81434,6 @@ is_a: GO:0090497 ! mesenchymal cell migration intersection_of: GO:0090497 ! mesenchymal cell migration intersection_of: part_of GO:0060174 ! limb bud formation relationship: part_of GO:0090496 ! mesenchyme migration involved in limb bud formation -created_by: bf creation_date: 2010-02-24T02:05:14Z [Term] @@ -75980,7 +81444,6 @@ def: "An immunoglobulin-like complex that is present in at least the plasma memb comment: Despite its name, the pre-BCR is not a receptor complex, as it appears to provide a low level of signal not dependent on a ligand, but rather simply on correct assembly of the complex as a measure for correct Ig heavy chain recombination and folding. A significant proportion of pre-BCR complexes fail to reach the cell surface, and in some cases may provide their signaling function from the trans-Golgi network or lysosome. synonym: "pre-BCR" EXACT [] is_a: GO:0098796 ! membrane protein complex -created_by: bf creation_date: 2010-03-11T10:46:10Z [Term] @@ -75993,7 +81456,6 @@ is_a: GO:0072698 ! protein localization to microtubule cytoskeleton intersection_of: GO:0008104 ! protein localization intersection_of: has_target_end_location GO:0005874 ! microtubule relationship: has_target_end_location GO:0005874 ! microtubule -created_by: bf creation_date: 2010-03-11T11:00:56Z [Term] @@ -76006,7 +81468,6 @@ is_a: GO:0005488 ! binding intersection_of: GO:0005488 ! binding intersection_of: has_primary_input CHEBI:37397 relationship: has_primary_input CHEBI:37397 -created_by: bf creation_date: 2010-03-12T10:25:34Z [Term] @@ -76019,7 +81480,6 @@ is_a: GO:0042045 ! epithelial fluid transport intersection_of: GO:0042044 ! fluid transport intersection_of: has_primary_input CHEBI:15377 intersection_of: results_in_transport_across UBERON:0000483 ! epithelium -created_by: bf creation_date: 2010-03-18T10:55:38Z [Term] @@ -76032,7 +81492,6 @@ is_a: GO:1902414 ! protein localization to cell junction intersection_of: GO:0008104 ! protein localization intersection_of: has_target_end_location GO:0045202 ! synapse relationship: has_target_end_location GO:0045202 ! synapse -created_by: bf creation_date: 2010-03-29T10:58:53Z [Term] @@ -76047,7 +81506,6 @@ is_a: GO:0055085 ! transmembrane transport intersection_of: GO:0006810 ! transport intersection_of: has_primary_input CHEBI:43474 intersection_of: results_in_transport_across GO:0016020 ! membrane -created_by: bf creation_date: 2010-04-08T11:24:06Z [Term] @@ -76059,7 +81517,6 @@ is_a: GO:0016477 ! cell migration intersection_of: GO:0016477 ! cell migration intersection_of: part_of GO:0001570 ! vasculogenesis relationship: part_of GO:0001570 ! vasculogenesis -created_by: bf creation_date: 2010-04-09T03:53:01Z [Term] @@ -76071,7 +81528,6 @@ is_a: GO:0051239 ! regulation of multicellular organismal process intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0002540 ! leukotriene production involved in inflammatory response relationship: regulates GO:0002540 ! leukotriene production involved in inflammatory response -created_by: bf creation_date: 2010-04-26T10:49:22Z [Term] @@ -76085,7 +81541,6 @@ is_a: GO:0051240 ! positive regulation of multicellular organismal process intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0002540 ! leukotriene production involved in inflammatory response relationship: positively_regulates GO:0002540 ! leukotriene production involved in inflammatory response -created_by: bf creation_date: 2010-04-26T10:50:14Z [Term] @@ -76099,17 +81554,12 @@ is_a: GO:0051241 ! negative regulation of multicellular organismal process intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0002540 ! leukotriene production involved in inflammatory response relationship: negatively_regulates GO:0002540 ! leukotriene production involved in inflammatory response -created_by: bf creation_date: 2010-04-26T10:50:55Z [Term] id: GO:0035556 name: intracellular signal transduction namespace: biological_process -alt_id: GO:0007242 -alt_id: GO:0007243 -alt_id: GO:0023013 -alt_id: GO:0023034 def: "The process in which a signal is passed on to downstream components within the cell, which become activated themselves to further propagate the signal and finally trigger a change in the function or state of the cell." [GOC:bf, GOC:jl, GOC:signaling, ISBN:3527303782] subset: goslim_drosophila synonym: "intracellular signal transduction pathway" NARROW [] @@ -76120,7 +81570,6 @@ is_a: GO:0007165 ! signal transduction intersection_of: GO:0007165 ! signal transduction intersection_of: occurs_in GO:0005622 ! intracellular anatomical structure relationship: occurs_in GO:0005622 ! intracellular anatomical structure -created_by: bf creation_date: 2010-05-14T01:14:37Z [Term] @@ -76133,7 +81582,6 @@ is_a: GO:0051098 ! regulation of binding intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0003682 ! chromatin binding relationship: regulates GO:0003682 ! chromatin binding -created_by: bf creation_date: 2010-05-19T10:28:36Z [Term] @@ -76147,7 +81595,6 @@ is_a: GO:0051100 ! negative regulation of binding intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0003682 ! chromatin binding relationship: negatively_regulates GO:0003682 ! chromatin binding -created_by: bf creation_date: 2010-05-19T10:29:06Z [Term] @@ -76161,7 +81608,6 @@ is_a: GO:0051099 ! positive regulation of binding intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0003682 ! chromatin binding relationship: positively_regulates GO:0003682 ! chromatin binding -created_by: bf creation_date: 2010-05-19T10:29:41Z [Term] @@ -76176,7 +81622,6 @@ intersection_of: GO:0016020 ! membrane intersection_of: bounding_layer_of GO:0042582 ! azurophil granule relationship: bounding_layer_of GO:0042582 ! azurophil granule relationship: part_of GO:0042582 ! azurophil granule -created_by: bf creation_date: 2010-10-05T01:29:10Z [Term] @@ -76190,7 +81635,6 @@ is_a: GO:0045184 ! establishment of protein localization is_a: GO:0071692 ! protein localization to extracellular region intersection_of: GO:0045184 ! establishment of protein localization intersection_of: has_target_end_location GO:0005576 ! extracellular region -created_by: bf creation_date: 2010-11-09T10:25:08Z [Term] @@ -76205,7 +81649,6 @@ intersection_of: GO:0048856 ! anatomical structure development intersection_of: results_in_development_of UBERON:0003704 ! intrahepatic bile duct relationship: part_of GO:0001889 ! liver development relationship: results_in_development_of UBERON:0003704 ! intrahepatic bile duct -created_by: bf creation_date: 2010-12-08T04:10:50Z [Term] @@ -76217,7 +81660,6 @@ is_a: GO:0061009 ! common bile duct development intersection_of: GO:0048856 ! anatomical structure development intersection_of: results_in_development_of UBERON:0001152 ! cystic duct relationship: results_in_development_of UBERON:0001152 ! cystic duct -created_by: bf creation_date: 2010-12-10T01:24:28Z [Term] @@ -76230,7 +81672,6 @@ is_a: GO:0030282 ! bone mineralization intersection_of: GO:0030282 ! bone mineralization intersection_of: part_of GO:0043931 ! ossification involved in bone maturation relationship: part_of GO:0043931 ! ossification involved in bone maturation -created_by: bf creation_date: 2010-12-20T01:57:31Z [Term] @@ -76244,7 +81685,6 @@ intersection_of: GO:0030154 ! cell differentiation intersection_of: results_in_acquisition_of_features_of CL:0002504 ! enteric smooth muscle cell relationship: part_of GO:0048565 ! digestive tract development relationship: results_in_acquisition_of_features_of CL:0002504 ! enteric smooth muscle cell -created_by: bf creation_date: 2011-01-21T02:58:58Z [Term] @@ -76257,7 +81697,6 @@ intersection_of: GO:0048856 ! anatomical structure development intersection_of: results_in_development_of CL:0000856 ! neuromast hair cell relationship: part_of GO:0048886 ! neuromast hair cell differentiation relationship: results_in_development_of CL:0000856 ! neuromast hair cell -created_by: bf creation_date: 2011-02-14T11:01:42Z [Term] @@ -76270,7 +81709,6 @@ intersection_of: GO:0048468 ! cell development intersection_of: results_in_development_of CL:2000034 ! anterior lateral line neuromast hair cell relationship: part_of GO:0048903 ! anterior lateral line neuromast hair cell differentiation relationship: results_in_development_of CL:2000034 ! anterior lateral line neuromast hair cell -created_by: bf creation_date: 2011-02-14T11:03:57Z [Term] @@ -76283,7 +81721,6 @@ intersection_of: GO:0048468 ! cell development intersection_of: results_in_development_of CL:2000037 ! posterior lateral line neuromast hair cell relationship: part_of GO:0048923 ! posterior lateral line neuromast hair cell differentiation relationship: results_in_development_of CL:2000037 ! posterior lateral line neuromast hair cell -created_by: bf creation_date: 2011-02-14T11:04:57Z [Term] @@ -76296,7 +81733,6 @@ intersection_of: GO:0009653 ! anatomical structure morphogenesis intersection_of: results_in_morphogenesis_of CL:0000856 ! neuromast hair cell relationship: part_of GO:0035675 ! neuromast hair cell development relationship: results_in_morphogenesis_of CL:0000856 ! neuromast hair cell -created_by: bf creation_date: 2011-02-14T11:06:15Z [Term] @@ -76308,7 +81744,6 @@ is_a: GO:0043615 ! astrocyte cell migration is_a: GO:0060326 ! cell chemotaxis intersection_of: GO:0006935 ! chemotaxis intersection_of: results_in_movement_of CL:0000127 ! astrocyte -created_by: bf creation_date: 2011-02-28T03:17:52Z [Term] @@ -76322,7 +81757,6 @@ is_a: GO:0016477 ! cell migration intersection_of: GO:0016477 ! cell migration intersection_of: results_in_movement_of CL:0000037 ! hematopoietic stem cell relationship: results_in_movement_of CL:0000037 ! hematopoietic stem cell -created_by: bf creation_date: 2011-02-28T03:20:36Z [Term] @@ -76335,7 +81769,6 @@ is_a: GO:0002262 ! myeloid cell homeostasis intersection_of: GO:0048872 ! homeostasis of number of cells intersection_of: acts_on_population_of CL:0000576 ! monocyte relationship: acts_on_population_of CL:0000576 ! monocyte -created_by: bf creation_date: 2011-03-02T11:32:57Z [Term] @@ -76348,7 +81781,6 @@ is_a: GO:0010818 ! T cell chemotaxis intersection_of: GO:0006935 ! chemotaxis intersection_of: results_in_movement_of CL:0000912 ! helper T cell relationship: results_in_movement_of CL:0000912 ! helper T cell -created_by: bf creation_date: 2011-03-02T02:31:48Z [Term] @@ -76361,7 +81793,6 @@ is_a: GO:0010818 ! T cell chemotaxis intersection_of: GO:0006935 ! chemotaxis intersection_of: results_in_movement_of CL:0000899 ! T-helper 17 cell relationship: results_in_movement_of CL:0000899 ! T-helper 17 cell -created_by: bf creation_date: 2011-03-02T02:35:16Z [Term] @@ -76374,7 +81805,6 @@ is_a: GO:0010818 ! T cell chemotaxis intersection_of: GO:0006935 ! chemotaxis intersection_of: results_in_movement_of CL:0000545 ! T-helper 1 cell relationship: results_in_movement_of CL:0000545 ! T-helper 1 cell -created_by: bf creation_date: 2011-03-02T02:36:49Z [Term] @@ -76387,7 +81817,6 @@ is_a: GO:0010818 ! T cell chemotaxis intersection_of: GO:0006935 ! chemotaxis intersection_of: results_in_movement_of CL:0000546 ! T-helper 2 cell relationship: results_in_movement_of CL:0000546 ! T-helper 2 cell -created_by: bf creation_date: 2011-03-02T02:37:44Z [Term] @@ -76399,7 +81828,6 @@ is_a: GO:0042110 ! T cell activation intersection_of: GO:0001775 ! cell activation intersection_of: has_primary_input CL:0000813 ! memory T cell relationship: has_primary_input CL:0000813 ! memory T cell -created_by: bf creation_date: 2011-03-02T03:03:02Z [Term] @@ -76411,7 +81839,6 @@ is_a: GO:0046631 ! alpha-beta T cell activation intersection_of: GO:0001775 ! cell activation intersection_of: has_primary_input CL:0000624 ! CD4-positive, alpha-beta T cell relationship: has_primary_input CL:0000624 ! CD4-positive, alpha-beta T cell -created_by: bf creation_date: 2011-03-02T03:04:11Z [Term] @@ -76424,7 +81851,6 @@ is_a: GO:0035710 ! CD4-positive, alpha-beta T cell activation intersection_of: GO:0001775 ! cell activation intersection_of: has_primary_input CL:0000545 ! T-helper 1 cell relationship: has_primary_input CL:0000545 ! T-helper 1 cell -created_by: bf creation_date: 2011-03-02T03:05:08Z [Term] @@ -76437,7 +81863,6 @@ is_a: GO:0035710 ! CD4-positive, alpha-beta T cell activation intersection_of: GO:0001775 ! cell activation intersection_of: has_primary_input CL:0000546 ! T-helper 2 cell relationship: has_primary_input CL:0000546 ! T-helper 2 cell -created_by: bf creation_date: 2011-03-02T03:05:59Z [Term] @@ -76451,7 +81876,6 @@ is_a: GO:0006814 ! sodium ion transport is_a: GO:0034220 ! monoatomic ion transmembrane transport intersection_of: GO:0055085 ! transmembrane transport intersection_of: has_primary_input CHEBI:29101 -created_by: bf creation_date: 2011-03-10T02:52:36Z [Term] @@ -76463,7 +81887,6 @@ is_a: GO:0072537 ! fibroblast activation intersection_of: GO:0001775 ! cell activation intersection_of: has_primary_input CL:0000632 ! hepatic stellate cell relationship: has_primary_input CL:0000632 ! hepatic stellate cell -created_by: bf creation_date: 2011-03-11T10:04:12Z [Term] @@ -76478,7 +81901,6 @@ is_a: GO:0042073 ! intraciliary transport intersection_of: GO:0042073 ! intraciliary transport intersection_of: part_of GO:0060271 ! cilium assembly relationship: part_of GO:0060271 ! cilium assembly -created_by: bf creation_date: 2011-03-17T10:55:42Z [Term] @@ -76490,7 +81912,6 @@ is_a: GO:0008283 ! cell population proliferation intersection_of: GO:0008283 ! cell population proliferation intersection_of: part_of GO:0001745 ! compound eye morphogenesis relationship: part_of GO:0001745 ! compound eye morphogenesis -created_by: bf creation_date: 2011-03-17T10:57:03Z [Term] @@ -76503,7 +81924,6 @@ is_a: GO:0046633 ! alpha-beta T cell proliferation intersection_of: GO:0008283 ! cell population proliferation intersection_of: acts_on_population_of CL:0000624 ! CD4-positive, alpha-beta T cell relationship: acts_on_population_of CL:0000624 ! CD4-positive, alpha-beta T cell -created_by: bf creation_date: 2011-03-17T02:12:48Z [Term] @@ -76516,7 +81936,6 @@ is_a: GO:0046633 ! alpha-beta T cell proliferation intersection_of: GO:0008283 ! cell population proliferation intersection_of: acts_on_population_of CL:0000625 ! CD8-positive, alpha-beta T cell relationship: acts_on_population_of CL:0000625 ! CD8-positive, alpha-beta T cell -created_by: bf creation_date: 2011-03-17T02:13:54Z [Term] @@ -76528,7 +81947,6 @@ is_a: GO:0035739 ! CD4-positive, alpha-beta T cell proliferation intersection_of: GO:0008283 ! cell population proliferation intersection_of: acts_on_population_of CL:0000896 ! activated CD4-positive, alpha-beta T cell relationship: acts_on_population_of CL:0000896 ! activated CD4-positive, alpha-beta T cell -created_by: bf creation_date: 2011-03-17T02:18:39Z [Term] @@ -76540,7 +81958,6 @@ is_a: GO:0035740 ! CD8-positive, alpha-beta T cell proliferation intersection_of: GO:0008283 ! cell population proliferation intersection_of: acts_on_population_of CL:0000906 ! activated CD8-positive, alpha-beta T cell relationship: acts_on_population_of CL:0000906 ! activated CD8-positive, alpha-beta T cell -created_by: bf creation_date: 2011-03-17T02:19:58Z [Term] @@ -76554,7 +81971,6 @@ is_a: GO:0002369 ! T cell cytokine production intersection_of: GO:0001816 ! cytokine production intersection_of: process_has_causal_agent CL:0000624 ! CD4-positive, alpha-beta T cell relationship: process_has_causal_agent CL:0000624 ! CD4-positive, alpha-beta T cell -created_by: bf creation_date: 2011-03-17T02:21:51Z [Term] @@ -76570,7 +81986,6 @@ intersection_of: GO:0001816 ! cytokine production intersection_of: process_has_causal_agent CL:0000545 ! T-helper 1 cell relationship: part_of GO:0042088 ! T-helper 1 type immune response relationship: process_has_causal_agent CL:0000545 ! T-helper 1 cell -created_by: bf creation_date: 2011-03-17T02:22:54Z [Term] @@ -76586,7 +82001,6 @@ intersection_of: GO:0001816 ! cytokine production intersection_of: process_has_causal_agent CL:0000546 ! T-helper 2 cell relationship: part_of GO:0042092 ! type 2 immune response relationship: process_has_causal_agent CL:0000546 ! T-helper 2 cell -created_by: bf creation_date: 2011-03-17T02:23:32Z [Term] @@ -76598,7 +82012,6 @@ is_a: GO:0048247 ! lymphocyte chemotaxis intersection_of: GO:0006935 ! chemotaxis intersection_of: results_in_movement_of CL:0000623 ! natural killer cell relationship: results_in_movement_of CL:0000623 ! natural killer cell -created_by: bf creation_date: 2011-03-17T02:40:10Z [Term] @@ -76610,7 +82023,6 @@ is_a: GO:0048247 ! lymphocyte chemotaxis intersection_of: GO:0006935 ! chemotaxis intersection_of: results_in_movement_of CL:0000236 ! B cell relationship: results_in_movement_of CL:0000236 ! B cell -created_by: bf creation_date: 2011-03-23T10:30:33Z [Term] @@ -76622,7 +82034,6 @@ is_a: GO:0043542 ! endothelial cell migration is_a: GO:0060326 ! cell chemotaxis intersection_of: GO:0006935 ! chemotaxis intersection_of: results_in_movement_of CL:0000115 ! endothelial cell -created_by: bf creation_date: 2011-03-31T04:31:37Z [Term] @@ -76636,7 +82047,6 @@ is_a: GO:0051649 ! establishment of localization in cell intersection_of: GO:0030073 ! insulin secretion intersection_of: part_of GO:0071333 ! cellular response to glucose stimulus relationship: part_of GO:0071333 ! cellular response to glucose stimulus -created_by: bf creation_date: 2011-04-01T01:14:40Z [Term] @@ -76650,7 +82060,6 @@ is_a: GO:0061178 ! regulation of insulin secretion involved in cellular response intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0035773 ! insulin secretion involved in cellular response to glucose stimulus relationship: positively_regulates GO:0035773 ! insulin secretion involved in cellular response to glucose stimulus -created_by: bf creation_date: 2011-04-01T01:49:09Z [Term] @@ -76664,7 +82073,6 @@ intersection_of: GO:0009653 ! anatomical structure morphogenesis intersection_of: results_in_morphogenesis_of UBERON:0004739 ! pronephric glomerulus relationship: part_of GO:0039021 ! pronephric glomerulus development relationship: results_in_morphogenesis_of UBERON:0004739 ! pronephric glomerulus -created_by: bf creation_date: 2011-04-04T10:59:28Z [Term] @@ -76677,7 +82085,6 @@ is_a: GO:0072014 ! proximal tubule development intersection_of: GO:0048856 ! anatomical structure development intersection_of: results_in_development_of UBERON:0006173 ! pronephric proximal tubule relationship: results_in_development_of UBERON:0006173 ! pronephric proximal tubule -created_by: bf creation_date: 2011-04-04T11:02:54Z [Term] @@ -76690,7 +82097,6 @@ is_a: GO:0072017 ! distal tubule development intersection_of: GO:0048856 ! anatomical structure development intersection_of: results_in_development_of UBERON:0006175 ! pronephric distal tubule relationship: results_in_development_of UBERON:0006175 ! pronephric distal tubule -created_by: bf creation_date: 2011-04-04T11:06:01Z [Term] @@ -76704,7 +82110,6 @@ intersection_of: GO:0030154 ! cell differentiation intersection_of: results_in_acquisition_of_features_of CL:1000090 ! pronephric nephron tubule epithelial cell relationship: part_of GO:0039020 ! pronephric nephron tubule development relationship: results_in_acquisition_of_features_of CL:1000090 ! pronephric nephron tubule epithelial cell -created_by: bf creation_date: 2011-04-04T11:07:47Z [Term] @@ -76718,7 +82123,6 @@ intersection_of: GO:0030154 ! cell differentiation intersection_of: results_in_acquisition_of_features_of CL:0000566 ! angioblastic mesenchymal cell relationship: part_of GO:0001568 ! blood vessel development relationship: results_in_acquisition_of_features_of CL:0000566 ! angioblastic mesenchymal cell -created_by: bf creation_date: 2011-04-04T11:10:38Z [Term] @@ -76730,7 +82134,6 @@ is_a: GO:0016477 ! cell migration intersection_of: GO:0016477 ! cell migration intersection_of: part_of GO:0001822 ! kidney development relationship: part_of GO:0001822 ! kidney development -created_by: bf creation_date: 2011-04-06T10:39:52Z [Term] @@ -76743,7 +82146,6 @@ is_a: GO:0035787 ! cell migration involved in kidney development intersection_of: GO:0016477 ! cell migration intersection_of: part_of GO:0001656 ! metanephros development relationship: part_of GO:0001656 ! metanephros development -created_by: bf creation_date: 2011-04-06T10:42:21Z [Term] @@ -76756,7 +82158,6 @@ intersection_of: GO:0071695 ! anatomical structure maturation intersection_of: results_in_maturation_of UBERON:0000056 ! ureter relationship: part_of GO:0072189 ! ureter development relationship: results_in_maturation_of UBERON:0000056 ! ureter -created_by: bf creation_date: 2011-04-14T01:13:39Z [Term] @@ -76770,7 +82171,6 @@ intersection_of: GO:0048856 ! anatomical structure development intersection_of: results_in_development_of UBERON:0001235 ! adrenal cortex relationship: part_of GO:0030325 ! adrenal gland development relationship: results_in_development_of UBERON:0001235 ! adrenal cortex -created_by: bf creation_date: 2011-04-18T10:25:39Z [Term] @@ -76785,7 +82185,6 @@ intersection_of: GO:0048646 ! anatomical structure formation involved in morphog intersection_of: results_in_formation_of UBERON:0001235 ! adrenal cortex relationship: part_of GO:0035801 ! adrenal cortex development relationship: results_in_formation_of UBERON:0001235 ! adrenal cortex -created_by: bf creation_date: 2011-04-18T10:26:49Z [Term] @@ -76801,7 +82200,6 @@ intersection_of: part_of CL:0000025 ! egg cell relationship: part_of CL:0000025 ! egg cell relationship: RO:0002160 NCBITaxon:33208 ! only in taxon Metazoa relationship: RO:0002162 NCBITaxon:33208 {all_only="true"} ! in taxon Metazoa -created_by: bf creation_date: 2011-04-19T02:07:23Z [Term] @@ -76813,7 +82211,6 @@ synonym: "regulation of urinary volume" EXACT [] synonym: "regulation of urine flow" EXACT [] is_a: GO:0003014 ! renal system process is_a: GO:0050878 ! regulation of body fluid levels -created_by: bf creation_date: 2011-04-20T01:17:38Z [Term] @@ -76828,7 +82225,6 @@ intersection_of: results_in_development_of UBERON:0000162 ! cloaca relationship: part_of GO:0001655 ! urogenital system development relationship: part_of GO:0048546 ! digestive tract morphogenesis relationship: results_in_development_of UBERON:0000162 ! cloaca -created_by: bf creation_date: 2011-05-06T01:54:35Z [Term] @@ -76843,7 +82239,6 @@ intersection_of: GO:0048856 ! anatomical structure development intersection_of: results_in_development_of UBERON:0004804 ! oviduct epithelium relationship: part_of GO:0060066 ! oviduct development relationship: results_in_development_of UBERON:0004804 ! oviduct epithelium -created_by: bf creation_date: 2011-05-10T10:53:05Z [Term] @@ -76857,7 +82252,6 @@ intersection_of: GO:0048856 ! anatomical structure development intersection_of: results_in_development_of UBERON:0006955 ! uterine epithelium relationship: part_of GO:0060065 ! uterus development relationship: results_in_development_of UBERON:0006955 ! uterine epithelium -created_by: bf creation_date: 2011-05-10T10:57:45Z [Term] @@ -76872,7 +82266,6 @@ intersection_of: GO:0009653 ! anatomical structure morphogenesis intersection_of: results_in_morphogenesis_of UBERON:0000993 ! oviduct relationship: part_of GO:0060066 ! oviduct development relationship: results_in_morphogenesis_of UBERON:0000993 ! oviduct -created_by: bf creation_date: 2011-05-10T11:01:20Z [Term] @@ -76884,7 +82277,6 @@ is_a: GO:0030855 ! epithelial cell differentiation is_a: GO:0061005 ! cell differentiation involved in kidney development intersection_of: GO:0030855 ! epithelial cell differentiation intersection_of: part_of GO:0001822 ! kidney development -created_by: bf creation_date: 2011-05-11T11:34:21Z [Term] @@ -76898,7 +82290,6 @@ intersection_of: GO:0048856 ! anatomical structure development intersection_of: results_in_development_of CL:0000556 ! megakaryocyte relationship: part_of GO:0030219 ! megakaryocyte differentiation relationship: results_in_development_of CL:0000556 ! megakaryocyte -created_by: bf creation_date: 2011-05-13T01:28:06Z [Term] @@ -76913,7 +82304,6 @@ is_a: GO:0050896 ! response to stimulus intersection_of: GO:0050896 ! response to stimulus intersection_of: has_primary_input CHEBI:29103 relationship: has_primary_input CHEBI:29103 -created_by: bf creation_date: 2011-05-25T02:58:45Z [Term] @@ -76927,7 +82317,6 @@ is_a: GO:0035864 ! response to potassium ion is_a: GO:0070887 ! cellular response to chemical stimulus intersection_of: GO:0070887 ! cellular response to chemical stimulus intersection_of: has_primary_input CHEBI:29103 -created_by: bf creation_date: 2011-05-25T02:59:11Z [Term] @@ -76939,9 +82328,8 @@ comment: Depending on the species, this region may have a distinct geometrically synonym: "cilial transition zone" EXACT [] synonym: "cilium transition zone" EXACT [] synonym: "connecting cilium" RELATED [] -is_a: GO:0110165 ! cellular anatomical entity +is_a: GO:0110165 ! cellular anatomical structure relationship: part_of GO:0005929 ! cilium -created_by: bf creation_date: 2011-05-25T03:09:58Z [Term] @@ -76954,7 +82342,6 @@ intersection_of: GO:0048856 ! anatomical structure development intersection_of: results_in_development_of UBERON:0001705 ! nail relationship: part_of GO:0060173 ! limb development relationship: results_in_development_of UBERON:0001705 ! nail -created_by: bf creation_date: 2011-05-31T02:30:34Z [Term] @@ -76963,12 +82350,11 @@ name: amacrine cell differentiation namespace: biological_process def: "The process in which a relatively unspecialized cell acquires specialized features of an amacrine cell, an interneuron generated in the inner nuclear layer (INL) of the vertebrate retina. Amacrine cells integrate, modulate, and interpose a temporal domain in the visual message presented to the retinal ganglion cells, with which they synapse in the inner plexiform layer. Amacrine cells lack large axons." [CL:0000561, GOC:bf] synonym: "amacrine neuron differentiation" EXACT [CL:0000561] -is_a: GO:0030182 ! neuron differentiation +is_a: GO:0021953 ! central nervous system neuron differentiation intersection_of: GO:0030154 ! cell differentiation intersection_of: results_in_acquisition_of_features_of CL:0000561 ! amacrine cell relationship: part_of GO:0003407 ! neural retina development relationship: results_in_acquisition_of_features_of CL:0000561 ! amacrine cell -created_by: bf creation_date: 2011-06-06T11:32:50Z [Term] @@ -76976,11 +82362,10 @@ id: GO:0035883 name: enteroendocrine cell differentiation namespace: biological_process def: "The process in which a relatively unspecialized cell acquires specialized structural and/or functional features of an enteroendocrine cell. Enteroendocrine cells are hormonally active epithelial cells in the gut that constitute the diffuse neuroendocrine system." [CL:0000164, GOC:bf] -is_a: GO:0002067 ! glandular epithelial cell differentiation +is_a: GO:0030855 ! epithelial cell differentiation intersection_of: GO:0030154 ! cell differentiation intersection_of: results_in_acquisition_of_features_of CL:0000164 ! enteroendocrine cell relationship: results_in_acquisition_of_features_of CL:0000164 ! enteroendocrine cell -created_by: bf creation_date: 2011-06-06T11:48:51Z [Term] @@ -76995,7 +82380,6 @@ intersection_of: GO:0030154 ! cell differentiation intersection_of: results_in_acquisition_of_features_of CL:0000359 ! vascular associated smooth muscle cell relationship: part_of GO:0001944 ! vasculature development relationship: results_in_acquisition_of_features_of CL:0000359 ! vascular associated smooth muscle cell -created_by: bf creation_date: 2011-06-08T11:23:52Z [Term] @@ -77007,7 +82391,6 @@ is_a: GO:0035886 ! vascular associated smooth muscle cell differentiation intersection_of: GO:0030154 ! cell differentiation intersection_of: results_in_acquisition_of_features_of CL:0002539 ! aortic smooth muscle cell relationship: results_in_acquisition_of_features_of CL:0002539 ! aortic smooth muscle cell -created_by: bf creation_date: 2011-06-08T11:34:26Z [Term] @@ -77019,7 +82402,6 @@ synonym: "parathormone secretion" EXACT [PR:000013429] synonym: "parathyrin secretion" EXACT [PR:000013429] synonym: "PTH secretion" EXACT [PMID:12171519, PR:000013429] is_a: GO:0060986 ! endocrine hormone secretion -created_by: bf creation_date: 2011-06-22T09:28:54Z [Term] @@ -77031,7 +82413,6 @@ is_a: GO:0060840 ! artery development intersection_of: GO:0048856 ! anatomical structure development intersection_of: results_in_development_of UBERON:0000947 ! aorta relationship: results_in_development_of UBERON:0000947 ! aorta -created_by: bf creation_date: 2011-06-24T11:00:07Z [Term] @@ -77044,7 +82425,6 @@ intersection_of: GO:0048856 ! anatomical structure development intersection_of: results_in_development_of UBERON:0001496 ! ascending aorta relationship: part_of GO:0035904 ! aorta development relationship: results_in_development_of UBERON:0001496 ! ascending aorta -created_by: bf creation_date: 2011-06-24T11:02:01Z [Term] @@ -77057,7 +82437,6 @@ intersection_of: GO:0048856 ! anatomical structure development intersection_of: results_in_development_of UBERON:0001514 ! descending aorta relationship: part_of GO:0035904 ! aorta development relationship: results_in_development_of UBERON:0001514 ! descending aorta -created_by: bf creation_date: 2011-06-24T11:05:22Z [Term] @@ -77069,7 +82448,6 @@ is_a: GO:0035904 ! aorta development intersection_of: GO:0048856 ! anatomical structure development intersection_of: results_in_development_of UBERON:0005805 ! dorsal aorta relationship: results_in_development_of UBERON:0005805 ! dorsal aorta -created_by: bf creation_date: 2011-06-24T11:07:01Z [Term] @@ -77082,7 +82460,6 @@ intersection_of: GO:0009653 ! anatomical structure morphogenesis intersection_of: results_in_morphogenesis_of UBERON:0000947 ! aorta relationship: part_of GO:0035904 ! aorta development relationship: results_in_morphogenesis_of UBERON:0000947 ! aorta -created_by: bf creation_date: 2011-06-24T11:11:11Z [Term] @@ -77097,7 +82474,6 @@ intersection_of: results_in_morphogenesis_of UBERON:0001496 ! ascending aorta relationship: part_of GO:0035905 ! ascending aorta development relationship: part_of GO:0035909 ! aorta morphogenesis relationship: results_in_morphogenesis_of UBERON:0001496 ! ascending aorta -created_by: bf creation_date: 2011-06-24T11:14:52Z [Term] @@ -77112,7 +82488,6 @@ intersection_of: results_in_morphogenesis_of UBERON:0001514 ! descending aorta relationship: part_of GO:0035906 ! descending aorta development relationship: part_of GO:0035909 ! aorta morphogenesis relationship: results_in_morphogenesis_of UBERON:0001514 ! descending aorta -created_by: bf creation_date: 2011-06-24T11:19:24Z [Term] @@ -77125,7 +82500,6 @@ intersection_of: GO:0009653 ! anatomical structure morphogenesis intersection_of: results_in_morphogenesis_of UBERON:0005805 ! dorsal aorta relationship: part_of GO:0035907 ! dorsal aorta development relationship: results_in_morphogenesis_of UBERON:0005805 ! dorsal aorta -created_by: bf creation_date: 2011-06-24T11:22:14Z [Term] @@ -77138,7 +82512,6 @@ intersection_of: GO:0030154 ! cell differentiation intersection_of: results_in_acquisition_of_features_of CL:0000188 ! cell of skeletal muscle relationship: part_of GO:0007519 ! skeletal muscle tissue development relationship: results_in_acquisition_of_features_of CL:0000188 ! cell of skeletal muscle -created_by: bf creation_date: 2011-06-24T02:36:19Z [Term] @@ -77151,7 +82524,6 @@ is_a: GO:0140353 ! lipid export from cell intersection_of: GO:0046903 ! secretion intersection_of: has_primary_input CHEBI:26764 relationship: has_primary_input CHEBI:26764 -created_by: bf creation_date: 2011-07-20T01:01:00Z [Term] @@ -77164,7 +82536,6 @@ is_a: GO:0035929 ! steroid hormone secretion intersection_of: GO:0046903 ! secretion intersection_of: has_primary_input CHEBI:36699 relationship: has_primary_input CHEBI:36699 -created_by: bf creation_date: 2011-07-20T01:03:22Z [Term] @@ -77176,7 +82547,6 @@ is_a: GO:0035930 ! corticosteroid hormone secretion intersection_of: GO:0046903 ! secretion intersection_of: has_primary_input CHEBI:25354 relationship: has_primary_input CHEBI:25354 -created_by: bf creation_date: 2011-07-20T01:04:59Z [Term] @@ -77189,7 +82559,6 @@ is_a: GO:0035931 ! mineralocorticoid secretion intersection_of: GO:0046903 ! secretion intersection_of: has_primary_input CHEBI:27584 relationship: has_primary_input CHEBI:27584 -created_by: bf creation_date: 2011-07-20T01:06:24Z [Term] @@ -77201,7 +82570,6 @@ is_a: GO:0035930 ! corticosteroid hormone secretion intersection_of: GO:0046903 ! secretion intersection_of: has_primary_input CHEBI:24261 relationship: has_primary_input CHEBI:24261 -created_by: bf creation_date: 2011-07-20T01:08:37Z [Term] @@ -77210,7 +82578,6 @@ name: androgen secretion namespace: biological_process def: "The regulated release of an androgen into the circulatory system. Androgens are steroid hormones that stimulate or control the development and maintenance of masculine characteristics in vertebrates." [GOC:sl] is_a: GO:0035929 ! steroid hormone secretion -created_by: bf creation_date: 2011-07-20T01:11:31Z [Term] @@ -77222,7 +82589,6 @@ is_a: GO:0046879 ! hormone secretion intersection_of: GO:0046903 ! secretion intersection_of: has_primary_input CHEBI:17347 relationship: has_primary_input CHEBI:17347 -created_by: bf creation_date: 2011-07-20T01:13:13Z [Term] @@ -77235,7 +82601,6 @@ is_a: GO:0035929 ! steroid hormone secretion intersection_of: GO:0046903 ! secretion intersection_of: has_primary_input CHEBI:23965 relationship: has_primary_input CHEBI:23965 -created_by: bf creation_date: 2011-07-20T01:16:45Z [Term] @@ -77247,7 +82612,6 @@ is_a: GO:0098528 ! skeletal muscle fiber differentiation intersection_of: GO:0030154 ! cell differentiation intersection_of: results_in_acquisition_of_features_of CL:0002673 ! tongue muscle cell relationship: results_in_acquisition_of_features_of CL:0002673 ! tongue muscle cell -created_by: bf creation_date: 2011-08-22T01:35:16Z [Term] @@ -77261,7 +82625,6 @@ intersection_of: GO:0030154 ! cell differentiation intersection_of: results_in_acquisition_of_features_of CL:0000223 ! endodermal cell relationship: part_of GO:0001706 ! endoderm formation relationship: results_in_acquisition_of_features_of CL:0000223 ! endodermal cell -created_by: bf creation_date: 2011-08-25T04:50:36Z [Term] @@ -77274,7 +82637,6 @@ is_a: GO:0061448 ! connective tissue development intersection_of: GO:0048856 ! anatomical structure development intersection_of: results_in_development_of UBERON:0000043 ! tendon relationship: results_in_development_of UBERON:0000043 ! tendon -created_by: bf creation_date: 2011-08-26T04:14:30Z [Term] @@ -77289,7 +82651,6 @@ intersection_of: GO:0030154 ! cell differentiation intersection_of: results_in_acquisition_of_features_of CL:0000388 ! tendon cell relationship: part_of GO:0035992 ! tendon formation relationship: results_in_acquisition_of_features_of CL:0000388 ! tendon cell -created_by: bf creation_date: 2011-08-26T04:16:06Z [Term] @@ -77303,7 +82664,6 @@ intersection_of: GO:0048646 ! anatomical structure formation involved in morphog intersection_of: results_in_formation_of UBERON:0000043 ! tendon relationship: part_of GO:0035989 ! tendon development relationship: results_in_formation_of UBERON:0000043 ! tendon -created_by: bf creation_date: 2011-08-30T01:35:10Z [Term] @@ -77317,7 +82677,6 @@ intersection_of: results_in_development_of UBERON:0002498 ! deltopectoral crest relationship: part_of GO:0060173 ! limb development relationship: part_of GO:0060348 ! bone development relationship: results_in_development_of UBERON:0002498 ! deltopectoral crest -created_by: bf creation_date: 2011-08-30T01:46:53Z [Term] @@ -77333,7 +82692,6 @@ intersection_of: GO:0009653 ! anatomical structure morphogenesis intersection_of: results_in_morphogenesis_of UBERON:0003657 ! limb joint relationship: part_of GO:0035108 ! limb morphogenesis relationship: results_in_morphogenesis_of UBERON:0003657 ! limb joint -created_by: bf creation_date: 2011-10-13T04:52:59Z [Term] @@ -77348,7 +82706,6 @@ intersection_of: GO:0048468 ! cell development intersection_of: results_in_development_of CL:0000092 ! osteoclast relationship: part_of GO:0030316 ! osteoclast differentiation relationship: results_in_development_of CL:0000092 ! osteoclast -created_by: bf creation_date: 2011-11-02T05:20:35Z [Term] @@ -77360,7 +82717,6 @@ is_a: GO:0046631 ! alpha-beta T cell activation intersection_of: GO:0001775 ! cell activation intersection_of: has_primary_input CL:0000625 ! CD8-positive, alpha-beta T cell relationship: has_primary_input CL:0000625 ! CD8-positive, alpha-beta T cell -created_by: bf creation_date: 2011-11-03T10:34:12Z [Term] @@ -77374,16 +82730,32 @@ is_a: GO:0046930 ! pore complex property_value: RO:0002161 NCBITaxon:2 property_value: RO:0002161 NCBITaxon:2157 property_value: RO:0002161 NCBITaxon:4751 -created_by: bf creation_date: 2011-12-12T10:53:24Z +[Term] +id: GO:0036064 +name: ciliary basal body +namespace: cellular_component +def: "A membrane-tethered, short cylindrical array of microtubules and associated proteins found at the base of a eukaryotic cilium (also called flagellum) that is similar in structure to a centriole and derives from it. The cilium basal body is the site of assembly and remodeling of the cilium and serves as a nucleation site for axoneme growth. As well as anchoring the cilium, it is thought to provide a selective gateway regulating the entry of ciliary proteins and vesicles by intraflagellar transport." [GOC:cilia, GOC:clt, PMID:21750193] +comment: In most eukaryotic cells, 'ciliary basal body' (GO:0036064) and 'centriole' (GO:0005814) represent a common entity that cycles through its function in cell division, then ciliogenesis, then cell division again. However, these structures are modified extensively as they transition into each other, and may contain different proteins, specific to each component. +synonym: "basal body" BROAD [] +synonym: "cilial basal body" EXACT [] +synonym: "cilium basal body" EXACT [GOC:bf] +synonym: "kinetosome" EXACT [PMID:11125699] +synonym: "microtubule basal body" EXACT [] +xref: NIF_Subcellular:sao11978067 +is_a: GO:0005815 ! microtubule organizing center +intersection_of: GO:0005815 ! microtubule organizing center +intersection_of: part_of GO:0005929 ! cilium +relationship: part_of GO:0005929 ! cilium +creation_date: 2011-12-15T10:40:20Z + [Term] id: GO:0036072 name: direct ossification namespace: biological_process def: "The formation of bone or of a bony substance, or the conversion of fibrous tissue or of cartilage into bone or a bony substance, that does not require the replacement of preexisting tissues." [GO_REF:0000034] is_a: GO:0001503 ! ossification -created_by: bf creation_date: 2011-12-19T01:47:22Z [Term] @@ -77393,7 +82765,6 @@ namespace: biological_process def: "Ossification that requires the replacement of a preexisting tissue prior to bone tissue formation." [GO_REF:0000034] synonym: "indirect ossification" EXACT [GO_REF:0000034] is_a: GO:0001503 ! ossification -created_by: bf creation_date: 2011-12-19T01:53:16Z [Term] @@ -77407,7 +82778,6 @@ intersection_of: GO:0008283 ! cell population proliferation intersection_of: acts_on_population_of CL:0000586 ! germ cell relationship: acts_on_population_of CL:0000586 ! germ cell relationship: part_of GO:0007276 ! gamete generation -created_by: bf creation_date: 2012-01-17T04:06:27Z [Term] @@ -77422,7 +82792,6 @@ subset: goslim_flybase_ribbon subset: goslim_plant_ribbon subset: goslim_prokaryote_ribbon is_a: GO:0005488 ! binding -created_by: bf creation_date: 2012-01-17T04:20:34Z [Term] @@ -77434,7 +82803,6 @@ is_a: GO:0030718 ! germ-line stem cell population maintenance intersection_of: GO:0098727 ! maintenance of cell number intersection_of: acts_on_population_of CL:0000016 ! male germ line stem cell relationship: acts_on_population_of CL:0000016 ! male germ line stem cell -created_by: bf creation_date: 2012-01-26T01:58:10Z [Term] @@ -77446,7 +82814,6 @@ is_a: GO:0030718 ! germ-line stem cell population maintenance intersection_of: GO:0098727 ! maintenance of cell number intersection_of: acts_on_population_of CL:0000022 ! female germ line stem cell relationship: acts_on_population_of CL:0000022 ! female germ line stem cell -created_by: bf creation_date: 2012-01-26T01:58:10Z [Term] @@ -77458,7 +82825,6 @@ is_a: GO:0008347 ! glial cell migration intersection_of: GO:0016477 ! cell migration intersection_of: results_in_movement_of CL:0002573 ! Schwann cell relationship: results_in_movement_of CL:0002573 ! Schwann cell -created_by: bf creation_date: 2012-03-06T10:44:39Z [Term] @@ -77471,7 +82837,6 @@ is_a: GO:0001776 ! leukocyte homeostasis intersection_of: GO:0048872 ! homeostasis of number of cells intersection_of: acts_on_population_of CL:0000451 ! dendritic cell relationship: acts_on_population_of CL:0000451 ! dendritic cell -created_by: bf creation_date: 2012-03-12T11:05:36Z [Term] @@ -77481,7 +82846,6 @@ namespace: cellular_component def: "Inner arm structure present on the outer doublet microtubules of ciliary and flagellar axonemes. The structure of inner dynein arms is complex and may vary within the axoneme. Inner dynein arms are heteromeric, comprising 8 different heavy chains and various subunits. Inner and outer dynein arms have different functions in the generation of microtubule-based motility." [GOC:BHF, GOC:vk, PMID:19347929, PMID:2557057, PMID:7962092] synonym: "inner dynein arm complex" EXACT [] is_a: GO:0005858 ! axonemal dynein complex -created_by: bf creation_date: 2012-03-21T01:24:54Z [Term] @@ -77491,7 +82855,6 @@ namespace: cellular_component def: "Outer arm structure present on the outer doublet microtubules of ciliary and flagellar axonemes. Outer dynein arms contain 2-3 heavy chains, two or more intermediate chains and a cluster of 4-8 light chains. Inner and outer dynein arms have different functions in the generation of microtubule-based motility." [GOC:BHF, GOC:vk, PMID:2557057, PMID:6218174] synonym: "outer dynein arm complex" EXACT [] is_a: GO:0005858 ! axonemal dynein complex -created_by: bf creation_date: 2012-03-21T01:25:03Z [Term] @@ -77504,7 +82867,6 @@ is_a: GO:0070286 ! axonemal dynein complex assembly intersection_of: GO:0022607 ! cellular component assembly intersection_of: results_in_assembly_of GO:0036157 ! outer dynein arm relationship: results_in_assembly_of GO:0036157 ! outer dynein arm -created_by: bf creation_date: 2012-03-21T02:25:01Z [Term] @@ -77517,7 +82879,6 @@ is_a: GO:0070286 ! axonemal dynein complex assembly intersection_of: GO:0022607 ! cellular component assembly intersection_of: results_in_assembly_of GO:0036156 ! inner dynein arm relationship: results_in_assembly_of GO:0036156 ! inner dynein arm -created_by: bf creation_date: 2012-03-21T02:25:01Z [Term] @@ -77527,7 +82888,6 @@ namespace: biological_process def: "The regulated release of a melanocyte-stimulating hormone, any of a group of peptide hormones that are produced by cells in the intermediate lobe of the pituitary gland, and stimulate the production of melanin to increase pigmentation." [GOC:cjm, Wikipedia:Melanocyte-stimulating_hormone] synonym: "MSH secretion" EXACT [GOC:cjm] is_a: GO:0030072 ! peptide hormone secretion -created_by: bf creation_date: 2012-03-26T01:16:55Z [Term] @@ -77539,7 +82899,6 @@ is_a: GO:0030072 ! peptide hormone secretion intersection_of: GO:0046903 ! secretion intersection_of: has_primary_input CHEBI:3306 relationship: has_primary_input CHEBI:3306 -created_by: bf creation_date: 2012-03-26T01:30:32Z [Term] @@ -77554,7 +82913,6 @@ is_a: GO:0010467 ! gene expression relationship: has_part GO:0030072 ! peptide hormone secretion property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/21535" xsd:anyURI property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/9542" xsd:anyURI -created_by: bf creation_date: 2012-03-26T01:43:46Z [Term] @@ -77568,7 +82926,6 @@ intersection_of: GO:0021700 ! developmental maturation intersection_of: results_in_maturation_of CL:0000092 ! osteoclast relationship: part_of GO:0036035 ! osteoclast development relationship: results_in_maturation_of CL:0000092 ! osteoclast -created_by: bf creation_date: 2012-03-29T02:04:00Z [Term] @@ -77583,7 +82940,6 @@ is_a: GO:0120025 ! plasma membrane bounded cell projection intersection_of: GO:0120025 ! plasma membrane bounded cell projection intersection_of: part_of CL:0000187 ! muscle cell relationship: part_of CL:0000187 ! muscle cell -created_by: bf creation_date: 2012-04-20T10:20:47Z [Term] @@ -77595,14 +82951,12 @@ is_a: GO:0031253 ! cell projection membrane intersection_of: GO:0031253 ! cell projection membrane intersection_of: part_of GO:0036194 ! muscle cell projection relationship: part_of GO:0036194 ! muscle cell projection -created_by: bf creation_date: 2012-04-20T10:21:51Z [Term] id: GO:0036211 name: protein modification process namespace: biological_process -alt_id: GO:0006464 def: "The covalent alteration of one or more amino acids occurring in proteins, peptides and nascent polypeptides (co-translational, post-translational modifications). Includes the modification of charged tRNAs that are destined to occur in a protein (pre-translation modification)." [GOC:bf, GOC:jl] subset: goslim_candida subset: goslim_chembl @@ -77615,7 +82969,6 @@ synonym: "protein modification" EXACT [GOC:bf] is_a: GO:0019538 ! protein metabolic process is_a: GO:0043412 ! macromolecule modification property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/23112" xsd:anyURI -created_by: bf creation_date: 2012-04-26T01:47:12Z [Term] @@ -77627,7 +82980,6 @@ is_a: GO:0002274 ! myeloid leukocyte activation intersection_of: GO:0001775 ! cell activation intersection_of: has_primary_input CL:0000094 ! granulocyte relationship: has_primary_input CL:0000094 ! granulocyte -created_by: bf creation_date: 2012-05-11T10:57:48Z [Term] @@ -77638,7 +82990,6 @@ def: "Any process that results in a change in state or activity of a cell or an comment: This term should be used when a decrease in oxygen levels is not considered a stress response. For a hypoxic stress response, consider instead 'response to hypoxia ; GO:0001666'. synonym: "response to lowered oxygen levels" EXACT [GOC:bf] is_a: GO:0070482 ! response to oxygen levels -created_by: bf creation_date: 2012-07-20T01:05:46Z [Term] @@ -77652,7 +83003,6 @@ intersection_of: GO:0009653 ! anatomical structure morphogenesis intersection_of: results_in_morphogenesis_of UBERON:0001473 ! lymphatic vessel relationship: part_of GO:0001945 ! lymph vessel development relationship: results_in_morphogenesis_of UBERON:0001473 ! lymphatic vessel -created_by: bf creation_date: 2012-08-08T10:08:47Z [Term] @@ -77666,7 +83016,6 @@ intersection_of: GO:0009653 ! anatomical structure morphogenesis intersection_of: results_in_morphogenesis_of UBERON:0002331 ! umbilical cord relationship: part_of GO:0061027 ! umbilical cord development relationship: results_in_morphogenesis_of UBERON:0002331 ! umbilical cord -created_by: bf creation_date: 2012-08-08T10:12:11Z [Term] @@ -77678,7 +83027,6 @@ is_a: GO:0002065 ! columnar/cuboidal epithelial cell differentiation intersection_of: GO:0030154 ! cell differentiation intersection_of: results_in_acquisition_of_features_of CL:0000059 ! ameloblast relationship: results_in_acquisition_of_features_of CL:0000059 ! ameloblast -created_by: bf creation_date: 2012-08-08T13:49:15Z [Term] @@ -77691,7 +83039,6 @@ is_a: GO:0030072 ! peptide hormone secretion intersection_of: GO:0046903 ! secretion intersection_of: has_primary_input CHEBI:75431 relationship: has_primary_input CHEBI:75431 -created_by: bf creation_date: 2012-09-04T14:16:43Z [Term] @@ -77701,7 +83048,6 @@ namespace: biological_process def: "The regulated release of pancreatic polypeptide (PP) from a cell. Pancreatic polypeptide is a 36 amino acid polypeptide secreted by islets of Langerhans cells in the pancreas." [GOC:cjm, PMID:12730894, Wikipedia:Pancreatic_polypeptide] synonym: "PP secretion" NARROW [GOC:cjm] is_a: GO:0030072 ! peptide hormone secretion -created_by: bf creation_date: 2012-09-04T14:39:03Z [Term] @@ -77714,7 +83060,6 @@ is_a: GO:0048872 ! homeostasis of number of cells intersection_of: GO:0048872 ! homeostasis of number of cells intersection_of: acts_on_population_of CL:0000182 ! hepatocyte relationship: acts_on_population_of CL:0000182 ! hepatocyte -created_by: bf creation_date: 2012-09-05T10:17:07Z [Term] @@ -77727,7 +83072,6 @@ is_a: GO:0048872 ! homeostasis of number of cells intersection_of: GO:0048872 ! homeostasis of number of cells intersection_of: acts_on_population_of CL:1000428 ! stem cell of epidermis relationship: acts_on_population_of CL:1000428 ! stem cell of epidermis -created_by: bf creation_date: 2012-09-05T10:21:23Z [Term] @@ -77739,7 +83083,6 @@ is_a: GO:0071674 ! mononuclear cell migration intersection_of: GO:0016477 ! cell migration intersection_of: results_in_movement_of CL:0000451 ! dendritic cell relationship: results_in_movement_of CL:0000451 ! dendritic cell -created_by: bf creation_date: 2012-09-05T10:24:46Z [Term] @@ -77754,7 +83097,6 @@ intersection_of: results_in_morphogenesis_of UBERON:0007812 ! post-anal tail relationship: results_in_morphogenesis_of UBERON:0007812 ! post-anal tail relationship: RO:0002160 NCBITaxon:7711 ! only in taxon Chordata relationship: RO:0002162 NCBITaxon:7711 {all_only="true"} ! in taxon Chordata -created_by: bf creation_date: 2012-09-11T13:54:49Z [Term] @@ -77763,7 +83105,6 @@ name: platelet morphogenesis namespace: biological_process def: "Generation and organization of a platelet, a non-nucleated disk-shaped cell formed by extrusion from megakaryocytes, found in the blood of all mammals, and mainly involved in blood coagulation." [CL:0000233, GOC:BHF, GOC:vk] is_a: GO:0000902 ! cell morphogenesis -created_by: bf creation_date: 2012-09-11T15:15:35Z [Term] @@ -77775,15 +83116,12 @@ is_a: GO:0048469 ! cell maturation intersection_of: GO:0021700 ! developmental maturation intersection_of: results_in_maturation_of CL:0000233 ! platelet relationship: results_in_maturation_of CL:0000233 ! platelet -created_by: bf creation_date: 2012-09-11T15:23:11Z [Term] id: GO:0036376 name: sodium ion export across plasma membrane namespace: biological_process -alt_id: GO:0071436 -alt_id: GO:0098667 def: "The directed movement of sodium ions from inside of a cell, across the plasma membrane and into the extracellular region." [GOC:vw, PMID:14674689] synonym: "sodium export" RELATED [GOC:mah] synonym: "sodium ion export" RELATED [] @@ -77795,7 +83133,6 @@ intersection_of: has_primary_input CHEBI:29101 intersection_of: has_target_end_location GO:0005576 ! extracellular region intersection_of: has_target_start_location GO:0005829 ! cytosol intersection_of: results_in_transport_across GO:0005886 ! plasma membrane -created_by: mah creation_date: 2009-12-16T11:13:55Z [Term] @@ -77804,9 +83141,8 @@ name: myofilament namespace: cellular_component def: "Any of the smallest contractile units of a myofibril (striated muscle fiber)." [Wikipedia:Myofilament] synonym: "striated muscle filament" EXACT [GOC:bf] -is_a: GO:0110165 ! cellular anatomical entity +is_a: GO:0110165 ! cellular anatomical structure relationship: part_of GO:0030016 ! myofibril -created_by: bf creation_date: 2013-05-22T14:39:06Z [Term] @@ -77819,7 +83155,6 @@ is_a: GO:0030154 ! cell differentiation intersection_of: GO:0030154 ! cell differentiation intersection_of: results_in_acquisition_of_features_of CL:0000186 ! myofibroblast cell relationship: results_in_acquisition_of_features_of CL:0000186 ! myofibroblast cell -created_by: bf creation_date: 2013-10-30T10:06:51Z [Term] @@ -77827,9 +83162,8 @@ id: GO:0036477 name: somatodendritic compartment namespace: cellular_component def: "The region of a neuron that includes the cell body (cell soma) and dendrite(s), but excludes the axon." [GOC:pad, GOC:PARL] -is_a: GO:0110165 ! cellular anatomical entity +is_a: GO:0110165 ! cellular anatomical structure relationship: part_of CL:0000540 ! neuron -created_by: bf creation_date: 2014-07-24T10:06:19Z [Term] @@ -77843,7 +83177,6 @@ intersection_of: GO:0016477 ! cell migration intersection_of: results_in_movement_of CL:0000011 ! migratory trunk neural crest cell relationship: part_of GO:0035290 ! trunk segmentation relationship: results_in_movement_of CL:0000011 ! migratory trunk neural crest cell -created_by: bf creation_date: 2014-08-26T15:27:44Z [Term] @@ -77859,7 +83192,6 @@ intersection_of: GO:0061025 ! membrane fusion intersection_of: results_in_fusion_of GO:0000139 ! Golgi membrane relationship: part_of GO:0090168 ! Golgi reassembly relationship: results_in_fusion_of GO:0000139 ! Golgi membrane -created_by: bf creation_date: 2015-05-21T10:05:06Z [Term] @@ -77877,15 +83209,12 @@ intersection_of: has_end_location CL:0000700 ! dopaminergic neuron intersection_of: has_start_location CL:0000127 ! astrocyte relationship: has_end_location CL:0000700 ! dopaminergic neuron relationship: has_start_location CL:0000127 ! astrocyte -created_by: bf creation_date: 2016-02-29T14:05:47Z [Term] id: GO:0038023 name: signaling receptor activity namespace: molecular_function -alt_id: GO:0004872 -alt_id: GO:0019041 def: "Receiving a signal and transmitting it in the cell to initiate a change in cell activity. A signal is a physical entity or change in state that is used to transfer information in order to trigger a response." [GOC:bf, GOC:signaling] subset: goslim_agr subset: goslim_chembl @@ -77900,7 +83229,6 @@ synonym: "receptor activity" BROAD [] synonym: "receptor activity involved in signal transduction" EXACT [GOC:bf] synonym: "signalling receptor activity" EXACT [] is_a: GO:0060089 ! molecular transducer activity -created_by: bf creation_date: 2011-08-01T02:45:27Z [Term] @@ -77915,6 +83243,7 @@ synonym: "endocytic receptor activity" NARROW [GOC:signaling, ISBN:0123645387, P synonym: "receptor activity" BROAD [] synonym: "receptor activity involved in receptor-mediated endocytosis" NARROW [GOC:bf] synonym: "transport receptor activity" BROAD [GOC:signaling] +xref: Reactome:R-HSA-203716 "eNOS:Caveolin-1 complex binds to Nostrin" xref: Reactome:R-HSA-3000103 "CUBN:AMN binds CBLIF:RCbl" xref: Reactome:R-HSA-3000112 "CD320-mediated TCN2:RCbl uptake and delivery to lysosome" xref: Reactome:R-HSA-3000122 "CD320 binds extracellular TCN2:RCbl" @@ -77926,7 +83255,6 @@ is_a: GO:0003674 ! molecular_function relationship: has_part GO:0060090 ! molecular adaptor activity relationship: part_of GO:0016192 ! vesicle-mediated transport property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/26872" xsd:anyURI -created_by: bf creation_date: 2011-08-01T02:50:45Z [Term] @@ -77939,7 +83267,6 @@ synonym: "prolactin-mediated signaling pathway" EXACT [GOC:bf] is_a: GO:0009755 ! hormone-mediated signaling pathway is_a: GO:0019221 ! cytokine-mediated signaling pathway property_value: RO:0002161 NCBITaxon:4751 -created_by: bf creation_date: 2012-05-14T01:52:59Z [Term] @@ -77951,7 +83278,6 @@ comment: In addition to somatostatin (SST), the somatostatin receptors (SSTRs) c synonym: "SST receptor signaling pathway" EXACT [GOC:bf] synonym: "SSTR signaling pathway" RELATED [GOC:bf] is_a: GO:0007186 ! G protein-coupled receptor signaling pathway -created_by: bf creation_date: 2012-06-12T10:30:01Z [Term] @@ -77968,14 +83294,12 @@ synonym: "SST signaling pathway" EXACT [Wikipedia:Somatostatin] is_a: GO:0009755 ! hormone-mediated signaling pathway is_a: GO:0038169 ! somatostatin receptor signaling pathway relationship: has_primary_input CHEBI:64628 -created_by: bf creation_date: 2012-06-12T10:33:21Z [Term] id: GO:0038187 name: pattern recognition receptor activity namespace: molecular_function -alt_id: GO:0008329 def: "Combining with a pathogen-associated molecular pattern (PAMP), a structure conserved among microbial species to initiate an innate immune response." [GOC:ar, GOC:bf] synonym: "macrophage receptor activity" RELATED [] synonym: "MAMP receptor activity" NARROW [] @@ -77989,7 +83313,6 @@ xref: Wikipedia:Pattern_recognition_receptor is_a: GO:0038023 ! signaling receptor activity property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/17995" xsd:anyURI property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/18588" xsd:anyURI -created_by: bf creation_date: 2013-05-29T15:24:44Z [Term] @@ -78001,7 +83324,6 @@ synonym: "CCK signaling" EXACT [PMID:11181948, Wikipedia:Cholecystokinin] synonym: "cholecystokinin receptor signaling pathway" RELATED [GOC:bf] xref: Wikipedia:Cholecystokinin is_a: GO:0007186 ! G protein-coupled receptor signaling pathway -created_by: bf creation_date: 2013-07-01T13:05:46Z [Term] @@ -78017,7 +83339,6 @@ intersection_of: results_in_formation_of UBERON:0005310 ! pronephric nephron tub relationship: part_of GO:0039008 ! pronephric nephron tubule morphogenesis relationship: part_of GO:0072116 ! pronephros formation relationship: results_in_formation_of UBERON:0005310 ! pronephric nephron tubule -created_by: bf creation_date: 2010-07-02T09:37:27Z [Term] @@ -78031,7 +83352,6 @@ intersection_of: results_in_morphogenesis_of UBERON:0005309 ! pronephric nephron relationship: part_of GO:0039019 ! pronephric nephron development relationship: part_of GO:0072114 ! pronephros morphogenesis relationship: results_in_morphogenesis_of UBERON:0005309 ! pronephric nephron -created_by: bf creation_date: 2010-07-02T09:38:53Z [Term] @@ -78045,7 +83365,6 @@ intersection_of: results_in_morphogenesis_of UBERON:0005310 ! pronephric nephron relationship: part_of GO:0039007 ! pronephric nephron morphogenesis relationship: part_of GO:0039020 ! pronephric nephron tubule development relationship: results_in_morphogenesis_of UBERON:0005310 ! pronephric nephron tubule -created_by: bf creation_date: 2010-07-02T09:45:55Z [Term] @@ -78060,7 +83379,6 @@ intersection_of: GO:0009653 ! anatomical structure morphogenesis intersection_of: results_in_morphogenesis_of UBERON:0006173 ! pronephric proximal tubule relationship: part_of GO:0035776 ! pronephric proximal tubule development relationship: results_in_morphogenesis_of UBERON:0006173 ! pronephric proximal tubule -created_by: bf creation_date: 2010-07-02T09:53:12Z [Term] @@ -78074,7 +83392,6 @@ intersection_of: GO:0009653 ! anatomical structure morphogenesis intersection_of: results_in_morphogenesis_of UBERON:0006175 ! pronephric distal tubule relationship: part_of GO:0035777 ! pronephric distal tubule development relationship: results_in_morphogenesis_of UBERON:0006175 ! pronephric distal tubule -created_by: bf creation_date: 2010-07-02T09:58:03Z [Term] @@ -78087,7 +83404,6 @@ is_a: GO:0061005 ! cell differentiation involved in kidney development intersection_of: GO:0030154 ! cell differentiation intersection_of: part_of GO:0048793 ! pronephros development relationship: part_of GO:0048793 ! pronephros development -created_by: bf creation_date: 2010-07-02T09:59:25Z [Term] @@ -78100,7 +83416,6 @@ is_a: GO:0072111 ! cell proliferation involved in kidney development intersection_of: GO:0008283 ! cell population proliferation intersection_of: part_of GO:0048793 ! pronephros development relationship: part_of GO:0048793 ! pronephros development -created_by: bf creation_date: 2010-07-02T10:01:49Z [Term] @@ -78114,7 +83429,6 @@ is_a: GO:0060995 ! cell-cell signaling involved in kidney development intersection_of: GO:0007267 ! cell-cell signaling intersection_of: part_of GO:0048793 ! pronephros development relationship: part_of GO:0048793 ! pronephros development -created_by: bf creation_date: 2010-07-02T10:03:16Z [Term] @@ -78127,7 +83441,6 @@ is_a: GO:0061004 ! pattern specification involved in kidney development intersection_of: GO:0007389 ! pattern specification process intersection_of: part_of GO:0048793 ! pronephros development relationship: part_of GO:0048793 ! pronephros development -created_by: bf creation_date: 2010-07-02T10:04:39Z [Term] @@ -78140,7 +83453,6 @@ intersection_of: GO:0048856 ! anatomical structure development intersection_of: results_in_development_of UBERON:0005309 ! pronephric nephron relationship: part_of GO:0048793 ! pronephros development relationship: results_in_development_of UBERON:0005309 ! pronephric nephron -created_by: bf creation_date: 2010-07-02T10:10:20Z [Term] @@ -78153,7 +83465,6 @@ intersection_of: GO:0048856 ! anatomical structure development intersection_of: results_in_development_of UBERON:0005310 ! pronephric nephron tubule relationship: part_of GO:0039019 ! pronephric nephron development relationship: results_in_development_of UBERON:0005310 ! pronephric nephron tubule -created_by: bf creation_date: 2010-07-02T10:11:36Z [Term] @@ -78167,7 +83478,6 @@ intersection_of: GO:0048856 ! anatomical structure development intersection_of: results_in_development_of UBERON:0004739 ! pronephric glomerulus relationship: part_of GO:0039019 ! pronephric nephron development relationship: results_in_development_of UBERON:0004739 ! pronephric glomerulus -created_by: bf creation_date: 2010-07-02T10:13:38Z [Term] @@ -78180,7 +83490,6 @@ intersection_of: GO:0048856 ! anatomical structure development intersection_of: results_in_development_of UBERON:0003060 ! pronephric duct relationship: part_of GO:0048793 ! pronephros development relationship: results_in_development_of UBERON:0003060 ! pronephric duct -created_by: bf creation_date: 2010-07-02T10:15:03Z [Term] @@ -78194,14 +83503,12 @@ intersection_of: results_in_morphogenesis_of UBERON:0003060 ! pronephric duct relationship: part_of GO:0039022 ! pronephric duct development relationship: part_of GO:0072114 ! pronephros morphogenesis relationship: results_in_morphogenesis_of UBERON:0003060 ! pronephric duct -created_by: bf creation_date: 2010-07-02T10:18:09Z [Term] id: GO:0040007 name: growth namespace: biological_process -alt_id: GO:0048590 def: "The increase in size or mass of an entire organism, a part of an organism or a cell." [GOC:bf, GOC:ma] comment: See also the biological process term 'cell growth ; GO:0016049'. subset: gocheck_do_not_annotate @@ -78466,7 +83773,6 @@ relationship: regulates GO:0006584 ! catecholamine metabolic process id: GO:0042073 name: intraciliary transport namespace: biological_process -alt_id: GO:0035734 def: "The bidirectional movement of large protein complexes along microtubules within a cilium, mediated by motor proteins." [GOC:cilia, GOC:kmv, PMID:17981739, PMID:18180368, PMID:22869374] comment: Note that we deem cilium and microtubule-based flagellum to be equivalent. synonym: "IFT" RELATED [] @@ -78505,7 +83811,6 @@ relationship: part_of GO:0007369 ! gastrulation id: GO:0042078 name: germ-line stem cell division namespace: biological_process -alt_id: GO:0048131 def: "The self-renewing division of a germline stem cell to produce a daughter stem cell and a daughter germ cell, which will divide to form the gametes." [GOC:jid, PMID:2279698] synonym: "germ-line stem cell renewal" EXACT [] is_a: GO:0017145 ! stem cell division @@ -78549,7 +83854,6 @@ relationship: results_in_acquisition_of_features_of CL:0000492 ! CD4-positive he id: GO:0042098 name: T cell proliferation namespace: biological_process -alt_id: GO:0042111 def: "The expansion of a T cell population by cell division. Follows T cell activation." [GOC:jl] synonym: "T lymphocyte proliferation" EXACT [] synonym: "T-cell proliferation" EXACT [] @@ -78564,7 +83868,6 @@ relationship: acts_on_population_of CL:0000084 ! T cell id: GO:0042100 name: B cell proliferation namespace: biological_process -alt_id: GO:0042114 def: "The expansion of a B cell population by cell division. Follows B cell activation." [GOC:jl] synonym: "B lymphocyte proliferation" EXACT [] synonym: "B-cell proliferation" EXACT [] @@ -78769,7 +84072,7 @@ namespace: cellular_component def: "An organelle found in cnidoblast (nematoblast) cells. When matured, these stinging organelles store toxins and can deliver them when the cnidocil (a short extension of the cnidocyst) is stimulated by a prey or another stimulus." [DOI:10.1139/z02-135, GOC:jl] synonym: "cnidocyst" EXACT [] xref: Wikipedia:Cnidocyte -is_a: GO:0043232 ! intracellular non-membrane-bounded organelle +is_a: GO:0043232 ! intracellular membraneless organelle relationship: part_of GO:0005938 ! cell cortex relationship: RO:0002160 NCBITaxon:33208 ! only in taxon Metazoa relationship: RO:0002162 NCBITaxon:33208 {all_only="true"} ! in taxon Metazoa @@ -78871,8 +84174,6 @@ relationship: part_of GO:0012505 ! endomembrane system id: GO:0042176 name: regulation of protein catabolic process namespace: biological_process -alt_id: GO:1903362 -alt_id: GO:2000598 def: "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of a protein by the destruction of the native, active configuration, with or without the hydrolysis of peptide bonds." [GOC:go_curators, GOC:jl] synonym: "regulation of cellular protein breakdown" EXACT [GOC:TermGenie] synonym: "regulation of cellular protein catabolic process" EXACT [] @@ -78892,15 +84193,12 @@ intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0030163 ! protein catabolic process relationship: regulates GO:0030163 ! protein catabolic process property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/23112" xsd:anyURI -created_by: kmv creation_date: 2014-08-21T15:05:45Z [Term] id: GO:0042177 name: negative regulation of protein catabolic process namespace: biological_process -alt_id: GO:1903363 -alt_id: GO:2000599 def: "Any process that stops, prevents or reduces the frequency, rate or extent of protein catabolic process." [GO_REF:0000058, GOC:kmv, GOC:obol, GOC:TermGenie, PMID:24785082] synonym: "down regulation of cellular protein breakdown" EXACT [GOC:TermGenie] synonym: "down regulation of cellular protein catabolic process" EXACT [GOC:TermGenie] @@ -78939,17 +84237,17 @@ property_value: term_tracker_item "https://github.com/geneontology/go-ontology/i [Term] id: GO:0042180 -name: cellular ketone metabolic process +name: ketone metabolic process namespace: biological_process def: "The chemical reactions and pathways involving any of a class of organic compounds that contain the carbonyl group, CO, and in which the carbonyl group is bonded only to carbon atoms, as carried out by individual cells. The general formula for a ketone is RCOR, where R and R are alkyl or aryl groups." [GOC:jl, ISBN:0787650153] subset: goslim_pir synonym: "ketone metabolism" EXACT [] is_a: BFO:0000003 -is_a: GO:0044237 ! cellular metabolic process -is_a: GO:0044281 ! small molecule metabolic process +is_a: GO:0008152 ! metabolic process intersection_of: GO:0008152 ! metabolic process intersection_of: has_primary_input_or_output CHEBI:17087 relationship: has_primary_input_or_output CHEBI:17087 +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28908" xsd:anyURI [Term] id: GO:0042181 @@ -78960,8 +84258,7 @@ synonym: "ketone anabolism" EXACT [] synonym: "ketone biosynthesis" EXACT [] synonym: "ketone formation" EXACT [] synonym: "ketone synthesis" EXACT [] -is_a: GO:0042180 ! cellular ketone metabolic process -is_a: GO:0044249 ! cellular biosynthetic process +is_a: GO:0042180 ! ketone metabolic process is_a: GO:0044283 ! small molecule biosynthetic process intersection_of: GO:0009058 ! biosynthetic process intersection_of: has_primary_output CHEBI:17087 @@ -78975,8 +84272,7 @@ def: "The chemical reactions and pathways resulting in the breakdown of ketones, synonym: "ketone breakdown" EXACT [] synonym: "ketone catabolism" EXACT [] synonym: "ketone degradation" EXACT [] -is_a: GO:0042180 ! cellular ketone metabolic process -is_a: GO:0044248 ! cellular catabolic process +is_a: GO:0042180 ! ketone metabolic process is_a: GO:0044282 ! small molecule catabolic process intersection_of: GO:0009056 ! catabolic process intersection_of: has_primary_input CHEBI:17087 @@ -78984,7 +84280,7 @@ relationship: has_primary_input CHEBI:17087 [Term] id: GO:0042219 -name: cellular modified amino acid catabolic process +name: modified amino acid catabolic process namespace: biological_process def: "The chemical reactions and pathways resulting in the breakdown of compounds derived from amino acids, organic acids containing one or more amino substituents." [GOC:ai] synonym: "amino acid derivative catabolic process" EXACT [] @@ -78993,15 +84289,16 @@ synonym: "cellular amino acid derivative catabolic process" EXACT [] synonym: "cellular amino acid derivative catabolism" EXACT [] synonym: "cellular amino acid derivative degradation" EXACT [] synonym: "cellular modified amino acid breakdown" EXACT [GOC:mah] +synonym: "cellular modified amino acid catabolic process" EXACT [GOC:mah] synonym: "cellular modified amino acid catabolism" EXACT [GOC:mah] synonym: "cellular modified amino acid degradation" EXACT [GOC:mah] -synonym: "modified amino acid catabolic process" EXACT [GOC:mah] synonym: "modified amino acid catabolism" EXACT [GOC:mah] -is_a: GO:0006575 ! cellular modified amino acid metabolic process +is_a: GO:0006575 ! modified amino acid metabolic process is_a: GO:0009056 ! catabolic process intersection_of: GO:0009056 ! catabolic process intersection_of: has_primary_input CHEBI:83821 relationship: has_primary_input CHEBI:83821 +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28908" xsd:anyURI [Term] id: GO:0042221 @@ -79040,7 +84337,6 @@ property_value: RO:0002161 NCBITaxon:4751 id: GO:0042254 name: ribosome biogenesis namespace: biological_process -alt_id: GO:0007046 def: "A cellular process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of ribosome subunits; includes transport to the sites of protein synthesis." [GOC:ma, PMID:26404467, Wikipedia:Ribosome_biogenesis] subset: goslim_candida subset: goslim_chembl @@ -79057,11 +84353,10 @@ is_a: GO:0022613 ! ribonucleoprotein complex biogenesis id: GO:0042255 name: ribosome assembly namespace: biological_process -alt_id: GO:0042257 def: "The aggregation, arrangement and bonding together of the mature ribosome and of its subunits." [GOC:ma, PMID:30467428] subset: goslim_yeast synonym: "ribosomal subunit assembly" NARROW [GOC:mah, GOC:vw] -is_a: GO:0140694 ! non-membrane-bounded organelle assembly +is_a: GO:0140694 ! membraneless organelle assembly intersection_of: GO:0022607 ! cellular component assembly intersection_of: results_in_assembly_of GO:0005840 ! ribosome relationship: part_of GO:0042254 ! ribosome biogenesis @@ -79338,7 +84633,7 @@ relationship: has_part GO:0034220 ! monoatomic ion transmembrane transport [Term] id: GO:0042398 -name: cellular modified amino acid biosynthetic process +name: modified amino acid biosynthetic process namespace: biological_process def: "The chemical reactions and pathways resulting in the formation of compounds derived from amino acids, organic acids containing one or more amino substituents." [GOC:ai] synonym: "amino acid derivative biosynthetic process" EXACT [] @@ -79351,11 +84646,12 @@ synonym: "cellular modified amino acid anabolism" EXACT [GOC:mah] synonym: "cellular modified amino acid biosynthesis" EXACT [GOC:mah] synonym: "cellular modified amino acid formation" EXACT [GOC:mah] synonym: "cellular modified amino acid synthesis" EXACT [GOC:mah] -is_a: GO:0006575 ! cellular modified amino acid metabolic process +is_a: GO:0006575 ! modified amino acid metabolic process is_a: GO:0009058 ! biosynthetic process intersection_of: GO:0009058 ! biosynthetic process intersection_of: has_primary_output CHEBI:83821 relationship: has_primary_output CHEBI:83821 +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28908" xsd:anyURI [Term] id: GO:0042401 @@ -79372,13 +84668,14 @@ is_a: GO:0009309 ! amine biosynthetic process [Term] id: GO:0042402 -name: cellular biogenic amine catabolic process +name: biogenic amine catabolic process namespace: biological_process def: "The chemical reactions and pathways occurring at the level of individual cells resulting in the breakdown of biogenic amines, any of a group of naturally occurring, biologically active amines, such as norepinephrine, histamine, and serotonin, many of which act as neurotransmitters." [GOC:go_curators, GOC:jl, ISBN:0198506732] synonym: "biogenic amine breakdown" EXACT [] synonym: "biogenic amine catabolism" EXACT [] synonym: "biogenic amine degradation" EXACT [] is_a: GO:0009310 ! amine catabolic process +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28908" xsd:anyURI [Term] id: GO:0042403 @@ -79386,7 +84683,7 @@ name: thyroid hormone metabolic process namespace: biological_process def: "The chemical reactions and pathways involving any of the compounds secreted by the thyroid gland, largely thyroxine and triiodothyronine." [GOC:jl, ISBN:0198506732] synonym: "thyroid hormone metabolism" EXACT [] -is_a: GO:0006575 ! cellular modified amino acid metabolic process +is_a: GO:0006575 ! modified amino acid metabolic process is_a: GO:0018958 ! phenol-containing compound metabolic process is_a: GO:0042445 ! hormone metabolic process @@ -79558,7 +84855,7 @@ synonym: "catecholamine breakdown" EXACT [] synonym: "catecholamine catabolism" EXACT [] synonym: "catecholamine degradation" EXACT [] is_a: GO:0006584 ! catecholamine metabolic process -is_a: GO:0042402 ! cellular biogenic amine catabolic process +is_a: GO:0042402 ! biogenic amine catabolic process intersection_of: GO:0009056 ! catabolic process intersection_of: has_primary_input CHEBI:33567 relationship: has_primary_input CHEBI:33567 @@ -79611,7 +84908,6 @@ relationship: has_primary_input CHEBI:350546 id: GO:0042430 name: indole-containing compound metabolic process namespace: biological_process -alt_id: GO:0042434 def: "The chemical reactions and pathways involving compounds that contain an indole (2,3-benzopyrrole) skeleton." [GOC:jl, GOC:mah] synonym: "indole and derivative metabolic process" EXACT [] synonym: "indole and derivative metabolism" EXACT [] @@ -79663,7 +84959,6 @@ relationship: has_primary_input CHEBI:24828 id: GO:0042442 name: melatonin catabolic process namespace: biological_process -alt_id: GO:0042449 def: "The chemical reactions and pathways resulting in the breakdown of melatonin (N-acetyl-5-methoxytryptamine)." [GOC:jl] synonym: "melatonin breakdown" EXACT [] synonym: "melatonin catabolism" EXACT [] @@ -79678,7 +84973,6 @@ relationship: has_primary_input CHEBI:16796 id: GO:0042445 name: hormone metabolic process namespace: biological_process -alt_id: GO:0034754 def: "The chemical reactions and pathways involving any hormone, naturally occurring substances secreted by specialized cells that affects the metabolism or behavior of other cells possessing functional receptors for the hormone." [GOC:jl] subset: goslim_pir synonym: "cellular hormone metabolic process" RELATED [] @@ -79725,7 +85019,6 @@ relationship: has_primary_input_or_output CHEBI:17026 id: GO:0042461 name: photoreceptor cell development namespace: biological_process -alt_id: GO:0046531 def: "Development of a photoreceptor, a cell that responds to incident electromagnetic radiation, particularly visible light." [GOC:go_curators] synonym: "photoreceptor morphogenesis" EXACT [] is_a: GO:0048666 ! neuron development @@ -79830,7 +85123,6 @@ relationship: RO:0002162 NCBITaxon:7711 {all_only="true"} ! in taxon Chordata id: GO:0042476 name: odontogenesis namespace: biological_process -alt_id: GO:0042477 def: "The process whose specific outcome is the progression of a tooth or teeth over time, from formation to the mature structure(s). A tooth is any hard bony, calcareous, or chitinous organ found in the mouth or pharynx of an animal and used in procuring or masticating food." [GOC:jl, GOC:mah] synonym: "odontogenesis of calcareous or chitinous tooth" NARROW [] synonym: "odontogeny" EXACT [] @@ -79894,7 +85186,6 @@ relationship: negatively_regulates GO:0042462 ! eye photoreceptor cell developme id: GO:0042481 name: regulation of odontogenesis namespace: biological_process -alt_id: GO:0042484 def: "Any process that modulates the frequency, rate or extent of the formation and development of a tooth or teeth." [GOC:jl] synonym: "regulation of odontogenesis of calcareous or chitinous tooth" NARROW [] synonym: "regulation of tooth development" EXACT [] @@ -79907,7 +85198,6 @@ relationship: regulates GO:0042476 ! odontogenesis id: GO:0042482 name: positive regulation of odontogenesis namespace: biological_process -alt_id: GO:0042485 def: "Any process that activates or increases the frequency, rate or extent of the formation and development of a tooth or teeth." [GOC:jl] synonym: "activation of odontogenesis" NARROW [] synonym: "positive regulation of odontogenesis of calcareous or chitinous tooth" NARROW [] @@ -79926,7 +85216,6 @@ relationship: positively_regulates GO:0042476 ! odontogenesis id: GO:0042483 name: negative regulation of odontogenesis namespace: biological_process -alt_id: GO:0042486 def: "Any process that stops, prevents, or reduces the frequency, rate or extent of the formation and development of a tooth or teeth." [GOC:jl] synonym: "down regulation of odontogenesis" EXACT [] synonym: "down-regulation of odontogenesis" EXACT [] @@ -80136,9 +85425,6 @@ is_a: GO:0002478 ! antigen processing and presentation of exogenous peptide anti id: GO:0042592 name: homeostatic process namespace: biological_process -alt_id: GO:0032844 -alt_id: GO:0032845 -alt_id: GO:0032846 def: "Any biological process involved in the maintenance of an internal steady state." [GOC:jl, ISBN:0395825172] subset: goslim_agr subset: goslim_chembl @@ -80268,7 +85554,7 @@ namespace: cellular_component def: "Any complex of actin, myosin, and accessory proteins." [GOC:go_curators] synonym: "actomyosin complex" EXACT [] synonym: "actomyosin structure" EXACT [] -is_a: GO:0110165 ! cellular anatomical entity +is_a: GO:0110165 ! cellular anatomical structure relationship: part_of GO:0015629 ! actin cytoskeleton [Term] @@ -80285,7 +85571,6 @@ relationship: results_in_acquisition_of_features_of CL:0000573 ! retinal cone ce id: GO:0042675 name: compound eye cone cell differentiation namespace: biological_process -alt_id: GO:0042674 def: "The process in which a relatively unspecialized cell acquires the specialized features of a compound eye cone cell, a cone-shaped cell, that focuses light in a compound eye." [GOC:mtg_sensu] is_a: GO:0030154 ! cell differentiation intersection_of: GO:0030154 ! cell differentiation @@ -80404,8 +85689,6 @@ relationship: part_of GO:0007320 ! insemination id: GO:0042742 name: defense response to bacterium namespace: biological_process -alt_id: GO:0009816 -alt_id: GO:0042830 def: "Reactions triggered in response to the presence of a bacterium that act to protect the cell or organism." [GOC:jl] synonym: "antibacterial peptide activity" RELATED [] synonym: "defence response to bacteria" EXACT [] @@ -80442,16 +85725,6 @@ intersection_of: has_primary_input CHEBI:32988 relationship: has_primary_input CHEBI:32988 relationship: part_of GO:0042886 ! amide transport -[Term] -id: GO:0042921 -name: nuclear receptor-mediated glucocorticoid signaling pathway -namespace: biological_process -def: "A nuclear receptor-mediated signaling pathway initiated by a glucocorticoid binding to an intracellular receptor of the nuclear receptor protein family, and ending with regulation of a downstream cellular process, e.g. transcription." [GOC:mah] -synonym: "glucocorticoid receptor signaling pathway" BROAD [] -synonym: "glucocorticoid receptor signalling pathway" BROAD [] -synonym: "intracellular glucocorticoid receptor signaling pathway" EXACT [] -is_a: GO:0031958 ! nuclear receptor-mediated corticosteroid signaling pathway - [Term] id: GO:0042923 name: neuropeptide binding @@ -80498,7 +85771,7 @@ subset: goslim_prokaryote_ribbon synonym: "cell process" BROAD [] synonym: "cellular process" BROAD [] synonym: "cellular projection" EXACT [] -is_a: GO:0110165 ! cellular anatomical entity +is_a: GO:0110165 ! cellular anatomical structure relationship: part_of CL:0000000 ! cell [Term] @@ -80590,8 +85863,6 @@ relationship: RO:0002162 NCBITaxon:7711 {all_only="true"} ! in taxon Chordata id: GO:0043010 name: camera-type eye development namespace: biological_process -alt_id: GO:0001747 -alt_id: GO:0031075 def: "The process whose specific outcome is the progression of the camera-type eye over time, from its formation to the mature structure. The camera-type eye is an organ of sight that receives light through an aperture and focuses it through a lens, projecting it on a photoreceptor field." [GOC:go_curators, GOC:mtg_sensu] is_a: GO:0001654 ! eye development intersection_of: GO:0048856 ! anatomical structure development @@ -80630,7 +85901,6 @@ relationship: has_primary_input GO:1990904 ! ribonucleoprotein complex id: GO:0043022 name: ribosome binding namespace: molecular_function -alt_id: GO:0030376 def: "Binding to a ribosome." [GOC:go_curators] synonym: "ribosome receptor activity" NARROW [] is_a: GO:0043021 ! ribonucleoprotein complex binding @@ -80776,7 +86046,6 @@ relationship: positively_regulates GO:0006915 ! apoptotic process id: GO:0043066 name: negative regulation of apoptotic process namespace: biological_process -alt_id: GO:0006916 def: "Any process that stops, prevents, or reduces the frequency, rate or extent of cell death by apoptotic process." [GOC:jl, GOC:mtg_apoptosis] comment: This term should only be used when it is not possible to determine which phase or subtype of the apoptotic process is negatively regulated by a gene product. Whenever detailed information is available, the more granular children terms should be used. synonym: "anti-apoptosis" EXACT [] @@ -80798,7 +86067,6 @@ property_value: RO:0002161 NCBITaxon:4896 id: GO:0043067 name: regulation of programmed cell death namespace: biological_process -alt_id: GO:0043070 def: "Any process that modulates the frequency, rate or extent of programmed cell death, cell death resulting from activation of endogenous cellular processes." [GOC:jl] synonym: "regulation of non-apoptotic programmed cell death" NARROW [] is_a: GO:0050794 ! regulation of cellular process @@ -80810,7 +86078,6 @@ relationship: regulates GO:0012501 ! programmed cell death id: GO:0043068 name: positive regulation of programmed cell death namespace: biological_process -alt_id: GO:0043071 def: "Any process that activates or increases the frequency, rate or extent of programmed cell death, cell death resulting from activation of endogenous cellular processes." [GOC:jl] synonym: "activation of programmed cell death" NARROW [] synonym: "positive regulation of non-apoptotic programmed cell death" NARROW [] @@ -80828,7 +86095,6 @@ relationship: positively_regulates GO:0012501 ! programmed cell death id: GO:0043069 name: negative regulation of programmed cell death namespace: biological_process -alt_id: GO:0043072 def: "Any process that stops, prevents, or reduces the frequency, rate or extent of programmed cell death, cell death resulting from activation of endogenous cellular processes." [GOC:jl] synonym: "down regulation of programmed cell death" EXACT [] synonym: "down-regulation of programmed cell death" EXACT [] @@ -80856,7 +86122,6 @@ relationship: part_of CL:0000586 ! germ cell id: GO:0043085 name: positive regulation of catalytic activity namespace: biological_process -alt_id: GO:0048554 def: "Any process that activates or increases the activity of an enzyme." [GOC:ebc, GOC:jl, GOC:tb, GOC:vw] subset: gocheck_obsoletion_candidate subset: goslim_chembl @@ -80882,7 +86147,6 @@ relationship: positively_regulates GO:0003824 ! catalytic activity id: GO:0043086 name: negative regulation of catalytic activity namespace: biological_process -alt_id: GO:0048553 def: "Any process that stops or reduces the activity of an enzyme." [GOC:ebc, GOC:jl, GOC:tb, GOC:vw] subset: gocheck_obsoletion_candidate synonym: "down regulation of enzyme activity" EXACT [] @@ -80936,7 +86200,6 @@ is_a: GO:0043114 ! regulation of vascular permeability id: GO:0043129 name: surfactant homeostasis namespace: biological_process -alt_id: GO:0050828 def: "Any process involved in the maintenance of a steady-state level of a surface-active agent that maintains the surface tension of a liquid." [PMID:23708874, PMID:9751757] synonym: "regulation of liquid surface tension" RELATED [] synonym: "regulation of surface tension of a liquid" RELATED [] @@ -80999,9 +86262,6 @@ relationship: results_in_developmental_progression_of CL:0000724 ! heterocyst id: GO:0043170 name: macromolecule metabolic process namespace: biological_process -alt_id: GO:0034960 -alt_id: GO:0043283 -alt_id: GO:0044259 def: "The chemical reactions and pathways involving macromolecules, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass." [GOC:mah] subset: gocheck_do_not_annotate subset: goslim_pir @@ -81085,7 +86345,6 @@ relationship: part_of GO:0043679 ! axon terminus id: GO:0043200 name: response to amino acid namespace: biological_process -alt_id: GO:0010237 def: "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an amino acid stimulus. An amino acid is a carboxylic acids containing one or more amino groups." [GOC:ef, GOC:mlg] synonym: "response to amino acid stimulus" EXACT [GOC:dos] is_a: GO:0001101 ! response to acid chemical @@ -81123,7 +86382,7 @@ synonym: "Schwann cell myelin sheath" NARROW [] xref: FMA:62983 xref: NIF_Subcellular:sao593830697 xref: Wikipedia:Myelin -is_a: GO:0110165 ! cellular anatomical entity +is_a: GO:0110165 ! cellular anatomical structure relationship: part_of CL:0000125 ! glial cell relationship: RO:0002160 NCBITaxon:33208 ! only in taxon Metazoa relationship: RO:0002162 NCBITaxon:33208 {all_only="true"} ! in taxon Metazoa @@ -81140,7 +86399,7 @@ subset: goslim_prokaryote subset: goslim_prokaryote_ribbon xref: NIF_Subcellular:sao1539965131 xref: Wikipedia:Organelle -is_a: GO:0110165 ! cellular anatomical entity +is_a: GO:0110165 ! cellular anatomical structure [Term] id: GO:0043227 @@ -81153,23 +86412,26 @@ xref: NIF_Subcellular:sao414196390 is_a: GO:0043226 ! organelle intersection_of: GO:0043226 ! organelle intersection_of: has_part GO:0016020 ! membrane -disjoint_from: GO:0043228 ! non-membrane-bounded organelle +disjoint_from: GO:0043228 ! membraneless organelle relationship: has_part GO:0016020 ! membrane property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28153" xsd:anyURI [Term] id: GO:0043228 -name: non-membrane-bounded organelle +name: membraneless organelle namespace: cellular_component def: "Organized structure of distinctive morphology and function, not bounded by a lipid bilayer membrane. Includes ribosomes, the cytoskeleton and chromosomes." [GOC:go_curators] subset: gocheck_do_not_annotate subset: goslim_mouse synonym: "biological condensate" RELATED [] +synonym: "membrane-less organelle" EXACT [] +synonym: "non-membrane-bounded organelle" EXACT [] synonym: "non-membrane-enclosed organelle" EXACT [] xref: NIF_Subcellular:sao1456184038 is_a: GO:0043226 ! organelle property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/21881" xsd:anyURI property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28153" xsd:anyURI +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29106" xsd:anyURI [Term] id: GO:0043229 @@ -81210,15 +86472,17 @@ intersection_of: part_of GO:0005622 ! intracellular anatomical structure [Term] id: GO:0043232 -name: intracellular non-membrane-bounded organelle +name: intracellular membraneless organelle namespace: cellular_component def: "Organized structure of distinctive morphology and function, not bounded by a lipid bilayer membrane and occurring within the cell. Includes ribosomes, the cytoskeleton and chromosomes." [GOC:go_curators] subset: goslim_pir +synonym: "intracellular non-membrane-bounded organelle" EXACT [] synonym: "intracellular non-membrane-enclosed organelle" EXACT [] -is_a: GO:0043228 ! non-membrane-bounded organelle +is_a: GO:0043228 ! membraneless organelle is_a: GO:0043229 ! intracellular organelle -intersection_of: GO:0043228 ! non-membrane-bounded organelle +intersection_of: GO:0043228 ! membraneless organelle intersection_of: part_of GO:0005622 ! intracellular anatomical structure +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29106" xsd:anyURI [Term] id: GO:0043233 @@ -81329,14 +86593,16 @@ relationship: regulates GO:0016051 ! carbohydrate biosynthetic process [Term] id: GO:0043264 -name: extracellular non-membrane-bounded organelle +name: extracellular membraneless organelle namespace: cellular_component def: "Organized structure of distinctive morphology and function, not bounded by a lipid bilayer membrane and occurring outside the cell." [GOC:jl] +synonym: "extracellular non-membrane-bounded organelle" EXACT [] synonym: "extracellular non-membrane-enclosed organelle" EXACT [] -is_a: GO:0043228 ! non-membrane-bounded organelle +is_a: GO:0043228 ! membraneless organelle is_a: GO:0043230 ! extracellular organelle -intersection_of: GO:0043228 ! non-membrane-bounded organelle +intersection_of: GO:0043228 ! membraneless organelle intersection_of: part_of GO:0005576 ! extracellular region +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29106" xsd:anyURI [Term] id: GO:0043266 @@ -81467,7 +86733,7 @@ name: contractile muscle fiber namespace: cellular_component def: "Fibers, composed of actin, myosin, and associated proteins, found in cells of smooth or striated muscle." [GOC:go_curators, ISBN:0815316194] synonym: "contractile fibre" EXACT [] -is_a: GO:0043232 ! intracellular non-membrane-bounded organelle +is_a: GO:0043232 ! intracellular membraneless organelle is_a: GO:0099512 ! supramolecular fiber relationship: part_of CL:0000187 ! muscle cell relationship: part_of GO:0005737 ! cytoplasm @@ -82290,25 +87556,6 @@ intersection_of: GO:0005488 ! binding intersection_of: has_primary_input CHEBI:37396 relationship: has_primary_input CHEBI:37396 -[Term] -id: GO:0043401 -name: steroid hormone receptor signaling pathway -namespace: biological_process -def: "The series of molecular signals mediated by a steroid hormone binding to a receptor." [PMID:12606724] -synonym: "steroid hormone mediated signalling" EXACT [] -synonym: "steroid hormone-mediated signaling pathway" EXACT [] -is_a: GO:0009755 ! hormone-mediated signaling pathway -relationship: part_of GO:0071383 ! cellular response to steroid hormone stimulus - -[Term] -id: GO:0043402 -name: glucocorticoid mediated signaling pathway -namespace: biological_process -def: "The series of molecular signals mediated by the detection of a glucocorticoid hormone." [PMID:15240347] -synonym: "glucocorticoid mediated signalling" EXACT [] -is_a: GO:0043401 ! steroid hormone receptor signaling pathway -relationship: part_of GO:0071385 ! cellular response to glucocorticoid stimulus - [Term] id: GO:0043403 name: skeletal muscle tissue regeneration @@ -82374,30 +87621,6 @@ intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0043403 ! skeletal muscle tissue regeneration relationship: negatively_regulates GO:0043403 ! skeletal muscle tissue regeneration -[Term] -id: GO:0043433 -name: negative regulation of DNA-binding transcription factor activity -namespace: biological_process -alt_id: GO:1904168 -alt_id: GO:2000824 -def: "Any process that stops, prevents, or reduces the frequency, rate or extent of the activity of a transcription factor, any factor involved in the initiation or regulation of transcription." [GOC:jl] -subset: gocheck_obsoletion_candidate -synonym: "down regulation of transcription factor activity" EXACT [] -synonym: "down-regulation of transcription factor activity" EXACT [] -synonym: "downregulation of transcription factor activity" EXACT [] -synonym: "inhibition of transcription factor activity" NARROW [] -synonym: "negative regulation of androgen receptor activity" NARROW [] -synonym: "negative regulation of DNA binding transcription factor activity" EXACT [] -synonym: "negative regulation of sequence-specific DNA binding transcription factor activity" EXACT [] -synonym: "negative regulation of thyroid hormone receptor activity" NARROW [] -synonym: "negative regulation of transcription factor activity" BROAD [GOC:dph, GOC:tb] -is_a: GO:0044092 ! negative regulation of molecular function -is_a: GO:0051090 ! regulation of DNA-binding transcription factor activity -intersection_of: GO:0065007 ! biological regulation -intersection_of: negatively_regulates GO:0003700 ! DNA-binding transcription factor activity -relationship: negatively_regulates GO:0003700 ! DNA-binding transcription factor activity -creation_date: 2011-07-15T10:56:12Z - [Term] id: GO:0043434 name: response to peptide hormone @@ -82458,7 +87681,7 @@ id: GO:0043467 name: regulation of generation of precursor metabolites and energy namespace: biological_process def: "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of precursor metabolites, substances from which energy is derived, and the processes involved in the liberation of energy from these substances." [GOC:jl] -is_a: GO:0031323 ! regulation of cellular metabolic process +is_a: GO:0019222 ! regulation of metabolic process intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0006091 ! generation of precursor metabolites and energy relationship: regulates GO:0006091 ! generation of precursor metabolites and energy @@ -82672,14 +87895,6 @@ intersection_of: has_primary_input PR:000009054 ! insulin gene translation produ relationship: has_primary_input PR:000009054 ! insulin gene translation product property_value: RO:0002161 NCBITaxon:4751 -[Term] -id: GO:0043565 -name: sequence-specific DNA binding -namespace: molecular_function -def: "Binding to DNA of a specific nucleotide composition, e.g. GC-rich DNA binding, or with a specific sequence motif or type of DNA e.g. promotor binding or rDNA binding." [GOC:jl] -synonym: "sequence specific DNA binding" EXACT [] -is_a: GO:0003677 ! DNA binding - [Term] id: GO:0043576 name: regulation of respiratory gaseous exchange @@ -82931,9 +88146,6 @@ relationship: part_of GO:0046849 ! bone remodeling id: GO:0043933 name: protein-containing complex organization namespace: biological_process -alt_id: GO:0034600 -alt_id: GO:0034621 -alt_id: GO:0071822 def: "Any process in which macromolecules aggregate, disaggregate, or are modified, resulting in the formation, disassembly, or alteration of a protein complex." [GOC:mah] synonym: "cellular macromolecular complex organization" RELATED [] synonym: "cellular macromolecular complex subunit organisation" RELATED [] @@ -82949,7 +88161,6 @@ intersection_of: GO:0016043 ! cellular component organization intersection_of: results_in_organization_of GO:0032991 ! protein-containing complex relationship: results_in_organization_of GO:0032991 ! protein-containing complex property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/22580" xsd:anyURI -created_by: mah creation_date: 2010-09-08T10:01:42Z [Term] @@ -83108,7 +88319,6 @@ relationship: regulates GO:0003016 ! respiratory system process id: GO:0044085 name: cellular component biogenesis namespace: biological_process -alt_id: GO:0071843 def: "A process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of a cellular component. Includes biosynthesis of constituent macromolecules, and those macromolecular modifications that are involved in synthesis or assembly of the cellular component." [GOC:jl, GOC:mah] subset: gocheck_do_not_annotate subset: goslim_pir @@ -83183,7 +88393,6 @@ is_a: GO:0065009 ! regulation of molecular function intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0003674 ! molecular_function relationship: negatively_regulates GO:0003674 ! molecular_function -created_by: jl creation_date: 2009-04-21T04:07:27Z [Term] @@ -83196,7 +88405,6 @@ is_a: GO:0065009 ! regulation of molecular function intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0003674 ! molecular_function relationship: positively_regulates GO:0003674 ! molecular_function -created_by: jl creation_date: 2009-04-21T04:11:06Z [Term] @@ -83209,21 +88417,8 @@ synonym: "translation initiation (ternary) complex" EXACT [] is_a: BFO:0000004 is_a: GO:1990904 ! ribonucleoprotein complex relationship: part_of GO:0005737 ! cytoplasm -created_by: jl creation_date: 2009-10-22T02:38:55Z -[Term] -id: GO:0044237 -name: cellular metabolic process -namespace: biological_process -def: "The chemical reactions and pathways by which individual cells transform chemical substances." [GOC:go_curators] -comment: This term should not be used for direct annotation. It should be possible to make a more specific annotation to one of the children of this term. -subset: gocheck_do_not_annotate -synonym: "cellular metabolism" EXACT [] -synonym: "intermediary metabolism" RELATED [GOC:mah] -is_a: GO:0008152 ! metabolic process -is_a: GO:0009987 ! cellular process - [Term] id: GO:0044238 name: primary metabolic process @@ -83239,18 +88434,6 @@ xref: Wikipedia:Primary_metabolite is_a: GO:0008152 ! metabolic process property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/26424" xsd:anyURI -[Term] -id: GO:0044242 -name: cellular lipid catabolic process -namespace: biological_process -def: "The chemical reactions and pathways resulting in the breakdown of lipids, as carried out by individual cells." [GOC:jl] -synonym: "cellular lipid breakdown" EXACT [] -synonym: "cellular lipid catabolism" EXACT [] -synonym: "cellular lipid degradation" EXACT [] -is_a: GO:0016042 ! lipid catabolic process -is_a: GO:0044248 ! cellular catabolic process -is_a: GO:0044255 ! cellular lipid metabolic process - [Term] id: GO:0044248 name: cellular catabolic process @@ -83260,32 +88443,6 @@ synonym: "cellular breakdown" EXACT [] synonym: "cellular catabolism" EXACT [] synonym: "cellular degradation" EXACT [] is_a: GO:0009056 ! catabolic process -is_a: GO:0044237 ! cellular metabolic process - -[Term] -id: GO:0044249 -name: cellular biosynthetic process -namespace: biological_process -def: "The chemical reactions and pathways resulting in the formation of substances, carried out by individual cells." [GOC:jl] -comment: This term should not be used for direct annotation. It should be possible to make a more specific annotation to one of the children of this term. -subset: gocheck_do_not_annotate -synonym: "cellular anabolism" EXACT [] -synonym: "cellular biosynthesis" EXACT [] -synonym: "cellular formation" EXACT [] -synonym: "cellular synthesis" EXACT [] -is_a: GO:0009058 ! biosynthetic process -is_a: GO:0044237 ! cellular metabolic process -property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27052" xsd:anyURI - -[Term] -id: GO:0044255 -name: cellular lipid metabolic process -namespace: biological_process -def: "The chemical reactions and pathways involving lipids, as carried out by individual cells." [GOC:jl] -subset: goslim_pir -synonym: "cellular lipid metabolism" EXACT [] -is_a: GO:0006629 ! lipid metabolic process -is_a: GO:0044237 ! cellular metabolic process [Term] id: GO:0044258 @@ -83311,7 +88468,6 @@ subset: goslim_flybase_ribbon subset: goslim_metagenomics synonym: "small molecule metabolism" EXACT [] is_a: GO:0008152 ! metabolic process -created_by: jl creation_date: 2010-01-26T12:05:20Z [Term] @@ -83323,7 +88479,6 @@ comment: Small molecules in GO include monosaccharides but exclude disaccharides synonym: "small molecule catabolism" EXACT [] is_a: GO:0009056 ! catabolic process is_a: GO:0044281 ! small molecule metabolic process -created_by: jl creation_date: 2010-01-26T12:06:10Z [Term] @@ -83337,7 +88492,6 @@ subset: goslim_prokaryote_ribbon synonym: "small molecule biosynthesis" EXACT [] is_a: GO:0009058 ! biosynthetic process is_a: GO:0044281 ! small molecule metabolic process -created_by: jl creation_date: 2010-01-26T12:06:49Z [Term] @@ -83350,10 +88504,9 @@ synonym: "cell soma" EXACT [] xref: FBbt:00005107 xref: FMA:67301 xref: Wikipedia:Cell_body -is_a: GO:0110165 ! cellular anatomical entity +is_a: GO:0110165 ! cellular anatomical structure relationship: part_of CL:0000000 ! cell property_value: RO:0002161 NCBITaxon:4890 -created_by: jl creation_date: 2010-02-05T10:37:16Z [Term] @@ -83364,9 +88517,8 @@ def: "The specialized, terminal region of a neuron projection such as an axon or synonym: "nerve terminal" RELATED [PMID:25972809, PMID:9650842] synonym: "neuron projection terminal" EXACT [] synonym: "neuron terminal specialization" EXACT [] -is_a: GO:0110165 ! cellular anatomical entity +is_a: GO:0110165 ! cellular anatomical structure relationship: part_of GO:0043005 ! neuron projection -created_by: jl creation_date: 2010-02-05T02:44:04Z [Term] @@ -83376,7 +88528,6 @@ namespace: cellular_component def: "A specialized axon terminus which is produced by retinal cone cells. Pedicles are large, conical, flat end-feet (8-10 micrometers diameter) of the retinal cone axon that lie more or less side by side on the same plane at the outer edge of the outer plexiform layer (OPL)." [PMID:10939333] synonym: "cone pedicle" EXACT [] is_a: GO:0043679 ! axon terminus -created_by: jl creation_date: 2010-07-14T01:30:02Z [Term] @@ -83390,7 +88541,6 @@ is_a: GO:0050673 ! epithelial cell proliferation intersection_of: GO:0008283 ! cell population proliferation intersection_of: acts_on_population_of CL:0000169 ! type B pancreatic cell relationship: acts_on_population_of CL:0000169 ! type B pancreatic cell -created_by: jl creation_date: 2010-08-25T01:44:51Z [Term] @@ -83403,7 +88553,6 @@ is_a: GO:0006915 ! apoptotic process intersection_of: GO:0006915 ! apoptotic process intersection_of: occurs_in CL:0000057 ! fibroblast relationship: occurs_in CL:0000057 ! fibroblast -created_by: jl creation_date: 2010-09-23T11:33:38Z [Term] @@ -83416,7 +88565,6 @@ is_a: GO:0033365 ! protein localization to organelle intersection_of: GO:0008104 ! protein localization intersection_of: has_target_end_location GO:0005856 ! cytoskeleton relationship: has_target_end_location GO:0005856 ! cytoskeleton -created_by: jl creation_date: 2011-12-13T11:43:24Z [Term] @@ -83439,7 +88587,6 @@ property_value: term_tracker_item "https://github.com/geneontology/go-ontology/i id: GO:0044458 name: motile cilium assembly namespace: biological_process -alt_id: GO:1903887 def: "The aggregation, arrangement and bonding together of a set of components to form a motile cilium." [GO_REF:0000079, GOC:cilia, GOC:krc, GOC:TermGenie, PMID:19776033, PMID:21129373, ZFIN:dsf] synonym: "motile primary cilia assembly" RELATED [GOC:TermGenie] synonym: "motile primary cilia formation" RELATED [GOC:TermGenie] @@ -83451,7 +88598,6 @@ is_a: GO:0060271 ! cilium assembly intersection_of: GO:0022607 ! cellular component assembly intersection_of: results_in_assembly_of GO:0031514 ! motile cilium relationship: results_in_assembly_of GO:0031514 ! motile cilium -created_by: krc creation_date: 2015-02-06T17:23:23Z [Term] @@ -83463,7 +88609,6 @@ is_a: GO:0032943 ! mononuclear cell proliferation intersection_of: GO:0008283 ! cell population proliferation intersection_of: acts_on_population_of CL:0000451 ! dendritic cell relationship: acts_on_population_of CL:0000451 ! dendritic cell -created_by: jl creation_date: 2012-04-05T04:31:39Z [Term] @@ -83476,7 +88621,6 @@ is_a: GO:0001775 ! cell activation intersection_of: GO:0001775 ! cell activation intersection_of: has_primary_input CL:0000138 ! chondrocyte relationship: has_primary_input CL:0000138 ! chondrocyte -created_by: jl creation_date: 2012-04-05T04:45:38Z [Term] @@ -83486,7 +88630,6 @@ namespace: biological_process def: "A biological process that directly contributes to the process of producing new individuals, involving another organism." [GOC:jl] subset: goslim_drosophila is_a: GO:0022414 ! reproductive process -created_by: jl creation_date: 2012-09-19T15:56:30Z [Term] @@ -83496,7 +88639,6 @@ namespace: biological_process def: "A multicellular organism process which involves another multicellular organism of the same or different species." [GOC:jl] is_a: GO:0032501 ! multicellular organismal process property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/21459" xsd:anyURI -created_by: jl creation_date: 2012-09-19T16:06:16Z [Term] @@ -83514,7 +88656,6 @@ intersection_of: results_in_transport_across GO:0031090 ! organelle membrane relationship: has_target_end_location GO:0043229 ! intracellular organelle relationship: has_target_start_location GO:0005829 ! cytosol relationship: results_in_transport_across GO:0031090 ! organelle membrane -created_by: jl creation_date: 2012-11-07T15:37:36Z [Term] @@ -83533,7 +88674,6 @@ intersection_of: results_in_organization_of GO:0005929 ! cilium relationship: results_in_organization_of GO:0005929 ! cilium relationship: RO:0002160 NCBITaxon:2759 ! only in taxon Eukaryota relationship: RO:0002162 NCBITaxon:2759 {all_only="true"} ! in taxon Eukaryota -created_by: jl creation_date: 2013-03-27T15:09:58Z [Term] @@ -83549,7 +88689,6 @@ disjoint_from: GO:0048511 ! rhythmic process disjoint_from: GO:0050896 ! response to stimulus disjoint_from: GO:0051179 ! localization disjoint_from: GO:0071840 ! cellular component organization or biogenesis -created_by: jl creation_date: 2014-07-16T13:12:40Z [Term] @@ -83562,7 +88701,6 @@ is_a: GO:0033036 ! macromolecule localization intersection_of: GO:0051179 ! localization intersection_of: has_primary_input CHEBI:6495 relationship: has_primary_input CHEBI:6495 -created_by: jl creation_date: 2014-11-25T16:27:06Z [Term] @@ -83574,7 +88712,6 @@ is_a: GO:0044872 ! lipoprotein localization is_a: GO:0051668 ! localization within membrane intersection_of: GO:0044872 ! lipoprotein localization intersection_of: has_target_end_location GO:0016020 ! membrane -created_by: jl creation_date: 2014-11-25T16:28:43Z [Term] @@ -83586,14 +88723,12 @@ is_a: GO:0044873 ! lipoprotein localization to membrane intersection_of: GO:0044872 ! lipoprotein localization intersection_of: has_target_end_location GO:0019867 ! outer membrane relationship: has_target_end_location GO:0019867 ! outer membrane -created_by: jl creation_date: 2014-11-25T16:30:30Z [Term] id: GO:0044877 name: protein-containing complex binding namespace: molecular_function -alt_id: GO:0032403 def: "Binding to a macromolecular complex." [GOC:jl] subset: goslim_chembl synonym: "macromolecular complex binding" RELATED [] @@ -83603,7 +88738,6 @@ is_a: GO:0005488 ! binding intersection_of: GO:0005488 ! binding intersection_of: has_primary_input GO:0032991 ! protein-containing complex relationship: has_primary_input GO:0032991 ! protein-containing complex -created_by: jl creation_date: 2014-12-16T11:38:58Z [Term] @@ -83613,11 +88747,30 @@ namespace: cellular_component def: "An intracellular membrane-bounded particle found in fungi and containing chitin synthase; it synthesizes chitin microfibrils. Chitin synthase activity exists in chitosomes and they are proposed to act as a reservoir for regulated transport of chitin synthase enzymes to the division septum." [ISBN:0198506732, PMID:8970154] is_a: GO:0031410 ! cytoplasmic vesicle +[Term] +id: GO:0045019 +name: negative regulation of nitric oxide biosynthetic process +namespace: biological_process +def: "Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of nitric oxide." [GOC:go_curators] +synonym: "down regulation of nitric oxide biosynthetic process" EXACT [] +synonym: "down-regulation of nitric oxide biosynthetic process" EXACT [] +synonym: "downregulation of nitric oxide biosynthetic process" EXACT [] +synonym: "inhibition of nitric oxide biosynthetic process" NARROW [] +synonym: "negative regulation of nitric oxide anabolism" EXACT [] +synonym: "negative regulation of nitric oxide biosynthesis" EXACT [] +synonym: "negative regulation of nitric oxide formation" EXACT [] +synonym: "negative regulation of nitric oxide synthesis" EXACT [] +is_a: GO:0009890 ! negative regulation of biosynthetic process +is_a: GO:0045428 ! regulation of nitric oxide biosynthetic process +is_a: GO:1904406 ! negative regulation of nitric oxide metabolic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0006809 ! nitric oxide biosynthetic process +relationship: negatively_regulates GO:0006809 ! nitric oxide biosynthetic process + [Term] id: GO:0045026 name: plasma membrane fusion namespace: biological_process -alt_id: GO:0006947 def: "The joining of the lipid bilayer membrane that surround a cell with that of another cell, producing a single cell." [GOC:elh, GOC:mtg_muscle] synonym: "cell fusion" BROAD [] synonym: "cell-cell fusion" BROAD [] @@ -83725,7 +88878,6 @@ relationship: results_in_acquisition_of_features_of CL:0000815 ! regulatory T ce id: GO:0045087 name: innate immune response namespace: biological_process -alt_id: GO:0002226 def: "Innate immune responses are defense responses mediated by germline encoded components that directly recognize components of potential pathogens." [GO_REF:0000022, GOC:add, GOC:ebc, GOC:mtg_sensu] synonym: "innate immunity" EXACT [GOC:pg] synonym: "nonspecific immune response" EXACT [] @@ -83963,8 +89115,6 @@ relationship: regulates GO:0045190 ! isotype switching id: GO:0045196 name: establishment or maintenance of neuroblast polarity namespace: biological_process -alt_id: GO:0043339 -alt_id: GO:0043342 def: "Any cellular process that results in the specification, formation or maintenance of the apicobasal polarity of a neuroblast cell, a progenitor of the central nervous system." [GOC:bf, GOC:mah, GOC:mtg_sensu, PMID:19375318, PMID:20066083] synonym: "establishment and/or maintenance of neuroblast cell polarity" EXACT [] is_a: GO:0007163 ! establishment or maintenance of cell polarity @@ -83974,8 +89124,6 @@ relationship: part_of GO:0055059 ! asymmetric neuroblast division id: GO:0045200 name: establishment of neuroblast polarity namespace: biological_process -alt_id: GO:0043340 -alt_id: GO:0043343 def: "The specification and formation of the apicobasal polarity of a neuroblast cell, a progenitor of the central nervous system." [GOC:bf, GOC:mtg_sensu] synonym: "establishment of neuroblast cell polarity" EXACT [] is_a: BFO:0000003 @@ -84020,7 +89168,6 @@ relationship: part_of GO:0098794 ! postsynapse id: GO:0045214 name: sarcomere organization namespace: biological_process -alt_id: GO:0006938 def: "The myofibril assembly process that results in the organization of muscle actomyosin into sarcomeres. The sarcomere is the repeating unit of a myofibril in a muscle cell, composed of an array of overlapping thick and thin filaments between two adjacent Z discs." [GOC:bf] synonym: "sarcomere alignment" EXACT [] synonym: "sarcomere organisation" EXACT [] @@ -84216,6 +89363,42 @@ relationship: has_primary_input CL:0000738 ! leukocyte relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata relationship: RO:0002162 NCBITaxon:7742 {all_only="true"} ! in taxon Vertebrata +[Term] +id: GO:0045428 +name: regulation of nitric oxide biosynthetic process +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of nitric oxide." [GOC:go_curators] +synonym: "regulation of nitric oxide anabolism" EXACT [] +synonym: "regulation of nitric oxide biosynthesis" EXACT [] +synonym: "regulation of nitric oxide formation" EXACT [] +synonym: "regulation of nitric oxide synthesis" EXACT [] +is_a: GO:0009889 ! regulation of biosynthetic process +is_a: GO:0080164 ! regulation of nitric oxide metabolic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0006809 ! nitric oxide biosynthetic process +relationship: regulates GO:0006809 ! nitric oxide biosynthetic process + +[Term] +id: GO:0045429 +name: positive regulation of nitric oxide biosynthetic process +namespace: biological_process +def: "Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of nitric oxide." [GOC:go_curators] +synonym: "activation of nitric oxide biosynthetic process" NARROW [] +synonym: "positive regulation of nitric oxide anabolism" EXACT [] +synonym: "positive regulation of nitric oxide biosynthesis" EXACT [] +synonym: "positive regulation of nitric oxide formation" EXACT [] +synonym: "positive regulation of nitric oxide synthesis" EXACT [] +synonym: "stimulation of nitric oxide biosynthetic process" NARROW [] +synonym: "up regulation of nitric oxide biosynthetic process" EXACT [] +synonym: "up-regulation of nitric oxide biosynthetic process" EXACT [] +synonym: "upregulation of nitric oxide biosynthetic process" EXACT [] +is_a: GO:0009891 ! positive regulation of biosynthetic process +is_a: GO:0045428 ! regulation of nitric oxide biosynthetic process +is_a: GO:1904407 ! positive regulation of nitric oxide metabolic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0006809 ! nitric oxide biosynthetic process +relationship: positively_regulates GO:0006809 ! nitric oxide biosynthetic process + [Term] id: GO:0045443 name: juvenile hormone secretion @@ -84278,7 +89461,7 @@ name: ecdysteroid metabolic process namespace: biological_process def: "The chemical reactions and pathways involving ecdysteroids, a group of polyhydroxylated ketosteroids ubiquitous in insects and other arthropods, in which they initiate post-embryonic development, including the metamorphosis of immature forms and the development of the reproductive system and the maturation of oocytes in adult females." [ISBN:0198506732] synonym: "ecdysteroid metabolism" EXACT [] -is_a: GO:0042180 ! cellular ketone metabolic process +is_a: GO:0042180 ! ketone metabolic process is_a: GO:0042445 ! hormone metabolic process intersection_of: GO:0008152 ! metabolic process intersection_of: has_primary_input_or_output CHEBI:23897 @@ -86195,7 +91378,7 @@ synonym: "down-regulation of gluconeogenesis" EXACT [] synonym: "downregulation of gluconeogenesis" EXACT [] synonym: "inhibition of gluconeogenesis" NARROW [] is_a: GO:0006111 ! regulation of gluconeogenesis -is_a: GO:0031327 ! negative regulation of cellular biosynthetic process +is_a: GO:0009890 ! negative regulation of biosynthetic process is_a: GO:0045912 ! negative regulation of carbohydrate metabolic process intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0006094 ! gluconeogenesis @@ -86212,8 +91395,8 @@ synonym: "up regulation of gluconeogenesis" EXACT [] synonym: "up-regulation of gluconeogenesis" EXACT [] synonym: "upregulation of gluconeogenesis" EXACT [] is_a: GO:0006111 ! regulation of gluconeogenesis +is_a: GO:0009891 ! positive regulation of biosynthetic process is_a: GO:0010907 ! positive regulation of glucose metabolic process -is_a: GO:0031328 ! positive regulation of cellular biosynthetic process intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0006094 ! gluconeogenesis relationship: positively_regulates GO:0006094 ! gluconeogenesis @@ -86262,7 +91445,6 @@ relationship: positively_regulates GO:0005978 ! glycogen biosynthetic process id: GO:0045727 name: positive regulation of translation namespace: biological_process -alt_id: GO:0045946 def: "Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of proteins by the translation of mRNA or circRNA." [GOC:dph, GOC:go_curators, GOC:tb] synonym: "activation of protein biosynthetic process" NARROW [] synonym: "positive regulation of protein anabolism" EXACT [] @@ -86307,8 +91489,6 @@ is_a: GO:0008152 ! metabolic process id: GO:0045732 name: positive regulation of protein catabolic process namespace: biological_process -alt_id: GO:1903364 -alt_id: GO:2000600 def: "Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of a protein by the destruction of the native, active configuration, with or without the hydrolysis of peptide bonds." [GOC:go_curators] synonym: "activation of cellular protein breakdown" NARROW [GOC:TermGenie] synonym: "activation of cellular protein catabolic process" NARROW [GOC:TermGenie] @@ -86430,7 +91610,7 @@ relationship: positively_regulates GO:0001508 ! action potential [Term] id: GO:0045763 -name: negative regulation of cellular amino acid metabolic process +name: negative regulation of amino acid metabolic process namespace: biological_process def: "Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving amino acid." [GOC:go_curators] synonym: "down regulation of amino acid metabolic process" EXACT [] @@ -86438,11 +91618,12 @@ synonym: "down-regulation of amino acid metabolic process" EXACT [] synonym: "downregulation of amino acid metabolic process" EXACT [] synonym: "inhibition of amino acid metabolic process" NARROW [] synonym: "negative regulation of amino acid metabolism" EXACT [] -is_a: GO:0006521 ! regulation of cellular amino acid metabolic process -is_a: GO:0033239 ! negative regulation of amine metabolic process +is_a: GO:0006521 ! regulation of amino acid metabolic process +is_a: GO:0009892 ! negative regulation of metabolic process intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0006520 ! amino acid metabolic process relationship: negatively_regulates GO:0006520 ! amino acid metabolic process +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28908" xsd:anyURI [Term] id: GO:0045764 @@ -86456,8 +91637,8 @@ synonym: "stimulation of amino acid metabolic process" NARROW [] synonym: "up regulation of amino acid metabolic process" EXACT [] synonym: "up-regulation of amino acid metabolic process" EXACT [] synonym: "upregulation of amino acid metabolic process" EXACT [] -is_a: GO:0006521 ! regulation of cellular amino acid metabolic process -is_a: GO:0033240 ! positive regulation of amine metabolic process +is_a: GO:0006521 ! regulation of amino acid metabolic process +is_a: GO:0009893 ! positive regulation of metabolic process intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0006520 ! amino acid metabolic process relationship: positively_regulates GO:0006520 ! amino acid metabolic process @@ -86667,11 +91848,12 @@ synonym: "negative regulation of glycogen catabolism" EXACT [] synonym: "negative regulation of glycogen degradation" EXACT [] synonym: "negative regulation of glycogenolysis" EXACT [GOC:sl] is_a: GO:0005981 ! regulation of glycogen catabolic process -is_a: GO:0031330 ! negative regulation of cellular catabolic process +is_a: GO:0009895 ! negative regulation of catabolic process is_a: GO:0070874 ! negative regulation of glycogen metabolic process intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0005980 ! glycogen catabolic process relationship: negatively_regulates GO:0005980 ! glycogen catabolic process +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29024" xsd:anyURI [Term] id: GO:0045819 @@ -86688,11 +91870,12 @@ synonym: "up regulation of glycogen catabolic process" EXACT [] synonym: "up-regulation of glycogen catabolic process" EXACT [] synonym: "upregulation of glycogen catabolic process" EXACT [] is_a: GO:0005981 ! regulation of glycogen catabolic process -is_a: GO:0031331 ! positive regulation of cellular catabolic process +is_a: GO:0009896 ! positive regulation of catabolic process is_a: GO:0070875 ! positive regulation of glycogen metabolic process intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0005980 ! glycogen catabolic process relationship: positively_regulates GO:0005980 ! glycogen catabolic process +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29024" xsd:anyURI [Term] id: GO:0045822 @@ -87042,60 +92225,6 @@ intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0030435 ! sporulation resulting in formation of a cellular spore relationship: positively_regulates GO:0030435 ! sporulation resulting in formation of a cellular spore -[Term] -id: GO:0045892 -name: negative regulation of DNA-templated transcription -namespace: biological_process -alt_id: GO:0016481 -alt_id: GO:0032582 -alt_id: GO:0061021 -def: "Any process that stops, prevents, or reduces the frequency, rate or extent of cellular DNA-templated transcription." [GOC:go_curators, GOC:txnOH] -synonym: "down regulation of gene-specific transcription" RELATED [] -synonym: "down regulation of transcription, DNA-dependent" EXACT [] -synonym: "down-regulation of gene-specific transcription" RELATED [] -synonym: "down-regulation of transcription, DNA-dependent" EXACT [] -synonym: "downregulation of gene-specific transcription" RELATED [] -synonym: "downregulation of transcription, DNA-dependent" EXACT [] -synonym: "inhibition of gene-specific transcription" RELATED [] -synonym: "inhibition of transcription, DNA-dependent" NARROW [] -synonym: "negative regulation of cellular transcription, DNA-dependent" EXACT [] -synonym: "negative regulation of gene-specific transcription" RELATED [] -synonym: "negative regulation of transcription, DNA-dependent" EXACT [GOC:txnOH] -synonym: "negative regulation of transcription, DNA-templated" EXACT [] -synonym: "transcription repressor activity" RELATED [] -is_a: GO:0006355 ! regulation of DNA-templated transcription -intersection_of: GO:0065007 ! biological regulation -intersection_of: negatively_regulates GO:0006351 ! DNA-templated transcription -relationship: negatively_regulates GO:0006351 ! DNA-templated transcription - -[Term] -id: GO:0045893 -name: positive regulation of DNA-templated transcription -namespace: biological_process -alt_id: GO:0043193 -alt_id: GO:0045941 -alt_id: GO:0061020 -def: "Any process that activates or increases the frequency, rate or extent of cellular DNA-templated transcription." [GOC:go_curators, GOC:txnOH] -synonym: "activation of gene-specific transcription" RELATED [] -synonym: "activation of transcription, DNA-dependent" NARROW [] -synonym: "positive regulation of cellular transcription, DNA-dependent" EXACT [] -synonym: "positive regulation of gene-specific transcription" RELATED [] -synonym: "positive regulation of transcription, DNA-dependent" EXACT [GOC:txnOH] -synonym: "positive regulation of transcription, DNA-templated" EXACT [] -synonym: "stimulation of gene-specific transcription" NARROW [] -synonym: "stimulation of transcription, DNA-dependent" NARROW [] -synonym: "transcription activator activity" RELATED [] -synonym: "up regulation of gene-specific transcription" RELATED [] -synonym: "up regulation of transcription, DNA-dependent" EXACT [] -synonym: "up-regulation of gene-specific transcription" RELATED [] -synonym: "up-regulation of transcription, DNA-dependent" EXACT [] -synonym: "upregulation of gene-specific transcription" RELATED [] -synonym: "upregulation of transcription, DNA-dependent" EXACT [] -is_a: GO:0006355 ! regulation of DNA-templated transcription -intersection_of: GO:0065007 ! biological regulation -intersection_of: positively_regulates GO:0006351 ! DNA-templated transcription -relationship: positively_regulates GO:0006351 ! DNA-templated transcription - [Term] id: GO:0045900 name: negative regulation of translational elongation @@ -87519,34 +92648,6 @@ intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0008202 ! steroid metabolic process relationship: positively_regulates GO:0008202 ! steroid metabolic process -[Term] -id: GO:0045944 -name: positive regulation of transcription by RNA polymerase II -namespace: biological_process -alt_id: GO:0010552 -alt_id: GO:0045817 -def: "Any process that activates or increases the frequency, rate or extent of transcription from an RNA polymerase II promoter." [GOC:go_curators, GOC:txnOH] -synonym: "activation of global transcription from RNA polymerase II promoter" RELATED [] -synonym: "activation of transcription from RNA polymerase II promoter" EXACT [] -synonym: "positive regulation of gene-specific transcription from RNA polymerase II promoter" RELATED [] -synonym: "positive regulation of global transcription from Pol II promoter" RELATED [] -synonym: "positive regulation of transcription from Pol II promoter" EXACT [] -synonym: "positive regulation of transcription from RNA polymerase II promoter" EXACT [] -synonym: "positive regulation of transcription from RNA polymerase II promoter, global" RELATED [] -synonym: "stimulation of global transcription from RNA polymerase II promoter" NARROW [] -synonym: "stimulation of transcription from RNA polymerase II promoter" EXACT [] -synonym: "up regulation of global transcription from RNA polymerase II promoter" RELATED [] -synonym: "up regulation of transcription from RNA polymerase II promoter" EXACT [] -synonym: "up-regulation of global transcription from RNA polymerase II promoter" RELATED [] -synonym: "up-regulation of transcription from RNA polymerase II promoter" EXACT [] -synonym: "upregulation of global transcription from RNA polymerase II promoter" RELATED [] -synonym: "upregulation of transcription from RNA polymerase II promoter" EXACT [] -is_a: GO:0006357 ! regulation of transcription by RNA polymerase II -is_a: GO:0045893 ! positive regulation of DNA-templated transcription -intersection_of: GO:0065007 ! biological regulation -intersection_of: positively_regulates GO:0006366 ! transcription by RNA polymerase II -relationship: positively_regulates GO:0006366 ! transcription by RNA polymerase II - [Term] id: GO:0045947 name: negative regulation of translational initiation @@ -87683,9 +92784,7 @@ synonym: "downregulation of ecdysteroid metabolic process" EXACT [] synonym: "inhibition of ecdysteroid metabolic process" NARROW [] synonym: "negative regulation of ecdysteroid metabolism" EXACT [] is_a: GO:0007553 ! regulation of ecdysteroid metabolic process -is_a: GO:0031324 ! negative regulation of cellular metabolic process is_a: GO:0032351 ! negative regulation of hormone metabolic process -is_a: GO:0062014 ! negative regulation of small molecule metabolic process intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0045455 ! ecdysteroid metabolic process relationship: negatively_regulates GO:0045455 ! ecdysteroid metabolic process @@ -87702,9 +92801,7 @@ synonym: "up regulation of ecdysteroid metabolic process" EXACT [] synonym: "up-regulation of ecdysteroid metabolic process" EXACT [] synonym: "upregulation of ecdysteroid metabolic process" EXACT [] is_a: GO:0007553 ! regulation of ecdysteroid metabolic process -is_a: GO:0031325 ! positive regulation of cellular metabolic process is_a: GO:0032352 ! positive regulation of hormone metabolic process -is_a: GO:0062013 ! positive regulation of small molecule metabolic process intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0045455 ! ecdysteroid metabolic process relationship: positively_regulates GO:0045455 ! ecdysteroid metabolic process @@ -87925,6 +93022,7 @@ synonym: "negative regulation of ecdysteroid formation" EXACT [] synonym: "negative regulation of ecdysteroid synthesis" EXACT [] is_a: GO:0007554 ! regulation of ecdysteroid biosynthetic process is_a: GO:0045965 ! negative regulation of ecdysteroid metabolic process +is_a: GO:0062014 ! negative regulation of small molecule metabolic process is_a: GO:0090032 ! negative regulation of steroid hormone biosynthetic process intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0045456 ! ecdysteroid biosynthetic process @@ -87946,6 +93044,7 @@ synonym: "up-regulation of ecdysteroid biosynthetic process" EXACT [] synonym: "upregulation of ecdysteroid biosynthetic process" EXACT [] is_a: GO:0007554 ! regulation of ecdysteroid biosynthetic process is_a: GO:0045966 ! positive regulation of ecdysteroid metabolic process +is_a: GO:0062013 ! positive regulation of small molecule metabolic process is_a: GO:0090031 ! positive regulation of steroid hormone biosynthetic process intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0045456 ! ecdysteroid biosynthetic process @@ -88062,8 +93161,8 @@ synonym: "aldehyde anabolism" EXACT [] synonym: "aldehyde biosynthesis" EXACT [] synonym: "aldehyde formation" EXACT [] synonym: "aldehyde synthesis" EXACT [] -is_a: GO:0006081 ! cellular aldehyde metabolic process -is_a: GO:0044249 ! cellular biosynthetic process +is_a: GO:0006081 ! aldehyde metabolic process +is_a: GO:0009058 ! biosynthetic process intersection_of: GO:0009058 ! biosynthetic process intersection_of: has_primary_output CHEBI:17478 relationship: has_primary_output CHEBI:17478 @@ -88076,8 +93175,8 @@ def: "The chemical reactions and pathways resulting in the breakdown of aldehyde synonym: "aldehyde breakdown" EXACT [] synonym: "aldehyde catabolism" EXACT [] synonym: "aldehyde degradation" EXACT [] -is_a: GO:0006081 ! cellular aldehyde metabolic process -is_a: GO:0044248 ! cellular catabolic process +is_a: GO:0006081 ! aldehyde metabolic process +is_a: GO:0009056 ! catabolic process intersection_of: GO:0009056 ! catabolic process intersection_of: has_primary_input CHEBI:17478 relationship: has_primary_input CHEBI:17478 @@ -88097,6 +93196,32 @@ intersection_of: GO:0009058 ! biosynthetic process intersection_of: has_primary_output CHEBI:33853 relationship: has_primary_output CHEBI:33853 +[Term] +id: GO:0046209 +name: nitric oxide metabolic process +namespace: biological_process +def: "The chemical reactions and pathways involving nitric oxide, nitrogen monoxide (NO), a colorless gas only slightly soluble in water." [GOC:ai] +synonym: "nitric oxide metabolism" EXACT [] +is_a: BFO:0000003 +is_a: GO:0008152 ! metabolic process +intersection_of: GO:0008152 ! metabolic process +intersection_of: has_primary_input_or_output CHEBI:16480 +relationship: has_primary_input_or_output CHEBI:16480 + +[Term] +id: GO:0046210 +name: nitric oxide catabolic process +namespace: biological_process +def: "The chemical reactions and pathways resulting in the breakdown of nitric oxide, nitrogen monoxide (NO), a colorless gas only slightly soluble in water." [GOC:ai] +synonym: "nitric oxide breakdown" EXACT [] +synonym: "nitric oxide catabolism" EXACT [] +synonym: "nitric oxide degradation" EXACT [] +is_a: GO:0009056 ! catabolic process +is_a: GO:0046209 ! nitric oxide metabolic process +intersection_of: GO:0009056 ! catabolic process +intersection_of: has_primary_input CHEBI:16480 +relationship: has_primary_input CHEBI:16480 + [Term] id: GO:0046344 name: ecdysteroid catabolic process @@ -88141,6 +93266,51 @@ intersection_of: GO:0009056 ! catabolic process intersection_of: has_primary_input CHEBI:29067 relationship: has_primary_input CHEBI:29067 +[Term] +id: GO:0046459 +name: short-chain fatty acid metabolic process +namespace: biological_process +def: "The chemical reactions and pathways involving a short-chain fatty acid. A short-chain fatty acid has an aliphatic tail containing fewer than 6 carbons." [Wikipedia:Fatty_acid_metabolism] +comment: While there is not universal consensus on the lengths of short-, medium-, long- and very-long-chain fatty acids, the GO uses the definitions in ChEBI (see CHEBI:26666, CHEBI:59554, CHEBI:15904 and CHEBI:27283). +synonym: "short-chain fatty acid metabolism" EXACT [] +is_a: BFO:0000003 +is_a: GO:0008152 ! metabolic process +intersection_of: GO:0008152 ! metabolic process +intersection_of: has_primary_input_or_output CHEBI:58951 +relationship: has_primary_input_or_output CHEBI:58951 +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/26445" xsd:anyURI + +[Term] +id: GO:0046466 +name: membrane lipid catabolic process +namespace: biological_process +def: "The chemical reactions and pathways resulting in the breakdown of membrane lipids, any lipid found in or associated with a biological membrane." [GOC:ai] +synonym: "membrane lipid breakdown" EXACT [] +synonym: "membrane lipid catabolism" EXACT [] +synonym: "membrane lipid degradation" EXACT [] +synonym: "membrane lipid peroxidation" BROAD [GOC:tb] +is_a: GO:0006643 ! membrane lipid metabolic process +is_a: GO:0016042 ! lipid catabolic process +intersection_of: GO:0009056 ! catabolic process +intersection_of: has_primary_input CHEBI:18059 +intersection_of: occurs_in GO:0016020 ! membrane +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28908" xsd:anyURI + +[Term] +id: GO:0046467 +name: membrane lipid biosynthetic process +namespace: biological_process +def: "The chemical reactions and pathways resulting in the formation of membrane lipids, any lipid found in or associated with a biological membrane." [GOC:ai] +synonym: "membrane lipid anabolism" EXACT [] +synonym: "membrane lipid biosynthesis" EXACT [] +synonym: "membrane lipid formation" EXACT [] +synonym: "membrane lipid synthesis" EXACT [] +is_a: GO:0006643 ! membrane lipid metabolic process +is_a: GO:0008610 ! lipid biosynthetic process +intersection_of: GO:0009058 ! biosynthetic process +intersection_of: has_primary_output CHEBI:18059 +intersection_of: occurs_in GO:0016020 ! membrane + [Term] id: GO:0046479 name: glycosphingolipid catabolic process @@ -88159,7 +93329,6 @@ relationship: has_primary_input CHEBI:24402 id: GO:0046530 name: photoreceptor cell differentiation namespace: biological_process -alt_id: GO:0007467 def: "The specialization of organization of a photoreceptor, a cell that responds to incident electromagnetic radiation, particularly visible light. An example of this process is found in Drosophila melanogaster." [GOC:ai, ISBN:0198506732] is_a: GO:0030182 ! neuron differentiation intersection_of: GO:0030154 ! cell differentiation @@ -88170,7 +93339,6 @@ relationship: results_in_acquisition_of_features_of CL:0000210 ! photoreceptor c id: GO:0046532 name: regulation of photoreceptor cell differentiation namespace: biological_process -alt_id: GO:0045673 def: "Any process that modulates the frequency, rate or extent of photoreceptor cell differentiation. An example of this process is found in Drosophila melanogaster." [GOC:go_curators] synonym: "regulation of photoreceptor differentiation" EXACT [] is_a: GO:0045664 ! regulation of neuron differentiation @@ -88182,7 +93350,6 @@ relationship: regulates GO:0046530 ! photoreceptor cell differentiation id: GO:0046533 name: negative regulation of photoreceptor cell differentiation namespace: biological_process -alt_id: GO:0045674 def: "Any process that stops, prevents, or reduces the frequency, rate or extent of photoreceptor cell differentiation. An example of this process is found in Drosophila melanogaster." [GOC:go_curators] synonym: "down regulation of photoreceptor cell differentiation" EXACT [] synonym: "down regulation of photoreceptor differentiation" EXACT [] @@ -88204,7 +93371,6 @@ relationship: negatively_regulates GO:0046530 ! photoreceptor cell differentiati id: GO:0046534 name: positive regulation of photoreceptor cell differentiation namespace: biological_process -alt_id: GO:0045675 def: "Any process that activates or increases the frequency, rate or extent of photoreceptor cell differentiation. An example of this process is found in Drosophila melanogaster." [GOC:go_curators] synonym: "activation of photoreceptor cell differentiation" NARROW [] synonym: "activation of photoreceptor differentiation" NARROW [] @@ -88860,6 +94026,17 @@ intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0030073 ! insulin secretion relationship: negatively_regulates GO:0030073 ! insulin secretion +[Term] +id: GO:0046697 +name: decidualization +namespace: biological_process +def: "The cellular and vascular changes occurring in the endometrium of the pregnant uterus just after the onset of blastocyst implantation. This process involves the proliferation and differentiation of the fibroblast-like endometrial stromal cells into large, polyploid decidual cells that eventually form the maternal component of the placenta." [ISBN:0721662544, PMID:11133685] +synonym: "decidual cell reaction" EXACT [] +xref: Wikipedia:Decidualization +is_a: GO:0003006 ! developmental process involved in reproduction +is_a: GO:0009888 ! tissue development +relationship: part_of GO:0001893 ! maternal placenta development + [Term] id: GO:0046716 name: muscle cell cellular homeostasis @@ -89225,7 +94402,7 @@ synonym: "regulation of hormone anabolism" EXACT [] synonym: "regulation of hormone biosynthesis" EXACT [] synonym: "regulation of hormone formation" EXACT [] synonym: "regulation of hormone synthesis" EXACT [] -is_a: GO:0031326 ! regulation of cellular biosynthetic process +is_a: GO:0009889 ! regulation of biosynthetic process is_a: GO:0032350 ! regulation of hormone metabolic process intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0042446 ! hormone biosynthetic process @@ -89245,7 +94422,7 @@ synonym: "stimulation of hormone biosynthetic process" NARROW [] synonym: "up regulation of hormone biosynthetic process" EXACT [] synonym: "up-regulation of hormone biosynthetic process" EXACT [] synonym: "upregulation of hormone biosynthetic process" EXACT [] -is_a: GO:0031328 ! positive regulation of cellular biosynthetic process +is_a: GO:0009891 ! positive regulation of biosynthetic process is_a: GO:0032352 ! positive regulation of hormone metabolic process is_a: GO:0046885 ! regulation of hormone biosynthetic process intersection_of: GO:0065007 ! biological regulation @@ -89337,7 +94514,6 @@ is_a: GO:0006810 ! transport id: GO:0046907 name: intracellular transport namespace: biological_process -alt_id: GO:1902582 def: "The directed movement of substances within a cell." [GOC:ai] synonym: "single organism intracellular transport" RELATED [GOC:TermGenie] synonym: "single-organism intracellular transport" RELATED [] @@ -89347,7 +94523,6 @@ is_a: GO:0051649 ! establishment of localization in cell intersection_of: GO:0006810 ! transport intersection_of: occurs_in GO:0005622 ! intracellular anatomical structure relationship: occurs_in GO:0005622 ! intracellular anatomical structure -created_by: jl creation_date: 2013-12-18T14:04:50Z [Term] @@ -89532,7 +94707,6 @@ relationship: has_primary_input CL:0000723 ! somatic stem cell id: GO:0048132 name: female germ-line stem cell asymmetric division namespace: biological_process -alt_id: GO:0048141 def: "The self-renewing division of a germline stem cell in the female gonad, to produce a daughter stem cell and a daughter germ cell, which will divide to form the female gametes." [GOC:jid, GOC:mtg_sensu] synonym: "female germ-line stem cell renewal" EXACT [] is_a: GO:0098728 ! germline stem cell asymmetric division @@ -90151,8 +95325,6 @@ property_value: term_tracker_item "https://github.com/geneontology/go-ontology/i id: GO:0048477 name: oogenesis namespace: biological_process -alt_id: GO:0009993 -alt_id: GO:0048157 def: "The complete process of formation and maturation of an ovum or female gamete from a primordial female germ cell. Examples of this process are found in Mus musculus and Drosophila melanogaster." [GOC:kmv, GOC:mtg_sensu, GOC:pr] synonym: "ovum development" EXACT systematic_synonym [] xref: Wikipedia:Oogenesis @@ -90268,7 +95440,6 @@ relationship: results_in_acquisition_of_features_of CL:0000018 ! spermatid id: GO:0048518 name: positive regulation of biological process namespace: biological_process -alt_id: GO:0043119 def: "Any process that activates or increases the frequency, rate or extent of a biological process. Biological processes are regulated by many means; examples include the control of gene expression, protein modification or interaction with a protein or substrate molecule." [GOC:jid] subset: gocheck_do_not_annotate synonym: "activation of biological process" NARROW [] @@ -90286,7 +95457,6 @@ relationship: positively_regulates GO:0008150 ! biological_process id: GO:0048519 name: negative regulation of biological process namespace: biological_process -alt_id: GO:0043118 def: "Any process that stops, prevents, or reduces the frequency, rate or extent of a biological process. Biological processes are regulated by many means; examples include the control of gene expression, protein modification or interaction with a protein or substrate molecule." [GOC:jid] subset: gocheck_do_not_annotate synonym: "down regulation of biological process" EXACT [] @@ -90334,7 +95504,6 @@ relationship: negatively_regulates GO:0007610 ! behavior id: GO:0048522 name: positive regulation of cellular process namespace: biological_process -alt_id: GO:0051242 def: "Any process that activates or increases the frequency, rate or extent of a cellular process, any of those that are carried out at the cellular level, but are not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level." [GOC:jid] subset: gocheck_do_not_annotate synonym: "activation of cellular process" NARROW [] @@ -90353,7 +95522,6 @@ relationship: positively_regulates GO:0009987 ! cellular process id: GO:0048523 name: negative regulation of cellular process namespace: biological_process -alt_id: GO:0051243 def: "Any process that stops, prevents, or reduces the frequency, rate or extent of a cellular process, any of those that are carried out at the cellular level, but are not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level." [GOC:jid] subset: gocheck_do_not_annotate synonym: "down regulation of cellular process" EXACT [] @@ -90484,7 +95652,6 @@ relationship: has_primary_input CHEBI:26764 id: GO:0048546 name: digestive tract morphogenesis namespace: biological_process -alt_id: GO:0048547 def: "The process in which the anatomical structures of the digestive tract are generated and organized. The digestive tract is the anatomical structure through which food passes and is processed." [GOC:dph, GOC:go_curators, PMID:12618131] synonym: "alimentary canal morphogenesis" EXACT [] synonym: "digestive tube morphogenesis" EXACT [] @@ -90660,7 +95827,6 @@ relationship: part_of GO:0032502 ! developmental process id: GO:0048592 name: eye morphogenesis namespace: biological_process -alt_id: GO:0048748 def: "The process in which the anatomical structures of the eye are generated and organized." [GOC:jid, GOC:mtg_sensu] is_a: GO:0090596 ! sensory organ morphogenesis intersection_of: GO:0009653 ! anatomical structure morphogenesis @@ -90672,8 +95838,6 @@ relationship: results_in_morphogenesis_of UBERON:0000970 ! eye id: GO:0048593 name: camera-type eye morphogenesis namespace: biological_process -alt_id: GO:0048594 -alt_id: GO:0048595 def: "The process in which the anatomical structures of the eye are generated and organized. The camera-type eye is an organ of sight that receives light through an aperture and focuses it through a lens, projecting it on a photoreceptor field." [GOC:jid, GOC:mtg_sensu] synonym: "camera-style eye morphogenesis" EXACT [GOC:dph] is_a: GO:0048592 ! eye morphogenesis @@ -90696,7 +95860,6 @@ relationship: part_of GO:0048593 ! camera-type eye morphogenesis id: GO:0048598 name: embryonic morphogenesis namespace: biological_process -alt_id: GO:0048828 def: "The process in which anatomical structures are generated and organized during the embryonic phase. The embryonic phase begins with zygote formation. The end of the embryonic phase is organism-specific. For example, it would be at birth for mammals, larval hatching for insects and seed dormancy in plants." [GOC:jid, GOC:mtg_sensu] synonym: "embryonic anatomical structure morphogenesis" EXACT [GOC:dph, GOC:tb] is_a: GO:0009653 ! anatomical structure morphogenesis @@ -91369,7 +96532,6 @@ relationship: results_in_development_of UBERON:0001135 ! smooth muscle tissue id: GO:0048749 name: compound eye development namespace: biological_process -alt_id: GO:0007456 def: "The process whose specific outcome is the progression of the compound eye over time, from its formation to the mature structure. The compound eye is an organ of sight that contains multiple repeating units, often arranged hexagonally. Each unit has its own lens and photoreceptor cell(s) and can generate either a single pixelated image or multiple images, per eye." [GOC:jid, GOC:mtg_sensu, Wikipedia:Eye] synonym: "insect-type retina development" EXACT [PMID:11735386] is_a: GO:0001654 ! eye development @@ -92324,7 +97486,6 @@ relationship: results_in_development_of UBERON:2001391 ! anterior lateral line g id: GO:0048909 name: anterior lateral line nerve development namespace: biological_process -alt_id: GO:0021734 def: "The process whose specific outcome is the progression of the anterior lateral line nerve over time, form its formation to the mature structure. The anterior lateral line nerve contains efferent axons that innervate hair cells of the ALL and afferent axons that project to an octavolateralis column in the hindbrain. The octavolateralis column consists of the medial octavolateralis nucleus (MON), the caudal octavolateralis nucleus, and the magnocellular nucleus." [GO_REF:0000021, GOC:cls, GOC:dgh, GOC:dph, GOC:jid, ISBN:0125296509] synonym: "ALLN development" EXACT [] synonym: "nALL development" EXACT [] @@ -92386,7 +97547,6 @@ relationship: results_in_development_of UBERON:2001314 ! posterior lateral line id: GO:0048918 name: posterior lateral line nerve development namespace: biological_process -alt_id: GO:0021733 def: "The process whose specific outcome is the progression of the posterior lateral line nerve over time, from its formation to the mature structure. The posterior lateral line nerve innervates hair cells of the PLL and projects to an octavolateralis column in the hindbrain that consists of the medial octavolateralis nucleus (MON), the caudal octavolateralis nucleus, and the magnocellular nucleus." [GO_REF:0000021, GOC:cls, GOC:dgh, GOC:dph, GOC:jid, ISBN:0125296509] synonym: "caudal lateral line nerve development" EXACT [] synonym: "PLLN development" EXACT [] @@ -92571,29 +97731,6 @@ intersection_of: GO:0051179 ! localization intersection_of: has_primary_input GO:0005694 ! chromosome relationship: has_primary_input GO:0005694 ! chromosome -[Term] -id: GO:0050369 -name: [tyrosine 3-monooxygenase] kinase activity -namespace: molecular_function -def: "Catalysis of the reaction: ATP + [tyrosine-3-monooxygenase] = ADP + phospho-[tyrosine-3-monooxygenase]." [EC:2.7.11.6, MetaCyc:TYROSINE-3-MONOOXYGENASE-KINASE-RXN] -synonym: "ATP:tyrosine-3-monoxygenase phosphotransferase activity" RELATED [EC:2.7.11.6] -synonym: "pheochromocytoma tyrosine hydroxylase-associated kinase activity" RELATED [EC:2.7.11.6] -synonym: "STK4" RELATED [EC:2.7.11.6] -synonym: "tyrosine 3-monooxygenase kinase (phosphorylating) activity" RELATED [EC:2.7.11.6] -synonym: "tyrosine 3-monooxygenase kinase activity" EXACT [] -xref: EC:2.7.11.6 -xref: MetaCyc:2.7.11.6-RXN -xref: RHEA:17133 -is_a: GO:0004672 ! protein kinase activity -intersection_of: GO:0016301 ! kinase activity -intersection_of: has_primary_input PR:000016301 ! tyrosine 3-monooxygenase -relationship: has_participant CHEBI:15378 -relationship: has_participant CHEBI:29999 -relationship: has_participant CHEBI:30616 -relationship: has_participant CHEBI:456216 -relationship: has_participant CHEBI:83421 -relationship: has_primary_input PR:000016301 ! tyrosine 3-monooxygenase - [Term] id: GO:0050432 name: catecholamine secretion @@ -92868,7 +98005,6 @@ relationship: regulates GO:0006954 ! inflammatory response id: GO:0050728 name: negative regulation of inflammatory response namespace: biological_process -alt_id: GO:0030236 def: "Any process that stops, prevents, or reduces the frequency, rate or extent of the inflammatory response." [GOC:ai] synonym: "anti-inflammatory response" EXACT [] synonym: "down regulation of inflammatory response" EXACT [] @@ -92916,6 +98052,7 @@ id: GO:0050731 name: positive regulation of peptidyl-tyrosine phosphorylation namespace: biological_process def: "Any process that activates or increases the frequency, rate or extent of the phosphorylation of peptidyl-tyrosine." [GOC:ai] +subset: gocheck_obsoletion_candidate synonym: "activation of peptidyl-tyrosine phosphorylation" NARROW [] synonym: "stimulation of peptidyl-tyrosine phosphorylation" NARROW [] synonym: "up regulation of peptidyl-tyrosine phosphorylation" EXACT [] @@ -92950,7 +98087,7 @@ name: regulation of lipoprotein metabolic process namespace: biological_process def: "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving lipoproteins, any conjugated, water-soluble protein in which the nonprotein group consists of a lipid or lipids." [GOC:ai] synonym: "regulation of lipoprotein metabolism" EXACT [] -is_a: GO:0031323 ! regulation of cellular metabolic process +is_a: GO:0019222 ! regulation of metabolic process intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0042157 ! lipoprotein metabolic process relationship: regulates GO:0042157 ! lipoprotein metabolic process @@ -92966,7 +98103,7 @@ synonym: "stimulation of lipoprotein metabolic process" NARROW [] synonym: "up regulation of lipoprotein metabolic process" EXACT [] synonym: "up-regulation of lipoprotein metabolic process" EXACT [] synonym: "upregulation of lipoprotein metabolic process" EXACT [] -is_a: GO:0031328 ! positive regulation of cellular biosynthetic process +is_a: GO:0009891 ! positive regulation of biosynthetic process is_a: GO:0050746 ! regulation of lipoprotein metabolic process intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0042157 ! lipoprotein metabolic process @@ -92982,7 +98119,7 @@ synonym: "down-regulation of lipoprotein metabolic process" EXACT [] synonym: "downregulation of lipoprotein metabolic process" EXACT [] synonym: "inhibition of lipoprotein metabolic process" NARROW [] synonym: "negative regulation of lipoprotein metabolism" EXACT [] -is_a: GO:0031324 ! negative regulation of cellular metabolic process +is_a: GO:0009892 ! negative regulation of metabolic process is_a: GO:0050746 ! regulation of lipoprotein metabolic process intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0042157 ! lipoprotein metabolic process @@ -93210,7 +98347,6 @@ relationship: positively_regulates GO:0006955 ! immune response id: GO:0050789 name: regulation of biological process namespace: biological_process -alt_id: GO:0050791 def: "Any process that modulates the frequency, rate or extent of a biological process. Biological processes are regulated by many means; examples include the control of gene expression, protein modification or interaction with a protein or substrate molecule." [GOC:ai, GOC:go_curators] subset: gocheck_do_not_annotate subset: goslim_candida @@ -93226,7 +98362,6 @@ relationship: regulates GO:0008150 ! biological_process id: GO:0050790 name: regulation of catalytic activity namespace: biological_process -alt_id: GO:0048552 def: "Any process that modulates the activity of an enzyme." [GOC:ai, GOC:ebc, GOC:vw] subset: gocheck_obsoletion_candidate subset: goslim_chembl @@ -93251,7 +98386,6 @@ relationship: regulates GO:0032502 ! developmental process id: GO:0050794 name: regulation of cellular process namespace: biological_process -alt_id: GO:0051244 def: "Any process that modulates the frequency, rate or extent of a cellular process, any of those that are carried out at the cellular level, but are not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level." [GOC:go_curators] subset: gocheck_do_not_annotate synonym: "regulation of cellular physiological process" EXACT [] @@ -93286,7 +98420,6 @@ relationship: regulates GO:0030073 ! insulin secretion id: GO:0050801 name: monoatomic ion homeostasis namespace: biological_process -alt_id: GO:2000021 def: "Any process involved in the maintenance of an internal steady state of monoatomic ions within an organism or cell. Monatomic ions (also called simple ions) are ions consisting of exactly one atom." [GOC:ai] synonym: "electrolyte homeostasis" RELATED [] synonym: "ion homeostasis" BROAD [] @@ -93473,9 +98606,6 @@ relationship: has_primary_input CHEBI:15377 id: GO:0050832 name: defense response to fungus namespace: biological_process -alt_id: GO:0009623 -alt_id: GO:0009817 -alt_id: GO:0042831 def: "Reactions triggered in response to the presence of a fungus that act to protect the cell or organism." [GOC:ai] synonym: "defence response to fungi" EXACT [] synonym: "defence response to fungus" EXACT [] @@ -93834,11 +98964,18 @@ intersection_of: regulates_levels_of CHEBI:15377 relationship: regulates_levels_of CHEBI:15377 property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/24554" xsd:anyURI +[Term] +id: GO:0050893 +name: sensory processing +namespace: biological_process +def: "Any neural process required for an organism to sense and interpret the dimensions of a sensory experience: modality, location, intensity and affect." [GOC:dph, ISBN:0721662544] +is_a: GO:0050890 ! cognition +relationship: part_of GO:0007600 ! sensory perception + [Term] id: GO:0050896 name: response to stimulus namespace: biological_process -alt_id: GO:0051869 def: "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus. The process begins with detection of the stimulus and ends with a change in state or activity or the cell or organism." [GOC:ai, GOC:bf] comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. subset: gocheck_do_not_annotate @@ -93944,8 +99081,6 @@ is_a: GO:0007606 ! sensory perception of chemical stimulus id: GO:0050910 name: detection of mechanical stimulus involved in sensory perception of sound namespace: biological_process -alt_id: GO:0009592 -alt_id: GO:0055128 def: "The series of events involved in the perception of sound vibration in which the vibration is received and converted into a molecular signal." [GOC:ai] synonym: "detection of sound" EXACT [] synonym: "hearing, sensory transduction of sound" EXACT [] @@ -94046,8 +99181,6 @@ relationship: negatively_regulates GO:0006935 ! chemotaxis id: GO:0050931 name: pigment cell differentiation namespace: biological_process -alt_id: GO:0043357 -alt_id: GO:0043358 def: "The process in which a relatively unspecialized cell acquires the specialized features of a pigmented cell, such as a melanocyte." [GOC:dgh] comment: Note that the chromatophore mentioned here is distinct from the pigment bearing structure found in certain photosynthetic bacteria and cyanobacteria. It is also different from the plant chromoplast, which is also sometimes called a chromatophore. synonym: "chromatophore differentiation" EXACT [] @@ -94566,7 +99699,6 @@ relationship: positively_regulates GO:0016042 ! lipid catabolic process id: GO:0051017 name: actin filament bundle assembly namespace: biological_process -alt_id: GO:0045011 def: "The assembly of actin filament bundles; actin filaments are on the same axis but may be oriented with the same or opposite polarities and may be packed with different levels of tightness." [GOC:ai] synonym: "actin bundling activity" RELATED [] synonym: "actin cable assembly" RELATED [GOC:mah] @@ -94824,49 +99956,6 @@ intersection_of: GO:0022411 ! cellular component disassembly intersection_of: results_in_disassembly_of GO:0031965 ! nuclear membrane relationship: results_in_disassembly_of GO:0031965 ! nuclear membrane -[Term] -id: GO:0051090 -name: regulation of DNA-binding transcription factor activity -namespace: biological_process -alt_id: GO:1904167 -alt_id: GO:2000823 -def: "Any process that modulates the frequency, rate or extent of the activity of a transcription factor, any factor involved in the initiation or regulation of transcription." [GOC:ai] -subset: gocheck_obsoletion_candidate -synonym: "regulation of androgen receptor activity" NARROW [] -synonym: "regulation of DNA binding transcription factor activity" EXACT [] -synonym: "regulation of sequence-specific DNA binding transcription factor activity" EXACT [] -synonym: "regulation of thyroid hormone receptor activity" NARROW [] -synonym: "regulation of transcription factor activity" BROAD [GOC:dph, GOC:tb] -is_a: GO:0006355 ! regulation of DNA-templated transcription -is_a: GO:0065009 ! regulation of molecular function -intersection_of: GO:0065007 ! biological regulation -intersection_of: regulates GO:0003700 ! DNA-binding transcription factor activity -relationship: regulates GO:0003700 ! DNA-binding transcription factor activity - -[Term] -id: GO:0051091 -name: positive regulation of DNA-binding transcription factor activity -namespace: biological_process -alt_id: GO:1904169 -def: "Any process that activates or increases the frequency, rate or extent of activity of a transcription factor, any factor involved in the initiation or regulation of transcription." [GOC:ai] -subset: gocheck_obsoletion_candidate -synonym: "activation of transcription factor activity" NARROW [] -synonym: "positive regulation of DNA binding transcription factor activity" EXACT [] -synonym: "positive regulation of sequence-specific DNA binding transcription factor activity" EXACT [] -synonym: "positive regulation of thyroid hormone receptor activity" NARROW [] -synonym: "positive regulation of transcription factor activity" BROAD [GOC:dph, GOC:tb] -synonym: "stimulation of transcription factor activity" NARROW [] -synonym: "up regulation of transcription factor activity" EXACT [] -synonym: "up-regulation of transcription factor activity" EXACT [] -synonym: "upregulation of transcription factor activity" EXACT [] -is_a: GO:0044093 ! positive regulation of molecular function -is_a: GO:0051090 ! regulation of DNA-binding transcription factor activity -intersection_of: GO:0065007 ! biological regulation -intersection_of: positively_regulates GO:0003700 ! DNA-binding transcription factor activity -relationship: positively_regulates GO:0003700 ! DNA-binding transcription factor activity -created_by: rph -creation_date: 2015-04-22T12:22:16Z - [Term] id: GO:0051093 name: negative regulation of developmental process @@ -95394,7 +100483,6 @@ relationship: results_in_transport_to_from_or_in GO:0005634 ! nucleus id: GO:0051170 name: import into nucleus namespace: biological_process -alt_id: GO:1902593 def: "The directed movement of substances into the nucleus." [GOC:ai] synonym: "nuclear import" EXACT [] synonym: "nuclear translocation" EXACT [] @@ -95405,14 +100493,12 @@ intersection_of: has_target_start_location GO:0005829 ! cytosol intersection_of: results_in_transport_across GO:0005635 ! nuclear envelope relationship: has_target_end_location GO:0031981 ! nuclear lumen relationship: has_target_start_location GO:0005829 ! cytosol -created_by: jl creation_date: 2013-12-19T15:26:34Z [Term] id: GO:0051179 name: localization namespace: biological_process -alt_id: GO:1902578 def: "Any process in which a cell, a substance, or a cellular entity, such as a protein complex or organelle, is transported, tethered to or otherwise maintained in a specific location. In the case of substances, localization may also be achieved via selective degradation." [GOC:ai, GOC:dos] subset: gocheck_do_not_annotate subset: goslim_pir @@ -95426,7 +100512,6 @@ synonym: "single organism localization" RELATED [GOC:TermGenie] synonym: "single-organism localization" RELATED [] is_a: GO:0008150 ! biological_process property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27052" xsd:anyURI -created_by: jl creation_date: 2013-12-18T13:51:04Z [Term] @@ -95619,7 +100704,6 @@ relationship: negatively_regulates GO:0032501 ! multicellular organismal process id: GO:0051246 name: regulation of protein metabolic process namespace: biological_process -alt_id: GO:0032268 def: "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving a protein." [GOC:ai] synonym: "regulation of cellular protein metabolic process" RELATED [] synonym: "regulation of cellular protein metabolism" RELATED [] @@ -95634,7 +100718,6 @@ property_value: term_tracker_item "https://github.com/geneontology/go-ontology/i id: GO:0051247 name: positive regulation of protein metabolic process namespace: biological_process -alt_id: GO:0032270 def: "Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving a protein." [GOC:ai] synonym: "activation of cellular protein metabolic process" NARROW [] synonym: "activation of protein metabolic process" NARROW [] @@ -95660,7 +100743,6 @@ property_value: term_tracker_item "https://github.com/geneontology/go-ontology/i id: GO:0051248 name: negative regulation of protein metabolic process namespace: biological_process -alt_id: GO:0032269 def: "Any process that stops, prevents, or reduces the frequency, rate or extent of chemical reactions and pathways involving a protein." [GOC:ai] synonym: "down regulation of cellular protein metabolic process" EXACT [] synonym: "down regulation of protein metabolic process" EXACT [] @@ -95792,9 +100874,6 @@ is_a: GO:0032984 ! protein-containing complex disassembly id: GO:0051276 name: chromosome organization namespace: biological_process -alt_id: GO:0006323 -alt_id: GO:0007001 -alt_id: GO:0051277 def: "A process that is carried out at the cellular level that results in the assembly, arrangement of constituent parts, or disassembly of chromosomes, structures composed of a very long molecule of DNA and associated proteins that carries hereditary information. This term covers covalent modifications at the molecular level as well as spatial relationships among the major components of a chromosome." [GOC:ai, GOC:dph, GOC:jl, GOC:mah] subset: goslim_chembl subset: goslim_drosophila @@ -95990,7 +101069,6 @@ intersection_of: has_primary_input GO:0005694 ! chromosome id: GO:0051321 name: meiotic cell cycle namespace: biological_process -alt_id: GO:0007126 def: "Progression through the phases of the meiotic cell cycle, in which canonically a cell replicates to produce four offspring with half the chromosomal content of the progenitor cell via two nuclear divisions." [GOC:ai] comment: Note that this term should not be confused with 'GO:0140013 ; meiotic nuclear division'. 'GO:0051321 ; meiotic cell cycle represents the entire mitotic cell cycle, while 'GO:0140013 meiotic nuclear division' specifically represents the actual nuclear division step of the mitotic cell cycle. subset: goslim_drosophila @@ -96236,6 +101314,20 @@ intersection_of: has_primary_input CHEBI:51143 relationship: has_primary_input CHEBI:51143 relationship: part_of GO:1901698 ! response to nitrogen compound +[Term] +id: GO:0051418 +name: microtubule nucleation by microtubule organizing center +namespace: biological_process +def: "The 'de novo' formation of a microtubule, mediated by the microtubule organizing center." [GOC:ai] +synonym: "microtubule nucleation by microtubule organising centre" EXACT [] +synonym: "microtubule nucleation by MTOC" EXACT [] +synonym: "microtubule organizing center-mediated microtubule nucleation" EXACT [] +synonym: "MTOC-mediated microtubule nucleation" EXACT [] +is_a: GO:0007020 ! microtubule nucleation +intersection_of: GO:0007020 ! microtubule nucleation +intersection_of: process_has_causal_agent GO:0005815 ! microtubule organizing center +relationship: process_has_causal_agent GO:0005815 ! microtubule organizing center + [Term] id: GO:0051445 name: regulation of meiotic cell cycle @@ -96419,7 +101511,6 @@ relationship: positively_regulates GO:0051458 ! corticotropin secretion id: GO:0051469 name: vesicle fusion with vacuole namespace: biological_process -alt_id: GO:0042146 def: "The joining of the lipid bilayer membrane around a vesicle with the lipid bilayer membrane around the vacuole." [GOC:ai] synonym: "heterotypic vacuole fusion (non-autophagic)" RELATED [] synonym: "heterotypic vacuole fusion, non-autophagic" RELATED [] @@ -96894,7 +101985,6 @@ property_value: term_tracker_item "https://github.com/geneontology/go-ontology/i id: GO:0051641 name: cellular localization namespace: biological_process -alt_id: GO:1902580 def: "A cellular localization process whereby a substance or cellular entity, such as a protein complex or organelle, is transported to, and/or maintained in, a specific location within a cell including the localization of substances or cellular entities to the cell membrane." [GOC:tb, GOC:vw] comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. subset: gocheck_do_not_annotate @@ -96909,7 +101999,6 @@ synonym: "single-organism cellular localization" RELATED [] is_a: GO:0009987 ! cellular process is_a: GO:0051179 ! localization property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27189" xsd:anyURI -created_by: jl creation_date: 2013-12-18T14:04:32Z [Term] @@ -97126,8 +102215,6 @@ intersection_of: has_primary_input GO:0005794 ! Golgi apparatus id: GO:0051707 name: response to other organism namespace: biological_process -alt_id: GO:0009613 -alt_id: GO:0042828 def: "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus from another living organism." [GOC:ai] is_a: GO:0043207 ! response to external biotic stimulus is_a: GO:0044419 ! biological process involved in interspecies interaction between organisms @@ -97146,12 +102233,6 @@ is_a: GO:0050896 ! response to stimulus id: GO:0051726 name: regulation of cell cycle namespace: biological_process -alt_id: GO:0000074 -alt_id: GO:0007050 -alt_id: GO:0071156 -alt_id: GO:0071157 -alt_id: GO:0071158 -alt_id: GO:0071850 def: "Any process that modulates the rate or extent of progression through the cell cycle." [GOC:ai, GOC:dph, GOC:tb] subset: goslim_yeast synonym: "arrest of mitotic cell cycle progression" NARROW [GOC:mah] @@ -97173,122 +102254,6 @@ intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0007049 ! cell cycle relationship: regulates GO:0007049 ! cell cycle -[Term] -id: GO:0051767 -name: nitric-oxide synthase biosynthetic process -namespace: biological_process -alt_id: GO:0051768 -def: "The chemical reactions and pathways resulting in the formation of a nitric-oxide synthase, an enzyme which catalyzes the reaction L-arginine + n NADPH + n H+ + m O2 = citrulline + nitric oxide + n NADP+." [GOC:ai] -synonym: "brain nitric-oxide synthase biosynthetic process" NARROW [GOC:bf] -synonym: "endothelial nitric-oxide synthase biosynthetic process" NARROW [GOC:bf] -synonym: "inducible nitric-oxide synthase biosynthetic process" NARROW [GOC:bf] -synonym: "nitric-oxide synthase (type 2) biosynthesis" NARROW [] -synonym: "nitric-oxide synthase (type 2) biosynthetic process" NARROW [] -synonym: "nitric-oxide synthase (type II) biosynthesis" NARROW [] -synonym: "nitric-oxide synthase (type II) biosynthetic process" NARROW [] -synonym: "nitric-oxide synthase 2 biosynthetic process" NARROW [] -synonym: "nitric-oxide synthase-1 biosynthetic process" NARROW [GOC:bf] -synonym: "nitric-oxide synthase-2 biosynthetic process" NARROW [GOC:bf] -synonym: "nitric-oxide synthase-3 biosynthetic process" NARROW [GOC:bf] -synonym: "NO synthase biosynthesis" EXACT [] -synonym: "NO synthase biosynthetic process" EXACT [] -synonym: "NOS biosynthesis" EXACT [] -synonym: "NOS biosynthetic process" EXACT [] -synonym: "NOS1 biosynthesis" NARROW [GOC:bf] -synonym: "NOS2 biosynthesis" NARROW [GOC:bf] -synonym: "NOS2 synthase biosynthesis" NARROW [] -synonym: "NOS2 synthase biosynthetic process" NARROW [] -synonym: "NOS3 biosynthesis" NARROW [GOC:bf] -is_a: GO:0009059 ! macromolecule biosynthetic process -property_value: RO:0002161 NCBITaxon:4751 -property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28860" xsd:anyURI - -[Term] -id: GO:0051769 -name: regulation of nitric-oxide synthase biosynthetic process -namespace: biological_process -alt_id: GO:0051772 -def: "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of a nitric-oxide synthase enzyme." [GOC:ai] -synonym: "regulation of nitric-oxide synthase (type 2) biosynthesis" NARROW [] -synonym: "regulation of nitric-oxide synthase (type 2) biosynthetic process" NARROW [] -synonym: "regulation of nitric-oxide synthase (type II) biosynthesis" NARROW [] -synonym: "regulation of nitric-oxide synthase (type II) biosynthetic process" NARROW [] -synonym: "regulation of nitric-oxide synthase 2 biosynthetic process" NARROW [] -synonym: "regulation of NO synthase biosynthesis" EXACT [] -synonym: "regulation of NO synthase biosynthetic process" EXACT [] -synonym: "regulation of NOS biosynthesis" EXACT [] -synonym: "regulation of NOS biosynthetic process" EXACT [] -synonym: "regulation of NOS2 synthase biosynthesis" NARROW [] -synonym: "regulation of NOS2 synthase biosynthetic process" NARROW [] -is_a: GO:0010556 ! regulation of macromolecule biosynthetic process -intersection_of: GO:0065007 ! biological regulation -intersection_of: regulates GO:0051767 ! nitric-oxide synthase biosynthetic process -relationship: regulates GO:0051767 ! nitric-oxide synthase biosynthetic process - -[Term] -id: GO:0051770 -name: positive regulation of nitric-oxide synthase biosynthetic process -namespace: biological_process -alt_id: GO:0051773 -def: "Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of a nitric oxide synthase enzyme." [GOC:ai] -synonym: "activation of nitric-oxide synthase 2 biosynthetic process" NARROW [] -synonym: "activation of nitric-oxide synthase biosynthetic process" NARROW [] -synonym: "positive regulation of nitric-oxide synthase (type 2) biosynthesis" NARROW [] -synonym: "positive regulation of nitric-oxide synthase (type 2) biosynthetic process" NARROW [] -synonym: "positive regulation of nitric-oxide synthase (type II) biosynthesis" NARROW [] -synonym: "positive regulation of nitric-oxide synthase (type II) biosynthetic process" NARROW [] -synonym: "positive regulation of nitric-oxide synthase 2 biosynthetic process" NARROW [] -synonym: "positive regulation of NO synthase biosynthesis" EXACT [] -synonym: "positive regulation of NO synthase biosynthetic process" EXACT [] -synonym: "positive regulation of NOS biosynthesis" EXACT [] -synonym: "positive regulation of NOS biosynthetic process" EXACT [] -synonym: "positive regulation of NOS2 synthase biosynthesis" NARROW [] -synonym: "positive regulation of NOS2 synthase biosynthetic process" NARROW [] -synonym: "stimulation of nitric-oxide synthase 2 biosynthetic process" NARROW [] -synonym: "stimulation of nitric-oxide synthase biosynthetic process" NARROW [] -synonym: "up regulation of nitric-oxide synthase 2 biosynthetic process" NARROW [] -synonym: "up regulation of nitric-oxide synthase biosynthetic process" EXACT [] -synonym: "up-regulation of nitric-oxide synthase 2 biosynthetic process" NARROW [] -synonym: "up-regulation of nitric-oxide synthase biosynthetic process" EXACT [] -synonym: "upregulation of nitric-oxide synthase 2 biosynthetic process" NARROW [] -synonym: "upregulation of nitric-oxide synthase biosynthetic process" EXACT [] -is_a: GO:0010557 ! positive regulation of macromolecule biosynthetic process -is_a: GO:0051769 ! regulation of nitric-oxide synthase biosynthetic process -intersection_of: GO:0065007 ! biological regulation -intersection_of: positively_regulates GO:0051767 ! nitric-oxide synthase biosynthetic process -relationship: positively_regulates GO:0051767 ! nitric-oxide synthase biosynthetic process - -[Term] -id: GO:0051771 -name: negative regulation of nitric-oxide synthase biosynthetic process -namespace: biological_process -alt_id: GO:0051774 -def: "Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of a nitric-oxide synthase enzyme." [GOC:ai] -synonym: "down regulation of nitric-oxide synthase 2 biosynthetic process" NARROW [] -synonym: "down regulation of nitric-oxide synthase biosynthetic process" EXACT [] -synonym: "down-regulation of nitric-oxide synthase 2 biosynthetic process" NARROW [] -synonym: "down-regulation of nitric-oxide synthase biosynthetic process" EXACT [] -synonym: "downregulation of nitric-oxide synthase 2 biosynthetic process" NARROW [] -synonym: "downregulation of nitric-oxide synthase biosynthetic process" EXACT [] -synonym: "inhibition of nitric-oxide synthase 2 biosynthetic process" NARROW [] -synonym: "inhibition of nitric-oxide synthase biosynthetic process" NARROW [] -synonym: "negative regulation of nitric-oxide synthase (type 2) biosynthesis" NARROW [] -synonym: "negative regulation of nitric-oxide synthase (type 2) biosynthetic process" NARROW [] -synonym: "negative regulation of nitric-oxide synthase (type II) biosynthesis" NARROW [] -synonym: "negative regulation of nitric-oxide synthase (type II) biosynthetic process" NARROW [] -synonym: "negative regulation of nitric-oxide synthase 2 biosynthetic process" NARROW [] -synonym: "negative regulation of NO synthase biosynthesis" EXACT [] -synonym: "negative regulation of NO synthase biosynthetic process" EXACT [] -synonym: "negative regulation of NOS biosynthesis" EXACT [] -synonym: "negative regulation of NOS biosynthetic process" EXACT [] -synonym: "negative regulation of NOS2 synthase biosynthesis" NARROW [] -synonym: "negative regulation of NOS2 synthase biosynthetic process" NARROW [] -is_a: GO:0010558 ! negative regulation of macromolecule biosynthetic process -is_a: GO:0051769 ! regulation of nitric-oxide synthase biosynthetic process -intersection_of: GO:0065007 ! biological regulation -intersection_of: negatively_regulates GO:0051767 ! nitric-oxide synthase biosynthetic process -relationship: negatively_regulates GO:0051767 ! nitric-oxide synthase biosynthetic process - [Term] id: GO:0051781 name: positive regulation of cell division @@ -97361,6 +102326,25 @@ intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0000280 ! nuclear division relationship: positively_regulates GO:0000280 ! nuclear division +[Term] +id: GO:0051790 +name: short-chain fatty acid biosynthetic process +namespace: biological_process +def: "The chemical reactions and pathways resulting in the formation of a short-chain fatty acid. A short-chain fatty acid has an aliphatic tail containing fewer than 6 carbons." [Wikipedia:Fatty_acid_metabolism] +comment: While there is not universal consensus on the lengths of short-, medium-, long- and very-long-chain fatty acids, the GO uses the definitions in ChEBI (see CHEBI:26666, CHEBI:59554, CHEBI:15904 and CHEBI:27283). +synonym: "short chain fatty acid biosynthesis" EXACT [] +synonym: "short chain fatty acid biosynthetic process" EXACT [] +synonym: "short-chain fatty acid anabolism" EXACT [] +synonym: "short-chain fatty acid biosynthesis" EXACT [] +synonym: "short-chain fatty acid formation" EXACT [] +synonym: "short-chain fatty acid synthesis" EXACT [] +is_a: GO:0009058 ! biosynthetic process +is_a: GO:0046459 ! short-chain fatty acid metabolic process +intersection_of: GO:0009058 ! biosynthetic process +intersection_of: has_primary_output CHEBI:58951 +relationship: has_primary_output CHEBI:58951 +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/26445" xsd:anyURI + [Term] id: GO:0051797 name: regulation of hair follicle development @@ -97556,6 +102540,9 @@ synonym: "synaptic transmission, GABA mediated" EXACT [] synonym: "synaptic transmission, gamma-aminobutyric acid mediated" EXACT [] synonym: "synaptic transmission, gamma-aminobutyric acid-ergic" EXACT [] is_a: GO:0007268 ! chemical synaptic transmission +intersection_of: GO:0007268 ! chemical synaptic transmission +intersection_of: has_participant CHEBI:59888 +intersection_of: has_participant CL:0000617 ! GABAergic neuron relationship: has_participant CHEBI:59888 relationship: has_participant CL:0000617 ! GABAergic neuron @@ -97935,7 +102922,6 @@ relationship: has_primary_input CHEBI:24780 id: GO:0055001 name: muscle cell development namespace: biological_process -alt_id: GO:0048747 def: "The process whose specific outcome is the progression of a muscle cell over time, from its formation to the mature structure. Muscle cell development does not include the steps involved in committing an unspecified cell to the muscle cell fate." [CL:0000187, GOC:devbiol] synonym: "muscle fiber development" EXACT [] synonym: "muscle fibre development" EXACT [] @@ -98058,7 +103044,6 @@ relationship: results_in_acquisition_of_features_of CL:0002129 ! regular atrial id: GO:0055013 name: cardiac muscle cell development namespace: biological_process -alt_id: GO:0048739 def: "The process whose specific outcome is the progression of a cardiac muscle cell over time, from its formation to the mature state." [GOC:devbiol, GOC:mtg_heart] synonym: "cardiac muscle fiber development" EXACT [] synonym: "cardiac muscle fibre development" EXACT [] @@ -98240,7 +103225,6 @@ relationship: negatively_regulates GO:0048738 ! cardiac muscle tissue developmen id: GO:0055056 name: D-glucose transmembrane transporter activity namespace: molecular_function -alt_id: GO:0015579 def: "Enables the transfer of the D-enantiomer of the hexose monosaccharide glucose from one side of a membrane to the other." [GOC:jid, GOC:jsg, GOC:mah] xref: Reactome:R-HSA-429094 "SLC2A6,8,10,12 transport Glc from extracellular region to cytosol" xref: Reactome:R-HSA-450095 "GLUT2 (SLC2A2) transports Glc from cytosol to extracellular region" @@ -98355,7 +103339,6 @@ property_value: term_tracker_item "https://github.com/geneontology/go-ontology/i id: GO:0055085 name: transmembrane transport namespace: biological_process -alt_id: GO:0090662 def: "The process in which a solute is transported across a lipid bilayer, from one side of a membrane to the other." [GOC:dph, GOC:jid] comment: Transmembrane transport is the transport of a solute across a lipid bilayer. Note that transport through the nuclear pore complex is not transmembrane because the nuclear membrane is a double membrane and is not traversed. For transport through the nuclear pore, consider instead the term 'nucleocytoplasmic transport ; GO:0006913' and its children. Note also that this term is not intended for use in annotating lateral movement within membranes. subset: goslim_chembl @@ -98372,7 +103355,6 @@ is_a: GO:0009987 ! cellular process intersection_of: GO:0006810 ! transport intersection_of: results_in_transport_across GO:0016020 ! membrane relationship: results_in_transport_across GO:0016020 ! membrane -created_by: tb creation_date: 2015-10-21T13:22:47Z [Term] @@ -98476,7 +103458,6 @@ namespace: biological_process def: "The transmission of vibrations via ossicles to the inner ear." [GOC:mh] is_a: GO:0032501 ! multicellular organismal process relationship: part_of GO:0007605 ! sensory perception of sound -created_by: jid creation_date: 2009-10-13T10:59:39Z [Term] @@ -98671,7 +103652,6 @@ relationship: results_in_acquisition_of_features_of CL:0000748 ! retinal bipolar id: GO:0060041 name: retina development in camera-type eye namespace: biological_process -alt_id: GO:0002073 def: "The process whose specific outcome is the progression of the retina over time, from its formation to the mature structure. The retina is the innermost layer or coating at the back of the eyeball, which is sensitive to light and in which the optic nerve terminates." [GOC:bf, GOC:dph, ISBN:0815340729] synonym: "retina development in camera-style eye" EXACT [] synonym: "retinal development" RELATED [GOC:dph, GOC:tb] @@ -98912,7 +103892,6 @@ is_a: GO:0003674 ! molecular_function id: GO:0060090 name: molecular adaptor activity namespace: molecular_function -alt_id: GO:0032947 def: "The binding activity of a molecule that brings together two or more molecules through a selective, non-covalent, often stoichiometric interaction, permitting those molecules to function in a coordinated way." [GOC:mtg_MIT_16mar07, GOC:vw] subset: goslim_drosophila subset: goslim_euk_cellular_processes_ribbon @@ -99294,7 +104273,6 @@ property_value: term_tracker_item "https://github.com/geneontology/go-ontology/i id: GO:0060170 name: ciliary membrane namespace: cellular_component -alt_id: GO:0020017 def: "The portion of the plasma membrane surrounding a cilium." [GOC:cilia, GOC:dph, GOC:rph] comment: Note that cilia and eukaryotic flagella are deemed to be equivalent. synonym: "cilial membrane" EXACT [] @@ -99563,7 +104541,6 @@ relationship: results_in_movement_of CL:0000671 ! centripetally migrating follic id: GO:0060271 name: cilium assembly namespace: biological_process -alt_id: GO:0042384 def: "The assembly of a cilium, a specialized eukaryotic organelle that consists of a filiform extrusion of the cell surface. Each cilium is bounded by an extrusion of the cytoplasmic membrane, and contains a regular longitudinal array of microtubules, anchored basally in a centriole." [GOC:BHF, GOC:cilia, GOC:dph, GOC:kmv, GOC:pr, GOC:vw, ISBN:0198506732, PMID:13978319, PMID:27350441] comment: Note that we deem cilium and microtubule-based flagellum to be equivalent. synonym: "ciliogenesis" EXACT [] @@ -99583,7 +104560,6 @@ relationship: has_part GO:0061512 ! protein localization to cilium relationship: has_part GO:0097712 ! vesicle targeting, trans-Golgi to periciliary membrane compartment relationship: has_part GO:1905349 ! ciliary transition zone assembly relationship: results_in_assembly_of GO:0005929 ! cilium -relationship: RO:0002162 NCBITaxon:2759 {all_only="true"} ! in taxon Eukaryota relationship: starts_with GO:0097711 ! ciliary basal body-plasma membrane docking property_value: RO:0002161 NCBITaxon:3176 property_value: RO:0002161 NCBITaxon:3312 @@ -99640,7 +104616,6 @@ relationship: regulates GO:0048468 ! cell development id: GO:0060285 name: cilium-dependent cell motility namespace: biological_process -alt_id: GO:0071974 def: "Cell motility due to the motion of one or more eukaryotic cilia. A eukaryotic cilium is a specialized organelle that consists of a filiform extrusion of the cell surface. Each cilium is bounded by an extrusion of the cytoplasmic (plasma) membrane, and contains a regular longitudinal array of microtubules, anchored basally in a centriole." [GOC:cilia, GOC:dgh, GOC:dph, GOC:krc, GOC:mlg, GOC:mtg_cambridge_2013] comment: Note that we deem eukaryotic cilia and microtubule-based flagella to be equivalent. synonym: "ciliary cell motility" RELATED [] @@ -99939,7 +104914,6 @@ relationship: part_of GO:0060350 ! endochondral bone morphogenesis id: GO:0060359 name: response to ammonium ion namespace: biological_process -alt_id: GO:1903717 def: "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an ammonium stimulus." [GO_REF:0000071, GOC:TermGenie, PMID:23509267] synonym: "response to ammonia" EXACT [] is_a: BFO:0000003 @@ -100072,7 +105046,6 @@ relationship: negatively_regulates GO:0008291 ! acetylcholine metabolic process id: GO:0060411 name: cardiac septum morphogenesis namespace: biological_process -alt_id: GO:0003280 def: "The process in which the anatomical structure of a cardiac septum is generated and organized. A cardiac septum is a partition that separates parts of the heart." [GOC:dph, GOC:mtg_heart] synonym: "heart septum morphogenesis" EXACT [] is_a: BFO:0000003 @@ -100099,7 +105072,6 @@ relationship: results_in_morphogenesis_of UBERON:0002094 ! interventricular sept id: GO:0060413 name: atrial septum morphogenesis namespace: biological_process -alt_id: GO:0003287 def: "The developmental process in which atrial septum is generated and organized. The atrial septum separates the upper chambers (the atria) of the heart from one another." [GOC:dph, GOC:mtg_heart] synonym: "interatrial septum morphogenesis" EXACT [GOC:dph] is_a: GO:0060411 ! cardiac septum morphogenesis @@ -100626,7 +105598,7 @@ name: lung goblet cell differentiation namespace: biological_process def: "The process in which a relatively unspecialized cell acquires specialized features of a lung goblet cell. A goblet cell is a cell of the epithelial lining that produces and secretes mucins." [GOC:dph, GOC:mtg_lung] synonym: "pulmonary goblet cell differentiation" EXACT [] -is_a: GO:0060487 ! lung epithelial cell differentiation +is_a: GO:0061140 ! lung secretory cell differentiation intersection_of: GO:0030154 ! cell differentiation intersection_of: results_in_acquisition_of_features_of CL:1000143 ! lung goblet cell relationship: part_of GO:0060481 ! lobar bronchus epithelium development @@ -100900,7 +105872,6 @@ intersection_of: GO:0048856 ! anatomical structure development intersection_of: results_in_development_of UBERON:0001956 ! cartilage of bronchus relationship: part_of GO:0060433 ! bronchus development relationship: results_in_development_of UBERON:0001956 ! cartilage of bronchus -created_by: dph creation_date: 2009-04-10T08:12:06Z [Term] @@ -100914,7 +105885,6 @@ intersection_of: results_in_morphogenesis_of UBERON:0001956 ! cartilage of bronc relationship: part_of GO:0060434 ! bronchus morphogenesis relationship: part_of GO:0060532 ! bronchus cartilage development relationship: results_in_morphogenesis_of UBERON:0001956 ! cartilage of bronchus -created_by: dph creation_date: 2009-04-10T08:47:41Z [Term] @@ -100927,7 +105897,6 @@ intersection_of: GO:0048856 ! anatomical structure development intersection_of: results_in_development_of UBERON:0003604 ! trachea cartilage relationship: part_of GO:0060438 ! trachea development relationship: results_in_development_of UBERON:0003604 ! trachea cartilage -created_by: dph creation_date: 2009-04-10T09:00:18Z [Term] @@ -100941,7 +105910,6 @@ intersection_of: results_in_morphogenesis_of UBERON:0003604 ! trachea cartilage relationship: part_of GO:0060439 ! trachea morphogenesis relationship: part_of GO:0060534 ! trachea cartilage development relationship: results_in_morphogenesis_of UBERON:0003604 ! trachea cartilage -created_by: dph creation_date: 2009-04-10T09:07:48Z [Term] @@ -100955,7 +105923,6 @@ intersection_of: GO:0009653 ! anatomical structure morphogenesis intersection_of: results_in_morphogenesis_of UBERON:0007844 ! cartilage element relationship: part_of GO:0051216 ! cartilage development relationship: results_in_morphogenesis_of UBERON:0007844 ! cartilage element -created_by: dph creation_date: 2009-04-10T09:13:27Z [Term] @@ -100967,7 +105934,6 @@ is_a: GO:0009888 ! tissue development intersection_of: GO:0048856 ! anatomical structure development intersection_of: results_in_development_of UBERON:0002385 ! muscle tissue relationship: results_in_development_of UBERON:0002385 ! muscle tissue -created_by: dph creation_date: 2009-04-10T08:05:37Z [Term] @@ -100979,7 +105945,6 @@ is_a: GO:0007517 ! muscle organ development intersection_of: GO:0048856 ! anatomical structure development intersection_of: results_in_development_of UBERON:0014892 ! skeletal muscle organ, vertebrate relationship: results_in_development_of UBERON:0014892 ! skeletal muscle organ, vertebrate -created_by: dph creation_date: 2009-04-10T08:25:12Z [Term] @@ -100993,7 +105958,6 @@ intersection_of: results_in_development_of UBERON:0001103 ! diaphragm relationship: part_of GO:0060541 ! respiratory system development relationship: results_in_development_of UBERON:0001103 ! diaphragm property_value: RO:0002161 NCBITaxon:8782 -created_by: dph creation_date: 2009-04-10T08:44:56Z [Term] @@ -101007,7 +105971,6 @@ intersection_of: results_in_morphogenesis_of UBERON:0001103 ! diaphragm relationship: part_of GO:0060539 ! diaphragm development relationship: results_in_morphogenesis_of UBERON:0001103 ! diaphragm property_value: RO:0002161 NCBITaxon:8782 -created_by: dph creation_date: 2009-04-10T08:47:51Z [Term] @@ -101020,7 +105983,6 @@ is_a: GO:0048731 ! system development intersection_of: GO:0048856 ! anatomical structure development intersection_of: results_in_development_of UBERON:0001004 ! respiratory system relationship: results_in_development_of UBERON:0001004 ! respiratory system -created_by: dph creation_date: 2009-04-10T08:55:42Z [Term] @@ -101033,7 +105995,6 @@ is_a: GO:0048589 ! developmental growth intersection_of: GO:0048589 ! developmental growth intersection_of: part_of GO:0009653 ! anatomical structure morphogenesis relationship: part_of GO:0009653 ! anatomical structure morphogenesis -created_by: dph creation_date: 2009-04-28T08:42:53Z [Term] @@ -101048,7 +106009,6 @@ is_a: GO:1902742 ! apoptotic process involved in development intersection_of: GO:0006915 ! apoptotic process intersection_of: part_of GO:0009653 ! anatomical structure morphogenesis relationship: part_of GO:0009653 ! anatomical structure morphogenesis -created_by: dph creation_date: 2009-04-28T09:17:27Z [Term] @@ -101061,7 +106021,6 @@ is_a: GO:0035239 ! tube morphogenesis intersection_of: GO:0009653 ! anatomical structure morphogenesis intersection_of: results_in_morphogenesis_of UBERON:0003914 ! epithelial tube relationship: results_in_morphogenesis_of UBERON:0003914 ! epithelial tube -created_by: dph creation_date: 2009-04-28T09:33:36Z [Term] @@ -101073,7 +106032,6 @@ is_a: GO:0002065 ! columnar/cuboidal epithelial cell differentiation intersection_of: GO:0030154 ! cell differentiation intersection_of: results_in_acquisition_of_features_of CL:0000710 ! neurecto-epithelial cell relationship: results_in_acquisition_of_features_of CL:0000710 ! neurecto-epithelial cell -created_by: dph creation_date: 2009-04-29T01:50:05Z [Term] @@ -101086,7 +106044,6 @@ is_a: GO:0070613 ! regulation of protein processing intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0016486 ! peptide hormone processing relationship: regulates GO:0016486 ! peptide hormone processing -created_by: dph creation_date: 2009-04-29T03:16:05Z [Term] @@ -101100,7 +106057,6 @@ is_a: GO:0060568 ! regulation of peptide hormone processing intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0016486 ! peptide hormone processing relationship: positively_regulates GO:0016486 ! peptide hormone processing -created_by: dph creation_date: 2009-04-29T03:22:05Z [Term] @@ -101114,7 +106070,6 @@ is_a: GO:0060568 ! regulation of peptide hormone processing intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0016486 ! peptide hormone processing relationship: negatively_regulates GO:0016486 ! peptide hormone processing -created_by: dph creation_date: 2009-04-29T03:24:55Z [Term] @@ -101128,7 +106083,6 @@ is_a: GO:0002009 ! morphogenesis of an epithelium intersection_of: GO:0009653 ! anatomical structure morphogenesis intersection_of: results_in_morphogenesis_of UBERON:0005157 ! epithelial fold relationship: results_in_morphogenesis_of UBERON:0005157 ! epithelial fold -created_by: dph creation_date: 2009-04-30T09:27:17Z [Term] @@ -101140,7 +106094,6 @@ is_a: GO:0060571 ! morphogenesis of an epithelial fold intersection_of: GO:0009653 ! anatomical structure morphogenesis intersection_of: results_in_morphogenesis_of UBERON:0005153 ! epithelial bud relationship: results_in_morphogenesis_of UBERON:0005153 ! epithelial bud -created_by: dph creation_date: 2009-04-30T09:38:35Z [Term] @@ -101153,7 +106106,6 @@ intersection_of: GO:0021700 ! developmental maturation intersection_of: results_in_maturation_of CL:0002563 ! intestinal epithelial cell relationship: part_of GO:0060576 ! intestinal epithelial cell development relationship: results_in_maturation_of CL:0002563 ! intestinal epithelial cell -created_by: dph creation_date: 2009-05-06T08:10:41Z [Term] @@ -101166,7 +106118,6 @@ intersection_of: GO:0030154 ! cell differentiation intersection_of: results_in_acquisition_of_features_of CL:0002563 ! intestinal epithelial cell relationship: part_of GO:0048565 ! digestive tract development relationship: results_in_acquisition_of_features_of CL:0002563 ! intestinal epithelial cell -created_by: dph creation_date: 2009-05-06T08:17:56Z [Term] @@ -101179,7 +106130,6 @@ intersection_of: GO:0048856 ! anatomical structure development intersection_of: results_in_development_of CL:0002563 ! intestinal epithelial cell relationship: part_of GO:0060575 ! intestinal epithelial cell differentiation relationship: results_in_development_of CL:0002563 ! intestinal epithelial cell -created_by: dph creation_date: 2009-05-06T08:20:24Z [Term] @@ -101192,7 +106142,6 @@ is_a: GO:0048845 ! venous blood vessel morphogenesis intersection_of: GO:0009653 ! anatomical structure morphogenesis intersection_of: results_in_morphogenesis_of UBERON:0002016 ! pulmonary vein relationship: results_in_morphogenesis_of UBERON:0002016 ! pulmonary vein -created_by: dph creation_date: 2009-05-06T08:44:04Z [Term] @@ -101204,7 +106153,6 @@ is_a: GO:0048845 ! venous blood vessel morphogenesis intersection_of: GO:0009653 ! anatomical structure morphogenesis intersection_of: results_in_morphogenesis_of UBERON:0001585 ! anterior vena cava relationship: results_in_morphogenesis_of UBERON:0001585 ! anterior vena cava -created_by: dph creation_date: 2009-05-06T08:47:21Z [Term] @@ -101216,7 +106164,6 @@ is_a: GO:0045165 ! cell fate commitment intersection_of: GO:0045165 ! cell fate commitment intersection_of: part_of GO:0007389 ! pattern specification process relationship: part_of GO:0007389 ! pattern specification process -created_by: dph creation_date: 2009-05-07T12:40:55Z [Term] @@ -101230,7 +106177,6 @@ intersection_of: GO:0048871 ! multicellular organismal-level homeostasis intersection_of: regulates_levels_of CHEBI:24875 relationship: regulates_levels_of CHEBI:24875 property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/24554" xsd:anyURI -created_by: dph creation_date: 2009-05-08T02:18:21Z [Term] @@ -101244,7 +106190,6 @@ intersection_of: GO:0030154 ! cell differentiation intersection_of: results_in_acquisition_of_features_of CL:0000058 ! chondroblast relationship: part_of GO:0051216 ! cartilage development relationship: results_in_acquisition_of_features_of CL:0000058 ! chondroblast -created_by: dph creation_date: 2009-05-11T07:47:36Z [Term] @@ -101262,7 +106207,6 @@ intersection_of: GO:0048646 ! anatomical structure formation involved in morphog intersection_of: results_in_formation_of UBERON:0001911 ! mammary gland relationship: part_of GO:0060443 ! mammary gland morphogenesis relationship: results_in_formation_of UBERON:0001911 ! mammary gland -created_by: dph creation_date: 2009-05-13T08:47:52Z [Term] @@ -101275,7 +106219,6 @@ intersection_of: GO:0048646 ! anatomical structure formation involved in morphog intersection_of: results_in_formation_of UBERON:0005311 ! mammary placode relationship: part_of GO:0060592 ! mammary gland formation relationship: results_in_formation_of UBERON:0005311 ! mammary placode -created_by: dph creation_date: 2009-05-13T11:55:20Z [Term] @@ -101288,7 +106231,6 @@ is_a: GO:0060601 ! lateral sprouting from an epithelium intersection_of: GO:0060601 ! lateral sprouting from an epithelium intersection_of: part_of GO:0060444 ! branching involved in mammary gland duct morphogenesis relationship: part_of GO:0060444 ! branching involved in mammary gland duct morphogenesis -created_by: dph creation_date: 2009-05-13T12:38:06Z [Term] @@ -101298,7 +106240,6 @@ namespace: biological_process def: "The process in which a branch forms along the side of an epithelium." [GOC:dph] is_a: GO:0002009 ! morphogenesis of an epithelium relationship: part_of GO:0061138 ! morphogenesis of a branching epithelium -created_by: dph creation_date: 2009-05-14T02:33:01Z [Term] @@ -101312,7 +106253,6 @@ intersection_of: results_in_morphogenesis_of UBERON:0001765 ! mammary duct relationship: part_of GO:0060443 ! mammary gland morphogenesis relationship: part_of GO:0061180 ! mammary gland epithelium development relationship: results_in_morphogenesis_of UBERON:0001765 ! mammary duct -created_by: dph creation_date: 2009-05-15T09:22:25Z [Term] @@ -101325,7 +106265,6 @@ is_a: GO:0048762 ! mesenchymal cell differentiation intersection_of: GO:0048762 ! mesenchymal cell differentiation intersection_of: part_of GO:0030879 ! mammary gland development relationship: part_of GO:0030879 ! mammary gland development -created_by: dph creation_date: 2009-05-15T12:17:06Z [Term] @@ -101338,7 +106277,6 @@ intersection_of: GO:0048856 ! anatomical structure development intersection_of: results_in_development_of UBERON:0004180 ! mammary gland fat relationship: part_of GO:0030879 ! mammary gland development relationship: results_in_development_of UBERON:0004180 ! mammary gland fat -created_by: dph creation_date: 2009-05-15T12:27:57Z [Term] @@ -101352,7 +106290,6 @@ intersection_of: GO:0048856 ! anatomical structure development intersection_of: results_in_development_of UBERON:0001013 ! adipose tissue relationship: part_of GO:0048513 ! animal organ development relationship: results_in_development_of UBERON:0001013 ! adipose tissue -created_by: dph creation_date: 2009-05-15T12:36:28Z [Term] @@ -101366,7 +106303,6 @@ intersection_of: GO:0048646 ! anatomical structure formation involved in morphog intersection_of: results_in_formation_of UBERON:0005333 ! mammary bud relationship: part_of GO:0060648 ! mammary gland bud morphogenesis relationship: results_in_formation_of UBERON:0005333 ! mammary bud -created_by: dph creation_date: 2009-05-18T08:43:14Z [Term] @@ -101381,7 +106317,6 @@ intersection_of: GO:0048646 ! anatomical structure formation involved in morphog intersection_of: results_in_formation_of UBERON:0004182 ! mammary gland cord relationship: part_of GO:0060652 ! mammary gland cord morphogenesis relationship: results_in_formation_of UBERON:0004182 ! mammary gland cord -created_by: dph creation_date: 2009-05-18T08:57:58Z [Term] @@ -101394,7 +106329,6 @@ intersection_of: GO:0048856 ! anatomical structure development intersection_of: results_in_development_of UBERON:0002030 ! nipple relationship: part_of GO:0030879 ! mammary gland development relationship: results_in_development_of UBERON:0002030 ! nipple -created_by: dph creation_date: 2009-05-18T09:29:38Z [Term] @@ -101406,7 +106340,6 @@ is_a: GO:0010631 ! epithelial cell migration intersection_of: GO:0016477 ! cell migration intersection_of: part_of GO:0060596 ! mammary placode formation relationship: part_of GO:0060596 ! mammary placode formation -created_by: dph creation_date: 2009-05-18T09:41:49Z [Term] @@ -101418,7 +106351,6 @@ is_a: GO:0033044 ! regulation of chromosome organization intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0030261 ! chromosome condensation relationship: regulates GO:0030261 ! chromosome condensation -created_by: dph creation_date: 2009-05-18T02:12:13Z [Term] @@ -101431,7 +106363,6 @@ is_a: GO:0051049 ! regulation of transport intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0016192 ! vesicle-mediated transport relationship: regulates GO:0016192 ! vesicle-mediated transport -created_by: dph creation_date: 2009-05-18T02:29:43Z [Term] @@ -101443,7 +106374,6 @@ is_a: GO:0032886 ! regulation of microtubule-based process intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0007018 ! microtubule-based movement relationship: regulates GO:0007018 ! microtubule-based movement -created_by: dph creation_date: 2009-05-18T03:07:02Z [Term] @@ -101458,7 +106388,6 @@ intersection_of: has_end_location CL:0000066 ! epithelial cell intersection_of: has_start_location CL:0008019 ! mesenchymal cell relationship: has_end_location CL:0000066 ! epithelial cell relationship: has_start_location CL:0008019 ! mesenchymal cell -created_by: dph creation_date: 2009-05-19T03:59:05Z [Term] @@ -101470,7 +106399,6 @@ is_a: GO:0050872 ! white fat cell differentiation intersection_of: GO:0050872 ! white fat cell differentiation intersection_of: part_of GO:0060611 ! mammary gland fat development relationship: part_of GO:0060611 ! mammary gland fat development -created_by: dph creation_date: 2009-05-27T05:50:56Z [Term] @@ -101482,7 +106410,6 @@ is_a: GO:0060644 ! mammary gland epithelial cell differentiation intersection_of: GO:0030855 ! epithelial cell differentiation intersection_of: part_of GO:0060648 ! mammary gland bud morphogenesis relationship: part_of GO:0060615 ! mammary gland bud formation -created_by: dph creation_date: 2009-05-29T07:58:13Z [Term] @@ -101495,7 +106422,6 @@ intersection_of: GO:0030154 ! cell differentiation intersection_of: results_in_acquisition_of_features_of CL:0002327 ! mammary gland epithelial cell relationship: part_of GO:0061180 ! mammary gland epithelium development relationship: results_in_acquisition_of_features_of CL:0002327 ! mammary gland epithelial cell -created_by: dph creation_date: 2009-05-29T08:03:07Z [Term] @@ -101507,7 +106433,6 @@ is_a: GO:0098609 ! cell-cell adhesion intersection_of: GO:0098609 ! cell-cell adhesion intersection_of: part_of GO:0060611 ! mammary gland fat development relationship: part_of GO:0060611 ! mammary gland fat development -created_by: dph creation_date: 2009-05-29T08:33:29Z [Term] @@ -101520,7 +106445,6 @@ intersection_of: GO:0009653 ! anatomical structure morphogenesis intersection_of: results_in_morphogenesis_of UBERON:0005333 ! mammary bud relationship: part_of GO:0060603 ! mammary gland duct morphogenesis relationship: results_in_morphogenesis_of UBERON:0005333 ! mammary bud -created_by: dph creation_date: 2009-05-29T08:42:22Z [Term] @@ -101534,7 +106458,6 @@ intersection_of: GO:0009653 ! anatomical structure morphogenesis intersection_of: results_in_morphogenesis_of UBERON:0004182 ! mammary gland cord relationship: part_of GO:0060603 ! mammary gland duct morphogenesis relationship: results_in_morphogenesis_of UBERON:0004182 ! mammary gland cord -created_by: dph creation_date: 2009-05-29T09:06:56Z [Term] @@ -101547,7 +106470,6 @@ is_a: GO:0060644 ! mammary gland epithelial cell differentiation intersection_of: GO:0030855 ! epithelial cell differentiation intersection_of: part_of GO:0060652 ! mammary gland cord morphogenesis relationship: part_of GO:0060652 ! mammary gland cord morphogenesis -created_by: dph creation_date: 2009-05-29T09:17:16Z [Term] @@ -101559,7 +106481,6 @@ is_a: GO:0060444 ! branching involved in mammary gland duct morphogenesis intersection_of: GO:0061138 ! morphogenesis of a branching epithelium intersection_of: part_of GO:0060652 ! mammary gland cord morphogenesis relationship: part_of GO:0060652 ! mammary gland cord morphogenesis -created_by: dph creation_date: 2009-05-29T09:29:32Z [Term] @@ -101574,7 +106495,6 @@ intersection_of: results_in_morphogenesis_of UBERON:0002030 ! nipple relationship: part_of GO:0060443 ! mammary gland morphogenesis relationship: part_of GO:0060618 ! nipple development relationship: results_in_morphogenesis_of UBERON:0002030 ! nipple -created_by: dph creation_date: 2009-05-29T10:45:44Z [Term] @@ -101586,7 +106506,6 @@ is_a: GO:0048730 ! epidermis morphogenesis intersection_of: GO:0048730 ! epidermis morphogenesis intersection_of: part_of GO:0060658 ! nipple morphogenesis relationship: part_of GO:0060658 ! nipple morphogenesis -created_by: dph creation_date: 2009-05-29T11:04:04Z [Term] @@ -101598,7 +106517,6 @@ is_a: GO:0050673 ! epithelial cell proliferation intersection_of: GO:0050673 ! epithelial cell proliferation intersection_of: part_of GO:0007435 ! salivary gland morphogenesis relationship: part_of GO:0007435 ! salivary gland morphogenesis -created_by: dph creation_date: 2009-06-01T08:36:13Z [Term] @@ -101612,7 +106530,6 @@ intersection_of: GO:0009653 ! anatomical structure morphogenesis intersection_of: results_in_morphogenesis_of UBERON:0007106 ! chorionic villus relationship: part_of GO:0001892 ! embryonic placenta development relationship: results_in_morphogenesis_of UBERON:0007106 ! chorionic villus -created_by: dph creation_date: 2009-06-02T09:33:37Z [Term] @@ -101625,7 +106542,6 @@ is_a: GO:0061138 ! morphogenesis of a branching epithelium intersection_of: GO:0061138 ! morphogenesis of a branching epithelium intersection_of: part_of GO:0060713 ! labyrinthine layer morphogenesis relationship: part_of GO:0060713 ! labyrinthine layer morphogenesis -created_by: dph creation_date: 2009-06-02T10:40:40Z [Term] @@ -101638,7 +106554,6 @@ is_a: GO:0060706 ! cell differentiation involved in embryonic placenta developme intersection_of: GO:0030855 ! epithelial cell differentiation intersection_of: part_of GO:0001892 ! embryonic placenta development relationship: part_of GO:0060711 ! labyrinthine layer development -created_by: dph creation_date: 2009-06-02T11:40:52Z [Term] @@ -101651,7 +106566,6 @@ is_a: GO:0007267 ! cell-cell signaling intersection_of: GO:0007267 ! cell-cell signaling intersection_of: part_of GO:0001890 ! placenta development relationship: part_of GO:0001892 ! embryonic placenta development -created_by: dph creation_date: 2009-06-02T12:58:03Z [Term] @@ -101661,7 +106575,6 @@ namespace: biological_process def: "The process whose specific outcome is the progression of a blood vessel of the placenta over time, from its formation to the mature structure." [GOC:dph, PMID:16916377] is_a: GO:0001568 ! blood vessel development relationship: part_of GO:0001890 ! placenta development -created_by: dph creation_date: 2009-06-02T01:09:43Z [Term] @@ -101674,7 +106587,6 @@ intersection_of: GO:0009653 ! anatomical structure morphogenesis intersection_of: results_in_morphogenesis_of UBERON:0000084 ! ureteric bud relationship: part_of GO:0001657 ! ureteric bud development relationship: results_in_morphogenesis_of UBERON:0000084 ! ureteric bud -created_by: dph creation_date: 2009-06-02T01:31:41Z [Term] @@ -101687,7 +106599,6 @@ intersection_of: GO:0048646 ! anatomical structure formation involved in morphog intersection_of: results_in_formation_of UBERON:0000084 ! ureteric bud relationship: part_of GO:0060675 ! ureteric bud morphogenesis relationship: results_in_formation_of UBERON:0000084 ! ureteric bud -created_by: dph creation_date: 2009-06-02T01:47:23Z [Term] @@ -101699,7 +106610,6 @@ is_a: GO:0060601 ! lateral sprouting from an epithelium intersection_of: GO:0060601 ! lateral sprouting from an epithelium intersection_of: part_of GO:0001658 ! branching involved in ureteric bud morphogenesis relationship: part_of GO:0001658 ! branching involved in ureteric bud morphogenesis -created_by: dph creation_date: 2009-06-02T02:44:27Z [Term] @@ -101714,7 +106624,6 @@ intersection_of: has_end_location CL:0008019 ! mesenchymal cell intersection_of: has_start_location CL:0000066 ! epithelial cell relationship: has_end_location CL:0008019 ! mesenchymal cell relationship: has_start_location CL:0000066 ! epithelial cell -created_by: dph creation_date: 2009-06-03T06:36:46Z [Term] @@ -101729,7 +106638,6 @@ is_a: GO:2000241 ! regulation of reproductive process intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0060513 ! prostatic bud formation relationship: regulates GO:0060513 ! prostatic bud formation -created_by: dph creation_date: 2009-06-05T12:29:26Z [Term] @@ -101743,7 +106651,6 @@ is_a: GO:2000242 ! negative regulation of reproductive process intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0060513 ! prostatic bud formation relationship: negatively_regulates GO:0060513 ! prostatic bud formation -created_by: dph creation_date: 2009-06-05T12:35:25Z [Term] @@ -101757,7 +106664,6 @@ is_a: GO:2000241 ! regulation of reproductive process intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0060442 ! branching involved in prostate gland morphogenesis relationship: regulates GO:0060442 ! branching involved in prostate gland morphogenesis -created_by: dph creation_date: 2009-06-05T12:37:14Z [Term] @@ -101770,7 +106676,6 @@ is_a: GO:0051239 ! regulation of multicellular organismal process intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0001763 ! morphogenesis of a branching structure relationship: regulates GO:0001763 ! morphogenesis of a branching structure -created_by: dph creation_date: 2009-06-05T12:41:44Z [Term] @@ -101782,7 +106687,6 @@ is_a: GO:0030154 ! cell differentiation intersection_of: GO:0030154 ! cell differentiation intersection_of: part_of GO:0007431 ! salivary gland development relationship: part_of GO:0007431 ! salivary gland development -created_by: dph creation_date: 2009-06-08T01:01:35Z [Term] @@ -101794,7 +106698,6 @@ is_a: GO:0030855 ! epithelial cell differentiation is_a: GO:0060689 ! cell differentiation involved in salivary gland development intersection_of: GO:0030855 ! epithelial cell differentiation intersection_of: part_of GO:0007431 ! salivary gland development -created_by: dph creation_date: 2009-06-08T01:04:19Z [Term] @@ -101806,7 +106709,6 @@ is_a: GO:0002070 ! epithelial cell maturation intersection_of: GO:0002070 ! epithelial cell maturation intersection_of: part_of GO:0007431 ! salivary gland development relationship: part_of GO:0060690 ! epithelial cell differentiation involved in salivary gland development -created_by: dph creation_date: 2009-06-08T01:06:00Z [Term] @@ -101818,7 +106720,6 @@ is_a: GO:0048762 ! mesenchymal cell differentiation is_a: GO:0060689 ! cell differentiation involved in salivary gland development intersection_of: GO:0048762 ! mesenchymal cell differentiation intersection_of: part_of GO:0007431 ! salivary gland development -created_by: dph creation_date: 2009-06-08T01:08:44Z [Term] @@ -101832,7 +106733,6 @@ is_a: GO:2000027 ! regulation of animal organ morphogenesis intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0060445 ! branching involved in salivary gland morphogenesis relationship: regulates GO:0060445 ! branching involved in salivary gland morphogenesis -created_by: dph creation_date: 2009-06-08T01:14:44Z [Term] @@ -101844,7 +106744,6 @@ is_a: GO:0060690 ! epithelial cell differentiation involved in salivary gland de is_a: GO:0090425 ! acinar cell differentiation intersection_of: GO:0090425 ! acinar cell differentiation intersection_of: part_of GO:0007431 ! salivary gland development -created_by: dph creation_date: 2009-06-09T09:32:46Z [Term] @@ -101856,7 +106755,6 @@ is_a: GO:0030182 ! neuron differentiation is_a: GO:0060689 ! cell differentiation involved in salivary gland development intersection_of: GO:0030182 ! neuron differentiation intersection_of: part_of GO:0007431 ! salivary gland development -created_by: dph creation_date: 2009-06-09T09:35:52Z [Term] @@ -101869,7 +106767,6 @@ is_a: GO:0030154 ! cell differentiation intersection_of: GO:0030154 ! cell differentiation intersection_of: part_of GO:0001892 ! embryonic placenta development relationship: part_of GO:0001892 ! embryonic placenta development -created_by: dph creation_date: 2009-06-09T10:26:42Z [Term] @@ -101881,7 +106778,6 @@ is_a: GO:0060706 ! cell differentiation involved in embryonic placenta developme intersection_of: GO:0030154 ! cell differentiation intersection_of: results_in_acquisition_of_features_of CL:0002488 ! trophoblast giant cell relationship: results_in_acquisition_of_features_of CL:0002488 ! trophoblast giant cell -created_by: dph creation_date: 2009-06-09T10:32:12Z [Term] @@ -101895,7 +106791,6 @@ intersection_of: GO:0030154 ! cell differentiation intersection_of: results_in_acquisition_of_features_of CL:0002499 ! spongiotrophoblast cell relationship: part_of GO:0060712 ! spongiotrophoblast layer development relationship: results_in_acquisition_of_features_of CL:0002499 ! spongiotrophoblast cell -created_by: dph creation_date: 2009-06-09T10:38:10Z [Term] @@ -101908,7 +106803,6 @@ intersection_of: GO:0048856 ! anatomical structure development intersection_of: results_in_development_of UBERON:0003946 ! placenta labyrinth relationship: part_of GO:0001892 ! embryonic placenta development relationship: results_in_development_of UBERON:0003946 ! placenta labyrinth -created_by: dph creation_date: 2009-06-09T03:27:43Z [Term] @@ -101921,7 +106815,6 @@ intersection_of: GO:0048856 ! anatomical structure development intersection_of: results_in_development_of UBERON:0004021 ! spongiotrophoblast layer relationship: part_of GO:0001892 ! embryonic placenta development relationship: results_in_development_of UBERON:0004021 ! spongiotrophoblast layer -created_by: dph creation_date: 2009-06-09T03:33:40Z [Term] @@ -101936,7 +106829,6 @@ intersection_of: results_in_morphogenesis_of UBERON:0003946 ! placenta labyrinth relationship: part_of GO:0060669 ! embryonic placenta morphogenesis relationship: part_of GO:0060711 ! labyrinthine layer development relationship: results_in_morphogenesis_of UBERON:0003946 ! placenta labyrinth -created_by: dph creation_date: 2009-06-10T08:10:19Z [Term] @@ -101950,7 +106842,6 @@ intersection_of: GO:0048646 ! anatomical structure formation involved in morphog intersection_of: results_in_formation_of UBERON:0003946 ! placenta labyrinth relationship: part_of GO:0060713 ! labyrinthine layer morphogenesis relationship: results_in_formation_of UBERON:0003946 ! placenta labyrinth -created_by: dph creation_date: 2009-06-10T08:13:14Z [Term] @@ -101964,7 +106855,6 @@ intersection_of: GO:0048856 ! anatomical structure development intersection_of: results_in_development_of UBERON:0004183 ! placental labyrinth blood vessel relationship: part_of GO:0060711 ! labyrinthine layer development relationship: results_in_development_of UBERON:0004183 ! placental labyrinth blood vessel -created_by: dph creation_date: 2009-06-11T09:04:38Z [Term] @@ -101976,7 +106866,6 @@ is_a: GO:1903867 ! extraembryonic membrane development intersection_of: GO:0048856 ! anatomical structure development intersection_of: results_in_development_of UBERON:0003124 ! chorion membrane relationship: results_in_development_of UBERON:0003124 ! chorion membrane -created_by: dph creation_date: 2009-06-11T02:37:50Z [Term] @@ -101989,7 +106878,6 @@ intersection_of: GO:0030154 ! cell differentiation intersection_of: results_in_acquisition_of_features_of CL:0011101 ! chorionic trophoblast cell relationship: part_of GO:0060717 ! chorion development relationship: results_in_acquisition_of_features_of CL:0011101 ! chorionic trophoblast cell -created_by: dph creation_date: 2009-06-11T02:48:27Z [Term] @@ -102002,7 +106890,6 @@ intersection_of: GO:0048468 ! cell development intersection_of: results_in_development_of CL:0011101 ! chorionic trophoblast cell relationship: part_of GO:0060718 ! chorionic trophoblast cell differentiation relationship: results_in_development_of CL:0011101 ! chorionic trophoblast cell -created_by: dph creation_date: 2009-06-11T02:58:45Z [Term] @@ -102014,7 +106901,6 @@ is_a: GO:0008283 ! cell population proliferation intersection_of: GO:0008283 ! cell population proliferation intersection_of: part_of GO:0001892 ! embryonic placenta development relationship: part_of GO:0001892 ! embryonic placenta development -created_by: dph creation_date: 2009-06-12T12:46:04Z [Term] @@ -102026,7 +106912,6 @@ is_a: GO:0042127 ! regulation of cell population proliferation intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0060722 ! cell proliferation involved in embryonic placenta development relationship: regulates GO:0060722 ! cell proliferation involved in embryonic placenta development -created_by: dph creation_date: 2009-06-12T12:50:23Z [Term] @@ -102040,7 +106925,6 @@ intersection_of: GO:0048589 ! developmental growth intersection_of: results_in_growth_of UBERON:0002367 ! prostate gland relationship: part_of GO:0030850 ! prostate gland development relationship: results_in_growth_of UBERON:0002367 ! prostate gland -created_by: dph creation_date: 2009-06-15T09:21:52Z [Term] @@ -102054,7 +106938,6 @@ is_a: GO:0060736 ! prostate gland growth intersection_of: GO:0060736 ! prostate gland growth intersection_of: part_of GO:0009653 ! anatomical structure morphogenesis relationship: part_of GO:0060512 ! prostate gland morphogenesis -created_by: dph creation_date: 2009-06-15T09:24:40Z [Term] @@ -102067,7 +106950,6 @@ is_a: GO:0060684 ! epithelial-mesenchymal cell signaling intersection_of: GO:0060684 ! epithelial-mesenchymal cell signaling intersection_of: part_of GO:0030850 ! prostate gland development relationship: part_of GO:0030850 ! prostate gland development -created_by: dph creation_date: 2009-06-15T09:31:31Z [Term] @@ -102080,7 +106962,6 @@ is_a: GO:0060638 ! mesenchymal-epithelial cell signaling intersection_of: GO:0060638 ! mesenchymal-epithelial cell signaling intersection_of: part_of GO:0030850 ! prostate gland development relationship: part_of GO:0030850 ! prostate gland development -created_by: dph creation_date: 2009-06-15T09:35:08Z [Term] @@ -102094,7 +106975,6 @@ intersection_of: GO:0009653 ! anatomical structure morphogenesis intersection_of: results_in_morphogenesis_of UBERON:0000428 ! prostate epithelium relationship: part_of GO:0060512 ! prostate gland morphogenesis relationship: results_in_morphogenesis_of UBERON:0000428 ! prostate epithelium -created_by: dph creation_date: 2009-06-16T09:23:22Z [Term] @@ -102110,7 +106990,6 @@ intersection_of: results_in_morphogenesis_of UBERON:0004184 ! prostate gland str relationship: part_of GO:0060512 ! prostate gland morphogenesis relationship: part_of GO:0061448 ! connective tissue development relationship: results_in_morphogenesis_of UBERON:0004184 ! prostate gland stroma -created_by: dph creation_date: 2009-06-16T09:27:01Z [Term] @@ -102123,7 +107002,6 @@ is_a: GO:0030855 ! epithelial cell differentiation intersection_of: GO:0030855 ! epithelial cell differentiation intersection_of: part_of GO:0030850 ! prostate gland development relationship: part_of GO:0030850 ! prostate gland development -created_by: dph creation_date: 2009-06-16T09:32:34Z [Term] @@ -102136,7 +107014,6 @@ is_a: GO:0002070 ! epithelial cell maturation intersection_of: GO:0002070 ! epithelial cell maturation intersection_of: part_of GO:0030850 ! prostate gland development relationship: part_of GO:0060742 ! epithelial cell differentiation involved in prostate gland development -created_by: dph creation_date: 2009-06-16T09:34:42Z [Term] @@ -102149,7 +107026,6 @@ intersection_of: GO:0048856 ! anatomical structure development intersection_of: results_in_development_of UBERON:0003214 ! mammary gland alveolus relationship: part_of GO:0061377 ! mammary gland lobule development relationship: results_in_development_of UBERON:0003214 ! mammary gland alveolus -created_by: dph creation_date: 2009-06-22T10:52:12Z [Term] @@ -102161,7 +107037,6 @@ is_a: GO:0002688 ! regulation of leukocyte chemotaxis intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0002551 ! mast cell chemotaxis relationship: regulates GO:0002551 ! mast cell chemotaxis -created_by: dph creation_date: 2009-06-22T02:36:06Z [Term] @@ -102174,7 +107049,6 @@ is_a: GO:0060753 ! regulation of mast cell chemotaxis intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0002551 ! mast cell chemotaxis relationship: positively_regulates GO:0002551 ! mast cell chemotaxis -created_by: dph creation_date: 2009-06-22T02:38:19Z [Term] @@ -102187,7 +107061,6 @@ is_a: GO:0060753 ! regulation of mast cell chemotaxis intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0002551 ! mast cell chemotaxis relationship: negatively_regulates GO:0002551 ! mast cell chemotaxis -created_by: dph creation_date: 2009-06-22T02:40:58Z [Term] @@ -102199,7 +107072,6 @@ is_a: GO:0048583 ! regulation of response to stimulus intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0034097 ! response to cytokine relationship: regulates GO:0034097 ! response to cytokine -created_by: dph creation_date: 2009-06-22T02:56:12Z [Term] @@ -102212,7 +107084,6 @@ is_a: GO:0060759 ! regulation of response to cytokine stimulus intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0034097 ! response to cytokine relationship: positively_regulates GO:0034097 ! response to cytokine -created_by: dph creation_date: 2009-06-22T02:58:04Z [Term] @@ -102225,7 +107096,6 @@ is_a: GO:0060759 ! regulation of response to cytokine stimulus intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0034097 ! response to cytokine relationship: negatively_regulates GO:0034097 ! response to cytokine -created_by: dph creation_date: 2009-06-22T02:59:57Z [Term] @@ -102239,7 +107109,6 @@ is_a: GO:2000027 ! regulation of animal organ morphogenesis intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0060444 ! branching involved in mammary gland duct morphogenesis relationship: regulates GO:0060444 ! branching involved in mammary gland duct morphogenesis -created_by: dph creation_date: 2009-06-22T05:20:33Z [Term] @@ -102252,7 +107121,6 @@ is_a: GO:0007267 ! cell-cell signaling intersection_of: GO:0007267 ! cell-cell signaling intersection_of: part_of GO:0030879 ! mammary gland development relationship: part_of GO:0030879 ! mammary gland development -created_by: dph creation_date: 2009-07-06T09:24:53Z [Term] @@ -102264,7 +107132,6 @@ is_a: GO:0050673 ! epithelial cell proliferation intersection_of: GO:0050673 ! epithelial cell proliferation intersection_of: part_of GO:0030850 ! prostate gland development relationship: part_of GO:0030850 ! prostate gland development -created_by: dph creation_date: 2009-07-08T07:32:34Z [Term] @@ -102276,7 +107143,6 @@ is_a: GO:0050678 ! regulation of epithelial cell proliferation intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0060767 ! epithelial cell proliferation involved in prostate gland development relationship: regulates GO:0060767 ! epithelial cell proliferation involved in prostate gland development -created_by: dph creation_date: 2009-07-08T07:34:56Z [Term] @@ -102291,7 +107157,6 @@ is_a: GO:2000243 ! positive regulation of reproductive process intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0060767 ! epithelial cell proliferation involved in prostate gland development relationship: positively_regulates GO:0060767 ! epithelial cell proliferation involved in prostate gland development -created_by: dph creation_date: 2009-07-08T07:38:02Z [Term] @@ -102307,7 +107172,6 @@ is_a: GO:2000242 ! negative regulation of reproductive process intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0060767 ! epithelial cell proliferation involved in prostate gland development relationship: negatively_regulates GO:0060767 ! epithelial cell proliferation involved in prostate gland development -created_by: dph creation_date: 2009-07-08T07:40:27Z [Term] @@ -102319,7 +107183,6 @@ is_a: GO:0010463 ! mesenchymal cell proliferation intersection_of: GO:0010463 ! mesenchymal cell proliferation intersection_of: part_of GO:0030850 ! prostate gland development relationship: part_of GO:0030850 ! prostate gland development -created_by: dph creation_date: 2009-07-28T11:50:56Z [Term] @@ -102331,7 +107194,6 @@ is_a: GO:0010464 ! regulation of mesenchymal cell proliferation intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0060781 ! mesenchymal cell proliferation involved in prostate gland development relationship: regulates GO:0060781 ! mesenchymal cell proliferation involved in prostate gland development -created_by: dph creation_date: 2009-07-28T11:54:20Z [Term] @@ -102343,7 +107205,6 @@ is_a: GO:0042127 ! regulation of cell population proliferation intersection_of: GO:0042127 ! regulation of cell population proliferation intersection_of: part_of GO:0001894 ! tissue homeostasis relationship: part_of GO:0048873 ! homeostasis of number of cells within a tissue -created_by: dph creation_date: 2009-07-31T01:46:28Z [Term] @@ -102355,7 +107216,6 @@ is_a: GO:0042981 ! regulation of apoptotic process intersection_of: GO:0042981 ! regulation of apoptotic process intersection_of: part_of GO:0001894 ! tissue homeostasis relationship: part_of GO:0048873 ! homeostasis of number of cells within a tissue -created_by: dph creation_date: 2009-07-31T01:49:54Z [Term] @@ -102367,7 +107227,6 @@ is_a: GO:0045595 ! regulation of cell differentiation intersection_of: GO:0045595 ! regulation of cell differentiation intersection_of: part_of GO:0001894 ! tissue homeostasis relationship: part_of GO:0048873 ! homeostasis of number of cells within a tissue -created_by: dph creation_date: 2009-07-31T01:55:19Z [Term] @@ -102381,7 +107240,6 @@ intersection_of: GO:0048646 ! anatomical structure formation involved in morphog intersection_of: results_in_formation_of UBERON:0005085 ! ectodermal placode relationship: part_of GO:0071697 ! ectodermal placode morphogenesis relationship: results_in_formation_of UBERON:0005085 ! ectodermal placode -created_by: dph creation_date: 2009-08-04T12:15:57Z [Term] @@ -102394,7 +107252,6 @@ intersection_of: GO:0048646 ! anatomical structure formation involved in morphog intersection_of: results_in_formation_of UBERON:0005086 ! hair follicle placode relationship: part_of GO:0001942 ! hair follicle development relationship: results_in_formation_of UBERON:0005086 ! hair follicle placode -created_by: dph creation_date: 2009-08-04T12:18:26Z [Term] @@ -102407,7 +107264,6 @@ intersection_of: GO:0048646 ! anatomical structure formation involved in morphog intersection_of: results_in_formation_of UBERON:0005087 ! tooth placode relationship: part_of GO:0042475 ! odontogenesis of dentin-containing tooth relationship: results_in_formation_of UBERON:0005087 ! tooth placode -created_by: dph creation_date: 2009-08-04T12:21:47Z [Term] @@ -102420,7 +107276,6 @@ intersection_of: GO:0048646 ! anatomical structure formation involved in morphog intersection_of: results_in_formation_of UBERON:0005088 ! sebaceous gland placode relationship: part_of GO:0048733 ! sebaceous gland development relationship: results_in_formation_of UBERON:0005088 ! sebaceous gland placode -created_by: dph creation_date: 2009-08-04T12:23:09Z [Term] @@ -102432,7 +107287,6 @@ is_a: GO:0048732 ! gland development intersection_of: GO:0048732 ! gland development intersection_of: results_in_development_of UBERON:0001820 ! sweat gland relationship: results_in_development_of UBERON:0001820 ! sweat gland -created_by: dph creation_date: 2009-08-04T12:35:12Z [Term] @@ -102445,7 +107299,6 @@ intersection_of: GO:0048646 ! anatomical structure formation involved in morphog intersection_of: results_in_formation_of UBERON:0005089 ! sweat gland placode relationship: part_of GO:0060792 ! sweat gland development relationship: results_in_formation_of UBERON:0005089 ! sweat gland placode -created_by: dph creation_date: 2009-08-04T12:38:10Z [Term] @@ -102457,7 +107310,6 @@ is_a: GO:0045165 ! cell fate commitment intersection_of: GO:0045165 ! cell fate commitment intersection_of: part_of GO:0001704 ! formation of primary germ layer relationship: part_of GO:0001704 ! formation of primary germ layer -created_by: dph creation_date: 2009-08-04T03:11:22Z [Term] @@ -102470,7 +107322,6 @@ is_a: GO:2000241 ! regulation of reproductive process intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0060706 ! cell differentiation involved in embryonic placenta development relationship: regulates GO:0060706 ! cell differentiation involved in embryonic placenta development -created_by: dph creation_date: 2009-08-06T01:20:25Z [Term] @@ -102484,7 +107335,6 @@ is_a: GO:2000242 ! negative regulation of reproductive process intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0060706 ! cell differentiation involved in embryonic placenta development relationship: negatively_regulates GO:0060706 ! cell differentiation involved in embryonic placenta development -created_by: dph creation_date: 2009-08-06T02:02:18Z [Term] @@ -102496,7 +107346,6 @@ is_a: GO:0006417 ! regulation of translation intersection_of: GO:0006417 ! regulation of translation intersection_of: part_of GO:0009948 ! anterior/posterior axis specification relationship: part_of GO:0009948 ! anterior/posterior axis specification -created_by: dph creation_date: 2009-08-07T10:02:31Z [Term] @@ -102509,7 +107358,6 @@ intersection_of: GO:0030154 ! cell differentiation intersection_of: results_in_acquisition_of_features_of CL:0002138 ! endothelial cell of lymphatic vessel relationship: part_of GO:0001945 ! lymph vessel development relationship: results_in_acquisition_of_features_of CL:0002138 ! endothelial cell of lymphatic vessel -created_by: dph creation_date: 2009-08-11T03:45:20Z [Term] @@ -102522,7 +107370,6 @@ intersection_of: GO:0030154 ! cell differentiation intersection_of: results_in_acquisition_of_features_of CL:0000071 ! blood vessel endothelial cell relationship: part_of GO:0001568 ! blood vessel development relationship: results_in_acquisition_of_features_of CL:0000071 ! blood vessel endothelial cell -created_by: dph creation_date: 2009-08-11T03:47:36Z [Term] @@ -102534,7 +107381,6 @@ is_a: GO:0001568 ! blood vessel development intersection_of: GO:0048856 ! anatomical structure development intersection_of: results_in_development_of UBERON:0001637 ! artery relationship: results_in_development_of UBERON:0001637 ! artery -created_by: dph creation_date: 2009-08-12T10:10:51Z [Term] @@ -102546,7 +107392,6 @@ is_a: GO:0001568 ! blood vessel development intersection_of: GO:0048856 ! anatomical structure development intersection_of: results_in_development_of UBERON:0001638 ! vein relationship: results_in_development_of UBERON:0001638 ! vein -created_by: dph creation_date: 2009-08-12T10:14:07Z [Term] @@ -102558,7 +107403,6 @@ is_a: GO:0060837 ! blood vessel endothelial cell differentiation intersection_of: GO:0030154 ! cell differentiation intersection_of: results_in_acquisition_of_features_of CL:1000413 ! endothelial cell of artery relationship: results_in_acquisition_of_features_of CL:1000413 ! endothelial cell of artery -created_by: dph creation_date: 2009-08-12T10:41:34Z [Term] @@ -102570,7 +107414,6 @@ is_a: GO:0060837 ! blood vessel endothelial cell differentiation intersection_of: GO:0030154 ! cell differentiation intersection_of: results_in_acquisition_of_features_of CL:0002543 ! vein endothelial cell relationship: results_in_acquisition_of_features_of CL:0002543 ! vein endothelial cell -created_by: dph creation_date: 2009-08-12T10:43:40Z [Term] @@ -102583,7 +107426,6 @@ is_a: GO:0048754 ! branching morphogenesis of an epithelial tube intersection_of: GO:0048754 ! branching morphogenesis of an epithelial tube intersection_of: part_of GO:0036303 ! lymph vessel morphogenesis relationship: part_of GO:0001946 ! lymphangiogenesis -created_by: dph creation_date: 2009-08-12T12:00:48Z [Term] @@ -102596,7 +107438,6 @@ intersection_of: GO:0048856 ! anatomical structure development intersection_of: results_in_development_of UBERON:0001840 ! semicircular canal relationship: part_of GO:0048839 ! inner ear development relationship: results_in_development_of UBERON:0001840 ! semicircular canal -created_by: dph creation_date: 2009-08-13T09:36:37Z [Term] @@ -102609,7 +107450,6 @@ intersection_of: GO:0048646 ! anatomical structure formation involved in morphog intersection_of: results_in_formation_of UBERON:0001840 ! semicircular canal relationship: part_of GO:0048752 ! semicircular canal morphogenesis relationship: results_in_formation_of UBERON:0001840 ! semicircular canal -created_by: dph creation_date: 2009-08-13T09:45:07Z [Term] @@ -102621,7 +107461,6 @@ is_a: GO:0003002 ! regionalization intersection_of: GO:0003002 ! regionalization intersection_of: part_of GO:0060876 ! semicircular canal formation relationship: part_of GO:0060876 ! semicircular canal formation -created_by: dph creation_date: 2009-08-13T09:56:45Z [Term] @@ -102634,7 +107473,6 @@ is_a: GO:0060571 ! morphogenesis of an epithelial fold intersection_of: GO:0060571 ! morphogenesis of an epithelial fold intersection_of: part_of GO:0060876 ! semicircular canal formation relationship: part_of GO:0060876 ! semicircular canal formation -created_by: dph creation_date: 2009-08-13T10:01:01Z [Term] @@ -102647,7 +107485,6 @@ intersection_of: GO:0048856 ! anatomical structure development intersection_of: results_in_development_of UBERON:0009200 ! limb epidermis relationship: part_of GO:0060173 ! limb development relationship: results_in_development_of UBERON:0009200 ! limb epidermis -created_by: dph creation_date: 2009-08-13T12:39:39Z [Term] @@ -102656,7 +107493,6 @@ name: neural plate pattern specification namespace: biological_process def: "The developmental process that results in the creation of defined areas or spaces within the neural plate to which cells respond and eventually are instructed to differentiate." [GOC:dph, GOC:sdb_2009, GOC:tb] is_a: GO:0007389 ! pattern specification process -created_by: dph creation_date: 2009-08-13T02:06:27Z [Term] @@ -102666,7 +107502,6 @@ namespace: biological_process def: "The pattern specification process that results in the subdivision of an axis or axes of the neural plate in space to define an area or volume in which specific patterns of cell differentiation will take place or in which cells interpret a specific environment." [GOC:dph, GOC:sdb_2009, GOC:tb] is_a: GO:0003002 ! regionalization is_a: GO:0060896 ! neural plate pattern specification -created_by: dph creation_date: 2009-08-13T02:09:04Z [Term] @@ -102676,7 +107511,6 @@ namespace: biological_process def: "The developmental process pertaining to the initial formation of a camera-type eye from unspecified neurectoderm. This process begins with the differentiation of cells that form the optic field and ends when the optic cup has attained its shape." [GOC:dph, GOC:sdb_2009, GOC:tb] is_a: GO:0048646 ! anatomical structure formation involved in morphogenesis relationship: part_of GO:0048596 ! embryonic camera-type eye morphogenesis -created_by: dph creation_date: 2009-08-13T02:26:54Z [Term] @@ -102689,7 +107523,6 @@ is_a: GO:0061081 ! positive regulation of myeloid leukocyte cytokine production intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0010934 ! macrophage cytokine production relationship: positively_regulates GO:0010934 ! macrophage cytokine production -created_by: dph creation_date: 2009-09-04T02:32:18Z [Term] @@ -102703,7 +107536,6 @@ intersection_of: GO:0048646 ! anatomical structure formation involved in morphog intersection_of: results_in_formation_of UBERON:0000948 ! heart relationship: part_of GO:0003007 ! heart morphogenesis relationship: results_in_formation_of UBERON:0000948 ! heart -created_by: dph creation_date: 2009-09-17T09:02:13Z [Term] @@ -102715,7 +107547,6 @@ is_a: GO:0048762 ! mesenchymal cell differentiation intersection_of: GO:0048762 ! mesenchymal cell differentiation intersection_of: part_of GO:0030324 ! lung development relationship: part_of GO:0030324 ! lung development -created_by: dph creation_date: 2009-09-18T11:45:33Z [Term] @@ -102727,7 +107558,6 @@ is_a: GO:0010463 ! mesenchymal cell proliferation intersection_of: GO:0010463 ! mesenchymal cell proliferation intersection_of: part_of GO:0030324 ! lung development relationship: part_of GO:0030324 ! lung development -created_by: dph creation_date: 2009-09-18T11:50:17Z [Term] @@ -102740,7 +107570,6 @@ is_a: GO:0055007 ! cardiac muscle cell differentiation intersection_of: GO:0030154 ! cell differentiation intersection_of: results_in_acquisition_of_features_of CL:0002072 ! nodal myocyte relationship: results_in_acquisition_of_features_of CL:0002072 ! nodal myocyte -created_by: dph creation_date: 2009-09-29T11:01:31Z [Term] @@ -102756,7 +107585,6 @@ intersection_of: GO:0030154 ! cell differentiation intersection_of: results_in_acquisition_of_features_of CL:1000409 ! myocyte of sinoatrial node relationship: part_of GO:0003163 ! sinoatrial node development relationship: results_in_acquisition_of_features_of CL:1000409 ! myocyte of sinoatrial node -created_by: dph creation_date: 2009-09-29T11:03:30Z [Term] @@ -102771,7 +107599,6 @@ intersection_of: GO:0030154 ! cell differentiation intersection_of: results_in_acquisition_of_features_of CL:1000410 ! myocyte of atrioventricular node relationship: part_of GO:0003162 ! atrioventricular node development relationship: results_in_acquisition_of_features_of CL:1000410 ! myocyte of atrioventricular node -created_by: dph creation_date: 2009-09-29T11:07:06Z [Term] @@ -102785,7 +107612,6 @@ intersection_of: GO:0048856 ! anatomical structure development intersection_of: results_in_development_of CL:0002072 ! nodal myocyte relationship: part_of GO:0060920 ! cardiac pacemaker cell differentiation relationship: results_in_development_of CL:0002072 ! nodal myocyte -created_by: dph creation_date: 2009-09-29T11:51:55Z [Term] @@ -102799,7 +107625,6 @@ intersection_of: GO:0048468 ! cell development intersection_of: results_in_development_of CL:1000410 ! myocyte of atrioventricular node relationship: part_of GO:0060922 ! atrioventricular node cell differentiation relationship: results_in_development_of CL:1000410 ! myocyte of atrioventricular node -created_by: dph creation_date: 2009-09-29T11:59:26Z [Term] @@ -102815,7 +107640,6 @@ intersection_of: GO:0048468 ! cell development intersection_of: results_in_development_of CL:1000409 ! myocyte of sinoatrial node relationship: part_of GO:0060921 ! sinoatrial node cell differentiation relationship: results_in_development_of CL:1000409 ! myocyte of sinoatrial node -created_by: dph creation_date: 2009-09-29T12:05:47Z [Term] @@ -102828,7 +107652,6 @@ intersection_of: GO:0030154 ! cell differentiation intersection_of: results_in_acquisition_of_features_of CL:0010007 ! His-Purkinje system cell relationship: part_of GO:0003164 ! His-Purkinje system development relationship: results_in_acquisition_of_features_of CL:0010007 ! His-Purkinje system cell -created_by: dph creation_date: 2009-09-29T01:10:32Z [Term] @@ -102841,7 +107664,6 @@ intersection_of: GO:0048468 ! cell development intersection_of: results_in_development_of CL:0010007 ! His-Purkinje system cell relationship: part_of GO:0060932 ! His-Purkinje system cell differentiation relationship: results_in_development_of CL:0010007 ! His-Purkinje system cell -created_by: dph creation_date: 2009-09-29T01:15:02Z [Term] @@ -102853,7 +107675,6 @@ is_a: GO:0035051 ! cardiocyte differentiation intersection_of: GO:0030154 ! cell differentiation intersection_of: results_in_acquisition_of_features_of CL:0002548 ! fibroblast of cardiac tissue relationship: results_in_acquisition_of_features_of CL:0002548 ! fibroblast of cardiac tissue -created_by: dph creation_date: 2009-09-29T01:20:04Z [Term] @@ -102866,7 +107687,6 @@ intersection_of: GO:0048468 ! cell development intersection_of: results_in_development_of CL:0002548 ! fibroblast of cardiac tissue relationship: part_of GO:0060935 ! cardiac fibroblast cell differentiation relationship: results_in_development_of CL:0002548 ! fibroblast of cardiac tissue -created_by: dph creation_date: 2009-09-29T01:23:03Z [Term] @@ -102875,13 +107695,12 @@ name: cardiac neuron differentiation namespace: biological_process def: "The process in which a relatively unspecialized cell acquires specialized features of a neuron of the heart." [GOC:mtg_heart] synonym: "heart neuron differentiation" EXACT [GOC:mtg_heart] -is_a: GO:0030182 ! neuron differentiation is_a: GO:0035051 ! cardiocyte differentiation +is_a: GO:0048934 ! peripheral nervous system neuron differentiation intersection_of: GO:0030154 ! cell differentiation intersection_of: results_in_acquisition_of_features_of CL:0010022 ! cardiac neuron relationship: part_of GO:0048483 ! autonomic nervous system development relationship: results_in_acquisition_of_features_of CL:0010022 ! cardiac neuron -created_by: dph creation_date: 2009-09-29T02:45:33Z [Term] @@ -102894,7 +107713,6 @@ is_a: GO:0060837 ! blood vessel endothelial cell differentiation intersection_of: GO:0030154 ! cell differentiation intersection_of: results_in_acquisition_of_features_of CL:0010006 ! cardiac blood vessel endothelial cell relationship: results_in_acquisition_of_features_of CL:0010006 ! cardiac blood vessel endothelial cell -created_by: dph creation_date: 2009-09-29T02:48:55Z [Term] @@ -102907,7 +107725,6 @@ is_a: GO:0035051 ! cardiocyte differentiation intersection_of: GO:0030154 ! cell differentiation intersection_of: results_in_acquisition_of_features_of CL:0010020 ! cardiac glial cell relationship: results_in_acquisition_of_features_of CL:0010020 ! cardiac glial cell -created_by: dph creation_date: 2009-09-29T03:06:37Z [Term] @@ -102921,7 +107738,6 @@ intersection_of: GO:0048468 ! cell development intersection_of: results_in_development_of CL:0010020 ! cardiac glial cell relationship: part_of GO:0060950 ! cardiac glial cell differentiation relationship: results_in_development_of CL:0010020 ! cardiac glial cell -created_by: dph creation_date: 2009-09-29T03:09:24Z [Term] @@ -102934,7 +107750,6 @@ intersection_of: GO:0030154 ! cell differentiation intersection_of: results_in_acquisition_of_features_of CL:0002350 ! endocardial cell relationship: part_of GO:0003157 ! endocardium development relationship: results_in_acquisition_of_features_of CL:0002350 ! endocardial cell -created_by: dph creation_date: 2009-09-29T03:20:39Z [Term] @@ -102948,7 +107763,6 @@ intersection_of: GO:0048856 ! anatomical structure development intersection_of: results_in_development_of CL:0002350 ! endocardial cell relationship: part_of GO:0060956 ! endocardial cell differentiation relationship: results_in_development_of CL:0002350 ! endocardial cell -created_by: dph creation_date: 2009-09-29T03:26:59Z [Term] @@ -102957,13 +107771,12 @@ name: cardiac neuron development namespace: biological_process def: "The process whose specific outcome is the progression of a cardiac neuron over time, from its formation to the mature state." [GOC:mtg_heart] synonym: "heart neuron development" EXACT [GOC:mtg_heart] -is_a: GO:0048666 ! neuron development +is_a: GO:0048935 ! peripheral nervous system neuron development is_a: GO:0055006 ! cardiac cell development intersection_of: GO:0048468 ! cell development intersection_of: results_in_development_of CL:0010022 ! cardiac neuron relationship: part_of GO:0060945 ! cardiac neuron differentiation relationship: results_in_development_of CL:0010022 ! cardiac neuron -created_by: dph creation_date: 2009-09-30T10:14:56Z [Term] @@ -102975,7 +107788,6 @@ is_a: GO:0016477 ! cell migration intersection_of: GO:0016477 ! cell migration intersection_of: part_of GO:0007507 ! heart development relationship: part_of GO:0007507 ! heart development -created_by: dph creation_date: 2009-10-06T10:53:49Z [Term] @@ -102987,7 +107799,6 @@ is_a: GO:0060973 ! cell migration involved in heart development intersection_of: GO:0016477 ! cell migration intersection_of: part_of GO:0060914 ! heart formation relationship: part_of GO:0060914 ! heart formation -created_by: dph creation_date: 2009-10-06T10:56:33Z [Term] @@ -103005,7 +107816,6 @@ intersection_of: GO:0048856 ! anatomical structure development intersection_of: results_in_development_of UBERON:0003498 ! heart blood vessel relationship: part_of GO:0007507 ! heart development relationship: results_in_development_of UBERON:0003498 ! heart blood vessel -created_by: dph creation_date: 2009-10-06T12:15:23Z [Term] @@ -103023,7 +107833,6 @@ intersection_of: GO:0009653 ! anatomical structure morphogenesis intersection_of: results_in_morphogenesis_of UBERON:0003498 ! heart blood vessel relationship: part_of GO:0060976 ! coronary vasculature development relationship: results_in_morphogenesis_of UBERON:0003498 ! heart blood vessel -created_by: dph creation_date: 2009-10-06T12:28:23Z [Term] @@ -103039,7 +107848,6 @@ is_a: GO:0001525 ! angiogenesis intersection_of: GO:0001525 ! angiogenesis intersection_of: part_of GO:0060976 ! coronary vasculature development relationship: part_of GO:0060977 ! coronary vasculature morphogenesis -created_by: dph creation_date: 2009-10-06T02:02:12Z [Term] @@ -103053,7 +107861,6 @@ is_a: GO:0001570 ! vasculogenesis intersection_of: GO:0001570 ! vasculogenesis intersection_of: part_of GO:0060977 ! coronary vasculature morphogenesis relationship: part_of GO:0060977 ! coronary vasculature morphogenesis -created_by: dph creation_date: 2009-10-06T02:19:42Z [Term] @@ -103066,7 +107873,6 @@ is_a: GO:0060973 ! cell migration involved in heart development intersection_of: GO:0016477 ! cell migration intersection_of: part_of GO:0060979 ! vasculogenesis involved in coronary vascular morphogenesis relationship: part_of GO:0060979 ! vasculogenesis involved in coronary vascular morphogenesis -created_by: dph creation_date: 2009-10-06T02:33:06Z [Term] @@ -103078,7 +107884,6 @@ is_a: GO:0060973 ! cell migration involved in heart development intersection_of: GO:0016477 ! cell migration intersection_of: part_of GO:0060978 ! angiogenesis involved in coronary vascular morphogenesis relationship: part_of GO:0060978 ! angiogenesis involved in coronary vascular morphogenesis -created_by: dph creation_date: 2009-10-06T02:49:12Z [Term] @@ -103091,7 +107896,6 @@ is_a: GO:0060977 ! coronary vasculature morphogenesis intersection_of: GO:0009653 ! anatomical structure morphogenesis intersection_of: results_in_morphogenesis_of UBERON:0001621 ! coronary artery relationship: results_in_morphogenesis_of UBERON:0001621 ! coronary artery -created_by: dph creation_date: 2009-10-06T02:58:52Z [Term] @@ -103101,7 +107905,6 @@ namespace: biological_process def: "The regulated release of a hormone into the circulatory system." [GOC:dph] is_a: GO:0046879 ! hormone secretion relationship: part_of GO:0050886 ! endocrine process -created_by: dph creation_date: 2010-01-11T09:03:48Z [Term] @@ -103114,7 +107917,6 @@ intersection_of: GO:0009653 ! anatomical structure morphogenesis intersection_of: results_in_morphogenesis_of UBERON:0002113 ! kidney relationship: part_of GO:0001822 ! kidney development relationship: results_in_morphogenesis_of UBERON:0002113 ! kidney -created_by: dph creation_date: 2010-01-19T08:16:55Z [Term] @@ -103127,7 +107929,6 @@ is_a: GO:0007267 ! cell-cell signaling intersection_of: GO:0007267 ! cell-cell signaling intersection_of: part_of GO:0001822 ! kidney development relationship: part_of GO:0001822 ! kidney development -created_by: dph creation_date: 2010-01-19T08:33:40Z [Term] @@ -103143,7 +107944,6 @@ intersection_of: GO:0007389 ! pattern specification process intersection_of: part_of GO:0001822 ! kidney development relationship: part_of GO:0001822 ! kidney development relationship: part_of GO:0072048 ! renal system pattern specification -created_by: dph creation_date: 2010-01-21T09:05:54Z [Term] @@ -103155,7 +107955,6 @@ is_a: GO:0030154 ! cell differentiation intersection_of: GO:0030154 ! cell differentiation intersection_of: part_of GO:0001822 ! kidney development relationship: part_of GO:0001822 ! kidney development -created_by: dph creation_date: 2010-01-21T09:13:55Z [Term] @@ -103167,7 +107966,6 @@ is_a: GO:0042127 ! regulation of cell population proliferation intersection_of: GO:0042127 ! regulation of cell population proliferation intersection_of: part_of GO:0060993 ! kidney morphogenesis relationship: part_of GO:0060993 ! kidney morphogenesis -created_by: dph creation_date: 2010-01-21T11:25:23Z [Term] @@ -103178,7 +107976,6 @@ def: "An system process carried out by any of the organs or tissues of the hepat subset: goslim_generic synonym: "hepatobiliary system process" EXACT [GOC:dph] is_a: GO:0003008 ! system process -created_by: dph creation_date: 2010-01-22T09:09:10Z [Term] @@ -103191,7 +107988,6 @@ is_a: GO:0048731 ! system development intersection_of: GO:0048856 ! anatomical structure development intersection_of: results_in_development_of UBERON:0002423 ! hepatobiliary system relationship: results_in_development_of UBERON:0002423 ! hepatobiliary system -created_by: dph creation_date: 2010-01-22T09:11:59Z [Term] @@ -103208,7 +108004,6 @@ intersection_of: GO:0048856 ! anatomical structure development intersection_of: results_in_development_of UBERON:0002394 ! bile duct relationship: part_of GO:0061008 ! hepaticobiliary system development relationship: results_in_development_of UBERON:0002394 ! bile duct -created_by: dph creation_date: 2010-01-22T09:17:13Z [Term] @@ -103221,7 +108016,6 @@ intersection_of: GO:0048856 ! anatomical structure development intersection_of: results_in_development_of UBERON:0002110 ! gallbladder relationship: part_of GO:0061008 ! hepaticobiliary system development relationship: results_in_development_of UBERON:0002110 ! gallbladder -created_by: dph creation_date: 2010-01-22T09:38:44Z [Term] @@ -103233,7 +108027,6 @@ is_a: GO:0061009 ! common bile duct development intersection_of: GO:0048856 ! anatomical structure development intersection_of: results_in_development_of UBERON:0001175 ! common hepatic duct relationship: results_in_development_of UBERON:0001175 ! common hepatic duct -created_by: dph creation_date: 2010-01-22T09:44:39Z [Term] @@ -103247,15 +108040,12 @@ intersection_of: GO:0030154 ! cell differentiation intersection_of: results_in_acquisition_of_features_of CL:1000488 ! cholangiocyte relationship: part_of GO:0001889 ! liver development relationship: results_in_acquisition_of_features_of CL:1000488 ! cholangiocyte -created_by: dph creation_date: 2010-02-02T09:08:03Z [Term] id: GO:0061024 name: membrane organization namespace: biological_process -alt_id: GO:0016044 -alt_id: GO:0044802 def: "A process which results in the assembly, arrangement of constituent parts, or disassembly of a membrane. A membrane is a double layer of lipid molecules that encloses all cells, and, in eukaryotes, many organelles; may be a single or double lipid bilayer; also includes associated proteins." [GOC:dph, GOC:tb] subset: goslim_chembl subset: goslim_drosophila @@ -103272,15 +108062,12 @@ is_a: GO:0016043 ! cellular component organization intersection_of: GO:0016043 ! cellular component organization intersection_of: results_in_organization_of GO:0016020 ! membrane relationship: results_in_organization_of GO:0016020 ! membrane -created_by: jl creation_date: 2010-02-08T02:43:11Z [Term] id: GO:0061025 name: membrane fusion namespace: biological_process -alt_id: GO:0006944 -alt_id: GO:0044801 def: "The membrane organization process that joins two lipid bilayers to form a single membrane." [GOC:dph, GOC:tb] subset: goslim_yeast synonym: "cellular membrane fusion" EXACT [] @@ -103290,7 +108077,6 @@ is_a: GO:0061024 ! membrane organization intersection_of: GO:0061024 ! membrane organization intersection_of: results_in_fusion_of GO:0016020 ! membrane relationship: results_in_fusion_of GO:0016020 ! membrane -created_by: jl creation_date: 2010-02-08T02:48:06Z [Term] @@ -103302,7 +108088,6 @@ is_a: GO:0048856 ! anatomical structure development intersection_of: GO:0048856 ! anatomical structure development intersection_of: results_in_development_of UBERON:0002331 ! umbilical cord relationship: results_in_development_of UBERON:0002331 ! umbilical cord -created_by: dph creation_date: 2010-02-09T09:09:22Z [Term] @@ -103315,7 +108100,6 @@ intersection_of: GO:0048856 ! anatomical structure development intersection_of: results_in_development_of UBERON:0001711 ! eyelid relationship: part_of GO:0043010 ! camera-type eye development relationship: results_in_development_of UBERON:0001711 ! eyelid -created_by: dph creation_date: 2010-02-09T09:36:11Z [Term] @@ -103327,7 +108111,6 @@ is_a: GO:0060644 ! mammary gland epithelial cell differentiation intersection_of: GO:0030855 ! epithelial cell differentiation intersection_of: part_of GO:0060749 ! mammary gland alveolus development relationship: part_of GO:0060749 ! mammary gland alveolus development -created_by: dph creation_date: 2010-02-09T09:43:00Z [Term] @@ -103341,7 +108124,6 @@ intersection_of: GO:0048856 ! anatomical structure development intersection_of: results_in_development_of UBERON:0002425 ! visceral serous pericardium relationship: part_of GO:0060039 ! pericardium development relationship: results_in_development_of UBERON:0002425 ! visceral serous pericardium -created_by: dph creation_date: 2010-02-09T09:52:49Z [Term] @@ -103354,7 +108136,6 @@ intersection_of: GO:0048856 ! anatomical structure development intersection_of: results_in_development_of UBERON:0004186 ! olfactory bulb mitral cell layer relationship: part_of GO:0021772 ! olfactory bulb development relationship: results_in_development_of UBERON:0004186 ! olfactory bulb mitral cell layer -created_by: dph creation_date: 2010-02-09T03:30:23Z [Term] @@ -103366,7 +108147,6 @@ is_a: GO:2000026 ! regulation of multicellular organismal development intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0051216 ! cartilage development relationship: regulates GO:0051216 ! cartilage development -created_by: dph creation_date: 2010-02-09T03:41:35Z [Term] @@ -103380,7 +108160,6 @@ is_a: GO:0061035 ! regulation of cartilage development intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0051216 ! cartilage development relationship: positively_regulates GO:0051216 ! cartilage development -created_by: dph creation_date: 2010-02-09T03:41:35Z [Term] @@ -103394,7 +108173,6 @@ is_a: GO:0061035 ! regulation of cartilage development intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0051216 ! cartilage development relationship: negatively_regulates GO:0051216 ! cartilage development -created_by: dph creation_date: 2010-02-09T03:41:35Z [Term] @@ -103408,7 +108186,6 @@ intersection_of: GO:0009653 ! anatomical structure morphogenesis intersection_of: results_in_morphogenesis_of UBERON:0000995 ! uterus relationship: part_of GO:0060065 ! uterus development relationship: results_in_morphogenesis_of UBERON:0000995 ! uterus -created_by: dph creation_date: 2010-02-22T11:12:35Z [Term] @@ -103422,7 +108199,6 @@ intersection_of: GO:0009653 ! anatomical structure morphogenesis intersection_of: results_in_morphogenesis_of UBERON:0000992 ! ovary relationship: part_of GO:0008585 ! female gonad development relationship: results_in_morphogenesis_of UBERON:0000992 ! ovary -created_by: dph creation_date: 2010-02-22T11:29:28Z [Term] @@ -103434,7 +108210,6 @@ is_a: GO:1903034 ! regulation of response to wounding intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0042060 ! wound healing relationship: regulates GO:0042060 ! wound healing -created_by: dph creation_date: 2010-02-25T10:14:37Z [Term] @@ -103448,7 +108223,6 @@ is_a: GO:1903035 ! negative regulation of response to wounding intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0042060 ! wound healing relationship: negatively_regulates GO:0042060 ! wound healing -created_by: dph creation_date: 2010-02-25T10:33:30Z [Term] @@ -103461,7 +108235,6 @@ is_a: GO:1905330 ! regulation of morphogenesis of an epithelium intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0060441 ! epithelial tube branching involved in lung morphogenesis relationship: regulates GO:0060441 ! epithelial tube branching involved in lung morphogenesis -created_by: dph creation_date: 2010-02-25T10:41:38Z [Term] @@ -103475,7 +108248,6 @@ is_a: GO:1905332 ! positive regulation of morphogenesis of an epithelium intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0060441 ! epithelial tube branching involved in lung morphogenesis relationship: positively_regulates GO:0060441 ! epithelial tube branching involved in lung morphogenesis -created_by: dph creation_date: 2010-02-25T10:50:01Z [Term] @@ -103489,7 +108261,6 @@ is_a: GO:1905331 ! negative regulation of morphogenesis of an epithelium intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0060441 ! epithelial tube branching involved in lung morphogenesis relationship: negatively_regulates GO:0060441 ! epithelial tube branching involved in lung morphogenesis -created_by: dph creation_date: 2010-02-25T10:51:31Z [Term] @@ -103505,7 +108276,6 @@ intersection_of: GO:0016049 ! cell growth intersection_of: part_of GO:0055013 ! cardiac muscle cell development relationship: part_of GO:0003301 ! physiological cardiac muscle hypertrophy relationship: part_of GO:0055013 ! cardiac muscle cell development -created_by: dph creation_date: 2010-02-25T12:56:07Z [Term] @@ -103518,7 +108288,6 @@ is_a: GO:0055021 ! regulation of cardiac muscle tissue growth intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0061049 ! cell growth involved in cardiac muscle cell development relationship: regulates GO:0061049 ! cell growth involved in cardiac muscle cell development -created_by: dph creation_date: 2010-02-25T01:05:16Z [Term] @@ -103534,7 +108303,6 @@ is_a: GO:0061050 ! regulation of cell growth involved in cardiac muscle cell dev intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0061049 ! cell growth involved in cardiac muscle cell development relationship: positively_regulates GO:0061049 ! cell growth involved in cardiac muscle cell development -created_by: dph creation_date: 2010-02-25T01:08:08Z [Term] @@ -103550,7 +108318,6 @@ is_a: GO:0061050 ! regulation of cell growth involved in cardiac muscle cell dev intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0061049 ! cell growth involved in cardiac muscle cell development relationship: negatively_regulates GO:0061049 ! cell growth involved in cardiac muscle cell development -created_by: dph creation_date: 2010-02-25T01:11:30Z [Term] @@ -103563,7 +108330,6 @@ intersection_of: GO:0048856 ! anatomical structure development intersection_of: results_in_development_of UBERON:0002329 ! somite relationship: part_of GO:0009790 ! embryo development relationship: results_in_development_of UBERON:0002329 ! somite -created_by: dph creation_date: 2010-03-02T12:05:13Z [Term] @@ -103576,7 +108342,6 @@ intersection_of: GO:0048856 ! anatomical structure development intersection_of: results_in_development_of UBERON:0004016 ! dermatome relationship: part_of GO:0061053 ! somite development relationship: results_in_development_of UBERON:0004016 ! dermatome -created_by: dph creation_date: 2010-03-02T12:07:37Z [Term] @@ -103589,7 +108354,6 @@ intersection_of: GO:0048856 ! anatomical structure development intersection_of: results_in_development_of UBERON:0003082 ! myotome relationship: part_of GO:0061053 ! somite development relationship: results_in_development_of UBERON:0003082 ! myotome -created_by: dph creation_date: 2010-03-02T12:11:01Z [Term] @@ -103602,7 +108366,6 @@ intersection_of: GO:0048856 ! anatomical structure development intersection_of: results_in_development_of UBERON:0003089 ! sclerotome relationship: part_of GO:0061053 ! somite development relationship: results_in_development_of UBERON:0003089 ! sclerotome -created_by: dph creation_date: 2010-03-02T12:12:40Z [Term] @@ -103617,7 +108380,6 @@ intersection_of: results_in_development_of UBERON:0005090 ! muscle structure relationship: results_in_development_of UBERON:0005090 ! muscle structure relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa relationship: RO:0002162 NCBITaxon:6072 {all_only="true"} ! in taxon Eumetazoa -created_by: dph creation_date: 2010-03-09T08:55:14Z [Term] @@ -103630,7 +108392,6 @@ intersection_of: GO:0048856 ! anatomical structure development intersection_of: results_in_development_of UBERON:0000057 ! urethra relationship: part_of GO:0072001 ! renal system development relationship: results_in_development_of UBERON:0000057 ! urethra -created_by: dph creation_date: 2010-03-12T08:24:52Z [Term] @@ -103642,7 +108403,6 @@ is_a: GO:0061068 ! urethra development intersection_of: GO:0048856 ! anatomical structure development intersection_of: results_in_development_of UBERON:0001333 ! male urethra relationship: results_in_development_of UBERON:0001333 ! male urethra -created_by: dph creation_date: 2010-03-12T08:28:19Z [Term] @@ -103654,7 +108414,6 @@ is_a: GO:0061068 ! urethra development intersection_of: GO:0048856 ! anatomical structure development intersection_of: results_in_development_of UBERON:0001334 ! female urethra relationship: results_in_development_of UBERON:0001334 ! female urethra -created_by: dph creation_date: 2010-03-12T08:29:43Z [Term] @@ -103668,7 +108427,6 @@ intersection_of: GO:0048856 ! anatomical structure development intersection_of: results_in_development_of UBERON:0002325 ! epithelium of urethra relationship: part_of GO:0061068 ! urethra development relationship: results_in_development_of UBERON:0002325 ! epithelium of urethra -created_by: dph creation_date: 2010-03-12T08:36:53Z [Term] @@ -103682,7 +108440,6 @@ intersection_of: GO:0009653 ! anatomical structure morphogenesis intersection_of: results_in_morphogenesis_of UBERON:0001769 ! iris relationship: part_of GO:0048593 ! camera-type eye morphogenesis relationship: results_in_morphogenesis_of UBERON:0001769 ! iris -created_by: dph creation_date: 2010-03-16T10:48:42Z [Term] @@ -103696,7 +108453,6 @@ intersection_of: GO:0009653 ! anatomical structure morphogenesis intersection_of: results_in_morphogenesis_of UBERON:0001775 ! ciliary body relationship: part_of GO:0048593 ! camera-type eye morphogenesis relationship: results_in_morphogenesis_of UBERON:0001775 ! ciliary body -created_by: dph creation_date: 2010-03-16T10:55:19Z [Term] @@ -103708,7 +108464,6 @@ is_a: GO:0050793 ! regulation of developmental process intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0003407 ! neural retina development relationship: regulates GO:0003407 ! neural retina development -created_by: dph creation_date: 2010-03-16T11:47:05Z [Term] @@ -103721,7 +108476,6 @@ is_a: GO:1902868 ! positive regulation of retina development in camera-type eye intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0003407 ! neural retina development relationship: positively_regulates GO:0003407 ! neural retina development -created_by: dph creation_date: 2010-03-16T11:59:48Z [Term] @@ -103734,7 +108488,6 @@ is_a: GO:1902867 ! negative regulation of retina development in camera-type eye intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0003407 ! neural retina development relationship: negatively_regulates GO:0003407 ! neural retina development -created_by: dph creation_date: 2010-03-16T12:46:11Z [Term] @@ -103747,7 +108500,6 @@ intersection_of: GO:0048856 ! anatomical structure development intersection_of: results_in_development_of UBERON:0005092 ! right horn of sinus venosus relationship: part_of GO:0003235 ! sinus venosus development relationship: results_in_development_of UBERON:0005092 ! right horn of sinus venosus -created_by: dph creation_date: 2010-04-08T02:45:10Z [Term] @@ -103760,7 +108512,6 @@ is_a: GO:0002720 ! positive regulation of cytokine production involved in immune intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0061082 ! myeloid leukocyte cytokine production relationship: positively_regulates GO:0061082 ! myeloid leukocyte cytokine production -created_by: dph creation_date: 2010-04-13T11:26:41Z [Term] @@ -103771,7 +108522,6 @@ def: "Any process that contributes to cytokine production by a myeloid cell." [G comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select one of the 'regulation' children terms. subset: gocheck_do_not_annotate is_a: GO:0002367 ! cytokine production involved in immune response -created_by: dph creation_date: 2010-04-13T11:29:42Z [Term] @@ -103785,7 +108535,6 @@ is_a: GO:0050730 ! regulation of peptidyl-tyrosine phosphorylation intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0004713 ! protein tyrosine kinase activity relationship: regulates GO:0004713 ! protein tyrosine kinase activity -created_by: dph creation_date: 2010-04-26T02:34:53Z [Term] @@ -103800,7 +108549,6 @@ is_a: GO:0061097 ! regulation of protein tyrosine kinase activity intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0004713 ! protein tyrosine kinase activity relationship: positively_regulates GO:0004713 ! protein tyrosine kinase activity -created_by: dph creation_date: 2010-04-26T02:34:53Z [Term] @@ -103815,7 +108563,6 @@ is_a: GO:0061097 ! regulation of protein tyrosine kinase activity intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0004713 ! protein tyrosine kinase activity relationship: negatively_regulates GO:0004713 ! protein tyrosine kinase activity -created_by: dph creation_date: 2010-04-26T02:34:53Z [Term] @@ -103826,9 +108573,8 @@ def: "The process in which a relatively unspecialized cell acquires specialized is_a: GO:0061101 ! neuroendocrine cell differentiation is_a: GO:0061140 ! lung secretory cell differentiation intersection_of: GO:0030154 ! cell differentiation -intersection_of: results_in_acquisition_of_features_of CL:1000223 ! lung neuroendocrine cell -relationship: results_in_acquisition_of_features_of CL:1000223 ! lung neuroendocrine cell -created_by: dph +intersection_of: results_in_acquisition_of_features_of CL:1000223 ! pulmonary neuroendocrine cell +relationship: results_in_acquisition_of_features_of CL:1000223 ! pulmonary neuroendocrine cell creation_date: 2010-04-27T03:28:46Z [Term] @@ -103841,7 +108587,6 @@ is_a: GO:0060563 ! neuroepithelial cell differentiation intersection_of: GO:0030154 ! cell differentiation intersection_of: results_in_acquisition_of_features_of CL:0000165 ! neuroendocrine cell relationship: results_in_acquisition_of_features_of CL:0000165 ! neuroendocrine cell -created_by: dph creation_date: 2010-04-28T09:42:20Z [Term] @@ -103856,7 +108601,6 @@ intersection_of: GO:0030154 ! cell differentiation intersection_of: results_in_acquisition_of_features_of CL:1000222 ! stomach neuroendocrine cell relationship: part_of GO:0062094 ! stomach development relationship: results_in_acquisition_of_features_of CL:1000222 ! stomach neuroendocrine cell -created_by: dph creation_date: 2010-04-28T09:47:07Z [Term] @@ -103870,7 +108614,6 @@ intersection_of: GO:0030154 ! cell differentiation intersection_of: results_in_acquisition_of_features_of CL:1000426 ! chromaffin cell of adrenal gland relationship: part_of GO:0030325 ! adrenal gland development relationship: results_in_acquisition_of_features_of CL:1000426 ! chromaffin cell of adrenal gland -created_by: dph creation_date: 2010-04-29T08:27:53Z [Term] @@ -103883,7 +108626,6 @@ is_a: GO:0045664 ! regulation of neuron differentiation intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0061102 ! stomach neuroendocrine cell differentiation relationship: regulates GO:0061102 ! stomach neuroendocrine cell differentiation -created_by: dph creation_date: 2010-04-29T12:19:37Z [Term] @@ -103897,7 +108639,6 @@ is_a: GO:0061105 ! regulation of stomach neuroendocrine cell differentiation intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0061102 ! stomach neuroendocrine cell differentiation relationship: negatively_regulates GO:0061102 ! stomach neuroendocrine cell differentiation -created_by: dph creation_date: 2010-04-29T12:23:05Z [Term] @@ -103910,7 +108651,6 @@ is_a: GO:0048732 ! gland development intersection_of: GO:0048856 ! anatomical structure development intersection_of: results_in_development_of UBERON:0000998 ! seminal vesicle relationship: results_in_development_of UBERON:0000998 ! seminal vesicle -created_by: dph creation_date: 2010-04-30T10:17:30Z [Term] @@ -103925,7 +108665,6 @@ intersection_of: GO:0048856 ! anatomical structure development intersection_of: results_in_development_of UBERON:0004805 ! seminal vesicle epithelium relationship: part_of GO:0061107 ! seminal vesicle development relationship: results_in_development_of UBERON:0004805 ! seminal vesicle epithelium -created_by: dph creation_date: 2010-04-30T10:19:54Z [Term] @@ -103938,7 +108677,6 @@ is_a: GO:0033363 ! secretory granule organization intersection_of: GO:0016043 ! cellular component organization intersection_of: results_in_organization_of GO:0031045 ! dense core granule relationship: results_in_organization_of GO:0031045 ! dense core granule -created_by: dph creation_date: 2010-05-01T09:34:37Z [Term] @@ -103951,7 +108689,6 @@ is_a: GO:0060495 ! cell-cell signaling involved in lung development is_a: GO:0060684 ! epithelial-mesenchymal cell signaling intersection_of: GO:0060684 ! epithelial-mesenchymal cell signaling intersection_of: part_of GO:0030324 ! lung development -created_by: dph creation_date: 2010-05-05T11:14:38Z [Term] @@ -103964,7 +108701,6 @@ intersection_of: GO:0009653 ! anatomical structure morphogenesis intersection_of: results_in_morphogenesis_of UBERON:0001264 ! pancreas relationship: part_of GO:0031016 ! pancreas development relationship: results_in_morphogenesis_of UBERON:0001264 ! pancreas -created_by: dph creation_date: 2010-05-05T11:55:30Z [Term] @@ -103976,7 +108712,6 @@ is_a: GO:0061138 ! morphogenesis of a branching epithelium intersection_of: GO:0061138 ! morphogenesis of a branching epithelium intersection_of: part_of GO:0061113 ! pancreas morphogenesis relationship: part_of GO:0061113 ! pancreas morphogenesis -created_by: dph creation_date: 2010-05-05T12:03:04Z [Term] @@ -103989,7 +108724,6 @@ is_a: GO:0060420 ! regulation of heart growth intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0060419 ! heart growth relationship: negatively_regulates GO:0060419 ! heart growth -created_by: dph creation_date: 2010-05-17T07:31:28Z [Term] @@ -104003,7 +108737,6 @@ is_a: GO:0072175 ! epithelial tube formation intersection_of: GO:0048646 ! anatomical structure formation involved in morphogenesis intersection_of: results_in_formation_of UBERON:0003922 ! pancreatic epithelial bud relationship: results_in_formation_of UBERON:0003922 ! pancreatic epithelial bud -created_by: dph creation_date: 2010-05-17T09:33:40Z [Term] @@ -104013,7 +108746,6 @@ namespace: biological_process def: "The process in which the anatomical structures of a branched epithelium are generated and organized." [GOC:dph] is_a: GO:0001763 ! morphogenesis of a branching structure is_a: GO:0002009 ! morphogenesis of an epithelium -created_by: dph creation_date: 2010-05-25T09:05:34Z [Term] @@ -104025,7 +108757,6 @@ is_a: GO:0060487 ! lung epithelial cell differentiation intersection_of: GO:0030154 ! cell differentiation intersection_of: results_in_acquisition_of_features_of CL:1000272 ! lung secretory cell relationship: results_in_acquisition_of_features_of CL:1000272 ! lung secretory cell -created_by: dph creation_date: 2010-05-25T09:28:53Z [Term] @@ -104034,10 +108765,10 @@ name: lung ciliated cell differentiation namespace: biological_process def: "The process in which a relatively unspecialized cell acquires specialized features of a lung ciliated cell. A lung ciliated cell is a specialized lung epithelial cell that contains cilia for moving substances released from lung secretory cells." [GOC:cilia, GOC:dph, GOC:krc] is_a: GO:0060487 ! lung epithelial cell differentiation +is_a: GO:1903251 ! multi-ciliated epithelial cell differentiation intersection_of: GO:0030154 ! cell differentiation -intersection_of: results_in_acquisition_of_features_of CL:1000271 ! lung ciliated cell -relationship: results_in_acquisition_of_features_of CL:1000271 ! lung ciliated cell -created_by: dph +intersection_of: results_in_acquisition_of_features_of CL:1000271 ! lung multiciliated epithelial cell +relationship: results_in_acquisition_of_features_of CL:1000271 ! lung multiciliated epithelial cell creation_date: 2010-05-25T09:31:14Z [Term] @@ -104050,7 +108781,6 @@ intersection_of: GO:0009653 ! anatomical structure morphogenesis intersection_of: results_in_morphogenesis_of UBERON:0001211 ! Peyer's patch relationship: part_of GO:0048541 ! Peyer's patch development relationship: results_in_morphogenesis_of UBERON:0001211 ! Peyer's patch -created_by: dph creation_date: 2010-05-26T06:46:23Z [Term] @@ -104063,7 +108793,6 @@ intersection_of: GO:0048856 ! anatomical structure development intersection_of: results_in_development_of UBERON:0005316 ! endocardial endothelium relationship: part_of GO:0003157 ! endocardium development relationship: results_in_development_of UBERON:0005316 ! endocardial endothelium -created_by: dph creation_date: 2010-06-03T09:15:31Z [Term] @@ -104076,7 +108805,6 @@ is_a: GO:0030198 ! extracellular matrix organization intersection_of: GO:0030198 ! extracellular matrix organization intersection_of: part_of GO:0003157 ! endocardium development relationship: part_of GO:0003157 ! endocardium development -created_by: dph creation_date: 2010-06-03T09:18:02Z [Term] @@ -104089,7 +108817,6 @@ intersection_of: GO:0048856 ! anatomical structure development intersection_of: results_in_development_of UBERON:0002202 ! submucosa of trachea relationship: part_of GO:0060438 ! trachea development relationship: results_in_development_of UBERON:0002202 ! submucosa of trachea -created_by: dph creation_date: 2010-06-07T09:58:40Z [Term] @@ -104102,7 +108829,6 @@ intersection_of: GO:0048856 ! anatomical structure development intersection_of: results_in_development_of UBERON:0005203 ! trachea gland relationship: part_of GO:0061152 ! trachea submucosa development relationship: results_in_development_of UBERON:0005203 ! trachea gland -created_by: dph creation_date: 2010-06-07T10:10:51Z [Term] @@ -104115,7 +108841,6 @@ is_a: GO:0060562 ! epithelial tube morphogenesis intersection_of: GO:0009653 ! anatomical structure morphogenesis intersection_of: results_in_morphogenesis_of UBERON:0003915 ! endothelial tube relationship: results_in_morphogenesis_of UBERON:0003915 ! endothelial tube -created_by: dph creation_date: 2010-06-15T09:05:00Z [Term] @@ -104128,7 +108853,6 @@ intersection_of: GO:0009653 ! anatomical structure morphogenesis intersection_of: results_in_morphogenesis_of UBERON:0005317 ! pulmonary artery endothelium relationship: part_of GO:0061156 ! pulmonary artery morphogenesis relationship: results_in_morphogenesis_of UBERON:0005317 ! pulmonary artery endothelium -created_by: dph creation_date: 2010-06-15T09:09:04Z [Term] @@ -104140,7 +108864,6 @@ is_a: GO:0048844 ! artery morphogenesis intersection_of: GO:0009653 ! anatomical structure morphogenesis intersection_of: results_in_morphogenesis_of UBERON:0002012 ! pulmonary artery relationship: results_in_morphogenesis_of UBERON:0002012 ! pulmonary artery -created_by: dph creation_date: 2010-06-15T09:13:47Z [Term] @@ -104152,7 +108875,6 @@ is_a: GO:0022603 ! regulation of anatomical structure morphogenesis intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0060789 ! hair follicle placode formation relationship: regulates GO:0060789 ! hair follicle placode formation -created_by: dph creation_date: 2010-06-25T01:03:29Z [Term] @@ -104165,7 +108887,6 @@ is_a: GO:0061168 ! regulation of hair follicle placode formation intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0060789 ! hair follicle placode formation relationship: positively_regulates GO:0060789 ! hair follicle placode formation -created_by: dph creation_date: 2010-06-25T01:08:50Z [Term] @@ -104178,7 +108899,6 @@ is_a: GO:0061168 ! regulation of hair follicle placode formation intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0060789 ! hair follicle placode formation relationship: negatively_regulates GO:0060789 ! hair follicle placode formation -created_by: dph creation_date: 2010-06-25T01:10:48Z [Term] @@ -104191,7 +108911,6 @@ is_a: GO:0050796 ! regulation of insulin secretion intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0035773 ! insulin secretion involved in cellular response to glucose stimulus relationship: regulates GO:0035773 ! insulin secretion involved in cellular response to glucose stimulus -created_by: dph creation_date: 2010-07-13T09:38:42Z [Term] @@ -104207,7 +108926,6 @@ is_a: GO:0061178 ! regulation of insulin secretion involved in cellular response intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0035773 ! insulin secretion involved in cellular response to glucose stimulus relationship: negatively_regulates GO:0035773 ! insulin secretion involved in cellular response to glucose stimulus -created_by: dph creation_date: 2010-07-13T09:41:46Z [Term] @@ -104221,7 +108939,6 @@ intersection_of: GO:0048856 ! anatomical structure development intersection_of: results_in_development_of UBERON:0008367 ! breast epithelium relationship: part_of GO:0030879 ! mammary gland development relationship: results_in_development_of UBERON:0008367 ! breast epithelium -created_by: dph creation_date: 2010-07-14T08:18:24Z [Term] @@ -104234,7 +108951,6 @@ is_a: GO:0060284 ! regulation of cell development intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0002063 ! chondrocyte development relationship: regulates GO:0002063 ! chondrocyte development -created_by: dph creation_date: 2010-07-14T08:28:52Z [Term] @@ -104248,7 +108964,6 @@ is_a: GO:0061181 ! regulation of chondrocyte development intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0002063 ! chondrocyte development relationship: negatively_regulates GO:0002063 ! chondrocyte development -created_by: dph creation_date: 2010-07-14T08:33:05Z [Term] @@ -104260,7 +108975,6 @@ is_a: GO:0050793 ! regulation of developmental process intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0061054 ! dermatome development relationship: regulates GO:0061054 ! dermatome development -created_by: dph creation_date: 2010-07-14T08:40:26Z [Term] @@ -104273,7 +108987,6 @@ is_a: GO:0061183 ! regulation of dermatome development intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0061054 ! dermatome development relationship: positively_regulates GO:0061054 ! dermatome development -created_by: dph creation_date: 2010-07-14T08:42:03Z [Term] @@ -104286,7 +108999,6 @@ is_a: GO:0061183 ! regulation of dermatome development intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0061054 ! dermatome development relationship: negatively_regulates GO:0061054 ! dermatome development -created_by: dph creation_date: 2010-07-14T08:43:08Z [Term] @@ -104299,7 +109011,6 @@ is_a: GO:0061190 ! regulation of sclerotome development intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0061056 ! sclerotome development relationship: positively_regulates GO:0061056 ! sclerotome development -created_by: dph creation_date: 2010-07-14T09:17:23Z [Term] @@ -104311,7 +109022,6 @@ is_a: GO:0050793 ! regulation of developmental process intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0061056 ! sclerotome development relationship: regulates GO:0061056 ! sclerotome development -created_by: dph creation_date: 2010-07-14T09:19:47Z [Term] @@ -104324,7 +109034,6 @@ intersection_of: GO:0048856 ! anatomical structure development intersection_of: results_in_development_of UBERON:0001727 ! taste bud relationship: part_of GO:0043586 ! tongue development relationship: results_in_development_of UBERON:0001727 ! taste bud -created_by: dph creation_date: 2010-07-27T10:55:08Z [Term] @@ -104338,7 +109047,6 @@ intersection_of: results_in_morphogenesis_of UBERON:0001727 ! taste bud relationship: part_of GO:0043587 ! tongue morphogenesis relationship: part_of GO:0061193 ! taste bud development relationship: results_in_morphogenesis_of UBERON:0001727 ! taste bud -created_by: dph creation_date: 2010-07-27T11:01:31Z [Term] @@ -104352,7 +109060,6 @@ intersection_of: GO:0048646 ! anatomical structure formation involved in morphog intersection_of: results_in_formation_of UBERON:0001727 ! taste bud relationship: part_of GO:0061194 ! taste bud morphogenesis relationship: results_in_formation_of UBERON:0001727 ! taste bud -created_by: dph creation_date: 2010-07-27T12:22:26Z [Term] @@ -104366,7 +109073,6 @@ is_a: GO:0035295 ! tube development intersection_of: GO:0048856 ! anatomical structure development intersection_of: results_in_development_of UBERON:0003890 ! Mullerian duct relationship: results_in_development_of UBERON:0003890 ! Mullerian duct -created_by: dph creation_date: 2010-07-30T10:54:47Z [Term] @@ -104380,7 +109086,6 @@ intersection_of: GO:0009653 ! anatomical structure morphogenesis intersection_of: results_in_morphogenesis_of UBERON:0000080 ! mesonephros relationship: part_of GO:0001823 ! mesonephros development relationship: results_in_morphogenesis_of UBERON:0000080 ! mesonephros -created_by: dph creation_date: 2010-08-17T03:11:10Z [Term] @@ -104392,7 +109097,6 @@ is_a: GO:0061005 ! cell differentiation involved in kidney development intersection_of: GO:0030154 ! cell differentiation intersection_of: part_of GO:0001823 ! mesonephros development relationship: part_of GO:0001823 ! mesonephros development -created_by: dph creation_date: 2010-08-17T03:21:23Z [Term] @@ -104404,7 +109108,6 @@ is_a: GO:0072111 ! cell proliferation involved in kidney development intersection_of: GO:0008283 ! cell population proliferation intersection_of: part_of GO:0001823 ! mesonephros development relationship: part_of GO:0001823 ! mesonephros development -created_by: dph creation_date: 2010-08-17T03:22:46Z [Term] @@ -104417,7 +109120,6 @@ is_a: GO:0060995 ! cell-cell signaling involved in kidney development intersection_of: GO:0007267 ! cell-cell signaling intersection_of: part_of GO:0001823 ! mesonephros development relationship: part_of GO:0001823 ! mesonephros development -created_by: dph creation_date: 2010-08-17T03:24:08Z [Term] @@ -104430,7 +109132,6 @@ intersection_of: GO:0048856 ! anatomical structure development intersection_of: results_in_development_of UBERON:0005319 ! mesonephric collecting duct relationship: part_of GO:0001823 ! mesonephros development relationship: results_in_development_of UBERON:0005319 ! mesonephric collecting duct -created_by: dph creation_date: 2010-08-17T03:25:51Z [Term] @@ -104443,7 +109144,6 @@ intersection_of: GO:0048856 ! anatomical structure development intersection_of: results_in_development_of UBERON:0005320 ! mesonephric juxtaglomerular apparatus relationship: part_of GO:0001823 ! mesonephros development relationship: results_in_development_of UBERON:0005320 ! mesonephric juxtaglomerular apparatus -created_by: dph creation_date: 2010-08-17T03:27:36Z [Term] @@ -104456,7 +109156,6 @@ is_a: GO:0090184 ! positive regulation of kidney development intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0001823 ! mesonephros development relationship: positively_regulates GO:0001823 ! mesonephros development -created_by: dph creation_date: 2010-08-17T03:39:35Z [Term] @@ -104469,7 +109168,6 @@ intersection_of: GO:0048856 ! anatomical structure development intersection_of: results_in_development_of UBERON:0005321 ! mesonephric smooth muscle tissue relationship: part_of GO:0001823 ! mesonephros development relationship: results_in_development_of UBERON:0005321 ! mesonephric smooth muscle tissue -created_by: dph creation_date: 2010-08-17T03:29:54Z [Term] @@ -104482,7 +109180,6 @@ intersection_of: GO:0048856 ! anatomical structure development intersection_of: results_in_development_of UBERON:0005322 ! mesonephric nephron relationship: part_of GO:0001823 ! mesonephros development relationship: results_in_development_of UBERON:0005322 ! mesonephric nephron -created_by: dph creation_date: 2010-08-17T03:31:08Z [Term] @@ -104494,7 +109191,6 @@ is_a: GO:0090183 ! regulation of kidney development intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0001823 ! mesonephros development relationship: regulates GO:0001823 ! mesonephros development -created_by: dph creation_date: 2010-08-17T03:35:31Z [Term] @@ -104507,7 +109203,6 @@ is_a: GO:0090185 ! negative regulation of kidney development intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0001823 ! mesonephros development relationship: negatively_regulates GO:0001823 ! mesonephros development -created_by: dph creation_date: 2010-08-17T03:43:06Z [Term] @@ -104520,7 +109215,6 @@ intersection_of: GO:0048856 ! anatomical structure development intersection_of: results_in_development_of UBERON:0005323 ! mesonephric mesenchyme relationship: part_of GO:0001823 ! mesonephros development relationship: results_in_development_of UBERON:0005323 ! mesonephric mesenchyme -created_by: dph creation_date: 2010-08-17T03:45:44Z [Term] @@ -104534,7 +109228,6 @@ intersection_of: GO:0048856 ! anatomical structure development intersection_of: results_in_development_of UBERON:0005324 ! mesonephric macula densa relationship: part_of GO:0061212 ! mesonephric juxtaglomerular apparatus development relationship: results_in_development_of UBERON:0005324 ! mesonephric macula densa -created_by: dph creation_date: 2010-08-19T01:11:41Z [Term] @@ -104547,7 +109240,6 @@ intersection_of: GO:0009653 ! anatomical structure morphogenesis intersection_of: results_in_morphogenesis_of UBERON:0005323 ! mesonephric mesenchyme relationship: part_of GO:0061219 ! mesonephric mesenchyme development relationship: results_in_morphogenesis_of UBERON:0005323 ! mesonephric mesenchyme -created_by: dph creation_date: 2010-08-19T01:17:38Z [Term] @@ -104560,7 +109252,6 @@ intersection_of: GO:0048856 ! anatomical structure development intersection_of: results_in_development_of UBERON:0005325 ! mesonephric glomerulus relationship: part_of GO:0061215 ! mesonephric nephron development relationship: results_in_development_of UBERON:0005325 ! mesonephric glomerulus -created_by: dph creation_date: 2010-08-19T01:26:00Z [Term] @@ -104574,7 +109265,6 @@ is_a: GO:0061004 ! pattern specification involved in kidney development intersection_of: GO:0007389 ! pattern specification process intersection_of: part_of GO:0001823 ! mesonephros development relationship: part_of GO:0001823 ! mesonephros development -created_by: dph creation_date: 2010-08-19T02:22:22Z [Term] @@ -104588,7 +109278,6 @@ intersection_of: results_in_morphogenesis_of UBERON:0005322 ! mesonephric nephro relationship: part_of GO:0061206 ! mesonephros morphogenesis relationship: part_of GO:0061215 ! mesonephric nephron development relationship: results_in_morphogenesis_of UBERON:0005322 ! mesonephric nephron -created_by: dph creation_date: 2010-08-19T02:26:24Z [Term] @@ -104601,7 +109290,6 @@ intersection_of: GO:0048856 ! anatomical structure development intersection_of: results_in_development_of UBERON:0005326 ! mesonephric glomerulus vasculature relationship: part_of GO:0061224 ! mesonephric glomerulus development relationship: results_in_development_of UBERON:0005326 ! mesonephric glomerulus vasculature -created_by: dph creation_date: 2010-08-19T02:47:06Z [Term] @@ -104615,7 +109303,6 @@ intersection_of: GO:0048856 ! anatomical structure development intersection_of: results_in_development_of UBERON:0005327 ! mesonephric glomerular epithelium relationship: part_of GO:0061224 ! mesonephric glomerulus development relationship: results_in_development_of UBERON:0005327 ! mesonephric glomerular epithelium -created_by: dph creation_date: 2010-08-19T02:49:46Z [Term] @@ -104629,7 +109316,6 @@ intersection_of: results_in_morphogenesis_of UBERON:0005325 ! mesonephric glomer relationship: part_of GO:0061224 ! mesonephric glomerulus development relationship: part_of GO:0061228 ! mesonephric nephron morphogenesis relationship: results_in_morphogenesis_of UBERON:0005325 ! mesonephric glomerulus -created_by: dph creation_date: 2010-08-19T02:53:35Z [Term] @@ -104639,7 +109325,6 @@ namespace: biological_process def: "The process in which an organism retains a population of mesenchymal stem cells that contributes to the shaping of a nephron in the mesonephros. A mesenchymal stem cell is a cell that retains the ability to divide and proliferate throughout life to provide progenitor cells that can differentiate into specialized mesenchymal cells." [GOC:mtg_kidney_jan10] is_a: GO:0072038 ! mesenchymal stem cell maintenance involved in nephron morphogenesis relationship: part_of GO:0061228 ! mesonephric nephron morphogenesis -created_by: dph creation_date: 2010-08-19T02:57:11Z [Term] @@ -104652,7 +109337,6 @@ intersection_of: GO:0009653 ! anatomical structure morphogenesis intersection_of: results_in_morphogenesis_of UBERON:0005328 ! mesonephric comma-shaped body relationship: part_of GO:0061228 ! mesonephric nephron morphogenesis relationship: results_in_morphogenesis_of UBERON:0005328 ! mesonephric comma-shaped body -created_by: dph creation_date: 2010-08-19T03:00:21Z [Term] @@ -104666,7 +109350,6 @@ intersection_of: results_in_morphogenesis_of UBERON:0005329 ! mesonephric nephro relationship: part_of GO:0061228 ! mesonephric nephron morphogenesis relationship: part_of GO:0061242 ! mesonephric nephron tubule development relationship: results_in_morphogenesis_of UBERON:0005329 ! mesonephric nephron tubule -created_by: dph creation_date: 2010-08-19T03:09:26Z [Term] @@ -104680,7 +109363,6 @@ intersection_of: GO:0048856 ! anatomical structure development intersection_of: results_in_development_of UBERON:0005330 ! mesonephric nephron epithelium relationship: part_of GO:0061215 ! mesonephric nephron development relationship: results_in_development_of UBERON:0005330 ! mesonephric nephron epithelium -created_by: dph creation_date: 2010-08-19T03:11:59Z [Term] @@ -104694,7 +109376,6 @@ is_a: GO:0072164 ! mesonephric tubule development intersection_of: GO:0048856 ! anatomical structure development intersection_of: results_in_development_of UBERON:0005329 ! mesonephric nephron tubule relationship: results_in_development_of UBERON:0005329 ! mesonephric nephron tubule -created_by: dph creation_date: 2010-08-19T03:17:00Z [Term] @@ -104707,7 +109388,6 @@ intersection_of: GO:0009653 ! anatomical structure morphogenesis intersection_of: results_in_morphogenesis_of UBERON:0005331 ! mesonephric renal vesicle relationship: part_of GO:0061228 ! mesonephric nephron morphogenesis relationship: results_in_morphogenesis_of UBERON:0005331 ! mesonephric renal vesicle -created_by: dph creation_date: 2010-08-19T03:20:21Z [Term] @@ -104720,7 +109400,6 @@ intersection_of: GO:0009653 ! anatomical structure morphogenesis intersection_of: results_in_morphogenesis_of UBERON:0005332 ! mesonephric S-shaped body relationship: part_of GO:0061228 ! mesonephric nephron morphogenesis relationship: results_in_morphogenesis_of UBERON:0005332 ! mesonephric S-shaped body -created_by: dph creation_date: 2010-08-19T03:23:55Z [Term] @@ -104733,7 +109412,6 @@ intersection_of: GO:0048856 ! anatomical structure development intersection_of: results_in_development_of UBERON:0006182 ! mesonephric glomerular mesangium relationship: part_of GO:0061231 ! mesonephric glomerulus vasculature development relationship: results_in_development_of UBERON:0006182 ! mesonephric glomerular mesangium -created_by: dph creation_date: 2010-08-30T12:59:25Z [Term] @@ -104747,7 +109425,6 @@ intersection_of: results_in_morphogenesis_of UBERON:0005326 ! mesonephric glomer relationship: part_of GO:0061231 ! mesonephric glomerulus vasculature development relationship: part_of GO:0061234 ! mesonephric glomerulus morphogenesis relationship: results_in_morphogenesis_of UBERON:0005326 ! mesonephric glomerulus vasculature -created_by: dph creation_date: 2010-08-30T01:11:34Z [Term] @@ -104760,7 +109437,6 @@ intersection_of: GO:0048646 ! anatomical structure formation involved in morphog intersection_of: results_in_formation_of UBERON:0006183 ! mesonephric glomerular capillary relationship: part_of GO:0061248 ! mesonephric glomerulus vasculature morphogenesis relationship: results_in_formation_of UBERON:0006183 ! mesonephric glomerular capillary -created_by: dph creation_date: 2010-08-30T01:17:08Z [Term] @@ -104771,7 +109447,6 @@ def: "The process in which a relatively unspecialized cell acquires specialized is_a: GO:0061208 ! cell differentiation involved in mesonephros development is_a: GO:0072311 ! glomerular epithelial cell differentiation relationship: part_of GO:0061232 ! mesonephric glomerular epithelium development -created_by: dph creation_date: 2010-08-30T01:20:03Z [Term] @@ -104781,7 +109456,6 @@ namespace: biological_process def: "The process whose specific outcome is the progression of a mesonephric glomerular epithelial cell over time, from its formation to the mature structure. Mesonephric glomerular epithelial cells are specialized epithelial cells that form part of the mesonephric glomerulus; there are two types, mesonephric glomerular parietal epithelial cells and mesonephric glomerular visceral epithelial cells." [GOC:mtg_kidney_jan10] is_a: GO:0072310 ! glomerular epithelial cell development relationship: part_of GO:0061250 ! mesonephric glomerular epithelial cell differentiation -created_by: dph creation_date: 2010-08-30T01:20:45Z [Term] @@ -104796,7 +109470,6 @@ intersection_of: GO:0030154 ! cell differentiation intersection_of: results_in_acquisition_of_features_of CL:0002523 ! mesonephric podocyte relationship: results_in_acquisition_of_features_of CL:0002523 ! mesonephric podocyte property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/23000" xsd:anyURI -created_by: dph creation_date: 2010-08-30T02:03:38Z [Term] @@ -104812,7 +109485,6 @@ intersection_of: results_in_development_of CL:0002523 ! mesonephric podocyte relationship: part_of GO:0061256 ! mesonephric podocyte differentiation relationship: results_in_development_of CL:0002523 ! mesonephric podocyte property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/23000" xsd:anyURI -created_by: dph creation_date: 2010-08-30T02:10:40Z [Term] @@ -104827,7 +109499,6 @@ is_a: GO:0061208 ! cell differentiation involved in mesonephros development intersection_of: GO:0060231 ! mesenchymal to epithelial transition intersection_of: part_of GO:0061206 ! mesonephros morphogenesis relationship: part_of GO:0061206 ! mesonephros morphogenesis -created_by: dph creation_date: 2010-08-30T02:35:15Z [Term] @@ -104841,7 +109512,6 @@ intersection_of: GO:0048646 ! anatomical structure formation involved in morphog intersection_of: results_in_formation_of UBERON:0005331 ! mesonephric renal vesicle relationship: part_of GO:0061243 ! mesonephric renal vesicle morphogenesis relationship: results_in_formation_of UBERON:0005331 ! mesonephric renal vesicle -created_by: dph creation_date: 2010-08-30T02:41:20Z [Term] @@ -104855,7 +109525,6 @@ intersection_of: GO:0030154 ! cell differentiation intersection_of: results_in_acquisition_of_features_of CL:1000022 ! mesonephric nephron tubule epithelial cell relationship: part_of GO:0061242 ! mesonephric nephron tubule development relationship: results_in_acquisition_of_features_of CL:1000022 ! mesonephric nephron tubule epithelial cell -created_by: dph creation_date: 2010-08-30T03:02:09Z [Term] @@ -104868,7 +109537,6 @@ is_a: GO:0072036 ! mesenchymal to epithelial transition involved in renal vesicl intersection_of: GO:0060231 ! mesenchymal to epithelial transition intersection_of: part_of GO:0061262 ! mesonephric renal vesicle formation relationship: part_of GO:0061262 ! mesonephric renal vesicle formation -created_by: dph creation_date: 2010-08-30T03:26:30Z [Term] @@ -104883,7 +109551,6 @@ is_a: GO:0072027 ! connecting tubule development intersection_of: GO:0048856 ! anatomical structure development intersection_of: results_in_development_of UBERON:0006189 ! mesonephric connecting tubule relationship: results_in_development_of UBERON:0006189 ! mesonephric connecting tubule -created_by: dph creation_date: 2010-09-02T12:00:56Z [Term] @@ -104897,7 +109564,6 @@ intersection_of: GO:0009653 ! anatomical structure morphogenesis intersection_of: results_in_morphogenesis_of UBERON:0006190 ! mesonephric distal tubule relationship: part_of GO:0061274 ! mesonephric distal tubule development relationship: results_in_morphogenesis_of UBERON:0006190 ! mesonephric distal tubule -created_by: dph creation_date: 2010-09-02T12:12:00Z [Term] @@ -104910,7 +109576,6 @@ is_a: GO:0072017 ! distal tubule development intersection_of: GO:0048856 ! anatomical structure development intersection_of: results_in_development_of UBERON:0006190 ! mesonephric distal tubule relationship: results_in_development_of UBERON:0006190 ! mesonephric distal tubule -created_by: dph creation_date: 2010-09-02T12:16:25Z [Term] @@ -104923,7 +109588,6 @@ is_a: GO:0072014 ! proximal tubule development intersection_of: GO:0048856 ! anatomical structure development intersection_of: results_in_development_of UBERON:0006192 ! mesonephric proximal tubule relationship: results_in_development_of UBERON:0006192 ! mesonephric proximal tubule -created_by: dph creation_date: 2010-09-02T01:08:05Z [Term] @@ -104937,7 +109601,6 @@ intersection_of: GO:0009653 ! anatomical structure morphogenesis intersection_of: results_in_morphogenesis_of UBERON:0006192 ! mesonephric proximal tubule relationship: part_of GO:0061275 ! mesonephric proximal tubule development relationship: results_in_morphogenesis_of UBERON:0006192 ! mesonephric proximal tubule -created_by: dph creation_date: 2010-09-02T01:11:02Z [Term] @@ -104950,7 +109613,6 @@ intersection_of: GO:0048646 ! anatomical structure formation involved in morphog intersection_of: results_in_formation_of UBERON:0005329 ! mesonephric nephron tubule relationship: part_of GO:0061240 ! mesonephric nephron tubule morphogenesis relationship: results_in_formation_of UBERON:0005329 ! mesonephric nephron tubule -created_by: dph creation_date: 2010-09-02T01:16:21Z [Term] @@ -104962,7 +109624,6 @@ is_a: GO:0072155 ! epithelial cell migration involved in nephron tubule morphoge intersection_of: GO:0010631 ! epithelial cell migration intersection_of: part_of GO:0061240 ! mesonephric nephron tubule morphogenesis relationship: part_of GO:0061240 ! mesonephric nephron tubule morphogenesis -created_by: dph creation_date: 2010-09-02T01:18:53Z [Term] @@ -104975,7 +109636,6 @@ is_a: GO:0072157 ! epithelial cell migration involved in distal tubule morphogen intersection_of: GO:0010631 ! epithelial cell migration intersection_of: part_of GO:0061273 ! mesonephric distal tubule morphogenesis relationship: part_of GO:0061273 ! mesonephric distal tubule morphogenesis -created_by: dph creation_date: 2010-09-02T01:20:56Z [Term] @@ -104988,7 +109648,6 @@ is_a: GO:0072159 ! epithelial cell migration involved in proximal tubule morphog intersection_of: GO:0010631 ! epithelial cell migration intersection_of: part_of GO:0061276 ! mesonephric proximal tubule morphogenesis relationship: part_of GO:0061276 ! mesonephric proximal tubule morphogenesis -created_by: dph creation_date: 2010-09-02T01:23:43Z [Term] @@ -105001,7 +109660,6 @@ intersection_of: GO:0048856 ! anatomical structure development intersection_of: results_in_development_of UBERON:0006170 ! mesonephric capsule relationship: part_of GO:0001823 ! mesonephros development relationship: results_in_development_of UBERON:0006170 ! mesonephric capsule -created_by: dph creation_date: 2010-09-02T01:50:06Z [Term] @@ -105014,7 +109672,6 @@ intersection_of: GO:0009653 ! anatomical structure morphogenesis intersection_of: results_in_morphogenesis_of UBERON:0006170 ! mesonephric capsule relationship: part_of GO:0061285 ! mesonephric capsule development relationship: results_in_morphogenesis_of UBERON:0006170 ! mesonephric capsule -created_by: dph creation_date: 2010-09-02T01:53:31Z [Term] @@ -105027,7 +109684,6 @@ intersection_of: GO:0048646 ! anatomical structure formation involved in morphog intersection_of: results_in_formation_of UBERON:0006170 ! mesonephric capsule relationship: part_of GO:0061286 ! mesonephric capsule morphogenesis relationship: results_in_formation_of UBERON:0006170 ! mesonephric capsule -created_by: dph creation_date: 2010-09-02T01:55:03Z [Term] @@ -105042,7 +109698,6 @@ intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:1901146 ! mesenchymal cell apoptotic process involved in mesonephric nephron morphogenesis relationship: regulates GO:0061235 ! mesenchymal stem cell maintenance involved in mesonephric nephron morphogenesis relationship: regulates GO:1901146 ! mesenchymal cell apoptotic process involved in mesonephric nephron morphogenesis -created_by: dph creation_date: 2010-09-06T09:48:56Z [Term] @@ -105059,7 +109714,6 @@ intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:1901146 ! mesenchymal cell apoptotic process involved in mesonephric nephron morphogenesis relationship: negatively_regulates GO:0061235 ! mesenchymal stem cell maintenance involved in mesonephric nephron morphogenesis relationship: negatively_regulates GO:1901146 ! mesenchymal cell apoptotic process involved in mesonephric nephron morphogenesis -created_by: dph creation_date: 2010-09-06T09:54:49Z [Term] @@ -105076,7 +109730,6 @@ intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:1901146 ! mesenchymal cell apoptotic process involved in mesonephric nephron morphogenesis relationship: positively_regulates GO:0061235 ! mesenchymal stem cell maintenance involved in mesonephric nephron morphogenesis relationship: positively_regulates GO:1901146 ! mesenchymal cell apoptotic process involved in mesonephric nephron morphogenesis -created_by: dph creation_date: 2010-09-06T09:58:59Z [Term] @@ -105090,7 +109743,6 @@ intersection_of: GO:0048856 ! anatomical structure development intersection_of: results_in_development_of UBERON:0004864 ! vasculature of retina relationship: part_of GO:0060041 ! retina development in camera-type eye relationship: results_in_development_of UBERON:0004864 ! vasculature of retina -created_by: dph creation_date: 2010-09-06T03:27:06Z [Term] @@ -105105,7 +109757,6 @@ intersection_of: GO:0009653 ! anatomical structure morphogenesis intersection_of: results_in_morphogenesis_of UBERON:0004864 ! vasculature of retina relationship: part_of GO:0061298 ! retina vasculature development in camera-type eye relationship: results_in_morphogenesis_of UBERON:0004864 ! vasculature of retina -created_by: dph creation_date: 2010-09-06T03:28:25Z [Term] @@ -105117,7 +109768,6 @@ is_a: GO:0001944 ! vasculature development intersection_of: GO:0048856 ! anatomical structure development intersection_of: results_in_development_of UBERON:0006694 ! cerebellum vasculature relationship: results_in_development_of UBERON:0006694 ! cerebellum vasculature -created_by: dph creation_date: 2010-09-06T03:36:40Z [Term] @@ -105132,7 +109782,6 @@ intersection_of: results_in_morphogenesis_of UBERON:0006694 ! cerebellum vascula relationship: part_of GO:0021549 ! cerebellum development relationship: part_of GO:0061300 ! cerebellum vasculature development relationship: results_in_morphogenesis_of UBERON:0006694 ! cerebellum vasculature -created_by: dph creation_date: 2010-09-06T03:38:05Z [Term] @@ -105145,7 +109794,6 @@ intersection_of: GO:0048856 ! anatomical structure development intersection_of: results_in_development_of UBERON:0000964 ! cornea relationship: part_of GO:0043010 ! camera-type eye development relationship: results_in_development_of UBERON:0000964 ! cornea -created_by: dph creation_date: 2010-09-14T02:09:08Z [Term] @@ -105158,7 +109806,6 @@ is_a: GO:0061299 ! retina vasculature morphogenesis in camera-type eye intersection_of: GO:0009653 ! anatomical structure morphogenesis intersection_of: results_in_morphogenesis_of UBERON:0003501 ! retina blood vessel relationship: results_in_morphogenesis_of UBERON:0003501 ! retina blood vessel -created_by: dph creation_date: 2010-09-16T09:02:59Z [Term] @@ -105170,7 +109817,6 @@ is_a: GO:0014033 ! neural crest cell differentiation is_a: GO:0035051 ! cardiocyte differentiation intersection_of: GO:0014033 ! neural crest cell differentiation intersection_of: part_of GO:0007507 ! heart development -created_by: dph creation_date: 2010-09-23T08:50:56Z [Term] @@ -105182,7 +109828,6 @@ is_a: GO:0014032 ! neural crest cell development intersection_of: GO:0014032 ! neural crest cell development intersection_of: part_of GO:0007507 ! heart development relationship: part_of GO:0061307 ! cardiac neural crest cell differentiation involved in heart development -created_by: dph creation_date: 2010-09-23T09:01:49Z [Term] @@ -105194,7 +109839,6 @@ is_a: GO:0061308 ! cardiac neural crest cell development involved in heart devel intersection_of: GO:0014032 ! neural crest cell development intersection_of: part_of GO:0003151 ! outflow tract morphogenesis relationship: part_of GO:0003151 ! outflow tract morphogenesis -created_by: dph creation_date: 2010-09-23T09:08:37Z [Term] @@ -105208,7 +109852,6 @@ is_a: GO:0007166 ! cell surface receptor signaling pathway intersection_of: GO:0007166 ! cell surface receptor signaling pathway intersection_of: part_of GO:0007507 ! heart development relationship: part_of GO:0007507 ! heart development -created_by: dph creation_date: 2010-09-23T09:18:32Z [Term] @@ -105221,7 +109864,6 @@ intersection_of: GO:0030154 ! cell differentiation intersection_of: results_in_acquisition_of_features_of CL:0002522 ! renal filtration cell relationship: part_of GO:0072001 ! renal system development relationship: results_in_acquisition_of_features_of CL:0002522 ! renal filtration cell -created_by: dph creation_date: 2010-09-24T12:18:35Z [Term] @@ -105235,28 +109877,24 @@ intersection_of: results_in_acquisition_of_features_of CL:0002520 ! nephrocyte relationship: results_in_acquisition_of_features_of CL:0002520 ! nephrocyte relationship: RO:0002160 NCBITaxon:50557 ! only in taxon Insecta relationship: RO:0002162 NCBITaxon:50557 {all_only="true"} ! in taxon Insecta -created_by: dph creation_date: 2010-09-24T12:23:29Z [Term] id: GO:0061320 name: pericardial nephrocyte differentiation namespace: biological_process -alt_id: GO:0007513 def: "The process in which a relatively unspecialized cell acquires the specialized structural and/or functional features of a pericardial nephrocyte. A pericardial nephrocyte is an insect renal cell that filters hemolymph and is found with other pericardial nephrocytes in two rows flanking the dorsal vessel. Differentiation includes the processes involved in commitment of a cell to a specific fate and its subsequent development to the mature state." [CL:0000474, GOC:dph, GOC:mtg_kidney_jan10, GOC:sart, PMID:19783135] synonym: "pericardial cell differentiation" NARROW [] is_a: GO:0061319 ! nephrocyte differentiation intersection_of: GO:0030154 ! cell differentiation intersection_of: results_in_acquisition_of_features_of CL:0000474 ! pericardial nephrocyte relationship: results_in_acquisition_of_features_of CL:0000474 ! pericardial nephrocyte -created_by: dph creation_date: 2010-09-24T12:25:53Z [Term] id: GO:0061321 name: garland nephrocyte differentiation namespace: biological_process -alt_id: GO:0007514 def: "The process in which a relatively unspecialized cell acquires the specialized structural and/or functional features of a garland nephrocyte. A garland nephrocyte is an insect renal cell that filters hemolymph and forms a ring with other garland nephrocytes around the esophagus. Differentiation includes the processes involved in commitment of a cell to a specific fate and its subsequent development to the mature state." [CL:0000486, GOC:dph, GOC:mtg_kidney_jan10, GOC:sart, PMID:19783135] synonym: "garland cell differentiation" EXACT [] is_a: GO:0061319 ! nephrocyte differentiation @@ -105264,7 +109902,6 @@ intersection_of: GO:0030154 ! cell differentiation intersection_of: results_in_acquisition_of_features_of CL:0000486 ! garland cell relationship: part_of GO:0001700 ! embryonic development via the syncytial blastoderm relationship: results_in_acquisition_of_features_of CL:0000486 ! garland cell -created_by: dph creation_date: 2010-09-24T12:28:16Z [Term] @@ -105276,7 +109913,6 @@ is_a: GO:0061319 ! nephrocyte differentiation intersection_of: GO:0030154 ! cell differentiation intersection_of: results_in_acquisition_of_features_of CL:0002524 ! disseminated nephrocyte relationship: results_in_acquisition_of_features_of CL:0002524 ! disseminated nephrocyte -created_by: dph creation_date: 2010-09-24T12:30:46Z [Term] @@ -105288,7 +109924,6 @@ is_a: GO:0008283 ! cell population proliferation intersection_of: GO:0008283 ! cell population proliferation intersection_of: part_of GO:0003007 ! heart morphogenesis relationship: part_of GO:0003007 ! heart morphogenesis -created_by: dph creation_date: 2010-09-28T09:05:26Z [Term] @@ -105300,7 +109935,6 @@ is_a: GO:0061323 ! cell proliferation involved in heart morphogenesis intersection_of: GO:0008283 ! cell population proliferation intersection_of: part_of GO:0003151 ! outflow tract morphogenesis relationship: part_of GO:0003151 ! outflow tract morphogenesis -created_by: dph creation_date: 2010-09-28T09:29:30Z [Term] @@ -105314,7 +109948,6 @@ intersection_of: GO:0048856 ! anatomical structure development intersection_of: results_in_development_of UBERON:0009773 ! renal tubule relationship: part_of GO:0072001 ! renal system development relationship: results_in_development_of UBERON:0009773 ! renal tubule -created_by: dph creation_date: 2010-09-28T12:50:43Z [Term] @@ -105327,7 +109960,6 @@ intersection_of: GO:0030154 ! cell differentiation intersection_of: results_in_acquisition_of_features_of CL:1000155 ! Malpighian tubule stellate cell relationship: part_of GO:0072002 ! Malpighian tubule development relationship: results_in_acquisition_of_features_of CL:1000155 ! Malpighian tubule stellate cell -created_by: dph creation_date: 2010-09-28T01:32:55Z [Term] @@ -105339,7 +109971,6 @@ is_a: GO:2001013 ! epithelial cell proliferation involved in renal tubule morpho intersection_of: GO:0050673 ! epithelial cell proliferation intersection_of: part_of GO:0007443 ! Malpighian tubule morphogenesis relationship: part_of GO:0007443 ! Malpighian tubule morphogenesis -created_by: dph creation_date: 2010-09-28T02:01:02Z [Term] @@ -105354,7 +109985,6 @@ intersection_of: GO:0048646 ! anatomical structure formation involved in morphog intersection_of: results_in_formation_of UBERON:0001054 ! Malpighian tubule relationship: part_of GO:0007443 ! Malpighian tubule morphogenesis relationship: results_in_formation_of UBERON:0001054 ! Malpighian tubule -created_by: dph creation_date: 2010-09-28T01:39:32Z [Term] @@ -105367,7 +109997,6 @@ intersection_of: GO:0009653 ! anatomical structure morphogenesis intersection_of: results_in_morphogenesis_of UBERON:0009773 ! renal tubule relationship: part_of GO:0061326 ! renal tubule development relationship: results_in_morphogenesis_of UBERON:0009773 ! renal tubule -created_by: dph creation_date: 2010-09-28T01:43:04Z [Term] @@ -105380,7 +110009,6 @@ is_a: GO:0016477 ! cell migration intersection_of: GO:0016477 ! cell migration intersection_of: part_of GO:0007443 ! Malpighian tubule morphogenesis relationship: part_of GO:0007443 ! Malpighian tubule morphogenesis -created_by: dph creation_date: 2010-09-28T02:04:05Z [Term] @@ -105393,7 +110021,6 @@ is_a: GO:0060560 ! developmental growth involved in morphogenesis intersection_of: GO:0048588 ! developmental cell growth intersection_of: part_of GO:0007443 ! Malpighian tubule morphogenesis relationship: part_of GO:0007443 ! Malpighian tubule morphogenesis -created_by: dph creation_date: 2010-09-28T02:08:25Z [Term] @@ -105405,7 +110032,6 @@ is_a: GO:0000902 ! cell morphogenesis intersection_of: GO:0000902 ! cell morphogenesis intersection_of: part_of GO:0007443 ! Malpighian tubule morphogenesis relationship: part_of GO:0007443 ! Malpighian tubule morphogenesis -created_by: dph creation_date: 2010-09-28T02:11:47Z [Term] @@ -105414,7 +110040,6 @@ name: cardiac conduction namespace: biological_process def: "Transfer of an organized electrical impulse across the heart to coordinate the contraction of cardiac muscles. The process begins with generation of an action potential (in the sinoatrial node (SA) in humans) and ends with a change in the rate, frequency, or extent of the contraction of the heart muscles." [GOC:dph] is_a: GO:0008016 ! regulation of heart contraction -created_by: dph creation_date: 2010-09-29T08:46:05Z [Term] @@ -105426,7 +110051,6 @@ is_a: GO:0007155 ! cell adhesion intersection_of: GO:0007155 ! cell adhesion intersection_of: part_of GO:0003007 ! heart morphogenesis relationship: part_of GO:0003007 ! heart morphogenesis -created_by: dph creation_date: 2010-09-29T11:34:06Z [Term] @@ -105438,7 +110062,6 @@ is_a: GO:0030155 ! regulation of cell adhesion intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0061343 ! cell adhesion involved in heart morphogenesis relationship: regulates GO:0061343 ! cell adhesion involved in heart morphogenesis -created_by: dph creation_date: 2010-09-29T11:35:27Z [Term] @@ -105447,7 +110070,6 @@ name: neural precursor cell proliferation namespace: biological_process def: "The multiplication or reproduction of neural precursor cells, resulting in the expansion of a cell population. A neural precursor cell is either a nervous system stem cell or a nervous system progenitor cell." [GOC:dph, GOC:yaf] is_a: GO:0008283 ! cell population proliferation -created_by: dph creation_date: 2010-10-01T11:06:04Z [Term] @@ -105459,7 +110081,6 @@ is_a: GO:0060326 ! cell chemotaxis is_a: GO:0061334 ! cell rearrangement involved in Malpighian tubule morphogenesis intersection_of: GO:0060326 ! cell chemotaxis intersection_of: part_of GO:0007443 ! Malpighian tubule morphogenesis -created_by: dph creation_date: 2010-10-01T11:57:28Z [Term] @@ -105473,7 +110094,6 @@ intersection_of: GO:0048856 ! anatomical structure development intersection_of: results_in_development_of UBERON:0000959 ! optic chiasma relationship: part_of GO:0021554 ! optic nerve development relationship: results_in_development_of UBERON:0000959 ! optic chiasma -created_by: dph creation_date: 2010-10-13T08:00:29Z [Term] @@ -105486,7 +110106,6 @@ is_a: GO:0009058 ! biosynthetic process intersection_of: GO:0009058 ! biosynthetic process intersection_of: has_primary_output CHEBI:17347 relationship: has_primary_output CHEBI:17347 -created_by: dph creation_date: 2010-10-27T02:50:48Z [Term] @@ -105499,7 +110118,6 @@ intersection_of: GO:0048856 ! anatomical structure development intersection_of: results_in_development_of UBERON:0001912 ! lobule of mammary gland relationship: part_of GO:0030879 ! mammary gland development relationship: results_in_development_of UBERON:0001912 ! lobule of mammary gland -created_by: dph creation_date: 2010-11-09T09:36:29Z [Term] @@ -105512,7 +110130,6 @@ intersection_of: GO:0030154 ! cell differentiation intersection_of: results_in_acquisition_of_features_of CL:1000182 ! malpighian tubule tip cell relationship: part_of GO:0072002 ! Malpighian tubule development relationship: results_in_acquisition_of_features_of CL:1000182 ! malpighian tubule tip cell -created_by: dph creation_date: 2010-11-23T09:52:44Z [Term] @@ -105525,7 +110142,6 @@ is_a: GO:0009653 ! anatomical structure morphogenesis intersection_of: GO:0009653 ! anatomical structure morphogenesis intersection_of: results_in_morphogenesis_of UBERON:0000440 ! trabecula relationship: results_in_morphogenesis_of UBERON:0000440 ! trabecula -created_by: dph creation_date: 2010-12-02T08:51:45Z [Term] @@ -105537,7 +110153,6 @@ is_a: GO:0061383 ! trabecula morphogenesis intersection_of: GO:0009653 ! anatomical structure morphogenesis intersection_of: results_in_morphogenesis_of UBERON:0002511 ! trabecula carnea relationship: results_in_morphogenesis_of UBERON:0002511 ! trabecula carnea -created_by: dph creation_date: 2010-12-02T08:54:20Z [Term] @@ -105549,7 +110164,6 @@ is_a: GO:0048144 ! fibroblast proliferation is_a: GO:0061323 ! cell proliferation involved in heart morphogenesis intersection_of: GO:0048144 ! fibroblast proliferation intersection_of: part_of GO:0003007 ! heart morphogenesis -created_by: dph creation_date: 2011-02-10T01:41:59Z [Term] @@ -105559,7 +110173,6 @@ namespace: biological_process def: "The process whose specific outcome is the progression of vasculature of the renal system over time, from its formation to the mature structure." [GOC:dph, GOC:mtg_kidney_jan10, PMID:11891195] is_a: GO:0001944 ! vasculature development relationship: part_of GO:0072001 ! renal system development -created_by: dph creation_date: 2012-03-08T12:16:24Z [Term] @@ -105569,7 +110182,6 @@ namespace: biological_process def: "The process in which the renal system vasculature is generated and organized. Morphogenesis pertains to the creation of form." [GOC:dph, GOC:mtg_kidney_jan10, PMID:11891195] is_a: GO:0009653 ! anatomical structure morphogenesis relationship: part_of GO:0061437 ! renal system vasculature development -created_by: dph creation_date: 2012-03-08T12:21:56Z [Term] @@ -105584,7 +110196,6 @@ intersection_of: results_in_morphogenesis_of UBERON:0006544 ! kidney vasculature relationship: part_of GO:0061438 ! renal system vasculature morphogenesis relationship: part_of GO:0061440 ! kidney vasculature development relationship: results_in_morphogenesis_of UBERON:0006544 ! kidney vasculature -created_by: dph creation_date: 2012-03-08T12:30:11Z [Term] @@ -105597,7 +110208,6 @@ intersection_of: GO:0048856 ! anatomical structure development intersection_of: results_in_development_of UBERON:0006544 ! kidney vasculature relationship: part_of GO:0001822 ! kidney development relationship: results_in_development_of UBERON:0006544 ! kidney vasculature -created_by: dph creation_date: 2012-03-08T12:39:09Z [Term] @@ -105610,7 +110220,6 @@ intersection_of: GO:0009653 ! anatomical structure morphogenesis intersection_of: results_in_morphogenesis_of UBERON:0001184 ! renal artery relationship: part_of GO:0061439 ! kidney vasculature morphogenesis relationship: results_in_morphogenesis_of UBERON:0001184 ! renal artery -created_by: dph creation_date: 2012-03-08T12:42:09Z [Term] @@ -105622,7 +110231,6 @@ is_a: GO:0009888 ! tissue development intersection_of: GO:0048856 ! anatomical structure development intersection_of: results_in_development_of UBERON:0002384 ! connective tissue relationship: results_in_development_of UBERON:0002384 ! connective tissue -created_by: dph creation_date: 2012-03-22T12:53:41Z [Term] @@ -105630,12 +110238,11 @@ id: GO:0061449 name: olfactory bulb tufted cell development namespace: biological_process def: "The process whose specific outcome is the progression of an olfactory bulb tufted cell over time, from initial commitment of the cell to a specific fate, to the fully functional differentiated cell." [GOC:dph] -is_a: GO:0048666 ! neuron development +is_a: GO:0021884 ! forebrain neuron development intersection_of: GO:0048468 ! cell development intersection_of: results_in_development_of CL:1001503 ! olfactory bulb tufted cell relationship: part_of GO:0021772 ! olfactory bulb development relationship: results_in_development_of CL:1001503 ! olfactory bulb tufted cell -created_by: dph creation_date: 2012-05-15T12:30:21Z [Term] @@ -105649,7 +110256,6 @@ intersection_of: GO:0016477 ! cell migration intersection_of: results_in_movement_of CL:0000351 ! trophoblast cell relationship: part_of GO:0007566 ! embryo implantation relationship: results_in_movement_of CL:0000351 ! trophoblast cell -created_by: dph creation_date: 2012-07-10T08:38:37Z [Term] @@ -105662,7 +110268,6 @@ intersection_of: GO:0048856 ! anatomical structure development intersection_of: results_in_development_of UBERON:0009918 ! retrotrapezoid nucleus relationship: part_of GO:0021550 ! medulla oblongata development relationship: results_in_development_of UBERON:0009918 ! retrotrapezoid nucleus -created_by: dph creation_date: 2012-07-19T12:38:30Z [Term] @@ -105675,7 +110280,6 @@ intersection_of: GO:0030154 ! cell differentiation intersection_of: results_in_acquisition_of_features_of CL:1000001 ! retrotrapezoid nucleus neuron relationship: part_of GO:0061451 ! retrotrapezoid nucleus development relationship: results_in_acquisition_of_features_of CL:1000001 ! retrotrapezoid nucleus neuron -created_by: dph creation_date: 2012-07-19T12:43:18Z [Term] @@ -105689,7 +110293,6 @@ is_a: GO:0060575 ! intestinal epithelial cell differentiation intersection_of: GO:0030154 ! cell differentiation intersection_of: results_in_acquisition_of_features_of CL:0002088 ! interstitial cell of Cajal relationship: results_in_acquisition_of_features_of CL:0002088 ! interstitial cell of Cajal -created_by: dph creation_date: 2012-07-20T08:20:50Z [Term] @@ -105706,7 +110309,6 @@ intersection_of: has_target_end_location GO:0005829 ! cytosol intersection_of: has_target_start_location GO:0005794 ! Golgi apparatus intersection_of: results_in_transport_across GO:0016020 ! membrane relationship: has_target_start_location GO:0005794 ! Golgi apparatus -created_by: dph creation_date: 2012-07-27T02:29:43Z [Term] @@ -105718,7 +110320,6 @@ is_a: GO:0048731 ! system development intersection_of: GO:0048856 ! anatomical structure development intersection_of: results_in_development_of UBERON:0000990 ! reproductive system relationship: results_in_development_of UBERON:0000990 ! reproductive system -created_by: dph creation_date: 2012-08-22T17:47:53Z [Term] @@ -105730,7 +110331,6 @@ is_a: GO:0072665 ! protein localization to vacuole intersection_of: GO:0008104 ! protein localization intersection_of: has_target_end_location GO:0005764 ! lysosome relationship: has_target_end_location GO:0005764 ! lysosome -created_by: dph creation_date: 2012-10-05T10:50:51Z [Term] @@ -105742,7 +110342,6 @@ is_a: GO:0050678 ! regulation of epithelial cell proliferation intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0044342 ! type B pancreatic cell proliferation relationship: regulates GO:0044342 ! type B pancreatic cell proliferation -created_by: dph creation_date: 2012-11-01T13:16:23Z [Term] @@ -105755,7 +110354,6 @@ is_a: GO:0042093 ! T-helper cell differentiation intersection_of: GO:0030154 ! cell differentiation intersection_of: results_in_acquisition_of_features_of CL:0002038 ! T follicular helper cell relationship: results_in_acquisition_of_features_of CL:0002038 ! T follicular helper cell -created_by: dph creation_date: 2012-11-02T09:01:48Z [Term] @@ -105768,7 +110366,6 @@ is_a: GO:0048872 ! homeostasis of number of cells intersection_of: GO:0048872 ! homeostasis of number of cells intersection_of: acts_on_population_of CL:0000037 ! hematopoietic stem cell relationship: acts_on_population_of CL:0000037 ! hematopoietic stem cell -created_by: dph creation_date: 2012-12-04T09:41:02Z [Term] @@ -105780,7 +110377,6 @@ is_a: GO:0042098 ! T cell proliferation intersection_of: GO:0008283 ! cell population proliferation intersection_of: acts_on_population_of CL:0000813 ! memory T cell relationship: acts_on_population_of CL:0000813 ! memory T cell -created_by: dph creation_date: 2012-12-04T09:52:54Z [Term] @@ -105800,7 +110396,6 @@ property_value: RO:0002161 NCBITaxon:3378 property_value: RO:0002161 NCBITaxon:3398 property_value: RO:0002161 NCBITaxon:4890 property_value: RO:0002161 NCBITaxon:5782 -created_by: dph creation_date: 2013-03-22T15:41:44Z [Term] @@ -105813,7 +110408,6 @@ intersection_of: GO:0048468 ! cell development intersection_of: results_in_development_of CL:0000763 ! myeloid cell relationship: part_of GO:0030099 ! myeloid cell differentiation relationship: results_in_development_of CL:0000763 ! myeloid cell -created_by: dph creation_date: 2013-04-18T13:03:16Z [Term] @@ -105826,7 +110420,6 @@ is_a: GO:0002262 ! myeloid cell homeostasis intersection_of: GO:0048872 ! homeostasis of number of cells intersection_of: acts_on_population_of CL:0000235 ! macrophage relationship: acts_on_population_of CL:0000235 ! macrophage -created_by: dph creation_date: 2013-04-18T13:25:33Z [Term] @@ -105838,7 +110431,6 @@ is_a: GO:0043011 ! myeloid dendritic cell differentiation intersection_of: GO:0030154 ! cell differentiation intersection_of: results_in_acquisition_of_features_of CL:0000453 ! Langerhans cell relationship: results_in_acquisition_of_features_of CL:0000453 ! Langerhans cell -created_by: dph creation_date: 2013-04-18T13:29:07Z [Term] @@ -105850,7 +110442,6 @@ is_a: GO:0030154 ! cell differentiation intersection_of: GO:0030154 ! cell differentiation intersection_of: results_in_acquisition_of_features_of CL:0000632 ! hepatic stellate cell relationship: results_in_acquisition_of_features_of CL:0000632 ! hepatic stellate cell -created_by: dph creation_date: 2013-04-18T13:36:08Z [Term] @@ -105865,7 +110456,6 @@ is_a: GO:1903008 ! organelle disassembly intersection_of: GO:0022411 ! cellular component disassembly intersection_of: results_in_disassembly_of GO:0005929 ! cilium relationship: results_in_disassembly_of GO:0005929 ! cilium -created_by: dph creation_date: 2013-04-18T14:59:59Z [Term] @@ -105878,7 +110468,6 @@ intersection_of: GO:0048856 ! anatomical structure development intersection_of: results_in_development_of UBERON:0002291 ! central canal of spinal cord relationship: part_of GO:0021510 ! spinal cord development relationship: results_in_development_of UBERON:0002291 ! central canal of spinal cord -created_by: dph creation_date: 2013-04-20T08:18:31Z [Term] @@ -105890,7 +110479,6 @@ is_a: GO:0048565 ! digestive tract development intersection_of: GO:0048856 ! anatomical structure development intersection_of: results_in_development_of UBERON:0001046 ! hindgut relationship: results_in_development_of UBERON:0001046 ! hindgut -created_by: dph creation_date: 2013-06-14T11:22:21Z [Term] @@ -105902,7 +110490,6 @@ is_a: GO:0015870 ! acetylcholine transport is_a: GO:0023061 ! signal release intersection_of: GO:0046903 ! secretion intersection_of: has_primary_input CHEBI:15355 -created_by: dph creation_date: 2013-06-21T15:40:39Z [Term] @@ -105915,7 +110502,6 @@ is_a: GO:0099124 ! axonal dopamine secretion intersection_of: GO:0007269 ! neurotransmitter secretion intersection_of: has_primary_input CHEBI:59905 relationship: part_of GO:0001963 ! synaptic transmission, dopaminergic -created_by: dph creation_date: 2013-06-21T15:43:15Z [Term] @@ -105928,7 +110514,6 @@ is_a: GO:0048243 ! norepinephrine secretion is_a: GO:0160043 ! catecholamine secretion, neurotransmission intersection_of: GO:0007269 ! neurotransmitter secretion intersection_of: has_primary_input CHEBI:72587 -created_by: dph creation_date: 2013-06-21T16:05:08Z [Term] @@ -105941,7 +110526,6 @@ is_a: GO:0014051 ! gamma-aminobutyric acid secretion intersection_of: GO:0007269 ! neurotransmitter secretion intersection_of: has_primary_input CHEBI:59888 relationship: part_of GO:0051932 ! synaptic transmission, GABAergic -created_by: dph creation_date: 2013-06-21T16:10:50Z [Term] @@ -105955,7 +110539,6 @@ is_a: GO:0051938 ! L-glutamate import intersection_of: GO:0007269 ! neurotransmitter secretion intersection_of: has_primary_input CHEBI:29985 relationship: part_of GO:0035249 ! synaptic transmission, glutamatergic -created_by: dph creation_date: 2013-06-21T16:14:47Z [Term] @@ -105967,7 +110550,6 @@ is_a: GO:0015816 ! glycine transport is_a: GO:0032940 ! secretion by cell intersection_of: GO:0046903 ! secretion intersection_of: has_primary_input CHEBI:57305 -created_by: dph creation_date: 2013-06-21T16:18:23Z [Term] @@ -105980,7 +110562,6 @@ is_a: GO:0061536 ! glycine secretion intersection_of: GO:0007269 ! neurotransmitter secretion intersection_of: has_primary_input CHEBI:57305 relationship: part_of GO:0060012 ! synaptic transmission, glycinergic -created_by: dph creation_date: 2013-06-21T16:19:02Z [Term] @@ -105993,7 +110574,6 @@ is_a: GO:0007269 ! neurotransmitter secretion intersection_of: GO:0007269 ! neurotransmitter secretion intersection_of: has_primary_input CHEBI:57595 relationship: has_primary_input CHEBI:57595 -created_by: dph creation_date: 2013-06-21T16:21:21Z [Term] @@ -106003,7 +110583,6 @@ namespace: biological_process def: "The controlled release of a peptide from a cell in which the peptide acts as a neurotransmitter." [GOC:dph] is_a: GO:0002790 ! peptide secretion is_a: GO:0007269 ! neurotransmitter secretion -created_by: dph creation_date: 2013-06-25T09:10:10Z [Term] @@ -106018,7 +110597,6 @@ intersection_of: GO:0048856 ! anatomical structure development intersection_of: results_in_development_of UBERON:0000045 ! ganglion relationship: part_of GO:0007399 ! nervous system development relationship: results_in_development_of UBERON:0000045 ! ganglion -created_by: dph creation_date: 2013-07-10T08:36:12Z [Term] @@ -106032,7 +110610,6 @@ intersection_of: GO:0048856 ! anatomical structure development intersection_of: results_in_development_of UBERON:0001806 ! sympathetic ganglion relationship: part_of GO:0048485 ! sympathetic nervous system development relationship: results_in_development_of UBERON:0001806 ! sympathetic ganglion -created_by: dph creation_date: 2013-07-10T08:38:01Z [Term] @@ -106046,7 +110623,6 @@ intersection_of: GO:0048856 ! anatomical structure development intersection_of: results_in_development_of UBERON:0001714 ! cranial ganglion relationship: part_of GO:0021545 ! cranial nerve development relationship: results_in_development_of UBERON:0001714 ! cranial ganglion -created_by: dph creation_date: 2013-07-10T08:40:14Z [Term] @@ -106059,7 +110635,6 @@ is_a: GO:0061550 ! cranial ganglion development intersection_of: GO:0048856 ! anatomical structure development intersection_of: results_in_development_of UBERON:0001675 ! trigeminal ganglion relationship: results_in_development_of UBERON:0001675 ! trigeminal ganglion -created_by: dph creation_date: 2013-07-10T08:42:19Z [Term] @@ -106073,7 +110648,6 @@ intersection_of: GO:0009653 ! anatomical structure morphogenesis intersection_of: results_in_morphogenesis_of UBERON:0000045 ! ganglion relationship: part_of GO:0061548 ! ganglion development relationship: results_in_morphogenesis_of UBERON:0000045 ! ganglion -created_by: dph creation_date: 2013-07-10T08:44:57Z [Term] @@ -106087,7 +110661,6 @@ intersection_of: GO:0071695 ! anatomical structure maturation intersection_of: results_in_maturation_of UBERON:0000045 ! ganglion relationship: part_of GO:0061548 ! ganglion development relationship: results_in_maturation_of UBERON:0000045 ! ganglion -created_by: dph creation_date: 2013-07-10T08:45:59Z [Term] @@ -106102,7 +110675,6 @@ intersection_of: GO:0048646 ! anatomical structure formation involved in morphog intersection_of: results_in_formation_of UBERON:0000045 ! ganglion relationship: part_of GO:0061552 ! ganglion morphogenesis relationship: results_in_formation_of UBERON:0000045 ! ganglion -created_by: dph creation_date: 2013-07-10T08:51:50Z [Term] @@ -106117,7 +110689,6 @@ intersection_of: results_in_morphogenesis_of UBERON:0001675 ! trigeminal ganglio relationship: part_of GO:0021636 ! trigeminal nerve morphogenesis relationship: part_of GO:0061551 ! trigeminal ganglion development relationship: results_in_morphogenesis_of UBERON:0001675 ! trigeminal ganglion -created_by: dph creation_date: 2013-07-10T08:57:12Z [Term] @@ -106132,7 +110703,6 @@ intersection_of: results_in_maturation_of UBERON:0001675 ! trigeminal ganglion relationship: part_of GO:0021635 ! trigeminal nerve maturation relationship: part_of GO:0061551 ! trigeminal ganglion development relationship: results_in_maturation_of UBERON:0001675 ! trigeminal ganglion -created_by: dph creation_date: 2013-07-10T08:58:24Z [Term] @@ -106147,7 +110717,6 @@ intersection_of: results_in_maturation_of UBERON:0001714 ! cranial ganglion relationship: part_of GO:0021605 ! cranial nerve maturation relationship: part_of GO:0061550 ! cranial ganglion development relationship: results_in_maturation_of UBERON:0001714 ! cranial ganglion -created_by: dph creation_date: 2013-07-10T08:59:52Z [Term] @@ -106162,7 +110731,6 @@ intersection_of: results_in_morphogenesis_of UBERON:0001714 ! cranial ganglion relationship: part_of GO:0021602 ! cranial nerve morphogenesis relationship: part_of GO:0061550 ! cranial ganglion development relationship: results_in_morphogenesis_of UBERON:0001714 ! cranial ganglion -created_by: dph creation_date: 2013-07-10T09:02:15Z [Term] @@ -106176,7 +110744,6 @@ intersection_of: GO:0048646 ! anatomical structure formation involved in morphog intersection_of: results_in_formation_of UBERON:0001714 ! cranial ganglion relationship: part_of GO:0061559 ! cranial ganglion morphogenesis relationship: results_in_formation_of UBERON:0001714 ! cranial ganglion -created_by: dph creation_date: 2013-07-10T09:07:27Z [Term] @@ -106190,7 +110757,6 @@ intersection_of: GO:0048646 ! anatomical structure formation involved in morphog intersection_of: results_in_formation_of UBERON:0001675 ! trigeminal ganglion relationship: part_of GO:0061556 ! trigeminal ganglion morphogenesis relationship: results_in_formation_of UBERON:0001675 ! trigeminal ganglion -created_by: dph creation_date: 2013-07-10T09:08:13Z [Term] @@ -106199,7 +110765,6 @@ name: axon development namespace: biological_process def: "The progression of an axon over time. Covers axonogenesis (de novo generation of an axon) and axon regeneration (regrowth), as well as processes pertaining to the progression of the axon over time (fasciculation and defasciculation)." [GOC:dph, GOC:pg, GOC:pr] is_a: GO:0031175 ! neuron projection development -created_by: dph creation_date: 2013-07-18T14:43:01Z [Term] @@ -106212,7 +110777,6 @@ is_a: GO:0007015 ! actin filament organization intersection_of: GO:0016043 ! cellular component organization intersection_of: results_in_organization_of GO:0032432 ! actin filament bundle relationship: results_in_organization_of GO:0032432 ! actin filament bundle -created_by: dph creation_date: 2013-08-02T11:24:11Z [Term] @@ -106224,7 +110788,6 @@ is_a: GO:0061582 ! intestinal epithelial cell migration intersection_of: GO:0016477 ! cell migration intersection_of: results_in_movement_of CL:0011108 ! colon epithelial cell relationship: results_in_movement_of CL:0011108 ! colon epithelial cell -created_by: dph creation_date: 2013-12-23T07:26:54Z [Term] @@ -106236,7 +110799,6 @@ is_a: GO:0010631 ! epithelial cell migration intersection_of: GO:0016477 ! cell migration intersection_of: results_in_movement_of CL:0000575 ! corneal epithelial cell relationship: results_in_movement_of CL:0000575 ! corneal epithelial cell -created_by: dph creation_date: 2013-12-23T07:28:29Z [Term] @@ -106248,7 +110810,6 @@ is_a: GO:0010631 ! epithelial cell migration intersection_of: GO:0016477 ! cell migration intersection_of: results_in_movement_of CL:0002563 ! intestinal epithelial cell relationship: results_in_movement_of CL:0002563 ! intestinal epithelial cell -created_by: dph creation_date: 2013-12-23T07:30:55Z [Term] @@ -106259,7 +110820,6 @@ def: "The controlled release of orexin from a cell or a tissue." [GOC:dph] synonym: "hypocretin secretion" EXACT [] is_a: GO:0002790 ! peptide secretion property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/23504" xsd:anyURI -created_by: dph creation_date: 2013-12-26T10:07:38Z [Term] @@ -106271,7 +110831,6 @@ synonym: "hypocretin secretion, neurotransmission" EXACT [] is_a: GO:0061544 ! peptide secretion, neurotransmission is_a: GO:0061584 ! orexin secretion property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/23504" xsd:anyURI -created_by: dph creation_date: 2013-12-26T10:09:37Z [Term] @@ -106285,16 +110844,12 @@ intersection_of: GO:0009653 ! anatomical structure morphogenesis intersection_of: results_in_morphogenesis_of UBERON:0004363 ! pharyngeal arch artery relationship: part_of GO:0060037 ! pharyngeal system development relationship: results_in_morphogenesis_of UBERON:0004363 ! pharyngeal arch artery -created_by: dph creation_date: 2014-05-09T15:34:06Z [Term] id: GO:0061629 name: RNA polymerase II-specific DNA-binding transcription factor binding namespace: molecular_function -alt_id: GO:0001085 -alt_id: GO:0001102 -alt_id: GO:0001103 def: "Binding to a sequence-specific DNA binding RNA polymerase II transcription factor, any of the factors that interact selectively and non-covalently with a specific DNA sequence in order to modulate transcription." [GOC:dph, GOC:vw] synonym: "RNA polymerase II activating transcription factor binding" RELATED [] synonym: "RNA polymerase II repressing transcription factor binding" RELATED [] @@ -106303,7 +110858,6 @@ synonym: "RNA polymerase II sequence-specific DNA-binding transcription factor b synonym: "RNA polymerase II transcription factor binding" RELATED [] is_a: GO:0140297 ! DNA-binding transcription factor binding property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/19354" xsd:anyURI -created_by: dph creation_date: 2014-05-15T09:12:24Z [Term] @@ -106316,7 +110870,6 @@ intersection_of: GO:0009653 ! anatomical structure morphogenesis intersection_of: results_in_morphogenesis_of UBERON:0000998 ! seminal vesicle relationship: part_of GO:0061107 ! seminal vesicle development relationship: results_in_morphogenesis_of UBERON:0000998 ! seminal vesicle -created_by: dph creation_date: 2015-03-04T13:33:49Z [Term] @@ -106333,7 +110886,6 @@ intersection_of: GO:0061138 ! morphogenesis of a branching epithelium intersection_of: part_of GO:0061682 ! seminal vesicle morphogenesis relationship: part_of GO:0061108 ! seminal vesicle epithelium development relationship: part_of GO:0061682 ! seminal vesicle morphogenesis -created_by: dph creation_date: 2015-03-04T13:39:47Z [Term] @@ -106345,7 +110897,6 @@ is_a: GO:1990234 ! transferase complex intersection_of: GO:0032991 ! protein-containing complex intersection_of: capable_of GO:0016772 ! transferase activity, transferring phosphorus-containing groups relationship: capable_of GO:0016772 ! transferase activity, transferring phosphorus-containing groups -created_by: dph creation_date: 2015-05-06T11:22:38Z [Term] @@ -106353,12 +110904,12 @@ id: GO:0061725 name: cytosolic lipolysis namespace: biological_process def: "The chemical reactions and pathways resulting in the breakdown of lipid droplets and hydrolysis of stored triglycerides occurring through the orchestrated activation of cytosolic lipases." [GOC:autophagy] -is_a: GO:0044242 ! cellular lipid catabolic process +is_a: GO:0016042 ! lipid catabolic process intersection_of: GO:0009056 ! catabolic process intersection_of: has_primary_input CHEBI:18059 intersection_of: occurs_in GO:0005829 ! cytosol relationship: occurs_in GO:0005829 ! cytosol -created_by: dph +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28908" xsd:anyURI creation_date: 2015-07-08T13:42:15Z [Term] @@ -106371,9 +110922,23 @@ is_a: GO:0071695 ! anatomical structure maturation intersection_of: GO:0021700 ! developmental maturation intersection_of: results_in_maturation_of GO:0030141 ! secretory granule relationship: results_in_maturation_of GO:0030141 ! secretory granule -created_by: dph creation_date: 2016-09-09T13:24:34Z +[Term] +id: GO:0061842 +name: microtubule organizing center localization +namespace: biological_process +def: "Any process in which the microtubule organizing center is transported to, and/or maintained in, a specific location within the cell." [PMID:21281821] +synonym: "microtubule organizing center polarity" NARROW [] +synonym: "MTOC localization" EXACT [] +synonym: "MTOC polarity" NARROW [] +is_a: BFO:0000003 +is_a: GO:0009987 ! cellular process +is_a: GO:0051179 ! localization +intersection_of: GO:0051179 ! localization +intersection_of: has_primary_input GO:0005815 ! microtubule organizing center +relationship: has_primary_input GO:0005815 ! microtubule organizing center + [Term] id: GO:0061844 name: antimicrobial humoral immune response mediated by antimicrobial peptide @@ -106412,7 +110977,6 @@ is_a: GO:0030334 ! regulation of cell migration intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0097402 ! neuroblast migration relationship: regulates GO:0097402 ! neuroblast migration -created_by: dph creation_date: 2017-03-08T18:17:07Z [Term] @@ -106425,7 +110989,6 @@ is_a: GO:0061853 ! regulation of neuroblast migration intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0097402 ! neuroblast migration relationship: positively_regulates GO:0097402 ! neuroblast migration -created_by: dph creation_date: 2017-03-08T18:22:30Z [Term] @@ -106438,7 +111001,6 @@ is_a: GO:0061853 ! regulation of neuroblast migration intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0097402 ! neuroblast migration relationship: negatively_regulates GO:0097402 ! neuroblast migration -created_by: dph creation_date: 2017-03-08T18:26:21Z [Term] @@ -106452,7 +111014,6 @@ intersection_of: GO:0006810 ! transport intersection_of: has_primary_input CHEBI:29108 intersection_of: results_in_transport_across GO:0016020 ! membrane intersection_of: results_in_transport_to_from_or_in GO:0005794 ! Golgi apparatus -created_by: dph creation_date: 2017-03-14T16:08:23Z [Term] @@ -106464,7 +111025,6 @@ is_a: GO:0010761 ! fibroblast migration intersection_of: GO:0016477 ! cell migration intersection_of: results_in_movement_of CL:0000632 ! hepatic stellate cell relationship: results_in_movement_of CL:0000632 ! hepatic stellate cell -created_by: dph creation_date: 2017-05-01T13:01:40Z [Term] @@ -106476,7 +111036,6 @@ is_a: GO:0010762 ! regulation of fibroblast migration intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0061868 ! hepatic stellate cell migration relationship: regulates GO:0061868 ! hepatic stellate cell migration -created_by: dph creation_date: 2017-05-01T13:04:20Z [Term] @@ -106489,7 +111048,6 @@ is_a: GO:0061869 ! regulation of hepatic stellate cell migration intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0061868 ! hepatic stellate cell migration relationship: positively_regulates GO:0061868 ! hepatic stellate cell migration -created_by: dph creation_date: 2017-05-01T13:17:23Z [Term] @@ -106502,7 +111060,6 @@ is_a: GO:0061869 ! regulation of hepatic stellate cell migration intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0061868 ! hepatic stellate cell migration relationship: negatively_regulates GO:0061868 ! hepatic stellate cell migration -created_by: dph creation_date: 2017-05-01T13:20:51Z [Term] @@ -106515,7 +111072,6 @@ is_a: GO:0050865 ! regulation of cell activation intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0048143 ! astrocyte activation relationship: regulates GO:0048143 ! astrocyte activation -created_by: dph creation_date: 2017-06-01T22:26:29Z [Term] @@ -106530,7 +111086,6 @@ is_a: GO:0150079 ! negative regulation of neuroinflammatory response intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0048143 ! astrocyte activation relationship: negatively_regulates GO:0048143 ! astrocyte activation -created_by: dph creation_date: 2017-06-01T22:29:43Z [Term] @@ -106545,7 +111100,6 @@ is_a: GO:0150078 ! positive regulation of neuroinflammatory response intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0048143 ! astrocyte activation relationship: positively_regulates GO:0048143 ! astrocyte activation -created_by: dph creation_date: 2017-06-01T22:31:50Z [Term] @@ -106559,7 +111113,6 @@ intersection_of: GO:0001775 ! cell activation intersection_of: has_primary_input CL:0000125 ! glial cell relationship: has_primary_input CL:0000125 ! glial cell relationship: part_of GO:0150076 ! neuroinflammatory response -created_by: dph creation_date: 2017-06-13T13:06:23Z [Term] @@ -106572,7 +111125,6 @@ is_a: GO:0008104 ! protein localization intersection_of: GO:0008104 ! protein localization intersection_of: has_target_end_location GO:0036477 ! somatodendritic compartment relationship: has_target_end_location GO:0036477 ! somatodendritic compartment -created_by: dph creation_date: 2017-09-08T13:22:26Z [Term] @@ -106585,7 +111137,6 @@ is_a: GO:0090150 ! establishment of protein localization to membrane intersection_of: GO:0045184 ! establishment of protein localization intersection_of: has_target_end_location GO:0005886 ! plasma membrane intersection_of: has_target_start_location GO:0005622 ! intracellular anatomical structure -created_by: dph creation_date: 2017-10-26T12:55:15Z [Term] @@ -106597,7 +111148,6 @@ is_a: GO:0060349 ! bone morphogenesis intersection_of: GO:0060349 ! bone morphogenesis intersection_of: results_in_morphogenesis_of UBERON:0012075 ! replacement bone relationship: results_in_morphogenesis_of UBERON:0012075 ! replacement bone -created_by: dph creation_date: 2018-02-12T18:10:59Z [Term] @@ -106609,7 +111159,6 @@ is_a: GO:0061973 ! membrane bone morphogenesis intersection_of: GO:0060349 ! bone morphogenesis intersection_of: results_in_morphogenesis_of UBERON:0008907 ! dermal bone relationship: results_in_morphogenesis_of UBERON:0008907 ! dermal bone -created_by: dph creation_date: 2018-02-12T18:16:21Z [Term] @@ -106621,7 +111170,6 @@ is_a: GO:0060349 ! bone morphogenesis intersection_of: GO:0060349 ! bone morphogenesis intersection_of: results_in_morphogenesis_of UBERON:0007842 ! membrane bone relationship: results_in_morphogenesis_of UBERON:0007842 ! membrane bone -created_by: dph creation_date: 2018-02-12T18:21:09Z [Term] @@ -106631,7 +111179,6 @@ namespace: biological_process def: "A process that coontributes to the second meiotic division. The second meiotic division separates chromatids resulting in a haploid number of chromosomes." [PMID:29385397] synonym: "second meiotic division" EXACT [PMID:29385397] is_a: GO:1903046 ! meiotic cell cycle process -created_by: dph creation_date: 2018-02-14T22:37:44Z [Term] @@ -106644,7 +111191,6 @@ is_a: GO:0019222 ! regulation of metabolic process intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0044281 ! small molecule metabolic process relationship: regulates GO:0044281 ! small molecule metabolic process -created_by: dph creation_date: 2018-03-19T14:11:54Z [Term] @@ -106658,7 +111204,6 @@ is_a: GO:0062012 ! regulation of small molecule metabolic process intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0044281 ! small molecule metabolic process relationship: positively_regulates GO:0044281 ! small molecule metabolic process -created_by: dph creation_date: 2018-03-19T14:25:10Z [Term] @@ -106672,7 +111217,6 @@ is_a: GO:0062012 ! regulation of small molecule metabolic process intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0044281 ! small molecule metabolic process relationship: negatively_regulates GO:0044281 ! small molecule metabolic process -created_by: dph creation_date: 2018-03-19T14:27:23Z [Term] @@ -106683,7 +111227,6 @@ def: "An extracellular matrix consisting mainly of proteins (especially collagen is_a: GO:0031012 ! extracellular matrix relationship: RO:0002160 NCBITaxon:33208 ! only in taxon Metazoa relationship: RO:0002162 NCBITaxon:33208 {all_only="true"} ! in taxon Metazoa -created_by: dph creation_date: 2018-04-13T12:47:21Z [Term] @@ -106697,7 +111240,6 @@ is_a: GO:2001252 ! positive regulation of chromosome organization intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0000070 ! mitotic sister chromatid segregation relationship: positively_regulates GO:0000070 ! mitotic sister chromatid segregation -created_by: dph creation_date: 2018-04-23T14:32:23Z [Term] @@ -106710,7 +111252,6 @@ intersection_of: GO:0048869 ! cellular developmental process intersection_of: results_in_acquisition_of_features_of CL:0001658 ! visual pigment cell (sensu Nematoda and Protostomia) relationship: part_of GO:0001745 ! compound eye morphogenesis relationship: results_in_acquisition_of_features_of CL:0001658 ! visual pigment cell (sensu Nematoda and Protostomia) -created_by: dph creation_date: 2018-08-01T12:59:42Z [Term] @@ -106723,7 +111264,6 @@ intersection_of: GO:0048856 ! anatomical structure development intersection_of: results_in_development_of UBERON:0000945 ! stomach relationship: part_of GO:0048565 ! digestive tract development relationship: results_in_development_of UBERON:0000945 ! stomach -created_by: dph creation_date: 2018-11-20T18:15:45Z [Term] @@ -106736,7 +111276,6 @@ intersection_of: GO:0032991 ! protein-containing complex intersection_of: capable_of GO:0038024 ! cargo receptor activity intersection_of: part_of GO:0016020 ! membrane relationship: capable_of GO:0038024 ! cargo receptor activity -created_by: dph creation_date: 2019-07-08T18:09:01Z [Term] @@ -106748,7 +111287,6 @@ is_a: GO:0050906 ! detection of stimulus involved in sensory perception intersection_of: GO:0051606 ! detection of stimulus intersection_of: part_of GO:0019233 ! sensory perception of pain relationship: part_of GO:0019233 ! sensory perception of pain -created_by: dph creation_date: 2019-09-13T13:48:47Z [Term] @@ -106762,7 +111300,6 @@ is_a: GO:0008152 ! metabolic process intersection_of: GO:0008152 ! metabolic process intersection_of: has_primary_input_or_output CHEBI:28838 relationship: has_primary_input_or_output CHEBI:28838 -created_by: dph creation_date: 2019-11-18T15:56:36Z [Term] @@ -106778,7 +111315,6 @@ is_a: GO:0062170 ! lutein metabolic process intersection_of: GO:0009058 ! biosynthetic process intersection_of: has_primary_output CHEBI:28838 relationship: has_primary_output CHEBI:28838 -created_by: dph creation_date: 2019-11-18T16:01:00Z [Term] @@ -106794,7 +111330,6 @@ is_a: GO:0062170 ! lutein metabolic process intersection_of: GO:0009056 ! catabolic process intersection_of: has_primary_input CHEBI:28838 relationship: has_primary_input CHEBI:28838 -created_by: dph creation_date: 2019-11-18T16:06:07Z [Term] @@ -106807,7 +111342,6 @@ intersection_of: GO:0009987 ! cellular process intersection_of: results_in_assembly_of GO:0001534 ! radial spoke relationship: part_of GO:0035082 ! axoneme assembly relationship: results_in_assembly_of GO:0001534 ! radial spoke -created_by: dph creation_date: 2019-11-20T17:50:08Z [Term] @@ -106819,7 +111353,6 @@ is_a: GO:0030855 ! epithelial cell differentiation intersection_of: GO:0030154 ! cell differentiation intersection_of: results_in_acquisition_of_features_of CL:0005006 ! ionocyte relationship: results_in_acquisition_of_features_of CL:0005006 ! ionocyte -created_by: dph creation_date: 2020-04-20T12:30:35Z [Term] @@ -106831,7 +111364,6 @@ is_a: GO:0035418 ! protein localization to synapse intersection_of: GO:0008104 ! protein localization intersection_of: has_target_end_location GO:0098794 ! postsynapse relationship: has_target_end_location GO:0098794 ! postsynapse -created_by: dph creation_date: 2020-04-20T13:58:43Z [Term] @@ -106854,9 +111386,6 @@ intersection_of: results_in_transport_across GO:0016020 ! membrane id: GO:0065003 name: protein-containing complex assembly namespace: biological_process -alt_id: GO:0006461 -alt_id: GO:0034622 -alt_id: GO:0043623 def: "The aggregation, arrangement and bonding together of a set of macromolecules to form a protein-containing complex." [GOC:jl] subset: goslim_chembl subset: goslim_drosophila @@ -107946,7 +112475,6 @@ intersection_of: GO:0009306 ! protein secretion intersection_of: process_has_causal_agent CL:0000233 ! platelet relationship: part_of GO:0002576 ! platelet degranulation relationship: process_has_causal_agent CL:0000233 ! platelet -created_by: mah creation_date: 2009-04-09T02:38:05Z [Term] @@ -107961,14 +112489,12 @@ is_a: GO:0006816 ! calcium ion transport is_a: GO:0055085 ! transmembrane transport intersection_of: GO:0055085 ! transmembrane transport intersection_of: has_primary_input CHEBI:29108 -created_by: mah creation_date: 2009-04-28T10:44:09Z [Term] id: GO:0070613 name: regulation of protein processing namespace: biological_process -alt_id: GO:0010953 def: "Any process that modulates the frequency, rate or extent of protein processing, a protein maturation process achieved by the cleavage of a peptide bond or bonds within a protein." [GOC:mah] synonym: "regulation of protein maturation by peptide bond cleavage" EXACT [] is_a: GO:0030162 ! regulation of proteolysis @@ -107976,7 +112502,6 @@ is_a: GO:1903317 ! regulation of protein maturation intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0016485 ! protein processing relationship: regulates GO:0016485 ! protein processing -created_by: mah creation_date: 2009-04-29T02:49:14Z [Term] @@ -107989,7 +112514,6 @@ is_a: GO:0006810 ! transport intersection_of: GO:0006810 ! transport intersection_of: results_in_transport_across UBERON:0000483 ! epithelium relationship: results_in_transport_across UBERON:0000483 ! epithelium -created_by: mah creation_date: 2009-05-06T03:31:02Z [Term] @@ -108001,7 +112525,6 @@ is_a: GO:0070633 ! transepithelial transport intersection_of: GO:0070633 ! transepithelial transport intersection_of: has_primary_input CHEBI:28938 relationship: has_primary_input CHEBI:28938 -created_by: mah creation_date: 2009-05-06T03:34:43Z [Term] @@ -108016,7 +112539,6 @@ intersection_of: acts_on_population_of CL:0000738 ! leukocyte relationship: acts_on_population_of CL:0000738 ! leukocyte relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata relationship: RO:0002162 NCBITaxon:7742 {all_only="true"} ! in taxon Vertebrata -created_by: mah creation_date: 2009-05-28T05:25:28Z [Term] @@ -108028,7 +112550,6 @@ is_a: GO:0070661 ! leukocyte proliferation intersection_of: GO:0008283 ! cell population proliferation intersection_of: acts_on_population_of CL:0000097 ! mast cell relationship: acts_on_population_of CL:0000097 ! mast cell -created_by: mah creation_date: 2009-05-28T05:27:51Z [Term] @@ -108040,7 +112561,6 @@ is_a: GO:0042127 ! regulation of cell population proliferation intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0070661 ! leukocyte proliferation relationship: regulates GO:0070661 ! leukocyte proliferation -created_by: mah creation_date: 2009-05-28T05:30:39Z [Term] @@ -108057,7 +112577,6 @@ is_a: GO:0070663 ! regulation of leukocyte proliferation intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0070661 ! leukocyte proliferation relationship: negatively_regulates GO:0070661 ! leukocyte proliferation -created_by: mah creation_date: 2009-05-28T05:34:50Z [Term] @@ -108075,7 +112594,6 @@ is_a: GO:0070663 ! regulation of leukocyte proliferation intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0070661 ! leukocyte proliferation relationship: positively_regulates GO:0070661 ! leukocyte proliferation -created_by: mah creation_date: 2009-05-28T05:36:46Z [Term] @@ -108087,7 +112605,6 @@ is_a: GO:0070663 ! regulation of leukocyte proliferation intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0070662 ! mast cell proliferation relationship: regulates GO:0070662 ! mast cell proliferation -created_by: mah creation_date: 2009-05-28T05:40:43Z [Term] @@ -108104,7 +112621,6 @@ is_a: GO:0070666 ! regulation of mast cell proliferation intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0070662 ! mast cell proliferation relationship: negatively_regulates GO:0070662 ! mast cell proliferation -created_by: mah creation_date: 2009-05-28T05:45:11Z [Term] @@ -108122,7 +112638,6 @@ is_a: GO:0070666 ! regulation of mast cell proliferation intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0070662 ! mast cell proliferation relationship: positively_regulates GO:0070662 ! mast cell proliferation -created_by: mah creation_date: 2009-05-28T05:48:30Z [Term] @@ -108133,7 +112648,6 @@ def: "Any process in which a macromolecule is transported to, and/or maintained synonym: "cellular macromolecule localisation" EXACT [GOC:mah] is_a: GO:0033036 ! macromolecule localization is_a: GO:0051641 ! cellular localization -created_by: mah creation_date: 2009-06-16T04:08:29Z [Term] @@ -108143,7 +112657,6 @@ namespace: cellular_component def: "A secretory granule that contains cathepsin and gelatinase and is readily exocytosed upon cell activation; found primarily in mature neutrophil cells." [GOC:BHF, GOC:mah, GOC:rl, PMID:12070036] synonym: "gelatinase granule" EXACT [PMID:23650620] is_a: GO:0030141 ! secretory granule -created_by: mah creation_date: 2009-07-20T03:57:00Z [Term] @@ -108156,7 +112669,6 @@ intersection_of: GO:0016020 ! membrane intersection_of: bounding_layer_of GO:0070820 ! tertiary granule relationship: bounding_layer_of GO:0070820 ! tertiary granule relationship: part_of GO:0070820 ! tertiary granule -created_by: mah creation_date: 2009-07-20T03:59:41Z [Term] @@ -108170,7 +112682,6 @@ intersection_of: GO:0022607 ! cellular component assembly intersection_of: results_in_assembly_of GO:0005923 ! bicellular tight junction relationship: part_of GO:0043297 ! apical junction assembly relationship: results_in_assembly_of GO:0005923 ! bicellular tight junction -created_by: mah creation_date: 2009-07-23T04:32:38Z [Term] @@ -108184,21 +112695,18 @@ is_a: GO:0085029 ! extracellular matrix assembly intersection_of: GO:0022607 ! cellular component assembly intersection_of: results_in_assembly_of GO:0005604 ! basement membrane relationship: results_in_assembly_of GO:0005604 ! basement membrane -created_by: mah creation_date: 2009-07-23T05:01:51Z [Term] id: GO:0070840 name: dynein complex binding namespace: molecular_function -alt_id: GO:0045502 def: "Binding to a dynein complex, a protein complex that contains two or three dynein heavy chains and several light chains, and has microtubule motor activity." [GOC:bf, GOC:BHF, GOC:mah] synonym: "dynein binding" RELATED [] is_a: GO:0044877 ! protein-containing complex binding intersection_of: GO:0005488 ! binding intersection_of: has_primary_input GO:0030286 ! dynein complex relationship: has_primary_input GO:0030286 ! dynein complex -created_by: mah creation_date: 2009-07-31T01:22:47Z [Term] @@ -108207,7 +112715,6 @@ name: growth factor receptor binding namespace: molecular_function def: "Binding to a growth factor receptor." [GOC:mah, GOC:vw] is_a: GO:0005102 ! signaling receptor binding -created_by: mah creation_date: 2009-08-07T11:23:02Z [Term] @@ -108219,14 +112726,12 @@ synonym: "regulation of bile acid anabolism" EXACT [GOC:mah] synonym: "regulation of bile acid biosynthesis" EXACT [GOC:mah] synonym: "regulation of bile acid formation" EXACT [GOC:mah] synonym: "regulation of bile acid synthesis" EXACT [GOC:mah] -is_a: GO:0010565 ! regulation of cellular ketone metabolic process -is_a: GO:0031326 ! regulation of cellular biosynthetic process +is_a: GO:0010565 ! regulation of ketone metabolic process is_a: GO:0050810 ! regulation of steroid biosynthetic process is_a: GO:1904251 ! regulation of bile acid metabolic process intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0006699 ! bile acid biosynthetic process relationship: regulates GO:0006699 ! bile acid biosynthetic process -created_by: mah creation_date: 2009-08-14T03:09:02Z [Term] @@ -108243,13 +112748,11 @@ synonym: "negative regulation of bile acid biosynthesis" EXACT [GOC:mah] synonym: "negative regulation of bile acid formation" EXACT [GOC:mah] synonym: "negative regulation of bile acid synthesis" EXACT [GOC:mah] is_a: GO:0010894 ! negative regulation of steroid biosynthetic process -is_a: GO:0031327 ! negative regulation of cellular biosynthetic process is_a: GO:0070857 ! regulation of bile acid biosynthetic process is_a: GO:1904252 ! negative regulation of bile acid metabolic process intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0006699 ! bile acid biosynthetic process relationship: negatively_regulates GO:0006699 ! bile acid biosynthetic process -created_by: mah creation_date: 2009-08-14T03:16:40Z [Term] @@ -108267,13 +112770,11 @@ synonym: "up regulation of bile acid biosynthetic process" EXACT [GOC:mah] synonym: "up-regulation of bile acid biosynthetic process" EXACT [GOC:mah] synonym: "upregulation of bile acid biosynthetic process" EXACT [GOC:mah] is_a: GO:0010893 ! positive regulation of steroid biosynthetic process -is_a: GO:0031328 ! positive regulation of cellular biosynthetic process is_a: GO:0070857 ! regulation of bile acid biosynthetic process is_a: GO:1904253 ! positive regulation of bile acid metabolic process intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0006699 ! bile acid biosynthetic process relationship: positively_regulates GO:0006699 ! bile acid biosynthetic process -created_by: mah creation_date: 2009-08-14T03:22:58Z [Term] @@ -108287,7 +112788,6 @@ is_a: GO:0043467 ! regulation of generation of precursor metabolites and energy intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0005977 ! glycogen metabolic process relationship: regulates GO:0005977 ! glycogen metabolic process -created_by: mah creation_date: 2009-08-20T02:44:53Z [Term] @@ -108297,13 +112797,11 @@ namespace: biological_process def: "Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving glycogen." [GOC:mah] synonym: "negative regulation of glycogen metabolism" EXACT [GOC:mah] is_a: GO:0010605 ! negative regulation of macromolecule metabolic process -is_a: GO:0031324 ! negative regulation of cellular metabolic process is_a: GO:0045912 ! negative regulation of carbohydrate metabolic process is_a: GO:0070873 ! regulation of glycogen metabolic process intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0005977 ! glycogen metabolic process relationship: negatively_regulates GO:0005977 ! glycogen metabolic process -created_by: mah creation_date: 2009-08-20T02:50:41Z [Term] @@ -108314,12 +112812,10 @@ def: "Any process that activates or increases the frequency, rate or extent of t synonym: "positive regulation of glycogen metabolism" EXACT [GOC:mah] is_a: GO:0010604 ! positive regulation of macromolecule metabolic process is_a: GO:0010907 ! positive regulation of glucose metabolic process -is_a: GO:0031325 ! positive regulation of cellular metabolic process is_a: GO:0070873 ! regulation of glycogen metabolic process intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0005977 ! glycogen metabolic process relationship: positively_regulates GO:0005977 ! glycogen metabolic process -created_by: mah creation_date: 2009-08-20T02:53:55Z [Term] @@ -108331,7 +112827,6 @@ comment: Note that this term is in the subset of terms that should not be used f subset: gocheck_do_not_annotate is_a: GO:0042221 ! response to chemical is_a: GO:0051716 ! cellular response to stimulus -created_by: mah creation_date: 2009-08-27T04:41:45Z [Term] @@ -108345,7 +112840,6 @@ is_a: GO:0022607 ! cellular component assembly intersection_of: GO:0022607 ! cellular component assembly intersection_of: results_in_assembly_of GO:0043226 ! organelle relationship: results_in_assembly_of GO:0043226 ! organelle -created_by: mah creation_date: 2009-09-15T03:00:51Z [Term] @@ -108358,7 +112852,6 @@ is_a: GO:0001909 ! leukocyte mediated cytotoxicity is_a: GO:0002446 ! neutrophil mediated immunity intersection_of: GO:0001906 ! cell killing intersection_of: process_has_causal_agent CL:0000775 ! neutrophil -created_by: mah creation_date: 2009-10-01T01:49:30Z [Term] @@ -108372,7 +112865,6 @@ is_a: GO:0002886 ! regulation of myeloid leukocyte mediated immunity intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0070942 ! neutrophil mediated cytotoxicity relationship: regulates GO:0070942 ! neutrophil mediated cytotoxicity -created_by: mah creation_date: 2009-10-01T02:14:36Z [Term] @@ -108391,7 +112883,6 @@ is_a: GO:0070948 ! regulation of neutrophil mediated cytotoxicity intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0070942 ! neutrophil mediated cytotoxicity relationship: negatively_regulates GO:0070942 ! neutrophil mediated cytotoxicity -created_by: mah creation_date: 2009-10-01T02:20:17Z [Term] @@ -108411,7 +112902,6 @@ is_a: GO:0070948 ! regulation of neutrophil mediated cytotoxicity intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0070942 ! neutrophil mediated cytotoxicity relationship: positively_regulates GO:0070942 ! neutrophil mediated cytotoxicity -created_by: mah creation_date: 2009-10-01T02:28:49Z [Term] @@ -108424,7 +112914,6 @@ intersection_of: GO:0021700 ! developmental maturation intersection_of: results_in_maturation_of UBERON:0001474 ! bone element relationship: part_of GO:0060348 ! bone development relationship: results_in_maturation_of UBERON:0001474 ! bone element -created_by: mah creation_date: 2009-10-05T04:35:31Z [Term] @@ -108433,7 +112922,6 @@ name: sensory perception of gravity namespace: biological_process def: "The series of events required for an organism to receive a gravitational stimulus, convert it to a molecular signal, and recognize and characterize the signal. This is a neurological process." [GOC:mah] is_a: GO:0007600 ! sensory perception -created_by: mah creation_date: 2009-11-03T03:25:12Z [Term] @@ -108446,7 +112934,6 @@ is_a: GO:0050974 ! detection of mechanical stimulus involved in sensory percepti intersection_of: GO:0050982 ! detection of mechanical stimulus intersection_of: part_of GO:0070998 ! sensory perception of gravity relationship: part_of GO:0070998 ! sensory perception of gravity -created_by: mah creation_date: 2009-11-03T03:27:30Z [Term] @@ -108459,7 +112946,6 @@ is_a: GO:0034502 ! protein localization to chromosome intersection_of: GO:0008104 ! protein localization intersection_of: has_target_end_location GO:0000785 ! chromatin relationship: has_target_end_location GO:0000785 ! chromatin -created_by: mah creation_date: 2009-11-20T11:51:20Z [Term] @@ -108472,7 +112958,6 @@ is_a: GO:0070199 ! establishment of protein localization to chromosome is_a: GO:0071168 ! protein localization to chromatin intersection_of: GO:0045184 ! establishment of protein localization intersection_of: has_target_end_location GO:0000785 ! chromatin -created_by: mah creation_date: 2009-11-20T11:52:43Z [Term] @@ -108485,7 +112970,6 @@ subset: gocheck_do_not_annotate synonym: "cellular response to abiotic stress" NARROW [GOC:mah] is_a: GO:0009628 ! response to abiotic stimulus is_a: GO:0104004 ! cellular response to environmental stimulus -created_by: mah creation_date: 2009-12-03T01:02:11Z [Term] @@ -108498,21 +112982,18 @@ is_a: GO:0043200 ! response to amino acid is_a: GO:0070887 ! cellular response to chemical stimulus intersection_of: GO:0070887 ! cellular response to chemical stimulus intersection_of: has_primary_input CHEBI:35238 -created_by: mah creation_date: 2009-12-03T02:08:11Z [Term] id: GO:0071242 name: cellular response to ammonium ion namespace: biological_process -alt_id: GO:1903718 def: "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an ammonium stimulus." [GO_REF:0000071, GOC:TermGenie, PMID:23509267] synonym: "cellular response to ammonia" EXACT [] is_a: GO:0060359 ! response to ammonium ion is_a: GO:0070887 ! cellular response to chemical stimulus intersection_of: GO:0070887 ! cellular response to chemical stimulus intersection_of: has_primary_input CHEBI:28938 -created_by: mah creation_date: 2009-12-03T02:39:40Z [Term] @@ -108525,7 +113006,6 @@ is_a: GO:0051592 ! response to calcium ion is_a: GO:0070887 ! cellular response to chemical stimulus intersection_of: GO:0070887 ! cellular response to chemical stimulus intersection_of: has_primary_input CHEBI:29108 -created_by: mah creation_date: 2009-12-10T03:55:01Z [Term] @@ -108538,7 +113018,6 @@ is_a: GO:0010039 ! response to iron ion is_a: GO:0070887 ! cellular response to chemical stimulus intersection_of: GO:0070887 ! cellular response to chemical stimulus intersection_of: has_primary_input CHEBI:24875 -created_by: mah creation_date: 2009-12-10T03:57:22Z [Term] @@ -108552,7 +113031,6 @@ is_a: GO:0033198 ! response to ATP is_a: GO:0070887 ! cellular response to chemical stimulus intersection_of: GO:0070887 ! cellular response to chemical stimulus intersection_of: has_primary_input CHEBI:30616 -created_by: mah creation_date: 2009-12-10T05:09:47Z [Term] @@ -108564,7 +113042,6 @@ is_a: GO:0009743 ! response to carbohydrate is_a: GO:0070887 ! cellular response to chemical stimulus intersection_of: GO:0070887 ! cellular response to chemical stimulus intersection_of: has_primary_input CHEBI:16646 -created_by: mah creation_date: 2009-12-10T05:13:33Z [Term] @@ -108576,7 +113053,6 @@ is_a: GO:0009746 ! response to hexose is_a: GO:0070887 ! cellular response to chemical stimulus intersection_of: GO:0070887 ! cellular response to chemical stimulus intersection_of: has_primary_input CHEBI:18133 -created_by: mah creation_date: 2009-12-10T05:37:00Z [Term] @@ -108589,7 +113065,6 @@ is_a: GO:0009749 ! response to glucose is_a: GO:0070887 ! cellular response to chemical stimulus intersection_of: GO:0070887 ! cellular response to chemical stimulus intersection_of: has_primary_input CHEBI:4167 -created_by: mah creation_date: 2009-12-10T05:38:03Z [Term] @@ -108598,7 +113073,6 @@ name: cellular response to cytokine stimulus namespace: biological_process def: "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a cytokine stimulus." [GOC:mah] is_a: GO:0034097 ! response to cytokine -created_by: mah creation_date: 2009-12-11T02:41:12Z [Term] @@ -108611,7 +113085,6 @@ is_a: GO:0043434 ! response to peptide hormone is_a: GO:0070887 ! cellular response to chemical stimulus intersection_of: GO:0070887 ! cellular response to chemical stimulus intersection_of: has_primary_input CHEBI:25905 -created_by: mah creation_date: 2009-12-11T03:24:18Z [Term] @@ -108623,7 +113096,6 @@ is_a: GO:0033762 ! response to glucagon is_a: GO:0070887 ! cellular response to chemical stimulus intersection_of: GO:0070887 ! cellular response to chemical stimulus intersection_of: has_primary_input CHEBI:5391 -created_by: mah creation_date: 2009-12-11T03:25:07Z [Term] @@ -108635,7 +113107,6 @@ is_a: GO:0048545 ! response to steroid hormone is_a: GO:0070887 ! cellular response to chemical stimulus intersection_of: GO:0070887 ! cellular response to chemical stimulus intersection_of: has_primary_input CHEBI:26764 -created_by: mah creation_date: 2009-12-11T03:49:02Z [Term] @@ -108647,7 +113118,6 @@ is_a: GO:0070887 ! cellular response to chemical stimulus intersection_of: GO:0070887 ! cellular response to chemical stimulus intersection_of: has_primary_input CHEBI:36699 relationship: has_primary_input CHEBI:36699 -created_by: mah creation_date: 2009-12-11T03:52:07Z [Term] @@ -108659,7 +113129,6 @@ is_a: GO:0051384 ! response to glucocorticoid is_a: GO:0070887 ! cellular response to chemical stimulus intersection_of: GO:0070887 ! cellular response to chemical stimulus intersection_of: has_primary_input CHEBI:24261 -created_by: mah creation_date: 2009-12-11T03:53:56Z [Term] @@ -108671,7 +113140,6 @@ is_a: GO:0051385 ! response to mineralocorticoid is_a: GO:0070887 ! cellular response to chemical stimulus intersection_of: GO:0070887 ! cellular response to chemical stimulus intersection_of: has_primary_input CHEBI:25354 -created_by: mah creation_date: 2009-12-11T03:59:02Z [Term] @@ -108684,7 +113152,6 @@ is_a: GO:0032355 ! response to estradiol is_a: GO:0070887 ! cellular response to chemical stimulus intersection_of: GO:0070887 ! cellular response to chemical stimulus intersection_of: has_primary_input CHEBI:23965 -created_by: mah creation_date: 2009-12-11T04:10:31Z [Term] @@ -108696,7 +113163,6 @@ is_a: GO:0032570 ! response to progesterone is_a: GO:0070887 ! cellular response to chemical stimulus intersection_of: GO:0070887 ! cellular response to chemical stimulus intersection_of: has_primary_input CHEBI:17026 -created_by: mah creation_date: 2009-12-11T04:11:13Z [Term] @@ -108708,7 +113174,6 @@ is_a: GO:0033574 ! response to testosterone is_a: GO:0070887 ! cellular response to chemical stimulus intersection_of: GO:0070887 ! cellular response to chemical stimulus intersection_of: has_primary_input CHEBI:17347 -created_by: mah creation_date: 2009-12-11T04:11:29Z [Term] @@ -108720,7 +113185,6 @@ is_a: GO:0033993 ! response to lipid is_a: GO:0070887 ! cellular response to chemical stimulus intersection_of: GO:0070887 ! cellular response to chemical stimulus intersection_of: has_primary_input CHEBI:18059 -created_by: mah creation_date: 2009-12-11T04:37:10Z [Term] @@ -108733,7 +113197,6 @@ is_a: GO:0051716 ! cellular response to stimulus intersection_of: GO:0051716 ! cellular response to stimulus intersection_of: has_primary_input GO:1990777 ! lipoprotein particle relationship: has_primary_input GO:1990777 ! lipoprotein particle -created_by: mah creation_date: 2009-12-14T02:48:51Z [Term] @@ -108745,7 +113208,6 @@ is_a: GO:0014075 ! response to amine is_a: GO:0070887 ! cellular response to chemical stimulus intersection_of: GO:0070887 ! cellular response to chemical stimulus intersection_of: has_primary_input CHEBI:32952 -created_by: mah creation_date: 2009-12-14T04:08:17Z [Term] @@ -108758,7 +113220,6 @@ is_a: GO:0034776 ! response to histamine is_a: GO:0070887 ! cellular response to chemical stimulus intersection_of: GO:0070887 ! cellular response to chemical stimulus intersection_of: has_primary_input CHEBI:58432 -created_by: mah creation_date: 2009-12-14T04:09:25Z [Term] @@ -108772,7 +113233,6 @@ intersection_of: GO:0008283 ! cell population proliferation intersection_of: acts_on_population_of CL:0000037 ! hematopoietic stem cell relationship: acts_on_population_of CL:0000037 ! hematopoietic stem cell relationship: part_of GO:0030097 ! hemopoiesis -created_by: mah creation_date: 2009-12-16T10:22:52Z [Term] @@ -108784,7 +113244,6 @@ is_a: GO:0000303 ! response to superoxide is_a: GO:0070887 ! cellular response to chemical stimulus intersection_of: GO:0070887 ! cellular response to chemical stimulus intersection_of: has_primary_input CHEBI:18421 -created_by: mah creation_date: 2009-12-16T04:39:14Z [Term] @@ -108797,7 +113256,6 @@ is_a: GO:0071214 ! cellular response to abiotic stimulus is_a: GO:1901701 ! cellular response to oxygen-containing compound intersection_of: GO:0070887 ! cellular response to chemical stimulus intersection_of: has_primary_input CHEBI:15377 -created_by: mah creation_date: 2009-12-18T11:32:44Z [Term] @@ -108808,7 +113266,6 @@ def: "Any process that results in a change in state or activity of a cell (in te comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. subset: gocheck_do_not_annotate is_a: GO:0009719 ! response to endogenous stimulus -created_by: mah creation_date: 2009-12-18T02:25:40Z [Term] @@ -108820,7 +113277,6 @@ is_a: GO:0030182 ! neuron differentiation intersection_of: GO:0030154 ! cell differentiation intersection_of: results_in_acquisition_of_features_of CL:0000700 ! dopaminergic neuron relationship: results_in_acquisition_of_features_of CL:0000700 ! dopaminergic neuron -created_by: mah creation_date: 2010-01-12T02:28:44Z [Term] @@ -108835,7 +113291,6 @@ is_a: GO:0060429 ! epithelium development intersection_of: GO:0048856 ! anatomical structure development intersection_of: results_in_development_of UBERON:0003051 ! ear vesicle relationship: results_in_development_of UBERON:0003051 ! ear vesicle -created_by: mah creation_date: 2010-02-04T04:07:17Z [Term] @@ -108850,7 +113305,6 @@ intersection_of: GO:0009653 ! anatomical structure morphogenesis intersection_of: results_in_morphogenesis_of UBERON:0003051 ! ear vesicle relationship: part_of GO:0071599 ! otic vesicle development relationship: results_in_morphogenesis_of UBERON:0003051 ! ear vesicle -created_by: mah creation_date: 2010-02-04T04:07:27Z [Term] @@ -108862,7 +113316,6 @@ is_a: GO:0030595 ! leukocyte chemotaxis is_a: GO:0097530 ! granulocyte migration intersection_of: GO:0006935 ! chemotaxis intersection_of: results_in_movement_of CL:0000094 ! granulocyte -created_by: mah creation_date: 2010-02-09T04:08:17Z [Term] @@ -108874,7 +113327,6 @@ is_a: GO:0002688 ! regulation of leukocyte chemotaxis intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0071621 ! granulocyte chemotaxis relationship: regulates GO:0071621 ! granulocyte chemotaxis -created_by: mah creation_date: 2010-02-09T04:09:24Z [Term] @@ -108887,7 +113339,6 @@ is_a: GO:0071622 ! regulation of granulocyte chemotaxis intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0071621 ! granulocyte chemotaxis relationship: negatively_regulates GO:0071621 ! granulocyte chemotaxis -created_by: mah creation_date: 2010-02-09T04:13:19Z [Term] @@ -108900,7 +113351,6 @@ is_a: GO:0071622 ! regulation of granulocyte chemotaxis intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0071621 ! granulocyte chemotaxis relationship: positively_regulates GO:0071621 ! granulocyte chemotaxis -created_by: mah creation_date: 2010-02-09T04:15:36Z [Term] @@ -108910,7 +113360,6 @@ namespace: biological_process def: "The process of biting and mashing food with the teeth prior to swallowing." [GOC:gvg] synonym: "chewing" EXACT [GOC:mah] is_a: GO:0022600 ! digestive system process -created_by: mah creation_date: 2010-02-10T11:19:48Z [Term] @@ -108922,7 +113371,6 @@ is_a: GO:0014909 ! smooth muscle cell migration is_a: GO:0060326 ! cell chemotaxis intersection_of: GO:0006935 ! chemotaxis intersection_of: results_in_movement_of CL:0000192 ! smooth muscle cell -created_by: mah creation_date: 2010-02-16T01:32:59Z [Term] @@ -108935,7 +113383,6 @@ is_a: GO:0050920 ! regulation of chemotaxis intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0071670 ! smooth muscle cell chemotaxis relationship: regulates GO:0071670 ! smooth muscle cell chemotaxis -created_by: mah creation_date: 2010-02-16T01:42:03Z [Term] @@ -108953,7 +113400,6 @@ is_a: GO:0071671 ! regulation of smooth muscle cell chemotaxis intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0071670 ! smooth muscle cell chemotaxis relationship: negatively_regulates GO:0071670 ! smooth muscle cell chemotaxis -created_by: mah creation_date: 2010-02-16T01:44:28Z [Term] @@ -108972,7 +113418,6 @@ is_a: GO:0071671 ! regulation of smooth muscle cell chemotaxis intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0071670 ! smooth muscle cell chemotaxis relationship: positively_regulates GO:0071670 ! smooth muscle cell chemotaxis -created_by: mah creation_date: 2010-02-16T01:48:14Z [Term] @@ -108984,7 +113429,6 @@ is_a: GO:0050900 ! leukocyte migration intersection_of: GO:0016477 ! cell migration intersection_of: results_in_movement_of CL:0000842 ! mononuclear cell relationship: results_in_movement_of CL:0000842 ! mononuclear cell -created_by: mah creation_date: 2010-02-16T02:11:00Z [Term] @@ -108996,7 +113440,6 @@ is_a: GO:0002685 ! regulation of leukocyte migration intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0071674 ! mononuclear cell migration relationship: regulates GO:0071674 ! mononuclear cell migration -created_by: mah creation_date: 2010-02-16T02:11:53Z [Term] @@ -109013,7 +113456,6 @@ is_a: GO:0071675 ! regulation of mononuclear cell migration intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0071674 ! mononuclear cell migration relationship: negatively_regulates GO:0071674 ! mononuclear cell migration -created_by: mah creation_date: 2010-02-16T02:13:55Z [Term] @@ -109031,7 +113473,6 @@ is_a: GO:0071675 ! regulation of mononuclear cell migration intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0071674 ! mononuclear cell migration relationship: positively_regulates GO:0071674 ! mononuclear cell migration -created_by: mah creation_date: 2010-02-16T02:15:29Z [Term] @@ -109045,7 +113486,6 @@ is_a: GO:0008104 ! protein localization intersection_of: GO:0008104 ! protein localization intersection_of: has_target_end_location GO:0005576 ! extracellular region relationship: has_target_end_location GO:0005576 ! extracellular region -created_by: mah creation_date: 2010-02-25T04:00:13Z [Term] @@ -109059,7 +113499,6 @@ intersection_of: GO:0021700 ! developmental maturation intersection_of: results_in_maturation_of UBERON:0000061 ! anatomical structure relationship: part_of GO:0048856 ! anatomical structure development relationship: results_in_maturation_of UBERON:0000061 ! anatomical structure -created_by: mah creation_date: 2010-03-02T11:43:38Z [Term] @@ -109071,7 +113510,6 @@ is_a: GO:0048856 ! anatomical structure development intersection_of: GO:0048856 ! anatomical structure development intersection_of: results_in_development_of UBERON:0005085 ! ectodermal placode relationship: results_in_development_of UBERON:0005085 ! ectodermal placode -created_by: mah creation_date: 2010-03-02T11:48:01Z [Term] @@ -109085,7 +113523,6 @@ intersection_of: GO:0009653 ! anatomical structure morphogenesis intersection_of: results_in_morphogenesis_of UBERON:0005085 ! ectodermal placode relationship: part_of GO:0071696 ! ectodermal placode development relationship: results_in_morphogenesis_of UBERON:0005085 ! ectodermal placode -created_by: mah creation_date: 2010-03-02T11:49:51Z [Term] @@ -109097,7 +113534,6 @@ is_a: GO:0071696 ! ectodermal placode development intersection_of: GO:0048856 ! anatomical structure development intersection_of: results_in_development_of UBERON:0003050 ! olfactory placode relationship: results_in_development_of UBERON:0003050 ! olfactory placode -created_by: mah creation_date: 2010-03-02T12:45:14Z [Term] @@ -109111,7 +113547,6 @@ intersection_of: GO:0009653 ! anatomical structure morphogenesis intersection_of: results_in_morphogenesis_of UBERON:0003050 ! olfactory placode relationship: part_of GO:0071698 ! olfactory placode development relationship: results_in_morphogenesis_of UBERON:0003050 ! olfactory placode -created_by: mah creation_date: 2010-03-02T12:45:45Z [Term] @@ -109124,7 +113559,6 @@ intersection_of: GO:0021700 ! developmental maturation intersection_of: results_in_maturation_of UBERON:0003050 ! olfactory placode relationship: part_of GO:0071698 ! olfactory placode development relationship: results_in_maturation_of UBERON:0003050 ! olfactory placode -created_by: mah creation_date: 2010-03-02T01:10:54Z [Term] @@ -109138,7 +113572,6 @@ is_a: GO:0006810 ! transport intersection_of: GO:0006810 ! transport intersection_of: has_primary_input CHEBI:51143 relationship: has_primary_input CHEBI:51143 -created_by: mah creation_date: 2010-03-08T03:56:28Z [Term] @@ -109151,7 +113584,6 @@ subset: gocheck_do_not_annotate synonym: "TNF superfamily production" RELATED [GOC:rv] synonym: "TNFSF cytokine production" EXACT [GOC:add] is_a: GO:0001816 ! cytokine production -created_by: mah creation_date: 2010-03-09T02:40:35Z [Term] @@ -109163,7 +113595,6 @@ synonym: "immunoglobulin V(D)J joining" BROAD [GOC:add] synonym: "immunoglobulin V(D)J recombination" BROAD [GOC:add] synonym: "immunoglobulin V-D-J joining" EXACT [GOC:add] is_a: GO:0033152 ! immunoglobulin V(D)J recombination -created_by: mah creation_date: 2010-03-09T04:20:31Z [Term] @@ -109175,7 +113606,6 @@ synonym: "immunoglobulin V(D)J joining" BROAD [GOC:add] synonym: "immunoglobulin V(D)J recombination" BROAD [GOC:add] synonym: "immunoglobulin V-J joining" EXACT [GOC:add] is_a: GO:0033152 ! immunoglobulin V(D)J recombination -created_by: mah creation_date: 2010-03-09T04:22:29Z [Term] @@ -109189,7 +113619,6 @@ intersection_of: GO:0022607 ! cellular component assembly intersection_of: results_in_assembly_of GO:0016020 ! membrane relationship: part_of GO:0044091 ! membrane biogenesis relationship: results_in_assembly_of GO:0016020 ! membrane -created_by: mah creation_date: 2010-03-10T11:19:17Z [Term] @@ -109203,9 +113632,31 @@ is_a: GO:0030198 ! extracellular matrix organization intersection_of: GO:0016043 ! cellular component organization intersection_of: results_in_organization_of GO:0005604 ! basement membrane relationship: results_in_organization_of GO:0005604 ! basement membrane -created_by: mah creation_date: 2010-03-10T11:57:10Z +[Term] +id: GO:0071731 +name: response to nitric oxide +namespace: biological_process +def: "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a nitric oxide stimulus." [GOC:mah, GOC:yaf] +is_a: BFO:0000003 +is_a: GO:0050896 ! response to stimulus +intersection_of: GO:0050896 ! response to stimulus +intersection_of: has_primary_input CHEBI:16480 +relationship: has_primary_input CHEBI:16480 +creation_date: 2010-03-17T04:03:38Z + +[Term] +id: GO:0071732 +name: cellular response to nitric oxide +namespace: biological_process +def: "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a nitric oxide stimulus." [GOC:mah, GOC:yaf] +is_a: GO:0070887 ! cellular response to chemical stimulus +is_a: GO:0071731 ! response to nitric oxide +intersection_of: GO:0070887 ! cellular response to chemical stimulus +intersection_of: has_primary_input CHEBI:16480 +creation_date: 2010-03-17T04:12:52Z + [Term] id: GO:0071735 name: IgG immunoglobulin complex @@ -109220,7 +113671,6 @@ synonym: "IgG2c" NARROW [GOC:add] synonym: "IgG3" NARROW [GOC:add] synonym: "IgG4" NARROW [GOC:add] is_a: GO:0019814 ! immunoglobulin complex -created_by: mah creation_date: 2010-03-24T01:44:53Z [Term] @@ -109239,7 +113689,6 @@ synonym: "IgG3 antibody" NARROW [GOC:add] synonym: "IgG4 antibody" NARROW [GOC:add] is_a: GO:0042571 ! immunoglobulin complex, circulating is_a: GO:0071735 ! IgG immunoglobulin complex -created_by: mah creation_date: 2010-03-24T01:44:53Z [Term] @@ -109249,7 +113698,6 @@ namespace: cellular_component def: "A protein complex composed of two identical immunoglobulin heavy chains of the IgD isotype and two identical immunoglobulin light chains, held together by disulfide bonds. An IgD immunoglobulin complex may be embedded in the plasma membrane or present in the extracellular space, in mucosal areas or other tissues, or circulating in the blood or lymph." [GOC:add, ISBN:0781765196, PMID:11282392] comment: Note that an IgD immunoglobulin complex has the function of antigen binding if a suitable antigen is available. is_a: GO:0019814 ! immunoglobulin complex -created_by: mah creation_date: 2010-03-24T01:44:53Z [Term] @@ -109261,7 +113709,6 @@ comment: Note that an IgD immunoglobulin complex has the function of antigen bin synonym: "IgD antibody" EXACT [GOC:add] is_a: GO:0042571 ! immunoglobulin complex, circulating is_a: GO:0071738 ! IgD immunoglobulin complex -created_by: mah creation_date: 2010-03-24T01:44:53Z [Term] @@ -109271,7 +113718,6 @@ namespace: cellular_component def: "A protein complex composed of two identical immunoglobulin heavy chains of the IgE isotype and two identical immunoglobulin light chains, held together by disulfide bonds. An IgE immunoglobulin complex may be embedded in the plasma membrane or present in the extracellular space, in mucosal areas or other tissues, or circulating in the blood or lymph." [GOC:add, ISBN:0781765196] comment: Note that an IgE immunoglobulin complex has the function of antigen binding if a suitable antigen is available. is_a: GO:0019814 ! immunoglobulin complex -created_by: mah creation_date: 2010-03-24T01:44:53Z [Term] @@ -109283,7 +113729,6 @@ comment: Note that an IgE immunoglobulin complex has the function of antigen bin synonym: "IgE antibody" EXACT [GOC:add] is_a: GO:0042571 ! immunoglobulin complex, circulating is_a: GO:0071742 ! IgE immunoglobulin complex -created_by: mah creation_date: 2010-03-24T01:44:53Z [Term] @@ -109295,7 +113740,6 @@ comment: Note that an IgA immunoglobulin complex has the function of antigen bin synonym: "IgA1 antibody" NARROW [GOC:add] synonym: "IgA2 antibody" NARROW [GOC:add] is_a: GO:0019814 ! immunoglobulin complex -created_by: mah creation_date: 2010-03-24T01:44:53Z [Term] @@ -109309,7 +113753,6 @@ synonym: "IgA1 antibody" NARROW [GOC:add] synonym: "IgA2 antibody" NARROW [GOC:add] is_a: GO:0042571 ! immunoglobulin complex, circulating is_a: GO:0071745 ! IgA immunoglobulin complex -created_by: mah creation_date: 2010-03-24T01:44:53Z [Term] @@ -109319,7 +113762,6 @@ namespace: cellular_component def: "A protein complex composed of two identical immunoglobulin heavy chains of the IgM isotype and two identical immunoglobulin light chains, held together by disulfide bonds, and in its circulating form complexed with J chain in polymeric forms. An IgM immunoglobulin complex may be embedded in the plasma membrane or present in the extracellular space, in mucosal areas or other tissues, or circulating in the blood or lymph." [GOC:add, ISBN:0781765196, PMID:20176268] comment: Note that an IgM immunoglobulin complex has the function of antigen binding if a suitable antigen is available. is_a: GO:0019814 ! immunoglobulin complex -created_by: mah creation_date: 2010-03-24T01:44:53Z [Term] @@ -109331,7 +113773,6 @@ comment: Note that an IgM immunoglobulin complex has the function of antigen bin synonym: "IgM antibody" EXACT [GOC:add] is_a: GO:0042571 ! immunoglobulin complex, circulating is_a: GO:0071753 ! IgM immunoglobulin complex -created_by: mah creation_date: 2010-03-24T01:44:53Z [Term] @@ -109346,7 +113787,6 @@ intersection_of: GO:0016043 ! cellular component organization intersection_of: results_in_organization_of GO:0031965 ! nuclear membrane relationship: part_of GO:0006998 ! nuclear envelope organization relationship: results_in_organization_of GO:0031965 ! nuclear membrane -created_by: mah creation_date: 2010-03-29T03:59:35Z [Term] @@ -109360,14 +113800,12 @@ is_a: GO:0071763 ! nuclear membrane organization intersection_of: GO:0016043 ! cellular component organization intersection_of: results_in_organization_of GO:0005640 ! nuclear outer membrane relationship: results_in_organization_of GO:0005640 ! nuclear outer membrane -created_by: mah creation_date: 2010-03-29T04:03:37Z [Term] id: GO:0071805 name: potassium ion transmembrane transport namespace: biological_process -alt_id: GO:0010163 def: "A process in which a potassium ion is transported from one side of a membrane to the other." [GOC:mah] comment: Note that this term is not intended for use in annotating lateral movement within membranes. synonym: "high affinity potassium ion import" NARROW [] @@ -109379,7 +113817,6 @@ is_a: GO:0006813 ! potassium ion transport is_a: GO:0034220 ! monoatomic ion transmembrane transport intersection_of: GO:0055085 ! transmembrane transport intersection_of: has_primary_input CHEBI:29103 -created_by: mah creation_date: 2010-09-03T02:43:49Z [Term] @@ -109394,7 +113831,6 @@ is_a: GO:0055085 ! transmembrane transport intersection_of: GO:0006810 ! transport intersection_of: has_primary_input CHEBI:36080 intersection_of: results_in_transport_across GO:0016020 ! membrane -created_by: mah creation_date: 2010-09-03T02:54:26Z [Term] @@ -109409,7 +113845,6 @@ is_a: GO:0071814 ! protein-lipid complex binding intersection_of: GO:0005488 ! binding intersection_of: has_primary_input GO:1990777 ! lipoprotein particle relationship: has_primary_input GO:1990777 ! lipoprotein particle -created_by: mah creation_date: 2010-09-06T03:16:01Z [Term] @@ -109421,7 +113856,6 @@ is_a: GO:0044877 ! protein-containing complex binding intersection_of: GO:0005488 ! binding intersection_of: has_primary_input GO:0032994 ! protein-lipid complex relationship: has_primary_input GO:0032994 ! protein-lipid complex -created_by: mah creation_date: 2010-09-06T04:26:27Z [Term] @@ -109436,7 +113870,6 @@ intersection_of: GO:0016043 ! cellular component organization intersection_of: results_in_organization_of GO:0032994 ! protein-lipid complex relationship: results_in_organization_of GO:0032994 ! protein-lipid complex property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/25143" xsd:anyURI -created_by: mah creation_date: 2010-09-08T10:04:36Z [Term] @@ -109453,14 +113886,12 @@ intersection_of: GO:0016043 ! cellular component organization intersection_of: results_in_organization_of GO:1990904 ! ribonucleoprotein complex relationship: results_in_organization_of GO:1990904 ! ribonucleoprotein complex property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/25143" xsd:anyURI -created_by: mah creation_date: 2010-09-08T10:10:35Z [Term] id: GO:0071840 name: cellular component organization or biogenesis namespace: biological_process -alt_id: GO:0071841 def: "A process that results in the biosynthesis of constituent macromolecules, assembly, arrangement of constituent parts, or disassembly of a cellular component." [GOC:mah] comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. subset: gocheck_do_not_annotate @@ -109471,7 +113902,6 @@ synonym: "cellular component organisation or biogenesis at cellular level" EXACT synonym: "cellular component organization or biogenesis at cellular level" EXACT [] is_a: GO:0009987 ! cellular process property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27189" xsd:anyURI -created_by: mah creation_date: 2010-09-10T01:39:16Z [Term] @@ -109485,7 +113915,6 @@ is_a: GO:0050896 ! response to stimulus intersection_of: GO:0050896 ! response to stimulus intersection_of: has_primary_input CHEBI:33567 relationship: has_primary_input CHEBI:33567 -created_by: mah creation_date: 2010-09-13T02:51:13Z [Term] @@ -109497,7 +113926,6 @@ is_a: GO:0070887 ! cellular response to chemical stimulus is_a: GO:0071869 ! response to catecholamine intersection_of: GO:0070887 ! cellular response to chemical stimulus intersection_of: has_primary_input CHEBI:33567 -created_by: mah creation_date: 2010-09-13T02:54:50Z [Term] @@ -109513,7 +113941,6 @@ is_a: GO:0050896 ! response to stimulus intersection_of: GO:0050896 ! response to stimulus intersection_of: has_primary_input CHEBI:72587 relationship: has_primary_input CHEBI:72587 -created_by: mah creation_date: 2010-09-13T03:31:53Z [Term] @@ -109527,7 +113954,6 @@ is_a: GO:0070887 ! cellular response to chemical stimulus is_a: GO:0071873 ! response to norepinephrine intersection_of: GO:0070887 ! cellular response to chemical stimulus intersection_of: has_primary_input CHEBI:72587 -created_by: mah creation_date: 2010-09-13T03:33:32Z [Term] @@ -109543,7 +113969,6 @@ intersection_of: occurs_in CL:0000738 ! leukocyte relationship: occurs_in CL:0000738 ! leukocyte relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata relationship: RO:0002162 NCBITaxon:7742 {all_only="true"} ! in taxon Vertebrata -created_by: mah creation_date: 2010-09-14T12:44:09Z [Term] @@ -109561,7 +113986,6 @@ is_a: GO:0071887 ! leukocyte apoptotic process intersection_of: GO:0006915 ! apoptotic process intersection_of: occurs_in CL:0000235 ! macrophage relationship: occurs_in CL:0000235 ! macrophage -created_by: mah creation_date: 2010-09-14T12:50:40Z [Term] @@ -109576,7 +114000,6 @@ is_a: GO:0005488 ! binding intersection_of: GO:0005488 ! binding intersection_of: has_primary_input CHEBI:17544 relationship: has_primary_input CHEBI:17544 -created_by: mah creation_date: 2010-09-14T01:47:43Z [Term] @@ -109588,7 +114011,6 @@ is_a: GO:0060563 ! neuroepithelial cell differentiation intersection_of: GO:0030154 ! cell differentiation intersection_of: results_in_acquisition_of_features_of CL:0000060 ! odontoblast relationship: results_in_acquisition_of_features_of CL:0000060 ! odontoblast -created_by: mah creation_date: 2010-09-14T04:00:40Z [Term] @@ -109605,7 +114027,6 @@ is_a: GO:0009058 ! biosynthetic process intersection_of: GO:0009058 ! biosynthetic process intersection_of: has_primary_output CHEBI:16991 relationship: has_primary_output CHEBI:16991 -created_by: mah creation_date: 2010-09-15T02:14:33Z [Term] @@ -109619,7 +114040,6 @@ subset: goslim_pombe subset: goslim_prokaryote xref: Wikipedia:Nitrogen_cycle is_a: GO:0008152 ! metabolic process -created_by: mah creation_date: 2010-09-30T05:21:03Z [Term] @@ -109628,8 +114048,7 @@ name: cell periphery namespace: cellular_component def: "The broad region around and including the plasma membrane of a cell, encompassing the cell cortex (inside the cell), the plasma membrane, and any external encapsulating structures." [GOC:pdt] subset: goslim_flybase_ribbon -is_a: GO:0110165 ! cellular anatomical entity -created_by: mah +is_a: GO:0110165 ! cellular anatomical structure creation_date: 2010-10-04T01:51:47Z [Term] @@ -109641,7 +114060,6 @@ synonym: "elastic fibre" EXACT [GOC:mah] synonym: "elastin fiber" EXACT [GOC:BHF] is_a: GO:0099512 ! supramolecular fiber relationship: part_of GO:0031012 ! extracellular matrix -created_by: mah creation_date: 2010-10-11T11:44:57Z [Term] @@ -109656,7 +114074,6 @@ intersection_of: GO:0022607 ! cellular component assembly intersection_of: results_in_assembly_of GO:0070062 ! extracellular exosome relationship: part_of GO:0097734 ! extracellular exosome biogenesis relationship: results_in_assembly_of GO:0070062 ! extracellular exosome -created_by: mah creation_date: 2010-10-18T03:44:18Z [Term] @@ -109671,7 +114088,6 @@ is_a: GO:0048731 ! system development intersection_of: GO:0048731 ! system development intersection_of: results_in_development_of UBERON:0001008 ! renal system relationship: results_in_development_of UBERON:0001008 ! renal system -created_by: mah creation_date: 2010-01-25T10:31:00Z [Term] @@ -109686,7 +114102,6 @@ intersection_of: results_in_development_of UBERON:0001054 ! Malpighian tubule relationship: results_in_development_of UBERON:0001054 ! Malpighian tubule relationship: RO:0002160 NCBITaxon:50557 ! only in taxon Insecta relationship: RO:0002162 NCBITaxon:50557 {all_only="true"} ! in taxon Insecta -created_by: mah creation_date: 2010-01-25T10:54:30Z [Term] @@ -109701,7 +114116,6 @@ intersection_of: GO:0048646 ! anatomical structure formation involved in morphog intersection_of: results_in_formation_of UBERON:0005095 ! kidney rudiment relationship: part_of GO:0060993 ! kidney morphogenesis relationship: results_in_formation_of UBERON:0005095 ! kidney rudiment -created_by: mah creation_date: 2010-01-25T11:18:58Z [Term] @@ -109715,7 +114129,6 @@ intersection_of: GO:0048856 ! anatomical structure development intersection_of: results_in_development_of UBERON:0001285 ! nephron relationship: part_of GO:0001822 ! kidney development relationship: results_in_development_of UBERON:0001285 ! nephron -created_by: mah creation_date: 2010-01-25T01:37:16Z [Term] @@ -109728,7 +114141,6 @@ is_a: GO:1904238 ! pericyte cell differentiation intersection_of: GO:0030154 ! cell differentiation intersection_of: results_in_acquisition_of_features_of CL:0000650 ! mesangial cell relationship: results_in_acquisition_of_features_of CL:0000650 ! mesangial cell -created_by: mah creation_date: 2010-01-25T01:59:09Z [Term] @@ -109742,7 +114154,6 @@ intersection_of: GO:0030154 ! cell differentiation intersection_of: results_in_acquisition_of_features_of CL:1000742 ! glomerular mesangial cell relationship: part_of GO:0072109 ! glomerular mesangium development relationship: results_in_acquisition_of_features_of CL:1000742 ! glomerular mesangial cell -created_by: mah creation_date: 2010-01-25T01:59:33Z [Term] @@ -109755,7 +114166,6 @@ intersection_of: GO:0048856 ! anatomical structure development intersection_of: results_in_development_of UBERON:0004211 ! nephron epithelium relationship: part_of GO:0072006 ! nephron development relationship: results_in_development_of UBERON:0004211 ! nephron epithelium -created_by: mah creation_date: 2010-01-25T02:01:39Z [Term] @@ -109768,7 +114178,6 @@ intersection_of: GO:0048856 ! anatomical structure development intersection_of: results_in_development_of UBERON:0004188 ! glomerular epithelium relationship: part_of GO:0032835 ! glomerulus development relationship: results_in_development_of UBERON:0004188 ! glomerular epithelium -created_by: mah creation_date: 2010-01-25T02:02:14Z [Term] @@ -109782,7 +114191,6 @@ intersection_of: GO:0048856 ! anatomical structure development intersection_of: results_in_development_of UBERON:0004189 ! glomerular endothelium relationship: part_of GO:0072012 ! glomerulus vasculature development relationship: results_in_development_of UBERON:0004189 ! glomerular endothelium -created_by: mah creation_date: 2010-01-25T02:02:57Z [Term] @@ -109797,7 +114205,6 @@ intersection_of: GO:0048856 ! anatomical structure development intersection_of: results_in_development_of UBERON:0004190 ! renal glomerulus vasculature relationship: part_of GO:0032835 ! glomerulus development relationship: results_in_development_of UBERON:0004190 ! renal glomerulus vasculature -created_by: mah creation_date: 2010-01-25T02:05:04Z [Term] @@ -109809,7 +114216,6 @@ is_a: GO:0072080 ! nephron tubule development intersection_of: GO:0048856 ! anatomical structure development intersection_of: results_in_development_of UBERON:0004134 ! proximal tubule relationship: results_in_development_of UBERON:0004134 ! proximal tubule -created_by: mah creation_date: 2010-01-25T02:33:46Z [Term] @@ -109824,7 +114230,6 @@ intersection_of: results_in_development_of CL:0000653 ! podocyte relationship: part_of GO:0072112 ! podocyte differentiation relationship: results_in_development_of CL:0000653 ! podocyte property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/23000" xsd:anyURI -created_by: mah creation_date: 2010-01-25T02:12:45Z [Term] @@ -109838,7 +114243,6 @@ intersection_of: GO:0048856 ! anatomical structure development intersection_of: results_in_development_of UBERON:0001230 ! glomerular capsule relationship: part_of GO:0072139 ! glomerular parietal epithelial cell differentiation relationship: results_in_development_of UBERON:0001230 ! glomerular capsule -created_by: mah creation_date: 2010-01-25T02:13:16Z [Term] @@ -109850,7 +114254,6 @@ is_a: GO:0072080 ! nephron tubule development intersection_of: GO:0048856 ! anatomical structure development intersection_of: results_in_development_of UBERON:0004135 ! distal tubule relationship: results_in_development_of UBERON:0004135 ! distal tubule -created_by: mah creation_date: 2010-01-25T02:34:19Z [Term] @@ -109863,7 +114266,6 @@ intersection_of: GO:0048856 ! anatomical structure development intersection_of: results_in_development_of UBERON:0001287 ! proximal convoluted tubule relationship: part_of GO:0072014 ! proximal tubule development relationship: results_in_development_of UBERON:0001287 ! proximal convoluted tubule -created_by: mah creation_date: 2010-01-25T02:35:35Z [Term] @@ -109877,7 +114279,6 @@ intersection_of: GO:0048856 ! anatomical structure development intersection_of: results_in_development_of UBERON:0001290 ! proximal straight tubule relationship: part_of GO:0072014 ! proximal tubule development relationship: results_in_development_of UBERON:0001290 ! proximal straight tubule -created_by: mah creation_date: 2010-01-25T02:36:14Z [Term] @@ -109890,7 +114291,6 @@ intersection_of: GO:0048856 ! anatomical structure development intersection_of: results_in_development_of UBERON:0004193 ! loop of Henle ascending limb thin segment relationship: part_of GO:0072070 ! loop of Henle development relationship: results_in_development_of UBERON:0004193 ! loop of Henle ascending limb thin segment -created_by: mah creation_date: 2010-01-25T02:37:13Z [Term] @@ -109903,14 +114303,12 @@ intersection_of: GO:0048856 ! anatomical structure development intersection_of: results_in_development_of UBERON:0005096 ! descending thin limb relationship: part_of GO:0072070 ! loop of Henle development relationship: results_in_development_of UBERON:0005096 ! descending thin limb -created_by: mah creation_date: 2010-01-25T02:37:47Z [Term] id: GO:0072023 name: thick ascending limb development namespace: biological_process -alt_id: GO:0072026 def: "The process whose specific outcome is the progression of the thick ascending limb over time, from its formation to the mature structure. The thick ascending limb is the last part of the loop of Henle. Its thick, mitochondria-rich epithelium characterizes the outer medulla, and is responsible for very avid active salt transport. At the macula densa, the thick ascending limb connects to the distal convoluted tubule." [GOC:mtg_kidney_jan10] synonym: "TAL development" EXACT [GOC:mtg_kidney_jan10] is_a: GO:0072080 ! nephron tubule development @@ -109918,7 +114316,6 @@ intersection_of: GO:0048856 ! anatomical structure development intersection_of: results_in_development_of UBERON:0001291 ! thick ascending limb of loop of Henle relationship: part_of GO:0072017 ! distal tubule development relationship: results_in_development_of UBERON:0001291 ! thick ascending limb of loop of Henle -created_by: mah creation_date: 2010-01-25T02:39:51Z [Term] @@ -109931,7 +114328,6 @@ intersection_of: GO:0048856 ! anatomical structure development intersection_of: results_in_development_of UBERON:0002335 ! macula densa relationship: part_of GO:0072051 ! juxtaglomerular apparatus development relationship: results_in_development_of UBERON:0002335 ! macula densa -created_by: mah creation_date: 2010-01-25T02:40:15Z [Term] @@ -109944,7 +114340,6 @@ intersection_of: GO:0048856 ! anatomical structure development intersection_of: results_in_development_of UBERON:0001292 ! distal convoluted tubule relationship: part_of GO:0072017 ! distal tubule development relationship: results_in_development_of UBERON:0001292 ! distal convoluted tubule -created_by: mah creation_date: 2010-01-25T02:40:45Z [Term] @@ -109957,7 +114352,6 @@ is_a: GO:0072080 ! nephron tubule development intersection_of: GO:0048856 ! anatomical structure development intersection_of: results_in_development_of UBERON:0005097 ! renal connecting tubule relationship: results_in_development_of UBERON:0005097 ! renal connecting tubule -created_by: mah creation_date: 2010-01-25T02:42:05Z [Term] @@ -109972,7 +114366,6 @@ intersection_of: results_in_morphogenesis_of UBERON:0001285 ! nephron relationship: part_of GO:0060993 ! kidney morphogenesis relationship: part_of GO:0072006 ! nephron development relationship: results_in_morphogenesis_of UBERON:0001285 ! nephron -created_by: mah creation_date: 2010-01-25T02:45:52Z [Term] @@ -109985,7 +114378,6 @@ is_a: GO:0072006 ! nephron development intersection_of: GO:0048856 ! anatomical structure development intersection_of: results_in_development_of UBERON:0004194 ! long nephron relationship: results_in_development_of UBERON:0004194 ! long nephron -created_by: mah creation_date: 2010-01-25T02:49:08Z [Term] @@ -109997,7 +114389,6 @@ is_a: GO:0072006 ! nephron development intersection_of: GO:0048856 ! anatomical structure development intersection_of: results_in_development_of UBERON:0004195 ! short nephron relationship: results_in_development_of UBERON:0004195 ! short nephron -created_by: mah creation_date: 2010-01-25T02:49:32Z [Term] @@ -110011,7 +114402,6 @@ intersection_of: GO:0048856 ! anatomical structure development intersection_of: results_in_development_of UBERON:0004196 ! proximal convoluted tubule segment 1 relationship: part_of GO:0072019 ! proximal convoluted tubule development relationship: results_in_development_of UBERON:0004196 ! proximal convoluted tubule segment 1 -created_by: mah creation_date: 2010-01-25T02:55:57Z [Term] @@ -110025,7 +114415,6 @@ intersection_of: GO:0048856 ! anatomical structure development intersection_of: results_in_development_of UBERON:0004197 ! proximal convoluted tubule segment 2 relationship: part_of GO:0072019 ! proximal convoluted tubule development relationship: results_in_development_of UBERON:0004197 ! proximal convoluted tubule segment 2 -created_by: mah creation_date: 2010-01-25T02:56:36Z [Term] @@ -110040,7 +114429,6 @@ intersection_of: GO:0048646 ! anatomical structure formation involved in morphog intersection_of: results_in_formation_of UBERON:0004209 ! renal vesicle relationship: part_of GO:0072077 ! renal vesicle morphogenesis relationship: results_in_formation_of UBERON:0004209 ! renal vesicle -created_by: mah creation_date: 2010-01-25T02:57:03Z [Term] @@ -110053,7 +114441,6 @@ is_a: GO:0060231 ! mesenchymal to epithelial transition intersection_of: GO:0060231 ! mesenchymal to epithelial transition intersection_of: part_of GO:0072033 ! renal vesicle formation relationship: part_of GO:0072033 ! renal vesicle formation -created_by: mah creation_date: 2010-01-25T03:04:24Z [Term] @@ -110066,7 +114453,6 @@ is_a: GO:0072497 ! mesenchymal stem cell differentiation intersection_of: GO:0072497 ! mesenchymal stem cell differentiation intersection_of: part_of GO:0072028 ! nephron morphogenesis relationship: part_of GO:0072028 ! nephron morphogenesis -created_by: mah creation_date: 2010-01-25T03:07:39Z [Term] @@ -110076,7 +114462,6 @@ namespace: biological_process def: "The process in which an organism retains a population of mesenchymal stem cells that contributes to the shaping of a nephron. A mesenchymal stem cell is a cell that retains the ability to divide and proliferate throughout life to provide progenitor cells that can differentiate into specialized mesenchymal cells." [GOC:mtg_kidney_jan10] is_a: GO:0035019 ! somatic stem cell population maintenance relationship: part_of GO:0072028 ! nephron morphogenesis -created_by: mah creation_date: 2010-01-25T03:08:05Z [Term] @@ -110093,7 +114478,6 @@ intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:1901145 ! mesenchymal cell apoptotic process involved in nephron morphogenesis relationship: regulates GO:0072038 ! mesenchymal stem cell maintenance involved in nephron morphogenesis relationship: regulates GO:1901145 ! mesenchymal cell apoptotic process involved in nephron morphogenesis -created_by: mah creation_date: 2010-01-25T03:08:34Z [Term] @@ -110111,7 +114495,6 @@ intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:1901145 ! mesenchymal cell apoptotic process involved in nephron morphogenesis relationship: negatively_regulates GO:0072038 ! mesenchymal stem cell maintenance involved in nephron morphogenesis relationship: negatively_regulates GO:1901145 ! mesenchymal cell apoptotic process involved in nephron morphogenesis -created_by: mah creation_date: 2010-01-25T03:09:30Z [Term] @@ -110129,7 +114512,6 @@ intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:1901145 ! mesenchymal cell apoptotic process involved in nephron morphogenesis relationship: positively_regulates GO:0072038 ! mesenchymal stem cell maintenance involved in nephron morphogenesis relationship: positively_regulates GO:1901145 ! mesenchymal cell apoptotic process involved in nephron morphogenesis -created_by: mah creation_date: 2010-01-25T03:10:32Z [Term] @@ -110142,7 +114524,6 @@ intersection_of: GO:0048856 ! anatomical structure development intersection_of: results_in_development_of UBERON:0001232 ! collecting duct of renal tubule relationship: part_of GO:0001822 ! kidney development relationship: results_in_development_of UBERON:0001232 ! collecting duct of renal tubule -created_by: mah creation_date: 2010-01-25T03:18:06Z [Term] @@ -110154,7 +114535,6 @@ subset: gocheck_do_not_annotate synonym: "renal system pattern formation" RELATED [GOC:mtg_kidney_jan10] is_a: GO:0007389 ! pattern specification process relationship: part_of GO:0072001 ! renal system development -created_by: mah creation_date: 2010-01-25T03:31:51Z [Term] @@ -110168,7 +114548,6 @@ intersection_of: GO:0009653 ! anatomical structure morphogenesis intersection_of: results_in_morphogenesis_of UBERON:0004198 ! comma-shaped body relationship: part_of GO:0072028 ! nephron morphogenesis relationship: results_in_morphogenesis_of UBERON:0004198 ! comma-shaped body -created_by: mah creation_date: 2010-01-25T03:44:48Z [Term] @@ -110182,7 +114561,6 @@ intersection_of: GO:0009653 ! anatomical structure morphogenesis intersection_of: results_in_morphogenesis_of UBERON:0004199 ! S-shaped body relationship: part_of GO:0072028 ! nephron morphogenesis relationship: results_in_morphogenesis_of UBERON:0004199 ! S-shaped body -created_by: mah creation_date: 2010-01-25T03:45:19Z [Term] @@ -110195,7 +114573,6 @@ intersection_of: GO:0048856 ! anatomical structure development intersection_of: results_in_development_of UBERON:0002303 ! juxtaglomerular apparatus relationship: part_of GO:0001822 ! kidney development relationship: results_in_development_of UBERON:0002303 ! juxtaglomerular apparatus -created_by: mah creation_date: 2010-01-25T03:52:23Z [Term] @@ -110208,7 +114585,6 @@ intersection_of: GO:0030154 ! cell differentiation intersection_of: results_in_acquisition_of_features_of CL:1000618 ! juxtaglomerular complex cell relationship: part_of GO:0072051 ! juxtaglomerular apparatus development relationship: results_in_acquisition_of_features_of CL:1000618 ! juxtaglomerular complex cell -created_by: mah creation_date: 2010-01-25T03:58:01Z [Term] @@ -110222,7 +114598,6 @@ intersection_of: GO:0048856 ! anatomical structure development intersection_of: results_in_development_of UBERON:0001294 ! inner medulla of kidney relationship: part_of GO:0001822 ! kidney development relationship: results_in_development_of UBERON:0001294 ! inner medulla of kidney -created_by: mah creation_date: 2010-01-25T03:59:37Z [Term] @@ -110236,7 +114611,6 @@ intersection_of: GO:0048856 ! anatomical structure development intersection_of: results_in_development_of UBERON:0001293 ! outer medulla of kidney relationship: part_of GO:0001822 ! kidney development relationship: results_in_development_of UBERON:0001293 ! outer medulla of kidney -created_by: mah creation_date: 2010-01-25T04:00:42Z [Term] @@ -110249,7 +114623,6 @@ intersection_of: GO:0048856 ! anatomical structure development intersection_of: results_in_development_of UBERON:0001225 ! cortex of kidney relationship: part_of GO:0001822 ! kidney development relationship: results_in_development_of UBERON:0001225 ! cortex of kidney -created_by: mah creation_date: 2010-01-25T04:01:12Z [Term] @@ -110266,7 +114639,6 @@ intersection_of: GO:0048856 ! anatomical structure development intersection_of: results_in_development_of UBERON:0004200 ! kidney pyramid relationship: part_of GO:0001822 ! kidney development relationship: results_in_development_of UBERON:0004200 ! kidney pyramid -created_by: mah creation_date: 2010-01-25T04:01:36Z [Term] @@ -110279,7 +114651,6 @@ intersection_of: GO:0048856 ! anatomical structure development intersection_of: results_in_development_of UBERON:0004201 ! kidney outer medulla inner stripe relationship: part_of GO:0072054 ! renal outer medulla development relationship: results_in_development_of UBERON:0004201 ! kidney outer medulla inner stripe -created_by: mah creation_date: 2010-01-25T04:01:58Z [Term] @@ -110292,7 +114663,6 @@ intersection_of: GO:0048856 ! anatomical structure development intersection_of: results_in_development_of UBERON:0004202 ! kidney outer medulla outer stripe relationship: part_of GO:0072054 ! renal outer medulla development relationship: results_in_development_of UBERON:0004202 ! kidney outer medulla outer stripe -created_by: mah creation_date: 2010-01-25T04:02:56Z [Term] @@ -110304,7 +114674,6 @@ is_a: GO:0048856 ! anatomical structure development intersection_of: GO:0048856 ! anatomical structure development intersection_of: results_in_development_of UBERON:0004203 ! cortical collecting duct relationship: results_in_development_of UBERON:0004203 ! cortical collecting duct -created_by: mah creation_date: 2010-01-25T04:07:07Z [Term] @@ -110316,7 +114685,6 @@ is_a: GO:0072044 ! collecting duct development intersection_of: GO:0048856 ! anatomical structure development intersection_of: results_in_development_of UBERON:0004204 ! outer medullary collecting duct relationship: results_in_development_of UBERON:0004204 ! outer medullary collecting duct -created_by: mah creation_date: 2010-01-25T04:08:18Z [Term] @@ -110328,7 +114696,6 @@ is_a: GO:0072044 ! collecting duct development intersection_of: GO:0048856 ! anatomical structure development intersection_of: results_in_development_of UBERON:0004205 ! inner medullary collecting duct relationship: results_in_development_of UBERON:0004205 ! inner medullary collecting duct -created_by: mah creation_date: 2010-01-25T04:08:45Z [Term] @@ -110342,7 +114709,6 @@ intersection_of: GO:0048856 ! anatomical structure development intersection_of: results_in_development_of UBERON:0005099 ! short descending thin limb relationship: part_of GO:0072030 ! short nephron development relationship: results_in_development_of UBERON:0005099 ! short descending thin limb -created_by: mah creation_date: 2010-01-25T04:12:39Z [Term] @@ -110356,7 +114722,6 @@ intersection_of: GO:0048856 ! anatomical structure development intersection_of: results_in_development_of UBERON:0005100 ! long descending thin limb relationship: part_of GO:0072029 ! long nephron development relationship: results_in_development_of UBERON:0005100 ! long descending thin limb -created_by: mah creation_date: 2010-01-25T04:13:17Z [Term] @@ -110369,7 +114734,6 @@ intersection_of: GO:0048856 ! anatomical structure development intersection_of: results_in_development_of UBERON:0005101 ! early distal convoluted tubule relationship: part_of GO:0072025 ! distal convoluted tubule development relationship: results_in_development_of UBERON:0005101 ! early distal convoluted tubule -created_by: mah creation_date: 2010-01-25T04:15:17Z [Term] @@ -110382,21 +114746,18 @@ intersection_of: GO:0048856 ! anatomical structure development intersection_of: results_in_development_of UBERON:0005102 ! late distal convoluted tubule relationship: part_of GO:0072025 ! distal convoluted tubule development relationship: results_in_development_of UBERON:0005102 ! late distal convoluted tubule -created_by: mah creation_date: 2010-01-25T04:15:50Z [Term] id: GO:0072070 name: loop of Henle development namespace: biological_process -alt_id: GO:0072018 def: "The process whose specific outcome is the progression of the loop of Henle over time, from its formation to the mature structure. The loop of Henle is a nephron tubule that connects the proximal convoluted tubule to the distal convoluted tubule." [GOC:mtg_kidney_jan10] synonym: "intermediate tubule development" EXACT [] is_a: GO:0072080 ! nephron tubule development intersection_of: GO:0048856 ! anatomical structure development intersection_of: results_in_development_of UBERON:0001288 ! loop of Henle relationship: results_in_development_of UBERON:0001288 ! loop of Henle -created_by: mah creation_date: 2010-01-25T04:20:27Z [Term] @@ -110409,7 +114770,6 @@ is_a: GO:0061005 ! cell differentiation involved in kidney development intersection_of: GO:0030154 ! cell differentiation intersection_of: results_in_acquisition_of_features_of CL:1000692 ! kidney interstitial fibroblast relationship: results_in_acquisition_of_features_of CL:1000692 ! kidney interstitial fibroblast -created_by: mah creation_date: 2010-01-25T04:34:31Z [Term] @@ -110422,7 +114782,6 @@ intersection_of: GO:0048856 ! anatomical structure development intersection_of: results_in_development_of UBERON:0004819 ! kidney epithelium relationship: part_of GO:0001822 ! kidney development relationship: results_in_development_of UBERON:0004819 ! kidney epithelium -created_by: mah creation_date: 2010-01-25T04:37:42Z [Term] @@ -110435,7 +114794,6 @@ intersection_of: GO:0048856 ! anatomical structure development intersection_of: results_in_development_of UBERON:0003918 ! kidney mesenchyme relationship: part_of GO:0001822 ! kidney development relationship: results_in_development_of UBERON:0003918 ! kidney mesenchyme -created_by: mah creation_date: 2010-01-25T04:39:04Z [Term] @@ -110448,7 +114806,6 @@ intersection_of: GO:0048856 ! anatomical structure development intersection_of: results_in_development_of UBERON:0003220 ! metanephric mesenchyme relationship: part_of GO:0001656 ! metanephros development relationship: results_in_development_of UBERON:0003220 ! metanephric mesenchyme -created_by: mah creation_date: 2010-01-25T04:40:11Z [Term] @@ -110461,7 +114818,6 @@ intersection_of: GO:0048856 ! anatomical structure development intersection_of: results_in_development_of UBERON:0004208 ! nephrogenic mesenchyme relationship: part_of GO:0072006 ! nephron development relationship: results_in_development_of UBERON:0004208 ! nephrogenic mesenchyme -created_by: mah creation_date: 2010-01-25T04:40:44Z [Term] @@ -110475,7 +114831,6 @@ intersection_of: results_in_morphogenesis_of UBERON:0004209 ! renal vesicle relationship: part_of GO:0072087 ! renal vesicle development relationship: part_of GO:0072088 ! nephron epithelium morphogenesis relationship: results_in_morphogenesis_of UBERON:0004209 ! renal vesicle -created_by: mah creation_date: 2010-02-01T02:21:06Z [Term] @@ -110489,7 +114844,6 @@ intersection_of: GO:0009653 ! anatomical structure morphogenesis intersection_of: results_in_morphogenesis_of UBERON:0001231 ! nephron tubule relationship: part_of GO:0072080 ! nephron tubule development relationship: results_in_morphogenesis_of UBERON:0001231 ! nephron tubule -created_by: mah creation_date: 2010-02-01T02:25:14Z [Term] @@ -110502,7 +114856,6 @@ intersection_of: GO:0048646 ! anatomical structure formation involved in morphog intersection_of: results_in_formation_of UBERON:0001231 ! nephron tubule relationship: part_of GO:0072078 ! nephron tubule morphogenesis relationship: results_in_formation_of UBERON:0001231 ! nephron tubule -created_by: mah creation_date: 2010-02-01T02:29:26Z [Term] @@ -110515,7 +114868,6 @@ is_a: GO:0072009 ! nephron epithelium development intersection_of: GO:0048856 ! anatomical structure development intersection_of: results_in_development_of UBERON:0001231 ! nephron tubule relationship: results_in_development_of UBERON:0001231 ! nephron tubule -created_by: mah creation_date: 2010-02-01T02:32:12Z [Term] @@ -110528,7 +114880,6 @@ intersection_of: GO:0048856 ! anatomical structure development intersection_of: results_in_development_of UBERON:0004209 ! renal vesicle relationship: part_of GO:0072009 ! nephron epithelium development relationship: results_in_development_of UBERON:0004209 ! renal vesicle -created_by: mah creation_date: 2010-02-08T01:18:31Z [Term] @@ -110542,7 +114893,6 @@ intersection_of: results_in_morphogenesis_of UBERON:0004211 ! nephron epithelium relationship: part_of GO:0072009 ! nephron epithelium development relationship: part_of GO:0072028 ! nephron morphogenesis relationship: results_in_morphogenesis_of UBERON:0004211 ! nephron epithelium -created_by: mah creation_date: 2010-02-08T01:19:06Z [Term] @@ -110556,7 +114906,6 @@ intersection_of: GO:0008283 ! cell population proliferation intersection_of: acts_on_population_of CL:0000034 ! stem cell relationship: acts_on_population_of CL:0000034 ! stem cell relationship: has_part GO:0017145 ! stem cell division -created_by: mah creation_date: 2010-02-08T02:03:36Z [Term] @@ -110568,7 +114917,6 @@ is_a: GO:0042127 ! regulation of cell population proliferation intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0072089 ! stem cell proliferation relationship: regulates GO:0072089 ! stem cell proliferation -created_by: mah creation_date: 2010-02-08T02:09:03Z [Term] @@ -110582,7 +114930,6 @@ intersection_of: GO:0048646 ! anatomical structure formation involved in morphog intersection_of: results_in_formation_of UBERON:0005147 ! metanephric renal vesicle relationship: part_of GO:0072283 ! metanephric renal vesicle morphogenesis relationship: results_in_formation_of UBERON:0005147 ! metanephric renal vesicle -created_by: mah creation_date: 2010-02-10T01:17:11Z [Term] @@ -110597,7 +114944,6 @@ is_a: GO:0009952 ! anterior/posterior pattern specification is_a: GO:0061004 ! pattern specification involved in kidney development intersection_of: GO:0009952 ! anterior/posterior pattern specification intersection_of: part_of GO:0001822 ! kidney development -created_by: mah creation_date: 2010-02-10T02:06:24Z [Term] @@ -110611,7 +114957,6 @@ is_a: GO:0072098 ! anterior/posterior pattern specification involved in kidney d intersection_of: GO:0009952 ! anterior/posterior pattern specification intersection_of: part_of GO:0001657 ! ureteric bud development relationship: part_of GO:0001657 ! ureteric bud development -created_by: mah creation_date: 2010-02-10T02:12:09Z [Term] @@ -110625,7 +114970,6 @@ intersection_of: GO:0009653 ! anatomical structure morphogenesis intersection_of: results_in_morphogenesis_of UBERON:0000074 ! renal glomerulus relationship: part_of GO:0032835 ! glomerulus development relationship: results_in_morphogenesis_of UBERON:0000074 ! renal glomerulus -created_by: mah creation_date: 2010-02-10T02:32:09Z [Term] @@ -110640,7 +114984,6 @@ intersection_of: results_in_morphogenesis_of UBERON:0004190 ! renal glomerulus v relationship: part_of GO:0072012 ! glomerulus vasculature development relationship: part_of GO:0072102 ! glomerulus morphogenesis relationship: results_in_morphogenesis_of UBERON:0004190 ! renal glomerulus vasculature -created_by: mah creation_date: 2010-02-10T02:34:54Z [Term] @@ -110653,7 +114996,6 @@ intersection_of: GO:0048646 ! anatomical structure formation involved in morphog intersection_of: results_in_formation_of UBERON:0004212 ! glomerular capillary relationship: part_of GO:0072103 ! glomerulus vasculature morphogenesis relationship: results_in_formation_of UBERON:0004212 ! glomerular capillary -created_by: mah creation_date: 2010-02-10T02:40:40Z [Term] @@ -110666,7 +115008,6 @@ is_a: GO:0030432 ! peristalsis intersection_of: GO:0030432 ! peristalsis intersection_of: occurs_in UBERON:0000056 ! ureter relationship: occurs_in UBERON:0000056 ! ureter -created_by: mah creation_date: 2010-02-10T03:07:54Z [Term] @@ -110680,7 +115021,6 @@ is_a: GO:2000027 ! regulation of animal organ morphogenesis intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0060676 ! ureteric bud formation relationship: regulates GO:0060676 ! ureteric bud formation -created_by: mah creation_date: 2010-02-12T02:34:40Z [Term] @@ -110694,7 +115034,6 @@ is_a: GO:1905278 ! positive regulation of epithelial tube formation intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0060676 ! ureteric bud formation relationship: positively_regulates GO:0060676 ! ureteric bud formation -created_by: mah creation_date: 2010-02-12T02:37:28Z [Term] @@ -110708,7 +115047,6 @@ is_a: GO:2000698 ! positive regulation of epithelial cell differentiation involv intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0003337 ! mesenchymal to epithelial transition involved in metanephros morphogenesis relationship: positively_regulates GO:0003337 ! mesenchymal to epithelial transition involved in metanephros morphogenesis -created_by: mah creation_date: 2010-02-12T02:45:57Z [Term] @@ -110721,7 +115059,6 @@ intersection_of: GO:0048856 ! anatomical structure development intersection_of: results_in_development_of UBERON:0002320 ! glomerular mesangium relationship: part_of GO:0072012 ! glomerulus vasculature development relationship: results_in_development_of UBERON:0002320 ! glomerular mesangium -created_by: mah creation_date: 2010-02-22T10:35:24Z [Term] @@ -110733,7 +115070,6 @@ is_a: GO:0008283 ! cell population proliferation intersection_of: GO:0008283 ! cell population proliferation intersection_of: part_of GO:0001822 ! kidney development relationship: part_of GO:0001822 ! kidney development -created_by: mah creation_date: 2010-02-22T10:48:45Z [Term] @@ -110748,7 +115084,6 @@ intersection_of: GO:0030154 ! cell differentiation intersection_of: results_in_acquisition_of_features_of CL:0000653 ! podocyte relationship: results_in_acquisition_of_features_of CL:0000653 ! podocyte property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/23000" xsd:anyURI -created_by: mah creation_date: 2010-02-22T10:52:11Z [Term] @@ -110762,7 +115097,6 @@ intersection_of: GO:0009653 ! anatomical structure morphogenesis intersection_of: results_in_morphogenesis_of UBERON:0002120 ! pronephros relationship: part_of GO:0048793 ! pronephros development relationship: results_in_morphogenesis_of UBERON:0002120 ! pronephros -created_by: mah creation_date: 2010-02-22T11:12:15Z [Term] @@ -110777,7 +115111,6 @@ intersection_of: GO:0048646 ! anatomical structure formation involved in morphog intersection_of: results_in_formation_of UBERON:0002120 ! pronephros relationship: part_of GO:0072114 ! pronephros morphogenesis relationship: results_in_formation_of UBERON:0002120 ! pronephros -created_by: mah creation_date: 2010-02-22T11:16:26Z [Term] @@ -110791,7 +115124,6 @@ intersection_of: GO:0021700 ! developmental maturation intersection_of: results_in_maturation_of UBERON:0002120 ! pronephros relationship: part_of GO:0048793 ! pronephros development relationship: results_in_maturation_of UBERON:0002120 ! pronephros -created_by: mah creation_date: 2010-02-22T11:25:48Z [Term] @@ -110804,7 +115136,6 @@ intersection_of: GO:0048856 ! anatomical structure development intersection_of: results_in_development_of UBERON:0002015 ! kidney capsule relationship: part_of GO:0001822 ! kidney development relationship: results_in_development_of UBERON:0002015 ! kidney capsule -created_by: mah creation_date: 2010-02-22T02:02:55Z [Term] @@ -110817,7 +115148,6 @@ intersection_of: GO:0009653 ! anatomical structure morphogenesis intersection_of: results_in_morphogenesis_of UBERON:0002015 ! kidney capsule relationship: part_of GO:0072127 ! renal capsule development relationship: results_in_morphogenesis_of UBERON:0002015 ! kidney capsule -created_by: mah creation_date: 2010-02-22T02:06:19Z [Term] @@ -110831,7 +115161,6 @@ intersection_of: GO:0048646 ! anatomical structure formation involved in morphog intersection_of: results_in_formation_of UBERON:0002015 ! kidney capsule relationship: part_of GO:0072128 ! renal capsule morphogenesis relationship: results_in_formation_of UBERON:0002015 ! kidney capsule -created_by: mah creation_date: 2010-02-22T02:08:14Z [Term] @@ -110844,7 +115173,6 @@ intersection_of: GO:0009653 ! anatomical structure morphogenesis intersection_of: results_in_morphogenesis_of UBERON:0003918 ! kidney mesenchyme relationship: part_of GO:0072074 ! kidney mesenchyme development relationship: results_in_morphogenesis_of UBERON:0003918 ! kidney mesenchyme -created_by: mah creation_date: 2010-02-22T02:16:43Z [Term] @@ -110858,7 +115186,6 @@ intersection_of: results_in_morphogenesis_of UBERON:0003104 ! mesenchyme relationship: part_of GO:0009887 ! animal organ morphogenesis relationship: part_of GO:0060485 ! mesenchyme development relationship: results_in_morphogenesis_of UBERON:0003104 ! mesenchyme -created_by: mah creation_date: 2010-02-22T02:17:15Z [Term] @@ -110871,7 +115198,6 @@ intersection_of: GO:0009653 ! anatomical structure morphogenesis intersection_of: results_in_morphogenesis_of UBERON:0003220 ! metanephric mesenchyme relationship: part_of GO:0072075 ! metanephric mesenchyme development relationship: results_in_morphogenesis_of UBERON:0003220 ! metanephric mesenchyme -created_by: mah creation_date: 2010-02-22T02:20:14Z [Term] @@ -110884,7 +115210,6 @@ intersection_of: GO:0009653 ! anatomical structure morphogenesis intersection_of: results_in_morphogenesis_of UBERON:0004208 ! nephrogenic mesenchyme relationship: part_of GO:0072076 ! nephrogenic mesenchyme development relationship: results_in_morphogenesis_of UBERON:0004208 ! nephrogenic mesenchyme -created_by: mah creation_date: 2010-02-22T02:21:16Z [Term] @@ -110898,7 +115223,6 @@ is_a: GO:0061209 ! cell proliferation involved in mesonephros development intersection_of: GO:0010463 ! mesenchymal cell proliferation intersection_of: part_of GO:0001657 ! ureteric bud development relationship: part_of GO:0001657 ! ureteric bud development -created_by: mah creation_date: 2010-02-22T02:40:38Z [Term] @@ -110907,7 +115231,6 @@ name: glomerular parietal epithelial cell differentiation namespace: biological_process def: "The process in which a relatively unspecialized cell acquires specialized features of a glomerular parietal epithelial cell. Glomerular parietal epithelial cells are specialized epithelial cells that form tight junctions as a barrier to protein transport." [GOC:mtg_kidney_jan10] is_a: GO:0072311 ! glomerular epithelial cell differentiation -created_by: mah creation_date: 2010-02-24T01:33:05Z [Term] @@ -110921,7 +115244,6 @@ intersection_of: GO:0048856 ! anatomical structure development intersection_of: results_in_development_of CL:1000692 ! kidney interstitial fibroblast relationship: part_of GO:0072071 ! kidney interstitial fibroblast differentiation relationship: results_in_development_of CL:1000692 ! kidney interstitial fibroblast -created_by: mah creation_date: 2010-02-24T01:39:05Z [Term] @@ -110934,7 +115256,6 @@ intersection_of: GO:0048468 ! cell development intersection_of: results_in_development_of CL:1000618 ! juxtaglomerular complex cell relationship: part_of GO:0072052 ! juxtaglomerulus cell differentiation relationship: results_in_development_of CL:1000618 ! juxtaglomerular complex cell -created_by: mah creation_date: 2010-02-24T01:42:53Z [Term] @@ -110947,7 +115268,6 @@ intersection_of: GO:0032502 ! developmental process intersection_of: results_in_development_of CL:0000650 ! mesangial cell relationship: part_of GO:0072007 ! mesangial cell differentiation relationship: results_in_development_of CL:0000650 ! mesangial cell -created_by: mah creation_date: 2010-02-24T01:44:28Z [Term] @@ -110961,7 +115281,6 @@ intersection_of: GO:0048856 ! anatomical structure development intersection_of: results_in_development_of CL:1000742 ! glomerular mesangial cell relationship: part_of GO:0072008 ! glomerular mesangial cell differentiation relationship: results_in_development_of CL:1000742 ! glomerular mesangial cell -created_by: mah creation_date: 2010-02-24T01:53:13Z [Term] @@ -110974,7 +115293,6 @@ is_a: GO:0035787 ! cell migration involved in kidney development intersection_of: GO:0010631 ! epithelial cell migration intersection_of: part_of GO:0072078 ! nephron tubule morphogenesis relationship: part_of GO:0072078 ! nephron tubule morphogenesis -created_by: mah creation_date: 2010-02-24T02:21:25Z [Term] @@ -110987,7 +115305,6 @@ intersection_of: GO:0009653 ! anatomical structure morphogenesis intersection_of: results_in_morphogenesis_of UBERON:0004135 ! distal tubule relationship: part_of GO:0072017 ! distal tubule development relationship: results_in_morphogenesis_of UBERON:0004135 ! distal tubule -created_by: mah creation_date: 2010-02-24T02:32:03Z [Term] @@ -110999,7 +115316,6 @@ is_a: GO:0072155 ! epithelial cell migration involved in nephron tubule morphoge intersection_of: GO:0010631 ! epithelial cell migration intersection_of: part_of GO:0072156 ! distal tubule morphogenesis relationship: part_of GO:0072156 ! distal tubule morphogenesis -created_by: mah creation_date: 2010-02-24T02:33:33Z [Term] @@ -111012,7 +115328,6 @@ intersection_of: GO:0009653 ! anatomical structure morphogenesis intersection_of: results_in_morphogenesis_of UBERON:0004134 ! proximal tubule relationship: part_of GO:0072014 ! proximal tubule development relationship: results_in_morphogenesis_of UBERON:0004134 ! proximal tubule -created_by: mah creation_date: 2010-02-24T02:35:36Z [Term] @@ -111024,7 +115339,6 @@ is_a: GO:0072155 ! epithelial cell migration involved in nephron tubule morphoge intersection_of: GO:0010631 ! epithelial cell migration intersection_of: part_of GO:0072158 ! proximal tubule morphogenesis relationship: part_of GO:0072158 ! proximal tubule morphogenesis -created_by: mah creation_date: 2010-02-24T02:37:08Z [Term] @@ -111037,7 +115351,6 @@ intersection_of: GO:0030154 ! cell differentiation intersection_of: results_in_acquisition_of_features_of CL:1000494 ! nephron tubule epithelial cell relationship: part_of GO:0072080 ! nephron tubule development relationship: results_in_acquisition_of_features_of CL:1000494 ! nephron tubule epithelial cell -created_by: mah creation_date: 2010-02-24T02:40:11Z [Term] @@ -111050,7 +115363,6 @@ is_a: GO:2001012 ! mesenchymal cell differentiation involved in renal system dev intersection_of: GO:0048762 ! mesenchymal cell differentiation intersection_of: part_of GO:0001822 ! kidney development relationship: part_of GO:0072074 ! kidney mesenchyme development -created_by: mah creation_date: 2010-02-26T01:31:49Z [Term] @@ -111063,7 +115375,6 @@ intersection_of: GO:0048856 ! anatomical structure development intersection_of: results_in_development_of UBERON:0005103 ! mesonephric epithelium relationship: part_of GO:0001823 ! mesonephros development relationship: results_in_development_of UBERON:0005103 ! mesonephric epithelium -created_by: mah creation_date: 2010-02-26T01:40:43Z [Term] @@ -111076,7 +115387,6 @@ is_a: GO:0072163 ! mesonephric epithelium development intersection_of: GO:0048856 ! anatomical structure development intersection_of: results_in_development_of UBERON:0000083 ! mesonephric tubule relationship: results_in_development_of UBERON:0000083 ! mesonephric tubule -created_by: mah creation_date: 2010-02-26T01:45:58Z [Term] @@ -111089,7 +115399,6 @@ is_a: GO:0072207 ! metanephric epithelium development intersection_of: GO:0048856 ! anatomical structure development intersection_of: results_in_development_of UBERON:0005106 ! metanephric tubule relationship: results_in_development_of UBERON:0005106 ! metanephric tubule -created_by: mah creation_date: 2010-02-26T01:58:18Z [Term] @@ -111102,7 +115411,6 @@ intersection_of: GO:0009653 ! anatomical structure morphogenesis intersection_of: results_in_morphogenesis_of UBERON:0000083 ! mesonephric tubule relationship: part_of GO:0072164 ! mesonephric tubule development relationship: results_in_morphogenesis_of UBERON:0000083 ! mesonephric tubule -created_by: mah creation_date: 2010-02-26T02:02:13Z [Term] @@ -111115,7 +115423,6 @@ intersection_of: GO:0048646 ! anatomical structure formation involved in morphog intersection_of: results_in_formation_of UBERON:0000083 ! mesonephric tubule relationship: part_of GO:0072171 ! mesonephric tubule morphogenesis relationship: results_in_formation_of UBERON:0000083 ! mesonephric tubule -created_by: mah creation_date: 2010-02-26T02:02:37Z [Term] @@ -111128,7 +115435,6 @@ intersection_of: GO:0009653 ! anatomical structure morphogenesis intersection_of: results_in_morphogenesis_of UBERON:0005106 ! metanephric tubule relationship: part_of GO:0072170 ! metanephric tubule development relationship: results_in_morphogenesis_of UBERON:0005106 ! metanephric tubule -created_by: mah creation_date: 2010-02-26T02:06:42Z [Term] @@ -111141,7 +115447,6 @@ intersection_of: GO:0048646 ! anatomical structure formation involved in morphog intersection_of: results_in_formation_of UBERON:0005106 ! metanephric tubule relationship: part_of GO:0072173 ! metanephric tubule morphogenesis relationship: results_in_formation_of UBERON:0005106 ! metanephric tubule -created_by: mah creation_date: 2010-02-26T02:07:41Z [Term] @@ -111155,7 +115460,6 @@ intersection_of: results_in_formation_of UBERON:0003914 ! epithelial tube relationship: part_of GO:0060562 ! epithelial tube morphogenesis relationship: results_in_formation_of UBERON:0003914 ! epithelial tube property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/22302" xsd:anyURI -created_by: mah creation_date: 2010-02-26T02:15:40Z [Term] @@ -111168,7 +115472,6 @@ is_a: GO:0072073 ! kidney epithelium development intersection_of: GO:0048856 ! anatomical structure development intersection_of: results_in_development_of UBERON:0009201 ! nephric duct relationship: results_in_development_of UBERON:0009201 ! nephric duct -created_by: mah creation_date: 2010-02-26T02:27:31Z [Term] @@ -111182,7 +115485,6 @@ is_a: GO:0072176 ! nephric duct development intersection_of: GO:0048856 ! anatomical structure development intersection_of: results_in_development_of UBERON:0003074 ! mesonephric duct relationship: results_in_development_of UBERON:0003074 ! mesonephric duct -created_by: mah creation_date: 2010-02-26T02:32:22Z [Term] @@ -111195,7 +115497,6 @@ intersection_of: GO:0009653 ! anatomical structure morphogenesis intersection_of: results_in_morphogenesis_of UBERON:0009201 ! nephric duct relationship: part_of GO:0072176 ! nephric duct development relationship: results_in_morphogenesis_of UBERON:0009201 ! nephric duct -created_by: mah creation_date: 2010-02-26T02:35:29Z [Term] @@ -111208,7 +115509,6 @@ intersection_of: GO:0048646 ! anatomical structure formation involved in morphog intersection_of: results_in_formation_of UBERON:0009201 ! nephric duct relationship: part_of GO:0072178 ! nephric duct morphogenesis relationship: results_in_formation_of UBERON:0009201 ! nephric duct -created_by: mah creation_date: 2010-02-26T02:35:55Z [Term] @@ -111223,7 +115523,6 @@ intersection_of: GO:0009653 ! anatomical structure morphogenesis intersection_of: results_in_morphogenesis_of UBERON:0003074 ! mesonephric duct relationship: part_of GO:0072177 ! mesonephric duct development relationship: results_in_morphogenesis_of UBERON:0003074 ! mesonephric duct -created_by: mah creation_date: 2010-02-26T02:37:13Z [Term] @@ -111238,7 +115537,6 @@ is_a: GO:0072180 ! mesonephric duct morphogenesis intersection_of: GO:0048646 ! anatomical structure formation involved in morphogenesis intersection_of: results_in_formation_of UBERON:0003074 ! mesonephric duct relationship: results_in_formation_of UBERON:0003074 ! mesonephric duct -created_by: mah creation_date: 2010-02-26T02:38:03Z [Term] @@ -111250,7 +115548,6 @@ is_a: GO:2000696 ! regulation of epithelial cell differentiation involved in kid intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0072160 ! nephron tubule epithelial cell differentiation relationship: regulates GO:0072160 ! nephron tubule epithelial cell differentiation -created_by: mah creation_date: 2010-02-26T02:45:09Z [Term] @@ -111264,7 +115561,6 @@ is_a: GO:2000697 ! negative regulation of epithelial cell differentiation involv intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0072160 ! nephron tubule epithelial cell differentiation relationship: negatively_regulates GO:0072160 ! nephron tubule epithelial cell differentiation -created_by: mah creation_date: 2010-02-26T02:47:25Z [Term] @@ -111278,7 +115574,6 @@ intersection_of: GO:0048856 ! anatomical structure development intersection_of: results_in_development_of UBERON:0000056 ! ureter relationship: part_of GO:0072001 ! renal system development relationship: results_in_development_of UBERON:0000056 ! ureter -created_by: mah creation_date: 2010-03-01T01:44:14Z [Term] @@ -111292,7 +115587,6 @@ intersection_of: GO:0048856 ! anatomical structure development intersection_of: results_in_development_of UBERON:0001254 ! urothelium of ureter relationship: part_of GO:0072189 ! ureter development relationship: results_in_development_of UBERON:0001254 ! urothelium of ureter -created_by: mah creation_date: 2010-03-01T01:46:31Z [Term] @@ -111305,7 +115599,6 @@ intersection_of: GO:0048856 ! anatomical structure development intersection_of: results_in_development_of UBERON:0009919 ! ureter smooth muscle relationship: part_of GO:0072189 ! ureter development relationship: results_in_development_of UBERON:0009919 ! ureter smooth muscle -created_by: mah creation_date: 2010-03-01T01:48:53Z [Term] @@ -111318,7 +115611,6 @@ intersection_of: GO:0030154 ! cell differentiation intersection_of: results_in_acquisition_of_features_of CL:1000979 ! ureter smooth muscle cell relationship: part_of GO:0072191 ! ureter smooth muscle development relationship: results_in_acquisition_of_features_of CL:1000979 ! ureter smooth muscle cell -created_by: mah creation_date: 2010-03-01T01:55:01Z [Term] @@ -111328,7 +115620,6 @@ namespace: biological_process def: "The process whose specific outcome is the progression of smooth muscle in the kidney over time, from its formation to the mature structure." [GOC:mtg_kidney_jan10] is_a: GO:0048745 ! smooth muscle tissue development relationship: part_of GO:0001822 ! kidney development -created_by: mah creation_date: 2010-03-01T02:05:30Z [Term] @@ -111342,7 +115633,6 @@ intersection_of: GO:0009653 ! anatomical structure morphogenesis intersection_of: results_in_morphogenesis_of UBERON:0000056 ! ureter relationship: part_of GO:0072189 ! ureter development relationship: results_in_morphogenesis_of UBERON:0000056 ! ureter -created_by: mah creation_date: 2010-03-01T02:24:55Z [Term] @@ -111356,7 +115646,6 @@ is_a: GO:0010463 ! mesenchymal cell proliferation intersection_of: GO:0010463 ! mesenchymal cell proliferation intersection_of: part_of GO:0072189 ! ureter development relationship: part_of GO:0072189 ! ureter development -created_by: mah creation_date: 2010-03-01T03:24:41Z [Term] @@ -111370,7 +115659,6 @@ is_a: GO:0010464 ! regulation of mesenchymal cell proliferation intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0072198 ! mesenchymal cell proliferation involved in ureter development relationship: regulates GO:0072198 ! mesenchymal cell proliferation involved in ureter development -created_by: mah creation_date: 2010-03-01T03:38:13Z [Term] @@ -111387,7 +115675,6 @@ is_a: GO:0072201 ! negative regulation of mesenchymal cell proliferation intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0072198 ! mesenchymal cell proliferation involved in ureter development relationship: negatively_regulates GO:0072198 ! mesenchymal cell proliferation involved in ureter development -created_by: mah creation_date: 2010-03-01T03:42:31Z [Term] @@ -111400,7 +115687,6 @@ is_a: GO:0010464 ! regulation of mesenchymal cell proliferation intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0010463 ! mesenchymal cell proliferation relationship: negatively_regulates GO:0010463 ! mesenchymal cell proliferation -created_by: mah creation_date: 2010-03-01T03:43:29Z [Term] @@ -111412,7 +115698,6 @@ is_a: GO:0061005 ! cell differentiation involved in kidney development intersection_of: GO:0030154 ! cell differentiation intersection_of: part_of GO:0001656 ! metanephros development relationship: part_of GO:0001656 ! metanephros development -created_by: mah creation_date: 2010-03-18T10:40:14Z [Term] @@ -111424,7 +115709,6 @@ is_a: GO:0072111 ! cell proliferation involved in kidney development intersection_of: GO:0008283 ! cell population proliferation intersection_of: part_of GO:0001656 ! metanephros development relationship: part_of GO:0001656 ! metanephros development -created_by: mah creation_date: 2010-03-18T10:42:27Z [Term] @@ -111437,7 +115721,6 @@ is_a: GO:0060995 ! cell-cell signaling involved in kidney development intersection_of: GO:0007267 ! cell-cell signaling intersection_of: part_of GO:0001656 ! metanephros development relationship: part_of GO:0001656 ! metanephros development -created_by: mah creation_date: 2010-03-18T10:54:36Z [Term] @@ -111450,7 +115733,6 @@ intersection_of: GO:0048856 ! anatomical structure development intersection_of: results_in_development_of UBERON:0004737 ! metanephric collecting duct relationship: part_of GO:0001656 ! metanephros development relationship: results_in_development_of UBERON:0004737 ! metanephric collecting duct -created_by: mah creation_date: 2010-03-18T11:15:37Z [Term] @@ -111463,7 +115745,6 @@ intersection_of: GO:0048856 ! anatomical structure development intersection_of: results_in_development_of UBERON:0004738 ! metanephric juxtaglomerular apparatus relationship: part_of GO:0001656 ! metanephros development relationship: results_in_development_of UBERON:0004738 ! metanephric juxtaglomerular apparatus -created_by: mah creation_date: 2010-03-18T11:17:47Z [Term] @@ -111476,7 +115757,6 @@ intersection_of: GO:0048856 ! anatomical structure development intersection_of: results_in_development_of UBERON:0005108 ! metanephric epithelium relationship: part_of GO:0001656 ! metanephros development relationship: results_in_development_of UBERON:0005108 ! metanephric epithelium -created_by: mah creation_date: 2010-03-18T11:50:37Z [Term] @@ -111489,7 +115769,6 @@ intersection_of: GO:0048856 ! anatomical structure development intersection_of: results_in_development_of UBERON:0005109 ! metanephric smooth muscle tissue relationship: part_of GO:0001656 ! metanephros development relationship: results_in_development_of UBERON:0005109 ! metanephric smooth muscle tissue -created_by: mah creation_date: 2010-03-18T11:51:59Z [Term] @@ -111502,7 +115781,6 @@ intersection_of: GO:0048856 ! anatomical structure development intersection_of: results_in_development_of UBERON:0005110 ! metanephric nephron relationship: part_of GO:0001656 ! metanephros development relationship: results_in_development_of UBERON:0005110 ! metanephric nephron -created_by: mah creation_date: 2010-03-18T12:52:57Z [Term] @@ -111519,7 +115797,6 @@ intersection_of: GO:0048856 ! anatomical structure development intersection_of: results_in_development_of UBERON:0005111 ! metanephric pyramid relationship: part_of GO:0001656 ! metanephros development relationship: results_in_development_of UBERON:0005111 ! metanephric pyramid -created_by: mah creation_date: 2010-03-18T01:04:51Z [Term] @@ -111532,7 +115809,6 @@ intersection_of: GO:0048856 ! anatomical structure development intersection_of: results_in_development_of UBERON:0005137 ! metanephric capsule relationship: part_of GO:0001656 ! metanephros development relationship: results_in_development_of UBERON:0005137 ! metanephric capsule -created_by: mah creation_date: 2010-03-18T01:25:19Z [Term] @@ -111546,7 +115822,6 @@ intersection_of: GO:0048856 ! anatomical structure development intersection_of: results_in_development_of UBERON:0005113 ! metanephric cortex mesenchyme relationship: part_of GO:0001656 ! metanephros development relationship: results_in_development_of UBERON:0005113 ! metanephric cortex mesenchyme -created_by: mah creation_date: 2010-03-18T01:29:49Z [Term] @@ -111569,7 +115844,6 @@ is_a: GO:0090184 ! positive regulation of kidney development intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0001656 ! metanephros development relationship: positively_regulates GO:0001656 ! metanephros development -created_by: mah creation_date: 2010-03-18T01:40:12Z [Term] @@ -111582,7 +115856,6 @@ is_a: GO:0090185 ! negative regulation of kidney development intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0001656 ! metanephros development relationship: negatively_regulates GO:0001656 ! metanephros development -created_by: mah creation_date: 2010-03-18T01:45:48Z [Term] @@ -111596,7 +115869,6 @@ intersection_of: GO:0048856 ! anatomical structure development intersection_of: results_in_development_of UBERON:0005114 ! metanephric ascending thin limb relationship: part_of GO:0072236 ! metanephric loop of Henle development relationship: results_in_development_of UBERON:0005114 ! metanephric ascending thin limb -created_by: mah creation_date: 2010-03-18T03:34:42Z [Term] @@ -111608,7 +115880,6 @@ is_a: GO:0072059 ! cortical collecting duct development intersection_of: GO:0048856 ! anatomical structure development intersection_of: results_in_development_of UBERON:0005115 ! metanephric cortical collecting duct relationship: results_in_development_of UBERON:0005115 ! metanephric cortical collecting duct -created_by: mah creation_date: 2010-03-18T03:34:52Z [Term] @@ -111621,7 +115892,6 @@ intersection_of: GO:0048856 ! anatomical structure development intersection_of: results_in_development_of UBERON:0005116 ! metanephric descending thin limb relationship: part_of GO:0072236 ! metanephric loop of Henle development relationship: results_in_development_of UBERON:0005116 ! metanephric descending thin limb -created_by: mah creation_date: 2010-03-18T03:35:05Z [Term] @@ -111635,7 +115905,6 @@ intersection_of: GO:0048856 ! anatomical structure development intersection_of: results_in_development_of UBERON:0005117 ! metanephric distal convoluted tubule relationship: part_of GO:0072235 ! metanephric distal tubule development relationship: results_in_development_of UBERON:0005117 ! metanephric distal convoluted tubule -created_by: mah creation_date: 2010-03-18T03:35:27Z [Term] @@ -111649,7 +115918,6 @@ intersection_of: GO:0048856 ! anatomical structure development intersection_of: results_in_development_of UBERON:0005118 ! metanephric early distal convoluted tubule relationship: part_of GO:0072221 ! metanephric distal convoluted tubule development relationship: results_in_development_of UBERON:0005118 ! metanephric early distal convoluted tubule -created_by: mah creation_date: 2010-03-18T03:35:46Z [Term] @@ -111662,7 +115930,6 @@ intersection_of: GO:0048856 ! anatomical structure development intersection_of: results_in_development_of UBERON:0005119 ! metanephric glomerular mesangium relationship: part_of GO:0072239 ! metanephric glomerulus vasculature development relationship: results_in_development_of UBERON:0005119 ! metanephric glomerular mesangium -created_by: mah creation_date: 2010-03-18T03:35:56Z [Term] @@ -111676,7 +115943,6 @@ intersection_of: GO:0048856 ! anatomical structure development intersection_of: results_in_development_of UBERON:0004736 ! metanephric glomerulus relationship: part_of GO:0072210 ! metanephric nephron development relationship: results_in_development_of UBERON:0004736 ! metanephric glomerulus -created_by: mah creation_date: 2010-03-18T03:36:20Z [Term] @@ -111690,7 +115956,6 @@ intersection_of: GO:0048856 ! anatomical structure development intersection_of: results_in_development_of UBERON:0005120 ! metanephric late distal convoluted tubule relationship: part_of GO:0072221 ! metanephric distal convoluted tubule development relationship: results_in_development_of UBERON:0005120 ! metanephric late distal convoluted tubule -created_by: mah creation_date: 2010-03-18T03:37:04Z [Term] @@ -111704,7 +115969,6 @@ intersection_of: GO:0048856 ! anatomical structure development intersection_of: results_in_development_of UBERON:0005122 ! metanephric macula densa relationship: part_of GO:0072206 ! metanephric juxtaglomerular apparatus development relationship: results_in_development_of UBERON:0005122 ! metanephric macula densa -created_by: mah creation_date: 2010-03-18T03:37:26Z [Term] @@ -111718,7 +115982,6 @@ intersection_of: GO:0048856 ! anatomical structure development intersection_of: results_in_development_of UBERON:0005124 ! metanephric proximal convoluted tubule relationship: part_of GO:0072237 ! metanephric proximal tubule development relationship: results_in_development_of UBERON:0005124 ! metanephric proximal convoluted tubule -created_by: mah creation_date: 2010-03-18T03:37:56Z [Term] @@ -111733,7 +115996,6 @@ intersection_of: GO:0048856 ! anatomical structure development intersection_of: results_in_development_of UBERON:0005125 ! metanephric proximal straight tubule relationship: part_of GO:0072237 ! metanephric proximal tubule development relationship: results_in_development_of UBERON:0005125 ! metanephric proximal straight tubule -created_by: mah creation_date: 2010-03-18T03:38:53Z [Term] @@ -111747,7 +116009,6 @@ intersection_of: GO:0048856 ! anatomical structure development intersection_of: results_in_development_of UBERON:0005126 ! metanephric S1 relationship: part_of GO:0072229 ! metanephric proximal convoluted tubule development relationship: results_in_development_of UBERON:0005126 ! metanephric S1 -created_by: mah creation_date: 2010-03-18T03:39:10Z [Term] @@ -111762,7 +116023,6 @@ intersection_of: GO:0048856 ! anatomical structure development intersection_of: results_in_development_of UBERON:0005127 ! metanephric thick ascending limb relationship: part_of GO:0072235 ! metanephric distal tubule development relationship: results_in_development_of UBERON:0005127 ! metanephric thick ascending limb -created_by: mah creation_date: 2010-03-18T03:39:36Z [Term] @@ -111776,7 +116036,6 @@ is_a: GO:0072243 ! metanephric nephron epithelium development intersection_of: GO:0048856 ! anatomical structure development intersection_of: results_in_development_of UBERON:0005146 ! metanephric nephron tubule relationship: results_in_development_of UBERON:0005146 ! metanephric nephron tubule -created_by: mah creation_date: 2010-03-18T03:41:23Z [Term] @@ -111789,7 +116048,6 @@ is_a: GO:0072234 ! metanephric nephron tubule development intersection_of: GO:0048856 ! anatomical structure development intersection_of: results_in_development_of UBERON:0005129 ! metanephric distal tubule relationship: results_in_development_of UBERON:0005129 ! metanephric distal tubule -created_by: mah creation_date: 2010-03-18T03:45:37Z [Term] @@ -111803,7 +116061,6 @@ is_a: GO:0072234 ! metanephric nephron tubule development intersection_of: GO:0048856 ! anatomical structure development intersection_of: results_in_development_of UBERON:0005130 ! metanephric loop of Henle relationship: results_in_development_of UBERON:0005130 ! metanephric loop of Henle -created_by: mah creation_date: 2010-03-18T03:46:18Z [Term] @@ -111816,7 +116073,6 @@ is_a: GO:0072234 ! metanephric nephron tubule development intersection_of: GO:0048856 ! anatomical structure development intersection_of: results_in_development_of UBERON:0005151 ! metanephric proximal tubule relationship: results_in_development_of UBERON:0005151 ! metanephric proximal tubule -created_by: mah creation_date: 2010-03-18T03:46:54Z [Term] @@ -111830,7 +116086,6 @@ is_a: GO:0072210 ! metanephric nephron development intersection_of: GO:0048856 ! anatomical structure development intersection_of: results_in_development_of UBERON:0005132 ! metanephric long nephron relationship: results_in_development_of UBERON:0005132 ! metanephric long nephron -created_by: mah creation_date: 2010-03-18T03:48:23Z [Term] @@ -111844,7 +116099,6 @@ intersection_of: GO:0048856 ! anatomical structure development intersection_of: results_in_development_of UBERON:0005133 ! metanephric glomerulus vasculature relationship: part_of GO:0072224 ! metanephric glomerulus development relationship: results_in_development_of UBERON:0005133 ! metanephric glomerulus vasculature -created_by: mah creation_date: 2010-03-18T03:50:29Z [Term] @@ -111857,7 +116111,6 @@ is_a: GO:0072207 ! metanephric epithelium development intersection_of: GO:0048856 ! anatomical structure development intersection_of: results_in_development_of UBERON:0005134 ! metanephric nephron epithelium relationship: results_in_development_of UBERON:0005134 ! metanephric nephron epithelium -created_by: mah creation_date: 2010-03-19T03:29:49Z [Term] @@ -111871,7 +116124,6 @@ intersection_of: GO:0048856 ! anatomical structure development intersection_of: results_in_development_of UBERON:0005135 ! metanephric glomerular epithelium relationship: part_of GO:0072224 ! metanephric glomerulus development relationship: results_in_development_of UBERON:0005135 ! metanephric glomerular epithelium -created_by: mah creation_date: 2010-03-19T03:38:47Z [Term] @@ -111886,7 +116138,6 @@ intersection_of: GO:0030154 ! cell differentiation intersection_of: results_in_acquisition_of_features_of CL:0002525 ! metanephric podocyte relationship: results_in_acquisition_of_features_of CL:0002525 ! metanephric podocyte property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/23000" xsd:anyURI -created_by: mah creation_date: 2010-03-19T03:44:57Z [Term] @@ -111902,7 +116153,6 @@ intersection_of: results_in_development_of CL:0002525 ! metanephric podocyte relationship: part_of GO:0072248 ! metanephric podocyte differentiation relationship: results_in_development_of CL:0002525 ! metanephric podocyte property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/23000" xsd:anyURI -created_by: mah creation_date: 2010-03-19T03:46:26Z [Term] @@ -111916,7 +116166,6 @@ intersection_of: GO:0030154 ! cell differentiation intersection_of: results_in_acquisition_of_features_of CL:1000123 ! metanephric nephron tubule epithelial cell relationship: part_of GO:0072234 ! metanephric nephron tubule development relationship: results_in_acquisition_of_features_of CL:1000123 ! metanephric nephron tubule epithelial cell -created_by: mah creation_date: 2010-03-19T04:11:02Z [Term] @@ -111930,7 +116179,6 @@ intersection_of: GO:0048856 ! anatomical structure development intersection_of: results_in_development_of UBERON:0005136 ! metanephric glomerular endothelium relationship: part_of GO:0072239 ! metanephric glomerulus vasculature development relationship: results_in_development_of UBERON:0005136 ! metanephric glomerular endothelium -created_by: mah creation_date: 2010-03-30T02:42:26Z [Term] @@ -111943,7 +116191,6 @@ intersection_of: GO:0009653 ! anatomical structure morphogenesis intersection_of: results_in_morphogenesis_of UBERON:0005137 ! metanephric capsule relationship: part_of GO:0072213 ! metanephric capsule development relationship: results_in_morphogenesis_of UBERON:0005137 ! metanephric capsule -created_by: mah creation_date: 2010-03-30T02:54:49Z [Term] @@ -111956,7 +116203,6 @@ intersection_of: GO:0048646 ! anatomical structure formation involved in morphog intersection_of: results_in_formation_of UBERON:0005137 ! metanephric capsule relationship: part_of GO:0072265 ! metanephric capsule morphogenesis relationship: results_in_formation_of UBERON:0005137 ! metanephric capsule -created_by: mah creation_date: 2010-03-30T02:56:35Z [Term] @@ -111971,7 +116217,6 @@ is_a: GO:0061004 ! pattern specification involved in kidney development intersection_of: GO:0007389 ! pattern specification process intersection_of: part_of GO:0001656 ! metanephros development relationship: part_of GO:0001656 ! metanephros development -created_by: mah creation_date: 2010-03-30T03:06:30Z [Term] @@ -111985,7 +116230,6 @@ intersection_of: GO:0048856 ! anatomical structure development intersection_of: results_in_development_of UBERON:0005139 ! metanephric long descending thin limb relationship: part_of GO:0072238 ! metanephric long nephron development relationship: results_in_development_of UBERON:0005139 ! metanephric long descending thin limb -created_by: mah creation_date: 2010-03-30T03:12:05Z [Term] @@ -111998,7 +116242,6 @@ is_a: GO:0072210 ! metanephric nephron development intersection_of: GO:0048856 ! anatomical structure development intersection_of: results_in_development_of UBERON:0005140 ! metanephric short nephron relationship: results_in_development_of UBERON:0005140 ! metanephric short nephron -created_by: mah creation_date: 2010-03-30T03:15:18Z [Term] @@ -112012,7 +116255,6 @@ intersection_of: GO:0048856 ! anatomical structure development intersection_of: results_in_development_of UBERON:0005141 ! metanephric short descending thin limb relationship: part_of GO:0072270 ! metanephric short nephron development relationship: results_in_development_of UBERON:0005141 ! metanephric short descending thin limb -created_by: mah creation_date: 2010-03-30T03:16:25Z [Term] @@ -112026,7 +116268,6 @@ intersection_of: results_in_morphogenesis_of UBERON:0005110 ! metanephric nephro relationship: part_of GO:0003338 ! metanephros morphogenesis relationship: part_of GO:0072210 ! metanephric nephron development relationship: results_in_morphogenesis_of UBERON:0005110 ! metanephric nephron -created_by: mah creation_date: 2010-03-30T03:33:19Z [Term] @@ -112039,7 +116280,6 @@ intersection_of: GO:0009653 ! anatomical structure morphogenesis intersection_of: results_in_morphogenesis_of UBERON:0004736 ! metanephric glomerulus relationship: part_of GO:0072224 ! metanephric glomerulus development relationship: results_in_morphogenesis_of UBERON:0004736 ! metanephric glomerulus -created_by: mah creation_date: 2010-04-01T02:46:58Z [Term] @@ -112053,7 +116293,6 @@ intersection_of: results_in_morphogenesis_of UBERON:0005133 ! metanephric glomer relationship: part_of GO:0072239 ! metanephric glomerulus vasculature development relationship: part_of GO:0072275 ! metanephric glomerulus morphogenesis relationship: results_in_morphogenesis_of UBERON:0005133 ! metanephric glomerulus vasculature -created_by: mah creation_date: 2010-04-01T02:47:32Z [Term] @@ -112066,7 +116305,6 @@ intersection_of: GO:0048646 ! anatomical structure formation involved in morphog intersection_of: results_in_formation_of UBERON:0005144 ! metanephric glomerular capillary relationship: part_of GO:0072276 ! metanephric glomerulus vasculature morphogenesis relationship: results_in_formation_of UBERON:0005144 ! metanephric glomerular capillary -created_by: mah creation_date: 2010-04-01T02:47:56Z [Term] @@ -112079,7 +116317,6 @@ intersection_of: GO:0009653 ! anatomical structure morphogenesis intersection_of: results_in_morphogenesis_of UBERON:0005145 ! metanephric comma-shaped body relationship: part_of GO:0072273 ! metanephric nephron morphogenesis relationship: results_in_morphogenesis_of UBERON:0005145 ! metanephric comma-shaped body -created_by: mah creation_date: 2010-04-01T03:14:42Z [Term] @@ -112093,7 +116330,6 @@ is_a: GO:0072202 ! cell differentiation involved in metanephros development intersection_of: GO:0072497 ! mesenchymal stem cell differentiation intersection_of: part_of GO:0072273 ! metanephric nephron morphogenesis relationship: part_of GO:0072273 ! metanephric nephron morphogenesis -created_by: mah creation_date: 2010-04-01T03:22:06Z [Term] @@ -112108,7 +116344,6 @@ intersection_of: results_in_morphogenesis_of UBERON:0005146 ! metanephric nephro relationship: part_of GO:0072234 ! metanephric nephron tubule development relationship: part_of GO:0072273 ! metanephric nephron morphogenesis relationship: results_in_morphogenesis_of UBERON:0005146 ! metanephric nephron tubule -created_by: mah creation_date: 2010-04-01T03:25:11Z [Term] @@ -112121,7 +116356,6 @@ intersection_of: GO:0009653 ! anatomical structure morphogenesis intersection_of: results_in_morphogenesis_of UBERON:0005147 ! metanephric renal vesicle relationship: part_of GO:0072273 ! metanephric nephron morphogenesis relationship: results_in_morphogenesis_of UBERON:0005147 ! metanephric renal vesicle -created_by: mah creation_date: 2010-04-01T03:28:00Z [Term] @@ -112134,7 +116368,6 @@ intersection_of: GO:0009653 ! anatomical structure morphogenesis intersection_of: results_in_morphogenesis_of UBERON:0005148 ! metanephric S-shaped body relationship: part_of GO:0072273 ! metanephric nephron morphogenesis relationship: results_in_morphogenesis_of UBERON:0005148 ! metanephric S-shaped body -created_by: mah creation_date: 2010-04-01T03:41:36Z [Term] @@ -112147,7 +116380,6 @@ is_a: GO:0072036 ! mesenchymal to epithelial transition involved in renal vesicl intersection_of: GO:0060231 ! mesenchymal to epithelial transition intersection_of: part_of GO:0072093 ! metanephric renal vesicle formation relationship: part_of GO:0072093 ! metanephric renal vesicle formation -created_by: mah creation_date: 2010-04-01T03:43:31Z [Term] @@ -112161,7 +116393,6 @@ is_a: GO:0072234 ! metanephric nephron tubule development intersection_of: GO:0048856 ! anatomical structure development intersection_of: results_in_development_of UBERON:0005149 ! metanephric connecting tubule relationship: results_in_development_of UBERON:0005149 ! metanephric connecting tubule -created_by: mah creation_date: 2010-04-09T03:30:09Z [Term] @@ -112175,7 +116406,6 @@ intersection_of: GO:0009653 ! anatomical structure morphogenesis intersection_of: results_in_morphogenesis_of UBERON:0005129 ! metanephric distal tubule relationship: part_of GO:0072235 ! metanephric distal tubule development relationship: results_in_morphogenesis_of UBERON:0005129 ! metanephric distal tubule -created_by: mah creation_date: 2010-04-09T03:41:47Z [Term] @@ -112189,7 +116419,6 @@ intersection_of: GO:0009653 ! anatomical structure morphogenesis intersection_of: results_in_morphogenesis_of UBERON:0005151 ! metanephric proximal tubule relationship: part_of GO:0072237 ! metanephric proximal tubule development relationship: results_in_morphogenesis_of UBERON:0005151 ! metanephric proximal tubule -created_by: mah creation_date: 2010-04-09T03:42:03Z [Term] @@ -112203,7 +116432,6 @@ intersection_of: GO:0048646 ! anatomical structure formation involved in morphog intersection_of: results_in_formation_of UBERON:0005146 ! metanephric nephron tubule relationship: part_of GO:0072282 ! metanephric nephron tubule morphogenesis relationship: results_in_formation_of UBERON:0005146 ! metanephric nephron tubule -created_by: mah creation_date: 2010-04-09T03:47:44Z [Term] @@ -112216,7 +116444,6 @@ is_a: GO:0072155 ! epithelial cell migration involved in nephron tubule morphoge intersection_of: GO:0010631 ! epithelial cell migration intersection_of: part_of GO:0072282 ! metanephric nephron tubule morphogenesis relationship: part_of GO:0072282 ! metanephric nephron tubule morphogenesis -created_by: mah creation_date: 2010-04-09T03:52:29Z [Term] @@ -112229,7 +116456,6 @@ is_a: GO:0072290 ! epithelial cell migration involved in metanephric nephron tub intersection_of: GO:0010631 ! epithelial cell migration intersection_of: part_of GO:0072287 ! metanephric distal tubule morphogenesis relationship: part_of GO:0072287 ! metanephric distal tubule morphogenesis -created_by: mah creation_date: 2010-04-09T03:53:37Z [Term] @@ -112242,7 +116468,6 @@ is_a: GO:0072290 ! epithelial cell migration involved in metanephric nephron tub intersection_of: GO:0010631 ! epithelial cell migration intersection_of: part_of GO:0072288 ! metanephric proximal tubule morphogenesis relationship: part_of GO:0072288 ! metanephric proximal tubule morphogenesis -created_by: mah creation_date: 2010-04-09T03:54:28Z [Term] @@ -112255,7 +116480,6 @@ is_a: GO:0090192 ! regulation of glomerulus development intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0072224 ! metanephric glomerulus development relationship: regulates GO:0072224 ! metanephric glomerulus development -created_by: mah creation_date: 2010-04-09T05:03:14Z [Term] @@ -112269,7 +116493,6 @@ is_a: GO:0090194 ! negative regulation of glomerulus development intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0072224 ! metanephric glomerulus development relationship: negatively_regulates GO:0072224 ! metanephric glomerulus development -created_by: mah creation_date: 2010-04-09T05:03:41Z [Term] @@ -112283,7 +116506,6 @@ is_a: GO:0090193 ! positive regulation of glomerulus development intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0072224 ! metanephric glomerulus development relationship: positively_regulates GO:0072224 ! metanephric glomerulus development -created_by: mah creation_date: 2010-04-09T05:03:41Z [Term] @@ -112299,7 +116521,6 @@ intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:1901147 ! mesenchymal cell apoptotic process involved in metanephric nephron morphogenesis relationship: regulates GO:0072309 ! mesenchymal stem cell maintenance involved in metanephric nephron morphogenesis relationship: regulates GO:1901147 ! mesenchymal cell apoptotic process involved in metanephric nephron morphogenesis -created_by: mah creation_date: 2010-04-09T05:03:41Z [Term] @@ -112316,7 +116537,6 @@ intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:1901147 ! mesenchymal cell apoptotic process involved in metanephric nephron morphogenesis relationship: negatively_regulates GO:0072309 ! mesenchymal stem cell maintenance involved in metanephric nephron morphogenesis relationship: negatively_regulates GO:1901147 ! mesenchymal cell apoptotic process involved in metanephric nephron morphogenesis -created_by: mah creation_date: 2010-04-09T05:03:41Z [Term] @@ -112333,7 +116553,6 @@ intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:1901147 ! mesenchymal cell apoptotic process involved in metanephric nephron morphogenesis relationship: positively_regulates GO:0072309 ! mesenchymal stem cell maintenance involved in metanephric nephron morphogenesis relationship: positively_regulates GO:1901147 ! mesenchymal cell apoptotic process involved in metanephric nephron morphogenesis -created_by: mah creation_date: 2010-04-09T05:03:41Z [Term] @@ -112345,7 +116564,6 @@ is_a: GO:0072182 ! regulation of nephron tubule epithelial cell differentiation intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0072257 ! metanephric nephron tubule epithelial cell differentiation relationship: regulates GO:0072257 ! metanephric nephron tubule epithelial cell differentiation -created_by: mah creation_date: 2010-04-09T05:03:41Z [Term] @@ -112358,7 +116576,6 @@ is_a: GO:0072307 ! regulation of metanephric nephron tubule epithelial cell diff intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0072257 ! metanephric nephron tubule epithelial cell differentiation relationship: negatively_regulates GO:0072257 ! metanephric nephron tubule epithelial cell differentiation -created_by: mah creation_date: 2010-04-09T05:03:41Z [Term] @@ -112368,7 +116585,6 @@ namespace: biological_process def: "The process in which an organism retains a population of mesenchymal stem cells that contributes to the shaping of a nephron in the metanephros. A mesenchymal stem cell is a cell that retains the ability to divide and proliferate throughout life to provide progenitor cells that can differentiate into specialized mesenchymal cells." [GOC:mtg_kidney_jan10] is_a: GO:0072038 ! mesenchymal stem cell maintenance involved in nephron morphogenesis relationship: part_of GO:0072273 ! metanephric nephron morphogenesis -created_by: mah creation_date: 2010-04-09T05:03:41Z [Term] @@ -112378,7 +116594,6 @@ namespace: biological_process def: "The process whose specific outcome is the progression of a glomerular epithelial cell over time, from its formation to the mature structure. Glomerular epithelial cells are specialized epithelial cells that form part of the glomerulus; there are two types, glomerular parietal epithelial cells and glomerular visceral epithelial cells." [GOC:mtg_kidney_jan10] is_a: GO:0002064 ! epithelial cell development relationship: part_of GO:0072311 ! glomerular epithelial cell differentiation -created_by: mah creation_date: 2010-04-09T06:47:31Z [Term] @@ -112388,7 +116603,6 @@ namespace: biological_process def: "The process in which a relatively unspecialized cell acquires specialized features of a glomerular epithelial cell. Glomerular epithelial cells are specialized epithelial cells that form part of the glomerulus; there are two types, glomerular parietal epithelial cells and glomerular visceral epithelial cells." [GOC:mtg_kidney_jan10] is_a: GO:0035850 ! epithelial cell differentiation involved in kidney development relationship: part_of GO:0072010 ! glomerular epithelium development -created_by: mah creation_date: 2010-04-09T06:49:21Z [Term] @@ -112399,7 +116613,6 @@ def: "The process in which a relatively unspecialized cell acquires specialized is_a: GO:0072202 ! cell differentiation involved in metanephros development is_a: GO:0072311 ! glomerular epithelial cell differentiation relationship: part_of GO:0072244 ! metanephric glomerular epithelium development -created_by: mah creation_date: 2010-04-09T06:54:15Z [Term] @@ -112409,7 +116622,6 @@ namespace: biological_process def: "The process whose specific outcome is the progression of a metanephric glomerular epithelial cell over time, from its formation to the mature structure. Metanephric glomerular epithelial cells are specialized epithelial cells that form part of the metanephric glomerulus; there are two types, metanephric glomerular parietal epithelial cells and metanephric glomerular visceral epithelial cells." [GOC:mtg_kidney_jan10] is_a: GO:0072310 ! glomerular epithelial cell development relationship: part_of GO:0072312 ! metanephric glomerular epithelial cell differentiation -created_by: mah creation_date: 2010-04-09T06:57:26Z [Term] @@ -112422,7 +116634,6 @@ is_a: GO:0032787 ! monocarboxylic acid metabolic process intersection_of: GO:0009056 ! catabolic process intersection_of: has_primary_input CHEBI:35757 relationship: has_primary_input CHEBI:35757 -created_by: mah creation_date: 2010-11-02T04:41:55Z [Term] @@ -112439,7 +116650,6 @@ is_a: GO:0046394 ! carboxylic acid biosynthetic process intersection_of: GO:0009058 ! biosynthetic process intersection_of: has_primary_output CHEBI:35757 relationship: has_primary_output CHEBI:35757 -created_by: mah creation_date: 2010-11-02T04:51:32Z [Term] @@ -112454,7 +116664,6 @@ is_a: GO:0006810 ! transport intersection_of: GO:0006810 ! transport intersection_of: has_primary_input CHEBI:83821 relationship: has_primary_input CHEBI:83821 -created_by: mah creation_date: 2010-11-04T12:18:23Z [Term] @@ -112468,7 +116677,6 @@ is_a: GO:0005488 ! binding intersection_of: GO:0005488 ! binding intersection_of: has_primary_input CHEBI:83821 relationship: has_primary_input CHEBI:83821 -created_by: mah creation_date: 2010-11-04T05:45:32Z [Term] @@ -112480,7 +116688,6 @@ is_a: GO:0048144 ! fibroblast proliferation intersection_of: GO:0008283 ! cell population proliferation intersection_of: acts_on_population_of CL:0002410 ! pancreatic stellate cell relationship: acts_on_population_of CL:0002410 ! pancreatic stellate cell -created_by: mah creation_date: 2010-11-05T03:04:50Z [Term] @@ -112495,14 +116702,12 @@ intersection_of: GO:0022857 ! transmembrane transporter activity intersection_of: has_primary_input CHEBI:83821 relationship: has_primary_input CHEBI:83821 relationship: part_of GO:0072337 ! modified amino acid transport -created_by: mah creation_date: 2010-11-11T11:50:31Z [Term] id: GO:0072359 name: circulatory system development namespace: biological_process -alt_id: GO:0072358 def: "The process whose specific outcome is the progression of the circulatory system over time, from its formation to the mature structure. The circulatory system is the organ system that passes nutrients (such as amino acids and electrolytes), gases, hormones, blood cells, etc. to and from cells in the body to help fight diseases and help stabilize body temperature and pH to maintain homeostasis." [GOC:mah, UBERON:0001009] subset: goslim_drosophila synonym: "cardiovascular system development" NARROW [] @@ -112510,7 +116715,6 @@ is_a: GO:0048731 ! system development intersection_of: GO:0048856 ! anatomical structure development intersection_of: results_in_development_of UBERON:0001009 ! circulatory system relationship: results_in_development_of UBERON:0001009 ! circulatory system -created_by: mah creation_date: 2010-11-16T11:27:39Z [Term] @@ -112523,7 +116727,6 @@ intersection_of: GO:0048856 ! anatomical structure development intersection_of: results_in_development_of UBERON:0006965 ! vascular cord relationship: part_of GO:0072359 ! circulatory system development relationship: results_in_development_of UBERON:0006965 ! vascular cord -created_by: mah creation_date: 2010-11-16T11:46:55Z [Term] @@ -112537,14 +116740,12 @@ is_a: GO:0051656 ! establishment of organelle localization intersection_of: GO:0046907 ! intracellular transport intersection_of: has_primary_input GO:0043226 ! organelle intersection_of: results_in_transport_along GO:0005874 ! microtubule -created_by: mah creation_date: 2010-12-01T04:59:11Z [Term] id: GO:0072488 name: ammonium transmembrane transport namespace: biological_process -alt_id: GO:0015696 def: "The process in which ammonium is transported across a membrane. Ammonium is the cation NH4+." [GOC:mah] comment: Note that this term is not intended for use in annotating lateral movement within membranes. synonym: "ammonia transport" BROAD [] @@ -112556,7 +116757,6 @@ intersection_of: has_primary_input CHEBI:28938 intersection_of: results_in_transport_across GO:0016020 ! membrane relationship: has_primary_input CHEBI:28938 property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/22228" xsd:anyURI -created_by: mah creation_date: 2010-12-10T10:29:57Z [Term] @@ -112565,7 +116765,6 @@ name: mesenchymal stem cell differentiation namespace: biological_process def: "The process in which a relatively unspecialized cell acquires specialized features of a mesenchymal stem cell. A mesenchymal stem cell is a cell that retains the ability to divide and proliferate throughout life to provide progenitor cells that can differentiate into specialized mesenchymal cells." [CL:0002452, GOC:BHF] is_a: GO:0048863 ! stem cell differentiation -created_by: mah creation_date: 2010-12-15T12:59:30Z [Term] @@ -112579,7 +116778,6 @@ intersection_of: GO:0048856 ! anatomical structure development intersection_of: results_in_development_of UBERON:0001343 ! seminiferous tubule of testis relationship: part_of GO:0008584 ! male gonad development relationship: results_in_development_of UBERON:0001343 ! seminiferous tubule of testis -created_by: mah creation_date: 2011-01-04T12:50:36Z [Term] @@ -112592,7 +116790,6 @@ is_a: GO:0001775 ! cell activation intersection_of: GO:0001775 ! cell activation intersection_of: has_primary_input CL:0000057 ! fibroblast relationship: has_primary_input CL:0000057 ! fibroblast -created_by: mah creation_date: 2011-01-14T04:35:08Z [Term] @@ -112604,7 +116801,6 @@ synonym: "Th17 immune response" EXACT [GOC:mah] is_a: BFO:0000003 is_a: GO:0002460 ! adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains relationship: has_participant CL:0000899 ! T-helper 17 cell -created_by: mah creation_date: 2011-01-17T11:13:53Z [Term] @@ -112619,7 +116815,6 @@ intersection_of: GO:0030154 ! cell differentiation intersection_of: results_in_acquisition_of_features_of CL:0000899 ! T-helper 17 cell relationship: part_of GO:0072538 ! T-helper 17 type immune response relationship: results_in_acquisition_of_features_of CL:0000899 ! T-helper 17 cell -created_by: mah creation_date: 2011-01-17T11:18:47Z [Term] @@ -112636,7 +116831,6 @@ is_a: GO:0099172 ! presynapse organization intersection_of: GO:0016043 ! cellular component organization intersection_of: results_in_organization_of GO:0043195 ! terminal bouton relationship: results_in_organization_of GO:0043195 ! terminal bouton -created_by: mah creation_date: 2011-01-25T04:09:35Z [Term] @@ -112647,12 +116841,11 @@ def: "A developmental process, independent of morphogenetic (shape) change, that comment: These processes continue to 60 DPA in Gossypium spp. synonym: "pancreatic B cell maturation" EXACT [CL:0000169, GOC:mah] synonym: "pancreatic beta cell maturation" EXACT [CL:0000169, GOC:mah] -is_a: GO:0002071 ! glandular epithelial cell maturation +is_a: GO:0002070 ! epithelial cell maturation intersection_of: GO:0021700 ! developmental maturation intersection_of: results_in_maturation_of CL:0000169 ! type B pancreatic cell relationship: part_of GO:0003323 ! type B pancreatic cell development relationship: results_in_maturation_of CL:0000169 ! type B pancreatic cell -created_by: mah creation_date: 2011-01-27T01:57:14Z [Term] @@ -112664,7 +116857,6 @@ is_a: GO:0050673 ! epithelial cell proliferation intersection_of: GO:0050673 ! epithelial cell proliferation intersection_of: part_of GO:0072576 ! liver morphogenesis relationship: part_of GO:0072576 ! liver morphogenesis -created_by: mah creation_date: 2011-02-02T03:37:50Z [Term] @@ -112677,7 +116869,6 @@ intersection_of: GO:0009653 ! anatomical structure morphogenesis intersection_of: results_in_morphogenesis_of UBERON:0002107 ! liver relationship: part_of GO:0001889 ! liver development relationship: results_in_morphogenesis_of UBERON:0002107 ! liver -created_by: mah creation_date: 2011-02-02T03:41:30Z [Term] @@ -112695,7 +116886,6 @@ is_a: GO:0006915 ! apoptotic process intersection_of: GO:0006915 ! apoptotic process intersection_of: occurs_in CL:0000115 ! endothelial cell relationship: occurs_in CL:0000115 ! endothelial cell -created_by: mah creation_date: 2011-02-02T03:56:24Z [Term] @@ -112706,11 +116896,10 @@ def: "The chemical reactions and pathways involving diatomic oxygen (O2)." [GOC: synonym: "diatomic oxygen metabolic process" EXACT [CHEBI:33263] synonym: "oxygen metabolism" EXACT [GOC:mah] is_a: BFO:0000003 -is_a: GO:0044237 ! cellular metabolic process +is_a: GO:0008152 ! metabolic process intersection_of: GO:0008152 ! metabolic process intersection_of: has_primary_input_or_output CHEBI:15379 relationship: has_primary_input_or_output CHEBI:15379 -created_by: mah creation_date: 2011-02-11T10:46:51Z [Term] @@ -112723,7 +116912,6 @@ is_a: GO:0033365 ! protein localization to organelle is_a: GO:0045184 ! establishment of protein localization intersection_of: GO:0045184 ! establishment of protein localization intersection_of: has_target_end_location GO:0043226 ! organelle -created_by: mah creation_date: 2011-02-14T01:56:51Z [Term] @@ -112738,7 +116926,6 @@ intersection_of: GO:0045185 ! maintenance of protein location intersection_of: occurs_in GO:0043226 ! organelle relationship: occurs_in GO:0043226 ! organelle relationship: part_of GO:0033365 ! protein localization to organelle -created_by: mah creation_date: 2011-02-14T02:09:13Z [Term] @@ -112753,15 +116940,12 @@ is_a: GO:0008104 ! protein localization is_a: GO:0051668 ! localization within membrane intersection_of: GO:0008104 ! protein localization intersection_of: has_target_end_location GO:0016020 ! membrane -created_by: mah creation_date: 2011-02-14T02:35:18Z [Term] id: GO:0072659 name: protein localization to plasma membrane namespace: biological_process -alt_id: GO:0072661 -alt_id: GO:0090002 def: "A process in which a protein is transported to, or maintained in, a specific location in the plasma membrane." [GOC:mah] subset: goslim_generic subset: goslim_pombe @@ -112776,7 +116960,6 @@ intersection_of: has_target_end_location GO:0005886 ! plasma membrane intersection_of: has_target_start_location GO:0005622 ! intracellular anatomical structure relationship: has_target_end_location GO:0005886 ! plasma membrane relationship: has_target_start_location GO:0005622 ! intracellular anatomical structure -created_by: tb creation_date: 2009-07-10T10:29:23Z [Term] @@ -112789,7 +116972,6 @@ is_a: GO:0033365 ! protein localization to organelle intersection_of: GO:0008104 ! protein localization intersection_of: has_target_end_location GO:0005773 ! vacuole relationship: has_target_end_location GO:0005773 ! vacuole -created_by: mah creation_date: 2011-02-14T02:55:35Z [Term] @@ -112802,7 +116984,6 @@ is_a: GO:0072594 ! establishment of protein localization to organelle is_a: GO:0072665 ! protein localization to vacuole intersection_of: GO:0045184 ! establishment of protein localization intersection_of: has_target_end_location GO:0005773 ! vacuole -created_by: mah creation_date: 2011-02-14T02:56:29Z [Term] @@ -112815,7 +116996,6 @@ intersection_of: GO:0045185 ! maintenance of protein location intersection_of: occurs_in GO:0005773 ! vacuole relationship: occurs_in GO:0005773 ! vacuole relationship: part_of GO:0072665 ! protein localization to vacuole -created_by: mah creation_date: 2011-02-14T02:56:57Z [Term] @@ -112829,7 +117009,6 @@ is_a: GO:0030316 ! osteoclast differentiation intersection_of: GO:0030154 ! cell differentiation intersection_of: results_in_acquisition_of_features_of CL:0000779 ! multinuclear osteoclast relationship: results_in_acquisition_of_features_of CL:0000779 ! multinuclear osteoclast -created_by: mah creation_date: 2011-02-22T02:10:38Z [Term] @@ -112841,7 +117020,6 @@ is_a: GO:0071674 ! mononuclear cell migration intersection_of: GO:0016477 ! cell migration intersection_of: results_in_movement_of CL:0000542 ! lymphocyte relationship: results_in_movement_of CL:0000542 ! lymphocyte -created_by: mah creation_date: 2011-02-22T03:38:12Z [Term] @@ -112853,7 +117031,6 @@ is_a: GO:0097530 ! granulocyte migration intersection_of: GO:0016477 ! cell migration intersection_of: results_in_movement_of CL:0000771 ! eosinophil relationship: results_in_movement_of CL:0000771 ! eosinophil -created_by: mah creation_date: 2011-02-22T03:39:31Z [Term] @@ -112868,7 +117045,6 @@ is_a: GO:0072676 ! lymphocyte migration intersection_of: GO:0016477 ! cell migration intersection_of: results_in_movement_of CL:0000084 ! T cell relationship: results_in_movement_of CL:0000084 ! T cell -created_by: mah creation_date: 2011-02-22T03:40:40Z [Term] @@ -112885,7 +117061,6 @@ is_a: GO:0072678 ! T cell migration intersection_of: GO:0016477 ! cell migration intersection_of: results_in_movement_of CL:0000893 ! thymocyte relationship: results_in_movement_of CL:0000893 ! thymocyte -created_by: mah creation_date: 2011-02-22T03:47:51Z [Term] @@ -112898,7 +117073,6 @@ is_a: GO:1990778 ! protein localization to cell periphery intersection_of: GO:0008104 ! protein localization intersection_of: has_target_end_location GO:0005938 ! cell cortex relationship: has_target_end_location GO:0005938 ! cell cortex -created_by: mah creation_date: 2012-04-11T01:16:33Z [Term] @@ -112911,7 +117085,6 @@ is_a: GO:0044380 ! protein localization to cytoskeleton intersection_of: GO:0008104 ! protein localization intersection_of: has_target_end_location GO:0015630 ! microtubule cytoskeleton relationship: has_target_end_location GO:0015630 ! microtubule cytoskeleton -created_by: mah creation_date: 2012-04-11T01:19:35Z [Term] @@ -113013,7 +117186,6 @@ is_a: GO:0019222 ! regulation of metabolic process intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0044238 ! primary metabolic process relationship: regulates GO:0044238 ! primary metabolic process -created_by: dhl creation_date: 2009-04-22T04:30:52Z [Term] @@ -113027,7 +117199,6 @@ is_a: GO:0048583 ! regulation of response to stimulus intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0006950 ! response to stress relationship: regulates GO:0006950 ! response to stress -created_by: dhl creation_date: 2009-05-06T04:51:28Z [Term] @@ -113041,7 +117212,6 @@ is_a: GO:0055082 ! intracellular chemical homeostasis intersection_of: GO:0055082 ! intracellular chemical homeostasis intersection_of: regulates_levels_of CHEBI:35238 relationship: regulates_levels_of CHEBI:35238 -created_by: dhl creation_date: 2010-01-27T04:47:27Z [Term] @@ -113053,9 +117223,19 @@ is_a: GO:2000241 ! regulation of reproductive process intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0009566 ! fertilization relationship: regulates GO:0009566 ! fertilization -created_by: dhl creation_date: 2010-09-01T03:44:27Z +[Term] +id: GO:0080164 +name: regulation of nitric oxide metabolic process +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving nitric oxide, nitrogen monoxide (NO), a colorless gas only slightly soluble in water." [GOC:DHL] +is_a: GO:0019222 ! regulation of metabolic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0046209 ! nitric oxide metabolic process +relationship: regulates GO:0046209 ! nitric oxide metabolic process +creation_date: 2010-09-23T04:02:50Z + [Term] id: GO:0080171 name: lytic vacuole organization @@ -113069,7 +117249,6 @@ is_a: GO:0007033 ! vacuole organization intersection_of: GO:0016043 ! cellular component organization intersection_of: results_in_organization_of GO:0000323 ! lytic vacuole relationship: results_in_organization_of GO:0000323 ! lytic vacuole -created_by: dhl creation_date: 2011-04-25T04:40:46Z [Term] @@ -113082,7 +117261,6 @@ is_a: GO:0030198 ! extracellular matrix organization intersection_of: GO:0022607 ! cellular component assembly intersection_of: results_in_assembly_of GO:0031012 ! extracellular matrix relationship: results_in_assembly_of GO:0031012 ! extracellular matrix -created_by: jl creation_date: 2010-07-14T12:52:49Z [Term] @@ -113094,7 +117272,6 @@ is_a: GO:0001508 ! action potential intersection_of: GO:0001508 ! action potential intersection_of: occurs_in CL:0000746 ! cardiac muscle cell relationship: occurs_in CL:0000746 ! cardiac muscle cell -created_by: tb creation_date: 2011-11-10T07:45:11Z [Term] @@ -113106,7 +117283,6 @@ is_a: GO:0086001 ! cardiac muscle cell action potential intersection_of: GO:0086001 ! cardiac muscle cell action potential intersection_of: part_of GO:0086003 ! cardiac muscle cell contraction relationship: part_of GO:0086003 ! cardiac muscle cell contraction -created_by: tb creation_date: 2011-11-10T07:45:11Z [Term] @@ -113117,7 +117293,6 @@ def: "The actin filament-based process in which cytoplasmic actin filaments slid is_a: BFO:0000003 is_a: GO:0070252 ! actin-mediated cell contraction relationship: part_of GO:0060048 ! cardiac muscle contraction -created_by: tb creation_date: 2011-11-10T07:48:15Z [Term] @@ -113130,7 +117305,6 @@ is_a: GO:1903115 ! regulation of actin filament-based movement intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0086003 ! cardiac muscle cell contraction relationship: regulates GO:0086003 ! cardiac muscle cell contraction -created_by: tb creation_date: 2011-11-10T07:49:10Z [Term] @@ -113142,7 +117316,6 @@ is_a: GO:0086002 ! cardiac muscle cell action potential involved in contraction intersection_of: GO:0001508 ! action potential intersection_of: occurs_in CL:0002131 ! regular ventricular cardiac myocyte relationship: occurs_in CL:0002131 ! regular ventricular cardiac myocyte -created_by: tb creation_date: 2011-11-10T07:59:36Z [Term] @@ -113155,7 +117328,6 @@ intersection_of: GO:0001508 ! action potential intersection_of: occurs_in CL:0002129 ! regular atrial cardiac myocyte relationship: occurs_in CL:0002129 ! regular atrial cardiac myocyte relationship: part_of GO:0086026 ! atrial cardiac muscle cell to AV node cell signaling -created_by: tb creation_date: 2011-11-10T08:49:13Z [Term] @@ -113172,7 +117344,6 @@ intersection_of: GO:0001508 ! action potential intersection_of: occurs_in CL:1000409 ! myocyte of sinoatrial node relationship: occurs_in CL:1000409 ! myocyte of sinoatrial node relationship: part_of GO:0086018 ! SA node cell to atrial cardiac muscle cell signaling -created_by: tb creation_date: 2011-11-10T08:50:15Z [Term] @@ -113187,7 +117358,6 @@ intersection_of: GO:0001508 ! action potential intersection_of: occurs_in CL:1000410 ! myocyte of atrioventricular node relationship: occurs_in CL:1000410 ! myocyte of atrioventricular node relationship: part_of GO:0086027 ! AV node cell to bundle of His cell signaling -created_by: tb creation_date: 2011-11-10T08:58:56Z [Term] @@ -113200,7 +117370,6 @@ intersection_of: GO:0001508 ! action potential intersection_of: occurs_in CL:0002068 ! Purkinje myocyte relationship: occurs_in CL:0002068 ! Purkinje myocyte relationship: part_of GO:0086029 ! Purkinje myocyte to ventricular cardiac muscle cell signaling -created_by: tb creation_date: 2011-11-10T08:58:56Z [Term] @@ -113215,7 +117384,6 @@ synonym: "sinoatrial node cardiomyocyte to atrial cardiomyocyte signalling" EXAC synonym: "sinus node cardiomyocyte to atrial cardiomyocyte signalling" NARROW [] is_a: GO:0086019 ! cell-cell signaling involved in cardiac conduction is_a: GO:0086070 ! SA node cell to atrial cardiac muscle cell communication -created_by: tb creation_date: 2011-11-10T09:15:01Z [Term] @@ -113228,7 +117396,6 @@ is_a: GO:0007267 ! cell-cell signaling is_a: GO:0086065 ! cell communication involved in cardiac conduction intersection_of: GO:0007267 ! cell-cell signaling intersection_of: part_of GO:0061337 ! cardiac conduction -created_by: dph creation_date: 2011-11-16T03:43:52Z [Term] @@ -113241,7 +117408,6 @@ synonym: "atrial cardiomyocyte to AV node cell signaling" EXACT [] synonym: "atrial cardiomyocyte to AV node cell signalling" EXACT [GOC:mah] is_a: GO:0086019 ! cell-cell signaling involved in cardiac conduction is_a: GO:0086066 ! atrial cardiac muscle cell to AV node cell communication -created_by: tb creation_date: 2011-11-11T02:02:14Z [Term] @@ -113253,7 +117419,6 @@ synonym: "atrioventricular node to bundle of His cell signaling" EXACT [] synonym: "AV node cell to bundle of His cell signalling" EXACT [GOC:mah] is_a: GO:0086019 ! cell-cell signaling involved in cardiac conduction is_a: GO:0086067 ! AV node cell to bundle of His cell communication -created_by: tb creation_date: 2011-11-11T02:02:14Z [Term] @@ -113265,7 +117430,6 @@ synonym: "bundle of His cardiac muscle cell to Purkinje myocyte signaling" EXACT synonym: "bundle of His cardiac muscle cell to Purkinje myocyte signalling" EXACT [GOC:mah] is_a: GO:0086019 ! cell-cell signaling involved in cardiac conduction is_a: GO:0086069 ! bundle of His cell to Purkinje myocyte communication -created_by: tb creation_date: 2011-11-11T02:02:14Z [Term] @@ -113281,7 +117445,6 @@ intersection_of: has_end_location CL:2000046 ! ventricular cardiac muscle cell intersection_of: has_start_location CL:0002068 ! Purkinje myocyte relationship: has_end_location CL:2000046 ! ventricular cardiac muscle cell relationship: has_start_location CL:0002068 ! Purkinje myocyte -created_by: tb creation_date: 2011-11-11T02:02:14Z [Term] @@ -113295,7 +117458,6 @@ intersection_of: GO:0001508 ! action potential intersection_of: occurs_in CL:0010005 ! atrioventricular bundle cell relationship: occurs_in CL:0010005 ! atrioventricular bundle cell relationship: part_of GO:0086028 ! bundle of His cell to Purkinje myocyte signaling -created_by: dph creation_date: 2011-11-15T12:01:18Z [Term] @@ -113308,7 +117470,6 @@ is_a: GO:0007154 ! cell communication intersection_of: GO:0007154 ! cell communication intersection_of: part_of GO:0061337 ! cardiac conduction relationship: part_of GO:0061337 ! cardiac conduction -created_by: dph creation_date: 2011-11-22T08:57:02Z [Term] @@ -113319,7 +117480,6 @@ def: "The process that mediates interactions between an atrial cardiomyocyte and synonym: "atrial cardiomyocyte to atrioventricular node cell communication" EXACT [] synonym: "atrial cardiomyocyte to AV node cell communication" EXACT [] is_a: GO:0086065 ! cell communication involved in cardiac conduction -created_by: dph creation_date: 2011-11-22T09:05:09Z [Term] @@ -113329,7 +117489,6 @@ namespace: biological_process def: "The process that mediates interactions between an AV node cell and its surroundings that contributes to the process of the AV node cell communicating with a bundle of His cell in cardiac conduction. Encompasses interactions such as signaling or attachment between one cell and another cell, between a cell and an extracellular matrix, or between a cell and any other aspect of its environment." [GOC:BHF, GOC:mtg_cardiac_conduct_nov11] synonym: "atrioventricular node cell to bundle of His cell communication" EXACT [] is_a: GO:0086065 ! cell communication involved in cardiac conduction -created_by: dph creation_date: 2011-11-22T09:11:44Z [Term] @@ -113338,7 +117497,6 @@ name: Purkinje myocyte to ventricular cardiac muscle cell communication namespace: biological_process def: "The process that mediates interactions between a Purkinje myocyte and its surroundings that contributes to the process of the Purkinje myocyte communicating with a ventricular cardiac muscle cell in cardiac conduction. Encompasses interactions such as signaling or attachment between one cell and another cell, between a cell and an extracellular matrix, or between a cell and any other aspect of its environment." [GOC:BHF, GOC:mtg_cardiac_conduct_nov11] is_a: GO:0086065 ! cell communication involved in cardiac conduction -created_by: dph creation_date: 2011-11-22T09:14:49Z [Term] @@ -113353,7 +117511,6 @@ synonym: "bundle of His myocyte to atrioventricular junction myocyte" NARROW [] synonym: "ventricular conduction system cell to cell communication" EXACT [] is_a: GO:0086065 ! cell communication involved in cardiac conduction property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/20731" xsd:anyURI -created_by: dph creation_date: 2011-11-22T09:18:49Z [Term] @@ -113367,7 +117524,6 @@ synonym: "SAN cardiomyocyte to atrial cardiomyocyte communication" EXACT [] synonym: "sinoatrial node cardiomyocyte to atrial cardiomyocyte communication" EXACT [] synonym: "sinus node cardiomyocyte to atrial cardiomyocyte communication" NARROW [] is_a: GO:0086065 ! cell communication involved in cardiac conduction -created_by: dph creation_date: 2011-11-22T09:32:45Z [Term] @@ -113383,7 +117539,6 @@ is_a: GO:0007213 ! G protein-coupled acetylcholine receptor signaling pathway is_a: GO:0086103 ! G protein-coupled receptor signaling pathway involved in heart process intersection_of: GO:0007213 ! G protein-coupled acetylcholine receptor signaling pathway intersection_of: part_of GO:0003015 ! heart process -created_by: bf [Term] id: GO:0086103 @@ -113398,7 +117553,6 @@ is_a: GO:0007186 ! G protein-coupled receptor signaling pathway intersection_of: GO:0007186 ! G protein-coupled receptor signaling pathway intersection_of: part_of GO:0003015 ! heart process relationship: part_of GO:0003015 ! heart process -created_by: bf creation_date: 2012-03-19T01:28:23Z [Term] @@ -113444,9 +117598,6 @@ relationship: has_primary_input CHEBI:57595 id: GO:0089718 name: amino acid import across plasma membrane namespace: biological_process -alt_id: GO:0043092 -alt_id: GO:0044745 -alt_id: GO:1902837 def: "The directed movement of an amino acid from outside of a cell, across the plasma membrane and into the cytosol." [GOC:krc, PMID:8195186] synonym: "amino acid import into cell" EXACT [] synonym: "amino acid transmembrane import" BROAD [] @@ -113459,7 +117610,6 @@ intersection_of: has_primary_input CHEBI:35238 intersection_of: has_target_end_location GO:0005829 ! cytosol intersection_of: has_target_start_location GO:0005576 ! extracellular region intersection_of: results_in_transport_across GO:0005886 ! plasma membrane -created_by: jl creation_date: 2012-11-14T14:21:41Z [Term] @@ -113474,7 +117624,6 @@ intersection_of: results_in_formation_of UBERON:0004341 ! primitive streak relationship: part_of GO:0001702 ! gastrulation with mouth forming second relationship: part_of GO:0009948 ! anterior/posterior axis specification relationship: results_in_formation_of UBERON:0004341 ! primitive streak -created_by: tb creation_date: 2009-07-29T10:31:31Z [Term] @@ -113487,7 +117636,6 @@ is_a: GO:1902622 ! regulation of neutrophil migration intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0030593 ! neutrophil chemotaxis relationship: regulates GO:0030593 ! neutrophil chemotaxis -created_by: tb creation_date: 2009-08-03T10:09:34Z [Term] @@ -113501,7 +117649,6 @@ is_a: GO:1902624 ! positive regulation of neutrophil migration intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0030593 ! neutrophil chemotaxis relationship: positively_regulates GO:0030593 ! neutrophil chemotaxis -created_by: tb creation_date: 2009-08-03T10:12:23Z [Term] @@ -113515,7 +117662,6 @@ is_a: GO:1902623 ! negative regulation of neutrophil migration intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0030593 ! neutrophil chemotaxis relationship: negatively_regulates GO:0030593 ! neutrophil chemotaxis -created_by: tb creation_date: 2009-08-03T10:13:09Z [Term] @@ -113528,7 +117674,6 @@ is_a: GO:0071675 ! regulation of mononuclear cell migration intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0002548 ! monocyte chemotaxis relationship: regulates GO:0002548 ! monocyte chemotaxis -created_by: tb creation_date: 2009-08-03T10:17:03Z [Term] @@ -113542,7 +117687,6 @@ is_a: GO:0090025 ! regulation of monocyte chemotaxis intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0002548 ! monocyte chemotaxis relationship: positively_regulates GO:0002548 ! monocyte chemotaxis -created_by: tb creation_date: 2009-08-03T10:18:54Z [Term] @@ -113556,7 +117700,6 @@ is_a: GO:0090025 ! regulation of monocyte chemotaxis intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0002548 ! monocyte chemotaxis relationship: negatively_regulates GO:0002548 ! monocyte chemotaxis -created_by: tb creation_date: 2009-08-03T10:19:40Z [Term] @@ -113566,7 +117709,6 @@ namespace: biological_process def: "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of steroid hormones,compounds with a 1, 2, cyclopentanoperhydrophenanthrene nucleus that act as hormones." [GOC:dph, GOC:tb] is_a: GO:0046885 ! regulation of hormone biosynthetic process is_a: GO:0050810 ! regulation of steroid biosynthetic process -created_by: tb creation_date: 2009-08-03T10:38:27Z [Term] @@ -113577,7 +117719,6 @@ def: "Any process that increases the frequency, rate or extent of the chemical r is_a: GO:0010893 ! positive regulation of steroid biosynthetic process is_a: GO:0046886 ! positive regulation of hormone biosynthetic process is_a: GO:0090030 ! regulation of steroid hormone biosynthetic process -created_by: tb creation_date: 2009-08-03T10:40:32Z [Term] @@ -113588,7 +117729,6 @@ def: "Any process that decreases the frequency, rate or extent of the chemical r is_a: GO:0010894 ! negative regulation of steroid biosynthetic process is_a: GO:0032353 ! negative regulation of hormone biosynthetic process is_a: GO:0090030 ! regulation of steroid hormone biosynthetic process -created_by: tb creation_date: 2009-08-03T10:41:35Z [Term] @@ -113601,7 +117741,6 @@ is_a: GO:0031116 ! positive regulation of microtubule polymerization intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0007020 ! microtubule nucleation relationship: positively_regulates GO:0007020 ! microtubule nucleation -created_by: tb creation_date: 2009-08-12T11:33:09Z [Term] @@ -113614,7 +117753,6 @@ is_a: GO:0045787 ! positive regulation of cell cycle intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0022402 ! cell cycle process relationship: positively_regulates GO:0022402 ! cell cycle process -created_by: tb creation_date: 2009-09-09T11:39:52Z [Term] @@ -113626,7 +117764,6 @@ is_a: GO:0044087 ! regulation of cellular component biogenesis intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0042254 ! ribosome biogenesis relationship: regulates GO:0042254 ! ribosome biogenesis -created_by: tb creation_date: 2009-09-11T10:32:17Z [Term] @@ -113639,7 +117776,6 @@ is_a: GO:0090069 ! regulation of ribosome biogenesis intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0042254 ! ribosome biogenesis relationship: positively_regulates GO:0042254 ! ribosome biogenesis -created_by: tb creation_date: 2009-09-11T10:32:17Z [Term] @@ -113652,7 +117788,6 @@ is_a: GO:0090069 ! regulation of ribosome biogenesis intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0042254 ! ribosome biogenesis relationship: negatively_regulates GO:0042254 ! ribosome biogenesis -created_by: tb creation_date: 2009-09-11T10:32:17Z [Term] @@ -113664,7 +117799,6 @@ is_a: GO:0030154 ! cell differentiation intersection_of: GO:0030154 ! cell differentiation intersection_of: results_in_acquisition_of_features_of CL:0000891 ! foam cell relationship: results_in_acquisition_of_features_of CL:0000891 ! foam cell -created_by: tb creation_date: 2009-09-15T03:46:30Z [Term] @@ -113677,7 +117811,6 @@ intersection_of: GO:0030154 ! cell differentiation intersection_of: results_in_acquisition_of_features_of CL:0000892 ! smooth muscle cell derived foam cell relationship: results_in_acquisition_of_features_of CL:0000892 ! smooth muscle cell derived foam cell property_value: RO:0002161 NCBITaxon:4751 -created_by: tb creation_date: 2009-09-15T03:48:10Z [Term] @@ -113689,7 +117822,6 @@ is_a: GO:0051049 ! regulation of transport intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0015833 ! peptide transport relationship: regulates GO:0015833 ! peptide transport -created_by: tb creation_date: 2009-10-23T11:21:38Z [Term] @@ -113702,7 +117834,6 @@ is_a: GO:1903055 ! positive regulation of extracellular matrix organization intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0022617 ! extracellular matrix disassembly relationship: positively_regulates GO:0022617 ! extracellular matrix disassembly -created_by: tb creation_date: 2009-11-04T10:03:25Z [Term] @@ -113715,7 +117846,6 @@ intersection_of: GO:0048856 ! anatomical structure development intersection_of: results_in_development_of UBERON:0001844 ! cochlea relationship: part_of GO:0048839 ! inner ear development relationship: results_in_development_of UBERON:0001844 ! cochlea -created_by: tb creation_date: 2009-11-18T11:42:15Z [Term] @@ -113730,7 +117860,6 @@ intersection_of: results_in_morphogenesis_of UBERON:0001844 ! cochlea relationship: part_of GO:0042472 ! inner ear morphogenesis relationship: part_of GO:0090102 ! cochlea development relationship: results_in_morphogenesis_of UBERON:0001844 ! cochlea -created_by: tb creation_date: 2009-11-18T11:45:11Z [Term] @@ -113744,7 +117873,6 @@ intersection_of: GO:0030154 ! cell differentiation intersection_of: results_in_acquisition_of_features_of CL:0005019 ! pancreatic epsilon cell relationship: part_of GO:0031018 ! endocrine pancreas development relationship: results_in_acquisition_of_features_of CL:0005019 ! pancreatic epsilon cell -created_by: tb creation_date: 2009-11-18T11:48:52Z [Term] @@ -113752,21 +117880,31 @@ id: GO:0090105 name: pancreatic E cell development namespace: biological_process def: "The process whose specific outcome is the progression of a pancreatic E cell over time, from its formation to the mature structure." [GOC:dph, GOC:tb] -is_a: GO:0002068 ! glandular epithelial cell development +is_a: GO:0002064 ! epithelial cell development intersection_of: GO:0048468 ! cell development intersection_of: results_in_development_of CL:0005019 ! pancreatic epsilon cell relationship: part_of GO:0090104 ! pancreatic epsilon cell differentiation relationship: results_in_development_of CL:0005019 ! pancreatic epsilon cell -created_by: tb creation_date: 2009-11-18T11:51:00Z +[Term] +id: GO:0090109 +name: regulation of cell-substrate junction assembly +namespace: biological_process +def: "Any process that modulates the rate, frequency, or extent of cell-substrate junction assembly. Cell-substrate junction assembly is the aggregation, arrangement and bonding together of a set of components to form a junction between a cell and its substrate." [GOC:dph, GOC:tb] +is_a: GO:0150116 ! regulation of cell-substrate junction organization +is_a: GO:1901888 ! regulation of cell junction assembly +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0007044 ! cell-substrate junction assembly +relationship: regulates GO:0007044 ! cell-substrate junction assembly +creation_date: 2009-11-25T11:00:58Z + [Term] id: GO:0090130 name: tissue migration namespace: biological_process def: "The process in which the population of cells that make up a tissue undergo directed movement." [GOC:ascb_2009, GOC:dph, GOC:tb] is_a: GO:0032501 ! multicellular organismal process -created_by: tb creation_date: 2009-12-07T03:13:55Z [Term] @@ -113776,7 +117914,6 @@ namespace: biological_process def: "The process in which the population of cells that make up a mesenchyme undergo directed movement." [GOC:ascb_2009, GOC:dph, GOC:tb] is_a: GO:0090130 ! tissue migration relationship: part_of GO:0072132 ! mesenchyme morphogenesis -created_by: tb creation_date: 2009-12-07T03:15:17Z [Term] @@ -113785,7 +117922,6 @@ name: epithelium migration namespace: biological_process def: "The process in which the population of cells that make up an epithelium undergo directed movement." [GOC:ascb_2009, GOC:dph, GOC:tb] is_a: GO:0090130 ! tissue migration -created_by: tb creation_date: 2009-12-07T03:19:34Z [Term] @@ -113798,7 +117934,6 @@ is_a: GO:0032956 ! regulation of actin cytoskeleton organization is_a: GO:0098609 ! cell-cell adhesion intersection_of: GO:0098609 ! cell-cell adhesion intersection_of: regulates GO:0030036 ! actin cytoskeleton organization -created_by: tb creation_date: 2009-12-08T02:05:00Z [Term] @@ -113812,7 +117947,6 @@ is_a: GO:0045184 ! establishment of protein localization is_a: GO:0072657 ! protein localization to membrane intersection_of: GO:0045184 ! establishment of protein localization intersection_of: has_target_end_location GO:0016020 ! membrane -created_by: tb creation_date: 2009-12-08T03:18:51Z [Term] @@ -113828,7 +117962,6 @@ intersection_of: has_target_end_location GO:0005764 ! lysosome intersection_of: has_target_start_location GO:0005794 ! Golgi apparatus intersection_of: occurs_in GO:0005829 ! cytosol relationship: has_target_end_location GO:0005764 ! lysosome -created_by: tb creation_date: 2009-12-08T08:35:13Z [Term] @@ -113841,7 +117974,6 @@ is_a: GO:0030010 ! establishment of cell polarity intersection_of: GO:0030010 ! establishment of cell polarity intersection_of: occurs_in CL:0000066 ! epithelial cell relationship: occurs_in CL:0000066 ! epithelial cell -created_by: tb creation_date: 2009-12-08T08:58:27Z [Term] @@ -113856,7 +117988,6 @@ intersection_of: GO:0022411 ! cellular component disassembly intersection_of: results_in_disassembly_of GO:0005794 ! Golgi apparatus relationship: part_of GO:0048313 ! Golgi inheritance relationship: results_in_disassembly_of GO:0005794 ! Golgi apparatus -created_by: tb creation_date: 2009-12-08T09:15:11Z [Term] @@ -113868,7 +117999,6 @@ synonym: "Golgi apparatus reassembly" EXACT [] is_a: GO:0007030 ! Golgi organization is_a: GO:0022607 ! cellular component assembly relationship: part_of GO:0048313 ! Golgi inheritance -created_by: tb creation_date: 2009-12-08T09:15:11Z [Term] @@ -113880,7 +118010,6 @@ is_a: GO:1903358 ! regulation of Golgi organization intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0048313 ! Golgi inheritance relationship: regulates GO:0048313 ! Golgi inheritance -created_by: tb creation_date: 2009-12-11T10:21:59Z [Term] @@ -113893,7 +118022,6 @@ intersection_of: GO:0009653 ! anatomical structure morphogenesis intersection_of: results_in_maturation_of CL:0000138 ! chondrocyte relationship: part_of GO:0002063 ! chondrocyte development relationship: results_in_maturation_of CL:0000138 ! chondrocyte -created_by: tb creation_date: 2009-12-11T10:36:02Z [Term] @@ -113906,7 +118034,6 @@ is_a: GO:0061025 ! membrane fusion intersection_of: GO:0061025 ! membrane fusion intersection_of: results_in_fusion_of GO:0031090 ! organelle membrane relationship: results_in_fusion_of GO:0031090 ! organelle membrane -created_by: tb creation_date: 2009-12-11T11:44:58Z [Term] @@ -113919,7 +118046,6 @@ is_a: GO:0050793 ! regulation of developmental process intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0001822 ! kidney development relationship: regulates GO:0001822 ! kidney development -created_by: tb creation_date: 2009-12-18T10:50:56Z [Term] @@ -113934,7 +118060,6 @@ is_a: GO:0090183 ! regulation of kidney development intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0001822 ! kidney development relationship: positively_regulates GO:0001822 ! kidney development -created_by: tb creation_date: 2009-12-18T10:52:01Z [Term] @@ -113949,7 +118074,6 @@ is_a: GO:0090183 ! regulation of kidney development intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0001822 ! kidney development relationship: negatively_regulates GO:0001822 ! kidney development -created_by: tb creation_date: 2009-12-18T10:58:45Z [Term] @@ -113964,7 +118088,6 @@ is_a: GO:2000027 ! regulation of animal organ morphogenesis intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0001658 ! branching involved in ureteric bud morphogenesis relationship: regulates GO:0001658 ! branching involved in ureteric bud morphogenesis -created_by: tb creation_date: 2009-12-18T11:11:17Z [Term] @@ -113978,7 +118101,6 @@ is_a: GO:1905332 ! positive regulation of morphogenesis of an epithelium intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0001658 ! branching involved in ureteric bud morphogenesis relationship: positively_regulates GO:0001658 ! branching involved in ureteric bud morphogenesis -created_by: tb creation_date: 2009-12-18T11:11:17Z [Term] @@ -113992,7 +118114,6 @@ is_a: GO:1905331 ! negative regulation of morphogenesis of an epithelium intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0001658 ! branching involved in ureteric bud morphogenesis relationship: negatively_regulates GO:0001658 ! branching involved in ureteric bud morphogenesis -created_by: tb creation_date: 2009-12-18T11:11:17Z [Term] @@ -114004,7 +118125,6 @@ is_a: GO:0090183 ! regulation of kidney development intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0032835 ! glomerulus development relationship: regulates GO:0032835 ! glomerulus development -created_by: tb creation_date: 2009-12-18T11:17:13Z [Term] @@ -114017,7 +118137,6 @@ is_a: GO:0090192 ! regulation of glomerulus development intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0032835 ! glomerulus development relationship: positively_regulates GO:0032835 ! glomerulus development -created_by: tb creation_date: 2009-12-18T11:17:13Z [Term] @@ -114030,7 +118149,6 @@ is_a: GO:0090192 ! regulation of glomerulus development intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0032835 ! glomerulus development relationship: negatively_regulates GO:0032835 ! glomerulus development -created_by: tb creation_date: 2009-12-18T11:17:13Z [Term] @@ -114044,7 +118162,6 @@ intersection_of: GO:0048589 ! developmental growth intersection_of: results_in_morphogenesis_of UBERON:0004021 ! spongiotrophoblast layer relationship: part_of GO:0060712 ! spongiotrophoblast layer development relationship: results_in_morphogenesis_of UBERON:0004021 ! spongiotrophoblast layer -created_by: tb creation_date: 2010-01-08T12:10:44Z [Term] @@ -114056,7 +118173,6 @@ is_a: GO:0044057 ! regulation of system process intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0003012 ! muscle system process relationship: regulates GO:0003012 ! muscle system process -created_by: tb creation_date: 2010-02-03T11:48:13Z [Term] @@ -114068,7 +118184,6 @@ is_a: GO:0090276 ! regulation of peptide hormone secretion intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0070253 ! somatostatin secretion relationship: regulates GO:0070253 ! somatostatin secretion -created_by: tb creation_date: 2010-02-05T02:54:14Z [Term] @@ -114081,7 +118196,6 @@ is_a: GO:0090277 ! positive regulation of peptide hormone secretion intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0070253 ! somatostatin secretion relationship: positively_regulates GO:0070253 ! somatostatin secretion -created_by: tb creation_date: 2010-02-05T02:54:14Z [Term] @@ -114094,7 +118208,6 @@ is_a: GO:0090278 ! negative regulation of peptide hormone secretion intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0070253 ! somatostatin secretion relationship: negatively_regulates GO:0070253 ! somatostatin secretion -created_by: tb creation_date: 2010-02-05T02:54:14Z [Term] @@ -114107,7 +118220,6 @@ is_a: GO:0046883 ! regulation of hormone secretion intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0030072 ! peptide hormone secretion relationship: regulates GO:0030072 ! peptide hormone secretion -created_by: tb creation_date: 2010-02-05T02:56:39Z [Term] @@ -114121,7 +118233,6 @@ is_a: GO:0090276 ! regulation of peptide hormone secretion intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0030072 ! peptide hormone secretion relationship: positively_regulates GO:0030072 ! peptide hormone secretion -created_by: tb creation_date: 2010-02-05T02:56:39Z [Term] @@ -114135,7 +118246,6 @@ is_a: GO:0090276 ! regulation of peptide hormone secretion intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0030072 ! peptide hormone secretion relationship: negatively_regulates GO:0030072 ! peptide hormone secretion -created_by: tb creation_date: 2010-02-05T02:56:39Z [Term] @@ -114148,7 +118258,6 @@ is_a: GO:0051924 ! regulation of calcium ion transport intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0070509 ! calcium ion import relationship: regulates GO:0070509 ! calcium ion import -created_by: tb creation_date: 2010-02-08T05:11:20Z [Term] @@ -114162,7 +118271,6 @@ is_a: GO:0090279 ! regulation of calcium ion import intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0070509 ! calcium ion import relationship: positively_regulates GO:0070509 ! calcium ion import -created_by: tb creation_date: 2010-02-08T05:11:20Z [Term] @@ -114176,7 +118284,6 @@ is_a: GO:0090279 ! regulation of calcium ion import intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0070509 ! calcium ion import relationship: negatively_regulates GO:0070509 ! calcium ion import -created_by: tb creation_date: 2010-02-08T05:11:20Z [Term] @@ -114188,7 +118295,6 @@ is_a: GO:0070663 ! regulation of leukocyte proliferation intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0002158 ! osteoclast proliferation relationship: regulates GO:0002158 ! osteoclast proliferation -created_by: tb creation_date: 2010-02-18T03:11:03Z [Term] @@ -114201,7 +118307,6 @@ is_a: GO:0090289 ! regulation of osteoclast proliferation intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0002158 ! osteoclast proliferation relationship: positively_regulates GO:0002158 ! osteoclast proliferation -created_by: tb creation_date: 2010-02-18T03:11:03Z [Term] @@ -114214,7 +118319,6 @@ is_a: GO:0090289 ! regulation of osteoclast proliferation intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0002158 ! osteoclast proliferation relationship: negatively_regulates GO:0002158 ! osteoclast proliferation -created_by: tb creation_date: 2010-02-18T03:11:03Z [Term] @@ -114227,7 +118331,6 @@ is_a: GO:0022603 ! regulation of anatomical structure morphogenesis intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0014029 ! neural crest formation relationship: regulates GO:0014029 ! neural crest formation -created_by: tb creation_date: 2010-03-12T04:08:26Z [Term] @@ -114240,7 +118343,6 @@ is_a: GO:0090299 ! regulation of neural crest formation intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0014029 ! neural crest formation relationship: positively_regulates GO:0014029 ! neural crest formation -created_by: tb creation_date: 2010-03-12T04:08:26Z [Term] @@ -114253,7 +118355,6 @@ is_a: GO:0090299 ! regulation of neural crest formation intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0014029 ! neural crest formation relationship: negatively_regulates GO:0014029 ! neural crest formation -created_by: tb creation_date: 2010-03-12T04:08:26Z [Term] @@ -114266,7 +118367,6 @@ is_a: GO:1903036 ! positive regulation of response to wounding intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0042060 ! wound healing relationship: positively_regulates GO:0042060 ! wound healing -created_by: tb creation_date: 2010-03-22T02:12:03Z [Term] @@ -114283,7 +118383,6 @@ intersection_of: has_primary_input_or_output CHEBI:33696 relationship: has_primary_input_or_output CHEBI:33696 property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/26133" xsd:anyURI property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27052" xsd:anyURI -created_by: tb creation_date: 2010-04-07T10:18:47Z [Term] @@ -114297,7 +118396,6 @@ is_a: GO:0051222 ! positive regulation of protein transport intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0006886 ! intracellular protein transport relationship: positively_regulates GO:0006886 ! intracellular protein transport -created_by: tb creation_date: 2010-04-16T03:45:07Z [Term] @@ -114311,7 +118409,6 @@ is_a: GO:0051224 ! negative regulation of protein transport intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0006886 ! intracellular protein transport relationship: negatively_regulates GO:0006886 ! intracellular protein transport -created_by: tb creation_date: 2010-04-16T03:45:07Z [Term] @@ -114324,7 +118421,6 @@ is_a: GO:0019222 ! regulation of metabolic process intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0006801 ! superoxide metabolic process relationship: regulates GO:0006801 ! superoxide metabolic process -created_by: tb creation_date: 2010-05-06T02:29:05Z [Term] @@ -114337,7 +118433,6 @@ is_a: GO:0050795 ! regulation of behavior intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0031987 ! locomotion involved in locomotory behavior relationship: regulates GO:0031987 ! locomotion involved in locomotory behavior -created_by: tb creation_date: 2010-05-14T10:24:29Z [Term] @@ -114351,7 +118446,6 @@ is_a: GO:0090325 ! regulation of locomotion involved in locomotory behavior intersection_of: GO:0050789 ! regulation of biological process intersection_of: positively_regulates GO:0031987 ! locomotion involved in locomotory behavior relationship: positively_regulates GO:0031987 ! locomotion involved in locomotory behavior -created_by: tb creation_date: 2010-05-14T10:26:58Z [Term] @@ -114365,7 +118459,6 @@ is_a: GO:0090325 ! regulation of locomotion involved in locomotory behavior intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0031987 ! locomotion involved in locomotory behavior relationship: negatively_regulates GO:0031987 ! locomotion involved in locomotory behavior -created_by: tb creation_date: 2010-05-14T10:26:58Z [Term] @@ -114379,7 +118472,6 @@ is_a: GO:0050795 ! regulation of behavior intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0008355 ! olfactory learning relationship: regulates GO:0008355 ! olfactory learning -created_by: tb creation_date: 2010-05-14T10:37:22Z [Term] @@ -114391,7 +118483,6 @@ is_a: GO:0045598 ! regulation of fat cell differentiation intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0050873 ! brown fat cell differentiation relationship: regulates GO:0050873 ! brown fat cell differentiation -created_by: tb creation_date: 2010-06-01T03:16:57Z [Term] @@ -114404,7 +118495,6 @@ is_a: GO:0090335 ! regulation of brown fat cell differentiation intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0050873 ! brown fat cell differentiation relationship: positively_regulates GO:0050873 ! brown fat cell differentiation -created_by: tb creation_date: 2010-06-01T03:19:26Z [Term] @@ -114420,7 +118510,6 @@ is_a: GO:0065007 ! biological regulation intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0060079 ! excitatory postsynaptic potential relationship: negatively_regulates GO:0060079 ! excitatory postsynaptic potential -created_by: tb creation_date: 2010-12-15T01:43:12Z [Term] @@ -114432,7 +118521,6 @@ is_a: GO:0002067 ! glandular epithelial cell differentiation intersection_of: GO:0030154 ! cell differentiation intersection_of: results_in_acquisition_of_features_of CL:0000622 ! acinar cell relationship: results_in_acquisition_of_features_of CL:0000622 ! acinar cell -created_by: tb creation_date: 2012-05-04T09:24:48Z [Term] @@ -114445,7 +118533,6 @@ is_a: GO:0034504 ! protein localization to nucleus intersection_of: GO:0008104 ! protein localization intersection_of: has_target_end_location GO:0005635 ! nuclear envelope relationship: has_target_end_location GO:0005635 ! nuclear envelope -created_by: tb creation_date: 2012-07-30T01:50:41Z [Term] @@ -114462,7 +118549,6 @@ intersection_of: has_target_end_location GO:0005775 ! vacuolar lumen intersection_of: has_target_start_location GO:0005829 ! cytosol intersection_of: results_in_transport_across GO:0016020 ! membrane relationship: has_primary_input CHEBI:14321 -created_by: tb creation_date: 2012-09-24T14:12:46Z [Term] @@ -114477,7 +118563,6 @@ intersection_of: GO:0019725 ! cellular homeostasis intersection_of: regulates_levels_of CHEBI:14321 relationship: regulates_levels_of CHEBI:14321 property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/24220" xsd:anyURI -created_by: tb creation_date: 2012-09-24T14:22:02Z [Term] @@ -114492,7 +118577,6 @@ intersection_of: has_target_end_location GO:0005622 ! intracellular anatomical s intersection_of: has_target_start_location GO:0005576 ! extracellular region relationship: has_target_end_location GO:0005622 ! intracellular anatomical structure relationship: has_target_start_location GO:0005576 ! extracellular region -created_by: tb creation_date: 2012-10-17T11:06:17Z [Term] @@ -114507,7 +118591,6 @@ intersection_of: has_target_end_location GO:0005622 ! intracellular anatomical s intersection_of: has_target_start_location GO:0005576 ! extracellular region relationship: has_target_end_location GO:0005622 ! intracellular anatomical structure relationship: has_target_start_location GO:0005576 ! extracellular region -created_by: tb creation_date: 2012-10-17T11:12:09Z [Term] @@ -114519,7 +118602,6 @@ is_a: GO:0090131 ! mesenchyme migration intersection_of: GO:0090131 ! mesenchyme migration intersection_of: part_of GO:0060174 ! limb bud formation relationship: part_of GO:0060174 ! limb bud formation -created_by: tb creation_date: 2012-10-17T12:04:20Z [Term] @@ -114532,14 +118614,12 @@ is_a: GO:0001667 ! ameboidal-type cell migration intersection_of: GO:0016477 ! cell migration intersection_of: results_in_movement_of CL:0008019 ! mesenchymal cell relationship: results_in_movement_of CL:0008019 ! mesenchymal cell -created_by: tb creation_date: 2012-10-17T12:08:17Z [Term] id: GO:0090513 name: L-histidine transmembrane import into vacuole namespace: biological_process -alt_id: GO:0090457 def: "The directed movement of L-histidine into the vacuole across the vacuolar membrane." [GOC:al] synonym: "histidine transmembrane import into vacuole" BROAD [] synonym: "vacuolar histidine import" BROAD [GOC:tb] @@ -114551,7 +118631,6 @@ intersection_of: has_primary_input CHEBI:57595 intersection_of: has_target_end_location GO:0005775 ! vacuolar lumen intersection_of: has_target_start_location GO:0005829 ! cytosol intersection_of: results_in_transport_across GO:0016020 ! membrane -created_by: tb creation_date: 2012-12-14T11:25:52Z [Term] @@ -114566,7 +118645,6 @@ intersection_of: has_primary_input CHEBI:29985 intersection_of: has_target_end_location GO:0005775 ! vacuolar lumen intersection_of: has_target_start_location GO:0005829 ! cytosol intersection_of: results_in_transport_across GO:0016020 ! membrane -created_by: tb creation_date: 2012-12-14T11:25:52Z [Term] @@ -114580,7 +118658,6 @@ intersection_of: GO:0016477 ! cell migration intersection_of: results_in_movement_of CL:0000653 ! podocyte relationship: results_in_movement_of CL:0000653 ! podocyte property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/23000" xsd:anyURI -created_by: tb creation_date: 2013-01-08T11:08:57Z [Term] @@ -114590,7 +118667,6 @@ namespace: biological_process def: "The immediate defensive reaction by vertebrate tissue to injury caused by chemical or physical agents." [GOC:add] is_a: GO:0006954 ! inflammatory response is_a: GO:0009611 ! response to wounding -created_by: tb creation_date: 2014-08-12T12:13:53Z [Term] @@ -114603,7 +118679,6 @@ intersection_of: GO:0009653 ! anatomical structure morphogenesis intersection_of: results_in_morphogenesis_of UBERON:0000020 ! sense organ relationship: part_of GO:0007423 ! sensory organ development relationship: results_in_morphogenesis_of UBERON:0000020 ! sense organ -created_by: tb creation_date: 2014-08-22T13:23:20Z [Term] @@ -114617,7 +118692,6 @@ intersection_of: GO:0009653 ! anatomical structure morphogenesis intersection_of: results_in_morphogenesis_of UBERON:0014403 ! male anatomical structure relationship: part_of GO:0046661 ! male sex differentiation relationship: results_in_morphogenesis_of UBERON:0014403 ! male anatomical structure -created_by: tb creation_date: 2014-08-22T13:29:45Z [Term] @@ -114630,7 +118704,6 @@ is_a: GO:0002444 ! myeloid leukocyte mediated immunity intersection_of: GO:0001906 ! cell killing intersection_of: process_has_causal_agent CL:0000129 ! microglial cell relationship: process_has_causal_agent CL:0000129 ! microglial cell -created_by: tb creation_date: 2015-04-14T14:04:54Z [Term] @@ -114643,7 +118716,6 @@ is_a: GO:0006403 ! RNA localization intersection_of: GO:0006403 ! RNA localization intersection_of: has_target_end_location GO:0005634 ! nucleus relationship: has_target_end_location GO:0005634 ! nucleus -created_by: tb creation_date: 2016-07-19T17:00:49Z [Term] @@ -114653,7 +118725,6 @@ namespace: biological_process def: "Any process of the immune system that can contribute to the formation of immunological memory or an immune response based upon activation of immunological memory." [GOC:add, PMID:26086132, PMID:26831526] is_a: GO:0002376 ! immune system process relationship: part_of GO:0006955 ! immune response -created_by: tb creation_date: 2016-11-11T12:20:30Z [Term] @@ -114662,7 +118733,6 @@ name: immunological memory formation process namespace: biological_process def: "Any immunological memory process that can contribute to the formation of immunological memory." [GOC:add, PMID:26086132, PMID:26831526] is_a: GO:0090713 ! immunological memory process -created_by: tb creation_date: 2016-11-11T12:25:47Z [Term] @@ -114675,7 +118745,6 @@ is_a: GO:0098588 ! bounding membrane of organelle intersection_of: GO:0016020 ! membrane intersection_of: bounding_layer_of GO:0048770 ! pigment granule relationship: bounding_layer_of GO:0048770 ! pigment granule -created_by: tb creation_date: 2017-05-16T22:33:39Z [Term] @@ -114708,7 +118777,6 @@ is_a: GO:0032838 ! plasma membrane bounded cell projection cytoplasm intersection_of: GO:0005737 ! cytoplasm intersection_of: part_of GO:0005929 ! cilium relationship: part_of GO:0005929 ! cilium -created_by: pr creation_date: 2011-03-23T01:52:31Z [Term] @@ -114722,7 +118790,6 @@ is_a: GO:0120031 ! plasma membrane bounded cell projection assembly intersection_of: GO:0022607 ! cellular component assembly intersection_of: results_in_assembly_of GO:0097511 ! dendritic cell dendrite relationship: results_in_assembly_of GO:0097511 ! dendritic cell dendrite -created_by: pr creation_date: 2011-03-31T04:52:53Z [Term] @@ -114735,7 +118802,6 @@ is_a: GO:1903131 ! mononuclear cell differentiation intersection_of: GO:0030154 ! cell differentiation intersection_of: results_in_acquisition_of_features_of CL:0000451 ! dendritic cell relationship: results_in_acquisition_of_features_of CL:0000451 ! dendritic cell -created_by: pr creation_date: 2011-04-01T10:08:42Z [Term] @@ -114749,7 +118815,6 @@ is_a: GO:0097028 ! dendritic cell differentiation intersection_of: GO:0030154 ! cell differentiation intersection_of: results_in_acquisition_of_features_of CL:0000841 ! mature conventional dendritic cell relationship: results_in_acquisition_of_features_of CL:0000841 ! mature conventional dendritic cell -created_by: pr creation_date: 2011-04-01T10:10:22Z [Term] @@ -114762,7 +118827,6 @@ is_a: GO:0071887 ! leukocyte apoptotic process intersection_of: GO:0006915 ! apoptotic process intersection_of: occurs_in CL:0000451 ! dendritic cell relationship: occurs_in CL:0000451 ! dendritic cell -created_by: pr creation_date: 2011-05-04T02:18:59Z [Term] @@ -114776,7 +118840,6 @@ is_a: GO:0051402 ! neuron apoptotic process intersection_of: GO:0006915 ! apoptotic process intersection_of: occurs_in CL:0000100 ! motor neuron relationship: occurs_in CL:0000100 ! motor neuron -created_by: pr creation_date: 2011-05-04T02:21:43Z [Term] @@ -114791,7 +118854,6 @@ is_a: GO:1904019 ! epithelial cell apoptotic process intersection_of: GO:0006915 ! apoptotic process intersection_of: occurs_in CL:0000169 ! type B pancreatic cell relationship: occurs_in CL:0000169 ! type B pancreatic cell -created_by: pr creation_date: 2011-05-04T02:24:38Z [Term] @@ -114807,7 +118869,6 @@ is_a: GO:0006537 ! glutamate biosynthetic process intersection_of: GO:0009058 ! biosynthetic process intersection_of: has_primary_output CHEBI:29985 relationship: has_primary_output CHEBI:29985 -created_by: pr creation_date: 2011-05-24T04:30:38Z [Term] @@ -114820,7 +118881,6 @@ is_a: GO:0098590 ! plasma membrane region intersection_of: GO:0098590 ! plasma membrane region intersection_of: part_of GO:0045202 ! synapse relationship: part_of GO:0045202 ! synapse -created_by: pr creation_date: 2011-06-07T11:22:09Z [Term] @@ -114834,7 +118894,6 @@ intersection_of: GO:0048856 ! anatomical structure development intersection_of: results_in_development_of CL:0000359 ! vascular associated smooth muscle cell relationship: part_of GO:0035886 ! vascular associated smooth muscle cell differentiation relationship: results_in_development_of CL:0000359 ! vascular associated smooth muscle cell -created_by: pr creation_date: 2011-06-20T04:03:08Z [Term] @@ -114846,7 +118905,6 @@ is_a: GO:0072497 ! mesenchymal stem cell differentiation intersection_of: GO:0030154 ! cell differentiation intersection_of: results_in_acquisition_of_features_of CL:0002639 ! amniotic stem cell relationship: results_in_acquisition_of_features_of CL:0002639 ! amniotic stem cell -created_by: pr creation_date: 2011-06-22T11:17:52Z [Term] @@ -114863,7 +118921,6 @@ relationship: part_of GO:1904888 ! cranial skeletal system development relationship: results_in_morphogenesis_of UBERON:0009198 ! craniofacial suture relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata relationship: RO:0002162 NCBITaxon:7742 {all_only="true"} ! in taxon Vertebrata -created_by: pr creation_date: 2011-07-05T02:51:54Z [Term] @@ -114875,7 +118932,6 @@ is_a: GO:0097094 ! craniofacial suture morphogenesis intersection_of: GO:0009653 ! anatomical structure morphogenesis intersection_of: results_in_morphogenesis_of UBERON:0009199 ! facial suture relationship: results_in_morphogenesis_of UBERON:0009199 ! facial suture -created_by: pr creation_date: 2011-07-05T03:06:27Z [Term] @@ -114891,7 +118947,6 @@ intersection_of: GO:0009987 ! cellular process intersection_of: results_in_assembly_of GO:0045211 ! postsynaptic membrane relationship: part_of GO:0099068 ! postsynapse assembly relationship: results_in_assembly_of GO:0045211 ! postsynaptic membrane -created_by: pr creation_date: 2011-07-27T01:26:49Z [Term] @@ -114906,7 +118961,6 @@ intersection_of: has_primary_input GO:0098802 ! plasma membrane signaling recept intersection_of: has_target_end_location GO:0045202 ! synapse relationship: has_primary_input GO:0098802 ! plasma membrane signaling receptor complex relationship: has_target_end_location GO:0045202 ! synapse -created_by: pr creation_date: 2011-07-31T09:20:30Z [Term] @@ -114919,7 +118973,6 @@ is_a: GO:0006915 ! apoptotic process intersection_of: GO:0006915 ! apoptotic process intersection_of: occurs_in CL:0008019 ! mesenchymal cell relationship: occurs_in CL:0008019 ! mesenchymal cell -created_by: pr creation_date: 2011-09-06T02:31:59Z [Term] @@ -114931,7 +118984,6 @@ is_a: GO:0030182 ! neuron differentiation intersection_of: GO:0030154 ! cell differentiation intersection_of: results_in_acquisition_of_features_of CL:0000617 ! GABAergic neuron relationship: results_in_acquisition_of_features_of CL:0000617 ! GABAergic neuron -created_by: pr creation_date: 2011-09-14T09:39:11Z [Term] @@ -114946,7 +118998,6 @@ is_a: GO:0008152 ! metabolic process intersection_of: GO:0008152 ! metabolic process intersection_of: has_primary_input_or_output CHEBI:28938 relationship: has_primary_input_or_output CHEBI:28938 -created_by: pr creation_date: 2011-09-28T04:21:30Z [Term] @@ -114960,7 +119011,6 @@ is_a: GO:0048646 ! anatomical structure formation involved in morphogenesis intersection_of: GO:0048646 ! anatomical structure formation involved in morphogenesis intersection_of: results_in_formation_of UBERON:0001752 ! enamel relationship: results_in_formation_of UBERON:0001752 ! enamel -created_by: pr creation_date: 2011-11-21T09:01:24Z [Term] @@ -114975,23 +119025,35 @@ is_a: GO:0048646 ! anatomical structure formation involved in morphogenesis intersection_of: GO:0048646 ! anatomical structure formation involved in morphogenesis intersection_of: results_in_formation_of UBERON:0001751 ! dentine relationship: results_in_formation_of UBERON:0001751 ! dentine -created_by: pr creation_date: 2011-11-21T09:04:17Z [Term] id: GO:0097190 name: apoptotic signaling pathway namespace: biological_process -alt_id: GO:0008624 def: "The series of molecular signals which triggers the apoptotic death of a cell. The pathway starts with reception of a signal, and ends when the execution phase of apoptosis is triggered." [GOC:mtg_apoptosis] comment: This term can be used to annotate gene products involved in apoptotic events happening downstream of the cross-talk point between the extrinsic and intrinsic apoptotic pathways. The cross-talk starts when caspase-8 cleaves Bid and truncated Bid interacts with mitochondria. From this point on it is not possible to distinguish between extrinsic and intrinsic pathways. synonym: "apoptotic signalling pathway" EXACT [GOC:mah] synonym: "induction of apoptosis by extracellular signals" EXACT [] is_a: GO:0007165 ! signal transduction relationship: part_of GO:0006915 ! apoptotic process -created_by: pr creation_date: 2011-11-23T09:30:23Z +[Term] +id: GO:0097191 +name: extrinsic apoptotic signaling pathway +namespace: biological_process +def: "The series of molecular signals in which a signal is conveyed from the cell surface to trigger the apoptotic death of a cell. The pathway starts with either a ligand binding to a cell surface receptor, or a ligand being withdrawn from a cell surface receptor (e.g. in the case of signaling by dependence receptors), and ends when the execution phase of apoptosis is triggered." [GOC:mtg_apoptosis, GOC:yaf, PMID:17340152] +comment: Fas acts as a death receptor with a role in apoptosis, but can also act as a non-apoptotic signal transducer. +synonym: "death receptor-mediated apoptosis" NARROW [] +synonym: "extrinsic apoptosis" NARROW [] +synonym: "extrinsic apoptotic pathway" EXACT [] +synonym: "extrinsic apoptotic signaling pathway in presence of ligand" NARROW [] +synonym: "extrinsic apoptotic signalling pathway" EXACT [GOC:mah] +is_a: GO:0007166 ! cell surface receptor signaling pathway +is_a: GO:0097190 ! apoptotic signaling pathway +creation_date: 2011-11-23T09:34:28Z + [Term] id: GO:0097194 name: execution phase of apoptosis @@ -115003,7 +119065,6 @@ is_a: BFO:0000003 is_a: GO:0009987 ! cellular process relationship: has_part GO:0032060 ! bleb assembly relationship: part_of GO:0006915 ! apoptotic process -created_by: pr creation_date: 2011-11-23T09:45:24Z [Term] @@ -115012,7 +119073,6 @@ name: renal filtration namespace: biological_process def: "A renal system process in which fluid circulating through the body is filtered through a barrier system." [GOC:pr, GOC:sart] is_a: GO:0003014 ! renal system process -created_by: pr creation_date: 2012-01-03T03:10:17Z [Term] @@ -115027,7 +119087,6 @@ intersection_of: GO:0016043 ! cellular component organization intersection_of: results_in_organization_of GO:0005765 ! lysosomal membrane relationship: part_of GO:0007040 ! lysosome organization relationship: results_in_organization_of GO:0005765 ! lysosomal membrane -created_by: pr creation_date: 2012-01-12T10:16:15Z [Term] @@ -115040,7 +119099,6 @@ intersection_of: GO:0016020 ! membrane intersection_of: bounding_layer_of GO:0042599 ! lamellar body relationship: bounding_layer_of GO:0042599 ! lamellar body relationship: part_of GO:0042599 ! lamellar body -created_by: pr creation_date: 2012-01-26T10:28:42Z [Term] @@ -115048,7 +119106,6 @@ id: GO:0097237 name: cellular response to toxic substance namespace: biological_process def: "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a toxic stimulus." [GOC:pr] -created_by: pr creation_date: 2012-02-02T12:23:31Z [Term] @@ -115061,7 +119118,6 @@ is_a: GO:0034349 ! glial cell apoptotic process intersection_of: GO:0006915 ! apoptotic process intersection_of: occurs_in CL:0000128 ! oligodendrocyte relationship: occurs_in CL:0000128 ! oligodendrocyte -created_by: pr creation_date: 2012-03-05T10:51:15Z [Term] @@ -115072,7 +119128,6 @@ def: "The elimination of substances from peritubular capillaries (or surrounding is_a: GO:0003014 ! renal system process is_a: GO:0007588 ! excretion property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/22368" xsd:anyURI -created_by: pr creation_date: 2012-03-05T02:03:58Z [Term] @@ -115085,7 +119140,6 @@ is_a: GO:0048878 ! chemical homeostasis intersection_of: GO:0048878 ! chemical homeostasis intersection_of: regulates_levels_of CHEBI:28938 relationship: regulates_levels_of CHEBI:28938 -created_by: pr creation_date: 2012-03-22T02:51:22Z [Term] @@ -115099,7 +119153,6 @@ is_a: GO:0055082 ! intracellular chemical homeostasis is_a: GO:0097272 ! ammonium homeostasis intersection_of: GO:0055082 ! intracellular chemical homeostasis intersection_of: regulates_levels_of CHEBI:28938 -created_by: pr creation_date: 2012-03-22T02:54:38Z [Term] @@ -115113,7 +119166,6 @@ intersection_of: GO:0006915 ! apoptotic process intersection_of: occurs_in CL:0000312 ! keratinocyte relationship: occurs_in CL:0000312 ! keratinocyte property_value: RO:0002161 NCBITaxon:6656 -created_by: pr creation_date: 2012-03-29T10:20:51Z [Term] @@ -115126,7 +119178,6 @@ is_a: GO:1904019 ! epithelial cell apoptotic process intersection_of: GO:0006915 ! apoptotic process intersection_of: occurs_in CL:0000182 ! hepatocyte relationship: occurs_in CL:0000182 ! hepatocyte -created_by: pr creation_date: 2012-03-29T10:23:21Z [Term] @@ -115138,7 +119189,6 @@ is_a: GO:0010631 ! epithelial cell migration intersection_of: GO:0016477 ! cell migration intersection_of: results_in_movement_of CL:0000148 ! melanocyte relationship: results_in_movement_of CL:0000148 ! melanocyte -created_by: pr creation_date: 2012-06-08T10:08:18Z [Term] @@ -115151,7 +119201,6 @@ is_a: GO:0071168 ! protein localization to chromatin intersection_of: GO:0008104 ! protein localization intersection_of: has_target_end_location GO:0000792 ! heterochromatin relationship: has_target_end_location GO:0000792 ! heterochromatin -created_by: pr creation_date: 2012-07-03T03:19:07Z [Term] @@ -115164,7 +119213,6 @@ is_a: GO:0008283 ! cell population proliferation intersection_of: GO:0008283 ! cell population proliferation intersection_of: acts_on_population_of CL:0011101 ! chorionic trophoblast cell relationship: acts_on_population_of CL:0011101 ! chorionic trophoblast cell -created_by: pr creation_date: 2012-07-19T10:17:37Z [Term] @@ -115179,7 +119227,6 @@ is_a: GO:0005488 ! binding intersection_of: GO:0005488 ! binding intersection_of: has_primary_input CHEBI:63299 relationship: has_primary_input CHEBI:63299 -created_by: pr creation_date: 2012-08-02T13:03:39Z [Term] @@ -115193,7 +119240,6 @@ is_a: GO:0120025 ! plasma membrane bounded cell projection intersection_of: GO:0120025 ! plasma membrane bounded cell projection intersection_of: part_of CL:0000125 ! glial cell relationship: part_of CL:0000125 ! glial cell -created_by: pr creation_date: 2012-10-22T13:55:54Z [Term] @@ -115206,7 +119252,6 @@ is_a: GO:0016477 ! cell migration intersection_of: GO:0016477 ! cell migration intersection_of: results_in_movement_of CL:0000031 ! neuroblast (sensu Vertebrata) relationship: results_in_movement_of CL:0000031 ! neuroblast (sensu Vertebrata) -created_by: pr creation_date: 2012-10-29T08:24:37Z [Term] @@ -115219,7 +119264,6 @@ intersection_of: GO:0030154 ! cell differentiation intersection_of: results_in_acquisition_of_features_of CL:1001569 ! hippocampal interneuron relationship: part_of GO:0021766 ! hippocampus development relationship: results_in_acquisition_of_features_of CL:1001569 ! hippocampal interneuron -created_by: pr creation_date: 2012-11-04T10:58:28Z [Term] @@ -115229,10 +119273,9 @@ namespace: cellular_component def: "An arrangement of closely apposed microtubules running parallel to each other." [NIF_Subcellular:sao1872343973] synonym: "microtubule fascicle" EXACT [] xref: NIF_Subcellular:sao1872343973 -is_a: GO:0110165 ! cellular anatomical entity +is_a: GO:0110165 ! cellular anatomical structure relationship: has_part GO:0005874 ! microtubule relationship: part_of GO:0005856 ! cytoskeleton -created_by: pr creation_date: 2012-11-07T15:01:27Z [Term] @@ -115245,14 +119288,12 @@ is_a: GO:0021895 ! cerebral cortex neuron differentiation intersection_of: GO:0030154 ! cell differentiation intersection_of: results_in_acquisition_of_features_of CL:1001571 ! hippocampal pyramidal neuron relationship: results_in_acquisition_of_features_of CL:1001571 ! hippocampal pyramidal neuron -created_by: pr creation_date: 2012-11-22T09:33:31Z [Term] id: GO:0097435 name: supramolecular fiber organization namespace: biological_process -alt_id: GO:0043206 def: "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a supramolecular fiber, a polymer consisting of an indefinite number of protein or protein complex subunits that have polymerised to form a fiber-shaped structure." [GOC:pr] synonym: "extracellular fibril organisation" NARROW [] synonym: "extracellular fibril organization" NARROW [] @@ -115263,7 +119304,6 @@ is_a: GO:0016043 ! cellular component organization intersection_of: GO:0016043 ! cellular component organization intersection_of: results_in_organization_of GO:0099512 ! supramolecular fiber relationship: results_in_organization_of GO:0099512 ! supramolecular fiber -created_by: pr creation_date: 2012-11-27T15:46:25Z [Term] @@ -115275,7 +119315,6 @@ xref: NIF_Subcellular:sao172297168 is_a: GO:0043005 ! neuron projection relationship: has_part GO:0030425 ! dendrite relationship: part_of GO:0036477 ! somatodendritic compartment -created_by: pr creation_date: 2012-12-17T12:31:49Z [Term] @@ -115291,7 +119330,6 @@ is_a: GO:0097386 ! glial cell projection intersection_of: GO:0120025 ! plasma membrane bounded cell projection intersection_of: part_of CL:0000127 ! astrocyte relationship: part_of CL:0000127 ! astrocyte -created_by: pr creation_date: 2012-12-17T13:29:55Z [Term] @@ -115305,7 +119343,6 @@ is_a: GO:0097386 ! glial cell projection intersection_of: GO:0005902 ! microvillus intersection_of: part_of CL:0002573 ! Schwann cell relationship: part_of CL:0002573 ! Schwann cell -created_by: pr creation_date: 2012-12-19T13:01:02Z [Term] @@ -115317,7 +119354,6 @@ xref: NIF_Subcellular:nlx_subcell_100312 is_a: GO:0030424 ! axon relationship: part_of CL:0001033 ! hippocampal granule cell property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/25796" xsd:anyURI -created_by: pr creation_date: 2012-12-19T16:51:57Z [Term] @@ -115331,7 +119367,6 @@ is_a: GO:1990009 ! retinal cell apoptotic process intersection_of: GO:0006915 ! apoptotic process intersection_of: occurs_in CL:0000604 ! retinal rod cell relationship: occurs_in CL:0000604 ! retinal rod cell -created_by: pr creation_date: 2013-03-21T09:44:45Z [Term] @@ -115345,7 +119380,6 @@ is_a: GO:1990009 ! retinal cell apoptotic process intersection_of: GO:0006915 ! apoptotic process intersection_of: occurs_in CL:0000573 ! retinal cone cell relationship: occurs_in CL:0000573 ! retinal cone cell -created_by: pr creation_date: 2013-03-21T09:46:22Z [Term] @@ -115357,7 +119391,6 @@ is_a: GO:0001764 ! neuron migration intersection_of: GO:0016477 ! cell migration intersection_of: results_in_movement_of CL:0000100 ! motor neuron relationship: results_in_movement_of CL:0000100 ! motor neuron -created_by: pr creation_date: 2013-04-23T13:00:46Z [Term] @@ -115369,7 +119402,6 @@ is_a: GO:0097475 ! motor neuron migration intersection_of: GO:0016477 ! cell migration intersection_of: results_in_movement_of CL:0011001 ! spinal cord motor neuron relationship: results_in_movement_of CL:0011001 ! spinal cord motor neuron -created_by: pr creation_date: 2013-04-23T13:03:46Z [Term] @@ -115381,7 +119413,6 @@ is_a: GO:0097476 ! spinal cord motor neuron migration intersection_of: GO:0016477 ! cell migration intersection_of: results_in_movement_of CL:0011002 ! lateral motor column neuron relationship: results_in_movement_of CL:0011002 ! lateral motor column neuron -created_by: pr creation_date: 2013-04-23T13:05:32Z [Term] @@ -115393,7 +119424,6 @@ is_a: GO:0120025 ! plasma membrane bounded cell projection intersection_of: GO:0120025 ! plasma membrane bounded cell projection intersection_of: part_of CL:0000451 ! dendritic cell relationship: part_of CL:0000451 ! dendritic cell -created_by: pr creation_date: 2013-10-16T13:02:25Z [Term] @@ -115405,7 +119435,6 @@ is_a: GO:0030016 ! myofibril intersection_of: GO:0030016 ! myofibril intersection_of: part_of CL:0000746 ! cardiac muscle cell relationship: part_of CL:0000746 ! cardiac muscle cell -created_by: pr creation_date: 2013-10-16T13:04:58Z [Term] @@ -115417,7 +119446,6 @@ is_a: GO:0005886 ! plasma membrane intersection_of: GO:0005886 ! plasma membrane intersection_of: part_of CL:0000019 ! sperm relationship: part_of CL:0000019 ! sperm -created_by: pr creation_date: 2013-10-18T11:31:17Z [Term] @@ -115429,7 +119457,6 @@ is_a: GO:0050900 ! leukocyte migration intersection_of: GO:0016477 ! cell migration intersection_of: results_in_movement_of CL:0000766 ! myeloid leukocyte relationship: results_in_movement_of CL:0000766 ! myeloid leukocyte -created_by: pr creation_date: 2013-11-11T13:59:43Z [Term] @@ -115441,7 +119468,6 @@ is_a: GO:0097529 ! myeloid leukocyte migration intersection_of: GO:0016477 ! cell migration intersection_of: results_in_movement_of CL:0000094 ! granulocyte relationship: results_in_movement_of CL:0000094 ! granulocyte -created_by: pr creation_date: 2013-11-11T14:00:44Z [Term] @@ -115453,7 +119479,6 @@ is_a: GO:0097529 ! myeloid leukocyte migration intersection_of: GO:0016477 ! cell migration intersection_of: results_in_movement_of CL:0000097 ! mast cell relationship: results_in_movement_of CL:0000097 ! mast cell -created_by: pr creation_date: 2013-11-11T14:01:41Z [Term] @@ -115467,7 +119492,6 @@ is_a: GO:0016477 ! cell migration intersection_of: GO:0016477 ! cell migration intersection_of: results_in_movement_of CL:0000838 ! lymphoid lineage restricted progenitor cell relationship: results_in_movement_of CL:0000838 ! lymphoid lineage restricted progenitor cell -created_by: pr creation_date: 2013-11-28T10:47:15Z [Term] @@ -115481,7 +119505,6 @@ intersection_of: GO:0009653 ! anatomical structure morphogenesis intersection_of: results_in_morphogenesis_of UBERON:0003846 ! thymus epithelium relationship: part_of GO:0048538 ! thymus development relationship: results_in_morphogenesis_of UBERON:0003846 ! thymus epithelium -created_by: pr creation_date: 2013-11-28T10:51:03Z [Term] @@ -115494,11 +119517,10 @@ synonym: "axoneme central pair" EXACT [] synonym: "axoneme microtubule central pair" EXACT [] synonym: "central pair" BROAD [] synonym: "central-pair microtubules" RELATED [] -is_a: GO:0110165 ! cellular anatomical entity +is_a: GO:0110165 ! cellular anatomical structure relationship: has_part GO:1990719 ! C1 axonemal microtubule relationship: has_part GO:1990720 ! C2 axonemal microtubule relationship: part_of GO:1990716 ! axonemal central apparatus -created_by: pr creation_date: 2013-12-12T11:07:09Z [Term] @@ -115511,19 +119533,17 @@ synonym: "axoneme outer doublet" EXACT [] synonym: "DMT" RELATED [] synonym: "outer doublet" BROAD [] synonym: "outer-doublet microtubules" RELATED [] -is_a: GO:0110165 ! cellular anatomical entity +is_a: GO:0110165 ! cellular anatomical structure relationship: has_part GO:0097649 ! A axonemal microtubule relationship: has_part GO:0097650 ! B axonemal microtubule relationship: part_of GO:0005930 ! axoneme property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/26128" xsd:anyURI -created_by: pr creation_date: 2013-12-12T11:19:29Z [Term] id: GO:0097553 name: calcium ion transmembrane import into cytosol namespace: biological_process -alt_id: GO:0060401 def: "A process in which a calcium ion is transported from one side of a membrane to the other into the cytosol by means of some agent such as a transporter or pore." [GOC:vw] synonym: "calcium transmembrane import into cytosol" BROAD [] synonym: "cytosolic calcium ion transport" BROAD [] @@ -115534,7 +119554,6 @@ intersection_of: has_target_end_location GO:0005829 ! cytosol intersection_of: results_in_transport_across GO:0016020 ! membrane relationship: has_target_end_location GO:0005829 ! cytosol property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/23015" xsd:anyURI -created_by: pr creation_date: 2014-01-23T11:05:13Z [Term] @@ -115547,15 +119566,12 @@ is_a: GO:0048284 ! organelle fusion intersection_of: GO:0009987 ! cellular process intersection_of: results_in_fusion_of GO:0005773 ! vacuole relationship: results_in_fusion_of GO:0005773 ! vacuole -created_by: pr creation_date: 2014-02-28T09:49:31Z [Term] id: GO:0097623 name: potassium ion export across plasma membrane namespace: biological_process -alt_id: GO:0071435 -alt_id: GO:0098668 def: "The directed movement of potassium ions from inside of a cell, across the plasma membrane and into the extracellular region." [GOC:vw, PMID:11932440] synonym: "potassium export" BROAD [GOC:mah] synonym: "potassium export across plasma membrane" EXACT [] @@ -115569,7 +119585,6 @@ intersection_of: has_target_end_location GO:0005576 ! extracellular region intersection_of: has_target_start_location GO:0005829 ! cytosol intersection_of: results_in_transport_across GO:0005886 ! plasma membrane property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/14265" xsd:anyURI -created_by: pr creation_date: 2009-12-16T11:10:45Z [Term] @@ -115582,7 +119597,6 @@ is_a: GO:0016477 ! cell migration intersection_of: GO:0016477 ! cell migration intersection_of: results_in_movement_of CL:0000661 ! distal tip cell (sensu Nematoda) relationship: results_in_movement_of CL:0000661 ! distal tip cell (sensu Nematoda) -created_by: pr creation_date: 2014-08-20T16:06:53Z [Term] @@ -115591,7 +119605,6 @@ name: calcitonin family receptor activity namespace: molecular_function def: "Combining with any member of the calcitonin family (e.g. adrenomedullin, adrenomedullin 2 (intermedin), amylin, calcitonin and calcitonin gene-related peptides (CGRPs)) to initiate a change in cell activity." [GOC:bhm, InterPro:IPR003287, PMID:10871296, PMID:12037140, PMID:18687416] is_a: GO:0008528 ! G protein-coupled peptide receptor activity -created_by: pr creation_date: 2014-09-08T15:32:19Z [Term] @@ -115600,7 +119613,6 @@ name: calcitonin family binding namespace: molecular_function def: "Binding to a member of the calcitonin family (e.g. adrenomedullin, adrenomedullin 2 (intermedin), amylin, calcitonin and calcitonin gene-related peptides (CGRPs))." [GOC:bhm, InterPro:IPR021116, PMID:10871296, PMID:12037140, PMID:18687416] is_a: GO:0017046 ! peptide hormone binding -created_by: pr creation_date: 2014-09-08T20:50:52Z [Term] @@ -115610,7 +119622,6 @@ namespace: cellular_component def: "A protein complex that contains G protein-coupled receptors." [GOC:bhm] synonym: "G-protein coupled receptor complex" EXACT [] is_a: GO:0098802 ! plasma membrane signaling receptor complex -created_by: pr creation_date: 2014-09-10T09:14:30Z [Term] @@ -115621,7 +119632,6 @@ def: "A complete microtubule with 13 protofilaments that fuses with an incomplet synonym: "A tubule" BROAD [] is_a: GO:0005879 ! axonemal microtubule relationship: part_of GO:0097545 ! axonemal doublet microtubule -created_by: pr creation_date: 2014-09-10T20:41:28Z [Term] @@ -115632,7 +119642,6 @@ def: "An incomplete microtubule containing 10 protofilaments that fuses with a c synonym: "B tubule" BROAD [] is_a: GO:0005879 ! axonemal microtubule relationship: part_of GO:0097545 ! axonemal doublet microtubule -created_by: pr creation_date: 2014-09-10T20:43:18Z [Term] @@ -115644,7 +119653,6 @@ is_a: GO:0031982 ! vesicle is_a: GO:0043231 ! intracellular membrane-bounded organelle intersection_of: GO:0031982 ! vesicle intersection_of: part_of GO:0005622 ! intracellular anatomical structure -created_by: pr creation_date: 2016-03-29T17:39:45Z [Term] @@ -115657,7 +119665,6 @@ synonym: "anchoring of the basal body to the plasma membrane" RELATED [] synonym: "ciliary basal body docking" EXACT [] is_a: GO:0140056 ! organelle localization by membrane tethering relationship: part_of GO:0060271 ! cilium assembly -created_by: pr creation_date: 2016-08-05T16:12:33Z [Term] @@ -115667,7 +119674,6 @@ namespace: biological_process def: "The process in which vesicles formed at the trans-Golgi network are directed to the plasma membrane surrounding the base of the cilium, including the ciliary pocket, mediated by molecules at the vesicle membrane and target membrane surfaces." [GOC:cilia, PMID:20106869, PMID:23351793, PMID:24814148, PMID:26485645] is_a: GO:0048199 ! vesicle targeting, to, from or within Golgi relationship: part_of GO:0060271 ! cilium assembly -created_by: pr creation_date: 2016-08-05T16:16:28Z [Term] @@ -115680,7 +119686,6 @@ is_a: GO:0042246 ! tissue regeneration intersection_of: GO:0031099 ! regeneration intersection_of: results_in_maturation_of UBERON:0003714 ! neural tissue relationship: results_in_maturation_of UBERON:0003714 ! neural tissue -created_by: pr creation_date: 2016-08-25T13:14:27Z [Term] @@ -115696,7 +119701,6 @@ is_a: GO:0048870 ! cell motility intersection_of: GO:0048870 ! cell motility intersection_of: results_in_movement_of CL:0000019 ! sperm relationship: results_in_movement_of CL:0000019 ! sperm -created_by: pr creation_date: 2016-09-01T12:00:45Z [Term] @@ -115714,7 +119718,6 @@ relationship: has_part GO:0036156 ! inner dynein arm relationship: has_part GO:0036157 ! outer dynein arm relationship: has_part GO:0097540 ! axonemal central pair relationship: has_part GO:0097545 ! axonemal doublet microtubule -created_by: pr creation_date: 2016-09-27T15:26:34Z [Term] @@ -115728,9 +119731,25 @@ synonym: "exosome production" EXACT [] synonym: "ILV assembly" RELATED [] synonym: "intraluminal vesicle assembly" RELATED [] is_a: GO:0140112 ! extracellular vesicle biogenesis -created_by: pr creation_date: 2016-10-03T14:35:25Z +[Term] +id: GO:0097742 +name: de novo centriole assembly +namespace: biological_process +def: "Centriole assembly in which a centriole arises de novo, rather than by replication from an existing centriole. This process may occur via different mechanisms. Examples include the deuterosome pathway in multicilated epithelial animal cells and formation of centrioles during parthenogenesis in some insects." [GOC:cilia, PMID:25047614, PMID:25291643] +synonym: "acentriolar basal body biogenesis" RELATED [] +synonym: "de novo basal body amplification" RELATED [] +synonym: "de novo basal body assembly" RELATED [] +synonym: "de novo basal body biogenesis" RELATED [] +synonym: "de novo basal body generation" RELATED [] +synonym: "de novo centriole amplification" RELATED [] +synonym: "de novo ciliary basal body assembly" RELATED [] +synonym: "multiciliation" RELATED [] +synonym: "multiciliogenesis" RELATED [] +is_a: GO:0098534 ! centriole assembly +creation_date: 2016-10-19T15:13:50Z + [Term] id: GO:0098520 name: excitatory neuromuscular junction @@ -115741,7 +119760,6 @@ is_a: GO:0060076 ! excitatory synapse intersection_of: GO:0060076 ! excitatory synapse intersection_of: overlaps CL:0000100 ! motor neuron intersection_of: overlaps CL:0000187 ! muscle cell -created_by: dos creation_date: 2013-10-14T12:02:51Z [Term] @@ -115757,7 +119775,6 @@ intersection_of: GO:0060076 ! excitatory synapse intersection_of: overlaps CL:0000100 ! motor neuron intersection_of: overlaps CL:0008002 ! skeletal muscle fiber relationship: overlaps CL:0008002 ! skeletal muscle fiber -created_by: dos creation_date: 2013-10-14T12:04:32Z [Term] @@ -115771,7 +119788,6 @@ intersection_of: GO:0045202 ! synapse intersection_of: overlaps CL:0000100 ! motor neuron intersection_of: overlaps CL:0002372 ! myotube relationship: overlaps CL:0002372 ! myotube -created_by: dos creation_date: 2013-10-14T12:05:12Z [Term] @@ -115785,7 +119801,6 @@ intersection_of: GO:0045202 ! synapse intersection_of: overlaps CL:0000100 ! motor neuron intersection_of: overlaps CL:0008003 ! somatic muscle myotube relationship: overlaps CL:0008003 ! somatic muscle myotube -created_by: dos creation_date: 2013-10-14T12:05:43Z [Term] @@ -115798,7 +119813,6 @@ is_a: GO:0098524 ! neuromuscular junction of somatic muscle myotube intersection_of: GO:0060076 ! excitatory synapse intersection_of: overlaps CL:0000100 ! motor neuron intersection_of: overlaps CL:0008003 ! somatic muscle myotube -created_by: dos creation_date: 2013-10-14T12:06:08Z [Term] @@ -115811,7 +119825,6 @@ intersection_of: GO:0045202 ! synapse intersection_of: overlaps CL:0000100 ! motor neuron intersection_of: overlaps CL:0008004 ! somatic muscle cell relationship: overlaps CL:0008004 ! somatic muscle cell -created_by: dos creation_date: 2013-10-14T12:07:05Z [Term] @@ -115824,7 +119837,6 @@ is_a: GO:0035914 ! skeletal muscle cell differentiation intersection_of: GO:0030154 ! cell differentiation intersection_of: results_in_acquisition_of_features_of CL:0008002 ! skeletal muscle fiber relationship: results_in_acquisition_of_features_of CL:0008002 ! skeletal muscle fiber -created_by: dos creation_date: 2013-10-15T14:00:34Z [Term] @@ -115839,16 +119851,47 @@ relationship: part_of GO:0048741 ! skeletal muscle fiber development relationship: results_in_organization_of GO:0098522 ! neuromuscular junction of skeletal muscle fiber [Term] -id: GO:0098531 -name: ligand-activated transcription factor activity -namespace: molecular_function -def: "A DNA-binding transcription factor activity regulated by binding to a ligand and that modulates the transcription of specific genes and gene sets. Examples include the lac and trp repressors in E.coli and steroid hormone receptors." [GOC:dos, PMID:25568920, PMID:8735275] -comment: For usage guidance, see comment in GO:0003700 ; DNA-binding transcription factor activity. -synonym: "direct ligand regulated sequence-specific DNA binding transcription factor activity" EXACT [] -synonym: "transcription factor activity, direct ligand regulated sequence-specific DNA binding" EXACT [] -is_a: GO:0003700 ! DNA-binding transcription factor activity -created_by: dos -creation_date: 2013-10-17T15:51:30Z +id: GO:0098534 +name: centriole assembly +namespace: biological_process +def: "A cellular process that results in the assembly of one or more centrioles." [GOC:dos, PMID:24075808] +is_a: GO:0031023 ! microtubule organizing center organization +is_a: GO:0140694 ! membraneless organelle assembly +intersection_of: GO:0022607 ! cellular component assembly +intersection_of: results_in_assembly_of GO:0005814 ! centriole +relationship: results_in_assembly_of GO:0005814 ! centriole +creation_date: 2013-10-22T15:55:22Z + +[Term] +id: GO:0098535 +name: de novo centriole assembly involved in multi-ciliated epithelial cell differentiation +namespace: biological_process +def: "Centriole assembly in which a centriole arises de novo by a process involving an electron-dense structure known as a deuterosome, rather than by duplication of an existing centriole, and occurring as part of multi-ciliated epithelial cell differentiation." [GOC:cilia, GOC:dos, PMID:24075808, PMID:5111878, PMID:5661997] +comment: In most eukaryotic cells, 'centriole' (GO:0005814) and 'ciliary basal body' (GO:0036064) represent a common entity that cycles through its function in cell division, then ciliogenesis, then cell division again. However, these structures are modified extensively as they transition into each other, and may contain different proteins, specific to each component. +synonym: "centriole amplification" RELATED [PMID:24075808] +synonym: "de novo centriole assembly" BROAD [] +synonym: "de novo centriole assembly via deuterosome" EXACT [] +synonym: "deuterosomal basal body biogenesis" RELATED [] +synonym: "deuterosome pathway" RELATED [PMID:25047614] +synonym: "deuterosome-mediated centriole biogenesis" RELATED [PMID:24075808] +synonym: "multiciliation" RELATED [] +synonym: "multiciliogenesis" RELATED [] +is_a: GO:0097742 ! de novo centriole assembly +intersection_of: GO:0097742 ! de novo centriole assembly +intersection_of: part_of GO:1903251 ! multi-ciliated epithelial cell differentiation +relationship: has_participant GO:0098536 ! deuterosome +relationship: part_of GO:1903251 ! multi-ciliated epithelial cell differentiation +creation_date: 2013-10-22T16:03:13Z + +[Term] +id: GO:0098536 +name: deuterosome +namespace: cellular_component +def: "A spherical, electron dense, cytoplasmic structure that is involved in de novo assembly of centrioles." [GOC:cilia, GOC:dos, PMID:24075808, PMID:25047614, PMID:5661997] +is_a: GO:0043232 ! intracellular membraneless organelle +relationship: RO:0002160 NCBITaxon:33208 ! only in taxon Metazoa +relationship: RO:0002162 NCBITaxon:33208 {all_only="true"} ! in taxon Metazoa +creation_date: 2013-10-22T16:21:19Z [Term] id: GO:0098537 @@ -115858,14 +119901,12 @@ def: "OBSOLETE. Nucleus with two or more lobes connected by a thin filament that comment: This term was obsoleted because it does not correspond to a specific type of nucleus, it is a morphologically different nucleus present in certain cell types. property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/20764" xsd:anyURI is_obsolete: true -created_by: dos creation_date: 2013-10-22T18:31:36Z [Term] id: GO:0098542 name: defense response to other organism namespace: biological_process -alt_id: GO:0009814 def: "Reactions triggered in response to the presence of another organism that act to protect the cell or organism from damage caused by that organism." [GOC:dos] subset: goslim_generic subset: goslim_prokaryote @@ -115875,7 +119916,6 @@ synonym: "defense response, incompatible interaction" NARROW [] synonym: "resistance response to pathogen" NARROW [] is_a: GO:0051707 ! response to other organism property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/22173" xsd:anyURI -created_by: dos creation_date: 2013-11-11T12:59:11Z [Term] @@ -115887,7 +119927,6 @@ is_a: GO:0031503 ! protein-containing complex localization is_a: GO:0051235 ! maintenance of location intersection_of: GO:0051235 ! maintenance of location intersection_of: has_primary_input GO:0032991 ! protein-containing complex -created_by: dos creation_date: 2013-11-15T18:20:16Z [Term] @@ -115901,7 +119940,6 @@ intersection_of: GO:0098544 ! maintenance of protein complex location intersection_of: has_primary_input GO:0032991 ! protein-containing complex intersection_of: occurs_in GO:0005737 ! cytoplasm relationship: occurs_in GO:0005737 ! cytoplasm -created_by: dos creation_date: 2013-11-15T20:49:15Z [Term] @@ -115914,7 +119952,6 @@ is_a: GO:0031090 ! organelle membrane intersection_of: GO:0016020 ! membrane intersection_of: bounding_layer_of GO:0043226 ! organelle relationship: bounding_layer_of GO:0043226 ! organelle -created_by: dos creation_date: 2014-02-26T13:41:31Z [Term] @@ -115929,7 +119966,6 @@ is_a: GO:0016020 ! membrane intersection_of: GO:0016020 ! membrane intersection_of: part_of GO:0005886 ! plasma membrane relationship: part_of GO:0005886 ! plasma membrane -created_by: dos creation_date: 2014-03-06T11:55:32Z [Term] @@ -115938,18 +119974,15 @@ name: mucin granule namespace: cellular_component def: "A secretory granule that contains mucin." [PMID:16377632] is_a: GO:0030141 ! secretory granule -created_by: dos creation_date: 2014-03-11T15:59:11Z [Term] id: GO:0098609 name: cell-cell adhesion namespace: biological_process -alt_id: GO:0016337 def: "The attachment of one cell to another cell via adhesion molecules." [GOC:dos] synonym: "single organismal cell-cell adhesion" RELATED [] is_a: GO:0007155 ! cell adhesion -created_by: dos creation_date: 2014-04-16T13:40:03Z [Term] @@ -116004,7 +120037,6 @@ relationship: capable_of_part_of GO:0098609 ! cell-cell adhesion id: GO:0098636 name: protein complex involved in cell adhesion namespace: cellular_component -alt_id: GO:1990307 def: "Any protein complex that is capable of carrying out some part of the process of cell adhesion to the cell matrix or to another cell." [GOC:dos] synonym: "cell adhesion complex" RELATED [] is_a: GO:0032991 ! protein-containing complex @@ -116049,7 +120081,6 @@ def: "A complex of collagen trimers such as a fibril or collagen network." [GOC: synonym: "Supramolecular aggregate of collagen" EXACT [PMID:19693541] synonym: "Supramolecular collagen assembly" EXACT [PMID:21421911] is_a: GO:0099080 ! supramolecular complex -is_a: PR:000050567 ! protein-containing material entity relationship: has_part GO:0005581 ! collagen trimer relationship: part_of GO:0062023 ! collagen-containing extracellular matrix @@ -116076,7 +120107,6 @@ relationship: part_of GO:0005604 ! basement membrane id: GO:0098655 name: monoatomic cation transmembrane transport namespace: biological_process -alt_id: GO:0099132 def: "The process in which a monoatomic cation is transported across a membrane. Monatomic cations (also called simple cations) are positively charged ions consisting of exactly one atom." [GOC:dos, GOC:vw] synonym: "ATP hydrolysis coupled cation transmembrane transport" NARROW [] synonym: "cation transmembrane transport" BROAD [] @@ -116112,7 +120142,6 @@ is_a: GO:0007186 ! G protein-coupled receptor signaling pathway intersection_of: GO:0007165 ! signal transduction intersection_of: starts_with GO:0004993 ! G protein-coupled serotonin receptor activity relationship: starts_with GO:0004993 ! G protein-coupled serotonin receptor activity -created_by: dos creation_date: 2016-12-21T12:07:58Z [Term] @@ -116127,7 +120156,6 @@ is_a: GO:0043235 ! receptor complex intersection_of: GO:0032991 ! protein-containing complex intersection_of: capable_of GO:0099589 ! serotonin receptor activity relationship: capable_of GO:0099589 ! serotonin receptor activity -created_by: dos creation_date: 2016-12-21T12:24:56Z [Term] @@ -116142,7 +120170,6 @@ intersection_of: capable_of GO:0004993 ! G protein-coupled serotonin receptor ac relationship: capable_of GO:0004993 ! G protein-coupled serotonin receptor activity relationship: capable_of_part_of GO:0098664 ! G protein-coupled serotonin receptor signaling pathway property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/12942" xsd:anyURI -created_by: dos creation_date: 2016-12-21T12:28:12Z [Term] @@ -116155,7 +120182,6 @@ is_a: GO:0045202 ! synapse intersection_of: GO:0045202 ! synapse intersection_of: capable_of GO:0060012 ! synaptic transmission, glycinergic relationship: capable_of GO:0060012 ! synaptic transmission, glycinergic -created_by: dos creation_date: 2017-03-07T14:50:33Z [Term] @@ -116168,7 +120194,6 @@ is_a: GO:0045202 ! synapse intersection_of: GO:0045202 ! synapse intersection_of: capable_of GO:0001963 ! synaptic transmission, dopaminergic relationship: capable_of GO:0001963 ! synaptic transmission, dopaminergic -created_by: dos creation_date: 2017-03-07T14:51:52Z [Term] @@ -116181,14 +120206,12 @@ is_a: GO:0060627 ! regulation of vesicle-mediated transport intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0099504 ! synaptic vesicle cycle relationship: regulates GO:0099504 ! synaptic vesicle cycle -created_by: dos creation_date: 2017-03-21T16:06:48Z [Term] id: GO:0098703 name: calcium ion import across plasma membrane namespace: biological_process -alt_id: GO:1990035 def: "The directed movement of calcium ions from outside of a cell, across the plasma membrane and into the cytosol." [GOC:dos] synonym: "calcium ion import into cell" EXACT [] synonym: "calcium ion uptake into cell" EXACT [GOC:vw] @@ -116202,14 +120225,12 @@ intersection_of: has_target_end_location GO:0005829 ! cytosol intersection_of: has_target_start_location GO:0005576 ! extracellular region intersection_of: results_in_transport_across GO:0005886 ! plasma membrane property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/24965" xsd:anyURI -created_by: mah creation_date: 2013-02-07T13:07:59Z [Term] id: GO:0098704 name: carbohydrate import across plasma membrane namespace: biological_process -alt_id: GO:0097319 def: "The directed movement of a carbohydrate from outside of a cell, across the plasma membrane and into the cytosol." [GOC:dos] synonym: "carbohydrate import into cell" EXACT [] is_a: GO:0034219 ! carbohydrate transmembrane transport @@ -116219,15 +120240,12 @@ intersection_of: has_primary_input CHEBI:16646 intersection_of: has_target_end_location GO:0005829 ! cytosol intersection_of: has_target_start_location GO:0005576 ! extracellular region intersection_of: results_in_transport_across GO:0005886 ! plasma membrane -created_by: pr creation_date: 2012-05-31T02:45:02Z [Term] id: GO:0098708 name: D-glucose import across plasma membrane namespace: biological_process -alt_id: GO:0061490 -alt_id: GO:1990821 def: "The directed movement of D-glucose from outside of a cell, across the plasma membrane and into the cytosol." [GOC:dos] synonym: "glucose import across plasma membrane" EXACT [] synonym: "glucose import into cell" EXACT [] @@ -116239,16 +120257,12 @@ intersection_of: has_primary_input CHEBI:4167 intersection_of: has_target_end_location GO:0005829 ! cytosol intersection_of: has_target_start_location GO:0005576 ! extracellular region intersection_of: results_in_transport_across GO:0005886 ! plasma membrane -created_by: al creation_date: 2012-12-06T14:54:07Z [Term] id: GO:0098711 name: iron ion import across plasma membrane namespace: biological_process -alt_id: GO:0097459 -alt_id: GO:0097460 -alt_id: GO:0098707 def: "The directed movement of iron ions from outside of a cell, across the plasma membrane and into the cytosol." [GOC:mah, PMID:8321236] synonym: "ferrous ion import into cell" RELATED [GOC:mah] synonym: "ferrous iron import across plasma membrane" RELATED [] @@ -116263,15 +120277,12 @@ intersection_of: has_primary_input CHEBI:24875 intersection_of: has_target_end_location GO:0005829 ! cytosol intersection_of: has_target_start_location GO:0005576 ! extracellular region intersection_of: results_in_transport_across GO:0005886 ! plasma membrane -created_by: pr creation_date: 2012-12-20T08:29:00Z [Term] id: GO:0098712 name: L-glutamate import across plasma membrane namespace: biological_process -alt_id: GO:1903802 -alt_id: GO:1990123 def: "The directed movement of L-glutamate from outside of a cell, across the plasma membrane and into the cytosol." [GOC:dos] synonym: "L-glutamate import into cell" EXACT [] synonym: "L-glutamate(1-) import across plasma membrane" BROAD [] @@ -116283,15 +120294,12 @@ intersection_of: has_primary_input CHEBI:29985 intersection_of: has_target_end_location GO:0005829 ! cytosol intersection_of: has_target_start_location GO:0005576 ! extracellular region intersection_of: results_in_transport_across GO:0005886 ! plasma membrane -created_by: mah creation_date: 2013-06-12T12:32:47Z [Term] id: GO:0098719 name: sodium ion import across plasma membrane namespace: biological_process -alt_id: GO:0097369 -alt_id: GO:1990118 def: "The directed movement of sodium ions from outside of a cell, across the plasma membrane and into the cytosol." [GOC:dos] synonym: "sodium import" EXACT [] synonym: "sodium ion import" RELATED [] @@ -116303,7 +120311,6 @@ intersection_of: has_primary_input CHEBI:29101 intersection_of: has_target_end_location GO:0005829 ! cytosol intersection_of: has_target_start_location GO:0005576 ! extracellular region intersection_of: results_in_transport_across GO:0005886 ! plasma membrane -created_by: pr creation_date: 2012-08-03T16:55:52Z [Term] @@ -116426,7 +120433,7 @@ namespace: cellular_component def: "The part of a synapse that is part of the presynaptic cell." [GOC:dos] subset: goslim_synapse synonym: "presynaptic terminal" EXACT [] -is_a: GO:0110165 ! cellular anatomical entity +is_a: GO:0110165 ! cellular anatomical structure relationship: part_of CL:0000540 ! neuron relationship: part_of GO:0045202 ! synapse @@ -116436,7 +120443,7 @@ name: postsynapse namespace: cellular_component def: "The part of a synapse that is part of the post-synaptic cell." [GOC:dos] subset: goslim_synapse -is_a: GO:0110165 ! cellular anatomical entity +is_a: GO:0110165 ! cellular anatomical structure relationship: part_of CL:0000000 ! cell relationship: part_of GO:0045202 ! synapse @@ -116540,7 +120547,7 @@ id: GO:0098862 name: cluster of actin-based cell projections namespace: cellular_component def: "A cell part consisting of multiple, closely packed actin-based cell projections." [GOC:dos] -is_a: GO:0110165 ! cellular anatomical entity +is_a: GO:0110165 ! cellular anatomical structure relationship: has_part GO:0098858 ! actin-based cell projection relationship: part_of CL:0000000 ! cell @@ -116663,7 +120670,6 @@ is_a: GO:0098901 ! regulation of cardiac muscle cell action potential intersection_of: GO:0050789 ! regulation of biological process intersection_of: regulates GO:0086016 ! AV node cell action potential relationship: regulates GO:0086016 ! AV node cell action potential -created_by: tb creation_date: 2011-11-10T08:58:56Z [Term] @@ -116676,7 +120682,6 @@ is_a: GO:0098901 ! regulation of cardiac muscle cell action potential intersection_of: GO:0050789 ! regulation of biological process intersection_of: regulates GO:0086043 ! bundle of His cell action potential relationship: regulates GO:0086043 ! bundle of His cell action potential -created_by: dph creation_date: 2011-11-15T12:01:18Z [Term] @@ -116689,7 +120694,6 @@ is_a: GO:0098901 ! regulation of cardiac muscle cell action potential intersection_of: GO:0050789 ! regulation of biological process intersection_of: regulates GO:0086017 ! Purkinje myocyte action potential relationship: regulates GO:0086017 ! Purkinje myocyte action potential -created_by: tb creation_date: 2011-11-10T08:58:56Z [Term] @@ -116706,7 +120710,6 @@ is_a: GO:0098901 ! regulation of cardiac muscle cell action potential intersection_of: GO:0050789 ! regulation of biological process intersection_of: regulates GO:0086015 ! SA node cell action potential relationship: regulates GO:0086015 ! SA node cell action potential -created_by: tb creation_date: 2011-11-10T08:50:15Z [Term] @@ -116733,7 +120736,6 @@ intersection_of: part_of GO:0086004 ! regulation of cardiac muscle cell contract intersection_of: regulates GO:0086001 ! cardiac muscle cell action potential relationship: part_of GO:0086004 ! regulation of cardiac muscle cell contraction relationship: regulates GO:0086001 ! cardiac muscle cell action potential -created_by: tb creation_date: 2011-11-10T07:45:11Z [Term] @@ -116747,7 +120749,6 @@ is_a: GO:1903779 ! regulation of cardiac conduction intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0086014 ! atrial cardiac muscle cell action potential relationship: regulates GO:0086014 ! atrial cardiac muscle cell action potential -created_by: tb creation_date: 2011-11-10T08:49:13Z [Term] @@ -116760,7 +120761,6 @@ is_a: GO:0098901 ! regulation of cardiac muscle cell action potential intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0086005 ! ventricular cardiac muscle cell action potential relationship: regulates GO:0086005 ! ventricular cardiac muscle cell action potential -created_by: tb creation_date: 2011-11-10T07:59:36Z [Term] @@ -116800,6 +120800,46 @@ intersection_of: has_end_location GO:0098793 ! presynapse intersection_of: has_start_location GO:0098794 ! postsynapse intersection_of: process_has_causal_agent CHEBI:18059 +[Term] +id: GO:0098923 +name: retrograde trans-synaptic signaling by soluble gas +namespace: biological_process +def: "Cell-cell signaling from postsynapse to presynapse, across the synaptic cleft, mediated by an soluble gas ligand." [GOC:dos] +subset: goslim_synapse +is_a: GO:0098917 ! retrograde trans-synaptic signaling +is_a: GO:0099543 ! trans-synaptic signaling by soluble gas +intersection_of: GO:0099543 ! trans-synaptic signaling by soluble gas +intersection_of: has_end_location GO:0098793 ! presynapse +intersection_of: has_start_location GO:0098794 ! postsynapse + +[Term] +id: GO:0098924 +name: retrograde trans-synaptic signaling by nitric oxide +namespace: biological_process +def: "Cell-cell signaling from postsynapse to presynapse, across the synaptic cleft, mediated by nitric oxide." [GOC:dos] +subset: goslim_synapse +is_a: GO:0098923 ! retrograde trans-synaptic signaling by soluble gas +is_a: GO:0099548 ! trans-synaptic signaling by nitric oxide +intersection_of: GO:0099537 ! trans-synaptic signaling +intersection_of: has_end_location GO:0098793 ! presynapse +intersection_of: has_start_location GO:0098794 ! postsynapse +intersection_of: process_has_causal_agent CHEBI:16480 + +[Term] +id: GO:0098925 +name: retrograde trans-synaptic signaling by nitric oxide, modulating synaptic transmission +namespace: biological_process +def: "Modulation of synaptic transmission by cell-cell signaling from postsynapse to presynapse, across the synaptic cleft, mediated by nitric oxide." [GOC:dos] +comment: Note that this term was created for the SynGO project, and will be obsoleted when the SynGO annotations are made in Noctua. +subset: goslim_synapse +is_a: GO:0098924 ! retrograde trans-synaptic signaling by nitric oxide +is_a: GO:0099555 ! trans-synaptic signaling by nitric oxide, modulating synaptic transmission +intersection_of: GO:0099537 ! trans-synaptic signaling +intersection_of: has_end_location GO:0098793 ! presynapse +intersection_of: has_start_location GO:0098794 ! postsynapse +intersection_of: process_has_causal_agent CHEBI:16480 +intersection_of: regulates GO:0007268 ! chemical synaptic transmission + [Term] id: GO:0098926 name: postsynaptic signal transduction @@ -116881,6 +120921,19 @@ intersection_of: results_in_transport_along GO:0005874 ! microtubule relationship: has_target_end_location GO:0098794 ! postsynapse relationship: occurs_in GO:0032839 ! dendrite cytoplasm +[Term] +id: GO:0098940 +name: anterograde trans-synaptic signaling by nitric oxide +namespace: biological_process +def: "Cell-cell signaling from presynapse to postynapse, across the synaptic cleft, mediated by nitric oxide." [GOC:dos] +subset: goslim_synapse +is_a: GO:0098916 ! anterograde trans-synaptic signaling +is_a: GO:0099548 ! trans-synaptic signaling by nitric oxide +intersection_of: GO:0099537 ! trans-synaptic signaling +intersection_of: has_end_location GO:0098794 ! postsynapse +intersection_of: has_start_location GO:0098793 ! presynapse +intersection_of: process_has_causal_agent CHEBI:16480 + [Term] id: GO:0098960 name: postsynaptic neurotransmitter receptor activity @@ -117142,7 +121195,7 @@ id: GO:0099080 name: supramolecular complex namespace: cellular_component def: "A cellular component that consists of an indeterminate number of proteins or macromolecular complexes, organized into a regular, higher-order structure such as a polymer, sheet, network or a fiber." [GOC:dos] -is_a: GO:0110165 ! cellular anatomical entity +is_a: GO:0110165 ! cellular anatomical structure [Term] id: GO:0099081 @@ -117285,7 +121338,6 @@ is_a: GO:0099187 ! presynaptic cytoskeleton organization intersection_of: GO:0016043 ! cellular component organization intersection_of: results_in_organization_of GO:0099143 ! presynaptic actin cytoskeleton relationship: results_in_organization_of GO:0099143 ! presynaptic actin cytoskeleton -created_by: dos creation_date: 2017-06-09T18:34:19Z [Term] @@ -117298,7 +121350,6 @@ is_a: GO:0015629 ! actin cytoskeleton is_a: GO:0099569 ! presynaptic cytoskeleton intersection_of: GO:0015629 ! actin cytoskeleton intersection_of: part_of GO:0098793 ! presynapse -created_by: dos creation_date: 2017-06-09T18:36:19Z [Term] @@ -117315,7 +121366,6 @@ is_a: GO:1905475 ! regulation of protein localization to membrane intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0098967 ! exocytic insertion of neurotransmitter receptor to postsynaptic membrane relationship: regulates GO:0098967 ! exocytic insertion of neurotransmitter receptor to postsynaptic membrane -created_by: dos creation_date: 2017-06-09T18:49:26Z [Term] @@ -117328,7 +121378,6 @@ is_a: GO:0007267 ! cell-cell signaling intersection_of: GO:0007267 ! cell-cell signaling intersection_of: process_has_causal_agent GO:0070062 ! extracellular exosome relationship: process_has_causal_agent GO:0070062 ! extracellular exosome -created_by: dos creation_date: 2017-07-05T16:40:45Z [Term] @@ -117343,7 +121392,6 @@ is_a: GO:0099156 ! cell-cell signaling via exosome is_a: GO:0099537 ! trans-synaptic signaling intersection_of: GO:0099537 ! trans-synaptic signaling intersection_of: process_has_causal_agent GO:0070062 ! extracellular exosome -created_by: dos creation_date: 2017-07-05T16:49:44Z [Term] @@ -117356,9 +121404,19 @@ is_a: GO:0045111 ! intermediate filament cytoskeleton is_a: GO:0099571 ! postsynaptic cytoskeleton intersection_of: GO:0045111 ! intermediate filament cytoskeleton intersection_of: part_of GO:0098794 ! postsynapse -created_by: dos creation_date: 2017-08-28T15:26:08Z +[Term] +id: GO:0099163 +name: synaptic signaling by nitric oxide +namespace: biological_process +def: "Cell-cell signaling to or from a synapse, mediated by nitric oxide." [GOC:dos, PMID:19038221] +subset: goslim_synapse +is_a: GO:0099536 ! synaptic signaling +intersection_of: GO:0099536 ! synaptic signaling +intersection_of: process_has_causal_agent CHEBI:16480 +relationship: process_has_causal_agent CHEBI:16480 + [Term] id: GO:0099170 name: postsynaptic modulation of chemical synaptic transmission @@ -117369,7 +121427,6 @@ is_a: GO:0050804 ! modulation of chemical synaptic transmission intersection_of: GO:0050804 ! modulation of chemical synaptic transmission intersection_of: occurs_in GO:0098794 ! postsynapse relationship: occurs_in GO:0098794 ! postsynapse -created_by: dos creation_date: 2017-09-11T17:09:17Z [Term] @@ -117382,7 +121439,6 @@ is_a: GO:0050804 ! modulation of chemical synaptic transmission intersection_of: GO:0050804 ! modulation of chemical synaptic transmission intersection_of: occurs_in GO:0098793 ! presynapse relationship: occurs_in GO:0098793 ! presynapse -created_by: dos creation_date: 2017-09-11T17:09:31Z [Term] @@ -117466,7 +121522,6 @@ is_a: GO:0045111 ! intermediate filament cytoskeleton is_a: GO:0099569 ! presynaptic cytoskeleton intersection_of: GO:0045111 ! intermediate filament cytoskeleton intersection_of: part_of GO:0098793 ! presynapse -created_by: dos creation_date: 2017-12-01T18:10:21Z [Term] @@ -117480,7 +121535,6 @@ is_a: GO:0099188 ! postsynaptic cytoskeleton organization intersection_of: GO:0016043 ! cellular component organization intersection_of: results_in_organization_of GO:0099160 ! postsynaptic intermediate filament cytoskeleton relationship: results_in_organization_of GO:0099160 ! postsynaptic intermediate filament cytoskeleton -created_by: dos creation_date: 2017-12-20T13:47:30Z [Term] @@ -117493,7 +121547,6 @@ intersection_of: GO:0009987 ! cellular process intersection_of: results_in_organization_of GO:0099569 ! presynaptic cytoskeleton relationship: part_of GO:0099172 ! presynapse organization relationship: results_in_organization_of GO:0099569 ! presynaptic cytoskeleton -created_by: dos creation_date: 2017-12-20T15:05:34Z [Term] @@ -117507,7 +121560,6 @@ intersection_of: GO:0016043 ! cellular component organization intersection_of: results_in_organization_of GO:0099571 ! postsynaptic cytoskeleton relationship: part_of GO:0099173 ! postsynapse organization relationship: results_in_organization_of GO:0099571 ! postsynaptic cytoskeleton -created_by: dos creation_date: 2017-12-20T15:06:57Z [Term] @@ -117559,7 +121611,6 @@ relationship: occurs_in GO:0098793 ! presynapse id: GO:0099512 name: supramolecular fiber namespace: cellular_component -alt_id: GO:0043205 def: "A polymer consisting of an indefinite number of protein or protein complex subunits that have polymerised to form a fiber-shaped structure." [GOC:dos] synonym: "fibril" RELATED [] is_a: GO:0099081 ! supramolecular polymer @@ -117588,7 +121639,6 @@ is_a: GO:0030705 ! cytoskeleton-dependent intracellular transport intersection_of: GO:0046907 ! intracellular transport intersection_of: results_in_transport_along GO:0005884 ! actin filament relationship: results_in_transport_along GO:0005884 ! actin filament -created_by: tb creation_date: 2009-05-27T10:56:08Z [Term] @@ -117756,6 +121806,14 @@ intersection_of: GO:0099537 ! trans-synaptic signaling intersection_of: process_has_causal_agent CHEBI:18059 relationship: process_has_causal_agent CHEBI:18059 +[Term] +id: GO:0099543 +name: trans-synaptic signaling by soluble gas +namespace: biological_process +def: "Cell-cell signaling between presynapse and postsynapse mediated by a soluble gas ligand crossing the synaptic cleft." [GOC:dos] +subset: goslim_synapse +is_a: GO:0099537 ! trans-synaptic signaling + [Term] id: GO:0099546 name: protein catabolic process, modulating synaptic transmission @@ -117769,7 +121827,6 @@ intersection_of: has_primary_input CHEBI:36080 intersection_of: occurs_in GO:0045202 ! synapse intersection_of: regulates GO:0007268 ! chemical synaptic transmission relationship: regulates GO:0007268 ! chemical synaptic transmission -relationship: RO:0002162 NCBITaxon:33208 {all_only="true"} ! in taxon Metazoa [Term] id: GO:0099547 @@ -117784,7 +121841,17 @@ intersection_of: GO:0065007 ! biological regulation intersection_of: occurs_in GO:0045202 ! synapse intersection_of: regulates GO:0006412 ! translation intersection_of: regulates GO:0007268 ! chemical synaptic transmission -relationship: RO:0002162 NCBITaxon:33208 {all_only="true"} ! in taxon Metazoa + +[Term] +id: GO:0099548 +name: trans-synaptic signaling by nitric oxide +namespace: biological_process +def: "Cell-cell signaling between presynapse and postsynapse mediated by nitric oxide." [GOC:dos] +subset: goslim_synapse +is_a: GO:0099163 ! synaptic signaling by nitric oxide +is_a: GO:0099543 ! trans-synaptic signaling by soluble gas +intersection_of: GO:0099537 ! trans-synaptic signaling +intersection_of: process_has_causal_agent CHEBI:16480 [Term] id: GO:0099550 @@ -117824,6 +121891,29 @@ intersection_of: GO:0099537 ! trans-synaptic signaling intersection_of: process_has_causal_agent CHEBI:18059 intersection_of: regulates GO:0007268 ! chemical synaptic transmission +[Term] +id: GO:0099554 +name: trans-synaptic signaling by soluble gas, modulating synaptic transmission +namespace: biological_process +def: "Cell-cell signaling between presynapse and postsynapse, via the release and reception of gaseous molecules, that modulates the synaptic transmission properties of the synapse." [GOC:dos] +comment: Note that this term was created for the SynGO project, and will be obsoleted when the SynGO annotations are made in Noctua. +subset: goslim_synapse +is_a: GO:0099543 ! trans-synaptic signaling by soluble gas +is_a: GO:0099550 ! trans-synaptic signaling, modulating synaptic transmission + +[Term] +id: GO:0099555 +name: trans-synaptic signaling by nitric oxide, modulating synaptic transmission +namespace: biological_process +def: "Cell-cell signaling between presynapse and postsynapse, via the release and reception of nitric oxide molecules, that modulates the synaptic transmission properties of the synapse." [GOC:dos] +comment: Note that this term was created for the SynGO project, and will be obsoleted when the SynGO annotations are made in Noctua. +subset: goslim_synapse +is_a: GO:0099548 ! trans-synaptic signaling by nitric oxide +is_a: GO:0099554 ! trans-synaptic signaling by soluble gas, modulating synaptic transmission +intersection_of: GO:0099537 ! trans-synaptic signaling +intersection_of: process_has_causal_agent CHEBI:16480 +intersection_of: regulates GO:0007268 ! chemical synaptic transmission + [Term] id: GO:0099565 name: chemical synaptic transmission, postsynaptic @@ -117886,7 +121976,6 @@ intersection_of: has_primary_input CHEBI:36080 intersection_of: occurs_in GO:0045202 ! synapse intersection_of: regulates GO:0007268 ! chemical synaptic transmission intersection_of: regulates GO:0009056 ! catabolic process -relationship: RO:0002162 NCBITaxon:33208 {all_only="true"} ! in taxon Metazoa [Term] id: GO:0099575 @@ -118141,7 +122230,6 @@ is_a: GO:0001508 ! action potential intersection_of: GO:0001508 ! action potential intersection_of: regulates GO:0003009 ! skeletal muscle contraction relationship: regulates GO:0003009 ! skeletal muscle contraction -created_by: cjm creation_date: 2015-04-02T04:13:19Z [Term] @@ -118199,7 +122287,6 @@ name: cellular response to environmental stimulus namespace: biological_process def: "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an environmental stimulus." [GOC:dos] is_a: GO:0051716 ! cellular response to stimulus -created_by: dos creation_date: 2017-02-17T16:02:42Z [Term] @@ -118212,7 +122299,6 @@ is_a: GO:1903034 ! regulation of response to wounding intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0090594 ! inflammatory response to wounding relationship: regulates GO:0090594 ! inflammatory response to wounding -created_by: hjd creation_date: 2017-04-28T20:03:14Z [Term] @@ -118226,7 +122312,6 @@ is_a: GO:1903035 ! negative regulation of response to wounding intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0090594 ! inflammatory response to wounding relationship: negatively_regulates GO:0090594 ! inflammatory response to wounding -created_by: hjd creation_date: 2017-04-28T20:09:46Z [Term] @@ -118240,7 +122325,6 @@ is_a: GO:1903036 ! positive regulation of response to wounding intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0090594 ! inflammatory response to wounding relationship: positively_regulates GO:0090594 ! inflammatory response to wounding -created_by: hjd creation_date: 2017-04-28T20:16:31Z [Term] @@ -118252,7 +122336,6 @@ is_a: GO:0120036 ! plasma membrane bounded cell projection organization intersection_of: GO:0016043 ! cellular component organization intersection_of: results_in_organization_of GO:0043005 ! neuron projection relationship: results_in_organization_of GO:0043005 ! neuron projection -created_by: hjd creation_date: 2017-06-23T18:30:18Z [Term] @@ -118265,7 +122348,6 @@ is_a: GO:1903116 ! positive regulation of actin filament-based movement intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0086003 ! cardiac muscle cell contraction relationship: positively_regulates GO:0086003 ! cardiac muscle cell contraction -created_by: hjd creation_date: 2018-07-26T16:05:16Z [Term] @@ -118279,7 +122361,6 @@ is_a: GO:0086004 ! regulation of cardiac muscle cell contraction intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0086003 ! cardiac muscle cell contraction relationship: negatively_regulates GO:0086003 ! cardiac muscle cell contraction -created_by: hjd creation_date: 2018-07-26T16:10:17Z [Term] @@ -118292,7 +122373,6 @@ is_a: GO:1903358 ! regulation of Golgi organization intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0048280 ! vesicle fusion with Golgi apparatus relationship: regulates GO:0048280 ! vesicle fusion with Golgi apparatus -created_by: hjd creation_date: 2019-06-27T15:12:22Z [Term] @@ -118305,7 +122385,6 @@ is_a: GO:0106214 ! regulation of vesicle fusion with Golgi apparatus intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0048280 ! vesicle fusion with Golgi apparatus relationship: negatively_regulates GO:0048280 ! vesicle fusion with Golgi apparatus -created_by: hjd creation_date: 2019-06-27T15:17:17Z [Term] @@ -118318,7 +122397,6 @@ is_a: GO:0106214 ! regulation of vesicle fusion with Golgi apparatus intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0048280 ! vesicle fusion with Golgi apparatus relationship: positively_regulates GO:0048280 ! vesicle fusion with Golgi apparatus -created_by: hjd creation_date: 2019-06-27T15:20:59Z [Term] @@ -118330,7 +122408,6 @@ is_a: GO:1900449 ! regulation of glutamate receptor signaling pathway intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0098991 ! kainate selective glutamate receptor signaling pathway relationship: regulates GO:0098991 ! kainate selective glutamate receptor signaling pathway -created_by: hjd [Term] id: GO:0106427 @@ -118342,7 +122419,6 @@ is_a: GO:0106426 ! regulation of kainate selective glutamate receptor signaling intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0106426 ! regulation of kainate selective glutamate receptor signaling pathway relationship: negatively_regulates GO:0106426 ! regulation of kainate selective glutamate receptor signaling pathway -created_by: hjd [Term] id: GO:0106428 @@ -118355,7 +122431,6 @@ intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0106426 ! regulation of kainate selective glutamate receptor signaling pathway relationship: positively_regulates GO:0106426 ! regulation of kainate selective glutamate receptor signaling pathway property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/23558" xsd:anyURI -created_by: hjd [Term] id: GO:0110011 @@ -118366,7 +122441,6 @@ is_a: GO:1903053 ! regulation of extracellular matrix organization intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0071711 ! basement membrane organization relationship: regulates GO:0071711 ! basement membrane organization -created_by: kmv [Term] id: GO:0110020 @@ -118377,7 +122451,6 @@ is_a: GO:0032956 ! regulation of actin cytoskeleton organization intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0031032 ! actomyosin structure organization relationship: regulates GO:0031032 ! actomyosin structure organization -created_by: kmv creation_date: 2017-06-20T19:28:58Z [Term] @@ -118389,7 +122462,6 @@ is_a: GO:0051450 ! myoblast proliferation intersection_of: GO:0008283 ! cell population proliferation intersection_of: acts_on_population_of CL:0000513 ! cardiac muscle myoblast relationship: acts_on_population_of CL:0000513 ! cardiac muscle myoblast -created_by: kmv creation_date: 2017-06-29T14:35:24Z [Term] @@ -118401,7 +122473,6 @@ is_a: GO:2000291 ! regulation of myoblast proliferation intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0110021 ! cardiac muscle myoblast proliferation relationship: regulates GO:0110021 ! cardiac muscle myoblast proliferation -created_by: kmv creation_date: 2017-06-29T15:11:47Z [Term] @@ -118414,7 +122485,6 @@ is_a: GO:2000818 ! negative regulation of myoblast proliferation intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0110021 ! cardiac muscle myoblast proliferation relationship: negatively_regulates GO:0110021 ! cardiac muscle myoblast proliferation -created_by: kmv creation_date: 2017-06-29T15:18:30Z [Term] @@ -118427,7 +122497,6 @@ is_a: GO:2000288 ! positive regulation of myoblast proliferation intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0110021 ! cardiac muscle myoblast proliferation relationship: positively_regulates GO:0110021 ! cardiac muscle myoblast proliferation -created_by: kmv creation_date: 2017-06-29T15:24:16Z [Term] @@ -118440,7 +122509,6 @@ is_a: GO:1902903 ! regulation of supramolecular fiber organization intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0007015 ! actin filament organization relationship: regulates GO:0007015 ! actin filament organization -created_by: kmv creation_date: 2017-09-20T19:52:57Z [Term] @@ -118452,7 +122520,6 @@ is_a: GO:0045601 ! regulation of endothelial cell differentiation intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0060837 ! blood vessel endothelial cell differentiation relationship: regulates GO:0060837 ! blood vessel endothelial cell differentiation -created_by: kmv creation_date: 2017-10-23T14:32:09Z [Term] @@ -118465,7 +122532,6 @@ is_a: GO:0110057 ! regulation of blood vessel endothelial cell differentiation intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0060837 ! blood vessel endothelial cell differentiation relationship: positively_regulates GO:0060837 ! blood vessel endothelial cell differentiation -created_by: kmv creation_date: 2017-10-23T14:38:19Z [Term] @@ -118478,7 +122544,6 @@ is_a: GO:0110057 ! regulation of blood vessel endothelial cell differentiation intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0060837 ! blood vessel endothelial cell differentiation relationship: negatively_regulates GO:0060837 ! blood vessel endothelial cell differentiation -created_by: kmv creation_date: 2017-10-23T14:47:29Z [Term] @@ -118492,7 +122557,6 @@ intersection_of: GO:0032991 ! protein-containing complex intersection_of: capable_of GO:0008519 ! ammonium channel activity relationship: capable_of GO:0008519 ! ammonium channel activity relationship: capable_of_part_of GO:0072488 ! ammonium transmembrane transport -created_by: kmv creation_date: 2017-11-20T15:21:10Z [Term] @@ -118506,7 +122570,6 @@ is_a: GO:0016192 ! vesicle-mediated transport intersection_of: GO:0010496 ! intercellular transport intersection_of: process_has_causal_agent GO:1903561 ! extracellular vesicle relationship: process_has_causal_agent GO:1903561 ! extracellular vesicle -created_by: kmv creation_date: 2018-01-29T14:46:52Z [Term] @@ -118518,7 +122581,6 @@ is_a: GO:1901342 ! regulation of vasculature development intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0060674 ! placenta blood vessel development relationship: regulates GO:0060674 ! placenta blood vessel development -created_by: kmv creation_date: 2018-02-01T14:49:12Z [Term] @@ -118531,7 +122593,6 @@ is_a: GO:0110079 ! regulation of placenta blood vessel development intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0060674 ! placenta blood vessel development relationship: positively_regulates GO:0060674 ! placenta blood vessel development -created_by: kmv creation_date: 2018-02-01T14:55:30Z [Term] @@ -118544,7 +122605,6 @@ is_a: GO:0110079 ! regulation of placenta blood vessel development intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0060674 ! placenta blood vessel development relationship: negatively_regulates GO:0060674 ! placenta blood vessel development -created_by: kmv creation_date: 2018-02-01T15:01:11Z [Term] @@ -118556,7 +122616,6 @@ is_a: GO:0051402 ! neuron apoptotic process intersection_of: GO:0006915 ! apoptotic process intersection_of: occurs_in CL:0002608 ! hippocampal neuron relationship: occurs_in CL:0002608 ! hippocampal neuron -created_by: kmv creation_date: 2018-02-13T21:06:23Z [Term] @@ -118568,7 +122627,6 @@ is_a: GO:0043523 ! regulation of neuron apoptotic process intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0110088 ! hippocampal neuron apoptotic process relationship: regulates GO:0110088 ! hippocampal neuron apoptotic process -created_by: kmv creation_date: 2018-02-13T21:18:29Z [Term] @@ -118581,7 +122639,6 @@ is_a: GO:0110089 ! regulation of hippocampal neuron apoptotic process intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0110088 ! hippocampal neuron apoptotic process relationship: positively_regulates GO:0110088 ! hippocampal neuron apoptotic process -created_by: kmv creation_date: 2018-02-13T21:22:18Z [Term] @@ -118594,7 +122651,6 @@ is_a: GO:0110089 ! regulation of hippocampal neuron apoptotic process intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0110088 ! hippocampal neuron apoptotic process relationship: negatively_regulates GO:0110088 ! hippocampal neuron apoptotic process -created_by: kmv creation_date: 2018-02-13T21:25:01Z [Term] @@ -118607,7 +122663,6 @@ intersection_of: GO:1990748 ! cellular detoxification intersection_of: has_primary_input CHEBI:17478 relationship: has_primary_input CHEBI:17478 relationship: part_of GO:0110096 ! cellular response to aldehyde -created_by: kmv creation_date: 2018-02-16T21:19:20Z [Term] @@ -118619,7 +122674,6 @@ is_a: GO:0070887 ! cellular response to chemical stimulus intersection_of: GO:0070887 ! cellular response to chemical stimulus intersection_of: has_primary_input CHEBI:17478 relationship: has_primary_input CHEBI:17478 -created_by: kmv creation_date: 2018-02-16T21:29:18Z [Term] @@ -118633,7 +122687,6 @@ is_a: GO:2000027 ! regulation of animal organ morphogenesis intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0009887 ! animal organ morphogenesis relationship: positively_regulates GO:0009887 ! animal organ morphogenesis -created_by: kmv creation_date: 2018-07-05T14:10:14Z [Term] @@ -118647,7 +122700,6 @@ is_a: GO:2000027 ! regulation of animal organ morphogenesis intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0009887 ! animal organ morphogenesis relationship: negatively_regulates GO:0009887 ! animal organ morphogenesis -created_by: kmv creation_date: 2018-07-05T14:25:21Z [Term] @@ -118661,7 +122713,6 @@ is_a: GO:0032409 ! regulation of transporter activity intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0005319 ! lipid transporter activity relationship: regulates GO:0005319 ! lipid transporter activity -created_by: kmv creation_date: 2018-07-06T18:53:55Z [Term] @@ -118676,7 +122727,6 @@ is_a: GO:0110112 ! regulation of lipid transporter activity intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0005319 ! lipid transporter activity relationship: positively_regulates GO:0005319 ! lipid transporter activity -created_by: kmv creation_date: 2018-07-06T19:14:13Z [Term] @@ -118691,7 +122741,6 @@ is_a: GO:0110112 ! regulation of lipid transporter activity intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0005319 ! lipid transporter activity relationship: negatively_regulates GO:0005319 ! lipid transporter activity -created_by: kmv creation_date: 2018-07-06T19:21:44Z [Term] @@ -118703,7 +122752,6 @@ is_a: GO:0046532 ! regulation of photoreceptor cell differentiation intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0001751 ! compound eye photoreceptor cell differentiation relationship: regulates GO:0001751 ! compound eye photoreceptor cell differentiation -created_by: kmv creation_date: 2018-07-16T18:08:49Z [Term] @@ -118716,7 +122764,6 @@ is_a: GO:0110116 ! regulation of compound eye photoreceptor cell differentiation intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0001751 ! compound eye photoreceptor cell differentiation relationship: positively_regulates GO:0001751 ! compound eye photoreceptor cell differentiation -created_by: kmv creation_date: 2018-07-16T18:13:28Z [Term] @@ -118729,7 +122776,6 @@ is_a: GO:0110116 ! regulation of compound eye photoreceptor cell differentiation intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0001751 ! compound eye photoreceptor cell differentiation relationship: negatively_regulates GO:0001751 ! compound eye photoreceptor cell differentiation -created_by: kmv creation_date: 2018-07-16T18:15:52Z [Term] @@ -118741,7 +122787,6 @@ is_a: GO:0014812 ! muscle cell migration intersection_of: GO:0016477 ! cell migration intersection_of: results_in_movement_of CL:0002372 ! myotube relationship: results_in_movement_of CL:0002372 ! myotube -created_by: kmv creation_date: 2018-08-22T20:58:09Z [Term] @@ -118753,7 +122798,6 @@ is_a: GO:0030334 ! regulation of cell migration intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0110122 ! myotube cell migration relationship: regulates GO:0110122 ! myotube cell migration -created_by: kmv creation_date: 2018-08-22T21:06:53Z [Term] @@ -118766,7 +122810,6 @@ is_a: GO:0110123 ! regulation of myotube cell migration intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0110122 ! myotube cell migration relationship: positively_regulates GO:0110122 ! myotube cell migration -created_by: kmv creation_date: 2018-08-22T21:09:38Z [Term] @@ -118779,22 +122822,22 @@ is_a: GO:0110123 ! regulation of myotube cell migration intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0110122 ! myotube cell migration relationship: negatively_regulates GO:0110122 ! myotube cell migration -created_by: kmv creation_date: 2018-08-22T21:12:47Z [Term] id: GO:0110165 -name: cellular anatomical entity +name: cellular anatomical structure namespace: cellular_component -def: "A part of a cellular organism that is either an immaterial entity or a material entity with granularity above the level of a protein complex but below that of an anatomical system. Or, a substance produced by a cellular organism with granularity above the level of a protein complex." [GOC:kmv] +def: "A part of a cellular organism consisting of a material entity with granularity above the level of a protein complex but below that of an anatomical system. Note that cellular organisms exclude viruses." [GOC:kmv] subset: gocheck_do_not_annotate subset: goslim_pir +synonym: "cellular anatomical entity" EXACT [] is_a: CARO:0000000 is_a: GO:0005575 ! cellular_component is_a: UBERON:0000061 ! anatomical structure property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/24200" xsd:anyURI property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/26424" xsd:anyURI -created_by: kmv +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28978" xsd:anyURI creation_date: 2019-08-12T18:01:37Z [Term] @@ -118807,7 +122850,6 @@ intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:1905962 ! glutamatergic neuron differentiation relationship: regulates GO:1905962 ! glutamatergic neuron differentiation property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/13107" xsd:anyURI -created_by: krc creation_date: 2017-03-01T16:10:27Z [Term] @@ -118821,7 +122863,6 @@ intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:1905962 ! glutamatergic neuron differentiation relationship: negatively_regulates GO:1905962 ! glutamatergic neuron differentiation property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/13107" xsd:anyURI -created_by: krc creation_date: 2017-03-01T16:25:50Z [Term] @@ -118835,7 +122876,6 @@ intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:1905962 ! glutamatergic neuron differentiation relationship: positively_regulates GO:1905962 ! glutamatergic neuron differentiation property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/13107" xsd:anyURI -created_by: krc creation_date: 2017-03-01T16:35:45Z [Term] @@ -118849,7 +122889,6 @@ intersection_of: GO:0005488 ! binding intersection_of: has_primary_input CHEBI:64628 relationship: has_primary_input CHEBI:64628 property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/13143" xsd:anyURI -created_by: krc creation_date: 2017-03-17T14:54:21Z [Term] @@ -118862,7 +122901,6 @@ intersection_of: GO:0042995 ! cell projection intersection_of: has_part GO:0098590 ! plasma membrane region relationship: has_part GO:0098590 ! plasma membrane region property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/13193" xsd:anyURI -created_by: krc creation_date: 2017-03-21T17:26:07Z [Term] @@ -118881,7 +122919,6 @@ intersection_of: has_target_end_location GO:0005576 ! extracellular region intersection_of: has_target_start_location GO:0005829 ! cytosol intersection_of: results_in_transport_across GO:0005886 ! plasma membrane property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/13271" xsd:anyURI -created_by: krc creation_date: 2017-03-31T17:39:03Z [Term] @@ -118896,7 +122933,6 @@ intersection_of: GO:0022607 ! cellular component assembly intersection_of: results_in_assembly_of GO:0120025 ! plasma membrane bounded cell projection relationship: results_in_assembly_of GO:0120025 ! plasma membrane bounded cell projection property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/13298" xsd:anyURI -created_by: krc creation_date: 2017-04-24T23:56:08Z [Term] @@ -118910,7 +122946,6 @@ intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0120031 ! plasma membrane bounded cell projection assembly relationship: regulates GO:0120031 ! plasma membrane bounded cell projection assembly property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/13298" xsd:anyURI -created_by: krc creation_date: 2017-04-26T04:27:04Z [Term] @@ -118924,7 +122959,6 @@ intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0120031 ! plasma membrane bounded cell projection assembly relationship: negatively_regulates GO:0120031 ! plasma membrane bounded cell projection assembly property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/13298" xsd:anyURI -created_by: krc creation_date: 2017-04-26T04:34:31Z [Term] @@ -118939,7 +122973,6 @@ intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0120031 ! plasma membrane bounded cell projection assembly relationship: positively_regulates GO:0120031 ! plasma membrane bounded cell projection assembly property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/13298" xsd:anyURI -created_by: krc creation_date: 2017-04-26T04:34:45Z [Term] @@ -118952,7 +122985,6 @@ intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0120036 ! plasma membrane bounded cell projection organization relationship: regulates GO:0120036 ! plasma membrane bounded cell projection organization property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/13298" xsd:anyURI -created_by: krc creation_date: 2017-04-26T16:02:06Z [Term] @@ -118965,7 +122997,6 @@ intersection_of: GO:0016043 ! cellular component organization intersection_of: results_in_organization_of GO:0120025 ! plasma membrane bounded cell projection relationship: results_in_organization_of GO:0120025 ! plasma membrane bounded cell projection property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/13298" xsd:anyURI -created_by: krc creation_date: 2017-04-26T16:07:02Z [Term] @@ -118978,7 +123009,6 @@ intersection_of: GO:0009653 ! anatomical structure morphogenesis intersection_of: results_in_morphogenesis_of GO:0120025 ! plasma membrane bounded cell projection relationship: results_in_morphogenesis_of GO:0120025 ! plasma membrane bounded cell projection property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/13298" xsd:anyURI -created_by: krc creation_date: 2017-04-28T23:39:37Z [Term] @@ -118991,7 +123021,6 @@ intersection_of: GO:0005737 ! cytoplasm intersection_of: part_of GO:0043005 ! neuron projection relationship: part_of GO:0043005 ! neuron projection property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/14472" xsd:anyURI -created_by: krc creation_date: 2017-11-01T18:58:12Z [Term] @@ -119004,7 +123033,6 @@ intersection_of: GO:0016485 ! protein processing intersection_of: has_primary_input_or_output CHEBI:5391 relationship: has_primary_input_or_output CHEBI:5391 property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/14505" xsd:anyURI -created_by: krc creation_date: 2017-11-08T19:31:42Z [Term] @@ -119026,7 +123054,6 @@ intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0030574 ! collagen catabolic process relationship: positively_regulates GO:0030574 ! collagen catabolic process property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/15720" xsd:anyURI -created_by: krc creation_date: 2018-05-11T16:31:42Z [Term] @@ -119039,9 +123066,21 @@ intersection_of: GO:0006694 ! steroid biosynthetic process intersection_of: has_primary_output CHEBI:26764 relationship: has_primary_output CHEBI:26764 property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/16000" xsd:anyURI -created_by: krc creation_date: 2019-05-20T22:34:00Z +[Term] +id: GO:0120180 +name: cell-substrate junction disassembly +namespace: biological_process +def: "The disaggregation of a cell-substrate junction into its constituent components." [GOC:aruk, GOC:bc, PMID:25490267] +is_a: GO:0150115 ! cell-substrate junction organization +is_a: GO:0150146 ! cell junction disassembly +intersection_of: GO:0022411 ! cellular component disassembly +intersection_of: results_in_disassembly_of GO:0030055 ! cell-substrate junction +relationship: results_in_disassembly_of GO:0030055 ! cell-substrate junction +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/15964" xsd:anyURI +creation_date: 2018-07-12T17:33:35Z + [Term] id: GO:0120186 name: negative regulation of protein localization to chromatin @@ -119054,7 +123093,6 @@ intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0071168 ! protein localization to chromatin relationship: negatively_regulates GO:0071168 ! protein localization to chromatin property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/16012" xsd:anyURI -created_by: krc creation_date: 2018-07-14T00:19:32Z [Term] @@ -119069,7 +123107,6 @@ intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0071168 ! protein localization to chromatin relationship: positively_regulates GO:0071168 ! protein localization to chromatin property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/16012" xsd:anyURI -created_by: krc creation_date: 2018-07-14T00:21:28Z [Term] @@ -119082,7 +123119,6 @@ intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0032782 ! bile acid secretion relationship: regulates GO:0032782 ! bile acid secretion property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/16040" xsd:anyURI -created_by: krc creation_date: 2018-07-16T22:28:58Z [Term] @@ -119096,7 +123132,6 @@ intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0032782 ! bile acid secretion relationship: positively_regulates GO:0032782 ! bile acid secretion property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/16040" xsd:anyURI -created_by: krc creation_date: 2018-07-16T22:36:17Z [Term] @@ -119110,7 +123145,6 @@ intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0032782 ! bile acid secretion relationship: negatively_regulates GO:0032782 ! bile acid secretion property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/16040" xsd:anyURI -created_by: krc creation_date: 2018-07-16T22:38:34Z [Term] @@ -119126,7 +123160,6 @@ intersection_of: GO:0022607 ! cellular component assembly intersection_of: results_in_assembly_of GO:0070160 ! tight junction relationship: results_in_assembly_of GO:0070160 ! tight junction property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/16187" xsd:anyURI -created_by: krc creation_date: 2018-08-14T22:48:05Z [Term] @@ -119141,7 +123174,6 @@ intersection_of: GO:0016043 ! cellular component organization intersection_of: results_in_organization_of GO:0070160 ! tight junction relationship: results_in_organization_of GO:0070160 ! tight junction property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/16187" xsd:anyURI -created_by: krc creation_date: 2018-08-14T23:05:40Z [Term] @@ -119158,7 +123190,6 @@ intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0000105 ! L-histidine biosynthetic process relationship: regulates GO:0000105 ! L-histidine biosynthetic process property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/17537" xsd:anyURI -created_by: krc creation_date: 2019-06-27T20:55:42Z [Term] @@ -119196,7 +123227,6 @@ intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0000105 ! L-histidine biosynthetic process relationship: negatively_regulates GO:0000105 ! L-histidine biosynthetic process property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/17537" xsd:anyURI -created_by: krc creation_date: 2019-06-27T20:56:35Z [Term] @@ -119234,7 +123264,6 @@ intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0000105 ! L-histidine biosynthetic process relationship: positively_regulates GO:0000105 ! L-histidine biosynthetic process property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/17537" xsd:anyURI -created_by: krc creation_date: 2019-06-27T20:57:28Z [Term] @@ -119247,7 +123276,6 @@ intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0001824 ! blastocyst development relationship: regulates GO:0001824 ! blastocyst development property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/18871" xsd:anyURI -created_by: krc creation_date: 2020-02-17T19:59:20Z [Term] @@ -119262,7 +123290,6 @@ intersection_of: results_in_morphogenesis_of UBERON:0001737 ! larynx relationship: part_of GO:0120224 ! larynx development relationship: results_in_morphogenesis_of UBERON:0001737 ! larynx property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/18924" xsd:anyURI -created_by: krc creation_date: 2020-02-22T01:42:04Z [Term] @@ -119276,7 +123303,6 @@ intersection_of: results_in_development_of UBERON:0001737 ! larynx relationship: part_of GO:0060541 ! respiratory system development relationship: results_in_development_of UBERON:0001737 ! larynx property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/18924" xsd:anyURI -created_by: krc creation_date: 2020-02-24T17:13:10Z [Term] @@ -119290,7 +123316,6 @@ intersection_of: GO:0008104 ! protein localization intersection_of: has_target_end_location GO:0031514 ! motile cilium relationship: has_target_end_location GO:0031514 ! motile cilium property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/19588" xsd:anyURI -created_by: krc creation_date: 2020-06-05T23:43:04Z [Term] @@ -119306,7 +123331,6 @@ intersection_of: GO:0008015 ! blood circulation intersection_of: occurs_in UBERON:0001893 ! telencephalon relationship: occurs_in UBERON:0001893 ! telencephalon property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/20107" xsd:anyURI -created_by: krc creation_date: 2020-10-20T19:13:51Z [Term] @@ -119321,7 +123345,6 @@ intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0120275 ! cerebral blood circulation relationship: regulates GO:0120275 ! cerebral blood circulation property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/20107" xsd:anyURI -created_by: krc creation_date: 2020-10-21T06:52:22Z [Term] @@ -119341,7 +123364,6 @@ intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0120275 ! cerebral blood circulation relationship: positively_regulates GO:0120275 ! cerebral blood circulation property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/20107" xsd:anyURI -created_by: krc creation_date: 2020-10-21T06:55:42Z [Term] @@ -119361,7 +123383,6 @@ intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0120275 ! cerebral blood circulation relationship: negatively_regulates GO:0120275 ! cerebral blood circulation property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/20107" xsd:anyURI -created_by: krc creation_date: 2020-10-21T07:02:05Z [Term] @@ -119374,7 +123395,6 @@ intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0043473 ! pigmentation relationship: regulates GO:0043473 ! pigmentation property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/20524" xsd:anyURI -created_by: krc creation_date: 2021-02-09T19:37:35Z [Term] @@ -119394,7 +123414,6 @@ intersection_of: results_in_assembly_of GO:0097545 ! axonemal doublet microtubul relationship: part_of GO:0035082 ! axoneme assembly relationship: results_in_assembly_of GO:0097545 ! axonemal doublet microtubule property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/21154" xsd:anyURI -created_by: krc creation_date: 2021-03-23T16:28:18Z [Term] @@ -119410,7 +123429,6 @@ relationship: occurs_in CL:0000019 ! sperm relationship: part_of GO:0007286 ! spermatid development relationship: part_of GO:0030317 ! flagellated sperm motility property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/21361" xsd:anyURI -created_by: krc creation_date: 2021-04-29T01:27:27Z [Term] @@ -119420,7 +123438,6 @@ namespace: cellular_component def: "A telopode is a plasma membrane bounded cell projection that is present on a telocyte and is tens to hundreds of microns long. Telopodes form a labyrinthine system communicating through gap junctions." [GOC:krc, MESH:D000067617, PMID:20367664] is_a: GO:0120025 ! plasma membrane bounded cell projection property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/21973" xsd:anyURI -created_by: krc creation_date: 2021-08-16T16:45:21Z [Term] @@ -119434,7 +123451,6 @@ intersection_of: results_in_formation_of UBERON:0003915 ! endothelial tube relationship: part_of GO:0061154 ! endothelial tube morphogenesis relationship: results_in_formation_of UBERON:0003915 ! endothelial tube property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/22302" xsd:anyURI -created_by: krc creation_date: 2022-05-25T16:17:59Z [Term] @@ -119449,7 +123465,6 @@ is_a: GO:1903046 ! meiotic cell cycle process intersection_of: GO:0000280 ! nuclear division intersection_of: part_of GO:0051321 ! meiotic cell cycle property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/19910" xsd:anyURI -created_by: pg creation_date: 2017-03-23T09:40:00Z [Term] @@ -119465,7 +123480,6 @@ is_a: GO:1903047 ! mitotic cell cycle process intersection_of: GO:0000280 ! nuclear division intersection_of: part_of GO:0000278 ! mitotic cell cycle property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/19910" xsd:anyURI -created_by: pg creation_date: 2017-03-23T14:44:23Z [Term] @@ -119478,7 +123492,6 @@ is_a: GO:0009987 ! cellular process intersection_of: GO:0009987 ! cellular process intersection_of: part_of GO:0006887 ! exocytosis relationship: part_of GO:0006887 ! exocytosis -created_by: pg creation_date: 2017-05-15T13:20:45Z [Term] @@ -119490,7 +123503,6 @@ is_a: GO:0098609 ! cell-cell adhesion intersection_of: GO:0098609 ! cell-cell adhesion intersection_of: part_of GO:0051716 ! cellular response to stimulus relationship: part_of GO:0051716 ! cellular response to stimulus -created_by: pg creation_date: 2017-05-24T11:37:30Z [Term] @@ -119501,7 +123513,6 @@ def: "The process by which an organelle membrane interacts with another membrane subset: goslim_pombe is_a: GO:0022406 ! membrane docking is_a: GO:0051640 ! organelle localization -created_by: pg creation_date: 2017-06-27T09:58:51Z [Term] @@ -119513,7 +123524,6 @@ is_a: GO:0051049 ! regulation of transport intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0042953 ! lipoprotein transport relationship: regulates GO:0042953 ! lipoprotein transport -created_by: pg creation_date: 2017-07-21T15:35:47Z [Term] @@ -119526,7 +123536,6 @@ is_a: GO:0140075 ! regulation of lipoprotein transport intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0042953 ! lipoprotein transport relationship: negatively_regulates GO:0042953 ! lipoprotein transport -created_by: pg creation_date: 2017-07-21T15:39:50Z [Term] @@ -119539,7 +123548,6 @@ is_a: GO:0140075 ! regulation of lipoprotein transport intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0042953 ! lipoprotein transport relationship: positively_regulates GO:0042953 ! lipoprotein transport -created_by: pg creation_date: 2017-07-21T15:41:54Z [Term] @@ -119555,7 +123563,6 @@ intersection_of: GO:0003824 ! catalytic activity intersection_of: has_primary_input PR:000000001 ! protein relationship: has_primary_input PR:000000001 ! protein property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/14225" xsd:anyURI -created_by: pg creation_date: 2017-09-14T10:32:59Z [Term] @@ -119571,7 +123578,6 @@ intersection_of: GO:0003824 ! catalytic activity intersection_of: has_primary_input CHEBI:16991 relationship: has_primary_input CHEBI:16991 property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/14225" xsd:anyURI -created_by: pg creation_date: 2017-09-14T12:03:51Z [Term] @@ -119588,7 +123594,6 @@ intersection_of: has_primary_input CHEBI:33697 relationship: has_primary_input CHEBI:33697 property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/14225" xsd:anyURI property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/21612" xsd:anyURI -created_by: pg creation_date: 2017-09-14T12:05:21Z [Term] @@ -119602,28 +123607,8 @@ intersection_of: GO:0003824 ! catalytic activity intersection_of: has_primary_input CHEBI:17089 relationship: has_primary_input CHEBI:17089 property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/14225" xsd:anyURI -created_by: pg creation_date: 2017-09-15T19:27:54Z -[Term] -id: GO:0140110 -name: transcription regulator activity -namespace: molecular_function -def: "A molecular function that controls the rate, timing and/or magnitude of gene transcription. The function of transcriptional regulators is to modulate gene expression at the transcription step so that they are expressed in the right cell at the right time and in the right amount throughout the life of the cell and the organism. Genes are transcriptional units, and include bacterial operons." [GOC:pg, GOC:txnOH-2018, Wikipedia:Transcription_factor] -subset: gocheck_do_not_annotate -subset: goslim_euk_cellular_processes_ribbon -subset: goslim_flybase_ribbon -subset: goslim_generic -subset: goslim_plant -subset: goslim_plant_ribbon -subset: goslim_prokaryote -subset: goslim_prokaryote_ribbon -is_a: GO:0003674 ! molecular_function -property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/13588" xsd:anyURI -property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/23609" xsd:anyURI -created_by: pg -creation_date: 2017-10-18T07:05:44Z - [Term] id: GO:0140112 name: extracellular vesicle biogenesis @@ -119632,7 +123617,6 @@ def: "The assembly and secretion a set of components to form an extracellular ve synonym: "extracellular vesicle assembly" EXACT [] is_a: GO:0044085 ! cellular component biogenesis property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/14256" xsd:anyURI -created_by: pg creation_date: 2017-10-23T11:53:42Z [Term] @@ -119649,7 +123633,6 @@ intersection_of: has_target_start_location GO:0005829 ! cytosol intersection_of: results_in_transport_across GO:0005886 ! plasma membrane relationship: has_target_start_location GO:0005829 ! cytosol relationship: results_in_transport_across GO:0005886 ! plasma membrane -created_by: pg creation_date: 2017-10-24T14:38:16Z [Term] @@ -119663,7 +123646,6 @@ is_a: GO:2000403 ! positive regulation of lymphocyte migration intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0048247 ! lymphocyte chemotaxis relationship: positively_regulates GO:0048247 ! lymphocyte chemotaxis -created_by: pg creation_date: 2017-11-02T10:26:40Z [Term] @@ -119681,7 +123663,6 @@ intersection_of: results_in_transport_across GO:0005774 ! vacuolar membrane relationship: has_target_end_location GO:0005775 ! vacuolar lumen relationship: has_target_start_location GO:0005829 ! cytosol relationship: results_in_transport_across GO:0005774 ! vacuolar membrane -created_by: pg creation_date: 2017-12-13T15:15:29Z [Term] @@ -119696,7 +123677,6 @@ intersection_of: has_primary_input CHEBI:28938 intersection_of: has_target_end_location GO:0005829 ! cytosol intersection_of: has_target_start_location GO:0005576 ! extracellular region intersection_of: results_in_transport_across GO:0005886 ! plasma membrane -created_by: pg creation_date: 2018-01-26T12:39:56Z [Term] @@ -119715,7 +123695,6 @@ intersection_of: GO:0007165 ! signal transduction intersection_of: has_part GO:0022850 ! serotonin-gated monoatomic cation channel activity intersection_of: starts_with GO:0099589 ! serotonin receptor activity relationship: has_part GO:0022850 ! serotonin-gated monoatomic cation channel activity -created_by: pg creation_date: 2018-06-02T13:34:51Z [Term] @@ -119732,7 +123711,6 @@ intersection_of: has_primary_input GO:0098878 ! neurotransmitter receptor comple intersection_of: has_target_end_location GO:0098793 ! presynapse intersection_of: occurs_in GO:1904115 ! axon cytoplasm intersection_of: results_in_transport_along GO:0005874 ! microtubule -created_by: pg creation_date: 2018-07-09T09:41:37Z [Term] @@ -119747,7 +123725,6 @@ intersection_of: GO:0006412 ! translation intersection_of: occurs_in GO:0098793 ! presynapse relationship: occurs_in GO:0098793 ! presynapse property_value: term_tracker_item "https://github.com/geneontology/synapse/issues/216" xsd:anyURI -created_by: pg creation_date: 2018-07-13T13:00:33Z [Term] @@ -119763,7 +123740,6 @@ intersection_of: occurs_in GO:0098793 ! presynapse intersection_of: regulates GO:0007268 ! chemical synaptic transmission relationship: regulates GO:0007268 ! chemical synaptic transmission property_value: term_tracker_item "https://github.com/geneontology/synapse/issues/216" xsd:anyURI -created_by: pg creation_date: 2018-07-13T13:07:23Z [Term] @@ -119780,7 +123756,6 @@ intersection_of: GO:0006897 ! endocytosis intersection_of: occurs_in GO:0098793 ! presynapse relationship: occurs_in GO:0098793 ! presynapse property_value: term_tracker_item "https://github.com/geneontology/synapse/issues/230" xsd:anyURI -created_by: pg creation_date: 2018-07-15T07:33:55Z [Term] @@ -119797,7 +123772,6 @@ intersection_of: GO:0006897 ! endocytosis intersection_of: occurs_in GO:0098794 ! postsynapse relationship: occurs_in GO:0098794 ! postsynapse property_value: term_tracker_item "https://github.com/geneontology/synapse/issues/230" xsd:anyURI -created_by: pg creation_date: 2018-07-15T07:38:27Z [Term] @@ -119814,7 +123788,6 @@ relationship: occurs_in GO:0045202 ! synapse relationship: RO:0002160 NCBITaxon:33208 ! only in taxon Metazoa relationship: RO:0002162 NCBITaxon:33208 {all_only="true"} ! in taxon Metazoa property_value: term_tracker_item "https://github.com/geneontology/synapse/issues/210" xsd:anyURI -created_by: pg creation_date: 2018-07-15T09:23:12Z [Term] @@ -119829,7 +123802,6 @@ intersection_of: GO:0006412 ! translation intersection_of: occurs_in GO:0098794 ! postsynapse relationship: occurs_in GO:0098794 ! postsynapse property_value: term_tracker_item "https://github.com/geneontology/synapse/issues/210" xsd:anyURI -created_by: pg creation_date: 2018-07-15T09:26:27Z [Term] @@ -119847,7 +123819,6 @@ relationship: occurs_in GO:0045202 ! synapse relationship: RO:0002160 NCBITaxon:33208 ! only in taxon Metazoa relationship: RO:0002162 NCBITaxon:33208 {all_only="true"} ! in taxon Metazoa property_value: term_tracker_item "https://github.com/geneontology/synapse/issues/210" xsd:anyURI -created_by: pg creation_date: 2018-07-15T09:38:26Z [Term] @@ -119863,7 +123834,6 @@ intersection_of: occurs_in GO:0098793 ! presynapse intersection_of: regulates GO:0006412 ! translation relationship: occurs_in GO:0098793 ! presynapse property_value: term_tracker_item "https://github.com/geneontology/synapse/issues/210" xsd:anyURI -created_by: pg creation_date: 2018-07-15T09:38:33Z [Term] @@ -119879,7 +123849,6 @@ intersection_of: occurs_in GO:0098794 ! postsynapse intersection_of: regulates GO:0006412 ! translation relationship: occurs_in GO:0098794 ! postsynapse property_value: term_tracker_item "https://github.com/geneontology/synapse/issues/210" xsd:anyURI -created_by: pg creation_date: 2018-07-15T09:38:54Z [Term] @@ -119898,7 +123867,6 @@ relationship: occurs_in GO:0045202 ! synapse relationship: RO:0002160 NCBITaxon:33208 ! only in taxon Metazoa relationship: RO:0002162 NCBITaxon:33208 {all_only="true"} ! in taxon Metazoa property_value: term_tracker_item "https://github.com/geneontology/synapse/issues/210" xsd:anyURI -created_by: pg creation_date: 2018-07-15T10:12:51Z [Term] @@ -119914,7 +123882,6 @@ intersection_of: has_primary_input CHEBI:36080 intersection_of: occurs_in GO:0098793 ! presynapse relationship: occurs_in GO:0098793 ! presynapse property_value: term_tracker_item "https://github.com/geneontology/synapse/issues/204" xsd:anyURI -created_by: pg creation_date: 2018-07-15T10:23:49Z [Term] @@ -119930,7 +123897,6 @@ intersection_of: has_primary_input CHEBI:36080 intersection_of: occurs_in GO:0098794 ! postsynapse relationship: occurs_in GO:0098794 ! postsynapse property_value: term_tracker_item "https://github.com/geneontology/synapse/issues/204" xsd:anyURI -created_by: pg creation_date: 2018-07-15T10:25:04Z [Term] @@ -119950,7 +123916,6 @@ relationship: occurs_in GO:0045202 ! synapse relationship: RO:0002160 NCBITaxon:33208 ! only in taxon Metazoa relationship: RO:0002162 NCBITaxon:33208 {all_only="true"} ! in taxon Metazoa property_value: term_tracker_item "https://github.com/geneontology/synapse/issues/204" xsd:anyURI -created_by: pg creation_date: 2018-07-15T10:34:56Z [Term] @@ -119967,7 +123932,6 @@ intersection_of: occurs_in GO:0098793 ! presynapse intersection_of: regulates GO:0009056 ! catabolic process relationship: occurs_in GO:0098793 ! presynapse property_value: term_tracker_item "https://github.com/geneontology/synapse/issues/204" xsd:anyURI -created_by: pg creation_date: 2018-07-15T10:35:39Z [Term] @@ -119984,7 +123948,6 @@ intersection_of: occurs_in GO:0098794 ! postsynapse intersection_of: regulates GO:0009056 ! catabolic process relationship: occurs_in GO:0098794 ! postsynapse property_value: term_tracker_item "https://github.com/geneontology/synapse/issues/204" xsd:anyURI -created_by: pg creation_date: 2018-07-15T10:35:56Z [Term] @@ -119998,7 +123961,6 @@ is_a: BFO:0000003 is_a: GO:0009987 ! cellular process relationship: has_part GO:0045026 ! plasma membrane fusion property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/15939" xsd:anyURI -created_by: pg creation_date: 2018-08-13T18:38:18Z [Term] @@ -120013,23 +123975,18 @@ intersection_of: has_primary_input CHEBI:18133 intersection_of: has_target_end_location GO:0005829 ! cytosol intersection_of: has_target_start_location GO:0005576 ! extracellular region intersection_of: results_in_transport_across GO:0005886 ! plasma membrane -created_by: pg creation_date: 2018-10-01T08:49:49Z [Term] id: GO:0140297 name: DNA-binding transcription factor binding namespace: molecular_function -alt_id: GO:0001107 -alt_id: GO:0033613 -alt_id: GO:0070491 def: "Binding to a DNA-binding transcription factor, a protein that interacts with a specific DNA sequence (sometimes referred to as a motif) within the regulatory region of a gene to modulate transcription." [GOC:txnOH-2018] synonym: "activating transcription factor binding" RELATED [] synonym: "repressing transcription factor binding" RELATED [] synonym: "transcription activator binding" RELATED [] is_a: GO:0008134 ! transcription factor binding property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/19354" xsd:anyURI -created_by: pg creation_date: 2018-11-28T12:48:20Z [Term] @@ -120049,7 +124006,6 @@ intersection_of: GO:0005215 ! transporter activity intersection_of: has_primary_input PR:000000001 ! protein relationship: has_primary_input PR:000000001 ! protein property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/17073" xsd:anyURI -created_by: pg creation_date: 2019-04-01T10:41:38Z [Term] @@ -120065,7 +124021,6 @@ intersection_of: has_target_end_location GO:0005576 ! extracellular region intersection_of: has_target_start_location GO:0005622 ! intracellular anatomical structure relationship: has_target_end_location GO:0005576 ! extracellular region relationship: has_target_start_location GO:0005622 ! intracellular anatomical structure -created_by: pg creation_date: 2019-05-22T11:20:45Z [Term] @@ -120080,7 +124035,6 @@ intersection_of: GO:0006810 ! transport intersection_of: has_primary_input CHEBI:18059 intersection_of: has_target_end_location GO:0005576 ! extracellular region intersection_of: has_target_start_location GO:0005622 ! intracellular anatomical structure -created_by: pg creation_date: 2019-05-22T11:33:07Z [Term] @@ -120096,7 +124050,6 @@ intersection_of: has_target_end_location GO:0005622 ! intracellular anatomical s intersection_of: has_target_start_location GO:0005576 ! extracellular region relationship: has_target_end_location GO:0005622 ! intracellular anatomical structure relationship: has_target_start_location GO:0005576 ! extracellular region -created_by: pg creation_date: 2019-05-22T11:38:15Z [Term] @@ -120105,20 +124058,17 @@ name: immune receptor activity namespace: molecular_function def: "Receiving a signal and transmitting it in a cell to initiate an immune response." [PMID:31415752, Wikipedia:Immune_receptor] is_a: GO:0038023 ! signaling receptor activity -created_by: pg creation_date: 2019-10-18T14:11:15Z [Term] id: GO:0140448 name: signaling receptor ligand precursor processing namespace: biological_process -alt_id: GO:0035638 def: "The cleavage of a peptide bond in a precursor form of a signaling receptor ligand, resulting in the mature (active) form of the ligand." [PMID:29247995] synonym: "ligand maturation" NARROW [GOC:bf] synonym: "signal maturation" RELATED [] is_a: GO:0016485 ! protein processing property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/19216" xsd:anyURI -created_by: pg creation_date: 2020-04-03T13:30:04Z [Term] @@ -120133,7 +124083,6 @@ is_a: GO:0032991 ! protein-containing complex intersection_of: GO:0032991 ! protein-containing complex intersection_of: part_of GO:0005634 ! nucleus relationship: part_of GO:0005634 ! nucleus -created_by: pg creation_date: 2020-09-09T05:12:38Z [Term] @@ -120143,7 +124092,6 @@ namespace: biological_process def: "Reactions triggered in response to the presence of a symbiont that act to protect or prevent damage to the host." [GOC:pg] is_a: GO:0098542 ! defense response to other organism property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/20261" xsd:anyURI -created_by: pg creation_date: 2020-11-11T17:19:06Z [Term] @@ -120156,7 +124104,6 @@ intersection_of: GO:0048285 ! organelle fission intersection_of: results_in_fission_of GO:0005773 ! vacuole relationship: results_in_fission_of GO:0005773 ! vacuole property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/20639" xsd:anyURI -created_by: pg creation_date: 2021-01-04T10:17:58Z [Term] @@ -120170,7 +124117,6 @@ intersection_of: GO:0003824 ! catalytic activity intersection_of: has_primary_input CHEBI:33696 relationship: has_primary_input CHEBI:33696 property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/21402" xsd:anyURI -created_by: pg creation_date: 2021-05-11T06:31:07Z [Term] @@ -120184,7 +124130,6 @@ intersection_of: GO:0016477 ! cell migration intersection_of: results_in_movement_of CL:0000598 ! pyramidal neuron relationship: results_in_movement_of CL:0000598 ! pyramidal neuron property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/21476" xsd:anyURI -created_by: pg creation_date: 2021-05-25T12:48:12Z [Term] @@ -120210,7 +124155,6 @@ intersection_of: has_part GO:0016887 ! ATP hydrolysis activity relationship: has_part GO:0016887 ! ATP hydrolysis activity property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/21612" xsd:anyURI property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/22371" xsd:anyURI -created_by: pg creation_date: 2021-06-15T07:35:06Z [Term] @@ -120223,7 +124167,6 @@ intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0036162 ! oxytocin production relationship: regulates GO:0036162 ! oxytocin production property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/21535" xsd:anyURI -created_by: pg creation_date: 2021-06-24T11:28:07Z [Term] @@ -120237,7 +124180,6 @@ intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0036162 ! oxytocin production relationship: positively_regulates GO:0036162 ! oxytocin production property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/21535" xsd:anyURI -created_by: pg creation_date: 2021-06-24T11:31:26Z [Term] @@ -120251,23 +124193,23 @@ intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0036162 ! oxytocin production relationship: negatively_regulates GO:0036162 ! oxytocin production property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/21535" xsd:anyURI -created_by: pg creation_date: 2021-06-24T11:31:45Z [Term] id: GO:0140694 -name: non-membrane-bounded organelle assembly +name: membraneless organelle assembly namespace: biological_process def: "The aggregation, arrangement and bonding together of a set of components to form a non-membrane-bounded organelle." [PMID:28225081] +synonym: "non-membrane-bounded organelle assembly" EXACT [] synonym: "non-membrane-bounded organelle formation" EXACT [] synonym: "non-membrane-enclosed organelle assembly" EXACT [] synonym: "non-membrane-enclosed organelle formation" EXACT [] is_a: GO:0070925 ! organelle assembly intersection_of: GO:0022607 ! cellular component assembly -intersection_of: results_in_assembly_of GO:0043228 ! non-membrane-bounded organelle -relationship: results_in_assembly_of GO:0043228 ! non-membrane-bounded organelle +intersection_of: results_in_assembly_of GO:0043228 ! membraneless organelle +relationship: results_in_assembly_of GO:0043228 ! membraneless organelle property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/21939" xsd:anyURI -created_by: pg +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29106" xsd:anyURI creation_date: 2021-08-09T15:30:06Z [Term] @@ -120282,7 +124224,6 @@ intersection_of: GO:0007588 ! excretion intersection_of: has_primary_input CHEBI:28938 relationship: has_primary_input CHEBI:28938 property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/22368" xsd:anyURI -created_by: pg creation_date: 2021-11-24T17:55:51Z [Term] @@ -120298,7 +124239,6 @@ intersection_of: results_in_transport_across GO:0016020 ! membrane relationship: has_target_end_location GO:0005794 ! Golgi apparatus relationship: has_target_start_location GO:0005829 ! cytosol property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/21524" xsd:anyURI -created_by: pg creation_date: 2022-05-16T06:59:22Z [Term] @@ -120313,7 +124253,6 @@ is_a: GO:0048878 ! chemical homeostasis intersection_of: GO:0048871 ! multicellular organismal-level homeostasis intersection_of: regulates_levels_of CHEBI:24431 property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/24554" xsd:anyURI -created_by: pg creation_date: 2022-12-12T09:11:06Z [Term] @@ -120325,7 +124264,6 @@ synonym: "intracellular signaling cascade" EXACT [] synonym: "intracellular signaling module" EXACT [] is_a: GO:0035556 ! intracellular signal transduction property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/26557" xsd:anyURI -created_by: pg creation_date: 2023-12-04T14:13:20Z [Term] @@ -120342,7 +124280,6 @@ intersection_of: has_primary_output CHEBI:33696 relationship: has_primary_output CHEBI:33696 property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27408" xsd:anyURI property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27633" xsd:anyURI -created_by: pg creation_date: 2024-03-25T07:33:40Z [Term] @@ -120359,20 +124296,8 @@ intersection_of: has_primary_input CHEBI:33696 relationship: has_primary_input CHEBI:33696 property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27408" xsd:anyURI property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27633" xsd:anyURI -created_by: pg creation_date: 2024-03-25T07:35:06Z -[Term] -id: GO:0141193 -name: nuclear receptor-mediated signaling pathway -namespace: biological_process -def: "The series of molecular signals initiated by a signaling molecule binding to an intracellular receptor of the nuclear receptor protein family, and ending with regulation of a downstream cellular process, e.g. transcription." [PMID:25614732] -synonym: "nuclear receptor signaling pathway" EXACT [] -is_a: GO:0030522 ! intracellular receptor signaling pathway -property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27599" xsd:anyURI -created_by: pg -creation_date: 2024-04-12T13:08:13Z - [Term] id: GO:0150031 name: regulation of protein localization to lysosome @@ -120382,7 +124307,6 @@ is_a: GO:0032880 ! regulation of protein localization intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0061462 ! protein localization to lysosome relationship: regulates GO:0061462 ! protein localization to lysosome -created_by: bc creation_date: 2018-02-06T17:07:03Z [Term] @@ -120395,7 +124319,6 @@ is_a: GO:1903829 ! positive regulation of protein localization intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0061462 ! protein localization to lysosome relationship: positively_regulates GO:0061462 ! protein localization to lysosome -created_by: bc creation_date: 2018-02-06T17:11:02Z [Term] @@ -120408,7 +124331,6 @@ is_a: GO:1903828 ! negative regulation of protein localization intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0061462 ! protein localization to lysosome relationship: negatively_regulates GO:0061462 ! protein localization to lysosome -created_by: bc creation_date: 2018-02-06T17:14:16Z [Term] @@ -120418,11 +124340,23 @@ namespace: cellular_component def: "That part of an axon close to and including the growth cone or the axon terminus." [GOC:aruk, GOC:bc, PMID:17202468] synonym: "distal part of axon" EXACT [] synonym: "distal part of the axon" EXACT [PMID:17202468] -is_a: GO:0110165 ! cellular anatomical entity +is_a: GO:0110165 ! cellular anatomical structure relationship: part_of GO:0030424 ! axon -created_by: bc creation_date: 2018-02-19T15:04:24Z +[Term] +id: GO:0150045 +name: regulation of synaptic signaling by nitric oxide +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of synaptic signaling by nitric oxide." [GOC:aruk, GOC:bc, PMID:26311509] +subset: goslim_synapse +is_a: GO:0010646 ! regulation of cell communication +is_a: GO:0023051 ! regulation of signaling +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0099163 ! synaptic signaling by nitric oxide +relationship: regulates GO:0099163 ! synaptic signaling by nitric oxide +creation_date: 2018-04-23T09:42:25Z + [Term] id: GO:0150052 name: regulation of postsynapse assembly @@ -120434,7 +124368,6 @@ is_a: GO:0099175 ! regulation of postsynapse organization intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0099068 ! postsynapse assembly relationship: regulates GO:0099068 ! postsynapse assembly -created_by: bc creation_date: 2018-05-08T16:38:55Z [Term] @@ -120445,7 +124378,6 @@ def: "The process whose specific outcome is the progression of the visual system synonym: "optic pathway development" RELATED [] synonym: "visual pathway development" RELATED [] is_a: GO:0048880 ! sensory system development -created_by: bc creation_date: 2018-07-23T10:31:58Z [Term] @@ -120457,7 +124389,6 @@ synonym: "nerve tissue inflammatory response" EXACT [] synonym: "nervous tissue inflammatory response" EXACT [] synonym: "neural tissue inflammatory response" EXACT [] is_a: GO:0006954 ! inflammatory response -created_by: bc creation_date: 2018-07-26T12:25:34Z [Term] @@ -120471,7 +124402,6 @@ intersection_of: regulates GO:0150076 ! neuroinflammatory response relationship: regulates GO:0150076 ! neuroinflammatory response relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata relationship: RO:0002162 NCBITaxon:7742 {all_only="true"} ! in taxon Vertebrata -created_by: bc creation_date: 2018-07-26T12:32:18Z [Term] @@ -120484,7 +124414,6 @@ is_a: GO:0150077 ! regulation of neuroinflammatory response intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0150076 ! neuroinflammatory response relationship: positively_regulates GO:0150076 ! neuroinflammatory response -created_by: bc creation_date: 2018-07-26T12:35:50Z [Term] @@ -120497,7 +124426,6 @@ is_a: GO:0150077 ! regulation of neuroinflammatory response intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0150076 ! neuroinflammatory response relationship: negatively_regulates GO:0150076 ! neuroinflammatory response -created_by: bc creation_date: 2018-07-26T12:38:08Z [Term] @@ -120518,7 +124446,6 @@ intersection_of: has_end_location CL:0000540 ! neuron intersection_of: has_start_location CL:0000125 ! glial cell relationship: has_end_location CL:0000540 ! neuron relationship: has_start_location CL:0000125 ! glial cell -created_by: bc creation_date: 2018-12-17T12:28:09Z [Term] @@ -120539,7 +124466,6 @@ intersection_of: has_end_location CL:0000125 ! glial cell intersection_of: has_start_location CL:0000540 ! neuron relationship: has_end_location CL:0000125 ! glial cell relationship: has_start_location CL:0000540 ! neuron -created_by: bc creation_date: 2018-12-17T12:30:12Z [Term] @@ -120552,7 +124478,6 @@ is_a: GO:0002695 ! negative regulation of leukocyte activation intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0042117 ! monocyte activation relationship: negatively_regulates GO:0042117 ! monocyte activation -created_by: bc creation_date: 2019-04-26T20:01:24Z [Term] @@ -120569,7 +124494,6 @@ intersection_of: results_in_transport_across UBERON:0000120 ! blood brain barrie relationship: results_in_transport_across UBERON:0000120 ! blood brain barrier relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa relationship: RO:0002162 NCBITaxon:6072 {all_only="true"} ! in taxon Eumetazoa -created_by: bc creation_date: 2019-05-27T09:12:03Z [Term] @@ -120581,7 +124505,6 @@ is_a: GO:1902414 ! protein localization to cell junction intersection_of: GO:0008104 ! protein localization intersection_of: has_target_end_location GO:0005911 ! cell-cell junction relationship: has_target_end_location GO:0005911 ! cell-cell junction -created_by: bc creation_date: 2019-06-11T11:00:18Z [Term] @@ -120593,7 +124516,6 @@ is_a: GO:0032880 ! regulation of protein localization intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0150105 ! protein localization to cell-cell junction relationship: regulates GO:0150105 ! protein localization to cell-cell junction -created_by: bc creation_date: 2019-06-11T11:17:15Z [Term] @@ -120606,7 +124528,6 @@ is_a: GO:1903829 ! positive regulation of protein localization intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0150105 ! protein localization to cell-cell junction relationship: positively_regulates GO:0150105 ! protein localization to cell-cell junction -created_by: bc creation_date: 2019-06-11T11:23:58Z [Term] @@ -120618,9 +124539,54 @@ is_a: GO:0051049 ! regulation of transport intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0070633 ! transepithelial transport relationship: regulates GO:0070633 ! transepithelial transport -created_by: bc creation_date: 2019-09-15T07:16:49Z +[Term] +id: GO:0150115 +name: cell-substrate junction organization +namespace: biological_process +def: "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a cell-substrate junction. A cell-substrate junction is a specialized region of connection between a cell and the extracellular matrix." [GOC:aruk, GOC:bc, PMID:10419689, PMID:1643657, PMID:16805308, PMID:26923917, PMID:8314002] +is_a: GO:0034330 ! cell junction organization +intersection_of: GO:0034330 ! cell junction organization +intersection_of: results_in_organization_of GO:0030055 ! cell-substrate junction +relationship: results_in_organization_of GO:0030055 ! cell-substrate junction +creation_date: 2019-11-14T11:06:29Z + +[Term] +id: GO:0150116 +name: regulation of cell-substrate junction organization +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of cell-substrate junction organization." [GOC:aruk] +is_a: GO:0051128 ! regulation of cellular component organization +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0150115 ! cell-substrate junction organization +relationship: regulates GO:0150115 ! cell-substrate junction organization +creation_date: 2019-11-14T12:12:27Z + +[Term] +id: GO:0150117 +name: positive regulation of cell-substrate junction organization +namespace: biological_process +def: "Any process that activates or increases the frequency, rate or extent of cell-substrate junction organization." [GOC:aruk] +is_a: GO:0051130 ! positive regulation of cellular component organization +is_a: GO:0150116 ! regulation of cell-substrate junction organization +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0150115 ! cell-substrate junction organization +relationship: positively_regulates GO:0150115 ! cell-substrate junction organization +creation_date: 2019-11-14T12:15:07Z + +[Term] +id: GO:0150118 +name: negative regulation of cell-substrate junction organization +namespace: biological_process +def: "Any process that stops, prevents or reduces the frequency, rate or extent of cell-substrate junction organization." [GOC:aruk] +is_a: GO:0051129 ! negative regulation of cellular component organization +is_a: GO:0150116 ! regulation of cell-substrate junction organization +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0150115 ! cell-substrate junction organization +relationship: negatively_regulates GO:0150115 ! cell-substrate junction organization +creation_date: 2019-11-14T12:16:32Z + [Term] id: GO:0150119 name: negative regulation of protein localization to cell-cell junction @@ -120632,7 +124598,6 @@ is_a: GO:1903828 ! negative regulation of protein localization intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0150105 ! protein localization to cell-cell junction relationship: negatively_regulates GO:0150105 ! protein localization to cell-cell junction -created_by: bc creation_date: 2019-11-21T13:53:34Z [Term] @@ -120645,7 +124610,6 @@ is_a: GO:0034330 ! cell junction organization intersection_of: GO:0022411 ! cellular component disassembly intersection_of: results_in_disassembly_of GO:0030054 ! cell junction relationship: results_in_disassembly_of GO:0030054 ! cell junction -created_by: bc creation_date: 2019-12-08T11:12:13Z [Term] @@ -120658,7 +124622,6 @@ is_a: GO:0150146 ! cell junction disassembly intersection_of: GO:0022411 ! cellular component disassembly intersection_of: results_in_disassembly_of GO:0005911 ! cell-cell junction relationship: results_in_disassembly_of GO:0005911 ! cell-cell junction -created_by: bc creation_date: 2019-12-08T11:16:14Z [Term] @@ -120675,7 +124638,6 @@ is_a: GO:0010232 ! vascular transport intersection_of: GO:0006810 ! transport intersection_of: results_in_transport_across UBERON:0003210 ! blood-cerebrospinal fluid barrier relationship: results_in_transport_across UBERON:0003210 ! blood-cerebrospinal fluid barrier -created_by: bc creation_date: 2020-03-26T14:43:04Z [Term] @@ -120689,7 +124651,6 @@ intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0150104 ! transport across blood-brain barrier relationship: part_of GO:0043114 ! regulation of vascular permeability relationship: regulates GO:0150104 ! transport across blood-brain barrier -created_by: bc creation_date: 2020-03-26T19:22:26Z [Term] @@ -120704,7 +124665,6 @@ intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0150104 ! transport across blood-brain barrier relationship: part_of GO:0043117 ! positive regulation of vascular permeability relationship: positively_regulates GO:0150104 ! transport across blood-brain barrier -created_by: bc creation_date: 2020-03-26T19:26:38Z [Term] @@ -120719,7 +124679,6 @@ intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0150104 ! transport across blood-brain barrier relationship: negatively_regulates GO:0150104 ! transport across blood-brain barrier relationship: part_of GO:0043116 ! negative regulation of vascular permeability -created_by: bc creation_date: 2020-03-26T19:28:51Z [Term] @@ -120732,7 +124691,6 @@ is_a: GO:0008283 ! cell population proliferation intersection_of: GO:0008283 ! cell population proliferation intersection_of: acts_on_population_of CL:0000178 ! Leydig cell relationship: acts_on_population_of CL:0000178 ! Leydig cell -created_by: rynl creation_date: 2022-02-08T20:09:53Z [Term] @@ -120745,7 +124703,6 @@ is_a: GO:0048880 ! sensory system development intersection_of: GO:0048856 ! anatomical structure development intersection_of: results_in_development_of UBERON:0003942 ! somatosensory system relationship: results_in_development_of UBERON:0003942 ! somatosensory system -created_by: rynl creation_date: 2022-07-07T16:49:26Z [Term] @@ -120758,7 +124715,6 @@ is_a: GO:0050432 ! catecholamine secretion intersection_of: GO:0007269 ! neurotransmitter secretion intersection_of: has_primary_input CHEBI:33567 property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/23804" xsd:anyURI -created_by: rynl creation_date: 2022-08-17T00:36:44Z [Term] @@ -120771,7 +124727,6 @@ intersection_of: GO:0060349 ! bone morphogenesis intersection_of: results_in_fusion_of UBERON:0009198 ! craniofacial suture relationship: results_in_fusion_of UBERON:0009198 ! craniofacial suture property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/23213" xsd:anyURI -created_by: rynl creation_date: 2022-08-19T23:18:54Z [Term] @@ -120786,7 +124741,6 @@ intersection_of: GO:0030154 ! cell differentiation intersection_of: results_in_acquisition_of_features_of CL:0011025 ! exhausted T cell relationship: results_in_acquisition_of_features_of CL:0011025 ! exhausted T cell property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/25698" xsd:anyURI -created_by: rynl creation_date: 2023-07-14T22:56:05Z [Term] @@ -120799,7 +124753,6 @@ intersection_of: GO:0048856 ! anatomical structure development intersection_of: results_in_development_of UBERON:0001042 ! chordate pharynx relationship: results_in_development_of UBERON:0001042 ! chordate pharynx property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/18285" xsd:anyURI -created_by: rynl creation_date: 2023-08-29T21:05:28Z [Term] @@ -120808,13 +124761,15 @@ name: bicarbonate channel activity namespace: molecular_function def: "Enables the energy-independent facilitated diffusion of bicarbonate through a transmembrane aqueous pore or channel." [PMID:18400985] synonym: "hydrogencarbonate channel activity" EXACT [] +xref: RHEA:28695 {source="skos:broadMatch"} is_a: GO:0015106 ! bicarbonate transmembrane transporter activity is_a: GO:0015267 ! channel activity intersection_of: GO:0015267 ! channel activity intersection_of: has_primary_input CHEBI:17544 +relationship: has_participant CHEBI:17544 property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/26601" xsd:anyURI property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/26780" xsd:anyURI -created_by: rynl +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27521" xsd:anyURI creation_date: 2023-12-13T00:09:44Z [Term] @@ -120829,7 +124784,6 @@ intersection_of: GO:0048872 ! homeostasis of number of cells intersection_of: acts_on_population_of CL:0000625 ! CD8-positive, alpha-beta T cell relationship: acts_on_population_of CL:0000625 ! CD8-positive, alpha-beta T cell property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27184" xsd:anyURI -created_by: rynl creation_date: 2024-03-04T23:49:25Z [Term] @@ -120842,9 +124796,22 @@ intersection_of: GO:0022857 ! transmembrane transporter activity intersection_of: has_primary_input CHEBI:58432 relationship: has_primary_input CHEBI:58432 property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27277" xsd:anyURI -created_by: rynl creation_date: 2024-03-15T16:40:36Z +[Term] +id: GO:0160212 +name: glycine-gated cation channel activity +namespace: molecular_function +def: "Enables the transmembrane transfer of a cation by a channel that opens when glycine is bound by the channel complex or one of its constituent parts on the extracellular side of the plasma membrane." [PMID:11823786] +is_a: GO:0022824 ! transmitter-gated monoatomic ion channel activity +is_a: GO:0099094 ! ligand-gated monoatomic cation channel activity +intersection_of: GO:0022836 ! gated channel activity +intersection_of: has_primary_input CHEBI:23906 +intersection_of: has_small_molecule_activator CHEBI:57305 +relationship: has_small_molecule_activator CHEBI:57305 +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28887" xsd:anyURI +creation_date: 2024-09-10T16:55:41Z + [Term] id: GO:0170055 name: lipid transmembrane transporter activity @@ -120856,7 +124823,6 @@ is_a: GO:0022857 ! transmembrane transporter activity intersection_of: GO:0022857 ! transmembrane transporter activity intersection_of: has_primary_input CHEBI:18059 property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27252" xsd:anyURI -created_by: ew creation_date: 2024-03-15T18:47:58Z [Term] @@ -120871,7 +124837,6 @@ is_a: GO:0051094 ! positive regulation of developmental process intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0016358 ! dendrite development relationship: positively_regulates GO:0016358 ! dendrite development -created_by: hjd creation_date: 2012-01-09T10:41:31Z [Term] @@ -120884,7 +124849,6 @@ is_a: GO:0001817 ! regulation of cytokine production intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0002534 ! cytokine production involved in inflammatory response relationship: regulates GO:0002534 ! cytokine production involved in inflammatory response -created_by: rph creation_date: 2012-01-11T09:34:27Z [Term] @@ -120900,7 +124864,6 @@ is_a: GO:1900015 ! regulation of cytokine production involved in inflammatory re intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0002534 ! cytokine production involved in inflammatory response relationship: negatively_regulates GO:0002534 ! cytokine production involved in inflammatory response -created_by: rph creation_date: 2012-01-11T09:34:31Z [Term] @@ -120916,7 +124879,6 @@ is_a: GO:1900015 ! regulation of cytokine production involved in inflammatory re intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0002534 ! cytokine production involved in inflammatory response relationship: positively_regulates GO:0002534 ! cytokine production involved in inflammatory response -created_by: rph creation_date: 2012-01-11T09:34:35Z [Term] @@ -120929,7 +124891,6 @@ is_a: GO:0050878 ! regulation of body fluid levels intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0007599 ! hemostasis relationship: regulates GO:0007599 ! hemostasis -created_by: jl creation_date: 2012-01-19T03:23:38Z [Term] @@ -120946,7 +124907,6 @@ is_a: GO:1900046 ! regulation of hemostasis intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0007599 ! hemostasis relationship: negatively_regulates GO:0007599 ! hemostasis -created_by: jl creation_date: 2012-01-19T03:23:42Z [Term] @@ -120963,7 +124923,6 @@ is_a: GO:1900046 ! regulation of hemostasis intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0007599 ! hemostasis relationship: positively_regulates GO:0007599 ! hemostasis -created_by: jl creation_date: 2012-01-19T03:23:45Z [Term] @@ -120975,7 +124934,6 @@ is_a: GO:0050804 ! modulation of chemical synaptic transmission intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0007274 ! neuromuscular synaptic transmission relationship: regulates GO:0007274 ! neuromuscular synaptic transmission -created_by: kmv creation_date: 2012-01-26T10:14:10Z [Term] @@ -120992,7 +124950,6 @@ is_a: GO:1900073 ! regulation of neuromuscular synaptic transmission intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0007274 ! neuromuscular synaptic transmission relationship: negatively_regulates GO:0007274 ! neuromuscular synaptic transmission -created_by: kmv creation_date: 2012-01-26T10:14:18Z [Term] @@ -121009,7 +124966,6 @@ is_a: GO:1900073 ! regulation of neuromuscular synaptic transmission intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0007274 ! neuromuscular synaptic transmission relationship: positively_regulates GO:0007274 ! neuromuscular synaptic transmission -created_by: kmv creation_date: 2012-01-26T10:14:22Z [Term] @@ -121022,7 +124978,6 @@ is_a: GO:0050794 ! regulation of cellular process intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0032869 ! cellular response to insulin stimulus relationship: regulates GO:0032869 ! cellular response to insulin stimulus -created_by: yaf creation_date: 2012-01-31T11:22:22Z [Term] @@ -121040,7 +124995,6 @@ is_a: GO:1900076 ! regulation of cellular response to insulin stimulus intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0032869 ! cellular response to insulin stimulus relationship: negatively_regulates GO:0032869 ! cellular response to insulin stimulus -created_by: yaf creation_date: 2012-01-31T11:23:15Z [Term] @@ -121058,7 +125012,6 @@ is_a: GO:1900076 ! regulation of cellular response to insulin stimulus intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0032869 ! cellular response to insulin stimulus relationship: positively_regulates GO:0032869 ! cellular response to insulin stimulus -created_by: yaf creation_date: 2012-01-31T11:24:30Z [Term] @@ -121073,7 +125026,6 @@ is_a: GO:0050776 ! regulation of immune response intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0002317 ! plasma cell differentiation relationship: regulates GO:0002317 ! plasma cell differentiation -created_by: bf creation_date: 2012-02-15T10:46:00Z [Term] @@ -121097,7 +125049,6 @@ is_a: GO:1900098 ! regulation of plasma cell differentiation intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0002317 ! plasma cell differentiation relationship: negatively_regulates GO:0002317 ! plasma cell differentiation -created_by: bf creation_date: 2012-02-15T10:46:05Z [Term] @@ -121121,7 +125072,6 @@ is_a: GO:1900098 ! regulation of plasma cell differentiation intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0002317 ! plasma cell differentiation relationship: positively_regulates GO:0002317 ! plasma cell differentiation -created_by: bf creation_date: 2012-02-15T10:46:08Z [Term] @@ -121135,7 +125085,6 @@ is_a: GO:0009966 ! regulation of signal transduction intersection_of: GO:0009966 ! regulation of signal transduction intersection_of: occurs_in GO:0005576 ! extracellular region relationship: occurs_in GO:0005576 ! extracellular region -created_by: bf creation_date: 2012-02-22T10:21:48Z [Term] @@ -121154,7 +125103,6 @@ is_a: GO:0009968 ! negative regulation of signal transduction is_a: GO:1900115 ! extracellular regulation of signal transduction intersection_of: GO:0009968 ! negative regulation of signal transduction intersection_of: occurs_in GO:0005576 ! extracellular region -created_by: bf creation_date: 2012-02-22T10:27:56Z [Term] @@ -121166,7 +125114,6 @@ is_a: GO:0050794 ! regulation of cellular process intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0097194 ! execution phase of apoptosis relationship: regulates GO:0097194 ! execution phase of apoptosis -created_by: pr creation_date: 2012-02-22T11:26:20Z [Term] @@ -121183,7 +125130,6 @@ is_a: GO:1900117 ! regulation of execution phase of apoptosis intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0097194 ! execution phase of apoptosis relationship: negatively_regulates GO:0097194 ! execution phase of apoptosis -created_by: pr creation_date: 2012-02-22T11:26:24Z [Term] @@ -121200,7 +125146,6 @@ is_a: GO:1900117 ! regulation of execution phase of apoptosis intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0097194 ! execution phase of apoptosis relationship: positively_regulates GO:0097194 ! execution phase of apoptosis -created_by: pr creation_date: 2012-02-22T11:26:27Z [Term] @@ -121214,7 +125159,6 @@ is_a: GO:0043393 ! regulation of protein binding intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0005102 ! signaling receptor binding relationship: regulates GO:0005102 ! signaling receptor binding -created_by: bf creation_date: 2012-02-22T11:40:53Z [Term] @@ -121234,7 +125178,6 @@ is_a: GO:1900120 ! regulation of receptor binding intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0005102 ! signaling receptor binding relationship: negatively_regulates GO:0005102 ! signaling receptor binding -created_by: bf creation_date: 2012-02-22T11:40:57Z [Term] @@ -121251,7 +125194,6 @@ is_a: GO:1900120 ! regulation of receptor binding intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0005102 ! signaling receptor binding relationship: positively_regulates GO:0005102 ! signaling receptor binding -created_by: bf creation_date: 2012-02-22T11:41:00Z [Term] @@ -121267,7 +125209,6 @@ is_a: GO:0032885 ! regulation of polysaccharide biosynthetic process intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0030213 ! hyaluronan biosynthetic process relationship: regulates GO:0030213 ! hyaluronan biosynthetic process -created_by: yaf creation_date: 2012-02-23T01:09:21Z [Term] @@ -121305,7 +125246,6 @@ is_a: GO:1900125 ! regulation of hyaluronan biosynthetic process intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0030213 ! hyaluronan biosynthetic process relationship: negatively_regulates GO:0030213 ! hyaluronan biosynthetic process -created_by: yaf creation_date: 2012-02-23T01:09:29Z [Term] @@ -121343,7 +125283,6 @@ is_a: GO:1900125 ! regulation of hyaluronan biosynthetic process intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0030213 ! hyaluronan biosynthetic process relationship: positively_regulates GO:0030213 ! hyaluronan biosynthetic process -created_by: yaf creation_date: 2012-02-23T01:09:33Z [Term] @@ -121356,7 +125295,6 @@ is_a: GO:0051098 ! regulation of binding intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0008289 ! lipid binding relationship: regulates GO:0008289 ! lipid binding -created_by: pm creation_date: 2012-02-23T04:05:03Z [Term] @@ -121374,7 +125312,6 @@ is_a: GO:1900130 ! regulation of lipid binding intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0008289 ! lipid binding relationship: negatively_regulates GO:0008289 ! lipid binding -created_by: pm creation_date: 2012-02-23T04:05:07Z [Term] @@ -121392,7 +125329,6 @@ is_a: GO:1900130 ! regulation of lipid binding intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0008289 ! lipid binding relationship: positively_regulates GO:0008289 ! lipid binding -created_by: pm creation_date: 2012-02-23T04:05:11Z [Term] @@ -121407,7 +125343,6 @@ is_a: GO:0098801 ! regulation of renal system process intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0002001 ! renin secretion into blood stream relationship: regulates GO:0002001 ! renin secretion into blood stream -created_by: rph creation_date: 2012-02-27T10:32:01Z [Term] @@ -121429,7 +125364,6 @@ is_a: GO:1900133 ! regulation of renin secretion into blood stream intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0002001 ! renin secretion into blood stream relationship: negatively_regulates GO:0002001 ! renin secretion into blood stream -created_by: rph creation_date: 2012-02-27T10:32:05Z [Term] @@ -121451,7 +125385,6 @@ is_a: GO:1900133 ! regulation of renin secretion into blood stream intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0002001 ! renin secretion into blood stream relationship: positively_regulates GO:0002001 ! renin secretion into blood stream -created_by: rph creation_date: 2012-02-27T10:32:08Z [Term] @@ -121464,7 +125397,6 @@ is_a: GO:0034350 ! regulation of glial cell apoptotic process intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0097252 ! oligodendrocyte apoptotic process relationship: regulates GO:0097252 ! oligodendrocyte apoptotic process -created_by: yaf creation_date: 2012-03-06T10:22:45Z [Term] @@ -121486,7 +125418,6 @@ is_a: GO:1900141 ! regulation of oligodendrocyte apoptotic process intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0097252 ! oligodendrocyte apoptotic process relationship: negatively_regulates GO:0097252 ! oligodendrocyte apoptotic process -created_by: yaf creation_date: 2012-03-06T10:22:50Z [Term] @@ -121508,7 +125439,6 @@ is_a: GO:1900141 ! regulation of oligodendrocyte apoptotic process intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0097252 ! oligodendrocyte apoptotic process relationship: positively_regulates GO:0097252 ! oligodendrocyte apoptotic process -created_by: yaf creation_date: 2012-03-06T10:22:54Z [Term] @@ -121520,7 +125450,6 @@ is_a: GO:1903975 ! regulation of glial cell migration intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0036135 ! Schwann cell migration relationship: regulates GO:0036135 ! Schwann cell migration -created_by: bf creation_date: 2012-03-06T04:14:50Z [Term] @@ -121537,7 +125466,6 @@ is_a: GO:1903976 ! negative regulation of glial cell migration intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0036135 ! Schwann cell migration relationship: negatively_regulates GO:0036135 ! Schwann cell migration -created_by: bf creation_date: 2012-03-06T04:14:55Z [Term] @@ -121554,14 +125482,12 @@ is_a: GO:1903977 ! positive regulation of glial cell migration intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0036135 ! Schwann cell migration relationship: positively_regulates GO:0036135 ! Schwann cell migration -created_by: bf creation_date: 2012-03-06T04:14:58Z [Term] id: GO:1900150 name: regulation of defense response to fungus namespace: biological_process -alt_id: GO:2000072 def: "Any process that modulates the frequency, rate or extent of defense response to fungus." [GOC:dhl, GOC:TermGenie, PMID:22242006] synonym: "regulation of defence response to fungi" EXACT [GOC:TermGenie] synonym: "regulation of defence response to fungus" EXACT [GOC:TermGenie] @@ -121577,7 +125503,6 @@ is_a: GO:0032101 ! regulation of response to external stimulus intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0050832 ! defense response to fungus relationship: regulates GO:0050832 ! defense response to fungus -created_by: dhl creation_date: 2012-03-06T10:00:16Z [Term] @@ -121589,7 +125514,6 @@ is_a: GO:0030500 ! regulation of bone mineralization intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0035630 ! bone mineralization involved in bone maturation relationship: regulates GO:0035630 ! bone mineralization involved in bone maturation -created_by: vk creation_date: 2012-03-07T08:55:07Z [Term] @@ -121606,7 +125530,6 @@ is_a: GO:1900157 ! regulation of bone mineralization involved in bone maturation intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0035630 ! bone mineralization involved in bone maturation relationship: negatively_regulates GO:0035630 ! bone mineralization involved in bone maturation -created_by: vk creation_date: 2012-03-07T08:55:12Z [Term] @@ -121623,66 +125546,8 @@ is_a: GO:1900157 ! regulation of bone mineralization involved in bone maturation intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0035630 ! bone mineralization involved in bone maturation relationship: positively_regulates GO:0035630 ! bone mineralization involved in bone maturation -created_by: vk creation_date: 2012-03-07T08:55:16Z -[Term] -id: GO:1900169 -name: regulation of glucocorticoid mediated signaling pathway -namespace: biological_process -def: "Any process that modulates the frequency, rate or extent of glucocorticoid mediated signaling pathway." [GOC:TermGenie] -synonym: "regulation of glucocorticoid mediated signalling" EXACT [GOC:TermGenie] -is_a: GO:0009966 ! regulation of signal transduction -intersection_of: GO:0065007 ! biological regulation -intersection_of: regulates GO:0043402 ! glucocorticoid mediated signaling pathway -relationship: regulates GO:0043402 ! glucocorticoid mediated signaling pathway -created_by: hjd -creation_date: 2012-03-08T08:33:16Z - -[Term] -id: GO:1900170 -name: negative regulation of glucocorticoid mediated signaling pathway -namespace: biological_process -def: "Any process that stops, prevents or reduces the frequency, rate or extent of glucocorticoid mediated signaling pathway." [GOC:TermGenie] -synonym: "down regulation of glucocorticoid mediated signaling pathway" EXACT [GOC:TermGenie] -synonym: "down regulation of glucocorticoid mediated signalling" EXACT [GOC:TermGenie] -synonym: "down-regulation of glucocorticoid mediated signaling pathway" EXACT [GOC:TermGenie] -synonym: "down-regulation of glucocorticoid mediated signalling" EXACT [GOC:TermGenie] -synonym: "downregulation of glucocorticoid mediated signaling pathway" EXACT [GOC:TermGenie] -synonym: "downregulation of glucocorticoid mediated signalling" EXACT [GOC:TermGenie] -synonym: "inhibition of glucocorticoid mediated signaling pathway" NARROW [GOC:TermGenie] -synonym: "inhibition of glucocorticoid mediated signalling" NARROW [GOC:TermGenie] -synonym: "negative regulation of glucocorticoid mediated signalling" EXACT [GOC:TermGenie] -is_a: GO:0009968 ! negative regulation of signal transduction -is_a: GO:1900169 ! regulation of glucocorticoid mediated signaling pathway -intersection_of: GO:0065007 ! biological regulation -intersection_of: negatively_regulates GO:0043402 ! glucocorticoid mediated signaling pathway -relationship: negatively_regulates GO:0043402 ! glucocorticoid mediated signaling pathway -created_by: hjd -creation_date: 2012-03-08T08:33:20Z - -[Term] -id: GO:1900171 -name: positive regulation of glucocorticoid mediated signaling pathway -namespace: biological_process -def: "Any process that activates or increases the frequency, rate or extent of glucocorticoid mediated signaling pathway." [GOC:TermGenie] -synonym: "activation of glucocorticoid mediated signaling pathway" NARROW [GOC:TermGenie] -synonym: "activation of glucocorticoid mediated signalling" NARROW [GOC:TermGenie] -synonym: "positive regulation of glucocorticoid mediated signalling" EXACT [GOC:TermGenie] -synonym: "up regulation of glucocorticoid mediated signaling pathway" EXACT [GOC:TermGenie] -synonym: "up regulation of glucocorticoid mediated signalling" EXACT [GOC:TermGenie] -synonym: "up-regulation of glucocorticoid mediated signaling pathway" EXACT [GOC:TermGenie] -synonym: "up-regulation of glucocorticoid mediated signalling" EXACT [GOC:TermGenie] -synonym: "upregulation of glucocorticoid mediated signaling pathway" EXACT [GOC:TermGenie] -synonym: "upregulation of glucocorticoid mediated signalling" EXACT [GOC:TermGenie] -is_a: GO:0009967 ! positive regulation of signal transduction -is_a: GO:1900169 ! regulation of glucocorticoid mediated signaling pathway -intersection_of: GO:0065007 ! biological regulation -intersection_of: positively_regulates GO:0043402 ! glucocorticoid mediated signaling pathway -relationship: positively_regulates GO:0043402 ! glucocorticoid mediated signaling pathway -created_by: hjd -creation_date: 2012-03-08T08:33:23Z - [Term] id: GO:1900180 name: regulation of protein localization to nucleus @@ -121695,7 +125560,6 @@ is_a: GO:0032880 ! regulation of protein localization intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0034504 ! protein localization to nucleus relationship: regulates GO:0034504 ! protein localization to nucleus -created_by: bf creation_date: 2012-03-12T01:23:44Z [Term] @@ -121727,7 +125591,6 @@ is_a: GO:1903828 ! negative regulation of protein localization intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0034504 ! protein localization to nucleus relationship: negatively_regulates GO:0034504 ! protein localization to nucleus -created_by: bf creation_date: 2012-03-12T01:23:48Z [Term] @@ -121759,7 +125622,6 @@ is_a: GO:1903829 ! positive regulation of protein localization intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0034504 ! protein localization to nucleus relationship: positively_regulates GO:0034504 ! protein localization to nucleus -created_by: bf creation_date: 2012-03-12T01:23:52Z [Term] @@ -121772,7 +125634,6 @@ is_a: GO:2000241 ! regulation of reproductive process intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0001556 ! oocyte maturation relationship: regulates GO:0001556 ! oocyte maturation -created_by: kmv creation_date: 2012-03-19T09:41:18Z [Term] @@ -121790,7 +125651,6 @@ is_a: GO:2000242 ! negative regulation of reproductive process intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0001556 ! oocyte maturation relationship: negatively_regulates GO:0001556 ! oocyte maturation -created_by: kmv creation_date: 2012-03-19T09:41:27Z [Term] @@ -121808,7 +125668,6 @@ is_a: GO:2000243 ! positive regulation of reproductive process intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0001556 ! oocyte maturation relationship: positively_regulates GO:0001556 ! oocyte maturation -created_by: kmv creation_date: 2012-03-19T09:41:35Z [Term] @@ -121822,7 +125681,6 @@ is_a: GO:1902742 ! apoptotic process involved in development intersection_of: GO:0097152 ! mesenchymal cell apoptotic process intersection_of: part_of GO:0001656 ! metanephros development relationship: part_of GO:0001656 ! metanephros development -created_by: yaf creation_date: 2012-03-21T11:58:05Z [Term] @@ -121842,7 +125700,6 @@ is_a: GO:1902742 ! apoptotic process involved in development intersection_of: GO:0006915 ! apoptotic process intersection_of: part_of GO:0072205 ! metanephric collecting duct development relationship: part_of GO:0072205 ! metanephric collecting duct development -created_by: yaf creation_date: 2012-03-21T01:21:32Z [Term] @@ -121862,7 +125719,6 @@ is_a: GO:1902742 ! apoptotic process involved in development intersection_of: GO:0006915 ! apoptotic process intersection_of: part_of GO:0072234 ! metanephric nephron tubule development relationship: part_of GO:0072234 ! metanephric nephron tubule development -created_by: yaf creation_date: 2012-03-21T01:21:45Z [Term] @@ -121874,7 +125730,6 @@ is_a: GO:0050793 ! regulation of developmental process intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0039020 ! pronephric nephron tubule development relationship: regulates GO:0039020 ! pronephric nephron tubule development -created_by: bf creation_date: 2012-03-22T09:23:13Z [Term] @@ -121891,7 +125746,6 @@ is_a: GO:1900206 ! regulation of pronephric nephron tubule development intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0039020 ! pronephric nephron tubule development relationship: negatively_regulates GO:0039020 ! pronephric nephron tubule development -created_by: bf creation_date: 2012-03-22T09:23:23Z [Term] @@ -121905,7 +125759,6 @@ is_a: GO:2001053 ! regulation of mesenchymal cell apoptotic process intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:1900200 ! mesenchymal cell apoptotic process involved in metanephros development relationship: regulates GO:1900200 ! mesenchymal cell apoptotic process involved in metanephros development -created_by: yaf creation_date: 2012-03-22T10:52:50Z [Term] @@ -121924,7 +125777,6 @@ is_a: GO:2001054 ! negative regulation of mesenchymal cell apoptotic process intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:1900200 ! mesenchymal cell apoptotic process involved in metanephros development relationship: negatively_regulates GO:1900200 ! mesenchymal cell apoptotic process involved in metanephros development -created_by: yaf creation_date: 2012-03-22T10:53:00Z [Term] @@ -121943,7 +125795,6 @@ is_a: GO:2001055 ! positive regulation of mesenchymal cell apoptotic process intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:1900200 ! mesenchymal cell apoptotic process involved in metanephros development relationship: positively_regulates GO:1900200 ! mesenchymal cell apoptotic process involved in metanephros development -created_by: yaf creation_date: 2012-03-22T10:53:09Z [Term] @@ -121963,7 +125814,6 @@ is_a: GO:1904748 ! regulation of apoptotic process involved in development intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:1900204 ! apoptotic process involved in metanephric collecting duct development relationship: regulates GO:1900204 ! apoptotic process involved in metanephric collecting duct development -created_by: yaf creation_date: 2012-03-22T10:53:21Z [Term] @@ -122020,7 +125870,6 @@ is_a: GO:1904746 ! negative regulation of apoptotic process involved in developm intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:1900204 ! apoptotic process involved in metanephric collecting duct development relationship: negatively_regulates GO:1900204 ! apoptotic process involved in metanephric collecting duct development -created_by: yaf creation_date: 2012-03-22T10:53:31Z [Term] @@ -122077,7 +125926,6 @@ is_a: GO:1904747 ! positive regulation of apoptotic process involved in developm intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:1900204 ! apoptotic process involved in metanephric collecting duct development relationship: positively_regulates GO:1900204 ! apoptotic process involved in metanephric collecting duct development -created_by: yaf creation_date: 2012-03-22T10:53:39Z [Term] @@ -122097,7 +125945,6 @@ is_a: GO:1904748 ! regulation of apoptotic process involved in development intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:1900205 ! apoptotic process involved in metanephric nephron tubule development relationship: regulates GO:1900205 ! apoptotic process involved in metanephric nephron tubule development -created_by: yaf creation_date: 2012-03-22T10:53:51Z [Term] @@ -122154,7 +126001,6 @@ is_a: GO:1904746 ! negative regulation of apoptotic process involved in developm intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:1900205 ! apoptotic process involved in metanephric nephron tubule development relationship: negatively_regulates GO:1900205 ! apoptotic process involved in metanephric nephron tubule development -created_by: yaf creation_date: 2012-03-22T10:54:01Z [Term] @@ -122211,7 +126057,6 @@ is_a: GO:1904747 ! positive regulation of apoptotic process involved in developm intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:1900205 ! apoptotic process involved in metanephric nephron tubule development relationship: positively_regulates GO:1900205 ! apoptotic process involved in metanephric nephron tubule development -created_by: yaf creation_date: 2012-03-22T10:54:09Z [Term] @@ -122223,7 +126068,6 @@ is_a: GO:0006448 ! regulation of translational elongation intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0002182 ! cytoplasmic translational elongation relationship: regulates GO:0002182 ! cytoplasmic translational elongation -created_by: vw creation_date: 2012-04-03T05:07:02Z [Term] @@ -122241,7 +126085,6 @@ is_a: GO:2000766 ! negative regulation of cytoplasmic translation intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0002182 ! cytoplasmic translational elongation relationship: negatively_regulates GO:0002182 ! cytoplasmic translational elongation -created_by: vw creation_date: 2012-04-03T05:07:14Z [Term] @@ -122258,7 +126101,6 @@ is_a: GO:1900247 ! regulation of cytoplasmic translational elongation intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0002182 ! cytoplasmic translational elongation relationship: positively_regulates GO:0002182 ! cytoplasmic translational elongation -created_by: vw creation_date: 2012-04-03T05:07:24Z [Term] @@ -122281,7 +126123,6 @@ is_a: GO:2000068 ! regulation of defense response to insect intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0002213 ! defense response to insect relationship: negatively_regulates GO:0002213 ! defense response to insect -created_by: dhl creation_date: 2012-04-12T04:44:00Z [Term] @@ -122303,14 +126144,12 @@ is_a: GO:2000068 ! regulation of defense response to insect intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0002213 ! defense response to insect relationship: positively_regulates GO:0002213 ! defense response to insect -created_by: dhl creation_date: 2012-04-12T04:44:10Z [Term] id: GO:1900424 name: regulation of defense response to bacterium namespace: biological_process -alt_id: GO:1902477 def: "Any process that modulates the frequency, rate or extent of defense response to bacterium." [GOC:TermGenie, PMID:22346749] synonym: "regulation of antibacterial peptide activity" RELATED [GOC:TermGenie] synonym: "regulation of defence response to bacteria" EXACT [GOC:TermGenie] @@ -122328,14 +126167,12 @@ is_a: GO:0032101 ! regulation of response to external stimulus intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0042742 ! defense response to bacterium relationship: regulates GO:0042742 ! defense response to bacterium -created_by: dhl creation_date: 2012-04-24T10:12:43Z [Term] id: GO:1900425 name: negative regulation of defense response to bacterium namespace: biological_process -alt_id: GO:1902478 def: "Any process that stops, prevents or reduces the frequency, rate or extent of defense response to bacterium." [GOC:TermGenie, PMID:22346749] synonym: "down regulation of antibacterial peptide activity" RELATED [GOC:TermGenie] synonym: "down regulation of defence response to bacteria" EXACT [GOC:TermGenie] @@ -122376,14 +126213,12 @@ is_a: GO:1900424 ! regulation of defense response to bacterium intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0042742 ! defense response to bacterium relationship: negatively_regulates GO:0042742 ! defense response to bacterium -created_by: dhl creation_date: 2012-04-24T10:12:54Z [Term] id: GO:1900426 name: positive regulation of defense response to bacterium namespace: biological_process -alt_id: GO:1902479 def: "Any process that activates or increases the frequency, rate or extent of defense response to bacterium." [GOC:TermGenie, PMID:22346749] synonym: "activation of antibacterial peptide activity" RELATED [GOC:TermGenie] synonym: "activation of defence response to bacteria" EXACT [GOC:TermGenie] @@ -122419,7 +126254,6 @@ is_a: GO:1900424 ! regulation of defense response to bacterium intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0042742 ! defense response to bacterium relationship: positively_regulates GO:0042742 ! defense response to bacterium -created_by: dhl creation_date: 2012-04-24T10:13:13Z [Term] @@ -122433,7 +126267,6 @@ is_a: GO:0009966 ! regulation of signal transduction intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0007215 ! glutamate receptor signaling pathway relationship: regulates GO:0007215 ! glutamate receptor signaling pathway -created_by: rl creation_date: 2012-04-27T03:45:43Z [Term] @@ -122460,7 +126293,6 @@ is_a: GO:1900449 ! regulation of glutamate receptor signaling pathway intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0007215 ! glutamate receptor signaling pathway relationship: negatively_regulates GO:0007215 ! glutamate receptor signaling pathway -created_by: rl creation_date: 2012-04-27T03:45:53Z [Term] @@ -122487,7 +126319,6 @@ is_a: GO:1900449 ! regulation of glutamate receptor signaling pathway intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0007215 ! glutamate receptor signaling pathway relationship: positively_regulates GO:0007215 ! glutamate receptor signaling pathway -created_by: rl creation_date: 2012-04-27T03:46:03Z [Term] @@ -122500,7 +126331,6 @@ is_a: GO:0010958 ! regulation of amino acid import across plasma membrane intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:1903804 ! glycine import across plasma membrane relationship: regulates GO:1903804 ! glycine import across plasma membrane -created_by: al creation_date: 2012-06-13T07:40:11Z [Term] @@ -122519,7 +126349,6 @@ is_a: GO:1900923 ! regulation of glycine import across plasma membrane intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:1903804 ! glycine import across plasma membrane relationship: negatively_regulates GO:1903804 ! glycine import across plasma membrane -created_by: al creation_date: 2012-06-13T07:40:32Z [Term] @@ -122538,7 +126367,6 @@ is_a: GO:1900923 ! regulation of glycine import across plasma membrane intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:1903804 ! glycine import across plasma membrane relationship: positively_regulates GO:1903804 ! glycine import across plasma membrane -created_by: al creation_date: 2012-06-13T07:40:40Z [Term] @@ -122553,7 +126381,6 @@ is_a: GO:1901379 ! regulation of potassium ion transmembrane transport intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0015079 ! potassium ion transmembrane transporter activity relationship: regulates GO:0015079 ! potassium ion transmembrane transporter activity -created_by: rl creation_date: 2012-06-15T01:13:49Z [Term] @@ -122577,7 +126404,6 @@ is_a: GO:1901380 ! negative regulation of potassium ion transmembrane transport intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0015079 ! potassium ion transmembrane transporter activity relationship: negatively_regulates GO:0015079 ! potassium ion transmembrane transporter activity -created_by: rl creation_date: 2012-06-15T01:14:10Z [Term] @@ -122601,7 +126427,6 @@ is_a: GO:1901381 ! positive regulation of potassium ion transmembrane transport intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0015079 ! potassium ion transmembrane transporter activity relationship: positively_regulates GO:0015079 ! potassium ion transmembrane transporter activity -created_by: rl creation_date: 2012-06-15T01:14:18Z [Term] @@ -122615,7 +126440,6 @@ is_a: GO:1903169 ! regulation of calcium ion transmembrane transport intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0015085 ! calcium ion transmembrane transporter activity relationship: regulates GO:0015085 ! calcium ion transmembrane transporter activity -created_by: rl creation_date: 2012-06-15T07:54:12Z [Term] @@ -122634,7 +126458,6 @@ is_a: GO:1903170 ! negative regulation of calcium ion transmembrane transport intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0015085 ! calcium ion transmembrane transporter activity relationship: negatively_regulates GO:0015085 ! calcium ion transmembrane transporter activity -created_by: rl creation_date: 2012-06-15T07:54:32Z [Term] @@ -122653,7 +126476,6 @@ is_a: GO:1904427 ! positive regulation of calcium ion transmembrane transport intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0015085 ! calcium ion transmembrane transporter activity relationship: positively_regulates GO:0015085 ! calcium ion transmembrane transporter activity -created_by: rl creation_date: 2012-06-15T07:54:40Z [Term] @@ -122671,7 +126493,6 @@ is_a: GO:0008152 ! metabolic process intersection_of: GO:0008152 ! metabolic process intersection_of: has_primary_input_or_output CHEBI:63299 relationship: has_primary_input_or_output CHEBI:63299 -created_by: bf creation_date: 2012-07-12T04:05:09Z [Term] @@ -122687,7 +126508,6 @@ is_a: GO:1901135 ! carbohydrate derivative metabolic process intersection_of: GO:0009056 ! catabolic process intersection_of: has_primary_input CHEBI:63299 relationship: has_primary_input CHEBI:63299 -created_by: bf creation_date: 2012-07-12T04:05:31Z [Term] @@ -122704,7 +126524,6 @@ is_a: GO:1901135 ! carbohydrate derivative metabolic process intersection_of: GO:0009058 ! biosynthetic process intersection_of: has_primary_output CHEBI:63299 relationship: has_primary_output CHEBI:63299 -created_by: bf creation_date: 2012-07-12T04:05:39Z [Term] @@ -122721,7 +126540,6 @@ property_value: RO:0002161 NCBITaxon:2 property_value: RO:0002161 NCBITaxon:2157 property_value: RO:0002161 NCBITaxon:33090 property_value: RO:0002161 NCBITaxon:4751 -created_by: pm creation_date: 2012-07-13T12:32:40Z [Term] @@ -122737,7 +126555,6 @@ is_a: GO:1901142 ! insulin metabolic process intersection_of: GO:0009056 ! catabolic process intersection_of: has_primary_input PR:000009054 ! insulin gene translation product relationship: has_primary_input PR:000009054 ! insulin gene translation product -created_by: pm creation_date: 2012-07-13T12:33:03Z [Term] @@ -122750,7 +126567,6 @@ is_a: GO:0097152 ! mesenchymal cell apoptotic process intersection_of: GO:0097152 ! mesenchymal cell apoptotic process intersection_of: part_of GO:0072028 ! nephron morphogenesis relationship: part_of GO:0072028 ! nephron morphogenesis -created_by: pr creation_date: 2012-07-13T01:43:51Z [Term] @@ -122762,7 +126578,6 @@ is_a: GO:1901145 ! mesenchymal cell apoptotic process involved in nephron morpho intersection_of: GO:0097152 ! mesenchymal cell apoptotic process intersection_of: part_of GO:0061228 ! mesonephric nephron morphogenesis relationship: part_of GO:0061228 ! mesonephric nephron morphogenesis -created_by: pr creation_date: 2012-07-13T02:40:43Z [Term] @@ -122775,7 +126590,6 @@ is_a: GO:1901145 ! mesenchymal cell apoptotic process involved in nephron morpho intersection_of: GO:0097152 ! mesenchymal cell apoptotic process intersection_of: part_of GO:0072273 ! metanephric nephron morphogenesis relationship: part_of GO:0072273 ! metanephric nephron morphogenesis -created_by: pr creation_date: 2012-07-13T02:41:12Z [Term] @@ -122789,7 +126603,6 @@ is_a: GO:0010467 ! gene expression intersection_of: GO:0010467 ! gene expression intersection_of: part_of GO:0030198 ! extracellular matrix organization relationship: part_of GO:0030198 ! extracellular matrix organization -created_by: bf creation_date: 2012-07-16T03:29:30Z [Term] @@ -122803,7 +126616,6 @@ is_a: GO:0008152 ! metabolic process intersection_of: GO:0008152 ! metabolic process intersection_of: has_primary_input_or_output CHEBI:50994 relationship: has_primary_input_or_output CHEBI:50994 -created_by: bf creation_date: 2012-07-18T04:44:39Z [Term] @@ -122819,7 +126631,6 @@ is_a: GO:1901160 ! primary amino compound metabolic process intersection_of: GO:0009056 ! catabolic process intersection_of: has_primary_input CHEBI:50994 relationship: has_primary_input CHEBI:50994 -created_by: bf creation_date: 2012-07-18T04:45:06Z [Term] @@ -122836,7 +126647,6 @@ is_a: GO:1901160 ! primary amino compound metabolic process intersection_of: GO:0009058 ! biosynthetic process intersection_of: has_primary_output CHEBI:50994 relationship: has_primary_output CHEBI:50994 -created_by: bf creation_date: 2012-07-18T04:45:14Z [Term] @@ -122848,7 +126658,6 @@ is_a: GO:0030334 ! regulation of cell migration intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0061450 ! trophoblast cell migration relationship: regulates GO:0061450 ! trophoblast cell migration -created_by: vk creation_date: 2012-07-19T07:53:06Z [Term] @@ -122867,7 +126676,6 @@ is_a: GO:2000242 ! negative regulation of reproductive process intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0061450 ! trophoblast cell migration relationship: negatively_regulates GO:0061450 ! trophoblast cell migration -created_by: vk creation_date: 2012-07-19T07:53:28Z [Term] @@ -122887,7 +126695,6 @@ is_a: GO:2000243 ! positive regulation of reproductive process intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0061450 ! trophoblast cell migration relationship: positively_regulates GO:0061450 ! trophoblast cell migration -created_by: vk creation_date: 2012-07-19T07:53:35Z [Term] @@ -122899,7 +126706,6 @@ is_a: GO:0001755 ! neural crest cell migration intersection_of: GO:0001755 ! neural crest cell migration intersection_of: part_of GO:0048483 ! autonomic nervous system development relationship: part_of GO:0048483 ! autonomic nervous system development -created_by: vk creation_date: 2012-07-19T08:39:56Z [Term] @@ -122912,7 +126718,6 @@ is_a: GO:0043254 ! regulation of protein-containing complex assembly intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0001677 ! formation of translation initiation ternary complex relationship: regulates GO:0001677 ! formation of translation initiation ternary complex -created_by: ss creation_date: 2012-07-25T02:26:58Z [Term] @@ -122935,7 +126740,6 @@ is_a: GO:1901190 ! regulation of formation of translation initiation ternary com intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0001677 ! formation of translation initiation ternary complex relationship: negatively_regulates GO:0001677 ! formation of translation initiation ternary complex -created_by: ss creation_date: 2012-07-25T02:27:21Z [Term] @@ -122957,7 +126761,6 @@ is_a: GO:1901190 ! regulation of formation of translation initiation ternary com intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0001677 ! formation of translation initiation ternary complex relationship: positively_regulates GO:0001677 ! formation of translation initiation ternary complex -created_by: ss creation_date: 2012-07-25T02:27:29Z [Term] @@ -122982,7 +126785,6 @@ is_a: GO:0050850 ! positive regulation of calcium-mediated signaling intersection_of: GO:0050850 ! positive regulation of calcium-mediated signaling intersection_of: part_of GO:0071277 ! cellular response to calcium ion relationship: part_of GO:0071277 ! cellular response to calcium ion -created_by: al creation_date: 2012-07-27T10:57:56Z [Term] @@ -122995,7 +126797,6 @@ is_a: GO:1903053 ! regulation of extracellular matrix organization intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0085029 ! extracellular matrix assembly relationship: regulates GO:0085029 ! extracellular matrix assembly -created_by: rl creation_date: 2012-07-27T04:04:00Z [Term] @@ -123012,7 +126813,6 @@ is_a: GO:1903054 ! negative regulation of extracellular matrix organization intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0085029 ! extracellular matrix assembly relationship: negatively_regulates GO:0085029 ! extracellular matrix assembly -created_by: rl creation_date: 2012-07-27T04:04:24Z [Term] @@ -123030,7 +126830,6 @@ is_a: GO:1903055 ! positive regulation of extracellular matrix organization intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0085029 ! extracellular matrix assembly relationship: positively_regulates GO:0085029 ! extracellular matrix assembly -created_by: rl creation_date: 2012-07-27T04:04:32Z [Term] @@ -123043,7 +126842,6 @@ is_a: GO:0050793 ! regulation of developmental process intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0003207 ! cardiac chamber formation relationship: regulates GO:0003207 ! cardiac chamber formation -created_by: rl creation_date: 2012-07-31T07:18:35Z [Term] @@ -123065,7 +126863,6 @@ is_a: GO:1901210 ! regulation of cardiac chamber formation intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0003207 ! cardiac chamber formation relationship: negatively_regulates GO:0003207 ! cardiac chamber formation -created_by: rl creation_date: 2012-07-31T07:18:57Z [Term] @@ -123087,7 +126884,6 @@ is_a: GO:1901221 ! positive regulation of cardiac chamber morphogenesis intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0003207 ! cardiac chamber formation relationship: positively_regulates GO:0003207 ! cardiac chamber formation -created_by: rl creation_date: 2012-07-31T07:19:05Z [Term] @@ -123100,7 +126896,6 @@ is_a: GO:2000826 ! regulation of heart morphogenesis intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0003206 ! cardiac chamber morphogenesis relationship: regulates GO:0003206 ! cardiac chamber morphogenesis -created_by: rl creation_date: 2012-08-06T17:59:11Z [Term] @@ -123122,7 +126917,6 @@ is_a: GO:1901219 ! regulation of cardiac chamber morphogenesis intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0003206 ! cardiac chamber morphogenesis relationship: negatively_regulates GO:0003206 ! cardiac chamber morphogenesis -created_by: rl creation_date: 2012-08-06T17:59:34Z [Term] @@ -123144,7 +126938,6 @@ is_a: GO:1901219 ! regulation of cardiac chamber morphogenesis intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0003206 ! cardiac chamber morphogenesis relationship: positively_regulates GO:0003206 ! cardiac chamber morphogenesis -created_by: rl creation_date: 2012-08-06T17:59:42Z [Term] @@ -123156,7 +126949,6 @@ is_a: GO:0030856 ! regulation of epithelial cell differentiation intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0061141 ! lung ciliated cell differentiation relationship: regulates GO:0061141 ! lung ciliated cell differentiation -created_by: vk creation_date: 2012-08-08T08:58:34Z [Term] @@ -123174,7 +126966,6 @@ is_a: GO:1901246 ! regulation of lung ciliated cell differentiation intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0061141 ! lung ciliated cell differentiation relationship: negatively_regulates GO:0061141 ! lung ciliated cell differentiation -created_by: vk creation_date: 2012-08-08T08:58:58Z [Term] @@ -123192,7 +126983,6 @@ is_a: GO:1901246 ! regulation of lung ciliated cell differentiation intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0061141 ! lung ciliated cell differentiation relationship: positively_regulates GO:0061141 ! lung ciliated cell differentiation -created_by: vk creation_date: 2012-08-08T08:59:05Z [Term] @@ -123205,7 +126995,6 @@ is_a: GO:0030856 ! regulation of epithelial cell differentiation intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0060480 ! lung goblet cell differentiation relationship: regulates GO:0060480 ! lung goblet cell differentiation -created_by: vk creation_date: 2012-08-08T08:59:12Z [Term] @@ -123228,7 +127017,6 @@ is_a: GO:1901249 ! regulation of lung goblet cell differentiation intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0060480 ! lung goblet cell differentiation relationship: negatively_regulates GO:0060480 ! lung goblet cell differentiation -created_by: vk creation_date: 2012-08-08T08:59:36Z [Term] @@ -123251,7 +127039,6 @@ is_a: GO:1901249 ! regulation of lung goblet cell differentiation intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0060480 ! lung goblet cell differentiation relationship: positively_regulates GO:0060480 ! lung goblet cell differentiation -created_by: vk creation_date: 2012-08-08T08:59:44Z [Term] @@ -123264,7 +127051,6 @@ is_a: GO:0006810 ! transport intersection_of: GO:0006810 ! transport intersection_of: has_primary_input CHEBI:63299 relationship: has_primary_input CHEBI:63299 -created_by: bf creation_date: 2012-08-16T14:51:22Z [Term] @@ -123279,7 +127065,6 @@ is_a: GO:2000241 ! regulation of reproductive process intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0030317 ! flagellated sperm motility relationship: regulates GO:0030317 ! flagellated sperm motility -created_by: hjd creation_date: 2012-08-22T20:50:14Z [Term] @@ -123304,7 +127089,6 @@ is_a: GO:2000242 ! negative regulation of reproductive process intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0030317 ! flagellated sperm motility relationship: negatively_regulates GO:0030317 ! flagellated sperm motility -created_by: hjd creation_date: 2012-08-22T20:50:35Z [Term] @@ -123316,7 +127100,6 @@ is_a: GO:0030856 ! regulation of epithelial cell differentiation intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0071895 ! odontoblast differentiation relationship: regulates GO:0071895 ! odontoblast differentiation -created_by: hjd creation_date: 2012-08-31T16:50:05Z [Term] @@ -123333,7 +127116,6 @@ is_a: GO:1901329 ! regulation of odontoblast differentiation intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0071895 ! odontoblast differentiation relationship: negatively_regulates GO:0071895 ! odontoblast differentiation -created_by: hjd creation_date: 2012-08-31T16:50:27Z [Term] @@ -123350,7 +127132,6 @@ is_a: GO:1902913 ! positive regulation of neuroepithelial cell differentiation intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0071895 ! odontoblast differentiation relationship: positively_regulates GO:0071895 ! odontoblast differentiation -created_by: hjd creation_date: 2012-08-31T16:50:35Z [Term] @@ -123363,7 +127144,6 @@ is_a: GO:0005488 ! binding intersection_of: GO:0005488 ! binding intersection_of: has_primary_input CHEBI:33567 relationship: has_primary_input CHEBI:33567 -created_by: bf creation_date: 2012-09-03T14:08:44Z [Term] @@ -123376,7 +127156,6 @@ is_a: GO:2000026 ! regulation of multicellular organismal development intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0001944 ! vasculature development relationship: regulates GO:0001944 ! vasculature development -created_by: bf creation_date: 2012-09-06T09:16:15Z [Term] @@ -123399,7 +127178,6 @@ is_a: GO:1901342 ! regulation of vasculature development intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0001944 ! vasculature development relationship: negatively_regulates GO:0001944 ! vasculature development -created_by: bf creation_date: 2012-09-06T09:17:24Z [Term] @@ -123413,7 +127191,6 @@ is_a: GO:0043266 ! regulation of potassium ion transport intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0071805 ! potassium ion transmembrane transport relationship: regulates GO:0071805 ! potassium ion transmembrane transport -created_by: rl creation_date: 2012-09-28T15:58:00Z [Term] @@ -123432,7 +127209,6 @@ is_a: GO:1901379 ! regulation of potassium ion transmembrane transport intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0071805 ! potassium ion transmembrane transport relationship: negatively_regulates GO:0071805 ! potassium ion transmembrane transport -created_by: rl creation_date: 2012-09-28T15:59:08Z [Term] @@ -123451,7 +127227,6 @@ is_a: GO:1901379 ! regulation of potassium ion transmembrane transport intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0071805 ! potassium ion transmembrane transport relationship: positively_regulates GO:0071805 ! potassium ion transmembrane transport -created_by: rl creation_date: 2012-09-28T15:59:25Z [Term] @@ -123463,7 +127238,6 @@ is_a: GO:0042127 ! regulation of cell population proliferation intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0097360 ! chorionic trophoblast cell proliferation relationship: regulates GO:0097360 ! chorionic trophoblast cell proliferation -created_by: vk creation_date: 2012-10-01T10:03:13Z [Term] @@ -123480,7 +127254,6 @@ is_a: GO:1901382 ! regulation of chorionic trophoblast cell proliferation intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0097360 ! chorionic trophoblast cell proliferation relationship: negatively_regulates GO:0097360 ! chorionic trophoblast cell proliferation -created_by: vk creation_date: 2012-10-01T10:04:23Z [Term] @@ -123497,7 +127270,6 @@ is_a: GO:1901382 ! regulation of chorionic trophoblast cell proliferation intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0097360 ! chorionic trophoblast cell proliferation relationship: positively_regulates GO:0097360 ! chorionic trophoblast cell proliferation -created_by: vk creation_date: 2012-10-01T10:04:41Z [Term] @@ -123509,7 +127281,6 @@ is_a: GO:0051279 ! regulation of release of sequestered calcium ion into cytosol intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0061454 ! release of sequestered calcium ion into cytosol by Golgi relationship: regulates GO:0061454 ! release of sequestered calcium ion into cytosol by Golgi -created_by: al creation_date: 2012-10-03T07:26:03Z [Term] @@ -123522,7 +127293,6 @@ is_a: GO:0022603 ! regulation of anatomical structure morphogenesis intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0001946 ! lymphangiogenesis relationship: regulates GO:0001946 ! lymphangiogenesis -created_by: dph creation_date: 2012-10-15T13:08:17Z [Term] @@ -123544,7 +127314,6 @@ is_a: GO:1901490 ! regulation of lymphangiogenesis intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0001946 ! lymphangiogenesis relationship: negatively_regulates GO:0001946 ! lymphangiogenesis -created_by: dph creation_date: 2012-10-15T13:08:21Z [Term] @@ -123566,7 +127335,6 @@ is_a: GO:1901490 ! regulation of lymphangiogenesis intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0001946 ! lymphangiogenesis relationship: positively_regulates GO:0001946 ! lymphangiogenesis -created_by: dph creation_date: 2012-10-15T13:08:25Z [Term] @@ -123580,7 +127348,6 @@ intersection_of: GO:0022857 ! transmembrane transporter activity intersection_of: has_primary_input CHEBI:63299 relationship: has_primary_input CHEBI:63299 relationship: part_of GO:1901264 {source="GO_REF:0000090"} ! carbohydrate derivative transport -created_by: pr creation_date: 2012-10-17T10:31:22Z [Term] @@ -123592,7 +127359,6 @@ is_a: GO:1905330 ! regulation of morphogenesis of an epithelium intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0061154 ! endothelial tube morphogenesis relationship: regulates GO:0061154 ! endothelial tube morphogenesis -created_by: dph creation_date: 2012-10-17T14:30:40Z [Term] @@ -123607,7 +127373,6 @@ is_a: GO:0045595 ! regulation of cell differentiation intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0002244 ! hematopoietic progenitor cell differentiation relationship: regulates GO:0002244 ! hematopoietic progenitor cell differentiation -created_by: vk creation_date: 2012-10-24T11:23:01Z [Term] @@ -123639,7 +127404,6 @@ is_a: GO:1901532 ! regulation of hematopoietic progenitor cell differentiation intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0002244 ! hematopoietic progenitor cell differentiation relationship: negatively_regulates GO:0002244 ! hematopoietic progenitor cell differentiation -created_by: vk creation_date: 2012-10-24T11:23:06Z [Term] @@ -123671,7 +127435,6 @@ is_a: GO:1901532 ! regulation of hematopoietic progenitor cell differentiation intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0002244 ! hematopoietic progenitor cell differentiation relationship: positively_regulates GO:0002244 ! hematopoietic progenitor cell differentiation -created_by: vk creation_date: 2012-10-24T11:23:14Z [Term] @@ -123684,7 +127447,6 @@ is_a: GO:0060284 ! regulation of cell development intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0001885 ! endothelial cell development relationship: regulates GO:0001885 ! endothelial cell development -created_by: pr creation_date: 2012-10-30T12:59:50Z [Term] @@ -123702,7 +127464,6 @@ is_a: GO:1901550 ! regulation of endothelial cell development intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0001885 ! endothelial cell development relationship: negatively_regulates GO:0001885 ! endothelial cell development -created_by: pr creation_date: 2012-10-30T12:59:54Z [Term] @@ -123719,7 +127480,6 @@ is_a: GO:1901550 ! regulation of endothelial cell development intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0001885 ! endothelial cell development relationship: positively_regulates GO:0001885 ! endothelial cell development -created_by: pr creation_date: 2012-10-30T12:59:58Z [Term] @@ -123734,7 +127494,6 @@ is_a: GO:0005874 ! microtubule intersection_of: GO:0005874 ! microtubule intersection_of: part_of GO:0030425 ! dendrite relationship: part_of GO:0030425 ! dendrite -created_by: pr creation_date: 2012-11-07T14:37:30Z [Term] @@ -123750,7 +127509,6 @@ is_a: GO:0097427 ! microtubule bundle intersection_of: GO:0097427 ! microtubule bundle intersection_of: part_of GO:0030424 ! axon relationship: part_of GO:0030424 ! axon -created_by: pr creation_date: 2012-11-07T15:37:12Z [Term] @@ -123764,7 +127522,6 @@ is_a: GO:0008152 ! metabolic process intersection_of: GO:0008152 ! metabolic process intersection_of: has_primary_input_or_output CHEBI:78608 relationship: has_primary_input_or_output CHEBI:78608 -created_by: tb creation_date: 2012-11-08T17:39:50Z [Term] @@ -123780,7 +127537,6 @@ is_a: GO:1901605 ! alpha-amino acid metabolic process intersection_of: GO:0009056 ! catabolic process intersection_of: has_primary_input CHEBI:78608 relationship: has_primary_input CHEBI:78608 -created_by: tb creation_date: 2012-11-08T17:39:54Z [Term] @@ -123797,7 +127553,6 @@ is_a: GO:1901605 ! alpha-amino acid metabolic process intersection_of: GO:0009058 ! biosynthetic process intersection_of: has_primary_output CHEBI:78608 relationship: has_primary_output CHEBI:78608 -created_by: tb creation_date: 2012-11-08T17:39:58Z [Term] @@ -123810,7 +127565,6 @@ is_a: GO:1902513 ! regulation of organelle transport along microtubule intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0047496 ! vesicle transport along microtubule relationship: regulates GO:0047496 ! vesicle transport along microtubule -created_by: hjd creation_date: 2012-11-08T21:49:44Z [Term] @@ -123832,7 +127586,6 @@ is_a: GO:1901608 ! regulation of vesicle transport along microtubule intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0047496 ! vesicle transport along microtubule relationship: negatively_regulates GO:0047496 ! vesicle transport along microtubule -created_by: hjd creation_date: 2012-11-08T21:49:48Z [Term] @@ -123854,7 +127607,6 @@ is_a: GO:1901608 ! regulation of vesicle transport along microtubule intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0047496 ! vesicle transport along microtubule relationship: positively_regulates GO:0047496 ! vesicle transport along microtubule -created_by: hjd creation_date: 2012-11-08T21:49:53Z [Term] @@ -123896,7 +127648,6 @@ is_a: GO:2000331 ! regulation of terminal button organization intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0072553 ! terminal button organization relationship: negatively_regulates GO:0072553 ! terminal button organization -created_by: lb creation_date: 2012-11-13T10:40:51Z [Term] @@ -123938,7 +127689,6 @@ is_a: GO:2000331 ! regulation of terminal button organization intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0072553 ! terminal button organization relationship: positively_regulates GO:0072553 ! terminal button organization -created_by: lb creation_date: 2012-11-13T10:40:58Z [Term] @@ -123952,7 +127702,6 @@ is_a: GO:0008152 ! metabolic process intersection_of: GO:0008152 ! metabolic process intersection_of: has_primary_input_or_output CHEBI:33822 relationship: has_primary_input_or_output CHEBI:33822 -created_by: pr creation_date: 2012-11-13T12:54:27Z [Term] @@ -123968,7 +127717,6 @@ is_a: GO:1901615 ! organic hydroxy compound metabolic process intersection_of: GO:0009056 ! catabolic process intersection_of: has_primary_input CHEBI:33822 relationship: has_primary_input CHEBI:33822 -created_by: pr creation_date: 2012-11-13T12:54:31Z [Term] @@ -123985,7 +127733,6 @@ is_a: GO:1901615 ! organic hydroxy compound metabolic process intersection_of: GO:0009058 ! biosynthetic process intersection_of: has_primary_output CHEBI:33822 relationship: has_primary_output CHEBI:33822 -created_by: pr creation_date: 2012-11-13T12:54:36Z [Term] @@ -123997,7 +127744,6 @@ is_a: GO:0022857 ! transmembrane transporter activity intersection_of: GO:0022857 ! transmembrane transporter activity intersection_of: has_primary_input CHEBI:33822 relationship: has_primary_input CHEBI:33822 -created_by: pr creation_date: 2012-11-13T12:59:01Z [Term] @@ -124010,7 +127756,6 @@ is_a: GO:2000401 ! regulation of lymphocyte migration intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0048247 ! lymphocyte chemotaxis relationship: regulates GO:0048247 ! lymphocyte chemotaxis -created_by: tb creation_date: 2012-11-13T23:03:23Z [Term] @@ -124028,7 +127773,6 @@ is_a: GO:2000402 ! negative regulation of lymphocyte migration intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0048247 ! lymphocyte chemotaxis relationship: negatively_regulates GO:0048247 ! lymphocyte chemotaxis -created_by: tb creation_date: 2012-11-13T23:03:28Z [Term] @@ -124042,7 +127786,6 @@ is_a: GO:0051128 ! regulation of cellular component organization intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0001941 ! postsynaptic membrane organization relationship: regulates GO:0001941 ! postsynaptic membrane organization -created_by: ans creation_date: 2012-11-15T11:40:15Z [Term] @@ -124065,7 +127808,6 @@ is_a: GO:1905809 ! negative regulation of synapse organization intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0001941 ! postsynaptic membrane organization relationship: negatively_regulates GO:0001941 ! postsynaptic membrane organization -created_by: ans creation_date: 2012-11-15T11:40:20Z [Term] @@ -124088,7 +127830,6 @@ is_a: GO:1901626 ! regulation of postsynaptic membrane organization intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0001941 ! postsynaptic membrane organization relationship: positively_regulates GO:0001941 ! postsynaptic membrane organization -created_by: ans creation_date: 2012-11-15T11:40:24Z [Term] @@ -124100,7 +127841,6 @@ is_a: GO:0050678 ! regulation of epithelial cell proliferation intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0002941 ! synoviocyte proliferation relationship: regulates GO:0002941 ! synoviocyte proliferation -created_by: hjd creation_date: 2012-11-16T20:16:23Z [Term] @@ -124117,7 +127857,6 @@ is_a: GO:1901645 ! regulation of synoviocyte proliferation intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0002941 ! synoviocyte proliferation relationship: negatively_regulates GO:0002941 ! synoviocyte proliferation -created_by: hjd creation_date: 2012-11-16T20:16:27Z [Term] @@ -124134,7 +127873,6 @@ is_a: GO:1901645 ! regulation of synoviocyte proliferation intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0002941 ! synoviocyte proliferation relationship: positively_regulates GO:0002941 ! synoviocyte proliferation -created_by: hjd creation_date: 2012-11-16T20:16:32Z [Term] @@ -124147,7 +127885,6 @@ is_a: GO:0050896 ! response to stimulus intersection_of: GO:0050896 ! response to stimulus intersection_of: has_primary_input CHEBI:60466 relationship: has_primary_input CHEBI:60466 -created_by: pr creation_date: 2012-11-20T09:45:15Z [Term] @@ -124159,14 +127896,12 @@ is_a: GO:0070887 ! cellular response to chemical stimulus is_a: GO:1901652 ! response to peptide intersection_of: GO:0070887 ! cellular response to chemical stimulus intersection_of: has_primary_input CHEBI:60466 -created_by: pr creation_date: 2012-11-20T09:45:19Z [Term] id: GO:1901654 name: response to ketone namespace: biological_process -alt_id: GO:1990369 def: "A response that results in a state of tolerance to ketone." [GOC:mengo_curators, PMID:23356676] synonym: "process resulting in tolerance to ketone" NARROW [] is_a: BFO:0000003 @@ -124174,7 +127909,6 @@ is_a: GO:0050896 ! response to stimulus intersection_of: GO:0050896 ! response to stimulus intersection_of: has_primary_input CHEBI:17087 relationship: has_primary_input CHEBI:17087 -created_by: pr creation_date: 2012-11-20T10:55:47Z [Term] @@ -124186,7 +127920,6 @@ is_a: GO:0070887 ! cellular response to chemical stimulus is_a: GO:1901654 ! response to ketone intersection_of: GO:0070887 ! cellular response to chemical stimulus intersection_of: has_primary_input CHEBI:17087 -created_by: pr creation_date: 2012-11-20T10:55:51Z [Term] @@ -124204,7 +127937,6 @@ is_a: GO:0050866 ! negative regulation of cell activation intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0014901 ! satellite cell activation involved in skeletal muscle regeneration relationship: negatively_regulates GO:0014901 ! satellite cell activation involved in skeletal muscle regeneration -created_by: dph creation_date: 2012-11-21T16:21:11Z [Term] @@ -124218,7 +127950,6 @@ is_a: GO:0005488 ! binding intersection_of: GO:0005488 ! binding intersection_of: has_primary_input CHEBI:15378 relationship: has_primary_input CHEBI:15378 -created_by: al creation_date: 2012-12-07T13:50:53Z [Term] @@ -124230,7 +127961,6 @@ is_a: GO:0042981 ! regulation of apoptotic process intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:1990010 ! compound eye retinal cell apoptotic process relationship: regulates GO:1990010 ! compound eye retinal cell apoptotic process -created_by: pr creation_date: 2012-12-12T10:28:35Z [Term] @@ -124247,14 +127977,12 @@ is_a: GO:1901692 ! regulation of compound eye retinal cell apoptotic process intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:1990010 ! compound eye retinal cell apoptotic process relationship: negatively_regulates GO:1990010 ! compound eye retinal cell apoptotic process -created_by: pr creation_date: 2012-12-12T10:28:40Z [Term] id: GO:1901694 name: positive regulation of compound eye retinal cell apoptotic process namespace: biological_process -alt_id: GO:0046675 def: "Any process that activates or increases the frequency, rate or extent of compound eye retinal cell apoptotic process." [GOC:mtg_apoptosis, GOC:TermGenie, PMID:12021768] synonym: "activation of compound eye retinal cell apoptotic process" NARROW [GOC:TermGenie] synonym: "induction of compound eye retinal cell programmed cell death" RELATED [] @@ -124267,7 +127995,6 @@ is_a: GO:1901692 ! regulation of compound eye retinal cell apoptotic process intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:1990010 ! compound eye retinal cell apoptotic process relationship: positively_regulates GO:1990010 ! compound eye retinal cell apoptotic process -created_by: pr creation_date: 2012-12-12T10:28:45Z [Term] @@ -124284,7 +128011,6 @@ intersection_of: GO:0050896 ! response to stimulus intersection_of: has_primary_input CHEBI:51143 relationship: has_primary_input CHEBI:51143 property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27194" xsd:anyURI -created_by: pr creation_date: 2012-12-13T15:06:08Z [Term] @@ -124300,7 +128026,6 @@ is_a: GO:1901698 ! response to nitrogen compound intersection_of: GO:0070887 ! cellular response to chemical stimulus intersection_of: has_primary_input CHEBI:51143 property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27194" xsd:anyURI -created_by: pr creation_date: 2012-12-13T15:06:13Z [Term] @@ -124316,7 +128041,6 @@ intersection_of: GO:0050896 ! response to stimulus intersection_of: has_primary_input CHEBI:25806 relationship: has_primary_input CHEBI:25806 property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27194" xsd:anyURI -created_by: pr creation_date: 2012-12-13T15:11:37Z [Term] @@ -124329,7 +128053,6 @@ is_a: GO:0070887 ! cellular response to chemical stimulus is_a: GO:1901700 ! response to oxygen-containing compound intersection_of: GO:0070887 ! cellular response to chemical stimulus intersection_of: has_primary_input CHEBI:25806 -created_by: pr creation_date: 2012-12-13T15:11:42Z [Term] @@ -124341,7 +128064,6 @@ is_a: GO:0048762 ! mesenchymal cell differentiation intersection_of: GO:0048762 ! mesenchymal cell differentiation intersection_of: part_of GO:0060348 ! bone development relationship: part_of GO:0060348 ! bone development -created_by: hjd creation_date: 2012-12-14T16:04:16Z [Term] @@ -124358,12 +128080,12 @@ synonym: "regulation of GABA catabolism" EXACT [GOC:TermGenie] synonym: "regulation of gamma-aminobutyric acid breakdown" EXACT [GOC:TermGenie] synonym: "regulation of gamma-aminobutyric acid catabolism" EXACT [GOC:TermGenie] synonym: "regulation of gamma-aminobutyric acid degradation" EXACT [GOC:TermGenie] -is_a: GO:0006521 ! regulation of cellular amino acid metabolic process +is_a: GO:0006521 ! regulation of amino acid metabolic process is_a: GO:0009894 ! regulation of catabolic process +is_a: GO:0062012 ! regulation of small molecule metabolic process intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0009450 ! gamma-aminobutyric acid catabolic process relationship: regulates GO:0009450 ! gamma-aminobutyric acid catabolic process -created_by: mcc creation_date: 2012-12-19T16:13:24Z [Term] @@ -124421,14 +128143,12 @@ synonym: "negative regulation of gamma-aminobutyric acid breakdown" EXACT [GOC:T synonym: "negative regulation of gamma-aminobutyric acid catabolism" EXACT [GOC:TermGenie] synonym: "negative regulation of gamma-aminobutyric acid degradation" EXACT [GOC:TermGenie] is_a: GO:0009895 ! negative regulation of catabolic process -is_a: GO:0031324 ! negative regulation of cellular metabolic process -is_a: GO:0045763 ! negative regulation of cellular amino acid metabolic process +is_a: GO:0045763 ! negative regulation of amino acid metabolic process is_a: GO:0062014 ! negative regulation of small molecule metabolic process is_a: GO:1901715 ! regulation of gamma-aminobutyric acid catabolic process intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0009450 ! gamma-aminobutyric acid catabolic process relationship: negatively_regulates GO:0009450 ! gamma-aminobutyric acid catabolic process -created_by: mcc creation_date: 2012-12-19T16:13:31Z [Term] @@ -124486,14 +128206,12 @@ synonym: "upregulation of gamma-aminobutyric acid catabolic process" EXACT [GOC: synonym: "upregulation of gamma-aminobutyric acid catabolism" EXACT [GOC:TermGenie] synonym: "upregulation of gamma-aminobutyric acid degradation" EXACT [GOC:TermGenie] is_a: GO:0009896 ! positive regulation of catabolic process -is_a: GO:0031325 ! positive regulation of cellular metabolic process is_a: GO:0045764 ! positive regulation of amino acid metabolic process is_a: GO:0062013 ! positive regulation of small molecule metabolic process is_a: GO:1901715 ! regulation of gamma-aminobutyric acid catabolic process intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0009450 ! gamma-aminobutyric acid catabolic process relationship: positively_regulates GO:0009450 ! gamma-aminobutyric acid catabolic process -created_by: mcc creation_date: 2012-12-19T16:13:36Z [Term] @@ -124505,7 +128223,6 @@ is_a: GO:0042127 ! regulation of cell population proliferation intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0072111 ! cell proliferation involved in kidney development relationship: regulates GO:0072111 ! cell proliferation involved in kidney development -created_by: krc creation_date: 2012-12-27T19:30:31Z [Term] @@ -124522,7 +128239,6 @@ is_a: GO:1901722 ! regulation of cell proliferation involved in kidney developme intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0072111 ! cell proliferation involved in kidney development relationship: negatively_regulates GO:0072111 ! cell proliferation involved in kidney development -created_by: krc creation_date: 2012-12-27T19:30:35Z [Term] @@ -124539,7 +128255,6 @@ is_a: GO:1901722 ! regulation of cell proliferation involved in kidney developme intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0072111 ! cell proliferation involved in kidney development relationship: positively_regulates GO:0072111 ! cell proliferation involved in kidney development -created_by: krc creation_date: 2012-12-27T19:30:40Z [Term] @@ -124553,7 +128268,6 @@ is_a: GO:0008152 ! metabolic process intersection_of: GO:0008152 ! metabolic process intersection_of: has_primary_input_or_output CHEBI:27547 relationship: has_primary_input_or_output CHEBI:27547 -created_by: yaf creation_date: 2013-01-22T11:36:55Z [Term] @@ -124569,7 +128283,6 @@ is_a: GO:1901825 ! zeaxanthin metabolic process intersection_of: GO:0009056 ! catabolic process intersection_of: has_primary_input CHEBI:27547 relationship: has_primary_input CHEBI:27547 -created_by: yaf creation_date: 2013-01-22T11:37:00Z [Term] @@ -124586,7 +128299,6 @@ is_a: GO:1901825 ! zeaxanthin metabolic process intersection_of: GO:0009058 ! biosynthetic process intersection_of: has_primary_output CHEBI:27547 relationship: has_primary_output CHEBI:27547 -created_by: yaf creation_date: 2013-01-22T11:37:07Z [Term] @@ -124598,7 +128310,6 @@ is_a: GO:0050793 ! regulation of developmental process intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0060537 ! muscle tissue development relationship: regulates GO:0060537 ! muscle tissue development -created_by: yaf creation_date: 2013-02-01T10:30:47Z [Term] @@ -124615,7 +128326,6 @@ is_a: GO:1901861 ! regulation of muscle tissue development intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0060537 ! muscle tissue development relationship: negatively_regulates GO:0060537 ! muscle tissue development -created_by: yaf creation_date: 2013-02-01T10:30:52Z [Term] @@ -124632,7 +128342,6 @@ is_a: GO:1901861 ! regulation of muscle tissue development intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0060537 ! muscle tissue development relationship: positively_regulates GO:0060537 ! muscle tissue development -created_by: yaf creation_date: 2013-02-01T10:30:57Z [Term] @@ -124646,7 +128355,6 @@ is_a: GO:0051098 ! regulation of binding intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0005509 ! calcium ion binding relationship: regulates GO:0005509 ! calcium ion binding -created_by: rl creation_date: 2013-02-06T12:38:12Z [Term] @@ -124669,7 +128377,6 @@ is_a: GO:1901876 ! regulation of calcium ion binding intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0005509 ! calcium ion binding relationship: negatively_regulates GO:0005509 ! calcium ion binding -created_by: rl creation_date: 2013-02-06T12:38:22Z [Term] @@ -124692,7 +128399,6 @@ is_a: GO:1901876 ! regulation of calcium ion binding intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0005509 ! calcium ion binding relationship: positively_regulates GO:0005509 ! calcium ion binding -created_by: rl creation_date: 2013-02-06T12:38:26Z [Term] @@ -124708,7 +128414,6 @@ is_a: GO:0043244 ! regulation of protein-containing complex disassembly intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0051261 ! protein depolymerization relationship: regulates GO:0051261 ! protein depolymerization -created_by: rl creation_date: 2013-02-06T13:57:23Z [Term] @@ -124745,7 +128450,6 @@ is_a: GO:1901879 ! regulation of protein depolymerization intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0051261 ! protein depolymerization relationship: negatively_regulates GO:0051261 ! protein depolymerization -created_by: rl creation_date: 2013-02-06T13:57:28Z [Term] @@ -124782,7 +128486,6 @@ is_a: GO:1901879 ! regulation of protein depolymerization intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0051261 ! protein depolymerization relationship: positively_regulates GO:0051261 ! protein depolymerization -created_by: rl creation_date: 2013-02-06T13:57:32Z [Term] @@ -124795,7 +128498,6 @@ is_a: GO:0051128 ! regulation of cellular component organization intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0034329 ! cell junction assembly relationship: regulates GO:0034329 ! cell junction assembly -created_by: tb creation_date: 2013-02-06T19:40:32Z [Term] @@ -124812,7 +128514,6 @@ is_a: GO:1901888 ! regulation of cell junction assembly intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0034329 ! cell junction assembly relationship: negatively_regulates GO:0034329 ! cell junction assembly -created_by: tb creation_date: 2013-02-06T19:40:41Z [Term] @@ -124830,7 +128531,6 @@ is_a: GO:1901888 ! regulation of cell junction assembly intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0034329 ! cell junction assembly relationship: positively_regulates GO:0034329 ! cell junction assembly -created_by: tb creation_date: 2013-02-06T19:40:46Z [Term] @@ -124846,7 +128546,6 @@ is_a: GO:0051650 ! establishment of vesicle localization intersection_of: GO:0006810 ! transport intersection_of: has_primary_input GO:0031045 ! dense core granule intersection_of: occurs_in GO:0005829 ! cytosol -created_by: pr creation_date: 2013-02-19T13:00:52Z [Term] @@ -124859,7 +128558,6 @@ is_a: GO:1904809 ! regulation of dense core granule transport intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:1990048 ! anterograde neuronal dense core vesicle transport relationship: regulates GO:1990048 ! anterograde neuronal dense core vesicle transport -created_by: pr creation_date: 2013-02-19T13:36:21Z [Term] @@ -124877,7 +128575,6 @@ is_a: GO:1904810 ! negative regulation of dense core granule transport intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:1990048 ! anterograde neuronal dense core vesicle transport relationship: negatively_regulates GO:1990048 ! anterograde neuronal dense core vesicle transport -created_by: pr creation_date: 2013-02-19T13:36:30Z [Term] @@ -124895,7 +128592,6 @@ is_a: GO:1904811 ! positive regulation of dense core granule transport intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:1990048 ! anterograde neuronal dense core vesicle transport relationship: positively_regulates GO:1990048 ! anterograde neuronal dense core vesicle transport -created_by: pr creation_date: 2013-02-19T13:36:35Z [Term] @@ -124909,7 +128605,6 @@ is_a: GO:2001017 ! regulation of retrograde axon cargo transport intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:1990049 ! retrograde neuronal dense core vesicle transport relationship: regulates GO:1990049 ! retrograde neuronal dense core vesicle transport -created_by: pr creation_date: 2013-02-19T13:36:43Z [Term] @@ -124928,7 +128623,6 @@ is_a: GO:2001018 ! negative regulation of retrograde axon cargo transport intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:1990049 ! retrograde neuronal dense core vesicle transport relationship: negatively_regulates GO:1990049 ! retrograde neuronal dense core vesicle transport -created_by: pr creation_date: 2013-02-19T13:36:47Z [Term] @@ -124947,7 +128641,6 @@ is_a: GO:2001019 ! positive regulation of retrograde axon cargo transport intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:1990049 ! retrograde neuronal dense core vesicle transport relationship: positively_regulates GO:1990049 ! retrograde neuronal dense core vesicle transport -created_by: pr creation_date: 2013-02-19T13:36:52Z [Term] @@ -124959,7 +128652,6 @@ is_a: GO:2000136 ! regulation of cell proliferation involved in heart morphogene intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0061325 ! cell proliferation involved in outflow tract morphogenesis relationship: regulates GO:0061325 ! cell proliferation involved in outflow tract morphogenesis -created_by: dph creation_date: 2013-02-20T20:30:26Z [Term] @@ -124976,7 +128668,6 @@ is_a: GO:2000138 ! positive regulation of cell proliferation involved in heart m intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0061325 ! cell proliferation involved in outflow tract morphogenesis relationship: positively_regulates GO:0061325 ! cell proliferation involved in outflow tract morphogenesis -created_by: dph creation_date: 2013-02-20T20:30:31Z [Term] @@ -124992,7 +128683,6 @@ intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0060271 ! cilium assembly relationship: regulates GO:0060271 ! cilium assembly property_value: RO:0002161 NCBITaxon:4751 -created_by: dph creation_date: 2013-03-26T18:10:51Z [Term] @@ -125020,7 +128710,6 @@ is_a: GO:1902116 ! negative regulation of organelle assembly intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0060271 ! cilium assembly relationship: negatively_regulates GO:0060271 ! cilium assembly -created_by: dph creation_date: 2013-03-26T18:10:56Z [Term] @@ -125034,7 +128723,6 @@ is_a: GO:2000145 ! regulation of cell motility intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0060285 ! cilium-dependent cell motility relationship: regulates GO:0060285 ! cilium-dependent cell motility -created_by: jl creation_date: 2013-03-27T14:42:38Z [Term] @@ -125053,7 +128741,6 @@ is_a: GO:2000146 ! negative regulation of cell motility intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0060285 ! cilium-dependent cell motility relationship: negatively_regulates GO:0060285 ! cilium-dependent cell motility -created_by: jl creation_date: 2013-03-27T14:42:42Z [Term] @@ -125065,7 +128752,6 @@ is_a: GO:0015802 ! basic amino acid transport intersection_of: GO:0015802 ! basic amino acid transport intersection_of: has_primary_input CHEBI:57595 relationship: has_primary_input CHEBI:57595 -created_by: kmv creation_date: 2013-03-27T16:09:15Z [Term] @@ -125078,7 +128764,6 @@ is_a: GO:0072091 ! regulation of stem cell proliferation intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0071425 ! hematopoietic stem cell proliferation relationship: regulates GO:0071425 ! hematopoietic stem cell proliferation -created_by: ss creation_date: 2013-04-02T05:13:19Z [Term] @@ -125101,7 +128786,6 @@ is_a: GO:2000647 ! negative regulation of stem cell proliferation intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0071425 ! hematopoietic stem cell proliferation relationship: negatively_regulates GO:0071425 ! hematopoietic stem cell proliferation -created_by: ss creation_date: 2013-04-02T05:13:24Z [Term] @@ -125123,7 +128807,6 @@ is_a: GO:2000648 ! positive regulation of stem cell proliferation intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0071425 ! hematopoietic stem cell proliferation relationship: positively_regulates GO:0071425 ! hematopoietic stem cell proliferation -created_by: ss creation_date: 2013-04-02T05:13:31Z [Term] @@ -125139,7 +128822,6 @@ is_a: GO:2000736 ! regulation of stem cell differentiation intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0060218 ! hematopoietic stem cell differentiation relationship: regulates GO:0060218 ! hematopoietic stem cell differentiation -created_by: ss creation_date: 2013-04-02T05:19:09Z [Term] @@ -125172,7 +128854,6 @@ is_a: GO:2000737 ! negative regulation of stem cell differentiation intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0060218 ! hematopoietic stem cell differentiation relationship: negatively_regulates GO:0060218 ! hematopoietic stem cell differentiation -created_by: ss creation_date: 2013-04-02T05:19:14Z [Term] @@ -125205,7 +128886,6 @@ is_a: GO:2000738 ! positive regulation of stem cell differentiation intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0060218 ! hematopoietic stem cell differentiation relationship: positively_regulates GO:0060218 ! hematopoietic stem cell differentiation -created_by: ss creation_date: 2013-04-02T05:19:19Z [Term] @@ -125218,7 +128898,6 @@ is_a: GO:0050896 ! response to stimulus intersection_of: GO:0050896 ! response to stimulus intersection_of: has_primary_input CHEBI:29985 relationship: has_primary_input CHEBI:29985 -created_by: tb creation_date: 2013-04-16T21:21:14Z [Term] @@ -125230,7 +128909,6 @@ is_a: GO:1905483 ! regulation of motor neuron migration intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0097477 ! lateral motor column neuron migration relationship: regulates GO:0097477 ! lateral motor column neuron migration -created_by: pr creation_date: 2013-04-23T14:42:18Z [Term] @@ -125247,7 +128925,6 @@ is_a: GO:1905484 ! negative regulation of motor neuron migration intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0097477 ! lateral motor column neuron migration relationship: negatively_regulates GO:0097477 ! lateral motor column neuron migration -created_by: pr creation_date: 2013-04-23T14:42:23Z [Term] @@ -125264,7 +128941,6 @@ is_a: GO:1905485 ! positive regulation of motor neuron migration intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0097477 ! lateral motor column neuron migration relationship: positively_regulates GO:0097477 ! lateral motor column neuron migration -created_by: pr creation_date: 2013-04-23T14:42:28Z [Term] @@ -125289,7 +128965,6 @@ is_a: GO:2000243 ! positive regulation of reproductive process intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0030317 ! flagellated sperm motility relationship: positively_regulates GO:0030317 ! flagellated sperm motility -created_by: bf creation_date: 2013-04-29T09:15:25Z [Term] @@ -125303,7 +128978,6 @@ is_a: GO:1903706 ! regulation of hemopoiesis intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0002521 ! leukocyte differentiation relationship: regulates GO:0002521 ! leukocyte differentiation -created_by: pr creation_date: 2013-05-02T17:32:42Z [Term] @@ -125330,7 +129004,6 @@ is_a: GO:1903707 ! negative regulation of hemopoiesis intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0002521 ! leukocyte differentiation relationship: negatively_regulates GO:0002521 ! leukocyte differentiation -created_by: pr creation_date: 2013-05-02T17:32:47Z [Term] @@ -125357,7 +129030,6 @@ is_a: GO:1903708 ! positive regulation of hemopoiesis intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0002521 ! leukocyte differentiation relationship: positively_regulates GO:0002521 ! leukocyte differentiation -created_by: pr creation_date: 2013-05-02T17:32:52Z [Term] @@ -125370,7 +129042,6 @@ is_a: GO:0044087 ! regulation of cellular component biogenesis intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0070925 ! organelle assembly relationship: regulates GO:0070925 ! organelle assembly -created_by: pr creation_date: 2013-05-14T09:43:21Z [Term] @@ -125387,7 +129058,6 @@ is_a: GO:1902115 ! regulation of organelle assembly intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0070925 ! organelle assembly relationship: negatively_regulates GO:0070925 ! organelle assembly -created_by: pr creation_date: 2013-05-14T09:43:31Z [Term] @@ -125405,7 +129075,6 @@ is_a: GO:1902115 ! regulation of organelle assembly intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0070925 ! organelle assembly relationship: positively_regulates GO:0070925 ! organelle assembly -created_by: pr creation_date: 2013-05-14T09:43:36Z [Term] @@ -125418,7 +129087,6 @@ is_a: GO:1904035 ! regulation of epithelial cell apoptotic process intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0097283 ! keratinocyte apoptotic process relationship: regulates GO:0097283 ! keratinocyte apoptotic process -created_by: rl creation_date: 2013-05-29T14:36:11Z [Term] @@ -125440,7 +129108,6 @@ is_a: GO:1904036 ! negative regulation of epithelial cell apoptotic process intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0097283 ! keratinocyte apoptotic process relationship: negatively_regulates GO:0097283 ! keratinocyte apoptotic process -created_by: rl creation_date: 2013-05-29T14:36:15Z [Term] @@ -125462,7 +129129,6 @@ is_a: GO:1904037 ! positive regulation of epithelial cell apoptotic process intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0097283 ! keratinocyte apoptotic process relationship: positively_regulates GO:0097283 ! keratinocyte apoptotic process -created_by: rl creation_date: 2013-05-29T14:36:21Z [Term] @@ -125476,7 +129142,6 @@ is_a: GO:0001959 ! regulation of cytokine-mediated signaling pathway intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0038161 ! prolactin signaling pathway relationship: regulates GO:0038161 ! prolactin signaling pathway -created_by: lb creation_date: 2013-06-12T10:10:07Z [Term] @@ -125503,7 +129168,6 @@ is_a: GO:1902211 ! regulation of prolactin signaling pathway intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0038161 ! prolactin signaling pathway relationship: negatively_regulates GO:0038161 ! prolactin signaling pathway -created_by: lb creation_date: 2013-06-12T10:10:12Z [Term] @@ -125530,7 +129194,6 @@ is_a: GO:1902211 ! regulation of prolactin signaling pathway intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0038161 ! prolactin signaling pathway relationship: positively_regulates GO:0038161 ! prolactin signaling pathway -created_by: lb creation_date: 2013-06-12T10:10:18Z [Term] @@ -125548,7 +129211,6 @@ intersection_of: GO:0006915 ! apoptotic process intersection_of: occurs_in CL:0000232 ! erythrocyte relationship: occurs_in CL:0000232 ! erythrocyte property_value: RO:0002161 NCBITaxon:4751 -created_by: rl creation_date: 2013-06-13T10:02:29Z [Term] @@ -125565,7 +129227,6 @@ is_a: GO:0033032 ! regulation of myeloid cell apoptotic process intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:1902217 ! erythrocyte apoptotic process relationship: regulates GO:1902217 ! erythrocyte apoptotic process -created_by: rl creation_date: 2013-06-20T19:30:53Z [Term] @@ -125608,7 +129269,6 @@ intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:1902217 ! erythrocyte apoptotic process relationship: negatively_regulates GO:1902217 ! erythrocyte apoptotic process property_value: RO:0002161 NCBITaxon:4751 -created_by: rl creation_date: 2013-06-20T19:30:59Z [Term] @@ -125651,7 +129311,6 @@ intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:1902217 ! erythrocyte apoptotic process relationship: positively_regulates GO:1902217 ! erythrocyte apoptotic process property_value: RO:0002161 NCBITaxon:4751 -created_by: rl creation_date: 2013-06-20T19:31:04Z [Term] @@ -125664,7 +129323,6 @@ is_a: GO:1902337 ! regulation of apoptotic process involved in morphogenesis intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0003275 ! apoptotic process involved in outflow tract morphogenesis relationship: regulates GO:0003275 ! apoptotic process involved in outflow tract morphogenesis -created_by: dph creation_date: 2013-06-24T19:12:24Z [Term] @@ -125686,7 +129344,6 @@ is_a: GO:1902338 ! negative regulation of apoptotic process involved in morphoge intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0003275 ! apoptotic process involved in outflow tract morphogenesis relationship: negatively_regulates GO:0003275 ! apoptotic process involved in outflow tract morphogenesis -created_by: dph creation_date: 2013-06-24T19:12:30Z [Term] @@ -125708,7 +129365,6 @@ is_a: GO:1902339 ! positive regulation of apoptotic process involved in morphoge intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0003275 ! apoptotic process involved in outflow tract morphogenesis relationship: positively_regulates GO:0003275 ! apoptotic process involved in outflow tract morphogenesis -created_by: dph creation_date: 2013-06-24T19:12:42Z [Term] @@ -125727,15 +129383,12 @@ is_a: GO:0060561 ! apoptotic process involved in morphogenesis intersection_of: GO:0006915 ! apoptotic process intersection_of: part_of GO:0048514 ! blood vessel morphogenesis relationship: part_of GO:0048514 ! blood vessel morphogenesis -created_by: dph creation_date: 2013-06-25T16:16:00Z [Term] id: GO:1902275 name: regulation of chromatin organization namespace: biological_process -alt_id: GO:0001672 -alt_id: GO:1903308 def: "Any process that modulates the frequency, rate or extent of chromatin organization." [GO_REF:0000058, GOC:bf, GOC:TermGenie, GOC:vw, PMID:18314879] synonym: "regulation of chromatin assembly or disassembly" RELATED [] synonym: "regulation of chromatin assembly/disassembly" RELATED [] @@ -125746,7 +129399,6 @@ is_a: GO:0051128 ! regulation of cellular component organization intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0006325 ! chromatin organization relationship: regulates GO:0006325 ! chromatin organization -created_by: bf creation_date: 2013-07-01T13:21:52Z [Term] @@ -125760,7 +129412,6 @@ is_a: GO:0034765 ! regulation of monoatomic ion transmembrane transport intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0035725 ! sodium ion transmembrane transport relationship: regulates GO:0035725 ! sodium ion transmembrane transport -created_by: rl creation_date: 2013-07-18T13:33:53Z [Term] @@ -125783,7 +129434,6 @@ is_a: GO:1902305 ! regulation of sodium ion transmembrane transport intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0035725 ! sodium ion transmembrane transport relationship: negatively_regulates GO:0035725 ! sodium ion transmembrane transport -created_by: rl creation_date: 2013-07-18T13:34:01Z [Term] @@ -125806,7 +129456,6 @@ is_a: GO:1902305 ! regulation of sodium ion transmembrane transport intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0035725 ! sodium ion transmembrane transport relationship: positively_regulates GO:0035725 ! sodium ion transmembrane transport -created_by: rl creation_date: 2013-07-18T13:34:18Z [Term] @@ -125821,7 +129470,6 @@ is_a: GO:1904748 ! regulation of apoptotic process involved in development intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0060561 ! apoptotic process involved in morphogenesis relationship: regulates GO:0060561 ! apoptotic process involved in morphogenesis -created_by: sart creation_date: 2013-07-29T15:03:16Z [Term] @@ -125853,7 +129501,6 @@ is_a: GO:1904746 ! negative regulation of apoptotic process involved in developm intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0060561 ! apoptotic process involved in morphogenesis relationship: negatively_regulates GO:0060561 ! apoptotic process involved in morphogenesis -created_by: sart creation_date: 2013-07-29T15:03:25Z [Term] @@ -125885,7 +129532,6 @@ is_a: GO:1904747 ! positive regulation of apoptotic process involved in developm intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0060561 ! apoptotic process involved in morphogenesis relationship: positively_regulates GO:0060561 ! apoptotic process involved in morphogenesis -created_by: sart creation_date: 2013-07-29T15:03:33Z [Term] @@ -125912,7 +129558,6 @@ is_a: GO:2001251 ! negative regulation of chromosome organization intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0030261 ! chromosome condensation relationship: negatively_regulates GO:0030261 ! chromosome condensation -created_by: dgf creation_date: 2013-07-29T20:54:14Z [Term] @@ -125927,7 +129572,6 @@ is_a: GO:0006915 ! apoptotic process intersection_of: GO:0006915 ! apoptotic process intersection_of: occurs_in CL:0000148 ! melanocyte relationship: occurs_in CL:0000148 ! melanocyte -created_by: pr creation_date: 2013-08-15T16:35:45Z [Term] @@ -125959,7 +129603,6 @@ is_a: GO:0051253 ! negative regulation of RNA metabolic process intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0006401 ! RNA catabolic process relationship: negatively_regulates GO:0006401 ! RNA catabolic process -created_by: bf creation_date: 2013-08-22T14:59:39Z [Term] @@ -125974,7 +129617,6 @@ is_a: GO:0150105 ! protein localization to cell-cell junction intersection_of: GO:0008104 ! protein localization intersection_of: has_target_end_location GO:0005923 ! bicellular tight junction relationship: has_target_end_location GO:0005923 ! bicellular tight junction -created_by: tb creation_date: 2013-09-11T21:43:13Z [Term] @@ -125989,7 +129631,6 @@ is_a: GO:0008104 ! protein localization intersection_of: GO:0008104 ! protein localization intersection_of: has_target_end_location GO:0030054 ! cell junction relationship: has_target_end_location GO:0030054 ! cell junction -created_by: tb creation_date: 2013-09-13T16:55:57Z [Term] @@ -126004,7 +129645,6 @@ is_a: GO:0022898 ! regulation of transmembrane transporter activity intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0015250 ! water channel activity relationship: regulates GO:0015250 ! water channel activity -created_by: bf creation_date: 2013-09-23T12:56:31Z [Term] @@ -126029,7 +129669,6 @@ is_a: GO:1902427 ! regulation of water channel activity intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0015250 ! water channel activity relationship: positively_regulates GO:0015250 ! water channel activity -created_by: bf creation_date: 2013-09-23T12:56:49Z [Term] @@ -126052,7 +129691,6 @@ is_a: GO:2000036 ! regulation of stem cell population maintenance intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0019827 ! stem cell population maintenance relationship: negatively_regulates GO:0019827 ! stem cell population maintenance -created_by: cjm creation_date: 2013-10-16T22:19:17Z [Term] @@ -126075,7 +129713,6 @@ is_a: GO:2000036 ! regulation of stem cell population maintenance intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0019827 ! stem cell population maintenance relationship: positively_regulates GO:0019827 ! stem cell population maintenance -created_by: cjm creation_date: 2013-10-16T22:27:47Z [Term] @@ -126090,7 +129727,6 @@ is_a: GO:0008104 ! protein localization intersection_of: GO:0008104 ! protein localization intersection_of: has_target_end_location GO:0031252 ! cell leading edge relationship: has_target_end_location GO:0031252 ! cell leading edge -created_by: jl creation_date: 2013-10-22T12:36:07Z [Term] @@ -126103,7 +129739,6 @@ is_a: GO:0032880 ! regulation of protein localization intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0035418 ! protein localization to synapse relationship: regulates GO:0035418 ! protein localization to synapse -created_by: kmv creation_date: 2013-10-25T15:09:09Z [Term] @@ -126125,7 +129760,6 @@ is_a: GO:1903829 ! positive regulation of protein localization intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0035418 ! protein localization to synapse relationship: positively_regulates GO:0035418 ! protein localization to synapse -created_by: kmv creation_date: 2013-10-25T15:09:18Z [Term] @@ -126144,7 +129778,6 @@ is_a: GO:0070231 ! T cell apoptotic process intersection_of: GO:0006915 ! apoptotic process intersection_of: occurs_in CL:0000815 ! regulatory T cell relationship: occurs_in CL:0000815 ! regulatory T cell -created_by: nhn creation_date: 2013-11-04T17:18:09Z [Term] @@ -126157,7 +129790,6 @@ is_a: GO:1904019 ! epithelial cell apoptotic process intersection_of: GO:0006915 ! apoptotic process intersection_of: occurs_in CL:0000216 ! Sertoli cell relationship: occurs_in CL:0000216 ! Sertoli cell -created_by: pr creation_date: 2013-11-06T11:27:34Z [Term] @@ -126172,7 +129804,6 @@ is_a: GO:1904019 ! epithelial cell apoptotic process intersection_of: GO:0006915 ! apoptotic process intersection_of: occurs_in CL:1000488 ! cholangiocyte relationship: occurs_in CL:1000488 ! cholangiocyte -created_by: cls creation_date: 2013-11-12T15:30:08Z [Term] @@ -126185,7 +129816,6 @@ is_a: GO:0006915 ! apoptotic process intersection_of: GO:0006915 ! apoptotic process intersection_of: occurs_in CL:0005026 ! hepatoblast relationship: occurs_in CL:0005026 ! hepatoblast -created_by: cls creation_date: 2013-11-12T17:02:52Z [Term] @@ -126200,7 +129830,6 @@ is_a: GO:2000241 ! regulation of reproductive process intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0048240 ! sperm capacitation relationship: regulates GO:0048240 ! sperm capacitation -created_by: hjd creation_date: 2013-11-12T21:17:03Z [Term] @@ -126224,7 +129853,6 @@ is_a: GO:2000242 ! negative regulation of reproductive process intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0048240 ! sperm capacitation relationship: negatively_regulates GO:0048240 ! sperm capacitation -created_by: hjd creation_date: 2013-11-12T21:17:12Z [Term] @@ -126248,7 +129876,6 @@ is_a: GO:2000243 ! positive regulation of reproductive process intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0048240 ! sperm capacitation relationship: positively_regulates GO:0048240 ! sperm capacitation -created_by: hjd creation_date: 2013-11-12T21:17:21Z [Term] @@ -126264,7 +129891,6 @@ intersection_of: GO:0032991 ! protein-containing complex intersection_of: capable_of GO:0003824 ! catalytic activity relationship: capable_of GO:0003824 ! catalytic activity property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/19980" xsd:anyURI -created_by: bhm creation_date: 2013-11-13T16:18:47Z [Term] @@ -126277,7 +129903,6 @@ is_a: GO:1990351 ! transporter complex intersection_of: GO:0032991 ! protein-containing complex intersection_of: capable_of GO:0022857 ! transmembrane transporter activity relationship: capable_of GO:0022857 ! transmembrane transporter activity -created_by: bhm creation_date: 2013-11-13T16:23:04Z [Term] @@ -126296,7 +129921,6 @@ is_a: GO:1903624 ! regulation of DNA catabolic process intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0006309 ! apoptotic DNA fragmentation relationship: regulates GO:0006309 ! apoptotic DNA fragmentation -created_by: hjd creation_date: 2013-11-15T18:28:32Z [Term] @@ -126333,7 +129957,6 @@ is_a: GO:1903625 ! negative regulation of DNA catabolic process intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0006309 ! apoptotic DNA fragmentation relationship: negatively_regulates GO:0006309 ! apoptotic DNA fragmentation -created_by: hjd creation_date: 2013-11-15T18:28:41Z [Term] @@ -126370,7 +129993,6 @@ is_a: GO:1903626 ! positive regulation of DNA catabolic process intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0006309 ! apoptotic DNA fragmentation relationship: positively_regulates GO:0006309 ! apoptotic DNA fragmentation -created_by: hjd creation_date: 2013-11-15T18:28:50Z [Term] @@ -126384,14 +130006,12 @@ is_a: GO:0060632 ! regulation of microtubule-based movement intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0072384 ! organelle transport along microtubule relationship: regulates GO:0072384 ! organelle transport along microtubule -created_by: dph creation_date: 2013-11-15T20:15:17Z [Term] id: GO:1902531 name: regulation of intracellular signal transduction namespace: biological_process -alt_id: GO:0010627 def: "Any process that modulates the frequency, rate or extent of intracellular signal transduction." [GOC:dph, GOC:signaling, GOC:tb, GOC:TermGenie] synonym: "regulation of intracellular protein kinase cascade" NARROW [] synonym: "regulation of intracellular signal transduction pathway" NARROW [GOC:TermGenie] @@ -126404,14 +130024,12 @@ is_a: GO:0009966 ! regulation of signal transduction intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0035556 ! intracellular signal transduction relationship: regulates GO:0035556 ! intracellular signal transduction -created_by: bf creation_date: 2013-12-02T11:32:52Z [Term] id: GO:1902532 name: negative regulation of intracellular signal transduction namespace: biological_process -alt_id: GO:0010741 def: "Any process that stops, prevents or reduces the frequency, rate or extent of intracellular signal transduction." [GOC:dph, GOC:signaling, GOC:tb, GOC:TermGenie] synonym: "down regulation of intracellular signal transduction" EXACT [GOC:TermGenie] synonym: "down regulation of intracellular signal transduction pathway" NARROW [GOC:TermGenie] @@ -126453,14 +130071,12 @@ is_a: GO:1902531 ! regulation of intracellular signal transduction intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0035556 ! intracellular signal transduction relationship: negatively_regulates GO:0035556 ! intracellular signal transduction -created_by: bf creation_date: 2013-12-02T11:33:01Z [Term] id: GO:1902533 name: positive regulation of intracellular signal transduction namespace: biological_process -alt_id: GO:0010740 def: "Any process that activates or increases the frequency, rate or extent of intracellular signal transduction." [GOC:BHF, GOC:dph, GOC:signaling, GOC:tb, GOC:TermGenie] synonym: "activation of intracellular signal transduction" NARROW [GOC:TermGenie] synonym: "activation of intracellular signal transduction pathway" NARROW [GOC:TermGenie] @@ -126502,7 +130118,6 @@ is_a: GO:1902531 ! regulation of intracellular signal transduction intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0035556 ! intracellular signal transduction relationship: positively_regulates GO:0035556 ! intracellular signal transduction -created_by: bf creation_date: 2013-12-02T11:33:10Z [Term] @@ -126514,7 +130129,6 @@ is_a: GO:0002694 ! regulation of leukocyte activation intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0042119 ! neutrophil activation relationship: regulates GO:0042119 ! neutrophil activation -created_by: ecu creation_date: 2013-12-10T15:33:08Z [Term] @@ -126531,7 +130145,6 @@ is_a: GO:1902563 ! regulation of neutrophil activation intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0042119 ! neutrophil activation relationship: negatively_regulates GO:0042119 ! neutrophil activation -created_by: ecu creation_date: 2013-12-10T15:33:16Z [Term] @@ -126548,7 +130161,6 @@ is_a: GO:1902563 ! regulation of neutrophil activation intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0042119 ! neutrophil activation relationship: positively_regulates GO:0042119 ! neutrophil activation -created_by: ecu creation_date: 2013-12-10T15:33:26Z [Term] @@ -126560,7 +130172,6 @@ is_a: GO:0002694 ! regulation of leukocyte activation intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0043307 ! eosinophil activation relationship: regulates GO:0043307 ! eosinophil activation -created_by: ecu creation_date: 2013-12-10T15:54:35Z [Term] @@ -126577,7 +130188,6 @@ is_a: GO:1902566 ! regulation of eosinophil activation intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0043307 ! eosinophil activation relationship: negatively_regulates GO:0043307 ! eosinophil activation -created_by: ecu creation_date: 2013-12-10T15:54:43Z [Term] @@ -126594,7 +130204,6 @@ is_a: GO:1902566 ! regulation of eosinophil activation intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0043307 ! eosinophil activation relationship: positively_regulates GO:0043307 ! eosinophil activation -created_by: ecu creation_date: 2013-12-10T15:54:52Z [Term] @@ -126609,7 +130218,6 @@ is_a: GO:0034504 ! protein localization to nucleus intersection_of: GO:0008104 ! protein localization intersection_of: has_target_end_location GO:0005730 ! nucleolus relationship: has_target_end_location GO:0005730 ! nucleolus -created_by: mah creation_date: 2013-12-10T16:25:28Z [Term] @@ -126646,16 +130254,12 @@ is_a: GO:2000070 ! regulation of response to water deprivation intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0009414 ! response to water deprivation relationship: positively_regulates GO:0009414 ! response to water deprivation -created_by: tb creation_date: 2013-12-19T00:31:58Z [Term] id: GO:1902600 name: proton transmembrane transport namespace: biological_process -alt_id: GO:0006818 -alt_id: GO:0015991 -alt_id: GO:0015992 def: "The directed movement of a proton across a membrane." [GO_REF:0000069, GOC:pr, GOC:TermGenie] subset: goslim_pir synonym: "ATP hydrolysis coupled proton transport" NARROW [] @@ -126670,7 +130274,6 @@ intersection_of: GO:0006810 ! transport intersection_of: has_primary_input CHEBI:15378 intersection_of: results_in_transport_across GO:0016020 ! membrane relationship: has_primary_input CHEBI:15378 -created_by: pr creation_date: 2013-12-20T11:08:37Z [Term] @@ -126682,7 +130285,6 @@ is_a: GO:0002685 ! regulation of leukocyte migration intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:1990266 ! neutrophil migration relationship: regulates GO:1990266 ! neutrophil migration -created_by: sl creation_date: 2014-01-15T18:58:39Z [Term] @@ -126699,7 +130301,6 @@ is_a: GO:1902622 ! regulation of neutrophil migration intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:1990266 ! neutrophil migration relationship: negatively_regulates GO:1990266 ! neutrophil migration -created_by: sl creation_date: 2014-01-15T18:58:49Z [Term] @@ -126716,7 +130317,6 @@ is_a: GO:1902622 ! regulation of neutrophil migration intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:1990266 ! neutrophil migration relationship: positively_regulates GO:1990266 ! neutrophil migration -created_by: sl creation_date: 2014-01-15T18:58:58Z [Term] @@ -126728,7 +130328,6 @@ is_a: GO:0014033 ! neural crest cell differentiation intersection_of: GO:0014033 ! neural crest cell differentiation intersection_of: part_of GO:0048538 ! thymus development relationship: part_of GO:0048538 ! thymus development -created_by: pr creation_date: 2014-01-21T10:03:20Z [Term] @@ -126740,7 +130339,6 @@ is_a: GO:0014033 ! neural crest cell differentiation intersection_of: GO:0014033 ! neural crest cell differentiation intersection_of: part_of GO:0060017 ! parathyroid gland development relationship: part_of GO:0060017 ! parathyroid gland development -created_by: pr creation_date: 2014-01-21T10:03:29Z [Term] @@ -126751,7 +130349,6 @@ def: "The directed movement of calcium ion into a cytosol." [GO_REF:0000075, GOC synonym: "calcium import into cytosol" BROAD [] is_a: GO:0006816 ! calcium ion transport relationship: has_target_end_location GO:0005829 ! cytosol -created_by: pr creation_date: 2014-01-22T13:41:11Z [Term] @@ -126789,7 +130386,6 @@ is_a: GO:2001141 ! regulation of RNA biosynthetic process intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0032774 ! RNA biosynthetic process relationship: negatively_regulates GO:0032774 ! RNA biosynthetic process -created_by: jl creation_date: 2014-02-05T16:32:01Z [Term] @@ -126827,7 +130423,6 @@ is_a: GO:2001141 ! regulation of RNA biosynthetic process intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0032774 ! RNA biosynthetic process relationship: positively_regulates GO:0032774 ! RNA biosynthetic process -created_by: jl creation_date: 2014-02-05T16:32:10Z [Term] @@ -126840,7 +130435,6 @@ is_a: GO:0032879 ! regulation of localization intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0097120 ! receptor localization to synapse relationship: regulates GO:0097120 ! receptor localization to synapse -created_by: kmv creation_date: 2014-02-07T17:38:31Z [Term] @@ -126862,7 +130456,6 @@ is_a: GO:1902683 ! regulation of receptor localization to synapse intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0097120 ! receptor localization to synapse relationship: negatively_regulates GO:0097120 ! receptor localization to synapse -created_by: kmv creation_date: 2014-02-07T17:38:41Z [Term] @@ -126884,7 +130477,6 @@ is_a: GO:1902683 ! regulation of receptor localization to synapse intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0097120 ! receptor localization to synapse relationship: positively_regulates GO:0097120 ! receptor localization to synapse -created_by: kmv creation_date: 2014-02-07T17:38:51Z [Term] @@ -126898,7 +130490,6 @@ is_a: GO:0048863 ! stem cell differentiation intersection_of: GO:0030154 ! cell differentiation intersection_of: results_in_acquisition_of_features_of CL:0002633 ! respiratory basal cell relationship: results_in_acquisition_of_features_of CL:0002633 ! respiratory basal cell -created_by: cjm creation_date: 2014-02-13T23:41:24Z [Term] @@ -126910,7 +130501,6 @@ is_a: GO:2000177 ! regulation of neural precursor cell proliferation intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0007405 ! neuroblast proliferation relationship: regulates GO:0007405 ! neuroblast proliferation -created_by: rl creation_date: 2014-02-18T10:03:31Z [Term] @@ -126923,7 +130513,6 @@ is_a: GO:0043235 ! receptor complex intersection_of: GO:0032991 ! protein-containing complex intersection_of: capable_of GO:0016917 ! GABA receptor activity relationship: capable_of GO:0016917 ! GABA receptor activity -created_by: bhm creation_date: 2014-02-20T16:07:48Z [Term] @@ -126940,7 +130529,6 @@ is_a: GO:0090278 ! negative regulation of peptide hormone secretion intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0070459 ! prolactin secretion relationship: negatively_regulates GO:0070459 ! prolactin secretion -created_by: mr creation_date: 2014-02-24T16:09:28Z [Term] @@ -126957,7 +130545,6 @@ is_a: GO:0090277 ! positive regulation of peptide hormone secretion intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0070459 ! prolactin secretion relationship: positively_regulates GO:0070459 ! prolactin secretion -created_by: mr creation_date: 2014-02-24T16:09:37Z [Term] @@ -126974,7 +130561,6 @@ is_a: GO:0014859 ! negative regulation of skeletal muscle cell proliferation intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0014841 ! skeletal muscle satellite cell proliferation relationship: negatively_regulates GO:0014841 ! skeletal muscle satellite cell proliferation -created_by: mr creation_date: 2014-02-24T16:09:46Z [Term] @@ -126991,7 +130577,6 @@ is_a: GO:0014858 ! positive regulation of skeletal muscle cell proliferation intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0014841 ! skeletal muscle satellite cell proliferation relationship: positively_regulates GO:0014841 ! skeletal muscle satellite cell proliferation -created_by: mr creation_date: 2014-02-24T16:09:56Z [Term] @@ -127007,7 +130592,6 @@ is_a: GO:2001015 ! negative regulation of skeletal muscle cell differentiation intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0014816 ! skeletal muscle satellite cell differentiation relationship: negatively_regulates GO:0014816 ! skeletal muscle satellite cell differentiation -created_by: mr creation_date: 2014-02-24T16:10:05Z [Term] @@ -127023,7 +130607,6 @@ is_a: GO:2001016 ! positive regulation of skeletal muscle cell differentiation intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0014816 ! skeletal muscle satellite cell differentiation relationship: positively_regulates GO:0014816 ! skeletal muscle satellite cell differentiation -created_by: mr creation_date: 2014-02-24T16:10:14Z [Term] @@ -127059,7 +130642,6 @@ is_a: GO:0009890 ! negative regulation of biosynthetic process intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0030166 ! proteoglycan biosynthetic process relationship: negatively_regulates GO:0030166 ! proteoglycan biosynthetic process -created_by: mr creation_date: 2014-02-24T16:10:43Z [Term] @@ -127095,7 +130677,6 @@ is_a: GO:0009891 ! positive regulation of biosynthetic process intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0030166 ! proteoglycan biosynthetic process relationship: positively_regulates GO:0030166 ! proteoglycan biosynthetic process -created_by: mr creation_date: 2014-02-24T16:10:52Z [Term] @@ -127107,7 +130688,6 @@ is_a: GO:1902738 ! regulation of chondrocyte differentiation involved in endocho intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0003418 ! growth plate cartilage chondrocyte differentiation relationship: regulates GO:0003418 ! growth plate cartilage chondrocyte differentiation -created_by: mr creation_date: 2014-02-24T16:11:28Z [Term] @@ -127121,7 +130701,6 @@ is_a: GO:2000027 ! regulation of animal organ morphogenesis intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0003413 ! chondrocyte differentiation involved in endochondral bone morphogenesis relationship: regulates GO:0003413 ! chondrocyte differentiation involved in endochondral bone morphogenesis -created_by: mr creation_date: 2014-02-26T15:36:15Z [Term] @@ -127161,7 +130740,6 @@ is_a: GO:0006915 ! apoptotic process intersection_of: GO:0006915 ! apoptotic process intersection_of: part_of GO:0048856 ! anatomical structure development relationship: part_of GO:0048856 ! anatomical structure development -created_by: pr creation_date: 2014-02-28T13:09:43Z [Term] @@ -127174,7 +130752,6 @@ is_a: GO:0030856 ! regulation of epithelial cell differentiation intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0070306 ! lens fiber cell differentiation relationship: regulates GO:0070306 ! lens fiber cell differentiation -created_by: mr creation_date: 2014-03-03T23:18:50Z [Term] @@ -127197,7 +130774,6 @@ is_a: GO:1902746 ! regulation of lens fiber cell differentiation intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0070306 ! lens fiber cell differentiation relationship: negatively_regulates GO:0070306 ! lens fiber cell differentiation -created_by: mr creation_date: 2014-03-03T23:19:32Z [Term] @@ -127220,7 +130796,6 @@ is_a: GO:1902746 ! regulation of lens fiber cell differentiation intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0070306 ! lens fiber cell differentiation relationship: positively_regulates GO:0070306 ! lens fiber cell differentiation -created_by: mr creation_date: 2014-03-03T23:20:12Z [Term] @@ -127238,7 +130813,6 @@ is_a: GO:0061181 ! regulation of chondrocyte development intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0002063 ! chondrocyte development relationship: positively_regulates GO:0002063 ! chondrocyte development -created_by: mr creation_date: 2014-03-07T17:45:55Z [Term] @@ -127251,7 +130825,6 @@ is_a: GO:0016477 ! cell migration intersection_of: GO:0016477 ! cell migration intersection_of: results_in_movement_of CL:0000594 ! skeletal muscle satellite cell relationship: results_in_movement_of CL:0000594 ! skeletal muscle satellite cell -created_by: mr creation_date: 2014-03-10T15:20:28Z [Term] @@ -127264,7 +130837,6 @@ is_a: GO:2001014 ! regulation of skeletal muscle cell differentiation intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0098528 ! skeletal muscle fiber differentiation relationship: regulates GO:0098528 ! skeletal muscle fiber differentiation -created_by: mr creation_date: 2014-03-26T21:18:26Z [Term] @@ -127282,7 +130854,6 @@ is_a: GO:2001015 ! negative regulation of skeletal muscle cell differentiation intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0098528 ! skeletal muscle fiber differentiation relationship: negatively_regulates GO:0098528 ! skeletal muscle fiber differentiation -created_by: mr creation_date: 2014-03-26T21:18:32Z [Term] @@ -127300,7 +130871,6 @@ is_a: GO:2001016 ! positive regulation of skeletal muscle cell differentiation intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0098528 ! skeletal muscle fiber differentiation relationship: positively_regulates GO:0098528 ! skeletal muscle fiber differentiation -created_by: mr creation_date: 2014-03-26T21:18:38Z [Term] @@ -127313,7 +130883,6 @@ is_a: GO:0032880 ! regulation of protein localization intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0035372 ! protein localization to microtubule relationship: regulates GO:0035372 ! protein localization to microtubule -created_by: tb creation_date: 2014-03-27T22:07:12Z [Term] @@ -127335,7 +130904,6 @@ is_a: GO:1903828 ! negative regulation of protein localization intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0035372 ! protein localization to microtubule relationship: negatively_regulates GO:0035372 ! protein localization to microtubule -created_by: tb creation_date: 2014-03-27T22:07:18Z [Term] @@ -127352,7 +130920,6 @@ is_a: GO:2000178 ! negative regulation of neural precursor cell proliferation intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0010456 ! cell proliferation in dorsal spinal cord relationship: negatively_regulates GO:0010456 ! cell proliferation in dorsal spinal cord -created_by: mr creation_date: 2014-03-31T17:42:50Z [Term] @@ -127369,7 +130936,6 @@ is_a: GO:2000179 ! positive regulation of neural precursor cell proliferation intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0010456 ! cell proliferation in dorsal spinal cord relationship: positively_regulates GO:0010456 ! cell proliferation in dorsal spinal cord -created_by: mr creation_date: 2014-03-31T17:43:33Z [Term] @@ -127391,7 +130957,6 @@ is_a: GO:1902513 ! regulation of organelle transport along microtubule intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0030473 ! nuclear migration along microtubule relationship: regulates GO:0030473 ! nuclear migration along microtubule -created_by: vw creation_date: 2014-04-01T13:50:23Z [Term] @@ -127448,7 +131013,6 @@ is_a: GO:1902838 ! regulation of nuclear migration along microtubule intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0030473 ! nuclear migration along microtubule relationship: negatively_regulates GO:0030473 ! nuclear migration along microtubule -created_by: vw creation_date: 2014-04-01T13:50:29Z [Term] @@ -127505,7 +131069,6 @@ is_a: GO:1902838 ! regulation of nuclear migration along microtubule intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0030473 ! nuclear migration along microtubule relationship: positively_regulates GO:0030473 ! nuclear migration along microtubule -created_by: vw creation_date: 2014-04-01T13:50:35Z [Term] @@ -127520,7 +131083,6 @@ is_a: GO:0000226 ! microtubule cytoskeleton organization is_a: GO:1903047 ! mitotic cell cycle process intersection_of: GO:0000226 ! microtubule cytoskeleton organization intersection_of: part_of GO:0000278 ! mitotic cell cycle -created_by: vw creation_date: 2014-04-02T14:19:38Z [Term] @@ -127533,7 +131095,6 @@ is_a: GO:0050793 ! regulation of developmental process intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0031076 ! embryonic camera-type eye development relationship: regulates GO:0031076 ! embryonic camera-type eye development -created_by: mr creation_date: 2014-04-03T15:24:00Z [Term] @@ -127555,7 +131116,6 @@ is_a: GO:1902863 ! regulation of embryonic camera-type eye development intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0031076 ! embryonic camera-type eye development relationship: negatively_regulates GO:0031076 ! embryonic camera-type eye development -created_by: mr creation_date: 2014-04-03T15:24:06Z [Term] @@ -127577,7 +131137,6 @@ is_a: GO:1902863 ! regulation of embryonic camera-type eye development intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0031076 ! embryonic camera-type eye development relationship: positively_regulates GO:0031076 ! embryonic camera-type eye development -created_by: mr creation_date: 2014-04-03T15:24:12Z [Term] @@ -127591,7 +131150,6 @@ is_a: GO:0050793 ! regulation of developmental process intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0060041 ! retina development in camera-type eye relationship: regulates GO:0060041 ! retina development in camera-type eye -created_by: mr creation_date: 2014-04-03T15:24:17Z [Term] @@ -127619,7 +131177,6 @@ is_a: GO:1902866 ! regulation of retina development in camera-type eye intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0060041 ! retina development in camera-type eye relationship: negatively_regulates GO:0060041 ! retina development in camera-type eye -created_by: mr creation_date: 2014-04-03T15:24:23Z [Term] @@ -127647,7 +131204,6 @@ is_a: GO:1902866 ! regulation of retina development in camera-type eye intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0060041 ! retina development in camera-type eye relationship: positively_regulates GO:0060041 ! retina development in camera-type eye -created_by: mr creation_date: 2014-04-03T15:24:29Z [Term] @@ -127660,7 +131216,6 @@ is_a: GO:0045664 ! regulation of neuron differentiation intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0035881 ! amacrine cell differentiation relationship: regulates GO:0035881 ! amacrine cell differentiation -created_by: mr creation_date: 2014-04-03T15:24:35Z [Term] @@ -127682,7 +131237,6 @@ is_a: GO:1902869 ! regulation of amacrine cell differentiation intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0035881 ! amacrine cell differentiation relationship: negatively_regulates GO:0035881 ! amacrine cell differentiation -created_by: mr creation_date: 2014-04-03T15:24:40Z [Term] @@ -127704,7 +131258,6 @@ is_a: GO:1902869 ! regulation of amacrine cell differentiation intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0035881 ! amacrine cell differentiation relationship: positively_regulates GO:0035881 ! amacrine cell differentiation -created_by: mr creation_date: 2014-04-03T15:24:46Z [Term] @@ -127719,7 +131272,6 @@ is_a: GO:0051239 ! regulation of multicellular organismal process intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0009880 ! embryonic pattern specification relationship: regulates GO:0009880 ! embryonic pattern specification -created_by: mr creation_date: 2014-04-03T15:25:15Z [Term] @@ -127741,7 +131293,6 @@ is_a: GO:1902875 ! regulation of embryonic pattern specification intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0009880 ! embryonic pattern specification relationship: negatively_regulates GO:0009880 ! embryonic pattern specification -created_by: mr creation_date: 2014-04-03T15:25:20Z [Term] @@ -127763,7 +131314,6 @@ is_a: GO:1902875 ! regulation of embryonic pattern specification intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0009880 ! embryonic pattern specification relationship: positively_regulates GO:0009880 ! embryonic pattern specification -created_by: mr creation_date: 2014-04-03T15:25:26Z [Term] @@ -127777,7 +131327,6 @@ is_a: GO:0051128 ! regulation of cellular component organization intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0097435 ! supramolecular fiber organization relationship: regulates GO:0097435 ! supramolecular fiber organization -created_by: rl creation_date: 2014-04-15T16:46:36Z [Term] @@ -127800,7 +131349,6 @@ is_a: GO:1902903 ! regulation of supramolecular fiber organization intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0097435 ! supramolecular fiber organization relationship: negatively_regulates GO:0097435 ! supramolecular fiber organization -created_by: rl creation_date: 2014-04-15T16:46:42Z [Term] @@ -127823,7 +131371,6 @@ is_a: GO:1902903 ! regulation of supramolecular fiber organization intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0097435 ! supramolecular fiber organization relationship: positively_regulates GO:0097435 ! supramolecular fiber organization -created_by: rl creation_date: 2014-04-15T16:46:48Z [Term] @@ -127836,7 +131383,6 @@ is_a: GO:0051049 ! regulation of transport intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0032402 ! melanosome transport relationship: regulates GO:0032402 ! melanosome transport -created_by: als creation_date: 2014-04-17T11:40:16Z [Term] @@ -127854,7 +131400,6 @@ is_a: GO:1902908 ! regulation of melanosome transport intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0032402 ! melanosome transport relationship: negatively_regulates GO:0032402 ! melanosome transport -created_by: als creation_date: 2014-04-17T11:40:28Z [Term] @@ -127872,7 +131417,6 @@ is_a: GO:1902908 ! regulation of melanosome transport intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0032402 ! melanosome transport relationship: positively_regulates GO:0032402 ! melanosome transport -created_by: als creation_date: 2014-04-17T11:40:34Z [Term] @@ -127885,7 +131429,6 @@ is_a: GO:0061695 ! transferase complex, transferring phosphorus-containing group intersection_of: GO:0032991 ! protein-containing complex intersection_of: capable_of GO:0004672 ! protein kinase activity relationship: capable_of GO:0004672 ! protein kinase activity -created_by: bhm creation_date: 2014-04-17T13:52:40Z [Term] @@ -127901,7 +131444,6 @@ is_a: GO:0030858 ! positive regulation of epithelial cell differentiation intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0060563 ! neuroepithelial cell differentiation relationship: positively_regulates GO:0060563 ! neuroepithelial cell differentiation -created_by: mr creation_date: 2014-04-18T21:06:42Z [Term] @@ -127917,7 +131459,6 @@ intersection_of: regulates GO:1990379 ! lipid transport across blood-brain barri relationship: regulates GO:1990379 ! lipid transport across blood-brain barrier relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa relationship: RO:0002162 NCBITaxon:6072 {all_only="true"} ! in taxon Eumetazoa -created_by: sjp creation_date: 2014-05-09T09:30:04Z [Term] @@ -127936,7 +131477,6 @@ is_a: GO:1903000 ! regulation of lipid transport across blood-brain barrier intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:1990379 ! lipid transport across blood-brain barrier relationship: negatively_regulates GO:1990379 ! lipid transport across blood-brain barrier -created_by: sjp creation_date: 2014-05-09T09:30:10Z [Term] @@ -127955,7 +131495,6 @@ is_a: GO:1903000 ! regulation of lipid transport across blood-brain barrier intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:1990379 ! lipid transport across blood-brain barrier relationship: positively_regulates GO:1990379 ! lipid transport across blood-brain barrier -created_by: sjp creation_date: 2014-05-09T09:30:16Z [Term] @@ -127969,7 +131508,6 @@ is_a: GO:0022411 ! cellular component disassembly intersection_of: GO:0022411 ! cellular component disassembly intersection_of: results_in_disassembly_of GO:0043226 ! organelle relationship: results_in_disassembly_of GO:0043226 ! organelle -created_by: jl creation_date: 2014-05-13T12:36:03Z [Term] @@ -127981,7 +131519,6 @@ is_a: GO:2000026 ! regulation of multicellular organismal development intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0060348 ! bone development relationship: regulates GO:0060348 ! bone development -created_by: mr creation_date: 2014-05-13T22:41:53Z [Term] @@ -127999,7 +131536,6 @@ is_a: GO:1903010 ! regulation of bone development intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0060348 ! bone development relationship: negatively_regulates GO:0060348 ! bone development -created_by: mr creation_date: 2014-05-13T22:42:00Z [Term] @@ -128017,7 +131553,6 @@ is_a: GO:1903010 ! regulation of bone development intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0060348 ! bone development relationship: positively_regulates GO:0060348 ! bone development -created_by: mr creation_date: 2014-05-13T22:42:06Z [Term] @@ -128031,7 +131566,6 @@ is_a: GO:0019222 ! regulation of metabolic process intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0009100 ! glycoprotein metabolic process relationship: regulates GO:0009100 ! glycoprotein metabolic process -created_by: rl creation_date: 2014-05-14T18:44:19Z [Term] @@ -128054,7 +131588,6 @@ is_a: GO:1903018 ! regulation of glycoprotein metabolic process intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0009100 ! glycoprotein metabolic process relationship: negatively_regulates GO:0009100 ! glycoprotein metabolic process -created_by: rl creation_date: 2014-05-14T18:44:25Z [Term] @@ -128077,40 +131610,8 @@ is_a: GO:1903018 ! regulation of glycoprotein metabolic process intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0009100 ! glycoprotein metabolic process relationship: positively_regulates GO:0009100 ! glycoprotein metabolic process -created_by: rl creation_date: 2014-05-14T18:44:31Z -[Term] -id: GO:1903025 -name: regulation of RNA polymerase II regulatory region sequence-specific DNA binding -namespace: biological_process -def: "Any process that modulates the frequency, rate or extent of RNA polymerase II regulatory region sequence-specific DNA binding." [GO_REF:0000059, GOC:dph, GOC:krc, GOC:TermGenie, PMID:20026326] -subset: gocheck_do_not_annotate -is_a: GO:2000677 ! regulation of transcription regulatory region DNA binding -intersection_of: GO:0065007 ! biological regulation -intersection_of: regulates GO:0000977 ! RNA polymerase II transcription regulatory region sequence-specific DNA binding -relationship: regulates GO:0000977 ! RNA polymerase II transcription regulatory region sequence-specific DNA binding -created_by: dph -creation_date: 2014-05-15T17:55:54Z - -[Term] -id: GO:1903026 -name: negative regulation of RNA polymerase II regulatory region sequence-specific DNA binding -namespace: biological_process -def: "Any process that stops, prevents or reduces the frequency, rate or extent of RNA polymerase II regulatory region sequence-specific DNA binding." [GO_REF:0000059, GOC:dph, GOC:krc, GOC:TermGenie, PMID:20026326] -subset: gocheck_do_not_annotate -synonym: "down regulation of RNA polymerase II regulatory region sequence-specific DNA binding" EXACT [GOC:TermGenie] -synonym: "down-regulation of RNA polymerase II regulatory region sequence-specific DNA binding" EXACT [GOC:TermGenie] -synonym: "downregulation of RNA polymerase II regulatory region sequence-specific DNA binding" EXACT [GOC:TermGenie] -synonym: "inhibition of RNA polymerase II regulatory region sequence-specific DNA binding" NARROW [GOC:TermGenie] -is_a: GO:1903025 ! regulation of RNA polymerase II regulatory region sequence-specific DNA binding -is_a: GO:2000678 ! negative regulation of transcription regulatory region DNA binding -intersection_of: GO:0065007 ! biological regulation -intersection_of: negatively_regulates GO:0000977 ! RNA polymerase II transcription regulatory region sequence-specific DNA binding -relationship: negatively_regulates GO:0000977 ! RNA polymerase II transcription regulatory region sequence-specific DNA binding -created_by: dph -creation_date: 2014-05-15T17:56:00Z - [Term] id: GO:1903034 name: regulation of response to wounding @@ -128121,7 +131622,6 @@ is_a: GO:0080134 ! regulation of response to stress intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0009611 ! response to wounding relationship: regulates GO:0009611 ! response to wounding -created_by: kmv creation_date: 2014-05-18T01:28:46Z [Term] @@ -128143,7 +131643,6 @@ is_a: GO:1903034 ! regulation of response to wounding intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0009611 ! response to wounding relationship: negatively_regulates GO:0009611 ! response to wounding -created_by: kmv creation_date: 2014-05-18T01:28:52Z [Term] @@ -128165,7 +131664,6 @@ is_a: GO:1903034 ! regulation of response to wounding intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0009611 ! response to wounding relationship: positively_regulates GO:0009611 ! response to wounding -created_by: kmv creation_date: 2014-05-18T01:28:58Z [Term] @@ -128180,7 +131678,6 @@ is_a: GO:0022407 ! regulation of cell-cell adhesion intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0007159 ! leukocyte cell-cell adhesion relationship: regulates GO:0007159 ! leukocyte cell-cell adhesion -created_by: rl creation_date: 2014-05-19T15:29:58Z [Term] @@ -128208,7 +131705,6 @@ is_a: GO:1903037 ! regulation of leukocyte cell-cell adhesion intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0007159 ! leukocyte cell-cell adhesion relationship: negatively_regulates GO:0007159 ! leukocyte cell-cell adhesion -created_by: rl creation_date: 2014-05-19T15:30:05Z [Term] @@ -128236,7 +131732,6 @@ is_a: GO:1903037 ! regulation of leukocyte cell-cell adhesion intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0007159 ! leukocyte cell-cell adhesion relationship: positively_regulates GO:0007159 ! leukocyte cell-cell adhesion -created_by: rl creation_date: 2014-05-19T15:30:15Z [Term] @@ -128250,7 +131745,6 @@ is_a: GO:0061181 ! regulation of chondrocyte development intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0003415 ! chondrocyte hypertrophy relationship: regulates GO:0003415 ! chondrocyte hypertrophy -created_by: mr creation_date: 2014-05-20T21:23:13Z [Term] @@ -128269,7 +131763,6 @@ is_a: GO:1903041 ! regulation of chondrocyte hypertrophy intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0003415 ! chondrocyte hypertrophy relationship: negatively_regulates GO:0003415 ! chondrocyte hypertrophy -created_by: mr creation_date: 2014-05-20T21:23:19Z [Term] @@ -128288,7 +131781,6 @@ is_a: GO:1903041 ! regulation of chondrocyte hypertrophy intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0003415 ! chondrocyte hypertrophy relationship: positively_regulates GO:0003415 ! chondrocyte hypertrophy -created_by: mr creation_date: 2014-05-20T21:23:25Z [Term] @@ -128301,7 +131793,6 @@ is_a: GO:1901166 ! neural crest cell migration involved in autonomic nervous sys intersection_of: GO:0001755 ! neural crest cell migration intersection_of: part_of GO:0048485 ! sympathetic nervous system development relationship: part_of GO:0048485 ! sympathetic nervous system development -created_by: rl creation_date: 2014-05-22T07:06:02Z [Term] @@ -128317,7 +131808,6 @@ intersection_of: GO:0009987 ! cellular process intersection_of: part_of GO:0051321 ! meiotic cell cycle disjoint_from: GO:1903047 ! mitotic cell cycle process relationship: part_of GO:0051321 ! meiotic cell cycle -created_by: jl creation_date: 2014-05-22T14:22:28Z [Term] @@ -128330,7 +131820,6 @@ is_a: GO:0022402 ! cell cycle process intersection_of: GO:0009987 ! cellular process intersection_of: part_of GO:0000278 ! mitotic cell cycle relationship: part_of GO:0000278 ! mitotic cell cycle -created_by: jl creation_date: 2014-05-22T14:22:34Z [Term] @@ -128346,7 +131835,6 @@ is_a: GO:2001257 ! regulation of cation channel activity intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0022848 ! acetylcholine-gated monoatomic cation-selective channel activity relationship: regulates GO:0022848 ! acetylcholine-gated monoatomic cation-selective channel activity -created_by: bf creation_date: 2014-05-22T14:46:53Z [Term] @@ -128367,7 +131855,6 @@ intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0051603 ! proteolysis involved in protein catabolic process relationship: regulates GO:0051603 ! proteolysis involved in protein catabolic process property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/23112" xsd:anyURI -created_by: rl creation_date: 2014-05-22T18:00:45Z [Term] @@ -128417,7 +131904,6 @@ intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0051603 ! proteolysis involved in protein catabolic process relationship: negatively_regulates GO:0051603 ! proteolysis involved in protein catabolic process property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/23112" xsd:anyURI -created_by: rl creation_date: 2014-05-22T18:00:51Z [Term] @@ -128467,7 +131953,6 @@ intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0051603 ! proteolysis involved in protein catabolic process relationship: positively_regulates GO:0051603 ! proteolysis involved in protein catabolic process property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/23112" xsd:anyURI -created_by: rl creation_date: 2014-05-22T18:00:57Z [Term] @@ -128481,7 +131966,6 @@ is_a: GO:0051128 ! regulation of cellular component organization intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0030198 ! extracellular matrix organization relationship: regulates GO:0030198 ! extracellular matrix organization -created_by: rl creation_date: 2014-05-23T17:15:41Z [Term] @@ -128508,7 +131992,6 @@ is_a: GO:1903053 ! regulation of extracellular matrix organization intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0030198 ! extracellular matrix organization relationship: negatively_regulates GO:0030198 ! extracellular matrix organization -created_by: rl creation_date: 2014-05-23T17:15:47Z [Term] @@ -128535,7 +132018,6 @@ is_a: GO:1903053 ! regulation of extracellular matrix organization intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0030198 ! extracellular matrix organization relationship: positively_regulates GO:0030198 ! extracellular matrix organization -created_by: rl creation_date: 2014-05-23T17:15:53Z [Term] @@ -128550,7 +132032,6 @@ is_a: GO:0033043 ! regulation of organelle organization intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0032438 ! melanosome organization relationship: regulates GO:0032438 ! melanosome organization -created_by: rl creation_date: 2014-05-27T13:27:49Z [Term] @@ -128578,7 +132059,6 @@ is_a: GO:1903056 ! regulation of melanosome organization intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0032438 ! melanosome organization relationship: negatively_regulates GO:0032438 ! melanosome organization -created_by: rl creation_date: 2014-05-27T13:27:55Z [Term] @@ -128606,15 +132086,12 @@ is_a: GO:1903056 ! regulation of melanosome organization intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0032438 ! melanosome organization relationship: positively_regulates GO:0032438 ! melanosome organization -created_by: rl creation_date: 2014-05-27T13:28:01Z [Term] id: GO:1903076 name: regulation of protein localization to plasma membrane namespace: biological_process -alt_id: GO:0090003 -alt_id: GO:1905963 def: "Any process that modulates the frequency, rate or extent of protein localization to plasma membrane." [GO_REF:0000058, GOC:BHF, GOC:rl, GOC:TermGenie, PMID:11602640] synonym: "regulation of establishment of protein localisation in plasma membrane" RELATED [GOC:mah] synonym: "regulation of establishment of protein localization in plasma membrane" RELATED [] @@ -128628,15 +132105,12 @@ is_a: GO:1905475 ! regulation of protein localization to membrane intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0072659 ! protein localization to plasma membrane relationship: regulates GO:0072659 ! protein localization to plasma membrane -created_by: tb creation_date: 2009-07-10T10:32:44Z [Term] id: GO:1903077 name: negative regulation of protein localization to plasma membrane namespace: biological_process -alt_id: GO:0090005 -alt_id: GO:1905964 def: "Any process that stops, prevents or reduces the frequency, rate or extent of protein localization to plasma membrane." [GO_REF:0000058, GOC:BHF, GOC:rl, GOC:TermGenie, PMID:11602640] synonym: "down regulation of protein localisation in plasma membrane" EXACT [GOC:TermGenie] synonym: "down regulation of protein localization in plasma membrane" EXACT [GOC:TermGenie] @@ -128671,15 +132145,12 @@ is_a: GO:1905476 ! negative regulation of protein localization to membrane intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0072659 ! protein localization to plasma membrane relationship: negatively_regulates GO:0072659 ! protein localization to plasma membrane -created_by: tb creation_date: 2014-05-29T17:10:16Z [Term] id: GO:1903078 name: positive regulation of protein localization to plasma membrane namespace: biological_process -alt_id: GO:0090004 -alt_id: GO:1905965 def: "Any process that activates or increases the frequency, rate or extent of protein localization to plasma membrane." [GO_REF:0000058, GOC:BHF, GOC:rl, GOC:TermGenie, PMID:11602640] synonym: "activation of protein localisation in plasma membrane" NARROW [GOC:TermGenie] synonym: "activation of protein localization in plasma membrane" NARROW [GOC:TermGenie] @@ -128713,7 +132184,6 @@ is_a: GO:1905477 ! positive regulation of protein localization to membrane intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0072659 ! protein localization to plasma membrane relationship: positively_regulates GO:0072659 ! protein localization to plasma membrane -created_by: tb creation_date: 2009-07-10T10:34:17Z [Term] @@ -128725,7 +132195,6 @@ is_a: GO:0032970 ! regulation of actin filament-based process intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0030048 ! actin filament-based movement relationship: regulates GO:0030048 ! actin filament-based movement -created_by: al creation_date: 2014-06-12T16:55:57Z [Term] @@ -128742,7 +132211,6 @@ is_a: GO:1903115 ! regulation of actin filament-based movement intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0030048 ! actin filament-based movement relationship: positively_regulates GO:0030048 ! actin filament-based movement -created_by: al creation_date: 2014-06-12T16:56:04Z [Term] @@ -128757,7 +132225,6 @@ is_a: GO:0044380 ! protein localization to cytoskeleton intersection_of: GO:0008104 ! protein localization intersection_of: has_target_end_location GO:0015629 ! actin cytoskeleton relationship: has_target_end_location GO:0015629 ! actin cytoskeleton -created_by: mah creation_date: 2014-06-16T11:27:09Z [Term] @@ -128773,7 +132240,6 @@ is_a: GO:1903119 ! protein localization to actin cytoskeleton intersection_of: GO:0008104 ! protein localization intersection_of: has_target_end_location GO:0032432 ! actin filament bundle relationship: has_target_end_location GO:0032432 ! actin filament bundle -created_by: mah creation_date: 2014-06-16T11:27:16Z [Term] @@ -128785,7 +132251,6 @@ is_a: GO:0002521 ! leukocyte differentiation intersection_of: GO:0030154 ! cell differentiation intersection_of: results_in_acquisition_of_features_of CL:0000842 ! mononuclear cell relationship: results_in_acquisition_of_features_of CL:0000842 ! mononuclear cell -created_by: cls creation_date: 2014-06-25T15:47:09Z [Term] @@ -128801,7 +132266,6 @@ is_a: GO:0051924 ! regulation of calcium ion transport intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0070588 ! calcium ion transmembrane transport relationship: regulates GO:0070588 ! calcium ion transmembrane transport -created_by: rl creation_date: 2014-07-11T17:09:26Z [Term] @@ -128830,7 +132294,6 @@ is_a: GO:1903169 ! regulation of calcium ion transmembrane transport intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0070588 ! calcium ion transmembrane transport relationship: negatively_regulates GO:0070588 ! calcium ion transmembrane transport -created_by: rl creation_date: 2014-07-11T17:09:32Z [Term] @@ -128847,7 +132310,6 @@ is_a: GO:0042053 ! regulation of dopamine metabolic process intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0042416 ! dopamine biosynthetic process relationship: regulates GO:0042416 ! dopamine biosynthetic process -created_by: bf creation_date: 2014-07-14T12:17:41Z [Term] @@ -128885,7 +132347,6 @@ is_a: GO:1903179 ! regulation of dopamine biosynthetic process intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0042416 ! dopamine biosynthetic process relationship: negatively_regulates GO:0042416 ! dopamine biosynthetic process -created_by: bf creation_date: 2014-07-14T12:17:47Z [Term] @@ -128923,7 +132384,6 @@ is_a: GO:1903179 ! regulation of dopamine biosynthetic process intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0042416 ! dopamine biosynthetic process relationship: positively_regulates GO:0042416 ! dopamine biosynthetic process -created_by: bf creation_date: 2014-07-14T12:17:53Z [Term] @@ -128941,7 +132401,6 @@ intersection_of: GO:0006915 ! apoptotic process intersection_of: occurs_in CL:0000653 ! podocyte relationship: occurs_in CL:0000653 ! podocyte property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/23000" xsd:anyURI -created_by: sl creation_date: 2014-07-23T17:07:55Z [Term] @@ -128954,7 +132413,6 @@ is_a: GO:0045595 ! regulation of cell differentiation intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0035987 ! endodermal cell differentiation relationship: regulates GO:0035987 ! endodermal cell differentiation -created_by: als creation_date: 2014-07-29T13:22:35Z [Term] @@ -128976,7 +132434,6 @@ is_a: GO:1903224 ! regulation of endodermal cell differentiation intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0035987 ! endodermal cell differentiation relationship: negatively_regulates GO:0035987 ! endodermal cell differentiation -created_by: als creation_date: 2014-07-29T13:22:41Z [Term] @@ -128998,7 +132455,6 @@ is_a: GO:1903224 ! regulation of endodermal cell differentiation intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0035987 ! endodermal cell differentiation relationship: positively_regulates GO:0035987 ! endodermal cell differentiation -created_by: als creation_date: 2014-07-29T13:22:47Z [Term] @@ -129012,7 +132468,6 @@ is_a: GO:0070925 ! organelle assembly intersection_of: GO:0022607 ! cellular component assembly intersection_of: results_in_assembly_of GO:0042470 ! melanosome relationship: results_in_assembly_of GO:0042470 ! melanosome -created_by: bf creation_date: 2014-07-31T10:41:38Z [Term] @@ -129023,16 +132478,14 @@ def: "The process in which a relatively unspecialized cell acquires the speciali synonym: "multiciliate cell differentiation" BROAD [] is_a: GO:0002065 ! columnar/cuboidal epithelial cell differentiation intersection_of: GO:0030154 ! cell differentiation -intersection_of: results_in_acquisition_of_features_of CL:0005012 ! multi-ciliated epithelial cell -relationship: results_in_acquisition_of_features_of CL:0005012 ! multi-ciliated epithelial cell -created_by: tb +intersection_of: results_in_acquisition_of_features_of CL:0005012 ! multiciliated epithelial cell +relationship: results_in_acquisition_of_features_of CL:0005012 ! multiciliated epithelial cell creation_date: 2014-08-05T19:21:21Z [Term] id: GO:1903276 name: regulation of sodium ion export across plasma membrane namespace: biological_process -alt_id: GO:1903273 def: "Any process that modulates the frequency, rate or extent of sodium ion export across the plasma membrane." [GO_REF:0000058, GOC:BHF, GOC:rl, GOC:TermGenie, PMID:17095720] synonym: "regulation of sodium export" RELATED [GOC:TermGenie] synonym: "regulation of sodium ion export" RELATED [] @@ -129041,14 +132494,12 @@ is_a: GO:1902305 ! regulation of sodium ion transmembrane transport intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0036376 ! sodium ion export across plasma membrane relationship: regulates GO:0036376 ! sodium ion export across plasma membrane -created_by: rl creation_date: 2014-08-08T17:06:46Z [Term] id: GO:1903277 name: negative regulation of sodium ion export across plasma membrane namespace: biological_process -alt_id: GO:1903274 def: "Any process that stops, prevents or reduces the frequency, rate or extent of sodium ion export across the plasma membrane." [GO_REF:0000058, GOC:BHF, GOC:rl, GOC:TermGenie, PMID:17095720] synonym: "down regulation of sodium export" RELATED [GOC:TermGenie] synonym: "down regulation of sodium ion export" RELATED [GOC:TermGenie] @@ -129070,14 +132521,12 @@ is_a: GO:1903276 ! regulation of sodium ion export across plasma membrane intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0036376 ! sodium ion export across plasma membrane relationship: negatively_regulates GO:0036376 ! sodium ion export across plasma membrane -created_by: rl creation_date: 2014-08-08T17:10:22Z [Term] id: GO:1903278 name: positive regulation of sodium ion export across plasma membrane namespace: biological_process -alt_id: GO:1903275 def: "Any process that activates or increases the frequency, rate or extent of sodium ion export across the plasma membrane." [GO_REF:0000058, GOC:BHF, GOC:rl, GOC:TermGenie, PMID:17095720] synonym: "activation of sodium export" NARROW [GOC:TermGenie] synonym: "activation of sodium ion export" NARROW [GOC:TermGenie] @@ -129099,7 +132548,6 @@ is_a: GO:1903276 ! regulation of sodium ion export across plasma membrane intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0036376 ! sodium ion export across plasma membrane relationship: positively_regulates GO:0036376 ! sodium ion export across plasma membrane -created_by: rl creation_date: 2014-08-08T17:10:30Z [Term] @@ -129113,7 +132561,6 @@ is_a: GO:1901379 ! regulation of potassium ion transmembrane transport intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:1990573 ! potassium ion import across plasma membrane relationship: regulates GO:1990573 ! potassium ion import across plasma membrane -created_by: rl creation_date: 2014-08-11T14:26:16Z [Term] @@ -129141,7 +132588,6 @@ is_a: GO:1903286 ! regulation of potassium ion import intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:1990573 ! potassium ion import across plasma membrane relationship: negatively_regulates GO:1990573 ! potassium ion import across plasma membrane -created_by: rl creation_date: 2014-08-11T14:26:24Z [Term] @@ -129169,7 +132615,6 @@ is_a: GO:1903286 ! regulation of potassium ion import intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:1990573 ! potassium ion import across plasma membrane relationship: positively_regulates GO:1990573 ! potassium ion import across plasma membrane -created_by: rl creation_date: 2014-08-11T14:26:32Z [Term] @@ -129185,7 +132630,6 @@ is_a: GO:0072657 ! protein localization to membrane intersection_of: GO:0008104 ! protein localization intersection_of: has_target_end_location GO:0000139 ! Golgi membrane relationship: has_target_end_location GO:0000139 ! Golgi membrane -created_by: mah creation_date: 2014-08-12T14:22:31Z [Term] @@ -129200,7 +132644,6 @@ is_a: GO:0051966 ! regulation of synaptic transmission, glutamatergic intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0061535 ! glutamate secretion, neurotransmission relationship: regulates GO:0061535 ! glutamate secretion, neurotransmission -created_by: pad creation_date: 2014-08-13T13:54:15Z [Term] @@ -129220,7 +132663,6 @@ is_a: GO:1903294 ! regulation of glutamate secretion, neurotransmission intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0061535 ! glutamate secretion, neurotransmission relationship: negatively_regulates GO:0061535 ! glutamate secretion, neurotransmission -created_by: pad creation_date: 2014-08-13T13:54:23Z [Term] @@ -129240,7 +132682,6 @@ is_a: GO:1903294 ! regulation of glutamate secretion, neurotransmission intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0061535 ! glutamate secretion, neurotransmission relationship: positively_regulates GO:0061535 ! glutamate secretion, neurotransmission -created_by: pad creation_date: 2014-08-13T13:54:31Z [Term] @@ -129253,7 +132694,6 @@ is_a: GO:0017157 ! regulation of exocytosis intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0045055 ! regulated exocytosis relationship: regulates GO:0045055 ! regulated exocytosis -created_by: pad creation_date: 2014-08-18T10:04:53Z [Term] @@ -129271,7 +132711,6 @@ is_a: GO:1903305 ! regulation of regulated secretory pathway intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0045055 ! regulated exocytosis relationship: negatively_regulates GO:0045055 ! regulated exocytosis -created_by: pad creation_date: 2014-08-18T10:05:02Z [Term] @@ -129289,7 +132728,6 @@ is_a: GO:1903305 ! regulation of regulated secretory pathway intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0045055 ! regulated exocytosis relationship: positively_regulates GO:0045055 ! regulated exocytosis -created_by: pad creation_date: 2014-08-18T10:05:10Z [Term] @@ -129301,7 +132739,6 @@ is_a: GO:0019222 ! regulation of metabolic process intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0071941 ! nitrogen cycle metabolic process relationship: regulates GO:0071941 ! nitrogen cycle metabolic process -created_by: vw creation_date: 2014-08-18T12:57:34Z [Term] @@ -129318,7 +132755,6 @@ is_a: GO:1903314 ! regulation of nitrogen cycle metabolic process intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0071941 ! nitrogen cycle metabolic process relationship: negatively_regulates GO:0071941 ! nitrogen cycle metabolic process -created_by: vw creation_date: 2014-08-18T12:57:42Z [Term] @@ -129335,7 +132771,6 @@ is_a: GO:1903314 ! regulation of nitrogen cycle metabolic process intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0071941 ! nitrogen cycle metabolic process relationship: positively_regulates GO:0071941 ! nitrogen cycle metabolic process -created_by: vw creation_date: 2014-08-18T12:57:50Z [Term] @@ -129348,7 +132783,6 @@ is_a: GO:0051246 ! regulation of protein metabolic process intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0051604 ! protein maturation relationship: regulates GO:0051604 ! protein maturation -created_by: vw creation_date: 2014-08-18T12:59:07Z [Term] @@ -129366,7 +132800,6 @@ is_a: GO:1903317 ! regulation of protein maturation intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0051604 ! protein maturation relationship: negatively_regulates GO:0051604 ! protein maturation -created_by: vw creation_date: 2014-08-18T12:59:15Z [Term] @@ -129384,7 +132817,6 @@ is_a: GO:1903317 ! regulation of protein maturation intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0051604 ! protein maturation relationship: positively_regulates GO:0051604 ! protein maturation -created_by: vw creation_date: 2014-08-18T12:59:23Z [Term] @@ -129396,7 +132828,6 @@ is_a: GO:0032386 ! regulation of intracellular transport intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0007034 ! vacuolar transport relationship: regulates GO:0007034 ! vacuolar transport -created_by: vw creation_date: 2014-08-18T13:16:04Z [Term] @@ -129413,7 +132844,6 @@ is_a: GO:1903335 ! regulation of vacuolar transport intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0007034 ! vacuolar transport relationship: negatively_regulates GO:0007034 ! vacuolar transport -created_by: vw creation_date: 2014-08-18T13:16:11Z [Term] @@ -129430,7 +132860,6 @@ is_a: GO:1903335 ! regulation of vacuolar transport intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0007034 ! vacuolar transport relationship: positively_regulates GO:0007034 ! vacuolar transport -created_by: vw creation_date: 2014-08-18T13:16:19Z [Term] @@ -129452,7 +132881,6 @@ is_a: GO:2000810 ! regulation of bicellular tight junction assembly intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0070830 ! bicellular tight junction assembly relationship: negatively_regulates GO:0070830 ! bicellular tight junction assembly -created_by: pr creation_date: 2014-08-19T11:02:14Z [Term] @@ -129474,7 +132902,6 @@ is_a: GO:2000810 ! regulation of bicellular tight junction assembly intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0070830 ! bicellular tight junction assembly relationship: positively_regulates GO:0070830 ! bicellular tight junction assembly -created_by: pr creation_date: 2014-08-19T11:05:06Z [Term] @@ -129487,7 +132914,6 @@ is_a: GO:0050896 ! response to stimulus intersection_of: GO:0050896 ! response to stimulus intersection_of: has_primary_input CHEBI:59905 relationship: has_primary_input CHEBI:59905 -created_by: mr creation_date: 2014-08-19T19:33:26Z [Term] @@ -129499,7 +132925,6 @@ is_a: GO:0070887 ! cellular response to chemical stimulus is_a: GO:1903350 ! response to dopamine intersection_of: GO:0070887 ! cellular response to chemical stimulus intersection_of: has_primary_input CHEBI:59905 -created_by: mr creation_date: 2014-08-19T19:33:35Z [Term] @@ -129516,7 +132941,6 @@ is_a: GO:0033043 ! regulation of organelle organization intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0006997 ! nucleus organization relationship: regulates GO:0006997 ! nucleus organization -created_by: hjd creation_date: 2014-08-20T19:36:16Z [Term] @@ -129528,7 +132952,6 @@ is_a: GO:0030334 ! regulation of cell migration intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0097628 ! distal tip cell migration relationship: regulates GO:0097628 ! distal tip cell migration -created_by: pr creation_date: 2014-08-21T10:05:08Z [Term] @@ -129545,7 +132968,6 @@ is_a: GO:1903354 ! regulation of distal tip cell migration intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0097628 ! distal tip cell migration relationship: negatively_regulates GO:0097628 ! distal tip cell migration -created_by: pr creation_date: 2014-08-21T10:05:17Z [Term] @@ -129562,7 +132984,6 @@ is_a: GO:1903354 ! regulation of distal tip cell migration intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0097628 ! distal tip cell migration relationship: positively_regulates GO:0097628 ! distal tip cell migration -created_by: pr creation_date: 2014-08-21T10:05:26Z [Term] @@ -129576,7 +132997,6 @@ is_a: GO:0033043 ! regulation of organelle organization intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0007030 ! Golgi organization relationship: regulates GO:0007030 ! Golgi organization -created_by: als creation_date: 2014-08-21T10:22:22Z [Term] @@ -129593,7 +133013,6 @@ is_a: GO:0061550 ! cranial ganglion development intersection_of: GO:0048856 ! anatomical structure development intersection_of: results_in_development_of UBERON:0012175 ! acoustico-facial VII-VIII ganglion complex relationship: results_in_development_of UBERON:0012175 ! acoustico-facial VII-VIII ganglion complex -created_by: bf creation_date: 2014-08-26T12:40:36Z [Term] @@ -129606,7 +133025,6 @@ is_a: GO:0060623 ! regulation of chromosome condensation intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0007076 ! mitotic chromosome condensation relationship: regulates GO:0007076 ! mitotic chromosome condensation -created_by: al creation_date: 2014-08-26T13:57:13Z [Term] @@ -129624,7 +133042,6 @@ is_a: GO:1905821 ! positive regulation of chromosome condensation intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0007076 ! mitotic chromosome condensation relationship: positively_regulates GO:0007076 ! mitotic chromosome condensation -created_by: al creation_date: 2014-08-26T13:57:29Z [Term] @@ -129637,7 +133054,6 @@ is_a: GO:0050896 ! response to stimulus intersection_of: GO:0050896 ! response to stimulus intersection_of: has_primary_input CHEBI:3098 relationship: has_primary_input CHEBI:3098 -created_by: rl creation_date: 2014-09-03T12:45:43Z [Term] @@ -129649,7 +133065,6 @@ is_a: GO:0070887 ! cellular response to chemical stimulus is_a: GO:1903412 ! response to bile acid intersection_of: GO:0070887 ! cellular response to chemical stimulus intersection_of: has_primary_input CHEBI:3098 -created_by: rl creation_date: 2014-09-03T12:45:51Z [Term] @@ -129662,7 +133077,6 @@ is_a: GO:0060284 ! regulation of cell development intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0048469 ! cell maturation relationship: regulates GO:0048469 ! cell maturation -created_by: jl creation_date: 2014-09-15T13:31:23Z [Term] @@ -129684,7 +133098,6 @@ is_a: GO:1903429 ! regulation of cell maturation intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0048469 ! cell maturation relationship: negatively_regulates GO:0048469 ! cell maturation -created_by: jl creation_date: 2014-09-15T13:31:32Z [Term] @@ -129706,7 +133119,6 @@ is_a: GO:1903429 ! regulation of cell maturation intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0048469 ! cell maturation relationship: positively_regulates GO:0048469 ! cell maturation -created_by: jl creation_date: 2014-09-15T13:31:41Z [Term] @@ -129718,7 +133130,6 @@ is_a: GO:0097648 ! G protein-coupled receptor complex intersection_of: GO:0032991 ! protein-containing complex intersection_of: capable_of GO:0097642 ! calcitonin family receptor activity relationship: capable_of GO:0097642 ! calcitonin family receptor activity -created_by: pr creation_date: 2014-09-16T13:25:11Z [Term] @@ -129735,7 +133146,6 @@ is_a: GO:1990778 ! protein localization to cell periphery intersection_of: GO:0008104 ! protein localization intersection_of: has_target_end_location GO:0060170 ! ciliary membrane relationship: has_target_end_location GO:0060170 ! ciliary membrane -created_by: pr creation_date: 2014-09-16T15:15:39Z [Term] @@ -129762,7 +133172,6 @@ is_a: GO:0090335 ! regulation of brown fat cell differentiation intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0050873 ! brown fat cell differentiation relationship: negatively_regulates GO:0050873 ! brown fat cell differentiation -created_by: hjd creation_date: 2014-09-17T19:15:00Z [Term] @@ -129776,7 +133185,6 @@ is_a: GO:2000026 ! regulation of multicellular organismal development intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0007595 ! lactation relationship: regulates GO:0007595 ! lactation -created_by: mr creation_date: 2014-09-24T14:44:13Z [Term] @@ -129795,7 +133203,6 @@ is_a: GO:1903487 ! regulation of lactation intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0007595 ! lactation relationship: negatively_regulates GO:0007595 ! lactation -created_by: mr creation_date: 2014-09-24T14:44:22Z [Term] @@ -129814,7 +133221,6 @@ is_a: GO:1903487 ! regulation of lactation intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0007595 ! lactation relationship: positively_regulates GO:0007595 ! lactation -created_by: mr creation_date: 2014-09-24T14:44:30Z [Term] @@ -129828,7 +133234,6 @@ is_a: GO:0008152 ! metabolic process intersection_of: GO:0008152 ! metabolic process intersection_of: has_primary_input_or_output CHEBI:37395 relationship: has_primary_input_or_output CHEBI:37395 -created_by: dph creation_date: 2014-10-01T21:55:47Z [Term] @@ -129841,7 +133246,6 @@ is_a: GO:0044057 ! regulation of system process intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0008015 ! blood circulation relationship: regulates GO:0008015 ! blood circulation -created_by: mr creation_date: 2014-10-06T18:38:56Z [Term] @@ -129863,7 +133267,6 @@ is_a: GO:1903522 ! regulation of blood circulation intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0008015 ! blood circulation relationship: negatively_regulates GO:0008015 ! blood circulation -created_by: mr creation_date: 2014-10-06T18:39:05Z [Term] @@ -129885,7 +133288,6 @@ is_a: GO:1903522 ! regulation of blood circulation intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0008015 ! blood circulation relationship: positively_regulates GO:0008015 ! blood circulation -created_by: mr creation_date: 2014-10-06T18:39:13Z [Term] @@ -129899,7 +133301,6 @@ is_a: GO:0051046 ! regulation of secretion intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0032940 ! secretion by cell relationship: regulates GO:0032940 ! secretion by cell -created_by: pm creation_date: 2014-10-08T13:24:59Z [Term] @@ -129922,7 +133323,6 @@ is_a: GO:1903530 ! regulation of secretion by cell intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0032940 ! secretion by cell relationship: negatively_regulates GO:0032940 ! secretion by cell -created_by: pm creation_date: 2014-10-08T13:25:08Z [Term] @@ -129945,7 +133345,6 @@ is_a: GO:1903530 ! regulation of secretion by cell intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0032940 ! secretion by cell relationship: positively_regulates GO:0032940 ! secretion by cell -created_by: pm creation_date: 2014-10-08T13:25:17Z [Term] @@ -129958,7 +133357,6 @@ is_a: GO:1903046 ! meiotic cell cycle process intersection_of: GO:1903046 ! meiotic cell cycle process intersection_of: part_of GO:0001556 ! oocyte maturation relationship: part_of GO:0001556 ! oocyte maturation -created_by: pr creation_date: 2014-10-09T10:46:14Z [Term] @@ -129972,7 +133370,6 @@ is_a: GO:2000241 ! regulation of reproductive process intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:1903537 ! meiotic cell cycle process involved in oocyte maturation relationship: regulates GO:1903537 ! meiotic cell cycle process involved in oocyte maturation -created_by: pr creation_date: 2014-10-09T10:52:38Z [Term] @@ -129989,7 +133386,6 @@ is_a: GO:1990778 ! protein localization to cell periphery intersection_of: GO:0008104 ! protein localization intersection_of: has_target_end_location GO:0045211 ! postsynaptic membrane relationship: has_target_end_location GO:0045211 ! postsynaptic membrane -created_by: kmv creation_date: 2014-10-10T11:23:53Z [Term] @@ -130004,7 +133400,6 @@ is_a: GO:0090150 ! establishment of protein localization to membrane is_a: GO:1903539 ! protein localization to postsynaptic membrane intersection_of: GO:0045184 ! establishment of protein localization intersection_of: has_target_end_location GO:0045211 ! postsynaptic membrane -created_by: kmv creation_date: 2014-10-10T11:24:03Z [Term] @@ -130020,7 +133415,6 @@ is_a: GO:0017157 ! regulation of exocytosis intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:1990182 ! exosomal secretion relationship: regulates GO:1990182 ! exosomal secretion -created_by: pga creation_date: 2014-10-14T11:38:52Z [Term] @@ -130057,7 +133451,6 @@ is_a: GO:1903541 ! regulation of exosomal secretion intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:1990182 ! exosomal secretion relationship: negatively_regulates GO:1990182 ! exosomal secretion -created_by: pga creation_date: 2014-10-14T11:39:02Z [Term] @@ -130095,7 +133488,6 @@ is_a: GO:1903541 ! regulation of exosomal secretion intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:1990182 ! exosomal secretion relationship: positively_regulates GO:1990182 ! exosomal secretion -created_by: pga creation_date: 2014-10-14T11:39:10Z [Term] @@ -130108,7 +133500,6 @@ is_a: GO:1902115 ! regulation of organelle assembly intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0071971 ! extracellular exosome assembly relationship: regulates GO:0071971 ! extracellular exosome assembly -created_by: pga creation_date: 2014-10-20T15:37:25Z [Term] @@ -130126,7 +133517,6 @@ is_a: GO:1903551 ! regulation of extracellular exosome assembly intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0071971 ! extracellular exosome assembly relationship: negatively_regulates GO:0071971 ! extracellular exosome assembly -created_by: pga creation_date: 2014-10-20T15:37:33Z [Term] @@ -130144,7 +133534,6 @@ is_a: GO:1903551 ! regulation of extracellular exosome assembly intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0071971 ! extracellular exosome assembly relationship: positively_regulates GO:0071971 ! extracellular exosome assembly -created_by: pga creation_date: 2014-10-20T15:37:42Z [Term] @@ -130158,7 +133547,6 @@ is_a: GO:0001817 ! regulation of cytokine production intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0071706 ! tumor necrosis factor superfamily cytokine production relationship: regulates GO:0071706 ! tumor necrosis factor superfamily cytokine production -created_by: pga creation_date: 2014-10-21T10:26:05Z [Term] @@ -130185,7 +133573,6 @@ is_a: GO:1903555 ! regulation of tumor necrosis factor superfamily cytokine prod intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0071706 ! tumor necrosis factor superfamily cytokine production relationship: negatively_regulates GO:0071706 ! tumor necrosis factor superfamily cytokine production -created_by: pga creation_date: 2014-10-21T10:26:14Z [Term] @@ -130212,7 +133599,6 @@ is_a: GO:1903555 ! regulation of tumor necrosis factor superfamily cytokine prod intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0071706 ! tumor necrosis factor superfamily cytokine production relationship: positively_regulates GO:0071706 ! tumor necrosis factor superfamily cytokine production -created_by: pga creation_date: 2014-10-21T10:26:23Z [Term] @@ -130225,7 +133611,6 @@ is_a: GO:0031982 ! vesicle is_a: GO:0065010 ! extracellular membrane-bounded organelle intersection_of: GO:0031982 ! vesicle intersection_of: part_of GO:0005576 ! extracellular region -created_by: jl creation_date: 2014-10-22T14:26:11Z [Term] @@ -130237,7 +133622,6 @@ is_a: GO:0032880 ! regulation of protein localization intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0061512 ! protein localization to cilium relationship: regulates GO:0061512 ! protein localization to cilium -created_by: krc creation_date: 2014-10-24T20:58:11Z [Term] @@ -130254,7 +133638,6 @@ is_a: GO:1903828 ! negative regulation of protein localization intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0061512 ! protein localization to cilium relationship: negatively_regulates GO:0061512 ! protein localization to cilium -created_by: krc creation_date: 2014-10-24T20:58:20Z [Term] @@ -130271,7 +133654,6 @@ is_a: GO:1903829 ! positive regulation of protein localization intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0061512 ! protein localization to cilium relationship: positively_regulates GO:0061512 ! protein localization to cilium -created_by: krc creation_date: 2014-10-24T20:58:28Z [Term] @@ -130288,7 +133670,6 @@ is_a: GO:1905475 ! regulation of protein localization to membrane intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:1903441 ! protein localization to ciliary membrane relationship: regulates GO:1903441 ! protein localization to ciliary membrane -created_by: krc creation_date: 2014-10-24T21:32:51Z [Term] @@ -130322,7 +133703,6 @@ is_a: GO:1905476 ! negative regulation of protein localization to membrane intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:1903441 ! protein localization to ciliary membrane relationship: negatively_regulates GO:1903441 ! protein localization to ciliary membrane -created_by: krc creation_date: 2014-10-24T21:32:59Z [Term] @@ -130356,7 +133736,6 @@ is_a: GO:1905477 ! positive regulation of protein localization to membrane intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:1903441 ! protein localization to ciliary membrane relationship: positively_regulates GO:1903441 ! protein localization to ciliary membrane -created_by: krc creation_date: 2014-10-24T21:33:08Z [Term] @@ -130369,7 +133748,6 @@ is_a: GO:0019222 ! regulation of metabolic process intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0046034 ! ATP metabolic process relationship: regulates GO:0046034 ! ATP metabolic process -created_by: sl creation_date: 2014-10-30T19:04:24Z [Term] @@ -130391,7 +133769,6 @@ is_a: GO:1903578 ! regulation of ATP metabolic process intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0046034 ! ATP metabolic process relationship: negatively_regulates GO:0046034 ! ATP metabolic process -created_by: sl creation_date: 2014-10-30T19:04:33Z [Term] @@ -130413,7 +133790,6 @@ is_a: GO:1903578 ! regulation of ATP metabolic process intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0046034 ! ATP metabolic process relationship: positively_regulates GO:0046034 ! ATP metabolic process -created_by: sl creation_date: 2014-10-30T19:04:42Z [Term] @@ -130427,7 +133803,6 @@ is_a: GO:0050776 ! regulation of immune response intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0002561 ! basophil degranulation relationship: regulates GO:0002561 ! basophil degranulation -created_by: sl creation_date: 2014-10-31T17:37:24Z [Term] @@ -130446,7 +133821,6 @@ is_a: GO:1903581 ! regulation of basophil degranulation intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0002561 ! basophil degranulation relationship: negatively_regulates GO:0002561 ! basophil degranulation -created_by: sl creation_date: 2014-10-31T17:37:33Z [Term] @@ -130465,7 +133839,6 @@ is_a: GO:1903581 ! regulation of basophil degranulation intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0002561 ! basophil degranulation relationship: positively_regulates GO:0002561 ! basophil degranulation -created_by: sl creation_date: 2014-10-31T17:37:42Z [Term] @@ -130479,7 +133852,6 @@ is_a: GO:0051239 ! regulation of multicellular organismal process intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0002553 ! histamine secretion by mast cell relationship: regulates GO:0002553 ! histamine secretion by mast cell -created_by: als creation_date: 2014-11-06T13:19:09Z [Term] @@ -130497,7 +133869,6 @@ is_a: GO:1903593 ! regulation of histamine secretion by mast cell intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0002553 ! histamine secretion by mast cell relationship: negatively_regulates GO:0002553 ! histamine secretion by mast cell -created_by: als creation_date: 2014-11-06T13:19:18Z [Term] @@ -130517,7 +133888,6 @@ is_a: GO:1903593 ! regulation of histamine secretion by mast cell intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0002553 ! histamine secretion by mast cell relationship: positively_regulates GO:0002553 ! histamine secretion by mast cell -created_by: als creation_date: 2014-11-06T13:19:26Z [Term] @@ -130534,7 +133904,6 @@ is_a: GO:0060255 ! regulation of macromolecule metabolic process intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0006308 ! DNA catabolic process relationship: regulates GO:0006308 ! DNA catabolic process -created_by: sl creation_date: 2014-11-19T22:36:35Z [Term] @@ -130568,7 +133937,6 @@ is_a: GO:1903624 ! regulation of DNA catabolic process intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0006308 ! DNA catabolic process relationship: negatively_regulates GO:0006308 ! DNA catabolic process -created_by: sl creation_date: 2014-11-19T22:36:43Z [Term] @@ -130602,7 +133970,6 @@ is_a: GO:1903624 ! regulation of DNA catabolic process intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0006308 ! DNA catabolic process relationship: positively_regulates GO:0006308 ! DNA catabolic process -created_by: sl creation_date: 2014-11-19T22:36:51Z [Term] @@ -130614,9 +133981,8 @@ synonym: "sebocyte differentiation" EXACT [CL:0002140] is_a: GO:0001949 ! sebaceous gland cell differentiation is_a: GO:0090425 ! acinar cell differentiation intersection_of: GO:0030154 ! cell differentiation -intersection_of: results_in_acquisition_of_features_of CL:0002140 ! acinar cell of sebaceous gland -relationship: results_in_acquisition_of_features_of CL:0002140 ! acinar cell of sebaceous gland -created_by: cls +intersection_of: results_in_acquisition_of_features_of CL:0002140 ! skin sebocyte +relationship: results_in_acquisition_of_features_of CL:0002140 ! skin sebocyte creation_date: 2014-11-30T11:51:57Z [Term] @@ -130629,7 +133995,6 @@ is_a: GO:0010632 ! regulation of epithelial cell migration intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0007298 ! border follicle cell migration relationship: regulates GO:0007298 ! border follicle cell migration -created_by: als creation_date: 2014-12-01T13:35:39Z [Term] @@ -130643,7 +134008,6 @@ is_a: GO:1903684 ! regulation of border follicle cell migration intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0007298 ! border follicle cell migration relationship: negatively_regulates GO:0007298 ! border follicle cell migration -created_by: als creation_date: 2014-12-01T13:41:05Z [Term] @@ -130657,7 +134021,6 @@ is_a: GO:1903684 ! regulation of border follicle cell migration intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0007298 ! border follicle cell migration relationship: positively_regulates GO:0007298 ! border follicle cell migration -created_by: als creation_date: 2014-12-01T13:41:19Z [Term] @@ -130679,7 +134042,6 @@ is_a: GO:0120033 ! negative regulation of plasma membrane bounded cell projectio intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0030033 ! microvillus assembly relationship: negatively_regulates GO:0030033 ! microvillus assembly -created_by: als creation_date: 2014-12-03T11:45:08Z [Term] @@ -130701,7 +134063,6 @@ is_a: GO:0120034 ! positive regulation of plasma membrane bounded cell projectio intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0030033 ! microvillus assembly relationship: positively_regulates GO:0030033 ! microvillus assembly -created_by: als creation_date: 2014-12-03T11:45:17Z [Term] @@ -130721,7 +134082,6 @@ is_a: GO:0048856 ! anatomical structure development intersection_of: GO:0048856 ! anatomical structure development intersection_of: results_in_development_of UBERON:0001153 ! caecum relationship: results_in_development_of UBERON:0001153 ! caecum -created_by: cls creation_date: 2014-12-03T12:05:00Z [Term] @@ -130736,7 +134096,6 @@ is_a: GO:0048856 ! anatomical structure development intersection_of: GO:0048856 ! anatomical structure development intersection_of: results_in_development_of UBERON:0001777 ! substantia propria of cornea relationship: results_in_development_of UBERON:0001777 ! substantia propria of cornea -created_by: cls creation_date: 2014-12-03T13:12:09Z [Term] @@ -130751,7 +134110,6 @@ is_a: GO:0048856 ! anatomical structure development intersection_of: GO:0048856 ! anatomical structure development intersection_of: results_in_development_of UBERON:0001043 ! esophagus relationship: results_in_development_of UBERON:0001043 ! esophagus -created_by: cls creation_date: 2014-12-03T14:41:30Z [Term] @@ -130763,7 +134121,6 @@ is_a: GO:0060575 ! intestinal epithelial cell differentiation intersection_of: GO:0030154 ! cell differentiation intersection_of: results_in_acquisition_of_features_of CL:0000584 ! enterocyte relationship: results_in_acquisition_of_features_of CL:0000584 ! enterocyte -created_by: cls creation_date: 2014-12-03T15:08:51Z [Term] @@ -130782,7 +134139,6 @@ is_a: GO:2000026 ! regulation of multicellular organismal development intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0030097 ! hemopoiesis relationship: regulates GO:0030097 ! hemopoiesis -created_by: pad creation_date: 2014-12-04T15:34:13Z [Term] @@ -130822,7 +134178,6 @@ is_a: GO:1903706 ! regulation of hemopoiesis intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0030097 ! hemopoiesis relationship: negatively_regulates GO:0030097 ! hemopoiesis -created_by: pad creation_date: 2014-12-04T15:34:21Z [Term] @@ -130862,7 +134217,6 @@ is_a: GO:1903706 ! regulation of hemopoiesis intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0030097 ! hemopoiesis relationship: positively_regulates GO:0030097 ! hemopoiesis -created_by: pad creation_date: 2014-12-04T15:34:30Z [Term] @@ -130881,7 +134235,6 @@ is_a: GO:0048732 ! gland development intersection_of: GO:0048856 ! anatomical structure development intersection_of: results_in_development_of UBERON:0002451 ! endometrial gland relationship: results_in_development_of UBERON:0002451 ! endometrial gland -created_by: cls creation_date: 2014-12-04T18:57:21Z [Term] @@ -130894,7 +134247,6 @@ is_a: GO:0030154 ! cell differentiation intersection_of: GO:0030154 ! cell differentiation intersection_of: results_in_acquisition_of_features_of CL:0000175 ! luteal cell relationship: results_in_acquisition_of_features_of CL:0000175 ! luteal cell -created_by: cjm creation_date: 2014-12-10T01:36:43Z [Term] @@ -130908,14 +134260,12 @@ is_a: GO:0051128 ! regulation of cellular component organization intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0007009 ! plasma membrane organization relationship: regulates GO:0007009 ! plasma membrane organization -created_by: al creation_date: 2014-12-10T18:59:44Z [Term] id: GO:1903764 name: regulation of potassium ion export across plasma membrane namespace: biological_process -alt_id: GO:1902302 def: "Any process that modulates the frequency, rate or extent of potassium ion export across the plasma membrane." [GO_REF:0000058, GOC:BHF, GOC:mtg_cardiac_conduct_nov11, GOC:rl, GOC:TermGenie, PMID:19646991] synonym: "regulation of potassium export" BROAD [GOC:TermGenie] synonym: "regulation of potassium export across plasma membrane" BROAD [GOC:TermGenie] @@ -130924,14 +134274,12 @@ is_a: GO:1901379 ! regulation of potassium ion transmembrane transport intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0097623 ! potassium ion export across plasma membrane relationship: regulates GO:0097623 ! potassium ion export across plasma membrane -created_by: rl creation_date: 2013-07-17T16:39:53Z [Term] id: GO:1903765 name: negative regulation of potassium ion export across plasma membrane namespace: biological_process -alt_id: GO:1902303 def: "Any process that stops, prevents or reduces the frequency, rate or extent of potassium ion export across the plasma membrane." [GO_REF:0000058, GOC:BHF, GOC:mtg_cardiac_conduct_nov11, GOC:rl, GOC:TermGenie, PMID:19646991] synonym: "down regulation of potassium export" BROAD [GOC:TermGenie] synonym: "down regulation of potassium ion export" BROAD [GOC:TermGenie] @@ -130952,14 +134300,12 @@ is_a: GO:1903764 ! regulation of potassium ion export across plasma membrane intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0097623 ! potassium ion export across plasma membrane relationship: negatively_regulates GO:0097623 ! potassium ion export across plasma membrane -created_by: rl creation_date: 2013-07-17T16:40:02Z [Term] id: GO:1903766 name: positive regulation of potassium ion export across plasma membrane namespace: biological_process -alt_id: GO:1902304 def: "Any process that activates or increases the frequency, rate or extent of potassium ion export across the plasma membrane." [GO_REF:0000058, GOC:BHF, GOC:mtg_cardiac_conduct_nov11, GOC:rl, GOC:TermGenie, PMID:19646991] synonym: "activation of potassium export" RELATED [GOC:TermGenie] synonym: "activation of potassium ion export" RELATED [GOC:TermGenie] @@ -130980,7 +134326,6 @@ is_a: GO:1903764 ! regulation of potassium ion export across plasma membrane intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0097623 ! potassium ion export across plasma membrane relationship: positively_regulates GO:0097623 ! potassium ion export across plasma membrane -created_by: rl creation_date: 2013-07-17T16:40:10Z [Term] @@ -130996,7 +134341,6 @@ is_a: GO:0072665 ! protein localization to vacuole intersection_of: GO:0008104 ! protein localization intersection_of: has_target_end_location GO:0005774 ! vacuolar membrane relationship: has_target_end_location GO:0005774 ! vacuolar membrane -created_by: mah creation_date: 2015-01-07T13:15:54Z [Term] @@ -131008,7 +134352,6 @@ is_a: GO:0008016 ! regulation of heart contraction intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0061337 ! cardiac conduction relationship: regulates GO:0061337 ! cardiac conduction -created_by: rph creation_date: 2015-01-07T13:20:11Z [Term] @@ -131025,7 +134368,6 @@ is_a: GO:1903779 ! regulation of cardiac conduction intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0061337 ! cardiac conduction relationship: negatively_regulates GO:0061337 ! cardiac conduction -created_by: rph creation_date: 2015-01-07T13:20:20Z [Term] @@ -131042,7 +134384,6 @@ is_a: GO:1903779 ! regulation of cardiac conduction intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0061337 ! cardiac conduction relationship: positively_regulates GO:0061337 ! cardiac conduction -created_by: rph creation_date: 2015-01-07T13:20:28Z [Term] @@ -131054,7 +134395,6 @@ is_a: GO:1902305 ! regulation of sodium ion transmembrane transport intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0098719 ! sodium ion import across plasma membrane relationship: regulates GO:0098719 ! sodium ion import across plasma membrane -created_by: nc creation_date: 2015-01-07T16:48:43Z [Term] @@ -131071,7 +134411,6 @@ is_a: GO:1903782 ! regulation of sodium ion import across plasma membrane intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0098719 ! sodium ion import across plasma membrane relationship: negatively_regulates GO:0098719 ! sodium ion import across plasma membrane -created_by: nc creation_date: 2015-01-07T16:48:51Z [Term] @@ -131088,7 +134427,6 @@ is_a: GO:1903782 ! regulation of sodium ion import across plasma membrane intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0098719 ! sodium ion import across plasma membrane relationship: positively_regulates GO:0098719 ! sodium ion import across plasma membrane -created_by: nc creation_date: 2015-01-07T16:49:00Z [Term] @@ -131102,14 +134440,12 @@ is_a: GO:0051955 ! regulation of amino acid transport intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0003333 ! amino acid transmembrane transport relationship: regulates GO:0003333 ! amino acid transmembrane transport -created_by: al creation_date: 2015-01-08T17:42:18Z [Term] id: GO:1903804 name: glycine import across plasma membrane namespace: biological_process -alt_id: GO:0036233 def: "The directed movement of glycine from outside of a cell, across the plasma membrane and into the cytosol." [GO_REF:0000075, GOC:TermGenie, PMID:23895341] synonym: "glycine import" BROAD [] synonym: "glycine import into cell" EXACT [] @@ -131120,15 +134456,12 @@ intersection_of: has_primary_input CHEBI:57305 intersection_of: has_target_end_location GO:0005829 ! cytosol intersection_of: has_target_start_location GO:0005576 ! extracellular region intersection_of: results_in_transport_across GO:0005886 ! plasma membrane -created_by: bf creation_date: 2012-05-11T01:16:45Z [Term] id: GO:1903810 name: L-histidine import across plasma membrane namespace: biological_process -alt_id: GO:0061460 -alt_id: GO:0090466 def: "The directed movement of L-histidine from outside of a cell, across the plasma membrane and into the cytosol." [GO_REF:0000075, GOC:TermGenie, PMID:23895341] synonym: "histidine import" BROAD [] synonym: "L-histidine import" BROAD [] @@ -131140,7 +134473,6 @@ intersection_of: has_primary_input CHEBI:57595 intersection_of: has_target_end_location GO:0005829 ! cytosol intersection_of: has_target_start_location GO:0005576 ! extracellular region intersection_of: results_in_transport_across GO:0005886 ! plasma membrane -created_by: dph creation_date: 2012-10-05T10:20:50Z [Term] @@ -131153,7 +134485,6 @@ is_a: GO:0055085 ! transmembrane transport intersection_of: GO:0006810 ! transport intersection_of: has_primary_input CHEBI:64709 intersection_of: results_in_transport_across GO:0016020 ! membrane -created_by: vw creation_date: 2015-01-20T10:20:58Z [Term] @@ -131177,7 +134508,6 @@ intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0008104 ! protein localization relationship: negatively_regulates GO:0008104 ! protein localization property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/22021" xsd:anyURI -created_by: jl creation_date: 2015-01-20T14:32:24Z [Term] @@ -131199,7 +134529,6 @@ intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0008104 ! protein localization relationship: positively_regulates GO:0008104 ! protein localization property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/22021" xsd:anyURI -created_by: jl creation_date: 2015-01-20T14:32:33Z [Term] @@ -131215,7 +134544,6 @@ is_a: GO:0007165 ! signal transduction intersection_of: GO:0007165 ! signal transduction intersection_of: part_of GO:0071242 ! cellular response to ammonium ion relationship: part_of GO:0071242 ! cellular response to ammonium ion -created_by: al creation_date: 2015-01-21T17:52:09Z [Term] @@ -131227,7 +134555,6 @@ is_a: GO:1905651 ! regulation of artery morphogenesis intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0035909 ! aorta morphogenesis relationship: regulates GO:0035909 ! aorta morphogenesis -created_by: rph creation_date: 2015-01-23T14:00:51Z [Term] @@ -131244,7 +134571,6 @@ is_a: GO:1905652 ! negative regulation of artery morphogenesis intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0035909 ! aorta morphogenesis relationship: negatively_regulates GO:0035909 ! aorta morphogenesis -created_by: rph creation_date: 2015-01-23T14:01:01Z [Term] @@ -131261,7 +134587,6 @@ is_a: GO:1905653 ! positive regulation of artery morphogenesis intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0035909 ! aorta morphogenesis relationship: positively_regulates GO:0035909 ! aorta morphogenesis -created_by: rph creation_date: 2015-01-23T14:01:09Z [Term] @@ -131273,7 +134598,6 @@ is_a: GO:0048856 ! anatomical structure development intersection_of: GO:0048856 ! anatomical structure development intersection_of: results_in_development_of UBERON:0005631 ! extraembryonic membrane relationship: results_in_development_of UBERON:0005631 ! extraembryonic membrane -created_by: cjm creation_date: 2015-02-05T00:42:16Z [Term] @@ -131291,7 +134615,6 @@ is_a: GO:2000114 ! regulation of establishment of cell polarity intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0001768 ! establishment of T cell polarity relationship: regulates GO:0001768 ! establishment of T cell polarity -created_by: als creation_date: 2015-02-09T10:50:21Z [Term] @@ -131338,7 +134661,6 @@ is_a: GO:1903903 ! regulation of establishment of T cell polarity intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0001768 ! establishment of T cell polarity relationship: negatively_regulates GO:0001768 ! establishment of T cell polarity -created_by: als creation_date: 2015-02-09T10:50:30Z [Term] @@ -131385,7 +134707,6 @@ is_a: GO:1903903 ! regulation of establishment of T cell polarity intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0001768 ! establishment of T cell polarity relationship: positively_regulates GO:0001768 ! establishment of T cell polarity -created_by: als creation_date: 2015-02-09T10:50:40Z [Term] @@ -131398,7 +134719,6 @@ is_a: GO:0005488 ! binding intersection_of: GO:0005488 ! binding intersection_of: has_primary_input CHEBI:23965 relationship: has_primary_input CHEBI:23965 -created_by: sl creation_date: 2015-02-11T00:11:34Z [Term] @@ -131415,7 +134735,6 @@ is_a: GO:0051241 ! negative regulation of multicellular organismal process intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0007585 ! respiratory gaseous exchange by respiratory system relationship: negatively_regulates GO:0007585 ! respiratory gaseous exchange by respiratory system -created_by: sl creation_date: 2015-02-17T20:26:24Z [Term] @@ -131432,7 +134751,6 @@ is_a: GO:0051240 ! positive regulation of multicellular organismal process intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0007585 ! respiratory gaseous exchange by respiratory system relationship: positively_regulates GO:0007585 ! respiratory gaseous exchange by respiratory system -created_by: sl creation_date: 2015-02-17T20:26:35Z [Term] @@ -131445,7 +134763,6 @@ is_a: GO:1904035 ! regulation of epithelial cell apoptotic process intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0097284 ! hepatocyte apoptotic process relationship: regulates GO:0097284 ! hepatocyte apoptotic process -created_by: sl creation_date: 2015-02-19T12:54:40Z [Term] @@ -131467,7 +134784,6 @@ is_a: GO:1904036 ! negative regulation of epithelial cell apoptotic process intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0097284 ! hepatocyte apoptotic process relationship: negatively_regulates GO:0097284 ! hepatocyte apoptotic process -created_by: sl creation_date: 2015-02-19T12:54:50Z [Term] @@ -131489,7 +134805,6 @@ is_a: GO:1904037 ! positive regulation of epithelial cell apoptotic process intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0097284 ! hepatocyte apoptotic process relationship: positively_regulates GO:0097284 ! hepatocyte apoptotic process -created_by: sl creation_date: 2015-02-19T12:54:59Z [Term] @@ -131507,7 +134822,6 @@ is_a: GO:0106135 ! negative regulation of cardiac muscle cell contraction intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0086005 ! ventricular cardiac muscle cell action potential relationship: negatively_regulates GO:0086005 ! ventricular cardiac muscle cell action potential -created_by: nc creation_date: 2015-02-20T14:31:55Z [Term] @@ -131525,7 +134839,6 @@ is_a: GO:0106134 ! positive regulation of cardiac muscle cell contraction intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0086005 ! ventricular cardiac muscle cell action potential relationship: positively_regulates GO:0086005 ! ventricular cardiac muscle cell action potential -created_by: nc creation_date: 2015-02-20T14:32:04Z [Term] @@ -131543,7 +134856,6 @@ is_a: GO:0106135 ! negative regulation of cardiac muscle cell contraction intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0086014 ! atrial cardiac muscle cell action potential relationship: negatively_regulates GO:0086014 ! atrial cardiac muscle cell action potential -created_by: nc creation_date: 2015-02-20T14:36:33Z [Term] @@ -131560,7 +134872,6 @@ is_a: GO:0098910 ! regulation of atrial cardiac muscle cell action potential intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0086014 ! atrial cardiac muscle cell action potential relationship: positively_regulates GO:0086014 ! atrial cardiac muscle cell action potential -created_by: nc creation_date: 2015-02-20T14:36:42Z [Term] @@ -131587,7 +134898,6 @@ is_a: GO:0098904 ! regulation of AV node cell action potential intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0086016 ! AV node cell action potential relationship: negatively_regulates GO:0086016 ! AV node cell action potential -created_by: nc creation_date: 2015-02-20T14:59:41Z [Term] @@ -131614,7 +134924,6 @@ is_a: GO:0098904 ! regulation of AV node cell action potential intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0086016 ! AV node cell action potential relationship: positively_regulates GO:0086016 ! AV node cell action potential -created_by: nc creation_date: 2015-02-20T14:59:50Z [Term] @@ -131627,7 +134936,6 @@ is_a: GO:0030334 ! regulation of cell migration intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0008347 ! glial cell migration relationship: regulates GO:0008347 ! glial cell migration -created_by: nc creation_date: 2015-03-02T15:13:31Z [Term] @@ -131649,7 +134957,6 @@ is_a: GO:1903975 ! regulation of glial cell migration intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0008347 ! glial cell migration relationship: negatively_regulates GO:0008347 ! glial cell migration -created_by: nc creation_date: 2015-03-02T15:13:38Z [Term] @@ -131671,7 +134978,6 @@ is_a: GO:1903975 ! regulation of glial cell migration intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0008347 ! glial cell migration relationship: positively_regulates GO:0008347 ! glial cell migration -created_by: nc creation_date: 2015-03-02T15:13:43Z [Term] @@ -131684,7 +134990,6 @@ is_a: GO:0150077 ! regulation of neuroinflammatory response intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0001774 ! microglial cell activation relationship: regulates GO:0001774 ! microglial cell activation -created_by: nc creation_date: 2015-03-02T15:17:33Z [Term] @@ -131702,7 +135007,6 @@ is_a: GO:1903978 ! regulation of microglial cell activation intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0001774 ! microglial cell activation relationship: negatively_regulates GO:0001774 ! microglial cell activation -created_by: nc creation_date: 2015-03-02T15:17:39Z [Term] @@ -131720,14 +135024,12 @@ is_a: GO:1903978 ! regulation of microglial cell activation intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0001774 ! microglial cell activation relationship: positively_regulates GO:0001774 ! microglial cell activation -created_by: nc creation_date: 2015-03-02T15:17:44Z [Term] id: GO:1903988 name: iron ion export across plasma membrane namespace: biological_process -alt_id: GO:1903414 def: "The directed movement of iron ions from inside of a cell, across the plasma membrane and into the extracellular region." [GO_REF:0000074, GOC:BHF, GOC:kom, GOC:rl, GOC:TermGenie, PMID:15514116] comment: An example of this is mouse ferroportin (symbol Slc40a1, UniProtKB identifier: Q9JHI9). synonym: "ferrous iron export" NARROW [] @@ -131741,7 +135043,6 @@ intersection_of: has_primary_input CHEBI:24875 intersection_of: has_target_end_location GO:0005576 ! extracellular region intersection_of: has_target_start_location GO:0005829 ! cytosol intersection_of: results_in_transport_across GO:0005886 ! plasma membrane -created_by: rl creation_date: 2014-09-03T13:01:37Z [Term] @@ -131750,11 +135051,10 @@ name: regulation of sebum secreting cell proliferation namespace: biological_process def: "Any process that modulates the frequency, rate or extent of sebum secreting cell proliferation." [GO_REF:0000058, GOC:hjd, GOC:TermGenie, PMID:16901790] synonym: "regulation of sebocyte proliferation" RELATED [GOC:TermGenie] -is_a: GO:0042127 ! regulation of cell population proliferation +is_a: GO:0050678 ! regulation of epithelial cell proliferation intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:1990654 ! sebum secreting cell proliferation relationship: regulates GO:1990654 ! sebum secreting cell proliferation -created_by: hjd creation_date: 2015-03-06T16:19:44Z [Term] @@ -131771,12 +135071,11 @@ synonym: "downregulation of sebum secreting cell proliferation" EXACT [GOC:TermG synonym: "inhibition of sebocyte proliferation" RELATED [GOC:TermGenie] synonym: "inhibition of sebum secreting cell proliferation" NARROW [GOC:TermGenie] synonym: "negative regulation of sebocyte proliferation" RELATED [GOC:TermGenie] -is_a: GO:0008285 ! negative regulation of cell population proliferation +is_a: GO:0050680 ! negative regulation of epithelial cell proliferation is_a: GO:1904002 ! regulation of sebum secreting cell proliferation intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:1990654 ! sebum secreting cell proliferation relationship: negatively_regulates GO:1990654 ! sebum secreting cell proliferation -created_by: hjd creation_date: 2015-03-06T16:19:50Z [Term] @@ -131793,12 +135092,11 @@ synonym: "up-regulation of sebocyte proliferation" RELATED [GOC:TermGenie] synonym: "up-regulation of sebum secreting cell proliferation" EXACT [GOC:TermGenie] synonym: "upregulation of sebocyte proliferation" RELATED [GOC:TermGenie] synonym: "upregulation of sebum secreting cell proliferation" EXACT [GOC:TermGenie] -is_a: GO:0008284 ! positive regulation of cell population proliferation +is_a: GO:0050679 ! positive regulation of epithelial cell proliferation is_a: GO:1904002 ! regulation of sebum secreting cell proliferation intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:1990654 ! sebum secreting cell proliferation relationship: positively_regulates GO:1990654 ! sebum secreting cell proliferation -created_by: hjd creation_date: 2015-03-06T16:19:56Z [Term] @@ -131811,7 +135109,6 @@ is_a: GO:0050896 ! response to stimulus intersection_of: GO:0050896 ! response to stimulus intersection_of: has_primary_input CHEBI:350546 relationship: has_primary_input CHEBI:350546 -created_by: sl creation_date: 2015-03-06T19:33:54Z [Term] @@ -131823,7 +135120,6 @@ is_a: GO:0070887 ! cellular response to chemical stimulus is_a: GO:1904014 ! response to serotonin intersection_of: GO:0070887 ! cellular response to chemical stimulus intersection_of: has_primary_input CHEBI:350546 -created_by: sl creation_date: 2015-03-06T19:34:00Z [Term] @@ -131846,7 +135142,6 @@ is_a: GO:1901342 ! regulation of vasculature development intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0001944 ! vasculature development relationship: positively_regulates GO:0001944 ! vasculature development -created_by: sl creation_date: 2015-03-06T22:17:04Z [Term] @@ -131865,7 +135160,6 @@ property_value: RO:0002161 NCBITaxon:2 property_value: RO:0002161 NCBITaxon:2157 property_value: RO:0002161 NCBITaxon:33090 property_value: RO:0002161 NCBITaxon:4751 -created_by: sl creation_date: 2015-03-06T22:27:17Z [Term] @@ -131881,7 +135175,6 @@ is_a: GO:1903053 ! regulation of extracellular matrix organization intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0030199 ! collagen fibril organization relationship: regulates GO:0030199 ! collagen fibril organization -created_by: ae creation_date: 2015-03-12T12:36:52Z [Term] @@ -131909,7 +135202,6 @@ is_a: GO:1904026 ! regulation of collagen fibril organization intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0030199 ! collagen fibril organization relationship: negatively_regulates GO:0030199 ! collagen fibril organization -created_by: ae creation_date: 2015-03-12T12:36:59Z [Term] @@ -131937,7 +135229,6 @@ is_a: GO:1904026 ! regulation of collagen fibril organization intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0030199 ! collagen fibril organization relationship: positively_regulates GO:0030199 ! collagen fibril organization -created_by: ae creation_date: 2015-03-12T12:37:06Z [Term] @@ -131952,7 +135243,6 @@ is_a: GO:0042981 ! regulation of apoptotic process intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:1904019 ! epithelial cell apoptotic process relationship: regulates GO:1904019 ! epithelial cell apoptotic process -created_by: sl creation_date: 2015-03-13T22:05:41Z [Term] @@ -131984,7 +135274,6 @@ is_a: GO:1904035 ! regulation of epithelial cell apoptotic process intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:1904019 ! epithelial cell apoptotic process relationship: negatively_regulates GO:1904019 ! epithelial cell apoptotic process -created_by: sl creation_date: 2015-03-13T22:05:47Z [Term] @@ -132016,7 +135305,6 @@ is_a: GO:1904035 ! regulation of epithelial cell apoptotic process intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:1904019 ! epithelial cell apoptotic process relationship: positively_regulates GO:1904019 ! epithelial cell apoptotic process -created_by: sl creation_date: 2015-03-13T22:05:53Z [Term] @@ -132030,7 +135318,6 @@ is_a: GO:0034759 ! regulation of iron ion transmembrane transport intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:1903988 ! iron ion export across plasma membrane relationship: regulates GO:1903988 ! iron ion export across plasma membrane -created_by: kom creation_date: 2015-03-16T15:36:37Z [Term] @@ -132053,7 +135340,6 @@ is_a: GO:1904038 ! regulation of iron export across plasma membrane intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:1903988 ! iron ion export across plasma membrane relationship: negatively_regulates GO:1903988 ! iron ion export across plasma membrane -created_by: kom creation_date: 2015-03-16T15:36:43Z [Term] @@ -132076,7 +135362,6 @@ is_a: GO:1904038 ! regulation of iron export across plasma membrane intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:1903988 ! iron ion export across plasma membrane relationship: positively_regulates GO:1903988 ! iron ion export across plasma membrane -created_by: kom creation_date: 2015-03-16T15:36:49Z [Term] @@ -132089,7 +135374,6 @@ is_a: GO:0050896 ! response to stimulus intersection_of: GO:0050896 ! response to stimulus intersection_of: has_primary_input CHEBI:27584 relationship: has_primary_input CHEBI:27584 -created_by: sl creation_date: 2015-03-16T23:07:53Z [Term] @@ -132101,7 +135385,6 @@ is_a: GO:0070887 ! cellular response to chemical stimulus is_a: GO:1904044 ! response to aldosterone intersection_of: GO:0070887 ! cellular response to chemical stimulus intersection_of: has_primary_input CHEBI:27584 -created_by: sl creation_date: 2015-03-16T23:07:59Z [Term] @@ -132114,7 +135397,6 @@ is_a: GO:0050678 ! regulation of epithelial cell proliferation intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:1990705 ! cholangiocyte proliferation relationship: regulates GO:1990705 ! cholangiocyte proliferation -created_by: sl creation_date: 2015-03-18T17:56:14Z [Term] @@ -132136,7 +135418,6 @@ is_a: GO:1904054 ! regulation of cholangiocyte proliferation intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:1990705 ! cholangiocyte proliferation relationship: negatively_regulates GO:1990705 ! cholangiocyte proliferation -created_by: sl creation_date: 2015-03-18T17:56:20Z [Term] @@ -132158,7 +135439,6 @@ is_a: GO:1904054 ! regulation of cholangiocyte proliferation intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:1990705 ! cholangiocyte proliferation relationship: positively_regulates GO:1990705 ! cholangiocyte proliferation -created_by: sl creation_date: 2015-03-18T17:56:26Z [Term] @@ -132185,7 +135465,6 @@ is_a: GO:0051930 ! regulation of sensory perception of pain intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0019233 ! sensory perception of pain relationship: negatively_regulates GO:0019233 ! sensory perception of pain -created_by: sl creation_date: 2015-03-18T20:33:57Z [Term] @@ -132212,7 +135491,6 @@ is_a: GO:0051930 ! regulation of sensory perception of pain intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0019233 ! sensory perception of pain relationship: positively_regulates GO:0019233 ! sensory perception of pain -created_by: sl creation_date: 2015-03-18T20:34:03Z [Term] @@ -132225,7 +135503,6 @@ is_a: GO:0034762 ! regulation of transmembrane transport intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0098655 ! monoatomic cation transmembrane transport relationship: regulates GO:0098655 ! monoatomic cation transmembrane transport -created_by: sl creation_date: 2015-03-18T21:11:43Z [Term] @@ -132242,7 +135519,6 @@ is_a: GO:1904062 ! regulation of monoatomic cation transmembrane transport intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0098655 ! monoatomic cation transmembrane transport relationship: negatively_regulates GO:0098655 ! monoatomic cation transmembrane transport -created_by: sl creation_date: 2015-03-18T21:11:50Z [Term] @@ -132259,7 +135535,6 @@ is_a: GO:1904062 ! regulation of monoatomic cation transmembrane transport intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0098655 ! monoatomic cation transmembrane transport relationship: positively_regulates GO:0098655 ! monoatomic cation transmembrane transport -created_by: sl creation_date: 2015-03-18T21:11:55Z [Term] @@ -132289,7 +135564,6 @@ is_a: GO:0007213 ! G protein-coupled acetylcholine receptor signaling pathway intersection_of: GO:0007213 ! G protein-coupled acetylcholine receptor signaling pathway intersection_of: part_of GO:0014057 ! positive regulation of acetylcholine secretion, neurotransmission relationship: part_of GO:0014057 ! positive regulation of acetylcholine secretion, neurotransmission -created_by: kmv creation_date: 2015-03-19T15:28:47Z [Term] @@ -132303,7 +135577,6 @@ is_a: GO:0048638 ! regulation of developmental growth intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0001834 ! trophectodermal cell proliferation relationship: regulates GO:0001834 ! trophectodermal cell proliferation -created_by: tb creation_date: 2015-03-20T16:55:56Z [Term] @@ -132325,7 +135598,6 @@ is_a: GO:1904073 ! regulation of trophectodermal cell proliferation intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0001834 ! trophectodermal cell proliferation relationship: negatively_regulates GO:0001834 ! trophectodermal cell proliferation -created_by: tb creation_date: 2015-03-20T16:56:02Z [Term] @@ -132347,7 +135619,6 @@ is_a: GO:1904073 ! regulation of trophectodermal cell proliferation intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0001834 ! trophectodermal cell proliferation relationship: positively_regulates GO:0001834 ! trophectodermal cell proliferation -created_by: tb creation_date: 2015-03-20T16:56:08Z [Term] @@ -132362,7 +135633,6 @@ is_a: GO:0008104 ! protein localization intersection_of: GO:0008104 ! protein localization intersection_of: has_target_end_location GO:0005902 ! microvillus relationship: has_target_end_location GO:0005902 ! microvillus -created_by: kmv creation_date: 2015-04-01T18:14:41Z [Term] @@ -132376,7 +135646,6 @@ intersection_of: GO:0005737 ! cytoplasm intersection_of: part_of GO:0030424 ! axon relationship: part_of GO:0030424 ! axon property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/14472" xsd:anyURI -created_by: sl creation_date: 2015-04-06T18:13:14Z [Term] @@ -132389,7 +135658,6 @@ is_a: GO:0050896 ! response to stimulus intersection_of: GO:0050896 ! response to stimulus intersection_of: has_primary_input CHEBI:9937 relationship: has_primary_input CHEBI:9937 -created_by: sl creation_date: 2015-04-06T19:39:42Z [Term] @@ -132401,7 +135669,6 @@ is_a: GO:0070887 ! cellular response to chemical stimulus is_a: GO:1904116 ! response to vasopressin intersection_of: GO:0070887 ! cellular response to chemical stimulus intersection_of: has_primary_input CHEBI:9937 -created_by: sl creation_date: 2015-04-06T19:39:48Z [Term] @@ -132414,7 +135681,6 @@ is_a: GO:2000027 ! regulation of animal organ morphogenesis intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0071600 ! otic vesicle morphogenesis relationship: regulates GO:0071600 ! otic vesicle morphogenesis -created_by: pga creation_date: 2015-04-07T14:00:56Z [Term] @@ -132432,7 +135698,6 @@ is_a: GO:1905331 ! negative regulation of morphogenesis of an epithelium intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0071600 ! otic vesicle morphogenesis relationship: negatively_regulates GO:0071600 ! otic vesicle morphogenesis -created_by: pga creation_date: 2015-04-07T14:01:02Z [Term] @@ -132450,7 +135715,6 @@ is_a: GO:1905332 ! positive regulation of morphogenesis of an epithelium intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0071600 ! otic vesicle morphogenesis relationship: positively_regulates GO:0071600 ! otic vesicle morphogenesis -created_by: pga creation_date: 2015-04-07T14:01:08Z [Term] @@ -132463,7 +135727,6 @@ is_a: GO:1905517 ! macrophage migration intersection_of: GO:0016477 ! cell migration intersection_of: results_in_movement_of CL:0000129 ! microglial cell relationship: results_in_movement_of CL:0000129 ! microglial cell -created_by: nc creation_date: 2015-04-10T16:04:49Z [Term] @@ -132476,7 +135739,6 @@ is_a: GO:1905521 ! regulation of macrophage migration intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:1904124 ! microglial cell migration relationship: regulates GO:1904124 ! microglial cell migration -created_by: nc creation_date: 2015-04-13T09:06:57Z [Term] @@ -132494,7 +135756,6 @@ is_a: GO:1905522 ! negative regulation of macrophage migration intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:1904124 ! microglial cell migration relationship: negatively_regulates GO:1904124 ! microglial cell migration -created_by: nc creation_date: 2015-04-13T09:07:03Z [Term] @@ -132512,7 +135773,6 @@ is_a: GO:1905523 ! positive regulation of macrophage migration intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:1904124 ! microglial cell migration relationship: positively_regulates GO:1904124 ! microglial cell migration -created_by: nc creation_date: 2015-04-13T09:07:11Z [Term] @@ -132531,7 +135791,6 @@ is_a: GO:1903538 ! regulation of meiotic cell cycle process involved in oocyte m intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:1903537 ! meiotic cell cycle process involved in oocyte maturation relationship: negatively_regulates GO:1903537 ! meiotic cell cycle process involved in oocyte maturation -created_by: tb creation_date: 2015-04-14T15:59:22Z [Term] @@ -132549,7 +135808,6 @@ is_a: GO:1903538 ! regulation of meiotic cell cycle process involved in oocyte m intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:1903537 ! meiotic cell cycle process involved in oocyte maturation relationship: positively_regulates GO:1903537 ! meiotic cell cycle process involved in oocyte maturation -created_by: tb creation_date: 2015-04-14T15:59:28Z [Term] @@ -132562,7 +135820,6 @@ is_a: GO:0002886 ! regulation of myeloid leukocyte mediated immunity intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0090634 ! microglial cell mediated cytotoxicity relationship: regulates GO:0090634 ! microglial cell mediated cytotoxicity -created_by: nc creation_date: 2015-04-15T08:05:29Z [Term] @@ -132580,7 +135837,6 @@ is_a: GO:1904149 ! regulation of microglial cell mediated cytotoxicity intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0090634 ! microglial cell mediated cytotoxicity relationship: negatively_regulates GO:0090634 ! microglial cell mediated cytotoxicity -created_by: nc creation_date: 2015-04-15T08:05:35Z [Term] @@ -132598,7 +135854,6 @@ is_a: GO:1904149 ! regulation of microglial cell mediated cytotoxicity intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0090634 ! microglial cell mediated cytotoxicity relationship: positively_regulates GO:0090634 ! microglial cell mediated cytotoxicity -created_by: nc creation_date: 2015-04-15T08:05:42Z [Term] @@ -132610,7 +135865,6 @@ is_a: GO:0033077 ! T cell differentiation in thymus intersection_of: GO:0030154 ! cell differentiation intersection_of: results_in_acquisition_of_features_of CL:0000806 ! DN2 thymocyte relationship: results_in_acquisition_of_features_of CL:0000806 ! DN2 thymocyte -created_by: dph creation_date: 2015-04-15T12:52:53Z [Term] @@ -132622,7 +135876,6 @@ is_a: GO:0033077 ! T cell differentiation in thymus intersection_of: GO:0030154 ! cell differentiation intersection_of: results_in_acquisition_of_features_of CL:0000807 ! DN3 thymocyte relationship: results_in_acquisition_of_features_of CL:0000807 ! DN3 thymocyte -created_by: dph creation_date: 2015-04-15T12:53:00Z [Term] @@ -132634,7 +135887,6 @@ is_a: GO:0033077 ! T cell differentiation in thymus intersection_of: GO:0030154 ! cell differentiation intersection_of: results_in_acquisition_of_features_of CL:0000808 ! DN4 thymocyte relationship: results_in_acquisition_of_features_of CL:0000808 ! DN4 thymocyte -created_by: dph creation_date: 2015-04-15T12:53:07Z [Term] @@ -132648,7 +135900,6 @@ intersection_of: GO:0022607 ! cellular component assembly intersection_of: results_in_assembly_of GO:1990716 ! axonemal central apparatus relationship: part_of GO:0035082 ! axoneme assembly relationship: results_in_assembly_of GO:1990716 ! axonemal central apparatus -created_by: krc creation_date: 2015-04-16T18:46:11Z [Term] @@ -132661,7 +135912,6 @@ is_a: GO:0120032 ! regulation of plasma membrane bounded cell projection assembl intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0032060 ! bleb assembly relationship: regulates GO:0032060 ! bleb assembly -created_by: als creation_date: 2015-04-23T09:32:19Z [Term] @@ -132683,7 +135933,6 @@ is_a: GO:1904170 ! regulation of bleb assembly intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0032060 ! bleb assembly relationship: negatively_regulates GO:0032060 ! bleb assembly -created_by: als creation_date: 2015-04-23T09:32:25Z [Term] @@ -132705,7 +135954,6 @@ is_a: GO:1904170 ! regulation of bleb assembly intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0032060 ! bleb assembly relationship: positively_regulates GO:0032060 ! bleb assembly -created_by: als creation_date: 2015-04-23T09:32:31Z [Term] @@ -132718,7 +135966,6 @@ is_a: GO:0050793 ! regulation of developmental process intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0060612 ! adipose tissue development relationship: regulates GO:0060612 ! adipose tissue development -created_by: sl creation_date: 2015-04-29T20:01:01Z [Term] @@ -132741,7 +135988,6 @@ is_a: GO:1904177 ! regulation of adipose tissue development intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0060612 ! adipose tissue development relationship: negatively_regulates GO:0060612 ! adipose tissue development -created_by: sl creation_date: 2015-04-29T20:01:07Z [Term] @@ -132764,7 +136010,6 @@ is_a: GO:1904177 ! regulation of adipose tissue development intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0060612 ! adipose tissue development relationship: positively_regulates GO:0060612 ! adipose tissue development -created_by: sl creation_date: 2015-04-29T20:01:13Z [Term] @@ -132779,7 +136024,6 @@ is_a: GO:1904035 ! regulation of epithelial cell apoptotic process intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:1902488 ! cholangiocyte apoptotic process relationship: regulates GO:1902488 ! cholangiocyte apoptotic process -created_by: sl creation_date: 2015-05-06T15:25:48Z [Term] @@ -132811,7 +136055,6 @@ is_a: GO:1904192 ! regulation of cholangiocyte apoptotic process intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:1902488 ! cholangiocyte apoptotic process relationship: negatively_regulates GO:1902488 ! cholangiocyte apoptotic process -created_by: sl creation_date: 2015-05-06T15:25:55Z [Term] @@ -132843,7 +136086,6 @@ is_a: GO:1904192 ! regulation of cholangiocyte apoptotic process intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:1902488 ! cholangiocyte apoptotic process relationship: positively_regulates GO:1902488 ! cholangiocyte apoptotic process -created_by: sl creation_date: 2015-05-06T15:26:00Z [Term] @@ -132855,7 +136097,6 @@ is_a: GO:0050678 ! regulation of epithelial cell proliferation intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:1990739 ! granulosa cell proliferation relationship: regulates GO:1990739 ! granulosa cell proliferation -created_by: sl creation_date: 2015-05-07T17:02:25Z [Term] @@ -132872,7 +136113,6 @@ is_a: GO:1904195 ! regulation of granulosa cell proliferation intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:1990739 ! granulosa cell proliferation relationship: negatively_regulates GO:1990739 ! granulosa cell proliferation -created_by: sl creation_date: 2015-05-07T17:02:34Z [Term] @@ -132889,7 +136129,6 @@ is_a: GO:1904195 ! regulation of granulosa cell proliferation intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:1990739 ! granulosa cell proliferation relationship: positively_regulates GO:1990739 ! granulosa cell proliferation -created_by: sl creation_date: 2015-05-07T17:02:40Z [Term] @@ -132902,7 +136141,6 @@ is_a: GO:0014743 ! regulation of muscle hypertrophy intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0014734 ! skeletal muscle hypertrophy relationship: regulates GO:0014734 ! skeletal muscle hypertrophy -created_by: sl creation_date: 2015-05-08T17:38:13Z [Term] @@ -132920,7 +136158,6 @@ is_a: GO:1904204 ! regulation of skeletal muscle hypertrophy intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0014734 ! skeletal muscle hypertrophy relationship: negatively_regulates GO:0014734 ! skeletal muscle hypertrophy -created_by: sl creation_date: 2015-05-08T17:38:19Z [Term] @@ -132938,7 +136175,6 @@ is_a: GO:1904204 ! regulation of skeletal muscle hypertrophy intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0014734 ! skeletal muscle hypertrophy relationship: positively_regulates GO:0014734 ! skeletal muscle hypertrophy -created_by: sl creation_date: 2015-05-08T17:38:25Z [Term] @@ -132950,7 +136186,6 @@ is_a: GO:0030154 ! cell differentiation intersection_of: GO:0030154 ! cell differentiation intersection_of: results_in_acquisition_of_features_of CL:0000669 ! pericyte relationship: results_in_acquisition_of_features_of CL:0000669 ! pericyte -created_by: dph creation_date: 2015-05-15T14:50:13Z [Term] @@ -132960,12 +136195,10 @@ namespace: biological_process def: "Any process that modulates the frequency, rate or extent of bile acid metabolic process." [GO_REF:0000058, GOC:bf, GOC:TermGenie] synonym: "regulation of bile acid metabolism" EXACT [GOC:TermGenie] is_a: GO:0019218 ! regulation of steroid metabolic process -is_a: GO:0031323 ! regulation of cellular metabolic process is_a: GO:0062012 ! regulation of small molecule metabolic process intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0008206 ! bile acid metabolic process relationship: regulates GO:0008206 ! bile acid metabolic process -created_by: bf creation_date: 2015-05-20T11:04:28Z [Term] @@ -132982,14 +136215,12 @@ synonym: "downregulation of bile acid metabolism" EXACT [GOC:TermGenie] synonym: "inhibition of bile acid metabolic process" NARROW [GOC:TermGenie] synonym: "inhibition of bile acid metabolism" NARROW [GOC:TermGenie] synonym: "negative regulation of bile acid metabolism" EXACT [GOC:TermGenie] -is_a: GO:0031324 ! negative regulation of cellular metabolic process is_a: GO:0045939 ! negative regulation of steroid metabolic process is_a: GO:0062014 ! negative regulation of small molecule metabolic process is_a: GO:1904251 ! regulation of bile acid metabolic process intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0008206 ! bile acid metabolic process relationship: negatively_regulates GO:0008206 ! bile acid metabolic process -created_by: bf creation_date: 2015-05-20T11:04:35Z [Term] @@ -133006,14 +136237,12 @@ synonym: "up-regulation of bile acid metabolic process" EXACT [GOC:TermGenie] synonym: "up-regulation of bile acid metabolism" EXACT [GOC:TermGenie] synonym: "upregulation of bile acid metabolic process" EXACT [GOC:TermGenie] synonym: "upregulation of bile acid metabolism" EXACT [GOC:TermGenie] -is_a: GO:0031325 ! positive regulation of cellular metabolic process is_a: GO:0045940 ! positive regulation of steroid metabolic process is_a: GO:0062013 ! positive regulation of small molecule metabolic process is_a: GO:1904251 ! regulation of bile acid metabolic process intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0008206 ! bile acid metabolic process relationship: positively_regulates GO:0008206 ! bile acid metabolic process -created_by: bf creation_date: 2015-05-20T11:04:40Z [Term] @@ -133030,39 +136259,8 @@ is_a: GO:0034759 ! regulation of iron ion transmembrane transport intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0005381 ! iron ion transmembrane transporter activity relationship: regulates GO:0005381 ! iron ion transmembrane transporter activity -created_by: kom creation_date: 2015-05-20T14:05:00Z -[Term] -id: GO:1904255 -name: negative regulation of iron ion transmembrane transporter activity -namespace: biological_process -def: "Any process that stops, prevents or reduces the frequency, rate or extent of an iron transmembrane transporter activity." [GO_REF:0000059, GOC:BHF, GOC:kom, GOC:TermGenie, PMID:15514116] -subset: gocheck_obsoletion_candidate -synonym: "down regulation of iron cation channel activity" EXACT [GOC:TermGenie] -synonym: "down regulation of iron channel activity" EXACT [GOC:TermGenie] -synonym: "down regulation of iron-specific channel activity" EXACT [GOC:TermGenie] -synonym: "down-regulation of iron cation channel activity" EXACT [GOC:TermGenie] -synonym: "down-regulation of iron channel activity" EXACT [GOC:TermGenie] -synonym: "down-regulation of iron-specific channel activity" EXACT [GOC:TermGenie] -synonym: "downregulation of iron cation channel activity" EXACT [GOC:TermGenie] -synonym: "downregulation of iron channel activity" EXACT [GOC:TermGenie] -synonym: "downregulation of iron-specific channel activity" EXACT [GOC:TermGenie] -synonym: "inhibition of iron cation channel activity" NARROW [GOC:TermGenie] -synonym: "inhibition of iron channel activity" NARROW [GOC:TermGenie] -synonym: "inhibition of iron-specific channel activity" NARROW [GOC:TermGenie] -synonym: "negative regulation of iron cation channel activity" EXACT [GOC:TermGenie] -synonym: "negative regulation of iron channel activity" EXACT [] -synonym: "negative regulation of iron-specific channel activity" EXACT [GOC:TermGenie] -is_a: GO:0032410 ! negative regulation of transporter activity -is_a: GO:0034760 ! negative regulation of iron ion transmembrane transport -is_a: GO:1904254 ! regulation of iron ion transmembrane transporter activity -intersection_of: GO:0065007 ! biological regulation -intersection_of: negatively_regulates GO:0005381 ! iron ion transmembrane transporter activity -relationship: negatively_regulates GO:0005381 ! iron ion transmembrane transporter activity -created_by: kom -creation_date: 2015-05-20T14:05:06Z - [Term] id: GO:1904266 name: regulation of Schwann cell chemotaxis @@ -133073,7 +136271,6 @@ is_a: GO:1900147 ! regulation of Schwann cell migration intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:1990751 ! Schwann cell chemotaxis relationship: regulates GO:1990751 ! Schwann cell chemotaxis -created_by: sl creation_date: 2015-05-28T17:47:41Z [Term] @@ -133091,7 +136288,6 @@ is_a: GO:1904266 ! regulation of Schwann cell chemotaxis intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:1990751 ! Schwann cell chemotaxis relationship: negatively_regulates GO:1990751 ! Schwann cell chemotaxis -created_by: sl creation_date: 2015-05-28T17:47:48Z [Term] @@ -133109,7 +136305,6 @@ is_a: GO:1904266 ! regulation of Schwann cell chemotaxis intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:1990751 ! Schwann cell chemotaxis relationship: positively_regulates GO:1990751 ! Schwann cell chemotaxis -created_by: sl creation_date: 2015-05-28T17:47:55Z [Term] @@ -133130,7 +136325,6 @@ is_a: GO:0099738 ! cell cortex region intersection_of: GO:0099738 ! cell cortex region intersection_of: part_of GO:0031252 ! cell leading edge relationship: part_of GO:0031252 ! cell leading edge -created_by: kmv creation_date: 2015-05-28T19:16:03Z [Term] @@ -133142,7 +136336,6 @@ is_a: GO:0006940 ! regulation of smooth muscle contraction intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0014831 ! gastro-intestinal system smooth muscle contraction relationship: regulates GO:0014831 ! gastro-intestinal system smooth muscle contraction -created_by: sl creation_date: 2015-06-09T23:18:42Z [Term] @@ -133159,7 +136352,6 @@ is_a: GO:1904304 ! regulation of gastro-intestinal system smooth muscle contract intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0014831 ! gastro-intestinal system smooth muscle contraction relationship: negatively_regulates GO:0014831 ! gastro-intestinal system smooth muscle contraction -created_by: sl creation_date: 2015-06-09T23:18:48Z [Term] @@ -133176,7 +136368,6 @@ is_a: GO:1904304 ! regulation of gastro-intestinal system smooth muscle contract intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0014831 ! gastro-intestinal system smooth muscle contraction relationship: positively_regulates GO:0014831 ! gastro-intestinal system smooth muscle contraction -created_by: sl creation_date: 2015-06-09T23:18:54Z [Term] @@ -133192,7 +136383,6 @@ is_a: GO:0022824 ! transmitter-gated monoatomic ion channel activity is_a: GO:0099529 ! neurotransmitter receptor activity involved in regulation of postsynaptic membrane potential intersection_of: GO:0022824 ! transmitter-gated monoatomic ion channel activity intersection_of: part_of GO:0060078 ! regulation of postsynaptic membrane potential -created_by: dos creation_date: 2015-06-10T18:02:07Z [Term] @@ -133208,7 +136398,6 @@ is_a: GO:0098801 ! regulation of renal system process intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0060083 ! smooth muscle contraction involved in micturition relationship: regulates GO:0060083 ! smooth muscle contraction involved in micturition -created_by: sl creation_date: 2015-06-10T18:46:11Z [Term] @@ -133235,7 +136424,6 @@ is_a: GO:1904318 ! regulation of smooth muscle contraction involved in micturiti intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0060083 ! smooth muscle contraction involved in micturition relationship: negatively_regulates GO:0060083 ! smooth muscle contraction involved in micturition -created_by: sl creation_date: 2015-06-10T18:46:17Z [Term] @@ -133262,7 +136450,6 @@ is_a: GO:1904318 ! regulation of smooth muscle contraction involved in micturiti intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0060083 ! smooth muscle contraction involved in micturition relationship: positively_regulates GO:0060083 ! smooth muscle contraction involved in micturition -created_by: sl creation_date: 2015-06-10T18:46:23Z [Term] @@ -133274,7 +136461,6 @@ is_a: GO:0045664 ! regulation of neuron differentiation intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0071542 ! dopaminergic neuron differentiation relationship: regulates GO:0071542 ! dopaminergic neuron differentiation -created_by: sl creation_date: 2015-06-11T18:06:19Z [Term] @@ -133291,7 +136477,6 @@ is_a: GO:1904338 ! regulation of dopaminergic neuron differentiation intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0071542 ! dopaminergic neuron differentiation relationship: negatively_regulates GO:0071542 ! dopaminergic neuron differentiation -created_by: sl creation_date: 2015-06-11T18:06:25Z [Term] @@ -133308,7 +136493,6 @@ is_a: GO:1904338 ! regulation of dopaminergic neuron differentiation intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0071542 ! dopaminergic neuron differentiation relationship: positively_regulates GO:0071542 ! dopaminergic neuron differentiation -created_by: sl creation_date: 2015-06-11T18:06:32Z [Term] @@ -133320,7 +136504,6 @@ is_a: GO:1904304 ! regulation of gastro-intestinal system smooth muscle contract intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:1990765 ! colon smooth muscle contraction relationship: regulates GO:1990765 ! colon smooth muscle contraction -created_by: sl creation_date: 2015-06-11T21:16:58Z [Term] @@ -133337,7 +136520,6 @@ is_a: GO:1904341 ! regulation of colon smooth muscle contraction intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:1990765 ! colon smooth muscle contraction relationship: negatively_regulates GO:1990765 ! colon smooth muscle contraction -created_by: sl creation_date: 2015-06-11T21:17:05Z [Term] @@ -133354,7 +136536,6 @@ is_a: GO:1904341 ! regulation of colon smooth muscle contraction intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:1990765 ! colon smooth muscle contraction relationship: positively_regulates GO:1990765 ! colon smooth muscle contraction -created_by: sl creation_date: 2015-06-11T21:17:11Z [Term] @@ -133367,7 +136548,6 @@ is_a: GO:1903522 ! regulation of blood circulation intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:1990768 ! gastric mucosal blood circulation relationship: regulates GO:1990768 ! gastric mucosal blood circulation -created_by: sl creation_date: 2015-06-11T21:20:31Z [Term] @@ -133389,7 +136569,6 @@ is_a: GO:1904344 ! regulation of gastric mucosal blood circulation intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:1990768 ! gastric mucosal blood circulation relationship: negatively_regulates GO:1990768 ! gastric mucosal blood circulation -created_by: sl creation_date: 2015-06-11T21:20:44Z [Term] @@ -133411,7 +136590,6 @@ is_a: GO:1904344 ! regulation of gastric mucosal blood circulation intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:1990768 ! gastric mucosal blood circulation relationship: positively_regulates GO:1990768 ! gastric mucosal blood circulation -created_by: sl creation_date: 2015-06-11T21:20:50Z [Term] @@ -133423,7 +136601,6 @@ is_a: GO:1904304 ! regulation of gastro-intestinal system smooth muscle contract intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:1990770 ! small intestine smooth muscle contraction relationship: regulates GO:1990770 ! small intestine smooth muscle contraction -created_by: sl creation_date: 2015-06-11T21:37:34Z [Term] @@ -133440,7 +136617,6 @@ is_a: GO:1904347 ! regulation of small intestine smooth muscle contraction intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:1990770 ! small intestine smooth muscle contraction relationship: negatively_regulates GO:1990770 ! small intestine smooth muscle contraction -created_by: sl creation_date: 2015-06-11T21:37:40Z [Term] @@ -133457,7 +136633,6 @@ is_a: GO:1904347 ! regulation of small intestine smooth muscle contraction intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:1990770 ! small intestine smooth muscle contraction relationship: positively_regulates GO:1990770 ! small intestine smooth muscle contraction -created_by: sl creation_date: 2015-06-11T21:37:46Z [Term] @@ -133473,7 +136648,6 @@ is_a: GO:0042176 ! regulation of protein catabolic process intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0007039 ! protein catabolic process in the vacuole relationship: regulates GO:0007039 ! protein catabolic process in the vacuole -created_by: rl creation_date: 2015-06-12T09:10:36Z [Term] @@ -133510,7 +136684,6 @@ is_a: GO:1904350 ! regulation of protein catabolic process in the vacuole intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0007039 ! protein catabolic process in the vacuole relationship: negatively_regulates GO:0007039 ! protein catabolic process in the vacuole -created_by: rl creation_date: 2015-06-12T09:10:42Z [Term] @@ -133547,7 +136720,6 @@ is_a: GO:1904350 ! regulation of protein catabolic process in the vacuole intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0007039 ! protein catabolic process in the vacuole relationship: positively_regulates GO:0007039 ! protein catabolic process in the vacuole -created_by: rl creation_date: 2015-06-12T09:10:49Z [Term] @@ -133559,7 +136731,6 @@ is_a: GO:0090276 ! regulation of peptide hormone secretion intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0036161 ! calcitonin secretion relationship: regulates GO:0036161 ! calcitonin secretion -created_by: sl creation_date: 2015-06-15T17:54:52Z [Term] @@ -133576,7 +136747,6 @@ is_a: GO:1904362 ! regulation of calcitonin secretion intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0036161 ! calcitonin secretion relationship: negatively_regulates GO:0036161 ! calcitonin secretion -created_by: sl creation_date: 2015-06-15T17:54:58Z [Term] @@ -133593,7 +136763,6 @@ is_a: GO:1904362 ! regulation of calcitonin secretion intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0036161 ! calcitonin secretion relationship: positively_regulates GO:0036161 ! calcitonin secretion -created_by: sl creation_date: 2015-06-15T17:55:05Z [Term] @@ -133605,7 +136774,6 @@ is_a: GO:0032880 ! regulation of protein localization intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:1990778 ! protein localization to cell periphery relationship: regulates GO:1990778 ! protein localization to cell periphery -created_by: sl creation_date: 2015-06-22T22:09:25Z [Term] @@ -133622,7 +136790,6 @@ is_a: GO:1904375 ! regulation of protein localization to cell periphery intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:1990778 ! protein localization to cell periphery relationship: negatively_regulates GO:1990778 ! protein localization to cell periphery -created_by: sl creation_date: 2015-06-22T22:09:32Z [Term] @@ -133639,7 +136806,6 @@ is_a: GO:1904375 ! regulation of protein localization to cell periphery intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:1990778 ! protein localization to cell periphery relationship: positively_regulates GO:1990778 ! protein localization to cell periphery -created_by: sl creation_date: 2015-06-22T22:09:37Z [Term] @@ -133651,7 +136817,6 @@ is_a: GO:0060040 ! retinal bipolar neuron differentiation intersection_of: GO:0030154 ! cell differentiation intersection_of: results_in_acquisition_of_features_of CL:0000751 ! rod bipolar cell relationship: results_in_acquisition_of_features_of CL:0000751 ! rod bipolar cell -created_by: sl creation_date: 2015-06-23T19:01:11Z [Term] @@ -133665,7 +136830,6 @@ is_a: GO:0060040 ! retinal bipolar neuron differentiation intersection_of: GO:0030154 ! cell differentiation intersection_of: results_in_acquisition_of_features_of CL:0000752 ! cone retinal bipolar cell relationship: results_in_acquisition_of_features_of CL:0000752 ! cone retinal bipolar cell -created_by: sl creation_date: 2015-06-23T19:01:16Z [Term] @@ -133680,7 +136844,6 @@ is_a: GO:0050807 ! regulation of synapse organization intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0007528 ! neuromuscular junction development relationship: regulates GO:0007528 ! neuromuscular junction development -created_by: sl creation_date: 2015-06-23T19:23:42Z [Term] @@ -133712,7 +136875,6 @@ is_a: GO:1905809 ! negative regulation of synapse organization intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0007528 ! neuromuscular junction development relationship: negatively_regulates GO:0007528 ! neuromuscular junction development -created_by: sl creation_date: 2015-06-23T19:23:48Z [Term] @@ -133744,9 +136906,50 @@ is_a: GO:1904396 ! regulation of neuromuscular junction development intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0007528 ! neuromuscular junction development relationship: positively_regulates GO:0007528 ! neuromuscular junction development -created_by: sl creation_date: 2015-06-23T19:23:54Z +[Term] +id: GO:1904406 +name: negative regulation of nitric oxide metabolic process +namespace: biological_process +def: "Any process that stops, prevents or reduces the frequency, rate or extent of nitric oxide metabolic process." [GO_REF:0000058, GOC:TermGenie, PMID:11991626] +synonym: "down regulation of nitric oxide metabolic process" EXACT [GOC:TermGenie] +synonym: "down regulation of nitric oxide metabolism" EXACT [GOC:TermGenie] +synonym: "down-regulation of nitric oxide metabolic process" EXACT [GOC:TermGenie] +synonym: "down-regulation of nitric oxide metabolism" EXACT [GOC:TermGenie] +synonym: "downregulation of nitric oxide metabolic process" EXACT [GOC:TermGenie] +synonym: "downregulation of nitric oxide metabolism" EXACT [GOC:TermGenie] +synonym: "inhibition of nitric oxide metabolic process" NARROW [GOC:TermGenie] +synonym: "inhibition of nitric oxide metabolism" NARROW [GOC:TermGenie] +synonym: "negative regulation of nitric oxide metabolism" EXACT [GOC:TermGenie] +is_a: GO:0009892 ! negative regulation of metabolic process +is_a: GO:0080164 ! regulation of nitric oxide metabolic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0046209 ! nitric oxide metabolic process +relationship: negatively_regulates GO:0046209 ! nitric oxide metabolic process +creation_date: 2015-06-24T20:56:41Z + +[Term] +id: GO:1904407 +name: positive regulation of nitric oxide metabolic process +namespace: biological_process +def: "Any process that activates or increases the frequency, rate or extent of nitric oxide metabolic process." [GO_REF:0000058, GOC:TermGenie, PMID:11991626] +synonym: "activation of nitric oxide metabolic process" NARROW [GOC:TermGenie] +synonym: "activation of nitric oxide metabolism" NARROW [GOC:TermGenie] +synonym: "positive regulation of nitric oxide metabolism" EXACT [GOC:TermGenie] +synonym: "up regulation of nitric oxide metabolic process" EXACT [GOC:TermGenie] +synonym: "up regulation of nitric oxide metabolism" EXACT [GOC:TermGenie] +synonym: "up-regulation of nitric oxide metabolic process" EXACT [GOC:TermGenie] +synonym: "up-regulation of nitric oxide metabolism" EXACT [GOC:TermGenie] +synonym: "upregulation of nitric oxide metabolic process" EXACT [GOC:TermGenie] +synonym: "upregulation of nitric oxide metabolism" EXACT [GOC:TermGenie] +is_a: GO:0009893 ! positive regulation of metabolic process +is_a: GO:0080164 ! regulation of nitric oxide metabolic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0046209 ! nitric oxide metabolic process +relationship: positively_regulates GO:0046209 ! nitric oxide metabolic process +creation_date: 2015-06-24T20:56:47Z + [Term] id: GO:1904408 name: melatonin binding @@ -133757,7 +136960,6 @@ is_a: GO:0005488 ! binding intersection_of: GO:0005488 ! binding intersection_of: has_primary_input CHEBI:16796 relationship: has_primary_input CHEBI:16796 -created_by: mr creation_date: 2015-06-25T19:19:53Z [Term] @@ -133771,7 +136973,6 @@ is_a: GO:0033043 ! regulation of organelle organization intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0033363 ! secretory granule organization relationship: regulates GO:0033363 ! secretory granule organization -created_by: sl creation_date: 2015-06-25T19:40:42Z [Term] @@ -133798,7 +136999,6 @@ is_a: GO:1904409 ! regulation of secretory granule organization intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0033363 ! secretory granule organization relationship: negatively_regulates GO:0033363 ! secretory granule organization -created_by: sl creation_date: 2015-06-25T19:40:49Z [Term] @@ -133825,7 +137025,6 @@ is_a: GO:1904409 ! regulation of secretory granule organization intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0033363 ! secretory granule organization relationship: positively_regulates GO:0033363 ! secretory granule organization -created_by: sl creation_date: 2015-06-25T19:40:55Z [Term] @@ -133837,7 +137036,6 @@ is_a: GO:0050793 ! regulation of developmental process intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0003231 ! cardiac ventricle development relationship: regulates GO:0003231 ! cardiac ventricle development -created_by: sl creation_date: 2015-06-25T19:52:15Z [Term] @@ -133855,7 +137053,6 @@ is_a: GO:1904412 ! regulation of cardiac ventricle development intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0003231 ! cardiac ventricle development relationship: negatively_regulates GO:0003231 ! cardiac ventricle development -created_by: sl creation_date: 2015-06-25T19:52:21Z [Term] @@ -133873,7 +137070,6 @@ is_a: GO:1904412 ! regulation of cardiac ventricle development intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0003231 ! cardiac ventricle development relationship: positively_regulates GO:0003231 ! cardiac ventricle development -created_by: sl creation_date: 2015-06-25T19:52:27Z [Term] @@ -133901,14 +137097,12 @@ is_a: GO:1903169 ! regulation of calcium ion transmembrane transport intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0070588 ! calcium ion transmembrane transport relationship: positively_regulates GO:0070588 ! calcium ion transmembrane transport -created_by: sl creation_date: 2015-07-02T20:44:25Z [Term] id: GO:1904438 name: regulation of iron ion import across plasma membrane namespace: biological_process -alt_id: GO:1903989 def: "Any process that modulates the frequency, rate or extent of iron ions import across plasma membrane." [GO_REF:0000058, GOC:BHF, GOC:kom, GOC:TermGenie, PMID:18353247] synonym: "regulation of ferrous ion import into cell" RELATED [GOC:TermGenie] synonym: "regulation of ferrous iron import across plasma membrane" RELATED [] @@ -133918,14 +137112,12 @@ is_a: GO:0060341 ! regulation of cellular localization intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0098711 ! iron ion import across plasma membrane relationship: regulates GO:0098711 ! iron ion import across plasma membrane -created_by: rl creation_date: 2015-03-04T14:37:36Z [Term] id: GO:1904439 name: negative regulation of iron ion import across plasma membrane namespace: biological_process -alt_id: GO:1903990 def: "Any process that stops, prevents or reduces the frequency, rate or extent of iron ions import across plasma membrane." [GO_REF:0000058, GOC:BHF, GOC:kom, GOC:TermGenie, PMID:18353247] synonym: "down regulation of ferrous ion import into cell" RELATED [GOC:TermGenie] synonym: "down regulation of ferrous iron import across plasma membrane" RELATED [GOC:TermGenie] @@ -133943,14 +137135,12 @@ is_a: GO:1904438 ! regulation of iron ion import across plasma membrane intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0098711 ! iron ion import across plasma membrane relationship: negatively_regulates GO:0098711 ! iron ion import across plasma membrane -created_by: rl creation_date: 2015-07-06T13:49:58Z [Term] id: GO:1904440 name: positive regulation of iron ion import across plasma membrane namespace: biological_process -alt_id: GO:1903991 def: "Any process that activates or increases the frequency, rate or extent of iron ions import across plasma membrane." [GO_REF:0000058, GOC:BHF, GOC:kom, GOC:TermGenie, PMID:18353247] synonym: "activation of ferrous ion import into cell" NARROW [GOC:TermGenie] synonym: "activation of ferrous iron import across plasma membrane" NARROW [GOC:TermGenie] @@ -133968,7 +137158,6 @@ is_a: GO:1904438 ! regulation of iron ion import across plasma membrane intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0098711 ! iron ion import across plasma membrane relationship: positively_regulates GO:0098711 ! iron ion import across plasma membrane -created_by: rl creation_date: 2015-07-06T13:50:04Z [Term] @@ -133991,7 +137180,6 @@ is_a: GO:0098908 ! regulation of neuronal action potential intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0019228 ! neuronal action potential relationship: negatively_regulates GO:0019228 ! neuronal action potential -created_by: sl creation_date: 2015-07-09T18:02:40Z [Term] @@ -134014,7 +137202,6 @@ is_a: GO:0098908 ! regulation of neuronal action potential intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0019228 ! neuronal action potential relationship: positively_regulates GO:0019228 ! neuronal action potential -created_by: sl creation_date: 2015-07-09T18:02:46Z [Term] @@ -134026,7 +137213,6 @@ is_a: GO:0048732 ! gland development intersection_of: GO:0048856 ! anatomical structure development intersection_of: results_in_development_of UBERON:0012478 ! cloacal gland relationship: results_in_development_of UBERON:0012478 ! cloacal gland -created_by: mr creation_date: 2015-07-15T22:14:39Z [Term] @@ -134041,7 +137227,6 @@ is_a: GO:0061512 ! protein localization to cilium intersection_of: GO:0008104 ! protein localization intersection_of: has_target_end_location GO:0035869 ! ciliary transition zone relationship: has_target_end_location GO:0035869 ! ciliary transition zone -created_by: kmv creation_date: 2015-07-17T20:43:21Z [Term] @@ -134056,7 +137241,6 @@ is_a: GO:0006915 ! apoptotic process intersection_of: GO:0006915 ! apoptotic process intersection_of: occurs_in CL:0000186 ! myofibroblast cell relationship: occurs_in CL:0000186 ! myofibroblast cell -created_by: sl creation_date: 2015-07-28T18:29:08Z [Term] @@ -134071,7 +137255,6 @@ is_a: GO:0042981 ! regulation of apoptotic process intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:1904516 ! myofibroblast cell apoptotic process relationship: regulates GO:1904516 ! myofibroblast cell apoptotic process -created_by: sl creation_date: 2015-07-29T15:52:14Z [Term] @@ -134103,7 +137286,6 @@ is_a: GO:1904520 ! regulation of myofibroblast cell apoptotic process intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:1904516 ! myofibroblast cell apoptotic process relationship: negatively_regulates GO:1904516 ! myofibroblast cell apoptotic process -created_by: sl creation_date: 2015-07-29T15:52:20Z [Term] @@ -134135,7 +137317,6 @@ is_a: GO:1904520 ! regulation of myofibroblast cell apoptotic process intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:1904516 ! myofibroblast cell apoptotic process relationship: positively_regulates GO:1904516 ! myofibroblast cell apoptotic process -created_by: sl creation_date: 2015-07-29T15:52:26Z [Term] @@ -134150,7 +137331,6 @@ is_a: GO:0043393 ! regulation of protein binding intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0008017 ! microtubule binding relationship: regulates GO:0008017 ! microtubule binding -created_by: als creation_date: 2015-07-30T10:32:13Z [Term] @@ -134178,7 +137358,6 @@ is_a: GO:1904526 ! regulation of microtubule binding intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0008017 ! microtubule binding relationship: negatively_regulates GO:0008017 ! microtubule binding -created_by: als creation_date: 2015-07-30T10:32:29Z [Term] @@ -134206,7 +137385,6 @@ is_a: GO:1904526 ! regulation of microtubule binding intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0008017 ! microtubule binding relationship: positively_regulates GO:0008017 ! microtubule binding -created_by: als creation_date: 2015-07-30T10:32:36Z [Term] @@ -134220,7 +137398,6 @@ is_a: GO:0050896 ! response to stimulus intersection_of: GO:0050896 ! response to stimulus intersection_of: has_primary_input CHEBI:17089 relationship: has_primary_input CHEBI:17089 -created_by: sl creation_date: 2015-08-20T16:46:24Z [Term] @@ -134233,7 +137410,6 @@ is_a: GO:0070887 ! cellular response to chemical stimulus is_a: GO:1904587 ! response to glycoprotein intersection_of: GO:0070887 ! cellular response to chemical stimulus intersection_of: has_primary_input CHEBI:17089 -created_by: sl creation_date: 2015-08-20T16:46:30Z [Term] @@ -134255,7 +137431,6 @@ intersection_of: capable_of GO:0022850 ! serotonin-gated monoatomic cation chann relationship: capable_of GO:0022850 ! serotonin-gated monoatomic cation channel activity relationship: capable_of_part_of GO:0007210 ! serotonin receptor signaling pathway property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/12942" xsd:anyURI -created_by: bhm creation_date: 2015-08-26T13:19:49Z [Term] @@ -134272,7 +137447,6 @@ is_a: GO:0006915 ! apoptotic process intersection_of: GO:0006915 ! apoptotic process intersection_of: occurs_in CL:0000136 ! adipocyte relationship: occurs_in CL:0000136 ! adipocyte -created_by: sl creation_date: 2015-08-27T18:13:06Z [Term] @@ -134286,7 +137460,6 @@ is_a: GO:0060092 ! regulation of synaptic transmission, glycinergic intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0061537 ! glycine secretion, neurotransmission relationship: regulates GO:0061537 ! glycine secretion, neurotransmission -created_by: hjd creation_date: 2015-08-27T20:03:38Z [Term] @@ -134305,7 +137478,6 @@ is_a: GO:1904624 ! regulation of glycine secretion, neurotransmission intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0061537 ! glycine secretion, neurotransmission relationship: negatively_regulates GO:0061537 ! glycine secretion, neurotransmission -created_by: hjd creation_date: 2015-08-27T20:03:44Z [Term] @@ -134324,7 +137496,6 @@ is_a: GO:1904624 ! regulation of glycine secretion, neurotransmission intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0061537 ! glycine secretion, neurotransmission relationship: positively_regulates GO:0061537 ! glycine secretion, neurotransmission -created_by: hjd creation_date: 2015-08-27T20:03:49Z [Term] @@ -134342,7 +137513,6 @@ intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:1903210 ! podocyte apoptotic process relationship: regulates GO:1903210 ! podocyte apoptotic process property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/23000" xsd:anyURI -created_by: sl creation_date: 2015-08-28T14:14:44Z [Term] @@ -134385,7 +137555,6 @@ intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:1903210 ! podocyte apoptotic process relationship: negatively_regulates GO:1903210 ! podocyte apoptotic process property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/23000" xsd:anyURI -created_by: sl creation_date: 2015-08-28T14:14:50Z [Term] @@ -134428,7 +137597,6 @@ intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:1903210 ! podocyte apoptotic process relationship: positively_regulates GO:1903210 ! podocyte apoptotic process property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/23000" xsd:anyURI -created_by: sl creation_date: 2015-08-28T14:14:56Z [Term] @@ -134445,7 +137613,6 @@ is_a: GO:0042981 ! regulation of apoptotic process intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:1904606 ! fat cell apoptotic process relationship: regulates GO:1904606 ! fat cell apoptotic process -created_by: sl creation_date: 2015-08-31T20:59:28Z [Term] @@ -134487,7 +137654,6 @@ is_a: GO:1904649 ! regulation of fat cell apoptotic process intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:1904606 ! fat cell apoptotic process relationship: negatively_regulates GO:1904606 ! fat cell apoptotic process -created_by: sl creation_date: 2015-08-31T20:59:34Z [Term] @@ -134529,7 +137695,6 @@ is_a: GO:1904649 ! regulation of fat cell apoptotic process intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:1904606 ! fat cell apoptotic process relationship: positively_regulates GO:1904606 ! fat cell apoptotic process -created_by: sl creation_date: 2015-08-31T20:59:40Z [Term] @@ -134543,7 +137708,6 @@ is_a: GO:0050793 ! regulation of developmental process intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0048286 ! lung alveolus development relationship: regulates GO:0048286 ! lung alveolus development -created_by: sl creation_date: 2015-09-03T22:44:44Z [Term] @@ -134571,7 +137735,6 @@ is_a: GO:1904653 ! regulation of lung alveolus development intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0048286 ! lung alveolus development relationship: negatively_regulates GO:0048286 ! lung alveolus development -created_by: sl creation_date: 2015-09-03T22:44:50Z [Term] @@ -134599,14 +137762,12 @@ is_a: GO:1904653 ! regulation of lung alveolus development intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0048286 ! lung alveolus development relationship: positively_regulates GO:0048286 ! lung alveolus development -created_by: sl creation_date: 2015-09-03T22:44:56Z [Term] id: GO:1904659 name: D-glucose transmembrane transport namespace: biological_process -alt_id: GO:0015758 def: "The process in which D-glucose is transported across a membrane." [GO_REF:0000069, GOC:TermGenie, PMID:9090050] synonym: "glucose transmembrane transport" EXACT [] synonym: "glucose transport" RELATED [] @@ -134615,7 +137776,6 @@ intersection_of: GO:0006810 ! transport intersection_of: has_primary_input CHEBI:4167 intersection_of: results_in_transport_across GO:0016020 ! membrane relationship: has_primary_input CHEBI:4167 -created_by: vw creation_date: 2015-09-04T17:20:16Z [Term] @@ -134636,7 +137796,6 @@ is_a: GO:0045596 ! negative regulation of cell differentiation intersection_of: GO:0045596 ! negative regulation of cell differentiation intersection_of: part_of GO:0019827 ! stem cell population maintenance relationship: part_of GO:0019827 ! stem cell population maintenance -created_by: tb creation_date: 2015-09-12T00:46:08Z [Term] @@ -134648,7 +137807,6 @@ is_a: GO:2000036 ! regulation of stem cell population maintenance intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0035019 ! somatic stem cell population maintenance relationship: regulates GO:0035019 ! somatic stem cell population maintenance -created_by: rph creation_date: 2015-09-14T08:40:19Z [Term] @@ -134665,7 +137823,6 @@ is_a: GO:1904672 ! regulation of somatic stem cell population maintenance intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0035019 ! somatic stem cell population maintenance relationship: negatively_regulates GO:0035019 ! somatic stem cell population maintenance -created_by: rph creation_date: 2015-09-14T08:40:25Z [Term] @@ -134682,7 +137839,6 @@ is_a: GO:1904672 ! regulation of somatic stem cell population maintenance intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0035019 ! somatic stem cell population maintenance relationship: positively_regulates GO:0035019 ! somatic stem cell population maintenance -created_by: rph creation_date: 2015-09-14T08:40:32Z [Term] @@ -134695,7 +137851,6 @@ is_a: GO:2000035 ! regulation of stem cell division intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0048103 ! somatic stem cell division relationship: regulates GO:0048103 ! somatic stem cell division -created_by: rph creation_date: 2015-09-14T08:47:22Z [Term] @@ -134717,7 +137872,6 @@ is_a: GO:1904675 ! regulation of somatic stem cell division intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0048103 ! somatic stem cell division relationship: negatively_regulates GO:0048103 ! somatic stem cell division -created_by: rph creation_date: 2015-09-14T08:47:28Z [Term] @@ -134739,15 +137893,12 @@ is_a: GO:1904675 ! regulation of somatic stem cell division intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0048103 ! somatic stem cell division relationship: positively_regulates GO:0048103 ! somatic stem cell division -created_by: rph creation_date: 2015-09-14T08:47:34Z [Term] id: GO:1904680 name: peptide transmembrane transporter activity namespace: molecular_function -alt_id: GO:0015197 -alt_id: GO:0015637 def: "Enables the transfer of a peptide from one side of a membrane to the other." [GO_REF:0000070, GOC:TermGenie, GOC:vw] synonym: "peptide transporter activity" RELATED [] synonym: "peptide uptake permease activity" RELATED [] @@ -134757,7 +137908,6 @@ intersection_of: GO:0005215 ! transporter activity intersection_of: has_primary_input CHEBI:60466 intersection_of: results_in_transport_across GO:0016020 ! membrane relationship: has_primary_input CHEBI:60466 -created_by: tb creation_date: 2015-09-22T18:50:41Z [Term] @@ -134771,7 +137921,6 @@ intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0002183 ! cytoplasmic translational initiation relationship: regulates GO:0002183 ! cytoplasmic translational initiation property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/21560" xsd:anyURI -created_by: dos creation_date: 2015-09-25T14:39:38Z [Term] @@ -134788,7 +137937,6 @@ is_a: GO:1904688 ! regulation of cytoplasmic translational initiation intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0002183 ! cytoplasmic translational initiation relationship: negatively_regulates GO:0002183 ! cytoplasmic translational initiation -created_by: dos creation_date: 2015-09-25T14:39:44Z [Term] @@ -134805,7 +137953,6 @@ is_a: GO:1904688 ! regulation of cytoplasmic translational initiation intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0002183 ! cytoplasmic translational initiation relationship: positively_regulates GO:0002183 ! cytoplasmic translational initiation -created_by: dos creation_date: 2015-09-25T14:39:50Z [Term] @@ -134832,7 +137979,6 @@ is_a: GO:0061469 ! regulation of type B pancreatic cell proliferation intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0044342 ! type B pancreatic cell proliferation relationship: negatively_regulates GO:0044342 ! type B pancreatic cell proliferation -created_by: sl creation_date: 2015-09-25T15:23:38Z [Term] @@ -134859,7 +138005,6 @@ is_a: GO:0061469 ! regulation of type B pancreatic cell proliferation intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0044342 ! type B pancreatic cell proliferation relationship: positively_regulates GO:0044342 ! type B pancreatic cell proliferation -created_by: sl creation_date: 2015-09-25T15:23:44Z [Term] @@ -134876,7 +138021,6 @@ intersection_of: results_in_morphogenesis_of UBERON:0001891 ! midbrain relationship: part_of GO:0030901 ! midbrain development relationship: part_of GO:0048854 ! brain morphogenesis relationship: results_in_morphogenesis_of UBERON:0001891 ! midbrain -created_by: bf creation_date: 2015-09-29T09:15:28Z [Term] @@ -134890,7 +138034,6 @@ is_a: GO:0050678 ! regulation of epithelial cell proliferation intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:1990863 ! acinar cell proliferation relationship: regulates GO:1990863 ! acinar cell proliferation -created_by: sl creation_date: 2015-09-30T15:19:50Z [Term] @@ -134917,7 +138060,6 @@ is_a: GO:1904697 ! regulation of acinar cell proliferation intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:1990863 ! acinar cell proliferation relationship: negatively_regulates GO:1990863 ! acinar cell proliferation -created_by: sl creation_date: 2015-09-30T15:19:57Z [Term] @@ -134944,7 +138086,6 @@ is_a: GO:1904697 ! regulation of acinar cell proliferation intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:1990863 ! acinar cell proliferation relationship: positively_regulates GO:1990863 ! acinar cell proliferation -created_by: sl creation_date: 2015-09-30T15:20:03Z [Term] @@ -134959,7 +138100,6 @@ is_a: GO:1904019 ! epithelial cell apoptotic process intersection_of: GO:0006915 ! apoptotic process intersection_of: occurs_in CL:0000501 ! granulosa cell relationship: occurs_in CL:0000501 ! granulosa cell -created_by: sl creation_date: 2015-09-30T21:29:54Z [Term] @@ -134973,7 +138113,6 @@ is_a: GO:0048660 ! regulation of smooth muscle cell proliferation intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:1990874 ! vascular associated smooth muscle cell proliferation relationship: regulates GO:1990874 ! vascular associated smooth muscle cell proliferation -created_by: sl creation_date: 2015-10-01T16:05:20Z [Term] @@ -134996,7 +138135,6 @@ is_a: GO:1904705 ! regulation of vascular associated smooth muscle cell prolifer intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:1990874 ! vascular associated smooth muscle cell proliferation relationship: negatively_regulates GO:1990874 ! vascular associated smooth muscle cell proliferation -created_by: sl creation_date: 2015-10-01T16:05:26Z [Term] @@ -135019,7 +138157,6 @@ is_a: GO:1904705 ! regulation of vascular associated smooth muscle cell prolifer intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:1990874 ! vascular associated smooth muscle cell proliferation relationship: positively_regulates GO:1990874 ! vascular associated smooth muscle cell proliferation -created_by: sl creation_date: 2015-10-01T16:05:32Z [Term] @@ -135034,7 +138171,6 @@ is_a: GO:1904035 ! regulation of epithelial cell apoptotic process intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:1904700 ! granulosa cell apoptotic process relationship: regulates GO:1904700 ! granulosa cell apoptotic process -created_by: sl creation_date: 2015-10-01T16:09:38Z [Term] @@ -135066,7 +138202,6 @@ is_a: GO:1904708 ! regulation of granulosa cell apoptotic process intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:1904700 ! granulosa cell apoptotic process relationship: negatively_regulates GO:1904700 ! granulosa cell apoptotic process -created_by: sl creation_date: 2015-10-01T16:09:45Z [Term] @@ -135098,7 +138233,6 @@ is_a: GO:1904708 ! regulation of granulosa cell apoptotic process intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:1904700 ! granulosa cell apoptotic process relationship: positively_regulates GO:1904700 ! granulosa cell apoptotic process -created_by: sl creation_date: 2015-10-01T16:09:51Z [Term] @@ -135114,7 +138248,6 @@ is_a: GO:0070013 ! intracellular organelle lumen intersection_of: GO:0031974 ! membrane-enclosed lumen intersection_of: part_of GO:0070820 ! tertiary granule relationship: part_of GO:0070820 ! tertiary granule -created_by: mec creation_date: 2015-10-12T12:53:10Z [Term] @@ -135127,7 +138260,6 @@ is_a: GO:0014909 ! smooth muscle cell migration intersection_of: GO:0016477 ! cell migration intersection_of: results_in_movement_of CL:0000359 ! vascular associated smooth muscle cell relationship: results_in_movement_of CL:0000359 ! vascular associated smooth muscle cell -created_by: rph creation_date: 2015-10-15T09:56:00Z [Term] @@ -135286,7 +138418,6 @@ is_a: GO:1904748 ! regulation of apoptotic process involved in development intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:1902742 ! apoptotic process involved in development relationship: negatively_regulates GO:1902742 ! apoptotic process involved in development -created_by: es creation_date: 2015-10-19T14:12:27Z [Term] @@ -135445,7 +138576,6 @@ is_a: GO:1904748 ! regulation of apoptotic process involved in development intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:1902742 ! apoptotic process involved in development relationship: positively_regulates GO:1902742 ! apoptotic process involved in development -created_by: es creation_date: 2015-10-19T14:12:34Z [Term] @@ -135487,7 +138617,6 @@ is_a: GO:0050793 ! regulation of developmental process intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:1902742 ! apoptotic process involved in development relationship: regulates GO:1902742 ! apoptotic process involved in development -created_by: es creation_date: 2015-10-19T15:02:28Z [Term] @@ -135502,7 +138631,6 @@ is_a: GO:1900180 ! regulation of protein localization to nucleus intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:1902570 ! protein localization to nucleolus relationship: regulates GO:1902570 ! protein localization to nucleolus -created_by: nc creation_date: 2015-10-19T15:16:17Z [Term] @@ -135534,7 +138662,6 @@ is_a: GO:1904749 ! regulation of protein localization to nucleolus intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:1902570 ! protein localization to nucleolus relationship: negatively_regulates GO:1902570 ! protein localization to nucleolus -created_by: nc creation_date: 2015-10-19T15:16:24Z [Term] @@ -135566,7 +138693,6 @@ is_a: GO:1904749 ! regulation of protein localization to nucleolus intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:1902570 ! protein localization to nucleolus relationship: positively_regulates GO:1902570 ! protein localization to nucleolus -created_by: nc creation_date: 2015-10-19T15:16:30Z [Term] @@ -135579,7 +138705,6 @@ is_a: GO:0014910 ! regulation of smooth muscle cell migration intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:1904738 ! vascular associated smooth muscle cell migration relationship: regulates GO:1904738 ! vascular associated smooth muscle cell migration -created_by: rph creation_date: 2015-10-19T15:49:52Z [Term] @@ -135601,7 +138726,6 @@ is_a: GO:1904752 ! regulation of vascular associated smooth muscle cell migratio intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:1904738 ! vascular associated smooth muscle cell migration relationship: negatively_regulates GO:1904738 ! vascular associated smooth muscle cell migration -created_by: rph creation_date: 2015-10-19T15:49:58Z [Term] @@ -135623,7 +138747,6 @@ is_a: GO:1904752 ! regulation of vascular associated smooth muscle cell migratio intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:1904738 ! vascular associated smooth muscle cell migration relationship: positively_regulates GO:1904738 ! vascular associated smooth muscle cell migration -created_by: rph creation_date: 2015-10-19T15:50:05Z [Term] @@ -135636,7 +138759,6 @@ is_a: GO:0045595 ! regulation of cell differentiation intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0036446 ! myofibroblast differentiation relationship: regulates GO:0036446 ! myofibroblast differentiation -created_by: rph creation_date: 2015-10-23T12:15:05Z [Term] @@ -135658,7 +138780,6 @@ is_a: GO:1904760 ! regulation of myofibroblast differentiation intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0036446 ! myofibroblast differentiation relationship: negatively_regulates GO:0036446 ! myofibroblast differentiation -created_by: rph creation_date: 2015-10-23T12:15:11Z [Term] @@ -135680,7 +138801,6 @@ is_a: GO:1904760 ! regulation of myofibroblast differentiation intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0036446 ! myofibroblast differentiation relationship: positively_regulates GO:0036446 ! myofibroblast differentiation -created_by: rph creation_date: 2015-10-23T12:15:17Z [Term] @@ -135694,7 +138814,6 @@ is_a: GO:0060349 ! bone morphogenesis intersection_of: GO:0009653 ! anatomical structure morphogenesis intersection_of: results_in_morphogenesis_of UBERON:0002514 ! intramembranous bone relationship: results_in_morphogenesis_of UBERON:0002514 ! intramembranous bone -created_by: dos creation_date: 2015-10-28T11:46:04Z [Term] @@ -135708,7 +138827,6 @@ is_a: GO:1904375 ! regulation of protein localization to cell periphery intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0072697 ! protein localization to cell cortex relationship: regulates GO:0072697 ! protein localization to cell cortex -created_by: es creation_date: 2015-10-29T16:55:01Z [Term] @@ -135731,7 +138849,6 @@ is_a: GO:1904776 ! regulation of protein localization to cell cortex intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0072697 ! protein localization to cell cortex relationship: negatively_regulates GO:0072697 ! protein localization to cell cortex -created_by: es creation_date: 2015-10-29T16:55:08Z [Term] @@ -135754,7 +138871,6 @@ is_a: GO:1904776 ! regulation of protein localization to cell cortex intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0072697 ! protein localization to cell cortex relationship: positively_regulates GO:0072697 ! protein localization to cell cortex -created_by: es creation_date: 2015-10-29T16:55:15Z [Term] @@ -135767,7 +138883,6 @@ is_a: GO:0035561 ! regulation of chromatin binding intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:1990188 ! euchromatin binding relationship: regulates GO:1990188 ! euchromatin binding -created_by: nc creation_date: 2015-11-09T11:43:04Z [Term] @@ -135785,7 +138900,6 @@ is_a: GO:1904793 ! regulation of euchromatin binding intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:1990188 ! euchromatin binding relationship: negatively_regulates GO:1990188 ! euchromatin binding -created_by: nc creation_date: 2015-11-09T11:43:12Z [Term] @@ -135803,7 +138917,6 @@ is_a: GO:1904793 ! regulation of euchromatin binding intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:1990188 ! euchromatin binding relationship: positively_regulates GO:1990188 ! euchromatin binding -created_by: nc creation_date: 2015-11-09T11:43:19Z [Term] @@ -135817,7 +138930,6 @@ is_a: GO:0032386 ! regulation of intracellular transport intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:1901950 ! dense core granule transport relationship: regulates GO:1901950 ! dense core granule transport -created_by: es creation_date: 2015-11-11T10:40:10Z [Term] @@ -135840,7 +138952,6 @@ is_a: GO:1904809 ! regulation of dense core granule transport intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:1901950 ! dense core granule transport relationship: negatively_regulates GO:1901950 ! dense core granule transport -created_by: es creation_date: 2015-11-11T10:40:18Z [Term] @@ -135863,7 +138974,6 @@ is_a: GO:1904809 ! regulation of dense core granule transport intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:1901950 ! dense core granule transport relationship: positively_regulates GO:1901950 ! dense core granule transport -created_by: es creation_date: 2015-11-11T10:40:25Z [Term] @@ -135878,7 +138988,6 @@ is_a: GO:0048856 ! anatomical structure development intersection_of: GO:0048856 ! anatomical structure development intersection_of: results_in_development_of UBERON:0000042 ! serous membrane relationship: results_in_development_of UBERON:0000042 ! serous membrane -created_by: dph creation_date: 2015-11-17T19:00:01Z [Term] @@ -135891,7 +139000,6 @@ intersection_of: GO:0048856 ! anatomical structure development intersection_of: results_in_development_of UBERON:0001178 ! visceral peritoneum relationship: part_of GO:1904820 ! peritoneum development relationship: results_in_development_of UBERON:0001178 ! visceral peritoneum -created_by: dph creation_date: 2015-11-17T19:00:17Z [Term] @@ -135905,7 +139013,6 @@ intersection_of: GO:0048856 ! anatomical structure development intersection_of: results_in_development_of UBERON:0001366 ! parietal peritoneum relationship: part_of GO:1904820 ! peritoneum development relationship: results_in_development_of UBERON:0001366 ! parietal peritoneum -created_by: dph creation_date: 2015-11-17T19:00:24Z [Term] @@ -135918,7 +139025,6 @@ is_a: GO:1904817 ! serous membrane development intersection_of: GO:0048856 ! anatomical structure development intersection_of: results_in_development_of UBERON:0002358 ! peritoneum relationship: results_in_development_of UBERON:0002358 ! peritoneum -created_by: dph creation_date: 2015-11-18T17:23:51Z [Term] @@ -135930,7 +139036,6 @@ is_a: GO:1905063 ! regulation of vascular associated smooth muscle cell differen intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0035887 ! aortic smooth muscle cell differentiation relationship: regulates GO:0035887 ! aortic smooth muscle cell differentiation -created_by: rph creation_date: 2015-11-24T10:20:40Z [Term] @@ -135947,7 +139052,6 @@ is_a: GO:1905064 ! negative regulation of vascular associated smooth muscle cell intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0035887 ! aortic smooth muscle cell differentiation relationship: negatively_regulates GO:0035887 ! aortic smooth muscle cell differentiation -created_by: rph creation_date: 2015-11-24T10:20:47Z [Term] @@ -135964,7 +139068,6 @@ is_a: GO:1905065 ! positive regulation of vascular associated smooth muscle cell intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0035887 ! aortic smooth muscle cell differentiation relationship: positively_regulates GO:0035887 ! aortic smooth muscle cell differentiation -created_by: rph creation_date: 2015-11-24T10:20:54Z [Term] @@ -135986,7 +139089,6 @@ intersection_of: GO:0009653 ! anatomical structure morphogenesis intersection_of: results_in_morphogenesis_of UBERON:0000044 ! dorsal root ganglion relationship: part_of GO:1990791 ! dorsal root ganglion development relationship: results_in_morphogenesis_of UBERON:0000044 ! dorsal root ganglion -created_by: bf creation_date: 2015-12-01T16:41:17Z [Term] @@ -136005,7 +139107,6 @@ intersection_of: GO:0009653 ! anatomical structure morphogenesis intersection_of: results_in_morphogenesis_of UBERON:0012175 ! acoustico-facial VII-VIII ganglion complex relationship: part_of GO:1903375 ! facioacoustic ganglion development relationship: results_in_morphogenesis_of UBERON:0012175 ! acoustico-facial VII-VIII ganglion complex -created_by: bf creation_date: 2015-12-01T17:02:06Z [Term] @@ -136020,7 +139121,6 @@ is_a: GO:2000035 ! regulation of stem cell division intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0048133 ! male germ-line stem cell asymmetric division relationship: regulates GO:0048133 ! male germ-line stem cell asymmetric division -created_by: sl creation_date: 2015-12-05T00:28:31Z [Term] @@ -136044,7 +139144,6 @@ is_a: GO:1904838 ! regulation of male germ-line stem cell asymmetric division intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0048133 ! male germ-line stem cell asymmetric division relationship: negatively_regulates GO:0048133 ! male germ-line stem cell asymmetric division -created_by: sl creation_date: 2015-12-05T00:28:39Z [Term] @@ -136067,7 +139166,6 @@ is_a: GO:1904838 ! regulation of male germ-line stem cell asymmetric division intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0048133 ! male germ-line stem cell asymmetric division relationship: positively_regulates GO:0048133 ! male germ-line stem cell asymmetric division -created_by: sl creation_date: 2015-12-05T00:28:46Z [Term] @@ -136080,7 +139178,6 @@ is_a: GO:0007416 ! synapse assembly intersection_of: GO:0009987 ! cellular process intersection_of: results_in_assembly_of GO:0060076 ! excitatory synapse relationship: results_in_assembly_of GO:0060076 ! excitatory synapse -created_by: bf creation_date: 2015-12-17T10:31:26Z [Term] @@ -136096,7 +139193,6 @@ is_a: GO:0048856 ! anatomical structure development intersection_of: GO:0048856 ! anatomical structure development intersection_of: results_in_development_of UBERON:0010323 ! cranial skeletal system relationship: results_in_development_of UBERON:0010323 ! cranial skeletal system -created_by: bf creation_date: 2016-01-07T13:45:06Z [Term] @@ -136109,7 +139205,6 @@ is_a: GO:0051963 ! regulation of synapse assembly intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:1904861 ! excitatory synapse assembly relationship: regulates GO:1904861 ! excitatory synapse assembly -created_by: bf creation_date: 2016-01-07T14:35:53Z [Term] @@ -136131,7 +139226,6 @@ is_a: GO:1904889 ! regulation of excitatory synapse assembly intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:1904861 ! excitatory synapse assembly relationship: negatively_regulates GO:1904861 ! excitatory synapse assembly -created_by: bf creation_date: 2016-01-07T14:36:00Z [Term] @@ -136153,7 +139247,6 @@ is_a: GO:1904889 ! regulation of excitatory synapse assembly intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:1904861 ! excitatory synapse assembly relationship: positively_regulates GO:1904861 ! excitatory synapse assembly -created_by: bf creation_date: 2016-01-07T14:36:07Z [Term] @@ -136168,7 +139261,6 @@ is_a: GO:0048145 ! regulation of fibroblast proliferation intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:1990922 ! hepatic stellate cell proliferation relationship: regulates GO:1990922 ! hepatic stellate cell proliferation -created_by: sl creation_date: 2016-01-14T15:56:59Z [Term] @@ -136200,7 +139292,6 @@ is_a: GO:1904897 ! regulation of hepatic stellate cell proliferation intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:1990922 ! hepatic stellate cell proliferation relationship: negatively_regulates GO:1990922 ! hepatic stellate cell proliferation -created_by: sl creation_date: 2016-01-14T15:57:06Z [Term] @@ -136232,7 +139323,6 @@ is_a: GO:1904897 ! regulation of hepatic stellate cell proliferation intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:1990922 ! hepatic stellate cell proliferation relationship: positively_regulates GO:1990922 ! hepatic stellate cell proliferation -created_by: sl creation_date: 2016-01-14T15:57:13Z [Term] @@ -136246,7 +139336,6 @@ is_a: GO:2000177 ! regulation of neural precursor cell proliferation intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0033278 ! cell proliferation in midbrain relationship: regulates GO:0033278 ! cell proliferation in midbrain -created_by: bf creation_date: 2016-02-01T13:16:11Z [Term] @@ -136273,7 +139362,6 @@ is_a: GO:2000178 ! negative regulation of neural precursor cell proliferation intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0033278 ! cell proliferation in midbrain relationship: negatively_regulates GO:0033278 ! cell proliferation in midbrain -created_by: bf creation_date: 2016-02-01T13:16:19Z [Term] @@ -136300,7 +139388,6 @@ is_a: GO:2000179 ! positive regulation of neural precursor cell proliferation intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0033278 ! cell proliferation in midbrain relationship: positively_regulates GO:0033278 ! cell proliferation in midbrain -created_by: bf creation_date: 2016-02-01T13:16:27Z [Term] @@ -136314,7 +139401,6 @@ is_a: GO:0001764 ! neuron migration intersection_of: GO:0016477 ! cell migration intersection_of: results_in_movement_of CL:0000099 ! interneuron relationship: results_in_movement_of CL:0000099 ! interneuron -created_by: ah creation_date: 2016-02-01T14:04:32Z [Term] @@ -136326,7 +139412,6 @@ is_a: GO:0001764 ! neuron migration intersection_of: GO:0016477 ! cell migration intersection_of: results_in_movement_of CL:0000101 ! sensory neuron relationship: results_in_movement_of CL:0000101 ! sensory neuron -created_by: ah creation_date: 2016-02-01T14:15:50Z [Term] @@ -136338,7 +139423,6 @@ is_a: GO:1901210 ! regulation of cardiac chamber formation intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0003211 ! cardiac ventricle formation relationship: regulates GO:0003211 ! cardiac ventricle formation -created_by: bc creation_date: 2016-02-02T16:37:16Z [Term] @@ -136356,7 +139440,6 @@ is_a: GO:1904942 ! regulation of cardiac ventricle formation intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0003211 ! cardiac ventricle formation relationship: negatively_regulates GO:0003211 ! cardiac ventricle formation -created_by: bc creation_date: 2016-02-02T16:37:24Z [Term] @@ -136373,7 +139456,6 @@ is_a: GO:1904942 ! regulation of cardiac ventricle formation intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0003211 ! cardiac ventricle formation relationship: positively_regulates GO:0003211 ! cardiac ventricle formation -created_by: bc creation_date: 2016-02-02T16:37:31Z [Term] @@ -136391,7 +139473,6 @@ intersection_of: GO:0030154 ! cell differentiation intersection_of: results_in_acquisition_of_features_of CL:2000097 ! midbrain dopaminergic neuron relationship: part_of GO:0030901 ! midbrain development relationship: results_in_acquisition_of_features_of CL:2000097 ! midbrain dopaminergic neuron -created_by: bf creation_date: 2016-02-04T14:38:10Z [Term] @@ -136405,7 +139486,6 @@ is_a: GO:1902494 ! catalytic complex intersection_of: GO:0032991 ! protein-containing complex intersection_of: capable_of GO:0016887 ! ATP hydrolysis activity relationship: capable_of GO:0016887 ! ATP hydrolysis activity -created_by: bhm creation_date: 2016-02-04T22:13:32Z [Term] @@ -136437,7 +139517,6 @@ is_a: GO:1903828 ! negative regulation of protein localization intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0045184 ! establishment of protein localization relationship: negatively_regulates GO:0045184 ! establishment of protein localization -created_by: mec creation_date: 2016-02-05T09:59:24Z [Term] @@ -136469,7 +139548,6 @@ is_a: GO:1903829 ! positive regulation of protein localization intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0045184 ! establishment of protein localization relationship: positively_regulates GO:0045184 ! establishment of protein localization -created_by: mec creation_date: 2016-02-05T09:59:32Z [Term] @@ -136485,7 +139563,6 @@ is_a: GO:1904338 ! regulation of dopaminergic neuron differentiation intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:1904948 ! midbrain dopaminergic neuron differentiation relationship: regulates GO:1904948 ! midbrain dopaminergic neuron differentiation -created_by: bf creation_date: 2016-02-09T12:00:21Z [Term] @@ -136522,7 +139599,6 @@ is_a: GO:1904956 ! regulation of midbrain dopaminergic neuron differentiation intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:1904948 ! midbrain dopaminergic neuron differentiation relationship: negatively_regulates GO:1904948 ! midbrain dopaminergic neuron differentiation -created_by: bf creation_date: 2016-02-09T12:00:29Z [Term] @@ -136559,7 +139635,6 @@ is_a: GO:1904956 ! regulation of midbrain dopaminergic neuron differentiation intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:1904948 ! midbrain dopaminergic neuron differentiation relationship: positively_regulates GO:1904948 ! midbrain dopaminergic neuron differentiation -created_by: bf creation_date: 2016-02-09T12:00:36Z [Term] @@ -136573,7 +139648,6 @@ is_a: GO:0110122 ! myotube cell migration intersection_of: GO:0016477 ! cell migration intersection_of: results_in_movement_of CL:0000189 ! slow muscle cell relationship: results_in_movement_of CL:0000189 ! slow muscle cell -created_by: ymb creation_date: 2016-02-16T21:20:11Z [Term] @@ -136587,7 +139661,6 @@ intersection_of: GO:0022607 ! cellular component assembly intersection_of: results_in_assembly_of GO:0005903 ! brush border relationship: results_in_assembly_of GO:0005903 ! brush border property_value: RO:0002161 NCBITaxon:4751 -created_by: tb creation_date: 2016-02-17T00:58:30Z [Term] @@ -136600,7 +139673,6 @@ intersection_of: GO:0016477 ! cell migration intersection_of: results_in_movement_of CL:0002138 ! endothelial cell of lymphatic vessel relationship: part_of GO:0036303 ! lymph vessel morphogenesis relationship: results_in_movement_of CL:0002138 ! endothelial cell of lymphatic vessel -created_by: dgh creation_date: 2016-02-18T20:49:43Z [Term] @@ -136612,7 +139684,6 @@ is_a: GO:0050865 ! regulation of cell activation intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0042118 ! endothelial cell activation relationship: regulates GO:0042118 ! endothelial cell activation -created_by: bc creation_date: 2016-02-29T16:16:09Z [Term] @@ -136629,7 +139700,6 @@ is_a: GO:1904987 ! regulation of endothelial cell activation intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0042118 ! endothelial cell activation relationship: negatively_regulates GO:0042118 ! endothelial cell activation -created_by: bc creation_date: 2016-02-29T16:16:18Z [Term] @@ -136646,14 +139716,12 @@ is_a: GO:1904987 ! regulation of endothelial cell activation intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0042118 ! endothelial cell activation relationship: positively_regulates GO:0042118 ! endothelial cell activation -created_by: bc creation_date: 2016-02-29T16:16:25Z [Term] id: GO:1905011 name: transmembrane phosphate ion transport from cytosol to vacuole namespace: biological_process -alt_id: GO:0007037 def: "The directed movement of phosphate ions from the cytosol across the vacuolar membrane and into the vacuolar lumen." [GO_REF:0000078, GOC:TermGenie, PMID:26554016] synonym: "vacuolar phosphate transport" BROAD [] is_a: GO:0034486 ! vacuolar transmembrane transport @@ -136666,9 +139734,20 @@ intersection_of: results_in_transport_across GO:0005774 ! vacuolar membrane relationship: has_target_end_location GO:0005775 ! vacuolar lumen relationship: has_target_start_location GO:0005829 ! cytosol relationship: results_in_transport_across GO:0005774 ! vacuolar membrane -created_by: tb creation_date: 2016-03-03T00:34:12Z +[Term] +id: GO:1905038 +name: regulation of membrane lipid metabolic process +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of membrane lipid metabolic process." [GO_REF:0000058, GOC:TermGenie, PMID:25954280] +synonym: "regulation of membrane lipid metabolism" EXACT [GOC:TermGenie] +is_a: GO:0019216 ! regulation of lipid metabolic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0006643 ! membrane lipid metabolic process +relationship: regulates GO:0006643 ! membrane lipid metabolic process +creation_date: 2016-03-08T20:41:32Z + [Term] id: GO:1905039 name: carboxylic acid transmembrane transport @@ -136679,7 +139758,6 @@ is_a: GO:0055085 ! transmembrane transport intersection_of: GO:0006810 ! transport intersection_of: has_primary_input CHEBI:29067 intersection_of: results_in_transport_across GO:0016020 ! membrane -created_by: vw creation_date: 2016-03-09T15:33:53Z [Term] @@ -136697,7 +139775,6 @@ is_a: GO:0071696 ! ectodermal placode development intersection_of: GO:0048856 ! anatomical structure development intersection_of: results_in_development_of UBERON:0003069 ! otic placode relationship: results_in_development_of UBERON:0003069 ! otic placode -created_by: bf creation_date: 2016-03-10T09:30:20Z [Term] @@ -136711,7 +139788,6 @@ is_a: GO:0051150 ! regulation of smooth muscle cell differentiation intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0035886 ! vascular associated smooth muscle cell differentiation relationship: regulates GO:0035886 ! vascular associated smooth muscle cell differentiation -created_by: rph creation_date: 2016-03-21T11:14:53Z [Term] @@ -136738,7 +139814,6 @@ is_a: GO:1905063 ! regulation of vascular associated smooth muscle cell differen intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0035886 ! vascular associated smooth muscle cell differentiation relationship: negatively_regulates GO:0035886 ! vascular associated smooth muscle cell differentiation -created_by: rph creation_date: 2016-03-21T11:15:03Z [Term] @@ -136765,7 +139840,6 @@ is_a: GO:1905063 ! regulation of vascular associated smooth muscle cell differen intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0035886 ! vascular associated smooth muscle cell differentiation relationship: positively_regulates GO:0035886 ! vascular associated smooth muscle cell differentiation -created_by: rph creation_date: 2016-03-21T11:15:13Z [Term] @@ -136778,7 +139852,6 @@ is_a: GO:1903867 ! extraembryonic membrane development intersection_of: GO:0048856 ! anatomical structure development intersection_of: results_in_development_of UBERON:0004340 ! allantois relationship: results_in_development_of UBERON:0004340 ! allantois -created_by: cls creation_date: 2016-03-21T15:18:21Z [Term] @@ -136791,7 +139864,6 @@ is_a: GO:0016477 ! cell migration intersection_of: GO:0016477 ! cell migration intersection_of: results_in_movement_of CL:2000075 ! anterior visceral endoderm cell relationship: results_in_movement_of CL:2000075 ! anterior visceral endoderm cell -created_by: cls creation_date: 2016-03-21T15:18:32Z [Term] @@ -136806,7 +139878,6 @@ is_a: GO:0150147 ! cell-cell junction disassembly intersection_of: GO:0022411 ! cellular component disassembly intersection_of: results_in_disassembly_of GO:0070160 ! tight junction relationship: results_in_disassembly_of GO:0070160 ! tight junction -created_by: rl creation_date: 2016-03-23T12:35:08Z [Term] @@ -136820,7 +139891,6 @@ is_a: GO:0051128 ! regulation of cellular component organization intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:1905071 ! tight junction disassembly relationship: regulates GO:1905071 ! tight junction disassembly -created_by: rl creation_date: 2016-03-23T19:32:51Z [Term] @@ -136844,7 +139914,6 @@ is_a: GO:1905073 ! regulation of tight junction disassembly intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:1905071 ! tight junction disassembly relationship: negatively_regulates GO:1905071 ! tight junction disassembly -created_by: rl creation_date: 2016-03-23T19:33:01Z [Term] @@ -136868,7 +139937,6 @@ is_a: GO:1905073 ! regulation of tight junction disassembly intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:1905071 ! tight junction disassembly relationship: positively_regulates GO:1905071 ! tight junction disassembly -created_by: rl creation_date: 2016-03-23T19:33:10Z [Term] @@ -136881,7 +139949,6 @@ is_a: GO:0060284 ! regulation of cell development intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0098749 ! cerebellar neuron development relationship: regulates GO:0098749 ! cerebellar neuron development -created_by: hjd creation_date: 2016-03-24T19:45:17Z [Term] @@ -136899,7 +139966,6 @@ is_a: GO:1905079 ! regulation of cerebellar neuron development intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0098749 ! cerebellar neuron development relationship: negatively_regulates GO:0098749 ! cerebellar neuron development -created_by: hjd creation_date: 2016-03-24T19:45:26Z [Term] @@ -136917,7 +139983,6 @@ is_a: GO:1905079 ! regulation of cerebellar neuron development intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0098749 ! cerebellar neuron development relationship: positively_regulates GO:0098749 ! cerebellar neuron development -created_by: hjd creation_date: 2016-03-24T19:45:35Z [Term] @@ -136930,7 +139995,6 @@ is_a: GO:0060312 ! regulation of blood vessel remodeling intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0101010 ! pulmonary blood vessel remodeling relationship: regulates GO:0101010 ! pulmonary blood vessel remodeling -created_by: bc creation_date: 2016-04-06T13:07:24Z [Term] @@ -136948,7 +140012,6 @@ is_a: GO:1905109 ! regulation of pulmonary blood vessel remodeling intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0101010 ! pulmonary blood vessel remodeling relationship: negatively_regulates GO:0101010 ! pulmonary blood vessel remodeling -created_by: bc creation_date: 2016-04-06T13:07:33Z [Term] @@ -136966,7 +140029,6 @@ is_a: GO:2000504 ! positive regulation of blood vessel remodeling intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0101010 ! pulmonary blood vessel remodeling relationship: positively_regulates GO:0101010 ! pulmonary blood vessel remodeling -created_by: bc creation_date: 2016-04-06T13:07:42Z [Term] @@ -136980,7 +140042,6 @@ is_a: GO:0060632 ! regulation of microtubule-based movement intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0099640 ! axo-dendritic protein transport relationship: regulates GO:0099640 ! axo-dendritic protein transport -created_by: sl creation_date: 2016-04-11T20:38:31Z [Term] @@ -137002,7 +140063,6 @@ is_a: GO:1905126 ! regulation of axo-dendritic protein transport intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0099640 ! axo-dendritic protein transport relationship: negatively_regulates GO:0099640 ! axo-dendritic protein transport -created_by: sl creation_date: 2016-04-11T20:38:40Z [Term] @@ -137024,7 +140084,6 @@ is_a: GO:1905126 ! regulation of axo-dendritic protein transport intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0099640 ! axo-dendritic protein transport relationship: positively_regulates GO:0099640 ! axo-dendritic protein transport -created_by: sl creation_date: 2016-04-11T20:38:48Z [Term] @@ -137041,7 +140100,6 @@ intersection_of: GO:0048646 ! anatomical structure formation involved in morphog intersection_of: results_in_formation_of UBERON:0004356 ! apical ectodermal ridge relationship: part_of GO:0035107 ! appendage morphogenesis relationship: results_in_formation_of UBERON:0004356 ! apical ectodermal ridge -created_by: dph creation_date: 2016-04-13T11:46:40Z [Term] @@ -137056,7 +140114,6 @@ is_a: GO:0022603 ! regulation of anatomical structure morphogenesis intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:1905139 ! apical ectodermal ridge formation relationship: regulates GO:1905139 ! apical ectodermal ridge formation -created_by: dph creation_date: 2016-04-13T12:16:40Z [Term] @@ -137089,7 +140146,6 @@ is_a: GO:1905140 ! regulation of apical ectodermal ridge formation intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:1905139 ! apical ectodermal ridge formation relationship: negatively_regulates GO:1905139 ! apical ectodermal ridge formation -created_by: dph creation_date: 2016-04-13T12:16:48Z [Term] @@ -137119,7 +140175,6 @@ is_a: GO:1905140 ! regulation of apical ectodermal ridge formation intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:1905139 ! apical ectodermal ridge formation relationship: positively_regulates GO:1905139 ! apical ectodermal ridge formation -created_by: dph creation_date: 2016-04-13T12:16:57Z [Term] @@ -137132,7 +140187,6 @@ is_a: GO:0050896 ! response to stimulus intersection_of: GO:0050896 ! response to stimulus intersection_of: has_primary_input CHEBI:15355 relationship: has_primary_input CHEBI:15355 -created_by: dos creation_date: 2016-04-14T08:54:49Z [Term] @@ -137144,7 +140198,6 @@ is_a: GO:0070887 ! cellular response to chemical stimulus is_a: GO:1905144 ! response to acetylcholine intersection_of: GO:0070887 ! cellular response to chemical stimulus intersection_of: has_primary_input CHEBI:15355 -created_by: dos creation_date: 2016-04-14T08:54:58Z [Term] @@ -137165,7 +140218,6 @@ is_a: GO:0007039 ! protein catabolic process in the vacuole intersection_of: GO:0030163 ! protein catabolic process intersection_of: occurs_in GO:0005764 ! lysosome relationship: occurs_in GO:0005764 ! lysosome -created_by: bf creation_date: 2016-04-14T12:50:34Z [Term] @@ -137178,7 +140230,6 @@ is_a: GO:0043502 ! regulation of muscle adaptation intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0014895 ! smooth muscle hypertrophy relationship: regulates GO:0014895 ! smooth muscle hypertrophy -created_by: bc creation_date: 2016-04-15T12:47:07Z [Term] @@ -137196,7 +140247,6 @@ is_a: GO:1905147 ! regulation of smooth muscle hypertrophy intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0014895 ! smooth muscle hypertrophy relationship: negatively_regulates GO:0014895 ! smooth muscle hypertrophy -created_by: bc creation_date: 2016-04-15T12:47:16Z [Term] @@ -137214,7 +140264,6 @@ is_a: GO:1905147 ! regulation of smooth muscle hypertrophy intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0014895 ! smooth muscle hypertrophy relationship: positively_regulates GO:0014895 ! smooth muscle hypertrophy -created_by: bc creation_date: 2016-04-15T12:47:24Z [Term] @@ -137226,7 +140275,6 @@ is_a: GO:0051128 ! regulation of cellular component organization intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0010324 ! membrane invagination relationship: regulates GO:0010324 ! membrane invagination -created_by: bf creation_date: 2016-04-18T15:43:54Z [Term] @@ -137243,7 +140291,6 @@ is_a: GO:1905153 ! regulation of membrane invagination intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0010324 ! membrane invagination relationship: negatively_regulates GO:0010324 ! membrane invagination -created_by: bf creation_date: 2016-04-18T15:44:04Z [Term] @@ -137260,7 +140307,6 @@ is_a: GO:1905153 ! regulation of membrane invagination intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0010324 ! membrane invagination relationship: positively_regulates GO:0010324 ! membrane invagination -created_by: bf creation_date: 2016-04-18T15:44:12Z [Term] @@ -137272,12 +140318,11 @@ synonym: "down regulation of photosynthesis" EXACT [GOC:TermGenie] synonym: "down-regulation of photosynthesis" EXACT [GOC:TermGenie] synonym: "downregulation of photosynthesis" EXACT [GOC:TermGenie] synonym: "inhibition of photosynthesis" NARROW [GOC:TermGenie] +is_a: GO:0009892 ! negative regulation of metabolic process is_a: GO:0010109 ! regulation of photosynthesis -is_a: GO:0031324 ! negative regulation of cellular metabolic process intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0015979 ! photosynthesis relationship: negatively_regulates GO:0015979 ! photosynthesis -created_by: tb creation_date: 2016-04-19T16:12:29Z [Term] @@ -137289,12 +140334,11 @@ synonym: "activation of photosynthesis" NARROW [GOC:TermGenie] synonym: "up regulation of photosynthesis" EXACT [GOC:TermGenie] synonym: "up-regulation of photosynthesis" EXACT [GOC:TermGenie] synonym: "upregulation of photosynthesis" EXACT [GOC:TermGenie] +is_a: GO:0009893 ! positive regulation of metabolic process is_a: GO:0010109 ! regulation of photosynthesis -is_a: GO:0031325 ! positive regulation of cellular metabolic process intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0015979 ! photosynthesis relationship: positively_regulates GO:0015979 ! photosynthesis -created_by: tb creation_date: 2016-04-19T16:12:39Z [Term] @@ -137314,7 +140358,6 @@ is_a: GO:1904350 ! regulation of protein catabolic process in the vacuole intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:1905146 ! lysosomal protein catabolic process relationship: regulates GO:1905146 ! lysosomal protein catabolic process -created_by: bf creation_date: 2016-04-26T12:10:01Z [Term] @@ -137371,7 +140414,6 @@ is_a: GO:1905165 ! regulation of lysosomal protein catabolic process intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:1905146 ! lysosomal protein catabolic process relationship: negatively_regulates GO:1905146 ! lysosomal protein catabolic process -created_by: bf creation_date: 2016-04-26T12:10:10Z [Term] @@ -137428,7 +140470,6 @@ is_a: GO:1905165 ! regulation of lysosomal protein catabolic process intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:1905146 ! lysosomal protein catabolic process relationship: positively_regulates GO:1905146 ! lysosomal protein catabolic process -created_by: bf creation_date: 2016-04-26T12:10:19Z [Term] @@ -137442,7 +140483,6 @@ is_a: GO:0045595 ! regulation of cell differentiation intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0035051 ! cardiocyte differentiation relationship: regulates GO:0035051 ! cardiocyte differentiation -created_by: bc creation_date: 2016-06-02T07:20:01Z [Term] @@ -137470,7 +140510,6 @@ is_a: GO:1905207 ! regulation of cardiocyte differentiation intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0035051 ! cardiocyte differentiation relationship: negatively_regulates GO:0035051 ! cardiocyte differentiation -created_by: bc creation_date: 2016-06-02T07:20:09Z [Term] @@ -137498,7 +140537,6 @@ is_a: GO:1905207 ! regulation of cardiocyte differentiation intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0035051 ! cardiocyte differentiation relationship: positively_regulates GO:0035051 ! cardiocyte differentiation -created_by: bc creation_date: 2016-06-02T07:20:16Z [Term] @@ -137512,7 +140550,6 @@ is_a: GO:1903379 ! regulation of mitotic chromosome condensation intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0007076 ! mitotic chromosome condensation relationship: negatively_regulates GO:0007076 ! mitotic chromosome condensation -created_by: vw creation_date: 2016-06-03T08:41:08Z [Term] @@ -137525,7 +140562,6 @@ is_a: GO:0051098 ! regulation of binding intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0003723 ! RNA binding relationship: regulates GO:0003723 ! RNA binding -created_by: bf creation_date: 2016-06-06T10:20:56Z [Term] @@ -137543,7 +140579,6 @@ is_a: GO:1905214 ! regulation of RNA binding intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0003723 ! RNA binding relationship: negatively_regulates GO:0003723 ! RNA binding -created_by: bf creation_date: 2016-06-06T10:21:04Z [Term] @@ -137561,7 +140596,6 @@ is_a: GO:1905214 ! regulation of RNA binding intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0003723 ! RNA binding relationship: positively_regulates GO:0003723 ! RNA binding -created_by: bf creation_date: 2016-06-06T10:21:12Z [Term] @@ -137575,7 +140609,6 @@ is_a: GO:0045637 ! regulation of myeloid cell differentiation intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0030220 ! platelet formation relationship: regulates GO:0030220 ! platelet formation -created_by: sl creation_date: 2016-06-06T22:15:46Z [Term] @@ -137597,7 +140630,6 @@ is_a: GO:1905219 ! regulation of platelet formation intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0030220 ! platelet formation relationship: negatively_regulates GO:0030220 ! platelet formation -created_by: sl creation_date: 2016-06-06T22:15:54Z [Term] @@ -137620,7 +140652,6 @@ is_a: GO:1905219 ! regulation of platelet formation intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0030220 ! platelet formation relationship: positively_regulates GO:0030220 ! platelet formation -created_by: sl creation_date: 2016-06-06T22:16:02Z [Term] @@ -137637,7 +140668,6 @@ is_a: GO:0009653 ! anatomical structure morphogenesis intersection_of: GO:0009653 ! anatomical structure morphogenesis intersection_of: results_in_morphogenesis_of UBERON:0002348 ! epicardium relationship: results_in_morphogenesis_of UBERON:0002348 ! epicardium -created_by: rl creation_date: 2016-06-07T10:02:32Z [Term] @@ -137650,15 +140680,12 @@ is_a: GO:0070887 ! cellular response to chemical stimulus is_a: GO:1902065 ! response to L-glutamate intersection_of: GO:0070887 ! cellular response to chemical stimulus intersection_of: has_primary_input CHEBI:29985 -created_by: sl creation_date: 2016-06-07T17:30:08Z [Term] id: GO:1905268 name: negative regulation of chromatin organization namespace: biological_process -alt_id: GO:0045798 -alt_id: GO:1903309 def: "Any process that stops, prevents or reduces the frequency, rate or extent of chromatin organization." [GO_REF:0000058, GOC:pr, GOC:TermGenie, GOC:vw, PMID:654321] synonym: "down regulation of chromatin assembly or disassembly" RELATED [] synonym: "down regulation of chromatin organisation" EXACT [GOC:TermGenie] @@ -137687,15 +140714,12 @@ intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0006325 ! chromatin organization relationship: negatively_regulates GO:0006325 ! chromatin organization property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/22766" xsd:anyURI -created_by: pr creation_date: 2016-06-15T20:14:47Z [Term] id: GO:1905269 name: positive regulation of chromatin organization namespace: biological_process -alt_id: GO:0045799 -alt_id: GO:1903310 def: "Any process that activates or increases the frequency, rate or extent of chromatin organization." [GO_REF:0000058, GOC:pr, GOC:TermGenie, GOC:vw, PMID:654321] synonym: "activation of chromatin assembly or disassembly" NARROW [] synonym: "activation of chromatin organisation" NARROW [GOC:TermGenie] @@ -137725,7 +140749,6 @@ intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0006325 ! chromatin organization relationship: positively_regulates GO:0006325 ! chromatin organization property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/22766" xsd:anyURI -created_by: pr creation_date: 2016-06-15T20:14:56Z [Term] @@ -137738,7 +140761,6 @@ is_a: GO:0021895 ! cerebral cortex neuron differentiation intersection_of: GO:0030154 ! cell differentiation intersection_of: results_in_acquisition_of_features_of CL:2000056 ! Meynert cell relationship: results_in_acquisition_of_features_of CL:2000056 ! Meynert cell -created_by: cjm creation_date: 2016-06-15T23:44:17Z [Term] @@ -137746,11 +140768,10 @@ id: GO:1905275 name: Rohon-Beard neuron differentiation namespace: biological_process def: "The process in which a relatively unspecialized cell acquires the specialized features of a Rohon-Beard neuron." [GO_REF:0000086, GOC:TermGenie, ZFIN:ZDB-PUB-120807-45] -is_a: GO:0030182 ! neuron differentiation +is_a: GO:0021953 ! central nervous system neuron differentiation intersection_of: GO:0030154 ! cell differentiation intersection_of: results_in_acquisition_of_features_of CL:0000247 ! Rohon-Beard neuron relationship: results_in_acquisition_of_features_of CL:0000247 ! Rohon-Beard neuron -created_by: cjm creation_date: 2016-06-16T23:17:04Z [Term] @@ -137764,7 +140785,6 @@ is_a: GO:2000026 ! regulation of multicellular organismal development intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0072175 ! epithelial tube formation relationship: regulates GO:0072175 ! epithelial tube formation -created_by: bhm creation_date: 2016-06-20T09:35:41Z [Term] @@ -137783,7 +140803,6 @@ is_a: GO:1905331 ! negative regulation of morphogenesis of an epithelium intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0072175 ! epithelial tube formation relationship: negatively_regulates GO:0072175 ! epithelial tube formation -created_by: bhm creation_date: 2016-06-20T09:35:49Z [Term] @@ -137802,7 +140821,6 @@ is_a: GO:1905332 ! positive regulation of morphogenesis of an epithelium intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0072175 ! epithelial tube formation relationship: positively_regulates GO:0072175 ! epithelial tube formation -created_by: bhm creation_date: 2016-06-20T09:35:57Z [Term] @@ -137821,7 +140839,6 @@ is_a: GO:0048729 ! tissue morphogenesis intersection_of: GO:0009653 ! anatomical structure morphogenesis intersection_of: results_in_morphogenesis_of UBERON:0006008 ! fibrous ring of heart relationship: results_in_morphogenesis_of UBERON:0006008 ! fibrous ring of heart -created_by: rl creation_date: 2016-06-21T09:46:54Z [Term] @@ -137838,7 +140855,6 @@ is_a: GO:0034390 ! smooth muscle cell apoptotic process intersection_of: GO:0006915 ! apoptotic process intersection_of: occurs_in CL:0000359 ! vascular associated smooth muscle cell relationship: occurs_in CL:0000359 ! vascular associated smooth muscle cell -created_by: rph creation_date: 2016-06-23T13:24:20Z [Term] @@ -137850,7 +140866,6 @@ is_a: GO:2000736 ! regulation of stem cell differentiation intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0014033 ! neural crest cell differentiation relationship: regulates GO:0014033 ! neural crest cell differentiation -created_by: rl creation_date: 2016-06-28T15:02:01Z [Term] @@ -137868,7 +140883,6 @@ is_a: GO:2000737 ! negative regulation of stem cell differentiation intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0014033 ! neural crest cell differentiation relationship: negatively_regulates GO:0014033 ! neural crest cell differentiation -created_by: rl creation_date: 2016-06-28T15:02:09Z [Term] @@ -137886,7 +140900,6 @@ is_a: GO:2000738 ! positive regulation of stem cell differentiation intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0014033 ! neural crest cell differentiation relationship: positively_regulates GO:0014033 ! neural crest cell differentiation -created_by: rl creation_date: 2016-06-28T15:02:16Z [Term] @@ -137899,7 +140912,6 @@ is_a: GO:0060284 ! regulation of cell development intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0060576 ! intestinal epithelial cell development relationship: regulates GO:0060576 ! intestinal epithelial cell development -created_by: rph creation_date: 2016-06-30T11:40:47Z [Term] @@ -137918,7 +140930,6 @@ is_a: GO:1905298 ! regulation of intestinal epithelial cell development intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0060576 ! intestinal epithelial cell development relationship: negatively_regulates GO:0060576 ! intestinal epithelial cell development -created_by: rph creation_date: 2016-06-30T11:40:55Z [Term] @@ -137936,7 +140947,6 @@ is_a: GO:1905298 ! regulation of intestinal epithelial cell development intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0060576 ! intestinal epithelial cell development relationship: positively_regulates GO:0060576 ! intestinal epithelial cell development -created_by: rph creation_date: 2016-06-30T11:41:02Z [Term] @@ -137954,7 +140964,6 @@ is_a: GO:1902903 ! regulation of supramolecular fiber organization intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0055003 ! cardiac myofibril assembly relationship: regulates GO:0055003 ! cardiac myofibril assembly -created_by: rl creation_date: 2016-07-06T10:01:49Z [Term] @@ -137989,7 +140998,6 @@ is_a: GO:2000726 ! negative regulation of cardiac muscle cell differentiation intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0055003 ! cardiac myofibril assembly relationship: negatively_regulates GO:0055003 ! cardiac myofibril assembly -created_by: rl creation_date: 2016-07-06T10:01:58Z [Term] @@ -138024,7 +141032,6 @@ is_a: GO:1905304 ! regulation of cardiac myofibril assembly intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0055003 ! cardiac myofibril assembly relationship: positively_regulates GO:0055003 ! cardiac myofibril assembly -created_by: rl creation_date: 2016-07-06T10:02:07Z [Term] @@ -138036,7 +141043,6 @@ is_a: GO:0030334 ! regulation of cell migration intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0003253 ! cardiac neural crest cell migration involved in outflow tract morphogenesis relationship: regulates GO:0003253 ! cardiac neural crest cell migration involved in outflow tract morphogenesis -created_by: rl creation_date: 2016-07-11T17:34:26Z [Term] @@ -138053,7 +141059,6 @@ is_a: GO:1905310 ! regulation of cardiac neural crest cell migration involved in intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0003253 ! cardiac neural crest cell migration involved in outflow tract morphogenesis relationship: negatively_regulates GO:0003253 ! cardiac neural crest cell migration involved in outflow tract morphogenesis -created_by: rl creation_date: 2016-07-11T17:34:35Z [Term] @@ -138070,7 +141075,6 @@ is_a: GO:1905310 ! regulation of cardiac neural crest cell migration involved in intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0003253 ! cardiac neural crest cell migration involved in outflow tract morphogenesis relationship: positively_regulates GO:0003253 ! cardiac neural crest cell migration involved in outflow tract morphogenesis -created_by: rl creation_date: 2016-07-11T17:34:43Z [Term] @@ -138082,7 +141086,6 @@ is_a: GO:0061323 ! cell proliferation involved in heart morphogenesis intersection_of: GO:0008283 ! cell population proliferation intersection_of: part_of GO:0003203 ! endocardial cushion morphogenesis relationship: part_of GO:0003203 ! endocardial cushion morphogenesis -created_by: rl creation_date: 2016-07-12T13:56:36Z [Term] @@ -138095,7 +141098,6 @@ is_a: GO:0016477 ! cell migration intersection_of: GO:0016477 ! cell migration intersection_of: results_in_movement_of CL:0000134 ! mesenchymal stem cell relationship: results_in_movement_of CL:0000134 ! mesenchymal stem cell -created_by: sl creation_date: 2016-07-14T17:13:02Z [Term] @@ -138107,7 +141109,6 @@ is_a: GO:0030334 ! regulation of cell migration intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:1905319 ! mesenchymal stem cell migration relationship: regulates GO:1905319 ! mesenchymal stem cell migration -created_by: sl creation_date: 2016-07-15T22:19:14Z [Term] @@ -138124,7 +141125,6 @@ is_a: GO:1905320 ! regulation of mesenchymal stem cell migration intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:1905319 ! mesenchymal stem cell migration relationship: negatively_regulates GO:1905319 ! mesenchymal stem cell migration -created_by: sl creation_date: 2016-07-15T22:19:22Z [Term] @@ -138141,7 +141141,6 @@ is_a: GO:1905320 ! regulation of mesenchymal stem cell migration intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:1905319 ! mesenchymal stem cell migration relationship: positively_regulates GO:1905319 ! mesenchymal stem cell migration -created_by: sl creation_date: 2016-07-15T22:19:29Z [Term] @@ -138155,7 +141154,6 @@ is_a: GO:0022603 ! regulation of anatomical structure morphogenesis intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0002009 ! morphogenesis of an epithelium relationship: regulates GO:0002009 ! morphogenesis of an epithelium -created_by: bhm creation_date: 2016-07-22T07:13:49Z [Term] @@ -138178,7 +141176,6 @@ is_a: GO:1905330 ! regulation of morphogenesis of an epithelium intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0002009 ! morphogenesis of an epithelium relationship: negatively_regulates GO:0002009 ! morphogenesis of an epithelium -created_by: bhm creation_date: 2016-07-22T07:13:57Z [Term] @@ -138201,7 +141198,6 @@ is_a: GO:1905330 ! regulation of morphogenesis of an epithelium intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0002009 ! morphogenesis of an epithelium relationship: positively_regulates GO:0002009 ! morphogenesis of an epithelium -created_by: bhm creation_date: 2016-07-22T07:14:05Z [Term] @@ -138219,7 +141215,6 @@ intersection_of: GO:0022607 ! cellular component assembly intersection_of: results_in_assembly_of GO:0035869 ! ciliary transition zone relationship: part_of GO:0060271 ! cilium assembly relationship: results_in_assembly_of GO:0035869 ! ciliary transition zone -created_by: pr creation_date: 2016-08-04T14:49:43Z [Term] @@ -138232,7 +141227,6 @@ is_a: GO:0016477 ! cell migration intersection_of: GO:0016477 ! cell migration intersection_of: results_in_movement_of CL:0000669 ! pericyte relationship: results_in_movement_of CL:0000669 ! pericyte -created_by: rph creation_date: 2016-08-05T12:01:48Z [Term] @@ -138248,7 +141242,6 @@ is_a: GO:0035418 ! protein localization to synapse intersection_of: GO:0008104 ! protein localization intersection_of: has_target_end_location GO:0098793 ! presynapse relationship: has_target_end_location GO:0098793 ! presynapse -created_by: dos creation_date: 2016-08-18T14:42:59Z [Term] @@ -138264,7 +141257,6 @@ is_a: GO:1902473 ! regulation of protein localization to synapse intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:1905383 ! protein localization to presynapse relationship: regulates GO:1905383 ! protein localization to presynapse -created_by: dos creation_date: 2016-08-18T14:56:00Z [Term] @@ -138301,7 +141293,6 @@ is_a: GO:1905384 ! regulation of protein localization to presynapse intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:1905383 ! protein localization to presynapse relationship: negatively_regulates GO:1905383 ! protein localization to presynapse -created_by: dos creation_date: 2016-08-18T14:56:08Z [Term] @@ -138338,7 +141329,6 @@ is_a: GO:1905384 ! regulation of protein localization to presynapse intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:1905383 ! protein localization to presynapse relationship: positively_regulates GO:1905383 ! protein localization to presynapse -created_by: dos creation_date: 2016-08-18T14:56:21Z [Term] @@ -138357,7 +141347,6 @@ is_a: GO:0070231 ! T cell apoptotic process intersection_of: GO:0006915 ! apoptotic process intersection_of: occurs_in CL:0000906 ! activated CD8-positive, alpha-beta T cell relationship: occurs_in CL:0000906 ! activated CD8-positive, alpha-beta T cell -created_by: pga creation_date: 2016-08-25T08:09:27Z [Term] @@ -138376,7 +141365,6 @@ is_a: GO:0070231 ! T cell apoptotic process intersection_of: GO:0006915 ! apoptotic process intersection_of: occurs_in CL:0000896 ! activated CD4-positive, alpha-beta T cell relationship: occurs_in CL:0000896 ! activated CD4-positive, alpha-beta T cell -created_by: pga creation_date: 2016-08-25T08:13:40Z [Term] @@ -138395,7 +141383,6 @@ is_a: GO:0070232 ! regulation of T cell apoptotic process intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:1905398 ! activated CD4-positive, alpha-beta T cell apoptotic process relationship: regulates GO:1905398 ! activated CD4-positive, alpha-beta T cell apoptotic process -created_by: pga creation_date: 2016-08-25T09:09:46Z [Term] @@ -138447,7 +141434,6 @@ is_a: GO:1905399 ! regulation of activated CD4-positive, alpha-beta T cell apopt intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:1905398 ! activated CD4-positive, alpha-beta T cell apoptotic process relationship: negatively_regulates GO:1905398 ! activated CD4-positive, alpha-beta T cell apoptotic process -created_by: pga creation_date: 2016-08-25T09:09:53Z [Term] @@ -138499,7 +141485,6 @@ is_a: GO:1905399 ! regulation of activated CD4-positive, alpha-beta T cell apopt intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:1905398 ! activated CD4-positive, alpha-beta T cell apoptotic process relationship: positively_regulates GO:1905398 ! activated CD4-positive, alpha-beta T cell apoptotic process -created_by: pga creation_date: 2016-08-25T09:10:00Z [Term] @@ -138518,7 +141503,6 @@ is_a: GO:0070232 ! regulation of T cell apoptotic process intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:1905397 ! activated CD8-positive, alpha-beta T cell apoptotic process relationship: regulates GO:1905397 ! activated CD8-positive, alpha-beta T cell apoptotic process -created_by: pga creation_date: 2016-08-25T09:13:56Z [Term] @@ -138570,7 +141554,6 @@ is_a: GO:1905402 ! regulation of activated CD8-positive, alpha-beta T cell apopt intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:1905397 ! activated CD8-positive, alpha-beta T cell apoptotic process relationship: negatively_regulates GO:1905397 ! activated CD8-positive, alpha-beta T cell apoptotic process -created_by: pga creation_date: 2016-08-25T09:14:03Z [Term] @@ -138622,7 +141605,6 @@ is_a: GO:1905402 ! regulation of activated CD8-positive, alpha-beta T cell apopt intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:1905397 ! activated CD8-positive, alpha-beta T cell apoptotic process relationship: positively_regulates GO:1905397 ! activated CD8-positive, alpha-beta T cell apoptotic process -created_by: pga creation_date: 2016-08-25T09:14:10Z [Term] @@ -138639,7 +141621,6 @@ is_a: GO:0050896 ! response to stimulus intersection_of: GO:0050896 ! response to stimulus intersection_of: has_primary_input CHEBI:57305 relationship: has_primary_input CHEBI:57305 -created_by: sl creation_date: 2016-09-08T22:09:15Z [Term] @@ -138655,7 +141636,6 @@ is_a: GO:0070887 ! cellular response to chemical stimulus is_a: GO:1905429 ! response to glycine intersection_of: GO:0070887 ! cellular response to chemical stimulus intersection_of: has_primary_input CHEBI:57305 -created_by: sl creation_date: 2016-09-08T22:09:23Z [Term] @@ -138668,7 +141648,6 @@ is_a: GO:0099177 ! regulation of trans-synaptic signaling intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0099082 ! retrograde trans-synaptic signaling by neuropeptide relationship: regulates GO:0099082 ! retrograde trans-synaptic signaling by neuropeptide -created_by: bf creation_date: 2016-09-14T10:56:47Z [Term] @@ -138688,7 +141667,6 @@ is_a: GO:1905432 ! regulation of retrograde trans-synaptic signaling by neuropep intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0099082 ! retrograde trans-synaptic signaling by neuropeptide relationship: negatively_regulates GO:0099082 ! retrograde trans-synaptic signaling by neuropeptide -created_by: bf creation_date: 2016-09-14T10:56:55Z [Term] @@ -138707,7 +141685,6 @@ is_a: GO:1905432 ! regulation of retrograde trans-synaptic signaling by neuropep intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0099082 ! retrograde trans-synaptic signaling by neuropeptide relationship: positively_regulates GO:0099082 ! retrograde trans-synaptic signaling by neuropeptide -created_by: bf creation_date: 2016-09-14T10:57:02Z [Term] @@ -138719,7 +141696,6 @@ is_a: GO:1901532 ! regulation of hematopoietic progenitor cell differentiation intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0002318 ! myeloid progenitor cell differentiation relationship: regulates GO:0002318 ! myeloid progenitor cell differentiation -created_by: rz creation_date: 2016-09-16T12:32:18Z [Term] @@ -138736,7 +141712,6 @@ is_a: GO:1905453 ! regulation of myeloid progenitor cell differentiation intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0002318 ! myeloid progenitor cell differentiation relationship: negatively_regulates GO:0002318 ! myeloid progenitor cell differentiation -created_by: rz creation_date: 2016-09-16T12:32:26Z [Term] @@ -138753,7 +141728,6 @@ is_a: GO:1905453 ! regulation of myeloid progenitor cell differentiation intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0002318 ! myeloid progenitor cell differentiation relationship: positively_regulates GO:0002318 ! myeloid progenitor cell differentiation -created_by: rz creation_date: 2016-09-16T12:32:33Z [Term] @@ -138765,7 +141739,6 @@ is_a: GO:1901532 ! regulation of hematopoietic progenitor cell differentiation intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0002320 ! lymphoid progenitor cell differentiation relationship: regulates GO:0002320 ! lymphoid progenitor cell differentiation -created_by: rz creation_date: 2016-09-16T12:32:40Z [Term] @@ -138782,7 +141755,6 @@ is_a: GO:1905456 ! regulation of lymphoid progenitor cell differentiation intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0002320 ! lymphoid progenitor cell differentiation relationship: negatively_regulates GO:0002320 ! lymphoid progenitor cell differentiation -created_by: rz creation_date: 2016-09-16T12:32:48Z [Term] @@ -138799,7 +141771,6 @@ is_a: GO:1905456 ! regulation of lymphoid progenitor cell differentiation intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0002320 ! lymphoid progenitor cell differentiation relationship: positively_regulates GO:0002320 ! lymphoid progenitor cell differentiation -created_by: rz creation_date: 2016-09-16T12:32:55Z [Term] @@ -138816,7 +141787,6 @@ is_a: GO:0034391 ! regulation of smooth muscle cell apoptotic process intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:1905288 ! vascular associated smooth muscle cell apoptotic process relationship: regulates GO:1905288 ! vascular associated smooth muscle cell apoptotic process -created_by: rph creation_date: 2016-09-19T11:33:54Z [Term] @@ -138858,7 +141828,6 @@ is_a: GO:1905459 ! regulation of vascular associated smooth muscle cell apoptoti intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:1905288 ! vascular associated smooth muscle cell apoptotic process relationship: negatively_regulates GO:1905288 ! vascular associated smooth muscle cell apoptotic process -created_by: rph creation_date: 2016-09-19T11:34:03Z [Term] @@ -138900,7 +141869,6 @@ is_a: GO:1905459 ! regulation of vascular associated smooth muscle cell apoptoti intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:1905288 ! vascular associated smooth muscle cell apoptotic process relationship: positively_regulates GO:1905288 ! vascular associated smooth muscle cell apoptotic process -created_by: rph creation_date: 2016-09-19T11:34:10Z [Term] @@ -138914,7 +141882,6 @@ is_a: GO:0032880 ! regulation of protein localization intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0072657 ! protein localization to membrane relationship: regulates GO:0072657 ! protein localization to membrane -created_by: bc creation_date: 2016-09-21T16:20:03Z [Term] @@ -138941,7 +141908,6 @@ is_a: GO:1905475 ! regulation of protein localization to membrane intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0072657 ! protein localization to membrane relationship: negatively_regulates GO:0072657 ! protein localization to membrane -created_by: bc creation_date: 2016-09-21T16:20:10Z [Term] @@ -138968,7 +141934,6 @@ is_a: GO:1905475 ! regulation of protein localization to membrane intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0072657 ! protein localization to membrane relationship: positively_regulates GO:0072657 ! protein localization to membrane -created_by: bc creation_date: 2016-09-21T16:20:18Z [Term] @@ -138980,7 +141945,6 @@ is_a: GO:2001222 ! regulation of neuron migration intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0097475 ! motor neuron migration relationship: regulates GO:0097475 ! motor neuron migration -created_by: hbye creation_date: 2016-09-23T12:49:54Z [Term] @@ -138997,7 +141961,6 @@ is_a: GO:2001223 ! negative regulation of neuron migration intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0097475 ! motor neuron migration relationship: negatively_regulates GO:0097475 ! motor neuron migration -created_by: hbye creation_date: 2016-09-23T12:50:11Z [Term] @@ -139014,7 +141977,6 @@ is_a: GO:2001224 ! positive regulation of neuron migration intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0097475 ! motor neuron migration relationship: positively_regulates GO:0097475 ! motor neuron migration -created_by: hbye creation_date: 2016-09-23T12:50:19Z [Term] @@ -139032,7 +141994,6 @@ is_a: GO:2000172 ! regulation of branching morphogenesis of a nerve intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0048755 ! branching morphogenesis of a nerve relationship: positively_regulates GO:0048755 ! branching morphogenesis of a nerve -created_by: hbye creation_date: 2016-09-23T14:11:52Z [Term] @@ -139050,7 +142011,6 @@ is_a: GO:1902017 ! regulation of cilium assembly intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0044458 ! motile cilium assembly relationship: regulates GO:0044458 ! motile cilium assembly -created_by: krc creation_date: 2016-09-27T18:27:47Z [Term] @@ -139093,7 +142053,6 @@ is_a: GO:1905503 ! regulation of motile cilium assembly intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0044458 ! motile cilium assembly relationship: negatively_regulates GO:0044458 ! motile cilium assembly -created_by: krc creation_date: 2016-09-27T18:27:55Z [Term] @@ -139136,9 +142095,22 @@ is_a: GO:1905503 ! regulation of motile cilium assembly intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0044458 ! motile cilium assembly relationship: positively_regulates GO:0044458 ! motile cilium assembly -created_by: krc creation_date: 2016-09-27T18:28:03Z +[Term] +id: GO:1905508 +name: protein localization to microtubule organizing center +namespace: biological_process +def: "A process in which a protein is transported to, or maintained in, a location within a microtubule organizing center." [GO_REF:0000087, GOC:TermGenie, PMID:19001497] +synonym: "protein localisation in microtubule organizing center" EXACT [GOC:TermGenie] +synonym: "protein localisation to microtubule organizing center" EXACT [GOC:TermGenie] +synonym: "protein localization in microtubule organizing center" EXACT [GOC:TermGenie] +is_a: GO:0072698 ! protein localization to microtubule cytoskeleton +intersection_of: GO:0008104 ! protein localization +intersection_of: has_target_end_location GO:0005815 ! microtubule organizing center +relationship: has_target_end_location GO:0005815 ! microtubule organizing center +creation_date: 2016-09-28T12:32:16Z + [Term] id: GO:1905516 name: positive regulation of fertilization @@ -139158,7 +142130,6 @@ is_a: GO:2000243 ! positive regulation of reproductive process intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0009566 ! fertilization relationship: positively_regulates GO:0009566 ! fertilization -created_by: pr creation_date: 2016-09-30T14:32:32Z [Term] @@ -139171,7 +142142,6 @@ is_a: GO:0097529 ! myeloid leukocyte migration intersection_of: GO:0016477 ! cell migration intersection_of: results_in_movement_of CL:0000235 ! macrophage relationship: results_in_movement_of CL:0000235 ! macrophage -created_by: sl creation_date: 2016-09-30T22:17:45Z [Term] @@ -139183,7 +142153,6 @@ is_a: GO:0071675 ! regulation of mononuclear cell migration intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:1905517 ! macrophage migration relationship: regulates GO:1905517 ! macrophage migration -created_by: sl creation_date: 2016-10-03T15:29:06Z [Term] @@ -139200,7 +142169,6 @@ is_a: GO:1905521 ! regulation of macrophage migration intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:1905517 ! macrophage migration relationship: negatively_regulates GO:1905517 ! macrophage migration -created_by: sl creation_date: 2016-10-03T15:29:14Z [Term] @@ -139217,7 +142185,6 @@ is_a: GO:1905521 ! regulation of macrophage migration intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:1905517 ! macrophage migration relationship: positively_regulates GO:1905517 ! macrophage migration -created_by: sl creation_date: 2016-10-03T15:29:21Z [Term] @@ -139232,7 +142199,6 @@ is_a: GO:1905330 ! regulation of morphogenesis of an epithelium intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0001569 ! branching involved in blood vessel morphogenesis relationship: regulates GO:0001569 ! branching involved in blood vessel morphogenesis -created_by: nc creation_date: 2016-10-12T14:19:33Z [Term] @@ -139255,7 +142221,6 @@ is_a: GO:1905553 ! regulation of blood vessel branching intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0001569 ! branching involved in blood vessel morphogenesis relationship: negatively_regulates GO:0001569 ! branching involved in blood vessel morphogenesis -created_by: nc creation_date: 2016-10-12T14:19:41Z [Term] @@ -139278,7 +142243,6 @@ is_a: GO:1905553 ! regulation of blood vessel branching intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0001569 ! branching involved in blood vessel morphogenesis relationship: positively_regulates GO:0001569 ! branching involved in blood vessel morphogenesis -created_by: nc creation_date: 2016-10-12T14:19:49Z [Term] @@ -139294,7 +142258,6 @@ is_a: GO:0010564 ! regulation of cell cycle process intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0007077 ! mitotic nuclear membrane disassembly relationship: regulates GO:0007077 ! mitotic nuclear membrane disassembly -created_by: hbye creation_date: 2016-10-14T13:14:57Z [Term] @@ -139327,7 +142290,6 @@ is_a: GO:1905557 ! regulation of mitotic nuclear envelope disassembly intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0007077 ! mitotic nuclear membrane disassembly relationship: negatively_regulates GO:0007077 ! mitotic nuclear membrane disassembly -created_by: hbye creation_date: 2016-10-14T13:15:08Z [Term] @@ -139360,7 +142322,6 @@ is_a: GO:1905557 ! regulation of mitotic nuclear envelope disassembly intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0007077 ! mitotic nuclear membrane disassembly relationship: positively_regulates GO:0007077 ! mitotic nuclear membrane disassembly -created_by: hbye creation_date: 2016-10-14T13:15:17Z [Term] @@ -139372,7 +142333,6 @@ is_a: GO:0001936 ! regulation of endothelial cell proliferation intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0101023 ! vascular endothelial cell proliferation relationship: regulates GO:0101023 ! vascular endothelial cell proliferation -created_by: nc creation_date: 2016-10-17T09:24:17Z [Term] @@ -139389,7 +142349,6 @@ is_a: GO:1905562 ! regulation of vascular endothelial cell proliferation intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0101023 ! vascular endothelial cell proliferation relationship: negatively_regulates GO:0101023 ! vascular endothelial cell proliferation -created_by: nc creation_date: 2016-10-17T09:24:26Z [Term] @@ -139406,7 +142365,6 @@ is_a: GO:1905562 ! regulation of vascular endothelial cell proliferation intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0101023 ! vascular endothelial cell proliferation relationship: positively_regulates GO:0101023 ! vascular endothelial cell proliferation -created_by: nc creation_date: 2016-10-17T09:24:35Z [Term] @@ -139421,7 +142379,6 @@ is_a: GO:0051402 ! neuron apoptotic process intersection_of: GO:0006915 ! apoptotic process intersection_of: occurs_in CL:0000601 ! cochlear outer hair cell relationship: occurs_in CL:0000601 ! cochlear outer hair cell -created_by: sl creation_date: 2016-10-21T22:42:13Z [Term] @@ -139436,7 +142393,6 @@ is_a: GO:0043523 ! regulation of neuron apoptotic process intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:1905584 ! outer hair cell apoptotic process relationship: regulates GO:1905584 ! outer hair cell apoptotic process -created_by: sl creation_date: 2016-10-24T22:35:34Z [Term] @@ -139468,7 +142424,6 @@ is_a: GO:1905585 ! regulation of outer hair cell apoptotic process intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:1905584 ! outer hair cell apoptotic process relationship: negatively_regulates GO:1905584 ! outer hair cell apoptotic process -created_by: sl creation_date: 2016-10-24T22:35:43Z [Term] @@ -139500,7 +142455,6 @@ is_a: GO:1905585 ! regulation of outer hair cell apoptotic process intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:1905584 ! outer hair cell apoptotic process relationship: positively_regulates GO:1905584 ! outer hair cell apoptotic process -created_by: sl creation_date: 2016-10-24T22:35:51Z [Term] @@ -139516,7 +142470,6 @@ is_a: GO:0099174 ! regulation of presynapse organization intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0099054 ! presynapse assembly relationship: regulates GO:0099054 ! presynapse assembly -created_by: bc creation_date: 2016-10-27T16:08:13Z [Term] @@ -139543,7 +142496,6 @@ is_a: GO:1905606 ! regulation of presynapse assembly intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0099054 ! presynapse assembly relationship: negatively_regulates GO:0099054 ! presynapse assembly -created_by: bc creation_date: 2016-10-27T16:08:20Z [Term] @@ -139570,7 +142522,6 @@ is_a: GO:1905606 ! regulation of presynapse assembly intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0099054 ! presynapse assembly relationship: positively_regulates GO:0099054 ! presynapse assembly -created_by: bc creation_date: 2016-10-27T16:08:28Z [Term] @@ -139586,7 +142537,6 @@ is_a: GO:0009889 ! regulation of biosynthetic process intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0042427 ! serotonin biosynthetic process relationship: regulates GO:0042427 ! serotonin biosynthetic process -created_by: pad creation_date: 2016-10-31T14:26:20Z [Term] @@ -139623,7 +142573,6 @@ is_a: GO:1905627 ! regulation of serotonin biosynthetic process intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0042427 ! serotonin biosynthetic process relationship: negatively_regulates GO:0042427 ! serotonin biosynthetic process -created_by: pad creation_date: 2016-10-31T14:26:28Z [Term] @@ -139660,7 +142609,6 @@ is_a: GO:1905627 ! regulation of serotonin biosynthetic process intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0042427 ! serotonin biosynthetic process relationship: positively_regulates GO:0042427 ! serotonin biosynthetic process -created_by: pad creation_date: 2016-10-31T14:26:36Z [Term] @@ -139675,7 +142623,6 @@ is_a: GO:0071168 ! protein localization to chromatin intersection_of: GO:0008104 ! protein localization intersection_of: has_target_end_location GO:0000791 ! euchromatin relationship: has_target_end_location GO:0000791 ! euchromatin -created_by: pga creation_date: 2016-11-01T16:16:14Z [Term] @@ -139690,7 +142637,6 @@ is_a: GO:0071169 ! establishment of protein localization to chromatin is_a: GO:1905632 ! protein localization to euchromatin intersection_of: GO:0045184 ! establishment of protein localization intersection_of: has_target_end_location GO:0000791 ! euchromatin -created_by: pga creation_date: 2016-11-01T16:16:22Z [Term] @@ -139703,27 +142649,8 @@ is_a: GO:0032880 ! regulation of protein localization intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0071168 ! protein localization to chromatin relationship: regulates GO:0071168 ! protein localization to chromatin -created_by: pga creation_date: 2016-11-01T16:33:52Z -[Term] -id: GO:1905636 -name: positive regulation of RNA polymerase II regulatory region sequence-specific DNA binding -namespace: biological_process -def: "Any process that activates or increases the frequency, rate or extent of RNA polymerase II regulatory region sequence-specific DNA binding." [GO_REF:0000059, GOC:bc, GOC:PARL, GOC:TermGenie, PMID:23675531] -subset: gocheck_do_not_annotate -synonym: "activation of RNA polymerase II regulatory region sequence-specific DNA binding" NARROW [GOC:TermGenie] -synonym: "up regulation of RNA polymerase II regulatory region sequence-specific DNA binding" EXACT [GOC:TermGenie] -synonym: "up-regulation of RNA polymerase II regulatory region sequence-specific DNA binding" EXACT [GOC:TermGenie] -synonym: "upregulation of RNA polymerase II regulatory region sequence-specific DNA binding" EXACT [GOC:TermGenie] -is_a: GO:1903025 ! regulation of RNA polymerase II regulatory region sequence-specific DNA binding -is_a: GO:2000679 ! positive regulation of transcription regulatory region DNA binding -intersection_of: GO:0065007 ! biological regulation -intersection_of: positively_regulates GO:0000977 ! RNA polymerase II transcription regulatory region sequence-specific DNA binding -relationship: positively_regulates GO:0000977 ! RNA polymerase II transcription regulatory region sequence-specific DNA binding -created_by: bc -creation_date: 2016-11-03T12:03:07Z - [Term] id: GO:1905651 name: regulation of artery morphogenesis @@ -139735,7 +142662,6 @@ is_a: GO:0022603 ! regulation of anatomical structure morphogenesis intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0048844 ! artery morphogenesis relationship: regulates GO:0048844 ! artery morphogenesis -created_by: rph creation_date: 2016-11-09T12:19:37Z [Term] @@ -139762,7 +142688,6 @@ is_a: GO:2000181 ! negative regulation of blood vessel morphogenesis intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0048844 ! artery morphogenesis relationship: negatively_regulates GO:0048844 ! artery morphogenesis -created_by: rph creation_date: 2016-11-09T12:19:53Z [Term] @@ -139789,7 +142714,6 @@ is_a: GO:1905651 ! regulation of artery morphogenesis intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0048844 ! artery morphogenesis relationship: positively_regulates GO:0048844 ! artery morphogenesis -created_by: rph creation_date: 2016-11-09T12:20:01Z [Term] @@ -139803,7 +142727,6 @@ is_a: GO:1903169 ! regulation of calcium ion transmembrane transport intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0098703 ! calcium ion import across plasma membrane relationship: regulates GO:0098703 ! calcium ion import across plasma membrane -created_by: bhm creation_date: 2016-11-11T09:26:06Z [Term] @@ -139822,7 +142745,6 @@ is_a: GO:1905664 ! regulation of calcium ion import across plasma membrane intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0098703 ! calcium ion import across plasma membrane relationship: positively_regulates GO:0098703 ! calcium ion import across plasma membrane -created_by: bhm creation_date: 2016-11-11T09:26:23Z [Term] @@ -139836,7 +142758,6 @@ is_a: GO:0044088 ! regulation of vacuole organization intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0007040 ! lysosome organization relationship: regulates GO:0007040 ! lysosome organization -created_by: sl creation_date: 2016-11-11T22:01:04Z [Term] @@ -139863,7 +142784,6 @@ is_a: GO:1905671 ! regulation of lysosome organization intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0007040 ! lysosome organization relationship: negatively_regulates GO:0007040 ! lysosome organization -created_by: sl creation_date: 2016-11-11T22:01:12Z [Term] @@ -139890,7 +142810,6 @@ is_a: GO:1905671 ! regulation of lysosome organization intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0007040 ! lysosome organization relationship: positively_regulates GO:0007040 ! lysosome organization -created_by: sl creation_date: 2016-11-11T22:01:20Z [Term] @@ -139904,7 +142823,6 @@ is_a: GO:1903008 ! organelle disassembly intersection_of: GO:0022411 ! cellular component disassembly intersection_of: results_in_disassembly_of GO:0005634 ! nucleus relationship: results_in_disassembly_of GO:0005634 ! nucleus -created_by: pr creation_date: 2016-11-14T13:38:57Z [Term] @@ -139918,7 +142836,6 @@ is_a: GO:0097427 ! microtubule bundle intersection_of: GO:0097427 ! microtubule bundle intersection_of: part_of GO:0005737 ! cytoplasm relationship: part_of GO:0005737 ! cytoplasm -created_by: mah creation_date: 2016-11-24T16:52:02Z [Term] @@ -139941,7 +142858,6 @@ is_a: GO:0060457 ! negative regulation of digestive system process intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0046541 ! saliva secretion relationship: negatively_regulates GO:0046541 ! saliva secretion -created_by: pga creation_date: 2016-12-09T10:24:00Z [Term] @@ -139954,7 +142870,6 @@ is_a: GO:0035372 ! protein localization to microtubule intersection_of: GO:0008104 ! protein localization intersection_of: has_target_end_location GO:0005881 ! cytoplasmic microtubule relationship: has_target_end_location GO:0005881 ! cytoplasmic microtubule -created_by: mah creation_date: 2016-12-12T15:31:07Z [Term] @@ -139967,7 +142882,6 @@ is_a: GO:0045595 ! regulation of cell differentiation intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0048333 ! mesodermal cell differentiation relationship: regulates GO:0048333 ! mesodermal cell differentiation -created_by: rph creation_date: 2016-12-21T12:44:13Z [Term] @@ -139989,7 +142903,6 @@ is_a: GO:1905770 ! regulation of mesodermal cell differentiation intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0048333 ! mesodermal cell differentiation relationship: negatively_regulates GO:0048333 ! mesodermal cell differentiation -created_by: rph creation_date: 2016-12-21T12:44:23Z [Term] @@ -140011,7 +142924,6 @@ is_a: GO:1905770 ! regulation of mesodermal cell differentiation intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0048333 ! mesodermal cell differentiation relationship: positively_regulates GO:0048333 ! mesodermal cell differentiation -created_by: rph creation_date: 2016-12-21T12:44:32Z [Term] @@ -140030,7 +142942,6 @@ is_a: GO:0051931 ! regulation of sensory perception intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0050976 ! detection of mechanical stimulus involved in sensory perception of touch relationship: regulates GO:0050976 ! detection of mechanical stimulus involved in sensory perception of touch -created_by: hbye creation_date: 2017-01-09T15:11:04Z [Term] @@ -140078,7 +142989,6 @@ is_a: GO:1905787 ! regulation of detection of mechanical stimulus involved in se intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0050976 ! detection of mechanical stimulus involved in sensory perception of touch relationship: negatively_regulates GO:0050976 ! detection of mechanical stimulus involved in sensory perception of touch -created_by: hbye creation_date: 2017-01-09T15:11:14Z [Term] @@ -140126,7 +143036,6 @@ is_a: GO:1905787 ! regulation of detection of mechanical stimulus involved in se intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0050976 ! detection of mechanical stimulus involved in sensory perception of touch relationship: positively_regulates GO:0050976 ! detection of mechanical stimulus involved in sensory perception of touch -created_by: hbye creation_date: 2017-01-09T15:11:23Z [Term] @@ -140142,7 +143051,6 @@ is_a: GO:0098883 ! synapse pruning intersection_of: GO:0022411 ! cellular component disassembly intersection_of: results_in_disassembly_of GO:0060076 ! excitatory synapse relationship: results_in_disassembly_of GO:0060076 ! excitatory synapse -created_by: tb creation_date: 2017-01-11T22:03:06Z [Term] @@ -140159,7 +143067,6 @@ is_a: GO:0050807 ! regulation of synapse organization intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0098883 ! synapse pruning relationship: regulates GO:0098883 ! synapse pruning -created_by: tb creation_date: 2017-01-11T22:03:15Z [Term] @@ -140180,7 +143087,6 @@ is_a: GO:1905809 ! negative regulation of synapse organization intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0098883 ! synapse pruning relationship: negatively_regulates GO:0098883 ! synapse pruning -created_by: tb creation_date: 2017-01-11T22:03:24Z [Term] @@ -140201,7 +143107,6 @@ is_a: GO:1905806 ! regulation of synapse pruning intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0098883 ! synapse pruning relationship: positively_regulates GO:0098883 ! synapse pruning -created_by: tb creation_date: 2017-01-11T22:03:33Z [Term] @@ -140238,7 +143143,6 @@ is_a: GO:0051129 ! negative regulation of cellular component organization intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0050808 ! synapse organization relationship: negatively_regulates GO:0050808 ! synapse organization -created_by: tb creation_date: 2017-01-11T22:03:41Z [Term] @@ -140254,7 +143158,6 @@ is_a: GO:1905806 ! regulation of synapse pruning intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:1905805 ! excitatory synapse pruning relationship: regulates GO:1905805 ! excitatory synapse pruning -created_by: tb creation_date: 2017-01-12T02:38:27Z [Term] @@ -140275,7 +143178,6 @@ is_a: GO:1905810 ! regulation of excitatory synapse pruning intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:1905805 ! excitatory synapse pruning relationship: negatively_regulates GO:1905805 ! excitatory synapse pruning -created_by: tb creation_date: 2017-01-12T02:38:36Z [Term] @@ -140302,7 +143204,6 @@ is_a: GO:2001252 ! positive regulation of chromosome organization intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0030261 ! chromosome condensation relationship: positively_regulates GO:0030261 ! chromosome condensation -created_by: bhm creation_date: 2017-01-13T14:13:44Z [Term] @@ -140319,7 +143220,6 @@ is_a: GO:0031115 ! negative regulation of microtubule polymerization intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0007020 ! microtubule nucleation relationship: negatively_regulates GO:0007020 ! microtubule nucleation -created_by: hbye creation_date: 2017-01-17T12:00:56Z [Term] @@ -140332,7 +143232,6 @@ is_a: GO:0035295 ! tube development intersection_of: GO:0048856 ! anatomical structure development intersection_of: results_in_development_of UBERON:0001301 ! epididymis relationship: results_in_development_of UBERON:0001301 ! epididymis -created_by: sl creation_date: 2017-01-27T00:00:33Z [Term] @@ -140347,7 +143246,6 @@ is_a: GO:0032880 ! regulation of protein localization intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:1902463 ! protein localization to cell leading edge relationship: regulates GO:1902463 ! protein localization to cell leading edge -created_by: sl creation_date: 2017-01-27T19:34:55Z [Term] @@ -140379,7 +143277,6 @@ is_a: GO:1905871 ! regulation of protein localization to cell leading edge intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:1902463 ! protein localization to cell leading edge relationship: negatively_regulates GO:1902463 ! protein localization to cell leading edge -created_by: sl creation_date: 2017-01-27T19:35:04Z [Term] @@ -140411,7 +143308,6 @@ is_a: GO:1905871 ! regulation of protein localization to cell leading edge intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:1902463 ! protein localization to cell leading edge relationship: positively_regulates GO:1902463 ! protein localization to cell leading edge -created_by: sl creation_date: 2017-01-27T19:35:13Z [Term] @@ -140426,7 +143322,6 @@ is_a: GO:2000241 ! regulation of reproductive process intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0048477 ! oogenesis relationship: regulates GO:0048477 ! oogenesis -created_by: hbye creation_date: 2017-01-31T09:31:05Z [Term] @@ -140450,7 +143345,6 @@ is_a: GO:2000242 ! negative regulation of reproductive process intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0048477 ! oogenesis relationship: negatively_regulates GO:0048477 ! oogenesis -created_by: hbye creation_date: 2017-01-31T09:31:15Z [Term] @@ -140474,7 +143368,6 @@ is_a: GO:2000243 ! positive regulation of reproductive process intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0048477 ! oogenesis relationship: positively_regulates GO:0048477 ! oogenesis -created_by: hbye creation_date: 2017-01-31T09:31:23Z [Term] @@ -140486,7 +143379,6 @@ is_a: GO:1901861 ! regulation of muscle tissue development intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0048745 ! smooth muscle tissue development relationship: regulates GO:0048745 ! smooth muscle tissue development -created_by: bhm creation_date: 2017-02-01T14:31:16Z [Term] @@ -140503,7 +143395,6 @@ is_a: GO:1905899 ! regulation of smooth muscle tissue development intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0048745 ! smooth muscle tissue development relationship: negatively_regulates GO:0048745 ! smooth muscle tissue development -created_by: bhm creation_date: 2017-02-01T14:31:24Z [Term] @@ -140520,7 +143411,6 @@ is_a: GO:1905899 ! regulation of smooth muscle tissue development intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0048745 ! smooth muscle tissue development relationship: positively_regulates GO:0048745 ! smooth muscle tissue development -created_by: bhm creation_date: 2017-02-01T14:31:33Z [Term] @@ -140532,7 +143422,6 @@ is_a: GO:0050793 ! regulation of developmental process intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0001707 ! mesoderm formation relationship: regulates GO:0001707 ! mesoderm formation -created_by: rph creation_date: 2017-02-03T12:28:20Z [Term] @@ -140549,7 +143438,6 @@ is_a: GO:2000381 ! negative regulation of mesoderm development intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0001707 ! mesoderm formation relationship: negatively_regulates GO:0001707 ! mesoderm formation -created_by: rph creation_date: 2017-02-03T12:28:29Z [Term] @@ -140566,7 +143454,6 @@ is_a: GO:2000382 ! positive regulation of mesoderm development intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0001707 ! mesoderm formation relationship: positively_regulates GO:0001707 ! mesoderm formation -created_by: rph creation_date: 2017-02-03T12:28:38Z [Term] @@ -140580,7 +143467,6 @@ is_a: GO:1903169 ! regulation of calcium ion transmembrane transport intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:1990034 ! calcium ion export across plasma membrane relationship: regulates GO:1990034 ! calcium ion export across plasma membrane -created_by: rph creation_date: 2017-02-07T13:20:39Z [Term] @@ -140603,7 +143489,6 @@ is_a: GO:1905912 ! regulation of calcium ion export across plasma membrane intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:1990034 ! calcium ion export across plasma membrane relationship: negatively_regulates GO:1990034 ! calcium ion export across plasma membrane -created_by: rph creation_date: 2017-02-07T13:20:48Z [Term] @@ -140626,7 +143511,6 @@ is_a: GO:1905912 ! regulation of calcium ion export across plasma membrane intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:1990034 ! calcium ion export across plasma membrane relationship: positively_regulates GO:1990034 ! calcium ion export across plasma membrane -created_by: rph creation_date: 2017-02-07T13:20:56Z [Term] @@ -140643,7 +143527,6 @@ is_a: GO:0060408 ! regulation of acetylcholine metabolic process intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0008292 ! acetylcholine biosynthetic process relationship: regulates GO:0008292 ! acetylcholine biosynthetic process -created_by: bc creation_date: 2017-02-08T13:08:30Z [Term] @@ -140681,7 +143564,6 @@ is_a: GO:1905921 ! regulation of acetylcholine biosynthetic process intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0008292 ! acetylcholine biosynthetic process relationship: negatively_regulates GO:0008292 ! acetylcholine biosynthetic process -created_by: bc creation_date: 2017-02-08T13:08:39Z [Term] @@ -140719,7 +143601,6 @@ is_a: GO:1905921 ! regulation of acetylcholine biosynthetic process intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0008292 ! acetylcholine biosynthetic process relationship: positively_regulates GO:0008292 ! acetylcholine biosynthetic process -created_by: bc creation_date: 2017-02-08T13:08:48Z [Term] @@ -140732,7 +143613,6 @@ is_a: GO:0051239 ! regulation of multicellular organismal process intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0036093 ! germ cell proliferation relationship: regulates GO:0036093 ! germ cell proliferation -created_by: hbye creation_date: 2017-02-09T14:51:31Z [Term] @@ -140750,7 +143630,6 @@ is_a: GO:1905936 ! regulation of germ cell proliferation intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0036093 ! germ cell proliferation relationship: negatively_regulates GO:0036093 ! germ cell proliferation -created_by: hbye creation_date: 2017-02-09T14:51:41Z [Term] @@ -140768,7 +143647,6 @@ is_a: GO:1905936 ! regulation of germ cell proliferation intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0036093 ! germ cell proliferation relationship: positively_regulates GO:0036093 ! germ cell proliferation -created_by: hbye creation_date: 2017-02-09T14:51:51Z [Term] @@ -140782,7 +143660,6 @@ is_a: GO:2000241 ! regulation of reproductive process intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0008406 ! gonad development relationship: regulates GO:0008406 ! gonad development -created_by: hbye creation_date: 2017-02-09T17:01:50Z [Term] @@ -140806,7 +143683,6 @@ is_a: GO:2000242 ! negative regulation of reproductive process intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0008406 ! gonad development relationship: negatively_regulates GO:0008406 ! gonad development -created_by: hbye creation_date: 2017-02-09T17:01:59Z [Term] @@ -140830,7 +143706,6 @@ is_a: GO:2000243 ! positive regulation of reproductive process intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0008406 ! gonad development relationship: positively_regulates GO:0008406 ! gonad development -created_by: hbye creation_date: 2017-02-09T17:02:08Z [Term] @@ -140843,7 +143718,6 @@ is_a: GO:0048583 ! regulation of response to stimulus intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0051592 ! response to calcium ion relationship: regulates GO:0051592 ! response to calcium ion -created_by: bc creation_date: 2017-02-13T10:56:34Z [Term] @@ -140865,7 +143739,6 @@ is_a: GO:1905945 ! regulation of response to calcium ion intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0051592 ! response to calcium ion relationship: negatively_regulates GO:0051592 ! response to calcium ion -created_by: bc creation_date: 2017-02-13T10:56:41Z [Term] @@ -140887,7 +143760,6 @@ is_a: GO:1905945 ! regulation of response to calcium ion intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0051592 ! response to calcium ion relationship: positively_regulates GO:0051592 ! response to calcium ion -created_by: bc creation_date: 2017-02-13T10:56:49Z [Term] @@ -140906,7 +143778,6 @@ is_a: GO:1905664 ! regulation of calcium ion import across plasma membrane intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0098703 ! calcium ion import across plasma membrane relationship: negatively_regulates GO:0098703 ! calcium ion import across plasma membrane -created_by: bhm creation_date: 2017-02-17T09:42:30Z [Term] @@ -140919,7 +143790,6 @@ is_a: GO:0032879 ! regulation of localization intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0010876 ! lipid localization relationship: regulates GO:0010876 ! lipid localization -created_by: rz creation_date: 2017-02-21T12:12:22Z [Term] @@ -140941,7 +143811,6 @@ is_a: GO:1905952 ! regulation of lipid localization intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0010876 ! lipid localization relationship: negatively_regulates GO:0010876 ! lipid localization -created_by: rz creation_date: 2017-02-21T12:12:41Z [Term] @@ -140963,7 +143832,6 @@ is_a: GO:1905952 ! regulation of lipid localization intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0010876 ! lipid localization relationship: positively_regulates GO:0010876 ! lipid localization -created_by: rz creation_date: 2017-02-21T12:12:49Z [Term] @@ -140981,7 +143849,6 @@ is_a: GO:1905331 ! negative regulation of morphogenesis of an epithelium intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0061154 ! endothelial tube morphogenesis relationship: negatively_regulates GO:0061154 ! endothelial tube morphogenesis -created_by: rph creation_date: 2017-02-21T15:17:31Z [Term] @@ -140999,7 +143866,6 @@ is_a: GO:1905332 ! positive regulation of morphogenesis of an epithelium intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0061154 ! endothelial tube morphogenesis relationship: positively_regulates GO:0061154 ! endothelial tube morphogenesis -created_by: rph creation_date: 2017-02-21T15:17:39Z [Term] @@ -141011,21 +143877,18 @@ is_a: GO:0030182 ! neuron differentiation intersection_of: GO:0030154 ! cell differentiation intersection_of: results_in_acquisition_of_features_of CL:0000679 ! glutamatergic neuron relationship: results_in_acquisition_of_features_of CL:0000679 ! glutamatergic neuron -created_by: sl creation_date: 2017-02-23T17:40:43Z [Term] id: GO:1990009 name: retinal cell apoptotic process namespace: biological_process -alt_id: GO:0046674 def: "Any apoptotic process in a retinal cell." [GOC:mtg_apoptosis, PMID:15558487, PMID:24664675] synonym: "induction of retinal programmed cell death" RELATED [] is_a: GO:0006915 ! apoptotic process intersection_of: GO:0006915 ! apoptotic process intersection_of: occurs_in CL:0009004 ! retinal cell relationship: occurs_in CL:0009004 ! retinal cell -created_by: pr creation_date: 2012-12-12T10:15:08Z [Term] @@ -141037,7 +143900,6 @@ is_a: GO:1990009 ! retinal cell apoptotic process intersection_of: GO:0006915 ! apoptotic process intersection_of: occurs_in CL:0009001 ! compound eye retinal cell relationship: occurs_in CL:0009001 ! compound eye retinal cell -created_by: pr creation_date: 2012-12-12T10:21:07Z [Term] @@ -141054,7 +143916,6 @@ intersection_of: has_primary_input CHEBI:29108 intersection_of: has_target_end_location GO:0005576 ! extracellular region intersection_of: has_target_start_location GO:0005829 ! cytosol intersection_of: results_in_transport_across GO:0005886 ! plasma membrane -created_by: mah creation_date: 2013-02-07T13:01:29Z [Term] @@ -141092,7 +143953,6 @@ intersection_of: has_target_start_location GO:0098793 ! presynapse intersection_of: occurs_in GO:1904115 ! axon cytoplasm intersection_of: results_in_transport_along GO:0005874 ! microtubule relationship: has_primary_input GO:0098992 ! neuronal dense core vesicle -created_by: pr creation_date: 2013-02-19T13:31:44Z [Term] @@ -141104,7 +143964,6 @@ is_a: GO:1904019 ! epithelial cell apoptotic process intersection_of: GO:0006915 ! apoptotic process intersection_of: occurs_in CL:0011004 ! lens fiber cell relationship: occurs_in CL:0011004 ! lens fiber cell -created_by: hjd creation_date: 2013-05-01T19:09:28Z [Term] @@ -141124,7 +143983,6 @@ intersection_of: has_primary_input GO:0070062 ! extracellular exosome relationship: has_primary_input GO:0070062 ! extracellular exosome relationship: part_of GO:0097734 ! extracellular exosome biogenesis property_value: RO:0002161 NCBITaxon:4890 -created_by: hjd creation_date: 2013-09-04T21:08:14Z [Term] @@ -141136,7 +143994,6 @@ is_a: GO:0003682 ! chromatin binding intersection_of: GO:0005488 ! binding intersection_of: has_primary_input GO:0000791 ! euchromatin relationship: has_primary_input GO:0000791 ! euchromatin -created_by: tb creation_date: 2013-09-11T19:18:38Z [Term] @@ -141148,7 +144005,6 @@ is_a: GO:1902494 ! catalytic complex intersection_of: GO:1902494 ! catalytic complex intersection_of: capable_of GO:0016740 ! transferase activity relationship: capable_of GO:0016740 ! transferase activity -created_by: bhm creation_date: 2013-11-12T13:20:12Z [Term] @@ -141161,7 +144017,6 @@ is_a: GO:0042562 ! hormone binding intersection_of: GO:0005488 ! binding intersection_of: has_primary_input CHEBI:26764 relationship: has_primary_input CHEBI:26764 -created_by: pr creation_date: 2013-11-15T09:26:18Z [Term] @@ -141173,7 +144028,6 @@ is_a: GO:0019215 ! intermediate filament binding intersection_of: GO:0005488 ! binding intersection_of: has_primary_input GO:0045095 ! keratin filament relationship: has_primary_input GO:0045095 ! keratin filament -created_by: tb creation_date: 2013-12-13T22:05:25Z [Term] @@ -141185,7 +144039,6 @@ is_a: GO:0097530 ! granulocyte migration intersection_of: GO:0016477 ! cell migration intersection_of: results_in_movement_of CL:0000775 ! neutrophil relationship: results_in_movement_of CL:0000775 ! neutrophil -created_by: sl creation_date: 2014-01-10T00:17:47Z [Term] @@ -141198,7 +144051,6 @@ is_a: GO:0006403 ! RNA localization intersection_of: GO:0006403 ! RNA localization intersection_of: has_target_end_location GO:0000785 ! chromatin relationship: has_target_end_location GO:0000785 ! chromatin -created_by: mah creation_date: 2014-01-30T15:55:34Z [Term] @@ -141212,7 +144064,6 @@ is_a: GO:0032991 ! protein-containing complex intersection_of: GO:0032991 ! protein-containing complex intersection_of: capable_of GO:0005215 ! transporter activity relationship: capable_of GO:0005215 ! transporter activity -created_by: bhm creation_date: 2014-03-26T14:23:27Z [Term] @@ -141227,7 +144078,6 @@ is_a: GO:0048608 ! reproductive structure development intersection_of: GO:0048856 ! anatomical structure development intersection_of: results_in_development_of UBERON:0006435 ! os penis relationship: results_in_development_of UBERON:0006435 ! os penis -created_by: sl creation_date: 2014-05-01T23:59:13Z [Term] @@ -141241,8 +144091,6 @@ is_a: GO:0150104 ! transport across blood-brain barrier intersection_of: GO:0150104 ! transport across blood-brain barrier intersection_of: has_primary_input CHEBI:18059 intersection_of: results_in_transport_across UBERON:0000120 ! blood brain barrier -relationship: RO:0002162 NCBITaxon:6072 {all_only="true"} ! in taxon Eumetazoa -created_by: sjp creation_date: 2014-05-08T09:52:28Z [Term] @@ -141256,7 +144104,6 @@ intersection_of: GO:0098754 ! detoxification intersection_of: has_primary_input CHEBI:24875 relationship: has_primary_input CHEBI:24875 relationship: part_of GO:0010039 ! response to iron ion -created_by: sart creation_date: 2014-08-19T10:12:46Z [Term] @@ -141269,14 +144116,12 @@ is_a: GO:0061792 ! secretory granule maturation intersection_of: GO:0021700 ! developmental maturation intersection_of: results_in_maturation_of GO:0031045 ! dense core granule relationship: results_in_maturation_of GO:0031045 ! dense core granule -created_by: kmv creation_date: 2014-09-30T20:35:11Z [Term] id: GO:1990573 name: potassium ion import across plasma membrane namespace: biological_process -alt_id: GO:0010107 def: "The directed movement of potassium ions from outside of a cell, across the plasma membrane and into the cytosol." [PMID:9139127] synonym: "potassium import" BROAD [] synonym: "potassium ion import" BROAD [] @@ -141288,7 +144133,6 @@ intersection_of: has_primary_input CHEBI:29103 intersection_of: has_target_end_location GO:0005829 ! cytosol intersection_of: has_target_start_location GO:0005576 ! extracellular region intersection_of: results_in_transport_across GO:0005886 ! plasma membrane -created_by: vw creation_date: 2014-12-04T09:48:12Z [Term] @@ -141301,7 +144145,6 @@ is_a: GO:2000765 ! regulation of cytoplasmic translation intersection_of: GO:0050789 ! regulation of biological process intersection_of: regulates GO:0002184 ! cytoplasmic translational termination relationship: regulates GO:0002184 ! cytoplasmic translational termination -created_by: vw creation_date: 2014-12-10T15:48:55Z [Term] @@ -141310,12 +144153,10 @@ name: sebum secreting cell proliferation namespace: biological_process def: "The multiplication or reproduction of sebocytes by cell division, resulting in the expansion of their population. A sebocyte is an epithelial cell that makes up the sebaceous glands, and secrete sebum." [GOC:hjd, PMID:16901790, PMID:18474083] synonym: "sebocyte proliferation" RELATED [GOC:dph] -is_a: BFO:0000003 -is_a: GO:0008283 ! cell population proliferation +is_a: GO:0050673 ! epithelial cell proliferation intersection_of: GO:0008283 ! cell population proliferation -intersection_of: acts_on_population_of CL:0000317 ! sebum secreting cell -relationship: acts_on_population_of CL:0000317 ! sebum secreting cell -created_by: hjd +intersection_of: acts_on_population_of CL:0000317 ! sebocyte +relationship: acts_on_population_of CL:0000317 ! sebocyte creation_date: 2015-02-23T19:43:49Z [Term] @@ -141335,9 +144176,8 @@ id: GO:1990716 name: axonemal central apparatus namespace: cellular_component def: "Part of the 9+2 axoneme, that occurs in most motile cilia, consisting of the pair of two single central microtubules and their associated structures which include the central pair projections, the central pair bridges linking the two tubules, and the central pair caps which are attached to the distal or plus ends of the microtubules." [GOC:cilia, PMID:21586547, PMID:9295136] -is_a: GO:0110165 ! cellular anatomical entity +is_a: GO:0110165 ! cellular anatomical structure relationship: part_of GO:0005930 ! axoneme -created_by: krc creation_date: 2015-03-27T22:33:23Z [Term] @@ -141348,7 +144188,6 @@ def: "One of two microtubules present in the axonemal central pair. It is distin synonym: "C1 tubule" BROAD [] is_a: GO:0005879 ! axonemal microtubule relationship: part_of GO:0097540 ! axonemal central pair -created_by: krc creation_date: 2015-03-27T22:55:12Z [Term] @@ -141359,7 +144198,6 @@ def: "One of two microtubules present in the axonemal central pair. It is distin synonym: "C2 tubule" BROAD [] is_a: GO:0005879 ! axonemal microtubule relationship: part_of GO:0097540 ! axonemal central pair -created_by: krc creation_date: 2015-03-27T22:58:40Z [Term] @@ -141371,7 +144209,6 @@ is_a: GO:0050673 ! epithelial cell proliferation intersection_of: GO:0008283 ! cell population proliferation intersection_of: acts_on_population_of CL:0000501 ! granulosa cell relationship: acts_on_population_of CL:0000501 ! granulosa cell -created_by: sl creation_date: 2015-05-06T18:56:04Z [Term] @@ -141386,7 +144223,6 @@ intersection_of: GO:0098754 ! detoxification intersection_of: occurs_in CL:0000000 ! cell relationship: occurs_in CL:0000000 ! cell relationship: part_of GO:0097237 ! cellular response to toxic substance -created_by: vw creation_date: 2015-05-18T16:17:46Z [Term] @@ -141398,7 +144234,6 @@ is_a: GO:0036135 ! Schwann cell migration is_a: GO:0060326 ! cell chemotaxis intersection_of: GO:0006935 ! chemotaxis intersection_of: results_in_movement_of CL:0002573 ! Schwann cell -created_by: sl creation_date: 2015-05-21T19:19:09Z [Term] @@ -141413,7 +144248,6 @@ relationship: occurs_in UBERON:0001155 ! colon relationship: part_of GO:0014827 ! intestine smooth muscle contraction relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata relationship: RO:0002162 NCBITaxon:7742 {all_only="true"} ! in taxon Vertebrata -created_by: sl creation_date: 2015-06-10T18:29:21Z [Term] @@ -141427,7 +144261,6 @@ is_a: GO:0008015 ! blood circulation intersection_of: GO:0008015 ! blood circulation intersection_of: occurs_in UBERON:0004786 ! gastrointestinal system mucosa relationship: occurs_in UBERON:0004786 ! gastrointestinal system mucosa -created_by: sl creation_date: 2015-06-10T20:11:09Z [Term] @@ -141442,7 +144275,6 @@ relationship: occurs_in UBERON:0002108 ! small intestine relationship: part_of GO:0014827 ! intestine smooth muscle contraction relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata relationship: RO:0002162 NCBITaxon:7742 {all_only="true"} ! in taxon Vertebrata -created_by: sl creation_date: 2015-06-11T18:02:33Z [Term] @@ -141451,7 +144283,6 @@ name: lipoprotein particle namespace: cellular_component def: "A spherical particle containing non-covalently associated proteins and lipids. Examples are plasma lipoprotein particles which transport lipids in the blood or lymph." [GOC:vesicles] is_a: GO:0032994 ! protein-lipid complex -created_by: pr creation_date: 2015-06-18T08:42:53Z [Term] @@ -141465,31 +144296,6 @@ intersection_of: has_target_end_location GO:0071944 ! cell periphery relationship: has_target_end_location GO:0071944 ! cell periphery creation_date: 2015-06-18T22:37:39Z -[Term] -id: GO:1990784 -name: response to dsDNA -namespace: biological_process -def: "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a double-stranded DNA stimulus." [PMID:10051633] -synonym: "response to double-stranded DNA" EXACT [] -is_a: GO:0042221 ! response to chemical -intersection_of: GO:0050896 ! response to stimulus -intersection_of: has_primary_input CHEBI:4705 -relationship: has_primary_input CHEBI:4705 -created_by: sl -creation_date: 2015-06-24T17:54:13Z - -[Term] -id: GO:1990786 -name: cellular response to dsDNA -namespace: biological_process -def: "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a double-stranded DNA stimulus." [PMID:10051633] -is_a: GO:0070887 ! cellular response to chemical stimulus -is_a: GO:1990784 ! response to dsDNA -intersection_of: GO:0070887 ! cellular response to chemical stimulus -intersection_of: has_primary_input CHEBI:4705 -created_by: sl -creation_date: 2015-06-24T22:48:25Z - [Term] id: GO:1990791 name: dorsal root ganglion development @@ -141500,7 +144306,6 @@ is_a: GO:0061548 ! ganglion development intersection_of: GO:0048856 ! anatomical structure development intersection_of: results_in_development_of UBERON:0000044 ! dorsal root ganglion relationship: results_in_development_of UBERON:0000044 ! dorsal root ganglion -created_by: sl creation_date: 2015-07-02T22:09:54Z [Term] @@ -141513,7 +144318,6 @@ is_a: GO:0007165 ! signal transduction intersection_of: GO:0007165 ! signal transduction intersection_of: has_part GO:0015276 ! ligand-gated monoatomic ion channel activity relationship: has_part GO:0015276 ! ligand-gated monoatomic ion channel activity -created_by: bhm creation_date: 2015-07-20T12:09:56Z [Term] @@ -141525,27 +144329,14 @@ is_a: GO:0003333 ! amino acid transmembrane transport is_a: GO:0015802 ! basic amino acid transport intersection_of: GO:0015802 ! basic amino acid transport intersection_of: results_in_transport_across GO:0016020 ! membrane -created_by: vw creation_date: 2015-08-19T07:47:00Z -[Term] -id: GO:1990837 -name: sequence-specific double-stranded DNA binding -namespace: molecular_function -def: "Binding to double-stranded DNA of a specific nucleotide composition, e.g. GC-rich DNA binding, or with a specific sequence motif or type of DNA, e.g. promotor binding or rDNA binding." [GOC:dos, GOC:sl] -synonym: "sequence-specific dsDNA binding" EXACT [] -is_a: GO:0003690 ! double-stranded DNA binding -is_a: GO:0043565 ! sequence-specific DNA binding -created_by: sl -creation_date: 2015-08-25T17:30:06Z - [Term] id: GO:1990845 name: adaptive thermogenesis namespace: biological_process def: "The regulated production of heat in response to short term environmental changes, such as stress, diet or reduced temperature." [PMID:17260010, PMID:20363363] is_a: GO:0008152 ! metabolic process -created_by: sl creation_date: 2015-08-31T18:19:49Z [Term] @@ -141562,7 +144353,6 @@ intersection_of: GO:0051179 ! localization intersection_of: has_primary_input GO:0005773 ! vacuole relationship: has_primary_input GO:0005773 ! vacuole property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/22182" xsd:anyURI -created_by: mcc creation_date: 2015-09-10T08:16:02Z [Term] @@ -141576,7 +144366,6 @@ is_a: GO:0050673 ! epithelial cell proliferation intersection_of: GO:0008283 ! cell population proliferation intersection_of: acts_on_population_of CL:0000622 ! acinar cell relationship: acts_on_population_of CL:0000622 ! acinar cell -created_by: sl creation_date: 2015-09-25T14:26:09Z [Term] @@ -141590,15 +144379,12 @@ is_a: GO:0048659 ! smooth muscle cell proliferation intersection_of: GO:0008283 ! cell population proliferation intersection_of: acts_on_population_of CL:0000359 ! vascular associated smooth muscle cell relationship: acts_on_population_of CL:0000359 ! vascular associated smooth muscle cell -created_by: sl creation_date: 2015-09-29T16:34:59Z [Term] id: GO:1990904 name: ribonucleoprotein complex namespace: cellular_component -alt_id: GO:0030529 -alt_id: GO:1990903 def: "A macromolecular complex that contains both RNA and protein molecules." [GOC:krc, GOC:vesicles] subset: goslim_pir synonym: "extracellular ribonucleoprotein complex" NARROW [] @@ -141609,7 +144395,6 @@ synonym: "RNP" EXACT [] xref: Wikipedia:Ribonucleoprotein is_a: GO:0032991 ! protein-containing complex relationship: has_part CHEBI:33697 -created_by: pr creation_date: 2015-11-19T12:26:37Z [Term] @@ -141622,7 +144407,6 @@ intersection_of: GO:0005737 ! cytoplasm intersection_of: part_of CL:0000025 ! egg cell relationship: part_of CL:0000025 ! egg cell property_value: RO:0002161 NCBITaxon:4751 -created_by: sl creation_date: 2015-12-10T21:40:16Z [Term] @@ -141637,7 +144421,6 @@ is_a: GO:0048144 ! fibroblast proliferation intersection_of: GO:0008283 ! cell population proliferation intersection_of: acts_on_population_of CL:0000632 ! hepatic stellate cell relationship: acts_on_population_of CL:0000632 ! hepatic stellate cell -created_by: sl creation_date: 2016-01-13T23:12:57Z [Term] @@ -141654,7 +144437,6 @@ is_a: GO:0002262 ! myeloid cell homeostasis intersection_of: GO:0048872 ! homeostasis of number of cells intersection_of: acts_on_population_of CL:0000771 ! eosinophil relationship: acts_on_population_of CL:0000771 ! eosinophil -created_by: sl creation_date: 2016-06-06T22:34:31Z [Term] @@ -141668,7 +144450,6 @@ is_a: GO:0002262 ! myeloid cell homeostasis intersection_of: GO:0048872 ! homeostasis of number of cells intersection_of: acts_on_population_of CL:0000767 ! basophil relationship: acts_on_population_of CL:0000767 ! basophil -created_by: sl creation_date: 2016-06-06T22:38:22Z [Term] @@ -141680,7 +144461,6 @@ is_a: GO:2000027 ! regulation of animal organ morphogenesis intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0072284 ! metanephric S-shaped body morphogenesis relationship: regulates GO:0072284 ! metanephric S-shaped body morphogenesis -created_by: jl creation_date: 2010-07-30T02:14:33Z [Term] @@ -141693,7 +144473,6 @@ is_a: GO:2000004 ! regulation of metanephric S-shaped body morphogenesis intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0072284 ! metanephric S-shaped body morphogenesis relationship: negatively_regulates GO:0072284 ! metanephric S-shaped body morphogenesis -created_by: jl creation_date: 2010-07-30T02:14:37Z [Term] @@ -141705,7 +144484,6 @@ is_a: GO:2000027 ! regulation of animal organ morphogenesis intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0072278 ! metanephric comma-shaped body morphogenesis relationship: regulates GO:0072278 ! metanephric comma-shaped body morphogenesis -created_by: jl creation_date: 2010-07-30T02:17:12Z [Term] @@ -141718,7 +144496,6 @@ is_a: GO:2000006 ! regulation of metanephric comma-shaped body morphogenesis intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0072278 ! metanephric comma-shaped body morphogenesis relationship: negatively_regulates GO:0072278 ! metanephric comma-shaped body morphogenesis -created_by: jl creation_date: 2010-07-30T02:17:17Z [Term] @@ -141732,7 +144509,6 @@ is_a: GO:1905939 ! regulation of gonad development intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0008584 ! male gonad development relationship: regulates GO:0008584 ! male gonad development -created_by: jl creation_date: 2010-07-15T03:29:05Z [Term] @@ -141747,7 +144523,6 @@ is_a: GO:2000018 ! regulation of male gonad development intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0008584 ! male gonad development relationship: negatively_regulates GO:0008584 ! male gonad development -created_by: jl creation_date: 2010-07-15T03:29:10Z [Term] @@ -141762,7 +144537,6 @@ is_a: GO:2000018 ! regulation of male gonad development intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0008584 ! male gonad development relationship: positively_regulates GO:0008584 ! male gonad development -created_by: jl creation_date: 2010-07-15T03:29:13Z [Term] @@ -141775,7 +144549,6 @@ is_a: GO:0051239 ! regulation of multicellular organismal process intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0007275 ! multicellular organism development relationship: regulates GO:0007275 ! multicellular organism development -created_by: tb creation_date: 2010-08-05T11:25:59Z [Term] @@ -141788,7 +144561,6 @@ is_a: GO:0022603 ! regulation of anatomical structure morphogenesis intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0009887 ! animal organ morphogenesis relationship: regulates GO:0009887 ! animal organ morphogenesis -created_by: tb creation_date: 2010-08-05T11:26:27Z [Term] @@ -141801,7 +144573,6 @@ is_a: GO:0051302 ! regulation of cell division intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0017145 ! stem cell division relationship: regulates GO:0017145 ! stem cell division -created_by: tb creation_date: 2010-08-05T11:34:53Z [Term] @@ -141816,7 +144587,6 @@ intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0019827 ! stem cell population maintenance relationship: regulates GO:0019827 ! stem cell population maintenance property_value: RO:0002161 NCBITaxon:4751 -created_by: tb creation_date: 2010-08-05T11:35:25Z [Term] @@ -141829,7 +144599,6 @@ is_a: GO:0051150 ! regulation of smooth muscle cell differentiation intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0072193 ! ureter smooth muscle cell differentiation relationship: regulates GO:0072193 ! ureter smooth muscle cell differentiation -created_by: jl creation_date: 2010-08-20T01:44:16Z [Term] @@ -141843,7 +144612,6 @@ is_a: GO:2000061 ! regulation of ureter smooth muscle cell differentiation intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0072193 ! ureter smooth muscle cell differentiation relationship: negatively_regulates GO:0072193 ! ureter smooth muscle cell differentiation -created_by: jl creation_date: 2010-08-20T01:44:23Z [Term] @@ -141857,7 +144625,6 @@ is_a: GO:2000061 ! regulation of ureter smooth muscle cell differentiation intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0072193 ! ureter smooth muscle cell differentiation relationship: positively_regulates GO:0072193 ! ureter smooth muscle cell differentiation -created_by: jl creation_date: 2010-08-20T01:44:28Z [Term] @@ -141870,7 +144637,6 @@ is_a: GO:0031347 ! regulation of defense response intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0002213 ! defense response to insect relationship: regulates GO:0002213 ! defense response to insect -created_by: tb creation_date: 2010-08-23T09:30:00Z [Term] @@ -141886,7 +144652,6 @@ is_a: GO:0080134 ! regulation of response to stress intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0009414 ! response to water deprivation relationship: regulates GO:0009414 ! response to water deprivation -created_by: tb creation_date: 2010-08-23T11:32:32Z [Term] @@ -141900,7 +144665,6 @@ is_a: GO:0060284 ! regulation of cell development intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0003323 ! type B pancreatic cell development relationship: regulates GO:0003323 ! type B pancreatic cell development -created_by: tb creation_date: 2010-08-27T11:19:37Z [Term] @@ -141916,7 +144680,6 @@ is_a: GO:2000074 ! regulation of type B pancreatic cell development intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0003323 ! type B pancreatic cell development relationship: negatively_regulates GO:0003323 ! type B pancreatic cell development -created_by: tb creation_date: 2010-08-27T11:21:17Z [Term] @@ -141933,7 +144696,6 @@ is_a: GO:2000074 ! regulation of type B pancreatic cell development intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0003323 ! type B pancreatic cell development relationship: positively_regulates GO:0003323 ! type B pancreatic cell development -created_by: tb creation_date: 2010-08-27T11:21:19Z [Term] @@ -141946,7 +144708,6 @@ is_a: GO:2000696 ! regulation of epithelial cell differentiation involved in kid intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0061261 ! mesenchymal to epithelial transition involved in mesonephros morphogenesis relationship: regulates GO:0061261 ! mesenchymal to epithelial transition involved in mesonephros morphogenesis -created_by: dph creation_date: 2010-09-03T06:06:41Z [Term] @@ -141960,7 +144721,6 @@ is_a: GO:2000697 ! negative regulation of epithelial cell differentiation involv intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0061261 ! mesenchymal to epithelial transition involved in mesonephros morphogenesis relationship: negatively_regulates GO:0061261 ! mesenchymal to epithelial transition involved in mesonephros morphogenesis -created_by: dph creation_date: 2010-09-03T06:08:21Z [Term] @@ -141974,7 +144734,6 @@ is_a: GO:2000698 ! positive regulation of epithelial cell differentiation involv intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0061261 ! mesenchymal to epithelial transition involved in mesonephros morphogenesis relationship: positively_regulates GO:0061261 ! mesenchymal to epithelial transition involved in mesonephros morphogenesis -created_by: dph creation_date: 2010-09-03T06:08:24Z [Term] @@ -141987,7 +144746,6 @@ is_a: GO:0090192 ! regulation of glomerulus development intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0061224 ! mesonephric glomerulus development relationship: regulates GO:0061224 ! mesonephric glomerulus development -created_by: dph creation_date: 2010-09-03T06:09:19Z [Term] @@ -142000,7 +144758,6 @@ is_a: GO:2000087 ! regulation of mesonephric glomerulus development intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0061224 ! mesonephric glomerulus development relationship: negatively_regulates GO:0061224 ! mesonephric glomerulus development -created_by: dph creation_date: 2010-09-03T06:09:22Z [Term] @@ -142013,7 +144770,6 @@ is_a: GO:2000087 ! regulation of mesonephric glomerulus development intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0061224 ! mesonephric glomerulus development relationship: positively_regulates GO:0061224 ! mesonephric glomerulus development -created_by: dph creation_date: 2010-09-03T06:09:24Z [Term] @@ -142025,7 +144781,6 @@ is_a: GO:0072182 ! regulation of nephron tubule epithelial cell differentiation intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0061265 ! mesonephric nephron tubule epithelial cell differentiation relationship: regulates GO:0061265 ! mesonephric nephron tubule epithelial cell differentiation -created_by: dph creation_date: 2010-09-03T06:12:25Z [Term] @@ -142038,7 +144793,6 @@ is_a: GO:2000093 ! regulation of mesonephric nephron tubule epithelial cell diff intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0061265 ! mesonephric nephron tubule epithelial cell differentiation relationship: negatively_regulates GO:0061265 ! mesonephric nephron tubule epithelial cell differentiation -created_by: dph creation_date: 2010-09-03T06:12:28Z [Term] @@ -142051,7 +144805,6 @@ is_a: GO:0042981 ! regulation of apoptotic process intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0071887 ! leukocyte apoptotic process relationship: regulates GO:0071887 ! leukocyte apoptotic process -created_by: mah creation_date: 2010-09-15T01:42:05Z [Term] @@ -142065,7 +144818,6 @@ is_a: GO:2000106 ! regulation of leukocyte apoptotic process intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0071887 ! leukocyte apoptotic process relationship: negatively_regulates GO:0071887 ! leukocyte apoptotic process -created_by: mah creation_date: 2010-09-15T01:42:09Z [Term] @@ -142079,7 +144831,6 @@ is_a: GO:2000106 ! regulation of leukocyte apoptotic process intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0071887 ! leukocyte apoptotic process relationship: positively_regulates GO:0071887 ! leukocyte apoptotic process -created_by: mah creation_date: 2010-09-15T01:42:12Z [Term] @@ -142095,7 +144846,6 @@ is_a: GO:2000106 ! regulation of leukocyte apoptotic process intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0071888 ! macrophage apoptotic process relationship: regulates GO:0071888 ! macrophage apoptotic process -created_by: mah creation_date: 2010-09-15T01:44:15Z [Term] @@ -142112,7 +144862,6 @@ is_a: GO:2000109 ! regulation of macrophage apoptotic process intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0071888 ! macrophage apoptotic process relationship: negatively_regulates GO:0071888 ! macrophage apoptotic process -created_by: mah creation_date: 2010-09-15T01:44:18Z [Term] @@ -142129,7 +144878,6 @@ is_a: GO:2000109 ! regulation of macrophage apoptotic process intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0071888 ! macrophage apoptotic process relationship: positively_regulates GO:0071888 ! macrophage apoptotic process -created_by: mah creation_date: 2010-09-15T01:44:21Z [Term] @@ -142143,7 +144891,6 @@ is_a: GO:0032878 ! regulation of establishment or maintenance of cell polarity intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0030010 ! establishment of cell polarity relationship: regulates GO:0030010 ! establishment of cell polarity -created_by: dph creation_date: 2010-09-16T01:22:36Z [Term] @@ -142155,7 +144902,6 @@ is_a: GO:0042127 ! regulation of cell population proliferation intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0061323 ! cell proliferation involved in heart morphogenesis relationship: regulates GO:0061323 ! cell proliferation involved in heart morphogenesis -created_by: dph creation_date: 2010-09-29T12:43:53Z [Term] @@ -142168,7 +144914,6 @@ is_a: GO:2000136 ! regulation of cell proliferation involved in heart morphogene intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0061323 ! cell proliferation involved in heart morphogenesis relationship: negatively_regulates GO:0061323 ! cell proliferation involved in heart morphogenesis -created_by: dph creation_date: 2010-09-29T12:43:55Z [Term] @@ -142181,7 +144926,6 @@ is_a: GO:2000136 ! regulation of cell proliferation involved in heart morphogene intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0061323 ! cell proliferation involved in heart morphogenesis relationship: positively_regulates GO:0061323 ! cell proliferation involved in heart morphogenesis -created_by: dph creation_date: 2010-09-29T12:43:57Z [Term] @@ -142197,7 +144941,6 @@ is_a: GO:0050794 ! regulation of cellular process intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0048870 ! cell motility relationship: regulates GO:0048870 ! cell motility -created_by: mah creation_date: 2010-10-01T09:41:21Z [Term] @@ -142214,7 +144957,6 @@ is_a: GO:2000145 ! regulation of cell motility intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0048870 ! cell motility relationship: negatively_regulates GO:0048870 ! cell motility -created_by: mah creation_date: 2010-10-01T09:41:26Z [Term] @@ -142231,7 +144973,6 @@ is_a: GO:2000145 ! regulation of cell motility intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0048870 ! cell motility relationship: positively_regulates GO:0048870 ! cell motility -created_by: mah creation_date: 2010-10-01T09:41:30Z [Term] @@ -142245,7 +144986,6 @@ is_a: GO:2000147 ! positive regulation of cell motility intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0060285 ! cilium-dependent cell motility relationship: positively_regulates GO:0060285 ! cilium-dependent cell motility -created_by: mah creation_date: 2010-10-04T12:41:05Z [Term] @@ -142259,7 +144999,6 @@ is_a: GO:0051093 ! negative regulation of developmental process intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0016358 ! dendrite development relationship: negatively_regulates GO:0016358 ! dendrite development -created_by: rl creation_date: 2010-10-07T10:53:15Z [Term] @@ -142271,7 +145010,6 @@ is_a: GO:0060688 ! regulation of morphogenesis of a branching structure intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0048755 ! branching morphogenesis of a nerve relationship: regulates GO:0048755 ! branching morphogenesis of a nerve -created_by: rl creation_date: 2010-10-07T12:07:54Z [Term] @@ -142285,7 +145023,6 @@ is_a: GO:2000172 ! regulation of branching morphogenesis of a nerve intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0048755 ! branching morphogenesis of a nerve relationship: negatively_regulates GO:0048755 ! branching morphogenesis of a nerve -created_by: rl creation_date: 2010-10-07T12:07:56Z [Term] @@ -142299,7 +145036,6 @@ is_a: GO:1905456 ! regulation of lymphoid progenitor cell differentiation intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0002572 ! pro-T cell differentiation relationship: regulates GO:0002572 ! pro-T cell differentiation -created_by: mah creation_date: 2010-10-11T10:24:30Z [Term] @@ -142314,7 +145050,6 @@ is_a: GO:2000174 ! regulation of pro-T cell differentiation intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0002572 ! pro-T cell differentiation relationship: negatively_regulates GO:0002572 ! pro-T cell differentiation -created_by: mah creation_date: 2010-10-11T10:24:33Z [Term] @@ -142329,7 +145064,6 @@ is_a: GO:2000174 ! regulation of pro-T cell differentiation intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0002572 ! pro-T cell differentiation relationship: positively_regulates GO:0002572 ! pro-T cell differentiation -created_by: mah creation_date: 2010-10-11T10:24:35Z [Term] @@ -142341,7 +145075,6 @@ is_a: GO:0042127 ! regulation of cell population proliferation intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0061351 ! neural precursor cell proliferation relationship: regulates GO:0061351 ! neural precursor cell proliferation -created_by: dph creation_date: 2010-10-13T12:40:41Z [Term] @@ -142354,7 +145087,6 @@ is_a: GO:2000177 ! regulation of neural precursor cell proliferation intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0061351 ! neural precursor cell proliferation relationship: negatively_regulates GO:0061351 ! neural precursor cell proliferation -created_by: dph creation_date: 2010-10-13T12:40:43Z [Term] @@ -142367,7 +145099,6 @@ is_a: GO:2000177 ! regulation of neural precursor cell proliferation intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0061351 ! neural precursor cell proliferation relationship: positively_regulates GO:0061351 ! neural precursor cell proliferation -created_by: dph creation_date: 2010-10-13T12:40:45Z [Term] @@ -142380,7 +145111,6 @@ is_a: GO:1901343 ! negative regulation of vasculature development intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0048514 ! blood vessel morphogenesis relationship: negatively_regulates GO:0048514 ! blood vessel morphogenesis -created_by: dph creation_date: 2010-10-13T12:46:31Z [Term] @@ -142396,7 +145126,6 @@ is_a: GO:0009889 ! regulation of biosynthetic process intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0006701 ! progesterone biosynthetic process relationship: regulates GO:0006701 ! progesterone biosynthetic process -created_by: dph creation_date: 2010-10-14T07:36:06Z [Term] @@ -142413,7 +145142,6 @@ is_a: GO:2000182 ! regulation of progesterone biosynthetic process intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0006701 ! progesterone biosynthetic process relationship: negatively_regulates GO:0006701 ! progesterone biosynthetic process -created_by: dph creation_date: 2010-10-14T07:36:10Z [Term] @@ -142430,7 +145158,6 @@ is_a: GO:2000182 ! regulation of progesterone biosynthetic process intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0006701 ! progesterone biosynthetic process relationship: positively_regulates GO:0006701 ! progesterone biosynthetic process -created_by: dph creation_date: 2010-10-14T07:36:14Z [Term] @@ -142444,7 +145171,6 @@ is_a: GO:0034762 ! regulation of transmembrane transport intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0035435 ! phosphate ion transmembrane transport relationship: regulates GO:0035435 ! phosphate ion transmembrane transport -created_by: vw creation_date: 2010-10-15T11:33:04Z [Term] @@ -142458,7 +145184,6 @@ is_a: GO:2000185 ! regulation of phosphate transmembrane transport intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0035435 ! phosphate ion transmembrane transport relationship: negatively_regulates GO:0035435 ! phosphate ion transmembrane transport -created_by: vw creation_date: 2010-10-15T11:33:08Z [Term] @@ -142472,7 +145197,6 @@ is_a: GO:2000185 ! regulation of phosphate transmembrane transport intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0035435 ! phosphate ion transmembrane transport relationship: positively_regulates GO:0035435 ! phosphate ion transmembrane transport -created_by: vw creation_date: 2010-10-15T11:33:10Z [Term] @@ -142487,7 +145211,6 @@ is_a: GO:2000026 ! regulation of multicellular organismal development intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0008585 ! female gonad development relationship: regulates GO:0008585 ! female gonad development -created_by: yaf creation_date: 2010-10-19T10:45:34Z [Term] @@ -142502,7 +145225,6 @@ is_a: GO:2000194 ! regulation of female gonad development intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0008585 ! female gonad development relationship: negatively_regulates GO:0008585 ! female gonad development -created_by: yaf creation_date: 2010-10-19T10:45:38Z [Term] @@ -142517,7 +145239,6 @@ is_a: GO:2000194 ! regulation of female gonad development intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0008585 ! female gonad development relationship: positively_regulates GO:0008585 ! female gonad development -created_by: yaf creation_date: 2010-10-19T10:45:41Z [Term] @@ -142529,10 +145250,10 @@ synonym: "regulation of glutamate metabolism" EXACT [GOC:obol] synonym: "regulation of glutamic acid metabolic process" EXACT [GOC:obol] synonym: "regulation of glutamic acid metabolism" EXACT [GOC:obol] is_a: GO:0000820 ! regulation of glutamine family amino acid metabolic process +is_a: GO:0062012 ! regulation of small molecule metabolic process intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0006536 ! glutamate metabolic process relationship: regulates GO:0006536 ! glutamate metabolic process -created_by: mah creation_date: 2010-11-03T02:43:51Z [Term] @@ -142543,14 +145264,12 @@ def: "Any process that stops, prevents, or reduces the frequency, rate or extent synonym: "negative regulation of glutamate metabolism" EXACT [GOC:obol] synonym: "negative regulation of glutamic acid metabolic process" EXACT [GOC:obol] synonym: "negative regulation of glutamic acid metabolism" EXACT [GOC:obol] -is_a: GO:0031324 ! negative regulation of cellular metabolic process -is_a: GO:0045763 ! negative regulation of cellular amino acid metabolic process +is_a: GO:0045763 ! negative regulation of amino acid metabolic process is_a: GO:0062014 ! negative regulation of small molecule metabolic process is_a: GO:2000211 ! regulation of glutamate metabolic process intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0006536 ! glutamate metabolic process relationship: negatively_regulates GO:0006536 ! glutamate metabolic process -created_by: mah creation_date: 2010-11-03T02:43:55Z [Term] @@ -142561,14 +145280,12 @@ def: "Any process that activates or increases the frequency, rate or extent of g synonym: "positive regulation of glutamate metabolism" EXACT [GOC:obol] synonym: "positive regulation of glutamic acid metabolic process" EXACT [GOC:obol] synonym: "positive regulation of glutamic acid metabolism" EXACT [GOC:obol] -is_a: GO:0031325 ! positive regulation of cellular metabolic process is_a: GO:0045764 ! positive regulation of amino acid metabolic process is_a: GO:0062013 ! positive regulation of small molecule metabolic process is_a: GO:2000211 ! regulation of glutamate metabolic process intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0006536 ! glutamate metabolic process relationship: positively_regulates GO:0006536 ! glutamate metabolic process -created_by: mah creation_date: 2010-11-03T02:43:59Z [Term] @@ -142580,7 +145297,6 @@ is_a: GO:0009889 ! regulation of biosynthetic process intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0061370 ! testosterone biosynthetic process relationship: regulates GO:0061370 ! testosterone biosynthetic process -created_by: yaf creation_date: 2010-11-09T10:38:33Z [Term] @@ -142593,7 +145309,6 @@ is_a: GO:2000224 ! regulation of testosterone biosynthetic process intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0061370 ! testosterone biosynthetic process relationship: negatively_regulates GO:0061370 ! testosterone biosynthetic process -created_by: yaf creation_date: 2010-11-09T10:38:37Z [Term] @@ -142606,7 +145321,6 @@ is_a: GO:0030856 ! regulation of epithelial cell differentiation intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0003310 ! pancreatic A cell differentiation relationship: regulates GO:0003310 ! pancreatic A cell differentiation -created_by: mah creation_date: 2010-11-09T03:43:37Z [Term] @@ -142621,7 +145335,6 @@ is_a: GO:2000226 ! regulation of pancreatic A cell differentiation intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0003310 ! pancreatic A cell differentiation relationship: negatively_regulates GO:0003310 ! pancreatic A cell differentiation -created_by: mah creation_date: 2010-11-09T03:43:40Z [Term] @@ -142636,7 +145349,6 @@ is_a: GO:2000226 ! regulation of pancreatic A cell differentiation intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0003310 ! pancreatic A cell differentiation relationship: positively_regulates GO:0003310 ! pancreatic A cell differentiation -created_by: mah creation_date: 2010-11-09T03:43:42Z [Term] @@ -142648,7 +145360,6 @@ is_a: GO:0048145 ! regulation of fibroblast proliferation intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0072343 ! pancreatic stellate cell proliferation relationship: regulates GO:0072343 ! pancreatic stellate cell proliferation -created_by: mah creation_date: 2010-11-09T03:45:18Z [Term] @@ -142661,7 +145372,6 @@ is_a: GO:2000229 ! regulation of pancreatic stellate cell proliferation intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0072343 ! pancreatic stellate cell proliferation relationship: negatively_regulates GO:0072343 ! pancreatic stellate cell proliferation -created_by: mah creation_date: 2010-11-09T03:45:21Z [Term] @@ -142674,7 +145384,6 @@ is_a: GO:2000229 ! regulation of pancreatic stellate cell proliferation intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0072343 ! pancreatic stellate cell proliferation relationship: positively_regulates GO:0072343 ! pancreatic stellate cell proliferation -created_by: mah creation_date: 2010-11-09T03:45:23Z [Term] @@ -142686,7 +145395,6 @@ is_a: GO:0050789 ! regulation of biological process intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0022414 ! reproductive process relationship: regulates GO:0022414 ! reproductive process -created_by: mah creation_date: 2010-11-10T02:44:02Z [Term] @@ -142699,7 +145407,6 @@ is_a: GO:2000241 ! regulation of reproductive process intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0022414 ! reproductive process relationship: negatively_regulates GO:0022414 ! reproductive process -created_by: mah creation_date: 2010-11-10T02:44:05Z [Term] @@ -142712,7 +145419,6 @@ is_a: GO:2000241 ! regulation of reproductive process intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0022414 ! reproductive process relationship: positively_regulates GO:0022414 ! reproductive process -created_by: mah creation_date: 2010-11-10T02:44:08Z [Term] @@ -142727,7 +145433,6 @@ is_a: GO:0045769 ! negative regulation of asymmetric cell division intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0045196 ! establishment or maintenance of neuroblast polarity relationship: negatively_regulates GO:0045196 ! establishment or maintenance of neuroblast polarity -created_by: vw creation_date: 2010-11-11T11:40:34Z [Term] @@ -142739,7 +145444,6 @@ is_a: GO:1905936 ! regulation of germ cell proliferation intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0002176 ! male germ cell proliferation relationship: regulates GO:0002176 ! male germ cell proliferation -created_by: dph creation_date: 2010-11-18T09:29:44Z [Term] @@ -142753,7 +145457,6 @@ is_a: GO:2000254 ! regulation of male germ cell proliferation intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0002176 ! male germ cell proliferation relationship: negatively_regulates GO:0002176 ! male germ cell proliferation -created_by: dph creation_date: 2010-11-18T09:29:47Z [Term] @@ -142767,7 +145470,6 @@ is_a: GO:2000254 ! regulation of male germ cell proliferation intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0002176 ! male germ cell proliferation relationship: positively_regulates GO:0002176 ! male germ cell proliferation -created_by: dph creation_date: 2010-11-18T09:29:50Z [Term] @@ -142780,7 +145482,6 @@ is_a: GO:0042981 ! regulation of apoptotic process intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0044346 ! fibroblast apoptotic process relationship: regulates GO:0044346 ! fibroblast apoptotic process -created_by: jl creation_date: 2010-11-23T01:07:23Z [Term] @@ -142794,7 +145495,6 @@ is_a: GO:2000269 ! regulation of fibroblast apoptotic process intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0044346 ! fibroblast apoptotic process relationship: negatively_regulates GO:0044346 ! fibroblast apoptotic process -created_by: jl creation_date: 2010-11-23T01:07:27Z [Term] @@ -142808,7 +145508,6 @@ is_a: GO:2000269 ! regulation of fibroblast apoptotic process intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0044346 ! fibroblast apoptotic process relationship: positively_regulates GO:0044346 ! fibroblast apoptotic process -created_by: jl creation_date: 2010-11-23T01:07:29Z [Term] @@ -142824,7 +145523,6 @@ is_a: GO:0044092 ! negative regulation of molecular function intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0038023 ! signaling receptor activity relationship: negatively_regulates GO:0038023 ! signaling receptor activity -created_by: bf creation_date: 2010-12-02T09:28:47Z [Term] @@ -142839,7 +145537,6 @@ is_a: GO:0044093 ! positive regulation of molecular function intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0038023 ! signaling receptor activity relationship: positively_regulates GO:0038023 ! signaling receptor activity -created_by: bf creation_date: 2010-12-02T09:28:50Z [Term] @@ -142856,7 +145553,6 @@ is_a: GO:0051052 ! regulation of DNA metabolic process intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0071897 ! DNA biosynthetic process relationship: regulates GO:0071897 ! DNA biosynthetic process -created_by: yaf creation_date: 2010-12-08T04:48:15Z [Term] @@ -142874,25 +145570,24 @@ is_a: GO:2000278 ! regulation of DNA biosynthetic process intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0071897 ! DNA biosynthetic process relationship: negatively_regulates GO:0071897 ! DNA biosynthetic process -created_by: yaf creation_date: 2010-12-08T04:48:20Z [Term] id: GO:2000282 -name: regulation of cellular amino acid biosynthetic process +name: regulation of amino acid biosynthetic process namespace: biological_process def: "Any process that modulates the frequency, rate or extent of cellular amino acid biosynthetic process." [GOC:obol] -synonym: "regulation of amino acid biosynthetic process" EXACT [GOC:obol] synonym: "regulation of cellular amino acid anabolism" EXACT [GOC:obol] synonym: "regulation of cellular amino acid biosynthesis" EXACT [GOC:obol] +synonym: "regulation of cellular amino acid biosynthetic process" EXACT [GOC:obol] synonym: "regulation of cellular amino acid formation" EXACT [GOC:obol] synonym: "regulation of cellular amino acid synthesis" EXACT [GOC:obol] -is_a: GO:0006521 ! regulation of cellular amino acid metabolic process +is_a: GO:0006521 ! regulation of amino acid metabolic process is_a: GO:0009889 ! regulation of biosynthetic process intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0008652 ! amino acid biosynthetic process relationship: regulates GO:0008652 ! amino acid biosynthetic process -created_by: vw +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28908" xsd:anyURI creation_date: 2010-12-10T11:54:19Z [Term] @@ -142906,12 +145601,11 @@ synonym: "negative regulation of amino acid formation" EXACT [GOC:obol] synonym: "negative regulation of amino acid synthesis" EXACT [GOC:obol] synonym: "negative regulation of cellular amino acid biosynthetic process" EXACT [GOC:obol] is_a: GO:0009890 ! negative regulation of biosynthetic process -is_a: GO:0045763 ! negative regulation of cellular amino acid metabolic process -is_a: GO:2000282 ! regulation of cellular amino acid biosynthetic process +is_a: GO:0045763 ! negative regulation of amino acid metabolic process +is_a: GO:2000282 ! regulation of amino acid biosynthetic process intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0008652 ! amino acid biosynthetic process relationship: negatively_regulates GO:0008652 ! amino acid biosynthetic process -created_by: vw creation_date: 2010-12-10T11:54:23Z [Term] @@ -142926,11 +145620,10 @@ synonym: "positive regulation of amino acid synthesis" EXACT [GOC:obol] synonym: "positive regulation of cellular amino acid biosynthetic process" EXACT [GOC:obol] is_a: GO:0009891 ! positive regulation of biosynthetic process is_a: GO:0045764 ! positive regulation of amino acid metabolic process -is_a: GO:2000282 ! regulation of cellular amino acid biosynthetic process +is_a: GO:2000282 ! regulation of amino acid biosynthetic process intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0008652 ! amino acid biosynthetic process relationship: positively_regulates GO:0008652 ! amino acid biosynthetic process -created_by: vw creation_date: 2010-12-10T11:54:27Z [Term] @@ -142943,7 +145636,6 @@ is_a: GO:2000290 ! regulation of myotome development intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0061055 ! myotome development relationship: positively_regulates GO:0061055 ! myotome development -created_by: rl creation_date: 2010-12-16T05:17:15Z [Term] @@ -142956,7 +145648,6 @@ is_a: GO:2000291 ! regulation of myoblast proliferation intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0051450 ! myoblast proliferation relationship: positively_regulates GO:0051450 ! myoblast proliferation -created_by: rl creation_date: 2010-12-16T05:20:52Z [Term] @@ -142968,7 +145659,6 @@ is_a: GO:0050793 ! regulation of developmental process intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0061055 ! myotome development relationship: regulates GO:0061055 ! myotome development -created_by: mah creation_date: 2010-12-20T10:22:05Z [Term] @@ -142980,7 +145670,6 @@ is_a: GO:0042127 ! regulation of cell population proliferation intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0051450 ! myoblast proliferation relationship: regulates GO:0051450 ! myoblast proliferation -created_by: mah creation_date: 2010-12-20T10:34:26Z [Term] @@ -142993,7 +145682,6 @@ is_a: GO:0044062 ! regulation of excretion intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0030421 ! defecation relationship: regulates GO:0030421 ! defecation -created_by: bf creation_date: 2010-12-21T09:23:08Z [Term] @@ -143007,7 +145695,6 @@ is_a: GO:2000292 ! regulation of defecation intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0030421 ! defecation relationship: negatively_regulates GO:0030421 ! defecation -created_by: bf creation_date: 2010-12-21T09:23:13Z [Term] @@ -143021,7 +145708,6 @@ is_a: GO:2000292 ! regulation of defecation intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0030421 ! defecation relationship: positively_regulates GO:0030421 ! defecation -created_by: bf creation_date: 2010-12-21T09:23:16Z [Term] @@ -143035,7 +145721,6 @@ is_a: GO:1903305 ! regulation of regulated secretory pathway intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0016079 ! synaptic vesicle exocytosis relationship: regulates GO:0016079 ! synaptic vesicle exocytosis -created_by: dph creation_date: 2011-01-03T08:20:40Z [Term] @@ -143048,7 +145733,6 @@ is_a: GO:2000300 ! regulation of synaptic vesicle exocytosis intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0016079 ! synaptic vesicle exocytosis relationship: negatively_regulates GO:0016079 ! synaptic vesicle exocytosis -created_by: dph creation_date: 2011-01-03T08:21:00Z [Term] @@ -143062,7 +145746,6 @@ is_a: GO:2000300 ! regulation of synaptic vesicle exocytosis intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0016079 ! synaptic vesicle exocytosis relationship: positively_regulates GO:0016079 ! synaptic vesicle exocytosis -created_by: dph creation_date: 2011-01-03T08:21:14Z [Term] @@ -143079,7 +145762,6 @@ is_a: GO:2001257 ! regulation of cation channel activity intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0015277 ! kainate selective glutamate receptor activity relationship: regulates GO:0015277 ! kainate selective glutamate receptor activity -created_by: bf creation_date: 2011-01-18T10:14:16Z [Term] @@ -143092,7 +145774,6 @@ is_a: GO:0002822 ! regulation of adaptive immune response based on somatic recom intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0072538 ! T-helper 17 type immune response relationship: regulates GO:0072538 ! T-helper 17 type immune response -created_by: mah creation_date: 2011-01-18T01:32:26Z [Term] @@ -143106,7 +145787,6 @@ is_a: GO:2000316 ! regulation of T-helper 17 type immune response intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0072538 ! T-helper 17 type immune response relationship: negatively_regulates GO:0072538 ! T-helper 17 type immune response -created_by: mah creation_date: 2011-01-18T01:33:00Z [Term] @@ -143120,7 +145800,6 @@ is_a: GO:2000316 ! regulation of T-helper 17 type immune response intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0072538 ! T-helper 17 type immune response relationship: positively_regulates GO:0072538 ! T-helper 17 type immune response -created_by: mah creation_date: 2011-01-18T01:33:24Z [Term] @@ -143134,7 +145813,6 @@ is_a: GO:2000316 ! regulation of T-helper 17 type immune response intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0072539 ! T-helper 17 cell differentiation relationship: regulates GO:0072539 ! T-helper 17 cell differentiation -created_by: mah creation_date: 2011-01-18T01:43:48Z [Term] @@ -143149,7 +145827,6 @@ is_a: GO:2000319 ! regulation of T-helper 17 cell differentiation intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0072539 ! T-helper 17 cell differentiation relationship: negatively_regulates GO:0072539 ! T-helper 17 cell differentiation -created_by: mah creation_date: 2011-01-18T01:44:31Z [Term] @@ -143164,50 +145841,8 @@ is_a: GO:2000319 ! regulation of T-helper 17 cell differentiation intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0072539 ! T-helper 17 cell differentiation relationship: positively_regulates GO:0072539 ! T-helper 17 cell differentiation -created_by: mah creation_date: 2011-01-18T01:45:08Z -[Term] -id: GO:2000322 -name: regulation of glucocorticoid receptor signaling pathway -namespace: biological_process -def: "Any process that modulates the frequency, rate or extent of glucocorticoid receptor signaling pathway." [GOC:BHF] -synonym: "regulation of glucocorticoid receptor signalling pathway" EXACT [GOC:obol] -is_a: GO:0033143 ! regulation of intracellular steroid hormone receptor signaling pathway -intersection_of: GO:0065007 ! biological regulation -intersection_of: regulates GO:0042921 ! nuclear receptor-mediated glucocorticoid signaling pathway -relationship: regulates GO:0042921 ! nuclear receptor-mediated glucocorticoid signaling pathway -created_by: vk -creation_date: 2011-01-18T04:38:10Z - -[Term] -id: GO:2000323 -name: negative regulation of glucocorticoid receptor signaling pathway -namespace: biological_process -def: "Any process that stops, prevents or reduces the frequency, rate or extent of glucocorticoid receptor signaling pathway." [GOC:BHF] -synonym: "negative regulation of glucocorticoid receptor signalling pathway" EXACT [GOC:obol] -is_a: GO:0033144 ! negative regulation of intracellular steroid hormone receptor signaling pathway -is_a: GO:2000322 ! regulation of glucocorticoid receptor signaling pathway -intersection_of: GO:0065007 ! biological regulation -intersection_of: negatively_regulates GO:0042921 ! nuclear receptor-mediated glucocorticoid signaling pathway -relationship: negatively_regulates GO:0042921 ! nuclear receptor-mediated glucocorticoid signaling pathway -created_by: vk -creation_date: 2011-01-18T04:38:43Z - -[Term] -id: GO:2000324 -name: positive regulation of glucocorticoid receptor signaling pathway -namespace: biological_process -def: "Any process that activates or increases the frequency, rate or extent of glucocorticoid receptor signaling pathway." [GOC:BHF] -synonym: "positive regulation of glucocorticoid receptor signalling pathway" EXACT [GOC:obol] -is_a: GO:0033145 ! positive regulation of intracellular steroid hormone receptor signaling pathway -is_a: GO:2000322 ! regulation of glucocorticoid receptor signaling pathway -intersection_of: GO:0065007 ! biological regulation -intersection_of: positively_regulates GO:0042921 ! nuclear receptor-mediated glucocorticoid signaling pathway -relationship: positively_regulates GO:0042921 ! nuclear receptor-mediated glucocorticoid signaling pathway -created_by: vk -creation_date: 2011-01-18T04:39:05Z - [Term] id: GO:2000331 name: regulation of terminal button organization @@ -143222,7 +145857,6 @@ is_a: GO:0099174 ! regulation of presynapse organization intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0072553 ! terminal button organization relationship: regulates GO:0072553 ! terminal button organization -created_by: mah creation_date: 2011-01-28T11:29:08Z [Term] @@ -143240,7 +145874,6 @@ is_a: GO:0042981 ! regulation of apoptotic process intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0072577 ! endothelial cell apoptotic process relationship: regulates GO:0072577 ! endothelial cell apoptotic process -created_by: mah creation_date: 2011-02-03T10:43:16Z [Term] @@ -143259,7 +145892,6 @@ is_a: GO:2000351 ! regulation of endothelial cell apoptotic process intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0072577 ! endothelial cell apoptotic process relationship: negatively_regulates GO:0072577 ! endothelial cell apoptotic process -created_by: mah creation_date: 2011-02-03T10:43:20Z [Term] @@ -143278,7 +145910,6 @@ is_a: GO:2000351 ! regulation of endothelial cell apoptotic process intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0072577 ! endothelial cell apoptotic process relationship: positively_regulates GO:0072577 ! endothelial cell apoptotic process -created_by: mah creation_date: 2011-02-03T10:43:23Z [Term] @@ -143291,7 +145922,6 @@ is_a: GO:0050793 ! regulation of developmental process intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0001541 ! ovarian follicle development relationship: regulates GO:0001541 ! ovarian follicle development -created_by: yaf creation_date: 2011-02-03T02:01:28Z [Term] @@ -143305,7 +145935,6 @@ is_a: GO:2000354 ! regulation of ovarian follicle development intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0001541 ! ovarian follicle development relationship: negatively_regulates GO:0001541 ! ovarian follicle development -created_by: yaf creation_date: 2011-02-03T02:01:32Z [Term] @@ -143315,11 +145944,10 @@ namespace: biological_process def: "Any process that modulates the frequency, rate or extent of oxygen metabolic process." [GOC:mah] synonym: "regulation of diatomic oxygen metabolic process" EXACT [GOC:obol] synonym: "regulation of oxygen metabolism" EXACT [GOC:obol] -is_a: GO:0031323 ! regulation of cellular metabolic process +is_a: GO:0019222 ! regulation of metabolic process intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0072592 ! oxygen metabolic process relationship: regulates GO:0072592 ! oxygen metabolic process -created_by: mah creation_date: 2011-02-11T02:03:32Z [Term] @@ -143329,12 +145957,11 @@ namespace: biological_process def: "Any process that stops, prevents or reduces the frequency, rate or extent of oxygen metabolic process." [GOC:mah] synonym: "negative regulation of diatomic oxygen metabolic process" EXACT [GOC:obol] synonym: "negative regulation of oxygen metabolism" EXACT [GOC:obol] -is_a: GO:0031324 ! negative regulation of cellular metabolic process +is_a: GO:0009892 ! negative regulation of metabolic process is_a: GO:2000374 ! regulation of oxygen metabolic process intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0072592 ! oxygen metabolic process relationship: negatively_regulates GO:0072592 ! oxygen metabolic process -created_by: mah creation_date: 2011-02-11T02:03:44Z [Term] @@ -143344,12 +145971,11 @@ namespace: biological_process def: "Any process that activates or increases the frequency, rate or extent of oxygen metabolic process." [GOC:mah] synonym: "positive regulation of diatomic oxygen metabolic process" EXACT [GOC:obol] synonym: "positive regulation of oxygen metabolism" EXACT [GOC:obol] -is_a: GO:0031325 ! positive regulation of cellular metabolic process +is_a: GO:0009893 ! positive regulation of metabolic process is_a: GO:2000374 ! regulation of oxygen metabolic process intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0072592 ! oxygen metabolic process relationship: positively_regulates GO:0072592 ! oxygen metabolic process -created_by: mah creation_date: 2011-02-11T02:03:52Z [Term] @@ -143361,7 +145987,6 @@ is_a: GO:0050793 ! regulation of developmental process intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0007498 ! mesoderm development relationship: regulates GO:0007498 ! mesoderm development -created_by: vk creation_date: 2011-02-15T03:09:46Z [Term] @@ -143374,7 +145999,6 @@ is_a: GO:2000380 ! regulation of mesoderm development intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0007498 ! mesoderm development relationship: negatively_regulates GO:0007498 ! mesoderm development -created_by: vk creation_date: 2011-02-15T03:10:02Z [Term] @@ -143387,7 +146011,6 @@ is_a: GO:2000380 ! regulation of mesoderm development intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0007498 ! mesoderm development relationship: positively_regulates GO:0007498 ! mesoderm development -created_by: vk creation_date: 2011-02-15T03:10:12Z [Term] @@ -143399,7 +146022,6 @@ is_a: GO:0050793 ! regulation of developmental process intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0007398 ! ectoderm development relationship: regulates GO:0007398 ! ectoderm development -created_by: vk creation_date: 2011-02-15T03:17:10Z [Term] @@ -143412,7 +146034,6 @@ is_a: GO:2000383 ! regulation of ectoderm development intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0007398 ! ectoderm development relationship: negatively_regulates GO:0007398 ! ectoderm development -created_by: vk creation_date: 2011-02-15T03:17:27Z [Term] @@ -143425,7 +146046,6 @@ is_a: GO:2000383 ! regulation of ectoderm development intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0007398 ! ectoderm development relationship: positively_regulates GO:0007398 ! ectoderm development -created_by: vk creation_date: 2011-02-15T03:17:39Z [Term] @@ -143439,7 +146059,6 @@ is_a: GO:2000354 ! regulation of ovarian follicle development intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0001541 ! ovarian follicle development relationship: positively_regulates GO:0001541 ! ovarian follicle development -created_by: yaf creation_date: 2011-02-16T02:21:21Z [Term] @@ -143452,7 +146071,6 @@ is_a: GO:2000241 ! regulation of reproductive process intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0001547 ! antral ovarian follicle growth relationship: regulates GO:0001547 ! antral ovarian follicle growth -created_by: yaf creation_date: 2011-02-16T04:53:43Z [Term] @@ -143466,7 +146084,6 @@ is_a: GO:2000387 ! regulation of antral ovarian follicle growth intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0001547 ! antral ovarian follicle growth relationship: positively_regulates GO:0001547 ! antral ovarian follicle growth -created_by: yaf creation_date: 2011-02-16T04:54:01Z [Term] @@ -143478,7 +146095,6 @@ is_a: GO:0071675 ! regulation of mononuclear cell migration intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0072676 ! lymphocyte migration relationship: regulates GO:0072676 ! lymphocyte migration -created_by: mah creation_date: 2011-02-23T10:45:19Z [Term] @@ -143491,7 +146107,6 @@ is_a: GO:2000401 ! regulation of lymphocyte migration intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0072676 ! lymphocyte migration relationship: negatively_regulates GO:0072676 ! lymphocyte migration -created_by: mah creation_date: 2011-02-23T10:45:47Z [Term] @@ -143504,7 +146119,6 @@ is_a: GO:2000401 ! regulation of lymphocyte migration intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0072676 ! lymphocyte migration relationship: positively_regulates GO:0072676 ! lymphocyte migration -created_by: mah creation_date: 2011-02-23T10:46:06Z [Term] @@ -143519,7 +146133,6 @@ is_a: GO:2000401 ! regulation of lymphocyte migration intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0072678 ! T cell migration relationship: regulates GO:0072678 ! T cell migration -created_by: mah creation_date: 2011-02-23T10:48:24Z [Term] @@ -143535,7 +146148,6 @@ is_a: GO:2000404 ! regulation of T cell migration intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0072678 ! T cell migration relationship: negatively_regulates GO:0072678 ! T cell migration -created_by: mah creation_date: 2011-02-23T10:48:52Z [Term] @@ -143551,7 +146163,6 @@ is_a: GO:2000404 ! regulation of T cell migration intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0072678 ! T cell migration relationship: positively_regulates GO:0072678 ! T cell migration -created_by: mah creation_date: 2011-02-23T10:49:12Z [Term] @@ -143568,7 +146179,6 @@ is_a: GO:2000404 ! regulation of T cell migration intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0072679 ! thymocyte migration relationship: regulates GO:0072679 ! thymocyte migration -created_by: mah creation_date: 2011-02-23T01:33:32Z [Term] @@ -143586,7 +146196,6 @@ is_a: GO:2000410 ! regulation of thymocyte migration intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0072679 ! thymocyte migration relationship: negatively_regulates GO:0072679 ! thymocyte migration -created_by: mah creation_date: 2011-02-23T01:34:01Z [Term] @@ -143604,7 +146213,6 @@ is_a: GO:2000410 ! regulation of thymocyte migration intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0072679 ! thymocyte migration relationship: positively_regulates GO:0072679 ! thymocyte migration -created_by: mah creation_date: 2011-02-23T01:34:23Z [Term] @@ -143616,7 +146224,6 @@ is_a: GO:0002685 ! regulation of leukocyte migration intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0072677 ! eosinophil migration relationship: regulates GO:0072677 ! eosinophil migration -created_by: mah creation_date: 2011-02-23T01:43:23Z [Term] @@ -143629,7 +146236,6 @@ is_a: GO:2000416 ! regulation of eosinophil migration intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0072677 ! eosinophil migration relationship: negatively_regulates GO:0072677 ! eosinophil migration -created_by: mah creation_date: 2011-02-23T01:43:52Z [Term] @@ -143642,7 +146248,6 @@ is_a: GO:2000416 ! regulation of eosinophil migration intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0072677 ! eosinophil migration relationship: positively_regulates GO:0072677 ! eosinophil migration -created_by: mah creation_date: 2011-02-23T01:44:14Z [Term] @@ -143655,7 +146260,6 @@ is_a: GO:2000416 ! regulation of eosinophil migration intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0048245 ! eosinophil chemotaxis relationship: regulates GO:0048245 ! eosinophil chemotaxis -created_by: bf creation_date: 2011-02-24T01:16:44Z [Term] @@ -143669,7 +146273,6 @@ is_a: GO:2000422 ! regulation of eosinophil chemotaxis intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0048245 ! eosinophil chemotaxis relationship: negatively_regulates GO:0048245 ! eosinophil chemotaxis -created_by: bf creation_date: 2011-02-24T01:17:12Z [Term] @@ -143683,7 +146286,6 @@ is_a: GO:2000422 ! regulation of eosinophil chemotaxis intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0048245 ! eosinophil chemotaxis relationship: positively_regulates GO:0048245 ! eosinophil chemotaxis -created_by: bf creation_date: 2011-02-24T01:17:35Z [Term] @@ -143698,7 +146300,6 @@ is_a: GO:0050764 ! regulation of phagocytosis intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0043277 ! apoptotic cell clearance relationship: regulates GO:0043277 ! apoptotic cell clearance -created_by: bf creation_date: 2011-02-25T11:50:11Z [Term] @@ -143714,7 +146315,6 @@ is_a: GO:2000425 ! regulation of apoptotic cell clearance intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0043277 ! apoptotic cell clearance relationship: negatively_regulates GO:0043277 ! apoptotic cell clearance -created_by: bf creation_date: 2011-02-25T11:50:39Z [Term] @@ -143730,7 +146330,6 @@ is_a: GO:2000425 ! regulation of apoptotic cell clearance intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0043277 ! apoptotic cell clearance relationship: positively_regulates GO:0043277 ! apoptotic cell clearance -created_by: bf creation_date: 2011-02-25T11:50:59Z [Term] @@ -143743,7 +146342,6 @@ is_a: GO:1903975 ! regulation of glial cell migration intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0035700 ! astrocyte chemotaxis relationship: regulates GO:0035700 ! astrocyte chemotaxis -created_by: bf creation_date: 2011-03-04T10:53:50Z [Term] @@ -143757,7 +146355,6 @@ is_a: GO:2000458 ! regulation of astrocyte chemotaxis intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0035700 ! astrocyte chemotaxis relationship: negatively_regulates GO:0035700 ! astrocyte chemotaxis -created_by: bf creation_date: 2011-03-04T10:54:28Z [Term] @@ -143772,7 +146369,6 @@ is_a: GO:0098815 ! modulation of excitatory postsynaptic potential intersection_of: GO:0050789 ! regulation of biological process intersection_of: positively_regulates GO:0060079 ! excitatory postsynaptic potential relationship: positively_regulates GO:0060079 ! excitatory postsynaptic potential -created_by: rl creation_date: 2011-03-04T02:43:32Z [Term] @@ -143786,7 +146382,6 @@ is_a: GO:2000458 ! regulation of astrocyte chemotaxis intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0035700 ! astrocyte chemotaxis relationship: positively_regulates GO:0035700 ! astrocyte chemotaxis -created_by: bf creation_date: 2011-03-04T04:43:29Z [Term] @@ -143799,7 +146394,6 @@ is_a: GO:0030334 ! regulation of cell migration intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0035701 ! hematopoietic stem cell migration relationship: regulates GO:0035701 ! hematopoietic stem cell migration -created_by: bf creation_date: 2011-03-09T09:34:08Z [Term] @@ -143813,7 +146407,6 @@ is_a: GO:2000471 ! regulation of hematopoietic stem cell migration intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0035701 ! hematopoietic stem cell migration relationship: negatively_regulates GO:0035701 ! hematopoietic stem cell migration -created_by: bf creation_date: 2011-03-09T09:34:54Z [Term] @@ -143827,7 +146420,6 @@ is_a: GO:2000471 ! regulation of hematopoietic stem cell migration intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0035701 ! hematopoietic stem cell migration relationship: positively_regulates GO:0035701 ! hematopoietic stem cell migration -created_by: bf creation_date: 2011-03-09T09:35:25Z [Term] @@ -143841,7 +146433,6 @@ intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0072249 ! metanephric podocyte development relationship: regulates GO:0072249 ! metanephric podocyte development property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/23000" xsd:anyURI -created_by: yaf creation_date: 2011-03-09T05:16:40Z [Term] @@ -143856,7 +146447,6 @@ intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0072249 ! metanephric podocyte development relationship: positively_regulates GO:0072249 ! metanephric podocyte development property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/23000" xsd:anyURI -created_by: yaf creation_date: 2011-03-09T05:17:26Z [Term] @@ -143868,7 +146458,6 @@ is_a: GO:0050865 ! regulation of cell activation intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0035733 ! hepatic stellate cell activation relationship: regulates GO:0035733 ! hepatic stellate cell activation -created_by: bf creation_date: 2011-03-14T03:48:32Z [Term] @@ -143881,7 +146470,6 @@ is_a: GO:2000489 ! regulation of hepatic stellate cell activation intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0035733 ! hepatic stellate cell activation relationship: negatively_regulates GO:0035733 ! hepatic stellate cell activation -created_by: bf creation_date: 2011-03-14T03:49:18Z [Term] @@ -143894,7 +146482,6 @@ is_a: GO:2000489 ! regulation of hepatic stellate cell activation intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0035733 ! hepatic stellate cell activation relationship: positively_regulates GO:0035733 ! hepatic stellate cell activation -created_by: bf creation_date: 2011-03-14T03:49:48Z [Term] @@ -143906,7 +146493,6 @@ is_a: GO:0042127 ! regulation of cell population proliferation intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0035736 ! cell proliferation involved in compound eye morphogenesis relationship: regulates GO:0035736 ! cell proliferation involved in compound eye morphogenesis -created_by: bf creation_date: 2011-03-18T02:18:34Z [Term] @@ -143919,7 +146505,6 @@ is_a: GO:2000495 ! regulation of cell proliferation involved in compound eye mor intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0035736 ! cell proliferation involved in compound eye morphogenesis relationship: negatively_regulates GO:0035736 ! cell proliferation involved in compound eye morphogenesis -created_by: bf creation_date: 2011-03-18T02:19:22Z [Term] @@ -143932,7 +146517,6 @@ is_a: GO:2000495 ! regulation of cell proliferation involved in compound eye mor intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0035736 ! cell proliferation involved in compound eye morphogenesis relationship: positively_regulates GO:0035736 ! cell proliferation involved in compound eye morphogenesis -created_by: bf creation_date: 2011-03-18T02:19:54Z [Term] @@ -143944,7 +146528,6 @@ is_a: GO:1901623 ! regulation of lymphocyte chemotaxis intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0035747 ! natural killer cell chemotaxis relationship: regulates GO:0035747 ! natural killer cell chemotaxis -created_by: bf creation_date: 2011-03-21T10:09:23Z [Term] @@ -143957,7 +146540,6 @@ is_a: GO:2000501 ! regulation of natural killer cell chemotaxis intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0035747 ! natural killer cell chemotaxis relationship: negatively_regulates GO:0035747 ! natural killer cell chemotaxis -created_by: bf creation_date: 2011-03-21T10:09:32Z [Term] @@ -143970,7 +146552,6 @@ is_a: GO:2000501 ! regulation of natural killer cell chemotaxis intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0035747 ! natural killer cell chemotaxis relationship: positively_regulates GO:0035747 ! natural killer cell chemotaxis -created_by: bf creation_date: 2011-03-21T10:09:38Z [Term] @@ -143984,7 +146565,6 @@ is_a: GO:0060312 ! regulation of blood vessel remodeling intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0001974 ! blood vessel remodeling relationship: positively_regulates GO:0001974 ! blood vessel remodeling -created_by: pr creation_date: 2011-03-21T10:33:20Z [Term] @@ -143997,7 +146577,6 @@ is_a: GO:0071675 ! regulation of mononuclear cell migration intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0002407 ! dendritic cell chemotaxis relationship: regulates GO:0002407 ! dendritic cell chemotaxis -created_by: ebc creation_date: 2011-03-22T10:21:38Z [Term] @@ -144011,7 +146590,6 @@ is_a: GO:2000508 ! regulation of dendritic cell chemotaxis intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0002407 ! dendritic cell chemotaxis relationship: negatively_regulates GO:0002407 ! dendritic cell chemotaxis -created_by: ebc creation_date: 2011-03-22T10:21:45Z [Term] @@ -144025,7 +146603,6 @@ is_a: GO:2000508 ! regulation of dendritic cell chemotaxis intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0002407 ! dendritic cell chemotaxis relationship: positively_regulates GO:0002407 ! dendritic cell chemotaxis -created_by: ebc creation_date: 2011-03-22T10:21:49Z [Term] @@ -144037,7 +146614,6 @@ is_a: GO:0046634 ! regulation of alpha-beta T cell activation intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0035710 ! CD4-positive, alpha-beta T cell activation relationship: regulates GO:0035710 ! CD4-positive, alpha-beta T cell activation -created_by: ebc creation_date: 2011-03-22T10:36:56Z [Term] @@ -144050,7 +146626,6 @@ is_a: GO:2000514 ! regulation of CD4-positive, alpha-beta T cell activation intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0035710 ! CD4-positive, alpha-beta T cell activation relationship: negatively_regulates GO:0035710 ! CD4-positive, alpha-beta T cell activation -created_by: ebc creation_date: 2011-03-22T10:37:02Z [Term] @@ -144063,7 +146638,6 @@ is_a: GO:2000514 ! regulation of CD4-positive, alpha-beta T cell activation intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0035710 ! CD4-positive, alpha-beta T cell activation relationship: positively_regulates GO:0035710 ! CD4-positive, alpha-beta T cell activation -created_by: ebc creation_date: 2011-03-22T10:37:06Z [Term] @@ -144076,7 +146650,6 @@ is_a: GO:2000514 ! regulation of CD4-positive, alpha-beta T cell activation intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0035711 ! T-helper 1 cell activation relationship: regulates GO:0035711 ! T-helper 1 cell activation -created_by: ebc creation_date: 2011-03-22T10:40:19Z [Term] @@ -144090,7 +146663,6 @@ is_a: GO:2000517 ! regulation of T-helper 1 cell activation intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0035711 ! T-helper 1 cell activation relationship: negatively_regulates GO:0035711 ! T-helper 1 cell activation -created_by: ebc creation_date: 2011-03-22T10:40:26Z [Term] @@ -144104,7 +146676,6 @@ is_a: GO:2000517 ! regulation of T-helper 1 cell activation intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0035711 ! T-helper 1 cell activation relationship: positively_regulates GO:0035711 ! T-helper 1 cell activation -created_by: ebc creation_date: 2011-03-22T10:40:31Z [Term] @@ -144122,7 +146693,6 @@ is_a: GO:1903037 ! regulation of leukocyte cell-cell adhesion intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0031295 ! T cell costimulation relationship: regulates GO:0031295 ! T cell costimulation -created_by: ebc creation_date: 2011-03-23T10:23:24Z [Term] @@ -144140,7 +146710,6 @@ is_a: GO:2000523 ! regulation of T cell costimulation intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0031295 ! T cell costimulation relationship: negatively_regulates GO:0031295 ! T cell costimulation -created_by: ebc creation_date: 2011-03-23T10:23:31Z [Term] @@ -144158,7 +146727,6 @@ is_a: GO:2000523 ! regulation of T cell costimulation intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0031295 ! T cell costimulation relationship: positively_regulates GO:0031295 ! T cell costimulation -created_by: ebc creation_date: 2011-03-23T10:23:36Z [Term] @@ -144170,7 +146738,6 @@ is_a: GO:2000508 ! regulation of dendritic cell chemotaxis intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0002408 ! myeloid dendritic cell chemotaxis relationship: regulates GO:0002408 ! myeloid dendritic cell chemotaxis -created_by: ebc creation_date: 2011-03-23T12:18:32Z [Term] @@ -144183,7 +146750,6 @@ is_a: GO:2000527 ! regulation of myeloid dendritic cell chemotaxis intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0002408 ! myeloid dendritic cell chemotaxis relationship: negatively_regulates GO:0002408 ! myeloid dendritic cell chemotaxis -created_by: ebc creation_date: 2011-03-23T12:18:39Z [Term] @@ -144196,7 +146762,6 @@ is_a: GO:2000527 ! regulation of myeloid dendritic cell chemotaxis intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0002408 ! myeloid dendritic cell chemotaxis relationship: positively_regulates GO:0002408 ! myeloid dendritic cell chemotaxis -created_by: ebc creation_date: 2011-03-23T12:18:45Z [Term] @@ -144208,7 +146773,6 @@ is_a: GO:1901623 ! regulation of lymphocyte chemotaxis intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0035754 ! B cell chemotaxis relationship: regulates GO:0035754 ! B cell chemotaxis -created_by: ebc creation_date: 2011-03-29T09:49:25Z [Term] @@ -144221,7 +146785,6 @@ is_a: GO:2000537 ! regulation of B cell chemotaxis intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0035754 ! B cell chemotaxis relationship: positively_regulates GO:0035754 ! B cell chemotaxis -created_by: ebc creation_date: 2011-03-29T09:49:33Z [Term] @@ -144234,7 +146797,6 @@ is_a: GO:0045992 ! negative regulation of embryonic development intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0007369 ! gastrulation relationship: negatively_regulates GO:0007369 ! gastrulation -created_by: yaf creation_date: 2011-04-01T04:10:08Z [Term] @@ -144247,7 +146809,6 @@ is_a: GO:0040019 ! positive regulation of embryonic development intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0007369 ! gastrulation relationship: positively_regulates GO:0007369 ! gastrulation -created_by: yaf creation_date: 2011-04-01T04:10:15Z [Term] @@ -144260,7 +146821,6 @@ is_a: GO:0120032 ! regulation of plasma membrane bounded cell projection assembl intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0097026 ! dendritic cell dendrite assembly relationship: regulates GO:0097026 ! dendritic cell dendrite assembly -created_by: ebc creation_date: 2011-04-03T07:21:55Z [Term] @@ -144274,7 +146834,6 @@ is_a: GO:2000547 ! regulation of dendritic cell dendrite assembly intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0097026 ! dendritic cell dendrite assembly relationship: negatively_regulates GO:0097026 ! dendritic cell dendrite assembly -created_by: ebc creation_date: 2011-04-03T07:22:01Z [Term] @@ -144288,7 +146847,6 @@ is_a: GO:2000547 ! regulation of dendritic cell dendrite assembly intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0097026 ! dendritic cell dendrite assembly relationship: positively_regulates GO:0097026 ! dendritic cell dendrite assembly -created_by: ebc creation_date: 2011-04-03T07:22:06Z [Term] @@ -144301,7 +146859,6 @@ is_a: GO:2000537 ! regulation of B cell chemotaxis intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0035754 ! B cell chemotaxis relationship: negatively_regulates GO:0035754 ! B cell chemotaxis -created_by: ebc creation_date: 2011-04-03T07:25:59Z [Term] @@ -144315,7 +146872,6 @@ is_a: GO:0002828 ! regulation of type 2 immune response intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0035745 ! T-helper 2 cell cytokine production relationship: regulates GO:0035745 ! T-helper 2 cell cytokine production -created_by: ebc creation_date: 2011-04-03T07:32:47Z [Term] @@ -144330,7 +146886,6 @@ is_a: GO:2000551 ! regulation of T-helper 2 cell cytokine production intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0035745 ! T-helper 2 cell cytokine production relationship: negatively_regulates GO:0035745 ! T-helper 2 cell cytokine production -created_by: ebc creation_date: 2011-04-03T07:32:54Z [Term] @@ -144345,7 +146900,6 @@ is_a: GO:2000551 ! regulation of T-helper 2 cell cytokine production intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0035745 ! T-helper 2 cell cytokine production relationship: positively_regulates GO:0035745 ! T-helper 2 cell cytokine production -created_by: ebc creation_date: 2011-04-03T07:32:58Z [Term] @@ -144359,7 +146913,6 @@ is_a: GO:0002825 ! regulation of T-helper 1 type immune response intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0035744 ! T-helper 1 cell cytokine production relationship: regulates GO:0035744 ! T-helper 1 cell cytokine production -created_by: ebc creation_date: 2011-04-03T07:35:43Z [Term] @@ -144374,7 +146927,6 @@ is_a: GO:2000554 ! regulation of T-helper 1 cell cytokine production intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0035744 ! T-helper 1 cell cytokine production relationship: negatively_regulates GO:0035744 ! T-helper 1 cell cytokine production -created_by: ebc creation_date: 2011-04-03T07:35:51Z [Term] @@ -144389,7 +146941,6 @@ is_a: GO:2000554 ! regulation of T-helper 1 cell cytokine production intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0035744 ! T-helper 1 cell cytokine production relationship: positively_regulates GO:0035744 ! T-helper 1 cell cytokine production -created_by: ebc creation_date: 2011-04-03T07:35:56Z [Term] @@ -144402,7 +146953,6 @@ is_a: GO:2000514 ! regulation of CD4-positive, alpha-beta T cell activation intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0035739 ! CD4-positive, alpha-beta T cell proliferation relationship: regulates GO:0035739 ! CD4-positive, alpha-beta T cell proliferation -created_by: ebc creation_date: 2011-04-03T09:01:04Z [Term] @@ -144416,7 +146966,6 @@ is_a: GO:2000561 ! regulation of CD4-positive, alpha-beta T cell proliferation intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0035739 ! CD4-positive, alpha-beta T cell proliferation relationship: negatively_regulates GO:0035739 ! CD4-positive, alpha-beta T cell proliferation -created_by: ebc creation_date: 2011-04-03T09:01:11Z [Term] @@ -144430,7 +146979,6 @@ is_a: GO:2000561 ! regulation of CD4-positive, alpha-beta T cell proliferation intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0035739 ! CD4-positive, alpha-beta T cell proliferation relationship: positively_regulates GO:0035739 ! CD4-positive, alpha-beta T cell proliferation -created_by: ebc creation_date: 2011-04-03T09:01:15Z [Term] @@ -144443,7 +146991,6 @@ is_a: GO:2001185 ! regulation of CD8-positive, alpha-beta T cell activation intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0035740 ! CD8-positive, alpha-beta T cell proliferation relationship: regulates GO:0035740 ! CD8-positive, alpha-beta T cell proliferation -created_by: ebc creation_date: 2011-04-03T09:03:13Z [Term] @@ -144457,7 +147004,6 @@ is_a: GO:2001186 ! negative regulation of CD8-positive, alpha-beta T cell activa intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0035740 ! CD8-positive, alpha-beta T cell proliferation relationship: negatively_regulates GO:0035740 ! CD8-positive, alpha-beta T cell proliferation -created_by: ebc creation_date: 2011-04-03T09:03:19Z [Term] @@ -144471,7 +147017,6 @@ is_a: GO:2001187 ! positive regulation of CD8-positive, alpha-beta T cell activa intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0035740 ! CD8-positive, alpha-beta T cell proliferation relationship: positively_regulates GO:0035740 ! CD8-positive, alpha-beta T cell proliferation -created_by: ebc creation_date: 2011-04-03T09:03:24Z [Term] @@ -144483,7 +147028,6 @@ is_a: GO:0050863 ! regulation of T cell activation intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0035709 ! memory T cell activation relationship: regulates GO:0035709 ! memory T cell activation -created_by: ebc creation_date: 2011-04-03T09:10:06Z [Term] @@ -144496,7 +147040,6 @@ is_a: GO:2000567 ! regulation of memory T cell activation intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0035709 ! memory T cell activation relationship: positively_regulates GO:0035709 ! memory T cell activation -created_by: ebc creation_date: 2011-04-03T09:10:12Z [Term] @@ -144509,7 +147052,6 @@ is_a: GO:2000514 ! regulation of CD4-positive, alpha-beta T cell activation intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0035712 ! T-helper 2 cell activation relationship: regulates GO:0035712 ! T-helper 2 cell activation -created_by: ebc creation_date: 2011-04-03T09:14:53Z [Term] @@ -144523,7 +147065,6 @@ is_a: GO:2000569 ! regulation of T-helper 2 cell activation intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0035712 ! T-helper 2 cell activation relationship: positively_regulates GO:0035712 ! T-helper 2 cell activation -created_by: ebc creation_date: 2011-04-03T09:14:59Z [Term] @@ -144541,7 +147082,6 @@ is_a: GO:2000278 ! regulation of DNA biosynthetic process intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0071897 ! DNA biosynthetic process relationship: positively_regulates GO:0071897 ! DNA biosynthetic process -created_by: yaf creation_date: 2011-04-04T10:01:20Z [Term] @@ -144555,7 +147095,6 @@ is_a: GO:0022603 ! regulation of anatomical structure morphogenesis intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0021634 ! optic nerve formation relationship: regulates GO:0021634 ! optic nerve formation -created_by: yaf creation_date: 2011-04-11T03:41:30Z [Term] @@ -144570,7 +147109,6 @@ is_a: GO:2000595 ! regulation of optic nerve formation intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0021634 ! optic nerve formation relationship: negatively_regulates GO:0021634 ! optic nerve formation -created_by: yaf creation_date: 2011-04-11T03:41:35Z [Term] @@ -144585,7 +147123,6 @@ is_a: GO:2000595 ! regulation of optic nerve formation intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0021634 ! optic nerve formation relationship: positively_regulates GO:0021634 ! optic nerve formation -created_by: yaf creation_date: 2011-04-11T03:41:39Z [Term] @@ -144597,7 +147134,6 @@ is_a: GO:1901722 ! regulation of cell proliferation involved in kidney developme intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0061209 ! cell proliferation involved in mesonephros development relationship: regulates GO:0061209 ! cell proliferation involved in mesonephros development -created_by: yaf creation_date: 2011-04-18T08:42:19Z [Term] @@ -144610,7 +147146,6 @@ is_a: GO:2000606 ! regulation of cell proliferation involved in mesonephros deve intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0061209 ! cell proliferation involved in mesonephros development relationship: negatively_regulates GO:0061209 ! cell proliferation involved in mesonephros development -created_by: yaf creation_date: 2011-04-18T08:42:23Z [Term] @@ -144623,7 +147158,6 @@ is_a: GO:2000606 ! regulation of cell proliferation involved in mesonephros deve intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0061209 ! cell proliferation involved in mesonephros development relationship: positively_regulates GO:0061209 ! cell proliferation involved in mesonephros development -created_by: yaf creation_date: 2011-04-18T08:42:25Z [Term] @@ -144631,12 +147165,10 @@ id: GO:2000609 name: regulation of thyroid hormone generation namespace: biological_process def: "Any process that modulates the frequency, rate or extent of thyroid hormone generation." [GOC:obol] -is_a: GO:0031323 ! regulation of cellular metabolic process is_a: GO:0032350 ! regulation of hormone metabolic process intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0006590 ! thyroid hormone generation relationship: regulates GO:0006590 ! thyroid hormone generation -created_by: yaf creation_date: 2011-04-18T10:12:14Z [Term] @@ -144644,13 +147176,11 @@ id: GO:2000610 name: negative regulation of thyroid hormone generation namespace: biological_process def: "Any process that stops, prevents or reduces the frequency, rate or extent of thyroid hormone generation." [GOC:obol] -is_a: GO:0031324 ! negative regulation of cellular metabolic process is_a: GO:0032351 ! negative regulation of hormone metabolic process is_a: GO:2000609 ! regulation of thyroid hormone generation intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0006590 ! thyroid hormone generation relationship: negatively_regulates GO:0006590 ! thyroid hormone generation -created_by: yaf creation_date: 2011-04-18T10:12:19Z [Term] @@ -144658,13 +147188,11 @@ id: GO:2000611 name: positive regulation of thyroid hormone generation namespace: biological_process def: "Any process that activates or increases the frequency, rate or extent of thyroid hormone generation." [GOC:obol] -is_a: GO:0031325 ! positive regulation of cellular metabolic process is_a: GO:0032352 ! positive regulation of hormone metabolic process is_a: GO:2000609 ! regulation of thyroid hormone generation intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0006590 ! thyroid hormone generation relationship: positively_regulates GO:0006590 ! thyroid hormone generation -created_by: yaf creation_date: 2011-04-18T10:12:22Z [Term] @@ -144678,7 +147206,6 @@ is_a: GO:0090276 ! regulation of peptide hormone secretion intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0070460 ! thyroid-stimulating hormone secretion relationship: regulates GO:0070460 ! thyroid-stimulating hormone secretion -created_by: yaf creation_date: 2011-04-18T12:56:16Z [Term] @@ -144693,7 +147220,6 @@ is_a: GO:2000612 ! regulation of thyroid-stimulating hormone secretion intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0070460 ! thyroid-stimulating hormone secretion relationship: negatively_regulates GO:0070460 ! thyroid-stimulating hormone secretion -created_by: yaf creation_date: 2011-04-18T12:56:20Z [Term] @@ -144708,7 +147234,6 @@ is_a: GO:2000612 ! regulation of thyroid-stimulating hormone secretion intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0070460 ! thyroid-stimulating hormone secretion relationship: positively_regulates GO:0070460 ! thyroid-stimulating hormone secretion -created_by: yaf creation_date: 2011-04-18T12:56:22Z [Term] @@ -144721,7 +147246,6 @@ is_a: GO:0072091 ! regulation of stem cell proliferation intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0072089 ! stem cell proliferation relationship: negatively_regulates GO:0072089 ! stem cell proliferation -created_by: dph creation_date: 2011-04-27T01:04:22Z [Term] @@ -144734,7 +147258,6 @@ is_a: GO:0072091 ! regulation of stem cell proliferation intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0072089 ! stem cell proliferation relationship: positively_regulates GO:0072089 ! stem cell proliferation -created_by: dph creation_date: 2011-04-27T01:04:25Z [Term] @@ -144749,7 +147272,6 @@ is_a: GO:1902305 ! regulation of sodium ion transmembrane transport intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0015081 ! sodium ion transmembrane transporter activity relationship: regulates GO:0015081 ! sodium ion transmembrane transporter activity -created_by: yaf creation_date: 2011-04-28T08:42:53Z [Term] @@ -144765,7 +147287,6 @@ is_a: GO:2000649 ! regulation of sodium ion transmembrane transporter activity intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0015081 ! sodium ion transmembrane transporter activity relationship: negatively_regulates GO:0015081 ! sodium ion transmembrane transporter activity -created_by: yaf creation_date: 2011-04-28T08:42:57Z [Term] @@ -144781,7 +147302,6 @@ is_a: GO:2000649 ! regulation of sodium ion transmembrane transporter activity intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0015081 ! sodium ion transmembrane transporter activity relationship: positively_regulates GO:0015081 ! sodium ion transmembrane transporter activity -created_by: yaf creation_date: 2011-04-28T08:43:00Z [Term] @@ -144794,7 +147314,6 @@ is_a: GO:0050794 ! regulation of cellular process intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0071394 ! cellular response to testosterone stimulus relationship: regulates GO:0071394 ! cellular response to testosterone stimulus -created_by: vk creation_date: 2011-05-02T03:23:56Z [Term] @@ -144808,7 +147327,6 @@ is_a: GO:2000654 ! regulation of cellular response to testosterone stimulus intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0071394 ! cellular response to testosterone stimulus relationship: negatively_regulates GO:0071394 ! cellular response to testosterone stimulus -created_by: vk creation_date: 2011-05-02T03:23:59Z [Term] @@ -144821,7 +147339,6 @@ is_a: GO:2000106 ! regulation of leukocyte apoptotic process intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0097048 ! dendritic cell apoptotic process relationship: regulates GO:0097048 ! dendritic cell apoptotic process -created_by: pr creation_date: 2011-05-09T07:34:16Z [Term] @@ -144835,7 +147352,6 @@ is_a: GO:2000668 ! regulation of dendritic cell apoptotic process intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0097048 ! dendritic cell apoptotic process relationship: negatively_regulates GO:0097048 ! dendritic cell apoptotic process -created_by: pr creation_date: 2011-05-09T07:34:21Z [Term] @@ -144849,7 +147365,6 @@ is_a: GO:2000668 ! regulation of dendritic cell apoptotic process intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0097048 ! dendritic cell apoptotic process relationship: positively_regulates GO:0097048 ! dendritic cell apoptotic process -created_by: pr creation_date: 2011-05-09T07:34:26Z [Term] @@ -144863,7 +147378,6 @@ is_a: GO:0043523 ! regulation of neuron apoptotic process intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0097049 ! motor neuron apoptotic process relationship: regulates GO:0097049 ! motor neuron apoptotic process -created_by: pr creation_date: 2011-05-09T10:56:17Z [Term] @@ -144878,7 +147392,6 @@ is_a: GO:2000671 ! regulation of motor neuron apoptotic process intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0097049 ! motor neuron apoptotic process relationship: negatively_regulates GO:0097049 ! motor neuron apoptotic process -created_by: pr creation_date: 2011-05-09T10:56:21Z [Term] @@ -144893,7 +147406,6 @@ is_a: GO:2000671 ! regulation of motor neuron apoptotic process intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0097049 ! motor neuron apoptotic process relationship: positively_regulates GO:0097049 ! motor neuron apoptotic process -created_by: pr creation_date: 2011-05-09T10:56:24Z [Term] @@ -144908,7 +147420,6 @@ is_a: GO:1904035 ! regulation of epithelial cell apoptotic process intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0097050 ! type B pancreatic cell apoptotic process relationship: regulates GO:0097050 ! type B pancreatic cell apoptotic process -created_by: pr creation_date: 2011-05-09T11:51:09Z [Term] @@ -144924,7 +147435,6 @@ is_a: GO:2000674 ! regulation of type B pancreatic cell apoptotic process intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0097050 ! type B pancreatic cell apoptotic process relationship: negatively_regulates GO:0097050 ! type B pancreatic cell apoptotic process -created_by: pr creation_date: 2011-05-09T11:51:12Z [Term] @@ -144940,50 +147450,8 @@ is_a: GO:2000674 ! regulation of type B pancreatic cell apoptotic process intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0097050 ! type B pancreatic cell apoptotic process relationship: positively_regulates GO:0097050 ! type B pancreatic cell apoptotic process -created_by: pr creation_date: 2011-05-09T11:51:15Z -[Term] -id: GO:2000677 -name: regulation of transcription regulatory region DNA binding -namespace: biological_process -def: "Any process that modulates the frequency, rate or extent of transcription regulatory region DNA binding." [GOC:obol] -subset: gocheck_do_not_annotate -is_a: GO:0051101 ! regulation of DNA binding -intersection_of: GO:0065007 ! biological regulation -intersection_of: regulates GO:0000976 ! transcription cis-regulatory region binding -relationship: regulates GO:0000976 ! transcription cis-regulatory region binding -created_by: yaf -creation_date: 2011-05-09T03:28:11Z - -[Term] -id: GO:2000678 -name: negative regulation of transcription regulatory region DNA binding -namespace: biological_process -def: "Any process that stops, prevents or reduces the frequency, rate or extent of transcription regulatory region DNA binding." [GOC:obol] -subset: gocheck_do_not_annotate -is_a: GO:0043392 ! negative regulation of DNA binding -is_a: GO:2000677 ! regulation of transcription regulatory region DNA binding -intersection_of: GO:0065007 ! biological regulation -intersection_of: negatively_regulates GO:0000976 ! transcription cis-regulatory region binding -relationship: negatively_regulates GO:0000976 ! transcription cis-regulatory region binding -created_by: yaf -creation_date: 2011-05-09T03:28:14Z - -[Term] -id: GO:2000679 -name: positive regulation of transcription regulatory region DNA binding -namespace: biological_process -def: "Any process that activates or increases the frequency, rate or extent of transcription regulatory region DNA binding." [GOC:obol] -subset: gocheck_do_not_annotate -is_a: GO:0043388 ! positive regulation of DNA binding -is_a: GO:2000677 ! regulation of transcription regulatory region DNA binding -intersection_of: GO:0065007 ! biological regulation -intersection_of: positively_regulates GO:0000976 ! transcription cis-regulatory region binding -relationship: positively_regulates GO:0000976 ! transcription cis-regulatory region binding -created_by: yaf -creation_date: 2011-05-09T03:28:17Z - [Term] id: GO:2000690 name: regulation of cardiac muscle cell myoblast differentiation @@ -144996,7 +147464,6 @@ is_a: GO:0051890 ! regulation of cardioblast differentiation intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0060379 ! cardiac muscle cell myoblast differentiation relationship: regulates GO:0060379 ! cardiac muscle cell myoblast differentiation -created_by: yaf creation_date: 2011-05-25T09:08:01Z [Term] @@ -145012,7 +147479,6 @@ is_a: GO:2000690 ! regulation of cardiac muscle cell myoblast differentiation intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0060379 ! cardiac muscle cell myoblast differentiation relationship: negatively_regulates GO:0060379 ! cardiac muscle cell myoblast differentiation -created_by: yaf creation_date: 2011-05-25T09:08:06Z [Term] @@ -145024,7 +147490,6 @@ is_a: GO:0030856 ! regulation of epithelial cell differentiation intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0035850 ! epithelial cell differentiation involved in kidney development relationship: regulates GO:0035850 ! epithelial cell differentiation involved in kidney development -created_by: bf creation_date: 2011-05-16T04:23:52Z [Term] @@ -145037,7 +147502,6 @@ is_a: GO:2000696 ! regulation of epithelial cell differentiation involved in kid intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0035850 ! epithelial cell differentiation involved in kidney development relationship: negatively_regulates GO:0035850 ! epithelial cell differentiation involved in kidney development -created_by: bf creation_date: 2011-05-16T04:23:55Z [Term] @@ -145050,7 +147514,6 @@ is_a: GO:2000696 ! regulation of epithelial cell differentiation involved in kid intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0035850 ! epithelial cell differentiation involved in kidney development relationship: positively_regulates GO:0035850 ! epithelial cell differentiation involved in kidney development -created_by: bf creation_date: 2011-05-16T04:23:57Z [Term] @@ -145066,7 +147529,6 @@ is_a: GO:2000690 ! regulation of cardiac muscle cell myoblast differentiation intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0060379 ! cardiac muscle cell myoblast differentiation relationship: positively_regulates GO:0060379 ! cardiac muscle cell myoblast differentiation -created_by: yaf creation_date: 2011-05-25T09:08:09Z [Term] @@ -145081,7 +147543,6 @@ is_a: GO:1905207 ! regulation of cardiocyte differentiation intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0055007 ! cardiac muscle cell differentiation relationship: regulates GO:0055007 ! cardiac muscle cell differentiation -created_by: vk creation_date: 2011-06-08T10:51:06Z [Term] @@ -145097,7 +147558,6 @@ is_a: GO:2000725 ! regulation of cardiac muscle cell differentiation intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0055007 ! cardiac muscle cell differentiation relationship: negatively_regulates GO:0055007 ! cardiac muscle cell differentiation -created_by: vk creation_date: 2011-06-08T10:51:11Z [Term] @@ -145113,7 +147573,6 @@ is_a: GO:2000725 ! regulation of cardiac muscle cell differentiation intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0055007 ! cardiac muscle cell differentiation relationship: positively_regulates GO:0055007 ! cardiac muscle cell differentiation -created_by: vk creation_date: 2011-06-08T10:51:15Z [Term] @@ -145129,7 +147588,6 @@ is_a: GO:0072199 ! regulation of mesenchymal cell proliferation involved in uret intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0072198 ! mesenchymal cell proliferation involved in ureter development relationship: positively_regulates GO:0072198 ! mesenchymal cell proliferation involved in ureter development -created_by: yaf creation_date: 2011-06-10T02:27:19Z [Term] @@ -145141,7 +147599,6 @@ is_a: GO:0045595 ! regulation of cell differentiation intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0048863 ! stem cell differentiation relationship: regulates GO:0048863 ! stem cell differentiation -created_by: yaf creation_date: 2011-06-14T02:05:16Z [Term] @@ -145154,7 +147611,6 @@ is_a: GO:2000736 ! regulation of stem cell differentiation intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0048863 ! stem cell differentiation relationship: negatively_regulates GO:0048863 ! stem cell differentiation -created_by: yaf creation_date: 2011-06-14T02:05:20Z [Term] @@ -145167,7 +147623,6 @@ is_a: GO:2000736 ! regulation of stem cell differentiation intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0048863 ! stem cell differentiation relationship: positively_regulates GO:0048863 ! stem cell differentiation -created_by: yaf creation_date: 2011-06-14T02:05:23Z [Term] @@ -145179,7 +147634,6 @@ is_a: GO:2000736 ! regulation of stem cell differentiation intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0072497 ! mesenchymal stem cell differentiation relationship: regulates GO:0072497 ! mesenchymal stem cell differentiation -created_by: yaf creation_date: 2011-06-14T02:31:27Z [Term] @@ -145192,7 +147646,6 @@ is_a: GO:2000739 ! regulation of mesenchymal stem cell differentiation intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0072497 ! mesenchymal stem cell differentiation relationship: negatively_regulates GO:0072497 ! mesenchymal stem cell differentiation -created_by: yaf creation_date: 2011-06-14T02:31:31Z [Term] @@ -145205,7 +147658,6 @@ is_a: GO:2000739 ! regulation of mesenchymal stem cell differentiation intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0072497 ! mesenchymal stem cell differentiation relationship: positively_regulates GO:0072497 ! mesenchymal stem cell differentiation -created_by: yaf creation_date: 2011-06-14T02:31:34Z [Term] @@ -145217,7 +147669,6 @@ is_a: GO:0006417 ! regulation of translation intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0002181 ! cytoplasmic translation relationship: regulates GO:0002181 ! cytoplasmic translation -created_by: vw creation_date: 2011-06-20T10:39:19Z [Term] @@ -145230,7 +147681,6 @@ is_a: GO:2000765 ! regulation of cytoplasmic translation intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0002181 ! cytoplasmic translation relationship: negatively_regulates GO:0002181 ! cytoplasmic translation -created_by: vw creation_date: 2011-06-20T10:39:23Z [Term] @@ -145243,7 +147693,6 @@ is_a: GO:2000765 ! regulation of cytoplasmic translation intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0002181 ! cytoplasmic translation relationship: positively_regulates GO:0002181 ! cytoplasmic translation -created_by: vw creation_date: 2011-06-20T10:39:26Z [Term] @@ -145256,7 +147705,6 @@ is_a: GO:2000698 ! positive regulation of epithelial cell differentiation involv intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0072160 ! nephron tubule epithelial cell differentiation relationship: positively_regulates GO:0072160 ! nephron tubule epithelial cell differentiation -created_by: yaf creation_date: 2011-06-22T11:55:06Z [Term] @@ -145268,7 +147716,6 @@ is_a: GO:0010464 ! regulation of mesenchymal cell proliferation intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0060916 ! mesenchymal cell proliferation involved in lung development relationship: regulates GO:0060916 ! mesenchymal cell proliferation involved in lung development -created_by: pr creation_date: 2011-06-24T01:53:50Z [Term] @@ -145283,7 +147730,6 @@ is_a: GO:2000790 ! regulation of mesenchymal cell proliferation involved in lung intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0060916 ! mesenchymal cell proliferation involved in lung development relationship: negatively_regulates GO:0060916 ! mesenchymal cell proliferation involved in lung development -created_by: pr creation_date: 2011-06-24T01:53:53Z [Term] @@ -145298,7 +147744,6 @@ is_a: GO:2000790 ! regulation of mesenchymal cell proliferation involved in lung intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0060916 ! mesenchymal cell proliferation involved in lung development relationship: positively_regulates GO:0060916 ! mesenchymal cell proliferation involved in lung development -created_by: pr creation_date: 2011-06-24T01:53:56Z [Term] @@ -145312,7 +147757,6 @@ is_a: GO:0008283 ! cell population proliferation intersection_of: GO:0008283 ! cell population proliferation intersection_of: part_of GO:0003170 ! heart valve development relationship: part_of GO:0003170 ! heart valve development -created_by: bf creation_date: 2011-06-24T03:12:15Z [Term] @@ -145324,7 +147768,6 @@ is_a: GO:0050678 ! regulation of epithelial cell proliferation intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0060502 ! epithelial cell proliferation involved in lung morphogenesis relationship: regulates GO:0060502 ! epithelial cell proliferation involved in lung morphogenesis -created_by: pr creation_date: 2011-06-25T07:22:38Z [Term] @@ -145337,7 +147780,6 @@ is_a: GO:2000794 ! regulation of epithelial cell proliferation involved in lung intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0060502 ! epithelial cell proliferation involved in lung morphogenesis relationship: negatively_regulates GO:0060502 ! epithelial cell proliferation involved in lung morphogenesis -created_by: pr creation_date: 2011-06-25T07:22:42Z [Term] @@ -145349,7 +147791,6 @@ is_a: GO:2000739 ! regulation of mesenchymal stem cell differentiation intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0097086 ! amniotic stem cell differentiation relationship: regulates GO:0097086 ! amniotic stem cell differentiation -created_by: yaf creation_date: 2011-06-29T02:18:59Z [Term] @@ -145362,7 +147803,6 @@ is_a: GO:2000797 ! regulation of amniotic stem cell differentiation intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0097086 ! amniotic stem cell differentiation relationship: negatively_regulates GO:0097086 ! amniotic stem cell differentiation -created_by: yaf creation_date: 2011-06-29T02:19:03Z [Term] @@ -145375,7 +147815,6 @@ is_a: GO:2000797 ! regulation of amniotic stem cell differentiation intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0097086 ! amniotic stem cell differentiation relationship: positively_regulates GO:0097086 ! amniotic stem cell differentiation -created_by: yaf creation_date: 2011-06-29T02:19:06Z [Term] @@ -145388,7 +147827,6 @@ is_a: GO:1901888 ! regulation of cell junction assembly intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0070830 ! bicellular tight junction assembly relationship: regulates GO:0070830 ! bicellular tight junction assembly -created_by: vk creation_date: 2011-07-06T01:08:28Z [Term] @@ -145401,24 +147839,8 @@ is_a: GO:2000291 ! regulation of myoblast proliferation intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0051450 ! myoblast proliferation relationship: negatively_regulates GO:0051450 ! myoblast proliferation -created_by: pr creation_date: 2011-07-12T03:06:04Z -[Term] -id: GO:2000825 -name: positive regulation of androgen receptor activity -namespace: biological_process -def: "Any process that activates or increases the frequency, rate or extent of androgen receptor activity." [GOC:obol] -subset: gocheck_obsoletion_candidate -is_a: GO:0006357 ! regulation of transcription by RNA polymerase II -is_a: GO:0051091 ! positive regulation of DNA-binding transcription factor activity -is_a: GO:2000273 ! positive regulation of signaling receptor activity -intersection_of: GO:0065007 ! biological regulation -intersection_of: positively_regulates GO:0004879 ! nuclear receptor activity -relationship: positively_regulates GO:0004879 ! nuclear receptor activity -created_by: yaf -creation_date: 2011-07-15T10:56:14Z - [Term] id: GO:2000826 name: regulation of heart morphogenesis @@ -145429,7 +147851,6 @@ is_a: GO:2000027 ! regulation of animal organ morphogenesis intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0003007 ! heart morphogenesis relationship: regulates GO:0003007 ! heart morphogenesis -created_by: vk creation_date: 2011-07-19T10:08:58Z [Term] @@ -145445,7 +147866,6 @@ is_a: GO:0046883 ! regulation of hormone secretion intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0035898 ! parathyroid hormone secretion relationship: regulates GO:0035898 ! parathyroid hormone secretion -created_by: bf creation_date: 2011-07-26T08:37:53Z [Term] @@ -145462,7 +147882,6 @@ is_a: GO:2000828 ! regulation of parathyroid hormone secretion intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0035898 ! parathyroid hormone secretion relationship: negatively_regulates GO:0035898 ! parathyroid hormone secretion -created_by: bf creation_date: 2011-07-26T08:37:57Z [Term] @@ -145479,7 +147898,6 @@ is_a: GO:2000828 ! regulation of parathyroid hormone secretion intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0035898 ! parathyroid hormone secretion relationship: positively_regulates GO:0035898 ! parathyroid hormone secretion -created_by: bf creation_date: 2011-07-26T08:38:00Z [Term] @@ -145493,7 +147911,6 @@ is_a: GO:0046883 ! regulation of hormone secretion intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0035929 ! steroid hormone secretion relationship: regulates GO:0035929 ! steroid hormone secretion -created_by: bf creation_date: 2011-07-26T08:38:46Z [Term] @@ -145508,7 +147925,6 @@ is_a: GO:2000831 ! regulation of steroid hormone secretion intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0035929 ! steroid hormone secretion relationship: negatively_regulates GO:0035929 ! steroid hormone secretion -created_by: bf creation_date: 2011-07-26T08:38:50Z [Term] @@ -145523,7 +147939,6 @@ is_a: GO:2000831 ! regulation of steroid hormone secretion intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0035929 ! steroid hormone secretion relationship: positively_regulates GO:0035929 ! steroid hormone secretion -created_by: bf creation_date: 2011-07-26T08:38:51Z [Term] @@ -145535,7 +147950,6 @@ is_a: GO:2000831 ! regulation of steroid hormone secretion intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0035935 ! androgen secretion relationship: regulates GO:0035935 ! androgen secretion -created_by: bf creation_date: 2011-07-26T08:39:45Z [Term] @@ -145548,7 +147962,6 @@ is_a: GO:2000834 ! regulation of androgen secretion intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0035935 ! androgen secretion relationship: negatively_regulates GO:0035935 ! androgen secretion -created_by: bf creation_date: 2011-07-26T08:39:48Z [Term] @@ -145561,7 +147974,6 @@ is_a: GO:2000834 ! regulation of androgen secretion intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0035935 ! androgen secretion relationship: positively_regulates GO:0035935 ! androgen secretion -created_by: bf creation_date: 2011-07-26T08:39:51Z [Term] @@ -145573,7 +147985,6 @@ is_a: GO:0046883 ! regulation of hormone secretion intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0035936 ! testosterone secretion relationship: regulates GO:0035936 ! testosterone secretion -created_by: bf creation_date: 2011-07-26T08:42:29Z [Term] @@ -145586,7 +147997,6 @@ is_a: GO:2000843 ! regulation of testosterone secretion intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0035936 ! testosterone secretion relationship: negatively_regulates GO:0035936 ! testosterone secretion -created_by: bf creation_date: 2011-07-26T08:42:33Z [Term] @@ -145599,7 +148009,6 @@ is_a: GO:2000843 ! regulation of testosterone secretion intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0035936 ! testosterone secretion relationship: positively_regulates GO:0035936 ! testosterone secretion -created_by: bf creation_date: 2011-07-26T08:42:36Z [Term] @@ -145612,7 +148021,6 @@ is_a: GO:2000831 ! regulation of steroid hormone secretion intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0035930 ! corticosteroid hormone secretion relationship: regulates GO:0035930 ! corticosteroid hormone secretion -created_by: bf creation_date: 2011-07-26T08:43:38Z [Term] @@ -145626,7 +148034,6 @@ is_a: GO:2000846 ! regulation of corticosteroid hormone secretion intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0035930 ! corticosteroid hormone secretion relationship: negatively_regulates GO:0035930 ! corticosteroid hormone secretion -created_by: bf creation_date: 2011-07-26T08:43:42Z [Term] @@ -145640,7 +148047,6 @@ is_a: GO:2000846 ! regulation of corticosteroid hormone secretion intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0035930 ! corticosteroid hormone secretion relationship: positively_regulates GO:0035930 ! corticosteroid hormone secretion -created_by: bf creation_date: 2011-07-26T08:43:45Z [Term] @@ -145652,7 +148058,6 @@ is_a: GO:2000846 ! regulation of corticosteroid hormone secretion intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0035933 ! glucocorticoid secretion relationship: regulates GO:0035933 ! glucocorticoid secretion -created_by: bf creation_date: 2011-07-26T08:44:43Z [Term] @@ -145665,7 +148070,6 @@ is_a: GO:2000849 ! regulation of glucocorticoid secretion intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0035933 ! glucocorticoid secretion relationship: negatively_regulates GO:0035933 ! glucocorticoid secretion -created_by: bf creation_date: 2011-07-26T08:44:48Z [Term] @@ -145678,7 +148082,6 @@ is_a: GO:2000849 ! regulation of glucocorticoid secretion intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0035933 ! glucocorticoid secretion relationship: positively_regulates GO:0035933 ! glucocorticoid secretion -created_by: bf creation_date: 2011-07-26T08:44:51Z [Term] @@ -145690,7 +148093,6 @@ is_a: GO:2000846 ! regulation of corticosteroid hormone secretion intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0035931 ! mineralocorticoid secretion relationship: regulates GO:0035931 ! mineralocorticoid secretion -created_by: bf creation_date: 2011-07-26T08:46:38Z [Term] @@ -145703,7 +148105,6 @@ is_a: GO:2000855 ! regulation of mineralocorticoid secretion intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0035931 ! mineralocorticoid secretion relationship: negatively_regulates GO:0035931 ! mineralocorticoid secretion -created_by: bf creation_date: 2011-07-26T08:46:42Z [Term] @@ -145716,7 +148117,6 @@ is_a: GO:2000855 ! regulation of mineralocorticoid secretion intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0035931 ! mineralocorticoid secretion relationship: positively_regulates GO:0035931 ! mineralocorticoid secretion -created_by: bf creation_date: 2011-07-26T08:46:45Z [Term] @@ -145728,7 +148128,6 @@ is_a: GO:2000855 ! regulation of mineralocorticoid secretion intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0035932 ! aldosterone secretion relationship: regulates GO:0035932 ! aldosterone secretion -created_by: bf creation_date: 2011-07-26T08:47:27Z [Term] @@ -145741,7 +148140,6 @@ is_a: GO:2000858 ! regulation of aldosterone secretion intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0035932 ! aldosterone secretion relationship: negatively_regulates GO:0035932 ! aldosterone secretion -created_by: bf creation_date: 2011-07-26T08:47:31Z [Term] @@ -145754,7 +148152,6 @@ is_a: GO:2000858 ! regulation of aldosterone secretion intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0035932 ! aldosterone secretion relationship: positively_regulates GO:0035932 ! aldosterone secretion -created_by: bf creation_date: 2011-07-26T08:47:34Z [Term] @@ -145767,7 +148164,6 @@ is_a: GO:2000831 ! regulation of steroid hormone secretion intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0035938 ! estradiol secretion relationship: regulates GO:0035938 ! estradiol secretion -created_by: bf creation_date: 2011-07-26T08:49:13Z [Term] @@ -145781,7 +148177,6 @@ is_a: GO:2000864 ! regulation of estradiol secretion intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0035938 ! estradiol secretion relationship: negatively_regulates GO:0035938 ! estradiol secretion -created_by: bf creation_date: 2011-07-26T08:49:17Z [Term] @@ -145795,7 +148190,6 @@ is_a: GO:2000864 ! regulation of estradiol secretion intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0035938 ! estradiol secretion relationship: positively_regulates GO:0035938 ! estradiol secretion -created_by: bf creation_date: 2011-07-26T08:49:20Z [Term] @@ -145808,7 +148202,6 @@ is_a: GO:2000831 ! regulation of steroid hormone secretion intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0042701 ! progesterone secretion relationship: regulates GO:0042701 ! progesterone secretion -created_by: bf creation_date: 2011-07-26T08:51:14Z [Term] @@ -145822,7 +148215,6 @@ is_a: GO:2000870 ! regulation of progesterone secretion intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0042701 ! progesterone secretion relationship: negatively_regulates GO:0042701 ! progesterone secretion -created_by: bf creation_date: 2011-07-26T08:51:19Z [Term] @@ -145836,7 +148228,6 @@ is_a: GO:2000870 ! regulation of progesterone secretion intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0042701 ! progesterone secretion relationship: positively_regulates GO:0042701 ! progesterone secretion -created_by: bf creation_date: 2011-07-26T08:51:22Z [Term] @@ -145850,7 +148241,6 @@ is_a: GO:1905456 ! regulation of lymphoid progenitor cell differentiation intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0002328 ! pro-B cell differentiation relationship: regulates GO:0002328 ! pro-B cell differentiation -created_by: yaf creation_date: 2011-08-02T03:05:45Z [Term] @@ -145865,7 +148255,6 @@ is_a: GO:2000973 ! regulation of pro-B cell differentiation intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0002328 ! pro-B cell differentiation relationship: negatively_regulates GO:0002328 ! pro-B cell differentiation -created_by: yaf creation_date: 2011-08-02T03:05:50Z [Term] @@ -145880,7 +148269,6 @@ is_a: GO:2000973 ! regulation of pro-B cell differentiation intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0002328 ! pro-B cell differentiation relationship: positively_regulates GO:0002328 ! pro-B cell differentiation -created_by: yaf creation_date: 2011-08-02T03:05:53Z [Term] @@ -145892,7 +148280,6 @@ is_a: GO:0045664 ! regulation of neuron differentiation intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0021879 ! forebrain neuron differentiation relationship: regulates GO:0021879 ! forebrain neuron differentiation -created_by: yaf creation_date: 2011-08-03T12:09:12Z [Term] @@ -145905,7 +148292,6 @@ is_a: GO:2000977 ! regulation of forebrain neuron differentiation intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0021879 ! forebrain neuron differentiation relationship: negatively_regulates GO:0021879 ! forebrain neuron differentiation -created_by: yaf creation_date: 2011-08-03T12:09:16Z [Term] @@ -145918,7 +148304,6 @@ is_a: GO:2000977 ! regulation of forebrain neuron differentiation intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0021879 ! forebrain neuron differentiation relationship: positively_regulates GO:0021879 ! forebrain neuron differentiation -created_by: yaf creation_date: 2011-08-03T12:09:19Z [Term] @@ -145931,7 +148316,6 @@ is_a: GO:0045631 ! regulation of mechanoreceptor differentiation intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0060113 ! inner ear receptor cell differentiation relationship: regulates GO:0060113 ! inner ear receptor cell differentiation -created_by: yaf creation_date: 2011-08-03T02:38:43Z [Term] @@ -145945,7 +148329,6 @@ is_a: GO:2000980 ! regulation of inner ear receptor cell differentiation intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0060113 ! inner ear receptor cell differentiation relationship: negatively_regulates GO:0060113 ! inner ear receptor cell differentiation -created_by: yaf creation_date: 2011-08-03T02:38:47Z [Term] @@ -145959,7 +148342,6 @@ is_a: GO:2000980 ! regulation of inner ear receptor cell differentiation intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0060113 ! inner ear receptor cell differentiation relationship: positively_regulates GO:0060113 ! inner ear receptor cell differentiation -created_by: yaf creation_date: 2011-08-03T02:38:51Z [Term] @@ -145973,7 +148355,6 @@ is_a: GO:0048762 ! mesenchymal cell differentiation intersection_of: GO:0048762 ! mesenchymal cell differentiation intersection_of: part_of GO:0072001 ! renal system development relationship: part_of GO:0072001 ! renal system development -created_by: yaf creation_date: 2011-08-09T04:05:14Z [Term] @@ -145985,7 +148366,6 @@ is_a: GO:0050673 ! epithelial cell proliferation intersection_of: GO:0050673 ! epithelial cell proliferation intersection_of: part_of GO:0061333 ! renal tubule morphogenesis relationship: part_of GO:0061333 ! renal tubule morphogenesis -created_by: yaf creation_date: 2011-08-12T11:37:29Z [Term] @@ -145997,7 +148377,6 @@ is_a: GO:0045595 ! regulation of cell differentiation intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0035914 ! skeletal muscle cell differentiation relationship: regulates GO:0035914 ! skeletal muscle cell differentiation -created_by: yaf creation_date: 2011-08-11T08:54:37Z [Term] @@ -146010,7 +148389,6 @@ is_a: GO:2001014 ! regulation of skeletal muscle cell differentiation intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0035914 ! skeletal muscle cell differentiation relationship: negatively_regulates GO:0035914 ! skeletal muscle cell differentiation -created_by: yaf creation_date: 2011-08-11T08:54:41Z [Term] @@ -146023,7 +148401,6 @@ is_a: GO:2001014 ! regulation of skeletal muscle cell differentiation intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0035914 ! skeletal muscle cell differentiation relationship: positively_regulates GO:0035914 ! skeletal muscle cell differentiation -created_by: yaf creation_date: 2011-08-11T08:54:44Z [Term] @@ -146037,7 +148414,6 @@ is_a: GO:0060632 ! regulation of microtubule-based movement intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0008090 ! retrograde axonal transport relationship: regulates GO:0008090 ! retrograde axonal transport -created_by: kmv creation_date: 2011-08-11T09:44:42Z [Term] @@ -146051,7 +148427,6 @@ is_a: GO:2001017 ! regulation of retrograde axon cargo transport intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0008090 ! retrograde axonal transport relationship: negatively_regulates GO:0008090 ! retrograde axonal transport -created_by: kmv creation_date: 2011-08-11T09:44:46Z [Term] @@ -146065,7 +148440,6 @@ is_a: GO:2001017 ! regulation of retrograde axon cargo transport intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0008090 ! retrograde axonal transport relationship: positively_regulates GO:0008090 ! retrograde axonal transport -created_by: kmv creation_date: 2011-08-11T09:44:49Z [Term] @@ -146078,7 +148452,6 @@ is_a: GO:0050920 ! regulation of chemotaxis intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0035767 ! endothelial cell chemotaxis relationship: regulates GO:0035767 ! endothelial cell chemotaxis -created_by: rl creation_date: 2011-08-22T01:07:26Z [Term] @@ -146092,7 +148465,6 @@ is_a: GO:2001026 ! regulation of endothelial cell chemotaxis intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0035767 ! endothelial cell chemotaxis relationship: negatively_regulates GO:0035767 ! endothelial cell chemotaxis -created_by: rl creation_date: 2011-08-22T01:07:31Z [Term] @@ -146106,7 +148478,6 @@ is_a: GO:2001026 ! regulation of endothelial cell chemotaxis intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0035767 ! endothelial cell chemotaxis relationship: positively_regulates GO:0035767 ! endothelial cell chemotaxis -created_by: rl creation_date: 2011-08-22T01:07:34Z [Term] @@ -146118,7 +148489,6 @@ is_a: GO:1902809 ! regulation of skeletal muscle fiber differentiation intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0035981 ! tongue muscle cell differentiation relationship: regulates GO:0035981 ! tongue muscle cell differentiation -created_by: yaf creation_date: 2011-08-24T11:10:16Z [Term] @@ -146131,7 +148501,6 @@ is_a: GO:2001035 ! regulation of tongue muscle cell differentiation intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0035981 ! tongue muscle cell differentiation relationship: negatively_regulates GO:0035981 ! tongue muscle cell differentiation -created_by: yaf creation_date: 2011-08-24T11:10:20Z [Term] @@ -146144,7 +148513,6 @@ is_a: GO:2001035 ! regulation of tongue muscle cell differentiation intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0035981 ! tongue muscle cell differentiation relationship: positively_regulates GO:0035981 ! tongue muscle cell differentiation -created_by: yaf creation_date: 2011-08-24T11:10:22Z [Term] @@ -146158,7 +148526,6 @@ is_a: GO:0045595 ! regulation of cell differentiation intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0035990 ! tendon cell differentiation relationship: regulates GO:0035990 ! tendon cell differentiation -created_by: yaf creation_date: 2011-09-01T09:20:32Z [Term] @@ -146173,7 +148540,6 @@ is_a: GO:2001049 ! regulation of tendon cell differentiation intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0035990 ! tendon cell differentiation relationship: negatively_regulates GO:0035990 ! tendon cell differentiation -created_by: yaf creation_date: 2011-09-01T09:20:38Z [Term] @@ -146188,7 +148554,6 @@ is_a: GO:2001049 ! regulation of tendon cell differentiation intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0035990 ! tendon cell differentiation relationship: positively_regulates GO:0035990 ! tendon cell differentiation -created_by: yaf creation_date: 2011-09-01T09:20:42Z [Term] @@ -146201,7 +148566,6 @@ is_a: GO:0042981 ! regulation of apoptotic process intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0097152 ! mesenchymal cell apoptotic process relationship: regulates GO:0097152 ! mesenchymal cell apoptotic process -created_by: yaf creation_date: 2011-09-08T02:49:59Z [Term] @@ -146215,7 +148579,6 @@ is_a: GO:2001053 ! regulation of mesenchymal cell apoptotic process intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0097152 ! mesenchymal cell apoptotic process relationship: negatively_regulates GO:0097152 ! mesenchymal cell apoptotic process -created_by: yaf creation_date: 2011-09-08T02:50:05Z [Term] @@ -146229,7 +148592,6 @@ is_a: GO:2001053 ! regulation of mesenchymal cell apoptotic process intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0097152 ! mesenchymal cell apoptotic process relationship: positively_regulates GO:0097152 ! mesenchymal cell apoptotic process -created_by: yaf creation_date: 2011-09-08T02:50:09Z [Term] @@ -146244,7 +148606,6 @@ is_a: GO:0005488 ! binding intersection_of: GO:0005488 ! binding intersection_of: has_primary_input CHEBI:28087 relationship: has_primary_input CHEBI:28087 -created_by: jl creation_date: 2011-09-14T12:01:06Z [Term] @@ -146261,7 +148622,6 @@ is_a: GO:0051252 ! regulation of RNA metabolic process intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0032774 ! RNA biosynthetic process relationship: regulates GO:0032774 ! RNA biosynthetic process -created_by: dph creation_date: 2011-10-17T11:36:25Z [Term] @@ -146275,7 +148635,6 @@ is_a: GO:0098801 ! regulation of renal system process intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0003097 ! renal water transport relationship: regulates GO:0003097 ! renal water transport -created_by: yaf creation_date: 2011-10-24T11:37:51Z [Term] @@ -146289,7 +148648,6 @@ is_a: GO:2001151 ! regulation of renal water transport intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0003097 ! renal water transport relationship: negatively_regulates GO:0003097 ! renal water transport -created_by: yaf creation_date: 2011-10-24T11:37:57Z [Term] @@ -146303,7 +148661,6 @@ is_a: GO:2001151 ! regulation of renal water transport intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0003097 ! renal water transport relationship: positively_regulates GO:0003097 ! renal water transport -created_by: yaf creation_date: 2011-10-24T11:38:01Z [Term] @@ -146321,7 +148678,6 @@ is_a: GO:1903578 ! regulation of ATP metabolic process intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0006754 ! ATP biosynthetic process relationship: regulates GO:0006754 ! ATP biosynthetic process -created_by: kmv creation_date: 2011-10-26T03:18:03Z [Term] @@ -146340,7 +148696,6 @@ is_a: GO:2001169 ! regulation of ATP biosynthetic process intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0006754 ! ATP biosynthetic process relationship: negatively_regulates GO:0006754 ! ATP biosynthetic process -created_by: kmv creation_date: 2011-10-26T03:18:13Z [Term] @@ -146359,7 +148714,6 @@ is_a: GO:2001169 ! regulation of ATP biosynthetic process intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0006754 ! ATP biosynthetic process relationship: positively_regulates GO:0006754 ! ATP biosynthetic process -created_by: kmv creation_date: 2011-10-26T03:18:26Z [Term] @@ -146371,7 +148725,6 @@ is_a: GO:0046634 ! regulation of alpha-beta T cell activation intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0036037 ! CD8-positive, alpha-beta T cell activation relationship: regulates GO:0036037 ! CD8-positive, alpha-beta T cell activation -created_by: yaf creation_date: 2011-11-03T01:16:51Z [Term] @@ -146384,7 +148737,6 @@ is_a: GO:2001185 ! regulation of CD8-positive, alpha-beta T cell activation intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0036037 ! CD8-positive, alpha-beta T cell activation relationship: negatively_regulates GO:0036037 ! CD8-positive, alpha-beta T cell activation -created_by: yaf creation_date: 2011-11-03T01:16:57Z [Term] @@ -146397,7 +148749,6 @@ is_a: GO:2001185 ! regulation of CD8-positive, alpha-beta T cell activation intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0036037 ! CD8-positive, alpha-beta T cell activation relationship: positively_regulates GO:0036037 ! CD8-positive, alpha-beta T cell activation -created_by: yaf creation_date: 2011-11-03T01:17:02Z [Term] @@ -146415,7 +148766,6 @@ is_a: GO:0050776 ! regulation of immune response intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0002290 ! gamma-delta T cell activation involved in immune response relationship: regulates GO:0002290 ! gamma-delta T cell activation involved in immune response -created_by: yaf creation_date: 2011-11-03T04:28:38Z [Term] @@ -146434,7 +148784,6 @@ is_a: GO:2001191 ! regulation of gamma-delta T cell activation involved in immun intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0002290 ! gamma-delta T cell activation involved in immune response relationship: negatively_regulates GO:0002290 ! gamma-delta T cell activation involved in immune response -created_by: yaf creation_date: 2011-11-03T04:28:44Z [Term] @@ -146453,7 +148802,6 @@ is_a: GO:2001191 ! regulation of gamma-delta T cell activation involved in immun intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0002290 ! gamma-delta T cell activation involved in immune response relationship: positively_regulates GO:0002290 ! gamma-delta T cell activation involved in immune response -created_by: yaf creation_date: 2011-11-03T04:28:48Z [Term] @@ -146465,7 +148813,6 @@ is_a: GO:1902105 ! regulation of leukocyte differentiation intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0097028 ! dendritic cell differentiation relationship: regulates GO:0097028 ! dendritic cell differentiation -created_by: yaf creation_date: 2011-11-04T02:01:27Z [Term] @@ -146478,7 +148825,6 @@ is_a: GO:2001198 ! regulation of dendritic cell differentiation intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0097028 ! dendritic cell differentiation relationship: negatively_regulates GO:0097028 ! dendritic cell differentiation -created_by: yaf creation_date: 2011-11-04T02:01:33Z [Term] @@ -146491,7 +148837,6 @@ is_a: GO:2001198 ! regulation of dendritic cell differentiation intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0097028 ! dendritic cell differentiation relationship: positively_regulates GO:0097028 ! dendritic cell differentiation -created_by: yaf creation_date: 2011-11-04T02:01:36Z [Term] @@ -146504,7 +148849,6 @@ is_a: GO:1903706 ! regulation of hemopoiesis intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0036035 ! osteoclast development relationship: regulates GO:0036035 ! osteoclast development -created_by: yaf creation_date: 2011-11-10T10:58:59Z [Term] @@ -146518,7 +148862,6 @@ is_a: GO:2001204 ! regulation of osteoclast development intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0036035 ! osteoclast development relationship: negatively_regulates GO:0036035 ! osteoclast development -created_by: yaf creation_date: 2011-11-10T10:59:06Z [Term] @@ -146532,7 +148875,6 @@ is_a: GO:2001204 ! regulation of osteoclast development intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0036035 ! osteoclast development relationship: positively_regulates GO:0036035 ! osteoclast development -created_by: yaf creation_date: 2011-11-10T10:59:12Z [Term] @@ -146545,7 +148887,6 @@ is_a: GO:0045595 ! regulation of cell differentiation intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0001570 ! vasculogenesis relationship: regulates GO:0001570 ! vasculogenesis -created_by: yaf creation_date: 2011-11-15T01:22:31Z [Term] @@ -146559,7 +148900,6 @@ is_a: GO:2001212 ! regulation of vasculogenesis intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0001570 ! vasculogenesis relationship: negatively_regulates GO:0001570 ! vasculogenesis -created_by: yaf creation_date: 2011-11-15T01:22:36Z [Term] @@ -146573,7 +148913,6 @@ is_a: GO:2001212 ! regulation of vasculogenesis intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0001570 ! vasculogenesis relationship: positively_regulates GO:0001570 ! vasculogenesis -created_by: yaf creation_date: 2011-11-15T01:22:39Z [Term] @@ -146590,7 +148929,6 @@ intersection_of: regulates GO:0001764 ! neuron migration relationship: regulates GO:0001764 ! neuron migration relationship: RO:0002160 NCBITaxon:33208 ! only in taxon Metazoa relationship: RO:0002162 NCBITaxon:33208 {all_only="true"} ! in taxon Metazoa -created_by: kmv creation_date: 2011-11-17T10:01:38Z [Term] @@ -146606,7 +148944,6 @@ is_a: GO:2001222 ! regulation of neuron migration intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0001764 ! neuron migration relationship: negatively_regulates GO:0001764 ! neuron migration -created_by: kmv creation_date: 2011-11-17T10:01:45Z [Term] @@ -146622,7 +148959,6 @@ is_a: GO:2001222 ! regulation of neuron migration intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0001764 ! neuron migration relationship: positively_regulates GO:0001764 ! neuron migration -created_by: kmv creation_date: 2011-11-17T10:01:49Z [Term] @@ -146636,7 +148972,6 @@ is_a: GO:0042981 ! regulation of apoptotic process intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0097190 ! apoptotic signaling pathway relationship: regulates GO:0097190 ! apoptotic signaling pathway -created_by: pr creation_date: 2011-11-24T01:20:49Z [Term] @@ -146651,7 +148986,6 @@ is_a: GO:2001233 ! regulation of apoptotic signaling pathway intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0097190 ! apoptotic signaling pathway relationship: negatively_regulates GO:0097190 ! apoptotic signaling pathway -created_by: pr creation_date: 2011-11-24T01:20:54Z [Term] @@ -146667,9 +149001,49 @@ intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0097190 ! apoptotic signaling pathway relationship: positively_regulates GO:0097190 ! apoptotic signaling pathway property_value: RO:0002161 NCBITaxon:4896 -created_by: pr creation_date: 2011-11-24T01:20:58Z +[Term] +id: GO:2001236 +name: regulation of extrinsic apoptotic signaling pathway +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of extrinsic apoptotic signaling pathway." [GOC:mtg_apoptosis] +synonym: "regulation of extrinsic apoptosis" NARROW [] +synonym: "regulation of extrinsic apoptotic signalling pathway" EXACT [GOC:mah] +is_a: GO:2001233 ! regulation of apoptotic signaling pathway +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0097191 ! extrinsic apoptotic signaling pathway +relationship: regulates GO:0097191 ! extrinsic apoptotic signaling pathway +creation_date: 2011-11-24T01:30:05Z + +[Term] +id: GO:2001237 +name: negative regulation of extrinsic apoptotic signaling pathway +namespace: biological_process +def: "Any process that stops, prevents or reduces the frequency, rate or extent of extrinsic apoptotic signaling pathway." [GOC:mtg_apoptosis] +synonym: "negative regulation of extrinsic apoptosis" NARROW [] +synonym: "negative regulation of extrinsic apoptotic signalling pathway" EXACT [GOC:mah] +is_a: GO:2001234 ! negative regulation of apoptotic signaling pathway +is_a: GO:2001236 ! regulation of extrinsic apoptotic signaling pathway +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0097191 ! extrinsic apoptotic signaling pathway +relationship: negatively_regulates GO:0097191 ! extrinsic apoptotic signaling pathway +creation_date: 2011-11-24T01:30:11Z + +[Term] +id: GO:2001238 +name: positive regulation of extrinsic apoptotic signaling pathway +namespace: biological_process +def: "Any process that activates or increases the frequency, rate or extent of extrinsic apoptotic signaling pathway." [GOC:mtg_apoptosis] +synonym: "positive regulation of extrinsic apoptosis" NARROW [] +synonym: "positive regulation of extrinsic apoptotic signalling pathway" EXACT [GOC:mah] +is_a: GO:2001235 ! positive regulation of apoptotic signaling pathway +is_a: GO:2001236 ! regulation of extrinsic apoptotic signaling pathway +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0097191 ! extrinsic apoptotic signaling pathway +relationship: positively_regulates GO:0097191 ! extrinsic apoptotic signaling pathway +creation_date: 2011-11-24T01:30:16Z + [Term] id: GO:2001251 name: negative regulation of chromosome organization @@ -146684,7 +149058,6 @@ is_a: GO:0033044 ! regulation of chromosome organization intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0051276 ! chromosome organization relationship: negatively_regulates GO:0051276 ! chromosome organization -created_by: yaf creation_date: 2011-12-02T02:01:20Z [Term] @@ -146701,7 +149074,6 @@ is_a: GO:0033044 ! regulation of chromosome organization intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0051276 ! chromosome organization relationship: positively_regulates GO:0051276 ! chromosome organization -created_by: yaf creation_date: 2011-12-02T02:01:26Z [Term] @@ -146717,7 +149089,6 @@ is_a: GO:1904062 ! regulation of monoatomic cation transmembrane transport intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0005261 ! monoatomic cation channel activity relationship: regulates GO:0005261 ! monoatomic cation channel activity -created_by: vk creation_date: 2011-12-07T07:14:43Z [Term] @@ -146734,7 +149105,6 @@ is_a: GO:2001257 ! regulation of cation channel activity intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0005261 ! monoatomic cation channel activity relationship: negatively_regulates GO:0005261 ! monoatomic cation channel activity -created_by: vk creation_date: 2011-12-07T07:14:51Z [Term] @@ -146751,7 +149121,6 @@ is_a: GO:2001257 ! regulation of cation channel activity intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0005261 ! monoatomic cation channel activity relationship: positively_regulates GO:0005261 ! monoatomic cation channel activity -created_by: vk creation_date: 2011-12-07T07:14:57Z [Term] @@ -146762,7 +149131,6 @@ is_a: IAO:0000030 ! information content entity [Term] id: IAO:0000030 name: information content entity -is_a: BFO:0000031 [Term] id: IAO:0000078 @@ -146821,7 +149189,6 @@ is_a: NCBITaxon:39107 ! Murinae id: NCBITaxon:10090 name: Mus musculus namespace: ncbi_taxonomy -alt_id: NCBITaxon:85055 synonym: "house mouse" EXACT genbank_common_name [] synonym: "mouse" EXACT OMO:0003003 [] xref: GC_ID:1 @@ -146838,7 +149205,6 @@ is_a: NCBITaxon:7776 ! Gnathostomata id: NCBITaxon:117571 name: Euteleostomi namespace: ncbi_taxonomy -alt_id: NCBITaxon:40673 synonym: "bony vertebrates" EXACT genbank_common_name [] xref: GC_ID:1 is_a: NCBITaxon:117570 ! Teleostomi @@ -146847,7 +149213,6 @@ is_a: NCBITaxon:117570 ! Teleostomi id: NCBITaxon:119089 name: Chromadorea namespace: ncbi_taxonomy -alt_id: NCBITaxon:27837 synonym: "Adenophorea" RELATED synonym [] xref: GC_ID:1 is_a: NCBITaxon:6231 ! Nematoda @@ -146958,6 +149323,7 @@ name: Saccharomycotina namespace: ncbi_taxonomy synonym: "true yeasts" EXACT genbank_common_name [] xref: GC_ID:1 +xref: PMID:38895705 is_a: NCBITaxon:716545 ! saccharomyceta [Term] @@ -147515,7 +149881,6 @@ disjoint_from: NCBITaxon:554915 ! Amoebozoa id: NCBITaxon:39107 name: Murinae namespace: ncbi_taxonomy -alt_id: NCBITaxon:109679 xref: GC_ID:1 is_a: NCBITaxon:10066 ! Muridae @@ -147615,6 +149980,7 @@ name: Saccharomycetes namespace: ncbi_taxonomy synonym: "Hemiascomycetes" RELATED synonym [] xref: GC_ID:1 +xref: PMID:38895705 is_a: NCBITaxon:147537 ! Saccharomycotina [Term] @@ -147624,14 +149990,13 @@ namespace: ncbi_taxonomy synonym: "budding yeasts" RELATED blast_name [] synonym: "Endomycetales" RELATED synonym [] xref: GC_ID:1 +xref: PMID:38895705 is_a: NCBITaxon:4891 ! Saccharomycetes [Term] id: NCBITaxon:4893 name: Saccharomycetaceae namespace: ncbi_taxonomy -alt_id: NCBITaxon:221665 -alt_id: NCBITaxon:44280 xref: GC_ID:1 is_a: NCBITaxon:4892 ! Saccharomycetales @@ -147655,7 +150020,6 @@ is_a: NCBITaxon:4894 ! Schizosaccharomycetaceae id: NCBITaxon:4896 name: Schizosaccharomyces pombe namespace: ncbi_taxonomy -alt_id: NCBITaxon:45042 synonym: "fission yeast" EXACT genbank_common_name [] synonym: "Schizosaccharomyces malidevorans" RELATED synonym [] xref: GC_ID:1 @@ -147665,7 +150029,6 @@ is_a: NCBITaxon:4895 ! Schizosaccharomyces id: NCBITaxon:4930 name: Saccharomyces namespace: ncbi_taxonomy -alt_id: NCBITaxon:36915 synonym: "Pachytichospora" RELATED synonym [] xref: GC_ID:1 is_a: NCBITaxon:4893 ! Saccharomycetaceae @@ -147674,14 +150037,13 @@ is_a: NCBITaxon:4893 ! Saccharomycetaceae id: NCBITaxon:4932 name: Saccharomyces cerevisiae namespace: ncbi_taxonomy -alt_id: NCBITaxon:2898199 -alt_id: NCBITaxon:41870 synonym: "baker's yeast" EXACT OMO:0003003 [] synonym: "brewer's yeast" EXACT genbank_common_name [] synonym: "Candida robusta" RELATED synonym [] synonym: "Mycoderma cerevisiae" RELATED synonym [] synonym: "Saccharomyces capensis" RELATED synonym [] synonym: "Saccharomyces cerevisiae 'var. diastaticus'" EXACT equivalent_name [] +synonym: "Saccharomyces cerevisiae (Desm.) Meyen ex E.C. Hansen, 1883" RELATED synonym [] synonym: "Saccharomyces diastaticus" RELATED synonym [] synonym: "Saccharomyces italicus" RELATED synonym [] synonym: "Saccharomyces oviformis" RELATED synonym [] @@ -147795,8 +150157,6 @@ disjoint_from: NCBITaxon:88770 ! Panarthropoda id: NCBITaxon:6236 name: Rhabditida namespace: ncbi_taxonomy -alt_id: NCBITaxon:33251 -alt_id: NCBITaxon:6308 synonym: "Strongylida" RELATED synonym [] xref: GC_ID:1 is_a: NCBITaxon:119089 ! Chromadorea @@ -147812,7 +150172,6 @@ is_a: NCBITaxon:55885 ! Peloderinae id: NCBITaxon:6243 name: Rhabditidae namespace: ncbi_taxonomy -alt_id: NCBITaxon:54603 xref: GC_ID:1 is_a: NCBITaxon:55879 ! Rhabditoidea @@ -148006,7 +150365,6 @@ is_a: NCBITaxon:9498 ! Cebidae id: NCBITaxon:9481 name: Callithrix namespace: ncbi_taxonomy -alt_id: NCBITaxon:9492 synonym: "Callithrix" EXACT scientific_name [] xref: GC_ID:1 is_a: NCBITaxon:9480 ! Callitrichinae @@ -148015,7 +150373,6 @@ is_a: NCBITaxon:9480 ! Callitrichinae id: NCBITaxon:9483 name: Callithrix jacchus namespace: ncbi_taxonomy -alt_id: NCBITaxon:9484 synonym: "Callithrix jacchus jacchus" RELATED synonym [] synonym: "common marmoset" EXACT OMO:0003003 [] synonym: "Simia jacchus" RELATED synonym [] @@ -148082,7 +150439,6 @@ is_a: NCBITaxon:338152 ! Felinae id: NCBITaxon:9685 name: Felis catus namespace: ncbi_taxonomy -alt_id: NCBITaxon:36475 synonym: "cat" EXACT OMO:0003003 [] synonym: "cats" EXACT OMO:0003003 [] synonym: "domestic cat" EXACT genbank_common_name [] @@ -148115,13 +150471,6 @@ is_a: NCBITaxon:9787 ! Perissodactyla id: NCBITaxon:9789 name: Equus namespace: ncbi_taxonomy -alt_id: NCBITaxon:1225530 -alt_id: NCBITaxon:35506 -alt_id: NCBITaxon:35507 -alt_id: NCBITaxon:35508 -alt_id: NCBITaxon:35509 -alt_id: NCBITaxon:35510 -alt_id: NCBITaxon:475184 synonym: "Amerhippus" RELATED synonym [] synonym: "Asinus" RELATED synonym [] synonym: "Dolichohippus" RELATED synonym [] @@ -148151,7 +150500,6 @@ is_a: NCBITaxon:314147 ! Glires id: PATO:0000001 name: quality namespace: quality -alt_id: PATO:0000072 def: "A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities" [PATOC:GVG] is_a: BFO:0000020 @@ -148159,7 +150507,6 @@ is_a: BFO:0000020 id: PATO:0000025 name: composition namespace: quality -alt_id: PATO:0002015 def: "A single physical entity inhering in an bearer by virtue of the bearer's quantities or relative ratios of subparts." [PATOC:GVG] comment: For example calcium composition (which may inhere in bone), haemoglobin composition (which may inhere in blood). subset: attribute_slim @@ -148190,7 +150537,6 @@ is_a: PATO:0001241 ! physical object quality id: PATO:0000052 name: shape namespace: quality -alt_id: PATO:0001647 def: "A morphological quality inhering in a bearer by virtue of the bearer's ratios of distances between its features (points, edges, surfaces and also holes etc)." [PATOC:GVG] comment: Shapes are invariant on size transformations. Shapes can be subdivided into 2D and 3D shapes, We can also make a distinction between shapes of complete self-connected objects, and shapes of parts of objects. subset: attribute_slim @@ -148234,7 +150580,6 @@ is_a: PATO:0000051 ! morphology id: PATO:0000141 name: structure namespace: quality -alt_id: PATO:0001452 def: "A morphology quality inhering in a bearer by virtue of the bearer's relative position, shape, arrangements and connectivity of an organism's various parts; the pattern underlying its form." [PATOC:GVG] subset: attribute_slim synonym: "conformation" BROAD [VT:1000738] @@ -148282,7 +150627,6 @@ is_a: PATO:0002009 ! branchiness id: PATO:0000404 name: coiled namespace: quality -alt_id: PATO:0001363 def: "A shape quality inhering in a bearer by virtue of the bearer's being curled or wound (especially in concentric rings or spirals)." [WordNet:WordNet] subset: cell_quality subset: mpath_slim @@ -148356,7 +150700,6 @@ is_a: PATO:0000068 ! qualitative id: PATO:0000586 name: increased size namespace: quality -alt_id: PATO:0001202 def: "A size quality which is relatively high." [PATOC:GVG] subset: value_slim synonym: "big" RELATED [] @@ -148481,7 +150824,6 @@ is_a: PATO:0000992 ! viscosity id: PATO:0001018 name: physical quality namespace: quality -alt_id: PATO:0002079 def: "A quality of a physical entity that exists through action of continuants at the physical level of organisation in relation to other entities." [PATOC:GVG] subset: attribute_slim synonym: "relational physical quality" EXACT [] @@ -148529,8 +150871,6 @@ is_a: PATO:0000261 ! maturity id: PATO:0001241 name: physical object quality namespace: quality -alt_id: PATO:0001237 -alt_id: PATO:0001238 def: "A quality which inheres in a continuant." [PATOC:GVG] comment: Relational qualities are qualities that hold between multiple entities. Normal (monadic) qualities such as the shape of a eyeball exist purely as a quality of that eyeball. A relational quality such as sensitivity to light is a quality of that eyeball (and connecting nervous system) as it relates to incoming light waves/particles. synonym: "monadic quality of a continuant" EXACT [] @@ -149029,7 +151369,6 @@ is_a: PATO:0002008 ! concave 3-D shape id: PATO:0001873 name: cylindrical namespace: quality -alt_id: PATO:0001203 def: "A convex 3-D shape quality inhering in a bearer by virtue of the bearer's exhibiting a consistently-sized round cross section." [PATOC:MAH] subset: cell_quality subset: value_slim @@ -149618,7 +151957,6 @@ def: "A quality inhering in a cell by virtue of the cell having a high nuclear/c comment: A high nuclear/cytolasmic ratio is 70% or higher. synonym: "high N:C ratio" EXACT [] is_a: PATO:0001396 ! cellular quality -created_by: http://orcid.org/0000-0001-5208-3432 [Term] id: PATO:0045001 @@ -150008,7 +152346,6 @@ name: anatomical structure quality namespace: quality def: "A quality of continuant that exist at the anatomical level of organisation and anything under it. This includes, but is not limited to, cells , tissues, and components." [] is_a: PATO:0001241 ! physical object quality -created_by: http://orcid.org/0000-0001-7258-9596 [Term] id: PATO:0070045 @@ -150016,7 +152353,6 @@ name: anatomical histological quality namespace: quality def: "A quality inhering in an anotomical structure by virtue of its capacity to be stained by specific histological dyes." [] is_a: PATO:0070044 ! anatomical structure quality -created_by: http://orcid.org/0000-0001-7258-9596 [Term] id: PATO:0070046 @@ -150024,7 +152360,6 @@ name: neutrophillic namespace: quality def: "An affinity inhering in an anatomical structure by virtue of the bearer exhibiting a molecular interaction that stains and colors, pale-pink, with Wright-Giemsa stain." [GOC:add] is_a: PATO:0070045 ! anatomical histological quality -created_by: http://orcid.org/0000-0001-7258-9596 [Term] id: PATO:0070047 @@ -150032,7 +152367,6 @@ name: polychromatophilic namespace: quality def: "An affinity inhering in an anatomical structure by virtue of the bearer exhibiting a molecular interaction for both basic and acid stains under specific pH conditions." [GOC:add] is_a: PATO:0070045 ! anatomical histological quality -created_by: http://orcid.org/0000-0001-7258-9596 [Term] id: PATO:0070060 @@ -150070,12 +152404,12 @@ id: PR:000000001 name: protein namespace: protein def: "An amino acid chain that is produced de novo by ribosome-mediated translation of a genetically-encoded mRNA, and any derivatives thereof." [PRO:DAN, PRO:WCB] -comment: The definition above excludes protein complexes, which some also consider a protein. Those who wish to refer to a class representing both senses of the word are directed to CHEBI:36080. Note that the definition allows for experimentally-manipulated genes, and allows for artifically-produced derivatives that mimic those found naturally. Proteins (in the sense defined here) that descended from a common ancestor can be classified into families and superfamilies composed of products of evolutionarily-related genes. The domain architecture of a protein is described by the order of its constituent domains. Proteins with the same domains in the same order are defined as homeomorphic [PRO:WCB]. +comment: The definition above excludes protein complexes, which some also consider a protein. Those who wish to refer to a class representing both senses of the word are directed to CHEBI:36080. Note that the definition allows for experimentally-manipulated genes, and allows for artifically-produced derivatives that mimic those found naturally. Proteins (in the sense defined here) that descended from a common ancestor can be classified into families and superfamilies composed of products of evolutionarily-related genes. The domain architecture of a protein is described by the order of its constituent domains. Proteins with the same domains in the same order are defined as homeomorphic [PRO:WCB). synonym: "native protein" NARROW [IEDB:BP] synonym: "natural protein" EXACT [PRO:DAN] is_a: BFO:0000002 is_a: PR:000018263 ! amino acid chain -is_a: PR:000050567 ! protein-containing material entity +is_a: PR:000064867 ! protein-containing molecular entity relationship: output_of GO:0006412 ! translation [Term] @@ -150090,7 +152424,6 @@ synonym: "differentiation antigen CD19" EXACT [] synonym: "T-cell surface antigen Leu-12" EXACT [] xref: IUPHARobj:2764 xref: PIRSF:PIRSF016630 -is_a: CHEBI:36080 is_a: PR:000000001 ! protein [Term] @@ -150102,7 +152435,6 @@ comment: Category=gene. Requested by=CL. synonym: "CD34" EXACT PRO-short-label [PRO:DNx] synonym: "hematopoietic progenitor cell antigen CD34" EXACT [] xref: PIRSF:PIRSF028749 -is_a: CHEBI:36080 is_a: PR:000000001 ! protein [Term] @@ -150116,7 +152448,6 @@ synonym: "T-cell differentiation antigen L3T4" EXACT [] synonym: "T-cell surface antigen T4/Leu-3" EXACT [] synonym: "T-cell surface glycoprotein CD4" EXACT [] xref: PIRSF:PIRSF001977 -is_a: CHEBI:36080 is_a: PR:000000001 ! protein [Term] @@ -150144,7 +152475,6 @@ synonym: "PTPRC" EXACT PRO-short-label [PRO:DNx] synonym: "T200" BROAD [PRO:DNx] xref: IUPHARobj:1852 xref: PIRSF:PIRSF002004 -is_a: CHEBI:36080 is_a: PR:000000001 ! protein [Term] @@ -150255,7 +152585,6 @@ def: "A protein that has a core domain composition consisting of an extracellula comment: Category=family. synonym: "CD3 subunit with Ig-like domain" EXACT [] xref: PIRSF:PIRSF001993 -is_a: CHEBI:36080 is_a: PR:000000001 ! protein [Term] @@ -150278,7 +152607,6 @@ namespace: protein def: "A protein with a domain composition consisting of a large extracellular domain, including five Ig-like C2-type domains followed by two copies of the Fibronectin type-III domain (Pfam:PF00041), a single-pass transmembrane domain and a short cytoplasmic C-terminal domain." [PRO:CNA] comment: Category=family. xref: PIRSF:PIRSF002507 -is_a: CHEBI:36080 is_a: PR:000000001 ! protein [Term] @@ -150311,7 +152639,6 @@ namespace: protein def: "A protein that is a type I transmembrane receptor with an N-terminal cysteine-rich domain, a single Fibronectin type II (FNII) domain (Pfam:PF00040) and eight to ten copies of the Lectin C-type domain (Pfam:PF00059) (CTLDs). The presence of multiple copies of the CTLD domain is a hallmark of this class." [PMID:12223280] comment: Category=family. xref: PIRSF:PIRSF002427 -is_a: CHEBI:36080 is_a: PR:000000001 ! protein [Term] @@ -150348,7 +152675,6 @@ synonym: "T-cell surface antigen T11/Leu-5" EXACT [] synonym: "T-cell surface glycoprotein CD2" EXACT [] xref: IUPHARobj:2600 xref: PIRSF:PIRSF001984 -is_a: CHEBI:36080 is_a: PR:000000001 ! protein [Term] @@ -150364,7 +152690,6 @@ synonym: "Lyt2" RELATED Gene-based [] synonym: "MAL" RELATED Gene-based [] synonym: "T-cell surface glycoprotein Lyt-2" EXACT [] synonym: "T-lymphocyte differentiation antigen T8/Leu-2" EXACT [] -is_a: CHEBI:36080 is_a: PR:000000001 ! protein [Term] @@ -150382,7 +152707,6 @@ synonym: "Lyt3" RELATED Gene-based [] synonym: "T-cell membrane glycoprotein Ly-3" EXACT [] synonym: "T-cell surface glycoprotein Lyt-3" EXACT [] xref: PIRSF:PIRSF002020 -is_a: CHEBI:36080 is_a: PR:000000001 ! protein [Term] @@ -150830,7 +153154,6 @@ namespace: protein def: "A protein that contains the ADP-ribosyl cyclase domain (Pfam:PF02267)." [PRO:WCB] comment: Category=family. xref: PIRSF:PIRSF005736 -is_a: CHEBI:36080 is_a: PR:000000001 ! protein [Term] @@ -150848,7 +153171,6 @@ synonym: "siglec-2" EXACT [] synonym: "SIGLEC2" RELATED Gene-based [] synonym: "T-cell surface antigen Leu-14" EXACT [] xref: IUPHARobj:2786 -is_a: CHEBI:36080 is_a: PR:000000001 ! protein [Term] @@ -150870,7 +153192,6 @@ synonym: "MS4A1" EXACT PRO-short-label [PRO:DNx] synonym: "Ms4a2" RELATED Gene-based [] xref: IUPHARobj:2628 xref: PIRSF:PIRSF001995 -is_a: CHEBI:36080 is_a: PR:000000001 ! protein [Term] @@ -150879,7 +153200,6 @@ name: B7-related protein namespace: protein def: "A protein that is a member of a family that includes translation products of genes CD86, CD276, ICOSLG, and others. These are membrane-anchored proteins with a small intracellular domain and an extracellular domain with signal sequence, an Immunoglobulin V-set domain (Pfam:PF07686), and a CD80-like C2-set immunoglobulin domain (Pfam:PF08205)." [PRO:WCB] comment: Category=family. -is_a: CHEBI:36080 is_a: PR:000000001 ! protein [Term] @@ -150900,7 +153220,6 @@ synonym: "dendritic lectin" EXACT [] synonym: "DLEC" RELATED Gene-based [] synonym: "HECL" RELATED Gene-based [] synonym: "UNQ9361/PRO34150" RELATED Gene-based [] -is_a: CHEBI:36080 is_a: PR:000000001 ! protein [Term] @@ -150912,7 +153231,6 @@ comment: Category=gene. Requested by=CL. synonym: "CD207" EXACT PRO-short-label [PRO:DNx] synonym: "CLEC4K" RELATED Gene-based [] synonym: "langerin" EXACT [] -is_a: CHEBI:36080 is_a: PR:000000001 ! protein [Term] @@ -150929,7 +153247,6 @@ synonym: "DC-SIGN" RELATED [] synonym: "DC-SIGN1" EXACT [] synonym: "dendritic cell-specific ICAM-3-grabbing non-integrin 1" EXACT [] xref: IUPHARobj:2930 -is_a: CHEBI:36080 is_a: PR:000000001 ! protein [Term] @@ -150959,7 +153276,6 @@ synonym: "PGP-1" EXACT [] synonym: "PGP-I" RELATED [] synonym: "phagocytic glycoprotein 1" EXACT [] synonym: "phagocytic glycoprotein I" EXACT [] -is_a: CHEBI:36080 is_a: PR:000000001 ! protein [Term] @@ -150985,7 +153301,6 @@ synonym: "SLAM family member 2" EXACT [] synonym: "SLAMF2" EXACT [] synonym: "TCT.1" EXACT [] xref: PIRSF:PIRSF001973 -is_a: CHEBI:36080 is_a: PR:000000001 ! protein [Term] @@ -150998,7 +153313,6 @@ synonym: "B-cell activation protein" EXACT [] synonym: "CD83" EXACT PRO-short-label [PRO:DNx] synonym: "CD83 antigen" EXACT [] synonym: "cell surface protein HB15" EXACT [] -is_a: CHEBI:36080 is_a: PR:000000001 ! protein [Term] @@ -151025,7 +153339,6 @@ synonym: "lymphocyte surface MEL-14 antigen" EXACT [] synonym: "SELL" EXACT PRO-short-label [PRO:DNx] synonym: "TQ1" EXACT [] xref: PIRSF:PIRSF002421 -is_a: CHEBI:36080 is_a: PR:000000001 ! protein [Term] @@ -151040,7 +153353,6 @@ synonym: "hly9-beta" EXACT [] synonym: "leukocyte differentiation antigen CD84" EXACT [] synonym: "signaling lymphocytic activation molecule 5" EXACT [] synonym: "SLAMF5" RELATED Gene-based [] -is_a: CHEBI:36080 is_a: PR:000000001 ! protein [Term] @@ -151050,7 +153362,15 @@ namespace: protein def: "A protein that is a stand alone version of the Glycosyltransferase family 10 (fucosyltransferase) (Pfam:PF00852) domain. Proteins in this class may catalyze alpha-1,3 glycosidic linkages." [PMID:9451017] comment: Category=family. xref: PIRSF:PIRSF005726 -is_a: CHEBI:36080 +is_a: PR:000000001 ! protein + +[Term] +id: PR:000001325 +name: beta-1,3-glucuronyltransferase +namespace: protein +def: "A protein with a core domain structure consisting of a very small cytoplasmic domain followed by a transmembrane domain and a Glycosyltransferase family 43 (Pfam:PF03360) domain." [PRO:WCB] +comment: Category=family. +xref: PIRSF:PIRSF016413 is_a: PR:000000001 ! protein [Term] @@ -151065,7 +153385,6 @@ synonym: "CD317" EXACT [] synonym: "HM1.24 antigen" EXACT [] synonym: "tetherin" EXACT [] xref: PIRSF:PIRSF023920 -is_a: CHEBI:36080 is_a: PR:000000001 ! protein [Term] @@ -151075,7 +153394,6 @@ namespace: protein def: "A protein that has a core domain structure of signal sequence, propeptide, five Cadherin domains (Pfam:PF00028), a transmembrane region, and a Cadherin cytoplasmic region (Pfam:PF01049). Cadherins function as adhesion molecules that mediate Ca2+-dependent cell-cell adhesion in solid tissues." [PRO:WCB] comment: Category=family. xref: PIRSF:PIRSF002504 -is_a: CHEBI:36080 is_a: PR:000000001 ! protein [Term] @@ -151090,7 +153408,6 @@ synonym: "CD67 antigen" EXACT [] synonym: "CEACAM8" EXACT PRO-short-label [PRO:DNx] synonym: "CGM6" RELATED Gene-based [] synonym: "non-specific cross-reacting antigen NCA-95" EXACT [] -is_a: CHEBI:36080 is_a: PR:000000001 ! protein [Term] @@ -151103,7 +153420,6 @@ synonym: "C3b/C4b receptor" EXACT [] synonym: "C3BR" RELATED Gene-based [] synonym: "CD35" EXACT [] synonym: "CR1" EXACT PRO-short-label [PRO:DNx] -is_a: CHEBI:36080 is_a: PR:000000001 ! protein [Term] @@ -151121,7 +153437,6 @@ synonym: "EBV receptor" EXACT [] synonym: "epstein-Barr virus receptor" EXACT [] xref: PIRSF:PIRSF002484 is_a: CHEBI:36080 -is_a: PR:000000001 ! protein [Term] id: PR:000001343 @@ -151141,7 +153456,6 @@ synonym: "early T-cell activation antigen p60" EXACT [] synonym: "GP32/28" EXACT [] synonym: "leukocyte surface antigen Leu-23" EXACT [] synonym: "MLR-3" EXACT [] -is_a: CHEBI:36080 is_a: PR:000000001 ! protein [Term] @@ -151158,7 +153472,6 @@ synonym: "PD-Ibeta" EXACT [] synonym: "PDNP3" RELATED Gene-based [] synonym: "phosphodiesterase I beta" EXACT [] synonym: "phosphodiesterase I/nucleotide pyrophosphatase 3" EXACT [] -is_a: CHEBI:36080 is_a: PR:000000001 ! protein [Term] @@ -151174,7 +153487,6 @@ synonym: "END" RELATED Gene-based [] synonym: "ENG" EXACT PRO-short-label [PRO:DNx] xref: IUPHARobj:2895 xref: PIRSF:PIRSF038746 -is_a: CHEBI:36080 is_a: PR:000000001 ! protein [Term] @@ -151187,7 +153499,6 @@ synonym: "FOXP3" EXACT PRO-short-label [PRO:DNx] synonym: "IPEX" RELATED Gene-based [] synonym: "JM2" RELATED Gene-based [] synonym: "scurfin" EXACT [] -is_a: CHEBI:36080 is_a: PR:000000001 ! protein [Term] @@ -151197,7 +153508,6 @@ namespace: protein def: "A protein that contains an extracellular Glycophorin A domain (Pfam:PF01102), followed by a single-pass transmembrane region and a small intracellular domain. A protein that is an integral protein of the red cell membrane. Proteins in this class are responsible for the molecular basis of the blood group antigens, surface markers on the outside of the red blood cell membrane." [InterPro:IPR001195, PRO:CNA] comment: Category=family. xref: PIRSF:PIRSF002466 -is_a: CHEBI:36080 is_a: PR:000000001 ! protein [Term] @@ -151207,7 +153517,6 @@ namespace: protein def: "A protein with a core domain architecture consisting of an extracellular domain containing two copies of the Immunoglobulin domain (Pfam:PF00047), followed by a single-pass transmembrane region and a small intracellular domain. The active protein is a low affinity receptor for immunoglobulin gamma chain Fc region. Human II-a, II-b, and II-c represent a recent gene expansion and are equally related to mouse II, III, and IV. Human III-A and III-B are closely related and closer to mouse IV than to mouse III." [PRO:WCB] comment: Category=family. xref: PIRSF:PIRSF001980 -is_a: CHEBI:36080 is_a: PR:000000001 ! protein [Term] @@ -151218,7 +153527,6 @@ def: "A protein with a core domain architecture consisting of an extracellular d comment: Category=family. Note: The active protein is a low affinity receptor for immunoglobulin gamma chain Fc region. It comprises the translation products of the FCGR1 gene (mouse) or one of the closely related FCGR1A, FCGR1B, or FCGR1C genes (human). FCGR1C may be a pseudogene in human. synonym: "Fc-gamma receptor" RELATED [] xref: PIRSF:PIRSF001981 -is_a: CHEBI:36080 is_a: PR:000000001 ! protein [Term] @@ -151238,7 +153546,6 @@ synonym: "p55" BROAD [PRO:DNx] synonym: "TAC antigen" EXACT [] xref: IUPHARobj:1695 xref: PIRSF:PIRSF001954 -is_a: CHEBI:36080 is_a: PR:000000001 ! protein [Term] @@ -151257,7 +153564,6 @@ synonym: "IL2RB" EXACT PRO-short-label [PRO:DNx] synonym: "p70-75" EXACT [] synonym: "p75" BROAD [PRO:DNx] xref: IUPHARobj:1696 -is_a: CHEBI:36080 is_a: PR:000000001 ! protein [Term] @@ -151286,7 +153592,6 @@ synonym: "KLRD1" EXACT PRO-short-label [PRO:DNx] synonym: "KP43" EXACT [] synonym: "natural killer cells antigen CD94" EXACT [] synonym: "NK cell receptor" EXACT [] -is_a: CHEBI:36080 is_a: PR:000000001 ! protein [Term] @@ -151296,7 +153601,6 @@ namespace: protein def: "A protein with four transmembrane domains, small intracellular amino- and carboxyl-terminal regions, and two extracellular loops, a small one (EC1) and a larger one (EC2) of about 100 residues. The EC2 loop contains at least 4 cysteine residues, including a highly conserved 'CCG' motif." [PRO:WCB, Wikipedia:Tetraspanin] comment: Category=family. xref: PIRSF:PIRSF002419 -is_a: CHEBI:36080 is_a: PR:000000001 ! protein [Term] @@ -151368,6 +153672,21 @@ synonym: "T-lymphocyte activation antigen CD80" EXACT [] xref: IUPHARobj:2744 is_a: PR:000001290 ! B7-related protein +[Term] +id: PR:000001440 +name: galactosylgalactosylxylosylprotein 3-beta-glucuronosyltransferase 1 +namespace: protein +def: "A beta-1,3-glucuronyltransferase that is a translation product of the human B3GAT1 gene or a 1:1 ortholog thereof." [PRO:WCB] +comment: Category=gene. +synonym: "B3GAT1" EXACT PRO-short-label [PRO:DNx] +synonym: "beta-1,3-glucuronyltransferase 1" EXACT [] +synonym: "GlcAT-P" EXACT [] +synonym: "GLCATP" RELATED Gene-based [] +synonym: "GlcUAT-P" EXACT [] +synonym: "glucuronosyltransferase P" EXACT [] +synonym: "UDP-GlcUA:glycoprotein beta-1,3-glucuronyltransferase" EXACT [] +is_a: PR:000001325 ! beta-1,3-glucuronyltransferase + [Term] id: PR:000001444 name: cadherin-5 @@ -151593,7 +153912,6 @@ def: "A protein that has a core domain composition consisting of a Rel homology comment: Category=family. synonym: "transcription factor NF-kappa-B" RELATED [] xref: PIRSF:PIRSF036310 -is_a: CHEBI:36080 is_a: PR:000000001 ! protein [Term] @@ -151602,9 +153920,7 @@ name: prominin namespace: protein def: "A protein with core architecture consisting of one Prominin (Pfam:PF05478) domain. The prominins are an emerging family of proteins that, among the multispan membrane proteins, display a novel topology. Mouse and human prominin and prominin-like 1 are predicted to contain five membrane spanning domains, with an N-terminal domain exposed to the extracellular space followed by four, alternating small cytoplasmic and large extracellular, loops and a cytoplasmic C-terminal domain." [InterPro:IPR008795, PMID:11467842] comment: Category=family. -xref: PANTHER:PTHR22730 xref: PIRSF:PIRSF017831 -is_a: CHEBI:36080 is_a: PR:000000001 ! protein [Term] @@ -151638,7 +153954,6 @@ synonym: "dectin-2" EXACT [] synonym: "DECTIN2" RELATED Gene-based [] synonym: "dendritic cell-associated C-type lectin 2" EXACT [] xref: IUPHARobj:2928 -is_a: CHEBI:36080 is_a: PR:000000001 ! protein [Term] @@ -151659,7 +153974,6 @@ synonym: "DECTIN1" RELATED Gene-based [] synonym: "dendritic cell-associated C-type lectin 1" EXACT [] synonym: "UNQ539/PRO1082" RELATED Gene-based [] xref: IUPHARobj:2927 -is_a: CHEBI:36080 is_a: PR:000000001 ! protein [Term] @@ -151671,7 +153985,6 @@ comment: Category=family. synonym: "fam:C/C-C chemokine" EXACT PRO-short-label [PRO:DAN] xref: PIRSF:PIRSF001950 is_a: CHEBI:36080 -is_a: PR:000000001 ! protein [Term] id: PR:000001809 @@ -151681,7 +153994,6 @@ def: "A protein that is a translation product of the human CD59 gene, a 1:1 orth comment: Category=gene. Requested by=CL. Pro-orthology refers to, in this case, after-speciation gene duplication in the non-human species (aka 1:many orthology). This gene is present as a single copy in human and has undergone a lineage-specific duplication in mouse. CD59 antigen has a core architecture consisting of one UPAR/Ly-6 domain (Pfam:PF00021), a small domain of about 70 amino acids and containing 5 conserved disulfide bonds. It is both N- and O-glycosylated and is a GPI-anchored protein that releases soluble forms in some tissues. synonym: "CD59-like" EXACT PRO-short-label [PRO:DNx] xref: PIRSF:PIRSF038782 -is_a: CHEBI:36080 is_a: PR:000000001 ! protein [Term] @@ -151691,7 +154003,6 @@ namespace: protein def: "A protein with core architecture consisting of asignal sequence, 5 Ig-like domains, followed by a transmembrane sequence, followed by a Protein tyrosine kinase domain (Pfam:PF07714). However, only 1-3 of the Ig domains are detected by the Pfam HMMs in most of the sequences. Pfam:PF00047 is most common, but other members of the Ig domain clan, Pfam:PF07679 and Pfam:PF07686 can be identified instead. The fourth Ig domain lacks the disulfide-bonded cysteines." [PRO:WCB] comment: Category=family. xref: PIRSF:PIRSF000615 -is_a: CHEBI:36080 is_a: PR:000000001 ! protein [Term] @@ -151719,7 +154030,6 @@ namespace: protein def: "A protein with core architecture consisting of a signal sequence, a Class II histocompatibility antigen, alpha domain (Pfam:PF00993) and an Immunoglobulin C1-set domain (Pfam:PF07654); these form the extracellular domain and are followed by a single-pass transmembrane region and a small cytoplasmic region." [PRO:WCB, Wikipedia:Human_leukocyte_antigen] comment: Category=family. Note: There are three major and two minor class II MHC (major histocompatability complex) alpha chain genes in human. Designations for the MHC complex loci are species specific: HLA (human leukocyte antigen) in human, H-2 in mouse. MHC class II loci are characterized by large numbers of allelic variants. In contrast to MHC Class I alpha chain genes, orthologies can be seen between some human and mouse genes. MHC class II alpha chains form heterodimers with MHLC class II beta chains. synonym: "MHCcIIalpha" EXACT PRO-short-label [PRO:DAN] -is_a: CHEBI:36080 is_a: PR:000000001 ! protein [Term] @@ -151729,7 +154039,6 @@ namespace: protein def: "A protein with core architecture consisting of a signal sequence, one Immunoglobulin V-set domain (Pfam:PF07686), two Immunoglobulin C1-set domains (Pfam:PF07654), a single-pass transmembrane region and a very small cytoplasmic region." [PRO:WCB] comment: Category=family. xref: PIRSF:PIRSF038063 -is_a: CHEBI:36080 is_a: PR:000000001 ! protein [Term] @@ -151743,7 +154052,6 @@ synonym: "CDw150" EXACT [] synonym: "IPO-3" EXACT [] synonym: "SLAM" RELATED Gene-based [] synonym: "SLAMF1" EXACT PRO-short-label [PRO:DNx] -is_a: CHEBI:36080 is_a: PR:000000001 ! protein [Term] @@ -151758,7 +154066,6 @@ synonym: "TBET" RELATED Gene-based [] synonym: "TBLYM" RELATED Gene-based [] synonym: "TBX21" EXACT PRO-short-label [PRO:DNx] synonym: "transcription factor TBLYM" EXACT [] -is_a: CHEBI:36080 is_a: PR:000000001 ! protein [Term] @@ -151774,7 +154081,6 @@ synonym: "T-cell leukemia antigen" EXACT [] synonym: "T-cell surface antigen Leu-9" EXACT [] synonym: "TP41" EXACT [] xref: PIRSF:PIRSF038791 -is_a: CHEBI:36080 is_a: PR:000000001 ! protein [Term] @@ -151785,7 +154091,6 @@ def: "A protein with core architecture consisting of a signal sequence, an extra comment: Category=family. synonym: "CD1" EXACT PRO-short-label [PRO:DAN] xref: PIRSF:PIRSF038798 -is_a: CHEBI:36080 is_a: PR:000000001 ! protein [Term] @@ -151800,7 +154105,6 @@ synonym: "ly-1" EXACT [] synonym: "lymphocyte antigen 1" EXACT [] synonym: "lymphocyte antigen T1/Leu-1" EXACT [] synonym: "Lyt-1" EXACT [] -is_a: CHEBI:36080 is_a: PR:000000001 ! protein [Term] @@ -151812,7 +154116,6 @@ comment: Category=gene. Requested by=CL. synonym: "CD28" EXACT PRO-short-label [PRO:DNx] synonym: "TP44" EXACT [] xref: IUPHARobj:2863 -is_a: CHEBI:36080 is_a: PR:000000001 ! protein [Term] @@ -151827,7 +154130,6 @@ synonym: "Thy-1" RELATED Gene-based [] synonym: "Thy-1 antigen" EXACT [] synonym: "THY1" EXACT PRO-short-label [PRO:DNx] xref: PIRSF:PIRSF038777 -is_a: CHEBI:36080 is_a: PR:000000001 ! protein [Term] @@ -151840,7 +154142,6 @@ synonym: "ARG1" EXACT PRO-short-label [PRO:DNx] synonym: "liver-type arginase" EXACT [] synonym: "type I arginase" EXACT [] xref: IUPHARobj:1244 -is_a: CHEBI:36080 is_a: PR:000000001 ! protein [Term] @@ -151869,7 +154170,6 @@ synonym: "CTLA-4" EXACT [] synonym: "CTLA4" EXACT PRO-short-label [PRO:DNx] synonym: "cytotoxic T-lymphocyte-associated antigen 4" EXACT [] xref: IUPHARobj:2743 -is_a: CHEBI:36080 is_a: PR:000000001 ! protein [Term] @@ -151886,7 +154186,6 @@ synonym: "VPREB" RELATED Gene-based [] synonym: "VpreB protein" EXACT [] synonym: "VPREB1" EXACT PRO-short-label [PRO:DNx] xref: PIRSF:PIRSF038787 -is_a: CHEBI:36080 is_a: PR:000000001 ! protein [Term] @@ -151903,7 +154202,6 @@ synonym: "IGL1" RELATED Gene-based [] synonym: "IGLL1" EXACT PRO-short-label [PRO:DNx] synonym: "immunoglobulin omega polypeptide" EXACT [] synonym: "immunoglobulin-related protein 14.1" EXACT [] -is_a: CHEBI:36080 is_a: PR:000000001 ! protein [Term] @@ -151921,7 +154219,6 @@ synonym: "CD28-related protein 1" EXACT [] synonym: "CRP-1" RELATED [] synonym: "ICOS" EXACT PRO-short-label [PRO:DNx] xref: IUPHARobj:2939 -is_a: CHEBI:36080 is_a: PR:000000001 ! protein [Term] @@ -151931,7 +154228,6 @@ namespace: protein def: "A protein with core architecture consisting of a large extracellular region containing one Integrin, beta chain domain (Pfam:PF00362), up to four EGF-like domains (Pfam:PF07974), and an Integrin beta tail domain (Pfam:PF07965), followed by a single-pass transmembrane region and a small cytoplasmic region often containing an Integrin beta cytoplasmic domain (Pfam:PF08725)." [PRO:WCB] comment: Category=family. xref: PIRSF:PIRSF002512 -is_a: CHEBI:36080 is_a: PR:000000001 ! protein [Term] @@ -151950,7 +154246,6 @@ synonym: "IL3RA" EXACT PRO-short-label [PRO:DNx] synonym: "interleukin-3 receptor class II alpha chain" EXACT [] synonym: "Sut-1" RELATED Gene-based [] xref: IUPHARobj:1705 -is_a: CHEBI:36080 is_a: PR:000000001 ! protein [Term] @@ -151969,7 +154264,6 @@ synonym: "IL5R" RELATED Gene-based [] synonym: "IL5RA" EXACT PRO-short-label [PRO:DNx] xref: IUPHARobj:1706 xref: PIRSF:PIRSF018419 -is_a: CHEBI:36080 is_a: PR:000000001 ! protein [Term] @@ -151987,7 +154281,6 @@ synonym: "IL-7RA" EXACT [] synonym: "IL7R" EXACT PRO-short-label [PRO:DNx] xref: IUPHARobj:1698 xref: PIRSF:PIRSF001960 -is_a: CHEBI:36080 is_a: PR:000000001 ! protein [Term] @@ -151997,7 +154290,6 @@ namespace: protein def: "A protein that is a translation product of the KLRB1 gene or its closely related paralogs (KLRB1A-F). There are lineage-specific expansions in mouse and rat." [PRO:WCB] comment: Category=family. Requested by=CL. xref: PIRSF:PIRSF038804 -is_a: CHEBI:36080 is_a: PR:000000001 ! protein [Term] @@ -152016,7 +154308,6 @@ synonym: "lymphocyte antigen 48" EXACT [] synonym: "sialophorin" EXACT [] synonym: "SPN" EXACT PRO-short-label [PRO:DNx] xref: PIRSF:PIRSF001994 -is_a: CHEBI:36080 is_a: PR:000000001 ! protein [Term] @@ -152039,7 +154330,6 @@ synonym: "immunoglobulin E-binding factor" EXACT [] synonym: "lymphocyte IgE receptor" EXACT [] xref: IUPHARobj:2935 xref: PIRSF:PIRSF002426 -is_a: CHEBI:36080 is_a: PR:000000001 ! protein [Term] @@ -152049,7 +154339,6 @@ namespace: protein def: "A protein with core architecture consisting of a Lysosome-associated membrane glycoprotein (Pfam:PF01299) domain. It is a single-pass type I membrane protein that shuttles between lysosomes, endosomes, and the plasma membrane." [PRO:WCB] comment: Category=family. xref: PIRSF:PIRSF002462 -is_a: CHEBI:36080 is_a: PR:000000001 ! protein [Term] @@ -152062,7 +154351,6 @@ synonym: "macrophage receptor with collagenous structure" EXACT [] synonym: "MARCO" EXACT PRO-short-label [PRO:DNx] synonym: "SCARA2" RELATED Gene-based [] synonym: "scavenger receptor class A member 2" EXACT [] -is_a: CHEBI:36080 is_a: PR:000000001 ! protein [Term] @@ -152079,7 +154367,6 @@ synonym: "scavenger receptor class A member 1" EXACT [] synonym: "scavenger receptor type A" EXACT [] synonym: "Scvr" RELATED Gene-based [] synonym: "SR-A" EXACT [] -is_a: CHEBI:36080 is_a: PR:000000001 ! protein [Term] @@ -152089,7 +154376,6 @@ namespace: protein def: "A protein with core architecture consisting of a Peptidase family M1 domain (Pfam:PF01433)." [PRO:WCB] comment: Category=family. xref: PIRSF:PIRSF005502 -is_a: CHEBI:36080 is_a: PR:000000001 ! protein [Term] @@ -152102,7 +154388,6 @@ synonym: "CD14" EXACT PRO-short-label [PRO:DNx] synonym: "monocyte differentiation antigen CD14" EXACT [] synonym: "myeloid cell-specific leucine-rich glycoprotein" EXACT [] xref: PIRSF:PIRSF002017 -is_a: CHEBI:36080 is_a: PR:000000001 ! protein [Term] @@ -152118,7 +154403,6 @@ synonym: "sialic acid-binding Ig-like lectin 3" EXACT [] synonym: "siglec-3" EXACT [] synonym: "SIGLEC3" RELATED Gene-based [] xref: IUPHARobj:2601 -is_a: CHEBI:36080 is_a: PR:000000001 ! protein [Term] @@ -152138,7 +154422,6 @@ synonym: "NCR1" EXACT PRO-short-label [PRO:DNx] synonym: "NK cell-activating receptor" BROAD [PRO:DNx] synonym: "NK-p46" EXACT [] synonym: "NKp46" EXACT [] -is_a: CHEBI:36080 is_a: PR:000000001 ! protein [Term] @@ -152156,7 +154439,6 @@ synonym: "NK cell-activating receptor" BROAD [PRO:DNx] synonym: "NK-p44" EXACT [] synonym: "NKp44" EXACT [] xref: PIRSF:PIRSF037963 -is_a: CHEBI:36080 is_a: PR:000000001 ! protein [Term] @@ -152176,7 +154458,6 @@ synonym: "non-MHC restricted killing associated" EXACT [] synonym: "signaling lymphocytic activation molecule 4" EXACT [] synonym: "SLAM family member 4" EXACT [] synonym: "SLAMF4" EXACT [] -is_a: CHEBI:36080 is_a: PR:000000001 ! protein [Term] @@ -152186,7 +154467,6 @@ namespace: protein def: "A protein with core architecture consisting of an as yet unnamed domain in the amino-terminal half and a carboxyl-terminal Lectin C-type domain (Pfam:PF00059)." [PRO:WCB] comment: Category=family. xref: PIRSF:PIRSF005558 -is_a: CHEBI:36080 is_a: PR:000000001 ! protein [Term] @@ -152209,7 +154489,6 @@ synonym: "SFE" EXACT [] synonym: "skin fibroblast elastase" EXACT [] xref: IUPHARobj:1611 xref: PIRSF:PIRSF501074 -is_a: CHEBI:36080 is_a: PR:000000001 ! protein [Term] @@ -152230,7 +154509,6 @@ synonym: "Thor" RELATED Gene-based [] synonym: "thymus orphan receptor" EXACT [] synonym: "TOR" EXACT [] xref: IUPHARobj:600 -is_a: CHEBI:36080 is_a: PR:000000001 ! protein [Term] @@ -152243,7 +154521,6 @@ synonym: "B-cell-specific transcription factor" EXACT [] synonym: "BSAP" EXACT [] synonym: "Pax-5" RELATED Gene-based [] synonym: "PAX5" EXACT PRO-short-label [PRO:DNx] -is_a: CHEBI:36080 is_a: PR:000000001 ! protein [Term] @@ -152266,7 +154543,6 @@ synonym: "PAS-4" EXACT [] synonym: "platelet collagen receptor" EXACT [] synonym: "platelet glycoprotein IV" EXACT [] synonym: "thrombospondin receptor" EXACT [] -is_a: CHEBI:36080 is_a: PR:000000001 ! protein [Term] @@ -152283,7 +154559,6 @@ synonym: "GP1BA" EXACT PRO-short-label [PRO:DNx] synonym: "GPIb-alpha" EXACT [] synonym: "GPIbA" EXACT [] xref: PIRSF:PIRSF002493 -is_a: CHEBI:36080 is_a: PR:000000001 ! protein [Term] @@ -152299,7 +154574,6 @@ synonym: "PDCD1" EXACT PRO-short-label [PRO:DNx] synonym: "protein PD-1" EXACT [] xref: IUPHARobj:2760 xref: PIRSF:PIRSF018380 -is_a: CHEBI:36080 is_a: PR:000000001 ! protein [Term] @@ -152311,7 +154585,6 @@ comment: Category=gene. Requested by=CL. synonym: "CD163" EXACT PRO-short-label [PRO:DNx] synonym: "hemoglobin scavenger receptor" EXACT [] synonym: "M130" RELATED Gene-based [] -is_a: CHEBI:36080 is_a: PR:000000001 ! protein [Term] @@ -152332,7 +154605,6 @@ synonym: "siglec-5" EXACT [] synonym: "siglec-F" EXACT [] synonym: "SIGLEC5" EXACT PRO-short-label [PRO:DNx] synonym: "Siglecf" RELATED [] -is_a: CHEBI:36080 is_a: PR:000000001 ! protein [Term] @@ -152351,7 +154623,6 @@ synonym: "OBBP1" RELATED Gene-based [] synonym: "obesity-binding protein 1" EXACT [] synonym: "siglec-6" EXACT [] synonym: "SIGLEC6" EXACT PRO-short-label [PRO:DNx] -is_a: CHEBI:36080 is_a: PR:000000001 ! protein [Term] @@ -152368,7 +154639,6 @@ synonym: "sialic acid-binding Ig-like lectin 1" EXACT [] synonym: "siglec-1" EXACT [] synonym: "SIGLEC1" EXACT PRO-short-label [PRO:DNx] synonym: "SN" RELATED Gene-based [] -is_a: CHEBI:36080 is_a: PR:000000001 ! protein [Term] @@ -152387,7 +154657,6 @@ synonym: "nectadrin" EXACT [] synonym: "R13-Ag" EXACT [] synonym: "small cell lung carcinoma cluster 4 antigen" EXACT [] synonym: "X62 heat stable antigen" EXACT [] -is_a: CHEBI:36080 is_a: PR:000000001 ! protein [Term] @@ -152402,7 +154671,6 @@ synonym: "SDC1" EXACT PRO-short-label [PRO:DNx] synonym: "Synd-1" RELATED Gene-based [] synonym: "SYND1" EXACT [] xref: PIRSF:PIRSF015854 -is_a: CHEBI:36080 is_a: PR:000000001 ! protein [Term] @@ -152419,7 +154687,6 @@ synonym: "Trap" RELATED Gene-based [] synonym: "TrATPase" EXACT [] synonym: "type 5 acid phosphatase" EXACT [] xref: PIRSF:PIRSF000898 -is_a: CHEBI:36080 is_a: PR:000000001 ! protein [Term] @@ -152429,7 +154696,6 @@ namespace: protein def: "A protein with core architecture consisting of a signal sequence, a Lectin C-type domain (Pfam:PF00059), 5 or 6 EGF-like domains (Pfam:PF00008, Pfam:PF09064, or Pfam:PF07645), a transmembrane region, and a small cytoplasmic region (36-51 amino acids)." [PRO:WCB] comment: Category=family. xref: PIRSF:PIRSF001775 -is_a: CHEBI:36080 is_a: PR:000000001 ! protein [Term] @@ -152441,7 +154707,6 @@ comment: Category=gene. Requested by=CL. synonym: "Gata-3" RELATED Gene-based [] synonym: "GATA-binding factor 3" EXACT [] synonym: "GATA3" EXACT PRO-short-label [PRO:DNx] -is_a: CHEBI:36080 is_a: PR:000000001 ! protein [Term] @@ -152455,7 +154720,6 @@ synonym: "SFFV proviral integration 1 protein" EXACT [] synonym: "Sfpi-1" RELATED Gene-based [] synonym: "Sfpi1" RELATED Gene-based [] synonym: "SPI1" EXACT PRO-short-label [PRO:DNx] -is_a: CHEBI:36080 is_a: PR:000000001 ! protein [Term] @@ -152472,7 +154736,6 @@ synonym: "TfR1" EXACT [] synonym: "TFRC" EXACT PRO-short-label [PRO:DNx] synonym: "TR" RELATED [] synonym: "Trfr" RELATED Gene-based [] -is_a: CHEBI:36080 is_a: PR:000000001 ! protein [Term] @@ -152490,7 +154753,6 @@ synonym: "TNF-related activation protein" EXACT [] synonym: "TNFSF5" RELATED Gene-based [] synonym: "TRAP" BROAD Gene-based [PRO:DNx] xref: PIRSF:PIRSF016527 -is_a: CHEBI:36080 is_a: PR:000000001 ! protein [Term] @@ -152507,7 +154769,6 @@ synonym: "receptor activator of NF-KB" EXACT [] synonym: "TNFRSF11A" EXACT PRO-short-label [PRO:DNx] xref: IUPHARobj:1881 xref: PIRSF:PIRSF038806 -is_a: CHEBI:36080 is_a: PR:000000001 ! protein [Term] @@ -152524,7 +154785,6 @@ synonym: "TNFRSF7" RELATED Gene-based [] synonym: "tumor necrosis factor receptor superfamily member 7" EXACT [] xref: IUPHARobj:1876 xref: PIRSF:PIRSF001966 -is_a: CHEBI:36080 is_a: PR:000000001 ! protein [Term] @@ -152573,7 +154833,6 @@ synonym: "U-PAR" EXACT [] synonym: "UPAR" RELATED Gene-based [] synonym: "uPAR" EXACT [] xref: PIRSF:PIRSF002022 -is_a: CHEBI:36080 is_a: PR:000000001 ! protein [Term] @@ -152584,7 +154843,6 @@ def: "A protein with core architecture consisting of a signal sequence, followed comment: Category=family. xref: PIRSF:PIRSF038502 is_a: CHEBI:36080 -is_a: PR:000000001 ! protein [Term] id: PR:000001998 @@ -152893,7 +155151,6 @@ namespace: protein def: "A protein that is the translation product of any of the LY6 genes (LY6A-LY6I)." [PRO:CNA] comment: Category=family. xref: PIRSF:PIRSF002021 -is_a: CHEBI:36080 is_a: PR:000000001 ! protein [Term] @@ -152970,7 +155227,6 @@ name: collagen alpha chain namespace: protein def: "A protein that is a component of collagen. Collagens are trimeric molecules in which each chain comprises a repeating Gly-X-Y triplet, in which X and Y can be any residue but are usually proline and hydroxyproline, respectively. This results in a left-handed helix that combines with other two to form a triple-helical structure." [Pfam:PF01391, PMID:15788652, PMID:1639194] comment: Category=family. -is_a: CHEBI:36080 is_a: PR:000000001 ! protein [Term] @@ -153010,7 +155266,6 @@ synonym: "zinc finger and BTB domain-containing protein 27" EXACT [] synonym: "zinc finger protein 51" EXACT [] synonym: "ZNF51" RELATED Gene-based [] xref: IUPHARobj:2957 -is_a: CHEBI:36080 is_a: PR:000000001 ! protein [Term] @@ -153032,7 +155287,6 @@ synonym: "RAG-1" EXACT [] synonym: "RAG1" EXACT PRO-short-label [PRO:DNx] synonym: "RING finger protein 74" EXACT [] synonym: "RNF74" RELATED Gene-based [] -is_a: CHEBI:36080 is_a: PR:000000001 ! protein [Term] @@ -153043,7 +155297,6 @@ def: "A protein that is a translation product of the human RAG2 gene or a 1:1 or comment: Category=gene. Requested by=CL. synonym: "RAG-2" EXACT [] synonym: "RAG2" EXACT PRO-short-label [PRO:DNx] -is_a: CHEBI:36080 is_a: PR:000000001 ! protein [Term] @@ -153071,7 +155324,6 @@ synonym: "P1" RELATED [] synonym: "PFP" RELATED Gene-based [] synonym: "PRF1" EXACT PRO-short-label [PRO:DNx] is_a: CHEBI:36080 -is_a: PR:000000001 ! protein [Term] id: PR:000003469 @@ -153087,9 +155339,20 @@ synonym: "Krox-20" RELATED Gene-based [] synonym: "KROX20" RELATED Gene-based [] synonym: "Zfp-25" RELATED Gene-based [] synonym: "zinc finger protein Krox-20" EXACT [] -is_a: CHEBI:36080 is_a: PR:000000001 ! protein +[Term] +id: PR:000003472 +name: granzyme K +namespace: protein +def: "A leukocyte granule-associated proteinase that is a translation product of the human GZMK gene or a 1:1 ortholog thereof." [PRO:CNA] +comment: Category=gene. +synonym: "GZMK" EXACT PRO-short-label [PRO:DNx] +synonym: "Gzmk" RELATED [] +synonym: "TRYP2" RELATED Gene-based [] +xref: IUPHARobj:2370 +is_a: PR:000003505 ! leukocyte granule-associated proteinase + [Term] id: PR:000003499 name: granzyme B @@ -153130,7 +155393,6 @@ namespace: protein def: "A protein that contains one copy of the T-box domain (Pfam:PF00907) and it is involved in the anterior neural specification." [PMID:10750050, PMID:12210112] comment: Category=family. synonym: "Eomes/Tbr1/Tbx21 family protein" EXACT [] -is_a: CHEBI:36080 is_a: PR:000000001 ! protein [Term] @@ -153150,7 +155412,6 @@ synonym: "Gb3 synthase" EXACT [] synonym: "globotriaosylceramide synthase" EXACT [] synonym: "P1/Pk synthase" EXACT [] synonym: "UDP-galactose:beta-D-galactosyl-beta1-R 4-alpha-D-galactosyltransferase" EXACT [] -is_a: CHEBI:36080 is_a: PR:000000001 ! protein [Term] @@ -153165,7 +155426,6 @@ synonym: "AXL" EXACT PRO-short-label [PRO:DNx] synonym: "AXL oncogene" EXACT [] synonym: "UFO" RELATED Gene-based [] xref: IUPHARobj:1835 -is_a: CHEBI:36080 is_a: PR:000000001 ! protein [Term] @@ -153182,7 +155442,6 @@ synonym: "CTIP2" RELATED Gene-based [] synonym: "radiation-induced tumor suppressor gene 1 protein" EXACT [] synonym: "RIT1" RELATED Gene-based [] synonym: "Rit1" EXACT [] -is_a: CHEBI:36080 is_a: PR:000000001 ! protein [Term] @@ -153194,9 +155453,21 @@ comment: Category=gene. synonym: "BEST4" EXACT PRO-short-label [PRO:DNx] synonym: "vitelliform macular dystrophy 2-like protein 2" EXACT [] synonym: "VMD2L2" RELATED Gene-based [] -is_a: CHEBI:36080 is_a: PR:000000001 ! protein +[Term] +id: PR:000004919 +name: carbonic anhydrase 3 +namespace: protein +def: "A single domain alpha-type carbonic anhydrase that is a translation product of the human CA3 gene or a 1:1 ortholog thereof." [PRO:DNx] +comment: Category=gene. +synonym: "CA-III" EXACT [] +synonym: "CA3" EXACT PRO-short-label [PRO:DNx] +synonym: "Car3" RELATED Gene-based [] +synonym: "carbonate dehydratase III" EXACT [] +synonym: "carbonic anhydrase III" EXACT [] +is_a: PR:000025841 ! single domain alpha-type carbonic anhydrase + [Term] id: PR:000005110 name: cholecystokinin @@ -153204,7 +155475,6 @@ namespace: protein def: "A protein that is a translation product of the human CCK gene or a 1:1 ortholog thereof." [PRO:DNx] comment: Category=gene. synonym: "CCK" EXACT PRO-short-label [PRO:DNx] -is_a: CHEBI:36080 is_a: PR:000000001 ! protein [Term] @@ -153237,7 +155507,6 @@ comment: Category=gene. Requested by=CL. synonym: "C/EBP alpha" EXACT [] synonym: "CEBP" RELATED Gene-based [] synonym: "CEBPA" EXACT PRO-short-label [PRO:DNx] -is_a: CHEBI:36080 is_a: PR:000000001 ! protein [Term] @@ -153249,7 +155518,6 @@ comment: Category=gene. Requested by=CL. synonym: "C/EBP epsilon" EXACT [] synonym: "CEBPE" EXACT PRO-short-label [PRO:DNx] synonym: "Gm294" RELATED Gene-based [] -is_a: CHEBI:36080 is_a: PR:000000001 ! protein [Term] @@ -153263,7 +155531,6 @@ synonym: "CHODL" EXACT PRO-short-label [PRO:DNx] synonym: "PRED12" RELATED Gene-based [] synonym: "transmembrane protein MT75" EXACT [] synonym: "UNQ872/PRO1890" RELATED Gene-based [] -is_a: CHEBI:36080 is_a: PR:000000001 ! protein [Term] @@ -153290,7 +155557,6 @@ synonym: "CD200 receptor-like 3" EXACT [] synonym: "Cd200r3" EXACT PRO-short-label [PRO:DNx] synonym: "CD200RLb" EXACT [] synonym: "cell surface glycoprotein OX2 receptor 3" EXACT [] -is_a: CHEBI:36080 is_a: PR:000000001 ! protein [Term] @@ -153303,7 +155569,6 @@ synonym: "Cd209b" EXACT PRO-short-label [PRO:DNx] synonym: "DC-SIGN-related protein 1" EXACT [] synonym: "DC-SIGNR1" EXACT [] synonym: "OtB7" EXACT [] -is_a: CHEBI:36080 is_a: PR:000000001 ! protein [Term] @@ -153317,7 +155582,6 @@ synonym: "TDT" RELATED Gene-based [] synonym: "terminal addition enzyme" EXACT [] synonym: "terminal deoxynucleotidyltransferase" EXACT [] synonym: "terminal transferase" EXACT [] -is_a: CHEBI:36080 is_a: PR:000000001 ! protein [Term] @@ -153330,7 +155594,6 @@ synonym: "EPER" RELATED Gene-based [] synonym: "EPO" BROAD Gene-based [PRO:DNx] synonym: "EPP" RELATED Gene-based [] synonym: "EPX" EXACT PRO-short-label [PRO:DNx] -is_a: CHEBI:36080 is_a: PR:000000001 ! protein [Term] @@ -153349,7 +155612,6 @@ synonym: "estradiol receptor" EXACT [] synonym: "NR3A1" RELATED Gene-based [] synonym: "nuclear receptor subfamily 3 group A member 1" EXACT [] xref: IUPHARobj:620 -is_a: CHEBI:36080 is_a: PR:000000001 ! protein [Term] @@ -153381,7 +155643,6 @@ synonym: "FGF1" EXACT PRO-short-label [PRO:DNx] synonym: "FGFA" RELATED Gene-based [] synonym: "HBGF-1" EXACT [] synonym: "heparin-binding growth factor 1" EXACT [] -is_a: CHEBI:36080 is_a: PR:000000001 ! protein [Term] @@ -153397,7 +155658,6 @@ synonym: "FGF2" EXACT PRO-short-label [PRO:DNx] synonym: "FGFB" RELATED Gene-based [] synonym: "HBGF-2" EXACT [] synonym: "heparin-binding growth factor 2" EXACT [] -is_a: CHEBI:36080 is_a: PR:000000001 ! protein [Term] @@ -153412,7 +155672,6 @@ synonym: "FGF-8" EXACT [] synonym: "FGF8" EXACT PRO-short-label [PRO:DNx] synonym: "HBGF-8" RELATED [] synonym: "heparin-binding growth factor 8" RELATED [] -is_a: CHEBI:36080 is_a: PR:000000001 ! protein [Term] @@ -153427,7 +155686,6 @@ synonym: "G0/G1 switch regulatory protein 7" EXACT [] synonym: "G0S7" RELATED Gene-based [] synonym: "proto-oncogene protein c-fos" EXACT [] synonym: "transcription factor AP-1 subunit c-Fos" EXACT [] -is_a: CHEBI:36080 is_a: PR:000000001 ! protein [Term] @@ -153446,7 +155704,6 @@ synonym: "RONU" RELATED Gene-based [] synonym: "WHN" RELATED Gene-based [] synonym: "winged-helix transcription factor nude" EXACT [] xref: IUPHARobj:2958 -is_a: CHEBI:36080 is_a: PR:000000001 ! protein [Term] @@ -153458,7 +155715,6 @@ comment: Category=gene. synonym: "forkhead-related transcription factor 1" RELATED [] synonym: "FOXP1" EXACT PRO-short-label [PRO:DNx] synonym: "HSPC215" RELATED Gene-based [] -is_a: CHEBI:36080 is_a: PR:000000001 ! protein [Term] @@ -153475,7 +155731,6 @@ synonym: "GAD67" RELATED Gene-based [] synonym: "glutamate decarboxylase 67 kDa isoform" EXACT [] xref: IUPHARobj:1272 is_a: CHEBI:36080 -is_a: PR:000000001 ! protein [Term] id: PR:000007857 @@ -153491,7 +155746,6 @@ synonym: "GATA1" EXACT PRO-short-label [PRO:DNx] synonym: "GF-1" RELATED [] synonym: "GF1" RELATED Gene-based [] synonym: "NF-E1 DNA-binding protein" EXACT [] -is_a: CHEBI:36080 is_a: PR:000000001 ! protein [Term] @@ -153502,7 +155756,6 @@ def: "A protein that is a translation product of the human GATA2 gene or a 1:1 o comment: Category=gene. Requested by=CL. synonym: "GATA-binding protein 2" EXACT [] synonym: "GATA2" EXACT PRO-short-label [PRO:DNx] -is_a: CHEBI:36080 is_a: PR:000000001 ! protein [Term] @@ -153512,7 +155765,6 @@ namespace: protein def: "A protein that is a translation product of the human GFAP gene or a 1:1 ortholog thereof." [PRO:DNx] comment: Category=gene. Requested by=CL. synonym: "GFAP" EXACT PRO-short-label [PRO:DNx] -is_a: CHEBI:36080 is_a: PR:000000001 ! protein [Term] @@ -153573,7 +155825,6 @@ synonym: "IL17Rh1" EXACT [] synonym: "interleukin-17B receptor" EXACT [] synonym: "UNQ2501/PRO19612" RELATED Gene-based [] xref: IUPHARobj:1739 -is_a: CHEBI:36080 is_a: PR:000000001 ! protein [Term] @@ -153592,7 +155843,6 @@ synonym: "ST2" RELATED Gene-based [] synonym: "Ste2" RELATED Gene-based [] synonym: "T1" RELATED Gene-based [] xref: IUPHARobj:1735 -is_a: CHEBI:36080 is_a: PR:000000001 ! protein [Term] @@ -153660,7 +155910,6 @@ comment: Category=gene. synonym: "KISS1" EXACT PRO-short-label [PRO:DNx] synonym: "kisspeptin-1" EXACT [] synonym: "PP5098" RELATED Gene-based [] -is_a: CHEBI:36080 is_a: PR:000000001 ! protein [Term] @@ -153678,7 +155927,6 @@ synonym: "MAFA-like receptor" EXACT [] synonym: "MAFAL" RELATED Gene-based [] synonym: "mast cell function-associated antigen" EXACT [] synonym: "mast cell function-associated antigen 2F1" EXACT [] -is_a: CHEBI:36080 is_a: PR:000000001 ! protein [Term] @@ -153694,7 +155942,6 @@ synonym: "Ly49" RELATED Gene-based [] synonym: "Ly49A" RELATED Gene-based [] synonym: "lymphocyte antigen 49a" EXACT [] synonym: "T lymphocyte antigen A1" EXACT [] -is_a: CHEBI:36080 is_a: PR:000000001 ! protein [Term] @@ -153709,7 +155956,6 @@ synonym: "ly-49c" EXACT [] synonym: "Ly49C" RELATED Gene-based [] synonym: "lymphocyte antigen 49c" EXACT [] synonym: "T-cell surface glycoprotein Ly-49C" EXACT [] -is_a: CHEBI:36080 is_a: PR:000000001 ! protein [Term] @@ -153724,7 +155970,6 @@ synonym: "Ly49-d" RELATED Gene-based [] synonym: "Ly49d" RELATED Gene-based [] synonym: "lymphocyte antigen 49d" EXACT [] synonym: "T-cell surface glycoprotein Ly-49D" EXACT [] -is_a: CHEBI:36080 is_a: PR:000000001 ! protein [Term] @@ -153739,7 +155984,6 @@ synonym: "Ly49-h" RELATED Gene-based [] synonym: "Ly49H" RELATED Gene-based [] synonym: "lymphocyte antigen 49h" EXACT [] synonym: "T-cell surface glycoprotein Ly-49H" EXACT [] -is_a: CHEBI:36080 is_a: PR:000000001 ! protein [Term] @@ -153756,7 +156000,6 @@ synonym: "NGAL" RELATED Gene-based [] synonym: "oncogene 24p3" EXACT [] synonym: "p25" BROAD [PRO:DNx] synonym: "SV-40-induced 24P3 protein" EXACT [] -is_a: CHEBI:36080 is_a: PR:000000001 ! protein [Term] @@ -153779,7 +156022,6 @@ synonym: "lectin galactoside-binding soluble 1" EXACT [] synonym: "LGALS1" EXACT PRO-short-label [PRO:DNx] synonym: "putative MAPK-activating protein PM12" EXACT [] synonym: "S-Lac lectin 1" EXACT [] -is_a: CHEBI:36080 is_a: PR:000000001 ! protein [Term] @@ -153795,7 +156037,6 @@ synonym: "LIM homeobox protein 3" EXACT [] synonym: "Lim-3" RELATED Gene-based [] synonym: "Lim3" RELATED Gene-based [] synonym: "Plim" RELATED Gene-based [] -is_a: CHEBI:36080 is_a: PR:000000001 ! protein [Term] @@ -153809,7 +156050,6 @@ synonym: "lactoferrin" EXACT [] synonym: "LF" RELATED Gene-based [] synonym: "LTF" EXACT PRO-short-label [PRO:DNx] synonym: "talalactoferrin" EXACT [] -is_a: CHEBI:36080 is_a: PR:000000001 ! protein [Term] @@ -153824,7 +156064,6 @@ synonym: "Lcn" RELATED Gene-based [] synonym: "LDC" RELATED Gene-based [] synonym: "LUM" EXACT PRO-short-label [PRO:DNx] synonym: "SLRR2D" RELATED Gene-based [] -is_a: CHEBI:36080 is_a: PR:000000001 ! protein [Term] @@ -153837,7 +156076,6 @@ synonym: "Meis1-related protein 1" EXACT [] synonym: "MEIS2" EXACT PRO-short-label [PRO:DNx] synonym: "MRG1" RELATED Gene-based [] synonym: "Stra10" RELATED Gene-based [] -is_a: CHEBI:36080 is_a: PR:000000001 ! protein [Term] @@ -153852,7 +156090,20 @@ synonym: "proto-oncogene c-Mer" EXACT [] synonym: "proto-oncogene tyrosine-protein kinase MER" EXACT [] synonym: "receptor tyrosine kinase MerTK" EXACT [] xref: IUPHARobj:1837 -is_a: CHEBI:36080 +is_a: PR:000000001 ! protein + +[Term] +id: PR:000010529 +name: DBH-like monooxygenase protein 1 +namespace: protein +def: "A protein that is a translation product of the human MOXD1 gene or a 1:1 ortholog thereof." [PRO:DNx] +comment: Category=gene. +synonym: "DBH-related protein" EXACT [] +synonym: "Dbhr" RELATED Gene-based [] +synonym: "monooxygenase X" EXACT [] +synonym: "MOX" RELATED Gene-based [] +synonym: "MOXD1" EXACT PRO-short-label [PRO:DNx] +synonym: "UNQ2493/PRO5780" RELATED Gene-based [] is_a: PR:000000001 ! protein [Term] @@ -153864,7 +156115,6 @@ comment: Category=gene. Requested by=CL. synonym: "MPO" EXACT PRO-short-label [PRO:DNx] xref: IUPHARobj:2789 is_a: CHEBI:36080 -is_a: PR:000000001 ! protein [Term] id: PR:000010799 @@ -153874,7 +156124,6 @@ def: "A protein that is a translation product of the human MYB gene or a 1:1 ort comment: Category=gene. Requested by=CL. synonym: "MYB" EXACT PRO-short-label [PRO:DNx] synonym: "proto-oncogene c-Myb" EXACT [] -is_a: CHEBI:36080 is_a: PR:000000001 ! protein [Term] @@ -153886,7 +156135,6 @@ comment: Category=gene. synonym: "brain-specific transmembrane protein containing 2 CUB and 1 LDL-receptor class A domains protein 1" EXACT [] synonym: "BTCL1" RELATED Gene-based [] synonym: "NETO1" EXACT PRO-short-label [PRO:DNx] -is_a: CHEBI:36080 is_a: PR:000000001 ! protein [Term] @@ -153916,9 +156164,22 @@ synonym: "laminet-1" EXACT [] synonym: "LMNT1" RELATED Gene-based [] synonym: "NTNG1" EXACT PRO-short-label [PRO:DNx] synonym: "UNQ571/PRO1133" RELATED Gene-based [] -is_a: CHEBI:36080 is_a: PR:000000001 ! protein +[Term] +id: PR:000012318 +name: paired box protein Pax-6 +namespace: protein +def: "A paired box protein PAX group IV that is a translation product of the human PAX6 gene or a 1:1 ortholog thereof." [PRO:DNx] +comment: Category=gene. +synonym: "AN2" RELATED Gene-based [] +synonym: "aniridia type II protein" EXACT [] +synonym: "oculorhombin" EXACT [] +synonym: "Pax-6" RELATED Gene-based [] +synonym: "PAX6" EXACT PRO-short-label [PRO:DNx] +synonym: "Sey" RELATED Gene-based [] +is_a: PR:000037798 ! paired box protein PAX group IV + [Term] id: PR:000012526 name: proenkephalin-B @@ -153928,7 +156189,17 @@ comment: Category=gene. synonym: "beta-neoendorphin-dynorphin" EXACT [] synonym: "PDYN" EXACT PRO-short-label [PRO:DNx] synonym: "preprodynorphin" EXACT [] -is_a: CHEBI:36080 +is_a: PR:000000001 ! protein + +[Term] +id: PR:000013015 +name: pro-opiomelanocortin +namespace: protein +def: "A protein that is a translation product of the human POMC gene or a 1:1 ortholog thereof." [PRO:DNx] +comment: Category=gene. +synonym: "corticotropin-lipotropin" EXACT [] +synonym: "POMC" EXACT PRO-short-label [PRO:DNx] +synonym: "Pomc1" RELATED Gene-based [] is_a: PR:000000001 ! protein [Term] @@ -153941,7 +156212,6 @@ synonym: "POU6F2" EXACT PRO-short-label [PRO:DNx] synonym: "retina-derived POU domain factor 1" EXACT [] synonym: "RPF-1" EXACT [] synonym: "RPF1" RELATED Gene-based [] -is_a: CHEBI:36080 is_a: PR:000000001 ! protein [Term] @@ -153955,7 +156225,6 @@ synonym: "MBP" RELATED Gene-based [] synonym: "Mbp-1" RELATED Gene-based [] synonym: "PRG2" EXACT PRO-short-label [PRO:DNx] synonym: "proteoglycan 2" EXACT [] -is_a: CHEBI:36080 is_a: PR:000000001 ! protein [Term] @@ -153979,7 +156248,6 @@ synonym: "PTH-rP" EXACT [] synonym: "PTHLH" EXACT PRO-short-label [PRO:DNx] synonym: "PTHRP" RELATED Gene-based [] synonym: "PTHrP" EXACT [] -is_a: CHEBI:36080 is_a: PR:000000001 ! protein [Term] @@ -153990,7 +156258,6 @@ def: "A protein that is a translation product of the human PVALB gene or a 1:1 o comment: Category=gene. synonym: "Pva" RELATED Gene-based [] synonym: "PVALB" EXACT PRO-short-label [PRO:DNx] -is_a: CHEBI:36080 is_a: PR:000000001 ! protein [Term] @@ -154002,7 +156269,6 @@ comment: Category=gene. synonym: "reeler protein" EXACT [] synonym: "RELN" EXACT PRO-short-label [PRO:DNx] synonym: "Rl" RELATED Gene-based [] -is_a: CHEBI:36080 is_a: PR:000000001 ! protein [Term] @@ -154033,7 +156299,6 @@ synonym: "RNase 2" EXACT [] synonym: "RNase UpI-2" EXACT [] synonym: "RNASE2" EXACT PRO-short-label [PRO:DNx] synonym: "RNS2" RELATED Gene-based [] -is_a: CHEBI:36080 is_a: PR:000000001 ! protein [Term] @@ -154047,7 +156312,6 @@ synonym: "ribonuclease 3" RELATED [] synonym: "RNase 3" EXACT [] synonym: "RNASE3" EXACT PRO-short-label [PRO:DNx] synonym: "RNS3" RELATED Gene-based [] -is_a: CHEBI:36080 is_a: PR:000000001 ! protein [Term] @@ -154069,7 +156333,18 @@ synonym: "polyomavirus enhancer-binding protein 2 alpha B subunit" EXACT [] synonym: "RUNX1" EXACT PRO-short-label [PRO:DNx] synonym: "SL3-3 enhancer factor 1 alpha B subunit" EXACT [] synonym: "SL3/AKV core-binding factor alpha B subunit" EXACT [] -is_a: CHEBI:36080 +is_a: PR:000000001 ! protein + +[Term] +id: PR:000014419 +name: protein S100-B +namespace: protein +def: "A protein that is a translation product of the human S100B gene or a 1:1 ortholog thereof." [PRO:DNx] +comment: Category=gene. +synonym: "S-100 protein beta chain" EXACT [] +synonym: "S-100 protein subunit beta" EXACT [] +synonym: "S100 calcium-binding protein B" EXACT [] +synonym: "S100B" EXACT PRO-short-label [PRO:DNx] is_a: PR:000000001 ! protein [Term] @@ -154095,7 +156370,6 @@ synonym: "UP1" EXACT [] synonym: "urinary protein 1" EXACT [] synonym: "urine protein 1" EXACT [] synonym: "Utg" RELATED Gene-based [] -is_a: CHEBI:36080 is_a: PR:000000001 ! protein [Term] @@ -154109,7 +156383,6 @@ synonym: "Hhg1" RELATED Gene-based [] synonym: "SHH" EXACT PRO-short-label [PRO:DNx] synonym: "Shh unprocessed N-terminal signaling and C-terminal autoprocessing domains" EXACT [] synonym: "ShhNC" EXACT [] -is_a: CHEBI:36080 is_a: PR:000000001 ! protein [Term] @@ -154120,7 +156393,6 @@ def: "A protein that is a translation product of the human SIX3 gene or a 1:1 or comment: Category=gene. synonym: "sine oculis homeobox homolog 3" EXACT [] synonym: "SIX3" EXACT PRO-short-label [PRO:DNx] -is_a: CHEBI:36080 is_a: PR:000000001 ! protein [Term] @@ -154137,7 +156409,6 @@ synonym: "PRSN" RELATED Gene-based [] synonym: "SNCG" EXACT PRO-short-label [PRO:DNx] synonym: "SR" EXACT [] synonym: "synoretin" EXACT [] -is_a: CHEBI:36080 is_a: PR:000000001 ! protein [Term] @@ -154148,7 +156419,6 @@ def: "A protein that is a translation product of the human SOX2 gene or a 1:1 or comment: Category=gene. synonym: "Sox-2" RELATED Gene-based [] synonym: "SOX2" EXACT PRO-short-label [PRO:DNx] -is_a: CHEBI:36080 is_a: PR:000000001 ! protein [Term] @@ -154162,7 +156432,6 @@ synonym: "KIAA0762" RELATED Gene-based [] synonym: "SPON1" EXACT PRO-short-label [PRO:DNx] synonym: "vascular smooth muscle cell growth-promoting factor" EXACT [] synonym: "VSGP" RELATED Gene-based [] -is_a: CHEBI:36080 is_a: PR:000000001 ! protein [Term] @@ -154174,7 +156443,6 @@ comment: Category=gene. synonym: "KIAA2036" RELATED Gene-based [] synonym: "SSPO" EXACT PRO-short-label [PRO:DNx] synonym: "SSPOP" RELATED Gene-based [] -is_a: CHEBI:36080 is_a: PR:000000001 ! protein [Term] @@ -154186,7 +156454,6 @@ comment: Category=gene. synonym: "growth hormone release-inhibiting factor" EXACT [] synonym: "Smst" RELATED Gene-based [] synonym: "SST" EXACT PRO-short-label [PRO:DNx] -is_a: CHEBI:36080 is_a: PR:000000001 ! protein [Term] @@ -154203,7 +156470,6 @@ synonym: "Tac2" RELATED Gene-based [] synonym: "TAC3" EXACT PRO-short-label [PRO:DNx] synonym: "UNQ585/PRO1155" RELATED Gene-based [] synonym: "ZNEUROK1" EXACT [] -is_a: CHEBI:36080 is_a: PR:000000001 ! protein [Term] @@ -154221,7 +156487,6 @@ synonym: "T-cell leukemia/lymphoma protein 5" EXACT [] synonym: "TAL-1" EXACT [] synonym: "TAL1" EXACT PRO-short-label [PRO:DNx] synonym: "TCL5" RELATED Gene-based [] -is_a: CHEBI:36080 is_a: PR:000000001 ! protein [Term] @@ -154234,7 +156499,6 @@ synonym: "TH" EXACT PRO-short-label [PRO:DNx] synonym: "TYH" RELATED Gene-based [] synonym: "tyrosine 3-hydroxylase" EXACT [] xref: IUPHARobj:1243 -is_a: CHEBI:36080 is_a: PR:000000001 ! protein [Term] @@ -154250,7 +156514,20 @@ synonym: "p24 family protein gamma-1" EXACT [] synonym: "p24gamma1" EXACT [] synonym: "putative T1/ST2 receptor-binding protein" EXACT [] synonym: "TMED1" EXACT PRO-short-label [PRO:DNx] -is_a: CHEBI:36080 +is_a: PR:000000001 ! protein + +[Term] +id: PR:000016626 +name: triggering receptor expressed on myeloid cells 2 +namespace: protein +def: "A protein that is a translation product of the human TREM2 gene or a 1:1 ortholog thereof." [PRO:DNx] +comment: Category=gene. +synonym: "TREM-2" EXACT [] +synonym: "TREM2" EXACT PRO-short-label [PRO:DNx] +synonym: "Trem2a" RELATED Gene-based [] +synonym: "Trem2b" RELATED Gene-based [] +synonym: "Trem2c" RELATED Gene-based [] +synonym: "triggering receptor expressed on monocytes 2" EXACT [] is_a: PR:000000001 ! protein [Term] @@ -154260,7 +156537,6 @@ namespace: protein def: "A protein that is a translation product of the human VIM gene or a 1:1 ortholog thereof." [PRO:DNx] comment: Category=gene. synonym: "VIM" EXACT PRO-short-label [PRO:DNx] -is_a: CHEBI:36080 is_a: PR:000000001 ! protein [Term] @@ -154273,7 +156549,6 @@ synonym: "vasoactive intestinal peptides" EXACT [PRO:DNx] synonym: "vasoactive intestinal polypeptides" EXACT [PRO:DNx] synonym: "vasoactive intestinal polypeptides precursor" EXACT [] synonym: "VIP" EXACT PRO-short-label [PRO:DNx] -is_a: CHEBI:36080 is_a: PR:000000001 ! protein [Term] @@ -154487,6 +156762,18 @@ is_a: PR:000018264 ! proteolytic cleavage product intersection_of: PR:000003264 ! collagen alpha-1(I) chain intersection_of: output_of GO:0016485 ! protein processing +[Term] +id: PR:000018820 +name: granzyme K proteolytic cleavage product +namespace: protein +def: "A granzyme K that has been processed by proteolytic cleavage." [PRO:DNx] +comment: Category=modification. +synonym: "GZMK/ClvPrd" EXACT PRO-short-label [PRO:DNx] +is_a: PR:000003472 ! granzyme K +is_a: PR:000018264 ! proteolytic cleavage product +intersection_of: PR:000003472 ! granzyme K +intersection_of: output_of GO:0016485 ! protein processing + [Term] id: PR:000019255 name: cholecystokinin proteolytic cleavage product @@ -154607,6 +156894,18 @@ is_a: PR:000018264 ! proteolytic cleavage product intersection_of: PR:000012526 ! proenkephalin-B intersection_of: output_of GO:0016485 ! protein processing +[Term] +id: PR:000021036 +name: pro-opiomelanocortin proteolytic cleavage product +namespace: protein +def: "A pro-opiomelanocortin that has been processed by proteolytic cleavage." [PRO:DNx] +comment: Category=modification. +synonym: "POMC/ClvPrd" EXACT PRO-short-label [PRO:DNx] +is_a: PR:000013015 ! pro-opiomelanocortin +is_a: PR:000018264 ! proteolytic cleavage product +intersection_of: PR:000013015 ! pro-opiomelanocortin +intersection_of: output_of GO:0016485 ! protein processing + [Term] id: PR:000021081 name: bone marrow proteoglycan, signal peptide removed form @@ -154824,7 +157123,6 @@ name: integrin alpha namespace: protein def: "A protein that is composed of a long N-terminal extracellular domain, a transmembrane domain and a short cytoplasmic C-terminal domain. The N-terminal domain contains beta-propeller repeats (interrupted by an A domain in a subset of integrins alpha), while the C-terminal domain contains a GFFxR motif." [PMID:19693543] comment: Category=family. Integrins are heterodimeric complexes of an alpha and a beta subunit. They are a structurally elaborate family of adhesion molecules that transmit signals bidirectionally across the plasma membrane by undergoing large-scale structural rearrangements. By regulating cell-cell and cell-matrix contacts, integrins participate in a wide-range of biological interactions including development, tissue repair, angiogenesis, inflammation and hemostasis. [PMID:10402956, PMID:11988479, PMID:9676575]. -is_a: CHEBI:36080 is_a: PR:000000001 ! protein [Term] @@ -154837,6 +157135,15 @@ synonym: "fam:ITGAsansA" EXACT PRO-short-label [PRO:DAN] xref: PIRSF:PIRSF005666 is_a: PR:000025796 ! integrin alpha +[Term] +id: PR:000025841 +name: single domain alpha-type carbonic anhydrase +namespace: protein +def: "A protein that contains a single copy of the Eukaryotic-type carbonic anhydrase domain (Pfam:PF00194) with no other conserved domains." [PRO:DAN] +comment: Category=family. +xref: PIRSF:PIRSF001392 +is_a: PR:000000001 ! protein + [Term] id: PR:000027795 name: trypsin @@ -154844,7 +157151,6 @@ namespace: protein def: "A protein that in active form is a serine protease that cleaves peptide bonds on the carboxyl side of lysine or arginine amino acids within amino acid chains." [PRO:DAN, Wikipedia:Trypsin] comment: Category=family. synonym: "PRSS" EXACT PRO-short-label [PRO:DNx] -is_a: CHEBI:36080 is_a: PR:000000001 ! protein [Term] @@ -154889,7 +157195,6 @@ synonym: "iroquois homeobox protein 6" EXACT [] synonym: "IRX6" EXACT PRO-short-label [PRO:DNx] synonym: "IRX7" RELATED Gene-based [] synonym: "IRXB3" RELATED Gene-based [] -is_a: CHEBI:36080 is_a: PR:000000001 ! protein [Term] @@ -154899,7 +157204,6 @@ namespace: protein def: "A protein that is a standalone version of the Hormone_1 domain (Pfam:PF00103). In the immature form, the domain is preceded by a signal peptide." [PRO:DAN] comment: Category=family. synonym: "fam:GH1" EXACT PRO-short-label [PRO:DNx] -is_a: CHEBI:36080 is_a: PR:000000001 ! protein [Term] @@ -154913,7 +157217,7 @@ synonym: "fam:GPCR" EXACT PRO-short-label [PRO:DAN] synonym: "seven-transmembrane receptor" BROAD [IUPHARfam:694] xref: IUPHARfam:694 is_a: BFO:0000004 -is_a: CHEBI:36080 +is_a: BFO:0000040 is_a: PR:000000001 ! protein intersection_of: PR:000000001 ! protein intersection_of: capable_of GO:0004930 ! G protein-coupled receptor activity @@ -154932,7 +157236,18 @@ synonym: "C20orf103" RELATED Gene-based [] synonym: "LAMP-5" EXACT [] synonym: "LAMP5" EXACT PRO-short-label [PRO:DNx] synonym: "lysosome-associated membrane protein 5" EXACT [] -is_a: CHEBI:36080 +is_a: PR:000000001 ! protein + +[Term] +id: PR:000032533 +name: LIM/homeobox protein Lhx6 +namespace: protein +def: "A protein that is a translation product of the human LHX6 gene or a 1:1 ortholog thereof." [PRO:DNx] +comment: Category=gene. +synonym: "LHX6" EXACT PRO-short-label [PRO:DNx] +synonym: "LHX6.1" RELATED Gene-based [] +synonym: "LIM homeobox protein 6" EXACT [] +synonym: "LIM/homeobox protein Lhx6.1" EXACT [] is_a: PR:000000001 ! protein [Term] @@ -154959,7 +157274,6 @@ name: eukaryotic protein namespace: protein def: "A protein that is encoded in the genome of some Eukaryota." [PRO:DAN] synonym: "Eukaryota protein" EXACT [PRO:DAN] -is_a: CHEBI:36080 is_a: PR:000000001 ! protein intersection_of: PR:000000001 ! protein intersection_of: RO:0002160 NCBITaxon:2759 ! only in taxon Eukaryota @@ -154988,9 +157302,27 @@ comment: Category=modification. synonym: "glycated protein" EXACT [PRO:DAN] synonym: "glycosylated protein" EXACT [PRO:DAN] synonym: "Prot/GlycoRes+" EXACT PRO-short-label [PRO:DAN] -is_a: CHEBI:36080 is_a: PR:000000001 ! protein +[Term] +id: PR:000037797 +name: paired box protein PAX +namespace: protein +def: "A protein that contains a copy of the 'Paired box' domain (Pfam:PF00292), a conserved amino acid motif with DNA-binding activity. Members of this class are transcription factors involved in pattern formation during embryogenesis, possibly by determining the time and place of organ initiation or morphogenesis." [PIRSF:PIRSF038195, PMID:9297966, PRO:CNA] +comment: Category=family. +xref: PIRSF:PIRSF038195 +is_a: PR:000000001 ! protein + +[Term] +id: PR:000037798 +name: paired box protein PAX group IV +namespace: protein +def: "A paired box protein PAX that contains, in addition to the 'Paired box' domain (Pfam:PF00292), a C-terminal Homeobox domain (Pfam:PF00046)." [PIRSF:PIRSF500778, PMID:11750700, PMID:24951566, PRO:CNA] +comment: Category=family. +synonym: "paired box protein, PAX6-type" EXACT [PIRSF:PIRSF500778] +xref: PIRSF:PIRSF500778 +is_a: PR:000037797 ! paired box protein PAX + [Term] id: PR:000040662 name: cathepsin-like protease @@ -155059,6 +157391,7 @@ synonym: "nonselective channel protein" EXACT [PRO:XQ] synonym: "pore class transporter protein" EXACT [PRO:XQ] synonym: "pore protein" EXACT [PRO:XQ] is_a: BFO:0000004 +is_a: BFO:0000040 is_a: CHEBI:36080 is_a: PR:000000001 ! protein intersection_of: PR:000000001 ! protein @@ -155071,7 +157404,6 @@ name: leukocyte immunoglobulin-like receptor subfamily member namespace: protein comment: Category=family. Requested by=HPO/MPO. synonym: "fam:LILR" EXACT PRO-short-label [PRO:DAN] -is_a: CHEBI:36080 is_a: PR:000000001 ! protein [Term] @@ -155081,7 +157413,6 @@ namespace: protein def: "A protein that is a translation product of a gene that encodes a standalone Insulin (Pfam:PF00049) domain preceded by a signal peptide." [PRO:DAN] comment: Category=family. synonym: "fam:INS" EXACT PRO-short-label [PRO:DAN] -is_a: CHEBI:36080 is_a: PR:000000001 ! protein [Term] @@ -155104,7 +157435,6 @@ namespace: protein def: "A protein that is a translation product of the mouse Ren1 or Ren2 genes, 1:1 orthologs thereof, or a semi-ortholog thereof." [PRO:DAN] comment: Category=family. synonym: "fam:angiotensinogenase" EXACT PRO-short-label [PRO:DAN] -is_a: CHEBI:36080 is_a: PR:000000001 ! protein [Term] @@ -155136,7 +157466,6 @@ namespace: protein def: "A protein that is a translation product of the human HBA1, HBA2, HBB, HBD, HBE1, HBG1, HBG2, HBM, HBQ1, or HBZ genes, 1:1 orthologs thereof, or semi-orthologs thereof." [PRO:DAN] comment: Category=family. synonym: "fam:Hb" EXACT PRO-short-label [PRO:DAN] -is_a: CHEBI:36080 is_a: PR:000000001 ! protein [Term] @@ -155158,17 +157487,17 @@ union_of: PR:P0DN77 ! medium-wave-sensitive opsin 2 (human) union_of: PR:P0DN78 ! medium-wave-sensitive opsin 3 (human) [Term] -id: PR:000050567 -name: protein-containing material entity +id: PR:000064867 +name: protein-containing molecular entity namespace: protein -def: "A material entity that minimally consists of a protein." [PRO:DAN] -comment: Note: This includes single proteins and derivatives thereof (PR:000000001), protein-containing complexes (GO:0032991), and protein aggregates (PR:000050566). +def: "A molecular entity that minimally consists of a protein." [PRO:DAN] +comment: Note: This includes single proteins and derivatives thereof (PR:000000001), protein-containing complexes (GO:0032991), and protein aggregates (PR:000050565). synonym: "protein" NARROW [PRO:DAN] synonym: "protein aggregate" NARROW [PRO:DAN] synonym: "protein complex" NARROW [PRO:DAN] synonym: "protein-containing complex" NARROW [PRO:DAN] -is_a: BFO:0000040 -intersection_of: BFO:0000040 +is_a: CHEBI:23367 +intersection_of: CHEBI:23367 intersection_of: has_part PR:000000001 ! protein relationship: has_part PR:000000001 ! protein @@ -155281,6 +157610,20 @@ is_a: PR:000029067 ! Homo sapiens protein intersection_of: PR:000001927 ! sialic acid-binding Ig-like lectin 5 intersection_of: RO:0002160 NCBITaxon:9606 ! only in taxon Homo sapiens +[Term] +id: PR:O35205 +name: granzyme K (mouse) +namespace: protein +def: "A granzyme K that is encoded in the genome of mouse." [OMA:O35205, PRO:DNx] +comment: Category=organism-gene. +synonym: "Gzmk" RELATED Gene-based [UniProtKB:O35205] +synonym: "mGZMK" EXACT PRO-short-label [PRO:DNx] +xref: UniProtKB:O35205 +is_a: PR:000003472 ! granzyme K +is_a: PR:000029032 ! Mus musculus protein +intersection_of: PR:000003472 ! granzyme K +intersection_of: RO:0002160 NCBITaxon:10090 ! only in taxon Mus musculus + [Term] id: PR:O35305 name: tumor necrosis factor receptor superfamily member 11A (mouse) @@ -155401,7 +157744,7 @@ intersection_of: RO:0002160 NCBITaxon:10090 ! only in taxon Mus musculus id: PR:O54707 name: natural killer cells antigen CD94 (mouse) namespace: protein -def: "A killer cell lectin-like receptor subfamily D member 1 that is encoded in the genome of mouse." [OMA:O54707, PANTHER:PTHR22800\:SF15, PRO:DNx] +def: "A killer cell lectin-like receptor subfamily D member 1 that is encoded in the genome of mouse." [OMA:O54707, PRO:DNx] comment: Category=organism-gene. synonym: "Cd94" RELATED Gene-based [UniProtKB:O54707] synonym: "CD94 (mouse)" EXACT [UniProtKB:O54707] @@ -155497,7 +157840,7 @@ intersection_of: RO:0002160 NCBITaxon:9606 ! only in taxon Homo sapiens id: PR:O88324 name: CD83 antigen (mouse) namespace: protein -def: "A CD83 molecule that is encoded in the genome of mouse." [OMA:O88324, PANTHER:PTHR15193\:SF0, PRO:DNx] +def: "A CD83 molecule that is encoded in the genome of mouse." [OMA:O88324, PRO:DNx] comment: Category=organism-gene. synonym: "Cd83" RELATED Gene-based [UniProtKB:O88324] synonym: "CD83 (mouse)" EXACT [UniProtKB:O88324] @@ -155597,6 +157940,7 @@ synonym: "T-box brain protein 2 (human)" EXACT [UniProtKB:O95936] synonym: "T-brain-2 (human)" EXACT [UniProtKB:O95936] synonym: "TBR-2 (human)" EXACT [UniProtKB:O95936] synonym: "TBR2" RELATED Gene-based [UniProtKB:O95936] +xref: Reactome:R-HSA-452232 "PR:O95936 located_in GO:0005654" xref: UniProtKB:O95936 is_a: PR:000003463 ! eomesodermin is_a: PR:000029067 ! Homo sapiens protein @@ -155677,6 +158021,38 @@ is_a: PR:000029032 ! Mus musculus protein intersection_of: PR:000007597 ! protein c-Fos intersection_of: RO:0002160 NCBITaxon:10090 ! only in taxon Mus musculus +[Term] +id: PR:P01189 +name: pro-opiomelanocortin (human) +namespace: protein +def: "A pro-opiomelanocortin that is encoded in the genome of human." [PRO:DNx, UniProtKB:P01189] +comment: Category=organism-gene. +synonym: "corticotropin-lipotropin (human)" EXACT [UniProtKB:P01189] +synonym: "hPOMC" EXACT PRO-short-label [PRO:DNx] +synonym: "POMC" RELATED Gene-based [UniProtKB:P01189] +xref: UniProtKB:P01189 +is_a: PR:000013015 ! pro-opiomelanocortin +is_a: PR:000029067 ! Homo sapiens protein +intersection_of: PR:000013015 ! pro-opiomelanocortin +intersection_of: RO:0002160 NCBITaxon:9606 ! only in taxon Homo sapiens + +[Term] +id: PR:P01193 +name: pro-opiomelanocortin (mouse) +namespace: protein +def: "A pro-opiomelanocortin that is encoded in the genome of mouse." [OMA:P01193, PRO:DNx] +comment: Category=organism-gene. +synonym: "corticotropin-lipotropin (mouse)" EXACT [UniProtKB:P01193] +synonym: "mPOMC" EXACT PRO-short-label [PRO:DNx] +synonym: "Pomc" RELATED Gene-based [UniProtKB:P01193] +synonym: "POMC (mouse)" EXACT [UniProtKB:P01193] +synonym: "Pomc1" RELATED Gene-based [UniProtKB:P01193] +xref: UniProtKB:P01193 +is_a: PR:000013015 ! pro-opiomelanocortin +is_a: PR:000029032 ! Mus musculus protein +intersection_of: PR:000013015 ! pro-opiomelanocortin +intersection_of: RO:0002160 NCBITaxon:10090 ! only in taxon Mus musculus + [Term] id: PR:P01213 name: proenkephalin-B (human) @@ -156102,6 +158478,23 @@ is_a: PR:000029067 ! Homo sapiens protein intersection_of: PR:000001843 ! Thy-1 membrane glycoprotein intersection_of: RO:0002160 NCBITaxon:9606 ! only in taxon Homo sapiens +[Term] +id: PR:P04271 +name: protein S100-B (human) +namespace: protein +def: "A protein S100-B that is encoded in the genome of human." [PRO:DNx, UniProtKB:P04271] +comment: Category=organism-gene. +synonym: "hS100B" EXACT PRO-short-label [PRO:DNx] +synonym: "S-100 protein beta chain (human)" EXACT [UniProtKB:P04271] +synonym: "S-100 protein subunit beta (human)" EXACT [UniProtKB:P04271] +synonym: "S100 calcium-binding protein B (human)" EXACT [UniProtKB:P04271] +synonym: "S100B" RELATED Gene-based [UniProtKB:P04271] +xref: UniProtKB:P04271 +is_a: PR:000014419 ! protein S100-B +is_a: PR:000029067 ! Homo sapiens protein +intersection_of: PR:000014419 ! protein S100-B +intersection_of: RO:0002160 NCBITaxon:9606 ! only in taxon Homo sapiens + [Term] id: PR:P05089 name: arginase-1 (human) @@ -156472,6 +158865,23 @@ is_a: PR:000029067 ! Homo sapiens protein intersection_of: PR:000001907 ! platelet glycoprotein Ib alpha chain intersection_of: RO:0002160 NCBITaxon:9606 ! only in taxon Homo sapiens +[Term] +id: PR:P07451 +name: carbonic anhydrase 3 (human) +namespace: protein +def: "A carbonic anhydrase 3 that is encoded in the genome of human." [PRO:DNx, UniProtKB:P07451] +comment: Category=organism-gene. +synonym: "CA-III (human)" EXACT [UniProtKB:P07451] +synonym: "CA3" RELATED Gene-based [UniProtKB:P07451] +synonym: "carbonate dehydratase III (human)" EXACT [UniProtKB:P07451] +synonym: "carbonic anhydrase III (human)" EXACT [UniProtKB:P07451] +synonym: "hCA3" EXACT PRO-short-label [PRO:DNx] +xref: UniProtKB:P07451 +is_a: PR:000004919 ! carbonic anhydrase 3 +is_a: PR:000029067 ! Homo sapiens protein +intersection_of: PR:000004919 ! carbonic anhydrase 3 +intersection_of: RO:0002160 NCBITaxon:9606 ! only in taxon Homo sapiens + [Term] id: PR:P07766 name: T-cell surface glycoprotein CD3 epsilon chain (human) @@ -157936,6 +160346,24 @@ is_a: PR:000029067 ! Homo sapiens protein intersection_of: PR:000007857 ! erythroid transcription factor intersection_of: RO:0002160 NCBITaxon:9606 ! only in taxon Homo sapiens +[Term] +id: PR:P16015 +name: carbonic anhydrase 3 (mouse) +namespace: protein +def: "A carbonic anhydrase 3 that is encoded in the genome of mouse." [OMA:P16015, PRO:DNx] +comment: Category=organism-gene. +synonym: "CA-III (mouse)" EXACT [UniProtKB:P16015] +synonym: "Ca3" RELATED Gene-based [UniProtKB:P16015] +synonym: "Car3" RELATED Gene-based [UniProtKB:P16015] +synonym: "carbonate dehydratase III (mouse)" EXACT [UniProtKB:P16015] +synonym: "carbonic anhydrase III (mouse)" EXACT [UniProtKB:P16015] +synonym: "mCA3" EXACT PRO-short-label [PRO:DNx] +xref: UniProtKB:P16015 +is_a: PR:000004919 ! carbonic anhydrase 3 +is_a: PR:000029032 ! Mus musculus protein +intersection_of: PR:000004919 ! carbonic anhydrase 3 +intersection_of: RO:0002160 NCBITaxon:10090 ! only in taxon Mus musculus + [Term] id: PR:P16045 name: galectin-1 (mouse) @@ -159033,6 +161461,24 @@ is_a: PR:000029032 ! Mus musculus protein intersection_of: PR:000001465 ! high affinity immunoglobulin gamma Fc receptor I intersection_of: RO:0002160 NCBITaxon:10090 ! only in taxon Mus musculus +[Term] +id: PR:P26367 +name: paired box protein Pax-6 (human) +namespace: protein +def: "A paired box protein Pax-6 that is encoded in the genome of human." [PRO:DNx, UniProtKB:P26367] +comment: Category=organism-gene. +synonym: "AN2" RELATED Gene-based [UniProtKB:P26367] +synonym: "aniridia type II protein (human)" EXACT [UniProtKB:P26367] +synonym: "hPAX6" EXACT PRO-short-label [PRO:DNx] +synonym: "oculorhombin (human)" EXACT [UniProtKB:P26367] +synonym: "PAX6" RELATED Gene-based [UniProtKB:P26367] +xref: Reactome:R-HSA-3009044 "PR:P26367 located_in GO:0005654" +xref: UniProtKB:P26367 +is_a: PR:000012318 ! paired box protein Pax-6 +is_a: PR:000029067 ! Homo sapiens protein +intersection_of: PR:000012318 ! paired box protein Pax-6 +intersection_of: RO:0002160 NCBITaxon:9606 ! only in taxon Homo sapiens + [Term] id: PR:P26618 name: platelet-derived growth factor receptor alpha (mouse) @@ -159206,7 +161652,7 @@ synonym: "2'-phospho-ADP-ribosyl cyclase/2'-phospho-cyclic-ADP-ribose transferas synonym: "2'-phospho-cyclic-ADP-ribose transferase (human)" EXACT [UniProtKB:P28907] synonym: "ADP-ribosyl cyclase 1 (human)" EXACT [] synonym: "ADPRC 1 (human)" EXACT [UniProtKB:P28907] -synonym: "cADPr hydrolase 1 (human)" EXACT [UniProtKB:P28907] +synonym: "cADPR hydrolase 1 (human)" EXACT [UniProtKB:P28907] synonym: "CD38" RELATED Gene-based [UniProtKB:P28907] synonym: "cyclic ADP-ribose hydrolase 1 (human)" EXACT [UniProtKB:P28907] synonym: "hCD38" EXACT PRO-short-label [PRO:DNx] @@ -160104,6 +162550,42 @@ is_a: PR:000029067 ! Homo sapiens protein intersection_of: PR:000005307 ! CCAAT/enhancer-binding protein alpha intersection_of: RO:0002160 NCBITaxon:9606 ! only in taxon Homo sapiens +[Term] +id: PR:P49863 +name: granzyme K (human) +namespace: protein +def: "A granzyme K that is encoded in the genome of human." [PRO:CNA, UniProtKB:P49863] +comment: Category=organism-gene. +synonym: "fragmentin-3 (human)" EXACT [UniProtKB:P49863] +synonym: "granzyme-3 (human)" EXACT [UniProtKB:P49863] +synonym: "GZMK" RELATED Gene-based [UniProtKB:P49863] +synonym: "hGZMK" EXACT PRO-short-label [PRO:DNx] +synonym: "NK-Tryp-2 (human)" EXACT [UniProtKB:P49863] +synonym: "NK-tryptase-2 (human)" EXACT [UniProtKB:P49863] +synonym: "TRYP2" RELATED Gene-based [UniProtKB:P49863] +xref: UniProtKB:P49863 +is_a: PR:000003472 ! granzyme K +is_a: PR:000029067 ! Homo sapiens protein +intersection_of: PR:000003472 ! granzyme K +intersection_of: RO:0002160 NCBITaxon:9606 ! only in taxon Homo sapiens + +[Term] +id: PR:P50114 +name: protein S100-B (mouse) +namespace: protein +def: "A protein S100-B that is encoded in the genome of mouse." [OMA:P50114, PRO:DNx] +comment: Category=organism-gene. +synonym: "mS100B" EXACT PRO-short-label [PRO:DNx] +synonym: "S-100 protein beta chain (mouse)" EXACT [UniProtKB:P50114] +synonym: "S-100 protein subunit beta (mouse)" EXACT [UniProtKB:P50114] +synonym: "S100 calcium-binding protein B (mouse)" EXACT [UniProtKB:P50114] +synonym: "S100b" RELATED Gene-based [UniProtKB:P50114] +xref: UniProtKB:P50114 +is_a: PR:000014419 ! protein S100-B +is_a: PR:000029032 ! Mus musculus protein +intersection_of: PR:000014419 ! protein S100-B +intersection_of: RO:0002160 NCBITaxon:10090 ! only in taxon Mus musculus + [Term] id: PR:P50283 name: T-cell antigen CD7 (mouse) @@ -160557,7 +163039,7 @@ synonym: "2'-phospho-ADP-ribosyl cyclase/2'-phospho-cyclic-ADP-ribose transferas synonym: "2'-phospho-cyclic-ADP-ribose transferase (mouse)" EXACT [UniProtKB:P56528] synonym: "ADP-ribosyl cyclase 1 (mouse)" EXACT [UniProtKB:P56528] synonym: "ADPRC 1 (mouse)" EXACT [UniProtKB:P56528] -synonym: "cADPr hydrolase 1 (mouse)" EXACT [UniProtKB:P56528] +synonym: "cADPR hydrolase 1 (mouse)" EXACT [UniProtKB:P56528] synonym: "Cd38" RELATED Gene-based [UniProtKB:P56528] synonym: "CD38 (mouse)" EXACT [UniProtKB:P56528] synonym: "cyclic ADP-ribose hydrolase 1 (mouse)" EXACT [UniProtKB:P56528] @@ -160701,6 +163183,23 @@ is_a: PR:000029067 ! Homo sapiens protein intersection_of: PR:000015665 ! somatostatin intersection_of: RO:0002160 NCBITaxon:9606 ! only in taxon Homo sapiens +[Term] +id: PR:P63015 +name: paired box protein Pax-6 (mouse) +namespace: protein +def: "A paired box protein Pax-6 that is encoded in the genome of mouse." [OMA:P63015, PRO:DNx] +comment: Category=organism-gene. +synonym: "mPAX6" EXACT PRO-short-label [PRO:DNx] +synonym: "oculorhombin (mouse)" EXACT [UniProtKB:P63015] +synonym: "Pax-6" RELATED Gene-based [UniProtKB:P63015] +synonym: "Pax6" RELATED Gene-based [UniProtKB:P63015] +synonym: "Sey" RELATED Gene-based [UniProtKB:P63015] +xref: UniProtKB:P63015 +is_a: PR:000012318 ! paired box protein Pax-6 +is_a: PR:000029032 ! Mus musculus protein +intersection_of: PR:000012318 ! paired box protein Pax-6 +intersection_of: RO:0002160 NCBITaxon:10090 ! only in taxon Mus musculus + [Term] id: PR:P70658 name: C-X-C chemokine receptor type 4 (mouse) @@ -162188,6 +164687,23 @@ is_a: PR:000029032 ! Mus musculus protein intersection_of: PR:000001666 ! relaxin receptor 1 intersection_of: RO:0002160 NCBITaxon:10090 ! only in taxon Mus musculus +[Term] +id: PR:Q6UVY6 +name: DBH-like monooxygenase protein 1 (human) +namespace: protein +def: "A DBH-like monooxygenase protein 1 that is encoded in the genome of human." [PRO:DNx, UniProtKB:Q6UVY6] +comment: Category=organism-gene. +synonym: "hMOXD1" EXACT PRO-short-label [PRO:DNx] +synonym: "monooxygenase X (human)" EXACT [UniProtKB:Q6UVY6] +synonym: "MOX" RELATED Gene-based [UniProtKB:Q6UVY6] +synonym: "MOXD1" RELATED Gene-based [UniProtKB:Q6UVY6] +synonym: "UNQ2493/PRO5780" RELATED Gene-based [UniProtKB:Q6UVY6] +xref: UniProtKB:Q6UVY6 +is_a: PR:000010529 ! DBH-like monooxygenase protein 1 +is_a: PR:000029067 ! Homo sapiens protein +intersection_of: PR:000010529 ! DBH-like monooxygenase protein 1 +intersection_of: RO:0002160 NCBITaxon:9606 ! only in taxon Homo sapiens + [Term] id: PR:Q6Y4S4 name: metastasis-suppressor KiSS-1 (mouse) @@ -162509,6 +165025,25 @@ is_a: PR:000029032 ! Mus musculus protein intersection_of: PR:000001350 ! forkhead box protein P3 intersection_of: RO:0002160 NCBITaxon:10090 ! only in taxon Mus musculus +[Term] +id: PR:Q99NH8 +name: triggering receptor expressed on myeloid cells 2 (mouse) +namespace: protein +def: "A triggering receptor expressed on myeloid cells 2 that is encoded in the genome of mouse." [OMA:Q99NH8, PRO:DNx] +comment: Category=organism-gene. +synonym: "mTREM2" EXACT PRO-short-label [PRO:DNx] +synonym: "TREM-2 (mouse)" EXACT [UniProtKB:Q99NH8] +synonym: "Trem2" RELATED Gene-based [UniProtKB:Q99NH8] +synonym: "Trem2a" RELATED Gene-based [UniProtKB:Q99NH8] +synonym: "Trem2b" RELATED Gene-based [UniProtKB:Q99NH8] +synonym: "Trem2c" RELATED Gene-based [UniProtKB:Q99NH8] +synonym: "triggering receptor expressed on monocytes 2 (mouse)" EXACT [UniProtKB:Q99NH8] +xref: UniProtKB:Q99NH8 +is_a: PR:000016626 ! triggering receptor expressed on myeloid cells 2 +is_a: PR:000029032 ! Mus musculus protein +intersection_of: PR:000016626 ! triggering receptor expressed on myeloid cells 2 +intersection_of: RO:0002160 NCBITaxon:10090 ! only in taxon Mus musculus + [Term] id: PR:Q99PV8 name: B-cell lymphoma/leukemia 11B (mouse) @@ -162635,6 +165170,43 @@ is_a: PR:000029067 ! Homo sapiens protein intersection_of: PR:000004691 ! B-cell lymphoma/leukemia 11B intersection_of: RO:0002160 NCBITaxon:9606 ! only in taxon Homo sapiens +[Term] +id: PR:Q9CW73 +name: galactosylgalactosylxylosylprotein 3-beta-glucuronosyltransferase 1 (mouse) +namespace: protein +def: "A galactosylgalactosylxylosylprotein 3-beta-glucuronosyltransferase 1 that is encoded in the genome of mouse." [OMA:Q9CW73, PRO:DNx] +comment: Category=organism-gene. +synonym: "B3gat1" RELATED Gene-based [UniProtKB:Q9CW73] +synonym: "beta-1,3-glucuronyltransferase 1 (mouse)" EXACT [UniProtKB:Q9CW73] +synonym: "GlcAT-P (mouse)" EXACT [UniProtKB:Q9CW73] +synonym: "GlcUAT-P (mouse)" EXACT [UniProtKB:Q9CW73] +synonym: "glucuronosyltransferase P (mouse)" EXACT [UniProtKB:Q9CW73] +synonym: "mB3GAT1" EXACT PRO-short-label [PRO:DNx] +synonym: "UDP-GlcUA:glycoprotein beta-1,3-glucuronyltransferase (mouse)" EXACT [UniProtKB:Q9CW73] +xref: UniProtKB:Q9CW73 +is_a: PR:000001440 ! galactosylgalactosylxylosylprotein 3-beta-glucuronosyltransferase 1 +is_a: PR:000029032 ! Mus musculus protein +intersection_of: PR:000001440 ! galactosylgalactosylxylosylprotein 3-beta-glucuronosyltransferase 1 +intersection_of: RO:0002160 NCBITaxon:10090 ! only in taxon Mus musculus + +[Term] +id: PR:Q9CXI3 +name: DBH-like monooxygenase protein 1 (mouse) +namespace: protein +def: "A DBH-like monooxygenase protein 1 that is encoded in the genome of mouse." [OMA:Q9CXI3, PRO:DNx] +comment: Category=organism-gene. +synonym: "DBH-related protein (mouse)" EXACT [UniProtKB:Q9CXI3] +synonym: "Dbhr" RELATED Gene-based [UniProtKB:Q9CXI3] +synonym: "mMOXD1" EXACT PRO-short-label [PRO:DNx] +synonym: "monooxygenase X (mouse)" EXACT [UniProtKB:Q9CXI3] +synonym: "Mox" RELATED Gene-based [UniProtKB:Q9CXI3] +synonym: "Moxd1" RELATED Gene-based [UniProtKB:Q9CXI3] +xref: UniProtKB:Q9CXI3 +is_a: PR:000010529 ! DBH-like monooxygenase protein 1 +is_a: PR:000029032 ! Mus musculus protein +intersection_of: PR:000010529 ! DBH-like monooxygenase protein 1 +intersection_of: RO:0002160 NCBITaxon:10090 ! only in taxon Mus musculus + [Term] id: PR:Q9CXM0 name: chondrolectin (mouse) @@ -162915,6 +165487,43 @@ is_a: PR:000029067 ! Homo sapiens protein intersection_of: PR:000008982 ! interleukin-17 receptor B intersection_of: RO:0002160 NCBITaxon:9606 ! only in taxon Homo sapiens +[Term] +id: PR:Q9NZC2 +name: triggering receptor expressed on myeloid cells 2 (human) +namespace: protein +def: "A triggering receptor expressed on myeloid cells 2 that is encoded in the genome of human." [PRO:DNx, UniProtKB:Q9NZC2] +comment: Category=organism-gene. Requested by=Alzforum. +synonym: "hTREM2" EXACT PRO-short-label [PRO:DNx] +synonym: "TREM-2 (human)" EXACT [UniProtKB:Q9NZC2] +synonym: "TREM2" RELATED Gene-based [UniProtKB:Q9NZC2] +synonym: "triggering receptor expressed on monocytes 2 (human)" EXACT [UniProtKB:Q9NZC2] +xref: UniProtKB:Q9NZC2 +is_a: PR:000016626 ! triggering receptor expressed on myeloid cells 2 +is_a: PR:000029067 ! Homo sapiens protein +intersection_of: PR:000016626 ! triggering receptor expressed on myeloid cells 2 +intersection_of: RO:0002160 NCBITaxon:9606 ! only in taxon Homo sapiens + +[Term] +id: PR:Q9P2W7 +name: galactosylgalactosylxylosylprotein 3-beta-glucuronosyltransferase 1 (human) +namespace: protein +def: "A galactosylgalactosylxylosylprotein 3-beta-glucuronosyltransferase 1 that is encoded in the genome of human." [PRO:WCB, UniProtKB:Q9P2W7] +comment: Category=organism-gene. +synonym: "B3GAT1" RELATED Gene-based [UniProtKB:Q9P2W7] +synonym: "beta-1,3-glucuronyltransferase 1 (human)" EXACT [UniProtKB:Q9P2W7] +synonym: "GlcAT-P (human)" EXACT [] +synonym: "GLCATP" RELATED Gene-based [UniProtKB:Q9P2W7] +synonym: "GlcUAT-P (human)" EXACT [UniProtKB:Q9P2W7] +synonym: "glucuronosyltransferase P (human)" EXACT [UniProtKB:Q9P2W7] +synonym: "hB3GAT1" EXACT PRO-short-label [PRO:DNx] +synonym: "UDP-GlcUA:glycoprotein beta-1,3-glucuronyltransferase (human)" EXACT [UniProtKB:Q9P2W7] +xref: Reactome:R-HSA-1889953 "PR:Q9P2W7 located_in GO:0000139" +xref: UniProtKB:Q9P2W7 +is_a: PR:000001440 ! galactosylgalactosylxylosylprotein 3-beta-glucuronosyltransferase 1 +is_a: PR:000029067 ! Homo sapiens protein +intersection_of: PR:000001440 ! galactosylgalactosylxylosylprotein 3-beta-glucuronosyltransferase 1 +intersection_of: RO:0002160 NCBITaxon:9606 ! only in taxon Homo sapiens + [Term] id: PR:Q9QUM0 name: integrin alpha-IIb (mouse) @@ -162985,6 +165594,23 @@ is_a: PR:000029032 ! Mus musculus protein intersection_of: PR:000001243 ! melanopsin intersection_of: RO:0002160 NCBITaxon:10090 ! only in taxon Mus musculus +[Term] +id: PR:Q9R1R0 +name: LIM/homeobox protein Lhx6 (mouse) +namespace: protein +def: "A LIM/homeobox protein Lhx6 that is encoded in the genome of mouse." [OMA:Q9R1R0, PRO:DNx] +comment: Category=organism-gene. +synonym: "Lhx6" RELATED Gene-based [UniProtKB:Q9R1R0] +synonym: "Lhx6.1" RELATED Gene-based [UniProtKB:Q9R1R0] +synonym: "LIM homeobox protein 6 (mouse)" EXACT [UniProtKB:Q9R1R0] +synonym: "LIM/homeobox protein Lhx6.1 (mouse)" EXACT [UniProtKB:Q9R1R0] +synonym: "mLHX6" EXACT PRO-short-label [PRO:DNx] +xref: UniProtKB:Q9R1R0 +is_a: PR:000029032 ! Mus musculus protein +is_a: PR:000032533 ! LIM/homeobox protein Lhx6 +intersection_of: PR:000032533 ! LIM/homeobox protein Lhx6 +intersection_of: RO:0002160 NCBITaxon:10090 ! only in taxon Mus musculus + [Term] id: PR:Q9UBR4 name: LIM/homeobox protein Lhx3 (human) @@ -163130,6 +165756,23 @@ is_a: PR:000029067 ! Homo sapiens protein intersection_of: PR:000001835 ! T-box transcription factor TBX21 intersection_of: RO:0002160 NCBITaxon:9606 ! only in taxon Homo sapiens +[Term] +id: PR:Q9UPM6 +name: LIM/homeobox protein Lhx6 (human) +namespace: protein +def: "A LIM/homeobox protein Lhx6 that is encoded in the genome of human." [PRO:DNx, UniProtKB:Q9UPM6] +comment: Category=organism-gene. +synonym: "hLHX6" EXACT PRO-short-label [PRO:DNx] +synonym: "LHX6" RELATED Gene-based [UniProtKB:Q9UPM6] +synonym: "LHX6.1" RELATED Gene-based [UniProtKB:Q9UPM6] +synonym: "LIM homeobox protein 6 (human)" EXACT [UniProtKB:Q9UPM6] +synonym: "LIM/homeobox protein Lhx6.1 (human)" EXACT [UniProtKB:Q9UPM6] +xref: UniProtKB:Q9UPM6 +is_a: PR:000029067 ! Homo sapiens protein +is_a: PR:000032533 ! LIM/homeobox protein Lhx6 +intersection_of: PR:000032533 ! LIM/homeobox protein Lhx6 +intersection_of: RO:0002160 NCBITaxon:9606 ! only in taxon Homo sapiens + [Term] id: PR:Q9WTK5 name: nuclear factor NF-kappa-B p100 subunit (mouse) @@ -163302,6 +165945,10 @@ def: "A material entity consisting of multiple components that are causally inte is_a: BFO:0000040 property_value: IAO:0000116 "May be replaced by a BFO class, as discussed in http://www.jbiomedsem.com/content/4/1/43" xsd:string +[Term] +id: SO:0001260 +name: sequence_collection + [Term] id: UBERON:0000000 name: processual entity @@ -163425,7 +166072,6 @@ is_a: UBERON:0000475 ! organism subdivision is_a: UBERON:0002268 ! olfactory organ is_a: UBERON:0004121 ! ectoderm-derived structure relationship: capable_of_part_of GO:0007608 ! sensory perception of smell -relationship: part_of UBERON:0001004 {gci_relation="part_of", gci_filler="NCBITaxon:32523", source="PMID:25312359"} ! respiratory system relationship: part_of UBERON:0001456 {source="FMA", source="ZFA-def"} ! face relationship: RO:0002162 NCBITaxon:7742 ! in taxon Vertebrata relationship: RO:0002202 UBERON:0003050 {source="ZFA"} ! develops from olfactory placode @@ -163484,7 +166130,6 @@ is_a: UBERON:0004119 ! endoderm-derived structure is_a: UBERON:0034922 ! cell cluster relationship: has_part CL:0000168 {source="PMID:16417468"} ! insulin secreting cell relationship: has_part CL:0000172 {source="PMID:16417468"} ! somatostatin secreting cell -relationship: has_part CL:0000696 {gci_filler="NCBITaxon:117570", gci_relation="part_of", source="PMID:16417468"} ! PP cell relationship: has_part CL:0002067 {source="PMID:16417468"} ! type A enteroendocrine cell relationship: part_of UBERON:0000016 ! endocrine pancreas relationship: RO:0002433 UBERON:0000016 ! contributes to morphology of endocrine pancreas @@ -163753,7 +166398,6 @@ xref: MIAA:0000284 xref: SCTID:20795001 xref: VHOG:0000860 xref: Wikipedia:Skin -is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0034944 {source="FMA"} ! zone of organ relationship: has_part UBERON:0001003 ! skin epidermis @@ -164167,11 +166811,9 @@ xref: VHOG:0001644 xref: WBbt:0005739 xref: Wikipedia:Head xref: XAO:0003024 -xref: ZFA:0001114 is_a: UBERON:0011676 ! subdivision of organism along main body axis relationship: part_of UBERON:0007811 ! craniocervical region relationship: RO:0002162 NCBITaxon:33213 ! in taxon Bilateria -relationship: RO:0002551 UBERON:0003129 {gci_relation="part_of", gci_filler="NCBITaxon:7776"} ! has skeleton skull [Term] id: UBERON:0000035 @@ -164192,7 +166834,6 @@ xref: EMAPA:35631 xref: FMA:18634 xref: MA:0002907 xref: SCTID:258665002 -is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0001305 ! ovarian follicle intersection_of: UBERON:0001305 ! ovarian follicle intersection_of: has_component UBERON:0005170 {cardinality="1"} ! granulosa cell layer @@ -164219,7 +166860,6 @@ synonym: "secondary follicle of ovary" EXACT [] xref: EMAPA:35632 xref: FMA:18637 xref: MA:0002908 -is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0001305 ! ovarian follicle intersection_of: UBERON:0001305 ! ovarian follicle intersection_of: has_component UBERON:0005170 {minCardinality="2"} ! granulosa cell layer @@ -164255,7 +166895,6 @@ xref: MA:0002909 xref: NCIT:C32692 xref: SCTID:362261008 xref: UMLS:C0600225 {source="ncithesaurus:Graafian_Follicle"} -is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0001305 ! ovarian follicle intersection_of: UBERON:0001305 ! ovarian follicle intersection_of: has_component UBERON:0005170 {minCardinality="2"} ! granulosa cell layer @@ -164340,7 +166979,6 @@ xref: TAO:0005425 xref: UMLS:C0036760 {source="ncithesaurus:Serosa"} xref: Wikipedia:Serous_membrane xref: ZFA:0005425 -is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0000481 ! multi-tissue structure is_a: UBERON:0004120 ! mesoderm-derived structure relationship: has_part UBERON:0001136 ! mesothelium @@ -164389,7 +167027,6 @@ property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/3/ id: UBERON:0000044 name: dorsal root ganglion namespace: uberon -alt_id: UBERON:0026602 def: "Sensory ganglia located on the dorsal spinal roots within the vertebral column. The spinal ganglion cells are pseudounipolar. The single primary branch bifurcates sending a peripheral process to carry sensory information from the periphery and a central branch which relays that information to the spinal cord or brain. (MSH) * ganglion found on the posterior root of each spinal nerve, composed of the unipolar nerve cell bodies of the sensory neurons of the nerve. (CSP)." [BIRNLEX:2596] subset: efo_slim subset: human_reference_atlas @@ -164720,7 +167357,6 @@ xref: UMLS:C0687028 {source="ncithesaurus:Duct"} xref: Wikipedia:Duct_(anatomy) xref: XAO:0004000 xref: ZFA:0005171 -is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0000063 ! organ subunit relationship: has_part UBERON:0034969 ! epithelial layer of duct relationship: RO:0000086 PATO:0002299 ! has quality tubular @@ -164769,7 +167405,6 @@ property_value: RO:0002175 NCBITaxon:9606 id: UBERON:0000060 name: anatomical wall namespace: uberon -alt_id: UBERON:0009915 def: "Organ component adjacent to an organ cavity and which consists of a maximal aggregate of organ component layers." [FMA:82482] subset: upper_level synonym: "organ wall" RELATED [FMA:82482] @@ -164812,7 +167447,6 @@ xref: XAO:0003000 xref: ZFA:0000037 is_a: BFO:0000004 is_a: UBERON:0000465 ! material anatomical entity -relationship: RO:0002496 UBERON:0000106 {gci_filler="NCBITaxon:33208", gci_relation="RO:0002162"} ! existence starts during or after zygote stage relationship: RO:0002497 UBERON:0000071 ! existence ends during or before death stage property_value: RO:0002175 NCBITaxon:33090 property_value: RO:0002175 NCBITaxon:33208 @@ -164846,7 +167480,6 @@ disjoint_from: UBERON:0034921 ! multi organ part structure relationship: capable_of GO:0008150 ! biological_process relationship: part_of UBERON:0000467 ! anatomical system relationship: RO:0002002 UBERON:0006984 ! has 2D boundary anatomical surface -relationship: RO:0002496 UBERON:0000111 {gci_filler="NCBITaxon:6072", gci_relation="RO:0002162"} ! existence starts during or after organogenesis stage property_value: RO:0002161 NCBITaxon:110815 {source="Wikipedia"} property_value: RO:0002175 NCBITaxon:33090 property_value: RO:0002175 NCBITaxon:33208 @@ -165108,7 +167741,6 @@ creation_date: 2009-06-18T09:26:37Z id: UBERON:0000075 name: subdivision of skeletal system namespace: uberon -alt_id: UBERON:0010322 def: "Anatomical cluster consisting of the skeletal elements and articular elements that are part of an individual subdivision of the organism." [https://orcid.org/0000-0002-6601-2165, UBERONREF:0000003] subset: non_informative synonym: "skeletal system part" RELATED [] @@ -165530,7 +168162,6 @@ def: "Nonparenchymatous organ that primarily consists of dense connective tissue synonym: "membrane" BROAD [] synonym: "membrane of organ" EXACT [] xref: FMA:7145 -is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0000062 ! organ relationship: RO:0002473 UBERON:0011823 {source="FMA-def"} ! composed primarily of dense connective tissue property_value: terms:contributor https://orcid.org/0000-0002-6601-2165 @@ -165613,7 +168244,6 @@ is_a: BFO:0000003 is_a: UBERON:0000000 ! processual entity relationship: ends_with UBERON:0000071 ! death stage relationship: has_part UBERON:0000105 ! life cycle stage -relationship: starts_with UBERON:0000106 {gci_filler="NCBITaxon:33208", gci_relation="RO:0002162"} ! zygote stage property_value: RO:0002175 NCBITaxon:33090 property_value: RO:0002175 NCBITaxon:33208 property_value: RO:0002175 NCBITaxon:4751 @@ -165796,7 +168426,6 @@ xref: Wikipedia:Organogenesis is_a: BFO:0000003 is_a: UBERON:0000105 ! life cycle stage relationship: part_of UBERON:0000068 ! embryo stage -relationship: preceded_by UBERON:0000110 {gci_relation="part_of", gci_filler="NCBITaxon:32523"} ! neurula stage relationship: RO:0002082 GO:0048513 ! simultaneous with animal organ development relationship: RO:0002162 NCBITaxon:6072 ! in taxon Eumetazoa property_value: seeAlso "https://github.com/obophenotype/developmental-stage-ontologies/issues/84" xsd:anyURI @@ -165905,7 +168534,6 @@ synonym: "segment of tracheobronchial tree" NARROW [FMA:12224] synonym: "tracheobronchial tree segment" NARROW [FMA:12224] xref: EMAPA:37946 {source="MA:th"} xref: FMA:12224 -is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0000025 ! tube is_a: UBERON:0004119 ! endoderm-derived structure intersection_of: UBERON:0000025 ! tube @@ -165995,7 +168623,6 @@ property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/9/ id: UBERON:0000122 name: neuron projection bundle namespace: uberon -alt_id: UBERON:0005163 def: "A fasciculated bundle of neuron projections (GO:0043005), largely or completely lacking synapses." [CARO:0001001, FBbt:00005099, FBC:DOS] synonym: "funiculus" EXACT [] synonym: "nerve fiber bundle" EXACT [FBbt:00005099] @@ -166152,6 +168779,56 @@ relationship: part_of UBERON:0001305 ! ovarian follicle relationship: RO:0002473 CL:0000503 ! composed primarily of theca cell property_value: RO:0002175 NCBITaxon:9606 +[Term] +id: UBERON:0000156 +name: theca externa +namespace: uberon +def: "The theca externa is the outer layers of the theca folliculi. It contains abundant collagen and is mainly supportive." [Wikipedia:Theca_externa] +subset: human_reference_atlas +subset: pheno_slim +synonym: "external coat of theca folliculi" RELATED [BTO:0002852] +synonym: "ovary theca externa" EXACT [MA:0001713] +synonym: "theca externa (folliculus ovaricus tertiarius)" EXACT [FMA:18657] +synonym: "tunica externa of theca folliculi" EXACT [FMA:18657] +synonym: "tunica externa thecae folliculi" RELATED OMO:0003011 [BTO:0002852, Wikipedia:Theca_externa] +xref: BTO:0002852 +xref: FMA:18657 +xref: MA:0001713 +xref: SCTID:258767003 +xref: Wikipedia:Theca_externa +is_a: UBERON:0000158 ! membranous layer +is_a: UBERON:0004120 ! mesoderm-derived structure +is_a: UBERON:0005156 ! reproductive structure +relationship: bounding_layer_of UBERON:0000155 ! theca cell layer +relationship: has_part GO:0005581 ! collagen trimer +relationship: RO:0002221 UBERON:0000157 ! surrounds theca interna +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/5/50/Mature_Graffian_follicle.jpg" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 + +[Term] +id: UBERON:0000157 +name: theca interna +namespace: uberon +def: "Theca interna cells express receptors for luteinizing hormone, which when activated will stimulate the production of androstenedione from cholesterol by the enzyme desmolase. Androstenedione ultimately gives the granulosa cells the precursor substrate for estrogen manufacturing." [Wikipedia:Theca_externa#Theca_interna] +subset: human_reference_atlas +subset: pheno_slim +synonym: "internal coat of capsule of Graafian follicle" RELATED [BTO:0002851] +synonym: "ovary theca interna" EXACT [MA:0001714] +synonym: "theca interna (folliculus ovaricus tertiarius)" EXACT [FMA:18658] +synonym: "tunica interna of theca folliculi" EXACT [FMA:18658] +synonym: "tunica interna thecae folliculi" RELATED [BTO:0002851] +xref: BTO:0002851 +xref: FMA:18658 +xref: MA:0001714 +xref: SCTID:258869006 +xref: Wikipedia:Theca_externa#Theca_interna +is_a: UBERON:0000158 ! membranous layer +is_a: UBERON:0004120 ! mesoderm-derived structure +is_a: UBERON:0005156 ! reproductive structure +relationship: part_of UBERON:0000155 ! theca cell layer +relationship: RO:0002433 UBERON:0000155 ! contributes to morphology of theca cell layer +property_value: RO:0002175 NCBITaxon:9606 + [Term] id: UBERON:0000158 name: membranous layer @@ -166403,7 +169080,6 @@ synonym: "oral orifice" EXACT [FMA:59806] synonym: "oral part of face" RELATED [] xref: FMA:59806 is_a: UBERON:0000161 {source="FMA"} ! orifice -relationship: overlaps UBERON:0001004 {gci_relation="part_of", gci_filler="NCBITaxon:32523"} ! respiratory system relationship: part_of UBERON:0000165 ! mouth [Term] @@ -166538,8 +169214,6 @@ relationship: RO:0002328 GO:0001701 ! functionally related to in utero embryonic id: UBERON:0000174 name: excreta namespace: uberon -alt_id: UBERON:0000324 -alt_id: UBERON:0007550 def: "A portion of organism substance that is the product of an excretion process that will be eliminated from the body. An excretion process is elimination by an organism of the waste products that arise as a result of metabolic activity." [GO:0007588, http://orcid.org/0000-0002-6601-2165] synonym: "excreted substance" EXACT [] synonym: "excretion" RELATED [BTO:0000491] @@ -166593,7 +169267,7 @@ xref: Wikipedia:Blood xref: XAO:0000124 xref: ZFA:0000007 is_a: BFO:0000002 -is_a: PR:000050567 ! protein-containing material entity +is_a: UBERON:0000061 ! anatomical structure is_a: UBERON:0000179 ! haemolymphatic fluid relationship: has_part CL:0000232 {source="CL:tm"} ! erythrocyte relationship: has_part UBERON:0001969 ! blood plasma @@ -166680,7 +169354,6 @@ creation_date: 2009-04-10T08:42:24Z id: UBERON:0000203 name: pallium namespace: uberon -alt_id: UBERON:0007333 def: "Dorsal part (roof region) of the telencephalon[GO]." [GO:0021543, https://github.com/obophenotype/uberon/issues/287, ISBN:0471888893, Wikipedia:Pallium_(neuroanatomy)] subset: developmental_classification subset: efo_slim @@ -166755,8 +169428,6 @@ is_a: UBERON:0010428 {source="FMA"} ! flat bone is_a: UBERON:0011164 ! neurocranium bone relationship: overlaps UBERON:0001697 ! orbit of skull relationship: part_of UBERON:0003113 {source="cjm"} ! dermatocranium -relationship: RO:0002170 UBERON:0001677 {gci_relation="part_of", gci_filler="NCBITaxon:9606", source="FMA"} ! connected to sphenoid bone -relationship: RO:0002170 UBERON:0001679 {gci_relation="part_of", gci_filler="NCBITaxon:9606", source="FMA"} ! connected to ethmoid bone property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/9/97/Gray136.png" xsd:anyURI property_value: foaf:depiction "https://upload.wikimedia.org/wikipedia/commons/5/5b/Frontal_bone.png" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 @@ -166862,7 +169533,6 @@ xref: SCTID:361885006 xref: UMLS:C0224856 {source="ncithesaurus:Tendon_Sheath"} xref: Wikipedia:Tendon_sheath is_a: BFO:0000002 -is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0004923 ! organ component layer intersection_of: UBERON:0004923 ! organ component layer intersection_of: bounding_layer_of UBERON:0000043 ! tendon @@ -166893,7 +169563,6 @@ xref: SCTID:181457005 xref: UMLS:C0002630 {source="ncithesaurus:Amnion"} xref: VHOG:0000721 xref: Wikipedia:Amnion -is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0005631 ! extraembryonic membrane relationship: has_part UBERON:0003254 ! amniotic ectoderm @@ -166911,7 +169580,6 @@ property_value: RO:0002175 NCBITaxon:9606 id: UBERON:0000307 name: blastula namespace: uberon -alt_id: UBERON:0007011 def: "Organism at the blastula stage - an early stage of embryonic development in animals. It is produced by cleavage of a fertilized ovum and consists of a spherical layer of around 128 cells surrounding a central fluid-filled cavity called the blastocoel. The blastula follows the morula and precedes the gastrula in the developmental sequence." [Wikipedia:Blastula] subset: inconsistent_with_fma synonym: "blastosphere" RELATED [Wikipedia:Blastula] @@ -167076,8 +169744,6 @@ relationship: produced_by UBERON:0000002 ! uterine cervix id: UBERON:0000317 name: colonic mucosa namespace: uberon -alt_id: UBERON:0003347 -alt_id: UBERON:0004981 def: "Mucosa that is part of a colon. The mucosa of the colon is lined by a simple columnar epithelium with a thin brush border and numerous goblet cells." [http://orcid.org/0000-0002-6601-2165] subset: efo_slim subset: human_reference_atlas @@ -167106,7 +169772,6 @@ property_value: RO:0002175 NCBITaxon:9606 id: UBERON:0000320 name: duodenal mucosa namespace: uberon -alt_id: UBERON:0003348 def: "A mucosa that is part of a duodenum [Automatically generated definition]." [OBOL:automatic] subset: human_reference_atlas synonym: "doudenal mucosa" EXACT [FMA:14942] @@ -167322,7 +169987,6 @@ xref: NCIT:C13166 xref: SCTID:361693009 xref: UMLS:C0026724 {source="ncithesaurus:Mucosa"} xref: Wikipedia:Mucous_membrane -is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0004923 ! organ component layer relationship: has_part UBERON:0000483 ! epithelium relationship: has_part UBERON:0002384 ! connective tissue @@ -167465,7 +170129,6 @@ relationship: RO:0002162 NCBITaxon:6072 ! in taxon Eumetazoa id: UBERON:0000355 name: pharyngeal mucosa namespace: uberon -alt_id: UBERON:0003344 def: "A mucosa that is part of a pharynx [Automatically generated definition]." [OBOL:automatic] synonym: "mucosa of organ of pharynx" EXACT [OBOL:automatic] synonym: "mucosa of pharynx" EXACT [OBOL:automatic] @@ -167614,7 +170277,6 @@ property_value: foaf:depiction "https://upload.wikimedia.org/wikipedia/commons/9 id: UBERON:0000369 name: corpus striatum namespace: uberon -alt_id: UBERON:0010082 def: "The corpus striatum (striated body) is a compound structure consisting of the caudate nucleus and the lentiform nucleus, which consists of the putamen and the globus pallidus[WP]." [Wikipedia:Corpus_striatum] comment: * According to the 1917 version of Gray's Anatomy, it is the combination of the lentiform nucleus (also known as the lenticular nucleus) and the caudate nucleus * According to BrainInfo it is a part of the basal ganglia comprising the globus pallidus and striatum subset: efo_slim @@ -168153,7 +170815,6 @@ xref: SCTID:181480002 xref: UMLS:C0036270 {source="ncithesaurus:Scalp"} xref: Wikipedia:Scalp is_a: BFO:0000002 -is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0034921 ! multi organ part structure relationship: has_part UBERON:0000014 ! zone of skin relationship: has_part UBERON:0002384 ! connective tissue @@ -168359,14 +171020,12 @@ xref: UMLS:C0013492 {source="ncithesaurus:Eccrine_Sweat_Gland"} xref: Wikipedia:Eccrine_sweat_gland is_a: UBERON:0001820 ! sweat gland is_a: UBERON:0010243 {source="MGI:anna"} ! merocrine gland -relationship: part_of UBERON:0008837 {gci_relation="part_of", gci_filler="NCBITaxon:10088", source="PMID:15843440"} ! palmar/plantar part of autopod property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0000424 name: gastric pit namespace: uberon -alt_id: UBERON:0000425 def: "Gastric pits are indentations in the stomach which denote entrances to the gastric glands. They are deeper in the pylorus than they are in the other parts of the stomach. The human stomach has several million of these pits." [Wikipedia:Gastric_pits] synonym: "foveola gastrica" RELATED [BTO:0002364] synonym: "foveolae gastricae" EXACT OMO:0003004 [FMA:76583, FMA:TA] @@ -168386,7 +171045,6 @@ property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/7/ id: UBERON:0000428 name: prostate epithelium namespace: uberon -alt_id: UBERON:0002452 def: "The prostate epithelium." [MP:0001168] subset: human_reference_atlas subset: pheno_slim @@ -168423,7 +171081,6 @@ property_value: RO:0002175 NCBITaxon:9606 id: UBERON:0000429 name: enteric plexus namespace: uberon -alt_id: UBERON:0012372 def: "A plexus of autonomic nerve fibers within the wall of the digestive tube, and made up of the submucosal, myenteric, and subserosal plexuses; it contains visceral afferent fibers, sympathetic postganglionic fibers, parasympathetic preganglionic and postganglionic fibers, and parasympathetic postganglionic cell bodies." [BTO:0002437] subset: human_reference_atlas synonym: "enteric nerve plexus" EXACT [FMA:77597] @@ -168465,7 +171122,6 @@ synonym: "trabecula arachnoideum" RELATED OMO:0003011 [] xref: BTO:0002500 xref: FMA:83979 xref: Wikipedia:Arachnoid_trabeculae -is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0000440 ! trabecula is_a: UBERON:0010313 ! neural crest-derived structure intersection_of: UBERON:0000440 ! trabecula @@ -168606,7 +171262,6 @@ relationship: part_of UBERON:0000955 ! brain id: UBERON:0000456 name: secretion of exocrine gland namespace: uberon -alt_id: UBERON:0006540 def: "A portion of organism substance that is produced by exocrine glands." [http://orcid.org/0000-0002-6601-2165] synonym: "bodily secretion" EXACT [MESH:D012634] synonym: "exocrine gland fluid" RELATED [] @@ -168658,7 +171313,6 @@ xref: FMA:86485 xref: NCIT:C12309 xref: SCTID:264460007 xref: UMLS:C0227837 {source="ncithesaurus:Endocervix"} -is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0000064 ! organ part is_a: UBERON:0005156 ! reproductive structure intersection_of: UBERON:0000064 ! organ part @@ -168853,7 +171507,6 @@ xref: ZFA:0001439 is_a: UBERON:0000061 ! anatomical structure relationship: has_part UBERON:0000062 ! organ relationship: part_of UBERON:0000468 ! multicellular organism -relationship: RO:0002496 UBERON:0000111 {gci_filler="NCBITaxon:6072", gci_relation="RO:0002162"} ! existence starts during or after organogenesis stage property_value: RO:0002175 NCBITaxon:33090 property_value: RO:0002175 NCBITaxon:33208 property_value: RO:0002175 NCBITaxon:4751 @@ -168934,7 +171587,6 @@ relationship: part_of UBERON:0003103 ! compound organ id: UBERON:0000473 name: testis namespace: uberon -alt_id: UBERON:0002117 def: "A gonad of a male animal. A gonad produces and releases sperm." [http://orcid.org/0000-0002-6601-2165] subset: efo_slim subset: organ_slim @@ -169074,13 +171726,6 @@ xref: Wikipedia:Body_part xref: XAO:0003013 xref: ZFA:0001308 is_a: UBERON:0010000 {source="CARO"} ! multicellular anatomical structure -relationship: has_part UBERON:0000075 {gci_relation="part_of", gci_filler="NCBITaxon:7742"} ! subdivision of skeletal system -relationship: has_part UBERON:0034929 {gci_relation="part_of", gci_filler="NCBITaxon:7742"} ! external soft tissue zone -relationship: overlaps UBERON:0001009 {gci_filler="NCBITaxon:33213", gci_relation="RO:0002162"} ! circulatory system -relationship: overlaps UBERON:0001015 {gci_filler="NCBITaxon:6072", gci_relation="RO:0002162"} ! musculature -relationship: overlaps UBERON:0001016 {gci_filler="NCBITaxon:6072", gci_relation="RO:0002162"} ! nervous system -relationship: overlaps UBERON:0001434 {gci_filler="NCBITaxon:33213", gci_relation="RO:0002162"} ! skeletal system -relationship: overlaps UBERON:0002416 {gci_filler="NCBITaxon:6072", gci_relation="RO:0002162"} ! integumental system relationship: part_of UBERON:0000468 ! multicellular organism property_value: IAO:0000116 "Reflects CARO2. todo - check the inclusion of FMA 'cardinal body part here', and check child terms for consistency" xsd:string property_value: RO:0002175 NCBITaxon:33090 @@ -169161,7 +171806,6 @@ is_a: UBERON:0005423 ! developing anatomical structure intersection_of: UBERON:0005423 ! developing anatomical structure intersection_of: part_of UBERON:0016887 ! entire extraembryonic component relationship: part_of UBERON:0016887 ! entire extraembryonic component -relationship: RO:0002491 UBERON:0000068 {gci_filler="NCBITaxon:6072", gci_relation="RO:0002162"} ! existence starts and ends during embryo stage [Term] id: UBERON:0000479 @@ -169227,11 +171871,46 @@ xref: XAO:0003037 xref: ZFA:0001488 is_a: UBERON:0010000 {source="CARO"} ! multicellular anatomical structure relationship: has_part UBERON:0000479 ! tissue -relationship: part_of NCBITaxon:6072 {gci_filler="NCBITaxon:6072", gci_relation="RO:0002162"} ! Eumetazoa property_value: RO:0002175 NCBITaxon:33090 property_value: RO:0002175 NCBITaxon:33208 property_value: RO:0002175 NCBITaxon:4751 +[Term] +id: UBERON:0000482 +name: basal lamina of epithelium +namespace: uberon +def: "Acellular anatomical structure that consists of a thin sheet of fibrous proteins that underlie and support the cells of an epithelium. It separates the cells of an epithelium from any underlying tissue." [http://orcid.org/0000-0001-9114-8737] +subset: human_reference_atlas +subset: uberon_slim +subset: vertebrate_core +synonym: "basal lamina" RELATED [CARO:0000065] +synonym: "basal lamina of connective tissue" EXACT [FMA:62918] +synonym: "basal laminae" RELATED OMO:0003004 [VHOG:0001592] +synonym: "lamina basalis" RELATED OMO:0003011 [Wikipedia:Basal_lamina] +xref: AAO:0010269 +xref: AEO:0000065 +xref: BILA:0000065 +xref: CARO:0000065 +xref: EHDAA2:0003065 +xref: FMA:62918 +xref: HAO:0000065 +xref: MESH:D001485 +xref: NCIT:C32186 +xref: NIF_Subcellular:sao1397492660 +xref: TAO:0001485 +xref: TGMA:0001850 +xref: UMLS:C0085872 {source="ncithesaurus:Basal_Lamina"} +xref: VHOG:0001592 +xref: WBbt:0005756 +xref: Wikipedia:Basal_lamina +xref: XAO:0003163 +xref: ZFA:0001485 +is_a: UBERON:0005764 {source="FMA"} ! acellular membrane +relationship: part_of UBERON:0005769 {source="FMA"} ! basement membrane of epithelium +relationship: RO:0002473 GO:0005604 ! composed primarily of basement membrane +property_value: foaf:depiction "https://upload.wikimedia.org/wikipedia/commons/6/65/Basal_lamina.jpg" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 + [Term] id: UBERON:0000483 name: epithelium @@ -169266,7 +171945,6 @@ xref: VHOG:0000387 xref: Wikipedia:Epithelium xref: XAO:0003045 xref: ZFA:0001486 -is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0000479 ! tissue intersection_of: UBERON:0000479 ! tissue intersection_of: RO:0002473 CL:0000066 ! composed primarily of epithelial cell @@ -169712,7 +172390,6 @@ property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/d/ id: UBERON:0000926 name: mesoderm namespace: uberon -alt_id: UBERON:0003263 def: "The middle germ layer of the embryo, between the endoderm and ectoderm." [Wikipedia:Mesoderm] subset: efo_slim subset: pheno_slim @@ -170254,9 +172931,7 @@ xref: ZFA:0000008 is_a: UBERON:0000062 {source="GO"} ! organ is_a: UBERON:0004121 ! ectoderm-derived structure relationship: BSPO:0000123 UBERON:0000468 ! multicellular organism -relationship: capable_of GO:0050890 {gci_relation="part_of", gci_filler="NCBITaxon:9606"} ! cognition relationship: part_of UBERON:0001017 {source="FMA"} ! central nervous system -relationship: RO:0002202 UBERON:0001049 {gci_relation="part_of", gci_filler="NCBITaxon:7711"} ! develops from neural tube relationship: RO:0002433 UBERON:0001016 ! contributes to morphology of nervous system relationship: RO:0002473 CL:0002319 ! composed primarily of neural cell relationship: RO:0002492 UBERON:0000066 ! existence ends during fully formed stage @@ -170511,7 +173186,6 @@ xref: VHOG:0000164 xref: Wikipedia:Cornea xref: XAO:0000180 xref: ZFA:0000640 -is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0010000 ! multicellular anatomical structure is_a: UBERON:0010313 ! neural crest-derived structure relationship: has_part UBERON:0001772 ! corneal epithelium @@ -170743,8 +173417,6 @@ relationship: part_of UBERON:0003252 {source="FMA"} ! thoracic rib cage relationship: RO:0002162 NCBITaxon:32523 {source="ISBN:0073040584"} ! in taxon Tetrapoda relationship: RO:0002170 UBERON:0002228 ! connected to rib relationship: RO:0002170 UBERON:0007831 ! connected to pectoral girdle skeleton -relationship: RO:0002170 UBERON:0008255 {gci_relation="part_of", gci_filler="NCBITaxon:9606", source="FMA"} ! connected to right clavicle -relationship: RO:0002170 UBERON:0008256 {gci_relation="part_of", gci_filler="NCBITaxon:9606", source="FMA"} ! connected to left clavicle relationship: RO:0002433 UBERON:0003252 ! contributes to morphology of thoracic rib cage property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/1/12/Illu_thoracic_cage.jpg" xsd:anyURI property_value: IAO:0000116 "in EMAPA and EHDAA2 this is part of the skeleton of pectoral girdle; the classic def of pectoral girdle (see WP) excludes the rib cage and sternum" xsd:string @@ -170938,9 +173610,6 @@ is_a: UBERON:0015052 ! femur endochondral element intersection_of: UBERON:0015052 ! femur endochondral element intersection_of: RO:0002473 UBERON:0002481 ! composed primarily of bone tissue relationship: proximally_connected_to UBERON:0007832 ! pelvic girdle skeleton -relationship: RO:0002170 UBERON:0000979 {gci_relation="part_of", gci_filler="NCBITaxon:9606", source="FMA"} ! connected to tibia -relationship: RO:0002170 UBERON:0001272 {gci_relation="part_of", gci_filler="NCBITaxon:9606", source="FMA"} ! connected to innominate bone -relationship: RO:0002170 UBERON:0002446 {gci_relation="part_of", gci_filler="NCBITaxon:9606", source="FMA"} ! connected to patella relationship: RO:0002202 UBERON:0010129 ! develops from femur cartilage element property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/7/73/Gray252.png" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 @@ -171302,7 +173971,6 @@ is_a: UBERON:0003134 ! female reproductive organ intersection_of: UBERON:0000991 ! gonad intersection_of: part_of UBERON:0000474 ! female reproductive system disjoint_from: UBERON:0009117 ! indifferent gonad -relationship: BSPO:0000126 UBERON:0003975 {gci_relation="part_of", gci_filler="NCBITaxon:40674", source="FMA-abduced-lr"} ! internal female genitalia relationship: RO:0002162 NCBITaxon:33208 ! in taxon Metazoa relationship: RO:0002202 UBERON:0009117 ! develops from indifferent gonad property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/d/d4/Gray589.png" xsd:anyURI @@ -171324,7 +173992,7 @@ synonym: "oviducts" RELATED OMO:0003004 [ZFA:0000560] synonym: "tuba uterina" RELATED [BTO:0000980] synonym: "tuba uterinae" RELATED [BTO:0000980] synonym: "tubular parts of female reproductive system" RELATED [http://orcid.org/0000-0002-6601-2165] -synonym: "uterine tube" EXACT [] +synonym: "uterine tube" NARROW [] xref: AAO:0010533 xref: BSA:0000083 xref: BTO:0000980 @@ -171824,7 +174492,6 @@ id: UBERON:0001009 name: circulatory system namespace: uberon def: "Organ system that passes nutrients (such as amino acids and electrolytes), gases, hormones, blood cells, etc. to and from cells in the body to help fight diseases and help stabilize body temperature and pH to maintain homeostasis[WP]." [Wikipedia:Circulatory_system] -subset: human_reference_atlas subset: uberon_slim synonym: "systema cardiovasculare" RELATED OMO:0003011 [Wikipedia:Circulatory_system] xref: AAO:0000959 @@ -171851,7 +174518,6 @@ property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/2/ property_value: RO:0002161 NCBITaxon:147099 {source="Wikipedia:Acoelomorpha"} property_value: RO:0002161 NCBITaxon:6073 property_value: RO:0002161 NCBITaxon:6157 -property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001013 @@ -172146,7 +174812,6 @@ xref: ZFA:0007009 is_a: UBERON:0000122 {source="FBbt"} ! neuron projection bundle relationship: part_of UBERON:0000010 ! peripheral nervous system relationship: RO:0000086 PATO:0002045 ! has quality dendritic -relationship: RO:0002254 UBERON:0002342 {gci_relation="part_of", gci_filler="NCBITaxon:7742", source="https://github.com/obophenotype/uberon/wiki/The-neural-crest"} ! has developmental contribution from neural crest property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -172408,12 +175073,9 @@ xref: XAO:0003227 xref: ZFA:0000056 is_a: BFO:0000002 is_a: UBERON:0006562 ! pharynx -relationship: distally_connected_to UBERON:0001043 {gci_relation="part_of", gci_filler="NCBITaxon:7742"} ! esophagus relationship: part_of UBERON:0001004 ! respiratory system -relationship: RO:0002150 UBERON:0001043 {gci_relation="part_of", gci_filler="NCBITaxon:7742"} ! continuous with esophagus relationship: RO:0002162 NCBITaxon:7711 ! in taxon Chordata relationship: RO:0002202 UBERON:0009145 {source="EHDAA2"} ! develops from pharyngeal region of foregut -relationship: RO:0002551 UBERON:0008895 {gci_relation="part_of", gci_filler="NCBITaxon:89593"} ! has skeleton splanchnocranium [Term] id: UBERON:0001043 @@ -172757,8 +175419,6 @@ xref: UMLS:C1515976 {source="ncithesaurus:Anatomic_Structure_System_or_Substance xref: WBbt:0000100 xref: XAO:0000000 xref: ZFA:0100000 -relationship: part_of UBERON:0003942 {gci_filler="GO:0050975", gci_relation="capable_of_part_of"} ! somatosensory system -relationship: part_of UBERON:0003942 {gci_relation="capable_of_part_of", gci_filler="GO:0019233"} ! somatosensory system property_value: RO:0002175 NCBITaxon:33090 property_value: RO:0002175 NCBITaxon:33208 property_value: RO:0002175 NCBITaxon:4751 @@ -172767,7 +175427,6 @@ property_value: RO:0002175 NCBITaxon:4751 id: UBERON:0001064 name: ventral pancreatic duct namespace: uberon -alt_id: UBERON:0005627 def: "A duct joining the pancreas to the common bile duct to supply pancreatic juices which aid in digestion provided by the exocrine pancreas. The pancreatic duct joins the common bile duct just prior to the ampulla of Vater, after which both ducts perforate the medial side of the second portion of the duodenum at the major duodenal papilla." [Wikipedia:Pancreatic_duct] comment: EDITOR_NOTE in EHDAA2 this is an epithelium, in FMA the wall consists of epithelium and connective tissue subset: human_reference_atlas @@ -172827,7 +175486,6 @@ xref: NCIT:C49571 xref: SCTID:244570000 xref: UMLS:C0021815 {source="ncithesaurus:Intervertebral_Disc"} xref: Wikipedia:Intervertebral_disk -is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0011135 ! intervertebral cartilage intersection_of: UBERON:0011135 ! intervertebral cartilage intersection_of: has_part UBERON:0002242 ! nucleus pulposus @@ -172946,10 +175604,8 @@ is_a: UBERON:0004087 ! vena cava intersection_of: UBERON:0004087 ! vena cava intersection_of: RO:0002179 UBERON:0000154 ! drains posterior region of body disjoint_from: UBERON:0001585 {source="lexical"} ! anterior vena cava -relationship: channels_into UBERON:0002078 {gci_relation="part_of", gci_filler="NCBITaxon:40674"} ! right cardiac atrium relationship: RO:0002170 UBERON:0002078 ! connected to right cardiac atrium relationship: RO:0002179 UBERON:0000154 ! drains posterior region of body -relationship: RO:0002202 UBERON:0005487 {gci_relation="part_of", gci_filler="NCBITaxon:40674", source="Wikipedia:Vitelline_vein"} ! develops from vitelline vein property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/4/4d/Gray577.png" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 @@ -173257,7 +175913,6 @@ is_a: UBERON:0000174 ! excreta intersection_of: UBERON:0000174 ! excreta intersection_of: produced_by UBERON:0002113 ! kidney relationship: produced_by UBERON:0002113 ! kidney -relationship: RO:0000086 PATO:0001548 {gci_relation="part_of", gci_filler="NCBITaxon:40674"} ! has quality quality of a liquid [Term] id: UBERON:0001089 @@ -173348,10 +176003,7 @@ xref: XAO:0000431 is_a: UBERON:0003913 ! tooth-like structure is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0010314 ! structure with developmental contribution from neural crest -relationship: BSPO:0000126 UBERON:0011595 {gci_relation="part_of", gci_filler="NCBITaxon:9606"} ! jaw region relationship: has_part UBERON:0001751 ! dentine -relationship: has_part UBERON:0001752 {gci_relation="part_of", gci_filler="NCBITaxon:9606"} ! enamel -relationship: part_of UBERON:0011595 {gci_relation="part_of", gci_filler="NCBITaxon:32523"} ! jaw region relationship: RO:0002254 UBERON:0000930 {source="XAO-modified"} ! has developmental contribution from stomodeum relationship: RO:0002254 UBERON:0005176 {source="ZFA-modified"} ! has developmental contribution from tooth enamel organ relationship: RO:0002495 UBERON:0008281 {source="cjm"} ! immediate transformation of tooth bud @@ -173394,9 +176046,7 @@ xref: UMLS:C0004170 {source="ncithesaurus:C1_Vertebra"} xref: Wikipedia:Atlas_(anatomy) xref: ZFA:0001167 is_a: UBERON:0002412 ! vertebra -relationship: anteriorly_connected_to UBERON:0001676 {gci_relation="part_of", gci_filler="NCBITaxon:40674", source="FMA"} ! occipital bone relationship: BSPO:0000096 UBERON:0001093 ! vertebral bone 2 -relationship: part_of UBERON:0006072 {gci_relation="part_of", gci_filler="NCBITaxon:32523"} ! cervical region of vertebral column property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -173432,14 +176082,12 @@ xref: Wikipedia:Axis_(anatomy) xref: ZFA:0001168 is_a: UBERON:0002412 ! vertebra relationship: anteriorly_connected_to UBERON:0001092 {source="FMA"} ! vertebral bone 1 -relationship: part_of UBERON:0006072 {gci_relation="part_of", gci_filler="NCBITaxon:32523"} ! cervical region of vertebral column property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001095 name: caudal vertebra namespace: uberon -alt_id: UBERON:0006070 def: "Any vertebral bone that is part of the caudal region of the vertebral column (tail or coccyx)." [http://orcid.org/0000-0002-6601-2165] comment: Taxon notes In zebrafish, Vertebra bearing a hemal arch and spine. The most posterior caudal vertebrae support the caudal fin and are referred to as preural vertebrae subset: human_reference_atlas @@ -173592,12 +176240,9 @@ xref: VHOG:0000849 xref: VSAO:0005031 xref: Wikipedia:Clavicle is_a: UBERON:0002495 {source="FMA"} ! long bone -is_a: UBERON:0003461 {gci_relation="part_of", gci_filler="NCBITaxon:32523"} ! shoulder bone is_a: UBERON:0007829 ! pectoral girdle bone is_a: UBERON:0015212 ! lateral structure relationship: BSPO:0000126 UBERON:0002091 ! appendicular skeleton -relationship: overlaps UBERON:0001469 {gci_relation="part_of", gci_filler="NCBITaxon:32523"} ! sternoclavicular joint -relationship: RO:0002170 UBERON:0000975 {gci_relation="part_of", gci_filler="NCBITaxon:9606", source="FMA"} ! connected to sternum relationship: RO:0002202 UBERON:0010905 ! develops from clavicle bone primordium relationship: RO:0002254 UBERON:0010843 ! has developmental contribution from clavicle cartilage element property_value: foaf:depiction "https://upload.wikimedia.org/wikipedia/commons/5/59/Pectoral_girdles-en.svg" xsd:anyURI @@ -173937,13 +176582,11 @@ is_a: UBERON:0002368 ! endocrine gland relationship: capable_of GO:0035898 ! parathyroid hormone secretion relationship: capable_of_part_of GO:0055074 {source="Wikipedia"} ! calcium ion homeostasis relationship: RO:0002162 NCBITaxon:32523 {source="PMID:16313389"} ! in taxon Tetrapoda -relationship: RO:0002202 UBERON:0007124 {gci_relation="part_of", gci_filler="NCBITaxon:10090", source="PMID:16313389"} ! develops from pharyngeal pouch 3 [Term] id: UBERON:0001133 name: cardiac muscle tissue namespace: uberon -alt_id: UBERON:0007096 def: "Muscle tissue composed of cardiac muscle cells, forming the muscles of the heart[ZFA,modified]." [ZFA:0005280] subset: pheno_slim subset: uberon_slim @@ -174294,7 +176937,6 @@ intersection_of: RO:0002179 UBERON:0002107 ! drains liver disjoint_from: UBERON:0001639 ! hepatic portal vein relationship: part_of UBERON:0006877 ! vasculature of liver relationship: RO:0002179 UBERON:0002107 ! drains liver -relationship: RO:0002202 UBERON:0005487 {gci_relation="part_of", gci_filler="NCBITaxon:40674", source="Wikipedia:Vitelline_vein"} ! develops from vitelline vein relationship: RO:0002376 UBERON:0001072 {source="FMA-abduced-lr"} ! tributary of inferior vena cava property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/6/61/Gray1121.png" xsd:anyURI property_value: IAO:0000116 "todo - add developmental relationships for other taxa" xsd:string @@ -174724,7 +177366,6 @@ xref: UMLS:C0017129 {source="ncithesaurus:Fundus_of_the_Stomach"} xref: VHOG:0000421 xref: Wikipedia:Fundus_(stomach) is_a: BFO:0000002 -is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0009870 ! zone of stomach relationship: has_part UBERON:0010038 ! fundic gastric gland relationship: RO:0002433 UBERON:0000945 ! contributes to morphology of stomach @@ -174760,7 +177401,6 @@ property_value: IAO:0000116 "we include this as zone of stomach even though it i id: UBERON:0001162 name: cardia of stomach namespace: uberon -alt_id: UBERON:0004712 def: "The part of the stomach attached to the esophagus. The cardia begins immediately distal to the z-line of the gastroeosphageal junction, where the squamous epithelium of the esophagus gives way to the columnar epithelium of the gastrointestinal tract[WP]." [BTO:0000198, Wikipedia:Cardia] subset: pheno_slim synonym: "antrum cardiacum" RELATED OMO:0003011 [Wikipedia:Cardia] @@ -174783,7 +177423,6 @@ xref: NCIT:C12256 xref: SCTID:362138004 xref: UMLS:C0007144 {source="ncithesaurus:Cardia"} xref: Wikipedia:Cardia -is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0009870 ! zone of stomach intersection_of: UBERON:0009870 ! zone of stomach intersection_of: has_part UBERON:0008859 ! cardiac gastric gland @@ -174861,7 +177500,6 @@ xref: UMLS:C0034196 {source="ncithesaurus:Pylorus"} xref: VHOG:0000420 xref: Wikipedia:Pylorus is_a: BFO:0000002 -is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0009870 ! zone of stomach intersection_of: UBERON:0009870 ! zone of stomach intersection_of: has_part UBERON:0001165 ! pyloric antrum @@ -175010,7 +177648,6 @@ xref: SCTID:181267003 xref: UMLS:C0005423 {source="ncithesaurus:Biliary_Tract"} xref: Wikipedia:Biliary_tract xref: XAO:0000455 -is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0004119 ! endoderm-derived structure is_a: UBERON:0013765 ! digestive system element intersection_of: UBERON:0000062 ! organ @@ -175969,7 +178606,6 @@ property_value: IAO:0000116 "currently defined as equivalent to any submucosal g id: UBERON:0001213 name: intestinal villus namespace: uberon -alt_id: UBERON:0007607 def: "The tiny hair-like projections that protrude from the inside of the small intestine that contain blood vessels that capture digested nutrients that are absorbed through the intestinal wall; the villi increase the absorptive surface area of the small intestine by approximately 30-fold." [MGI:csmith, MGI:rbabiuk, MP:0008108] subset: pheno_slim subset: uberon_slim @@ -175995,7 +178631,6 @@ xref: UMLS:C1519988 {source="ncithesaurus:Villus"} xref: Wikipedia:Intestinal_villus xref: ZFA:0005125 is_a: BFO:0000002 -is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0004923 {source="FMA"} ! organ component layer relationship: has_part CL:0000066 ! epithelial cell relationship: has_part UBERON:0001981 ! blood vessel @@ -176348,7 +178983,6 @@ property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/3/ id: UBERON:0001231 name: nephron tubule namespace: uberon -alt_id: UBERON:0004210 def: "An epithelial tube that is part of the nephron, the functional part of the kidney." [GO:0072078, Wikipedia:Renal_tubule] subset: efo_slim subset: human_reference_atlas @@ -176813,7 +179447,6 @@ property_value: foaf:depiction "https://cdn.humanatlas.io/digital-objects/ref-or id: UBERON:0001249 name: spleen lymphoid follicle namespace: uberon -alt_id: UBERON:0003969 def: "The area of the white pulp where the affinity maturation of B cells and the generation of memory B cells and plasma cells occur." [CL:tm, https://github.com/obophenotype/uberon/issues/6, MP:0008470] subset: pheno_slim synonym: "lymphatic follicle of spleen" EXACT [FMA:15843] @@ -177280,7 +179913,6 @@ xref: ZFA:0000140 is_a: BFO:0000002 is_a: UBERON:0002075 ! viscus relationship: has_part UBERON:0000016 ! endocrine pancreas -relationship: has_part UBERON:0000017 {gci_relation="part_of", gci_filler="NCBITaxon:89593"} ! exocrine pancreas relationship: RO:0002162 NCBITaxon:7742 {source="PMID:16417468"} ! in taxon Vertebrata relationship: RO:0002254 UBERON:0003923 {source="Wikipedia"} ! has developmental contribution from dorsal pancreatic bud relationship: RO:0002254 UBERON:0003924 {source="Wikipedia"} ! has developmental contribution from ventral pancreatic bud @@ -177586,7 +180218,6 @@ xref: NCIT:C33342 xref: SCTID:362192000 xref: UMLS:C0227514 {source="ncithesaurus:Portal_Triad"} xref: Wikipedia:Portal_triad -is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0004119 ! endoderm-derived structure is_a: UBERON:0034921 ! multi organ part structure relationship: has_part UBERON:0001193 ! hepatic artery @@ -177601,7 +180232,6 @@ property_value: RO:0002175 NCBITaxon:9606 id: UBERON:0001280 name: liver parenchyma namespace: uberon -alt_id: UBERON:0003223 def: "The functional units of the liver including the lobules." [MP:0008986] subset: pheno_slim synonym: "hepatic parenchyma" EXACT [FMA:17540] @@ -177631,7 +180261,6 @@ relationship: RO:0002433 UBERON:0002107 ! contributes to morphology of liver id: UBERON:0001281 name: hepatic sinusoid namespace: uberon -alt_id: UBERON:0003275 def: "Wide thin-walled blood vessels in the liver. In mammals they have neither veinous or arterial markers." [Wikipedia:Hepatic_sinusoid, ZFIN:curator] subset: human_reference_atlas subset: pheno_slim @@ -177871,7 +180500,6 @@ property_value: RO:0002175 NCBITaxon:9606 id: UBERON:0001290 name: proximal straight tubule namespace: uberon -alt_id: UBERON:0005166 def: "The proximal straight tubule is the part of the descending limb that extends from the proximal convoluted tubule to the descending thin tubule." [GO:0072020] subset: human_reference_atlas subset: uberon_slim @@ -178412,9 +181040,6 @@ xref: Wikipedia:Inferior_vesical_artery is_a: UBERON:0009027 ! vesical artery intersection_of: UBERON:0009027 ! vesical artery intersection_of: RO:0002178 UBERON:0006082 ! supplies fundus of urinary bladder -relationship: RO:0002178 UBERON:0000998 {gci_filler="UBERON:0003101", gci_relation="part_of"} ! supplies seminal vesicle -relationship: RO:0002178 UBERON:0001000 {gci_filler="UBERON:0003101", gci_relation="part_of"} ! supplies vas deferens -relationship: RO:0002178 UBERON:0002367 {gci_filler="UBERON:0003101", gci_relation="part_of"} ! supplies prostate gland relationship: RO:0002178 UBERON:0006082 ! supplies fundus of urinary bladder relationship: RO:0002252 UBERON:0001309 ! connecting branch of internal iliac artery property_value: foaf:depiction "https://upload.wikimedia.org/wikipedia/commons/1/13/Inferiorvesical.png" xsd:anyURI @@ -178845,7 +181470,6 @@ is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0005904 ! duct of male reproductive system relationship: BFO:0000067 GO:0007283 ! contains process spermatogenesis relationship: channel_for CL:0000019 ! sperm -relationship: channels_into UBERON:0003959 {gci_relation="part_of", gci_filler="NCBITaxon:40674"} ! rete testis relationship: part_of UBERON:0000473 ! testis relationship: RO:0002202 UBERON:0005297 {source="Wikipedia"} ! develops from testis sex cord property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/4/49/Seminiferous_tubule_and_sperm_low_mag.jpg" xsd:anyURI @@ -179166,7 +181790,6 @@ property_value: RO:0002175 NCBITaxon:9606 id: UBERON:0001366 name: parietal peritoneum namespace: uberon -alt_id: UBERON:0004459 def: "The outer layer of peritoneum that is attached to the abdominal and pelvic walls." [http://orcid.org/0000-0002-6601-2165, Wikipedia:Peritoneum#Types] subset: uberon_slim subset: vertebrate_core @@ -179191,7 +181814,6 @@ property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/5/ id: UBERON:0001383 name: muscle of leg namespace: uberon -alt_id: UBERON:0003270 def: "A muscle that is part of the region of the hindlimb between the pelvis and ankle." [https://orcid.org/0000-0002-6601-2165, Wikipedia:Leg_muscle] subset: human_reference_atlas subset: pheno_slim @@ -179958,7 +182580,6 @@ property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/5/ id: UBERON:0001449 name: phalanx of pes namespace: uberon -alt_id: UBERON:0004272 def: "A phalanx that is part of a hindlimb autopod[Automatically generated definition]." [https://orcid.org/0000-0002-6601-2165, Wikipedia:Phalanges_of_the_foot] subset: pheno_slim synonym: "bone of toe" RELATED [FMA:24493] @@ -180015,10 +182636,7 @@ xref: SCTID:302549007 xref: UMLS:C0015450 {source="ncithesaurus:Face"} xref: Wikipedia:Face is_a: UBERON:0001444 ! subdivision of head -relationship: has_part UBERON:0000018 {gci_filler="NCBITaxon:50557", gci_relation="part_of"} ! compound eye -relationship: has_part UBERON:0011156 {gci_relation="part_of", gci_filler="NCBITaxon:7742"} ! facial skeleton relationship: RO:0002433 UBERON:0000033 ! contributes to morphology of head -relationship: RO:0002551 UBERON:0011156 {gci_relation="part_of", gci_filler="NCBITaxon:7742"} ! has skeleton facial skeleton property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/5/55/Mona_Lisa_headcrop.jpg" xsd:anyURI [Term] @@ -180215,7 +182833,6 @@ property_value: RO:0002175 NCBITaxon:9606 id: UBERON:0001466 name: pedal digit namespace: uberon -alt_id: UBERON:0000027 def: "A digit that is part of a pes (foot)." [https://orcid.org/0000-0002-6601-2165] subset: pheno_slim subset: uberon_slim @@ -180327,7 +182944,6 @@ xref: SCTID:182165002 xref: UMLS:C0038291 {source="ncithesaurus:Sternoclavicular_Joint"} xref: Wikipedia:Sternoclavicular_articulation is_a: UBERON:0011108 {source="FMA"} ! synovial joint of pectoral girdle -is_a: UBERON:0011965 {gci_relation="part_of", gci_filler="NCBITaxon:9606", source="Wikipedia"} ! saddle joint intersection_of: UBERON:0000982 ! skeletal joint intersection_of: RO:0002176 UBERON:0000975 ! connects sternum intersection_of: RO:0002176 UBERON:0001105 ! connects clavicle bone @@ -180754,9 +183370,7 @@ intersection_of: UBERON:0000982 ! skeletal joint intersection_of: RO:0002176 UBERON:0001445 ! connects skeleton of pes intersection_of: RO:0002176 UBERON:0010720 ! connects hindlimb zeugopod skeleton relationship: overlaps UBERON:0002387 ! pes -relationship: RO:0002176 UBERON:0000979 {gci_relation="part_of", gci_filler="NCBITaxon:9606"} ! connects tibia relationship: RO:0002176 UBERON:0001445 ! connects skeleton of pes -relationship: RO:0002176 UBERON:0001446 {gci_relation="part_of", gci_filler="NCBITaxon:9606"} ! connects fibula relationship: RO:0002176 UBERON:0010720 ! connects hindlimb zeugopod skeleton property_value: foaf:depiction "https://upload.wikimedia.org/wikipedia/commons/b/bf/Ankle_en.svg" xsd:anyURI @@ -180941,7 +183555,6 @@ property_value: RO:0002175 NCBITaxon:9606 id: UBERON:0001497 name: muscle of pelvic girdle namespace: uberon -alt_id: UBERON:0003271 def: "Any muscle organ that is part of a pelvic girdle [Automatically generated definition]." [OBOL:automatic] subset: pheno_slim synonym: "girdle-pelvic muscle organ" EXACT [OBOL:automatic] @@ -180985,7 +183598,6 @@ relationship: part_of UBERON:0004488 {source="prolog"} ! musculature of pes id: UBERON:0001499 name: muscle of arm namespace: uberon -alt_id: UBERON:0003272 def: "A muscle organ that is part of an arm [Automatically generated definition]." [OBOL:automatic] subset: human_reference_atlas subset: pheno_slim @@ -181236,7 +183848,6 @@ property_value: RO:0002175 NCBITaxon:9606 id: UBERON:0001517 name: skin of elbow namespace: uberon -alt_id: UBERON:0003399 def: "A zone of skin that is part of a elbow [Automatically generated definition]." [OBOL:automatic] synonym: "cubital region zone of skin" EXACT [OBOL:automatic] synonym: "elbow skin" EXACT [] @@ -181385,7 +183996,6 @@ xref: UMLS:C0226086 {source="ncithesaurus:Right_Common_Carotid_Artery"} xref: Wikipedia:Right_common_carotid_artery is_a: UBERON:0001530 {source="FMA"} ! common carotid artery plus branches relationship: RO:0002170 UBERON:0001529 ! connected to brachiocephalic artery -relationship: RO:0002380 UBERON:0001529 {gci_relation="part_of", gci_filler="NCBITaxon:40674", source="FMA"} ! branching part of brachiocephalic artery property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/e/e6/Gray506.svg" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 @@ -181496,7 +184106,6 @@ intersection_of: UBERON:0001533 ! subclavian artery intersection_of: BSPO:0000121 UBERON:0000468 ! multicellular organism relationship: BSPO:0000121 UBERON:0000468 ! multicellular organism relationship: RO:0002170 UBERON:0001529 ! connected to brachiocephalic artery -relationship: RO:0002380 UBERON:0001529 {gci_relation="part_of", gci_filler="NCBITaxon:40674", source="FMA"} ! branching part of brachiocephalic artery property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/e/e6/Gray506.svg" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 @@ -182704,7 +185313,6 @@ is_a: UBERON:0002017 {source="MA"} ! portal vein relationship: channels_into UBERON:0002107 ! liver relationship: overlaps UBERON:0002107 ! liver relationship: part_of UBERON:0010194 ! hepatic portal system -relationship: RO:0002202 UBERON:0005487 {gci_relation="part_of", gci_filler="NCBITaxon:40674", source="Wikipedia:Vitelline_vein"} ! develops from vitelline vein property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/3/33/Gray591.png" xsd:anyURI property_value: foaf:depiction "https://cdn.humanatlas.io/digital-objects/ref-organ/blood-vasculature-female/v1.3/assets/3d-vh-f-blood-vasculature.glb" xsd:anyURI property_value: foaf:depiction "https://cdn.humanatlas.io/digital-objects/ref-organ/blood-vasculature-male/v1.3/assets/3d-vh-m-blood-vasculature.glb" xsd:anyURI @@ -182744,7 +185352,6 @@ relationship: indirectly_supplies UBERON:0000160 {source="ISBN:0073040584"} ! in relationship: indirectly_supplies UBERON:0000945 {source="ISBN:0073040584"} ! stomach relationship: indirectly_supplies UBERON:0002106 {source="ISBN:0073040584"} ! spleen relationship: indirectly_supplies UBERON:0002107 {source="ISBN:0073040584"} ! liver -relationship: RO:0002202 UBERON:0006002 {gci_relation="part_of", gci_filler="NCBITaxon:40674", source="Wikipedia"} ! develops from vitelline artery property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/6/65/Gray532.png" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 @@ -183263,8 +185870,6 @@ relationship: overlaps UBERON:0002241 ! chondrocranium relationship: overlaps UBERON:0003113 ! dermatocranium relationship: part_of UBERON:0005902 {source="FMA"} ! occipital region relationship: RO:0002162 NCBITaxon:117570 {source="WP"} ! in taxon Teleostomi -relationship: RO:0002170 UBERON:0001092 {gci_relation="part_of", gci_filler="NCBITaxon:9606", source="FMA"} ! connected to vertebral bone 1 -relationship: RO:0002170 UBERON:0001677 {gci_relation="part_of", gci_filler="NCBITaxon:9606", source="FMA"} ! connected to sphenoid bone relationship: RO:0002202 UBERON:0003089 {source="PMID:11523816"} ! develops from sclerotome relationship: RO:0002221 UBERON:0003687 ! surrounds foramen magnum property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/2/27/Gray194.png" xsd:anyURI @@ -183304,10 +185909,6 @@ intersection_of: RO:0002473 UBERON:0002481 ! composed primarily of bone tissue relationship: overlaps UBERON:0002241 ! chondrocranium relationship: overlaps UBERON:0003113 ! dermatocranium relationship: overlaps UBERON:0008895 ! splanchnocranium -relationship: RO:0002170 UBERON:0000209 {gci_relation="part_of", gci_filler="NCBITaxon:9606", source="FMA"} ! connected to tetrapod frontal bone -relationship: RO:0002170 UBERON:0001676 {gci_relation="part_of", gci_filler="NCBITaxon:9606", source="FMA"} ! connected to occipital bone -relationship: RO:0002170 UBERON:0001679 {gci_relation="part_of", gci_filler="NCBITaxon:9606", source="FMA"} ! connected to ethmoid bone -relationship: RO:0002170 UBERON:0002396 {gci_relation="part_of", gci_filler="NCBITaxon:9606", source="FMA"} ! connected to vomer relationship: RO:0002202 UBERON:0009193 {source="cjm"} ! develops from sphenoid cartilage element property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/6/66/Illu_cranial_bones2.jpg" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 @@ -183366,9 +185967,6 @@ is_a: UBERON:0003462 ! facial bone is_a: UBERON:0011164 ! neurocranium bone relationship: part_of UBERON:0002517 ! basicranium relationship: part_of UBERON:0011241 ! ethmoid region -relationship: RO:0002170 UBERON:0000209 {gci_relation="part_of", gci_filler="NCBITaxon:9606", source="FMA"} ! connected to tetrapod frontal bone -relationship: RO:0002170 UBERON:0001677 {gci_relation="part_of", gci_filler="NCBITaxon:9606", source="FMA"} ! connected to sphenoid bone -relationship: RO:0002170 UBERON:0002396 {gci_relation="part_of", gci_filler="NCBITaxon:9606", source="FMA"} ! connected to vomer relationship: RO:0002202 UBERON:0006227 ! develops from ethmoid bone primordium relationship: RO:0002433 UBERON:0011156 ! contributes to morphology of facial skeleton property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/6/66/Illu_cranial_bones2.jpg" xsd:anyURI @@ -183921,8 +186519,6 @@ property_value: foaf:depiction "https://upload.wikimedia.org/wikipedia/commons/8 id: UBERON:0001714 name: cranial ganglion namespace: uberon -alt_id: UBERON:0003213 -alt_id: UBERON:0026601 def: "The groups of nerve cell bodies associated with the twelve cranial nerves." [ISBN:0-683-40008-8, MGI:csmith, MP:0001081, PMID:9362461] subset: efo_slim subset: human_reference_atlas @@ -184364,7 +186960,6 @@ xref: EMAPA:37769 {source="MA:th"} xref: FMA:55515 xref: MA:0000730 xref: SCTID:371402001 -is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0000353 ! parenchyma is_a: UBERON:0004119 ! endoderm-derived structure is_a: UBERON:0010314 ! structure with developmental contribution from neural crest @@ -184386,7 +186981,6 @@ xref: FMA:55566 xref: MA:0002676 xref: NCIT:C33265 xref: UMLS:C0927176 {source="ncithesaurus:Parathyroid_Gland_Capsule"} -is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0003893 ! capsule intersection_of: UBERON:0003893 ! capsule intersection_of: bounding_layer_of UBERON:0001132 ! parathyroid gland @@ -184749,7 +187343,6 @@ intersection_of: part_of UBERON:0008281 ! tooth bud intersection_of: RO:0002473 CL:0007003 ! composed primarily of preodontoblast relationship: BSPO:0001107 UBERON:0005176 ! tooth enamel organ relationship: part_of UBERON:0008281 ! tooth bud -relationship: RO:0001025 UBERON:0001828 {gci_relation="part_of", gci_filler="NCBITaxon:9606", source="FMA-implied"} ! located in gingiva relationship: RO:0002202 UBERON:0003856 {source="ZFA"} ! develops from uncondensed odontogenic mesenchyme relationship: RO:0002473 CL:0007003 ! composed primarily of preodontoblast property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/2/22/Gray1011.png" xsd:anyURI @@ -184954,7 +187547,6 @@ xref: TAO:0002187 xref: UMLS:C0459875 {source="ncithesaurus:Corneal_Epithelium"} xref: Wikipedia:Corneal_epithelium xref: ZFA:0001683 -is_a: UBERON:0000488 {gci_relation="part_of", gci_filler="NCBITaxon:9606", source="FMA"} ! atypical epithelium is_a: UBERON:0010313 ! neural crest-derived structure is_a: UBERON:0015808 ! eye epithelium intersection_of: UBERON:0000483 ! epithelium @@ -185630,7 +188222,6 @@ property_value: RO:0002175 NCBITaxon:9606 id: UBERON:0001793 name: nerve fiber layer of retina namespace: uberon -alt_id: UBERON:0005888 def: "Layer of the retina formed by expansion of the fibers of the optic nerve." [ISBN:0-914294-08-3, MGI:smb] subset: pheno_slim subset: vertebrate_core @@ -185994,7 +188585,6 @@ xref: UMLS:C0229232 {source="ncithesaurus:Lens_Capsule"} xref: VHOG:0000550 xref: Wikipedia:Lens_(anatomy)#Lens_capsule xref: ZFA:0005574 -is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0005764 ! acellular membrane intersection_of: UBERON:0000476 ! acellular anatomical structure @@ -186073,7 +188663,6 @@ property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/f/ id: UBERON:0001807 name: paravertebral ganglion namespace: uberon -alt_id: UBERON:0005466 def: "Trunk ganglion which is part of a bilaterally paired set of sympathetic ganglia located anterior and lateral to the spinal cord." [Wikipedia:Paravertebral_ganglion, ZFIN:curator] subset: human_reference_atlas subset: uberon_slim @@ -186531,7 +189120,6 @@ xref: MESH:D013666 xref: NCIT:C33739 xref: UMLS:C0039409 {source="ncithesaurus:Tear"} xref: Wikipedia:Tear -is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0000456 ! secretion of exocrine gland intersection_of: UBERON:0000456 ! secretion of exocrine gland intersection_of: produced_by UBERON:0001817 ! lacrimal gland @@ -186612,7 +189200,6 @@ property_value: RO:0002161 NCBITaxon:8782 id: UBERON:0001834 name: upper lip namespace: uberon -alt_id: UBERON:0003391 def: "Lip that covers the upper portion of the mouth.[TAO]." [TAO:0001970, Wikipedia:Upper_lip] subset: pheno_slim subset: uberon_slim @@ -186639,7 +189226,6 @@ property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/d/ id: UBERON:0001835 name: lower lip namespace: uberon -alt_id: UBERON:0003392 def: "Lip that covers the lower portion of the mouth.[TAO]." [TAO:0002060, Wikipedia:Lower_lip] subset: pheno_slim subset: uberon_slim @@ -186826,7 +189412,6 @@ xref: ZFA:0000374 is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0034921 ! multi organ part structure relationship: part_of UBERON:0001839 {source="FMA", source="VHOG", source="XAO", source="ncit"} ! bony labyrinth -relationship: RO:0000086 PATO:0000404 {gci_relation="part_of", gci_filler="NCBITaxon:32525", source="Wikipedia"} ! has quality coiled relationship: RO:0002433 UBERON:0001846 ! contributes to morphology of internal ear property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/c/c7/Cochlea-crosssection.png" xsd:anyURI property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/c/cb/Cochlea-crosssection.svg" xsd:anyURI @@ -186923,7 +189508,6 @@ relationship: part_of UBERON:0001867 ! cartilage of external ear id: UBERON:0001849 name: membranous labyrinth namespace: uberon -alt_id: UBERON:0010113 def: "Organ with organ cavity which consists of the vestibular labyrinth and the cochlear labyrinth. The membranous labyrinth is lodged within the bony labyrinth and has the same general form; it is, however, considerably smaller and is partly separated from the bony walls by a quantity of fluid, the perilymph.[FMA, WP]." [FMA:61022, Wikipedia:Membranous_labyrinth] subset: organ_slim subset: pheno_slim @@ -187357,7 +189941,6 @@ property_value: RO:0002175 NCBITaxon:9606 id: UBERON:0001873 name: caudate nucleus namespace: uberon -alt_id: UBERON:0010122 def: "Subcortical nucleus of telecephalic origin consisting of an elongated gray mass lying lateral to and bordering the lateral ventricle. It is divided into a head, body and tail in some species." [BIRNLEX:1373] subset: efo_slim subset: human_reference_atlas @@ -187523,8 +190106,6 @@ xref: UMLS:C0262264 {source="BIRNLEX:1113"} xref: Wikipedia:Islands_of_Calleja is_a: UBERON:0009663 ! telencephalic nucleus relationship: part_of UBERON:0001869 ! cerebral hemisphere -relationship: part_of UBERON:0001882 {gci_relation="part_of", gci_filler="NCBITaxon:9443", source="MP"} ! nucleus accumbens -relationship: part_of UBERON:0001883 {gci_relation="part_of", gci_filler="NCBITaxon:9989", source="MP"} ! olfactory tubercle relationship: RO:0002433 UBERON:0001882 ! contributes to morphology of nucleus accumbens relationship: RO:0002433 UBERON:0001883 ! contributes to morphology of olfactory tubercle property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/c/c0/Islands_of_Calleja_Rat.jpg" xsd:anyURI @@ -187674,7 +190255,6 @@ xref: neuronames:179 xref: SCTID:279211002 xref: UMLS:C0152314 {source="ncithesaurus:Dentate_Gyrus"} xref: Wikipedia:Dentate_gyrus -is_a: UBERON:0000200 {gci_relation="part_of", gci_filler="NCBITaxon:9606", source="FMA"} ! gyrus is_a: UBERON:0002616 ! regional part of brain relationship: part_of UBERON:0002421 {source="MA"} ! hippocampal formation property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/a/ab/HippocampalRegions.jpg" xsd:anyURI @@ -188269,7 +190849,6 @@ property_value: RO:0002175 NCBITaxon:9606 id: UBERON:0001901 name: epithelium of trachea namespace: uberon -alt_id: UBERON:0003227 def: "The epithelial lining of the trachea which contains numerous ciliated cells." [ISBN:0-397-51047-0, MGI:cwg, MP:0002285] subset: human_reference_atlas subset: pheno_slim @@ -188541,7 +191120,6 @@ xref: UMLS:C1511310 {source="ncithesaurus:Breast_Fluid_or_Secretion"} xref: VHOG:0001263 xref: Wikipedia:Breast_milk is_a: BFO:0000002 -is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0006314 ! bodily fluid is_a: UBERON:0006539 ! mammary gland fluid/secretion relationship: has_part CHEBI:18059 @@ -188735,7 +191313,6 @@ xref: Wikipedia:Preoptic_area xref: ZFA:0000470 is_a: UBERON:0002616 ! regional part of brain relationship: part_of UBERON:0001894 ! diencephalon -relationship: part_of UBERON:0001898 {gci_relation="part_of", gci_filler="NCBITaxon:32524", source="PMC4038951"} ! hypothalamus property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/8/8c/HypothalamicNuclei.PNG" xsd:anyURI property_value: RO:0002175 NCBITaxon:7742 @@ -188960,7 +191537,6 @@ property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/7/ id: UBERON:0001951 name: epithelium of nasopharynx namespace: uberon -alt_id: UBERON:0003237 def: "An epithelium that is part of a nasopharynx [Automatically generated definition]." [OBOL:automatic] synonym: "epithelial tissue of nasal part of pharynx" EXACT [OBOL:automatic] synonym: "epithelial tissue of nasopharynx" EXACT [OBOL:automatic] @@ -188995,8 +191571,6 @@ relationship: part_of UBERON:0003929 {source="EHDAA2"} ! digestive tract epithel id: UBERON:0001954 name: Ammon's horn namespace: uberon -alt_id: UBERON:0003940 -alt_id: UBERON:0004165 def: "A part of the brain consisting of a three layered cortex located in the forebrain bordering the medial surface of the lateral ventricle. The term hippocampus is often used synonymously with hippocampal formation which consists of the hippocampus proper or Cornu Ammonis, the dentate gyrus and the subiculum." [BIRNLEX:721] subset: efo_slim subset: pheno_slim @@ -189091,7 +191665,6 @@ xref: MA:0001835 xref: NCIT:C49209 xref: SCTID:278980009 xref: UMLS:C0225604 {source="ncithesaurus:Bronchus_Cartilage"} -is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0003603 ! lower respiratory tract cartilage intersection_of: UBERON:0007844 ! cartilage element intersection_of: part_of UBERON:0002185 ! bronchus @@ -189326,7 +191899,6 @@ xref: MIAA:0000052 xref: NCIT:C13356 xref: UMLS:C0032105 {source="ncithesaurus:Plasma"} xref: Wikipedia:Blood_plasma -is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0000179 ! haemolymphatic fluid intersection_of: UBERON:0000463 ! organism substance intersection_of: has_part GO:0005577 ! fibrinogen complex @@ -189636,7 +192208,6 @@ xref: VHOG:0001250 xref: Wikipedia:Blood_vessel xref: XAO:0001011 xref: ZFA:0005314 -is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0000055 ! vessel is_a: UBERON:0004120 ! mesoderm-derived structure relationship: capable_of_part_of GO:0008015 ! blood circulation @@ -189933,7 +192504,6 @@ xref: NCIT:C94819 xref: UMLS:C0221930 {source="ncithesaurus:Stratum_Papillare"} xref: UMLS:C0682598 {source="ncithesaurus:Papillary_Dermis"} xref: Wikipedia:Papillary_dermis -is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0013754 ! integumentary system layer relationship: part_of UBERON:0002067 ! dermis @@ -189989,7 +192559,6 @@ xref: UMLS:C0225362 {source="ncithesaurus:Hyaline_Cartilage"} xref: VSAO:0000094 xref: Wikipedia:Hyaline_cartilage xref: XAO:0004029 -is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0002418 {source="FMA"} ! cartilage tissue relationship: RO:0002473 GO:0005585 {source="VSAO-text-def"} ! composed primarily of collagen type II trimer property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/2/2a/Gray292.png" xsd:anyURI @@ -190014,7 +192583,6 @@ xref: UMLS:C0684077 {source="ncithesaurus:Fibrocartilage"} xref: VSAO:0000103 xref: Wikipedia:Fibrocartilage xref: XAO:0004028 -is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0002418 ! cartilage tissue relationship: has_part GO:0005584 ! collagen type I trimer property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/2/2e/Gray295.png" xsd:anyURI @@ -190050,7 +192618,6 @@ property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/c/ id: UBERON:0001997 name: olfactory epithelium namespace: uberon -alt_id: UBERON:0004853 def: "A sensory epithelium inside the nasal cavity that is responsible for detecting odors[WP]." [Wikipedia:Olfactory_epithelium] comment: Genes: V1Rs, Trpc2 present in lamprey subset: efo_slim @@ -190610,7 +193177,6 @@ xref: NCIT:C12850 xref: SCTID:420086000 xref: UMLS:C0221924 {source="ncithesaurus:Stratum_Spinosum"} xref: Wikipedia:Stratum_spinosum -is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0013754 ! integumentary system layer intersection_of: UBERON:0013754 ! integumentary system layer @@ -190763,7 +193329,6 @@ xref: UMLS:C0028109 {source="ncithesaurus:Nipple"} xref: Wikipedia:Nipple is_a: UBERON:0000475 ! organism subdivision is_a: UBERON:0004121 ! ectoderm-derived structure -relationship: part_of UBERON:0000310 {gci_relation="part_of", gci_filler="NCBITaxon:9606", source="FMA"} ! breast relationship: part_of UBERON:0001911 ! mammary gland relationship: RO:0002162 NCBITaxon:32525 ! in taxon Theria relationship: RO:0002202 UBERON:0008425 {source="Stedmans"} ! develops from mammary ridge @@ -191138,10 +193703,10 @@ is_a: UBERON:0004119 ! endoderm-derived structure is_a: UBERON:0005178 ! thoracic cavity element is_a: UBERON:0015212 ! lateral structure relationship: BSPO:0000126 UBERON:0000170 ! pair of lungs -relationship: part_of UBERON:0000170 {note="some species only have a single lung"} ! pair of lungs +relationship: has_part UBERON:0002185 ! bronchus +relationship: part_of UBERON:0000170 ! pair of lungs relationship: RO:0002162 NCBITaxon:7776 ! in taxon Gnathostomata relationship: RO:0002202 UBERON:0000118 ! develops from lung bud -relationship: RO:0002219 UBERON:0009778 {gci_relation="part_of", gci_filler="NCBITaxon:9606", source="FMA"} ! surrounded by pleural sac relationship: RO:0002433 UBERON:0001004 ! contributes to morphology of respiratory system property_value: foaf:depiction "https://cdn.humanatlas.io/digital-objects/ref-organ/lung-female/v1.4/assets/3d-vh-f-lung.glb" xsd:anyURI property_value: foaf:depiction "https://cdn.humanatlas.io/digital-objects/ref-organ/lung-male/v1.4/assets/3d-vh-m-lung.glb" xsd:anyURI @@ -191230,8 +193795,8 @@ is_a: UBERON:0008397 ! tracheobronchial epithelium intersection_of: UBERON:0000483 ! epithelium intersection_of: part_of UBERON:0002186 ! bronchiole relationship: has_part CL:0000158 ! club cell -relationship: has_part CL:0002145 {source="FMA"} ! ciliated columnar cell of tracheobronchial tree -relationship: has_part CL:1000271 ! lung ciliated cell +relationship: has_part CL:0002145 {source="FMA"} ! multiciliated columnar cell of tracheobronchial tree +relationship: has_part CL:1000271 ! lung multiciliated epithelial cell relationship: part_of UBERON:0005039 ! mucosa of bronchiole relationship: RO:0002433 UBERON:0002186 ! contributes to morphology of bronchiole property_value: RO:0002175 NCBITaxon:9606 @@ -191249,7 +193814,6 @@ xref: FMA:69087 xref: MA:0000117 xref: NCIT:C32050 xref: UMLS:C1181304 {source="ncithesaurus:Adrenal_Gland_Capsule"} -is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0003893 ! capsule is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0010313 ! neural crest-derived structure @@ -191502,7 +194066,6 @@ xref: VHOG:0000108 xref: Wikipedia:Dermis xref: XAO:0000217 xref: ZFA:0001119 -is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0010314 ! structure with developmental contribution from neural crest is_a: UBERON:0013754 ! integumentary system layer @@ -191571,7 +194134,6 @@ xref: TAO:0001136 xref: UMLS:C0278403 {source="ncithesaurus:Subcutis"} xref: Wikipedia:Hypodermis xref: ZFA:0001136 -is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0013754 ! integumentary system layer relationship: BSPO:0000107 UBERON:0002067 ! dermis @@ -192198,7 +194760,6 @@ xref: SCTID:181469002 xref: UMLS:C1123023 {source="ncithesaurus:Skin"} xref: Wikipedia:Skin xref: XAO:0000023 -is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0000062 ! organ is_a: UBERON:0004121 ! ectoderm-derived structure relationship: part_of UBERON:0002199 ! integument @@ -192271,8 +194832,6 @@ xref: XAO:0003025 xref: ZFA:0001115 is_a: UBERON:0011676 ! subdivision of organism along main body axis disjoint_from: UBERON:0002464 ! nerve trunk -relationship: has_part UBERON:0000915 {gci_relation="part_of", gci_filler="NCBITaxon:7742"} ! thoracic segment of trunk -relationship: has_part UBERON:0000916 {gci_relation="part_of", gci_filler="NCBITaxon:7742"} ! abdomen relationship: part_of UBERON:0013702 ! body proper [Term] @@ -192314,7 +194873,7 @@ xref: XAO:0003027 is_a: UBERON:0004708 ! paired limb/fin intersection_of: UBERON:0000475 ! organism subdivision intersection_of: RO:0002551 UBERON:0004381 ! has skeleton skeleton of limb -relationship: RO:0002162 NCBITaxon:32523 {note="extends to stem tetrapods such as Eusthenopteron"} ! in taxon Tetrapoda +relationship: RO:0002162 NCBITaxon:32523 ! in taxon Tetrapoda relationship: RO:0002202 UBERON:0004347 ! develops from limb bud relationship: RO:0002492 UBERON:0000066 ! existence ends during fully formed stage relationship: RO:0002551 UBERON:0004381 ! has skeleton skeleton of limb @@ -192428,7 +194987,6 @@ property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/d/ id: UBERON:0002104 name: visual system namespace: uberon -alt_id: UBERON:0007036 def: "The sensory system subserving the sense of vision." [NIFSTD:FMAID_7191] subset: pheno_slim subset: uberon_slim @@ -192957,7 +195515,6 @@ relationship: BSPO:0000120 UBERON:0000468 ! multicellular organism id: UBERON:0002120 name: pronephros namespace: uberon -alt_id: UBERON:0005794 def: "In mammals, the pronephros is the first of the three embryonic kidneys to be established and exists only transiently. In lower vertebrates such as fish and amphibia, the pronephros is the fully functional embryonic kidney and is indispensible for larval life[GO]." [GO:0048793, Wikipedia:Pronephros] comment: Once the more complex mesonephros forms the pronephros undergoes apoptosis in amphibians. In fishes the nephron degenerates but the organ remains and becomes a component of the immune system[Wikipedia:Pronephros]. // TODO - check developmental relationships. Note that we previously include the ZFA/XAO terms under the more specific 'pronephric kidney', but these are now merged. TODO GCI: relationship: capable_of GO:0030104 subset: efo_slim @@ -193201,7 +195758,6 @@ xref: TAO:0000683 xref: UMLS:C0038533 {source="BIRNLEX:1028"} xref: Wikipedia:Subcommissural_organ xref: ZFA:0000683 -is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0010134 {source="MA"} ! secretory circumventricular organ relationship: has_part CL:0000065 ! ependymal cell relationship: part_of UBERON:0002314 {source="MA"} ! midbrain tectum @@ -193299,7 +195855,6 @@ property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/6/ id: UBERON:0002165 name: endocardium namespace: uberon -alt_id: UBERON:0006225 def: "The endocardium is an anatomical structure comprised of an endothelium and an extracellular matrix that forms the innermost layer of tissue of the heart, and lines the heart chambers[GO]." [GO:0003157] comment: fixed in GO to reflect FMA. See email to David/Varsha June 18 2010 subset: efo_slim @@ -193423,7 +195978,6 @@ property_value: foaf:depiction "https://cdn.humanatlas.io/digital-objects/ref-or id: UBERON:0002169 name: alveolar sac namespace: uberon -alt_id: UBERON:0008871 def: "The small terminal dilation of the alveolar ducts around which the alveoli form pocket-like clusters." [MP:0010902, Wikipedia:Alveolar_sac] subset: pheno_slim subset: uberon_slim @@ -193694,7 +196248,6 @@ property_value: RO:0002175 NCBITaxon:9606 id: UBERON:0002190 name: subcutaneous adipose tissue namespace: uberon -alt_id: UBERON:0008875 def: "A portion of adipose tissue that is part of the hypodermis, beneath the dermis." [http://orcid.org/0000-0002-6601-2165] subset: human_reference_atlas subset: pheno_slim @@ -194023,7 +196576,6 @@ xref: VSAO:0000029 xref: Wikipedia:Integument xref: ZFA:0000368 is_a: BFO:0000002 -is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0011216 {source="FMA"} ! organ system subdivision relationship: bounding_layer_of UBERON:0000468 ! multicellular organism relationship: has_part UBERON:0002072 ! hypodermis @@ -194387,7 +196939,6 @@ xref: FMA:7497 xref: MA:0001501 xref: SCTID:42903008 xref: Wikipedia:Synchondrosis -is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0002209 ! fibrous joint is_a: UBERON:0002213 ! cartilaginous joint intersection_of: UBERON:0002209 ! fibrous joint @@ -194727,7 +197278,6 @@ xref: FMA:76703 xref: MA:0000112 xref: SCTID:316586000 xref: Wikipedia:Nucleus_pulposus -is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0000062 ! organ is_a: UBERON:0002384 ! connective tissue is_a: UBERON:0004120 ! mesoderm-derived structure @@ -194775,7 +197325,6 @@ is_a: UBERON:0004121 ! ectoderm-derived structure relationship: capable_of GO:0043695 {source="Wikipedia"} ! detection of pheromone relationship: part_of UBERON:0000004 ! nose relationship: part_of UBERON:0009954 ! vomeronasal system -relationship: RO:0000086 PATO:0000588 {gci_relation="part_of", gci_filler="NCBITaxon:314295"} ! has quality vestigial relationship: RO:0002162 NCBITaxon:8287 ! in taxon Sarcopterygii relationship: RO:0002202 UBERON:0003050 {source="Wikipedia"} ! develops from olfactory placode relationship: RO:0002254 UBERON:0009714 {source="EHDAA2-abduced"} ! has developmental contribution from intermaxillary process @@ -195343,7 +197892,6 @@ relationship: part_of UBERON:0002422 ! fourth ventricle id: UBERON:0002291 name: central canal of spinal cord namespace: uberon -alt_id: UBERON:0002220 def: "Spinal cord structure that is part of the ventricular system and is filled with cerebral-spinal fluid and runs the length of the spinal cord." [PMID:23409159, ZFIN:curator] comment: previously mapped to FMA:75364. Note some ontologies (NIF, SNOMED) subdivide this into lumbar, thoracic, etc. Note we follow FMA in distinguishing between the canal and the lumen subset: human_reference_atlas @@ -195402,7 +197950,6 @@ xref: NCIT:C12678 xref: SCTID:361354009 xref: Wikipedia:Biliary_system is_a: BFO:0000002 -is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0011216 ! organ system subdivision intersection_of: UBERON:0011216 ! organ system subdivision intersection_of: capable_of GO:0006699 ! bile acid biosynthetic process @@ -195590,7 +198137,6 @@ xref: SCTID:362219002 xref: UMLS:C0022445 {source="ncithesaurus:Juxtaglomerular_Apparatus"} xref: Wikipedia:Juxtaglomerular_apparatus is_a: BFO:0000002 -is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0000061 ! anatomical structure relationship: capable_of GO:0003093 {source="GO"} ! regulation of glomerular filtration relationship: has_part CL:0000648 ! kidney granular cell @@ -195754,7 +198300,6 @@ property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/6/ id: UBERON:0002313 name: hippocampus pyramidal layer namespace: uberon -alt_id: UBERON:0005369 def: "A cytoarchitectural term denoting the layer of the hippocampus in which pyramidal cells are predominant. Its location is superficial to the Stratum oriens; it is deep to the Stratum radiatum in area CA1 and area CA2 and deep to the Stratum lucidum in area CA3 (Stephan-75) (NeuroNames)." [BIRNLEX:1444] comment: EDITOR_NOTE this layer changes in its depthwise spatial relation across its extent subset: pheno_slim @@ -196001,7 +198546,6 @@ is_a: UBERON:0002308 ! nucleus of brain id: UBERON:0002323 name: coelemic cavity lumen namespace: uberon -alt_id: UBERON:0000169 def: "The cavity within the body of all animals higher than the coelenterates and certain primitive worms, formed by the splitting of the embryonic mesoderm into two layers. In mammals it forms the peritoneal, pleural, and pericardial cavities." [BTO:0001707] comment: EDITOR_NOTE check the FMA placement here; ncit placement of body cavity here probably not correct subset: uberon_slim @@ -196027,7 +198571,6 @@ xref: RETIRED_EHDAA2:0003186 xref: SCTID:361348008 xref: TAO:0001438 xref: UMLS:C0333343 {source="ncithesaurus:Cavity"} -xref: ZFA:0001438 is_a: BFO:0000002 is_a: UBERON:0002553 ! anatomical cavity relationship: RO:0002494 UBERON:0003886 ! transformation of future coelemic cavity lumen @@ -196151,7 +198694,6 @@ is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0004121 ! ectoderm-derived structure relationship: BSPO:0000098 UBERON:0001555 ! digestive tract relationship: BSPO:0000102 UBERON:0001049 ! neural tube -relationship: part_of UBERON:0000922 {gci_relation="part_of", gci_filler="NCBITaxon:40674"} ! embryo relationship: part_of UBERON:0011137 ! axial skeletal system relationship: produces PR:000014841 ! sonic hedgehog protein relationship: RO:0002162 NCBITaxon:7711 {source="http://tolweb.org/Chordata/2499"} ! in taxon Chordata @@ -196220,7 +198762,6 @@ xref: NCIT:C12957 xref: UMLS:C1516995 {source="ncithesaurus:Exocrine_System"} xref: Wikipedia:Exocrine_gland xref: WikipediaCategory:Exocrine_system -is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0000467 ! anatomical system disjoint_from: UBERON:0002390 ! hematopoietic system disjoint_from: UBERON:0002405 ! immune system @@ -196296,7 +198837,6 @@ xref: VHOG:0001134 is_a: UBERON:0001637 {source="MA"} ! artery relationship: part_of UBERON:0008886 ! pulmonary vascular system relationship: RO:0002150 UBERON:0000948 ! continuous with heart -relationship: RO:0002150 UBERON:0002080 {gci_relation="part_of", gci_filler="NCBITaxon:40674"} ! continuous with heart right ventricle relationship: RO:0002170 UBERON:0002080 ! connected to heart right ventricle property_value: foaf:depiction "https://cdn.humanatlas.io/digital-objects/ref-organ/blood-vasculature-female/v1.3/assets/3d-vh-f-blood-vasculature.glb" xsd:anyURI property_value: foaf:depiction "https://cdn.humanatlas.io/digital-objects/ref-organ/blood-vasculature-male/v1.3/assets/3d-vh-m-blood-vasculature.glb" xsd:anyURI @@ -196402,7 +198942,7 @@ is_a: UBERON:0002031 ! epithelium of bronchus intersection_of: UBERON:0000483 ! epithelium intersection_of: part_of UBERON:0002183 ! lobar bronchus relationship: has_part CL:0002329 ! basal epithelial cell of tracheobronchial tree -relationship: has_part CL:0002332 ! ciliated cell of the bronchus +relationship: has_part CL:0002332 ! multiciliated epithelial cell of the bronchus relationship: has_part CL:0017000 ! pulmonary ionocyte relationship: part_of UBERON:0002183 ! lobar bronchus property_value: RO:0002175 NCBITaxon:9606 @@ -196433,10 +198973,10 @@ intersection_of: part_of UBERON:0002184 ! segmental bronchus relationship: has_part CL:0000158 ! club cell relationship: has_part CL:0002208 ! brush cell of bronchus relationship: has_part CL:0002329 ! basal epithelial cell of tracheobronchial tree -relationship: has_part CL:0002332 ! ciliated cell of the bronchus +relationship: has_part CL:0002332 ! multiciliated epithelial cell of the bronchus relationship: has_part CL:0017000 ! pulmonary ionocyte relationship: has_part CL:1000143 ! lung goblet cell -relationship: has_part CL:1000223 ! lung neuroendocrine cell +relationship: has_part CL:1000223 ! pulmonary neuroendocrine cell relationship: part_of UBERON:0002184 ! segmental bronchus property_value: RO:0002175 NCBITaxon:9606 property_value: terms:contributor https://orcid.org/0000-0001-6677-8489 @@ -196845,7 +199385,6 @@ property_value: RO:0002175 NCBITaxon:9606 id: UBERON:0002354 name: cardiac Purkinje fiber namespace: uberon -alt_id: UBERON:0004147 def: "The cardiac Purkinje fiber is part of the cardiac conduction system that receives signals from the bundle of His and innervates the ventricular cardiac muscle." [GO:0003165] subset: pheno_slim subset: uberon_slim @@ -197175,7 +199714,6 @@ xref: NCIT:C12712 xref: SCTID:115976003 xref: UMLS:C0015282 {source="ncithesaurus:Exocrine_Gland"} xref: Wikipedia:Exocrine_gland -is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0002530 ! gland intersection_of: UBERON:0002530 ! gland intersection_of: part_of UBERON:0002330 ! exocrine system @@ -197337,7 +199875,6 @@ xref: VHOG:0000253 xref: Wikipedia:Thymus xref: XAO:0000163 xref: ZFA:0001078 -is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0000077 ! mixed endoderm/mesoderm-derived structure is_a: UBERON:0002368 {source="EHDAA2"} ! endocrine gland is_a: UBERON:0004177 ! hemopoietic organ @@ -197409,6 +199946,7 @@ name: tonsil namespace: uberon def: "Either of the two small almond-shaped masses of lymph tissue found on either side of the oropharynx." [MGI:cwg, MP:0002380] subset: efo_slim +subset: human_reference_atlas subset: pheno_slim subset: uberon_slim synonym: "Mandel" RELATED [BTO:0001387] @@ -197432,6 +199970,7 @@ is_a: UBERON:0001962 ! gut-associated lymphoid tissue relationship: part_of UBERON:0001735 {source="cjm"} ! tonsillar ring relationship: RO:0001025 UBERON:0000167 ! located in oral cavity relationship: RO:0002433 UBERON:0001735 ! contributes to morphology of tonsillar ring +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0002374 @@ -197467,7 +200006,6 @@ property_value: foaf:depiction "https://upload.wikimedia.org/wikipedia/commons/2 id: UBERON:0002376 name: cranial muscle namespace: uberon -alt_id: UBERON:0003899 def: "Any skeletal muscle that is part of the head region." [http://orcid.org/0000-0002-6601-2165] comment: defined generically so could in theory encompass FBbt:00003260 'skeletal muscle of head', or the muscle of a starfish Aristotle's lantern, but we restrict this to craniates. Skeletal muscles of the head originate from the non-segmented head mesoderm (Noden, 1983; Wachtler et al., 1984) subset: efo_slim @@ -197501,7 +200039,6 @@ intersection_of: part_of UBERON:0000033 ! head intersection_of: RO:0002371 UBERON:0003129 ! attached to skull relationship: part_of UBERON:0004461 {source="https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships"} ! skeletal musculature of head relationship: RO:0002202 UBERON:0006904 {source="EHDAA2-abduced"} ! develops from head mesenchyme from mesoderm -relationship: RO:0002254 UBERON:0002342 {gci_relation="part_of", gci_filler="NCBITaxon:7742", source="https://github.com/obophenotype/uberon/wiki/The-neural-crest"} ! has developmental contribution from neural crest relationship: RO:0002371 UBERON:0003129 ! attached to skull property_value: RO:0002175 NCBITaxon:9606 @@ -197803,7 +200340,6 @@ property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/a/ id: UBERON:0002389 name: manual digit namespace: uberon -alt_id: UBERON:0000028 def: "A digit that is part of a manus (hand)." [http://orcid.org/0000-0002-6601-2165] subset: pheno_slim subset: uberon_slim @@ -198019,8 +200555,6 @@ is_a: UBERON:0008001 {source="FMA"} ! irregular bone is_a: UBERON:0011597 ! bone of upper jaw is_a: UBERON:0012071 ! palate bone relationship: part_of UBERON:0011085 ! palatoquadrate arch -relationship: RO:0002170 UBERON:0001677 {gci_relation="part_of", gci_filler="NCBITaxon:9606", source="FMA"} ! connected to sphenoid bone -relationship: RO:0002170 UBERON:0001679 {gci_relation="part_of", gci_filler="NCBITaxon:9606", source="FMA"} ! connected to ethmoid bone relationship: RO:0002433 UBERON:0011156 ! contributes to morphology of facial skeleton property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/7/77/Illu_facial_bones.jpg" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 @@ -198252,7 +200786,6 @@ xref: Wikipedia:Pericardium xref: XAO:0004182 xref: ZFA:0000054 is_a: BFO:0000002 -is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0000481 ! multi-tissue structure relationship: has_part UBERON:0002359 ! fibrous pericardium relationship: has_part UBERON:0002406 ! pericardial sac @@ -198287,7 +200820,6 @@ is_a: UBERON:0022351 ! parietal serous membrane intersection_of: UBERON:0022351 ! parietal serous membrane intersection_of: part_of UBERON:0002357 ! serous pericardium relationship: part_of UBERON:0002357 ! serous pericardium -relationship: RO:0002371 UBERON:0006670 {gci_relation="part_of", gci_filler="NCBITaxon:40674", source="FMA"} ! attached to central tendon of diaphragm property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/7/7e/Gray489.png" xsd:anyURI [Term] @@ -198438,7 +200970,6 @@ xref: SCTID:181820005 xref: Wikipedia:Cervical_vertebrae xref: XAO:0003076 is_a: UBERON:0003458 ! neck bone -is_a: UBERON:0004247 ! bone of dorsum is_a: UBERON:0004451 {is_inferred="true"} ! trunk or cervical vertebra is_a: UBERON:0015007 ! cervical vertebra endochondral element intersection_of: UBERON:0015007 ! cervical vertebra endochondral element @@ -198478,7 +201009,6 @@ property_value: RO:0002161 NCBITaxon:9606 id: UBERON:0002416 name: integumental system namespace: uberon -alt_id: UBERON:0007029 def: "Connected anatomical system that forms a barrier between an animal and its environment. In vertebrates, the integumental system consists of the epidermis, dermis plus associated glands and adnexa such as hair and scales. In invertebrates, the integumental system may include cuticle." [CARO:0002001, http://orcid.org/0000-0002-6601-2165, https://github.com/obophenotype/uberon/issues/29] subset: efo_slim subset: grouping_class @@ -198517,7 +201047,6 @@ xref: VHOG:0000403 xref: Wikipedia:Integumentary_system xref: XAO:0000176 is_a: BFO:0000002 -is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0000467 ! anatomical system disjoint_from: UBERON:0002423 ! hepatobiliary system disjoint_from: UBERON:0004456 ! entire sense organ system @@ -198767,7 +201296,6 @@ xref: Wikipedia:Hepatobiliary_system xref: XAO:0000132 xref: ZFA:0000036 is_a: BFO:0000002 -is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0011216 ! organ system subdivision disjoint_from: UBERON:0004456 ! entire sense organ system disjoint_from: UBERON:8450002 ! excretory system @@ -198803,7 +201331,6 @@ xref: XAO:0003201 xref: ZFA:0000816 is_a: UBERON:0003350 ! epithelium of mucosa is_a: UBERON:0003929 ! digestive tract epithelium -is_a: UBERON:0006915 {gci_relation="part_of", gci_filler="NCBITaxon:9606", source="FMA"} ! stratified squamous epithelium intersection_of: UBERON:0000483 ! epithelium intersection_of: part_of UBERON:0003729 ! mouth mucosa relationship: adjacent_to UBERON:0000167 {source="AAO-modified"} ! oral cavity @@ -199217,7 +201744,6 @@ property_value: RO:0002175 NCBITaxon:9606 id: UBERON:0002457 name: intersomitic artery namespace: uberon -alt_id: UBERON:0006001 def: "The small branching sprouts of the dorsal aorta that grow across the medial surface of the somite, turn right angles to grow over that surface and then fuse with other sprouts and form the vertebral arteries adjacent to the neural tube; the intersomitic arteries supply the body wall and persist in the adult as the posterior intercostal, subcostal and the lumbar arteries." [MP:0010662] subset: pheno_slim subset: vertebrate_core @@ -199284,7 +201810,6 @@ property_value: RO:0002175 NCBITaxon:9606 id: UBERON:0002464 name: nerve trunk namespace: uberon -alt_id: UBERON:0001147 synonym: "peripheral nerve trunk" EXACT [EMAPA:16986] synonym: "trunk of nerve" EXACT [] synonym: "trunk of peripheral nerve" EXACT [] @@ -199307,8 +201832,8 @@ relationship: trunk_part_of UBERON:0001021 ! nerve id: UBERON:0002465 name: lymphoid system namespace: uberon -alt_id: UBERON:0002096 def: "The lymphatic system in vertebrates is a network of conduits that carry a clear fluid called lymph. It also includes the lymphoid tissue through which the lymph travels. Lymphoid tissue is found in many organs, particularly the lymph nodes, and in the lymphoid follicles associated with the digestive system such as the tonsils. The system also includes all the structures dedicated to the circulation and production of lymphocytes, which includes the spleen, thymus, bone marrow and the lymphoid tissue associated with the digestive system[WP]." [Wikipedia:Lymphoid_system] +subset: human_reference_atlas subset: uberon_slim subset: vertebrate_core synonym: "lymphatic circulatory system" RELATED [https://orcid.org/0000-0002-6601-2165] @@ -199336,6 +201861,7 @@ relationship: part_of UBERON:0002193 {source="FMA"} ! hemolymphoid system relationship: part_of UBERON:0002405 ! immune system relationship: RO:0002162 NCBITaxon:7711 ! in taxon Chordata property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/b/b3/TE-Lymphatic_system_diagram.svg" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0002466 @@ -199364,7 +201890,6 @@ relationship: produced_by UBERON:0000160 ! intestine id: UBERON:0002469 name: esophagus mucosa namespace: uberon -alt_id: UBERON:0003345 def: "A mucosa that is part of a esophagus [Automatically generated definition]." [OBOL:automatic] synonym: "esophageal mucosa" EXACT [] synonym: "esophageal mucous membrane" EXACT [] @@ -199516,7 +202041,6 @@ xref: Wikipedia:Lesser_wing_of_sphenoid_bone xref: ZFA:0000253 is_a: UBERON:0002513 ! endochondral bone is_a: UBERON:0003462 ! facial bone -is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0011164 ! neurocranium bone is_a: UBERON:0015059 ! orbitosphenoid endochondral element is_a: UBERON:0015212 ! lateral structure @@ -199969,7 +202493,6 @@ xref: NCIT:C13184 xref: SCTID:33840008 xref: UMLS:C0031110 {source="ncithesaurus:Periosteum"} xref: Wikipedia:Periosteum -is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0000158 ! membranous layer relationship: part_of UBERON:0001474 ! bone element relationship: RO:0002473 UBERON:0011822 ! composed primarily of dense irregular connective tissue @@ -200098,7 +202621,6 @@ xref: SCTID:87483006 xref: UMLS:C0162864 {source="ncithesaurus:Tunica_Intima"} xref: Wikipedia:Tunica_intima is_a: BFO:0000002 -is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0004923 {source="FMA"} ! organ component layer relationship: adjacent_to UBERON:0010161 {source="ISBN:0073040584"} ! lumen of blood vessel relationship: has_part UBERON:0001986 ! endothelium @@ -200324,7 +202846,7 @@ is_a: UBERON:0000481 ! multi-tissue structure is_a: UBERON:0010188 {source="EHDAA2"} ! protuberance is_a: UBERON:0010314 ! structure with developmental contribution from neural crest relationship: part_of UBERON:0008814 ! pharyngeal arch system -relationship: part_of UBERON:0008816 {source="PMID:16313389"} ! embryonic head +relationship: part_of UBERON:8450003 {source="PMID:16313389"} ! embryonic craniocervical region relationship: RO:0002162 NCBITaxon:7711 {source="http://tolweb.org/Chordata/2499"} ! in taxon Chordata relationship: RO:0002256 UBERON:0007690 {source="PMID:16313389"} ! developmentally induced by early pharyngeal endoderm property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/8/8b/Gray41.png" xsd:anyURI @@ -200534,7 +203056,6 @@ is_a: UBERON:0002558 ! organ cavity intersection_of: UBERON:0002558 ! organ cavity intersection_of: RO:0002572 UBERON:0001017 ! luminal space of central nervous system relationship: part_of UBERON:0001017 ! central nervous system -relationship: RO:0002202 UBERON:0003842 {gci_relation="part_of", gci_filler="NCBITaxon:7742", source="cjm"} ! develops from neural tube lumen relationship: RO:0002572 UBERON:0001017 ! luminal space of central nervous system property_value: RO:0002175 NCBITaxon:569425 {source="DOI:10.1186/s12983-014-0089-2"} @@ -200758,7 +203279,6 @@ property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/1/ id: UBERON:0002707 name: corticospinal tract namespace: uberon -alt_id: UBERON:0004095 def: "The corticospinal fibers that arise from the pyramidal cells within the cerebral cortex layer V of the precentral motor area, the premotor area and the postcentral gyrus, then descend into and through the medulla to form the lateral corticospinal tract and the anterior corticospinal tract." [ISBN:0-683-40008-8, MP:0002878] subset: human_reference_atlas subset: pheno_slim @@ -201478,7 +203998,6 @@ intersection_of: UBERON:0006934 ! sensory epithelium intersection_of: part_of UBERON:0001033 ! gustatory system relationship: part_of UBERON:0000012 {source="NIFSTD"} ! somatic nervous system relationship: part_of UBERON:0001033 ! gustatory system -relationship: part_of UBERON:0001723 {gci_relation="part_of", gci_filler="NCBITaxon:9606"} ! tongue [Term] id: UBERON:0002928 @@ -201735,7 +204254,6 @@ relationship: RO:0002202 UBERON:0002346 ! develops from neurectoderm id: UBERON:0003051 name: ear vesicle namespace: uberon -alt_id: UBERON:0004373 def: "An epithelial sac of invaginated ectoderm formed from the otic placode that gives rise to the structures of the inner ear[MP]." [MP:0009806, Wikipedia:Otic_vesicle] subset: pheno_slim subset: vertebrate_core @@ -201883,6 +204401,7 @@ xref: VHOG:0000559 xref: XAO:0000057 xref: ZFA:0000279 is_a: BFO:0000002 +is_a: UBERON:0000061 ! anatomical structure is_a: UBERON:0006598 ! presumptive structure intersection_of: UBERON:0005423 ! developing anatomical structure intersection_of: RO:0002387 UBERON:0002329 ! has potential to develop into somite @@ -201910,7 +204429,6 @@ xref: Wikipedia:Pronephric_duct xref: XAO:0000063 xref: ZFA:0000150 is_a: UBERON:0009201 {source="GO"} ! nephric duct -is_a: UBERON:0012275 ! meso-epithelium relationship: part_of UBERON:0002120 ! pronephros relationship: RO:0002202 UBERON:0003064 {source="Wikipedia"} ! develops from intermediate mesoderm relationship: RO:0002202 UBERON:0005721 {source="XAO"} ! develops from pronephric mesoderm @@ -201951,7 +204469,6 @@ relationship: RO:0002387 UBERON:0002390 ! has potential to develop into hematopo id: UBERON:0003063 name: prechordal plate namespace: uberon -alt_id: UBERON:0004881 def: "A horseshoe-shaped thickening of the endoderm at the cranial (rostral) end of the primitive streak formed by the involution of Spemann's organizer cells which, together with the notochord, induces the formation of the neural plate from the overlying ectodermal cells and contributes mesodermal type cells to the surrounding tissue." [ISBN:0838580343, MP:0004387] subset: pheno_slim subset: uberon_slim @@ -202134,7 +204651,6 @@ relationship: RO:0002385 UBERON:0003942 ! has potential to developmentally contr id: UBERON:0003071 name: eye primordium namespace: uberon -alt_id: UBERON:0005060 def: "Portion of tissue that is part of the anterior neural keel and will form the optic vesicle[ZFA]. A paired ectodermal placode that becomes invaginated to form the embryonic lens vesicles." [GO:0046619, ZFA:0000570] subset: efo_slim synonym: "eye anlage" RELATED [XAO:0000227] @@ -202415,7 +204931,6 @@ property_value: IAO:0000116 "TODO - add grouping class for the anterior end of t id: UBERON:0003081 name: lateral plate mesoderm namespace: uberon -alt_id: UBERON:0006258 def: "Portion of the middle of the three primary germ layers of the embryo that resides on the periphery of the embryo, is continuous with the extra-embryonic mesoderm, splits into two layers enclosing the intra-embryonic coelom, and gives rise to body wall structures[MP]." [MP:0010117, Wikipedia:Lateral_plate_mesoderm] subset: pheno_slim subset: uberon_slim @@ -202785,7 +205300,6 @@ is_a: UBERON:0000479 ! tissue intersection_of: UBERON:0000479 ! tissue intersection_of: RO:0002473 CL:0008019 ! composed primarily of mesenchymal cell relationship: RO:0002162 NCBITaxon:6072 ! in taxon Eumetazoa -relationship: RO:0002254 UBERON:0000926 {gci_relation="part_of", gci_filler="NCBITaxon:7711"} ! has developmental contribution from mesoderm relationship: RO:0002328 GO:0032502 ! functionally related to developmental process relationship: RO:0002473 CL:0008019 ! composed primarily of mesenchymal cell property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/f/f4/Mesenchymal_Stem_Cell.jpg" xsd:anyURI @@ -202947,7 +205461,6 @@ is_a: UBERON:0002539 ! pharyngeal arch id: UBERON:0003117 name: pharyngeal arch 6 namespace: uberon -alt_id: UBERON:0004349 def: "The 6th pharyngeal arch. contributes to the development of the sternocleidomastoid and trapezius muscles." [MP:0006347] subset: pheno_slim synonym: "6th arch" EXACT [EHDAA2:0004075] @@ -202975,7 +205488,6 @@ is_a: UBERON:0002539 ! pharyngeal arch id: UBERON:0003118 name: pharyngeal arch artery 1 namespace: uberon -alt_id: UBERON:0004371 def: "The vessels formed within the first pair of branchial arches in embryogenesis." [MP:0010355] subset: pheno_slim subset: vertebrate_core @@ -203008,7 +205520,6 @@ relationship: RO:0002433 UBERON:0004362 ! contributes to morphology of pharyngea id: UBERON:0003119 name: pharyngeal arch artery 2 namespace: uberon -alt_id: UBERON:0004372 def: "The vessels formed within the second pair of branchial arches in embryogenesis." [MP:0010356] subset: pheno_slim subset: vertebrate_core @@ -203041,7 +205552,6 @@ relationship: RO:0002433 UBERON:0003066 ! contributes to morphology of pharyngea id: UBERON:0003120 name: pharyngeal arch artery 3 namespace: uberon -alt_id: UBERON:0004352 def: "The vessels formed within the third pair of branchial arches in embryogenesis." [MP:0006356] subset: pheno_slim subset: vertebrate_core @@ -203073,7 +205583,6 @@ relationship: RO:0002433 UBERON:0003114 ! contributes to morphology of pharyngea id: UBERON:0003121 name: pharyngeal arch artery 4 namespace: uberon -alt_id: UBERON:0004350 def: "The vessels formed within the fourth pair of branchial arches in embryogenesis." [MP:0006354] comment: proximal right subclavian subset: pheno_slim @@ -203125,7 +205634,6 @@ relationship: part_of UBERON:0003116 ! pharyngeal arch 5 id: UBERON:0003123 name: pharyngeal arch artery 6 namespace: uberon -alt_id: UBERON:0004351 def: "The vessels formed within the sixth pair of branchial arches in embryogenesis." [MP:0006355] subset: pheno_slim subset: vertebrate_core @@ -203252,7 +205760,6 @@ synonym: "trachea" BROAD SENSU [FBbt:00005043] xref: SPD:0000434 xref: TADS:0000315 xref: Wikipedia:Invertebrate_trachea -is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0001005 ! respiratory airway relationship: has_part UBERON:0003914 ! epithelial tube relationship: part_of UBERON:0005155 ! open tracheal system @@ -203837,7 +206344,6 @@ is_a: UBERON:0010371 ! ecto-epithelium intersection_of: UBERON:0000483 ! epithelium intersection_of: part_of UBERON:0001911 ! mammary gland relationship: part_of UBERON:0001911 ! mammary gland -relationship: part_of UBERON:0005200 {gci_relation="part_of", gci_filler="NCBITaxon:9606", source="EHDAA2"} ! thoracic mammary gland relationship: RO:0002202 UBERON:0011272 {source="EHDAA2", source="Wikipathways:WP2062"} ! develops from embryonic skin basal layer relationship: RO:0002433 UBERON:0001911 ! contributes to morphology of mammary gland @@ -203942,7 +206448,6 @@ property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/5/ id: UBERON:0003254 name: amniotic ectoderm namespace: uberon -alt_id: UBERON:0008359 subset: human_reference_atlas synonym: "amnion ectoderm" EXACT [EHDAA2:0000117, OBOL:automatic] synonym: "amnion epithelium" RELATED [BTO:0000897] @@ -204031,7 +206536,6 @@ property_value: IAO:0000116 "TODO - check" xsd:string id: UBERON:0003261 name: thyroid primordium endoderm namespace: uberon -alt_id: UBERON:0005235 def: "An endoderm that is part of a thyroid primordium." [OBOL:automatic] synonym: "endoderm of thyroid primordium" EXACT [OBOL:automatic] xref: EHDAA:956 @@ -204049,7 +206553,6 @@ relationship: RO:0002202 UBERON:0007690 {source="ZFA-propagated"} ! develops fro id: UBERON:0003262 name: amniotic mesoderm namespace: uberon -alt_id: UBERON:0003411 def: "A mesenchyme that is part of a amnion." [OBOL:automatic] subset: human_reference_atlas synonym: "amnion mesenchyme" EXACT [EHDAA2:0000118] @@ -204076,7 +206579,6 @@ property_value: RO:0002175 NCBITaxon:9606 id: UBERON:0003265 name: chorionic mesenchyme namespace: uberon -alt_id: UBERON:0003423 def: "A mesenchyme that is part of a chorion." [OBOL:automatic] synonym: "chorion mesenchyme" EXACT [OBOL:automatic] synonym: "chorion mesoderm" EXACT [RETIRED_EHDAA2:0000247] @@ -204503,7 +207005,6 @@ relationship: part_of UBERON:0002416 ! integumental system id: UBERON:0003304 name: mesoderm blood island namespace: uberon -alt_id: UBERON:0003305 def: "A blood island that is part of a mesoderm." [OBOL:automatic] synonym: "mesenchyme blood island" RELATED [OBOL:automatic] synonym: "mesoderm blood islands" EXACT OMO:0003004 [EHDAA2:0003241] @@ -204758,7 +207259,6 @@ property_value: RO:0002175 NCBITaxon:9606 id: UBERON:0003316 name: mesenchyme of yolk sac namespace: uberon -alt_id: UBERON:0003264 def: "The portion of the yolk sac that is derived from mesoderm and consists of mesenchyme." [UBERON:cjm] synonym: "yolk sac mesenchyme" EXACT [OBOL:automatic] xref: EHDAA2:0002216 @@ -204967,7 +207467,6 @@ relationship: part_of UBERON:0002386 ! forelimb zeugopod id: UBERON:0003328 name: mesenchyme of footplate namespace: uberon -alt_id: UBERON:0005260 def: "Mesenchyme that is part of a footplate." [OBOL:automatic] synonym: "foot plate mesenchyme" EXACT [] xref: EHDAA2:0000549 @@ -205296,6 +207795,7 @@ id: UBERON:0003346 name: mucosa of rectum namespace: uberon def: "A mucosa that is part of a rectum [Automatically generated definition]." [OBOL:automatic] +subset: human_reference_atlas synonym: "mucosa of organ of rectum" EXACT [OBOL:automatic] synonym: "mucous membrane of rectum" EXACT [OBOL:automatic] synonym: "organ mucosa of rectum" EXACT [OBOL:automatic] @@ -205314,6 +207814,7 @@ is_a: UBERON:0001207 ! mucosa of large intestine intersection_of: UBERON:0000344 ! mucosa intersection_of: part_of UBERON:0001052 ! rectum relationship: part_of UBERON:0001052 ! rectum +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0003350 @@ -205496,7 +207997,6 @@ property_value: IAO:0000116 "TODO - add cell types" xsd:string id: UBERON:0003371 name: pelvic appendage bud ectoderm namespace: uberon -alt_id: UBERON:0005232 def: "An unilaminar epithelium that surrounds a pelvic appendage bud." [OBOL:automatic] synonym: "hindlimb bud ectoderm" NARROW SENSU [EMAPA:16780] synonym: "hindlimb ectoderm" EXACT [VHOG:0001048] @@ -205521,8 +208021,6 @@ relationship: RO:0002202 UBERON:0000076 {source="EHDAA2"} ! develops from extern id: UBERON:0003372 name: pectoral appendage bud ectoderm namespace: uberon -alt_id: UBERON:0005231 -alt_id: UBERON:0005663 def: "An unilaminar epithelium that surrounds a pectoral appendage bud." [OBOL:automatic] synonym: "arm ectoderm" RELATED [OBOL:automatic] synonym: "forelimb bud ectoderm" NARROW SENSU [EMAPA:16407] @@ -205717,7 +208215,6 @@ property_value: IAO:0000116 "Not clear if we need this and intra-ocular muscle. id: UBERON:0003387 name: smooth muscle of trachea namespace: uberon -alt_id: UBERON:0004244 def: "A portion of smooth muscle tissue that is part of a trachea [Automatically generated definition]." [OBOL:automatic] subset: human_reference_atlas subset: pheno_slim @@ -206014,7 +208511,6 @@ relationship: RO:0002202 UBERON:0005730 ! develops from pelvic appendage field id: UBERON:0003413 name: pectoral appendage bud mesenchyme namespace: uberon -alt_id: UBERON:0005703 def: "Mesenchyme that is part of a pectoral appendage bud." [OBOL:automatic] synonym: "arm mesenchyme" NARROW [OBOL:automatic] synonym: "forelimb bud mesenchyme" NARROW SENSU [EMAPA:16408] @@ -207357,7 +209853,6 @@ relationship: part_of UBERON:0001004 ! respiratory system id: UBERON:0003505 name: trachea blood vessel namespace: uberon -alt_id: UBERON:0003525 def: "A blood vessel that is part of a trachea." [OBOL:automatic] synonym: "blood vessel of trachea" EXACT [OBOL:automatic] xref: EMAPA:35874 @@ -207891,7 +210386,6 @@ relationship: part_of UBERON:0007812 ! post-anal tail id: UBERON:0003535 name: vagus X nerve trunk namespace: uberon -alt_id: UBERON:0006308 def: "A nerve trunk that is part of a vagus nerve." [OBOL:automatic] synonym: "trunk of vagal nerve" EXACT [] synonym: "trunk of vagus nerve" EXACT [FMA:6221] @@ -209696,7 +212190,6 @@ property_value: RO:0002175 NCBITaxon:9606 id: UBERON:0003662 name: forelimb muscle namespace: uberon -alt_id: UBERON:0005634 def: "Any muscle organ that is part of a forelimb." [OBOL:automatic] synonym: "arm muscle system" RELATED [EHDAA2:0000141] synonym: "fore limb muscle organ" EXACT [OBOL:automatic] @@ -209821,7 +212314,6 @@ is_a: UBERON:0034925 ! anatomical collection intersection_of: UBERON:0034925 ! anatomical collection intersection_of: RO:0002351 UBERON:0001091 ! has member calcareous tooth relationship: part_of UBERON:0010323 ! cranial skeletal system -relationship: part_of UBERON:0011595 {gci_relation="part_of", gci_filler="NCBITaxon:32523"} ! jaw region relationship: RO:0002351 UBERON:0001091 ! has member calcareous tooth [Term] @@ -209895,7 +212387,6 @@ is_a: UBERON:0009198 {source="GO"} ! craniofacial suture intersection_of: UBERON:0002209 ! fibrous joint intersection_of: part_of UBERON:0003128 ! cranium relationship: part_of UBERON:0003128 ! cranium -relationship: RO:0002256 UBERON:0002363 {gci_relation="part_of", gci_filler="NCBITaxon:40674", source="PMID:16496288"} ! developmentally induced by dura mater relationship: RO:0002433 UBERON:0003128 ! contributes to morphology of cranium [Term] @@ -210948,7 +213439,6 @@ relationship: part_of UBERON:0002470 ! autopod region id: UBERON:0003842 name: neural tube lumen namespace: uberon -alt_id: UBERON:0005713 def: "An anatomical space that surrounded_by a neural tube." [OBOL:automatic] synonym: "cavity of neural tube" EXACT [https://orcid.org/0000-0002-6601-2165] synonym: "central lumen" RELATED [] @@ -211032,7 +213522,6 @@ intersection_of: part_of UBERON:0002370 ! thymus relationship: has_part CL:0002293 ! epithelial cell of thymus relationship: has_part PR:000007636 {source="PMID:21293377"} ! forkhead box protein N1 relationship: part_of UBERON:0002370 ! thymus -relationship: RO:0002202 UBERON:0010026 {gci_relation="part_of", gci_filler="NCBITaxon:40674", source="MP"} ! develops from ventral part of pharyngeal pouch 3 relationship: RO:0002433 UBERON:0002370 ! contributes to morphology of thymus property_value: RO:0002175 NCBITaxon:9606 @@ -211228,7 +213717,6 @@ intersection_of: part_of UBERON:0008281 ! tooth bud relationship: adjacent_to UBERON:0005176 ! tooth enamel organ relationship: part_of UBERON:0008281 ! tooth bud relationship: RO:0002202 UBERON:0007213 ! develops from mesenchyme derived from head neural crest -relationship: RO:0002202 UBERON:0010259 {gci_relation="part_of", gci_filler="NCBITaxon:32523", source="JB"} ! develops from 1st arch mesenchyme from neural crest property_value: IAO:0000116 "we follow ZFA in introducing an additional distinction between the dental papilla and the (uncondensed) mesenchyme. Note that in some species such as zebrafish teeth are not part of the mouth, and sharks have dermal denticles which share similar developmental origins with teeth. For now we assume a NC origin for all and add a taxon restriction to 1st arch mesenchyme" xsd:string [Term] @@ -211445,6 +213933,58 @@ intersection_of: UBERON:0006598 ! presumptive structure intersection_of: RO:0002387 UBERON:0000045 ! has potential to develop into ganglion relationship: RO:0002387 UBERON:0000045 ! has potential to develop into ganglion +[Term] +id: UBERON:0003876 +name: hippocampal field +namespace: uberon +def: "A part or parts of the hippocampus that have a particular function." [MGI:csmith, MP:0008262] +subset: non_informative +subset: pheno_slim +synonym: "hippocampal region" RELATED [BAMS:HIP] +synonym: "hippocampus region" RELATED [MA:0002428] +synonym: "hippocampus subdivision" EXACT [FMA:74041] +synonym: "subdivision of hippocampus" EXACT [FMA:74041] +xref: BAMS:Hi/CA +xref: BAMS:HIP +xref: EMAPA:32772 +xref: FMA:74041 +xref: MA:0002428 +is_a: UBERON:0002616 ! regional part of brain +disjoint_from: UBERON:0007688 ! anlage +relationship: part_of UBERON:0002421 ! hippocampal formation +relationship: RO:0002433 UBERON:0001954 ! contributes to morphology of Ammon's horn + +[Term] +id: UBERON:0003884 +name: CA4 field of hippocampus +namespace: uberon +def: "The last of four regions in the cornu ammonis of the hippocampus and is also part of the hilus of the dentate gyrus. This area contains mostly mossy cells that receive inputs from the dentate gyrus and pyramidal cells in the CA3 region and also projects back to the dentate gyrus." [ncithesaurus:CA4_Field_of_the_Cornu_Ammonis] +subset: efo_slim +subset: pheno_slim +synonym: "CA4" EXACT [] +synonym: "CA4 field" EXACT [] +synonym: "CA4 field of Ammon's horn" EXACT [] +synonym: "CA4 field of cornu ammonis" EXACT [] +synonym: "hippocampus CA4" EXACT [] +synonym: "regio IV cornus ammonis" EXACT OMO:0003011 [FMA:75741, FMA:TA] +synonym: "regio IV hippocampi proprii" EXACT OMO:0003011 [FMA:75741, FMA:TA] +synonym: "region 4 of Ammon's horn" EXACT [] +synonym: "region IV of ammon's horn" EXACT [FMA:75741] +synonym: "region IV of hippocampus proper" EXACT [FMA:75741] +xref: DHBA:10300 +xref: EFO:0002457 +xref: EMAPA:32771 +xref: FMA:75741 +xref: HBA:12895 +xref: MA:0000953 +xref: NCIT:C32249 +xref: neuronames:181 +xref: PBA:10074 +xref: UMLS:C2328406 {source="ncithesaurus:CA4_Field_of_the_Cornu_Ammonis"} +xref: Wikipedia:Region_IV_of_hippocampus_proper +is_a: UBERON:0003876 ! hippocampal field +property_value: IAO:0000116 "consider obsoleting. consider - CA3c, hilus" xsd:string + [Term] id: UBERON:0003885 name: mesometrium @@ -211509,9 +214049,9 @@ subset: efo_slim subset: human_reference_atlas subset: pheno_slim subset: uberon_slim -synonym: "fallopian tubes" RELATED [] +synonym: "fallopian tubes" RELATED OMO:0003004 [] synonym: "female paramesonephric duct" RELATED [EHDAA2:0000504] -synonym: "mammalian oviduct" EXACT [https://sourceforge.net/p/geneontology/ontology-requests/8397/] +synonym: "mammalian oviduct" BROAD [https://sourceforge.net/p/geneontology/ontology-requests/8397/] synonym: "paramesonephric duct of female" RELATED [EMAPA:35660] synonym: "salpinges" BROAD OMO:0003004 [] synonym: "salpinx" BROAD [] @@ -211546,7 +214086,6 @@ property_value: RO:0002175 NCBITaxon:9606 id: UBERON:0003890 name: Mullerian duct namespace: uberon -alt_id: UBERON:0005318 def: "Paired ducts of the embryo that run down the lateral sides of the urogenital ridge and terminate at the mullerian eminence in the primitive urogenital sinus. In the female, they will develop to form the fallopian tubes, uterus, and the upper portion of the vagina; in the male, they are lost. These ducts are made of tissue of mesodermal origin[WP]. develops either by lengthwise splitting of the archinephric duct (in chondrichthyans and some amphibians) or by a elongated invagination of the coelomic epithelium (other vertebrates) In males, the oviducts regress. The cranial end of the oviduct maintains an opening into the coelom (which primitively may have been the anteriormost coelomic funnels connecting the nephrocoel with the coelom). This opening is the ostium tubae[USM]." [GO:0061205, http://www.usm.maine.edu/bio/courses/bio205/bio205_26_sex.html, Wikipedia:Paramesonephric_duct] subset: pheno_slim synonym: "ductus paramesonephricus" EXACT [] @@ -211930,8 +214469,6 @@ xref: ZFA:0001370 is_a: UBERON:0003922 ! pancreatic epithelial bud relationship: part_of UBERON:0010375 {source="EHDAA2"} ! pancreas dorsal primordium relationship: RO:0002202 UBERON:0001045 {source="XAO"} ! develops from midgut -relationship: RO:0002256 UBERON:0002328 {gci_relation="part_of", gci_filler="NCBITaxon:10088", source="PMID:16417468"} ! developmentally induced by notochord -relationship: RO:0002256 UBERON:0005805 {gci_relation="part_of", gci_filler="NCBITaxon:10088", source="PMID:16417468"} ! developmentally induced by dorsal aorta property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/d/db/Gray982.png" xsd:anyURI [Term] @@ -212010,7 +214547,6 @@ relationship: part_of UBERON:0001555 ! digestive tract id: UBERON:0003931 name: diencephalic white matter namespace: uberon -alt_id: UBERON:0023148 def: "White matter that is part of a diencephalon [Automatically generated definition]." [OBOL:automatic] subset: vertebrate_core synonym: "diencephalic tract/commissure" EXACT [ZFA:0000338] @@ -212082,7 +214618,6 @@ intersection_of: part_of UBERON:0000990 ! reproductive system id: UBERON:0003942 name: somatosensory system namespace: uberon -alt_id: UBERON:0014511 def: "The sensory system for the sense of touch and pain." [NLXANAT:090818] subset: pheno_slim synonym: "somatic sensory system" EXACT [] @@ -212339,7 +214874,6 @@ xref: FMA:18307 xref: SCTID:362262001 xref: Wikipedia:Infundibulum_of_uterine_tube is_a: UBERON:0013515 {source="FMA"} ! subdivision of oviduct -relationship: part_of UBERON:0003889 {gci_relation="part_of", gci_filler="NCBITaxon:40674", source="FMA"} ! fallopian tube relationship: RO:0002162 NCBITaxon:7742 ! in taxon Vertebrata property_value: foaf:depiction "https://upload.wikimedia.org/wikipedia/commons/6/66/Illu_cervix.jpg" xsd:anyURI property_value: RO:0002175 NCBITaxon:8782 @@ -212361,7 +214895,6 @@ synonym: "thymus cortico-medullary boundary" EXACT [MP:0009543] synonym: "thymus corticomedullary junction" EXACT [MP:0009543] synonym: "thymus corticomedullary zone" EXACT [MP:0009543] xref: EMAPA:37974 {source="MA:th"} -is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0000077 ! mixed endoderm/mesoderm-derived structure is_a: UBERON:0007651 ! anatomical junction intersection_of: UBERON:0007651 ! anatomical junction @@ -212863,7 +215396,6 @@ relationship: RO:0002433 UBERON:0004061 ! contributes to morphology of neural tu id: UBERON:0004066 name: frontonasal prominence namespace: uberon -alt_id: UBERON:0006237 def: "The unpaired embryonic prominence that is formed by the tissues surrounding the forebrain vesicle and develops into the forehead and bridge of the nose/snout." [MP:0009901] subset: pheno_slim synonym: "embryonic frontonasal prominence" EXACT [http://orcid.org/0000-0002-6601-2165] @@ -213129,7 +215661,6 @@ property_value: RO:0002175 NCBITaxon:4751 id: UBERON:0004113 name: muscle of auditory ossicle namespace: uberon -alt_id: UBERON:0004112 def: "A muscle of the tympanic cavity that attaches to an auditory ossicle." [http://orcid.org/0000-0002-6601-2165] synonym: "auditory ossicles muscle" EXACT [FMA:49026] synonym: "muscle of auditory ossicles" EXACT [FMA:49026] @@ -213356,7 +215887,6 @@ intersection_of: has_part UBERON:0000990 ! reproductive system intersection_of: has_part UBERON:0001008 ! renal system relationship: has_part UBERON:0000990 ! reproductive system relationship: has_part UBERON:0001008 ! renal system -relationship: RO:0002202 UBERON:0003064 {gci_relation="part_of", gci_filler="NCBITaxon:7742", source="AAO", source="https://github.com/geneontology/go-ontology/issues/16143"} ! develops from intermediate mesoderm relationship: RO:0002492 UBERON:0000066 ! existence ends during fully formed stage [Term] @@ -213919,7 +216449,6 @@ relationship: part_of UBERON:0003970 ! placental labyrinth vasculature id: UBERON:0004184 name: prostate gland stroma namespace: uberon -alt_id: UBERON:0005084 def: "The prostate gland stroma is made up of the mesenchymal or fibroblast cells of the prostate gland." [GO:0060741] subset: human_reference_atlas synonym: "prostate stroma" EXACT [OBOL:automatic] @@ -214076,7 +216605,6 @@ is_a: UBERON:0001285 ! nephron id: UBERON:0004196 name: proximal convoluted tubule segment 1 namespace: uberon -alt_id: UBERON:0006432 def: "The S1 portion is the initial portion of the proximal convoluted tubule and is responsible for avid reabsorption of water and solutes[GO]." [GO:0072031, http://sourceforge.net/tracker/?func=detail&atid=440764&aid=3298740&group_id=36855] subset: human_reference_atlas synonym: "proximal tubule segment 1" EXACT [MA:0002612] @@ -214096,7 +216624,6 @@ property_value: RO:0002175 NCBITaxon:9606 id: UBERON:0004197 name: proximal convoluted tubule segment 2 namespace: uberon -alt_id: UBERON:0006433 def: "The S2 portion of the tubule is involved in reabsorption of water and sodium chloride[GO]." [GO:0072032] subset: human_reference_atlas synonym: "proximal tubule segment 2" EXACT [MA:0002613] @@ -214146,8 +216673,6 @@ property_value: IAO:0000116 "TODO" xsd:string id: UBERON:0004200 name: kidney pyramid namespace: uberon -alt_id: UBERON:0002449 -alt_id: UBERON:0005098 def: "Kidney pyramids are the conical arrangements of tubules that constitute the renal medulla in a multi-lobed mammalian kidney; they contain the loops of Henle and the medullary collecting ducts." [GO:0072056, http://anatomy.uams.edu/anatomyhtml/kidney.html] subset: human_reference_atlas subset: pheno_slim @@ -214227,7 +216752,6 @@ property_value: RO:0002175 NCBITaxon:9606 id: UBERON:0004203 name: cortical collecting duct namespace: uberon -alt_id: UBERON:0005267 def: "The cortical collecting duct is the portion of the collecting duct that resides in the renal cortex." [GO:0072059] subset: human_reference_atlas synonym: "kidney cortex collecting duct" EXACT [MA:0002600] @@ -214247,7 +216771,6 @@ property_value: RO:0002175 NCBITaxon:9606 id: UBERON:0004204 name: outer medullary collecting duct namespace: uberon -alt_id: UBERON:0005186 def: "The outer medullary collecting duct is the portion of the collecting duct that lies in the renal outer medulla." [GO:0072060] subset: human_reference_atlas synonym: "kidney outer medulla collecting duct" EXACT [MA:0002599] @@ -214264,7 +216787,6 @@ property_value: RO:0002175 NCBITaxon:9606 id: UBERON:0004205 name: inner medullary collecting duct namespace: uberon -alt_id: UBERON:0005187 def: "The inner medullary collecting duct is the portion of the collecting duct that lies in the renal inner medulla." [GO:0072061] subset: human_reference_atlas synonym: "inner renal medulla collecting duct" EXACT [MA:0002598] @@ -214912,7 +217434,6 @@ relationship: part_of UBERON:0001980 ! arteriole id: UBERON:0004237 name: blood vessel smooth muscle namespace: uberon -alt_id: UBERON:0010508 def: "Smooth muscle found within, and composing the majority of the wall of blood vessels." [Wikipedia:Vascular_smooth_muscle] subset: human_reference_atlas subset: pheno_slim @@ -215301,7 +217822,6 @@ relationship: part_of UBERON:0003823 ! hindlimb zeugopod id: UBERON:0004252 name: hindlimb stylopod muscle namespace: uberon -alt_id: UBERON:0000374 def: "Any muscle organ that is part of a hindlimb stylopod (upper leg)[Automatically generated definition]." [OBOL:automatic] subset: pheno_slim synonym: "muscle of thigh" EXACT [FMA:22470] @@ -215321,7 +217841,6 @@ relationship: part_of UBERON:0004463 {source="prolog"} ! musculature of hindlimb id: UBERON:0004253 name: skin muscle namespace: uberon -alt_id: UBERON:0015797 def: "Any muscle organ that is part of a skin of body [Automatically generated definition]." [OBOL:automatic] synonym: "integumental system muscle" EXACT [MA:0003139] synonym: "muscle of integumental system" EXACT [EMAPA:18187] @@ -216047,7 +218566,6 @@ xref: VHOG:0001202 xref: Wikipedia:Primitive_streak is_a: UBERON:0000485 {source="EHDAA2"} ! simple columnar epithelium is_a: UBERON:0005291 ! embryonic tissue -relationship: RO:0002202 UBERON:0008780 {gci_relation="part_of", gci_filler="NCBITaxon:40674", source="ISBN:9780878932504"} ! develops from inner cell mass derived epiblast relationship: RO:0002387 UBERON:0000925 ! has potential to develop into endoderm relationship: RO:0002387 UBERON:0000926 ! has potential to develop into mesoderm property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/f/f4/Gray13.png" xsd:anyURI @@ -216196,7 +218714,6 @@ property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/2/ id: UBERON:0004363 name: pharyngeal arch artery namespace: uberon -alt_id: UBERON:0004342 def: "One of a series of paired embryological vascular structures formed within a pharyngeal arch; in the adult, some of these vessels give rise to the great vessels[MP]." [MP:0002672] subset: efo_slim subset: pheno_slim @@ -216229,7 +218746,6 @@ xref: Wikipedia:Aortic_arches xref: XAO:0000341 xref: ZFA:0005004 is_a: UBERON:0003469 ! respiratory system artery -is_a: UBERON:0003496 ! head blood vessel is_a: UBERON:0006598 ! presumptive structure is_a: UBERON:0010314 ! structure with developmental contribution from neural crest relationship: part_of UBERON:0002539 ! pharyngeal arch @@ -216704,6 +219220,7 @@ xref: EMAPA:37722 {source="MA:th"} xref: MA:0002869 xref: XAO:0003077 is_a: UBERON:0002412 ! vertebra +is_a: UBERON:0004247 ! bone of dorsum intersection_of: UBERON:0002412 ! vertebra intersection_of: BSPO:0000096 UBERON:0001095 ! caudal vertebra union_of: UBERON:0002413 ! cervical vertebra @@ -216714,7 +219231,6 @@ relationship: BSPO:0000096 UBERON:0001095 ! caudal vertebra id: UBERON:0004452 name: carpal region namespace: uberon -alt_id: UBERON:0001462 def: "A mesopodium that is part of a manus. Includes as parts the carpal skeleton and associated tissues[cjm]. The anatomical region surrounding the carpus including the distal parts of the bones of the forearm and the proximal parts of the metacarpus or five metacarpal bones and the series of joints between these bones, thus referred to as wrist joints. This region also includes the carpal tunnel, the anatomical snuff box, the flexor retinaculum, and the extensor retinaculum[WP,unvetted]." [https://orcid.org/0000-0002-6601-2165, Wikipedia:Wrist] subset: pheno_slim subset: uberon_slim @@ -216784,7 +219300,6 @@ property_value: IAO:0000116 "Note that along with FMA we treat this as a limb se id: UBERON:0004454 name: tarsal region namespace: uberon -alt_id: UBERON:0002388 def: "Mesopodial segment of the pes, including the tarsal skeleton and associated tissues." [https://orcid.org/0000-0002-6601-2165, Wikipedia:Ankle] subset: efo_slim subset: pheno_slim @@ -216820,7 +219335,6 @@ property_value: foaf:depiction "https://upload.wikimedia.org/wikipedia/commons/b id: UBERON:0004455 name: neurula embryo namespace: uberon -alt_id: UBERON:0007013 def: "An embryo at the neurula stage." [http://orcid.org/0000-0002-6601-2165] synonym: "neurula" EXACT [BTO:0001766] xref: BILA:0000061 @@ -216950,7 +219464,6 @@ relationship: part_of UBERON:0000974 ! neck id: UBERON:0004466 name: musculature of leg namespace: uberon -alt_id: UBERON:0005632 def: "Any collection of muscles that is part of a lower leg or upper leg [Automatically generated definition]." [OBOL:automatic] synonym: "leg muscle system" EXACT [EHDAA2:0000973] xref: EHDAA2:0000973 @@ -217004,8 +219517,6 @@ relationship: part_of UBERON:0001137 ! dorsum id: UBERON:0004470 name: musculature of pelvic girdle namespace: uberon -alt_id: UBERON:0004485 -alt_id: UBERON:0005633 def: "Any collection of muscles that is part of a pelvic girdle [Automatically generated definition]." [OBOL:automatic] subset: pheno_slim synonym: "muscle group of pelvic girdle" EXACT [FMA:50205] @@ -217155,7 +219666,6 @@ property_value: IAO:0000116 "currently defined by location rather than attachmen id: UBERON:0004480 name: musculature of limb namespace: uberon -alt_id: UBERON:0005635 def: "Any collection of muscles that is part of a limb [Automatically generated definition]." [OBOL:automatic] subset: pheno_slim synonym: "limb muscle system" EXACT [EHDAA2:0000995] @@ -217612,7 +220122,6 @@ xref: XAO:0000100 xref: XAO:0001010 xref: ZFA:0000010 is_a: BFO:0000002 -is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0000467 ! anatomical system intersection_of: UBERON:0000467 ! anatomical system intersection_of: has_part UBERON:0000948 ! heart @@ -217664,7 +220173,6 @@ synonym: "set of blood vessels" EXACT [] xref: TAO:0001079 xref: ZFA:0001079 is_a: BFO:0000002 -is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0002049 ! vasculature intersection_of: UBERON:0002049 ! vasculature intersection_of: RO:0002473 UBERON:0001981 ! composed primarily of blood vessel @@ -217877,7 +220385,6 @@ id: UBERON:0004572 name: arterial system namespace: uberon def: "The part of the cardiovascular system consisting of all arteries." [https://orcid.org/0000-0002-6601-2165] -subset: human_reference_atlas subset: pheno_slim xref: BTO:0004690 xref: EHDAA2:0000143 @@ -217888,10 +220395,8 @@ xref: MA:0002719 xref: SCTID:362030008 xref: VHOG:0000273 is_a: BFO:0000002 -is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0007798 {source="MA"} ! vascular system relationship: RO:0002351 UBERON:0001637 ! has member artery -property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0004573 @@ -217926,7 +220431,6 @@ id: UBERON:0004582 name: venous system namespace: uberon def: "The part of the cardiovascular system consisting of all venous vessels. In vertebrates with a double circulation, this can be divided into systemic and pulmonary portions." [https://orcid.org/0000-0002-6601-2165] -subset: human_reference_atlas synonym: "vein system" EXACT [] xref: BTO:0004692 xref: EHDAA2:0002171 @@ -217938,10 +220442,8 @@ xref: SCTID:362060003 xref: UMLS:C1267406 {source="ncithesaurus:Venous_System"} xref: VHOG:0000277 is_a: BFO:0000002 -is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0007798 {source="MA"} ! vascular system relationship: RO:0002473 UBERON:0001638 ! composed primarily of vein -property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0004590 @@ -218299,7 +220801,6 @@ relationship: part_of UBERON:0000998 ! seminal vesicle id: UBERON:0004666 name: interventricular septum membranous part namespace: uberon -alt_id: UBERON:0004143 def: "The membranous portion of the wall between the two lower chambers of the heart." [MP:0008823] subset: pheno_slim synonym: "cardiac ventricular membranous septum" EXACT [http://orcid.org/0000-0002-6601-2165] @@ -218332,7 +220833,6 @@ relationship: RO:0002433 UBERON:0002094 ! contributes to morphology of intervent id: UBERON:0004667 name: interventricular septum muscular part namespace: uberon -alt_id: UBERON:0004144 def: "The muscular portion of the wall between the two lower chambers of the heart." [http://orcid.org/0000-0002-6601-2165, Wikipedia:Interventricular_septum#Portions] subset: pheno_slim synonym: "cardiac ventricular muscular septum" EXACT [http://orcid.org/0000-0002-6601-2165] @@ -218458,7 +220958,6 @@ relationship: part_of UBERON:0001895 ! metencephalon id: UBERON:0004675 name: hypoglossal nerve root namespace: uberon -alt_id: UBERON:0022760 def: "A nerve root that extends_fibers_into a hypoglossal nerve." [OBOL:automatic] synonym: "central part of hypoglossal nerve" EXACT [FMA:72632] synonym: "central part of hypoglossal nerve" RELATED [BIRNLEX:1288] @@ -218603,9 +221102,9 @@ relationship: part_of UBERON:0005928 ! external naris id: UBERON:0004693 name: Peyer's patch epithelium namespace: uberon -def: "The specialized epithelium of the Peyer's patch." [ISBN:0-8153-1691-7, MGI:cwg, MP:0002388] +def: "The specialized epithelial layer covering the entire Peyer's patch, including both the follicular and interfollicular areas and forming part of the gut-associated lymphoid tissue." [ISBN:0-8153-1691-7, MGI:cwg, MP:0002388] subset: pheno_slim -synonym: "Peyer's patch epithelium" EXACT [MA:0000731] +synonym: "Peyer's patch epithelium" EXACT [MA:0000731, PMID:31813624] xref: EMAPA:36506 xref: MA:0000731 is_a: UBERON:0001277 ! intestinal epithelium @@ -218826,7 +221325,6 @@ relationship: RO:0002162 NCBITaxon:6072 ! in taxon Eumetazoa id: UBERON:0004708 name: paired limb/fin namespace: uberon -alt_id: UBERON:0009872 def: "An appendage that is part of an appendage girdle complex." [https://github.com/geneontology/go-ontology/issues/9029, UBERON:cjm] subset: homology_grouping synonym: "girdle-associated appendage" EXACT [https://orcid.org/0000-0002-6601-2165] @@ -218838,7 +221336,6 @@ synonym: "pectoral or pelvic appendage" EXACT [https://orcid.org/0000-0002-6601- synonym: "pelvic/pectoral appendage" EXACT [https://orcid.org/0000-0002-6601-2165] xref: VSAO:0000067 is_a: BFO:0000002 -is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0000026 {source="VSAO"} ! appendage intersection_of: UBERON:0000026 ! appendage intersection_of: part_of UBERON:0010707 ! appendage girdle complex @@ -218855,7 +221352,6 @@ relationship: RO:0002551 UBERON:0011582 ! has skeleton paired limb/fin skeleton id: UBERON:0004709 name: pelvic appendage namespace: uberon -alt_id: UBERON:0009876 def: "Paired appendage that consists of the posterior appendicular skeleton and associated soft and hard tissues, but excludes the pelvic girdle and its associated soft and hard tissues." [VSAO:0000150] subset: homology_grouping synonym: "hindlimb/pelvic fin" EXACT [https://orcid.org/0000-0002-6601-2165] @@ -218878,7 +221374,6 @@ relationship: RO:0002551 UBERON:0007273 ! has skeleton pelvic appendage skeleton id: UBERON:0004710 name: pectoral appendage namespace: uberon -alt_id: UBERON:0009875 def: "Paired appendage that consists of the anterior appendicular skeleton and associated soft and hard tissues, but excludes the pectoral girdle and its associated soft and hard tissues." [VSAO:0000150-modified] subset: homology_grouping synonym: "anterior appendage" BROAD [] @@ -218916,7 +221411,6 @@ xref: SCTID:244403000 xref: UMLS:C0022427 {source="ncithesaurus:Jugular_Vein"} xref: Wikipedia:Jugular_vein is_a: UBERON:0001638 ! vein -relationship: part_of UBERON:0000974 {gci_filler="NCBITaxon:8287", gci_relation="RO:0002162"} ! neck relationship: RO:0002179 UBERON:0000033 ! drains head property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/f/f8/Gray558.png" xsd:anyURI @@ -219086,18 +221580,16 @@ property_value: RO:0002175 NCBITaxon:9606 id: UBERON:0004726 name: vasa recta namespace: uberon -def: "In the blood supply of the kidney, the vasa recta renis (or straight arteries of kidney, or straight arterioles of kidney) form a series of straight capillaries in the medulla. They lie parallel to the loop of Henle. These vessels branch off the efferent arterioles of juxtamedullary nephrons (those nephrons closest to the medulla), enter the medulla, and surround the loop of Henle." [Wikipedia:Vasa_recta] +def: "A group of microvessels that are part of the kidney. A vasa recta has a hairpin-like shape, entering the renal medulla as the straight arterioles and surrounds the loop of Henle, forming a capillary network. Finally it leaves the renal medulla to ascend to the cortex as the straight venules. The primary function of the vasa recta is to facilitate countercurrent exchange, which is essential for the kidney's ability to concentrate urine" [PMID:23126245, Wikipedia:Vasa_recta] subset: human_reference_atlas subset: pheno_slim -synonym: "arteria recta" RELATED [Wikipedia:Vasa_recta] -synonym: "arteriae rectae" RELATED [Wikipedia:Vasa_recta] -synonym: "arteriolae rectae renis" EXACT OMO:0003011 [FMA:72006, FMA:TA] +synonym: "arteriolae rectae renis" NARROW OMO:0003011 [FMA:72006, FMA:TA] synonym: "arteriolae rectae renis" RELATED OMO:0003011 [Wikipedia:Vasa_recta] synonym: "arteriolae recti" RELATED [Wikipedia:Vasa_recta] synonym: "kidney vasa recta" EXACT [MP:0011324] -synonym: "renal medullary capillary" EXACT [EMAPA:30043] -synonym: "set of straight arterioles of kidney" EXACT [FMA:72006] -synonym: "straight arterioles of kidney" EXACT [FMA:72006] +synonym: "renal medullary capillary" NARROW [EMAPA:30043] +synonym: "set of straight arterioles of kidney" NARROW [FMA:72006] +synonym: "straight arterioles of kidney" NARROW [FMA:72006] synonym: "vasa recta of kidney" EXACT [FMA:72006] synonym: "vasa recta renis" EXACT OMO:0003011 [FMA:72006, FMA:TA] synonym: "vasa rectae" RELATED [Wikipedia:Vasa_recta] @@ -219106,10 +221598,9 @@ xref: FMA:72006 xref: galen:ArteriaeRectae xref: MA:0002595 xref: Wikipedia:Vasa_recta -is_a: UBERON:0001140 ! renal vein +is_a: UBERON:0006544 ! kidney vasculature relationship: RO:0002170 UBERON:0004640 ! connected to renal efferent arteriole property_value: foaf:depiction "https://upload.wikimedia.org/wikipedia/commons/2/21/Kidney_nephron.png" xsd:anyURI -property_value: IAO:0000116 "TODO - is this a vein or set of veins? in MA it is a venous blood vessel" xsd:string property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -219209,7 +221700,6 @@ relationship: part_of UBERON:0002028 ! hindbrain id: UBERON:0004734 name: gastrula namespace: uberon -alt_id: UBERON:0007012 def: "Organism at the gastrula stage." [Wikipedia:Gastrula, Wikipedia:Trilaminar_blastocyst] subset: pheno_slim synonym: "blastocystis trilaminaris" RELATED [https://orcid.org/0000-0002-6601-2165] @@ -219285,7 +221775,6 @@ relationship: part_of UBERON:0010533 {is_inferred="true", source="https://github id: UBERON:0004739 name: pronephric glomerulus namespace: uberon -alt_id: UBERON:0004191 def: "The glomus forms from the splanchnic intermediate mesoderm and is the vascularized filtration unit, filtering the blood before it enters the tubules. The glomus is external to the nephron and extends over more than one body segment." [DOI:10.1371/journal.pone.0099864, GO:0072013, GOC:mtg_kidney_jan10, PMID:10572058, PMID:15647339, PMID:9268568, XAO:0000318] synonym: "corpuscle" RELATED [XAO:0000318] synonym: "glomera" RELATED OMO:0003004 [XAO:0000318] @@ -219663,8 +222152,6 @@ synonym: "vasa recta of outer zone of renal medulla" EXACT [OBOL:automatic] xref: EMAPA:36560 xref: MA:0002597 is_a: UBERON:0004726 ! vasa recta -is_a: UBERON:0013126 ! vein of abdomen -is_a: UBERON:0014401 ! renal venous blood vessel intersection_of: UBERON:0004726 ! vasa recta intersection_of: part_of UBERON:0001293 ! outer medulla of kidney relationship: part_of UBERON:0001293 ! outer medulla of kidney @@ -219688,8 +222175,6 @@ synonym: "vasa recta of set of inner region of renal pyramids" EXACT [OBOL:autom xref: EMAPA:36559 xref: MA:0002596 is_a: UBERON:0004726 ! vasa recta -is_a: UBERON:0013126 ! vein of abdomen -is_a: UBERON:0014401 ! renal venous blood vessel intersection_of: UBERON:0004726 ! vasa recta intersection_of: part_of UBERON:0001294 ! inner medulla of kidney relationship: part_of UBERON:0001294 ! inner medulla of kidney @@ -220100,7 +222585,6 @@ relationship: part_of UBERON:0001264 ! pancreas id: UBERON:0004796 name: prostate gland secretion namespace: uberon -alt_id: UBERON:0010142 def: "A bodily secretion that is produced by the prostate gland." [http://orcid.org/0000-0002-6601-2165] synonym: "prostate fluid" RELATED [BTO:0001232] synonym: "prostate secretion" EXACT [OBOL:automatic] @@ -220132,6 +222616,66 @@ intersection_of: part_of UBERON:0001981 ! blood vessel relationship: part_of UBERON:0035965 ! wall of blood vessel property_value: foaf:depiction "https://upload.wikimedia.org/wikipedia/commons/6/61/Blood_vessels.svg" xsd:anyURI +[Term] +id: UBERON:0004798 +name: respiratory system basal lamina +namespace: uberon +def: "A basal lamina that is part of a respiratory system [Automatically generated definition]." [OBOL:automatic] +synonym: "apparatus respiratorius basal lamina" EXACT [OBOL:automatic] +synonym: "apparatus respiratorius basal lamina of connective tissue" EXACT [OBOL:automatic] +synonym: "basal lamina of apparatus respiratorius" EXACT [OBOL:automatic] +synonym: "basal lamina of connective tissue of apparatus respiratorius" EXACT [OBOL:automatic] +synonym: "basal lamina of connective tissue of respiratory system" EXACT [OBOL:automatic] +synonym: "basal lamina of respiratory system" EXACT [OBOL:automatic] +synonym: "respiratory system basal lamina of connective tissue" EXACT [OBOL:automatic] +xref: EMAPA:37571 {source="MA:th"} +xref: MA:0001816 +is_a: UBERON:0000482 ! basal lamina of epithelium +intersection_of: UBERON:0000482 ! basal lamina of epithelium +intersection_of: part_of UBERON:0001004 ! respiratory system +relationship: part_of UBERON:0001004 ! respiratory system + +[Term] +id: UBERON:0004799 +name: trachea basal lamina +namespace: uberon +def: "A basal lamina that is part of a respiratory airway [Automatically generated definition]." [OBOL:automatic] +synonym: "basal lamina of connective tissue of respiratory airway" EXACT [OBOL:automatic] +xref: EMAPA:37553 {source="MA:th"} +xref: MA:0001855 +xref: NCIT:C49303 +xref: UMLS:C1710454 {source="ncithesaurus:Trachea_Basal_Lamina"} +is_a: UBERON:0004798 ! respiratory system basal lamina +intersection_of: UBERON:0000482 ! basal lamina of epithelium +intersection_of: part_of UBERON:0001005 ! respiratory airway +relationship: part_of UBERON:0001005 ! respiratory airway + +[Term] +id: UBERON:0004800 +name: bronchus basal lamina +namespace: uberon +def: "A basal lamina that is part of a bronchus [Automatically generated definition]." [OBOL:automatic] +synonym: "basal lamina of bronchi" EXACT [OBOL:automatic] +synonym: "basal lamina of bronchial trunk" EXACT [OBOL:automatic] +synonym: "basal lamina of bronchus" EXACT [OBOL:automatic] +synonym: "basal lamina of connective tissue of bronchi" EXACT [OBOL:automatic] +synonym: "basal lamina of connective tissue of bronchial trunk" EXACT [OBOL:automatic] +synonym: "basal lamina of connective tissue of bronchus" EXACT [OBOL:automatic] +synonym: "bronchi basal lamina" EXACT [OBOL:automatic] +synonym: "bronchi basal lamina of connective tissue" EXACT [OBOL:automatic] +synonym: "bronchial trunk basal lamina" EXACT [OBOL:automatic] +synonym: "bronchial trunk basal lamina of connective tissue" EXACT [OBOL:automatic] +synonym: "bronchus basal lamina of connective tissue" EXACT [OBOL:automatic] +xref: EMAPA:37810 {source="MA:th"} +xref: MA:0001833 +xref: NCIT:C49207 +xref: UMLS:C1707050 {source="ncithesaurus:Bronchus_Basal_Lamina"} +is_a: UBERON:0004119 ! endoderm-derived structure +is_a: UBERON:0004799 ! trachea basal lamina +intersection_of: UBERON:0000482 ! basal lamina of epithelium +intersection_of: part_of UBERON:0002185 ! bronchus +relationship: part_of UBERON:0002185 ! bronchus + [Term] id: UBERON:0004801 name: cervix epithelium @@ -220341,7 +222885,6 @@ is_a: UBERON:0003929 ! digestive tract epithelium intersection_of: UBERON:0000483 ! epithelium intersection_of: part_of UBERON:0001044 ! saliva-secreting gland relationship: part_of UBERON:0001044 ! saliva-secreting gland -relationship: RO:0002202 UBERON:0011272 {gci_relation="part_of", gci_filler="NCBITaxon:7742", source="Wikipathways:WP2062"} ! develops from embryonic skin basal layer [Term] id: UBERON:0004810 @@ -221260,7 +223803,6 @@ relationship: part_of UBERON:0006524 ! alveolar system id: UBERON:0004894 name: alveolar wall namespace: uberon -alt_id: UBERON:0008872 def: "A wall that contains the alveoli." [LG:0012626, MP:0010903] subset: pheno_slim synonym: "alveolus wall" RELATED [EMAPA:35120] @@ -222265,6 +224807,7 @@ id: UBERON:0004990 name: mucosa of ascending colon namespace: uberon def: "A mucosa that is part of an ascending colon [Automatically generated definition]." [OBOL:automatic] +subset: human_reference_atlas synonym: "ascending colon mucosa" EXACT [OBOL:automatic] synonym: "ascending colon mucosa of organ" EXACT [OBOL:automatic] synonym: "ascending colon mucous membrane" EXACT [OBOL:automatic] @@ -222277,12 +224820,14 @@ is_a: UBERON:0000317 ! colonic mucosa intersection_of: UBERON:0000344 ! mucosa intersection_of: part_of UBERON:0001156 ! ascending colon relationship: part_of UBERON:0001156 ! ascending colon +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0004991 name: mucosa of transverse colon namespace: uberon def: "A mucosa that is part of a transverse colon [Automatically generated definition]." [OBOL:automatic] +subset: human_reference_atlas synonym: "mucosa of organ of transverse colon" EXACT [OBOL:automatic] synonym: "mucous membrane of transverse colon" EXACT [OBOL:automatic] synonym: "organ mucosa of transverse colon" EXACT [OBOL:automatic] @@ -222295,12 +224840,14 @@ is_a: UBERON:0000317 ! colonic mucosa intersection_of: UBERON:0000344 ! mucosa intersection_of: part_of UBERON:0001157 ! transverse colon relationship: part_of UBERON:0001157 ! transverse colon +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0004992 name: mucosa of descending colon namespace: uberon def: "A mucosa that is part of a descending colon [Automatically generated definition]." [OBOL:automatic] +subset: human_reference_atlas synonym: "descending colon mucosa" EXACT [OBOL:automatic] synonym: "descending colon mucosa of organ" EXACT [OBOL:automatic] synonym: "descending colon mucous membrane" EXACT [OBOL:automatic] @@ -222313,12 +224860,14 @@ is_a: UBERON:0000317 ! colonic mucosa intersection_of: UBERON:0000344 ! mucosa intersection_of: part_of UBERON:0001158 ! descending colon relationship: part_of UBERON:0001158 ! descending colon +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0004993 name: mucosa of sigmoid colon namespace: uberon def: "A mucosa that is part of a sigmoid colon [Automatically generated definition]." [OBOL:automatic] +subset: human_reference_atlas synonym: "mucosa of organ of sigmoid colon" EXACT [OBOL:automatic] synonym: "mucous membrane of sigmoid colon" EXACT [OBOL:automatic] synonym: "organ mucosa of sigmoid colon" EXACT [OBOL:automatic] @@ -222331,6 +224880,7 @@ is_a: UBERON:0000317 ! colonic mucosa intersection_of: UBERON:0000344 ! mucosa intersection_of: part_of UBERON:0001159 ! sigmoid colon relationship: part_of UBERON:0001159 ! sigmoid colon +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0004994 @@ -223658,7 +226208,6 @@ is_a: UBERON:0006598 ! presumptive structure is_a: UBERON:0011814 {source="NCBIBook:NBK53175"} ! non-neurogenic ectodermal placode intersection_of: UBERON:0005085 ! ectodermal placode intersection_of: RO:0002387 UBERON:0001091 ! has potential to develop into calcareous tooth -relationship: part_of UBERON:0011595 {gci_relation="part_of", gci_filler="NCBITaxon:40674"} ! jaw region relationship: RO:0002254 UBERON:0004362 ! has developmental contribution from pharyngeal arch 1 relationship: RO:0002387 UBERON:0001091 ! has potential to develop into calcareous tooth @@ -223732,7 +226281,6 @@ property_value: IAO:0000116 "class added for consistency with GO - consider merg id: UBERON:0005096 name: descending thin limb namespace: uberon -alt_id: UBERON:0005165 def: "The descending thin limb is a part of the loop of Henle situated just after the proximal straight tubule (S3). It extends to the tip of the loop of Henle[GO]." [GO:0072022, Wikipedia:Descending_limb_of_loop_of_Henle] subset: human_reference_atlas subset: uberon_slim @@ -223863,7 +226411,6 @@ relationship: part_of UBERON:0000081 ! metanephros id: UBERON:0005110 name: metanephric nephron namespace: uberon -alt_id: UBERON:0005142 def: "A metanephric nephron is the functional unit of the metanephros[GO]." [GO:0072273] xref: VHOG:0000719 is_a: UBERON:0001285 ! nephron @@ -224033,7 +226580,6 @@ intersection_of: part_of UBERON:0000081 ! metanephros id: UBERON:0005129 name: metanephric distal tubule namespace: uberon -alt_id: UBERON:0005150 def: "The metanephric distal tubule is a metanephric nephron tubule that begins at the metanephric macula densa and extends to the metanephric connecting tubule[GO]." [GO:0072235] is_a: UBERON:0004135 ! distal tubule is_a: UBERON:0005146 ! metanephric nephron tubule @@ -224065,7 +226611,6 @@ intersection_of: part_of UBERON:0000081 ! metanephros id: UBERON:0005133 name: metanephric glomerulus vasculature namespace: uberon -alt_id: UBERON:0005143 def: "The metanephric glomerulus vasculature is composed of the tubule structures that carry blood or lymph in the metanephric glomerulus[GO]." [GO:0072239] is_a: UBERON:0004190 ! renal glomerulus vasculature intersection_of: UBERON:0004190 ! renal glomerulus vasculature @@ -224109,7 +226654,6 @@ relationship: part_of UBERON:0005133 {is_inferred="true", source="https://github id: UBERON:0005137 name: metanephric capsule namespace: uberon -alt_id: UBERON:0005112 def: "The metanephric capsule is the tough fibrous layer surrounding the metanephros, covered in a thick layer of perinephric adipose tissue. It provides some protection from trauma and damage[GO]." [GO:0072213] is_a: UBERON:0002015 ! kidney capsule is_a: UBERON:0004120 ! mesoderm-derived structure @@ -224171,8 +226715,6 @@ relationship: part_of UBERON:0000081 ! metanephros id: UBERON:0005146 name: metanephric nephron tubule namespace: uberon -alt_id: UBERON:0005128 -alt_id: UBERON:0005152 def: "A metanephric nephron tubule is an epithelial tube that is part of the metanephric nephron, the functional part of the metanephros[GO]." [GO:0072282] is_a: UBERON:0001231 ! nephron tubule is_a: UBERON:0005106 ! metanephric tubule @@ -224221,7 +226763,6 @@ intersection_of: part_of UBERON:0000081 ! metanephros id: UBERON:0005151 name: metanephric proximal tubule namespace: uberon -alt_id: UBERON:0005131 def: "The metanephric proximal tubule is a metanephric nephron tubule that connects Bowman's capsule to the descending thin limb of the loop of Henle in the metanephros. It has a brush border epithelial morphology[GO]." [GO:0072288] is_a: UBERON:0004134 ! proximal tubule is_a: UBERON:0005146 ! metanephric nephron tubule @@ -224825,7 +227366,6 @@ def: "Stromal matrix surrounding blood vessels within the choroid plexus." [PMCI synonym: "choroid plexus stromal matrix" EXACT [PMCID:PMC3496674] xref: EMAPA:36609 xref: MA:0000825 -is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0003891 ! stroma is_a: UBERON:0004121 ! ectoderm-derived structure intersection_of: UBERON:0003891 ! stroma @@ -225413,7 +227953,6 @@ xref: EMAPA:28136 xref: MA:0002608 xref: SCTID:243707006 xref: Wikipedia:Medullary_interstitium -is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0005215 ! kidney interstitium intersection_of: UBERON:0005169 ! interstitial tissue intersection_of: part_of UBERON:0001225 ! cortex of kidney @@ -226061,7 +228600,6 @@ relationship: part_of UBERON:0000080 ! mesonephros id: UBERON:0005333 name: mammary bud namespace: uberon -alt_id: UBERON:0004181 def: "A bulb of epithelial cells that forms from the mammary placode that develops into the mammary gland." [http://orcid.org/0000-0002-6601-2165] synonym: "lactiferous gland bud" EXACT [] synonym: "mammary gland bud" EXACT [GO:0060648] @@ -226165,7 +228703,6 @@ xref: NCIT:C12329 xref: SCTID:181433005 xref: UMLS:C0037855 {source="ncithesaurus:Spermatic_Cord"} xref: Wikipedia:Spermatic_cord -is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0005156 ! reproductive structure is_a: UBERON:0034921 ! multi organ part structure relationship: has_part UBERON:0001000 ! vas deferens @@ -227072,7 +229609,6 @@ property_value: IAO:0000116 "the decision to split digestive and gastrointestina id: UBERON:0005410 name: cartilaginous otic capsule namespace: uberon -alt_id: UBERON:0010351 def: "An otic capsule endochondral element that is composed primarily of cartilage tissue." [OBOL:automatic] subset: vertebrate_core synonym: "auditory capsule" EXACT [ZFA:0001500] @@ -227980,7 +230516,6 @@ xref: TAO:0001077 xref: ZFA:0001077 is_a: UBERON:0001048 ! primordium is_a: UBERON:0003351 ! pharyngeal epithelium -relationship: part_of UBERON:0000974 {gci_relation="part_of", gci_filler="NCBITaxon:40674", source="EHDAA2"} ! neck relationship: part_of UBERON:0002405 {source="ZFA"} ! immune system relationship: part_of UBERON:0003295 {source="EHDAA2"} ! pharyngeal gland relationship: RO:0002254 UBERON:0005428 ! has developmental contribution from vagal neural crest @@ -228352,7 +230887,6 @@ xref: EMAPA:35904 xref: FMA:5900 xref: XAO:0004143 is_a: BFO:0000002 -is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0002049 ! vasculature relationship: has_part UBERON:0001981 ! blood vessel @@ -228772,7 +231306,6 @@ relationship: RO:0002495 UBERON:0007297 {source="Bgee:AN"} ! immediate transform id: UBERON:0005723 name: floor plate spinal cord region namespace: uberon -alt_id: UBERON:0005247 def: "A multi-tissue structure that is part of a spinal cord and is part of a floor plate." [OBOL:automatic] subset: vertebrate_core synonym: "floor plate spinal cord" EXACT [VHOG:0000787] @@ -228926,7 +231459,6 @@ xref: NCIT:C33818 xref: SCTID:61066005 xref: UMLS:C0225342 {source="ncithesaurus:Tunica_Adventitia"} xref: Wikipedia:Tunica_externa_(vessels) -is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0004797 {source="cjm"} ! blood vessel layer is_a: UBERON:0005742 ! adventitia relationship: RO:0000086 PATO:0002462 ! has quality collagenous @@ -228991,7 +231523,6 @@ property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/8/ id: UBERON:0005745 name: optic foramen namespace: uberon -alt_id: UBERON:0006269 def: "An opening in the skull through which cranial nerve II passes.[MP]." [https://github.com/obophenotype/uberon/issues/1213, ISBN:0-683-40008-8, MP:0010704, Wikipedia:Optic_canal] comment: In teleost fishes the opening is wider that in mammals. Due to the longer and deeper shape in mammals, this is usually called the optic canal; sometimes the term optic foramen may be used for the opening of the canal, but here we use this term to denote the entire space together with surrounding bone surface. subset: pheno_slim @@ -229183,7 +231714,6 @@ xref: NCIT:C13191 xref: SCTID:68989006 xref: UMLS:C0004799 {source="ncithesaurus:Basement_Membrane"} xref: Wikipedia:Basement_membrane -is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0005764 {source="FMA"} ! acellular membrane relationship: adjacent_to CL:0000066 ! epithelial cell relationship: has_part GO:0005587 ! collagen type IV trimer @@ -229521,7 +232051,6 @@ relationship: RO:0002202 UBERON:0005866 ! develops from pre-cartilage condensati id: UBERON:0005865 name: pre-muscle condensation namespace: uberon -alt_id: UBERON:0008714 synonym: "pre muscle mass" EXACT [] synonym: "premuscle mass" EXACT [] xref: AEO:0000149 @@ -229976,7 +232505,6 @@ comment: See notes for serous membrane xref: FMA:9689 xref: SCTID:362890006 is_a: BFO:0000002 -is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0000062 ! organ relationship: has_part UBERON:0000042 ! serous membrane relationship: has_part UBERON:0002553 ! anatomical cavity @@ -230160,7 +232688,6 @@ xref: XAO:0004011 is_a: BFO:0000002 is_a: UBERON:0010912 ! subdivision of skeleton relationship: part_of UBERON:0011137 ! axial skeletal system -relationship: RO:0002170 UBERON:0002091 {gci_relation="part_of", gci_filler="NCBITaxon:7776"} ! connected to appendicular skeleton relationship: RO:0002202 UBERON:0003089 ! develops from sclerotome relationship: RO:0002433 UBERON:0001434 ! contributes to morphology of skeletal system property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/8/8b/Axial_skeleton_diagram.svg" xsd:anyURI @@ -230277,7 +232804,6 @@ relationship: part_of UBERON:0002079 ! left cardiac atrium id: UBERON:0005969 name: eye trabecular meshwork namespace: uberon -alt_id: UBERON:0004028 def: "A pore-like structure surrounding the entire circumference of the anterior chamber of the eye through which aqueous humor circulates[MP]." [MP:0005203, Wikipedia:Trabecular_meshwork] subset: efo_slim subset: pheno_slim @@ -231009,7 +233535,6 @@ relationship: part_of UBERON:0003956 ! aqueous drainage system id: UBERON:0006207 name: aortico-pulmonary spiral septum namespace: uberon -alt_id: UBERON:0005999 def: "The spiral septum that separates the truncus arteriosus into a ventral pulmonary trunk and the dorsal aorta[MP]. The aorticopulmonary septum is developmentally formed from neural crest, specifically the cardiac neural crest, and actively separates the aorta and pulmonary arteries and fuses with the interventricular septum within the heart during development. The actual mechanism of septation of the outflow tract is poorly understood, but is recognized as a dynamic process with contributions from contractile, hemodynamic, and extracellular matrix interactions." [MP:0010650, Wikipedia:Aorticopulmonary_septum] subset: emapa_ehdaa2 subset: pheno_slim @@ -231138,7 +233663,6 @@ relationship: RO:0002387 UBERON:0001435 ! has potential to develop into carpal b id: UBERON:0006215 name: rhombic lip namespace: uberon -alt_id: UBERON:0013163 def: "The posterior section of the developing metencephalon recognized transiently within the vertebrate embryo; the rhombic lip extends posteriorly from the roof of the fourth ventricle to dorsal neuroepithelial cell and can be divided into eight structural units based on rhombomeres 1-8 (r1-r8), recognized at early stages of hindbrain development; producing granule cells and five brainstem nuclei, the rhombic lip plays an important role in developing a complex cerebellar neural system." [MGI:anna, MP:0012525] subset: pheno_slim subset: vertebrate_core @@ -231745,7 +234269,6 @@ relationship: part_of UBERON:0001697 ! orbit of skull id: UBERON:0006273 name: otic pit namespace: uberon -alt_id: UBERON:0009123 def: "The pair of depressions of thickened otic placode epithelium, that further develops into the otic vesicles." [ISBN:0-683-40008-8, MP:0011172] subset: emapa_ehdaa2 subset: pheno_slim @@ -231787,7 +234310,6 @@ relationship: RO:0002176 UBERON:0002402 ! connects pleural cavity id: UBERON:0006283 name: future cardiac ventricle namespace: uberon -alt_id: UBERON:0010226 def: "Multi-tissue structure that is part of the heart tube and will become the cardiac ventricle." [ZFA:0001719] comment: The embryonic ventricle or primitive ventricle of the developing heart gives rise to the trabeculated parts of the left and right ventricles. In contrast, the smooth parts of the left and right ventricles originate from the embryological bulbus cordis. The primitive ventricle becomes divided by a septum, the septum inferius or ventricular septum, which grows upward from the lower part of the ventricle, its position being indicated on the surface of the heart by a furrow. Its dorsal part increases more rapidly than its ventral portion, and fuses with the dorsal part of the septum intermedium. For a time an interventricular foramen exists above its ventral portion, but this foramen is ultimately closed by the fusion of the aortic septum with the ventricular septum[WP] synonym: "early heart ventricle" EXACT [] @@ -231897,7 +234419,6 @@ xref: EHDAA2:0001778 xref: EHDAA:6041 xref: EMAPA:18027 xref: VHOG:0000960 -is_a: BFO:0000002 is_a: UBERON:0015057 ! scapula endochondral element intersection_of: UBERON:0015057 ! scapula endochondral element intersection_of: RO:0002473 UBERON:0005866 ! composed primarily of pre-cartilage condensation @@ -231923,7 +234444,6 @@ relationship: RO:0002387 UBERON:0001470 ! has potential to develop into glenohum id: UBERON:0006293 name: spleen primordium namespace: uberon -alt_id: UBERON:0009750 def: "A dense syncitial-like mesenchymal thickening in the dorsal mesogastrium[ISBN]. the embryonic connective tissue made up of loosely aggregated mesenchymal cells, supported by interlaminar jelly, that gives rise to the developing spleen[MP]." [ISBN:0123747295, MP:0011263] subset: pheno_slim synonym: "left spleen primordium" NARROW [XAO:0000326] @@ -232436,6 +234956,7 @@ name: lymphatic part of lymphoid system namespace: uberon def: "An organ system subdivision that is a network of vessels capable of removing accumulating protein and fluid from the interstitial space and returning it to the vascular space. In some species, this network is connected to the immune system via lymph nodes and lymphocyte-producing organs, with the whole being the lymphoid system." [http://orcid.org/0000-0002-6601-2165] subset: efo_slim +subset: human_reference_atlas subset: pheno_slim synonym: "lymphatic system" EXACT [FMA:7162, MA:0002435] synonym: "lymphatic tree system" EXACT [FMA:7162] @@ -232454,6 +234975,7 @@ is_a: UBERON:0011216 ! organ system subdivision relationship: part_of UBERON:0001009 {source="AAO"} ! circulatory system relationship: part_of UBERON:0002465 {source="FMA", source="MA"} ! lymphoid system property_value: IAO:0000116 "consider merging with lymph vasculature" xsd:string +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0006561 @@ -232650,7 +235172,6 @@ relationship: part_of UBERON:0004681 ! vestibular system id: UBERON:0006586 name: otolymph namespace: uberon -alt_id: UBERON:0007793 def: "Transudate located within the osseus labyrinth. Otolymph can be further classified with respect to whether it is within the membranous labyrinth (endolymph) or outside the mebranous labyrinth (perilymph)." [http://orcid.org/0000-0002-6601-2165] synonym: "labyrinthine fluid" RELATED [MESH:A12.207.571] xref: EMAPA:36547 @@ -233316,7 +235837,6 @@ property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/1/ id: UBERON:0006725 name: spiral ligament namespace: uberon -alt_id: UBERON:0028186 def: "A spiral thickening of the fibrous lining of the cochlear wall. Spiral ligament secures the membranous cochlear duct to the bony spiral canal of the cochlea. Its spiral ligament fibrocytes function in conjunction with the stria vascularis to mediate cochlear ion homeostasis." [https://github.com/obophenotype/mouse-anatomy-ontology/issues/71, Wikipedia:Spiral_ligament] subset: pheno_slim synonym: "ligamentum spirale ductus cochlearis" EXACT OMO:0003011 [Wikipedia:Spiral_ligament] @@ -233448,8 +235968,8 @@ xref: UMLS:C0682578 {source="ncithesaurus:Glandular_Epithelium"} xref: UMLS:C1708242 {source="ncithesaurus:Glandular_Epithelial_Tissue"} is_a: UBERON:0000483 ! epithelium intersection_of: UBERON:0000483 ! epithelium -intersection_of: RO:0002473 CL:0000150 ! composed primarily of glandular epithelial cell -relationship: RO:0002473 CL:0000150 ! composed primarily of glandular epithelial cell +intersection_of: RO:0002473 CL:0000150 ! composed primarily of glandular secretory epithelial cell +relationship: RO:0002473 CL:0000150 ! composed primarily of glandular secretory epithelial cell property_value: IAO:0000116 "consider splitting epithelium from epithelial tissue" xsd:string [Term] @@ -233606,8 +236126,6 @@ property_value: seeAlso "https://github.com/obophenotype/uberon/issues/2667" xsd id: UBERON:0006849 name: scapula namespace: uberon -alt_id: UBERON:0001124 -alt_id: UBERON:0010904 def: "Endochondral bone that is dorsoventrally compressed and provides attachment site for muscles of the pectoral appendage." [https://github.com/obophenotype/uberon/issues/204, https://github.com/obophenotype/uberon/issues/339, VSAO:0000157] subset: efo_slim subset: human_reference_atlas @@ -233640,11 +236158,7 @@ is_a: UBERON:0007829 ! pectoral girdle bone is_a: UBERON:0015057 ! scapula endochondral element intersection_of: UBERON:0015057 ! scapula endochondral element intersection_of: RO:0002473 UBERON:0002481 ! composed primarily of bone tissue -relationship: distally_connected_to UBERON:0000976 {gci_relation="part_of", gci_filler="NCBITaxon:32523"} ! humerus relationship: distally_connected_to UBERON:0007272 ! pectoral appendage skeleton -relationship: overlaps UBERON:0001470 {gci_relation="part_of", gci_filler="NCBITaxon:32523"} ! glenohumeral joint -relationship: overlaps UBERON:0003692 {gci_relation="part_of", gci_filler="NCBITaxon:32523"} ! acromioclavicular joint -relationship: part_of UBERON:0001467 {gci_relation="part_of", gci_filler="NCBITaxon:32523", source="FMA"} ! shoulder relationship: RO:0002202 UBERON:0004753 {source="ZFA"} ! develops from scapulocoracoid relationship: RO:0002202 UBERON:0006290 ! develops from scapula cartilage element property_value: foaf:depiction "https://upload.wikimedia.org/wikipedia/commons/5/59/Pectoral_girdles-en.svg" xsd:anyURI @@ -233833,7 +236347,6 @@ relationship: produces UBERON:0006530 ! seminal fluid id: UBERON:0006871 name: embryonic footplate namespace: uberon -alt_id: UBERON:0004343 def: "The distal elements of the developing limb of vertebrates that will give rise to the pes (foot)." [https://github.com/obophenotype/mammalian-phenotype-ontology/issues/2218, MGI:csmith, MP:0004576, UBERON:cjm] subset: pheno_slim synonym: "distal part of hindlimb bud" RELATED [EMAPA:17249] @@ -234203,7 +236716,7 @@ xref: UMLS:C0225337 {source="ncithesaurus:Columnar_Epithelium"} is_a: UBERON:0000485 ! simple columnar epithelium is_a: UBERON:0006799 ! glandular epithelium intersection_of: UBERON:0000485 ! simple columnar epithelium -intersection_of: RO:0002473 CL:0000150 ! composed primarily of glandular epithelial cell +intersection_of: RO:0002473 CL:0000150 ! composed primarily of glandular secretory epithelial cell [Term] id: UBERON:0006930 @@ -234213,7 +236726,7 @@ xref: FMA:66809 is_a: UBERON:0000484 ! simple cuboidal epithelium is_a: UBERON:0006799 ! glandular epithelium intersection_of: UBERON:0000484 ! simple cuboidal epithelium -intersection_of: RO:0002473 CL:0000150 ! composed primarily of glandular epithelial cell +intersection_of: RO:0002473 CL:0000150 ! composed primarily of glandular secretory epithelial cell [Term] id: UBERON:0006931 @@ -234354,7 +236867,6 @@ property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/b/ id: UBERON:0006947 name: male genital duct namespace: uberon -alt_id: UBERON:0010140 def: "A duct or series of ducts that transports sperm from the gonad. In mammals this is from the seminiferous tubules through rete testis, vas efferentia, epididymis, vas deferens, ejeculatory duct to the urethra." [https://orcid.org/0000-0002-6601-2165] subset: grouping_class synonym: "sperm duct" EXACT [ZFA:0001268] @@ -234508,7 +237020,6 @@ xref: EFO:0003709 xref: TAO:0005077 xref: ZFA:0005077 is_a: BFO:0000002 -is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0005423 ! developing anatomical structure relationship: has_part CL:0000115 ! endothelial cell relationship: has_part CL:0000566 ! angioblastic mesenchymal cell @@ -234764,7 +237275,6 @@ property_value: RO:0002175 NCBITaxon:9606 id: UBERON:0007122 name: pharyngeal pouch 1 namespace: uberon -alt_id: UBERON:0005718 def: "A pharyngeal pouch that is between pharyngeal arches 1 and 2." [ISBN:0124020607, PMID:16313389, VHOG:0000970] subset: efo_slim subset: pheno_slim @@ -234806,7 +237316,6 @@ relationship: overlaps UBERON:0004362 ! pharyngeal arch 1 id: UBERON:0007123 name: pharyngeal pouch 2 namespace: uberon -alt_id: UBERON:0005715 def: "A pharyngeal puch that is between the pharyngeal arches 2 and 3." [ISBN:0124020607, PMID:16313389] subset: efo_slim subset: pheno_slim @@ -234847,7 +237356,6 @@ relationship: overlaps UBERON:0003114 ! pharyngeal arch 3 id: UBERON:0007124 name: pharyngeal pouch 3 namespace: uberon -alt_id: UBERON:0005716 def: "A pharyngeal pouch that between pharyngeal arches 3 and 4." [ISBN:0124020607, PMID:16313389, Wikipedia:Pharyngeal_pouch_(embryology)#Third_pouch] subset: efo_slim subset: pheno_slim @@ -235242,7 +237750,6 @@ synonym: "bone marrow stroma" EXACT [FMA:21426] xref: CALOHA:TS-0085 xref: FMA:21426 xref: Wikipedia:Bone_marrow#Stroma -is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0003891 ! stroma is_a: UBERON:0004120 ! mesoderm-derived structure intersection_of: UBERON:0003891 ! stroma @@ -235256,7 +237763,6 @@ relationship: part_of UBERON:0002371 ! bone marrow id: UBERON:0007196 name: tracheobronchial tree namespace: uberon -alt_id: UBERON:0004102 def: "The structure from the trachea, bronchi, and bronchioles that forms the airways that supply air to the lungs. The lining of the tracheobronchial tree consists of ciliated columnar epithelial cells." [Wikipedia:Tracheobronchial_tree] subset: human_reference_atlas subset: organ_slim @@ -235267,7 +237773,6 @@ xref: FMA:7393 xref: NCIT:C117875 xref: SCTID:361384001 xref: Wikipedia:Tracheobronchial_tree -is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0000062 ! organ is_a: UBERON:0004119 ! endoderm-derived structure relationship: has_part UBERON:0002185 ! bronchus @@ -235407,7 +237912,6 @@ xref: Wikipedia:Infant is_a: BFO:0000003 is_a: UBERON:0000105 ! life cycle stage relationship: part_of UBERON:0000112 ! sexually immature stage -relationship: part_of UBERON:0018685 {gci_relation="part_of", gci_filler="NCBITaxon:40674"} ! nursing stage property_value: IAO:0000116 "consider splitting infant/newborn" xsd:string property_value: seeAlso "https://github.com/obophenotype/uberon/issues/350" xsd:anyURI @@ -236034,7 +238538,6 @@ synonym: "pancreatic lobule" EXACT [FMA:16012] xref: EMAPA:37710 {source="MA:th"} xref: FMA:16012 xref: MA:0000721 -is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0000064 ! organ part is_a: UBERON:0004119 ! endoderm-derived structure relationship: has_part UBERON:0001263 ! pancreatic acinus @@ -236275,7 +238778,6 @@ relationship: RO:0002162 NCBITaxon:7742 ! in taxon Vertebrata id: UBERON:0007414 name: nucleus of midbrain tegmentum namespace: uberon -alt_id: UBERON:0012277 def: "A nucleus of brain that spans a midbrain tegmentum." [OBOL:automatic] synonym: "tegmental nuclei" EXACT OMO:0003004 [] synonym: "tegmental nucleus" EXACT [ZFA:0005577] @@ -236723,7 +239225,6 @@ intersection_of: part_of UBERON:0000915 ! thoracic segment of trunk id: UBERON:0007645 name: future meninx namespace: uberon -alt_id: UBERON:0004065 def: "A developing mesenchymal capsule that covers the developing brain and spinal cord and is the precursor of the meningeal cluster. In mammals this gives rise to the arachnoid mater, pia mater and dura mater. In cyclostomes and fishes, the future meninx gives rise to a single meningeal layer, the primitive meninx." [http://orcid.org/0000-0002-6601-2165] subset: pheno_slim synonym: "meninx primitiva" RELATED [MP:0009726] @@ -236757,7 +239258,6 @@ relationship: RO:0002387 UBERON:0000391 ! has potential to develop into leptomen id: UBERON:0007647 name: ectomeninx namespace: uberon -alt_id: UBERON:0010115 def: "The outermost layer of the mesenchymal capsule that surrounds the developing brain, of mixed paraxial mesoderm and neural crest origin. The ectomeninx forms the dura mater (both inner layer and outer chondrogenic layer)." [ISBN:9781607950325] synonym: "future dura mater" EXACT [EHDAA2:0004317] xref: EHDAA2:0004317 @@ -237177,9 +239677,9 @@ xref: NCIT:C12418 xref: SCTID:361355005 xref: UMLS:C0460004 {source="ncithesaurus:Head_and_Neck"} xref: WikipediaCategory:Head_and_neck +xref: ZFA:0001114 is_a: UBERON:0000475 {source="MA"} ! organism subdivision relationship: has_part UBERON:0000033 ! head -relationship: has_part UBERON:0000974 {gci_relation="part_of", gci_filler="NCBITaxon:32523"} ! neck relationship: has_part UBERON:0006562 ! pharynx relationship: part_of UBERON:0000153 ! anterior region of body relationship: part_of UBERON:0013702 ! body proper @@ -237216,7 +239716,6 @@ property_value: RO:0002161 NCBITaxon:314295 id: UBERON:0007823 name: appendage girdle region namespace: uberon -alt_id: UBERON:0007824 def: "An organism subdivision that encompasses the region containing the pectoral or pelvic girdle. Note that this includes both the skeletal elements and associated tissues (integument, muscle, etc)." [https://orcid.org/0000-0002-6601-2165, UBERONREF:0000003] synonym: "fin girdle" RELATED SENSU [] synonym: "fin girdle region" RELATED SENSU [] @@ -237449,7 +239948,6 @@ namespace: uberon def: "Connective tissue, which consists of fibroblasts, the intercellular matrix of which contains a regular network of collagen and elastic fiber bundles. Examples: bone (tissue), cartilage (tissue), dense regular connective tissue." [FMA:20103] xref: FMA:20103 is_a: BFO:0000002 -is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0002384 {source="FMA"} ! connective tissue disjoint_from: UBERON:0011821 ! irregular connective tissue relationship: has_part CL:0000057 ! fibroblast @@ -237779,7 +240277,6 @@ xref: SCTID:53301001 xref: UMLS:C0040442 {source="ncithesaurus:Tooth_Bud"} is_a: BFO:0000002 is_a: UBERON:0005423 ! developing anatomical structure -relationship: part_of UBERON:0011595 {gci_relation="part_of", gci_filler="NCBITaxon:40674"} ! jaw region relationship: RO:0002202 UBERON:0005087 ! develops from tooth placode [Term] @@ -238032,7 +240529,6 @@ xref: EMAPA:18541 xref: Wikipedia:Milk_line is_a: BFO:0000002 is_a: UBERON:0006598 ! presumptive structure -relationship: part_of UBERON:0000915 {gci_relation="part_of", gci_filler="NCBITaxon:9443"} ! thoracic segment of trunk relationship: part_of UBERON:0002100 ! trunk relationship: RO:0002202 UBERON:0000924 ! develops from ectoderm relationship: RO:0002387 UBERON:0001911 ! has potential to develop into mammary gland @@ -238520,7 +241016,6 @@ xref: SCTID:410744003 xref: VSAO:0000072 xref: Wikipedia:Ligament#Articular_ligaments is_a: BFO:0000002 -is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0000211 ! ligament intersection_of: UBERON:0000211 ! ligament intersection_of: part_of UBERON:0001434 ! skeletal system @@ -238685,7 +241180,6 @@ property_value: terms:contributor https://orcid.org/0000-0001-6677-8489 id: UBERON:0008876 name: hypodermis skeletal muscle layer namespace: uberon -alt_id: UBERON:0010934 def: "Any skeletal muscle organ in the hypodermis / superficial fascia." [ISBN:0123813611, MP:0011157] subset: pheno_slim synonym: "hypodermal muscle layer" EXACT [MP:0011157] @@ -238788,7 +241282,6 @@ synonym: "pulmonary system" EXACT [ISBN:0073040584] xref: FMA:45621 xref: Wikipedia:Pulmonary_circulation is_a: BFO:0000002 -is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0007798 {source="Obol"} ! vascular system relationship: has_part UBERON:0002012 ! pulmonary artery relationship: has_part UBERON:0002016 ! pulmonary vein @@ -238840,7 +241333,6 @@ xref: ZFA:0001216 is_a: BFO:0000002 is_a: UBERON:0011159 ! primary subdivision of cranial skeletal system disjoint_from: UBERON:0011156 ! facial skeleton -relationship: overlaps UBERON:0011156 {gci_relation="part_of", gci_filler="NCBITaxon:89593"} ! facial skeleton relationship: RO:0002202 UBERON:0002539 {source="https://github.com/obophenotype/uberon/issues/83"} ! develops from pharyngeal arch relationship: RO:0002254 UBERON:0003099 ! has developmental contribution from cranial neural crest property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/7/77/Illu_facial_bones.jpg" xsd:anyURI @@ -238964,10 +241456,7 @@ namespace: uberon def: "A retinal neural layer that is immediately adjacent to the inner nuclear layer and comprises 20 percent of the inner plexiform layer of retina." [GOC:tfm] xref: CP:0000113 is_a: UBERON:0008927 ! sublaminar layers S1 or S2 -is_a: UBERON:0009732 ! sublaminar layers S1 or S2 or S5 -is_a: UBERON:0009733 ! sublaminar layers S1 or S2 or S3 is_a: UBERON:0009735 ! sublaminar layers S1 or S3 or S4 -is_a: UBERON:0009737 ! sublaminar layers S1 or S2 or S3 or S4 intersection_of: UBERON:0008921 ! substratum of layer of retina intersection_of: adjacent_to UBERON:0001791 ! inner nuclear layer of retina intersection_of: adjacent_to UBERON:0008923 ! sublaminar layer S2 @@ -238983,10 +241472,6 @@ def: "A retinal neural layer that is immediately adjacent to the S1 and S3 layer xref: CP:0000114 is_a: UBERON:0008927 ! sublaminar layers S1 or S2 is_a: UBERON:0008928 ! sublaminar layers S2 or S3 -is_a: UBERON:0009732 ! sublaminar layers S1 or S2 or S5 -is_a: UBERON:0009733 ! sublaminar layers S1 or S2 or S3 -is_a: UBERON:0009734 ! sublaminar layers S2 or S3 or S4 -is_a: UBERON:0009737 ! sublaminar layers S1 or S2 or S3 or S4 intersection_of: UBERON:0008921 ! substratum of layer of retina intersection_of: adjacent_to UBERON:0008922 ! sublaminar layer S1 intersection_of: adjacent_to UBERON:0008924 ! sublaminar layer S3 @@ -239003,11 +241488,6 @@ def: "A retinal neural layer that is immediately adjacent to the S2 and S4 layer xref: CP:0000115 is_a: UBERON:0008928 ! sublaminar layers S2 or S3 is_a: UBERON:0009731 ! sublaminar layers S3 or S4 -is_a: UBERON:0009733 ! sublaminar layers S1 or S2 or S3 -is_a: UBERON:0009734 ! sublaminar layers S2 or S3 or S4 -is_a: UBERON:0009735 ! sublaminar layers S1 or S3 or S4 -is_a: UBERON:0009736 ! sublaminar layers S3 or S4 or S5 -is_a: UBERON:0009737 ! sublaminar layers S1 or S2 or S3 or S4 intersection_of: UBERON:0008921 ! substratum of layer of retina intersection_of: adjacent_to UBERON:0008923 ! sublaminar layer S2 intersection_of: adjacent_to UBERON:0008925 ! sublaminar layer S4 @@ -239023,10 +241503,6 @@ def: "A retinal neural layer that is immediately adjacent to the S3 and S5 layer xref: CP:0000116 is_a: UBERON:0008929 ! sublaminar layers S4 or S5 is_a: UBERON:0009731 ! sublaminar layers S3 or S4 -is_a: UBERON:0009734 ! sublaminar layers S2 or S3 or S4 -is_a: UBERON:0009735 ! sublaminar layers S1 or S3 or S4 -is_a: UBERON:0009736 ! sublaminar layers S3 or S4 or S5 -is_a: UBERON:0009737 ! sublaminar layers S1 or S2 or S3 or S4 intersection_of: UBERON:0008921 ! substratum of layer of retina intersection_of: adjacent_to UBERON:0008924 ! sublaminar layer S3 intersection_of: adjacent_to UBERON:0008926 ! sublaminar layer S5 @@ -239042,7 +241518,6 @@ def: "A retinal neural layer that is immediately adjacent to the retinal ganglio xref: CP:0000117 is_a: UBERON:0008929 ! sublaminar layers S4 or S5 is_a: UBERON:0009732 ! sublaminar layers S1 or S2 or S5 -is_a: UBERON:0009736 ! sublaminar layers S3 or S4 or S5 intersection_of: UBERON:0008921 ! substratum of layer of retina intersection_of: adjacent_to UBERON:0001792 ! ganglionic layer of retina intersection_of: adjacent_to UBERON:0008925 ! sublaminar layer S4 @@ -239056,7 +241531,8 @@ name: sublaminar layers S1 or S2 namespace: uberon def: "One of sublaminar layers S1 or S2." [GOC:tfm, https://github.com/obophenotype/uberon/issues/31] xref: CP:0000118 -is_a: UBERON:0008921 ! substratum of layer of retina +is_a: UBERON:0009732 ! sublaminar layers S1 or S2 or S5 +is_a: UBERON:0009733 ! sublaminar layers S1 or S2 or S3 union_of: UBERON:0008922 ! sublaminar layer S1 union_of: UBERON:0008923 ! sublaminar layer S2 relationship: part_of UBERON:0001795 ! inner plexiform layer of retina @@ -239067,7 +241543,8 @@ name: sublaminar layers S2 or S3 namespace: uberon def: "One of sublaminar layers S2 or S3." [GOC:tfm, https://github.com/obophenotype/uberon/issues/31] xref: CP:0000119 -is_a: UBERON:0008921 ! substratum of layer of retina +is_a: UBERON:0009733 ! sublaminar layers S1 or S2 or S3 +is_a: UBERON:0009734 ! sublaminar layers S2 or S3 or S4 union_of: UBERON:0008923 ! sublaminar layer S2 union_of: UBERON:0008924 ! sublaminar layer S3 relationship: part_of UBERON:0001795 ! inner plexiform layer of retina @@ -239078,7 +241555,7 @@ name: sublaminar layers S4 or S5 namespace: uberon def: "One of sublaminar layers S4 or S5." [GOC:tfm, https://github.com/obophenotype/uberon/issues/31] xref: CP:0000120 -is_a: UBERON:0008921 ! substratum of layer of retina +is_a: UBERON:0009736 ! sublaminar layers S3 or S4 or S5 union_of: UBERON:0008925 ! sublaminar layer S4 union_of: UBERON:0008926 ! sublaminar layer S5 relationship: part_of UBERON:0001795 ! inner plexiform layer of retina @@ -239227,7 +241704,6 @@ property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/e/ id: UBERON:0008998 name: vasculature of brain namespace: uberon -alt_id: UBERON:0005284 def: "System pertaining to blood vessels in the brain." [BTO:0003840] subset: efo_slim synonym: "brain vasculature" EXACT [] @@ -239389,49 +241865,44 @@ property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0009089 -name: inner medulla vasa recta descending limb +name: inner medulla descending vasa recta namespace: uberon xref: KUPO:0001003 is_a: UBERON:0000064 ! organ part -is_a: UBERON:0004120 ! mesoderm-derived structure relationship: part_of UBERON:0004776 {source="KUPO"} ! inner renal medulla vasa recta [Term] id: UBERON:0009090 -name: outer medulla vasa recta descending limb +name: outer medulla descending vasa recta namespace: uberon xref: KUPO:0001004 is_a: UBERON:0000064 ! organ part -is_a: UBERON:0004120 ! mesoderm-derived structure relationship: part_of UBERON:0004775 {source="KUPO"} ! outer renal medulla vasa recta [Term] id: UBERON:0009091 -name: vasa recta ascending limb +name: ascending vasa recta namespace: uberon subset: human_reference_atlas xref: KUPO:0001005 is_a: UBERON:0000064 ! organ part -is_a: UBERON:0004120 ! mesoderm-derived structure relationship: part_of UBERON:0004726 {source="KUPO"} ! vasa recta property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0009092 -name: inner medulla vasa recta ascending limb +name: inner medulla ascending vasa recta namespace: uberon xref: KUPO:0001006 is_a: UBERON:0000064 ! organ part -is_a: UBERON:0004120 ! mesoderm-derived structure relationship: part_of UBERON:0004776 {source="KUPO"} ! inner renal medulla vasa recta [Term] id: UBERON:0009093 -name: outer medulla vasa recta ascending limb +name: outer medulla ascending vasa recta namespace: uberon xref: KUPO:0001007 is_a: UBERON:0000064 ! organ part -is_a: UBERON:0004120 ! mesoderm-derived structure relationship: part_of UBERON:0004775 {source="KUPO"} ! outer renal medulla vasa recta [Term] @@ -239631,7 +242102,6 @@ relationship: RO:0002202 UBERON:0005092 {source="EHDAA2"} ! develops from right id: UBERON:0009133 name: pleuroperitoneal membrane namespace: uberon -alt_id: UBERON:0009146 def: "A fold of tissue which extends into the peritoneal cavity of the developing embryo and participates in the separation of the pleural and peritoneal cavities." [http://medical-dictionary.thefreedictionary.com/pleuroperitoneal+membrane, Wikipedia:Pleuroperitoneal] synonym: "pleuroperitoneal fold" EXACT [VHOG:0000757] synonym: "pleuroperitoneal membranes" EXACT OMO:0003004 [EHDAA2:0001483] @@ -239666,7 +242136,6 @@ relationship: part_of UBERON:0007811 ! craniocervical region id: UBERON:0009142 name: entire embryonic mesenchyme namespace: uberon -alt_id: UBERON:0003313 def: "Sum total of mesenchyme in the embryo." [https://github.com/obophenotype/human-developmental-anatomy-ontology/issues/7] xref: EHDAA2:0001113 xref: EHDAA:177 @@ -239780,17 +242249,17 @@ is_a: UBERON:0003914 {source="EHDAA2"} ! epithelial tube is_a: UBERON:0004819 ! kidney epithelium is_a: UBERON:0006553 ! renal duct is_a: UBERON:0006555 ! excretory tube +is_a: UBERON:0012275 ! meso-epithelium union_of: UBERON:0003060 ! pronephric duct union_of: UBERON:0003074 ! mesonephric duct [Term] id: UBERON:0009202 -name: vasa recta descending limb +name: descending vasa recta namespace: uberon subset: human_reference_atlas xref: KUPO:0001002 is_a: UBERON:0000064 ! organ part -is_a: UBERON:0004120 ! mesoderm-derived structure relationship: part_of UBERON:0004726 {source="KUPO"} ! vasa recta property_value: RO:0002175 NCBITaxon:9606 @@ -240028,7 +242497,7 @@ synonym: "branchial arch mesenchyme" EXACT [MP:0011262] synonym: "pharyngeal arch mesenchyme" EXACT [https://orcid.org/0000-0002-6601-2165] xref: EMAPA:32755 xref: FMA:295694 -is_a: UBERON:0005253 ! head mesenchyme +is_a: UBERON:0005291 ! embryonic tissue is_a: UBERON:0007524 {source="EHDAA2"} ! dense mesenchyme tissue intersection_of: UBERON:0003104 ! mesenchyme intersection_of: part_of UBERON:0002539 ! pharyngeal arch @@ -240298,7 +242767,6 @@ relationship: part_of UBERON:0002544 ! digit id: UBERON:0009552 name: distal segment of manual digit namespace: uberon -alt_id: UBERON:0004093 def: "A segment of the manual digit containing the distal phalanx." [http://orcid.org/0000-0002-6601-2165] subset: pheno_slim synonym: "finger digit tip" EXACT [DOI:10.1038/nature10346] @@ -240600,7 +243068,6 @@ relationship: part_of UBERON:0006241 ! future spinal cord id: UBERON:0009584 name: 1st arch mandibular mesenchyme namespace: uberon -alt_id: UBERON:0010043 def: "Mesenchyme that is part of a 1st arch mandibular component." [OBOL:automatic] synonym: "mandibular component mesenchyme" RELATED [] synonym: "mandibular mesenchyme" RELATED [] @@ -240687,7 +243154,7 @@ synonym: "MHB neural plate" EXACT [https://orcid.org/0000-0002-6601-2165] synonym: "midbrain-hindbrain boundary neural plate" EXACT [ZFA:0007044] xref: TAO:0007044 xref: ZFA:0007044 -is_a: BFO:0000002 +is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0006598 ! presumptive structure relationship: part_of UBERON:0003075 {source="ZFA"} ! neural plate relationship: RO:0002495 UBERON:0007281 ! immediate transformation of presumptive midbrain hindbrain boundary @@ -241276,7 +243743,9 @@ name: sublaminar layers S3 or S4 namespace: uberon def: "One of sublaminar layers S3 or S4." [GOC:plr, https://github.com/obophenotype/uberon/issues/31] xref: CP:0001040 -is_a: UBERON:0008921 ! substratum of layer of retina +is_a: UBERON:0009734 ! sublaminar layers S2 or S3 or S4 +is_a: UBERON:0009735 ! sublaminar layers S1 or S3 or S4 +is_a: UBERON:0009736 ! sublaminar layers S3 or S4 or S5 union_of: UBERON:0008924 ! sublaminar layer S3 union_of: UBERON:0008925 ! sublaminar layer S4 @@ -241297,7 +243766,7 @@ name: sublaminar layers S1 or S2 or S3 namespace: uberon def: "One of sublaminar layers S1, S2, or S3." [GOC:plr, https://github.com/obophenotype/uberon/issues/31] xref: CP:0001042 -is_a: UBERON:0008921 ! substratum of layer of retina +is_a: UBERON:0009737 ! sublaminar layers S1 or S2 or S3 or S4 union_of: UBERON:0008922 ! sublaminar layer S1 union_of: UBERON:0008923 ! sublaminar layer S2 union_of: UBERON:0008924 ! sublaminar layer S3 @@ -241308,7 +243777,7 @@ name: sublaminar layers S2 or S3 or S4 namespace: uberon def: "One of sublaminar layers S2, S3, or S4." [GOC:plr, https://github.com/obophenotype/uberon/issues/31] xref: CP:0001043 -is_a: UBERON:0008921 ! substratum of layer of retina +is_a: UBERON:0009737 ! sublaminar layers S1 or S2 or S3 or S4 union_of: UBERON:0008923 ! sublaminar layer S2 union_of: UBERON:0008924 ! sublaminar layer S3 union_of: UBERON:0008925 ! sublaminar layer S4 @@ -241319,7 +243788,7 @@ name: sublaminar layers S1 or S3 or S4 namespace: uberon def: "One of sublaminar layers S1, S3, or S4." [GOC:plr, https://github.com/obophenotype/uberon/issues/31] xref: CP:0001044 -is_a: UBERON:0008921 ! substratum of layer of retina +is_a: UBERON:0009737 ! sublaminar layers S1 or S2 or S3 or S4 union_of: UBERON:0008922 ! sublaminar layer S1 union_of: UBERON:0008924 ! sublaminar layer S3 union_of: UBERON:0008925 ! sublaminar layer S4 @@ -241734,7 +244203,6 @@ property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/9/ id: UBERON:0009870 name: zone of stomach namespace: uberon -alt_id: UBERON:0009034 def: "A division of the stomach. The stomach can be divided based on mucosal histology (glandular epithelium and gastric glands) and the relative position and type of gastric gland." [ISBN:0073040584, Wikipedia:Stomach#Sections] synonym: "gastric zone" EXACT [FMA:14558] synonym: "region of stomach" EXACT [] @@ -242723,7 +245191,6 @@ relationship: RO:0002254 UBERON:0003099 {source="cjm"} ! has developmental contr id: UBERON:0010047 name: oral gland namespace: uberon -alt_id: UBERON:0003293 def: "Gland of the epithelium lining the oral cavity. The most common are the salivary glands." [ISBN:0073040584] synonym: "buccal gland" NARROW [] synonym: "gland of oral opening" RELATED [] @@ -243447,7 +245914,6 @@ xref: BTO:0000102 xref: galen:BloodClot xref: Wikipedia:Thrombus is_a: BFO:0000002 -is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0000463 ! organism substance intersection_of: UBERON:0000463 ! organism substance intersection_of: output_of GO:0007596 ! blood coagulation @@ -244162,7 +246628,6 @@ namespace: uberon def: "Mesenchyme that develops_from a head mesenchyme from mesoderm and is part of a 1st arch mesenchyme." [OBOL:automatic] synonym: "mesenchyme derived from head mesoderm of mesenchyme of 1st arch" EXACT [EMAPA:16130] xref: EMAPA:16130 -is_a: UBERON:0006904 ! head mesenchyme from mesoderm is_a: UBERON:0010042 ! 1st arch mesenchyme is_a: UBERON:0010360 ! pharyngeal arch mesenchyme from head mesenchyme intersection_of: UBERON:0003104 ! mesenchyme @@ -244182,7 +246647,6 @@ synonym: "pharyngeal arch 2 mesenchyme from head mesenchyme" EXACT [] xref: EHDAA2:0000067 xref: EMAPA:16280 is_a: UBERON:0005689 ! 2nd arch mesenchyme -is_a: UBERON:0006904 ! head mesenchyme from mesoderm is_a: UBERON:0010360 ! pharyngeal arch mesenchyme from head mesenchyme intersection_of: UBERON:0003104 ! mesenchyme intersection_of: part_of UBERON:0005689 ! 2nd arch mesenchyme @@ -244201,7 +246665,6 @@ synonym: "pharyngeal arch 3 mesenchyme from head mesenchyme" EXACT [] xref: EHDAA2:0000082 xref: EMAPA:16403 is_a: UBERON:0005690 ! 3rd arch mesenchyme -is_a: UBERON:0006904 ! head mesenchyme from mesoderm is_a: UBERON:0010360 ! pharyngeal arch mesenchyme from head mesenchyme intersection_of: UBERON:0003104 ! mesenchyme intersection_of: part_of UBERON:0005690 ! 3rd arch mesenchyme @@ -244220,7 +246683,6 @@ synonym: "pharyngeal arch 4 mesenchyme from head mesenchyme" EXACT [] xref: EHDAA2:0000097 xref: EMAPA:16771 is_a: UBERON:0005691 ! 4th arch mesenchyme -is_a: UBERON:0006904 ! head mesenchyme from mesoderm is_a: UBERON:0010360 ! pharyngeal arch mesenchyme from head mesenchyme intersection_of: UBERON:0003104 ! mesenchyme intersection_of: part_of UBERON:0005691 ! 4th arch mesenchyme @@ -244236,7 +246698,6 @@ synonym: "branchial arch 6 mesenchyme from head mesenchyme" RELATED [] synonym: "head mesenchyme derived arch 6 mesenchyme" EXACT [] synonym: "pharyngeal arch 6 mesenchyme from head mesenchyme" EXACT [] xref: EHDAA2:0004078 -is_a: UBERON:0006904 ! head mesenchyme from mesoderm is_a: UBERON:0010031 ! 6th arch mesenchyme is_a: UBERON:0010360 ! pharyngeal arch mesenchyme from head mesenchyme intersection_of: UBERON:0003104 ! mesenchyme @@ -244364,7 +246825,6 @@ relationship: RO:0002162 NCBITaxon:7742 ! in taxon Vertebrata id: UBERON:0010365 name: odontoid tissue namespace: uberon -alt_id: UBERON:0001973 def: "Skeletal tissue that is part of the exoskeleton and derived from an odontogenic papilla." [GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070, PSPUB:0000170, VSAO:0000063] subset: uberon_slim synonym: "dental tissue" RELATED [VSAO:curator] @@ -244387,7 +246847,6 @@ is_a: UBERON:0010313 ! neural crest-derived structure intersection_of: UBERON:0004755 ! skeletal tissue intersection_of: part_of UBERON:0010364 ! dermal skeleton intersection_of: RO:0002202 UBERON:0001763 ! develops from odontogenic papilla -relationship: part_of UBERON:0001091 {gci_relation="part_of", gci_filler="NCBITaxon:32524"} ! calcareous tooth relationship: part_of UBERON:0010364 ! dermal skeleton relationship: RO:0002202 UBERON:0001763 ! develops from odontogenic papilla relationship: RO:0002433 UBERON:0001091 ! contributes to morphology of calcareous tooth @@ -244880,7 +247339,6 @@ synonym: "primary follicle" RELATED [] synonym: "primary lymphoid follicle" EXACT [] synonym: "primary lymphoid nodule" EXACT [FMA:55223] xref: FMA:55223 -is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0000444 {source="FMA"} ! lymphoid follicle relationship: has_part CL:0000788 {source="CL:tm"} ! naive B cell @@ -245608,7 +248066,6 @@ is_a: UBERON:0010707 ! appendage girdle complex intersection_of: UBERON:0010707 ! appendage girdle complex intersection_of: has_part UBERON:0001421 ! pectoral girdle region relationship: has_part UBERON:0001421 ! pectoral girdle region -relationship: part_of UBERON:0000153 {gci_relation="part_of", gci_filler="NCBITaxon:32523"} ! anterior region of body relationship: RO:0002551 UBERON:0012475 ! has skeleton skeleton of pectoral complex [Term] @@ -245632,7 +248089,6 @@ is_a: UBERON:0010707 ! appendage girdle complex intersection_of: UBERON:0010707 ! appendage girdle complex intersection_of: has_part UBERON:0001271 ! pelvic girdle region relationship: has_part UBERON:0001271 ! pelvic girdle region -relationship: part_of UBERON:0000154 {gci_relation="part_of", gci_filler="NCBITaxon:32523"} ! posterior region of body relationship: RO:0002551 UBERON:0012476 ! has skeleton skeleton of pelvic complex [Term] @@ -245786,7 +248242,6 @@ xref: UMLS:C0228116 xref: Wikipedia:Meninges is_a: BFO:0000002 is_a: BFO:0000004 -is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0034925 ! anatomical collection intersection_of: UBERON:0034925 ! anatomical collection intersection_of: bounding_layer_of UBERON:0001017 ! central nervous system @@ -246087,7 +248542,6 @@ property_value: IAO:0000116 "the MA class belongs here, based on its current chi id: UBERON:0010893 name: median external naris namespace: uberon -alt_id: UBERON:0012123 def: "Am unpaired external naris that lies in the midline of the head." [OBOL:automatic] subset: cyclostome_subset synonym: "median anterior naris" EXACT [] @@ -246183,7 +248637,6 @@ relationship: part_of UBERON:0004288 {source="VSAO"} ! skeleton id: UBERON:0010913 name: vertebral element namespace: uberon -alt_id: UBERON:0015005 def: "Skeletal element that forms around the notochord and is part of the vertebral column." [GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070, https://github.com/obophenotype/uberon/issues/294, VSAO:0000184] synonym: "vertebra element" EXACT [https://github.com/obophenotype/uberon/wiki/Modeling-endochondral-elements-Design-Pattern] synonym: "vertebra endochondral element" NARROW [https://github.com/obophenotype/uberon/issues/82] @@ -247119,7 +249572,6 @@ id: UBERON:0011234 name: fibrous membrane of synovial tendon sheath namespace: uberon xref: FMA:40877 -is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0004923 ! organ component layer intersection_of: UBERON:0004923 ! organ component layer intersection_of: bounding_layer_of UBERON:0000304 ! tendon sheath @@ -247227,8 +249679,6 @@ relationship: part_of UBERON:0003889 ! fallopian tube id: UBERON:0011299 name: white matter of telencephalon namespace: uberon -alt_id: UBERON:0013202 -alt_id: UBERON:0022550 def: "A partion of white matter that is part of a telencephalon. This can be further subdivided in some species, for example, into hemisphere white matter and the corpus callosum." [https://orcid.org/0000-0002-6601-2165] synonym: "predominantly white regional part of telencephalon" EXACT [BIRNLEX:1075] synonym: "telencephalic tract/commissure" EXACT [ZFA:0000597] @@ -247249,7 +249699,6 @@ relationship: part_of UBERON:0001893 ! telencephalon id: UBERON:0011300 name: gray matter of telencephalon namespace: uberon -alt_id: UBERON:0024186 def: "A portion of gray matter that is part of a telencephalon." [OBOL:automatic] synonym: "predominantly gray regional part of telencephalon" EXACT [BIRNLEX:1067] xref: BIRNLEX:1067 @@ -247277,7 +249726,6 @@ def: "An acellular strand that runs from subcommissural organ caudally through t synonym: "Reissner's fibre" EXACT [] xref: NLX:151878 xref: Wikipedia:Reissner's_fiber -is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0000476 ! acellular anatomical structure is_a: UBERON:0004121 ! ectoderm-derived structure relationship: part_of UBERON:0001017 ! central nervous system @@ -247445,7 +249893,6 @@ is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0010712 ! limb skeleton subdivision intersection_of: UBERON:0010912 ! subdivision of skeleton intersection_of: RO:0002576 UBERON:0002472 ! skeleton of stylopod -relationship: distally_connected_to UBERON:0011584 {gci_relation="part_of", gci_filler="NCBITaxon:32523"} ! zeugopodial skeleton relationship: part_of UBERON:0002472 ! stylopod relationship: part_of UBERON:0004381 {source="VSAO"} ! skeleton of limb relationship: RO:0002576 UBERON:0002472 ! skeleton of stylopod @@ -247467,7 +249914,6 @@ is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0010712 ! limb skeleton subdivision intersection_of: UBERON:0010912 ! subdivision of skeleton intersection_of: RO:0002576 UBERON:0002471 ! skeleton of zeugopod -relationship: distally_connected_to UBERON:0006717 {gci_relation="part_of", gci_filler="NCBITaxon:32523"} ! autopodial skeleton relationship: part_of UBERON:0002471 ! zeugopod relationship: part_of UBERON:0004381 {source="VSAO"} ! skeleton of limb relationship: proximally_connected_to UBERON:0011583 ! stylopodial skeleton @@ -247712,7 +250158,6 @@ subset: pheno_slim synonym: "presacral vertebra" RELATED [http://orcid.org/0000-0002-6601-2165] synonym: "thoracolumbar vertebra" EXACT [] is_a: UBERON:0003463 ! trunk bone -is_a: UBERON:0004247 ! bone of dorsum is_a: UBERON:0004451 {is_inferred="true"} ! trunk or cervical vertebra intersection_of: UBERON:0002412 ! vertebra intersection_of: part_of UBERON:0009568 ! trunk region of vertebral column @@ -247995,7 +250440,6 @@ xref: AAO:0000121 xref: NCIT:C32450 xref: UMLS:C1511770 {source="ncithesaurus:Dense_Connective_Tissue"} xref: Wikipedia:Dense_connective_tissue -is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0002384 ! connective tissue intersection_of: UBERON:0002384 ! connective tissue intersection_of: RO:0002473 UBERON:0011860 ! composed primarily of collection of collagen fibrils @@ -248108,7 +250552,6 @@ xref: FMA:63212 xref: MESH:D024022 xref: NCIT:C32339 xref: NIF_Subcellular:sao7547390221 -is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0000476 {source="ZFA"} ! acellular anatomical structure relationship: RO:0002473 GO:0005581 ! composed primarily of collagen trimer relationship: RO:0002473 GO:0098643 ! composed primarily of banded collagen fibril @@ -248388,7 +250831,6 @@ xref: EMAPA:36582 xref: FMA:70661 xref: Wikipedia:Pilosebaceous_unit is_a: BFO:0000002 -is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0000063 ! organ subunit relationship: has_part UBERON:0001821 ! sebaceous gland relationship: has_part UBERON:0002033 ! arrector muscle of hair @@ -248471,7 +250913,6 @@ xref: MA:0001613 xref: NCIT:C77661 xref: SCTID:27633001 xref: UMLS:C0227197 {source="ncithesaurus:Glandular_Stomach"} -is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0009870 ! zone of stomach intersection_of: UBERON:0009870 ! zone of stomach intersection_of: has_part UBERON:0006924 ! stomach glandular epithelium @@ -248678,6 +251119,7 @@ synonym: "haemocoelom" NARROW [] synonym: "schizocoelom" NARROW [] xref: EHDAA2:0004731 xref: Wikipedia:Coelom +xref: ZFA:0001438 is_a: UBERON:0000481 {source="EHDAA2"} ! multi-tissue structure relationship: RO:0002162 NCBITaxon:33213 ! in taxon Bilateria property_value: IAO:0000116 "EHDAA2 distingsuishes between the lumen, the lining, and the 'coelomic cavity', which despire it's name, is not a space - it is the aggregate of space plus lining." xsd:string @@ -249151,7 +251593,6 @@ relationship: part_of UBERON:0000002 ! uterine cervix id: UBERON:0012249 name: ectocervix namespace: uberon -alt_id: UBERON:0010182 def: "The part of the cervix uteri that protrudes into the vagina and is lined with stratified squamous epithelium." [BTO:0001850, Wikipedia:Vaginal_portion_of_cervix] subset: human_reference_atlas synonym: "ectocervix" EXACT [BTO:0001850, FMA:86484] @@ -249168,7 +251609,6 @@ xref: NCIT:C12310 xref: SCTID:264459002 xref: UMLS:C0227829 {source="ncithesaurus:Ectocervix"} xref: Wikipedia:Vaginal_portion_of_cervix -is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0000064 ! organ part is_a: UBERON:0005156 ! reproductive structure intersection_of: UBERON:0000064 ! organ part @@ -249974,7 +252414,6 @@ is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0034769 {source="FMA"} ! lymphomyeloid tissue intersection_of: UBERON:0000479 ! tissue intersection_of: site_of GO:0030097 ! hemopoiesis -relationship: part_of UBERON:0002371 {gci_relation="part_of", gci_filler="NCBITaxon:9606", source="FMA"} ! bone marrow relationship: part_of UBERON:0002390 {source="defitional"} ! hematopoietic system relationship: site_of GO:0030097 ! hemopoiesis @@ -249990,7 +252429,6 @@ synonym: "tunica fibrosa" BROAD [] xref: FMA:58102 xref: SCTID:361318005 xref: Wikipedia:Fibrous_tunic_of_eyeball -is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0004923 {source="FMA"} ! organ component layer is_a: UBERON:0010314 ! structure with developmental contribution from neural crest @@ -250181,7 +252619,6 @@ relationship: part_of UBERON:0000162 ! cloaca id: UBERON:0012480 name: cloacal mucosa namespace: uberon -alt_id: UBERON:0003349 def: "A mucosa that is part of a cloaca [Automatically generated definition]." [OBOL:automatic] synonym: "cloaca mucosa" EXACT [] synonym: "cloaca mucosa of organ" EXACT [] @@ -251099,7 +253536,6 @@ relationship: part_of UBERON:0003116 ! pharyngeal arch 5 id: UBERON:0013503 name: caudal vertebra cartilage element namespace: uberon -alt_id: UBERON:0013517 def: "A caudal vertebra endochondral element that is composed primarily of cartilage tissue." [OBOL:automatic] synonym: "coccygeal vertebra cartilage element" EXACT [http://orcid.org/0000-0002-6601-2165] synonym: "coccygeal vertebral cartilage condensation group" EXACT [EHDAA2:0000260] @@ -251118,7 +253554,6 @@ relationship: RO:0002387 UBERON:0001095 ! has potential to develop into caudal v id: UBERON:0013504 name: caudal vertebra pre-cartilage condensation namespace: uberon -alt_id: UBERON:0013518 def: "A caudal vertebra endochondral element that is composed primarily of a pre-cartilage condensation." [OBOL:automatic] synonym: "coccygeal vertebra pre-cartilage condensation" EXACT [http://orcid.org/0000-0002-6601-2165] synonym: "tail vertebral pre-cartilage condensation" EXACT [EMAPA:18045] @@ -252373,6 +254808,7 @@ synonym: "rib skeleton" RELATED [] synonym: "set of all ribs" RELATED [FMA:265719] xref: FMA:265719 xref: TAO:0002100 +is_a: BFO:0000002 is_a: UBERON:0000075 ! subdivision of skeletal system relationship: has_part UBERON:0003252 ! thoracic rib cage relationship: part_of UBERON:0011138 ! postcranial axial skeletal system @@ -253352,6 +255788,7 @@ namespace: uberon def: "A rib bone or its cartilage or pre-cartilage precursor." [https://github.com/obophenotype/uberon/wiki/Modeling-endochondral-elements-Design-Pattern] synonym: "rib element" EXACT [https://github.com/obophenotype/uberon/wiki/Modeling-endochondral-elements-Design-Pattern] synonym: "rib skeletal element" BROAD [https://github.com/obophenotype/uberon/wiki/Modeling-endochondral-elements-Design-Pattern] +is_a: BFO:0000002 is_a: UBERON:0010363 ! endochondral element union_of: UBERON:0002228 ! rib union_of: UBERON:0006288 ! rib cartilage element @@ -253565,6 +256002,7 @@ namespace: uberon def: "A scapula bone or its cartilage or pre-cartilage precursor." [https://github.com/obophenotype/uberon/wiki/Modeling-endochondral-elements-Design-Pattern] synonym: "scapula element" EXACT [https://github.com/obophenotype/uberon/wiki/Modeling-endochondral-elements-Design-Pattern] synonym: "scapula skeletal element" BROAD [https://github.com/obophenotype/uberon/wiki/Modeling-endochondral-elements-Design-Pattern] +is_a: BFO:0000002 is_a: UBERON:0010363 ! endochondral element union_of: UBERON:0006290 ! scapula cartilage element union_of: UBERON:0006291 ! scapula pre-cartilage condensation @@ -253578,6 +256016,8 @@ namespace: uberon def: "An orbitosphenoid bone or its cartilage or pre-cartilage precursor." [https://github.com/obophenotype/uberon/wiki/Modeling-endochondral-elements-Design-Pattern] synonym: "orbitosphenoid element" EXACT [https://github.com/obophenotype/uberon/wiki/Modeling-endochondral-elements-Design-Pattern] synonym: "orbitosphenoid skeletal element" BROAD [https://github.com/obophenotype/uberon/wiki/Modeling-endochondral-elements-Design-Pattern] +is_a: UBERON:0004120 ! mesoderm-derived structure +is_a: UBERON:0010313 ! neural crest-derived structure is_a: UBERON:0010363 ! endochondral element union_of: UBERON:0002478 ! orbitosphenoid union_of: UBERON:0005687 ! orbitosphenoid cartilage element @@ -254764,7 +257204,6 @@ synonym: "tunica fibrosa hepatis" EXACT OMO:0003011 [FMA:15813, FMA:TA] xref: FMA:15813 xref: SCTID:362185005 xref: Wikipedia:Fibrous_capsule_of_Glisson -is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0003893 ! capsule is_a: UBERON:0004119 ! endoderm-derived structure intersection_of: UBERON:0003893 ! capsule @@ -255025,7 +257464,6 @@ property_value: RO:0002175 NCBITaxon:9606 id: UBERON:0016526 name: lobe of cerebral hemisphere namespace: uberon -alt_id: UBERON:0000322 def: "Subdivision of telencephalon which is one of a number of subdivisions of each hemisphere separated by both real landmarks (sulci and fissures) and arbitrary boundaries[FMA,modified]." [FMA:61823] comment: We use the term lobe broadly as a rough regional area, encompassing homologous regions in smooth-brained mammals. We subdivide the lobes into white matter and neocortical parts. synonym: "cerebral cortical segment" RELATED [FMA:68603] @@ -255183,7 +257621,6 @@ relationship: part_of UBERON:0002600 ! limbic lobe id: UBERON:0016545 name: pharyngeal ectoderm namespace: uberon -alt_id: UBERON:2001379 def: "The external part of the developing pharynx that is made of ectoderm. During vertebrate development, pockets form in pharyngeal ectoderm between the pharyngeal arches." [http://orcid.org/0000-0002-6601-2165, PMID:23020903] xref: TAO:0001379 xref: ZFA:0001379 @@ -255366,7 +257803,6 @@ relationship: part_of UBERON:0003072 ! optic cup id: UBERON:0016879 name: future central nervous system namespace: uberon -alt_id: UBERON:3000469 def: "Primordium that develops into the central nervous system." [http://orcid.org/0000-0002-6601-2165] synonym: "future CNS" EXACT [] synonym: "presumptive central nervous system" EXACT [] @@ -255376,14 +257812,12 @@ intersection_of: UBERON:0006598 ! presumptive structure intersection_of: RO:0002387 UBERON:0001017 ! has potential to develop into central nervous system relationship: part_of UBERON:0016880 ! future nervous system relationship: RO:0002202 UBERON:0000924 ! develops from ectoderm -relationship: RO:0002202 UBERON:0002346 {gci_relation="part_of", gci_filler="NCBITaxon:7742"} ! develops from neurectoderm relationship: RO:0002387 UBERON:0001017 ! has potential to develop into central nervous system [Term] id: UBERON:0016880 name: future nervous system namespace: uberon -alt_id: UBERON:3000477 def: "Primordium that develops into the nervous system." [http://orcid.org/0000-0002-6601-2165] synonym: "presumptive nervous system" EXACT [AAO:0000477] xref: AAO:0000477 @@ -255777,7 +258211,6 @@ relationship: RO:0000086 PATO:0002462 ! has quality collagenous id: UBERON:0018142 name: caudal vertebra endochondral element namespace: uberon -alt_id: UBERON:0015006 def: "Any vertebra endochondral element that is part of the caudal region of the vertebral column (tail or coccyx)." [http://orcid.org/0000-0002-6601-2165] synonym: "caudal vertebra element" EXACT [] synonym: "coccygeal vertebra element" NARROW [] @@ -255865,7 +258298,6 @@ subset: pheno_slim synonym: "pulmonary lymphatic chain" EXACT [FMA:67999] synonym: "pulmonary lymphatic vasculature" RELATED [] xref: FMA:67999 -is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0004119 ! endoderm-derived structure is_a: UBERON:0011216 ! organ system subdivision intersection_of: UBERON:0011216 ! organ system subdivision @@ -255884,7 +258316,6 @@ subset: human_reference_atlas synonym: "lymphatic vessel of lung" EXACT [] xref: FMA:234006 xref: SCTID:321862009 -is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0003456 ! respiratory system lymphatic vessel is_a: UBERON:0004119 ! endoderm-derived structure intersection_of: UBERON:0001473 ! lymphatic vessel @@ -256558,7 +258989,6 @@ relationship: part_of UBERON:0000988 ! pons id: UBERON:0019293 name: white matter of pontine tegmentum namespace: uberon -alt_id: UBERON:0025819 synonym: "pontine white matter tracts" EXACT [HBA:PoWM] synonym: "predominantly white regional part of pontine tegmentum" EXACT [BIRNLEX:1069] synonym: "substantia alba tegmenti pontis" EXACT [FMA:TA] @@ -257614,7 +260044,6 @@ name: external soft tissue zone namespace: uberon def: "A region or zone on the surface of an organism that encompasses skin and any adnexa, down through muscles and bounded by underlying skeletal support structures." [http://orcid.org/0000-0002-6601-2165] is_a: BFO:0000002 -is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0010000 ! multicellular anatomical structure relationship: has_part UBERON:0000014 ! zone of skin relationship: has_part UBERON:0001015 ! musculature @@ -260027,7 +262456,6 @@ xref: TAO:0001053 xref: ZFA:0001053 is_a: UBERON:0004573 ! systemic artery relationship: part_of UBERON:0001530 {source="EHDAA2"} ! common carotid artery plus branches -relationship: RO:0002202 UBERON:0003120 {gci_relation="part_of", gci_filler="NCBITaxon:40674", source="EHDAA2"} ! develops from pharyngeal arch artery 3 relationship: RO:0002202 UBERON:0004363 ! develops from pharyngeal arch artery [Term] @@ -260979,7 +263407,6 @@ name: ductal plate namespace: uberon def: "In human, ductal plate is a double-layered cylindrical structure of bile duct epithelium that surrounds the portal ramifications by the eighth gestational week. After approximately the 12th gestational week, remodelling of ductal plate begins, and maturity is attained by the end of gestation or early postnatal period." [http://orcid.org/0000-0002-7073-9172, PMID:28515578] subset: added_for_HCA -is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0004119 ! endoderm-derived structure is_a: UBERON:0010000 ! multicellular anatomical structure relationship: has_part UBERON:0004820 ! bile duct epithelium @@ -261619,7 +264046,6 @@ is_a: UBERON:0000361 ! red bone marrow intersection_of: UBERON:0000361 ! red bone marrow intersection_of: part_of UBERON:0000975 ! sternum relationship: part_of UBERON:0000975 ! sternum -created_by: http://orcid.org/0000-0002-2825-0621 [Term] id: UBERON:8410081 @@ -261631,7 +264057,6 @@ synonym: "microvessel" BROAD [] is_a: UBERON:0001981 ! blood vessel is_a: UBERON:0010523 ! microcirculatory vessel property_value: seeAlso "https://github.com/obophenotype/uberon/issues/2186" xsd:string -created_by: http://orcid.org/0000-0002-2825-0621 [Term] id: UBERON:8420000 @@ -261758,9 +264183,20 @@ intersection_of: UBERON:0000467 ! anatomical system intersection_of: capable_of GO:0046903 ! secretion relationship: capable_of GO:0046903 ! secretion property_value: RO:0002175 NCBITaxon:9606 -created_by: http://orcid.org/0000-0002-6095-8718 creation_date: 2022-05-25T18:21:29Z +[Term] +id: UBERON:8450003 +name: embryonic craniocervical region +namespace: uberon +def: "A craniocervical region that is part of an embryo." [https://orcid.org/0000-0002-6095-8718] +is_a: UBERON:0007811 ! craniocervical region +intersection_of: UBERON:0007811 ! craniocervical region +intersection_of: part_of UBERON:0000922 ! embryo +relationship: part_of UBERON:0000922 ! embryo +property_value: terms:contributor https://orcid.org/0000-0002-6095-8718 +property_value: terms:date "2024-09-12T14:40:00Z" xsd:dateTime + [Term] id: UBERON:8470000 name: placental blood @@ -262272,6 +264708,426 @@ relationship: RO:0002572 UBERON:0002299 ! luminal space of alveolus of lung property_value: terms:contributor https://orcid.org/0009-0000-8480-9277 property_value: terms:date "2024-06-28T10:50:18Z" xsd:dateTime +[Term] +id: http://identifiers.org/ensembl/ENSG00000006128 +name: TAC1 +is_a: SO:0000704 + +[Term] +id: http://identifiers.org/ensembl/ENSG00000010327 +name: STAB1 +is_a: SO:0000704 + +[Term] +id: http://identifiers.org/ensembl/ENSG00000038295 +name: TLL1 +is_a: SO:0000704 + +[Term] +id: http://identifiers.org/ensembl/ENSG00000038945 +name: MSR1 +is_a: SO:0000704 + +[Term] +id: http://identifiers.org/ensembl/ENSG00000041982 +name: TNC +is_a: SO:0000704 + +[Term] +id: http://identifiers.org/ensembl/ENSG00000047936 +name: ROS1 +is_a: SO:0000704 + +[Term] +id: http://identifiers.org/ensembl/ENSG00000050730 +name: TNIP3 +is_a: SO:0000704 + +[Term] +id: http://identifiers.org/ensembl/ENSG00000051128 +name: HOMER3 +is_a: SO:0000704 + +[Term] +id: http://identifiers.org/ensembl/ENSG00000072694 +name: FCGR2B +is_a: SO:0000704 + +[Term] +id: http://identifiers.org/ensembl/ENSG00000078898 +name: BPIFB2 +is_a: SO:0000704 + +[Term] +id: http://identifiers.org/ensembl/ENSG00000082482 +name: KCNK2 +is_a: SO:0000704 + +[Term] +id: http://identifiers.org/ensembl/ENSG00000082684 +name: SEMA5B +is_a: SO:0000704 + +[Term] +id: http://identifiers.org/ensembl/ENSG00000100292 +name: HMOX1 +is_a: SO:0000704 + +[Term] +id: http://identifiers.org/ensembl/ENSG00000100362 +name: PVALB +is_a: SO:0000704 + +[Term] +id: http://identifiers.org/ensembl/ENSG00000100604 +name: CHGA +is_a: SO:0000704 + +[Term] +id: http://identifiers.org/ensembl/ENSG00000107796 +name: ACTA2 +is_a: SO:0000704 + +[Term] +id: http://identifiers.org/ensembl/ENSG00000111215 +name: PRR4 +is_a: SO:0000704 + +[Term] +id: http://identifiers.org/ensembl/ENSG00000113532 +name: ST8SIA4 +is_a: SO:0000704 + +[Term] +id: http://identifiers.org/ensembl/ENSG00000114805 +name: PLCH1 +is_a: SO:0000704 + +[Term] +id: http://identifiers.org/ensembl/ENSG00000115593 +name: SMYD1 +is_a: SO:0000704 + +[Term] +id: http://identifiers.org/ensembl/ENSG00000118513 +name: MYB +is_a: SO:0000704 + +[Term] +id: http://identifiers.org/ensembl/ENSG00000118523 +name: CCN2 +is_a: SO:0000704 + +[Term] +id: http://identifiers.org/ensembl/ENSG00000119547 +name: ONECUT2 +is_a: SO:0000704 + +[Term] +id: http://identifiers.org/ensembl/ENSG00000122585 +name: NPY +is_a: SO:0000704 + +[Term] +id: http://identifiers.org/ensembl/ENSG00000122852 +name: SFTPA1 +is_a: SO:0000704 + +[Term] +id: http://identifiers.org/ensembl/ENSG00000124302 +name: CHST8 +is_a: SO:0000704 + +[Term] +id: http://identifiers.org/ensembl/ENSG00000124491 +name: F13A1 +is_a: SO:0000704 + +[Term] +id: http://identifiers.org/ensembl/ENSG00000125869 +name: LAMP5 +is_a: SO:0000704 + +[Term] +id: http://identifiers.org/ensembl/ENSG00000131097 +name: HIGD1B +is_a: SO:0000704 + +[Term] +id: http://identifiers.org/ensembl/ENSG00000131471 +name: AOC3 +is_a: SO:0000704 + +[Term] +id: http://identifiers.org/ensembl/ENSG00000131747 +name: TOP2A +is_a: SO:0000704 + +[Term] +id: http://identifiers.org/ensembl/ENSG00000134443 +name: GRP +is_a: SO:0000704 + +[Term] +id: http://identifiers.org/ensembl/ENSG00000137252 +name: HCRTR2 +is_a: SO:0000704 + +[Term] +id: http://identifiers.org/ensembl/ENSG00000137573 +name: SULF1 +is_a: SO:0000704 + +[Term] +id: http://identifiers.org/ensembl/ENSG00000137709 +name: POU2F3 +is_a: SO:0000704 + +[Term] +id: http://identifiers.org/ensembl/ENSG00000137804 +name: NUSAP1 +is_a: SO:0000704 + +[Term] +id: http://identifiers.org/ensembl/ENSG00000139329 +name: LUM +is_a: SO:0000704 + +[Term] +id: http://identifiers.org/ensembl/ENSG00000143171 +name: RXRG +is_a: SO:0000704 + +[Term] +id: http://identifiers.org/ensembl/ENSG00000143196 +name: DPT +is_a: SO:0000704 + +[Term] +id: http://identifiers.org/ensembl/ENSG00000144229 +name: THSD7B +is_a: SO:0000704 + +[Term] +id: http://identifiers.org/ensembl/ENSG00000146469 +name: VIP +is_a: SO:0000704 + +[Term] +id: http://identifiers.org/ensembl/ENSG00000149591 +name: TAGLN +is_a: SO:0000704 + +[Term] +id: http://identifiers.org/ensembl/ENSG00000154080 +name: CHST9 +is_a: SO:0000704 + +[Term] +id: http://identifiers.org/ensembl/ENSG00000156689 +name: GLYATL2 +is_a: SO:0000704 + +[Term] +id: http://identifiers.org/ensembl/ENSG00000157005 +name: SST +is_a: SO:0000704 + +[Term] +id: http://identifiers.org/ensembl/ENSG00000157404 +name: KIT +is_a: SO:0000704 + +[Term] +id: http://identifiers.org/ensembl/ENSG00000162399 +name: BSND +is_a: SO:0000704 + +[Term] +id: http://identifiers.org/ensembl/ENSG00000163735 +name: CXCL5 +is_a: SO:0000704 + +[Term] +id: http://identifiers.org/ensembl/ENSG00000164120 +name: HPGD +is_a: SO:0000704 + +[Term] +id: http://identifiers.org/ensembl/ENSG00000166803 +name: PCLAF +is_a: SO:0000704 + +[Term] +id: http://identifiers.org/ensembl/ENSG00000166959 +name: MS4A8 +is_a: SO:0000704 + +[Term] +id: http://identifiers.org/ensembl/ENSG00000167306 +name: MYO5B +is_a: SO:0000704 + +[Term] +id: http://identifiers.org/ensembl/ENSG00000168079 +name: SCARA5 +is_a: SO:0000704 + +[Term] +id: http://identifiers.org/ensembl/ENSG00000170323 +name: FABP4 +is_a: SO:0000704 + +[Term] +id: http://identifiers.org/ensembl/ENSG00000171303 +name: KCNK3 +is_a: SO:0000704 + +[Term] +id: http://identifiers.org/ensembl/ENSG00000171346 +name: KRT15 +is_a: SO:0000704 + +[Term] +id: http://identifiers.org/ensembl/ENSG00000171848 +name: RRM2 +is_a: SO:0000704 + +[Term] +id: http://identifiers.org/ensembl/ENSG00000172673 +name: THEMIS +is_a: SO:0000704 + +[Term] +id: http://identifiers.org/ensembl/ENSG00000174501 +name: ANKRD36C +is_a: SO:0000704 + +[Term] +id: http://identifiers.org/ensembl/ENSG00000174807 +name: CD248 +is_a: SO:0000704 + +[Term] +id: http://identifiers.org/ensembl/ENSG00000174948 +name: GPR149 +is_a: SO:0000704 + +[Term] +id: http://identifiers.org/ensembl/ENSG00000175063 +name: UBE2C +is_a: SO:0000704 + +[Term] +id: http://identifiers.org/ensembl/ENSG00000176009 +name: ASCL3 +is_a: SO:0000704 + +[Term] +id: http://identifiers.org/ensembl/ENSG00000178031 +name: ADAMTSL1 +is_a: SO:0000704 + +[Term] +id: http://identifiers.org/ensembl/ENSG00000178538 +name: CA8 +is_a: SO:0000704 + +[Term] +id: http://identifiers.org/ensembl/ENSG00000179902 +name: C1orf194 +is_a: SO:0000704 + +[Term] +id: http://identifiers.org/ensembl/ENSG00000180801 +name: ARSJ +is_a: SO:0000704 + +[Term] +id: http://identifiers.org/ensembl/ENSG00000184530 +name: C6orf58 +is_a: SO:0000704 + +[Term] +id: http://identifiers.org/ensembl/ENSG00000185668 +name: POU3F1 +is_a: SO:0000704 + +[Term] +id: http://identifiers.org/ensembl/ENSG00000187908 +name: DMBT1 +is_a: SO:0000704 + +[Term] +id: http://identifiers.org/ensembl/ENSG00000189056 +name: RELN +is_a: SO:0000704 + +[Term] +id: http://identifiers.org/ensembl/ENSG00000189058 +name: APOD +is_a: SO:0000704 + +[Term] +id: http://identifiers.org/ensembl/ENSG00000197085 +name: NPSR1-AS1 +is_a: SO:0000704 + +[Term] +id: http://identifiers.org/ensembl/ENSG00000197353 +name: LYPD2 +is_a: SO:0000704 + +[Term] +id: http://identifiers.org/ensembl/ENSG00000197943 +name: PLCG2 +is_a: SO:0000704 + +[Term] +id: http://identifiers.org/ensembl/ENSG00000198901 +name: PRC1 +is_a: SO:0000704 + +[Term] +id: http://identifiers.org/ensembl/ENSG00000198963 +name: RORB +is_a: SO:0000704 + +[Term] +id: http://identifiers.org/ensembl/ENSG00000204262 +name: COL5A2 +is_a: SO:0000704 + +[Term] +id: http://identifiers.org/ensembl/ENSG00000204305 +name: AGER +is_a: SO:0000704 + +[Term] +id: http://identifiers.org/ensembl/ENSG00000206073 +name: SERPINB4 +is_a: SO:0000704 + +[Term] +id: http://identifiers.org/ensembl/ENSG00000215182 +name: MUC5AC +is_a: SO:0000704 + +[Term] +id: http://identifiers.org/ensembl/ENSG00000235665 +name: LINC00298 +is_a: SO:0000704 + +[Term] +id: http://identifiers.org/ensembl/ENSG00000242265 +name: PEG10 +is_a: SO:0000704 + +[Term] +id: http://identifiers.org/ensembl/ENSG00000256193 +name: LINC00507 +is_a: SO:0000704 + [Term] id: http://purl.obolibrary.org/obo/D96882F1-8709-49AB-BCA9-772A67EA6C33 name: obsolete D96882F1-8709-49AB-BCA9-772A67EA6C33 @@ -262398,7 +265254,6 @@ id: RO:0002021 name: occurs across def: "A relationship between a process and a barrier, where the process occurs in a region spanning the barrier. For cellular processes the barrier is typically a membrane. Examples include transport across a membrane and membrane depolarization." [] is_a: RO:0002479 ! has part that occurs in -created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-07-20T17:19:37Z [Typedef] @@ -263287,7 +266142,6 @@ name: causally upstream of or within, negative effect property_value: RO:0004050 RO:0002418 property_value: seeAlso "https://wiki.geneontology.org/Causally_upstream_of_or_within,_negative_effect" xsd:anyURI is_a: causally_upstream_of_or_within ! causally upstream of or within -created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-03-13T23:55:05Z [Typedef] @@ -263295,7 +266149,6 @@ id: RO:0004047 name: causally upstream of or within, positive effect property_value: seeAlso https://wiki.geneontology.org/Causally_upstream_of_or_within,_positive_effect is_a: causally_upstream_of_or_within ! causally upstream of or within -created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-03-13T23:55:19Z [Typedef] @@ -263304,7 +266157,6 @@ name: has small molecule regulator def: "a relation between a process and a continuant, in which the process is regulated by the small molecule continuant" [] is_a: has_participant ! has participant inverse_of: RO:0012004 ! is small molecule regulator of -created_by: https://orcid.org/0000-0003-1813-6857 creation_date: 2020-04-22T20:27:26Z [Typedef] @@ -263312,7 +266164,6 @@ id: RO:0012004 name: is small molecule regulator of def: "a relation between a continuant and a process, in which the continuant is a small molecule that regulates the process" [] is_a: RO:0002596 ! capable of regulating -created_by: https://orcid.org/0000-0003-1813-6857 creation_date: 2020-06-24T13:15:17Z [Typedef] @@ -263322,7 +266173,6 @@ def: "a relation between a continuant and a process, in which the continuant is property_value: seeAlso "https://wiki.geneontology.org/Is_small_molecule_activator_of" xsd:anyURI is_a: RO:0002598 ! capable of positively regulating is_a: RO:0012004 ! is small molecule regulator of -created_by: https://orcid.org/0000-0003-1813-6857 creation_date: 2020-06-24T13:15:26Z [Typedef] @@ -263332,7 +266182,6 @@ def: "A relationship between a neuron and a region, where the neuron has a funct synonym: "has synaptic input or output in" EXACT [] is_a: RO:0002130 ! has synaptic terminal in transitive_over: part_of ! part of -created_by: https://orcid.org/0000-0002-1373-1705 creation_date: 2020-07-17T09:26:52Z [Typedef] @@ -263345,9 +266194,18 @@ synonym: "has sensory terminal location" EXACT [] domain: CL:0000101 ! sensory neuron is_a: RO:0002360 ! has dendrite location transitive_over: part_of ! part of -created_by: https://orcid.org/0000-0002-1373-1705 creation_date: 2020-07-20T12:10:09Z +[Typedef] +id: RO:0015004 +name: has characterizing marker set +def: "A relation that applies between a cell type and a set of markers that can be used to uniquely identify that cell type." [] +synonym: "has marker gene combination" EXACT [] +synonym: "has marker signature set" EXACT [] +property_value: IAO:0000116 "C has_characterizing_marker_set y iff: C is a cell type and y is a collection of genes or proteins whose expression is sufficient to distinguish cell type C from most or all other cell types." xsd:string +property_value: terms:contributor https://orcid.org/0000-0001-7258-9596 +domain: CL:0000000 ! cell + [Typedef] id: RO:0015006 name: different in magnitude relative to @@ -263421,7 +266279,6 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0012003 is_a: has_participant ! has participant -created_by: https://orcid.org/0000-0003-1813-6857 creation_date: 2020-06-08T17:21:33Z [Typedef] @@ -263730,7 +266587,6 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_ontology xref: RO:0004009 is_a: has_input ! has input is_a: has_primary_input_or_output ! has primary input or output -created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-12-13T11:26:56Z [Typedef] @@ -263741,7 +266597,6 @@ def: "p 'has primary input ot output' c iff either (a) p 'has primary input' c o subset: http://purl.obolibrary.org/obo/valid_for_go_ontology xref: RO:0004007 is_a: has_participant ! has participant -created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-12-13T11:26:17Z [Typedef] @@ -263753,7 +266608,6 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_ontology xref: RO:0004008 is_a: has_output ! has output is_a: has_primary_input_or_output ! has primary input or output -created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-12-13T11:26:32Z [Typedef] @@ -263764,7 +266618,6 @@ def: "a relation between a process and a continuant, in which the process is act xref: RO:0012001 is_a: RO:0012000 ! has small molecule regulator inverse_of: RO:0012005 ! is small molecule activator of -created_by: https://orcid.org/0000-0003-1813-6857 creation_date: 2020-04-22T20:28:37Z [Typedef] @@ -264111,7 +266964,6 @@ namespace: external def: "p has anatomical participant c iff p has participant c, and c is an anatomical entity" [] xref: RO:0040036 is_a: has_participant ! has participant -created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-09-26T01:08:58Z [Typedef] @@ -264183,7 +267035,6 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0012008 is_a: results_in_organization_of ! results in organization of -created_by: https://orcid.org/0000-0003-1813-6857 creation_date: 2021-02-26T07:28:29Z [Typedef] @@ -264235,7 +267086,6 @@ name: results in organization of namespace: external def: "p results in organization of c iff p results in the assembly, arrangement of constituent parts, or disassembly of c" [] xref: RO:0002592 -is_a: has_participant ! has participant is_a: results_in_changes_to_anatomical_or_cellular_structure ! results in changes to anatomical or cellular structure [Typedef] diff --git a/patterns/definitions.owl b/patterns/definitions.owl index 5455e8867..c94c5e8de 100644 --- a/patterns/definitions.owl +++ b/patterns/definitions.owl @@ -7,8 +7,8 @@ Prefix(rdfs:=) Ontology( - -Annotation(owl:versionInfo "2024-09-25") + +Annotation(owl:versionInfo "2025-01-06") Declaration(Class()) Declaration(Class()) @@ -55,8 +55,6 @@ Declaration(Class()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) @@ -69,7 +67,7 @@ Declaration(AnnotationProperty( () -AnnotationAssertion(Annotation( "DOI:10.1016/j.coi.2005.11.008") Annotation( "DOI:10.1038/nri3087") Annotation( "DOI:10.3389/fimmu.2019.01893") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. +AnnotationAssertion(Annotation( "DOI:10.1016/j.coi.2005.11.008") Annotation( "DOI:10.1038/nri3087") Annotation( "DOI:10.3389/fimmu.2019.01893") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. Mononuclear phagocytes are immune cells that form a critical part of the body's innate immune system, the body's first line of defense against infections. Mononuclear phagocytes are characterized by the presence of a single, large nucleus. The ‘Mononuclear Phagocyte System’ nomenclature was introduced to distinguish mononuclear monocytes and macrophages from other cells with multiple nuclei. However, the cells within the mononuclear phagocyte system represent a highly heterogeneous group, all of which are able to perform highly efficient phagocytosis - engulfing and digesting microbes and cellular debris to fight infections and to maintain normal tissue homeostasis. In addition to phagocytosis, mononuclear phagocytes also secrete chemical compounds to recruit other immune cells to a site of infection. These cells produce different types of signaling molecules, including cytokines, chemokines, and reactive oxygen species, triggering a cascade of responses to ensure rapid and efficient containment and neutralization of invading pathogens. These cells are also involved in antigen presentation, a process essential for stimulating an adaptive immune response. They can process and present antigens to T cells, thereby linking the innate and adaptive immune responses. @@ -78,7 +76,7 @@ AnnotationAssertion( () -AnnotationAssertion(Annotation( "DOI:10.1002/glia.24343") Annotation( "DOI:10.1038/nn1988") Annotation( "DOI:10.1101/cshperspect.a020602") Annotation( "DOI:10.1126/science.aat0473") Annotation( "DOI:10.3389/fncel.2017.00024") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. +AnnotationAssertion(Annotation( "DOI:10.1002/glia.24343") Annotation( "DOI:10.1038/nn1988") Annotation( "DOI:10.1101/cshperspect.a020602") Annotation( "DOI:10.1126/science.aat0473") Annotation( "DOI:10.3389/fncel.2017.00024") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. Glial cells, also known as neuroglia or simply glia, are non-neuronal cells in the central and peripheral nervous systems that provide support and protection for neurons. They constitute approximately half of the total cells in the human brain and more than half in other parts of the nervous system. Glial cells perform several key functions including, but not limited to, maintaining homeostasis, forming the myelin sheath around the neuron axons, and providing support and nutrition to neurons. These different functions are performed by various glial cell types, including astrocytes, oligodendrocytes, microglia and other specialized types. Astrocytes, for example, are the most abundant glial cells and provide metabolic and nutrient support to neurons, help regulate the extracellular ion and neurotransmitter levels, and play a role in the formation and maintenance of the blood-brain barrier, contributing to the overall homeostasis and functioning of the nervous system. Additionally, astrocytes are involved in synaptic communication and participate in processes such as synaptogenesis and synaptic pruning. @@ -89,7 +87,7 @@ AnnotationAssertion( () -AnnotationAssertion(Annotation( "DOI:10.1016/0166-4328(96)00075-7") Annotation( "DOI:10.1016/j.cell.2017.05.034") Annotation( "DOI:10.1038/s41574-019-0168-8") Annotation( "DOI:10.1073/pnas.1804938115") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. +AnnotationAssertion(Annotation( "DOI:10.1016/0166-4328(96)00075-7") Annotation( "DOI:10.1016/j.cell.2017.05.034") Annotation( "DOI:10.1038/s41574-019-0168-8") Annotation( "DOI:10.1073/pnas.1804938115") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. Type EC enteroendocrine cells, also known as enterochromaffin cells, are a vital hormone-secreting cell type found in the gastrointestinal tract. These cells are named after their location in the intestines (“entero”) and because they are stainable by chromium salts (“chromaffin”). The primary function of type EC enteroendocrine cells is to act as chemosensors and lies in their capacity to produce and secrete serotonin, also known as 5-hydroxytryptamine (5-HT). Serotonin is a neurotransmitter that plays a significant role in modulating motility, secretion, vasodilation, perception of pain, and appetite in the gastrointestinal system. However, its function is not limited to the gastrointestinal tract; once secreted, serotonin is distributed via the bloodstream and contributes to regulating mood, appetite, and sleep in the brain. @@ -98,18 +96,25 @@ AnnotationAssertion( () -AnnotationAssertion(Annotation( "DOI:10.1007/s00424-017-1965-3") Annotation( "DOI:10.1016/j.cellimm.2018.01.005") Annotation( "DOI:10.1038/nri3600") Annotation( "DOI:10.14348/molcells.2021.0058") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. +AnnotationAssertion(Annotation( "DOI:10.1007/s00424-017-1965-3") Annotation( "DOI:10.1016/j.cellimm.2018.01.005") Annotation( "DOI:10.1038/nri3600") Annotation( "DOI:10.14348/molcells.2021.0058") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. Alveolar macrophages are unique tissue-resident macrophages found in the lungs, specifically in the air sacs or alveoli where gas exchange occurs. They are characterized by specific surface markers including: F4/80-positive, CD11b-/low, CD11c-positive, CD68-positive, sialoadhesin-positive, dectin-1-positive, MR-positive, CX3CR1-negative. These specialized immune cells form a crucial part of the body's defense mechanism, playing important roles in pulmonary health and homeostasis. They are the first line of defense in the pulmonary immune response, acting as scavengers that patrol the alveoli and engulf foreign particles like bacteria, dust, and other debris that enter the lungs through inhalation. The primary function of these alveolar macrophages is phagocytosis, whereby they consume and digest foreign substances, dead cells, and other particulates. In the lung, alveolar macrophages are also responsible for clearing surfactant. Additionally, alveolar macrophages also play an integral role in initiating the immune response, as they secrete several pro-inflammatory cytokines and chemokines that recruit other immune cells to the site of infection or inflammation. Beyond their role in host defense, alveolar macrophages contribute to tissue remodeling and wound repair in the lungs, aiding in maintaining lung integrity. They also regulate local inflammation and control the immune response to prevent excessive inflammation that may be harmful. However, an imbalance in the function of alveolar macrophages can contribute to various lung diseases. Abnormal alveolar macrophage activation has been implicated in chronic inflammatory diseases such as emphysema, asthma, and fibrosis.") AnnotationAssertion( "https://cellxgene.cziscience.com/cellguide/CL_0000583") +# Class: () + +AnnotationAssertion(Annotation( "DOI:10.1016/j.it.2022.10.010") Annotation( "DOI:10.1038/s41577-020-0281-x") Annotation( "DOI:10.3389/fimmu.2019.00036") Annotation( "DOI:10.3389/fphys.2020.00509/full") Annotation( "DOI:10.3892/mco.2017.1356") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Endothelial cells of lymphatic vessels are specialized type of cells that form the interior lining of the lymphatic system, which primarily comprises the lymph vessels and nodes. These cells play a critical role in creating a barrier between the lymphatic system and the surrounding tissues. They are structurally different from the endothelial cells of the blood vessels due to the presence of anchoring filaments and lack of a continuous basement membrane, and have a unique phenotype marked by the expression of various cell-specific markers such as Prox-1, VEGFR-3, and LYVE-1. +A significant function of these endothelial cells is to maintain the fluid balance within the body. They facilitate the uptake of excess interstitial fluid that collects in the body tissues, and ensure its transport back into the bloodstream via the lymphatic vessels. These cells also enable the absorption of fats and fat-soluble vitamins from the digestive system, and their subsequent transport in the form of chyle, a milky fluid, to the blood. +Furthermore, endothelial cells of lymphatic vessels play a pivotal role in the body's immune response. They enable the passage of lymphocytes, that are crucial for the body's defense mechanism, from the tissues into the lymph where these cells are activated to fight against foreign bodies and infections. Also, they regulate inflammation reactions by controlling the migration of inflammatory cells, and are thus involved in pathological conditions with an inflammatory component. Lastly, these cells have been noted for their involvement in various disease states related to tissue edema, metastasis, and tumor growth, thus highlighting their importance in both health and disease states.") +AnnotationAssertion( "https://cellxgene.cziscience.com/cellguide/CL_0002138") + # Class: (cycling B cell) AnnotationAssertion(Annotation( "PMID:31348891") "A(n) B cell that is cycling.") -AnnotationAssertion( ) -AnnotationAssertion( "2024-07-02T09:14:23Z") AnnotationAssertion(Annotation( "PMID:31348891") "proliferating B cell") AnnotationAssertion(rdfs:label "cycling B cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) @@ -117,8 +122,6 @@ EquivalentClasses( ObjectIntersection # Class: (cycling T cell) AnnotationAssertion(Annotation( "PMID:37291214") "A(n) T cell that is cycling.") -AnnotationAssertion( ) -AnnotationAssertion( "2024-07-02T09:14:23Z") AnnotationAssertion(Annotation( "PMID:37291214") "proliferating T cell") AnnotationAssertion(rdfs:label "cycling T cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) @@ -126,8 +129,6 @@ EquivalentClasses( ObjectIntersection # Class: (cycling dendritic cell) AnnotationAssertion(Annotation( "PMID:32066951") "A(n) dendritic cell that is cycling.") -AnnotationAssertion( ) -AnnotationAssertion( "2024-07-02T09:14:23Z") AnnotationAssertion(Annotation( "PMID:32066951") "proliferating dendritic cell") AnnotationAssertion(rdfs:label "cycling dendritic cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) @@ -135,8 +136,6 @@ EquivalentClasses( ObjectIntersection # Class: (cycling natural killer cell) AnnotationAssertion(Annotation( "PMID:34062119") "A(n) natural killer cell that is cycling.") -AnnotationAssertion( ) -AnnotationAssertion( "2024-07-02T09:14:23Z") AnnotationAssertion(Annotation( "PMID:34062119") "proliferating natural killer cell") AnnotationAssertion(rdfs:label "cycling natural killer cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) @@ -144,8 +143,6 @@ EquivalentClasses( ObjectIntersection # Class: (cycling gamma-delta T cell) AnnotationAssertion(Annotation( "PMID:32066951") "A(n) gamma-delta T cell that is cycling.") -AnnotationAssertion( ) -AnnotationAssertion( "2024-07-02T09:14:23Z") AnnotationAssertion(Annotation( "PMID:32066951") "proliferating gamma-delta T cell") AnnotationAssertion(rdfs:label "cycling gamma-delta T cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) @@ -153,8 +150,6 @@ EquivalentClasses( ObjectIntersection # Class: (cycling monocyte) AnnotationAssertion(Annotation( "PMID:31348891") "A(n) monocyte that is cycling.") -AnnotationAssertion( ) -AnnotationAssertion( "2024-07-02T09:14:23Z") AnnotationAssertion(Annotation( "PMID:31348891") "proliferating monocyte") AnnotationAssertion(rdfs:label "cycling monocyte") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) @@ -162,8 +157,6 @@ EquivalentClasses( ObjectIntersection # Class: (cycling CD8-positive, alpha-beta T cell) AnnotationAssertion(Annotation( "PMID:34062119") "A(n) CD8-positive, alpha-beta T cell that is cycling.") -AnnotationAssertion( ) -AnnotationAssertion( "2024-07-02T09:14:23Z") AnnotationAssertion(Annotation( "PMID:34062119") "proliferating CD8-positive, alpha-beta T cell") AnnotationAssertion(rdfs:label "cycling CD8-positive, alpha-beta T cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) @@ -171,8 +164,6 @@ EquivalentClasses( ObjectIntersection # Class: (cycling CD4-positive, alpha-beta T cell) AnnotationAssertion(Annotation( "PMID:34062119") "A(n) CD4-positive, alpha-beta T cell that is cycling.") -AnnotationAssertion( ) -AnnotationAssertion( "2024-07-02T09:14:23Z") AnnotationAssertion(Annotation( "PMID:34062119") "proliferating CD4-positive, alpha-beta T cell") AnnotationAssertion(rdfs:label "cycling CD4-positive, alpha-beta T cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) @@ -180,8 +171,6 @@ EquivalentClasses( ObjectIntersection # Class: (cycling macrophage) AnnotationAssertion(Annotation( "PMID:33208946") "A(n) macrophage that is cycling.") -AnnotationAssertion( ) -AnnotationAssertion( "2024-07-02T09:14:23Z") AnnotationAssertion(Annotation( "PMID:33208946") "proliferating macrophage") AnnotationAssertion(rdfs:label "cycling macrophage") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) @@ -189,8 +178,6 @@ EquivalentClasses( ObjectIntersection # Class: (cycling alveolar macrophage) AnnotationAssertion(Annotation( "PMID:37291214") "A(n) alveolar macrophage that is cycling.") -AnnotationAssertion( ) -AnnotationAssertion( "2024-07-02T09:14:23Z") AnnotationAssertion(Annotation( "PMID:37291214") "proliferating alveolar macrophage") AnnotationAssertion(rdfs:label "cycling alveolar macrophage") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) @@ -198,8 +185,6 @@ EquivalentClasses( ObjectIntersection # Class: (cycling mononuclear phagocyte) AnnotationAssertion(Annotation( "PMID:37468583") "A(n) mononuclear phagocyte that is cycling.") -AnnotationAssertion( ) -AnnotationAssertion( "2024-07-02T09:14:23Z") AnnotationAssertion(Annotation( "PMID:37468583") "proliferating mononuclear phagocyte") AnnotationAssertion(rdfs:label "cycling mononuclear phagocyte") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) @@ -207,8 +192,6 @@ EquivalentClasses( ObjectIntersection # Class: (cycling endothelial cell of lymphatic vessel) AnnotationAssertion(Annotation( "PMID:37291214") "A(n) endothelial cell of lymphatic vessel that is cycling.") -AnnotationAssertion( ) -AnnotationAssertion( "2024-07-02T09:14:23Z") AnnotationAssertion(Annotation( "PMID:37291214") "proliferating endothelial cell of lymphatic vessel") AnnotationAssertion(rdfs:label "cycling endothelial cell of lymphatic vessel") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) @@ -216,8 +199,6 @@ EquivalentClasses( ObjectIntersection # Class: (cycling pulmonary alveolar type 2 cell) AnnotationAssertion(Annotation( "PMID:37291214") "A(n) pulmonary alveolar type 2 cell that is cycling.") -AnnotationAssertion( ) -AnnotationAssertion( "2024-07-02T09:14:23Z") AnnotationAssertion(Annotation( "PMID:37291214") "proliferating pulmonary alveolar type 2 cell") AnnotationAssertion(rdfs:label "cycling pulmonary alveolar type 2 cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) @@ -225,8 +206,6 @@ EquivalentClasses( ObjectIntersection # Class: (cycling myeloid cell) AnnotationAssertion(Annotation( "PMID:38301653") "A(n) myeloid cell that is cycling.") -AnnotationAssertion( ) -AnnotationAssertion( "2024-07-02T09:14:23Z") AnnotationAssertion(Annotation( "PMID:38301653") "proliferating myeloid cell") AnnotationAssertion(rdfs:label "cycling myeloid cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) @@ -234,8 +213,6 @@ EquivalentClasses( ObjectIntersection # Class: (cycling basal cell) AnnotationAssertion(Annotation( "PMID:33208946") "A(n) basal cell that is cycling.") -AnnotationAssertion( ) -AnnotationAssertion( "2024-07-02T09:14:23Z") AnnotationAssertion(Annotation( "PMID:33208946") "proliferating basal cell") AnnotationAssertion(rdfs:label "cycling basal cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) @@ -243,8 +220,6 @@ EquivalentClasses( ObjectIntersection # Class: (cycling stromal cell) AnnotationAssertion(Annotation( "PMID:34497389") "A(n) stromal cell that is cycling.") -AnnotationAssertion( ) -AnnotationAssertion( "2024-07-19T09:14:23Z") AnnotationAssertion(Annotation( "PMID:34497389") "proliferating stromal cell") AnnotationAssertion(rdfs:label "cycling stromal cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) @@ -252,8 +227,6 @@ EquivalentClasses( ObjectIntersection # Class: (cycling glial cell) AnnotationAssertion(Annotation( "PMID:34497389") "A(n) glial cell that is cycling.") -AnnotationAssertion( ) -AnnotationAssertion( "2024-07-19T09:14:23Z") AnnotationAssertion(Annotation( "PMID:34497389") "proliferating glial cell") AnnotationAssertion(rdfs:label "cycling glial cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) @@ -261,8 +234,6 @@ EquivalentClasses( ObjectIntersection # Class: (cycling plasma cell) AnnotationAssertion(Annotation( "PMID:34497389") "A(n) plasma cell that is cycling.") -AnnotationAssertion( ) -AnnotationAssertion( "2024-07-19T09:14:23Z") AnnotationAssertion(Annotation( "PMID:34497389") "proliferating plasma cell") AnnotationAssertion(rdfs:label "cycling plasma cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) @@ -270,8 +241,6 @@ EquivalentClasses( ObjectIntersection # Class: (cycling type EC enteroendocrine cell) AnnotationAssertion(Annotation( "PMID:34497389") "A(n) type EC enteroendocrine cell that is cycling.") -AnnotationAssertion( ) -AnnotationAssertion( "2024-07-19T09:14:23Z") AnnotationAssertion(Annotation( "PMID:34497389") "proliferating type EC enteroendocrine cell") AnnotationAssertion(rdfs:label "cycling type EC enteroendocrine cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) @@ -279,90 +248,204 @@ EquivalentClasses( ObjectIntersection # Class: (cycling neuroblast (sensu Vertebrata)) AnnotationAssertion(Annotation( "PMID:34497389") "A(n) neuroblast (sensu Vertebrata) that is cycling.") -AnnotationAssertion( ) -AnnotationAssertion( "2024-07-19T09:14:23Z") AnnotationAssertion(Annotation( "PMID:34497389") "proliferating neuroblast (sensu Vertebrata)") AnnotationAssertion(rdfs:label "cycling neuroblast (sensu Vertebrata)") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) -AnnotationAssertion(Annotation( "DOI:10.1002/cphy.c120026") Annotation( "DOI:10.1007/978-1-4939-1311-4_10") Annotation( "DOI:10.1016/j.immuni.2022.08.002") Annotation( "DOI:10.1038/nri.2017.11") Annotation( "DOI:10.1111/j.1478-3231.2006.01342.x") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. +AnnotationAssertion(Annotation( "DOI:10.1016/S0092-8674(00)81834-6") Annotation( "DOI:10.1016/S1534-5807(02)00173-9") Annotation( "DOI:10.1242/dev.202046") Annotation( "https://www.ncbi.nlm.nih.gov/books/NBK553142/") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Male germ cells are specialized cells that give rise to the male gametes and are therefore crucial for sexual reproduction in males. Through a complex process called spermatogenesis in the testes male germ cells undergo several stages of development, each with distinctive morphological and physiological characteristics, eventually differentiating into mature spermatozoa (sperm). +Male germ cells are responsible for transferring genetic material from male to offspring as part of sexual reproduction. In the initial stage of their life cycle, they exist as spermatogonial stem cells, which multiply by mitotic division to self-renew and to produce daughter cells. The daughter cells then undergo meiotic division, a process that reduces the number of chromosomes in each cell by half, from diploid to haploid – the formation of spermatids. This is critical for maintaining genetic stability from generation to generation, as it ensures that when an egg and sperm cell unite during fertilization, the resulting offspring will have the correct number of chromosomes. The final phase of spermatogenesis is called spermiogenesis, during which spermatozoa - mature and motile sperm cells – are produced from round spermatids. +The matured male germ cells or sperm cells are highly specialized, having a streamlined shape designed for efficient movement towards the female egg. A sperm cell is divided into three main parts, namely the head, midpiece, and tail. The head contains the genetic material, the midpiece contains mitochondria that provide energy, and the tail, termed as the flagellum, propels the sperm cell forward. Each of these parts play significant roles in fertilization.") +AnnotationAssertion( "https://cellxgene.cziscience.com/cellguide/CL_0000015") +AnnotationAssertion(Annotation( "DOI:10.1080/19420889.2015.1017156") Annotation( "DOI:10.1152/physrev.00009.2020") Annotation( "https://www.ncbi.nlm.nih.gov/books/NBK26914/") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Sperm cells, also known as spermatozoa or male gametes, are highly specialized cells that are pivotal for sexual reproduction in animals. Produced in the male reproductive organs, specifically the testes, sperm cells play an important role in the process of fertilization, where they fuse with a female gamete or egg cell (ovum) to form a zygote, which marks the beginning of a new organism. +Sperm cells hold several unique traits that set them apart from other body cells. Structurally, a sperm cell possesses two main structures: the head, containing the nucleus carrying the paternal genetic information, and the flagellum, which generates energy and grants the sperm cell mobility +The process of fertilization occurs when one sperm cell successfully penetrates the egg, delivering its genetic information, and ultimately leading to the formation of a new individual combining both paternal and maternal genetic materials. Notably, while hundreds of millions of sperm cells may be released during ejaculation, only one has the opportunity to successfully fertilize the egg, underscoring the highly competitive nature of this biological process.") +AnnotationAssertion( "https://cellxgene.cziscience.com/cellguide/CL_0000019") +AnnotationAssertion(Annotation( "DOI:10.1002/cphy.c120026") Annotation( "DOI:10.1007/978-1-4939-1311-4_10") Annotation( "DOI:10.1016/j.immuni.2022.08.002") Annotation( "DOI:10.1038/nri.2017.11") Annotation( "DOI:10.1111/j.1478-3231.2006.01342.x") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. Kupffer cells are tissue-resident macrophages located in the liver. They are an integral part of the mononuclear phagocyte system and are responsible for the phagocytosis of dead or dying cells, microbes, and other foreign substances. Kupffer cells account for approximately 80-90% of tissue-resident macrophages in the body. They are found within the lumen of liver sinusoids and interface with microbial populations and products. The primary role of Kupffer cells is to maintain homeostasis in the liver. They continuously filter and cleanse the blood that flows through the liver, removing pathogens, endotoxins, particulate matter, aged and dysfunctional red blood cells, and miscellaneous waste products. These cells also play an important role in maintaining iron homeostasis. During the process of phagocytosis, Kupffer cells recycle iron from degraded red blood cells, which is then utilized in the formation of new erythrocytes. Kupffer cells also play key roles in various immune responses and inflammatory processes. They secrete various types of cytokines and chemokines, which contribute to the activation and mobilization of other immune cells. They can also produce reactive oxygen species and nitric oxide, which have microbicidal actions. Although their activity is essential for host defense, excessive or prolonged activation of Kupffer cells may contribute to hepatic injury, inflammation, and fibrosis.") AnnotationAssertion( "https://cellxgene.cziscience.com/cellguide/CL_0000091") -AnnotationAssertion(Annotation( "DOI:10.1007/s12311-018-0985-7") Annotation( "DOI:10.1038/nrn3886") Annotation( "DOI:10.7554/eLife.63668") Annotation( "https://www.ncbi.nlm.nih.gov/books/NBK545154/") Annotation( "https://www.sciencedirect.com/topics/agricultural-and-biological-sciences/purkinje-cell") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. +AnnotationAssertion(Annotation( "DOI:10.3389/fmed.2017.00234") Annotation( "DOI:10.37175/stemedicine.v1i4.57") Annotation( "https://www.sciencedirect.com/topics/medicine-and-dentistry/osteoclast") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Osteoclasts, derived from the monocyte/macrophage lineage, play a crucial role in bone remodeling through bone resorption. They are distinguished from other cells by their large size and their unique ability to secrete enzymes and acids that dissolve the calcium phosphate in bone. The formation of osteoclasts is influenced by two primary factors: macrophage colony-stimulating factor (M-CSF) and the ligand-activated receptor (RANKL) of nuclear factor kappa B (NF-κB). +Osteoclasts also collaborate with osteoblasts, responsible for new bone formation, to maintain bone health and adapt bone structure. Their coordinated actions allow continuous remodeling while preserving overall bone strength and integrity. Imbalances in osteoclast activity can lead to pathological conditions. For example, excessive activity may contribute to diseases like osteoporosis, periprosthetic osteolysis, bone tumors, and Paget's disease. Other the other hand, osteoclast deficiency ca result in conditions like osteopetrosis.") +AnnotationAssertion( "https://cellxgene.cziscience.com/cellguide/CL_0000092") +AnnotationAssertion(Annotation( "DOI:10.1038/srep32007") Annotation( "https://www.ncbi.nlm.nih.gov/books/NBK539836/") Annotation( "https://www.ncbi.nlm.nih.gov/books/NBK563130") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Surface ectoderm cells give rise to external structures such as the epidermis, hair, nails, and sweat glands. They are critical during the early stages of embryonic development, where they delineate and create the organism's exterior body plan. Beyond forming the organism's physical exterior, surface ectodermal cells have other significant roles. For instance, these cells lead to the development of the anterior pituitary gland and the enamel of the teeth. They are also integral to the formation of the sensory organs, including the eyes and the ears. In the eyes, they form the cornea and lens epithelium. In the ears, they form the external ear canal and certain parts of the inner ear. Therefore, these cells are instrumental in the development of various sensory systems in an organism. +Certain abnormalities or mutations in surface ectodermal cells could lead to medical conditions known as ectodermal dysplasias. These are a group of inherited disorders affecting the development or function of teeth, hair, nails, and sweat glands. Therefore, understanding the formation and function of surface ectodermal cells is also important in identifying and addressing certain genetic disorders and conditions. In summary, surface ectodermal cells are essential in embryonic development, contributing to the creation of the external physical appearance and the sensory organs of an organism.") +AnnotationAssertion( "https://cellxgene.cziscience.com/cellguide/CL_0000114") +AnnotationAssertion(Annotation( "DOI:10.1007/s12311-018-0985-7") Annotation( "DOI:10.1038/nrn3886") Annotation( "DOI:10.7554/eLife.63668") Annotation( "https://www.ncbi.nlm.nih.gov/books/NBK545154/") Annotation( "https://www.sciencedirect.com/topics/agricultural-and-biological-sciences/purkinje-cell") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. Purkinje cells, named after the Czech anatomist Jan Evangelista Purkyně who discovered them, are unique inhibitory neurons in the cerebellar cortex. They are a critical part of the vertebrate nervous system as they provide the only signal output from the cortex to the cerebellar nuclei. They are one of the few types of neurons that are large enough to be seen with the naked eye. The most distinct hallmark of Purkinje cells is their elaborate dendritic arbor, which forms a broad and intricately branching structure resembling a tree. These numerous branches each receive excitatory synaptic inputs from more than 100,000 parallel fibers; in addition, a single climbing fiber makes hundreds of synapses to the soma and proximal dendrites. A single long axon forms an inhibitory projection to the cerebellar nuclei. Purkinje cells play key roles in the coordination of fine, voluntary motor movements and balance. As the sole output of all motor coordination in the cerebellar cortex, they serve as a central relay in the cerebro-cerebellar loop. Each Purkinje cell receives two types of synaptic input: one from parallel fibers (which are axons of granule cells), and the other from climbing fibers (originating from the inferior olivary nucleus). The Purkinje cells process and integrate these diverse kinds of input signals to generate output that controls timing and coordination of movements. Purkinje neurons show considerable synaptic plasticity. Throughout life, these cells continue to undergo long-term potentiation and depression at parallel fiber synapses, which cause long-lasting increase or decrease, respectively, of synaptic transmission and have been proposed as mechanisms for motor learning. Purkinje cells are also known to be implicated in a variety of diseases. Their progressive loss is a prime feature in certain types of ataxia, a collective term used to describe conditions characterized by loss of muscular control and coordination. Furthermore, a significant reduction in the density of Purkinje cells has been reported in conditions such as autism and Huntington’s disease.") AnnotationAssertion( "https://cellxgene.cziscience.com/cellguide/CL_0000121") -AnnotationAssertion(Annotation( "DOI:10.1016/S1357-2725(02)00083-3") Annotation( "DOI:10.1038/s41575-022-00675-x") Annotation( "DOI:10.1165/ajrcmb.25.5.f218") Annotation( "DOI:10.1242/bio.20121701") Annotation( "https://www.ncbi.nlm.nih.gov/books/NBK553208/") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. +AnnotationAssertion(Annotation( "DOI:10.1016/j.cell.2019.08.053") Annotation( "DOI:10.1016/j.conb.2022.102674") Annotation( "DOI:10.1016/j.tins.2021.11.001") Annotation( "DOI:10.1038/nri3086") Annotation( "DOI:10.3389/fnins.2021.742065") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Microglial cells, sometimes referred to as microglia, are a type of glial cell that primarily exist within the central nervous system (CNS), notably in the brain and the spinal cord. Classified among the resident immune cells, microglial cells represent about 10% of all cells found within the CNS. These cells are derived from progenitor cells in the yolk sac, which differentiates them from other types of glial cells (such as astrocytes and oligodendrocytes) that are derived from neuroectodermal cell lineages. +The primary role of microglial cells is to act as the first and main active form of immune defense in the CNS. They express a vast repertoire of pattern recognition receptors, which allow them to sense and eliminate microbes invading the CNS parenchyma. They represent one of the macrophage populations of the CNS and are responsible for phagocytosis (engulfing and destroying cellular waste or pathogens) in the neural environment. +Microglial cells are particularly responsive to pathogens and injuries and change their morphology in reaction to inflammation or insult: In the normal state they are characterized by a ramified shape with small processes; in response to stimuli, some microglia mature and change to an amoeboid shape. +Beyond their macrophagic activity, they also perform synaptic pruning during brain development, eliminate unnecessarily produced neurons, and facilitate tissue regeneration and repair. they play integral roles in regulating neural development and supporting cell survival and are important for maintaining tissue homeostasis. +While their protective role generally benefits the brain, their over-activation can occasionally lead to neuro-inflammatory diseases, underlining the importance of balanced microglial cell functions. They have been extensively studied for their association with neurodegenerative diseases, such as Alzheimer's disease, Parkinson's disease, and multiple sclerosis.") +AnnotationAssertion( "https://cellxgene.cziscience.com/cellguide/CL_0000129") +AnnotationAssertion(Annotation( "DOI:10.1038/nri2171") Annotation( "DOI:10.1111/bph.14527") Annotation( "DOI:10.3390/ijms23073698") Annotation( "DOI:10.3748/wjg.v17.i5.578") Annotation( "DOI:full/10.15252/emmm.202114121") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Gut endothelial cells are a crucial component of the endothelium, a thin layer of single cells that line the interior surface of blood vessels and lymphatic vessels, including those in the digestive system or \"gut\". These cells plays an integral role in various physiological and metabolic functions, actively participating in nutrient absorption, host defense, and vascular homeostasis in the gut. +The primary function of gut endothelial cells lies in their ability to control the passage of materials and the transit of white blood cells into and out of the bloodstream. They achieve this through the formation of a semi-permeable barrier, in which permeability is regulated by tight junctions; complex structures that bring the cells together, sealing the space between them. This ensures a controlled, selective passage of nutrients, ions, and water from the bloodstream into the gut and vice versa, helping maintain homeostasis and overall health. +Gut endothelial cells also play a significant role in angiogenesis and serve as a critical regulator of the gut immune responses playing a modulative role in gut immune homeostasis and inflammatory responses. In addition, they generate nitric oxide, a potent vasodilator, which helps in maintaining vascular tonus, preventing platelet and leukocyte adhesion, and decreasing smooth muscle proliferation. These multi-faceted roles make gut endothelial cells indispensable for the normal functioning of the gut and overall health.") +AnnotationAssertion( "https://cellxgene.cziscience.com/cellguide/CL_0000131") +AnnotationAssertion(Annotation( "DOI:10.1002/med.21754") Annotation( "DOI:10.1038/nrc.2016.37") Annotation( "DOI:10.1111/j.1751-1097.2007.00226.x") Annotation( "DOI:10.3390/ijms21249769") Annotation( "https://www.sciencedirect.com/topics/agricultural-and-biological-sciences/melanocyte") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Melanocytes are specialized cells prevalently found in the skin, but also present in the hair follicles, eyes, inner ear, bones, heart, and brain. Their primary function is the synthesis of melanin, a pigment responsible for coloration of skin, hair, and eyes. The presence and distribution of this pigment play a crucial role in the body's defense mechanism against harmful ultraviolet radiation. +In addition to melanin production, melanocytes also engage in a variety of other biological functions. They play a fundamental role in the immune response, owing to their ability to present antigens to T cells. Furthermore, they contribute to the maintenance of the skin's homeostasis by regulating processes such as extracellular matrix remodeling and cytokine production. A balance in melanocyte function is pivotal, as dysfunctions often result in dermatological disorders. For instance, the loss of melanocytes or reduction in their function may lead to hypopigmentation conditions such as vitiligo, whereas an abnormal increase could result in hyperpigmentation disorders or melanoma, a dangerous type of skin cancer.") +AnnotationAssertion( "https://cellxgene.cziscience.com/cellguide/CL_0000148") +AnnotationAssertion(Annotation( "DOI:10.1016/S1357-2725(02)00083-3") Annotation( "DOI:10.1038/s41575-022-00675-x") Annotation( "DOI:10.1165/ajrcmb.25.5.f218") Annotation( "DOI:10.1242/bio.20121701") Annotation( "https://www.ncbi.nlm.nih.gov/books/NBK553208/") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. Goblet cells are specialized, simple columnar, secretory epithelial cells that are mostly found in the respiratory and intestinal tracts. The term \"goblet\" refers to their shape, which resembles a flask or goblet, specially at their apical end which is swollen due to the accumulation of secretory granules. The primary function of goblet cells is to to protect and lubricate the underlying tissues by secreting large quantities of mucin, a complex glycoprotein, which forms mucus when hydrated. In the respiratory tract, the mucus secreted by these cells traps dust, bacteria, viruses, and other potentially harmful particles in the inhaled air, preventing them from reaching the delicate tissues of the lungs. In the intestines, the goblet cells secrete mucus that acts as a protective barrier shielding the intestinal epithelium from dietary antigens, pathogens and prevents the intestinal epithelium from being eroded by the actions of the digestive enzymes and the abrasive action of passing food material. Goblet cells are capable of rapidly altering their secretory output in response to stimuli. For example, irritants like smoke or dust can trigger an increased rate of mucus production, as the body attempts to flush out the harmful particles. Conversely, in conditions such as chronic bronchitis and cystic fibrosis, overactive goblet cells can create a thick accumulation of mucus that obstructs the airways and fosters bacterial growth. Lastly, goblet cells are not static, rather, they undergo a dynamic process known as goblet cell metaplasia-differentiation, wherein non-goblet cells in response to chronic injury or inflammation, can differentiate into goblet cells leading to an accumulation of these cells in the tissue, known as goblet cell hyperplasia.") AnnotationAssertion( "https://cellxgene.cziscience.com/cellguide/CL_0000160") -AnnotationAssertion(Annotation( "DOI:10.1038/s41574-019-0168-8") Annotation( "DOI:10.1111/j.1463-1326.2011.01438.x") Annotation( "DOI:10.1196/annals.1294.001") Annotation( "DOI:10.1210/endrev/bnaa018") Annotation( "DOI:10.7554/elife.78512") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. +AnnotationAssertion(Annotation( "DOI:10.1038/s41574-019-0168-8") Annotation( "DOI:10.1111/j.1463-1326.2011.01438.x") Annotation( "DOI:10.1196/annals.1294.001") Annotation( "DOI:10.1210/endrev/bnaa018") Annotation( "DOI:10.7554/elife.78512") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. Enteroendocrine cells are a specialized subset of cells located within the epithelial lining of both the small and large intestines, as well as the stomach and pancreas. Constituting less than 1% of the total population of intestinal cells, they are differentiated from a common intestinal cell progenitor, thus sharing lineage with absorptive and goblet cells of the intestines. The distinct characteristic feature of an enteroendocrine cell is its inherent capacity to synthesize and secrete a plethora of gut hormones such as serotonin, somatostatin, neurotensin, cholecystokinin, secretin, gastric inhibitory peptide, motilin, and glucagon-like peptide-1. Integrated within this complex network of signaling agents, these substances control various aspects of the digestive system. Each enteroendocrine cell has its unique combination of hormones to release, determined by its position along the intestinal tract. Intriguingly, these hormones not only modulate local gut function, including motility, absorption and secretion, but also potentiate distant actions on other systems such as endocrine, nervous and immune and play a role in the feeling of satiety. The release of these hormones from enteroendocrine cells is a highly regulated and dynamic process. The cells are equipped with sensory receptors localized on its luminal side that respond to various stimuli, including changes in nutrient composition, chemical or mechanical changes in the gut lumen, or even signals arising from commensal microbiota. This sensory input stimulates a signaling cascade within the cell, culminating in the release of specific hormones into the interstitial fluid. These hormones then make their way into the bloodstream, acting on their respective target receptors to mediate their duties. The multifunctional characteristics of enteroendocrine cells make them crucial for maintaining gut homeostasis and the overall physiological well being of the body.") AnnotationAssertion( "https://cellxgene.cziscience.com/cellguide/CL_0000164") -AnnotationAssertion(Annotation( "DOI:10.1002/cphy.c190003") Annotation( "DOI:10.1016/j.biocel.2016.02.003") Annotation( "DOI:10.3389/fendo.2018.00711") Annotation( "DOI:10.3389/fimmu.2022.977175") Annotation( "DOI:10.3389/fimmu.2022.977175/full") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. +AnnotationAssertion(Annotation( "DOI:10.1002/cphy.c190003") Annotation( "DOI:10.1016/j.biocel.2016.02.003") Annotation( "DOI:10.3389/fendo.2018.00711") Annotation( "DOI:10.3389/fimmu.2022.977175") Annotation( "DOI:10.3389/fimmu.2022.977175/full") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. Chromaffin cells, also known as pheochromocytes, are neuroendocrine cells that are typically located in the adrenal medulla, the innermost part of the adrenal gland, which is situated on top of each kidney. Chromaffin cells are also found in small clusters, known as paraganglia, in various locations throughout the body, including the sympathetic nervous system. They derive their name from their ability to stain a brownish-black color upon exposure to chromic salts, a feature made possible due to their high content of granules rich in catecholamines and catecholamine-related neurotransmitters. The primary function of chromaffin cells is the synthesis and release of catecholamines, specifically epinephrine (adrenaline) and norepinephrine (noradrenaline). These neurotransmitters are vital stress hormones that, when released by the adrenal chromaffing cells into the bloodstream, prepare the body for the 'fight or flight' response. This response can enhance the body's performance in a dangerous situation by increasing heart rate, elevating blood sugar, and increasing blood flow to the muscles. The chromaffin cells in paraganglia are responsible for the local release of catecholamines and play a role in regulating blood pressure and other autonomic functions. In addition to their role in stress response, chromaffin cells also contribute to the body's immune response. They secrete several peptides including antimicrobial peptides, and the discovery of LPS and cytokine receptors on chromaffin cells suggests that the adrenal medulla may participate in some aspects of the immune response.") AnnotationAssertion( "https://cellxgene.cziscience.com/cellguide/CL_0000166") -AnnotationAssertion(Annotation( "DOI:10.1016/j.coemr.2019.03.001") Annotation( "DOI:10.1093/biolre/ioy059") Annotation( "DOI:10.1210/clinem/dgaa603") Annotation( "DOI:10.3389/fendo.2014.00006") Annotation( "https://www.ncbi.nlm.nih.gov/books/NBK556007/#:~:text=Leydig%20cells%20are%20the%20primary,secondary%20sexual%20characteristics%20and%20behaviors.") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. +AnnotationAssertion(Annotation( "DOI:10.1016/j.coemr.2019.03.001") Annotation( "DOI:10.1093/biolre/ioy059") Annotation( "DOI:10.1210/clinem/dgaa603") Annotation( "DOI:10.3389/fendo.2014.00006") Annotation( "https://www.ncbi.nlm.nih.gov/books/NBK556007/#:~:text=Leydig%20cells%20are%20the%20primary,secondary%20sexual%20characteristics%20and%20behaviors.") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. Leydig cells are a testosterone-secreting cell in the interstitial area in the testes of males. They are named after Franz Leydig, a German anatomist who discovered these cells in 1850. Uniquely situated within the soft connective tissue surrounding the seminiferous tubules, Leydig cells form an integral part of the male reproductive system. They are usually polygonal cells characterized by well developed smooth endoplasmic reticulum, high lipid content and a large round nucleus. They are found across mammalian species, including humans. The primary function of Leydig cells is the production of androgens, the male sex hormones, the most notable of which is testosterone. Leydig cells synthesize testosterone from cholesterol through a series of enzymatic reactions. The production and release of testosterone are mainly regulated by the luteinizing hormone (LH) released by the anterior pituitary gland. In response to LH, Leydig cells convert cholesterol into testosterone, which then plays a crucial role in the development and maintenance of primary and secondary male sexual characteristics. These include the formation and maturation of male reproductive organs, onset of spermatogenesis, and the presentation of male secondary sexual traits such as the deepening of the voice, growth of facial hair, development of muscles, and a broadening of shoulders. Apart from testosterone production, Leydig cells also secrete insulin-like factor 3 (INSL3) that is essential for testicular descent during embryonic development in males. Dysregulation or loss of Leydig cells can lead to numerous conditions like testosterone deficiency, infertility, and certain forms of testicular cancer. Although not typical, Leydig cells can regenerate if they are damaged, ensuring the continuous production of testosterone and maintaining male reproductive health. They provide an excellent model to study cell differentiation and hormone regulation, thereby enhancing our understanding of reproductive biology and associated disorders.") AnnotationAssertion( "https://cellxgene.cziscience.com/cellguide/CL_0000178") -AnnotationAssertion(Annotation( "DOI:10.1016/j.biocel.2011.11.011") Annotation( "DOI:10.1055/s-2007-1007096") Annotation( "DOI:10.1083/jcb.201903090") Annotation( "DOI:10.1111/j.1439-0396.2007.00752.x") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. +AnnotationAssertion(Annotation( "DOI:10.1016/j.biocel.2011.11.011") Annotation( "DOI:10.1055/s-2007-1007096") Annotation( "DOI:10.1083/jcb.201903090") Annotation( "DOI:10.1111/j.1439-0396.2007.00752.x") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. Hepatocytes are the major cell type constituting 70-80% of the liver's cytoplasmic mass, playing crucial roles in maintaining the body's metabolic homeostasis. Dimensions of mature hepatocytes typically range from 20 to 30 μm in humans, but size may vary depending on their location within the liver lobule. Hepatocytes are characterized by high biosynthetic, enzymatic, and endocytic activity. They contain abundant mitochondria, smooth and rough endoplasmic reticulum, peroxisomes, lysosomes, and a large nucleus that is often binucleate. The liver consists of three zones - the periportal Zone 1, midzone 2, and pericentral Zone 3 - which have differential nutrient and oxygen status, and damage susceptibility; hepatocytes in the different zones show signifcant functional heterogeneity ('hepatocyte functional zonation'). Hepatocytes are involved in a multitude of critical functions including the metabolism of lipids, carbohydrates, and proteins, the synthesis of serum proteins (e.g., albumin, transferrin, and lipoproteins), the detoxification and excretion of endogenous and exogenous substances, the storage of vitamins and minerals, and the production and secretion of bile. Heterocytes demonstrate a remarkable regenerative capacity, which enables the liver to recover from injury and loss of tissue mass. Notably, hepatocytes perform biotransformation with both phase I and phase II enzymes, which modify drugs, xenobiotics, and various substances for elimination from the body. Phase I enzymes, such as cytochrome P450, catalyze both oxidative and reductive reactions of many xenobiotics; many of the products of phase I enzymes are substrates for the phase II enzymes, which catalyze conjugation reactions. Alterations in hepatocyte function have significant implications for overall human health and disease. Certain conditions, such as hepatitis, cirrhosis, and liver cancer, can profoundly affect hepatocyte structure and function, thereby disrupting the liver's ability to perform its vital roles within the body. As the primary site for drug metabolism, changes in hepatocyte function can also impact the effectiveness and toxicity of pharmaceuticals. The regenerative ability of hepatocytes makes them valuable cells for liver regenerative medicine and bioartificial liver support systems, and their study has provided significant insights into liver biology and disease.") AnnotationAssertion( "https://cellxgene.cziscience.com/cellguide/CL_0000182") -AnnotationAssertion(Annotation( "DOI:10.1016/j.ejogrb.2004.01.010") Annotation( "DOI:10.1093/humrep/del408") Annotation( "DOI:10.1093/humupd/6.3.279") Annotation( "DOI:10.1210/jcem-28-3-355") Annotation( "DOI:10.3389/fendo.2019.00832/full") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. +AnnotationAssertion(Annotation( "DOI:10.1002/cphy.c160033") Annotation( "DOI:10.3390/biology10101056") Annotation( "https://www.nature.com/scitable/topicpage/the-sliding-filament-theory-of-muscle-contraction-14567666/") Annotation( "https://www.ncbi.nlm.nih.gov/books/NBK537139") Annotation( "https://www.ncbi.nlm.nih.gov/books/NBK9961/") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Skeletal muscle cells, or myocytes, are essential for the musculoskeletal system, featuring a striated appearance from tightly packed sarcomeres. These elongated, multi-nucleated cells convert ATP into mechanical energ and are key for voluntary movement and posture. They also are responsible for maintaining body temperature, storing nutrients, and stabilizing joints. +Skeletal muscle cells organize themselves tightly into bundles to form muscle fibers. Embedded within each of these cells are thousands of myofibrils, which are made up of the contractile proteins, actin (the thin filament), and myosin (the thick filament). Contraction of a skeletal muscle cell occurs when these myofibrils shorten, a process driven by the sliding of actin and myosin filaments over each other in a mechanism famously known as the sliding filament theory. +Additionally, skeletal muscle cells exhibit a high degree of plasticity, which allows for their adaptation in response to alterations in functional demands or damages. They have an innate regenerative capacity due to the presence of satellite cells—quiescent muscle stem cells that reside within the muscle fibers. Upon muscle injury, these satellite cells become activated, proliferate, and differentiate into new muscle cells, thereby contributing to the repair and growth of injured skeletal muscle. With this, skeletal muscle cells serve not only a pivotal biomechanical function but also possess a great capacity for self-healing and regeneration.") +AnnotationAssertion( "https://cellxgene.cziscience.com/cellguide/CL_0000188") +AnnotationAssertion(Annotation( "DOI:10.1093/ptj/81.11.1810") Annotation( "DOI:10.1186/s13578-015-0054-6") Annotation( "DOI:10.3389/fphys.2021.747214") Annotation( "https://www.sciencedirect.com/topics/biochemistry-genetics-and-molecular-biology/slow-muscle-fiber") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Slow muscle cells, as the name implies, are a type of muscle cell well known for their slow contractile speed. They are also referred to as type I, slow-twitch, or red muscles because of their high myoglobin content which gives them a dark, reddish appearance. These cells are predominantly found in the postural muscles of the body, such as those in the back and lower limbs. +A defining characteristic of slow muscle cells is their significant resistance to fatigue. This is largely due to their efficient oxidative metabolism, which allows them to continuously contract over extended periods without succumbing to fatigue. This extraordinary endurance is facilitated by a high concentration of mitochondria, which enables the efficient use of oxygen for energy production, and capillaries, which supplies the necessary oxygen and nutrients. Additionally, these cells have an abundant supply of myoglobin, a protein that stores and transports oxygen within the muscle cell, further supporting their aerobic metabolism. +The primary role of slow muscle cells in the human body is to provide sustained, low-intensity contractions over a prolonged period. They are responsible for maintaining posture and providing stability, rather than delivering short, powerful bursts of activity. They play a pivotal role in supporting various physical activities such as standing, walking, or any form of exercise that requires endurance over speed.") +AnnotationAssertion( "https://cellxgene.cziscience.com/cellguide/CL_0000189") +AnnotationAssertion(Annotation( "DOI:10.1152/japplphysiol.00636.2019") Annotation( "DOI:10.3389/fcell.2018.00125") Annotation( "DOI:10.4161/org.4.3.6312") Annotation( "https://www.sciencedirect.com/topics/biochemistry-genetics-and-molecular-biology/fast-muscle-fiber") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Fast muscle cells, also known as type II muscle fibers, are a particular type of muscle cell that specializes in conducting rapid, high-intensity contractions. These cells are primarily found within skeletal muscle groups that are directly involved in gross motor activities, such as running, jumping, or lifting heavy weights. The designation \"fast\" refers to their speed of contraction in response to neural stimuli, which is significantly quicker when compared to other muscle cell types such as slow-twitch or type I muscle fibers. +The primary function of fast muscle cells revolves around their role in anaerobic metabolism, which provides the energy needed for short, forceful bursts of power. They contain a high concentration of glycolytic enzymes that facilitate this process, leading to a swift break down of glucose to generate ATP (adenosine triphosphate), the primary energy currency in biological systems. On the downside, the byproduct of this very rapid, anaerobic metabolic process is lactic acid, which can build up and cause muscle fatigue. +Fast muscle cells can be further classified into two subtypes based on their metabolic characteristics: type IIa and type IIb/x. Type IIa cells, also known as fast oxidative-glycolytic fibers, possess a good oxygen supply and can function in both anaerobic and aerobic conditions, exhibiting moderate resistance to fatigue. On the other hand, type IIb/x cells, also known as fast glycolytic fibers, primarily rely on anaerobic metabolism and tire out a lot quicker. Both these subtypes can adapt to changing demands due to exercise and conditioning, highlighting the plasticity that is a key characteristic of these versatile muscle cells.") +AnnotationAssertion( "https://cellxgene.cziscience.com/cellguide/CL_0000190") +AnnotationAssertion(Annotation( "DOI:10.1093/ptj/81.11.1810") Annotation( "https://training.seer.cancer.gov/anatomy/muscular/types.html") Annotation( "https://www.ncbi.nlm.nih.gov/books/NBK10854/") Annotation( "https://www.ncbi.nlm.nih.gov/books/NBK526125") Annotation( "https://www.ncbi.nlm.nih.gov/books/NBK556137/") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Smooth muscle cells are a specialized type of muscle cells that are primarily found within the walls of hollow organs such as the intestine, stomach, bladder, uterus, and blood vessels. These cells are an essential component of the autonomic nervous system controling involuntary movements within the body. +Smooth muscle cells play a vital role in many physiological processes due to their unique functionality. They can contract and relax in a slow, sustained, and controlled manner to help modulate the size and shape of the lumens of the organs they surround. For example, in the digestive system, coordinated contraction and relaxation of smooth muscle cells propels food along the gastrointestinal tract - a process known as peristalsis. In the blood vessels, the smooth muscle cells, by contracting or relaxing, either constrict or dilate the vessels, which in turn, help regulate blood flow and pressure. +On a cellular level, smooth muscle cells possess a single, centrally located nucleus and contain an arranged network of actin and myosin filaments, which are the proteins responsible for muscle contraction. Unlike their counterparts in skeletal or cardiac muscles, these cells lack specific contact points for these filaments, hence the lack of visible striations. Furthermore, the contraction of smooth muscle cells is regulated by hormones and neurotransmitters, such as acetylcholine and norepinephrine, adding an additional layer of complex regulation to these highly specialized cells.") +AnnotationAssertion( "https://cellxgene.cziscience.com/cellguide/CL_0000192") +AnnotationAssertion(Annotation( "DOI:10.1016/j.ceb.2019.07.012") Annotation( "DOI:10.5535/arm.2016.40.1.162") Annotation( "https://www.sciencedirect.com/topics/biochemistry-genetics-and-molecular-biology/mesoderm") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Mesodermal cells are pluripotent and the most abundant in the human body. They contribute to the development of several structures such as the skeletal muscles, bones, heart and blood vessels, kidneys, gonads, connective tissues, and certain layers of the skin. Hence, the mesoderm is often regarded as an active and diverse layer due to its role in forming many bodily structures. +In embryonic development, these cells are instrumental, contributing to the body's structures through a carefully coordinated sequence of morphogenetic movements. This process forms the complex multicellular architecture of tissues and organs from a simple ball of cells. Without the function of mesodermal cells, the body's integral structures and systems would cease to form correctly, leading to developmental disorders such as axial mesodermal dysplasia complex") +AnnotationAssertion( "https://cellxgene.cziscience.com/cellguide/CL_0000222") +AnnotationAssertion(Annotation( "DOI:10.1038/s41586-020-2347-0") Annotation( "DOI:10.3389/fcell.2022.1040708") Annotation( "https://www.ncbi.nlm.nih.gov/books/NBK10008/") Annotation( "https://www.ncbi.nlm.nih.gov/books/NBK553142/") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Gametes are reproductive cells essential for sexual reproduction in eukaryotic organisms, including humans, animals, and many plants. These cells are haploid, containing half the genome or only one set of chromosomes, which is a contrast to the diploid state (two sets of chromosomes) found in most cells in a multicellular organism. This reduction in genetic material is crucial since it allows for the re-establishment of the diploid number of chromosomes when two gametes merge to form a diploid zygote during fertilization. +There are two major types of gametes in animals: sperm cells in males and egg (or ova) in females. These gametes contribute equally to the genetic makeup of the offspring but are morphologically and functionally distinct. Sperm cells (or spermatozoa) are characterized by their motility, small size, and large quantities; they are produced continuously in vast numbers through a process called spermatogenesis in the male gonads or testes. Female gametes are much larger, fewer in numbers, and are not motile; they undergo a development process known as oogenesis, which takes place within the ovaries. The egg also contributes most of the cytoplasm and organelles (including mitochondria) to the zygote that are required for initial cell division stages after fertilization. +Gametes have a primary role in sexual reproduction and genetic variation, which aids in evolution. The formation of gametes involves a special type of cell division called meiosis that introduces genetic diversity via the process of recombination and independent assortment. Following the fusion of male and female gametes, the combination of paternal and maternal genetic material in the zygote allows for genetic recombination, which is a fundamental source of genetic variation and, thus, evolution. Therefore, gametes not only are critical to the inception of new individuals but also contribute to species survival and evolution.") +AnnotationAssertion( "https://cellxgene.cziscience.com/cellguide/CL_0000300") +AnnotationAssertion(Annotation( "DOI:10.1016/j.jri.2023.103811") Annotation( "DOI:10.1530/JOE-17-0402") Annotation( "https://www.ncbi.nlm.nih.gov/books/NBK53245") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Trophoblast cells, originating from the blastocyst's outer layer, are highly specialized and pivotal for embryo development. Their crucial roles include facilitating implantation and contributing to the formation of the placenta, an essential organ for fetal nutrition, gas exchange, and waste removal during pregnancy. +These cells play a crucial role in implantation by adhering to the uterus lining. Post-implantation, some trophoblast cells differentiate, forming syncytiotrophoblasts. These multi-nucleated cells absorb nutrients, release waste, and secrete hormones, including human chorionic gonadotropin (hCG), sustaining pregnancy. +Trophoblast cells also play a crucial role in immune tolerance, preventing the maternal immune system from treating the fetus as foreign. This balance is vital for a healthy pregnancy. Dysfunctional trophoblast cells may lead to complications like miscarriages or preeclampsia, emphasizing their importance in both embryology and reproductive medicine.") +AnnotationAssertion( "https://cellxgene.cziscience.com/cellguide/CL_0000351") +AnnotationAssertion(Annotation( "https://www.ncbi.nlm.nih.gov/books/NBK482438/") Annotation( "https://www.ncbi.nlm.nih.gov/books/NBK532857/") Annotation( "https://www.ncbi.nlm.nih.gov/books/NBK557452/") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Smooth muscle cells, as a broader category, are non-striated, involuntary muscle cells that usually exhibit contractions and dilation to facilitate numerous physiological functions. Sphincter associated smooth muscle cells are a specific type of smooth muscle cell that are primarily associated with the functioning of various anatomical sphincters in the human body. +The traits that distinguishes sphincter associated smooth muscle cells from other smooth muscle cells are their location and specialized function in sphincter mechanisms. Sphincter associated smooth muscle cells play a pivotal role in regulating the opening and closure of the bodily sphincters. These sphincters can be found at multiple locations within the body including the gastrointestinal tract (namely the esophagus, stomach, small intestine, and rectum), the urinary tract, and the circulatory system. Upon receiving signals from the autonomous nervous system, these cells contract or relax to modulate the aperture of sphincters, thus controlling the movement of substances through them. Due to their precise and vital functional role, any dysfunction or dysregulation in these cells can lead to serious medical conditions, such as gastroesophageal reflux or urinary incontinence.") +AnnotationAssertion( "https://cellxgene.cziscience.com/cellguide/CL_0000358") +AnnotationAssertion(Annotation( "DOI:10.1093/cvr/cvs135") Annotation( "DOI:10.1093/cvr/cvy023") Annotation( "DOI:10.1161/ATVBAHA.118.311229") Annotation( "DOI:10.3389/fimmu.2020.599415") Annotation( "DOI:10.3390/ijms20225694") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Vascular associated smooth muscle cells (VSMCs) are specialized cells that constitute a major component of the blood vessel wall in the circulatory system. They derive their name from the predominantly smooth appearance under microscopic examination, as opposed to the striated appearance of cardiac and skeletal muscles. +A principal function of VSMCs is to regulate vascular tone, which directly dictates blood pressure and blood flow distribution across various body parts. This is achieved through coordinated contraction and relaxation of the muscles in response to a variety of extracellular signals. When a blood vessel is exposed to stimuli like pressure or injury, VSMCs contract, resulting in vasoconstriction and ultimately, an increase in blood pressure. Conversely, in response to vasodilators, these cells relax, leading to vasodilation and a consequent decrease in blood pressure. +VSMCs are also involved in vascular remodeling, a process where blood vessels adapt their structure to long-term changes in hemodynamic conditions or disease states. In diseases like atherosclerosis and hypertension, an aberrant proliferative and synthetic phenotype of VSMCs contributes to the formation of plaques, leading to vessel hardening or even occlusion. Recent research has further implicated these cells in immune responses, recognizing their function in leukocyte recruitment and inflammation, factors that are largely instrumental in vascular pathologies.") +AnnotationAssertion( "https://cellxgene.cziscience.com/cellguide/CL_0000359") +AnnotationAssertion(Annotation( "DOI:10.1016/j.semcdb.2016.04.009") Annotation( "DOI:10.1242/dev.202046") Annotation( "https://www.ncbi.nlm.nih.gov/books/NBK26843/") Annotation( "https://www.ncbi.nlm.nih.gov/books/NBK553142/") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +The male gamete, also known as a sperm cell, is a highly specialized cell type critical to sexual reproduction. Sperm are produced during a process called spermatogenesis within the male reproductive organ, specifically the testes. They are haploid cells, carrying the genetic material from the male parent, and fuse with the ovum, the female gamete, to form a diploid zygote during fertilization, thereby initiating gestation and the development of a new organism. +The male gamete is distinguished by its morphology, notably its elongated shape which is geared towards locomotion. One of the primary characteristics of a male gamete is its flagellum, or tail, which propels the cell towards the female gamete. It additionally contains an elongated head region housing the nucleus, where the genetic material is stored. The anterior section of the head, the acrosome, releases enzymes essential for penetrating the protective layers of the ovum during the fertilization process. +The function of male gametes does not cease upon fertilization. In addition to delivering the paternal set of chromosomes, fusion of the sperm cell with the ovum causes an increase in cytosolic Ca2+ which then activates the female egg cell to undergo the so-called cortical reaction during which the egg’s zona pellucida is changed so fusion with additional sperm is prevented. The Ca2+ signal also initiates the development of the zygote and eventual formation of an embryo. Male gametes also contribute towards forming the placenta, which supplies nutrients and removes waste products during gestation.") +AnnotationAssertion( "https://cellxgene.cziscience.com/cellguide/CL_0000408") +AnnotationAssertion(Annotation( "DOI:10.1016/j.ejogrb.2004.01.010") Annotation( "DOI:10.1093/humrep/del408") Annotation( "DOI:10.1093/humupd/6.3.279") Annotation( "DOI:10.1210/jcem-28-3-355") Annotation( "DOI:10.3389/fendo.2019.00832/full") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. Granulosa cells are a type of somatic cell most commonly known for their crucial role within the ovarian follicles of female mammalian species. Named for their grainy appearance, they are situated in the follicular epithelium, lining the inner part of the follicle and directly surrounding the oocyte. These cells stand as an integral part of the ovarian structure and function. One of the primary roles of granulosa cells is to aid in the production and secretion of sex hormones, particularly estrogen. They achieve this by working in tandem with theca cells, which stay attached to the external layer of the follicle. Theca cells produce androstenedione (a type of androgen) which granulosa cells then convert into estradiol, a form of estrogen, with the help of the enzyme aromatase. Moreover, granulosa cells participate in luteinization, transforming into luteal granulosa cells as a response to the luteinizing hormone during ovulation. This allows the formation of the corpus luteum, responsible for the secretion of progesterone necessary to maintain pregnancy. Granulosa cells also play a significant role in follicular development and oocyte maturation, involving close communication with the contained oocyte. They support the oocyte through the provision of nutrients and growth factors, control its meiotic cycle and ensure it is appropriately oriented and instructed for impending ovulation. Furthermore, granulosa cells contribute to the formation of the zona pellucida and the follicular fluid, providing an optimal environment for the oocyte's growth and maturation. These cells, thus, perform multiple vital roles, underscoring their importance in fertility and reproductive health.") AnnotationAssertion( "https://cellxgene.cziscience.com/cellguide/CL_0000501") -AnnotationAssertion(Annotation( "DOI:10.1016/j.pharmthera.2015.05.007") Annotation( "DOI:10.1038/s41574-018-0020-6") Annotation( "DOI:10.1093/annonc/mdh216") Annotation( "https://www.sciencedirect.com/topics/neuroscience/somatostatin-cell") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. +AnnotationAssertion(Annotation( "DOI:10.1016/j.pharmthera.2015.05.007") Annotation( "DOI:10.1038/s41574-018-0020-6") Annotation( "DOI:10.1093/annonc/mdh216") Annotation( "https://www.sciencedirect.com/topics/neuroscience/somatostatin-cell") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. Type D enteroendocrine cells, also known as D or delta cells, are specialized hormone-releasing cells found in the pancreas and also scattered throughout the lining of the gastrointestinal tract in mammals, notably within the stomach and the upper part of the small intestine known as the duodenum. The primary role of D cells is to produce and secrete somatostatin, a potent paracrine inhibitor. In the gastrointestinal tract, somatostatin slows down digestion. It reduces gastric acid secretion and slows down the rate of gastric emptying, thereby prolonging and controling the digestive p. Functionally, these effects are aimed at sustaining nutrient absorption to optimize energy extraction from consumed food. In the pancreas, D cells maintain a vital role in endocrine regulation. D cells in the pancreatic islands secrete somatostatin to inhibit the release of both insulin and glucagon from type A cells and B cells, glucoregulatory hormones that control blood sugar levels. Hence, D cells contribute considerably to the homeostasis of the body's metabolic processes. It is also noteworthy that dysfunctional D cells or irregular somatostatin signaling has been associated with certain pathologies such as neuroendocrine tumors and gastric ulcers.") AnnotationAssertion( "https://cellxgene.cziscience.com/cellguide/CL_0000502") -AnnotationAssertion(Annotation( "DOI:10.1007/s00018-002-8412-z") Annotation( "DOI:10.1038/nature09637") Annotation( "DOI:10.1038/nrmicro2546") Annotation( "DOI:10.1146/annurev-physiol-030212-183744") Annotation( "DOI:10.3389/fimmu.2020.00587") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. +AnnotationAssertion(Annotation( "DOI:10.1007/s00018-002-8412-z") Annotation( "DOI:10.1038/nature09637") Annotation( "DOI:10.1038/nrmicro2546") Annotation( "DOI:10.1146/annurev-physiol-030212-183744") Annotation( "DOI:10.3389/fimmu.2020.00587") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. Paneth cells are specialized epithelial cells that are primarily located at the bottom of the crypts of Lieberkühn in the small intestine, where they play a pivotal role in maintaining gut homeostasis. They have also been found in smaller numbers in the colonic crypts and other parts of the gastrointestinal tract. Paneth cells are characterized by large acidophilic granules, which take up most of the cytoplasmic volume, causing the nucleus to be pushed toward the base of the cell. Paneth cells function as a part of the innate immune system. The large granules inside the cells are filled with antimicrobial peptides, such as defensins and lysozymes. Upon bacterial intrusion or cellular signaling indicating a potential infection, Paneth cells release the granules containing the antimicrobial substances into the crypt lumen, effectively serving as the first line of defense against bacterial invasion within the gastrointestinal tract. In essence, Paneth cells serve as guardians, protecting the intestinal stem cells from harmful pathogens that may disturb the gut ecosystem. In addition to their primary role in immunity, Paneth cells are also crucial for supporting the stem cell niche in the intestinal crypts. They are located adjacent to Lgr5+ stem cells and secrete various growth factors such as EGF, TGF-alpha, Wnt3, and Notch ligand Dll4. These factors regulate the self-renewal and differentiation of these stem cells, which continuously replenish the intestinal epithelium. Consequently, any abnormality or dysfunction in Paneth cells could lead to a disturbance in gut homeostasis, possibly resulting in various illnesses such as inflammatory bowel disease.") AnnotationAssertion( "https://cellxgene.cziscience.com/cellguide/CL_0000510") -AnnotationAssertion(Annotation( "DOI:10.1007/BF00710764") Annotation( "DOI:10.1038/nrgastro.2013.36") Annotation( "DOI:10.1097/MOG.0b013e32832ebfac") Annotation( "DOI:10.1111/prd.12116") Annotation( "DOI:10.1152/physrev.00011.2011") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. +AnnotationAssertion(Annotation( "DOI:10.1074/jbc.RA118.001739") Annotation( "https://www.ncbi.nlm.nih.gov/books/NBK544225/") Annotation( "https://www.sciencedirect.com/topics/medicine-and-dentistry/smooth-muscle") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +A precursor to the smooth muscle cell, the smooth muscle myoblast, is integral to various body systems, including the cardiovascular, gastrointestinal, and respiratory systems. Smooth muscle myoblasts arise from the differentiation of mesenchymal stem cells, a process tightly regulated by specific genetic factors and environmental signals. Their role extends to myogenesis, particularly in the formation of muscular tissue, especially during embryonic development. +Smooth muscle myoblasts possess distinctive cellular characteristics. In contrast to skeletal muscle myoblasts, they do not fuse to create multinucleated fibers. Instead, they differentiate into individual, uninucleated smooth muscle cells. This differentiation unfolds in two distinct phases: proliferation, marked by rapid division to increase cell numbers, and differentiation, involving structural and functional transformation into mature smooth muscle cells. This intricate process is intricately mediated by various signaling molecules and transcription factors. +Functionally, smooth muscle myoblasts and the mature muscle cells they generate play pivotal roles in various physiological processes. Smooth muscle cells orchestrate involuntary muscle responses and are integral to body systems that regulate blood flow, propel food along the digestive tract, and control airflow in the respiratory tract. These diverse functions underscore the significance of smooth muscle myoblasts in the body's growth, maintenance, and overall function.") +AnnotationAssertion( "https://cellxgene.cziscience.com/cellguide/CL_0000514") +AnnotationAssertion(Annotation( "DOI:10.1016/j.immuni.2017.10.021") Annotation( "DOI:10.1146/annurev-immunol-081022113627") Annotation( "DOI:10.1186/2050-7771-2-1") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Granulocyte monocyte progenitor cells (GMP cells), originating from hematopoietic stem cells in the bone marrow, are a critical intermediate in myeloid cell development. Positioned at a key differentiation juncture, these cells exhibit bidirectional potential, giving rise to both granulocyte and monocyte lineages. +Their primary role is to generate mature granulocytes and monocytes, essential components of the body's innate immunity and inflammatory responses. Granulocytes, such as neutrophils, eosinophils, and basophils, contribute to the first line of defense against infections by migrating to the infection site and phagocytosing pathogens. Monocytes can differentiate into macrophages or dendritic cells, playing diverse roles in immune responses.") +AnnotationAssertion( "https://cellxgene.cziscience.com/cellguide/CL_0000557") +AnnotationAssertion(Annotation( "DOI:10.1016/s1357-2725(03)00042-6") Annotation( "DOI:10.1152/physrev.00061.2017") Annotation( "DOI:10.1186/s13287-022-02706-5") Annotation( "DOI:10.1369/0022155411426780") Annotation( "DOI:10.22074/cellj.2016.4714") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Skeletal muscle satellite cells (SMSCs) are a type of adult stem cell that nestles on the outer surface of the myofiber, positioned between the sarcolemma (plasma membrane of the muscle cell) and peripheral basement membrane. +The primary function of SMSCs lies in their capacity to facilitate the growth and repair of damaged skeletal muscle. Upon muscle injury or trauma, these normally quiescent cells activate, proliferate, and differentiate into myoblasts. These myoblasts subsequently mature and fuse to form myotubes, which ultimately help in the repair and rebuilding of muscle fibers. This response is an integral part of the skeletal muscle's ability to recover from injury and adapt to enhanced or changing physical demands, thereby maintaining and improving muscle function. +Furthermore, SMSCs also contribute to hypertrophic muscle growth due to resistance exercise and endurance training, with the notable feature of their multi-nucleated nature resulting from the fusion of differentiated myoblasts. The additional nuclei support enhanced protein synthesis, thus allowing the muscle fibers to grow and strengthen in response to exercise. In aging and in diseases, the number or functionality of these cells can decrease, leading to impaired muscle regeneration and progressive muscle weakness.") +AnnotationAssertion( "https://cellxgene.cziscience.com/cellguide/CL_0000594") +AnnotationAssertion(Annotation( "DOI:10.1007/BF00710764") Annotation( "DOI:10.1038/nrgastro.2013.36") Annotation( "DOI:10.1097/MOG.0b013e32832ebfac") Annotation( "DOI:10.1111/prd.12116") Annotation( "DOI:10.1152/physrev.00011.2011") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. Acinar cells are specialized exocrine gland cells that secrete specific enzymes and fluids to aid in digestion. Found primarily in the pancreas and salivary glands, the term acinar is derived from the Latin word 'acinus' which means 'grape'; this is because acinar cells are arranged in a grape-like cluster around small ducts, formulating an acinus structure. In the salivary glands, acinar cells secrete digestive enzymes as well as other substances such as mucus and water. These secretions service the initial stages of the digestive process, preparing the consumed food for onward digestion in the stomach and intestines by lubricating and partially breaking it down. In the pancreas, acinar cells are responsible for synthesizing and secreting a significant amount of digestive enzymes, such as trypsin, chymotrypsin, and amylase. These enzymes are stored in zymogen granules inside the acinar cells until they are dispatched into the small intestine. Once within the small intestine, they break down proteins, carbohydrates, and fats into substances that can be absorbed. This is vital to the effective and efficient digestion and absorption of nutrients from the food we consume. Acinar cells have high protein synthesis rates and are susceptible to accumulation of misfolded proteins; the subsequential induction of ER stress is thought to be involved in the development of pancreatitis, a serious inflammatory disease of the exocrine pancreas.") AnnotationAssertion( "https://cellxgene.cziscience.com/cellguide/CL_0000622") -AnnotationAssertion(Annotation( "DOI:10.1038/s41467-022-33748-1") Annotation( "DOI:10.1038/s41572-020-0196-7") Annotation( "DOI:10.1146/annurev-physiol-020911-153238") Annotation( "DOI:10.1159/000481633") Annotation( "DOI:10.3389/fcell.2021.771931") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. +AnnotationAssertion(Annotation( "DOI:10.1038/s41467-022-33748-1") Annotation( "DOI:10.1038/s41572-020-0196-7") Annotation( "DOI:10.1146/annurev-physiol-020911-153238") Annotation( "DOI:10.1159/000481633") Annotation( "DOI:10.3389/fcell.2021.771931") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. Podocytes are highly specialized, terminally differentiated glomerular visceral epithelial cells that wrap around the capillaries in the kidneys. They play an essential role in kidney function, particularly in the filtration selectivity of the glomerulus. Each podocyte is characterized by a unique architecture with a large cell body, ‘major processes’ extending outwardly from the cell body and ‘foot processes’, also known as pedicels, which surround. the glomerular capillary loops Podocytes represent the last barrier of the glomerular filtration membrane in the kidney. This barrier prevents the leakage of plasma proteins from the blood into the urine, hence maintaining protein homeostasis in the body. The foot processes of the podocytes interdigitate with those from neighboring cells. The cell-cell junctions between the foot processes, the slit-diaphragms, are thought to create a molecular sensor of renal filtration that prevents the passage of macromolecules while allowing water and small solutes to pass. Podocytes also contribute to the glomerular basement membrane by secreting collagen and maintain glomerular endothelial cell fenestration by secreting VEGFA. They have been shown to play a role in inducing cytoskeletal regulation, cell adhesion, and inflammatory response, consistent with their essential function in the kidney. The importance of podocytes is further emphasized by the effects of their damage or loss. Abnormalities in podocytes often result in severe kidney diseases (podocytopathies), including focal segmental glomerulosclerosis (FSGS) and minimal change disease (MCD). Injury to the podocytes can result in \"effacement\" or flattening of foot processes, leading to increased permeability of the filtration barrier and proteinuria (an excess of serum protein in urine) which is a common symptom of kidney diseases.") AnnotationAssertion( "https://cellxgene.cziscience.com/cellguide/CL_0000653") -AnnotationAssertion(Annotation( "DOI:10.1002/ar.1092200109") Annotation( "DOI:10.1016/0306-4522(86)90162-4") Annotation( "DOI:10.1016/j.devcel.2012.11.003") Annotation( "DOI:10.1038/s41467-022-31571-2") Annotation( "DOI:10.1152/ajprenal.90601.2008") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. +AnnotationAssertion(Annotation( "DOI:10.1002/ar.1092200109") Annotation( "DOI:10.1016/0306-4522(86)90162-4") Annotation( "DOI:10.1016/j.devcel.2012.11.003") Annotation( "DOI:10.1038/s41467-022-31571-2") Annotation( "DOI:10.1152/ajprenal.90601.2008") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. Fenestrated cells are specialized epithelial cells that are characterized by a distinctive structural feature, fenestrations or tiny pores, which allow an exchange of substances such as fluids, nutrients, and waste between blood vessels and the surrounding tissue environments. These cells are present in various types of epithelial tissues in the human body, including the intestinal tract, endocrine glands, and certain parts of the renal system. There are multiple types of endothelial cell fenestrations. The most common type is found in systemic capillaries of the endocrine tissue (e.g., pancreatic islets), gastrointestinal mucosa, and renal peritubular capillaries. Here, the fenestrated cells have fenestrations in their peripheral cytoplasm with a unique thin and permeable diaphragm that provides a high degree of selectivity, blocking the passage of larger molecules while allowing the free movement of smaller ones. In contrast, other types of fenestrations, such as the discontinuous epithelium of the liver sinusoidal endothelial cells, do not have diaphragms. @@ -370,336 +453,805 @@ Characteristically, fenestrated cells play a vital role in the filtering process In the endocrine system, fenestrated cells in glandular capillaries allow the prompt release of hormones into the bloodstream. These cells have tightly clustered fenestrations which increase the surface area available for passive diffusion, improving the efficiency of hormone secretion. In villi of the small intestine, these cells increase absorption efficiency, permitting the exchange of water, electrolytes, and nutrients. Overall, fenestrated cells contribute immensely to important physiological processes of filtration, absorption, and secretion, primarily connecting our body's circulation system with the surrounding tissues and organs.") AnnotationAssertion( "https://cellxgene.cziscience.com/cellguide/CL_0000666") -AnnotationAssertion(Annotation( "DOI:10.1038/nature08529") Annotation( "DOI:10.1093/jb/mvv121") Annotation( "DOI:10.1136/gut.47.5.735") Annotation( "https://www.ncbi.nlm.nih.gov/books/NBK534232/") Annotation( "https://www.sciencedirect.com/topics/medicine-and-dentistry/microfold-cell") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. +AnnotationAssertion(Annotation( "DOI:10.1038/nature08529") Annotation( "DOI:10.1093/jb/mvv121") Annotation( "DOI:10.1136/gut.47.5.735") Annotation( "https://www.ncbi.nlm.nih.gov/books/NBK534232/") Annotation( "https://www.sciencedirect.com/topics/medicine-and-dentistry/microfold-cell") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. M cells, or microfold cells, of the gut are specialized epithelial cells found in the lining of the gut, specifically in the follicle-associated epithelium of mucosa-associated lymphoid tissue, where they function as sentries against toxins and pathogens. M cells are characterized by apical microfolds (hence their alternate name) which express unique adhesion molecules that enable them to sample the luminal macromolecules. Other morphological features that distinguish M cells from other intestinal mucosal cells include sparse microvilli and a reduced thickness of the glycocalyx, which permits adhesion while not hindering the transport of molecules. They also have unique intraepithelial invaginations on the basolateral side which are filled with macrophages and other immune cells that can process the engulfed macromolecules quickly. These morphological characteristics enable M cells to serve a dual role in immune responses. They initiate the immune response by transporting antigens (such as toxic or pathogenic substances) across the epithelial layer to lymphocytes and antigen-presenting cells in the underlying lymphoid tissue. This specialized transport process is called 'transcytosis.' They also have specialized molecules like glycoprotein-2 for bacterial uptake. Simultaneously, M cells help maintain immune tolerance to food antigens and commensal bacteria, preventing unnecessary reactions to non-pathogenic substances and hypersensitivity conditions. While these functions are crucial for well-being, M cell dysfunction can lead to serious conditions like Crohn's disease and other inflammatory bowel diseases.") AnnotationAssertion( "https://cellxgene.cziscience.com/cellguide/CL_0000682") -AnnotationAssertion(Annotation( "DOI:10.1016/j.febslet.2014.07.005") Annotation( "DOI:10.1016/j.mce.2015.06.028") Annotation( "DOI:10.1038/s41580-020-00317-7") Annotation( "DOI:10.1210/jc.2003-030630") Annotation( "DOI:10.1369/00221554155835") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. +AnnotationAssertion(Annotation( "DOI:10.1016/j.febslet.2014.07.005") Annotation( "DOI:10.1016/j.mce.2015.06.028") Annotation( "DOI:10.1038/s41580-020-00317-7") Annotation( "DOI:10.1210/jc.2003-030630") Annotation( "DOI:10.1369/00221554155835") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. PP cells, also known as pancreatic polypeptide cells (and previously called F cells or gamma cells), are enteroendocrine cells predominantly found in the islets of Langerhans in the head of the pancreas. They are one of the four main endocrine cell types present in the pancreatic islets, along with type A, B and D cells. PP cells are notable for their production of pancreatic polypeptide, an anorexigenic hormone that modulates food intake and energy homeostasis. By secreting pancreatic polypeptide, PP cells play a significant role in the management of both digestive and appetite regulation. Upon ingestion of food, there is a significant increase in the secretion of pancreatic polypeptide, which then reduces biliary secretion and helps slow down the movement of food through the digestive tract. This allows more time for digestion to take place and nutrients to be absorbed, promoting the efficient use of dietary intake. The pancreatic polypeptide further reduces appetite by interacting with the hypothalamus, the area of the brain responsible for control of hunger. Given their important role in digestion, malfunction or damage to PP cells can lead to a disturbance in the digestive process and contribute to some disease conditions. For example, an overproduction of pancreatic polypeptide can result in conditions such as pancreatic tumors and diabetes. Conversely, an under secretion might contribute to obesity due to impaired dietary control. Furthermore, PP cells may also play a role in the body's energy balance, suggesting their implication in conditions related to energy metabolism.") AnnotationAssertion( "https://cellxgene.cziscience.com/cellguide/CL_0000696") -AnnotationAssertion(Annotation( "DOI:10.1002/nau.22195") Annotation( "DOI:10.1038/ki.2009.73") Annotation( "DOI:10.1038/ncpuro0672") Annotation( "DOI:10.1038/s41579-020-0324-0") Annotation( "DOI:10.1152/physrev.00041.2019") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. +AnnotationAssertion(Annotation( "DOI:10.1002/nau.22195") Annotation( "DOI:10.1038/ki.2009.73") Annotation( "DOI:10.1038/ncpuro0672") Annotation( "DOI:10.1038/s41579-020-0324-0") Annotation( "DOI:10.1152/physrev.00041.2019") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. Urothelial cells are a unique type of epithelial cell found lining the urinary tract system. They form the urothelium, a specialized, multi-layered epithelium that lines major portions of the urinary tract, including the renal pelvis, ureters, bladder, and the proximal part of the urethra. The distinct characteristic of urothelial cells is their ability to stretch and contract depending on the volume of liquid they contain - a feature that facilitates the essential role they play in maintaining the functionality and integrity of the urinary system. The primary function of urothelial cells is to provide an impermeable barrier to urine, preventing the toxic components present in the urine from seeping back into the body's bloodstream. The urothelium consists of a superficial umbrella cell layer, 1–2 layers of intermediate cells, and a basal cell layer. The umbrella layer is composed of large, mostly binucleated cells that are covered in an asymmetrical unit membrane, the uroplakin plaques. These plaques function to seal the apical membrane of the bladder from the toxic and highly variable contents of urine. The lipid bilayer structure of uroplakin plaques has an exceptionally high concentration of uroplakins that contribute to the barrier function of the urothelium. Beyond their mechanical function, urothelial cells also play a role in sensing and signaling changes in the urinary system. They express a number of sensor molecules or respond to thermal, mechanical and chemical stimuli and can release chemical mediators. This allows them to act as sensory transducers because they detect changes in the filling state of the bladder and transmit this information to the nervous system. Moreover, these versatile cells contribute to the defense mechanism against urinary tract pathogens. They respond to bacterial infections by releasing chemical messengers, cytokines and chemokines, to attract immune cells, and also can engulf pathogens via endocytosis.") AnnotationAssertion( "https://cellxgene.cziscience.com/cellguide/CL_0000731") -AnnotationAssertion(Annotation( "DOI:10.1038/nri.2017.28") Annotation( "DOI:10.1111/sji.12883") Annotation( "DOI:10.1182/blood-2009-07-235028") Annotation( "DOI:10.3389/fimmu.2015.00423/full") Annotation( "DOI:10.3389/fimmu.2019.02035") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. +AnnotationAssertion(Annotation( "DOI:10.1016/j.ccep.2010.10.012") Annotation( "DOI:10.1038/nrcardio.2016.203") Annotation( "https://www.ncbi.nlm.nih.gov/books/NBK572070") Annotation( "https://www.sciencedirect.com/topics/agricultural-and-biological-sciences/cardiac-muscle") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Cardiac muscle cells, also known as cardiomyocytes or cardiac myocytes, are specialized cells that form the heart tissue. These cells are elongated, branched, and contain a single centrally located nucleus. Their anatomy is composed primarily of densely packed myofibrils, which are protein structures that consist of sarcomeres - the fundamental units of muscle contraction. Cardiac muscle cells are united at their ends through specialized junctions known as intercalated discs, which allow the heart to contract in a unified, powerful and rhythmic way. +Functionally, cardiac muscle cells are responsible for the heart's consistent pumping action that circulates blood throughout the body. Unlike most cells in the body, cardiac muscle cells spontaneously depolarize and generate action potentials without external stimulation. This unique trait stems from the presence of ion channels in the cells' membrane that allow a cyclic flow of ions across the membrane, which create the electrical impulses necessary for heart contraction. The spread of these electrical signals from one cardiac muscle cell to another - facilitated by the interconnected network made by the intercalated disks - results in a synchronized contraction of the heart muscle. +Unlike skeletal muscle cells which can tire and need rest, cardiac muscle cells have to work ceaselessly throughout the entire lifespan, without the opportunity for rest, to ensure continuous circulation of blood. This is made possible through the high volume of mitochondria and a constant supply of oxygen from coronary circulation. In conclusion, cardiac muscle cells, through their unique structure and vital functionality, play a pivotal role in sustaining life by providing the means for blood to reach every cell in the body.") +AnnotationAssertion( "https://cellxgene.cziscience.com/cellguide/CL_0000746") +AnnotationAssertion(Annotation( "DOI:10.1038/nri.2017.28") Annotation( "DOI:10.1111/sji.12883") Annotation( "DOI:10.1182/blood-2009-07-235028") Annotation( "DOI:10.3389/fimmu.2015.00423/full") Annotation( "DOI:10.3389/fimmu.2019.02035") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. Classical monocytes are a subtype of monocytes that are characterized by high CD14 but no CD16 expression. Emerging from the bone marrow and entering the bloodstream, these cells play central roles in immune responses and regulation of inflammation. CD14-positive CD16-negative monocytes form the majority of circulating monocytes in the body, typically contributing to around 80-90% of the total monocyte pool. The primary function of the classical monocytes is to serve in the frontline of host defense against infections. They are primed to migrate to sites of infection, and they express pattern recognition receptors that help them identify and phagocytose pathogens, leading to their destruction. Classical monocytes also contribute to inflammation by producing several pro-inflammatory cytokines including interleukins and tumor necrosis factors. In response to specific signals from tissues under pathological conditions, such as infection or injury, classical monocytes can leave the bloodstream and migrate towards the affected sites. Following their arrival, these cells differentiate into diverse cell types including macrophages and dendritic cells to combat specific pathogens or injury. Dysregulated monocyte activity can lead to the development of many human diseases including inflammation, infection, tissue injury, and various autoimmune diseases.") AnnotationAssertion( "https://cellxgene.cziscience.com/cellguide/CL_0000860") -AnnotationAssertion(Annotation( "DOI:10.1038/s41392-023-01452-1") Annotation( "DOI:10.1186/s12935-021-02089-2") Annotation( "DOI:10.3389/fimmu.2015.00263") Annotation( "DOI:10.3389/fimmu.2020.583084") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. +AnnotationAssertion(Annotation( "DOI:10.1038/s41392-023-01452-1") Annotation( "DOI:10.1186/s12935-021-02089-2") Annotation( "DOI:10.3389/fimmu.2015.00263") Annotation( "DOI:10.3389/fimmu.2020.583084") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. Inflammatory macrophages, also sometimes referred to as M1 or classically activated macrophages, play an important role in the inflammatory response. The M1/M2 classification is based upon macrophage polarization rather than macrophage location and refers to macrophage activation towards either a more inflammatory or more resolving phenotype, respectively, although the functional diversity of macrophages is more nuanced than such a dichotomy suggests. Inflammatory macrophages are derived from monocytes recruited to a site of infection or injury. M1 macrophages are classically activated, typically by IFN-γ or lipopolysaccharide (LPS). Upon sensing signs of inflammation, they quickly respond by increasing their pro-inflammatory activity. They achieve this by producing a range of signaling molecules, such as nitric oxide, reactive oxygen species, and numerous cytokines such as tumor necrosis factor-alpha (TNF-alpha) and interleukin-1, -6 and -12. The release of these potent molecules helps to recruit other immune cells to the site, killing off pathogenic organisms and facilitation inflammation. At the same time, M1 macrophages can also present antigens to T cells, thereby helping to induce an adaptive immune response. Over time, these macrophages may transition in phenotype and function to help resolve the inflammation and promote tissue repair. Despite the beneficial role of inflammatory macrophages in dealing with pathogens, chronic activation of these cells can lead to harmful effects. Over time, continuous production of pro-inflammatory molecules can cause damage to tissues and organs. This is seen in certain chronic inflammatory diseases, such as atherosclerosis, diabetes, obesity, asthma, and various autoimmune disorders. In such situations, the normally protective function of inflammatory macrophages is not properly controlled, which can contribute to disease pathology.") AnnotationAssertion( "https://cellxgene.cziscience.com/cellguide/CL_0000863") -AnnotationAssertion(Annotation( "DOI:10.1038/s41392-023-01452-1") Annotation( "DOI:10.1186/s12935-021-02089-2") Annotation( "DOI:10.3389/fimmu.2015.00263") Annotation( "DOI:10.3389/fimmu.2020.583084") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. +AnnotationAssertion(Annotation( "DOI:10.1007/s00281-013-0382-8") Annotation( "DOI:10.1016/j.immuni.2022.10.005") Annotation( "DOI:10.1016/j.tins.2021.07.002") Annotation( "DOI:10.1038/s41583-019-0201-x") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Central Nervous System (CNS) macrophages represent an integral part of the brain's innate immune system. These immune cells play crucial roles in maintenance and regulation, homeostasis, and disease response, thereby helping in the overall cognitive functioning of an organism. +There are different macrophage populations in the CNS, often classified into microglial cells, which reside in the parenchyma, and non-parenchymal macrophages at the interface between the brain and the periphery, including the perivascular spaces, the choroid plexus, and the meninges. CNS macrophages are derived from erythromyeloid progenitors in the yolk sac. CNS macrophages have distinct morphologies: Meningeal and perivascular macrophages have a more elongated shape than microglia, which are characterized by a small cell body with fine processes; in contrast, choroid plexus macrophages typically have a stellate shape. +Microglia are the most abundant abundant mononuclear phagocytes and have been shown to play a number of physiological roles, including proinflammatory and anti-inflammatory functions, synaptic pruning and remodeling, and apoptotic cell removal through phagocytosis. Non-parenchymal CAMs primarily support the barrier function against external antigens. Meningeal macrophages have been shown to respond to peripheral microbial challenges and to protect the brain against fatal viral infection. +CNS macrophages are also involved in the initiation and progression of many neurological diseases, such as Alzheimer's disease and Parkinson's disease as well as multiple sclerosis.") +AnnotationAssertion( "https://cellxgene.cziscience.com/cellguide/CL_0000878") +AnnotationAssertion(Annotation( "DOI:10.1038/s41392-023-01452-1") Annotation( "DOI:10.1186/s12935-021-02089-2") Annotation( "DOI:10.3389/fimmu.2015.00263") Annotation( "DOI:10.3389/fimmu.2020.583084") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. Alternatively activated macrophages, also referred to as M2 macrophages, are immune cells originating from monocytes. The M1/M2 classification is based upon macrophage polarization rather than macrophage location and refers to macrophage activation towards either a more inflammatory or more resolving phenotype, respectively, although the functional diversity of macrophages is more nuanced than such a dichotomy suggests. M2 macrophages cells are differentiated from their precursors generally in response to Th2 cytokines, such as interleukin-4 (IL-4), interleukin-10 (IL-10), and interleukin-13 (IL-13). Tissue-resident macrophages are also sometimes said to have an “M2-like” phenotype. M2 macrophages play key roles in immunoregulation and disease resolution. Functionally, alternatively activated macrophages are essential in wound healing and tissue repair and remodeling, largely due to their potent anti-inflammatory actions and their ability to promote angiogenesis. They achieve these functions by the production of specific growth factors and signaling proteins including Arg1, Ym1/2, Fizz1, and TGF-β. Additionally, they provide defense against specific categories of pathogens, particularly parasites, through specific communication with Th2 cells. However, dysfunction of M2 macrophages can be harmful. Alternatively activated macrophages have been associated with several pathological conditions such as asthma, fibrosis, and tumor progression. This is due to their capacity to inhibit inflammatory responses, promote unneeded wound healing processes, and support tumour growth and spreading. Furthermore, complex roles have been observed in metabolic disorders, cardiovascular diseases, and neurodegenerative diseases, showing the diverse functional spectrum of these cells.") AnnotationAssertion( "https://cellxgene.cziscience.com/cellguide/CL_0000890") -AnnotationAssertion(Annotation( "DOI:10.1016/0165-6147(89)90192-2") Annotation( "DOI:10.1038/nrgastro.2013.36") Annotation( "DOI:10.1097/01.mog.0000239863.96833.c0") Annotation( "https://www.ncbi.nlm.nih.gov/books/NBK54134/") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. +AnnotationAssertion(Annotation( "DOI:10.1007/s00795-015-0099-y") Annotation( "DOI:10.1007/s11914-012-0105-4") Annotation( "DOI:10.1016/j.jot.2021.04.005") Annotation( "DOI:10.1038/s41413-020-0099-y") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Bone cells, also known as osteocytes, form the building blocks of the skeletal system. They represent the most common type of bone cell, making up approximately 95% of the total bone cell population in mature adult bone tissue. Osteocytes are a stellate shape with numerous long, slender dendritic processes. +The formation of bone is a complex process involving the action of osteoclasts - cells that break down and reabsorb old bone, followed by osteoblasts that rebuild the bone. Osteocytes serve as coordinators for these two types of bone cells to ensure a balance in the bone remodeling process, contributing to maintaining both bone strength and mineral homeostasis. +The primary functions of osteocytes involve the creation, maintenance, and repair of bone tissue. They ensure that bone remodeling is performed by forming a network within the bone and communicating with other cells to help them respond to mechanical strain and damage. +A remarkable aspect of osteocytes is their ability to perceive mechanical forces, translating them into biochemical signals that regulate bone remodeling and adaptation. Defects in osteocyte function, aside from other bone cells, have been associated with several bone disorders such as osteoporosis, renal osteodystrophy, and skeletal manifestations of diabetes.") +AnnotationAssertion( "https://cellxgene.cziscience.com/cellguide/CL_0001035") +AnnotationAssertion(Annotation( "DOI:10.1016/0165-6147(89)90192-2") Annotation( "DOI:10.1038/nrgastro.2013.36") Annotation( "DOI:10.1097/01.mog.0000239863.96833.c0") Annotation( "https://www.ncbi.nlm.nih.gov/books/NBK54134/") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. Pancreatic acinar cells are the functional units of the exocrine pancreas. These cells are structurally arranged in small clusters - or acini - with a small central lumen, and their primary function is to produce and secrete enzymes that facilitate digestion of proteins, carbohydrates, and fats within the small intestine. Some of the most important digestive enzymes synthesized by the pancreatic acinar cells include amylase, which digests carbohydrates, lipase, which breaks down fats, and several proteases such as trypsin and chymotrypsin which are vital for the digestion of proteins. Importantly, these enzymes are produced as proenzymes or zymogens to avoid autolysis, or the breakdown of the pancreas itself. The release of these enzymes by the pancreatic acinar cells is strictly regulated by hormones and neurochemicals. Cholecystokinin (CCK) released from the enteroendocrine cells in the duodenum cause the release of these enzymes. Moreover, acinar cells also respond to another hormone, secretin, by releasing bicarbonate-rich fluid which helps to neutralize the gastric acid in the duodenum. Dysregulation in the function of pancreatic acinar cells can lead to severe health issues, including pancreatitis, which is characterized by inflammatory damage to the organ due to the premature activation of digestive enzymes.") AnnotationAssertion( "https://cellxgene.cziscience.com/cellguide/CL_0002064") -AnnotationAssertion(Annotation( "DOI:10.1016/j.diabres.2018.06.013") Annotation( "DOI:10.1210/en.2016-1748") Annotation( "DOI:10.2337/db15-1541") Annotation( "DOI:10.2337/dbi19-0002") Annotation( "DOI:10.3389/fphys.2012.00349/full") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. +AnnotationAssertion(Annotation( "DOI:10.1016/j.diabres.2018.06.013") Annotation( "DOI:10.1210/en.2016-1748") Annotation( "DOI:10.2337/db15-1541") Annotation( "DOI:10.2337/dbi19-0002") Annotation( "DOI:10.3389/fphys.2012.00349/full") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. Type A enteroendocrine cells, also known as alpha cells or A cells, are a species of endocrine cells primarily located in the pancreatic islets of Langerhans; they have also been identified within the lining of the stomach. Functionally, these cells are pivotal in glucose metabolism and homeostasis, accounting for about 20% of the total population of cells in the pancreatic islets. The primary role of type A enteroendocrine cells involves the synthesis, storage, and secretion of the peptide hormone glucagon, which is critical in energy regulation throughout the body. In response to a decrease in blood glucose levels, the pancreatic A cells are stimulated to secrete glucagon into the bloodstream. Glucagon acts on its target cells, mainly in the liver, to stimulate glycogenolysis and gluconeogenesis processes, thereby increasing blood glucose levels back to normal. In this way, pancreatic A cells play an integral role in maintaining glucose homeostasis and preventing hypoglycemia. Pancreatic A cells also participate in the local regulation of islet activities as glucagon acts through glucagon receptors on A, B and D type cells within the islets. Recent studies have also shown that Pancreatic A cells play a role in the generation and regeneration of B type cells. Following beta cell injuries pancreatic A cells increase in numbers and produce Glucagon-like peptide-1 (GLP-1), which increases the proliferation and cytoprotection of beta cells. In response to extreme injury of B type cells pancreatic A cells can transform (transdifferentiate) into functioning B type cells. Until recently, glucagon has been considered a pancreas-specific hormone; however, extrapancreatic glucagon has been reported in patients who had undergone complete, and glucagon-positive cells been identified in the human stomach, indicating that Type A enteroendocrine cells are not restricted to the pancreas.") AnnotationAssertion( "https://cellxgene.cziscience.com/cellguide/CL_0002067") -AnnotationAssertion(Annotation( "DOI:10.1101/cshperspect.a028241") Annotation( "DOI:10.1146/annurev-physiol-021014-071931") Annotation( "DOI:10.1152/ajplung.00329.2019") Annotation( "DOI:10.1159/000196486") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. +AnnotationAssertion(Annotation( "DOI:10.3389/fphys.2013.00102") Annotation( "https://www.ncbi.nlm.nih.gov/books/NBK572070") Annotation( "https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3164530") Annotation( "https://www.sciencedirect.com/topics/agricultural-and-biological-sciences/cardiac-muscle") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Cardiac myocytes, also known as cardiac muscle cells, form the majority of the cardiac tissue and are responsible for the contractile function of the heart. These myocytes are columnar-shaped cells with centrally located nuclei, and they exhibit visibly striated cytoplasm due to the organized array of myofibrils, which are composed of filaments of actin and myosin. Cardiac myocytes connect with each other through specialized structures called intercalated discs, facilitating electrical and mechanical continuity and enabling synchronous contraction of the heart. They also possess a high number of mitochondria to meet their high energy demand for continuous heartbeat action. +Cardiac myocytes are capable of automaticity, meaning they have the unique ability to spontaneously and rhythmically generate their electrical impulses, a characteristic led by pacemaker cells. The electrical signals initiated and propagated in these cells are responsible for heartbeats. They also respond to the electrical signals transmitted by the autonomic nervous system and chemical signals like hormones. Thus, cardiac myocytes not only participate in maintaining the heart’s function but also play a role in modulating heart rate and strength of contraction in response to the body's changing needs. Consequently, malfunction of these cells leads to serious cardiac diseases such as heart failure and arrhythmias.") +AnnotationAssertion( "https://cellxgene.cziscience.com/cellguide/CL_0002098") +AnnotationAssertion(Annotation( "DOI:10.1016/j.bbamcr.2015.11.025") Annotation( "DOI:10.1111/pace.14107") Annotation( "DOI:10.1172/JCI25417") Annotation( "https://www.sciencedirect.com/topics/agricultural-and-biological-sciences/cardiac-muscle") Annotation( "https://www.sciencedirect.com/topics/neuroscience/cardiac-action-potential") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Regular atrial cardiac myocytes, also known as atrial myocytes, are specialized muscle cells found in the atria – the upper chambers of the heart. They contract and relax during the heart's cycle, modulating the pumping of blood through the atria and into the ventricles. Additionally, endowed with inherent rhythmic electrical activity, atrial myocytes contribute significantly to the initiation and propagation of the heart’s electrical impulses. +A distinguishing feature that separates atrial myocytes from other cardiac myocytes is their ability to synthesize and secrete atrial natriuretic peptide (ANP) in response to atrial stretch or dilatation. ANP acts as a potent vasodilator and diuretic, helping to maintain blood pressure and volume homeostasis. The phenomena of atrial stretch or distension, which triggers ANP release, is often in response to excess blood volume entering the heart, providing a mechanism at the cellular level which actively regulates systemic cardiovascular balance. +Like all cardiac myocytes, atrial myocytes are embedded in a dense network of connective tissue that provides structural support. These cells are characterized by a single, centrally located nucleus, and overall, have a rod-like appearance with branching ends that connect with adjacent cells to form a continuous, synchronized ensemble. Their cytoplasm is abundant with mitochondria, reflecting the high energy demand associated with constant contraction and relaxation. At the ultrastructural level, atrial myocytes display striations due to the regular arrangement of actin and myosin proteins, which facilitate the contraction process essential for the heart's pump function.") +AnnotationAssertion( "https://cellxgene.cziscience.com/cellguide/CL_0002129") +AnnotationAssertion(Annotation( "DOI:10.1038/s41569-022-00770-1") Annotation( "DOI:10.1186/s12872-015-0124-z") Annotation( "DOI:10.3389/fphys.2022.863265/full") Annotation( "https://www.sciencedirect.com/topics/medicine-and-dentistry/vascular-endothelial-cell") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Endothelial cells of the vascular tree, commonly referred to as vascular endothelial cells, line the entire circulatory system, from the heart to the smallest capillaries. These cells have a unique, flattened shape, and are tightly bound together, forming a thin layer known as the endothelium. The endothelium is responsible for maintaining the interior surface of blood vessels, and plays a critical role in ensuring the smooth flow of blood. +Vascular endothelial cells act as a semi-permeable membrane, controlling the passage of materials and the transit of white blood cells into and out of the bloodstream. These cells are also involved in blood coagulation. When a blood vessel is damaged, endothelial cells promote clotting to prevent excessive bleeding and facilitate wound healing. Other functions include regulation of blood pressure and blood volume by releasing vasodilators and vasoconstrictors to either widen or constrict blood vessels, accordingly. +Furthermore, the endothelial cells are crucial in the formation of new blood vessels, a process known as angiogenesis. This is particularly important in wound healing and the growth of new tissues during development or after injury. In the context of diseases such as cancer, angiogenesis helps facilitate tumor growth by providing nutrients and oxygen.") +AnnotationAssertion( "https://cellxgene.cziscience.com/cellguide/CL_0002139") +AnnotationAssertion(Annotation( "DOI:10.1101/cshperspect.a028241") Annotation( "DOI:10.1146/annurev-physiol-021014-071931") Annotation( "DOI:10.1152/ajplung.00329.2019") Annotation( "DOI:10.1159/000196486") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. Ciliated columnar cells of the tracheobronchial tree compose the inner lining of the tracheobronchial tree, the system of airways consisting of trachea, bronchi and bronchioles that allow passage of air into the lungs, where gas exchange occurs. A defining feature of these endo-epithelial cells are the tiny hair-like structures covering their surface, known as cilia. The nucleus is located at the base of the cell, and the area above it is rich in mitochondria and well-developed endoplasmic reticulum, both crucial for the energy-intensive process of cilia operation. The primary function of these ciliated cells is to keep the respiratory tract clean via mucociliary clearance or the respiratory escalator. These cells create a two-layered 'coat': The lower \"sol\" layer is watery where the cilia can beat in coordinated waves, and the upper \"gel\" layer is thick and sticky, trapping inhaled particles, such as dust, bacteria, viruses, and other potentially harmful substances. This rhythmical beating of the cilia then moves the mucus and trapped particles upwards and out of the respiratory tract, which is then either coughed out or swallowed. Damage or dysfunction of these ciliated cells, as seen in diseases such as primary ciliary dyskinesia, cystic fibrosis, or chronic bronchitis, may lead to reduced or ineffective mucociliary clearance and an increased susceptibility to respiratory infections.") AnnotationAssertion( "https://cellxgene.cziscience.com/cellguide/CL_0002145") -AnnotationAssertion(Annotation( "DOI:10.1007/978-3-211-99390-3_83") Annotation( "DOI:10.1038/nature16161") Annotation( "DOI:10.1111/j.1469-7580.2005.00403.x") Annotation( "DOI:10.3389/fphys.2015.00087") Annotation( "DOI:10.5114/ceji.2022.124416") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. +AnnotationAssertion(Annotation( "DOI:10.1038/leu.2010.214") Annotation( "DOI:10.1126/science.75570") Annotation( "DOI:10.1182/blood-2004-06-2480") Annotation( "DOI:10.1182/blood-2009-08-239194") Annotation( "https://www.sciencedirect.com/topics/engineering/endosteum") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Endosteal cells, also known as osteogenic cells, are a specialized type of cell that resides in the endosteum of the bone marrow cavity. The endosteum is a thin vascular membrane of connective tissue that lines the inner surface of the bony tissue that forms the medullary cavity of long bones. This specific location assigns endosteal cells critical roles in the bone maintenance and regeneration process as they actively participate in bone remodeling, a process that involves both the formation and resorption of bone tissue. +Endosteal cells function by regulating the activity of both osteoblasts and osteoclasts. Osteoblasts are cells that deposit new bone, and osteoclasts are responsible for bone resorption, a process important for the maintenance, repair, and remodelling of bones. When new bone tissue is required, such as in instances of bone fractures or increased mechanical stress, endosteal cells differentiate into osteoblasts to facilitate the bone formation process. Conversely, when bone resorption is necessary, these cells are known to release signals that lead to the recruitment and activation of osteoclasts. +In addition to this, endosteal cells play a significant role in hematopoiesis, which is the formation of blood cellular components. They function in this process by providing a niche for hematopoietic stem cells, serving to support their maintenance and differentiation. Understanding the functionality of endosteal cells is important in the field of regenerative medicine and stem cell therapy, especially in diseases affecting bone remodeling and hematopoiesis.") +AnnotationAssertion( "https://cellxgene.cziscience.com/cellguide/CL_0002157") +AnnotationAssertion(Annotation( "DOI:10.1007/978-3-211-99390-3_83") Annotation( "DOI:10.1038/nature16161") Annotation( "DOI:10.1111/j.1469-7580.2005.00403.x") Annotation( "DOI:10.3389/fphys.2015.00087") Annotation( "DOI:10.5114/ceji.2022.124416") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. Brush cells, also referred to as tuft cells or multivesicular cells, are a specialized type of epithelial cell mainly noted for their characteristic 'brush border' composed of microvilli. These cells reside in the epithelial lining of tissue organs such as the respiratory tract, gastrointestinal tract, and the bile ducts. The name derives from their distinct appearance under the microscope, which resembles a brush due to the dense layer of microvilli protruding into the lumen. A key function of brush cells is chemosensation: They express a variety of signaling molecules and receptors that enable them to detect specific chemical stimuli in the environment and act as sensory transducers. Many of these receptors are responsive to luminal content, which makes brush cells vital for regulating and coordinating appropriate physiological responses to changes in these substances. Recent research has also elucidated an important role for these cells in immunity. Intestinal brush cells have been found to be the source of a cytokine called interleukin-25, which can initiate type 2 immune responses during parasitic infections. This immune function, along with the chemosensing abilities, signifies that brush cells could serve crucial roles in health and disease, although much research is still required to fully elucidate their myriad roles in physiology and pathology. Overall, brush cells are a versatile cell type, whose distinct morphology and functional capabilities allow them to perform a unique set of functions within the body.") AnnotationAssertion( "https://cellxgene.cziscience.com/cellguide/CL_0002204") -AnnotationAssertion(Annotation( "DOI:10.1016/B978-1-4377-1926-0.10005-0") Annotation( "DOI:10.1016/j.biocel.2007.10.034") Annotation( "DOI:10.1098/rstb.2010.0324") Annotation( "DOI:10.1136/bmjophth-2020-000459") Annotation( "https://www.sciencedirect.com/topics/immunology-and-microbiology/lens-fiber") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. +AnnotationAssertion(Annotation( "DOI:10.1016/j.biocel.2007.10.034") Annotation( "DOI:10.1111/aos.14600") Annotation( "DOI:10.1155/2021/9951032") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +The anterior lens cells, also known as lens epithelial cells, are an integral part of the eye's structure and play a critical role in the organ's physiological functioning. They are situated in the anterior portion of the lens, precisely in the lens capsule, and stretch over the lens' frontal surface. +The primary function of anterior lens cells is to facilitate eye accommodation by controlling the shape and thickness of the eye lens. +The cells are involved in continuous proliferation, migration, and differentiation into lens fiber cells, helping to maintain lens growth and transparency. Anterior lens cells have a prolonged life span and reveal an extraordinary ability to function indefinitely, a characteristic that is critical for maintaining lens transparency. Damage or disturbance to the anterior lens cells can give rise to lens opacity, eventually leading to cataracts, which is a common cause of vision loss.") +AnnotationAssertion( "https://cellxgene.cziscience.com/cellguide/CL_0002223") +AnnotationAssertion(Annotation( "DOI:10.1016/B978-1-4377-1926-0.10005-0") Annotation( "DOI:10.1016/j.biocel.2007.10.034") Annotation( "DOI:10.1098/rstb.2010.0324") Annotation( "DOI:10.1136/bmjophth-2020-000459") Annotation( "https://www.sciencedirect.com/topics/immunology-and-microbiology/lens-fiber") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. Secondary lens fibers are a specialized type of elongated cells located within the structure of the eye's lens. They play an essential role in vision by enabling light transmission and focus on the retina, which allows for clear, distinct vision. These cells are characterized by their lack of nuclei and organelles, their orderly alignment, and their high protein content, particularly crystallins. Lens fibers are differentiated from equatorial epithelial cells of the lens in a process that involves cell elongation, denucleation and tight packing, which serve to reduce light scattering occurrences in the eye. This differentiation accelerates substantially after birth in comparison to during embryogenesis and continues throughout life, contributing to the growth of the eye lens. Secondary lens fibers are specifically those cells that are newly differentiated and cover the old lens fiber core. This process also leads to the removal of light-obstructing cellular components, mainly nuclei and organelles, making these fibers transparent and ideal for their function. The fibers carry out their primary function of light refraction via a high concentration of specialized proteins known as crystallins, which form a gradient of refractive index together with the cytoplasm. This index manipulation facilitates precise light focus onto the retina. Secondary lens fibers also contribute to the lens's shape and biomechanical properties through intercellular interactions, particularly at the sutures where the ends of the fibers meet. Any disruption to secondary lens fibers can lead to vision problems, including cataracts, which is the clouding of the lens resulting from the aggregation of crystallin proteins.") AnnotationAssertion( "https://cellxgene.cziscience.com/cellguide/CL_0002225") -AnnotationAssertion(Annotation( "DOI:10.1016/j.cell.2013.07.004") Annotation( "DOI:10.1038/s41575-018-0081-y") Annotation( "DOI:10.1038/s41580-020-0278-0") Annotation( "DOI:10.1101/gad.1674008") Annotation( "DOI:10.1111/j.1365-2184.2009.00642.x") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. +AnnotationAssertion(Annotation( "https://www.ncbi.nlm.nih.gov/books/NBK532252/") Annotation( "https://www.ncbi.nlm.nih.gov/books/NBK537180/") Annotation( "https://www.sciencedirect.com/topics/neuroscience/iris-dilator-muscle") Annotation( "https://www.sciencedirect.com/topics/neuroscience/iris-sphincter-muscle") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +The smooth muscle cell of sphincter of pupil is a specialized cell type typically found within the eye, more specifically within the sphincter muscle of the iris. +These cells can constrict and dilate in response to light signals, tightly regulating the amount of light reaching the retina. Contraction narrows the pupil in bright conditions (pupillary constriction), protecting the retina from excessive light. In low light, relaxation allows dilation (pupillary dilation), enhancing visual perception in dim conditions. +These cells are also innervated by parasympathetic fibers from the oculomotor nerve. Light signals to the Edinger-Westphal nucleus stimulate the release of acetylcholine, contracting the cells. On the contrary, sympathetic stimulation induces relaxation. This precise control plays a crucial role in optimizing visual function, highlighting their essential role in vision biology.") +AnnotationAssertion( "https://cellxgene.cziscience.com/cellguide/CL_0002243") +AnnotationAssertion(Annotation( "DOI:10.1016/j.cell.2013.07.004") Annotation( "DOI:10.1038/s41575-018-0081-y") Annotation( "DOI:10.1038/s41580-020-0278-0") Annotation( "DOI:10.1101/gad.1674008") Annotation( "DOI:10.1111/j.1365-2184.2009.00642.x") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. Intestinal crypt stem cells, also known as crypt base columnar cells, are a unique type of cell, characterized by the highly specific marker LGR5, found in the intestinal epithelium. Situated at the bottom of the minute pockets known as crypts of Lieberkühn, these are undifferentiated cells that have the ability to perpetually self-renew, as well as differentiate into various other cell types that constitute the epithelial lining of the intestine. The fundamental role of intestinal crypt stem cells is to provide a constant supply of new cells to maintain the cellular turnover of the intestinal epithelium, a tissue known for rapid self-renewal. These stem cells are nurtured and protected by specialized epithelial and mesenchymal cells, and together constitute the intestinal stem cell niche. An important function of intestinal crypt stem cells is to sustain the balance between cell division and programmed cell death, called apoptosis, to ensure the integrity of the intestinal lining. Given their active proliferation rate, these stem cells initiate the creation of diverse differentiated cell types, including enterocytes (the primary absorptive cells in the intestinal lumen), goblet cells (that produce mucus to protect the epithelial layer), enteroendocrine cells (involved in producing gastrointestinal hormones), and Paneth cells (involved in secreting antimicrobial peptides). This diversity in output regulates the physiological activities of the gut ranging from nutrient absorption, hormone secretion, bacterial balance, to immunity. Research studies suggest that dysregulation in intestinal crypt stem cell proliferation and differentiation is associated with several intestinal disorders including intestinal cancer, and various enteropathies.") AnnotationAssertion( "https://cellxgene.cziscience.com/cellguide/CL_0002250") -AnnotationAssertion(Annotation( "DOI:10.1016/B978-0-12-819402-7.00001-2") Annotation( "DOI:10.1016/B978-012369442-3/50154-9") Annotation( "DOI:10.1016/j.mce.2015.06.028") Annotation( "DOI:10.1038/s42255-019-0148-2") Annotation( "DOI:10.3389/fendo.2023.1192311") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. +AnnotationAssertion(Annotation( "DOI:10.1007/s10456-021-09780-y") Annotation( "DOI:10.1016/j.jhep.2016.07.009") Annotation( "DOI:10.1038/s41575-018-0020-y") Annotation( "DOI:10.1038/s41598-020-57652-0") Annotation( "DOI:10.1186/1476-5926-1-1") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Endothelial cells of sinusoids, often referred to as sinusoidal endothelial cells (SECs), are a specialized type of endothelial cell that primarily reside in the capillaries of the liver, spleen, and bone marrow. These cells form the innermost monolayer of the sinusoidal blood vessels, also known as sinusoids, that mediate the exchange of nutrients, metabolites, and waste materials between the blood and the surrounding organ tissue. SECs possess distinctive morphological features including a large, flattened shape, an abundance of fenestrations or pores, and the lack of a continuous basement membrane. These structural characteristics distinguish sinusoidal endothelial cells from other, more regularly structured endothelial cells in the body. +Due to their special fenestrated structure, SECs facilitate the exchange of macromolecules, like lipoproteins and hyaluronan, between plasma and the surrounding organ parenchymal cells. These fenestrations act like sieves, allowing the passage of substances based on their size and charge. It's noteworthy that the permeability characteristics of SECs can be regulated dynamically according to the body's homeostatic needs. +Beyond their key role in exchange mechanisms, endothelial cells of sinusoids are involved in several other functions. In the liver, for example, they help in the removal and endocytic degradation of waste macromolecules, immune response, and regulation of liver regeneration. They also participate in the formation and remodeling of blood vessels, a process known as angiogenesis. Additionally, in recent years, it has been discovered that these cells may have a role in disease conditions like cirrhosis and liver cancer.") +AnnotationAssertion( "https://cellxgene.cziscience.com/cellguide/CL_0002262") +AnnotationAssertion(Annotation( "DOI:10.1016/B978-0-12-819402-7.00001-2") Annotation( "DOI:10.1016/B978-012369442-3/50154-9") Annotation( "DOI:10.1016/j.mce.2015.06.028") Annotation( "DOI:10.1038/s42255-019-0148-2") Annotation( "DOI:10.3389/fendo.2023.1192311") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. Pancreatic polypeptide (PP) cells (also called F or gamma cells) are unique endocrine cells located within the Islets of Langerhans in the pancreas. PP cells are one of the rarer pancreatic cell types and are more prevalent in the head and neck of the pancreas. They are critical in normal pancreatic physiological functions and are involved in the development of pancreatic endocrine disorders. The primary function of PP cells is the production and secretion of the pancreatic polypeptide hormone (PP). This hormone plays a crucial role in several gastrointestinal functions and metabolic responses. The release of the PP hormone is stimulated after eating, especially in protein-rich meals, leading to it being present in large amounts during digestion. The fundamental role of PP is to self-regulate pancreatic secretion activities ensuring its exocrine and endocrine functions are under control. The pancreatic polypeptide hormone from PP cells also aids in adapting to low physical activity and fasting by reducing the production of insulin and glucagon and inhibiting the hepatic glucose production. Additionally, this hormone influences gut motility by slowing down the gastric emptying and reducing small intestinal transit, thereby controlling the pace at which nutritional substances are absorbed. Because of these functions, any malfunction or irregularity in PP cells can result in various disorders such as diabetes and pancreatic diseases.") AnnotationAssertion( "https://cellxgene.cziscience.com/cellguide/CL_0002275") -AnnotationAssertion(Annotation( "DOI:10.1016/S1569-2590(05)10005-6") Annotation( "DOI:10.1111/j.1444-0938.2002.tb02384.x") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. +AnnotationAssertion(Annotation( "DOI:10.1016/S1569-2590(05)10005-6") Annotation( "DOI:10.1111/j.1444-0938.2002.tb02384.x") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. Pigmented ciliary epithelial cells, which are a type of pigment cell, have a crucial function within the eye's ciliary body. The ciliary body, located behind the iris, is one of the eye’s most vital structures and consists of two types of epithelial cells: the pigmented and the non-pigmented ciliary epithelial cells. The pigmented ciliary epithelial cells form the outer layer of the ciliary body and exhibit a black or brown pigmentation due to the melanin they contain. One key function of pigmented ciliary epithelial cells is to aid in the formation of aqueous humor, an intraocular fluid that nourishes the cornea and lens, and maintains intraocular pressure which is essential for the eye’s shape and light refraction. These cells facilitate this function in conjunction with the non-pigmented ciliary epithelial cells. Together, the pigmented and non-pigmented ciliary epithelial cells form a bilayer epithelium that allows the secretion of aqueous humor through a bi-directional fluid transport mechanism. Pigmented ciliary epithelial cells also contribute to the blood-aqueous barrier, a physiological frontier that controls the entry and exit of various substances from the blood to the aqueous humor and vice versa. The pigmentation in these cells, intensified by melanin, helps to absorb scattered light coming into the eye, reducing any potential damage and glare.") AnnotationAssertion( "https://cellxgene.cziscience.com/cellguide/CL_0002303") -AnnotationAssertion(Annotation( "DOI:10.1165/rcmb.2013-0049OC") Annotation( "DOI:10.1186/s12931-014-0160-8") Annotation( "DOI:10.2353/ajpath.2010.090870") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. +AnnotationAssertion(Annotation( "DOI:10.1002/iub.1404") Annotation( "DOI:10.1093/molehr/gan048") Annotation( "https://www.ncbi.nlm.nih.gov/books/NBK9906/") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Embryonic cells in metazoans, which include all multicellular animals, are biological units in their earliest developmental stages from conception until the organism is fully formed. +They are derived from a fertilized egg, which undergoes a series of cell divisions to produce a multicellular organism. During the early phases of embryonic development, these cells exhibit pluripotency, meaning they possess the potential to differentiate into a diverse array of specialized cell types that constitute different body tissues and structures. +The balance between cell proliferation and differentiation in embryonic cells is crucial for successful development. When cells continue to divide without differentiating, overgrowth may occur leading to conditions such as teratomas (tumors of embryonic cells). Conversely, if cell differentiation proceeds at the expense of cell proliferation, developmental anomalies could occur regarding size or mass of the organism or its parts.") +AnnotationAssertion( "https://cellxgene.cziscience.com/cellguide/CL_0002321") +AnnotationAssertion(Annotation( "DOI:10.1165/rcmb.2013-0049OC") Annotation( "DOI:10.1186/s12931-014-0160-8") Annotation( "DOI:10.2353/ajpath.2010.090870") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. The basal epithelial cells of the tracheobronchial tree are critical components found in the lining of the airway passages, including the trachea and bronchi. They are keratin-5-positive, nonciliated, cuboidal cells and typically tightly attached to the basement membrane. In humans, the proportion of basal cells in the respiratory epithelium gradually decreases going down the tracheobronchial tree: they represent approximately 34% of the cells in the trachea, 27% in the large airways, and 10% in the small airways, although it is worth noting that there are differences in the compositions of the tracheobronchial epithelia between different species. Basal epithelial cells serve as the basal layer of the tracheobronchial epithelium, providing both structural and regenerative support for the epithelial tissue that lines the upper regions of the respiratory tract. They serve as progenitor or stem cells that are capable of differentiating into multiple cell types, such as ciliated and secretory cells. This gives them a central role in homeostatic maintenance of the epithelium, and in repairing damaged epithelium after an injury or during disease. This regenerative capacity is crucial in maintaining the integrity of the tracheobronchial surface, especially given its continual exposure to inhaled irritants and microorganisms. In addition to their primary restorative function, basal epithelial cells are also involved in the initial immune response within the tracheobronchial tree. Equipped with pattern recognition receptors, these cells can identify and respond to pathogenic organisms, triggering an immune response and producing a range of inflammatory mediators, such as cytokines and chemokines, to help combat infections.") AnnotationAssertion( "https://cellxgene.cziscience.com/cellguide/CL_0002329") -AnnotationAssertion(Annotation( "DOI:10.1016/S1357-2725(02)00083-3") Annotation( "DOI:10.1111/febs.15731") Annotation( "DOI:10.1165/ajrcmb.25.5.f218") Annotation( "DOI:10.2147/COPD.S38938") Annotation( "DOI:10.3109/01902148.2013.791733") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. +AnnotationAssertion(Annotation( "DOI:10.1016/j.medici.2017.08.003") Annotation( "DOI:10.1016/j.ydbio.2009.06.033") Annotation( "DOI:10.1101/cshperspect.a036723") Annotation( "DOI:10.1161/ATVBAHA.121.313788") Annotation( "DOI:10.1161/CIRCRESAHA.117.312136") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Endocardial cells, often referred to as endothelial cells of the heart, constitute the innermost lining layer of the heart tissues, forming the endocardium. They play a critical role in maintaining heart functionality and homeostasis. These cells, flat and squamous in structure, are adjoined closely to form a tight barrier that separates the heart's muscular layer, the myocardium, from the blood flowing through the heart chambers. +Functionally, endocardial cells are key players in several crucial physiological processes within the heart. Synthesizing matrix molecules that contribute to the structural formation of the heart, these cells actively partake in maintaining its structural integrity. They also exhibit unique metabolic activity, which aids in maintaining optimal cardiac functioning in both healthy and pathological conditions. Importantly, they are known for their involvement in modulating myocardial contraction and relaxation, that is crucial for normal heart rhythm and function. They achieve this by producing factors like nitric oxide (NO) which, amongst other things, aids in the regulation of blood pressure, prevents blood clotting and inhibits the adherence of blood cells to the vessel wall. +In pathological states, endocardial cells can undergo a transformation process known as endothelial-mesenchymal transition (EndMT), which is inherently involved in several cardiac diseases. In this transition, they acquire the ability to migrate and differentiate into several other types of cells contributing to disease progression. Moreover, their dysfunction can lead to endocarditis, an inflammation of the endocardium, as well as increase the risk of other heart diseases.") +AnnotationAssertion( "https://cellxgene.cziscience.com/cellguide/CL_0002350") +AnnotationAssertion(Annotation( "DOI:10.1016/bs.ai.2014.09.003") Annotation( "DOI:10.1038/nri3667") Annotation( "DOI:10.1111/sji.13094") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Cortical thymic epithelial cells (cTECs) are a vital cell type located in the thymus, a lymphoid organ that plays a key role in the development of T cells, which are essential for the adaptive immune system. cTECs also have a role in forming barriers and lining surfaces. In the thymus, their presence contributes to the distinctive architecture of both the cortex and medulla. +cTECs also play a significant part in the selection and development of T cells. During T cell maturation, these cells express both self and non-self proteins via the major histocompatibility complex (MHC) to immature T cells. cTECs then stimulate the T cells that can recognize such proteins, an important event known as positive selection. This process aids in the creation of a diverse T cell receptor (TCR) repertoire that can react to a wide range of antigens, therefore ensuring effective immunity. +Apart from aiding in T cells' positive selection, cTECs also contribute to eliminating self-reactive T cells, a role essential in preventing autoimmune diseases. These cells induce an apoptosis-driven process known as \"negative selection\" which eliminates T cells that are too highly reactive to self-antigens.") +AnnotationAssertion( "https://cellxgene.cziscience.com/cellguide/CL_0002364") +AnnotationAssertion(Annotation( "DOI:10.1007/s11427-013-4482-4") Annotation( "DOI:10.4049/jimmunol.2100692") Annotation( "DOI:10.7554/eLife.60188") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Medullary thymic epithelial cells (mTECs) are distinct cells situated in the thymic medulla, a vital organ where T cells mature. mTECs are recognized by their unique appearance, characterized by large, plump cells with abundant cytoplasm and irregularly shaped nuclei. They inhabit a microenvironment closely interacting with various thymic cell types, including conventional dendritic cells and thymocytes. +The primary function of mTECs revolves around negative selection of developing T cells, thus preventing autoimmune responses. mTECs allow developing T cells to recognize and be responsive to foreign antigens while remaining tolerant to the body's own tissues. They achieve this through a process called promiscuous gene expression where they express and display a vast array of self-antigens. This process is regulated by a transcriptional regulator called autoimmune regulator (Aire), which contributes to immunological self-tolerance. +mTECs themselves have a self-renewing ability and sustain the continuous export of mature T cells. They also express a number of genes that encode for chemokines and other signaling molecules which draw in and retain developing T cells for the process of negative selection. The three-dimensional network formed by these cells provides a physical platform for such selection. Together, mTECs hold a critical place in the maintenance of immune homeostasis, demonstrating the conceptual links that exist between population of stromal cells, thymocytes development, tissue-restricted antigen expression, and negative selection.") +AnnotationAssertion( "https://cellxgene.cziscience.com/cellguide/CL_0002365") +AnnotationAssertion(Annotation( "DOI:10.1073/pnas.070447210") Annotation( "DOI:10.1093/humupd/dmr031") Annotation( "DOI:10.1177/1535370220938741") Annotation( "https://www.sciencedirect.com/topics/medicine-and-dentistry/uterine-contraction") Annotation( "https://www.sciencedirect.com/topics/veterinary-science-and-veterinary-medicine/myometrium") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Myometrial cells are specialized smooth muscle cells located in the myometrium, the middle layer of the uterine wall. Unique to female reproductive physiology, they play a key role in pregnancy and childbirth. +These cells are distinctive in their capability to substantially increase in size and number during pregnancy, preparing the uterus to accommodate the growing fetus. As pregnancy progresses, myometrial cells demonstrate a progressive growth in uterine mass through cellular hypertrophy. They are also responsible for the production of extracellular matrix proteins like collagen, which aids in supporting cell structure and function, further facilitating uterine enlargement. +During childbirth, myometrial cells are responsible for the expansion and contraction of the uterus. They can propagate action potentials and generate considerable force, which is critical to their function in the reproductive system. After pregnancy, these cells can reduce in size, a process known as uterine involution. Given the important role these cells play in female reproductive physiology, dysregulation of the myometrial cell function can contribute to uterine pathologies such as uterine fibroids.") +AnnotationAssertion( "https://cellxgene.cziscience.com/cellguide/CL_0002366") +AnnotationAssertion(Annotation( "DOI:10.1016/S1357-2725(02)00083-3") Annotation( "DOI:10.1111/febs.15731") Annotation( "DOI:10.1165/ajrcmb.25.5.f218") Annotation( "DOI:10.2147/COPD.S38938") Annotation( "DOI:10.3109/01902148.2013.791733") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. The respiratory goblet cell is a highly specialized cell type found primarily within the respiratory tract, including the nose, trachea, and lungs. Named because their shape resembles a goblet - a drinking vessel with a wide body and narrow neck - these cells form a vital part of the respiratory system's protective mechanisms. They are found within the columnar epithelium lining these organs, which forms a barrier between the internal body and the exterior environment. A principal function of the respiratory goblet cell is the production and secretion of mucus, a carbohydrate-rich, viscous and gel-like substance that plays a critical role in trapping dust, bacteria, viruses, and other airborne particles that are inhaled. The mucus secreted by the goblet cells covers the lining of the respiratory tract, effectively catching these particles and preventing them from reaching the lungs and causing infection. Mucus also provides hydration and lubrication to the respiratory tract surfaces, which is important in maintaining the tissue's health and functioning. In addition to their mucus-secreting capabilities, respiratory goblet cells also play a significant role in the body's inflammatory responses. When the respiratory system is exposed to irritants or pathogens, the number and activity of goblet cells often increase, leading to a higher production of mucus. This is a protective response designed to trap and neutralize the harmful substances more effectively. However, in conditions like chronic obstructive pulmonary disease (COPD) and asthma, an overproliferation of goblet cells, also known as goblet cell hyperplasia, can lead to excessive mucus production and airway obstruction.") AnnotationAssertion( "https://cellxgene.cziscience.com/cellguide/CL_0002370") -AnnotationAssertion(Annotation( "DOI:10.1002/hep.31252") Annotation( "DOI:10.1016/j.ajpath.2023.02.012") Annotation( "DOI:10.1016/j.biocel.2010.06.020") Annotation( "DOI:10.1016/j.gastha.2022.07.015") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. +AnnotationAssertion(Annotation( "DOI:10.1038/nrm3980") Annotation( "https://www.genome.gov/genetics-glossary/Somatic-Cells") Annotation( "https://www.ncbi.nlm.nih.gov/books/NBK557896/") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Somatic cells represent the majority of the cell types in the human body. They are fundamental building blocks of organs, tissues, and other bodily structures, with every organ being composed of distinct subpopulations of these cells. +The primary function of somatic cells is to maintain the function and survival of an organism. They carry significant information in the form of DNA, and through the process of mitosis, contribute to the repair and regeneration of body tissues. +Further, some types of somatic cells work in a collaborative manner to form complex functional structures such as the skin and lining of the gut, demonstrating a higher level of organization. However, it's important to note that somatic cells are distinct from germ cells, which are responsible for sexual reproduction by forming sperm or eggs. Any alterations in the DNA of somatic cells, due to mutations, will not affect the offspring as they aren't involved in transmission of genetic information to the next generation. +While most somatic cells contain two copies of each chromosome (diploid), a certain subset may possess a single set of chromosomes (haploid), specifically found in male ants, bees, and other hymenopterans. Hence, diversity is a defining characteristic of somatic cells, reflecting in their structures, roles, and genetic makeup.") +AnnotationAssertion( "https://cellxgene.cziscience.com/cellguide/CL_0002371") +AnnotationAssertion(Annotation( "DOI:10.1038/nrgastro.2012.168") Annotation( "DOI:10.1111/j.1365-2982.2012.01986.x") Annotation( "DOI:10.1371/journal.pcbi.1009644") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Enteric smooth muscle cells are a specialized type of cell found in the gastrointestinal tract. They are an integral part of the enteric nervous system, which regulates the functions of the gastrointestinal system. These cells have a unique structural organization that enables their primary function: the contraction and relaxation necessary for the propulsion of gastrointestinal contents. +Smooth muscle cells in the enteric system possess unique attributes that distinguish them from other smooth muscle cells in the body. One crucial function is peristalsis, where these cells contract in a coordinated manner, generating a wave of contraction and relaxation. This peristaltic movement facilitates the movement of food particles through the digestive tract, playing a vital role in the digestion and absorption processes in animals. Additionally, these cells are responsible for maintaining the tone of gastrointestinal sphincters, controlling passage and preventing one-sided movement of the contents. +Enteric smooth muscle cells are also involved in local immune responses of the gastrointestinal tract. They can communicate with local immune cells and secrete cytokines or other signaling molecules in response to infectious organisms, which makes them crucial mediocellular players in gastrointestinal homeostasis and response to disease. Their interactions with other cell types, such as neurons, myofibroblasts, and interstitial cells of Cajal, further contribute to these cells' role in maintaining the physiological functions of the gastrointestinal system. Overall, enteric smooth muscle cells provide an indispensable contribution to the complex operations of the digestive tract.") +AnnotationAssertion( "https://cellxgene.cziscience.com/cellguide/CL_0002504") +AnnotationAssertion(Annotation( "DOI:10.1002/hep.31252") Annotation( "DOI:10.1016/j.ajpath.2023.02.012") Annotation( "DOI:10.1016/j.biocel.2010.06.020") Annotation( "DOI:10.1016/j.gastha.2022.07.015") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. Intrahepatic cholangiocytes represent a subset of the biliary epithelial cells that form a network of tubes in the liver called the biliary tree The intrahepatic cholangiocytes reside specifically in the intrahepatic bile ducts and play a crucial role in liver physiology and bile production and secretion, thereby aiding in the digestion and absorption of fats in the small intestine. These specific cholangiocytes arise from bipotent hepatoblasts, whereas extrahepatic cholangiocytes share an embryologic origin with the ventral pancreas. Recent research suggests that there is also heterogeneity within populations of intrahepatic cholangiocytes with different transcriptional profiles, proliferative capacity, and biological function; for example, subpopulations differ in calcium-mobilizing receptors. The primary function of intrahepatic cholangiocytes is related to bile formation and maintenance of its flow. In addition to their secretory and absorptive activities, they are involved in the regulation of bile composition, volume, and alkalinization, contributing to the neutralization of the acidic chyme (partly digested food) that enters the intestine from the stomach. Intrahepatic cholangiocytes are also recognized for their role in liver regeneration and repair, often proliferating in response to injury. Intrahepatic cholangiocytes take part in certain pathological conditions, like primary biliary cirrhosis and cholangiocarcinoma. Changes in these cells often lead to abnormalities in bile formation and transport, causing cholestatic liver diseases. Overall, the primary and secondary functional activities of intrahepatic cholangiocytes are vital in maintaining liver function, digestive processes, and contributing to the body's response to liver injury.") AnnotationAssertion( "https://cellxgene.cziscience.com/cellguide/CL_0002538") -AnnotationAssertion(Annotation( "DOI:10.1007/s00441-008-0706-5") Annotation( "DOI:10.1038/s41569-022-00770-1") Annotation( "DOI:10.1038/s41598-021-01360-w") Annotation( "DOI:10.3390/ijms20184411") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. +AnnotationAssertion(Annotation( "DOI:10.1016/j.devcel.2005.05.017") Annotation( "DOI:10.1111/febs.12414") Annotation( "DOI:10.7150/ijbs.49871") Annotation( "https://training.seer.cancer.gov/anatomy/cells_tissues_membranes/tissues/muscle.html") Annotation( "https://www.sciencedirect.com/topics/medicine-and-dentistry/aortic-smooth-muscle-cell") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Aortic smooth muscle cells are specialized and highly differentiated muscle cells that are located in the tunica media layer of the aorta. They consist of spindle-shaped cells with a centrally located nucleus. These cells are rich in actin and myosin, muscle contractile proteins, that allow them to exert force and change shape. +Aortic smooth muscle cells play a vital role in maintaining blood pressure and circulation, and are essential for vascular integrity and function. The primary function of these cells is contraction and relaxation, which enables the regulation of blood flow and pressure in the aorta, and helps in the distribution of oxygen and nutrients throughout the body. +Additionally, a critical characteristic of smooth muscle cells is their plasticity. They can undergo phenotypic modulation in response to changes in their environment or vascular injury, switching from a contractile to a synthetic phenotype. The contractile phenotype is characterized by high contractility and low proliferation rate, while the synthetic phenotype is marked by increased cell proliferation and matrix synthesis but reduced contractile function. +Aortic smooth muscle cells have a significant role in the physiological and pathological processes of the cardiovascular system. In the normal physiological state, they contribute to the elasticity and flexibility of the aorta. Conversely, in pathological states, changes in the function and structure of aortic smooth muscle cells are connected with various vascular diseases, including atherosclerosis, hypertension, and aneurysm.") +AnnotationAssertion( "https://cellxgene.cziscience.com/cellguide/CL_0002539") +AnnotationAssertion(Annotation( "DOI:10.1007/s00441-008-0706-5") Annotation( "DOI:10.1038/s41569-022-00770-1") Annotation( "DOI:10.1038/s41598-021-01360-w") Annotation( "DOI:10.3390/ijms20184411") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. Vein endothelial cells form a thin layer of squamous cells, the endothelium, lining the interior surface of veins throughout the body. They shape the inner cellular lining of the entire vascular system, including the heart, playing a crucial role in blood circulation. The unique characteristic compact arrangement of these cells enables veins to act as a barrier between the blood (that can contain foreign substances) and the surrounding venous tissue and maintain the integrity of the vascular system. The primary function of vein endothelial cells is to control the exchange of substances between the bloodstream and the surrounding tissues. They facilitate selective transportation of molecules depending on their size and solubility, including gases, nutrients, hormones, and waste products. Vein endothelial cells also play a protective role by inhibiting the translocation of toxins or pathogens from blood to tissues. Additionally, these cells are involved in blood coagulation and inflammation response, primarily by producing substances that inhibit blood clot formation under normal conditions and initiating clotting when necessary. Another significant function of vein endothelial cells is the regulation of blood flow and blood pressure. They produce and release several substances, including nitric oxide and prostacyclin, which help in controlling vasodilation and vasoconstriction, thereby regulating blood pressure. These cells are also responsible for angiogenesis, the formation of new blood vessels, which is crucial during wound healing and in the formation of granulation tissue. Consequently, any dysfunction in vein endothelial cells can lead to severe health problems like atherosclerosis, hypertension, and thrombosis.") AnnotationAssertion( "https://cellxgene.cziscience.com/cellguide/CL_0002543") -AnnotationAssertion(Annotation( "DOI:10.1016/j.biopha.2019.108765") Annotation( "DOI:10.1016/j.tibtech.2006.01.010") Annotation( "DOI:10.1038/s41536-019-0083-6") Annotation( "DOI:10.1096/fj.202100332R") Annotation( "DOI:10.1111/dgd.12049") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. +AnnotationAssertion(Annotation( "DOI:10.1016/j.biopha.2019.108765") Annotation( "DOI:10.1016/j.tibtech.2006.01.010") Annotation( "DOI:10.1038/s41536-019-0083-6") Annotation( "DOI:10.1096/fj.202100332R") Annotation( "DOI:10.1111/dgd.12049") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. Mesenchymal stem cells of adipose tissue, also known commonly as adipose-derived stem cells (ADSCs), are a population of adult stem cells that can be obtained easily from adipose tissues. They have many of the same regenerative properties as other mesenchymal stem cells, but are more easily accessible than bone marrow-derived stem cells. Adipose-derived stem cells show immense promise in the field of regenerative medicine due to their ability to differentiate into adipocytes, chondrocytes, myocytes, osteoblasts, and other cell types. ADSCs also possess immunomodulatory and homeostatic functions: they have the ability to suppress immune responses and provide a therapeutic environment for tissue repair and regeneration, as well as supporting the proliferation of adipocytes and the overall expansion of adipose tissue and contributing to the tissue's ability to react to demands of energy storage and mobilization. Dysfunction of these cells may contribute to metabolic complications observed in obesity and diabetes. ADSCs have been used for therapeutic applications such as pathological wound healing, severe refractory acute graft-versus-host disease, and idiopathic thrombocytopenic purpura.") AnnotationAssertion( "https://cellxgene.cziscience.com/cellguide/CL_0002570") -AnnotationAssertion(Annotation( "DOI:10.1002/glia.23892") Annotation( "DOI:10.1016/B978-0-444-52902-2.00005-9") Annotation( "DOI:10.1016/j.biocel.2006.05.007") Annotation( "DOI:10.1186/1742-2094-8-110") Annotation( "DOI:10.1186/s13064-020-00140-y") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. +AnnotationAssertion(Annotation( "DOI:10.1002/glia.23892") Annotation( "DOI:10.1016/B978-0-444-52902-2.00005-9") Annotation( "DOI:10.1016/j.biocel.2006.05.007") Annotation( "DOI:10.1186/1742-2094-8-110") Annotation( "DOI:10.1186/s13064-020-00140-y") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. Schwann cells, also known as neurolemmocytes, are a type of glial cell located in the peripheral nervous system. These cells play a significant role in the healthy functioning of nerves by producing myelin, a fatty substance that forms a coating around nerve fibers. Myelin serves as an insulator and enhances the speed and efficiency of electrical nerve impulses; a single Schwann cell can myelinate a single axon. Myelination starts by the elongation and envelopment of the Schwann cell around the axon, followed by the synthesis and deposition of myelin layers. Some studies suggest that Schwann cells may regulate neuronal action potential, muscular contraction, and the sensitive response. While Schwann cells are most commonly known for the formation of the myelin sheath, some Schwann cells do not form myelin: Remak Schwann cells, a class of nonmyelinating Schwann cells, ensheath axons with smaller diameter, such as C fiber nociceptors in sciatic nerves and form Remak bundles. Schwann cells are found along both motor and sensory neurons and are crucial for the advancement and recovery of peripheral nerve injuries, due to their capacity to support nerve regeneration. In cases of nerve injury, Schwann cells play a vital role in recovery by initiating Wallerian degeneration, a process in which the part of the axon distal to the injury site degrades and is then cleared away. Following this, Schwann cells can guide the regrowth of the nerve, providing a conducive environment for axon regeneration. They remodel themselves into a regenerative phenotype, proliferate, and organize themselves into bands of Büngner that provide physical and chemical guidance for the regrowths of axons. This function of Schwann cells in the repair and regeneration of nervous system highlights their therapeutic potential in peripheral nerve injury treatments.") AnnotationAssertion( "https://cellxgene.cziscience.com/cellguide/CL_0002573") -AnnotationAssertion(Annotation( "DOI:0.1016/j.preteyeres.2015.08.001") Annotation( "DOI:10.1016/j.preteyeres.2012.08.004") Annotation( "DOI:10.1038/nature04482") Annotation( "DOI:10.5301/EJO.2010.6049") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. +AnnotationAssertion(Annotation( "DOI:0.1016/j.preteyeres.2015.08.001") Annotation( "DOI:10.1016/j.preteyeres.2012.08.004") Annotation( "DOI:10.1038/nature04482") Annotation( "DOI:10.5301/EJO.2010.6049") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. Retinal blood vessel endothelial cells constitute the innermost lining of the blood vessels found in the retina, the light-sensitive layer of tissue at the back of the eye. The primary role of these cells revolves around their location within the retinal vascular system, forming the structure of the blood-retinal barrier, a subset of the larger blood-ocular barrier system. The endothelial cells are particularly involved in the growth of new retinal blood vessels from pre-existing ones (angiogenesis); this is critical in managing the amount of oxygen and essential nutrients delivered to the ocular tissues. They are crucial for maintaining homeostasis in the retinal environment by controlling the exchange of molecules between the blood and the retina. Furthermore, they mediate immune cell trafficking, supporting the immune privilege of the eye by preventing the unrestricted infiltration of inflammatory cells into the retina, thus maintaining ocular health and normal vision. The malfunction or dysfunction of retinal blood vessel endothelial cells is implicated in numerous ocular pathologies, particularly diabetic retinopathy, which is one of the leading causes of blindness worldwide. In such conditions, the compromise in the integrity of the blood-retinal barrier and excess angiogenesis can lead to retinal edema and pathological neovascularization, resulting in vision loss.") AnnotationAssertion( "https://cellxgene.cziscience.com/cellguide/CL_0002585") -AnnotationAssertion(Annotation( "DOI:10.1111/febs.16018") Annotation( "DOI:10.1152/physrev.00021.2004") Annotation( "DOI:10.3389/fphar.2021.727870/full") Annotation( "https://www.sciencedirect.com/topics/chemistry/retinal-pigment") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. +AnnotationAssertion(Annotation( "DOI:10.1111/febs.16018") Annotation( "DOI:10.1152/physrev.00021.2004") Annotation( "DOI:10.3389/fphar.2021.727870/full") Annotation( "https://www.sciencedirect.com/topics/chemistry/retinal-pigment") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. Retinal pigment epithelial (RPE) cells form a single layer of cells at the back of the eye sandwiched between the neurosensory retina and the choroid, playing a significant role in maintaining vision health. These pigment-laden cells are highly specialized and perform an array of metabolic and transport functions essential for the maintenance of the photoreceptor cells (rods and cones) in the retina. The pigmentation of RPE cells actively aids in the absorption of excess light and the prevention of light scattering, thus enhancing the eye's optical properties. The retinal pigment epithelium forms a key part of the blood/retina barrier. The cells have long sheet-like microvilli on their apical membrane that project into the light-sensitive outer segments of the photoreceptors, forming a close structural interaction. The basolateral membrane of the RPE interacts with the underlying Bruch’s membrane, which separates the RPE cells from fenestrated endothelium of the choriocapillaris. RPE cells support the photoreceptor by providing them with oxygen and nutrients (such as glucose, retinol and fatty acids) and removing waste products. They also recycle the visual pigment, in a process called the \"visual cycle\", where the RPE cells play a vital role in the regeneration of visual pigment (11-cis retinol) following the absorption of light. This is essential for the maintenance of photoreceptor excitability. Beyond this, RPE cells take part in the phagocytosis process, where they digest the shed ends of photoreceptor outer segments, thus, preventing the build-up of waste residue that could otherwise harm retinal health. They also secrete various factors, including growth factors required to maintain the structural integrity of choriocapillaris endothelium and photoreceptors, as well as immunosuppressive factors that play an important role in establishing the immune privilege of the eye.") AnnotationAssertion( "https://cellxgene.cziscience.com/cellguide/CL_0002586") -AnnotationAssertion(Annotation( "DOI:10.1002/cyto.a.20952") Annotation( "DOI:10.1007/s12015-006-0015-x") Annotation( "DOI:10.1172/JCI107470") Annotation( "DOI:10.3390/app10030938") Annotation( "https://www.ncbi.nlm.nih.gov/books/NBK53254/") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. +AnnotationAssertion(Annotation( "DOI:10.1016/j.apsb.2012.12.007") Annotation( "DOI:10.1124/pr.115.010652") Annotation( "https://www.sciencedirect.com/topics/medicine-and-dentistry/pulmonary-artery-smooth-muscle-cell") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Smooth muscle cells of the pulmonary artery form a principal component of the pulmonary artery's media layer, the middle section of the artery wall typically found between endothelial inner layer (intima) and the outermost connective tissue layer (adventitia). The unique structure of these cells, defined by fusiform shape and the absence of striations, sets them apart from other muscle cell types, including cardiac and skeletal. +The primary function of smooth muscle cells of the pulmonary artery is to regulate the diameter of the pulmonary artery, which in turn controls the flow of blood into the lungs. They accomplish this task through the contraction and relaxation, indicative of vasoconstriction and vasodilation respectively. When these cells contract, the diameter of the artery narrows, leading to reduced blood flow. Conversely, relaxation of these cells widens the artery, facilitating increased blood flow. Such blood flow modulation is crucial for the maintenance of blood pressure and ensuring that the lungs receive an adequate blood supply for efficient oxygen exchange. +As a result, abnormal function or proliferation of these cells can contribute to conditions such as pulmonary hypertension, a condition characterized by high blood pressure in the arteries leading to the lungs. This can occur due to hypoxia (lack of enough oxygen), leading to excessive constriction or proliferation of the smooth muscle cells.") +AnnotationAssertion( "https://cellxgene.cziscience.com/cellguide/CL_0002591") +AnnotationAssertion(Annotation( "DOI:10.1152/japplphysiol.00313.2006") Annotation( "DOI:10.1183/09031936.00019810") Annotation( "https://www.ncbi.nlm.nih.gov/books/NBK537353/") Annotation( "https://www.sciencedirect.com/topics/agricultural-and-biological-sciences/bronchial-muscle") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Bronchial smooth muscle cells are specialized types of cells found in the bronchi of the respiratory system in mammals. These bronchi are tubular structures that function to carry air from the trachea into the lungs. As part of the smooth muscle tissue, bronchial smooth muscle cells are involuntary cells, meaning they function with minimal direct voluntary control. They are characterized by their elongated spindle-shaped structure, with each cell containing a single central nucleus. +The primary function of bronchial smooth muscle cells is to control airway diameter, which directly influences the flow of air into and out of the lungs. Muscular contractions and relaxations mediated by these cells enable the bronchi to constrict or expand, facilitating the regulation of respiratory airflow. Additionally, these cells play a pivotal role in immune responses as they produce and release various substances that can instigate or lessen inflammation of airway tissue. Furthermore, bronchial smooth muscle cells can proliferate and lay down collagen and other extracellular matrix proteins, contributing to the structural integrity of the bronchial tubes. +In pathological conditions, such as asthma and chronic obstructive pulmonary disease, the function and biology of bronchial smooth muscle cells change. Asthma, for example, is associated with an abnormal increase in the mass of the bronchial smooth muscles, leading to narrowing of the airways and resultant breathing difficulties. These cells also exhibit altered contractile behavior and an augmented immune response during inflammatory lung diseases.") +AnnotationAssertion( "https://cellxgene.cziscience.com/cellguide/CL_0002598") +AnnotationAssertion(Annotation( "DOI:10.1016/s1357-2725(02)00259-5") Annotation( "https://www.ncbi.nlm.nih.gov/books/NBK9961") Annotation( "https://www.sciencedirect.com/topics/agricultural-and-biological-sciences/airway-smooth-muscle") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Smooth muscle cells of the trachea have a characteristic 'smooth' (non-striated) appearance under the microscope, a distinguishing feature that differentiates them from skeletal and cardiac muscle cells. The smooth appearance is due to the organization of actin and myosin filaments in the cell, which allows for a controlled, contractile function. +These cells play a key role in controlling the diameter of the trachea, thus regulating the airflow. They are responsible for the involuntary constriction and relaxation of the trachea influencing the air passage during various physiological behaviors like breathing, coughing, and sneezing. This autonomic control allows for adaptations to specific body requirements without conscious control, such as increasing air flow during exercise or restricting it during rest. +In conditions such as asthma, chronic bronchitis, and emphysema, there are changes in smooth muscle cells. For example, the mass of smooth muscle cells increases in chronic airway diseases, possibly in response to chronic inflammation. This increase may indicate a pathological condition or be a part of the body's response to injury and repair.") +AnnotationAssertion( "https://cellxgene.cziscience.com/cellguide/CL_0002600") +AnnotationAssertion(Annotation( "DOI:10.1177/0036850419850431") Annotation( "DOI:10.1203/00006450-199811000-00001") Annotation( "DOI:10.3791/56639") Annotation( "https://www.ncbi.nlm.nih.gov/books/NBK532927/") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Uterine smooth muscle cells are specialized cells that make up the majority of the uterus and in particular, the myometrium. The myometrium is a thick, involuntary muscle layer, principally consisting of verticillate cell bundles that sculpt the helical architecture of the uterus. This dense muscular tissue, packed with uterine smooth muscle cells, is responsible for the significant contractile force witnessed during the physical processes of labor and childbirth. +In the non-pregnant uterus, they exist in a quiescent phase. Upon implantation, these cells are primarily responsible for the expansion consequently allowing the uterus to accommodate the growing fetus. Towards the end of pregnancy, under the influence of hormonal and mechanical signals, uterine smooth muscle cells transition from a relaxed phase to an active contractile phase, culminating in the delivery of the fetus. +At the cellular level, these transitions involve significant changes in the electrophysiological properties of uterine smooth muscle cells. Governed by a complex interplay of ion channels, transporters, and signaling proteins, these cells adjust their electrical activity, conduction properties, and contracting mechanisms. Any issues with these processes can result in problems such as preterm birth or labor dysfunction.") +AnnotationAssertion( "https://cellxgene.cziscience.com/cellguide/CL_0002601") +AnnotationAssertion(Annotation( "DOI:10.1002/cyto.a.20952") Annotation( "DOI:10.1007/s12015-006-0015-x") Annotation( "DOI:10.1172/JCI107470") Annotation( "DOI:10.3390/app10030938") Annotation( "https://www.ncbi.nlm.nih.gov/books/NBK53254/") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. Endothelial cells of the umbilical vein form the inner lining of the veins found in the umbilical cord. They are involved in tube formation and migration which are essential for angiogenesis, the process of generating new blood vessels; this is critical during the fetal stage for the development of the circulatory system. Endothelial cells of the umbilical vein also play a role in controlling the passage of white blood cells into tissues during inflammatory responses. Because human umbilical vein endothelial cells (HUVECs) can easily be derived from the umbilical cord, and because they express common endothelial cell markers, they have been used as an epithelial cell model for studies on cell proliferation, migration, angiogenesis, and inflammation. They have been used as models for vascular diseases like atherosclerosis, for investigating how tumor cells infiltrate blood vessels and form metastases. Thus, while endothelial cells of the umbilical vein play a critical role in vascular biology, they also represent a powerful tool in disease studies and potential treatment strategies.") AnnotationAssertion( "https://cellxgene.cziscience.com/cellguide/CL_0002618") -AnnotationAssertion(Annotation( "DOI:10.1186/s12931-022-02042-5") Annotation( "DOI:10.3389/falgy.2021.787128") Annotation( "DOI:110.1038/s41385-020-00370-7") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. +AnnotationAssertion(Annotation( "DOI:10.1111/j.1745-7254.2007.00625.x") Annotation( "DOI:10.1111/jnc.15689") Annotation( "DOI:10.3389/fimmu.2022.997786") Annotation( "DOI:10.4103/1673-5374.226386") Annotation( "DOI:10.4103/1673-5374.322423") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Mature microglial cells represented one of the macrophage populations within the central nervous system (CNS). Microglial cells serve as the primary immune defense mechanism within the CNS, playing active roles in maintaining brain homeostasis and responding to pathological processes. In response to pathogens and injuries, microglial cells mature and change their morphology from a ramified shape with small processes (normal state) to an amoeboid shape (mature state). +Mature microglial cells possess multiple functional abilities, thereby enabling them to execute diverse roles in order to maintain the health of surrounding neural cells. They act to clear away cellular debris, dead neurons, or plaque formations through the process of phagocytosis. They are also continuously scanning their environment and are able to detect subtle changes in the neural landscape caused by injury, disease, or infection. Upon detection of such changes, these cells become activated and present antigens and secrete cytokines and chemokines to initiate an inflammation response, which sustains the brain’s defense against injurious agents. +Their role is not solely destructive or defensive: mature microglial cells also contribute to neurodevelopment by guiding the formation of neural circuits, synaptogenesis, and remodeling. Furthermore, they assist in managing synaptic plasticity, a key process in learning and memory functions. While the dysregulation of microglial cells has been implicated in various neurodegenerative diseases, they are also regarded as potential therapeutic targets for such conditions, given their crucial roles in maintaining CNS health.") +AnnotationAssertion( "https://cellxgene.cziscience.com/cellguide/CL_0002629") +AnnotationAssertion(Annotation( "DOI:10.1186/s12931-022-02042-5") Annotation( "DOI:10.3389/falgy.2021.787128") Annotation( "DOI:110.1038/s41385-020-00370-7") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. Respiratory basal cells are highly specialized cells that serve a crucial role in the human airway epithelium, predominantly found lining the surfaces of the trachea and bronchi. These cells exhibit a distinctive columnar shape and are attached directly to the basal lamina. They are characterized by the presence of high amounts of cytoplasmic keratins, predominantly keratin 5 and 14, and transcription factor tumor protein (tp63), which set them apart from other types of lung epithelial cells such as ciliated cells and secretory cells. Basal cells are essential for maintaining airway integrity. They make up one third of all respiratory epithelial cells and serve as stem cells as they can transform into different cell types, like goblet cells, ciliated cells, and club cells, when needed for homeostatic maintenance of the epithelial barrier or to repair and restore a healthy cellular environment after injury. Their position at the interface between the internal environment and the external atmosphere makes these cells a first line of defense against air-borne irritants, allergens, and pathogens. Their robust, intrinsic reparative properties facilitate effective recovery from such adversities. However, damage to respiratory basal cells or abnormalities in their function are associated with several respiratory pathologies such as asthma, chronic obstructive pulmonary disease, and lung cancer. Therefore, understanding these cells' function, and their role in disease, is crucial for the development of new therapeutic strategies for respiratory disorders.") AnnotationAssertion( "https://cellxgene.cziscience.com/cellguide/CL_0002633") -AnnotationAssertion(Annotation( "DOI:10.1007/s12079-019-00511-z") Annotation( "DOI:10.1016/j.cmet.2013.08.001") Annotation( "DOI:10.1101/cshperspect.a006569") Annotation( "DOI:10.3389/fcell.2021.642352") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. +AnnotationAssertion(Annotation( "DOI:10.1007/s12079-019-00511-z") Annotation( "DOI:10.1016/j.cmet.2013.08.001") Annotation( "DOI:10.1101/cshperspect.a006569") Annotation( "DOI:10.3389/fcell.2021.642352") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. Endothelial stalk cells are specialized vascular cells vital in angiogenesis, a process through which new blood vessels are formed from pre-existing ones; specifically, endothelial stalk cells are involved in sprouting angiogenesis, where they help form the body of new blood vessels. Vascular sprouting relies on the coordinated activity of migrating endothelial tip cells at the forefront and proliferating stalk cells that elongate the sprout. The process is tightly controlled by different growths factors: Vascular Endothelial Growth Factor acts on endothelial cells, inducing them to become endothelial tip cells that initiate sprouting. After sprouting initiation, activation of Notch signaling suppresses differentiation toward a tip cell phenotype and some of the endothelial cells differentiate into stalk cells, which follow tip cells, multiply, and elongate to provide a structural backbone to the growing vessel sprout. In contrast to endothelial tip cells, which migrate and lead the angiogenic sprout, endothelial stalk cells behind the sprouts continue forming the tube or lumen for blood flow and facilitate maturation and stability of the new vessel. The delicate balance between the activities of stalk and tip cells during angiogenesis is crucial to build a functional vascular network. Dysfunctions in endothelial stalk cells can lead to pathological conditions such as impaired wound healing, unregulated tumor growth, and metastasis due to abnormal angiogenesis.") AnnotationAssertion( "https://cellxgene.cziscience.com/cellguide/CL_0002671") -AnnotationAssertion(Annotation( "DOI:10.1016/j.jcf.2019.09.010") Annotation( "DOI:10.1038/s41586-018-0393-7") Annotation( "DOI:10.1038/s41598-023-30603-1") Annotation( "DOI:10.1146/annurev-pathol-042420-094031") Annotation( "DOI:10.3389/fmars.2020.00709") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. +AnnotationAssertion(Annotation( "DOI:10.1002/ca.21011") Annotation( "https://www.ncbi.nlm.nih.gov/books/NBK507782/") Annotation( "https://www.ncbi.nlm.nih.gov/books/NBK554405/") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Tongue muscle cells are responsible for essential functions like mastication, deglutition (swallowing), phonation (speech), and taste receptivity. They can be classified into two functional classes - extrinsic and intrinsic muscle cells. +The extrinsic tongue muscle cells originate outside the tongue and are primarily involved in determining the position of the tongue within the mouth. Muscle groups such as the genioglossus, hyoglossus, and styloglossus are composed of these extrinsic muscle cells and grant the tongue its wide range of motion. +The intrinsic tongue muscle cells, on the other hand, originate and function within the tongue itself, influencing the shape of the tongue during speech, eating, and swallowing. These cells can contract to alter the tongue's shape, making it long, short, curled, or flat, as needed. Together, these two types of muscle cells allow the tongue to perform its vital functions effectively. Moreover, they play a critical role in maintaining oral health by facilitating physical cleaning of the oral cavity and assisting in the mechanical breakdown of food.") +AnnotationAssertion( "https://cellxgene.cziscience.com/cellguide/CL_0002673") +AnnotationAssertion(Annotation( "DOI:10.1016/j.jcf.2019.09.010") Annotation( "DOI:10.1038/s41586-018-0393-7") Annotation( "DOI:10.1038/s41598-023-30603-1") Annotation( "DOI:10.1146/annurev-pathol-042420-094031") Annotation( "DOI:10.3389/fmars.2020.00709") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. Ionocytes are specialized cells predominantly found in the mammalian respiratory and renal systems as well as in the gills, skin, and intestinal tract of fish. These cells play crucial roles in maintaining ion and acid-base homeostasis. Ionocytes demonstrate remarkable plasticity and are able to adapt themselves in response to changes in environmental conditions such as pH, salinity, ion concentration, and temperature. These cells work by selectively absorbing specific ions from the environment, thus maintaining the body's internal ionic balance. The most commonly absorbed ions include sodium (Na+), chloride (Cl-), calcium (Ca2+), and hydrogen (H+). Moreover, ionocytes contribute to acid-base regulation. In response to acidosis or alkalosis, ionocytes can either excrete or retain hydrogen (H+) and bicarbonate (HCO3-) ions to readjust the blood pH. Further, experimental evidence suggests a functional complexity of ionocytes, implying diverse roles beyond ion regulation. Recent research highlights ionocytes' involvement in ammonia excretion and the regulation of extracellular fluid volume, highlighting their contribution to the overall homeostatic process. Malfunctioning ionocytes have been implicated in various diseases, including cystic fibrosis which is caused by mutations in the chloride channel CFTR, an ionocyte marker.") AnnotationAssertion( "https://cellxgene.cziscience.com/cellguide/CL_0005006") -AnnotationAssertion(Annotation( "DOI:10.1016/j.krcp.2013.07.005") Annotation( "DOI:10.2215/CJN.05760513") Annotation( "DOI:10.2215/CJN.08580813") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. +AnnotationAssertion(Annotation( "DOI:10.1016/j.krcp.2013.07.005") Annotation( "DOI:10.2215/CJN.05760513") Annotation( "DOI:10.2215/CJN.08580813") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. Renal principal cells are the major cell type in the initial collecting tubule and the cortical and outer medullary collecting ducts, as well as the connecting tubule, in the nephrons of the kidneys. A key function of renal principal cells is the regulation of water balance in the body. These cells express aquaporin-2 (AQP2) water channels, which facilitate the reabsorption of water from the fluid within the renal tubule lumen back into the blood. The translocation of AQP2 to the cell membrane is controlled by the hormone vasopressin: In response to high vasopressin levels, AQP2 moves to the cell membrane, allowing water to pass through effectively and be reabsorbed, therefore concentrating the urine. Conversely, in low vasopressin conditions, AQP2 is removed from the membrane, reducing water reabsorption and diluting the urine. Renal principal cells are also involved in the regulation of sodium and potassium levels in the body. They have sodium channels (ENaC) in their luminal membranes which permit the reabsorption of sodium ions from the tubule fluid back into the blood, resulting in a net reabsorption of sodium ions into the systemic circulation. This process is controlled, in part, by the hormone aldosterone. Additionally, renal principal cells contain potassium channels that facilitate the secretion of potassium ions into the urine. The activities of these channels, in coordination with other cell types in the nephron, are critical for maintaining electrolyte balance and overall body homeostasis.") AnnotationAssertion( "https://cellxgene.cziscience.com/cellguide/CL_0005009") -AnnotationAssertion(Annotation( "DOI:10.1152/ajprenal.2000.279.1.F195") Annotation( "DOI:10.1161/HYPERTENSIONAHA.121.16492") Annotation( "DOI:10.1681/ASN.V1011") Annotation( "DOI:10.2215/CJN.08880914") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. +AnnotationAssertion(Annotation( "DOI:10.1152/ajprenal.2000.279.1.F195") Annotation( "DOI:10.1161/HYPERTENSIONAHA.121.16492") Annotation( "DOI:10.1681/ASN.V1011") Annotation( "DOI:10.2215/CJN.08880914") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. Renal intercalated cells are specialized cells located in the collecting duct system of the kidneys. The primary role of intercalated cells is to reabsorb bicarbonate ions and secrete hydrogen ions, thereby maintaining the acid-base homeostasis in the blood. They comprise two main subtypes primarily distinguished by their functional and morphological attributes: alpha and beta intercalated cells. Alpha intercalated cells are more predominant when the body is in a state of acidosis, a condition characterized by an increased acidity of the blood. These cells are specialized in secreting excessive hydrogen ions into the urine through a mechanism involving vacuolar H+-ATPase and H+/K+-ATPase pumps on their apical membranes. They simultaneously reabsorb bicarbonate ions from the tubular fluid and return them to the bloodstream via mechanisms involving carbonic anhydrase II and bicarbonate/chloride exchangers on the basolateral membrane. This dual process helps to increase blood pH towards normal levels. When the body is in a state of alkalosis, a condition characterized by lowered levels of hydrogen ions in the blood, beta intercalated cells are more predominant. They primarily reabsorb hydrogen ions from the tubular fluid through vacuolar H+-ATPase and H+/K+-ATPase pumps on their basolateral membranes, while secreting bicarbonate ions into the urine via pendrin, a bicarbonate/chloride exchanger in the apical membrane. These mechanisms work together to decrease blood pH towards normal levels. In summary, renal intercalated cells play a critical role in the delicate balance of the body’s pH, safeguarding the body from potential harm caused by acidemia or alkalemia.") AnnotationAssertion( "https://cellxgene.cziscience.com/cellguide/CL_0005010") -AnnotationAssertion(Annotation( "DOI:10.1016/j.semnephrol.2019.04.005") Annotation( "DOI:10.1152/physiol.00008.2011") Annotation( "DOI:10.1172/JCI63492") Annotation( "DOI:10.3390/diseases2020071") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. +AnnotationAssertion(Annotation( "DOI:10.1016/j.semnephrol.2019.04.005") Annotation( "DOI:10.1152/physiol.00008.2011") Annotation( "DOI:10.1172/JCI63492") Annotation( "DOI:10.3390/diseases2020071") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. Renal alpha-intercalated cells are located within the connecting tubules and collecting ducts of the kidneys, which are components of the kidney's complex nephron system. Along with beta-intercalated cells, they play a critical role in the body’s acid-base balance. Renal alpha-intercalated cells contain an abundance of proton pumps and enzymes like carbonic anhydrase, which aid in the transport of hydrogen ions for secretion in the urine. The bicarbonate/chloride transporters on their apical membrane meanwhile take up bicarbonate ions from the urine and supply them back into the blood. Through this mechanism, these cells contribute significantly to the neutrality of blood pH, and dysfunction of renal alpha-intercalated cells often leads to distal renal tubular acidosis, a condition resulting in acidic blood and alkaline urine.") AnnotationAssertion( "https://cellxgene.cziscience.com/cellguide/CL_0005011") -AnnotationAssertion(Annotation( "DOI:10.1016/j.cub.2014.08.047") Annotation( "DOI:10.1038/nrm.2017.21") Annotation( "DOI:10.1101/cshperspect.a028233") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. +AnnotationAssertion(Annotation( "DOI:10.1016/j.cub.2014.08.047") Annotation( "DOI:10.1038/nrm.2017.21") Annotation( "DOI:10.1101/cshperspect.a028233") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. The multi-ciliated epithelial cell are terminally differentiated epithelia that line brain ventricles, the respiratory tract and parts of the female and male reproductive organs in animals, playing critical roles in the maintenance of homeostasis through ciliary motion. They are characterized by the presence of hundreds of motile cilia, hair-like microtubule-based organelles that beat in a coordinated fashion to direct fluid flow over the cell surface. Multi-ciliated epithelial cells have fundamental roles in the proper functioning of many organ systems. In the respiratory system, they line the airways and orchestrate the coordinated movement of mucus, effectively clearing the airways of inhaled particles and pathogens. These cells are also vital in the ventricular system of the brain where they facilitate cerebrospinal fluid circulation, thus contributing to the maintenance of the brain's microenvironment. In the fallopian tube, multi-ciliated epithelial cells aid in the transport of oocytes from the ovary to the uterus, a process crucial to reproduction. The formation and function of multi-ciliated epithelial cells is a highly regulated process that involves several stages of development including cell specification, centriole multiplication, and ciliogenesis. Any disruption in these processes can result in dysfunctional or decreased numbers of cilia, which can lead to a myriad of health issues, ranging from chronic respiratory infections to infertility.") AnnotationAssertion( "https://cellxgene.cziscience.com/cellguide/CL_0005012") -AnnotationAssertion(Annotation( "DOI:10.1007/s00125-008-1238-y") Annotation( "DOI:10.1152/physrev.00012.2004") Annotation( "DOI:10.1210/en.2018-00833") Annotation( "DOI:10.3389/fendo.2022.904004") Annotation( "DOI:10.3390/ijms20081867") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. +AnnotationAssertion(Annotation( "DOI:10.1007/s00125-008-1238-y") Annotation( "DOI:10.1152/physrev.00012.2004") Annotation( "DOI:10.1210/en.2018-00833") Annotation( "DOI:10.3389/fendo.2022.904004") Annotation( "DOI:10.3390/ijms20081867") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. Pancreatic epsilon cells are a specialized type of endocrine cell found in the islets of Langerhans, a region of the pancreas responsible for hormone production. These clusters of cells constitute only about 1% of the pancreatic islet cell population, making them a relatively small yet significant component of the pancreas. Pancreatic epsilon cells have a round or ovoid shape with occasional cytoplasmic extensions and are characterized by small and spherical granules. The principal function of pancreatic epsilon cells involves the synthesis and release of the hormone ghrelin, a peptide hormone predominantly produced in the stomach; pancreatic epsilon cells are one of the few sites outside the gastrointestinal tract known to produce this hormone. Ghrelin has multiple vital roles, playing a significant part in generating hunger sensations, promoting fat storage, and influencing various metabolic processes. It also stimulates the release of Growth Hormone (GH) from the anterior pituitary gland. During fetal development, when they form a layer around the islet, epsilon cells are an important source of ghrelin, likely secreting the hormone into the circulation; their numbers decrease in adults. While research on pancreatic epsilon cells is still ongoing, these cells have been implicated in several disease states, most notably Type 2 diabetes and metabolic syndrome. The dysfunction or reduction in the number of pancreatic epsilon cells can lead to anomalies in ghrelin production, impacting overall metabolic homeostasis and glucose regulation.") AnnotationAssertion( "https://cellxgene.cziscience.com/cellguide/CL_0005019") -AnnotationAssertion(Annotation( "DOI:10.1016/j.stem.2014.04.010") Annotation( "DOI:10.1093/jb/mvr001") Annotation( "DOI:10.1242/dev.031369") Annotation( "DOI:10.1242/dev.114215") Annotation( "DOI:10.5966/sctm.2015-0051") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. +AnnotationAssertion(Annotation( "DOI:10.1016/j.stem.2014.04.010") Annotation( "DOI:10.1093/jb/mvr001") Annotation( "DOI:10.1242/dev.031369") Annotation( "DOI:10.1242/dev.114215") Annotation( "DOI:10.5966/sctm.2015-0051") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. Hepatoblasts are immature precursor cells that predominate during the early stages of liver development, specifically in the embryonic phase of life. They first arise from the endoderm, one of the three primary germ layers in the very early embryo, and then differentiate into two distinct mature liver cell types - the hepatocytes and cholangiocytes. During liver organogenesis hepatoblasts proliferate and migrate into the septum transversum to form the liver bud. Proliferation and differentiation of these cells are regulated by several soluble factors, such as hepatocyte growth factor, which is a mitogen of both hepatoblasts and mature hepatocytes. As they start to differentiate into hepatocytes and cholangiocytes, the cells begin to express hepatic markers like albumin and alpha-fetoprotein. Although hepatoblasts are specified embryonic liver cells that are bipotential for hepatocytes and cholangiocytes, a subset of liver cells (called oval cells) has been identified in adults that express stem cell markers, such as CD133 and cKIT, and has been suggested to have the same potential as hepatoblasts to differentiate into hepatocytes and cholangiocytes.") AnnotationAssertion( "https://cellxgene.cziscience.com/cellguide/CL_0005026") -AnnotationAssertion(Annotation( "DOI:10.1016/j.celrep.2020.107952") Annotation( "DOI:10.1038/s41575-018-0081-y") Annotation( "DOI:10.1073/pnas.1607327113") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. +AnnotationAssertion(Annotation( "DOI:10.1038/srep32884") Annotation( "DOI:10.1096/fba.2020-00058") Annotation( "DOI:10.1210/endo.141.9.7634") Annotation( "DOI:10.12659/MSMBR.901142") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Preosteoblast is a critical cell type involved in bone formation, crucial in a process known as ossification or osteogenesis. They are derived from mesenchymal stem cells and are an intermediate stage marking the transition from an osteoprogenitor cell to a fully differentiated osteoblast. The presence of preosteoblasts signifies the site of new bone deposition, highlighting their crucial role in skeletal development and in response to bone injury repairs. +The primary function of preosteoblasts is to differentiate into osteoblasts, which are responsible for secreting osteoid (the unmineralized portion of bone matrix) and regulating the process of bone mineralization. Preosteoblasts are regulated by various growth factors and hormones, including bone morphogenic proteins (BMPs), fibroblast growth factors (FGFs), parathyroid hormone (PTH) and Vitamin D. +However, the function of preosteoblasts is not limited to bone formation alone. In addition to osteogenesis, preosteoblasts significantly contribute to the maintenance of bone homeostasis through regulating the activity of osteoclasts - the cells responsible for bone resorption. This regulation is mediated through RANK/RANKL/OPG pathway signaling. Osteoprotegerin (OPG) released from the preosteoblasts acts as a decoy receptor for RANKL impairing osteoclast formation, hence preventing excessive bone resorption. This regulatory role indicates the dual functionality of preosteoblasts, which are indispensable for both the formation of new bone and the maintenance of existing bone tissue.") +AnnotationAssertion( "https://cellxgene.cziscience.com/cellguide/CL_0007010") +AnnotationAssertion(Annotation( "DOI:10.1007/s12522-011-0102-9") Annotation( "DOI:10.1016/j.it.2017.01.009") Annotation( "DOI:10.1016/j.preghy.2010.10.003") Annotation( "DOI:10.1080/19336918.2015.1089376") Annotation( "DOI:10.1080/19336918.2015.1120397") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Extravillous trophoblasts (EVTs), a specialized subset of trophoblast cells, play crucial roles in establishing and sustaining pregnancy. +Firstly, they anchor the fetus to the maternal tissue, providing structural stability. Secondly, they are instrumental in modifying the maternal spiral arteries to ensure an adequate supply of maternal blood to the placenta and the developing fetus. EVTs invade maternal decidua and myometrium and replace the endothelial lining of the spiral arteries, transforming these high-resistance, narrow vessels into low-resistance, wide vessels, favouring higher blood flow. Thirdly, these cells also play an immunological role, creating an environment conducive to the acceptance of the semi-allogeneic fetus, by expressing non-classical MHC molecules, thereby averting any potential maternal immune response towards fetal tissues. +While EVTs are commonly associated with healthy pregnancies, abnormalities in their function or development have been connected to problematic pregnancies. Conditions like pre-eclampsia and fetal growth restriction (FGR) may arise if EVT cells do not effectively invade the maternal decidua or adequately remodel.") +AnnotationAssertion( "https://cellxgene.cziscience.com/cellguide/CL_0008036") +AnnotationAssertion(Annotation( "DOI:10.1016/j.coph.2013.09.008") Annotation( "DOI:10.1038/mi.2017.73") Annotation( "DOI:10.1038/nature24489") Annotation( "DOI:10.1111/j.1365-2613.2011.00767.x") Annotation( "DOI:10.1146/annurev-physiol-021115-105439") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +The enteroendocrine cell of the small intestine is a specialized type of cell that forms part of the lining of the intestinal wall. These cells are interspersed among absorptive cells, mucus-secreting goblet cells, and other gut cell types, forming the crypt-villus axis, which is the functional unit of the small intestinal epithelium. +Functionally, enteroendocrine cells play a pivotal role in the gut-endocrine system, which is responsible for the digestive process. These cells translate the luminal nutrient status into hormonal signals thereby acting as chemosensors. They contain secretory granules at their base which release hormones into the bloodstream following chemo-sensation. The hormones they secrete perform diverse functions including regulating gastric secretion, gut motility, insulin release, appetite control and other local and systemic effects. +In addition to their endocrine functions, enteroendocrine cells also play a part in the modulation of the immune response in the gut. They can secrete cytokines and chemokines that have a role in directing the immune response to invading pathogens. Moreover, emerging research suggests that these cells play a role in maintaining the balance between gut resident bacteria, known as the gut microbiota, and the host. As such, a comprehensive understanding of the enteroendocrine cells of the small intestine underpins knowledge in nutrition, endocrinology, and various gastroenterological conditions.") +AnnotationAssertion( "https://cellxgene.cziscience.com/cellguide/CL_0009006") +AnnotationAssertion(Annotation( "DOI:10.1002/ibd.20197") Annotation( "DOI:10.1038/nature09637") Annotation( "DOI:10.1038/nrmicro2546") Annotation( "DOI:10.1093/ecco-jcc/jjac190.0884") Annotation( "DOI:10.1136/gut.48.2.176") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Paneth cells of the colon are specialized secretory epithelial cells that can be found in the large intestine, albeit in small numbers compared with the small intestine where Paneth cells are more abundant. Under disease conditions such as inflammatory bowel disease, Paneth cells increase in numbers in the colon. They reside in the crypts of Lieberkühn, which are glandular structures embedded within the mucosal layer of the small and large intestine. +Paneth cells play a crucial role in maintaining intestinal homeostasis and acting as a frontline of defense in our bodies against ingested microbes. They achieve this through the secretion of antimicrobial peptides and proteins such as lysozyme and defensins, which can directly kill or inhibit the growth of various bacteria, fungi, and viruses. They degranulate these substances into the intestinal lumen, especially under conditions of pathogenic invasion or damage to the epithelial lining. +Moreover, Paneth cells are essential for the maintenance of intestinal stem cells, which continually replace the epithelium of the intestine. They create a niche for these stem cells at the base of the crypts, secreting various signaling molecules and factors that are essential for the growth and differentiation of intestinal stem cells. In essence, the existence and function of Paneth cells are fundamental to the overall gut health and immune defense system, by providing both antimicrobial functions and a conducive environment for the renewal of the intestinal lining. +The role of Paneth cells specifically in the colon is of interest in the context of inflammatory bowel disease, such as ulcerative colitis and Crohn’s disease: Their presence in the colon is thought to represent Paneth cell metaplasia and indicates a chronic inflammatory state.") +AnnotationAssertion( "https://cellxgene.cziscience.com/cellguide/CL_0009009") +AnnotationAssertion(Annotation( "DOI:10.1016/j.cell.2014.02.057") Annotation( "DOI:10.1053/j.gastro.2018.08.016") Annotation( "DOI:10.1172/jci.insight.150894") Annotation( "DOI:10.3389/fbioe.2023.1189225") Annotation( "https://www.sciencedirect.com/topics/immunology-and-microbiology/intestinal-stem-cell") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Transit amplifying cells (TACs) are an intermediate, undifferentiated population between stem cells and differentiated cells. They can be found in multiple regions such as the small intestine and the colon. TACs of the colon, are integral components of the colonic crypts and vital players in the maintenance of colonic tissue. +These cells serve a critical function in the rapid and constant renewal of the epithelium lining the colon, with the whole epithelial surface renewed approximately every 5-7 days. They divide rapidly and progressively differentiate into mature columnar epithelium cells, including enterocytes, goblet cells, and enteroendocrine cells. The continued proliferation of transit amplifying cells is fundamental to maintain the balance in cell population while preventing tissue degeneration and maintaining a state of homeostasis. However, uncontrolled proliferation and compromised differentiation capacity can contribute to the development of colon cancers.") +AnnotationAssertion( "https://cellxgene.cziscience.com/cellguide/CL_0009011") +AnnotationAssertion(Annotation( "DOI:10.1007/s11894-010-0130-3") Annotation( "DOI:10.1016/j.cell.2014.02.057") Annotation( "DOI:10.1101/gad.1674008") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Transit amplifying cells (TACs) represent an intermediate population between stem cells and fully differentiated cells, and can be found in multiple regions such as the colon and the small intestine. The small intestine's efficiency in absorbing nutrients, its protective barrier function, and its innate cellular renewal every few days is largely dependent on the role played by these TACs. +TACs of the small intestine are primarily present in the crypt-villus structure of the intestine, more specifically in the crypt region. They originate from Lgr5+ intestinal stem cells that reside at the base of the crypts. Following their derivation from stem cells, TACs undergo up to six rounds of rapid division over a 48-72 hour period, effectively amplifying the cell population, hence their name. During this process, they gradually migrate upward along the walls of the crypt from where they differentiate into diverse mature cell types such as enterocytes, goblet cells, and Paneth cells. +TACs serve as an important element in the homeostasis and regeneration of the intestinal epithelium, amplifying the pool of cells available for differentiation. They also minimize genetic errors during DNA replication by serving as a 'buffer zone' between the long-lived stem cells and the terminal differentiated cells of the gut lining, thus reducing the potential for propagation of mutation-causing defects. Lastly, TACs play an essential part in gastrointestinal tissue repair following injury or inflammation. Their rapid proliferation and subsequent differentiation abilities often help expedite the wound healing process in the intestinal epithelium.") +AnnotationAssertion( "https://cellxgene.cziscience.com/cellguide/CL_0009012") +AnnotationAssertion(Annotation( "DOI:10.1016/j.celrep.2020.107952") Annotation( "DOI:10.1038/s41575-018-0081-y") Annotation( "DOI:10.1073/pnas.1607327113") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. Intestinal crypt stem cells of the small intestine are a type of adult stem cell intimately involved in the continuous replenishment of the intestinal epithelium, the innermost layer of the intestine responsible for nutrient absorption. These cells, located within the crypts of Lieberkühn, are the origin of various cell lineages that make up the functional units of the small intestine. They possess self-renewal ability, an essential feature of stem cells, which allows them to maintain a steady population in the small intestine. One of the critical roles of intestinal crypt stem cells is to drive the continual renewal process taking place in the small intestine every 3-5 days. By proliferating intensively, these cells produce transient amplifying (TA) cells that are characterized by quick division and progressive differentiation. These cells eventually differentiate into specialized cell types, encompassing absorptive enterocytes, mucin-secreting goblet cells, hormone-secreting enteroendocrine cells, and Paneth cells, all of which have essential roles in digestion and nutrient absorption in the small intestine. Intestinal crypt stem cells of the small intestine are also play a significant part in injury recovery. Under regular conditions, these cells primarily exist in an active state, facilitating the constant renovation of the gut lining. However, upon injury or loss of regular intestinal crypt stem cells reserve intestinal stem cells, a slow-cycling and radio-resistant population, can be stimulated to take over the duties of active crypt stem cells. Such plasticity provides a powerful regenerative mechanism that ensures the intestinal epithelium's function and structural integrity amidst diverse conditions.") AnnotationAssertion( "https://cellxgene.cziscience.com/cellguide/CL_0009017") -AnnotationAssertion(Annotation( "DOI:10.1016/j.cell.2013.07.004") Annotation( "DOI:10.1038/s41575-018-0081-y") Annotation( "DOI:10.1073/pnas.1607327113") Annotation( "DOI:10.1111/j.1365-2184.2009.00642.x") Annotation( "DOI:10.1186/s12943-019-0962-x") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. +AnnotationAssertion(Annotation( "DOI:10.1016/j.immuni.2022.08.005") Annotation( "DOI:10.1016/j.jcmgh.2021.08.021") Annotation( "DOI:10.1038/s41575-019-0172-4") Annotation( "DOI:10.1038/s41575-023-00769-0") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Colon macrophages are a heterogeneous population of macrophages in the gastrointestinal tract. Intestinal macrophages represent the largest group of macrophages in the body and play a key role as sentinels for pathogen recognition and elimination. Because the gastrointestinal tract is continually exposed to a high antigenic load derived from microbes and food intake, macrophages in the intestines are crucial not only for the gut’s immune defense but also for maintaining gastrointestinal homeostasis, avoiding chronic inflammation despite constantly facing foreign antigens. The phenotypic profiles and cytokine production of intestinal macrophages therefore differ from conventional macrophages elsewhere in the body. +Colon macrophages orchestrate a wide variety of immune responses. They interact with the colon’s microflora thanks to their location in the mucosal layer, thus playing an important role in shaping gut immunity. By presenting antigens, they help to activate and steer an appropriate immune response either by triggering inflammation against harmful pathogens or by supporting tolerance for beneficial microbes. Therefore, disturbances in the colon macrophage population is thought to contribute to colon-related diseases such as inflammatory bowel disease and colon cancer. +These immune cells are versatile and multifunctional, not just limited to defensive actions. Colon macrophages interact with the enteric nervous system to regulate gut secretion and motility. They also play a crucial role in maintaining colon tissue health and integrity by contributing to tissue repair processes. This occurs either through phagocytosis of dead cells and remnants, or indirectly through the release of growth factor molecules, which stimulate cellular proliferation and differentiation necessary for tissue regeneration.") +AnnotationAssertion( "https://cellxgene.cziscience.com/cellguide/CL_0009038") +AnnotationAssertion(Annotation( "DOI:10.1038/mi.2015.32") Annotation( "DOI:10.1038/mi.2016.132") Annotation( "DOI:10.1038/nrgastro.2013.35") Annotation( "DOI:10.1038/s41385-018-0039-y") Annotation( "DOI:10.1073/pnas.1006451107") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Colon goblet cells are a subset of intestinal goblet cells that are localized in the epithelial lining of the colon. They are specialized secretory epithelial cells that are recognized by their characteristic ‘goblet’ or flask-like shape and typically have a distinctive appearance due to the accumulation of secretory vesicles in their cytoplasm. +The primary function of goblet cells is the secretion of mucus, which is an essential substance for the protection and successful functioning of the intestinal tract. In the colon, goblet cells continuously renew the inner mucus layer, which is attached and impervious to bacteria (the outer layer of the colon is unattached and is the habitat of commensal bacteria) +The mucus secreted by goblet cells is rich in glycoproteins known as mucins, especially MUC2, forming a complex web of molecules that comprises the foundational structure of the mucus layer. It traps and eliminates harmful bacteria, while selectively allowing beneficial microbiota to access the epithelial surface and aid in digestion and nutrient absorption. The mucus layer not only provides a provides a protective barrier against pathogen invasion, as well as mechanical damage, and the erosive effects of digestive enzymes, it also acts as a lubricant to facilitate the passage of food material. +Colon goblet cells are also involved in regulating the local immune response within the gut, maintaining the delicate balance between necessary immune reactions to harmful pathogens and tolerance to beneficial microbiota and dietary substances. Goblet cells can modulate immune responses by presenting antigens to dendritic cells, as well as through the production of immunomodulatory molecules that can alter the behavior of immune cells. When the inner mucus layer of the colon is defective, it might be a pathophysiological mechanism for colitis and infectious diseases.") +AnnotationAssertion( "https://cellxgene.cziscience.com/cellguide/CL_0009039") +AnnotationAssertion(Annotation( "DOI:10.1152/ajpgi.00073.2017") Annotation( "DOI:10.1371/journal.ppat.1010318") Annotation( "DOI:10.3389/fimmu.2022.822867") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Tuft cells, also often referred to as brush cells or caveolated cells, are highly specialized sensory cells found in the colon, among other organs. They were named for their unique appearance under an electron microscope, which presents a distinctive ‘tuft-like’ morphology. They are characterized by apical microvilli, arranged in an irregular tuft that confers a dome-like shape. These cells comprise only a small fraction of the cells in the epithelial layer of the colon, making them among the least populous cell types in this region. +Tuft cells in the colon primarily function as chemosensory cells that can sense and respond to environmental changes. These cells can detect and respond to microbial metabolites, helping initiate immune responses against potential threats. +Recent studies have revealed that tuft cells play a role in responding to intestinal parasitic infections. When a gastrointestinal parasite infects the colon, tuft cells are activated and release the cytokine IL-25. This action increases the production of tuft cells and triggers essential Th2 immune responses to expel the parasites. Also, the removal of tuft cells has been linked to increased susceptibility to these infections. However, overactivity of tuft cells has been associated with inflammatory bowel disease, highlighting the need for a delicate balance of tuft cell function to maintain colon homeostasis.") +AnnotationAssertion( "https://cellxgene.cziscience.com/cellguide/CL_0009041") +AnnotationAssertion(Annotation( "DOI:10.1016/j.cell.2013.07.004") Annotation( "DOI:10.1038/s41575-018-0081-y") Annotation( "DOI:10.1073/pnas.1607327113") Annotation( "DOI:10.1111/j.1365-2184.2009.00642.x") Annotation( "DOI:10.1186/s12943-019-0962-x") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. Intestinal crypt stem cells of the colon, also known as colon crypt base columnar (CBC) cells, are highly specialized cells primarily responsible for the constant self-renewal of the colonic epithelium. These cells are found in the crypts of Lieberkühn - deeply invaginated sections of the colon's mucosal layer. The prime function of intestinal crypt stem cells of the colon is to serve as the source of constant cell regeneration in the colon. Every few days, these stem cells divide and differentiate into the various other types of intestinal cells, such as enterocytes, goblet cells, and enteroendocrine cells. A constant renewal cycle is necessary due to the harsh environment of the colon where cells continuously encounter abrasive food matter and potential pathogens, leading to a high turnover rate. When the colon's mucosal layer suffers damage, a rapid response is triggered whereby colon crypt stem cells divide faster and are directed to injured sites to repair the epithelial layer. Dysregulation of these cells' function or proliferation can contribute to disorders such as colorectal cancer.") AnnotationAssertion( "https://cellxgene.cziscience.com/cellguide/CL_0009043") -AnnotationAssertion(Annotation( "DOI:10.1002/dvg.23276") Annotation( "DOI:10.1242/dev.193193") Annotation( "DOI:10.3389/fcell.2020.00635/full") Annotation( "https://doi.org/10.1016/j.ydbio.2011.12.042") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. +AnnotationAssertion(Annotation( "DOI:10.1002/cphy.c190015") Annotation( "DOI:10.1111/aji.12128") Annotation( "DOI:10.1172/jci.insight.163422") Annotation( "DOI:10.1530/REP-09-0147") Annotation( "DOI:10.2174/1570161111311050010") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +The endothelial cell of the uterus is a specialized type of endothelial cell found in the inner lining of blood vessels, specifically those in the uterus. These cells play critical roles in maintaining uterine health, fertilization, and pregnancy processes. They form the interior surface of blood vessels, creating a barrier between the vessel lumen and surrounding tissue. This fluid environment, maintained by these endothelial cells, provides a platform for the material exchange between blood and tissues, thereby modulating blood coagulation, immune responses, and controlling vasodilation and vasoconstriction. +Functionally, the endothelial cells of the uterus are paramount in regulating the uterine blood flow, an important determinant of successful conception and pregnancy outcomes. They support the vascular changes during the reproductive cycle, particularly the spiral arteriolar development and function, essential in endometrial thickening, maturation, and eventual shedding during menstruation periods. The cells also contribute to angiogenesis, a process crucial during implantation and placenta development, whereby new blood vessels form from pre-existing vessels to supply the growing fetus with oxygen and nutrients. Uterine endothelial cells are also implicated in mediating immune responses within the uterus. Changes in these cells can influence various conditions such as reproductive disorders and complications including heavy menstrual bleeding, endometrial hyperplasia, fertility problems, and cancer.") +AnnotationAssertion( "https://cellxgene.cziscience.com/cellguide/CL_0009095") +AnnotationAssertion(Annotation( "DOI:10.1007/s00441-021-03471-2") Annotation( "DOI:10.1530/VB-20-0006") Annotation( "DOI:10.3389/fcvm.2018.00101") Annotation( "DOI:10.3389/fphys.2018.00382") Annotation( "DOI:10.3390/ijms20184411") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Cardiac endothelial cells are a specialized subset of endothelial cells, the cell type responsible for forming the inner lining of cardiovascular structures such as the heart, and blood vessels. They are a pivotal component of the heart's microenvironment and play a key role in regulating blood pressure, maintaining cardiac homeostasis, in addition to cooperating with other cardiac cells like cardiomyocytes and fibroblasts in the orchestration of a coordinated heart function. +Cardiac endothelial cells contribute to the each stage of the heart's operation, whether during relaxation or contraction. Cardiac endothelial cells release nitric oxide, a potent vasodilator that regulates blood vessel dilation consequently controlling blood pressure and flow. They also produce a myriad of growth factors that aid in new blood vessel formation, known as angiogenesis, crucially needed for tissue repair and regeneration when the heart undergoes damage, as in cases of myocardial infarction. +Furthermore, cardiac endothelial cells control the passage of nutrients, hormones, and gases between the bloodstream and the heart tissue, ensuring its complex metabolic demands are met adequately. They serve as a selective barrier, regulating the transit of cells and signaling molecules, thereby playing a pivotal role in inflammatory responses and immune cell trafficking. They also contribute to the maintenance of blood fluidity and clotting balance through a complex interplay of anti-thrombic and pro-thrombic factors.") +AnnotationAssertion( "https://cellxgene.cziscience.com/cellguide/CL_0010008") +AnnotationAssertion(Annotation( "DOI:10.1016/j.exer.2016.03.016") Annotation( "DOI:10.1016/j.pbiomolbio.2003.11.012") Annotation( "DOI:10.1098/rstb.2010.0300") Annotation( "DOI:10.1242/dev.107953") Annotation( "https://www.sciencedirect.com/topics/immunology-and-microbiology/lens-fiber") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Lens fiber cells are specialized, elongated cells located in the ocular lens, an important part of the eye responsible for focusing light onto the retina to create clear defined images. These cells are unique among body cells, as they are transparent and filled with a clear protein called crystallin to facilitate the passage of light. +The entire life cycle of a lens fiber cell includes differentiation from lens epithelial cells, which are the progenitor cells lying at the anterior surface of the lens. In response to various signals, these cells elongate and migrate towards the posterior pole, while simultaneously undergoing a process of denucleation and degradation of cellular organelles. This unique process ensures that the cells do not scatter light, which is critical for the transparency of the lens. After reaching full maturity, lens fiber cells form tightly packed layers, known as laminae, to make up the distinctive architecture of the ocular lens. +Lens fiber cells play pivotal roles in vision. Their primary function is to transmit and focus the light that enters the eye onto the retina, providing the sharpness and clarity necessary for vision. The precise alignment and organization of these cells allow for optimal light transmittance and minimizes scattering, thereby maintaining the transparency of the lens. As such, disruptions or abnormalities in lens fiber cells can lead to serious vision impairment, including conditions like cataracts, a common condition characterized by the opacification of the lens.") +AnnotationAssertion( "https://cellxgene.cziscience.com/cellguide/CL_0011004") +AnnotationAssertion(Annotation( "DOI:10.1002/dvg.23276") Annotation( "DOI:10.1242/dev.193193") Annotation( "DOI:10.3389/fcell.2020.00635/full") Annotation( "https://doi.org/10.1016/j.ydbio.2011.12.042") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. Neural crest cells are a group of transient and highly migratory cells that originate from the neuroectoderm during the early stages of embryonic development. They are multipotent cells with an exceptional degree of plasticity, capable of differentiating into various somatic cell types and therefore play a fundamental role in the formation of various organs and tissues, making them critical contributors to the developing embryo. After the initiation of neurulation (the formation of the neural tube) neural crest cells start to undergo epithelial-to-mesenchymal transition and delaminate and migrate from the dorsal neural tube to several regions throughout the embryo. They differentiate into a range of diverse cell types, such as neurons and glial cells of the peripheral nervous system, including sensory and autonomic neurons. They also contribute to the formation of adrenal glands, pigment cells in the skin (melanocytes), cardiac structures, including parts of the heart septum and major arteries, as well as bones and cartilage of the face and skull. Disorders or aberrations in the development or migration of the neural crest cells can lead to serious congenital malformations, such as neurocristopathies, including Hirschsprung disease, neuroblastoma, and neurofibromatosis.") AnnotationAssertion( "https://cellxgene.cziscience.com/cellguide/CL_0011012") -AnnotationAssertion(Annotation( "DOI:10.1038/s41586-018-0393-7") Annotation( "DOI:10.1146/annurev-pathol-042420-094031") Annotation( "DOI:10.1172/JCI171268") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. +AnnotationAssertion(Annotation( "DOI:10.1016/j.diff.2016.05.007") Annotation( "DOI:10.1186/s13578-021-00579-4") Annotation( "DOI:10.1186/s13578-022-00856-w") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Skeletal muscle fibroblasts (SMFs), with their spindle-shaped morphology, play a crucial role in maintaining the structure and function of skeletal muscles. They produce connective tissues enveloping muscle fibers, offering vital structural support for optimal muscle contraction. SMFs are integral components of the dynamic and complex microenvironment of muscle tissue, contributing significantly to healthy muscle development and homeostasis. +SMFs primarily synthesize and secrete extracellular matrix (ECM) components, such as collagen, fibronectin, and proteoglycans. The resulting ECM exhibits mechanical properties that resist tensile forces from muscle contractions, ensuring muscle efficiency. It also crucially transmits force during muscle movement, aids muscle attachment to the skeletal structure, and serves as a scaffold for muscle regeneration and repair. +Following injury, they proliferate and transform into myofibroblasts, aiding wound contraction and depositing new ECM for tissue repair. Additionally, these fibroblasts modulate inflammatory responses by secreting cytokines and interact with other cell types, like immune cells and satellite cells, to coordinate muscle healing. In diseases, an imbalance in SMF activity may lead to conditions such as fibrosis, marked by excessive ECM deposition and impaired muscle function.") +AnnotationAssertion( "https://cellxgene.cziscience.com/cellguide/CL_0011027") +AnnotationAssertion(Annotation( "DOI:10.1007/s00018-019-03104-6") Annotation( "DOI:10.1093/biolre/ioy070") Annotation( "DOI:10.1155/2014/579279") Annotation( "https://www.ncbi.nlm.nih.gov/books/NBK53245/") Annotation( "https://www.sciencedirect.com/topics/medicine-and-dentistry/placenta-development") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +The chorionic trophoblast cell, vital for placental development in mammals, originates from the blastocyst's outer layer, the trophectoderm. As a significant component of the placenta, the chorion forms the external fetal-maternal interface and consists primarily of chorionic trophoblast cells. These cells are pivotal in embryogenesis, fetal nutrition, waste removal, and immune response generation, contributing crucially to the success of pregnancy. +Chorionic trophoblast cells undergo trophoblast differentiation, giving rise to specialized sub-types: cytotrophoblasts and syncytiotrophoblasts. Cytotrophoblasts, found in the inner layer, serve as stem cells and contribute to proliferative activities. In contrast, syncytiotrophoblasts, originating from cytotrophoblasts, form the outer layer with a distinctive multinucleated, continuous, and non-proliferative structure. These cells play a key role in maternal-fetal gas and nutrient exchange, producing essential hormones like human chorionic gonadotropin (hCG), progesterone, and estrogen, vital for sustaining pregnancy. +Apart from their physiological roles, chorionic trophoblast cells play a crucial role in shielding the fetus from the maternal immune system. They accomplish this by modifying the expression of major histocompatibility complex (MHC) molecules, which are self-identifying proteins utilized by the immune system to identify foreign cells. Through selective expression of specific types of these molecules, trophoblast cells can evade cytotoxic T cells that might otherwise attack them, while still retaining the ability to attract natural killer cells. These natural killer cells assist in trophoblast invasion and the remodeling of blood vessels in the uterus.") +AnnotationAssertion( "https://cellxgene.cziscience.com/cellguide/CL_0011101") +AnnotationAssertion(Annotation( "DOI:10.1038/s41586-018-0393-7") Annotation( "DOI:10.1146/annurev-pathol-042420-094031") Annotation( "DOI:10.1172/JCI171268") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. The pulmonary ionocyte is a relatively newly identified, specific epithelial cell type found primarily in the pulmonary or respiratory system. Discovered through novel mapping techniques in 2018, these cells are surprisingly rare, making up less than 2% of the cells in the lung's airway, yet they play an essential role in the airway surface liquid and mucus regulation, a crucial factor in lung health. The main responsibility of the pulmonary ionocyte pertains to the regulation and mobilization of chloride ions. They express a high level of CFTR (Cystic Fibrosis Transmembrane Conductance Regulator) gene, which encodes a protein channel across the membrane of cells that produce mucus, sweat, saliva, tears, and digestive enzymes. The activity of CFTR regulates the movement of chloride ions and fluids in and out of cells, which helps maintain a balance of fluid in the organs they are expressed in. If CFTR is dysfunctional, it can cause conditions such as cystic fibrosis, characterized by thick, sticky mucus that can clog the lungs and obstruct the pancreas, leading to respiratory and digestive issues. The discovery of this cell type offers new doors to the treatment and further understanding of diseases like cystic fibrosis. Increased understanding of pulmonary ionocytes could contribute to the development of novel therapeutic approaches to manipulate the function of CFTR in the lungs and other organs affected by dysfunctional CFTR.") AnnotationAssertion( "https://cellxgene.cziscience.com/cellguide/CL_0017000") -AnnotationAssertion(Annotation( "DOI:10.1038/s41385-018-0039-y") Annotation( "DOI:10.1038/s41385-020-00370-7") Annotation( "DOI:10.1159/000512268") Annotation( "DOI:10.1513/AnnalsATS.201802-128AW") Annotation( "https://www.ncbi.nlm.nih.gov/books/NBK553208/") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. +AnnotationAssertion(Annotation( "DOI:10.1016/j.resp.2007.06.017") Annotation( "DOI:10.1113/jphysiol.2003.052779") Annotation( "DOI:10.1146/annurev.ph.52.030190.000525") Annotation( "DOI:10.1152/ajplung.00068.2019") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Serous cells of the tracheobronchial are found on the surface epithelium, submucosal glands, or both, depending on species. They appear in tubulo-acinar arrangements in submucosal glands. +Tracheobronchial serous cells play a vital role in maintaining respiratory health by secreting serous fluid, which is rich in enzymes, ions, and antimicrobial proteins. This serous fluid is essential in clearing out debris, trapping and neutralizing inhaled pathogens and particulate matters, thereby helping in preventing infections. Their secretory products also include water and electrolytes that, combined with mucus (from mucous cells), maintain proper humidity within the airway and lubricate its surfaces, facilitating unhindered airflow. Dysfunction of these cells may lead to diseases such as cystic fibrosis.") +AnnotationAssertion( "https://cellxgene.cziscience.com/cellguide/CL_0019001") +AnnotationAssertion(Annotation( "DOI:10.1007/978-3-540-79090-7_5") Annotation( "DOI:10.1152/japplphysiol.00950.2012") Annotation( "https://www.ncbi.nlm.nih.gov/books/NBK556044/") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Tracheobronchial smooth muscle cells are universally located in the tracheobronchial tree and play a critical role in controlling and modulating the size of the airway lumen, thereby contributing significantly to the airflow resistance. +These cells display both phasic and tonic characteristics, which are vital for airway contractility. Phasic activity manifests as cyclic contraction and relaxation, similar to the behavior seen in gastrointestinal smooth muscle cells, whilst tonic activity resembles vascular smooth muscle cells, maintaining a constant degree of tension. These features enable tracheobronchial smooth muscle cells to constrict the airways in response to various mechanical and chemical stimuli, including allergens, parasympathetic nervous stimulation, changes in gas composition, and cold air, thus protecting the delicate alveoli from potential damage. +Tracheobronchial smooth muscle cells, beyond their contractile function, actively contribute to airway remodeling in conditions like asthma. Their proliferative and synthetic capabilities lead to smooth muscle hypertrophy, hyperplasia, and the production of extracellular matrix components, collectively causing abnormal airway narrowing.") +AnnotationAssertion( "https://cellxgene.cziscience.com/cellguide/CL_0019019") +AnnotationAssertion(Annotation( "DOI:10.1038/s41385-018-0039-y") Annotation( "DOI:10.1038/s41385-020-00370-7") Annotation( "DOI:10.1159/000512268") Annotation( "DOI:10.1513/AnnalsATS.201802-128AW") Annotation( "https://www.ncbi.nlm.nih.gov/books/NBK553208/") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. Lung goblet cells are critical components of the respiratory tract, specifically found in the bronchial segments. They are secretory epithelial cells known for their signature \"goblet\" or cup-like shape. Their primary function is to produce and secrete mucus that aids in trapping airborne particles and pathogens, preventing them from reaching the delicate environment of the lung. As part of the lung's epithelial lining, they act as frontline defenders, maintaining lung health and function. The lung goblet cells are densely packed with granules containing mucin glycoproteins, the primary component of mucus. As mucus is produced and secreted, it moves towards the lumen of the lungs where the cilia, hair-like structures of the neighboring ciliated epithelial cells, help to navigate it upwards and out of the respiratory tract. This coordinated action ensures the expulsion of unwanted particles and pathogens, effectively cleaning the respiratory tract. Dysfunction or abnormal proliferation of lung goblet cells can result in pathological conditions such as chronic obstructive pulmonary disorder (COPD) and asthma, where excessive mucus production leads to airway obstruction. Furthermore, lung goblet cells respond to a variety of stimuli, including toxins, allergens, irritants, and infections, adjusting their mucus production accordingly.") AnnotationAssertion( "https://cellxgene.cziscience.com/cellguide/CL_1000143") -AnnotationAssertion(Annotation( "DOI:10.1016/bs.ctdb.2018.12.002") Annotation( "DOI:10.1016/j.devcel.2020.09.024") Annotation( "DOI:10.1242/dmm.046920") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. +AnnotationAssertion(Annotation( "DOI:10.1016/bs.ctdb.2018.12.002") Annotation( "DOI:10.1016/j.devcel.2020.09.024") Annotation( "DOI:10.1242/dmm.046920") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. Lung neuroendocrine cells, also commonly known as pulmonary neuroendocrine cells (PNECs), are predominantly located in the respiratory epithelium of the bronchial and bronchiolar airways in the lungs. These cells, characterised by their small size and granular appearance, have a distinctive morphology that sets them apart from other lung cells. They are considered part of the diffuse neuroendocrine system due to their scattered distribution through the epithelium and have been classified into solitary cells and clustered forms known as neuroepithelial bodies. The primary function of PNECs is linked to regulation and maintenance of the lung environment. They are sensory in nature and can secrete various bioactive substances such as serotonin, calcitonin, calcitonin gene-related peptides, and bombesin-like peptides which modulate airway smooth muscle tone and influence gut motility. For example, they act as oxygen sensors in response to hypoxia and are responsible for releasing neuropeptides that can induce responses. Moreover, PNECs provide an afferent function as they are equipped with long microvilli that project into the lumen of the bronchus and react to changes in the chemical composition of the luminal content.") AnnotationAssertion( "https://cellxgene.cziscience.com/cellguide/CL_1000223") -AnnotationAssertion(Annotation( "DOI:10.1038/nrgastro.2013.35") Annotation( "DOI:10.1038/nri3738") Annotation( "DOI:10.1084/jem.20191130") Annotation( "DOI:10.3389/fphys.2021.699152/full") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. +AnnotationAssertion(Annotation( "DOI:10.1007/978-981-13-5895-1_1") Annotation( "DOI:10.1038/nrgastro.2012.168") Annotation( "DOI:10.1038/s41575-020-0271-2") Annotation( "DOI:10.1053/j.gastro.2016.02.030") Annotation( "DOI:10.1111/j.1582-4934.2008.00352.x") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Smooth muscle cells of the small intestine form a key component of the enteric system which is imperative for gastrointestinal motility. These cells are a specialized subgroup of smooth muscle cells, specifically found in the layers of the small intestine. The small intestine represents a significant part of the digestive system and plays a crucial role in the absorption of nutrients into the bloodstream. +Smooth muscle cells of the small intestine are predominantly responsible for creating the contractions and relaxations that constitute intestinal motility. They trigger these movements in a coordinated and rhythmic manner known as peristalsis and segmentation. Peristalsis is a form of longitudinal and sequential contraction that pushes food from the upper gastrointestinal tract to the lower parts. Segmentation works by squeezing the intestine randomly, thereby facilitating the mixing of food particles and increasing contact with absorptive surfaces. These two processes are critical for intestinal motility and an effective digestive process. +Apart from facilitating transit of food through contractions, these smooth muscle cells play a role in controlling the diameter of the vessels and the blood flow in the small intestine by their constrictive ability. These smooth muscle cells also contribute to the structural integrity of the small intestine by forming a part of its muscularis externa and muscularis mucosae. Additionally, they interact with other cell types such as enteric neurons and interstitial cells of Cajal (ICC), forming an integrated cellular network that ensures optimal functioning of the intestinal tract.") +AnnotationAssertion( "https://cellxgene.cziscience.com/cellguide/CL_1000275") +AnnotationAssertion(Annotation( "DOI:10.1152/advan.00025.2003") Annotation( "https://www.ncbi.nlm.nih.gov/books/NBK532857/") Annotation( "https://www.ncbi.nlm.nih.gov/books/NBK556137/") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +The smooth muscle fiber of the ileum primarily refers to a specific class of muscle cells present in the ileum, the final segment of the small intestine. Distinguished from skeletal muscle and cardiac muscle, smooth muscle does not possess striations and is under the control of the involuntary nervous system. +These cells primarily facilitate the movement of digested food, a process known as peristalsis. These cells coordinate rhythmic contractions and relaxations, propelling the chyme toward the colon. This process is vital for efficient nutrient absorption in the small intestine and the transfer of undigested material to the large intestine. Moreover, the smooth muscle fibers enhance the ileum's ability to expand and adapt to volume changes without elevating internal pressure, known as compliance. +The smooth muscle fiber of the ileum contributes to reflex responses, enhancing muscle contractions to propel intestinal contents in different physiological conditions. This involves intricate molecular signaling with neurotransmitters, hormones, and local signals. Thus, beyond its structural role, the smooth muscle fiber is crucial for the physiological functions of digestion and absorption in the small intestine.") +AnnotationAssertion( "https://cellxgene.cziscience.com/cellguide/CL_1000278") +AnnotationAssertion(Annotation( "DOI:10.1016/j.celrep.2018.11.086") Annotation( "DOI:10.1038/s41385-022-00565-0") Annotation( "DOI:10.1089/ten.teb.2016.0352") Annotation( "DOI:10.1101/2020.02.19.937615v2.full") Annotation( "DOI:10.1152/ajprenal.00327.2009") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Epithelial cells of the urethra constitute the inner lining of the urethra, forming a mucosal barrier that helps protect the body from external contaminants. The type of epithelial cells found in the urethra can vary along its length. In general, the urethra is lined with stratified squamous epithelium in its distal or external portion, which is closer to the external environment. This type of epithelium provides protection against mechanical stress and pathogens. Closer to the bladder, the urethra transitions to a different type of epithelium. In males, the proximal part of the urethra is lined with pseudostratified columnar epithelium in the region where it passes through the prostate gland. In females, the transitional epithelium may be present in the proximal part of the urethra near the bladder. +Epithelial cells of the urethra are primarily dedicated to the protection of underlying tissues from mechanical stress and pathogens during micturition (urination). They do this by creating a tight, impermeable barrier that prevents the entry and colonization of invading microbes. They produce a variety of antimicrobials and are tightly packed to prevent infiltration between cells, forming an integral part of the body's innate immune system. +In addition to their protective role, these cells are involved in the secretion of mucus. This mucus acts as a lubricant that ensures the smooth and easy passage of urine from the bladder through the urethra and out of the body, reducing any potential damage from the erosive action of urine. Epithelial cells of the urethra are dynamic, constantly renewing their numbers to replace any cells lost through wear and tear. Any disruptions to the function or integrity of these cells may contribute to urinary tract infections and other urological disorders.") +AnnotationAssertion( "https://cellxgene.cziscience.com/cellguide/CL_1000296") +AnnotationAssertion(Annotation( "DOI:10.1016/S0165-6147(00)01600-X") Annotation( "DOI:10.1016/S1357-2725(02)00083-3") Annotation( "DOI:10.1080/07853890600585795") Annotation( "DOI:10.2147/COPD.S38938") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Bronchial goblet cells are a subset of goblet cells that are predominantly found in the respiratory tract, specifically within the bronchi and bronchioles. Named for their flask-like shape and their apparent similarity to a goblet, these cells contribute significantly to the maintenance of lung health and homeostasis. In humans, goblet cells comprise up to 25% of the bronchial epithelial columnar cells and are an integral part of the mucus-secreting system of the respiratory tract and are primarily responsible for the production and secretion of mucus. +The mucus secreted by bronchial goblet cells serves as a protective layer over the delicate and sensitive structures of the bronchi. The mucus, an amalgamation of glycoproteins, lipids, and other substances, traps any inhaled dust, microorganisms, and pollutants, preventing them from reaching deeper lung tissues and causing potential damage. Additionally, the mucus secretion aids in moistening the airway surface, thereby facilitating effective gas exchange and maintaining the overall health of the respiratory tract. +Bronchial goblet cells have an innate defense mechanism wherein they increase secretion of mucus in response to irritants, infection or inflammation in the airway. This strategy, however, if incessantly stimulated, can lead to airway obstruction and health complications like asthma and chronic obstructive pulmonary disease (COPD).") +AnnotationAssertion( "https://cellxgene.cziscience.com/cellguide/CL_1000312") +AnnotationAssertion(Annotation( "DOI:10.1038/mi.2015.32") Annotation( "DOI:10.1042/BSR20201471") Annotation( "DOI:10.1111/imr.12182") Annotation( "DOI:10.1146/annurev-physiol-021115-105447") Annotation( "DOI:full/10.1111/febs.15731") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +The large intestine goblet cell is a highly specialized type of mucosal epithelial cell that is located within the epithelial lining of the large intestine. The key function of goblet cells is the production and secretion of a protective layer of mucus which is essential for maintaining gut homeostasis. Goblet cells have a characteristic 'goblet-like' shape, which adapts them for this specific function: organelles such as the nucleus, mitochondria, ER, and Golgi apparatus are located in the basal portion of the cell; while the vesicles with mucins (required for mucus production) are located apically, close to the apical membrane where their exocytosis takes place. +The goblet cells of the large intestine produce a thick layer of mucus that coats the intestinal lumen. This mucus provides a barrier that prevents the direct contact of intestinal cells with bacteria and other potentially toxic substances present in the digestive tract. It also lubricates the intestine to facilitate the smooth passage of digested food material. It is worth noting that the mucus system differs between the small and large intestine: although in both the mucus is built around MUC2 mucin polymers produced by goblet cells, it is becoming clear that there are several types of goblet cells that function in different ways. +From an immunological perspective, large intestine goblet cells participate in promoting a balanced gut immune response. They contribute to the process known as immune tolerance, where they prevent the body's immune system from overreacting to the trillions of bacteria present in the gut. These cells achieve this by secreting molecules that help maintain a calm environment, limiting inflammatory reactions unless absolutely necessary. Any dysfunction or decrease in the number of goblet cells can result in a compromised intestinal barrier leading to various health issues, including inflammatory bowel disease.") +AnnotationAssertion( "https://cellxgene.cziscience.com/cellguide/CL_1000320") +AnnotationAssertion(Annotation( "DOI:10.1007/s11894-010-0131-2") Annotation( "DOI:10.1038/nature10863") Annotation( "DOI:10.1038/s41575-022-00675-x") Annotation( "DOI:10.1111/imr.12182") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +The ileal goblet cell is a subset of intestinal goblet cells that are a key component of the epithelium of the ileum, a portion of the small intestine. Goblet cells are named and characterized by their distinctive 'goblet' shape with a narrow base tapering to a broad apical surface; located between the lumen of the intestine and the internal environment of the body, they serve an integral role in maintaining gut homeostasis. +Like all intestinal goblet cells, the primary function of ileal goblet cells is the production and secretion of mucins, large, heavily glycosylated proteins that combine to form mucus. This mucus lining serves as a protective barrier, shielding the underlying tissue from the potentially damaging effects of digestive enzymes, acids, or pathogenic microbes present in the gut lumen. Their strategic location in the ileal segment of the intestinal tract aids in efficient nutrient absorption while also maintaining an impregnable barrier against potential pathogens, ensuring an intricate balance. +Goblet cells of the ileum also play a significant role in immune modulation. They are thought to promote oral tolerance (the immune unresponsiveness to orally ingested antigens such as food) by delivering luminal antigens to underlying dendritic cells, thereby driving immune education and tolerogenic responses. They also secrete bioactive molecules, such as the trefoil factor peptide TFF3, which aids in repairing damaged epithelium. By performing these crucial functions, ileal goblet cells not only aid in maintaining intestinal health, but also contribute significantly to the overall well-being of the organism.") +AnnotationAssertion( "https://cellxgene.cziscience.com/cellguide/CL_1000326") +AnnotationAssertion(Annotation( "DOI:10.1016/S1357-2725(02)00083-3") Annotation( "DOI:10.1164/ajrccm.154.6.8970383") Annotation( "DOI:10.1165/ajrcmb.25.5.f218") Annotation( "DOI:10.2147/COPD.S38938") Annotation( "DOI:10.3109/01902148.2013.791733") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Tracheal goblet cells are specialized cells found in the lining of the trachea. They are a key component of the tracheobronchial epithelium, a critical region responsible for maintaining open airways and preventing the ingress of harmful particles or irritants. Goblet cells are filled with membrane-bound secretory granules, which are responsible for their distinctive, goblet-like shape. +Goblet cells specialize in the production and secretion of mucus, a slimy substance composed primarily of glycoproteins (mucins) and water. This sticky mucus serves to trap foreign particles and pollutants, such as dust, bacteria, and viruses that an organism breathes in. After trapping these particles, the cilia on neighboring ciliated epithelial cells beat synchronously, forming a coordinated escalator to push mucus upwards toward the pharynx, where it's either swallowed or expectorated. This system, known as the mucociliary clearance or escalator, forms a crucial barrier in the lungs against respiratory pathogens and external insults. +Changes in the number or function of tracheal goblet cells can engender health complications. For example, goblet cell hyperplasia, or excessive growth of goblet cells, is a common feature of chronic inflammatory lung diseases such as asthma and Chronic Obstructive Pulmonary Disease (COPD). This condition results in mucus hypersecretion, airway blockage, and increased risk of respiratory tract infections.") +AnnotationAssertion( "https://cellxgene.cziscience.com/cellguide/CL_1000329") +AnnotationAssertion(Annotation( "DOI:10.1002/dvdy.24250") Annotation( "DOI:10.1016/B978-012330215-1/50029-6") Annotation( "DOI:10.1016/S0034-5687(01)00214-") Annotation( "DOI:10.1074/jbc.M208826200") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Serous cells are specialized epithelial cells and can be found lining the trachea and brochus. They are among the major components of the respiratory epithelium. +These cells are known for their production and release of serous secretions, which form a key component of airway mucus. These secretions primarily comprise of water, proteins, and enzymes, such as lysozyme and peroxidases. Their main purposes are to provide hydration and lubrication to the airway tissue and to act as a defense mechanism against pathogens. While the lysozyme and peroxidases contribute to the destruction of bacteria, the water in the secretions helps to liquefy the mucus, facilitating the effective functioning of the ciliated cells that propel the mucus up the trachea. +The coordinated action between serous cells and other cell types in the tracheal epithelium proves essential for maintaining a healthy respiratory tract. Dysfunction or damage of these cells can lead to various respiratory tract disorders, such as cystic fibrosis and asthma.") +AnnotationAssertion( "https://cellxgene.cziscience.com/cellguide/CL_1000330") +AnnotationAssertion(Annotation( "DOI:10.1152/physrev.00039.2014") Annotation( "https://www.ncbi.nlm.nih.gov/books/NBK534789/") Annotation( "https://www.sciencedirect.com/topics/neuroscience/secretory-cell") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Serous cells of the epithelium of the bronchus, also termed bronchial serous cells, are predominantly found within the seromucous glands located in the bronchial submucosa. Serous cells can also be found in the trachea and are characterized by small, sparse, electron-dense granules. +Serous cells are specialized cells responsible for the production and secretion of serous fluid. Serous fluid, mainly composed of water, proteins, and various types of salts, provides many benefits: it helps moisturize the airways, keep the bronchial tube walls moist, and safeguard the bronchial tubes against various foreign particles and infectious agents such as bacteria and viruses. Moreover, the fluid released by these cells assists in the lubrication and reduced friction in the bronchi, allowing for smoother airflow.") +AnnotationAssertion( "https://cellxgene.cziscience.com/cellguide/CL_1000331") +AnnotationAssertion(Annotation( "DOI:10.1038/nrgastro.2013.35") Annotation( "DOI:10.1038/nri3738") Annotation( "DOI:10.1084/jem.20191130") Annotation( "DOI:10.3389/fphys.2021.699152/full") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. Enterocytes of the epithelium of the small intestine are specialized cells that reside in the lining of the small intestine, and are primarily responsible for the essential process of nutrient absorption. These cells are columnar epithelial cells with an apical surface lined with microvilli, a feature referred to as the 'brush border', to maximize the surface area available for absorption. Enterocytes play a critical role in both the digestion and absorption of nutrients from food. Their extensive brush border contains enzymes that further assist in nutrient breakdown and transport proteins that transfer nutrients, such as glucose, amino acids, lipids, and vitamins, across the cell membrane. The enterocytes of the small intestine also participate in the barrier function of the gut lining. Enterocytes are connected by tight junctions, which act as a primary defense line against pathogenic invasion by maintaining intestinal barrier integrity. Additionally, their cell surface is coated in glycocalyx and mucus which forms a defensive barrier preventing the penetration of harmful bacteria into the systemic circulation.") AnnotationAssertion( "https://cellxgene.cziscience.com/cellguide/CL_1000334") -AnnotationAssertion(Annotation( "DOI:10.1038/nri3738") Annotation( "DOI:10.1084/jem.20191130") Annotation( "DOI:10.1111/j.1365-2249.2011.04523.x") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. +AnnotationAssertion(Annotation( "DOI:10.1038/nri3738") Annotation( "DOI:10.1084/jem.20191130") Annotation( "DOI:10.1111/j.1365-2249.2011.04523.x") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. Enterocytes of the epithelium proper of the ileum, commonly known as ileal enterocytes, are specialized epithelial cells found lining the inner surface of the ileum, the final section of the small intestine in the human body. They play a pivotal role in nutrient absorption, digestive metabolic functions, and the maintenance of the host’s immune response. Like enterocytes in other parts of the intestine, ileal enterocytes exhibit distinct characteristics specific to their function and role. They have microvilli on their apical surfaces to increase absorption and are important in the absorption of vitamins and the reabsorption of bile salts. These cells also produce enzymes that metabolize lipids and xenobiotics.") AnnotationAssertion( "https://cellxgene.cziscience.com/cellguide/CL_1000342") -AnnotationAssertion(Annotation( "DOI:10.1007/s11894-010-0130-3") Annotation( "DOI:10.1038/nrgastro.2013.35") Annotation( "DOI:10.1038/nri3738") Annotation( "DOI:10.1084/jem.20191130") Annotation( "DOI:10.3389/fimmu.2019.00277") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. +AnnotationAssertion(Annotation( "DOI:10.1007/s00018-002-8412-z") Annotation( "DOI:10.1038/nature09637") Annotation( "DOI:10.1038/nrmicro2546") Annotation( "DOI:10.1146/annurev-physiol-030212-183744") Annotation( "DOI:10.3389/fimmu.2020.00587") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Paneth cells of the epithelium of the small intestine, often referred to simply as Paneth cells, are a type of specialized secretory cell that forms an integral part of the intestinal crypts of Lieberkühn – gland-like invaginations lining the small intestine. Named after the Austrian physician Josef Paneth, who first identified them in the late 19th century, these cells are significant because of their substantial involvement in the mucosal immune system and intestinal stem cell maintenance. +Functionally, Paneth cells play a key role in maintaining gut homeostasis and in the first line of antimicrobial defense, mainly through the secretion of a range of antimicrobial peptides and proteins. These include lysozymes, cryptdins, or alpha-defensins, which have potent activity against various gut pathogens including bacteria, fungi, and parasites. Furthermore, Paneth cells of the small intestine are also known to release secretory phospholipase A2, an enzyme active against gram-positive bacteria. Additionally, they secrete several growth factors like EGF, TGF-alpha, and Wnt3, which are crucial for stem cell support and the overall maintenance of intestinal mucosal integrity. +The unique location of Paneth cells at the base of the crypts positions them in very close proximity to intestinal stem cells. This not only facilitates their role in stem cell maintenance but also involves them in epithelial regeneration and repair following injury. Dysfunctional Paneth cells have been associated with several gut disorders, like Crohn’s disease and necrotizing enterocolitis.") +AnnotationAssertion( "https://cellxgene.cziscience.com/cellguide/CL_1000343") +AnnotationAssertion(Annotation( "DOI:10.1007/s11894-010-0130-3") Annotation( "DOI:10.1038/nrgastro.2013.35") Annotation( "DOI:10.1038/nri3738") Annotation( "DOI:10.1084/jem.20191130") Annotation( "DOI:10.3389/fimmu.2019.00277") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. Enterocytes of the colon are specialized epithelial cells located in the lining of the colon, the largest part of the large intestine. These cells play a critical role in absorbing water, electrolytes, and certain vitamins from the food material passed on from the small intestine. With a unique structure of finger-like protrusions referred to as microvilli, the enterocytes increase their surface area for effective absorption. The colon is the last part of the digestive system, and as such, it is responsible for compacting undigested food materials and forming fecal matter. Enterocytes of the colon facilitate this process effectively through absorption of water. Enterocytes are known for their high regeneration potential, replenishing every 4-5 days, enabling the healthy functioning of the colon. They originate from stem cells located in the crypt of the colon and differentiate into mature enterocytes as they migrate upwards towards the luminal surface. This constant turnover aids in maintaining the intestinal barrier, preventing the entry of detrimental substances into the systemic circulation. Their tight junctions with other epithelial cells provide a robust barrier against invasive pathogens. Enterocytes of the colon are involved in the communication with the gut microbiota. These cells harbor enzymes necessary for the metabolism of short-chain fatty acids, which are the byproducts of the fermentation process by gut bacteria. Short-chain fatty acids serve as a major energy source for colonocytes and are important for maintaining colonic health. The dysfunction of enterocytes, therefore, could lead to disorders such as inflammatory bowel disease or colorectal cancer.") AnnotationAssertion( "https://cellxgene.cziscience.com/cellguide/CL_1000347") -AnnotationAssertion(Annotation( "DOI:10.1007/s00441-008-0706-5") Annotation( "DOI:10.1007/s10456-021-09785-7") Annotation( "DOI:10.1016/j.ccm.2021.08.005") Annotation( "DOI:10.1016/j.jvs.2004.03.043") Annotation( "DOI:10.1177/153857440303700107") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. +AnnotationAssertion(Annotation( "DOI:10.1164/rccm.201408-1492PP") Annotation( "DOI:10.1165/rcmb.2021-0150ED") Annotation( "DOI:10.1242/dmm.006031") Annotation( "DOI:10.3389/falgy.2021.787128") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Basal cells of epithelium of trachea are a vital cell population within the respiratory tract's lining, specifically in the trachea's epithelium. These cells are located at the base of the columnar epithelial cell layer and can be identified by their characteristic cuboidal shape, a large nucleus and few organelles, as well as scattered microvilli. The basal cells are not in direct contact with the lumen, which is covered by a layer of ciliated and non-ciliated columnar cells. Instead, the basal cells are connected to, and line, a thin basement membrane. +The primary function of basal cells involves stem cell activity and epithelial tissue maintenance. Basal cells in the trachea play a crucial role in the regeneration and repair of the tracheal epithelium during damage or injury, acting as progenitor cells for ciliated and secretory cells. They serve as a reserve pool of cells, ready to proliferate and differentiate as needed for homeostatic tissue maintenance or in repair processes when the epithelium has been compromised, whether by injury or disease. +These cells are also implicated in numerous disease pathways. Conditions like chronic obstructive pulmonary disease and lung cancer exhibit unusual behavior and quantities of tracheal basal cells, making these cells a focal point in respiratory disease research. In summary, basal cells in the tracheal epithelium have a multifaceted role in maintaining, repairing, and influencing tracheal health, playing a crucial role in the stability of the respiratory system.") +AnnotationAssertion( "https://cellxgene.cziscience.com/cellguide/CL_1000348") +AnnotationAssertion(Annotation( "DOI:10.1002/ar.1092380310") Annotation( "DOI:10.1038/labinvest.2015.114") Annotation( "DOI:10.1136/thx.2004.la0104") Annotation( "DOI:10.3389/falgy.2021.787128") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +The basal cells of the epithelium of the bronchus are a vital component of the cellular linings found within the bronchial tubes of the respiratory system. They are typically nonciliated, cuboidal cells that are tightly attached to the basement membrane, thereby providing structural support for the epithelial tissues. +The function of the basal cell of the bronchial epithelium is multifaceted, underscoring the importance of these cells for respiratory health. One of their primary roles involves regeneration and cellular turnover. They serve as local stem cells, being able to proliferate and differentiate into other cell types such as ciliated and secretory epithelial cells. This regenerative function of basal cells is required for maintaining the integrity of the bronchial epithelium and is especially critical after injury or during disease states when there is an increased need for new cells to repair damaged tissue or replace lost cells. +In addition to these regenerative duties, basal cells of the bronchial epithelium play a crucial role in providing a defensive barrier against inhaled substances. They participate in the coordinated immune response directed against airborne pathogens, foreign particles, and toxins that enter the respiratory tract. Basal cells can respond to inflammation or irritation by altering their activities, which include proliferating, differentiating, or producing bioactive substances. Throughout all these responses, the basal cells help to maintain the homeostasis of the bronchial tubes, allowing for the efficient transport of air to and from the lungs.") +AnnotationAssertion( "https://cellxgene.cziscience.com/cellguide/CL_1000349") +AnnotationAssertion(Annotation( "DOI:10.1038/mi.2013.30") Annotation( "DOI:10.1093/jb/mvv121") Annotation( "DOI:10.1111/j.1574-695X.2007.00359.x") Annotation( "DOI:10.3389/fimmu.2019.01499") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Microfold cells, also widely known as M cells, are a distinct type of epithelial cell found in the gut, including the small intestine, specifically within the Peyer’s patches, a component of the gut-associated lymphoid tissue (GALT). M cells play a crucial role in the immune response within the intestine environment. +These cells are characterized by microfolds (short microvilli, which give them their name), a reduced, thin glycocalyx, and a deeply invaginated basolateral membrane next to immune cells such as B cells, T cells, and macrophages, and DCs. +These features allow the M cells to form the first point of contact between the gut lumen and the intestinal immune system. They are well-regulated gateways that capture and transport antigens, such as bacteria, viruses, and other foreign substances found in the lumen, to the underlying cells of the immune system. This specialized transport mechanism, called ‘transcytosis’, involves engulfment of these antigens from the apical side, transport across their cytoplasm, and release on the basolateral side of the cells, where immune responses can be initiated. +Furthermore, M cells have complex interactions with members of the gut microbiota and other immune cells, making them essential for maintaining gut homeostasis. This cross-talk shapes the diversity and makeup of the gut microbiota, subsequently having a substantial impact on the host's health. In certain situations, pathogenic organisms can exploit the transcytosis mechanism to infiltrate the host's system, causing various infectious diseases. +The overarching significance of M cells in the small intestine lies in their role of surveillance and protection against a wide range of potentially harmful pathogens, while also facilitating beneficial interactions with commensal microbes.") +AnnotationAssertion( "https://cellxgene.cziscience.com/cellguide/CL_1000353") +AnnotationAssertion(Annotation( "DOI:10.1016/j.jhep.2016.07.009") Annotation( "DOI:10.1038/cmi.2016.5") Annotation( "DOI:10.1038/s41575-018-0020-y") Annotation( "DOI:10.1038/s41575-020-00411-3") Annotation( "https://www.sciencedirect.com/topics/immunology-and-microbiology/disse-space") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Endothelial cells of hepatic sinusoids, also known as hepatic or liver sinusoidal endothelial cells (HSEC or LSEC), are unique, specialized type of endothelial cells located in the liver. They are the building units of the hepatic sinusoid, which functions as a specialized capillary system that facilitates the exchange of various substances between the blood and hepatocytes. This finely tuned environment, facilitated by HSEC, is primordial for the liver's multiple physiologic functions that include nutrient metabolism, toxin inactivation, and immunomodulation. +The HSEC have a distinctive morphology that sets them apart from the typical endothelial cells found in other organs. These cells are exceptionally thin to allow for efficient transfer of molecules and characterized by fenestrations, which are non-diaphragmatic, sieve-like openings that provide an open filtration pathway from the sinusoidal lumen to the space of Disse, where hepatocytes are exposed. The fenestration is a crucial feature that allows lipoproteins, nutrients, and other plasma components easy access to hepatocytes for essential liver functions, including clearance of waste products and metabolic regulation. +HSECs further play a vital role in immune functionality in the liver. They act as a sentinel, determining the nature of the immune response to encountered particulates. They possess a capacity for antigen presentation and express a series of immune-related surface molecules, which helps in immunosurveillance and immunoregulation. The HSEC also aid in the removal and destruction of virus-infected cells, harmful microorganisms, and circulatory waste products to safeguard liver health and general systemic cleanliness.") +AnnotationAssertion( "https://cellxgene.cziscience.com/cellguide/CL_1000398") +AnnotationAssertion(Annotation( "DOI:10.1007/s00441-008-0706-5") Annotation( "DOI:10.1007/s10456-021-09785-7") Annotation( "DOI:10.1016/j.ccm.2021.08.005") Annotation( "DOI:10.1016/j.jvs.2004.03.043") Annotation( "DOI:10.1177/153857440303700107") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. Endothelial cells of the artery, also referred to as arterial endothelial cells, form an integral part of the arterial system. They form a single layer, known as the endothelium, lining the interior surface of arteries, and are able to respond to the high-pressure and flow conditions present in arteries. The primary role of these cells is to provide a barrier between the vessel wall and the blood, exhibiting selective permeability to regulate the movement of liquids, gases, and blood-borne substances across the vascular wall. Arterial endothelial cells significantly contribute to maintaining vascular homeostasis. They are at the forefront of sensations and responses to mechanical stimuli, like shear stress and blood pressure changes. An additional key function pertains to the production of nitric oxide, which helps to regulate vascular tone and blood pressure, prevents platelet aggregation, limits leukocyte adhesion to the endothelium, and inhibits smooth muscle cell proliferation. These varied but connected functions help to preclude the development of atherosclerosis, ensuring normal circulation and arterial health. Moreover, these cells play a pivotal role in inflammation and coagulation processes. During inflammatory events, they express various adhesion molecules, aiding in leukocyte recruitment and rolling onto the vessel walls for immune response. They also produce anticoagulant and procoagulant substances, involved in blood clotting and clot dissolution, respectively. Dysregulation of the usual functions of arterial endothelial cells can result in serious pathophysiological conditions, such as atherosclerosis, hypertension, and other cardiovascular diseases.") AnnotationAssertion( "https://cellxgene.cziscience.com/cellguide/CL_1000413") -AnnotationAssertion(Annotation( "DOI:10.1007/s004290050160") Annotation( "DOI:10.1111/j.1442-9071.2012.02818.x") Annotation( "DOI:10.1167/tvst.8.4.32") Annotation( "DOI:10.2147/OPTH.S26048") Annotation( "DOI:10.3389/fimmu.2022.918619") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. +AnnotationAssertion(Annotation( "DOI:10.1007/s004290050160") Annotation( "DOI:10.1111/j.1442-9071.2012.02818.x") Annotation( "DOI:10.1167/tvst.8.4.32") Annotation( "DOI:10.2147/OPTH.S26048") Annotation( "DOI:10.3389/fimmu.2022.918619") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. Epithelial cells of the lacrimal sac play a significant role in the physiology of tear drainage, acting as an integral part of the lacrimal drainage system. The lacrimal sac is part of the nasolacrimal duct system, a conduit which connects the eye to the nasal cavity, and is lined by multilayered, non-keratinizing, squamous epithelial cells. The epithelial cells of the lacrimal sac are specialized for the purpose of maintaining a moist environment and protecting the surface of the eye. They form a barrier that traps and removes potential contaminants from the tear film during the drainage process. These cells also actively contribute to tear turnover by expediting the drainage of excess tears. Dysfunctional epithelial cells of the lacrimal sac can lead to dacryocystitis, a condition characterized by inflammation of the lacrimal sac. Epithelial cells of the lacrimal sac also perform various other tasks which ensure the overall health of the eye. They are involved in the regulation of immune responses within the lacrimal apparatus and may have a possible role in host-microbiome interactions. Thus, epithelial cells of the lacrimal sac play a multifaceted role in tear drainage and ocular surface defence, directly translating to eye health and vision quality.") AnnotationAssertion( "https://cellxgene.cziscience.com/cellguide/CL_1000436") -AnnotationAssertion(Annotation( "DOI:10.1016/j.ajpath.2014.01.014") Annotation( "DOI:10.1016/j.semnephrol.2019.04.005") Annotation( "DOI:10.2215/CJN.05760513") Annotation( "DOI:10.2215/CJN.08880914") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. +AnnotationAssertion(Annotation( "DOI:10.1016/S1350-9462(98)00011-1") Annotation( "DOI:10.1038/srep31171") Annotation( "DOI:10.1111/j.1444-0938.2008.00260.x") Annotation( "https://www.sciencedirect.com/topics/medicine-and-dentistry/ciliary-muscle") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Ciliary muscle cells are specialized contractile cells that constitute the ciliary muscle, a component of the eye in vertebrates. These cells form a ring around the iris, the eye's colored part. Ciliary muscle cells fall into the category of smooth muscle cells, characterized by their lack of the striations typical of skeletal and cardiac muscle cells. Their shape is elongated and pointed at both ends, and they occur in multi-nucleated syncytia where many cells share the same cytoplasm. +Ciliary muscle cells primarily control the eye's accommodation, adjusting the thickness and curvature of the lens to fine-tune the focus of light on the retina. When ciliary muscle cells contract, tension on the zonular fibers holding the lens in place is reduced, allowing the lens to become thicker and increase its refractive power. Conversely, when the ciliary muscle cells relax, the tension on the zonular fibers increases, causing the lens to become flatter and decrease its refractive power. This adjustment facilitates clear vision at different distances, ranging from near to far objects. +Additionally, ciliary muscle cells play a role in draining the eye's aqueous humor, which is the clear fluid that fills the anterior chamber of the eye between the cornea and the lens. By controlling the shape of the surrounding trabecular meshwork through muscle contractions and relaxations, ciliary muscle cells indirectly regulate intraocular pressure, a factor critical for preventing ocular conditions like glaucoma.") +AnnotationAssertion( "https://cellxgene.cziscience.com/cellguide/CL_1000443") +AnnotationAssertion(Annotation( "DOI:10.1007/978-94-011-2354-9_6") Annotation( "DOI:10.1007/s004670050586") Annotation( "DOI:10.1016/B978-0-323-35775-3.00011-4") Annotation( "DOI:10.1146/annurev-physiol-052521-121841") Annotation( "DOI:10.1681/ASN.2012010029") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Epithelial cells of the nephron form the epithelial lining of the nephron, the functional unit of the kidney that filters the blood to produce urine. Each kidney holds approximately one million nephrons, each of which is composed of several distinct parts, including the renal corpuscle, the proximal tubule, the loop of Henle, and the distal tubule. All sections are lined with highly specialized epithelial cells adapted to perform different functions within the sections of the nephron. +The different epithelial cells of the nephron play crucial roles in the process of filtration, reabsorption, secretion, and excretion, essential tasks for the regulation of body fluid composition and volume. During filtration, the blood is forced through the walls of glomerular capillaries into the Bowman's capsule, where waste products, electrolytes, and water are separated from the blood cells and proteins. As the filtrate then passes through the nephron, epithelial cells of the tubular portion reabsorb useful substances such as glucose, amino acids, and electrolytes, along with most of the water back into the bloodstream. Waste products like urea and creatinine, as well as excess ions and water, remain in the tubule for elimination. +In addition, epithelial cells of the nephron also play a vital part in maintaining the body's acid-base balance by actively secreting hydrogen ions into the urine while reabsorbing bicarbonate from the urine back into the blood. They are also involved in the regulation of blood pressure through the renin-angiotensin-aldosterone system and contribute to erythrocyte production by releasing the hormone erythropoietin in response to low oxygen levels in the blood. Abnormalities or damage in renal epithelial cells often result in impaired kidney function, leading to various renal diseases.") +AnnotationAssertion( "https://cellxgene.cziscience.com/cellguide/CL_1000449") +AnnotationAssertion(Annotation( "DOI:10.1016/j.ajpath.2014.01.014") Annotation( "DOI:10.1016/j.semnephrol.2019.04.005") Annotation( "DOI:10.2215/CJN.05760513") Annotation( "DOI:10.2215/CJN.08880914") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. Kidney collecting duct epithelial cells are a specialized type of cells that form an integral part of the renal system. Located in the collecting duct system of the kidneys, these cells are responsible for one of the final steps in the process of urine formation, and they are instrumental in the fine tuning of the volume and composition of urine by reabsorbing water and certain solutes back into the bloodstream. These cells express specific channels and carriers that actively and passively transport ions and water. They also have channels on their membranes, such as sodium channels and potassium channels, involved in reabsorbing or secreting these electrolytes depending upon the body's needs. The function of renal collecting duct epithelial cells can be regulated by a variety of hormones, including vasopressin (antidiuretic hormone), which can modulate the ion channels and carriers and hence indirectly influence body fluid homeostasis. Aside from their function in ion and water balance, kidney collecting duct epithelial cells also aid in maintaining the body's acid-base balance. They have specialized functionality to secret hydrogen ions into the tubular lumen, which contributes to acid excretion. Any dysfunction may have serious implications and lead to various renal or systemic diseases, exemplifying the importance of these cells in maintaining overall body homeostasis.") AnnotationAssertion( "https://cellxgene.cziscience.com/cellguide/CL_1000454") -AnnotationAssertion(Annotation( "DOI:10.1016/j.jcmgh.2015.05.005") Annotation( "DOI:10.1016/j.jhep.2012.10.011") Annotation( "DOI:10.1038/s41575-019-0125-y") Annotation( "DOI:10.1152/ajpgi.00227.2012") Annotation( "DOI:10.5009/gnl16033") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. +AnnotationAssertion(Annotation( "DOI:10.1016/j.jinf.2015.06.006") Annotation( "DOI:10.1111/j.1751-1097.2007.00226.x") Annotation( "DOI:10.1615/CritRevEukaryotGeneExpr.2020028454") Annotation( "DOI:10.5114/pdia.2013.33376") Annotation( "https://www.sciencedirect.com/topics/biochemistry-genetics-and-molecular-biology/melanocyte") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Melanocytes of the skin are specialized pigment cells crucial for producing and distributing melanin, the pigment determining skin, in addition to hair and eye color. Located in the basal layer of the epidermis, melanocytes serve as a natural sunscreen, protecting skin cells from harmful UV radiation. Structurally dendritic, they synthesize melanin through melanogenesis, transferring melanosomes to keratinocytes for UV shielding +Beyond pigmentation and UV protection, melanocytes play roles in immune and inflammatory responses. They respond to environmental changes, communicate with skin cell types, and secrete cytokines and growth factors influencing skin homeostasis. Dysregulation may lead to pigment disorders like vitiligo and melasma or contribute to skin cancer, particularly malignant melanoma.") +AnnotationAssertion( "https://cellxgene.cziscience.com/cellguide/CL_1000458") +AnnotationAssertion(Annotation( "DOI:10.1101/cshperspect.a030510") Annotation( "https://www.ncbi.nlm.nih.gov/books/NBK279291") Annotation( "https://www.sciencedirect.com/topics/immunology-and-microbiology/smooth-muscle-cell") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Smooth muscle cells of the prostate constitute a critical component of the prostatic stroma, enveloping glandular structures to support functions like secretion and fluid expulsion. Like other smooth muscles, smooth muscle cells of the prostate lack the striations characteristic of skeletal and cardiac muscle cell. +Functionally, they play a crucial role in reproductive and urinary functions. Smooth muscle cells of the prostate contribute to the transport and expulsion of prostatic secretions into the urethra and respond dynamically to signaling molecules such as hormones and neurotransmitters. For instance, under sympathetic nervous stimulation, they contract and apply pressure on the gland's ducts, facilitating the secretion process.") +AnnotationAssertion( "https://cellxgene.cziscience.com/cellguide/CL_1000487") +AnnotationAssertion(Annotation( "DOI:10.1016/j.jcmgh.2015.05.005") Annotation( "DOI:10.1016/j.jhep.2012.10.011") Annotation( "DOI:10.1038/s41575-019-0125-y") Annotation( "DOI:10.1152/ajpgi.00227.2012") Annotation( "DOI:10.5009/gnl16033") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. Cholangiocytes, also known as biliary epithelial cells, are specialized epithelial cells that line the biliary tract, which constitutes the gall bladder and bile ducts inside the liver. Crucial to the maintenance of the liver's health and function, cholangiocytes have a key role in the modification and secretion of bile, a fluid produced by hepatocytes that is essential to digestion and the absorption of fats and vitamins. Cholangiocytes accomplish their primary function through the expression of a variety of transport proteins located on their apical and basolateral membranes, which propel bile acids and other contents of the bile into the biliary lumen. The hepatic bile, once secreted by the hepatocytes, is further modified by cholangiocytes via secretion and absorption processes. These processes help in the regulation of bile volume and composition, which is fundamental in ensuring the efficient digestion of dietary fats and fat-soluble vitamins and the excretion of cholesterol. In addition to their role in bile modification, cholangiocytes also perform several other integral functions. For instance, these cells express Toll-like receptors (TLRs) which allow cholangiocytes to initiate an immune response against pathogens in the biliary lumen. When functioning normally, these cells contribute to biliary integrity, hepatic architecture, and overall hepatic physiology. However, when they become pathological, they are involved in the progression of liver diseases, such as primary biliary cirrhosis and cholangiocarcinoma – the malignancy of the biliary tract.") AnnotationAssertion( "https://cellxgene.cziscience.com/cellguide/CL_1000488") -AnnotationAssertion(Annotation( "DOI:10.1016/j.ccm.2021.08.005") Annotation( "DOI:10.1016/j.coi.2020.04.005") Annotation( "DOI:10.1152/ajplung.90587.2008") Annotation( "DOI:10.3389/fphys.2014.00284") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. +AnnotationAssertion(Annotation( "DOI:10.1016/j.ccm.2021.08.005") Annotation( "DOI:10.1016/j.coi.2020.04.005") Annotation( "DOI:10.1152/ajplung.90587.2008") Annotation( "DOI:10.3389/fphys.2014.00284") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. Mesothelial cells of the pleura form a significant part of the pleural membrane, a thin, double-layered serous membrane that lines the thoracic cavity and encompasses the lungs. These specialized cells contribute to the pleura's key function of producing a lubricating serous fluid, which reduces friction between the lung's outer surface (visceral pleura) and the inner lining of the thoracic cavity (parietal pleura) during respiration. The cellular structure of mesothelial cells, characterized by microvilli on their surface, aids in the secretion and absorption of the pleural fluid, effectively supporting the smooth expansion and contraction of the lungs. Dysregulation in mesothelial cells can lead to pathologies, including pleural effusion and malignant mesothelioma. Mesothelial cells of the pleura display unique immunologic properties. They act as a first line of defense against infection because they are able to recognize pathogens and respond by secreting various cytokines and chemokines. Additionally, these cells are directly involved in the translocation of immune cells into the pleural cavity during inflammatory response, thereby playing an active role in the immune response within the pleural environment. In the event of pleural injury, these cells are also involved in the mesothelial-mesenchymal transition, a process that allows mesothelial cells to transdifferentiate into myofibroblasts and promote tissue repair.") AnnotationAssertion( "https://cellxgene.cziscience.com/cellguide/CL_1000491") -AnnotationAssertion(Annotation( "DOI:10.1016/S1357-2725(03)00242-5") Annotation( "DOI:10.1152/physrev.00026.2003") Annotation( "DOI:10.1371/journal.pone.0276978") Annotation( "DOI:10.3389/fphys.2014.00221") Annotation( "DOI:10.3390/jdb7020007") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. +AnnotationAssertion(Annotation( "DOI:10.1016/S1357-2725(03)00242-5") Annotation( "DOI:10.1152/physrev.00026.2003") Annotation( "DOI:10.1371/journal.pone.0276978") Annotation( "DOI:10.3389/fphys.2014.00221") Annotation( "DOI:10.3390/jdb7020007") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. Mesothelial cells of visceral pleura are specialized epithelial cells that line the inner layer of the pleura, the membrane that envelops the lungs. Positioned adjacent to the lung tissue, these cells form a protective barrier and contribute to the structure of the visceral pleura. They are characterized by their cuboidal to squamous epithelial shape and the presence of microvilli on their surface, a feature aiding in fluid and solute exchange between the pleura and the lungs. The primary function of mesothelial cells of visceral pleura is to secrete a lubricating serous fluid to facilitate smooth, frictionless lung movement within the thoracic cavity during respiration. This helps in the prevention of trauma or damage stemming from the constant rubbing of the lung tissue against the chest wall, hence playing a pivotal role in maintaining respiratory function. Besides fluid secretion, these cells have an essential role in the transportation of fluids and particles across the pleura, as well as in inflammation, wound healing, and tissue repair processes within the pleura. Mesothelial cells of visceral pleura are notably implicated in the development of pleural diseases such as pleural effusion and pleural mesothelioma, a rare and aggressive form of cancer primarily linked with exposure to asbestos. Alterations, such as hyperplasia or metaplasia, may occur in these mesothelial cells under pathological conditions.") AnnotationAssertion( "https://cellxgene.cziscience.com/cellguide/CL_1000493") -AnnotationAssertion(Annotation( "DOI:10.1016/j.biocel.2010.05.015") Annotation( "DOI:10.1016/j.yexcr.2012.02.032") Annotation( "DOI:10.1111/j.1523-1755.2005.00260.x") Annotation( "DOI:10.2337/diacare.28.1.164") Annotation( "DOI:10.3389/fphys.2021.689083") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. +AnnotationAssertion(Annotation( "DOI:10.1016/bs.ircmb.2022.01.005") Annotation( "DOI:10.1172/jci.insight.161078") Annotation( "DOI:10.3389/fimmu.2021.681748") Annotation( "DOI:10.3389/fphys.2017.00837") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Kidney resident macrophages are a heterogeneous population of immune cell found in the cortex and medullary regions of the kidney as well as within and surround the glomeruli. Their primary role involves maintaining homeostasis and immune surveillance in the kidney microenvironment, defending against ascending urinary infections. Beyond traditional macrophage roles such as phagocytosis and antigen presentation, kidney resident macrophages also contribute significantly to the response to kidney injury including tissue repair and angiogenesis. +Under normal physiological conditions, kidney resident macrophages work to maintain the balance of the kidney's microenvironment by removing dead cells, pathogens and cellular debris, to limit inflammation and tissue damage. They are ‘professional’ phagocytes, clearing pathogens and debris by engulfing and digesting these harmful materials. Moreover, they are capable of presenting antigens to other immune cells, which aids in the activation of the adaptive immune response. +Kidney resident macrophages show a high degree of plasticity: in response to environmental stimuli they change their morphology and cell surface markers. For example, in response to acute injury, some macrophages adopt a pro-inflammatory phenotype and augment tissue damage; once the injury stimulus is removed, they may change to mediate tissue repair. +While kidney macrophages contribute to wound healing, tissue repair and regeneration by producing key growth factors and cytokines that stimulate cell proliferation, collagen production, and blood vessel formation, dysregulation in their activity can also lead to progressive inflammation and fibrosis, common features in chronic kidney disease.") +AnnotationAssertion( "https://cellxgene.cziscience.com/cellguide/CL_1000698") +AnnotationAssertion(Annotation( "DOI:10.1002/cphy.c110052") Annotation( "DOI:10.1007/s00418-021-02033-5") Annotation( "DOI:10.1097/MNH.0b013e32820ac850") Annotation( "DOI:10.1681/ASN.2019040415") Annotation( "DOI:10.23876/j.krcp.2017.36.4.305") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Kidney connecting tubule epithelial cells are found in collecting duct system of the kidney, specifically in at the interconnection segment between the nephron and the collecting ducts. The epithelial cells lining the connecting tubule are crucial for the journey of filtrate before it empties into urine-collecting ducts and therefore play a critical role in maintaining the body’s fluid and electrolyte balance. +One of the principal functions of connecting tubule epithelial cells involves the selective reabsorption and secretion of various solutes. This reabsorption process includes critical regulatory electrolytes such as sodium ions (Na+), chloride ions (Cl-), and bicarbonate ions (HCO3-), thus playing a role in the regulation of the acid-base homeostasis. Their function also involves the secretion of potassium ions (K+) into the renal tubular fluid. +The connecting tubule epithelial cells are primarily intercalated cells, which can be categorized into two types according to their specific functions: type A intercalated cells, which secrete acid, and the type B intercalated cells, which secrete base (bicarbonate) and reabsorb chloride. By regulating the concentrations of these ions, as well as reabsorption of water, connecting tubule epithelial cells contribute substantively to maintaining the body's electrolyte levels, pH balance, and overall homeostasis. +In addition to intercalating cells, the collecting duct system also has principal cells, which are characterized by the expression of the water channel AQP2. AQP2-expressing cells have also been identified in connecting tubules, but there is some controversy whether these represent a unique cell type as there are some morphologic differences compared with principal cells.") +AnnotationAssertion( "https://cellxgene.cziscience.com/cellguide/CL_1000768") +AnnotationAssertion(Annotation( "DOI:10.1002/cphy.c110060") Annotation( "DOI:10.1146/annurev-physiol-052521-121841") Annotation( "DOI:10.1159/000092212") Annotation( "DOI:10.1681/ASN.2019040415") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Kidney proximal convoluted tubule epithelial cells line the most voluminous part of the kidney's nephron, the proximal convoluted tubule, located in the cortex of the kidney. These cells are primarily involved in reabsorption and secretion processes, key functions that facilitate homeostasis within the body. +Proximal convoluted tubule epithelial cells extensively function in the reabsorption process to a greater degree than their counterparts in the proximal straight tubule. Approximately two-thirds of filtrated sodium and water, nearly all nutrient sugars and amino acids, and a significant portion of bicarbonates pass through the proximal convoluted tubule, are effectively absorbed by the epithelial cells, and reenter the bodily circulation. By absorbing bicarbonates and secreting protons into the tubular fluid, proximal convoluted tubule epithelial cells also contribute to the pH regulation in the body . +In addition to reabsorption, proximal convoluted tubule epithelial cells also play a critical role in the excretion of waste metabolites and xenobiotics. These cells possess a range of transporters that secrete metabolic end products and certain drugs, hence aiding in their elimination. This function underlines their importance for body detoxification.") +AnnotationAssertion( "https://cellxgene.cziscience.com/cellguide/CL_1000838") +AnnotationAssertion(Annotation( "DOI:10.1002/cphy.c110061") Annotation( "DOI:10.1038/nrd4461") Annotation( "DOI:10.1146/annurev-physiol-052521-121841") Annotation( "DOI:10.1681/ASN.2019040415") Annotation( "DOI:10.2215/CJN.10391012") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Kidney proximal straight tubule epithelial cells line the straight portion of the proximal tubule of the nephron, extending from the cortical medullary ray into the outer stripe of the outer medulla. They are characterized by a brush border of dense microvilli on their apical surface, enhancing the cell's surface area and aiding reabsorption, though reabsorption occurs more heavily in the proximal convoluted tubule preceding the straight portion of the tubule. +The primary function of the kidney proximal straight tubule epithelial cells is to reabsorb the filtrate that the kidney produces, which includes glucose, sodium, and water. The reabsorption occurs through both passive and active transport methods. These cells exhibit enzyme-rich microvilli that also absorb small proteins and peptides. Consequently, they are involved in the regulation of plasma levels of various substances, including glucose, amino acids, and electrolytes, and maintain the body's pH homeostasis by secreting H+ ions into the urine and absorbing bicarbonate ions. +These cells are also reported to be involved in drug metabolism. Many drugs are filtered from the blood by the kidneys and subsequently reabsorbed by the kidney proximal tubule epithelial cells back into the bloodstream. Furthermore, these cells play a significant role in the progression of kidney diseases. For example, in diabetic nephropathy and acute kidney injury, kidney proximal straight tubule epithelial cells can undergo cellular changes and result in malfunctions such as reduced reabsorption and increased excretion.") +AnnotationAssertion( "https://cellxgene.cziscience.com/cellguide/CL_1000839") +AnnotationAssertion(Annotation( "DOI:10.1002/cphy.c140002") Annotation( "DOI:10.1007/s40620-021-01032-y") Annotation( "DOI:10.1152/physrev.2000.80.1.277") Annotation( "DOI:10.1681/ASN.2019040415") Annotation( "DOI:10.2215/CJN.05920613") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Kidney distal convoluted tubule epithelial cells, often referred to simply as distal convoluted tubule (DCT) cells, constitute a significant portion of the nephron -- the functional building unit of the kidney involved in filtration and reabsorption of substances from blood. The DCT epithelial cells form lining of the distal convoluted tubule, a segment of the nephron located after the loop of Henle and before the collecting tubule. These cells are characterized by unique morphological features such as small size, low height and fewer microvilli compared to proximal convoluted tubule epithelial cells. +These cells perform a host of vital functions contributing to the regulation of extracellular fluid volume and electrolyte balance, blood pressure and pH. While the DCT is less prominent in water and sodium reabsorption compared to the proximal tubule and the loop of Henle, it plays a crucial role in fine-tuning the process. DCT epithelial cells are responsible for the final adjustments of sodium, potassium and calcium reabsorption, thereby affecting overall fluid and electrolyte balance, blood pressure regulation and bone health. The reabsorption process is regulated by hormones including aldosterone and parathyroid hormone. +The distal convoluted tubule (DCT) also plays a significant role in acid-base homeostasis by secreting protons (H+) into the tubular fluid and reabsorbing bicarbonate ions (HCO3-), thus regulating the pH of the blood. The ability of DCT cells to adjust urine concentration plays a part in maintaining the body’s pH balance and preventing conditions like acidosis or alkalosis. In summary, kidney distal convoluted tubule epithelial cells perform functions that are crucial to maintaining body's homeostasis.") +AnnotationAssertion( "https://cellxgene.cziscience.com/cellguide/CL_1000849") +AnnotationAssertion(Annotation( "DOI:10.1073/pnas.0736323100") Annotation( "DOI:10.1146/annurev-physiol-052521-121841") Annotation( "DOI:10.1161/HYPERTENSIONAHA.115.04739") Annotation( "DOI:10.1681/ASN.2009070759") Annotation( "DOI:10.1681/ASN.2015050515") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Macula densa epithelial cells, as part of the complex nephron structure, play a crucial role in kidney function. These cells, which make up the macula densa, help regulate blood pressure and the filtration rate of the glomerulus by sensing sodium chloride amounts in the kidney tubules. Found where the thick ascending limb of the Loop of Henle touches the afferent arteriole, macula densa epithelial cells are positioned in an optimal location to monitor and respond to changes in the filtrate composition. +These cells maintain intraglomerular homeostasis. When the sodium chloride concentration is high, macula densa cells respond by secreting adenosine and vasoconstricting the afferent arteriole to decrease the glomerular filtration rate. Conversely, if the sodium chloride concentration in the filtrate is low, the production and release of nitric oxide cause vasodilation to enhance the glomerular filtration rate. +Macula densa epithelial cells also have a role in tubuloglomerular feedback mechanisms, an essential autoregulatory renal response. They send feedback to the glomerular mesangial cells, allowing constriction or relaxation of the afferent arteriole as needed depending on the content of the filtrate.") +AnnotationAssertion( "https://cellxgene.cziscience.com/cellguide/CL_1000850") +AnnotationAssertion(Annotation( "DOI:10.1016/j.biocel.2010.05.015") Annotation( "DOI:10.1016/j.yexcr.2012.02.032") Annotation( "DOI:10.1111/j.1523-1755.2005.00260.x") Annotation( "DOI:10.2337/diacare.28.1.164") Annotation( "DOI:10.3389/fphys.2021.689083") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. The glomerular capillary endothelial cell comprises an intrinsic component of the glomerulus in the kidney. Glomeruli contain a network of capillaries where the first step of blood filtration takes place, with glomerular capillary endothelial cells acting as an integral part of this process. Unlike regular endothelial cells that line the vasculature, unique fenestrations (openings) characterize these cells, allowing for enhanced permeability and filtration efficacy. Together with the glomerular basement membrane and podocytes, the glomerular endothelial cells form the glomerular filtration barrier, which is responsible for blood filtration and therefore critical for removal of waste products, such as urea and creatinine, and excess substances, such as glucose and ions, from the bloodstream. The glomerular capillary endothelial cells' fenestrations permit the free flow of a variety of particles, barring larger, negatively charged proteins like serum albumin, enabling the formation of an ultrafiltrate. This ultrafiltrate is the primitive form of urine, which then passes through the proximal tubule for further processing and ultimately helps maintain systemic fluid and electrolyte balance. Moreover, the glomerular capillary endothelial cells are also believed to play a crucial role in renal pathologies. Any compromise to their structural integrity or functional performance can lead to kidney diseases, including but not limited to, diabetic nephropathy and glomerulonephritis. For instance, in diabetes, persistent hyperglycemia can injure these cells, leading to a compromised glomerular filtration barrier and proteinuria, indicating the loss of proteins in the urine.") AnnotationAssertion( "https://cellxgene.cziscience.com/cellguide/CL_1001005") -AnnotationAssertion(Annotation( "DOI:10.1046/j.0001-6772.2003.01205.x") Annotation( "DOI:10.1093/ndt/gfl308") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. +AnnotationAssertion(Annotation( "DOI:10.1007/s00424-012-1126-7") Annotation( "DOI:10.1152/ajpregu.00332.2006") Annotation( "DOI:10.1152/physrev.00042.2012") Annotation( "DOI:10.2174/15701611113116660149") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Kidney afferent arteriole cells are specialized cell types found in the renal vasculature, specifically in the afferent arterioles which help in maintaining the renal blood flow and glomerular filtration rate. They are essential for the proper functioning of the kidneys, contributing to the regulation of blood pressure and fluid balance within the organism. Located before the glomerulus, a tiny, intricate network of capillaries within the nephron, these cells help control the expansion or contraction of the arteriole, thus regulating the pressure and flow of blood into the glomerulus. +Functionally, kidney afferent arteriole cells are largely involved in responding to changes in blood volume and systemic blood pressure. They achieve this by modulating the diameter of the afferent arteriole through a process known as autoregulation. Autoregulation involves two primary mechanisms: the myogenic response and the tubuloglomerular feedback. The myogenic response is essentially the intrinsic ability of the vascular smooth muscle to respond to pressure changes, while the tubuloglomerular feedback is the process where the macula densa cells located near the glomerulus respond to changes in fluid delivery rates in the tubules, sending signals to afferent arterioles to constrict or dilate accordingly. These cells also have significant interaction with renin-containing juxtaglomerular cells, which are located in the wall of afferent arterioles. Juxtaglomerular cells secrete the enzyme renin in response to low blood pressure or sympathetic nerve activity, initiating the renin-angiotensin-aldosterone system cascade that ultimately helps retain sodium and water to increase blood volume and pressure.") +AnnotationAssertion( "https://cellxgene.cziscience.com/cellguide/CL_1001006") +AnnotationAssertion(Annotation( "DOI:10.1152/ajpregu.2000.279.2.R629") Annotation( "DOI:10.1152/physrev.00042.2012") Annotation( "DOI:10.1159/000072054") Annotation( "DOI:10.1161/01.HYP.29.1.222") Annotation( "DOI:10.3748/wjg.v12.i34.5429") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Kidney efferent arteriole cells are highly adaptable vascular cells that make up the efferent arterioles in the kidney. These units are integral components of the renal microcirculation system, conducting blood away from the glomeruli after filtration occurs. Efferent arterioles directly affect glomerular hydrostatic pressure and, subsequently, the rate of glomerular filtration. They are the downstream channels that ensure the effective transportation of blood to the peritubular capillaries and vasa recta, critical for maintaining fluid balance and electrolyte homeostasis. +Kidney efferent arteriole cells are exceptional in their ability to perform autoregulation—a critical dynamic control of intrarenal blood flow ensuring stable glomerular filtration rates. This is primarily achieved via myogenic and tubuloglomerular feedback mechanisms, where the cells respond to changes in pressure and the concentration of sodium chloride in the tubular fluid, and constrict or dilate depending on the detected changes. +Cells associated with the efferent arteriole also respond to several systemic influences. Through complex intracellular signaling pathways, they respond to fluctuations in hormones (like angiotensin II and endothelin) and several other mediators such as nitric oxide and prostaglandins. Their adaptive capability helps maintain homeostasis and ensures the entire system's optimal performance under various physiological conditions. Dysfunctions in kidney efferent arteriole cells can lead to severe pathologies like hypertension and chronic kidney disease.") +AnnotationAssertion( "https://cellxgene.cziscience.com/cellguide/CL_1001009") +AnnotationAssertion(Annotation( "DOI:10.1007/s00360-018-1164-3") Annotation( "DOI:10.1146/annurev-physiol-021113-170350") Annotation( "DOI:10.1152/advan.00227.2022") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +The kidney loop of Henle descending limb epithelial cells are highly specialized cells that play a crucial role in maintaining the body's salt and water balance. These cells line the descending limb of the loop of Henle, which is a portion of the renal tubule located in the kidneys, an organ responsible for filtering waste products, ions and extra water from the blood and converting them into urine. However, the descending limb epithelial cells are specifically involved in the countercurrent multiplication system, a mechanism to concentrate urine that involves both active and passive transport processes. +These cells are notably permeable to water but relatively impermeable to solutes, a characteristic that dramatically influences the osmotic gradient in the renal medulla. As filtrate initially descends down the loop of Henle, water gets drawn out due to the increasing osmotic gradient, thereby concentrating the filtrate. Additionally, these epithelial cells are exceptionally thin walled, allowing water to freely diffuse across the membrane. +Furthermore, the kidney loop of Henle descending limb epithelial cells are inextricably linked to the functioning of numerous diuretic drugs, which work by blocking the reabsorption of water and certain electrolytes in the kidneys, leading to increased urine production to rid the body of excess fluids.") +AnnotationAssertion( "https://cellxgene.cziscience.com/cellguide/CL_1001021") +AnnotationAssertion(Annotation( "DOI:10.1046/j.0001-6772.2003.01205.x") Annotation( "DOI:10.1093/ndt/gfl308") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. Kidney afferent arteriole endothelial cells are a specialized type of cell located within the kidneys, forming the inner lining of the afferent arterioles, which are responsible for delivering blood to the glomeruli - capillary networks responsible for filtration - from where the process of urine formation begins in the nephrons. The endothelial cells in the kidney afferent arterioles have a key function in regulating the blood flow and filtration. They have autocrine and paracrine signaling capabilities, meaning they can signal to themselves and other nearby cells. They produce nitric oxide, prostacyclin, and endothelin, which are powerful vasodilators and vasoconstrictors that regulate renal blood flow. These cells also engage in the mitigation of kidney injury and inflammation by promoting repair and regeneration, demonstrating the multifaceted roles these cells play in maintaining renal health.") AnnotationAssertion( "https://cellxgene.cziscience.com/cellguide/CL_1001096") -AnnotationAssertion(Annotation( "DOI:10.1016/j.semcdb.2014.08.002") Annotation( "DOI:10.1016/j.semnephrol.2015.01.010") Annotation( "DOI:10.1038/s41581-021-00411-9") Annotation( "DOI:10.1681/ASN.2019111179") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. +AnnotationAssertion(Annotation( "DOI:10.1016/j.semcdb.2014.08.002") Annotation( "DOI:10.1016/j.semnephrol.2015.01.010") Annotation( "DOI:10.1038/s41581-021-00411-9") Annotation( "DOI:10.1681/ASN.2019111179") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. Kidney efferent arteriole endothelial cells constitute a vital component of the kidney's microvascular system. They are unique endothelial cells found lining the walls of efferent arterioles, which transport blood away from the glomeruli in the kidney. The primary responsibilities of the kidney efferent arteriole endothelial cells involve controling renal blood flow, regulating glomerular filtration rate (GFR), and managing perfusion pressure. They do this by contracting and relaxing, effectively narrowing and widening the arteriole's lumen thereby controling the volume and rate of blood flow to the peritubular capillaries and creating the pressure gradient necessary for filtration in the glomerulus. Furthermore, kidney efferent arteriole endothelial cells show a high degree of plasticity in response to pathophysiological stimuli and can undergo structural and functional changes based on local needs. In conditions like hypertension and diabetes, these cells can experience hypertrophy and endothelial dysfunction, contributing to the progression of renal disease.") AnnotationAssertion( "https://cellxgene.cziscience.com/cellguide/CL_1001099") -AnnotationAssertion(Annotation( "DOI:10.1016/B978-0-323-35515-5.00009-9") Annotation( "DOI:10.1053/j.ajkd.2005.01.008") Annotation( "DOI:10.1081/jdi-100101958") Annotation( "DOI:10.1111/apha.12026") Annotation( "DOI:10.1152/ajpregu.00657.2002") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. +AnnotationAssertion(Annotation( "DOI:10.1016/B978-0-323-35515-5.00009-9") Annotation( "DOI:10.1053/j.ajkd.2005.01.008") Annotation( "DOI:10.1081/jdi-100101958") Annotation( "DOI:10.1111/apha.12026") Annotation( "DOI:10.1152/ajpregu.00657.2002") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. The vasa recta ascending limb cells are specialized epithelial cells that are part of the vasa recta in the kidney, a crucial component of the renal medulla that functions as a counter-current exchanger to maintain the concentration gradient required for water reabsorption. These particular cells are located in the ascending limb of the vasa recta, which takes blood flow from the medulla back to the cortex. The primary function of vasa recta ascending limb cells is to preserve the renal medulla's hypertonicity, necessary for the kidney's urine concentration mechanism. Unlike the vasa recta descending limb cells, the venous-like epithelial cells of the ascending vasa recta are highly fenestrated and lack pericyte coverage, which facilitates water reuptake. As the blood flows through the ascending limb, it loses solutes and gains water, which is driven by the high solute concentration in the surrounding interstitium. This process acts in concert with cellular action in the descending limb and contributions from the so-called Loop of Henle, which helps with water and sodium chloride retrieval from the urine. In the context of normal physiological processes, the function of the vasa recta ascending limb cells is essential in maintaining the body's overall fluid balance, electrolyte concentration, and systemic blood pressure. Any dysfunction in these cells may lead to impaired urine concentration or dilution capability of the kidney, potentially resulting in conditions like diabetes insipidus or hyponatremia.") AnnotationAssertion( "https://cellxgene.cziscience.com/cellguide/CL_1001131") -AnnotationAssertion(Annotation( "DOI:10.1053/j.ajkd.2005.01.008") Annotation( "DOI:10.1081/jdi-100101958") Annotation( "DOI:10.1111/apha.12026#apha12026-bib-0039") Annotation( "DOI:10.1152/ajpregu.00657.2002") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. +AnnotationAssertion(Annotation( "DOI:10.1053/j.ajkd.2005.01.008") Annotation( "DOI:10.1081/jdi-100101958") Annotation( "DOI:10.1111/apha.12026#apha12026-bib-0039") Annotation( "DOI:10.1152/ajpregu.00657.2002") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. Vasa recta descending limb cells are specialized epithelial cells found in the vasa recta, a network of blood vessels in the renal medulla. These cells line the interior surface of the descending limb of the vasa recta and play a crucial role in the filtering and regulation of substances within the blood. In contrast to vasa recta ascending limb cells, the arterial-like epithelial cells of the descending vasa recta are non-fenestrated and covered by a pericyte layer that regulates the medullary blood flow. They help keeping the body’s fluid and electrolyte balance in check through a process known as countercurrent exchange system, in which the cells of the descending limb are permeable to water but relatively impermeable to solutes, such as sodium and urea. As the blood descends into the medulla along its descending limb, water passively diffuses out of the vasa recta, concentrating the blood in solutes. In addition to their central role in water and solute exchange, these cells contribute to maintaining the medullary osmotic gradient, a critical function to concentrate urine. The osmotic gradient is created by the counterflow of water and solutes between the descending and ascending limbs of the vasa recta and the adjacent Loop of Henle. The selective permeability of the descending limb cells allows them to maintain this gradient, which in turn helps to conserve water, a vital role in the overall function of the renal system. Thus, vasa recta descending limb cells have a significant function in renal physiology, particularly in osmoregulation and fluid balance.") AnnotationAssertion( "https://cellxgene.cziscience.com/cellguide/CL_1001285") -AnnotationAssertion(Annotation( "DOI:10.1007/s11906-015-0538-0") Annotation( "DOI:10.1016/B978-0-12-386456-7.05402-2") Annotation( "DOI:10.1016/j.biocel.2022.106261") Annotation( "DOI:10.1073/pnas.1710964114") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. +AnnotationAssertion(Annotation( "DOI:10.1038/nrurol.2011.144") Annotation( "DOI:10.1038/nrurol.2016.13") Annotation( "DOI:10.1038/s41579-020-0324-0") Annotation( "DOI:10.1038/s41585-020-0350-8") Annotation( "DOI:10.1080/03008880410015165") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Bladder urothelial cells form the urothelium in the bladder - a specific type of epithelial tissue that constitutes the inner lining of the bladder and other parts of the urinary tract including the renal pelvis, ureters and urethra. These unique cells are specialized to withstand the highly variable and sometimes harsh conditions present in the urinary system. Their key function is maintaining the barrier integrity of the urinary tract even when exposed to high volumes of urine and its solutes, and they play a crucial role in protecting underlying tissues from damage and infection. +The bladder urothelial cells exhibit a remarkable spectrum of phenotypic versatility and have an extraordinary capacity to stretch and retract based on the degree of bladder filling and emptying. In their relaxed state, these cells appear large and cuboidal, but upon stretching, they become thinner and exhibit a squamous cell-like appearance. This distinctive feature enables them to adjust to the changes in the urinary bladder volume while remaining impermeable to urinary solutes, thereby preventing a potential toxicity to the bladder wall and infiltration into the bloodstream. +Apart from their barrier function, bladder urothelial cells also express a number of sensor molecules or respond to thermal, mechanical and chemical stimuli and can release signaling molecules, thereby playing a key role in sensory mechanisms that communicate vital information about the bladder's mechanical state to the nervous system. This communication helps regulate the micturition cycle and maintain urinary continence. Recent studies have also indicated that these cells may play a role in immune responses, highlighting their importance in bladder physiology. +Altered proliferation and differentiation of bladder urothelial cells are implicated in various diseases and conditions such as bladder cancer, interstitial cystitis, and urinary tract infections.") +AnnotationAssertion( "https://cellxgene.cziscience.com/cellguide/CL_1001428") +AnnotationAssertion(Annotation( "DOI:10.1038/nrurol.2016.13") Annotation( "DOI:10.1038/s41385-022-00565-0") Annotation( "DOI:10.1152/physrev.00030.2012") Annotation( "DOI:10.1152/physrev.00041.2019") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Urethra urothelial cells are highly specialized epithelial cells in the urethra, which is a tubelike structure that carries urine from the bladder to the external urethral orifice. Urothelial cells form the urothelium – a stratified, transitional epithelium lining the bladder, ureters, renal pelvis and urethra. These cells are highly adapted to their specific environment and maintain the crucial function of sustaining the urinary tract's core roles, primarily to transit and store urine without auto-corrosion or pathogen proliferation. +Within the urethra urothelial cells are primarily found in proximal two-thirds of the urethra, while the distal third is lined by stratified squamous epithelial cells. The urothelial cells are renowned for their remarkable impermeability and ability to stretch and recoil during the various stages of urine filling and emptying. They form a tight barrier that prevents reabsorption of harmful byproducts and toxic substances present in the urine, guarding the deeper tissues and bloodstream against potential damage. This is largely attributed to specialized junctions, namely zonulae occludentes or tight junctions, in the umbrella cell layer (one of three layers of the urothelium) that seal the intercellular space between adjacent cells. Together with the urothelial plaque (an apical membrane plaque comprised of uroplakin proteins covering the umbrella cells at the luminal surface), the junctional complexes form a very effective permeability barrier that regulates the passage of water and ion from urine to the underlying tissue. +A noteworthy feature of urothelial cells is their regulatory and sensory roles involving communication with the underlying layers about the filling and emptying status of the urinary tract. The cells also manage a fine balance between proliferation and differentiation, with the basal cells providing a ready pool of cells to replace the superficial layer when damaged. Their remarkable ability for regeneration and turnover, and their response to signals for repair underpins the durability and functionality of the urothelial tract.") +AnnotationAssertion( "https://cellxgene.cziscience.com/cellguide/CL_1001430") +AnnotationAssertion(Annotation( "DOI:10.1007/s11906-015-0538-0") Annotation( "DOI:10.1016/B978-0-12-386456-7.05402-2") Annotation( "DOI:10.1016/j.biocel.2022.106261") Annotation( "DOI:10.1073/pnas.1710964114") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. The kidney collecting duct principal cell is a highly specialized type of cell found in the late distal convoluted tubule and collecting duct of the kidney's nephron. Principal cells are located at the final segments of the renal tubules, where they play a pivotal role in key homeostatic processes. One of their fundamental functions of kidney collecting duct principal cells is the regulation of water reabsorption, which is mediated by aquaporins (water channel proteins). Antidiuretic hormones, such as vasopressin, can stimulate the redistribution of these water channels from an intracellular pools to the apical plasma membrane of the principal cell; translocation of aquaporin (specifically, AQP2) is associated with an increase of osmotic water permeability. The water reabsorption affects the concentration of the final urine; these cells are therefore directly involved in the maintenance of the body's fluid balance. Kidney collecting duct principal cells also participate in sodium and potassium ions regulation. They reabsorb sodium ions from the tubular fluid back into the bloodstream, a process facilitated by the action of aldosterone, a hormone released by the adrenal glands. Similarly, the principal cells secrete potassium ions into the tubular fluid in response to aldosterone, contributing to the regulation of potassium levels in the body. Impaired function of cells can lead to various renal diseases and disorders, highlighting the vital role of kidney collecting duct principal cells in the body's homeostatic processes.") AnnotationAssertion( "https://cellxgene.cziscience.com/cellguide/CL_1001431") -AnnotationAssertion(Annotation( "DOI:10.1007/978-3-030-32300-4_26") Annotation( "DOI:10.1007/s00265-006-0178-0") Annotation( "DOI:10.1111/j.1439-0272.1992.tb02636.x") Annotation( "https://www.ncbi.nlm.nih.gov/books/NBK499854/") Annotation( "https://www.sciencedirect.com/topics/veterinary-science-and-veterinary-medicine/seminal-vesicle") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. +AnnotationAssertion(Annotation( "DOI:10.1007/978-3-211-99390-3_106") Annotation( "DOI:10.1152/physiol.00008.2011") Annotation( "DOI:10.1152/physrev.00011.2019") Annotation( "DOI:10.2215/CJN.08880914") Annotation( "DOI:10.3390/diseases2020071") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +The kidney collecting duct intercalated cell, otherwise referred to simply as the intercalated cell, is a specialized epithelial cell type primarily found in the kidney's collecting duct system. It is among the main cells that line this final component of the nephron, crucial in the physiological system that maintains acid-base homeostasis. This unique cell type comes in mainly three subtypes as per the localization of their proton pumps: type A, type B, and non-A, non-B cells. Each subtype plays different roles in regulating acid-base balance and electrolyte homeostasis in the body under varying physiological conditions. +Type A intercalated cells reabsorb bicarbonate and secrete protons into urine, leading to the production of acidic urine. These cells are typically prevalent on the renal cortex and function particularly in states of metabolic acidosis or potassium depletion. On the other hand, type B intercalated cells secrete bicarbonate and reabsorb protons; thus, they are crucial in alkaline urine production and potassium conservation. These cells are essential to counter metabolic alkalosis or situations of potassium surplus. The non-A, non-B cells have the characteristic features of both type A and B cells, but play a prominent role under conditions of chronically elevated aldosterone and angiotensin II levels. +Through their differentiated roles, intercalated cells also facilitate the reabsorption of sodium and chloride ions, and water to maintain osmolarity. These cells' activity is finely regulated by hormonal signals like aldosterone, angiotensin II, vasopressin, and the parathyroid hormone. Intercalated cell activity can undergo a significant transformation under pathological conditions, and their dysregulation is associated with diseases such as distal renal tubular acidosis, hypertension, and chronic kidney disease.") +AnnotationAssertion( "https://cellxgene.cziscience.com/cellguide/CL_1001432") +AnnotationAssertion(Annotation( "DOI:10.1016/j.coph.2013.09.008") Annotation( "DOI:10.1038/mi.2017.73") Annotation( "DOI:10.1038/s41574-019-0168-8") Annotation( "DOI:10.1111/j.1365-2613.2011.00767.x") Annotation( "DOI:10.1146/annurev-physiol-021115-105439") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Intestinal enteroendocrine cells are a highly specialized cell type found within the gastrointestinal epithelium. They account for approximately 1% of the intestinal epithelial cells in what is known as the largest endocrine organ in the human body. Intestinal enteroendocrine cells exhibit an exceptional diversity, both in terms of their secretory products and their distribution along the intestines, varying from the small intestine to the colon. +The primary function of intestinal enteroendocrine cells is to maintain gut physiology and homeostasis. They are known for their hormone production and are the source of numerous bioactive molecules including somatostatin, serotonin, cholecystokinin, glucose-dependent insulinotropic peptide, motilin, neurotensin, and others. These hormones and neuropeptides act in autocrine, paracrine, or endocrine signaling, impacting various functions including intestinal motility, secretion, nutrient absorption, and gut barrier functions. +Intestinal enteroendocrine cells also serve as the body's frontline of defense, playing an integral role in surveillance against lumen-occurring hazards including pathogen attack. Enteroendocrine cells are divided into ‘closed type’ and ‘open type’. Closed type cells are located close to the basal membrane and do not reach the lumen of the gut. In contrast, the apical side of the open-type intestinal enteroendocrine cells is directly exposed to luminal contents and thus can recognize bacterial metabolites and dietary nutrients. In response, these cells can modulate the immune system responses and thereby function as a key communicator between the gut microbiota and the host.") +AnnotationAssertion( "https://cellxgene.cziscience.com/cellguide/CL_1001516") +AnnotationAssertion(Annotation( "DOI:10.1007/978-3-030-32300-4_26") Annotation( "DOI:10.1007/s00265-006-0178-0") Annotation( "DOI:10.1111/j.1439-0272.1992.tb02636.x") Annotation( "https://www.ncbi.nlm.nih.gov/books/NBK499854/") Annotation( "https://www.sciencedirect.com/topics/veterinary-science-and-veterinary-medicine/seminal-vesicle") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. Seminal vesicle glandular cells belong to a specialized group of epithelial cells that form the internal lining of the seminal vesicles, a pair of male reproductive organs. These cells are located within the complex tubuloalveolar glands that make up the seminal vesicles and are known for their unique pseudostratified columnar epithelium structure. The primary function of these cells is the secretion of a variety of substances that ultimately constitute around 70% of the fluid volume of semen. Seminal cells produce a high-fructose fluid that serves as an energy source for the spermatozoa and promotes their motility. They also secrete other essential substances like proteins, enzymes, vitamin C, prostaglandins, and various other compounds. Collectively, these substances help in the nourishment, protection, and transportation of the spermatozoa throughout the male reproductive system and during the ejaculation process. Secondary to the production of seminal fluid, the seminal vesicle glandular cells also play a role in the contraction of the seminal vesicles during ejaculation. The contraction of these glands, induced by sympathetic nerves, ensures the efficient propulsion of the seminal fluid mixed with spermatozoa into the ejaculatory ducts and subsequently to the urethra. Notably, any malfunction or pathological condition affecting these cells can impact male fertility, emphasizing the importance of understanding the intricate functions of seminal vesicle glandular cells in maintaining the healthy physiological function of male reproduction.") AnnotationAssertion( "https://cellxgene.cziscience.com/cellguide/CL_1001597") -AnnotationAssertion(Annotation( "DOI:10.1002/(SICI)1097-0029(19980415)41:2<98::AID-JEMT2>3.0.CO;2-M") Annotation( "DOI:10.1111/joa.13709") Annotation( "DOI:10.3389/fncel.2015.00480") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. +AnnotationAssertion(Annotation( "DOI:10.1038/nbt.2247") Annotation( "DOI:10.1038/nrn1824") Annotation( "DOI:10.1177/0271678X156179") Annotation( "DOI:10.1186/s12987-020-00230-3") Annotation( "DOI:10.3389/fnins.2023.1047778") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Cerebral cortex endothelial cells are unique endothelial cells responsible for the formation and regulation of the blood-brain barrier (BBB), a specialized structure that separates the circulating blood from the cerebral neural tissue. These cells line the inner surface of nearly all blood vessels that irrigate the cerebral cortex, the outermost layer of the brain involved with complex cognitive functions such as thought, perception, and memory formation. Cerebral cortex endothelial cells are integral to maintaining brain health and function due to their role in regulating brain microenvironment and controlling the passage of essential molecules and cells. +The endothelial cells in the cerebral cortex are distinctive due to their highly selective permeability, largely attributable to the existence of unique tight junctions which maintain the barrier function of the BBB. The tightly interconnected structures of these cells prevent most substances from freely diffusing into the brain tissue, ensuring that harmful agents such as toxins, pathogens, or peripheral immune cells don't reach the brain and compromise its function. These cells also express multiple transporters and enzymes, allowing the selective entry of necessary nutrients and metabolites while excluding toxic substances. +Cerebral cortex endothelial cells also participate in neurovascular coupling, a process where localized neuronal activity increases cerebral blood flow to satisfy the local metabolic demands. The endothelial cells work in coordination with neurons and other cell types such as astrocytes and pericytes to mediate this process. They have been thought to regulate local blood flow by releasing substances in response to neuronal activity. Additionally, these cells are involved in many pathological conditions. Breakdown or dysfunction of the BBB often marked by altered endothelial cell function is linked to numerous neurological disorders including stroke, multiple sclerosis, Alzheimer’s disease, and brain tumors.") +AnnotationAssertion( "https://cellxgene.cziscience.com/cellguide/CL_1001602") +AnnotationAssertion(Annotation( "DOI:10.1002/JLB.3RU0720-418R") Annotation( "DOI:10.1016/j.immuni.2022.08.010") Annotation( "DOI:10.1189/jlb.70.2.163") Annotation( "DOI:10.3389/fimmu.2021.753940/full") Annotation( "DOI:10.3390/cells10040897") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Lung macrophages refer to macrophage populations in the lungs, including the tissue-resident alveolar macrophages and interstitial macrophages, located in the air spaces and the connective tissue of the lung, respectively, and recruited macrophages. They are important in maintaining tissue homeostasis and immunity. +The primary function of lung macrophages is to patrol and maintain the pulmonary system, where they serve as the first line of defense against airborne pathogens and inhaled particles. They perform phagocytosis of pathogens, particulate matter, dead cells, and other cellular debris from the lungs to maintain clear air passages and optimize gas exchange. They may also participate in tissue repair and the resolution of inflammation following injury. +Lung macrophages also play a critical role in immune regulation. They help to initiate an immune response by secreting cytokines and other inflammatory mediators and by presenting antigens from the pathogens they have engulfed to induce T cell responses. However, if activated improperly, lung macrophages can contribute to inflammatory diseases of the lung such as chronic obstructive pulmonary disease (COPD) or asthma.") +AnnotationAssertion( "https://cellxgene.cziscience.com/cellguide/CL_1001603") +AnnotationAssertion(Annotation( "DOI:10.1002/rmb2.12088") Annotation( "DOI:10.1093/humupd/dmw004") Annotation( "DOI:10.1111/j.1749-6632.2010.05938.x") Annotation( "DOI:10.3390/ijms21114092") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Decidual cells, originating from the endometrial lining in the uterus, undergo significant transformations during pregnancy and are integral to its preparation and maintenance. Their conversion from endometrial fibroblast to a secretory phenotype, known as decidualization, occurs as a normal process in the menstrual cycle or in response to embryo implantation. +With crucial roles in regulating maternal immune responses and placental development, decidual cells have a twofold function: preventing rejection of the conceptus by the mother's immune system and guiding placental development to avoid excessive trophoblast invasion leading to pre-eclampsia. During decidualization, these cells secrete proteins and growth factors supporting embryo implantation and sustaining early pregnancy. Furthermore, decidual cells modulate the activities of natural killer cells, macrophages, and T cells in the uterus, maintaining a balance of pro-inflammatory and anti-inflammatory conditions during pregnancy.") +AnnotationAssertion( "https://cellxgene.cziscience.com/cellguide/CL_2000002") +AnnotationAssertion(Annotation( "DOI:10.1038/s41423-023-01042-9") Annotation( "DOI:10.1038/s41467-019-14127-9") Annotation( "DOI:10.3389/fimmu.2023.1235812") Annotation( "DOI:10.3389/fphys.2020.00509") Annotation( "DOI:10.3389/fphys.2020.577584") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +A dermis lymphatic vessel endothelial cell is a specialized type of cell that lines the interior surface of lymphatic vessels present in the dermal layer of the skin. These cells are organized into a single layer, forming an integral part of the lymphatic system which acts as the body's secondary circulatory system. The primary function of dermis lymphatic vessel endothelial cells is to facilitate the transportation and regulation of the lymph fluid within the dermis. They act as a barrier, contributing to fluid homeostasis, lipid transport, and immune cell trafficking. These cells are uniquely equipped to let fluid and larger molecules, including proteins and immune cells, into the lymphatic vessels from the surrounding interstitial space. This is enabled by the specialized junctions between the endothelial cells and the presence of primary lymphatic valves that prevent the backflow of lymph. +Another paramount role of dermis lymphatic vessel endothelial cells is their involvement in immune response. By interacting with white blood cells, especially T-cells and dendritic cells, they can mediate local immune surveillance and contribute to both innate and adaptive immune responses. These cells are also implicated in a variety of pathological conditions, including lymphedema and metastasis in cancer.") +AnnotationAssertion( "https://cellxgene.cziscience.com/cellguide/CL_2000011") +AnnotationAssertion(Annotation( "DOI:10.1016/j.jid.2016.10.017") Annotation( "DOI:10.1080/19381980.2017.1375636") Annotation( "DOI:10.4161/derm.1.2.8472") Annotation( "https://doi.org/10.2147/CLEP.S323744") Annotation( "https://www.sciencedirect.com/topics/agricultural-and-biological-sciences/sebum") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Sebaceous gland cells, also known as sebocytes, are small, oil-producing glands present in the skin of mammals. These specialized cells are predominantly located in the dermis, particularly on the face, scalp, and upper body. +The primary function of sebaceous gland cells is the production and secretion of sebum, a complex mixture of lipids including triglycerides, wax esters, squalene, and metabolites of fat-soluble vitamins (such as vitamin E), as well as free fatty acids. The production process involves a unique form of programmed cell death called holocrine secretion. In this process, as sebaceous gland cells mature, they progressively accumulate lipid droplets, before ultimately disintegrating and releasing their lipid-rich contents into the gland's ductal system. +The sebum generated by these cells serves multiple purposes. It acts as a waterproofing agent, preventing excessive wetting or drying of the skin and averaging skin's water-holding capacity. Sebum also has antimicrobial properties, providing a natural defense barrier against certain bacterial and fungal species. Additionally, it contributes to the skin’s suppleness and prevents it from becoming brittle. An overproduction or imbalance of sebaceous gland cells can lead to common skin disorders, such as acne, seborrhea, or rosacea, illustrating their importance in skin health.") +AnnotationAssertion( "https://cellxgene.cziscience.com/cellguide/CL_2000021") +AnnotationAssertion(Annotation( "DOI:10.1016/j.peptides.2018.05.012") Annotation( "DOI:10.1126/science.aam5894") Annotation( "https://www.ncbi.nlm.nih.gov/books/NBK535355") Annotation( "https://www.ncbi.nlm.nih.gov/books/NBK572070/") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Ventricular cardiac muscle cells, or cardiomyocytes, are specialized cells found in the ventricular walls of the heart. They exhibit unique features, including centrally located nuclei, robust cytoskeletal structures, high mitochondria content, and intercalated discs, which contribute to their efficient pumping of blood throughout the body. +The main role of ventricular cardiac muscle cells is to coordinate contractions, enabling the heart to pump blood throughout the body. This is achieved through controlled ion movement across cell membranes, generating rhythmic electrical signals called action potentials. Intercalated discs between these cells aid synchronized contractions by allowing efficient signal spread through gap junctions. The high mitochondrial content ensures a constant energy supply for this ongoing contraction cycle. +Ventricular cardiac muscle cells contribute not only mechanically but also biochemically by secreting essential hormones like atrial natriuretic peptide and B-type natriuretic peptide for blood pressure regulation and cardiac remodeling. These cells exhibit low turnover under normal conditions, emphasizing their long-term stability, yet have limited regenerative capacity following cardiac injuries. Dysfunction in these cells can result in significant cardiac issues, including heart failure.") +AnnotationAssertion( "https://cellxgene.cziscience.com/cellguide/CL_2000046") +AnnotationAssertion(Annotation( "DOI:10.1007/s00018-019-03104-6") Annotation( "DOI:10.3389/fimmu.2020.00343") Annotation( "DOI:10.3390/nu15163564") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +The placental villous trophoblast, a highly specialized cell type crucial for placental development, plays a key role in facilitating exchanges between the maternal bloodstream and the developing fetus. +Structurally, placental villous trophoblasts are situated on the villous tree structures, forming an outer epithelial layer. Comprising two subtypes—proliferating cytotrophoblasts forming the inner layer and terminally differentiated syncytiotrophoblasts constituting the outer layer in contact with maternal blood—these cells define the placental architecture. +Functionally, placental villous trophoblasts play pivotal roles in forming and maintaining the placenta, ensuring the safe development of the fetus. Their primary function involves managing substance exchange between the mother and fetus, mediating the transfer of gases, nutrients, hormones, and waste materials to support optimal fetal growth. Additionally, these trophoblasts synthesize and release crucial hormones like human chorionic gonadotropin (hCG), which maintains the decidua and signals the mother's body to sustain pregnancy. Acting as a physical and immunological barrier, they protect the fetus from maternal immune cells and prevent the transmission of pathogens, contributing significantly to the success of pregnancy.") +AnnotationAssertion( "https://cellxgene.cziscience.com/cellguide/CL_2000060") +AnnotationAssertion(Annotation( "DOI:10.1002/(SICI)1097-0029(19980415)41:2<98::AID-JEMT2>3.0.CO;2-M") Annotation( "DOI:10.1111/joa.13709") Annotation( "DOI:10.3389/fncel.2015.00480") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. Hypendymal cells are secretory cells located between the ependymal layer and the posterior commissure, forming the hypendmal layer of the subcommissural organ (SCO), a highly conserved gland that is part of the circumventricular system within the brain. Hypendymal cells are bipolar cells with a thin apical pole and basal process. Most of the ultrastructural characteristics of these cells are similar to those described for the ependymal cells (which are arranged into another layer – the ependyma). However, ependymal cells release their secretion into the ventricular cerebrospinal fluid whereas hypendymal cells project processes to the local blood vessels and to the subarachnoidal space.") diff --git a/src/ontology/components/cellxgene_subset.owl b/src/ontology/components/cellxgene_subset.owl index ec40c578f..7c12f6d0f 100644 --- a/src/ontology/components/cellxgene_subset.owl +++ b/src/ontology/components/cellxgene_subset.owl @@ -7,8 +7,8 @@ Prefix(rdfs:=) Ontology( - -Annotation(owl:versionInfo "2025-01-06") + +Annotation(owl:versionInfo "2025-01-07") Declaration(Class()) Declaration(Class()) diff --git a/src/ontology/mirror/README.md b/src/ontology/mirror/README.md deleted file mode 100644 index 1db2fb47c..000000000 --- a/src/ontology/mirror/README.md +++ /dev/null @@ -1 +0,0 @@ -This folder is used by the release process to stage external ontologies diff --git a/src/ontology/reports/cl-base-diff.md b/src/ontology/reports/cl-base-diff.md index 5d76b1e39..06d5efb78 100644 --- a/src/ontology/reports/cl-base-diff.md +++ b/src/ontology/reports/cl-base-diff.md @@ -2,12 +2,12 @@ ## Left - Ontology IRI: `http://purl.obolibrary.org/obo/cl/cl-base.owl` -- Version IRI: `http://purl.obolibrary.org/obo/cl/cl-base/cl/releases/2024-08-16/cl-base.owl/cl/cl-base.owl` +- Version IRI: `http://purl.obolibrary.org/obo/cl/cl-base/cl/releases/2024-09-26/cl-base.owl/cl/cl-base.owl` - Loaded from: `file:/work/src/ontology/tmp/current-base-release.obo` ## Right - Ontology IRI: `http://purl.obolibrary.org/obo/cl/cl-base.owl` -- Version IRI: `http://purl.obolibrary.org/obo/cl/cl-base/cl/releases/2024-09-26/cl-base.owl/cl/cl-base.owl` +- Version IRI: `http://purl.obolibrary.org/obo/cl/cl-base/cl/releases/2025-01-08/cl-base.owl/cl/cl-base.owl` - Loaded from: `file:/work/src/ontology/../../cl-base.obo` ### Ontology imports @@ -16,5558 +16,11944 @@ ### Ontology annotations #### Removed -- [versionInfo](http://www.w3.org/2002/07/owl#versionInfo) "2024-08-16"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [versionInfo](http://www.w3.org/2002/07/owl#versionInfo) "2024-09-26"^^[string](http://www.w3.org/2001/XMLSchema#string) #### Added -- [versionInfo](http://www.w3.org/2002/07/owl#versionInfo) "2024-09-26"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [versionInfo](http://www.w3.org/2002/07/owl#versionInfo) "2025-01-08"^^[string](http://www.w3.org/2001/XMLSchema#string) -### B cell, CD19-positive `http://purl.obolibrary.org/obo/CL_0001201` +### A2 amacrine cell `http://purl.obolibrary.org/obo/CL_0004219` #### Removed -- [B cell, CD19-positive](http://purl.obolibrary.org/obo/CL_0001201) EquivalentTo [lymphocyte of B lineage, CD19-positive](http://purl.obolibrary.org/obo/CL_0001200) and ([RO_0002104](http://purl.obolibrary.org/obo/RO_0002104) some [PR_000001002](http://purl.obolibrary.org/obo/PR_000001002)) and ([RO_0002162](http://purl.obolibrary.org/obo/RO_0002162) some [NCBITaxon_40674](http://purl.obolibrary.org/obo/NCBITaxon_40674)) and ([RO_0002215](http://purl.obolibrary.org/obo/RO_0002215) some [GO_0019724](http://purl.obolibrary.org/obo/GO_0019724)) - -#### Added -- [B cell, CD19-positive](http://purl.obolibrary.org/obo/CL_0001201) EquivalentTo [lymphocyte of B lineage, CD19-positive](http://purl.obolibrary.org/obo/CL_0001200) and ([RO_0002104](http://purl.obolibrary.org/obo/RO_0002104) some [PR_000001002](http://purl.obolibrary.org/obo/PR_000001002)) and ([RO_0002215](http://purl.obolibrary.org/obo/RO_0002215) some [GO_0019724](http://purl.obolibrary.org/obo/GO_0019724)) +- [A2 amacrine cell](http://purl.obolibrary.org/obo/CL_0004219) [RO_0002175](http://purl.obolibrary.org/obo/RO_0002175) [NCBITaxon_9606](http://purl.obolibrary.org/obo/NCBITaxon_9606) +- [A2 amacrine cell](http://purl.obolibrary.org/obo/CL_0004219) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [human_reference_atlas](http://purl.obolibrary.org/obo/cl/cl-base#human_reference_atlas) -### BEST4+ colonocyte `http://purl.obolibrary.org/obo/CL_4047052` -#### Added -- [BEST4+ colonocyte](http://purl.obolibrary.org/obo/CL_4047052) [label](http://www.w3.org/2000/01/rdf-schema#label) "BEST4+ colonocyte"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [BEST4+ colonocyte](http://purl.obolibrary.org/obo/CL_4047052) [contributor](http://purl.org/dc/terms/contributor) [0009-0005-7919-4905](https://orcid.org/0009-0005-7919-4905) +### Axl+ dendritic cell, human `http://purl.obolibrary.org/obo/CL_0017009` +#### Removed +- [Axl+ dendritic cell, human](http://purl.obolibrary.org/obo/CL_0017009) [created by](http://www.geneontology.org/formats/oboInOwl#created_by) "http://orcid.org/0000-0003-2473-2313"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [BEST4+ colonocyte](http://purl.obolibrary.org/obo/CL_4047052) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "An enterocyte of the human colon expressing bestrophin-4 (BEST4) calcium-activated ion channels. These cells have a distinct transcriptomic profile compared to other enterocytes and are scattered through the colon epithelium."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:34497389"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [Axl+ dendritic cell, human](http://purl.obolibrary.org/obo/CL_0017009) [date](http://purl.org/dc/elements/1.1/date) "2022-08-25T14:18:37Z"^^[dateTime](http://www.w3.org/2001/XMLSchema#dateTime) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:24223998"^^[string](http://www.w3.org/2001/XMLSchema#string) +#### Added +- [Axl+ dendritic cell, human](http://purl.obolibrary.org/obo/CL_0017009) [date](http://purl.org/dc/terms/date) "2022-08-25T14:18:37Z"^^[dateTime](http://www.w3.org/2001/XMLSchema#dateTime) -- [BEST4+ colonocyte](http://purl.obolibrary.org/obo/CL_4047052) [id](http://www.geneontology.org/formats/oboInOwl#id) "CL:4047052"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [Axl+ dendritic cell, human](http://purl.obolibrary.org/obo/CL_0017009) [contributor](http://purl.org/dc/terms/contributor) [0000-0003-2473-2313](http://orcid.org/0000-0003-2473-2313) -- [BEST4+ colonocyte](http://purl.obolibrary.org/obo/CL_4047052) [date](http://purl.org/dc/terms/date) "2024-07-25T13:21:19Z"^^[dateTime](http://www.w3.org/2001/XMLSchema#dateTime) -- Class: [BEST4+ colonocyte](http://purl.obolibrary.org/obo/CL_4047052) +### B-lymphoblast `http://purl.obolibrary.org/obo/CL_0017006` +#### Removed +- [B-lymphoblast](http://purl.obolibrary.org/obo/CL_0017006) [created by](http://www.geneontology.org/formats/oboInOwl#created_by) "http://orcid.org/0000-0003-2473-2313"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [BEST4+ colonocyte](http://purl.obolibrary.org/obo/CL_4047052) EquivalentTo [enterocyte of colon](http://purl.obolibrary.org/obo/CL_1000347) and ([RO_0002292](http://purl.obolibrary.org/obo/RO_0002292) some [PR_Q8NFU0](http://purl.obolibrary.org/obo/PR_Q8NFU0)) +- [B-lymphoblast](http://purl.obolibrary.org/obo/CL_0017006) [date](http://purl.org/dc/elements/1.1/date) "2022-08-17T14:30:32Z"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [BEST4+ colonocyte](http://purl.obolibrary.org/obo/CL_4047052) SubClassOf [BEST4+ intestinal epithelial cell, human](http://purl.obolibrary.org/obo/CL_4030026) +#### Added +- [B-lymphoblast](http://purl.obolibrary.org/obo/CL_0017006) [date](http://purl.org/dc/terms/date) "2022-08-17T14:30:32Z"^^[dateTime](http://www.w3.org/2001/XMLSchema#dateTime) -- [BEST4+ colonocyte](http://purl.obolibrary.org/obo/CL_4047052) SubClassOf [enterocyte of colon](http://purl.obolibrary.org/obo/CL_1000347) +- [B-lymphoblast](http://purl.obolibrary.org/obo/CL_0017006) [contributor](http://purl.org/dc/terms/contributor) [0000-0003-2473-2313](http://orcid.org/0000-0003-2473-2313) -### BEST4+ intestinal epithelial cell, human `http://purl.obolibrary.org/obo/CL_4030026` +### BEST4+ enterocyte `http://purl.obolibrary.org/obo/CL_4030026` #### Removed -- [BEST4+ intestinal epithelial cell, human](http://purl.obolibrary.org/obo/CL_4030026) [label](http://www.w3.org/2000/01/rdf-schema#label) "BEST4+ intestinal epithelial cell, human"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [BEST4+ enterocyte](http://purl.obolibrary.org/obo/CL_4030026) [label](http://www.w3.org/2000/01/rdf-schema#label) "BEST4+ enteroycte"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [BEST4+ intestinal epithelial cell, human](http://purl.obolibrary.org/obo/CL_4030026) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "An absorptive epithelial cell of the human intestine expressing bestrophin-4 (BEST4) calcium-activated ion channels."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:35176508"^^[string](http://www.w3.org/2001/XMLSchema#string) - - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:24223998"^^[string](http://www.w3.org/2001/XMLSchema#string) - - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://orcid.org/0000-0002-7431-4139"^^[string](http://www.w3.org/2001/XMLSchema#string) +#### Added +- [BEST4+ enterocyte](http://purl.obolibrary.org/obo/CL_4030026) [label](http://www.w3.org/2000/01/rdf-schema#label) "BEST4+ enterocyte"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [BEST4+ intestinal epithelial cell, human](http://purl.obolibrary.org/obo/CL_4030026) SubClassOf [gut absorptive cell](http://purl.obolibrary.org/obo/CL_0000677) -- [BEST4+ intestinal epithelial cell, human](http://purl.obolibrary.org/obo/CL_4030026) SubClassOf [eukaryotic cell](http://purl.obolibrary.org/obo/CL_0000255) +### CAP motoneuron `http://purl.obolibrary.org/obo/CL_0000532` -- [BEST4+ intestinal epithelial cell, human](http://purl.obolibrary.org/obo/CL_4030026) SubClassOf [RO_0002160](http://purl.obolibrary.org/obo/RO_0002160) some [NCBITaxon_9606](http://purl.obolibrary.org/obo/NCBITaxon_9606) +#### Added +- [CAP motoneuron](http://purl.obolibrary.org/obo/CL_0000532) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "cap cell"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:17971221"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [BEST4+ intestinal epithelial cell, human](http://purl.obolibrary.org/obo/CL_4030026) SubClassOf [BFO_0000002](http://purl.obolibrary.org/obo/BFO_0000002) +- [CAP motoneuron](http://purl.obolibrary.org/obo/CL_0000532) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "caudal primary motor neuron"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:18077593"^^[string](http://www.w3.org/2001/XMLSchema#string) -#### Added -- [BEST4+ intestinal epithelial cell, human](http://purl.obolibrary.org/obo/CL_4030026) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "An enterocyte of the human intestine expressing bestrophin-4 (BEST4) calcium-activated ion channels."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:35176508"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [CAP motoneuron](http://purl.obolibrary.org/obo/CL_0000532) [has_exact_synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "CaP motorneuron"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:3746410"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:24223998"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [CAP motoneuron](http://purl.obolibrary.org/obo/CL_0000532) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A primary motor neuron with its soma in the caudal region of a spinal cord. The axon of this motoneuron exit the spinal cord from one single point and innervates the lateral surface of ventral axial muscles"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:35431796"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://orcid.org/0000-0002-7431-4139"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:17971221"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [BEST4+ intestinal epithelial cell, human](http://purl.obolibrary.org/obo/CL_4030026) [label](http://www.w3.org/2000/01/rdf-schema#label) "BEST4+ enteroycte"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [BEST4+ intestinal epithelial cell, human](http://purl.obolibrary.org/obo/CL_4030026) EquivalentTo [enterocyte](http://purl.obolibrary.org/obo/CL_0000584) and ([RO_0002292](http://purl.obolibrary.org/obo/RO_0002292) some [PR_Q8NFU0](http://purl.obolibrary.org/obo/PR_Q8NFU0)) +### CCL3-positive alveolar macrophage `http://purl.obolibrary.org/obo/CL_4033041` -- [BEST4+ intestinal epithelial cell, human](http://purl.obolibrary.org/obo/CL_4030026) SubClassOf [RO_0002162](http://purl.obolibrary.org/obo/RO_0002162) some [NCBITaxon_9606](http://purl.obolibrary.org/obo/NCBITaxon_9606) +#### Added +- [CCL3-positive alveolar macrophage](http://purl.obolibrary.org/obo/CL_4033041) [comment](http://www.w3.org/2000/01/rdf-schema#comment) "The marker set TNIP3, CXCL5 can identify the Human cell type CCL3-positive alveolar macrophage in the Lung with a confidence of 0.67 (NS-Forest FBeta value)."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://doi.org/10.5281/zenodo.11165918"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [BEST4+ intestinal epithelial cell, human](http://purl.obolibrary.org/obo/CL_4030026) SubClassOf [enterocyte](http://purl.obolibrary.org/obo/CL_0000584) +- [CCL3-positive alveolar macrophage](http://purl.obolibrary.org/obo/CL_4033041) SubClassOf [RO_0015004](http://purl.obolibrary.org/obo/RO_0015004) some [CLM_1000004](http://purl.obolibrary.org/obo/CLM_1000004) ### CD115-positive monocyte `http://purl.obolibrary.org/obo/CL_0001022` - -#### Added +#### Removed - [CD115-positive monocyte](http://purl.obolibrary.org/obo/CL_0001022) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) -### CD14-positive monocyte `http://purl.obolibrary.org/obo/CL_0001054` + +### CD115-positive monocyte OR common dendritic progenitor `http://purl.obolibrary.org/obo/CL_0001019` #### Added -- [CD14-positive monocyte](http://purl.obolibrary.org/obo/CL_0001054) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) +- [CD115-positive monocyte OR common dendritic progenitor](http://purl.obolibrary.org/obo/CL_0001019) SubClassOf [myeloid cell](http://purl.obolibrary.org/obo/CL_0000763) -### CD16-negative, CD56-bright natural killer cell, human `http://purl.obolibrary.org/obo/CL_0000938` +### CD117-positive common myeloid progenitor OR CD217-positive common lymphoid progenitor `http://purl.obolibrary.org/obo/CL_0001030` #### Added -- [CD16-negative, CD56-bright natural killer cell, human](http://purl.obolibrary.org/obo/CL_0000938) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) +- [CD117-positive common myeloid progenitor OR CD217-positive common lymphoid progenitor](http://purl.obolibrary.org/obo/CL_0001030) SubClassOf [progenitor cell](http://purl.obolibrary.org/obo/CL_0011026) -### CD16-positive, CD56-dim natural killer cell, human `http://purl.obolibrary.org/obo/CL_0000939` +### CD14-positive monocyte `http://purl.obolibrary.org/obo/CL_0001054` +#### Removed +- [CD14-positive monocyte](http://purl.obolibrary.org/obo/CL_0001054) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) -#### Added -- [CD16-positive, CD56-dim natural killer cell, human](http://purl.obolibrary.org/obo/CL_0000939) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) -### CD1c-positive myeloid dendritic cell `http://purl.obolibrary.org/obo/CL_0002399` +### CD141-positive myeloid dendritic cell `http://purl.obolibrary.org/obo/CL_0002394` #### Removed -- [CD1c-positive myeloid dendritic cell](http://purl.obolibrary.org/obo/CL_0002399) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A myeloid dendritic cell found in the blood that is CD1c-positive."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:20628149"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [CD141-positive myeloid dendritic cell](http://purl.obolibrary.org/obo/CL_0002394) [comment](http://www.w3.org/2000/01/rdf-schema#comment) "Markers are found in human cells. Normally they represent 3-5% of peripheral blood mDCs (human). These cells express high levels of CD283 (TLR3), are capable of producing IL-12p70 and IFN-beta upon stimulation, and inducing a TH1 response [PMCID:PMC2882828]. They are also Necl2-positive. May be human equivalent of murine CD8alpha-positive DCs."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:dsd"^^[string](http://www.w3.org/2001/XMLSchema#string) +#### Added +- [CD141-positive myeloid dendritic cell](http://purl.obolibrary.org/obo/CL_0002394) [comment](http://www.w3.org/2000/01/rdf-schema#comment) "Markers are found in human cells. Normally they represent 3-5% of peripheral blood mDCs (human). These cells express high levels of CD283 (TLR3), are capable of producing IL-12p70 and IFN-beta upon stimulation, and inducing a TH1 response [PMCID:PMC2882828]. They are also Necl2-positive. May be human equivalent of murine CD8-alpha-positive DCs."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:20204387"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:tfm"^^[string](http://www.w3.org/2001/XMLSchema#string) +### CD16-negative, CD56-bright natural killer cell, human `http://purl.obolibrary.org/obo/CL_0000938` +#### Removed +- [CD16-negative, CD56-bright natural killer cell, human](http://purl.obolibrary.org/obo/CL_0000938) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) -#### Added -- [CD1c-positive myeloid dendritic cell](http://purl.obolibrary.org/obo/CL_0002399) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A myeloid dendritic cell that is CD1c-positive."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:20628149"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:dsd"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:20204387"^^[string](http://www.w3.org/2001/XMLSchema#string) +### CD16-positive, CD56-dim natural killer cell, human `http://purl.obolibrary.org/obo/CL_0000939` +#### Removed +- [CD16-positive, CD56-dim natural killer cell, human](http://purl.obolibrary.org/obo/CL_0000939) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:tfm"^^[string](http://www.w3.org/2001/XMLSchema#string) ### CD25+ mast cell `http://purl.obolibrary.org/obo/CL_0011023` - -#### Added +#### Removed - [CD25+ mast cell](http://purl.obolibrary.org/obo/CL_0011023) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) -### CD27-high, CD11b-high natural killer cell, mouse `http://purl.obolibrary.org/obo/CL_0002347` -#### Added +### CD27-high, CD11b-high natural killer cell, mouse `http://purl.obolibrary.org/obo/CL_0002347` +#### Removed - [CD27-high, CD11b-high natural killer cell, mouse](http://purl.obolibrary.org/obo/CL_0002347) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) -### CD27-high, CD11b-low natural killer cell, mouse `http://purl.obolibrary.org/obo/CL_0002349` -#### Added +### CD27-high, CD11b-low natural killer cell, mouse `http://purl.obolibrary.org/obo/CL_0002349` +#### Removed - [CD27-high, CD11b-low natural killer cell, mouse](http://purl.obolibrary.org/obo/CL_0002349) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) -### CD27-low, CD11b-high natural killer cell, mouse `http://purl.obolibrary.org/obo/CL_0002348` -#### Added +### CD27-low, CD11b-high natural killer cell, mouse `http://purl.obolibrary.org/obo/CL_0002348` +#### Removed - [CD27-low, CD11b-high natural killer cell, mouse](http://purl.obolibrary.org/obo/CL_0002348) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) -### CD27-low, CD11b-low immature natural killer cell, mouse `http://purl.obolibrary.org/obo/CL_0002345` -#### Added +### CD27-low, CD11b-low immature natural killer cell, mouse `http://purl.obolibrary.org/obo/CL_0002345` +#### Removed - [CD27-low, CD11b-low immature natural killer cell, mouse](http://purl.obolibrary.org/obo/CL_0002345) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) -### CD34-negative, CD117-positive innate lymphoid cell, human `http://purl.obolibrary.org/obo/CL_0001072` -#### Added +### CD34-negative, CD117-positive innate lymphoid cell, human `http://purl.obolibrary.org/obo/CL_0001072` +#### Removed - [CD34-negative, CD117-positive innate lymphoid cell, human](http://purl.obolibrary.org/obo/CL_0001072) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) -### CD34-negative, CD41-positive, CD42-positive megakaryocyte cell `http://purl.obolibrary.org/obo/CL_0002026` -#### Added +### CD34-negative, CD41-positive, CD42-positive megakaryocyte cell `http://purl.obolibrary.org/obo/CL_0002026` +#### Removed - [CD34-negative, CD41-positive, CD42-positive megakaryocyte cell](http://purl.obolibrary.org/obo/CL_0002026) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) -### CD34-positive, CD38-negative hematopoietic stem cell `http://purl.obolibrary.org/obo/CL_0001024` -#### Added +### CD34-positive, CD38-negative hematopoietic stem cell `http://purl.obolibrary.org/obo/CL_0001024` +#### Removed - [CD34-positive, CD38-negative hematopoietic stem cell](http://purl.obolibrary.org/obo/CL_0001024) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) -### CD34-positive, CD38-positive common lymphoid progenitor `http://purl.obolibrary.org/obo/CL_0001021` -#### Added +### CD34-positive, CD38-positive common lymphoid progenitor `http://purl.obolibrary.org/obo/CL_0001021` +#### Removed - [CD34-positive, CD38-positive common lymphoid progenitor](http://purl.obolibrary.org/obo/CL_0001021) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) -### CD34-positive, CD38-positive megakaryocyte erythroid progenitor cell `http://purl.obolibrary.org/obo/CL_0002005` + +### CD34-positive, CD38-positive common myeloid progenitor OR CD34-positive, CD38-positive common lymphoid progenitor `http://purl.obolibrary.org/obo/CL_0000995` #### Added +- [CD34-positive, CD38-positive common myeloid progenitor OR CD34-positive, CD38-positive common lymphoid progenitor](http://purl.obolibrary.org/obo/CL_0000995) SubClassOf [progenitor cell](http://purl.obolibrary.org/obo/CL_0011026) + + +### CD34-positive, CD38-positive megakaryocyte erythroid progenitor cell `http://purl.obolibrary.org/obo/CL_0002005` +#### Removed - [CD34-positive, CD38-positive megakaryocyte erythroid progenitor cell](http://purl.obolibrary.org/obo/CL_0002005) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) -### CD34-positive, CD41-positive, CD42-negative megakaryocyte progenitor cell `http://purl.obolibrary.org/obo/CL_0002025` -#### Added +### CD34-positive, CD41-positive, CD42-negative megakaryocyte progenitor cell `http://purl.obolibrary.org/obo/CL_0002025` +#### Removed - [CD34-positive, CD41-positive, CD42-negative megakaryocyte progenitor cell](http://purl.obolibrary.org/obo/CL_0002025) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) -### CD34-positive, CD41-positive, CD42-positive megakaryocyte progenitor cell `http://purl.obolibrary.org/obo/CL_0002023` -#### Added +### CD34-positive, CD41-positive, CD42-positive megakaryocyte progenitor cell `http://purl.obolibrary.org/obo/CL_0002023` +#### Removed - [CD34-positive, CD41-positive, CD42-positive megakaryocyte progenitor cell](http://purl.obolibrary.org/obo/CL_0002023) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) -### CD34-positive, CD56-positive, CD117-positive common innate lymphoid precursor, human `http://purl.obolibrary.org/obo/CL_0001074` -#### Added +### CD34-positive, CD56-positive, CD117-positive common innate lymphoid precursor, human `http://purl.obolibrary.org/obo/CL_0001074` +#### Removed - [CD34-positive, CD56-positive, CD117-positive common innate lymphoid precursor, human](http://purl.obolibrary.org/obo/CL_0001074) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) -### CD4-positive, alpha-beta memory T cell, CD45RO-positive `http://purl.obolibrary.org/obo/CL_0001204` -#### Removed -- [CD4-positive, alpha-beta memory T cell, CD45RO-positive](http://purl.obolibrary.org/obo/CL_0001204) EquivalentTo [CD4-positive, alpha-beta memory T cell](http://purl.obolibrary.org/obo/CL_0000897) and ([lacks_plasma_membrane_part](http://purl.obolibrary.org/obo/CL_4030046) some [PR_000001380](http://purl.obolibrary.org/obo/PR_000001380)) and ([RO_0002104](http://purl.obolibrary.org/obo/RO_0002104) some [PR_000001017](http://purl.obolibrary.org/obo/PR_000001017)) and ([RO_0002104](http://purl.obolibrary.org/obo/RO_0002104) some [PR_000001869](http://purl.obolibrary.org/obo/PR_000001869)) and ([RO_0002160](http://purl.obolibrary.org/obo/RO_0002160) some [NCBITaxon_9606](http://purl.obolibrary.org/obo/NCBITaxon_9606)) and ([RO_0002353](http://purl.obolibrary.org/obo/RO_0002353) some [GO_0043379](http://purl.obolibrary.org/obo/GO_0043379)) and ([RO_0015015](http://purl.obolibrary.org/obo/RO_0015015) some [PR_000001307](http://purl.obolibrary.org/obo/PR_000001307)) and ([RO_0015015](http://purl.obolibrary.org/obo/RO_0015015) some [PR_000001381](http://purl.obolibrary.org/obo/PR_000001381)) -- [CD4-positive, alpha-beta memory T cell, CD45RO-positive](http://purl.obolibrary.org/obo/CL_0001204) SubClassOf [RO_0002160](http://purl.obolibrary.org/obo/RO_0002160) some [NCBITaxon_9606](http://purl.obolibrary.org/obo/NCBITaxon_9606) +### CD38-negative naive B cell `http://purl.obolibrary.org/obo/CL_0002102` #### Added -- [CD4-positive, alpha-beta memory T cell, CD45RO-positive](http://purl.obolibrary.org/obo/CL_0001204) EquivalentTo [CD4-positive, alpha-beta memory T cell](http://purl.obolibrary.org/obo/CL_0000897) and ([lacks_plasma_membrane_part](http://purl.obolibrary.org/obo/CL_4030046) some [PR_000001380](http://purl.obolibrary.org/obo/PR_000001380)) and ([RO_0002104](http://purl.obolibrary.org/obo/RO_0002104) some [PR_000001017](http://purl.obolibrary.org/obo/PR_000001017)) and ([RO_0002104](http://purl.obolibrary.org/obo/RO_0002104) some [PR_000001869](http://purl.obolibrary.org/obo/PR_000001869)) and ([RO_0002162](http://purl.obolibrary.org/obo/RO_0002162) some [NCBITaxon_9606](http://purl.obolibrary.org/obo/NCBITaxon_9606)) and ([RO_0002353](http://purl.obolibrary.org/obo/RO_0002353) some [GO_0043379](http://purl.obolibrary.org/obo/GO_0043379)) and ([RO_0015015](http://purl.obolibrary.org/obo/RO_0015015) some [PR_000001307](http://purl.obolibrary.org/obo/PR_000001307)) and ([RO_0015015](http://purl.obolibrary.org/obo/RO_0015015) some [PR_000001381](http://purl.obolibrary.org/obo/PR_000001381)) +- [CD38-negative naive B cell](http://purl.obolibrary.org/obo/CL_0002102) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl/cl-base#cellxgene_subset) -- [CD4-positive, alpha-beta memory T cell, CD45RO-positive](http://purl.obolibrary.org/obo/CL_0001204) SubClassOf [RO_0002162](http://purl.obolibrary.org/obo/RO_0002162) some [NCBITaxon_9606](http://purl.obolibrary.org/obo/NCBITaxon_9606) +### CD4-negative, CD8-alpha-negative, CD11b-positive dendritic cell `http://purl.obolibrary.org/obo/CL_0002454` +#### Removed +- [CD4-negative, CD8-alpha-negative, CD11b-positive dendritic cell](http://purl.obolibrary.org/obo/CL_0002454) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "Cd4-negative, CD8_alpha-negative, CD11b-positive dendritic cell is a conventional dendritic cell that is CD11b-positive, CD4-negative, CD8_alpha-negative and is CD205-positive."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:tfm"^^[string](http://www.w3.org/2001/XMLSchema#string) -### CD56-negative, CD161-positive immature natural killer cell, human `http://purl.obolibrary.org/obo/CL_0002344` + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "http://www.immgen.org/index_content.html"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [CD4-negative, CD8-alpha-negative, CD11b-positive dendritic cell](http://purl.obolibrary.org/obo/CL_0002454) [label](http://www.w3.org/2000/01/rdf-schema#label) "Cd4-negative, CD8_alpha-negative, CD11b-positive dendritic cell"^^[string](http://www.w3.org/2001/XMLSchema#string) #### Added -- [CD56-negative, CD161-positive immature natural killer cell, human](http://purl.obolibrary.org/obo/CL_0002344) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) +- [CD4-negative, CD8-alpha-negative, CD11b-positive dendritic cell](http://purl.obolibrary.org/obo/CL_0002454) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "CD4-negative, CD8-alpha-negative, CD11b-positive dendritic cell is a conventional dendritic cell that is CD11b-positive, CD4-negative, CD8-alpha-negative and is CD205-positive."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:tfm"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "http://www.immgen.org/index_content.html"^^[string](http://www.w3.org/2001/XMLSchema#string) -### CD56-positive, CD161-positive immature natural killer cell, human `http://purl.obolibrary.org/obo/CL_0002338` +- [CD4-negative, CD8-alpha-negative, CD11b-positive dendritic cell](http://purl.obolibrary.org/obo/CL_0002454) [label](http://www.w3.org/2000/01/rdf-schema#label) "CD4-negative, CD8-alpha-negative, CD11b-positive dendritic cell"^^[string](http://www.w3.org/2001/XMLSchema#string) -#### Added -- [CD56-positive, CD161-positive immature natural killer cell, human](http://purl.obolibrary.org/obo/CL_0002338) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) +### CD4-positive CD11b-positive dendritic cell `http://purl.obolibrary.org/obo/CL_0000999` +#### Removed +- [CD4-positive CD11b-positive dendritic cell](http://purl.obolibrary.org/obo/CL_0000999) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "CD8_alpha-negative CD11b-positive dendritic cell is a conventional dendritic cell that is CD11b-positive, CD4-positive and is CD205-negative and CD8_alpha-negative."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:amm"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMCID:PMC2346585"^^[string](http://www.w3.org/2001/XMLSchema#string) -### CD7-negative lymphoid progenitor cell `http://purl.obolibrary.org/obo/CL_0001027` + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GO_REF:0000031"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:tfm"^^[string](http://www.w3.org/2001/XMLSchema#string) #### Added -- [CD7-negative lymphoid progenitor cell](http://purl.obolibrary.org/obo/CL_0001027) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) +- [CD4-positive CD11b-positive dendritic cell](http://purl.obolibrary.org/obo/CL_0000999) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "CD8-alpha-negative CD11b-positive dendritic cell is a conventional dendritic cell that is CD11b-positive, CD4-positive and is CD205-negative and CD8-alpha-negative."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:amm"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMCID:PMC2346585"^^[string](http://www.w3.org/2001/XMLSchema#string) -### CD7-positive lymphoid progenitor cell `http://purl.obolibrary.org/obo/CL_0001028` + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GO_REF:0000031"^^[string](http://www.w3.org/2001/XMLSchema#string) -#### Added -- [CD7-positive lymphoid progenitor cell](http://purl.obolibrary.org/obo/CL_0001028) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:tfm"^^[string](http://www.w3.org/2001/XMLSchema#string) -### CD71-negative, GlyA-positive orthochromatic erythroblast `http://purl.obolibrary.org/obo/CL_0002018` +### CD56-negative, CD161-positive immature natural killer cell, human `http://purl.obolibrary.org/obo/CL_0002344` +#### Removed +- [CD56-negative, CD161-positive immature natural killer cell, human](http://purl.obolibrary.org/obo/CL_0002344) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) -#### Added -- [CD71-negative, GlyA-positive orthochromatic erythroblast](http://purl.obolibrary.org/obo/CL_0002018) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) -### CD8-positive, alpha-beta memory T cell, CD45RO-positive `http://purl.obolibrary.org/obo/CL_0001203` +### CD56-positive, CD161-positive immature natural killer cell, human `http://purl.obolibrary.org/obo/CL_0002338` #### Removed -- [CD8-positive, alpha-beta memory T cell, CD45RO-positive](http://purl.obolibrary.org/obo/CL_0001203) EquivalentTo [CD8-positive, alpha-beta memory T cell](http://purl.obolibrary.org/obo/CL_0000909) and ([lacks_plasma_membrane_part](http://purl.obolibrary.org/obo/CL_4030046) some [PR_000001380](http://purl.obolibrary.org/obo/PR_000001380)) and ([RO_0002104](http://purl.obolibrary.org/obo/RO_0002104) some [PR_000001017](http://purl.obolibrary.org/obo/PR_000001017)) and ([RO_0002104](http://purl.obolibrary.org/obo/RO_0002104) some [PR_000001869](http://purl.obolibrary.org/obo/PR_000001869)) and ([RO_0002160](http://purl.obolibrary.org/obo/RO_0002160) some [NCBITaxon_9606](http://purl.obolibrary.org/obo/NCBITaxon_9606)) and ([RO_0002353](http://purl.obolibrary.org/obo/RO_0002353) some [GO_0043379](http://purl.obolibrary.org/obo/GO_0043379)) and ([RO_0015015](http://purl.obolibrary.org/obo/RO_0015015) some [PR_000001307](http://purl.obolibrary.org/obo/PR_000001307)) and ([RO_0015015](http://purl.obolibrary.org/obo/RO_0015015) some [PR_000001381](http://purl.obolibrary.org/obo/PR_000001381)) +- [CD56-positive, CD161-positive immature natural killer cell, human](http://purl.obolibrary.org/obo/CL_0002338) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) + -- [CD8-positive, alpha-beta memory T cell, CD45RO-positive](http://purl.obolibrary.org/obo/CL_0001203) SubClassOf [RO_0002160](http://purl.obolibrary.org/obo/RO_0002160) some [NCBITaxon_9606](http://purl.obolibrary.org/obo/NCBITaxon_9606) + +### CD57-positive enterocyte `http://purl.obolibrary.org/obo/CL_4033092` #### Added -- [CD8-positive, alpha-beta memory T cell, CD45RO-positive](http://purl.obolibrary.org/obo/CL_0001203) EquivalentTo [CD8-positive, alpha-beta memory T cell](http://purl.obolibrary.org/obo/CL_0000909) and ([lacks_plasma_membrane_part](http://purl.obolibrary.org/obo/CL_4030046) some [PR_000001380](http://purl.obolibrary.org/obo/PR_000001380)) and ([RO_0002104](http://purl.obolibrary.org/obo/RO_0002104) some [PR_000001017](http://purl.obolibrary.org/obo/PR_000001017)) and ([RO_0002104](http://purl.obolibrary.org/obo/RO_0002104) some [PR_000001869](http://purl.obolibrary.org/obo/PR_000001869)) and ([RO_0002162](http://purl.obolibrary.org/obo/RO_0002162) some [NCBITaxon_9606](http://purl.obolibrary.org/obo/NCBITaxon_9606)) and ([RO_0002353](http://purl.obolibrary.org/obo/RO_0002353) some [GO_0043379](http://purl.obolibrary.org/obo/GO_0043379)) and ([RO_0015015](http://purl.obolibrary.org/obo/RO_0015015) some [PR_000001307](http://purl.obolibrary.org/obo/PR_000001307)) and ([RO_0015015](http://purl.obolibrary.org/obo/RO_0015015) some [PR_000001381](http://purl.obolibrary.org/obo/PR_000001381)) +- [CD57-positive enterocyte](http://purl.obolibrary.org/obo/CL_4033092) [label](http://www.w3.org/2000/01/rdf-schema#label) "CD57-positive enterocyte"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [CD8-positive, alpha-beta memory T cell, CD45RO-positive](http://purl.obolibrary.org/obo/CL_0001203) SubClassOf [RO_0002162](http://purl.obolibrary.org/obo/RO_0002162) some [NCBITaxon_9606](http://purl.obolibrary.org/obo/NCBITaxon_9606) +- [CD57-positive enterocyte](http://purl.obolibrary.org/obo/CL_4033092) [has_exact_synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "CD57+ enterocyte"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:37468586"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [CD57-positive enterocyte](http://purl.obolibrary.org/obo/CL_4033092) [contributor](http://purl.org/dc/terms/contributor) [0000-0001-6677-8489](https://orcid.org/0000-0001-6677-8489) -### CD9-positive, CD41-positive megakaryocyte cell `http://purl.obolibrary.org/obo/CL_0002027` +- [CD57-positive enterocyte](http://purl.obolibrary.org/obo/CL_4033092) [date](http://purl.org/dc/terms/date) "2024-12-06T14:32:49Z"^^[dateTime](http://www.w3.org/2001/XMLSchema#dateTime) -#### Added -- [CD9-positive, CD41-positive megakaryocyte cell](http://purl.obolibrary.org/obo/CL_0002027) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) +- [CD57-positive enterocyte](http://purl.obolibrary.org/obo/CL_4033092) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "An enterocyte that is part of a duodenal epithelium and expresses beta-1,3-glucuronyltransferase 1 (B3GAT1), also known as CD57 or HNK-1."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:37468586"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [CD57-positive enterocyte](http://purl.obolibrary.org/obo/CL_4033092) [contributor](http://purl.org/dc/terms/contributor) [0000-0001-9961-7673](https://orcid.org/0000-0001-9961-7673) -### DN1 thymic pro-T cell `http://purl.obolibrary.org/obo/CL_0000894` +- [CD57-positive enterocyte](http://purl.obolibrary.org/obo/CL_4033092) [contributor](http://purl.org/dc/terms/contributor) [0000-0001-7655-4833](https://orcid.org/0000-0001-7655-4833) -#### Added -- [DN1 thymic pro-T cell](http://purl.obolibrary.org/obo/CL_0000894) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) +- [CD57-positive enterocyte](http://purl.obolibrary.org/obo/CL_4033092) [id](http://www.geneontology.org/formats/oboInOwl#id) "CL:4033092"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [CD57-positive enterocyte](http://purl.obolibrary.org/obo/CL_4033092) [comment](http://www.w3.org/2000/01/rdf-schema#comment) "While CD57 is traditionally associated with immune cells (e.g., NK cells), its expression on enterocytes marks unique epithelial subsets with specific functions or maturation states. These cells are specially enriched in areas of the duodenum within submucosal glands."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:37468586"^^[string](http://www.w3.org/2001/XMLSchema#string) -### DN2 thymocyte `http://purl.obolibrary.org/obo/CL_0000806` +- Class: [CD57-positive enterocyte](http://purl.obolibrary.org/obo/CL_4033092) -#### Added -- [DN2 thymocyte](http://purl.obolibrary.org/obo/CL_0000806) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) +- [CD57-positive enterocyte](http://purl.obolibrary.org/obo/CL_4033092) EquivalentTo [enterocyte](http://purl.obolibrary.org/obo/CL_0000584) and ([BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0008346](http://purl.obolibrary.org/obo/UBERON_0008346)) and ([RO_0002292](http://purl.obolibrary.org/obo/RO_0002292) some [PR_000001440](http://purl.obolibrary.org/obo/PR_000001440)) +- [CD57-positive enterocyte](http://purl.obolibrary.org/obo/CL_4033092) SubClassOf [RO_0002292](http://purl.obolibrary.org/obo/RO_0002292) some [PR_000001440](http://purl.obolibrary.org/obo/PR_000001440) -### DN3 thymocyte `http://purl.obolibrary.org/obo/CL_0000807` +- [CD57-positive enterocyte](http://purl.obolibrary.org/obo/CL_4033092) SubClassOf [BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0008346](http://purl.obolibrary.org/obo/UBERON_0008346) -#### Added -- [DN3 thymocyte](http://purl.obolibrary.org/obo/CL_0000807) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) +- [CD57-positive enterocyte](http://purl.obolibrary.org/obo/CL_4033092) SubClassOf [enterocyte of epithelium of intestinal villus](http://purl.obolibrary.org/obo/CL_1000335) -### DN4 thymocyte `http://purl.obolibrary.org/obo/CL_0000808` +### CD7-negative lymphoid progenitor OR granulocyte monocyte progenitor `http://purl.obolibrary.org/obo/CL_0001012` #### Added -- [DN4 thymocyte](http://purl.obolibrary.org/obo/CL_0000808) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) +- [CD7-negative lymphoid progenitor OR granulocyte monocyte progenitor](http://purl.obolibrary.org/obo/CL_0001012) SubClassOf [progenitor cell](http://purl.obolibrary.org/obo/CL_0011026) -### Dx5-negative, NK1.1-positive immature natural killer cell, mouse `http://purl.obolibrary.org/obo/CL_0002346` +### CD7-negative lymphoid progenitor cell `http://purl.obolibrary.org/obo/CL_0001027` +#### Removed +- [CD7-negative lymphoid progenitor cell](http://purl.obolibrary.org/obo/CL_0001027) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) -#### Added -- [Dx5-negative, NK1.1-positive immature natural killer cell, mouse](http://purl.obolibrary.org/obo/CL_0002346) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) -### Eumycetozoan cell `http://purl.obolibrary.org/obo/CL_0000257` +### CD7-positive lymphoid progenitor cell `http://purl.obolibrary.org/obo/CL_0001028` #### Removed -- [Eumycetozoan cell](http://purl.obolibrary.org/obo/CL_0000257) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "Any cell that only exists in Eumycetozoa."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBC:Autogenerated"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [CD7-positive lymphoid progenitor cell](http://purl.obolibrary.org/obo/CL_0001028) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) -- [Eumycetozoan cell](http://purl.obolibrary.org/obo/CL_0000257) EquivalentTo [cell](http://purl.obolibrary.org/obo/CL_0000000) and ([RO_0002160](http://purl.obolibrary.org/obo/RO_0002160) some [NCBITaxon_142796](http://purl.obolibrary.org/obo/NCBITaxon_142796)) -- [Eumycetozoan cell](http://purl.obolibrary.org/obo/CL_0000257) SubClassOf [RO_0002160](http://purl.obolibrary.org/obo/RO_0002160) some [NCBITaxon_142796](http://purl.obolibrary.org/obo/NCBITaxon_142796) -#### Added -- [Eumycetozoan cell](http://purl.obolibrary.org/obo/CL_0000257) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "Any cell that in taxon some Eumycetozoa."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBC:Autogenerated"^^[string](http://www.w3.org/2001/XMLSchema#string) +### CD71-negative, GlyA-positive orthochromatic erythroblast `http://purl.obolibrary.org/obo/CL_0002018` +#### Removed +- [CD71-negative, GlyA-positive orthochromatic erythroblast](http://purl.obolibrary.org/obo/CL_0002018) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) + -- [Eumycetozoan cell](http://purl.obolibrary.org/obo/CL_0000257) EquivalentTo [cell](http://purl.obolibrary.org/obo/CL_0000000) and ([RO_0002162](http://purl.obolibrary.org/obo/RO_0002162) some [NCBITaxon_142796](http://purl.obolibrary.org/obo/NCBITaxon_142796)) -- [Eumycetozoan cell](http://purl.obolibrary.org/obo/CL_0000257) SubClassOf [RO_0002162](http://purl.obolibrary.org/obo/RO_0002162) some [NCBITaxon_142796](http://purl.obolibrary.org/obo/NCBITaxon_142796) +### CD8-alpha-low Langerhans cell `http://purl.obolibrary.org/obo/CL_0001015` +#### Removed +- [CD8-alpha-low Langerhans cell](http://purl.obolibrary.org/obo/CL_0001015) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "CD8_alpha-low Langerhans cell is a Langerhans cell that is CD205-high and is CD8_alpha-low."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:amm"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMCID:PMC2346585"^^[string](http://www.w3.org/2001/XMLSchema#string) -### GABAergic interneuron of the anterior substantia nigra pars reticulata `http://purl.obolibrary.org/obo/CL_4042026` + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GO_REF:0000031"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [CD8-alpha-low Langerhans cell](http://purl.obolibrary.org/obo/CL_0001015) [label](http://www.w3.org/2000/01/rdf-schema#label) "CD8_alpha-low Langerhans cell"^^[string](http://www.w3.org/2001/XMLSchema#string) #### Added -- [GABAergic interneuron of the anterior substantia nigra pars reticulata](http://purl.obolibrary.org/obo/CL_4042026) [date](http://purl.org/dc/terms/date) "2024-09-23T13:56:01Z"^^[dateTime](http://www.w3.org/2001/XMLSchema#dateTime) +- [CD8-alpha-low Langerhans cell](http://purl.obolibrary.org/obo/CL_0001015) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "CD8-alpha-low Langerhans cell is a Langerhans cell that is CD205-high and is CD8-alpha-low."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:amm"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [GABAergic interneuron of the anterior substantia nigra pars reticulata](http://purl.obolibrary.org/obo/CL_4042026) [label](http://www.w3.org/2000/01/rdf-schema#label) "GABAergic interneuron of the anterior substantia nigra pars reticulata"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMCID:PMC2346585"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GO_REF:0000031"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [CD8-alpha-low Langerhans cell](http://purl.obolibrary.org/obo/CL_0001015) [label](http://www.w3.org/2000/01/rdf-schema#label) "CD8-alpha-low Langerhans cell"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [GABAergic interneuron of the anterior substantia nigra pars reticulata](http://purl.obolibrary.org/obo/CL_4042026) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "aSNpr"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003000](http://purl.obolibrary.org/obo/OMO_0003000) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:36148148"^^[string](http://www.w3.org/2001/XMLSchema#string) +### CD8-alpha-negative CD11b-negative dendritic cell `http://purl.obolibrary.org/obo/CL_0000998` +#### Removed +- [CD8-alpha-negative CD11b-negative dendritic cell](http://purl.obolibrary.org/obo/CL_0000998) [label](http://www.w3.org/2000/01/rdf-schema#label) "CD8_alpha-negative CD11b-negative dendritic cell"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [GABAergic interneuron of the anterior substantia nigra pars reticulata](http://purl.obolibrary.org/obo/CL_4042026) [id](http://www.geneontology.org/formats/oboInOwl#id) "CL:4042026"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [CD8-alpha-negative CD11b-negative dendritic cell](http://purl.obolibrary.org/obo/CL_0000998) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "CD8_alpha-negative CD11b-negative dendritic cell is a conventional dendritic cell that is CD11b-negative, CD4-negative CD8_alpha-negative and is CD205-positive. This cell is able to cross- present antigen to CD8-alpha-positive T cells."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:amm"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [GABAergic interneuron of the anterior substantia nigra pars reticulata](http://purl.obolibrary.org/obo/CL_4042026) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A GABAergic interneuron that has its soma in the anterior section of the substantia nigra pars reticulata. This GABAergic interneuron is characterized by the expression of Six3 and Foxp1 and it develops from Nkx6-2 expressing neuronal progenitors in the ventrolateral midbrain-diencephalon region."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:36148148"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMCID:PMC2346585"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [GABAergic interneuron of the anterior substantia nigra pars reticulata](http://purl.obolibrary.org/obo/CL_4042026) [contributor](http://purl.org/dc/terms/contributor) [0000-0002-0098-8958](https://orcid.org/0000-0002-0098-8958) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GO_REF:0000031"^^[string](http://www.w3.org/2001/XMLSchema#string) -- Class: [GABAergic interneuron of the anterior substantia nigra pars reticulata](http://purl.obolibrary.org/obo/CL_4042026) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "http://www.immgen.org/index_content.html"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [GABAergic interneuron of the anterior substantia nigra pars reticulata](http://purl.obolibrary.org/obo/CL_4042026) SubClassOf [RO_0002292](http://purl.obolibrary.org/obo/RO_0002292) some [PR_000014898](http://purl.obolibrary.org/obo/PR_000014898) +#### Added +- [CD8-alpha-negative CD11b-negative dendritic cell](http://purl.obolibrary.org/obo/CL_0000998) [label](http://www.w3.org/2000/01/rdf-schema#label) "CD8-alpha-negative CD11b-negative dendritic cell"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [GABAergic interneuron of the anterior substantia nigra pars reticulata](http://purl.obolibrary.org/obo/CL_4042026) SubClassOf [RO_0002292](http://purl.obolibrary.org/obo/RO_0002292) some [PR_000007643](http://purl.obolibrary.org/obo/PR_000007643) +- [CD8-alpha-negative CD11b-negative dendritic cell](http://purl.obolibrary.org/obo/CL_0000998) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "CD8-alpha-negative CD11b-negative dendritic cell is a conventional dendritic cell that is CD11b-negative, CD4-negative CD8-alpha-negative and is CD205-positive. This cell is able to cross- present antigen to CD8-alpha-positive T cells."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:amm"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [GABAergic interneuron of the anterior substantia nigra pars reticulata](http://purl.obolibrary.org/obo/CL_4042026) SubClassOf [RO_0002292](http://purl.obolibrary.org/obo/RO_0002292) some [PR_000013047](http://purl.obolibrary.org/obo/PR_000013047) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMCID:PMC2346585"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [GABAergic interneuron of the anterior substantia nigra pars reticulata](http://purl.obolibrary.org/obo/CL_4042026) SubClassOf [neuron of the substantia nigra](http://purl.obolibrary.org/obo/CL_0002614) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GO_REF:0000031"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "http://www.immgen.org/index_content.html"^^[string](http://www.w3.org/2001/XMLSchema#string) -### GABAergic interneuron of the posterior substantia nigra pars reticulata `http://purl.obolibrary.org/obo/CL_4042027` -#### Added -- [GABAergic interneuron of the posterior substantia nigra pars reticulata](http://purl.obolibrary.org/obo/CL_4042027) [id](http://www.geneontology.org/formats/oboInOwl#id) "CL:4042027"^^[string](http://www.w3.org/2001/XMLSchema#string) +### CD8-alpha-negative plasmacytoid dendritic cell `http://purl.obolibrary.org/obo/CL_0002455` +#### Removed +- [CD8-alpha-negative plasmacytoid dendritic cell](http://purl.obolibrary.org/obo/CL_0002455) [label](http://www.w3.org/2000/01/rdf-schema#label) "CD8_alpha-negative plasmacytoid dendritic cell"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [GABAergic interneuron of the posterior substantia nigra pars reticulata](http://purl.obolibrary.org/obo/CL_4042027) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A GABAergic interneuron that has its soma in the posterior section of the substantia nigra pars reticulata. This GABAergic interneuron is characterised by the expression of the transcription factors Pax5, Ctip2 and Pou6f2 and it develops from the ventrolateral r1 neuroepithelium expresing NKX61."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:36148148"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [CD8-alpha-negative plasmacytoid dendritic cell](http://purl.obolibrary.org/obo/CL_0002455) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A CD11c-low plasmacytoid dendritic cell that is CD8alpha-negative and CD4-positive."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:tfm"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [GABAergic interneuron of the posterior substantia nigra pars reticulata](http://purl.obolibrary.org/obo/CL_4042027) [contributor](http://purl.org/dc/terms/contributor) [0000-0002-0098-8958](https://orcid.org/0000-0002-0098-8958) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "http://www.immgen.org/index_content.html"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [GABAergic interneuron of the posterior substantia nigra pars reticulata](http://purl.obolibrary.org/obo/CL_4042027) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "pSNpr"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:36148148"^^[string](http://www.w3.org/2001/XMLSchema#string) +#### Added +- [CD8-alpha-negative plasmacytoid dendritic cell](http://purl.obolibrary.org/obo/CL_0002455) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A CD11c-low plasmacytoid dendritic cell that is CD8-alpha-negative and CD4-positive."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:tfm"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [GABAergic interneuron of the posterior substantia nigra pars reticulata](http://purl.obolibrary.org/obo/CL_4042027) [date](http://purl.org/dc/terms/date) "2024-09-23T14:49:11Z"^^[dateTime](http://www.w3.org/2001/XMLSchema#dateTime) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "http://www.immgen.org/index_content.html"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [GABAergic interneuron of the posterior substantia nigra pars reticulata](http://purl.obolibrary.org/obo/CL_4042027) [label](http://www.w3.org/2000/01/rdf-schema#label) "GABAergic interneuron of the posterior substantia nigra pars reticulata"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [CD8-alpha-negative plasmacytoid dendritic cell](http://purl.obolibrary.org/obo/CL_0002455) [label](http://www.w3.org/2000/01/rdf-schema#label) "CD8-alpha-negative plasmacytoid dendritic cell"^^[string](http://www.w3.org/2001/XMLSchema#string) -- Class: [GABAergic interneuron of the posterior substantia nigra pars reticulata](http://purl.obolibrary.org/obo/CL_4042027) -- [GABAergic interneuron of the posterior substantia nigra pars reticulata](http://purl.obolibrary.org/obo/CL_4042027) SubClassOf [neuron of the substantia nigra](http://purl.obolibrary.org/obo/CL_0002614) +### CD8-alpha-negative thymic conventional dendritic cell `http://purl.obolibrary.org/obo/CL_0002460` +#### Removed +- [CD8-alpha-negative thymic conventional dendritic cell](http://purl.obolibrary.org/obo/CL_0002460) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A conventional thymic dendritic cell that is CD8alpha-negative."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:19273629"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [GABAergic interneuron of the posterior substantia nigra pars reticulata](http://purl.obolibrary.org/obo/CL_4042027) SubClassOf [RO_0002292](http://purl.obolibrary.org/obo/RO_0002292) some [PR_000001903](http://purl.obolibrary.org/obo/PR_000001903) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:tfm"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "http://www.immgen.org/index_content.html"^^[string](http://www.w3.org/2001/XMLSchema#string) -### GO_0000768 `http://purl.obolibrary.org/obo/GO_0000768` +- [CD8-alpha-negative thymic conventional dendritic cell](http://purl.obolibrary.org/obo/CL_0002460) [label](http://www.w3.org/2000/01/rdf-schema#label) "CD8alpha-negative thymic conventional dendritic cell"^^[string](http://www.w3.org/2001/XMLSchema#string) #### Added -- Class: [GO_0000768](http://purl.obolibrary.org/obo/GO_0000768) +- [CD8-alpha-negative thymic conventional dendritic cell](http://purl.obolibrary.org/obo/CL_0002460) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A conventional thymic dendritic cell that is CD8-alpha-negative."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:19273629"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:tfm"^^[string](http://www.w3.org/2001/XMLSchema#string) -### GO_0036376 `http://purl.obolibrary.org/obo/GO_0036376` + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "http://www.immgen.org/index_content.html"^^[string](http://www.w3.org/2001/XMLSchema#string) -#### Added -- Class: [GO_0036376](http://purl.obolibrary.org/obo/GO_0036376) +- [CD8-alpha-negative thymic conventional dendritic cell](http://purl.obolibrary.org/obo/CL_0002460) [label](http://www.w3.org/2000/01/rdf-schema#label) "CD8-alpha-negative thymic conventional dendritic cell"^^[string](http://www.w3.org/2001/XMLSchema#string) -### GO_0050962 `http://purl.obolibrary.org/obo/GO_0050962` +### CD8-alpha-positive CD11b-negative dendritic cell `http://purl.obolibrary.org/obo/CL_0001000` #### Removed -- Class: [GO_0050962](http://purl.obolibrary.org/obo/GO_0050962) +- [CD8-alpha-positive CD11b-negative dendritic cell](http://purl.obolibrary.org/obo/CL_0001000) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "CD8_alpha-positive CD11b-negative dendritic cell is a conventional dendritic cell that is CD11b-negative, CD4-negative and is CD205-positive and CD8_alpha-positive."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:amm"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMCID:PMC2346585"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GO_REF:0000031"^^[string](http://www.w3.org/2001/XMLSchema#string) -### GO_1990573 `http://purl.obolibrary.org/obo/GO_1990573` + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:tfm"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [CD8-alpha-positive CD11b-negative dendritic cell](http://purl.obolibrary.org/obo/CL_0001000) [label](http://www.w3.org/2000/01/rdf-schema#label) "CD8_alpha-positive CD11b-negative dendritic cell"^^[string](http://www.w3.org/2001/XMLSchema#string) #### Added -- Class: [GO_1990573](http://purl.obolibrary.org/obo/GO_1990573) +- [CD8-alpha-positive CD11b-negative dendritic cell](http://purl.obolibrary.org/obo/CL_0001000) [label](http://www.w3.org/2000/01/rdf-schema#label) "CD8-alpha-positive CD11b-negative dendritic cell"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [CD8-alpha-positive CD11b-negative dendritic cell](http://purl.obolibrary.org/obo/CL_0001000) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "CD8-alpha-positive CD11b-negative dendritic cell is a conventional dendritic cell that is CD11b-negative, CD4-negative and is CD205-positive and CD8-alpha-positive."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:amm"^^[string](http://www.w3.org/2001/XMLSchema#string) -### GlyA-positive erythrocyte `http://purl.obolibrary.org/obo/CL_0002021` + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMCID:PMC2346585"^^[string](http://www.w3.org/2001/XMLSchema#string) -#### Added -- [GlyA-positive erythrocyte](http://purl.obolibrary.org/obo/CL_0002021) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GO_REF:0000031"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:tfm"^^[string](http://www.w3.org/2001/XMLSchema#string) -### ILC1, human `http://purl.obolibrary.org/obo/CL_0001077` -#### Added -- [ILC1, human](http://purl.obolibrary.org/obo/CL_0001077) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) +### CD8-alpha-positive plasmacytoid dendritic cell `http://purl.obolibrary.org/obo/CL_0002456` +#### Removed +- [CD8-alpha-positive plasmacytoid dendritic cell](http://purl.obolibrary.org/obo/CL_0002456) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A CD11c-low plasmacytoid dendritic cell that is CD8alpha-positive and CD4-positive."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:tfm"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "http://www.immgen.org/index_content.html"^^[string](http://www.w3.org/2001/XMLSchema#string) -### Kit and Sca1-positive hematopoietic stem cell `http://purl.obolibrary.org/obo/CL_0001008` +- [CD8-alpha-positive plasmacytoid dendritic cell](http://purl.obolibrary.org/obo/CL_0002456) [label](http://www.w3.org/2000/01/rdf-schema#label) "CD8_alpha-positive plasmacytoid dendritic cell"^^[string](http://www.w3.org/2001/XMLSchema#string) #### Added -- [Kit and Sca1-positive hematopoietic stem cell](http://purl.obolibrary.org/obo/CL_0001008) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) +- [CD8-alpha-positive plasmacytoid dendritic cell](http://purl.obolibrary.org/obo/CL_0002456) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A CD11c-low plasmacytoid dendritic cell that is CD8-alpha-positive and CD4-positive."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:tfm"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "http://www.immgen.org/index_content.html"^^[string](http://www.w3.org/2001/XMLSchema#string) -### Kit-negative, Ly-76 high orthochromatophilic erythroblasts `http://purl.obolibrary.org/obo/CL_0002017` +- [CD8-alpha-positive plasmacytoid dendritic cell](http://purl.obolibrary.org/obo/CL_0002456) [label](http://www.w3.org/2000/01/rdf-schema#label) "CD8-alpha-positive plasmacytoid dendritic cell"^^[string](http://www.w3.org/2001/XMLSchema#string) -#### Added -- [Kit-negative, Ly-76 high orthochromatophilic erythroblasts](http://purl.obolibrary.org/obo/CL_0002017) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) +### CD8-alpha-positive thymic conventional dendritic cell `http://purl.obolibrary.org/obo/CL_0002059` +#### Removed +- [CD8-alpha-positive thymic conventional dendritic cell](http://purl.obolibrary.org/obo/CL_0002059) [label](http://www.w3.org/2000/01/rdf-schema#label) "CD8alpha-positive thymic conventional dendritic cell"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [CD8-alpha-positive thymic conventional dendritic cell](http://purl.obolibrary.org/obo/CL_0002059) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A conventional thymic dendritic cell that is CD8alpha-positive."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:19273629"^^[string](http://www.w3.org/2001/XMLSchema#string) -### Kit-positive macrophage dendritic cell progenitor `http://purl.obolibrary.org/obo/CL_0002011` + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:tfm"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "http://www.immgen.org/index_content.html"^^[string](http://www.w3.org/2001/XMLSchema#string) #### Added -- [Kit-positive macrophage dendritic cell progenitor](http://purl.obolibrary.org/obo/CL_0002011) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) +- [CD8-alpha-positive thymic conventional dendritic cell](http://purl.obolibrary.org/obo/CL_0002059) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A conventional thymic dendritic cell that is CD8-alpha-positive."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:19273629"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:tfm"^^[string](http://www.w3.org/2001/XMLSchema#string) -### Kit-positive megakaryocyte progenitor cell `http://purl.obolibrary.org/obo/CL_0002024` + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "http://www.immgen.org/index_content.html"^^[string](http://www.w3.org/2001/XMLSchema#string) -#### Added -- [Kit-positive megakaryocyte progenitor cell](http://purl.obolibrary.org/obo/CL_0002024) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) +- [CD8-alpha-positive thymic conventional dendritic cell](http://purl.obolibrary.org/obo/CL_0002059) [label](http://www.w3.org/2000/01/rdf-schema#label) "CD8-alpha-positive thymic conventional dendritic cell"^^[string](http://www.w3.org/2001/XMLSchema#string) -### Kit-positive, CD34-negative megakaryocyte erythroid progenitor cell `http://purl.obolibrary.org/obo/CL_0002006` +### CD9-positive, CD41-positive megakaryocyte cell `http://purl.obolibrary.org/obo/CL_0002027` +#### Removed +- [CD9-positive, CD41-positive megakaryocyte cell](http://purl.obolibrary.org/obo/CL_0002027) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) -#### Added -- [Kit-positive, CD34-negative megakaryocyte erythroid progenitor cell](http://purl.obolibrary.org/obo/CL_0002006) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) -### Kit-positive, Sca1-positive common lymphoid progenitor `http://purl.obolibrary.org/obo/CL_0001025` +### CGRP-expressing neuron `http://purl.obolibrary.org/obo/CL_4042034` #### Added -- [Kit-positive, Sca1-positive common lymphoid progenitor](http://purl.obolibrary.org/obo/CL_0001025) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) +- [CGRP-expressing neuron](http://purl.obolibrary.org/obo/CL_4042034) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "CGRP-positive neuron"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:34061020"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [CGRP-expressing neuron](http://purl.obolibrary.org/obo/CL_4042034) [id](http://www.geneontology.org/formats/oboInOwl#id) "CL:4042034"^^[string](http://www.w3.org/2001/XMLSchema#string) -### Kupffer cell `http://purl.obolibrary.org/obo/CL_0000091` +- [CGRP-expressing neuron](http://purl.obolibrary.org/obo/CL_4042034) [date](http://purl.org/dc/terms/date) "2024-10-30T15:35:08Z"^^[dateTime](http://www.w3.org/2001/XMLSchema#dateTime) -#### Added -- [Kupffer cell](http://purl.obolibrary.org/obo/CL_0000091) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://cellxgene.cziscience.com/cellguide/CL_0000091"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [CGRP-expressing neuron](http://purl.obolibrary.org/obo/CL_4042034) [contributor](http://purl.org/dc/terms/contributor) [0000-0002-0098-8958](https://orcid.org/0000-0002-0098-8958) -- [Kupffer cell](http://purl.obolibrary.org/obo/CL_0000091) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. +- [CGRP-expressing neuron](http://purl.obolibrary.org/obo/CL_4042034) [label](http://www.w3.org/2000/01/rdf-schema#label) "CGRP-expressing neuron"^^[string](http://www.w3.org/2001/XMLSchema#string) -Kupffer cells are tissue-resident macrophages located in the liver. They are an integral part of the mononuclear phagocyte system and are responsible for the phagocytosis of dead or dying cells, microbes, and other foreign substances. Kupffer cells account for approximately 80-90% of tissue-resident macrophages in the body. They are found within the lumen of liver sinusoids and interface with microbial populations and products. -The primary role of Kupffer cells is to maintain homeostasis in the liver. They continuously filter and cleanse the blood that flows through the liver, removing pathogens, endotoxins, particulate matter, aged and dysfunctional red blood cells, and miscellaneous waste products. These cells also play an important role in maintaining iron homeostasis. During the process of phagocytosis, Kupffer cells recycle iron from degraded red blood cells, which is then utilized in the formation of new erythrocytes. -Kupffer cells also play key roles in various immune responses and inflammatory processes. They secrete various types of cytokines and chemokines, which contribute to the activation and mobilization of other immune cells. They can also produce reactive oxygen species and nitric oxide, which have microbicidal actions. Although their activity is essential for host defense, excessive or prolonged activation of Kupffer cells may contribute to hepatic injury, inflammation, and fibrosis."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1038/nri.2017.11"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [CGRP-expressing neuron](http://purl.obolibrary.org/obo/CL_4042034) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "CGRP-expressing interneuron"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:34061020"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1007/978-1-4939-1311-4_10"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [CGRP-expressing neuron](http://purl.obolibrary.org/obo/CL_4042034) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "An interneuron neuron characterized by the expression of calcitonin gene-related peptide (CGRP), a 37-amino acid neuropeptide. This neuron type is involved in nociception and pain modulation by facilitating the transmission of nociceptive signals from peripheral sensory nerve endings to central nervous system structures. This neuron type is found in the dorsal root ganglia (DRG) and trigeminal ganglion, and the spinal cord dorsal horn."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:34061020"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1111/j.1478-3231.2006.01342.x"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [CGRP-expressing neuron](http://purl.obolibrary.org/obo/CL_4042034) [has_exact_synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "Calcitonin gene-related peptide neuron"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:34061020"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1002/cphy.c120026"^^[string](http://www.w3.org/2001/XMLSchema#string) +- Class: [CGRP-expressing neuron](http://purl.obolibrary.org/obo/CL_4042034) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1016/j.immuni.2022.08.002"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [CGRP-expressing neuron](http://purl.obolibrary.org/obo/CL_4042034) SubClassOf [central nervous system neuron](http://purl.obolibrary.org/obo/CL_2000029) -- [Kupffer cell](http://purl.obolibrary.org/obo/CL_0000091) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) +- [CGRP-expressing neuron](http://purl.obolibrary.org/obo/CL_4042034) SubClassOf [afferent neuron](http://purl.obolibrary.org/obo/CL_0000526) -### L cone cell `http://purl.obolibrary.org/obo/CL_0003048` +### CLM_1000001 `http://purl.obolibrary.org/obo/CLM_1000001` #### Added -- [L cone cell](http://purl.obolibrary.org/obo/CL_0003048) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) +- Class: [CLM_1000001](http://purl.obolibrary.org/obo/CLM_1000001) -### L2/3/5 fan Martinotti sst GABAergic interneuron (Mmus) `http://purl.obolibrary.org/obo/CL_4023030` -#### Removed -- [L2/3/5 fan Martinotti sst GABAergic interneuron (Mmus)](http://purl.obolibrary.org/obo/CL_4023030) SubClassOf [sst GABAergic cortical interneuron](http://purl.obolibrary.org/obo/CL_4023017) +### CLM_1000002 `http://purl.obolibrary.org/obo/CLM_1000002` #### Added -- [L2/3/5 fan Martinotti sst GABAergic interneuron (Mmus)](http://purl.obolibrary.org/obo/CL_4023030) SubClassOf [BFO_0000002](http://purl.obolibrary.org/obo/BFO_0000002) +- Class: [CLM_1000002](http://purl.obolibrary.org/obo/CLM_1000002) -- [L2/3/5 fan Martinotti sst GABAergic interneuron (Mmus)](http://purl.obolibrary.org/obo/CL_4023030) SubClassOf [cerebral cortex GABAergic interneuron](http://purl.obolibrary.org/obo/CL_0010011) - -### L4 sst Martinotti interneuron (Mmus) `http://purl.obolibrary.org/obo/CL_4023031` -#### Removed -- [L4 sst Martinotti interneuron (Mmus)](http://purl.obolibrary.org/obo/CL_4023031) SubClassOf [sst GABAergic cortical interneuron](http://purl.obolibrary.org/obo/CL_4023017) +### CLM_1000003 `http://purl.obolibrary.org/obo/CLM_1000003` #### Added -- [L4 sst Martinotti interneuron (Mmus)](http://purl.obolibrary.org/obo/CL_4023031) SubClassOf [cerebral cortex GABAergic interneuron](http://purl.obolibrary.org/obo/CL_0010011) +- Class: [CLM_1000003](http://purl.obolibrary.org/obo/CLM_1000003) -- [L4 sst Martinotti interneuron (Mmus)](http://purl.obolibrary.org/obo/CL_4023031) SubClassOf [BFO_0000002](http://purl.obolibrary.org/obo/BFO_0000002) +### CLM_1000004 `http://purl.obolibrary.org/obo/CLM_1000004` -### L5 extratelencephalic projecting glutamatergic cortical neuron `http://purl.obolibrary.org/obo/CL_4023041` -#### Removed -- [L5 extratelencephalic projecting glutamatergic cortical neuron](http://purl.obolibrary.org/obo/CL_4023041) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A glutamatergic neuron, with a soma found in the deeper portion of L5, that has long-range axonal projections including deep subcortical targets outside of the telencephalon and, in some cases, the spinal cord. While the L5 ET neuron projections are not limited to ET targets, they are clearly differentiated from the neuron subclasses whose projections are constrained to intratelencephalic (IT) targets. L5 ET neurons are generally the largest excitatory cortical neurons, typically having a thick apical dendrite with a prominent dendritic tuft in layer 1 and displaying burst-firing physiological characteristics."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:34616075"^^[string](http://www.w3.org/2001/XMLSchema#string) +#### Added +- Class: [CLM_1000004](http://purl.obolibrary.org/obo/CLM_1000004) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:37824655"^^[string](http://www.w3.org/2001/XMLSchema#string) + +### CLM_1000005 `http://purl.obolibrary.org/obo/CLM_1000005` #### Added -- [L5 extratelencephalic projecting glutamatergic cortical neuron](http://purl.obolibrary.org/obo/CL_4023041) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A transcriptomically distinct glutamatergic neuron, with a soma found in the deeper portion of L5, that has long-range axonal projections including deep subcortical targets outside of the telencephalon and, in some cases, the spinal cord. While the L5 ET neuron projections are not limited to ET targets, they are clearly differentiated from the neuron subclasses whose projections are constrained to intratelencephalic (IT) targets. L5 ET neurons are generally the largest excitatory cortical neurons, typically having a thick apical dendrite with a prominent dendritic tuft in layer 1 and displaying burst-firing physiological characteristics. The standard transcriptomic reference data for this cell type can be found on the CellxGene census under the collection: 'Transcriptomic cytoarchitecture reveals principles of human neocortex organization', dataset: 'Supercluster: Deep layer (non-IT) excitatory neurons ', Author Categories: 'CrossArea_subclass', clusters L5 ET."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:34616075"^^[string](http://www.w3.org/2001/XMLSchema#string) +- Class: [CLM_1000005](http://purl.obolibrary.org/obo/CLM_1000005) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:37824655"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://cellxgene.cziscience.com/e/d01c9dff-abd1-4825-bf30-2eb2ba74597e.cxg/"^^[string](http://www.w3.org/2001/XMLSchema#string) +### CLM_1000006 `http://purl.obolibrary.org/obo/CLM_1000006` +#### Added +- Class: [CLM_1000006](http://purl.obolibrary.org/obo/CLM_1000006) -### L5 non-Martinotti sst GABAergic interneuron (Mmus) `http://purl.obolibrary.org/obo/CL_4023028` -#### Removed -- [L5 non-Martinotti sst GABAergic interneuron (Mmus)](http://purl.obolibrary.org/obo/CL_4023028) SubClassOf [sst GABAergic cortical interneuron](http://purl.obolibrary.org/obo/CL_4023017) -#### Added -- [L5 non-Martinotti sst GABAergic interneuron (Mmus)](http://purl.obolibrary.org/obo/CL_4023028) SubClassOf [BFO_0000002](http://purl.obolibrary.org/obo/BFO_0000002) +### CLM_1000008 `http://purl.obolibrary.org/obo/CLM_1000008` -- [L5 non-Martinotti sst GABAergic interneuron (Mmus)](http://purl.obolibrary.org/obo/CL_4023028) SubClassOf [cerebral cortex GABAergic interneuron](http://purl.obolibrary.org/obo/CL_0010011) +#### Added +- Class: [CLM_1000008](http://purl.obolibrary.org/obo/CLM_1000008) -### L5 sst T-Martinotti interneuron (Mmus) `http://purl.obolibrary.org/obo/CL_4023027` -#### Removed -- [L5 sst T-Martinotti interneuron (Mmus)](http://purl.obolibrary.org/obo/CL_4023027) SubClassOf [sst GABAergic cortical interneuron](http://purl.obolibrary.org/obo/CL_4023017) +### CLM_1000009 `http://purl.obolibrary.org/obo/CLM_1000009` #### Added -- [L5 sst T-Martinotti interneuron (Mmus)](http://purl.obolibrary.org/obo/CL_4023027) SubClassOf [cerebral cortex GABAergic interneuron](http://purl.obolibrary.org/obo/CL_0010011) +- Class: [CLM_1000009](http://purl.obolibrary.org/obo/CLM_1000009) -- [L5 sst T-Martinotti interneuron (Mmus)](http://purl.obolibrary.org/obo/CL_4023027) SubClassOf [BFO_0000002](http://purl.obolibrary.org/obo/BFO_0000002) +### CLM_1000010 `http://purl.obolibrary.org/obo/CLM_1000010` + +#### Added +- Class: [CLM_1000010](http://purl.obolibrary.org/obo/CLM_1000010) -### L5/6 near-projecting glutamatergic neuron of the primary motor cortex `http://purl.obolibrary.org/obo/CL_4023043` -#### Removed -- [L5/6 near-projecting glutamatergic neuron of the primary motor cortex](http://purl.obolibrary.org/obo/CL_4023043) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A near-projecting glutamatergic neuron with a soma found in layer 5/6 of the primary motor cortex."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:31209381"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:34616075"^^[string](http://www.w3.org/2001/XMLSchema#string) +### CLM_1000026 `http://purl.obolibrary.org/obo/CLM_1000026` #### Added -- [L5/6 near-projecting glutamatergic neuron of the primary motor cortex](http://purl.obolibrary.org/obo/CL_4023043) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A transcriptomically distinct near-projecting glutamatergic neuron with a soma found in layer 5/6 of the primary motor cortex. The standard transcriptomic reference data for this cell type can be found on the CellxGene census under the collection: 'Transcriptomic cytoarchitecture reveals principles of human neocortex organization', dataset: 'Supercluster: Deep layer (non-IT) excitatory neurons', Author Categories: 'CrossArea_subclass', cluster L5/6 NP."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:31209381"^^[string](http://www.w3.org/2001/XMLSchema#string) +- Class: [CLM_1000026](http://purl.obolibrary.org/obo/CLM_1000026) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:34616075"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://cellxgene.cziscience.com/e/d01c9dff-abd1-4825-bf30-2eb2ba74597e.cxg/"^^[string](http://www.w3.org/2001/XMLSchema#string) +### CLM_1000027 `http://purl.obolibrary.org/obo/CLM_1000027` +#### Added +- Class: [CLM_1000027](http://purl.obolibrary.org/obo/CLM_1000027) -### L5/6 non-Martinotti sst GABAergic interneuron (Mmus) `http://purl.obolibrary.org/obo/CL_4023118` -#### Removed -- [L5/6 non-Martinotti sst GABAergic interneuron (Mmus)](http://purl.obolibrary.org/obo/CL_4023118) SubClassOf [sst GABAergic cortical interneuron](http://purl.obolibrary.org/obo/CL_4023017) + +### CLM_1000031 `http://purl.obolibrary.org/obo/CLM_1000031` #### Added -- [L5/6 non-Martinotti sst GABAergic interneuron (Mmus)](http://purl.obolibrary.org/obo/CL_4023118) SubClassOf [cerebral cortex GABAergic interneuron](http://purl.obolibrary.org/obo/CL_0010011) +- Class: [CLM_1000031](http://purl.obolibrary.org/obo/CLM_1000031) -- [L5/6 non-Martinotti sst GABAergic interneuron (Mmus)](http://purl.obolibrary.org/obo/CL_4023118) SubClassOf [BFO_0000002](http://purl.obolibrary.org/obo/BFO_0000002) +### CLM_1000032 `http://purl.obolibrary.org/obo/CLM_1000032` -### L6 corticothalamic-projecting glutamatergic cortical neuron `http://purl.obolibrary.org/obo/CL_4023042` -#### Removed -- [L6 corticothalamic-projecting glutamatergic cortical neuron](http://purl.obolibrary.org/obo/CL_4023042) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A corticothalamic-projecting neuron with a soma found in cortical layer 6."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:34616075"^^[string](http://www.w3.org/2001/XMLSchema#string) +#### Added +- Class: [CLM_1000032](http://purl.obolibrary.org/obo/CLM_1000032) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:37824655"^^[string](http://www.w3.org/2001/XMLSchema#string) + +### CLM_1000041 `http://purl.obolibrary.org/obo/CLM_1000041` #### Added -- [L6 corticothalamic-projecting glutamatergic cortical neuron](http://purl.obolibrary.org/obo/CL_4023042) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A transcriptomically distinct corticothalamic-projecting neuron with a soma found in cortical layer 6. The standard transcriptomic reference data for this cell type can be found on the CellxGene census under the collection: 'Transcriptomic cytoarchitecture reveals principles of human neocortex organization', dataset: 'Supercluster: Deep layer (non-IT) excitatory neurons', Author Categories: 'CrossArea_subclass', clusters L6 CT."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:34616075"^^[string](http://www.w3.org/2001/XMLSchema#string) +- Class: [CLM_1000041](http://purl.obolibrary.org/obo/CLM_1000041) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:37824655"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://cellxgene.cziscience.com/e/d01c9dff-abd1-4825-bf30-2eb2ba74597e.cxg/"^^[string](http://www.w3.org/2001/XMLSchema#string) +### CLM_1000043 `http://purl.obolibrary.org/obo/CLM_1000043` + +#### Added +- Class: [CLM_1000043](http://purl.obolibrary.org/obo/CLM_1000043) -### L6 th sst GABAergic interneuron (Mmus) `http://purl.obolibrary.org/obo/CL_4023075` -#### Removed -- [L6 th sst GABAergic interneuron (Mmus)](http://purl.obolibrary.org/obo/CL_4023075) SubClassOf [sst GABAergic cortical interneuron](http://purl.obolibrary.org/obo/CL_4023017) +### CLM_1000046 `http://purl.obolibrary.org/obo/CLM_1000046` #### Added -- [L6 th sst GABAergic interneuron (Mmus)](http://purl.obolibrary.org/obo/CL_4023075) SubClassOf [cerebral cortex GABAergic interneuron](http://purl.obolibrary.org/obo/CL_0010011) +- Class: [CLM_1000046](http://purl.obolibrary.org/obo/CLM_1000046) -- [L6 th sst GABAergic interneuron (Mmus)](http://purl.obolibrary.org/obo/CL_4023075) SubClassOf [BFO_0000002](http://purl.obolibrary.org/obo/BFO_0000002) +### CLM_1000047 `http://purl.obolibrary.org/obo/CLM_1000047` -### L6b glutamatergic cortical neuron `http://purl.obolibrary.org/obo/CL_4023038` -#### Removed -- [L6b glutamatergic cortical neuron](http://purl.obolibrary.org/obo/CL_4023038) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A glutamatergic neuron with a soma found in cortical layer 6b. They are transcriptomically related to corticothalamic-projecting neurons but have differential projections to the thalamus or anterior cingulate."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:30382198"^^[string](http://www.w3.org/2001/XMLSchema#string) +#### Added +- Class: [CLM_1000047](http://purl.obolibrary.org/obo/CLM_1000047) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:37824655"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1101/2020.10.19.34312"^^[string](http://www.w3.org/2001/XMLSchema#string) +### CLM_1000052 `http://purl.obolibrary.org/obo/CLM_1000052` #### Added -- [L6b glutamatergic cortical neuron](http://purl.obolibrary.org/obo/CL_4023038) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [human_reference_atlas](http://purl.obolibrary.org/obo/cl/cl-base#human_reference_atlas) +- Class: [CLM_1000052](http://purl.obolibrary.org/obo/CLM_1000052) -- [L6b glutamatergic cortical neuron](http://purl.obolibrary.org/obo/CL_4023038) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A glutamatergic neuron with a soma found in cortical layer 6b. They are transcriptomically related to corticothalamic-projecting neurons but have differential projections to the thalamus or anterior cingulate. The standard transcriptomic reference data for this cell type can be found on the CellxGene census under the collection: 'Transcriptomic cytoarchitecture reveals principles of human neocortex organization', dataset: 'Supercluster: Deep layer (non-IT) excitatory neuron', Author Categories: 'CrossArea_subclass', cluster L6b."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:30382198"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:37824655"^^[string](http://www.w3.org/2001/XMLSchema#string) +### CLM_1000053 `http://purl.obolibrary.org/obo/CLM_1000053` - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1101/2020.10.19.34312"^^[string](http://www.w3.org/2001/XMLSchema#string) +#### Added +- Class: [CLM_1000053](http://purl.obolibrary.org/obo/CLM_1000053) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://cellxgene.cziscience.com/e/d01c9dff-abd1-4825-bf30-2eb2ba74597e.cxg/"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [L6b glutamatergic cortical neuron](http://purl.obolibrary.org/obo/CL_4023038) [RO_0002175](http://purl.obolibrary.org/obo/RO_0002175) [NCBITaxon_9606](http://purl.obolibrary.org/obo/NCBITaxon_9606) +### CLM_1000054 `http://purl.obolibrary.org/obo/CLM_1000054` - -### Lamp5 Lhx6 neuron `http://purl.obolibrary.org/obo/CL_4042013` -#### Removed -- [Lamp5 Lhx6 neuron](http://purl.obolibrary.org/obo/CL_4042013) SubClassOf [lamp5 GABAergic cortical interneuron](http://purl.obolibrary.org/obo/CL_4023011) +#### Added +- Class: [CLM_1000054](http://purl.obolibrary.org/obo/CLM_1000054) - -### Leydig cell `http://purl.obolibrary.org/obo/CL_0000178` +### CLM_1000056 `http://purl.obolibrary.org/obo/CLM_1000056` #### Added -- [Leydig cell](http://purl.obolibrary.org/obo/CL_0000178) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. +- Class: [CLM_1000056](http://purl.obolibrary.org/obo/CLM_1000056) -Leydig cells are a testosterone-secreting cell in the interstitial area in the testes of males. They are named after Franz Leydig, a German anatomist who discovered these cells in 1850. Uniquely situated within the soft connective tissue surrounding the seminiferous tubules, Leydig cells form an integral part of the male reproductive system. They are usually polygonal cells characterized by well developed smooth endoplasmic reticulum, high lipid content and a large round nucleus. They are found across mammalian species, including humans. -The primary function of Leydig cells is the production of androgens, the male sex hormones, the most notable of which is testosterone. Leydig cells synthesize testosterone from cholesterol through a series of enzymatic reactions. The production and release of testosterone are mainly regulated by the luteinizing hormone (LH) released by the anterior pituitary gland. In response to LH, Leydig cells convert cholesterol into testosterone, which then plays a crucial role in the development and maintenance of primary and secondary male sexual characteristics. These include the formation and maturation of male reproductive organs, onset of spermatogenesis, and the presentation of male secondary sexual traits such as the deepening of the voice, growth of facial hair, development of muscles, and a broadening of shoulders. -Apart from testosterone production, Leydig cells also secrete insulin-like factor 3 (INSL3) that is essential for testicular descent during embryonic development in males. Dysregulation or loss of Leydig cells can lead to numerous conditions like testosterone deficiency, infertility, and certain forms of testicular cancer. Although not typical, Leydig cells can regenerate if they are damaged, ensuring the continuous production of testosterone and maintaining male reproductive health. They provide an excellent model to study cell differentiation and hormone regulation, thereby enhancing our understanding of reproductive biology and associated disorders."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1093/biolre/ioy059"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1210/clinem/dgaa603"^^[string](http://www.w3.org/2001/XMLSchema#string) +### CLM_1000059 `http://purl.obolibrary.org/obo/CLM_1000059` - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://www.ncbi.nlm.nih.gov/books/NBK556007/#:~:text=Leydig%20cells%20are%20the%20primary,secondary%20sexual%20characteristics%20and%20behaviors."^^[string](http://www.w3.org/2001/XMLSchema#string) +#### Added +- Class: [CLM_1000059](http://purl.obolibrary.org/obo/CLM_1000059) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1016/j.coemr.2019.03.001"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.3389/fendo.2014.00006"^^[string](http://www.w3.org/2001/XMLSchema#string) +### CLM_1000061 `http://purl.obolibrary.org/obo/CLM_1000061` -- [Leydig cell](http://purl.obolibrary.org/obo/CL_0000178) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://cellxgene.cziscience.com/cellguide/CL_0000178"^^[string](http://www.w3.org/2001/XMLSchema#string) +#### Added +- Class: [CLM_1000061](http://purl.obolibrary.org/obo/CLM_1000061) -### Ly-76 high positive erythrocyte `http://purl.obolibrary.org/obo/CL_0002022` +### CLM_1000063 `http://purl.obolibrary.org/obo/CLM_1000063` #### Added -- [Ly-76 high positive erythrocyte](http://purl.obolibrary.org/obo/CL_0002022) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) +- Class: [CLM_1000063](http://purl.obolibrary.org/obo/CLM_1000063) -### M cell of gut `http://purl.obolibrary.org/obo/CL_0000682` +### CLM_1000065 `http://purl.obolibrary.org/obo/CLM_1000065` #### Added -- [M cell of gut](http://purl.obolibrary.org/obo/CL_0000682) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://cellxgene.cziscience.com/cellguide/CL_0000682"^^[string](http://www.w3.org/2001/XMLSchema#string) +- Class: [CLM_1000065](http://purl.obolibrary.org/obo/CLM_1000065) -- [M cell of gut](http://purl.obolibrary.org/obo/CL_0000682) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. -M cells, or microfold cells, of the gut are specialized epithelial cells found in the lining of the gut, specifically in the follicle-associated epithelium of mucosa-associated lymphoid tissue, where they function as sentries against toxins and pathogens. M cells are characterized by apical microfolds (hence their alternate name) which express unique adhesion molecules that enable them to sample the luminal macromolecules. -Other morphological features that distinguish M cells from other intestinal mucosal cells include sparse microvilli and a reduced thickness of the glycocalyx, which permits adhesion while not hindering the transport of molecules. They also have unique intraepithelial invaginations on the basolateral side which are filled with macrophages and other immune cells that can process the engulfed macromolecules quickly. -These morphological characteristics enable M cells to serve a dual role in immune responses. They initiate the immune response by transporting antigens (such as toxic or pathogenic substances) across the epithelial layer to lymphocytes and antigen-presenting cells in the underlying lymphoid tissue. This specialized transport process is called 'transcytosis.' They also have specialized molecules like glycoprotein-2 for bacterial uptake. Simultaneously, M cells help maintain immune tolerance to food antigens and commensal bacteria, preventing unnecessary reactions to non-pathogenic substances and hypersensitivity conditions. While these functions are crucial for well-being, M cell dysfunction can lead to serious conditions like Crohn's disease and other inflammatory bowel diseases."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1038/nature08529"^^[string](http://www.w3.org/2001/XMLSchema#string) +### CLM_1000066 `http://purl.obolibrary.org/obo/CLM_1000066` - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1093/jb/mvv121"^^[string](http://www.w3.org/2001/XMLSchema#string) +#### Added +- Class: [CLM_1000066](http://purl.obolibrary.org/obo/CLM_1000066) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1136/gut.47.5.735"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://www.ncbi.nlm.nih.gov/books/NBK534232/"^^[string](http://www.w3.org/2001/XMLSchema#string) +### CLM_1000067 `http://purl.obolibrary.org/obo/CLM_1000067` - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://www.sciencedirect.com/topics/medicine-and-dentistry/microfold-cell"^^[string](http://www.w3.org/2001/XMLSchema#string) +#### Added +- Class: [CLM_1000067](http://purl.obolibrary.org/obo/CLM_1000067) -### M cone cell `http://purl.obolibrary.org/obo/CL_0003049` +### CLM_1000068 `http://purl.obolibrary.org/obo/CLM_1000068` #### Added -- [M cone cell](http://purl.obolibrary.org/obo/CL_0003049) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) +- Class: [CLM_1000068](http://purl.obolibrary.org/obo/CLM_1000068) -### Malpighian tubule stellate cell `http://purl.obolibrary.org/obo/CL_1000155` +### CLM_1000069 `http://purl.obolibrary.org/obo/CLM_1000069` #### Added -- [Malpighian tubule stellate cell](http://purl.obolibrary.org/obo/CL_1000155) SubClassOf [eukaryotic cell](http://purl.obolibrary.org/obo/CL_0000255) +- Class: [CLM_1000069](http://purl.obolibrary.org/obo/CLM_1000069) -### NK1.1-positive natural killer cell, mouse `http://purl.obolibrary.org/obo/CL_0002438` +### CLM_1000070 `http://purl.obolibrary.org/obo/CLM_1000070` #### Added -- [NK1.1-positive natural killer cell, mouse](http://purl.obolibrary.org/obo/CL_0002438) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) +- Class: [CLM_1000070](http://purl.obolibrary.org/obo/CLM_1000070) -### PATO_0010007 `http://purl.obolibrary.org/obo/PATO_0010007` +### CLM_1000071 `http://purl.obolibrary.org/obo/CLM_1000071` #### Added -- Class: [PATO_0010007](http://purl.obolibrary.org/obo/PATO_0010007) +- Class: [CLM_1000071](http://purl.obolibrary.org/obo/CLM_1000071) -### PP cell `http://purl.obolibrary.org/obo/CL_0000696` +### CLM_1000072 `http://purl.obolibrary.org/obo/CLM_1000072` #### Added -- [PP cell](http://purl.obolibrary.org/obo/CL_0000696) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. +- Class: [CLM_1000072](http://purl.obolibrary.org/obo/CLM_1000072) -PP cells, also known as pancreatic polypeptide cells (and previously called F cells or gamma cells), are enteroendocrine cells predominantly found in the islets of Langerhans in the head of the pancreas. They are one of the four main endocrine cell types present in the pancreatic islets, along with type A, B and D cells. PP cells are notable for their production of pancreatic polypeptide, an anorexigenic hormone that modulates food intake and energy homeostasis. -By secreting pancreatic polypeptide, PP cells play a significant role in the management of both digestive and appetite regulation. Upon ingestion of food, there is a significant increase in the secretion of pancreatic polypeptide, which then reduces biliary secretion and helps slow down the movement of food through the digestive tract. This allows more time for digestion to take place and nutrients to be absorbed, promoting the efficient use of dietary intake. The pancreatic polypeptide further reduces appetite by interacting with the hypothalamus, the area of the brain responsible for control of hunger. -Given their important role in digestion, malfunction or damage to PP cells can lead to a disturbance in the digestive process and contribute to some disease conditions. For example, an overproduction of pancreatic polypeptide can result in conditions such as pancreatic tumors and diabetes. Conversely, an under secretion might contribute to obesity due to impaired dietary control. Furthermore, PP cells may also play a role in the body's energy balance, suggesting their implication in conditions related to energy metabolism."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1210/jc.2003-030630"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1016/j.mce.2015.06.028"^^[string](http://www.w3.org/2001/XMLSchema#string) +### CLM_1000073 `http://purl.obolibrary.org/obo/CLM_1000073` - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1016/j.febslet.2014.07.005"^^[string](http://www.w3.org/2001/XMLSchema#string) +#### Added +- Class: [CLM_1000073](http://purl.obolibrary.org/obo/CLM_1000073) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1369/00221554155835"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1038/s41580-020-00317-7"^^[string](http://www.w3.org/2001/XMLSchema#string) +### CLM_1000074 `http://purl.obolibrary.org/obo/CLM_1000074` -- [PP cell](http://purl.obolibrary.org/obo/CL_0000696) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://cellxgene.cziscience.com/cellguide/CL_0000696"^^[string](http://www.w3.org/2001/XMLSchema#string) +#### Added +- Class: [CLM_1000074](http://purl.obolibrary.org/obo/CLM_1000074) -### PR_000007479 `http://purl.obolibrary.org/obo/PR_000007479` +### CLM_1000075 `http://purl.obolibrary.org/obo/CLM_1000075` #### Added -- Class: [PR_000007479](http://purl.obolibrary.org/obo/PR_000007479) +- Class: [CLM_1000075](http://purl.obolibrary.org/obo/CLM_1000075) -### PR_000007489 `http://purl.obolibrary.org/obo/PR_000007489` +### CLM_1000079 `http://purl.obolibrary.org/obo/CLM_1000079` #### Added -- Class: [PR_000007489](http://purl.obolibrary.org/obo/PR_000007489) +- Class: [CLM_1000079](http://purl.obolibrary.org/obo/CLM_1000079) -### PR_000007643 `http://purl.obolibrary.org/obo/PR_000007643` +### CLM_1000080 `http://purl.obolibrary.org/obo/CLM_1000080` #### Added -- Class: [PR_000007643](http://purl.obolibrary.org/obo/PR_000007643) +- Class: [CLM_1000080](http://purl.obolibrary.org/obo/CLM_1000080) -### PR_000010529 `http://purl.obolibrary.org/obo/PR_000010529` +### CLM_1000081 `http://purl.obolibrary.org/obo/CLM_1000081` #### Added -- Class: [PR_000010529](http://purl.obolibrary.org/obo/PR_000010529) +- Class: [CLM_1000081](http://purl.obolibrary.org/obo/CLM_1000081) -### PR_000013047 `http://purl.obolibrary.org/obo/PR_000013047` +### CLM_1000082 `http://purl.obolibrary.org/obo/CLM_1000082` #### Added -- Class: [PR_000013047](http://purl.obolibrary.org/obo/PR_000013047) +- Class: [CLM_1000082](http://purl.obolibrary.org/obo/CLM_1000082) -### PR_000013433 `http://purl.obolibrary.org/obo/PR_000013433` +### CLM_1000083 `http://purl.obolibrary.org/obo/CLM_1000083` #### Added -- Class: [PR_000013433](http://purl.obolibrary.org/obo/PR_000013433) +- Class: [CLM_1000083](http://purl.obolibrary.org/obo/CLM_1000083) -### PR_000014419 `http://purl.obolibrary.org/obo/PR_000014419` +### CLM_1000085 `http://purl.obolibrary.org/obo/CLM_1000085` #### Added -- Class: [PR_000014419](http://purl.obolibrary.org/obo/PR_000014419) +- Class: [CLM_1000085](http://purl.obolibrary.org/obo/CLM_1000085) -### PR_000014898 `http://purl.obolibrary.org/obo/PR_000014898` +### CNS long range interneuron `http://purl.obolibrary.org/obo/CL_0000410` +#### Removed +- [CNS long range interneuron](http://purl.obolibrary.org/obo/CL_0000410) SubClassOf [obsolete CNS interneuron](http://purl.obolibrary.org/obo/CL_0000402) #### Added -- Class: [PR_000014898](http://purl.obolibrary.org/obo/PR_000014898) +- [CNS long range interneuron](http://purl.obolibrary.org/obo/CL_0000410) SubClassOf [interneuron](http://purl.obolibrary.org/obo/CL_0000099) -### Peyer's patch follicular dendritic cell `http://purl.obolibrary.org/obo/CL_0009015` +### CNS neuron (sensu Nematoda and Protostomia) `http://purl.obolibrary.org/obo/CL_0000028` +#### Removed +- [CNS neuron (sensu Nematoda and Protostomia)](http://purl.obolibrary.org/obo/CL_0000028) SubClassOf [neuron](http://purl.obolibrary.org/obo/CL_0000540) #### Added -- [Peyer's patch follicular dendritic cell](http://purl.obolibrary.org/obo/CL_0009015) SubClassOf [eukaryotic cell](http://purl.obolibrary.org/obo/CL_0000255) +- [CNS neuron (sensu Nematoda and Protostomia)](http://purl.obolibrary.org/obo/CL_0000028) SubClassOf [central nervous system neuron](http://purl.obolibrary.org/obo/CL_2000029) -### Purkinje cell `http://purl.obolibrary.org/obo/CL_0000121` +### CNS neuron (sensu Vertebrata) `http://purl.obolibrary.org/obo/CL_0000117` +#### Removed +- [CNS neuron (sensu Vertebrata)](http://purl.obolibrary.org/obo/CL_0000117) SubClassOf [RO_0002202](http://purl.obolibrary.org/obo/RO_0002202) some [neuroblast (sensu Vertebrata)](http://purl.obolibrary.org/obo/CL_0000031) + +- [CNS neuron (sensu Vertebrata)](http://purl.obolibrary.org/obo/CL_0000117) SubClassOf [neuron](http://purl.obolibrary.org/obo/CL_0000540) + +- [CNS neuron (sensu Vertebrata)](http://purl.obolibrary.org/obo/CL_0000117) SubClassOf [BFO_0000002](http://purl.obolibrary.org/obo/BFO_0000002) #### Added -- [Purkinje cell](http://purl.obolibrary.org/obo/CL_0000121) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://cellxgene.cziscience.com/cellguide/CL_0000121"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [CNS neuron (sensu Vertebrata)](http://purl.obolibrary.org/obo/CL_0000117) SubClassOf [central nervous system neuron](http://purl.obolibrary.org/obo/CL_2000029) -- [Purkinje cell](http://purl.obolibrary.org/obo/CL_0000121) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. -Purkinje cells, named after the Czech anatomist Jan Evangelista Purkyně who discovered them, are unique inhibitory neurons in the cerebellar cortex. They are a critical part of the vertebrate nervous system as they provide the only signal output from the cortex to the cerebellar nuclei. They are one of the few types of neurons that are large enough to be seen with the naked eye. The most distinct hallmark of Purkinje cells is their elaborate dendritic arbor, which forms a broad and intricately branching structure resembling a tree. These numerous branches each receive excitatory synaptic inputs from more than 100,000 parallel fibers; in addition, a single climbing fiber makes hundreds of synapses to the soma and proximal dendrites. A single long axon forms an inhibitory projection to the cerebellar nuclei. -Purkinje cells play key roles in the coordination of fine, voluntary motor movements and balance. As the sole output of all motor coordination in the cerebellar cortex, they serve as a central relay in the cerebro-cerebellar loop. Each Purkinje cell receives two types of synaptic input: one from parallel fibers (which are axons of granule cells), and the other from climbing fibers (originating from the inferior olivary nucleus). The Purkinje cells process and integrate these diverse kinds of input signals to generate output that controls timing and coordination of movements. -Purkinje neurons show considerable synaptic plasticity. Throughout life, these cells continue to undergo long-term potentiation and depression at parallel fiber synapses, which cause long-lasting increase or decrease, respectively, of synaptic transmission and have been proposed as mechanisms for motor learning. -Purkinje cells are also known to be implicated in a variety of diseases. Their progressive loss is a prime feature in certain types of ataxia, a collective term used to describe conditions characterized by loss of muscular control and coordination. Furthermore, a significant reduction in the density of Purkinje cells has been reported in conditions such as autism and Huntington’s disease."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.7554/eLife.63668"^^[string](http://www.w3.org/2001/XMLSchema#string) +### CNS short range interneuron `http://purl.obolibrary.org/obo/CL_0000406` +#### Removed +- [CNS short range interneuron](http://purl.obolibrary.org/obo/CL_0000406) SubClassOf [obsolete CNS interneuron](http://purl.obolibrary.org/obo/CL_0000402) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://www.sciencedirect.com/topics/agricultural-and-biological-sciences/purkinje-cell"^^[string](http://www.w3.org/2001/XMLSchema#string) +#### Added +- [CNS short range interneuron](http://purl.obolibrary.org/obo/CL_0000406) SubClassOf [interneuron](http://purl.obolibrary.org/obo/CL_0000099) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1038/nrn3886"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://www.ncbi.nlm.nih.gov/books/NBK545154/"^^[string](http://www.w3.org/2001/XMLSchema#string) +### Cajal-Retzius cell `http://purl.obolibrary.org/obo/CL_0000695` +#### Removed +- [Cajal-Retzius cell](http://purl.obolibrary.org/obo/CL_0000695) SubClassOf [CNS neuron (sensu Vertebrata)](http://purl.obolibrary.org/obo/CL_0000117) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1007/s12311-018-0985-7"^^[string](http://www.w3.org/2001/XMLSchema#string) -### Schwann cell `http://purl.obolibrary.org/obo/CL_0002573` +### D1/D2-hybrid medium spiny neuron `http://purl.obolibrary.org/obo/CL_4030050` #### Added -- [Schwann cell](http://purl.obolibrary.org/obo/CL_0002573) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://cellxgene.cziscience.com/cellguide/CL_0002573"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [D1/D2-hybrid medium spiny neuron](http://purl.obolibrary.org/obo/CL_4030050) SubClassOf [striatum neuron](http://purl.obolibrary.org/obo/CL_0002613) -- [Schwann cell](http://purl.obolibrary.org/obo/CL_0002573) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. -Schwann cells, also known as neurolemmocytes, are a type of glial cell located in the peripheral nervous system. These cells play a significant role in the healthy functioning of nerves by producing myelin, a fatty substance that forms a coating around nerve fibers. Myelin serves as an insulator and enhances the speed and efficiency of electrical nerve impulses; a single Schwann cell can myelinate a single axon. Myelination starts by the elongation and envelopment of the Schwann cell around the axon, followed by the synthesis and deposition of myelin layers. Some studies suggest that Schwann cells may regulate neuronal action potential, muscular contraction, and the sensitive response. -While Schwann cells are most commonly known for the formation of the myelin sheath, some Schwann cells do not form myelin: Remak Schwann cells, a class of nonmyelinating Schwann cells, ensheath axons with smaller diameter, such as C fiber nociceptors in sciatic nerves and form Remak bundles. -Schwann cells are found along both motor and sensory neurons and are crucial for the advancement and recovery of peripheral nerve injuries, due to their capacity to support nerve regeneration. In cases of nerve injury, Schwann cells play a vital role in recovery by initiating Wallerian degeneration, a process in which the part of the axon distal to the injury site degrades and is then cleared away. Following this, Schwann cells can guide the regrowth of the nerve, providing a conducive environment for axon regeneration. They remodel themselves into a regenerative phenotype, proliferate, and organize themselves into bands of Büngner that provide physical and chemical guidance for the regrowths of axons. This function of Schwann cells in the repair and regeneration of nervous system highlights their therapeutic potential in peripheral nerve injury treatments."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1016/j.biocel.2006.05.007"^^[string](http://www.w3.org/2001/XMLSchema#string) +### DN1 thymic pro-T cell `http://purl.obolibrary.org/obo/CL_0000894` +#### Removed +- [DN1 thymic pro-T cell](http://purl.obolibrary.org/obo/CL_0000894) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1016/B978-0-444-52902-2.00005-9"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1002/glia.23892"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1186/s13064-020-00140-y"^^[string](http://www.w3.org/2001/XMLSchema#string) +### DN2 thymocyte `http://purl.obolibrary.org/obo/CL_0000806` +#### Removed +- [DN2 thymocyte](http://purl.obolibrary.org/obo/CL_0000806) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1186/1742-2094-8-110"^^[string](http://www.w3.org/2001/XMLSchema#string) -### Schwann cell precursor `http://purl.obolibrary.org/obo/CL_0002375` +### DN3 thymocyte `http://purl.obolibrary.org/obo/CL_0000807` #### Removed -- [Schwann cell precursor](http://purl.obolibrary.org/obo/CL_0002375) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A glioblast cell that develops from a migratory neural crest cell. The SCP is embedded among neurons (axons) with minimal extracellular spaces separating them from nerve cell membranes and has no basal lamina. In rodents SCPs are the only cells in the Schwann cell linage that expresses Cdh19."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:tfm"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [DN3 thymocyte](http://purl.obolibrary.org/obo/CL_0000807) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) -- [Schwann cell precursor](http://purl.obolibrary.org/obo/CL_0002375) SubClassOf [glioblast](http://purl.obolibrary.org/obo/CL_0000030) -#### Added -- [Schwann cell precursor](http://purl.obolibrary.org/obo/CL_0002375) [comment](http://www.w3.org/2000/01/rdf-schema#comment) "Schwann cell precursor are capable of differentiating into Schwann cells and other cell types such as melanocytes, neurons, and mesenchymal cells."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:35815410"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [Schwann cell precursor](http://purl.obolibrary.org/obo/CL_0002375) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "SCP"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003000](http://purl.obolibrary.org/obo/OMO_0003000) +### DN4 thymocyte `http://purl.obolibrary.org/obo/CL_0000808` +#### Removed +- [DN4 thymocyte](http://purl.obolibrary.org/obo/CL_0000808) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:35815410"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [Schwann cell precursor](http://purl.obolibrary.org/obo/CL_0002375) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A multipotent progenitor cell that develops from a migratory neural crest cell. The schwann cell precursor is embedded among axons, with minimal extracellular space separating them from nerve cell membranes. This cell lacks a basal lamina, which distinguishes it from more mature Schwann cells. In rodents, cadherin-19 (Cdh19) serves as a specific marker for this developmental stage."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:30971890"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:tfm"^^[string](http://www.w3.org/2001/XMLSchema#string) +### Dx5-negative, NK1.1-positive immature natural killer cell, mouse `http://purl.obolibrary.org/obo/CL_0002346` +#### Removed +- [Dx5-negative, NK1.1-positive immature natural killer cell, mouse](http://purl.obolibrary.org/obo/CL_0002346) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:15580626"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:35815410"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [Schwann cell precursor](http://purl.obolibrary.org/obo/CL_0002375) SubClassOf [RO_0002387](http://purl.obolibrary.org/obo/RO_0002387) some [Schwann cell](http://purl.obolibrary.org/obo/CL_0002573) +### FMA_83808 `http://purl.obolibrary.org/obo/FMA_83808` +#### Removed +- [FMA_83808](http://purl.obolibrary.org/obo/FMA_83808) [IAO_0000231](http://purl.obolibrary.org/obo/IAO_0000231) [IAO_0000227](http://purl.obolibrary.org/obo/IAO_0000227) -- [Schwann cell precursor](http://purl.obolibrary.org/obo/CL_0002375) SubClassOf [RO_0000053](http://purl.obolibrary.org/obo/RO_0000053) some [PATO_0001402](http://purl.obolibrary.org/obo/PATO_0001402) +- [FMA_83808](http://purl.obolibrary.org/obo/FMA_83808) [term replaced by](http://purl.obolibrary.org/obo/IAO_0100001) [cardiac muscle cell](http://purl.obolibrary.org/obo/CL_0000746) +- [FMA_83808](http://purl.obolibrary.org/obo/FMA_83808) [deprecated](http://www.w3.org/2002/07/owl#deprecated) true -### TAC3-positive medium spiny neuron `http://purl.obolibrary.org/obo/CL_4042002` +- Class: [FMA_83808](http://purl.obolibrary.org/obo/FMA_83808) -#### Added -- [TAC3-positive medium spiny neuron](http://purl.obolibrary.org/obo/CL_4042002) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) -### TAC3-positive striatal interneuron `http://purl.obolibrary.org/obo/CL_4042001` +### GABAergic interneuron `http://purl.obolibrary.org/obo/CL_0011005` #### Removed -- [TAC3-positive striatal interneuron](http://purl.obolibrary.org/obo/CL_4042001) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A GABAergic interneuron that has its soma located in the striatum and that has an enriched expression of the gene TAC3."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:32999462"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [GABAergic interneuron](http://purl.obolibrary.org/obo/CL_0011005) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [human_reference_atlas](http://purl.obolibrary.org/obo/cl/cl-base#human_reference_atlas) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:34727523"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [GABAergic interneuron](http://purl.obolibrary.org/obo/CL_0011005) [RO_0002175](http://purl.obolibrary.org/obo/RO_0002175) [NCBITaxon_9606](http://purl.obolibrary.org/obo/NCBITaxon_9606) #### Added -- [TAC3-positive striatal interneuron](http://purl.obolibrary.org/obo/CL_4042001) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A GABAergic interneuron that has its soma located in the striatum and that has an enriched expression of the genes TAC3 and LHX6."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:32999462"^^[string](http://www.w3.org/2001/XMLSchema#string) - - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:34727523"^^[string](http://www.w3.org/2001/XMLSchema#string) - -- [TAC3-positive striatal interneuron](http://purl.obolibrary.org/obo/CL_4042001) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) +- [GABAergic interneuron](http://purl.obolibrary.org/obo/CL_0011005) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl/cl-base#cellxgene_subset) -### TCR-positive macrophage `http://purl.obolibrary.org/obo/CL_4030058` +### GABAergic interneuron of the anterior substantia nigra pars reticulata `http://purl.obolibrary.org/obo/CL_4042026` #### Added -- [TCR-positive macrophage](http://purl.obolibrary.org/obo/CL_4030058) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) +- [GABAergic interneuron of the anterior substantia nigra pars reticulata](http://purl.obolibrary.org/obo/CL_4042026) SubClassOf [BFO_0000002](http://purl.obolibrary.org/obo/BFO_0000002) -### UBERON_0001136 `http://purl.obolibrary.org/obo/UBERON_0001136` +### GABAergic interneuron of the posterior substantia nigra pars reticulata `http://purl.obolibrary.org/obo/CL_4042027` #### Added -- Class: [UBERON_0001136](http://purl.obolibrary.org/obo/UBERON_0001136) +- [GABAergic interneuron of the posterior substantia nigra pars reticulata](http://purl.obolibrary.org/obo/CL_4042027) SubClassOf [BFO_0000002](http://purl.obolibrary.org/obo/BFO_0000002) -### UBERON_0001243 `http://purl.obolibrary.org/obo/UBERON_0001243` - -#### Added -- Class: [UBERON_0001243](http://purl.obolibrary.org/obo/UBERON_0001243) +### GCIs +#### Removed +- [cell](http://purl.obolibrary.org/obo/CL_0000000) and ([RO_0000053](http://purl.obolibrary.org/obo/RO_0000053) some [PATO_0001908](http://purl.obolibrary.org/obo/PATO_0001908)) SubClassOf [BFO_0000051](http://purl.obolibrary.org/obo/BFO_0000051) some [GO_0005634](http://purl.obolibrary.org/obo/GO_0005634) +- [cell](http://purl.obolibrary.org/obo/CL_0000000) and ([RO_0000053](http://purl.obolibrary.org/obo/RO_0000053) some [PATO_0001407](http://purl.obolibrary.org/obo/PATO_0001407)) SubClassOf [BFO_0000051](http://purl.obolibrary.org/obo/BFO_0000051) some [GO_0005634](http://purl.obolibrary.org/obo/GO_0005634) -### UBERON_0002197 `http://purl.obolibrary.org/obo/UBERON_0002197` +- [endocrine cell](http://purl.obolibrary.org/obo/CL_0000163) and ([BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0000160](http://purl.obolibrary.org/obo/UBERON_0000160)) SubClassOf [enteroendocrine cell](http://purl.obolibrary.org/obo/CL_0000164) -#### Added -- Class: [UBERON_0002197](http://purl.obolibrary.org/obo/UBERON_0002197) +- [endocrine cell](http://purl.obolibrary.org/obo/CL_0000163) and ([BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0001264](http://purl.obolibrary.org/obo/UBERON_0001264)) SubClassOf [enteroendocrine cell](http://purl.obolibrary.org/obo/CL_0000164) +- [neuron](http://purl.obolibrary.org/obo/CL_0000540) and ([RO_0002162](http://purl.obolibrary.org/obo/RO_0002162) some [NCBITaxon_7742](http://purl.obolibrary.org/obo/NCBITaxon_7742)) SubClassOf [RO_0002202](http://purl.obolibrary.org/obo/RO_0002202) some [neuroblast (sensu Vertebrata)](http://purl.obolibrary.org/obo/CL_0000031) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://github.com/obophenotype/cell-ontology/issues/757"^^[string](http://www.w3.org/2001/XMLSchema#string) -### UBERON_0003981 `http://purl.obolibrary.org/obo/UBERON_0003981` +- [endocrine cell](http://purl.obolibrary.org/obo/CL_0000163) and ([BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0000945](http://purl.obolibrary.org/obo/UBERON_0000945)) SubClassOf [enteroendocrine cell](http://purl.obolibrary.org/obo/CL_0000164) -#### Added -- Class: [UBERON_0003981](http://purl.obolibrary.org/obo/UBERON_0003981) -### UBERON_0004642 `http://purl.obolibrary.org/obo/UBERON_0004642` +### GO_0001552 `http://purl.obolibrary.org/obo/GO_0001552` #### Added -- Class: [UBERON_0004642](http://purl.obolibrary.org/obo/UBERON_0004642) +- Class: [GO_0001552](http://purl.obolibrary.org/obo/GO_0001552) -### UBERON_0004670 `http://purl.obolibrary.org/obo/UBERON_0004670` +### GO_0001696 `http://purl.obolibrary.org/obo/GO_0001696` #### Added -- Class: [UBERON_0004670](http://purl.obolibrary.org/obo/UBERON_0004670) +- Class: [GO_0001696](http://purl.obolibrary.org/obo/GO_0001696) -### UBERON_0005357 `http://purl.obolibrary.org/obo/UBERON_0005357` +### GO_0005773 `http://purl.obolibrary.org/obo/GO_0005773` #### Added -- Class: [UBERON_0005357](http://purl.obolibrary.org/obo/UBERON_0005357) +- Class: [GO_0005773](http://purl.obolibrary.org/obo/GO_0005773) -### UBERON_0006250 `http://purl.obolibrary.org/obo/UBERON_0006250` +### GO_0005927 `http://purl.obolibrary.org/obo/GO_0005927` #### Added -- Class: [UBERON_0006250](http://purl.obolibrary.org/obo/UBERON_0006250) +- Class: [GO_0005927](http://purl.obolibrary.org/obo/GO_0005927) -### UBERON_0006914 `http://purl.obolibrary.org/obo/UBERON_0006914` +### GO_0019626 `http://purl.obolibrary.org/obo/GO_0019626` #### Added -- Class: [UBERON_0006914](http://purl.obolibrary.org/obo/UBERON_0006914) +- Class: [GO_0019626](http://purl.obolibrary.org/obo/GO_0019626) -### UBERON_0006915 `http://purl.obolibrary.org/obo/UBERON_0006915` +### GO_0035377 `http://purl.obolibrary.org/obo/GO_0035377` #### Added -- Class: [UBERON_0006915](http://purl.obolibrary.org/obo/UBERON_0006915) +- Class: [GO_0035377](http://purl.obolibrary.org/obo/GO_0035377) -### UBERON_0010077 `http://purl.obolibrary.org/obo/UBERON_0010077` +### GO_0035898 `http://purl.obolibrary.org/obo/GO_0035898` #### Added -- Class: [UBERON_0010077](http://purl.obolibrary.org/obo/UBERON_0010077) +- Class: [GO_0035898](http://purl.obolibrary.org/obo/GO_0035898) -### UBERON_0012186 `http://purl.obolibrary.org/obo/UBERON_0012186` +### GO_0045428 `http://purl.obolibrary.org/obo/GO_0045428` #### Added -- Class: [UBERON_0012186](http://purl.obolibrary.org/obo/UBERON_0012186) +- Class: [GO_0045428](http://purl.obolibrary.org/obo/GO_0045428) -### UBERON_0012375 `http://purl.obolibrary.org/obo/UBERON_0012375` +### GO_0045765 `http://purl.obolibrary.org/obo/GO_0045765` #### Added -- Class: [UBERON_0012375](http://purl.obolibrary.org/obo/UBERON_0012375) +- Class: [GO_0045765](http://purl.obolibrary.org/obo/GO_0045765) -### UBERON_0013739 `http://purl.obolibrary.org/obo/UBERON_0013739` +### GO_0046697 `http://purl.obolibrary.org/obo/GO_0046697` #### Added -- Class: [UBERON_0013739](http://purl.obolibrary.org/obo/UBERON_0013739) +- Class: [GO_0046697](http://purl.obolibrary.org/obo/GO_0046697) -### UBERON_0013740 `http://purl.obolibrary.org/obo/UBERON_0013740` +### GO_0050893 `http://purl.obolibrary.org/obo/GO_0050893` #### Added -- Class: [UBERON_0013740](http://purl.obolibrary.org/obo/UBERON_0013740) +- Class: [GO_0050893](http://purl.obolibrary.org/obo/GO_0050893) -### UBERON_0014727 `http://purl.obolibrary.org/obo/UBERON_0014727` +### GO_0051767 `http://purl.obolibrary.org/obo/GO_0051767` +#### Removed +- Class: [GO_0051767](http://purl.obolibrary.org/obo/GO_0051767) -#### Added -- Class: [UBERON_0014727](http://purl.obolibrary.org/obo/UBERON_0014727) -### UBERON_0014729 `http://purl.obolibrary.org/obo/UBERON_0014729` +### GO_0098522 `http://purl.obolibrary.org/obo/GO_0098522` #### Added -- Class: [UBERON_0014729](http://purl.obolibrary.org/obo/UBERON_0014729) +- Class: [GO_0098522](http://purl.obolibrary.org/obo/GO_0098522) -### UBERON_0015766 `http://purl.obolibrary.org/obo/UBERON_0015766` +### GO_0098535 `http://purl.obolibrary.org/obo/GO_0098535` #### Added -- Class: [UBERON_0015766](http://purl.obolibrary.org/obo/UBERON_0015766) +- Class: [GO_0098535](http://purl.obolibrary.org/obo/GO_0098535) -### VIP GABAergic cortical interneuron `http://purl.obolibrary.org/obo/CL_4023016` +### GlyA-positive erythrocyte `http://purl.obolibrary.org/obo/CL_0002021` #### Removed -- [VIP GABAergic cortical interneuron](http://purl.obolibrary.org/obo/CL_4023016) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A GABAergic neuron located in the cerebral cortex that expresses vasoactive intestinal polypeptide"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:33186530"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [GlyA-positive erythrocyte](http://purl.obolibrary.org/obo/CL_0002021) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:37824655"^^[string](http://www.w3.org/2001/XMLSchema#string) -#### Added -- [VIP GABAergic cortical interneuron](http://purl.obolibrary.org/obo/CL_4023016) [description](http://purl.org/dc/terms/description) "This neuronal type is distinguished by its heterogeneous morphology and electrophysiological characteristics (Pronneke et al., 2015,2020; Apicella and Marchionni, 2022). Variations in morphology and firing patterns are observed in human cortical VIP interneurons. In a study by Lee et al., 2023, four distinct subtypes of VIP neurons were identified, each exhibiting unique morphologies, soma locations, and electrophysiological properties. These subtypes are defined according to their transcriptomic markers: LBH-VIP and CCD184-VIP, both of which display a bipolar morphology with axons and dendrites extending across cortical layers; and SY16-VIP and ADAMTSL1-VIP, characterized by a dendritic arbor that spreads horizontally within the same layer as the soma (Lee et al., 2023). Disruption or malfunction of VIP cortical interneuron is implicated in neurodevelopmental disorders such as Rett Syndrome and Dravet Syndrome (Goff and Goldberg 2021)."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:26420784"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:31210267"^^[string](http://www.w3.org/2001/XMLSchema#string) +### H1 horizontal cell `http://purl.obolibrary.org/obo/CL_0004217` - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:35221922"^^[string](http://www.w3.org/2001/XMLSchema#string) +#### Added +- [H1 horizontal cell](http://purl.obolibrary.org/obo/CL_0004217) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl/cl-base#cellxgene_subset) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:33794534"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [VIP GABAergic cortical interneuron](http://purl.obolibrary.org/obo/CL_4023016) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A transcriptomically distinct cortical GABAergic neuron that expresses the vasocactive intestinal polypeptide and that has its soma located in the cerebral cortex. The standard transcriptomic reference data for this cell type can be found on the CellxGene census under the collection: 'Transcriptomic cytoarchitecture reveals principles of human neocortex organization', dataset: 'Supercluster: CGE-derived interneurons', Author Categories: 'CrossArea_subclass', cluster Vip."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://cellxgene.cziscience.com/e/e4ddac12-f48f-4455-8e8d-c2a48a683437.cxg/"^^[string](http://www.w3.org/2001/XMLSchema#string) +### H2 horizontal cell `http://purl.obolibrary.org/obo/CL_0004218` - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:33186530"^^[string](http://www.w3.org/2001/XMLSchema#string) +#### Added +- [H2 horizontal cell](http://purl.obolibrary.org/obo/CL_0004218) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl/cl-base#cellxgene_subset) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:37824655"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [VIP GABAergic cortical interneuron](http://purl.obolibrary.org/obo/CL_4023016) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "VIP-IN"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:33794534"^^[string](http://www.w3.org/2001/XMLSchema#string) +### Hofbauer cell `http://purl.obolibrary.org/obo/CL_3000001` +#### Removed +- [Hofbauer cell](http://purl.obolibrary.org/obo/CL_3000001) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A tissue-resident macrophage that is part of the placenta. A Hofbauer cell expresses high levels of growth factors and metalloproteinases that support vasculogenesis, angiogenesis, branching morphogenesis and tissue remodeling. A Hofbauer cell has a fetal origin and is present throughout pregnancy."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:30498493"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [VIP GABAergic cortical interneuron](http://purl.obolibrary.org/obo/CL_4023016) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "cortical VIP neuron"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:36384143"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:35438172"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [VIP GABAergic cortical interneuron](http://purl.obolibrary.org/obo/CL_4023016) [has_broad_synonym](http://www.geneontology.org/formats/oboInOwl#hasBroadSynonym) "VIP-Expressing GABAergic Neuron"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:35221922"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:CellBLAST"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [VIP GABAergic cortical interneuron](http://purl.obolibrary.org/obo/CL_4023016) [has_broad_synonym](http://www.geneontology.org/formats/oboInOwl#hasBroadSynonym) "VIP neuron"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:33108272"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:30429548"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [VIP GABAergic cortical interneuron](http://purl.obolibrary.org/obo/CL_4023016) [has_broad_synonym](http://www.geneontology.org/formats/oboInOwl#hasBroadSynonym) "Vip GABAergic neuron"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ILX:0770151"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:34745147"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [VIP GABAergic cortical interneuron](http://purl.obolibrary.org/obo/CL_4023016) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "VIP type"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:37824655"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [Hofbauer cell](http://purl.obolibrary.org/obo/CL_3000001) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "HBC"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003000](http://purl.obolibrary.org/obo/OMO_0003000) -- [VIP GABAergic cortical interneuron](http://purl.obolibrary.org/obo/CL_4023016) [has_broad_synonym](http://www.geneontology.org/formats/oboInOwl#hasBroadSynonym) "VIP interneuron"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:33108272"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [Hofbauer cell](http://purl.obolibrary.org/obo/CL_3000001) SubClassOf [tissue-resident macrophage](http://purl.obolibrary.org/obo/CL_0000864) -- [VIP GABAergic cortical interneuron](http://purl.obolibrary.org/obo/CL_4023016) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "Vip"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ILX:0770151"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [Hofbauer cell](http://purl.obolibrary.org/obo/CL_3000001) SubClassOf [BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0001987](http://purl.obolibrary.org/obo/UBERON_0001987) +#### Added +- [Hofbauer cell](http://purl.obolibrary.org/obo/CL_3000001) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "HBC"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003000](http://purl.obolibrary.org/obo/OMO_0003000) -### acinar cell `http://purl.obolibrary.org/obo/CL_0000622` + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:39007150"^^[string](http://www.w3.org/2001/XMLSchema#string) -#### Added -- [acinar cell](http://purl.obolibrary.org/obo/CL_0000622) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://cellxgene.cziscience.com/cellguide/CL_0000622"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [Hofbauer cell](http://purl.obolibrary.org/obo/CL_3000001) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A tissue-resident macrophage that is part of the placenta. A Hofbauer cell expresses high levels of growth factors and metalloproteinases that support vasculogenesis, angiogenesis, branching morphogenesis and tissue remodeling. A Hofbauer cell has a fetal origin, is found in the villous stroma, chorion, and amnion, and is present throughout pregnancy."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:30498493"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [acinar cell](http://purl.obolibrary.org/obo/CL_0000622) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:35438172"^^[string](http://www.w3.org/2001/XMLSchema#string) -Acinar cells are specialized exocrine gland cells that secrete specific enzymes and fluids to aid in digestion. Found primarily in the pancreas and salivary glands, the term acinar is derived from the Latin word 'acinus' which means 'grape'; this is because acinar cells are arranged in a grape-like cluster around small ducts, formulating an acinus structure. -In the salivary glands, acinar cells secrete digestive enzymes as well as other substances such as mucus and water. These secretions service the initial stages of the digestive process, preparing the consumed food for onward digestion in the stomach and intestines by lubricating and partially breaking it down. -In the pancreas, acinar cells are responsible for synthesizing and secreting a significant amount of digestive enzymes, such as trypsin, chymotrypsin, and amylase. These enzymes are stored in zymogen granules inside the acinar cells until they are dispatched into the small intestine. Once within the small intestine, they break down proteins, carbohydrates, and fats into substances that can be absorbed. This is vital to the effective and efficient digestion and absorption of nutrients from the food we consume. -Acinar cells have high protein synthesis rates and are susceptible to accumulation of misfolded proteins; the subsequential induction of ER stress is thought to be involved in the development of pancreatitis, a serious inflammatory disease of the exocrine pancreas."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1111/prd.12116"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:CellBLAST"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1152/physrev.00011.2011"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:30429548"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1007/BF00710764"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:34745147"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1097/MOG.0b013e32832ebfac"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [Hofbauer cell](http://purl.obolibrary.org/obo/CL_3000001) [has_exact_synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "fetal Hofbauer cell"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:39007150"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1038/nrgastro.2013.36"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [Hofbauer cell](http://purl.obolibrary.org/obo/CL_3000001) SubClassOf [placental resident macrophage](http://purl.obolibrary.org/obo/CL_4033087) -### adepithelial cell `http://purl.obolibrary.org/obo/CL_0000462` +### ILC1, human `http://purl.obolibrary.org/obo/CL_0001077` #### Removed -- [adepithelial cell](http://purl.obolibrary.org/obo/CL_0000462) SubClassOf [eukaryotic cell](http://purl.obolibrary.org/obo/CL_0000255) - -- [adepithelial cell](http://purl.obolibrary.org/obo/CL_0000462) SubClassOf [RO_0002160](http://purl.obolibrary.org/obo/RO_0002160) some [NCBITaxon_50557](http://purl.obolibrary.org/obo/NCBITaxon_50557) +- [ILC1, human](http://purl.obolibrary.org/obo/CL_0001077) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) -#### Added -- [adepithelial cell](http://purl.obolibrary.org/obo/CL_0000462) SubClassOf [RO_0002162](http://purl.obolibrary.org/obo/RO_0002162) some [NCBITaxon_50557](http://purl.obolibrary.org/obo/NCBITaxon_50557) -### adipose macrophage `http://purl.obolibrary.org/obo/CL_0002477` +### Island of Calleja granule cell `http://purl.obolibrary.org/obo/CL_4030053` #### Added -- [adipose macrophage](http://purl.obolibrary.org/obo/CL_0002477) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) +- [Island of Calleja granule cell](http://purl.obolibrary.org/obo/CL_4030053) SubClassOf [BFO_0000002](http://purl.obolibrary.org/obo/BFO_0000002) -### alarm substance cell `http://purl.obolibrary.org/obo/CL_0007021` +### Kit and Sca1-positive hematopoietic stem cell `http://purl.obolibrary.org/obo/CL_0001008` +#### Removed +- [Kit and Sca1-positive hematopoietic stem cell](http://purl.obolibrary.org/obo/CL_0001008) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) -#### Added -- [alarm substance cell](http://purl.obolibrary.org/obo/CL_0007021) SubClassOf [eukaryotic cell](http://purl.obolibrary.org/obo/CL_0000255) -### alpha-beta T cell `http://purl.obolibrary.org/obo/CL_0000789` +### Kit-negative, Ly-76 high orthochromatophilic erythroblasts `http://purl.obolibrary.org/obo/CL_0002017` +#### Removed +- [Kit-negative, Ly-76 high orthochromatophilic erythroblasts](http://purl.obolibrary.org/obo/CL_0002017) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) + -#### Added -- [alpha-beta T cell](http://purl.obolibrary.org/obo/CL_0000789) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) +### Kit-positive macrophage dendritic cell progenitor `http://purl.obolibrary.org/obo/CL_0002011` +#### Removed +- [Kit-positive macrophage dendritic cell progenitor](http://purl.obolibrary.org/obo/CL_0002011) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) -### alpha1-tanycyte `http://purl.obolibrary.org/obo/CL_4042017` -#### Added -- [alpha1-tanycyte](http://purl.obolibrary.org/obo/CL_4042017) [id](http://www.geneontology.org/formats/oboInOwl#id) "CL:4042017"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [alpha1-tanycyte](http://purl.obolibrary.org/obo/CL_4042017) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A tanycyte cell found in the ventromedial and dorsomedial nuclei of the hypothalamus. This type of tanycyte extends its protrusions close to parenchymal neurons without contacting blood vessels. It expresses the glial marker S-100β."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:16344112"^^[string](http://www.w3.org/2001/XMLSchema#string) +### Kit-positive megakaryocyte progenitor cell `http://purl.obolibrary.org/obo/CL_0002024` +#### Removed +- [Kit-positive megakaryocyte progenitor cell](http://purl.obolibrary.org/obo/CL_0002024) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "wikipedia:Tanycyte"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:26578855"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [alpha1-tanycyte](http://purl.obolibrary.org/obo/CL_4042017) [comment](http://www.w3.org/2000/01/rdf-schema#comment) "In rodents, a1 tanycytes are known to express DARPP-32, GPR50, NA Vimentin, Connexin 43, GLT-1, GLUT1(+) (Goodman and Hajihosseini 2015; Prevot et al., 2018)."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:26578855"^^[string](http://www.w3.org/2001/XMLSchema#string) +### Kit-positive, CD34-negative megakaryocyte erythroid progenitor cell `http://purl.obolibrary.org/obo/CL_0002006` +#### Removed +- [Kit-positive, CD34-negative megakaryocyte erythroid progenitor cell](http://purl.obolibrary.org/obo/CL_0002006) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) -- [alpha1-tanycyte](http://purl.obolibrary.org/obo/CL_4042017) [contributor](http://purl.org/dc/terms/contributor) [0000-0002-0098-8958](https://orcid.org/0000-0002-0098-8958) -- [alpha1-tanycyte](http://purl.obolibrary.org/obo/CL_4042017) [label](http://www.w3.org/2000/01/rdf-schema#label) "alpha1-tanycyte"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [alpha1-tanycyte](http://purl.obolibrary.org/obo/CL_4042017) [date](http://purl.org/dc/terms/date) "2024-08-19T13:06:16Z"^^[dateTime](http://www.w3.org/2001/XMLSchema#dateTime) +### Kit-positive, Sca1-positive common lymphoid progenitor `http://purl.obolibrary.org/obo/CL_0001025` +#### Removed +- [Kit-positive, Sca1-positive common lymphoid progenitor](http://purl.obolibrary.org/obo/CL_0001025) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) -- [alpha1-tanycyte](http://purl.obolibrary.org/obo/CL_4042017) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "DMH tanycyte"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:29351662"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [alpha1-tanycyte](http://purl.obolibrary.org/obo/CL_4042017) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "VMH tanycyte"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:29351662"^^[string](http://www.w3.org/2001/XMLSchema#string) -- Class: [alpha1-tanycyte](http://purl.obolibrary.org/obo/CL_4042017) +### Kupffer cell `http://purl.obolibrary.org/obo/CL_0000091` +#### Removed +- [Kupffer cell](http://purl.obolibrary.org/obo/CL_0000091) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. -- [alpha1-tanycyte](http://purl.obolibrary.org/obo/CL_4042017) SubClassOf [BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0004642](http://purl.obolibrary.org/obo/UBERON_0004642) +Kupffer cells are tissue-resident macrophages located in the liver. They are an integral part of the mononuclear phagocyte system and are responsible for the phagocytosis of dead or dying cells, microbes, and other foreign substances. Kupffer cells account for approximately 80-90% of tissue-resident macrophages in the body. They are found within the lumen of liver sinusoids and interface with microbial populations and products. +The primary role of Kupffer cells is to maintain homeostasis in the liver. They continuously filter and cleanse the blood that flows through the liver, removing pathogens, endotoxins, particulate matter, aged and dysfunctional red blood cells, and miscellaneous waste products. These cells also play an important role in maintaining iron homeostasis. During the process of phagocytosis, Kupffer cells recycle iron from degraded red blood cells, which is then utilized in the formation of new erythrocytes. +Kupffer cells also play key roles in various immune responses and inflammatory processes. They secrete various types of cytokines and chemokines, which contribute to the activation and mobilization of other immune cells. They can also produce reactive oxygen species and nitric oxide, which have microbicidal actions. Although their activity is essential for host defense, excessive or prolonged activation of Kupffer cells may contribute to hepatic injury, inflammation, and fibrosis."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1038/nri.2017.11"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [alpha1-tanycyte](http://purl.obolibrary.org/obo/CL_4042017) SubClassOf [tanycyte](http://purl.obolibrary.org/obo/CL_0002085) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1007/978-1-4939-1311-4_10"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [alpha1-tanycyte](http://purl.obolibrary.org/obo/CL_4042017) SubClassOf [RO_0002292](http://purl.obolibrary.org/obo/RO_0002292) some [PR_000014419](http://purl.obolibrary.org/obo/PR_000014419) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1111/j.1478-3231.2006.01342.x"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [alpha1-tanycyte](http://purl.obolibrary.org/obo/CL_4042017) SubClassOf [astrocyte of the forebrain](http://purl.obolibrary.org/obo/CL_0012000) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1002/cphy.c120026"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1016/j.immuni.2022.08.002"^^[string](http://www.w3.org/2001/XMLSchema#string) -### alpha2-tanycyte `http://purl.obolibrary.org/obo/CL_4042018` +- [Kupffer cell](http://purl.obolibrary.org/obo/CL_0000091) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) #### Added -- [alpha2-tanycyte](http://purl.obolibrary.org/obo/CL_4042018) [comment](http://www.w3.org/2000/01/rdf-schema#comment) "In rodents, this type of tanycyte is more developmentally advanced than alpha1 tanycytes, shows a high neurogenic competence and expresses the following markers DARPP-32, Vimentin, GPR50, Connexin-43, GLT-1, GLUT1(+) (Goodman and Hajihosseini 2015; Prevot et al., 2018)"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:26578855"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [Kupffer cell](http://purl.obolibrary.org/obo/CL_0000091) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. -- [alpha2-tanycyte](http://purl.obolibrary.org/obo/CL_4042018) [id](http://www.geneontology.org/formats/oboInOwl#id) "CL:4042018"^^[string](http://www.w3.org/2001/XMLSchema#string) +Kupffer cells are tissue-resident macrophages located in the liver. They are an integral part of the mononuclear phagocyte system and are responsible for the phagocytosis of dead or dying cells, microbes, and other foreign substances. Kupffer cells account for approximately 80-90% of tissue-resident macrophages in the body. They are found within the lumen of liver sinusoids and interface with microbial populations and products. +The primary role of Kupffer cells is to maintain homeostasis in the liver. They continuously filter and cleanse the blood that flows through the liver, removing pathogens, endotoxins, particulate matter, aged and dysfunctional red blood cells, and miscellaneous waste products. These cells also play an important role in maintaining iron homeostasis. During the process of phagocytosis, Kupffer cells recycle iron from degraded red blood cells, which is then utilized in the formation of new erythrocytes. +Kupffer cells also play key roles in various immune responses and inflammatory processes. They secrete various types of cytokines and chemokines, which contribute to the activation and mobilization of other immune cells. They can also produce reactive oxygen species and nitric oxide, which have microbicidal actions. Although their activity is essential for host defense, excessive or prolonged activation of Kupffer cells may contribute to hepatic injury, inflammation, and fibrosis."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1038/nri.2017.11"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [alpha2-tanycyte](http://purl.obolibrary.org/obo/CL_4042018) [label](http://www.w3.org/2000/01/rdf-schema#label) "alpha2-tanycyte"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1007/978-1-4939-1311-4_10"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [alpha2-tanycyte](http://purl.obolibrary.org/obo/CL_4042018) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "dmARH tanycyte"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:29351662"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1111/j.1478-3231.2006.01342.x"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [alpha2-tanycyte](http://purl.obolibrary.org/obo/CL_4042018) [contributor](http://purl.org/dc/terms/contributor) [0000-0002-0098-8958](https://orcid.org/0000-0002-0098-8958) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1002/cphy.c120026"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [alpha2-tanycyte](http://purl.obolibrary.org/obo/CL_4042018) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A type of tanycyte found in the dorsomedial arcuate nucleus of the hypothalamus. This mono-ciliated tanycyte extends its protrusion to the arcuate nucleus and expresses the glial marker S-100β."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:16344112"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1016/j.immuni.2022.08.002"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "wikipedia:Tanycyte"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:29351662"^^[string](http://www.w3.org/2001/XMLSchema#string) +### L cone cell `http://purl.obolibrary.org/obo/CL_0003048` +#### Removed +- [L cone cell](http://purl.obolibrary.org/obo/CL_0003048) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:26578855"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [alpha2-tanycyte](http://purl.obolibrary.org/obo/CL_4042018) [date](http://purl.org/dc/terms/date) "2024-08-19T13:13:20Z"^^[dateTime](http://www.w3.org/2001/XMLSchema#dateTime) -- Class: [alpha2-tanycyte](http://purl.obolibrary.org/obo/CL_4042018) +### L2/3 intratelencephalic projecting glutamatergic neuron `http://purl.obolibrary.org/obo/CL_4030059` +#### Removed +- [L2/3 intratelencephalic projecting glutamatergic neuron](http://purl.obolibrary.org/obo/CL_4030059) [comment](http://www.w3.org/2000/01/rdf-schema#comment) "Hystorically, the L2/3 intratelencephalic projectic glutametergic neuron was known to have its soma in cortical layer 2/3. MERFISH data showed that this intratelencephalic-projecting glutametergic neuron can have its soma in layer 2/3, 4B, 4C. The position of the soma in layer 4b and 4C is less frequent for this neuronal type in comparison to cortical layer 2/3."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:37824655"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [alpha2-tanycyte](http://purl.obolibrary.org/obo/CL_4042018) SubClassOf [RO_0002131](http://purl.obolibrary.org/obo/RO_0002131) some [UBERON_0001932](http://purl.obolibrary.org/obo/UBERON_0001932) +#### Added +- [L2/3 intratelencephalic projecting glutamatergic neuron](http://purl.obolibrary.org/obo/CL_4030059) [RO_0002175](http://purl.obolibrary.org/obo/RO_0002175) [NCBITaxon_9606](http://purl.obolibrary.org/obo/NCBITaxon_9606) -- [alpha2-tanycyte](http://purl.obolibrary.org/obo/CL_4042018) SubClassOf [RO_0002292](http://purl.obolibrary.org/obo/RO_0002292) some [PR_000014419](http://purl.obolibrary.org/obo/PR_000014419) +- [L2/3 intratelencephalic projecting glutamatergic neuron](http://purl.obolibrary.org/obo/CL_4030059) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl/cl-base#cellxgene_subset) -- [alpha2-tanycyte](http://purl.obolibrary.org/obo/CL_4042018) SubClassOf [tanycyte](http://purl.obolibrary.org/obo/CL_0002085) +- [L2/3 intratelencephalic projecting glutamatergic neuron](http://purl.obolibrary.org/obo/CL_4030059) [comment](http://www.w3.org/2000/01/rdf-schema#comment) "Hystorically, the L2/3 intratelencephalic projectic glutametergic neuron was known to have its soma in cortical layer 2/3. MERFISH data showed that this intratelencephalic-projecting glutametergic neuron can have its soma in layer 2/3, 4B, 4C. The position of the soma in layer 4b and 4C is less frequent for this neuronal type in comparison to cortical layer 2/3. The marker set ONECUT2, COL5A2 can identify the Human cell type L2/3 intratelencephalic projecting glutamatergic neuron in the Brain with a confidence of 0.670149932 (NS-Forest FBeta value)."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://doi.org/10.5281/zenodo.11165918"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:37824655"^^[string](http://www.w3.org/2001/XMLSchema#string) -### alternatively activated macrophage `http://purl.obolibrary.org/obo/CL_0000890` +- [L2/3 intratelencephalic projecting glutamatergic neuron](http://purl.obolibrary.org/obo/CL_4030059) SubClassOf [RO_0015004](http://purl.obolibrary.org/obo/RO_0015004) some [CLM_1000065](http://purl.obolibrary.org/obo/CLM_1000065) -#### Added -- [alternatively activated macrophage](http://purl.obolibrary.org/obo/CL_0000890) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://cellxgene.cziscience.com/cellguide/CL_0000890"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [alternatively activated macrophage](http://purl.obolibrary.org/obo/CL_0000890) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. +### L4 intratelencephalic projecting glutamatergic neuron `http://purl.obolibrary.org/obo/CL_4030063` +#### Removed +- [L4 intratelencephalic projecting glutamatergic neuron](http://purl.obolibrary.org/obo/CL_4030063) [comment](http://www.w3.org/2000/01/rdf-schema#comment) "Historically, the L4 intratelencephalic projectic glutametergic neuron was known to have its soma in cortical layer 4. MERFISH data showed that this intratelencephalic-projecting glutametergic neuron can also have its soma in layer 3."^^[string](http://www.w3.org/2001/XMLSchema#string) -Alternatively activated macrophages, also referred to as M2 macrophages, are immune cells originating from monocytes. The M1/M2 classification is based upon macrophage polarization rather than macrophage location and refers to macrophage activation towards either a more inflammatory or more resolving phenotype, respectively, although the functional diversity of macrophages is more nuanced than such a dichotomy suggests. -M2 macrophages cells are differentiated from their precursors generally in response to Th2 cytokines, such as interleukin-4 (IL-4), interleukin-10 (IL-10), and interleukin-13 (IL-13). Tissue-resident macrophages are also sometimes said to have an “M2-like” phenotype. M2 macrophages play key roles in immunoregulation and disease resolution. -Functionally, alternatively activated macrophages are essential in wound healing and tissue repair and remodeling, largely due to their potent anti-inflammatory actions and their ability to promote angiogenesis. They achieve these functions by the production of specific growth factors and signaling proteins including Arg1, Ym1/2, Fizz1, and TGF-β. Additionally, they provide defense against specific categories of pathogens, particularly parasites, through specific communication with Th2 cells. -However, dysfunction of M2 macrophages can be harmful. Alternatively activated macrophages have been associated with several pathological conditions such as asthma, fibrosis, and tumor progression. This is due to their capacity to inhibit inflammatory responses, promote unneeded wound healing processes, and support tumour growth and spreading. Furthermore, complex roles have been observed in metabolic disorders, cardiovascular diseases, and neurodegenerative diseases, showing the diverse functional spectrum of these cells."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1186/s12935-021-02089-2"^^[string](http://www.w3.org/2001/XMLSchema#string) +#### Added +- [L4 intratelencephalic projecting glutamatergic neuron](http://purl.obolibrary.org/obo/CL_4030063) [RO_0002175](http://purl.obolibrary.org/obo/RO_0002175) [NCBITaxon_9606](http://purl.obolibrary.org/obo/NCBITaxon_9606) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.3389/fimmu.2020.583084"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [L4 intratelencephalic projecting glutamatergic neuron](http://purl.obolibrary.org/obo/CL_4030063) [comment](http://www.w3.org/2000/01/rdf-schema#comment) "The marker set RORB, ST8SIA4 can identify the Human cell type L4 intratelencephalic projecting glutamatergic neuron in the Brain with a confidence of 0.720108696 (NS-Forest FBeta value). Historically, the L4 intratelencephalic projectic glutametergic neuron was known to have its soma in cortical layer 4. MERFISH data showed that this intratelencephalic-projecting glutametergic neuron can also have its soma in layer 3."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://doi.org/10.5281/zenodo.11165918"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.3389/fimmu.2015.00263"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [L4 intratelencephalic projecting glutamatergic neuron](http://purl.obolibrary.org/obo/CL_4030063) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl/cl-base#cellxgene_subset) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1038/s41392-023-01452-1"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [L4 intratelencephalic projecting glutamatergic neuron](http://purl.obolibrary.org/obo/CL_4030063) SubClassOf [RO_0015004](http://purl.obolibrary.org/obo/RO_0015004) some [CLM_1000066](http://purl.obolibrary.org/obo/CLM_1000066) -### alveolar macrophage `http://purl.obolibrary.org/obo/CL_0000583` +### L5 extratelencephalic projecting glutamatergic cortical neuron `http://purl.obolibrary.org/obo/CL_4023041` #### Added -- [alveolar macrophage](http://purl.obolibrary.org/obo/CL_0000583) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. +- [L5 extratelencephalic projecting glutamatergic cortical neuron](http://purl.obolibrary.org/obo/CL_4023041) [RO_0002175](http://purl.obolibrary.org/obo/RO_0002175) [NCBITaxon_9606](http://purl.obolibrary.org/obo/NCBITaxon_9606) -Alveolar macrophages are unique tissue-resident macrophages found in the lungs, specifically in the air sacs or alveoli where gas exchange occurs. They are characterized by specific surface markers including: F4/80-positive, CD11b-/low, CD11c-positive, CD68-positive, sialoadhesin-positive, dectin-1-positive, MR-positive, CX3CR1-negative. These specialized immune cells form a crucial part of the body's defense mechanism, playing important roles in pulmonary health and homeostasis. They are the first line of defense in the pulmonary immune response, acting as scavengers that patrol the alveoli and engulf foreign particles like bacteria, dust, and other debris that enter the lungs through inhalation. -The primary function of these alveolar macrophages is phagocytosis, whereby they consume and digest foreign substances, dead cells, and other particulates. In the lung, alveolar macrophages are also responsible for clearing surfactant. Additionally, alveolar macrophages also play an integral role in initiating the immune response, as they secrete several pro-inflammatory cytokines and chemokines that recruit other immune cells to the site of infection or inflammation. -Beyond their role in host defense, alveolar macrophages contribute to tissue remodeling and wound repair in the lungs, aiding in maintaining lung integrity. They also regulate local inflammation and control the immune response to prevent excessive inflammation that may be harmful. However, an imbalance in the function of alveolar macrophages can contribute to various lung diseases. Abnormal alveolar macrophage activation has been implicated in chronic inflammatory diseases such as emphysema, asthma, and fibrosis."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1016/j.cellimm.2018.01.005"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [L5 extratelencephalic projecting glutamatergic cortical neuron](http://purl.obolibrary.org/obo/CL_4023041) [comment](http://www.w3.org/2000/01/rdf-schema#comment) "The marker set CHST8, POU3F1 can identify the Human cell type L5 extratelencephalic projecting glutamatergic cortical neuron in the Brain with a confidence of 0.815891473 (NS-Forest FBeta value)."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://doi.org/10.5281/zenodo.11165918"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1007/s00424-017-1965-3"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [L5 extratelencephalic projecting glutamatergic cortical neuron](http://purl.obolibrary.org/obo/CL_4023041) SubClassOf [RO_0015004](http://purl.obolibrary.org/obo/RO_0015004) some [CLM_1000067](http://purl.obolibrary.org/obo/CLM_1000067) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.14348/molcells.2021.0058"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1038/nri3600"^^[string](http://www.w3.org/2001/XMLSchema#string) +### L5 intratelencephalic projecting glutamatergic neuron `http://purl.obolibrary.org/obo/CL_4030064` -- [alveolar macrophage](http://purl.obolibrary.org/obo/CL_0000583) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://cellxgene.cziscience.com/cellguide/CL_0000583"^^[string](http://www.w3.org/2001/XMLSchema#string) +#### Added +- [L5 intratelencephalic projecting glutamatergic neuron](http://purl.obolibrary.org/obo/CL_4030064) [RO_0002175](http://purl.obolibrary.org/obo/RO_0002175) [NCBITaxon_9606](http://purl.obolibrary.org/obo/NCBITaxon_9606) -- [alveolar macrophage](http://purl.obolibrary.org/obo/CL_0000583) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) +- [L5 intratelencephalic projecting glutamatergic neuron](http://purl.obolibrary.org/obo/CL_4030064) [comment](http://www.w3.org/2000/01/rdf-schema#comment) "The marker set ARSJ, RORB, KCNK2 can identify the Human cell type L5 intratelencephalic projecting glutamatergic neuron in the Brain with a confidence of 0.764261336 (NS-Forest FBeta value)."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://doi.org/10.5281/zenodo.11165918"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [L5 intratelencephalic projecting glutamatergic neuron](http://purl.obolibrary.org/obo/CL_4030064) SubClassOf [RO_0015004](http://purl.obolibrary.org/obo/RO_0015004) some [CLM_1000068](http://purl.obolibrary.org/obo/CLM_1000068) -### angioblastic mesenchymal cell `http://purl.obolibrary.org/obo/CL_0000566` + +### L5/6 near-projecting glutamatergic neuron `http://purl.obolibrary.org/obo/CL_4030067` #### Added -- [angioblastic mesenchymal cell](http://purl.obolibrary.org/obo/CL_0000566) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) +- [L5/6 near-projecting glutamatergic neuron](http://purl.obolibrary.org/obo/CL_4030067) [comment](http://www.w3.org/2000/01/rdf-schema#comment) "The marker set NPSR1-AS1, TLL1 can identify the Human cell type L5/6 near-projecting glutamatergic neuron in the Brain with a confidence of 0.899288218 (NS-Forest FBeta value)."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://doi.org/10.5281/zenodo.11165918"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [L5/6 near-projecting glutamatergic neuron](http://purl.obolibrary.org/obo/CL_4030067) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl/cl-base#cellxgene_subset) -### angiogenic pericyte `http://purl.obolibrary.org/obo/CL_4047012` +- [L5/6 near-projecting glutamatergic neuron](http://purl.obolibrary.org/obo/CL_4030067) [RO_0002175](http://purl.obolibrary.org/obo/RO_0002175) [NCBITaxon_9606](http://purl.obolibrary.org/obo/NCBITaxon_9606) -#### Added -- [angiogenic pericyte](http://purl.obolibrary.org/obo/CL_4047012) [contributor](http://purl.org/dc/terms/contributor) [0009-0005-7919-4905](https://orcid.org/0009-0005-7919-4905) +- [L5/6 near-projecting glutamatergic neuron](http://purl.obolibrary.org/obo/CL_4030067) SubClassOf [RO_0015004](http://purl.obolibrary.org/obo/RO_0015004) some [CLM_1000069](http://purl.obolibrary.org/obo/CLM_1000069) -- [angiogenic pericyte](http://purl.obolibrary.org/obo/CL_4047012) [date](http://purl.org/dc/terms/date) "2024-09-06T08:41:39Z"^^[dateTime](http://www.w3.org/2001/XMLSchema#dateTime) -- [angiogenic pericyte](http://purl.obolibrary.org/obo/CL_4047012) [id](http://www.geneontology.org/formats/oboInOwl#id) "CL:4047012"^^[string](http://www.w3.org/2001/XMLSchema#string) +### L6 corticothalamic-projecting glutamatergic cortical neuron `http://purl.obolibrary.org/obo/CL_4023042` -- [angiogenic pericyte](http://purl.obolibrary.org/obo/CL_4047012) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A specialized pericyte that actively participates in the formation of new blood vessels during angiogenesis by undergoing phenotypic changes, increasing proliferation, and interacting closely with endothelial cells."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:34497389"^^[string](http://www.w3.org/2001/XMLSchema#string) +#### Added +- [L6 corticothalamic-projecting glutamatergic cortical neuron](http://purl.obolibrary.org/obo/CL_4023042) [RO_0002175](http://purl.obolibrary.org/obo/RO_0002175) [NCBITaxon_9606](http://purl.obolibrary.org/obo/NCBITaxon_9606) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:24853910"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [L6 corticothalamic-projecting glutamatergic cortical neuron](http://purl.obolibrary.org/obo/CL_4023042) [comment](http://www.w3.org/2000/01/rdf-schema#comment) "The marker set SEMA5B, ADAMTSL1, SULF1 can identify the Human cell type L6 corticothalamic-projecting glutamatergic cortical neuron in the Brain with a confidence of 0.631898455 (NS-Forest FBeta value)."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://doi.org/10.5281/zenodo.11165918"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [angiogenic pericyte](http://purl.obolibrary.org/obo/CL_4047012) [label](http://www.w3.org/2000/01/rdf-schema#label) "angiogenic pericyte"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [L6 corticothalamic-projecting glutamatergic cortical neuron](http://purl.obolibrary.org/obo/CL_4023042) SubClassOf [RO_0015004](http://purl.obolibrary.org/obo/RO_0015004) some [CLM_1000070](http://purl.obolibrary.org/obo/CLM_1000070) -- Class: [angiogenic pericyte](http://purl.obolibrary.org/obo/CL_4047012) -- [angiogenic pericyte](http://purl.obolibrary.org/obo/CL_4047012) SubClassOf [pericyte](http://purl.obolibrary.org/obo/CL_0000669) +### L6 intratelencephalic projecting Car3 glutamatergic neuron `http://purl.obolibrary.org/obo/CL_4030068` +#### Added +- [L6 intratelencephalic projecting Car3 glutamatergic neuron](http://purl.obolibrary.org/obo/CL_4030068) [comment](http://www.w3.org/2000/01/rdf-schema#comment) "The marker set SMYD1, THEMIS can identify the Human cell type L6 intratelencephalic projecting Car3 glutamatergic neuron in the Brain with a confidence of 0.877752028 (NS-Forest FBeta value)."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://doi.org/10.5281/zenodo.11165918"^^[string](http://www.w3.org/2001/XMLSchema#string) -### animal zygote `http://purl.obolibrary.org/obo/CL_0000365` -#### Removed -- [animal zygote](http://purl.obolibrary.org/obo/CL_0000365) EquivalentTo [zygote](http://purl.obolibrary.org/obo/CL_0010017) and ([RO_0002160](http://purl.obolibrary.org/obo/RO_0002160) some [NCBITaxon_33208](http://purl.obolibrary.org/obo/NCBITaxon_33208)) +- [L6 intratelencephalic projecting Car3 glutamatergic neuron](http://purl.obolibrary.org/obo/CL_4030068) [RO_0002175](http://purl.obolibrary.org/obo/RO_0002175) [NCBITaxon_9606](http://purl.obolibrary.org/obo/NCBITaxon_9606) -- [animal zygote](http://purl.obolibrary.org/obo/CL_0000365) SubClassOf [RO_0002160](http://purl.obolibrary.org/obo/RO_0002160) some [NCBITaxon_33208](http://purl.obolibrary.org/obo/NCBITaxon_33208) +- [L6 intratelencephalic projecting Car3 glutamatergic neuron](http://purl.obolibrary.org/obo/CL_4030068) SubClassOf [RO_0015004](http://purl.obolibrary.org/obo/RO_0015004) some [CLM_1000072](http://purl.obolibrary.org/obo/CLM_1000072) + + +### L6 intratelencephalic projecting glutamatergic neuron `http://purl.obolibrary.org/obo/CL_4030065` #### Added -- [animal zygote](http://purl.obolibrary.org/obo/CL_0000365) EquivalentTo [zygote](http://purl.obolibrary.org/obo/CL_0010017) and ([RO_0002162](http://purl.obolibrary.org/obo/RO_0002162) some [NCBITaxon_33208](http://purl.obolibrary.org/obo/NCBITaxon_33208)) +- [L6 intratelencephalic projecting glutamatergic neuron](http://purl.obolibrary.org/obo/CL_4030065) [comment](http://www.w3.org/2000/01/rdf-schema#comment) "The marker set LINC00507, THEMIS can identify the Human cell type L6 intratelencephalic projecting glutamatergic neuron in the Brain with a confidence of 0.641695703 (NS-Forest FBeta value)."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://doi.org/10.5281/zenodo.11165918"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [animal zygote](http://purl.obolibrary.org/obo/CL_0000365) SubClassOf [RO_0002162](http://purl.obolibrary.org/obo/RO_0002162) some [NCBITaxon_33208](http://purl.obolibrary.org/obo/NCBITaxon_33208) +- [L6 intratelencephalic projecting glutamatergic neuron](http://purl.obolibrary.org/obo/CL_4030065) [RO_0002175](http://purl.obolibrary.org/obo/RO_0002175) [NCBITaxon_9606](http://purl.obolibrary.org/obo/NCBITaxon_9606) +- [L6 intratelencephalic projecting glutamatergic neuron](http://purl.obolibrary.org/obo/CL_4030065) SubClassOf [RO_0015004](http://purl.obolibrary.org/obo/RO_0015004) some [CLM_1000071](http://purl.obolibrary.org/obo/CLM_1000071) -### astrocyte of the cerebral cortex `http://purl.obolibrary.org/obo/CL_0002605` + +### L6 intratelencephalic projecting glutamatergic neuron of the primary motor cortex `http://purl.obolibrary.org/obo/CL_4023050` #### Removed -- [astrocyte of the cerebral cortex](http://purl.obolibrary.org/obo/CL_0002605) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "An astrocyte of the cerebral cortex."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:tfm"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [L6 intratelencephalic projecting glutamatergic neuron of the primary motor cortex](http://purl.obolibrary.org/obo/CL_4023050) SubClassOf [RO_0000053](http://purl.obolibrary.org/obo/RO_0000053) some [PATO_0070019](http://purl.obolibrary.org/obo/PATO_0070019) #### Added -- [astrocyte of the cerebral cortex](http://purl.obolibrary.org/obo/CL_0002605) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A transcriptomically distinct astrocyte that is found in the cerebral cortex."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:tfm"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [L6 intratelencephalic projecting glutamatergic neuron of the primary motor cortex](http://purl.obolibrary.org/obo/CL_4023050) SubClassOf [untufted pyramidal neuron](http://purl.obolibrary.org/obo/CL_4023095) -### astrocyte-restricted precursor `http://purl.obolibrary.org/obo/CL_4042022` +### L6b glutamatergic neuron of the primary motor cortex `http://purl.obolibrary.org/obo/CL_4023046` #### Added -- [astrocyte-restricted precursor](http://purl.obolibrary.org/obo/CL_4042022) [id](http://www.geneontology.org/formats/oboInOwl#id) "CL:4042022"^^[string](http://www.w3.org/2001/XMLSchema#string) - -- [astrocyte-restricted precursor](http://purl.obolibrary.org/obo/CL_4042022) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "astrocyte precursor cell"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:33052610"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [L6b glutamatergic neuron of the primary motor cortex](http://purl.obolibrary.org/obo/CL_4023046) [RO_0002175](http://purl.obolibrary.org/obo/RO_0002175) [NCBITaxon_9606](http://purl.obolibrary.org/obo/NCBITaxon_9606) -- [astrocyte-restricted precursor](http://purl.obolibrary.org/obo/CL_4042022) [date](http://purl.org/dc/terms/date) "2024-09-02T11:44:45Z"^^[dateTime](http://www.w3.org/2001/XMLSchema#dateTime) +- [L6b glutamatergic neuron of the primary motor cortex](http://purl.obolibrary.org/obo/CL_4023046) [comment](http://www.w3.org/2000/01/rdf-schema#comment) "The marker set CCN2, ROS1 can identify the Human cell type L6b glutamatergic neuron of the primary motor cortex in the Brain with a confidence of 0.819940964 (NS-Forest FBeta value)."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://doi.org/10.5281/zenodo.11165918"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [astrocyte-restricted precursor](http://purl.obolibrary.org/obo/CL_4042022) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "ARP"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [synonym_type_property](http://www.geneontology.org/formats/oboInOwl#SynonymTypeProperty) "OMO:0003000"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [L6b glutamatergic neuron of the primary motor cortex](http://purl.obolibrary.org/obo/CL_4023046) SubClassOf [RO_0015004](http://purl.obolibrary.org/obo/RO_0015004) some [CLM_1000073](http://purl.obolibrary.org/obo/CLM_1000073) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:33052610"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [astrocyte-restricted precursor](http://purl.obolibrary.org/obo/CL_4042022) [comment](http://www.w3.org/2000/01/rdf-schema#comment) "In vitro, this progenitor cell can differentiate from glial-restricted precursor cells."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:33052610"^^[string](http://www.w3.org/2001/XMLSchema#string) +### Lamp5 Lhx6 neuron `http://purl.obolibrary.org/obo/CL_4042013` -- [astrocyte-restricted precursor](http://purl.obolibrary.org/obo/CL_4042022) [label](http://www.w3.org/2000/01/rdf-schema#label) "astrocyte-restricted precursor"^^[string](http://www.w3.org/2001/XMLSchema#string) +#### Added +- [Lamp5 Lhx6 neuron](http://purl.obolibrary.org/obo/CL_4042013) [RO_0002175](http://purl.obolibrary.org/obo/RO_0002175) [NCBITaxon_9606](http://purl.obolibrary.org/obo/NCBITaxon_9606) -- [astrocyte-restricted precursor](http://purl.obolibrary.org/obo/CL_4042022) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A progenitor cell of the central nervous system that differentiates exclusively onto astrocytes. This progenitor cell expresses CD44 and S100 calcium-binding protein B."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:15531362"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [Lamp5 Lhx6 neuron](http://purl.obolibrary.org/obo/CL_4042013) [comment](http://www.w3.org/2000/01/rdf-schema#comment) "The marker set CHST9, LAMP5 can identify the Human cell type Lamp5 Lhx6 neuron in the Brain with a confidence of 0.821678322 (NS-Forest FBeta value)."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://doi.org/10.5281/zenodo.11165918"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:33052610"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [Lamp5 Lhx6 neuron](http://purl.obolibrary.org/obo/CL_4042013) SubClassOf [RO_0015004](http://purl.obolibrary.org/obo/RO_0015004) some [CLM_1000075](http://purl.obolibrary.org/obo/CLM_1000075) -- [astrocyte-restricted precursor](http://purl.obolibrary.org/obo/CL_4042022) [contributor](http://purl.org/dc/terms/contributor) [0000-0002-0098-8958](https://orcid.org/0000-0002-0098-8958) +- [Lamp5 Lhx6 neuron](http://purl.obolibrary.org/obo/CL_4042013) SubClassOf [lamp5 GABAergic cortical interneuron](http://purl.obolibrary.org/obo/CL_4023011) -- Class: [astrocyte-restricted precursor](http://purl.obolibrary.org/obo/CL_4042022) +- [Lamp5 Lhx6 neuron](http://purl.obolibrary.org/obo/CL_4042013) SubClassOf [RO_0002292](http://purl.obolibrary.org/obo/RO_0002292) some [PR_000032533](http://purl.obolibrary.org/obo/PR_000032533) -- [astrocyte-restricted precursor](http://purl.obolibrary.org/obo/CL_4042022) SubClassOf [BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0001017](http://purl.obolibrary.org/obo/UBERON_0001017) -- [astrocyte-restricted precursor](http://purl.obolibrary.org/obo/CL_4042022) SubClassOf [RO_0002292](http://purl.obolibrary.org/obo/RO_0002292) some [PR_000001307](http://purl.obolibrary.org/obo/PR_000001307) +### Leydig cell `http://purl.obolibrary.org/obo/CL_0000178` +#### Removed +- [Leydig cell](http://purl.obolibrary.org/obo/CL_0000178) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. -- [astrocyte-restricted precursor](http://purl.obolibrary.org/obo/CL_4042022) SubClassOf [progenitor cell](http://purl.obolibrary.org/obo/CL_0011026) +Leydig cells are a testosterone-secreting cell in the interstitial area in the testes of males. They are named after Franz Leydig, a German anatomist who discovered these cells in 1850. Uniquely situated within the soft connective tissue surrounding the seminiferous tubules, Leydig cells form an integral part of the male reproductive system. They are usually polygonal cells characterized by well developed smooth endoplasmic reticulum, high lipid content and a large round nucleus. They are found across mammalian species, including humans. +The primary function of Leydig cells is the production of androgens, the male sex hormones, the most notable of which is testosterone. Leydig cells synthesize testosterone from cholesterol through a series of enzymatic reactions. The production and release of testosterone are mainly regulated by the luteinizing hormone (LH) released by the anterior pituitary gland. In response to LH, Leydig cells convert cholesterol into testosterone, which then plays a crucial role in the development and maintenance of primary and secondary male sexual characteristics. These include the formation and maturation of male reproductive organs, onset of spermatogenesis, and the presentation of male secondary sexual traits such as the deepening of the voice, growth of facial hair, development of muscles, and a broadening of shoulders. +Apart from testosterone production, Leydig cells also secrete insulin-like factor 3 (INSL3) that is essential for testicular descent during embryonic development in males. Dysregulation or loss of Leydig cells can lead to numerous conditions like testosterone deficiency, infertility, and certain forms of testicular cancer. Although not typical, Leydig cells can regenerate if they are damaged, ensuring the continuous production of testosterone and maintaining male reproductive health. They provide an excellent model to study cell differentiation and hormone regulation, thereby enhancing our understanding of reproductive biology and associated disorders."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1093/biolre/ioy059"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [astrocyte-restricted precursor](http://purl.obolibrary.org/obo/CL_4042022) SubClassOf [neuron associated cell (sensu Vertebrata)](http://purl.obolibrary.org/obo/CL_0000123) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1210/clinem/dgaa603"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [astrocyte-restricted precursor](http://purl.obolibrary.org/obo/CL_4042022) SubClassOf [RO_0002203](http://purl.obolibrary.org/obo/RO_0002203) some [astrocyte](http://purl.obolibrary.org/obo/CL_0000127) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://www.ncbi.nlm.nih.gov/books/NBK556007/#:~:text=Leydig%20cells%20are%20the%20primary,secondary%20sexual%20characteristics%20and%20behaviors."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1016/j.coemr.2019.03.001"^^[string](http://www.w3.org/2001/XMLSchema#string) -### basal epithelial cell of tracheobronchial tree `http://purl.obolibrary.org/obo/CL_0002329` + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.3389/fendo.2014.00006"^^[string](http://www.w3.org/2001/XMLSchema#string) #### Added -- [basal epithelial cell of tracheobronchial tree](http://purl.obolibrary.org/obo/CL_0002329) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://cellxgene.cziscience.com/cellguide/CL_0002329"^^[string](http://www.w3.org/2001/XMLSchema#string) - -- [basal epithelial cell of tracheobronchial tree](http://purl.obolibrary.org/obo/CL_0002329) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. +- [Leydig cell](http://purl.obolibrary.org/obo/CL_0000178) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. -The basal epithelial cells of the tracheobronchial tree are critical components found in the lining of the airway passages, including the trachea and bronchi. They are keratin-5-positive, nonciliated, cuboidal cells and typically tightly attached to the basement membrane. In humans, the proportion of basal cells in the respiratory epithelium gradually decreases going down the tracheobronchial tree: they represent approximately 34% of the cells in the trachea, 27% in the large airways, and 10% in the small airways, although it is worth noting that there are differences in the compositions of the tracheobronchial epithelia between different species. -Basal epithelial cells serve as the basal layer of the tracheobronchial epithelium, providing both structural and regenerative support for the epithelial tissue that lines the upper regions of the respiratory tract. They serve as progenitor or stem cells that are capable of differentiating into multiple cell types, such as ciliated and secretory cells. This gives them a central role in homeostatic maintenance of the epithelium, and in repairing damaged epithelium after an injury or during disease. This regenerative capacity is crucial in maintaining the integrity of the tracheobronchial surface, especially given its continual exposure to inhaled irritants and microorganisms. -In addition to their primary restorative function, basal epithelial cells are also involved in the initial immune response within the tracheobronchial tree. Equipped with pattern recognition receptors, these cells can identify and respond to pathogenic organisms, triggering an immune response and producing a range of inflammatory mediators, such as cytokines and chemokines, to help combat infections."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.2353/ajpath.2010.090870"^^[string](http://www.w3.org/2001/XMLSchema#string) - - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1186/s12931-014-0160-8"^^[string](http://www.w3.org/2001/XMLSchema#string) - - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1165/rcmb.2013-0049OC"^^[string](http://www.w3.org/2001/XMLSchema#string) - - -### basophil mast progenitor cell `http://purl.obolibrary.org/obo/CL_0002028` +Leydig cells are a testosterone-secreting cell in the interstitial area in the testes of males. They are named after Franz Leydig, a German anatomist who discovered these cells in 1850. Uniquely situated within the soft connective tissue surrounding the seminiferous tubules, Leydig cells form an integral part of the male reproductive system. They are usually polygonal cells characterized by well developed smooth endoplasmic reticulum, high lipid content and a large round nucleus. They are found across mammalian species, including humans. +The primary function of Leydig cells is the production of androgens, the male sex hormones, the most notable of which is testosterone. Leydig cells synthesize testosterone from cholesterol through a series of enzymatic reactions. The production and release of testosterone are mainly regulated by the luteinizing hormone (LH) released by the anterior pituitary gland. In response to LH, Leydig cells convert cholesterol into testosterone, which then plays a crucial role in the development and maintenance of primary and secondary male sexual characteristics. These include the formation and maturation of male reproductive organs, onset of spermatogenesis, and the presentation of male secondary sexual traits such as the deepening of the voice, growth of facial hair, development of muscles, and a broadening of shoulders. +Apart from testosterone production, Leydig cells also secrete insulin-like factor 3 (INSL3) that is essential for testicular descent during embryonic development in males. Dysregulation or loss of Leydig cells can lead to numerous conditions like testosterone deficiency, infertility, and certain forms of testicular cancer. Although not typical, Leydig cells can regenerate if they are damaged, ensuring the continuous production of testosterone and maintaining male reproductive health. They provide an excellent model to study cell differentiation and hormone regulation, thereby enhancing our understanding of reproductive biology and associated disorders."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1093/biolre/ioy059"^^[string](http://www.w3.org/2001/XMLSchema#string) -#### Added -- [basophil mast progenitor cell](http://purl.obolibrary.org/obo/CL_0002028) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1210/clinem/dgaa603"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://www.ncbi.nlm.nih.gov/books/NBK556007/#:~:text=Leydig%20cells%20are%20the%20primary,secondary%20sexual%20characteristics%20and%20behaviors."^^[string](http://www.w3.org/2001/XMLSchema#string) -### basophil progenitor cell `http://purl.obolibrary.org/obo/CL_0000613` + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1016/j.coemr.2019.03.001"^^[string](http://www.w3.org/2001/XMLSchema#string) -#### Added -- [basophil progenitor cell](http://purl.obolibrary.org/obo/CL_0000613) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.3389/fendo.2014.00006"^^[string](http://www.w3.org/2001/XMLSchema#string) -### basophilic erythroblast `http://purl.obolibrary.org/obo/CL_0000549` +### Lugaro cell `http://purl.obolibrary.org/obo/CL_0011006` #### Added -- [basophilic erythroblast](http://purl.obolibrary.org/obo/CL_0000549) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) +- [Lugaro cell](http://purl.obolibrary.org/obo/CL_0011006) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "globular cell"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:34194302"^^[string](http://www.w3.org/2001/XMLSchema#string) -### beta1-tanycyte `http://purl.obolibrary.org/obo/CL_4042019` +### Ly-76 high positive erythrocyte `http://purl.obolibrary.org/obo/CL_0002022` +#### Removed +- [Ly-76 high positive erythrocyte](http://purl.obolibrary.org/obo/CL_0002022) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) -#### Added -- [beta1-tanycyte](http://purl.obolibrary.org/obo/CL_4042019) [id](http://www.geneontology.org/formats/oboInOwl#id) "CL:4042019"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [beta1-tanycyte](http://purl.obolibrary.org/obo/CL_4042019) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A type of tanycyte found in the lateral infundibular recess of the brain. This tanycyte has an elongated morphology with multiple microvilli extending to the third ventricle in the lateral zones of the median eminence. This type of tanycyte expresses FGF receptors 1 and 2, is in contact with GnRH neurons, and is involved in the release of gonadotropin-releasing hormone (GnRH)."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:16344112"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:29351662"^^[string](http://www.w3.org/2001/XMLSchema#string) +### M cell of gut `http://purl.obolibrary.org/obo/CL_0000682` +#### Removed +- [M cell of gut](http://purl.obolibrary.org/obo/CL_0000682) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Tanycyte"^^[string](http://www.w3.org/2001/XMLSchema#string) +M cells, or microfold cells, of the gut are specialized epithelial cells found in the lining of the gut, specifically in the follicle-associated epithelium of mucosa-associated lymphoid tissue, where they function as sentries against toxins and pathogens. M cells are characterized by apical microfolds (hence their alternate name) which express unique adhesion molecules that enable them to sample the luminal macromolecules. +Other morphological features that distinguish M cells from other intestinal mucosal cells include sparse microvilli and a reduced thickness of the glycocalyx, which permits adhesion while not hindering the transport of molecules. They also have unique intraepithelial invaginations on the basolateral side which are filled with macrophages and other immune cells that can process the engulfed macromolecules quickly. +These morphological characteristics enable M cells to serve a dual role in immune responses. They initiate the immune response by transporting antigens (such as toxic or pathogenic substances) across the epithelial layer to lymphocytes and antigen-presenting cells in the underlying lymphoid tissue. This specialized transport process is called 'transcytosis.' They also have specialized molecules like glycoprotein-2 for bacterial uptake. Simultaneously, M cells help maintain immune tolerance to food antigens and commensal bacteria, preventing unnecessary reactions to non-pathogenic substances and hypersensitivity conditions. While these functions are crucial for well-being, M cell dysfunction can lead to serious conditions like Crohn's disease and other inflammatory bowel diseases."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1038/nature08529"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:26578855"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1093/jb/mvv121"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [beta1-tanycyte](http://purl.obolibrary.org/obo/CL_4042019) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "vmARH tanycyte"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:29351662"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1136/gut.47.5.735"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [beta1-tanycyte](http://purl.obolibrary.org/obo/CL_4042019) [contributor](http://purl.org/dc/terms/contributor) [0000-0002-0098-8958](https://orcid.org/0000-0002-0098-8958) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://www.ncbi.nlm.nih.gov/books/NBK534232/"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [beta1-tanycyte](http://purl.obolibrary.org/obo/CL_4042019) [date](http://purl.org/dc/terms/date) "2024-08-19T13:17:32Z"^^[dateTime](http://www.w3.org/2001/XMLSchema#dateTime) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://www.sciencedirect.com/topics/medicine-and-dentistry/microfold-cell"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [beta1-tanycyte](http://purl.obolibrary.org/obo/CL_4042019) [label](http://www.w3.org/2000/01/rdf-schema#label) "beta1-tanycyte"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [M cell of gut](http://purl.obolibrary.org/obo/CL_0000682) SubClassOf [BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0003929](http://purl.obolibrary.org/obo/UBERON_0003929) -- Class: [beta1-tanycyte](http://purl.obolibrary.org/obo/CL_4042019) +#### Added +- [M cell of gut](http://purl.obolibrary.org/obo/CL_0000682) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. -- [beta1-tanycyte](http://purl.obolibrary.org/obo/CL_4042019) SubClassOf [astrocyte of the forebrain](http://purl.obolibrary.org/obo/CL_0012000) +M cells, or microfold cells, of the gut are specialized epithelial cells found in the lining of the gut, specifically in the follicle-associated epithelium of mucosa-associated lymphoid tissue, where they function as sentries against toxins and pathogens. M cells are characterized by apical microfolds (hence their alternate name) which express unique adhesion molecules that enable them to sample the luminal macromolecules. +Other morphological features that distinguish M cells from other intestinal mucosal cells include sparse microvilli and a reduced thickness of the glycocalyx, which permits adhesion while not hindering the transport of molecules. They also have unique intraepithelial invaginations on the basolateral side which are filled with macrophages and other immune cells that can process the engulfed macromolecules quickly. +These morphological characteristics enable M cells to serve a dual role in immune responses. They initiate the immune response by transporting antigens (such as toxic or pathogenic substances) across the epithelial layer to lymphocytes and antigen-presenting cells in the underlying lymphoid tissue. This specialized transport process is called 'transcytosis.' They also have specialized molecules like glycoprotein-2 for bacterial uptake. Simultaneously, M cells help maintain immune tolerance to food antigens and commensal bacteria, preventing unnecessary reactions to non-pathogenic substances and hypersensitivity conditions. While these functions are crucial for well-being, M cell dysfunction can lead to serious conditions like Crohn's disease and other inflammatory bowel diseases."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1038/nature08529"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [beta1-tanycyte](http://purl.obolibrary.org/obo/CL_4042019) SubClassOf [BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0006250](http://purl.obolibrary.org/obo/UBERON_0006250) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1093/jb/mvv121"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [beta1-tanycyte](http://purl.obolibrary.org/obo/CL_4042019) SubClassOf [RO_0002131](http://purl.obolibrary.org/obo/RO_0002131) some [UBERON_0002197](http://purl.obolibrary.org/obo/UBERON_0002197) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1136/gut.47.5.735"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [beta1-tanycyte](http://purl.obolibrary.org/obo/CL_4042019) SubClassOf [tanycyte](http://purl.obolibrary.org/obo/CL_0002085) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://www.ncbi.nlm.nih.gov/books/NBK534232/"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [beta1-tanycyte](http://purl.obolibrary.org/obo/CL_4042019) SubClassOf [RO_0002292](http://purl.obolibrary.org/obo/RO_0002292) some [PR_000007489](http://purl.obolibrary.org/obo/PR_000007489) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://www.sciencedirect.com/topics/medicine-and-dentistry/microfold-cell"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [beta1-tanycyte](http://purl.obolibrary.org/obo/CL_4042019) SubClassOf [RO_0002292](http://purl.obolibrary.org/obo/RO_0002292) some [PR_000007479](http://purl.obolibrary.org/obo/PR_000007479) -- [beta1-tanycyte](http://purl.obolibrary.org/obo/CL_4042019) SubClassOf [secretory cell](http://purl.obolibrary.org/obo/CL_0000151) +### M cone cell `http://purl.obolibrary.org/obo/CL_0003049` +#### Removed +- [M cone cell](http://purl.obolibrary.org/obo/CL_0003049) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) -- [beta1-tanycyte](http://purl.obolibrary.org/obo/CL_4042019) SubClassOf [RO_0002215](http://purl.obolibrary.org/obo/RO_0002215) some [GO_0032274](http://purl.obolibrary.org/obo/GO_0032274) -### beta2-tanycyte `http://purl.obolibrary.org/obo/CL_4042020` +### M6 retinal ganglion cell `http://purl.obolibrary.org/obo/CL_0003035` #### Added -- [beta2-tanycyte](http://purl.obolibrary.org/obo/CL_4042020) [label](http://www.w3.org/2000/01/rdf-schema#label) "beta2-tanycyte"^^[string](http://www.w3.org/2001/XMLSchema#string) - -- [beta2-tanycyte](http://purl.obolibrary.org/obo/CL_4042020) [date](http://purl.org/dc/terms/date) "2024-08-19T13:21:39Z"^^[dateTime](http://www.w3.org/2001/XMLSchema#dateTime) - -- [beta2-tanycyte](http://purl.obolibrary.org/obo/CL_4042020) [id](http://www.geneontology.org/formats/oboInOwl#id) "CL:4042020"^^[string](http://www.w3.org/2001/XMLSchema#string) - -- [beta2-tanycyte](http://purl.obolibrary.org/obo/CL_4042020) [contributor](http://purl.org/dc/terms/contributor) [0000-0002-0098-8958](https://orcid.org/0000-0002-0098-8958) - -- [beta2-tanycyte](http://purl.obolibrary.org/obo/CL_4042020) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A type of tanycyte found in the floor of the infundibular recess in the brain. This tanycyte has an elongated morphology with multiple microvilli extending medially and ventrally to the median eminence, contacting the pial surface and blood vessels. This type of tanycyte expresses FGF receptors 1 and 2, is in contact with GnRH neurons, and is involved in the release of gonadotropin-releasing hormone (GnRH)."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:16344112"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [M6 retinal ganglion cell](http://purl.obolibrary.org/obo/CL_0003035) SubClassOf [BFO_0000002](http://purl.obolibrary.org/obo/BFO_0000002) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "wikipedia:Tanycyte"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:29351662"^^[string](http://www.w3.org/2001/XMLSchema#string) - - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:26578855"^^[string](http://www.w3.org/2001/XMLSchema#string) - -- [beta2-tanycyte](http://purl.obolibrary.org/obo/CL_4042020) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "ME tanycyte"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:29351662"^^[string](http://www.w3.org/2001/XMLSchema#string) +### Martinotti neuron `http://purl.obolibrary.org/obo/CL_4023076` +#### Removed +- [Martinotti neuron](http://purl.obolibrary.org/obo/CL_4023076) SubClassOf [multipolar neuron](http://purl.obolibrary.org/obo/CL_0000104) -- Class: [beta2-tanycyte](http://purl.obolibrary.org/obo/CL_4042020) -- [beta2-tanycyte](http://purl.obolibrary.org/obo/CL_4042020) SubClassOf [RO_0002131](http://purl.obolibrary.org/obo/RO_0002131) some [UBERON_0002197](http://purl.obolibrary.org/obo/UBERON_0002197) -- [beta2-tanycyte](http://purl.obolibrary.org/obo/CL_4042020) SubClassOf [RO_0002292](http://purl.obolibrary.org/obo/RO_0002292) some [PR_000007479](http://purl.obolibrary.org/obo/PR_000007479) +### NK1.1-positive natural killer cell, mouse `http://purl.obolibrary.org/obo/CL_0002438` +#### Removed +- [NK1.1-positive natural killer cell, mouse](http://purl.obolibrary.org/obo/CL_0002438) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) -- [beta2-tanycyte](http://purl.obolibrary.org/obo/CL_4042020) SubClassOf [RO_0002292](http://purl.obolibrary.org/obo/RO_0002292) some [PR_000007489](http://purl.obolibrary.org/obo/PR_000007489) -- [beta2-tanycyte](http://purl.obolibrary.org/obo/CL_4042020) SubClassOf [tanycyte](http://purl.obolibrary.org/obo/CL_0002085) -- [beta2-tanycyte](http://purl.obolibrary.org/obo/CL_4042020) SubClassOf [astrocyte of the forebrain](http://purl.obolibrary.org/obo/CL_0012000) +### OFFx cell `http://purl.obolibrary.org/obo/CL_4033036` -- [beta2-tanycyte](http://purl.obolibrary.org/obo/CL_4042020) SubClassOf [BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0006250](http://purl.obolibrary.org/obo/UBERON_0006250) +#### Added +- [OFFx cell](http://purl.obolibrary.org/obo/CL_4033036) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl/cl-base#cellxgene_subset) -### blood vessel endothelial cell `http://purl.obolibrary.org/obo/CL_0000071` +### ON-blue cone bipolar cell `http://purl.obolibrary.org/obo/CL_4033019` #### Removed -- [blood vessel endothelial cell](http://purl.obolibrary.org/obo/CL_0000071) SubClassOf [RO_0002202](http://purl.obolibrary.org/obo/RO_0002202) some [embryonic blood vessel endothelial progenitor cell](http://purl.obolibrary.org/obo/CL_0002546) - +- [ON-blue cone bipolar cell](http://purl.obolibrary.org/obo/CL_4033019) [RO_0002175](http://purl.obolibrary.org/obo/RO_0002175) [NCBITaxon_9606](http://purl.obolibrary.org/obo/NCBITaxon_9606) - -### bone cell `http://purl.obolibrary.org/obo/CL_0001035` -#### Removed -- [bone cell](http://purl.obolibrary.org/obo/CL_0001035) SubClassOf [cell](http://purl.obolibrary.org/obo/CL_0000000) +- [ON-blue cone bipolar cell](http://purl.obolibrary.org/obo/CL_4033019) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [human_reference_atlas](http://purl.obolibrary.org/obo/cl/cl-base#human_reference_atlas) #### Added -- [bone cell](http://purl.obolibrary.org/obo/CL_0001035) SubClassOf [eukaryotic cell](http://purl.obolibrary.org/obo/CL_0000255) +- [ON-blue cone bipolar cell](http://purl.obolibrary.org/obo/CL_4033019) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl/cl-base#cellxgene_subset) -### bone marrow macrophage `http://purl.obolibrary.org/obo/CL_0002476` +### PAX6 GABAergic cortical interneuron `http://purl.obolibrary.org/obo/CL_4042032` #### Added -- [bone marrow macrophage](http://purl.obolibrary.org/obo/CL_0002476) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) +- [PAX6 GABAergic cortical interneuron](http://purl.obolibrary.org/obo/CL_4042032) [id](http://www.geneontology.org/formats/oboInOwl#id) "CL:4042032"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [PAX6 GABAergic cortical interneuron](http://purl.obolibrary.org/obo/CL_4042032) [date](http://purl.org/dc/terms/date) "2024-10-11T13:25:51Z"^^[dateTime](http://www.w3.org/2001/XMLSchema#dateTime) -### brush cell `http://purl.obolibrary.org/obo/CL_0002204` +- [PAX6 GABAergic cortical interneuron](http://purl.obolibrary.org/obo/CL_4042032) [RO_0002175](http://purl.obolibrary.org/obo/RO_0002175) [NCBITaxon_9606](http://purl.obolibrary.org/obo/NCBITaxon_9606) -#### Added -- [brush cell](http://purl.obolibrary.org/obo/CL_0002204) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://cellxgene.cziscience.com/cellguide/CL_0002204"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [PAX6 GABAergic cortical interneuron](http://purl.obolibrary.org/obo/CL_4042032) [comment](http://www.w3.org/2000/01/rdf-schema#comment) "The marker set RELN, HCRTR2 can identify the Human cell type http://purl.obolibrary.org/obo/CL_4042032 in the Brain with a confidence of 0.724125093 (NS-Forest FBeta value)."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://doi.org/10.5281/zenodo.11165918"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [brush cell](http://purl.obolibrary.org/obo/CL_0002204) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. +- [PAX6 GABAergic cortical interneuron](http://purl.obolibrary.org/obo/CL_4042032) [label](http://www.w3.org/2000/01/rdf-schema#label) "PAX6 GABAergic cortical interneuron"^^[string](http://www.w3.org/2001/XMLSchema#string) -Brush cells, also referred to as tuft cells or multivesicular cells, are a specialized type of epithelial cell mainly noted for their characteristic 'brush border' composed of microvilli. These cells reside in the epithelial lining of tissue organs such as the respiratory tract, gastrointestinal tract, and the bile ducts. The name derives from their distinct appearance under the microscope, which resembles a brush due to the dense layer of microvilli protruding into the lumen. -A key function of brush cells is chemosensation: They express a variety of signaling molecules and receptors that enable them to detect specific chemical stimuli in the environment and act as sensory transducers. Many of these receptors are responsive to luminal content, which makes brush cells vital for regulating and coordinating appropriate physiological responses to changes in these substances. -Recent research has also elucidated an important role for these cells in immunity. Intestinal brush cells have been found to be the source of a cytokine called interleukin-25, which can initiate type 2 immune responses during parasitic infections. This immune function, along with the chemosensing abilities, signifies that brush cells could serve crucial roles in health and disease, although much research is still required to fully elucidate their myriad roles in physiology and pathology. Overall, brush cells are a versatile cell type, whose distinct morphology and functional capabilities allow them to perform a unique set of functions within the body."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.3389/fphys.2015.00087"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [PAX6 GABAergic cortical interneuron](http://purl.obolibrary.org/obo/CL_4042032) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A transcriptomically distinct GABAergic neuron located in the cerebral cortex that expresses the transcript PAX6. The standard transcriptomic reference data for this cell type can be found on the CellxGene census under the collection: 'Transcriptomic cytoarchitecture reveals principles of human neocortex organization', dataset: 'Supercluster: CGE-derived interneurons', Author Categories: 'CrossArea_subclass', clusters PAX6."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://cellxgene.cziscience.com/e/e4ddac12-f48f-4455-8e8d-c2a48a683437.cxg/"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1007/978-3-211-99390-3_83"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:37824655"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.5114/ceji.2022.124416"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [PAX6 GABAergic cortical interneuron](http://purl.obolibrary.org/obo/CL_4042032) [contributor](http://purl.org/dc/terms/contributor) [0000-0002-0098-8958](https://orcid.org/0000-0002-0098-8958) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1038/nature16161"^^[string](http://www.w3.org/2001/XMLSchema#string) +- Class: [PAX6 GABAergic cortical interneuron](http://purl.obolibrary.org/obo/CL_4042032) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1111/j.1469-7580.2005.00403.x"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [PAX6 GABAergic cortical interneuron](http://purl.obolibrary.org/obo/CL_4042032) SubClassOf [RO_0002292](http://purl.obolibrary.org/obo/RO_0002292) some [PR_000012318](http://purl.obolibrary.org/obo/PR_000012318) + +- [PAX6 GABAergic cortical interneuron](http://purl.obolibrary.org/obo/CL_4042032) SubClassOf [RO_0015004](http://purl.obolibrary.org/obo/RO_0015004) some [CLM_1000079](http://purl.obolibrary.org/obo/CLM_1000079) + +- [PAX6 GABAergic cortical interneuron](http://purl.obolibrary.org/obo/CL_4042032) SubClassOf [caudal ganglionic eminence derived cortical interneuron](http://purl.obolibrary.org/obo/CL_4023064) -### cardioblast (sensu Arthropoda) `http://purl.obolibrary.org/obo/CL_0000465` +### PP cell `http://purl.obolibrary.org/obo/CL_0000696` #### Removed -- [cardioblast (sensu Arthropoda)](http://purl.obolibrary.org/obo/CL_0000465) SubClassOf [RO_0002160](http://purl.obolibrary.org/obo/RO_0002160) some [NCBITaxon_6656](http://purl.obolibrary.org/obo/NCBITaxon_6656) +- [PP cell](http://purl.obolibrary.org/obo/CL_0000696) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +PP cells, also known as pancreatic polypeptide cells (and previously called F cells or gamma cells), are enteroendocrine cells predominantly found in the islets of Langerhans in the head of the pancreas. They are one of the four main endocrine cell types present in the pancreatic islets, along with type A, B and D cells. PP cells are notable for their production of pancreatic polypeptide, an anorexigenic hormone that modulates food intake and energy homeostasis. +By secreting pancreatic polypeptide, PP cells play a significant role in the management of both digestive and appetite regulation. Upon ingestion of food, there is a significant increase in the secretion of pancreatic polypeptide, which then reduces biliary secretion and helps slow down the movement of food through the digestive tract. This allows more time for digestion to take place and nutrients to be absorbed, promoting the efficient use of dietary intake. The pancreatic polypeptide further reduces appetite by interacting with the hypothalamus, the area of the brain responsible for control of hunger. +Given their important role in digestion, malfunction or damage to PP cells can lead to a disturbance in the digestive process and contribute to some disease conditions. For example, an overproduction of pancreatic polypeptide can result in conditions such as pancreatic tumors and diabetes. Conversely, an under secretion might contribute to obesity due to impaired dietary control. Furthermore, PP cells may also play a role in the body's energy balance, suggesting their implication in conditions related to energy metabolism."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1210/jc.2003-030630"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [cardioblast (sensu Arthropoda)](http://purl.obolibrary.org/obo/CL_0000465) SubClassOf [eukaryotic cell](http://purl.obolibrary.org/obo/CL_0000255) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1016/j.mce.2015.06.028"^^[string](http://www.w3.org/2001/XMLSchema#string) -#### Added -- [cardioblast (sensu Arthropoda)](http://purl.obolibrary.org/obo/CL_0000465) SubClassOf [RO_0002162](http://purl.obolibrary.org/obo/RO_0002162) some [NCBITaxon_6656](http://purl.obolibrary.org/obo/NCBITaxon_6656) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1016/j.febslet.2014.07.005"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1369/00221554155835"^^[string](http://www.w3.org/2001/XMLSchema#string) -### cardiocyte `http://purl.obolibrary.org/obo/CL_0002494` -#### Removed -- [cardiocyte](http://purl.obolibrary.org/obo/CL_0002494) SubClassOf [cell](http://purl.obolibrary.org/obo/CL_0000000) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1038/s41580-020-00317-7"^^[string](http://www.w3.org/2001/XMLSchema#string) #### Added -- [cardiocyte](http://purl.obolibrary.org/obo/CL_0002494) SubClassOf [eukaryotic cell](http://purl.obolibrary.org/obo/CL_0000255) +- [PP cell](http://purl.obolibrary.org/obo/CL_0000696) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. +PP cells, also known as pancreatic polypeptide cells (and previously called F cells or gamma cells), are enteroendocrine cells predominantly found in the islets of Langerhans in the head of the pancreas. They are one of the four main endocrine cell types present in the pancreatic islets, along with type A, B and D cells. PP cells are notable for their production of pancreatic polypeptide, an anorexigenic hormone that modulates food intake and energy homeostasis. +By secreting pancreatic polypeptide, PP cells play a significant role in the management of both digestive and appetite regulation. Upon ingestion of food, there is a significant increase in the secretion of pancreatic polypeptide, which then reduces biliary secretion and helps slow down the movement of food through the digestive tract. This allows more time for digestion to take place and nutrients to be absorbed, promoting the efficient use of dietary intake. The pancreatic polypeptide further reduces appetite by interacting with the hypothalamus, the area of the brain responsible for control of hunger. +Given their important role in digestion, malfunction or damage to PP cells can lead to a disturbance in the digestive process and contribute to some disease conditions. For example, an overproduction of pancreatic polypeptide can result in conditions such as pancreatic tumors and diabetes. Conversely, an under secretion might contribute to obesity due to impaired dietary control. Furthermore, PP cells may also play a role in the body's energy balance, suggesting their implication in conditions related to energy metabolism."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1210/jc.2003-030630"^^[string](http://www.w3.org/2001/XMLSchema#string) -### caudal ganglionic eminence derived interneuron `http://purl.obolibrary.org/obo/CL_4023064` -#### Removed -- [caudal ganglionic eminence derived interneuron](http://purl.obolibrary.org/obo/CL_4023064) [label](http://www.w3.org/2000/01/rdf-schema#label) "caudal ganglionic eminence derived interneuron"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1016/j.mce.2015.06.028"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [caudal ganglionic eminence derived interneuron](http://purl.obolibrary.org/obo/CL_4023064) [has_exact_synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "CGE interneuron"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003000](http://purl.obolibrary.org/obo/OMO_0003000) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1016/j.febslet.2014.07.005"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:37824663"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1369/00221554155835"^^[string](http://www.w3.org/2001/XMLSchema#string) -#### Added -- [caudal ganglionic eminence derived interneuron](http://purl.obolibrary.org/obo/CL_4023064) [label](http://www.w3.org/2000/01/rdf-schema#label) "caudal ganglionic eminence derived cortical interneuron"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1038/s41580-020-00317-7"^^[string](http://www.w3.org/2001/XMLSchema#string) -### cell `http://purl.obolibrary.org/obo/CL_0000000` +### PP cell of intestine `http://purl.obolibrary.org/obo/CL_0002680` #### Removed -- [cell](http://purl.obolibrary.org/obo/CL_0000000) SubClassOf [RO_0002160](http://purl.obolibrary.org/obo/RO_0002160) some [NCBITaxon_131567](http://purl.obolibrary.org/obo/NCBITaxon_131567) +- [PP cell of intestine](http://purl.obolibrary.org/obo/CL_0002680) EquivalentTo [PP cell](http://purl.obolibrary.org/obo/CL_0000696) and ([BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0000160](http://purl.obolibrary.org/obo/UBERON_0000160)) #### Added -- [cell](http://purl.obolibrary.org/obo/CL_0000000) SubClassOf [RO_0002162](http://purl.obolibrary.org/obo/RO_0002162) some [NCBITaxon_131567](http://purl.obolibrary.org/obo/NCBITaxon_131567) +- [PP cell of intestine](http://purl.obolibrary.org/obo/CL_0002680) EquivalentTo [PP cell](http://purl.obolibrary.org/obo/CL_0000696) and ([BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0001277](http://purl.obolibrary.org/obo/UBERON_0001277)) -### cell of skeletal muscle `http://purl.obolibrary.org/obo/CL_0000188` -#### Removed -- [cell of skeletal muscle](http://purl.obolibrary.org/obo/CL_0000188) SubClassOf [cell](http://purl.obolibrary.org/obo/CL_0000000) +### PR_000001440 `http://purl.obolibrary.org/obo/PR_000001440` #### Added -- [cell of skeletal muscle](http://purl.obolibrary.org/obo/CL_0000188) SubClassOf [eukaryotic cell](http://purl.obolibrary.org/obo/CL_0000255) +- Class: [PR_000001440](http://purl.obolibrary.org/obo/PR_000001440) -### cerebral cortex endothelial cell `http://purl.obolibrary.org/obo/CL_1001602` -#### Removed -- [cerebral cortex endothelial cell](http://purl.obolibrary.org/obo/CL_1001602) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "Endothelial cells forming the walls of the capillaries within the cerebral cortex."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NPX:PDR"^^[string](http://www.w3.org/2001/XMLSchema#string) +### PR_000003472 `http://purl.obolibrary.org/obo/PR_000003472` #### Added -- [cerebral cortex endothelial cell](http://purl.obolibrary.org/obo/CL_1001602) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A distinct endothelial cell forming the walls of the capillaries within the cerebral cortex."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NPX:PDR"^^[string](http://www.w3.org/2001/XMLSchema#string) +- Class: [PR_000003472](http://purl.obolibrary.org/obo/PR_000003472) -### chandelier pvalb GABAergic cortical interneuron `http://purl.obolibrary.org/obo/CL_4023036` -#### Removed -- [chandelier pvalb GABAergic cortical interneuron](http://purl.obolibrary.org/obo/CL_4023036) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A pvalb GABAergic cortical interneuron that is recognizable by the straight terminal axonal 'cartridges' of vertically oriented strings of synaptic boutons. Chandelier PV cells' boutons target exclusively the axon initial segment (AIS) of pyramidal cells, with a single cell innervating hundreds of pyramidal cells in a clustered manner."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:27477017"^^[string](http://www.w3.org/2001/XMLSchema#string) +### PR_000012318 `http://purl.obolibrary.org/obo/PR_000012318` #### Added -- [chandelier pvalb GABAergic cortical interneuron](http://purl.obolibrary.org/obo/CL_4023036) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A transcriptomically distinct pvalb GABAergic cortical interneuron that is recognizable by the straight terminal axonal 'cartridges' of vertically oriented strings of synaptic boutons. Chandelier PV cells' boutons target exclusively the axon initial segment (AIS) of pyramidal cells, with a single cell innervating hundreds of pyramidal cells in a clustered manner. The standard transcriptomic reference data for this cell type can be found on the CellxGene census under the collection: 'Transcriptomic cytoarchitecture reveals principles of human neocortex organization', dataset: 'Supercluster: CGE-derived interneurons', Author Categories: 'CrossArea_subclass', clusters Chandelier."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:27477017"^^[string](http://www.w3.org/2001/XMLSchema#string) - - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://cellxgene.cziscience.com/e/9c63201d-bfd9-41a8-bbbc-18d947556f3d.cxg/"^^[string](http://www.w3.org/2001/XMLSchema#string) +- Class: [PR_000012318](http://purl.obolibrary.org/obo/PR_000012318) -### cholangiocyte `http://purl.obolibrary.org/obo/CL_1000488` +### PR_000013015 `http://purl.obolibrary.org/obo/PR_000013015` #### Added -- [cholangiocyte](http://purl.obolibrary.org/obo/CL_1000488) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://cellxgene.cziscience.com/cellguide/CL_1000488"^^[string](http://www.w3.org/2001/XMLSchema#string) +- Class: [PR_000013015](http://purl.obolibrary.org/obo/PR_000013015) -- [cholangiocyte](http://purl.obolibrary.org/obo/CL_1000488) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. -Cholangiocytes, also known as biliary epithelial cells, are specialized epithelial cells that line the biliary tract, which constitutes the gall bladder and bile ducts inside the liver. Crucial to the maintenance of the liver's health and function, cholangiocytes have a key role in the modification and secretion of bile, a fluid produced by hepatocytes that is essential to digestion and the absorption of fats and vitamins. -Cholangiocytes accomplish their primary function through the expression of a variety of transport proteins located on their apical and basolateral membranes, which propel bile acids and other contents of the bile into the biliary lumen. The hepatic bile, once secreted by the hepatocytes, is further modified by cholangiocytes via secretion and absorption processes. These processes help in the regulation of bile volume and composition, which is fundamental in ensuring the efficient digestion of dietary fats and fat-soluble vitamins and the excretion of cholesterol. -In addition to their role in bile modification, cholangiocytes also perform several other integral functions. For instance, these cells express Toll-like receptors (TLRs) which allow cholangiocytes to initiate an immune response against pathogens in the biliary lumen. When functioning normally, these cells contribute to biliary integrity, hepatic architecture, and overall hepatic physiology. However, when they become pathological, they are involved in the progression of liver diseases, such as primary biliary cirrhosis and cholangiocarcinoma – the malignancy of the biliary tract."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1016/j.jhep.2012.10.011"^^[string](http://www.w3.org/2001/XMLSchema#string) +### PR_000016626 `http://purl.obolibrary.org/obo/PR_000016626` - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1152/ajpgi.00227.2012"^^[string](http://www.w3.org/2001/XMLSchema#string) +#### Added +- Class: [PR_000016626](http://purl.obolibrary.org/obo/PR_000016626) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1038/s41575-019-0125-y"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.5009/gnl16033"^^[string](http://www.w3.org/2001/XMLSchema#string) +### PR_000032533 `http://purl.obolibrary.org/obo/PR_000032533` - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1016/j.jcmgh.2015.05.005"^^[string](http://www.w3.org/2001/XMLSchema#string) +#### Added +- Class: [PR_000032533](http://purl.obolibrary.org/obo/PR_000032533) -### choroid plexus epithelial cell `http://purl.obolibrary.org/obo/CL_0000706` +### Purkinje cell `http://purl.obolibrary.org/obo/CL_0000121` #### Removed -- [choroid plexus epithelial cell](http://purl.obolibrary.org/obo/CL_0000706) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "Specialized ependymal cell that produces the cerebrospinal fluid from the blood and secretes it into the lumen of the brain and spinal chord."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:add"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [Purkinje cell](http://purl.obolibrary.org/obo/CL_0000121) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +Purkinje cells, named after the Czech anatomist Jan Evangelista Purkyně who discovered them, are unique inhibitory neurons in the cerebellar cortex. They are a critical part of the vertebrate nervous system as they provide the only signal output from the cortex to the cerebellar nuclei. They are one of the few types of neurons that are large enough to be seen with the naked eye. The most distinct hallmark of Purkinje cells is their elaborate dendritic arbor, which forms a broad and intricately branching structure resembling a tree. These numerous branches each receive excitatory synaptic inputs from more than 100,000 parallel fibers; in addition, a single climbing fiber makes hundreds of synapses to the soma and proximal dendrites. A single long axon forms an inhibitory projection to the cerebellar nuclei. +Purkinje cells play key roles in the coordination of fine, voluntary motor movements and balance. As the sole output of all motor coordination in the cerebellar cortex, they serve as a central relay in the cerebro-cerebellar loop. Each Purkinje cell receives two types of synaptic input: one from parallel fibers (which are axons of granule cells), and the other from climbing fibers (originating from the inferior olivary nucleus). The Purkinje cells process and integrate these diverse kinds of input signals to generate output that controls timing and coordination of movements. +Purkinje neurons show considerable synaptic plasticity. Throughout life, these cells continue to undergo long-term potentiation and depression at parallel fiber synapses, which cause long-lasting increase or decrease, respectively, of synaptic transmission and have been proposed as mechanisms for motor learning. +Purkinje cells are also known to be implicated in a variety of diseases. Their progressive loss is a prime feature in certain types of ataxia, a collective term used to describe conditions characterized by loss of muscular control and coordination. Furthermore, a significant reduction in the density of Purkinje cells has been reported in conditions such as autism and Huntington’s disease."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.7554/eLife.63668"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "JB:jb"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://www.sciencedirect.com/topics/agricultural-and-biological-sciences/purkinje-cell"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:tfm"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1038/nrn3886"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:9550134"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://www.ncbi.nlm.nih.gov/books/NBK545154/"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [choroid plexus epithelial cell](http://purl.obolibrary.org/obo/CL_0000706) EquivalentTo [ependymal cell](http://purl.obolibrary.org/obo/CL_0000065) and ([BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0001886](http://purl.obolibrary.org/obo/UBERON_0001886)) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1007/s12311-018-0985-7"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [choroid plexus epithelial cell](http://purl.obolibrary.org/obo/CL_0000706) SubClassOf [BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0001886](http://purl.obolibrary.org/obo/UBERON_0001886) +- [Purkinje cell](http://purl.obolibrary.org/obo/CL_0000121) SubClassOf [efferent neuron](http://purl.obolibrary.org/obo/CL_0000527) -- [choroid plexus epithelial cell](http://purl.obolibrary.org/obo/CL_0000706) SubClassOf [neural cell](http://purl.obolibrary.org/obo/CL_0002319) +- [Purkinje cell](http://purl.obolibrary.org/obo/CL_0000121) SubClassOf [CNS neuron (sensu Vertebrata)](http://purl.obolibrary.org/obo/CL_0000117) #### Added -- [choroid plexus epithelial cell](http://purl.obolibrary.org/obo/CL_0000706) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A specialized ependymal cell that is part of the choroid plexus epithelium, responsible for producing cerebrospinal fluid (CSF) by selectively filtering and modifying blood plasma components before secreting it into the brain and spinal cord. This cell is characterized by a brush border on its apical surface, which enhances the secretion of CSF."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:add"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [Purkinje cell](http://purl.obolibrary.org/obo/CL_0000121) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "JB:jb"^^[string](http://www.w3.org/2001/XMLSchema#string) +Purkinje cells, named after the Czech anatomist Jan Evangelista Purkyně who discovered them, are unique inhibitory neurons in the cerebellar cortex. They are a critical part of the vertebrate nervous system as they provide the only signal output from the cortex to the cerebellar nuclei. They are one of the few types of neurons that are large enough to be seen with the naked eye. The most distinct hallmark of Purkinje cells is their elaborate dendritic arbor, which forms a broad and intricately branching structure resembling a tree. These numerous branches each receive excitatory synaptic inputs from more than 100,000 parallel fibers; in addition, a single climbing fiber makes hundreds of synapses to the soma and proximal dendrites. A single long axon forms an inhibitory projection to the cerebellar nuclei. +Purkinje cells play key roles in the coordination of fine, voluntary motor movements and balance. As the sole output of all motor coordination in the cerebellar cortex, they serve as a central relay in the cerebro-cerebellar loop. Each Purkinje cell receives two types of synaptic input: one from parallel fibers (which are axons of granule cells), and the other from climbing fibers (originating from the inferior olivary nucleus). The Purkinje cells process and integrate these diverse kinds of input signals to generate output that controls timing and coordination of movements. +Purkinje neurons show considerable synaptic plasticity. Throughout life, these cells continue to undergo long-term potentiation and depression at parallel fiber synapses, which cause long-lasting increase or decrease, respectively, of synaptic transmission and have been proposed as mechanisms for motor learning. +Purkinje cells are also known to be implicated in a variety of diseases. Their progressive loss is a prime feature in certain types of ataxia, a collective term used to describe conditions characterized by loss of muscular control and coordination. Furthermore, a significant reduction in the density of Purkinje cells has been reported in conditions such as autism and Huntington’s disease."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.7554/eLife.63668"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:15561411"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://www.sciencedirect.com/topics/agricultural-and-biological-sciences/purkinje-cell"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:tfm"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1038/nrn3886"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:9550134"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://www.ncbi.nlm.nih.gov/books/NBK545154/"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [choroid plexus epithelial cell](http://purl.obolibrary.org/obo/CL_0000706) [comment](http://www.w3.org/2000/01/rdf-schema#comment) "A choroid plexus epithelial cell possesses non-motile 9+0 cilia. While these cilia can exhibit transient motility during development, they generally do not contribute significantly to the directional flow of cerebrospinal fluid (CSF). Instead, they are primarily involved in sensory functions."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:25729351"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1007/s12311-018-0985-7"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [choroid plexus epithelial cell](http://purl.obolibrary.org/obo/CL_0000706) EquivalentTo [ependymal cell](http://purl.obolibrary.org/obo/CL_0000065) and ([BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0003911](http://purl.obolibrary.org/obo/UBERON_0003911)) -- [choroid plexus epithelial cell](http://purl.obolibrary.org/obo/CL_0000706) SubClassOf [BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0003911](http://purl.obolibrary.org/obo/UBERON_0003911) +### RXFP1-positive interface island D1-medium spiny neuron `http://purl.obolibrary.org/obo/CL_4030054` -- [choroid plexus epithelial cell](http://purl.obolibrary.org/obo/CL_0000706) SubClassOf [RO_0002215](http://purl.obolibrary.org/obo/RO_0002215) some [GO_0033326](http://purl.obolibrary.org/obo/GO_0033326) +#### Added +- [RXFP1-positive interface island D1-medium spiny neuron](http://purl.obolibrary.org/obo/CL_4030054) SubClassOf [striatum neuron](http://purl.obolibrary.org/obo/CL_0002613) -- [choroid plexus epithelial cell](http://purl.obolibrary.org/obo/CL_0000706) SubClassOf [brush border epithelial cell](http://purl.obolibrary.org/obo/CL_0000239) +### Rohon-Beard neuron `http://purl.obolibrary.org/obo/CL_0000247` +#### Removed +- [Rohon-Beard neuron](http://purl.obolibrary.org/obo/CL_0000247) SubClassOf [somatosensory neuron](http://purl.obolibrary.org/obo/CL_4023168) -### choroidal cell of the eye `http://purl.obolibrary.org/obo/CL_0000348` +- [Rohon-Beard neuron](http://purl.obolibrary.org/obo/CL_0000247) SubClassOf [neuronal receptor cell](http://purl.obolibrary.org/obo/CL_0000006) -#### Added -- [choroidal cell of the eye](http://purl.obolibrary.org/obo/CL_0000348) SubClassOf [eukaryotic cell](http://purl.obolibrary.org/obo/CL_0000255) -### chromaffin cell `http://purl.obolibrary.org/obo/CL_0000166` +### Schwann cell `http://purl.obolibrary.org/obo/CL_0002573` +#### Removed +- [Schwann cell](http://purl.obolibrary.org/obo/CL_0002573) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. -#### Added -- [chromaffin cell](http://purl.obolibrary.org/obo/CL_0000166) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://cellxgene.cziscience.com/cellguide/CL_0000166"^^[string](http://www.w3.org/2001/XMLSchema#string) +Schwann cells, also known as neurolemmocytes, are a type of glial cell located in the peripheral nervous system. These cells play a significant role in the healthy functioning of nerves by producing myelin, a fatty substance that forms a coating around nerve fibers. Myelin serves as an insulator and enhances the speed and efficiency of electrical nerve impulses; a single Schwann cell can myelinate a single axon. Myelination starts by the elongation and envelopment of the Schwann cell around the axon, followed by the synthesis and deposition of myelin layers. Some studies suggest that Schwann cells may regulate neuronal action potential, muscular contraction, and the sensitive response. +While Schwann cells are most commonly known for the formation of the myelin sheath, some Schwann cells do not form myelin: Remak Schwann cells, a class of nonmyelinating Schwann cells, ensheath axons with smaller diameter, such as C fiber nociceptors in sciatic nerves and form Remak bundles. +Schwann cells are found along both motor and sensory neurons and are crucial for the advancement and recovery of peripheral nerve injuries, due to their capacity to support nerve regeneration. In cases of nerve injury, Schwann cells play a vital role in recovery by initiating Wallerian degeneration, a process in which the part of the axon distal to the injury site degrades and is then cleared away. Following this, Schwann cells can guide the regrowth of the nerve, providing a conducive environment for axon regeneration. They remodel themselves into a regenerative phenotype, proliferate, and organize themselves into bands of Büngner that provide physical and chemical guidance for the regrowths of axons. This function of Schwann cells in the repair and regeneration of nervous system highlights their therapeutic potential in peripheral nerve injury treatments."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1016/j.biocel.2006.05.007"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [chromaffin cell](http://purl.obolibrary.org/obo/CL_0000166) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1016/B978-0-444-52902-2.00005-9"^^[string](http://www.w3.org/2001/XMLSchema#string) -Chromaffin cells, also known as pheochromocytes, are neuroendocrine cells that are typically located in the adrenal medulla, the innermost part of the adrenal gland, which is situated on top of each kidney. Chromaffin cells are also found in small clusters, known as paraganglia, in various locations throughout the body, including the sympathetic nervous system. They derive their name from their ability to stain a brownish-black color upon exposure to chromic salts, a feature made possible due to their high content of granules rich in catecholamines and catecholamine-related neurotransmitters. -The primary function of chromaffin cells is the synthesis and release of catecholamines, specifically epinephrine (adrenaline) and norepinephrine (noradrenaline). These neurotransmitters are vital stress hormones that, when released by the adrenal chromaffing cells into the bloodstream, prepare the body for the 'fight or flight' response. This response can enhance the body's performance in a dangerous situation by increasing heart rate, elevating blood sugar, and increasing blood flow to the muscles. The chromaffin cells in paraganglia are responsible for the local release of catecholamines and play a role in regulating blood pressure and other autonomic functions. -In addition to their role in stress response, chromaffin cells also contribute to the body's immune response. They secrete several peptides including antimicrobial peptides, and the discovery of LPS and cytokine receptors on chromaffin cells suggests that the adrenal medulla may participate in some aspects of the immune response."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.3389/fendo.2018.00711"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1002/glia.23892"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.3389/fimmu.2022.977175/full"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1186/s13064-020-00140-y"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1002/cphy.c190003"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1186/1742-2094-8-110"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.3389/fimmu.2022.977175"^^[string](http://www.w3.org/2001/XMLSchema#string) +#### Added +- [Schwann cell](http://purl.obolibrary.org/obo/CL_0002573) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1016/j.biocel.2016.02.003"^^[string](http://www.w3.org/2001/XMLSchema#string) +Schwann cells, also known as neurolemmocytes, are a type of glial cell located in the peripheral nervous system. These cells play a significant role in the healthy functioning of nerves by producing myelin, a fatty substance that forms a coating around nerve fibers. Myelin serves as an insulator and enhances the speed and efficiency of electrical nerve impulses; a single Schwann cell can myelinate a single axon. Myelination starts by the elongation and envelopment of the Schwann cell around the axon, followed by the synthesis and deposition of myelin layers. Some studies suggest that Schwann cells may regulate neuronal action potential, muscular contraction, and the sensitive response. +While Schwann cells are most commonly known for the formation of the myelin sheath, some Schwann cells do not form myelin: Remak Schwann cells, a class of nonmyelinating Schwann cells, ensheath axons with smaller diameter, such as C fiber nociceptors in sciatic nerves and form Remak bundles. +Schwann cells are found along both motor and sensory neurons and are crucial for the advancement and recovery of peripheral nerve injuries, due to their capacity to support nerve regeneration. In cases of nerve injury, Schwann cells play a vital role in recovery by initiating Wallerian degeneration, a process in which the part of the axon distal to the injury site degrades and is then cleared away. Following this, Schwann cells can guide the regrowth of the nerve, providing a conducive environment for axon regeneration. They remodel themselves into a regenerative phenotype, proliferate, and organize themselves into bands of Büngner that provide physical and chemical guidance for the regrowths of axons. This function of Schwann cells in the repair and regeneration of nervous system highlights their therapeutic potential in peripheral nerve injury treatments."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1016/j.biocel.2006.05.007"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1016/B978-0-444-52902-2.00005-9"^^[string](http://www.w3.org/2001/XMLSchema#string) -### ciliated cell `http://purl.obolibrary.org/obo/CL_0000064` -#### Removed -- [ciliated cell](http://purl.obolibrary.org/obo/CL_0000064) SubClassOf [cell](http://purl.obolibrary.org/obo/CL_0000000) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1002/glia.23892"^^[string](http://www.w3.org/2001/XMLSchema#string) -#### Added -- [ciliated cell](http://purl.obolibrary.org/obo/CL_0000064) SubClassOf [eukaryotic cell](http://purl.obolibrary.org/obo/CL_0000255) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1186/s13064-020-00140-y"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [ciliated cell](http://purl.obolibrary.org/obo/CL_0000064) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1186/1742-2094-8-110"^^[string](http://www.w3.org/2001/XMLSchema#string) -### ciliated cell of the bronchus `http://purl.obolibrary.org/obo/CL_0002332` -#### Removed -- [ciliated cell of the bronchus](http://purl.obolibrary.org/obo/CL_0002332) EquivalentTo [ciliated cell](http://purl.obolibrary.org/obo/CL_0000064) and ([BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0002185](http://purl.obolibrary.org/obo/UBERON_0002185)) +### Sertoli cell `http://purl.obolibrary.org/obo/CL_0000216` #### Added -- [ciliated cell of the bronchus](http://purl.obolibrary.org/obo/CL_0002332) EquivalentTo [ciliated cell](http://purl.obolibrary.org/obo/CL_0000064) and ([BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0002031](http://purl.obolibrary.org/obo/UBERON_0002031)) +- [Sertoli cell](http://purl.obolibrary.org/obo/CL_0000216) SubClassOf [secretory epithelial cell](http://purl.obolibrary.org/obo/CL_1100001) -### ciliated columnar cell of tracheobronchial tree `http://purl.obolibrary.org/obo/CL_0002145` +### TAC3-positive medium spiny neuron `http://purl.obolibrary.org/obo/CL_4042002` #### Removed -- [ciliated columnar cell of tracheobronchial tree](http://purl.obolibrary.org/obo/CL_0002145) SubClassOf [BFO_0000051](http://purl.obolibrary.org/obo/BFO_0000051) some [GO_0031514](http://purl.obolibrary.org/obo/GO_0031514) +- [TAC3-positive medium spiny neuron](http://purl.obolibrary.org/obo/CL_4042002) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) -#### Added -- [ciliated columnar cell of tracheobronchial tree](http://purl.obolibrary.org/obo/CL_0002145) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://cellxgene.cziscience.com/cellguide/CL_0002145"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [ciliated columnar cell of tracheobronchial tree](http://purl.obolibrary.org/obo/CL_0002145) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. -Ciliated columnar cells of the tracheobronchial tree compose the inner lining of the tracheobronchial tree, the system of airways consisting of trachea, bronchi and bronchioles that allow passage of air into the lungs, where gas exchange occurs. A defining feature of these endo-epithelial cells are the tiny hair-like structures covering their surface, known as cilia. The nucleus is located at the base of the cell, and the area above it is rich in mitochondria and well-developed endoplasmic reticulum, both crucial for the energy-intensive process of cilia operation. -The primary function of these ciliated cells is to keep the respiratory tract clean via mucociliary clearance or the respiratory escalator. These cells create a two-layered 'coat': The lower "sol" layer is watery where the cilia can beat in coordinated waves, and the upper "gel" layer is thick and sticky, trapping inhaled particles, such as dust, bacteria, viruses, and other potentially harmful substances. This rhythmical beating of the cilia then moves the mucus and trapped particles upwards and out of the respiratory tract, which is then either coughed out or swallowed. -Damage or dysfunction of these ciliated cells, as seen in diseases such as primary ciliary dyskinesia, cystic fibrosis, or chronic bronchitis, may lead to reduced or ineffective mucociliary clearance and an increased susceptibility to respiratory infections."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1146/annurev-physiol-021014-071931"^^[string](http://www.w3.org/2001/XMLSchema#string) +### TAC3-positive striatal interneuron `http://purl.obolibrary.org/obo/CL_4042001` +#### Removed +- [TAC3-positive striatal interneuron](http://purl.obolibrary.org/obo/CL_4042001) SubClassOf [obsolete CNS interneuron](http://purl.obolibrary.org/obo/CL_0000402) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1159/000196486"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [TAC3-positive striatal interneuron](http://purl.obolibrary.org/obo/CL_4042001) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1152/ajplung.00329.2019"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [TAC3-positive striatal interneuron](http://purl.obolibrary.org/obo/CL_4042001) SubClassOf [RO_0002100](http://purl.obolibrary.org/obo/RO_0002100) some [UBERON_0002435](http://purl.obolibrary.org/obo/UBERON_0002435) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1101/cshperspect.a028241"^^[string](http://www.w3.org/2001/XMLSchema#string) +#### Added +- [TAC3-positive striatal interneuron](http://purl.obolibrary.org/obo/CL_4042001) SubClassOf [striatum neuron](http://purl.obolibrary.org/obo/CL_0002613) -### circulating cell `http://purl.obolibrary.org/obo/CL_0000080` +### TCR-positive macrophage `http://purl.obolibrary.org/obo/CL_4030058` #### Removed -- [circulating cell](http://purl.obolibrary.org/obo/CL_0000080) SubClassOf [cell](http://purl.obolibrary.org/obo/CL_0000000) +- [TCR-positive macrophage](http://purl.obolibrary.org/obo/CL_4030058) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) -#### Added -- [circulating cell](http://purl.obolibrary.org/obo/CL_0000080) SubClassOf [eukaryotic cell](http://purl.obolibrary.org/obo/CL_0000255) -### classical monocyte `http://purl.obolibrary.org/obo/CL_0000860` +### Tc1 cell `http://purl.obolibrary.org/obo/CL_0000917` #### Added -- [classical monocyte](http://purl.obolibrary.org/obo/CL_0000860) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://cellxgene.cziscience.com/cellguide/CL_0000860"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [Tc1 cell](http://purl.obolibrary.org/obo/CL_0000917) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl/cl-base#cellxgene_subset) -- [classical monocyte](http://purl.obolibrary.org/obo/CL_0000860) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. - -Classical monocytes are a subtype of monocytes that are characterized by high CD14 but no CD16 expression. Emerging from the bone marrow and entering the bloodstream, these cells play central roles in immune responses and regulation of inflammation. CD14-positive CD16-negative monocytes form the majority of circulating monocytes in the body, typically contributing to around 80-90% of the total monocyte pool. -The primary function of the classical monocytes is to serve in the frontline of host defense against infections. They are primed to migrate to sites of infection, and they express pattern recognition receptors that help them identify and phagocytose pathogens, leading to their destruction. Classical monocytes also contribute to inflammation by producing several pro-inflammatory cytokines including interleukins and tumor necrosis factors. -In response to specific signals from tissues under pathological conditions, such as infection or injury, classical monocytes can leave the bloodstream and migrate towards the affected sites. Following their arrival, these cells differentiate into diverse cell types including macrophages and dendritic cells to combat specific pathogens or injury. Dysregulated monocyte activity can lead to the development of many human diseases including inflammation, infection, tissue injury, and various autoimmune diseases."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1038/nri.2017.28"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1182/blood-2009-07-235028"^^[string](http://www.w3.org/2001/XMLSchema#string) +### UBERON_0000155 `http://purl.obolibrary.org/obo/UBERON_0000155` - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1111/sji.12883"^^[string](http://www.w3.org/2001/XMLSchema#string) +#### Added +- Class: [UBERON_0000155](http://purl.obolibrary.org/obo/UBERON_0000155) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.3389/fimmu.2015.00423/full"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.3389/fimmu.2019.02035"^^[string](http://www.w3.org/2001/XMLSchema#string) +### UBERON_0000156 `http://purl.obolibrary.org/obo/UBERON_0000156` -- [classical monocyte](http://purl.obolibrary.org/obo/CL_0000860) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) +#### Added +- Class: [UBERON_0000156](http://purl.obolibrary.org/obo/UBERON_0000156) -### cnidocyte `http://purl.obolibrary.org/obo/CL_0011029` +### UBERON_0000157 `http://purl.obolibrary.org/obo/UBERON_0000157` #### Added -- [cnidocyte](http://purl.obolibrary.org/obo/CL_0011029) SubClassOf [eukaryotic cell](http://purl.obolibrary.org/obo/CL_0000255) +- Class: [UBERON_0000157](http://purl.obolibrary.org/obo/UBERON_0000157) -### common dendritic progenitor `http://purl.obolibrary.org/obo/CL_0001029` +### UBERON_0000400 `http://purl.obolibrary.org/obo/UBERON_0000400` #### Added -- [common dendritic progenitor](http://purl.obolibrary.org/obo/CL_0001029) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) +- Class: [UBERON_0000400](http://purl.obolibrary.org/obo/UBERON_0000400) -### common myeloid progenitor, CD34-positive `http://purl.obolibrary.org/obo/CL_0001059` +### UBERON_0000482 `http://purl.obolibrary.org/obo/UBERON_0000482` #### Added -- [common myeloid progenitor, CD34-positive](http://purl.obolibrary.org/obo/CL_0001059) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) +- Class: [UBERON_0000482](http://purl.obolibrary.org/obo/UBERON_0000482) -### connective tissue cell `http://purl.obolibrary.org/obo/CL_0002320` +### UBERON_0001160 `http://purl.obolibrary.org/obo/UBERON_0001160` #### Removed -- [connective tissue cell](http://purl.obolibrary.org/obo/CL_0002320) SubClassOf [cell](http://purl.obolibrary.org/obo/CL_0000000) +- Class: [UBERON_0001160](http://purl.obolibrary.org/obo/UBERON_0001160) -#### Added -- [connective tissue cell](http://purl.obolibrary.org/obo/CL_0002320) SubClassOf [eukaryotic cell](http://purl.obolibrary.org/obo/CL_0000255) -### corneocyte `http://purl.obolibrary.org/obo/CL_0002153` +### UBERON_0001206 `http://purl.obolibrary.org/obo/UBERON_0001206` #### Added -- [corneocyte](http://purl.obolibrary.org/obo/CL_0002153) SubClassOf [eukaryotic cell](http://purl.obolibrary.org/obo/CL_0000255) +- Class: [UBERON_0001206](http://purl.obolibrary.org/obo/UBERON_0001206) -### crypt-bottom fibroblast `http://purl.obolibrary.org/obo/CL_4052008` +### UBERON_0001242 `http://purl.obolibrary.org/obo/UBERON_0001242` +#### Removed +- Class: [UBERON_0001242](http://purl.obolibrary.org/obo/UBERON_0001242) -#### Added -- [crypt-bottom fibroblast](http://purl.obolibrary.org/obo/CL_4052008) [label](http://www.w3.org/2000/01/rdf-schema#label) "crypt-bottom fibroblast"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [crypt-bottom fibroblast](http://purl.obolibrary.org/obo/CL_4052008) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "bottom pericryptic-associated fibroblasts"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:33916891"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [crypt-bottom fibroblast](http://purl.obolibrary.org/obo/CL_4052008) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "CBFs"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003000](http://purl.obolibrary.org/obo/OMO_0003000) +### UBERON_0001295 `http://purl.obolibrary.org/obo/UBERON_0001295` +#### Removed +- Class: [UBERON_0001295](http://purl.obolibrary.org/obo/UBERON_0001295) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "doi:/10.1371/journal.pbio.3001032"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [crypt-bottom fibroblast](http://purl.obolibrary.org/obo/CL_4052008) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A subepithelial intestinal fibroblast that is located adjacent to the base of the crypt of Lieberkühn, near the intestinal stem cells. Characterized by low PDGFRα expression, this cell is crucial for maintaining the intestinal stem cell niche. Crypt-bottom fibroblast secretes key signaling molecules including canonical Wnt ligands (Wnt2, Wnt2b), Wnt potentiators (Rspo3), and BMP inhibitors (Grem1), which collectively regulate intestinal stem cell function and epithelial homeostasis."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "doi:/10.1371/journal.pbio.3001032"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:33916891"^^[string](http://www.w3.org/2001/XMLSchema#string) +### UBERON_0002368 `http://purl.obolibrary.org/obo/UBERON_0002368` -- [crypt-bottom fibroblast](http://purl.obolibrary.org/obo/CL_4052008) [date](http://purl.org/dc/terms/date) "2024-09-23T10:23:18Z"^^[dateTime](http://www.w3.org/2001/XMLSchema#dateTime) +#### Added +- Class: [UBERON_0002368](http://purl.obolibrary.org/obo/UBERON_0002368) -- [crypt-bottom fibroblast](http://purl.obolibrary.org/obo/CL_4052008) [id](http://www.geneontology.org/formats/oboInOwl#id) "CL:4052008"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [crypt-bottom fibroblast](http://purl.obolibrary.org/obo/CL_4052008) [contributor](http://purl.org/dc/terms/contributor) [0009-0000-8480-9277](https://orcid.org/0009-0000-8480-9277) +### UBERON_0002420 `http://purl.obolibrary.org/obo/UBERON_0002420` -- Class: [crypt-bottom fibroblast](http://purl.obolibrary.org/obo/CL_4052008) +#### Added +- Class: [UBERON_0002420](http://purl.obolibrary.org/obo/UBERON_0002420) -- [crypt-bottom fibroblast](http://purl.obolibrary.org/obo/CL_4052008) SubClassOf [subepithelial intestinal fibroblast](http://purl.obolibrary.org/obo/CL_4052007) -- [crypt-bottom fibroblast](http://purl.obolibrary.org/obo/CL_4052008) SubClassOf [RO_0002220](http://purl.obolibrary.org/obo/RO_0002220) some [UBERON_0013739](http://purl.obolibrary.org/obo/UBERON_0013739) +### UBERON_0002530 `http://purl.obolibrary.org/obo/UBERON_0002530` -- [crypt-bottom fibroblast](http://purl.obolibrary.org/obo/CL_4052008) SubClassOf [RO_0002220](http://purl.obolibrary.org/obo/RO_0002220) some [intestinal crypt stem cell](http://purl.obolibrary.org/obo/CL_0002250) +#### Added +- Class: [UBERON_0002530](http://purl.obolibrary.org/obo/UBERON_0002530) -### crypt-top fibroblast `http://purl.obolibrary.org/obo/CL_4052009` +### UBERON_0003335 `http://purl.obolibrary.org/obo/UBERON_0003335` #### Added -- [crypt-top fibroblast](http://purl.obolibrary.org/obo/CL_4052009) [id](http://www.geneontology.org/formats/oboInOwl#id) "CL:4052009"^^[string](http://www.w3.org/2001/XMLSchema#string) - -- [crypt-top fibroblast](http://purl.obolibrary.org/obo/CL_4052009) [contributor](http://purl.org/dc/terms/contributor) [0009-0000-8480-9277](https://orcid.org/0009-0000-8480-9277) +- Class: [UBERON_0003335](http://purl.obolibrary.org/obo/UBERON_0003335) -- [crypt-top fibroblast](http://purl.obolibrary.org/obo/CL_4052009) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "S2b fibroblast"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:37495570"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [crypt-top fibroblast](http://purl.obolibrary.org/obo/CL_4052009) [date](http://purl.org/dc/terms/date) "2024-09-23T11:14:04Z"^^[dateTime](http://www.w3.org/2001/XMLSchema#dateTime) +### UBERON_0004997 `http://purl.obolibrary.org/obo/UBERON_0004997` +#### Removed +- Class: [UBERON_0004997](http://purl.obolibrary.org/obo/UBERON_0004997) -- [crypt-top fibroblast](http://purl.obolibrary.org/obo/CL_4052009) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "CTFs"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003000](http://purl.obolibrary.org/obo/OMO_0003000) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "doi:/10.1371/journal.pbio.3001032"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [crypt-top fibroblast](http://purl.obolibrary.org/obo/CL_4052009) [comment](http://www.w3.org/2000/01/rdf-schema#comment) "S2b fibroblasts are located at the top of the crypt and express NRG1 and NPY."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:37495570"^^[string](http://www.w3.org/2001/XMLSchema#string) +### UBERON_0005357 `http://purl.obolibrary.org/obo/UBERON_0005357` +#### Removed +- Class: [UBERON_0005357](http://purl.obolibrary.org/obo/UBERON_0005357) -- [crypt-top fibroblast](http://purl.obolibrary.org/obo/CL_4052009) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "top pericryptic fibroblast"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:33916891"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [crypt-top fibroblast](http://purl.obolibrary.org/obo/CL_4052009) [label](http://www.w3.org/2000/01/rdf-schema#label) "crypt-top fibroblast"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [crypt-top fibroblast](http://purl.obolibrary.org/obo/CL_4052009) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A subepithelial intestinal fibroblast that is located adjacent to the top of the crypt of Lieberkuhn. Characterized by high experession of PDGFRα, this cell secretes a range of signaling factors, including WNTs and BMPs, that drive epithelial differentiation, creating a gradient that regulates the balance between stem cell maintenance and differentiation."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "doi:/10.1371/journal.pbio.3001032"^^[string](http://www.w3.org/2001/XMLSchema#string) +### UBERON_0006761 `http://purl.obolibrary.org/obo/UBERON_0006761` - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:33916891"^^[string](http://www.w3.org/2001/XMLSchema#string) +#### Added +- Class: [UBERON_0006761](http://purl.obolibrary.org/obo/UBERON_0006761) -- Class: [crypt-top fibroblast](http://purl.obolibrary.org/obo/CL_4052009) -- [crypt-top fibroblast](http://purl.obolibrary.org/obo/CL_4052009) SubClassOf [subepithelial intestinal fibroblast](http://purl.obolibrary.org/obo/CL_4052007) +### UBERON_0006799 `http://purl.obolibrary.org/obo/UBERON_0006799` +#### Removed +- Class: [UBERON_0006799](http://purl.obolibrary.org/obo/UBERON_0006799) -- [crypt-top fibroblast](http://purl.obolibrary.org/obo/CL_4052009) SubClassOf [RO_0002220](http://purl.obolibrary.org/obo/RO_0002220) some [UBERON_0013740](http://purl.obolibrary.org/obo/UBERON_0013740) -### cuboidal granulosa cell `http://purl.obolibrary.org/obo/CL_4033084` +### UBERON_0007240 `http://purl.obolibrary.org/obo/UBERON_0007240` #### Added -- [cuboidal granulosa cell](http://purl.obolibrary.org/obo/CL_4033084) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "cuboidal GC"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003000](http://purl.obolibrary.org/obo/OMO_0003000) +- Class: [UBERON_0007240](http://purl.obolibrary.org/obo/UBERON_0007240) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:33914868"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [cuboidal granulosa cell](http://purl.obolibrary.org/obo/CL_4033084) [label](http://www.w3.org/2000/01/rdf-schema#label) "cuboidal granulosa cell"^^[string](http://www.w3.org/2001/XMLSchema#string) +### UBERON_0008345 `http://purl.obolibrary.org/obo/UBERON_0008345` -- [cuboidal granulosa cell](http://purl.obolibrary.org/obo/CL_4033084) [date](http://purl.org/dc/terms/date) "2024-09-24T13:14:57Z"^^[dateTime](http://www.w3.org/2001/XMLSchema#dateTime) +#### Added +- Class: [UBERON_0008345](http://purl.obolibrary.org/obo/UBERON_0008345) -- [cuboidal granulosa cell](http://purl.obolibrary.org/obo/CL_4033084) [has_exact_synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "cuboidal epithelial granulosa cell"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:31849844"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [cuboidal granulosa cell](http://purl.obolibrary.org/obo/CL_4033084) [contributor](http://purl.org/dc/terms/contributor) [0000-0001-6677-8489](https://orcid.org/0000-0001-6677-8489) +### UBERON_0010038 `http://purl.obolibrary.org/obo/UBERON_0010038` -- [cuboidal granulosa cell](http://purl.obolibrary.org/obo/CL_4033084) [id](http://www.geneontology.org/formats/oboInOwl#id) "CL:4033084"^^[string](http://www.w3.org/2001/XMLSchema#string) +#### Added +- Class: [UBERON_0010038](http://purl.obolibrary.org/obo/UBERON_0010038) -- [cuboidal granulosa cell](http://purl.obolibrary.org/obo/CL_4033084) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A granulosa cell that has a cuboidal morphology and develops from squamous granulosa cell during the transition between primordial follicle to primary follicle. Cuboidal granulosa cells proliferate to form a second layer within secondary follicles."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:28892263"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [cuboidal granulosa cell](http://purl.obolibrary.org/obo/CL_4033084) [has_exact_synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "columnar granulosa cell"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:19001500"^^[string](http://www.w3.org/2001/XMLSchema#string) +### UBERON_0012498 `http://purl.obolibrary.org/obo/UBERON_0012498` -- [cuboidal granulosa cell](http://purl.obolibrary.org/obo/CL_4033084) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "columnar GC"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003000](http://purl.obolibrary.org/obo/OMO_0003000) +#### Added +- Class: [UBERON_0012498](http://purl.obolibrary.org/obo/UBERON_0012498) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:19001500"^^[string](http://www.w3.org/2001/XMLSchema#string) -- Class: [cuboidal granulosa cell](http://purl.obolibrary.org/obo/CL_4033084) +### UBERON_0015716 `http://purl.obolibrary.org/obo/UBERON_0015716` -- [cuboidal granulosa cell](http://purl.obolibrary.org/obo/CL_4033084) SubClassOf [granulosa cell](http://purl.obolibrary.org/obo/CL_0000501) +#### Added +- Class: [UBERON_0015716](http://purl.obolibrary.org/obo/UBERON_0015716) -- [cuboidal granulosa cell](http://purl.obolibrary.org/obo/CL_4033084) SubClassOf [UBERON_0004120](http://purl.obolibrary.org/obo/UBERON_0004120) -- [cuboidal granulosa cell](http://purl.obolibrary.org/obo/CL_4033084) SubClassOf [RO_0002207](http://purl.obolibrary.org/obo/RO_0002207) some [squamous granulosa cell](http://purl.obolibrary.org/obo/CL_4033083) +### UBERON_0022281 `http://purl.obolibrary.org/obo/UBERON_0022281` +#### Added +- Class: [UBERON_0022281](http://purl.obolibrary.org/obo/UBERON_0022281) -### cumulus cell `http://purl.obolibrary.org/obo/CL_0000711` -#### Removed -- [cumulus cell](http://purl.obolibrary.org/obo/CL_0000711) SubClassOf [RO_0002202](http://purl.obolibrary.org/obo/RO_0002202) some [granulosa cell](http://purl.obolibrary.org/obo/CL_0000501) -- [cumulus cell](http://purl.obolibrary.org/obo/CL_0000711) SubClassOf [follicular cell of ovary](http://purl.obolibrary.org/obo/CL_0002174) +### VIP GABAergic cortical interneuron `http://purl.obolibrary.org/obo/CL_4023016` #### Added -- [cumulus cell](http://purl.obolibrary.org/obo/CL_0000711) SubClassOf [UBERON_0004120](http://purl.obolibrary.org/obo/UBERON_0004120) +- [VIP GABAergic cortical interneuron](http://purl.obolibrary.org/obo/CL_4023016) [comment](http://www.w3.org/2000/01/rdf-schema#comment) "The marker set VIP can identify the Human cell type VIP GABAergic cortical interneuron in the Brain with a confidence of 0.855531344 (NS-Forest FBeta value)."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://doi.org/10.5281/zenodo.11165918"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [cumulus cell](http://purl.obolibrary.org/obo/CL_0000711) SubClassOf [RO_0002202](http://purl.obolibrary.org/obo/RO_0002202) some [cuboidal granulosa cell](http://purl.obolibrary.org/obo/CL_4033084) +- [VIP GABAergic cortical interneuron](http://purl.obolibrary.org/obo/CL_4023016) [RO_0002175](http://purl.obolibrary.org/obo/RO_0002175) [NCBITaxon_9606](http://purl.obolibrary.org/obo/NCBITaxon_9606) -- [cumulus cell](http://purl.obolibrary.org/obo/CL_0000711) SubClassOf [granulosa cell](http://purl.obolibrary.org/obo/CL_0000501) +- [VIP GABAergic cortical interneuron](http://purl.obolibrary.org/obo/CL_4023016) SubClassOf [RO_0015004](http://purl.obolibrary.org/obo/RO_0015004) some [CLM_1000085](http://purl.obolibrary.org/obo/CLM_1000085) -### cyanophore `http://purl.obolibrary.org/obo/CL_0000747` +### VIP-ChAT interneuron `http://purl.obolibrary.org/obo/CL_4042015` #### Added -- [cyanophore](http://purl.obolibrary.org/obo/CL_0000747) SubClassOf [eukaryotic cell](http://purl.obolibrary.org/obo/CL_0000255) +- [VIP-ChAT interneuron](http://purl.obolibrary.org/obo/CL_4042015) SubClassOf [VIP GABAergic cortical interneuron](http://purl.obolibrary.org/obo/CL_4023016) -### cystoblast `http://purl.obolibrary.org/obo/CL_0000722` +### Vgamma5-negative CD8-alpha alpha positive gamma-delta intraepithelial T cell `http://purl.obolibrary.org/obo/CL_0002514` #### Removed -- [cystoblast](http://purl.obolibrary.org/obo/CL_0000722) SubClassOf [RO_0002160](http://purl.obolibrary.org/obo/RO_0002160) some [NCBITaxon_6656](http://purl.obolibrary.org/obo/NCBITaxon_6656) +- [Vgamma5-negative CD8-alpha alpha positive gamma-delta intraepithelial T cell](http://purl.obolibrary.org/obo/CL_0002514) [label](http://www.w3.org/2000/01/rdf-schema#label) "Vgamma5-negative CD8alpha alpha positive gamma-delta intraepithelial T cell"^^[string](http://www.w3.org/2001/XMLSchema#string) -#### Added -- [cystoblast](http://purl.obolibrary.org/obo/CL_0000722) SubClassOf [RO_0002162](http://purl.obolibrary.org/obo/RO_0002162) some [NCBITaxon_6656](http://purl.obolibrary.org/obo/NCBITaxon_6656) +- [Vgamma5-negative CD8-alpha alpha positive gamma-delta intraepithelial T cell](http://purl.obolibrary.org/obo/CL_0002514) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A CD8alpha alpha positive gamma-delta intraepithelial T cell that does not express a TCR partially encoded by the Vgamma5 gene segment."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:tfm"^^[string](http://www.w3.org/2001/XMLSchema#string) - -### decidual natural killer cell, human `http://purl.obolibrary.org/obo/CL_0002343` - -#### Added -- [decidual natural killer cell, human](http://purl.obolibrary.org/obo/CL_0002343) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) - - -### dendritic cell `http://purl.obolibrary.org/obo/CL_0000451` + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "http://www.immgen.org/index_content.html"^^[string](http://www.w3.org/2001/XMLSchema#string) #### Added -- [dendritic cell](http://purl.obolibrary.org/obo/CL_0000451) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) - - -### dermal chromatophore `http://purl.obolibrary.org/obo/CL_4040006` +- [Vgamma5-negative CD8-alpha alpha positive gamma-delta intraepithelial T cell](http://purl.obolibrary.org/obo/CL_0002514) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A CD8-alpha alpha positive gamma-delta intraepithelial T cell that does not express a TCR partially encoded by the Vgamma5 gene segment."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:tfm"^^[string](http://www.w3.org/2001/XMLSchema#string) -#### Added -- [dermal chromatophore](http://purl.obolibrary.org/obo/CL_4040006) SubClassOf [eukaryotic cell](http://purl.obolibrary.org/obo/CL_0000255) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "http://www.immgen.org/index_content.html"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [Vgamma5-negative CD8-alpha alpha positive gamma-delta intraepithelial T cell](http://purl.obolibrary.org/obo/CL_0002514) [label](http://www.w3.org/2000/01/rdf-schema#label) "Vgamma5-negative CD8-alpha alpha positive gamma-delta intraepithelial T cell"^^[string](http://www.w3.org/2001/XMLSchema#string) -### early T lineage precursor `http://purl.obolibrary.org/obo/CL_0002425` -#### Added -- [early T lineage precursor](http://purl.obolibrary.org/obo/CL_0002425) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) +### Vgamma5-positive CD8-alpha alpha positive gamma-delta intraepithelial T cell `http://purl.obolibrary.org/obo/CL_0002513` +#### Removed +- [Vgamma5-positive CD8-alpha alpha positive gamma-delta intraepithelial T cell](http://purl.obolibrary.org/obo/CL_0002513) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A CD8alpha alpha positive gamma-delta intraepithelial T cell that expresses a TCR encoded in part by the Vgamma5 gene segment."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:tfm"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "http://www.immgen.org/index_content.html"^^[string](http://www.w3.org/2001/XMLSchema#string) -### early colonocyte `http://purl.obolibrary.org/obo/CL_4047018` +- [Vgamma5-positive CD8-alpha alpha positive gamma-delta intraepithelial T cell](http://purl.obolibrary.org/obo/CL_0002513) [label](http://www.w3.org/2000/01/rdf-schema#label) "Vgamma5-positive CD8alpha alpha positive gamma-delta intraepithelial T cell"^^[string](http://www.w3.org/2001/XMLSchema#string) #### Added -- [early colonocyte](http://purl.obolibrary.org/obo/CL_4047018) [contributor](http://purl.org/dc/terms/contributor) [0009-0005-7919-4905](https://orcid.org/0009-0005-7919-4905) +- [Vgamma5-positive CD8-alpha alpha positive gamma-delta intraepithelial T cell](http://purl.obolibrary.org/obo/CL_0002513) [label](http://www.w3.org/2000/01/rdf-schema#label) "Vgamma5-positive CD8-alpha alpha positive gamma-delta intraepithelial T cell"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [early colonocyte](http://purl.obolibrary.org/obo/CL_4047018) [label](http://www.w3.org/2000/01/rdf-schema#label) "early colonocyte"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [Vgamma5-positive CD8-alpha alpha positive gamma-delta intraepithelial T cell](http://purl.obolibrary.org/obo/CL_0002513) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A CD8-alpha alpha positive gamma-delta intraepithelial T cell that expresses a TCR encoded in part by the Vgamma5 gene segment."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:tfm"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [early colonocyte](http://purl.obolibrary.org/obo/CL_4047018) [id](http://www.geneontology.org/formats/oboInOwl#id) "CL:4047018"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "http://www.immgen.org/index_content.html"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [early colonocyte](http://purl.obolibrary.org/obo/CL_4047018) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "An enterocyte that is part of the colon, in the early stages of differentiation, located in the intestinal crypt-villus axis."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:36060223"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:28049136"^^[string](http://www.w3.org/2001/XMLSchema#string) +### absorptive cell `http://purl.obolibrary.org/obo/CL_0000212` -- [early colonocyte](http://purl.obolibrary.org/obo/CL_4047018) [has_exact_synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "early enterocyte of colon"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "doi:10.1101/2021.01.13.426602"^^[string](http://www.w3.org/2001/XMLSchema#string) +#### Added +- [absorptive cell](http://purl.obolibrary.org/obo/CL_0000212) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl/cl-base#cellxgene_subset) -- [early colonocyte](http://purl.obolibrary.org/obo/CL_4047018) [date](http://purl.org/dc/terms/date) "2024-09-24T11:50:13Z"^^[dateTime](http://www.w3.org/2001/XMLSchema#dateTime) -- Class: [early colonocyte](http://purl.obolibrary.org/obo/CL_4047018) +### acinar cell `http://purl.obolibrary.org/obo/CL_0000622` +#### Removed +- [acinar cell](http://purl.obolibrary.org/obo/CL_0000622) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. -- [early colonocyte](http://purl.obolibrary.org/obo/CL_4047018) EquivalentTo [early enterocyte](http://purl.obolibrary.org/obo/CL_4047019) and ([BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0001155](http://purl.obolibrary.org/obo/UBERON_0001155)) +Acinar cells are specialized exocrine gland cells that secrete specific enzymes and fluids to aid in digestion. Found primarily in the pancreas and salivary glands, the term acinar is derived from the Latin word 'acinus' which means 'grape'; this is because acinar cells are arranged in a grape-like cluster around small ducts, formulating an acinus structure. +In the salivary glands, acinar cells secrete digestive enzymes as well as other substances such as mucus and water. These secretions service the initial stages of the digestive process, preparing the consumed food for onward digestion in the stomach and intestines by lubricating and partially breaking it down. +In the pancreas, acinar cells are responsible for synthesizing and secreting a significant amount of digestive enzymes, such as trypsin, chymotrypsin, and amylase. These enzymes are stored in zymogen granules inside the acinar cells until they are dispatched into the small intestine. Once within the small intestine, they break down proteins, carbohydrates, and fats into substances that can be absorbed. This is vital to the effective and efficient digestion and absorption of nutrients from the food we consume. +Acinar cells have high protein synthesis rates and are susceptible to accumulation of misfolded proteins; the subsequential induction of ER stress is thought to be involved in the development of pancreatitis, a serious inflammatory disease of the exocrine pancreas."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1111/prd.12116"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [early colonocyte](http://purl.obolibrary.org/obo/CL_4047018) SubClassOf [early enterocyte](http://purl.obolibrary.org/obo/CL_4047019) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1152/physrev.00011.2011"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [early colonocyte](http://purl.obolibrary.org/obo/CL_4047018) SubClassOf [enterocyte of colon](http://purl.obolibrary.org/obo/CL_1000347) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1007/BF00710764"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1097/MOG.0b013e32832ebfac"^^[string](http://www.w3.org/2001/XMLSchema#string) -### early enterocyte `http://purl.obolibrary.org/obo/CL_4047019` + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1038/nrgastro.2013.36"^^[string](http://www.w3.org/2001/XMLSchema#string) #### Added -- [early enterocyte](http://purl.obolibrary.org/obo/CL_4047019) [label](http://www.w3.org/2000/01/rdf-schema#label) "early enterocyte"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [acinar cell](http://purl.obolibrary.org/obo/CL_0000622) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. -- [early enterocyte](http://purl.obolibrary.org/obo/CL_4047019) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "An enterocyte in the early stages of development, located above the transit-amplifying cell zone in the intestinal crypt-villus axis."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:35235783"^^[string](http://www.w3.org/2001/XMLSchema#string) +Acinar cells are specialized exocrine gland cells that secrete specific enzymes and fluids to aid in digestion. Found primarily in the pancreas and salivary glands, the term acinar is derived from the Latin word 'acinus' which means 'grape'; this is because acinar cells are arranged in a grape-like cluster around small ducts, formulating an acinus structure. +In the salivary glands, acinar cells secrete digestive enzymes as well as other substances such as mucus and water. These secretions service the initial stages of the digestive process, preparing the consumed food for onward digestion in the stomach and intestines by lubricating and partially breaking it down. +In the pancreas, acinar cells are responsible for synthesizing and secreting a significant amount of digestive enzymes, such as trypsin, chymotrypsin, and amylase. These enzymes are stored in zymogen granules inside the acinar cells until they are dispatched into the small intestine. Once within the small intestine, they break down proteins, carbohydrates, and fats into substances that can be absorbed. This is vital to the effective and efficient digestion and absorption of nutrients from the food we consume. +Acinar cells have high protein synthesis rates and are susceptible to accumulation of misfolded proteins; the subsequential induction of ER stress is thought to be involved in the development of pancreatitis, a serious inflammatory disease of the exocrine pancreas."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1111/prd.12116"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:20683682"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1152/physrev.00011.2011"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [early enterocyte](http://purl.obolibrary.org/obo/CL_4047019) [id](http://www.geneontology.org/formats/oboInOwl#id) "CL:4047019"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1007/BF00710764"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [early enterocyte](http://purl.obolibrary.org/obo/CL_4047019) [date](http://purl.org/dc/terms/date) "2024-09-24T12:11:09Z"^^[dateTime](http://www.w3.org/2001/XMLSchema#dateTime) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1097/MOG.0b013e32832ebfac"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [early enterocyte](http://purl.obolibrary.org/obo/CL_4047019) [contributor](http://purl.org/dc/terms/contributor) [0009-0005-7919-4905](https://orcid.org/0009-0005-7919-4905) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1038/nrgastro.2013.36"^^[string](http://www.w3.org/2001/XMLSchema#string) -- Class: [early enterocyte](http://purl.obolibrary.org/obo/CL_4047019) +- [acinar cell](http://purl.obolibrary.org/obo/CL_0000622) EquivalentTo [glandular secretory epithelial cell](http://purl.obolibrary.org/obo/CL_0000150) and [protein secreting cell](http://purl.obolibrary.org/obo/CL_0000154) and ([BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0009842](http://purl.obolibrary.org/obo/UBERON_0009842)) -- [early enterocyte](http://purl.obolibrary.org/obo/CL_4047019) EquivalentTo [enterocyte](http://purl.obolibrary.org/obo/CL_0000584) and ([BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0013740](http://purl.obolibrary.org/obo/UBERON_0013740)) -- [early enterocyte](http://purl.obolibrary.org/obo/CL_4047019) SubClassOf [enterocyte](http://purl.obolibrary.org/obo/CL_0000584) +### activated CD4-negative, CD8-negative type I NK T cell `http://purl.obolibrary.org/obo/CL_0000928` -- [early enterocyte](http://purl.obolibrary.org/obo/CL_4047019) SubClassOf [BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0013740](http://purl.obolibrary.org/obo/UBERON_0013740) +#### Added +- [activated CD4-negative, CD8-negative type I NK T cell](http://purl.obolibrary.org/obo/CL_0000928) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl/cl-base#cellxgene_subset) -### ectodermal cell `http://purl.obolibrary.org/obo/CL_0000221` +### adipose macrophage `http://purl.obolibrary.org/obo/CL_0002477` +#### Removed +- [adipose macrophage](http://purl.obolibrary.org/obo/CL_0002477) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) #### Added -- [ectodermal cell](http://purl.obolibrary.org/obo/CL_0000221) SubClassOf [eukaryotic cell](http://purl.obolibrary.org/obo/CL_0000255) +- [adipose macrophage](http://purl.obolibrary.org/obo/CL_0002477) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl/cl-base#cellxgene_subset) -### elicited macrophage `http://purl.obolibrary.org/obo/CL_0000861` +### adventitial fibroblast `http://purl.obolibrary.org/obo/CL_4052030` #### Added -- [elicited macrophage](http://purl.obolibrary.org/obo/CL_0000861) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) +- [adventitial fibroblast](http://purl.obolibrary.org/obo/CL_4052030) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A fibroblast of the adventitia of a blood vessel. This cell contributes to vascular homeostasis, remodeling, and inflammation by producing extracellular matrix components, cytokines, and growth factors. Adventitial fibroblast can transition into an activated state during injury or disease, marked by increased proliferation, migration, matrix deposition, and contractile protein expression"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:28705796"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:36718802"^^[string](http://www.w3.org/2001/XMLSchema#string) -### endocrine cell `http://purl.obolibrary.org/obo/CL_0000163` +- [adventitial fibroblast](http://purl.obolibrary.org/obo/CL_4052030) [label](http://www.w3.org/2000/01/rdf-schema#label) "adventitial fibroblast"^^[string](http://www.w3.org/2001/XMLSchema#string) -#### Added -- [endocrine cell](http://purl.obolibrary.org/obo/CL_0000163) SubClassOf [eukaryotic cell](http://purl.obolibrary.org/obo/CL_0000255) +- [adventitial fibroblast](http://purl.obolibrary.org/obo/CL_4052030) [contributor](http://purl.org/dc/terms/contributor) [0009-0000-8480-9277](https://orcid.org/0009-0000-8480-9277) +- [adventitial fibroblast](http://purl.obolibrary.org/obo/CL_4052030) [comment](http://www.w3.org/2000/01/rdf-schema#comment) "Single-cell transcriptomics of murine aorta identifies two adventitial fibroblast-specific markers, PDGFRA and DPEP1, which were validated at the protein level by immunohistochemistry and flow cytometry across human and murine arteries, highlighting fibroblast heterogeneity in health and cardiovascular disease (CVD) in humans and mice."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:36718802"^^[string](http://www.w3.org/2001/XMLSchema#string) -### endodermal cell `http://purl.obolibrary.org/obo/CL_0000223` +- [adventitial fibroblast](http://purl.obolibrary.org/obo/CL_4052030) [id](http://www.geneontology.org/formats/oboInOwl#id) "CL:4052030"^^[string](http://www.w3.org/2001/XMLSchema#string) -#### Added -- [endodermal cell](http://purl.obolibrary.org/obo/CL_0000223) SubClassOf [eukaryotic cell](http://purl.obolibrary.org/obo/CL_0000255) +- [adventitial fibroblast](http://purl.obolibrary.org/obo/CL_4052030) [date](http://purl.org/dc/terms/date) "2024-12-05T11:01:15Z"^^[dateTime](http://www.w3.org/2001/XMLSchema#dateTime) +- Class: [adventitial fibroblast](http://purl.obolibrary.org/obo/CL_4052030) -### endothelial cell `http://purl.obolibrary.org/obo/CL_0000115` +- [adventitial fibroblast](http://purl.obolibrary.org/obo/CL_4052030) EquivalentTo [fibroblast](http://purl.obolibrary.org/obo/CL_0000057) and ([BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0005734](http://purl.obolibrary.org/obo/UBERON_0005734)) -#### Added -- [endothelial cell](http://purl.obolibrary.org/obo/CL_0000115) SubClassOf [eukaryotic cell](http://purl.obolibrary.org/obo/CL_0000255) +- [adventitial fibroblast](http://purl.obolibrary.org/obo/CL_4052030) SubClassOf [RO_0002215](http://purl.obolibrary.org/obo/RO_0002215) some [GO_0070278](http://purl.obolibrary.org/obo/GO_0070278) +- [adventitial fibroblast](http://purl.obolibrary.org/obo/CL_4052030) SubClassOf [fibroblast](http://purl.obolibrary.org/obo/CL_0000057) -### endothelial cell of artery `http://purl.obolibrary.org/obo/CL_1000413` +- [adventitial fibroblast](http://purl.obolibrary.org/obo/CL_4052030) SubClassOf [secretory cell](http://purl.obolibrary.org/obo/CL_0000151) -#### Added -- [endothelial cell of artery](http://purl.obolibrary.org/obo/CL_1000413) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. +- [adventitial fibroblast](http://purl.obolibrary.org/obo/CL_4052030) SubClassOf [adventitial cell](http://purl.obolibrary.org/obo/CL_0002503) -Endothelial cells of the artery, also referred to as arterial endothelial cells, form an integral part of the arterial system. They form a single layer, known as the endothelium, lining the interior surface of arteries, and are able to respond to the high-pressure and flow conditions present in arteries. The primary role of these cells is to provide a barrier between the vessel wall and the blood, exhibiting selective permeability to regulate the movement of liquids, gases, and blood-borne substances across the vascular wall. -Arterial endothelial cells significantly contribute to maintaining vascular homeostasis. They are at the forefront of sensations and responses to mechanical stimuli, like shear stress and blood pressure changes. An additional key function pertains to the production of nitric oxide, which helps to regulate vascular tone and blood pressure, prevents platelet aggregation, limits leukocyte adhesion to the endothelium, and inhibits smooth muscle cell proliferation. These varied but connected functions help to preclude the development of atherosclerosis, ensuring normal circulation and arterial health. -Moreover, these cells play a pivotal role in inflammation and coagulation processes. During inflammatory events, they express various adhesion molecules, aiding in leukocyte recruitment and rolling onto the vessel walls for immune response. They also produce anticoagulant and procoagulant substances, involved in blood clotting and clot dissolution, respectively. Dysregulation of the usual functions of arterial endothelial cells can result in serious pathophysiological conditions, such as atherosclerosis, hypertension, and other cardiovascular diseases."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1177/153857440303700107"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [adventitial fibroblast](http://purl.obolibrary.org/obo/CL_4052030) SubClassOf [BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0005734](http://purl.obolibrary.org/obo/UBERON_0005734) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1007/s00441-008-0706-5"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [adventitial fibroblast](http://purl.obolibrary.org/obo/CL_4052030) SubClassOf [RO_0002215](http://purl.obolibrary.org/obo/RO_0002215) some [GO_0001816](http://purl.obolibrary.org/obo/GO_0001816) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1016/j.jvs.2004.03.043"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1016/j.ccm.2021.08.005"^^[string](http://www.w3.org/2001/XMLSchema#string) +### airway submucosal gland collecting duct epithelial cell `http://purl.obolibrary.org/obo/CL_4033023` - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1007/s10456-021-09785-7"^^[string](http://www.w3.org/2001/XMLSchema#string) +#### Added +- [airway submucosal gland collecting duct epithelial cell](http://purl.obolibrary.org/obo/CL_4033023) [comment](http://www.w3.org/2000/01/rdf-schema#comment) "The marker set GLYATL2, DMBT1 can identify the Human cell type airway submucosal gland collecting duct epithelial cell in the Lung with a confidence of 0.46 (NS-Forest FBeta value)."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://doi.org/10.5281/zenodo.11165918"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [endothelial cell of artery](http://purl.obolibrary.org/obo/CL_1000413) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://cellxgene.cziscience.com/cellguide/CL_1000413"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [airway submucosal gland collecting duct epithelial cell](http://purl.obolibrary.org/obo/CL_4033023) SubClassOf [RO_0015004](http://purl.obolibrary.org/obo/RO_0015004) some [CLM_1000052](http://purl.obolibrary.org/obo/CLM_1000052) -### endothelial cell of umbilical vein `http://purl.obolibrary.org/obo/CL_0002618` +### airway submucosal gland duct basal cell `http://purl.obolibrary.org/obo/CL_4033024` #### Added -- [endothelial cell of umbilical vein](http://purl.obolibrary.org/obo/CL_0002618) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://cellxgene.cziscience.com/cellguide/CL_0002618"^^[string](http://www.w3.org/2001/XMLSchema#string) - -- [endothelial cell of umbilical vein](http://purl.obolibrary.org/obo/CL_0002618) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. - -Endothelial cells of the umbilical vein form the inner lining of the veins found in the umbilical cord. They are involved in tube formation and migration which are essential for angiogenesis, the process of generating new blood vessels; this is critical during the fetal stage for the development of the circulatory system. Endothelial cells of the umbilical vein also play a role in controlling the passage of white blood cells into tissues during inflammatory responses. -Because human umbilical vein endothelial cells (HUVECs) can easily be derived from the umbilical cord, and because they express common endothelial cell markers, they have been used as an epithelial cell model for studies on cell proliferation, migration, angiogenesis, and inflammation. They have been used as models for vascular diseases like atherosclerosis, for investigating how tumor cells infiltrate blood vessels and form metastases. -Thus, while endothelial cells of the umbilical vein play a critical role in vascular biology, they also represent a powerful tool in disease studies and potential treatment strategies."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1007/s12015-006-0015-x"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [airway submucosal gland duct basal cell](http://purl.obolibrary.org/obo/CL_4033024) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl/cl-base#cellxgene_subset) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1172/JCI107470"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://www.ncbi.nlm.nih.gov/books/NBK53254/"^^[string](http://www.w3.org/2001/XMLSchema#string) +### airway submucosal gland duct multiciliated cell `http://purl.obolibrary.org/obo/CL_4033055` +#### Removed +- [airway submucosal gland duct multiciliated cell](http://purl.obolibrary.org/obo/CL_4033055) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A ciliated cell that is part of a ciliated duct of an airway submucosal gland."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:17707699"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.3390/app10030938"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:30864819"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1002/cyto.a.20952"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [airway submucosal gland duct multiciliated cell](http://purl.obolibrary.org/obo/CL_4033055) [label](http://www.w3.org/2000/01/rdf-schema#label) "airway submucosal gland duct ciliated cell"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [airway submucosal gland duct multiciliated cell](http://purl.obolibrary.org/obo/CL_4033055) EquivalentTo [ciliated cell](http://purl.obolibrary.org/obo/CL_0000064) and ([BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_8410077](http://purl.obolibrary.org/obo/UBERON_8410077)) and ([BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_8600014](http://purl.obolibrary.org/obo/UBERON_8600014)) -### endothelial stalk cell `http://purl.obolibrary.org/obo/CL_0002671` +- [airway submucosal gland duct multiciliated cell](http://purl.obolibrary.org/obo/CL_4033055) SubClassOf [ciliated cell](http://purl.obolibrary.org/obo/CL_0000064) #### Added -- [endothelial stalk cell](http://purl.obolibrary.org/obo/CL_0002671) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://cellxgene.cziscience.com/cellguide/CL_0002671"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [airway submucosal gland duct multiciliated cell](http://purl.obolibrary.org/obo/CL_4033055) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A multi-ciliated epithelial cell located in ciliated duct of an airway submucosal gland, characterized by a columnar shape and motile cilia on its apical surface."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:17707699"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [endothelial stalk cell](http://purl.obolibrary.org/obo/CL_0002671) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. - -Endothelial stalk cells are specialized vascular cells vital in angiogenesis, a process through which new blood vessels are formed from pre-existing ones; specifically, endothelial stalk cells are involved in sprouting angiogenesis, where they help form the body of new blood vessels. -Vascular sprouting relies on the coordinated activity of migrating endothelial tip cells at the forefront and proliferating stalk cells that elongate the sprout. The process is tightly controlled by different growths factors: Vascular Endothelial Growth Factor acts on endothelial cells, inducing them to become endothelial tip cells that initiate sprouting. After sprouting initiation, activation of Notch signaling suppresses differentiation toward a tip cell phenotype and some of the endothelial cells differentiate into stalk cells, which follow tip cells, multiply, and elongate to provide a structural backbone to the growing vessel sprout. -In contrast to endothelial tip cells, which migrate and lead the angiogenic sprout, endothelial stalk cells behind the sprouts continue forming the tube or lumen for blood flow and facilitate maturation and stability of the new vessel. The delicate balance between the activities of stalk and tip cells during angiogenesis is crucial to build a functional vascular network. Dysfunctions in endothelial stalk cells can lead to pathological conditions such as impaired wound healing, unregulated tumor growth, and metastasis due to abnormal angiogenesis."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1016/j.cmet.2013.08.001"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:30864819"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.3389/fcell.2021.642352"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [airway submucosal gland duct multiciliated cell](http://purl.obolibrary.org/obo/CL_4033055) [has_exact_synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "airway submucosal gland duct ciliated cell"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1007/s12079-019-00511-z"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [airway submucosal gland duct multiciliated cell](http://purl.obolibrary.org/obo/CL_4033055) [label](http://www.w3.org/2000/01/rdf-schema#label) "airway submucosal gland duct multiciliated cell"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1101/cshperspect.a006569"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [airway submucosal gland duct multiciliated cell](http://purl.obolibrary.org/obo/CL_4033055) EquivalentTo [columnar/cuboidal epithelial cell](http://purl.obolibrary.org/obo/CL_0000075) and ([BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_8410077](http://purl.obolibrary.org/obo/UBERON_8410077)) and ([BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_8600014](http://purl.obolibrary.org/obo/UBERON_8600014)) and ([BFO_0000051](http://purl.obolibrary.org/obo/BFO_0000051) some [GO_0031514](http://purl.obolibrary.org/obo/GO_0031514)) and ([RO_0000053](http://purl.obolibrary.org/obo/RO_0000053) some [PATO_0010007](http://purl.obolibrary.org/obo/PATO_0010007)) +- [airway submucosal gland duct multiciliated cell](http://purl.obolibrary.org/obo/CL_4033055) SubClassOf [multiciliated epithelial cell](http://purl.obolibrary.org/obo/CL_0005012) -### enterocyte of colon `http://purl.obolibrary.org/obo/CL_1000347` -#### Removed -- [enterocyte of colon](http://purl.obolibrary.org/obo/CL_1000347) [label](http://www.w3.org/2000/01/rdf-schema#label) "enterocyte of colon"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [airway submucosal gland duct multiciliated cell](http://purl.obolibrary.org/obo/CL_4033055) SubClassOf [duct epithelial cell](http://purl.obolibrary.org/obo/CL_0000068) -#### Added -- [enterocyte of colon](http://purl.obolibrary.org/obo/CL_1000347) [label](http://www.w3.org/2000/01/rdf-schema#label) "colonocyte"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [enterocyte of colon](http://purl.obolibrary.org/obo/CL_1000347) [has_exact_synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "enterocyte of colon"^^[string](http://www.w3.org/2001/XMLSchema#string) +### alpha-beta T cell `http://purl.obolibrary.org/obo/CL_0000789` +#### Removed +- [alpha-beta T cell](http://purl.obolibrary.org/obo/CL_0000789) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) -- [enterocyte of colon](http://purl.obolibrary.org/obo/CL_1000347) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. -Enterocytes of the colon are specialized epithelial cells located in the lining of the colon, the largest part of the large intestine. These cells play a critical role in absorbing water, electrolytes, and certain vitamins from the food material passed on from the small intestine. With a unique structure of finger-like protrusions referred to as microvilli, the enterocytes increase their surface area for effective absorption. The colon is the last part of the digestive system, and as such, it is responsible for compacting undigested food materials and forming fecal matter. Enterocytes of the colon facilitate this process effectively through absorption of water. -Enterocytes are known for their high regeneration potential, replenishing every 4-5 days, enabling the healthy functioning of the colon. They originate from stem cells located in the crypt of the colon and differentiate into mature enterocytes as they migrate upwards towards the luminal surface. This constant turnover aids in maintaining the intestinal barrier, preventing the entry of detrimental substances into the systemic circulation. Their tight junctions with other epithelial cells provide a robust barrier against invasive pathogens. -Enterocytes of the colon are involved in the communication with the gut microbiota. These cells harbor enzymes necessary for the metabolism of short-chain fatty acids, which are the byproducts of the fermentation process by gut bacteria. Short-chain fatty acids serve as a major energy source for colonocytes and are important for maintaining colonic health. The dysfunction of enterocytes, therefore, could lead to disorders such as inflammatory bowel disease or colorectal cancer."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1038/nrgastro.2013.35"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1038/nri3738"^^[string](http://www.w3.org/2001/XMLSchema#string) +### alternatively activated macrophage `http://purl.obolibrary.org/obo/CL_0000890` +#### Removed +- [alternatively activated macrophage](http://purl.obolibrary.org/obo/CL_0000890) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1084/jem.20191130"^^[string](http://www.w3.org/2001/XMLSchema#string) +Alternatively activated macrophages, also referred to as M2 macrophages, are immune cells originating from monocytes. The M1/M2 classification is based upon macrophage polarization rather than macrophage location and refers to macrophage activation towards either a more inflammatory or more resolving phenotype, respectively, although the functional diversity of macrophages is more nuanced than such a dichotomy suggests. +M2 macrophages cells are differentiated from their precursors generally in response to Th2 cytokines, such as interleukin-4 (IL-4), interleukin-10 (IL-10), and interleukin-13 (IL-13). Tissue-resident macrophages are also sometimes said to have an “M2-like” phenotype. M2 macrophages play key roles in immunoregulation and disease resolution. +Functionally, alternatively activated macrophages are essential in wound healing and tissue repair and remodeling, largely due to their potent anti-inflammatory actions and their ability to promote angiogenesis. They achieve these functions by the production of specific growth factors and signaling proteins including Arg1, Ym1/2, Fizz1, and TGF-β. Additionally, they provide defense against specific categories of pathogens, particularly parasites, through specific communication with Th2 cells. +However, dysfunction of M2 macrophages can be harmful. Alternatively activated macrophages have been associated with several pathological conditions such as asthma, fibrosis, and tumor progression. This is due to their capacity to inhibit inflammatory responses, promote unneeded wound healing processes, and support tumour growth and spreading. Furthermore, complex roles have been observed in metabolic disorders, cardiovascular diseases, and neurodegenerative diseases, showing the diverse functional spectrum of these cells."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1186/s12935-021-02089-2"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.3389/fimmu.2019.00277"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.3389/fimmu.2020.583084"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1007/s11894-010-0130-3"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.3389/fimmu.2015.00263"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [enterocyte of colon](http://purl.obolibrary.org/obo/CL_1000347) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://cellxgene.cziscience.com/cellguide/CL_1000347"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1038/s41392-023-01452-1"^^[string](http://www.w3.org/2001/XMLSchema#string) +#### Added +- [alternatively activated macrophage](http://purl.obolibrary.org/obo/CL_0000890) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. -### enterocyte of epithelium of small intestine `http://purl.obolibrary.org/obo/CL_1000334` +Alternatively activated macrophages, also referred to as M2 macrophages, are immune cells originating from monocytes. The M1/M2 classification is based upon macrophage polarization rather than macrophage location and refers to macrophage activation towards either a more inflammatory or more resolving phenotype, respectively, although the functional diversity of macrophages is more nuanced than such a dichotomy suggests. +M2 macrophages cells are differentiated from their precursors generally in response to Th2 cytokines, such as interleukin-4 (IL-4), interleukin-10 (IL-10), and interleukin-13 (IL-13). Tissue-resident macrophages are also sometimes said to have an “M2-like” phenotype. M2 macrophages play key roles in immunoregulation and disease resolution. +Functionally, alternatively activated macrophages are essential in wound healing and tissue repair and remodeling, largely due to their potent anti-inflammatory actions and their ability to promote angiogenesis. They achieve these functions by the production of specific growth factors and signaling proteins including Arg1, Ym1/2, Fizz1, and TGF-β. Additionally, they provide defense against specific categories of pathogens, particularly parasites, through specific communication with Th2 cells. +However, dysfunction of M2 macrophages can be harmful. Alternatively activated macrophages have been associated with several pathological conditions such as asthma, fibrosis, and tumor progression. This is due to their capacity to inhibit inflammatory responses, promote unneeded wound healing processes, and support tumour growth and spreading. Furthermore, complex roles have been observed in metabolic disorders, cardiovascular diseases, and neurodegenerative diseases, showing the diverse functional spectrum of these cells."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1186/s12935-021-02089-2"^^[string](http://www.w3.org/2001/XMLSchema#string) -#### Added -- [enterocyte of epithelium of small intestine](http://purl.obolibrary.org/obo/CL_1000334) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.3389/fimmu.2020.583084"^^[string](http://www.w3.org/2001/XMLSchema#string) -Enterocytes of the epithelium of the small intestine are specialized cells that reside in the lining of the small intestine, and are primarily responsible for the essential process of nutrient absorption. These cells are columnar epithelial cells with an apical surface lined with microvilli, a feature referred to as the 'brush border', to maximize the surface area available for absorption. -Enterocytes play a critical role in both the digestion and absorption of nutrients from food. Their extensive brush border contains enzymes that further assist in nutrient breakdown and transport proteins that transfer nutrients, such as glucose, amino acids, lipids, and vitamins, across the cell membrane. -The enterocytes of the small intestine also participate in the barrier function of the gut lining. Enterocytes are connected by tight junctions, which act as a primary defense line against pathogenic invasion by maintaining intestinal barrier integrity. Additionally, their cell surface is coated in glycocalyx and mucus which forms a defensive barrier preventing the penetration of harmful bacteria into the systemic circulation."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1038/nrgastro.2013.35"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.3389/fimmu.2015.00263"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.3389/fphys.2021.699152/full"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1038/s41392-023-01452-1"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1038/nri3738"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1084/jem.20191130"^^[string](http://www.w3.org/2001/XMLSchema#string) +### alveolar adventitial fibroblast `http://purl.obolibrary.org/obo/CL_4028006` -- [enterocyte of epithelium of small intestine](http://purl.obolibrary.org/obo/CL_1000334) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://cellxgene.cziscience.com/cellguide/CL_1000334"^^[string](http://www.w3.org/2001/XMLSchema#string) +#### Added +- [alveolar adventitial fibroblast](http://purl.obolibrary.org/obo/CL_4028006) [comment](http://www.w3.org/2000/01/rdf-schema#comment) "The marker set SCARA5, CD248 can identify the Human cell type alveolar adventitial fibroblast in the Lung with a confidence of 0.85 (NS-Forest FBeta value)."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://doi.org/10.5281/zenodo.11165918"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [alveolar adventitial fibroblast](http://purl.obolibrary.org/obo/CL_4028006) SubClassOf [RO_0015004](http://purl.obolibrary.org/obo/RO_0015004) some [CLM_1000001](http://purl.obolibrary.org/obo/CLM_1000001) -### enterocyte of epithelium proper of ileum `http://purl.obolibrary.org/obo/CL_1000342` -#### Added -- [enterocyte of epithelium proper of ileum](http://purl.obolibrary.org/obo/CL_1000342) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://cellxgene.cziscience.com/cellguide/CL_1000342"^^[string](http://www.w3.org/2001/XMLSchema#string) +### alveolar macrophage `http://purl.obolibrary.org/obo/CL_0000583` +#### Removed +- [alveolar macrophage](http://purl.obolibrary.org/obo/CL_0000583) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. -- [enterocyte of epithelium proper of ileum](http://purl.obolibrary.org/obo/CL_1000342) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. +Alveolar macrophages are unique tissue-resident macrophages found in the lungs, specifically in the air sacs or alveoli where gas exchange occurs. They are characterized by specific surface markers including: F4/80-positive, CD11b-/low, CD11c-positive, CD68-positive, sialoadhesin-positive, dectin-1-positive, MR-positive, CX3CR1-negative. These specialized immune cells form a crucial part of the body's defense mechanism, playing important roles in pulmonary health and homeostasis. They are the first line of defense in the pulmonary immune response, acting as scavengers that patrol the alveoli and engulf foreign particles like bacteria, dust, and other debris that enter the lungs through inhalation. +The primary function of these alveolar macrophages is phagocytosis, whereby they consume and digest foreign substances, dead cells, and other particulates. In the lung, alveolar macrophages are also responsible for clearing surfactant. Additionally, alveolar macrophages also play an integral role in initiating the immune response, as they secrete several pro-inflammatory cytokines and chemokines that recruit other immune cells to the site of infection or inflammation. +Beyond their role in host defense, alveolar macrophages contribute to tissue remodeling and wound repair in the lungs, aiding in maintaining lung integrity. They also regulate local inflammation and control the immune response to prevent excessive inflammation that may be harmful. However, an imbalance in the function of alveolar macrophages can contribute to various lung diseases. Abnormal alveolar macrophage activation has been implicated in chronic inflammatory diseases such as emphysema, asthma, and fibrosis."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1016/j.cellimm.2018.01.005"^^[string](http://www.w3.org/2001/XMLSchema#string) -Enterocytes of the epithelium proper of the ileum, commonly known as ileal enterocytes, are specialized epithelial cells found lining the inner surface of the ileum, the final section of the small intestine in the human body. They play a pivotal role in nutrient absorption, digestive metabolic functions, and the maintenance of the host’s immune response. -Like enterocytes in other parts of the intestine, ileal enterocytes exhibit distinct characteristics specific to their function and role. They have microvilli on their apical surfaces to increase absorption and are important in the absorption of vitamins and the reabsorption of bile salts. These cells also produce enzymes that metabolize lipids and xenobiotics."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1038/nri3738"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1007/s00424-017-1965-3"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1084/jem.20191130"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.14348/molcells.2021.0058"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1111/j.1365-2249.2011.04523.x"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1038/nri3600"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [alveolar macrophage](http://purl.obolibrary.org/obo/CL_0000583) [comment](http://www.w3.org/2000/01/rdf-schema#comment) "Markers: Mouse: F4/80mid, CD11b-/low, CD11c+, CD68+, sialoadhesin+, dectin-1+, MR+, CX3CR1-."^^[string](http://www.w3.org/2001/XMLSchema#string) -### enteroendocrine cell `http://purl.obolibrary.org/obo/CL_0000164` +- [alveolar macrophage](http://purl.obolibrary.org/obo/CL_0000583) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) #### Added -- [enteroendocrine cell](http://purl.obolibrary.org/obo/CL_0000164) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://cellxgene.cziscience.com/cellguide/CL_0000164"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [alveolar macrophage](http://purl.obolibrary.org/obo/CL_0000583) [comment](http://www.w3.org/2000/01/rdf-schema#comment) "The marker set MSR1, FABP4 can identify the Human cell type alveolar macrophage in the Lung with a confidence of 0.80 (NS-Forest FBeta value). Markers: Mouse: F4/80mid, CD11b-/low, CD11c+, CD68+, sialoadhesin+, dectin-1+, MR+, CX3CR1-."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://doi.org/10.5281/zenodo.11165918"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [enteroendocrine cell](http://purl.obolibrary.org/obo/CL_0000164) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. +- [alveolar macrophage](http://purl.obolibrary.org/obo/CL_0000583) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. -Enteroendocrine cells are a specialized subset of cells located within the epithelial lining of both the small and large intestines, as well as the stomach and pancreas. Constituting less than 1% of the total population of intestinal cells, they are differentiated from a common intestinal cell progenitor, thus sharing lineage with absorptive and goblet cells of the intestines. -The distinct characteristic feature of an enteroendocrine cell is its inherent capacity to synthesize and secrete a plethora of gut hormones such as serotonin, somatostatin, neurotensin, cholecystokinin, secretin, gastric inhibitory peptide, motilin, and glucagon-like peptide-1. Integrated within this complex network of signaling agents, these substances control various aspects of the digestive system. Each enteroendocrine cell has its unique combination of hormones to release, determined by its position along the intestinal tract. Intriguingly, these hormones not only modulate local gut function, including motility, absorption and secretion, but also potentiate distant actions on other systems such as endocrine, nervous and immune and play a role in the feeling of satiety. -The release of these hormones from enteroendocrine cells is a highly regulated and dynamic process. The cells are equipped with sensory receptors localized on its luminal side that respond to various stimuli, including changes in nutrient composition, chemical or mechanical changes in the gut lumen, or even signals arising from commensal microbiota. This sensory input stimulates a signaling cascade within the cell, culminating in the release of specific hormones into the interstitial fluid. These hormones then make their way into the bloodstream, acting on their respective target receptors to mediate their duties. The multifunctional characteristics of enteroendocrine cells make them crucial for maintaining gut homeostasis and the overall physiological well being of the body."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.7554/elife.78512"^^[string](http://www.w3.org/2001/XMLSchema#string) +Alveolar macrophages are unique tissue-resident macrophages found in the lungs, specifically in the air sacs or alveoli where gas exchange occurs. They are characterized by specific surface markers including: F4/80-positive, CD11b-/low, CD11c-positive, CD68-positive, sialoadhesin-positive, dectin-1-positive, MR-positive, CX3CR1-negative. These specialized immune cells form a crucial part of the body's defense mechanism, playing important roles in pulmonary health and homeostasis. They are the first line of defense in the pulmonary immune response, acting as scavengers that patrol the alveoli and engulf foreign particles like bacteria, dust, and other debris that enter the lungs through inhalation. +The primary function of these alveolar macrophages is phagocytosis, whereby they consume and digest foreign substances, dead cells, and other particulates. In the lung, alveolar macrophages are also responsible for clearing surfactant. Additionally, alveolar macrophages also play an integral role in initiating the immune response, as they secrete several pro-inflammatory cytokines and chemokines that recruit other immune cells to the site of infection or inflammation. +Beyond their role in host defense, alveolar macrophages contribute to tissue remodeling and wound repair in the lungs, aiding in maintaining lung integrity. They also regulate local inflammation and control the immune response to prevent excessive inflammation that may be harmful. However, an imbalance in the function of alveolar macrophages can contribute to various lung diseases. Abnormal alveolar macrophage activation has been implicated in chronic inflammatory diseases such as emphysema, asthma, and fibrosis."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1016/j.cellimm.2018.01.005"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1111/j.1463-1326.2011.01438.x"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1007/s00424-017-1965-3"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1196/annals.1294.001"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.14348/molcells.2021.0058"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1210/endrev/bnaa018"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1038/nri3600"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1038/s41574-019-0168-8"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [alveolar macrophage](http://purl.obolibrary.org/obo/CL_0000583) SubClassOf [RO_0015004](http://purl.obolibrary.org/obo/RO_0015004) some [CLM_1000003](http://purl.obolibrary.org/obo/CLM_1000003) -### eosinophil progenitor cell `http://purl.obolibrary.org/obo/CL_0000611` +### alveolar type 1 fibroblast cell `http://purl.obolibrary.org/obo/CL_4028004` #### Added -- [eosinophil progenitor cell](http://purl.obolibrary.org/obo/CL_0000611) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) - +- [alveolar type 1 fibroblast cell](http://purl.obolibrary.org/obo/CL_4028004) [comment](http://www.w3.org/2000/01/rdf-schema#comment) "The marker set AOC3, LUM can identify the Human cell type alveolar type 1 fibroblast cell in the Lung with a confidence of 0.70 (NS-Forest FBeta value)."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://doi.org/10.5281/zenodo.11165918"^^[string](http://www.w3.org/2001/XMLSchema#string) -### ependymal cell `http://purl.obolibrary.org/obo/CL_0000065` -#### Removed -- [ependymal cell](http://purl.obolibrary.org/obo/CL_0000065) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A neurectoderm derived cell that lines the neural lumen."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "JB:jb"^^[string](http://www.w3.org/2001/XMLSchema#string) - - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:tfm"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [alveolar type 1 fibroblast cell](http://purl.obolibrary.org/obo/CL_4028004) SubClassOf [RO_0015004](http://purl.obolibrary.org/obo/RO_0015004) some [CLM_1000002](http://purl.obolibrary.org/obo/CLM_1000002) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:9550134"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [ependymal cell](http://purl.obolibrary.org/obo/CL_0000065) [has_exact_synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "ependymocyte"^^[string](http://www.w3.org/2001/XMLSchema#string) +### ameloblast `http://purl.obolibrary.org/obo/CL_0000059` +#### Removed +- [ameloblast](http://purl.obolibrary.org/obo/CL_0000059) SubClassOf [secretory cell](http://purl.obolibrary.org/obo/CL_0000151) #### Added -- [ependymal cell](http://purl.obolibrary.org/obo/CL_0000065) [has_narrow_synonym](http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym) "ependymocyte"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "doi:10.53347/rID-51713"^^[string](http://www.w3.org/2001/XMLSchema#string) - -- [ependymal cell](http://purl.obolibrary.org/obo/CL_0000065) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A neuroepithelial glial cell, derived from a radial glial cell originating from the neuroectoderm, lines the ventricles of the brain and the central canal of the spinal cord. This cell is characterized by the presence of cilia on its apical surface, which can be motile or non-motile."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:34335193"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [ameloblast](http://purl.obolibrary.org/obo/CL_0000059) SubClassOf [secretory epithelial cell](http://purl.obolibrary.org/obo/CL_1100001) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "JB:jb"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "doi:/10.3389/fncel.2021.703951"^^[string](http://www.w3.org/2001/XMLSchema#string) - - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:37008045"^^[string](http://www.w3.org/2001/XMLSchema#string) +### amygdala excitatory neuron `http://purl.obolibrary.org/obo/CL_4023039` +#### Removed +- [amygdala excitatory neuron](http://purl.obolibrary.org/obo/CL_4023039) SubClassOf [central nervous system neuron](http://purl.obolibrary.org/obo/CL_2000029) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://www.britannica.com/science/ependymal-cell"^^[string](http://www.w3.org/2001/XMLSchema#string) +#### Added +- [amygdala excitatory neuron](http://purl.obolibrary.org/obo/CL_4023039) SubClassOf [neuron of the forebrain](http://purl.obolibrary.org/obo/CL_0012001) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:tfm"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:9550134"^^[string](http://www.w3.org/2001/XMLSchema#string) +### amygdala pyramidal neuron `http://purl.obolibrary.org/obo/CL_4023110` +#### Removed +- [amygdala pyramidal neuron](http://purl.obolibrary.org/obo/CL_4023110) SubClassOf [central nervous system neuron](http://purl.obolibrary.org/obo/CL_2000029) -- [ependymal cell](http://purl.obolibrary.org/obo/CL_0000065) EquivalentTo [neurecto-epithelial cell](http://purl.obolibrary.org/obo/CL_0000710) and ([BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0004670](http://purl.obolibrary.org/obo/UBERON_0004670)) +#### Added +- [amygdala pyramidal neuron](http://purl.obolibrary.org/obo/CL_4023110) SubClassOf [neuron of the forebrain](http://purl.obolibrary.org/obo/CL_0012001) -- [ependymal cell](http://purl.obolibrary.org/obo/CL_0000065) SubClassOf [glial cell](http://purl.obolibrary.org/obo/CL_0000125) -- [ependymal cell](http://purl.obolibrary.org/obo/CL_0000065) SubClassOf [RO_0002207](http://purl.obolibrary.org/obo/RO_0002207) some [radial glial cell](http://purl.obolibrary.org/obo/CL_0000681) +### angioblastic mesenchymal cell `http://purl.obolibrary.org/obo/CL_0000566` +#### Removed +- [angioblastic mesenchymal cell](http://purl.obolibrary.org/obo/CL_0000566) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) -- [ependymal cell](http://purl.obolibrary.org/obo/CL_0000065) SubClassOf [BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0004670](http://purl.obolibrary.org/obo/UBERON_0004670) -### epidermal cell (sensu Arthropoda) `http://purl.obolibrary.org/obo/CL_0000463` +### anorectum goblet cell `http://purl.obolibrary.org/obo/CL_0009057` #### Removed -- [epidermal cell (sensu Arthropoda)](http://purl.obolibrary.org/obo/CL_0000463) SubClassOf [eukaryotic cell](http://purl.obolibrary.org/obo/CL_0000255) - -- [epidermal cell (sensu Arthropoda)](http://purl.obolibrary.org/obo/CL_0000463) SubClassOf [RO_0002160](http://purl.obolibrary.org/obo/RO_0002160) some [NCBITaxon_6656](http://purl.obolibrary.org/obo/NCBITaxon_6656) +- [anorectum goblet cell](http://purl.obolibrary.org/obo/CL_0009057) EquivalentTo [goblet cell](http://purl.obolibrary.org/obo/CL_0000160) and ([BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_8410050](http://purl.obolibrary.org/obo/UBERON_8410050)) #### Added -- [epidermal cell (sensu Arthropoda)](http://purl.obolibrary.org/obo/CL_0000463) SubClassOf [RO_0002162](http://purl.obolibrary.org/obo/RO_0002162) some [NCBITaxon_6656](http://purl.obolibrary.org/obo/NCBITaxon_6656) +- [anorectum goblet cell](http://purl.obolibrary.org/obo/CL_0009057) EquivalentTo [large intestine goblet cell](http://purl.obolibrary.org/obo/CL_1000320) and ([BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_8410050](http://purl.obolibrary.org/obo/UBERON_8410050)) -### epithelial cell `http://purl.obolibrary.org/obo/CL_0000066` +### anterior horn motor neuron `http://purl.obolibrary.org/obo/CL_2000048` #### Removed -- [epithelial cell](http://purl.obolibrary.org/obo/CL_0000066) SubClassOf [cell](http://purl.obolibrary.org/obo/CL_0000000) +- [anterior horn motor neuron](http://purl.obolibrary.org/obo/CL_2000048) SubClassOf [RO_0002100](http://purl.obolibrary.org/obo/RO_0002100) some [UBERON_0002257](http://purl.obolibrary.org/obo/UBERON_0002257) #### Added -- [epithelial cell](http://purl.obolibrary.org/obo/CL_0000066) SubClassOf [eukaryotic cell](http://purl.obolibrary.org/obo/CL_0000255) +- [anterior horn motor neuron](http://purl.obolibrary.org/obo/CL_2000048) SubClassOf [neuron of the ventral spinal cord](http://purl.obolibrary.org/obo/CL_0002612) -### epithelial cell of alveolus of lung `http://purl.obolibrary.org/obo/CL_0010003` +### anterior lateral line ganglion neuron `http://purl.obolibrary.org/obo/CL_0008021` #### Removed -- [epithelial cell of alveolus of lung](http://purl.obolibrary.org/obo/CL_0010003) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "An epithelial cell that is part_of a alveolus of lung."^^[string](http://www.w3.org/2001/XMLSchema#string) +- [anterior lateral line ganglion neuron](http://purl.obolibrary.org/obo/CL_0008021) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "Any neuron that has its soma located in some anterior lateral line ganglion."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBC:Autogenerated"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [epithelial cell of alveolus of lung](http://purl.obolibrary.org/obo/CL_0010003) [comment](http://www.w3.org/2000/01/rdf-schema#comment) "May be merged with pneumocyte in future"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [anterior lateral line ganglion neuron](http://purl.obolibrary.org/obo/CL_0008021) EquivalentTo [neuron](http://purl.obolibrary.org/obo/CL_0000540) and ([RO_0002100](http://purl.obolibrary.org/obo/RO_0002100) some [UBERON_2001391](http://purl.obolibrary.org/obo/UBERON_2001391)) -- [epithelial cell of alveolus of lung](http://purl.obolibrary.org/obo/CL_0010003) [label](http://www.w3.org/2000/01/rdf-schema#label) "epithelial cell of alveolus of lung"^^[string](http://www.w3.org/2001/XMLSchema#string) +#### Added +- [anterior lateral line ganglion neuron](http://purl.obolibrary.org/obo/CL_0008021) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "Any peripheral nervous system neuron that has its soma located in some anterior lateral line ganglion."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBC:Autogenerated"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [epithelial cell of alveolus of lung](http://purl.obolibrary.org/obo/CL_0010003) EquivalentTo [epithelial cell](http://purl.obolibrary.org/obo/CL_0000066) and ([BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0002299](http://purl.obolibrary.org/obo/UBERON_0002299)) +- [anterior lateral line ganglion neuron](http://purl.obolibrary.org/obo/CL_0008021) EquivalentTo [peripheral nervous system neuron](http://purl.obolibrary.org/obo/CL_2000032) and ([RO_0002100](http://purl.obolibrary.org/obo/RO_0002100) some [UBERON_2001391](http://purl.obolibrary.org/obo/UBERON_2001391)) -- [epithelial cell of alveolus of lung](http://purl.obolibrary.org/obo/CL_0010003) SubClassOf [epithelial cell](http://purl.obolibrary.org/obo/CL_0000066) -- [epithelial cell of alveolus of lung](http://purl.obolibrary.org/obo/CL_0010003) SubClassOf [BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0002299](http://purl.obolibrary.org/obo/UBERON_0002299) +### anterior lens cell `http://purl.obolibrary.org/obo/CL_0002223` #### Added -- [epithelial cell of alveolus of lung](http://purl.obolibrary.org/obo/CL_0010003) [IAO_0000233](http://purl.obolibrary.org/obo/IAO_0000233) [2429](https://github.com/obophenotype/cell-ontology/issues/2429) +- [anterior lens cell](http://purl.obolibrary.org/obo/CL_0002223) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. -- [epithelial cell of alveolus of lung](http://purl.obolibrary.org/obo/CL_0010003) [label](http://www.w3.org/2000/01/rdf-schema#label) "obsolete epithelial cell of alveolus of lung"^^[string](http://www.w3.org/2001/XMLSchema#string) - -- [epithelial cell of alveolus of lung](http://purl.obolibrary.org/obo/CL_0010003) [deprecated](http://www.w3.org/2002/07/owl#deprecated) true +The anterior lens cells, also known as lens epithelial cells, are an integral part of the eye's structure and play a critical role in the organ's physiological functioning. They are situated in the anterior portion of the lens, precisely in the lens capsule, and stretch over the lens' frontal surface. +The primary function of anterior lens cells is to facilitate eye accommodation by controlling the shape and thickness of the eye lens. +The cells are involved in continuous proliferation, migration, and differentiation into lens fiber cells, helping to maintain lens growth and transparency. Anterior lens cells have a prolonged life span and reveal an extraordinary ability to function indefinitely, a characteristic that is critical for maintaining lens transparency. Damage or disturbance to the anterior lens cells can give rise to lens opacity, eventually leading to cataracts, which is a common cause of vision loss."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1016/j.biocel.2007.10.034"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [epithelial cell of alveolus of lung](http://purl.obolibrary.org/obo/CL_0010003) [comment](http://www.w3.org/2000/01/rdf-schema#comment) "This cell type is exactly the same as 'pulmonary alveolar epithelial cell'."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1111/aos.14600"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [epithelial cell of alveolus of lung](http://purl.obolibrary.org/obo/CL_0010003) [term replaced by](http://purl.obolibrary.org/obo/IAO_0100001) [pulmonary alveolar epithelial cell](http://purl.obolibrary.org/obo/CL_0000322) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1155/2021/9951032"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [epithelial cell of alveolus of lung](http://purl.obolibrary.org/obo/CL_0010003) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "OBSOLETE. An epithelial cell that is part_of a alveolus of lung."^^[string](http://www.w3.org/2001/XMLSchema#string) +- [anterior lens cell](http://purl.obolibrary.org/obo/CL_0002223) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://cellxgene.cziscience.com/cellguide/CL_0002223"^^[string](http://www.w3.org/2001/XMLSchema#string) -### epithelial cell of lacrimal sac `http://purl.obolibrary.org/obo/CL_1000436` +### aortic smooth muscle cell `http://purl.obolibrary.org/obo/CL_0002539` #### Added -- [epithelial cell of lacrimal sac](http://purl.obolibrary.org/obo/CL_1000436) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. +- [aortic smooth muscle cell](http://purl.obolibrary.org/obo/CL_0002539) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://cellxgene.cziscience.com/cellguide/CL_0002539"^^[string](http://www.w3.org/2001/XMLSchema#string) -Epithelial cells of the lacrimal sac play a significant role in the physiology of tear drainage, acting as an integral part of the lacrimal drainage system. The lacrimal sac is part of the nasolacrimal duct system, a conduit which connects the eye to the nasal cavity, and is lined by multilayered, non-keratinizing, squamous epithelial cells. -The epithelial cells of the lacrimal sac are specialized for the purpose of maintaining a moist environment and protecting the surface of the eye. They form a barrier that traps and removes potential contaminants from the tear film during the drainage process. These cells also actively contribute to tear turnover by expediting the drainage of excess tears. Dysfunctional epithelial cells of the lacrimal sac can lead to dacryocystitis, a condition characterized by inflammation of the lacrimal sac. -Epithelial cells of the lacrimal sac also perform various other tasks which ensure the overall health of the eye. They are involved in the regulation of immune responses within the lacrimal apparatus and may have a possible role in host-microbiome interactions. Thus, epithelial cells of the lacrimal sac play a multifaceted role in tear drainage and ocular surface defence, directly translating to eye health and vision quality."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.2147/OPTH.S26048"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [aortic smooth muscle cell](http://purl.obolibrary.org/obo/CL_0002539) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1167/tvst.8.4.32"^^[string](http://www.w3.org/2001/XMLSchema#string) +Aortic smooth muscle cells are specialized and highly differentiated muscle cells that are located in the tunica media layer of the aorta. They consist of spindle-shaped cells with a centrally located nucleus. These cells are rich in actin and myosin, muscle contractile proteins, that allow them to exert force and change shape. +Aortic smooth muscle cells play a vital role in maintaining blood pressure and circulation, and are essential for vascular integrity and function. The primary function of these cells is contraction and relaxation, which enables the regulation of blood flow and pressure in the aorta, and helps in the distribution of oxygen and nutrients throughout the body. +Additionally, a critical characteristic of smooth muscle cells is their plasticity. They can undergo phenotypic modulation in response to changes in their environment or vascular injury, switching from a contractile to a synthetic phenotype. The contractile phenotype is characterized by high contractility and low proliferation rate, while the synthetic phenotype is marked by increased cell proliferation and matrix synthesis but reduced contractile function. +Aortic smooth muscle cells have a significant role in the physiological and pathological processes of the cardiovascular system. In the normal physiological state, they contribute to the elasticity and flexibility of the aorta. Conversely, in pathological states, changes in the function and structure of aortic smooth muscle cells are connected with various vascular diseases, including atherosclerosis, hypertension, and aneurysm."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://training.seer.cancer.gov/anatomy/cells_tissues_membranes/tissues/muscle.html"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1007/s004290050160"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.7150/ijbs.49871"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1111/j.1442-9071.2012.02818.x"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1016/j.devcel.2005.05.017"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.3389/fimmu.2022.918619"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1111/febs.12414"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [epithelial cell of lacrimal sac](http://purl.obolibrary.org/obo/CL_1000436) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://cellxgene.cziscience.com/cellguide/CL_1000436"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://www.sciencedirect.com/topics/medicine-and-dentistry/aortic-smooth-muscle-cell"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### appendix glandular cell `http://purl.obolibrary.org/obo/CL_1001585` +#### Removed +- [appendix glandular cell](http://purl.obolibrary.org/obo/CL_1001585) SubClassOf [BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0009697](http://purl.obolibrary.org/obo/UBERON_0009697) -### erythroid progenitor cell, mammalian `http://purl.obolibrary.org/obo/CL_0001066` + +### appendix goblet cell `http://purl.obolibrary.org/obo/CL_1000327` +#### Removed +- [appendix goblet cell](http://purl.obolibrary.org/obo/CL_1000327) EquivalentTo [goblet cell](http://purl.obolibrary.org/obo/CL_0000160) and ([BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0001154](http://purl.obolibrary.org/obo/UBERON_0001154)) #### Added -- [erythroid progenitor cell, mammalian](http://purl.obolibrary.org/obo/CL_0001066) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) +- [appendix goblet cell](http://purl.obolibrary.org/obo/CL_1000327) EquivalentTo [goblet cell](http://purl.obolibrary.org/obo/CL_0000160) and ([BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0009697](http://purl.obolibrary.org/obo/UBERON_0009697)) -### erythrophore `http://purl.obolibrary.org/obo/CL_0000574` +### atretic follicular cell of ovary `http://purl.obolibrary.org/obo/CL_4033089` #### Added -- [erythrophore](http://purl.obolibrary.org/obo/CL_0000574) SubClassOf [eukaryotic cell](http://purl.obolibrary.org/obo/CL_0000255) +- [atretic follicular cell of ovary](http://purl.obolibrary.org/obo/CL_4033089) [date](http://purl.org/dc/terms/date) "2024-11-05T11:23:25Z"^^[dateTime](http://www.w3.org/2001/XMLSchema#dateTime) +- [atretic follicular cell of ovary](http://purl.obolibrary.org/obo/CL_4033089) [id](http://www.geneontology.org/formats/oboInOwl#id) "CL:4033089"^^[string](http://www.w3.org/2001/XMLSchema#string) -### eukaryotic cell `http://purl.obolibrary.org/obo/CL_0000255` -#### Removed -- [eukaryotic cell](http://purl.obolibrary.org/obo/CL_0000255) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "Any cell that only exists in Eukaryota."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBC:Autogenerated"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [atretic follicular cell of ovary](http://purl.obolibrary.org/obo/CL_4033089) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A follicular cell of ovary that has begun to degenerate and undergo atresia, a specialized apoptosis. This cell is found in an atretic follicle, which is an ovarian follicle that started to mature but failed to reach full development and instead regresses."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:38069168"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [eukaryotic cell](http://purl.obolibrary.org/obo/CL_0000255) EquivalentTo [cell](http://purl.obolibrary.org/obo/CL_0000000) and ([RO_0002160](http://purl.obolibrary.org/obo/RO_0002160) some [NCBITaxon_2759](http://purl.obolibrary.org/obo/NCBITaxon_2759)) +- [atretic follicular cell of ovary](http://purl.obolibrary.org/obo/CL_4033089) [label](http://www.w3.org/2000/01/rdf-schema#label) "atretic follicular cell of ovary"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [eukaryotic cell](http://purl.obolibrary.org/obo/CL_0000255) SubClassOf [RO_0002160](http://purl.obolibrary.org/obo/RO_0002160) some [NCBITaxon_2759](http://purl.obolibrary.org/obo/NCBITaxon_2759) +- [atretic follicular cell of ovary](http://purl.obolibrary.org/obo/CL_4033089) [contributor](http://purl.org/dc/terms/contributor) [0000-0001-6677-8489](https://orcid.org/0000-0001-6677-8489) -#### Added -- [eukaryotic cell](http://purl.obolibrary.org/obo/CL_0000255) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "Any cell that in taxon some Eukaryota."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBC:Autogenerated"^^[string](http://www.w3.org/2001/XMLSchema#string) +- Class: [atretic follicular cell of ovary](http://purl.obolibrary.org/obo/CL_4033089) -- [eukaryotic cell](http://purl.obolibrary.org/obo/CL_0000255) EquivalentTo [cell](http://purl.obolibrary.org/obo/CL_0000000) and ([RO_0002162](http://purl.obolibrary.org/obo/RO_0002162) some [NCBITaxon_2759](http://purl.obolibrary.org/obo/NCBITaxon_2759)) +- [atretic follicular cell of ovary](http://purl.obolibrary.org/obo/CL_4033089) EquivalentTo [follicular cell of ovary](http://purl.obolibrary.org/obo/CL_0002174) and ([RO_0000056](http://purl.obolibrary.org/obo/RO_0000056) some [GO_0001552](http://purl.obolibrary.org/obo/GO_0001552)) -- [eukaryotic cell](http://purl.obolibrary.org/obo/CL_0000255) SubClassOf [RO_0002162](http://purl.obolibrary.org/obo/RO_0002162) some [NCBITaxon_2759](http://purl.obolibrary.org/obo/NCBITaxon_2759) +- [atretic follicular cell of ovary](http://purl.obolibrary.org/obo/CL_4033089) SubClassOf [follicular cell of ovary](http://purl.obolibrary.org/obo/CL_0002174) +- [atretic follicular cell of ovary](http://purl.obolibrary.org/obo/CL_4033089) SubClassOf [RO_0000056](http://purl.obolibrary.org/obo/RO_0000056) some [GO_0001552](http://purl.obolibrary.org/obo/GO_0001552) -### exocrine cell `http://purl.obolibrary.org/obo/CL_0000152` + +### atretic granulosa cell `http://purl.obolibrary.org/obo/CL_4033090` #### Added -- [exocrine cell](http://purl.obolibrary.org/obo/CL_0000152) SubClassOf [eukaryotic cell](http://purl.obolibrary.org/obo/CL_0000255) +- [atretic granulosa cell](http://purl.obolibrary.org/obo/CL_4033090) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A granulosa cell that is undergoing atresia. This cell type displays distinct morphological alterations compared with a healthy granulosa cell, including pyknosis (nuclear condensation) and cellular shrinkage."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:15353131"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:38069168"^^[string](http://www.w3.org/2001/XMLSchema#string) -### extraembryonic cell `http://purl.obolibrary.org/obo/CL_0000349` -#### Removed -- [extraembryonic cell](http://purl.obolibrary.org/obo/CL_0000349) SubClassOf [cell](http://purl.obolibrary.org/obo/CL_0000000) +- [atretic granulosa cell](http://purl.obolibrary.org/obo/CL_4033090) [contributor](http://purl.org/dc/terms/contributor) [0000-0001-6677-8489](https://orcid.org/0000-0001-6677-8489) -#### Added -- [extraembryonic cell](http://purl.obolibrary.org/obo/CL_0000349) SubClassOf [eukaryotic cell](http://purl.obolibrary.org/obo/CL_0000255) +- [atretic granulosa cell](http://purl.obolibrary.org/obo/CL_4033090) [id](http://www.geneontology.org/formats/oboInOwl#id) "CL:4033090"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [atretic granulosa cell](http://purl.obolibrary.org/obo/CL_4033090) [label](http://www.w3.org/2000/01/rdf-schema#label) "atretic granulosa cell"^^[string](http://www.w3.org/2001/XMLSchema#string) -### eye photoreceptor cell `http://purl.obolibrary.org/obo/CL_0000287` +- [atretic granulosa cell](http://purl.obolibrary.org/obo/CL_4033090) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "apoptotic granulosa cell"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:15353131"^^[string](http://www.w3.org/2001/XMLSchema#string) -#### Added -- [eye photoreceptor cell](http://purl.obolibrary.org/obo/CL_0000287) SubClassOf [neuronal receptor cell](http://purl.obolibrary.org/obo/CL_0000006) +- [atretic granulosa cell](http://purl.obolibrary.org/obo/CL_4033090) [date](http://purl.org/dc/terms/date) "2024-11-05T11:25:28Z"^^[dateTime](http://www.w3.org/2001/XMLSchema#dateTime) +- Class: [atretic granulosa cell](http://purl.obolibrary.org/obo/CL_4033090) -### fallopian tube ciliated cell `http://purl.obolibrary.org/obo/CL_4030007` -#### Removed -- [fallopian tube ciliated cell](http://purl.obolibrary.org/obo/CL_4030007) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "An epithelial ciliated cell that is part of the fallopian tube. This cell type is found mainly on the apex of the mucosal folds and contributes, together with peristaltic contractions, to the self-propulsion of spermatozoa, the transport of ovum during ovulation and the transport of the fertilized ovum to the intramural fallopian tube. A fallopian tube ciliated cell has a columnar shape and contains an oval or round nucleus, often located perpendicular or parallel to the long axis of the cell."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:16565155"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [atretic granulosa cell](http://purl.obolibrary.org/obo/CL_4033090) SubClassOf [atretic follicular cell of ovary](http://purl.obolibrary.org/obo/CL_4033089) - - [contributor](http://purl.org/dc/terms/contributor) "https://orcid.org/0000-0002-0819-0473"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [atretic granulosa cell](http://purl.obolibrary.org/obo/CL_4033090) SubClassOf [RO_0002202](http://purl.obolibrary.org/obo/RO_0002202) some [granulosa cell](http://purl.obolibrary.org/obo/CL_0000501) -#### Added -- [fallopian tube ciliated cell](http://purl.obolibrary.org/obo/CL_4030007) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "An epithelial ciliated cell that is part of the fallopian tube. This cell type is found mainly on the apex of the mucosal folds and contributes, together with peristaltic contractions, to the self-propulsion of spermatozoa, the transport of ovum during ovulation and the transport of the fertilized ovum to the intramural fallopian tube. A fallopian tube ciliated cell has a columnar shape and contains an oval or round nucleus, often located perpendicular or parallel to the long axis of the cell."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:16565155"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [fallopian tube ciliated cell](http://purl.obolibrary.org/obo/CL_4030007) [contributor](http://purl.org/dc/terms/contributor) [0000-0002-0819-0473](https://orcid.org/0000-0002-0819-0473) +### atretic theca cell `http://purl.obolibrary.org/obo/CL_4052027` +#### Added +- [atretic theca cell](http://purl.obolibrary.org/obo/CL_4052027) [contributor](http://purl.org/dc/terms/contributor) [0009-0000-8480-9277](https://orcid.org/0009-0000-8480-9277) -### fallopian tube secretory epithelial cell `http://purl.obolibrary.org/obo/CL_4030006` -#### Removed -- [fallopian tube secretory epithelial cell](http://purl.obolibrary.org/obo/CL_4030006) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "An epithelial cell that is part of the fallopian tube epithelium that secretes mucous fluid and oviduct-specific products through the stimulation of estrogen and luteinizing hormone. The fallopian tube secretory cell has approximately the same height as the ciliated cell and is usually a more narrow columnar cell. The nucleus is ovoid and perpendicular to the long axis of the cell. The chromatin is more dense and the nucleolus smaller than that seen in the ciliated cell."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://doi.org/10.3390/cells8080933"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [atretic theca cell](http://purl.obolibrary.org/obo/CL_4052027) [comment](http://www.w3.org/2000/01/rdf-schema#comment) "During atresia, theca interna and externa cells undergo distinct morphological and functional changes. Theca interna cells round up, expand in cytoplasmic area, and thicken the internal layer as organization degrades, while showing reduced STAR expression, which lowers androgen production. Theca externa cells display decreased ACTA2 expression, weakening structural integrity."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:38069168"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://doi.org/10.1186/1477-7827-7-129"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [atretic theca cell](http://purl.obolibrary.org/obo/CL_4052027) [id](http://www.geneontology.org/formats/oboInOwl#id) "CL:4052027"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://www.proteinatlas.org/learn/dictionary/normal/fallopian+tube"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [atretic theca cell](http://purl.obolibrary.org/obo/CL_4052027) [label](http://www.w3.org/2000/01/rdf-schema#label) "atretic theca cell"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [contributor](http://purl.org/dc/terms/contributor) "https://orcid.org/0000-0002-0819-0473"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [atretic theca cell](http://purl.obolibrary.org/obo/CL_4052027) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A theca cell undergoing atresia, characterized by distinct morphological changes including hypertrophy, altered cell shape, and disrupted layered organization. This cell exhibits reduced steroidogenic capacity and changes in surrounding vascularization. The onset of theca cell atresia can vary, occurring at different stages of follicle atresia depending on the phase of folliculogenesis."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:20628033"^^[string](http://www.w3.org/2001/XMLSchema#string) -#### Added -- [fallopian tube secretory epithelial cell](http://purl.obolibrary.org/obo/CL_4030006) [contributor](http://purl.org/dc/terms/contributor) [0000-0002-0819-0473](https://orcid.org/0000-0002-0819-0473) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:38069168"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [fallopian tube secretory epithelial cell](http://purl.obolibrary.org/obo/CL_4030006) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "An epithelial cell that is part of the fallopian tube epithelium that secretes mucous fluid and oviduct-specific products through the stimulation of estrogen and luteinizing hormone. The fallopian tube secretory cell has approximately the same height as the ciliated cell and is usually a more narrow columnar cell. The nucleus is ovoid and perpendicular to the long axis of the cell. The chromatin is more dense and the nucleolus smaller than that seen in the ciliated cell."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://doi.org/10.3390/cells8080933"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [atretic theca cell](http://purl.obolibrary.org/obo/CL_4052027) [date](http://purl.org/dc/terms/date) "2024-11-06T10:10:51Z"^^[dateTime](http://www.w3.org/2001/XMLSchema#dateTime) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://doi.org/10.1186/1477-7827-7-129"^^[string](http://www.w3.org/2001/XMLSchema#string) +- Class: [atretic theca cell](http://purl.obolibrary.org/obo/CL_4052027) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://www.proteinatlas.org/learn/dictionary/normal/fallopian+tube"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [atretic theca cell](http://purl.obolibrary.org/obo/CL_4052027) SubClassOf [atretic follicular cell of ovary](http://purl.obolibrary.org/obo/CL_4033089) +- [atretic theca cell](http://purl.obolibrary.org/obo/CL_4052027) SubClassOf [RO_0002202](http://purl.obolibrary.org/obo/RO_0002202) some [theca cell](http://purl.obolibrary.org/obo/CL_0000503) -### female germ cell `http://purl.obolibrary.org/obo/CL_0000021` + +### auditory epithelial cell `http://purl.obolibrary.org/obo/CL_0002491` #### Added -- [female germ cell](http://purl.obolibrary.org/obo/CL_0000021) SubClassOf [eukaryotic cell](http://purl.obolibrary.org/obo/CL_0000255) +- [auditory epithelial cell](http://purl.obolibrary.org/obo/CL_0002491) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl/cl-base#cellxgene_subset) -### fenestrated endothelial cell `http://purl.obolibrary.org/obo/CL_0000666` +### basal cell of epithelium of bronchus `http://purl.obolibrary.org/obo/CL_1000349` #### Added -- [fenestrated endothelial cell](http://purl.obolibrary.org/obo/CL_0000666) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://cellxgene.cziscience.com/cellguide/CL_0000666"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [basal cell of epithelium of bronchus](http://purl.obolibrary.org/obo/CL_1000349) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. -- [fenestrated endothelial cell](http://purl.obolibrary.org/obo/CL_0000666) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. - -Fenestrated cells are specialized epithelial cells that are characterized by a distinctive structural feature, fenestrations or tiny pores, which allow an exchange of substances such as fluids, nutrients, and waste between blood vessels and the surrounding tissue environments. These cells are present in various types of epithelial tissues in the human body, including the intestinal tract, endocrine glands, and certain parts of the renal system. -There are multiple types of endothelial cell fenestrations. The most common type is found in systemic capillaries of the endocrine tissue (e.g., pancreatic islets), gastrointestinal mucosa, and renal peritubular capillaries. Here, the fenestrated cells have fenestrations in their peripheral cytoplasm with a unique thin and permeable diaphragm that provides a high degree of selectivity, blocking the passage of larger molecules while allowing the free movement of smaller ones. In contrast, other types of fenestrations, such as the discontinuous epithelium of the liver sinusoidal endothelial cells, do not have diaphragms. -Characteristically, fenestrated cells play a vital role in the filtering process of body systems. They are a key part of the glomeruli in the kidneys where blood is filtered under high pressure. The fenestrations present in the endothelial cells lining the capillaries of the glomerulus allow the free passage of water and small solute molecules towards the Bowman's capsule, leaving behind larger proteins and cells in the blood, thereby aiding in the filtration and waste removal process. -In the endocrine system, fenestrated cells in glandular capillaries allow the prompt release of hormones into the bloodstream. These cells have tightly clustered fenestrations which increase the surface area available for passive diffusion, improving the efficiency of hormone secretion. In villi of the small intestine, these cells increase absorption efficiency, permitting the exchange of water, electrolytes, and nutrients. -Overall, fenestrated cells contribute immensely to important physiological processes of filtration, absorption, and secretion, primarily connecting our body's circulation system with the surrounding tissues and organs."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1002/ar.1092200109"^^[string](http://www.w3.org/2001/XMLSchema#string) +The basal cells of the epithelium of the bronchus are a vital component of the cellular linings found within the bronchial tubes of the respiratory system. They are typically nonciliated, cuboidal cells that are tightly attached to the basement membrane, thereby providing structural support for the epithelial tissues. +The function of the basal cell of the bronchial epithelium is multifaceted, underscoring the importance of these cells for respiratory health. One of their primary roles involves regeneration and cellular turnover. They serve as local stem cells, being able to proliferate and differentiate into other cell types such as ciliated and secretory epithelial cells. This regenerative function of basal cells is required for maintaining the integrity of the bronchial epithelium and is especially critical after injury or during disease states when there is an increased need for new cells to repair damaged tissue or replace lost cells. +In addition to these regenerative duties, basal cells of the bronchial epithelium play a crucial role in providing a defensive barrier against inhaled substances. They participate in the coordinated immune response directed against airborne pathogens, foreign particles, and toxins that enter the respiratory tract. Basal cells can respond to inflammation or irritation by altering their activities, which include proliferating, differentiating, or producing bioactive substances. Throughout all these responses, the basal cells help to maintain the homeostasis of the bronchial tubes, allowing for the efficient transport of air to and from the lungs."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1002/ar.1092380310"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1038/s41467-022-31571-2"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1136/thx.2004.la0104"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1016/j.devcel.2012.11.003"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.3389/falgy.2021.787128"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1152/ajprenal.90601.2008"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1038/labinvest.2015.114"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1016/0306-4522(86)90162-4"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [basal cell of epithelium of bronchus](http://purl.obolibrary.org/obo/CL_1000349) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://cellxgene.cziscience.com/cellguide/CL_1000349"^^[string](http://www.w3.org/2001/XMLSchema#string) -### fetal artery endothelial cell `http://purl.obolibrary.org/obo/CL_4047006` +### basal cell of epithelium of trachea `http://purl.obolibrary.org/obo/CL_1000348` #### Added -- [fetal artery endothelial cell](http://purl.obolibrary.org/obo/CL_4047006) [has_exact_synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "endothelial cell of fetal artery"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:34497389"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [basal cell of epithelium of trachea](http://purl.obolibrary.org/obo/CL_1000348) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://cellxgene.cziscience.com/cellguide/CL_1000348"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [fetal artery endothelial cell](http://purl.obolibrary.org/obo/CL_4047006) [has_exact_synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "fetal arterial EC"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:34497389"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [basal cell of epithelium of trachea](http://purl.obolibrary.org/obo/CL_1000348) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. -- [fetal artery endothelial cell](http://purl.obolibrary.org/obo/CL_4047006) [has_exact_synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "fetal artery EC"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:34497389"^^[string](http://www.w3.org/2001/XMLSchema#string) +Basal cells of epithelium of trachea are a vital cell population within the respiratory tract's lining, specifically in the trachea's epithelium. These cells are located at the base of the columnar epithelial cell layer and can be identified by their characteristic cuboidal shape, a large nucleus and few organelles, as well as scattered microvilli. The basal cells are not in direct contact with the lumen, which is covered by a layer of ciliated and non-ciliated columnar cells. Instead, the basal cells are connected to, and line, a thin basement membrane. +The primary function of basal cells involves stem cell activity and epithelial tissue maintenance. Basal cells in the trachea play a crucial role in the regeneration and repair of the tracheal epithelium during damage or injury, acting as progenitor cells for ciliated and secretory cells. They serve as a reserve pool of cells, ready to proliferate and differentiate as needed for homeostatic tissue maintenance or in repair processes when the epithelium has been compromised, whether by injury or disease. +These cells are also implicated in numerous disease pathways. Conditions like chronic obstructive pulmonary disease and lung cancer exhibit unusual behavior and quantities of tracheal basal cells, making these cells a focal point in respiratory disease research. In summary, basal cells in the tracheal epithelium have a multifaceted role in maintaining, repairing, and influencing tracheal health, playing a crucial role in the stability of the respiratory system."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1165/rcmb.2021-0150ED"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [fetal artery endothelial cell](http://purl.obolibrary.org/obo/CL_4047006) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "An endothelial cell that lines an artery in the fetal circulatory system."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:34497389"^^[string](http://www.w3.org/2001/XMLSchema#string) - -- [fetal artery endothelial cell](http://purl.obolibrary.org/obo/CL_4047006) [contributor](http://purl.org/dc/terms/contributor) [0009-0005-7919-4905](https://orcid.org/0009-0005-7919-4905) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1242/dmm.006031"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [fetal artery endothelial cell](http://purl.obolibrary.org/obo/CL_4047006) [label](http://www.w3.org/2000/01/rdf-schema#label) "fetal artery endothelial cell"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.3389/falgy.2021.787128"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [fetal artery endothelial cell](http://purl.obolibrary.org/obo/CL_4047006) [id](http://www.geneontology.org/formats/oboInOwl#id) "CL:4047006"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1164/rccm.201408-1492PP"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [fetal artery endothelial cell](http://purl.obolibrary.org/obo/CL_4047006) [date](http://purl.org/dc/terms/date) "2024-08-16T13:52:25Z"^^[dateTime](http://www.w3.org/2001/XMLSchema#dateTime) -- Class: [fetal artery endothelial cell](http://purl.obolibrary.org/obo/CL_4047006) +### basal epithelial cell of tracheobronchial tree `http://purl.obolibrary.org/obo/CL_0002329` +#### Removed +- [basal epithelial cell of tracheobronchial tree](http://purl.obolibrary.org/obo/CL_0002329) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. -- [fetal artery endothelial cell](http://purl.obolibrary.org/obo/CL_4047006) SubClassOf [endothelial cell of artery](http://purl.obolibrary.org/obo/CL_1000413) +The basal epithelial cells of the tracheobronchial tree are critical components found in the lining of the airway passages, including the trachea and bronchi. They are keratin-5-positive, nonciliated, cuboidal cells and typically tightly attached to the basement membrane. In humans, the proportion of basal cells in the respiratory epithelium gradually decreases going down the tracheobronchial tree: they represent approximately 34% of the cells in the trachea, 27% in the large airways, and 10% in the small airways, although it is worth noting that there are differences in the compositions of the tracheobronchial epithelia between different species. +Basal epithelial cells serve as the basal layer of the tracheobronchial epithelium, providing both structural and regenerative support for the epithelial tissue that lines the upper regions of the respiratory tract. They serve as progenitor or stem cells that are capable of differentiating into multiple cell types, such as ciliated and secretory cells. This gives them a central role in homeostatic maintenance of the epithelium, and in repairing damaged epithelium after an injury or during disease. This regenerative capacity is crucial in maintaining the integrity of the tracheobronchial surface, especially given its continual exposure to inhaled irritants and microorganisms. +In addition to their primary restorative function, basal epithelial cells are also involved in the initial immune response within the tracheobronchial tree. Equipped with pattern recognition receptors, these cells can identify and respond to pathogenic organisms, triggering an immune response and producing a range of inflammatory mediators, such as cytokines and chemokines, to help combat infections."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.2353/ajpath.2010.090870"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1186/s12931-014-0160-8"^^[string](http://www.w3.org/2001/XMLSchema#string) -### fetal derived definitive erythrocyte `http://purl.obolibrary.org/obo/CL_0002357` + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1165/rcmb.2013-0049OC"^^[string](http://www.w3.org/2001/XMLSchema#string) #### Added -- [fetal derived definitive erythrocyte](http://purl.obolibrary.org/obo/CL_0002357) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) - - -### fetal liver hematopoietic progenitor cell `http://purl.obolibrary.org/obo/CL_0002353` +- [basal epithelial cell of tracheobronchial tree](http://purl.obolibrary.org/obo/CL_0002329) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. -#### Added -- [fetal liver hematopoietic progenitor cell](http://purl.obolibrary.org/obo/CL_0002353) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) +The basal epithelial cells of the tracheobronchial tree are critical components found in the lining of the airway passages, including the trachea and bronchi. They are keratin-5-positive, nonciliated, cuboidal cells and typically tightly attached to the basement membrane. In humans, the proportion of basal cells in the respiratory epithelium gradually decreases going down the tracheobronchial tree: they represent approximately 34% of the cells in the trachea, 27% in the large airways, and 10% in the small airways, although it is worth noting that there are differences in the compositions of the tracheobronchial epithelia between different species. +Basal epithelial cells serve as the basal layer of the tracheobronchial epithelium, providing both structural and regenerative support for the epithelial tissue that lines the upper regions of the respiratory tract. They serve as progenitor or stem cells that are capable of differentiating into multiple cell types, such as ciliated and secretory cells. This gives them a central role in homeostatic maintenance of the epithelium, and in repairing damaged epithelium after an injury or during disease. This regenerative capacity is crucial in maintaining the integrity of the tracheobronchial surface, especially given its continual exposure to inhaled irritants and microorganisms. +In addition to their primary restorative function, basal epithelial cells are also involved in the initial immune response within the tracheobronchial tree. Equipped with pattern recognition receptors, these cells can identify and respond to pathogenic organisms, triggering an immune response and producing a range of inflammatory mediators, such as cytokines and chemokines, to help combat infections."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.2353/ajpath.2010.090870"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1186/s12931-014-0160-8"^^[string](http://www.w3.org/2001/XMLSchema#string) -### fetal vein endothelial cell `http://purl.obolibrary.org/obo/CL_4047011` + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1165/rcmb.2013-0049OC"^^[string](http://www.w3.org/2001/XMLSchema#string) -#### Added -- [fetal vein endothelial cell](http://purl.obolibrary.org/obo/CL_4047011) [contributor](http://purl.org/dc/terms/contributor) [0009-0005-7919-4905](https://orcid.org/0009-0005-7919-4905) -- [fetal vein endothelial cell](http://purl.obolibrary.org/obo/CL_4047011) [label](http://www.w3.org/2000/01/rdf-schema#label) "fetal vein endothelial cell"^^[string](http://www.w3.org/2001/XMLSchema#string) +### basket cell `http://purl.obolibrary.org/obo/CL_0000118` +#### Removed +- [basket cell](http://purl.obolibrary.org/obo/CL_0000118) SubClassOf [multipolar neuron](http://purl.obolibrary.org/obo/CL_0000104) -- [fetal vein endothelial cell](http://purl.obolibrary.org/obo/CL_4047011) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "fetal venous EC"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003000](http://purl.obolibrary.org/obo/OMO_0003000) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "doi:10.1101/2021.04.07.438755"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [fetal vein endothelial cell](http://purl.obolibrary.org/obo/CL_4047011) [date](http://purl.org/dc/terms/date) "2024-09-05T15:45:32Z"^^[dateTime](http://www.w3.org/2001/XMLSchema#dateTime) +### basophil mast progenitor cell `http://purl.obolibrary.org/obo/CL_0002028` +#### Removed +- [basophil mast progenitor cell](http://purl.obolibrary.org/obo/CL_0002028) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) -- [fetal vein endothelial cell](http://purl.obolibrary.org/obo/CL_4047011) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "An endothelial cell that lines the veins in the fetal circulatory system."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "doi:10.1101/2021.04.07.438755"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [fetal vein endothelial cell](http://purl.obolibrary.org/obo/CL_4047011) [has_exact_synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "fetal venous endothelial cell"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "doi:10.1101/2021.04.07.438755"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [fetal vein endothelial cell](http://purl.obolibrary.org/obo/CL_4047011) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "fetal vein EC"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003000](http://purl.obolibrary.org/obo/OMO_0003000) +### basophil progenitor cell `http://purl.obolibrary.org/obo/CL_0000613` +#### Removed +- [basophil progenitor cell](http://purl.obolibrary.org/obo/CL_0000613) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "doi:10.1101/2021.04.07.438755"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [fetal vein endothelial cell](http://purl.obolibrary.org/obo/CL_4047011) [id](http://www.geneontology.org/formats/oboInOwl#id) "CL:4047011"^^[string](http://www.w3.org/2001/XMLSchema#string) -- Class: [fetal vein endothelial cell](http://purl.obolibrary.org/obo/CL_4047011) +### basophilic erythroblast `http://purl.obolibrary.org/obo/CL_0000549` +#### Removed +- [basophilic erythroblast](http://purl.obolibrary.org/obo/CL_0000549) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) -- [fetal vein endothelial cell](http://purl.obolibrary.org/obo/CL_4047011) SubClassOf [vein endothelial cell](http://purl.obolibrary.org/obo/CL_0002543) -### fibroblastic reticular cell `http://purl.obolibrary.org/obo/CL_0009101` +### bistratified cell `http://purl.obolibrary.org/obo/CL_0004247` +#### Removed +- [bistratified cell](http://purl.obolibrary.org/obo/CL_0004247) SubClassOf [neuron](http://purl.obolibrary.org/obo/CL_0000540) #### Added -- [fibroblastic reticular cell](http://purl.obolibrary.org/obo/CL_0009101) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "FRC"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003000](http://purl.obolibrary.org/obo/OMO_0003000) +- [bistratified cell](http://purl.obolibrary.org/obo/CL_0004247) SubClassOf [central nervous system neuron](http://purl.obolibrary.org/obo/CL_2000029) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:35440118"^^[string](http://www.w3.org/2001/XMLSchema#string) - -### flask cell `http://purl.obolibrary.org/obo/CL_0007023` -#### Removed -- [flask cell](http://purl.obolibrary.org/obo/CL_0007023) SubClassOf [cell](http://purl.obolibrary.org/obo/CL_0000000) +### bistratified retinal ganglion cell `http://purl.obolibrary.org/obo/CL_0003001` #### Added -- [flask cell](http://purl.obolibrary.org/obo/CL_0007023) SubClassOf [eukaryotic cell](http://purl.obolibrary.org/obo/CL_0000255) +- [bistratified retinal ganglion cell](http://purl.obolibrary.org/obo/CL_0003001) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl/cl-base#cellxgene_subset) -### follicle associated enterocyte `http://purl.obolibrary.org/obo/CL_4052011` +### bladder urothelial cell `http://purl.obolibrary.org/obo/CL_1001428` #### Added -- [follicle associated enterocyte](http://purl.obolibrary.org/obo/CL_4052011) [has_exact_synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "follicle-associated epithelium enterocyte"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:7107724"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [bladder urothelial cell](http://purl.obolibrary.org/obo/CL_1001428) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. -- [follicle associated enterocyte](http://purl.obolibrary.org/obo/CL_4052011) [contributor](http://purl.org/dc/terms/contributor) [0009-0000-8480-9277](https://orcid.org/0009-0000-8480-9277) +Bladder urothelial cells form the urothelium in the bladder - a specific type of epithelial tissue that constitutes the inner lining of the bladder and other parts of the urinary tract including the renal pelvis, ureters and urethra. These unique cells are specialized to withstand the highly variable and sometimes harsh conditions present in the urinary system. Their key function is maintaining the barrier integrity of the urinary tract even when exposed to high volumes of urine and its solutes, and they play a crucial role in protecting underlying tissues from damage and infection. +The bladder urothelial cells exhibit a remarkable spectrum of phenotypic versatility and have an extraordinary capacity to stretch and retract based on the degree of bladder filling and emptying. In their relaxed state, these cells appear large and cuboidal, but upon stretching, they become thinner and exhibit a squamous cell-like appearance. This distinctive feature enables them to adjust to the changes in the urinary bladder volume while remaining impermeable to urinary solutes, thereby preventing a potential toxicity to the bladder wall and infiltration into the bloodstream. +Apart from their barrier function, bladder urothelial cells also express a number of sensor molecules or respond to thermal, mechanical and chemical stimuli and can release signaling molecules, thereby playing a key role in sensory mechanisms that communicate vital information about the bladder's mechanical state to the nervous system. This communication helps regulate the micturition cycle and maintain urinary continence. Recent studies have also indicated that these cells may play a role in immune responses, highlighting their importance in bladder physiology. +Altered proliferation and differentiation of bladder urothelial cells are implicated in various diseases and conditions such as bladder cancer, interstitial cystitis, and urinary tract infections."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1038/s41579-020-0324-0"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [follicle associated enterocyte](http://purl.obolibrary.org/obo/CL_4052011) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "follicular enterocyte"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:7107724"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1038/nrurol.2016.13"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [follicle associated enterocyte](http://purl.obolibrary.org/obo/CL_4052011) [label](http://www.w3.org/2000/01/rdf-schema#label) "follicle associated enterocyte"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1038/nrurol.2011.144"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [follicle associated enterocyte](http://purl.obolibrary.org/obo/CL_4052011) [date](http://purl.org/dc/terms/date) "2024-09-25T15:28:25Z"^^[dateTime](http://www.w3.org/2001/XMLSchema#dateTime) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1080/03008880410015165"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [follicle associated enterocyte](http://purl.obolibrary.org/obo/CL_4052011) [id](http://www.geneontology.org/formats/oboInOwl#id) "CL:4052011"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1038/s41585-020-0350-8"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [follicle associated enterocyte](http://purl.obolibrary.org/obo/CL_4052011) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "An enterocyte found in the follicle-associated epithelium (FAE) that covers Peyer's patches and other mucosa-associated lymphoid tissues. This cell has reduced absorptive capacity and expresses higher levels of chemokines CCL20 and CXCL16, compared to regular villus enterocytes. It contributes to antigen sampling and immune interactions, supporting the specialized function of the FAE in mucosal immunity."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:7107724"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [bladder urothelial cell](http://purl.obolibrary.org/obo/CL_1001428) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://cellxgene.cziscience.com/cellguide/CL_1001428"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:29339448"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:34634036"^^[string](http://www.w3.org/2001/XMLSchema#string) +### blood vessel smooth muscle cell `http://purl.obolibrary.org/obo/CL_0019018` -- [follicle associated enterocyte](http://purl.obolibrary.org/obo/CL_4052011) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "FAE enterocyte"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003000](http://purl.obolibrary.org/obo/OMO_0003000) +#### Added +- [blood vessel smooth muscle cell](http://purl.obolibrary.org/obo/CL_0019018) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl/cl-base#cellxgene_subset) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:7107724"^^[string](http://www.w3.org/2001/XMLSchema#string) -- Class: [follicle associated enterocyte](http://purl.obolibrary.org/obo/CL_4052011) +### bone cell `http://purl.obolibrary.org/obo/CL_0001035` -- [follicle associated enterocyte](http://purl.obolibrary.org/obo/CL_4052011) SubClassOf [enterocyte](http://purl.obolibrary.org/obo/CL_0000584) +#### Added +- [bone cell](http://purl.obolibrary.org/obo/CL_0001035) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. +Bone cells, also known as osteocytes, form the building blocks of the skeletal system. They represent the most common type of bone cell, making up approximately 95% of the total bone cell population in mature adult bone tissue. Osteocytes are a stellate shape with numerous long, slender dendritic processes. +The formation of bone is a complex process involving the action of osteoclasts - cells that break down and reabsorb old bone, followed by osteoblasts that rebuild the bone. Osteocytes serve as coordinators for these two types of bone cells to ensure a balance in the bone remodeling process, contributing to maintaining both bone strength and mineral homeostasis. +The primary functions of osteocytes involve the creation, maintenance, and repair of bone tissue. They ensure that bone remodeling is performed by forming a network within the bone and communicating with other cells to help them respond to mechanical strain and damage. +A remarkable aspect of osteocytes is their ability to perceive mechanical forces, translating them into biochemical signals that regulate bone remodeling and adaptation. Defects in osteocyte function, aside from other bone cells, have been associated with several bone disorders such as osteoporosis, renal osteodystrophy, and skeletal manifestations of diabetes."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1038/s41413-020-0099-y"^^[string](http://www.w3.org/2001/XMLSchema#string) -### follicle cell of egg chamber `http://purl.obolibrary.org/obo/CL_0000477` -#### Removed -- [follicle cell of egg chamber](http://purl.obolibrary.org/obo/CL_0000477) SubClassOf [eukaryotic cell](http://purl.obolibrary.org/obo/CL_0000255) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1007/s00795-015-0099-y"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [follicle cell of egg chamber](http://purl.obolibrary.org/obo/CL_0000477) SubClassOf [RO_0002160](http://purl.obolibrary.org/obo/RO_0002160) some [NCBITaxon_50557](http://purl.obolibrary.org/obo/NCBITaxon_50557) - - [source](http://www.geneontology.org/formats/oboInOwl#source) "https://github.com/obophenotype/cell-ontology/issues/589"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1016/j.jot.2021.04.005"^^[string](http://www.w3.org/2001/XMLSchema#string) -#### Added -- [follicle cell of egg chamber](http://purl.obolibrary.org/obo/CL_0000477) SubClassOf [RO_0002162](http://purl.obolibrary.org/obo/RO_0002162) some [NCBITaxon_50557](http://purl.obolibrary.org/obo/NCBITaxon_50557) - - [source](http://www.geneontology.org/formats/oboInOwl#source) "https://github.com/obophenotype/cell-ontology/issues/589"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1007/s11914-012-0105-4"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [bone cell](http://purl.obolibrary.org/obo/CL_0001035) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://cellxgene.cziscience.com/cellguide/CL_0001035"^^[string](http://www.w3.org/2001/XMLSchema#string) -### follicle stem cell (sensu Arthropoda) `http://purl.obolibrary.org/obo/CL_0000441` -#### Removed -- [follicle stem cell (sensu Arthropoda)](http://purl.obolibrary.org/obo/CL_0000441) SubClassOf [RO_0002160](http://purl.obolibrary.org/obo/RO_0002160) some [NCBITaxon_6656](http://purl.obolibrary.org/obo/NCBITaxon_6656) - - [IAO_0000233](http://purl.obolibrary.org/obo/IAO_0000233) "https://github.com/obophenotype/cell-ontology/issues/1943"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [follicle stem cell (sensu Arthropoda)](http://purl.obolibrary.org/obo/CL_0000441) SubClassOf [eukaryotic cell](http://purl.obolibrary.org/obo/CL_0000255) +### bone marrow macrophage `http://purl.obolibrary.org/obo/CL_0002476` +#### Removed +- [bone marrow macrophage](http://purl.obolibrary.org/obo/CL_0002476) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) -#### Added -- [follicle stem cell (sensu Arthropoda)](http://purl.obolibrary.org/obo/CL_0000441) SubClassOf [RO_0002162](http://purl.obolibrary.org/obo/RO_0002162) some [NCBITaxon_6656](http://purl.obolibrary.org/obo/NCBITaxon_6656) - - [IAO_0000233](http://purl.obolibrary.org/obo/IAO_0000233) "https://github.com/obophenotype/cell-ontology/issues/1943"^^[string](http://www.w3.org/2001/XMLSchema#string) -### follicular cell of ovary `http://purl.obolibrary.org/obo/CL_0002174` +### brain vascular cell `http://purl.obolibrary.org/obo/CL_4023072` #### Added -- [follicular cell of ovary](http://purl.obolibrary.org/obo/CL_0002174) SubClassOf [ovarian surface epithelial cell](http://purl.obolibrary.org/obo/CL_2000064) +- [brain vascular cell](http://purl.obolibrary.org/obo/CL_4023072) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl/cl-base#cellxgene_subset) -- [follicular cell of ovary](http://purl.obolibrary.org/obo/CL_0002174) SubClassOf [BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0001305](http://purl.obolibrary.org/obo/UBERON_0001305) +### brainstem motor neuron `http://purl.obolibrary.org/obo/CL_2000047` -### fungal cell `http://purl.obolibrary.org/obo/CL_0000521` -#### Removed -- [fungal cell](http://purl.obolibrary.org/obo/CL_0000521) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "Any cell that only exists in Fungi."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBC:Autogenerated"^^[string](http://www.w3.org/2001/XMLSchema#string) +#### Added +- [brainstem motor neuron](http://purl.obolibrary.org/obo/CL_2000047) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl/cl-base#cellxgene_subset) -- [fungal cell](http://purl.obolibrary.org/obo/CL_0000521) EquivalentTo [cell](http://purl.obolibrary.org/obo/CL_0000000) and ([RO_0002160](http://purl.obolibrary.org/obo/RO_0002160) some [NCBITaxon_4751](http://purl.obolibrary.org/obo/NCBITaxon_4751)) -- [fungal cell](http://purl.obolibrary.org/obo/CL_0000521) SubClassOf [RO_0002160](http://purl.obolibrary.org/obo/RO_0002160) some [NCBITaxon_4751](http://purl.obolibrary.org/obo/NCBITaxon_4751) +### bronchial goblet cell `http://purl.obolibrary.org/obo/CL_1000312` #### Added -- [fungal cell](http://purl.obolibrary.org/obo/CL_0000521) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "Any cell that in taxon some Fungi."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBC:Autogenerated"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [bronchial goblet cell](http://purl.obolibrary.org/obo/CL_1000312) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. -- [fungal cell](http://purl.obolibrary.org/obo/CL_0000521) EquivalentTo [cell](http://purl.obolibrary.org/obo/CL_0000000) and ([RO_0002162](http://purl.obolibrary.org/obo/RO_0002162) some [NCBITaxon_4751](http://purl.obolibrary.org/obo/NCBITaxon_4751)) +Bronchial goblet cells are a subset of goblet cells that are predominantly found in the respiratory tract, specifically within the bronchi and bronchioles. Named for their flask-like shape and their apparent similarity to a goblet, these cells contribute significantly to the maintenance of lung health and homeostasis. In humans, goblet cells comprise up to 25% of the bronchial epithelial columnar cells and are an integral part of the mucus-secreting system of the respiratory tract and are primarily responsible for the production and secretion of mucus. +The mucus secreted by bronchial goblet cells serves as a protective layer over the delicate and sensitive structures of the bronchi. The mucus, an amalgamation of glycoproteins, lipids, and other substances, traps any inhaled dust, microorganisms, and pollutants, preventing them from reaching deeper lung tissues and causing potential damage. Additionally, the mucus secretion aids in moistening the airway surface, thereby facilitating effective gas exchange and maintaining the overall health of the respiratory tract. +Bronchial goblet cells have an innate defense mechanism wherein they increase secretion of mucus in response to irritants, infection or inflammation in the airway. This strategy, however, if incessantly stimulated, can lead to airway obstruction and health complications like asthma and chronic obstructive pulmonary disease (COPD)."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1016/S1357-2725(02)00083-3"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [fungal cell](http://purl.obolibrary.org/obo/CL_0000521) SubClassOf [RO_0002162](http://purl.obolibrary.org/obo/RO_0002162) some [NCBITaxon_4751](http://purl.obolibrary.org/obo/NCBITaxon_4751) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.2147/COPD.S38938"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1080/07853890600585795"^^[string](http://www.w3.org/2001/XMLSchema#string) -### gamma-delta T cell `http://purl.obolibrary.org/obo/CL_0000798` + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1016/S0165-6147(00)01600-X"^^[string](http://www.w3.org/2001/XMLSchema#string) -#### Added -- [gamma-delta T cell](http://purl.obolibrary.org/obo/CL_0000798) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) +- [bronchial goblet cell](http://purl.obolibrary.org/obo/CL_1000312) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://cellxgene.cziscience.com/cellguide/CL_1000312"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [bronchial goblet cell](http://purl.obolibrary.org/obo/CL_1000312) [comment](http://www.w3.org/2000/01/rdf-schema#comment) "The marker set PLCG2, ANKRD36C can identify the Human cell type bronchial goblet cell in the Lung with a confidence of 0.55 (NS-Forest FBeta value)."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://doi.org/10.5281/zenodo.11165918"^^[string](http://www.w3.org/2001/XMLSchema#string) -### ganglion mother cell `http://purl.obolibrary.org/obo/CL_0000469` +- [bronchial goblet cell](http://purl.obolibrary.org/obo/CL_1000312) [RO_0002175](http://purl.obolibrary.org/obo/RO_0002175) [NCBITaxon_9606](http://purl.obolibrary.org/obo/NCBITaxon_9606) -#### Added -- [ganglion mother cell](http://purl.obolibrary.org/obo/CL_0000469) SubClassOf [eukaryotic cell](http://purl.obolibrary.org/obo/CL_0000255) +- [bronchial goblet cell](http://purl.obolibrary.org/obo/CL_1000312) SubClassOf [RO_0015004](http://purl.obolibrary.org/obo/RO_0015004) some [CLM_1000026](http://purl.obolibrary.org/obo/CLM_1000026) -### gingival epithelial cell `http://purl.obolibrary.org/obo/CL_0002621` -#### Removed -- [gingival epithelial cell](http://purl.obolibrary.org/obo/CL_0002621) SubClassOf [epithelial cell of alimentary canal](http://purl.obolibrary.org/obo/CL_0002251) +### bronchial smooth muscle cell `http://purl.obolibrary.org/obo/CL_0002598` #### Added -- [gingival epithelial cell](http://purl.obolibrary.org/obo/CL_0002621) SubClassOf [oral mucosa squamous cell](http://purl.obolibrary.org/obo/CL_1001576) +- [bronchial smooth muscle cell](http://purl.obolibrary.org/obo/CL_0002598) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://cellxgene.cziscience.com/cellguide/CL_0002598"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [bronchial smooth muscle cell](http://purl.obolibrary.org/obo/CL_0002598) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. -### glial cell `http://purl.obolibrary.org/obo/CL_0000125` - -#### Added -- [glial cell](http://purl.obolibrary.org/obo/CL_0000125) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://cellxgene.cziscience.com/cellguide/CL_0000125"^^[string](http://www.w3.org/2001/XMLSchema#string) +Bronchial smooth muscle cells are specialized types of cells found in the bronchi of the respiratory system in mammals. These bronchi are tubular structures that function to carry air from the trachea into the lungs. As part of the smooth muscle tissue, bronchial smooth muscle cells are involuntary cells, meaning they function with minimal direct voluntary control. They are characterized by their elongated spindle-shaped structure, with each cell containing a single central nucleus. +The primary function of bronchial smooth muscle cells is to control airway diameter, which directly influences the flow of air into and out of the lungs. Muscular contractions and relaxations mediated by these cells enable the bronchi to constrict or expand, facilitating the regulation of respiratory airflow. Additionally, these cells play a pivotal role in immune responses as they produce and release various substances that can instigate or lessen inflammation of airway tissue. Furthermore, bronchial smooth muscle cells can proliferate and lay down collagen and other extracellular matrix proteins, contributing to the structural integrity of the bronchial tubes. +In pathological conditions, such as asthma and chronic obstructive pulmonary disease, the function and biology of bronchial smooth muscle cells change. Asthma, for example, is associated with an abnormal increase in the mass of the bronchial smooth muscles, leading to narrowing of the airways and resultant breathing difficulties. These cells also exhibit altered contractile behavior and an augmented immune response during inflammatory lung diseases."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://www.sciencedirect.com/topics/agricultural-and-biological-sciences/bronchial-muscle"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [glial cell](http://purl.obolibrary.org/obo/CL_0000125) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1152/japplphysiol.00313.2006"^^[string](http://www.w3.org/2001/XMLSchema#string) -Glial cells, also known as neuroglia or simply glia, are non-neuronal cells in the central and peripheral nervous systems that provide support and protection for neurons. They constitute approximately half of the total cells in the human brain and more than half in other parts of the nervous system. Glial cells perform several key functions including, but not limited to, maintaining homeostasis, forming the myelin sheath around the neuron axons, and providing support and nutrition to neurons. -These different functions are performed by various glial cell types, including astrocytes, oligodendrocytes, microglia and other specialized types. Astrocytes, for example, are the most abundant glial cells and provide metabolic and nutrient support to neurons, help regulate the extracellular ion and neurotransmitter levels, and play a role in the formation and maintenance of the blood-brain barrier, contributing to the overall homeostasis and functioning of the nervous system. Additionally, astrocytes are involved in synaptic communication and participate in processes such as synaptogenesis and synaptic pruning. -Oligodendrocytes in the central nervous system function to insulate neurons by producing a fatty substance known as myelin. The myelin sheath enhances the speed and efficiency of nerve impulse conduction along the axons. -Microglia, the immune cells of the central nervous system, protect neurons from pathogens and clear away dead neurons through phagocytosis, a process also known as cellular eating. They also contribute to the regulation of inflammation in response to signals of tissue damage or infection in the central nervous system by releasing cytokines and other signaling molecules that modulate the immune response. -Despite their overarching function in the support and protection of neurons, glial cells have also been shown to play significant roles in the pathophysiology of many psychiatric and neurodegenerative diseases, such as Alzheimer’s, Parkinson’s Disease and multiple sclerosis."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1101/cshperspect.a020602"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://www.ncbi.nlm.nih.gov/books/NBK537353/"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1126/science.aat0473"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1183/09031936.00019810"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1038/nn1988"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1002/glia.24343"^^[string](http://www.w3.org/2001/XMLSchema#string) +### brown adipocyte `http://purl.obolibrary.org/obo/CL_0000449` - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.3389/fncel.2017.00024"^^[string](http://www.w3.org/2001/XMLSchema#string) +#### Added +- [brown adipocyte](http://purl.obolibrary.org/obo/CL_0000449) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl/cl-base#cellxgene_subset) -### glioblast `http://purl.obolibrary.org/obo/CL_0000030` +### brown preadipocyte `http://purl.obolibrary.org/obo/CL_0002335` #### Added -- [glioblast](http://purl.obolibrary.org/obo/CL_0000030) SubClassOf [eukaryotic cell](http://purl.obolibrary.org/obo/CL_0000255) +- [brown preadipocyte](http://purl.obolibrary.org/obo/CL_0002335) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl/cl-base#cellxgene_subset) -### glomerular capillary endothelial cell `http://purl.obolibrary.org/obo/CL_1001005` +### brush cell `http://purl.obolibrary.org/obo/CL_0002204` +#### Removed +- [brush cell](http://purl.obolibrary.org/obo/CL_0002204) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. -#### Added -- [glomerular capillary endothelial cell](http://purl.obolibrary.org/obo/CL_1001005) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://cellxgene.cziscience.com/cellguide/CL_1001005"^^[string](http://www.w3.org/2001/XMLSchema#string) +Brush cells, also referred to as tuft cells or multivesicular cells, are a specialized type of epithelial cell mainly noted for their characteristic 'brush border' composed of microvilli. These cells reside in the epithelial lining of tissue organs such as the respiratory tract, gastrointestinal tract, and the bile ducts. The name derives from their distinct appearance under the microscope, which resembles a brush due to the dense layer of microvilli protruding into the lumen. +A key function of brush cells is chemosensation: They express a variety of signaling molecules and receptors that enable them to detect specific chemical stimuli in the environment and act as sensory transducers. Many of these receptors are responsive to luminal content, which makes brush cells vital for regulating and coordinating appropriate physiological responses to changes in these substances. +Recent research has also elucidated an important role for these cells in immunity. Intestinal brush cells have been found to be the source of a cytokine called interleukin-25, which can initiate type 2 immune responses during parasitic infections. This immune function, along with the chemosensing abilities, signifies that brush cells could serve crucial roles in health and disease, although much research is still required to fully elucidate their myriad roles in physiology and pathology. Overall, brush cells are a versatile cell type, whose distinct morphology and functional capabilities allow them to perform a unique set of functions within the body."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.3389/fphys.2015.00087"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [glomerular capillary endothelial cell](http://purl.obolibrary.org/obo/CL_1001005) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1007/978-3-211-99390-3_83"^^[string](http://www.w3.org/2001/XMLSchema#string) -The glomerular capillary endothelial cell comprises an intrinsic component of the glomerulus in the kidney. Glomeruli contain a network of capillaries where the first step of blood filtration takes place, with glomerular capillary endothelial cells acting as an integral part of this process. Unlike regular endothelial cells that line the vasculature, unique fenestrations (openings) characterize these cells, allowing for enhanced permeability and filtration efficacy. -Together with the glomerular basement membrane and podocytes, the glomerular endothelial cells form the glomerular filtration barrier, which is responsible for blood filtration and therefore critical for removal of waste products, such as urea and creatinine, and excess substances, such as glucose and ions, from the bloodstream. The glomerular capillary endothelial cells' fenestrations permit the free flow of a variety of particles, barring larger, negatively charged proteins like serum albumin, enabling the formation of an ultrafiltrate. This ultrafiltrate is the primitive form of urine, which then passes through the proximal tubule for further processing and ultimately helps maintain systemic fluid and electrolyte balance. -Moreover, the glomerular capillary endothelial cells are also believed to play a crucial role in renal pathologies. Any compromise to their structural integrity or functional performance can lead to kidney diseases, including but not limited to, diabetic nephropathy and glomerulonephritis. For instance, in diabetes, persistent hyperglycemia can injure these cells, leading to a compromised glomerular filtration barrier and proteinuria, indicating the loss of proteins in the urine."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1016/j.biocel.2010.05.015"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.5114/ceji.2022.124416"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.2337/diacare.28.1.164"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1038/nature16161"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1111/j.1523-1755.2005.00260.x"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1111/j.1469-7580.2005.00403.x"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.3389/fphys.2021.689083"^^[string](http://www.w3.org/2001/XMLSchema#string) +#### Added +- [brush cell](http://purl.obolibrary.org/obo/CL_0002204) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1016/j.yexcr.2012.02.032"^^[string](http://www.w3.org/2001/XMLSchema#string) +Brush cells, also referred to as tuft cells or multivesicular cells, are a specialized type of epithelial cell mainly noted for their characteristic 'brush border' composed of microvilli. These cells reside in the epithelial lining of tissue organs such as the respiratory tract, gastrointestinal tract, and the bile ducts. The name derives from their distinct appearance under the microscope, which resembles a brush due to the dense layer of microvilli protruding into the lumen. +A key function of brush cells is chemosensation: They express a variety of signaling molecules and receptors that enable them to detect specific chemical stimuli in the environment and act as sensory transducers. Many of these receptors are responsive to luminal content, which makes brush cells vital for regulating and coordinating appropriate physiological responses to changes in these substances. +Recent research has also elucidated an important role for these cells in immunity. Intestinal brush cells have been found to be the source of a cytokine called interleukin-25, which can initiate type 2 immune responses during parasitic infections. This immune function, along with the chemosensing abilities, signifies that brush cells could serve crucial roles in health and disease, although much research is still required to fully elucidate their myriad roles in physiology and pathology. Overall, brush cells are a versatile cell type, whose distinct morphology and functional capabilities allow them to perform a unique set of functions within the body."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.3389/fphys.2015.00087"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1007/978-3-211-99390-3_83"^^[string](http://www.w3.org/2001/XMLSchema#string) -### glomerular endothelial cell `http://purl.obolibrary.org/obo/CL_0002188` + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.5114/ceji.2022.124416"^^[string](http://www.w3.org/2001/XMLSchema#string) -#### Added -- [glomerular endothelial cell](http://purl.obolibrary.org/obo/CL_0002188) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1038/nature16161"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1111/j.1469-7580.2005.00403.x"^^[string](http://www.w3.org/2001/XMLSchema#string) -### glycinergic amacrine cell `http://purl.obolibrary.org/obo/CL_4030028` +### brush cell of tracheobronchial tree `http://purl.obolibrary.org/obo/CL_0002075` #### Removed -- [glycinergic amacrine cell](http://purl.obolibrary.org/obo/CL_4030028) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "An amacrine cell that uses glycine as a neurotransmitter."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [definition](http://purl.obolibrary.org/obo/IAO_0000115) "https://doi.org/10.1016/j.cell.2020.08.013"^^[string](http://www.w3.org/2001/XMLSchema#string) - -#### Added -- [glycinergic amacrine cell](http://purl.obolibrary.org/obo/CL_4030028) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "An amacrine cell that uses glycine as a neurotransmitter."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://doi.org/10.1016/j.cell.2020.08.013"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [brush cell of tracheobronchial tree](http://purl.obolibrary.org/obo/CL_0002075) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "Infrequent type of columnar epithelial cell. This cell is characterized by the presence of a tuft of blunt, squat microvilli (approximately 120-140/cell) on the cell surface. The microvilli contain filaments that stretch into the underlying cytoplasm. They have a distinctive pear shape with a wide base and a narrow microvillous apex. Function not known."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ISBN:0517223651"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:15817800"^^[string](http://www.w3.org/2001/XMLSchema#string) -### goblet cell `http://purl.obolibrary.org/obo/CL_0000160` + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:tfm"^^[string](http://www.w3.org/2001/XMLSchema#string) #### Added -- [goblet cell](http://purl.obolibrary.org/obo/CL_0000160) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. - -Goblet cells are specialized, simple columnar, secretory epithelial cells that are mostly found in the respiratory and intestinal tracts. The term "goblet" refers to their shape, which resembles a flask or goblet, specially at their apical end which is swollen due to the accumulation of secretory granules. -The primary function of goblet cells is to to protect and lubricate the underlying tissues by secreting large quantities of mucin, a complex glycoprotein, which forms mucus when hydrated. In the respiratory tract, the mucus secreted by these cells traps dust, bacteria, viruses, and other potentially harmful particles in the inhaled air, preventing them from reaching the delicate tissues of the lungs. In the intestines, the goblet cells secrete mucus that acts as a protective barrier shielding the intestinal epithelium from dietary antigens, pathogens and prevents the intestinal epithelium from being eroded by the actions of the digestive enzymes and the abrasive action of passing food material. -Goblet cells are capable of rapidly altering their secretory output in response to stimuli. For example, irritants like smoke or dust can trigger an increased rate of mucus production, as the body attempts to flush out the harmful particles. Conversely, in conditions such as chronic bronchitis and cystic fibrosis, overactive goblet cells can create a thick accumulation of mucus that obstructs the airways and fosters bacterial growth. Lastly, goblet cells are not static, rather, they undergo a dynamic process known as goblet cell metaplasia-differentiation, wherein non-goblet cells in response to chronic injury or inflammation, can differentiate into goblet cells leading to an accumulation of these cells in the tissue, known as goblet cell hyperplasia."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1038/s41575-022-00675-x"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [brush cell of tracheobronchial tree](http://purl.obolibrary.org/obo/CL_0002075) [RO_0002175](http://purl.obolibrary.org/obo/RO_0002175) [NCBITaxon_9606](http://purl.obolibrary.org/obo/NCBITaxon_9606) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1242/bio.20121701"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [brush cell of tracheobronchial tree](http://purl.obolibrary.org/obo/CL_0002075) [comment](http://www.w3.org/2000/01/rdf-schema#comment) "The marker set POU2F3, HOMER3, MYB can identify the Human cell type brush cell of tracheobronchial tree in the Lung with a confidence of 0.56 (NS-Forest FBeta value)."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://doi.org/10.5281/zenodo.11165918"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1016/S1357-2725(02)00083-3"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [brush cell of tracheobronchial tree](http://purl.obolibrary.org/obo/CL_0002075) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A rare type of columnar epithelial cell that is part of the tracheobronchial epithelium. This cell is characterized by a distinctive tuft of apical microvilli, which extends into the cytoplasm, and a pear-shaped morphology, broad at the base and tapering to a narrow apex. It plays vital roles in chemosensation, producing cytokines like IL-25, and enhancing mucociliary clearance through acetylcholine release to support mucus movement and airway defense."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:37925434"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1165/ajrcmb.25.5.f218"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:30291131"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://www.ncbi.nlm.nih.gov/books/NBK553208/"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ISBN:0517223651"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [goblet cell](http://purl.obolibrary.org/obo/CL_0000160) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://cellxgene.cziscience.com/cellguide/CL_0000160"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:15817800"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:tfm"^^[string](http://www.w3.org/2001/XMLSchema#string) -### granulocyte `http://purl.obolibrary.org/obo/CL_0000094` +- [brush cell of tracheobronchial tree](http://purl.obolibrary.org/obo/CL_0002075) SubClassOf [columnar/cuboidal epithelial cell](http://purl.obolibrary.org/obo/CL_0000075) -#### Added -- [granulocyte](http://purl.obolibrary.org/obo/CL_0000094) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) +- [brush cell of tracheobronchial tree](http://purl.obolibrary.org/obo/CL_0002075) SubClassOf [RO_0015004](http://purl.obolibrary.org/obo/RO_0015004) some [CLM_1000061](http://purl.obolibrary.org/obo/CLM_1000061) -### granulocyte monocyte progenitor cell `http://purl.obolibrary.org/obo/CL_0000557` +### candelabrum cell `http://purl.obolibrary.org/obo/CL_4042030` #### Added -- [granulocyte monocyte progenitor cell](http://purl.obolibrary.org/obo/CL_0000557) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) +- [candelabrum cell](http://purl.obolibrary.org/obo/CL_4042030) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "CC"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003000](http://purl.obolibrary.org/obo/OMO_0003000) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:35578131"^^[string](http://www.w3.org/2001/XMLSchema#string) -### granulosa cell `http://purl.obolibrary.org/obo/CL_0000501` -#### Removed -- [granulosa cell](http://purl.obolibrary.org/obo/CL_0000501) SubClassOf [RO_0002207](http://purl.obolibrary.org/obo/RO_0002207) some [pre-granulosa cell](http://purl.obolibrary.org/obo/CL_4033066) +- [candelabrum cell](http://purl.obolibrary.org/obo/CL_4042030) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A GABAergic interneuron located in the cerebellar cortex. This GABAergic interneuron type has a distinct morphology, it presents a small cell soma near the Purkinje cell layer (PCL), dendrites that extend to the surface of the molecular layer, and beaded axons that make local synapses contacts within the molecular layer. A candelabrum cell is excited by mossy fibers and granule cells but inhibited by Purkinje cells, and it inhibits molecular layer interneurons, which leads to the disinhibition of Purkinje cells."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:35578131"^^[string](http://www.w3.org/2001/XMLSchema#string) -#### Added -- [granulosa cell](http://purl.obolibrary.org/obo/CL_0000501) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. +- [candelabrum cell](http://purl.obolibrary.org/obo/CL_4042030) [label](http://www.w3.org/2000/01/rdf-schema#label) "candelabrum cell"^^[string](http://www.w3.org/2001/XMLSchema#string) -Granulosa cells are a type of somatic cell most commonly known for their crucial role within the ovarian follicles of female mammalian species. Named for their grainy appearance, they are situated in the follicular epithelium, lining the inner part of the follicle and directly surrounding the oocyte. These cells stand as an integral part of the ovarian structure and function. -One of the primary roles of granulosa cells is to aid in the production and secretion of sex hormones, particularly estrogen. They achieve this by working in tandem with theca cells, which stay attached to the external layer of the follicle. Theca cells produce androstenedione (a type of androgen) which granulosa cells then convert into estradiol, a form of estrogen, with the help of the enzyme aromatase. Moreover, granulosa cells participate in luteinization, transforming into luteal granulosa cells as a response to the luteinizing hormone during ovulation. This allows the formation of the corpus luteum, responsible for the secretion of progesterone necessary to maintain pregnancy. -Granulosa cells also play a significant role in follicular development and oocyte maturation, involving close communication with the contained oocyte. They support the oocyte through the provision of nutrients and growth factors, control its meiotic cycle and ensure it is appropriately oriented and instructed for impending ovulation. Furthermore, granulosa cells contribute to the formation of the zona pellucida and the follicular fluid, providing an optimal environment for the oocyte's growth and maturation. These cells, thus, perform multiple vital roles, underscoring their importance in fertility and reproductive health."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1093/humupd/6.3.279"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [candelabrum cell](http://purl.obolibrary.org/obo/CL_4042030) [contributor](http://purl.org/dc/terms/contributor) [0000-0002-0098-8958](https://orcid.org/0000-0002-0098-8958) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.3389/fendo.2019.00832/full"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [candelabrum cell](http://purl.obolibrary.org/obo/CL_4042030) [comment](http://www.w3.org/2000/01/rdf-schema#comment) "Candelabrum cells are the most abundant interneurons in the Purkinje cell layer and are present in all cerebellar lobules."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:35578131"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1016/j.ejogrb.2004.01.010"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [candelabrum cell](http://purl.obolibrary.org/obo/CL_4042030) [has_exact_synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "candelabrum interneuron"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:35578131"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1093/humrep/del408"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [candelabrum cell](http://purl.obolibrary.org/obo/CL_4042030) [date](http://purl.org/dc/terms/date) "2024-10-15T11:06:31Z"^^[dateTime](http://www.w3.org/2001/XMLSchema#dateTime) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1210/jcem-28-3-355"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [candelabrum cell](http://purl.obolibrary.org/obo/CL_4042030) [id](http://www.geneontology.org/formats/oboInOwl#id) "CL:4042030"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [granulosa cell](http://purl.obolibrary.org/obo/CL_0000501) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://cellxgene.cziscience.com/cellguide/CL_0000501"^^[string](http://www.w3.org/2001/XMLSchema#string) +- Class: [candelabrum cell](http://purl.obolibrary.org/obo/CL_4042030) -- [granulosa cell](http://purl.obolibrary.org/obo/CL_0000501) SubClassOf [RO_0002202](http://purl.obolibrary.org/obo/RO_0002202) some [pre-granulosa cell](http://purl.obolibrary.org/obo/CL_4033066) +- [candelabrum cell](http://purl.obolibrary.org/obo/CL_4042030) SubClassOf [cerebellar neuron](http://purl.obolibrary.org/obo/CL_1001611) -### group 2 innate lymphoid cell, human `http://purl.obolibrary.org/obo/CL_0001081` +### cardiac endothelial cell `http://purl.obolibrary.org/obo/CL_0010008` #### Added -- [group 2 innate lymphoid cell, human](http://purl.obolibrary.org/obo/CL_0001081) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) +- [cardiac endothelial cell](http://purl.obolibrary.org/obo/CL_0010008) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. +Cardiac endothelial cells are a specialized subset of endothelial cells, the cell type responsible for forming the inner lining of cardiovascular structures such as the heart, and blood vessels. They are a pivotal component of the heart's microenvironment and play a key role in regulating blood pressure, maintaining cardiac homeostasis, in addition to cooperating with other cardiac cells like cardiomyocytes and fibroblasts in the orchestration of a coordinated heart function. +Cardiac endothelial cells contribute to the each stage of the heart's operation, whether during relaxation or contraction. Cardiac endothelial cells release nitric oxide, a potent vasodilator that regulates blood vessel dilation consequently controlling blood pressure and flow. They also produce a myriad of growth factors that aid in new blood vessel formation, known as angiogenesis, crucially needed for tissue repair and regeneration when the heart undergoes damage, as in cases of myocardial infarction. +Furthermore, cardiac endothelial cells control the passage of nutrients, hormones, and gases between the bloodstream and the heart tissue, ensuring its complex metabolic demands are met adequately. They serve as a selective barrier, regulating the transit of cells and signaling molecules, thereby playing a pivotal role in inflammatory responses and immune cell trafficking. They also contribute to the maintenance of blood fluidity and clotting balance through a complex interplay of anti-thrombic and pro-thrombic factors."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1007/s00441-021-03471-2"^^[string](http://www.w3.org/2001/XMLSchema#string) -### group 2 innate lymphoid cell, mouse `http://purl.obolibrary.org/obo/CL_0002089` + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.3389/fphys.2018.00382"^^[string](http://www.w3.org/2001/XMLSchema#string) -#### Added -- [group 2 innate lymphoid cell, mouse](http://purl.obolibrary.org/obo/CL_0002089) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.3390/ijms20184411"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.3389/fcvm.2018.00101"^^[string](http://www.w3.org/2001/XMLSchema#string) -### group 3 innate lymphoid cell `http://purl.obolibrary.org/obo/CL_0001071` + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1530/VB-20-0006"^^[string](http://www.w3.org/2001/XMLSchema#string) -#### Added -- [group 3 innate lymphoid cell](http://purl.obolibrary.org/obo/CL_0001071) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) +- [cardiac endothelial cell](http://purl.obolibrary.org/obo/CL_0010008) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://cellxgene.cziscience.com/cellguide/CL_0010008"^^[string](http://www.w3.org/2001/XMLSchema#string) -### gut absorptive cell `http://purl.obolibrary.org/obo/CL_0000677` +### cardiac muscle cell `http://purl.obolibrary.org/obo/CL_0000746` #### Removed -- [gut absorptive cell](http://purl.obolibrary.org/obo/CL_0000677) SubClassOf [cell](http://purl.obolibrary.org/obo/CL_0000000) +- [cardiac muscle cell](http://purl.obolibrary.org/obo/CL_0000746) [has_alternative_id](http://www.geneontology.org/formats/oboInOwl#hasAlternativeId) "FMA:83808"^^[string](http://www.w3.org/2001/XMLSchema#string) #### Added -- [gut absorptive cell](http://purl.obolibrary.org/obo/CL_0000677) SubClassOf [eukaryotic cell](http://purl.obolibrary.org/obo/CL_0000255) +- [cardiac muscle cell](http://purl.obolibrary.org/obo/CL_0000746) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://cellxgene.cziscience.com/cellguide/CL_0000746"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [cardiac muscle cell](http://purl.obolibrary.org/obo/CL_0000746) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. -### hair follicle cell `http://purl.obolibrary.org/obo/CL_0002559` -#### Removed -- [hair follicle cell](http://purl.obolibrary.org/obo/CL_0002559) SubClassOf [cell](http://purl.obolibrary.org/obo/CL_0000000) +Cardiac muscle cells, also known as cardiomyocytes or cardiac myocytes, are specialized cells that form the heart tissue. These cells are elongated, branched, and contain a single centrally located nucleus. Their anatomy is composed primarily of densely packed myofibrils, which are protein structures that consist of sarcomeres - the fundamental units of muscle contraction. Cardiac muscle cells are united at their ends through specialized junctions known as intercalated discs, which allow the heart to contract in a unified, powerful and rhythmic way. +Functionally, cardiac muscle cells are responsible for the heart's consistent pumping action that circulates blood throughout the body. Unlike most cells in the body, cardiac muscle cells spontaneously depolarize and generate action potentials without external stimulation. This unique trait stems from the presence of ion channels in the cells' membrane that allow a cyclic flow of ions across the membrane, which create the electrical impulses necessary for heart contraction. The spread of these electrical signals from one cardiac muscle cell to another - facilitated by the interconnected network made by the intercalated disks - results in a synchronized contraction of the heart muscle. +Unlike skeletal muscle cells which can tire and need rest, cardiac muscle cells have to work ceaselessly throughout the entire lifespan, without the opportunity for rest, to ensure continuous circulation of blood. This is made possible through the high volume of mitochondria and a constant supply of oxygen from coronary circulation. In conclusion, cardiac muscle cells, through their unique structure and vital functionality, play a pivotal role in sustaining life by providing the means for blood to reach every cell in the body."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://www.sciencedirect.com/topics/agricultural-and-biological-sciences/cardiac-muscle"^^[string](http://www.w3.org/2001/XMLSchema#string) -#### Added -- [hair follicle cell](http://purl.obolibrary.org/obo/CL_0002559) SubClassOf [eukaryotic cell](http://purl.obolibrary.org/obo/CL_0000255) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1016/j.ccep.2010.10.012"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1038/nrcardio.2016.203"^^[string](http://www.w3.org/2001/XMLSchema#string) -### hematopoietic lineage restricted progenitor cell `http://purl.obolibrary.org/obo/CL_0002031` + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://www.ncbi.nlm.nih.gov/books/NBK572070"^^[string](http://www.w3.org/2001/XMLSchema#string) -#### Added -- [hematopoietic lineage restricted progenitor cell](http://purl.obolibrary.org/obo/CL_0002031) SubClassOf [eukaryotic cell](http://purl.obolibrary.org/obo/CL_0000255) +### cardiac neuron `http://purl.obolibrary.org/obo/CL_0010022` +#### Removed +- [cardiac neuron](http://purl.obolibrary.org/obo/CL_0010022) EquivalentTo [neuron](http://purl.obolibrary.org/obo/CL_0000540) and ([RO_0002100](http://purl.obolibrary.org/obo/RO_0002100) some [UBERON_0000948](http://purl.obolibrary.org/obo/UBERON_0000948)) -### hematopoietic multipotent progenitor cell `http://purl.obolibrary.org/obo/CL_0000837` +- [cardiac neuron](http://purl.obolibrary.org/obo/CL_0010022) SubClassOf [neuron](http://purl.obolibrary.org/obo/CL_0000540) #### Added -- [hematopoietic multipotent progenitor cell](http://purl.obolibrary.org/obo/CL_0000837) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) +- [cardiac neuron](http://purl.obolibrary.org/obo/CL_0010022) EquivalentTo [peripheral nervous system neuron](http://purl.obolibrary.org/obo/CL_2000032) and ([RO_0002100](http://purl.obolibrary.org/obo/RO_0002100) some [UBERON_0000948](http://purl.obolibrary.org/obo/UBERON_0000948)) -- [hematopoietic multipotent progenitor cell](http://purl.obolibrary.org/obo/CL_0000837) SubClassOf [eukaryotic cell](http://purl.obolibrary.org/obo/CL_0000255) +- [cardiac neuron](http://purl.obolibrary.org/obo/CL_0010022) SubClassOf [peripheral nervous system neuron](http://purl.obolibrary.org/obo/CL_2000032) -### hematopoietic oligopotent progenitor cell `http://purl.obolibrary.org/obo/CL_0002032` +### catecholaminergic neuron `http://purl.obolibrary.org/obo/CL_4033050` #### Added -- [hematopoietic oligopotent progenitor cell](http://purl.obolibrary.org/obo/CL_0002032) SubClassOf [eukaryotic cell](http://purl.obolibrary.org/obo/CL_0000255) +- [catecholaminergic neuron](http://purl.obolibrary.org/obo/CL_4033050) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [human_reference_atlas](http://purl.obolibrary.org/obo/cl/cl-base#human_reference_atlas) +- [catecholaminergic neuron](http://purl.obolibrary.org/obo/CL_4033050) [RO_0002175](http://purl.obolibrary.org/obo/RO_0002175) [NCBITaxon_9606](http://purl.obolibrary.org/obo/NCBITaxon_9606) -### hemocyte (sensu Arthropoda) `http://purl.obolibrary.org/obo/CL_0000387` -#### Removed -- [hemocyte (sensu Arthropoda)](http://purl.obolibrary.org/obo/CL_0000387) SubClassOf [RO_0002160](http://purl.obolibrary.org/obo/RO_0002160) some [NCBITaxon_6656](http://purl.obolibrary.org/obo/NCBITaxon_6656) - -#### Added -- [hemocyte (sensu Arthropoda)](http://purl.obolibrary.org/obo/CL_0000387) SubClassOf [RO_0002162](http://purl.obolibrary.org/obo/RO_0002162) some [NCBITaxon_6656](http://purl.obolibrary.org/obo/NCBITaxon_6656) +### caudal ganglionic eminence derived cortical interneuron `http://purl.obolibrary.org/obo/CL_4023064` +#### Removed +- [caudal ganglionic eminence derived cortical interneuron](http://purl.obolibrary.org/obo/CL_4023064) SubClassOf [RO_0002202](http://purl.obolibrary.org/obo/RO_0002202) some [UBERON_0004026](http://purl.obolibrary.org/obo/UBERON_0004026) -### hepatic stellate cell `http://purl.obolibrary.org/obo/CL_0000632` +- [caudal ganglionic eminence derived cortical interneuron](http://purl.obolibrary.org/obo/CL_4023064) SubClassOf [BFO_0000002](http://purl.obolibrary.org/obo/BFO_0000002) #### Added -- [hepatic stellate cell](http://purl.obolibrary.org/obo/CL_0000632) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) +- [caudal ganglionic eminence derived cortical interneuron](http://purl.obolibrary.org/obo/CL_4023064) SubClassOf [caudal ganglionic eminence derived neuron](http://purl.obolibrary.org/obo/CL_4042039) -### hepatoblast `http://purl.obolibrary.org/obo/CL_0005026` +### caudal ganglionic eminence derived neuron `http://purl.obolibrary.org/obo/CL_4042039` #### Added -- [hepatoblast](http://purl.obolibrary.org/obo/CL_0005026) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. +- [caudal ganglionic eminence derived neuron](http://purl.obolibrary.org/obo/CL_4042039) [label](http://www.w3.org/2000/01/rdf-schema#label) "caudal ganglionic eminence derived neuron"^^[string](http://www.w3.org/2001/XMLSchema#string) -Hepatoblasts are immature precursor cells that predominate during the early stages of liver development, specifically in the embryonic phase of life. They first arise from the endoderm, one of the three primary germ layers in the very early embryo, and then differentiate into two distinct mature liver cell types - the hepatocytes and cholangiocytes. -During liver organogenesis hepatoblasts proliferate and migrate into the septum transversum to form the liver bud. Proliferation and differentiation of these cells are regulated by several soluble factors, such as hepatocyte growth factor, which is a mitogen of both hepatoblasts and mature hepatocytes. As they start to differentiate into hepatocytes and cholangiocytes, the cells begin to express hepatic markers like albumin and alpha-fetoprotein. -Although hepatoblasts are specified embryonic liver cells that are bipotential for hepatocytes and cholangiocytes, a subset of liver cells (called oval cells) has been identified in adults that express stem cell markers, such as CD133 and cKIT, and has been suggested to have the same potential as hepatoblasts to differentiate into hepatocytes and cholangiocytes."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1242/dev.031369"^^[string](http://www.w3.org/2001/XMLSchema#string) - - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1242/dev.114215"^^[string](http://www.w3.org/2001/XMLSchema#string) - - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.5966/sctm.2015-0051"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [caudal ganglionic eminence derived neuron](http://purl.obolibrary.org/obo/CL_4042039) [date](http://purl.org/dc/terms/date) "2024-11-14T11:27:25Z"^^[dateTime](http://www.w3.org/2001/XMLSchema#dateTime) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1093/jb/mvr001"^^[string](http://www.w3.org/2001/XMLSchema#string) - - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1016/j.stem.2014.04.010"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [caudal ganglionic eminence derived neuron](http://purl.obolibrary.org/obo/CL_4042039) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A neuron of the central nervous system that develops from a caudal ganglionic eminence."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:12637172"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [hepatoblast](http://purl.obolibrary.org/obo/CL_0005026) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://cellxgene.cziscience.com/cellguide/CL_0005026"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://www.ncbi.nlm.nih.gov/books/NBK98190/"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:20130169"^^[string](http://www.w3.org/2001/XMLSchema#string) -### hepatocyte `http://purl.obolibrary.org/obo/CL_0000182` + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:12593982"^^[string](http://www.w3.org/2001/XMLSchema#string) -#### Added -- [hepatocyte](http://purl.obolibrary.org/obo/CL_0000182) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. +- [caudal ganglionic eminence derived neuron](http://purl.obolibrary.org/obo/CL_4042039) [comment](http://www.w3.org/2000/01/rdf-schema#comment) "Neurons derived from the caudal ganglionic eminence consist mostly of neurons populating the cortical layers of the brain and some subcortical areas such as the globus pallidus, the striatus and the hippocampus. Amongst neurons derived from the caudal ganglionic eminence there are cortical GABAergic neurons such as Pax6, Lamp5, VIP, sncg, GABAergic; in the hippocampus, mossy fibers, pyramidal neurons, granule neurons and interneurons; in the striatum and globus pallidus, medium spiny projection neurons."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:12637172"^^[string](http://www.w3.org/2001/XMLSchema#string) -Hepatocytes are the major cell type constituting 70-80% of the liver's cytoplasmic mass, playing crucial roles in maintaining the body's metabolic homeostasis. Dimensions of mature hepatocytes typically range from 20 to 30 μm in humans, but size may vary depending on their location within the liver lobule. Hepatocytes are characterized by high biosynthetic, enzymatic, and endocytic activity. They contain abundant mitochondria, smooth and rough endoplasmic reticulum, peroxisomes, lysosomes, and a large nucleus that is often binucleate. -The liver consists of three zones - the periportal Zone 1, midzone 2, and pericentral Zone 3 - which have differential nutrient and oxygen status, and damage susceptibility; hepatocytes in the different zones show signifcant functional heterogeneity ('hepatocyte functional zonation'). Hepatocytes are involved in a multitude of critical functions including the metabolism of lipids, carbohydrates, and proteins, the synthesis of serum proteins (e.g., albumin, transferrin, and lipoproteins), the detoxification and excretion of endogenous and exogenous substances, the storage of vitamins and minerals, and the production and secretion of bile. -Heterocytes demonstrate a remarkable regenerative capacity, which enables the liver to recover from injury and loss of tissue mass. Notably, hepatocytes perform biotransformation with both phase I and phase II enzymes, which modify drugs, xenobiotics, and various substances for elimination from the body. Phase I enzymes, such as cytochrome P450, catalyze both oxidative and reductive reactions of many xenobiotics; many of the products of phase I enzymes are substrates for the phase II enzymes, which catalyze conjugation reactions. -Alterations in hepatocyte function have significant implications for overall human health and disease. Certain conditions, such as hepatitis, cirrhosis, and liver cancer, can profoundly affect hepatocyte structure and function, thereby disrupting the liver's ability to perform its vital roles within the body. As the primary site for drug metabolism, changes in hepatocyte function can also impact the effectiveness and toxicity of pharmaceuticals. The regenerative ability of hepatocytes makes them valuable cells for liver regenerative medicine and bioartificial liver support systems, and their study has provided significant insights into liver biology and disease."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1083/jcb.201903090"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://www.ncbi.nlm.nih.gov/books/NBK98190/"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1016/j.biocel.2011.11.011"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:20130169"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1111/j.1439-0396.2007.00752.x"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:12593982"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1055/s-2007-1007096"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [caudal ganglionic eminence derived neuron](http://purl.obolibrary.org/obo/CL_4042039) [id](http://www.geneontology.org/formats/oboInOwl#id) "CL:4042039"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [hepatocyte](http://purl.obolibrary.org/obo/CL_0000182) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://cellxgene.cziscience.com/cellguide/CL_0000182"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [caudal ganglionic eminence derived neuron](http://purl.obolibrary.org/obo/CL_4042039) [contributor](http://purl.org/dc/terms/contributor) [0000-0002-0098-8958](https://orcid.org/0000-0002-0098-8958) +- Class: [caudal ganglionic eminence derived neuron](http://purl.obolibrary.org/obo/CL_4042039) -### histoblast `http://purl.obolibrary.org/obo/CL_0000373` -#### Removed -- [histoblast](http://purl.obolibrary.org/obo/CL_0000373) SubClassOf [eukaryotic cell](http://purl.obolibrary.org/obo/CL_0000255) +- [caudal ganglionic eminence derived neuron](http://purl.obolibrary.org/obo/CL_4042039) SubClassOf [BFO_0000002](http://purl.obolibrary.org/obo/BFO_0000002) -- [histoblast](http://purl.obolibrary.org/obo/CL_0000373) SubClassOf [RO_0002160](http://purl.obolibrary.org/obo/RO_0002160) some [NCBITaxon_50557](http://purl.obolibrary.org/obo/NCBITaxon_50557) +- [caudal ganglionic eminence derived neuron](http://purl.obolibrary.org/obo/CL_4042039) SubClassOf [RO_0002202](http://purl.obolibrary.org/obo/RO_0002202) some [UBERON_0004026](http://purl.obolibrary.org/obo/UBERON_0004026) -#### Added -- [histoblast](http://purl.obolibrary.org/obo/CL_0000373) SubClassOf [RO_0002162](http://purl.obolibrary.org/obo/RO_0002162) some [NCBITaxon_50557](http://purl.obolibrary.org/obo/NCBITaxon_50557) +- [caudal ganglionic eminence derived neuron](http://purl.obolibrary.org/obo/CL_4042039) SubClassOf [central nervous system neuron](http://purl.obolibrary.org/obo/CL_2000029) -### hypendymal cell `http://purl.obolibrary.org/obo/CL_4023181` +### cell of skeletal muscle `http://purl.obolibrary.org/obo/CL_0000188` #### Added -- [hypendymal cell](http://purl.obolibrary.org/obo/CL_4023181) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. - -Hypendymal cells are secretory cells located between the ependymal layer and the posterior commissure, forming the hypendmal layer of the subcommissural organ (SCO), a highly conserved gland that is part of the circumventricular system within the brain. -Hypendymal cells are bipolar cells with a thin apical pole and basal process. Most of the ultrastructural characteristics of these cells are similar to those described for the ependymal cells (which are arranged into another layer – the ependyma). However, ependymal cells release their secretion into the ventricular cerebrospinal fluid whereas hypendymal cells project processes to the local blood vessels and to the subarachnoidal space."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.3389/fncel.2015.00480"^^[string](http://www.w3.org/2001/XMLSchema#string) - - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1002/(SICI)1097-0029(19980415)41:2<98::AID-JEMT2>3.0.CO;2-M"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [cell of skeletal muscle](http://purl.obolibrary.org/obo/CL_0000188) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://cellxgene.cziscience.com/cellguide/CL_0000188"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1111/joa.13709"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [cell of skeletal muscle](http://purl.obolibrary.org/obo/CL_0000188) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. -- [hypendymal cell](http://purl.obolibrary.org/obo/CL_4023181) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://cellxgene.cziscience.com/cellguide/CL_4023181"^^[string](http://www.w3.org/2001/XMLSchema#string) +Skeletal muscle cells, or myocytes, are essential for the musculoskeletal system, featuring a striated appearance from tightly packed sarcomeres. These elongated, multi-nucleated cells convert ATP into mechanical energ and are key for voluntary movement and posture. They also are responsible for maintaining body temperature, storing nutrients, and stabilizing joints. +Skeletal muscle cells organize themselves tightly into bundles to form muscle fibers. Embedded within each of these cells are thousands of myofibrils, which are made up of the contractile proteins, actin (the thin filament), and myosin (the thick filament). Contraction of a skeletal muscle cell occurs when these myofibrils shorten, a process driven by the sliding of actin and myosin filaments over each other in a mechanism famously known as the sliding filament theory. +Additionally, skeletal muscle cells exhibit a high degree of plasticity, which allows for their adaptation in response to alterations in functional demands or damages. They have an innate regenerative capacity due to the presence of satellite cells—quiescent muscle stem cells that reside within the muscle fibers. Upon muscle injury, these satellite cells become activated, proliferate, and differentiate into new muscle cells, thereby contributing to the repair and growth of injured skeletal muscle. With this, skeletal muscle cells serve not only a pivotal biomechanical function but also possess a great capacity for self-healing and regeneration."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.3390/biology10101056"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1002/cphy.c160033"^^[string](http://www.w3.org/2001/XMLSchema#string) -### imaginal disc cell `http://purl.obolibrary.org/obo/CL_0000429` -#### Removed -- [imaginal disc cell](http://purl.obolibrary.org/obo/CL_0000429) SubClassOf [eukaryotic cell](http://purl.obolibrary.org/obo/CL_0000255) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://www.ncbi.nlm.nih.gov/books/NBK537139"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [imaginal disc cell](http://purl.obolibrary.org/obo/CL_0000429) SubClassOf [RO_0002160](http://purl.obolibrary.org/obo/RO_0002160) some [NCBITaxon_50557](http://purl.obolibrary.org/obo/NCBITaxon_50557) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://www.nature.com/scitable/topicpage/the-sliding-filament-theory-of-muscle-contraction-14567666/"^^[string](http://www.w3.org/2001/XMLSchema#string) -#### Added -- [imaginal disc cell](http://purl.obolibrary.org/obo/CL_0000429) SubClassOf [RO_0002162](http://purl.obolibrary.org/obo/RO_0002162) some [NCBITaxon_50557](http://purl.obolibrary.org/obo/NCBITaxon_50557) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://www.ncbi.nlm.nih.gov/books/NBK9961/"^^[string](http://www.w3.org/2001/XMLSchema#string) -### immature pericyte `http://purl.obolibrary.org/obo/CL_4047007` +### central nervous system macrophage `http://purl.obolibrary.org/obo/CL_0000878` #### Added -- [immature pericyte](http://purl.obolibrary.org/obo/CL_4047007) [contributor](http://purl.org/dc/terms/contributor) [0009-0005-7919-4905](https://orcid.org/0009-0005-7919-4905) +- [central nervous system macrophage](http://purl.obolibrary.org/obo/CL_0000878) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://cellxgene.cziscience.com/cellguide/CL_0000878"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [immature pericyte](http://purl.obolibrary.org/obo/CL_4047007) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A pericyte that is in an early stage of development, found in newly forming or remodeling blood vessels. An immature pericyte is characterized by it's mesenchymal stem cell-like properties and high proliferative capacity, which allows it to differentiate into various types of pericytes and contribute to the structural and functional maturation of the vasculature. Immature pericytes are stellate in new vessels and elongated with less protrusions in remodeling vessels."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:32466671"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [central nervous system macrophage](http://purl.obolibrary.org/obo/CL_0000878) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:34497389"^^[string](http://www.w3.org/2001/XMLSchema#string) +Central Nervous System (CNS) macrophages represent an integral part of the brain's innate immune system. These immune cells play crucial roles in maintenance and regulation, homeostasis, and disease response, thereby helping in the overall cognitive functioning of an organism. +There are different macrophage populations in the CNS, often classified into microglial cells, which reside in the parenchyma, and non-parenchymal macrophages at the interface between the brain and the periphery, including the perivascular spaces, the choroid plexus, and the meninges. CNS macrophages are derived from erythromyeloid progenitors in the yolk sac. CNS macrophages have distinct morphologies: Meningeal and perivascular macrophages have a more elongated shape than microglia, which are characterized by a small cell body with fine processes; in contrast, choroid plexus macrophages typically have a stellate shape. +Microglia are the most abundant abundant mononuclear phagocytes and have been shown to play a number of physiological roles, including proinflammatory and anti-inflammatory functions, synaptic pruning and remodeling, and apoptotic cell removal through phagocytosis. Non-parenchymal CAMs primarily support the barrier function against external antigens. Meningeal macrophages have been shown to respond to peripheral microbial challenges and to protect the brain against fatal viral infection. +CNS macrophages are also involved in the initiation and progression of many neurological diseases, such as Alzheimer's disease and Parkinson's disease as well as multiple sclerosis."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1007/s00281-013-0382-8"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:36685855"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1038/s41583-019-0201-x"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:21839917"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1016/j.tins.2021.07.002"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:28564607"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1016/j.immuni.2022.10.005"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [immature pericyte](http://purl.obolibrary.org/obo/CL_4047007) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "imPCs"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003000](http://purl.obolibrary.org/obo/OMO_0003000) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:28564607"^^[string](http://www.w3.org/2001/XMLSchema#string) +### cerebellar granule cell precursor `http://purl.obolibrary.org/obo/CL_0002362` -- [immature pericyte](http://purl.obolibrary.org/obo/CL_4047007) [id](http://www.geneontology.org/formats/oboInOwl#id) "CL:4047007"^^[string](http://www.w3.org/2001/XMLSchema#string) +#### Added +- [cerebellar granule cell precursor](http://purl.obolibrary.org/obo/CL_0002362) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl/cl-base#cellxgene_subset) -- [immature pericyte](http://purl.obolibrary.org/obo/CL_4047007) [date](http://purl.org/dc/terms/date) "2024-08-19T11:32:32Z"^^[dateTime](http://www.w3.org/2001/XMLSchema#dateTime) -- [immature pericyte](http://purl.obolibrary.org/obo/CL_4047007) [label](http://www.w3.org/2000/01/rdf-schema#label) "immature pericyte"^^[string](http://www.w3.org/2001/XMLSchema#string) +### cerebellar inhibitory GABAergic interneuron `http://purl.obolibrary.org/obo/CL_4023057` +#### Removed +- [cerebellar inhibitory GABAergic interneuron](http://purl.obolibrary.org/obo/CL_4023057) SubClassOf [obsolete CNS interneuron](http://purl.obolibrary.org/obo/CL_0000402) -- [immature pericyte](http://purl.obolibrary.org/obo/CL_4047007) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "immature PCs"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003000](http://purl.obolibrary.org/obo/OMO_0003000) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:28564607"^^[string](http://www.w3.org/2001/XMLSchema#string) -- Class: [immature pericyte](http://purl.obolibrary.org/obo/CL_4047007) +### cerebellum basket cell `http://purl.obolibrary.org/obo/CL_2000027` +#### Removed +- [cerebellum basket cell](http://purl.obolibrary.org/obo/CL_2000027) SubClassOf [obsolete CNS interneuron](http://purl.obolibrary.org/obo/CL_0000402) -- [immature pericyte](http://purl.obolibrary.org/obo/CL_4047007) SubClassOf [pericyte](http://purl.obolibrary.org/obo/CL_0000669) -### immature single positive thymocyte `http://purl.obolibrary.org/obo/CL_0000805` +### cerebral cortex endothelial cell `http://purl.obolibrary.org/obo/CL_1001602` #### Added -- [immature single positive thymocyte](http://purl.obolibrary.org/obo/CL_0000805) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) - - -### inflammatory macrophage `http://purl.obolibrary.org/obo/CL_0000863` +- [cerebral cortex endothelial cell](http://purl.obolibrary.org/obo/CL_1001602) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://cellxgene.cziscience.com/cellguide/CL_1001602"^^[string](http://www.w3.org/2001/XMLSchema#string) -#### Added -- [inflammatory macrophage](http://purl.obolibrary.org/obo/CL_0000863) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. +- [cerebral cortex endothelial cell](http://purl.obolibrary.org/obo/CL_1001602) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. -Inflammatory macrophages, also sometimes referred to as M1 or classically activated macrophages, play an important role in the inflammatory response. The M1/M2 classification is based upon macrophage polarization rather than macrophage location and refers to macrophage activation towards either a more inflammatory or more resolving phenotype, respectively, although the functional diversity of macrophages is more nuanced than such a dichotomy suggests. -Inflammatory macrophages are derived from monocytes recruited to a site of infection or injury. M1 macrophages are classically activated, typically by IFN-γ or lipopolysaccharide (LPS). Upon sensing signs of inflammation, they quickly respond by increasing their pro-inflammatory activity. They achieve this by producing a range of signaling molecules, such as nitric oxide, reactive oxygen species, and numerous cytokines such as tumor necrosis factor-alpha (TNF-alpha) and interleukin-1, -6 and -12. The release of these potent molecules helps to recruit other immune cells to the site, killing off pathogenic organisms and facilitation inflammation. At the same time, M1 macrophages can also present antigens to T cells, thereby helping to induce an adaptive immune response. Over time, these macrophages may transition in phenotype and function to help resolve the inflammation and promote tissue repair. -Despite the beneficial role of inflammatory macrophages in dealing with pathogens, chronic activation of these cells can lead to harmful effects. Over time, continuous production of pro-inflammatory molecules can cause damage to tissues and organs. This is seen in certain chronic inflammatory diseases, such as atherosclerosis, diabetes, obesity, asthma, and various autoimmune disorders. In such situations, the normally protective function of inflammatory macrophages is not properly controlled, which can contribute to disease pathology."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1186/s12935-021-02089-2"^^[string](http://www.w3.org/2001/XMLSchema#string) +Cerebral cortex endothelial cells are unique endothelial cells responsible for the formation and regulation of the blood-brain barrier (BBB), a specialized structure that separates the circulating blood from the cerebral neural tissue. These cells line the inner surface of nearly all blood vessels that irrigate the cerebral cortex, the outermost layer of the brain involved with complex cognitive functions such as thought, perception, and memory formation. Cerebral cortex endothelial cells are integral to maintaining brain health and function due to their role in regulating brain microenvironment and controlling the passage of essential molecules and cells. +The endothelial cells in the cerebral cortex are distinctive due to their highly selective permeability, largely attributable to the existence of unique tight junctions which maintain the barrier function of the BBB. The tightly interconnected structures of these cells prevent most substances from freely diffusing into the brain tissue, ensuring that harmful agents such as toxins, pathogens, or peripheral immune cells don't reach the brain and compromise its function. These cells also express multiple transporters and enzymes, allowing the selective entry of necessary nutrients and metabolites while excluding toxic substances. +Cerebral cortex endothelial cells also participate in neurovascular coupling, a process where localized neuronal activity increases cerebral blood flow to satisfy the local metabolic demands. The endothelial cells work in coordination with neurons and other cell types such as astrocytes and pericytes to mediate this process. They have been thought to regulate local blood flow by releasing substances in response to neuronal activity. Additionally, these cells are involved in many pathological conditions. Breakdown or dysfunction of the BBB often marked by altered endothelial cell function is linked to numerous neurological disorders including stroke, multiple sclerosis, Alzheimer’s disease, and brain tumors."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1038/nbt.2247"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.3389/fimmu.2020.583084"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1186/s12987-020-00230-3"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.3389/fimmu.2015.00263"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1177/0271678X156179"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1038/s41392-023-01452-1"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1038/nrn1824"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [inflammatory macrophage](http://purl.obolibrary.org/obo/CL_0000863) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://cellxgene.cziscience.com/cellguide/CL_0000863"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.3389/fnins.2023.1047778"^^[string](http://www.w3.org/2001/XMLSchema#string) -### inner cell mass cell `http://purl.obolibrary.org/obo/CL_2000020` +### cerebral cortex neuron `http://purl.obolibrary.org/obo/CL_0010012` #### Removed -- [inner cell mass cell](http://purl.obolibrary.org/obo/CL_2000020) SubClassOf [cell](http://purl.obolibrary.org/obo/CL_0000000) +- [cerebral cortex neuron](http://purl.obolibrary.org/obo/CL_0010012) SubClassOf [central nervous system neuron](http://purl.obolibrary.org/obo/CL_2000029) #### Added -- [inner cell mass cell](http://purl.obolibrary.org/obo/CL_2000020) SubClassOf [eukaryotic cell](http://purl.obolibrary.org/obo/CL_0000255) +- [cerebral cortex neuron](http://purl.obolibrary.org/obo/CL_0010012) SubClassOf [neuron of the forebrain](http://purl.obolibrary.org/obo/CL_0012001) -### insulin secreting cell `http://purl.obolibrary.org/obo/CL_0000168` +### cerebrospinal fluid secreting cell `http://purl.obolibrary.org/obo/CL_0000686` +#### Removed +- [cerebrospinal fluid secreting cell](http://purl.obolibrary.org/obo/CL_0000686) SubClassOf [secretory cell](http://purl.obolibrary.org/obo/CL_0000151) + - [is_inferred](http://www.geneontology.org/formats/oboInOwl#is_inferred) "true"^^[string](http://www.w3.org/2001/XMLSchema#string) #### Added -- [insulin secreting cell](http://purl.obolibrary.org/obo/CL_0000168) SubClassOf [eukaryotic cell](http://purl.obolibrary.org/obo/CL_0000255) +- [cerebrospinal fluid secreting cell](http://purl.obolibrary.org/obo/CL_0000686) SubClassOf [secretory epithelial cell](http://purl.obolibrary.org/obo/CL_1100001) -### intercalated cell of salivary gland `http://purl.obolibrary.org/obo/CL_4052048` +### chandelier cell `http://purl.obolibrary.org/obo/CL_4023083` #### Added -- [intercalated cell of salivary gland](http://purl.obolibrary.org/obo/CL_4052048) [id](http://www.geneontology.org/formats/oboInOwl#id) "CL:4052048"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [chandelier cell](http://purl.obolibrary.org/obo/CL_4023083) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl/cl-base#cellxgene_subset) + -- [intercalated cell of salivary gland](http://purl.obolibrary.org/obo/CL_4052048) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A cuboidal epithelial cell that is part of the intercalated duct of salivary gland. This cell expresses proteins commonly associated with acinar cells and displays calcium signaling characteristics similar to secretory cells, indicating an active role in the secretory process rather than ion reabsorption."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:37724716"^^[string](http://www.w3.org/2001/XMLSchema#string) +### chandelier pvalb GABAergic cortical interneuron `http://purl.obolibrary.org/obo/CL_4023036` +#### Removed +- [chandelier pvalb GABAergic cortical interneuron](http://purl.obolibrary.org/obo/CL_4023036) [comment](http://www.w3.org/2000/01/rdf-schema#comment) "In mice, Chandelier PV cells have soma found in in upper L2/3, with some in deep L5 and exhibit fast-spiking but lower firing rate compared to basket cells, and have practically absent hyperpolarization sag."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:27477017"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:30855909"^^[string](http://www.w3.org/2001/XMLSchema#string) +#### Added +- [chandelier pvalb GABAergic cortical interneuron](http://purl.obolibrary.org/obo/CL_4023036) [comment](http://www.w3.org/2000/01/rdf-schema#comment) "The marker set GPR149, CA8 can identify the Human cell type chandelier pvalb GABAergic cortical interneuron in the Brain with a confidence of 0.799748111 (NS-Forest FBeta value). In mice, Chandelier PV cells have soma found in in upper L2/3, with some in deep L5 and exhibit fast-spiking but lower firing rate compared to basket cells, and have practically absent hyperpolarization sag."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:27477017"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:35799078"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://doi.org/10.5281/zenodo.11165918"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:36726292"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [chandelier pvalb GABAergic cortical interneuron](http://purl.obolibrary.org/obo/CL_4023036) [RO_0002175](http://purl.obolibrary.org/obo/RO_0002175) [NCBITaxon_9606](http://purl.obolibrary.org/obo/NCBITaxon_9606) -- [intercalated cell of salivary gland](http://purl.obolibrary.org/obo/CL_4052048) [label](http://www.w3.org/2000/01/rdf-schema#label) "intercalated cell of salivary gland"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [chandelier pvalb GABAergic cortical interneuron](http://purl.obolibrary.org/obo/CL_4023036) SubClassOf [RO_0015004](http://purl.obolibrary.org/obo/RO_0015004) some [CLM_1000063](http://purl.obolibrary.org/obo/CLM_1000063) -- [intercalated cell of salivary gland](http://purl.obolibrary.org/obo/CL_4052048) [contributor](http://purl.org/dc/terms/contributor) [0009-0000-8480-9277](https://orcid.org/0009-0000-8480-9277) -- [intercalated cell of salivary gland](http://purl.obolibrary.org/obo/CL_4052048) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "Id cell"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:35799078"^^[string](http://www.w3.org/2001/XMLSchema#string) +### chief cell of parathyroid gland `http://purl.obolibrary.org/obo/CL_0000446` +#### Removed +- [chief cell of parathyroid gland](http://purl.obolibrary.org/obo/CL_0000446) SubClassOf [epithelial cell of parathyroid gland](http://purl.obolibrary.org/obo/CL_0002260) -- [intercalated cell of salivary gland](http://purl.obolibrary.org/obo/CL_4052048) [has_exact_synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "salivary intercalated duct cells"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:37724716"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [chief cell of parathyroid gland](http://purl.obolibrary.org/obo/CL_0000446) SubClassOf [peptide hormone secreting cell](http://purl.obolibrary.org/obo/CL_0000167) -- [intercalated cell of salivary gland](http://purl.obolibrary.org/obo/CL_4052048) [has_broad_synonym](http://www.geneontology.org/formats/oboInOwl#hasBroadSynonym) "intercalated duct cell"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:37724716"^^[string](http://www.w3.org/2001/XMLSchema#string) +#### Added +- [chief cell of parathyroid gland](http://purl.obolibrary.org/obo/CL_0000446) SubClassOf [RO_0002215](http://purl.obolibrary.org/obo/RO_0002215) some [GO_0035898](http://purl.obolibrary.org/obo/GO_0035898) -- [intercalated cell of salivary gland](http://purl.obolibrary.org/obo/CL_4052048) [date](http://purl.org/dc/terms/date) "2024-09-11T09:55:55Z"^^[dateTime](http://www.w3.org/2001/XMLSchema#dateTime) +- [chief cell of parathyroid gland](http://purl.obolibrary.org/obo/CL_0000446) SubClassOf [BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0011197](http://purl.obolibrary.org/obo/UBERON_0011197) -- [intercalated cell of salivary gland](http://purl.obolibrary.org/obo/CL_4052048) [contributor](http://purl.org/dc/terms/contributor) [0000-0003-4389-9821](https://orcid.org/0000-0003-4389-9821) +- [chief cell of parathyroid gland](http://purl.obolibrary.org/obo/CL_0000446) SubClassOf [parathyroid glandular cell](http://purl.obolibrary.org/obo/CL_1001593) -- Class: [intercalated cell of salivary gland](http://purl.obolibrary.org/obo/CL_4052048) -- [intercalated cell of salivary gland](http://purl.obolibrary.org/obo/CL_4052048) SubClassOf [BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0015766](http://purl.obolibrary.org/obo/UBERON_0015766) +### cholangiocyte `http://purl.obolibrary.org/obo/CL_1000488` +#### Removed +- [cholangiocyte](http://purl.obolibrary.org/obo/CL_1000488) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. -- [intercalated cell of salivary gland](http://purl.obolibrary.org/obo/CL_4052048) SubClassOf [duct epithelial cell](http://purl.obolibrary.org/obo/CL_0000068) +Cholangiocytes, also known as biliary epithelial cells, are specialized epithelial cells that line the biliary tract, which constitutes the gall bladder and bile ducts inside the liver. Crucial to the maintenance of the liver's health and function, cholangiocytes have a key role in the modification and secretion of bile, a fluid produced by hepatocytes that is essential to digestion and the absorption of fats and vitamins. +Cholangiocytes accomplish their primary function through the expression of a variety of transport proteins located on their apical and basolateral membranes, which propel bile acids and other contents of the bile into the biliary lumen. The hepatic bile, once secreted by the hepatocytes, is further modified by cholangiocytes via secretion and absorption processes. These processes help in the regulation of bile volume and composition, which is fundamental in ensuring the efficient digestion of dietary fats and fat-soluble vitamins and the excretion of cholesterol. +In addition to their role in bile modification, cholangiocytes also perform several other integral functions. For instance, these cells express Toll-like receptors (TLRs) which allow cholangiocytes to initiate an immune response against pathogens in the biliary lumen. When functioning normally, these cells contribute to biliary integrity, hepatic architecture, and overall hepatic physiology. However, when they become pathological, they are involved in the progression of liver diseases, such as primary biliary cirrhosis and cholangiocarcinoma – the malignancy of the biliary tract."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1016/j.jhep.2012.10.011"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [intercalated cell of salivary gland](http://purl.obolibrary.org/obo/CL_4052048) SubClassOf [BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0014727](http://purl.obolibrary.org/obo/UBERON_0014727) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1152/ajpgi.00227.2012"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [intercalated cell of salivary gland](http://purl.obolibrary.org/obo/CL_4052048) SubClassOf [salivary gland glandular cell](http://purl.obolibrary.org/obo/CL_1001596) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1038/s41575-019-0125-y"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.5009/gnl16033"^^[string](http://www.w3.org/2001/XMLSchema#string) -### interstitial cell `http://purl.obolibrary.org/obo/CL_4030031` -#### Removed -- [interstitial cell](http://purl.obolibrary.org/obo/CL_4030031) SubClassOf [cell](http://purl.obolibrary.org/obo/CL_0000000) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1016/j.jcmgh.2015.05.005"^^[string](http://www.w3.org/2001/XMLSchema#string) #### Added -- [interstitial cell](http://purl.obolibrary.org/obo/CL_4030031) SubClassOf [eukaryotic cell](http://purl.obolibrary.org/obo/CL_0000255) - +- [cholangiocyte](http://purl.obolibrary.org/obo/CL_1000488) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. -### intestinal crypt stem cell `http://purl.obolibrary.org/obo/CL_0002250` +Cholangiocytes, also known as biliary epithelial cells, are specialized epithelial cells that line the biliary tract, which constitutes the gall bladder and bile ducts inside the liver. Crucial to the maintenance of the liver's health and function, cholangiocytes have a key role in the modification and secretion of bile, a fluid produced by hepatocytes that is essential to digestion and the absorption of fats and vitamins. +Cholangiocytes accomplish their primary function through the expression of a variety of transport proteins located on their apical and basolateral membranes, which propel bile acids and other contents of the bile into the biliary lumen. The hepatic bile, once secreted by the hepatocytes, is further modified by cholangiocytes via secretion and absorption processes. These processes help in the regulation of bile volume and composition, which is fundamental in ensuring the efficient digestion of dietary fats and fat-soluble vitamins and the excretion of cholesterol. +In addition to their role in bile modification, cholangiocytes also perform several other integral functions. For instance, these cells express Toll-like receptors (TLRs) which allow cholangiocytes to initiate an immune response against pathogens in the biliary lumen. When functioning normally, these cells contribute to biliary integrity, hepatic architecture, and overall hepatic physiology. However, when they become pathological, they are involved in the progression of liver diseases, such as primary biliary cirrhosis and cholangiocarcinoma – the malignancy of the biliary tract."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1016/j.jhep.2012.10.011"^^[string](http://www.w3.org/2001/XMLSchema#string) -#### Added -- [intestinal crypt stem cell](http://purl.obolibrary.org/obo/CL_0002250) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1152/ajpgi.00227.2012"^^[string](http://www.w3.org/2001/XMLSchema#string) -Intestinal crypt stem cells, also known as crypt base columnar cells, are a unique type of cell, characterized by the highly specific marker LGR5, found in the intestinal epithelium. Situated at the bottom of the minute pockets known as crypts of Lieberkühn, these are undifferentiated cells that have the ability to perpetually self-renew, as well as differentiate into various other cell types that constitute the epithelial lining of the intestine. -The fundamental role of intestinal crypt stem cells is to provide a constant supply of new cells to maintain the cellular turnover of the intestinal epithelium, a tissue known for rapid self-renewal. These stem cells are nurtured and protected by specialized epithelial and mesenchymal cells, and together constitute the intestinal stem cell niche. -An important function of intestinal crypt stem cells is to sustain the balance between cell division and programmed cell death, called apoptosis, to ensure the integrity of the intestinal lining. Given their active proliferation rate, these stem cells initiate the creation of diverse differentiated cell types, including enterocytes (the primary absorptive cells in the intestinal lumen), goblet cells (that produce mucus to protect the epithelial layer), enteroendocrine cells (involved in producing gastrointestinal hormones), and Paneth cells (involved in secreting antimicrobial peptides). This diversity in output regulates the physiological activities of the gut ranging from nutrient absorption, hormone secretion, bacterial balance, to immunity. -Research studies suggest that dysregulation in intestinal crypt stem cell proliferation and differentiation is associated with several intestinal disorders including intestinal cancer, and various enteropathies."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1101/gad.1674008"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1038/s41575-019-0125-y"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1038/s41575-018-0081-y"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.5009/gnl16033"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1016/j.cell.2013.07.004"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1016/j.jcmgh.2015.05.005"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1038/s41580-020-0278-0"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1111/j.1365-2184.2009.00642.x"^^[string](http://www.w3.org/2001/XMLSchema#string) +### chorionic girdle cell `http://purl.obolibrary.org/obo/CL_4040001` +#### Removed +- [chorionic girdle cell](http://purl.obolibrary.org/obo/CL_4040001) [note](http://www.geneontology.org/formats/oboInOwl#note) "Humans, mice and rats have a highly invasive (hemochorial) placentation. Horses have a non-invasive epitheliochorial placenta, except for the transient endometrial cup."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:27280409"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [intestinal crypt stem cell](http://purl.obolibrary.org/obo/CL_0002250) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://cellxgene.cziscience.com/cellguide/CL_0002250"^^[string](http://www.w3.org/2001/XMLSchema#string) +#### Added +- [chorionic girdle cell](http://purl.obolibrary.org/obo/CL_4040001) [comment](http://www.w3.org/2000/01/rdf-schema#comment) "Humans, mice and rats have a highly invasive (hemochorial) placentation. Horses have a non-invasive epitheliochorial placenta, except for the transient endometrial cup."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:27280409"^^[string](http://www.w3.org/2001/XMLSchema#string) -### intestinal crypt stem cell of colon `http://purl.obolibrary.org/obo/CL_0009043` +### chorionic trophoblast cell `http://purl.obolibrary.org/obo/CL_0011101` #### Added -- [intestinal crypt stem cell of colon](http://purl.obolibrary.org/obo/CL_0009043) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. +- [chorionic trophoblast cell](http://purl.obolibrary.org/obo/CL_0011101) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://cellxgene.cziscience.com/cellguide/CL_0011101"^^[string](http://www.w3.org/2001/XMLSchema#string) -Intestinal crypt stem cells of the colon, also known as colon crypt base columnar (CBC) cells, are highly specialized cells primarily responsible for the constant self-renewal of the colonic epithelium. These cells are found in the crypts of Lieberkühn - deeply invaginated sections of the colon's mucosal layer. -The prime function of intestinal crypt stem cells of the colon is to serve as the source of constant cell regeneration in the colon. Every few days, these stem cells divide and differentiate into the various other types of intestinal cells, such as enterocytes, goblet cells, and enteroendocrine cells. -A constant renewal cycle is necessary due to the harsh environment of the colon where cells continuously encounter abrasive food matter and potential pathogens, leading to a high turnover rate. When the colon's mucosal layer suffers damage, a rapid response is triggered whereby colon crypt stem cells divide faster and are directed to injured sites to repair the epithelial layer. Dysregulation of these cells' function or proliferation can contribute to disorders such as colorectal cancer."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1186/s12943-019-0962-x"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [chorionic trophoblast cell](http://purl.obolibrary.org/obo/CL_0011101) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1038/s41575-018-0081-y"^^[string](http://www.w3.org/2001/XMLSchema#string) +The chorionic trophoblast cell, vital for placental development in mammals, originates from the blastocyst's outer layer, the trophectoderm. As a significant component of the placenta, the chorion forms the external fetal-maternal interface and consists primarily of chorionic trophoblast cells. These cells are pivotal in embryogenesis, fetal nutrition, waste removal, and immune response generation, contributing crucially to the success of pregnancy. +Chorionic trophoblast cells undergo trophoblast differentiation, giving rise to specialized sub-types: cytotrophoblasts and syncytiotrophoblasts. Cytotrophoblasts, found in the inner layer, serve as stem cells and contribute to proliferative activities. In contrast, syncytiotrophoblasts, originating from cytotrophoblasts, form the outer layer with a distinctive multinucleated, continuous, and non-proliferative structure. These cells play a key role in maternal-fetal gas and nutrient exchange, producing essential hormones like human chorionic gonadotropin (hCG), progesterone, and estrogen, vital for sustaining pregnancy. +Apart from their physiological roles, chorionic trophoblast cells play a crucial role in shielding the fetus from the maternal immune system. They accomplish this by modifying the expression of major histocompatibility complex (MHC) molecules, which are self-identifying proteins utilized by the immune system to identify foreign cells. Through selective expression of specific types of these molecules, trophoblast cells can evade cytotoxic T cells that might otherwise attack them, while still retaining the ability to attract natural killer cells. These natural killer cells assist in trophoblast invasion and the remodeling of blood vessels in the uterus."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://www.ncbi.nlm.nih.gov/books/NBK53245/"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1016/j.cell.2013.07.004"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1007/s00018-019-03104-6"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1073/pnas.1607327113"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1155/2014/579279"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1111/j.1365-2184.2009.00642.x"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1093/biolre/ioy070"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [intestinal crypt stem cell of colon](http://purl.obolibrary.org/obo/CL_0009043) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://cellxgene.cziscience.com/cellguide/CL_0009043"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://www.sciencedirect.com/topics/medicine-and-dentistry/placenta-development"^^[string](http://www.w3.org/2001/XMLSchema#string) -### intestinal crypt stem cell of small intestine `http://purl.obolibrary.org/obo/CL_0009017` +### choroid plexus capillary endothelial cell `http://purl.obolibrary.org/obo/CL_4052017` #### Added -- [intestinal crypt stem cell of small intestine](http://purl.obolibrary.org/obo/CL_0009017) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. +- [choroid plexus capillary endothelial cell](http://purl.obolibrary.org/obo/CL_4052017) [id](http://www.geneontology.org/formats/oboInOwl#id) "CL:4052017"^^[string](http://www.w3.org/2001/XMLSchema#string) -Intestinal crypt stem cells of the small intestine are a type of adult stem cell intimately involved in the continuous replenishment of the intestinal epithelium, the innermost layer of the intestine responsible for nutrient absorption. These cells, located within the crypts of Lieberkühn, are the origin of various cell lineages that make up the functional units of the small intestine. They possess self-renewal ability, an essential feature of stem cells, which allows them to maintain a steady population in the small intestine. -One of the critical roles of intestinal crypt stem cells is to drive the continual renewal process taking place in the small intestine every 3-5 days. By proliferating intensively, these cells produce transient amplifying (TA) cells that are characterized by quick division and progressive differentiation. These cells eventually differentiate into specialized cell types, encompassing absorptive enterocytes, mucin-secreting goblet cells, hormone-secreting enteroendocrine cells, and Paneth cells, all of which have essential roles in digestion and nutrient absorption in the small intestine. -Intestinal crypt stem cells of the small intestine are also play a significant part in injury recovery. Under regular conditions, these cells primarily exist in an active state, facilitating the constant renovation of the gut lining. However, upon injury or loss of regular intestinal crypt stem cells reserve intestinal stem cells, a slow-cycling and radio-resistant population, can be stimulated to take over the duties of active crypt stem cells. Such plasticity provides a powerful regenerative mechanism that ensures the intestinal epithelium's function and structural integrity amidst diverse conditions."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1016/j.celrep.2020.107952"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [choroid plexus capillary endothelial cell](http://purl.obolibrary.org/obo/CL_4052017) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A capillary endothelial cell that is part of the choroid plexus, characterized by its fenestrated nature with 60 to 80 nm fenestrations and lack of tight junctions. This fenestrated structure allows for the rapid delivery of water and other components, aiding in the production of cerebrospinal fluid (CSF)."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:18480313"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1038/s41575-018-0081-y"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://www.ncbi.nlm.nih.gov/books/NBK27998/"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1073/pnas.1607327113"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:32375819"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [intestinal crypt stem cell of small intestine](http://purl.obolibrary.org/obo/CL_0009017) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://cellxgene.cziscience.com/cellguide/CL_0009017"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [choroid plexus capillary endothelial cell](http://purl.obolibrary.org/obo/CL_4052017) [contributor](http://purl.org/dc/terms/contributor) [0009-0000-8480-9277](https://orcid.org/0009-0000-8480-9277) +- [choroid plexus capillary endothelial cell](http://purl.obolibrary.org/obo/CL_4052017) [date](http://purl.org/dc/terms/date) "2024-10-01T11:38:22Z"^^[dateTime](http://www.w3.org/2001/XMLSchema#dateTime) -### intestinal enteroendocrine progenitor `http://purl.obolibrary.org/obo/CL_4052006` +- [choroid plexus capillary endothelial cell](http://purl.obolibrary.org/obo/CL_4052017) [label](http://www.w3.org/2000/01/rdf-schema#label) "choroid plexus capillary endothelial cell"^^[string](http://www.w3.org/2001/XMLSchema#string) -#### Added -- [intestinal enteroendocrine progenitor](http://purl.obolibrary.org/obo/CL_4052006) [comment](http://www.w3.org/2000/01/rdf-schema#comment) "The EEC progenitor is also present in other organisms; for example, flies have EEC progenitors but lack intestinal crypts and do not express the same markers. Instead, they are Dl+ and Pros+."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:25670791"^^[string](http://www.w3.org/2001/XMLSchema#string) +- Class: [choroid plexus capillary endothelial cell](http://purl.obolibrary.org/obo/CL_4052017) -- [intestinal enteroendocrine progenitor](http://purl.obolibrary.org/obo/CL_4052006) [contributor](http://purl.org/dc/terms/contributor) [0009-0000-8480-9277](https://orcid.org/0009-0000-8480-9277) +- [choroid plexus capillary endothelial cell](http://purl.obolibrary.org/obo/CL_4052017) EquivalentTo [capillary endothelial cell](http://purl.obolibrary.org/obo/CL_0002144) and ([BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0001886](http://purl.obolibrary.org/obo/UBERON_0001886)) -- [intestinal enteroendocrine progenitor](http://purl.obolibrary.org/obo/CL_4052006) [id](http://www.geneontology.org/formats/oboInOwl#id) "CL:4052006"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [choroid plexus capillary endothelial cell](http://purl.obolibrary.org/obo/CL_4052017) SubClassOf [BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0001886](http://purl.obolibrary.org/obo/UBERON_0001886) -- [intestinal enteroendocrine progenitor](http://purl.obolibrary.org/obo/CL_4052006) [label](http://www.w3.org/2000/01/rdf-schema#label) "intestinal enteroendocrine progenitor"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [choroid plexus capillary endothelial cell](http://purl.obolibrary.org/obo/CL_4052017) SubClassOf [fenestrated endothelial cell](http://purl.obolibrary.org/obo/CL_0000666) -- [intestinal enteroendocrine progenitor](http://purl.obolibrary.org/obo/CL_4052006) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "EEC Progenitor"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003000](http://purl.obolibrary.org/obo/OMO_0003000) +- [choroid plexus capillary endothelial cell](http://purl.obolibrary.org/obo/CL_4052017) SubClassOf [brain microvascular endothelial cell](http://purl.obolibrary.org/obo/CL_2000044) + +- [choroid plexus capillary endothelial cell](http://purl.obolibrary.org/obo/CL_4052017) SubClassOf [capillary endothelial cell](http://purl.obolibrary.org/obo/CL_0002144) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:31756561"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [intestinal enteroendocrine progenitor](http://purl.obolibrary.org/obo/CL_4052006) [date](http://purl.org/dc/terms/date) "2024-09-20T12:13:26Z"^^[dateTime](http://www.w3.org/2001/XMLSchema#dateTime) +### chromaffin cell `http://purl.obolibrary.org/obo/CL_0000166` +#### Removed +- [chromaffin cell](http://purl.obolibrary.org/obo/CL_0000166) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +Chromaffin cells, also known as pheochromocytes, are neuroendocrine cells that are typically located in the adrenal medulla, the innermost part of the adrenal gland, which is situated on top of each kidney. Chromaffin cells are also found in small clusters, known as paraganglia, in various locations throughout the body, including the sympathetic nervous system. They derive their name from their ability to stain a brownish-black color upon exposure to chromic salts, a feature made possible due to their high content of granules rich in catecholamines and catecholamine-related neurotransmitters. +The primary function of chromaffin cells is the synthesis and release of catecholamines, specifically epinephrine (adrenaline) and norepinephrine (noradrenaline). These neurotransmitters are vital stress hormones that, when released by the adrenal chromaffing cells into the bloodstream, prepare the body for the 'fight or flight' response. This response can enhance the body's performance in a dangerous situation by increasing heart rate, elevating blood sugar, and increasing blood flow to the muscles. The chromaffin cells in paraganglia are responsible for the local release of catecholamines and play a role in regulating blood pressure and other autonomic functions. +In addition to their role in stress response, chromaffin cells also contribute to the body's immune response. They secrete several peptides including antimicrobial peptides, and the discovery of LPS and cytokine receptors on chromaffin cells suggests that the adrenal medulla may participate in some aspects of the immune response."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.3389/fendo.2018.00711"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [intestinal enteroendocrine progenitor](http://purl.obolibrary.org/obo/CL_4052006) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "An epithelial cell that is part of the crypt of Lieberkuhn, originating from intestinal stem cells and giving rise to enteroendocrine cells (EECs). In mouse and human, this cell can be characterized by the expression of Neurog3, and has the ability to proliferate and differentiate into multiple EEC subtypes. Its proliferative potential contributes to crypt growth, distinguishing it from fully differentiated EECs."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:32531023"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.3389/fimmu.2022.977175/full"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:38260422"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1002/cphy.c190003"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "doi:/10.1038/s41467-021-27901-5"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.3389/fimmu.2022.977175"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:35913117"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1016/j.biocel.2016.02.003"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:31756561"^^[string](http://www.w3.org/2001/XMLSchema#string) +#### Added +- [chromaffin cell](http://purl.obolibrary.org/obo/CL_0000166) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. -- Class: [intestinal enteroendocrine progenitor](http://purl.obolibrary.org/obo/CL_4052006) +Chromaffin cells, also known as pheochromocytes, are neuroendocrine cells that are typically located in the adrenal medulla, the innermost part of the adrenal gland, which is situated on top of each kidney. Chromaffin cells are also found in small clusters, known as paraganglia, in various locations throughout the body, including the sympathetic nervous system. They derive their name from their ability to stain a brownish-black color upon exposure to chromic salts, a feature made possible due to their high content of granules rich in catecholamines and catecholamine-related neurotransmitters. +The primary function of chromaffin cells is the synthesis and release of catecholamines, specifically epinephrine (adrenaline) and norepinephrine (noradrenaline). These neurotransmitters are vital stress hormones that, when released by the adrenal chromaffing cells into the bloodstream, prepare the body for the 'fight or flight' response. This response can enhance the body's performance in a dangerous situation by increasing heart rate, elevating blood sugar, and increasing blood flow to the muscles. The chromaffin cells in paraganglia are responsible for the local release of catecholamines and play a role in regulating blood pressure and other autonomic functions. +In addition to their role in stress response, chromaffin cells also contribute to the body's immune response. They secrete several peptides including antimicrobial peptides, and the discovery of LPS and cytokine receptors on chromaffin cells suggests that the adrenal medulla may participate in some aspects of the immune response."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.3389/fendo.2018.00711"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [intestinal enteroendocrine progenitor](http://purl.obolibrary.org/obo/CL_4052006) SubClassOf [RO_0002202](http://purl.obolibrary.org/obo/RO_0002202) some [intestinal crypt stem cell](http://purl.obolibrary.org/obo/CL_0002250) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.3389/fimmu.2022.977175/full"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [intestinal enteroendocrine progenitor](http://purl.obolibrary.org/obo/CL_4052006) SubClassOf [BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0011184](http://purl.obolibrary.org/obo/UBERON_0011184) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1002/cphy.c190003"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [intestinal enteroendocrine progenitor](http://purl.obolibrary.org/obo/CL_4052006) SubClassOf [intestinal epithelial cell](http://purl.obolibrary.org/obo/CL_0002563) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.3389/fimmu.2022.977175"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [intestinal enteroendocrine progenitor](http://purl.obolibrary.org/obo/CL_4052006) SubClassOf [progenitor cell](http://purl.obolibrary.org/obo/CL_0011026) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1016/j.biocel.2016.02.003"^^[string](http://www.w3.org/2001/XMLSchema#string) -### intestinal fibroblastic reticular cell `http://purl.obolibrary.org/obo/CL_4052004` +### ciliary muscle cell `http://purl.obolibrary.org/obo/CL_1000443` #### Added -- [intestinal fibroblastic reticular cell](http://purl.obolibrary.org/obo/CL_4052004) [label](http://www.w3.org/2000/01/rdf-schema#label) "intestinal fibroblastic reticular cell"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [ciliary muscle cell](http://purl.obolibrary.org/obo/CL_1000443) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://cellxgene.cziscience.com/cellguide/CL_1000443"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [ciliary muscle cell](http://purl.obolibrary.org/obo/CL_1000443) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. -- [intestinal fibroblastic reticular cell](http://purl.obolibrary.org/obo/CL_4052004) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "gut-associated secondary lymphoid organs fibroblastic reticular cell"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:35440118"^^[string](http://www.w3.org/2001/XMLSchema#string) +Ciliary muscle cells are specialized contractile cells that constitute the ciliary muscle, a component of the eye in vertebrates. These cells form a ring around the iris, the eye's colored part. Ciliary muscle cells fall into the category of smooth muscle cells, characterized by their lack of the striations typical of skeletal and cardiac muscle cells. Their shape is elongated and pointed at both ends, and they occur in multi-nucleated syncytia where many cells share the same cytoplasm. +Ciliary muscle cells primarily control the eye's accommodation, adjusting the thickness and curvature of the lens to fine-tune the focus of light on the retina. When ciliary muscle cells contract, tension on the zonular fibers holding the lens in place is reduced, allowing the lens to become thicker and increase its refractive power. Conversely, when the ciliary muscle cells relax, the tension on the zonular fibers increases, causing the lens to become flatter and decrease its refractive power. This adjustment facilitates clear vision at different distances, ranging from near to far objects. +Additionally, ciliary muscle cells play a role in draining the eye's aqueous humor, which is the clear fluid that fills the anterior chamber of the eye between the cornea and the lens. By controlling the shape of the surrounding trabecular meshwork through muscle contractions and relaxations, ciliary muscle cells indirectly regulate intraocular pressure, a factor critical for preventing ocular conditions like glaucoma."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1038/srep31171"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [intestinal fibroblastic reticular cell](http://purl.obolibrary.org/obo/CL_4052004) [date](http://purl.org/dc/terms/date) "2024-09-19T11:22:18Z"^^[dateTime](http://www.w3.org/2001/XMLSchema#dateTime) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1016/S1350-9462(98)00011-1"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [intestinal fibroblastic reticular cell](http://purl.obolibrary.org/obo/CL_4052004) [has_narrow_synonym](http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym) "Ccl19-expressing fibroblastic reticular cell"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:35440118"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://www.sciencedirect.com/topics/medicine-and-dentistry/ciliary-muscle"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [intestinal fibroblastic reticular cell](http://purl.obolibrary.org/obo/CL_4052004) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A specialized fibroblastic reticular cell that is part of gut-associated lymphoid tissue (GALT), responsible for forming a structural network that facilitates immune cell interactions. This cell is found in Peyer's patches, cryptopatches, and isolated lymphoid follicles. It plays crucial roles in maintaining intestinal immunity by controlling innate lymphoid cell homeostasis and function, organizing lymphoid structures, and contributing to intestinal microbiome balance."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:35440118"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1111/j.1444-0938.2008.00260.x"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:33707780"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [intestinal fibroblastic reticular cell](http://purl.obolibrary.org/obo/CL_4052004) [contributor](http://purl.org/dc/terms/contributor) [0009-0000-8480-9277](https://orcid.org/0009-0000-8480-9277) +### ciliated cell `http://purl.obolibrary.org/obo/CL_0000064` +#### Removed +- [ciliated cell](http://purl.obolibrary.org/obo/CL_0000064) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) -- [intestinal fibroblastic reticular cell](http://purl.obolibrary.org/obo/CL_4052004) [id](http://www.geneontology.org/formats/oboInOwl#id) "CL:4052004"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [intestinal fibroblastic reticular cell](http://purl.obolibrary.org/obo/CL_4052004) [has_narrow_synonym](http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym) "solitary intestinal lymphoid tissue fibroblastic reticular cell"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:35440118"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [intestinal fibroblastic reticular cell](http://purl.obolibrary.org/obo/CL_4052004) [description](http://purl.org/dc/terms/description) "Intestinal fibroblastic reticular cells develop from both perivascular and subepithelial progenitors during Peyer's patch formation. Intestinal fibroblastic reticular cells express key markers such as CCL19, CCL21, CXCL13, TNFSF13B (also known as BAFF), and produce IL-7, which are important for their immune regulatory functions and the organization of lymphoid structures."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:35440118"^^[string](http://www.w3.org/2001/XMLSchema#string) +### ciliated epithelial cell of esophagus `http://purl.obolibrary.org/obo/CL_3000000` +#### Removed +- [ciliated epithelial cell of esophagus](http://purl.obolibrary.org/obo/CL_3000000) EquivalentTo [ciliated epithelial cell](http://purl.obolibrary.org/obo/CL_0000067) and ([BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0001976](http://purl.obolibrary.org/obo/UBERON_0001976)) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:33707780"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [ciliated epithelial cell of esophagus](http://purl.obolibrary.org/obo/CL_3000000) SubClassOf [ciliated epithelial cell](http://purl.obolibrary.org/obo/CL_0000067) -- Class: [intestinal fibroblastic reticular cell](http://purl.obolibrary.org/obo/CL_4052004) +- [ciliated epithelial cell of esophagus](http://purl.obolibrary.org/obo/CL_3000000) SubClassOf [BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0001976](http://purl.obolibrary.org/obo/UBERON_0001976) -- [intestinal fibroblastic reticular cell](http://purl.obolibrary.org/obo/CL_4052004) SubClassOf [fibroblastic reticular cell](http://purl.obolibrary.org/obo/CL_0009101) -- [intestinal fibroblastic reticular cell](http://purl.obolibrary.org/obo/CL_4052004) SubClassOf [BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0001962](http://purl.obolibrary.org/obo/UBERON_0001962) +### classical monocyte `http://purl.obolibrary.org/obo/CL_0000860` +#### Removed +- [classical monocyte](http://purl.obolibrary.org/obo/CL_0000860) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. -### intestinal subserosal fibroblast `http://purl.obolibrary.org/obo/CL_4052005` +Classical monocytes are a subtype of monocytes that are characterized by high CD14 but no CD16 expression. Emerging from the bone marrow and entering the bloodstream, these cells play central roles in immune responses and regulation of inflammation. CD14-positive CD16-negative monocytes form the majority of circulating monocytes in the body, typically contributing to around 80-90% of the total monocyte pool. +The primary function of the classical monocytes is to serve in the frontline of host defense against infections. They are primed to migrate to sites of infection, and they express pattern recognition receptors that help them identify and phagocytose pathogens, leading to their destruction. Classical monocytes also contribute to inflammation by producing several pro-inflammatory cytokines including interleukins and tumor necrosis factors. +In response to specific signals from tissues under pathological conditions, such as infection or injury, classical monocytes can leave the bloodstream and migrate towards the affected sites. Following their arrival, these cells differentiate into diverse cell types including macrophages and dendritic cells to combat specific pathogens or injury. Dysregulated monocyte activity can lead to the development of many human diseases including inflammation, infection, tissue injury, and various autoimmune diseases."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1038/nri.2017.28"^^[string](http://www.w3.org/2001/XMLSchema#string) -#### Added -- [intestinal subserosal fibroblast](http://purl.obolibrary.org/obo/CL_4052005) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A fibroblast that is part of the subserosa of intestine. This cell interacts with immune cells and play roles in inflammation and fibrosis. In certain conditions, such as Crohn's disease, subserosal fibroblast may differentiate into myofibroblasts."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:23143399"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1182/blood-2009-07-235028"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:26694715"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1111/sji.12883"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:38877292"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.3389/fimmu.2015.00423/full"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [intestinal subserosal fibroblast](http://purl.obolibrary.org/obo/CL_4052005) [id](http://www.geneontology.org/formats/oboInOwl#id) "CL:4052005"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.3389/fimmu.2019.02035"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [intestinal subserosal fibroblast](http://purl.obolibrary.org/obo/CL_4052005) [label](http://www.w3.org/2000/01/rdf-schema#label) "intestinal subserosal fibroblast"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [classical monocyte](http://purl.obolibrary.org/obo/CL_0000860) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) -- [intestinal subserosal fibroblast](http://purl.obolibrary.org/obo/CL_4052005) [date](http://purl.org/dc/terms/date) "2024-09-19T12:58:29Z"^^[dateTime](http://www.w3.org/2001/XMLSchema#dateTime) +#### Added +- [classical monocyte](http://purl.obolibrary.org/obo/CL_0000860) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. -- [intestinal subserosal fibroblast](http://purl.obolibrary.org/obo/CL_4052005) [contributor](http://purl.org/dc/terms/contributor) [0009-0000-8480-9277](https://orcid.org/0009-0000-8480-9277) +Classical monocytes are a subtype of monocytes that are characterized by high CD14 but no CD16 expression. Emerging from the bone marrow and entering the bloodstream, these cells play central roles in immune responses and regulation of inflammation. CD14-positive CD16-negative monocytes form the majority of circulating monocytes in the body, typically contributing to around 80-90% of the total monocyte pool. +The primary function of the classical monocytes is to serve in the frontline of host defense against infections. They are primed to migrate to sites of infection, and they express pattern recognition receptors that help them identify and phagocytose pathogens, leading to their destruction. Classical monocytes also contribute to inflammation by producing several pro-inflammatory cytokines including interleukins and tumor necrosis factors. +In response to specific signals from tissues under pathological conditions, such as infection or injury, classical monocytes can leave the bloodstream and migrate towards the affected sites. Following their arrival, these cells differentiate into diverse cell types including macrophages and dendritic cells to combat specific pathogens or injury. Dysregulated monocyte activity can lead to the development of many human diseases including inflammation, infection, tissue injury, and various autoimmune diseases."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1038/nri.2017.28"^^[string](http://www.w3.org/2001/XMLSchema#string) -- Class: [intestinal subserosal fibroblast](http://purl.obolibrary.org/obo/CL_4052005) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1182/blood-2009-07-235028"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [intestinal subserosal fibroblast](http://purl.obolibrary.org/obo/CL_4052005) SubClassOf [fibroblast](http://purl.obolibrary.org/obo/CL_0000057) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1111/sji.12883"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [intestinal subserosal fibroblast](http://purl.obolibrary.org/obo/CL_4052005) SubClassOf [BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0001243](http://purl.obolibrary.org/obo/UBERON_0001243) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.3389/fimmu.2015.00423/full"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [intestinal subserosal fibroblast](http://purl.obolibrary.org/obo/CL_4052005) SubClassOf [BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0012375](http://purl.obolibrary.org/obo/UBERON_0012375) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.3389/fimmu.2019.02035"^^[string](http://www.w3.org/2001/XMLSchema#string) -### intestinal villus capillary endothelial cell `http://purl.obolibrary.org/obo/CL_4052003` +### club cell `http://purl.obolibrary.org/obo/CL_0000158` #### Added -- [intestinal villus capillary endothelial cell](http://purl.obolibrary.org/obo/CL_4052003) [date](http://purl.org/dc/terms/date) "2024-09-17T10:03:25Z"^^[dateTime](http://www.w3.org/2001/XMLSchema#dateTime) +- [club cell](http://purl.obolibrary.org/obo/CL_0000158) SubClassOf [secretory epithelial cell](http://purl.obolibrary.org/obo/CL_1100001) -- [intestinal villus capillary endothelial cell](http://purl.obolibrary.org/obo/CL_4052003) [id](http://www.geneontology.org/formats/oboInOwl#id) "CL:4052003"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [intestinal villus capillary endothelial cell](http://purl.obolibrary.org/obo/CL_4052003) [label](http://www.w3.org/2000/01/rdf-schema#label) "intestinal villus capillary endothelial cell"^^[string](http://www.w3.org/2001/XMLSchema#string) +### cochlea auditory hair cell `http://purl.obolibrary.org/obo/CL_4023120` -- [intestinal villus capillary endothelial cell](http://purl.obolibrary.org/obo/CL_4052003) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "villus tip endothelial cell"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:38051275"^^[string](http://www.w3.org/2001/XMLSchema#string) +#### Added +- [cochlea auditory hair cell](http://purl.obolibrary.org/obo/CL_4023120) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl/cl-base#cellxgene_subset) -- [intestinal villus capillary endothelial cell](http://purl.obolibrary.org/obo/CL_4052003) [contributor](http://purl.org/dc/terms/contributor) [0009-0000-8480-9277](https://orcid.org/0009-0000-8480-9277) -- [intestinal villus capillary endothelial cell](http://purl.obolibrary.org/obo/CL_4052003) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A capillary endothelial cell that is part of the intestinal villus. This cell is highly fenestrated, with fenestrations most numerous at the villus tips, and plays a vital role in nutrient absorption and maintaining the selective permeability of the intestinal barrier."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:18480313"^^[string](http://www.w3.org/2001/XMLSchema#string) +### colon epithelial cell `http://purl.obolibrary.org/obo/CL_0011108` +#### Removed +- [colon epithelial cell](http://purl.obolibrary.org/obo/CL_0011108) EquivalentTo [epithelial cell](http://purl.obolibrary.org/obo/CL_0000066) and ([BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0001155](http://purl.obolibrary.org/obo/UBERON_0001155)) + +#### Added +- [colon epithelial cell](http://purl.obolibrary.org/obo/CL_0011108) EquivalentTo [epithelial cell](http://purl.obolibrary.org/obo/CL_0000066) and ([BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0000397](http://purl.obolibrary.org/obo/UBERON_0000397)) + + +### colon goblet cell `http://purl.obolibrary.org/obo/CL_0009039` +#### Removed +- [colon goblet cell](http://purl.obolibrary.org/obo/CL_0009039) EquivalentTo [goblet cell](http://purl.obolibrary.org/obo/CL_0000160) and ([BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0001155](http://purl.obolibrary.org/obo/UBERON_0001155)) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:35810168"^^[string](http://www.w3.org/2001/XMLSchema#string) +#### Added +- [colon goblet cell](http://purl.obolibrary.org/obo/CL_0009039) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:38051275"^^[string](http://www.w3.org/2001/XMLSchema#string) +Colon goblet cells are a subset of intestinal goblet cells that are localized in the epithelial lining of the colon. They are specialized secretory epithelial cells that are recognized by their characteristic ‘goblet’ or flask-like shape and typically have a distinctive appearance due to the accumulation of secretory vesicles in their cytoplasm. +The primary function of goblet cells is the secretion of mucus, which is an essential substance for the protection and successful functioning of the intestinal tract. In the colon, goblet cells continuously renew the inner mucus layer, which is attached and impervious to bacteria (the outer layer of the colon is unattached and is the habitat of commensal bacteria) +The mucus secreted by goblet cells is rich in glycoproteins known as mucins, especially MUC2, forming a complex web of molecules that comprises the foundational structure of the mucus layer. It traps and eliminates harmful bacteria, while selectively allowing beneficial microbiota to access the epithelial surface and aid in digestion and nutrient absorption. The mucus layer not only provides a provides a protective barrier against pathogen invasion, as well as mechanical damage, and the erosive effects of digestive enzymes, it also acts as a lubricant to facilitate the passage of food material. +Colon goblet cells are also involved in regulating the local immune response within the gut, maintaining the delicate balance between necessary immune reactions to harmful pathogens and tolerance to beneficial microbiota and dietary substances. Goblet cells can modulate immune responses by presenting antigens to dendritic cells, as well as through the production of immunomodulatory molecules that can alter the behavior of immune cells. When the inner mucus layer of the colon is defective, it might be a pathophysiological mechanism for colitis and infectious diseases."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1038/mi.2015.32"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [intestinal villus capillary endothelial cell](http://purl.obolibrary.org/obo/CL_4052003) [has_broad_synonym](http://www.geneontology.org/formats/oboInOwl#hasBroadSynonym) "villus blood capillary endothelial cells"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:35810168"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1038/s41385-018-0039-y"^^[string](http://www.w3.org/2001/XMLSchema#string) -- Class: [intestinal villus capillary endothelial cell](http://purl.obolibrary.org/obo/CL_4052003) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1038/nrgastro.2013.35"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [intestinal villus capillary endothelial cell](http://purl.obolibrary.org/obo/CL_4052003) EquivalentTo [capillary endothelial cell](http://purl.obolibrary.org/obo/CL_0002144) and ([BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0001213](http://purl.obolibrary.org/obo/UBERON_0001213)) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1038/mi.2016.132"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [intestinal villus capillary endothelial cell](http://purl.obolibrary.org/obo/CL_4052003) SubClassOf [fenestrated endothelial cell](http://purl.obolibrary.org/obo/CL_0000666) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1073/pnas.1006451107"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [intestinal villus capillary endothelial cell](http://purl.obolibrary.org/obo/CL_4052003) SubClassOf [capillary endothelial cell](http://purl.obolibrary.org/obo/CL_0002144) +- [colon goblet cell](http://purl.obolibrary.org/obo/CL_0009039) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://cellxgene.cziscience.com/cellguide/CL_0009039"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [intestinal villus capillary endothelial cell](http://purl.obolibrary.org/obo/CL_4052003) SubClassOf [BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0001213](http://purl.obolibrary.org/obo/UBERON_0001213) +- [colon goblet cell](http://purl.obolibrary.org/obo/CL_0009039) EquivalentTo [goblet cell](http://purl.obolibrary.org/obo/CL_0000160) and ([BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0000397](http://purl.obolibrary.org/obo/UBERON_0000397)) -### intrahepatic cholangiocyte `http://purl.obolibrary.org/obo/CL_0002538` +### colon macrophage `http://purl.obolibrary.org/obo/CL_0009038` #### Added -- [intrahepatic cholangiocyte](http://purl.obolibrary.org/obo/CL_0002538) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. +- [colon macrophage](http://purl.obolibrary.org/obo/CL_0009038) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://cellxgene.cziscience.com/cellguide/CL_0009038"^^[string](http://www.w3.org/2001/XMLSchema#string) -Intrahepatic cholangiocytes represent a subset of the biliary epithelial cells that form a network of tubes in the liver called the biliary tree The intrahepatic cholangiocytes reside specifically in the intrahepatic bile ducts and play a crucial role in liver physiology and bile production and secretion, thereby aiding in the digestion and absorption of fats in the small intestine. These specific cholangiocytes arise from bipotent hepatoblasts, whereas extrahepatic cholangiocytes share an embryologic origin with the ventral pancreas. -Recent research suggests that there is also heterogeneity within populations of intrahepatic cholangiocytes with different transcriptional profiles, proliferative capacity, and biological function; for example, subpopulations differ in calcium-mobilizing receptors. -The primary function of intrahepatic cholangiocytes is related to bile formation and maintenance of its flow. In addition to their secretory and absorptive activities, they are involved in the regulation of bile composition, volume, and alkalinization, contributing to the neutralization of the acidic chyme (partly digested food) that enters the intestine from the stomach. Intrahepatic cholangiocytes are also recognized for their role in liver regeneration and repair, often proliferating in response to injury. -Intrahepatic cholangiocytes take part in certain pathological conditions, like primary biliary cirrhosis and cholangiocarcinoma. Changes in these cells often lead to abnormalities in bile formation and transport, causing cholestatic liver diseases. Overall, the primary and secondary functional activities of intrahepatic cholangiocytes are vital in maintaining liver function, digestive processes, and contributing to the body's response to liver injury."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1016/j.ajpath.2023.02.012"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [colon macrophage](http://purl.obolibrary.org/obo/CL_0009038) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1002/hep.31252"^^[string](http://www.w3.org/2001/XMLSchema#string) +Colon macrophages are a heterogeneous population of macrophages in the gastrointestinal tract. Intestinal macrophages represent the largest group of macrophages in the body and play a key role as sentinels for pathogen recognition and elimination. Because the gastrointestinal tract is continually exposed to a high antigenic load derived from microbes and food intake, macrophages in the intestines are crucial not only for the gut’s immune defense but also for maintaining gastrointestinal homeostasis, avoiding chronic inflammation despite constantly facing foreign antigens. The phenotypic profiles and cytokine production of intestinal macrophages therefore differ from conventional macrophages elsewhere in the body. +Colon macrophages orchestrate a wide variety of immune responses. They interact with the colon’s microflora thanks to their location in the mucosal layer, thus playing an important role in shaping gut immunity. By presenting antigens, they help to activate and steer an appropriate immune response either by triggering inflammation against harmful pathogens or by supporting tolerance for beneficial microbes. Therefore, disturbances in the colon macrophage population is thought to contribute to colon-related diseases such as inflammatory bowel disease and colon cancer. +These immune cells are versatile and multifunctional, not just limited to defensive actions. Colon macrophages interact with the enteric nervous system to regulate gut secretion and motility. They also play a crucial role in maintaining colon tissue health and integrity by contributing to tissue repair processes. This occurs either through phagocytosis of dead cells and remnants, or indirectly through the release of growth factor molecules, which stimulate cellular proliferation and differentiation necessary for tissue regeneration."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1038/s41575-023-00769-0"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1016/j.gastha.2022.07.015"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1038/s41575-019-0172-4"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1016/j.biocel.2010.06.020"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1016/j.immuni.2022.08.005"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [intrahepatic cholangiocyte](http://purl.obolibrary.org/obo/CL_0002538) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://cellxgene.cziscience.com/cellguide/CL_0002538"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1016/j.jcmgh.2021.08.021"^^[string](http://www.w3.org/2001/XMLSchema#string) -### invertebrate nurse cell `http://purl.obolibrary.org/obo/CL_0000026` +### colonocyte `http://purl.obolibrary.org/obo/CL_1000347` +#### Removed +- [colonocyte](http://purl.obolibrary.org/obo/CL_1000347) [has_exact_synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "colonocyte"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:34497389"^^[string](http://www.w3.org/2001/XMLSchema#string) -#### Added -- [invertebrate nurse cell](http://purl.obolibrary.org/obo/CL_0000026) SubClassOf [eukaryotic cell](http://purl.obolibrary.org/obo/CL_0000255) +- [colonocyte](http://purl.obolibrary.org/obo/CL_1000347) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. +Enterocytes of the colon are specialized epithelial cells located in the lining of the colon, the largest part of the large intestine. These cells play a critical role in absorbing water, electrolytes, and certain vitamins from the food material passed on from the small intestine. With a unique structure of finger-like protrusions referred to as microvilli, the enterocytes increase their surface area for effective absorption. The colon is the last part of the digestive system, and as such, it is responsible for compacting undigested food materials and forming fecal matter. Enterocytes of the colon facilitate this process effectively through absorption of water. +Enterocytes are known for their high regeneration potential, replenishing every 4-5 days, enabling the healthy functioning of the colon. They originate from stem cells located in the crypt of the colon and differentiate into mature enterocytes as they migrate upwards towards the luminal surface. This constant turnover aids in maintaining the intestinal barrier, preventing the entry of detrimental substances into the systemic circulation. Their tight junctions with other epithelial cells provide a robust barrier against invasive pathogens. +Enterocytes of the colon are involved in the communication with the gut microbiota. These cells harbor enzymes necessary for the metabolism of short-chain fatty acids, which are the byproducts of the fermentation process by gut bacteria. Short-chain fatty acids serve as a major energy source for colonocytes and are important for maintaining colonic health. The dysfunction of enterocytes, therefore, could lead to disorders such as inflammatory bowel disease or colorectal cancer."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1038/nrgastro.2013.35"^^[string](http://www.w3.org/2001/XMLSchema#string) -### ionocyte `http://purl.obolibrary.org/obo/CL_0005006` + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1038/nri3738"^^[string](http://www.w3.org/2001/XMLSchema#string) -#### Added -- [ionocyte](http://purl.obolibrary.org/obo/CL_0005006) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1084/jem.20191130"^^[string](http://www.w3.org/2001/XMLSchema#string) -Ionocytes are specialized cells predominantly found in the mammalian respiratory and renal systems as well as in the gills, skin, and intestinal tract of fish. These cells play crucial roles in maintaining ion and acid-base homeostasis. Ionocytes demonstrate remarkable plasticity and are able to adapt themselves in response to changes in environmental conditions such as pH, salinity, ion concentration, and temperature. -These cells work by selectively absorbing specific ions from the environment, thus maintaining the body's internal ionic balance. The most commonly absorbed ions include sodium (Na+), chloride (Cl-), calcium (Ca2+), and hydrogen (H+). Moreover, ionocytes contribute to acid-base regulation. In response to acidosis or alkalosis, ionocytes can either excrete or retain hydrogen (H+) and bicarbonate (HCO3-) ions to readjust the blood pH. Further, experimental evidence suggests a functional complexity of ionocytes, implying diverse roles beyond ion regulation. Recent research highlights ionocytes' involvement in ammonia excretion and the regulation of extracellular fluid volume, highlighting their contribution to the overall homeostatic process. -Malfunctioning ionocytes have been implicated in various diseases, including cystic fibrosis which is caused by mutations in the chloride channel CFTR, an ionocyte marker."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1146/annurev-pathol-042420-094031"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.3389/fimmu.2019.00277"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1016/j.jcf.2019.09.010"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1007/s11894-010-0130-3"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1038/s41586-018-0393-7"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [colonocyte](http://purl.obolibrary.org/obo/CL_1000347) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A columnar cell of the colon that is part of the colonic epithelium."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:tfm"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1038/s41598-023-30603-1"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [colonocyte](http://purl.obolibrary.org/obo/CL_1000347) SubClassOf [enterocyte of epithelium of large intestine](http://purl.obolibrary.org/obo/CL_0002071) + - [is_inferred](http://www.geneontology.org/formats/oboInOwl#is_inferred) "true"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.3389/fmars.2020.00709"^^[string](http://www.w3.org/2001/XMLSchema#string) +#### Added +- [colonocyte](http://purl.obolibrary.org/obo/CL_1000347) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Enterocytes of the colon are specialized epithelial cells located in the lining of the colon, the largest part of the large intestine. These cells play a critical role in absorbing water, electrolytes, and certain vitamins from the food material passed on from the small intestine. With a unique structure of finger-like protrusions referred to as microvilli, the enterocytes increase their surface area for effective absorption. The colon is the last part of the digestive system, and as such, it is responsible for compacting undigested food materials and forming fecal matter. Enterocytes of the colon facilitate this process effectively through absorption of water. +Enterocytes are known for their high regeneration potential, replenishing every 4-5 days, enabling the healthy functioning of the colon. They originate from stem cells located in the crypt of the colon and differentiate into mature enterocytes as they migrate upwards towards the luminal surface. This constant turnover aids in maintaining the intestinal barrier, preventing the entry of detrimental substances into the systemic circulation. Their tight junctions with other epithelial cells provide a robust barrier against invasive pathogens. +Enterocytes of the colon are involved in the communication with the gut microbiota. These cells harbor enzymes necessary for the metabolism of short-chain fatty acids, which are the byproducts of the fermentation process by gut bacteria. Short-chain fatty acids serve as a major energy source for colonocytes and are important for maintaining colonic health. The dysfunction of enterocytes, therefore, could lead to disorders such as inflammatory bowel disease or colorectal cancer."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1038/nrgastro.2013.35"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1038/nri3738"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [ionocyte](http://purl.obolibrary.org/obo/CL_0005006) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://cellxgene.cziscience.com/cellguide/CL_0005006"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1084/jem.20191130"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.3389/fimmu.2019.00277"^^[string](http://www.w3.org/2001/XMLSchema#string) -### iridophore `http://purl.obolibrary.org/obo/CL_0000431` + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1007/s11894-010-0130-3"^^[string](http://www.w3.org/2001/XMLSchema#string) -#### Added -- [iridophore](http://purl.obolibrary.org/obo/CL_0000431) SubClassOf [eukaryotic cell](http://purl.obolibrary.org/obo/CL_0000255) +- [colonocyte](http://purl.obolibrary.org/obo/CL_1000347) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "An enterocyte (absorptive epithelial cell) of the colonic epithelium, characterized by a columnar shape. This cell is responsible for the absorption, transport, and metabolization of short-chain fatty acids (SCFAs) produced by gut bacteria, as well as the transport and absorption of water and electrolytes."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:16870803"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:34497389"^^[string](http://www.w3.org/2001/XMLSchema#string) -### kidney afferent arteriole endothelial cell `http://purl.obolibrary.org/obo/CL_1001096` + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:23821742"^^[string](http://www.w3.org/2001/XMLSchema#string) -#### Added -- [kidney afferent arteriole endothelial cell](http://purl.obolibrary.org/obo/CL_1001096) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:tfm"^^[string](http://www.w3.org/2001/XMLSchema#string) -Kidney afferent arteriole endothelial cells are a specialized type of cell located within the kidneys, forming the inner lining of the afferent arterioles, which are responsible for delivering blood to the glomeruli - capillary networks responsible for filtration - from where the process of urine formation begins in the nephrons. -The endothelial cells in the kidney afferent arterioles have a key function in regulating the blood flow and filtration. They have autocrine and paracrine signaling capabilities, meaning they can signal to themselves and other nearby cells. They produce nitric oxide, prostacyclin, and endothelin, which are powerful vasodilators and vasoconstrictors that regulate renal blood flow. These cells also engage in the mitigation of kidney injury and inflammation by promoting repair and regeneration, demonstrating the multifaceted roles these cells play in maintaining renal health."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1046/j.0001-6772.2003.01205.x"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [colonocyte](http://purl.obolibrary.org/obo/CL_1000347) SubClassOf [RO_0002215](http://purl.obolibrary.org/obo/RO_0002215) some [GO_0035377](http://purl.obolibrary.org/obo/GO_0035377) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1093/ndt/gfl308"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [colonocyte](http://purl.obolibrary.org/obo/CL_1000347) SubClassOf [enterocyte of epithelium of large intestine](http://purl.obolibrary.org/obo/CL_0002071) -- [kidney afferent arteriole endothelial cell](http://purl.obolibrary.org/obo/CL_1001096) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://cellxgene.cziscience.com/cellguide/CL_1001096"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [colonocyte](http://purl.obolibrary.org/obo/CL_1000347) SubClassOf [RO_0002215](http://purl.obolibrary.org/obo/RO_0002215) some [GO_0019626](http://purl.obolibrary.org/obo/GO_0019626) -### kidney cell `http://purl.obolibrary.org/obo/CL_1000497` +### columnar neuron `http://purl.obolibrary.org/obo/CL_0000112` #### Removed -- [kidney cell](http://purl.obolibrary.org/obo/CL_1000497) SubClassOf [cell](http://purl.obolibrary.org/obo/CL_0000000) +- [columnar neuron](http://purl.obolibrary.org/obo/CL_0000112) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "columnar neuron"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [columnar neuron](http://purl.obolibrary.org/obo/CL_0000112) SubClassOf [neuron](http://purl.obolibrary.org/obo/CL_0000540) #### Added -- [kidney cell](http://purl.obolibrary.org/obo/CL_1000497) SubClassOf [eukaryotic cell](http://purl.obolibrary.org/obo/CL_0000255) +- [columnar neuron](http://purl.obolibrary.org/obo/CL_0000112) [comment](http://www.w3.org/2000/01/rdf-schema#comment) "Columnar neurons have been widely studied in Diptera, locusts, honey bees and other insects. In the mammalian brain, a "columnar organisation" is referred to neurons of the neocortex, however these differ from columnar neurons which are found in the insects central nervous system."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:9153131"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:32374034"^^[string](http://www.w3.org/2001/XMLSchema#string) -### kidney collecting duct alpha-intercalated cell `http://purl.obolibrary.org/obo/CL_4030015` -#### Removed -- [kidney collecting duct alpha-intercalated cell](http://purl.obolibrary.org/obo/CL_4030015) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A renal alpha-intercalated cell that is part of the collecting duct of the renal tubule."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [contributor](http://purl.org/dc/terms/contributor) "https://orcid.org/0000-0003-2804-127X"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:34696823"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:31249312"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:18837039"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:9890303"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:37608556"^^[string](http://www.w3.org/2001/XMLSchema#string) -#### Added -- [kidney collecting duct alpha-intercalated cell](http://purl.obolibrary.org/obo/CL_4030015) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A renal alpha-intercalated cell that is part of the collecting duct of the renal tubule."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:31249312"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [columnar neuron](http://purl.obolibrary.org/obo/CL_0000112) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A neuron of the invertebrate central nervous system. This neuron innervates the central complex (CX) of an invertebrate brain and it forms columnar patterns with its dendrites. It is involved in navigation and spatial processing."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:34696823"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:9890303"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:37608556"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [kidney collecting duct alpha-intercalated cell](http://purl.obolibrary.org/obo/CL_4030015) [contributor](http://purl.org/dc/terms/contributor) [X](https://orcid.org/0000-0003-2804-127X) +- [columnar neuron](http://purl.obolibrary.org/obo/CL_0000112) SubClassOf [CNS neuron (sensu Nematoda and Protostomia)](http://purl.obolibrary.org/obo/CL_0000028) +- [columnar neuron](http://purl.obolibrary.org/obo/CL_0000112) SubClassOf [RO_0002215](http://purl.obolibrary.org/obo/RO_0002215) some [GO_0007601](http://purl.obolibrary.org/obo/GO_0007601) -### kidney collecting duct epithelial cell `http://purl.obolibrary.org/obo/CL_1000454` +- [columnar neuron](http://purl.obolibrary.org/obo/CL_0000112) SubClassOf [visual system neuron](http://purl.obolibrary.org/obo/CL_0008028) + + +### commissural neuron `http://purl.obolibrary.org/obo/CL_0000678` +#### Removed +- [commissural neuron](http://purl.obolibrary.org/obo/CL_0000678) SubClassOf [neuron](http://purl.obolibrary.org/obo/CL_0000540) #### Added -- [kidney collecting duct epithelial cell](http://purl.obolibrary.org/obo/CL_1000454) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. +- [commissural neuron](http://purl.obolibrary.org/obo/CL_0000678) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A neuron with soma location in the central nervous system that project its axon to the contralateral side of a central nervous system. This neuron can have its soma in the spinal cord, in the hemisphere of the brain, in the retina or in the ventral nerve cord of invertebrates."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:17560562"^^[string](http://www.w3.org/2001/XMLSchema#string) -Kidney collecting duct epithelial cells are a specialized type of cells that form an integral part of the renal system. Located in the collecting duct system of the kidneys, these cells are responsible for one of the final steps in the process of urine formation, and they are instrumental in the fine tuning of the volume and composition of urine by reabsorbing water and certain solutes back into the bloodstream. -These cells express specific channels and carriers that actively and passively transport ions and water. They also have channels on their membranes, such as sodium channels and potassium channels, involved in reabsorbing or secreting these electrolytes depending upon the body's needs. The function of renal collecting duct epithelial cells can be regulated by a variety of hormones, including vasopressin (antidiuretic hormone), which can modulate the ion channels and carriers and hence indirectly influence body fluid homeostasis. -Aside from their function in ion and water balance, kidney collecting duct epithelial cells also aid in maintaining the body's acid-base balance. They have specialized functionality to secret hydrogen ions into the tubular lumen, which contributes to acid excretion. Any dysfunction may have serious implications and lead to various renal or systemic diseases, exemplifying the importance of these cells in maintaining overall body homeostasis."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.2215/CJN.05760513"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:31693445"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1016/j.semnephrol.2019.04.005"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [commissural neuron](http://purl.obolibrary.org/obo/CL_0000678) [comment](http://www.w3.org/2000/01/rdf-schema#comment) "Historically, commissural neurons, particularly in the spinal cord, have been used as a model to understand axon guidance during development."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:31514748"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1016/j.ajpath.2014.01.014"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:27532244"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.2215/CJN.08880914"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:33438755"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [kidney collecting duct epithelial cell](http://purl.obolibrary.org/obo/CL_1000454) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://cellxgene.cziscience.com/cellguide/CL_1000454"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:25960414"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [commissural neuron](http://purl.obolibrary.org/obo/CL_0000678) SubClassOf [central nervous system neuron](http://purl.obolibrary.org/obo/CL_2000029) -### kidney collecting duct principal cell `http://purl.obolibrary.org/obo/CL_1001431` -#### Added -- [kidney collecting duct principal cell](http://purl.obolibrary.org/obo/CL_1001431) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://cellxgene.cziscience.com/cellguide/CL_1001431"^^[string](http://www.w3.org/2001/XMLSchema#string) +### common dendritic progenitor `http://purl.obolibrary.org/obo/CL_0001029` +#### Removed +- [common dendritic progenitor](http://purl.obolibrary.org/obo/CL_0001029) SubClassOf [myeloid cell](http://purl.obolibrary.org/obo/CL_0000763) -- [kidney collecting duct principal cell](http://purl.obolibrary.org/obo/CL_1001431) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. +- [common dendritic progenitor](http://purl.obolibrary.org/obo/CL_0001029) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) -The kidney collecting duct principal cell is a highly specialized type of cell found in the late distal convoluted tubule and collecting duct of the kidney's nephron. Principal cells are located at the final segments of the renal tubules, where they play a pivotal role in key homeostatic processes. -One of their fundamental functions of kidney collecting duct principal cells is the regulation of water reabsorption, which is mediated by aquaporins (water channel proteins). Antidiuretic hormones, such as vasopressin, can stimulate the redistribution of these water channels from an intracellular pools to the apical plasma membrane of the principal cell; translocation of aquaporin (specifically, AQP2) is associated with an increase of osmotic water permeability. The water reabsorption affects the concentration of the final urine; these cells are therefore directly involved in the maintenance of the body's fluid balance. -Kidney collecting duct principal cells also participate in sodium and potassium ions regulation. They reabsorb sodium ions from the tubular fluid back into the bloodstream, a process facilitated by the action of aldosterone, a hormone released by the adrenal glands. Similarly, the principal cells secrete potassium ions into the tubular fluid in response to aldosterone, contributing to the regulation of potassium levels in the body. Impaired function of cells can lead to various renal diseases and disorders, highlighting the vital role of kidney collecting duct principal cells in the body's homeostatic processes."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1007/s11906-015-0538-0"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1073/pnas.1710964114"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1016/B978-0-12-386456-7.05402-2"^^[string](http://www.w3.org/2001/XMLSchema#string) +### common myeloid progenitor, CD34-positive `http://purl.obolibrary.org/obo/CL_0001059` +#### Removed +- [common myeloid progenitor, CD34-positive](http://purl.obolibrary.org/obo/CL_0001059) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1016/j.biocel.2022.106261"^^[string](http://www.w3.org/2001/XMLSchema#string) -### kidney efferent arteriole endothelial cell `http://purl.obolibrary.org/obo/CL_1001099` +### cone retinal bipolar cell `http://purl.obolibrary.org/obo/CL_0000752` #### Added -- [kidney efferent arteriole endothelial cell](http://purl.obolibrary.org/obo/CL_1001099) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://cellxgene.cziscience.com/cellguide/CL_1001099"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [cone retinal bipolar cell](http://purl.obolibrary.org/obo/CL_0000752) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl/cl-base#cellxgene_subset) -- [kidney efferent arteriole endothelial cell](http://purl.obolibrary.org/obo/CL_1001099) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. -Kidney efferent arteriole endothelial cells constitute a vital component of the kidney's microvascular system. They are unique endothelial cells found lining the walls of efferent arterioles, which transport blood away from the glomeruli in the kidney. -The primary responsibilities of the kidney efferent arteriole endothelial cells involve controling renal blood flow, regulating glomerular filtration rate (GFR), and managing perfusion pressure. They do this by contracting and relaxing, effectively narrowing and widening the arteriole's lumen thereby controling the volume and rate of blood flow to the peritubular capillaries and creating the pressure gradient necessary for filtration in the glomerulus. -Furthermore, kidney efferent arteriole endothelial cells show a high degree of plasticity in response to pathophysiological stimuli and can undergo structural and functional changes based on local needs. In conditions like hypertension and diabetes, these cells can experience hypertrophy and endothelial dysfunction, contributing to the progression of renal disease."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1016/j.semcdb.2014.08.002"^^[string](http://www.w3.org/2001/XMLSchema#string) +### conjunctiva goblet cell `http://purl.obolibrary.org/obo/CL_2000084` - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1038/s41581-021-00411-9"^^[string](http://www.w3.org/2001/XMLSchema#string) +#### Added +- [conjunctiva goblet cell](http://purl.obolibrary.org/obo/CL_2000084) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl/cl-base#cellxgene_subset) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1681/ASN.2019111179"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1016/j.semnephrol.2015.01.010"^^[string](http://www.w3.org/2001/XMLSchema#string) +### cortical granule cell `http://purl.obolibrary.org/obo/CL_0001032` +#### Removed +- [cortical granule cell](http://purl.obolibrary.org/obo/CL_0001032) SubClassOf [neuron of the forebrain](http://purl.obolibrary.org/obo/CL_0012001) -### kidney loop of Henle short descending thin limb epithelial cell `http://purl.obolibrary.org/obo/CL_4030012` -#### Removed -- [kidney loop of Henle short descending thin limb epithelial cell](http://purl.obolibrary.org/obo/CL_4030012) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "Epithelial cell of the descending thin limb of the short loop (cortical) nephron limited to the outer medulla (mainly inner strip). It is known in some mammalian species that the short descending limb of the loop of Henle selectively expresses the serine protease Corin, the homeobox TF Uncx, and the urea channel Slc14a2."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [contributor](http://purl.org/dc/terms/contributor) "https://orcid.org/0000-0003-2804-127X"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:33769951"^^[string](http://www.w3.org/2001/XMLSchema#string) +### cortical immature neuron `http://purl.obolibrary.org/obo/CL_4042029` #### Added -- [kidney loop of Henle short descending thin limb epithelial cell](http://purl.obolibrary.org/obo/CL_4030012) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "Epithelial cell of the descending thin limb of the short loop (cortical) nephron limited to the outer medulla (mainly inner strip). It is known in some mammalian species that the short descending limb of the loop of Henle selectively expresses the serine protease Corin, the homeobox TF Uncx, and the urea channel Slc14a2."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:33769951"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [cortical immature neuron](http://purl.obolibrary.org/obo/CL_4042029) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "cIN"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003000](http://purl.obolibrary.org/obo/OMO_0003000) -- [kidney loop of Henle short descending thin limb epithelial cell](http://purl.obolibrary.org/obo/CL_4030012) [contributor](http://purl.org/dc/terms/contributor) [X](https://orcid.org/0000-0003-2804-127X) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:37833544"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [kidney loop of Henle short descending thin limb epithelial cell](http://purl.obolibrary.org/obo/CL_4030012) SubClassOf [squamous epithelial cell](http://purl.obolibrary.org/obo/CL_0000076) +- [cortical immature neuron](http://purl.obolibrary.org/obo/CL_4042029) [date](http://purl.org/dc/terms/date) "2024-10-10T09:14:54Z"^^[dateTime](http://www.w3.org/2001/XMLSchema#dateTime) +- [cortical immature neuron](http://purl.obolibrary.org/obo/CL_4042029) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "An immature neuron of a cerebral cortex. This neuron develops prenatally and remains in an immature state throughout the lifespan of the organism."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:37833544"^^[string](http://www.w3.org/2001/XMLSchema#string) -### lamp5 GABAergic cortical interneuron `http://purl.obolibrary.org/obo/CL_4023011` -#### Removed -- [lamp5 GABAergic cortical interneuron](http://purl.obolibrary.org/obo/CL_4023011) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A GABAergic neuron located in the cerebral cortex that expresses Lamp5"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:30382198"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [cortical immature neuron](http://purl.obolibrary.org/obo/CL_4042029) [id](http://www.geneontology.org/formats/oboInOwl#id) "CL:4042029"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:37824655"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [cortical immature neuron](http://purl.obolibrary.org/obo/CL_4042029) [label](http://www.w3.org/2000/01/rdf-schema#label) "cortical immature neuron"^^[string](http://www.w3.org/2001/XMLSchema#string) -#### Added -- [lamp5 GABAergic cortical interneuron](http://purl.obolibrary.org/obo/CL_4023011) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A transcriptomically distinct GABAergic neuron located in the cerebral cortex that expresses Lamp5. The standard transcriptomic reference data for this cell type can be found on the CellxGene census under the collection: 'Transcriptomic cytoarchitecture reveals principles of human neocortex organization', dataset: 'Supercluster: CGE-derived interneurons', Author Categories: 'CrossArea_subclass', clusters Lamp5."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://cellxgene.cziscience.com/e/e4ddac12-f48f-4455-8e8d-c2a48a683437.cxg/"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [cortical immature neuron](http://purl.obolibrary.org/obo/CL_4042029) [contributor](http://purl.org/dc/terms/contributor) [0000-0002-0098-8958](https://orcid.org/0000-0002-0098-8958) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:30382198"^^[string](http://www.w3.org/2001/XMLSchema#string) +- Class: [cortical immature neuron](http://purl.obolibrary.org/obo/CL_4042029) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:37824655"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [cortical immature neuron](http://purl.obolibrary.org/obo/CL_4042029) SubClassOf [immature neuron](http://purl.obolibrary.org/obo/CL_4042028) +- [cortical immature neuron](http://purl.obolibrary.org/obo/CL_4042029) SubClassOf [BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0000956](http://purl.obolibrary.org/obo/UBERON_0000956) -### larval midgut cell `http://purl.obolibrary.org/obo/CL_0009003` + +### cortical interneuron `http://purl.obolibrary.org/obo/CL_0008031` #### Removed -- [larval midgut cell](http://purl.obolibrary.org/obo/CL_0009003) SubClassOf [cell](http://purl.obolibrary.org/obo/CL_0000000) +- [cortical interneuron](http://purl.obolibrary.org/obo/CL_0008031) SubClassOf [obsolete CNS interneuron](http://purl.obolibrary.org/obo/CL_0000402) #### Added -- [larval midgut cell](http://purl.obolibrary.org/obo/CL_0009003) SubClassOf [eukaryotic cell](http://purl.obolibrary.org/obo/CL_0000255) +- [cortical interneuron](http://purl.obolibrary.org/obo/CL_0008031) SubClassOf [interneuron](http://purl.obolibrary.org/obo/CL_0000099) -### leucophore `http://purl.obolibrary.org/obo/CL_0000571` +### cortical thymic epithelial cell `http://purl.obolibrary.org/obo/CL_0002364` #### Added -- [leucophore](http://purl.obolibrary.org/obo/CL_0000571) SubClassOf [eukaryotic cell](http://purl.obolibrary.org/obo/CL_0000255) +- [cortical thymic epithelial cell](http://purl.obolibrary.org/obo/CL_0002364) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://cellxgene.cziscience.com/cellguide/CL_0002364"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [cortical thymic epithelial cell](http://purl.obolibrary.org/obo/CL_0002364) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. -### leukocyte `http://purl.obolibrary.org/obo/CL_0000738` -#### Removed -- [leukocyte](http://purl.obolibrary.org/obo/CL_0000738) SubClassOf [RO_0002160](http://purl.obolibrary.org/obo/RO_0002160) some [NCBITaxon_7742](http://purl.obolibrary.org/obo/NCBITaxon_7742) +Cortical thymic epithelial cells (cTECs) are a vital cell type located in the thymus, a lymphoid organ that plays a key role in the development of T cells, which are essential for the adaptive immune system. cTECs also have a role in forming barriers and lining surfaces. In the thymus, their presence contributes to the distinctive architecture of both the cortex and medulla. +cTECs also play a significant part in the selection and development of T cells. During T cell maturation, these cells express both self and non-self proteins via the major histocompatibility complex (MHC) to immature T cells. cTECs then stimulate the T cells that can recognize such proteins, an important event known as positive selection. This process aids in the creation of a diverse T cell receptor (TCR) repertoire that can react to a wide range of antigens, therefore ensuring effective immunity. +Apart from aiding in T cells' positive selection, cTECs also contribute to eliminating self-reactive T cells, a role essential in preventing autoimmune diseases. These cells induce an apoptosis-driven process known as "negative selection" which eliminates T cells that are too highly reactive to self-antigens."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1111/sji.13094"^^[string](http://www.w3.org/2001/XMLSchema#string) -#### Added -- [leukocyte](http://purl.obolibrary.org/obo/CL_0000738) SubClassOf [RO_0002162](http://purl.obolibrary.org/obo/RO_0002162) some [NCBITaxon_7742](http://purl.obolibrary.org/obo/NCBITaxon_7742) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1016/bs.ai.2014.09.003"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1038/nri3667"^^[string](http://www.w3.org/2001/XMLSchema#string) -### lower urinary tract cell `http://purl.obolibrary.org/obo/CL_1000600` +### corticothalamic VAL/VM projecting glutamatergic neuron of the primary motor cortex `http://purl.obolibrary.org/obo/CL_4023055` #### Removed -- [lower urinary tract cell](http://purl.obolibrary.org/obo/CL_1000600) SubClassOf [cell](http://purl.obolibrary.org/obo/CL_0000000) +- [corticothalamic VAL/VM projecting glutamatergic neuron of the primary motor cortex](http://purl.obolibrary.org/obo/CL_4023055) SubClassOf [RO_0000053](http://purl.obolibrary.org/obo/RO_0000053) some [PATO_0070019](http://purl.obolibrary.org/obo/PATO_0070019) #### Added -- [lower urinary tract cell](http://purl.obolibrary.org/obo/CL_1000600) SubClassOf [eukaryotic cell](http://purl.obolibrary.org/obo/CL_0000255) +- [corticothalamic VAL/VM projecting glutamatergic neuron of the primary motor cortex](http://purl.obolibrary.org/obo/CL_4023055) SubClassOf [untufted pyramidal neuron](http://purl.obolibrary.org/obo/CL_4023095) -### luminal hormone-sensing cell of mammary gland `http://purl.obolibrary.org/obo/CL_4033058` +### cranial motor neuron `http://purl.obolibrary.org/obo/CL_0015000` #### Added -- [luminal hormone-sensing cell of mammary gland](http://purl.obolibrary.org/obo/CL_4033058) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) +- [cranial motor neuron](http://purl.obolibrary.org/obo/CL_0015000) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl/cl-base#cellxgene_subset) -### lung ciliated cell `http://purl.obolibrary.org/obo/CL_1000271` +### created by `http://www.geneontology.org/formats/oboInOwl#created_by` #### Removed -- [lung ciliated cell](http://purl.obolibrary.org/obo/CL_1000271) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "Any ciliated cell that is part of some lung."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBC:Autogenerated"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [created by](http://www.geneontology.org/formats/oboInOwl#created_by) [label](http://www.w3.org/2000/01/rdf-schema#label) "created by"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [lung ciliated cell](http://purl.obolibrary.org/obo/CL_1000271) EquivalentTo [ciliated cell](http://purl.obolibrary.org/obo/CL_0000064) and ([BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0002048](http://purl.obolibrary.org/obo/UBERON_0002048)) +- AnnotationProperty: [created by](http://www.geneontology.org/formats/oboInOwl#created_by) -- [lung ciliated cell](http://purl.obolibrary.org/obo/CL_1000271) SubClassOf [BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0002048](http://purl.obolibrary.org/obo/UBERON_0002048) -#### Added -- [lung ciliated cell](http://purl.obolibrary.org/obo/CL_1000271) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "An epithelial cell that is part of the lung epithelium. This cell is characterised by the presence of cilia on its apical surface."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:27864314"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [lung ciliated cell](http://purl.obolibrary.org/obo/CL_1000271) EquivalentTo [ciliated epithelial cell](http://purl.obolibrary.org/obo/CL_0000067) and ([BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0000115](http://purl.obolibrary.org/obo/UBERON_0000115)) +### cycling B cell `http://purl.obolibrary.org/obo/CL_4033068` +#### Removed +- [cycling B cell](http://purl.obolibrary.org/obo/CL_4033068) [contributor](http://purl.org/dc/terms/contributor) [0000-0001-6677-8489](https://orcid.org/0000-0001-6677-8489) -- [lung ciliated cell](http://purl.obolibrary.org/obo/CL_1000271) SubClassOf [epithelial cell of lung](http://purl.obolibrary.org/obo/CL_0000082) +- [cycling B cell](http://purl.obolibrary.org/obo/CL_4033068) [date](http://purl.org/dc/terms/date) "2024-07-02T09:14:23Z"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [lung ciliated cell](http://purl.obolibrary.org/obo/CL_1000271) SubClassOf [ciliated epithelial cell](http://purl.obolibrary.org/obo/CL_0000067) -### lung goblet cell `http://purl.obolibrary.org/obo/CL_1000143` +### cycling CD4-positive, alpha-beta T cell `http://purl.obolibrary.org/obo/CL_4033075` +#### Removed +- [cycling CD4-positive, alpha-beta T cell](http://purl.obolibrary.org/obo/CL_4033075) [date](http://purl.org/dc/terms/date) "2024-07-02T09:14:23Z"^^[string](http://www.w3.org/2001/XMLSchema#string) -#### Added -- [lung goblet cell](http://purl.obolibrary.org/obo/CL_1000143) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. +- [cycling CD4-positive, alpha-beta T cell](http://purl.obolibrary.org/obo/CL_4033075) [contributor](http://purl.org/dc/terms/contributor) [0000-0001-6677-8489](https://orcid.org/0000-0001-6677-8489) -Lung goblet cells are critical components of the respiratory tract, specifically found in the bronchial segments. They are secretory epithelial cells known for their signature "goblet" or cup-like shape. Their primary function is to produce and secrete mucus that aids in trapping airborne particles and pathogens, preventing them from reaching the delicate environment of the lung. As part of the lung's epithelial lining, they act as frontline defenders, maintaining lung health and function. -The lung goblet cells are densely packed with granules containing mucin glycoproteins, the primary component of mucus. As mucus is produced and secreted, it moves towards the lumen of the lungs where the cilia, hair-like structures of the neighboring ciliated epithelial cells, help to navigate it upwards and out of the respiratory tract. This coordinated action ensures the expulsion of unwanted particles and pathogens, effectively cleaning the respiratory tract. -Dysfunction or abnormal proliferation of lung goblet cells can result in pathological conditions such as chronic obstructive pulmonary disorder (COPD) and asthma, where excessive mucus production leads to airway obstruction. Furthermore, lung goblet cells respond to a variety of stimuli, including toxins, allergens, irritants, and infections, adjusting their mucus production accordingly."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1159/000512268"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1038/s41385-018-0039-y"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1513/AnnalsATS.201802-128AW"^^[string](http://www.w3.org/2001/XMLSchema#string) +### cycling CD8-positive, alpha-beta T cell `http://purl.obolibrary.org/obo/CL_4033074` +#### Removed +- [cycling CD8-positive, alpha-beta T cell](http://purl.obolibrary.org/obo/CL_4033074) [date](http://purl.org/dc/terms/date) "2024-07-02T09:14:23Z"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1038/s41385-020-00370-7"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [cycling CD8-positive, alpha-beta T cell](http://purl.obolibrary.org/obo/CL_4033074) [contributor](http://purl.org/dc/terms/contributor) [0000-0001-6677-8489](https://orcid.org/0000-0001-6677-8489) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://www.ncbi.nlm.nih.gov/books/NBK553208/"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [lung goblet cell](http://purl.obolibrary.org/obo/CL_1000143) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://cellxgene.cziscience.com/cellguide/CL_1000143"^^[string](http://www.w3.org/2001/XMLSchema#string) +### cycling T cell `http://purl.obolibrary.org/obo/CL_4033069` +#### Removed +- [cycling T cell](http://purl.obolibrary.org/obo/CL_4033069) [date](http://purl.org/dc/terms/date) "2024-07-02T09:14:23Z"^^[string](http://www.w3.org/2001/XMLSchema#string) -### lung neuroendocrine cell `http://purl.obolibrary.org/obo/CL_1000223` +- [cycling T cell](http://purl.obolibrary.org/obo/CL_4033069) [contributor](http://purl.org/dc/terms/contributor) [0000-0001-6677-8489](https://orcid.org/0000-0001-6677-8489) -#### Added -- [lung neuroendocrine cell](http://purl.obolibrary.org/obo/CL_1000223) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://cellxgene.cziscience.com/cellguide/CL_1000223"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [lung neuroendocrine cell](http://purl.obolibrary.org/obo/CL_1000223) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. -Lung neuroendocrine cells, also commonly known as pulmonary neuroendocrine cells (PNECs), are predominantly located in the respiratory epithelium of the bronchial and bronchiolar airways in the lungs. These cells, characterised by their small size and granular appearance, have a distinctive morphology that sets them apart from other lung cells. They are considered part of the diffuse neuroendocrine system due to their scattered distribution through the epithelium and have been classified into solitary cells and clustered forms known as neuroepithelial bodies. -The primary function of PNECs is linked to regulation and maintenance of the lung environment. They are sensory in nature and can secrete various bioactive substances such as serotonin, calcitonin, calcitonin gene-related peptides, and bombesin-like peptides which modulate airway smooth muscle tone and influence gut motility. For example, they act as oxygen sensors in response to hypoxia and are responsible for releasing neuropeptides that can induce responses. Moreover, PNECs provide an afferent function as they are equipped with long microvilli that project into the lumen of the bronchus and react to changes in the chemical composition of the luminal content."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1016/bs.ctdb.2018.12.002"^^[string](http://www.w3.org/2001/XMLSchema#string) +### cycling alveolar macrophage `http://purl.obolibrary.org/obo/CL_4033077` +#### Removed +- [cycling alveolar macrophage](http://purl.obolibrary.org/obo/CL_4033077) [contributor](http://purl.org/dc/terms/contributor) [0000-0001-6677-8489](https://orcid.org/0000-0001-6677-8489) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1016/j.devcel.2020.09.024"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [cycling alveolar macrophage](http://purl.obolibrary.org/obo/CL_4033077) [date](http://purl.org/dc/terms/date) "2024-07-02T09:14:23Z"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1242/dmm.046920"^^[string](http://www.w3.org/2001/XMLSchema#string) +#### Added +- [cycling alveolar macrophage](http://purl.obolibrary.org/obo/CL_4033077) [RO_0002175](http://purl.obolibrary.org/obo/RO_0002175) [NCBITaxon_9606](http://purl.obolibrary.org/obo/NCBITaxon_9606) +- [cycling alveolar macrophage](http://purl.obolibrary.org/obo/CL_4033077) [comment](http://www.w3.org/2000/01/rdf-schema#comment) "The marker set PCLAF, RRM2, UBE2C, NUSAP1 can identify the Human cell type cycling alveolar macrophage in the Lung with a confidence of 0.26 (NS-Forest FBeta value)."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://doi.org/10.5281/zenodo.11165918"^^[string](http://www.w3.org/2001/XMLSchema#string) -### lung secretory cell `http://purl.obolibrary.org/obo/CL_1000272` +- [cycling alveolar macrophage](http://purl.obolibrary.org/obo/CL_4033077) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [human_reference_atlas](http://purl.obolibrary.org/obo/cl/cl-base#human_reference_atlas) -#### Added -- [lung secretory cell](http://purl.obolibrary.org/obo/CL_1000272) SubClassOf [eukaryotic cell](http://purl.obolibrary.org/obo/CL_0000255) +- [cycling alveolar macrophage](http://purl.obolibrary.org/obo/CL_4033077) SubClassOf [RO_0015004](http://purl.obolibrary.org/obo/RO_0015004) some [CLM_1000006](http://purl.obolibrary.org/obo/CLM_1000006) -### lymph node macrophage `http://purl.obolibrary.org/obo/CL_0000868` +### cycling basal cell `http://purl.obolibrary.org/obo/CL_4033082` +#### Removed +- [cycling basal cell](http://purl.obolibrary.org/obo/CL_4033082) [contributor](http://purl.org/dc/terms/contributor) [0000-0001-6677-8489](https://orcid.org/0000-0001-6677-8489) -#### Added -- [lymph node macrophage](http://purl.obolibrary.org/obo/CL_0000868) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) +- [cycling basal cell](http://purl.obolibrary.org/obo/CL_4033082) [date](http://purl.org/dc/terms/date) "2024-07-02T09:14:23Z"^^[string](http://www.w3.org/2001/XMLSchema#string) -### lymphocyte of B lineage, CD19-positive `http://purl.obolibrary.org/obo/CL_0001200` -#### Added -- [lymphocyte of B lineage, CD19-positive](http://purl.obolibrary.org/obo/CL_0001200) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) +### cycling dendritic cell `http://purl.obolibrary.org/obo/CL_4033070` +#### Removed +- [cycling dendritic cell](http://purl.obolibrary.org/obo/CL_4033070) [date](http://purl.org/dc/terms/date) "2024-07-02T09:14:23Z"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [cycling dendritic cell](http://purl.obolibrary.org/obo/CL_4033070) [contributor](http://purl.org/dc/terms/contributor) [0000-0001-6677-8489](https://orcid.org/0000-0001-6677-8489) -### macrophage derived foam cell `http://purl.obolibrary.org/obo/CL_0000517` -#### Added -- [macrophage derived foam cell](http://purl.obolibrary.org/obo/CL_0000517) SubClassOf [eukaryotic cell](http://purl.obolibrary.org/obo/CL_0000255) +### cycling endothelial cell of lymphatic vessel `http://purl.obolibrary.org/obo/CL_4033079` +#### Removed +- [cycling endothelial cell of lymphatic vessel](http://purl.obolibrary.org/obo/CL_4033079) [contributor](http://purl.org/dc/terms/contributor) [0000-0001-6677-8489](https://orcid.org/0000-0001-6677-8489) -### malpighian tubule tip cell `http://purl.obolibrary.org/obo/CL_1000182` +- [cycling endothelial cell of lymphatic vessel](http://purl.obolibrary.org/obo/CL_4033079) [date](http://purl.org/dc/terms/date) "2024-07-02T09:14:23Z"^^[string](http://www.w3.org/2001/XMLSchema#string) -#### Added -- [malpighian tubule tip cell](http://purl.obolibrary.org/obo/CL_1000182) SubClassOf [eukaryotic cell](http://purl.obolibrary.org/obo/CL_0000255) -### mast cell `http://purl.obolibrary.org/obo/CL_0000097` +### cycling gamma-delta T cell `http://purl.obolibrary.org/obo/CL_4033072` +#### Removed +- [cycling gamma-delta T cell](http://purl.obolibrary.org/obo/CL_4033072) [date](http://purl.org/dc/terms/date) "2024-07-02T09:14:23Z"^^[string](http://www.w3.org/2001/XMLSchema#string) -#### Added -- [mast cell](http://purl.obolibrary.org/obo/CL_0000097) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) +- [cycling gamma-delta T cell](http://purl.obolibrary.org/obo/CL_4033072) [contributor](http://purl.org/dc/terms/contributor) [0000-0001-6677-8489](https://orcid.org/0000-0001-6677-8489) -### mast cell progenitor `http://purl.obolibrary.org/obo/CL_0000831` + +### cycling glial cell `http://purl.obolibrary.org/obo/CL_4047002` +#### Removed +- [cycling glial cell](http://purl.obolibrary.org/obo/CL_4047002) [date](http://purl.org/dc/terms/date) "2024-07-19T09:14:23Z"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [cycling glial cell](http://purl.obolibrary.org/obo/CL_4047002) [contributor](http://purl.org/dc/terms/contributor) [0009-0005-7919-4905](https://orcid.org/0009-0005-7919-4905) + + + +### cycling macrophage `http://purl.obolibrary.org/obo/CL_4033076` +#### Removed +- [cycling macrophage](http://purl.obolibrary.org/obo/CL_4033076) [contributor](http://purl.org/dc/terms/contributor) [0000-0001-6677-8489](https://orcid.org/0000-0001-6677-8489) + +- [cycling macrophage](http://purl.obolibrary.org/obo/CL_4033076) [date](http://purl.org/dc/terms/date) "2024-07-02T09:14:23Z"^^[string](http://www.w3.org/2001/XMLSchema#string) + + + +### cycling monocyte `http://purl.obolibrary.org/obo/CL_4033073` +#### Removed +- [cycling monocyte](http://purl.obolibrary.org/obo/CL_4033073) [contributor](http://purl.org/dc/terms/contributor) [0000-0001-6677-8489](https://orcid.org/0000-0001-6677-8489) + +- [cycling monocyte](http://purl.obolibrary.org/obo/CL_4033073) [date](http://purl.org/dc/terms/date) "2024-07-02T09:14:23Z"^^[string](http://www.w3.org/2001/XMLSchema#string) + + + +### cycling mononuclear phagocyte `http://purl.obolibrary.org/obo/CL_4033078` +#### Removed +- [cycling mononuclear phagocyte](http://purl.obolibrary.org/obo/CL_4033078) [contributor](http://purl.org/dc/terms/contributor) [0000-0001-6677-8489](https://orcid.org/0000-0001-6677-8489) + +- [cycling mononuclear phagocyte](http://purl.obolibrary.org/obo/CL_4033078) [date](http://purl.org/dc/terms/date) "2024-07-02T09:14:23Z"^^[string](http://www.w3.org/2001/XMLSchema#string) + + + +### cycling myeloid cell `http://purl.obolibrary.org/obo/CL_4033081` +#### Removed +- [cycling myeloid cell](http://purl.obolibrary.org/obo/CL_4033081) [contributor](http://purl.org/dc/terms/contributor) [0000-0001-6677-8489](https://orcid.org/0000-0001-6677-8489) + +- [cycling myeloid cell](http://purl.obolibrary.org/obo/CL_4033081) [date](http://purl.org/dc/terms/date) "2024-07-02T09:14:23Z"^^[string](http://www.w3.org/2001/XMLSchema#string) + + + +### cycling natural killer cell `http://purl.obolibrary.org/obo/CL_4033071` +#### Removed +- [cycling natural killer cell](http://purl.obolibrary.org/obo/CL_4033071) [date](http://purl.org/dc/terms/date) "2024-07-02T09:14:23Z"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [cycling natural killer cell](http://purl.obolibrary.org/obo/CL_4033071) [contributor](http://purl.org/dc/terms/contributor) [0000-0001-6677-8489](https://orcid.org/0000-0001-6677-8489) + + + +### cycling neuroblast (sensu Vertebrata) `http://purl.obolibrary.org/obo/CL_4047005` +#### Removed +- [cycling neuroblast (sensu Vertebrata)](http://purl.obolibrary.org/obo/CL_4047005) [contributor](http://purl.org/dc/terms/contributor) [0009-0005-7919-4905](https://orcid.org/0009-0005-7919-4905) + +- [cycling neuroblast (sensu Vertebrata)](http://purl.obolibrary.org/obo/CL_4047005) [date](http://purl.org/dc/terms/date) "2024-07-19T09:14:23Z"^^[string](http://www.w3.org/2001/XMLSchema#string) + + + +### cycling plasma cell `http://purl.obolibrary.org/obo/CL_4047003` +#### Removed +- [cycling plasma cell](http://purl.obolibrary.org/obo/CL_4047003) [date](http://purl.org/dc/terms/date) "2024-07-19T09:14:23Z"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [cycling plasma cell](http://purl.obolibrary.org/obo/CL_4047003) [contributor](http://purl.org/dc/terms/contributor) [0009-0005-7919-4905](https://orcid.org/0009-0005-7919-4905) + + + +### cycling pulmonary alveolar type 2 cell `http://purl.obolibrary.org/obo/CL_4033080` +#### Removed +- [cycling pulmonary alveolar type 2 cell](http://purl.obolibrary.org/obo/CL_4033080) [date](http://purl.org/dc/terms/date) "2024-07-02T09:14:23Z"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [cycling pulmonary alveolar type 2 cell](http://purl.obolibrary.org/obo/CL_4033080) [contributor](http://purl.org/dc/terms/contributor) [0000-0001-6677-8489](https://orcid.org/0000-0001-6677-8489) + +#### Added +- [cycling pulmonary alveolar type 2 cell](http://purl.obolibrary.org/obo/CL_4033080) [comment](http://www.w3.org/2000/01/rdf-schema#comment) "The marker set PEG10, PRC1, TOP2A can identify the Human cell type cycling pulmonary alveolar type 2 cell in the Lung with a confidence of 0.61 (NS-Forest FBeta value)."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://doi.org/10.5281/zenodo.11165918"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [cycling pulmonary alveolar type 2 cell](http://purl.obolibrary.org/obo/CL_4033080) [RO_0002175](http://purl.obolibrary.org/obo/RO_0002175) [NCBITaxon_9606](http://purl.obolibrary.org/obo/NCBITaxon_9606) + +- [cycling pulmonary alveolar type 2 cell](http://purl.obolibrary.org/obo/CL_4033080) SubClassOf [RO_0015004](http://purl.obolibrary.org/obo/RO_0015004) some [CLM_1000010](http://purl.obolibrary.org/obo/CLM_1000010) + + +### cycling stromal cell `http://purl.obolibrary.org/obo/CL_4047001` +#### Removed +- [cycling stromal cell](http://purl.obolibrary.org/obo/CL_4047001) [contributor](http://purl.org/dc/terms/contributor) [0009-0005-7919-4905](https://orcid.org/0009-0005-7919-4905) + +- [cycling stromal cell](http://purl.obolibrary.org/obo/CL_4047001) [date](http://purl.org/dc/terms/date) "2024-07-19T09:14:23Z"^^[string](http://www.w3.org/2001/XMLSchema#string) + + + +### cycling type EC enteroendocrine cell `http://purl.obolibrary.org/obo/CL_4047004` +#### Removed +- [cycling type EC enteroendocrine cell](http://purl.obolibrary.org/obo/CL_4047004) [contributor](http://purl.org/dc/terms/contributor) [0009-0005-7919-4905](https://orcid.org/0009-0005-7919-4905) + +- [cycling type EC enteroendocrine cell](http://purl.obolibrary.org/obo/CL_4047004) [date](http://purl.org/dc/terms/date) "2024-07-19T09:14:23Z"^^[string](http://www.w3.org/2001/XMLSchema#string) + + + +### decidual cell `http://purl.obolibrary.org/obo/CL_2000002` + +#### Added +- [decidual cell](http://purl.obolibrary.org/obo/CL_2000002) [has_exact_synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "decidualized endometrial stromal cell"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:31907034"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [decidual cell](http://purl.obolibrary.org/obo/CL_2000002) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://cellxgene.cziscience.com/cellguide/CL_2000002"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [decidual cell](http://purl.obolibrary.org/obo/CL_2000002) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Decidual cells, originating from the endometrial lining in the uterus, undergo significant transformations during pregnancy and are integral to its preparation and maintenance. Their conversion from endometrial fibroblast to a secretory phenotype, known as decidualization, occurs as a normal process in the menstrual cycle or in response to embryo implantation. +With crucial roles in regulating maternal immune responses and placental development, decidual cells have a twofold function: preventing rejection of the conceptus by the mother's immune system and guiding placental development to avoid excessive trophoblast invasion leading to pre-eclampsia. During decidualization, these cells secrete proteins and growth factors supporting embryo implantation and sustaining early pregnancy. Furthermore, decidual cells modulate the activities of natural killer cells, macrophages, and T cells in the uterus, maintaining a balance of pro-inflammatory and anti-inflammatory conditions during pregnancy."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1002/rmb2.12088"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1093/humupd/dmw004"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1111/j.1749-6632.2010.05938.x"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.3390/ijms21114092"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### decidual natural killer cell, human `http://purl.obolibrary.org/obo/CL_0002343` +#### Removed +- [decidual natural killer cell, human](http://purl.obolibrary.org/obo/CL_0002343) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) + +#### Added +- [decidual natural killer cell, human](http://purl.obolibrary.org/obo/CL_0002343) SubClassOf [uterine natural killer cell](http://purl.obolibrary.org/obo/CL_4052028) + +- [decidual natural killer cell, human](http://purl.obolibrary.org/obo/CL_0002343) SubClassOf [BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0002450](http://purl.obolibrary.org/obo/UBERON_0002450) + +- [decidual natural killer cell, human](http://purl.obolibrary.org/obo/CL_0002343) SubClassOf [extraembryonic cell](http://purl.obolibrary.org/obo/CL_0000349) + + +### decidual resident macrophage `http://purl.obolibrary.org/obo/CL_4033088` + +#### Added +- [decidual resident macrophage](http://purl.obolibrary.org/obo/CL_4033088) [contributor](http://purl.org/dc/terms/contributor) [0000-0001-7655-4833](https://orcid.org/0000-0001-7655-4833) + +- [decidual resident macrophage](http://purl.obolibrary.org/obo/CL_4033088) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A resident macrophage that is part of the decidua. Some decidual macrophages are derived from maternal blood monocytes that are recruited to the uterus shortly after conception. The main functions of a decidual macrophage are implantation, placental development, immune regulation and vascular remodeling."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:39007150"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [decidual resident macrophage](http://purl.obolibrary.org/obo/CL_4033088) [label](http://www.w3.org/2000/01/rdf-schema#label) "decidual resident macrophage"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [decidual resident macrophage](http://purl.obolibrary.org/obo/CL_4033088) [date](http://purl.org/dc/terms/date) "2024-10-31T10:33:04Z"^^[dateTime](http://www.w3.org/2001/XMLSchema#dateTime) + +- [decidual resident macrophage](http://purl.obolibrary.org/obo/CL_4033088) [has_broad_synonym](http://www.geneontology.org/formats/oboInOwl#hasBroadSynonym) "decidual macrophage"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:39007150"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [decidual resident macrophage](http://purl.obolibrary.org/obo/CL_4033088) [has_broad_synonym](http://www.geneontology.org/formats/oboInOwl#hasBroadSynonym) "maternal decidual macrophage"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:39007150"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [decidual resident macrophage](http://purl.obolibrary.org/obo/CL_4033088) [contributor](http://purl.org/dc/terms/contributor) [0000-0001-6677-8489](https://orcid.org/0000-0001-6677-8489) + +- [decidual resident macrophage](http://purl.obolibrary.org/obo/CL_4033088) [id](http://www.geneontology.org/formats/oboInOwl#id) "CL:4033088"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- Class: [decidual resident macrophage](http://purl.obolibrary.org/obo/CL_4033088) + +- [decidual resident macrophage](http://purl.obolibrary.org/obo/CL_4033088) SubClassOf [BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0002450](http://purl.obolibrary.org/obo/UBERON_0002450) + +- [decidual resident macrophage](http://purl.obolibrary.org/obo/CL_4033088) SubClassOf [placental resident macrophage](http://purl.obolibrary.org/obo/CL_4033087) + +- [decidual resident macrophage](http://purl.obolibrary.org/obo/CL_4033088) SubClassOf [extraembryonic cell](http://purl.obolibrary.org/obo/CL_0000349) + + +### dendritic cell `http://purl.obolibrary.org/obo/CL_0000451` +#### Removed +- [dendritic cell](http://purl.obolibrary.org/obo/CL_0000451) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) + + + +### dentate gyrus of hippocampal formation stellate cell `http://purl.obolibrary.org/obo/CL_2000090` +#### Removed +- [dentate gyrus of hippocampal formation stellate cell](http://purl.obolibrary.org/obo/CL_2000090) SubClassOf [neuron of the forebrain](http://purl.obolibrary.org/obo/CL_0012001) + + + +### dermis lymphatic vessel endothelial cell `http://purl.obolibrary.org/obo/CL_2000011` + +#### Added +- [dermis lymphatic vessel endothelial cell](http://purl.obolibrary.org/obo/CL_2000011) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://cellxgene.cziscience.com/cellguide/CL_2000011"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [dermis lymphatic vessel endothelial cell](http://purl.obolibrary.org/obo/CL_2000011) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +A dermis lymphatic vessel endothelial cell is a specialized type of cell that lines the interior surface of lymphatic vessels present in the dermal layer of the skin. These cells are organized into a single layer, forming an integral part of the lymphatic system which acts as the body's secondary circulatory system. The primary function of dermis lymphatic vessel endothelial cells is to facilitate the transportation and regulation of the lymph fluid within the dermis. They act as a barrier, contributing to fluid homeostasis, lipid transport, and immune cell trafficking. These cells are uniquely equipped to let fluid and larger molecules, including proteins and immune cells, into the lymphatic vessels from the surrounding interstitial space. This is enabled by the specialized junctions between the endothelial cells and the presence of primary lymphatic valves that prevent the backflow of lymph. +Another paramount role of dermis lymphatic vessel endothelial cells is their involvement in immune response. By interacting with white blood cells, especially T-cells and dendritic cells, they can mediate local immune surveillance and contribute to both innate and adaptive immune responses. These cells are also implicated in a variety of pathological conditions, including lymphedema and metastasis in cancer."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1038/s41467-019-14127-9"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.3389/fphys.2020.00509"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1038/s41423-023-01042-9"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.3389/fphys.2020.577584"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.3389/fimmu.2023.1235812"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### deuterosomal cell `http://purl.obolibrary.org/obo/CL_4033044` + +#### Added +- [deuterosomal cell](http://purl.obolibrary.org/obo/CL_4033044) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl/cl-base#cellxgene_subset) + +- [deuterosomal cell](http://purl.obolibrary.org/obo/CL_4033044) SubClassOf [RO_0002215](http://purl.obolibrary.org/obo/RO_0002215) some [GO_0098535](http://purl.obolibrary.org/obo/GO_0098535) + + +### diffuse bipolar 1 cell `http://purl.obolibrary.org/obo/CL_4033027` +#### Removed +- [diffuse bipolar 1 cell](http://purl.obolibrary.org/obo/CL_4033027) [RO_0002175](http://purl.obolibrary.org/obo/RO_0002175) [NCBITaxon_9606](http://purl.obolibrary.org/obo/NCBITaxon_9606) + +- [diffuse bipolar 1 cell](http://purl.obolibrary.org/obo/CL_4033027) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [human_reference_atlas](http://purl.obolibrary.org/obo/cl/cl-base#human_reference_atlas) + +#### Added +- [diffuse bipolar 1 cell](http://purl.obolibrary.org/obo/CL_4033027) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl/cl-base#cellxgene_subset) + + +### diffuse bipolar 2 cell `http://purl.obolibrary.org/obo/CL_4033028` +#### Removed +- [diffuse bipolar 2 cell](http://purl.obolibrary.org/obo/CL_4033028) [RO_0002175](http://purl.obolibrary.org/obo/RO_0002175) [NCBITaxon_9606](http://purl.obolibrary.org/obo/NCBITaxon_9606) + +- [diffuse bipolar 2 cell](http://purl.obolibrary.org/obo/CL_4033028) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [human_reference_atlas](http://purl.obolibrary.org/obo/cl/cl-base#human_reference_atlas) + +#### Added +- [diffuse bipolar 2 cell](http://purl.obolibrary.org/obo/CL_4033028) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl/cl-base#cellxgene_subset) + + +### diffuse bipolar 3a cell `http://purl.obolibrary.org/obo/CL_4033029` +#### Removed +- [diffuse bipolar 3a cell](http://purl.obolibrary.org/obo/CL_4033029) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [human_reference_atlas](http://purl.obolibrary.org/obo/cl/cl-base#human_reference_atlas) + +- [diffuse bipolar 3a cell](http://purl.obolibrary.org/obo/CL_4033029) [RO_0002175](http://purl.obolibrary.org/obo/RO_0002175) [NCBITaxon_9606](http://purl.obolibrary.org/obo/NCBITaxon_9606) + +#### Added +- [diffuse bipolar 3a cell](http://purl.obolibrary.org/obo/CL_4033029) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl/cl-base#cellxgene_subset) + + +### diffuse bipolar 3b cell `http://purl.obolibrary.org/obo/CL_4033030` +#### Removed +- [diffuse bipolar 3b cell](http://purl.obolibrary.org/obo/CL_4033030) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [human_reference_atlas](http://purl.obolibrary.org/obo/cl/cl-base#human_reference_atlas) + +- [diffuse bipolar 3b cell](http://purl.obolibrary.org/obo/CL_4033030) [RO_0002175](http://purl.obolibrary.org/obo/RO_0002175) [NCBITaxon_9606](http://purl.obolibrary.org/obo/NCBITaxon_9606) + +#### Added +- [diffuse bipolar 3b cell](http://purl.obolibrary.org/obo/CL_4033030) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl/cl-base#cellxgene_subset) + + +### diffuse bipolar 4 cell `http://purl.obolibrary.org/obo/CL_4033031` +#### Removed +- [diffuse bipolar 4 cell](http://purl.obolibrary.org/obo/CL_4033031) [RO_0002175](http://purl.obolibrary.org/obo/RO_0002175) [NCBITaxon_9606](http://purl.obolibrary.org/obo/NCBITaxon_9606) + +- [diffuse bipolar 4 cell](http://purl.obolibrary.org/obo/CL_4033031) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [human_reference_atlas](http://purl.obolibrary.org/obo/cl/cl-base#human_reference_atlas) + +#### Added +- [diffuse bipolar 4 cell](http://purl.obolibrary.org/obo/CL_4033031) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl/cl-base#cellxgene_subset) + + +### diffuse bipolar 5 cell `http://purl.obolibrary.org/obo/CL_4033085` + +#### Added +- [diffuse bipolar 5 cell](http://purl.obolibrary.org/obo/CL_4033085) [contributor](http://purl.org/dc/terms/contributor) [0000-0001-6677-8489](https://orcid.org/0000-0001-6677-8489) + +- [diffuse bipolar 5 cell](http://purl.obolibrary.org/obo/CL_4033085) [comment](http://www.w3.org/2000/01/rdf-schema#comment) "A diffuse bipolar 5 cell typically contacts 7–8 cone photoreceptors. The number and thickness of its dendritic processes are intermediate between those of a diffuse bipolar 6 cell (less dense and thinner) and a diffuse bipolar 4 cell (denser and thicker)."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:27833534"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [diffuse bipolar 5 cell](http://purl.obolibrary.org/obo/CL_4033085) [id](http://www.geneontology.org/formats/oboInOwl#id) "CL:4033085"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [diffuse bipolar 5 cell](http://purl.obolibrary.org/obo/CL_4033085) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "DB5 cell"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:32032773"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003000](http://purl.obolibrary.org/obo/OMO_0003000) + +- [diffuse bipolar 5 cell](http://purl.obolibrary.org/obo/CL_4033085) [label](http://www.w3.org/2000/01/rdf-schema#label) "diffuse bipolar 5 cell"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [diffuse bipolar 5 cell](http://purl.obolibrary.org/obo/CL_4033085) [date](http://purl.org/dc/terms/date) "2024-10-16T12:46:53Z"^^[dateTime](http://www.w3.org/2001/XMLSchema#dateTime) + +- [diffuse bipolar 5 cell](http://purl.obolibrary.org/obo/CL_4033085) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "An ON diffuse bipolar cell that stratifies in the stratum 3 of the inner plexiform layer to make synapses with ON parasol ganglion cells. A diffuse bipolar 5 cell has high expression of MYO16 compared with other bipolar cells."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:32032773"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:27833534"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [diffuse bipolar 5 cell](http://purl.obolibrary.org/obo/CL_4033085) [RO_0002175](http://purl.obolibrary.org/obo/RO_0002175) [NCBITaxon_9443](http://purl.obolibrary.org/obo/NCBITaxon_9443) + +- Class: [diffuse bipolar 5 cell](http://purl.obolibrary.org/obo/CL_4033085) + +- [diffuse bipolar 5 cell](http://purl.obolibrary.org/obo/CL_4033085) SubClassOf [ON-bipolar cell](http://purl.obolibrary.org/obo/CL_0000749) + + +### diffuse bipolar 6 cell `http://purl.obolibrary.org/obo/CL_4033032` +#### Removed +- [diffuse bipolar 6 cell](http://purl.obolibrary.org/obo/CL_4033032) [RO_0002175](http://purl.obolibrary.org/obo/RO_0002175) [NCBITaxon_9606](http://purl.obolibrary.org/obo/NCBITaxon_9606) + +- [diffuse bipolar 6 cell](http://purl.obolibrary.org/obo/CL_4033032) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [human_reference_atlas](http://purl.obolibrary.org/obo/cl/cl-base#human_reference_atlas) + +#### Added +- [diffuse bipolar 6 cell](http://purl.obolibrary.org/obo/CL_4033032) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl/cl-base#cellxgene_subset) + + +### direct pathway medium spiny neuron `http://purl.obolibrary.org/obo/CL_4023026` + +#### Added +- [direct pathway medium spiny neuron](http://purl.obolibrary.org/obo/CL_4023026) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl/cl-base#cellxgene_subset) + + +### dorsal horn interneuron `http://purl.obolibrary.org/obo/CL_0011000` +#### Removed +- [dorsal horn interneuron](http://purl.obolibrary.org/obo/CL_0011000) SubClassOf [RO_0002100](http://purl.obolibrary.org/obo/RO_0002100) some [UBERON_0002256](http://purl.obolibrary.org/obo/UBERON_0002256) + +#### Added +- [dorsal horn interneuron](http://purl.obolibrary.org/obo/CL_0011000) SubClassOf [neuron of the dorsal spinal cord](http://purl.obolibrary.org/obo/CL_0002611) + + +### duodenal goblet cell `http://purl.obolibrary.org/obo/CL_1000324` +#### Removed +- [duodenal goblet cell](http://purl.obolibrary.org/obo/CL_1000324) EquivalentTo [goblet cell](http://purl.obolibrary.org/obo/CL_0000160) and ([BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0002114](http://purl.obolibrary.org/obo/UBERON_0002114)) + +- [duodenal goblet cell](http://purl.obolibrary.org/obo/CL_1000324) SubClassOf [BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0008346](http://purl.obolibrary.org/obo/UBERON_0008346) + +#### Added +- [duodenal goblet cell](http://purl.obolibrary.org/obo/CL_1000324) EquivalentTo [goblet cell](http://purl.obolibrary.org/obo/CL_0000160) and ([BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0008346](http://purl.obolibrary.org/obo/UBERON_0008346)) + +- [duodenal goblet cell](http://purl.obolibrary.org/obo/CL_1000324) SubClassOf [duodenum secretory cell](http://purl.obolibrary.org/obo/CL_1001589) + + +### duodenum secretory cell `http://purl.obolibrary.org/obo/CL_1001589` +#### Removed +- [duodenum secretory cell](http://purl.obolibrary.org/obo/CL_1001589) [label](http://www.w3.org/2000/01/rdf-schema#label) "duodenum glandular cell"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [duodenum secretory cell](http://purl.obolibrary.org/obo/CL_1001589) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "duodenum glandular cells"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "CALOHA:TS-1275"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [duodenum secretory cell](http://purl.obolibrary.org/obo/CL_1001589) EquivalentTo [glandular secretory epithelial cell](http://purl.obolibrary.org/obo/CL_0000150) and ([BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0002114](http://purl.obolibrary.org/obo/UBERON_0002114)) + +#### Added +- [duodenum secretory cell](http://purl.obolibrary.org/obo/CL_1001589) [label](http://www.w3.org/2000/01/rdf-schema#label) "duodenum secretory cell"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [duodenum secretory cell](http://purl.obolibrary.org/obo/CL_1001589) [has_narrow_synonym](http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym) "duodenum glandular cells"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "CALOHA:TS-1275"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [duodenum secretory cell](http://purl.obolibrary.org/obo/CL_1001589) EquivalentTo [secretory epithelial cell](http://purl.obolibrary.org/obo/CL_1100001) and ([BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0002114](http://purl.obolibrary.org/obo/UBERON_0002114)) + + +### early T lineage precursor `http://purl.obolibrary.org/obo/CL_0002425` +#### Removed +- [early T lineage precursor](http://purl.obolibrary.org/obo/CL_0002425) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) + + + +### early colonocyte `http://purl.obolibrary.org/obo/CL_4047018` +#### Removed +- [early colonocyte](http://purl.obolibrary.org/obo/CL_4047018) EquivalentTo [early enterocyte](http://purl.obolibrary.org/obo/CL_4047019) and ([BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0001155](http://purl.obolibrary.org/obo/UBERON_0001155)) + +#### Added +- [early colonocyte](http://purl.obolibrary.org/obo/CL_4047018) EquivalentTo [early enterocyte](http://purl.obolibrary.org/obo/CL_4047019) and ([BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0000397](http://purl.obolibrary.org/obo/UBERON_0000397)) + + +### eccrine cell `http://purl.obolibrary.org/obo/CL_0000434` +#### Removed +- [eccrine cell](http://purl.obolibrary.org/obo/CL_0000434) SubClassOf [glandular secretory epithelial cell](http://purl.obolibrary.org/obo/CL_0000150) + +#### Added +- [eccrine cell](http://purl.obolibrary.org/obo/CL_0000434) SubClassOf [secretory epithelial cell](http://purl.obolibrary.org/obo/CL_1100001) + + +### ectodermal cell `http://purl.obolibrary.org/obo/CL_0000221` + +#### Added +- [ectodermal cell](http://purl.obolibrary.org/obo/CL_0000221) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl/cl-base#cellxgene_subset) + + +### efferent neuron `http://purl.obolibrary.org/obo/CL_0000527` + +#### Added +- [efferent neuron](http://purl.obolibrary.org/obo/CL_0000527) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl/cl-base#cellxgene_subset) + + +### elicited macrophage `http://purl.obolibrary.org/obo/CL_0000861` +#### Removed +- [elicited macrophage](http://purl.obolibrary.org/obo/CL_0000861) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) + + + +### embryonic blood vessel endothelial progenitor cell `http://purl.obolibrary.org/obo/CL_0002546` + +#### Added +- [embryonic blood vessel endothelial progenitor cell](http://purl.obolibrary.org/obo/CL_0002546) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl/cl-base#cellxgene_subset) + + +### embryonic cell (metazoa) `http://purl.obolibrary.org/obo/CL_0002321` + +#### Added +- [embryonic cell (metazoa)](http://purl.obolibrary.org/obo/CL_0002321) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://cellxgene.cziscience.com/cellguide/CL_0002321"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [embryonic cell (metazoa)](http://purl.obolibrary.org/obo/CL_0002321) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Embryonic cells in metazoans, which include all multicellular animals, are biological units in their earliest developmental stages from conception until the organism is fully formed. +They are derived from a fertilized egg, which undergoes a series of cell divisions to produce a multicellular organism. During the early phases of embryonic development, these cells exhibit pluripotency, meaning they possess the potential to differentiate into a diverse array of specialized cell types that constitute different body tissues and structures. +The balance between cell proliferation and differentiation in embryonic cells is crucial for successful development. When cells continue to divide without differentiating, overgrowth may occur leading to conditions such as teratomas (tumors of embryonic cells). Conversely, if cell differentiation proceeds at the expense of cell proliferation, developmental anomalies could occur regarding size or mass of the organism or its parts."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://www.ncbi.nlm.nih.gov/books/NBK9906/"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1093/molehr/gan048"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1002/iub.1404"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### endo-epithelial cell `http://purl.obolibrary.org/obo/CL_0002076` + +#### Added +- [endo-epithelial cell](http://purl.obolibrary.org/obo/CL_0002076) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl/cl-base#cellxgene_subset) + + +### endocardial cell `http://purl.obolibrary.org/obo/CL_0002350` + +#### Added +- [endocardial cell](http://purl.obolibrary.org/obo/CL_0002350) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Endocardial cells, often referred to as endothelial cells of the heart, constitute the innermost lining layer of the heart tissues, forming the endocardium. They play a critical role in maintaining heart functionality and homeostasis. These cells, flat and squamous in structure, are adjoined closely to form a tight barrier that separates the heart's muscular layer, the myocardium, from the blood flowing through the heart chambers. +Functionally, endocardial cells are key players in several crucial physiological processes within the heart. Synthesizing matrix molecules that contribute to the structural formation of the heart, these cells actively partake in maintaining its structural integrity. They also exhibit unique metabolic activity, which aids in maintaining optimal cardiac functioning in both healthy and pathological conditions. Importantly, they are known for their involvement in modulating myocardial contraction and relaxation, that is crucial for normal heart rhythm and function. They achieve this by producing factors like nitric oxide (NO) which, amongst other things, aids in the regulation of blood pressure, prevents blood clotting and inhibits the adherence of blood cells to the vessel wall. +In pathological states, endocardial cells can undergo a transformation process known as endothelial-mesenchymal transition (EndMT), which is inherently involved in several cardiac diseases. In this transition, they acquire the ability to migrate and differentiate into several other types of cells contributing to disease progression. Moreover, their dysfunction can lead to endocarditis, an inflammation of the endocardium, as well as increase the risk of other heart diseases."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1101/cshperspect.a036723"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1016/j.ydbio.2009.06.033"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1161/ATVBAHA.121.313788"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1161/CIRCRESAHA.117.312136"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1016/j.medici.2017.08.003"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [endocardial cell](http://purl.obolibrary.org/obo/CL_0002350) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://cellxgene.cziscience.com/cellguide/CL_0002350"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### endocrine gland capillary endothelial cell `http://purl.obolibrary.org/obo/CL_4052015` + +#### Added +- [endocrine gland capillary endothelial cell](http://purl.obolibrary.org/obo/CL_4052015) [id](http://www.geneontology.org/formats/oboInOwl#id) "CL:4052015"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [endocrine gland capillary endothelial cell](http://purl.obolibrary.org/obo/CL_4052015) [label](http://www.w3.org/2000/01/rdf-schema#label) "endocrine gland capillary endothelial cell"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [endocrine gland capillary endothelial cell](http://purl.obolibrary.org/obo/CL_4052015) [contributor](http://purl.org/dc/terms/contributor) [0009-0000-8480-9277](https://orcid.org/0009-0000-8480-9277) + +- [endocrine gland capillary endothelial cell](http://purl.obolibrary.org/obo/CL_4052015) [date](http://purl.org/dc/terms/date) "2024-09-30T15:27:49Z"^^[dateTime](http://www.w3.org/2001/XMLSchema#dateTime) + +- [endocrine gland capillary endothelial cell](http://purl.obolibrary.org/obo/CL_4052015) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "Any capillary endothelial cell that is part of an endocrine gland."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:18480313"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- Class: [endocrine gland capillary endothelial cell](http://purl.obolibrary.org/obo/CL_4052015) + +- [endocrine gland capillary endothelial cell](http://purl.obolibrary.org/obo/CL_4052015) EquivalentTo [capillary endothelial cell](http://purl.obolibrary.org/obo/CL_0002144) and ([BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0002368](http://purl.obolibrary.org/obo/UBERON_0002368)) + +- [endocrine gland capillary endothelial cell](http://purl.obolibrary.org/obo/CL_4052015) SubClassOf [BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0002368](http://purl.obolibrary.org/obo/UBERON_0002368) + +- [endocrine gland capillary endothelial cell](http://purl.obolibrary.org/obo/CL_4052015) SubClassOf [capillary endothelial cell](http://purl.obolibrary.org/obo/CL_0002144) + + +### endometrial multiciliated epithelial cell `http://purl.obolibrary.org/obo/CL_4030040` +#### Removed +- [endometrial multiciliated epithelial cell](http://purl.obolibrary.org/obo/CL_4030040) [label](http://www.w3.org/2000/01/rdf-schema#label) "endometrial ciliated epithelial cell"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [endometrial multiciliated epithelial cell](http://purl.obolibrary.org/obo/CL_4030040) EquivalentTo [multiciliated epithelial cell](http://purl.obolibrary.org/obo/CL_0005012) and ([BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0004811](http://purl.obolibrary.org/obo/UBERON_0004811)) and ([BFO_0000051](http://purl.obolibrary.org/obo/BFO_0000051) some [GO_0097729](http://purl.obolibrary.org/obo/GO_0097729)) + +#### Added +- [endometrial multiciliated epithelial cell](http://purl.obolibrary.org/obo/CL_4030040) [label](http://www.w3.org/2000/01/rdf-schema#label) "endometrial multiciliated epithelial cell"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [endometrial multiciliated epithelial cell](http://purl.obolibrary.org/obo/CL_4030040) [has_exact_synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "endometrial ciliated epithelial cell"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [endometrial multiciliated epithelial cell](http://purl.obolibrary.org/obo/CL_4030040) EquivalentTo [columnar/cuboidal epithelial cell](http://purl.obolibrary.org/obo/CL_0000075) and ([BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0004811](http://purl.obolibrary.org/obo/UBERON_0004811)) and ([BFO_0000051](http://purl.obolibrary.org/obo/BFO_0000051) some [GO_0097729](http://purl.obolibrary.org/obo/GO_0097729)) and ([RO_0000053](http://purl.obolibrary.org/obo/RO_0000053) some [PATO_0010007](http://purl.obolibrary.org/obo/PATO_0010007)) + + +### endosteal cell `http://purl.obolibrary.org/obo/CL_0002157` + +#### Added +- [endosteal cell](http://purl.obolibrary.org/obo/CL_0002157) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://cellxgene.cziscience.com/cellguide/CL_0002157"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [endosteal cell](http://purl.obolibrary.org/obo/CL_0002157) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Endosteal cells, also known as osteogenic cells, are a specialized type of cell that resides in the endosteum of the bone marrow cavity. The endosteum is a thin vascular membrane of connective tissue that lines the inner surface of the bony tissue that forms the medullary cavity of long bones. This specific location assigns endosteal cells critical roles in the bone maintenance and regeneration process as they actively participate in bone remodeling, a process that involves both the formation and resorption of bone tissue. +Endosteal cells function by regulating the activity of both osteoblasts and osteoclasts. Osteoblasts are cells that deposit new bone, and osteoclasts are responsible for bone resorption, a process important for the maintenance, repair, and remodelling of bones. When new bone tissue is required, such as in instances of bone fractures or increased mechanical stress, endosteal cells differentiate into osteoblasts to facilitate the bone formation process. Conversely, when bone resorption is necessary, these cells are known to release signals that lead to the recruitment and activation of osteoclasts. +In addition to this, endosteal cells play a significant role in hematopoiesis, which is the formation of blood cellular components. They function in this process by providing a niche for hematopoietic stem cells, serving to support their maintenance and differentiation. Understanding the functionality of endosteal cells is important in the field of regenerative medicine and stem cell therapy, especially in diseases affecting bone remodeling and hematopoiesis."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1126/science.75570"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://www.sciencedirect.com/topics/engineering/endosteum"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1182/blood-2004-06-2480"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1038/leu.2010.214"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1182/blood-2009-08-239194"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### endothelial cell of artery `http://purl.obolibrary.org/obo/CL_1000413` +#### Removed +- [endothelial cell of artery](http://purl.obolibrary.org/obo/CL_1000413) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +Endothelial cells of the artery, also referred to as arterial endothelial cells, form an integral part of the arterial system. They form a single layer, known as the endothelium, lining the interior surface of arteries, and are able to respond to the high-pressure and flow conditions present in arteries. The primary role of these cells is to provide a barrier between the vessel wall and the blood, exhibiting selective permeability to regulate the movement of liquids, gases, and blood-borne substances across the vascular wall. +Arterial endothelial cells significantly contribute to maintaining vascular homeostasis. They are at the forefront of sensations and responses to mechanical stimuli, like shear stress and blood pressure changes. An additional key function pertains to the production of nitric oxide, which helps to regulate vascular tone and blood pressure, prevents platelet aggregation, limits leukocyte adhesion to the endothelium, and inhibits smooth muscle cell proliferation. These varied but connected functions help to preclude the development of atherosclerosis, ensuring normal circulation and arterial health. +Moreover, these cells play a pivotal role in inflammation and coagulation processes. During inflammatory events, they express various adhesion molecules, aiding in leukocyte recruitment and rolling onto the vessel walls for immune response. They also produce anticoagulant and procoagulant substances, involved in blood clotting and clot dissolution, respectively. Dysregulation of the usual functions of arterial endothelial cells can result in serious pathophysiological conditions, such as atherosclerosis, hypertension, and other cardiovascular diseases."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1177/153857440303700107"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1007/s00441-008-0706-5"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1016/j.jvs.2004.03.043"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1016/j.ccm.2021.08.005"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1007/s10456-021-09785-7"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [endothelial cell of artery](http://purl.obolibrary.org/obo/CL_1000413) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Endothelial cells of the artery, also referred to as arterial endothelial cells, form an integral part of the arterial system. They form a single layer, known as the endothelium, lining the interior surface of arteries, and are able to respond to the high-pressure and flow conditions present in arteries. The primary role of these cells is to provide a barrier between the vessel wall and the blood, exhibiting selective permeability to regulate the movement of liquids, gases, and blood-borne substances across the vascular wall. +Arterial endothelial cells significantly contribute to maintaining vascular homeostasis. They are at the forefront of sensations and responses to mechanical stimuli, like shear stress and blood pressure changes. An additional key function pertains to the production of nitric oxide, which helps to regulate vascular tone and blood pressure, prevents platelet aggregation, limits leukocyte adhesion to the endothelium, and inhibits smooth muscle cell proliferation. These varied but connected functions help to preclude the development of atherosclerosis, ensuring normal circulation and arterial health. +Moreover, these cells play a pivotal role in inflammation and coagulation processes. During inflammatory events, they express various adhesion molecules, aiding in leukocyte recruitment and rolling onto the vessel walls for immune response. They also produce anticoagulant and procoagulant substances, involved in blood clotting and clot dissolution, respectively. Dysregulation of the usual functions of arterial endothelial cells can result in serious pathophysiological conditions, such as atherosclerosis, hypertension, and other cardiovascular diseases."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1177/153857440303700107"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1007/s00441-008-0706-5"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1016/j.jvs.2004.03.043"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1016/j.ccm.2021.08.005"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1007/s10456-021-09785-7"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### endothelial cell of hepatic sinusoid `http://purl.obolibrary.org/obo/CL_1000398` + +#### Added +- [endothelial cell of hepatic sinusoid](http://purl.obolibrary.org/obo/CL_1000398) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://cellxgene.cziscience.com/cellguide/CL_1000398"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [endothelial cell of hepatic sinusoid](http://purl.obolibrary.org/obo/CL_1000398) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Endothelial cells of hepatic sinusoids, also known as hepatic or liver sinusoidal endothelial cells (HSEC or LSEC), are unique, specialized type of endothelial cells located in the liver. They are the building units of the hepatic sinusoid, which functions as a specialized capillary system that facilitates the exchange of various substances between the blood and hepatocytes. This finely tuned environment, facilitated by HSEC, is primordial for the liver's multiple physiologic functions that include nutrient metabolism, toxin inactivation, and immunomodulation. +The HSEC have a distinctive morphology that sets them apart from the typical endothelial cells found in other organs. These cells are exceptionally thin to allow for efficient transfer of molecules and characterized by fenestrations, which are non-diaphragmatic, sieve-like openings that provide an open filtration pathway from the sinusoidal lumen to the space of Disse, where hepatocytes are exposed. The fenestration is a crucial feature that allows lipoproteins, nutrients, and other plasma components easy access to hepatocytes for essential liver functions, including clearance of waste products and metabolic regulation. +HSECs further play a vital role in immune functionality in the liver. They act as a sentinel, determining the nature of the immune response to encountered particulates. They possess a capacity for antigen presentation and express a series of immune-related surface molecules, which helps in immunosurveillance and immunoregulation. The HSEC also aid in the removal and destruction of virus-infected cells, harmful microorganisms, and circulatory waste products to safeguard liver health and general systemic cleanliness."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1038/s41575-018-0020-y"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1038/cmi.2016.5"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1016/j.jhep.2016.07.009"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1038/s41575-020-00411-3"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://www.sciencedirect.com/topics/immunology-and-microbiology/disse-space"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### endothelial cell of lymphatic vessel `http://purl.obolibrary.org/obo/CL_0002138` + +#### Added +- [endothelial cell of lymphatic vessel](http://purl.obolibrary.org/obo/CL_0002138) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Endothelial cells of lymphatic vessels are specialized type of cells that form the interior lining of the lymphatic system, which primarily comprises the lymph vessels and nodes. These cells play a critical role in creating a barrier between the lymphatic system and the surrounding tissues. They are structurally different from the endothelial cells of the blood vessels due to the presence of anchoring filaments and lack of a continuous basement membrane, and have a unique phenotype marked by the expression of various cell-specific markers such as Prox-1, VEGFR-3, and LYVE-1. +A significant function of these endothelial cells is to maintain the fluid balance within the body. They facilitate the uptake of excess interstitial fluid that collects in the body tissues, and ensure its transport back into the bloodstream via the lymphatic vessels. These cells also enable the absorption of fats and fat-soluble vitamins from the digestive system, and their subsequent transport in the form of chyle, a milky fluid, to the blood. +Furthermore, endothelial cells of lymphatic vessels play a pivotal role in the body's immune response. They enable the passage of lymphocytes, that are crucial for the body's defense mechanism, from the tissues into the lymph where these cells are activated to fight against foreign bodies and infections. Also, they regulate inflammation reactions by controlling the migration of inflammatory cells, and are thus involved in pathological conditions with an inflammatory component. Lastly, these cells have been noted for their involvement in various disease states related to tissue edema, metastasis, and tumor growth, thus highlighting their importance in both health and disease states."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.3892/mco.2017.1356"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1038/s41577-020-0281-x"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.3389/fimmu.2019.00036"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1016/j.it.2022.10.010"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.3389/fphys.2020.00509/full"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [endothelial cell of lymphatic vessel](http://purl.obolibrary.org/obo/CL_0002138) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://cellxgene.cziscience.com/cellguide/CL_0002138"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### endothelial cell of sinusoid `http://purl.obolibrary.org/obo/CL_0002262` + +#### Added +- [endothelial cell of sinusoid](http://purl.obolibrary.org/obo/CL_0002262) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://cellxgene.cziscience.com/cellguide/CL_0002262"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [endothelial cell of sinusoid](http://purl.obolibrary.org/obo/CL_0002262) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Endothelial cells of sinusoids, often referred to as sinusoidal endothelial cells (SECs), are a specialized type of endothelial cell that primarily reside in the capillaries of the liver, spleen, and bone marrow. These cells form the innermost monolayer of the sinusoidal blood vessels, also known as sinusoids, that mediate the exchange of nutrients, metabolites, and waste materials between the blood and the surrounding organ tissue. SECs possess distinctive morphological features including a large, flattened shape, an abundance of fenestrations or pores, and the lack of a continuous basement membrane. These structural characteristics distinguish sinusoidal endothelial cells from other, more regularly structured endothelial cells in the body. +Due to their special fenestrated structure, SECs facilitate the exchange of macromolecules, like lipoproteins and hyaluronan, between plasma and the surrounding organ parenchymal cells. These fenestrations act like sieves, allowing the passage of substances based on their size and charge. It's noteworthy that the permeability characteristics of SECs can be regulated dynamically according to the body's homeostatic needs. +Beyond their key role in exchange mechanisms, endothelial cells of sinusoids are involved in several other functions. In the liver, for example, they help in the removal and endocytic degradation of waste macromolecules, immune response, and regulation of liver regeneration. They also participate in the formation and remodeling of blood vessels, a process known as angiogenesis. Additionally, in recent years, it has been discovered that these cells may have a role in disease conditions like cirrhosis and liver cancer."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1038/s41575-018-0020-y"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1007/s10456-021-09780-y"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1186/1476-5926-1-1"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1016/j.jhep.2016.07.009"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1038/s41598-020-57652-0"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### endothelial cell of umbilical vein `http://purl.obolibrary.org/obo/CL_0002618` +#### Removed +- [endothelial cell of umbilical vein](http://purl.obolibrary.org/obo/CL_0002618) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +Endothelial cells of the umbilical vein form the inner lining of the veins found in the umbilical cord. They are involved in tube formation and migration which are essential for angiogenesis, the process of generating new blood vessels; this is critical during the fetal stage for the development of the circulatory system. Endothelial cells of the umbilical vein also play a role in controlling the passage of white blood cells into tissues during inflammatory responses. +Because human umbilical vein endothelial cells (HUVECs) can easily be derived from the umbilical cord, and because they express common endothelial cell markers, they have been used as an epithelial cell model for studies on cell proliferation, migration, angiogenesis, and inflammation. They have been used as models for vascular diseases like atherosclerosis, for investigating how tumor cells infiltrate blood vessels and form metastases. +Thus, while endothelial cells of the umbilical vein play a critical role in vascular biology, they also represent a powerful tool in disease studies and potential treatment strategies."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1007/s12015-006-0015-x"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1172/JCI107470"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://www.ncbi.nlm.nih.gov/books/NBK53254/"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.3390/app10030938"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1002/cyto.a.20952"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [endothelial cell of umbilical vein](http://purl.obolibrary.org/obo/CL_0002618) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Endothelial cells of the umbilical vein form the inner lining of the veins found in the umbilical cord. They are involved in tube formation and migration which are essential for angiogenesis, the process of generating new blood vessels; this is critical during the fetal stage for the development of the circulatory system. Endothelial cells of the umbilical vein also play a role in controlling the passage of white blood cells into tissues during inflammatory responses. +Because human umbilical vein endothelial cells (HUVECs) can easily be derived from the umbilical cord, and because they express common endothelial cell markers, they have been used as an epithelial cell model for studies on cell proliferation, migration, angiogenesis, and inflammation. They have been used as models for vascular diseases like atherosclerosis, for investigating how tumor cells infiltrate blood vessels and form metastases. +Thus, while endothelial cells of the umbilical vein play a critical role in vascular biology, they also represent a powerful tool in disease studies and potential treatment strategies."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1007/s12015-006-0015-x"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1172/JCI107470"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://www.ncbi.nlm.nih.gov/books/NBK53254/"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.3390/app10030938"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1002/cyto.a.20952"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### endothelial cell of uterus `http://purl.obolibrary.org/obo/CL_0009095` + +#### Added +- [endothelial cell of uterus](http://purl.obolibrary.org/obo/CL_0009095) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://cellxgene.cziscience.com/cellguide/CL_0009095"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [endothelial cell of uterus](http://purl.obolibrary.org/obo/CL_0009095) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +The endothelial cell of the uterus is a specialized type of endothelial cell found in the inner lining of blood vessels, specifically those in the uterus. These cells play critical roles in maintaining uterine health, fertilization, and pregnancy processes. They form the interior surface of blood vessels, creating a barrier between the vessel lumen and surrounding tissue. This fluid environment, maintained by these endothelial cells, provides a platform for the material exchange between blood and tissues, thereby modulating blood coagulation, immune responses, and controlling vasodilation and vasoconstriction. +Functionally, the endothelial cells of the uterus are paramount in regulating the uterine blood flow, an important determinant of successful conception and pregnancy outcomes. They support the vascular changes during the reproductive cycle, particularly the spiral arteriolar development and function, essential in endometrial thickening, maturation, and eventual shedding during menstruation periods. The cells also contribute to angiogenesis, a process crucial during implantation and placenta development, whereby new blood vessels form from pre-existing vessels to supply the growing fetus with oxygen and nutrients. Uterine endothelial cells are also implicated in mediating immune responses within the uterus. Changes in these cells can influence various conditions such as reproductive disorders and complications including heavy menstrual bleeding, endometrial hyperplasia, fertility problems, and cancer."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.2174/1570161111311050010"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1002/cphy.c190015"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1111/aji.12128"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1530/REP-09-0147"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1172/jci.insight.163422"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### endothelial cell of vascular tree `http://purl.obolibrary.org/obo/CL_0002139` + +#### Added +- [endothelial cell of vascular tree](http://purl.obolibrary.org/obo/CL_0002139) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Endothelial cells of the vascular tree, commonly referred to as vascular endothelial cells, line the entire circulatory system, from the heart to the smallest capillaries. These cells have a unique, flattened shape, and are tightly bound together, forming a thin layer known as the endothelium. The endothelium is responsible for maintaining the interior surface of blood vessels, and plays a critical role in ensuring the smooth flow of blood. +Vascular endothelial cells act as a semi-permeable membrane, controlling the passage of materials and the transit of white blood cells into and out of the bloodstream. These cells are also involved in blood coagulation. When a blood vessel is damaged, endothelial cells promote clotting to prevent excessive bleeding and facilitate wound healing. Other functions include regulation of blood pressure and blood volume by releasing vasodilators and vasoconstrictors to either widen or constrict blood vessels, accordingly. +Furthermore, the endothelial cells are crucial in the formation of new blood vessels, a process known as angiogenesis. This is particularly important in wound healing and the growth of new tissues during development or after injury. In the context of diseases such as cancer, angiogenesis helps facilitate tumor growth by providing nutrients and oxygen."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://www.sciencedirect.com/topics/medicine-and-dentistry/vascular-endothelial-cell"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1186/s12872-015-0124-z"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1038/s41569-022-00770-1"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.3389/fphys.2022.863265/full"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [endothelial cell of vascular tree](http://purl.obolibrary.org/obo/CL_0002139) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://cellxgene.cziscience.com/cellguide/CL_0002139"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### endothelial stalk cell `http://purl.obolibrary.org/obo/CL_0002671` +#### Removed +- [endothelial stalk cell](http://purl.obolibrary.org/obo/CL_0002671) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +Endothelial stalk cells are specialized vascular cells vital in angiogenesis, a process through which new blood vessels are formed from pre-existing ones; specifically, endothelial stalk cells are involved in sprouting angiogenesis, where they help form the body of new blood vessels. +Vascular sprouting relies on the coordinated activity of migrating endothelial tip cells at the forefront and proliferating stalk cells that elongate the sprout. The process is tightly controlled by different growths factors: Vascular Endothelial Growth Factor acts on endothelial cells, inducing them to become endothelial tip cells that initiate sprouting. After sprouting initiation, activation of Notch signaling suppresses differentiation toward a tip cell phenotype and some of the endothelial cells differentiate into stalk cells, which follow tip cells, multiply, and elongate to provide a structural backbone to the growing vessel sprout. +In contrast to endothelial tip cells, which migrate and lead the angiogenic sprout, endothelial stalk cells behind the sprouts continue forming the tube or lumen for blood flow and facilitate maturation and stability of the new vessel. The delicate balance between the activities of stalk and tip cells during angiogenesis is crucial to build a functional vascular network. Dysfunctions in endothelial stalk cells can lead to pathological conditions such as impaired wound healing, unregulated tumor growth, and metastasis due to abnormal angiogenesis."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1016/j.cmet.2013.08.001"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.3389/fcell.2021.642352"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1007/s12079-019-00511-z"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1101/cshperspect.a006569"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [endothelial stalk cell](http://purl.obolibrary.org/obo/CL_0002671) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Endothelial stalk cells are specialized vascular cells vital in angiogenesis, a process through which new blood vessels are formed from pre-existing ones; specifically, endothelial stalk cells are involved in sprouting angiogenesis, where they help form the body of new blood vessels. +Vascular sprouting relies on the coordinated activity of migrating endothelial tip cells at the forefront and proliferating stalk cells that elongate the sprout. The process is tightly controlled by different growths factors: Vascular Endothelial Growth Factor acts on endothelial cells, inducing them to become endothelial tip cells that initiate sprouting. After sprouting initiation, activation of Notch signaling suppresses differentiation toward a tip cell phenotype and some of the endothelial cells differentiate into stalk cells, which follow tip cells, multiply, and elongate to provide a structural backbone to the growing vessel sprout. +In contrast to endothelial tip cells, which migrate and lead the angiogenic sprout, endothelial stalk cells behind the sprouts continue forming the tube or lumen for blood flow and facilitate maturation and stability of the new vessel. The delicate balance between the activities of stalk and tip cells during angiogenesis is crucial to build a functional vascular network. Dysfunctions in endothelial stalk cells can lead to pathological conditions such as impaired wound healing, unregulated tumor growth, and metastasis due to abnormal angiogenesis."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1016/j.cmet.2013.08.001"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.3389/fcell.2021.642352"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1007/s12079-019-00511-z"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1101/cshperspect.a006569"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### enteric smooth muscle cell `http://purl.obolibrary.org/obo/CL_0002504` + +#### Added +- [enteric smooth muscle cell](http://purl.obolibrary.org/obo/CL_0002504) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://cellxgene.cziscience.com/cellguide/CL_0002504"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [enteric smooth muscle cell](http://purl.obolibrary.org/obo/CL_0002504) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Enteric smooth muscle cells are a specialized type of cell found in the gastrointestinal tract. They are an integral part of the enteric nervous system, which regulates the functions of the gastrointestinal system. These cells have a unique structural organization that enables their primary function: the contraction and relaxation necessary for the propulsion of gastrointestinal contents. +Smooth muscle cells in the enteric system possess unique attributes that distinguish them from other smooth muscle cells in the body. One crucial function is peristalsis, where these cells contract in a coordinated manner, generating a wave of contraction and relaxation. This peristaltic movement facilitates the movement of food particles through the digestive tract, playing a vital role in the digestion and absorption processes in animals. Additionally, these cells are responsible for maintaining the tone of gastrointestinal sphincters, controlling passage and preventing one-sided movement of the contents. +Enteric smooth muscle cells are also involved in local immune responses of the gastrointestinal tract. They can communicate with local immune cells and secrete cytokines or other signaling molecules in response to infectious organisms, which makes them crucial mediocellular players in gastrointestinal homeostasis and response to disease. Their interactions with other cell types, such as neurons, myofibroblasts, and interstitial cells of Cajal, further contribute to these cells' role in maintaining the physiological functions of the gastrointestinal system. Overall, enteric smooth muscle cells provide an indispensable contribution to the complex operations of the digestive tract."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1038/nrgastro.2012.168"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1371/journal.pcbi.1009644"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1111/j.1365-2982.2012.01986.x"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### enterocyte `http://purl.obolibrary.org/obo/CL_0000584` + +#### Added +- [enterocyte](http://purl.obolibrary.org/obo/CL_0000584) SubClassOf [RO_0002202](http://purl.obolibrary.org/obo/RO_0002202) some [early enterocyte](http://purl.obolibrary.org/obo/CL_4047019) + + +### enterocyte of anorectum `http://purl.obolibrary.org/obo/CL_0009058` +#### Removed +- [enterocyte of anorectum](http://purl.obolibrary.org/obo/CL_0009058) SubClassOf [epithelial cell of large intestine](http://purl.obolibrary.org/obo/CL_0002253) + +- [enterocyte of anorectum](http://purl.obolibrary.org/obo/CL_0009058) SubClassOf [enterocyte](http://purl.obolibrary.org/obo/CL_0000584) + +#### Added +- [enterocyte of anorectum](http://purl.obolibrary.org/obo/CL_0009058) SubClassOf [enterocyte of epithelium of large intestine](http://purl.obolibrary.org/obo/CL_0002071) + + +### enterocyte of appendix `http://purl.obolibrary.org/obo/CL_0009026` +#### Removed +- [enterocyte of appendix](http://purl.obolibrary.org/obo/CL_0009026) SubClassOf [enterocyte](http://purl.obolibrary.org/obo/CL_0000584) + +#### Added +- [enterocyte of appendix](http://purl.obolibrary.org/obo/CL_0009026) SubClassOf [enterocyte of epithelium of large intestine](http://purl.obolibrary.org/obo/CL_0002071) + + +### enterocyte of epithelium of duodenal gland `http://purl.obolibrary.org/obo/CL_1000337` +#### Removed +- [enterocyte of epithelium of duodenal gland](http://purl.obolibrary.org/obo/CL_1000337) SubClassOf [epithelial cell of small intestine](http://purl.obolibrary.org/obo/CL_0002254) + +- [enterocyte of epithelium of duodenal gland](http://purl.obolibrary.org/obo/CL_1000337) SubClassOf [enterocyte](http://purl.obolibrary.org/obo/CL_0000584) + +#### Added +- [enterocyte of epithelium of duodenal gland](http://purl.obolibrary.org/obo/CL_1000337) SubClassOf [enterocyte of epithelium of small intestine](http://purl.obolibrary.org/obo/CL_1000334) + + +### enterocyte of epithelium of large intestine `http://purl.obolibrary.org/obo/CL_0002071` +#### Removed +- [enterocyte of epithelium of large intestine](http://purl.obolibrary.org/obo/CL_0002071) SubClassOf [BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0001278](http://purl.obolibrary.org/obo/UBERON_0001278) + + + +### enterocyte of epithelium of small intestine `http://purl.obolibrary.org/obo/CL_1000334` +#### Removed +- [enterocyte of epithelium of small intestine](http://purl.obolibrary.org/obo/CL_1000334) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +Enterocytes of the epithelium of the small intestine are specialized cells that reside in the lining of the small intestine, and are primarily responsible for the essential process of nutrient absorption. These cells are columnar epithelial cells with an apical surface lined with microvilli, a feature referred to as the 'brush border', to maximize the surface area available for absorption. +Enterocytes play a critical role in both the digestion and absorption of nutrients from food. Their extensive brush border contains enzymes that further assist in nutrient breakdown and transport proteins that transfer nutrients, such as glucose, amino acids, lipids, and vitamins, across the cell membrane. +The enterocytes of the small intestine also participate in the barrier function of the gut lining. Enterocytes are connected by tight junctions, which act as a primary defense line against pathogenic invasion by maintaining intestinal barrier integrity. Additionally, their cell surface is coated in glycocalyx and mucus which forms a defensive barrier preventing the penetration of harmful bacteria into the systemic circulation."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1038/nrgastro.2013.35"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.3389/fphys.2021.699152/full"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1038/nri3738"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1084/jem.20191130"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [enterocyte of epithelium of small intestine](http://purl.obolibrary.org/obo/CL_1000334) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Enterocytes of the epithelium of the small intestine are specialized cells that reside in the lining of the small intestine, and are primarily responsible for the essential process of nutrient absorption. These cells are columnar epithelial cells with an apical surface lined with microvilli, a feature referred to as the 'brush border', to maximize the surface area available for absorption. +Enterocytes play a critical role in both the digestion and absorption of nutrients from food. Their extensive brush border contains enzymes that further assist in nutrient breakdown and transport proteins that transfer nutrients, such as glucose, amino acids, lipids, and vitamins, across the cell membrane. +The enterocytes of the small intestine also participate in the barrier function of the gut lining. Enterocytes are connected by tight junctions, which act as a primary defense line against pathogenic invasion by maintaining intestinal barrier integrity. Additionally, their cell surface is coated in glycocalyx and mucus which forms a defensive barrier preventing the penetration of harmful bacteria into the systemic circulation."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1038/nrgastro.2013.35"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.3389/fphys.2021.699152/full"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1038/nri3738"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1084/jem.20191130"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [enterocyte of epithelium of small intestine](http://purl.obolibrary.org/obo/CL_1000334) [depiction](http://xmlns.com/foaf/0.1/depiction) [Small-intestine-cells.png](http://purl.obolibrary.org/obo/cl/images/Small-intestine-cells.png) + - [comment](http://www.w3.org/2000/01/rdf-schema#comment) "Figure depicts a cross section of intestinal villi in the small intestine, including the crypts of Lieberkuhn (seen here as ‘crypt’), as well as the layer specific locations of cells that exist within the gastrointestinal tract. Layers depicted here include epithelium (rows of cells bordering villus), submucosa (white space below the epithelium containing networks of neurons and ganglia depicted in pink), muscularis mucosae (blue layer), muscularis propria (referred to here as muscle layer). + +ISC: Intestinal Stem Cell +TA: Transit Amplifying Cells"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [license](http://purl.org/dc/elements/1.1/license) "http://creativecommons.org/licenses/by/4.0/"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### enterocyte of epithelium proper of ileum `http://purl.obolibrary.org/obo/CL_1000342` +#### Removed +- [enterocyte of epithelium proper of ileum](http://purl.obolibrary.org/obo/CL_1000342) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +Enterocytes of the epithelium proper of the ileum, commonly known as ileal enterocytes, are specialized epithelial cells found lining the inner surface of the ileum, the final section of the small intestine in the human body. They play a pivotal role in nutrient absorption, digestive metabolic functions, and the maintenance of the host’s immune response. +Like enterocytes in other parts of the intestine, ileal enterocytes exhibit distinct characteristics specific to their function and role. They have microvilli on their apical surfaces to increase absorption and are important in the absorption of vitamins and the reabsorption of bile salts. These cells also produce enzymes that metabolize lipids and xenobiotics."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1038/nri3738"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1084/jem.20191130"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1111/j.1365-2249.2011.04523.x"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [enterocyte of epithelium proper of ileum](http://purl.obolibrary.org/obo/CL_1000342) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Enterocytes of the epithelium proper of the ileum, commonly known as ileal enterocytes, are specialized epithelial cells found lining the inner surface of the ileum, the final section of the small intestine in the human body. They play a pivotal role in nutrient absorption, digestive metabolic functions, and the maintenance of the host’s immune response. +Like enterocytes in other parts of the intestine, ileal enterocytes exhibit distinct characteristics specific to their function and role. They have microvilli on their apical surfaces to increase absorption and are important in the absorption of vitamins and the reabsorption of bile salts. These cells also produce enzymes that metabolize lipids and xenobiotics."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1038/nri3738"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1084/jem.20191130"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1111/j.1365-2249.2011.04523.x"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### enteroendocrine cell `http://purl.obolibrary.org/obo/CL_0000164` +#### Removed +- [enteroendocrine cell](http://purl.obolibrary.org/obo/CL_0000164) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +Enteroendocrine cells are a specialized subset of cells located within the epithelial lining of both the small and large intestines, as well as the stomach and pancreas. Constituting less than 1% of the total population of intestinal cells, they are differentiated from a common intestinal cell progenitor, thus sharing lineage with absorptive and goblet cells of the intestines. +The distinct characteristic feature of an enteroendocrine cell is its inherent capacity to synthesize and secrete a plethora of gut hormones such as serotonin, somatostatin, neurotensin, cholecystokinin, secretin, gastric inhibitory peptide, motilin, and glucagon-like peptide-1. Integrated within this complex network of signaling agents, these substances control various aspects of the digestive system. Each enteroendocrine cell has its unique combination of hormones to release, determined by its position along the intestinal tract. Intriguingly, these hormones not only modulate local gut function, including motility, absorption and secretion, but also potentiate distant actions on other systems such as endocrine, nervous and immune and play a role in the feeling of satiety. +The release of these hormones from enteroendocrine cells is a highly regulated and dynamic process. The cells are equipped with sensory receptors localized on its luminal side that respond to various stimuli, including changes in nutrient composition, chemical or mechanical changes in the gut lumen, or even signals arising from commensal microbiota. This sensory input stimulates a signaling cascade within the cell, culminating in the release of specific hormones into the interstitial fluid. These hormones then make their way into the bloodstream, acting on their respective target receptors to mediate their duties. The multifunctional characteristics of enteroendocrine cells make them crucial for maintaining gut homeostasis and the overall physiological well being of the body."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.7554/elife.78512"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1111/j.1463-1326.2011.01438.x"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1196/annals.1294.001"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1210/endrev/bnaa018"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1038/s41574-019-0168-8"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [enteroendocrine cell](http://purl.obolibrary.org/obo/CL_0000164) SubClassOf [glandular secretory epithelial cell](http://purl.obolibrary.org/obo/CL_0000150) + +#### Added +- [enteroendocrine cell](http://purl.obolibrary.org/obo/CL_0000164) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Enteroendocrine cells are a specialized subset of cells located within the epithelial lining of both the small and large intestines, as well as the stomach and pancreas. Constituting less than 1% of the total population of intestinal cells, they are differentiated from a common intestinal cell progenitor, thus sharing lineage with absorptive and goblet cells of the intestines. +The distinct characteristic feature of an enteroendocrine cell is its inherent capacity to synthesize and secrete a plethora of gut hormones such as serotonin, somatostatin, neurotensin, cholecystokinin, secretin, gastric inhibitory peptide, motilin, and glucagon-like peptide-1. Integrated within this complex network of signaling agents, these substances control various aspects of the digestive system. Each enteroendocrine cell has its unique combination of hormones to release, determined by its position along the intestinal tract. Intriguingly, these hormones not only modulate local gut function, including motility, absorption and secretion, but also potentiate distant actions on other systems such as endocrine, nervous and immune and play a role in the feeling of satiety. +The release of these hormones from enteroendocrine cells is a highly regulated and dynamic process. The cells are equipped with sensory receptors localized on its luminal side that respond to various stimuli, including changes in nutrient composition, chemical or mechanical changes in the gut lumen, or even signals arising from commensal microbiota. This sensory input stimulates a signaling cascade within the cell, culminating in the release of specific hormones into the interstitial fluid. These hormones then make their way into the bloodstream, acting on their respective target receptors to mediate their duties. The multifunctional characteristics of enteroendocrine cells make them crucial for maintaining gut homeostasis and the overall physiological well being of the body."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.7554/elife.78512"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1111/j.1463-1326.2011.01438.x"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1196/annals.1294.001"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1210/endrev/bnaa018"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1038/s41574-019-0168-8"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [enteroendocrine cell](http://purl.obolibrary.org/obo/CL_0000164) SubClassOf [secretory epithelial cell](http://purl.obolibrary.org/obo/CL_1100001) + + +### enteroendocrine cell of anorectum `http://purl.obolibrary.org/obo/CL_0009063` +#### Removed +- [enteroendocrine cell of anorectum](http://purl.obolibrary.org/obo/CL_0009063) SubClassOf [glandular cell of the large intestine](http://purl.obolibrary.org/obo/CL_0002658) + +#### Added +- [enteroendocrine cell of anorectum](http://purl.obolibrary.org/obo/CL_0009063) SubClassOf [epithelial cell of large intestine](http://purl.obolibrary.org/obo/CL_0002253) + + +### enteroendocrine cell of appendix `http://purl.obolibrary.org/obo/CL_0009030` +#### Removed +- [enteroendocrine cell of appendix](http://purl.obolibrary.org/obo/CL_0009030) SubClassOf [appendix glandular cell](http://purl.obolibrary.org/obo/CL_1001585) + +#### Added +- [enteroendocrine cell of appendix](http://purl.obolibrary.org/obo/CL_0009030) SubClassOf [epithelial cell of appendix](http://purl.obolibrary.org/obo/CL_1000405) + + +### enteroendocrine cell of colon `http://purl.obolibrary.org/obo/CL_0009042` +#### Removed +- [enteroendocrine cell of colon](http://purl.obolibrary.org/obo/CL_0009042) SubClassOf [colon glandular cell](http://purl.obolibrary.org/obo/CL_1001588) + +#### Added +- [enteroendocrine cell of colon](http://purl.obolibrary.org/obo/CL_0009042) SubClassOf [colon epithelial cell](http://purl.obolibrary.org/obo/CL_0011108) + + +### enteroendocrine cell of small intestine `http://purl.obolibrary.org/obo/CL_0009006` + +#### Added +- [enteroendocrine cell of small intestine](http://purl.obolibrary.org/obo/CL_0009006) [depiction](http://xmlns.com/foaf/0.1/depiction) [Small-intestine-cells.png](http://purl.obolibrary.org/obo/cl/images/Small-intestine-cells.png) + - [comment](http://www.w3.org/2000/01/rdf-schema#comment) "Figure depicts a cross section of intestinal villi in the small intestine, including the crypts of Lieberkuhn (seen here as ‘crypt’), as well as the layer specific locations of cells that exist within the gastrointestinal tract. Layers depicted here include epithelium (rows of cells bordering villus), submucosa (white space below the epithelium containing networks of neurons and ganglia depicted in pink), muscularis mucosae (blue layer), muscularis propria (referred to here as muscle layer). + +ISC: Intestinal Stem Cell +TA: Transit Amplifying Cells"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [license](http://purl.org/dc/elements/1.1/license) "http://creativecommons.org/licenses/by/4.0/"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [enteroendocrine cell of small intestine](http://purl.obolibrary.org/obo/CL_0009006) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +The enteroendocrine cell of the small intestine is a specialized type of cell that forms part of the lining of the intestinal wall. These cells are interspersed among absorptive cells, mucus-secreting goblet cells, and other gut cell types, forming the crypt-villus axis, which is the functional unit of the small intestinal epithelium. +Functionally, enteroendocrine cells play a pivotal role in the gut-endocrine system, which is responsible for the digestive process. These cells translate the luminal nutrient status into hormonal signals thereby acting as chemosensors. They contain secretory granules at their base which release hormones into the bloodstream following chemo-sensation. The hormones they secrete perform diverse functions including regulating gastric secretion, gut motility, insulin release, appetite control and other local and systemic effects. +In addition to their endocrine functions, enteroendocrine cells also play a part in the modulation of the immune response in the gut. They can secrete cytokines and chemokines that have a role in directing the immune response to invading pathogens. Moreover, emerging research suggests that these cells play a role in maintaining the balance between gut resident bacteria, known as the gut microbiota, and the host. As such, a comprehensive understanding of the enteroendocrine cells of the small intestine underpins knowledge in nutrition, endocrinology, and various gastroenterological conditions."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1111/j.1365-2613.2011.00767.x"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1146/annurev-physiol-021115-105439"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1038/nature24489"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1016/j.coph.2013.09.008"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1038/mi.2017.73"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [enteroendocrine cell of small intestine](http://purl.obolibrary.org/obo/CL_0009006) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://cellxgene.cziscience.com/cellguide/CL_0009006"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### eosinophil progenitor cell `http://purl.obolibrary.org/obo/CL_0000611` +#### Removed +- [eosinophil progenitor cell](http://purl.obolibrary.org/obo/CL_0000611) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) + + + +### ependymal cell `http://purl.obolibrary.org/obo/CL_0000065` +#### Removed +- [ependymal cell](http://purl.obolibrary.org/obo/CL_0000065) EquivalentTo [neurecto-epithelial cell](http://purl.obolibrary.org/obo/CL_0000710) and ([BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0004670](http://purl.obolibrary.org/obo/UBERON_0004670)) + +#### Added +- [ependymal cell](http://purl.obolibrary.org/obo/CL_0000065) EquivalentTo [epithelial cell](http://purl.obolibrary.org/obo/CL_0000066) and ([BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0004670](http://purl.obolibrary.org/obo/UBERON_0004670)) + + +### epididymis secretory cell `http://purl.obolibrary.org/obo/CL_1001590` +#### Removed +- [epididymis secretory cell](http://purl.obolibrary.org/obo/CL_1001590) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "epididymis glandular cells"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "CALOHA:TS-1276"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [epididymis secretory cell](http://purl.obolibrary.org/obo/CL_1001590) [label](http://www.w3.org/2000/01/rdf-schema#label) "epididymis glandular cell"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [epididymis secretory cell](http://purl.obolibrary.org/obo/CL_1001590) EquivalentTo [glandular secretory epithelial cell](http://purl.obolibrary.org/obo/CL_0000150) and ([BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0001301](http://purl.obolibrary.org/obo/UBERON_0001301)) + +- [epididymis secretory cell](http://purl.obolibrary.org/obo/CL_1001590) SubClassOf [glandular secretory epithelial cell](http://purl.obolibrary.org/obo/CL_0000150) + +#### Added +- [epididymis secretory cell](http://purl.obolibrary.org/obo/CL_1001590) [label](http://www.w3.org/2000/01/rdf-schema#label) "epididymis secretory cell"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [epididymis secretory cell](http://purl.obolibrary.org/obo/CL_1001590) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "epididymis glandular cell"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "CALOHA:TS-1276"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [epididymis secretory cell](http://purl.obolibrary.org/obo/CL_1001590) EquivalentTo [secretory epithelial cell](http://purl.obolibrary.org/obo/CL_1100001) and ([BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0001301](http://purl.obolibrary.org/obo/UBERON_0001301)) + +- [epididymis secretory cell](http://purl.obolibrary.org/obo/CL_1001590) SubClassOf [secretory epithelial cell](http://purl.obolibrary.org/obo/CL_1100001) + + +### epithelial cell of Malassez `http://purl.obolibrary.org/obo/CL_0002166` +#### Removed +- [epithelial cell of Malassez](http://purl.obolibrary.org/obo/CL_0002166) SubClassOf [epithelial cell of alimentary canal](http://purl.obolibrary.org/obo/CL_0002251) + + + +### epithelial cell of alimentary canal `http://purl.obolibrary.org/obo/CL_0002251` +#### Removed +- [epithelial cell of alimentary canal](http://purl.obolibrary.org/obo/CL_0002251) EquivalentTo [epithelial cell](http://purl.obolibrary.org/obo/CL_0000066) and ([BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0001555](http://purl.obolibrary.org/obo/UBERON_0001555)) + +- [epithelial cell of alimentary canal](http://purl.obolibrary.org/obo/CL_0002251) SubClassOf [BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0001555](http://purl.obolibrary.org/obo/UBERON_0001555) + +#### Added +- [epithelial cell of alimentary canal](http://purl.obolibrary.org/obo/CL_0002251) EquivalentTo [epithelial cell](http://purl.obolibrary.org/obo/CL_0000066) and ([BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0003929](http://purl.obolibrary.org/obo/UBERON_0003929)) + +- [epithelial cell of alimentary canal](http://purl.obolibrary.org/obo/CL_0002251) SubClassOf [BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0003929](http://purl.obolibrary.org/obo/UBERON_0003929) + + +### epithelial cell of amnion `http://purl.obolibrary.org/obo/CL_0002536` + +#### Added +- [epithelial cell of amnion](http://purl.obolibrary.org/obo/CL_0002536) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl/cl-base#cellxgene_subset) + + +### epithelial cell of appendix `http://purl.obolibrary.org/obo/CL_1000405` +#### Removed +- [epithelial cell of appendix](http://purl.obolibrary.org/obo/CL_1000405) EquivalentTo [epithelial cell](http://purl.obolibrary.org/obo/CL_0000066) and ([BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0001154](http://purl.obolibrary.org/obo/UBERON_0001154)) + +- [epithelial cell of appendix](http://purl.obolibrary.org/obo/CL_1000405) SubClassOf [BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0001154](http://purl.obolibrary.org/obo/UBERON_0001154) + +#### Added +- [epithelial cell of appendix](http://purl.obolibrary.org/obo/CL_1000405) EquivalentTo [epithelial cell](http://purl.obolibrary.org/obo/CL_0000066) and ([BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0009697](http://purl.obolibrary.org/obo/UBERON_0009697)) + +- [epithelial cell of appendix](http://purl.obolibrary.org/obo/CL_1000405) SubClassOf [BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0009697](http://purl.obolibrary.org/obo/UBERON_0009697) + + +### epithelial cell of endometrial gland `http://purl.obolibrary.org/obo/CL_0009084` +#### Removed +- [epithelial cell of endometrial gland](http://purl.obolibrary.org/obo/CL_0009084) EquivalentTo [epithelial cell](http://purl.obolibrary.org/obo/CL_0000066) and ([BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0002451](http://purl.obolibrary.org/obo/UBERON_0002451)) + +- [epithelial cell of endometrial gland](http://purl.obolibrary.org/obo/CL_0009084) SubClassOf [BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0002451](http://purl.obolibrary.org/obo/UBERON_0002451) + +#### Added +- [epithelial cell of endometrial gland](http://purl.obolibrary.org/obo/CL_0009084) EquivalentTo [epithelial cell](http://purl.obolibrary.org/obo/CL_0000066) and ([BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0012276](http://purl.obolibrary.org/obo/UBERON_0012276)) + +- [epithelial cell of endometrial gland](http://purl.obolibrary.org/obo/CL_0009084) SubClassOf [BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0012276](http://purl.obolibrary.org/obo/UBERON_0012276) + + +### epithelial cell of esophagus `http://purl.obolibrary.org/obo/CL_0002252` +#### Removed +- [epithelial cell of esophagus](http://purl.obolibrary.org/obo/CL_0002252) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "An epithelial cell of the esophagus."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:tfm"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [epithelial cell of esophagus](http://purl.obolibrary.org/obo/CL_0002252) EquivalentTo [epithelial cell](http://purl.obolibrary.org/obo/CL_0000066) and ([BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0001043](http://purl.obolibrary.org/obo/UBERON_0001043)) + +- [epithelial cell of esophagus](http://purl.obolibrary.org/obo/CL_0002252) SubClassOf [BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0001043](http://purl.obolibrary.org/obo/UBERON_0001043) + +#### Added +- [epithelial cell of esophagus](http://purl.obolibrary.org/obo/CL_0002252) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "An epithelial cell of the lining of the esophagus."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:tfm"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [epithelial cell of esophagus](http://purl.obolibrary.org/obo/CL_0002252) EquivalentTo [epithelial cell](http://purl.obolibrary.org/obo/CL_0000066) and ([BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0001976](http://purl.obolibrary.org/obo/UBERON_0001976)) + +- [epithelial cell of esophagus](http://purl.obolibrary.org/obo/CL_0002252) SubClassOf [BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0001976](http://purl.obolibrary.org/obo/UBERON_0001976) + + +### epithelial cell of lacrimal sac `http://purl.obolibrary.org/obo/CL_1000436` +#### Removed +- [epithelial cell of lacrimal sac](http://purl.obolibrary.org/obo/CL_1000436) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +Epithelial cells of the lacrimal sac play a significant role in the physiology of tear drainage, acting as an integral part of the lacrimal drainage system. The lacrimal sac is part of the nasolacrimal duct system, a conduit which connects the eye to the nasal cavity, and is lined by multilayered, non-keratinizing, squamous epithelial cells. +The epithelial cells of the lacrimal sac are specialized for the purpose of maintaining a moist environment and protecting the surface of the eye. They form a barrier that traps and removes potential contaminants from the tear film during the drainage process. These cells also actively contribute to tear turnover by expediting the drainage of excess tears. Dysfunctional epithelial cells of the lacrimal sac can lead to dacryocystitis, a condition characterized by inflammation of the lacrimal sac. +Epithelial cells of the lacrimal sac also perform various other tasks which ensure the overall health of the eye. They are involved in the regulation of immune responses within the lacrimal apparatus and may have a possible role in host-microbiome interactions. Thus, epithelial cells of the lacrimal sac play a multifaceted role in tear drainage and ocular surface defence, directly translating to eye health and vision quality."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.2147/OPTH.S26048"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1167/tvst.8.4.32"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1007/s004290050160"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1111/j.1442-9071.2012.02818.x"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.3389/fimmu.2022.918619"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [epithelial cell of lacrimal sac](http://purl.obolibrary.org/obo/CL_1000436) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Epithelial cells of the lacrimal sac play a significant role in the physiology of tear drainage, acting as an integral part of the lacrimal drainage system. The lacrimal sac is part of the nasolacrimal duct system, a conduit which connects the eye to the nasal cavity, and is lined by multilayered, non-keratinizing, squamous epithelial cells. +The epithelial cells of the lacrimal sac are specialized for the purpose of maintaining a moist environment and protecting the surface of the eye. They form a barrier that traps and removes potential contaminants from the tear film during the drainage process. These cells also actively contribute to tear turnover by expediting the drainage of excess tears. Dysfunctional epithelial cells of the lacrimal sac can lead to dacryocystitis, a condition characterized by inflammation of the lacrimal sac. +Epithelial cells of the lacrimal sac also perform various other tasks which ensure the overall health of the eye. They are involved in the regulation of immune responses within the lacrimal apparatus and may have a possible role in host-microbiome interactions. Thus, epithelial cells of the lacrimal sac play a multifaceted role in tear drainage and ocular surface defence, directly translating to eye health and vision quality."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.2147/OPTH.S26048"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1167/tvst.8.4.32"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1007/s004290050160"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1111/j.1442-9071.2012.02818.x"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.3389/fimmu.2022.918619"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### epithelial cell of large intestine `http://purl.obolibrary.org/obo/CL_0002253` +#### Removed +- [epithelial cell of large intestine](http://purl.obolibrary.org/obo/CL_0002253) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "An epithelial cell of the large intestine."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:tfm"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [epithelial cell of large intestine](http://purl.obolibrary.org/obo/CL_0002253) SubClassOf [BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0000059](http://purl.obolibrary.org/obo/UBERON_0000059) + +#### Added +- [epithelial cell of large intestine](http://purl.obolibrary.org/obo/CL_0002253) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "An epithelial cell of the lining of the large intestine."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:tfm"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [epithelial cell of large intestine](http://purl.obolibrary.org/obo/CL_0002253) SubClassOf [BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0001278](http://purl.obolibrary.org/obo/UBERON_0001278) + + +### epithelial cell of nephron `http://purl.obolibrary.org/obo/CL_1000449` + +#### Added +- [epithelial cell of nephron](http://purl.obolibrary.org/obo/CL_1000449) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Epithelial cells of the nephron form the epithelial lining of the nephron, the functional unit of the kidney that filters the blood to produce urine. Each kidney holds approximately one million nephrons, each of which is composed of several distinct parts, including the renal corpuscle, the proximal tubule, the loop of Henle, and the distal tubule. All sections are lined with highly specialized epithelial cells adapted to perform different functions within the sections of the nephron. +The different epithelial cells of the nephron play crucial roles in the process of filtration, reabsorption, secretion, and excretion, essential tasks for the regulation of body fluid composition and volume. During filtration, the blood is forced through the walls of glomerular capillaries into the Bowman's capsule, where waste products, electrolytes, and water are separated from the blood cells and proteins. As the filtrate then passes through the nephron, epithelial cells of the tubular portion reabsorb useful substances such as glucose, amino acids, and electrolytes, along with most of the water back into the bloodstream. Waste products like urea and creatinine, as well as excess ions and water, remain in the tubule for elimination. +In addition, epithelial cells of the nephron also play a vital part in maintaining the body's acid-base balance by actively secreting hydrogen ions into the urine while reabsorbing bicarbonate from the urine back into the blood. They are also involved in the regulation of blood pressure through the renin-angiotensin-aldosterone system and contribute to erythrocyte production by releasing the hormone erythropoietin in response to low oxygen levels in the blood. Abnormalities or damage in renal epithelial cells often result in impaired kidney function, leading to various renal diseases."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1016/B978-0-323-35775-3.00011-4"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1007/978-94-011-2354-9_6"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1681/ASN.2012010029"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1007/s004670050586"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1146/annurev-physiol-052521-121841"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [epithelial cell of nephron](http://purl.obolibrary.org/obo/CL_1000449) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://cellxgene.cziscience.com/cellguide/CL_1000449"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### epithelial cell of pancreas `http://purl.obolibrary.org/obo/CL_0000083` + +#### Added +- [epithelial cell of pancreas](http://purl.obolibrary.org/obo/CL_0000083) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl/cl-base#cellxgene_subset) + + +### epithelial cell of parathyroid gland `http://purl.obolibrary.org/obo/CL_0002260` +#### Removed +- [epithelial cell of parathyroid gland](http://purl.obolibrary.org/obo/CL_0002260) EquivalentTo [endo-epithelial cell](http://purl.obolibrary.org/obo/CL_0002076) and ([BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0001132](http://purl.obolibrary.org/obo/UBERON_0001132)) + +- [epithelial cell of parathyroid gland](http://purl.obolibrary.org/obo/CL_0002260) SubClassOf [endo-epithelial cell](http://purl.obolibrary.org/obo/CL_0002076) + - [is_inferred](http://www.geneontology.org/formats/oboInOwl#is_inferred) "true"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [epithelial cell of parathyroid gland](http://purl.obolibrary.org/obo/CL_0002260) SubClassOf [parathyroid glandular cell](http://purl.obolibrary.org/obo/CL_1001593) + +#### Added +- [epithelial cell of parathyroid gland](http://purl.obolibrary.org/obo/CL_0002260) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl/cl-base#cellxgene_subset) + +- [epithelial cell of parathyroid gland](http://purl.obolibrary.org/obo/CL_0002260) EquivalentTo [epithelial cell](http://purl.obolibrary.org/obo/CL_0000066) and ([BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0001132](http://purl.obolibrary.org/obo/UBERON_0001132)) + +- [epithelial cell of parathyroid gland](http://purl.obolibrary.org/obo/CL_0002260) SubClassOf [BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0001132](http://purl.obolibrary.org/obo/UBERON_0001132) + +- [epithelial cell of parathyroid gland](http://purl.obolibrary.org/obo/CL_0002260) SubClassOf [endo-epithelial cell](http://purl.obolibrary.org/obo/CL_0002076) + + +### epithelial cell of prostatic urethra `http://purl.obolibrary.org/obo/CL_0017003` +#### Removed +- [epithelial cell of prostatic urethra](http://purl.obolibrary.org/obo/CL_0017003) [created by](http://www.geneontology.org/formats/oboInOwl#created_by) "http://orcid.org/0000-0003-2473-2313"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [epithelial cell of prostatic urethra](http://purl.obolibrary.org/obo/CL_0017003) [contributor](http://purl.org/dc/terms/contributor) [0000-0003-2473-2313](http://orcid.org/0000-0003-2473-2313) + + +### epithelial cell of small intestine `http://purl.obolibrary.org/obo/CL_0002254` +#### Removed +- [epithelial cell of small intestine](http://purl.obolibrary.org/obo/CL_0002254) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "An epithelial cell of the small intestine."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:tfm"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [epithelial cell of small intestine](http://purl.obolibrary.org/obo/CL_0002254) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "An epithelial cell of the lining of the small intestine."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:tfm"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### epithelial cell of stomach `http://purl.obolibrary.org/obo/CL_0002178` +#### Removed +- [epithelial cell of stomach](http://purl.obolibrary.org/obo/CL_0002178) EquivalentTo [epithelial cell](http://purl.obolibrary.org/obo/CL_0000066) and ([BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0000945](http://purl.obolibrary.org/obo/UBERON_0000945)) + +- [epithelial cell of stomach](http://purl.obolibrary.org/obo/CL_0002178) SubClassOf [BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0000945](http://purl.obolibrary.org/obo/UBERON_0000945) + +#### Added +- [epithelial cell of stomach](http://purl.obolibrary.org/obo/CL_0002178) EquivalentTo [epithelial cell](http://purl.obolibrary.org/obo/CL_0000066) and ([BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0001276](http://purl.obolibrary.org/obo/UBERON_0001276)) + +- [epithelial cell of stomach](http://purl.obolibrary.org/obo/CL_0002178) SubClassOf [BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0001276](http://purl.obolibrary.org/obo/UBERON_0001276) + + +### epithelial cell of thyroid gland `http://purl.obolibrary.org/obo/CL_0002257` + +#### Added +- [epithelial cell of thyroid gland](http://purl.obolibrary.org/obo/CL_0002257) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl/cl-base#cellxgene_subset) + + +### epithelial cell of urethra `http://purl.obolibrary.org/obo/CL_1000296` + +#### Added +- [epithelial cell of urethra](http://purl.obolibrary.org/obo/CL_1000296) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Epithelial cells of the urethra constitute the inner lining of the urethra, forming a mucosal barrier that helps protect the body from external contaminants. The type of epithelial cells found in the urethra can vary along its length. In general, the urethra is lined with stratified squamous epithelium in its distal or external portion, which is closer to the external environment. This type of epithelium provides protection against mechanical stress and pathogens. Closer to the bladder, the urethra transitions to a different type of epithelium. In males, the proximal part of the urethra is lined with pseudostratified columnar epithelium in the region where it passes through the prostate gland. In females, the transitional epithelium may be present in the proximal part of the urethra near the bladder. +Epithelial cells of the urethra are primarily dedicated to the protection of underlying tissues from mechanical stress and pathogens during micturition (urination). They do this by creating a tight, impermeable barrier that prevents the entry and colonization of invading microbes. They produce a variety of antimicrobials and are tightly packed to prevent infiltration between cells, forming an integral part of the body's innate immune system. +In addition to their protective role, these cells are involved in the secretion of mucus. This mucus acts as a lubricant that ensures the smooth and easy passage of urine from the bladder through the urethra and out of the body, reducing any potential damage from the erosive action of urine. Epithelial cells of the urethra are dynamic, constantly renewing their numbers to replace any cells lost through wear and tear. Any disruptions to the function or integrity of these cells may contribute to urinary tract infections and other urological disorders."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1152/ajprenal.00327.2009"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1089/ten.teb.2016.0352"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1101/2020.02.19.937615v2.full"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1016/j.celrep.2018.11.086"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1038/s41385-022-00565-0"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [epithelial cell of urethra](http://purl.obolibrary.org/obo/CL_1000296) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://cellxgene.cziscience.com/cellguide/CL_1000296"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### erythroid progenitor cell, mammalian `http://purl.obolibrary.org/obo/CL_0001066` +#### Removed +- [erythroid progenitor cell, mammalian](http://purl.obolibrary.org/obo/CL_0001066) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) + + + +### eukaryotic cell `http://purl.obolibrary.org/obo/CL_0000255` +#### Removed +- [eukaryotic cell](http://purl.obolibrary.org/obo/CL_0000255) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl/cl-base#cellxgene_subset) + + + +### excretory cell `http://purl.obolibrary.org/obo/CL_0000424` +#### Removed +- [excretory cell](http://purl.obolibrary.org/obo/CL_0000424) SubClassOf [secretory cell](http://purl.obolibrary.org/obo/CL_0000151) + +#### Added +- [excretory cell](http://purl.obolibrary.org/obo/CL_0000424) SubClassOf [cell](http://purl.obolibrary.org/obo/CL_0000000) + + +### externa theca cell `http://purl.obolibrary.org/obo/CL_4052013` + +#### Added +- [externa theca cell](http://purl.obolibrary.org/obo/CL_4052013) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "externa TC"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003000](http://purl.obolibrary.org/obo/OMO_0003000) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:31320652"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [externa theca cell](http://purl.obolibrary.org/obo/CL_4052013) [date](http://purl.org/dc/terms/date) "2024-09-30T11:10:15Z"^^[dateTime](http://www.w3.org/2001/XMLSchema#dateTime) + +- [externa theca cell](http://purl.obolibrary.org/obo/CL_4052013) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "exTC"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003000](http://purl.obolibrary.org/obo/OMO_0003000) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:31320652"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [externa theca cell](http://purl.obolibrary.org/obo/CL_4052013) [contributor](http://purl.org/dc/terms/contributor) [0009-0000-8480-9277](https://orcid.org/0009-0000-8480-9277) + +- [externa theca cell](http://purl.obolibrary.org/obo/CL_4052013) [id](http://www.geneontology.org/formats/oboInOwl#id) "CL:4052013"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [externa theca cell](http://purl.obolibrary.org/obo/CL_4052013) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A specialized theca cell that forms the outer layer of the theca surrounding the ovarian follicle, appearing at the antral follicle. Originating from progenitor theca cells, theca externa cell is characterized by its fibroblast-like appearance and primarily function to provide structural support to the developing follicle. This cell produces collagen fibers and extracellular matrix components such as Col1a1 and Col1a2."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:31320652"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:32530882"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Theca_externa"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:36758341"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [externa theca cell](http://purl.obolibrary.org/obo/CL_4052013) [label](http://www.w3.org/2000/01/rdf-schema#label) "externa theca cell"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- Class: [externa theca cell](http://purl.obolibrary.org/obo/CL_4052013) + +- [externa theca cell](http://purl.obolibrary.org/obo/CL_4052013) EquivalentTo [theca cell](http://purl.obolibrary.org/obo/CL_0000503) and ([BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0000156](http://purl.obolibrary.org/obo/UBERON_0000156)) + +- [externa theca cell](http://purl.obolibrary.org/obo/CL_4052013) SubClassOf [RO_0002202](http://purl.obolibrary.org/obo/RO_0002202) some [pre-theca cell](http://purl.obolibrary.org/obo/CL_4052010) + +- [externa theca cell](http://purl.obolibrary.org/obo/CL_4052013) SubClassOf [BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0000156](http://purl.obolibrary.org/obo/UBERON_0000156) + +- [externa theca cell](http://purl.obolibrary.org/obo/CL_4052013) SubClassOf [theca cell](http://purl.obolibrary.org/obo/CL_0000503) + + +### extraembryonic cell `http://purl.obolibrary.org/obo/CL_0000349` + +#### Added +- [extraembryonic cell](http://purl.obolibrary.org/obo/CL_0000349) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl/cl-base#cellxgene_subset) + + +### extravillous trophoblast `http://purl.obolibrary.org/obo/CL_0008036` + +#### Added +- [extravillous trophoblast](http://purl.obolibrary.org/obo/CL_0008036) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Extravillous trophoblasts (EVTs), a specialized subset of trophoblast cells, play crucial roles in establishing and sustaining pregnancy. +Firstly, they anchor the fetus to the maternal tissue, providing structural stability. Secondly, they are instrumental in modifying the maternal spiral arteries to ensure an adequate supply of maternal blood to the placenta and the developing fetus. EVTs invade maternal decidua and myometrium and replace the endothelial lining of the spiral arteries, transforming these high-resistance, narrow vessels into low-resistance, wide vessels, favouring higher blood flow. Thirdly, these cells also play an immunological role, creating an environment conducive to the acceptance of the semi-allogeneic fetus, by expressing non-classical MHC molecules, thereby averting any potential maternal immune response towards fetal tissues. +While EVTs are commonly associated with healthy pregnancies, abnormalities in their function or development have been connected to problematic pregnancies. Conditions like pre-eclampsia and fetal growth restriction (FGR) may arise if EVT cells do not effectively invade the maternal decidua or adequately remodel."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1016/j.preghy.2010.10.003"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1016/j.it.2017.01.009"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1080/19336918.2015.1120397"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1080/19336918.2015.1089376"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1007/s12522-011-0102-9"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [extravillous trophoblast](http://purl.obolibrary.org/obo/CL_0008036) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://cellxgene.cziscience.com/cellguide/CL_0008036"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### fallopian tube epithelial cell `http://purl.obolibrary.org/obo/CL_4052018` + +#### Added +- [fallopian tube epithelial cell](http://purl.obolibrary.org/obo/CL_4052018) [label](http://www.w3.org/2000/01/rdf-schema#label) "fallopian tube epithelial cell"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [fallopian tube epithelial cell](http://purl.obolibrary.org/obo/CL_4052018) [has_exact_synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "uterine tube epithelial cell"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Fallopian_tube"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [fallopian tube epithelial cell](http://purl.obolibrary.org/obo/CL_4052018) [date](http://purl.org/dc/terms/date) "2024-10-01T12:09:12Z"^^[dateTime](http://www.w3.org/2001/XMLSchema#dateTime) + +- [fallopian tube epithelial cell](http://purl.obolibrary.org/obo/CL_4052018) [has_broad_synonym](http://www.geneontology.org/formats/oboInOwl#hasBroadSynonym) "oviduct epithelial cell"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Fallopian_tube"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [fallopian tube epithelial cell](http://purl.obolibrary.org/obo/CL_4052018) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "Any epithelial cell that is part of the fallopian tube."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Fallopian_tube"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [fallopian tube epithelial cell](http://purl.obolibrary.org/obo/CL_4052018) [contributor](http://purl.org/dc/terms/contributor) [0009-0000-8480-9277](https://orcid.org/0009-0000-8480-9277) + +- [fallopian tube epithelial cell](http://purl.obolibrary.org/obo/CL_4052018) [id](http://www.geneontology.org/formats/oboInOwl#id) "CL:4052018"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- Class: [fallopian tube epithelial cell](http://purl.obolibrary.org/obo/CL_4052018) + +- [fallopian tube epithelial cell](http://purl.obolibrary.org/obo/CL_4052018) EquivalentTo [epithelial cell](http://purl.obolibrary.org/obo/CL_0000066) and ([BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0003889](http://purl.obolibrary.org/obo/UBERON_0003889)) + +- [fallopian tube epithelial cell](http://purl.obolibrary.org/obo/CL_4052018) SubClassOf [BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0003889](http://purl.obolibrary.org/obo/UBERON_0003889) + +- [fallopian tube epithelial cell](http://purl.obolibrary.org/obo/CL_4052018) SubClassOf [epithelial cell](http://purl.obolibrary.org/obo/CL_0000066) + + +### fallopian tube multiciliated cell `http://purl.obolibrary.org/obo/CL_4030007` +#### Removed +- [fallopian tube multiciliated cell](http://purl.obolibrary.org/obo/CL_4030007) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "An epithelial ciliated cell that is part of the fallopian tube. This cell type is found mainly on the apex of the mucosal folds and contributes, together with peristaltic contractions, to the self-propulsion of spermatozoa, the transport of ovum during ovulation and the transport of the fertilized ovum to the intramural fallopian tube. A fallopian tube ciliated cell has a columnar shape and contains an oval or round nucleus, often located perpendicular or parallel to the long axis of the cell."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:16565155"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [fallopian tube multiciliated cell](http://purl.obolibrary.org/obo/CL_4030007) [label](http://www.w3.org/2000/01/rdf-schema#label) "fallopian tube ciliated cell"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [fallopian tube multiciliated cell](http://purl.obolibrary.org/obo/CL_4030007) SubClassOf [BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0003889](http://purl.obolibrary.org/obo/UBERON_0003889) + +#### Added +- [fallopian tube multiciliated cell](http://purl.obolibrary.org/obo/CL_4030007) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A multi-ciliated epithelial cell that is part of the fallopian tube, mainly found on the apex of the mucosal folds. This cell exhibits a columnar shape with an oval nucleus and is characterized by the presence of cilia on its surface. The coordinated beating of these cilia, together with peristaltic contractions, contributes to the self-propulsion of spermatozoa, the transport of ovum during ovulation and the transport of the fertilized ovum to the intramural fallopian tube."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://www.proteinatlas.org/humanproteome/tissue/fallopian+tube"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:16565155"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [fallopian tube multiciliated cell](http://purl.obolibrary.org/obo/CL_4030007) [has_exact_synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "fallopian tube ciliated cell"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [fallopian tube multiciliated cell](http://purl.obolibrary.org/obo/CL_4030007) [label](http://www.w3.org/2000/01/rdf-schema#label) "fallopian tube multiciliated cell"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [fallopian tube multiciliated cell](http://purl.obolibrary.org/obo/CL_4030007) SubClassOf [fallopian tube epithelial cell](http://purl.obolibrary.org/obo/CL_4052018) + + +### fallopian tube non-ciliated cell `http://purl.obolibrary.org/obo/CL_4052019` + +#### Added +- [fallopian tube non-ciliated cell](http://purl.obolibrary.org/obo/CL_4052019) [contributor](http://purl.org/dc/terms/contributor) [0009-0000-8480-9277](https://orcid.org/0009-0000-8480-9277) + +- [fallopian tube non-ciliated cell](http://purl.obolibrary.org/obo/CL_4052019) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "Any epithelial cell that is part of the fallopian tube and lacks cilia."^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [fallopian tube non-ciliated cell](http://purl.obolibrary.org/obo/CL_4052019) [label](http://www.w3.org/2000/01/rdf-schema#label) "fallopian tube non-ciliated cell"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [fallopian tube non-ciliated cell](http://purl.obolibrary.org/obo/CL_4052019) [date](http://purl.org/dc/terms/date) "2024-10-01T12:12:12Z"^^[dateTime](http://www.w3.org/2001/XMLSchema#dateTime) + +- [fallopian tube non-ciliated cell](http://purl.obolibrary.org/obo/CL_4052019) [id](http://www.geneontology.org/formats/oboInOwl#id) "CL:4052019"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- Class: [fallopian tube non-ciliated cell](http://purl.obolibrary.org/obo/CL_4052019) + +- [fallopian tube non-ciliated cell](http://purl.obolibrary.org/obo/CL_4052019) SubClassOf [fallopian tube epithelial cell](http://purl.obolibrary.org/obo/CL_4052018) + +- [fallopian tube non-ciliated cell](http://purl.obolibrary.org/obo/CL_4052019) SubClassOf [lacks_part](http://purl.obolibrary.org/obo/CL_4030045) some [GO_0005929](http://purl.obolibrary.org/obo/GO_0005929) + + +### fallopian tube secretory epithelial cell `http://purl.obolibrary.org/obo/CL_4030006` +#### Removed +- [fallopian tube secretory epithelial cell](http://purl.obolibrary.org/obo/CL_4030006) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "An epithelial cell that is part of the fallopian tube epithelium that secretes mucous fluid and oviduct-specific products through the stimulation of estrogen and luteinizing hormone. The fallopian tube secretory cell has approximately the same height as the ciliated cell and is usually a more narrow columnar cell. The nucleus is ovoid and perpendicular to the long axis of the cell. The chromatin is more dense and the nucleolus smaller than that seen in the ciliated cell."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://doi.org/10.3390/cells8080933"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://doi.org/10.1186/1477-7827-7-129"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://www.proteinatlas.org/learn/dictionary/normal/fallopian+tube"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [fallopian tube secretory epithelial cell](http://purl.obolibrary.org/obo/CL_4030006) SubClassOf [BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0003889](http://purl.obolibrary.org/obo/UBERON_0003889) + +#### Added +- [fallopian tube secretory epithelial cell](http://purl.obolibrary.org/obo/CL_4030006) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "An epithelial cell that is part of the fallopian tube that secretes mucus and oviduct-specific products in response to hormonal stimulation from estrogen and luteinizing hormone. This fallopian tube secretory cell is similar in height to the ciliated cell, but typically exhibits a more narrow, columnar shape. Its nucleus is ovoid and oriented perpendicular to the cell's long axis, with denser chromatin and a smaller nucleolus compared to the ciliated cell."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://doi.org/10.3390/cells8080933"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://doi.org/10.1186/1477-7827-7-129"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://www.proteinatlas.org/learn/dictionary/normal/fallopian+tube"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [fallopian tube secretory epithelial cell](http://purl.obolibrary.org/obo/CL_4030006) SubClassOf [fallopian tube non-ciliated cell](http://purl.obolibrary.org/obo/CL_4052019) + + +### fallopian tube smooth muscle cell `http://purl.obolibrary.org/obo/CL_4052022` + +#### Added +- [fallopian tube smooth muscle cell](http://purl.obolibrary.org/obo/CL_4052022) [contributor](http://purl.org/dc/terms/contributor) [0009-0000-8480-9277](https://orcid.org/0009-0000-8480-9277) + +- [fallopian tube smooth muscle cell](http://purl.obolibrary.org/obo/CL_4052022) [label](http://www.w3.org/2000/01/rdf-schema#label) "fallopian tube smooth muscle cell"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [fallopian tube smooth muscle cell](http://purl.obolibrary.org/obo/CL_4052022) [comment](http://www.w3.org/2000/01/rdf-schema#comment) "The fallopian tube smooth muscle cell in the human contracts dynamically in response to hormones and signaling molecules. Prostaglandins, particularly PGF2α and PGE2, have been shown to increase muscular contractions, while progesterone, levonorgestrel, mifepristone, oxytocin, and human chorionic gonadotropin (hCG) decrease them. These contractile responses are crucial for regulating gamete and embryo transport through the fallopian tube."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:18621753"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [fallopian tube smooth muscle cell](http://purl.obolibrary.org/obo/CL_4052022) [has_broad_synonym](http://www.geneontology.org/formats/oboInOwl#hasBroadSynonym) "oviduct smooth muscle cell"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:31613440"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [fallopian tube smooth muscle cell](http://purl.obolibrary.org/obo/CL_4052022) [id](http://www.geneontology.org/formats/oboInOwl#id) "CL:4052022"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [fallopian tube smooth muscle cell](http://purl.obolibrary.org/obo/CL_4052022) [date](http://purl.org/dc/terms/date) "2024-10-21T12:16:54Z"^^[dateTime](http://www.w3.org/2001/XMLSchema#dateTime) + +- [fallopian tube smooth muscle cell](http://purl.obolibrary.org/obo/CL_4052022) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A smooth muscle cell that is part of the fallopian tube. This cell is responsible for peristaltic contractions that facilitate gamete and embryo transport, fluid mixing, and embryo admission to the uterus."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:31613440"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:31183831"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [fallopian tube smooth muscle cell](http://purl.obolibrary.org/obo/CL_4052022) [has_exact_synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "uterine tube smooth muscle cell"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:31613440"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- Class: [fallopian tube smooth muscle cell](http://purl.obolibrary.org/obo/CL_4052022) + +- [fallopian tube smooth muscle cell](http://purl.obolibrary.org/obo/CL_4052022) EquivalentTo [smooth muscle cell](http://purl.obolibrary.org/obo/CL_0000192) and ([BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0003889](http://purl.obolibrary.org/obo/UBERON_0003889)) + +- [fallopian tube smooth muscle cell](http://purl.obolibrary.org/obo/CL_4052022) SubClassOf [smooth muscle cell](http://purl.obolibrary.org/obo/CL_0000192) + +- [fallopian tube smooth muscle cell](http://purl.obolibrary.org/obo/CL_4052022) SubClassOf [BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0003889](http://purl.obolibrary.org/obo/UBERON_0003889) + + +### fast muscle cell `http://purl.obolibrary.org/obo/CL_0000190` + +#### Added +- [fast muscle cell](http://purl.obolibrary.org/obo/CL_0000190) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Fast muscle cells, also known as type II muscle fibers, are a particular type of muscle cell that specializes in conducting rapid, high-intensity contractions. These cells are primarily found within skeletal muscle groups that are directly involved in gross motor activities, such as running, jumping, or lifting heavy weights. The designation "fast" refers to their speed of contraction in response to neural stimuli, which is significantly quicker when compared to other muscle cell types such as slow-twitch or type I muscle fibers. +The primary function of fast muscle cells revolves around their role in anaerobic metabolism, which provides the energy needed for short, forceful bursts of power. They contain a high concentration of glycolytic enzymes that facilitate this process, leading to a swift break down of glucose to generate ATP (adenosine triphosphate), the primary energy currency in biological systems. On the downside, the byproduct of this very rapid, anaerobic metabolic process is lactic acid, which can build up and cause muscle fatigue. +Fast muscle cells can be further classified into two subtypes based on their metabolic characteristics: type IIa and type IIb/x. Type IIa cells, also known as fast oxidative-glycolytic fibers, possess a good oxygen supply and can function in both anaerobic and aerobic conditions, exhibiting moderate resistance to fatigue. On the other hand, type IIb/x cells, also known as fast glycolytic fibers, primarily rely on anaerobic metabolism and tire out a lot quicker. Both these subtypes can adapt to changing demands due to exercise and conditioning, highlighting the plasticity that is a key characteristic of these versatile muscle cells."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.3389/fcell.2018.00125"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1152/japplphysiol.00636.2019"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.4161/org.4.3.6312"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://www.sciencedirect.com/topics/biochemistry-genetics-and-molecular-biology/fast-muscle-fiber"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [fast muscle cell](http://purl.obolibrary.org/obo/CL_0000190) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://cellxgene.cziscience.com/cellguide/CL_0000190"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### fenestrated endothelial cell `http://purl.obolibrary.org/obo/CL_0000666` +#### Removed +- [fenestrated endothelial cell](http://purl.obolibrary.org/obo/CL_0000666) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +Fenestrated cells are specialized epithelial cells that are characterized by a distinctive structural feature, fenestrations or tiny pores, which allow an exchange of substances such as fluids, nutrients, and waste between blood vessels and the surrounding tissue environments. These cells are present in various types of epithelial tissues in the human body, including the intestinal tract, endocrine glands, and certain parts of the renal system. +There are multiple types of endothelial cell fenestrations. The most common type is found in systemic capillaries of the endocrine tissue (e.g., pancreatic islets), gastrointestinal mucosa, and renal peritubular capillaries. Here, the fenestrated cells have fenestrations in their peripheral cytoplasm with a unique thin and permeable diaphragm that provides a high degree of selectivity, blocking the passage of larger molecules while allowing the free movement of smaller ones. In contrast, other types of fenestrations, such as the discontinuous epithelium of the liver sinusoidal endothelial cells, do not have diaphragms. +Characteristically, fenestrated cells play a vital role in the filtering process of body systems. They are a key part of the glomeruli in the kidneys where blood is filtered under high pressure. The fenestrations present in the endothelial cells lining the capillaries of the glomerulus allow the free passage of water and small solute molecules towards the Bowman's capsule, leaving behind larger proteins and cells in the blood, thereby aiding in the filtration and waste removal process. +In the endocrine system, fenestrated cells in glandular capillaries allow the prompt release of hormones into the bloodstream. These cells have tightly clustered fenestrations which increase the surface area available for passive diffusion, improving the efficiency of hormone secretion. In villi of the small intestine, these cells increase absorption efficiency, permitting the exchange of water, electrolytes, and nutrients. +Overall, fenestrated cells contribute immensely to important physiological processes of filtration, absorption, and secretion, primarily connecting our body's circulation system with the surrounding tissues and organs."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1002/ar.1092200109"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1038/s41467-022-31571-2"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1016/j.devcel.2012.11.003"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1152/ajprenal.90601.2008"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1016/0306-4522(86)90162-4"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [fenestrated endothelial cell](http://purl.obolibrary.org/obo/CL_0000666) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Fenestrated cells are specialized epithelial cells that are characterized by a distinctive structural feature, fenestrations or tiny pores, which allow an exchange of substances such as fluids, nutrients, and waste between blood vessels and the surrounding tissue environments. These cells are present in various types of epithelial tissues in the human body, including the intestinal tract, endocrine glands, and certain parts of the renal system. +There are multiple types of endothelial cell fenestrations. The most common type is found in systemic capillaries of the endocrine tissue (e.g., pancreatic islets), gastrointestinal mucosa, and renal peritubular capillaries. Here, the fenestrated cells have fenestrations in their peripheral cytoplasm with a unique thin and permeable diaphragm that provides a high degree of selectivity, blocking the passage of larger molecules while allowing the free movement of smaller ones. In contrast, other types of fenestrations, such as the discontinuous epithelium of the liver sinusoidal endothelial cells, do not have diaphragms. +Characteristically, fenestrated cells play a vital role in the filtering process of body systems. They are a key part of the glomeruli in the kidneys where blood is filtered under high pressure. The fenestrations present in the endothelial cells lining the capillaries of the glomerulus allow the free passage of water and small solute molecules towards the Bowman's capsule, leaving behind larger proteins and cells in the blood, thereby aiding in the filtration and waste removal process. +In the endocrine system, fenestrated cells in glandular capillaries allow the prompt release of hormones into the bloodstream. These cells have tightly clustered fenestrations which increase the surface area available for passive diffusion, improving the efficiency of hormone secretion. In villi of the small intestine, these cells increase absorption efficiency, permitting the exchange of water, electrolytes, and nutrients. +Overall, fenestrated cells contribute immensely to important physiological processes of filtration, absorption, and secretion, primarily connecting our body's circulation system with the surrounding tissues and organs."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1002/ar.1092200109"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1038/s41467-022-31571-2"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1016/j.devcel.2012.11.003"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1152/ajprenal.90601.2008"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1016/0306-4522(86)90162-4"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### fetal derived definitive erythrocyte `http://purl.obolibrary.org/obo/CL_0002357` +#### Removed +- [fetal derived definitive erythrocyte](http://purl.obolibrary.org/obo/CL_0002357) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) + + + +### fetal liver hematopoietic progenitor cell `http://purl.obolibrary.org/obo/CL_0002353` +#### Removed +- [fetal liver hematopoietic progenitor cell](http://purl.obolibrary.org/obo/CL_0002353) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) + + + +### fetal pre-type II pulmonary alveolar epithelial cell `http://purl.obolibrary.org/obo/CL_4040003` +#### Removed +- [fetal pre-type II pulmonary alveolar epithelial cell](http://purl.obolibrary.org/obo/CL_4040003) [note](http://www.geneontology.org/formats/oboInOwl#note) "According to PMID:1316350 this cell type does not yet produce surfactant. According to PMID:9109447 and PMID:12114192 this cell type produces low levels of surfactant that can be increased by administration of very low-density lipoproteins. This cell type is of medical relevance, as a central feature of the fetal respiratory distress syndrome seems to be the presence in the lung of abundant pre-type II alveolar epithelial cells (PMID:1316350)."^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [fetal pre-type II pulmonary alveolar epithelial cell](http://purl.obolibrary.org/obo/CL_4040003) [comment](http://www.w3.org/2000/01/rdf-schema#comment) "According to PMID:1316350 this cell type does not yet produce surfactant. According to PMID:9109447 and PMID:12114192 this cell type produces low levels of surfactant that can be increased by administration of very low-density lipoproteins. This cell type is of medical relevance, as a central feature of the fetal respiratory distress syndrome seems to be the presence in the lung of abundant pre-type II alveolar epithelial cells (PMID:1316350)."^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### fibroblast `http://purl.obolibrary.org/obo/CL_0000057` +#### Removed +- [fibroblast](http://purl.obolibrary.org/obo/CL_0000057) SubClassOf [RO_0002202](http://purl.obolibrary.org/obo/RO_0002202) some [mesenchymal stem cell](http://purl.obolibrary.org/obo/CL_0000134) + +- [fibroblast](http://purl.obolibrary.org/obo/CL_0000057) SubClassOf [connective tissue cell](http://purl.obolibrary.org/obo/CL_0002320) + +- [fibroblast](http://purl.obolibrary.org/obo/CL_0000057) SubClassOf [BFO_0000002](http://purl.obolibrary.org/obo/BFO_0000002) + +#### Added +- [fibroblast](http://purl.obolibrary.org/obo/CL_0000057) SubClassOf [stromal cell](http://purl.obolibrary.org/obo/CL_0000499) + + +### fibroblast of connective tissue of glandular part of prostate `http://purl.obolibrary.org/obo/CL_1000305` +#### Removed +- [fibroblast of connective tissue of glandular part of prostate](http://purl.obolibrary.org/obo/CL_1000305) SubClassOf [BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0002367](http://purl.obolibrary.org/obo/UBERON_0002367) + +#### Added +- [fibroblast of connective tissue of glandular part of prostate](http://purl.obolibrary.org/obo/CL_1000305) SubClassOf [prostate stromal cell](http://purl.obolibrary.org/obo/CL_0002622) + + +### fibroblast of connective tissue of nonglandular part of prostate `http://purl.obolibrary.org/obo/CL_1000304` +#### Removed +- [fibroblast of connective tissue of nonglandular part of prostate](http://purl.obolibrary.org/obo/CL_1000304) SubClassOf [BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0002367](http://purl.obolibrary.org/obo/UBERON_0002367) + +#### Added +- [fibroblast of connective tissue of nonglandular part of prostate](http://purl.obolibrary.org/obo/CL_1000304) SubClassOf [prostate stromal cell](http://purl.obolibrary.org/obo/CL_0002622) + + +### fibroblast of connective tissue of prostate `http://purl.obolibrary.org/obo/CL_1000299` +#### Removed +- [fibroblast of connective tissue of prostate](http://purl.obolibrary.org/obo/CL_1000299) SubClassOf [BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0002367](http://purl.obolibrary.org/obo/UBERON_0002367) + +#### Added +- [fibroblast of connective tissue of prostate](http://purl.obolibrary.org/obo/CL_1000299) SubClassOf [prostate stromal cell](http://purl.obolibrary.org/obo/CL_0002622) + + +### fibroblast of lymphatic vessel `http://purl.obolibrary.org/obo/CL_0002554` + +#### Added +- [fibroblast of lymphatic vessel](http://purl.obolibrary.org/obo/CL_0002554) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl/cl-base#cellxgene_subset) + + +### fibroblast of outer membrane of prostatic capsule `http://purl.obolibrary.org/obo/CL_1000300` +#### Removed +- [fibroblast of outer membrane of prostatic capsule](http://purl.obolibrary.org/obo/CL_1000300) SubClassOf [BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0002367](http://purl.obolibrary.org/obo/UBERON_0002367) + +#### Added +- [fibroblast of outer membrane of prostatic capsule](http://purl.obolibrary.org/obo/CL_1000300) SubClassOf [prostate stromal cell](http://purl.obolibrary.org/obo/CL_0002622) + + +### fibroblast of subepithelial connective tissue of prostatic gland `http://purl.obolibrary.org/obo/CL_1000301` +#### Removed +- [fibroblast of subepithelial connective tissue of prostatic gland](http://purl.obolibrary.org/obo/CL_1000301) SubClassOf [BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0002367](http://purl.obolibrary.org/obo/UBERON_0002367) + +#### Added +- [fibroblast of subepithelial connective tissue of prostatic gland](http://purl.obolibrary.org/obo/CL_1000301) SubClassOf [prostate stromal cell](http://purl.obolibrary.org/obo/CL_0002622) + + +### fibroblast of tunica adventitia of artery `http://purl.obolibrary.org/obo/CL_1000306` +#### Removed +- [fibroblast of tunica adventitia of artery](http://purl.obolibrary.org/obo/CL_1000306) EquivalentTo [fibroblast](http://purl.obolibrary.org/obo/CL_0000057) and ([BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0005734](http://purl.obolibrary.org/obo/UBERON_0005734)) + +- [fibroblast of tunica adventitia of artery](http://purl.obolibrary.org/obo/CL_1000306) SubClassOf [BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0005734](http://purl.obolibrary.org/obo/UBERON_0005734) + +- [fibroblast of tunica adventitia of artery](http://purl.obolibrary.org/obo/CL_1000306) SubClassOf [adventitial cell](http://purl.obolibrary.org/obo/CL_0002503) + +- [fibroblast of tunica adventitia of artery](http://purl.obolibrary.org/obo/CL_1000306) SubClassOf [fibroblast](http://purl.obolibrary.org/obo/CL_0000057) + - [is_inferred](http://www.geneontology.org/formats/oboInOwl#is_inferred) "true"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [fibroblast of tunica adventitia of artery](http://purl.obolibrary.org/obo/CL_1000306) EquivalentTo [fibroblast](http://purl.obolibrary.org/obo/CL_0000057) and ([BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0007240](http://purl.obolibrary.org/obo/UBERON_0007240)) + +- [fibroblast of tunica adventitia of artery](http://purl.obolibrary.org/obo/CL_1000306) SubClassOf [adventitial fibroblast](http://purl.obolibrary.org/obo/CL_4052030) + +- [fibroblast of tunica adventitia of artery](http://purl.obolibrary.org/obo/CL_1000306) SubClassOf [BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0007240](http://purl.obolibrary.org/obo/UBERON_0007240) + + +### flat midget bipolar cell `http://purl.obolibrary.org/obo/CL_4033033` +#### Removed +- [flat midget bipolar cell](http://purl.obolibrary.org/obo/CL_4033033) [RO_0002175](http://purl.obolibrary.org/obo/RO_0002175) [NCBITaxon_9606](http://purl.obolibrary.org/obo/NCBITaxon_9606) + +- [flat midget bipolar cell](http://purl.obolibrary.org/obo/CL_4033033) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [human_reference_atlas](http://purl.obolibrary.org/obo/cl/cl-base#human_reference_atlas) + +#### Added +- [flat midget bipolar cell](http://purl.obolibrary.org/obo/CL_4033033) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl/cl-base#cellxgene_subset) + + +### forebrain neuroblast `http://purl.obolibrary.org/obo/CL_1000042` + +#### Added +- [forebrain neuroblast](http://purl.obolibrary.org/obo/CL_1000042) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl/cl-base#cellxgene_subset) + + +### foveolar cell of stomach `http://purl.obolibrary.org/obo/CL_0002179` +#### Removed +- [foveolar cell of stomach](http://purl.obolibrary.org/obo/CL_0002179) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "An epithelial cell within one of the pits in the embryonic gastric mucosa from which the gastric glands develop ."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "http://www.merriam-webster.com/medical/foveolar"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:tfm"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [foveolar cell of stomach](http://purl.obolibrary.org/obo/CL_0002179) SubClassOf [epithelial cell of stomach](http://purl.obolibrary.org/obo/CL_0002178) + +#### Added +- [foveolar cell of stomach](http://purl.obolibrary.org/obo/CL_0002179) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A simple columnar cell that populates the entire luminal surface including the gastric pits. This cell types secrete mucus to form a thick protective, lubricant layer over the gastric wall."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Foveolar_cell"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ISBN:0517223651"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:tfm"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [foveolar cell of stomach](http://purl.obolibrary.org/obo/CL_0002179) [has_exact_synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "surface mucosal cell of stomach"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [foveolar cell of stomach](http://purl.obolibrary.org/obo/CL_0002179) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:62949"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [foveolar cell of stomach](http://purl.obolibrary.org/obo/CL_0002179) SubClassOf [columnar/cuboidal epithelial cell](http://purl.obolibrary.org/obo/CL_0000075) + +- [foveolar cell of stomach](http://purl.obolibrary.org/obo/CL_0002179) SubClassOf [mucous cell of stomach](http://purl.obolibrary.org/obo/CL_0002180) + + +### gamete `http://purl.obolibrary.org/obo/CL_0000300` + +#### Added +- [gamete](http://purl.obolibrary.org/obo/CL_0000300) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://cellxgene.cziscience.com/cellguide/CL_0000300"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [gamete](http://purl.obolibrary.org/obo/CL_0000300) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Gametes are reproductive cells essential for sexual reproduction in eukaryotic organisms, including humans, animals, and many plants. These cells are haploid, containing half the genome or only one set of chromosomes, which is a contrast to the diploid state (two sets of chromosomes) found in most cells in a multicellular organism. This reduction in genetic material is crucial since it allows for the re-establishment of the diploid number of chromosomes when two gametes merge to form a diploid zygote during fertilization. +There are two major types of gametes in animals: sperm cells in males and egg (or ova) in females. These gametes contribute equally to the genetic makeup of the offspring but are morphologically and functionally distinct. Sperm cells (or spermatozoa) are characterized by their motility, small size, and large quantities; they are produced continuously in vast numbers through a process called spermatogenesis in the male gonads or testes. Female gametes are much larger, fewer in numbers, and are not motile; they undergo a development process known as oogenesis, which takes place within the ovaries. The egg also contributes most of the cytoplasm and organelles (including mitochondria) to the zygote that are required for initial cell division stages after fertilization. +Gametes have a primary role in sexual reproduction and genetic variation, which aids in evolution. The formation of gametes involves a special type of cell division called meiosis that introduces genetic diversity via the process of recombination and independent assortment. Following the fusion of male and female gametes, the combination of paternal and maternal genetic material in the zygote allows for genetic recombination, which is a fundamental source of genetic variation and, thus, evolution. Therefore, gametes not only are critical to the inception of new individuals but also contribute to species survival and evolution."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://www.ncbi.nlm.nih.gov/books/NBK553142/"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://www.ncbi.nlm.nih.gov/books/NBK10008/"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.3389/fcell.2022.1040708"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1038/s41586-020-2347-0"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### gamma-delta T cell `http://purl.obolibrary.org/obo/CL_0000798` +#### Removed +- [gamma-delta T cell](http://purl.obolibrary.org/obo/CL_0000798) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) + + + +### gastric cardiac gland goblet cell `http://purl.obolibrary.org/obo/CL_1000314` + +#### Added +- [gastric cardiac gland goblet cell](http://purl.obolibrary.org/obo/CL_1000314) SubClassOf [glandular epithelial cell of stomach](http://purl.obolibrary.org/obo/CL_0002659) + + +### gastric goblet cell `http://purl.obolibrary.org/obo/CL_1000313` +#### Removed +- [gastric goblet cell](http://purl.obolibrary.org/obo/CL_1000313) SubClassOf [BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0001276](http://purl.obolibrary.org/obo/UBERON_0001276) + + + +### giant bipolar cell `http://purl.obolibrary.org/obo/CL_4033035` + +#### Added +- [giant bipolar cell](http://purl.obolibrary.org/obo/CL_4033035) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl/cl-base#cellxgene_subset) + + +### gingival epithelial cell `http://purl.obolibrary.org/obo/CL_0002621` + +#### Added +- [gingival epithelial cell](http://purl.obolibrary.org/obo/CL_0002621) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl/cl-base#cellxgene_subset) + + +### glandular cell of esophagus `http://purl.obolibrary.org/obo/CL_0002657` +#### Removed +- [glandular cell of esophagus](http://purl.obolibrary.org/obo/CL_0002657) EquivalentTo [glandular secretory epithelial cell](http://purl.obolibrary.org/obo/CL_0000150) and ([BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0001043](http://purl.obolibrary.org/obo/UBERON_0001043)) + +#### Added +- [glandular cell of esophagus](http://purl.obolibrary.org/obo/CL_0002657) EquivalentTo [glandular secretory epithelial cell](http://purl.obolibrary.org/obo/CL_0000150) and ([BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0001976](http://purl.obolibrary.org/obo/UBERON_0001976)) + + +### glandular endometrial multiciliated epithelial cell `http://purl.obolibrary.org/obo/CL_4030042` +#### Removed +- [glandular endometrial multiciliated epithelial cell](http://purl.obolibrary.org/obo/CL_4030042) [label](http://www.w3.org/2000/01/rdf-schema#label) "glandular endometrial ciliated epithelial cell"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [glandular endometrial multiciliated epithelial cell](http://purl.obolibrary.org/obo/CL_4030042) SubClassOf [BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0012276](http://purl.obolibrary.org/obo/UBERON_0012276) + +#### Added +- [glandular endometrial multiciliated epithelial cell](http://purl.obolibrary.org/obo/CL_4030042) [label](http://www.w3.org/2000/01/rdf-schema#label) "glandular endometrial multiciliated epithelial cell"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [glandular endometrial multiciliated epithelial cell](http://purl.obolibrary.org/obo/CL_4030042) [has_exact_synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "glandular endometrial ciliated epithelial cell"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [glandular endometrial multiciliated epithelial cell](http://purl.obolibrary.org/obo/CL_4030042) SubClassOf [epithelial cell of endometrial gland](http://purl.obolibrary.org/obo/CL_0009084) + + +### glandular endometrial unciliated epithelial cell `http://purl.obolibrary.org/obo/CL_0002656` +#### Removed +- [glandular endometrial unciliated epithelial cell](http://purl.obolibrary.org/obo/CL_0002656) [label](http://www.w3.org/2000/01/rdf-schema#label) "glandular cell of endometrium"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [glandular endometrial unciliated epithelial cell](http://purl.obolibrary.org/obo/CL_0002656) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A glandular epithelial cell of the endometrium."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:tfm"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [glandular endometrial unciliated epithelial cell](http://purl.obolibrary.org/obo/CL_0002656) EquivalentTo [glandular secretory epithelial cell](http://purl.obolibrary.org/obo/CL_0000150) and ([BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0004811](http://purl.obolibrary.org/obo/UBERON_0004811)) + +- [glandular endometrial unciliated epithelial cell](http://purl.obolibrary.org/obo/CL_0002656) SubClassOf [BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0004811](http://purl.obolibrary.org/obo/UBERON_0004811) + +- [glandular endometrial unciliated epithelial cell](http://purl.obolibrary.org/obo/CL_0002656) SubClassOf [epithelial cell of uterus](http://purl.obolibrary.org/obo/CL_0002149) + +#### Added +- [glandular endometrial unciliated epithelial cell](http://purl.obolibrary.org/obo/CL_0002656) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A glandular epithelial cell of the endometrium. Following ovulation, these cells secrete a glycogen-rich substance known as histotroph or uterine milk, which nourishes the embryo if implantation occurs."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:25023676"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:tfm"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [glandular endometrial unciliated epithelial cell](http://purl.obolibrary.org/obo/CL_0002656) [label](http://www.w3.org/2000/01/rdf-schema#label) "glandular endometrial unciliated epithelial cell"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [glandular endometrial unciliated epithelial cell](http://purl.obolibrary.org/obo/CL_0002656) [has_broad_synonym](http://www.geneontology.org/formats/oboInOwl#hasBroadSynonym) "glandular cell of endometrium"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [glandular endometrial unciliated epithelial cell](http://purl.obolibrary.org/obo/CL_0002656) EquivalentTo [epithelial cell](http://purl.obolibrary.org/obo/CL_0000066) and ([BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0002451](http://purl.obolibrary.org/obo/UBERON_0002451)) and ([RO_0002215](http://purl.obolibrary.org/obo/RO_0002215) some [GO_0032940](http://purl.obolibrary.org/obo/GO_0032940)) + +- [glandular endometrial unciliated epithelial cell](http://purl.obolibrary.org/obo/CL_0002656) SubClassOf [BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0002451](http://purl.obolibrary.org/obo/UBERON_0002451) + +- [glandular endometrial unciliated epithelial cell](http://purl.obolibrary.org/obo/CL_0002656) SubClassOf [exocrine cell](http://purl.obolibrary.org/obo/CL_0000152) + +- [glandular endometrial unciliated epithelial cell](http://purl.obolibrary.org/obo/CL_0002656) SubClassOf [epithelial cell of endometrial gland](http://purl.obolibrary.org/obo/CL_0009084) + +- [glandular endometrial unciliated epithelial cell](http://purl.obolibrary.org/obo/CL_0002656) SubClassOf [glandular secretory epithelial cell](http://purl.obolibrary.org/obo/CL_0000150) + + +### glandular epithelial cell of stomach `http://purl.obolibrary.org/obo/CL_0002659` +#### Removed +- [glandular epithelial cell of stomach](http://purl.obolibrary.org/obo/CL_0002659) EquivalentTo [glandular secretory epithelial cell](http://purl.obolibrary.org/obo/CL_0000150) and ([BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0000945](http://purl.obolibrary.org/obo/UBERON_0000945)) + +#### Added +- [glandular epithelial cell of stomach](http://purl.obolibrary.org/obo/CL_0002659) EquivalentTo [glandular secretory epithelial cell](http://purl.obolibrary.org/obo/CL_0000150) and ([BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0001276](http://purl.obolibrary.org/obo/UBERON_0001276)) + + +### glandular secretory epithelial cell `http://purl.obolibrary.org/obo/CL_0000150` +#### Removed +- [glandular secretory epithelial cell](http://purl.obolibrary.org/obo/CL_0000150) [label](http://www.w3.org/2000/01/rdf-schema#label) "glandular epithelial cell"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [glandular secretory epithelial cell](http://purl.obolibrary.org/obo/CL_0000150) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A specialized epithelial cell that is capable of synthesizing and secreting certain biomolecules."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:tfm"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [glandular secretory epithelial cell](http://purl.obolibrary.org/obo/CL_0000150) SubClassOf [secretory cell](http://purl.obolibrary.org/obo/CL_0000151) + +- [glandular secretory epithelial cell](http://purl.obolibrary.org/obo/CL_0000150) SubClassOf [epithelial cell](http://purl.obolibrary.org/obo/CL_0000066) + +- [glandular secretory epithelial cell](http://purl.obolibrary.org/obo/CL_0000150) SubClassOf [BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0006799](http://purl.obolibrary.org/obo/UBERON_0006799) + +#### Added +- [glandular secretory epithelial cell](http://purl.obolibrary.org/obo/CL_0000150) [has_exact_synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "glandular epithelial cell"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [glandular secretory epithelial cell](http://purl.obolibrary.org/obo/CL_0000150) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "An epithelial cell, located in a gland, that is specialised for the synthesis and secretion of specific biomolecules, such as hormones, or mucous."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ORCID:0000-0002-7073-9172"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:tfm"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [glandular secretory epithelial cell](http://purl.obolibrary.org/obo/CL_0000150) [label](http://www.w3.org/2000/01/rdf-schema#label) "glandular secretory epithelial cell"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [glandular secretory epithelial cell](http://purl.obolibrary.org/obo/CL_0000150) EquivalentTo [epithelial cell](http://purl.obolibrary.org/obo/CL_0000066) and [secretory cell](http://purl.obolibrary.org/obo/CL_0000151) and ([BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0002530](http://purl.obolibrary.org/obo/UBERON_0002530)) + +- [glandular secretory epithelial cell](http://purl.obolibrary.org/obo/CL_0000150) SubClassOf [BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0002530](http://purl.obolibrary.org/obo/UBERON_0002530) + +- [glandular secretory epithelial cell](http://purl.obolibrary.org/obo/CL_0000150) SubClassOf [secretory epithelial cell](http://purl.obolibrary.org/obo/CL_1100001) + + +### glial cell `http://purl.obolibrary.org/obo/CL_0000125` +#### Removed +- [glial cell](http://purl.obolibrary.org/obo/CL_0000125) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +Glial cells, also known as neuroglia or simply glia, are non-neuronal cells in the central and peripheral nervous systems that provide support and protection for neurons. They constitute approximately half of the total cells in the human brain and more than half in other parts of the nervous system. Glial cells perform several key functions including, but not limited to, maintaining homeostasis, forming the myelin sheath around the neuron axons, and providing support and nutrition to neurons. +These different functions are performed by various glial cell types, including astrocytes, oligodendrocytes, microglia and other specialized types. Astrocytes, for example, are the most abundant glial cells and provide metabolic and nutrient support to neurons, help regulate the extracellular ion and neurotransmitter levels, and play a role in the formation and maintenance of the blood-brain barrier, contributing to the overall homeostasis and functioning of the nervous system. Additionally, astrocytes are involved in synaptic communication and participate in processes such as synaptogenesis and synaptic pruning. +Oligodendrocytes in the central nervous system function to insulate neurons by producing a fatty substance known as myelin. The myelin sheath enhances the speed and efficiency of nerve impulse conduction along the axons. +Microglia, the immune cells of the central nervous system, protect neurons from pathogens and clear away dead neurons through phagocytosis, a process also known as cellular eating. They also contribute to the regulation of inflammation in response to signals of tissue damage or infection in the central nervous system by releasing cytokines and other signaling molecules that modulate the immune response. +Despite their overarching function in the support and protection of neurons, glial cells have also been shown to play significant roles in the pathophysiology of many psychiatric and neurodegenerative diseases, such as Alzheimer’s, Parkinson’s Disease and multiple sclerosis."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1101/cshperspect.a020602"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1126/science.aat0473"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1038/nn1988"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1002/glia.24343"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.3389/fncel.2017.00024"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [glial cell](http://purl.obolibrary.org/obo/CL_0000125) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Glial cells, also known as neuroglia or simply glia, are non-neuronal cells in the central and peripheral nervous systems that provide support and protection for neurons. They constitute approximately half of the total cells in the human brain and more than half in other parts of the nervous system. Glial cells perform several key functions including, but not limited to, maintaining homeostasis, forming the myelin sheath around the neuron axons, and providing support and nutrition to neurons. +These different functions are performed by various glial cell types, including astrocytes, oligodendrocytes, microglia and other specialized types. Astrocytes, for example, are the most abundant glial cells and provide metabolic and nutrient support to neurons, help regulate the extracellular ion and neurotransmitter levels, and play a role in the formation and maintenance of the blood-brain barrier, contributing to the overall homeostasis and functioning of the nervous system. Additionally, astrocytes are involved in synaptic communication and participate in processes such as synaptogenesis and synaptic pruning. +Oligodendrocytes in the central nervous system function to insulate neurons by producing a fatty substance known as myelin. The myelin sheath enhances the speed and efficiency of nerve impulse conduction along the axons. +Microglia, the immune cells of the central nervous system, protect neurons from pathogens and clear away dead neurons through phagocytosis, a process also known as cellular eating. They also contribute to the regulation of inflammation in response to signals of tissue damage or infection in the central nervous system by releasing cytokines and other signaling molecules that modulate the immune response. +Despite their overarching function in the support and protection of neurons, glial cells have also been shown to play significant roles in the pathophysiology of many psychiatric and neurodegenerative diseases, such as Alzheimer’s, Parkinson’s Disease and multiple sclerosis."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1101/cshperspect.a020602"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1126/science.aat0473"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1038/nn1988"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1002/glia.24343"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.3389/fncel.2017.00024"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### glioblast `http://purl.obolibrary.org/obo/CL_0000030` + +#### Added +- [glioblast](http://purl.obolibrary.org/obo/CL_0000030) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A non-terminally differentiated cell that develops form the neuroectoderm. Glioblast has the potential to differentiate into various types of glial cells, including astrocytes and oligodendrocytes."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Glioblast"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:37824650"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### glomerular capillary endothelial cell `http://purl.obolibrary.org/obo/CL_1001005` +#### Removed +- [glomerular capillary endothelial cell](http://purl.obolibrary.org/obo/CL_1001005) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +The glomerular capillary endothelial cell comprises an intrinsic component of the glomerulus in the kidney. Glomeruli contain a network of capillaries where the first step of blood filtration takes place, with glomerular capillary endothelial cells acting as an integral part of this process. Unlike regular endothelial cells that line the vasculature, unique fenestrations (openings) characterize these cells, allowing for enhanced permeability and filtration efficacy. +Together with the glomerular basement membrane and podocytes, the glomerular endothelial cells form the glomerular filtration barrier, which is responsible for blood filtration and therefore critical for removal of waste products, such as urea and creatinine, and excess substances, such as glucose and ions, from the bloodstream. The glomerular capillary endothelial cells' fenestrations permit the free flow of a variety of particles, barring larger, negatively charged proteins like serum albumin, enabling the formation of an ultrafiltrate. This ultrafiltrate is the primitive form of urine, which then passes through the proximal tubule for further processing and ultimately helps maintain systemic fluid and electrolyte balance. +Moreover, the glomerular capillary endothelial cells are also believed to play a crucial role in renal pathologies. Any compromise to their structural integrity or functional performance can lead to kidney diseases, including but not limited to, diabetic nephropathy and glomerulonephritis. For instance, in diabetes, persistent hyperglycemia can injure these cells, leading to a compromised glomerular filtration barrier and proteinuria, indicating the loss of proteins in the urine."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1016/j.biocel.2010.05.015"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.2337/diacare.28.1.164"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1111/j.1523-1755.2005.00260.x"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.3389/fphys.2021.689083"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1016/j.yexcr.2012.02.032"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [glomerular capillary endothelial cell](http://purl.obolibrary.org/obo/CL_1001005) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +The glomerular capillary endothelial cell comprises an intrinsic component of the glomerulus in the kidney. Glomeruli contain a network of capillaries where the first step of blood filtration takes place, with glomerular capillary endothelial cells acting as an integral part of this process. Unlike regular endothelial cells that line the vasculature, unique fenestrations (openings) characterize these cells, allowing for enhanced permeability and filtration efficacy. +Together with the glomerular basement membrane and podocytes, the glomerular endothelial cells form the glomerular filtration barrier, which is responsible for blood filtration and therefore critical for removal of waste products, such as urea and creatinine, and excess substances, such as glucose and ions, from the bloodstream. The glomerular capillary endothelial cells' fenestrations permit the free flow of a variety of particles, barring larger, negatively charged proteins like serum albumin, enabling the formation of an ultrafiltrate. This ultrafiltrate is the primitive form of urine, which then passes through the proximal tubule for further processing and ultimately helps maintain systemic fluid and electrolyte balance. +Moreover, the glomerular capillary endothelial cells are also believed to play a crucial role in renal pathologies. Any compromise to their structural integrity or functional performance can lead to kidney diseases, including but not limited to, diabetic nephropathy and glomerulonephritis. For instance, in diabetes, persistent hyperglycemia can injure these cells, leading to a compromised glomerular filtration barrier and proteinuria, indicating the loss of proteins in the urine."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1016/j.biocel.2010.05.015"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.2337/diacare.28.1.164"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1111/j.1523-1755.2005.00260.x"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.3389/fphys.2021.689083"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1016/j.yexcr.2012.02.032"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### glomerular endothelial cell `http://purl.obolibrary.org/obo/CL_0002188` +#### Removed +- [glomerular endothelial cell](http://purl.obolibrary.org/obo/CL_0002188) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) + + + +### glutamatergic neuron of the basal ganglia `http://purl.obolibrary.org/obo/CL_4042040` + +#### Added +- [glutamatergic neuron of the basal ganglia](http://purl.obolibrary.org/obo/CL_4042040) [contributor](http://purl.org/dc/terms/contributor) [0000-0002-0098-8958](https://orcid.org/0000-0002-0098-8958) + +- [glutamatergic neuron of the basal ganglia](http://purl.obolibrary.org/obo/CL_4042040) [date](http://purl.org/dc/terms/date) "2024-11-18T13:37:58Z"^^[dateTime](http://www.w3.org/2001/XMLSchema#dateTime) + +- [glutamatergic neuron of the basal ganglia](http://purl.obolibrary.org/obo/CL_4042040) [label](http://www.w3.org/2000/01/rdf-schema#label) "glutamatergic neuron of the basal ganglia"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [glutamatergic neuron of the basal ganglia](http://purl.obolibrary.org/obo/CL_4042040) [comment](http://www.w3.org/2000/01/rdf-schema#comment) "The glutametergic neurons in the basal ganglia are part of a series of different circuits such as the corticolstriatal circuit, which is involved in regulating voluntary movements. The subthalamic nucleus circuit, which is involved in modulating the output of the basal ganglia, particularly in controlling movement initiation and inhibition. The thalamocortical loop, which is involved in refining motor movements and integrating sensory information with motor commanding."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:22498715"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:33785138"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:30498197"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [glutamatergic neuron of the basal ganglia](http://purl.obolibrary.org/obo/CL_4042040) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A glutametergic neuron with its soma located in a basal ganglia. This neuron type is involved in motor control, decision making and learning."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1016/j.jocn.2021.05.056"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:16276355"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:11307040"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [glutamatergic neuron of the basal ganglia](http://purl.obolibrary.org/obo/CL_4042040) [id](http://www.geneontology.org/formats/oboInOwl#id) "CL:4042040"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- Class: [glutamatergic neuron of the basal ganglia](http://purl.obolibrary.org/obo/CL_4042040) + +- [glutamatergic neuron of the basal ganglia](http://purl.obolibrary.org/obo/CL_4042040) SubClassOf [central nervous system neuron](http://purl.obolibrary.org/obo/CL_2000029) + +- [glutamatergic neuron of the basal ganglia](http://purl.obolibrary.org/obo/CL_4042040) SubClassOf [RO_0002100](http://purl.obolibrary.org/obo/RO_0002100) some [UBERON_0002420](http://purl.obolibrary.org/obo/UBERON_0002420) + +- [glutamatergic neuron of the basal ganglia](http://purl.obolibrary.org/obo/CL_4042040) SubClassOf [glutamatergic neuron](http://purl.obolibrary.org/obo/CL_0000679) + + +### glycinergic amacrine cell `http://purl.obolibrary.org/obo/CL_4030028` +#### Removed +- [glycinergic amacrine cell](http://purl.obolibrary.org/obo/CL_4030028) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [human_reference_atlas](http://purl.obolibrary.org/obo/cl/cl-base#human_reference_atlas) + +- [glycinergic amacrine cell](http://purl.obolibrary.org/obo/CL_4030028) [RO_0002175](http://purl.obolibrary.org/obo/RO_0002175) [NCBITaxon_9606](http://purl.obolibrary.org/obo/NCBITaxon_9606) + + + +### glycinergic-GABAergic amacrine cell `http://purl.obolibrary.org/obo/CL_4033091` + +#### Added +- [glycinergic-GABAergic amacrine cell](http://purl.obolibrary.org/obo/CL_4033091) [id](http://www.geneontology.org/formats/oboInOwl#id) "CL:4033091"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [glycinergic-GABAergic amacrine cell](http://purl.obolibrary.org/obo/CL_4033091) [label](http://www.w3.org/2000/01/rdf-schema#label) "glycinergic-GABAergic amacrine cell"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [glycinergic-GABAergic amacrine cell](http://purl.obolibrary.org/obo/CL_4033091) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "An amacrine cell that uses both GABA and glycine as neurotransmitters."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:37124720"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [glycinergic-GABAergic amacrine cell](http://purl.obolibrary.org/obo/CL_4033091) [date](http://purl.org/dc/terms/date) "2024-12-02T13:44:17Z"^^[dateTime](http://www.w3.org/2001/XMLSchema#dateTime) + +- [glycinergic-GABAergic amacrine cell](http://purl.obolibrary.org/obo/CL_4033091) [has_exact_synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "glycinergic/GABAergic amacrine neuron"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:37124720"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [glycinergic-GABAergic amacrine cell](http://purl.obolibrary.org/obo/CL_4033091) [contributor](http://purl.org/dc/terms/contributor) [0000-0001-6677-8489](https://orcid.org/0000-0001-6677-8489) + +- Class: [glycinergic-GABAergic amacrine cell](http://purl.obolibrary.org/obo/CL_4033091) + +- [glycinergic-GABAergic amacrine cell](http://purl.obolibrary.org/obo/CL_4033091) EquivalentTo [amacrine cell](http://purl.obolibrary.org/obo/CL_0000561) and ([RO_0002215](http://purl.obolibrary.org/obo/RO_0002215) some [GO_0061534](http://purl.obolibrary.org/obo/GO_0061534)) and ([RO_0002215](http://purl.obolibrary.org/obo/RO_0002215) some [GO_0061537](http://purl.obolibrary.org/obo/GO_0061537)) + +- [glycinergic-GABAergic amacrine cell](http://purl.obolibrary.org/obo/CL_4033091) SubClassOf [glycinergic amacrine cell](http://purl.obolibrary.org/obo/CL_4030028) + +- [glycinergic-GABAergic amacrine cell](http://purl.obolibrary.org/obo/CL_4033091) SubClassOf [GABAergic amacrine cell](http://purl.obolibrary.org/obo/CL_4030027) + + +### goblet cell `http://purl.obolibrary.org/obo/CL_0000160` +#### Removed +- [goblet cell](http://purl.obolibrary.org/obo/CL_0000160) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +Goblet cells are specialized, simple columnar, secretory epithelial cells that are mostly found in the respiratory and intestinal tracts. The term "goblet" refers to their shape, which resembles a flask or goblet, specially at their apical end which is swollen due to the accumulation of secretory granules. +The primary function of goblet cells is to to protect and lubricate the underlying tissues by secreting large quantities of mucin, a complex glycoprotein, which forms mucus when hydrated. In the respiratory tract, the mucus secreted by these cells traps dust, bacteria, viruses, and other potentially harmful particles in the inhaled air, preventing them from reaching the delicate tissues of the lungs. In the intestines, the goblet cells secrete mucus that acts as a protective barrier shielding the intestinal epithelium from dietary antigens, pathogens and prevents the intestinal epithelium from being eroded by the actions of the digestive enzymes and the abrasive action of passing food material. +Goblet cells are capable of rapidly altering their secretory output in response to stimuli. For example, irritants like smoke or dust can trigger an increased rate of mucus production, as the body attempts to flush out the harmful particles. Conversely, in conditions such as chronic bronchitis and cystic fibrosis, overactive goblet cells can create a thick accumulation of mucus that obstructs the airways and fosters bacterial growth. Lastly, goblet cells are not static, rather, they undergo a dynamic process known as goblet cell metaplasia-differentiation, wherein non-goblet cells in response to chronic injury or inflammation, can differentiate into goblet cells leading to an accumulation of these cells in the tissue, known as goblet cell hyperplasia."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1038/s41575-022-00675-x"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1242/bio.20121701"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1016/S1357-2725(02)00083-3"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1165/ajrcmb.25.5.f218"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://www.ncbi.nlm.nih.gov/books/NBK553208/"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [goblet cell](http://purl.obolibrary.org/obo/CL_0000160) SubClassOf [RO_0002215](http://purl.obolibrary.org/obo/RO_0002215) some [GO_0070254](http://purl.obolibrary.org/obo/GO_0070254) + +- [goblet cell](http://purl.obolibrary.org/obo/CL_0000160) SubClassOf [epithelial cell](http://purl.obolibrary.org/obo/CL_0000066) + +#### Added +- [goblet cell](http://purl.obolibrary.org/obo/CL_0000160) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Goblet cells are specialized, simple columnar, secretory epithelial cells that are mostly found in the respiratory and intestinal tracts. The term "goblet" refers to their shape, which resembles a flask or goblet, specially at their apical end which is swollen due to the accumulation of secretory granules. +The primary function of goblet cells is to to protect and lubricate the underlying tissues by secreting large quantities of mucin, a complex glycoprotein, which forms mucus when hydrated. In the respiratory tract, the mucus secreted by these cells traps dust, bacteria, viruses, and other potentially harmful particles in the inhaled air, preventing them from reaching the delicate tissues of the lungs. In the intestines, the goblet cells secrete mucus that acts as a protective barrier shielding the intestinal epithelium from dietary antigens, pathogens and prevents the intestinal epithelium from being eroded by the actions of the digestive enzymes and the abrasive action of passing food material. +Goblet cells are capable of rapidly altering their secretory output in response to stimuli. For example, irritants like smoke or dust can trigger an increased rate of mucus production, as the body attempts to flush out the harmful particles. Conversely, in conditions such as chronic bronchitis and cystic fibrosis, overactive goblet cells can create a thick accumulation of mucus that obstructs the airways and fosters bacterial growth. Lastly, goblet cells are not static, rather, they undergo a dynamic process known as goblet cell metaplasia-differentiation, wherein non-goblet cells in response to chronic injury or inflammation, can differentiate into goblet cells leading to an accumulation of these cells in the tissue, known as goblet cell hyperplasia."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1038/s41575-022-00675-x"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1242/bio.20121701"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1016/S1357-2725(02)00083-3"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1165/ajrcmb.25.5.f218"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://www.ncbi.nlm.nih.gov/books/NBK553208/"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [goblet cell](http://purl.obolibrary.org/obo/CL_0000160) SubClassOf [mucus secreting cell](http://purl.obolibrary.org/obo/CL_0000319) + +- [goblet cell](http://purl.obolibrary.org/obo/CL_0000160) SubClassOf [secretory epithelial cell](http://purl.obolibrary.org/obo/CL_1100001) + + +### granule cell `http://purl.obolibrary.org/obo/CL_0000120` +#### Removed +- [granule cell](http://purl.obolibrary.org/obo/CL_0000120) SubClassOf [CNS neuron (sensu Vertebrata)](http://purl.obolibrary.org/obo/CL_0000117) + +#### Added +- [granule cell](http://purl.obolibrary.org/obo/CL_0000120) SubClassOf [central nervous system neuron](http://purl.obolibrary.org/obo/CL_2000029) + + +### granulocyte `http://purl.obolibrary.org/obo/CL_0000094` +#### Removed +- [granulocyte](http://purl.obolibrary.org/obo/CL_0000094) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) + + + +### granulocyte monocyte progenitor cell `http://purl.obolibrary.org/obo/CL_0000557` +#### Removed +- [granulocyte monocyte progenitor cell](http://purl.obolibrary.org/obo/CL_0000557) SubClassOf [progenitor cell](http://purl.obolibrary.org/obo/CL_0011026) + +- [granulocyte monocyte progenitor cell](http://purl.obolibrary.org/obo/CL_0000557) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) + +#### Added +- [granulocyte monocyte progenitor cell](http://purl.obolibrary.org/obo/CL_0000557) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://cellxgene.cziscience.com/cellguide/CL_0000557"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [granulocyte monocyte progenitor cell](http://purl.obolibrary.org/obo/CL_0000557) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Granulocyte monocyte progenitor cells (GMP cells), originating from hematopoietic stem cells in the bone marrow, are a critical intermediate in myeloid cell development. Positioned at a key differentiation juncture, these cells exhibit bidirectional potential, giving rise to both granulocyte and monocyte lineages. +Their primary role is to generate mature granulocytes and monocytes, essential components of the body's innate immunity and inflammatory responses. Granulocytes, such as neutrophils, eosinophils, and basophils, contribute to the first line of defense against infections by migrating to the infection site and phagocytosing pathogens. Monocytes can differentiate into macrophages or dendritic cells, playing diverse roles in immune responses."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1146/annurev-immunol-081022113627"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1016/j.immuni.2017.10.021"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1186/2050-7771-2-1"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### granulosa cell `http://purl.obolibrary.org/obo/CL_0000501` +#### Removed +- [granulosa cell](http://purl.obolibrary.org/obo/CL_0000501) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +Granulosa cells are a type of somatic cell most commonly known for their crucial role within the ovarian follicles of female mammalian species. Named for their grainy appearance, they are situated in the follicular epithelium, lining the inner part of the follicle and directly surrounding the oocyte. These cells stand as an integral part of the ovarian structure and function. +One of the primary roles of granulosa cells is to aid in the production and secretion of sex hormones, particularly estrogen. They achieve this by working in tandem with theca cells, which stay attached to the external layer of the follicle. Theca cells produce androstenedione (a type of androgen) which granulosa cells then convert into estradiol, a form of estrogen, with the help of the enzyme aromatase. Moreover, granulosa cells participate in luteinization, transforming into luteal granulosa cells as a response to the luteinizing hormone during ovulation. This allows the formation of the corpus luteum, responsible for the secretion of progesterone necessary to maintain pregnancy. +Granulosa cells also play a significant role in follicular development and oocyte maturation, involving close communication with the contained oocyte. They support the oocyte through the provision of nutrients and growth factors, control its meiotic cycle and ensure it is appropriately oriented and instructed for impending ovulation. Furthermore, granulosa cells contribute to the formation of the zona pellucida and the follicular fluid, providing an optimal environment for the oocyte's growth and maturation. These cells, thus, perform multiple vital roles, underscoring their importance in fertility and reproductive health."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1093/humupd/6.3.279"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.3389/fendo.2019.00832/full"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1016/j.ejogrb.2004.01.010"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1093/humrep/del408"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1210/jcem-28-3-355"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [granulosa cell](http://purl.obolibrary.org/obo/CL_0000501) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Granulosa cells are a type of somatic cell most commonly known for their crucial role within the ovarian follicles of female mammalian species. Named for their grainy appearance, they are situated in the follicular epithelium, lining the inner part of the follicle and directly surrounding the oocyte. These cells stand as an integral part of the ovarian structure and function. +One of the primary roles of granulosa cells is to aid in the production and secretion of sex hormones, particularly estrogen. They achieve this by working in tandem with theca cells, which stay attached to the external layer of the follicle. Theca cells produce androstenedione (a type of androgen) which granulosa cells then convert into estradiol, a form of estrogen, with the help of the enzyme aromatase. Moreover, granulosa cells participate in luteinization, transforming into luteal granulosa cells as a response to the luteinizing hormone during ovulation. This allows the formation of the corpus luteum, responsible for the secretion of progesterone necessary to maintain pregnancy. +Granulosa cells also play a significant role in follicular development and oocyte maturation, involving close communication with the contained oocyte. They support the oocyte through the provision of nutrients and growth factors, control its meiotic cycle and ensure it is appropriately oriented and instructed for impending ovulation. Furthermore, granulosa cells contribute to the formation of the zona pellucida and the follicular fluid, providing an optimal environment for the oocyte's growth and maturation. These cells, thus, perform multiple vital roles, underscoring their importance in fertility and reproductive health."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1093/humupd/6.3.279"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.3389/fendo.2019.00832/full"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1016/j.ejogrb.2004.01.010"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1093/humrep/del408"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1210/jcem-28-3-355"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [granulosa cell](http://purl.obolibrary.org/obo/CL_0000501) SubClassOf [secretory epithelial cell](http://purl.obolibrary.org/obo/CL_1100001) + + +### granzyme K-associated CD8 T cell `http://purl.obolibrary.org/obo/CL_4052021` + +#### Added +- [granzyme K-associated CD8 T cell](http://purl.obolibrary.org/obo/CL_4052021) [has_exact_synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "tissue-enriched expressing GzmK CD8 cell"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:35704599"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [granzyme K-associated CD8 T cell](http://purl.obolibrary.org/obo/CL_4052021) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "CD8-GZMK cell"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003000](http://purl.obolibrary.org/obo/OMO_0003000) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "doi:/10.1101/2022.06.17.496207"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [granzyme K-associated CD8 T cell](http://purl.obolibrary.org/obo/CL_4052021) [has_narrow_synonym](http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym) "GZMK high CD8+ T effector memory cell"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:36347862"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [granzyme K-associated CD8 T cell](http://purl.obolibrary.org/obo/CL_4052021) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "TteK CD8 cell"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003000](http://purl.obolibrary.org/obo/OMO_0003000) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:35704599"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [granzyme K-associated CD8 T cell](http://purl.obolibrary.org/obo/CL_4052021) [has_exact_synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "granzyme K+ CD8 T cell"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:35704599"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [granzyme K-associated CD8 T cell](http://purl.obolibrary.org/obo/CL_4052021) [contributor](http://purl.org/dc/terms/contributor) [0009-0000-8480-9277](https://orcid.org/0009-0000-8480-9277) + +- [granzyme K-associated CD8 T cell](http://purl.obolibrary.org/obo/CL_4052021) [label](http://www.w3.org/2000/01/rdf-schema#label) "granzyme K-associated CD8 T cell"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [granzyme K-associated CD8 T cell](http://purl.obolibrary.org/obo/CL_4052021) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A CD8 T cell characterized by high expression of Granzyme K (GZMK). This cell is enriched in both inflamed tissues, such as synovial tissue in rheumatoid arthritis and respiratory tissues during COVID-19, as well as non-inflamed tissues like the gut and kidneys. Unlike highly cytotoxic GZMB+ CD8+ T cell, GZMK+ CD8+ T cell exhibits lower direct cytotoxic potential, and is involved in producing pro-inflammatory cytokines such as IFN-γ and TNF-α."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:37449888"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:35704599"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [granzyme K-associated CD8 T cell](http://purl.obolibrary.org/obo/CL_4052021) [date](http://purl.org/dc/terms/date) "2024-10-18T09:51:48Z"^^[dateTime](http://www.w3.org/2001/XMLSchema#dateTime) + +- [granzyme K-associated CD8 T cell](http://purl.obolibrary.org/obo/CL_4052021) [id](http://www.geneontology.org/formats/oboInOwl#id) "CL:4052021"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- Class: [granzyme K-associated CD8 T cell](http://purl.obolibrary.org/obo/CL_4052021) + +- [granzyme K-associated CD8 T cell](http://purl.obolibrary.org/obo/CL_4052021) EquivalentTo [CD8-positive, alpha-beta memory T cell](http://purl.obolibrary.org/obo/CL_0000909) and ([RO_0002292](http://purl.obolibrary.org/obo/RO_0002292) some [PR_000003472](http://purl.obolibrary.org/obo/PR_000003472)) + +- [granzyme K-associated CD8 T cell](http://purl.obolibrary.org/obo/CL_4052021) SubClassOf [RO_0002292](http://purl.obolibrary.org/obo/RO_0002292) some [PR_000003472](http://purl.obolibrary.org/obo/PR_000003472) + +- [granzyme K-associated CD8 T cell](http://purl.obolibrary.org/obo/CL_4052021) SubClassOf [CD8-positive, alpha-beta memory T cell](http://purl.obolibrary.org/obo/CL_0000909) + + +### group 2 innate lymphoid cell, human `http://purl.obolibrary.org/obo/CL_0001081` +#### Removed +- [group 2 innate lymphoid cell, human](http://purl.obolibrary.org/obo/CL_0001081) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) + + + +### group 2 innate lymphoid cell, mouse `http://purl.obolibrary.org/obo/CL_0002089` +#### Removed +- [group 2 innate lymphoid cell, mouse](http://purl.obolibrary.org/obo/CL_0002089) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) + + + +### group 3 innate lymphoid cell `http://purl.obolibrary.org/obo/CL_0001071` +#### Removed +- [group 3 innate lymphoid cell](http://purl.obolibrary.org/obo/CL_0001071) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) + + + +### gut endothelial cell `http://purl.obolibrary.org/obo/CL_0000131` + +#### Added +- [gut endothelial cell](http://purl.obolibrary.org/obo/CL_0000131) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Gut endothelial cells are a crucial component of the endothelium, a thin layer of single cells that line the interior surface of blood vessels and lymphatic vessels, including those in the digestive system or "gut". These cells plays an integral role in various physiological and metabolic functions, actively participating in nutrient absorption, host defense, and vascular homeostasis in the gut. +The primary function of gut endothelial cells lies in their ability to control the passage of materials and the transit of white blood cells into and out of the bloodstream. They achieve this through the formation of a semi-permeable barrier, in which permeability is regulated by tight junctions; complex structures that bring the cells together, sealing the space between them. This ensures a controlled, selective passage of nutrients, ions, and water from the bloodstream into the gut and vice versa, helping maintain homeostasis and overall health. +Gut endothelial cells also play a significant role in angiogenesis and serve as a critical regulator of the gut immune responses playing a modulative role in gut immune homeostasis and inflammatory responses. In addition, they generate nitric oxide, a potent vasodilator, which helps in maintaining vascular tonus, preventing platelet and leukocyte adhesion, and decreasing smooth muscle proliferation. These multi-faceted roles make gut endothelial cells indispensable for the normal functioning of the gut and overall health."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1038/nri2171"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1111/bph.14527"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.3748/wjg.v17.i5.578"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:full/10.15252/emmm.202114121"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.3390/ijms23073698"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [gut endothelial cell](http://purl.obolibrary.org/obo/CL_0000131) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://cellxgene.cziscience.com/cellguide/CL_0000131"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### hematopoietic multipotent progenitor cell `http://purl.obolibrary.org/obo/CL_0000837` +#### Removed +- [hematopoietic multipotent progenitor cell](http://purl.obolibrary.org/obo/CL_0000837) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) + + + +### hepatic pit cell `http://purl.obolibrary.org/obo/CL_2000054` +#### Removed +- [hepatic pit cell](http://purl.obolibrary.org/obo/CL_2000054) SubClassOf [natural killer cell](http://purl.obolibrary.org/obo/CL_0000623) + +- [hepatic pit cell](http://purl.obolibrary.org/obo/CL_2000054) SubClassOf [RO_0001025](http://purl.obolibrary.org/obo/RO_0001025) some [UBERON_0001281](http://purl.obolibrary.org/obo/UBERON_0001281) + +#### Added +- [hepatic pit cell](http://purl.obolibrary.org/obo/CL_2000054) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl/cl-base#cellxgene_subset) + +- [hepatic pit cell](http://purl.obolibrary.org/obo/CL_2000054) SubClassOf [liver-resident natural killer cell](http://purl.obolibrary.org/obo/CL_4047101) + + +### hepatic stellate cell `http://purl.obolibrary.org/obo/CL_0000632` +#### Removed +- [hepatic stellate cell](http://purl.obolibrary.org/obo/CL_0000632) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) + + + +### hepatoblast `http://purl.obolibrary.org/obo/CL_0005026` +#### Removed +- [hepatoblast](http://purl.obolibrary.org/obo/CL_0005026) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +Hepatoblasts are immature precursor cells that predominate during the early stages of liver development, specifically in the embryonic phase of life. They first arise from the endoderm, one of the three primary germ layers in the very early embryo, and then differentiate into two distinct mature liver cell types - the hepatocytes and cholangiocytes. +During liver organogenesis hepatoblasts proliferate and migrate into the septum transversum to form the liver bud. Proliferation and differentiation of these cells are regulated by several soluble factors, such as hepatocyte growth factor, which is a mitogen of both hepatoblasts and mature hepatocytes. As they start to differentiate into hepatocytes and cholangiocytes, the cells begin to express hepatic markers like albumin and alpha-fetoprotein. +Although hepatoblasts are specified embryonic liver cells that are bipotential for hepatocytes and cholangiocytes, a subset of liver cells (called oval cells) has been identified in adults that express stem cell markers, such as CD133 and cKIT, and has been suggested to have the same potential as hepatoblasts to differentiate into hepatocytes and cholangiocytes."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1242/dev.031369"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1242/dev.114215"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.5966/sctm.2015-0051"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1093/jb/mvr001"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1016/j.stem.2014.04.010"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [hepatoblast](http://purl.obolibrary.org/obo/CL_0005026) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Hepatoblasts are immature precursor cells that predominate during the early stages of liver development, specifically in the embryonic phase of life. They first arise from the endoderm, one of the three primary germ layers in the very early embryo, and then differentiate into two distinct mature liver cell types - the hepatocytes and cholangiocytes. +During liver organogenesis hepatoblasts proliferate and migrate into the septum transversum to form the liver bud. Proliferation and differentiation of these cells are regulated by several soluble factors, such as hepatocyte growth factor, which is a mitogen of both hepatoblasts and mature hepatocytes. As they start to differentiate into hepatocytes and cholangiocytes, the cells begin to express hepatic markers like albumin and alpha-fetoprotein. +Although hepatoblasts are specified embryonic liver cells that are bipotential for hepatocytes and cholangiocytes, a subset of liver cells (called oval cells) has been identified in adults that express stem cell markers, such as CD133 and cKIT, and has been suggested to have the same potential as hepatoblasts to differentiate into hepatocytes and cholangiocytes."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1242/dev.031369"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1242/dev.114215"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.5966/sctm.2015-0051"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1093/jb/mvr001"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1016/j.stem.2014.04.010"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### hepatocyte `http://purl.obolibrary.org/obo/CL_0000182` +#### Removed +- [hepatocyte](http://purl.obolibrary.org/obo/CL_0000182) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +Hepatocytes are the major cell type constituting 70-80% of the liver's cytoplasmic mass, playing crucial roles in maintaining the body's metabolic homeostasis. Dimensions of mature hepatocytes typically range from 20 to 30 μm in humans, but size may vary depending on their location within the liver lobule. Hepatocytes are characterized by high biosynthetic, enzymatic, and endocytic activity. They contain abundant mitochondria, smooth and rough endoplasmic reticulum, peroxisomes, lysosomes, and a large nucleus that is often binucleate. +The liver consists of three zones - the periportal Zone 1, midzone 2, and pericentral Zone 3 - which have differential nutrient and oxygen status, and damage susceptibility; hepatocytes in the different zones show signifcant functional heterogeneity ('hepatocyte functional zonation'). Hepatocytes are involved in a multitude of critical functions including the metabolism of lipids, carbohydrates, and proteins, the synthesis of serum proteins (e.g., albumin, transferrin, and lipoproteins), the detoxification and excretion of endogenous and exogenous substances, the storage of vitamins and minerals, and the production and secretion of bile. +Heterocytes demonstrate a remarkable regenerative capacity, which enables the liver to recover from injury and loss of tissue mass. Notably, hepatocytes perform biotransformation with both phase I and phase II enzymes, which modify drugs, xenobiotics, and various substances for elimination from the body. Phase I enzymes, such as cytochrome P450, catalyze both oxidative and reductive reactions of many xenobiotics; many of the products of phase I enzymes are substrates for the phase II enzymes, which catalyze conjugation reactions. +Alterations in hepatocyte function have significant implications for overall human health and disease. Certain conditions, such as hepatitis, cirrhosis, and liver cancer, can profoundly affect hepatocyte structure and function, thereby disrupting the liver's ability to perform its vital roles within the body. As the primary site for drug metabolism, changes in hepatocyte function can also impact the effectiveness and toxicity of pharmaceuticals. The regenerative ability of hepatocytes makes them valuable cells for liver regenerative medicine and bioartificial liver support systems, and their study has provided significant insights into liver biology and disease."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1083/jcb.201903090"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1016/j.biocel.2011.11.011"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1111/j.1439-0396.2007.00752.x"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1055/s-2007-1007096"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [hepatocyte](http://purl.obolibrary.org/obo/CL_0000182) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Hepatocytes are the major cell type constituting 70-80% of the liver's cytoplasmic mass, playing crucial roles in maintaining the body's metabolic homeostasis. Dimensions of mature hepatocytes typically range from 20 to 30 μm in humans, but size may vary depending on their location within the liver lobule. Hepatocytes are characterized by high biosynthetic, enzymatic, and endocytic activity. They contain abundant mitochondria, smooth and rough endoplasmic reticulum, peroxisomes, lysosomes, and a large nucleus that is often binucleate. +The liver consists of three zones - the periportal Zone 1, midzone 2, and pericentral Zone 3 - which have differential nutrient and oxygen status, and damage susceptibility; hepatocytes in the different zones show signifcant functional heterogeneity ('hepatocyte functional zonation'). Hepatocytes are involved in a multitude of critical functions including the metabolism of lipids, carbohydrates, and proteins, the synthesis of serum proteins (e.g., albumin, transferrin, and lipoproteins), the detoxification and excretion of endogenous and exogenous substances, the storage of vitamins and minerals, and the production and secretion of bile. +Heterocytes demonstrate a remarkable regenerative capacity, which enables the liver to recover from injury and loss of tissue mass. Notably, hepatocytes perform biotransformation with both phase I and phase II enzymes, which modify drugs, xenobiotics, and various substances for elimination from the body. Phase I enzymes, such as cytochrome P450, catalyze both oxidative and reductive reactions of many xenobiotics; many of the products of phase I enzymes are substrates for the phase II enzymes, which catalyze conjugation reactions. +Alterations in hepatocyte function have significant implications for overall human health and disease. Certain conditions, such as hepatitis, cirrhosis, and liver cancer, can profoundly affect hepatocyte structure and function, thereby disrupting the liver's ability to perform its vital roles within the body. As the primary site for drug metabolism, changes in hepatocyte function can also impact the effectiveness and toxicity of pharmaceuticals. The regenerative ability of hepatocytes makes them valuable cells for liver regenerative medicine and bioartificial liver support systems, and their study has provided significant insights into liver biology and disease."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1083/jcb.201903090"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1016/j.biocel.2011.11.011"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1111/j.1439-0396.2007.00752.x"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1055/s-2007-1007096"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### hippocampal CA4 neuron `http://purl.obolibrary.org/obo/CL_4023061` +#### Removed +- [hippocampal CA4 neuron](http://purl.obolibrary.org/obo/CL_4023061) SubClassOf [neuron](http://purl.obolibrary.org/obo/CL_0000540) + +#### Added +- [hippocampal CA4 neuron](http://purl.obolibrary.org/obo/CL_4023061) SubClassOf [central nervous system neuron](http://purl.obolibrary.org/obo/CL_2000029) + + +### horizontal pyramidal neuron `http://purl.obolibrary.org/obo/CL_4023066` +#### Removed +- [horizontal pyramidal neuron](http://purl.obolibrary.org/obo/CL_4023066) EquivalentTo [CNS neuron (sensu Vertebrata)](http://purl.obolibrary.org/obo/CL_0000117) and ([RO_0000053](http://purl.obolibrary.org/obo/RO_0000053) some [PATO_0070016](http://purl.obolibrary.org/obo/PATO_0070016)) + +- [horizontal pyramidal neuron](http://purl.obolibrary.org/obo/CL_4023066) SubClassOf [CNS neuron (sensu Vertebrata)](http://purl.obolibrary.org/obo/CL_0000117) + +#### Added +- [horizontal pyramidal neuron](http://purl.obolibrary.org/obo/CL_4023066) EquivalentTo [neuron](http://purl.obolibrary.org/obo/CL_0000540) and ([RO_0000053](http://purl.obolibrary.org/obo/RO_0000053) some [PATO_0070016](http://purl.obolibrary.org/obo/PATO_0070016)) + + +### hypendymal cell `http://purl.obolibrary.org/obo/CL_4023181` +#### Removed +- [hypendymal cell](http://purl.obolibrary.org/obo/CL_4023181) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +Hypendymal cells are secretory cells located between the ependymal layer and the posterior commissure, forming the hypendmal layer of the subcommissural organ (SCO), a highly conserved gland that is part of the circumventricular system within the brain. +Hypendymal cells are bipolar cells with a thin apical pole and basal process. Most of the ultrastructural characteristics of these cells are similar to those described for the ependymal cells (which are arranged into another layer – the ependyma). However, ependymal cells release their secretion into the ventricular cerebrospinal fluid whereas hypendymal cells project processes to the local blood vessels and to the subarachnoidal space."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.3389/fncel.2015.00480"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1002/(SICI)1097-0029(19980415)41:2<98::AID-JEMT2>3.0.CO;2-M"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1111/joa.13709"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [hypendymal cell](http://purl.obolibrary.org/obo/CL_4023181) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Hypendymal cells are secretory cells located between the ependymal layer and the posterior commissure, forming the hypendmal layer of the subcommissural organ (SCO), a highly conserved gland that is part of the circumventricular system within the brain. +Hypendymal cells are bipolar cells with a thin apical pole and basal process. Most of the ultrastructural characteristics of these cells are similar to those described for the ependymal cells (which are arranged into another layer – the ependyma). However, ependymal cells release their secretion into the ventricular cerebrospinal fluid whereas hypendymal cells project processes to the local blood vessels and to the subarachnoidal space."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.3389/fncel.2015.00480"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1002/(SICI)1097-0029(19980415)41:2<98::AID-JEMT2>3.0.CO;2-M"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1111/joa.13709"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### hypothalamus cell `http://purl.obolibrary.org/obo/CL_2000030` + +#### Added +- [hypothalamus cell](http://purl.obolibrary.org/obo/CL_2000030) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl/cl-base#cellxgene_subset) + + +### hypothalamus kisspeptin neuron `http://purl.obolibrary.org/obo/CL_4023123` +#### Removed +- [hypothalamus kisspeptin neuron](http://purl.obolibrary.org/obo/CL_4023123) SubClassOf [central nervous system neuron](http://purl.obolibrary.org/obo/CL_2000029) + +#### Added +- [hypothalamus kisspeptin neuron](http://purl.obolibrary.org/obo/CL_4023123) SubClassOf [neuron of the forebrain](http://purl.obolibrary.org/obo/CL_0012001) + + +### ileal goblet cell `http://purl.obolibrary.org/obo/CL_1000326` +#### Removed +- [ileal goblet cell](http://purl.obolibrary.org/obo/CL_1000326) EquivalentTo [goblet cell](http://purl.obolibrary.org/obo/CL_0000160) and ([BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0002116](http://purl.obolibrary.org/obo/UBERON_0002116)) + +#### Added +- [ileal goblet cell](http://purl.obolibrary.org/obo/CL_1000326) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +The ileal goblet cell is a subset of intestinal goblet cells that are a key component of the epithelium of the ileum, a portion of the small intestine. Goblet cells are named and characterized by their distinctive 'goblet' shape with a narrow base tapering to a broad apical surface; located between the lumen of the intestine and the internal environment of the body, they serve an integral role in maintaining gut homeostasis. +Like all intestinal goblet cells, the primary function of ileal goblet cells is the production and secretion of mucins, large, heavily glycosylated proteins that combine to form mucus. This mucus lining serves as a protective barrier, shielding the underlying tissue from the potentially damaging effects of digestive enzymes, acids, or pathogenic microbes present in the gut lumen. Their strategic location in the ileal segment of the intestinal tract aids in efficient nutrient absorption while also maintaining an impregnable barrier against potential pathogens, ensuring an intricate balance. +Goblet cells of the ileum also play a significant role in immune modulation. They are thought to promote oral tolerance (the immune unresponsiveness to orally ingested antigens such as food) by delivering luminal antigens to underlying dendritic cells, thereby driving immune education and tolerogenic responses. They also secrete bioactive molecules, such as the trefoil factor peptide TFF3, which aids in repairing damaged epithelium. By performing these crucial functions, ileal goblet cells not only aid in maintaining intestinal health, but also contribute significantly to the overall well-being of the organism."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1038/s41575-022-00675-x"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1038/nature10863"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1007/s11894-010-0131-2"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1111/imr.12182"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [ileal goblet cell](http://purl.obolibrary.org/obo/CL_1000326) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://cellxgene.cziscience.com/cellguide/CL_1000326"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [ileal goblet cell](http://purl.obolibrary.org/obo/CL_1000326) EquivalentTo [goblet cell](http://purl.obolibrary.org/obo/CL_0000160) and ([BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0008345](http://purl.obolibrary.org/obo/UBERON_0008345)) + +- [ileal goblet cell](http://purl.obolibrary.org/obo/CL_1000326) SubClassOf [BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0008345](http://purl.obolibrary.org/obo/UBERON_0008345) + + +### immature CD8-alpha-low Langerhans cell `http://purl.obolibrary.org/obo/CL_0001018` +#### Removed +- [immature CD8-alpha-low Langerhans cell](http://purl.obolibrary.org/obo/CL_0001018) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "Immature CD8_alpha-low Langerhans cell is a CD8_alpha-low Langerhans cell that is CD80-low, CD86-low, and MHCII-low."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:amm"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMCID:PMC2346585"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GO_REF:0000031"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:tfm"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [immature CD8-alpha-low Langerhans cell](http://purl.obolibrary.org/obo/CL_0001018) [label](http://www.w3.org/2000/01/rdf-schema#label) "immature CD8_alpha-low Langerhans cell"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [immature CD8-alpha-low Langerhans cell](http://purl.obolibrary.org/obo/CL_0001018) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "Immature CD8-alpha-low Langerhans cell is a CD8-alpha-low Langerhans cell that is CD80-low, CD86-low, and MHCII-low."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:amm"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMCID:PMC2346585"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GO_REF:0000031"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:tfm"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [immature CD8-alpha-low Langerhans cell](http://purl.obolibrary.org/obo/CL_0001018) [label](http://www.w3.org/2000/01/rdf-schema#label) "immature CD8-alpha-low Langerhans cell"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### immature CD8-alpha-negative CD11b-negative dendritic cell `http://purl.obolibrary.org/obo/CL_0001001` +#### Removed +- [immature CD8-alpha-negative CD11b-negative dendritic cell](http://purl.obolibrary.org/obo/CL_0001001) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "Immature CD8_alpha-negative CD11b-negative dendritic cell is a CD8_alpha-negative CD11b-negative dendritic cell that is CD80-low, CD86-low, and MHCII-low."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:amm"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMCID:PMC2346585"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GO_REF:0000031"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [immature CD8-alpha-negative CD11b-negative dendritic cell](http://purl.obolibrary.org/obo/CL_0001001) [label](http://www.w3.org/2000/01/rdf-schema#label) "immature CD8_alpha-negative CD11b-negative dendritic cell"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [immature CD8-alpha-negative CD11b-negative dendritic cell](http://purl.obolibrary.org/obo/CL_0001001) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "Immature CD8-alpha-negative CD11b-negative dendritic cell is a CD8-alpha-negative CD11b-negative dendritic cell that is CD80-low, CD86-low, and MHCII-low."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:amm"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMCID:PMC2346585"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GO_REF:0000031"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [immature CD8-alpha-negative CD11b-negative dendritic cell](http://purl.obolibrary.org/obo/CL_0001001) [label](http://www.w3.org/2000/01/rdf-schema#label) "immature CD8-alpha-negative CD11b-negative dendritic cell"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### immature CD8-alpha-negative CD11b-positive dendritic cell `http://purl.obolibrary.org/obo/CL_0000997` +#### Removed +- [immature CD8-alpha-negative CD11b-positive dendritic cell](http://purl.obolibrary.org/obo/CL_0000997) [label](http://www.w3.org/2000/01/rdf-schema#label) "immature CD8_alpha-negative CD11b-positive dendritic cell"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [immature CD8-alpha-negative CD11b-positive dendritic cell](http://purl.obolibrary.org/obo/CL_0000997) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "Immature CD8_alpha-negative CD11b-positive dendritic cell is a CD8_alpha-negative CD11b-positive dendritic cell that is CD80-low, CD86-low, and MHCII-low."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:amm"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMCID:PMC2346585"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GO_REF:0000031"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:tfm"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [immature CD8-alpha-negative CD11b-positive dendritic cell](http://purl.obolibrary.org/obo/CL_0000997) [label](http://www.w3.org/2000/01/rdf-schema#label) "immature CD8-alpha-negative CD11b-positive dendritic cell"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [immature CD8-alpha-negative CD11b-positive dendritic cell](http://purl.obolibrary.org/obo/CL_0000997) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "Immature CD8-alpha-negative CD11b-positive dendritic cell is a CD8-alpha-negative CD11b-positive dendritic cell that is CD80-low, CD86-low, and MHCII-low."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:amm"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMCID:PMC2346585"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GO_REF:0000031"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:tfm"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### immature CD8-alpha-positive CD11b-negative dendritic cell `http://purl.obolibrary.org/obo/CL_0001004` +#### Removed +- [immature CD8-alpha-positive CD11b-negative dendritic cell](http://purl.obolibrary.org/obo/CL_0001004) [label](http://www.w3.org/2000/01/rdf-schema#label) "immature CD8_alpha-positive CD11b-negative dendritic cell"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [immature CD8-alpha-positive CD11b-negative dendritic cell](http://purl.obolibrary.org/obo/CL_0001004) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "Immature CD8_alpha-positive CD11b-negative dendritic cell is a CD8_alpha-positive CD11b-negative dendritic cell that is CD80-low, CD86-low, and MHCII-low."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:amm"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMCID:PMC2346585"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GO_REF:0000031"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:tfm"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [immature CD8-alpha-positive CD11b-negative dendritic cell](http://purl.obolibrary.org/obo/CL_0001004) [label](http://www.w3.org/2000/01/rdf-schema#label) "immature CD8-alpha-positive CD11b-negative dendritic cell"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [immature CD8-alpha-positive CD11b-negative dendritic cell](http://purl.obolibrary.org/obo/CL_0001004) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "Immature CD8-alpha-positive CD11b-negative dendritic cell is a CD8-alpha-positive CD11b-negative dendritic cell that is CD80-low, CD86-low, and MHCII-low."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:amm"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMCID:PMC2346585"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GO_REF:0000031"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:tfm"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### immature astrocyte `http://purl.obolibrary.org/obo/CL_0002626` + +#### Added +- [immature astrocyte](http://purl.obolibrary.org/obo/CL_0002626) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl/cl-base#cellxgene_subset) + + +### immature neuron `http://purl.obolibrary.org/obo/CL_4042028` + +#### Added +- [immature neuron](http://purl.obolibrary.org/obo/CL_4042028) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A neuron in the central nervous system that is not committed to a differentiated fate, has not been newly derived from neurogenesis, and does not integrate into any circuit."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:37833544"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:32116519"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:31096632"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [immature neuron](http://purl.obolibrary.org/obo/CL_4042028) [comment](http://www.w3.org/2000/01/rdf-schema#comment) "It is hypothesised that immature neurons can be utilised as a neurogenic reserve and that they can be involved in circuit plasticity."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:32116519"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [immature neuron](http://purl.obolibrary.org/obo/CL_4042028) [id](http://www.geneontology.org/formats/oboInOwl#id) "CL:4042028"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [immature neuron](http://purl.obolibrary.org/obo/CL_4042028) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "IN"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003000](http://purl.obolibrary.org/obo/OMO_0003000) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:32116519"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [immature neuron](http://purl.obolibrary.org/obo/CL_4042028) [date](http://purl.org/dc/terms/date) "2024-10-10T09:14:45Z"^^[dateTime](http://www.w3.org/2001/XMLSchema#dateTime) + +- [immature neuron](http://purl.obolibrary.org/obo/CL_4042028) [contributor](http://purl.org/dc/terms/contributor) [0000-0002-0098-8958](https://orcid.org/0000-0002-0098-8958) + +- [immature neuron](http://purl.obolibrary.org/obo/CL_4042028) [label](http://www.w3.org/2000/01/rdf-schema#label) "immature neuron"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- Class: [immature neuron](http://purl.obolibrary.org/obo/CL_4042028) + +- [immature neuron](http://purl.obolibrary.org/obo/CL_4042028) SubClassOf [central nervous system neuron](http://purl.obolibrary.org/obo/CL_2000029) + + +### immature single positive thymocyte `http://purl.obolibrary.org/obo/CL_0000805` +#### Removed +- [immature single positive thymocyte](http://purl.obolibrary.org/obo/CL_0000805) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) + + + +### immune oligodendroglia `http://purl.obolibrary.org/obo/CL_4042031` + +#### Added +- [immune oligodendroglia](http://purl.obolibrary.org/obo/CL_4042031) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "imOLG"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003000](http://purl.obolibrary.org/obo/OMO_0003000) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:30747918"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [immune oligodendroglia](http://purl.obolibrary.org/obo/CL_4042031) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "An oligodendrocyte of the central nervous system that exhibits immune properties such as self-presentation and non-self antigen presentation to T cells, phagocytosis of debris, and cytokine and chemokine production. Immune oligodendroglia is immunoreactive during inflammation, neurodegenerative disorders, chronic stress and major depressive disorder."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:30747918"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:35662200"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:35301426"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:35615276"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [immune oligodendroglia](http://purl.obolibrary.org/obo/CL_4042031) [comment](http://www.w3.org/2000/01/rdf-schema#comment) "During inflammation, immuno oligodendroglia express MHC II to interact with immune cells in mouse models (Harrington et al., 2023; Madeira et al., 2022). In a mouse model of major depressive disorder and chronic stress, immuno oligodendroglia were associated with prefrontal cortex hypomyelination (Kokkosis et al., 2022)."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:37057892"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:35301426"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:35615276"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [immune oligodendroglia](http://purl.obolibrary.org/obo/CL_4042031) [date](http://purl.org/dc/terms/date) "2024-10-11T12:51:17Z"^^[dateTime](http://www.w3.org/2001/XMLSchema#dateTime) + +- [immune oligodendroglia](http://purl.obolibrary.org/obo/CL_4042031) [label](http://www.w3.org/2000/01/rdf-schema#label) "immune oligodendroglia"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [immune oligodendroglia](http://purl.obolibrary.org/obo/CL_4042031) [id](http://www.geneontology.org/formats/oboInOwl#id) "CL:4042031"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [immune oligodendroglia](http://purl.obolibrary.org/obo/CL_4042031) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "ImOL"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003000](http://purl.obolibrary.org/obo/OMO_0003000) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:35615276"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [immune oligodendroglia](http://purl.obolibrary.org/obo/CL_4042031) [has_exact_synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "immune oligodendrocyte"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:35615276"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [immune oligodendroglia](http://purl.obolibrary.org/obo/CL_4042031) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "ImOLG"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003000](http://purl.obolibrary.org/obo/OMO_0003000) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:30747918"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [immune oligodendroglia](http://purl.obolibrary.org/obo/CL_4042031) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "Im-OL"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003000](http://purl.obolibrary.org/obo/OMO_0003000) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:35301426"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [immune oligodendroglia](http://purl.obolibrary.org/obo/CL_4042031) [contributor](http://purl.org/dc/terms/contributor) [0000-0002-0098-8958](https://orcid.org/0000-0002-0098-8958) + +- Class: [immune oligodendroglia](http://purl.obolibrary.org/obo/CL_4042031) + +- [immune oligodendroglia](http://purl.obolibrary.org/obo/CL_4042031) SubClassOf [RO_0002215](http://purl.obolibrary.org/obo/RO_0002215) some [GO_0002504](http://purl.obolibrary.org/obo/GO_0002504) + +- [immune oligodendroglia](http://purl.obolibrary.org/obo/CL_4042031) SubClassOf [oligodendrocyte](http://purl.obolibrary.org/obo/CL_0000128) + + +### indirect pathway medium spiny neuron `http://purl.obolibrary.org/obo/CL_4023029` + +#### Added +- [indirect pathway medium spiny neuron](http://purl.obolibrary.org/obo/CL_4023029) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl/cl-base#cellxgene_subset) + + +### inflammatory macrophage `http://purl.obolibrary.org/obo/CL_0000863` +#### Removed +- [inflammatory macrophage](http://purl.obolibrary.org/obo/CL_0000863) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +Inflammatory macrophages, also sometimes referred to as M1 or classically activated macrophages, play an important role in the inflammatory response. The M1/M2 classification is based upon macrophage polarization rather than macrophage location and refers to macrophage activation towards either a more inflammatory or more resolving phenotype, respectively, although the functional diversity of macrophages is more nuanced than such a dichotomy suggests. +Inflammatory macrophages are derived from monocytes recruited to a site of infection or injury. M1 macrophages are classically activated, typically by IFN-γ or lipopolysaccharide (LPS). Upon sensing signs of inflammation, they quickly respond by increasing their pro-inflammatory activity. They achieve this by producing a range of signaling molecules, such as nitric oxide, reactive oxygen species, and numerous cytokines such as tumor necrosis factor-alpha (TNF-alpha) and interleukin-1, -6 and -12. The release of these potent molecules helps to recruit other immune cells to the site, killing off pathogenic organisms and facilitation inflammation. At the same time, M1 macrophages can also present antigens to T cells, thereby helping to induce an adaptive immune response. Over time, these macrophages may transition in phenotype and function to help resolve the inflammation and promote tissue repair. +Despite the beneficial role of inflammatory macrophages in dealing with pathogens, chronic activation of these cells can lead to harmful effects. Over time, continuous production of pro-inflammatory molecules can cause damage to tissues and organs. This is seen in certain chronic inflammatory diseases, such as atherosclerosis, diabetes, obesity, asthma, and various autoimmune disorders. In such situations, the normally protective function of inflammatory macrophages is not properly controlled, which can contribute to disease pathology."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1186/s12935-021-02089-2"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.3389/fimmu.2020.583084"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.3389/fimmu.2015.00263"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1038/s41392-023-01452-1"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [inflammatory macrophage](http://purl.obolibrary.org/obo/CL_0000863) EquivalentTo [elicited macrophage](http://purl.obolibrary.org/obo/CL_0000861) and ([RO_0002215](http://purl.obolibrary.org/obo/RO_0002215) some [GO_0032611](http://purl.obolibrary.org/obo/GO_0032611)) and ([RO_0002215](http://purl.obolibrary.org/obo/RO_0002215) some [GO_0032635](http://purl.obolibrary.org/obo/GO_0032635)) and ([RO_0002215](http://purl.obolibrary.org/obo/RO_0002215) some [GO_0032640](http://purl.obolibrary.org/obo/GO_0032640)) and ([RO_0002215](http://purl.obolibrary.org/obo/RO_0002215) some [GO_0042554](http://purl.obolibrary.org/obo/GO_0042554)) and ([RO_0002215](http://purl.obolibrary.org/obo/RO_0002215) some [GO_0042742](http://purl.obolibrary.org/obo/GO_0042742)) and ([RO_0002215](http://purl.obolibrary.org/obo/RO_0002215) some [GO_0051767](http://purl.obolibrary.org/obo/GO_0051767)) + +- [inflammatory macrophage](http://purl.obolibrary.org/obo/CL_0000863) SubClassOf [RO_0002215](http://purl.obolibrary.org/obo/RO_0002215) some [GO_0051767](http://purl.obolibrary.org/obo/GO_0051767) + +#### Added +- [inflammatory macrophage](http://purl.obolibrary.org/obo/CL_0000863) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Inflammatory macrophages, also sometimes referred to as M1 or classically activated macrophages, play an important role in the inflammatory response. The M1/M2 classification is based upon macrophage polarization rather than macrophage location and refers to macrophage activation towards either a more inflammatory or more resolving phenotype, respectively, although the functional diversity of macrophages is more nuanced than such a dichotomy suggests. +Inflammatory macrophages are derived from monocytes recruited to a site of infection or injury. M1 macrophages are classically activated, typically by IFN-γ or lipopolysaccharide (LPS). Upon sensing signs of inflammation, they quickly respond by increasing their pro-inflammatory activity. They achieve this by producing a range of signaling molecules, such as nitric oxide, reactive oxygen species, and numerous cytokines such as tumor necrosis factor-alpha (TNF-alpha) and interleukin-1, -6 and -12. The release of these potent molecules helps to recruit other immune cells to the site, killing off pathogenic organisms and facilitation inflammation. At the same time, M1 macrophages can also present antigens to T cells, thereby helping to induce an adaptive immune response. Over time, these macrophages may transition in phenotype and function to help resolve the inflammation and promote tissue repair. +Despite the beneficial role of inflammatory macrophages in dealing with pathogens, chronic activation of these cells can lead to harmful effects. Over time, continuous production of pro-inflammatory molecules can cause damage to tissues and organs. This is seen in certain chronic inflammatory diseases, such as atherosclerosis, diabetes, obesity, asthma, and various autoimmune disorders. In such situations, the normally protective function of inflammatory macrophages is not properly controlled, which can contribute to disease pathology."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1186/s12935-021-02089-2"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.3389/fimmu.2020.583084"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.3389/fimmu.2015.00263"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1038/s41392-023-01452-1"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [inflammatory macrophage](http://purl.obolibrary.org/obo/CL_0000863) EquivalentTo [elicited macrophage](http://purl.obolibrary.org/obo/CL_0000861) and ([RO_0002215](http://purl.obolibrary.org/obo/RO_0002215) some [GO_0032611](http://purl.obolibrary.org/obo/GO_0032611)) and ([RO_0002215](http://purl.obolibrary.org/obo/RO_0002215) some [GO_0032635](http://purl.obolibrary.org/obo/GO_0032635)) and ([RO_0002215](http://purl.obolibrary.org/obo/RO_0002215) some [GO_0032640](http://purl.obolibrary.org/obo/GO_0032640)) and ([RO_0002215](http://purl.obolibrary.org/obo/RO_0002215) some [GO_0042554](http://purl.obolibrary.org/obo/GO_0042554)) and ([RO_0002215](http://purl.obolibrary.org/obo/RO_0002215) some [GO_0042742](http://purl.obolibrary.org/obo/GO_0042742)) and ([RO_0002215](http://purl.obolibrary.org/obo/RO_0002215) some [GO_0045428](http://purl.obolibrary.org/obo/GO_0045428)) + +- [inflammatory macrophage](http://purl.obolibrary.org/obo/CL_0000863) SubClassOf [RO_0002215](http://purl.obolibrary.org/obo/RO_0002215) some [GO_0045428](http://purl.obolibrary.org/obo/GO_0045428) + + +### inner medulla vasa recta ascending limb cell `http://purl.obolibrary.org/obo/CL_1001209` +#### Removed +- [inner medulla vasa recta ascending limb cell](http://purl.obolibrary.org/obo/CL_1001209) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "Any vasa recta ascending limb cell that is part of some inner medulla vasa recta ascending limb."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBC:Autogenerated"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [inner medulla vasa recta ascending limb cell](http://purl.obolibrary.org/obo/CL_1001209) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "Any vasa recta ascending limb cell that is part of some inner medulla ascending vasa recta."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBC:Autogenerated"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### inner medulla vasa recta descending limb cell `http://purl.obolibrary.org/obo/CL_1001286` +#### Removed +- [inner medulla vasa recta descending limb cell](http://purl.obolibrary.org/obo/CL_1001286) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "Any vasa recta descending limb cell that is part of some inner medulla vasa recta descending limb."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBC:Autogenerated"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [inner medulla vasa recta descending limb cell](http://purl.obolibrary.org/obo/CL_1001286) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "Any vasa recta descending limb cell that is part of some inner medulla descending vasa recta."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBC:Autogenerated"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### inner renal medulla vasa recta cell `http://purl.obolibrary.org/obo/CL_1001126` +#### Removed +- [inner renal medulla vasa recta cell](http://purl.obolibrary.org/obo/CL_1001126) SubClassOf [kidney venous blood vessel cell](http://purl.obolibrary.org/obo/CL_1000893) + + + +### intermediate mesodermal cell `http://purl.obolibrary.org/obo/CL_0011011` + +#### Added +- [intermediate mesodermal cell](http://purl.obolibrary.org/obo/CL_0011011) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl/cl-base#cellxgene_subset) + + +### interna theca cell `http://purl.obolibrary.org/obo/CL_4052012` + +#### Added +- [interna theca cell](http://purl.obolibrary.org/obo/CL_4052012) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "inTC"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003000](http://purl.obolibrary.org/obo/OMO_0003000) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:31320652"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [interna theca cell](http://purl.obolibrary.org/obo/CL_4052012) [contributor](http://purl.org/dc/terms/contributor) [0009-0000-8480-9277](https://orcid.org/0009-0000-8480-9277) + +- [interna theca cell](http://purl.obolibrary.org/obo/CL_4052012) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A specialized theca cell that forms the inner, highly vascularized layer of the theca surrounding ovarian follicles. Originating from progenitor theca cells, the theca interna cell is steroidogenic, playing a crucial role in the production of androgens, which serves as a precursor for estrogen synthesis in granulosa cells. This cell expresses luteinizing hormone receptors, enabling it to respond to hormonal signals that regulate steroidogenesis."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:31320652"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:32530882"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Theca_interna"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:15833266"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [interna theca cell](http://purl.obolibrary.org/obo/CL_4052012) [label](http://www.w3.org/2000/01/rdf-schema#label) "interna theca cell"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [interna theca cell](http://purl.obolibrary.org/obo/CL_4052012) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "interna TC"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003000](http://purl.obolibrary.org/obo/OMO_0003000) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:31320652"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [interna theca cell](http://purl.obolibrary.org/obo/CL_4052012) [id](http://www.geneontology.org/formats/oboInOwl#id) "CL:4052012"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [interna theca cell](http://purl.obolibrary.org/obo/CL_4052012) [date](http://purl.org/dc/terms/date) "2024-09-30T11:10:15Z"^^[dateTime](http://www.w3.org/2001/XMLSchema#dateTime) + +- Class: [interna theca cell](http://purl.obolibrary.org/obo/CL_4052012) + +- [interna theca cell](http://purl.obolibrary.org/obo/CL_4052012) DisjointWith [externa theca cell](http://purl.obolibrary.org/obo/CL_4052013) + +- [interna theca cell](http://purl.obolibrary.org/obo/CL_4052012) EquivalentTo [theca cell](http://purl.obolibrary.org/obo/CL_0000503) and ([BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0000157](http://purl.obolibrary.org/obo/UBERON_0000157)) + +- [interna theca cell](http://purl.obolibrary.org/obo/CL_4052012) SubClassOf [RO_0002202](http://purl.obolibrary.org/obo/RO_0002202) some [pre-theca cell](http://purl.obolibrary.org/obo/CL_4052010) + +- [interna theca cell](http://purl.obolibrary.org/obo/CL_4052012) SubClassOf [androgen secreting cell](http://purl.obolibrary.org/obo/CL_0000593) + +- [interna theca cell](http://purl.obolibrary.org/obo/CL_4052012) SubClassOf [BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0000157](http://purl.obolibrary.org/obo/UBERON_0000157) + +- [interna theca cell](http://purl.obolibrary.org/obo/CL_4052012) SubClassOf [theca cell](http://purl.obolibrary.org/obo/CL_0000503) + + +### interneuron `http://purl.obolibrary.org/obo/CL_0000099` +#### Removed +- [interneuron](http://purl.obolibrary.org/obo/CL_0000099) SubClassOf [neuron](http://purl.obolibrary.org/obo/CL_0000540) + +#### Added +- [interneuron](http://purl.obolibrary.org/obo/CL_0000099) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "CNS interneuron"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [interneuron](http://purl.obolibrary.org/obo/CL_0000099) SubClassOf [central nervous system neuron](http://purl.obolibrary.org/obo/CL_2000029) + + +### intestinal crypt stem cell `http://purl.obolibrary.org/obo/CL_0002250` +#### Removed +- [intestinal crypt stem cell](http://purl.obolibrary.org/obo/CL_0002250) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +Intestinal crypt stem cells, also known as crypt base columnar cells, are a unique type of cell, characterized by the highly specific marker LGR5, found in the intestinal epithelium. Situated at the bottom of the minute pockets known as crypts of Lieberkühn, these are undifferentiated cells that have the ability to perpetually self-renew, as well as differentiate into various other cell types that constitute the epithelial lining of the intestine. +The fundamental role of intestinal crypt stem cells is to provide a constant supply of new cells to maintain the cellular turnover of the intestinal epithelium, a tissue known for rapid self-renewal. These stem cells are nurtured and protected by specialized epithelial and mesenchymal cells, and together constitute the intestinal stem cell niche. +An important function of intestinal crypt stem cells is to sustain the balance between cell division and programmed cell death, called apoptosis, to ensure the integrity of the intestinal lining. Given their active proliferation rate, these stem cells initiate the creation of diverse differentiated cell types, including enterocytes (the primary absorptive cells in the intestinal lumen), goblet cells (that produce mucus to protect the epithelial layer), enteroendocrine cells (involved in producing gastrointestinal hormones), and Paneth cells (involved in secreting antimicrobial peptides). This diversity in output regulates the physiological activities of the gut ranging from nutrient absorption, hormone secretion, bacterial balance, to immunity. +Research studies suggest that dysregulation in intestinal crypt stem cell proliferation and differentiation is associated with several intestinal disorders including intestinal cancer, and various enteropathies."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1101/gad.1674008"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1038/s41575-018-0081-y"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1016/j.cell.2013.07.004"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1038/s41580-020-0278-0"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1111/j.1365-2184.2009.00642.x"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [intestinal crypt stem cell](http://purl.obolibrary.org/obo/CL_0002250) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Intestinal crypt stem cells, also known as crypt base columnar cells, are a unique type of cell, characterized by the highly specific marker LGR5, found in the intestinal epithelium. Situated at the bottom of the minute pockets known as crypts of Lieberkühn, these are undifferentiated cells that have the ability to perpetually self-renew, as well as differentiate into various other cell types that constitute the epithelial lining of the intestine. +The fundamental role of intestinal crypt stem cells is to provide a constant supply of new cells to maintain the cellular turnover of the intestinal epithelium, a tissue known for rapid self-renewal. These stem cells are nurtured and protected by specialized epithelial and mesenchymal cells, and together constitute the intestinal stem cell niche. +An important function of intestinal crypt stem cells is to sustain the balance between cell division and programmed cell death, called apoptosis, to ensure the integrity of the intestinal lining. Given their active proliferation rate, these stem cells initiate the creation of diverse differentiated cell types, including enterocytes (the primary absorptive cells in the intestinal lumen), goblet cells (that produce mucus to protect the epithelial layer), enteroendocrine cells (involved in producing gastrointestinal hormones), and Paneth cells (involved in secreting antimicrobial peptides). This diversity in output regulates the physiological activities of the gut ranging from nutrient absorption, hormone secretion, bacterial balance, to immunity. +Research studies suggest that dysregulation in intestinal crypt stem cell proliferation and differentiation is associated with several intestinal disorders including intestinal cancer, and various enteropathies."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1101/gad.1674008"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1038/s41575-018-0081-y"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1016/j.cell.2013.07.004"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1038/s41580-020-0278-0"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1111/j.1365-2184.2009.00642.x"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### intestinal crypt stem cell of anorectum `http://purl.obolibrary.org/obo/CL_0009061` +#### Removed +- [intestinal crypt stem cell of anorectum](http://purl.obolibrary.org/obo/CL_0009061) EquivalentTo [intestinal crypt stem cell](http://purl.obolibrary.org/obo/CL_0002250) and ([BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_8410050](http://purl.obolibrary.org/obo/UBERON_8410050)) + +- [intestinal crypt stem cell of anorectum](http://purl.obolibrary.org/obo/CL_0009061) SubClassOf [epithelial cell of large intestine](http://purl.obolibrary.org/obo/CL_0002253) + +- [intestinal crypt stem cell of anorectum](http://purl.obolibrary.org/obo/CL_0009061) SubClassOf [intestinal crypt stem cell](http://purl.obolibrary.org/obo/CL_0002250) + +#### Added +- [intestinal crypt stem cell of anorectum](http://purl.obolibrary.org/obo/CL_0009061) EquivalentTo [intestinal crypt stem cell of large intestine](http://purl.obolibrary.org/obo/CL_0009016) and ([BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_8410050](http://purl.obolibrary.org/obo/UBERON_8410050)) + +- [intestinal crypt stem cell of anorectum](http://purl.obolibrary.org/obo/CL_0009061) SubClassOf [intestinal crypt stem cell of large intestine](http://purl.obolibrary.org/obo/CL_0009016) + + +### intestinal crypt stem cell of appendix `http://purl.obolibrary.org/obo/CL_0009028` +#### Removed +- [intestinal crypt stem cell of appendix](http://purl.obolibrary.org/obo/CL_0009028) SubClassOf [epithelial cell of appendix](http://purl.obolibrary.org/obo/CL_1000405) + + + +### intestinal crypt stem cell of colon `http://purl.obolibrary.org/obo/CL_0009043` +#### Removed +- [intestinal crypt stem cell of colon](http://purl.obolibrary.org/obo/CL_0009043) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "An intestinal crypt stem cell that is located in the colon."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "http://orcid.org/0000-0003-3440-1876"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [intestinal crypt stem cell of colon](http://purl.obolibrary.org/obo/CL_0009043) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +Intestinal crypt stem cells of the colon, also known as colon crypt base columnar (CBC) cells, are highly specialized cells primarily responsible for the constant self-renewal of the colonic epithelium. These cells are found in the crypts of Lieberkühn - deeply invaginated sections of the colon's mucosal layer. +The prime function of intestinal crypt stem cells of the colon is to serve as the source of constant cell regeneration in the colon. Every few days, these stem cells divide and differentiate into the various other types of intestinal cells, such as enterocytes, goblet cells, and enteroendocrine cells. +A constant renewal cycle is necessary due to the harsh environment of the colon where cells continuously encounter abrasive food matter and potential pathogens, leading to a high turnover rate. When the colon's mucosal layer suffers damage, a rapid response is triggered whereby colon crypt stem cells divide faster and are directed to injured sites to repair the epithelial layer. Dysregulation of these cells' function or proliferation can contribute to disorders such as colorectal cancer."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1186/s12943-019-0962-x"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1038/s41575-018-0081-y"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1016/j.cell.2013.07.004"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1073/pnas.1607327113"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1111/j.1365-2184.2009.00642.x"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [intestinal crypt stem cell of colon](http://purl.obolibrary.org/obo/CL_0009043) EquivalentTo [intestinal crypt stem cell](http://purl.obolibrary.org/obo/CL_0002250) and ([BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0001155](http://purl.obolibrary.org/obo/UBERON_0001155)) + +- [intestinal crypt stem cell of colon](http://purl.obolibrary.org/obo/CL_0009043) SubClassOf [intestinal crypt stem cell](http://purl.obolibrary.org/obo/CL_0002250) + +- [intestinal crypt stem cell of colon](http://purl.obolibrary.org/obo/CL_0009043) SubClassOf [colon epithelial cell](http://purl.obolibrary.org/obo/CL_0011108) + +#### Added +- [intestinal crypt stem cell of colon](http://purl.obolibrary.org/obo/CL_0009043) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Intestinal crypt stem cells of the colon, also known as colon crypt base columnar (CBC) cells, are highly specialized cells primarily responsible for the constant self-renewal of the colonic epithelium. These cells are found in the crypts of Lieberkühn - deeply invaginated sections of the colon's mucosal layer. +The prime function of intestinal crypt stem cells of the colon is to serve as the source of constant cell regeneration in the colon. Every few days, these stem cells divide and differentiate into the various other types of intestinal cells, such as enterocytes, goblet cells, and enteroendocrine cells. +A constant renewal cycle is necessary due to the harsh environment of the colon where cells continuously encounter abrasive food matter and potential pathogens, leading to a high turnover rate. When the colon's mucosal layer suffers damage, a rapid response is triggered whereby colon crypt stem cells divide faster and are directed to injured sites to repair the epithelial layer. Dysregulation of these cells' function or proliferation can contribute to disorders such as colorectal cancer."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1186/s12943-019-0962-x"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1038/s41575-018-0081-y"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1016/j.cell.2013.07.004"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1073/pnas.1607327113"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1111/j.1365-2184.2009.00642.x"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [intestinal crypt stem cell of colon](http://purl.obolibrary.org/obo/CL_0009043) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "An intestinal crypt stem cell that is located in the crypt of Lieberkuhn of colon."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "http://orcid.org/0000-0003-3440-1876"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:10841502"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [intestinal crypt stem cell of colon](http://purl.obolibrary.org/obo/CL_0009043) EquivalentTo [intestinal crypt stem cell](http://purl.obolibrary.org/obo/CL_0002250) and ([BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0013485](http://purl.obolibrary.org/obo/UBERON_0013485)) + +- [intestinal crypt stem cell of colon](http://purl.obolibrary.org/obo/CL_0009043) SubClassOf [intestinal crypt stem cell of large intestine](http://purl.obolibrary.org/obo/CL_0009016) + +- [intestinal crypt stem cell of colon](http://purl.obolibrary.org/obo/CL_0009043) SubClassOf [BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0013485](http://purl.obolibrary.org/obo/UBERON_0013485) + + +### intestinal crypt stem cell of small intestine `http://purl.obolibrary.org/obo/CL_0009017` +#### Removed +- [intestinal crypt stem cell of small intestine](http://purl.obolibrary.org/obo/CL_0009017) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +Intestinal crypt stem cells of the small intestine are a type of adult stem cell intimately involved in the continuous replenishment of the intestinal epithelium, the innermost layer of the intestine responsible for nutrient absorption. These cells, located within the crypts of Lieberkühn, are the origin of various cell lineages that make up the functional units of the small intestine. They possess self-renewal ability, an essential feature of stem cells, which allows them to maintain a steady population in the small intestine. +One of the critical roles of intestinal crypt stem cells is to drive the continual renewal process taking place in the small intestine every 3-5 days. By proliferating intensively, these cells produce transient amplifying (TA) cells that are characterized by quick division and progressive differentiation. These cells eventually differentiate into specialized cell types, encompassing absorptive enterocytes, mucin-secreting goblet cells, hormone-secreting enteroendocrine cells, and Paneth cells, all of which have essential roles in digestion and nutrient absorption in the small intestine. +Intestinal crypt stem cells of the small intestine are also play a significant part in injury recovery. Under regular conditions, these cells primarily exist in an active state, facilitating the constant renovation of the gut lining. However, upon injury or loss of regular intestinal crypt stem cells reserve intestinal stem cells, a slow-cycling and radio-resistant population, can be stimulated to take over the duties of active crypt stem cells. Such plasticity provides a powerful regenerative mechanism that ensures the intestinal epithelium's function and structural integrity amidst diverse conditions."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1016/j.celrep.2020.107952"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1038/s41575-018-0081-y"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1073/pnas.1607327113"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [intestinal crypt stem cell of small intestine](http://purl.obolibrary.org/obo/CL_0009017) [depiction](http://xmlns.com/foaf/0.1/depiction) [Small-intestine-cells.png](http://purl.obolibrary.org/obo/cl/images/Small-intestine-cells.png) + - [comment](http://www.w3.org/2000/01/rdf-schema#comment) "Figure depicts a cross section of intestinal villi in the small intestine, including the crypts of Lieberkuhn (seen here as ‘crypt’), as well as the layer specific locations of cells that exist within the gastrointestinal tract. Layers depicted here include epithelium (rows of cells bordering villus), submucosa (white space below the epithelium containing networks of neurons and ganglia depicted in pink), muscularis mucosae (blue layer), muscularis propria (referred to here as muscle layer). + +ISC: Intestinal Stem Cell +TA: Transit Amplifying Cells"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [license](http://purl.org/dc/elements/1.1/license) "http://creativecommons.org/licenses/by/4.0/"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [intestinal crypt stem cell of small intestine](http://purl.obolibrary.org/obo/CL_0009017) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Intestinal crypt stem cells of the small intestine are a type of adult stem cell intimately involved in the continuous replenishment of the intestinal epithelium, the innermost layer of the intestine responsible for nutrient absorption. These cells, located within the crypts of Lieberkühn, are the origin of various cell lineages that make up the functional units of the small intestine. They possess self-renewal ability, an essential feature of stem cells, which allows them to maintain a steady population in the small intestine. +One of the critical roles of intestinal crypt stem cells is to drive the continual renewal process taking place in the small intestine every 3-5 days. By proliferating intensively, these cells produce transient amplifying (TA) cells that are characterized by quick division and progressive differentiation. These cells eventually differentiate into specialized cell types, encompassing absorptive enterocytes, mucin-secreting goblet cells, hormone-secreting enteroendocrine cells, and Paneth cells, all of which have essential roles in digestion and nutrient absorption in the small intestine. +Intestinal crypt stem cells of the small intestine are also play a significant part in injury recovery. Under regular conditions, these cells primarily exist in an active state, facilitating the constant renovation of the gut lining. However, upon injury or loss of regular intestinal crypt stem cells reserve intestinal stem cells, a slow-cycling and radio-resistant population, can be stimulated to take over the duties of active crypt stem cells. Such plasticity provides a powerful regenerative mechanism that ensures the intestinal epithelium's function and structural integrity amidst diverse conditions."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1016/j.celrep.2020.107952"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1038/s41575-018-0081-y"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1073/pnas.1607327113"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### intestinal enteroendocrine cell `http://purl.obolibrary.org/obo/CL_1001516` +#### Removed +- [intestinal enteroendocrine cell](http://purl.obolibrary.org/obo/CL_1001516) EquivalentTo [enteroendocrine cell](http://purl.obolibrary.org/obo/CL_0000164) and ([BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0001242](http://purl.obolibrary.org/obo/UBERON_0001242)) + +#### Added +- [intestinal enteroendocrine cell](http://purl.obolibrary.org/obo/CL_1001516) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Intestinal enteroendocrine cells are a highly specialized cell type found within the gastrointestinal epithelium. They account for approximately 1% of the intestinal epithelial cells in what is known as the largest endocrine organ in the human body. Intestinal enteroendocrine cells exhibit an exceptional diversity, both in terms of their secretory products and their distribution along the intestines, varying from the small intestine to the colon. +The primary function of intestinal enteroendocrine cells is to maintain gut physiology and homeostasis. They are known for their hormone production and are the source of numerous bioactive molecules including somatostatin, serotonin, cholecystokinin, glucose-dependent insulinotropic peptide, motilin, neurotensin, and others. These hormones and neuropeptides act in autocrine, paracrine, or endocrine signaling, impacting various functions including intestinal motility, secretion, nutrient absorption, and gut barrier functions. +Intestinal enteroendocrine cells also serve as the body's frontline of defense, playing an integral role in surveillance against lumen-occurring hazards including pathogen attack. Enteroendocrine cells are divided into ‘closed type’ and ‘open type’. Closed type cells are located close to the basal membrane and do not reach the lumen of the gut. In contrast, the apical side of the open-type intestinal enteroendocrine cells is directly exposed to luminal contents and thus can recognize bacterial metabolites and dietary nutrients. In response, these cells can modulate the immune system responses and thereby function as a key communicator between the gut microbiota and the host."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1111/j.1365-2613.2011.00767.x"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1146/annurev-physiol-021115-105439"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1016/j.coph.2013.09.008"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1038/s41574-019-0168-8"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1038/mi.2017.73"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [intestinal enteroendocrine cell](http://purl.obolibrary.org/obo/CL_1001516) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://cellxgene.cziscience.com/cellguide/CL_1001516"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [intestinal enteroendocrine cell](http://purl.obolibrary.org/obo/CL_1001516) EquivalentTo [enteroendocrine cell](http://purl.obolibrary.org/obo/CL_0000164) and ([BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0001277](http://purl.obolibrary.org/obo/UBERON_0001277)) + +- [intestinal enteroendocrine cell](http://purl.obolibrary.org/obo/CL_1001516) SubClassOf [RO_0002207](http://purl.obolibrary.org/obo/RO_0002207) some [intestinal enteroendocrine progenitor](http://purl.obolibrary.org/obo/CL_4052006) + + +### intestinal epithelial cell `http://purl.obolibrary.org/obo/CL_0002563` +#### Removed +- [intestinal epithelial cell](http://purl.obolibrary.org/obo/CL_0002563) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "An epithelial cell of the intestine."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:tfm"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [intestinal epithelial cell](http://purl.obolibrary.org/obo/CL_0002563) EquivalentTo [epithelial cell](http://purl.obolibrary.org/obo/CL_0000066) and ([BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0000160](http://purl.obolibrary.org/obo/UBERON_0000160)) + +#### Added +- [intestinal epithelial cell](http://purl.obolibrary.org/obo/CL_0002563) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "An epithelial cell of the lining of the intestine."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:tfm"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [intestinal epithelial cell](http://purl.obolibrary.org/obo/CL_0002563) EquivalentTo [epithelial cell](http://purl.obolibrary.org/obo/CL_0000066) and ([BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0001277](http://purl.obolibrary.org/obo/UBERON_0001277)) + + +### intestinal lamina propria fibroblast `http://purl.obolibrary.org/obo/CL_4047023` + +#### Added +- [intestinal lamina propria fibroblast](http://purl.obolibrary.org/obo/CL_4047023) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "S1 fibroblast"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:30270042"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [intestinal lamina propria fibroblast](http://purl.obolibrary.org/obo/CL_4047023) [label](http://www.w3.org/2000/01/rdf-schema#label) "intestinal lamina propria fibroblast"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [intestinal lamina propria fibroblast](http://purl.obolibrary.org/obo/CL_4047023) [contributor](http://purl.org/dc/terms/contributor) [0009-0005-7919-4905](https://orcid.org/0009-0005-7919-4905) + +- [intestinal lamina propria fibroblast](http://purl.obolibrary.org/obo/CL_4047023) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A fibroblast located in the lamina propria of the intestinal mucosa. This cell expresses PDGFRα and CD81 and is negative for α-smooth muscle actin (α-SMA). This cell is predominantly located in the small intestine adjacent to myofibroblasts surrounding the crypts. It is capable of synthesizing extracellular matrix components and structural proteins such as collagen and elastin."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:21252048"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:36032088"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [intestinal lamina propria fibroblast](http://purl.obolibrary.org/obo/CL_4047023) [date](http://purl.org/dc/terms/date) "2024-09-24T15:45:18Z"^^[dateTime](http://www.w3.org/2001/XMLSchema#dateTime) + +- [intestinal lamina propria fibroblast](http://purl.obolibrary.org/obo/CL_4047023) [id](http://www.geneontology.org/formats/oboInOwl#id) "CL:4047023"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- Class: [intestinal lamina propria fibroblast](http://purl.obolibrary.org/obo/CL_4047023) + +- [intestinal lamina propria fibroblast](http://purl.obolibrary.org/obo/CL_4047023) EquivalentTo [fibroblast](http://purl.obolibrary.org/obo/CL_0000057) and ([BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0004780](http://purl.obolibrary.org/obo/UBERON_0004780)) and ([RO_0002215](http://purl.obolibrary.org/obo/RO_0002215) some [GO_0070278](http://purl.obolibrary.org/obo/GO_0070278)) + +- [intestinal lamina propria fibroblast](http://purl.obolibrary.org/obo/CL_4047023) SubClassOf [BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0004780](http://purl.obolibrary.org/obo/UBERON_0004780) + +- [intestinal lamina propria fibroblast](http://purl.obolibrary.org/obo/CL_4047023) SubClassOf [fibroblast](http://purl.obolibrary.org/obo/CL_0000057) + +- [intestinal lamina propria fibroblast](http://purl.obolibrary.org/obo/CL_4047023) SubClassOf [secretory cell](http://purl.obolibrary.org/obo/CL_0000151) + +- [intestinal lamina propria fibroblast](http://purl.obolibrary.org/obo/CL_4047023) SubClassOf [RO_0002215](http://purl.obolibrary.org/obo/RO_0002215) some [GO_0070278](http://purl.obolibrary.org/obo/GO_0070278) + + +### intestinal tuft cell `http://purl.obolibrary.org/obo/CL_0019032` +#### Removed +- [intestinal tuft cell](http://purl.obolibrary.org/obo/CL_0019032) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "Any brush cell that is part of the intestinal epithelium."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:22527717"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [intestinal tuft cell](http://purl.obolibrary.org/obo/CL_0019032) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "Any brush cell that is part of the intestinal epithelium."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:22527717"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:39358509"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [intestinal tuft cell](http://purl.obolibrary.org/obo/CL_0019032) SubClassOf [RO_0002202](http://purl.obolibrary.org/obo/RO_0002202) some [intestinal crypt stem cell](http://purl.obolibrary.org/obo/CL_0002250) + + +### intestinal villus goblet cell `http://purl.obolibrary.org/obo/CL_1000317` +#### Removed +- [intestinal villus goblet cell](http://purl.obolibrary.org/obo/CL_1000317) EquivalentTo [goblet cell](http://purl.obolibrary.org/obo/CL_0000160) and ([BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0001213](http://purl.obolibrary.org/obo/UBERON_0001213)) + +#### Added +- [intestinal villus goblet cell](http://purl.obolibrary.org/obo/CL_1000317) EquivalentTo [goblet cell](http://purl.obolibrary.org/obo/CL_0000160) and ([BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0013636](http://purl.obolibrary.org/obo/UBERON_0013636)) + + +### intestine goblet cell `http://purl.obolibrary.org/obo/CL_0019031` +#### Removed +- [intestine goblet cell](http://purl.obolibrary.org/obo/CL_0019031) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "Goblet cells reside throughout the length of the small and large intestine and are responsible for the production and maintenance of the protective mucus blanket by synthesizing and secreting high-molecular-weight glycoproteins known as mucins. Human intestinal goblet cells secrete the MUC2 mucin, as well as a number of typical mucus components: CLCA1, FCGBP, AGR2, ZG16, and TFF3."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:24942678"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:1996606"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [intestine goblet cell](http://purl.obolibrary.org/obo/CL_0019031) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "Goblet cells reside throughout the length of the small and large intestine and are responsible for the production and maintenance of the protective mucus blanket by synthesizing and secreting high-molecular-weight glycoproteins known as mucins. Human intestinal goblet cells secrete the MUC2 mucin, as well as a number of typical mucus components: CLCA1, FCGBP, AGR2, ZG16, and TFF3."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:33484640"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:24942678"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:1996606"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [intestine goblet cell](http://purl.obolibrary.org/obo/CL_0019031) SubClassOf [RO_0002202](http://purl.obolibrary.org/obo/RO_0002202) some [transit amplifying cell of gut](http://purl.obolibrary.org/obo/CL_4047017) + + +### intrahepatic cholangiocyte `http://purl.obolibrary.org/obo/CL_0002538` +#### Removed +- [intrahepatic cholangiocyte](http://purl.obolibrary.org/obo/CL_0002538) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +Intrahepatic cholangiocytes represent a subset of the biliary epithelial cells that form a network of tubes in the liver called the biliary tree The intrahepatic cholangiocytes reside specifically in the intrahepatic bile ducts and play a crucial role in liver physiology and bile production and secretion, thereby aiding in the digestion and absorption of fats in the small intestine. These specific cholangiocytes arise from bipotent hepatoblasts, whereas extrahepatic cholangiocytes share an embryologic origin with the ventral pancreas. +Recent research suggests that there is also heterogeneity within populations of intrahepatic cholangiocytes with different transcriptional profiles, proliferative capacity, and biological function; for example, subpopulations differ in calcium-mobilizing receptors. +The primary function of intrahepatic cholangiocytes is related to bile formation and maintenance of its flow. In addition to their secretory and absorptive activities, they are involved in the regulation of bile composition, volume, and alkalinization, contributing to the neutralization of the acidic chyme (partly digested food) that enters the intestine from the stomach. Intrahepatic cholangiocytes are also recognized for their role in liver regeneration and repair, often proliferating in response to injury. +Intrahepatic cholangiocytes take part in certain pathological conditions, like primary biliary cirrhosis and cholangiocarcinoma. Changes in these cells often lead to abnormalities in bile formation and transport, causing cholestatic liver diseases. Overall, the primary and secondary functional activities of intrahepatic cholangiocytes are vital in maintaining liver function, digestive processes, and contributing to the body's response to liver injury."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1016/j.ajpath.2023.02.012"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1002/hep.31252"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1016/j.gastha.2022.07.015"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1016/j.biocel.2010.06.020"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [intrahepatic cholangiocyte](http://purl.obolibrary.org/obo/CL_0002538) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Intrahepatic cholangiocytes represent a subset of the biliary epithelial cells that form a network of tubes in the liver called the biliary tree The intrahepatic cholangiocytes reside specifically in the intrahepatic bile ducts and play a crucial role in liver physiology and bile production and secretion, thereby aiding in the digestion and absorption of fats in the small intestine. These specific cholangiocytes arise from bipotent hepatoblasts, whereas extrahepatic cholangiocytes share an embryologic origin with the ventral pancreas. +Recent research suggests that there is also heterogeneity within populations of intrahepatic cholangiocytes with different transcriptional profiles, proliferative capacity, and biological function; for example, subpopulations differ in calcium-mobilizing receptors. +The primary function of intrahepatic cholangiocytes is related to bile formation and maintenance of its flow. In addition to their secretory and absorptive activities, they are involved in the regulation of bile composition, volume, and alkalinization, contributing to the neutralization of the acidic chyme (partly digested food) that enters the intestine from the stomach. Intrahepatic cholangiocytes are also recognized for their role in liver regeneration and repair, often proliferating in response to injury. +Intrahepatic cholangiocytes take part in certain pathological conditions, like primary biliary cirrhosis and cholangiocarcinoma. Changes in these cells often lead to abnormalities in bile formation and transport, causing cholestatic liver diseases. Overall, the primary and secondary functional activities of intrahepatic cholangiocytes are vital in maintaining liver function, digestive processes, and contributing to the body's response to liver injury."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1016/j.ajpath.2023.02.012"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1002/hep.31252"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1016/j.gastha.2022.07.015"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1016/j.biocel.2010.06.020"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### invaginating midget bipolar cell `http://purl.obolibrary.org/obo/CL_4033034` +#### Removed +- [invaginating midget bipolar cell](http://purl.obolibrary.org/obo/CL_4033034) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [human_reference_atlas](http://purl.obolibrary.org/obo/cl/cl-base#human_reference_atlas) + +- [invaginating midget bipolar cell](http://purl.obolibrary.org/obo/CL_4033034) [RO_0002175](http://purl.obolibrary.org/obo/RO_0002175) [NCBITaxon_9606](http://purl.obolibrary.org/obo/NCBITaxon_9606) + +#### Added +- [invaginating midget bipolar cell](http://purl.obolibrary.org/obo/CL_4033034) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl/cl-base#cellxgene_subset) + + +### inverted L6 intratelencephalic projecting glutamatergic neuron of the primary motor cortex (Mmus) `http://purl.obolibrary.org/obo/CL_4023081` +#### Removed +- [inverted L6 intratelencephalic projecting glutamatergic neuron of the primary motor cortex (Mmus)](http://purl.obolibrary.org/obo/CL_4023081) SubClassOf [RO_0000053](http://purl.obolibrary.org/obo/RO_0000053) some [PATO_0070021](http://purl.obolibrary.org/obo/PATO_0070021) + +#### Added +- [inverted L6 intratelencephalic projecting glutamatergic neuron of the primary motor cortex (Mmus)](http://purl.obolibrary.org/obo/CL_4023081) SubClassOf [inverted pyramidal neuron](http://purl.obolibrary.org/obo/CL_4023092) + + +### inverted pyramidal neuron `http://purl.obolibrary.org/obo/CL_4023092` +#### Removed +- [inverted pyramidal neuron](http://purl.obolibrary.org/obo/CL_4023092) EquivalentTo [CNS neuron (sensu Vertebrata)](http://purl.obolibrary.org/obo/CL_0000117) and ([RO_0000053](http://purl.obolibrary.org/obo/RO_0000053) some [PATO_0070021](http://purl.obolibrary.org/obo/PATO_0070021)) + +- [inverted pyramidal neuron](http://purl.obolibrary.org/obo/CL_4023092) SubClassOf [CNS neuron (sensu Vertebrata)](http://purl.obolibrary.org/obo/CL_0000117) + +#### Added +- [inverted pyramidal neuron](http://purl.obolibrary.org/obo/CL_4023092) EquivalentTo [neuron](http://purl.obolibrary.org/obo/CL_0000540) and ([RO_0000053](http://purl.obolibrary.org/obo/RO_0000053) some [PATO_0070021](http://purl.obolibrary.org/obo/PATO_0070021)) + + +### ionocyte `http://purl.obolibrary.org/obo/CL_0005006` +#### Removed +- [ionocyte](http://purl.obolibrary.org/obo/CL_0005006) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +Ionocytes are specialized cells predominantly found in the mammalian respiratory and renal systems as well as in the gills, skin, and intestinal tract of fish. These cells play crucial roles in maintaining ion and acid-base homeostasis. Ionocytes demonstrate remarkable plasticity and are able to adapt themselves in response to changes in environmental conditions such as pH, salinity, ion concentration, and temperature. +These cells work by selectively absorbing specific ions from the environment, thus maintaining the body's internal ionic balance. The most commonly absorbed ions include sodium (Na+), chloride (Cl-), calcium (Ca2+), and hydrogen (H+). Moreover, ionocytes contribute to acid-base regulation. In response to acidosis or alkalosis, ionocytes can either excrete or retain hydrogen (H+) and bicarbonate (HCO3-) ions to readjust the blood pH. Further, experimental evidence suggests a functional complexity of ionocytes, implying diverse roles beyond ion regulation. Recent research highlights ionocytes' involvement in ammonia excretion and the regulation of extracellular fluid volume, highlighting their contribution to the overall homeostatic process. +Malfunctioning ionocytes have been implicated in various diseases, including cystic fibrosis which is caused by mutations in the chloride channel CFTR, an ionocyte marker."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1146/annurev-pathol-042420-094031"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1016/j.jcf.2019.09.010"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1038/s41586-018-0393-7"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1038/s41598-023-30603-1"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.3389/fmars.2020.00709"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [ionocyte](http://purl.obolibrary.org/obo/CL_0005006) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Ionocytes are specialized cells predominantly found in the mammalian respiratory and renal systems as well as in the gills, skin, and intestinal tract of fish. These cells play crucial roles in maintaining ion and acid-base homeostasis. Ionocytes demonstrate remarkable plasticity and are able to adapt themselves in response to changes in environmental conditions such as pH, salinity, ion concentration, and temperature. +These cells work by selectively absorbing specific ions from the environment, thus maintaining the body's internal ionic balance. The most commonly absorbed ions include sodium (Na+), chloride (Cl-), calcium (Ca2+), and hydrogen (H+). Moreover, ionocytes contribute to acid-base regulation. In response to acidosis or alkalosis, ionocytes can either excrete or retain hydrogen (H+) and bicarbonate (HCO3-) ions to readjust the blood pH. Further, experimental evidence suggests a functional complexity of ionocytes, implying diverse roles beyond ion regulation. Recent research highlights ionocytes' involvement in ammonia excretion and the regulation of extracellular fluid volume, highlighting their contribution to the overall homeostatic process. +Malfunctioning ionocytes have been implicated in various diseases, including cystic fibrosis which is caused by mutations in the chloride channel CFTR, an ionocyte marker."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1146/annurev-pathol-042420-094031"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1016/j.jcf.2019.09.010"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1038/s41586-018-0393-7"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1038/s41598-023-30603-1"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.3389/fmars.2020.00709"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### iris pigment epithelial cell `http://purl.obolibrary.org/obo/CL_0002565` + +#### Added +- [iris pigment epithelial cell](http://purl.obolibrary.org/obo/CL_0002565) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl/cl-base#cellxgene_subset) + + +### jejunal goblet cell `http://purl.obolibrary.org/obo/CL_1000325` +#### Removed +- [jejunal goblet cell](http://purl.obolibrary.org/obo/CL_1000325) EquivalentTo [goblet cell](http://purl.obolibrary.org/obo/CL_0000160) and ([BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0002115](http://purl.obolibrary.org/obo/UBERON_0002115)) + +#### Added +- [jejunal goblet cell](http://purl.obolibrary.org/obo/CL_1000325) EquivalentTo [goblet cell](http://purl.obolibrary.org/obo/CL_0000160) and ([BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0000400](http://purl.obolibrary.org/obo/UBERON_0000400)) + +- [jejunal goblet cell](http://purl.obolibrary.org/obo/CL_1000325) SubClassOf [BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0000400](http://purl.obolibrary.org/obo/UBERON_0000400) + + +### keratinized cell of the oral mucosa `http://purl.obolibrary.org/obo/CL_0002170` +#### Removed +- [keratinized cell of the oral mucosa](http://purl.obolibrary.org/obo/CL_0002170) SubClassOf [epithelial cell of alimentary canal](http://purl.obolibrary.org/obo/CL_0002251) + + + +### keratinized epithelial cell of the anal canal `http://purl.obolibrary.org/obo/CL_0002637` +#### Removed +- [keratinized epithelial cell of the anal canal](http://purl.obolibrary.org/obo/CL_0002637) SubClassOf [stratified squamous epithelial cell of anal canal](http://purl.obolibrary.org/obo/CL_0009066) + + + +### kidney afferent arteriole cell `http://purl.obolibrary.org/obo/CL_1001006` + +#### Added +- [kidney afferent arteriole cell](http://purl.obolibrary.org/obo/CL_1001006) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://cellxgene.cziscience.com/cellguide/CL_1001006"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [kidney afferent arteriole cell](http://purl.obolibrary.org/obo/CL_1001006) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Kidney afferent arteriole cells are specialized cell types found in the renal vasculature, specifically in the afferent arterioles which help in maintaining the renal blood flow and glomerular filtration rate. They are essential for the proper functioning of the kidneys, contributing to the regulation of blood pressure and fluid balance within the organism. Located before the glomerulus, a tiny, intricate network of capillaries within the nephron, these cells help control the expansion or contraction of the arteriole, thus regulating the pressure and flow of blood into the glomerulus. +Functionally, kidney afferent arteriole cells are largely involved in responding to changes in blood volume and systemic blood pressure. They achieve this by modulating the diameter of the afferent arteriole through a process known as autoregulation. Autoregulation involves two primary mechanisms: the myogenic response and the tubuloglomerular feedback. The myogenic response is essentially the intrinsic ability of the vascular smooth muscle to respond to pressure changes, while the tubuloglomerular feedback is the process where the macula densa cells located near the glomerulus respond to changes in fluid delivery rates in the tubules, sending signals to afferent arterioles to constrict or dilate accordingly. These cells also have significant interaction with renin-containing juxtaglomerular cells, which are located in the wall of afferent arterioles. Juxtaglomerular cells secrete the enzyme renin in response to low blood pressure or sympathetic nerve activity, initiating the renin-angiotensin-aldosterone system cascade that ultimately helps retain sodium and water to increase blood volume and pressure."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1152/ajpregu.00332.2006"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.2174/15701611113116660149"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1152/physrev.00042.2012"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1007/s00424-012-1126-7"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### kidney afferent arteriole endothelial cell `http://purl.obolibrary.org/obo/CL_1001096` +#### Removed +- [kidney afferent arteriole endothelial cell](http://purl.obolibrary.org/obo/CL_1001096) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +Kidney afferent arteriole endothelial cells are a specialized type of cell located within the kidneys, forming the inner lining of the afferent arterioles, which are responsible for delivering blood to the glomeruli - capillary networks responsible for filtration - from where the process of urine formation begins in the nephrons. +The endothelial cells in the kidney afferent arterioles have a key function in regulating the blood flow and filtration. They have autocrine and paracrine signaling capabilities, meaning they can signal to themselves and other nearby cells. They produce nitric oxide, prostacyclin, and endothelin, which are powerful vasodilators and vasoconstrictors that regulate renal blood flow. These cells also engage in the mitigation of kidney injury and inflammation by promoting repair and regeneration, demonstrating the multifaceted roles these cells play in maintaining renal health."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1046/j.0001-6772.2003.01205.x"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1093/ndt/gfl308"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [kidney afferent arteriole endothelial cell](http://purl.obolibrary.org/obo/CL_1001096) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Kidney afferent arteriole endothelial cells are a specialized type of cell located within the kidneys, forming the inner lining of the afferent arterioles, which are responsible for delivering blood to the glomeruli - capillary networks responsible for filtration - from where the process of urine formation begins in the nephrons. +The endothelial cells in the kidney afferent arterioles have a key function in regulating the blood flow and filtration. They have autocrine and paracrine signaling capabilities, meaning they can signal to themselves and other nearby cells. They produce nitric oxide, prostacyclin, and endothelin, which are powerful vasodilators and vasoconstrictors that regulate renal blood flow. These cells also engage in the mitigation of kidney injury and inflammation by promoting repair and regeneration, demonstrating the multifaceted roles these cells play in maintaining renal health."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1046/j.0001-6772.2003.01205.x"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1093/ndt/gfl308"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### kidney collecting duct epithelial cell `http://purl.obolibrary.org/obo/CL_1000454` +#### Removed +- [kidney collecting duct epithelial cell](http://purl.obolibrary.org/obo/CL_1000454) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +Kidney collecting duct epithelial cells are a specialized type of cells that form an integral part of the renal system. Located in the collecting duct system of the kidneys, these cells are responsible for one of the final steps in the process of urine formation, and they are instrumental in the fine tuning of the volume and composition of urine by reabsorbing water and certain solutes back into the bloodstream. +These cells express specific channels and carriers that actively and passively transport ions and water. They also have channels on their membranes, such as sodium channels and potassium channels, involved in reabsorbing or secreting these electrolytes depending upon the body's needs. The function of renal collecting duct epithelial cells can be regulated by a variety of hormones, including vasopressin (antidiuretic hormone), which can modulate the ion channels and carriers and hence indirectly influence body fluid homeostasis. +Aside from their function in ion and water balance, kidney collecting duct epithelial cells also aid in maintaining the body's acid-base balance. They have specialized functionality to secret hydrogen ions into the tubular lumen, which contributes to acid excretion. Any dysfunction may have serious implications and lead to various renal or systemic diseases, exemplifying the importance of these cells in maintaining overall body homeostasis."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.2215/CJN.05760513"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1016/j.semnephrol.2019.04.005"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1016/j.ajpath.2014.01.014"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.2215/CJN.08880914"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [kidney collecting duct epithelial cell](http://purl.obolibrary.org/obo/CL_1000454) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Kidney collecting duct epithelial cells are a specialized type of cells that form an integral part of the renal system. Located in the collecting duct system of the kidneys, these cells are responsible for one of the final steps in the process of urine formation, and they are instrumental in the fine tuning of the volume and composition of urine by reabsorbing water and certain solutes back into the bloodstream. +These cells express specific channels and carriers that actively and passively transport ions and water. They also have channels on their membranes, such as sodium channels and potassium channels, involved in reabsorbing or secreting these electrolytes depending upon the body's needs. The function of renal collecting duct epithelial cells can be regulated by a variety of hormones, including vasopressin (antidiuretic hormone), which can modulate the ion channels and carriers and hence indirectly influence body fluid homeostasis. +Aside from their function in ion and water balance, kidney collecting duct epithelial cells also aid in maintaining the body's acid-base balance. They have specialized functionality to secret hydrogen ions into the tubular lumen, which contributes to acid excretion. Any dysfunction may have serious implications and lead to various renal or systemic diseases, exemplifying the importance of these cells in maintaining overall body homeostasis."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.2215/CJN.05760513"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1016/j.semnephrol.2019.04.005"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1016/j.ajpath.2014.01.014"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.2215/CJN.08880914"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### kidney collecting duct intercalated cell `http://purl.obolibrary.org/obo/CL_1001432` + +#### Added +- [kidney collecting duct intercalated cell](http://purl.obolibrary.org/obo/CL_1001432) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://cellxgene.cziscience.com/cellguide/CL_1001432"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [kidney collecting duct intercalated cell](http://purl.obolibrary.org/obo/CL_1001432) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +The kidney collecting duct intercalated cell, otherwise referred to simply as the intercalated cell, is a specialized epithelial cell type primarily found in the kidney's collecting duct system. It is among the main cells that line this final component of the nephron, crucial in the physiological system that maintains acid-base homeostasis. This unique cell type comes in mainly three subtypes as per the localization of their proton pumps: type A, type B, and non-A, non-B cells. Each subtype plays different roles in regulating acid-base balance and electrolyte homeostasis in the body under varying physiological conditions. +Type A intercalated cells reabsorb bicarbonate and secrete protons into urine, leading to the production of acidic urine. These cells are typically prevalent on the renal cortex and function particularly in states of metabolic acidosis or potassium depletion. On the other hand, type B intercalated cells secrete bicarbonate and reabsorb protons; thus, they are crucial in alkaline urine production and potassium conservation. These cells are essential to counter metabolic alkalosis or situations of potassium surplus. The non-A, non-B cells have the characteristic features of both type A and B cells, but play a prominent role under conditions of chronically elevated aldosterone and angiotensin II levels. +Through their differentiated roles, intercalated cells also facilitate the reabsorption of sodium and chloride ions, and water to maintain osmolarity. These cells' activity is finely regulated by hormonal signals like aldosterone, angiotensin II, vasopressin, and the parathyroid hormone. Intercalated cell activity can undergo a significant transformation under pathological conditions, and their dysregulation is associated with diseases such as distal renal tubular acidosis, hypertension, and chronic kidney disease."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1152/physrev.00011.2019"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.3390/diseases2020071"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1007/978-3-211-99390-3_106"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1152/physiol.00008.2011"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.2215/CJN.08880914"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### kidney collecting duct principal cell `http://purl.obolibrary.org/obo/CL_1001431` +#### Removed +- [kidney collecting duct principal cell](http://purl.obolibrary.org/obo/CL_1001431) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +The kidney collecting duct principal cell is a highly specialized type of cell found in the late distal convoluted tubule and collecting duct of the kidney's nephron. Principal cells are located at the final segments of the renal tubules, where they play a pivotal role in key homeostatic processes. +One of their fundamental functions of kidney collecting duct principal cells is the regulation of water reabsorption, which is mediated by aquaporins (water channel proteins). Antidiuretic hormones, such as vasopressin, can stimulate the redistribution of these water channels from an intracellular pools to the apical plasma membrane of the principal cell; translocation of aquaporin (specifically, AQP2) is associated with an increase of osmotic water permeability. The water reabsorption affects the concentration of the final urine; these cells are therefore directly involved in the maintenance of the body's fluid balance. +Kidney collecting duct principal cells also participate in sodium and potassium ions regulation. They reabsorb sodium ions from the tubular fluid back into the bloodstream, a process facilitated by the action of aldosterone, a hormone released by the adrenal glands. Similarly, the principal cells secrete potassium ions into the tubular fluid in response to aldosterone, contributing to the regulation of potassium levels in the body. Impaired function of cells can lead to various renal diseases and disorders, highlighting the vital role of kidney collecting duct principal cells in the body's homeostatic processes."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1007/s11906-015-0538-0"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1073/pnas.1710964114"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1016/B978-0-12-386456-7.05402-2"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1016/j.biocel.2022.106261"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [kidney collecting duct principal cell](http://purl.obolibrary.org/obo/CL_1001431) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +The kidney collecting duct principal cell is a highly specialized type of cell found in the late distal convoluted tubule and collecting duct of the kidney's nephron. Principal cells are located at the final segments of the renal tubules, where they play a pivotal role in key homeostatic processes. +One of their fundamental functions of kidney collecting duct principal cells is the regulation of water reabsorption, which is mediated by aquaporins (water channel proteins). Antidiuretic hormones, such as vasopressin, can stimulate the redistribution of these water channels from an intracellular pools to the apical plasma membrane of the principal cell; translocation of aquaporin (specifically, AQP2) is associated with an increase of osmotic water permeability. The water reabsorption affects the concentration of the final urine; these cells are therefore directly involved in the maintenance of the body's fluid balance. +Kidney collecting duct principal cells also participate in sodium and potassium ions regulation. They reabsorb sodium ions from the tubular fluid back into the bloodstream, a process facilitated by the action of aldosterone, a hormone released by the adrenal glands. Similarly, the principal cells secrete potassium ions into the tubular fluid in response to aldosterone, contributing to the regulation of potassium levels in the body. Impaired function of cells can lead to various renal diseases and disorders, highlighting the vital role of kidney collecting duct principal cells in the body's homeostatic processes."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1007/s11906-015-0538-0"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1073/pnas.1710964114"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1016/B978-0-12-386456-7.05402-2"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1016/j.biocel.2022.106261"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### kidney connecting tubule epithelial cell `http://purl.obolibrary.org/obo/CL_1000768` + +#### Added +- [kidney connecting tubule epithelial cell](http://purl.obolibrary.org/obo/CL_1000768) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://cellxgene.cziscience.com/cellguide/CL_1000768"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [kidney connecting tubule epithelial cell](http://purl.obolibrary.org/obo/CL_1000768) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Kidney connecting tubule epithelial cells are found in collecting duct system of the kidney, specifically in at the interconnection segment between the nephron and the collecting ducts. The epithelial cells lining the connecting tubule are crucial for the journey of filtrate before it empties into urine-collecting ducts and therefore play a critical role in maintaining the body’s fluid and electrolyte balance. +One of the principal functions of connecting tubule epithelial cells involves the selective reabsorption and secretion of various solutes. This reabsorption process includes critical regulatory electrolytes such as sodium ions (Na+), chloride ions (Cl-), and bicarbonate ions (HCO3-), thus playing a role in the regulation of the acid-base homeostasis. Their function also involves the secretion of potassium ions (K+) into the renal tubular fluid. +The connecting tubule epithelial cells are primarily intercalated cells, which can be categorized into two types according to their specific functions: type A intercalated cells, which secrete acid, and the type B intercalated cells, which secrete base (bicarbonate) and reabsorb chloride. By regulating the concentrations of these ions, as well as reabsorption of water, connecting tubule epithelial cells contribute substantively to maintaining the body's electrolyte levels, pH balance, and overall homeostasis. +In addition to intercalating cells, the collecting duct system also has principal cells, which are characterized by the expression of the water channel AQP2. AQP2-expressing cells have also been identified in connecting tubules, but there is some controversy whether these represent a unique cell type as there are some morphologic differences compared with principal cells."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1681/ASN.2019040415"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1002/cphy.c110052"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.23876/j.krcp.2017.36.4.305"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1097/MNH.0b013e32820ac850"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1007/s00418-021-02033-5"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### kidney distal convoluted tubule epithelial cell `http://purl.obolibrary.org/obo/CL_1000849` + +#### Added +- [kidney distal convoluted tubule epithelial cell](http://purl.obolibrary.org/obo/CL_1000849) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://cellxgene.cziscience.com/cellguide/CL_1000849"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [kidney distal convoluted tubule epithelial cell](http://purl.obolibrary.org/obo/CL_1000849) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Kidney distal convoluted tubule epithelial cells, often referred to simply as distal convoluted tubule (DCT) cells, constitute a significant portion of the nephron -- the functional building unit of the kidney involved in filtration and reabsorption of substances from blood. The DCT epithelial cells form lining of the distal convoluted tubule, a segment of the nephron located after the loop of Henle and before the collecting tubule. These cells are characterized by unique morphological features such as small size, low height and fewer microvilli compared to proximal convoluted tubule epithelial cells. +These cells perform a host of vital functions contributing to the regulation of extracellular fluid volume and electrolyte balance, blood pressure and pH. While the DCT is less prominent in water and sodium reabsorption compared to the proximal tubule and the loop of Henle, it plays a crucial role in fine-tuning the process. DCT epithelial cells are responsible for the final adjustments of sodium, potassium and calcium reabsorption, thereby affecting overall fluid and electrolyte balance, blood pressure regulation and bone health. The reabsorption process is regulated by hormones including aldosterone and parathyroid hormone. +The distal convoluted tubule (DCT) also plays a significant role in acid-base homeostasis by secreting protons (H+) into the tubular fluid and reabsorbing bicarbonate ions (HCO3-), thus regulating the pH of the blood. The ability of DCT cells to adjust urine concentration plays a part in maintaining the body’s pH balance and preventing conditions like acidosis or alkalosis. In summary, kidney distal convoluted tubule epithelial cells perform functions that are crucial to maintaining body's homeostasis."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1681/ASN.2019040415"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1007/s40620-021-01032-y"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1152/physrev.2000.80.1.277"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1002/cphy.c140002"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.2215/CJN.05920613"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### kidney efferent arteriole cell `http://purl.obolibrary.org/obo/CL_1001009` + +#### Added +- [kidney efferent arteriole cell](http://purl.obolibrary.org/obo/CL_1001009) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Kidney efferent arteriole cells are highly adaptable vascular cells that make up the efferent arterioles in the kidney. These units are integral components of the renal microcirculation system, conducting blood away from the glomeruli after filtration occurs. Efferent arterioles directly affect glomerular hydrostatic pressure and, subsequently, the rate of glomerular filtration. They are the downstream channels that ensure the effective transportation of blood to the peritubular capillaries and vasa recta, critical for maintaining fluid balance and electrolyte homeostasis. +Kidney efferent arteriole cells are exceptional in their ability to perform autoregulation—a critical dynamic control of intrarenal blood flow ensuring stable glomerular filtration rates. This is primarily achieved via myogenic and tubuloglomerular feedback mechanisms, where the cells respond to changes in pressure and the concentration of sodium chloride in the tubular fluid, and constrict or dilate depending on the detected changes. +Cells associated with the efferent arteriole also respond to several systemic influences. Through complex intracellular signaling pathways, they respond to fluctuations in hormones (like angiotensin II and endothelin) and several other mediators such as nitric oxide and prostaglandins. Their adaptive capability helps maintain homeostasis and ensures the entire system's optimal performance under various physiological conditions. Dysfunctions in kidney efferent arteriole cells can lead to severe pathologies like hypertension and chronic kidney disease."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1152/ajpregu.2000.279.2.R629"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1161/01.HYP.29.1.222"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1159/000072054"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.3748/wjg.v12.i34.5429"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1152/physrev.00042.2012"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [kidney efferent arteriole cell](http://purl.obolibrary.org/obo/CL_1001009) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://cellxgene.cziscience.com/cellguide/CL_1001009"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### kidney efferent arteriole endothelial cell `http://purl.obolibrary.org/obo/CL_1001099` +#### Removed +- [kidney efferent arteriole endothelial cell](http://purl.obolibrary.org/obo/CL_1001099) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +Kidney efferent arteriole endothelial cells constitute a vital component of the kidney's microvascular system. They are unique endothelial cells found lining the walls of efferent arterioles, which transport blood away from the glomeruli in the kidney. +The primary responsibilities of the kidney efferent arteriole endothelial cells involve controling renal blood flow, regulating glomerular filtration rate (GFR), and managing perfusion pressure. They do this by contracting and relaxing, effectively narrowing and widening the arteriole's lumen thereby controling the volume and rate of blood flow to the peritubular capillaries and creating the pressure gradient necessary for filtration in the glomerulus. +Furthermore, kidney efferent arteriole endothelial cells show a high degree of plasticity in response to pathophysiological stimuli and can undergo structural and functional changes based on local needs. In conditions like hypertension and diabetes, these cells can experience hypertrophy and endothelial dysfunction, contributing to the progression of renal disease."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1016/j.semcdb.2014.08.002"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1038/s41581-021-00411-9"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1681/ASN.2019111179"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1016/j.semnephrol.2015.01.010"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [kidney efferent arteriole endothelial cell](http://purl.obolibrary.org/obo/CL_1001099) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Kidney efferent arteriole endothelial cells constitute a vital component of the kidney's microvascular system. They are unique endothelial cells found lining the walls of efferent arterioles, which transport blood away from the glomeruli in the kidney. +The primary responsibilities of the kidney efferent arteriole endothelial cells involve controling renal blood flow, regulating glomerular filtration rate (GFR), and managing perfusion pressure. They do this by contracting and relaxing, effectively narrowing and widening the arteriole's lumen thereby controling the volume and rate of blood flow to the peritubular capillaries and creating the pressure gradient necessary for filtration in the glomerulus. +Furthermore, kidney efferent arteriole endothelial cells show a high degree of plasticity in response to pathophysiological stimuli and can undergo structural and functional changes based on local needs. In conditions like hypertension and diabetes, these cells can experience hypertrophy and endothelial dysfunction, contributing to the progression of renal disease."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1016/j.semcdb.2014.08.002"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1038/s41581-021-00411-9"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1681/ASN.2019111179"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1016/j.semnephrol.2015.01.010"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### kidney interstitial alternatively activated macrophage `http://purl.obolibrary.org/obo/CL_1000695` + +#### Added +- [kidney interstitial alternatively activated macrophage](http://purl.obolibrary.org/obo/CL_1000695) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl/cl-base#cellxgene_subset) + + +### kidney loop of Henle descending limb epithelial cell `http://purl.obolibrary.org/obo/CL_1001021` + +#### Added +- [kidney loop of Henle descending limb epithelial cell](http://purl.obolibrary.org/obo/CL_1001021) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://cellxgene.cziscience.com/cellguide/CL_1001021"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [kidney loop of Henle descending limb epithelial cell](http://purl.obolibrary.org/obo/CL_1001021) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +The kidney loop of Henle descending limb epithelial cells are highly specialized cells that play a crucial role in maintaining the body's salt and water balance. These cells line the descending limb of the loop of Henle, which is a portion of the renal tubule located in the kidneys, an organ responsible for filtering waste products, ions and extra water from the blood and converting them into urine. However, the descending limb epithelial cells are specifically involved in the countercurrent multiplication system, a mechanism to concentrate urine that involves both active and passive transport processes. +These cells are notably permeable to water but relatively impermeable to solutes, a characteristic that dramatically influences the osmotic gradient in the renal medulla. As filtrate initially descends down the loop of Henle, water gets drawn out due to the increasing osmotic gradient, thereby concentrating the filtrate. Additionally, these epithelial cells are exceptionally thin walled, allowing water to freely diffuse across the membrane. +Furthermore, the kidney loop of Henle descending limb epithelial cells are inextricably linked to the functioning of numerous diuretic drugs, which work by blocking the reabsorption of water and certain electrolytes in the kidneys, leading to increased urine production to rid the body of excess fluids."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1007/s00360-018-1164-3"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1152/advan.00227.2022"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1146/annurev-physiol-021113-170350"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### kidney proximal convoluted tubule epithelial cell `http://purl.obolibrary.org/obo/CL_1000838` + +#### Added +- [kidney proximal convoluted tubule epithelial cell](http://purl.obolibrary.org/obo/CL_1000838) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://cellxgene.cziscience.com/cellguide/CL_1000838"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [kidney proximal convoluted tubule epithelial cell](http://purl.obolibrary.org/obo/CL_1000838) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Kidney proximal convoluted tubule epithelial cells line the most voluminous part of the kidney's nephron, the proximal convoluted tubule, located in the cortex of the kidney. These cells are primarily involved in reabsorption and secretion processes, key functions that facilitate homeostasis within the body. +Proximal convoluted tubule epithelial cells extensively function in the reabsorption process to a greater degree than their counterparts in the proximal straight tubule. Approximately two-thirds of filtrated sodium and water, nearly all nutrient sugars and amino acids, and a significant portion of bicarbonates pass through the proximal convoluted tubule, are effectively absorbed by the epithelial cells, and reenter the bodily circulation. By absorbing bicarbonates and secreting protons into the tubular fluid, proximal convoluted tubule epithelial cells also contribute to the pH regulation in the body . +In addition to reabsorption, proximal convoluted tubule epithelial cells also play a critical role in the excretion of waste metabolites and xenobiotics. These cells possess a range of transporters that secrete metabolic end products and certain drugs, hence aiding in their elimination. This function underlines their importance for body detoxification."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1002/cphy.c110060"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1681/ASN.2019040415"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1146/annurev-physiol-052521-121841"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1159/000092212"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### kidney proximal straight tubule epithelial cell `http://purl.obolibrary.org/obo/CL_1000839` + +#### Added +- [kidney proximal straight tubule epithelial cell](http://purl.obolibrary.org/obo/CL_1000839) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Kidney proximal straight tubule epithelial cells line the straight portion of the proximal tubule of the nephron, extending from the cortical medullary ray into the outer stripe of the outer medulla. They are characterized by a brush border of dense microvilli on their apical surface, enhancing the cell's surface area and aiding reabsorption, though reabsorption occurs more heavily in the proximal convoluted tubule preceding the straight portion of the tubule. +The primary function of the kidney proximal straight tubule epithelial cells is to reabsorb the filtrate that the kidney produces, which includes glucose, sodium, and water. The reabsorption occurs through both passive and active transport methods. These cells exhibit enzyme-rich microvilli that also absorb small proteins and peptides. Consequently, they are involved in the regulation of plasma levels of various substances, including glucose, amino acids, and electrolytes, and maintain the body's pH homeostasis by secreting H+ ions into the urine and absorbing bicarbonate ions. +These cells are also reported to be involved in drug metabolism. Many drugs are filtered from the blood by the kidneys and subsequently reabsorbed by the kidney proximal tubule epithelial cells back into the bloodstream. Furthermore, these cells play a significant role in the progression of kidney diseases. For example, in diabetic nephropathy and acute kidney injury, kidney proximal straight tubule epithelial cells can undergo cellular changes and result in malfunctions such as reduced reabsorption and increased excretion."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1681/ASN.2019040415"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.2215/CJN.10391012"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1146/annurev-physiol-052521-121841"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1002/cphy.c110061"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1038/nrd4461"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [kidney proximal straight tubule epithelial cell](http://purl.obolibrary.org/obo/CL_1000839) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://cellxgene.cziscience.com/cellguide/CL_1000839"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### kidney resident macrophage `http://purl.obolibrary.org/obo/CL_1000698` + +#### Added +- [kidney resident macrophage](http://purl.obolibrary.org/obo/CL_1000698) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Kidney resident macrophages are a heterogeneous population of immune cell found in the cortex and medullary regions of the kidney as well as within and surround the glomeruli. Their primary role involves maintaining homeostasis and immune surveillance in the kidney microenvironment, defending against ascending urinary infections. Beyond traditional macrophage roles such as phagocytosis and antigen presentation, kidney resident macrophages also contribute significantly to the response to kidney injury including tissue repair and angiogenesis. +Under normal physiological conditions, kidney resident macrophages work to maintain the balance of the kidney's microenvironment by removing dead cells, pathogens and cellular debris, to limit inflammation and tissue damage. They are ‘professional’ phagocytes, clearing pathogens and debris by engulfing and digesting these harmful materials. Moreover, they are capable of presenting antigens to other immune cells, which aids in the activation of the adaptive immune response. +Kidney resident macrophages show a high degree of plasticity: in response to environmental stimuli they change their morphology and cell surface markers. For example, in response to acute injury, some macrophages adopt a pro-inflammatory phenotype and augment tissue damage; once the injury stimulus is removed, they may change to mediate tissue repair. +While kidney macrophages contribute to wound healing, tissue repair and regeneration by producing key growth factors and cytokines that stimulate cell proliferation, collagen production, and blood vessel formation, dysregulation in their activity can also lead to progressive inflammation and fibrosis, common features in chronic kidney disease."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.3389/fimmu.2021.681748"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1016/bs.ircmb.2022.01.005"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1172/jci.insight.161078"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.3389/fphys.2017.00837"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [kidney resident macrophage](http://purl.obolibrary.org/obo/CL_1000698) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://cellxgene.cziscience.com/cellguide/CL_1000698"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### kisspeptin neuron `http://purl.obolibrary.org/obo/CL_4023130` +#### Removed +- [kisspeptin neuron](http://purl.obolibrary.org/obo/CL_4023130) SubClassOf [neuron](http://purl.obolibrary.org/obo/CL_0000540) + +#### Added +- [kisspeptin neuron](http://purl.obolibrary.org/obo/CL_4023130) SubClassOf [central nervous system neuron](http://purl.obolibrary.org/obo/CL_2000029) + + +### koniocellular cell `http://purl.obolibrary.org/obo/CL_4023187` +#### Removed +- [koniocellular cell](http://purl.obolibrary.org/obo/CL_4023187) SubClassOf [central nervous system neuron](http://purl.obolibrary.org/obo/CL_2000029) + +#### Added +- [koniocellular cell](http://purl.obolibrary.org/obo/CL_4023187) SubClassOf [neuron of the forebrain](http://purl.obolibrary.org/obo/CL_0012001) + + +### lamp5 GABAergic cortical interneuron `http://purl.obolibrary.org/obo/CL_4023011` + +#### Added +- [lamp5 GABAergic cortical interneuron](http://purl.obolibrary.org/obo/CL_4023011) [RO_0002175](http://purl.obolibrary.org/obo/RO_0002175) [NCBITaxon_9606](http://purl.obolibrary.org/obo/NCBITaxon_9606) + +- [lamp5 GABAergic cortical interneuron](http://purl.obolibrary.org/obo/CL_4023011) [comment](http://www.w3.org/2000/01/rdf-schema#comment) "The marker set LINC00298, KIT can identify the Human cell type lamp5 GABAergic cortical interneuron in the Brain with a confidence of 0.814687838 (NS-Forest FBeta value)."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://doi.org/10.5281/zenodo.11165918"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [lamp5 GABAergic cortical interneuron](http://purl.obolibrary.org/obo/CL_4023011) SubClassOf [RO_0015004](http://purl.obolibrary.org/obo/RO_0015004) some [CLM_1000074](http://purl.obolibrary.org/obo/CLM_1000074) + + +### large intestine crypt goblet cell `http://purl.obolibrary.org/obo/CL_1000321` + +#### Added +- [large intestine crypt goblet cell](http://purl.obolibrary.org/obo/CL_1000321) EquivalentTo [goblet cell](http://purl.obolibrary.org/obo/CL_0000160) and ([BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0022281](http://purl.obolibrary.org/obo/UBERON_0022281)) + +- [large intestine crypt goblet cell](http://purl.obolibrary.org/obo/CL_1000321) SubClassOf [glandular cell of the large intestine](http://purl.obolibrary.org/obo/CL_0002658) + +- [large intestine crypt goblet cell](http://purl.obolibrary.org/obo/CL_1000321) SubClassOf [BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0022281](http://purl.obolibrary.org/obo/UBERON_0022281) + + +### large intestine goblet cell `http://purl.obolibrary.org/obo/CL_1000320` +#### Removed +- [large intestine goblet cell](http://purl.obolibrary.org/obo/CL_1000320) EquivalentTo [goblet cell](http://purl.obolibrary.org/obo/CL_0000160) and ([BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0000059](http://purl.obolibrary.org/obo/UBERON_0000059)) + +- [large intestine goblet cell](http://purl.obolibrary.org/obo/CL_1000320) SubClassOf [BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0001278](http://purl.obolibrary.org/obo/UBERON_0001278) + +#### Added +- [large intestine goblet cell](http://purl.obolibrary.org/obo/CL_1000320) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +The large intestine goblet cell is a highly specialized type of mucosal epithelial cell that is located within the epithelial lining of the large intestine. The key function of goblet cells is the production and secretion of a protective layer of mucus which is essential for maintaining gut homeostasis. Goblet cells have a characteristic 'goblet-like' shape, which adapts them for this specific function: organelles such as the nucleus, mitochondria, ER, and Golgi apparatus are located in the basal portion of the cell; while the vesicles with mucins (required for mucus production) are located apically, close to the apical membrane where their exocytosis takes place. +The goblet cells of the large intestine produce a thick layer of mucus that coats the intestinal lumen. This mucus provides a barrier that prevents the direct contact of intestinal cells with bacteria and other potentially toxic substances present in the digestive tract. It also lubricates the intestine to facilitate the smooth passage of digested food material. It is worth noting that the mucus system differs between the small and large intestine: although in both the mucus is built around MUC2 mucin polymers produced by goblet cells, it is becoming clear that there are several types of goblet cells that function in different ways. +From an immunological perspective, large intestine goblet cells participate in promoting a balanced gut immune response. They contribute to the process known as immune tolerance, where they prevent the body's immune system from overreacting to the trillions of bacteria present in the gut. These cells achieve this by secreting molecules that help maintain a calm environment, limiting inflammatory reactions unless absolutely necessary. Any dysfunction or decrease in the number of goblet cells can result in a compromised intestinal barrier leading to various health issues, including inflammatory bowel disease."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1038/mi.2015.32"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:full/10.1111/febs.15731"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1146/annurev-physiol-021115-105447"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1111/imr.12182"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1042/BSR20201471"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [large intestine goblet cell](http://purl.obolibrary.org/obo/CL_1000320) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://cellxgene.cziscience.com/cellguide/CL_1000320"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [large intestine goblet cell](http://purl.obolibrary.org/obo/CL_1000320) EquivalentTo [goblet cell](http://purl.obolibrary.org/obo/CL_0000160) and ([BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0001278](http://purl.obolibrary.org/obo/UBERON_0001278)) + + +### lateral ganglionic eminence derived neuron `http://purl.obolibrary.org/obo/CL_4023035` +#### Removed +- [lateral ganglionic eminence derived neuron](http://purl.obolibrary.org/obo/CL_4023035) SubClassOf [neuron](http://purl.obolibrary.org/obo/CL_0000540) + +#### Added +- [lateral ganglionic eminence derived neuron](http://purl.obolibrary.org/obo/CL_4023035) SubClassOf [central nervous system neuron](http://purl.obolibrary.org/obo/CL_2000029) + + +### lateral line ganglion neuron `http://purl.obolibrary.org/obo/CL_2000031` +#### Removed +- [lateral line ganglion neuron](http://purl.obolibrary.org/obo/CL_2000031) EquivalentTo [neuron](http://purl.obolibrary.org/obo/CL_0000540) and ([RO_0002100](http://purl.obolibrary.org/obo/RO_0002100) some [UBERON_2000120](http://purl.obolibrary.org/obo/UBERON_2000120)) + +- [lateral line ganglion neuron](http://purl.obolibrary.org/obo/CL_2000031) SubClassOf [neuron](http://purl.obolibrary.org/obo/CL_0000540) + +#### Added +- [lateral line ganglion neuron](http://purl.obolibrary.org/obo/CL_2000031) EquivalentTo [peripheral nervous system neuron](http://purl.obolibrary.org/obo/CL_2000032) and ([RO_0002100](http://purl.obolibrary.org/obo/RO_0002100) some [UBERON_2000120](http://purl.obolibrary.org/obo/UBERON_2000120)) + +- [lateral line ganglion neuron](http://purl.obolibrary.org/obo/CL_2000031) SubClassOf [RO_0002162](http://purl.obolibrary.org/obo/RO_0002162) some [NCBITaxon_32443](http://purl.obolibrary.org/obo/NCBITaxon_32443) + +- [lateral line ganglion neuron](http://purl.obolibrary.org/obo/CL_2000031) SubClassOf [peripheral nervous system neuron](http://purl.obolibrary.org/obo/CL_2000032) + +- [lateral line ganglion neuron](http://purl.obolibrary.org/obo/CL_2000031) SubClassOf [BFO_0000002](http://purl.obolibrary.org/obo/BFO_0000002) + + +### lateral mesodermal cell `http://purl.obolibrary.org/obo/CL_0011010` + +#### Added +- [lateral mesodermal cell](http://purl.obolibrary.org/obo/CL_0011010) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl/cl-base#cellxgene_subset) + + +### lateral ventricle neuron `http://purl.obolibrary.org/obo/CL_1001582` +#### Removed +- [lateral ventricle neuron](http://purl.obolibrary.org/obo/CL_1001582) SubClassOf [central nervous system neuron](http://purl.obolibrary.org/obo/CL_2000029) + +#### Added +- [lateral ventricle neuron](http://purl.obolibrary.org/obo/CL_1001582) SubClassOf [neuron of the forebrain](http://purl.obolibrary.org/obo/CL_0012001) + + +### lens fiber cell `http://purl.obolibrary.org/obo/CL_0011004` + +#### Added +- [lens fiber cell](http://purl.obolibrary.org/obo/CL_0011004) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Lens fiber cells are specialized, elongated cells located in the ocular lens, an important part of the eye responsible for focusing light onto the retina to create clear defined images. These cells are unique among body cells, as they are transparent and filled with a clear protein called crystallin to facilitate the passage of light. +The entire life cycle of a lens fiber cell includes differentiation from lens epithelial cells, which are the progenitor cells lying at the anterior surface of the lens. In response to various signals, these cells elongate and migrate towards the posterior pole, while simultaneously undergoing a process of denucleation and degradation of cellular organelles. This unique process ensures that the cells do not scatter light, which is critical for the transparency of the lens. After reaching full maturity, lens fiber cells form tightly packed layers, known as laminae, to make up the distinctive architecture of the ocular lens. +Lens fiber cells play pivotal roles in vision. Their primary function is to transmit and focus the light that enters the eye onto the retina, providing the sharpness and clarity necessary for vision. The precise alignment and organization of these cells allow for optimal light transmittance and minimizes scattering, thereby maintaining the transparency of the lens. As such, disruptions or abnormalities in lens fiber cells can lead to serious vision impairment, including conditions like cataracts, a common condition characterized by the opacification of the lens."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://www.sciencedirect.com/topics/immunology-and-microbiology/lens-fiber"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1016/j.exer.2016.03.016"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1242/dev.107953"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1098/rstb.2010.0300"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1016/j.pbiomolbio.2003.11.012"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [lens fiber cell](http://purl.obolibrary.org/obo/CL_0011004) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://cellxgene.cziscience.com/cellguide/CL_0011004"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### license `http://purl.org/dc/elements/1.1/license` + +#### Added +- AnnotationProperty: [license](http://purl.org/dc/elements/1.1/license) + + +### license `http://purl.org/dc/terms/license` + +#### Added +- AnnotationProperty: [license](http://purl.org/dc/terms/license) + + +### limbal epithelial stem cell of cornea `http://purl.obolibrary.org/obo/CL_4033093` + +#### Added +- [limbal epithelial stem cell of cornea](http://purl.obolibrary.org/obo/CL_4033093) [has_exact_synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "limbal stem cell"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:17562792"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [limbal epithelial stem cell of cornea](http://purl.obolibrary.org/obo/CL_4033093) [has_exact_synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "limbal epithelial stem cell"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:20614614"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [limbal epithelial stem cell of cornea](http://purl.obolibrary.org/obo/CL_4033093) [label](http://www.w3.org/2000/01/rdf-schema#label) "limbal epithelial stem cell of cornea"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [limbal epithelial stem cell of cornea](http://purl.obolibrary.org/obo/CL_4033093) [id](http://www.geneontology.org/formats/oboInOwl#id) "CL:4033093"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [limbal epithelial stem cell of cornea](http://purl.obolibrary.org/obo/CL_4033093) [contributor](http://purl.org/dc/terms/contributor) [0000-0001-7655-4833](https://orcid.org/0000-0001-7655-4833) + +- [limbal epithelial stem cell of cornea](http://purl.obolibrary.org/obo/CL_4033093) [date](http://purl.org/dc/terms/date) "2024-12-11T13:59:19Z"^^[dateTime](http://www.w3.org/2001/XMLSchema#dateTime) + +- [limbal epithelial stem cell of cornea](http://purl.obolibrary.org/obo/CL_4033093) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "LESC"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003000](http://purl.obolibrary.org/obo/OMO_0003000) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:20614614"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [limbal epithelial stem cell of cornea](http://purl.obolibrary.org/obo/CL_4033093) [contributor](http://purl.org/dc/terms/contributor) [0000-0001-6677-8489](https://orcid.org/0000-0001-6677-8489) + +- [limbal epithelial stem cell of cornea](http://purl.obolibrary.org/obo/CL_4033093) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A stem cell that is part of the corneo-scleral limbus. This cell type resides at the basal layer of the epithelium and has a small size and high nuclear to cytoplasmatic ratio (Secker and Daniels, 2009). A limbal stem cell is responsible for corneal epithelial renewal and repair (Li et al., 2023), and to help maintain a clear corneal surface by preventing conjunctival epithelial cells from migrating onto the cornea (Wang et al., 2023)."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:36983561"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:29105366"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:37768272"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:20614614"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [limbal epithelial stem cell of cornea](http://purl.obolibrary.org/obo/CL_4033093) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "LSC"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003000](http://purl.obolibrary.org/obo/OMO_0003000) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:36983561"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- Class: [limbal epithelial stem cell of cornea](http://purl.obolibrary.org/obo/CL_4033093) + +- [limbal epithelial stem cell of cornea](http://purl.obolibrary.org/obo/CL_4033093) EquivalentTo [stem cell](http://purl.obolibrary.org/obo/CL_0000034) and ([BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0006761](http://purl.obolibrary.org/obo/UBERON_0006761)) + +- [limbal epithelial stem cell of cornea](http://purl.obolibrary.org/obo/CL_4033093) SubClassOf [BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0000482](http://purl.obolibrary.org/obo/UBERON_0000482) + +- [limbal epithelial stem cell of cornea](http://purl.obolibrary.org/obo/CL_4033093) SubClassOf [BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0006761](http://purl.obolibrary.org/obo/UBERON_0006761) + +- [limbal epithelial stem cell of cornea](http://purl.obolibrary.org/obo/CL_4033093) SubClassOf [RO_0002203](http://purl.obolibrary.org/obo/RO_0002203) some [corneal epithelial cell](http://purl.obolibrary.org/obo/CL_0000575) + +- [limbal epithelial stem cell of cornea](http://purl.obolibrary.org/obo/CL_4033093) SubClassOf [epithelial fate stem cell](http://purl.obolibrary.org/obo/CL_0000036) + + +### lipid-associated macrophage `http://purl.obolibrary.org/obo/CL_4033086` + +#### Added +- [lipid-associated macrophage](http://purl.obolibrary.org/obo/CL_4033086) [contributor](http://purl.org/dc/terms/contributor) [0000-0001-8134-3037](https://orcid.org/0000-0001-8134-3037) + +- [lipid-associated macrophage](http://purl.obolibrary.org/obo/CL_4033086) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "LAM"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003000](http://purl.obolibrary.org/obo/OMO_0003000) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:31257031"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [lipid-associated macrophage](http://purl.obolibrary.org/obo/CL_4033086) [id](http://www.geneontology.org/formats/oboInOwl#id) "CL:4033086"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [lipid-associated macrophage](http://purl.obolibrary.org/obo/CL_4033086) [contributor](http://purl.org/dc/terms/contributor) [0000-0001-6677-8489](https://orcid.org/0000-0001-6677-8489) + +- [lipid-associated macrophage](http://purl.obolibrary.org/obo/CL_4033086) [label](http://www.w3.org/2000/01/rdf-schema#label) "lipid-associated macrophage"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [lipid-associated macrophage](http://purl.obolibrary.org/obo/CL_4033086) [comment](http://www.w3.org/2000/01/rdf-schema#comment) "Distinct from “adipose macrophage” in Trem2 expression, and is not limited to adipose tissue. Guilliams et al. describe these cells as being distinct from Kupffer cells."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:35021063"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:37153549"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [lipid-associated macrophage](http://purl.obolibrary.org/obo/CL_4033086) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A tissue-resident macrophage that is associated with lipids. This cell responsible of anti-inflammatory functions, lipid accumulation and enhancing phagocytosis (Wculek et al., 2022, Liu et al., 2022). In mice and humans, a lipid-associated macrophage is characterized by the marker Trem2 (Jaitlin et al., 2019)."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:34876704"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:31257031"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:35712121"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [lipid-associated macrophage](http://purl.obolibrary.org/obo/CL_4033086) [date](http://purl.org/dc/terms/date) "2024-10-17T10:20:13Z"^^[dateTime](http://www.w3.org/2001/XMLSchema#dateTime) + +- Class: [lipid-associated macrophage](http://purl.obolibrary.org/obo/CL_4033086) + +- [lipid-associated macrophage](http://purl.obolibrary.org/obo/CL_4033086) SubClassOf [RO_0002292](http://purl.obolibrary.org/obo/RO_0002292) some [PR_000016626](http://purl.obolibrary.org/obo/PR_000016626) + +- [lipid-associated macrophage](http://purl.obolibrary.org/obo/CL_4033086) SubClassOf [macrophage](http://purl.obolibrary.org/obo/CL_0000235) + + +### liver-resident natural killer cell `http://purl.obolibrary.org/obo/CL_4047101` + +#### Added +- [liver-resident natural killer cell](http://purl.obolibrary.org/obo/CL_4047101) [label](http://www.w3.org/2000/01/rdf-schema#label) "liver-resident natural killer cell"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [liver-resident natural killer cell](http://purl.obolibrary.org/obo/CL_4047101) [has_exact_synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "liver NK cell"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:26639736"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [liver-resident natural killer cell](http://purl.obolibrary.org/obo/CL_4047101) [has_exact_synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "hepatic NK"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "doi:10.3389/fimmu.2019.00946"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [liver-resident natural killer cell](http://purl.obolibrary.org/obo/CL_4047101) [has_exact_synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "liver-specific natural killer cell"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [liver-resident natural killer cell](http://purl.obolibrary.org/obo/CL_4047101) [has_exact_synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "intrahepatic NK"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:33828559"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [liver-resident natural killer cell](http://purl.obolibrary.org/obo/CL_4047101) [contributor](http://purl.org/dc/terms/contributor) [0009-0005-7919-4905](https://orcid.org/0009-0005-7919-4905) + +- [liver-resident natural killer cell](http://purl.obolibrary.org/obo/CL_4047101) [has_exact_synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "hepatic natural killer cells"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "doi:10.3389/fimmu.2019.00946"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [liver-resident natural killer cell](http://purl.obolibrary.org/obo/CL_4047101) [contributor](http://purl.org/dc/terms/contributor) "https://orcid.org/0000-0001-8134-3037"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [liver-resident natural killer cell](http://purl.obolibrary.org/obo/CL_4047101) [has_exact_synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "lr-NK"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:35726345"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [liver-resident natural killer cell](http://purl.obolibrary.org/obo/CL_4047101) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A natural killer cell resident to the liver, located in the hepatic sinusoids. In humans this cell type is distinguished from circulating natural killer cells by CD49a or CD69 gene expression. Liver-resident natural killer cells have also been shown to express CCR5, EOMES, KLRB1, GZMK, and CXCR6 in humans."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:26639736"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:35865550"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:32351704"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:34230995"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:27798170"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:31114585"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:26330348"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [liver-resident natural killer cell](http://purl.obolibrary.org/obo/CL_4047101) [comment](http://www.w3.org/2000/01/rdf-schema#comment) "Liver-resident natural killer cells play a crucial role in modulating the immune response during inflammation by balancing cytotoxic activity and cytokine production, thereby contributing to the maintenance of liver homeostasis and protection against excessive tissue damage."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:34230995"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [liver-resident natural killer cell](http://purl.obolibrary.org/obo/CL_4047101) [id](http://www.geneontology.org/formats/oboInOwl#id) "CL:4047101"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [liver-resident natural killer cell](http://purl.obolibrary.org/obo/CL_4047101) [has_exact_synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "liver resident natural killer cell"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:26330348"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [liver-resident natural killer cell](http://purl.obolibrary.org/obo/CL_4047101) [date](http://purl.org/dc/terms/date) "2024-07-29T13:43:11Z"^^[dateTime](http://www.w3.org/2001/XMLSchema#dateTime) + +- [liver-resident natural killer cell](http://purl.obolibrary.org/obo/CL_4047101) [has_exact_synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "he-NK"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:31114585"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- Class: [liver-resident natural killer cell](http://purl.obolibrary.org/obo/CL_4047101) + +- [liver-resident natural killer cell](http://purl.obolibrary.org/obo/CL_4047101) EquivalentTo [natural killer cell](http://purl.obolibrary.org/obo/CL_0000623) and ([RO_0001025](http://purl.obolibrary.org/obo/RO_0001025) some [UBERON_0001281](http://purl.obolibrary.org/obo/UBERON_0001281)) + +- [liver-resident natural killer cell](http://purl.obolibrary.org/obo/CL_4047101) SubClassOf [RO_0001025](http://purl.obolibrary.org/obo/RO_0001025) some [UBERON_0001281](http://purl.obolibrary.org/obo/UBERON_0001281) + +- [liver-resident natural killer cell](http://purl.obolibrary.org/obo/CL_4047101) SubClassOf [natural killer cell](http://purl.obolibrary.org/obo/CL_0000623) + + +### local interneuron `http://purl.obolibrary.org/obo/CL_0004001` +#### Removed +- [local interneuron](http://purl.obolibrary.org/obo/CL_0004001) SubClassOf [obsolete CNS interneuron](http://purl.obolibrary.org/obo/CL_0000402) + +#### Added +- [local interneuron](http://purl.obolibrary.org/obo/CL_0004001) SubClassOf [interneuron](http://purl.obolibrary.org/obo/CL_0000099) + + +### luminal adaptive secretory precursor cell of mammary gland `http://purl.obolibrary.org/obo/CL_4033057` + +#### Added +- [luminal adaptive secretory precursor cell of mammary gland](http://purl.obolibrary.org/obo/CL_4033057) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl/cl-base#cellxgene_subset) + + +### luminal endometrial multiciliated epithelial cell `http://purl.obolibrary.org/obo/CL_4030041` +#### Removed +- [luminal endometrial multiciliated epithelial cell](http://purl.obolibrary.org/obo/CL_4030041) [label](http://www.w3.org/2000/01/rdf-schema#label) "luminal endometrial ciliated epithelial cell"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [luminal endometrial multiciliated epithelial cell](http://purl.obolibrary.org/obo/CL_4030041) [has_exact_synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "luminal endometrial ciliated epithelial cell"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [luminal endometrial multiciliated epithelial cell](http://purl.obolibrary.org/obo/CL_4030041) [label](http://www.w3.org/2000/01/rdf-schema#label) "luminal endometrial multiciliated epithelial cell"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### luminal endometrial unciliated epithelial cell `http://purl.obolibrary.org/obo/CL_4052023` + +#### Added +- [luminal endometrial unciliated epithelial cell](http://purl.obolibrary.org/obo/CL_4052023) [comment](http://www.w3.org/2000/01/rdf-schema#comment) "The luminal endometrial unciliated epithelial cell expresses WNT7A, and LGR5 during the proliferative phase, transitioning to express VTCN1 and SULT1E1 in the early secretory phase, and LEFTY1, IL6, and PTGS1 in the mid- to late-secretory phases."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:39198675"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [luminal endometrial unciliated epithelial cell](http://purl.obolibrary.org/obo/CL_4052023) [id](http://www.geneontology.org/formats/oboInOwl#id) "CL:4052023"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [luminal endometrial unciliated epithelial cell](http://purl.obolibrary.org/obo/CL_4052023) [has_broad_synonym](http://www.geneontology.org/formats/oboInOwl#hasBroadSynonym) "luminal cell of endometrium"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [luminal endometrial unciliated epithelial cell](http://purl.obolibrary.org/obo/CL_4052023) [has_broad_synonym](http://www.geneontology.org/formats/oboInOwl#hasBroadSynonym) "endometrial luminal epithelial cell"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:31317179"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [luminal endometrial unciliated epithelial cell](http://purl.obolibrary.org/obo/CL_4052023) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "An epithelial cell that is part of the endometrial luminal epithelium, forming a continuous layer lining the uterine cavity. This cell undergoes cyclical changes during the menstrual cycle, proliferating under estrogen in the proliferative phase, and differentiating under progesterone in the secretory phase to prepare for potential implantation. During the window of implantation, this cell changes from a tall columnar shape to a shorter columnar or cuboidal form, loses polarity, and becomes receptive to blastocyst implantation."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:38559249"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:36581776"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:32929266"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:39198675"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [luminal endometrial unciliated epithelial cell](http://purl.obolibrary.org/obo/CL_4052023) [label](http://www.w3.org/2000/01/rdf-schema#label) "luminal endometrial unciliated epithelial cell"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [luminal endometrial unciliated epithelial cell](http://purl.obolibrary.org/obo/CL_4052023) [contributor](http://purl.org/dc/terms/contributor) [0009-0000-8480-9277](https://orcid.org/0009-0000-8480-9277) + +- [luminal endometrial unciliated epithelial cell](http://purl.obolibrary.org/obo/CL_4052023) [date](http://purl.org/dc/terms/date) "2024-10-22T12:02:23Z"^^[dateTime](http://www.w3.org/2001/XMLSchema#dateTime) + +- Class: [luminal endometrial unciliated epithelial cell](http://purl.obolibrary.org/obo/CL_4052023) + +- [luminal endometrial unciliated epithelial cell](http://purl.obolibrary.org/obo/CL_4052023) EquivalentTo [epithelial cell](http://purl.obolibrary.org/obo/CL_0000066) and ([BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0011949](http://purl.obolibrary.org/obo/UBERON_0011949)) and ([RO_0002215](http://purl.obolibrary.org/obo/RO_0002215) some [GO_0032940](http://purl.obolibrary.org/obo/GO_0032940)) + +- [luminal endometrial unciliated epithelial cell](http://purl.obolibrary.org/obo/CL_4052023) SubClassOf [epithelial cell of uterus](http://purl.obolibrary.org/obo/CL_0002149) + +- [luminal endometrial unciliated epithelial cell](http://purl.obolibrary.org/obo/CL_4052023) SubClassOf [oviduct secretory cell](http://purl.obolibrary.org/obo/CL_1001591) + +- [luminal endometrial unciliated epithelial cell](http://purl.obolibrary.org/obo/CL_4052023) SubClassOf [BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0011949](http://purl.obolibrary.org/obo/UBERON_0011949) + + +### luminal hormone-sensing cell of mammary gland `http://purl.obolibrary.org/obo/CL_4033058` +#### Removed +- [luminal hormone-sensing cell of mammary gland](http://purl.obolibrary.org/obo/CL_4033058) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) + +#### Added +- [luminal hormone-sensing cell of mammary gland](http://purl.obolibrary.org/obo/CL_4033058) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl/cl-base#cellxgene_subset) + + +### lung endothelial cell `http://purl.obolibrary.org/obo/CL_1001567` + +#### Added +- [lung endothelial cell](http://purl.obolibrary.org/obo/CL_1001567) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl/cl-base#cellxgene_subset) + + +### lung goblet cell `http://purl.obolibrary.org/obo/CL_1000143` +#### Removed +- [lung goblet cell](http://purl.obolibrary.org/obo/CL_1000143) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +Lung goblet cells are critical components of the respiratory tract, specifically found in the bronchial segments. They are secretory epithelial cells known for their signature "goblet" or cup-like shape. Their primary function is to produce and secrete mucus that aids in trapping airborne particles and pathogens, preventing them from reaching the delicate environment of the lung. As part of the lung's epithelial lining, they act as frontline defenders, maintaining lung health and function. +The lung goblet cells are densely packed with granules containing mucin glycoproteins, the primary component of mucus. As mucus is produced and secreted, it moves towards the lumen of the lungs where the cilia, hair-like structures of the neighboring ciliated epithelial cells, help to navigate it upwards and out of the respiratory tract. This coordinated action ensures the expulsion of unwanted particles and pathogens, effectively cleaning the respiratory tract. +Dysfunction or abnormal proliferation of lung goblet cells can result in pathological conditions such as chronic obstructive pulmonary disorder (COPD) and asthma, where excessive mucus production leads to airway obstruction. Furthermore, lung goblet cells respond to a variety of stimuli, including toxins, allergens, irritants, and infections, adjusting their mucus production accordingly."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1159/000512268"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1038/s41385-018-0039-y"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1513/AnnalsATS.201802-128AW"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1038/s41385-020-00370-7"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://www.ncbi.nlm.nih.gov/books/NBK553208/"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [lung goblet cell](http://purl.obolibrary.org/obo/CL_1000143) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Lung goblet cells are critical components of the respiratory tract, specifically found in the bronchial segments. They are secretory epithelial cells known for their signature "goblet" or cup-like shape. Their primary function is to produce and secrete mucus that aids in trapping airborne particles and pathogens, preventing them from reaching the delicate environment of the lung. As part of the lung's epithelial lining, they act as frontline defenders, maintaining lung health and function. +The lung goblet cells are densely packed with granules containing mucin glycoproteins, the primary component of mucus. As mucus is produced and secreted, it moves towards the lumen of the lungs where the cilia, hair-like structures of the neighboring ciliated epithelial cells, help to navigate it upwards and out of the respiratory tract. This coordinated action ensures the expulsion of unwanted particles and pathogens, effectively cleaning the respiratory tract. +Dysfunction or abnormal proliferation of lung goblet cells can result in pathological conditions such as chronic obstructive pulmonary disorder (COPD) and asthma, where excessive mucus production leads to airway obstruction. Furthermore, lung goblet cells respond to a variety of stimuli, including toxins, allergens, irritants, and infections, adjusting their mucus production accordingly."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1159/000512268"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1038/s41385-018-0039-y"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1513/AnnalsATS.201802-128AW"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1038/s41385-020-00370-7"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://www.ncbi.nlm.nih.gov/books/NBK553208/"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [lung goblet cell](http://purl.obolibrary.org/obo/CL_1000143) SubClassOf [lung secretory cell](http://purl.obolibrary.org/obo/CL_1000272) + + +### lung interstitial macrophage `http://purl.obolibrary.org/obo/CL_4033043` + +#### Added +- [lung interstitial macrophage](http://purl.obolibrary.org/obo/CL_4033043) [comment](http://www.w3.org/2000/01/rdf-schema#comment) "The marker set F13A1, STAB1, FCGR2B can identify the Human cell type lung interstitial macrophage in the Lung with a confidence of 0.46 (NS-Forest FBeta value)."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://doi.org/10.5281/zenodo.11165918"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [lung interstitial macrophage](http://purl.obolibrary.org/obo/CL_4033043) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl/cl-base#cellxgene_subset) + +- [lung interstitial macrophage](http://purl.obolibrary.org/obo/CL_4033043) SubClassOf [RO_0015004](http://purl.obolibrary.org/obo/RO_0015004) some [CLM_1000031](http://purl.obolibrary.org/obo/CLM_1000031) + + +### lung macrophage `http://purl.obolibrary.org/obo/CL_1001603` + +#### Added +- [lung macrophage](http://purl.obolibrary.org/obo/CL_1001603) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://cellxgene.cziscience.com/cellguide/CL_1001603"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [lung macrophage](http://purl.obolibrary.org/obo/CL_1001603) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Lung macrophages refer to macrophage populations in the lungs, including the tissue-resident alveolar macrophages and interstitial macrophages, located in the air spaces and the connective tissue of the lung, respectively, and recruited macrophages. They are important in maintaining tissue homeostasis and immunity. +The primary function of lung macrophages is to patrol and maintain the pulmonary system, where they serve as the first line of defense against airborne pathogens and inhaled particles. They perform phagocytosis of pathogens, particulate matter, dead cells, and other cellular debris from the lungs to maintain clear air passages and optimize gas exchange. They may also participate in tissue repair and the resolution of inflammation following injury. +Lung macrophages also play a critical role in immune regulation. They help to initiate an immune response by secreting cytokines and other inflammatory mediators and by presenting antigens from the pathogens they have engulfed to induce T cell responses. However, if activated improperly, lung macrophages can contribute to inflammatory diseases of the lung such as chronic obstructive pulmonary disease (COPD) or asthma."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1189/jlb.70.2.163"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1016/j.immuni.2022.08.010"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.3390/cells10040897"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1002/JLB.3RU0720-418R"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.3389/fimmu.2021.753940/full"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### lung multiciliated epithelial cell `http://purl.obolibrary.org/obo/CL_1000271` +#### Removed +- [lung multiciliated epithelial cell](http://purl.obolibrary.org/obo/CL_1000271) [label](http://www.w3.org/2000/01/rdf-schema#label) "lung ciliated cell"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [lung multiciliated epithelial cell](http://purl.obolibrary.org/obo/CL_1000271) EquivalentTo [ciliated epithelial cell](http://purl.obolibrary.org/obo/CL_0000067) and ([BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0000115](http://purl.obolibrary.org/obo/UBERON_0000115)) + +- [lung multiciliated epithelial cell](http://purl.obolibrary.org/obo/CL_1000271) SubClassOf [ciliated epithelial cell](http://purl.obolibrary.org/obo/CL_0000067) + +#### Added +- [lung multiciliated epithelial cell](http://purl.obolibrary.org/obo/CL_1000271) [has_exact_synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "lung ciliated cell"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [lung multiciliated epithelial cell](http://purl.obolibrary.org/obo/CL_1000271) [label](http://www.w3.org/2000/01/rdf-schema#label) "lung multiciliated epithelial cell"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [lung multiciliated epithelial cell](http://purl.obolibrary.org/obo/CL_1000271) EquivalentTo [columnar/cuboidal epithelial cell](http://purl.obolibrary.org/obo/CL_0000075) and ([BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0000115](http://purl.obolibrary.org/obo/UBERON_0000115)) and ([BFO_0000051](http://purl.obolibrary.org/obo/BFO_0000051) some [GO_0031514](http://purl.obolibrary.org/obo/GO_0031514)) and ([RO_0000053](http://purl.obolibrary.org/obo/RO_0000053) some [PATO_0010007](http://purl.obolibrary.org/obo/PATO_0010007)) + + +### lung perichondrial fibroblast `http://purl.obolibrary.org/obo/CL_4033026` + +#### Added +- [lung perichondrial fibroblast](http://purl.obolibrary.org/obo/CL_4033026) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl/cl-base#cellxgene_subset) + + +### lung pericyte `http://purl.obolibrary.org/obo/CL_0009089` + +#### Added +- [lung pericyte](http://purl.obolibrary.org/obo/CL_0009089) [comment](http://www.w3.org/2000/01/rdf-schema#comment) "The marker set HIGD1B, KCNK3 can identify the Human cell type lung pericyte in the Lung with a confidence of 0.84 (NS-Forest FBeta value)."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://doi.org/10.5281/zenodo.11165918"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [lung pericyte](http://purl.obolibrary.org/obo/CL_0009089) SubClassOf [RO_0015004](http://purl.obolibrary.org/obo/RO_0015004) some [CLM_1000047](http://purl.obolibrary.org/obo/CLM_1000047) + + +### lung resident granzyme K-associated CD8 T cell `http://purl.obolibrary.org/obo/CL_4052020` + +#### Added +- [lung resident granzyme K-associated CD8 T cell](http://purl.obolibrary.org/obo/CL_4052020) [contributor](http://purl.org/dc/terms/contributor) [0009-0000-8480-9277](https://orcid.org/0009-0000-8480-9277) + +- [lung resident granzyme K-associated CD8 T cell](http://purl.obolibrary.org/obo/CL_4052020) [date](http://purl.org/dc/terms/date) "2024-10-14T15:42:41Z"^^[dateTime](http://www.w3.org/2001/XMLSchema#dateTime) + +- [lung resident granzyme K-associated CD8 T cell](http://purl.obolibrary.org/obo/CL_4052020) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "lung resident CD8-GZMK"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003000](http://purl.obolibrary.org/obo/OMO_0003000) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "doi:/10.1101/2022.06.17.496207"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [lung resident granzyme K-associated CD8 T cell](http://purl.obolibrary.org/obo/CL_4052020) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A granzyme K-associated CD8 T cell that resides in the lung, characterized by the expression of granzyme K (GZMK), and tissue residency markers CD103 and CD49a. This cell exhibits cytotoxic potential through its expression of multiple granzymes (GZMA, GZMB, GZMH, GZMM) in addition to GZMK."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "doi:/10.1101/2022.06.17.496207"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [lung resident granzyme K-associated CD8 T cell](http://purl.obolibrary.org/obo/CL_4052020) [comment](http://www.w3.org/2000/01/rdf-schema#comment) "Lung resident granzyme K-associated CD8 T cell represents an intermediate stage of T cell differentiation, with GZMK expression peaking during this phase."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:28322863"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "doi:/10.1101/2022.06.17.496207"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [lung resident granzyme K-associated CD8 T cell](http://purl.obolibrary.org/obo/CL_4052020) [label](http://www.w3.org/2000/01/rdf-schema#label) "lung resident granzyme K-associated CD8 T cell"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [lung resident granzyme K-associated CD8 T cell](http://purl.obolibrary.org/obo/CL_4052020) [id](http://www.geneontology.org/formats/oboInOwl#id) "CL:4052020"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [lung resident granzyme K-associated CD8 T cell](http://purl.obolibrary.org/obo/CL_4052020) [contributor](http://purl.org/dc/terms/contributor) [0000-0002-2336-2552](https://orcid.org/0000-0002-2336-2552) + +- Class: [lung resident granzyme K-associated CD8 T cell](http://purl.obolibrary.org/obo/CL_4052020) + +- [lung resident granzyme K-associated CD8 T cell](http://purl.obolibrary.org/obo/CL_4052020) EquivalentTo [lung resident memory CD8-positive, CD103-positive, alpha-beta T cell](http://purl.obolibrary.org/obo/CL_4033040) and ([RO_0002292](http://purl.obolibrary.org/obo/RO_0002292) some [PR_000003472](http://purl.obolibrary.org/obo/PR_000003472)) + +- [lung resident granzyme K-associated CD8 T cell](http://purl.obolibrary.org/obo/CL_4052020) SubClassOf [granzyme K-associated CD8 T cell](http://purl.obolibrary.org/obo/CL_4052021) + +- [lung resident granzyme K-associated CD8 T cell](http://purl.obolibrary.org/obo/CL_4052020) SubClassOf [lung resident memory CD8-positive, CD103-positive, alpha-beta T cell](http://purl.obolibrary.org/obo/CL_4033040) + + +### lung resident memory CD4-positive, alpha-beta T cell `http://purl.obolibrary.org/obo/CL_4033038` + +#### Added +- [lung resident memory CD4-positive, alpha-beta T cell](http://purl.obolibrary.org/obo/CL_4033038) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl/cl-base#cellxgene_subset) + + +### lung resident memory CD8-positive, alpha-beta T cell `http://purl.obolibrary.org/obo/CL_4033039` + +#### Added +- [lung resident memory CD8-positive, alpha-beta T cell](http://purl.obolibrary.org/obo/CL_4033039) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl/cl-base#cellxgene_subset) + + +### lymph node macrophage `http://purl.obolibrary.org/obo/CL_0000868` +#### Removed +- [lymph node macrophage](http://purl.obolibrary.org/obo/CL_0000868) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) + + + +### lymphoblast `http://purl.obolibrary.org/obo/CL_0017005` +#### Removed +- [lymphoblast](http://purl.obolibrary.org/obo/CL_0017005) [date](http://purl.org/dc/elements/1.1/date) "2022-08-17T14:20:01Z"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [lymphoblast](http://purl.obolibrary.org/obo/CL_0017005) [created by](http://www.geneontology.org/formats/oboInOwl#created_by) "http://orcid.org/0000-0003-2473-2313"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [lymphoblast](http://purl.obolibrary.org/obo/CL_0017005) [date](http://purl.org/dc/terms/date) "2022-08-17T14:20:01Z"^^[dateTime](http://www.w3.org/2001/XMLSchema#dateTime) + +- [lymphoblast](http://purl.obolibrary.org/obo/CL_0017005) [contributor](http://purl.org/dc/terms/contributor) [0000-0003-2473-2313](http://orcid.org/0000-0003-2473-2313) + + +### lymphocyte of B lineage `http://purl.obolibrary.org/obo/CL_0000945` + +#### Added +- [lymphocyte of B lineage](http://purl.obolibrary.org/obo/CL_0000945) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl/cl-base#cellxgene_subset) + + +### lymphocyte of B lineage, CD19-positive `http://purl.obolibrary.org/obo/CL_0001200` +#### Removed +- [lymphocyte of B lineage, CD19-positive](http://purl.obolibrary.org/obo/CL_0001200) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) + + + +### lymphocyte of small intestine lamina propria `http://purl.obolibrary.org/obo/CL_0009044` + +#### Added +- [lymphocyte of small intestine lamina propria](http://purl.obolibrary.org/obo/CL_0009044) [depiction](http://xmlns.com/foaf/0.1/depiction) [Small-intestine-cells.png](http://purl.obolibrary.org/obo/cl/images/Small-intestine-cells.png) + - [comment](http://www.w3.org/2000/01/rdf-schema#comment) "Figure depicts a cross section of intestinal villi in the small intestine, including the crypts of Lieberkuhn (seen here as ‘crypt’), as well as the layer specific locations of cells that exist within the gastrointestinal tract. Layers depicted here include epithelium (rows of cells bordering villus), submucosa (white space below the epithelium containing networks of neurons and ganglia depicted in pink), muscularis mucosae (blue layer), muscularis propria (referred to here as muscle layer). + +ISC: Intestinal Stem Cell +TA: Transit Amplifying Cells"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [license](http://purl.org/dc/elements/1.1/license) "http://creativecommons.org/licenses/by/4.0/"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### macula densa epithelial cell `http://purl.obolibrary.org/obo/CL_1000850` + +#### Added +- [macula densa epithelial cell](http://purl.obolibrary.org/obo/CL_1000850) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Macula densa epithelial cells, as part of the complex nephron structure, play a crucial role in kidney function. These cells, which make up the macula densa, help regulate blood pressure and the filtration rate of the glomerulus by sensing sodium chloride amounts in the kidney tubules. Found where the thick ascending limb of the Loop of Henle touches the afferent arteriole, macula densa epithelial cells are positioned in an optimal location to monitor and respond to changes in the filtrate composition. +These cells maintain intraglomerular homeostasis. When the sodium chloride concentration is high, macula densa cells respond by secreting adenosine and vasoconstricting the afferent arteriole to decrease the glomerular filtration rate. Conversely, if the sodium chloride concentration in the filtrate is low, the production and release of nitric oxide cause vasodilation to enhance the glomerular filtration rate. +Macula densa epithelial cells also have a role in tubuloglomerular feedback mechanisms, an essential autoregulatory renal response. They send feedback to the glomerular mesangial cells, allowing constriction or relaxation of the afferent arteriole as needed depending on the content of the filtrate."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1073/pnas.0736323100"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1161/HYPERTENSIONAHA.115.04739"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1146/annurev-physiol-052521-121841"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1681/ASN.2015050515"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1681/ASN.2009070759"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [macula densa epithelial cell](http://purl.obolibrary.org/obo/CL_1000850) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://cellxgene.cziscience.com/cellguide/CL_1000850"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### magnocellular neurosecretory cell `http://purl.obolibrary.org/obo/CL_0011003` +#### Removed +- [magnocellular neurosecretory cell](http://purl.obolibrary.org/obo/CL_0011003) SubClassOf [central nervous system neuron](http://purl.obolibrary.org/obo/CL_2000029) + +#### Added +- [magnocellular neurosecretory cell](http://purl.obolibrary.org/obo/CL_0011003) SubClassOf [neuron of the forebrain](http://purl.obolibrary.org/obo/CL_0012001) + + +### male gamete `http://purl.obolibrary.org/obo/CL_0000408` + +#### Added +- [male gamete](http://purl.obolibrary.org/obo/CL_0000408) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +The male gamete, also known as a sperm cell, is a highly specialized cell type critical to sexual reproduction. Sperm are produced during a process called spermatogenesis within the male reproductive organ, specifically the testes. They are haploid cells, carrying the genetic material from the male parent, and fuse with the ovum, the female gamete, to form a diploid zygote during fertilization, thereby initiating gestation and the development of a new organism. +The male gamete is distinguished by its morphology, notably its elongated shape which is geared towards locomotion. One of the primary characteristics of a male gamete is its flagellum, or tail, which propels the cell towards the female gamete. It additionally contains an elongated head region housing the nucleus, where the genetic material is stored. The anterior section of the head, the acrosome, releases enzymes essential for penetrating the protective layers of the ovum during the fertilization process. +The function of male gametes does not cease upon fertilization. In addition to delivering the paternal set of chromosomes, fusion of the sperm cell with the ovum causes an increase in cytosolic Ca2+ which then activates the female egg cell to undergo the so-called cortical reaction during which the egg’s zona pellucida is changed so fusion with additional sperm is prevented. The Ca2+ signal also initiates the development of the zygote and eventual formation of an embryo. Male gametes also contribute towards forming the placenta, which supplies nutrients and removes waste products during gestation."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1016/j.semcdb.2016.04.009"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://www.ncbi.nlm.nih.gov/books/NBK553142/"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1242/dev.202046"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://www.ncbi.nlm.nih.gov/books/NBK26843/"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [male gamete](http://purl.obolibrary.org/obo/CL_0000408) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://cellxgene.cziscience.com/cellguide/CL_0000408"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### male germ cell `http://purl.obolibrary.org/obo/CL_0000015` + +#### Added +- [male germ cell](http://purl.obolibrary.org/obo/CL_0000015) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Male germ cells are specialized cells that give rise to the male gametes and are therefore crucial for sexual reproduction in males. Through a complex process called spermatogenesis in the testes male germ cells undergo several stages of development, each with distinctive morphological and physiological characteristics, eventually differentiating into mature spermatozoa (sperm). +Male germ cells are responsible for transferring genetic material from male to offspring as part of sexual reproduction. In the initial stage of their life cycle, they exist as spermatogonial stem cells, which multiply by mitotic division to self-renew and to produce daughter cells. The daughter cells then undergo meiotic division, a process that reduces the number of chromosomes in each cell by half, from diploid to haploid – the formation of spermatids. This is critical for maintaining genetic stability from generation to generation, as it ensures that when an egg and sperm cell unite during fertilization, the resulting offspring will have the correct number of chromosomes. The final phase of spermatogenesis is called spermiogenesis, during which spermatozoa - mature and motile sperm cells – are produced from round spermatids. +The matured male germ cells or sperm cells are highly specialized, having a streamlined shape designed for efficient movement towards the female egg. A sperm cell is divided into three main parts, namely the head, midpiece, and tail. The head contains the genetic material, the midpiece contains mitochondria that provide energy, and the tail, termed as the flagellum, propels the sperm cell forward. Each of these parts play significant roles in fertilization."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://www.ncbi.nlm.nih.gov/books/NBK553142/"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1242/dev.202046"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1016/S1534-5807(02)00173-9"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1016/S0092-8674(00)81834-6"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [male germ cell](http://purl.obolibrary.org/obo/CL_0000015) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://cellxgene.cziscience.com/cellguide/CL_0000015"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### mammillary body neuron `http://purl.obolibrary.org/obo/CL_4023074` +#### Removed +- [mammillary body neuron](http://purl.obolibrary.org/obo/CL_4023074) SubClassOf [central nervous system neuron](http://purl.obolibrary.org/obo/CL_2000029) + +#### Added +- [mammillary body neuron](http://purl.obolibrary.org/obo/CL_4023074) SubClassOf [neuron of the forebrain](http://purl.obolibrary.org/obo/CL_0012001) + + +### marrow fibroblast `http://purl.obolibrary.org/obo/CL_0002240` +#### Removed +- [marrow fibroblast](http://purl.obolibrary.org/obo/CL_0002240) SubClassOf [bone marrow cell](http://purl.obolibrary.org/obo/CL_0002092) + +#### Added +- [marrow fibroblast](http://purl.obolibrary.org/obo/CL_0002240) SubClassOf [stromal cell of bone marrow](http://purl.obolibrary.org/obo/CL_0010001) + + +### mast cell `http://purl.obolibrary.org/obo/CL_0000097` +#### Removed +- [mast cell](http://purl.obolibrary.org/obo/CL_0000097) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) + + + +### mast cell progenitor `http://purl.obolibrary.org/obo/CL_0000831` +#### Removed +- [mast cell progenitor](http://purl.obolibrary.org/obo/CL_0000831) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) + + + +### matrix D1 medium spiny neuron `http://purl.obolibrary.org/obo/CL_4030043` + +#### Added +- [matrix D1 medium spiny neuron](http://purl.obolibrary.org/obo/CL_4030043) SubClassOf [striatum neuron](http://purl.obolibrary.org/obo/CL_0002613) + + +### matrix D2 medium spiny neuron `http://purl.obolibrary.org/obo/CL_4030047` + +#### Added +- [matrix D2 medium spiny neuron](http://purl.obolibrary.org/obo/CL_4030047) SubClassOf [striatum neuron](http://purl.obolibrary.org/obo/CL_0002613) + + +### mature CD8-alpha-low Langerhans cell `http://purl.obolibrary.org/obo/CL_0001020` +#### Removed +- [mature CD8-alpha-low Langerhans cell](http://purl.obolibrary.org/obo/CL_0001020) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "Mature CD8_alpha-low Langerhans cell is a CD8_alpha-low Langerhans cell that that is CD80-high, CD86-high, MHCII-high and is CD83-positive."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:amm"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMCID:PMC2346585"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GO_REF:0000031"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [mature CD8-alpha-low Langerhans cell](http://purl.obolibrary.org/obo/CL_0001020) [label](http://www.w3.org/2000/01/rdf-schema#label) "mature CD8_alpha-low Langerhans cell"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [mature CD8-alpha-low Langerhans cell](http://purl.obolibrary.org/obo/CL_0001020) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "Mature CD8-alpha-low Langerhans cell is a CD8-alpha-low Langerhans cell that that is CD80-high, CD86-high, MHCII-high and is CD83-positive."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:amm"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMCID:PMC2346585"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GO_REF:0000031"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [mature CD8-alpha-low Langerhans cell](http://purl.obolibrary.org/obo/CL_0001020) [label](http://www.w3.org/2000/01/rdf-schema#label) "mature CD8-alpha-low Langerhans cell"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### mature CD8-alpha-negative CD11b-negative dendritic cell `http://purl.obolibrary.org/obo/CL_0001002` +#### Removed +- [mature CD8-alpha-negative CD11b-negative dendritic cell](http://purl.obolibrary.org/obo/CL_0001002) [label](http://www.w3.org/2000/01/rdf-schema#label) "mature CD8_alpha-negative CD11b-negative dendritic cell"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [mature CD8-alpha-negative CD11b-negative dendritic cell](http://purl.obolibrary.org/obo/CL_0001002) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "Mature CD8_alpha-negative CD11b-negative dendritic cell is a CD8_alpha-negative CD11b-negative dendritic cell that is CD80-high, CD86-high, MHCII-high and is CD83-positive."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:amm"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMCID:PMC2346585"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GO_REF:0000031"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:tfm"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [mature CD8-alpha-negative CD11b-negative dendritic cell](http://purl.obolibrary.org/obo/CL_0001002) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "Mature CD8-alpha-negative CD11b-negative dendritic cell is a CD8-alpha-negative CD11b-negative dendritic cell that is CD80-high, CD86-high, MHCII-high and is CD83-positive."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:amm"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMCID:PMC2346585"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GO_REF:0000031"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:tfm"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [mature CD8-alpha-negative CD11b-negative dendritic cell](http://purl.obolibrary.org/obo/CL_0001002) [label](http://www.w3.org/2000/01/rdf-schema#label) "mature CD8-alpha-negative CD11b-negative dendritic cell"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### mature CD8-alpha-negative CD11b-positive dendritic cell `http://purl.obolibrary.org/obo/CL_0001003` +#### Removed +- [mature CD8-alpha-negative CD11b-positive dendritic cell](http://purl.obolibrary.org/obo/CL_0001003) [label](http://www.w3.org/2000/01/rdf-schema#label) "mature CD8_alpha-negative CD11b-positive dendritic cell"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [mature CD8-alpha-negative CD11b-positive dendritic cell](http://purl.obolibrary.org/obo/CL_0001003) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "Mature CD8_alpha-negative CD11b-positive dendritic cell is a CD8_alpha-negative CD11b-positive dendritic cell that is CD80-high, CD86-high, MHCII-high and is CD83-positive."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:amm"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMCID:PMC2346585"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GO_REF:0000031"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:tfm"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [mature CD8-alpha-negative CD11b-positive dendritic cell](http://purl.obolibrary.org/obo/CL_0001003) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "Mature CD8-alpha-negative CD11b-positive dendritic cell is a CD8-alpha-negative CD11b-positive dendritic cell that is CD80-high, CD86-high, MHCII-high and is CD83-positive."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:amm"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMCID:PMC2346585"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GO_REF:0000031"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:tfm"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [mature CD8-alpha-negative CD11b-positive dendritic cell](http://purl.obolibrary.org/obo/CL_0001003) [label](http://www.w3.org/2000/01/rdf-schema#label) "mature CD8-alpha-negative CD11b-positive dendritic cell"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### mature CD8-alpha-positive CD11b-negative dendritic cell `http://purl.obolibrary.org/obo/CL_0001005` +#### Removed +- [mature CD8-alpha-positive CD11b-negative dendritic cell](http://purl.obolibrary.org/obo/CL_0001005) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "Mature CD8_alpha-positive CD11b-negative dendritic cell is a CD8_alpha-positive CD11b-negative dendritic cell that is CD80-high, CD86-high, MHCII-high and is CD83-positive."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:amm"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMCID:PMC2346585"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GO_REF:0000031"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [mature CD8-alpha-positive CD11b-negative dendritic cell](http://purl.obolibrary.org/obo/CL_0001005) [label](http://www.w3.org/2000/01/rdf-schema#label) "mature CD8_alpha-positive CD11b-negative dendritic cell"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [mature CD8-alpha-positive CD11b-negative dendritic cell](http://purl.obolibrary.org/obo/CL_0001005) [label](http://www.w3.org/2000/01/rdf-schema#label) "mature CD8-alpha-positive CD11b-negative dendritic cell"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [mature CD8-alpha-positive CD11b-negative dendritic cell](http://purl.obolibrary.org/obo/CL_0001005) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "Mature CD8-alpha-positive CD11b-negative dendritic cell is a CD8-alpha-positive CD11b-negative dendritic cell that is CD80-high, CD86-high, MHCII-high and is CD83-positive."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:amm"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMCID:PMC2346585"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GO_REF:0000031"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### mature T cell `http://purl.obolibrary.org/obo/CL_0002419` +#### Removed +- [mature T cell](http://purl.obolibrary.org/obo/CL_0002419) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) + + + +### mature microglial cell `http://purl.obolibrary.org/obo/CL_0002629` + +#### Added +- [mature microglial cell](http://purl.obolibrary.org/obo/CL_0002629) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Mature microglial cells represented one of the macrophage populations within the central nervous system (CNS). Microglial cells serve as the primary immune defense mechanism within the CNS, playing active roles in maintaining brain homeostasis and responding to pathological processes. In response to pathogens and injuries, microglial cells mature and change their morphology from a ramified shape with small processes (normal state) to an amoeboid shape (mature state). +Mature microglial cells possess multiple functional abilities, thereby enabling them to execute diverse roles in order to maintain the health of surrounding neural cells. They act to clear away cellular debris, dead neurons, or plaque formations through the process of phagocytosis. They are also continuously scanning their environment and are able to detect subtle changes in the neural landscape caused by injury, disease, or infection. Upon detection of such changes, these cells become activated and present antigens and secrete cytokines and chemokines to initiate an inflammation response, which sustains the brain’s defense against injurious agents. +Their role is not solely destructive or defensive: mature microglial cells also contribute to neurodevelopment by guiding the formation of neural circuits, synaptogenesis, and remodeling. Furthermore, they assist in managing synaptic plasticity, a key process in learning and memory functions. While the dysregulation of microglial cells has been implicated in various neurodegenerative diseases, they are also regarded as potential therapeutic targets for such conditions, given their crucial roles in maintaining CNS health."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.3389/fimmu.2022.997786"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1111/j.1745-7254.2007.00625.x"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1111/jnc.15689"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.4103/1673-5374.226386"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.4103/1673-5374.322423"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [mature microglial cell](http://purl.obolibrary.org/obo/CL_0002629) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://cellxgene.cziscience.com/cellguide/CL_0002629"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### medium field retinal amacrine cell `http://purl.obolibrary.org/obo/CL_0004252` +#### Removed +- [medium field retinal amacrine cell](http://purl.obolibrary.org/obo/CL_0004252) [RO_0002175](http://purl.obolibrary.org/obo/RO_0002175) [NCBITaxon_9606](http://purl.obolibrary.org/obo/NCBITaxon_9606) + +- [medium field retinal amacrine cell](http://purl.obolibrary.org/obo/CL_0004252) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [human_reference_atlas](http://purl.obolibrary.org/obo/cl/cl-base#human_reference_atlas) + + + +### medullary thymic epithelial cell `http://purl.obolibrary.org/obo/CL_0002365` + +#### Added +- [medullary thymic epithelial cell](http://purl.obolibrary.org/obo/CL_0002365) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://cellxgene.cziscience.com/cellguide/CL_0002365"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [medullary thymic epithelial cell](http://purl.obolibrary.org/obo/CL_0002365) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Medullary thymic epithelial cells (mTECs) are distinct cells situated in the thymic medulla, a vital organ where T cells mature. mTECs are recognized by their unique appearance, characterized by large, plump cells with abundant cytoplasm and irregularly shaped nuclei. They inhabit a microenvironment closely interacting with various thymic cell types, including conventional dendritic cells and thymocytes. +The primary function of mTECs revolves around negative selection of developing T cells, thus preventing autoimmune responses. mTECs allow developing T cells to recognize and be responsive to foreign antigens while remaining tolerant to the body's own tissues. They achieve this through a process called promiscuous gene expression where they express and display a vast array of self-antigens. This process is regulated by a transcriptional regulator called autoimmune regulator (Aire), which contributes to immunological self-tolerance. +mTECs themselves have a self-renewing ability and sustain the continuous export of mature T cells. They also express a number of genes that encode for chemokines and other signaling molecules which draw in and retain developing T cells for the process of negative selection. The three-dimensional network formed by these cells provides a physical platform for such selection. Together, mTECs hold a critical place in the maintenance of immune homeostasis, demonstrating the conceptual links that exist between population of stromal cells, thymocytes development, tissue-restricted antigen expression, and negative selection."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1007/s11427-013-4482-4"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.4049/jimmunol.2100692"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.7554/eLife.60188"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### melanin-concentrating hormone neuron `http://purl.obolibrary.org/obo/CL_4042036` + +#### Added +- [melanin-concentrating hormone neuron](http://purl.obolibrary.org/obo/CL_4042036) [comment](http://www.w3.org/2000/01/rdf-schema#comment) "Nearly all melanin-concentrating hormone neurons express the glutamate transporter VGlut2, however a small subset of them expresses the machinery for GABA release and neurotransmission."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:38020069"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [melanin-concentrating hormone neuron](http://purl.obolibrary.org/obo/CL_4042036) [id](http://www.geneontology.org/formats/oboInOwl#id) "CL:4042036"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [melanin-concentrating hormone neuron](http://purl.obolibrary.org/obo/CL_4042036) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A neuron of the central nervous system with its soma primarily located in the lateral hypothalamic area and surrounding regions, including the zona incerta. This neuron type expresses melanin-concentrating hormone and is involved in regulating various physiological processes, including sleep, feeding behavior, and energy homeostasis."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:38020069"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:30284033"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:39035036"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [melanin-concentrating hormone neuron](http://purl.obolibrary.org/obo/CL_4042036) [label](http://www.w3.org/2000/01/rdf-schema#label) "melanin-concentrating hormone neuron"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [melanin-concentrating hormone neuron](http://purl.obolibrary.org/obo/CL_4042036) [date](http://purl.org/dc/terms/date) "2024-10-31T16:03:26Z"^^[dateTime](http://www.w3.org/2001/XMLSchema#dateTime) + +- [melanin-concentrating hormone neuron](http://purl.obolibrary.org/obo/CL_4042036) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "MCH neuron"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:30284033"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [melanin-concentrating hormone neuron](http://purl.obolibrary.org/obo/CL_4042036) [contributor](http://purl.org/dc/terms/contributor) [0000-0002-0098-8958](https://orcid.org/0000-0002-0098-8958) + +- Class: [melanin-concentrating hormone neuron](http://purl.obolibrary.org/obo/CL_4042036) + +- [melanin-concentrating hormone neuron](http://purl.obolibrary.org/obo/CL_4042036) SubClassOf [central nervous system neuron](http://purl.obolibrary.org/obo/CL_2000029) + + +### melanocyte `http://purl.obolibrary.org/obo/CL_0000148` + +#### Added +- [melanocyte](http://purl.obolibrary.org/obo/CL_0000148) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://cellxgene.cziscience.com/cellguide/CL_0000148"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [melanocyte](http://purl.obolibrary.org/obo/CL_0000148) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Melanocytes are specialized cells prevalently found in the skin, but also present in the hair follicles, eyes, inner ear, bones, heart, and brain. Their primary function is the synthesis of melanin, a pigment responsible for coloration of skin, hair, and eyes. The presence and distribution of this pigment play a crucial role in the body's defense mechanism against harmful ultraviolet radiation. +In addition to melanin production, melanocytes also engage in a variety of other biological functions. They play a fundamental role in the immune response, owing to their ability to present antigens to T cells. Furthermore, they contribute to the maintenance of the skin's homeostasis by regulating processes such as extracellular matrix remodeling and cytokine production. A balance in melanocyte function is pivotal, as dysfunctions often result in dermatological disorders. For instance, the loss of melanocytes or reduction in their function may lead to hypopigmentation conditions such as vitiligo, whereas an abnormal increase could result in hyperpigmentation disorders or melanoma, a dangerous type of skin cancer."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1002/med.21754"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1038/nrc.2016.37"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1111/j.1751-1097.2007.00226.x"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://www.sciencedirect.com/topics/agricultural-and-biological-sciences/melanocyte"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.3390/ijms21249769"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### melanocyte of skin `http://purl.obolibrary.org/obo/CL_1000458` + +#### Added +- [melanocyte of skin](http://purl.obolibrary.org/obo/CL_1000458) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://cellxgene.cziscience.com/cellguide/CL_1000458"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [melanocyte of skin](http://purl.obolibrary.org/obo/CL_1000458) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Melanocytes of the skin are specialized pigment cells crucial for producing and distributing melanin, the pigment determining skin, in addition to hair and eye color. Located in the basal layer of the epidermis, melanocytes serve as a natural sunscreen, protecting skin cells from harmful UV radiation. Structurally dendritic, they synthesize melanin through melanogenesis, transferring melanosomes to keratinocytes for UV shielding +Beyond pigmentation and UV protection, melanocytes play roles in immune and inflammatory responses. They respond to environmental changes, communicate with skin cell types, and secrete cytokines and growth factors influencing skin homeostasis. Dysregulation may lead to pigment disorders like vitiligo and melasma or contribute to skin cancer, particularly malignant melanoma."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1111/j.1751-1097.2007.00226.x"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1615/CritRevEukaryotGeneExpr.2020028454"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1016/j.jinf.2015.06.006"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.5114/pdia.2013.33376"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://www.sciencedirect.com/topics/biochemistry-genetics-and-molecular-biology/melanocyte"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### meningeal macrophage `http://purl.obolibrary.org/obo/CL_0000879` + +#### Added +- [meningeal macrophage](http://purl.obolibrary.org/obo/CL_0000879) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl/cl-base#cellxgene_subset) + + +### mesenchymal stem cell of adipose tissue `http://purl.obolibrary.org/obo/CL_0002570` +#### Removed +- [mesenchymal stem cell of adipose tissue](http://purl.obolibrary.org/obo/CL_0002570) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +Mesenchymal stem cells of adipose tissue, also known commonly as adipose-derived stem cells (ADSCs), are a population of adult stem cells that can be obtained easily from adipose tissues. They have many of the same regenerative properties as other mesenchymal stem cells, but are more easily accessible than bone marrow-derived stem cells. +Adipose-derived stem cells show immense promise in the field of regenerative medicine due to their ability to differentiate into adipocytes, chondrocytes, myocytes, osteoblasts, and other cell types. ADSCs also possess immunomodulatory and homeostatic functions: they have the ability to suppress immune responses and provide a therapeutic environment for tissue repair and regeneration, as well as supporting the proliferation of adipocytes and the overall expansion of adipose tissue and contributing to the tissue's ability to react to demands of energy storage and mobilization. Dysfunction of these cells may contribute to metabolic complications observed in obesity and diabetes. +ADSCs have been used for therapeutic applications such as pathological wound healing, severe refractory acute graft-versus-host disease, and idiopathic thrombocytopenic purpura."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1111/dgd.12049"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1016/j.tibtech.2006.01.010"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1096/fj.202100332R"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1016/j.biopha.2019.108765"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1038/s41536-019-0083-6"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [mesenchymal stem cell of adipose tissue](http://purl.obolibrary.org/obo/CL_0002570) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Mesenchymal stem cells of adipose tissue, also known commonly as adipose-derived stem cells (ADSCs), are a population of adult stem cells that can be obtained easily from adipose tissues. They have many of the same regenerative properties as other mesenchymal stem cells, but are more easily accessible than bone marrow-derived stem cells. +Adipose-derived stem cells show immense promise in the field of regenerative medicine due to their ability to differentiate into adipocytes, chondrocytes, myocytes, osteoblasts, and other cell types. ADSCs also possess immunomodulatory and homeostatic functions: they have the ability to suppress immune responses and provide a therapeutic environment for tissue repair and regeneration, as well as supporting the proliferation of adipocytes and the overall expansion of adipose tissue and contributing to the tissue's ability to react to demands of energy storage and mobilization. Dysfunction of these cells may contribute to metabolic complications observed in obesity and diabetes. +ADSCs have been used for therapeutic applications such as pathological wound healing, severe refractory acute graft-versus-host disease, and idiopathic thrombocytopenic purpura."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1111/dgd.12049"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1016/j.tibtech.2006.01.010"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1096/fj.202100332R"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1016/j.biopha.2019.108765"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1038/s41536-019-0083-6"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### mesodermal cell `http://purl.obolibrary.org/obo/CL_0000222` + +#### Added +- [mesodermal cell](http://purl.obolibrary.org/obo/CL_0000222) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://cellxgene.cziscience.com/cellguide/CL_0000222"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [mesodermal cell](http://purl.obolibrary.org/obo/CL_0000222) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Mesodermal cells are pluripotent and the most abundant in the human body. They contribute to the development of several structures such as the skeletal muscles, bones, heart and blood vessels, kidneys, gonads, connective tissues, and certain layers of the skin. Hence, the mesoderm is often regarded as an active and diverse layer due to its role in forming many bodily structures. +In embryonic development, these cells are instrumental, contributing to the body's structures through a carefully coordinated sequence of morphogenetic movements. This process forms the complex multicellular architecture of tissues and organs from a simple ball of cells. Without the function of mesodermal cells, the body's integral structures and systems would cease to form correctly, leading to developmental disorders such as axial mesodermal dysplasia complex"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://www.sciencedirect.com/topics/biochemistry-genetics-and-molecular-biology/mesoderm"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1016/j.ceb.2019.07.012"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.5535/arm.2016.40.1.162"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### mesothelial cell of appendix `http://purl.obolibrary.org/obo/CL_0009029` +#### Removed +- [mesothelial cell of appendix](http://purl.obolibrary.org/obo/CL_0009029) EquivalentTo [mesothelial cell](http://purl.obolibrary.org/obo/CL_0000077) and ([BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0001154](http://purl.obolibrary.org/obo/UBERON_0001154)) + +- [mesothelial cell of appendix](http://purl.obolibrary.org/obo/CL_0009029) SubClassOf [epithelial cell of appendix](http://purl.obolibrary.org/obo/CL_1000405) + +#### Added +- [mesothelial cell of appendix](http://purl.obolibrary.org/obo/CL_0009029) EquivalentTo [mesothelial cell](http://purl.obolibrary.org/obo/CL_0000077) and ([BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0012498](http://purl.obolibrary.org/obo/UBERON_0012498)) + +- [mesothelial cell of appendix](http://purl.obolibrary.org/obo/CL_0009029) SubClassOf [BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0012498](http://purl.obolibrary.org/obo/UBERON_0012498) + + +### mesothelial cell of colon `http://purl.obolibrary.org/obo/CL_0009025` +#### Removed +- [mesothelial cell of colon](http://purl.obolibrary.org/obo/CL_0009025) EquivalentTo [mesothelial cell](http://purl.obolibrary.org/obo/CL_0000077) and ([BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0001155](http://purl.obolibrary.org/obo/UBERON_0001155)) + +- [mesothelial cell of colon](http://purl.obolibrary.org/obo/CL_0009025) SubClassOf [colon epithelial cell](http://purl.obolibrary.org/obo/CL_0011108) + +#### Added +- [mesothelial cell of colon](http://purl.obolibrary.org/obo/CL_0009025) EquivalentTo [mesothelial cell](http://purl.obolibrary.org/obo/CL_0000077) and ([BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0003335](http://purl.obolibrary.org/obo/UBERON_0003335)) + +- [mesothelial cell of colon](http://purl.obolibrary.org/obo/CL_0009025) SubClassOf [BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0003335](http://purl.obolibrary.org/obo/UBERON_0003335) + + +### mesothelial cell of pleura `http://purl.obolibrary.org/obo/CL_1000491` +#### Removed +- [mesothelial cell of pleura](http://purl.obolibrary.org/obo/CL_1000491) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +Mesothelial cells of the pleura form a significant part of the pleural membrane, a thin, double-layered serous membrane that lines the thoracic cavity and encompasses the lungs. These specialized cells contribute to the pleura's key function of producing a lubricating serous fluid, which reduces friction between the lung's outer surface (visceral pleura) and the inner lining of the thoracic cavity (parietal pleura) during respiration. +The cellular structure of mesothelial cells, characterized by microvilli on their surface, aids in the secretion and absorption of the pleural fluid, effectively supporting the smooth expansion and contraction of the lungs. Dysregulation in mesothelial cells can lead to pathologies, including pleural effusion and malignant mesothelioma. +Mesothelial cells of the pleura display unique immunologic properties. They act as a first line of defense against infection because they are able to recognize pathogens and respond by secreting various cytokines and chemokines. Additionally, these cells are directly involved in the translocation of immune cells into the pleural cavity during inflammatory response, thereby playing an active role in the immune response within the pleural environment. +In the event of pleural injury, these cells are also involved in the mesothelial-mesenchymal transition, a process that allows mesothelial cells to transdifferentiate into myofibroblasts and promote tissue repair."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1152/ajplung.90587.2008"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1016/j.coi.2020.04.005"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.3389/fphys.2014.00284"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1016/j.ccm.2021.08.005"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [mesothelial cell of pleura](http://purl.obolibrary.org/obo/CL_1000491) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Mesothelial cells of the pleura form a significant part of the pleural membrane, a thin, double-layered serous membrane that lines the thoracic cavity and encompasses the lungs. These specialized cells contribute to the pleura's key function of producing a lubricating serous fluid, which reduces friction between the lung's outer surface (visceral pleura) and the inner lining of the thoracic cavity (parietal pleura) during respiration. +The cellular structure of mesothelial cells, characterized by microvilli on their surface, aids in the secretion and absorption of the pleural fluid, effectively supporting the smooth expansion and contraction of the lungs. Dysregulation in mesothelial cells can lead to pathologies, including pleural effusion and malignant mesothelioma. +Mesothelial cells of the pleura display unique immunologic properties. They act as a first line of defense against infection because they are able to recognize pathogens and respond by secreting various cytokines and chemokines. Additionally, these cells are directly involved in the translocation of immune cells into the pleural cavity during inflammatory response, thereby playing an active role in the immune response within the pleural environment. +In the event of pleural injury, these cells are also involved in the mesothelial-mesenchymal transition, a process that allows mesothelial cells to transdifferentiate into myofibroblasts and promote tissue repair."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1152/ajplung.90587.2008"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1016/j.coi.2020.04.005"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.3389/fphys.2014.00284"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1016/j.ccm.2021.08.005"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### mesothelial cell of small intestine `http://purl.obolibrary.org/obo/CL_0009024` +#### Removed +- [mesothelial cell of small intestine](http://purl.obolibrary.org/obo/CL_0009024) EquivalentTo [mesothelial cell](http://purl.obolibrary.org/obo/CL_0000077) and ([BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0002108](http://purl.obolibrary.org/obo/UBERON_0002108)) + +- [mesothelial cell of small intestine](http://purl.obolibrary.org/obo/CL_0009024) SubClassOf [epithelial cell of small intestine](http://purl.obolibrary.org/obo/CL_0002254) + +#### Added +- [mesothelial cell of small intestine](http://purl.obolibrary.org/obo/CL_0009024) EquivalentTo [mesothelial cell](http://purl.obolibrary.org/obo/CL_0000077) and ([BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0001206](http://purl.obolibrary.org/obo/UBERON_0001206)) + +- [mesothelial cell of small intestine](http://purl.obolibrary.org/obo/CL_0009024) SubClassOf [BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0001206](http://purl.obolibrary.org/obo/UBERON_0001206) + + +### mesothelial cell of visceral pleura `http://purl.obolibrary.org/obo/CL_1000493` +#### Removed +- [mesothelial cell of visceral pleura](http://purl.obolibrary.org/obo/CL_1000493) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +Mesothelial cells of visceral pleura are specialized epithelial cells that line the inner layer of the pleura, the membrane that envelops the lungs. Positioned adjacent to the lung tissue, these cells form a protective barrier and contribute to the structure of the visceral pleura. They are characterized by their cuboidal to squamous epithelial shape and the presence of microvilli on their surface, a feature aiding in fluid and solute exchange between the pleura and the lungs. +The primary function of mesothelial cells of visceral pleura is to secrete a lubricating serous fluid to facilitate smooth, frictionless lung movement within the thoracic cavity during respiration. This helps in the prevention of trauma or damage stemming from the constant rubbing of the lung tissue against the chest wall, hence playing a pivotal role in maintaining respiratory function. Besides fluid secretion, these cells have an essential role in the transportation of fluids and particles across the pleura, as well as in inflammation, wound healing, and tissue repair processes within the pleura. +Mesothelial cells of visceral pleura are notably implicated in the development of pleural diseases such as pleural effusion and pleural mesothelioma, a rare and aggressive form of cancer primarily linked with exposure to asbestos. Alterations, such as hyperplasia or metaplasia, may occur in these mesothelial cells under pathological conditions."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1152/physrev.00026.2003"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1371/journal.pone.0276978"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.3389/fphys.2014.00221"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.3390/jdb7020007"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1016/S1357-2725(03)00242-5"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [mesothelial cell of visceral pleura](http://purl.obolibrary.org/obo/CL_1000493) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Mesothelial cells of visceral pleura are specialized epithelial cells that line the inner layer of the pleura, the membrane that envelops the lungs. Positioned adjacent to the lung tissue, these cells form a protective barrier and contribute to the structure of the visceral pleura. They are characterized by their cuboidal to squamous epithelial shape and the presence of microvilli on their surface, a feature aiding in fluid and solute exchange between the pleura and the lungs. +The primary function of mesothelial cells of visceral pleura is to secrete a lubricating serous fluid to facilitate smooth, frictionless lung movement within the thoracic cavity during respiration. This helps in the prevention of trauma or damage stemming from the constant rubbing of the lung tissue against the chest wall, hence playing a pivotal role in maintaining respiratory function. Besides fluid secretion, these cells have an essential role in the transportation of fluids and particles across the pleura, as well as in inflammation, wound healing, and tissue repair processes within the pleura. +Mesothelial cells of visceral pleura are notably implicated in the development of pleural diseases such as pleural effusion and pleural mesothelioma, a rare and aggressive form of cancer primarily linked with exposure to asbestos. Alterations, such as hyperplasia or metaplasia, may occur in these mesothelial cells under pathological conditions."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1152/physrev.00026.2003"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1371/journal.pone.0276978"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.3389/fphys.2014.00221"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.3390/jdb7020007"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1016/S1357-2725(03)00242-5"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### metallothionein-positive alveolar macrophage `http://purl.obolibrary.org/obo/CL_4033042` + +#### Added +- [metallothionein-positive alveolar macrophage](http://purl.obolibrary.org/obo/CL_4033042) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl/cl-base#cellxgene_subset) + +- [metallothionein-positive alveolar macrophage](http://purl.obolibrary.org/obo/CL_4033042) [comment](http://www.w3.org/2000/01/rdf-schema#comment) "The marker set HMOX1, HPGD can identify the Human cell type metallothionein-positive alveolar macrophage in the Lung with a confidence of 0.41 (NS-Forest FBeta value)."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://doi.org/10.5281/zenodo.11165918"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [metallothionein-positive alveolar macrophage](http://purl.obolibrary.org/obo/CL_4033042) SubClassOf [RO_0015004](http://purl.obolibrary.org/obo/RO_0015004) some [CLM_1000005](http://purl.obolibrary.org/obo/CLM_1000005) + + +### metanephric mesenchyme stem cell `http://purl.obolibrary.org/obo/CL_0000324` + +#### Added +- [metanephric mesenchyme stem cell](http://purl.obolibrary.org/obo/CL_0000324) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl/cl-base#cellxgene_subset) + + +### microfold cell of epithelium of small intestine `http://purl.obolibrary.org/obo/CL_1000353` + +#### Added +- [microfold cell of epithelium of small intestine](http://purl.obolibrary.org/obo/CL_1000353) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://cellxgene.cziscience.com/cellguide/CL_1000353"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [microfold cell of epithelium of small intestine](http://purl.obolibrary.org/obo/CL_1000353) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Microfold cells, also widely known as M cells, are a distinct type of epithelial cell found in the gut, including the small intestine, specifically within the Peyer’s patches, a component of the gut-associated lymphoid tissue (GALT). M cells play a crucial role in the immune response within the intestine environment. +These cells are characterized by microfolds (short microvilli, which give them their name), a reduced, thin glycocalyx, and a deeply invaginated basolateral membrane next to immune cells such as B cells, T cells, and macrophages, and DCs. +These features allow the M cells to form the first point of contact between the gut lumen and the intestinal immune system. They are well-regulated gateways that capture and transport antigens, such as bacteria, viruses, and other foreign substances found in the lumen, to the underlying cells of the immune system. This specialized transport mechanism, called ‘transcytosis’, involves engulfment of these antigens from the apical side, transport across their cytoplasm, and release on the basolateral side of the cells, where immune responses can be initiated. +Furthermore, M cells have complex interactions with members of the gut microbiota and other immune cells, making them essential for maintaining gut homeostasis. This cross-talk shapes the diversity and makeup of the gut microbiota, subsequently having a substantial impact on the host's health. In certain situations, pathogenic organisms can exploit the transcytosis mechanism to infiltrate the host's system, causing various infectious diseases. +The overarching significance of M cells in the small intestine lies in their role of surveillance and protection against a wide range of potentially harmful pathogens, while also facilitating beneficial interactions with commensal microbes."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1111/j.1574-695X.2007.00359.x"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1038/mi.2013.30"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1093/jb/mvv121"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.3389/fimmu.2019.01499"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### microfold cell of epithelium proper of appendix `http://purl.obolibrary.org/obo/CL_1000359` +#### Removed +- [microfold cell of epithelium proper of appendix](http://purl.obolibrary.org/obo/CL_1000359) SubClassOf [BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0009697](http://purl.obolibrary.org/obo/UBERON_0009697) + + + +### microglial cell `http://purl.obolibrary.org/obo/CL_0000129` +#### Removed +- [microglial cell](http://purl.obolibrary.org/obo/CL_0000129) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) + +#### Added +- [microglial cell](http://purl.obolibrary.org/obo/CL_0000129) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://cellxgene.cziscience.com/cellguide/CL_0000129"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [microglial cell](http://purl.obolibrary.org/obo/CL_0000129) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Microglial cells, sometimes referred to as microglia, are a type of glial cell that primarily exist within the central nervous system (CNS), notably in the brain and the spinal cord. Classified among the resident immune cells, microglial cells represent about 10% of all cells found within the CNS. These cells are derived from progenitor cells in the yolk sac, which differentiates them from other types of glial cells (such as astrocytes and oligodendrocytes) that are derived from neuroectodermal cell lineages. +The primary role of microglial cells is to act as the first and main active form of immune defense in the CNS. They express a vast repertoire of pattern recognition receptors, which allow them to sense and eliminate microbes invading the CNS parenchyma. They represent one of the macrophage populations of the CNS and are responsible for phagocytosis (engulfing and destroying cellular waste or pathogens) in the neural environment. +Microglial cells are particularly responsive to pathogens and injuries and change their morphology in reaction to inflammation or insult: In the normal state they are characterized by a ramified shape with small processes; in response to stimuli, some microglia mature and change to an amoeboid shape. +Beyond their macrophagic activity, they also perform synaptic pruning during brain development, eliminate unnecessarily produced neurons, and facilitate tissue regeneration and repair. they play integral roles in regulating neural development and supporting cell survival and are important for maintaining tissue homeostasis. +While their protective role generally benefits the brain, their over-activation can occasionally lead to neuro-inflammatory diseases, underlining the importance of balanced microglial cell functions. They have been extensively studied for their association with neurodegenerative diseases, such as Alzheimer's disease, Parkinson's disease, and multiple sclerosis."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1016/j.tins.2021.11.001"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1038/nri3086"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1016/j.cell.2019.08.053"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.3389/fnins.2021.742065"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1016/j.conb.2022.102674"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### microvascular endothelial cell `http://purl.obolibrary.org/obo/CL_2000008` + +#### Added +- [microvascular endothelial cell](http://purl.obolibrary.org/obo/CL_2000008) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl/cl-base#cellxgene_subset) + + +### midbrain-derived inhibitory neuron `http://purl.obolibrary.org/obo/CL_4023079` +#### Removed +- [midbrain-derived inhibitory neuron](http://purl.obolibrary.org/obo/CL_4023079) SubClassOf [neuron](http://purl.obolibrary.org/obo/CL_0000540) + +#### Added +- [midbrain-derived inhibitory neuron](http://purl.obolibrary.org/obo/CL_4023079) SubClassOf [central nervous system neuron](http://purl.obolibrary.org/obo/CL_2000029) + + +### middle primary motoneuron `http://purl.obolibrary.org/obo/CL_4042041` + +#### Added +- [middle primary motoneuron](http://purl.obolibrary.org/obo/CL_4042041) [label](http://www.w3.org/2000/01/rdf-schema#label) "middle primary motoneuron"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [middle primary motoneuron](http://purl.obolibrary.org/obo/CL_4042041) [date](http://purl.org/dc/terms/date) "2024-11-13T13:39:28Z"^^[dateTime](http://www.w3.org/2001/XMLSchema#dateTime) + +- [middle primary motoneuron](http://purl.obolibrary.org/obo/CL_4042041) [id](http://www.geneontology.org/formats/oboInOwl#id) "CL:4042041"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [middle primary motoneuron](http://purl.obolibrary.org/obo/CL_4042041) [contributor](http://purl.org/dc/terms/contributor) [0000-0002-0098-8958](https://orcid.org/0000-0002-0098-8958) + +- [middle primary motoneuron](http://purl.obolibrary.org/obo/CL_4042041) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A type of primary motor neuron located in the middle region of the spinal cord. This primary motor neuron type is characterized by their distinct axonal pathways that innervate the middle trunk muscles."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:35431796"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:3746410"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [middle primary motoneuron](http://purl.obolibrary.org/obo/CL_4042041) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0005179"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [middle primary motoneuron](http://purl.obolibrary.org/obo/CL_4042041) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "MiP"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003000](http://purl.obolibrary.org/obo/OMO_0003000) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:3746410"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- Class: [middle primary motoneuron](http://purl.obolibrary.org/obo/CL_4042041) + +- [middle primary motoneuron](http://purl.obolibrary.org/obo/CL_4042041) SubClassOf [primary motor neuron (sensu Teleostei)](http://purl.obolibrary.org/obo/CL_0000533) + + +### midget ganglion cell of retina `http://purl.obolibrary.org/obo/CL_4023188` + +#### Added +- [midget ganglion cell of retina](http://purl.obolibrary.org/obo/CL_4023188) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl/cl-base#cellxgene_subset) + + +### molecular layer interneuron `http://purl.obolibrary.org/obo/CL_4042035` + +#### Added +- [molecular layer interneuron](http://purl.obolibrary.org/obo/CL_4042035) [date](http://purl.org/dc/terms/date) "2024-10-31T15:55:31Z"^^[dateTime](http://www.w3.org/2001/XMLSchema#dateTime) + +- [molecular layer interneuron](http://purl.obolibrary.org/obo/CL_4042035) [id](http://www.geneontology.org/formats/oboInOwl#id) "CL:4042035"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [molecular layer interneuron](http://purl.obolibrary.org/obo/CL_4042035) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A type of cerebellar inhibitory GABAergic interneuron that is located in the molecular layer of the cerebellum. This cell type inhibits Purkinje cells and other molecular layer interneurons. This interneuron plays a crucial role in regulating cerebellar output through feedforward inhibition and is characterized by its fast-spiking properties."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:30742002"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:34616064"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:33075461"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:38692278"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [molecular layer interneuron](http://purl.obolibrary.org/obo/CL_4042035) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "MLI"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "OMO:0003000"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:33075461"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [molecular layer interneuron](http://purl.obolibrary.org/obo/CL_4042035) [contributor](http://purl.org/dc/terms/contributor) [0000-0002-0098-8958](https://orcid.org/0000-0002-0098-8958) + +- [molecular layer interneuron](http://purl.obolibrary.org/obo/CL_4042035) [label](http://www.w3.org/2000/01/rdf-schema#label) "molecular layer interneuron"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- Class: [molecular layer interneuron](http://purl.obolibrary.org/obo/CL_4042035) + +- [molecular layer interneuron](http://purl.obolibrary.org/obo/CL_4042035) SubClassOf [cerebellar neuron](http://purl.obolibrary.org/obo/CL_1001611) + + +### monoblast `http://purl.obolibrary.org/obo/CL_0000040` +#### Removed +- [monoblast](http://purl.obolibrary.org/obo/CL_0000040) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) + + + +### monocyte-derived dendritic cell `http://purl.obolibrary.org/obo/CL_0011031` + +#### Added +- [monocyte-derived dendritic cell](http://purl.obolibrary.org/obo/CL_0011031) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl/cl-base#cellxgene_subset) + + +### mononuclear phagocyte `http://purl.obolibrary.org/obo/CL_0000113` +#### Removed +- [mononuclear phagocyte](http://purl.obolibrary.org/obo/CL_0000113) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +Mononuclear phagocytes are immune cells that form a critical part of the body's innate immune system, the body's first line of defense against infections. Mononuclear phagocytes are characterized by the presence of a single, large nucleus. The ‘Mononuclear Phagocyte System’ nomenclature was introduced to distinguish mononuclear monocytes and macrophages from other cells with multiple nuclei. However, the cells within the mononuclear phagocyte system represent a highly heterogeneous group, all of which are able to perform highly efficient phagocytosis - engulfing and digesting microbes and cellular debris to fight infections and to maintain normal tissue homeostasis. +In addition to phagocytosis, mononuclear phagocytes also secrete chemical compounds to recruit other immune cells to a site of infection. These cells produce different types of signaling molecules, including cytokines, chemokines, and reactive oxygen species, triggering a cascade of responses to ensure rapid and efficient containment and neutralization of invading pathogens. These cells are also involved in antigen presentation, a process essential for stimulating an adaptive immune response. They can process and present antigens to T cells, thereby linking the innate and adaptive immune responses. +Mononuclear phagocytes play key roles in tissue repair and remodeling. After infection or injury, these cells help in the clearance of dead cells and debris, a crucial step in the initiation of tissue remodeling and the resolution of inflammation. Overall, mononuclear phagocytes are versatile cells that have tailored their functions to meet the unique challenges of different tissues within the body. They are pivotal in homeostasis, immunity, and inflammation, making them important aspects in a range of human diseases including infection, autoimmunity, and cancer."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1016/j.coi.2005.11.008"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1038/nri3087"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.3389/fimmu.2019.01893"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [mononuclear phagocyte](http://purl.obolibrary.org/obo/CL_0000113) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Mononuclear phagocytes are immune cells that form a critical part of the body's innate immune system, the body's first line of defense against infections. Mononuclear phagocytes are characterized by the presence of a single, large nucleus. The ‘Mononuclear Phagocyte System’ nomenclature was introduced to distinguish mononuclear monocytes and macrophages from other cells with multiple nuclei. However, the cells within the mononuclear phagocyte system represent a highly heterogeneous group, all of which are able to perform highly efficient phagocytosis - engulfing and digesting microbes and cellular debris to fight infections and to maintain normal tissue homeostasis. +In addition to phagocytosis, mononuclear phagocytes also secrete chemical compounds to recruit other immune cells to a site of infection. These cells produce different types of signaling molecules, including cytokines, chemokines, and reactive oxygen species, triggering a cascade of responses to ensure rapid and efficient containment and neutralization of invading pathogens. These cells are also involved in antigen presentation, a process essential for stimulating an adaptive immune response. They can process and present antigens to T cells, thereby linking the innate and adaptive immune responses. +Mononuclear phagocytes play key roles in tissue repair and remodeling. After infection or injury, these cells help in the clearance of dead cells and debris, a crucial step in the initiation of tissue remodeling and the resolution of inflammation. Overall, mononuclear phagocytes are versatile cells that have tailored their functions to meet the unique challenges of different tissues within the body. They are pivotal in homeostasis, immunity, and inflammation, making them important aspects in a range of human diseases including infection, autoimmunity, and cancer."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1016/j.coi.2005.11.008"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1038/nri3087"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.3389/fimmu.2019.01893"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### monostratified amacrine cell `http://purl.obolibrary.org/obo/CL_0004226` +#### Removed +- [monostratified amacrine cell](http://purl.obolibrary.org/obo/CL_0004226) SubClassOf [RO_0000053](http://purl.obolibrary.org/obo/RO_0000053) some [PATO_0070063](http://purl.obolibrary.org/obo/PATO_0070063) + +#### Added +- [monostratified amacrine cell](http://purl.obolibrary.org/obo/CL_0004226) SubClassOf [monostratified cell](http://purl.obolibrary.org/obo/CL_0004246) + + +### mucous cell of stomach `http://purl.obolibrary.org/obo/CL_0002180` +#### Removed +- [mucous cell of stomach](http://purl.obolibrary.org/obo/CL_0002180) EquivalentTo [epithelial cell](http://purl.obolibrary.org/obo/CL_0000066) and ([BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0000945](http://purl.obolibrary.org/obo/UBERON_0000945)) and ([RO_0002215](http://purl.obolibrary.org/obo/RO_0002215) some [GO_0070254](http://purl.obolibrary.org/obo/GO_0070254)) + +- [mucous cell of stomach](http://purl.obolibrary.org/obo/CL_0002180) SubClassOf [glandular epithelial cell of stomach](http://purl.obolibrary.org/obo/CL_0002659) + +#### Added +- [mucous cell of stomach](http://purl.obolibrary.org/obo/CL_0002180) EquivalentTo [epithelial cell](http://purl.obolibrary.org/obo/CL_0000066) and ([BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0001276](http://purl.obolibrary.org/obo/UBERON_0001276)) and ([RO_0002215](http://purl.obolibrary.org/obo/RO_0002215) some [GO_0070254](http://purl.obolibrary.org/obo/GO_0070254)) + +- [mucous cell of stomach](http://purl.obolibrary.org/obo/CL_0002180) SubClassOf [epithelial cell of stomach](http://purl.obolibrary.org/obo/CL_0002178) + +- [mucous cell of stomach](http://purl.obolibrary.org/obo/CL_0002180) SubClassOf [secretory epithelial cell](http://purl.obolibrary.org/obo/CL_1100001) + + +### mucous neck cell of gastric gland `http://purl.obolibrary.org/obo/CL_0002181` + +#### Added +- [mucous neck cell of gastric gland](http://purl.obolibrary.org/obo/CL_0002181) SubClassOf [glandular epithelial cell of stomach](http://purl.obolibrary.org/obo/CL_0002659) + + +### mucus secreting cell `http://purl.obolibrary.org/obo/CL_0000319` +#### Removed +- [mucus secreting cell](http://purl.obolibrary.org/obo/CL_0000319) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "Any secretory cell that is capable of some mucus secretion."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBC:Autogenerated"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [mucus secreting cell](http://purl.obolibrary.org/obo/CL_0000319) EquivalentTo [secretory cell](http://purl.obolibrary.org/obo/CL_0000151) and ([RO_0002215](http://purl.obolibrary.org/obo/RO_0002215) some [GO_0070254](http://purl.obolibrary.org/obo/GO_0070254)) + +#### Added +- [mucus secreting cell](http://purl.obolibrary.org/obo/CL_0000319) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "Any cell that is capable of some mucus secretion."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBC:Autogenerated"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [mucus secreting cell](http://purl.obolibrary.org/obo/CL_0000319) EquivalentTo [cell](http://purl.obolibrary.org/obo/CL_0000000) and ([RO_0002215](http://purl.obolibrary.org/obo/RO_0002215) some [GO_0070254](http://purl.obolibrary.org/obo/GO_0070254)) + + +### mucus secreting cell of bronchus submucosal gland `http://purl.obolibrary.org/obo/CL_4033022` + +#### Added +- [mucus secreting cell of bronchus submucosal gland](http://purl.obolibrary.org/obo/CL_4033022) [comment](http://www.w3.org/2000/01/rdf-schema#comment) "The marker set BPIFB2 can identify the Human cell type mucus secreting cell of bronchus submucosal gland in the Lung with a confidence of 0.93 (NS-Forest FBeta value)."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://doi.org/10.5281/zenodo.11165918"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [mucus secreting cell of bronchus submucosal gland](http://purl.obolibrary.org/obo/CL_4033022) SubClassOf [RO_0015004](http://purl.obolibrary.org/obo/RO_0015004) some [CLM_1000053](http://purl.obolibrary.org/obo/CLM_1000053) + + +### mucus secreting cell of tracheobronchial tree submucosal gland `http://purl.obolibrary.org/obo/CL_4033037` + +#### Added +- [mucus secreting cell of tracheobronchial tree submucosal gland](http://purl.obolibrary.org/obo/CL_4033037) SubClassOf [glandular secretory epithelial cell](http://purl.obolibrary.org/obo/CL_0000150) + + +### multiciliated columnar cell of tracheobronchial tree `http://purl.obolibrary.org/obo/CL_0002145` +#### Removed +- [multiciliated columnar cell of tracheobronchial tree](http://purl.obolibrary.org/obo/CL_0002145) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +Ciliated columnar cells of the tracheobronchial tree compose the inner lining of the tracheobronchial tree, the system of airways consisting of trachea, bronchi and bronchioles that allow passage of air into the lungs, where gas exchange occurs. A defining feature of these endo-epithelial cells are the tiny hair-like structures covering their surface, known as cilia. The nucleus is located at the base of the cell, and the area above it is rich in mitochondria and well-developed endoplasmic reticulum, both crucial for the energy-intensive process of cilia operation. +The primary function of these ciliated cells is to keep the respiratory tract clean via mucociliary clearance or the respiratory escalator. These cells create a two-layered 'coat': The lower "sol" layer is watery where the cilia can beat in coordinated waves, and the upper "gel" layer is thick and sticky, trapping inhaled particles, such as dust, bacteria, viruses, and other potentially harmful substances. This rhythmical beating of the cilia then moves the mucus and trapped particles upwards and out of the respiratory tract, which is then either coughed out or swallowed. +Damage or dysfunction of these ciliated cells, as seen in diseases such as primary ciliary dyskinesia, cystic fibrosis, or chronic bronchitis, may lead to reduced or ineffective mucociliary clearance and an increased susceptibility to respiratory infections."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1146/annurev-physiol-021014-071931"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1159/000196486"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1152/ajplung.00329.2019"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1101/cshperspect.a028241"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [multiciliated columnar cell of tracheobronchial tree](http://purl.obolibrary.org/obo/CL_0002145) [comment](http://www.w3.org/2000/01/rdf-schema#comment) "These cells possess numerous cilia on their surface, typically ranging from 200 to 300 per cell. The cilia vary in length, measuring between 6 to 7 μm in the upper airways (trachea) and becoming shorter, around 4 μm, in the smaller airways (terminal bronchioles). These cells form a two-layered 'coat' in the airway: the lower 'sol' layer is watery, allowing the cilia to beat in coordinated waves, while the upper 'gel' layer is thick and sticky, trapping inhaled particles."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://doi.org/10.1016/B978-032304048-8.50071-2"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:25386990"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [multiciliated columnar cell of tracheobronchial tree](http://purl.obolibrary.org/obo/CL_0002145) [label](http://www.w3.org/2000/01/rdf-schema#label) "ciliated columnar cell of tracheobronchial tree"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [multiciliated columnar cell of tracheobronchial tree](http://purl.obolibrary.org/obo/CL_0002145) SubClassOf [multiciliated epithelial cell](http://purl.obolibrary.org/obo/CL_0005012) + +#### Added +- [multiciliated columnar cell of tracheobronchial tree](http://purl.obolibrary.org/obo/CL_0002145) [label](http://www.w3.org/2000/01/rdf-schema#label) "multiciliated columnar cell of tracheobronchial tree"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [multiciliated columnar cell of tracheobronchial tree](http://purl.obolibrary.org/obo/CL_0002145) [comment](http://www.w3.org/2000/01/rdf-schema#comment) "The marker set C1orf194, MS4A8 can identify the Human cell type ciliated columnar cell of tracheobronchial tree in the Lung with a confidence of 0.86 (NS-Forest FBeta value). These cells possess numerous cilia on their surface, typically ranging from 200 to 300 per cell. The cilia vary in length, measuring between 6 to 7 μm in the upper airways (trachea) and becoming shorter, around 4 μm, in the smaller airways (terminal bronchioles). These cells form a two-layered 'coat' in the airway: the lower 'sol' layer is watery, allowing the cilia to beat in coordinated waves, while the upper 'gel' layer is thick and sticky, trapping inhaled particles."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://doi.org/10.1016/B978-032304048-8.50071-2"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://doi.org/10.5281/zenodo.11165918"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:25386990"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [multiciliated columnar cell of tracheobronchial tree](http://purl.obolibrary.org/obo/CL_0002145) [has_exact_synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "ciliated columnar cell of tracheobronchial tree"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [multiciliated columnar cell of tracheobronchial tree](http://purl.obolibrary.org/obo/CL_0002145) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Ciliated columnar cells of the tracheobronchial tree compose the inner lining of the tracheobronchial tree, the system of airways consisting of trachea, bronchi and bronchioles that allow passage of air into the lungs, where gas exchange occurs. A defining feature of these endo-epithelial cells are the tiny hair-like structures covering their surface, known as cilia. The nucleus is located at the base of the cell, and the area above it is rich in mitochondria and well-developed endoplasmic reticulum, both crucial for the energy-intensive process of cilia operation. +The primary function of these ciliated cells is to keep the respiratory tract clean via mucociliary clearance or the respiratory escalator. These cells create a two-layered 'coat': The lower "sol" layer is watery where the cilia can beat in coordinated waves, and the upper "gel" layer is thick and sticky, trapping inhaled particles, such as dust, bacteria, viruses, and other potentially harmful substances. This rhythmical beating of the cilia then moves the mucus and trapped particles upwards and out of the respiratory tract, which is then either coughed out or swallowed. +Damage or dysfunction of these ciliated cells, as seen in diseases such as primary ciliary dyskinesia, cystic fibrosis, or chronic bronchitis, may lead to reduced or ineffective mucociliary clearance and an increased susceptibility to respiratory infections."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1146/annurev-physiol-021014-071931"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1159/000196486"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1152/ajplung.00329.2019"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1101/cshperspect.a028241"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [multiciliated columnar cell of tracheobronchial tree](http://purl.obolibrary.org/obo/CL_0002145) EquivalentTo [columnar/cuboidal epithelial cell](http://purl.obolibrary.org/obo/CL_0000075) and ([BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0008397](http://purl.obolibrary.org/obo/UBERON_0008397)) and ([BFO_0000051](http://purl.obolibrary.org/obo/BFO_0000051) some [GO_0031514](http://purl.obolibrary.org/obo/GO_0031514)) and ([RO_0000053](http://purl.obolibrary.org/obo/RO_0000053) some [PATO_0010007](http://purl.obolibrary.org/obo/PATO_0010007)) + +- [multiciliated columnar cell of tracheobronchial tree](http://purl.obolibrary.org/obo/CL_0002145) SubClassOf [RO_0015004](http://purl.obolibrary.org/obo/RO_0015004) some [CLM_1000041](http://purl.obolibrary.org/obo/CLM_1000041) + + +### multiciliated ependymal cell `http://purl.obolibrary.org/obo/CL_4052001` +#### Removed +- [multiciliated ependymal cell](http://purl.obolibrary.org/obo/CL_4052001) SubClassOf [BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0005357](http://purl.obolibrary.org/obo/UBERON_0005357) + +#### Added +- [multiciliated ependymal cell](http://purl.obolibrary.org/obo/CL_4052001) EquivalentTo [columnar/cuboidal epithelial cell](http://purl.obolibrary.org/obo/CL_0000075) and ([BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0004670](http://purl.obolibrary.org/obo/UBERON_0004670)) and ([BFO_0000051](http://purl.obolibrary.org/obo/BFO_0000051) some [GO_0031514](http://purl.obolibrary.org/obo/GO_0031514)) and ([RO_0000053](http://purl.obolibrary.org/obo/RO_0000053) some [PATO_0010007](http://purl.obolibrary.org/obo/PATO_0010007)) + + +### multiciliated epithelial cell `http://purl.obolibrary.org/obo/CL_0005012` +#### Removed +- [multiciliated epithelial cell](http://purl.obolibrary.org/obo/CL_0005012) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +The multi-ciliated epithelial cell are terminally differentiated epithelia that line brain ventricles, the respiratory tract and parts of the female and male reproductive organs in animals, playing critical roles in the maintenance of homeostasis through ciliary motion. They are characterized by the presence of hundreds of motile cilia, hair-like microtubule-based organelles that beat in a coordinated fashion to direct fluid flow over the cell surface. +Multi-ciliated epithelial cells have fundamental roles in the proper functioning of many organ systems. In the respiratory system, they line the airways and orchestrate the coordinated movement of mucus, effectively clearing the airways of inhaled particles and pathogens. These cells are also vital in the ventricular system of the brain where they facilitate cerebrospinal fluid circulation, thus contributing to the maintenance of the brain's microenvironment. In the fallopian tube, multi-ciliated epithelial cells aid in the transport of oocytes from the ovary to the uterus, a process crucial to reproduction. +The formation and function of multi-ciliated epithelial cells is a highly regulated process that involves several stages of development including cell specification, centriole multiplication, and ciliogenesis. Any disruption in these processes can result in dysfunctional or decreased numbers of cilia, which can lead to a myriad of health issues, ranging from chronic respiratory infections to infertility."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1101/cshperspect.a028233"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1016/j.cub.2014.08.047"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1038/nrm.2017.21"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [multiciliated epithelial cell](http://purl.obolibrary.org/obo/CL_0005012) [label](http://www.w3.org/2000/01/rdf-schema#label) "multi-ciliated epithelial cell"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [multiciliated epithelial cell](http://purl.obolibrary.org/obo/CL_0005012) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +The multi-ciliated epithelial cell are terminally differentiated epithelia that line brain ventricles, the respiratory tract and parts of the female and male reproductive organs in animals, playing critical roles in the maintenance of homeostasis through ciliary motion. They are characterized by the presence of hundreds of motile cilia, hair-like microtubule-based organelles that beat in a coordinated fashion to direct fluid flow over the cell surface. +Multi-ciliated epithelial cells have fundamental roles in the proper functioning of many organ systems. In the respiratory system, they line the airways and orchestrate the coordinated movement of mucus, effectively clearing the airways of inhaled particles and pathogens. These cells are also vital in the ventricular system of the brain where they facilitate cerebrospinal fluid circulation, thus contributing to the maintenance of the brain's microenvironment. In the fallopian tube, multi-ciliated epithelial cells aid in the transport of oocytes from the ovary to the uterus, a process crucial to reproduction. +The formation and function of multi-ciliated epithelial cells is a highly regulated process that involves several stages of development including cell specification, centriole multiplication, and ciliogenesis. Any disruption in these processes can result in dysfunctional or decreased numbers of cilia, which can lead to a myriad of health issues, ranging from chronic respiratory infections to infertility."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1101/cshperspect.a028233"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1016/j.cub.2014.08.047"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1038/nrm.2017.21"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [multiciliated epithelial cell](http://purl.obolibrary.org/obo/CL_0005012) [has_exact_synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "multi-ciliated epithelial cell"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [multiciliated epithelial cell](http://purl.obolibrary.org/obo/CL_0005012) [label](http://www.w3.org/2000/01/rdf-schema#label) "multiciliated epithelial cell"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### multiciliated epithelial cell of the bronchus `http://purl.obolibrary.org/obo/CL_0002332` +#### Removed +- [multiciliated epithelial cell of the bronchus](http://purl.obolibrary.org/obo/CL_0002332) [label](http://www.w3.org/2000/01/rdf-schema#label) "ciliated cell of the bronchus"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [multiciliated epithelial cell of the bronchus](http://purl.obolibrary.org/obo/CL_0002332) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A ciliated cell of the bronchus."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:18757316"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:tfm"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [multiciliated epithelial cell of the bronchus](http://purl.obolibrary.org/obo/CL_0002332) EquivalentTo [ciliated cell](http://purl.obolibrary.org/obo/CL_0000064) and ([BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0002031](http://purl.obolibrary.org/obo/UBERON_0002031)) + +#### Added +- [multiciliated epithelial cell of the bronchus](http://purl.obolibrary.org/obo/CL_0002332) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A multi-ciliated epithelial cell located in the bronchus epithelium, characterized by a columnar shape and motile cilia on its apical surface."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:18757316"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:tfm"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [multiciliated epithelial cell of the bronchus](http://purl.obolibrary.org/obo/CL_0002332) [has_exact_synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "ciliated epithelial cell of the bronchus"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [multiciliated epithelial cell of the bronchus](http://purl.obolibrary.org/obo/CL_0002332) [label](http://www.w3.org/2000/01/rdf-schema#label) "multiciliated epithelial cell of the bronchus"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [multiciliated epithelial cell of the bronchus](http://purl.obolibrary.org/obo/CL_0002332) EquivalentTo [columnar/cuboidal epithelial cell](http://purl.obolibrary.org/obo/CL_0000075) and ([BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0002031](http://purl.obolibrary.org/obo/UBERON_0002031)) and ([BFO_0000051](http://purl.obolibrary.org/obo/BFO_0000051) some [GO_0031514](http://purl.obolibrary.org/obo/GO_0031514)) and ([RO_0000053](http://purl.obolibrary.org/obo/RO_0000053) some [PATO_0010007](http://purl.obolibrary.org/obo/PATO_0010007)) + + +### multipolar neuron `http://purl.obolibrary.org/obo/CL_0000104` +#### Removed +- [multipolar neuron](http://purl.obolibrary.org/obo/CL_0000104) EquivalentTo [neuron](http://purl.obolibrary.org/obo/CL_0000540) and ([RO_0000053](http://purl.obolibrary.org/obo/RO_0000053) some [PATO_0070026](http://purl.obolibrary.org/obo/PATO_0070026)) + +- [multipolar neuron](http://purl.obolibrary.org/obo/CL_0000104) SubClassOf [neuron](http://purl.obolibrary.org/obo/CL_0000540) + +#### Added +- [multipolar neuron](http://purl.obolibrary.org/obo/CL_0000104) SubClassOf [central nervous system neuron](http://purl.obolibrary.org/obo/CL_2000029) + + +### myelinating Schwann cell `http://purl.obolibrary.org/obo/CL_0000218` + +#### Added +- [myelinating Schwann cell](http://purl.obolibrary.org/obo/CL_0000218) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl/cl-base#cellxgene_subset) + + +### myeloid suppressor cell `http://purl.obolibrary.org/obo/CL_0000889` +#### Removed +- [myeloid suppressor cell](http://purl.obolibrary.org/obo/CL_0000889) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) + +#### Added +- [myeloid suppressor cell](http://purl.obolibrary.org/obo/CL_0000889) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl/cl-base#cellxgene_subset) + + +### myoblast `http://purl.obolibrary.org/obo/CL_0000056` + +#### Added +- [myoblast](http://purl.obolibrary.org/obo/CL_0000056) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl/cl-base#cellxgene_subset) + + +### myocyte of sinoatrial node `http://purl.obolibrary.org/obo/CL_1000409` + +#### Added +- [myocyte of sinoatrial node](http://purl.obolibrary.org/obo/CL_1000409) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl/cl-base#cellxgene_subset) + + +### myometrial cell `http://purl.obolibrary.org/obo/CL_0002366` + +#### Added +- [myometrial cell](http://purl.obolibrary.org/obo/CL_0002366) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Myometrial cells are specialized smooth muscle cells located in the myometrium, the middle layer of the uterine wall. Unique to female reproductive physiology, they play a key role in pregnancy and childbirth. +These cells are distinctive in their capability to substantially increase in size and number during pregnancy, preparing the uterus to accommodate the growing fetus. As pregnancy progresses, myometrial cells demonstrate a progressive growth in uterine mass through cellular hypertrophy. They are also responsible for the production of extracellular matrix proteins like collagen, which aids in supporting cell structure and function, further facilitating uterine enlargement. +During childbirth, myometrial cells are responsible for the expansion and contraction of the uterus. They can propagate action potentials and generate considerable force, which is critical to their function in the reproductive system. After pregnancy, these cells can reduce in size, a process known as uterine involution. Given the important role these cells play in female reproductive physiology, dysregulation of the myometrial cell function can contribute to uterine pathologies such as uterine fibroids."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1177/1535370220938741"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://www.sciencedirect.com/topics/veterinary-science-and-veterinary-medicine/myometrium"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1093/humupd/dmr031"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1073/pnas.070447210"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://www.sciencedirect.com/topics/medicine-and-dentistry/uterine-contraction"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [myometrial cell](http://purl.obolibrary.org/obo/CL_0002366) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://cellxgene.cziscience.com/cellguide/CL_0002366"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### myotendinous junction nucleus `http://purl.obolibrary.org/obo/CL_4052024` + +#### Added +- [myotendinous junction nucleus](http://purl.obolibrary.org/obo/CL_4052024) [contributor](http://purl.org/dc/terms/contributor) [0009-0000-8480-9277](https://orcid.org/0009-0000-8480-9277) + +- [myotendinous junction nucleus](http://purl.obolibrary.org/obo/CL_4052024) [id](http://www.geneontology.org/formats/oboInOwl#id) "CL:4052024"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [myotendinous junction nucleus](http://purl.obolibrary.org/obo/CL_4052024) [has_exact_synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "myotendinous junction myonuclei"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:33311464"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003004](http://purl.obolibrary.org/obo/OMO_0003004) + +- [myotendinous junction nucleus](http://purl.obolibrary.org/obo/CL_4052024) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "MTJ nucleus"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003000](http://purl.obolibrary.org/obo/OMO_0003000) + +- [myotendinous junction nucleus](http://purl.obolibrary.org/obo/CL_4052024) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A specialized muscle nucleus that is part of an extrafusal muscle fiber and overlaps the muscle-tendon junction, where muscle fibers connect to tendons. Characterized by a distinct transcriptional profile with the expression of genes like COL22A1, this myonucleus supports the structural integrity and function of the junction, playing a key role in transmitting the force generated by muscle contraction to the tendon."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:33311457"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:33311464"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:38398025"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [myotendinous junction nucleus](http://purl.obolibrary.org/obo/CL_4052024) [date](http://purl.org/dc/terms/date) "2024-10-30T13:47:39Z"^^[dateTime](http://www.w3.org/2001/XMLSchema#dateTime) + +- [myotendinous junction nucleus](http://purl.obolibrary.org/obo/CL_4052024) [label](http://www.w3.org/2000/01/rdf-schema#label) "myotendinous junction nucleus"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [myotendinous junction nucleus](http://purl.obolibrary.org/obo/CL_4052024) [has_exact_synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "myotendinous junction nuclei"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:33311457"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003004](http://purl.obolibrary.org/obo/OMO_0003004) + +- [myotendinous junction nucleus](http://purl.obolibrary.org/obo/CL_4052024) [contributor](http://purl.org/dc/terms/contributor) [X](https://orcid.org/0009-0001-6947-615X) + +- Class: [myotendinous junction nucleus](http://purl.obolibrary.org/obo/CL_4052024) + +- [myotendinous junction nucleus](http://purl.obolibrary.org/obo/CL_4052024) EquivalentTo [GO_0005634](http://purl.obolibrary.org/obo/GO_0005634) and ([BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [extrafusal muscle fiber](http://purl.obolibrary.org/obo/CL_0008046)) and ([RO_0002131](http://purl.obolibrary.org/obo/RO_0002131) some [GO_0005927](http://purl.obolibrary.org/obo/GO_0005927)) + +- [myotendinous junction nucleus](http://purl.obolibrary.org/obo/CL_4052024) SubClassOf [RO_0002131](http://purl.obolibrary.org/obo/RO_0002131) some [GO_0005927](http://purl.obolibrary.org/obo/GO_0005927) + +- [myotendinous junction nucleus](http://purl.obolibrary.org/obo/CL_4052024) SubClassOf [GO_0005634](http://purl.obolibrary.org/obo/GO_0005634) + +- [myotendinous junction nucleus](http://purl.obolibrary.org/obo/CL_4052024) SubClassOf [BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [extrafusal muscle fiber](http://purl.obolibrary.org/obo/CL_0008046) + + +### myotube `http://purl.obolibrary.org/obo/CL_0002372` + +#### Added +- [myotube](http://purl.obolibrary.org/obo/CL_0002372) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl/cl-base#cellxgene_subset) + + +### nasal mucosa goblet cell `http://purl.obolibrary.org/obo/CL_0002480` + +#### Added +- [nasal mucosa goblet cell](http://purl.obolibrary.org/obo/CL_0002480) [RO_0002175](http://purl.obolibrary.org/obo/RO_0002175) [NCBITaxon_9606](http://purl.obolibrary.org/obo/NCBITaxon_9606) + +- [nasal mucosa goblet cell](http://purl.obolibrary.org/obo/CL_0002480) [comment](http://www.w3.org/2000/01/rdf-schema#comment) "The marker set LYPD2, MUC5AC can identify the Human cell type nasal mucosa goblet cell in the Lung with a confidence of 0.81 (NS-Forest FBeta value)."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://doi.org/10.5281/zenodo.11165918"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [nasal mucosa goblet cell](http://purl.obolibrary.org/obo/CL_0002480) SubClassOf [RO_0015004](http://purl.obolibrary.org/obo/RO_0015004) some [CLM_1000027](http://purl.obolibrary.org/obo/CLM_1000027) + + +### natural helper lymphocyte `http://purl.obolibrary.org/obo/CL_0002679` +#### Removed +- [natural helper lymphocyte](http://purl.obolibrary.org/obo/CL_0002679) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) + + + +### neural crest cell `http://purl.obolibrary.org/obo/CL_0011012` +#### Removed +- [neural crest cell](http://purl.obolibrary.org/obo/CL_0011012) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +Neural crest cells are a group of transient and highly migratory cells that originate from the neuroectoderm during the early stages of embryonic development. They are multipotent cells with an exceptional degree of plasticity, capable of differentiating into various somatic cell types and therefore play a fundamental role in the formation of various organs and tissues, making them critical contributors to the developing embryo. +After the initiation of neurulation (the formation of the neural tube) neural crest cells start to undergo epithelial-to-mesenchymal transition and delaminate and migrate from the dorsal neural tube to several regions throughout the embryo. They differentiate into a range of diverse cell types, such as neurons and glial cells of the peripheral nervous system, including sensory and autonomic neurons. They also contribute to the formation of adrenal glands, pigment cells in the skin (melanocytes), cardiac structures, including parts of the heart septum and major arteries, as well as bones and cartilage of the face and skull. +Disorders or aberrations in the development or migration of the neural crest cells can lead to serious congenital malformations, such as neurocristopathies, including Hirschsprung disease, neuroblastoma, and neurofibromatosis."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.3389/fcell.2020.00635/full"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1242/dev.193193"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1002/dvg.23276"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://doi.org/10.1016/j.ydbio.2011.12.042"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [neural crest cell](http://purl.obolibrary.org/obo/CL_0011012) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Neural crest cells are a group of transient and highly migratory cells that originate from the neuroectoderm during the early stages of embryonic development. They are multipotent cells with an exceptional degree of plasticity, capable of differentiating into various somatic cell types and therefore play a fundamental role in the formation of various organs and tissues, making them critical contributors to the developing embryo. +After the initiation of neurulation (the formation of the neural tube) neural crest cells start to undergo epithelial-to-mesenchymal transition and delaminate and migrate from the dorsal neural tube to several regions throughout the embryo. They differentiate into a range of diverse cell types, such as neurons and glial cells of the peripheral nervous system, including sensory and autonomic neurons. They also contribute to the formation of adrenal glands, pigment cells in the skin (melanocytes), cardiac structures, including parts of the heart septum and major arteries, as well as bones and cartilage of the face and skull. +Disorders or aberrations in the development or migration of the neural crest cells can lead to serious congenital malformations, such as neurocristopathies, including Hirschsprung disease, neuroblastoma, and neurofibromatosis."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.3389/fcell.2020.00635/full"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1242/dev.193193"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1002/dvg.23276"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://doi.org/10.1016/j.ydbio.2011.12.042"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### neuroendocrine cell `http://purl.obolibrary.org/obo/CL_0000165` + +#### Added +- [neuroendocrine cell](http://purl.obolibrary.org/obo/CL_0000165) SubClassOf [secretory epithelial cell](http://purl.obolibrary.org/obo/CL_1100001) + + +### neuroendocrine cell of epithelium of crypt of Lieberkuhn `http://purl.obolibrary.org/obo/CL_4033002` + +#### Added +- [neuroendocrine cell of epithelium of crypt of Lieberkuhn](http://purl.obolibrary.org/obo/CL_4033002) SubClassOf [glandular secretory epithelial cell](http://purl.obolibrary.org/obo/CL_0000150) + + +### neurogliaform cell `http://purl.obolibrary.org/obo/CL_0000693` +#### Removed +- [neurogliaform cell](http://purl.obolibrary.org/obo/CL_0000693) SubClassOf [multipolar neuron](http://purl.obolibrary.org/obo/CL_0000104) + + + +### neuromuscular junction nucleus `http://purl.obolibrary.org/obo/CL_4052025` + +#### Added +- [neuromuscular junction nucleus](http://purl.obolibrary.org/obo/CL_4052025) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A specialized muscle nucleus that is part of an extrafusal muscle fiber, clustered at the postsynaptic side of the neuromuscular junction. This nucleus exhibits a distinct transcriptional profile, including acetylcholine receptor (AChR) subunit genes. It regulates the production of proteins essential for maintaining the structure and function of the neuromuscular junction, supporting efficient nerve-muscle signaling for muscle contraction."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:33311457"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:33311464"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:33037211"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [neuromuscular junction nucleus](http://purl.obolibrary.org/obo/CL_4052025) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "NMJ nuclues"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003000](http://purl.obolibrary.org/obo/OMO_0003000) + +- [neuromuscular junction nucleus](http://purl.obolibrary.org/obo/CL_4052025) [contributor](http://purl.org/dc/terms/contributor) [0009-0000-8480-9277](https://orcid.org/0009-0000-8480-9277) + +- [neuromuscular junction nucleus](http://purl.obolibrary.org/obo/CL_4052025) [has_exact_synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "neuromuscular junction myonuclei"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:33311464"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003004](http://purl.obolibrary.org/obo/OMO_0003004) + +- [neuromuscular junction nucleus](http://purl.obolibrary.org/obo/CL_4052025) [date](http://purl.org/dc/terms/date) "2024-10-31T11:09:04Z"^^[dateTime](http://www.w3.org/2001/XMLSchema#dateTime) + +- [neuromuscular junction nucleus](http://purl.obolibrary.org/obo/CL_4052025) [has_exact_synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "neuromuscular junction nuclei"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:33311457"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003004](http://purl.obolibrary.org/obo/OMO_0003004) + +- [neuromuscular junction nucleus](http://purl.obolibrary.org/obo/CL_4052025) [id](http://www.geneontology.org/formats/oboInOwl#id) "CL:4052025"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [neuromuscular junction nucleus](http://purl.obolibrary.org/obo/CL_4052025) [label](http://www.w3.org/2000/01/rdf-schema#label) "neuromuscular junction nucleus"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [neuromuscular junction nucleus](http://purl.obolibrary.org/obo/CL_4052025) [contributor](http://purl.org/dc/terms/contributor) [X](https://orcid.org/0009-0001-6947-615X) + +- Class: [neuromuscular junction nucleus](http://purl.obolibrary.org/obo/CL_4052025) + +- [neuromuscular junction nucleus](http://purl.obolibrary.org/obo/CL_4052025) EquivalentTo [GO_0005634](http://purl.obolibrary.org/obo/GO_0005634) and ([BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [extrafusal muscle fiber](http://purl.obolibrary.org/obo/CL_0008046)) and ([RO_0002131](http://purl.obolibrary.org/obo/RO_0002131) some [GO_0098522](http://purl.obolibrary.org/obo/GO_0098522)) + +- [neuromuscular junction nucleus](http://purl.obolibrary.org/obo/CL_4052025) SubClassOf [RO_0002131](http://purl.obolibrary.org/obo/RO_0002131) some [GO_0098522](http://purl.obolibrary.org/obo/GO_0098522) + +- [neuromuscular junction nucleus](http://purl.obolibrary.org/obo/CL_4052025) SubClassOf [BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [extrafusal muscle fiber](http://purl.obolibrary.org/obo/CL_0008046) + +- [neuromuscular junction nucleus](http://purl.obolibrary.org/obo/CL_4052025) SubClassOf [GO_0005634](http://purl.obolibrary.org/obo/GO_0005634) + + +### neuron of the dorsal spinal cord `http://purl.obolibrary.org/obo/CL_0002611` +#### Removed +- [neuron of the dorsal spinal cord](http://purl.obolibrary.org/obo/CL_0002611) EquivalentTo [CNS neuron (sensu Vertebrata)](http://purl.obolibrary.org/obo/CL_0000117) and ([RO_0002100](http://purl.obolibrary.org/obo/RO_0002100) some [UBERON_0002256](http://purl.obolibrary.org/obo/UBERON_0002256)) + +- [neuron of the dorsal spinal cord](http://purl.obolibrary.org/obo/CL_0002611) SubClassOf [CNS neuron (sensu Vertebrata)](http://purl.obolibrary.org/obo/CL_0000117) + - [is_inferred](http://www.geneontology.org/formats/oboInOwl#is_inferred) "true"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [neuron of the dorsal spinal cord](http://purl.obolibrary.org/obo/CL_0002611) EquivalentTo [neuron](http://purl.obolibrary.org/obo/CL_0000540) and ([RO_0002100](http://purl.obolibrary.org/obo/RO_0002100) some [UBERON_0002256](http://purl.obolibrary.org/obo/UBERON_0002256)) + + +### neuron of the forebrain `http://purl.obolibrary.org/obo/CL_0012001` +#### Removed +- [neuron of the forebrain](http://purl.obolibrary.org/obo/CL_0012001) EquivalentTo [CNS neuron (sensu Vertebrata)](http://purl.obolibrary.org/obo/CL_0000117) and ([RO_0002100](http://purl.obolibrary.org/obo/RO_0002100) some [UBERON_0001890](http://purl.obolibrary.org/obo/UBERON_0001890)) + +- [neuron of the forebrain](http://purl.obolibrary.org/obo/CL_0012001) SubClassOf [CNS neuron (sensu Vertebrata)](http://purl.obolibrary.org/obo/CL_0000117) + - [is_inferred](http://www.geneontology.org/formats/oboInOwl#is_inferred) "true"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [neuron of the forebrain](http://purl.obolibrary.org/obo/CL_0012001) EquivalentTo [neuron](http://purl.obolibrary.org/obo/CL_0000540) and ([RO_0002100](http://purl.obolibrary.org/obo/RO_0002100) some [UBERON_0001890](http://purl.obolibrary.org/obo/UBERON_0001890)) + + +### neuron of the substantia nigra `http://purl.obolibrary.org/obo/CL_0002614` +#### Removed +- [neuron of the substantia nigra](http://purl.obolibrary.org/obo/CL_0002614) EquivalentTo [CNS neuron (sensu Vertebrata)](http://purl.obolibrary.org/obo/CL_0000117) and ([RO_0002100](http://purl.obolibrary.org/obo/RO_0002100) some [UBERON_0002038](http://purl.obolibrary.org/obo/UBERON_0002038)) + +- [neuron of the substantia nigra](http://purl.obolibrary.org/obo/CL_0002614) SubClassOf [CNS neuron (sensu Vertebrata)](http://purl.obolibrary.org/obo/CL_0000117) + - [is_inferred](http://www.geneontology.org/formats/oboInOwl#is_inferred) "true"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [neuron of the substantia nigra](http://purl.obolibrary.org/obo/CL_0002614) EquivalentTo [neuron](http://purl.obolibrary.org/obo/CL_0000540) and ([RO_0002100](http://purl.obolibrary.org/obo/RO_0002100) some [UBERON_0002038](http://purl.obolibrary.org/obo/UBERON_0002038)) + + +### neuron of the ventral spinal cord `http://purl.obolibrary.org/obo/CL_0002612` +#### Removed +- [neuron of the ventral spinal cord](http://purl.obolibrary.org/obo/CL_0002612) EquivalentTo [CNS neuron (sensu Vertebrata)](http://purl.obolibrary.org/obo/CL_0000117) and ([RO_0002100](http://purl.obolibrary.org/obo/RO_0002100) some [UBERON_0002257](http://purl.obolibrary.org/obo/UBERON_0002257)) + +- [neuron of the ventral spinal cord](http://purl.obolibrary.org/obo/CL_0002612) SubClassOf [CNS neuron (sensu Vertebrata)](http://purl.obolibrary.org/obo/CL_0000117) + - [is_inferred](http://www.geneontology.org/formats/oboInOwl#is_inferred) "true"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [neuron of the ventral spinal cord](http://purl.obolibrary.org/obo/CL_0002612) EquivalentTo [neuron](http://purl.obolibrary.org/obo/CL_0000540) and ([RO_0002100](http://purl.obolibrary.org/obo/RO_0002100) some [UBERON_0002257](http://purl.obolibrary.org/obo/UBERON_0002257)) + + +### neuronal brush cell `http://purl.obolibrary.org/obo/CL_0000555` +#### Removed +- [neuronal brush cell](http://purl.obolibrary.org/obo/CL_0000555) SubClassOf [CNS neuron (sensu Vertebrata)](http://purl.obolibrary.org/obo/CL_0000117) + +#### Added +- [neuronal brush cell](http://purl.obolibrary.org/obo/CL_0000555) SubClassOf [central nervous system neuron](http://purl.obolibrary.org/obo/CL_2000029) + + +### neutrophilic myeloblast `http://purl.obolibrary.org/obo/CL_0000042` +#### Removed +- [neutrophilic myeloblast](http://purl.obolibrary.org/obo/CL_0000042) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) + + + +### non-classical monocyte `http://purl.obolibrary.org/obo/CL_0000875` +#### Removed +- [non-classical monocyte](http://purl.obolibrary.org/obo/CL_0000875) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) + + + +### non-myelinating Schwann cell `http://purl.obolibrary.org/obo/CL_0002376` + +#### Added +- [non-myelinating Schwann cell](http://purl.obolibrary.org/obo/CL_0002376) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl/cl-base#cellxgene_subset) + + +### noradrenergic cell `http://purl.obolibrary.org/obo/CL_0000459` + +#### Added +- [noradrenergic cell](http://purl.obolibrary.org/obo/CL_0000459) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl/cl-base#cellxgene_subset) + + +### notochordal cell `http://purl.obolibrary.org/obo/CL_0007005` + +#### Added +- [notochordal cell](http://purl.obolibrary.org/obo/CL_0007005) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl/cl-base#cellxgene_subset) + + +### nucleus accumbens shell and olfactory tubercle D1 medium spiny neuron `http://purl.obolibrary.org/obo/CL_4030051` + +#### Added +- [nucleus accumbens shell and olfactory tubercle D1 medium spiny neuron](http://purl.obolibrary.org/obo/CL_4030051) SubClassOf [striatum neuron](http://purl.obolibrary.org/obo/CL_0002613) + + +### nucleus accumbens shell and olfactory tubercle D2 medium spiny neuron `http://purl.obolibrary.org/obo/CL_4030052` + +#### Added +- [nucleus accumbens shell and olfactory tubercle D2 medium spiny neuron](http://purl.obolibrary.org/obo/CL_4030052) SubClassOf [striatum neuron](http://purl.obolibrary.org/obo/CL_0002613) + + +### obsolete CNS interneuron `http://purl.obolibrary.org/obo/CL_0000402` +#### Removed +- [obsolete CNS interneuron](http://purl.obolibrary.org/obo/CL_0000402) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009191"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [obsolete CNS interneuron](http://purl.obolibrary.org/obo/CL_0000402) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "An interneuron that has its cell body in a central nervous system."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "doi:10.1016/B978-0-12-817424-1.00001-X"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [obsolete CNS interneuron](http://purl.obolibrary.org/obo/CL_0000402) [label](http://www.w3.org/2000/01/rdf-schema#label) "CNS interneuron"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [obsolete CNS interneuron](http://purl.obolibrary.org/obo/CL_0000402) EquivalentTo [interneuron](http://purl.obolibrary.org/obo/CL_0000099) and ([RO_0002100](http://purl.obolibrary.org/obo/RO_0002100) some [UBERON_0001017](http://purl.obolibrary.org/obo/UBERON_0001017)) + +- [obsolete CNS interneuron](http://purl.obolibrary.org/obo/CL_0000402) SubClassOf [interneuron](http://purl.obolibrary.org/obo/CL_0000099) + +- [obsolete CNS interneuron](http://purl.obolibrary.org/obo/CL_0000402) SubClassOf [central nervous system neuron](http://purl.obolibrary.org/obo/CL_2000029) + +#### Added +- [obsolete CNS interneuron](http://purl.obolibrary.org/obo/CL_0000402) [deprecated](http://www.w3.org/2002/07/owl#deprecated) true + +- [obsolete CNS interneuron](http://purl.obolibrary.org/obo/CL_0000402) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "OBSOLETE. An interneuron that has its cell body in a central nervous system."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "doi:10.1016/B978-0-12-817424-1.00001-X"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [obsolete CNS interneuron](http://purl.obolibrary.org/obo/CL_0000402) [IAO_0000233](http://purl.obolibrary.org/obo/IAO_0000233) [2869](https://github.com/obophenotype/cell-ontology/issues/2869) + +- [obsolete CNS interneuron](http://purl.obolibrary.org/obo/CL_0000402) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl/cl-base#cellxgene_subset) + +- [obsolete CNS interneuron](http://purl.obolibrary.org/obo/CL_0000402) [term replaced by](http://purl.obolibrary.org/obo/IAO_0100001) [interneuron](http://purl.obolibrary.org/obo/CL_0000099) + +- [obsolete CNS interneuron](http://purl.obolibrary.org/obo/CL_0000402) [label](http://www.w3.org/2000/01/rdf-schema#label) "obsolete CNS interneuron"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### obsolete animal cell `http://purl.obolibrary.org/obo/CL_0000548` +#### Removed +- [obsolete animal cell](http://purl.obolibrary.org/obo/CL_0000548) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl/cl-base#cellxgene_subset) + + + +### obsolete native cell `http://purl.obolibrary.org/obo/CL_0000003` +#### Removed +- [obsolete native cell](http://purl.obolibrary.org/obo/CL_0000003) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl/cl-base#cellxgene_subset) + + + +### obsolete somatic cell `http://purl.obolibrary.org/obo/CL_0002371` +#### Removed +- [obsolete somatic cell](http://purl.obolibrary.org/obo/CL_0002371) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl/cl-base#cellxgene_subset) + +#### Added +- [obsolete somatic cell](http://purl.obolibrary.org/obo/CL_0002371) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Somatic cells represent the majority of the cell types in the human body. They are fundamental building blocks of organs, tissues, and other bodily structures, with every organ being composed of distinct subpopulations of these cells. +The primary function of somatic cells is to maintain the function and survival of an organism. They carry significant information in the form of DNA, and through the process of mitosis, contribute to the repair and regeneration of body tissues. +Further, some types of somatic cells work in a collaborative manner to form complex functional structures such as the skin and lining of the gut, demonstrating a higher level of organization. However, it's important to note that somatic cells are distinct from germ cells, which are responsible for sexual reproduction by forming sperm or eggs. Any alterations in the DNA of somatic cells, due to mutations, will not affect the offspring as they aren't involved in transmission of genetic information to the next generation. +While most somatic cells contain two copies of each chromosome (diploid), a certain subset may possess a single set of chromosomes (haploid), specifically found in male ants, bees, and other hymenopterans. Hence, diversity is a defining characteristic of somatic cells, reflecting in their structures, roles, and genetic makeup."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://www.ncbi.nlm.nih.gov/books/NBK557896/"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://www.genome.gov/genetics-glossary/Somatic-Cells"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1038/nrm3980"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [obsolete somatic cell](http://purl.obolibrary.org/obo/CL_0002371) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://cellxgene.cziscience.com/cellguide/CL_0002371"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### obsolete surface mucosal cell of stomach `http://purl.obolibrary.org/obo/CL_0002182` +#### Removed +- [obsolete surface mucosal cell of stomach](http://purl.obolibrary.org/obo/CL_0002182) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A simple columnar cell that populates the entire luminal surface including the gastric pits. This cell types secrete mucus to form a thick protective, lubricant layer over the gastric wall."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ISBN:0517223651"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:tfm"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [obsolete surface mucosal cell of stomach](http://purl.obolibrary.org/obo/CL_0002182) [label](http://www.w3.org/2000/01/rdf-schema#label) "surface mucosal cell of stomach"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [obsolete surface mucosal cell of stomach](http://purl.obolibrary.org/obo/CL_0002182) SubClassOf [mucous cell of stomach](http://purl.obolibrary.org/obo/CL_0002180) + +- [obsolete surface mucosal cell of stomach](http://purl.obolibrary.org/obo/CL_0002182) SubClassOf [BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0001276](http://purl.obolibrary.org/obo/UBERON_0001276) + +- [obsolete surface mucosal cell of stomach](http://purl.obolibrary.org/obo/CL_0002182) SubClassOf [columnar/cuboidal epithelial cell](http://purl.obolibrary.org/obo/CL_0000075) + +#### Added +- [obsolete surface mucosal cell of stomach](http://purl.obolibrary.org/obo/CL_0002182) [comment](http://www.w3.org/2000/01/rdf-schema#comment) "Duplicate with foveolar cell of stomach"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [obsolete surface mucosal cell of stomach](http://purl.obolibrary.org/obo/CL_0002182) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "OBSOLETE. A simple columnar cell that populates the entire luminal surface including the gastric pits. This cell types secrete mucus to form a thick protective, lubricant layer over the gastric wall."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ISBN:0517223651"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:tfm"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [obsolete surface mucosal cell of stomach](http://purl.obolibrary.org/obo/CL_0002182) [deprecated](http://www.w3.org/2002/07/owl#deprecated) true + +- [obsolete surface mucosal cell of stomach](http://purl.obolibrary.org/obo/CL_0002182) [label](http://www.w3.org/2000/01/rdf-schema#label) "obsolete surface mucosal cell of stomach"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [obsolete surface mucosal cell of stomach](http://purl.obolibrary.org/obo/CL_0002182) [term replaced by](http://purl.obolibrary.org/obo/IAO_0100001) [foveolar cell of stomach](http://purl.obolibrary.org/obo/CL_0002179) + + +### olfactory bulb interneuron `http://purl.obolibrary.org/obo/CL_1001434` +#### Removed +- [olfactory bulb interneuron](http://purl.obolibrary.org/obo/CL_1001434) SubClassOf [obsolete CNS interneuron](http://purl.obolibrary.org/obo/CL_0000402) + +- [olfactory bulb interneuron](http://purl.obolibrary.org/obo/CL_1001434) SubClassOf [BFO_0000002](http://purl.obolibrary.org/obo/BFO_0000002) + +#### Added +- [olfactory bulb interneuron](http://purl.obolibrary.org/obo/CL_1001434) SubClassOf [neuron of the forebrain](http://purl.obolibrary.org/obo/CL_0012001) + +- [olfactory bulb interneuron](http://purl.obolibrary.org/obo/CL_1001434) SubClassOf [interneuron](http://purl.obolibrary.org/obo/CL_0000099) + + +### olfactory bulb tufted cell `http://purl.obolibrary.org/obo/CL_1001503` +#### Removed +- [olfactory bulb tufted cell](http://purl.obolibrary.org/obo/CL_1001503) SubClassOf [BFO_0000002](http://purl.obolibrary.org/obo/BFO_0000002) + +- [olfactory bulb tufted cell](http://purl.obolibrary.org/obo/CL_1001503) SubClassOf [BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0005376](http://purl.obolibrary.org/obo/UBERON_0005376) + +- [olfactory bulb tufted cell](http://purl.obolibrary.org/obo/CL_1001503) SubClassOf [neuron](http://purl.obolibrary.org/obo/CL_0000540) + +#### Added +- [olfactory bulb tufted cell](http://purl.obolibrary.org/obo/CL_1001503) SubClassOf [RO_0002100](http://purl.obolibrary.org/obo/RO_0002100) some [UBERON_0005376](http://purl.obolibrary.org/obo/UBERON_0005376) + +- [olfactory bulb tufted cell](http://purl.obolibrary.org/obo/CL_1001503) SubClassOf [neuron of the forebrain](http://purl.obolibrary.org/obo/CL_0012001) + + +### olfactory ensheathing cell `http://purl.obolibrary.org/obo/CL_0011028` + +#### Added +- [olfactory ensheathing cell](http://purl.obolibrary.org/obo/CL_0011028) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl/cl-base#cellxgene_subset) + + +### olfactory epithelial cell `http://purl.obolibrary.org/obo/CL_0002167` + +#### Added +- [olfactory epithelial cell](http://purl.obolibrary.org/obo/CL_0002167) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl/cl-base#cellxgene_subset) + + +### olfactory granule cell `http://purl.obolibrary.org/obo/CL_0000626` +#### Removed +- [olfactory granule cell](http://purl.obolibrary.org/obo/CL_0000626) SubClassOf [neuron of the forebrain](http://purl.obolibrary.org/obo/CL_0012001) + + + +### olfactory receptor cell `http://purl.obolibrary.org/obo/CL_0000207` + +#### Added +- [olfactory receptor cell](http://purl.obolibrary.org/obo/CL_0000207) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl/cl-base#cellxgene_subset) + + +### oligodendrocyte precursor cell `http://purl.obolibrary.org/obo/CL_0002453` + +#### Added +- [oligodendrocyte precursor cell](http://purl.obolibrary.org/obo/CL_0002453) SubClassOf [BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0001017](http://purl.obolibrary.org/obo/UBERON_0001017) + +- [oligodendrocyte precursor cell](http://purl.obolibrary.org/obo/CL_0002453) SubClassOf [neuron associated cell (sensu Vertebrata)](http://purl.obolibrary.org/obo/CL_0000123) + + +### osteoclast `http://purl.obolibrary.org/obo/CL_0000092` +#### Removed +- [osteoclast](http://purl.obolibrary.org/obo/CL_0000092) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) + +#### Added +- [osteoclast](http://purl.obolibrary.org/obo/CL_0000092) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Osteoclasts, derived from the monocyte/macrophage lineage, play a crucial role in bone remodeling through bone resorption. They are distinguished from other cells by their large size and their unique ability to secrete enzymes and acids that dissolve the calcium phosphate in bone. The formation of osteoclasts is influenced by two primary factors: macrophage colony-stimulating factor (M-CSF) and the ligand-activated receptor (RANKL) of nuclear factor kappa B (NF-κB). +Osteoclasts also collaborate with osteoblasts, responsible for new bone formation, to maintain bone health and adapt bone structure. Their coordinated actions allow continuous remodeling while preserving overall bone strength and integrity. Imbalances in osteoclast activity can lead to pathological conditions. For example, excessive activity may contribute to diseases like osteoporosis, periprosthetic osteolysis, bone tumors, and Paget's disease. Other the other hand, osteoclast deficiency ca result in conditions like osteopetrosis."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.3389/fmed.2017.00234"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://www.sciencedirect.com/topics/medicine-and-dentistry/osteoclast"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.37175/stemedicine.v1i4.57"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [osteoclast](http://purl.obolibrary.org/obo/CL_0000092) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://cellxgene.cziscience.com/cellguide/CL_0000092"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### outer medulla vasa recta ascending limb cell `http://purl.obolibrary.org/obo/CL_1001210` +#### Removed +- [outer medulla vasa recta ascending limb cell](http://purl.obolibrary.org/obo/CL_1001210) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "Any vasa recta ascending limb cell that is part of some outer medulla vasa recta ascending limb."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBC:Autogenerated"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [outer medulla vasa recta ascending limb cell](http://purl.obolibrary.org/obo/CL_1001210) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "Any vasa recta ascending limb cell that is part of some outer medulla ascending vasa recta."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBC:Autogenerated"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### outer medulla vasa recta descending limb cell `http://purl.obolibrary.org/obo/CL_1001287` +#### Removed +- [outer medulla vasa recta descending limb cell](http://purl.obolibrary.org/obo/CL_1001287) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "Any vasa recta descending limb cell that is part of some outer medulla vasa recta descending limb."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBC:Autogenerated"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [outer medulla vasa recta descending limb cell](http://purl.obolibrary.org/obo/CL_1001287) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "Any vasa recta descending limb cell that is part of some outer medulla descending vasa recta."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBC:Autogenerated"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### outer renal medulla vasa recta cell `http://purl.obolibrary.org/obo/CL_1001127` +#### Removed +- [outer renal medulla vasa recta cell](http://purl.obolibrary.org/obo/CL_1001127) SubClassOf [kidney venous blood vessel cell](http://purl.obolibrary.org/obo/CL_1000893) + + + +### ovarian fibroblast `http://purl.obolibrary.org/obo/CL_2000063` +#### Removed +- [ovarian fibroblast](http://purl.obolibrary.org/obo/CL_2000063) SubClassOf [BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0000992](http://purl.obolibrary.org/obo/UBERON_0000992) + +#### Added +- [ovarian fibroblast](http://purl.obolibrary.org/obo/CL_2000063) SubClassOf [stromal cell of ovary](http://purl.obolibrary.org/obo/CL_0002132) + + +### oviduct secretory cell `http://purl.obolibrary.org/obo/CL_1001591` +#### Removed +- [oviduct secretory cell](http://purl.obolibrary.org/obo/CL_1001591) [label](http://www.w3.org/2000/01/rdf-schema#label) "oviduct glandular cell"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [oviduct secretory cell](http://purl.obolibrary.org/obo/CL_1001591) EquivalentTo [glandular secretory epithelial cell](http://purl.obolibrary.org/obo/CL_0000150) and ([BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0000993](http://purl.obolibrary.org/obo/UBERON_0000993)) + +- [oviduct secretory cell](http://purl.obolibrary.org/obo/CL_1001591) SubClassOf [glandular secretory epithelial cell](http://purl.obolibrary.org/obo/CL_0000150) + +#### Added +- [oviduct secretory cell](http://purl.obolibrary.org/obo/CL_1001591) [label](http://www.w3.org/2000/01/rdf-schema#label) "oviduct secretory cell"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [oviduct secretory cell](http://purl.obolibrary.org/obo/CL_1001591) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "oviduct glandular cell"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [oviduct secretory cell](http://purl.obolibrary.org/obo/CL_1001591) EquivalentTo [secretory epithelial cell](http://purl.obolibrary.org/obo/CL_1100001) and ([BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0000993](http://purl.obolibrary.org/obo/UBERON_0000993)) + +- [oviduct secretory cell](http://purl.obolibrary.org/obo/CL_1001591) SubClassOf [secretory epithelial cell](http://purl.obolibrary.org/obo/CL_1100001) + + +### pancreatic PP cell `http://purl.obolibrary.org/obo/CL_0002275` +#### Removed +- [pancreatic PP cell](http://purl.obolibrary.org/obo/CL_0002275) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +Pancreatic polypeptide (PP) cells (also called F or gamma cells) are unique endocrine cells located within the Islets of Langerhans in the pancreas. PP cells are one of the rarer pancreatic cell types and are more prevalent in the head and neck of the pancreas. They are critical in normal pancreatic physiological functions and are involved in the development of pancreatic endocrine disorders. +The primary function of PP cells is the production and secretion of the pancreatic polypeptide hormone (PP). This hormone plays a crucial role in several gastrointestinal functions and metabolic responses. The release of the PP hormone is stimulated after eating, especially in protein-rich meals, leading to it being present in large amounts during digestion. The fundamental role of PP is to self-regulate pancreatic secretion activities ensuring its exocrine and endocrine functions are under control. +The pancreatic polypeptide hormone from PP cells also aids in adapting to low physical activity and fasting by reducing the production of insulin and glucagon and inhibiting the hepatic glucose production. Additionally, this hormone influences gut motility by slowing down the gastric emptying and reducing small intestinal transit, thereby controlling the pace at which nutritional substances are absorbed. Because of these functions, any malfunction or irregularity in PP cells can result in various disorders such as diabetes and pancreatic diseases."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1038/s42255-019-0148-2"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1016/j.mce.2015.06.028"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1016/B978-0-12-819402-7.00001-2"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.3389/fendo.2023.1192311"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1016/B978-012369442-3/50154-9"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [pancreatic PP cell](http://purl.obolibrary.org/obo/CL_0002275) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Pancreatic polypeptide (PP) cells (also called F or gamma cells) are unique endocrine cells located within the Islets of Langerhans in the pancreas. PP cells are one of the rarer pancreatic cell types and are more prevalent in the head and neck of the pancreas. They are critical in normal pancreatic physiological functions and are involved in the development of pancreatic endocrine disorders. +The primary function of PP cells is the production and secretion of the pancreatic polypeptide hormone (PP). This hormone plays a crucial role in several gastrointestinal functions and metabolic responses. The release of the PP hormone is stimulated after eating, especially in protein-rich meals, leading to it being present in large amounts during digestion. The fundamental role of PP is to self-regulate pancreatic secretion activities ensuring its exocrine and endocrine functions are under control. +The pancreatic polypeptide hormone from PP cells also aids in adapting to low physical activity and fasting by reducing the production of insulin and glucagon and inhibiting the hepatic glucose production. Additionally, this hormone influences gut motility by slowing down the gastric emptying and reducing small intestinal transit, thereby controlling the pace at which nutritional substances are absorbed. Because of these functions, any malfunction or irregularity in PP cells can result in various disorders such as diabetes and pancreatic diseases."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1038/s42255-019-0148-2"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1016/j.mce.2015.06.028"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1016/B978-0-12-819402-7.00001-2"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.3389/fendo.2023.1192311"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1016/B978-012369442-3/50154-9"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### pancreatic acinar cell `http://purl.obolibrary.org/obo/CL_0002064` +#### Removed +- [pancreatic acinar cell](http://purl.obolibrary.org/obo/CL_0002064) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +Pancreatic acinar cells are the functional units of the exocrine pancreas. These cells are structurally arranged in small clusters - or acini - with a small central lumen, and their primary function is to produce and secrete enzymes that facilitate digestion of proteins, carbohydrates, and fats within the small intestine. +Some of the most important digestive enzymes synthesized by the pancreatic acinar cells include amylase, which digests carbohydrates, lipase, which breaks down fats, and several proteases such as trypsin and chymotrypsin which are vital for the digestion of proteins. Importantly, these enzymes are produced as proenzymes or zymogens to avoid autolysis, or the breakdown of the pancreas itself. +The release of these enzymes by the pancreatic acinar cells is strictly regulated by hormones and neurochemicals. Cholecystokinin (CCK) released from the enteroendocrine cells in the duodenum cause the release of these enzymes. Moreover, acinar cells also respond to another hormone, secretin, by releasing bicarbonate-rich fluid which helps to neutralize the gastric acid in the duodenum. +Dysregulation in the function of pancreatic acinar cells can lead to severe health issues, including pancreatitis, which is characterized by inflammatory damage to the organ due to the premature activation of digestive enzymes."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1097/01.mog.0000239863.96833.c0"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://www.ncbi.nlm.nih.gov/books/NBK54134/"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1016/0165-6147(89)90192-2"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1038/nrgastro.2013.36"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [pancreatic acinar cell](http://purl.obolibrary.org/obo/CL_0002064) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Pancreatic acinar cells are the functional units of the exocrine pancreas. These cells are structurally arranged in small clusters - or acini - with a small central lumen, and their primary function is to produce and secrete enzymes that facilitate digestion of proteins, carbohydrates, and fats within the small intestine. +Some of the most important digestive enzymes synthesized by the pancreatic acinar cells include amylase, which digests carbohydrates, lipase, which breaks down fats, and several proteases such as trypsin and chymotrypsin which are vital for the digestion of proteins. Importantly, these enzymes are produced as proenzymes or zymogens to avoid autolysis, or the breakdown of the pancreas itself. +The release of these enzymes by the pancreatic acinar cells is strictly regulated by hormones and neurochemicals. Cholecystokinin (CCK) released from the enteroendocrine cells in the duodenum cause the release of these enzymes. Moreover, acinar cells also respond to another hormone, secretin, by releasing bicarbonate-rich fluid which helps to neutralize the gastric acid in the duodenum. +Dysregulation in the function of pancreatic acinar cells can lead to severe health issues, including pancreatitis, which is characterized by inflammatory damage to the organ due to the premature activation of digestive enzymes."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1097/01.mog.0000239863.96833.c0"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://www.ncbi.nlm.nih.gov/books/NBK54134/"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1016/0165-6147(89)90192-2"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1038/nrgastro.2013.36"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### pancreatic epsilon cell `http://purl.obolibrary.org/obo/CL_0005019` +#### Removed +- [pancreatic epsilon cell](http://purl.obolibrary.org/obo/CL_0005019) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +Pancreatic epsilon cells are a specialized type of endocrine cell found in the islets of Langerhans, a region of the pancreas responsible for hormone production. These clusters of cells constitute only about 1% of the pancreatic islet cell population, making them a relatively small yet significant component of the pancreas. Pancreatic epsilon cells have a round or ovoid shape with occasional cytoplasmic extensions and are characterized by small and spherical granules. +The principal function of pancreatic epsilon cells involves the synthesis and release of the hormone ghrelin, a peptide hormone predominantly produced in the stomach; pancreatic epsilon cells are one of the few sites outside the gastrointestinal tract known to produce this hormone. Ghrelin has multiple vital roles, playing a significant part in generating hunger sensations, promoting fat storage, and influencing various metabolic processes. It also stimulates the release of Growth Hormone (GH) from the anterior pituitary gland. +During fetal development, when they form a layer around the islet, epsilon cells are an important source of ghrelin, likely secreting the hormone into the circulation; their numbers decrease in adults. While research on pancreatic epsilon cells is still ongoing, these cells have been implicated in several disease states, most notably Type 2 diabetes and metabolic syndrome. The dysfunction or reduction in the number of pancreatic epsilon cells can lead to anomalies in ghrelin production, impacting overall metabolic homeostasis and glucose regulation."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.3389/fendo.2022.904004"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.3390/ijms20081867"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1007/s00125-008-1238-y"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1210/en.2018-00833"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1152/physrev.00012.2004"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [pancreatic epsilon cell](http://purl.obolibrary.org/obo/CL_0005019) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Pancreatic epsilon cells are a specialized type of endocrine cell found in the islets of Langerhans, a region of the pancreas responsible for hormone production. These clusters of cells constitute only about 1% of the pancreatic islet cell population, making them a relatively small yet significant component of the pancreas. Pancreatic epsilon cells have a round or ovoid shape with occasional cytoplasmic extensions and are characterized by small and spherical granules. +The principal function of pancreatic epsilon cells involves the synthesis and release of the hormone ghrelin, a peptide hormone predominantly produced in the stomach; pancreatic epsilon cells are one of the few sites outside the gastrointestinal tract known to produce this hormone. Ghrelin has multiple vital roles, playing a significant part in generating hunger sensations, promoting fat storage, and influencing various metabolic processes. It also stimulates the release of Growth Hormone (GH) from the anterior pituitary gland. +During fetal development, when they form a layer around the islet, epsilon cells are an important source of ghrelin, likely secreting the hormone into the circulation; their numbers decrease in adults. While research on pancreatic epsilon cells is still ongoing, these cells have been implicated in several disease states, most notably Type 2 diabetes and metabolic syndrome. The dysfunction or reduction in the number of pancreatic epsilon cells can lead to anomalies in ghrelin production, impacting overall metabolic homeostasis and glucose regulation."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.3389/fendo.2022.904004"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.3390/ijms20081867"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1007/s00125-008-1238-y"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1210/en.2018-00833"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1152/physrev.00012.2004"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### pancreatic goblet cell `http://purl.obolibrary.org/obo/CL_1000322` +#### Removed +- [pancreatic goblet cell](http://purl.obolibrary.org/obo/CL_1000322) SubClassOf [epithelial cell of exocrine pancreas](http://purl.obolibrary.org/obo/CL_1001433) + +#### Added +- [pancreatic goblet cell](http://purl.obolibrary.org/obo/CL_1000322) SubClassOf [pancreas exocrine glandular cell](http://purl.obolibrary.org/obo/CL_1001599) + + +### pancreatic islet capillary endothelial cell `http://purl.obolibrary.org/obo/CL_4052014` + +#### Added +- [pancreatic islet capillary endothelial cell](http://purl.obolibrary.org/obo/CL_4052014) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A capillary endothelial cell that is part of islet of Langerhans, characterized by a high density of fenestrations —approximately ten times greater than those in exocrine pancreatic capillaries. These fenestrations facilitate efficient hormone exchange, which is essential for maintaining glucose homeostasis. The cell's structure and function are regulated by the local production of vascular endothelial growth factor-A (VEGF-A), which maintains its fenestrated architecture."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:16607697"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:28396983"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:33200981"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:27124642"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [pancreatic islet capillary endothelial cell](http://purl.obolibrary.org/obo/CL_4052014) [contributor](http://purl.org/dc/terms/contributor) [0009-0000-8480-9277](https://orcid.org/0009-0000-8480-9277) + +- [pancreatic islet capillary endothelial cell](http://purl.obolibrary.org/obo/CL_4052014) [label](http://www.w3.org/2000/01/rdf-schema#label) "pancreatic islet capillary endothelial cell"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [pancreatic islet capillary endothelial cell](http://purl.obolibrary.org/obo/CL_4052014) [id](http://www.geneontology.org/formats/oboInOwl#id) "CL:4052014"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [pancreatic islet capillary endothelial cell](http://purl.obolibrary.org/obo/CL_4052014) [has_broad_synonym](http://www.geneontology.org/formats/oboInOwl#hasBroadSynonym) "pancreatic islet endothelial cell"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:16607697"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [pancreatic islet capillary endothelial cell](http://purl.obolibrary.org/obo/CL_4052014) [has_broad_synonym](http://www.geneontology.org/formats/oboInOwl#hasBroadSynonym) "islet endothelial cell"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:16607697"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:28396983"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [pancreatic islet capillary endothelial cell](http://purl.obolibrary.org/obo/CL_4052014) [date](http://purl.org/dc/terms/date) "2024-09-30T14:36:12Z"^^[dateTime](http://www.w3.org/2001/XMLSchema#dateTime) + +- Class: [pancreatic islet capillary endothelial cell](http://purl.obolibrary.org/obo/CL_4052014) + +- [pancreatic islet capillary endothelial cell](http://purl.obolibrary.org/obo/CL_4052014) EquivalentTo [capillary endothelial cell](http://purl.obolibrary.org/obo/CL_0002144) and ([BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0000006](http://purl.obolibrary.org/obo/UBERON_0000006)) + +- [pancreatic islet capillary endothelial cell](http://purl.obolibrary.org/obo/CL_4052014) SubClassOf [fenestrated endothelial cell](http://purl.obolibrary.org/obo/CL_0000666) + +- [pancreatic islet capillary endothelial cell](http://purl.obolibrary.org/obo/CL_4052014) SubClassOf [BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0000006](http://purl.obolibrary.org/obo/UBERON_0000006) + +- [pancreatic islet capillary endothelial cell](http://purl.obolibrary.org/obo/CL_4052014) SubClassOf [capillary endothelial cell](http://purl.obolibrary.org/obo/CL_0002144) + + +### pancreatic stellate cell `http://purl.obolibrary.org/obo/CL_0002410` +#### Removed +- [pancreatic stellate cell](http://purl.obolibrary.org/obo/CL_0002410) SubClassOf [BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0001264](http://purl.obolibrary.org/obo/UBERON_0001264) + +#### Added +- [pancreatic stellate cell](http://purl.obolibrary.org/obo/CL_0002410) SubClassOf [stromal cell of pancreas](http://purl.obolibrary.org/obo/CL_0002574) + + +### paneth cell `http://purl.obolibrary.org/obo/CL_0000510` +#### Removed +- [paneth cell](http://purl.obolibrary.org/obo/CL_0000510) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +Paneth cells are specialized epithelial cells that are primarily located at the bottom of the crypts of Lieberkühn in the small intestine, where they play a pivotal role in maintaining gut homeostasis. They have also been found in smaller numbers in the colonic crypts and other parts of the gastrointestinal tract. Paneth cells are characterized by large acidophilic granules, which take up most of the cytoplasmic volume, causing the nucleus to be pushed toward the base of the cell. +Paneth cells function as a part of the innate immune system. The large granules inside the cells are filled with antimicrobial peptides, such as defensins and lysozymes. Upon bacterial intrusion or cellular signaling indicating a potential infection, Paneth cells release the granules containing the antimicrobial substances into the crypt lumen, effectively serving as the first line of defense against bacterial invasion within the gastrointestinal tract. In essence, Paneth cells serve as guardians, protecting the intestinal stem cells from harmful pathogens that may disturb the gut ecosystem. +In addition to their primary role in immunity, Paneth cells are also crucial for supporting the stem cell niche in the intestinal crypts. They are located adjacent to Lgr5+ stem cells and secrete various growth factors such as EGF, TGF-alpha, Wnt3, and Notch ligand Dll4. These factors regulate the self-renewal and differentiation of these stem cells, which continuously replenish the intestinal epithelium. Consequently, any abnormality or dysfunction in Paneth cells could lead to a disturbance in gut homeostasis, possibly resulting in various illnesses such as inflammatory bowel disease."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1038/nature09637"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.3389/fimmu.2020.00587"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1146/annurev-physiol-030212-183744"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1038/nrmicro2546"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1007/s00018-002-8412-z"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [paneth cell](http://purl.obolibrary.org/obo/CL_0000510) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "An epithelial cell found in the basal part of the intestinal glands (crypts of Lieberkuhn) including the appendix. Paneth cells synthesize and secrete lysozyme and cryptdins. Numerous in the deeper parts of the intestinal crypts, particularly in the duodenum, rich in zinc, contain large acidophilic granules, with irregular apical microvilli and prominent membrane-bound vacuoles containing matrix."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:32308658"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:29184701"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ISBN:0517223651"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "MESH:D019879"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:tfm"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [paneth cell](http://purl.obolibrary.org/obo/CL_0000510) SubClassOf [glandular secretory epithelial cell](http://purl.obolibrary.org/obo/CL_0000150) + - [is_inferred](http://www.geneontology.org/formats/oboInOwl#is_inferred) "true"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [paneth cell](http://purl.obolibrary.org/obo/CL_0000510) SubClassOf [BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0001983](http://purl.obolibrary.org/obo/UBERON_0001983) + +#### Added +- [paneth cell](http://purl.obolibrary.org/obo/CL_0000510) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Paneth cells are specialized epithelial cells that are primarily located at the bottom of the crypts of Lieberkühn in the small intestine, where they play a pivotal role in maintaining gut homeostasis. They have also been found in smaller numbers in the colonic crypts and other parts of the gastrointestinal tract. Paneth cells are characterized by large acidophilic granules, which take up most of the cytoplasmic volume, causing the nucleus to be pushed toward the base of the cell. +Paneth cells function as a part of the innate immune system. The large granules inside the cells are filled with antimicrobial peptides, such as defensins and lysozymes. Upon bacterial intrusion or cellular signaling indicating a potential infection, Paneth cells release the granules containing the antimicrobial substances into the crypt lumen, effectively serving as the first line of defense against bacterial invasion within the gastrointestinal tract. In essence, Paneth cells serve as guardians, protecting the intestinal stem cells from harmful pathogens that may disturb the gut ecosystem. +In addition to their primary role in immunity, Paneth cells are also crucial for supporting the stem cell niche in the intestinal crypts. They are located adjacent to Lgr5+ stem cells and secrete various growth factors such as EGF, TGF-alpha, Wnt3, and Notch ligand Dll4. These factors regulate the self-renewal and differentiation of these stem cells, which continuously replenish the intestinal epithelium. Consequently, any abnormality or dysfunction in Paneth cells could lead to a disturbance in gut homeostasis, possibly resulting in various illnesses such as inflammatory bowel disease."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1038/nature09637"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.3389/fimmu.2020.00587"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1146/annurev-physiol-030212-183744"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1038/nrmicro2546"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1007/s00018-002-8412-z"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [paneth cell](http://purl.obolibrary.org/obo/CL_0000510) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "An epithelial cell found in the basal part of the intestinal glands (crypts of Lieberkuhn) including the appendix. Paneth cells synthesize and secrete lysozyme and cryptdins. Numerous in the deeper parts of the intestinal crypts, particularly in the duodenum, rich in zinc, contain large acidophilic granules, with irregular apical microvilli and prominent membrane-bound vacuoles containing matrix."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:32308658"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:29184701"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:33484640"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ISBN:0517223651"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "MESH:D019879"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:tfm"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [paneth cell](http://purl.obolibrary.org/obo/CL_0000510) SubClassOf [RO_0002202](http://purl.obolibrary.org/obo/RO_0002202) some [transit amplifying cell of gut](http://purl.obolibrary.org/obo/CL_4047017) + +- [paneth cell](http://purl.obolibrary.org/obo/CL_0000510) SubClassOf [BFO_0000051](http://purl.obolibrary.org/obo/BFO_0000051) some [GO_0005773](http://purl.obolibrary.org/obo/GO_0005773) + +- [paneth cell](http://purl.obolibrary.org/obo/CL_0000510) SubClassOf [glandular secretory epithelial cell](http://purl.obolibrary.org/obo/CL_0000150) + +- [paneth cell](http://purl.obolibrary.org/obo/CL_0000510) SubClassOf [BFO_0000051](http://purl.obolibrary.org/obo/BFO_0000051) some [GO_0005902](http://purl.obolibrary.org/obo/GO_0005902) + +- [paneth cell](http://purl.obolibrary.org/obo/CL_0000510) SubClassOf [BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0011184](http://purl.obolibrary.org/obo/UBERON_0011184) + + +### paneth cell of colon `http://purl.obolibrary.org/obo/CL_0009009` + +#### Added +- [paneth cell of colon](http://purl.obolibrary.org/obo/CL_0009009) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Paneth cells of the colon are specialized secretory epithelial cells that can be found in the large intestine, albeit in small numbers compared with the small intestine where Paneth cells are more abundant. Under disease conditions such as inflammatory bowel disease, Paneth cells increase in numbers in the colon. They reside in the crypts of Lieberkühn, which are glandular structures embedded within the mucosal layer of the small and large intestine. +Paneth cells play a crucial role in maintaining intestinal homeostasis and acting as a frontline of defense in our bodies against ingested microbes. They achieve this through the secretion of antimicrobial peptides and proteins such as lysozyme and defensins, which can directly kill or inhibit the growth of various bacteria, fungi, and viruses. They degranulate these substances into the intestinal lumen, especially under conditions of pathogenic invasion or damage to the epithelial lining. +Moreover, Paneth cells are essential for the maintenance of intestinal stem cells, which continually replace the epithelium of the intestine. They create a niche for these stem cells at the base of the crypts, secreting various signaling molecules and factors that are essential for the growth and differentiation of intestinal stem cells. In essence, the existence and function of Paneth cells are fundamental to the overall gut health and immune defense system, by providing both antimicrobial functions and a conducive environment for the renewal of the intestinal lining. +The role of Paneth cells specifically in the colon is of interest in the context of inflammatory bowel disease, such as ulcerative colitis and Crohn’s disease: Their presence in the colon is thought to represent Paneth cell metaplasia and indicates a chronic inflammatory state."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1093/ecco-jcc/jjac190.0884"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1002/ibd.20197"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1136/gut.48.2.176"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1038/nature09637"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1038/nrmicro2546"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [paneth cell of colon](http://purl.obolibrary.org/obo/CL_0009009) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://cellxgene.cziscience.com/cellguide/CL_0009009"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### paneth cell of epithelium of small intestine `http://purl.obolibrary.org/obo/CL_1000343` + +#### Added +- [paneth cell of epithelium of small intestine](http://purl.obolibrary.org/obo/CL_1000343) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Paneth cells of the epithelium of the small intestine, often referred to simply as Paneth cells, are a type of specialized secretory cell that forms an integral part of the intestinal crypts of Lieberkühn – gland-like invaginations lining the small intestine. Named after the Austrian physician Josef Paneth, who first identified them in the late 19th century, these cells are significant because of their substantial involvement in the mucosal immune system and intestinal stem cell maintenance. +Functionally, Paneth cells play a key role in maintaining gut homeostasis and in the first line of antimicrobial defense, mainly through the secretion of a range of antimicrobial peptides and proteins. These include lysozymes, cryptdins, or alpha-defensins, which have potent activity against various gut pathogens including bacteria, fungi, and parasites. Furthermore, Paneth cells of the small intestine are also known to release secretory phospholipase A2, an enzyme active against gram-positive bacteria. Additionally, they secrete several growth factors like EGF, TGF-alpha, and Wnt3, which are crucial for stem cell support and the overall maintenance of intestinal mucosal integrity. +The unique location of Paneth cells at the base of the crypts positions them in very close proximity to intestinal stem cells. This not only facilitates their role in stem cell maintenance but also involves them in epithelial regeneration and repair following injury. Dysfunctional Paneth cells have been associated with several gut disorders, like Crohn’s disease and necrotizing enterocolitis."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1038/nature09637"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.3389/fimmu.2020.00587"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1146/annurev-physiol-030212-183744"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1038/nrmicro2546"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1007/s00018-002-8412-z"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [paneth cell of epithelium of small intestine](http://purl.obolibrary.org/obo/CL_1000343) [depiction](http://xmlns.com/foaf/0.1/depiction) [Small-intestine-cells.png](http://purl.obolibrary.org/obo/cl/images/Small-intestine-cells.png) + - [comment](http://www.w3.org/2000/01/rdf-schema#comment) "Figure depicts a cross section of intestinal villi in the small intestine , including the crypts of Lieberkuhn (seen here as ‘crypt’), as well as the layer specific locations of cells that exist within the gastrointestinal tract. Layers depicted here include epithelium (rows of cells bordering villus), submucosa (white space below the epithelium containing networks of neurons and ganglia depicted in pink), muscularis mucosae (blue layer), muscularis propria (referred to here as muscle layer). + +ISC: Intestinal Stem Cell +TA: Transit Amplifying Cells"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [license](http://purl.org/dc/elements/1.1/license) "http://creativecommons.org/licenses/by/4.0/"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [paneth cell of epithelium of small intestine](http://purl.obolibrary.org/obo/CL_1000343) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://cellxgene.cziscience.com/cellguide/CL_1000343"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### parafollicular cell `http://purl.obolibrary.org/obo/CL_0000570` +#### Removed +- [parafollicular cell](http://purl.obolibrary.org/obo/CL_0000570) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) + +#### Added +- [parafollicular cell](http://purl.obolibrary.org/obo/CL_0000570) SubClassOf [glandular secretory epithelial cell](http://purl.obolibrary.org/obo/CL_0000150) + + +### parasol ganglion cell of retina `http://purl.obolibrary.org/obo/CL_4023189` + +#### Added +- [parasol ganglion cell of retina](http://purl.obolibrary.org/obo/CL_4023189) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl/cl-base#cellxgene_subset) + + +### parasympathetic neuron `http://purl.obolibrary.org/obo/CL_0011102` + +#### Added +- [parasympathetic neuron](http://purl.obolibrary.org/obo/CL_0011102) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl/cl-base#cellxgene_subset) + + +### parathyroid glandular cell `http://purl.obolibrary.org/obo/CL_1001593` +#### Removed +- [parathyroid glandular cell](http://purl.obolibrary.org/obo/CL_1001593) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "Glandular cell of parathyroid epithelium. Example: Parathyroid chief cell and parathyroid oxyphil cells."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NPX:PDR"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "HPA:HPA"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [parathyroid glandular cell](http://purl.obolibrary.org/obo/CL_1001593) SubClassOf [BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0011197](http://purl.obolibrary.org/obo/UBERON_0011197) + +#### Added +- [parathyroid glandular cell](http://purl.obolibrary.org/obo/CL_1001593) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "Glandular (secretory) cell of parathyroid epithelium."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NPX:PDR"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "HPA:HPA"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [parathyroid glandular cell](http://purl.obolibrary.org/obo/CL_1001593) SubClassOf [epithelial cell of parathyroid gland](http://purl.obolibrary.org/obo/CL_0002260) + + +### parietal cell `http://purl.obolibrary.org/obo/CL_0000162` +#### Removed +- [parietal cell](http://purl.obolibrary.org/obo/CL_0000162) [has_exact_synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "oxyntic cell"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [parietal cell](http://purl.obolibrary.org/obo/CL_0000162) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A large, oval stomach epithelial cell with a central nucleus; source of gastric acid. Secretes HCl."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ISBN:0517223651"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:tfm"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [parietal cell](http://purl.obolibrary.org/obo/CL_0000162) SubClassOf [RO_0002215](http://purl.obolibrary.org/obo/RO_0002215) some [GO_0046717](http://purl.obolibrary.org/obo/GO_0046717) + +#### Added +- [parietal cell](http://purl.obolibrary.org/obo/CL_0000162) [has_exact_synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "gastric parietal cell"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:29263912"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [parietal cell](http://purl.obolibrary.org/obo/CL_0000162) [comment](http://www.w3.org/2000/01/rdf-schema#comment) "Parietal cells have dynamic, actin-supported microvilli that increase in number during active secretion, playing a crucial role in secreting hydrochloric acid and intrinsic factor. The structure and regulation of these microvilli are influenced by proteins such as ASAP3, which modulates Arf6 activity and actin assembly, thereby controlling microvilli formation and parietal cell function."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:29263912"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:31613538"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [parietal cell](http://purl.obolibrary.org/obo/CL_0000162) [has_exact_synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "oxyntic cell"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Parietal_cell"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [parietal cell](http://purl.obolibrary.org/obo/CL_0000162) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "An epithelial cell of the stomach that is part of the fundic gastric gland. This cell is characterized by its pyramidal shape, abundant mitochondria, and a complex network of secretory canaliculi lined with microvilli. It secretes hydrochloric acid into the stomach lumen and produces intrinsic factor, essential for vitamin B12 absorption."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:31670611"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:31613538"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ISBN:0517223651"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:tfm"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [parietal cell](http://purl.obolibrary.org/obo/CL_0000162) SubClassOf [RO_0002215](http://purl.obolibrary.org/obo/RO_0002215) some [GO_0001696](http://purl.obolibrary.org/obo/GO_0001696) + +- [parietal cell](http://purl.obolibrary.org/obo/CL_0000162) SubClassOf [exocrine cell](http://purl.obolibrary.org/obo/CL_0000152) + +- [parietal cell](http://purl.obolibrary.org/obo/CL_0000162) SubClassOf [BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0010038](http://purl.obolibrary.org/obo/UBERON_0010038) + +- [parietal cell](http://purl.obolibrary.org/obo/CL_0000162) SubClassOf [BFO_0000051](http://purl.obolibrary.org/obo/BFO_0000051) some [GO_0005902](http://purl.obolibrary.org/obo/GO_0005902) + + +### peg cell `http://purl.obolibrary.org/obo/CL_4033014` +#### Removed +- [peg cell](http://purl.obolibrary.org/obo/CL_4033014) SubClassOf [epithelial cell](http://purl.obolibrary.org/obo/CL_0000066) + +#### Added +- [peg cell](http://purl.obolibrary.org/obo/CL_4033014) SubClassOf [fallopian tube non-ciliated cell](http://purl.obolibrary.org/obo/CL_4052019) + + +### peptic cell `http://purl.obolibrary.org/obo/CL_0000155` +#### Removed +- [peptic cell](http://purl.obolibrary.org/obo/CL_0000155) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A cell that is usually basal in position, cuboidal with round nucleus, short microvilli, secretes pepsinogen."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:tfm"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [peptic cell](http://purl.obolibrary.org/obo/CL_0000155) [has_exact_synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "gastric chief cell"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [peptic cell](http://purl.obolibrary.org/obo/CL_0000155) [has_exact_synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "zymogenic cell"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [peptic cell](http://purl.obolibrary.org/obo/CL_0000155) [has_exact_synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "gastric chief cell"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Chief_cell"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [peptic cell](http://purl.obolibrary.org/obo/CL_0000155) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "An epithelial cell of the stomach that is part of the fundic gastric gland. This cell is characterized by a basally located nucleus, abundant rough endoplasmic reticulum, and large apical secretory granules. It produces and secretes pepsinogen, the inactive precursor of the digestive enzyme pepsin."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Gastric_chief_cell"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:30571046"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:tfm"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:21907708"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [peptic cell](http://purl.obolibrary.org/obo/CL_0000155) [has_exact_synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "zymogenic cell"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Chief_cell"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [peptic cell](http://purl.obolibrary.org/obo/CL_0000155) SubClassOf [exocrine cell](http://purl.obolibrary.org/obo/CL_0000152) + +- [peptic cell](http://purl.obolibrary.org/obo/CL_0000155) SubClassOf [BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0010038](http://purl.obolibrary.org/obo/UBERON_0010038) + + +### perineuronal satellite cell `http://purl.obolibrary.org/obo/CL_0000516` + +#### Added +- [perineuronal satellite cell](http://purl.obolibrary.org/obo/CL_0000516) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl/cl-base#cellxgene_subset) + + +### peripheral sensory neuron `http://purl.obolibrary.org/obo/CL_3000004` +#### Removed +- [peripheral sensory neuron](http://purl.obolibrary.org/obo/CL_3000004) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "Peripheral sensory neuron."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:CellBLAST"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:30096314"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [peripheral sensory neuron](http://purl.obolibrary.org/obo/CL_3000004) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A neuron type that is located in a peripheral nervous system and it transmits sensory information from the peripheral (PNS) to the central nervous system (CNS). A sensory neuron converts physical (light, sound, touch) or chemical (such as taste and smell) stimuli into an electrical signal through a process known as sensory transduction. The function of a sensory neuron is to carry informations from the external environment and internal body conditions to the central nervous system for further processing."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:31554486"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://www.britannica.com/science/sensory-neuron"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:CellBLAST"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:30096314"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://www.ncbi.nlm.nih.gov/books/NBK539846/"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:35858549"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Sensory_neuron"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [peripheral sensory neuron](http://purl.obolibrary.org/obo/CL_3000004) [comment](http://www.w3.org/2000/01/rdf-schema#comment) "Typically, a sensory neuron has a pseudounipolar morphology."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Sensory_neuron"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### peritoneal macrophage `http://purl.obolibrary.org/obo/CL_0000581` +#### Removed +- [peritoneal macrophage](http://purl.obolibrary.org/obo/CL_0000581) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) + + + +### perivascular cell `http://purl.obolibrary.org/obo/CL_4033054` + +#### Added +- [perivascular cell](http://purl.obolibrary.org/obo/CL_4033054) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl/cl-base#cellxgene_subset) + + +### perivascular macrophage `http://purl.obolibrary.org/obo/CL_0000881` +#### Removed +- [perivascular macrophage](http://purl.obolibrary.org/obo/CL_0000881) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) + + + +### phagocyte `http://purl.obolibrary.org/obo/CL_0000234` +#### Removed +- [phagocyte](http://purl.obolibrary.org/obo/CL_0000234) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl/cl-base#cellxgene_subset) + + + +### pigmented ciliary epithelial cell `http://purl.obolibrary.org/obo/CL_0002303` +#### Removed +- [pigmented ciliary epithelial cell](http://purl.obolibrary.org/obo/CL_0002303) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +Pigmented ciliary epithelial cells, which are a type of pigment cell, have a crucial function within the eye's ciliary body. The ciliary body, located behind the iris, is one of the eye’s most vital structures and consists of two types of epithelial cells: the pigmented and the non-pigmented ciliary epithelial cells. The pigmented ciliary epithelial cells form the outer layer of the ciliary body and exhibit a black or brown pigmentation due to the melanin they contain. +One key function of pigmented ciliary epithelial cells is to aid in the formation of aqueous humor, an intraocular fluid that nourishes the cornea and lens, and maintains intraocular pressure which is essential for the eye’s shape and light refraction. These cells facilitate this function in conjunction with the non-pigmented ciliary epithelial cells. Together, the pigmented and non-pigmented ciliary epithelial cells form a bilayer epithelium that allows the secretion of aqueous humor through a bi-directional fluid transport mechanism. +Pigmented ciliary epithelial cells also contribute to the blood-aqueous barrier, a physiological frontier that controls the entry and exit of various substances from the blood to the aqueous humor and vice versa. The pigmentation in these cells, intensified by melanin, helps to absorb scattered light coming into the eye, reducing any potential damage and glare."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1111/j.1444-0938.2002.tb02384.x"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1016/S1569-2590(05)10005-6"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [pigmented ciliary epithelial cell](http://purl.obolibrary.org/obo/CL_0002303) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Pigmented ciliary epithelial cells, which are a type of pigment cell, have a crucial function within the eye's ciliary body. The ciliary body, located behind the iris, is one of the eye’s most vital structures and consists of two types of epithelial cells: the pigmented and the non-pigmented ciliary epithelial cells. The pigmented ciliary epithelial cells form the outer layer of the ciliary body and exhibit a black or brown pigmentation due to the melanin they contain. +One key function of pigmented ciliary epithelial cells is to aid in the formation of aqueous humor, an intraocular fluid that nourishes the cornea and lens, and maintains intraocular pressure which is essential for the eye’s shape and light refraction. These cells facilitate this function in conjunction with the non-pigmented ciliary epithelial cells. Together, the pigmented and non-pigmented ciliary epithelial cells form a bilayer epithelium that allows the secretion of aqueous humor through a bi-directional fluid transport mechanism. +Pigmented ciliary epithelial cells also contribute to the blood-aqueous barrier, a physiological frontier that controls the entry and exit of various substances from the blood to the aqueous humor and vice versa. The pigmentation in these cells, intensified by melanin, helps to absorb scattered light coming into the eye, reducing any potential damage and glare."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1111/j.1444-0938.2002.tb02384.x"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1016/S1569-2590(05)10005-6"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### pinealocyte `http://purl.obolibrary.org/obo/CL_0000652` + +#### Added +- [pinealocyte](http://purl.obolibrary.org/obo/CL_0000652) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl/cl-base#cellxgene_subset) + +- [pinealocyte](http://purl.obolibrary.org/obo/CL_0000652) SubClassOf [glandular secretory epithelial cell](http://purl.obolibrary.org/obo/CL_0000150) + + +### pituitary gland capillary endothelial cell `http://purl.obolibrary.org/obo/CL_4052016` + +#### Added +- [pituitary gland capillary endothelial cell](http://purl.obolibrary.org/obo/CL_4052016) [id](http://www.geneontology.org/formats/oboInOwl#id) "CL:4052016"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [pituitary gland capillary endothelial cell](http://purl.obolibrary.org/obo/CL_4052016) [comment](http://www.w3.org/2000/01/rdf-schema#comment) "In the anterior pituitary gland of rats, capillary endothelial cells are distinguished by numerous fenestrations, which are covered by a single-layered diaphragm. The diaphragm features a dense ring-like structure."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:4899902"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [pituitary gland capillary endothelial cell](http://purl.obolibrary.org/obo/CL_4052016) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A capillary endothelial cell that is part of the pituitary gland. This cell is characterized by its fenestrated structure which facilitates the efficient transport of hormones and other signaling molecules, essential for endocrine signalling."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:32910242"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:10810312"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [pituitary gland capillary endothelial cell](http://purl.obolibrary.org/obo/CL_4052016) [label](http://www.w3.org/2000/01/rdf-schema#label) "pituitary gland capillary endothelial cell"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [pituitary gland capillary endothelial cell](http://purl.obolibrary.org/obo/CL_4052016) [date](http://purl.org/dc/terms/date) "2024-09-30T15:31:45Z"^^[dateTime](http://www.w3.org/2001/XMLSchema#dateTime) + +- [pituitary gland capillary endothelial cell](http://purl.obolibrary.org/obo/CL_4052016) [contributor](http://purl.org/dc/terms/contributor) [0009-0000-8480-9277](https://orcid.org/0009-0000-8480-9277) + +- Class: [pituitary gland capillary endothelial cell](http://purl.obolibrary.org/obo/CL_4052016) + +- [pituitary gland capillary endothelial cell](http://purl.obolibrary.org/obo/CL_4052016) EquivalentTo [capillary endothelial cell](http://purl.obolibrary.org/obo/CL_0002144) and ([BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0000007](http://purl.obolibrary.org/obo/UBERON_0000007)) + +- [pituitary gland capillary endothelial cell](http://purl.obolibrary.org/obo/CL_4052016) SubClassOf [pituitary gland cell](http://purl.obolibrary.org/obo/CL_2000004) + +- [pituitary gland capillary endothelial cell](http://purl.obolibrary.org/obo/CL_4052016) SubClassOf [fenestrated endothelial cell](http://purl.obolibrary.org/obo/CL_0000666) + +- [pituitary gland capillary endothelial cell](http://purl.obolibrary.org/obo/CL_4052016) SubClassOf [brain microvascular endothelial cell](http://purl.obolibrary.org/obo/CL_2000044) + +- [pituitary gland capillary endothelial cell](http://purl.obolibrary.org/obo/CL_4052016) SubClassOf [endocrine gland capillary endothelial cell](http://purl.obolibrary.org/obo/CL_4052015) + + +### placental resident macrophage `http://purl.obolibrary.org/obo/CL_4033087` + +#### Added +- [placental resident macrophage](http://purl.obolibrary.org/obo/CL_4033087) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A tissue-resident macrophage that is part of the placenta. This cell helps preventing immunological rejection of the fetus by modulating the immune environment. A placental resident macrophage has high plasticity to adapt to the changing needs of each phase of pregnancy."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:39007150"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [placental resident macrophage](http://purl.obolibrary.org/obo/CL_4033087) [label](http://www.w3.org/2000/01/rdf-schema#label) "placental resident macrophage"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [placental resident macrophage](http://purl.obolibrary.org/obo/CL_4033087) [contributor](http://purl.org/dc/terms/contributor) [0000-0001-6677-8489](https://orcid.org/0000-0001-6677-8489) + +- [placental resident macrophage](http://purl.obolibrary.org/obo/CL_4033087) [contributor](http://purl.org/dc/terms/contributor) [0000-0001-7655-4833](https://orcid.org/0000-0001-7655-4833) + +- [placental resident macrophage](http://purl.obolibrary.org/obo/CL_4033087) [date](http://purl.org/dc/terms/date) "2024-10-31T10:24:21Z"^^[dateTime](http://www.w3.org/2001/XMLSchema#dateTime) + +- [placental resident macrophage](http://purl.obolibrary.org/obo/CL_4033087) [has_broad_synonym](http://www.geneontology.org/formats/oboInOwl#hasBroadSynonym) "placental macrophage"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:39007150"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [placental resident macrophage](http://purl.obolibrary.org/obo/CL_4033087) [id](http://www.geneontology.org/formats/oboInOwl#id) "CL:4033087"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- Class: [placental resident macrophage](http://purl.obolibrary.org/obo/CL_4033087) + +- [placental resident macrophage](http://purl.obolibrary.org/obo/CL_4033087) EquivalentTo [tissue-resident macrophage](http://purl.obolibrary.org/obo/CL_0000864) and ([BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0001987](http://purl.obolibrary.org/obo/UBERON_0001987)) + +- [placental resident macrophage](http://purl.obolibrary.org/obo/CL_4033087) SubClassOf [BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0001987](http://purl.obolibrary.org/obo/UBERON_0001987) + +- [placental resident macrophage](http://purl.obolibrary.org/obo/CL_4033087) SubClassOf [tissue-resident macrophage](http://purl.obolibrary.org/obo/CL_0000864) + + +### placental villous trophoblast `http://purl.obolibrary.org/obo/CL_2000060` + +#### Added +- [placental villous trophoblast](http://purl.obolibrary.org/obo/CL_2000060) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +The placental villous trophoblast, a highly specialized cell type crucial for placental development, plays a key role in facilitating exchanges between the maternal bloodstream and the developing fetus. +Structurally, placental villous trophoblasts are situated on the villous tree structures, forming an outer epithelial layer. Comprising two subtypes—proliferating cytotrophoblasts forming the inner layer and terminally differentiated syncytiotrophoblasts constituting the outer layer in contact with maternal blood—these cells define the placental architecture. +Functionally, placental villous trophoblasts play pivotal roles in forming and maintaining the placenta, ensuring the safe development of the fetus. Their primary function involves managing substance exchange between the mother and fetus, mediating the transfer of gases, nutrients, hormones, and waste materials to support optimal fetal growth. Additionally, these trophoblasts synthesize and release crucial hormones like human chorionic gonadotropin (hCG), which maintains the decidua and signals the mother's body to sustain pregnancy. Acting as a physical and immunological barrier, they protect the fetus from maternal immune cells and prevent the transmission of pathogens, contributing significantly to the success of pregnancy."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1007/s00018-019-03104-6"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.3389/fimmu.2020.00343"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.3390/nu15163564"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [placental villous trophoblast](http://purl.obolibrary.org/obo/CL_2000060) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://cellxgene.cziscience.com/cellguide/CL_2000060"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### plasma cell `http://purl.obolibrary.org/obo/CL_0000786` +#### Removed +- [plasma cell](http://purl.obolibrary.org/obo/CL_0000786) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) + + + +### podocyte `http://purl.obolibrary.org/obo/CL_0000653` +#### Removed +- [podocyte](http://purl.obolibrary.org/obo/CL_0000653) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +Podocytes are highly specialized, terminally differentiated glomerular visceral epithelial cells that wrap around the capillaries in the kidneys. They play an essential role in kidney function, particularly in the filtration selectivity of the glomerulus. Each podocyte is characterized by a unique architecture with a large cell body, ‘major processes’ extending outwardly from the cell body and ‘foot processes’, also known as pedicels, which surround. the glomerular capillary loops +Podocytes represent the last barrier of the glomerular filtration membrane in the kidney. This barrier prevents the leakage of plasma proteins from the blood into the urine, hence maintaining protein homeostasis in the body. The foot processes of the podocytes interdigitate with those from neighboring cells. The cell-cell junctions between the foot processes, the slit-diaphragms, are thought to create a molecular sensor of renal filtration that prevents the passage of macromolecules while allowing water and small solutes to pass. +Podocytes also contribute to the glomerular basement membrane by secreting collagen and maintain glomerular endothelial cell fenestration by secreting VEGFA. They have been shown to play a role in inducing cytoskeletal regulation, cell adhesion, and inflammatory response, consistent with their essential function in the kidney. +The importance of podocytes is further emphasized by the effects of their damage or loss. Abnormalities in podocytes often result in severe kidney diseases (podocytopathies), including focal segmental glomerulosclerosis (FSGS) and minimal change disease (MCD). Injury to the podocytes can result in "effacement" or flattening of foot processes, leading to increased permeability of the filtration barrier and proteinuria (an excess of serum protein in urine) which is a common symptom of kidney diseases."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1038/s41572-020-0196-7"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1146/annurev-physiol-020911-153238"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1038/s41467-022-33748-1"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1159/000481633"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.3389/fcell.2021.771931"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [podocyte](http://purl.obolibrary.org/obo/CL_0000653) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Podocytes are highly specialized, terminally differentiated glomerular visceral epithelial cells that wrap around the capillaries in the kidneys. They play an essential role in kidney function, particularly in the filtration selectivity of the glomerulus. Each podocyte is characterized by a unique architecture with a large cell body, ‘major processes’ extending outwardly from the cell body and ‘foot processes’, also known as pedicels, which surround. the glomerular capillary loops +Podocytes represent the last barrier of the glomerular filtration membrane in the kidney. This barrier prevents the leakage of plasma proteins from the blood into the urine, hence maintaining protein homeostasis in the body. The foot processes of the podocytes interdigitate with those from neighboring cells. The cell-cell junctions between the foot processes, the slit-diaphragms, are thought to create a molecular sensor of renal filtration that prevents the passage of macromolecules while allowing water and small solutes to pass. +Podocytes also contribute to the glomerular basement membrane by secreting collagen and maintain glomerular endothelial cell fenestration by secreting VEGFA. They have been shown to play a role in inducing cytoskeletal regulation, cell adhesion, and inflammatory response, consistent with their essential function in the kidney. +The importance of podocytes is further emphasized by the effects of their damage or loss. Abnormalities in podocytes often result in severe kidney diseases (podocytopathies), including focal segmental glomerulosclerosis (FSGS) and minimal change disease (MCD). Injury to the podocytes can result in "effacement" or flattening of foot processes, leading to increased permeability of the filtration barrier and proteinuria (an excess of serum protein in urine) which is a common symptom of kidney diseases."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1038/s41572-020-0196-7"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1146/annurev-physiol-020911-153238"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1038/s41467-022-33748-1"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1159/000481633"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.3389/fcell.2021.771931"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### polychromatophilic erythroblast `http://purl.obolibrary.org/obo/CL_0000550` +#### Removed +- [polychromatophilic erythroblast](http://purl.obolibrary.org/obo/CL_0000550) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) + + + +### polymodal neuron `http://purl.obolibrary.org/obo/CL_0000102` +#### Removed +- [polymodal neuron](http://purl.obolibrary.org/obo/CL_0000102) SubClassOf [neuron](http://purl.obolibrary.org/obo/CL_0000540) + +#### Added +- [polymodal neuron](http://purl.obolibrary.org/obo/CL_0000102) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "polymodal sensory neuron"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:23749412"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [polymodal neuron](http://purl.obolibrary.org/obo/CL_0000102) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A neuron type that respond to multiple stimuli such as mechanical, thermal and chemical. This neuron type is responsible for integrating different types of sensory inputs, allowing organisms to respond appropriately to diverse environmental challenges."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:36381588"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:23749412"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [polymodal neuron](http://purl.obolibrary.org/obo/CL_0000102) SubClassOf [peripheral nervous system neuron](http://purl.obolibrary.org/obo/CL_2000032) + + +### post-arteriole capillary cell `http://purl.obolibrary.org/obo/CL_4047029` + +#### Added +- [post-arteriole capillary cell](http://purl.obolibrary.org/obo/CL_4047029) [contributor](http://purl.org/dc/terms/contributor) [0009-0005-7919-4905](https://orcid.org/0009-0005-7919-4905) + +- [post-arteriole capillary cell](http://purl.obolibrary.org/obo/CL_4047029) [id](http://www.geneontology.org/formats/oboInOwl#id) "CL:4047029"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [post-arteriole capillary cell](http://purl.obolibrary.org/obo/CL_4047029) [date](http://purl.org/dc/terms/date) "2024-11-07T12:50:06Z"^^[dateTime](http://www.w3.org/2001/XMLSchema#dateTime) + +- [post-arteriole capillary cell](http://purl.obolibrary.org/obo/CL_4047029) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "An endothelial cell forming the walls of capillaries immediately downstream from arterioles, facilitating the exchange of substances between blood and interstitial fluid. This cell is characterized by a small diameter and may be continuous, fenestrated, or sinusoidal, depending on their location and function. This cell plays a crucial role in tissue oxygenation, nutrient delivery, and maintaining homeostasis within the microvascular network."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:35406678"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:17893694"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [post-arteriole capillary cell](http://purl.obolibrary.org/obo/CL_4047029) [label](http://www.w3.org/2000/01/rdf-schema#label) "post-arteriole capillary cell"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- Class: [post-arteriole capillary cell](http://purl.obolibrary.org/obo/CL_4047029) + +- [post-arteriole capillary cell](http://purl.obolibrary.org/obo/CL_4047029) SubClassOf [capillary endothelial cell](http://purl.obolibrary.org/obo/CL_0002144) + + +### posterior lateral line ganglion neuron `http://purl.obolibrary.org/obo/CL_1000245` +#### Removed +- [posterior lateral line ganglion neuron](http://purl.obolibrary.org/obo/CL_1000245) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "Any neuron that has its soma located in some posterior lateral line ganglion."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBC:Autogenerated"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [posterior lateral line ganglion neuron](http://purl.obolibrary.org/obo/CL_1000245) EquivalentTo [neuron](http://purl.obolibrary.org/obo/CL_0000540) and ([RO_0002100](http://purl.obolibrary.org/obo/RO_0002100) some [UBERON_2001314](http://purl.obolibrary.org/obo/UBERON_2001314)) + +#### Added +- [posterior lateral line ganglion neuron](http://purl.obolibrary.org/obo/CL_1000245) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "Any peripheral nervous system neuron that has its soma located in some posterior lateral line ganglion."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBC:Autogenerated"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [posterior lateral line ganglion neuron](http://purl.obolibrary.org/obo/CL_1000245) EquivalentTo [peripheral nervous system neuron](http://purl.obolibrary.org/obo/CL_2000032) and ([RO_0002100](http://purl.obolibrary.org/obo/RO_0002100) some [UBERON_2001314](http://purl.obolibrary.org/obo/UBERON_2001314)) + + +### pre-conventional dendritic cell `http://purl.obolibrary.org/obo/CL_0002010` +#### Removed +- [pre-conventional dendritic cell](http://purl.obolibrary.org/obo/CL_0002010) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) + + + +### pre-natural killer cell `http://purl.obolibrary.org/obo/CL_0000937` +#### Removed +- [pre-natural killer cell](http://purl.obolibrary.org/obo/CL_0000937) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) + + + +### pre-venule capillary cell `http://purl.obolibrary.org/obo/CL_4047030` #### Added -- [mast cell progenitor](http://purl.obolibrary.org/obo/CL_0000831) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) +- [pre-venule capillary cell](http://purl.obolibrary.org/obo/CL_4047030) [date](http://purl.org/dc/terms/date) "2024-11-07T13:22:16Z"^^[dateTime](http://www.w3.org/2001/XMLSchema#dateTime) + +- [pre-venule capillary cell](http://purl.obolibrary.org/obo/CL_4047030) [has_exact_synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "Cap-Venous endothelial cell"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1038/s41467-022-33324-7"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [pre-venule capillary cell](http://purl.obolibrary.org/obo/CL_4047030) [id](http://www.geneontology.org/formats/oboInOwl#id) "CL:4047030"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [pre-venule capillary cell](http://purl.obolibrary.org/obo/CL_4047030) [contributor](http://purl.org/dc/terms/contributor) [0009-0005-7919-4905](https://orcid.org/0009-0005-7919-4905) + +- [pre-venule capillary cell](http://purl.obolibrary.org/obo/CL_4047030) [label](http://www.w3.org/2000/01/rdf-schema#label) "pre-venule capillary cell"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [pre-venule capillary cell](http://purl.obolibrary.org/obo/CL_4047030) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A specialized endothelial cell located in the transition zone between capillaries and small venules in the microvascular system. It exhibits characteristics of both capillary and venous cells, expressing markers from both types. This cell plays a role in regulating blood flow and substance exchange between blood and tissues."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:23620236"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1038/s41467-022-33324-7"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- Class: [pre-venule capillary cell](http://purl.obolibrary.org/obo/CL_4047030) + +- [pre-venule capillary cell](http://purl.obolibrary.org/obo/CL_4047030) SubClassOf [capillary endothelial cell](http://purl.obolibrary.org/obo/CL_0002144) + + +### preadipocyte `http://purl.obolibrary.org/obo/CL_0002334` + +#### Added +- [preadipocyte](http://purl.obolibrary.org/obo/CL_0002334) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl/cl-base#cellxgene_subset) + + +### preosteoblast `http://purl.obolibrary.org/obo/CL_0007010` + +#### Added +- [preosteoblast](http://purl.obolibrary.org/obo/CL_0007010) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Preosteoblast is a critical cell type involved in bone formation, crucial in a process known as ossification or osteogenesis. They are derived from mesenchymal stem cells and are an intermediate stage marking the transition from an osteoprogenitor cell to a fully differentiated osteoblast. The presence of preosteoblasts signifies the site of new bone deposition, highlighting their crucial role in skeletal development and in response to bone injury repairs. +The primary function of preosteoblasts is to differentiate into osteoblasts, which are responsible for secreting osteoid (the unmineralized portion of bone matrix) and regulating the process of bone mineralization. Preosteoblasts are regulated by various growth factors and hormones, including bone morphogenic proteins (BMPs), fibroblast growth factors (FGFs), parathyroid hormone (PTH) and Vitamin D. +However, the function of preosteoblasts is not limited to bone formation alone. In addition to osteogenesis, preosteoblasts significantly contribute to the maintenance of bone homeostasis through regulating the activity of osteoclasts - the cells responsible for bone resorption. This regulation is mediated through RANK/RANKL/OPG pathway signaling. Osteoprotegerin (OPG) released from the preosteoblasts acts as a decoy receptor for RANKL impairing osteoclast formation, hence preventing excessive bone resorption. This regulatory role indicates the dual functionality of preosteoblasts, which are indispensable for both the formation of new bone and the maintenance of existing bone tissue."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1210/endo.141.9.7634"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1096/fba.2020-00058"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.12659/MSMBR.901142"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1038/srep32884"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [preosteoblast](http://purl.obolibrary.org/obo/CL_0007010) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://cellxgene.cziscience.com/cellguide/CL_0007010"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### primary interneuron (sensu Teleostei) `http://purl.obolibrary.org/obo/CL_0000534` +#### Removed +- [primary interneuron (sensu Teleostei)](http://purl.obolibrary.org/obo/CL_0000534) SubClassOf [interneuron](http://purl.obolibrary.org/obo/CL_0000099) + +#### Added +- [primary interneuron (sensu Teleostei)](http://purl.obolibrary.org/obo/CL_0000534) SubClassOf [spinal cord interneuron](http://purl.obolibrary.org/obo/CL_0005000) + + +### primary motor neuron (sensu Teleostei) `http://purl.obolibrary.org/obo/CL_0000533` +#### Removed +- [primary motor neuron (sensu Teleostei)](http://purl.obolibrary.org/obo/CL_0000533) SubClassOf [motor neuron](http://purl.obolibrary.org/obo/CL_0000100) + +#### Added +- [primary motor neuron (sensu Teleostei)](http://purl.obolibrary.org/obo/CL_0000533) SubClassOf [spinal cord motor neuron](http://purl.obolibrary.org/obo/CL_0011001) + + +### primary neuron (sensu Teleostei) `http://purl.obolibrary.org/obo/CL_0000530` +#### Removed +- [primary neuron (sensu Teleostei)](http://purl.obolibrary.org/obo/CL_0000530) SubClassOf [neuron](http://purl.obolibrary.org/obo/CL_0000540) + +#### Added +- [primary neuron (sensu Teleostei)](http://purl.obolibrary.org/obo/CL_0000530) SubClassOf [RO_0002100](http://purl.obolibrary.org/obo/RO_0002100) some [UBERON_0002240](http://purl.obolibrary.org/obo/UBERON_0002240) + +- [primary neuron (sensu Teleostei)](http://purl.obolibrary.org/obo/CL_0000530) SubClassOf [central nervous system neuron](http://purl.obolibrary.org/obo/CL_2000029) + + +### primitive erythroid progenitor `http://purl.obolibrary.org/obo/CL_0002361` +#### Removed +- [primitive erythroid progenitor](http://purl.obolibrary.org/obo/CL_0002361) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) + +#### Added +- [primitive erythroid progenitor](http://purl.obolibrary.org/obo/CL_0002361) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl/cl-base#cellxgene_subset) + + +### primitive red blood cell `http://purl.obolibrary.org/obo/CL_0002355` +#### Removed +- [primitive red blood cell](http://purl.obolibrary.org/obo/CL_0002355) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) + + + +### principal gastric gland goblet cell `http://purl.obolibrary.org/obo/CL_1000315` + +#### Added +- [principal gastric gland goblet cell](http://purl.obolibrary.org/obo/CL_1000315) SubClassOf [glandular epithelial cell of stomach](http://purl.obolibrary.org/obo/CL_0002659) + + +### pro-B cell `http://purl.obolibrary.org/obo/CL_0000826` +#### Removed +- [pro-B cell](http://purl.obolibrary.org/obo/CL_0000826) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) + + + +### pro-NK cell `http://purl.obolibrary.org/obo/CL_0000825` +#### Removed +- [pro-NK cell](http://purl.obolibrary.org/obo/CL_0000825) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) + + + +### pro-opiomelanocortin neuron `http://purl.obolibrary.org/obo/CL_4042033` + +#### Added +- [pro-opiomelanocortin neuron](http://purl.obolibrary.org/obo/CL_4042033) [date](http://purl.org/dc/terms/date) "2024-10-15T10:17:41Z"^^[dateTime](http://www.w3.org/2001/XMLSchema#dateTime) + +- [pro-opiomelanocortin neuron](http://purl.obolibrary.org/obo/CL_4042033) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A neuron of the central nervous system that expresses POMC and synthesizes the POMC precursor polypeptide. This neuron type is located in the arcuate nucleus of the hypothalamus and in the nucleus tractus solitarius of the brainstem. The pro-opiomelanocortin neuron is part of the central melanocortin system and it is involved in regulating energy homeostasis, metabolism, and appetite. This neuronal type responds to hormonal signals such as levels of leptin and insulin, and its activation results in the release of α-melanocyte-stimulating hormone (α-MSH), which acts on melanocortin receptors to suppress food intake and increase energy expenditure."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:28192062"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:25870542"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [pro-opiomelanocortin neuron](http://purl.obolibrary.org/obo/CL_4042033) [label](http://www.w3.org/2000/01/rdf-schema#label) "pro-opiomelanocortin neuron"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [pro-opiomelanocortin neuron](http://purl.obolibrary.org/obo/CL_4042033) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "POMC-expressing neuron"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:34002087"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [pro-opiomelanocortin neuron](http://purl.obolibrary.org/obo/CL_4042033) [id](http://www.geneontology.org/formats/oboInOwl#id) "CL:4042033"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [pro-opiomelanocortin neuron](http://purl.obolibrary.org/obo/CL_4042033) [contributor](http://purl.org/dc/terms/contributor) [0000-0002-0098-8958](https://orcid.org/0000-0002-0098-8958) + +- [pro-opiomelanocortin neuron](http://purl.obolibrary.org/obo/CL_4042033) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "POMC neuron"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:34002087"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [pro-opiomelanocortin neuron](http://purl.obolibrary.org/obo/CL_4042033) [comment](http://www.w3.org/2000/01/rdf-schema#comment) "Pro-opiomelanocortin neurons have a diverse projection pattern. The neurons in the rostral arcuate nucleus project to autonomic areas, caudal arcuate POMC neurons project mainly to hypothalamic areas (Toda et al., 2017). Dysregulation of pro-opiomelanocortin neurons is associated with obesity and metabolic disorders (Quarta et al., 2020)."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:28192062"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:33633406"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- Class: [pro-opiomelanocortin neuron](http://purl.obolibrary.org/obo/CL_4042033) + +- [pro-opiomelanocortin neuron](http://purl.obolibrary.org/obo/CL_4042033) SubClassOf [RO_0002292](http://purl.obolibrary.org/obo/RO_0002292) some [PR_000013015](http://purl.obolibrary.org/obo/PR_000013015) + +- [pro-opiomelanocortin neuron](http://purl.obolibrary.org/obo/CL_4042033) SubClassOf [neuroendocrine cell](http://purl.obolibrary.org/obo/CL_0000165) + + +### proerythroblast `http://purl.obolibrary.org/obo/CL_0000547` +#### Removed +- [proerythroblast](http://purl.obolibrary.org/obo/CL_0000547) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) + + + +### promonocyte `http://purl.obolibrary.org/obo/CL_0000559` +#### Removed +- [promonocyte](http://purl.obolibrary.org/obo/CL_0000559) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) + + + +### promyelocyte `http://purl.obolibrary.org/obo/CL_0000836` +#### Removed +- [promyelocyte](http://purl.obolibrary.org/obo/CL_0000836) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) + + + +### prostate neuroendocrine cell `http://purl.obolibrary.org/obo/CL_0017002` +#### Removed +- [prostate neuroendocrine cell](http://purl.obolibrary.org/obo/CL_0017002) [created by](http://www.geneontology.org/formats/oboInOwl#created_by) "http://orcid.org/0000-0003-2473-2313"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [prostate neuroendocrine cell](http://purl.obolibrary.org/obo/CL_0017002) [contributor](http://purl.org/dc/terms/contributor) [0000-0003-2473-2313](http://orcid.org/0000-0003-2473-2313) + +- [prostate neuroendocrine cell](http://purl.obolibrary.org/obo/CL_0017002) SubClassOf [glandular secretory epithelial cell](http://purl.obolibrary.org/obo/CL_0000150) + + +### pseudounipolar neuron `http://purl.obolibrary.org/obo/CL_0000105` +#### Removed +- [pseudounipolar neuron](http://purl.obolibrary.org/obo/CL_0000105) SubClassOf [neuron](http://purl.obolibrary.org/obo/CL_0000540) + +#### Added +- [pseudounipolar neuron](http://purl.obolibrary.org/obo/CL_0000105) SubClassOf [peripheral nervous system neuron](http://purl.obolibrary.org/obo/CL_2000032) + + +### pulmonary alveolar type 1 cell `http://purl.obolibrary.org/obo/CL_0002062` + +#### Added +- [pulmonary alveolar type 1 cell](http://purl.obolibrary.org/obo/CL_0002062) [comment](http://www.w3.org/2000/01/rdf-schema#comment) "The marker set AGER can identify the Human cell type pulmonary alveolar type 1 cell in the Lung with a confidence of 0.85 (NS-Forest FBeta value)."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://doi.org/10.5281/zenodo.11165918"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [pulmonary alveolar type 1 cell](http://purl.obolibrary.org/obo/CL_0002062) SubClassOf [RO_0015004](http://purl.obolibrary.org/obo/RO_0015004) some [CLM_1000008](http://purl.obolibrary.org/obo/CLM_1000008) + + +### pulmonary alveolar type 2 cell `http://purl.obolibrary.org/obo/CL_0002063` + +#### Added +- [pulmonary alveolar type 2 cell](http://purl.obolibrary.org/obo/CL_0002063) [comment](http://www.w3.org/2000/01/rdf-schema#comment) "The marker set SFTPA1 can identify the Human cell type pulmonary alveolar type 2 cell in the Lung with a confidence of 0.95 (NS-Forest FBeta value)."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://doi.org/10.5281/zenodo.11165918"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [pulmonary alveolar type 2 cell](http://purl.obolibrary.org/obo/CL_0002063) SubClassOf [secretory epithelial cell](http://purl.obolibrary.org/obo/CL_1100001) + +- [pulmonary alveolar type 2 cell](http://purl.obolibrary.org/obo/CL_0002063) SubClassOf [RO_0015004](http://purl.obolibrary.org/obo/RO_0015004) some [CLM_1000009](http://purl.obolibrary.org/obo/CLM_1000009) + + +### pulmonary interstitial fibroblast `http://purl.obolibrary.org/obo/CL_0002241` + +#### Added +- [pulmonary interstitial fibroblast](http://purl.obolibrary.org/obo/CL_0002241) [comment](http://www.w3.org/2000/01/rdf-schema#comment) "The marker set DPT, APOD can identify the Human cell type pulmonary interstitial fibroblast in the Lung with a confidence of 0.58 (NS-Forest FBeta value)."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://doi.org/10.5281/zenodo.11165918"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [pulmonary interstitial fibroblast](http://purl.obolibrary.org/obo/CL_0002241) [RO_0002175](http://purl.obolibrary.org/obo/RO_0002175) [NCBITaxon_9606](http://purl.obolibrary.org/obo/NCBITaxon_9606) + +- [pulmonary interstitial fibroblast](http://purl.obolibrary.org/obo/CL_0002241) SubClassOf [RO_0015004](http://purl.obolibrary.org/obo/RO_0015004) some [CLM_1000046](http://purl.obolibrary.org/obo/CLM_1000046) + + +### pulmonary ionocyte `http://purl.obolibrary.org/obo/CL_0017000` +#### Removed +- [pulmonary ionocyte](http://purl.obolibrary.org/obo/CL_0017000) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +The pulmonary ionocyte is a relatively newly identified, specific epithelial cell type found primarily in the pulmonary or respiratory system. Discovered through novel mapping techniques in 2018, these cells are surprisingly rare, making up less than 2% of the cells in the lung's airway, yet they play an essential role in the airway surface liquid and mucus regulation, a crucial factor in lung health. +The main responsibility of the pulmonary ionocyte pertains to the regulation and mobilization of chloride ions. They express a high level of CFTR (Cystic Fibrosis Transmembrane Conductance Regulator) gene, which encodes a protein channel across the membrane of cells that produce mucus, sweat, saliva, tears, and digestive enzymes. The activity of CFTR regulates the movement of chloride ions and fluids in and out of cells, which helps maintain a balance of fluid in the organs they are expressed in. If CFTR is dysfunctional, it can cause conditions such as cystic fibrosis, characterized by thick, sticky mucus that can clog the lungs and obstruct the pancreas, leading to respiratory and digestive issues. +The discovery of this cell type offers new doors to the treatment and further understanding of diseases like cystic fibrosis. Increased understanding of pulmonary ionocytes could contribute to the development of novel therapeutic approaches to manipulate the function of CFTR in the lungs and other organs affected by dysfunctional CFTR."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1146/annurev-pathol-042420-094031"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1038/s41586-018-0393-7"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1172/JCI171268"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [pulmonary ionocyte](http://purl.obolibrary.org/obo/CL_0017000) [comment](http://www.w3.org/2000/01/rdf-schema#comment) "The marker set ASCL3, BSND can identify the Human cell type pulmonary ionocyte in the Lung with a confidence of 0.82 (NS-Forest FBeta value)."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://doi.org/10.5281/zenodo.11165918"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [pulmonary ionocyte](http://purl.obolibrary.org/obo/CL_0017000) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +The pulmonary ionocyte is a relatively newly identified, specific epithelial cell type found primarily in the pulmonary or respiratory system. Discovered through novel mapping techniques in 2018, these cells are surprisingly rare, making up less than 2% of the cells in the lung's airway, yet they play an essential role in the airway surface liquid and mucus regulation, a crucial factor in lung health. +The main responsibility of the pulmonary ionocyte pertains to the regulation and mobilization of chloride ions. They express a high level of CFTR (Cystic Fibrosis Transmembrane Conductance Regulator) gene, which encodes a protein channel across the membrane of cells that produce mucus, sweat, saliva, tears, and digestive enzymes. The activity of CFTR regulates the movement of chloride ions and fluids in and out of cells, which helps maintain a balance of fluid in the organs they are expressed in. If CFTR is dysfunctional, it can cause conditions such as cystic fibrosis, characterized by thick, sticky mucus that can clog the lungs and obstruct the pancreas, leading to respiratory and digestive issues. +The discovery of this cell type offers new doors to the treatment and further understanding of diseases like cystic fibrosis. Increased understanding of pulmonary ionocytes could contribute to the development of novel therapeutic approaches to manipulate the function of CFTR in the lungs and other organs affected by dysfunctional CFTR."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1146/annurev-pathol-042420-094031"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1038/s41586-018-0393-7"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1172/JCI171268"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [pulmonary ionocyte](http://purl.obolibrary.org/obo/CL_0017000) SubClassOf [RO_0015004](http://purl.obolibrary.org/obo/RO_0015004) some [CLM_1000032](http://purl.obolibrary.org/obo/CLM_1000032) + + +### pulmonary neuroendocrine cell `http://purl.obolibrary.org/obo/CL_1000223` +#### Removed +- [pulmonary neuroendocrine cell](http://purl.obolibrary.org/obo/CL_1000223) [has_exact_synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "pulmonary neuroendocrine cell"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:33355253"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [pulmonary neuroendocrine cell](http://purl.obolibrary.org/obo/CL_1000223) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +Lung neuroendocrine cells, also commonly known as pulmonary neuroendocrine cells (PNECs), are predominantly located in the respiratory epithelium of the bronchial and bronchiolar airways in the lungs. These cells, characterised by their small size and granular appearance, have a distinctive morphology that sets them apart from other lung cells. They are considered part of the diffuse neuroendocrine system due to their scattered distribution through the epithelium and have been classified into solitary cells and clustered forms known as neuroepithelial bodies. +The primary function of PNECs is linked to regulation and maintenance of the lung environment. They are sensory in nature and can secrete various bioactive substances such as serotonin, calcitonin, calcitonin gene-related peptides, and bombesin-like peptides which modulate airway smooth muscle tone and influence gut motility. For example, they act as oxygen sensors in response to hypoxia and are responsible for releasing neuropeptides that can induce responses. Moreover, PNECs provide an afferent function as they are equipped with long microvilli that project into the lumen of the bronchus and react to changes in the chemical composition of the luminal content."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1016/bs.ctdb.2018.12.002"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1016/j.devcel.2020.09.024"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1242/dmm.046920"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [pulmonary neuroendocrine cell](http://purl.obolibrary.org/obo/CL_1000223) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A neuroendocrine cell that is part of respiratory epithelium of the lung and is involved in the sensory detection of environmental stimuli, including hypoxia, nicotine and air pressure. Ultrastructurally, this cell type is characterized by the presence of cytoplasmic dense core granules, which are considered the storage sites of amine and peptide hormones. Lung neuroendocrine cells are innervated and appear as solitary cells or as clustered masses, localized at airway bifurcation sites, called neuroepithelial bodies that can release serotonin in response to hypoxia and interact with sensory nerve terminals. Lung neuroendocrine cells also function as reserve stem cells that repair the surrounding epithelium after injury."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "doi:10.3109/01902148209069653"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "doi:10.7554/eLife.78216"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:33355253"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [pulmonary neuroendocrine cell](http://purl.obolibrary.org/obo/CL_1000223) [label](http://www.w3.org/2000/01/rdf-schema#label) "lung neuroendocrine cell"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [pulmonary neuroendocrine cell](http://purl.obolibrary.org/obo/CL_1000223) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A neuroendocrine cell that is part of respiratory epithelium of the lung and is involved in the sensory detection of environmental stimuli, including hypoxia, nicotine and air pressure. Ultrastructurally, this cell type is characterized by the presence of cytoplasmic dense core granules, which are considered the storage sites of amine and peptide hormones. Pulmonary neuroendocrine cells are innervated and appear as solitary cells or as clustered masses, localized at airway bifurcation sites, called neuroepithelial bodies that can release serotonin in response to hypoxia and interact with sensory nerve terminals. Pulmonary neuroendocrine cells also function as reserve stem cells that repair the surrounding epithelium after injury."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "doi:10.3109/01902148209069653"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "doi:10.7554/eLife.78216"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:33355253"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [pulmonary neuroendocrine cell](http://purl.obolibrary.org/obo/CL_1000223) [comment](http://www.w3.org/2000/01/rdf-schema#comment) "The marker set CHGA, GRP can identify the Human cell type lung neuroendocrine cell in the Lung with a confidence of 0.94 (NS-Forest FBeta value)."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://doi.org/10.5281/zenodo.11165918"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [pulmonary neuroendocrine cell](http://purl.obolibrary.org/obo/CL_1000223) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Lung neuroendocrine cells, also commonly known as pulmonary neuroendocrine cells (PNECs), are predominantly located in the respiratory epithelium of the bronchial and bronchiolar airways in the lungs. These cells, characterised by their small size and granular appearance, have a distinctive morphology that sets them apart from other lung cells. They are considered part of the diffuse neuroendocrine system due to their scattered distribution through the epithelium and have been classified into solitary cells and clustered forms known as neuroepithelial bodies. +The primary function of PNECs is linked to regulation and maintenance of the lung environment. They are sensory in nature and can secrete various bioactive substances such as serotonin, calcitonin, calcitonin gene-related peptides, and bombesin-like peptides which modulate airway smooth muscle tone and influence gut motility. For example, they act as oxygen sensors in response to hypoxia and are responsible for releasing neuropeptides that can induce responses. Moreover, PNECs provide an afferent function as they are equipped with long microvilli that project into the lumen of the bronchus and react to changes in the chemical composition of the luminal content."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1016/bs.ctdb.2018.12.002"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1016/j.devcel.2020.09.024"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1242/dmm.046920"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [pulmonary neuroendocrine cell](http://purl.obolibrary.org/obo/CL_1000223) [has_exact_synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "lung neuroendocrine cell"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:15018448"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [pulmonary neuroendocrine cell](http://purl.obolibrary.org/obo/CL_1000223) [label](http://www.w3.org/2000/01/rdf-schema#label) "pulmonary neuroendocrine cell"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [pulmonary neuroendocrine cell](http://purl.obolibrary.org/obo/CL_1000223) SubClassOf [RO_0015004](http://purl.obolibrary.org/obo/RO_0015004) some [CLM_1000043](http://purl.obolibrary.org/obo/CLM_1000043) + + +### pvalb GABAergic cortical interneuron `http://purl.obolibrary.org/obo/CL_4023018` + +#### Added +- [pvalb GABAergic cortical interneuron](http://purl.obolibrary.org/obo/CL_4023018) [comment](http://www.w3.org/2000/01/rdf-schema#comment) "The marker set PVALB, TAC1, MYO5B can identify the Human cell type pvalb GABAergic cortical interneuron in the Brain with a confidence of 0.691998764 (NS-Forest FBeta value)."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://doi.org/10.5281/zenodo.11165918"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [pvalb GABAergic cortical interneuron](http://purl.obolibrary.org/obo/CL_4023018) [RO_0002175](http://purl.obolibrary.org/obo/RO_0002175) [NCBITaxon_9606](http://purl.obolibrary.org/obo/NCBITaxon_9606) + +- [pvalb GABAergic cortical interneuron](http://purl.obolibrary.org/obo/CL_4023018) SubClassOf [RO_0015004](http://purl.obolibrary.org/obo/RO_0015004) some [CLM_1000080](http://purl.obolibrary.org/obo/CLM_1000080) + + +### pyloric gastric gland goblet cell `http://purl.obolibrary.org/obo/CL_1000323` + +#### Added +- [pyloric gastric gland goblet cell](http://purl.obolibrary.org/obo/CL_1000323) SubClassOf [glandular epithelial cell of stomach](http://purl.obolibrary.org/obo/CL_0002659) + + +### pyramidal neuron `http://purl.obolibrary.org/obo/CL_0000598` +#### Removed +- [pyramidal neuron](http://purl.obolibrary.org/obo/CL_0000598) SubClassOf [multipolar neuron](http://purl.obolibrary.org/obo/CL_0000104) + +#### Added +- [pyramidal neuron](http://purl.obolibrary.org/obo/CL_0000598) SubClassOf [central nervous system neuron](http://purl.obolibrary.org/obo/CL_2000029) + + +### raphe nuclei neuron `http://purl.obolibrary.org/obo/CL_0002610` +#### Removed +- [raphe nuclei neuron](http://purl.obolibrary.org/obo/CL_0002610) EquivalentTo [CNS neuron (sensu Vertebrata)](http://purl.obolibrary.org/obo/CL_0000117) and ([RO_0002100](http://purl.obolibrary.org/obo/RO_0002100) some [UBERON_0004684](http://purl.obolibrary.org/obo/UBERON_0004684)) + +- [raphe nuclei neuron](http://purl.obolibrary.org/obo/CL_0002610) SubClassOf [CNS neuron (sensu Vertebrata)](http://purl.obolibrary.org/obo/CL_0000117) + - [is_inferred](http://www.geneontology.org/formats/oboInOwl#is_inferred) "true"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [raphe nuclei neuron](http://purl.obolibrary.org/obo/CL_0002610) EquivalentTo [neuron](http://purl.obolibrary.org/obo/CL_0000540) and ([RO_0002100](http://purl.obolibrary.org/obo/RO_0002100) some [UBERON_0004684](http://purl.obolibrary.org/obo/UBERON_0004684)) + + +### regular atrial cardiac myocyte `http://purl.obolibrary.org/obo/CL_0002129` + +#### Added +- [regular atrial cardiac myocyte](http://purl.obolibrary.org/obo/CL_0002129) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Regular atrial cardiac myocytes, also known as atrial myocytes, are specialized muscle cells found in the atria – the upper chambers of the heart. They contract and relax during the heart's cycle, modulating the pumping of blood through the atria and into the ventricles. Additionally, endowed with inherent rhythmic electrical activity, atrial myocytes contribute significantly to the initiation and propagation of the heart’s electrical impulses. +A distinguishing feature that separates atrial myocytes from other cardiac myocytes is their ability to synthesize and secrete atrial natriuretic peptide (ANP) in response to atrial stretch or dilatation. ANP acts as a potent vasodilator and diuretic, helping to maintain blood pressure and volume homeostasis. The phenomena of atrial stretch or distension, which triggers ANP release, is often in response to excess blood volume entering the heart, providing a mechanism at the cellular level which actively regulates systemic cardiovascular balance. +Like all cardiac myocytes, atrial myocytes are embedded in a dense network of connective tissue that provides structural support. These cells are characterized by a single, centrally located nucleus, and overall, have a rod-like appearance with branching ends that connect with adjacent cells to form a continuous, synchronized ensemble. Their cytoplasm is abundant with mitochondria, reflecting the high energy demand associated with constant contraction and relaxation. At the ultrastructural level, atrial myocytes display striations due to the regular arrangement of actin and myosin proteins, which facilitate the contraction process essential for the heart's pump function."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://www.sciencedirect.com/topics/agricultural-and-biological-sciences/cardiac-muscle"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1016/j.bbamcr.2015.11.025"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1172/JCI25417"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://www.sciencedirect.com/topics/neuroscience/cardiac-action-potential"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1111/pace.14107"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [regular atrial cardiac myocyte](http://purl.obolibrary.org/obo/CL_0002129) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://cellxgene.cziscience.com/cellguide/CL_0002129"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### regular cardiac myocyte `http://purl.obolibrary.org/obo/CL_0002098` + +#### Added +- [regular cardiac myocyte](http://purl.obolibrary.org/obo/CL_0002098) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://cellxgene.cziscience.com/cellguide/CL_0002098"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [regular cardiac myocyte](http://purl.obolibrary.org/obo/CL_0002098) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Cardiac myocytes, also known as cardiac muscle cells, form the majority of the cardiac tissue and are responsible for the contractile function of the heart. These myocytes are columnar-shaped cells with centrally located nuclei, and they exhibit visibly striated cytoplasm due to the organized array of myofibrils, which are composed of filaments of actin and myosin. Cardiac myocytes connect with each other through specialized structures called intercalated discs, facilitating electrical and mechanical continuity and enabling synchronous contraction of the heart. They also possess a high number of mitochondria to meet their high energy demand for continuous heartbeat action. +Cardiac myocytes are capable of automaticity, meaning they have the unique ability to spontaneously and rhythmically generate their electrical impulses, a characteristic led by pacemaker cells. The electrical signals initiated and propagated in these cells are responsible for heartbeats. They also respond to the electrical signals transmitted by the autonomic nervous system and chemical signals like hormones. Thus, cardiac myocytes not only participate in maintaining the heart’s function but also play a role in modulating heart rate and strength of contraction in response to the body's changing needs. Consequently, malfunction of these cells leads to serious cardiac diseases such as heart failure and arrhythmias."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://www.sciencedirect.com/topics/agricultural-and-biological-sciences/cardiac-muscle"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.3389/fphys.2013.00102"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3164530"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://www.ncbi.nlm.nih.gov/books/NBK572070"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### renal alpha-intercalated cell `http://purl.obolibrary.org/obo/CL_0005011` +#### Removed +- [renal alpha-intercalated cell](http://purl.obolibrary.org/obo/CL_0005011) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +Renal alpha-intercalated cells are located within the connecting tubules and collecting ducts of the kidneys, which are components of the kidney's complex nephron system. Along with beta-intercalated cells, they play a critical role in the body’s acid-base balance. +Renal alpha-intercalated cells contain an abundance of proton pumps and enzymes like carbonic anhydrase, which aid in the transport of hydrogen ions for secretion in the urine. The bicarbonate/chloride transporters on their apical membrane meanwhile take up bicarbonate ions from the urine and supply them back into the blood. Through this mechanism, these cells contribute significantly to the neutrality of blood pH, and dysfunction of renal alpha-intercalated cells often leads to distal renal tubular acidosis, a condition resulting in acidic blood and alkaline urine."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1172/JCI63492"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.3390/diseases2020071"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1016/j.semnephrol.2019.04.005"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1152/physiol.00008.2011"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [renal alpha-intercalated cell](http://purl.obolibrary.org/obo/CL_0005011) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Renal alpha-intercalated cells are located within the connecting tubules and collecting ducts of the kidneys, which are components of the kidney's complex nephron system. Along with beta-intercalated cells, they play a critical role in the body’s acid-base balance. +Renal alpha-intercalated cells contain an abundance of proton pumps and enzymes like carbonic anhydrase, which aid in the transport of hydrogen ions for secretion in the urine. The bicarbonate/chloride transporters on their apical membrane meanwhile take up bicarbonate ions from the urine and supply them back into the blood. Through this mechanism, these cells contribute significantly to the neutrality of blood pH, and dysfunction of renal alpha-intercalated cells often leads to distal renal tubular acidosis, a condition resulting in acidic blood and alkaline urine."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1172/JCI63492"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.3390/diseases2020071"^^[string](http://www.w3.org/2001/XMLSchema#string) -### mature T cell `http://purl.obolibrary.org/obo/CL_0002419` + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1016/j.semnephrol.2019.04.005"^^[string](http://www.w3.org/2001/XMLSchema#string) -#### Added -- [mature T cell](http://purl.obolibrary.org/obo/CL_0002419) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1152/physiol.00008.2011"^^[string](http://www.w3.org/2001/XMLSchema#string) -### melanocyte `http://purl.obolibrary.org/obo/CL_0000148` +### renal intercalated cell `http://purl.obolibrary.org/obo/CL_0005010` +#### Removed +- [renal intercalated cell](http://purl.obolibrary.org/obo/CL_0005010) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +Renal intercalated cells are specialized cells located in the collecting duct system of the kidneys. The primary role of intercalated cells is to reabsorb bicarbonate ions and secrete hydrogen ions, thereby maintaining the acid-base homeostasis in the blood. They comprise two main subtypes primarily distinguished by their functional and morphological attributes: alpha and beta intercalated cells. +Alpha intercalated cells are more predominant when the body is in a state of acidosis, a condition characterized by an increased acidity of the blood. These cells are specialized in secreting excessive hydrogen ions into the urine through a mechanism involving vacuolar H+-ATPase and H+/K+-ATPase pumps on their apical membranes. They simultaneously reabsorb bicarbonate ions from the tubular fluid and return them to the bloodstream via mechanisms involving carbonic anhydrase II and bicarbonate/chloride exchangers on the basolateral membrane. This dual process helps to increase blood pH towards normal levels. +When the body is in a state of alkalosis, a condition characterized by lowered levels of hydrogen ions in the blood, beta intercalated cells are more predominant. They primarily reabsorb hydrogen ions from the tubular fluid through vacuolar H+-ATPase and H+/K+-ATPase pumps on their basolateral membranes, while secreting bicarbonate ions into the urine via pendrin, a bicarbonate/chloride exchanger in the apical membrane. These mechanisms work together to decrease blood pH towards normal levels. +In summary, renal intercalated cells play a critical role in the delicate balance of the body’s pH, safeguarding the body from potential harm caused by acidemia or alkalemia."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1681/ASN.V1011"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1161/HYPERTENSIONAHA.121.16492"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1152/ajprenal.2000.279.1.F195"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.2215/CJN.08880914"^^[string](http://www.w3.org/2001/XMLSchema#string) #### Added -- [melanocyte](http://purl.obolibrary.org/obo/CL_0000148) SubClassOf [eukaryotic cell](http://purl.obolibrary.org/obo/CL_0000255) +- [renal intercalated cell](http://purl.obolibrary.org/obo/CL_0005010) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Renal intercalated cells are specialized cells located in the collecting duct system of the kidneys. The primary role of intercalated cells is to reabsorb bicarbonate ions and secrete hydrogen ions, thereby maintaining the acid-base homeostasis in the blood. They comprise two main subtypes primarily distinguished by their functional and morphological attributes: alpha and beta intercalated cells. +Alpha intercalated cells are more predominant when the body is in a state of acidosis, a condition characterized by an increased acidity of the blood. These cells are specialized in secreting excessive hydrogen ions into the urine through a mechanism involving vacuolar H+-ATPase and H+/K+-ATPase pumps on their apical membranes. They simultaneously reabsorb bicarbonate ions from the tubular fluid and return them to the bloodstream via mechanisms involving carbonic anhydrase II and bicarbonate/chloride exchangers on the basolateral membrane. This dual process helps to increase blood pH towards normal levels. +When the body is in a state of alkalosis, a condition characterized by lowered levels of hydrogen ions in the blood, beta intercalated cells are more predominant. They primarily reabsorb hydrogen ions from the tubular fluid through vacuolar H+-ATPase and H+/K+-ATPase pumps on their basolateral membranes, while secreting bicarbonate ions into the urine via pendrin, a bicarbonate/chloride exchanger in the apical membrane. These mechanisms work together to decrease blood pH towards normal levels. +In summary, renal intercalated cells play a critical role in the delicate balance of the body’s pH, safeguarding the body from potential harm caused by acidemia or alkalemia."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1681/ASN.V1011"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1161/HYPERTENSIONAHA.121.16492"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1152/ajprenal.2000.279.1.F195"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.2215/CJN.08880914"^^[string](http://www.w3.org/2001/XMLSchema#string) -### memory CCR4-positive regulatory T cell `http://purl.obolibrary.org/obo/CL_0001046` +### renal principal cell `http://purl.obolibrary.org/obo/CL_0005009` #### Removed -- [memory CCR4-positive regulatory T cell](http://purl.obolibrary.org/obo/CL_0001046) EquivalentTo [memory regulatory T cell](http://purl.obolibrary.org/obo/CL_0002678) and ([RO_0002104](http://purl.obolibrary.org/obo/RO_0002104) some [PR_000001017](http://purl.obolibrary.org/obo/PR_000001017)) and ([RO_0002104](http://purl.obolibrary.org/obo/RO_0002104) some [PR_000001200](http://purl.obolibrary.org/obo/PR_000001200)) and ([RO_0002160](http://purl.obolibrary.org/obo/RO_0002160) some [NCBITaxon_9606](http://purl.obolibrary.org/obo/NCBITaxon_9606)) +- [renal principal cell](http://purl.obolibrary.org/obo/CL_0005009) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +Renal principal cells are the major cell type in the initial collecting tubule and the cortical and outer medullary collecting ducts, as well as the connecting tubule, in the nephrons of the kidneys. +A key function of renal principal cells is the regulation of water balance in the body. These cells express aquaporin-2 (AQP2) water channels, which facilitate the reabsorption of water from the fluid within the renal tubule lumen back into the blood. The translocation of AQP2 to the cell membrane is controlled by the hormone vasopressin: In response to high vasopressin levels, AQP2 moves to the cell membrane, allowing water to pass through effectively and be reabsorbed, therefore concentrating the urine. Conversely, in low vasopressin conditions, AQP2 is removed from the membrane, reducing water reabsorption and diluting the urine. +Renal principal cells are also involved in the regulation of sodium and potassium levels in the body. They have sodium channels (ENaC) in their luminal membranes which permit the reabsorption of sodium ions from the tubule fluid back into the blood, resulting in a net reabsorption of sodium ions into the systemic circulation. This process is controlled, in part, by the hormone aldosterone. Additionally, renal principal cells contain potassium channels that facilitate the secretion of potassium ions into the urine. The activities of these channels, in coordination with other cell types in the nephron, are critical for maintaining electrolyte balance and overall body homeostasis."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.2215/CJN.05760513"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.2215/CJN.08580813"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [memory CCR4-positive regulatory T cell](http://purl.obolibrary.org/obo/CL_0001046) SubClassOf [RO_0002160](http://purl.obolibrary.org/obo/RO_0002160) some [NCBITaxon_9606](http://purl.obolibrary.org/obo/NCBITaxon_9606) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1016/j.krcp.2013.07.005"^^[string](http://www.w3.org/2001/XMLSchema#string) #### Added -- [memory CCR4-positive regulatory T cell](http://purl.obolibrary.org/obo/CL_0001046) EquivalentTo [memory regulatory T cell](http://purl.obolibrary.org/obo/CL_0002678) and ([RO_0002104](http://purl.obolibrary.org/obo/RO_0002104) some [PR_000001017](http://purl.obolibrary.org/obo/PR_000001017)) and ([RO_0002104](http://purl.obolibrary.org/obo/RO_0002104) some [PR_000001200](http://purl.obolibrary.org/obo/PR_000001200)) and ([RO_0002162](http://purl.obolibrary.org/obo/RO_0002162) some [NCBITaxon_9606](http://purl.obolibrary.org/obo/NCBITaxon_9606)) +- [renal principal cell](http://purl.obolibrary.org/obo/CL_0005009) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Renal principal cells are the major cell type in the initial collecting tubule and the cortical and outer medullary collecting ducts, as well as the connecting tubule, in the nephrons of the kidneys. +A key function of renal principal cells is the regulation of water balance in the body. These cells express aquaporin-2 (AQP2) water channels, which facilitate the reabsorption of water from the fluid within the renal tubule lumen back into the blood. The translocation of AQP2 to the cell membrane is controlled by the hormone vasopressin: In response to high vasopressin levels, AQP2 moves to the cell membrane, allowing water to pass through effectively and be reabsorbed, therefore concentrating the urine. Conversely, in low vasopressin conditions, AQP2 is removed from the membrane, reducing water reabsorption and diluting the urine. +Renal principal cells are also involved in the regulation of sodium and potassium levels in the body. They have sodium channels (ENaC) in their luminal membranes which permit the reabsorption of sodium ions from the tubule fluid back into the blood, resulting in a net reabsorption of sodium ions into the systemic circulation. This process is controlled, in part, by the hormone aldosterone. Additionally, renal principal cells contain potassium channels that facilitate the secretion of potassium ions into the urine. The activities of these channels, in coordination with other cell types in the nephron, are critical for maintaining electrolyte balance and overall body homeostasis."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.2215/CJN.05760513"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.2215/CJN.08580813"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [memory CCR4-positive regulatory T cell](http://purl.obolibrary.org/obo/CL_0001046) SubClassOf [RO_0002162](http://purl.obolibrary.org/obo/RO_0002162) some [NCBITaxon_9606](http://purl.obolibrary.org/obo/NCBITaxon_9606) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1016/j.krcp.2013.07.005"^^[string](http://www.w3.org/2001/XMLSchema#string) -### mesenchymal cell `http://purl.obolibrary.org/obo/CL_0008019` +### respiratory airway secretory cell `http://purl.obolibrary.org/obo/CL_4052031` #### Added -- [mesenchymal cell](http://purl.obolibrary.org/obo/CL_0008019) SubClassOf [eukaryotic cell](http://purl.obolibrary.org/obo/CL_0000255) +- [respiratory airway secretory cell](http://purl.obolibrary.org/obo/CL_4052031) [id](http://www.geneontology.org/formats/oboInOwl#id) "CL:4052031"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [respiratory airway secretory cell](http://purl.obolibrary.org/obo/CL_4052031) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A secretory epithelial cell of the respiratory and terminal bronchioles."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:35355013"^^[string](http://www.w3.org/2001/XMLSchema#string) -### mesenchymal stem cell of adipose tissue `http://purl.obolibrary.org/obo/CL_0002570` + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:36796082"^^[string](http://www.w3.org/2001/XMLSchema#string) -#### Added -- [mesenchymal stem cell of adipose tissue](http://purl.obolibrary.org/obo/CL_0002570) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. +- [respiratory airway secretory cell](http://purl.obolibrary.org/obo/CL_4052031) [comment](http://www.w3.org/2000/01/rdf-schema#comment) "The respiratory airway secretory cell is cuboidal and has a unique transcriptomic profile compared to other epithelial cells in the same region. In humans, it functions as a multipotent progenitor, capable of regenerating alveolar type 2 (AT2) cells."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:35355013"^^[string](http://www.w3.org/2001/XMLSchema#string) -Mesenchymal stem cells of adipose tissue, also known commonly as adipose-derived stem cells (ADSCs), are a population of adult stem cells that can be obtained easily from adipose tissues. They have many of the same regenerative properties as other mesenchymal stem cells, but are more easily accessible than bone marrow-derived stem cells. -Adipose-derived stem cells show immense promise in the field of regenerative medicine due to their ability to differentiate into adipocytes, chondrocytes, myocytes, osteoblasts, and other cell types. ADSCs also possess immunomodulatory and homeostatic functions: they have the ability to suppress immune responses and provide a therapeutic environment for tissue repair and regeneration, as well as supporting the proliferation of adipocytes and the overall expansion of adipose tissue and contributing to the tissue's ability to react to demands of energy storage and mobilization. Dysfunction of these cells may contribute to metabolic complications observed in obesity and diabetes. -ADSCs have been used for therapeutic applications such as pathological wound healing, severe refractory acute graft-versus-host disease, and idiopathic thrombocytopenic purpura."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1111/dgd.12049"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:36796082"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1016/j.tibtech.2006.01.010"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [respiratory airway secretory cell](http://purl.obolibrary.org/obo/CL_4052031) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "terminal and respiratory bronchioles secretory cell"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:35355018"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1096/fj.202100332R"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [respiratory airway secretory cell](http://purl.obolibrary.org/obo/CL_4052031) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "RAS cell"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003000](http://purl.obolibrary.org/obo/OMO_0003000) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1016/j.biopha.2019.108765"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:36796082"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1038/s41536-019-0083-6"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [respiratory airway secretory cell](http://purl.obolibrary.org/obo/CL_4052031) [label](http://www.w3.org/2000/01/rdf-schema#label) "respiratory airway secretory cell"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [mesenchymal stem cell of adipose tissue](http://purl.obolibrary.org/obo/CL_0002570) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://cellxgene.cziscience.com/cellguide/CL_0002570"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [respiratory airway secretory cell](http://purl.obolibrary.org/obo/CL_4052031) [date](http://purl.org/dc/terms/date) "2024-11-29T16:14:31Z"^^[dateTime](http://www.w3.org/2001/XMLSchema#dateTime) +- [respiratory airway secretory cell](http://purl.obolibrary.org/obo/CL_4052031) [contributor](http://purl.org/dc/terms/contributor) [0009-0000-8480-9277](https://orcid.org/0009-0000-8480-9277) -### mesodermal cell `http://purl.obolibrary.org/obo/CL_0000222` +- Class: [respiratory airway secretory cell](http://purl.obolibrary.org/obo/CL_4052031) -#### Added -- [mesodermal cell](http://purl.obolibrary.org/obo/CL_0000222) SubClassOf [eukaryotic cell](http://purl.obolibrary.org/obo/CL_0000255) +- [respiratory airway secretory cell](http://purl.obolibrary.org/obo/CL_4052031) SubClassOf [BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0002051](http://purl.obolibrary.org/obo/UBERON_0002051) + +- [respiratory airway secretory cell](http://purl.obolibrary.org/obo/CL_4052031) SubClassOf [epithelial cell of lung](http://purl.obolibrary.org/obo/CL_0000082) + +- [respiratory airway secretory cell](http://purl.obolibrary.org/obo/CL_4052031) SubClassOf [secretory epithelial cell](http://purl.obolibrary.org/obo/CL_1100001) +- [respiratory airway secretory cell](http://purl.obolibrary.org/obo/CL_4052031) SubClassOf [epithelial cell of tracheobronchial tree](http://purl.obolibrary.org/obo/CL_0002202) -### mesonephric podocyte `http://purl.obolibrary.org/obo/CL_0002523` +- [respiratory airway secretory cell](http://purl.obolibrary.org/obo/CL_4052031) SubClassOf [lung secretory cell](http://purl.obolibrary.org/obo/CL_1000272) + + +### respiratory basal cell `http://purl.obolibrary.org/obo/CL_0002633` #### Removed -- [mesonephric podocyte](http://purl.obolibrary.org/obo/CL_0002523) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A specialized epithelial cell that contains "feet" that interdigitate with the "feet" of other glomerular epithelial cells in the mesonephros."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [contributor](http://purl.org/dc/terms/contributor) "https://orcid.org/0000-0002-2244-7917"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [respiratory basal cell](http://purl.obolibrary.org/obo/CL_0002633) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +Respiratory basal cells are highly specialized cells that serve a crucial role in the human airway epithelium, predominantly found lining the surfaces of the trachea and bronchi. These cells exhibit a distinctive columnar shape and are attached directly to the basal lamina. They are characterized by the presence of high amounts of cytoplasmic keratins, predominantly keratin 5 and 14, and transcription factor tumor protein (tp63), which set them apart from other types of lung epithelial cells such as ciliated cells and secretory cells. +Basal cells are essential for maintaining airway integrity. They make up one third of all respiratory epithelial cells and serve as stem cells as they can transform into different cell types, like goblet cells, ciliated cells, and club cells, when needed for homeostatic maintenance of the epithelial barrier or to repair and restore a healthy cellular environment after injury. +Their position at the interface between the internal environment and the external atmosphere makes these cells a first line of defense against air-borne irritants, allergens, and pathogens. Their robust, intrinsic reparative properties facilitate effective recovery from such adversities. However, damage to respiratory basal cells or abnormalities in their function are associated with several respiratory pathologies such as asthma, chronic obstructive pulmonary disease, and lung cancer. Therefore, understanding these cells' function, and their role in disease, is crucial for the development of new therapeutic strategies for respiratory disorders."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:110.1038/s41385-020-00370-7"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1186/s12931-022-02042-5"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.3389/falgy.2021.787128"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [respiratory basal cell](http://purl.obolibrary.org/obo/CL_0002633) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Respiratory basal cells are highly specialized cells that serve a crucial role in the human airway epithelium, predominantly found lining the surfaces of the trachea and bronchi. These cells exhibit a distinctive columnar shape and are attached directly to the basal lamina. They are characterized by the presence of high amounts of cytoplasmic keratins, predominantly keratin 5 and 14, and transcription factor tumor protein (tp63), which set them apart from other types of lung epithelial cells such as ciliated cells and secretory cells. +Basal cells are essential for maintaining airway integrity. They make up one third of all respiratory epithelial cells and serve as stem cells as they can transform into different cell types, like goblet cells, ciliated cells, and club cells, when needed for homeostatic maintenance of the epithelial barrier or to repair and restore a healthy cellular environment after injury. +Their position at the interface between the internal environment and the external atmosphere makes these cells a first line of defense against air-borne irritants, allergens, and pathogens. Their robust, intrinsic reparative properties facilitate effective recovery from such adversities. However, damage to respiratory basal cells or abnormalities in their function are associated with several respiratory pathologies such as asthma, chronic obstructive pulmonary disease, and lung cancer. Therefore, understanding these cells' function, and their role in disease, is crucial for the development of new therapeutic strategies for respiratory disorders."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:110.1038/s41385-020-00370-7"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1186/s12931-022-02042-5"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.3389/falgy.2021.787128"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### respiratory tract epithelial cell `http://purl.obolibrary.org/obo/CL_0002368` +#### Removed +- [respiratory tract epithelial cell](http://purl.obolibrary.org/obo/CL_0002368) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "An endo-epithelial cell of the respiratory tract."^^[string](http://www.w3.org/2001/XMLSchema#string) - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:tfm"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [respiratory tract epithelial cell](http://purl.obolibrary.org/obo/CL_0002368) [label](http://www.w3.org/2000/01/rdf-schema#label) "respiratory epithelial cell"^^[string](http://www.w3.org/2001/XMLSchema#string) + #### Added -- [mesonephric podocyte](http://purl.obolibrary.org/obo/CL_0002523) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A specialized epithelial cell that contains "feet" that interdigitate with the "feet" of other glomerular epithelial cells in the mesonephros."^^[string](http://www.w3.org/2001/XMLSchema#string) +- [respiratory tract epithelial cell](http://purl.obolibrary.org/obo/CL_0002368) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "An epithelial cell of the respiratory tract epithelium. These cells have an endodermal origin."^^[string](http://www.w3.org/2001/XMLSchema#string) - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:tfm"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [mesonephric podocyte](http://purl.obolibrary.org/obo/CL_0002523) [contributor](http://purl.org/dc/terms/contributor) [0000-0002-2244-7917](https://orcid.org/0000-0002-2244-7917) +- [respiratory tract epithelial cell](http://purl.obolibrary.org/obo/CL_0002368) [label](http://www.w3.org/2000/01/rdf-schema#label) "respiratory tract epithelial cell"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [respiratory tract epithelial cell](http://purl.obolibrary.org/obo/CL_0002368) [has_exact_synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "respiratory epithelial cell"^^[string](http://www.w3.org/2001/XMLSchema#string) -### mesothelial cell `http://purl.obolibrary.org/obo/CL_0000077` +### respiratory tract goblet cell `http://purl.obolibrary.org/obo/CL_0002370` #### Removed -- [mesothelial cell](http://purl.obolibrary.org/obo/CL_0000077) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A flattened epithelial cell of mesenchymal origin that lines the serous cavity."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:tfm"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [respiratory tract goblet cell](http://purl.obolibrary.org/obo/CL_0002370) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +The respiratory goblet cell is a highly specialized cell type found primarily within the respiratory tract, including the nose, trachea, and lungs. Named because their shape resembles a goblet - a drinking vessel with a wide body and narrow neck - these cells form a vital part of the respiratory system's protective mechanisms. They are found within the columnar epithelium lining these organs, which forms a barrier between the internal body and the exterior environment. +A principal function of the respiratory goblet cell is the production and secretion of mucus, a carbohydrate-rich, viscous and gel-like substance that plays a critical role in trapping dust, bacteria, viruses, and other airborne particles that are inhaled. The mucus secreted by the goblet cells covers the lining of the respiratory tract, effectively catching these particles and preventing them from reaching the lungs and causing infection. Mucus also provides hydration and lubrication to the respiratory tract surfaces, which is important in maintaining the tissue's health and functioning. +In addition to their mucus-secreting capabilities, respiratory goblet cells also play a significant role in the body's inflammatory responses. When the respiratory system is exposed to irritants or pathogens, the number and activity of goblet cells often increase, leading to a higher production of mucus. This is a protective response designed to trap and neutralize the harmful substances more effectively. However, in conditions like chronic obstructive pulmonary disease (COPD) and asthma, an overproliferation of goblet cells, also known as goblet cell hyperplasia, can lead to excessive mucus production and airway obstruction."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1111/febs.15731"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1016/S1357-2725(02)00083-3"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ISBN:0721662544"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1165/ajrcmb.25.5.f218"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.3109/01902148.2013.791733"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.2147/COPD.S38938"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [respiratory tract goblet cell](http://purl.obolibrary.org/obo/CL_0002370) [label](http://www.w3.org/2000/01/rdf-schema#label) "respiratory goblet cell"^^[string](http://www.w3.org/2001/XMLSchema#string) #### Added -- [mesothelial cell](http://purl.obolibrary.org/obo/CL_0000077) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A flat, squamous-like epithelial cell of mesodermal origin. It forms the mesothelium, which lines the body's serous cavities including the pleural, peritoneal, and pericardial spaces. This cell plays a crucial role in synthesizing and secreting lubricants, such as glycosaminoglycans and surfactants, which minimize friction between adjacent tissues during movement."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:26106328"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [respiratory tract goblet cell](http://purl.obolibrary.org/obo/CL_0002370) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:tfm"^^[string](http://www.w3.org/2001/XMLSchema#string) +The respiratory goblet cell is a highly specialized cell type found primarily within the respiratory tract, including the nose, trachea, and lungs. Named because their shape resembles a goblet - a drinking vessel with a wide body and narrow neck - these cells form a vital part of the respiratory system's protective mechanisms. They are found within the columnar epithelium lining these organs, which forms a barrier between the internal body and the exterior environment. +A principal function of the respiratory goblet cell is the production and secretion of mucus, a carbohydrate-rich, viscous and gel-like substance that plays a critical role in trapping dust, bacteria, viruses, and other airborne particles that are inhaled. The mucus secreted by the goblet cells covers the lining of the respiratory tract, effectively catching these particles and preventing them from reaching the lungs and causing infection. Mucus also provides hydration and lubrication to the respiratory tract surfaces, which is important in maintaining the tissue's health and functioning. +In addition to their mucus-secreting capabilities, respiratory goblet cells also play a significant role in the body's inflammatory responses. When the respiratory system is exposed to irritants or pathogens, the number and activity of goblet cells often increase, leading to a higher production of mucus. This is a protective response designed to trap and neutralize the harmful substances more effectively. However, in conditions like chronic obstructive pulmonary disease (COPD) and asthma, an overproliferation of goblet cells, also known as goblet cell hyperplasia, can lead to excessive mucus production and airway obstruction."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1111/febs.15731"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ISBN:0721662544"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1016/S1357-2725(02)00083-3"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [mesothelial cell](http://purl.obolibrary.org/obo/CL_0000077) [comment](http://www.w3.org/2000/01/rdf-schema#comment) "Mesothelial cells, which morphologically resemble squamous epithelial cells, express both epithelial markers (cytokeratins) and mesenchymal markers (vimentin), reflecting their mesodermal origin. They feature surface microvilli and apical-basal polarity. Under certain conditions, they can undergo mesothelial-to-mesenchymal transition. These cells also produce extracellular matrix proteins, maintain serosal homeostasis, and facilitate fluid transport."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:26106328"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1165/ajrcmb.25.5.f218"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [mesothelial cell](http://purl.obolibrary.org/obo/CL_0000077) SubClassOf [BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0001136](http://purl.obolibrary.org/obo/UBERON_0001136) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.3109/01902148.2013.791733"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.2147/COPD.S38938"^^[string](http://www.w3.org/2001/XMLSchema#string) -### mesothelial cell of pleura `http://purl.obolibrary.org/obo/CL_1000491` +- [respiratory tract goblet cell](http://purl.obolibrary.org/obo/CL_0002370) [has_exact_synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "respiratory goblet cell"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [respiratory tract goblet cell](http://purl.obolibrary.org/obo/CL_0002370) [label](http://www.w3.org/2000/01/rdf-schema#label) "respiratory tract goblet cell"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### respiratory tract hillock cell `http://purl.obolibrary.org/obo/CL_4030023` +#### Removed +- [respiratory tract hillock cell](http://purl.obolibrary.org/obo/CL_4030023) [has_narrow_synonym](http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym) "hillock cell of respiratory tract"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [respiratory tract hillock cell](http://purl.obolibrary.org/obo/CL_4030023) [label](http://www.w3.org/2000/01/rdf-schema#label) "respiratory hillock cell"^^[string](http://www.w3.org/2001/XMLSchema#string) #### Added -- [mesothelial cell of pleura](http://purl.obolibrary.org/obo/CL_1000491) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. +- [respiratory tract hillock cell](http://purl.obolibrary.org/obo/CL_4030023) [has_exact_synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "hillock cell of respiratory tract"^^[string](http://www.w3.org/2001/XMLSchema#string) -Mesothelial cells of the pleura form a significant part of the pleural membrane, a thin, double-layered serous membrane that lines the thoracic cavity and encompasses the lungs. These specialized cells contribute to the pleura's key function of producing a lubricating serous fluid, which reduces friction between the lung's outer surface (visceral pleura) and the inner lining of the thoracic cavity (parietal pleura) during respiration. -The cellular structure of mesothelial cells, characterized by microvilli on their surface, aids in the secretion and absorption of the pleural fluid, effectively supporting the smooth expansion and contraction of the lungs. Dysregulation in mesothelial cells can lead to pathologies, including pleural effusion and malignant mesothelioma. -Mesothelial cells of the pleura display unique immunologic properties. They act as a first line of defense against infection because they are able to recognize pathogens and respond by secreting various cytokines and chemokines. Additionally, these cells are directly involved in the translocation of immune cells into the pleural cavity during inflammatory response, thereby playing an active role in the immune response within the pleural environment. -In the event of pleural injury, these cells are also involved in the mesothelial-mesenchymal transition, a process that allows mesothelial cells to transdifferentiate into myofibroblasts and promote tissue repair."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1152/ajplung.90587.2008"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [respiratory tract hillock cell](http://purl.obolibrary.org/obo/CL_4030023) [has_exact_synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "respiratory hillock cell"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1016/j.coi.2020.04.005"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [respiratory tract hillock cell](http://purl.obolibrary.org/obo/CL_4030023) [label](http://www.w3.org/2000/01/rdf-schema#label) "respiratory tract hillock cell"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.3389/fphys.2014.00284"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1016/j.ccm.2021.08.005"^^[string](http://www.w3.org/2001/XMLSchema#string) +### respiratory tract multiciliated cell `http://purl.obolibrary.org/obo/CL_4030034` +#### Removed +- [respiratory tract multiciliated cell](http://purl.obolibrary.org/obo/CL_4030034) [label](http://www.w3.org/2000/01/rdf-schema#label) "respiratory ciliated cell"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [mesothelial cell of pleura](http://purl.obolibrary.org/obo/CL_1000491) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://cellxgene.cziscience.com/cellguide/CL_1000491"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [respiratory tract multiciliated cell](http://purl.obolibrary.org/obo/CL_4030034) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A ciliated cell of the respiratory system. Ciliated cells are present in airway epithelium."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:18757316"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:21364219"^^[string](http://www.w3.org/2001/XMLSchema#string) -### mesothelial cell of visceral pleura `http://purl.obolibrary.org/obo/CL_1000493` +- [respiratory tract multiciliated cell](http://purl.obolibrary.org/obo/CL_4030034) EquivalentTo [ciliated cell](http://purl.obolibrary.org/obo/CL_0000064) and ([BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0004802](http://purl.obolibrary.org/obo/UBERON_0004802)) + +- [respiratory tract multiciliated cell](http://purl.obolibrary.org/obo/CL_4030034) SubClassOf [BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0004802](http://purl.obolibrary.org/obo/UBERON_0004802) + +- [respiratory tract multiciliated cell](http://purl.obolibrary.org/obo/CL_4030034) SubClassOf [ciliated cell](http://purl.obolibrary.org/obo/CL_0000064) #### Added -- [mesothelial cell of visceral pleura](http://purl.obolibrary.org/obo/CL_1000493) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. +- [respiratory tract multiciliated cell](http://purl.obolibrary.org/obo/CL_4030034) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A multiciliated epithelial cell located in the respiratory tract epithelium, characterized by a columnar shape and motile cilia on its apical surface. This cell develops through a highly orchestrated process, transitioning from a basal progenitor via an intermediate deuterosomal cell stage that generates centrioles essential for ciliogenesis."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:18757316"^^[string](http://www.w3.org/2001/XMLSchema#string) -Mesothelial cells of visceral pleura are specialized epithelial cells that line the inner layer of the pleura, the membrane that envelops the lungs. Positioned adjacent to the lung tissue, these cells form a protective barrier and contribute to the structure of the visceral pleura. They are characterized by their cuboidal to squamous epithelial shape and the presence of microvilli on their surface, a feature aiding in fluid and solute exchange between the pleura and the lungs. -The primary function of mesothelial cells of visceral pleura is to secrete a lubricating serous fluid to facilitate smooth, frictionless lung movement within the thoracic cavity during respiration. This helps in the prevention of trauma or damage stemming from the constant rubbing of the lung tissue against the chest wall, hence playing a pivotal role in maintaining respiratory function. Besides fluid secretion, these cells have an essential role in the transportation of fluids and particles across the pleura, as well as in inflammation, wound healing, and tissue repair processes within the pleura. -Mesothelial cells of visceral pleura are notably implicated in the development of pleural diseases such as pleural effusion and pleural mesothelioma, a rare and aggressive form of cancer primarily linked with exposure to asbestos. Alterations, such as hyperplasia or metaplasia, may occur in these mesothelial cells under pathological conditions."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1152/physrev.00026.2003"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:21364219"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1371/journal.pone.0276978"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:34044844"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.3389/fphys.2014.00221"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:37834236"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.3390/jdb7020007"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [respiratory tract multiciliated cell](http://purl.obolibrary.org/obo/CL_4030034) [has_exact_synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "respiratory multiciliated cell"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1016/S1357-2725(03)00242-5"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [respiratory tract multiciliated cell](http://purl.obolibrary.org/obo/CL_4030034) [has_exact_synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "respiratory ciliated cell"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [mesothelial cell of visceral pleura](http://purl.obolibrary.org/obo/CL_1000493) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://cellxgene.cziscience.com/cellguide/CL_1000493"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [respiratory tract multiciliated cell](http://purl.obolibrary.org/obo/CL_4030034) [label](http://www.w3.org/2000/01/rdf-schema#label) "respiratory tract multiciliated cell"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [respiratory tract multiciliated cell](http://purl.obolibrary.org/obo/CL_4030034) EquivalentTo [columnar/cuboidal epithelial cell](http://purl.obolibrary.org/obo/CL_0000075) and ([BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0004802](http://purl.obolibrary.org/obo/UBERON_0004802)) and ([BFO_0000051](http://purl.obolibrary.org/obo/BFO_0000051) some [GO_0031514](http://purl.obolibrary.org/obo/GO_0031514)) and ([RO_0000053](http://purl.obolibrary.org/obo/RO_0000053) some [PATO_0010007](http://purl.obolibrary.org/obo/PATO_0010007)) -### microglial cell `http://purl.obolibrary.org/obo/CL_0000129` +- [respiratory tract multiciliated cell](http://purl.obolibrary.org/obo/CL_4030034) SubClassOf [UBERON_0004119](http://purl.obolibrary.org/obo/UBERON_0004119) + +- [respiratory tract multiciliated cell](http://purl.obolibrary.org/obo/CL_4030034) SubClassOf [multiciliated epithelial cell](http://purl.obolibrary.org/obo/CL_0005012) + +- [respiratory tract multiciliated cell](http://purl.obolibrary.org/obo/CL_4030034) SubClassOf [respiratory tract epithelial cell](http://purl.obolibrary.org/obo/CL_0002368) + +- [respiratory tract multiciliated cell](http://purl.obolibrary.org/obo/CL_4030034) SubClassOf [RO_0002207](http://purl.obolibrary.org/obo/RO_0002207) some [deuterosomal cell](http://purl.obolibrary.org/obo/CL_4033044) + + +### respiratory tract suprabasal cell `http://purl.obolibrary.org/obo/CL_4033048` #### Removed -- [microglial cell](http://purl.obolibrary.org/obo/CL_0000129) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A central nervous system macrophage found in the parenchyma of the central nervous system. Marker include CD11b-positive, F4/80-positive, and CD68-positive."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:add"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [respiratory tract suprabasal cell](http://purl.obolibrary.org/obo/CL_4033048) [comment](http://www.w3.org/2000/01/rdf-schema#comment) "In humans, respiratory suprabasal cells have been noted to have enriched expression of the following: CK8, KRT13, IVL, and SERPINB3."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:25658372"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "doi:10.1101/2023.04.20.537495"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:14561199"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [respiratory tract suprabasal cell](http://purl.obolibrary.org/obo/CL_4033048) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A respiratory epithelial cell with topographic nuclear position in between the basal and luminal cell of the airway epithelium. This non-basal, intermediate cell has limited proliferative capacity, ultrastructural features of basal cells and no defined features of the typically differentiated cellular phenotypes."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:25564622"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "http://en.wikipedia.org/wiki/Microglia"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [respiratory tract suprabasal cell](http://purl.obolibrary.org/obo/CL_4033048) [label](http://www.w3.org/2000/01/rdf-schema#label) "respiratory suprabasal cell"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:2089275"^^[string](http://www.w3.org/2001/XMLSchema#string) +#### Added +- [respiratory tract suprabasal cell](http://purl.obolibrary.org/obo/CL_4033048) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A respiratory epithelial cell derived from a basal cell, with a topographic nuclear position between the basal and luminal cells of the airway epithelium. This non-basal, intermediate progenitor cell has limited proliferative capacity and can differentiate into multiciliated, secretory, or rare airway cells (ionocytes, tuft cells, neuroendocrine cells). It shares some ultrastructural features with basal cells but lacks the defined characteristics of fully differentiated cellular phenotypes."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:25564622"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:14612429"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:35387001"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:dsd"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:34044844"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:12430718"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:37834236"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "MESH:D017628"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [respiratory tract suprabasal cell](http://purl.obolibrary.org/obo/CL_4033048) [has_exact_synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "respiratory suprabasal cell"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:11517395"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [respiratory tract suprabasal cell](http://purl.obolibrary.org/obo/CL_4033048) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl/cl-base#cellxgene_subset) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:tfm"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [respiratory tract suprabasal cell](http://purl.obolibrary.org/obo/CL_4033048) [comment](http://www.w3.org/2000/01/rdf-schema#comment) "The marker set TNC, KRT15, SERPINB4 can identify the Human cell type respiratory suprabasal cell in the Lung with a confidence of 0.62 (NS-Forest FBeta value). In humans, respiratory tract suprabasal cells have been noted to have enriched expression of the following: CK8, KRT13, IVL, and SERPINB3. Single-cell sequencing indicates that suprabasal cells derived from the nasal epithelium are distinct from those in the tracheobronchial epithelium."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://doi.org/10.5281/zenodo.11165918"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:32726565"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:25658372"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "doi:10.1101/2023.04.20.537495"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [respiratory tract suprabasal cell](http://purl.obolibrary.org/obo/CL_4033048) [label](http://www.w3.org/2000/01/rdf-schema#label) "respiratory tract suprabasal cell"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:16177057"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [respiratory tract suprabasal cell](http://purl.obolibrary.org/obo/CL_4033048) SubClassOf [RO_0015004](http://purl.obolibrary.org/obo/RO_0015004) some [CLM_1000059](http://purl.obolibrary.org/obo/CLM_1000059) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ISBN:0721601464"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:19461673"^^[string](http://www.w3.org/2001/XMLSchema#string) +### reticulocyte `http://purl.obolibrary.org/obo/CL_0000558` +#### Removed +- [reticulocyte](http://purl.obolibrary.org/obo/CL_0000558) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) + + + +### retinal astrocyte `http://purl.obolibrary.org/obo/CL_4033015` #### Added -- [microglial cell](http://purl.obolibrary.org/obo/CL_0000129) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A transcriptomically distinct central nervous system macrophage found in the parenchyma of the central nervous system. Marker include CD11b-positive, F4/80-positive, and CD68-positive."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:add"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [retinal astrocyte](http://purl.obolibrary.org/obo/CL_4033015) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl/cl-base#cellxgene_subset) + + +### retinal bipolar neuron `http://purl.obolibrary.org/obo/CL_0000748` +#### Removed +- [retinal bipolar neuron](http://purl.obolibrary.org/obo/CL_0000748) EquivalentTo [bipolar neuron](http://purl.obolibrary.org/obo/CL_0000103) and ([RO_0002100](http://purl.obolibrary.org/obo/RO_0002100) some [UBERON_0001791](http://purl.obolibrary.org/obo/UBERON_0001791)) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:14561199"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [retinal bipolar neuron](http://purl.obolibrary.org/obo/CL_0000748) SubClassOf [bipolar neuron](http://purl.obolibrary.org/obo/CL_0000103) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "http://en.wikipedia.org/wiki/Microglia"^^[string](http://www.w3.org/2001/XMLSchema#string) +#### Added +- [retinal bipolar neuron](http://purl.obolibrary.org/obo/CL_0000748) EquivalentTo [neuron](http://purl.obolibrary.org/obo/CL_0000540) and ([RO_0002100](http://purl.obolibrary.org/obo/RO_0002100) some [UBERON_0001791](http://purl.obolibrary.org/obo/UBERON_0001791)) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:2089275"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:14612429"^^[string](http://www.w3.org/2001/XMLSchema#string) +### retinal blood vessel endothelial cell `http://purl.obolibrary.org/obo/CL_0002585` +#### Removed +- [retinal blood vessel endothelial cell](http://purl.obolibrary.org/obo/CL_0002585) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:dsd"^^[string](http://www.w3.org/2001/XMLSchema#string) +Retinal blood vessel endothelial cells constitute the innermost lining of the blood vessels found in the retina, the light-sensitive layer of tissue at the back of the eye. The primary role of these cells revolves around their location within the retinal vascular system, forming the structure of the blood-retinal barrier, a subset of the larger blood-ocular barrier system. +The endothelial cells are particularly involved in the growth of new retinal blood vessels from pre-existing ones (angiogenesis); this is critical in managing the amount of oxygen and essential nutrients delivered to the ocular tissues. They are crucial for maintaining homeostasis in the retinal environment by controlling the exchange of molecules between the blood and the retina. Furthermore, they mediate immune cell trafficking, supporting the immune privilege of the eye by preventing the unrestricted infiltration of inflammatory cells into the retina, thus maintaining ocular health and normal vision. +The malfunction or dysfunction of retinal blood vessel endothelial cells is implicated in numerous ocular pathologies, particularly diabetic retinopathy, which is one of the leading causes of blindness worldwide. In such conditions, the compromise in the integrity of the blood-retinal barrier and excess angiogenesis can lead to retinal edema and pathological neovascularization, resulting in vision loss."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.5301/EJO.2010.6049"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:12430718"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:0.1016/j.preteyeres.2015.08.001"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "MESH:D017628"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1016/j.preteyeres.2012.08.004"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:11517395"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1038/nature04482"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:tfm"^^[string](http://www.w3.org/2001/XMLSchema#string) +#### Added +- [retinal blood vessel endothelial cell](http://purl.obolibrary.org/obo/CL_0002585) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:16177057"^^[string](http://www.w3.org/2001/XMLSchema#string) +Retinal blood vessel endothelial cells constitute the innermost lining of the blood vessels found in the retina, the light-sensitive layer of tissue at the back of the eye. The primary role of these cells revolves around their location within the retinal vascular system, forming the structure of the blood-retinal barrier, a subset of the larger blood-ocular barrier system. +The endothelial cells are particularly involved in the growth of new retinal blood vessels from pre-existing ones (angiogenesis); this is critical in managing the amount of oxygen and essential nutrients delivered to the ocular tissues. They are crucial for maintaining homeostasis in the retinal environment by controlling the exchange of molecules between the blood and the retina. Furthermore, they mediate immune cell trafficking, supporting the immune privilege of the eye by preventing the unrestricted infiltration of inflammatory cells into the retina, thus maintaining ocular health and normal vision. +The malfunction or dysfunction of retinal blood vessel endothelial cells is implicated in numerous ocular pathologies, particularly diabetic retinopathy, which is one of the leading causes of blindness worldwide. In such conditions, the compromise in the integrity of the blood-retinal barrier and excess angiogenesis can lead to retinal edema and pathological neovascularization, resulting in vision loss."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.5301/EJO.2010.6049"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ISBN:0721601464"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:0.1016/j.preteyeres.2015.08.001"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:19461673"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1016/j.preteyeres.2012.08.004"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [microglial cell](http://purl.obolibrary.org/obo/CL_0000129) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1038/nature04482"^^[string](http://www.w3.org/2001/XMLSchema#string) -### micropylar cell `http://purl.obolibrary.org/obo/CL_0007022` +### retinal ganglion cell `http://purl.obolibrary.org/obo/CL_0000740` #### Removed -- [micropylar cell](http://purl.obolibrary.org/obo/CL_0007022) SubClassOf [cell](http://purl.obolibrary.org/obo/CL_0000000) +- [retinal ganglion cell](http://purl.obolibrary.org/obo/CL_0000740) SubClassOf [CNS neuron (sensu Vertebrata)](http://purl.obolibrary.org/obo/CL_0000117) #### Added -- [micropylar cell](http://purl.obolibrary.org/obo/CL_0007022) SubClassOf [eukaryotic cell](http://purl.obolibrary.org/obo/CL_0000255) +- [retinal ganglion cell](http://purl.obolibrary.org/obo/CL_0000740) SubClassOf [neuron](http://purl.obolibrary.org/obo/CL_0000540) -### monoblast `http://purl.obolibrary.org/obo/CL_0000040` +### retinal pigment epithelial cell `http://purl.obolibrary.org/obo/CL_0002586` +#### Removed +- [retinal pigment epithelial cell](http://purl.obolibrary.org/obo/CL_0002586) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. -#### Added -- [monoblast](http://purl.obolibrary.org/obo/CL_0000040) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) +Retinal pigment epithelial (RPE) cells form a single layer of cells at the back of the eye sandwiched between the neurosensory retina and the choroid, playing a significant role in maintaining vision health. These pigment-laden cells are highly specialized and perform an array of metabolic and transport functions essential for the maintenance of the photoreceptor cells (rods and cones) in the retina. The pigmentation of RPE cells actively aids in the absorption of excess light and the prevention of light scattering, thus enhancing the eye's optical properties. +The retinal pigment epithelium forms a key part of the blood/retina barrier. The cells have long sheet-like microvilli on their apical membrane that project into the light-sensitive outer segments of the photoreceptors, forming a close structural interaction. The basolateral membrane of the RPE interacts with the underlying Bruch’s membrane, which separates the RPE cells from fenestrated endothelium of the choriocapillaris. +RPE cells support the photoreceptor by providing them with oxygen and nutrients (such as glucose, retinol and fatty acids) and removing waste products. They also recycle the visual pigment, in a process called the "visual cycle", where the RPE cells play a vital role in the regeneration of visual pigment (11-cis retinol) following the absorption of light. This is essential for the maintenance of photoreceptor excitability. +Beyond this, RPE cells take part in the phagocytosis process, where they digest the shed ends of photoreceptor outer segments, thus, preventing the build-up of waste residue that could otherwise harm retinal health. They also secrete various factors, including growth factors required to maintain the structural integrity of choriocapillaris endothelium and photoreceptors, as well as immunosuppressive factors that play an important role in establishing the immune privilege of the eye."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1111/febs.16018"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1152/physrev.00021.2004"^^[string](http://www.w3.org/2001/XMLSchema#string) -### mononuclear phagocyte `http://purl.obolibrary.org/obo/CL_0000113` + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.3389/fphar.2021.727870/full"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://www.sciencedirect.com/topics/chemistry/retinal-pigment"^^[string](http://www.w3.org/2001/XMLSchema#string) #### Added -- [mononuclear phagocyte](http://purl.obolibrary.org/obo/CL_0000113) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. +- [retinal pigment epithelial cell](http://purl.obolibrary.org/obo/CL_0002586) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. -Mononuclear phagocytes are immune cells that form a critical part of the body's innate immune system, the body's first line of defense against infections. Mononuclear phagocytes are characterized by the presence of a single, large nucleus. The ‘Mononuclear Phagocyte System’ nomenclature was introduced to distinguish mononuclear monocytes and macrophages from other cells with multiple nuclei. However, the cells within the mononuclear phagocyte system represent a highly heterogeneous group, all of which are able to perform highly efficient phagocytosis - engulfing and digesting microbes and cellular debris to fight infections and to maintain normal tissue homeostasis. -In addition to phagocytosis, mononuclear phagocytes also secrete chemical compounds to recruit other immune cells to a site of infection. These cells produce different types of signaling molecules, including cytokines, chemokines, and reactive oxygen species, triggering a cascade of responses to ensure rapid and efficient containment and neutralization of invading pathogens. These cells are also involved in antigen presentation, a process essential for stimulating an adaptive immune response. They can process and present antigens to T cells, thereby linking the innate and adaptive immune responses. -Mononuclear phagocytes play key roles in tissue repair and remodeling. After infection or injury, these cells help in the clearance of dead cells and debris, a crucial step in the initiation of tissue remodeling and the resolution of inflammation. Overall, mononuclear phagocytes are versatile cells that have tailored their functions to meet the unique challenges of different tissues within the body. They are pivotal in homeostasis, immunity, and inflammation, making them important aspects in a range of human diseases including infection, autoimmunity, and cancer."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1016/j.coi.2005.11.008"^^[string](http://www.w3.org/2001/XMLSchema#string) +Retinal pigment epithelial (RPE) cells form a single layer of cells at the back of the eye sandwiched between the neurosensory retina and the choroid, playing a significant role in maintaining vision health. These pigment-laden cells are highly specialized and perform an array of metabolic and transport functions essential for the maintenance of the photoreceptor cells (rods and cones) in the retina. The pigmentation of RPE cells actively aids in the absorption of excess light and the prevention of light scattering, thus enhancing the eye's optical properties. +The retinal pigment epithelium forms a key part of the blood/retina barrier. The cells have long sheet-like microvilli on their apical membrane that project into the light-sensitive outer segments of the photoreceptors, forming a close structural interaction. The basolateral membrane of the RPE interacts with the underlying Bruch’s membrane, which separates the RPE cells from fenestrated endothelium of the choriocapillaris. +RPE cells support the photoreceptor by providing them with oxygen and nutrients (such as glucose, retinol and fatty acids) and removing waste products. They also recycle the visual pigment, in a process called the "visual cycle", where the RPE cells play a vital role in the regeneration of visual pigment (11-cis retinol) following the absorption of light. This is essential for the maintenance of photoreceptor excitability. +Beyond this, RPE cells take part in the phagocytosis process, where they digest the shed ends of photoreceptor outer segments, thus, preventing the build-up of waste residue that could otherwise harm retinal health. They also secrete various factors, including growth factors required to maintain the structural integrity of choriocapillaris endothelium and photoreceptors, as well as immunosuppressive factors that play an important role in establishing the immune privilege of the eye."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1111/febs.16018"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1038/nri3087"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1152/physrev.00021.2004"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.3389/fimmu.2019.01893"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.3389/fphar.2021.727870/full"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [mononuclear phagocyte](http://purl.obolibrary.org/obo/CL_0000113) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://cellxgene.cziscience.com/cellguide/CL_0000113"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://www.sciencedirect.com/topics/chemistry/retinal-pigment"^^[string](http://www.w3.org/2001/XMLSchema#string) -### morula cell `http://purl.obolibrary.org/obo/CL_0000360` +### retinal progenitor cell `http://purl.obolibrary.org/obo/CL_0002672` #### Added -- [morula cell](http://purl.obolibrary.org/obo/CL_0000360) SubClassOf [eukaryotic cell](http://purl.obolibrary.org/obo/CL_0000255) +- [retinal progenitor cell](http://purl.obolibrary.org/obo/CL_0002672) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl/cl-base#cellxgene_subset) -### multi-ciliated epithelial cell `http://purl.obolibrary.org/obo/CL_0005012` +### rod bipolar cell `http://purl.obolibrary.org/obo/CL_0000751` #### Removed -- [multi-ciliated epithelial cell](http://purl.obolibrary.org/obo/CL_0005012) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A ciliated epithelial cell with many cilia."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "CL:CVS"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [rod bipolar cell](http://purl.obolibrary.org/obo/CL_0000751) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [human_reference_atlas](http://purl.obolibrary.org/obo/cl/cl-base#human_reference_atlas) + +- [rod bipolar cell](http://purl.obolibrary.org/obo/CL_0000751) [RO_0002175](http://purl.obolibrary.org/obo/RO_0002175) [NCBITaxon_9606](http://purl.obolibrary.org/obo/NCBITaxon_9606) + + + +### rostral primary motorneuron `http://purl.obolibrary.org/obo/CL_4042038` #### Added -- [multi-ciliated epithelial cell](http://purl.obolibrary.org/obo/CL_0005012) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A columnar/cuboidal epithelial cell with multiple motile cilia on its apical surface. These cells facilitate the movement of liquids such as mucus or cerebrospinal fluid across the epithelial surface."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:30422572"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [rostral primary motorneuron](http://purl.obolibrary.org/obo/CL_4042038) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A type of primary motor neuron situated in the rostral region of the spinal cord. RoP neurons extend their axons to innervate the ventral trunk musculature."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:35431796"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "CL:CVS"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:3746410"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:28400610"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [rostral primary motorneuron](http://purl.obolibrary.org/obo/CL_4042038) [date](http://purl.org/dc/terms/date) "2024-11-13T13:42:01Z"^^[dateTime](http://www.w3.org/2001/XMLSchema#dateTime) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:38032388"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [rostral primary motorneuron](http://purl.obolibrary.org/obo/CL_4042038) [id](http://www.geneontology.org/formats/oboInOwl#id) "CL:4042038"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [multi-ciliated epithelial cell](http://purl.obolibrary.org/obo/CL_0005012) [comment](http://www.w3.org/2000/01/rdf-schema#comment) "While the term 'multi-ciliated epithelial cell' refers to cells with multiple motile cilia, there are exceptions where epithelial cells may have multiple non-motile cilia. Examples include olfactory sensory neurons, which have non-motile cilia for sensory detection, and choroid plexus epithelial cells, which possess multiple non-motile cilia with transient motility during development. Multiciliated cells are essential for human health, and their dysfunction can lead to various diseases known as ciliopathies, such as primary ciliary dyskinesia. This condition affects the respiratory system, brain ventricles, and reproductive system, leading to chronic respiratory infections, hydrocephalus, and infertility"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:23959957"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [rostral primary motorneuron](http://purl.obolibrary.org/obo/CL_4042038) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "RoP"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003000](http://purl.obolibrary.org/obo/OMO_0003000) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:22118931"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:3746410"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:26378583"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [rostral primary motorneuron](http://purl.obolibrary.org/obo/CL_4042038) [contributor](http://purl.org/dc/terms/contributor) [0000-0002-0098-8958](https://orcid.org/0000-0002-0098-8958) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:25729351"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [rostral primary motorneuron](http://purl.obolibrary.org/obo/CL_4042038) [label](http://www.w3.org/2000/01/rdf-schema#label) "rostral primary motorneuron"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [multi-ciliated epithelial cell](http://purl.obolibrary.org/obo/CL_0005012) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://cellxgene.cziscience.com/cellguide/CL_0005012"^^[string](http://www.w3.org/2001/XMLSchema#string) +- Class: [rostral primary motorneuron](http://purl.obolibrary.org/obo/CL_4042038) -- [multi-ciliated epithelial cell](http://purl.obolibrary.org/obo/CL_0005012) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. +- [rostral primary motorneuron](http://purl.obolibrary.org/obo/CL_4042038) SubClassOf [primary motor neuron (sensu Teleostei)](http://purl.obolibrary.org/obo/CL_0000533) -The multi-ciliated epithelial cell are terminally differentiated epithelia that line brain ventricles, the respiratory tract and parts of the female and male reproductive organs in animals, playing critical roles in the maintenance of homeostasis through ciliary motion. They are characterized by the presence of hundreds of motile cilia, hair-like microtubule-based organelles that beat in a coordinated fashion to direct fluid flow over the cell surface. -Multi-ciliated epithelial cells have fundamental roles in the proper functioning of many organ systems. In the respiratory system, they line the airways and orchestrate the coordinated movement of mucus, effectively clearing the airways of inhaled particles and pathogens. These cells are also vital in the ventricular system of the brain where they facilitate cerebrospinal fluid circulation, thus contributing to the maintenance of the brain's microenvironment. In the fallopian tube, multi-ciliated epithelial cells aid in the transport of oocytes from the ovary to the uterus, a process crucial to reproduction. -The formation and function of multi-ciliated epithelial cells is a highly regulated process that involves several stages of development including cell specification, centriole multiplication, and ciliogenesis. Any disruption in these processes can result in dysfunctional or decreased numbers of cilia, which can lead to a myriad of health issues, ranging from chronic respiratory infections to infertility."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1101/cshperspect.a028233"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1016/j.cub.2014.08.047"^^[string](http://www.w3.org/2001/XMLSchema#string) +### sebaceous gland cell `http://purl.obolibrary.org/obo/CL_2000021` - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1038/nrm.2017.21"^^[string](http://www.w3.org/2001/XMLSchema#string) +#### Added +- [sebaceous gland cell](http://purl.obolibrary.org/obo/CL_2000021) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. -- [multi-ciliated epithelial cell](http://purl.obolibrary.org/obo/CL_0005012) EquivalentTo [columnar/cuboidal epithelial cell](http://purl.obolibrary.org/obo/CL_0000075) and ([BFO_0000051](http://purl.obolibrary.org/obo/BFO_0000051) some [GO_0031514](http://purl.obolibrary.org/obo/GO_0031514)) and ([RO_0000053](http://purl.obolibrary.org/obo/RO_0000053) some [PATO_0010007](http://purl.obolibrary.org/obo/PATO_0010007)) +Sebaceous gland cells, also known as sebocytes, are small, oil-producing glands present in the skin of mammals. These specialized cells are predominantly located in the dermis, particularly on the face, scalp, and upper body. +The primary function of sebaceous gland cells is the production and secretion of sebum, a complex mixture of lipids including triglycerides, wax esters, squalene, and metabolites of fat-soluble vitamins (such as vitamin E), as well as free fatty acids. The production process involves a unique form of programmed cell death called holocrine secretion. In this process, as sebaceous gland cells mature, they progressively accumulate lipid droplets, before ultimately disintegrating and releasing their lipid-rich contents into the gland's ductal system. +The sebum generated by these cells serves multiple purposes. It acts as a waterproofing agent, preventing excessive wetting or drying of the skin and averaging skin's water-holding capacity. Sebum also has antimicrobial properties, providing a natural defense barrier against certain bacterial and fungal species. Additionally, it contributes to the skin’s suppleness and prevents it from becoming brittle. An overproduction or imbalance of sebaceous gland cells can lead to common skin disorders, such as acne, seborrhea, or rosacea, illustrating their importance in skin health."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://doi.org/10.2147/CLEP.S323744"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [multi-ciliated epithelial cell](http://purl.obolibrary.org/obo/CL_0005012) SubClassOf [columnar/cuboidal epithelial cell](http://purl.obolibrary.org/obo/CL_0000075) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.4161/derm.1.2.8472"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [multi-ciliated epithelial cell](http://purl.obolibrary.org/obo/CL_0005012) SubClassOf [RO_0000053](http://purl.obolibrary.org/obo/RO_0000053) some [PATO_0010007](http://purl.obolibrary.org/obo/PATO_0010007) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1080/19381980.2017.1375636"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [multi-ciliated epithelial cell](http://purl.obolibrary.org/obo/CL_0005012) SubClassOf [BFO_0000051](http://purl.obolibrary.org/obo/BFO_0000051) some [GO_0031514](http://purl.obolibrary.org/obo/GO_0031514) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1016/j.jid.2016.10.017"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://www.sciencedirect.com/topics/agricultural-and-biological-sciences/sebum"^^[string](http://www.w3.org/2001/XMLSchema#string) -### multiciliated ependymal cell `http://purl.obolibrary.org/obo/CL_4052001` +- [sebaceous gland cell](http://purl.obolibrary.org/obo/CL_2000021) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://cellxgene.cziscience.com/cellguide/CL_2000021"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### sebocyte `http://purl.obolibrary.org/obo/CL_0000317` +#### Removed +- [sebocyte](http://purl.obolibrary.org/obo/CL_0000317) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A cell secreting sebun, an oily substance secreted by sebaceous glands, composed of keratin, fat, and cellular debris."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "MESH:D012629"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [sebocyte](http://purl.obolibrary.org/obo/CL_0000317) [label](http://www.w3.org/2000/01/rdf-schema#label) "sebum secreting cell"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [sebocyte](http://purl.obolibrary.org/obo/CL_0000317) [has_exact_synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "sebocyte"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [sebocyte](http://purl.obolibrary.org/obo/CL_0000317) EquivalentTo [secretory cell](http://purl.obolibrary.org/obo/CL_0000151) and ([BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0001821](http://purl.obolibrary.org/obo/UBERON_0001821)) #### Added -- [multiciliated ependymal cell](http://purl.obolibrary.org/obo/CL_4052001) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "An ependymal cell that lines the lateral, third, and fourth ventricles of the brain. The cell is characterized by multiple motile cilia on its apical surface, which beats in a coordinated manner to facilitate the movement of cerebrospinal fluid (CSF), contributing to brain homeostasis."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:28067220"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [sebocyte](http://purl.obolibrary.org/obo/CL_0000317) [has_exact_synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "sebum secreting cell"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:25045600"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [sebocyte](http://purl.obolibrary.org/obo/CL_0000317) [label](http://www.w3.org/2000/01/rdf-schema#label) "sebocyte"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:37008045"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [sebocyte](http://purl.obolibrary.org/obo/CL_0000317) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl/cl-base#cellxgene_subset) -- [multiciliated ependymal cell](http://purl.obolibrary.org/obo/CL_4052001) [date](http://purl.org/dc/terms/date) "2024-08-20T10:06:15Z"^^[dateTime](http://www.w3.org/2001/XMLSchema#dateTime) +- [sebocyte](http://purl.obolibrary.org/obo/CL_0000317) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "An epithelial cell that is part of a sebaceous gland. This cell produces and secretes sebum, an oily, lipid-rich substance, through holocrine secretion where the entire cell ruptures to release its contents."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "MESH:D012629"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:19944183"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [sebocyte](http://purl.obolibrary.org/obo/CL_0000317) EquivalentTo [epithelial cell](http://purl.obolibrary.org/obo/CL_0000066) and ([BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0001821](http://purl.obolibrary.org/obo/UBERON_0001821)) + +- [sebocyte](http://purl.obolibrary.org/obo/CL_0000317) SubClassOf [glandular secretory epithelial cell](http://purl.obolibrary.org/obo/CL_0000150) + +- [sebocyte](http://purl.obolibrary.org/obo/CL_0000317) SubClassOf [epidermal cell](http://purl.obolibrary.org/obo/CL_0000362) + +- [sebocyte](http://purl.obolibrary.org/obo/CL_0000317) SubClassOf [epithelial cell of skin gland](http://purl.obolibrary.org/obo/CL_0002308) -- [multiciliated ependymal cell](http://purl.obolibrary.org/obo/CL_4052001) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "E1"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003000](http://purl.obolibrary.org/obo/OMO_0003000) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:28067220"^^[string](http://www.w3.org/2001/XMLSchema#string) +### secondary lens fiber `http://purl.obolibrary.org/obo/CL_0002225` +#### Removed +- [secondary lens fiber](http://purl.obolibrary.org/obo/CL_0002225) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:37008045"^^[string](http://www.w3.org/2001/XMLSchema#string) +Secondary lens fibers are a specialized type of elongated cells located within the structure of the eye's lens. They play an essential role in vision by enabling light transmission and focus on the retina, which allows for clear, distinct vision. These cells are characterized by their lack of nuclei and organelles, their orderly alignment, and their high protein content, particularly crystallins. +Lens fibers are differentiated from equatorial epithelial cells of the lens in a process that involves cell elongation, denucleation and tight packing, which serve to reduce light scattering occurrences in the eye. This differentiation accelerates substantially after birth in comparison to during embryogenesis and continues throughout life, contributing to the growth of the eye lens. Secondary lens fibers are specifically those cells that are newly differentiated and cover the old lens fiber core. This process also leads to the removal of light-obstructing cellular components, mainly nuclei and organelles, making these fibers transparent and ideal for their function. +The fibers carry out their primary function of light refraction via a high concentration of specialized proteins known as crystallins, which form a gradient of refractive index together with the cytoplasm. This index manipulation facilitates precise light focus onto the retina. Secondary lens fibers also contribute to the lens's shape and biomechanical properties through intercellular interactions, particularly at the sutures where the ends of the fibers meet. Any disruption to secondary lens fibers can lead to vision problems, including cataracts, which is the clouding of the lens resulting from the aggregation of crystallin proteins."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1136/bmjophth-2020-000459"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [multiciliated ependymal cell](http://purl.obolibrary.org/obo/CL_4052001) [has_broad_synonym](http://www.geneontology.org/formats/oboInOwl#hasBroadSynonym) "multiciliated ependymal cells"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:25045600"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://www.sciencedirect.com/topics/immunology-and-microbiology/lens-fiber"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [multiciliated ependymal cell](http://purl.obolibrary.org/obo/CL_4052001) [comment](http://www.w3.org/2000/01/rdf-schema#comment) "multiciliated ependymal cell, with an average of 16 motile cilia per cell, exhibits two types of planar cell polarity (PCP): rotational polarity, with unidirectional cilia orientation, and translational polarity, with asymmetric cilia positioning in the apical area. This location-specific PCP varies across the ventricular wall, aligning with the direction of CSF flow. These cells are interconnected by adherens and gap junctions, which support intercellular communication and maintain the structural integrity of the ependymal layer. Unlike some other cell types, these cells lack tight junctions."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:27311928"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1016/j.biocel.2007.10.034"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:25045600"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1098/rstb.2010.0324"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [multiciliated ependymal cell](http://purl.obolibrary.org/obo/CL_4052001) [contributor](http://purl.org/dc/terms/contributor) [0009-0000-8480-9277](https://orcid.org/0009-0000-8480-9277) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1016/B978-1-4377-1926-0.10005-0"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [multiciliated ependymal cell](http://purl.obolibrary.org/obo/CL_4052001) [id](http://www.geneontology.org/formats/oboInOwl#id) "CL:4052001"^^[string](http://www.w3.org/2001/XMLSchema#string) +#### Added +- [secondary lens fiber](http://purl.obolibrary.org/obo/CL_0002225) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. -- [multiciliated ependymal cell](http://purl.obolibrary.org/obo/CL_4052001) [label](http://www.w3.org/2000/01/rdf-schema#label) "multiciliated ependymal cell"^^[string](http://www.w3.org/2001/XMLSchema#string) +Secondary lens fibers are a specialized type of elongated cells located within the structure of the eye's lens. They play an essential role in vision by enabling light transmission and focus on the retina, which allows for clear, distinct vision. These cells are characterized by their lack of nuclei and organelles, their orderly alignment, and their high protein content, particularly crystallins. +Lens fibers are differentiated from equatorial epithelial cells of the lens in a process that involves cell elongation, denucleation and tight packing, which serve to reduce light scattering occurrences in the eye. This differentiation accelerates substantially after birth in comparison to during embryogenesis and continues throughout life, contributing to the growth of the eye lens. Secondary lens fibers are specifically those cells that are newly differentiated and cover the old lens fiber core. This process also leads to the removal of light-obstructing cellular components, mainly nuclei and organelles, making these fibers transparent and ideal for their function. +The fibers carry out their primary function of light refraction via a high concentration of specialized proteins known as crystallins, which form a gradient of refractive index together with the cytoplasm. This index manipulation facilitates precise light focus onto the retina. Secondary lens fibers also contribute to the lens's shape and biomechanical properties through intercellular interactions, particularly at the sutures where the ends of the fibers meet. Any disruption to secondary lens fibers can lead to vision problems, including cataracts, which is the clouding of the lens resulting from the aggregation of crystallin proteins."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1136/bmjophth-2020-000459"^^[string](http://www.w3.org/2001/XMLSchema#string) -- Class: [multiciliated ependymal cell](http://purl.obolibrary.org/obo/CL_4052001) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://www.sciencedirect.com/topics/immunology-and-microbiology/lens-fiber"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [multiciliated ependymal cell](http://purl.obolibrary.org/obo/CL_4052001) SubClassOf [BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0005357](http://purl.obolibrary.org/obo/UBERON_0005357) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1016/j.biocel.2007.10.034"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [multiciliated ependymal cell](http://purl.obolibrary.org/obo/CL_4052001) SubClassOf [multi-ciliated epithelial cell](http://purl.obolibrary.org/obo/CL_0005012) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1098/rstb.2010.0324"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [multiciliated ependymal cell](http://purl.obolibrary.org/obo/CL_4052001) SubClassOf [ependymal cell](http://purl.obolibrary.org/obo/CL_0000065) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1016/B978-1-4377-1926-0.10005-0"^^[string](http://www.w3.org/2001/XMLSchema#string) -### multinuclear osteoclast `http://purl.obolibrary.org/obo/CL_0000779` +### secondary motor neuron (sensu Teleostei) `http://purl.obolibrary.org/obo/CL_0000536` #### Removed -- [multinuclear osteoclast](http://purl.obolibrary.org/obo/CL_0000779) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A specialized multinuclear osteoclast associated with the absorption and removal of bone."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:12713016"^^[string](http://www.w3.org/2001/XMLSchema#string) - - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:add"^^[string](http://www.w3.org/2001/XMLSchema#string) - - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:9415452"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [secondary motor neuron (sensu Teleostei)](http://purl.obolibrary.org/obo/CL_0000536) SubClassOf [motor neuron](http://purl.obolibrary.org/obo/CL_0000100) #### Added -- [multinuclear osteoclast](http://purl.obolibrary.org/obo/CL_0000779) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A specialized multinuclear osteoclast, forming a syncytium through the fusion of mononuclear precursor cells, associated with the absorption and removal of bone."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:12713016"^^[string](http://www.w3.org/2001/XMLSchema#string) - - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:add"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [secondary motor neuron (sensu Teleostei)](http://purl.obolibrary.org/obo/CL_0000536) SubClassOf [spinal cord motor neuron](http://purl.obolibrary.org/obo/CL_0011001) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:38903088"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:29379067"^^[string](http://www.w3.org/2001/XMLSchema#string) - - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:9415452"^^[string](http://www.w3.org/2001/XMLSchema#string) - -- [multinuclear osteoclast](http://purl.obolibrary.org/obo/CL_0000779) SubClassOf [syncytial cell](http://purl.obolibrary.org/obo/CL_4052002) - - -### multinucleate cell `http://purl.obolibrary.org/obo/CL_0000228` +### secondary neuron (sensu Teleostei) `http://purl.obolibrary.org/obo/CL_0000535` #### Removed -- [multinucleate cell](http://purl.obolibrary.org/obo/CL_0000228) [has_exact_synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "syncytial cell"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [secondary neuron (sensu Teleostei)](http://purl.obolibrary.org/obo/CL_0000535) SubClassOf [neuron](http://purl.obolibrary.org/obo/CL_0000540) + +- [secondary neuron (sensu Teleostei)](http://purl.obolibrary.org/obo/CL_0000535) SubClassOf [BFO_0000002](http://purl.obolibrary.org/obo/BFO_0000002) -- [multinucleate cell](http://purl.obolibrary.org/obo/CL_0000228) [has_exact_synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "syncytium"^^[string](http://www.w3.org/2001/XMLSchema#string) +#### Added +- [secondary neuron (sensu Teleostei)](http://purl.obolibrary.org/obo/CL_0000535) SubClassOf [RO_0002100](http://purl.obolibrary.org/obo/RO_0002100) some [UBERON_0002240](http://purl.obolibrary.org/obo/UBERON_0002240) -- [multinucleate cell](http://purl.obolibrary.org/obo/CL_0000228) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "AEO:0000203"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [secondary neuron (sensu Teleostei)](http://purl.obolibrary.org/obo/CL_0000535) SubClassOf [UBERON_0010313](http://purl.obolibrary.org/obo/UBERON_0010313) -- [multinucleate cell](http://purl.obolibrary.org/obo/CL_0000228) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A cell with more than one nucleus."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FB:ma"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [secondary neuron (sensu Teleostei)](http://purl.obolibrary.org/obo/CL_0000535) SubClassOf [central nervous system neuron](http://purl.obolibrary.org/obo/CL_2000029) -- [multinucleate cell](http://purl.obolibrary.org/obo/CL_0000228) [has_exact_synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "syncitium"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [multinucleate cell](http://purl.obolibrary.org/obo/CL_0000228) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "WBbt:0008074"^^[string](http://www.w3.org/2001/XMLSchema#string) +### secretory epithelial cell `http://purl.obolibrary.org/obo/CL_1100001` #### Added -- [multinucleate cell](http://purl.obolibrary.org/obo/CL_0000228) [has_exact_synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "polynuclear cells"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Multinucleate"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [secretory epithelial cell](http://purl.obolibrary.org/obo/CL_1100001) [id](http://www.geneontology.org/formats/oboInOwl#id) "CL:1100001"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [multinucleate cell](http://purl.obolibrary.org/obo/CL_0000228) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A cell with more than one nucleus."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FB:ma"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [secretory epithelial cell](http://purl.obolibrary.org/obo/CL_1100001) [label](http://www.w3.org/2000/01/rdf-schema#label) "secretory epithelial cell"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Multinucleate"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [secretory epithelial cell](http://purl.obolibrary.org/obo/CL_1100001) [date](http://purl.org/dc/terms/date) "2024-07-21T09:24:44Z"^^[dateTime](http://www.w3.org/2001/XMLSchema#dateTime) -- [multinucleate cell](http://purl.obolibrary.org/obo/CL_0000228) [has_exact_synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "multinucleated cells"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Multinucleate"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [secretory epithelial cell](http://purl.obolibrary.org/obo/CL_1100001) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "An epithelial cell that is specialised for the synthesis and secretion of specific biomolecules."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://orcid.org/0000-0002-7073-9172"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [multinucleate cell](http://purl.obolibrary.org/obo/CL_0000228) SubClassOf [eukaryotic cell](http://purl.obolibrary.org/obo/CL_0000255) +- [secretory epithelial cell](http://purl.obolibrary.org/obo/CL_1100001) [contributor](http://purl.org/dc/terms/contributor) [0000-0002-7073-9172](https://orcid.org/0000-0002-7073-9172) +- Class: [secretory epithelial cell](http://purl.obolibrary.org/obo/CL_1100001) -### multinucleated giant cell `http://purl.obolibrary.org/obo/CL_0000647` -#### Removed -- [multinucleated giant cell](http://purl.obolibrary.org/obo/CL_0000647) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A phagocytic cell formed by the fusion of macrophages, occurs in chronic inflammatory responses to persistent microorganism such as M.tuberculosis, component of granulomas. Sometimes used to refer to megakaryocytes."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:add"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [secretory epithelial cell](http://purl.obolibrary.org/obo/CL_1100001) EquivalentTo [epithelial cell](http://purl.obolibrary.org/obo/CL_0000066) and [secretory cell](http://purl.obolibrary.org/obo/CL_0000151) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ISBN:0702022918"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [secretory epithelial cell](http://purl.obolibrary.org/obo/CL_1100001) SubClassOf [secretory cell](http://purl.obolibrary.org/obo/CL_0000151) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:tfm"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [secretory epithelial cell](http://purl.obolibrary.org/obo/CL_1100001) SubClassOf [epithelial cell](http://purl.obolibrary.org/obo/CL_0000066) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ISBN:0702024783"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [multinucleated giant cell](http://purl.obolibrary.org/obo/CL_0000647) SubClassOf [multinucleate cell](http://purl.obolibrary.org/obo/CL_0000228) +### secretory pericyte `http://purl.obolibrary.org/obo/CL_4047032` #### Added -- [multinucleated giant cell](http://purl.obolibrary.org/obo/CL_0000647) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "MGC"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003000](http://purl.obolibrary.org/obo/OMO_0003000) +- [secretory pericyte](http://purl.obolibrary.org/obo/CL_4047032) [contributor](http://purl.org/dc/terms/contributor) [0009-0005-7919-4905](https://orcid.org/0009-0005-7919-4905) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:33348900"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [secretory pericyte](http://purl.obolibrary.org/obo/CL_4047032) [id](http://www.geneontology.org/formats/oboInOwl#id) "CL:4047032"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [multinucleated giant cell](http://purl.obolibrary.org/obo/CL_0000647) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A phagocytic syncytial cell formed by the fusion of macrophages, occurs in chronic inflammatory responses to persistent microorganism such as M.tuberculosis, component of granulomas. Sometimes used to refer to megakaryocytes."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:add"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [secretory pericyte](http://purl.obolibrary.org/obo/CL_4047032) [label](http://www.w3.org/2000/01/rdf-schema#label) "secretory pericyte"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ISBN:0702022918"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [secretory pericyte](http://purl.obolibrary.org/obo/CL_4047032) [date](http://purl.org/dc/terms/date) "2024-11-07T15:36:16Z"^^[dateTime](http://www.w3.org/2001/XMLSchema#dateTime) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:tfm"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [secretory pericyte](http://purl.obolibrary.org/obo/CL_4047032) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A specialized pericyte located within the basement membrane of a blood capillary. This cell is characterized by its ability to produce and release a variety of bioactive molecules, collectively known as the pericyte secretome, including cytokines and regulators of angiogenesis."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.3389/fncel.2019.00282"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- Class: [secretory pericyte](http://purl.obolibrary.org/obo/CL_4047032) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:33348900"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [secretory pericyte](http://purl.obolibrary.org/obo/CL_4047032) SubClassOf [RO_0002215](http://purl.obolibrary.org/obo/RO_0002215) some [GO_0045765](http://purl.obolibrary.org/obo/GO_0045765) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ISBN:0702024783"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [secretory pericyte](http://purl.obolibrary.org/obo/CL_4047032) SubClassOf [pericyte](http://purl.obolibrary.org/obo/CL_0000669) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Giant_cell"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [secretory pericyte](http://purl.obolibrary.org/obo/CL_4047032) SubClassOf [secretory cell](http://purl.obolibrary.org/obo/CL_0000151) -- [multinucleated giant cell](http://purl.obolibrary.org/obo/CL_0000647) SubClassOf [syncytial cell](http://purl.obolibrary.org/obo/CL_4052002) +- [secretory pericyte](http://purl.obolibrary.org/obo/CL_4047032) SubClassOf [RO_0002215](http://purl.obolibrary.org/obo/RO_0002215) some [GO_0001816](http://purl.obolibrary.org/obo/GO_0001816) -### mural granulosa cell `http://purl.obolibrary.org/obo/CL_4033067` +### seminal vesicle glandular cell `http://purl.obolibrary.org/obo/CL_1001597` #### Removed -- [mural granulosa cell](http://purl.obolibrary.org/obo/CL_4033067) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A follicular cell of ovary that differentiates from a granulosa cell during the secondary follicle stage. Mural granulosa cells line the inner surface of the follicle wall, surrounding the fluid-filled antral cavity. These cells produce oestrogen during the follicular phase in response to follicle-stimulating hormone (FSH), and progesterone after ovulation in response to luteinizing hormone (LH)."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:33970370"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [seminal vesicle glandular cell](http://purl.obolibrary.org/obo/CL_1001597) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:27815559"^^[string](http://www.w3.org/2001/XMLSchema#string) +Seminal vesicle glandular cells belong to a specialized group of epithelial cells that form the internal lining of the seminal vesicles, a pair of male reproductive organs. These cells are located within the complex tubuloalveolar glands that make up the seminal vesicles and are known for their unique pseudostratified columnar epithelium structure. +The primary function of these cells is the secretion of a variety of substances that ultimately constitute around 70% of the fluid volume of semen. Seminal cells produce a high-fructose fluid that serves as an energy source for the spermatozoa and promotes their motility. They also secrete other essential substances like proteins, enzymes, vitamin C, prostaglandins, and various other compounds. Collectively, these substances help in the nourishment, protection, and transportation of the spermatozoa throughout the male reproductive system and during the ejaculation process. +Secondary to the production of seminal fluid, the seminal vesicle glandular cells also play a role in the contraction of the seminal vesicles during ejaculation. The contraction of these glands, induced by sympathetic nerves, ensures the efficient propulsion of the seminal fluid mixed with spermatozoa into the ejaculatory ducts and subsequently to the urethra. Notably, any malfunction or pathological condition affecting these cells can impact male fertility, emphasizing the importance of understanding the intricate functions of seminal vesicle glandular cells in maintaining the healthy physiological function of male reproduction."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1007/978-3-030-32300-4_26"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:34198768"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://www.ncbi.nlm.nih.gov/books/NBK499854/"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [mural granulosa cell](http://purl.obolibrary.org/obo/CL_4033067) SubClassOf [RO_0002207](http://purl.obolibrary.org/obo/RO_0002207) some [granulosa cell](http://purl.obolibrary.org/obo/CL_0000501) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://www.sciencedirect.com/topics/veterinary-science-and-veterinary-medicine/seminal-vesicle"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [mural granulosa cell](http://purl.obolibrary.org/obo/CL_4033067) SubClassOf [ovarian surface epithelial cell](http://purl.obolibrary.org/obo/CL_2000064) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1111/j.1439-0272.1992.tb02636.x"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [mural granulosa cell](http://purl.obolibrary.org/obo/CL_4033067) SubClassOf [follicular cell of ovary](http://purl.obolibrary.org/obo/CL_0002174) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1007/s00265-006-0178-0"^^[string](http://www.w3.org/2001/XMLSchema#string) #### Added -- [mural granulosa cell](http://purl.obolibrary.org/obo/CL_4033067) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A follicular cell of ovary that differentiates from a cuboidal granulosa cell during the secondary follicle stage. Mural granulosa cells line the inner surface of the follicle wall, surrounding the fluid-filled antral cavity. These cells produce oestrogen during the follicular phase in response to follicle-stimulating hormone (FSH), and progesterone after ovulation in response to luteinizing hormone (LH)."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:33970370"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [seminal vesicle glandular cell](http://purl.obolibrary.org/obo/CL_1001597) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:27815559"^^[string](http://www.w3.org/2001/XMLSchema#string) +Seminal vesicle glandular cells belong to a specialized group of epithelial cells that form the internal lining of the seminal vesicles, a pair of male reproductive organs. These cells are located within the complex tubuloalveolar glands that make up the seminal vesicles and are known for their unique pseudostratified columnar epithelium structure. +The primary function of these cells is the secretion of a variety of substances that ultimately constitute around 70% of the fluid volume of semen. Seminal cells produce a high-fructose fluid that serves as an energy source for the spermatozoa and promotes their motility. They also secrete other essential substances like proteins, enzymes, vitamin C, prostaglandins, and various other compounds. Collectively, these substances help in the nourishment, protection, and transportation of the spermatozoa throughout the male reproductive system and during the ejaculation process. +Secondary to the production of seminal fluid, the seminal vesicle glandular cells also play a role in the contraction of the seminal vesicles during ejaculation. The contraction of these glands, induced by sympathetic nerves, ensures the efficient propulsion of the seminal fluid mixed with spermatozoa into the ejaculatory ducts and subsequently to the urethra. Notably, any malfunction or pathological condition affecting these cells can impact male fertility, emphasizing the importance of understanding the intricate functions of seminal vesicle glandular cells in maintaining the healthy physiological function of male reproduction."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1007/978-3-030-32300-4_26"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:34198768"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://www.ncbi.nlm.nih.gov/books/NBK499854/"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [mural granulosa cell](http://purl.obolibrary.org/obo/CL_4033067) SubClassOf [RO_0002202](http://purl.obolibrary.org/obo/RO_0002202) some [cuboidal granulosa cell](http://purl.obolibrary.org/obo/CL_4033084) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://www.sciencedirect.com/topics/veterinary-science-and-veterinary-medicine/seminal-vesicle"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [mural granulosa cell](http://purl.obolibrary.org/obo/CL_4033067) SubClassOf [UBERON_0004120](http://purl.obolibrary.org/obo/UBERON_0004120) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1111/j.1439-0272.1992.tb02636.x"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [mural granulosa cell](http://purl.obolibrary.org/obo/CL_4033067) SubClassOf [granulosa cell](http://purl.obolibrary.org/obo/CL_0000501) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1007/s00265-006-0178-0"^^[string](http://www.w3.org/2001/XMLSchema#string) -### muscle cell `http://purl.obolibrary.org/obo/CL_0000187` +### sensory neuron `http://purl.obolibrary.org/obo/CL_0000101` #### Added -- [muscle cell](http://purl.obolibrary.org/obo/CL_0000187) SubClassOf [eukaryotic cell](http://purl.obolibrary.org/obo/CL_0000255) +- [sensory neuron](http://purl.obolibrary.org/obo/CL_0000101) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl/cl-base#cellxgene_subset) -### muscle precursor cell `http://purl.obolibrary.org/obo/CL_0000680` +### sensory neuron of dorsal root ganglion `http://purl.obolibrary.org/obo/CL_1001451` #### Added -- [muscle precursor cell](http://purl.obolibrary.org/obo/CL_0000680) SubClassOf [eukaryotic cell](http://purl.obolibrary.org/obo/CL_0000255) +- [sensory neuron of dorsal root ganglion](http://purl.obolibrary.org/obo/CL_1001451) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl/cl-base#cellxgene_subset) +- [sensory neuron of dorsal root ganglion](http://purl.obolibrary.org/obo/CL_1001451) SubClassOf [peripheral sensory neuron](http://purl.obolibrary.org/obo/CL_3000004) -### myeloid cell `http://purl.obolibrary.org/obo/CL_0000763` -#### Added -- [myeloid cell](http://purl.obolibrary.org/obo/CL_0000763) SubClassOf [eukaryotic cell](http://purl.obolibrary.org/obo/CL_0000255) +### sensory processing neuron `http://purl.obolibrary.org/obo/CL_0000379` +#### Removed +- [sensory processing neuron](http://purl.obolibrary.org/obo/CL_0000379) SubClassOf [neuron](http://purl.obolibrary.org/obo/CL_0000540) +#### Added +- [sensory processing neuron](http://purl.obolibrary.org/obo/CL_0000379) SubClassOf [central nervous system neuron](http://purl.obolibrary.org/obo/CL_2000029) -### myeloid suppressor cell `http://purl.obolibrary.org/obo/CL_0000889` +- [sensory processing neuron](http://purl.obolibrary.org/obo/CL_0000379) SubClassOf [RO_0002215](http://purl.obolibrary.org/obo/RO_0002215) some [GO_0050893](http://purl.obolibrary.org/obo/GO_0050893) -#### Added -- [myeloid suppressor cell](http://purl.obolibrary.org/obo/CL_0000889) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) +### serous cell of epithelium of bronchus `http://purl.obolibrary.org/obo/CL_1000331` -### myotube `http://purl.obolibrary.org/obo/CL_0002372` -#### Removed -- [myotube](http://purl.obolibrary.org/obo/CL_0002372) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A transversely striated, synctial muscle cell, formed by the fusion of myoblasts."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:dos"^^[string](http://www.w3.org/2001/XMLSchema#string) +#### Added +- [serous cell of epithelium of bronchus](http://purl.obolibrary.org/obo/CL_1000331) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ISBN:0323052908"^^[string](http://www.w3.org/2001/XMLSchema#string) +Serous cells of the epithelium of the bronchus, also termed bronchial serous cells, are predominantly found within the seromucous glands located in the bronchial submucosa. Serous cells can also be found in the trachea and are characterized by small, sparse, electron-dense granules. +Serous cells are specialized cells responsible for the production and secretion of serous fluid. Serous fluid, mainly composed of water, proteins, and various types of salts, provides many benefits: it helps moisturize the airways, keep the bronchial tube walls moist, and safeguard the bronchial tubes against various foreign particles and infectious agents such as bacteria and viruses. Moreover, the fluid released by these cells assists in the lubrication and reduced friction in the bronchi, allowing for smoother airflow."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1152/physrev.00039.2014"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:tfm"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://www.ncbi.nlm.nih.gov/books/NBK534789/"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:22274696"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://www.sciencedirect.com/topics/neuroscience/secretory-cell"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [myotube](http://purl.obolibrary.org/obo/CL_0002372) [has_exact_synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "single cell sarcomere"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [serous cell of epithelium of bronchus](http://purl.obolibrary.org/obo/CL_1000331) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://cellxgene.cziscience.com/cellguide/CL_1000331"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [myotube](http://purl.obolibrary.org/obo/CL_0002372) [has_exact_synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "myotubule"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [myotube](http://purl.obolibrary.org/obo/CL_0002372) SubClassOf [multinucleate cell](http://purl.obolibrary.org/obo/CL_0000228) +### serous cell of epithelium of trachea `http://purl.obolibrary.org/obo/CL_1000330` #### Added -- [myotube](http://purl.obolibrary.org/obo/CL_0002372) [has_exact_synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "myofibril"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00005812"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [serous cell of epithelium of trachea](http://purl.obolibrary.org/obo/CL_1000330) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. -- [myotube](http://purl.obolibrary.org/obo/CL_0002372) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A transversely striated, multinucleated syncytial muscle cell, formed by the fusion of myoblasts during muscle development."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:dos"^^[string](http://www.w3.org/2001/XMLSchema#string) +Serous cells are specialized epithelial cells and can be found lining the trachea and brochus. They are among the major components of the respiratory epithelium. +These cells are known for their production and release of serous secretions, which form a key component of airway mucus. These secretions primarily comprise of water, proteins, and enzymes, such as lysozyme and peroxidases. Their main purposes are to provide hydration and lubrication to the airway tissue and to act as a defense mechanism against pathogens. While the lysozyme and peroxidases contribute to the destruction of bacteria, the water in the secretions helps to liquefy the mucus, facilitating the effective functioning of the ciliated cells that propel the mucus up the trachea. +The coordinated action between serous cells and other cell types in the tracheal epithelium proves essential for maintaining a healthy respiratory tract. Dysfunction or damage of these cells can lead to various respiratory tract disorders, such as cystic fibrosis and asthma."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1002/dvdy.24250"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ISBN:0323052908"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1074/jbc.M208826200"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:tfm"^^[string](http://www.w3.org/2001/XMLSchema#string) - - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:22274696"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1016/B978-012330215-1/50029-6"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [myotube](http://purl.obolibrary.org/obo/CL_0002372) [has_exact_synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "myofiber"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00005812"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1016/S0034-5687(01)00214-"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [myotube](http://purl.obolibrary.org/obo/CL_0002372) SubClassOf [syncytial cell](http://purl.obolibrary.org/obo/CL_4052002) +- [serous cell of epithelium of trachea](http://purl.obolibrary.org/obo/CL_1000330) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://cellxgene.cziscience.com/cellguide/CL_1000330"^^[string](http://www.w3.org/2001/XMLSchema#string) -### natural helper lymphocyte `http://purl.obolibrary.org/obo/CL_0002679` +### serous secreting cell of bronchus submucosal gland `http://purl.obolibrary.org/obo/CL_4033005` #### Added -- [natural helper lymphocyte](http://purl.obolibrary.org/obo/CL_0002679) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) +- [serous secreting cell of bronchus submucosal gland](http://purl.obolibrary.org/obo/CL_4033005) [comment](http://www.w3.org/2000/01/rdf-schema#comment) "The marker set PRR4, C6orf58 can identify the Human cell type serous secreting cell of bronchus submucosal gland in the Lung with a confidence of 0.75 (NS-Forest FBeta value)."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://doi.org/10.5281/zenodo.11165918"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [serous secreting cell of bronchus submucosal gland](http://purl.obolibrary.org/obo/CL_4033005) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl/cl-base#cellxgene_subset) + +- [serous secreting cell of bronchus submucosal gland](http://purl.obolibrary.org/obo/CL_4033005) SubClassOf [RO_0015004](http://purl.obolibrary.org/obo/RO_0015004) some [CLM_1000054](http://purl.obolibrary.org/obo/CLM_1000054) -### nephrocyte `http://purl.obolibrary.org/obo/CL_0002520` -#### Removed -- [nephrocyte](http://purl.obolibrary.org/obo/CL_0002520) SubClassOf [eukaryotic cell](http://purl.obolibrary.org/obo/CL_0000255) -- [nephrocyte](http://purl.obolibrary.org/obo/CL_0002520) SubClassOf [RO_0002160](http://purl.obolibrary.org/obo/RO_0002160) some [NCBITaxon_50557](http://purl.obolibrary.org/obo/NCBITaxon_50557) +### skeletal muscle fibroblast `http://purl.obolibrary.org/obo/CL_0011027` #### Added -- [nephrocyte](http://purl.obolibrary.org/obo/CL_0002520) SubClassOf [RO_0002162](http://purl.obolibrary.org/obo/RO_0002162) some [NCBITaxon_50557](http://purl.obolibrary.org/obo/NCBITaxon_50557) +- [skeletal muscle fibroblast](http://purl.obolibrary.org/obo/CL_0011027) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. +Skeletal muscle fibroblasts (SMFs), with their spindle-shaped morphology, play a crucial role in maintaining the structure and function of skeletal muscles. They produce connective tissues enveloping muscle fibers, offering vital structural support for optimal muscle contraction. SMFs are integral components of the dynamic and complex microenvironment of muscle tissue, contributing significantly to healthy muscle development and homeostasis. +SMFs primarily synthesize and secrete extracellular matrix (ECM) components, such as collagen, fibronectin, and proteoglycans. The resulting ECM exhibits mechanical properties that resist tensile forces from muscle contractions, ensuring muscle efficiency. It also crucially transmits force during muscle movement, aids muscle attachment to the skeletal structure, and serves as a scaffold for muscle regeneration and repair. +Following injury, they proliferate and transform into myofibroblasts, aiding wound contraction and depositing new ECM for tissue repair. Additionally, these fibroblasts modulate inflammatory responses by secreting cytokines and interact with other cell types, like immune cells and satellite cells, to coordinate muscle healing. In diseases, an imbalance in SMF activity may lead to conditions such as fibrosis, marked by excessive ECM deposition and impaired muscle function."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1186/s13578-021-00579-4"^^[string](http://www.w3.org/2001/XMLSchema#string) -### neural cell `http://purl.obolibrary.org/obo/CL_0002319` -#### Removed -- [neural cell](http://purl.obolibrary.org/obo/CL_0002319) SubClassOf [cell](http://purl.obolibrary.org/obo/CL_0000000) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1186/s13578-022-00856-w"^^[string](http://www.w3.org/2001/XMLSchema#string) -#### Added -- [neural cell](http://purl.obolibrary.org/obo/CL_0002319) SubClassOf [eukaryotic cell](http://purl.obolibrary.org/obo/CL_0000255) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1016/j.diff.2016.05.007"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [skeletal muscle fibroblast](http://purl.obolibrary.org/obo/CL_0011027) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://cellxgene.cziscience.com/cellguide/CL_0011027"^^[string](http://www.w3.org/2001/XMLSchema#string) -### neural crest cell `http://purl.obolibrary.org/obo/CL_0011012` + +### skeletal muscle satellite cell `http://purl.obolibrary.org/obo/CL_0000594` #### Added -- [neural crest cell](http://purl.obolibrary.org/obo/CL_0011012) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://cellxgene.cziscience.com/cellguide/CL_0011012"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [skeletal muscle satellite cell](http://purl.obolibrary.org/obo/CL_0000594) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. -- [neural crest cell](http://purl.obolibrary.org/obo/CL_0011012) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. +Skeletal muscle satellite cells (SMSCs) are a type of adult stem cell that nestles on the outer surface of the myofiber, positioned between the sarcolemma (plasma membrane of the muscle cell) and peripheral basement membrane. +The primary function of SMSCs lies in their capacity to facilitate the growth and repair of damaged skeletal muscle. Upon muscle injury or trauma, these normally quiescent cells activate, proliferate, and differentiate into myoblasts. These myoblasts subsequently mature and fuse to form myotubes, which ultimately help in the repair and rebuilding of muscle fibers. This response is an integral part of the skeletal muscle's ability to recover from injury and adapt to enhanced or changing physical demands, thereby maintaining and improving muscle function. +Furthermore, SMSCs also contribute to hypertrophic muscle growth due to resistance exercise and endurance training, with the notable feature of their multi-nucleated nature resulting from the fusion of differentiated myoblasts. The additional nuclei support enhanced protein synthesis, thus allowing the muscle fibers to grow and strengthen in response to exercise. In aging and in diseases, the number or functionality of these cells can decrease, leading to impaired muscle regeneration and progressive muscle weakness."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1369/0022155411426780"^^[string](http://www.w3.org/2001/XMLSchema#string) -Neural crest cells are a group of transient and highly migratory cells that originate from the neuroectoderm during the early stages of embryonic development. They are multipotent cells with an exceptional degree of plasticity, capable of differentiating into various somatic cell types and therefore play a fundamental role in the formation of various organs and tissues, making them critical contributors to the developing embryo. -After the initiation of neurulation (the formation of the neural tube) neural crest cells start to undergo epithelial-to-mesenchymal transition and delaminate and migrate from the dorsal neural tube to several regions throughout the embryo. They differentiate into a range of diverse cell types, such as neurons and glial cells of the peripheral nervous system, including sensory and autonomic neurons. They also contribute to the formation of adrenal glands, pigment cells in the skin (melanocytes), cardiac structures, including parts of the heart septum and major arteries, as well as bones and cartilage of the face and skull. -Disorders or aberrations in the development or migration of the neural crest cells can lead to serious congenital malformations, such as neurocristopathies, including Hirschsprung disease, neuroblastoma, and neurofibromatosis."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.3389/fcell.2020.00635/full"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.22074/cellj.2016.4714"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1242/dev.193193"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1152/physrev.00061.2017"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1002/dvg.23276"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1016/s1357-2725(03)00042-6"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://doi.org/10.1016/j.ydbio.2011.12.042"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1186/s13287-022-02706-5"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [skeletal muscle satellite cell](http://purl.obolibrary.org/obo/CL_0000594) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://cellxgene.cziscience.com/cellguide/CL_0000594"^^[string](http://www.w3.org/2001/XMLSchema#string) -### neuroblast (sensu Nematoda and Protostomia) `http://purl.obolibrary.org/obo/CL_0000338` + +### skin sebocyte `http://purl.obolibrary.org/obo/CL_0002140` #### Removed -- [neuroblast (sensu Nematoda and Protostomia)](http://purl.obolibrary.org/obo/CL_0000338) SubClassOf [eukaryotic cell](http://purl.obolibrary.org/obo/CL_0000255) +- [skin sebocyte](http://purl.obolibrary.org/obo/CL_0002140) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A sebum secreting cell of the skin that secretes sebum into the hair follicles."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:tfm"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [neuroblast (sensu Nematoda and Protostomia)](http://purl.obolibrary.org/obo/CL_0000338) SubClassOf [RO_0002160](http://purl.obolibrary.org/obo/RO_0002160) some [NCBITaxon_33317](http://purl.obolibrary.org/obo/NCBITaxon_33317) +- [skin sebocyte](http://purl.obolibrary.org/obo/CL_0002140) [label](http://www.w3.org/2000/01/rdf-schema#label) "acinar cell of sebaceous gland"^^[string](http://www.w3.org/2001/XMLSchema#string) -#### Added -- [neuroblast (sensu Nematoda and Protostomia)](http://purl.obolibrary.org/obo/CL_0000338) SubClassOf [RO_0002162](http://purl.obolibrary.org/obo/RO_0002162) some [NCBITaxon_33317](http://purl.obolibrary.org/obo/NCBITaxon_33317) +- [skin sebocyte](http://purl.obolibrary.org/obo/CL_0002140) [has_broad_synonym](http://www.geneontology.org/formats/oboInOwl#hasBroadSynonym) "sebocyte"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [skin sebocyte](http://purl.obolibrary.org/obo/CL_0002140) EquivalentTo [sebocyte](http://purl.obolibrary.org/obo/CL_0000317) and ([BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0003487](http://purl.obolibrary.org/obo/UBERON_0003487)) -### neuroblast (sensu Vertebrata) `http://purl.obolibrary.org/obo/CL_0000031` -#### Removed -- [neuroblast (sensu Vertebrata)](http://purl.obolibrary.org/obo/CL_0000031) SubClassOf [RO_0002160](http://purl.obolibrary.org/obo/RO_0002160) some [NCBITaxon_7742](http://purl.obolibrary.org/obo/NCBITaxon_7742) +- [skin sebocyte](http://purl.obolibrary.org/obo/CL_0002140) SubClassOf [epithelial cell of sweat gland](http://purl.obolibrary.org/obo/CL_1000448) #### Added -- [neuroblast (sensu Vertebrata)](http://purl.obolibrary.org/obo/CL_0000031) SubClassOf [RO_0002162](http://purl.obolibrary.org/obo/RO_0002162) some [NCBITaxon_7742](http://purl.obolibrary.org/obo/NCBITaxon_7742) +- [skin sebocyte](http://purl.obolibrary.org/obo/CL_0002140) [has_exact_synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "acinar cell of skin sebaceous gland"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [skin sebocyte](http://purl.obolibrary.org/obo/CL_0002140) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "An acinar cell that is part of a skin sebaceous gland. This cell produces and secretes sebum into hair follicles."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:tfm"^^[string](http://www.w3.org/2001/XMLSchema#string) -### neuroglioblast (sensu Nematoda and Protostomia) `http://purl.obolibrary.org/obo/CL_0000468` -#### Removed -- [neuroglioblast (sensu Nematoda and Protostomia)](http://purl.obolibrary.org/obo/CL_0000468) SubClassOf [eukaryotic cell](http://purl.obolibrary.org/obo/CL_0000255) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:37205445"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [neuroglioblast (sensu Nematoda and Protostomia)](http://purl.obolibrary.org/obo/CL_0000468) SubClassOf [RO_0002160](http://purl.obolibrary.org/obo/RO_0002160) some [NCBITaxon_33317](http://purl.obolibrary.org/obo/NCBITaxon_33317) +- [skin sebocyte](http://purl.obolibrary.org/obo/CL_0002140) [label](http://www.w3.org/2000/01/rdf-schema#label) "skin sebocyte"^^[string](http://www.w3.org/2001/XMLSchema#string) -#### Added -- [neuroglioblast (sensu Nematoda and Protostomia)](http://purl.obolibrary.org/obo/CL_0000468) SubClassOf [RO_0002162](http://purl.obolibrary.org/obo/RO_0002162) some [NCBITaxon_33317](http://purl.obolibrary.org/obo/NCBITaxon_33317) +- [skin sebocyte](http://purl.obolibrary.org/obo/CL_0002140) [has_broad_synonym](http://www.geneontology.org/formats/oboInOwl#hasBroadSynonym) "acinar cell of sebaceous gland"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [skin sebocyte](http://purl.obolibrary.org/obo/CL_0002140) EquivalentTo [acinar cell](http://purl.obolibrary.org/obo/CL_0000622) and ([BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0003487](http://purl.obolibrary.org/obo/UBERON_0003487)) -### neuromast mantle cell `http://purl.obolibrary.org/obo/CL_0000851` +### slow muscle cell `http://purl.obolibrary.org/obo/CL_0000189` #### Added -- [neuromast mantle cell](http://purl.obolibrary.org/obo/CL_0000851) SubClassOf [eukaryotic cell](http://purl.obolibrary.org/obo/CL_0000255) +- [slow muscle cell](http://purl.obolibrary.org/obo/CL_0000189) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. +Slow muscle cells, as the name implies, are a type of muscle cell well known for their slow contractile speed. They are also referred to as type I, slow-twitch, or red muscles because of their high myoglobin content which gives them a dark, reddish appearance. These cells are predominantly found in the postural muscles of the body, such as those in the back and lower limbs. +A defining characteristic of slow muscle cells is their significant resistance to fatigue. This is largely due to their efficient oxidative metabolism, which allows them to continuously contract over extended periods without succumbing to fatigue. This extraordinary endurance is facilitated by a high concentration of mitochondria, which enables the efficient use of oxygen for energy production, and capillaries, which supplies the necessary oxygen and nutrients. Additionally, these cells have an abundant supply of myoglobin, a protein that stores and transports oxygen within the muscle cell, further supporting their aerobic metabolism. +The primary role of slow muscle cells in the human body is to provide sustained, low-intensity contractions over a prolonged period. They are responsible for maintaining posture and providing stability, rather than delivering short, powerful bursts of activity. They play a pivotal role in supporting various physical activities such as standing, walking, or any form of exercise that requires endurance over speed."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1093/ptj/81.11.1810"^^[string](http://www.w3.org/2001/XMLSchema#string) -### neuromast supporting cell `http://purl.obolibrary.org/obo/CL_0000852` + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.3389/fphys.2021.747214"^^[string](http://www.w3.org/2001/XMLSchema#string) -#### Added -- [neuromast supporting cell](http://purl.obolibrary.org/obo/CL_0000852) SubClassOf [eukaryotic cell](http://purl.obolibrary.org/obo/CL_0000255) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://www.sciencedirect.com/topics/biochemistry-genetics-and-molecular-biology/slow-muscle-fiber"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1186/s13578-015-0054-6"^^[string](http://www.w3.org/2001/XMLSchema#string) -### neuron associated cell (sensu Nematoda and Protostomia) `http://purl.obolibrary.org/obo/CL_0000130` -#### Removed -- [neuron associated cell (sensu Nematoda and Protostomia)](http://purl.obolibrary.org/obo/CL_0000130) SubClassOf [RO_0002160](http://purl.obolibrary.org/obo/RO_0002160) some [NCBITaxon_33317](http://purl.obolibrary.org/obo/NCBITaxon_33317) +- [slow muscle cell](http://purl.obolibrary.org/obo/CL_0000189) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://cellxgene.cziscience.com/cellguide/CL_0000189"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [neuron associated cell (sensu Nematoda and Protostomia)](http://purl.obolibrary.org/obo/CL_0000130) SubClassOf [eukaryotic cell](http://purl.obolibrary.org/obo/CL_0000255) + +### small bistratified retinal ganglion cell `http://purl.obolibrary.org/obo/CL_4033053` #### Added -- [neuron associated cell (sensu Nematoda and Protostomia)](http://purl.obolibrary.org/obo/CL_0000130) SubClassOf [RO_0002162](http://purl.obolibrary.org/obo/RO_0002162) some [NCBITaxon_33317](http://purl.obolibrary.org/obo/NCBITaxon_33317) +- [small bistratified retinal ganglion cell](http://purl.obolibrary.org/obo/CL_4033053) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl/cl-base#cellxgene_subset) -### neuron associated cell (sensu Vertebrata) `http://purl.obolibrary.org/obo/CL_0000123` +### small intestine goblet cell `http://purl.obolibrary.org/obo/CL_1000495` #### Removed -- [neuron associated cell (sensu Vertebrata)](http://purl.obolibrary.org/obo/CL_0000123) SubClassOf [eukaryotic cell](http://purl.obolibrary.org/obo/CL_0000255) +- [small intestine goblet cell](http://purl.obolibrary.org/obo/CL_1000495) EquivalentTo [goblet cell](http://purl.obolibrary.org/obo/CL_0000160) and ([BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0002108](http://purl.obolibrary.org/obo/UBERON_0002108)) + +- [small intestine goblet cell](http://purl.obolibrary.org/obo/CL_1000495) SubClassOf [epithelial cell of small intestine](http://purl.obolibrary.org/obo/CL_0002254) -- [neuron associated cell (sensu Vertebrata)](http://purl.obolibrary.org/obo/CL_0000123) SubClassOf [RO_0002160](http://purl.obolibrary.org/obo/RO_0002160) some [NCBITaxon_7742](http://purl.obolibrary.org/obo/NCBITaxon_7742) +- [small intestine goblet cell](http://purl.obolibrary.org/obo/CL_1000495) SubClassOf [BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0001902](http://purl.obolibrary.org/obo/UBERON_0001902) #### Added -- [neuron associated cell (sensu Vertebrata)](http://purl.obolibrary.org/obo/CL_0000123) SubClassOf [RO_0002162](http://purl.obolibrary.org/obo/RO_0002162) some [NCBITaxon_7742](http://purl.obolibrary.org/obo/NCBITaxon_7742) +- [small intestine goblet cell](http://purl.obolibrary.org/obo/CL_1000495) EquivalentTo [goblet cell](http://purl.obolibrary.org/obo/CL_0000160) and ([BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0001902](http://purl.obolibrary.org/obo/UBERON_0001902)) +- [small intestine goblet cell](http://purl.obolibrary.org/obo/CL_1000495) SubClassOf [small intestine secretory cell](http://purl.obolibrary.org/obo/CL_1001598) -### neuronal-restricted precursor `http://purl.obolibrary.org/obo/CL_4042021` -#### Added -- [neuronal-restricted precursor](http://purl.obolibrary.org/obo/CL_4042021) [comment](http://www.w3.org/2000/01/rdf-schema#comment) "In vitro cultures of embryonic mouse neural tubes show that neuronal-restricted precursors (NRPs) are derived from multipotent neuroepithelial cells to give rise to neurons. This progression suggests a linear relationship between multipotent progenitors and neuronal-restricted differentiation. (Mayer-Proschel et al., 1997). In the spinal cord of rats, neural-restricted precursor cells give rise cholinergic, GABAergic, glutametergic neurons (Cao and Howard et al., 2002)."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:9354325"^^[string](http://www.w3.org/2001/XMLSchema#string) +### small intestine secretory cell `http://purl.obolibrary.org/obo/CL_1001598` +#### Removed +- [small intestine secretory cell](http://purl.obolibrary.org/obo/CL_1001598) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "small intestinal glandular cell"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "CALOHA:TS-1286"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:12429182"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [small intestine secretory cell](http://purl.obolibrary.org/obo/CL_1001598) [label](http://www.w3.org/2000/01/rdf-schema#label) "small intestine glandular cell"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [neuronal-restricted precursor](http://purl.obolibrary.org/obo/CL_4042021) [date](http://purl.org/dc/terms/date) "2024-09-02T11:42:12Z"^^[dateTime](http://www.w3.org/2001/XMLSchema#dateTime) +- [small intestine secretory cell](http://purl.obolibrary.org/obo/CL_1001598) EquivalentTo [glandular secretory epithelial cell](http://purl.obolibrary.org/obo/CL_0000150) and ([BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0002108](http://purl.obolibrary.org/obo/UBERON_0002108)) -- [neuronal-restricted precursor](http://purl.obolibrary.org/obo/CL_4042021) [id](http://www.geneontology.org/formats/oboInOwl#id) "CL:4042021"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [small intestine secretory cell](http://purl.obolibrary.org/obo/CL_1001598) SubClassOf [glandular secretory epithelial cell](http://purl.obolibrary.org/obo/CL_0000150) -- [neuronal-restricted precursor](http://purl.obolibrary.org/obo/CL_4042021) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A progenitor cell of the central nervous system that differentiates exclusively onto neurons. This progenitor cell is found in a hippocampus subventricular zone, developing cortex and spinal cord of the central nervous system."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:10467245"^^[string](http://www.w3.org/2001/XMLSchema#string) +#### Added +- [small intestine secretory cell](http://purl.obolibrary.org/obo/CL_1001598) [label](http://www.w3.org/2000/01/rdf-schema#label) "small intestine secretory cell"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [neuronal-restricted precursor](http://purl.obolibrary.org/obo/CL_4042021) [contributor](http://purl.org/dc/terms/contributor) [0000-0002-0098-8958](https://orcid.org/0000-0002-0098-8958) +- [small intestine secretory cell](http://purl.obolibrary.org/obo/CL_1001598) [has_narrow_synonym](http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym) "small intestinal glandular cell"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "CALOHA:TS-1286"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [neuronal-restricted precursor](http://purl.obolibrary.org/obo/CL_4042021) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "NRP"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [synonym_type_property](http://www.geneontology.org/formats/oboInOwl#SynonymTypeProperty) "OMO:0003000"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [small intestine secretory cell](http://purl.obolibrary.org/obo/CL_1001598) EquivalentTo [secretory epithelial cell](http://purl.obolibrary.org/obo/CL_1100001) and ([BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0002108](http://purl.obolibrary.org/obo/UBERON_0002108)) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:12429182"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [small intestine secretory cell](http://purl.obolibrary.org/obo/CL_1001598) SubClassOf [secretory epithelial cell](http://purl.obolibrary.org/obo/CL_1100001) -- [neuronal-restricted precursor](http://purl.obolibrary.org/obo/CL_4042021) [label](http://www.w3.org/2000/01/rdf-schema#label) "neuronal-restricted precursor"^^[string](http://www.w3.org/2001/XMLSchema#string) -- Class: [neuronal-restricted precursor](http://purl.obolibrary.org/obo/CL_4042021) +### small intestine serosal dendritic cell `http://purl.obolibrary.org/obo/CL_0002466` -- [neuronal-restricted precursor](http://purl.obolibrary.org/obo/CL_4042021) SubClassOf [BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0001017](http://purl.obolibrary.org/obo/UBERON_0001017) +#### Added +- [small intestine serosal dendritic cell](http://purl.obolibrary.org/obo/CL_0002466) [depiction](http://xmlns.com/foaf/0.1/depiction) [Small-intestine-cells.png](http://purl.obolibrary.org/obo/cl/images/Small-intestine-cells.png) + - [comment](http://www.w3.org/2000/01/rdf-schema#comment) "Figure depicts a cross section of intestinal villi in the small intestine, including the crypts of Lieberkuhn (seen here as ‘crypt’), as well as the layer specific locations of cells that exist within the gastrointestinal tract. Layers depicted here include epithelium (rows of cells bordering villus), submucosa (white space below the epithelium containing networks of neurons and ganglia depicted in pink), muscularis mucosae (blue layer), muscularis propria (referred to here as muscle layer). -- [neuronal-restricted precursor](http://purl.obolibrary.org/obo/CL_4042021) SubClassOf [neuron associated cell (sensu Vertebrata)](http://purl.obolibrary.org/obo/CL_0000123) +ISC: Intestinal Stem Cell +TA: Transit Amplifying Cells"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [neuronal-restricted precursor](http://purl.obolibrary.org/obo/CL_4042021) SubClassOf [progenitor cell](http://purl.obolibrary.org/obo/CL_0011026) + - [license](http://purl.org/dc/elements/1.1/license) "http://creativecommons.org/licenses/by/4.0/"^^[string](http://www.w3.org/2001/XMLSchema#string) -### neuroplacodal cell `http://purl.obolibrary.org/obo/CL_0000032` +### smooth muscle cell `http://purl.obolibrary.org/obo/CL_0000192` #### Added -- [neuroplacodal cell](http://purl.obolibrary.org/obo/CL_0000032) SubClassOf [eukaryotic cell](http://purl.obolibrary.org/obo/CL_0000255) +- [smooth muscle cell](http://purl.obolibrary.org/obo/CL_0000192) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. +Smooth muscle cells are a specialized type of muscle cells that are primarily found within the walls of hollow organs such as the intestine, stomach, bladder, uterus, and blood vessels. These cells are an essential component of the autonomic nervous system controling involuntary movements within the body. +Smooth muscle cells play a vital role in many physiological processes due to their unique functionality. They can contract and relax in a slow, sustained, and controlled manner to help modulate the size and shape of the lumens of the organs they surround. For example, in the digestive system, coordinated contraction and relaxation of smooth muscle cells propels food along the gastrointestinal tract - a process known as peristalsis. In the blood vessels, the smooth muscle cells, by contracting or relaxing, either constrict or dilate the vessels, which in turn, help regulate blood flow and pressure. +On a cellular level, smooth muscle cells possess a single, centrally located nucleus and contain an arranged network of actin and myosin filaments, which are the proteins responsible for muscle contraction. Unlike their counterparts in skeletal or cardiac muscles, these cells lack specific contact points for these filaments, hence the lack of visible striations. Furthermore, the contraction of smooth muscle cells is regulated by hormones and neurotransmitters, such as acetylcholine and norepinephrine, adding an additional layer of complex regulation to these highly specialized cells."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1093/ptj/81.11.1810"^^[string](http://www.w3.org/2001/XMLSchema#string) -### neutrophilic myeloblast `http://purl.obolibrary.org/obo/CL_0000042` + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://www.ncbi.nlm.nih.gov/books/NBK526125"^^[string](http://www.w3.org/2001/XMLSchema#string) -#### Added -- [neutrophilic myeloblast](http://purl.obolibrary.org/obo/CL_0000042) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://training.seer.cancer.gov/anatomy/muscular/types.html"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://www.ncbi.nlm.nih.gov/books/NBK556137/"^^[string](http://www.w3.org/2001/XMLSchema#string) -### non-classical monocyte `http://purl.obolibrary.org/obo/CL_0000875` + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://www.ncbi.nlm.nih.gov/books/NBK10854/"^^[string](http://www.w3.org/2001/XMLSchema#string) -#### Added -- [non-classical monocyte](http://purl.obolibrary.org/obo/CL_0000875) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) +- [smooth muscle cell](http://purl.obolibrary.org/obo/CL_0000192) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://cellxgene.cziscience.com/cellguide/CL_0000192"^^[string](http://www.w3.org/2001/XMLSchema#string) -### notochordal cell `http://purl.obolibrary.org/obo/CL_0007005` -#### Removed -- [notochordal cell](http://purl.obolibrary.org/obo/CL_0007005) SubClassOf [cell](http://purl.obolibrary.org/obo/CL_0000000) +### smooth muscle cell of colon `http://purl.obolibrary.org/obo/CL_1000280` #### Added -- [notochordal cell](http://purl.obolibrary.org/obo/CL_0007005) SubClassOf [eukaryotic cell](http://purl.obolibrary.org/obo/CL_0000255) - - -### obliquely striated somatic muscle cell `http://purl.obolibrary.org/obo/CL_0008005` -#### Removed -- [obliquely striated somatic muscle cell](http://purl.obolibrary.org/obo/CL_0008005) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A somatic muscle cell that is oblquely striated. Examples include the somatic muscles of nematodes."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:8720463"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [smooth muscle cell of colon](http://purl.obolibrary.org/obo/CL_1000280) SubClassOf [BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0001278](http://purl.obolibrary.org/obo/UBERON_0001278) -- [obliquely striated somatic muscle cell](http://purl.obolibrary.org/obo/CL_0008005) EquivalentTo [somatic muscle cell](http://purl.obolibrary.org/obo/CL_0008004) and ([BFO_0000051](http://purl.obolibrary.org/obo/BFO_0000051) some [GO_0030017](http://purl.obolibrary.org/obo/GO_0030017)) and ([RO_0000053](http://purl.obolibrary.org/obo/RO_0000053) some [PATO_0001908](http://purl.obolibrary.org/obo/PATO_0001908)) and ([RO_0000053](http://purl.obolibrary.org/obo/RO_0000053) some [PATO_0002479](http://purl.obolibrary.org/obo/PATO_0002479)) -- [obliquely striated somatic muscle cell](http://purl.obolibrary.org/obo/CL_0008005) SubClassOf [multinucleate cell](http://purl.obolibrary.org/obo/CL_0000228) +### smooth muscle cell of large intestine smooth muscle circular layer `http://purl.obolibrary.org/obo/CL_4033011` #### Added -- [obliquely striated somatic muscle cell](http://purl.obolibrary.org/obo/CL_0008005) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A somatic muscle cell that is obliquely striated and mononucleated. Examples include the somatic muscles of nematodes."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "doi:10.3908/wormatlas.1.7"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [smooth muscle cell of large intestine smooth muscle circular layer](http://purl.obolibrary.org/obo/CL_4033011) SubClassOf [BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0001278](http://purl.obolibrary.org/obo/UBERON_0001278) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:8720463"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [obliquely striated somatic muscle cell](http://purl.obolibrary.org/obo/CL_0008005) EquivalentTo [somatic muscle cell](http://purl.obolibrary.org/obo/CL_0008004) and ([BFO_0000051](http://purl.obolibrary.org/obo/BFO_0000051) some [GO_0030017](http://purl.obolibrary.org/obo/GO_0030017)) and ([RO_0000053](http://purl.obolibrary.org/obo/RO_0000053) some [PATO_0001407](http://purl.obolibrary.org/obo/PATO_0001407)) and ([RO_0000053](http://purl.obolibrary.org/obo/RO_0000053) some [PATO_0002479](http://purl.obolibrary.org/obo/PATO_0002479)) +### smooth muscle cell of large intestine smooth muscle longitudinal layer `http://purl.obolibrary.org/obo/CL_4033012` -- [obliquely striated somatic muscle cell](http://purl.obolibrary.org/obo/CL_0008005) SubClassOf [single nucleate cell](http://purl.obolibrary.org/obo/CL_0000226) +#### Added +- [smooth muscle cell of large intestine smooth muscle longitudinal layer](http://purl.obolibrary.org/obo/CL_4033012) SubClassOf [BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0001278](http://purl.obolibrary.org/obo/UBERON_0001278) -### oenocyte `http://purl.obolibrary.org/obo/CL_0000487` -#### Removed -- [oenocyte](http://purl.obolibrary.org/obo/CL_0000487) SubClassOf [RO_0002160](http://purl.obolibrary.org/obo/RO_0002160) some [NCBITaxon_6656](http://purl.obolibrary.org/obo/NCBITaxon_6656) +### smooth muscle cell of prostate `http://purl.obolibrary.org/obo/CL_1000487` #### Added -- [oenocyte](http://purl.obolibrary.org/obo/CL_0000487) SubClassOf [RO_0002162](http://purl.obolibrary.org/obo/RO_0002162) some [NCBITaxon_6656](http://purl.obolibrary.org/obo/NCBITaxon_6656) +- [smooth muscle cell of prostate](http://purl.obolibrary.org/obo/CL_1000487) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. +Smooth muscle cells of the prostate constitute a critical component of the prostatic stroma, enveloping glandular structures to support functions like secretion and fluid expulsion. Like other smooth muscles, smooth muscle cells of the prostate lack the striations characteristic of skeletal and cardiac muscle cell. +Functionally, they play a crucial role in reproductive and urinary functions. Smooth muscle cells of the prostate contribute to the transport and expulsion of prostatic secretions into the urethra and respond dynamically to signaling molecules such as hormones and neurotransmitters. For instance, under sympathetic nervous stimulation, they contract and apply pressure on the gland's ducts, facilitating the secretion process."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://www.ncbi.nlm.nih.gov/books/NBK279291"^^[string](http://www.w3.org/2001/XMLSchema#string) -### oligodendrocyte precursor cell `http://purl.obolibrary.org/obo/CL_0002453` -#### Removed -- [oligodendrocyte precursor cell](http://purl.obolibrary.org/obo/CL_0002453) [comment](http://www.w3.org/2000/01/rdf-schema#comment) "This cell type can be purified from optic nerves and other regions of the embryonic, postnatal and adult rat CNS and can be differentiated in vitro to oligodendrocytes and type-2 astrocytes. Some references use the terms 'oligodendrocyte precursor cell' and 'oligodendrocyte type-2 astrocyte (O-2A) progenitor' to refer to the same entity (e.g., PMID:10704434), while others describe an oligodendrocyte type-2 astrocyte (O-2A) progenitor cell as the precurosr to oligodendrocyte- and type-2 astrocyte- progenitor cells (e.g, ISBN:9780702028991)."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:2182078"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://www.sciencedirect.com/topics/immunology-and-microbiology/smooth-muscle-cell"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ISBN:9780702028991"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1101/cshperspect.a030510"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:10704434"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [smooth muscle cell of prostate](http://purl.obolibrary.org/obo/CL_1000487) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://cellxgene.cziscience.com/cellguide/CL_1000487"^^[string](http://www.w3.org/2001/XMLSchema#string) -#### Added -- [oligodendrocyte precursor cell](http://purl.obolibrary.org/obo/CL_0002453) [description](http://purl.org/dc/terms/description) "This cell type can be purified from optic nerves and other regions of the embryonic, postnatal and adult rat CNS and can be differentiated in vitro to oligodendrocytes and type-2 astrocytes. Some references use the terms 'oligodendrocyte precursor cell' and 'oligodendrocyte type-2 astrocyte (O-2A) progenitor' to refer to the same entity (e.g., PMID:10704434), while others describe an oligodendrocyte type-2 astrocyte (O-2A) progenitor cell as the precurosr to oligodendrocyte- and type-2 astrocyte- progenitor cells (e.g, ISBN:9780702028991)."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:2182078"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ISBN:9780702028991"^^[string](http://www.w3.org/2001/XMLSchema#string) +### smooth muscle cell of rectum `http://purl.obolibrary.org/obo/CL_1000286` - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:10704434"^^[string](http://www.w3.org/2001/XMLSchema#string) +#### Added +- [smooth muscle cell of rectum](http://purl.obolibrary.org/obo/CL_1000286) SubClassOf [BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0001278](http://purl.obolibrary.org/obo/UBERON_0001278) -### ooblast `http://purl.obolibrary.org/obo/CL_0002239` +### smooth muscle cell of small intestine `http://purl.obolibrary.org/obo/CL_1000275` #### Added -- [ooblast](http://purl.obolibrary.org/obo/CL_0002239) SubClassOf [eukaryotic cell](http://purl.obolibrary.org/obo/CL_0000255) - +- [smooth muscle cell of small intestine](http://purl.obolibrary.org/obo/CL_1000275) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. -### oocyte `http://purl.obolibrary.org/obo/CL_0000023` -#### Removed -- [oocyte](http://purl.obolibrary.org/obo/CL_0000023) SubClassOf [eukaryotic cell](http://purl.obolibrary.org/obo/CL_0000255) +Smooth muscle cells of the small intestine form a key component of the enteric system which is imperative for gastrointestinal motility. These cells are a specialized subgroup of smooth muscle cells, specifically found in the layers of the small intestine. The small intestine represents a significant part of the digestive system and plays a crucial role in the absorption of nutrients into the bloodstream. +Smooth muscle cells of the small intestine are predominantly responsible for creating the contractions and relaxations that constitute intestinal motility. They trigger these movements in a coordinated and rhythmic manner known as peristalsis and segmentation. Peristalsis is a form of longitudinal and sequential contraction that pushes food from the upper gastrointestinal tract to the lower parts. Segmentation works by squeezing the intestine randomly, thereby facilitating the mixing of food particles and increasing contact with absorptive surfaces. These two processes are critical for intestinal motility and an effective digestive process. +Apart from facilitating transit of food through contractions, these smooth muscle cells play a role in controlling the diameter of the vessels and the blood flow in the small intestine by their constrictive ability. These smooth muscle cells also contribute to the structural integrity of the small intestine by forming a part of its muscularis externa and muscularis mucosae. Additionally, they interact with other cell types such as enteric neurons and interstitial cells of Cajal (ICC), forming an integrated cellular network that ensures optimal functioning of the intestinal tract."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1053/j.gastro.2016.02.030"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [oocyte](http://purl.obolibrary.org/obo/CL_0000023) SubClassOf [RO_0002160](http://purl.obolibrary.org/obo/RO_0002160) some [NCBITaxon_33208](http://purl.obolibrary.org/obo/NCBITaxon_33208) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1038/nrgastro.2012.168"^^[string](http://www.w3.org/2001/XMLSchema#string) -#### Added -- [oocyte](http://purl.obolibrary.org/obo/CL_0000023) SubClassOf [RO_0002162](http://purl.obolibrary.org/obo/RO_0002162) some [NCBITaxon_33208](http://purl.obolibrary.org/obo/NCBITaxon_33208) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1111/j.1582-4934.2008.00352.x"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1038/s41575-020-0271-2"^^[string](http://www.w3.org/2001/XMLSchema#string) -### osteoclast `http://purl.obolibrary.org/obo/CL_0000092` + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1007/978-981-13-5895-1_1"^^[string](http://www.w3.org/2001/XMLSchema#string) -#### Added -- [osteoclast](http://purl.obolibrary.org/obo/CL_0000092) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) +- [smooth muscle cell of small intestine](http://purl.obolibrary.org/obo/CL_1000275) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://cellxgene.cziscience.com/cellguide/CL_1000275"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [smooth muscle cell of small intestine](http://purl.obolibrary.org/obo/CL_1000275) [depiction](http://xmlns.com/foaf/0.1/depiction) [Small-intestine-cells.png](http://purl.obolibrary.org/obo/cl/images/Small-intestine-cells.png) + - [comment](http://www.w3.org/2000/01/rdf-schema#comment) "Figure depicts a cross section of intestinal villi in the small intestine, including the crypts of Lieberkuhn (seen here as ‘crypt’), as well as the layer specific locations of cells that exist within the gastrointestinal tract. Layers depicted here include epithelium (rows of cells bordering villus), submucosa (white space below the epithelium containing networks of neurons and ganglia depicted in pink), muscularis mucosae (blue layer), muscularis propria (referred to here as muscle layer). -### oxytocin receptor sst GABAergic cortical interneuron `http://purl.obolibrary.org/obo/CL_4023122` -#### Removed -- [oxytocin receptor sst GABAergic cortical interneuron](http://purl.obolibrary.org/obo/CL_4023122) SubClassOf [sst GABAergic cortical interneuron](http://purl.obolibrary.org/obo/CL_4023017) +ISC: Intestinal Stem Cell +TA: Transit Amplifying Cells"^^[string](http://www.w3.org/2001/XMLSchema#string) -#### Added -- [oxytocin receptor sst GABAergic cortical interneuron](http://purl.obolibrary.org/obo/CL_4023122) SubClassOf [RO_0002292](http://purl.obolibrary.org/obo/RO_0002292) some [PR_000015665](http://purl.obolibrary.org/obo/PR_000015665) + - [license](http://purl.org/dc/elements/1.1/license) "http://creativecommons.org/licenses/by/4.0/"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [oxytocin receptor sst GABAergic cortical interneuron](http://purl.obolibrary.org/obo/CL_4023122) SubClassOf [BFO_0000002](http://purl.obolibrary.org/obo/BFO_0000002) -- [oxytocin receptor sst GABAergic cortical interneuron](http://purl.obolibrary.org/obo/CL_4023122) SubClassOf [cerebral cortex GABAergic interneuron](http://purl.obolibrary.org/obo/CL_0010011) +### smooth muscle cell of sphincter of pupil `http://purl.obolibrary.org/obo/CL_0002243` +#### Added +- [smooth muscle cell of sphincter of pupil](http://purl.obolibrary.org/obo/CL_0002243) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. -### pancreatic PP cell `http://purl.obolibrary.org/obo/CL_0002275` +The smooth muscle cell of sphincter of pupil is a specialized cell type typically found within the eye, more specifically within the sphincter muscle of the iris. +These cells can constrict and dilate in response to light signals, tightly regulating the amount of light reaching the retina. Contraction narrows the pupil in bright conditions (pupillary constriction), protecting the retina from excessive light. In low light, relaxation allows dilation (pupillary dilation), enhancing visual perception in dim conditions. +These cells are also innervated by parasympathetic fibers from the oculomotor nerve. Light signals to the Edinger-Westphal nucleus stimulate the release of acetylcholine, contracting the cells. On the contrary, sympathetic stimulation induces relaxation. This precise control plays a crucial role in optimizing visual function, highlighting their essential role in vision biology."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://www.sciencedirect.com/topics/neuroscience/iris-dilator-muscle"^^[string](http://www.w3.org/2001/XMLSchema#string) -#### Added -- [pancreatic PP cell](http://purl.obolibrary.org/obo/CL_0002275) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://cellxgene.cziscience.com/cellguide/CL_0002275"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://www.ncbi.nlm.nih.gov/books/NBK537180/"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [pancreatic PP cell](http://purl.obolibrary.org/obo/CL_0002275) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://www.sciencedirect.com/topics/neuroscience/iris-sphincter-muscle"^^[string](http://www.w3.org/2001/XMLSchema#string) -Pancreatic polypeptide (PP) cells (also called F or gamma cells) are unique endocrine cells located within the Islets of Langerhans in the pancreas. PP cells are one of the rarer pancreatic cell types and are more prevalent in the head and neck of the pancreas. They are critical in normal pancreatic physiological functions and are involved in the development of pancreatic endocrine disorders. -The primary function of PP cells is the production and secretion of the pancreatic polypeptide hormone (PP). This hormone plays a crucial role in several gastrointestinal functions and metabolic responses. The release of the PP hormone is stimulated after eating, especially in protein-rich meals, leading to it being present in large amounts during digestion. The fundamental role of PP is to self-regulate pancreatic secretion activities ensuring its exocrine and endocrine functions are under control. -The pancreatic polypeptide hormone from PP cells also aids in adapting to low physical activity and fasting by reducing the production of insulin and glucagon and inhibiting the hepatic glucose production. Additionally, this hormone influences gut motility by slowing down the gastric emptying and reducing small intestinal transit, thereby controlling the pace at which nutritional substances are absorbed. Because of these functions, any malfunction or irregularity in PP cells can result in various disorders such as diabetes and pancreatic diseases."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1038/s42255-019-0148-2"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://www.ncbi.nlm.nih.gov/books/NBK532252/"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1016/j.mce.2015.06.028"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [smooth muscle cell of sphincter of pupil](http://purl.obolibrary.org/obo/CL_0002243) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://cellxgene.cziscience.com/cellguide/CL_0002243"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1016/B978-0-12-819402-7.00001-2"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.3389/fendo.2023.1192311"^^[string](http://www.w3.org/2001/XMLSchema#string) +### smooth muscle cell of stomach `http://purl.obolibrary.org/obo/CL_4047034` - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1016/B978-012369442-3/50154-9"^^[string](http://www.w3.org/2001/XMLSchema#string) +#### Added +- [smooth muscle cell of stomach](http://purl.obolibrary.org/obo/CL_4047034) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A smooth muscle cell that is part of the muscularis externa of the stomach wall. It is characterized by its fusiform shape, involuntary control, and ability to generate slow, sustained contractions. This cell is organized in distinct layers and is essential for gastric motility and digestion."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:21443757"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:33630273"^^[string](http://www.w3.org/2001/XMLSchema#string) -### pancreatic acinar cell `http://purl.obolibrary.org/obo/CL_0002064` +- [smooth muscle cell of stomach](http://purl.obolibrary.org/obo/CL_4047034) [date](http://purl.org/dc/terms/date) "2024-12-05T11:10:18Z"^^[dateTime](http://www.w3.org/2001/XMLSchema#dateTime) -#### Added -- [pancreatic acinar cell](http://purl.obolibrary.org/obo/CL_0002064) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://cellxgene.cziscience.com/cellguide/CL_0002064"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [smooth muscle cell of stomach](http://purl.obolibrary.org/obo/CL_4047034) [label](http://www.w3.org/2000/01/rdf-schema#label) "smooth muscle cell of stomach"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [pancreatic acinar cell](http://purl.obolibrary.org/obo/CL_0002064) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. +- [smooth muscle cell of stomach](http://purl.obolibrary.org/obo/CL_4047034) [id](http://www.geneontology.org/formats/oboInOwl#id) "CL:4047034"^^[string](http://www.w3.org/2001/XMLSchema#string) -Pancreatic acinar cells are the functional units of the exocrine pancreas. These cells are structurally arranged in small clusters - or acini - with a small central lumen, and their primary function is to produce and secrete enzymes that facilitate digestion of proteins, carbohydrates, and fats within the small intestine. -Some of the most important digestive enzymes synthesized by the pancreatic acinar cells include amylase, which digests carbohydrates, lipase, which breaks down fats, and several proteases such as trypsin and chymotrypsin which are vital for the digestion of proteins. Importantly, these enzymes are produced as proenzymes or zymogens to avoid autolysis, or the breakdown of the pancreas itself. -The release of these enzymes by the pancreatic acinar cells is strictly regulated by hormones and neurochemicals. Cholecystokinin (CCK) released from the enteroendocrine cells in the duodenum cause the release of these enzymes. Moreover, acinar cells also respond to another hormone, secretin, by releasing bicarbonate-rich fluid which helps to neutralize the gastric acid in the duodenum. -Dysregulation in the function of pancreatic acinar cells can lead to severe health issues, including pancreatitis, which is characterized by inflammatory damage to the organ due to the premature activation of digestive enzymes."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1097/01.mog.0000239863.96833.c0"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [smooth muscle cell of stomach](http://purl.obolibrary.org/obo/CL_4047034) [contributor](http://purl.org/dc/terms/contributor) [0009-0005-7919-4905](https://orcid.org/0009-0005-7919-4905) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://www.ncbi.nlm.nih.gov/books/NBK54134/"^^[string](http://www.w3.org/2001/XMLSchema#string) +- Class: [smooth muscle cell of stomach](http://purl.obolibrary.org/obo/CL_4047034) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1016/0165-6147(89)90192-2"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [smooth muscle cell of stomach](http://purl.obolibrary.org/obo/CL_4047034) SubClassOf [BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [smooth muscle cell of stomach](http://purl.obolibrary.org/obo/CL_4047034) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1038/nrgastro.2013.36"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [smooth muscle cell of stomach](http://purl.obolibrary.org/obo/CL_4047034) SubClassOf [smooth muscle cell](http://purl.obolibrary.org/obo/CL_0000192) -### pancreatic epsilon cell `http://purl.obolibrary.org/obo/CL_0005019` +### smooth muscle cell of taenia coli `http://purl.obolibrary.org/obo/CL_4033004` #### Added -- [pancreatic epsilon cell](http://purl.obolibrary.org/obo/CL_0005019) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://cellxgene.cziscience.com/cellguide/CL_0005019"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [smooth muscle cell of taenia coli](http://purl.obolibrary.org/obo/CL_4033004) SubClassOf [BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0001278](http://purl.obolibrary.org/obo/UBERON_0001278) -- [pancreatic epsilon cell](http://purl.obolibrary.org/obo/CL_0005019) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. - -Pancreatic epsilon cells are a specialized type of endocrine cell found in the islets of Langerhans, a region of the pancreas responsible for hormone production. These clusters of cells constitute only about 1% of the pancreatic islet cell population, making them a relatively small yet significant component of the pancreas. Pancreatic epsilon cells have a round or ovoid shape with occasional cytoplasmic extensions and are characterized by small and spherical granules. -The principal function of pancreatic epsilon cells involves the synthesis and release of the hormone ghrelin, a peptide hormone predominantly produced in the stomach; pancreatic epsilon cells are one of the few sites outside the gastrointestinal tract known to produce this hormone. Ghrelin has multiple vital roles, playing a significant part in generating hunger sensations, promoting fat storage, and influencing various metabolic processes. It also stimulates the release of Growth Hormone (GH) from the anterior pituitary gland. -During fetal development, when they form a layer around the islet, epsilon cells are an important source of ghrelin, likely secreting the hormone into the circulation; their numbers decrease in adults. While research on pancreatic epsilon cells is still ongoing, these cells have been implicated in several disease states, most notably Type 2 diabetes and metabolic syndrome. The dysfunction or reduction in the number of pancreatic epsilon cells can lead to anomalies in ghrelin production, impacting overall metabolic homeostasis and glucose regulation."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.3389/fendo.2022.904004"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.3390/ijms20081867"^^[string](http://www.w3.org/2001/XMLSchema#string) +### smooth muscle cell of the pulmonary artery `http://purl.obolibrary.org/obo/CL_0002591` - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1007/s00125-008-1238-y"^^[string](http://www.w3.org/2001/XMLSchema#string) +#### Added +- [smooth muscle cell of the pulmonary artery](http://purl.obolibrary.org/obo/CL_0002591) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://cellxgene.cziscience.com/cellguide/CL_0002591"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1210/en.2018-00833"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [smooth muscle cell of the pulmonary artery](http://purl.obolibrary.org/obo/CL_0002591) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1152/physrev.00012.2004"^^[string](http://www.w3.org/2001/XMLSchema#string) +Smooth muscle cells of the pulmonary artery form a principal component of the pulmonary artery's media layer, the middle section of the artery wall typically found between endothelial inner layer (intima) and the outermost connective tissue layer (adventitia). The unique structure of these cells, defined by fusiform shape and the absence of striations, sets them apart from other muscle cell types, including cardiac and skeletal. +The primary function of smooth muscle cells of the pulmonary artery is to regulate the diameter of the pulmonary artery, which in turn controls the flow of blood into the lungs. They accomplish this task through the contraction and relaxation, indicative of vasoconstriction and vasodilation respectively. When these cells contract, the diameter of the artery narrows, leading to reduced blood flow. Conversely, relaxation of these cells widens the artery, facilitating increased blood flow. Such blood flow modulation is crucial for the maintenance of blood pressure and ensuring that the lungs receive an adequate blood supply for efficient oxygen exchange. +As a result, abnormal function or proliferation of these cells can contribute to conditions such as pulmonary hypertension, a condition characterized by high blood pressure in the arteries leading to the lungs. This can occur due to hypoxia (lack of enough oxygen), leading to excessive constriction or proliferation of the smooth muscle cells."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://www.sciencedirect.com/topics/medicine-and-dentistry/pulmonary-artery-smooth-muscle-cell"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1016/j.apsb.2012.12.007"^^[string](http://www.w3.org/2001/XMLSchema#string) -### paneth cell `http://purl.obolibrary.org/obo/CL_0000510` + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1124/pr.115.010652"^^[string](http://www.w3.org/2001/XMLSchema#string) -#### Added -- [paneth cell](http://purl.obolibrary.org/obo/CL_0000510) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://cellxgene.cziscience.com/cellguide/CL_0000510"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [paneth cell](http://purl.obolibrary.org/obo/CL_0000510) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. +### smooth muscle cell of trachea `http://purl.obolibrary.org/obo/CL_0002600` -Paneth cells are specialized epithelial cells that are primarily located at the bottom of the crypts of Lieberkühn in the small intestine, where they play a pivotal role in maintaining gut homeostasis. They have also been found in smaller numbers in the colonic crypts and other parts of the gastrointestinal tract. Paneth cells are characterized by large acidophilic granules, which take up most of the cytoplasmic volume, causing the nucleus to be pushed toward the base of the cell. -Paneth cells function as a part of the innate immune system. The large granules inside the cells are filled with antimicrobial peptides, such as defensins and lysozymes. Upon bacterial intrusion or cellular signaling indicating a potential infection, Paneth cells release the granules containing the antimicrobial substances into the crypt lumen, effectively serving as the first line of defense against bacterial invasion within the gastrointestinal tract. In essence, Paneth cells serve as guardians, protecting the intestinal stem cells from harmful pathogens that may disturb the gut ecosystem. -In addition to their primary role in immunity, Paneth cells are also crucial for supporting the stem cell niche in the intestinal crypts. They are located adjacent to Lgr5+ stem cells and secrete various growth factors such as EGF, TGF-alpha, Wnt3, and Notch ligand Dll4. These factors regulate the self-renewal and differentiation of these stem cells, which continuously replenish the intestinal epithelium. Consequently, any abnormality or dysfunction in Paneth cells could lead to a disturbance in gut homeostasis, possibly resulting in various illnesses such as inflammatory bowel disease."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1038/nature09637"^^[string](http://www.w3.org/2001/XMLSchema#string) +#### Added +- [smooth muscle cell of trachea](http://purl.obolibrary.org/obo/CL_0002600) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://cellxgene.cziscience.com/cellguide/CL_0002600"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.3389/fimmu.2020.00587"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [smooth muscle cell of trachea](http://purl.obolibrary.org/obo/CL_0002600) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1146/annurev-physiol-030212-183744"^^[string](http://www.w3.org/2001/XMLSchema#string) +Smooth muscle cells of the trachea have a characteristic 'smooth' (non-striated) appearance under the microscope, a distinguishing feature that differentiates them from skeletal and cardiac muscle cells. The smooth appearance is due to the organization of actin and myosin filaments in the cell, which allows for a controlled, contractile function. +These cells play a key role in controlling the diameter of the trachea, thus regulating the airflow. They are responsible for the involuntary constriction and relaxation of the trachea influencing the air passage during various physiological behaviors like breathing, coughing, and sneezing. This autonomic control allows for adaptations to specific body requirements without conscious control, such as increasing air flow during exercise or restricting it during rest. +In conditions such as asthma, chronic bronchitis, and emphysema, there are changes in smooth muscle cells. For example, the mass of smooth muscle cells increases in chronic airway diseases, possibly in response to chronic inflammation. This increase may indicate a pathological condition or be a part of the body's response to injury and repair."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://www.sciencedirect.com/topics/agricultural-and-biological-sciences/airway-smooth-muscle"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1038/nrmicro2546"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://www.ncbi.nlm.nih.gov/books/NBK9961"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1007/s00018-002-8412-z"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1016/s1357-2725(02)00259-5"^^[string](http://www.w3.org/2001/XMLSchema#string) -### parafollicular cell `http://purl.obolibrary.org/obo/CL_0000570` +### smooth muscle fiber of duodenum `http://purl.obolibrary.org/obo/CL_1000276` #### Added -- [parafollicular cell](http://purl.obolibrary.org/obo/CL_0000570) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) +- [smooth muscle fiber of duodenum](http://purl.obolibrary.org/obo/CL_1000276) SubClassOf [BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0001902](http://purl.obolibrary.org/obo/UBERON_0001902) -### parietal epithelial cell `http://purl.obolibrary.org/obo/CL_1000452` +### smooth muscle fiber of ileum `http://purl.obolibrary.org/obo/CL_1000278` #### Added -- [parietal epithelial cell](http://purl.obolibrary.org/obo/CL_1000452) SubClassOf [squamous epithelial cell](http://purl.obolibrary.org/obo/CL_0000076) +- [smooth muscle fiber of ileum](http://purl.obolibrary.org/obo/CL_1000278) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://cellxgene.cziscience.com/cellguide/CL_1000278"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [smooth muscle fiber of ileum](http://purl.obolibrary.org/obo/CL_1000278) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. -### perineurial cell `http://purl.obolibrary.org/obo/CL_0002576` -#### Removed -- [perineurial cell](http://purl.obolibrary.org/obo/CL_0002576) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A glial cell that is part of the perineurium. This cell type has thin long bipolar cytoplasmic processes, pinocytotic vesicles, fragments of external lamina and/or external lamina-like material, attachment plaques, and desmosome-like junctions. Perineurial cells historically have been referred to as fibroblasts because of shape; however, unlike fibroblasts, a perineurial cell: does not have a compact nucleus and large endoplasmic reticulum; does have a double basement membrane opposed to a single basal lamina; is carefully joined to other perineurial cells by tight junctions into a single sheet as opposed to arranged in a large mass; and finally, can surround a small axon bundle at a nerve terminal whereas a fibroblast cannot."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:25818566"^^[string](http://www.w3.org/2001/XMLSchema#string) +The smooth muscle fiber of the ileum primarily refers to a specific class of muscle cells present in the ileum, the final segment of the small intestine. Distinguished from skeletal muscle and cardiac muscle, smooth muscle does not possess striations and is under the control of the involuntary nervous system. +These cells primarily facilitate the movement of digested food, a process known as peristalsis. These cells coordinate rhythmic contractions and relaxations, propelling the chyme toward the colon. This process is vital for efficient nutrient absorption in the small intestine and the transfer of undigested material to the large intestine. Moreover, the smooth muscle fibers enhance the ileum's ability to expand and adapt to volume changes without elevating internal pressure, known as compliance. +The smooth muscle fiber of the ileum contributes to reflex responses, enhancing muscle contractions to propel intestinal contents in different physiological conditions. This involves intricate molecular signaling with neurotransmitters, hormones, and local signals. Thus, beyond its structural role, the smooth muscle fiber is crucial for the physiological functions of digestion and absorption in the small intestine."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1152/advan.00025.2003"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GO:tfm"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://www.ncbi.nlm.nih.gov/books/NBK532857/"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NCIT:C41442"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://www.ncbi.nlm.nih.gov/books/NBK556137/"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "http://en.wikipedia.org/wiki/Perineurium"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [smooth muscle fiber of ileum](http://purl.obolibrary.org/obo/CL_1000278) SubClassOf [BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0001902](http://purl.obolibrary.org/obo/UBERON_0001902) - - [comment](http://www.w3.org/2000/01/rdf-schema#comment) "https://orcid.org/0000-0001-7655-4833"^^[string](http://www.w3.org/2001/XMLSchema#string) + +### smooth muscle myoblast `http://purl.obolibrary.org/obo/CL_0000514` #### Added -- [perineurial cell](http://purl.obolibrary.org/obo/CL_0002576) [contributor](http://purl.org/dc/terms/contributor) [0000-0001-7655-4833](https://orcid.org/0000-0001-7655-4833) +- [smooth muscle myoblast](http://purl.obolibrary.org/obo/CL_0000514) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://cellxgene.cziscience.com/cellguide/CL_0000514"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [perineurial cell](http://purl.obolibrary.org/obo/CL_0002576) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A glial cell that is part of the perineurium. This cell type has thin long bipolar cytoplasmic processes, pinocytotic vesicles, fragments of external lamina and/or external lamina-like material, attachment plaques, and desmosome-like junctions. Perineurial cells historically have been referred to as fibroblasts because of shape; however, unlike fibroblasts, a perineurial cell: does not have a compact nucleus and large endoplasmic reticulum; does have a double basement membrane opposed to a single basal lamina; is carefully joined to other perineurial cells by tight junctions into a single sheet as opposed to arranged in a large mass; and finally, can surround a small axon bundle at a nerve terminal whereas a fibroblast cannot."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:25818566"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [smooth muscle myoblast](http://purl.obolibrary.org/obo/CL_0000514) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GO:tfm"^^[string](http://www.w3.org/2001/XMLSchema#string) +A precursor to the smooth muscle cell, the smooth muscle myoblast, is integral to various body systems, including the cardiovascular, gastrointestinal, and respiratory systems. Smooth muscle myoblasts arise from the differentiation of mesenchymal stem cells, a process tightly regulated by specific genetic factors and environmental signals. Their role extends to myogenesis, particularly in the formation of muscular tissue, especially during embryonic development. +Smooth muscle myoblasts possess distinctive cellular characteristics. In contrast to skeletal muscle myoblasts, they do not fuse to create multinucleated fibers. Instead, they differentiate into individual, uninucleated smooth muscle cells. This differentiation unfolds in two distinct phases: proliferation, marked by rapid division to increase cell numbers, and differentiation, involving structural and functional transformation into mature smooth muscle cells. This intricate process is intricately mediated by various signaling molecules and transcription factors. +Functionally, smooth muscle myoblasts and the mature muscle cells they generate play pivotal roles in various physiological processes. Smooth muscle cells orchestrate involuntary muscle responses and are integral to body systems that regulate blood flow, propel food along the digestive tract, and control airflow in the respiratory tract. These diverse functions underscore the significance of smooth muscle myoblasts in the body's growth, maintenance, and overall function."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1074/jbc.RA118.001739"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NCIT:C41442"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://www.sciencedirect.com/topics/medicine-and-dentistry/smooth-muscle"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "http://en.wikipedia.org/wiki/Perineurium"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://www.ncbi.nlm.nih.gov/books/NBK544225/"^^[string](http://www.w3.org/2001/XMLSchema#string) -### peripheral blood mesothelial cell `http://purl.obolibrary.org/obo/CL_0002318` +### sncg GABAergic cortical interneuron `http://purl.obolibrary.org/obo/CL_4023015` #### Added -- [peripheral blood mesothelial cell](http://purl.obolibrary.org/obo/CL_0002318) SubClassOf [eukaryotic cell](http://purl.obolibrary.org/obo/CL_0000255) +- [sncg GABAergic cortical interneuron](http://purl.obolibrary.org/obo/CL_4023015) [RO_0002175](http://purl.obolibrary.org/obo/RO_0002175) [NCBITaxon_9606](http://purl.obolibrary.org/obo/NCBITaxon_9606) +- [sncg GABAergic cortical interneuron](http://purl.obolibrary.org/obo/CL_4023015) [comment](http://www.w3.org/2000/01/rdf-schema#comment) "The marker set RXRG, THSD7B can identify the Human cell type sncg GABAergic cortical interneuron in the Brain with a confidence of 0.628943702 (NS-Forest FBeta value)."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://doi.org/10.5281/zenodo.11165918"^^[string](http://www.w3.org/2001/XMLSchema#string) -### peritoneal macrophage `http://purl.obolibrary.org/obo/CL_0000581` +- [sncg GABAergic cortical interneuron](http://purl.obolibrary.org/obo/CL_4023015) SubClassOf [RO_0015004](http://purl.obolibrary.org/obo/RO_0015004) some [CLM_1000081](http://purl.obolibrary.org/obo/CLM_1000081) -#### Added -- [peritoneal macrophage](http://purl.obolibrary.org/obo/CL_0000581) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) +### somatosensory neuron `http://purl.obolibrary.org/obo/CL_4023168` +#### Removed +- [somatosensory neuron](http://purl.obolibrary.org/obo/CL_4023168) EquivalentTo [neuron](http://purl.obolibrary.org/obo/CL_0000540) and ([BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0003942](http://purl.obolibrary.org/obo/UBERON_0003942)) -### perivascular macrophage `http://purl.obolibrary.org/obo/CL_0000881` +- [somatosensory neuron](http://purl.obolibrary.org/obo/CL_4023168) SubClassOf [neuron](http://purl.obolibrary.org/obo/CL_0000540) #### Added -- [perivascular macrophage](http://purl.obolibrary.org/obo/CL_0000881) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) +- [somatosensory neuron](http://purl.obolibrary.org/obo/CL_4023168) EquivalentTo [neuron](http://purl.obolibrary.org/obo/CL_0000540) and ([BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0003942](http://purl.obolibrary.org/obo/UBERON_0003942)) and ([RO_0002100](http://purl.obolibrary.org/obo/RO_0002100) some [UBERON_0000010](http://purl.obolibrary.org/obo/UBERON_0000010)) +- [somatosensory neuron](http://purl.obolibrary.org/obo/CL_4023168) SubClassOf [peripheral nervous system neuron](http://purl.obolibrary.org/obo/CL_2000032) -### phagocyte (sensu Vertebrata) `http://purl.obolibrary.org/obo/CL_0000518` -#### Removed -- [phagocyte (sensu Vertebrata)](http://purl.obolibrary.org/obo/CL_0000518) SubClassOf [RO_0002160](http://purl.obolibrary.org/obo/RO_0002160) some [NCBITaxon_7742](http://purl.obolibrary.org/obo/NCBITaxon_7742) + +### sperm `http://purl.obolibrary.org/obo/CL_0000019` #### Added -- [phagocyte (sensu Vertebrata)](http://purl.obolibrary.org/obo/CL_0000518) SubClassOf [RO_0002162](http://purl.obolibrary.org/obo/RO_0002162) some [NCBITaxon_7742](http://purl.obolibrary.org/obo/NCBITaxon_7742) +- [sperm](http://purl.obolibrary.org/obo/CL_0000019) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. +Sperm cells, also known as spermatozoa or male gametes, are highly specialized cells that are pivotal for sexual reproduction in animals. Produced in the male reproductive organs, specifically the testes, sperm cells play an important role in the process of fertilization, where they fuse with a female gamete or egg cell (ovum) to form a zygote, which marks the beginning of a new organism. +Sperm cells hold several unique traits that set them apart from other body cells. Structurally, a sperm cell possesses two main structures: the head, containing the nucleus carrying the paternal genetic information, and the flagellum, which generates energy and grants the sperm cell mobility +The process of fertilization occurs when one sperm cell successfully penetrates the egg, delivering its genetic information, and ultimately leading to the formation of a new individual combining both paternal and maternal genetic materials. Notably, while hundreds of millions of sperm cells may be released during ejaculation, only one has the opportunity to successfully fertilize the egg, underscoring the highly competitive nature of this biological process."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1080/19420889.2015.1017156"^^[string](http://www.w3.org/2001/XMLSchema#string) -### photoreceptor cell `http://purl.obolibrary.org/obo/CL_0000210` -#### Removed -- [photoreceptor cell](http://purl.obolibrary.org/obo/CL_0000210) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A cell specialized to detect and transduce light."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "MESH:D010786"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://www.ncbi.nlm.nih.gov/books/NBK26914/"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [photoreceptor cell](http://purl.obolibrary.org/obo/CL_0000210) EquivalentTo [neuron](http://purl.obolibrary.org/obo/CL_0000540) and ([RO_0002215](http://purl.obolibrary.org/obo/RO_0002215) some [GO_0050962](http://purl.obolibrary.org/obo/GO_0050962)) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1152/physrev.00009.2020"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [sperm](http://purl.obolibrary.org/obo/CL_0000019) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://cellxgene.cziscience.com/cellguide/CL_0000019"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [photoreceptor cell](http://purl.obolibrary.org/obo/CL_0000210) SubClassOf [neuronal receptor cell](http://purl.obolibrary.org/obo/CL_0000006) - - [is_inferred](http://www.geneontology.org/formats/oboInOwl#is_inferred) "true"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [photoreceptor cell](http://purl.obolibrary.org/obo/CL_0000210) SubClassOf [RO_0002215](http://purl.obolibrary.org/obo/RO_0002215) some [GO_0050962](http://purl.obolibrary.org/obo/GO_0050962) +### sphincter associated smooth muscle cell `http://purl.obolibrary.org/obo/CL_0000358` #### Added -- [photoreceptor cell](http://purl.obolibrary.org/obo/CL_0000210) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A cell specialized in detecting light stimuli that are involved in visual perception."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "MESH:D010786"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [sphincter associated smooth muscle cell](http://purl.obolibrary.org/obo/CL_0000358) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. -- [photoreceptor cell](http://purl.obolibrary.org/obo/CL_0000210) EquivalentTo [neuron](http://purl.obolibrary.org/obo/CL_0000540) and ([RO_0002215](http://purl.obolibrary.org/obo/RO_0002215) some [GO_0050908](http://purl.obolibrary.org/obo/GO_0050908)) +Smooth muscle cells, as a broader category, are non-striated, involuntary muscle cells that usually exhibit contractions and dilation to facilitate numerous physiological functions. Sphincter associated smooth muscle cells are a specific type of smooth muscle cell that are primarily associated with the functioning of various anatomical sphincters in the human body. +The traits that distinguishes sphincter associated smooth muscle cells from other smooth muscle cells are their location and specialized function in sphincter mechanisms. Sphincter associated smooth muscle cells play a pivotal role in regulating the opening and closure of the bodily sphincters. These sphincters can be found at multiple locations within the body including the gastrointestinal tract (namely the esophagus, stomach, small intestine, and rectum), the urinary tract, and the circulatory system. Upon receiving signals from the autonomous nervous system, these cells contract or relax to modulate the aperture of sphincters, thus controlling the movement of substances through them. Due to their precise and vital functional role, any dysfunction or dysregulation in these cells can lead to serious medical conditions, such as gastroesophageal reflux or urinary incontinence."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://www.ncbi.nlm.nih.gov/books/NBK557452/"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [photoreceptor cell](http://purl.obolibrary.org/obo/CL_0000210) SubClassOf [sensory neuron](http://purl.obolibrary.org/obo/CL_0000101) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://www.ncbi.nlm.nih.gov/books/NBK482438/"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [photoreceptor cell](http://purl.obolibrary.org/obo/CL_0000210) SubClassOf [visual system neuron](http://purl.obolibrary.org/obo/CL_0008028) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://www.ncbi.nlm.nih.gov/books/NBK532857/"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [photoreceptor cell](http://purl.obolibrary.org/obo/CL_0000210) SubClassOf [RO_0002215](http://purl.obolibrary.org/obo/RO_0002215) some [GO_0050908](http://purl.obolibrary.org/obo/GO_0050908) +- [sphincter associated smooth muscle cell](http://purl.obolibrary.org/obo/CL_0000358) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://cellxgene.cziscience.com/cellguide/CL_0000358"^^[string](http://www.w3.org/2001/XMLSchema#string) -### pigment cell (sensu Vertebrata) `http://purl.obolibrary.org/obo/CL_0000342` +### spinal cord interneuron `http://purl.obolibrary.org/obo/CL_0005000` #### Removed -- [pigment cell (sensu Vertebrata)](http://purl.obolibrary.org/obo/CL_0000342) SubClassOf [RO_0002160](http://purl.obolibrary.org/obo/RO_0002160) some [NCBITaxon_7742](http://purl.obolibrary.org/obo/NCBITaxon_7742) +- [spinal cord interneuron](http://purl.obolibrary.org/obo/CL_0005000) SubClassOf [obsolete CNS interneuron](http://purl.obolibrary.org/obo/CL_0000402) + - [is_inferred](http://www.geneontology.org/formats/oboInOwl#is_inferred) "true"^^[string](http://www.w3.org/2001/XMLSchema#string) #### Added -- [pigment cell (sensu Vertebrata)](http://purl.obolibrary.org/obo/CL_0000342) SubClassOf [RO_0002162](http://purl.obolibrary.org/obo/RO_0002162) some [NCBITaxon_7742](http://purl.obolibrary.org/obo/NCBITaxon_7742) +- [spinal cord interneuron](http://purl.obolibrary.org/obo/CL_0005000) SubClassOf [interneuron](http://purl.obolibrary.org/obo/CL_0000099) + - [is_inferred](http://www.geneontology.org/formats/oboInOwl#is_inferred) "true"^^[string](http://www.w3.org/2001/XMLSchema#string) -### pigmented ciliary epithelial cell `http://purl.obolibrary.org/obo/CL_0002303` +### spinal cord motor neuron `http://purl.obolibrary.org/obo/CL_0011001` #### Added -- [pigmented ciliary epithelial cell](http://purl.obolibrary.org/obo/CL_0002303) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://cellxgene.cziscience.com/cellguide/CL_0002303"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [spinal cord motor neuron](http://purl.obolibrary.org/obo/CL_0011001) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl/cl-base#cellxgene_subset) -- [pigmented ciliary epithelial cell](http://purl.obolibrary.org/obo/CL_0002303) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. -Pigmented ciliary epithelial cells, which are a type of pigment cell, have a crucial function within the eye's ciliary body. The ciliary body, located behind the iris, is one of the eye’s most vital structures and consists of two types of epithelial cells: the pigmented and the non-pigmented ciliary epithelial cells. The pigmented ciliary epithelial cells form the outer layer of the ciliary body and exhibit a black or brown pigmentation due to the melanin they contain. -One key function of pigmented ciliary epithelial cells is to aid in the formation of aqueous humor, an intraocular fluid that nourishes the cornea and lens, and maintains intraocular pressure which is essential for the eye’s shape and light refraction. These cells facilitate this function in conjunction with the non-pigmented ciliary epithelial cells. Together, the pigmented and non-pigmented ciliary epithelial cells form a bilayer epithelium that allows the secretion of aqueous humor through a bi-directional fluid transport mechanism. -Pigmented ciliary epithelial cells also contribute to the blood-aqueous barrier, a physiological frontier that controls the entry and exit of various substances from the blood to the aqueous humor and vice versa. The pigmentation in these cells, intensified by melanin, helps to absorb scattered light coming into the eye, reducing any potential damage and glare."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1111/j.1444-0938.2002.tb02384.x"^^[string](http://www.w3.org/2001/XMLSchema#string) +### spiral ganglion neuron `http://purl.obolibrary.org/obo/CL_0011113` +#### Removed +- [spiral ganglion neuron](http://purl.obolibrary.org/obo/CL_0011113) EquivalentTo [neuron](http://purl.obolibrary.org/obo/CL_0000540) and ([RO_0002100](http://purl.obolibrary.org/obo/RO_0002100) some [UBERON_0000395](http://purl.obolibrary.org/obo/UBERON_0000395)) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1016/S1569-2590(05)10005-6"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [spiral ganglion neuron](http://purl.obolibrary.org/obo/CL_0011113) SubClassOf [neuron](http://purl.obolibrary.org/obo/CL_0000540) +#### Added +- [spiral ganglion neuron](http://purl.obolibrary.org/obo/CL_0011113) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl/cl-base#cellxgene_subset) -### plasma cell `http://purl.obolibrary.org/obo/CL_0000786` +- [spiral ganglion neuron](http://purl.obolibrary.org/obo/CL_0011113) EquivalentTo [peripheral nervous system neuron](http://purl.obolibrary.org/obo/CL_2000032) and ([RO_0002100](http://purl.obolibrary.org/obo/RO_0002100) some [UBERON_0000395](http://purl.obolibrary.org/obo/UBERON_0000395)) -#### Added -- [plasma cell](http://purl.obolibrary.org/obo/CL_0000786) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) +- [spiral ganglion neuron](http://purl.obolibrary.org/obo/CL_0011113) SubClassOf [peripheral nervous system neuron](http://purl.obolibrary.org/obo/CL_2000032) -### podocyte `http://purl.obolibrary.org/obo/CL_0000653` +### splanchnic mesodermal cell `http://purl.obolibrary.org/obo/CL_0017001` #### Added -- [podocyte](http://purl.obolibrary.org/obo/CL_0000653) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. +- [splanchnic mesodermal cell](http://purl.obolibrary.org/obo/CL_0017001) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl/cl-base#cellxgene_subset) -Podocytes are highly specialized, terminally differentiated glomerular visceral epithelial cells that wrap around the capillaries in the kidneys. They play an essential role in kidney function, particularly in the filtration selectivity of the glomerulus. Each podocyte is characterized by a unique architecture with a large cell body, ‘major processes’ extending outwardly from the cell body and ‘foot processes’, also known as pedicels, which surround. the glomerular capillary loops -Podocytes represent the last barrier of the glomerular filtration membrane in the kidney. This barrier prevents the leakage of plasma proteins from the blood into the urine, hence maintaining protein homeostasis in the body. The foot processes of the podocytes interdigitate with those from neighboring cells. The cell-cell junctions between the foot processes, the slit-diaphragms, are thought to create a molecular sensor of renal filtration that prevents the passage of macromolecules while allowing water and small solutes to pass. -Podocytes also contribute to the glomerular basement membrane by secreting collagen and maintain glomerular endothelial cell fenestration by secreting VEGFA. They have been shown to play a role in inducing cytoskeletal regulation, cell adhesion, and inflammatory response, consistent with their essential function in the kidney. -The importance of podocytes is further emphasized by the effects of their damage or loss. Abnormalities in podocytes often result in severe kidney diseases (podocytopathies), including focal segmental glomerulosclerosis (FSGS) and minimal change disease (MCD). Injury to the podocytes can result in "effacement" or flattening of foot processes, leading to increased permeability of the filtration barrier and proteinuria (an excess of serum protein in urine) which is a common symptom of kidney diseases."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1038/s41572-020-0196-7"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1146/annurev-physiol-020911-153238"^^[string](http://www.w3.org/2001/XMLSchema#string) +### splenic marginal zone macrophage `http://purl.obolibrary.org/obo/CL_0000872` +#### Removed +- [splenic marginal zone macrophage](http://purl.obolibrary.org/obo/CL_0000872) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1038/s41467-022-33748-1"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1159/000481633"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.3389/fcell.2021.771931"^^[string](http://www.w3.org/2001/XMLSchema#string) +### splenic metallophillic macrophage `http://purl.obolibrary.org/obo/CL_0000873` +#### Removed +- [splenic metallophillic macrophage](http://purl.obolibrary.org/obo/CL_0000873) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) -- [podocyte](http://purl.obolibrary.org/obo/CL_0000653) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://cellxgene.cziscience.com/cellguide/CL_0000653"^^[string](http://www.w3.org/2001/XMLSchema#string) -### polychromatophilic erythroblast `http://purl.obolibrary.org/obo/CL_0000550` +### splenic red pulp macrophage `http://purl.obolibrary.org/obo/CL_0000874` +#### Removed +- [splenic red pulp macrophage](http://purl.obolibrary.org/obo/CL_0000874) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) -#### Added -- [polychromatophilic erythroblast](http://purl.obolibrary.org/obo/CL_0000550) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) -### pre-conventional dendritic cell `http://purl.obolibrary.org/obo/CL_0002010` +### splenic white pulp macrophage `http://purl.obolibrary.org/obo/CL_0000876` +#### Removed +- [splenic white pulp macrophage](http://purl.obolibrary.org/obo/CL_0000876) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) -#### Added -- [pre-conventional dendritic cell](http://purl.obolibrary.org/obo/CL_0002010) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) -### pre-granulosa cell `http://purl.obolibrary.org/obo/CL_4033066` +### squamous endothelial cell of venule `http://purl.obolibrary.org/obo/CL_0008040` #### Removed -- [pre-granulosa cell](http://purl.obolibrary.org/obo/CL_4033066) SubClassOf [RO_0002210](http://purl.obolibrary.org/obo/RO_0002210) some [granulosa cell](http://purl.obolibrary.org/obo/CL_0000501) +- [squamous endothelial cell of venule](http://purl.obolibrary.org/obo/CL_0008040) [date](http://purl.org/dc/elements/1.1/date) "2024-07-03T19:52:47Z"^^[string](http://www.w3.org/2001/XMLSchema#string) #### Added -- [pre-granulosa cell](http://purl.obolibrary.org/obo/CL_4033066) SubClassOf [eukaryotic cell](http://purl.obolibrary.org/obo/CL_0000255) +- [squamous endothelial cell of venule](http://purl.obolibrary.org/obo/CL_0008040) [date](http://purl.org/dc/terms/date) "2024-07-03T19:52:47Z"^^[dateTime](http://www.w3.org/2001/XMLSchema#dateTime) -- [pre-granulosa cell](http://purl.obolibrary.org/obo/CL_4033066) SubClassOf [RO_0002210](http://purl.obolibrary.org/obo/RO_0002210) some [squamous granulosa cell](http://purl.obolibrary.org/obo/CL_4033083) +### sst GABAergic cortical interneuron `http://purl.obolibrary.org/obo/CL_4023017` +#### Removed +- [sst GABAergic cortical interneuron](http://purl.obolibrary.org/obo/CL_4023017) [comment](http://www.w3.org/2000/01/rdf-schema#comment) "In the mouse cortex, sst GABAergic cortical interneurons show heterogeneous electrophysiological signatures varying between low-threshold spiking (LTS), regular-spiking and fast-spiking (Song, Y. H., Yoon, J., & Lee, S. H. 2021). Sst GABAergic cortical interneurons have multiple functional roles in the brain. In the mouse, they involved in the generation of slow-waves during the sleep phase of non-rapid eye-movement (NREM) (Funk, C. M. et al., 2017), they maintain synaptic plasticity during motor learning (Adler, A., Zhao, R., et al., 2021), they enhance visual perception in the V1 cortical area by suppressing the activity of pyramidal excitatory neurons (Song, YH. et al., 2020). In humans, malfunctioning of sst GABAergic cortical interneurons is associated with neurodegenerative and psychiatric disorders such as Parkinson's disease, Alzheimer's disease, major depressive disorder, bipolar disorder and schizophrenia as individuals affected by these pathologies show a decrease of expression of SST in the brain (Song YH., Yoon J. et al., 2021)."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:32494634"^^[string](http://www.w3.org/2001/XMLSchema#string) -### pre-natural killer cell `http://purl.obolibrary.org/obo/CL_0000937` - -#### Added -- [pre-natural killer cell](http://purl.obolibrary.org/obo/CL_0000937) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:30792151"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:33742131"^^[string](http://www.w3.org/2001/XMLSchema#string) -### pre-theca cell `http://purl.obolibrary.org/obo/CL_4052010` + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:28821651"^^[string](http://www.w3.org/2001/XMLSchema#string) #### Added -- [pre-theca cell](http://purl.obolibrary.org/obo/CL_4052010) [has_exact_synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "progenitor theca cell"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:31320652"^^[string](http://www.w3.org/2001/XMLSchema#string) - -- [pre-theca cell](http://purl.obolibrary.org/obo/CL_4052010) [date](http://purl.org/dc/terms/date) "2024-09-25T11:15:57Z"^^[dateTime](http://www.w3.org/2001/XMLSchema#dateTime) - -- [pre-theca cell](http://purl.obolibrary.org/obo/CL_4052010) [label](http://www.w3.org/2000/01/rdf-schema#label) "pre-theca cell"^^[string](http://www.w3.org/2001/XMLSchema#string) - -- [pre-theca cell](http://purl.obolibrary.org/obo/CL_4052010) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A stromal cell that serves as a precursor to the theca cell layers in the ovary growing follicles. This cell is present in the early stages of follicular growth, particularly in smaller follicles. Unlike mature theca cell, a pre-theca cell is initially non-steroidogenic and lacks luteinizing hormone receptors."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:20628033"^^[string](http://www.w3.org/2001/XMLSchema#string) - - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:31320652"^^[string](http://www.w3.org/2001/XMLSchema#string) - - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:36205477"^^[string](http://www.w3.org/2001/XMLSchema#string) - -- [pre-theca cell](http://purl.obolibrary.org/obo/CL_4052010) [contributor](http://purl.org/dc/terms/contributor) [0009-0000-8480-9277](https://orcid.org/0009-0000-8480-9277) - -- [pre-theca cell](http://purl.obolibrary.org/obo/CL_4052010) [has_exact_synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "early theca cell"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:36205477"^^[string](http://www.w3.org/2001/XMLSchema#string) - -- [pre-theca cell](http://purl.obolibrary.org/obo/CL_4052010) [id](http://www.geneontology.org/formats/oboInOwl#id) "CL:4052010"^^[string](http://www.w3.org/2001/XMLSchema#string) - -- Class: [pre-theca cell](http://purl.obolibrary.org/obo/CL_4052010) +- [sst GABAergic cortical interneuron](http://purl.obolibrary.org/obo/CL_4023017) [comment](http://www.w3.org/2000/01/rdf-schema#comment) "In the mouse cortex, sst GABAergic cortical interneurons show heterogeneous electrophysiological signatures varying between low-threshold spiking (LTS), regular-spiking and fast-spiking (Song, Y. H., Yoon, J., & Lee, S. H. 2021). Sst GABAergic cortical interneurons have multiple functional roles in the brain. In the mouse, they involved in the generation of slow-waves during the sleep phase of non-rapid eye-movement (NREM) (Funk, C. M. et al., 2017), they maintain synaptic plasticity during motor learning (Adler, A., Zhao, R., et al., 2021), they enhance visual perception in the V1 cortical area by suppressing the activity of pyramidal excitatory neurons (Song, YH. et al., 2020). In humans, malfunctioning of sst GABAergic cortical interneurons is associated with neurodegenerative and psychiatric disorders such as Parkinson's disease, Alzheimer's disease, major depressive disorder, bipolar disorder and schizophrenia as individuals affected by these pathologies show a decrease of expression of SST in the brain (Song YH., Yoon J. et al., 2021). The marker set SST, PLCH1 can identify the Human cell type sst GABAergic cortical interneuron in the Brain with a confidence of 0.842367005 (NS-Forest FBeta value)."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:32494634"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [pre-theca cell](http://purl.obolibrary.org/obo/CL_4052010) SubClassOf [RO_0002203](http://purl.obolibrary.org/obo/RO_0002203) some [theca cell](http://purl.obolibrary.org/obo/CL_0000503) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://doi.org/10.5281/zenodo.11165918"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [pre-theca cell](http://purl.obolibrary.org/obo/CL_4052010) SubClassOf [stromal cell of ovary](http://purl.obolibrary.org/obo/CL_0002132) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:30792151"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [pre-theca cell](http://purl.obolibrary.org/obo/CL_4052010) SubClassOf [BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0012186](http://purl.obolibrary.org/obo/UBERON_0012186) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:33742131"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:28821651"^^[string](http://www.w3.org/2001/XMLSchema#string) -### preameloblast `http://purl.obolibrary.org/obo/CL_0007000` +- [sst GABAergic cortical interneuron](http://purl.obolibrary.org/obo/CL_4023017) [RO_0002175](http://purl.obolibrary.org/obo/RO_0002175) [NCBITaxon_9606](http://purl.obolibrary.org/obo/NCBITaxon_9606) -#### Added -- [preameloblast](http://purl.obolibrary.org/obo/CL_0007000) SubClassOf [eukaryotic cell](http://purl.obolibrary.org/obo/CL_0000255) +- [sst GABAergic cortical interneuron](http://purl.obolibrary.org/obo/CL_4023017) SubClassOf [RO_0015004](http://purl.obolibrary.org/obo/RO_0015004) some [CLM_1000082](http://purl.obolibrary.org/obo/CLM_1000082) -### precementoblast `http://purl.obolibrary.org/obo/CL_0007002` +### sst GABAergic neuron of the striatum `http://purl.obolibrary.org/obo/CL_4042037` #### Added -- [precementoblast](http://purl.obolibrary.org/obo/CL_0007002) SubClassOf [eukaryotic cell](http://purl.obolibrary.org/obo/CL_0000255) +- [sst GABAergic neuron of the striatum](http://purl.obolibrary.org/obo/CL_4042037) [id](http://www.geneontology.org/formats/oboInOwl#id) "CL:4042037"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [sst GABAergic neuron of the striatum](http://purl.obolibrary.org/obo/CL_4042037) [comment](http://www.w3.org/2000/01/rdf-schema#comment) "Some striatal SST GABAergic neurons can co-release glutamate and generate excitation-inhibition responses in postsynaptic neurons. This interneuron type has the least dense dendritic branches in the striatum. In the dorsomedial striatum these neurons regulate the activity of striatal projection neurons."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:33742131"^^[string](http://www.w3.org/2001/XMLSchema#string) -### primary neuron (sensu Teleostei) `http://purl.obolibrary.org/obo/CL_0000530` -#### Removed -- [primary neuron (sensu Teleostei)](http://purl.obolibrary.org/obo/CL_0000530) SubClassOf [eukaryotic cell](http://purl.obolibrary.org/obo/CL_0000255) - -- [primary neuron (sensu Teleostei)](http://purl.obolibrary.org/obo/CL_0000530) SubClassOf [RO_0002160](http://purl.obolibrary.org/obo/RO_0002160) some [NCBITaxon_32443](http://purl.obolibrary.org/obo/NCBITaxon_32443) - - [IAO_0000233](http://purl.obolibrary.org/obo/IAO_0000233) "https://github.com/obophenotype/cell-ontology/pull/1950"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:30467465"^^[string](http://www.w3.org/2001/XMLSchema#string) -#### Added -- [primary neuron (sensu Teleostei)](http://purl.obolibrary.org/obo/CL_0000530) SubClassOf [RO_0002162](http://purl.obolibrary.org/obo/RO_0002162) some [NCBITaxon_32443](http://purl.obolibrary.org/obo/NCBITaxon_32443) - - [IAO_0000233](http://purl.obolibrary.org/obo/IAO_0000233) "https://github.com/obophenotype/cell-ontology/pull/1950"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [sst GABAergic neuron of the striatum](http://purl.obolibrary.org/obo/CL_4042037) [date](http://purl.org/dc/terms/date) "2024-11-27T18:33:46Z"^^[dateTime](http://www.w3.org/2001/XMLSchema#dateTime) +- [sst GABAergic neuron of the striatum](http://purl.obolibrary.org/obo/CL_4042037) [label](http://www.w3.org/2000/01/rdf-schema#label) "sst GABAergic neuron of the striatum"^^[string](http://www.w3.org/2001/XMLSchema#string) -### primary spermatocyte `http://purl.obolibrary.org/obo/CL_0000656` +- [sst GABAergic neuron of the striatum](http://purl.obolibrary.org/obo/CL_4042037) [contributor](http://purl.org/dc/terms/contributor) [0000-0002-0098-8958](https://orcid.org/0000-0002-0098-8958) -#### Added -- [primary spermatocyte](http://purl.obolibrary.org/obo/CL_0000656) SubClassOf [eukaryotic cell](http://purl.obolibrary.org/obo/CL_0000255) +- [sst GABAergic neuron of the striatum](http://purl.obolibrary.org/obo/CL_4042037) [has_broad_synonym](http://www.geneontology.org/formats/oboInOwl#hasBroadSynonym) "SOM cell"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:30131490"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [sst GABAergic neuron of the striatum](http://purl.obolibrary.org/obo/CL_4042037) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A interneuron of the striatum expressing gamma-aminobutyric acid and somatostatin. This interneuron has a fusiform soma with a diameter between 9 - 25 µm, it has a long axon up to the length of 1mm. This neuron type displays a low threshold Ca2+ spike (LTS), a high input resistance, and the expression of long-lasting plateau potentials following depolarization from rest."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:30131490"^^[string](http://www.w3.org/2001/XMLSchema#string) -### primitive erythroid progenitor `http://purl.obolibrary.org/obo/CL_0002361` + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:33742131"^^[string](http://www.w3.org/2001/XMLSchema#string) -#### Added -- [primitive erythroid progenitor](http://purl.obolibrary.org/obo/CL_0002361) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:30467465"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [sst GABAergic neuron of the striatum](http://purl.obolibrary.org/obo/CL_4042037) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "striatal SST+ IN"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:33742131"^^[string](http://www.w3.org/2001/XMLSchema#string) -### primitive red blood cell `http://purl.obolibrary.org/obo/CL_0002355` +- Class: [sst GABAergic neuron of the striatum](http://purl.obolibrary.org/obo/CL_4042037) -#### Added -- [primitive red blood cell](http://purl.obolibrary.org/obo/CL_0002355) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) +- [sst GABAergic neuron of the striatum](http://purl.obolibrary.org/obo/CL_4042037) SubClassOf [striatum neuron](http://purl.obolibrary.org/obo/CL_0002613) +- [sst GABAergic neuron of the striatum](http://purl.obolibrary.org/obo/CL_4042037) SubClassOf [RO_0002292](http://purl.obolibrary.org/obo/RO_0002292) some [PR_000015665](http://purl.obolibrary.org/obo/PR_000015665) -### pro-B cell `http://purl.obolibrary.org/obo/CL_0000826` +- [sst GABAergic neuron of the striatum](http://purl.obolibrary.org/obo/CL_4042037) SubClassOf [GABAergic neuron](http://purl.obolibrary.org/obo/CL_0000617) -#### Added -- [pro-B cell](http://purl.obolibrary.org/obo/CL_0000826) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) +- [sst GABAergic neuron of the striatum](http://purl.obolibrary.org/obo/CL_4042037) SubClassOf [BFO_0000002](http://purl.obolibrary.org/obo/BFO_0000002) -### pro-NK cell `http://purl.obolibrary.org/obo/CL_0000825` +### sst chodl GABAergic cortical interneuron `http://purl.obolibrary.org/obo/CL_4023121` #### Added -- [pro-NK cell](http://purl.obolibrary.org/obo/CL_0000825) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) +- [sst chodl GABAergic cortical interneuron](http://purl.obolibrary.org/obo/CL_4023121) [RO_0002175](http://purl.obolibrary.org/obo/RO_0002175) [NCBITaxon_9606](http://purl.obolibrary.org/obo/NCBITaxon_9606) +- [sst chodl GABAergic cortical interneuron](http://purl.obolibrary.org/obo/CL_4023121) [comment](http://www.w3.org/2000/01/rdf-schema#comment) "The marker set NPY can identify the Human cell type sst chodl GABAergic cortical interneuron in the Brain with a confidence of 0.894026187 (NS-Forest FBeta value)."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://doi.org/10.5281/zenodo.11165918"^^[string](http://www.w3.org/2001/XMLSchema#string) -### proerythroblast `http://purl.obolibrary.org/obo/CL_0000547` +- [sst chodl GABAergic cortical interneuron](http://purl.obolibrary.org/obo/CL_4023121) SubClassOf [RO_0015004](http://purl.obolibrary.org/obo/RO_0015004) some [CLM_1000083](http://purl.obolibrary.org/obo/CLM_1000083) -#### Added -- [proerythroblast](http://purl.obolibrary.org/obo/CL_0000547) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) +### starburst amacrine cell `http://purl.obolibrary.org/obo/CL_0004232` +#### Removed +- [starburst amacrine cell](http://purl.obolibrary.org/obo/CL_0004232) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [human_reference_atlas](http://purl.obolibrary.org/obo/cl/cl-base#human_reference_atlas) -### progenitor cell `http://purl.obolibrary.org/obo/CL_0011026` +- [starburst amacrine cell](http://purl.obolibrary.org/obo/CL_0004232) [RO_0002175](http://purl.obolibrary.org/obo/RO_0002175) [NCBITaxon_9606](http://purl.obolibrary.org/obo/NCBITaxon_9606) -#### Added -- [progenitor cell](http://purl.obolibrary.org/obo/CL_0011026) SubClassOf [eukaryotic cell](http://purl.obolibrary.org/obo/CL_0000255) -### progesterone secreting cell `http://purl.obolibrary.org/obo/CL_0000179` +### stellate L6 intratelencephalic projecting glutamatergic neuron of the primary motor cortex (Mmus) `http://purl.obolibrary.org/obo/CL_4023080` +#### Removed +- [stellate L6 intratelencephalic projecting glutamatergic neuron of the primary motor cortex (Mmus)](http://purl.obolibrary.org/obo/CL_4023080) SubClassOf [RO_0000053](http://purl.obolibrary.org/obo/RO_0000053) some [PATO_0070020](http://purl.obolibrary.org/obo/PATO_0070020) #### Added -- [progesterone secreting cell](http://purl.obolibrary.org/obo/CL_0000179) SubClassOf [eukaryotic cell](http://purl.obolibrary.org/obo/CL_0000255) +- [stellate L6 intratelencephalic projecting glutamatergic neuron of the primary motor cortex (Mmus)](http://purl.obolibrary.org/obo/CL_4023080) SubClassOf [stellate pyramidal neuron](http://purl.obolibrary.org/obo/CL_4023093) -### promonocyte `http://purl.obolibrary.org/obo/CL_0000559` +### stellate interneuron `http://purl.obolibrary.org/obo/CL_0000691` +#### Removed +- [stellate interneuron](http://purl.obolibrary.org/obo/CL_0000691) SubClassOf [multipolar neuron](http://purl.obolibrary.org/obo/CL_0000104) + +- [stellate interneuron](http://purl.obolibrary.org/obo/CL_0000691) SubClassOf [RO_0000053](http://purl.obolibrary.org/obo/RO_0000053) some [PATO_0070010](http://purl.obolibrary.org/obo/PATO_0070010) #### Added -- [promonocyte](http://purl.obolibrary.org/obo/CL_0000559) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) +- [stellate interneuron](http://purl.obolibrary.org/obo/CL_0000691) SubClassOf [stellate neuron](http://purl.obolibrary.org/obo/CL_0000122) -### promyelocyte `http://purl.obolibrary.org/obo/CL_0000836` +### stellate neuron `http://purl.obolibrary.org/obo/CL_0000122` +#### Removed +- [stellate neuron](http://purl.obolibrary.org/obo/CL_0000122) EquivalentTo [CNS neuron (sensu Vertebrata)](http://purl.obolibrary.org/obo/CL_0000117) and ([RO_0000053](http://purl.obolibrary.org/obo/RO_0000053) some [PATO_0070010](http://purl.obolibrary.org/obo/PATO_0070010)) + +- [stellate neuron](http://purl.obolibrary.org/obo/CL_0000122) SubClassOf [CNS neuron (sensu Vertebrata)](http://purl.obolibrary.org/obo/CL_0000117) + +- [stellate neuron](http://purl.obolibrary.org/obo/CL_0000122) SubClassOf [multipolar neuron](http://purl.obolibrary.org/obo/CL_0000104) #### Added -- [promyelocyte](http://purl.obolibrary.org/obo/CL_0000836) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) +- [stellate neuron](http://purl.obolibrary.org/obo/CL_0000122) EquivalentTo [neuron](http://purl.obolibrary.org/obo/CL_0000540) and ([RO_0000053](http://purl.obolibrary.org/obo/RO_0000053) some [PATO_0070010](http://purl.obolibrary.org/obo/PATO_0070010)) + +- [stellate neuron](http://purl.obolibrary.org/obo/CL_0000122) SubClassOf [central nervous system neuron](http://purl.obolibrary.org/obo/CL_2000029) -### pronephric podocyte `http://purl.obolibrary.org/obo/CL_4030008` +### stellate pyramidal neuron `http://purl.obolibrary.org/obo/CL_4023093` #### Removed -- [pronephric podocyte](http://purl.obolibrary.org/obo/CL_4030008) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A specialized epithelial cell that contains "feet" that interdigitate with the "feet" of other glomerular epithelial cells in the pronephros."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [contributor](http://purl.org/dc/terms/contributor) "https://orcid.org/0000-0002-2244-7917"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [stellate pyramidal neuron](http://purl.obolibrary.org/obo/CL_4023093) EquivalentTo [CNS neuron (sensu Vertebrata)](http://purl.obolibrary.org/obo/CL_0000117) and ([RO_0000053](http://purl.obolibrary.org/obo/RO_0000053) some [PATO_0070020](http://purl.obolibrary.org/obo/PATO_0070020)) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:10322630"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [stellate pyramidal neuron](http://purl.obolibrary.org/obo/CL_4023093) SubClassOf [CNS neuron (sensu Vertebrata)](http://purl.obolibrary.org/obo/CL_0000117) #### Added -- [pronephric podocyte](http://purl.obolibrary.org/obo/CL_4030008) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A specialized epithelial cell that contains "feet" that interdigitate with the "feet" of other glomerular epithelial cells in the pronephros."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:10322630"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [stellate pyramidal neuron](http://purl.obolibrary.org/obo/CL_4023093) EquivalentTo [neuron](http://purl.obolibrary.org/obo/CL_0000540) and ([RO_0000053](http://purl.obolibrary.org/obo/RO_0000053) some [PATO_0070020](http://purl.obolibrary.org/obo/PATO_0070020)) -- [pronephric podocyte](http://purl.obolibrary.org/obo/CL_4030008) [contributor](http://purl.org/dc/terms/contributor) [0000-0002-2244-7917](https://orcid.org/0000-0002-2244-7917) - -### pulmonary alveolar epithelial cell `http://purl.obolibrary.org/obo/CL_0000322` +### stomach enteroendocrine cell `http://purl.obolibrary.org/obo/CL_1001517` #### Removed -- [pulmonary alveolar epithelial cell](http://purl.obolibrary.org/obo/CL_0000322) SubClassOf [epithelial cell of alveolus of lung](http://purl.obolibrary.org/obo/CL_0010003) +- [stomach enteroendocrine cell](http://purl.obolibrary.org/obo/CL_1001517) EquivalentTo [enteroendocrine cell](http://purl.obolibrary.org/obo/CL_0000164) and ([BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0001160](http://purl.obolibrary.org/obo/UBERON_0001160)) -#### Added -- [pulmonary alveolar epithelial cell](http://purl.obolibrary.org/obo/CL_0000322) [has_exact_synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "alveolus of lung epithelial cell"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [stomach enteroendocrine cell](http://purl.obolibrary.org/obo/CL_1001517) SubClassOf [glandular epithelial cell of stomach](http://purl.obolibrary.org/obo/CL_0002659) -- [pulmonary alveolar epithelial cell](http://purl.obolibrary.org/obo/CL_0000322) [has_exact_synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "epithelial cell of alveolus of lung"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [stomach enteroendocrine cell](http://purl.obolibrary.org/obo/CL_1001517) SubClassOf [BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0001160](http://purl.obolibrary.org/obo/UBERON_0001160) -- [pulmonary alveolar epithelial cell](http://purl.obolibrary.org/obo/CL_0000322) [date](http://purl.org/dc/terms/date) "2024-09-02T08:27:21Z"^^[dateTime](http://www.w3.org/2001/XMLSchema#dateTime) +#### Added +- [stomach enteroendocrine cell](http://purl.obolibrary.org/obo/CL_1001517) EquivalentTo [enteroendocrine cell](http://purl.obolibrary.org/obo/CL_0000164) and ([BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0000945](http://purl.obolibrary.org/obo/UBERON_0000945)) -- [pulmonary alveolar epithelial cell](http://purl.obolibrary.org/obo/CL_0000322) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "MESH:D056809"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [stomach enteroendocrine cell](http://purl.obolibrary.org/obo/CL_1001517) SubClassOf [epithelial cell of stomach](http://purl.obolibrary.org/obo/CL_0002178) -- [pulmonary alveolar epithelial cell](http://purl.obolibrary.org/obo/CL_0000322) [contributor](http://purl.org/dc/terms/contributor) [0000-0001-6677-8489](https://orcid.org/0000-0001-6677-8489) -- [pulmonary alveolar epithelial cell](http://purl.obolibrary.org/obo/CL_0000322) EquivalentTo [epithelial cell](http://purl.obolibrary.org/obo/CL_0000066) and ([BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0004821](http://purl.obolibrary.org/obo/UBERON_0004821)) +### stomach neuroendocrine cell `http://purl.obolibrary.org/obo/CL_1000222` +#### Removed +- [stomach neuroendocrine cell](http://purl.obolibrary.org/obo/CL_1000222) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "Any neuroendocrine cell that is part of some stomach."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBC:Autogenerated"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [pulmonary alveolar epithelial cell](http://purl.obolibrary.org/obo/CL_0000322) SubClassOf [squamous epithelial cell](http://purl.obolibrary.org/obo/CL_0000076) +- [stomach neuroendocrine cell](http://purl.obolibrary.org/obo/CL_1000222) EquivalentTo [neuroendocrine cell](http://purl.obolibrary.org/obo/CL_0000165) and ([BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0000945](http://purl.obolibrary.org/obo/UBERON_0000945)) +- [stomach neuroendocrine cell](http://purl.obolibrary.org/obo/CL_1000222) SubClassOf [glandular epithelial cell of stomach](http://purl.obolibrary.org/obo/CL_0002659) -### pulmonary ionocyte `http://purl.obolibrary.org/obo/CL_0017000` +- [stomach neuroendocrine cell](http://purl.obolibrary.org/obo/CL_1000222) SubClassOf [enteroendocrine cell](http://purl.obolibrary.org/obo/CL_0000164) #### Added -- [pulmonary ionocyte](http://purl.obolibrary.org/obo/CL_0017000) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. +- [stomach neuroendocrine cell](http://purl.obolibrary.org/obo/CL_1000222) [has_broad_synonym](http://www.geneontology.org/formats/oboInOwl#hasBroadSynonym) "DES cell"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:15153415"^^[string](http://www.w3.org/2001/XMLSchema#string) -The pulmonary ionocyte is a relatively newly identified, specific epithelial cell type found primarily in the pulmonary or respiratory system. Discovered through novel mapping techniques in 2018, these cells are surprisingly rare, making up less than 2% of the cells in the lung's airway, yet they play an essential role in the airway surface liquid and mucus regulation, a crucial factor in lung health. -The main responsibility of the pulmonary ionocyte pertains to the regulation and mobilization of chloride ions. They express a high level of CFTR (Cystic Fibrosis Transmembrane Conductance Regulator) gene, which encodes a protein channel across the membrane of cells that produce mucus, sweat, saliva, tears, and digestive enzymes. The activity of CFTR regulates the movement of chloride ions and fluids in and out of cells, which helps maintain a balance of fluid in the organs they are expressed in. If CFTR is dysfunctional, it can cause conditions such as cystic fibrosis, characterized by thick, sticky mucus that can clog the lungs and obstruct the pancreas, leading to respiratory and digestive issues. -The discovery of this cell type offers new doors to the treatment and further understanding of diseases like cystic fibrosis. Increased understanding of pulmonary ionocytes could contribute to the development of novel therapeutic approaches to manipulate the function of CFTR in the lungs and other organs affected by dysfunctional CFTR."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1146/annurev-pathol-042420-094031"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [stomach neuroendocrine cell](http://purl.obolibrary.org/obo/CL_1000222) [has_broad_synonym](http://www.geneontology.org/formats/oboInOwl#hasBroadSynonym) "diffuse endocrine system cell"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:15153415"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1038/s41586-018-0393-7"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [stomach neuroendocrine cell](http://purl.obolibrary.org/obo/CL_1000222) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A specialised neuroendocrine cell located in the gastric mucosa that regulates digestive processes including acid secretion and gut motility. This cell stores hormones in large dense core vesicles and synaptic-like microvesicles."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:15153415"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1172/JCI171268"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [stomach neuroendocrine cell](http://purl.obolibrary.org/obo/CL_1000222) EquivalentTo [neuroendocrine cell](http://purl.obolibrary.org/obo/CL_0000165) and ([BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0001276](http://purl.obolibrary.org/obo/UBERON_0001276)) -- [pulmonary ionocyte](http://purl.obolibrary.org/obo/CL_0017000) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://cellxgene.cziscience.com/cellguide/CL_0017000"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [stomach neuroendocrine cell](http://purl.obolibrary.org/obo/CL_1000222) SubClassOf [RO_0002215](http://purl.obolibrary.org/obo/RO_0002215) some [GO_0046717](http://purl.obolibrary.org/obo/GO_0046717) +- [stomach neuroendocrine cell](http://purl.obolibrary.org/obo/CL_1000222) SubClassOf [stomach enteroendocrine cell](http://purl.obolibrary.org/obo/CL_1001517) -### pvalb GABAergic cortical interneuron `http://purl.obolibrary.org/obo/CL_4023018` -#### Removed -- [pvalb GABAergic cortical interneuron](http://purl.obolibrary.org/obo/CL_4023018) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A GABAergic interneuron located in the cerebral cortex that expresses Parvalbumin."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:27477017"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:37824655"^^[string](http://www.w3.org/2001/XMLSchema#string) +### stomach smooth muscle outer longitudinal layer cell `http://purl.obolibrary.org/obo/CL_4047035` -- [pvalb GABAergic cortical interneuron](http://purl.obolibrary.org/obo/CL_4023018) EquivalentTo [interneuron](http://purl.obolibrary.org/obo/CL_0000099) and ([RO_0002100](http://purl.obolibrary.org/obo/RO_0002100) some [UBERON_0000956](http://purl.obolibrary.org/obo/UBERON_0000956)) and ([RO_0002215](http://purl.obolibrary.org/obo/RO_0002215) some [GO_0061534](http://purl.obolibrary.org/obo/GO_0061534)) and ([RO_0002292](http://purl.obolibrary.org/obo/RO_0002292) some [PR_000013502](http://purl.obolibrary.org/obo/PR_000013502)) +#### Added +- [stomach smooth muscle outer longitudinal layer cell](http://purl.obolibrary.org/obo/CL_4047035) [contributor](http://purl.org/dc/terms/contributor) [0009-0005-7919-4905](https://orcid.org/0009-0005-7919-4905) -- [pvalb GABAergic cortical interneuron](http://purl.obolibrary.org/obo/CL_4023018) SubClassOf [cerebral cortex GABAergic interneuron](http://purl.obolibrary.org/obo/CL_0010011) +- [stomach smooth muscle outer longitudinal layer cell](http://purl.obolibrary.org/obo/CL_4047035) [id](http://www.geneontology.org/formats/oboInOwl#id) "CL:4047035"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [pvalb GABAergic cortical interneuron](http://purl.obolibrary.org/obo/CL_4023018) SubClassOf [BFO_0000002](http://purl.obolibrary.org/obo/BFO_0000002) +- [stomach smooth muscle outer longitudinal layer cell](http://purl.obolibrary.org/obo/CL_4047035) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A specialized smooth muscle cell located in the outermost layer of the muscularis externa of the stomach wall. This cell is arranged longitudinally along the stomach's axis and is responsible for the contractions that facilitate food movement toward the pylorus."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:21443757"^^[string](http://www.w3.org/2001/XMLSchema#string) -#### Added -- [pvalb GABAergic cortical interneuron](http://purl.obolibrary.org/obo/CL_4023018) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A transcriptomically distinct GABAergic interneuron with a soma located in a cerebral cortex and it expresses Parvalbumin. The standard transcriptomic reference data for this cell type can be found on the CellxGene census under the collection: 'Transcriptomic cytoarchitecture reveals principles of human neocortex organization', dataset: 'Supercluster: MGE-derived interneurons', Author Categories: 'CrossArea_subclass', cluster Pvalb."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:27477017"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:33630273"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:37824655"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [stomach smooth muscle outer longitudinal layer cell](http://purl.obolibrary.org/obo/CL_4047035) [date](http://purl.org/dc/terms/date) "2024-12-05T16:13:49Z"^^[dateTime](http://www.w3.org/2001/XMLSchema#dateTime) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://cellxgene.cziscience.com/e/9c63201d-bfd9-41a8-bbbc-18d947556f3d.cxg/"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [stomach smooth muscle outer longitudinal layer cell](http://purl.obolibrary.org/obo/CL_4047035) [label](http://www.w3.org/2000/01/rdf-schema#label) "stomach smooth muscle outer longitudinal layer cell"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [pvalb GABAergic cortical interneuron](http://purl.obolibrary.org/obo/CL_4023018) EquivalentTo [medial ganglionic eminence derived GABAergic cortical interneuron](http://purl.obolibrary.org/obo/CL_4023069) and ([RO_0002100](http://purl.obolibrary.org/obo/RO_0002100) some [UBERON_0000956](http://purl.obolibrary.org/obo/UBERON_0000956)) and ([RO_0002215](http://purl.obolibrary.org/obo/RO_0002215) some [GO_0061534](http://purl.obolibrary.org/obo/GO_0061534)) and ([RO_0002292](http://purl.obolibrary.org/obo/RO_0002292) some [PR_000013502](http://purl.obolibrary.org/obo/PR_000013502)) +- Class: [stomach smooth muscle outer longitudinal layer cell](http://purl.obolibrary.org/obo/CL_4047035) -- [pvalb GABAergic cortical interneuron](http://purl.obolibrary.org/obo/CL_4023018) SubClassOf [medial ganglionic eminence derived GABAergic cortical interneuron](http://purl.obolibrary.org/obo/CL_4023069) +- [stomach smooth muscle outer longitudinal layer cell](http://purl.obolibrary.org/obo/CL_4047035) SubClassOf [smooth muscle cell of stomach](http://purl.obolibrary.org/obo/CL_4047034) -### renal alpha-intercalated cell `http://purl.obolibrary.org/obo/CL_0005011` +### stratified squamous epithelial cell of anal canal `http://purl.obolibrary.org/obo/CL_0009066` +#### Removed +- [stratified squamous epithelial cell of anal canal](http://purl.obolibrary.org/obo/CL_0009066) EquivalentTo [stratified squamous epithelial cell](http://purl.obolibrary.org/obo/CL_0000240) and ([BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0000159](http://purl.obolibrary.org/obo/UBERON_0000159)) + +- [stratified squamous epithelial cell of anal canal](http://purl.obolibrary.org/obo/CL_0009066) SubClassOf [BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0000159](http://purl.obolibrary.org/obo/UBERON_0000159) #### Added -- [renal alpha-intercalated cell](http://purl.obolibrary.org/obo/CL_0005011) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://cellxgene.cziscience.com/cellguide/CL_0005011"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [stratified squamous epithelial cell of anal canal](http://purl.obolibrary.org/obo/CL_0009066) EquivalentTo [stratified squamous epithelial cell](http://purl.obolibrary.org/obo/CL_0000240) and ([BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0015716](http://purl.obolibrary.org/obo/UBERON_0015716)) -- [renal alpha-intercalated cell](http://purl.obolibrary.org/obo/CL_0005011) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. +- [stratified squamous epithelial cell of anal canal](http://purl.obolibrary.org/obo/CL_0009066) SubClassOf [BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0015716](http://purl.obolibrary.org/obo/UBERON_0015716) -Renal alpha-intercalated cells are located within the connecting tubules and collecting ducts of the kidneys, which are components of the kidney's complex nephron system. Along with beta-intercalated cells, they play a critical role in the body’s acid-base balance. -Renal alpha-intercalated cells contain an abundance of proton pumps and enzymes like carbonic anhydrase, which aid in the transport of hydrogen ions for secretion in the urine. The bicarbonate/chloride transporters on their apical membrane meanwhile take up bicarbonate ions from the urine and supply them back into the blood. Through this mechanism, these cells contribute significantly to the neutrality of blood pH, and dysfunction of renal alpha-intercalated cells often leads to distal renal tubular acidosis, a condition resulting in acidic blood and alkaline urine."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1172/JCI63492"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.3390/diseases2020071"^^[string](http://www.w3.org/2001/XMLSchema#string) +### striatal pthlh-expressing interneuron `http://purl.obolibrary.org/obo/CL_4042023` +#### Removed +- [striatal pthlh-expressing interneuron](http://purl.obolibrary.org/obo/CL_4042023) SubClassOf [RO_0002100](http://purl.obolibrary.org/obo/RO_0002100) some [UBERON_0002435](http://purl.obolibrary.org/obo/UBERON_0002435) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1016/j.semnephrol.2019.04.005"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [striatal pthlh-expressing interneuron](http://purl.obolibrary.org/obo/CL_4042023) SubClassOf [obsolete CNS interneuron](http://purl.obolibrary.org/obo/CL_0000402) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1152/physiol.00008.2011"^^[string](http://www.w3.org/2001/XMLSchema#string) +#### Added +- [striatal pthlh-expressing interneuron](http://purl.obolibrary.org/obo/CL_4042023) SubClassOf [striatum neuron](http://purl.obolibrary.org/obo/CL_0002613) -### renal filtration cell `http://purl.obolibrary.org/obo/CL_0002522` +### striatum neuron `http://purl.obolibrary.org/obo/CL_0002613` +#### Removed +- [striatum neuron](http://purl.obolibrary.org/obo/CL_0002613) EquivalentTo [CNS neuron (sensu Vertebrata)](http://purl.obolibrary.org/obo/CL_0000117) and ([RO_0002100](http://purl.obolibrary.org/obo/RO_0002100) some [UBERON_0002435](http://purl.obolibrary.org/obo/UBERON_0002435)) #### Added -- [renal filtration cell](http://purl.obolibrary.org/obo/CL_0002522) SubClassOf [eukaryotic cell](http://purl.obolibrary.org/obo/CL_0000255) +- [striatum neuron](http://purl.obolibrary.org/obo/CL_0002613) EquivalentTo [neuron](http://purl.obolibrary.org/obo/CL_0000540) and ([RO_0002100](http://purl.obolibrary.org/obo/RO_0002100) some [UBERON_0002435](http://purl.obolibrary.org/obo/UBERON_0002435)) -### renal intercalated cell `http://purl.obolibrary.org/obo/CL_0005010` +### striosomal D1 medium spiny neuron `http://purl.obolibrary.org/obo/CL_4030048` #### Added -- [renal intercalated cell](http://purl.obolibrary.org/obo/CL_0005010) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://cellxgene.cziscience.com/cellguide/CL_0005010"^^[string](http://www.w3.org/2001/XMLSchema#string) - -- [renal intercalated cell](http://purl.obolibrary.org/obo/CL_0005010) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. +- [striosomal D1 medium spiny neuron](http://purl.obolibrary.org/obo/CL_4030048) SubClassOf [striatum neuron](http://purl.obolibrary.org/obo/CL_0002613) -Renal intercalated cells are specialized cells located in the collecting duct system of the kidneys. The primary role of intercalated cells is to reabsorb bicarbonate ions and secrete hydrogen ions, thereby maintaining the acid-base homeostasis in the blood. They comprise two main subtypes primarily distinguished by their functional and morphological attributes: alpha and beta intercalated cells. -Alpha intercalated cells are more predominant when the body is in a state of acidosis, a condition characterized by an increased acidity of the blood. These cells are specialized in secreting excessive hydrogen ions into the urine through a mechanism involving vacuolar H+-ATPase and H+/K+-ATPase pumps on their apical membranes. They simultaneously reabsorb bicarbonate ions from the tubular fluid and return them to the bloodstream via mechanisms involving carbonic anhydrase II and bicarbonate/chloride exchangers on the basolateral membrane. This dual process helps to increase blood pH towards normal levels. -When the body is in a state of alkalosis, a condition characterized by lowered levels of hydrogen ions in the blood, beta intercalated cells are more predominant. They primarily reabsorb hydrogen ions from the tubular fluid through vacuolar H+-ATPase and H+/K+-ATPase pumps on their basolateral membranes, while secreting bicarbonate ions into the urine via pendrin, a bicarbonate/chloride exchanger in the apical membrane. These mechanisms work together to decrease blood pH towards normal levels. -In summary, renal intercalated cells play a critical role in the delicate balance of the body’s pH, safeguarding the body from potential harm caused by acidemia or alkalemia."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1681/ASN.V1011"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1161/HYPERTENSIONAHA.121.16492"^^[string](http://www.w3.org/2001/XMLSchema#string) +### striosomal D2 medium spiny neuron `http://purl.obolibrary.org/obo/CL_4030049` - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1152/ajprenal.2000.279.1.F195"^^[string](http://www.w3.org/2001/XMLSchema#string) +#### Added +- [striosomal D2 medium spiny neuron](http://purl.obolibrary.org/obo/CL_4030049) SubClassOf [striatum neuron](http://purl.obolibrary.org/obo/CL_0002613) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.2215/CJN.08880914"^^[string](http://www.w3.org/2001/XMLSchema#string) +### stromal cell `http://purl.obolibrary.org/obo/CL_0000499` +#### Removed +- [stromal cell](http://purl.obolibrary.org/obo/CL_0000499) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A connective tissue cell of an organ found in the loose connective tissue. These are most often associated with the uterine mucosa and the ovary as well as the hematopoietic system and elsewhere."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "MESH:D017154"^^[string](http://www.w3.org/2001/XMLSchema#string) -### renal principal cell `http://purl.obolibrary.org/obo/CL_0005009` + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:tfm"^^[string](http://www.w3.org/2001/XMLSchema#string) #### Added -- [renal principal cell](http://purl.obolibrary.org/obo/CL_0005009) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://cellxgene.cziscience.com/cellguide/CL_0005009"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [stromal cell](http://purl.obolibrary.org/obo/CL_0000499) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A connective tissue cell of an organ found in the loose connective tissue."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "MESH:D017154"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [renal principal cell](http://purl.obolibrary.org/obo/CL_0005009) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:tfm"^^[string](http://www.w3.org/2001/XMLSchema#string) -Renal principal cells are the major cell type in the initial collecting tubule and the cortical and outer medullary collecting ducts, as well as the connecting tubule, in the nephrons of the kidneys. -A key function of renal principal cells is the regulation of water balance in the body. These cells express aquaporin-2 (AQP2) water channels, which facilitate the reabsorption of water from the fluid within the renal tubule lumen back into the blood. The translocation of AQP2 to the cell membrane is controlled by the hormone vasopressin: In response to high vasopressin levels, AQP2 moves to the cell membrane, allowing water to pass through effectively and be reabsorbed, therefore concentrating the urine. Conversely, in low vasopressin conditions, AQP2 is removed from the membrane, reducing water reabsorption and diluting the urine. -Renal principal cells are also involved in the regulation of sodium and potassium levels in the body. They have sodium channels (ENaC) in their luminal membranes which permit the reabsorption of sodium ions from the tubule fluid back into the blood, resulting in a net reabsorption of sodium ions into the systemic circulation. This process is controlled, in part, by the hormone aldosterone. Additionally, renal principal cells contain potassium channels that facilitate the secretion of potassium ions into the urine. The activities of these channels, in coordination with other cell types in the nephron, are critical for maintaining electrolyte balance and overall body homeostasis."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.2215/CJN.05760513"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.2215/CJN.08580813"^^[string](http://www.w3.org/2001/XMLSchema#string) +### stromal cell of endometrium `http://purl.obolibrary.org/obo/CL_0002255` +#### Removed +- [stromal cell of endometrium](http://purl.obolibrary.org/obo/CL_0002255) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A stromal cell of the endometrium that is fibroblastic in appearance. During decidualization this cell may differentiate into a decidual stromal cell."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://doi.org/10.1038/s41591-020-1040-z"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1016/j.krcp.2013.07.005"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:11331626"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:30309298"^^[string](http://www.w3.org/2001/XMLSchema#string) -### respiratory basal cell `http://purl.obolibrary.org/obo/CL_0002633` + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:30013421"^^[string](http://www.w3.org/2001/XMLSchema#string) -#### Added -- [respiratory basal cell](http://purl.obolibrary.org/obo/CL_0002633) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wiki:Decidualization&oldid=908981933#Endometrial_stromal_cells_(ESCs)"^^[string](http://www.w3.org/2001/XMLSchema#string) -Respiratory basal cells are highly specialized cells that serve a crucial role in the human airway epithelium, predominantly found lining the surfaces of the trachea and bronchi. These cells exhibit a distinctive columnar shape and are attached directly to the basal lamina. They are characterized by the presence of high amounts of cytoplasmic keratins, predominantly keratin 5 and 14, and transcription factor tumor protein (tp63), which set them apart from other types of lung epithelial cells such as ciliated cells and secretory cells. -Basal cells are essential for maintaining airway integrity. They make up one third of all respiratory epithelial cells and serve as stem cells as they can transform into different cell types, like goblet cells, ciliated cells, and club cells, when needed for homeostatic maintenance of the epithelial barrier or to repair and restore a healthy cellular environment after injury. -Their position at the interface between the internal environment and the external atmosphere makes these cells a first line of defense against air-borne irritants, allergens, and pathogens. Their robust, intrinsic reparative properties facilitate effective recovery from such adversities. However, damage to respiratory basal cells or abnormalities in their function are associated with several respiratory pathologies such as asthma, chronic obstructive pulmonary disease, and lung cancer. Therefore, understanding these cells' function, and their role in disease, is crucial for the development of new therapeutic strategies for respiratory disorders."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:110.1038/s41385-020-00370-7"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [stromal cell of endometrium](http://purl.obolibrary.org/obo/CL_0002255) EquivalentTo [stromal cell](http://purl.obolibrary.org/obo/CL_0000499) and ([BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0001295](http://purl.obolibrary.org/obo/UBERON_0001295)) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1186/s12931-022-02042-5"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [stromal cell of endometrium](http://purl.obolibrary.org/obo/CL_0002255) SubClassOf [stromal cell](http://purl.obolibrary.org/obo/CL_0000499) + - [is_inferred](http://www.geneontology.org/formats/oboInOwl#is_inferred) "true"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.3389/falgy.2021.787128"^^[string](http://www.w3.org/2001/XMLSchema#string) +#### Added +- [stromal cell of endometrium](http://purl.obolibrary.org/obo/CL_0002255) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A stromal cell of the endometrium, characterized by its fibroblast-like morphology, regenerative capacity, and ability to undergo decidualization. It differentiates into a decidual stromal cell during pregnancy, essential for embryo implantation and maintenance. This cell is involved in tissue proliferation, remodeling, and breakdown, responding to hormonal changes, particularly estrogen and progesterone."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:31907034"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [respiratory basal cell](http://purl.obolibrary.org/obo/CL_0002633) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://cellxgene.cziscience.com/cellguide/CL_0002633"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://doi.org/10.1038/s41591-020-1040-z"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:11331626"^^[string](http://www.w3.org/2001/XMLSchema#string) -### respiratory goblet cell `http://purl.obolibrary.org/obo/CL_0002370` + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Decidualization"^^[string](http://www.w3.org/2001/XMLSchema#string) -#### Added -- [respiratory goblet cell](http://purl.obolibrary.org/obo/CL_0002370) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://cellxgene.cziscience.com/cellguide/CL_0002370"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:30309298"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [respiratory goblet cell](http://purl.obolibrary.org/obo/CL_0002370) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:30013421"^^[string](http://www.w3.org/2001/XMLSchema#string) -The respiratory goblet cell is a highly specialized cell type found primarily within the respiratory tract, including the nose, trachea, and lungs. Named because their shape resembles a goblet - a drinking vessel with a wide body and narrow neck - these cells form a vital part of the respiratory system's protective mechanisms. They are found within the columnar epithelium lining these organs, which forms a barrier between the internal body and the exterior environment. -A principal function of the respiratory goblet cell is the production and secretion of mucus, a carbohydrate-rich, viscous and gel-like substance that plays a critical role in trapping dust, bacteria, viruses, and other airborne particles that are inhaled. The mucus secreted by the goblet cells covers the lining of the respiratory tract, effectively catching these particles and preventing them from reaching the lungs and causing infection. Mucus also provides hydration and lubrication to the respiratory tract surfaces, which is important in maintaining the tissue's health and functioning. -In addition to their mucus-secreting capabilities, respiratory goblet cells also play a significant role in the body's inflammatory responses. When the respiratory system is exposed to irritants or pathogens, the number and activity of goblet cells often increase, leading to a higher production of mucus. This is a protective response designed to trap and neutralize the harmful substances more effectively. However, in conditions like chronic obstructive pulmonary disease (COPD) and asthma, an overproliferation of goblet cells, also known as goblet cell hyperplasia, can lead to excessive mucus production and airway obstruction."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1111/febs.15731"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [stromal cell of endometrium](http://purl.obolibrary.org/obo/CL_0002255) [has_broad_synonym](http://www.geneontology.org/formats/oboInOwl#hasBroadSynonym) "stromal cell of uterus"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1016/S1357-2725(02)00083-3"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [stromal cell of endometrium](http://purl.obolibrary.org/obo/CL_0002255) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl/cl-base#cellxgene_subset) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1165/ajrcmb.25.5.f218"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [stromal cell of endometrium](http://purl.obolibrary.org/obo/CL_0002255) EquivalentTo [stromal cell](http://purl.obolibrary.org/obo/CL_0000499) and ([BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0002337](http://purl.obolibrary.org/obo/UBERON_0002337)) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.3109/01902148.2013.791733"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [stromal cell of endometrium](http://purl.obolibrary.org/obo/CL_0002255) SubClassOf [RO_0002215](http://purl.obolibrary.org/obo/RO_0002215) some [GO_0046697](http://purl.obolibrary.org/obo/GO_0046697) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.2147/COPD.S38938"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [stromal cell of endometrium](http://purl.obolibrary.org/obo/CL_0002255) SubClassOf [stromal cell](http://purl.obolibrary.org/obo/CL_0000499) -### reticulocyte `http://purl.obolibrary.org/obo/CL_0000558` +### subpleural fibroblast `http://purl.obolibrary.org/obo/CL_4052029` #### Added -- [reticulocyte](http://purl.obolibrary.org/obo/CL_0000558) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) +- [subpleural fibroblast](http://purl.obolibrary.org/obo/CL_4052029) [id](http://www.geneontology.org/formats/oboInOwl#id) "CL:4052029"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [subpleural fibroblast](http://purl.obolibrary.org/obo/CL_4052029) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A fibroblast that is located beneath the visceral pleura of the lung. This cell contributes to the development of idiopathic pulmonary fibrosis (IPF) by forming fibrotic lesions that originate subpleurally and extend into lung tissue through activation, proliferation, migration, and differentiation into a myofibroblast."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:37291214"^^[string](http://www.w3.org/2001/XMLSchema#string) -### retinal blood vessel endothelial cell `http://purl.obolibrary.org/obo/CL_0002585` + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:36543915"^^[string](http://www.w3.org/2001/XMLSchema#string) -#### Added -- [retinal blood vessel endothelial cell](http://purl.obolibrary.org/obo/CL_0002585) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:36769178"^^[string](http://www.w3.org/2001/XMLSchema#string) -Retinal blood vessel endothelial cells constitute the innermost lining of the blood vessels found in the retina, the light-sensitive layer of tissue at the back of the eye. The primary role of these cells revolves around their location within the retinal vascular system, forming the structure of the blood-retinal barrier, a subset of the larger blood-ocular barrier system. -The endothelial cells are particularly involved in the growth of new retinal blood vessels from pre-existing ones (angiogenesis); this is critical in managing the amount of oxygen and essential nutrients delivered to the ocular tissues. They are crucial for maintaining homeostasis in the retinal environment by controlling the exchange of molecules between the blood and the retina. Furthermore, they mediate immune cell trafficking, supporting the immune privilege of the eye by preventing the unrestricted infiltration of inflammatory cells into the retina, thus maintaining ocular health and normal vision. -The malfunction or dysfunction of retinal blood vessel endothelial cells is implicated in numerous ocular pathologies, particularly diabetic retinopathy, which is one of the leading causes of blindness worldwide. In such conditions, the compromise in the integrity of the blood-retinal barrier and excess angiogenesis can lead to retinal edema and pathological neovascularization, resulting in vision loss."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.5301/EJO.2010.6049"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [subpleural fibroblast](http://purl.obolibrary.org/obo/CL_4052029) [contributor](http://purl.org/dc/terms/contributor) [0009-0000-8480-9277](https://orcid.org/0009-0000-8480-9277) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:0.1016/j.preteyeres.2015.08.001"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [subpleural fibroblast](http://purl.obolibrary.org/obo/CL_4052029) [label](http://www.w3.org/2000/01/rdf-schema#label) "subpleural fibroblast"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1016/j.preteyeres.2012.08.004"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [subpleural fibroblast](http://purl.obolibrary.org/obo/CL_4052029) [date](http://purl.org/dc/terms/date) "2024-11-29T13:54:15Z"^^[dateTime](http://www.w3.org/2001/XMLSchema#dateTime) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1038/nature04482"^^[string](http://www.w3.org/2001/XMLSchema#string) +- Class: [subpleural fibroblast](http://purl.obolibrary.org/obo/CL_4052029) -- [retinal blood vessel endothelial cell](http://purl.obolibrary.org/obo/CL_0002585) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://cellxgene.cziscience.com/cellguide/CL_0002585"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [subpleural fibroblast](http://purl.obolibrary.org/obo/CL_4052029) SubClassOf [fibroblast of lung](http://purl.obolibrary.org/obo/CL_0002553) -### retinal pigment epithelial cell `http://purl.obolibrary.org/obo/CL_0002586` +### suprabasal keratinocyte `http://purl.obolibrary.org/obo/CL_4033013` #### Added -- [retinal pigment epithelial cell](http://purl.obolibrary.org/obo/CL_0002586) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://cellxgene.cziscience.com/cellguide/CL_0002586"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [suprabasal keratinocyte](http://purl.obolibrary.org/obo/CL_4033013) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl/cl-base#cellxgene_subset) -- [retinal pigment epithelial cell](http://purl.obolibrary.org/obo/CL_0002586) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. -Retinal pigment epithelial (RPE) cells form a single layer of cells at the back of the eye sandwiched between the neurosensory retina and the choroid, playing a significant role in maintaining vision health. These pigment-laden cells are highly specialized and perform an array of metabolic and transport functions essential for the maintenance of the photoreceptor cells (rods and cones) in the retina. The pigmentation of RPE cells actively aids in the absorption of excess light and the prevention of light scattering, thus enhancing the eye's optical properties. -The retinal pigment epithelium forms a key part of the blood/retina barrier. The cells have long sheet-like microvilli on their apical membrane that project into the light-sensitive outer segments of the photoreceptors, forming a close structural interaction. The basolateral membrane of the RPE interacts with the underlying Bruch’s membrane, which separates the RPE cells from fenestrated endothelium of the choriocapillaris. -RPE cells support the photoreceptor by providing them with oxygen and nutrients (such as glucose, retinol and fatty acids) and removing waste products. They also recycle the visual pigment, in a process called the "visual cycle", where the RPE cells play a vital role in the regeneration of visual pigment (11-cis retinol) following the absorption of light. This is essential for the maintenance of photoreceptor excitability. -Beyond this, RPE cells take part in the phagocytosis process, where they digest the shed ends of photoreceptor outer segments, thus, preventing the build-up of waste residue that could otherwise harm retinal health. They also secrete various factors, including growth factors required to maintain the structural integrity of choriocapillaris endothelium and photoreceptors, as well as immunosuppressive factors that play an important role in establishing the immune privilege of the eye."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1111/febs.16018"^^[string](http://www.w3.org/2001/XMLSchema#string) +### surface ectodermal cell `http://purl.obolibrary.org/obo/CL_0000114` - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1152/physrev.00021.2004"^^[string](http://www.w3.org/2001/XMLSchema#string) +#### Added +- [surface ectodermal cell](http://purl.obolibrary.org/obo/CL_0000114) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.3389/fphar.2021.727870/full"^^[string](http://www.w3.org/2001/XMLSchema#string) +Surface ectoderm cells give rise to external structures such as the epidermis, hair, nails, and sweat glands. They are critical during the early stages of embryonic development, where they delineate and create the organism's exterior body plan. Beyond forming the organism's physical exterior, surface ectodermal cells have other significant roles. For instance, these cells lead to the development of the anterior pituitary gland and the enamel of the teeth. They are also integral to the formation of the sensory organs, including the eyes and the ears. In the eyes, they form the cornea and lens epithelium. In the ears, they form the external ear canal and certain parts of the inner ear. Therefore, these cells are instrumental in the development of various sensory systems in an organism. +Certain abnormalities or mutations in surface ectodermal cells could lead to medical conditions known as ectodermal dysplasias. These are a group of inherited disorders affecting the development or function of teeth, hair, nails, and sweat glands. Therefore, understanding the formation and function of surface ectodermal cells is also important in identifying and addressing certain genetic disorders and conditions. In summary, surface ectodermal cells are essential in embryonic development, contributing to the creation of the external physical appearance and the sensory organs of an organism."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://www.ncbi.nlm.nih.gov/books/NBK563130"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://www.sciencedirect.com/topics/chemistry/retinal-pigment"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1038/srep32007"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://www.ncbi.nlm.nih.gov/books/NBK539836/"^^[string](http://www.w3.org/2001/XMLSchema#string) -### rod bipolar cell `http://purl.obolibrary.org/obo/CL_0000751` +- [surface ectodermal cell](http://purl.obolibrary.org/obo/CL_0000114) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://cellxgene.cziscience.com/cellguide/CL_0000114"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### taste receptor cell of tongue `http://purl.obolibrary.org/obo/CL_4033049` #### Removed -- [rod bipolar cell](http://purl.obolibrary.org/obo/CL_0000751) SubClassOf [BFO_0000002](http://purl.obolibrary.org/obo/BFO_0000002) +- [taste receptor cell of tongue](http://purl.obolibrary.org/obo/CL_4033049) SubClassOf [epithelial cell of alimentary canal](http://purl.obolibrary.org/obo/CL_0002251) -- [rod bipolar cell](http://purl.obolibrary.org/obo/CL_0000751) SubClassOf [RO_0002160](http://purl.obolibrary.org/obo/RO_0002160) some [NCBITaxon_40674](http://purl.obolibrary.org/obo/NCBITaxon_40674) -- [rod bipolar cell](http://purl.obolibrary.org/obo/CL_0000751) SubClassOf [eukaryotic cell](http://purl.obolibrary.org/obo/CL_0000255) + +### telocyte `http://purl.obolibrary.org/obo/CL_0017004` +#### Removed +- [telocyte](http://purl.obolibrary.org/obo/CL_0017004) [created by](http://www.geneontology.org/formats/oboInOwl#created_by) "http://orcid.org/0000-0003-2473-2313"^^[string](http://www.w3.org/2001/XMLSchema#string) #### Added -- [rod bipolar cell](http://purl.obolibrary.org/obo/CL_0000751) [RO_0002175](http://purl.obolibrary.org/obo/RO_0002175) [NCBITaxon_32443](http://purl.obolibrary.org/obo/NCBITaxon_32443) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:38627529"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [telocyte](http://purl.obolibrary.org/obo/CL_0017004) [contributor](http://purl.org/dc/terms/contributor) [0000-0003-2473-2313](http://orcid.org/0000-0003-2473-2313) -### rosehip neuron `http://purl.obolibrary.org/obo/CL_0008032` +### thalamic excitatory neuron `http://purl.obolibrary.org/obo/CL_4023068` #### Removed -- [rosehip neuron](http://purl.obolibrary.org/obo/CL_0008032) SubClassOf [RO_0002160](http://purl.obolibrary.org/obo/RO_0002160) some [NCBITaxon_9606](http://purl.obolibrary.org/obo/NCBITaxon_9606) +- [thalamic excitatory neuron](http://purl.obolibrary.org/obo/CL_4023068) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "An excitatory neuron that has its soma located in the thalamic complex."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1101/2022.10.12.511898"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [rosehip neuron](http://purl.obolibrary.org/obo/CL_0008032) SubClassOf [eukaryotic cell](http://purl.obolibrary.org/obo/CL_0000255) +- [thalamic excitatory neuron](http://purl.obolibrary.org/obo/CL_4023068) SubClassOf [central nervous system neuron](http://purl.obolibrary.org/obo/CL_2000029) #### Added -- [rosehip neuron](http://purl.obolibrary.org/obo/CL_0008032) SubClassOf [RO_0002162](http://purl.obolibrary.org/obo/RO_0002162) some [NCBITaxon_9606](http://purl.obolibrary.org/obo/NCBITaxon_9606) +- [thalamic excitatory neuron](http://purl.obolibrary.org/obo/CL_4023068) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl/cl-base#cellxgene_subset) +- [thalamic excitatory neuron](http://purl.obolibrary.org/obo/CL_4023068) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "An excitatory neuron that has its soma located in the thalamic complex. This neuron type can be involved in a series of circuits related to sensory integration, motor integration, pain processing, social behaviour and reward response."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:31196673"^^[string](http://www.w3.org/2001/XMLSchema#string) -### salivary gland cell `http://purl.obolibrary.org/obo/CL_0009005` -#### Removed -- [salivary gland cell](http://purl.obolibrary.org/obo/CL_0009005) SubClassOf [cell](http://purl.obolibrary.org/obo/CL_0000000) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:35278647"^^[string](http://www.w3.org/2001/XMLSchema#string) -#### Added -- [salivary gland cell](http://purl.obolibrary.org/obo/CL_0009005) SubClassOf [eukaryotic cell](http://purl.obolibrary.org/obo/CL_0000255) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:37163009"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:37824663"^^[string](http://www.w3.org/2001/XMLSchema#string) -### salivary gland glandular cell `http://purl.obolibrary.org/obo/CL_1001596` + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:30083593"^^[string](http://www.w3.org/2001/XMLSchema#string) -#### Added -- [salivary gland glandular cell](http://purl.obolibrary.org/obo/CL_1001596) SubClassOf [salivary gland cell](http://purl.obolibrary.org/obo/CL_0009005) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:38739251"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [thalamic excitatory neuron](http://purl.obolibrary.org/obo/CL_4023068) [comment](http://www.w3.org/2000/01/rdf-schema#comment) "Abnormalities in glutametergic neurons of the thalamic complex are associated with pathologies such as schizophrenia, colorectal visceral pain and Parkinson's disease."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:11532718"^^[string](http://www.w3.org/2001/XMLSchema#string) -### scleral cell `http://purl.obolibrary.org/obo/CL_0000347` + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:30083593"^^[string](http://www.w3.org/2001/XMLSchema#string) -#### Added -- [scleral cell](http://purl.obolibrary.org/obo/CL_0000347) SubClassOf [eukaryotic cell](http://purl.obolibrary.org/obo/CL_0000255) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:38739251"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [thalamic excitatory neuron](http://purl.obolibrary.org/obo/CL_4023068) SubClassOf [neuron of the forebrain](http://purl.obolibrary.org/obo/CL_0012001) -### scolopale cell `http://purl.obolibrary.org/obo/CL_0000382` -#### Added -- [scolopale cell](http://purl.obolibrary.org/obo/CL_0000382) SubClassOf [eukaryotic cell](http://purl.obolibrary.org/obo/CL_0000255) +### theca cell `http://purl.obolibrary.org/obo/CL_0000503` +#### Removed +- [theca cell](http://purl.obolibrary.org/obo/CL_0000503) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A flattened stroma cell forming a sheath or theca outside the basal lamina lining the mature ovarian follicle. Thecal interstitial or stromal cells are steroidogenic, and produce primarily androgens which serve as precusors of estrogens in the granulosa cells."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "MESH:D013799"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [theca cell](http://purl.obolibrary.org/obo/CL_0000503) SubClassOf [androgen secreting cell](http://purl.obolibrary.org/obo/CL_0000593) -### scolopidial ligament cell `http://purl.obolibrary.org/obo/CL_0000407` +- [theca cell](http://purl.obolibrary.org/obo/CL_0000503) SubClassOf [BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0001305](http://purl.obolibrary.org/obo/UBERON_0001305) #### Added -- [scolopidial ligament cell](http://purl.obolibrary.org/obo/CL_0000407) SubClassOf [eukaryotic cell](http://purl.obolibrary.org/obo/CL_0000255) +- [theca cell](http://purl.obolibrary.org/obo/CL_0000503) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A specialized stromal cell that forms the theca layer outside the basal lamina lining the ovarian follicle, appearing during the secondary follicle stage."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:36758341"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:15833266"^^[string](http://www.w3.org/2001/XMLSchema#string) -### sebaceous gland cell `http://purl.obolibrary.org/obo/CL_2000021` -#### Removed -- [sebaceous gland cell](http://purl.obolibrary.org/obo/CL_2000021) SubClassOf [cell](http://purl.obolibrary.org/obo/CL_0000000) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "MESH:D013799"^^[string](http://www.w3.org/2001/XMLSchema#string) -#### Added -- [sebaceous gland cell](http://purl.obolibrary.org/obo/CL_2000021) SubClassOf [eukaryotic cell](http://purl.obolibrary.org/obo/CL_0000255) +- [theca cell](http://purl.obolibrary.org/obo/CL_0000503) SubClassOf [BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0000155](http://purl.obolibrary.org/obo/UBERON_0000155) -### secondary lens fiber `http://purl.obolibrary.org/obo/CL_0002225` +### thymic fibroblast type 1 `http://purl.obolibrary.org/obo/CL_0009078` #### Added -- [secondary lens fiber](http://purl.obolibrary.org/obo/CL_0002225) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. +- [thymic fibroblast type 1](http://purl.obolibrary.org/obo/CL_0009078) SubClassOf [stromal cell of thymus](http://purl.obolibrary.org/obo/CL_4030001) -Secondary lens fibers are a specialized type of elongated cells located within the structure of the eye's lens. They play an essential role in vision by enabling light transmission and focus on the retina, which allows for clear, distinct vision. These cells are characterized by their lack of nuclei and organelles, their orderly alignment, and their high protein content, particularly crystallins. -Lens fibers are differentiated from equatorial epithelial cells of the lens in a process that involves cell elongation, denucleation and tight packing, which serve to reduce light scattering occurrences in the eye. This differentiation accelerates substantially after birth in comparison to during embryogenesis and continues throughout life, contributing to the growth of the eye lens. Secondary lens fibers are specifically those cells that are newly differentiated and cover the old lens fiber core. This process also leads to the removal of light-obstructing cellular components, mainly nuclei and organelles, making these fibers transparent and ideal for their function. -The fibers carry out their primary function of light refraction via a high concentration of specialized proteins known as crystallins, which form a gradient of refractive index together with the cytoplasm. This index manipulation facilitates precise light focus onto the retina. Secondary lens fibers also contribute to the lens's shape and biomechanical properties through intercellular interactions, particularly at the sutures where the ends of the fibers meet. Any disruption to secondary lens fibers can lead to vision problems, including cataracts, which is the clouding of the lens resulting from the aggregation of crystallin proteins."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1136/bmjophth-2020-000459"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://www.sciencedirect.com/topics/immunology-and-microbiology/lens-fiber"^^[string](http://www.w3.org/2001/XMLSchema#string) +### thymic fibroblast type 2 `http://purl.obolibrary.org/obo/CL_0009079` - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1016/j.biocel.2007.10.034"^^[string](http://www.w3.org/2001/XMLSchema#string) +#### Added +- [thymic fibroblast type 2](http://purl.obolibrary.org/obo/CL_0009079) SubClassOf [stromal cell of thymus](http://purl.obolibrary.org/obo/CL_4030001) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1098/rstb.2010.0324"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1016/B978-1-4377-1926-0.10005-0"^^[string](http://www.w3.org/2001/XMLSchema#string) +### tongue muscle cell `http://purl.obolibrary.org/obo/CL_0002673` -- [secondary lens fiber](http://purl.obolibrary.org/obo/CL_0002225) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://cellxgene.cziscience.com/cellguide/CL_0002225"^^[string](http://www.w3.org/2001/XMLSchema#string) +#### Added +- [tongue muscle cell](http://purl.obolibrary.org/obo/CL_0002673) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://cellxgene.cziscience.com/cellguide/CL_0002673"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [tongue muscle cell](http://purl.obolibrary.org/obo/CL_0002673) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. -### secondary neuron (sensu Teleostei) `http://purl.obolibrary.org/obo/CL_0000535` -#### Removed -- [secondary neuron (sensu Teleostei)](http://purl.obolibrary.org/obo/CL_0000535) SubClassOf [eukaryotic cell](http://purl.obolibrary.org/obo/CL_0000255) +Tongue muscle cells are responsible for essential functions like mastication, deglutition (swallowing), phonation (speech), and taste receptivity. They can be classified into two functional classes - extrinsic and intrinsic muscle cells. +The extrinsic tongue muscle cells originate outside the tongue and are primarily involved in determining the position of the tongue within the mouth. Muscle groups such as the genioglossus, hyoglossus, and styloglossus are composed of these extrinsic muscle cells and grant the tongue its wide range of motion. +The intrinsic tongue muscle cells, on the other hand, originate and function within the tongue itself, influencing the shape of the tongue during speech, eating, and swallowing. These cells can contract to alter the tongue's shape, making it long, short, curled, or flat, as needed. Together, these two types of muscle cells allow the tongue to perform its vital functions effectively. Moreover, they play a critical role in maintaining oral health by facilitating physical cleaning of the oral cavity and assisting in the mechanical breakdown of food."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://www.ncbi.nlm.nih.gov/books/NBK554405/"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [secondary neuron (sensu Teleostei)](http://purl.obolibrary.org/obo/CL_0000535) SubClassOf [RO_0002160](http://purl.obolibrary.org/obo/RO_0002160) some [NCBITaxon_32443](http://purl.obolibrary.org/obo/NCBITaxon_32443) - - [IAO_0000233](http://purl.obolibrary.org/obo/IAO_0000233) "https://github.com/obophenotype/cell-ontology/pull/1950"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://www.ncbi.nlm.nih.gov/books/NBK507782/"^^[string](http://www.w3.org/2001/XMLSchema#string) -#### Added -- [secondary neuron (sensu Teleostei)](http://purl.obolibrary.org/obo/CL_0000535) SubClassOf [RO_0002162](http://purl.obolibrary.org/obo/RO_0002162) some [NCBITaxon_32443](http://purl.obolibrary.org/obo/NCBITaxon_32443) - - [IAO_0000233](http://purl.obolibrary.org/obo/IAO_0000233) "https://github.com/obophenotype/cell-ontology/pull/1950"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1002/ca.21011"^^[string](http://www.w3.org/2001/XMLSchema#string) -### secondary spermatocyte `http://purl.obolibrary.org/obo/CL_0000657` +### tracheal goblet cell `http://purl.obolibrary.org/obo/CL_1000329` #### Added -- [secondary spermatocyte](http://purl.obolibrary.org/obo/CL_0000657) SubClassOf [eukaryotic cell](http://purl.obolibrary.org/obo/CL_0000255) +- [tracheal goblet cell](http://purl.obolibrary.org/obo/CL_1000329) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://cellxgene.cziscience.com/cellguide/CL_1000329"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [tracheal goblet cell](http://purl.obolibrary.org/obo/CL_1000329) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. -### seminal vesicle glandular cell `http://purl.obolibrary.org/obo/CL_1001597` +Tracheal goblet cells are specialized cells found in the lining of the trachea. They are a key component of the tracheobronchial epithelium, a critical region responsible for maintaining open airways and preventing the ingress of harmful particles or irritants. Goblet cells are filled with membrane-bound secretory granules, which are responsible for their distinctive, goblet-like shape. +Goblet cells specialize in the production and secretion of mucus, a slimy substance composed primarily of glycoproteins (mucins) and water. This sticky mucus serves to trap foreign particles and pollutants, such as dust, bacteria, and viruses that an organism breathes in. After trapping these particles, the cilia on neighboring ciliated epithelial cells beat synchronously, forming a coordinated escalator to push mucus upwards toward the pharynx, where it's either swallowed or expectorated. This system, known as the mucociliary clearance or escalator, forms a crucial barrier in the lungs against respiratory pathogens and external insults. +Changes in the number or function of tracheal goblet cells can engender health complications. For example, goblet cell hyperplasia, or excessive growth of goblet cells, is a common feature of chronic inflammatory lung diseases such as asthma and Chronic Obstructive Pulmonary Disease (COPD). This condition results in mucus hypersecretion, airway blockage, and increased risk of respiratory tract infections."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1016/S1357-2725(02)00083-3"^^[string](http://www.w3.org/2001/XMLSchema#string) -#### Added -- [seminal vesicle glandular cell](http://purl.obolibrary.org/obo/CL_1001597) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1165/ajrcmb.25.5.f218"^^[string](http://www.w3.org/2001/XMLSchema#string) -Seminal vesicle glandular cells belong to a specialized group of epithelial cells that form the internal lining of the seminal vesicles, a pair of male reproductive organs. These cells are located within the complex tubuloalveolar glands that make up the seminal vesicles and are known for their unique pseudostratified columnar epithelium structure. -The primary function of these cells is the secretion of a variety of substances that ultimately constitute around 70% of the fluid volume of semen. Seminal cells produce a high-fructose fluid that serves as an energy source for the spermatozoa and promotes their motility. They also secrete other essential substances like proteins, enzymes, vitamin C, prostaglandins, and various other compounds. Collectively, these substances help in the nourishment, protection, and transportation of the spermatozoa throughout the male reproductive system and during the ejaculation process. -Secondary to the production of seminal fluid, the seminal vesicle glandular cells also play a role in the contraction of the seminal vesicles during ejaculation. The contraction of these glands, induced by sympathetic nerves, ensures the efficient propulsion of the seminal fluid mixed with spermatozoa into the ejaculatory ducts and subsequently to the urethra. Notably, any malfunction or pathological condition affecting these cells can impact male fertility, emphasizing the importance of understanding the intricate functions of seminal vesicle glandular cells in maintaining the healthy physiological function of male reproduction."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1007/978-3-030-32300-4_26"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.3109/01902148.2013.791733"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://www.ncbi.nlm.nih.gov/books/NBK499854/"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1164/ajrccm.154.6.8970383"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://www.sciencedirect.com/topics/veterinary-science-and-veterinary-medicine/seminal-vesicle"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.2147/COPD.S38938"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1111/j.1439-0272.1992.tb02636.x"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1007/s00265-006-0178-0"^^[string](http://www.w3.org/2001/XMLSchema#string) +### tracheobronchial serous cell `http://purl.obolibrary.org/obo/CL_0019001` -- [seminal vesicle glandular cell](http://purl.obolibrary.org/obo/CL_1001597) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://cellxgene.cziscience.com/cellguide/CL_1001597"^^[string](http://www.w3.org/2001/XMLSchema#string) +#### Added +- [tracheobronchial serous cell](http://purl.obolibrary.org/obo/CL_0019001) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. +Serous cells of the tracheobronchial are found on the surface epithelium, submucosal glands, or both, depending on species. They appear in tubulo-acinar arrangements in submucosal glands. +Tracheobronchial serous cells play a vital role in maintaining respiratory health by secreting serous fluid, which is rich in enzymes, ions, and antimicrobial proteins. This serous fluid is essential in clearing out debris, trapping and neutralizing inhaled pathogens and particulate matters, thereby helping in preventing infections. Their secretory products also include water and electrolytes that, combined with mucus (from mucous cells), maintain proper humidity within the airway and lubricate its surfaces, facilitating unhindered airflow. Dysfunction of these cells may lead to diseases such as cystic fibrosis."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1016/j.resp.2007.06.017"^^[string](http://www.w3.org/2001/XMLSchema#string) -### sensory receptor cell `http://purl.obolibrary.org/obo/CL_0000197` -#### Removed -- [sensory receptor cell](http://purl.obolibrary.org/obo/CL_0000197) SubClassOf [cell](http://purl.obolibrary.org/obo/CL_0000000) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1146/annurev.ph.52.030190.000525"^^[string](http://www.w3.org/2001/XMLSchema#string) -#### Added -- [sensory receptor cell](http://purl.obolibrary.org/obo/CL_0000197) SubClassOf [eukaryotic cell](http://purl.obolibrary.org/obo/CL_0000255) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1113/jphysiol.2003.052779"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1152/ajplung.00068.2019"^^[string](http://www.w3.org/2001/XMLSchema#string) -### single nucleate cell `http://purl.obolibrary.org/obo/CL_0000226` +- [tracheobronchial serous cell](http://purl.obolibrary.org/obo/CL_0019001) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://cellxgene.cziscience.com/cellguide/CL_0019001"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### tracheobronchial smooth muscle cell `http://purl.obolibrary.org/obo/CL_0019019` #### Added -- [single nucleate cell](http://purl.obolibrary.org/obo/CL_0000226) SubClassOf [eukaryotic cell](http://purl.obolibrary.org/obo/CL_0000255) +- [tracheobronchial smooth muscle cell](http://purl.obolibrary.org/obo/CL_0019019) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. +Tracheobronchial smooth muscle cells are universally located in the tracheobronchial tree and play a critical role in controlling and modulating the size of the airway lumen, thereby contributing significantly to the airflow resistance. +These cells display both phasic and tonic characteristics, which are vital for airway contractility. Phasic activity manifests as cyclic contraction and relaxation, similar to the behavior seen in gastrointestinal smooth muscle cells, whilst tonic activity resembles vascular smooth muscle cells, maintaining a constant degree of tension. These features enable tracheobronchial smooth muscle cells to constrict the airways in response to various mechanical and chemical stimuli, including allergens, parasympathetic nervous stimulation, changes in gas composition, and cold air, thus protecting the delicate alveoli from potential damage. +Tracheobronchial smooth muscle cells, beyond their contractile function, actively contribute to airway remodeling in conditions like asthma. Their proliferative and synthetic capabilities lead to smooth muscle hypertrophy, hyperplasia, and the production of extracellular matrix components, collectively causing abnormal airway narrowing."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1152/japplphysiol.00950.2012"^^[string](http://www.w3.org/2001/XMLSchema#string) -### small intestine BEST4+ enterocyte `http://purl.obolibrary.org/obo/CL_4047051` + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://www.ncbi.nlm.nih.gov/books/NBK556044/"^^[string](http://www.w3.org/2001/XMLSchema#string) -#### Added -- [small intestine BEST4+ enterocyte](http://purl.obolibrary.org/obo/CL_4047051) [id](http://www.geneontology.org/formats/oboInOwl#id) "CL:4047051"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1007/978-3-540-79090-7_5"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [small intestine BEST4+ enterocyte](http://purl.obolibrary.org/obo/CL_4047051) [date](http://purl.org/dc/terms/date) "2024-07-25T13:05:50Z"^^[dateTime](http://www.w3.org/2001/XMLSchema#dateTime) +- [tracheobronchial smooth muscle cell](http://purl.obolibrary.org/obo/CL_0019019) [comment](http://www.w3.org/2000/01/rdf-schema#comment) "The marker set ACTA2, TAGLN can identify the Human cell type tracheobronchial smooth muscle cell in the Lung with a confidence of 0.69 (NS-Forest FBeta value)."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://doi.org/10.5281/zenodo.11165918"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [small intestine BEST4+ enterocyte](http://purl.obolibrary.org/obo/CL_4047051) [label](http://www.w3.org/2000/01/rdf-schema#label) "small intestine BEST4+ enterocyte"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [tracheobronchial smooth muscle cell](http://purl.obolibrary.org/obo/CL_0019019) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://cellxgene.cziscience.com/cellguide/CL_0019019"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [small intestine BEST4+ enterocyte](http://purl.obolibrary.org/obo/CL_4047051) [contributor](http://purl.org/dc/terms/contributor) [0009-0005-7919-4905](https://orcid.org/0009-0005-7919-4905) +- [tracheobronchial smooth muscle cell](http://purl.obolibrary.org/obo/CL_0019019) SubClassOf [RO_0015004](http://purl.obolibrary.org/obo/RO_0015004) some [CLM_1000056](http://purl.obolibrary.org/obo/CLM_1000056) -- [small intestine BEST4+ enterocyte](http://purl.obolibrary.org/obo/CL_4047051) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "An enterocyte of the human small intestine expressing bestrophin-4 (BEST4) calcium-activated ion channels. These enterocytes have a disinctive transcriptomic profile and are scattered through the small intestine epithelium."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:34497389"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:24223998"^^[string](http://www.w3.org/2001/XMLSchema#string) +### transit amplifying cell of anorectum `http://purl.obolibrary.org/obo/CL_0009056` +#### Removed +- [transit amplifying cell of anorectum](http://purl.obolibrary.org/obo/CL_0009056) EquivalentTo [transit amplifying cell](http://purl.obolibrary.org/obo/CL_0009010) and ([BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_8410050](http://purl.obolibrary.org/obo/UBERON_8410050)) -- Class: [small intestine BEST4+ enterocyte](http://purl.obolibrary.org/obo/CL_4047051) +- [transit amplifying cell of anorectum](http://purl.obolibrary.org/obo/CL_0009056) SubClassOf [transit amplifying cell](http://purl.obolibrary.org/obo/CL_0009010) -- [small intestine BEST4+ enterocyte](http://purl.obolibrary.org/obo/CL_4047051) EquivalentTo [enterocyte](http://purl.obolibrary.org/obo/CL_0000584) and ([BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0001902](http://purl.obolibrary.org/obo/UBERON_0001902)) and ([RO_0002292](http://purl.obolibrary.org/obo/RO_0002292) some [PR_Q8NFU0](http://purl.obolibrary.org/obo/PR_Q8NFU0)) +#### Added +- [transit amplifying cell of anorectum](http://purl.obolibrary.org/obo/CL_0009056) EquivalentTo [transit amplifying cell of gut](http://purl.obolibrary.org/obo/CL_4047017) and ([BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_8410050](http://purl.obolibrary.org/obo/UBERON_8410050)) -- [small intestine BEST4+ enterocyte](http://purl.obolibrary.org/obo/CL_4047051) SubClassOf [enterocyte of epithelium of small intestine](http://purl.obolibrary.org/obo/CL_1000334) +- [transit amplifying cell of anorectum](http://purl.obolibrary.org/obo/CL_0009056) SubClassOf [transit amplifying cell of gut](http://purl.obolibrary.org/obo/CL_4047017) -- [small intestine BEST4+ enterocyte](http://purl.obolibrary.org/obo/CL_4047051) SubClassOf [BEST4+ intestinal epithelial cell, human](http://purl.obolibrary.org/obo/CL_4030026) +### transit amplifying cell of appendix `http://purl.obolibrary.org/obo/CL_0009027` +#### Removed +- [transit amplifying cell of appendix](http://purl.obolibrary.org/obo/CL_0009027) EquivalentTo [transit amplifying cell](http://purl.obolibrary.org/obo/CL_0009010) and ([BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0013486](http://purl.obolibrary.org/obo/UBERON_0013486)) -### smooth muscle cell derived foam cell `http://purl.obolibrary.org/obo/CL_0000892` +- [transit amplifying cell of appendix](http://purl.obolibrary.org/obo/CL_0009027) SubClassOf [transit amplifying cell](http://purl.obolibrary.org/obo/CL_0009010) #### Added -- [smooth muscle cell derived foam cell](http://purl.obolibrary.org/obo/CL_0000892) SubClassOf [eukaryotic cell](http://purl.obolibrary.org/obo/CL_0000255) +- [transit amplifying cell of appendix](http://purl.obolibrary.org/obo/CL_0009027) EquivalentTo [transit amplifying cell of gut](http://purl.obolibrary.org/obo/CL_4047017) and ([BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0013486](http://purl.obolibrary.org/obo/UBERON_0013486)) +- [transit amplifying cell of appendix](http://purl.obolibrary.org/obo/CL_0009027) SubClassOf [transit amplifying cell of gut](http://purl.obolibrary.org/obo/CL_4047017) -### sncg GABAergic cortical interneuron `http://purl.obolibrary.org/obo/CL_4023015` + +### transit amplifying cell of colon `http://purl.obolibrary.org/obo/CL_0009011` #### Removed -- [sncg GABAergic cortical interneuron](http://purl.obolibrary.org/obo/CL_4023015) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A GABAergic neuron located in the cerebral cortex that expresses Gamma-synuclein"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:33186530"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [transit amplifying cell of colon](http://purl.obolibrary.org/obo/CL_0009011) EquivalentTo [transit amplifying cell](http://purl.obolibrary.org/obo/CL_0009010) and ([BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0013485](http://purl.obolibrary.org/obo/UBERON_0013485)) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:37824655"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [transit amplifying cell of colon](http://purl.obolibrary.org/obo/CL_0009011) SubClassOf [transit amplifying cell](http://purl.obolibrary.org/obo/CL_0009010) #### Added -- [sncg GABAergic cortical interneuron](http://purl.obolibrary.org/obo/CL_4023015) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A transcriptomically distinct GABAergic neuron located in the cerebral cortex that expresses Gamma-synuclein. The standard transcriptomic reference data for this cell type can be found on the CellxGene census under the collection: 'Transcriptomic cytoarchitecture reveals principles of human neocortex organization', dataset: 'Supercluster: CGE-derived interneurons', Author Categories: 'CrossArea_subclass', clusters Sncg."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://cellxgene.cziscience.com/e/e4ddac12-f48f-4455-8e8d-c2a48a683437.cxg/"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [transit amplifying cell of colon](http://purl.obolibrary.org/obo/CL_0009011) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://cellxgene.cziscience.com/cellguide/CL_0009011"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:33186530"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [transit amplifying cell of colon](http://purl.obolibrary.org/obo/CL_0009011) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:37824655"^^[string](http://www.w3.org/2001/XMLSchema#string) +Transit amplifying cells (TACs) are an intermediate, undifferentiated population between stem cells and differentiated cells. They can be found in multiple regions such as the small intestine and the colon. TACs of the colon, are integral components of the colonic crypts and vital players in the maintenance of colonic tissue. +These cells serve a critical function in the rapid and constant renewal of the epithelium lining the colon, with the whole epithelial surface renewed approximately every 5-7 days. They divide rapidly and progressively differentiate into mature columnar epithelium cells, including enterocytes, goblet cells, and enteroendocrine cells. The continued proliferation of transit amplifying cells is fundamental to maintain the balance in cell population while preventing tissue degeneration and maintaining a state of homeostasis. However, uncontrolled proliferation and compromised differentiation capacity can contribute to the development of colon cancers."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1172/jci.insight.150894"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.3389/fbioe.2023.1189225"^^[string](http://www.w3.org/2001/XMLSchema#string) -### sperm `http://purl.obolibrary.org/obo/CL_0000019` + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://www.sciencedirect.com/topics/immunology-and-microbiology/intestinal-stem-cell"^^[string](http://www.w3.org/2001/XMLSchema#string) -#### Added -- [sperm](http://purl.obolibrary.org/obo/CL_0000019) SubClassOf [eukaryotic cell](http://purl.obolibrary.org/obo/CL_0000255) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1053/j.gastro.2018.08.016"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1016/j.cell.2014.02.057"^^[string](http://www.w3.org/2001/XMLSchema#string) -### spermatid `http://purl.obolibrary.org/obo/CL_0000018` +- [transit amplifying cell of colon](http://purl.obolibrary.org/obo/CL_0009011) EquivalentTo [transit amplifying cell of gut](http://purl.obolibrary.org/obo/CL_4047017) and ([BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0013485](http://purl.obolibrary.org/obo/UBERON_0013485)) -#### Added -- [spermatid](http://purl.obolibrary.org/obo/CL_0000018) SubClassOf [eukaryotic cell](http://purl.obolibrary.org/obo/CL_0000255) +- [transit amplifying cell of colon](http://purl.obolibrary.org/obo/CL_0009011) SubClassOf [transit amplifying cell of gut](http://purl.obolibrary.org/obo/CL_4047017) -### splenic marginal zone macrophage `http://purl.obolibrary.org/obo/CL_0000872` +### transit amplifying cell of gut `http://purl.obolibrary.org/obo/CL_4047017` #### Added -- [splenic marginal zone macrophage](http://purl.obolibrary.org/obo/CL_0000872) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) +- [transit amplifying cell of gut](http://purl.obolibrary.org/obo/CL_4047017) [id](http://www.geneontology.org/formats/oboInOwl#id) "CL:4047017"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [transit amplifying cell of gut](http://purl.obolibrary.org/obo/CL_4047017) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "TA cell"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:20683682"^^[string](http://www.w3.org/2001/XMLSchema#string) -### splenic metallophillic macrophage `http://purl.obolibrary.org/obo/CL_0000873` +- [transit amplifying cell of gut](http://purl.obolibrary.org/obo/CL_4047017) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A transit amplifying cell of the gut epithelium, located in the wall of the intestinal crypt, just above intestinal stem cells from which they derive. These are rapidly dividing cells, capable of multiple rounds of division before differentiating into the various cell types of the gut epithelium (enterocyte, goblet, eneterodendocrine, paneth cells)."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:34497389"^^[string](http://www.w3.org/2001/XMLSchema#string) -#### Added -- [splenic metallophillic macrophage](http://purl.obolibrary.org/obo/CL_0000873) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:20683682"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:33195268"^^[string](http://www.w3.org/2001/XMLSchema#string) -### splenic red pulp macrophage `http://purl.obolibrary.org/obo/CL_0000874` +- [transit amplifying cell of gut](http://purl.obolibrary.org/obo/CL_4047017) [has_broad_synonym](http://www.geneontology.org/formats/oboInOwl#hasBroadSynonym) "transit-amplifying cell"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:24813615"^^[string](http://www.w3.org/2001/XMLSchema#string) -#### Added -- [splenic red pulp macrophage](http://purl.obolibrary.org/obo/CL_0000874) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) +- [transit amplifying cell of gut](http://purl.obolibrary.org/obo/CL_4047017) [contributor](http://purl.org/dc/terms/contributor) [0009-0005-7919-4905](https://orcid.org/0009-0005-7919-4905) +- [transit amplifying cell of gut](http://purl.obolibrary.org/obo/CL_4047017) [label](http://www.w3.org/2000/01/rdf-schema#label) "transit amplifying cell of gut"^^[string](http://www.w3.org/2001/XMLSchema#string) -### splenic white pulp macrophage `http://purl.obolibrary.org/obo/CL_0000876` +- [transit amplifying cell of gut](http://purl.obolibrary.org/obo/CL_4047017) [date](http://purl.org/dc/terms/date) "2024-09-24T10:48:47Z"^^[dateTime](http://www.w3.org/2001/XMLSchema#dateTime) -#### Added -- [splenic white pulp macrophage](http://purl.obolibrary.org/obo/CL_0000876) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) +- Class: [transit amplifying cell of gut](http://purl.obolibrary.org/obo/CL_4047017) +- [transit amplifying cell of gut](http://purl.obolibrary.org/obo/CL_4047017) EquivalentTo [transit amplifying cell](http://purl.obolibrary.org/obo/CL_0009010) and ([BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0013740](http://purl.obolibrary.org/obo/UBERON_0013740)) -### squamous endothelial cell of venule `http://purl.obolibrary.org/obo/CL_0008040` +- [transit amplifying cell of gut](http://purl.obolibrary.org/obo/CL_4047017) SubClassOf [RO_0002207](http://purl.obolibrary.org/obo/RO_0002207) some [intestinal crypt stem cell](http://purl.obolibrary.org/obo/CL_0002250) + +- [transit amplifying cell of gut](http://purl.obolibrary.org/obo/CL_4047017) SubClassOf [transit amplifying cell](http://purl.obolibrary.org/obo/CL_0009010) + +- [transit amplifying cell of gut](http://purl.obolibrary.org/obo/CL_4047017) SubClassOf [BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0013740](http://purl.obolibrary.org/obo/UBERON_0013740) + + +### transit amplifying cell of small intestine `http://purl.obolibrary.org/obo/CL_0009012` #### Removed -- [squamous endothelial cell of venule](http://purl.obolibrary.org/obo/CL_0008040) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "An endothelial cell of the venule that is squamous shaped. This is in contrast to the cubodial shape of high endothelial venule cells."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [comment](http://www.w3.org/2000/01/rdf-schema#comment) "GOC:tfm"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [transit amplifying cell of small intestine](http://purl.obolibrary.org/obo/CL_0009012) EquivalentTo [transit amplifying cell](http://purl.obolibrary.org/obo/CL_0009010) and ([BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0001241](http://purl.obolibrary.org/obo/UBERON_0001241)) + +- [transit amplifying cell of small intestine](http://purl.obolibrary.org/obo/CL_0009012) SubClassOf [transit amplifying cell](http://purl.obolibrary.org/obo/CL_0009010) #### Added -- [squamous endothelial cell of venule](http://purl.obolibrary.org/obo/CL_0008040) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "An endothelial cell of the venule that is squamous shaped. This is in contrast to the cubodial shape of high endothelial venule cells."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:tfm"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [transit amplifying cell of small intestine](http://purl.obolibrary.org/obo/CL_0009012) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://cellxgene.cziscience.com/cellguide/CL_0009012"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [transit amplifying cell of small intestine](http://purl.obolibrary.org/obo/CL_0009012) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. -### squamous epithelial cell `http://purl.obolibrary.org/obo/CL_0000076` +Transit amplifying cells (TACs) represent an intermediate population between stem cells and fully differentiated cells, and can be found in multiple regions such as the colon and the small intestine. The small intestine's efficiency in absorbing nutrients, its protective barrier function, and its innate cellular renewal every few days is largely dependent on the role played by these TACs. +TACs of the small intestine are primarily present in the crypt-villus structure of the intestine, more specifically in the crypt region. They originate from Lgr5+ intestinal stem cells that reside at the base of the crypts. Following their derivation from stem cells, TACs undergo up to six rounds of rapid division over a 48-72 hour period, effectively amplifying the cell population, hence their name. During this process, they gradually migrate upward along the walls of the crypt from where they differentiate into diverse mature cell types such as enterocytes, goblet cells, and Paneth cells. +TACs serve as an important element in the homeostasis and regeneration of the intestinal epithelium, amplifying the pool of cells available for differentiation. They also minimize genetic errors during DNA replication by serving as a 'buffer zone' between the long-lived stem cells and the terminal differentiated cells of the gut lining, thus reducing the potential for propagation of mutation-causing defects. Lastly, TACs play an essential part in gastrointestinal tissue repair following injury or inflammation. Their rapid proliferation and subsequent differentiation abilities often help expedite the wound healing process in the intestinal epithelium."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1101/gad.1674008"^^[string](http://www.w3.org/2001/XMLSchema#string) -#### Added -- [squamous epithelial cell](http://purl.obolibrary.org/obo/CL_0000076) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "Any epithelial cell that is part of some squamous epithelium."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBC:Autogenerated"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1016/j.cell.2014.02.057"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [squamous epithelial cell](http://purl.obolibrary.org/obo/CL_0000076) EquivalentTo [epithelial cell](http://purl.obolibrary.org/obo/CL_0000066) and ([BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0006914](http://purl.obolibrary.org/obo/UBERON_0006914)) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1007/s11894-010-0130-3"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [squamous epithelial cell](http://purl.obolibrary.org/obo/CL_0000076) SubClassOf [BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0006914](http://purl.obolibrary.org/obo/UBERON_0006914) +- [transit amplifying cell of small intestine](http://purl.obolibrary.org/obo/CL_0009012) [depiction](http://xmlns.com/foaf/0.1/depiction) [Small-intestine-cells.png](http://purl.obolibrary.org/obo/cl/images/Small-intestine-cells.png) + - [comment](http://www.w3.org/2000/01/rdf-schema#comment) "Figure depicts a cross section of intestinal villi in the small intestine , including the crypts of Lieberkhun (seen here as ‘crypt’), as well as the layer specific locations of cells that exist within the gastrointestinal tract. Layers depicted here include epithelium (rows of cells bordering villus), submucosa (white space below the epithelium containing networks of neurons and ganglia depicted in pink), muscularis mucosae (blue layer), muscularis propria (referred to here as muscle layer). +ISC: Intestinal Stem Cell +TA: Transit Amplifying Cells"^^[string](http://www.w3.org/2001/XMLSchema#string) -### squamous granulosa cell `http://purl.obolibrary.org/obo/CL_4033083` + - [license](http://purl.org/dc/elements/1.1/license) "http://creativecommons.org/licenses/by/4.0/"^^[string](http://www.w3.org/2001/XMLSchema#string) -#### Added -- [squamous granulosa cell](http://purl.obolibrary.org/obo/CL_4033083) [contributor](http://purl.org/dc/terms/contributor) [0000-0001-6677-8489](https://orcid.org/0000-0001-6677-8489) +- [transit amplifying cell of small intestine](http://purl.obolibrary.org/obo/CL_0009012) EquivalentTo [transit amplifying cell of gut](http://purl.obolibrary.org/obo/CL_4047017) and ([BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0001241](http://purl.obolibrary.org/obo/UBERON_0001241)) -- [squamous granulosa cell](http://purl.obolibrary.org/obo/CL_4033083) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "pre-granulosa cell"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:33914868"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [transit amplifying cell of small intestine](http://purl.obolibrary.org/obo/CL_0009012) SubClassOf [transit amplifying cell of gut](http://purl.obolibrary.org/obo/CL_4047017) -- [squamous granulosa cell](http://purl.obolibrary.org/obo/CL_4033083) [date](http://purl.org/dc/terms/date) "2024-09-24T13:13:24Z"^^[dateTime](http://www.w3.org/2001/XMLSchema#dateTime) -- [squamous granulosa cell](http://purl.obolibrary.org/obo/CL_4033083) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "squamous GC"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003000](http://purl.obolibrary.org/obo/OMO_0003000) +### trigeminal neuron `http://purl.obolibrary.org/obo/CL_4023169` +#### Removed +- [trigeminal neuron](http://purl.obolibrary.org/obo/CL_4023169) SubClassOf [neuron](http://purl.obolibrary.org/obo/CL_0000540) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:33914868"^^[string](http://www.w3.org/2001/XMLSchema#string) +#### Added +- [trigeminal neuron](http://purl.obolibrary.org/obo/CL_4023169) SubClassOf [central nervous system neuron](http://purl.obolibrary.org/obo/CL_2000029) -- [squamous granulosa cell](http://purl.obolibrary.org/obo/CL_4033083) [id](http://www.geneontology.org/formats/oboInOwl#id) "CL:4033083"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [squamous granulosa cell](http://purl.obolibrary.org/obo/CL_4033083) [label](http://www.w3.org/2000/01/rdf-schema#label) "squamous granulosa cell"^^[string](http://www.w3.org/2001/XMLSchema#string) +### trigeminal sensory neuron `http://purl.obolibrary.org/obo/CL_4023170` +#### Removed +- [trigeminal sensory neuron](http://purl.obolibrary.org/obo/CL_4023170) SubClassOf [somatosensory neuron](http://purl.obolibrary.org/obo/CL_4023168) -- [squamous granulosa cell](http://purl.obolibrary.org/obo/CL_4033083) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A granulosa cell that has a squamous morphology and form a single layer around the oocyte in primordial follicles. This cell develops directly into a cuboidal granulosa cell during the primordial-to-primary follicle transition."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:28892263"^^[string](http://www.w3.org/2001/XMLSchema#string) +#### Added +- [trigeminal sensory neuron](http://purl.obolibrary.org/obo/CL_4023170) SubClassOf [BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0003942](http://purl.obolibrary.org/obo/UBERON_0003942) -- [squamous granulosa cell](http://purl.obolibrary.org/obo/CL_4033083) [comment](http://www.w3.org/2000/01/rdf-schema#comment) "Often in literature squamous granulosa cell and pre-granulosa cell are used as synonyms. However, this term only makes reference to the quiescent granulosa cells that surround the primordial ovarian follicle, while a pre-granulosa cell proliferates to form the primordial follicle (and thus cells become the squamous granulosa cells)."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://orcid.org/0000-0001-6677-8489"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [squamous granulosa cell](http://purl.obolibrary.org/obo/CL_4033083) [has_exact_synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "flattened granulosa cell"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:22402964"^^[string](http://www.w3.org/2001/XMLSchema#string) +### trophoblast cell `http://purl.obolibrary.org/obo/CL_0000351` -- Class: [squamous granulosa cell](http://purl.obolibrary.org/obo/CL_4033083) +#### Added +- [trophoblast cell](http://purl.obolibrary.org/obo/CL_0000351) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://cellxgene.cziscience.com/cellguide/CL_0000351"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [squamous granulosa cell](http://purl.obolibrary.org/obo/CL_4033083) SubClassOf [RO_0002210](http://purl.obolibrary.org/obo/RO_0002210) some [cuboidal granulosa cell](http://purl.obolibrary.org/obo/CL_4033084) +- [trophoblast cell](http://purl.obolibrary.org/obo/CL_0000351) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. -- [squamous granulosa cell](http://purl.obolibrary.org/obo/CL_4033083) SubClassOf [RO_0002207](http://purl.obolibrary.org/obo/RO_0002207) some [pre-granulosa cell](http://purl.obolibrary.org/obo/CL_4033066) +Trophoblast cells, originating from the blastocyst's outer layer, are highly specialized and pivotal for embryo development. Their crucial roles include facilitating implantation and contributing to the formation of the placenta, an essential organ for fetal nutrition, gas exchange, and waste removal during pregnancy. +These cells play a crucial role in implantation by adhering to the uterus lining. Post-implantation, some trophoblast cells differentiate, forming syncytiotrophoblasts. These multi-nucleated cells absorb nutrients, release waste, and secrete hormones, including human chorionic gonadotropin (hCG), sustaining pregnancy. +Trophoblast cells also play a crucial role in immune tolerance, preventing the maternal immune system from treating the fetus as foreign. This balance is vital for a healthy pregnancy. Dysfunctional trophoblast cells may lead to complications like miscarriages or preeclampsia, emphasizing their importance in both embryology and reproductive medicine."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://www.ncbi.nlm.nih.gov/books/NBK53245"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [squamous granulosa cell](http://purl.obolibrary.org/obo/CL_4033083) SubClassOf [granulosa cell](http://purl.obolibrary.org/obo/CL_0000501) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1530/JOE-17-0402"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [squamous granulosa cell](http://purl.obolibrary.org/obo/CL_4033083) SubClassOf [BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0003981](http://purl.obolibrary.org/obo/UBERON_0003981) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1016/j.jri.2023.103811"^^[string](http://www.w3.org/2001/XMLSchema#string) -### sst GABAergic cortical interneuron `http://purl.obolibrary.org/obo/CL_4023017` +### tuft cell of appendix `http://purl.obolibrary.org/obo/CL_0009020` #### Removed -- [sst GABAergic cortical interneuron](http://purl.obolibrary.org/obo/CL_4023017) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A GABAergic neuron located in the cerebral cortex that expresses somatostatin (sst)"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:27477017"^^[string](http://www.w3.org/2001/XMLSchema#string) - - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:37824655"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [tuft cell of appendix](http://purl.obolibrary.org/obo/CL_0009020) SubClassOf [epithelial cell of appendix](http://purl.obolibrary.org/obo/CL_1000405) -- [sst GABAergic cortical interneuron](http://purl.obolibrary.org/obo/CL_4023017) EquivalentTo [interneuron](http://purl.obolibrary.org/obo/CL_0000099) and ([RO_0002100](http://purl.obolibrary.org/obo/RO_0002100) some [UBERON_0000956](http://purl.obolibrary.org/obo/UBERON_0000956)) and ([RO_0002215](http://purl.obolibrary.org/obo/RO_0002215) some [GO_0061534](http://purl.obolibrary.org/obo/GO_0061534)) and ([RO_0002292](http://purl.obolibrary.org/obo/RO_0002292) some [PR_000015665](http://purl.obolibrary.org/obo/PR_000015665)) +#### Added +- [tuft cell of appendix](http://purl.obolibrary.org/obo/CL_0009020) SubClassOf [BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0001154](http://purl.obolibrary.org/obo/UBERON_0001154) -- [sst GABAergic cortical interneuron](http://purl.obolibrary.org/obo/CL_4023017) SubClassOf [cerebral cortex GABAergic interneuron](http://purl.obolibrary.org/obo/CL_0010011) -- [sst GABAergic cortical interneuron](http://purl.obolibrary.org/obo/CL_4023017) SubClassOf [BFO_0000002](http://purl.obolibrary.org/obo/BFO_0000002) +### tuft cell of colon `http://purl.obolibrary.org/obo/CL_0009041` +#### Removed +- [tuft cell of colon](http://purl.obolibrary.org/obo/CL_0009041) SubClassOf [colon epithelial cell](http://purl.obolibrary.org/obo/CL_0011108) #### Added -- [sst GABAergic cortical interneuron](http://purl.obolibrary.org/obo/CL_4023017) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "SOM+ inhibitory interneuron"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:30001424"^^[string](http://www.w3.org/2001/XMLSchema#string) - -- [sst GABAergic cortical interneuron](http://purl.obolibrary.org/obo/CL_4023017) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "SST+ IN"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:33742131"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [tuft cell of colon](http://purl.obolibrary.org/obo/CL_0009041) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. -- [sst GABAergic cortical interneuron](http://purl.obolibrary.org/obo/CL_4023017) [comment](http://www.w3.org/2000/01/rdf-schema#comment) "In the mouse cortex, sst GABAergic cortical interneurons show heterogeneous electrophysiological signatures varying between low-threshold spiking (LTS), regular-spiking and fast-spiking (Song, Y. H., Yoon, J., & Lee, S. H. 2021). Sst GABAergic cortical interneurons have multiple functional roles in the brain. In the mouse, they involved in the generation of slow-waves during the sleep phase of non-rapid eye-movement (NREM) (Funk, C. M. et al., 2017), they maintain synaptic plasticity during motor learning (Adler, A., Zhao, R., et al., 2021), they enhance visual perception in the V1 cortical area by suppressing the activity of pyramidal excitatory neurons (Song, YH. et al., 2020). In humans, malfunctioning of sst GABAergic cortical interneurons is associated with neurodegenerative and psychiatric disorders such as Parkinson's disease, Alzheimer's disease, major depressive disorder, bipolar disorder and schizophrenia as individuals affected by these pathologies show a decrease of expression of SST in the brain (Song YH., Yoon J. et al., 2021)."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:32494634"^^[string](http://www.w3.org/2001/XMLSchema#string) +Tuft cells, also often referred to as brush cells or caveolated cells, are highly specialized sensory cells found in the colon, among other organs. They were named for their unique appearance under an electron microscope, which presents a distinctive ‘tuft-like’ morphology. They are characterized by apical microvilli, arranged in an irregular tuft that confers a dome-like shape. These cells comprise only a small fraction of the cells in the epithelial layer of the colon, making them among the least populous cell types in this region. +Tuft cells in the colon primarily function as chemosensory cells that can sense and respond to environmental changes. These cells can detect and respond to microbial metabolites, helping initiate immune responses against potential threats. +Recent studies have revealed that tuft cells play a role in responding to intestinal parasitic infections. When a gastrointestinal parasite infects the colon, tuft cells are activated and release the cytokine IL-25. This action increases the production of tuft cells and triggers essential Th2 immune responses to expel the parasites. Also, the removal of tuft cells has been linked to increased susceptibility to these infections. However, overactivity of tuft cells has been associated with inflammatory bowel disease, highlighting the need for a delicate balance of tuft cell function to maintain colon homeostasis."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.3389/fimmu.2022.822867"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:30792151"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1371/journal.ppat.1010318"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:33742131"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1152/ajpgi.00073.2017"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:28821651"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [tuft cell of colon](http://purl.obolibrary.org/obo/CL_0009041) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://cellxgene.cziscience.com/cellguide/CL_0009041"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [sst GABAergic cortical interneuron](http://purl.obolibrary.org/obo/CL_4023017) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "somatostatin-expressing inhibitory interneuron"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:30001424"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [tuft cell of colon](http://purl.obolibrary.org/obo/CL_0009041) SubClassOf [BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0001155](http://purl.obolibrary.org/obo/UBERON_0001155) -- [sst GABAergic cortical interneuron](http://purl.obolibrary.org/obo/CL_4023017) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A transcriptomically distinct GABAergic neuron located in the cerebral cortex that expresses somatostatin (sst). The standard transcriptomic reference data for this cell type can be found on the CellxGene census under the collection: 'Transcriptomic cytoarchitecture reveals principles of human neocortex organization', dataset: 'Supercluster: MGE-derived interneurons', Author Categories: 'CrossArea_subclass', cluster Sst."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:27477017"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:37824655"^^[string](http://www.w3.org/2001/XMLSchema#string) +### tuft cell of small intestine `http://purl.obolibrary.org/obo/CL_0009080` - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:33742131"^^[string](http://www.w3.org/2001/XMLSchema#string) +#### Added +- [tuft cell of small intestine](http://purl.obolibrary.org/obo/CL_0009080) [depiction](http://xmlns.com/foaf/0.1/depiction) [Small-intestine-cells.png](http://purl.obolibrary.org/obo/cl/images/Small-intestine-cells.png) + - [license](http://purl.org/dc/terms/license) "http://creativecommons.org/licenses/by/4.0/"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://cellxgene.cziscience.com/e/9c63201d-bfd9-41a8-bbbc-18d947556f3d.cxg/"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [comment](http://www.w3.org/2000/01/rdf-schema#comment) "Figure depicts a cross section of intestinal villi in the small intestine, including the crypts of Lieberkuhn (seen here as ‘crypt’), as well as the layer specific locations of cells that exist within the gastrointestinal tract. Layers depicted here include epithelium (rows of cells bordering villus), submucosa (white space below the epithelium containing networks of neurons and ganglia depicted in pink), muscularis mucosae (blue layer), muscularis propria (referred to here as muscle layer). -- [sst GABAergic cortical interneuron](http://purl.obolibrary.org/obo/CL_4023017) EquivalentTo [medial ganglionic eminence derived GABAergic cortical interneuron](http://purl.obolibrary.org/obo/CL_4023069) and ([RO_0002100](http://purl.obolibrary.org/obo/RO_0002100) some [UBERON_0000956](http://purl.obolibrary.org/obo/UBERON_0000956)) and ([RO_0002215](http://purl.obolibrary.org/obo/RO_0002215) some [GO_0061534](http://purl.obolibrary.org/obo/GO_0061534)) and ([RO_0002292](http://purl.obolibrary.org/obo/RO_0002292) some [PR_000015665](http://purl.obolibrary.org/obo/PR_000015665)) +ISC: Intestinal Stem Cell +TA: Transit Amplifying Cells"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [sst GABAergic cortical interneuron](http://purl.obolibrary.org/obo/CL_4023017) SubClassOf [medial ganglionic eminence derived GABAergic cortical interneuron](http://purl.obolibrary.org/obo/CL_4023069) +- [tuft cell of small intestine](http://purl.obolibrary.org/obo/CL_0009080) SubClassOf [BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0001902](http://purl.obolibrary.org/obo/UBERON_0001902) -### sst chodl GABAergic cortical interneuron `http://purl.obolibrary.org/obo/CL_4023121` +### tufted pyramidal neuron `http://purl.obolibrary.org/obo/CL_4023094` #### Removed -- [sst chodl GABAergic cortical interneuron](http://purl.obolibrary.org/obo/CL_4023121) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A sst GABAergic cortical interneuron that also expresses Chodl. These neurons are rare and correspond to the only known cortical interneurons with long-range projection."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:15845086"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [tufted pyramidal neuron](http://purl.obolibrary.org/obo/CL_4023094) EquivalentTo [CNS neuron (sensu Vertebrata)](http://purl.obolibrary.org/obo/CL_0000117) and ([RO_0000053](http://purl.obolibrary.org/obo/RO_0000053) some [PATO_0070018](http://purl.obolibrary.org/obo/PATO_0070018)) + +- [tufted pyramidal neuron](http://purl.obolibrary.org/obo/CL_4023094) SubClassOf [CNS neuron (sensu Vertebrata)](http://purl.obolibrary.org/obo/CL_0000117) + +#### Added +- [tufted pyramidal neuron](http://purl.obolibrary.org/obo/CL_4023094) EquivalentTo [neuron](http://purl.obolibrary.org/obo/CL_0000540) and ([RO_0000053](http://purl.obolibrary.org/obo/RO_0000053) some [PATO_0070018](http://purl.obolibrary.org/obo/PATO_0070018)) + - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:31209381"^^[string](http://www.w3.org/2001/XMLSchema#string) +### type 1 cone bipolar cell (sensu Mus) `http://purl.obolibrary.org/obo/CL_0000753` + +#### Added +- [type 1 cone bipolar cell (sensu Mus)](http://purl.obolibrary.org/obo/CL_0000753) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl/cl-base#cellxgene_subset) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:33372656"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:37824655"^^[string](http://www.w3.org/2001/XMLSchema#string) +### type 2 cone bipolar cell (sensu Mus) `http://purl.obolibrary.org/obo/CL_0000754` #### Added -- [sst chodl GABAergic cortical interneuron](http://purl.obolibrary.org/obo/CL_4023121) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A transcriptomically distinct sst GABAergic cortical interneuron that also expresses Chodl. These neurons are rare and correspond to the only known cortical interneurons with long-range projection. The standard transcriptomic reference data for this cell type can be found on the CellxGene census under the collection: 'Transcriptomic cytoarchitecture reveals principles of human neocortex organization', dataset: 'Supercluster: MGE-derived interneurons', Author Categories: 'CrossArea_subclass', clusters Sst Chodl."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:15845086"^^[string](http://www.w3.org/2001/XMLSchema#string) - - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:31209381"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [type 2 cone bipolar cell (sensu Mus)](http://purl.obolibrary.org/obo/CL_0000754) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl/cl-base#cellxgene_subset) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:33372656"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:37824655"^^[string](http://www.w3.org/2001/XMLSchema#string) +### type 3a cone bipolar cell `http://purl.obolibrary.org/obo/CL_0004213` - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://cellxgene.cziscience.com/e/9c63201d-bfd9-41a8-bbbc-18d947556f3d.cxg/"^^[string](http://www.w3.org/2001/XMLSchema#string) +#### Added +- [type 3a cone bipolar cell](http://purl.obolibrary.org/obo/CL_0004213) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl/cl-base#cellxgene_subset) -### stem cell `http://purl.obolibrary.org/obo/CL_0000034` +### type 3b cone bipolar cell `http://purl.obolibrary.org/obo/CL_0004214` #### Added -- [stem cell](http://purl.obolibrary.org/obo/CL_0000034) SubClassOf [eukaryotic cell](http://purl.obolibrary.org/obo/CL_0000255) +- [type 3b cone bipolar cell](http://purl.obolibrary.org/obo/CL_0004214) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl/cl-base#cellxgene_subset) -### stratified cuboidal epithelial cell `http://purl.obolibrary.org/obo/CL_0000241` +### type 4 cone bipolar cell (sensu Mus) `http://purl.obolibrary.org/obo/CL_0000756` #### Added -- [stratified cuboidal epithelial cell](http://purl.obolibrary.org/obo/CL_0000241) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A stratified epithelial cell that is part of cuboidal epithelium, characterized by multiple layers of cuboidal cells forming the apical layer. This provides a protective lining for ducts in large glands, such as sweat glands."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:30422572"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [type 4 cone bipolar cell (sensu Mus)](http://purl.obolibrary.org/obo/CL_0000756) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl/cl-base#cellxgene_subset) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Stratified_cuboidal_epithelium"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [stratified cuboidal epithelial cell](http://purl.obolibrary.org/obo/CL_0000241) EquivalentTo [stratified epithelial cell](http://purl.obolibrary.org/obo/CL_0000079) and ([BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0010077](http://purl.obolibrary.org/obo/UBERON_0010077)) +### type 5 cone bipolar cell (sensu Mus) `http://purl.obolibrary.org/obo/CL_0000757` -- [stratified cuboidal epithelial cell](http://purl.obolibrary.org/obo/CL_0000241) SubClassOf [BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0010077](http://purl.obolibrary.org/obo/UBERON_0010077) +#### Added +- [type 5 cone bipolar cell (sensu Mus)](http://purl.obolibrary.org/obo/CL_0000757) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl/cl-base#cellxgene_subset) -### stratified epithelial cell `http://purl.obolibrary.org/obo/CL_0000079` +### type 5a cone bipolar cell `http://purl.obolibrary.org/obo/CL_0004215` #### Added -- [stratified epithelial cell](http://purl.obolibrary.org/obo/CL_0000079) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "An epithelial cell, organized into multiple layers, with only the basal layer being in contact with the basement membrane."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "doi:/10.1016/B978-0-12-410424-2.00003-2"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [type 5a cone bipolar cell](http://purl.obolibrary.org/obo/CL_0004215) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl/cl-base#cellxgene_subset) + - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Epithelium"^^[string](http://www.w3.org/2001/XMLSchema#string) +### type 5b cone bipolar cell `http://purl.obolibrary.org/obo/CL_0004216` - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://www.biologyonline.com/dictionary/stratified-epithelium"^^[string](http://www.w3.org/2001/XMLSchema#string) +#### Added +- [type 5b cone bipolar cell](http://purl.obolibrary.org/obo/CL_0004216) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl/cl-base#cellxgene_subset) -### stratified squamous epithelial cell `http://purl.obolibrary.org/obo/CL_0000240` +### type 6 cone bipolar cell (sensu Mus) `http://purl.obolibrary.org/obo/CL_0000758` #### Added -- [stratified squamous epithelial cell](http://purl.obolibrary.org/obo/CL_0000240) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A stratified epithelial cell that is part of squamous epithelium, characterized by multiple layers of cells. The basal layer is directly attached to the basement membrane and the apical layer consists of flattened squamous cells. This provides a protective barrier, commonly found in areas subject to abrasion, such as the skin, oral cavity, and esophagus."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Epithelium"^^[string](http://www.w3.org/2001/XMLSchema#string) - - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:30422572"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [type 6 cone bipolar cell (sensu Mus)](http://purl.obolibrary.org/obo/CL_0000758) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl/cl-base#cellxgene_subset) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Stratified_squamous_epithelium"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [stratified squamous epithelial cell](http://purl.obolibrary.org/obo/CL_0000240) EquivalentTo [stratified epithelial cell](http://purl.obolibrary.org/obo/CL_0000079) and ([BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0006915](http://purl.obolibrary.org/obo/UBERON_0006915)) +### type 7 cone bipolar cell (sensu Mus) `http://purl.obolibrary.org/obo/CL_0000759` -- [stratified squamous epithelial cell](http://purl.obolibrary.org/obo/CL_0000240) SubClassOf [BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0006915](http://purl.obolibrary.org/obo/UBERON_0006915) +#### Added +- [type 7 cone bipolar cell (sensu Mus)](http://purl.obolibrary.org/obo/CL_0000759) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl/cl-base#cellxgene_subset) -### striatal PTHLH MOXD1 expressing interneuron `http://purl.obolibrary.org/obo/CL_4042024` +### type 8 cone bipolar cell (sensu Mus) `http://purl.obolibrary.org/obo/CL_0000760` #### Added -- [striatal PTHLH MOXD1 expressing interneuron](http://purl.obolibrary.org/obo/CL_4042024) [date](http://purl.org/dc/terms/date) "2024-09-17T10:26:57Z"^^[dateTime](http://www.w3.org/2001/XMLSchema#dateTime) +- [type 8 cone bipolar cell (sensu Mus)](http://purl.obolibrary.org/obo/CL_0000760) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl/cl-base#cellxgene_subset) -- [striatal PTHLH MOXD1 expressing interneuron](http://purl.obolibrary.org/obo/CL_4042024) [id](http://www.geneontology.org/formats/oboInOwl#id) "CL:4042024"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [striatal PTHLH MOXD1 expressing interneuron](http://purl.obolibrary.org/obo/CL_4042024) [contributor](http://purl.org/dc/terms/contributor) [0000-0002-0098-8958](https://orcid.org/0000-0002-0098-8958) +### type 9 cone bipolar cell (sensu Mus) `http://purl.obolibrary.org/obo/CL_0000761` -- [striatal PTHLH MOXD1 expressing interneuron](http://purl.obolibrary.org/obo/CL_4042024) [label](http://www.w3.org/2000/01/rdf-schema#label) "striatal PTHLH MOXD1 expressing interneuron"^^[string](http://www.w3.org/2001/XMLSchema#string) +#### Added +- [type 9 cone bipolar cell (sensu Mus)](http://purl.obolibrary.org/obo/CL_0000761) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl/cl-base#cellxgene_subset) -- [striatal PTHLH MOXD1 expressing interneuron](http://purl.obolibrary.org/obo/CL_4042024) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A pthlh-expressing interneuron that expresses MOXD1 and has its soma in a striatum."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:30134177"^^[string](http://www.w3.org/2001/XMLSchema#string) -- Class: [striatal PTHLH MOXD1 expressing interneuron](http://purl.obolibrary.org/obo/CL_4042024) +### type A cell of stomach `http://purl.obolibrary.org/obo/CL_0002264` +#### Removed +- [type A cell of stomach](http://purl.obolibrary.org/obo/CL_0002264) EquivalentTo [type A enteroendocrine cell](http://purl.obolibrary.org/obo/CL_0002067) and ([BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0000945](http://purl.obolibrary.org/obo/UBERON_0000945)) -- [striatal PTHLH MOXD1 expressing interneuron](http://purl.obolibrary.org/obo/CL_4042024) SubClassOf [RO_0002292](http://purl.obolibrary.org/obo/RO_0002292) some [PR_000010529](http://purl.obolibrary.org/obo/PR_000010529) +- [type A cell of stomach](http://purl.obolibrary.org/obo/CL_0002264) SubClassOf [glandular epithelial cell of stomach](http://purl.obolibrary.org/obo/CL_0002659) -- [striatal PTHLH MOXD1 expressing interneuron](http://purl.obolibrary.org/obo/CL_4042024) SubClassOf [striatal pthlh-expressing interneuron](http://purl.obolibrary.org/obo/CL_4042023) +#### Added +- [type A cell of stomach](http://purl.obolibrary.org/obo/CL_0002264) EquivalentTo [type A enteroendocrine cell](http://purl.obolibrary.org/obo/CL_0002067) and ([BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0001276](http://purl.obolibrary.org/obo/UBERON_0001276)) +- [type A cell of stomach](http://purl.obolibrary.org/obo/CL_0002264) SubClassOf [stomach enteroendocrine cell](http://purl.obolibrary.org/obo/CL_1001517) -### striatal pthlh-expressing interneuron `http://purl.obolibrary.org/obo/CL_4042023` -#### Added -- [striatal pthlh-expressing interneuron](http://purl.obolibrary.org/obo/CL_4042023) [comment](http://www.w3.org/2000/01/rdf-schema#comment) "According to spatial transcriptomic data in the human striatum, pthlh-expressing interneurons are one of the most abundant population of interneurons in the striatum (Leonardo D. Garma, et al., 2024)."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:37292997"^^[string](http://www.w3.org/2001/XMLSchema#string) +### type A enteroendocrine cell `http://purl.obolibrary.org/obo/CL_0002067` +#### Removed +- [type A enteroendocrine cell](http://purl.obolibrary.org/obo/CL_0002067) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. -- [striatal pthlh-expressing interneuron](http://purl.obolibrary.org/obo/CL_4042023) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "PTHLH/PVALB cell"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:37292997"^^[string](http://www.w3.org/2001/XMLSchema#string) +Type A enteroendocrine cells, also known as alpha cells or A cells, are a species of endocrine cells primarily located in the pancreatic islets of Langerhans; they have also been identified within the lining of the stomach. Functionally, these cells are pivotal in glucose metabolism and homeostasis, accounting for about 20% of the total population of cells in the pancreatic islets. +The primary role of type A enteroendocrine cells involves the synthesis, storage, and secretion of the peptide hormone glucagon, which is critical in energy regulation throughout the body. In response to a decrease in blood glucose levels, the pancreatic A cells are stimulated to secrete glucagon into the bloodstream. Glucagon acts on its target cells, mainly in the liver, to stimulate glycogenolysis and gluconeogenesis processes, thereby increasing blood glucose levels back to normal. In this way, pancreatic A cells play an integral role in maintaining glucose homeostasis and preventing hypoglycemia. +Pancreatic A cells also participate in the local regulation of islet activities as glucagon acts through glucagon receptors on A, B and D type cells within the islets. Recent studies have also shown that Pancreatic A cells play a role in the generation and regeneration of B type cells. Following beta cell injuries pancreatic A cells increase in numbers and produce Glucagon-like peptide-1 (GLP-1), which increases the proliferation and cytoprotection of beta cells. In response to extreme injury of B type cells pancreatic A cells can transform (transdifferentiate) into functioning B type cells. +Until recently, glucagon has been considered a pancreas-specific hormone; however, extrapancreatic glucagon has been reported in patients who had undergone complete, and glucagon-positive cells been identified in the human stomach, indicating that Type A enteroendocrine cells are not restricted to the pancreas."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.2337/dbi19-0002"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [striatal pthlh-expressing interneuron](http://purl.obolibrary.org/obo/CL_4042023) [date](http://purl.org/dc/terms/date) "2024-09-17T10:20:15Z"^^[dateTime](http://www.w3.org/2001/XMLSchema#dateTime) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.2337/db15-1541"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [striatal pthlh-expressing interneuron](http://purl.obolibrary.org/obo/CL_4042023) [label](http://www.w3.org/2000/01/rdf-schema#label) "striatal pthlh-expressing interneuron"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.3389/fphys.2012.00349/full"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [striatal pthlh-expressing interneuron](http://purl.obolibrary.org/obo/CL_4042023) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A GABAergic interneuron expressing PTHLH and PVALB that has its soma in a striatum. This GABAergic interneuron type presents a spatial expression gradient of PVALB in the mouse striatum."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:30134177"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1016/j.diabres.2018.06.013"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:37292997"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1210/en.2016-1748"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [striatal pthlh-expressing interneuron](http://purl.obolibrary.org/obo/CL_4042023) [id](http://www.geneontology.org/formats/oboInOwl#id) "CL:4042023"^^[string](http://www.w3.org/2001/XMLSchema#string) +#### Added +- [type A enteroendocrine cell](http://purl.obolibrary.org/obo/CL_0002067) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl/cl-base#cellxgene_subset) -- [striatal pthlh-expressing interneuron](http://purl.obolibrary.org/obo/CL_4042023) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "PTHLH +/PVALB+ interneuron"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:37292997"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [type A enteroendocrine cell](http://purl.obolibrary.org/obo/CL_0002067) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. -- [striatal pthlh-expressing interneuron](http://purl.obolibrary.org/obo/CL_4042023) [contributor](http://purl.org/dc/terms/contributor) [0000-0002-0098-8958](https://orcid.org/0000-0002-0098-8958) +Type A enteroendocrine cells, also known as alpha cells or A cells, are a species of endocrine cells primarily located in the pancreatic islets of Langerhans; they have also been identified within the lining of the stomach. Functionally, these cells are pivotal in glucose metabolism and homeostasis, accounting for about 20% of the total population of cells in the pancreatic islets. +The primary role of type A enteroendocrine cells involves the synthesis, storage, and secretion of the peptide hormone glucagon, which is critical in energy regulation throughout the body. In response to a decrease in blood glucose levels, the pancreatic A cells are stimulated to secrete glucagon into the bloodstream. Glucagon acts on its target cells, mainly in the liver, to stimulate glycogenolysis and gluconeogenesis processes, thereby increasing blood glucose levels back to normal. In this way, pancreatic A cells play an integral role in maintaining glucose homeostasis and preventing hypoglycemia. +Pancreatic A cells also participate in the local regulation of islet activities as glucagon acts through glucagon receptors on A, B and D type cells within the islets. Recent studies have also shown that Pancreatic A cells play a role in the generation and regeneration of B type cells. Following beta cell injuries pancreatic A cells increase in numbers and produce Glucagon-like peptide-1 (GLP-1), which increases the proliferation and cytoprotection of beta cells. In response to extreme injury of B type cells pancreatic A cells can transform (transdifferentiate) into functioning B type cells. +Until recently, glucagon has been considered a pancreas-specific hormone; however, extrapancreatic glucagon has been reported in patients who had undergone complete, and glucagon-positive cells been identified in the human stomach, indicating that Type A enteroendocrine cells are not restricted to the pancreas."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.2337/dbi19-0002"^^[string](http://www.w3.org/2001/XMLSchema#string) -- Class: [striatal pthlh-expressing interneuron](http://purl.obolibrary.org/obo/CL_4042023) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.2337/db15-1541"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [striatal pthlh-expressing interneuron](http://purl.obolibrary.org/obo/CL_4042023) SubClassOf [CNS interneuron](http://purl.obolibrary.org/obo/CL_0000402) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.3389/fphys.2012.00349/full"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [striatal pthlh-expressing interneuron](http://purl.obolibrary.org/obo/CL_4042023) SubClassOf [RO_0002292](http://purl.obolibrary.org/obo/RO_0002292) some [PR_000013502](http://purl.obolibrary.org/obo/PR_000013502) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1016/j.diabres.2018.06.013"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [striatal pthlh-expressing interneuron](http://purl.obolibrary.org/obo/CL_4042023) SubClassOf [BFO_0000002](http://purl.obolibrary.org/obo/BFO_0000002) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1210/en.2016-1748"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [striatal pthlh-expressing interneuron](http://purl.obolibrary.org/obo/CL_4042023) SubClassOf [RO_0002100](http://purl.obolibrary.org/obo/RO_0002100) some [UBERON_0002435](http://purl.obolibrary.org/obo/UBERON_0002435) -- [striatal pthlh-expressing interneuron](http://purl.obolibrary.org/obo/CL_4042023) SubClassOf [RO_0002292](http://purl.obolibrary.org/obo/RO_0002292) some [PR_000013433](http://purl.obolibrary.org/obo/PR_000013433) +### type D cell of colon `http://purl.obolibrary.org/obo/CL_0002265` -- [striatal pthlh-expressing interneuron](http://purl.obolibrary.org/obo/CL_4042023) SubClassOf [GABAergic interneuron](http://purl.obolibrary.org/obo/CL_0011005) +#### Added +- [type D cell of colon](http://purl.obolibrary.org/obo/CL_0002265) SubClassOf [colon glandular cell](http://purl.obolibrary.org/obo/CL_1001588) -### striated cell of salivary gland `http://purl.obolibrary.org/obo/CL_4052049` +### type D cell of stomach `http://purl.obolibrary.org/obo/CL_0002267` +#### Removed +- [type D cell of stomach](http://purl.obolibrary.org/obo/CL_0002267) EquivalentTo [type D enteroendocrine cell](http://purl.obolibrary.org/obo/CL_0000502) and ([BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0000945](http://purl.obolibrary.org/obo/UBERON_0000945)) #### Added -- [striated cell of salivary gland](http://purl.obolibrary.org/obo/CL_4052049) [has_broad_synonym](http://www.geneontology.org/formats/oboInOwl#hasBroadSynonym) "SD cells"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:11590591"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [type D cell of stomach](http://purl.obolibrary.org/obo/CL_0002267) EquivalentTo [type D enteroendocrine cell](http://purl.obolibrary.org/obo/CL_0000502) and ([BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0001276](http://purl.obolibrary.org/obo/UBERON_0001276)) -- [striated cell of salivary gland](http://purl.obolibrary.org/obo/CL_4052049) [contributor](http://purl.org/dc/terms/contributor) [0009-0000-8480-9277](https://orcid.org/0009-0000-8480-9277) +- [type D cell of stomach](http://purl.obolibrary.org/obo/CL_0002267) SubClassOf [stomach neuroendocrine cell](http://purl.obolibrary.org/obo/CL_1000222) -- [striated cell of salivary gland](http://purl.obolibrary.org/obo/CL_4052049) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "An columnar/cuboidal epithelial cell that is part of the striated duct of salivary gland, characterized by basal striations formed by infoldings of the plasma membrane. This cell play a crucial role in modifying the electrolyte composition and concentration of saliva through active ion transport, particularly the absorption of sodium and secretion of potassium."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:30855909"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:36726292"^^[string](http://www.w3.org/2001/XMLSchema#string) +### type D enteroendocrine cell `http://purl.obolibrary.org/obo/CL_0000502` +#### Removed +- [type D enteroendocrine cell](http://purl.obolibrary.org/obo/CL_0000502) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:34147989"^^[string](http://www.w3.org/2001/XMLSchema#string) +Type D enteroendocrine cells, also known as D or delta cells, are specialized hormone-releasing cells found in the pancreas and also scattered throughout the lining of the gastrointestinal tract in mammals, notably within the stomach and the upper part of the small intestine known as the duodenum. The primary role of D cells is to produce and secrete somatostatin, a potent paracrine inhibitor. +In the gastrointestinal tract, somatostatin slows down digestion. It reduces gastric acid secretion and slows down the rate of gastric emptying, thereby prolonging and controling the digestive p. Functionally, these effects are aimed at sustaining nutrient absorption to optimize energy extraction from consumed food. +In the pancreas, D cells maintain a vital role in endocrine regulation. D cells in the pancreatic islands secrete somatostatin to inhibit the release of both insulin and glucagon from type A cells and B cells, glucoregulatory hormones that control blood sugar levels. Hence, D cells contribute considerably to the homeostasis of the body's metabolic processes. It is also noteworthy that dysfunctional D cells or irregular somatostatin signaling has been associated with certain pathologies such as neuroendocrine tumors and gastric ulcers."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1093/annonc/mdh216"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [striated cell of salivary gland](http://purl.obolibrary.org/obo/CL_4052049) [contributor](http://purl.org/dc/terms/contributor) [0000-0003-4389-9821](https://orcid.org/0000-0003-4389-9821) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1038/s41574-018-0020-6"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [striated cell of salivary gland](http://purl.obolibrary.org/obo/CL_4052049) [has_broad_synonym](http://www.geneontology.org/formats/oboInOwl#hasBroadSynonym) "striated duct cells"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:11590591"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1016/j.pharmthera.2015.05.007"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [striated cell of salivary gland](http://purl.obolibrary.org/obo/CL_4052049) [label](http://www.w3.org/2000/01/rdf-schema#label) "striated cell of salivary gland"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://www.sciencedirect.com/topics/neuroscience/somatostatin-cell"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [striated cell of salivary gland](http://purl.obolibrary.org/obo/CL_4052049) [date](http://purl.org/dc/terms/date) "2024-09-11T10:00:25Z"^^[dateTime](http://www.w3.org/2001/XMLSchema#dateTime) +#### Added +- [type D enteroendocrine cell](http://purl.obolibrary.org/obo/CL_0000502) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. -- [striated cell of salivary gland](http://purl.obolibrary.org/obo/CL_4052049) [id](http://www.geneontology.org/formats/oboInOwl#id) "CL:4052049"^^[string](http://www.w3.org/2001/XMLSchema#string) +Type D enteroendocrine cells, also known as D or delta cells, are specialized hormone-releasing cells found in the pancreas and also scattered throughout the lining of the gastrointestinal tract in mammals, notably within the stomach and the upper part of the small intestine known as the duodenum. The primary role of D cells is to produce and secrete somatostatin, a potent paracrine inhibitor. +In the gastrointestinal tract, somatostatin slows down digestion. It reduces gastric acid secretion and slows down the rate of gastric emptying, thereby prolonging and controling the digestive p. Functionally, these effects are aimed at sustaining nutrient absorption to optimize energy extraction from consumed food. +In the pancreas, D cells maintain a vital role in endocrine regulation. D cells in the pancreatic islands secrete somatostatin to inhibit the release of both insulin and glucagon from type A cells and B cells, glucoregulatory hormones that control blood sugar levels. Hence, D cells contribute considerably to the homeostasis of the body's metabolic processes. It is also noteworthy that dysfunctional D cells or irregular somatostatin signaling has been associated with certain pathologies such as neuroendocrine tumors and gastric ulcers."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1093/annonc/mdh216"^^[string](http://www.w3.org/2001/XMLSchema#string) -- Class: [striated cell of salivary gland](http://purl.obolibrary.org/obo/CL_4052049) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1038/s41574-018-0020-6"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [striated cell of salivary gland](http://purl.obolibrary.org/obo/CL_4052049) EquivalentTo [columnar/cuboidal epithelial cell](http://purl.obolibrary.org/obo/CL_0000075) and ([BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0014729](http://purl.obolibrary.org/obo/UBERON_0014729)) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1016/j.pharmthera.2015.05.007"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [striated cell of salivary gland](http://purl.obolibrary.org/obo/CL_4052049) SubClassOf [duct epithelial cell](http://purl.obolibrary.org/obo/CL_0000068) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://www.sciencedirect.com/topics/neuroscience/somatostatin-cell"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [striated cell of salivary gland](http://purl.obolibrary.org/obo/CL_4052049) SubClassOf [BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0015766](http://purl.obolibrary.org/obo/UBERON_0015766) +- [type D enteroendocrine cell](http://purl.obolibrary.org/obo/CL_0000502) SubClassOf [neuroendocrine cell](http://purl.obolibrary.org/obo/CL_0000165) -- [striated cell of salivary gland](http://purl.obolibrary.org/obo/CL_4052049) SubClassOf [salivary gland glandular cell](http://purl.obolibrary.org/obo/CL_1001596) -- [striated cell of salivary gland](http://purl.obolibrary.org/obo/CL_4052049) SubClassOf [RO_0002215](http://purl.obolibrary.org/obo/RO_0002215) some [GO_0036376](http://purl.obolibrary.org/obo/GO_0036376) +### type EC enteroendocrine cell `http://purl.obolibrary.org/obo/CL_0000577` +#### Removed +- [type EC enteroendocrine cell](http://purl.obolibrary.org/obo/CL_0000577) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. -- [striated cell of salivary gland](http://purl.obolibrary.org/obo/CL_4052049) SubClassOf [BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0014729](http://purl.obolibrary.org/obo/UBERON_0014729) +Type EC enteroendocrine cells, also known as enterochromaffin cells, are a vital hormone-secreting cell type found in the gastrointestinal tract. These cells are named after their location in the intestines (“entero”) and because they are stainable by chromium salts (“chromaffin”). +The primary function of type EC enteroendocrine cells is to act as chemosensors and lies in their capacity to produce and secrete serotonin, also known as 5-hydroxytryptamine (5-HT). Serotonin is a neurotransmitter that plays a significant role in modulating motility, secretion, vasodilation, perception of pain, and appetite in the gastrointestinal system. However, its function is not limited to the gastrointestinal tract; once secreted, serotonin is distributed via the bloodstream and contributes to regulating mood, appetite, and sleep in the brain. +Via specific chemosensory receptors type EC enteroendocrine cells are able to respond to various environmental, metabolic, and homeostatic stimuli and transduce information from the gut to the nervous system: Food intake, particularly the ingestion of fats and carbohydrates, prompts these cells to produce and release serotonin; the mechanical stimulus of food in the lumen can also trigger release. The distribution, function, and responsiveness of type EC cells reveal them as a crucial link between the intestinal environment, the nervous system, and the regulation of numerous bodily functions."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1016/0166-4328(96)00075-7"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [striated cell of salivary gland](http://purl.obolibrary.org/obo/CL_4052049) SubClassOf [columnar/cuboidal epithelial cell](http://purl.obolibrary.org/obo/CL_0000075) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1073/pnas.1804938115"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [striated cell of salivary gland](http://purl.obolibrary.org/obo/CL_4052049) SubClassOf [RO_0002215](http://purl.obolibrary.org/obo/RO_0002215) some [GO_1990573](http://purl.obolibrary.org/obo/GO_1990573) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1038/s41574-019-0168-8"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1016/j.cell.2017.05.034"^^[string](http://www.w3.org/2001/XMLSchema#string) -### subepithelial intestinal fibroblast `http://purl.obolibrary.org/obo/CL_4052007` +- [type EC enteroendocrine cell](http://purl.obolibrary.org/obo/CL_0000577) SubClassOf [epithelial cell of alimentary canal](http://purl.obolibrary.org/obo/CL_0002251) #### Added -- [subepithelial intestinal fibroblast](http://purl.obolibrary.org/obo/CL_4052007) [contributor](http://purl.org/dc/terms/contributor) [0009-0000-8480-9277](https://orcid.org/0009-0000-8480-9277) +- [type EC enteroendocrine cell](http://purl.obolibrary.org/obo/CL_0000577) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. -- [subepithelial intestinal fibroblast](http://purl.obolibrary.org/obo/CL_4052007) [comment](http://www.w3.org/2000/01/rdf-schema#comment) "The S2 fibroblast population has been identified as a subset of intestinal fibroblasts located near the epithelial lining. This population is divided into two subtypes: S2a and S2b. S2a is involved in epithelial differentiation, while S2b, located at the top of the crypt, regulates intestinal stem cell proliferation, niche formation, and wound healing."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:37495570"^^[string](http://www.w3.org/2001/XMLSchema#string) +Type EC enteroendocrine cells, also known as enterochromaffin cells, are a vital hormone-secreting cell type found in the gastrointestinal tract. These cells are named after their location in the intestines (“entero”) and because they are stainable by chromium salts (“chromaffin”). +The primary function of type EC enteroendocrine cells is to act as chemosensors and lies in their capacity to produce and secrete serotonin, also known as 5-hydroxytryptamine (5-HT). Serotonin is a neurotransmitter that plays a significant role in modulating motility, secretion, vasodilation, perception of pain, and appetite in the gastrointestinal system. However, its function is not limited to the gastrointestinal tract; once secreted, serotonin is distributed via the bloodstream and contributes to regulating mood, appetite, and sleep in the brain. +Via specific chemosensory receptors type EC enteroendocrine cells are able to respond to various environmental, metabolic, and homeostatic stimuli and transduce information from the gut to the nervous system: Food intake, particularly the ingestion of fats and carbohydrates, prompts these cells to produce and release serotonin; the mechanical stimulus of food in the lumen can also trigger release. The distribution, function, and responsiveness of type EC cells reveal them as a crucial link between the intestinal environment, the nervous system, and the regulation of numerous bodily functions."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1016/0166-4328(96)00075-7"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:33916891"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1073/pnas.1804938115"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:30270042"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1038/s41574-019-0168-8"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [subepithelial intestinal fibroblast](http://purl.obolibrary.org/obo/CL_4052007) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A fibroblast located adjacent to the intestinal epithelium in both the small intestine and colon, specifically around the crypts. This cell is characterized by the expression of PDGFRα and various collagen isoforms, including COL4A5 and COL4A6. It secretes signalling molecules like TGF-β, Wnt ligands, and BMPs, which are crucial for epithelial homeostasis, intestinal stem cell support, and basement membrane formation."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:33916891"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1016/j.cell.2017.05.034"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:30270042"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:33430285"^^[string](http://www.w3.org/2001/XMLSchema#string) +### type G cell of stomach `http://purl.obolibrary.org/obo/CL_4047025` - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:37080817"^^[string](http://www.w3.org/2001/XMLSchema#string) +#### Added +- [type G cell of stomach](http://purl.obolibrary.org/obo/CL_4047025) [date](http://purl.org/dc/terms/date) "2024-10-24T10:43:22Z"^^[dateTime](http://www.w3.org/2001/XMLSchema#dateTime) -- [subepithelial intestinal fibroblast](http://purl.obolibrary.org/obo/CL_4052007) [date](http://purl.org/dc/terms/date) "2024-09-23T09:59:27Z"^^[dateTime](http://www.w3.org/2001/XMLSchema#dateTime) +- [type G cell of stomach](http://purl.obolibrary.org/obo/CL_4047025) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "Any type G enteroendocrine cell that is part of some epithelium of stomach."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBC:Autogenerated"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [subepithelial intestinal fibroblast](http://purl.obolibrary.org/obo/CL_4052007) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "S2 fibroblast"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:33916891"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [type G cell of stomach](http://purl.obolibrary.org/obo/CL_4047025) [contributor](http://purl.org/dc/terms/contributor) [0009-0005-7919-4905](https://orcid.org/0009-0005-7919-4905) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:30270042"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [type G cell of stomach](http://purl.obolibrary.org/obo/CL_4047025) [id](http://www.geneontology.org/formats/oboInOwl#id) "CL:4047025"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [subepithelial intestinal fibroblast](http://purl.obolibrary.org/obo/CL_4052007) [label](http://www.w3.org/2000/01/rdf-schema#label) "subepithelial intestinal fibroblast"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [type G cell of stomach](http://purl.obolibrary.org/obo/CL_4047025) [label](http://www.w3.org/2000/01/rdf-schema#label) "type G cell of stomach"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [subepithelial intestinal fibroblast](http://purl.obolibrary.org/obo/CL_4052007) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "S2 mesenchymal cells"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:33916891"^^[string](http://www.w3.org/2001/XMLSchema#string) +- Class: [type G cell of stomach](http://purl.obolibrary.org/obo/CL_4047025) -- [subepithelial intestinal fibroblast](http://purl.obolibrary.org/obo/CL_4052007) [id](http://www.geneontology.org/formats/oboInOwl#id) "CL:4052007"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [type G cell of stomach](http://purl.obolibrary.org/obo/CL_4047025) EquivalentTo [type G enteroendocrine cell](http://purl.obolibrary.org/obo/CL_0000508) and ([BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0001276](http://purl.obolibrary.org/obo/UBERON_0001276)) -- Class: [subepithelial intestinal fibroblast](http://purl.obolibrary.org/obo/CL_4052007) +- [type G cell of stomach](http://purl.obolibrary.org/obo/CL_4047025) SubClassOf [stomach neuroendocrine cell](http://purl.obolibrary.org/obo/CL_1000222) -- [subepithelial intestinal fibroblast](http://purl.obolibrary.org/obo/CL_4052007) SubClassOf [RO_0002220](http://purl.obolibrary.org/obo/RO_0002220) some [UBERON_0001277](http://purl.obolibrary.org/obo/UBERON_0001277) +- [type G cell of stomach](http://purl.obolibrary.org/obo/CL_4047025) SubClassOf [type G enteroendocrine cell](http://purl.obolibrary.org/obo/CL_0000508) -- [subepithelial intestinal fibroblast](http://purl.obolibrary.org/obo/CL_4052007) SubClassOf [fibroblast](http://purl.obolibrary.org/obo/CL_0000057) +### type G enteroendocrine cell `http://purl.obolibrary.org/obo/CL_0000508` +#### Removed +- [type G enteroendocrine cell](http://purl.obolibrary.org/obo/CL_0000508) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "An endocrine cell found in the pyloric gland mucosa (antral mucosa) of the stomach of mammals and responsible for the secretion of gastrin and enkephalin. Most abundant in pyloric antrum, pyramidal in form with a narrow apex bearing long microvilli."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ISBN:0517223651"^^[string](http://www.w3.org/2001/XMLSchema#string) -### substantia nigra dopaminergic neuron `http://purl.obolibrary.org/obo/CL_4042025` + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:tfm"^^[string](http://www.w3.org/2001/XMLSchema#string) -#### Added -- [substantia nigra dopaminergic neuron](http://purl.obolibrary.org/obo/CL_4042025) [id](http://www.geneontology.org/formats/oboInOwl#id) "CL:4042025"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "MESH:D019863"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [substantia nigra dopaminergic neuron](http://purl.obolibrary.org/obo/CL_4042025) [contributor](http://purl.org/dc/terms/contributor) [0000-0002-0098-8958](https://orcid.org/0000-0002-0098-8958) +- [type G enteroendocrine cell](http://purl.obolibrary.org/obo/CL_0000508) SubClassOf [glandular epithelial cell of stomach](http://purl.obolibrary.org/obo/CL_0002659) -- [substantia nigra dopaminergic neuron](http://purl.obolibrary.org/obo/CL_4042025) [label](http://www.w3.org/2000/01/rdf-schema#label) "substantia nigra dopaminergic neuron"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [type G enteroendocrine cell](http://purl.obolibrary.org/obo/CL_0000508) SubClassOf [BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0004997](http://purl.obolibrary.org/obo/UBERON_0004997) -- [substantia nigra dopaminergic neuron](http://purl.obolibrary.org/obo/CL_4042025) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A midbrain dopaminergic neuron that has its soma located in a substantia nigra. This dopaminergic neuron type is highly metabolically active and it is involved in the regulation of movement, cognition, motivation and reward. Neurodegeneration of this dopaminergic neuronal type causes loss in fine motor control in Parkinson's Disease."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:35308118"^^[string](http://www.w3.org/2001/XMLSchema#string) +#### Added +- [type G enteroendocrine cell](http://purl.obolibrary.org/obo/CL_0000508) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "An endocrine cell found in the stomach and duodenum and is responsible for the secretion of gastrin and enkephalin. Most abundant in pyloric antrum, pyramidal in form with a narrow apex bearing long microvilli."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:35674015"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:32826893"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ISBN:0517223651"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [substantia nigra dopaminergic neuron](http://purl.obolibrary.org/obo/CL_4042025) [has_narrow_synonym](http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym) "SNpc dopaminergic neuron"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:35308118"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:tfm"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [substantia nigra dopaminergic neuron](http://purl.obolibrary.org/obo/CL_4042025) [date](http://purl.org/dc/terms/date) "2024-09-16T13:09:29Z"^^[dateTime](http://www.w3.org/2001/XMLSchema#dateTime) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "MESH:D019863"^^[string](http://www.w3.org/2001/XMLSchema#string) -- Class: [substantia nigra dopaminergic neuron](http://purl.obolibrary.org/obo/CL_4042025) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:10700044"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [substantia nigra dopaminergic neuron](http://purl.obolibrary.org/obo/CL_4042025) SubClassOf [midbrain dopaminergic neuron](http://purl.obolibrary.org/obo/CL_2000097) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:37240181"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [substantia nigra dopaminergic neuron](http://purl.obolibrary.org/obo/CL_4042025) SubClassOf [neuron of the substantia nigra](http://purl.obolibrary.org/obo/CL_0002614) +- [type G enteroendocrine cell](http://purl.obolibrary.org/obo/CL_0000508) SubClassOf [neuroendocrine cell](http://purl.obolibrary.org/obo/CL_0000165) -### syncytial cell `http://purl.obolibrary.org/obo/CL_4052002` +### type I cell of adrenal cortex `http://purl.obolibrary.org/obo/CL_0002099` #### Added -- [syncytial cell](http://purl.obolibrary.org/obo/CL_4052002) [id](http://www.geneontology.org/formats/oboInOwl#id) "CL:4052002"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [type I cell of adrenal cortex](http://purl.obolibrary.org/obo/CL_0002099) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl/cl-base#cellxgene_subset) -- [syncytial cell](http://purl.obolibrary.org/obo/CL_4052002) [contributor](http://purl.org/dc/terms/contributor) [0009-0000-8480-9277](https://orcid.org/0009-0000-8480-9277) -- [syncytial cell](http://purl.obolibrary.org/obo/CL_4052002) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "SC"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003000](http://purl.obolibrary.org/obo/OMO_0003000) +### type IIx muscle cell `http://purl.obolibrary.org/obo/CL_4052026` - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:9067520"^^[string](http://www.w3.org/2001/XMLSchema#string) +#### Added +- [type IIx muscle cell](http://purl.obolibrary.org/obo/CL_4052026) [has_exact_synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "type 2x fiber"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:34727990"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [syncytial cell](http://purl.obolibrary.org/obo/CL_4052002) [date](http://purl.org/dc/terms/date) "2024-08-15T10:38:46Z"^^[dateTime](http://www.w3.org/2001/XMLSchema#dateTime) +- [type IIx muscle cell](http://purl.obolibrary.org/obo/CL_4052026) [has_exact_synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "type 2x muscle fiber"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:34727990"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [syncytial cell](http://purl.obolibrary.org/obo/CL_4052002) [has_exact_synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "syncytium"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "WBbt:0008074"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [type IIx muscle cell](http://purl.obolibrary.org/obo/CL_4052026) [comment](http://www.w3.org/2000/01/rdf-schema#comment) "In humans, type IIx fiber contains high levels of MYLK2, enhancing contraction speed and force via myosin phosphorylation, especially under low calcium. This mechanism supports post-activation potentiation, increasing force output in fast-twitch muscles. Additionally, this fiber has abundant ACTN3 (α-actinin-3), linked to muscle power, and exhibits the highest shortening velocity among human muscle fiber types. Notably, type IIx fiber is selectively lost in aging-related sarcopenia, increases in proportion in type 2 diabetes and obesity, and is the first to degenerate in Duchenne Muscular Dystrophy, impacting muscle function across various conditions."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:34727990"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [syncytial cell](http://purl.obolibrary.org/obo/CL_4052002) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A multinucleate cell formed by the fusion of multiple uninuclear cells through plasma membrane fusion. This process leads to a single large cell containing multiple nuclei within a shared cytoplasm."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Syncytium"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:27199166"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:20851884"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [type IIx muscle cell](http://purl.obolibrary.org/obo/CL_4052026) [id](http://www.geneontology.org/formats/oboInOwl#id) "CL:4052026"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [syncytial cell](http://purl.obolibrary.org/obo/CL_4052002) [label](http://www.w3.org/2000/01/rdf-schema#label) "syncytial cell"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [type IIx muscle cell](http://purl.obolibrary.org/obo/CL_4052026) [has_exact_synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "type 2x muscle cell"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:34727990"^^[string](http://www.w3.org/2001/XMLSchema#string) -- Class: [syncytial cell](http://purl.obolibrary.org/obo/CL_4052002) +- [type IIx muscle cell](http://purl.obolibrary.org/obo/CL_4052026) [has_exact_synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "type IIx muscle fiber"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "doi:10.1101/2024.05.15.594276"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [syncytial cell](http://purl.obolibrary.org/obo/CL_4052002) EquivalentTo [cell](http://purl.obolibrary.org/obo/CL_0000000) and ([RO_0000053](http://purl.obolibrary.org/obo/RO_0000053) some [PATO_0001908](http://purl.obolibrary.org/obo/PATO_0001908)) and ([RO_0002353](http://purl.obolibrary.org/obo/RO_0002353) some [GO_0000768](http://purl.obolibrary.org/obo/GO_0000768)) +- [type IIx muscle cell](http://purl.obolibrary.org/obo/CL_4052026) [contributor](http://purl.org/dc/terms/contributor) [0009-0000-8480-9277](https://orcid.org/0009-0000-8480-9277) -- [syncytial cell](http://purl.obolibrary.org/obo/CL_4052002) SubClassOf [multinucleate cell](http://purl.obolibrary.org/obo/CL_0000228) +- [type IIx muscle cell](http://purl.obolibrary.org/obo/CL_4052026) [label](http://www.w3.org/2000/01/rdf-schema#label) "type IIx muscle cell"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [syncytial cell](http://purl.obolibrary.org/obo/CL_4052002) SubClassOf [RO_0002353](http://purl.obolibrary.org/obo/RO_0002353) some [GO_0000768](http://purl.obolibrary.org/obo/GO_0000768) +- [type IIx muscle cell](http://purl.obolibrary.org/obo/CL_4052026) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A fast type II muscle cell that is part of the skeletal muscle tissue. This cell is characterized by its intermediate metabolic profile, utilizing both glycolytic and oxidative pathways for energy production. In humans, it is distinguished by the expression of myosin heavy chain 1 (MYH1)."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:35908794"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [syncytial cell](http://purl.obolibrary.org/obo/CL_4052002) SubClassOf [BFO_0000002](http://purl.obolibrary.org/obo/BFO_0000002) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:36361732"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:34727990"^^[string](http://www.w3.org/2001/XMLSchema#string) -### syncytial epithelial cell `http://purl.obolibrary.org/obo/CL_0000420` -#### Removed -- [syncytial epithelial cell](http://purl.obolibrary.org/obo/CL_0000420) SubClassOf [multinucleate cell](http://purl.obolibrary.org/obo/CL_0000228) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "doi:10.1101/2024.05.15.594276"^^[string](http://www.w3.org/2001/XMLSchema#string) -#### Added -- [syncytial epithelial cell](http://purl.obolibrary.org/obo/CL_0000420) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "An epithelial cell that forms a syncytium, which is a multinucleated cell resulting from the fusion of multiple cells."^^[string](http://www.w3.org/2001/XMLSchema#string) +- [type IIx muscle cell](http://purl.obolibrary.org/obo/CL_4052026) [date](http://purl.org/dc/terms/date) "2024-11-04T10:26:29Z"^^[dateTime](http://www.w3.org/2001/XMLSchema#dateTime) -- [syncytial epithelial cell](http://purl.obolibrary.org/obo/CL_0000420) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Syncytium"^^[string](http://www.w3.org/2001/XMLSchema#string) +- Class: [type IIx muscle cell](http://purl.obolibrary.org/obo/CL_4052026) -- [syncytial epithelial cell](http://purl.obolibrary.org/obo/CL_0000420) SubClassOf [syncytial cell](http://purl.obolibrary.org/obo/CL_4052002) +- [type IIx muscle cell](http://purl.obolibrary.org/obo/CL_4052026) SubClassOf [type II muscle cell](http://purl.obolibrary.org/obo/CL_0002212) -### syncytiotrophoblast cell `http://purl.obolibrary.org/obo/CL_0000525` +### unipolar brush cell `http://purl.obolibrary.org/obo/CL_4023161` #### Removed -- [syncytiotrophoblast cell](http://purl.obolibrary.org/obo/CL_0000525) SubClassOf [multinucleate cell](http://purl.obolibrary.org/obo/CL_0000228) +- [unipolar brush cell](http://purl.obolibrary.org/obo/CL_4023161) SubClassOf [obsolete CNS interneuron](http://purl.obolibrary.org/obo/CL_0000402) #### Added -- [syncytiotrophoblast cell](http://purl.obolibrary.org/obo/CL_0000525) SubClassOf [syncytial cell](http://purl.obolibrary.org/obo/CL_4052002) +- [unipolar brush cell](http://purl.obolibrary.org/obo/CL_4023161) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl/cl-base#cellxgene_subset) +- [unipolar brush cell](http://purl.obolibrary.org/obo/CL_4023161) SubClassOf [interneuron](http://purl.obolibrary.org/obo/CL_0000099) -### tanycyte `http://purl.obolibrary.org/obo/CL_0002085` -#### Removed -- [tanycyte](http://purl.obolibrary.org/obo/CL_0002085) [has_exact_synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "stretch cell"^^[string](http://www.w3.org/2001/XMLSchema#string) - -- [tanycyte](http://purl.obolibrary.org/obo/CL_0002085) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "Specialized elongated ventricular ependymal cell that has processes that extend to the outer, or pial, surface of the CNS. Resemble spongioblasts seen in developing brain. Found in the adult brain in the third ventricle, cerebral aqueduct, spinal canal and floor of the fourth ventricle."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "http://neurolex.org/wiki/Category:Tanycyte"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:tfm"^^[string](http://www.w3.org/2001/XMLSchema#string) +### unipolar neuron `http://purl.obolibrary.org/obo/CL_0000106` +#### Removed +- [unipolar neuron](http://purl.obolibrary.org/obo/CL_0000106) SubClassOf [neuron](http://purl.obolibrary.org/obo/CL_0000540) #### Added -- [tanycyte](http://purl.obolibrary.org/obo/CL_0002085) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A specialized elongated ventricular ependymal cell that has processes that extend to the outer, or pial, surface of the CNS. A tanycyte is found in the adult brain, specifically in the third ventricle, cerebral aqueduct, spinal canal, and floor of the fourth ventricle. This cell type is involved in hormonal regulation, gatekeeping molecules between the bloodstream and cerebrospinal fluid, metabolic sensing, and regulating food intake."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "http://neurolex.org/wiki/Category:Tanycyte"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [unipolar neuron](http://purl.obolibrary.org/obo/CL_0000106) SubClassOf [peripheral nervous system neuron](http://purl.obolibrary.org/obo/CL_2000032) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:tfm"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [tanycyte](http://purl.obolibrary.org/obo/CL_0002085) [has_exact_synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "stretch cell"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:29351662"^^[string](http://www.w3.org/2001/XMLSchema#string) +### untufted pyramidal neuron `http://purl.obolibrary.org/obo/CL_4023095` +#### Removed +- [untufted pyramidal neuron](http://purl.obolibrary.org/obo/CL_4023095) EquivalentTo [CNS neuron (sensu Vertebrata)](http://purl.obolibrary.org/obo/CL_0000117) and ([RO_0000053](http://purl.obolibrary.org/obo/RO_0000053) some [PATO_0070019](http://purl.obolibrary.org/obo/PATO_0070019)) + +- [untufted pyramidal neuron](http://purl.obolibrary.org/obo/CL_4023095) SubClassOf [CNS neuron (sensu Vertebrata)](http://purl.obolibrary.org/obo/CL_0000117) -- [tanycyte](http://purl.obolibrary.org/obo/CL_0002085) SubClassOf [BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0004670](http://purl.obolibrary.org/obo/UBERON_0004670) +#### Added +- [untufted pyramidal neuron](http://purl.obolibrary.org/obo/CL_4023095) EquivalentTo [neuron](http://purl.obolibrary.org/obo/CL_0000540) and ([RO_0000053](http://purl.obolibrary.org/obo/RO_0000053) some [PATO_0070019](http://purl.obolibrary.org/obo/PATO_0070019)) -### thymic nurse cell `http://purl.obolibrary.org/obo/CL_4030004` +### ureter urothelial cell `http://purl.obolibrary.org/obo/CL_1000706` #### Removed -- [thymic nurse cell](http://purl.obolibrary.org/obo/CL_4030004) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A large epithelial cell found in the thymus. This cell type may internalize thymocytes through extensions of plasma membrane. The cell surface and cytoplasmic vacuoles of a thymic nurse cell express MHC Class I and MHC Class II antigens. The interaction of these antigens with a developing thymocyte determines whether the thymocyte undergoes positive or negative selection."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://en.wikipedia.org/wiki/Thymic_nurse_cell"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [ureter urothelial cell](http://purl.obolibrary.org/obo/CL_1000706) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "Any urothelial cell that is part of some urothelium of ureter."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBC:Autogenerated"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [ureter urothelial cell](http://purl.obolibrary.org/obo/CL_1000706) SubClassOf [ureteral cell](http://purl.obolibrary.org/obo/CL_1000601) + - [is_inferred](http://www.geneontology.org/formats/oboInOwl#is_inferred) "true"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [contributor](http://purl.org/dc/terms/contributor) "https://orcid.org/0000-0002-0819-0473"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [ureter urothelial cell](http://purl.obolibrary.org/obo/CL_1000706) SubClassOf [urothelial cell](http://purl.obolibrary.org/obo/CL_0000731) + - [is_inferred](http://www.geneontology.org/formats/oboInOwl#is_inferred) "true"^^[string](http://www.w3.org/2001/XMLSchema#string) #### Added -- [thymic nurse cell](http://purl.obolibrary.org/obo/CL_4030004) [contributor](http://purl.org/dc/terms/contributor) [0000-0002-0819-0473](https://orcid.org/0000-0002-0819-0473) +- [ureter urothelial cell](http://purl.obolibrary.org/obo/CL_1000706) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A urothelial cell that is part of the urothelium of ureter."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:36180582"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [thymic nurse cell](http://purl.obolibrary.org/obo/CL_4030004) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A large epithelial cell found in the thymus. This cell type may internalize thymocytes through extensions of plasma membrane. The cell surface and cytoplasmic vacuoles of a thymic nurse cell express MHC Class I and MHC Class II antigens. The interaction of these antigens with a developing thymocyte determines whether the thymocyte undergoes positive or negative selection."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://en.wikipedia.org/wiki/Thymic_nurse_cell"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [ureter urothelial cell](http://purl.obolibrary.org/obo/CL_1000706) SubClassOf [urothelial cell](http://purl.obolibrary.org/obo/CL_0000731) +- [ureter urothelial cell](http://purl.obolibrary.org/obo/CL_1000706) SubClassOf [ureteral cell](http://purl.obolibrary.org/obo/CL_1000601) -### tracheobronchial serous cell `http://purl.obolibrary.org/obo/CL_0019001` + +### ureteric bud cell `http://purl.obolibrary.org/obo/CL_4030066` #### Added -- [tracheobronchial serous cell](http://purl.obolibrary.org/obo/CL_0019001) SubClassOf [eukaryotic cell](http://purl.obolibrary.org/obo/CL_0000255) +- [ureteric bud cell](http://purl.obolibrary.org/obo/CL_4030066) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl/cl-base#cellxgene_subset) -### transit amplifying cell `http://purl.obolibrary.org/obo/CL_0009010` +### urethra urothelial cell `http://purl.obolibrary.org/obo/CL_1001430` #### Removed -- [transit amplifying cell](http://purl.obolibrary.org/obo/CL_0009010) SubClassOf [cell](http://purl.obolibrary.org/obo/CL_0000000) +- [urethra urothelial cell](http://purl.obolibrary.org/obo/CL_1001430) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "Any urothelial cell that is part of some urethra urothelium."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBC:Autogenerated"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [urethra urothelial cell](http://purl.obolibrary.org/obo/CL_1001430) SubClassOf [urothelial cell](http://purl.obolibrary.org/obo/CL_0000731) + - [is_inferred](http://www.geneontology.org/formats/oboInOwl#is_inferred) "true"^^[string](http://www.w3.org/2001/XMLSchema#string) #### Added -- [transit amplifying cell](http://purl.obolibrary.org/obo/CL_0009010) SubClassOf [eukaryotic cell](http://purl.obolibrary.org/obo/CL_0000255) +- [urethra urothelial cell](http://purl.obolibrary.org/obo/CL_1001430) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. +Urethra urothelial cells are highly specialized epithelial cells in the urethra, which is a tubelike structure that carries urine from the bladder to the external urethral orifice. Urothelial cells form the urothelium – a stratified, transitional epithelium lining the bladder, ureters, renal pelvis and urethra. These cells are highly adapted to their specific environment and maintain the crucial function of sustaining the urinary tract's core roles, primarily to transit and store urine without auto-corrosion or pathogen proliferation. +Within the urethra urothelial cells are primarily found in proximal two-thirds of the urethra, while the distal third is lined by stratified squamous epithelial cells. The urothelial cells are renowned for their remarkable impermeability and ability to stretch and recoil during the various stages of urine filling and emptying. They form a tight barrier that prevents reabsorption of harmful byproducts and toxic substances present in the urine, guarding the deeper tissues and bloodstream against potential damage. This is largely attributed to specialized junctions, namely zonulae occludentes or tight junctions, in the umbrella cell layer (one of three layers of the urothelium) that seal the intercellular space between adjacent cells. Together with the urothelial plaque (an apical membrane plaque comprised of uroplakin proteins covering the umbrella cells at the luminal surface), the junctional complexes form a very effective permeability barrier that regulates the passage of water and ion from urine to the underlying tissue. +A noteworthy feature of urothelial cells is their regulatory and sensory roles involving communication with the underlying layers about the filling and emptying status of the urinary tract. The cells also manage a fine balance between proliferation and differentiation, with the basal cells providing a ready pool of cells to replace the superficial layer when damaged. Their remarkable ability for regeneration and turnover, and their response to signals for repair underpins the durability and functionality of the urothelial tract."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1152/physrev.00041.2019"^^[string](http://www.w3.org/2001/XMLSchema#string) -### trophoblast cell `http://purl.obolibrary.org/obo/CL_0000351` -#### Removed -- [trophoblast cell](http://purl.obolibrary.org/obo/CL_0000351) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "An extraembryonic cell that develops from a trophectodermal cell. This cell is found in the outer layer of the blastocyst and can invade other structures in the uterus once the blastocyst implants into the uterine wall. A trophoblast cell is involved in the implantation of the embryo into the uterine wall, placental formation, remodelling of maternal vasculature in the uterus, nutrient and gas exchange, hormone production, and immune modulation to support fetal development."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "MESH:D014327"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1038/nrurol.2016.13"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [comment](http://www.w3.org/2000/01/rdf-schema#comment) "doi:10.1007/978-3-030-84725-8"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1152/physrev.00030.2012"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:tfm"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1038/s41385-022-00565-0"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:37630754"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [urethra urothelial cell](http://purl.obolibrary.org/obo/CL_1001430) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A urothelial cell that is part of the urethra urothelium. This cell plays a crucial role in maintaining the urethral barrier function, protecting against toxic substances in urine, sensing environmental changes, and defending against pathogen entry."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:36180582"^^[string](http://www.w3.org/2001/XMLSchema#string) -#### Added -- [trophoblast cell](http://purl.obolibrary.org/obo/CL_0000351) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "An extraembryonic cell that develops from a trophectodermal cell. This cell is found in the outer layer of the blastocyst and can invade other structures in the uterus once the blastocyst implants into the uterine wall. A trophoblast cell is involved in the implantation of the embryo into the uterine wall, placental formation, remodelling of maternal vasculature in the uterus, nutrient and gas exchange, hormone production, and immune modulation to support fetal development."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "MESH:D014327"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:23589830"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "doi:10.1007/978-3-030-84725-8"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [urethra urothelial cell](http://purl.obolibrary.org/obo/CL_1001430) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://cellxgene.cziscience.com/cellguide/CL_1001430"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:tfm"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [urethra urothelial cell](http://purl.obolibrary.org/obo/CL_1001430) SubClassOf [urothelial cell](http://purl.obolibrary.org/obo/CL_0000731) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:37630754"^^[string](http://www.w3.org/2001/XMLSchema#string) +### urothelial cell `http://purl.obolibrary.org/obo/CL_0000731` +#### Removed +- [urothelial cell](http://purl.obolibrary.org/obo/CL_0000731) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. -### type A enteroendocrine cell `http://purl.obolibrary.org/obo/CL_0002067` +Urothelial cells are a unique type of epithelial cell found lining the urinary tract system. They form the urothelium, a specialized, multi-layered epithelium that lines major portions of the urinary tract, including the renal pelvis, ureters, bladder, and the proximal part of the urethra. The distinct characteristic of urothelial cells is their ability to stretch and contract depending on the volume of liquid they contain - a feature that facilitates the essential role they play in maintaining the functionality and integrity of the urinary system. +The primary function of urothelial cells is to provide an impermeable barrier to urine, preventing the toxic components present in the urine from seeping back into the body's bloodstream. The urothelium consists of a superficial umbrella cell layer, 1–2 layers of intermediate cells, and a basal cell layer. The umbrella layer is composed of large, mostly binucleated cells that are covered in an asymmetrical unit membrane, the uroplakin plaques. These plaques function to seal the apical membrane of the bladder from the toxic and highly variable contents of urine. The lipid bilayer structure of uroplakin plaques has an exceptionally high concentration of uroplakins that contribute to the barrier function of the urothelium. +Beyond their mechanical function, urothelial cells also play a role in sensing and signaling changes in the urinary system. They express a number of sensor molecules or respond to thermal, mechanical and chemical stimuli and can release chemical mediators. This allows them to act as sensory transducers because they detect changes in the filling state of the bladder and transmit this information to the nervous system. Moreover, these versatile cells contribute to the defense mechanism against urinary tract pathogens. They respond to bacterial infections by releasing chemical messengers, cytokines and chemokines, to attract immune cells, and also can engulf pathogens via endocytosis."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1038/ncpuro0672"^^[string](http://www.w3.org/2001/XMLSchema#string) -#### Added -- [type A enteroendocrine cell](http://purl.obolibrary.org/obo/CL_0002067) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://cellxgene.cziscience.com/cellguide/CL_0002067"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1038/ki.2009.73"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [type A enteroendocrine cell](http://purl.obolibrary.org/obo/CL_0002067) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1038/s41579-020-0324-0"^^[string](http://www.w3.org/2001/XMLSchema#string) -Type A enteroendocrine cells, also known as alpha cells or A cells, are a species of endocrine cells primarily located in the pancreatic islets of Langerhans; they have also been identified within the lining of the stomach. Functionally, these cells are pivotal in glucose metabolism and homeostasis, accounting for about 20% of the total population of cells in the pancreatic islets. -The primary role of type A enteroendocrine cells involves the synthesis, storage, and secretion of the peptide hormone glucagon, which is critical in energy regulation throughout the body. In response to a decrease in blood glucose levels, the pancreatic A cells are stimulated to secrete glucagon into the bloodstream. Glucagon acts on its target cells, mainly in the liver, to stimulate glycogenolysis and gluconeogenesis processes, thereby increasing blood glucose levels back to normal. In this way, pancreatic A cells play an integral role in maintaining glucose homeostasis and preventing hypoglycemia. -Pancreatic A cells also participate in the local regulation of islet activities as glucagon acts through glucagon receptors on A, B and D type cells within the islets. Recent studies have also shown that Pancreatic A cells play a role in the generation and regeneration of B type cells. Following beta cell injuries pancreatic A cells increase in numbers and produce Glucagon-like peptide-1 (GLP-1), which increases the proliferation and cytoprotection of beta cells. In response to extreme injury of B type cells pancreatic A cells can transform (transdifferentiate) into functioning B type cells. -Until recently, glucagon has been considered a pancreas-specific hormone; however, extrapancreatic glucagon has been reported in patients who had undergone complete, and glucagon-positive cells been identified in the human stomach, indicating that Type A enteroendocrine cells are not restricted to the pancreas."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.2337/dbi19-0002"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1152/physrev.00041.2019"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.2337/db15-1541"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1002/nau.22195"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.3389/fphys.2012.00349/full"^^[string](http://www.w3.org/2001/XMLSchema#string) +#### Added +- [urothelial cell](http://purl.obolibrary.org/obo/CL_0000731) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1016/j.diabres.2018.06.013"^^[string](http://www.w3.org/2001/XMLSchema#string) +Urothelial cells are a unique type of epithelial cell found lining the urinary tract system. They form the urothelium, a specialized, multi-layered epithelium that lines major portions of the urinary tract, including the renal pelvis, ureters, bladder, and the proximal part of the urethra. The distinct characteristic of urothelial cells is their ability to stretch and contract depending on the volume of liquid they contain - a feature that facilitates the essential role they play in maintaining the functionality and integrity of the urinary system. +The primary function of urothelial cells is to provide an impermeable barrier to urine, preventing the toxic components present in the urine from seeping back into the body's bloodstream. The urothelium consists of a superficial umbrella cell layer, 1–2 layers of intermediate cells, and a basal cell layer. The umbrella layer is composed of large, mostly binucleated cells that are covered in an asymmetrical unit membrane, the uroplakin plaques. These plaques function to seal the apical membrane of the bladder from the toxic and highly variable contents of urine. The lipid bilayer structure of uroplakin plaques has an exceptionally high concentration of uroplakins that contribute to the barrier function of the urothelium. +Beyond their mechanical function, urothelial cells also play a role in sensing and signaling changes in the urinary system. They express a number of sensor molecules or respond to thermal, mechanical and chemical stimuli and can release chemical mediators. This allows them to act as sensory transducers because they detect changes in the filling state of the bladder and transmit this information to the nervous system. Moreover, these versatile cells contribute to the defense mechanism against urinary tract pathogens. They respond to bacterial infections by releasing chemical messengers, cytokines and chemokines, to attract immune cells, and also can engulf pathogens via endocytosis."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1038/ncpuro0672"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1210/en.2016-1748"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1038/ki.2009.73"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1038/s41579-020-0324-0"^^[string](http://www.w3.org/2001/XMLSchema#string) -### type A synovial cell `http://purl.obolibrary.org/obo/CL_0002302` + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1152/physrev.00041.2019"^^[string](http://www.w3.org/2001/XMLSchema#string) -#### Added -- [type A synovial cell](http://purl.obolibrary.org/obo/CL_0002302) SubClassOf [squamous epithelial cell](http://purl.obolibrary.org/obo/CL_0000076) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1002/nau.22195"^^[string](http://www.w3.org/2001/XMLSchema#string) -### type B synovial cell `http://purl.obolibrary.org/obo/CL_0002301` +### uterine cervix secretory cell `http://purl.obolibrary.org/obo/CL_1001587` #### Removed -- [type B synovial cell](http://purl.obolibrary.org/obo/CL_0002301) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A resident stromal cell located in the synovial membrane and responsible for the production of immune-related cytokines and chemokines. This cell type secretes glycoproteins and hyaluronic acid, has abundant granular endoplasmic reticulum, but contains fewer vacuoles and vesicles."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:34433485"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [uterine cervix secretory cell](http://purl.obolibrary.org/obo/CL_1001587) [label](http://www.w3.org/2000/01/rdf-schema#label) "uterine cervix glandular cell"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:34772990"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [uterine cervix secretory cell](http://purl.obolibrary.org/obo/CL_1001587) EquivalentTo [glandular secretory epithelial cell](http://purl.obolibrary.org/obo/CL_0000150) and ([BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0000002](http://purl.obolibrary.org/obo/UBERON_0000002)) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ISBN:0517223651"^^[string](http://www.w3.org/2001/XMLSchema#string) +#### Added +- [uterine cervix secretory cell](http://purl.obolibrary.org/obo/CL_1001587) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "uterine cervix glandular cell"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:tfm"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [uterine cervix secretory cell](http://purl.obolibrary.org/obo/CL_1001587) [label](http://www.w3.org/2000/01/rdf-schema#label) "uterine cervix secretory cell"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [uterine cervix secretory cell](http://purl.obolibrary.org/obo/CL_1001587) EquivalentTo [secretory epithelial cell](http://purl.obolibrary.org/obo/CL_1100001) and ([BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0000002](http://purl.obolibrary.org/obo/UBERON_0000002)) - - [contributor](http://purl.org/dc/terms/contributor) "https://orcid.org/0000-0002-0819-0473"^^[string](http://www.w3.org/2001/XMLSchema#string) + +### uterine natural killer cell `http://purl.obolibrary.org/obo/CL_4052028` #### Added -- [type B synovial cell](http://purl.obolibrary.org/obo/CL_0002301) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A resident stromal cell located in the synovial membrane and responsible for the production of immune-related cytokines and chemokines. This cell type secretes glycoproteins and hyaluronic acid, has abundant granular endoplasmic reticulum, but contains fewer vacuoles and vesicles."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:34433485"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [uterine natural killer cell](http://purl.obolibrary.org/obo/CL_4052028) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "uNK cell"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003000](http://purl.obolibrary.org/obo/OMO_0003000) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:34772990"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:39198675"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ISBN:0517223651"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [uterine natural killer cell](http://purl.obolibrary.org/obo/CL_4052028) [contributor](http://purl.org/dc/terms/contributor) [0009-0000-8480-9277](https://orcid.org/0009-0000-8480-9277) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:tfm"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [uterine natural killer cell](http://purl.obolibrary.org/obo/CL_4052028) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A natural killer cell that is part of the uterus, specifically within the endometrium during the non-pregnant state and in the decidua during pregnancy. This cell exhibits dynamic changes in frequency throughout the menstrual cycle, with lower levels during menstruation and a significant increase during the mid-secretory phase and early pregnancy."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:35720413"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [type B synovial cell](http://purl.obolibrary.org/obo/CL_0002301) [contributor](http://purl.org/dc/terms/contributor) [0000-0002-0819-0473](https://orcid.org/0000-0002-0819-0473) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:39198675"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [type B synovial cell](http://purl.obolibrary.org/obo/CL_0002301) SubClassOf [squamous epithelial cell](http://purl.obolibrary.org/obo/CL_0000076) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Uterine_natural_killer_cells"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [uterine natural killer cell](http://purl.obolibrary.org/obo/CL_4052028) [label](http://www.w3.org/2000/01/rdf-schema#label) "uterine natural killer cell"^^[string](http://www.w3.org/2001/XMLSchema#string) -### type D enteroendocrine cell `http://purl.obolibrary.org/obo/CL_0000502` +- [uterine natural killer cell](http://purl.obolibrary.org/obo/CL_4052028) [has_narrow_synonym](http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym) "endometrial natural killer cell"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:35720413"^^[string](http://www.w3.org/2001/XMLSchema#string) -#### Added -- [type D enteroendocrine cell](http://purl.obolibrary.org/obo/CL_0000502) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://cellxgene.cziscience.com/cellguide/CL_0000502"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [uterine natural killer cell](http://purl.obolibrary.org/obo/CL_4052028) [date](http://purl.org/dc/terms/date) "2024-11-15T10:12:40Z"^^[dateTime](http://www.w3.org/2001/XMLSchema#dateTime) -- [type D enteroendocrine cell](http://purl.obolibrary.org/obo/CL_0000502) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. +- [uterine natural killer cell](http://purl.obolibrary.org/obo/CL_4052028) [id](http://www.geneontology.org/formats/oboInOwl#id) "CL:4052028"^^[string](http://www.w3.org/2001/XMLSchema#string) -Type D enteroendocrine cells, also known as D or delta cells, are specialized hormone-releasing cells found in the pancreas and also scattered throughout the lining of the gastrointestinal tract in mammals, notably within the stomach and the upper part of the small intestine known as the duodenum. The primary role of D cells is to produce and secrete somatostatin, a potent paracrine inhibitor. -In the gastrointestinal tract, somatostatin slows down digestion. It reduces gastric acid secretion and slows down the rate of gastric emptying, thereby prolonging and controling the digestive p. Functionally, these effects are aimed at sustaining nutrient absorption to optimize energy extraction from consumed food. -In the pancreas, D cells maintain a vital role in endocrine regulation. D cells in the pancreatic islands secrete somatostatin to inhibit the release of both insulin and glucagon from type A cells and B cells, glucoregulatory hormones that control blood sugar levels. Hence, D cells contribute considerably to the homeostasis of the body's metabolic processes. It is also noteworthy that dysfunctional D cells or irregular somatostatin signaling has been associated with certain pathologies such as neuroendocrine tumors and gastric ulcers."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1093/annonc/mdh216"^^[string](http://www.w3.org/2001/XMLSchema#string) +- Class: [uterine natural killer cell](http://purl.obolibrary.org/obo/CL_4052028) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1038/s41574-018-0020-6"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [uterine natural killer cell](http://purl.obolibrary.org/obo/CL_4052028) EquivalentTo [natural killer cell](http://purl.obolibrary.org/obo/CL_0000623) and ([BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0000995](http://purl.obolibrary.org/obo/UBERON_0000995)) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1016/j.pharmthera.2015.05.007"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [uterine natural killer cell](http://purl.obolibrary.org/obo/CL_4052028) SubClassOf [BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0000995](http://purl.obolibrary.org/obo/UBERON_0000995) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://www.sciencedirect.com/topics/neuroscience/somatostatin-cell"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [uterine natural killer cell](http://purl.obolibrary.org/obo/CL_4052028) SubClassOf [natural killer cell](http://purl.obolibrary.org/obo/CL_0000623) -### type EC enteroendocrine cell `http://purl.obolibrary.org/obo/CL_0000577` +### uterine smooth muscle cell `http://purl.obolibrary.org/obo/CL_0002601` #### Added -- [type EC enteroendocrine cell](http://purl.obolibrary.org/obo/CL_0000577) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://cellxgene.cziscience.com/cellguide/CL_0000577"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [uterine smooth muscle cell](http://purl.obolibrary.org/obo/CL_0002601) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. -- [type EC enteroendocrine cell](http://purl.obolibrary.org/obo/CL_0000577) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. +Uterine smooth muscle cells are specialized cells that make up the majority of the uterus and in particular, the myometrium. The myometrium is a thick, involuntary muscle layer, principally consisting of verticillate cell bundles that sculpt the helical architecture of the uterus. This dense muscular tissue, packed with uterine smooth muscle cells, is responsible for the significant contractile force witnessed during the physical processes of labor and childbirth. +In the non-pregnant uterus, they exist in a quiescent phase. Upon implantation, these cells are primarily responsible for the expansion consequently allowing the uterus to accommodate the growing fetus. Towards the end of pregnancy, under the influence of hormonal and mechanical signals, uterine smooth muscle cells transition from a relaxed phase to an active contractile phase, culminating in the delivery of the fetus. +At the cellular level, these transitions involve significant changes in the electrophysiological properties of uterine smooth muscle cells. Governed by a complex interplay of ion channels, transporters, and signaling proteins, these cells adjust their electrical activity, conduction properties, and contracting mechanisms. Any issues with these processes can result in problems such as preterm birth or labor dysfunction."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1177/0036850419850431"^^[string](http://www.w3.org/2001/XMLSchema#string) -Type EC enteroendocrine cells, also known as enterochromaffin cells, are a vital hormone-secreting cell type found in the gastrointestinal tract. These cells are named after their location in the intestines (“entero”) and because they are stainable by chromium salts (“chromaffin”). -The primary function of type EC enteroendocrine cells is to act as chemosensors and lies in their capacity to produce and secrete serotonin, also known as 5-hydroxytryptamine (5-HT). Serotonin is a neurotransmitter that plays a significant role in modulating motility, secretion, vasodilation, perception of pain, and appetite in the gastrointestinal system. However, its function is not limited to the gastrointestinal tract; once secreted, serotonin is distributed via the bloodstream and contributes to regulating mood, appetite, and sleep in the brain. -Via specific chemosensory receptors type EC enteroendocrine cells are able to respond to various environmental, metabolic, and homeostatic stimuli and transduce information from the gut to the nervous system: Food intake, particularly the ingestion of fats and carbohydrates, prompts these cells to produce and release serotonin; the mechanical stimulus of food in the lumen can also trigger release. The distribution, function, and responsiveness of type EC cells reveal them as a crucial link between the intestinal environment, the nervous system, and the regulation of numerous bodily functions."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1016/0166-4328(96)00075-7"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1203/00006450-199811000-00001"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1073/pnas.1804938115"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.3791/56639"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1038/s41574-019-0168-8"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://www.ncbi.nlm.nih.gov/books/NBK532927/"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1016/j.cell.2017.05.034"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [uterine smooth muscle cell](http://purl.obolibrary.org/obo/CL_0002601) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://cellxgene.cziscience.com/cellguide/CL_0002601"^^[string](http://www.w3.org/2001/XMLSchema#string) -### ureteral cell `http://purl.obolibrary.org/obo/CL_1000601` -#### Removed -- [ureteral cell](http://purl.obolibrary.org/obo/CL_1000601) SubClassOf [cell](http://purl.obolibrary.org/obo/CL_0000000) +### valve endothelial cell `http://purl.obolibrary.org/obo/CL_4030033` #### Added -- [ureteral cell](http://purl.obolibrary.org/obo/CL_1000601) SubClassOf [eukaryotic cell](http://purl.obolibrary.org/obo/CL_0000255) +- [valve endothelial cell](http://purl.obolibrary.org/obo/CL_4030033) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl/cl-base#cellxgene_subset) -### urothelial cell `http://purl.obolibrary.org/obo/CL_0000731` +### valve interstitial cell `http://purl.obolibrary.org/obo/CL_4030032` #### Added -- [urothelial cell](http://purl.obolibrary.org/obo/CL_0000731) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://cellxgene.cziscience.com/cellguide/CL_0000731"^^[string](http://www.w3.org/2001/XMLSchema#string) - -- [urothelial cell](http://purl.obolibrary.org/obo/CL_0000731) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. - -Urothelial cells are a unique type of epithelial cell found lining the urinary tract system. They form the urothelium, a specialized, multi-layered epithelium that lines major portions of the urinary tract, including the renal pelvis, ureters, bladder, and the proximal part of the urethra. The distinct characteristic of urothelial cells is their ability to stretch and contract depending on the volume of liquid they contain - a feature that facilitates the essential role they play in maintaining the functionality and integrity of the urinary system. -The primary function of urothelial cells is to provide an impermeable barrier to urine, preventing the toxic components present in the urine from seeping back into the body's bloodstream. The urothelium consists of a superficial umbrella cell layer, 1–2 layers of intermediate cells, and a basal cell layer. The umbrella layer is composed of large, mostly binucleated cells that are covered in an asymmetrical unit membrane, the uroplakin plaques. These plaques function to seal the apical membrane of the bladder from the toxic and highly variable contents of urine. The lipid bilayer structure of uroplakin plaques has an exceptionally high concentration of uroplakins that contribute to the barrier function of the urothelium. -Beyond their mechanical function, urothelial cells also play a role in sensing and signaling changes in the urinary system. They express a number of sensor molecules or respond to thermal, mechanical and chemical stimuli and can release chemical mediators. This allows them to act as sensory transducers because they detect changes in the filling state of the bladder and transmit this information to the nervous system. Moreover, these versatile cells contribute to the defense mechanism against urinary tract pathogens. They respond to bacterial infections by releasing chemical messengers, cytokines and chemokines, to attract immune cells, and also can engulf pathogens via endocytosis."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1038/ncpuro0672"^^[string](http://www.w3.org/2001/XMLSchema#string) - - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1038/ki.2009.73"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [valve interstitial cell](http://purl.obolibrary.org/obo/CL_4030032) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl/cl-base#cellxgene_subset) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1038/s41579-020-0324-0"^^[string](http://www.w3.org/2001/XMLSchema#string) - - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1152/physrev.00041.2019"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1002/nau.22195"^^[string](http://www.w3.org/2001/XMLSchema#string) +### vasa recta ascending limb cell `http://purl.obolibrary.org/obo/CL_1001131` +#### Removed +- [vasa recta ascending limb cell](http://purl.obolibrary.org/obo/CL_1001131) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. +The vasa recta ascending limb cells are specialized epithelial cells that are part of the vasa recta in the kidney, a crucial component of the renal medulla that functions as a counter-current exchanger to maintain the concentration gradient required for water reabsorption. These particular cells are located in the ascending limb of the vasa recta, which takes blood flow from the medulla back to the cortex. +The primary function of vasa recta ascending limb cells is to preserve the renal medulla's hypertonicity, necessary for the kidney's urine concentration mechanism. Unlike the vasa recta descending limb cells, the venous-like epithelial cells of the ascending vasa recta are highly fenestrated and lack pericyte coverage, which facilitates water reuptake. +As the blood flows through the ascending limb, it loses solutes and gains water, which is driven by the high solute concentration in the surrounding interstitium. This process acts in concert with cellular action in the descending limb and contributions from the so-called Loop of Henle, which helps with water and sodium chloride retrieval from the urine. +In the context of normal physiological processes, the function of the vasa recta ascending limb cells is essential in maintaining the body's overall fluid balance, electrolyte concentration, and systemic blood pressure. Any dysfunction in these cells may lead to impaired urine concentration or dilution capability of the kidney, potentially resulting in conditions like diabetes insipidus or hyponatremia."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1053/j.ajkd.2005.01.008"^^[string](http://www.w3.org/2001/XMLSchema#string) -### vaginal lubricant secreting cell `http://purl.obolibrary.org/obo/CL_0000436` + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1152/ajpregu.00657.2002"^^[string](http://www.w3.org/2001/XMLSchema#string) -#### Added -- [vaginal lubricant secreting cell](http://purl.obolibrary.org/obo/CL_0000436) SubClassOf [eukaryotic cell](http://purl.obolibrary.org/obo/CL_0000255) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1016/B978-0-323-35515-5.00009-9"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1111/apha.12026"^^[string](http://www.w3.org/2001/XMLSchema#string) -### vasa recta ascending limb cell `http://purl.obolibrary.org/obo/CL_1001131` + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1081/jdi-100101958"^^[string](http://www.w3.org/2001/XMLSchema#string) #### Added -- [vasa recta ascending limb cell](http://purl.obolibrary.org/obo/CL_1001131) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://cellxgene.cziscience.com/cellguide/CL_1001131"^^[string](http://www.w3.org/2001/XMLSchema#string) - -- [vasa recta ascending limb cell](http://purl.obolibrary.org/obo/CL_1001131) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. +- [vasa recta ascending limb cell](http://purl.obolibrary.org/obo/CL_1001131) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. The vasa recta ascending limb cells are specialized epithelial cells that are part of the vasa recta in the kidney, a crucial component of the renal medulla that functions as a counter-current exchanger to maintain the concentration gradient required for water reabsorption. These particular cells are located in the ascending limb of the vasa recta, which takes blood flow from the medulla back to the cortex. The primary function of vasa recta ascending limb cells is to preserve the renal medulla's hypertonicity, necessary for the kidney's urine concentration mechanism. Unlike the vasa recta descending limb cells, the venous-like epithelial cells of the ascending vasa recta are highly fenestrated and lack pericyte coverage, which facilitates water reuptake. @@ -5584,9 +11970,14 @@ In the context of normal physiological processes, the function of the vasa recta - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1081/jdi-100101958"^^[string](http://www.w3.org/2001/XMLSchema#string) -### vasa recta descending limb cell `http://purl.obolibrary.org/obo/CL_1001285` +### vasa recta cell `http://purl.obolibrary.org/obo/CL_1001036` +#### Removed +- [vasa recta cell](http://purl.obolibrary.org/obo/CL_1001036) SubClassOf [vein endothelial cell](http://purl.obolibrary.org/obo/CL_0002543) -#### Added + + +### vasa recta descending limb cell `http://purl.obolibrary.org/obo/CL_1001285` +#### Removed - [vasa recta descending limb cell](http://purl.obolibrary.org/obo/CL_1001285) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. Vasa recta descending limb cells are specialized epithelial cells found in the vasa recta, a network of blood vessels in the renal medulla. These cells line the interior surface of the descending limb of the vasa recta and play a crucial role in the filtering and regulation of substances within the blood. @@ -5600,36 +11991,44 @@ In addition to their central role in water and solute exchange, these cells cont - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1081/jdi-100101958"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [vasa recta descending limb cell](http://purl.obolibrary.org/obo/CL_1001285) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://cellxgene.cziscience.com/cellguide/CL_1001285"^^[string](http://www.w3.org/2001/XMLSchema#string) +#### Added +- [vasa recta descending limb cell](http://purl.obolibrary.org/obo/CL_1001285) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Vasa recta descending limb cells are specialized epithelial cells found in the vasa recta, a network of blood vessels in the renal medulla. These cells line the interior surface of the descending limb of the vasa recta and play a crucial role in the filtering and regulation of substances within the blood. +In contrast to vasa recta ascending limb cells, the arterial-like epithelial cells of the descending vasa recta are non-fenestrated and covered by a pericyte layer that regulates the medullary blood flow. They help keeping the body’s fluid and electrolyte balance in check through a process known as countercurrent exchange system, in which the cells of the descending limb are permeable to water but relatively impermeable to solutes, such as sodium and urea. As the blood descends into the medulla along its descending limb, water passively diffuses out of the vasa recta, concentrating the blood in solutes. +In addition to their central role in water and solute exchange, these cells contribute to maintaining the medullary osmotic gradient, a critical function to concentrate urine. The osmotic gradient is created by the counterflow of water and solutes between the descending and ascending limbs of the vasa recta and the adjacent Loop of Henle. The selective permeability of the descending limb cells allows them to maintain this gradient, which in turn helps to conserve water, a vital role in the overall function of the renal system. Thus, vasa recta descending limb cells have a significant function in renal physiology, particularly in osmoregulation and fluid balance."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1111/apha.12026#apha12026-bib-0039"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1053/j.ajkd.2005.01.008"^^[string](http://www.w3.org/2001/XMLSchema#string) -### vascular leptomeningeal cell `http://purl.obolibrary.org/obo/CL_4023051` -#### Removed -- [vascular leptomeningeal cell](http://purl.obolibrary.org/obo/CL_4023051) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A type of mesothelial fibroblast that is derived from the neural crest, is localized on blood vessels, and is a key component of the pia and arachnoid membranes surrounding the brain."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:27284195"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1152/ajpregu.00657.2002"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:37824655"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1081/jdi-100101958"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:30096314"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:29443965"^^[string](http://www.w3.org/2001/XMLSchema#string) +### vascular associated smooth muscle cell `http://purl.obolibrary.org/obo/CL_0000359` #### Added -- [vascular leptomeningeal cell](http://purl.obolibrary.org/obo/CL_4023051) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A transcriptomically distinct type of mesothelial fibroblast that is derived from the neural crest, is localized on blood vessels, and is a key component of the pia and arachnoid membranes surrounding the brain. The standard transcriptomic reference data for this cell type can be found on the CellxGene census under the collection: 'Transcriptomic cytoarchitecture reveals principles of human neocortex organization', dataset: 'Supercluster: Non-neuronal cells', Author Categories: 'CrossArea_subclass', clusters VLMC."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:27284195"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [vascular associated smooth muscle cell](http://purl.obolibrary.org/obo/CL_0000359) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:37824655"^^[string](http://www.w3.org/2001/XMLSchema#string) +Vascular associated smooth muscle cells (VSMCs) are specialized cells that constitute a major component of the blood vessel wall in the circulatory system. They derive their name from the predominantly smooth appearance under microscopic examination, as opposed to the striated appearance of cardiac and skeletal muscles. +A principal function of VSMCs is to regulate vascular tone, which directly dictates blood pressure and blood flow distribution across various body parts. This is achieved through coordinated contraction and relaxation of the muscles in response to a variety of extracellular signals. When a blood vessel is exposed to stimuli like pressure or injury, VSMCs contract, resulting in vasoconstriction and ultimately, an increase in blood pressure. Conversely, in response to vasodilators, these cells relax, leading to vasodilation and a consequent decrease in blood pressure. +VSMCs are also involved in vascular remodeling, a process where blood vessels adapt their structure to long-term changes in hemodynamic conditions or disease states. In diseases like atherosclerosis and hypertension, an aberrant proliferative and synthetic phenotype of VSMCs contributes to the formation of plaques, leading to vessel hardening or even occlusion. Recent research has further implicated these cells in immune responses, recognizing their function in leukocyte recruitment and inflammation, factors that are largely instrumental in vascular pathologies."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1093/cvr/cvs135"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://cellxgene.cziscience.com/e/5346f9c6-755e-4336-94cc-38706ec00c2f.cxg/"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1161/ATVBAHA.118.311229"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:30096314"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1093/cvr/cvy023"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:29443965"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.3389/fimmu.2020.599415"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.3390/ijms20225694"^^[string](http://www.w3.org/2001/XMLSchema#string) -### vein endothelial cell `http://purl.obolibrary.org/obo/CL_0002543` +- [vascular associated smooth muscle cell](http://purl.obolibrary.org/obo/CL_0000359) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://cellxgene.cziscience.com/cellguide/CL_0000359"^^[string](http://www.w3.org/2001/XMLSchema#string) -#### Added + +### vein endothelial cell `http://purl.obolibrary.org/obo/CL_0002543` +#### Removed - [vein endothelial cell](http://purl.obolibrary.org/obo/CL_0002543) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. Vein endothelial cells form a thin layer of squamous cells, the endothelium, lining the interior surface of veins throughout the body. They shape the inner cellular lining of the entire vascular system, including the heart, playing a crucial role in blood circulation. The unique characteristic compact arrangement of these cells enables veins to act as a barrier between the blood (that can contain foreign substances) and the surrounding venous tissue and maintain the integrity of the vascular system. @@ -5643,16 +12042,49 @@ Another significant function of vein endothelial cells is the regulation of bloo - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1038/s41569-022-00770-1"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [vein endothelial cell](http://purl.obolibrary.org/obo/CL_0002543) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://cellxgene.cziscience.com/cellguide/CL_0002543"^^[string](http://www.w3.org/2001/XMLSchema#string) +#### Added +- [vein endothelial cell](http://purl.obolibrary.org/obo/CL_0002543) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. +Vein endothelial cells form a thin layer of squamous cells, the endothelium, lining the interior surface of veins throughout the body. They shape the inner cellular lining of the entire vascular system, including the heart, playing a crucial role in blood circulation. The unique characteristic compact arrangement of these cells enables veins to act as a barrier between the blood (that can contain foreign substances) and the surrounding venous tissue and maintain the integrity of the vascular system. +The primary function of vein endothelial cells is to control the exchange of substances between the bloodstream and the surrounding tissues. They facilitate selective transportation of molecules depending on their size and solubility, including gases, nutrients, hormones, and waste products. Vein endothelial cells also play a protective role by inhibiting the translocation of toxins or pathogens from blood to tissues. Additionally, these cells are involved in blood coagulation and inflammation response, primarily by producing substances that inhibit blood clot formation under normal conditions and initiating clotting when necessary. +Another significant function of vein endothelial cells is the regulation of blood flow and blood pressure. They produce and release several substances, including nitric oxide and prostacyclin, which help in controlling vasodilation and vasoconstriction, thereby regulating blood pressure. These cells are also responsible for angiogenesis, the formation of new blood vessels, which is crucial during wound healing and in the formation of granulation tissue. Consequently, any dysfunction in vein endothelial cells can lead to severe health problems like atherosclerosis, hypertension, and thrombosis."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1007/s00441-008-0706-5"^^[string](http://www.w3.org/2001/XMLSchema#string) -### xanthophore cell `http://purl.obolibrary.org/obo/CL_0000430` + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1038/s41598-021-01360-w"^^[string](http://www.w3.org/2001/XMLSchema#string) -#### Added -- [xanthophore cell](http://purl.obolibrary.org/obo/CL_0000430) SubClassOf [eukaryotic cell](http://purl.obolibrary.org/obo/CL_0000255) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.3390/ijms20184411"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1038/s41569-022-00770-1"^^[string](http://www.w3.org/2001/XMLSchema#string) -### yolk sac hematopoietic stem cell `http://purl.obolibrary.org/obo/CL_0002354` + +### ventricular cardiac muscle cell `http://purl.obolibrary.org/obo/CL_2000046` #### Added +- [ventricular cardiac muscle cell](http://purl.obolibrary.org/obo/CL_2000046) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://cellxgene.cziscience.com/cellguide/CL_2000046"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [ventricular cardiac muscle cell](http://purl.obolibrary.org/obo/CL_2000046) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Ventricular cardiac muscle cells, or cardiomyocytes, are specialized cells found in the ventricular walls of the heart. They exhibit unique features, including centrally located nuclei, robust cytoskeletal structures, high mitochondria content, and intercalated discs, which contribute to their efficient pumping of blood throughout the body. +The main role of ventricular cardiac muscle cells is to coordinate contractions, enabling the heart to pump blood throughout the body. This is achieved through controlled ion movement across cell membranes, generating rhythmic electrical signals called action potentials. Intercalated discs between these cells aid synchronized contractions by allowing efficient signal spread through gap junctions. The high mitochondrial content ensures a constant energy supply for this ongoing contraction cycle. +Ventricular cardiac muscle cells contribute not only mechanically but also biochemically by secreting essential hormones like atrial natriuretic peptide and B-type natriuretic peptide for blood pressure regulation and cardiac remodeling. These cells exhibit low turnover under normal conditions, emphasizing their long-term stability, yet have limited regenerative capacity following cardiac injuries. Dysfunction in these cells can result in significant cardiac issues, including heart failure."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://www.ncbi.nlm.nih.gov/books/NBK572070/"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://www.ncbi.nlm.nih.gov/books/NBK535355"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1016/j.peptides.2018.05.012"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1126/science.aam5894"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### wide field retinal amacrine cell `http://purl.obolibrary.org/obo/CL_0004253` +#### Removed +- [wide field retinal amacrine cell](http://purl.obolibrary.org/obo/CL_0004253) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [human_reference_atlas](http://purl.obolibrary.org/obo/cl/cl-base#human_reference_atlas) + +- [wide field retinal amacrine cell](http://purl.obolibrary.org/obo/CL_0004253) [RO_0002175](http://purl.obolibrary.org/obo/RO_0002175) [NCBITaxon_9606](http://purl.obolibrary.org/obo/NCBITaxon_9606) + + + +### yolk sac hematopoietic stem cell `http://purl.obolibrary.org/obo/CL_0002354` +#### Removed - [yolk sac hematopoietic stem cell](http://purl.obolibrary.org/obo/CL_0002354) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) + diff --git a/src/ontology/reports/cl-edit.owl-obo-report.tsv b/src/ontology/reports/cl-edit.owl-obo-report.tsv index 164583607..c322af952 100644 --- a/src/ontology/reports/cl-edit.owl-obo-report.tsv +++ b/src/ontology/reports/cl-edit.owl-obo-report.tsv @@ -1,16 +1,137 @@ Level Rule Name Subject Property Value -WARN duplicate_label_synonym CL:1000347 oboInOwl:hasExactSynonym colonocyte +WARN missing_definition http://identifiers.org/ensembl/ENSG00000006128 IAO:0000115 +WARN missing_definition http://identifiers.org/ensembl/ENSG00000010327 IAO:0000115 +WARN missing_definition http://identifiers.org/ensembl/ENSG00000038295 IAO:0000115 +WARN missing_definition http://identifiers.org/ensembl/ENSG00000038945 IAO:0000115 +WARN missing_definition http://identifiers.org/ensembl/ENSG00000041982 IAO:0000115 +WARN missing_definition http://identifiers.org/ensembl/ENSG00000047936 IAO:0000115 +WARN missing_definition http://identifiers.org/ensembl/ENSG00000050730 IAO:0000115 +WARN missing_definition http://identifiers.org/ensembl/ENSG00000051128 IAO:0000115 +WARN missing_definition http://identifiers.org/ensembl/ENSG00000072694 IAO:0000115 +WARN missing_definition http://identifiers.org/ensembl/ENSG00000078898 IAO:0000115 +WARN missing_definition http://identifiers.org/ensembl/ENSG00000082482 IAO:0000115 +WARN missing_definition http://identifiers.org/ensembl/ENSG00000082684 IAO:0000115 +WARN missing_definition http://identifiers.org/ensembl/ENSG00000100292 IAO:0000115 +WARN missing_definition http://identifiers.org/ensembl/ENSG00000100362 IAO:0000115 +WARN missing_definition http://identifiers.org/ensembl/ENSG00000100604 IAO:0000115 +WARN missing_definition http://identifiers.org/ensembl/ENSG00000107796 IAO:0000115 +WARN missing_definition http://identifiers.org/ensembl/ENSG00000111215 IAO:0000115 +WARN missing_definition http://identifiers.org/ensembl/ENSG00000113532 IAO:0000115 +WARN missing_definition http://identifiers.org/ensembl/ENSG00000114805 IAO:0000115 +WARN missing_definition http://identifiers.org/ensembl/ENSG00000115593 IAO:0000115 +WARN missing_definition http://identifiers.org/ensembl/ENSG00000118513 IAO:0000115 +WARN missing_definition http://identifiers.org/ensembl/ENSG00000118523 IAO:0000115 +WARN missing_definition http://identifiers.org/ensembl/ENSG00000119547 IAO:0000115 +WARN missing_definition http://identifiers.org/ensembl/ENSG00000122585 IAO:0000115 +WARN missing_definition http://identifiers.org/ensembl/ENSG00000122852 IAO:0000115 +WARN missing_definition http://identifiers.org/ensembl/ENSG00000124302 IAO:0000115 +WARN missing_definition http://identifiers.org/ensembl/ENSG00000124491 IAO:0000115 +WARN missing_definition http://identifiers.org/ensembl/ENSG00000125869 IAO:0000115 +WARN missing_definition http://identifiers.org/ensembl/ENSG00000131097 IAO:0000115 +WARN missing_definition http://identifiers.org/ensembl/ENSG00000131471 IAO:0000115 +WARN missing_definition http://identifiers.org/ensembl/ENSG00000131747 IAO:0000115 +WARN missing_definition http://identifiers.org/ensembl/ENSG00000134443 IAO:0000115 +WARN missing_definition http://identifiers.org/ensembl/ENSG00000137252 IAO:0000115 +WARN missing_definition http://identifiers.org/ensembl/ENSG00000137573 IAO:0000115 +WARN missing_definition http://identifiers.org/ensembl/ENSG00000137709 IAO:0000115 +WARN missing_definition http://identifiers.org/ensembl/ENSG00000137804 IAO:0000115 +WARN missing_definition http://identifiers.org/ensembl/ENSG00000139329 IAO:0000115 +WARN missing_definition http://identifiers.org/ensembl/ENSG00000143171 IAO:0000115 +WARN missing_definition http://identifiers.org/ensembl/ENSG00000143196 IAO:0000115 +WARN missing_definition http://identifiers.org/ensembl/ENSG00000144229 IAO:0000115 +WARN missing_definition http://identifiers.org/ensembl/ENSG00000146469 IAO:0000115 +WARN missing_definition http://identifiers.org/ensembl/ENSG00000149591 IAO:0000115 +WARN missing_definition http://identifiers.org/ensembl/ENSG00000154080 IAO:0000115 +WARN missing_definition http://identifiers.org/ensembl/ENSG00000156689 IAO:0000115 +WARN missing_definition http://identifiers.org/ensembl/ENSG00000157005 IAO:0000115 +WARN missing_definition http://identifiers.org/ensembl/ENSG00000157404 IAO:0000115 +WARN missing_definition http://identifiers.org/ensembl/ENSG00000162399 IAO:0000115 +WARN missing_definition http://identifiers.org/ensembl/ENSG00000163735 IAO:0000115 +WARN missing_definition http://identifiers.org/ensembl/ENSG00000164120 IAO:0000115 +WARN missing_definition http://identifiers.org/ensembl/ENSG00000166803 IAO:0000115 +WARN missing_definition http://identifiers.org/ensembl/ENSG00000166959 IAO:0000115 +WARN missing_definition http://identifiers.org/ensembl/ENSG00000167306 IAO:0000115 +WARN missing_definition http://identifiers.org/ensembl/ENSG00000168079 IAO:0000115 +WARN missing_definition http://identifiers.org/ensembl/ENSG00000170323 IAO:0000115 +WARN missing_definition http://identifiers.org/ensembl/ENSG00000171303 IAO:0000115 +WARN missing_definition http://identifiers.org/ensembl/ENSG00000171346 IAO:0000115 +WARN missing_definition http://identifiers.org/ensembl/ENSG00000171848 IAO:0000115 +WARN missing_definition http://identifiers.org/ensembl/ENSG00000172673 IAO:0000115 +WARN missing_definition http://identifiers.org/ensembl/ENSG00000174501 IAO:0000115 +WARN missing_definition http://identifiers.org/ensembl/ENSG00000174807 IAO:0000115 +WARN missing_definition http://identifiers.org/ensembl/ENSG00000174948 IAO:0000115 +WARN missing_definition http://identifiers.org/ensembl/ENSG00000175063 IAO:0000115 +WARN missing_definition http://identifiers.org/ensembl/ENSG00000176009 IAO:0000115 +WARN missing_definition http://identifiers.org/ensembl/ENSG00000178031 IAO:0000115 +WARN missing_definition http://identifiers.org/ensembl/ENSG00000178538 IAO:0000115 +WARN missing_definition http://identifiers.org/ensembl/ENSG00000179902 IAO:0000115 +WARN missing_definition http://identifiers.org/ensembl/ENSG00000180801 IAO:0000115 +WARN missing_definition http://identifiers.org/ensembl/ENSG00000184530 IAO:0000115 +WARN missing_definition http://identifiers.org/ensembl/ENSG00000185668 IAO:0000115 +WARN missing_definition http://identifiers.org/ensembl/ENSG00000187908 IAO:0000115 +WARN missing_definition http://identifiers.org/ensembl/ENSG00000189056 IAO:0000115 +WARN missing_definition http://identifiers.org/ensembl/ENSG00000189058 IAO:0000115 +WARN missing_definition http://identifiers.org/ensembl/ENSG00000197085 IAO:0000115 +WARN missing_definition http://identifiers.org/ensembl/ENSG00000197353 IAO:0000115 +WARN missing_definition http://identifiers.org/ensembl/ENSG00000197943 IAO:0000115 +WARN missing_definition http://identifiers.org/ensembl/ENSG00000198901 IAO:0000115 +WARN missing_definition http://identifiers.org/ensembl/ENSG00000198963 IAO:0000115 +WARN missing_definition http://identifiers.org/ensembl/ENSG00000204262 IAO:0000115 +WARN missing_definition http://identifiers.org/ensembl/ENSG00000204305 IAO:0000115 +WARN missing_definition http://identifiers.org/ensembl/ENSG00000206073 IAO:0000115 +WARN missing_definition http://identifiers.org/ensembl/ENSG00000215182 IAO:0000115 +WARN missing_definition http://identifiers.org/ensembl/ENSG00000235665 IAO:0000115 +WARN missing_definition http://identifiers.org/ensembl/ENSG00000242265 IAO:0000115 +WARN missing_definition http://identifiers.org/ensembl/ENSG00000256193 IAO:0000115 +WARN missing_definition obo:CLM_1000001 IAO:0000115 +WARN missing_definition obo:CLM_1000002 IAO:0000115 +WARN missing_definition obo:CLM_1000003 IAO:0000115 +WARN missing_definition obo:CLM_1000004 IAO:0000115 +WARN missing_definition obo:CLM_1000005 IAO:0000115 +WARN missing_definition obo:CLM_1000006 IAO:0000115 +WARN missing_definition obo:CLM_1000008 IAO:0000115 +WARN missing_definition obo:CLM_1000009 IAO:0000115 +WARN missing_definition obo:CLM_1000010 IAO:0000115 +WARN missing_definition obo:CLM_1000026 IAO:0000115 +WARN missing_definition obo:CLM_1000027 IAO:0000115 +WARN missing_definition obo:CLM_1000031 IAO:0000115 +WARN missing_definition obo:CLM_1000032 IAO:0000115 +WARN missing_definition obo:CLM_1000041 IAO:0000115 +WARN missing_definition obo:CLM_1000043 IAO:0000115 +WARN missing_definition obo:CLM_1000046 IAO:0000115 +WARN missing_definition obo:CLM_1000047 IAO:0000115 +WARN missing_definition obo:CLM_1000052 IAO:0000115 +WARN missing_definition obo:CLM_1000053 IAO:0000115 +WARN missing_definition obo:CLM_1000054 IAO:0000115 +WARN missing_definition obo:CLM_1000056 IAO:0000115 +WARN missing_definition obo:CLM_1000059 IAO:0000115 +WARN missing_definition obo:CLM_1000061 IAO:0000115 +WARN missing_definition obo:CLM_1000063 IAO:0000115 +WARN missing_definition obo:CLM_1000065 IAO:0000115 +WARN missing_definition obo:CLM_1000066 IAO:0000115 +WARN missing_definition obo:CLM_1000067 IAO:0000115 +WARN missing_definition obo:CLM_1000068 IAO:0000115 +WARN missing_definition obo:CLM_1000069 IAO:0000115 +WARN missing_definition obo:CLM_1000070 IAO:0000115 +WARN missing_definition obo:CLM_1000071 IAO:0000115 +WARN missing_definition obo:CLM_1000072 IAO:0000115 +WARN missing_definition obo:CLM_1000073 IAO:0000115 +WARN missing_definition obo:CLM_1000074 IAO:0000115 +WARN missing_definition obo:CLM_1000075 IAO:0000115 +WARN missing_definition obo:CLM_1000079 IAO:0000115 +WARN missing_definition obo:CLM_1000080 IAO:0000115 +WARN missing_definition obo:CLM_1000081 IAO:0000115 +WARN missing_definition obo:CLM_1000082 IAO:0000115 +WARN missing_definition obo:CLM_1000083 IAO:0000115 +WARN missing_definition obo:CLM_1000085 IAO:0000115 WARN missing_definition CL:0000028 IAO:0000115 -WARN missing_definition CL:0000030 IAO:0000115 WARN missing_definition CL:0000036 IAO:0000115 WARN missing_definition CL:0000054 IAO:0000115 WARN missing_definition CL:0000069 IAO:0000115 WARN missing_definition CL:0000072 IAO:0000115 WARN missing_definition CL:0000078 IAO:0000115 WARN missing_definition CL:0000095 IAO:0000115 -WARN missing_definition CL:0000102 IAO:0000115 WARN missing_definition CL:0000109 IAO:0000115 -WARN missing_definition CL:0000112 IAO:0000115 WARN missing_definition CL:0000114 IAO:0000115 WARN missing_definition CL:0000117 IAO:0000115 WARN missing_definition CL:0000123 IAO:0000115 @@ -72,7 +193,6 @@ WARN missing_definition CL:0000489 IAO:0000115 WARN missing_definition CL:0000490 IAO:0000115 WARN missing_definition CL:0000520 IAO:0000115 WARN missing_definition CL:0000529 IAO:0000115 -WARN missing_definition CL:0000532 IAO:0000115 WARN missing_definition CL:0000544 IAO:0000115 WARN missing_definition CL:0000551 IAO:0000115 WARN missing_definition CL:0000555 IAO:0000115 @@ -82,7 +202,6 @@ WARN missing_definition CL:0000619 IAO:0000115 WARN missing_definition CL:0000661 IAO:0000115 WARN missing_definition CL:0000662 IAO:0000115 WARN missing_definition CL:0000676 IAO:0000115 -WARN missing_definition CL:0000678 IAO:0000115 WARN missing_definition CL:0000684 IAO:0000115 WARN missing_definition CL:0000687 IAO:0000115 WARN missing_definition CL:0000690 IAO:0000115 @@ -127,13 +246,17 @@ WARN missing_definition IAO:0000115 IAO:0000115 WARN missing_definition IAO:0000424 IAO:0000115 WARN missing_definition IAO:0000700 IAO:0000115 WARN missing_definition IAO:0100001 IAO:0000115 +WARN missing_definition RO:0015004 IAO:0000115 +WARN missing_definition SO:0001260 IAO:0000115 WARN missing_definition obo:uberon#HUMAN_PREFERRED IAO:0000115 WARN missing_definition obo:uberon#LATIN IAO:0000115 WARN missing_definition obo:uberon#PLURAL IAO:0000115 +WARN missing_definition dc:description IAO:0000115 +WARN missing_definition dc:license IAO:0000115 +WARN missing_definition dc:title IAO:0000115 WARN missing_definition oboInOwl:SubsetProperty IAO:0000115 WARN missing_definition oboInOwl:SynonymTypeProperty IAO:0000115 WARN missing_definition oboInOwl:consider IAO:0000115 -WARN missing_definition oboInOwl:hasAlternativeId IAO:0000115 WARN missing_definition oboInOwl:hasBroadSynonym IAO:0000115 WARN missing_definition oboInOwl:hasDbXref IAO:0000115 WARN missing_definition oboInOwl:hasExactSynonym IAO:0000115 @@ -158,11 +281,10 @@ INFO missing_superclass CL:0000076 rdfs:subClassOf INFO missing_superclass CL:0000080 rdfs:subClassOf INFO missing_superclass CL:0000082 rdfs:subClassOf INFO missing_superclass CL:0000103 rdfs:subClassOf -INFO missing_superclass CL:0000104 rdfs:subClassOf INFO missing_superclass CL:0000108 rdfs:subClassOf INFO missing_superclass CL:0000118 rdfs:subClassOf -INFO missing_superclass CL:0000122 rdfs:subClassOf INFO missing_superclass CL:0000148 rdfs:subClassOf +INFO missing_superclass CL:0000150 rdfs:subClassOf INFO missing_superclass CL:0000151 rdfs:subClassOf INFO missing_superclass CL:0000154 rdfs:subClassOf INFO missing_superclass CL:0000167 rdfs:subClassOf @@ -194,7 +316,6 @@ INFO missing_superclass CL:0000322 rdfs:subClassOf INFO missing_superclass CL:0000329 rdfs:subClassOf INFO missing_superclass CL:0000349 rdfs:subClassOf INFO missing_superclass CL:0000350 rdfs:subClassOf -INFO missing_superclass CL:0000402 rdfs:subClassOf INFO missing_superclass CL:0000412 rdfs:subClassOf INFO missing_superclass CL:0000413 rdfs:subClassOf INFO missing_superclass CL:0000438 rdfs:subClassOf @@ -210,7 +331,7 @@ INFO missing_superclass CL:0000514 rdfs:subClassOf INFO missing_superclass CL:0000531 rdfs:subClassOf INFO missing_superclass CL:0000536 rdfs:subClassOf INFO missing_superclass CL:0000593 rdfs:subClassOf -INFO missing_superclass CL:0000598 rdfs:subClassOf +INFO missing_superclass CL:0000622 rdfs:subClassOf INFO missing_superclass CL:0000656 rdfs:subClassOf INFO missing_superclass CL:0000691 rdfs:subClassOf INFO missing_superclass CL:0000693 rdfs:subClassOf @@ -243,9 +364,7 @@ INFO missing_superclass CL:0001079 rdfs:subClassOf INFO missing_superclass CL:0001080 rdfs:subClassOf INFO missing_superclass CL:0001081 rdfs:subClassOf INFO missing_superclass CL:0001082 rdfs:subClassOf -INFO missing_superclass CL:0002062 rdfs:subClassOf INFO missing_superclass CL:0002067 rdfs:subClassOf -INFO missing_superclass CL:0002075 rdfs:subClassOf INFO missing_superclass CL:0002076 rdfs:subClassOf INFO missing_superclass CL:0002077 rdfs:subClassOf INFO missing_superclass CL:0002078 rdfs:subClassOf @@ -253,7 +372,7 @@ INFO missing_superclass CL:0002089 rdfs:subClassOf INFO missing_superclass CL:0002132 rdfs:subClassOf INFO missing_superclass CL:0002148 rdfs:subClassOf INFO missing_superclass CL:0002152 rdfs:subClassOf -INFO missing_superclass CL:0002181 rdfs:subClassOf +INFO missing_superclass CL:0002180 rdfs:subClassOf INFO missing_superclass CL:0002200 rdfs:subClassOf INFO missing_superclass CL:0002202 rdfs:subClassOf INFO missing_superclass CL:0002205 rdfs:subClassOf @@ -272,7 +391,7 @@ INFO missing_superclass CL:0002316 rdfs:subClassOf INFO missing_superclass CL:0002319 rdfs:subClassOf INFO missing_superclass CL:0002320 rdfs:subClassOf INFO missing_superclass CL:0002327 rdfs:subClassOf -INFO missing_superclass CL:0002343 rdfs:subClassOf +INFO missing_superclass CL:0002332 rdfs:subClassOf INFO missing_superclass CL:0002344 rdfs:subClassOf INFO missing_superclass CL:0002346 rdfs:subClassOf INFO missing_superclass CL:0002366 rdfs:subClassOf @@ -299,21 +418,26 @@ INFO missing_superclass CL:0002537 rdfs:subClassOf INFO missing_superclass CL:0002540 rdfs:subClassOf INFO missing_superclass CL:0002541 rdfs:subClassOf INFO missing_superclass CL:0002559 rdfs:subClassOf +INFO missing_superclass CL:0002563 rdfs:subClassOf INFO missing_superclass CL:0002569 rdfs:subClassOf INFO missing_superclass CL:0002570 rdfs:subClassOf INFO missing_superclass CL:0002608 rdfs:subClassOf +INFO missing_superclass CL:0002610 rdfs:subClassOf +INFO missing_superclass CL:0002611 rdfs:subClassOf +INFO missing_superclass CL:0002612 rdfs:subClassOf +INFO missing_superclass CL:0002613 rdfs:subClassOf +INFO missing_superclass CL:0002614 rdfs:subClassOf INFO missing_superclass CL:0002621 rdfs:subClassOf INFO missing_superclass CL:0002631 rdfs:subClassOf INFO missing_superclass CL:0002632 rdfs:subClassOf INFO missing_superclass CL:0002633 rdfs:subClassOf -INFO missing_superclass CL:0002634 rdfs:subClassOf INFO missing_superclass CL:0002652 rdfs:subClassOf +INFO missing_superclass CL:0002656 rdfs:subClassOf INFO missing_superclass CL:0002659 rdfs:subClassOf INFO missing_superclass CL:0002673 rdfs:subClassOf INFO missing_superclass CL:0002681 rdfs:subClassOf INFO missing_superclass CL:0003001 rdfs:subClassOf INFO missing_superclass CL:0004246 rdfs:subClassOf -INFO missing_superclass CL:0004247 rdfs:subClassOf INFO missing_superclass CL:0004250 rdfs:subClassOf INFO missing_superclass CL:0005012 rdfs:subClassOf INFO missing_superclass CL:0005018 rdfs:subClassOf @@ -334,7 +458,6 @@ INFO missing_superclass CL:0008028 rdfs:subClassOf INFO missing_superclass CL:0008031 rdfs:subClassOf INFO missing_superclass CL:0008047 rdfs:subClassOf INFO missing_superclass CL:0009001 rdfs:subClassOf -INFO missing_superclass CL:0009006 rdfs:subClassOf INFO missing_superclass CL:0009007 rdfs:subClassOf INFO missing_superclass CL:0009008 rdfs:subClassOf INFO missing_superclass CL:0009014 rdfs:subClassOf @@ -349,10 +472,8 @@ INFO missing_superclass CL:0009022 rdfs:subClassOf INFO missing_superclass CL:0009023 rdfs:subClassOf INFO missing_superclass CL:0009024 rdfs:subClassOf INFO missing_superclass CL:0009025 rdfs:subClassOf -INFO missing_superclass CL:0009026 rdfs:subClassOf INFO missing_superclass CL:0009028 rdfs:subClassOf INFO missing_superclass CL:0009029 rdfs:subClassOf -INFO missing_superclass CL:0009030 rdfs:subClassOf INFO missing_superclass CL:0009031 rdfs:subClassOf INFO missing_superclass CL:0009032 rdfs:subClassOf INFO missing_superclass CL:0009033 rdfs:subClassOf @@ -364,7 +485,6 @@ INFO missing_superclass CL:0009038 rdfs:subClassOf INFO missing_superclass CL:0009039 rdfs:subClassOf INFO missing_superclass CL:0009040 rdfs:subClassOf INFO missing_superclass CL:0009041 rdfs:subClassOf -INFO missing_superclass CL:0009042 rdfs:subClassOf INFO missing_superclass CL:0009043 rdfs:subClassOf INFO missing_superclass CL:0009044 rdfs:subClassOf INFO missing_superclass CL:0009045 rdfs:subClassOf @@ -376,8 +496,6 @@ INFO missing_superclass CL:0009050 rdfs:subClassOf INFO missing_superclass CL:0009051 rdfs:subClassOf INFO missing_superclass CL:0009052 rdfs:subClassOf INFO missing_superclass CL:0009053 rdfs:subClassOf -INFO missing_superclass CL:0009054 rdfs:subClassOf -INFO missing_superclass CL:0009055 rdfs:subClassOf INFO missing_superclass CL:0009056 rdfs:subClassOf INFO missing_superclass CL:0009057 rdfs:subClassOf INFO missing_superclass CL:0009058 rdfs:subClassOf @@ -385,13 +503,10 @@ INFO missing_superclass CL:0009059 rdfs:subClassOf INFO missing_superclass CL:0009060 rdfs:subClassOf INFO missing_superclass CL:0009061 rdfs:subClassOf INFO missing_superclass CL:0009062 rdfs:subClassOf -INFO missing_superclass CL:0009063 rdfs:subClassOf INFO missing_superclass CL:0009064 rdfs:subClassOf INFO missing_superclass CL:0009065 rdfs:subClassOf INFO missing_superclass CL:0009066 rdfs:subClassOf -INFO missing_superclass CL:0009080 rdfs:subClassOf INFO missing_superclass CL:0009084 rdfs:subClassOf -INFO missing_superclass CL:0009089 rdfs:subClassOf INFO missing_superclass CL:0009092 rdfs:subClassOf INFO missing_superclass CL:0009093 rdfs:subClassOf INFO missing_superclass CL:0009094 rdfs:subClassOf @@ -419,7 +534,9 @@ INFO missing_superclass CL:0011013 rdfs:subClassOf INFO missing_superclass CL:0011030 rdfs:subClassOf INFO missing_superclass CL:0011105 rdfs:subClassOf INFO missing_superclass CL:0011106 rdfs:subClassOf +INFO missing_superclass CL:0011108 rdfs:subClassOf INFO missing_superclass CL:0011115 rdfs:subClassOf +INFO missing_superclass CL:0012001 rdfs:subClassOf INFO missing_superclass CL:0017002 rdfs:subClassOf INFO missing_superclass CL:0017003 rdfs:subClassOf INFO missing_superclass CL:0017010 rdfs:subClassOf @@ -433,15 +550,12 @@ INFO missing_superclass CL:0019003 rdfs:subClassOf INFO missing_superclass CL:0019015 rdfs:subClassOf INFO missing_superclass CL:0019017 rdfs:subClassOf INFO missing_superclass CL:0019018 rdfs:subClassOf -INFO missing_superclass CL:0019019 rdfs:subClassOf INFO missing_superclass CL:0019020 rdfs:subClassOf INFO missing_superclass CL:0019021 rdfs:subClassOf INFO missing_superclass CL:0019022 rdfs:subClassOf INFO missing_superclass CL:0019026 rdfs:subClassOf INFO missing_superclass CL:0019028 rdfs:subClassOf INFO missing_superclass CL:0019029 rdfs:subClassOf -INFO missing_superclass CL:0019031 rdfs:subClassOf -INFO missing_superclass CL:0019032 rdfs:subClassOf INFO missing_superclass CL:1000001 rdfs:subClassOf INFO missing_superclass CL:1000022 rdfs:subClassOf INFO missing_superclass CL:1000042 rdfs:subClassOf @@ -453,7 +567,6 @@ INFO missing_superclass CL:1000143 rdfs:subClassOf INFO missing_superclass CL:1000147 rdfs:subClassOf INFO missing_superclass CL:1000182 rdfs:subClassOf INFO missing_superclass CL:1000217 rdfs:subClassOf -INFO missing_superclass CL:1000222 rdfs:subClassOf INFO missing_superclass CL:1000236 rdfs:subClassOf INFO missing_superclass CL:1000239 rdfs:subClassOf INFO missing_superclass CL:1000245 rdfs:subClassOf @@ -461,11 +574,14 @@ INFO missing_superclass CL:1000271 rdfs:subClassOf INFO missing_superclass CL:1000272 rdfs:subClassOf INFO missing_superclass CL:1000296 rdfs:subClassOf INFO missing_superclass CL:1000298 rdfs:subClassOf +INFO missing_superclass CL:1000320 rdfs:subClassOf +INFO missing_superclass CL:1000321 rdfs:subClassOf +INFO missing_superclass CL:1000325 rdfs:subClassOf +INFO missing_superclass CL:1000327 rdfs:subClassOf INFO missing_superclass CL:1000330 rdfs:subClassOf INFO missing_superclass CL:1000331 rdfs:subClassOf INFO missing_superclass CL:1000332 rdfs:subClassOf INFO missing_superclass CL:1000333 rdfs:subClassOf -INFO missing_superclass CL:1000337 rdfs:subClassOf INFO missing_superclass CL:1000378 rdfs:subClassOf INFO missing_superclass CL:1000381 rdfs:subClassOf INFO missing_superclass CL:1000382 rdfs:subClassOf @@ -487,6 +603,7 @@ INFO missing_superclass CL:1000491 rdfs:subClassOf INFO missing_superclass CL:1000492 rdfs:subClassOf INFO missing_superclass CL:1000493 rdfs:subClassOf INFO missing_superclass CL:1000494 rdfs:subClassOf +INFO missing_superclass CL:1000495 rdfs:subClassOf INFO missing_superclass CL:1000497 rdfs:subClassOf INFO missing_superclass CL:1000500 rdfs:subClassOf INFO missing_superclass CL:1000504 rdfs:subClassOf @@ -496,6 +613,7 @@ INFO missing_superclass CL:1000546 rdfs:subClassOf INFO missing_superclass CL:1000549 rdfs:subClassOf INFO missing_superclass CL:1000612 rdfs:subClassOf INFO missing_superclass CL:1000692 rdfs:subClassOf +INFO missing_superclass CL:1000706 rdfs:subClassOf INFO missing_superclass CL:1000746 rdfs:subClassOf INFO missing_superclass CL:1001005 rdfs:subClassOf INFO missing_superclass CL:1001009 rdfs:subClassOf @@ -504,9 +622,8 @@ INFO missing_superclass CL:1001123 rdfs:subClassOf INFO missing_superclass CL:1001124 rdfs:subClassOf INFO missing_superclass CL:1001225 rdfs:subClassOf INFO missing_superclass CL:1001428 rdfs:subClassOf +INFO missing_superclass CL:1001430 rdfs:subClassOf INFO missing_superclass CL:1001433 rdfs:subClassOf -INFO missing_superclass CL:1001516 rdfs:subClassOf -INFO missing_superclass CL:1001517 rdfs:subClassOf INFO missing_superclass CL:1001561 rdfs:subClassOf INFO missing_superclass CL:1001569 rdfs:subClassOf INFO missing_superclass CL:1001576 rdfs:subClassOf @@ -514,6 +631,7 @@ INFO missing_superclass CL:1001579 rdfs:subClassOf INFO missing_superclass CL:1001580 rdfs:subClassOf INFO missing_superclass CL:1001581 rdfs:subClassOf INFO missing_superclass CL:1001582 rdfs:subClassOf +INFO missing_superclass CL:1001593 rdfs:subClassOf INFO missing_superclass CL:1001601 rdfs:subClassOf INFO missing_superclass CL:1001603 rdfs:subClassOf INFO missing_superclass CL:1001606 rdfs:subClassOf @@ -521,6 +639,7 @@ INFO missing_superclass CL:1001607 rdfs:subClassOf INFO missing_superclass CL:1001608 rdfs:subClassOf INFO missing_superclass CL:1001609 rdfs:subClassOf INFO missing_superclass CL:1001611 rdfs:subClassOf +INFO missing_superclass CL:1100001 rdfs:subClassOf INFO missing_superclass CL:2000000 rdfs:subClassOf INFO missing_superclass CL:2000001 rdfs:subClassOf INFO missing_superclass CL:2000004 rdfs:subClassOf @@ -547,7 +666,6 @@ INFO missing_superclass CL:2000027 rdfs:subClassOf INFO missing_superclass CL:2000028 rdfs:subClassOf INFO missing_superclass CL:2000029 rdfs:subClassOf INFO missing_superclass CL:2000030 rdfs:subClassOf -INFO missing_superclass CL:2000031 rdfs:subClassOf INFO missing_superclass CL:2000032 rdfs:subClassOf INFO missing_superclass CL:2000033 rdfs:subClassOf INFO missing_superclass CL:2000034 rdfs:subClassOf @@ -609,7 +727,6 @@ INFO missing_superclass CL:2000094 rdfs:subClassOf INFO missing_superclass CL:2000095 rdfs:subClassOf INFO missing_superclass CL:2000096 rdfs:subClassOf INFO missing_superclass CL:2000097 rdfs:subClassOf -INFO missing_superclass CL:3000000 rdfs:subClassOf INFO missing_superclass CL:3000002 rdfs:subClassOf INFO missing_superclass CL:3000003 rdfs:subClassOf INFO missing_superclass CL:3000004 rdfs:subClassOf @@ -618,7 +735,6 @@ INFO missing_superclass CL:4023009 rdfs:subClassOf INFO missing_superclass CL:4023012 rdfs:subClassOf INFO missing_superclass CL:4023013 rdfs:subClassOf INFO missing_superclass CL:4023019 rdfs:subClassOf -INFO missing_superclass CL:4023035 rdfs:subClassOf INFO missing_superclass CL:4023038 rdfs:subClassOf INFO missing_superclass CL:4023039 rdfs:subClassOf INFO missing_superclass CL:4023043 rdfs:subClassOf @@ -635,7 +751,6 @@ INFO missing_superclass CL:4023072 rdfs:subClassOf INFO missing_superclass CL:4023074 rdfs:subClassOf INFO missing_superclass CL:4023076 rdfs:subClassOf INFO missing_superclass CL:4023077 rdfs:subClassOf -INFO missing_superclass CL:4023079 rdfs:subClassOf INFO missing_superclass CL:4023083 rdfs:subClassOf INFO missing_superclass CL:4023086 rdfs:subClassOf INFO missing_superclass CL:4023087 rdfs:subClassOf @@ -657,7 +772,6 @@ INFO missing_superclass CL:4023124 rdfs:subClassOf INFO missing_superclass CL:4023125 rdfs:subClassOf INFO missing_superclass CL:4023127 rdfs:subClassOf INFO missing_superclass CL:4023128 rdfs:subClassOf -INFO missing_superclass CL:4023130 rdfs:subClassOf INFO missing_superclass CL:4023154 rdfs:subClassOf INFO missing_superclass CL:4023159 rdfs:subClassOf INFO missing_superclass CL:4023168 rdfs:subClassOf @@ -681,34 +795,23 @@ INFO missing_superclass CL:4030031 rdfs:subClassOf INFO missing_superclass CL:4030033 rdfs:subClassOf INFO missing_superclass CL:4030040 rdfs:subClassOf INFO missing_superclass CL:4030058 rdfs:subClassOf -INFO missing_superclass CL:4030059 rdfs:subClassOf INFO missing_superclass CL:4030060 rdfs:subClassOf INFO missing_superclass CL:4030061 rdfs:subClassOf INFO missing_superclass CL:4030062 rdfs:subClassOf -INFO missing_superclass CL:4030063 rdfs:subClassOf -INFO missing_superclass CL:4030064 rdfs:subClassOf -INFO missing_superclass CL:4030065 rdfs:subClassOf -INFO missing_superclass CL:4030067 rdfs:subClassOf -INFO missing_superclass CL:4030068 rdfs:subClassOf INFO missing_superclass CL:4032001 rdfs:subClassOf INFO missing_superclass CL:4033000 rdfs:subClassOf INFO missing_superclass CL:4033001 rdfs:subClassOf INFO missing_superclass CL:4033002 rdfs:subClassOf INFO missing_superclass CL:4033003 rdfs:subClassOf -INFO missing_superclass CL:4033004 rdfs:subClassOf -INFO missing_superclass CL:4033005 rdfs:subClassOf INFO missing_superclass CL:4033006 rdfs:subClassOf INFO missing_superclass CL:4033007 rdfs:subClassOf INFO missing_superclass CL:4033008 rdfs:subClassOf INFO missing_superclass CL:4033009 rdfs:subClassOf INFO missing_superclass CL:4033010 rdfs:subClassOf -INFO missing_superclass CL:4033011 rdfs:subClassOf -INFO missing_superclass CL:4033012 rdfs:subClassOf INFO missing_superclass CL:4033013 rdfs:subClassOf INFO missing_superclass CL:4033015 rdfs:subClassOf INFO missing_superclass CL:4033020 rdfs:subClassOf INFO missing_superclass CL:4033021 rdfs:subClassOf -INFO missing_superclass CL:4033022 rdfs:subClassOf INFO missing_superclass CL:4033025 rdfs:subClassOf INFO missing_superclass CL:4033026 rdfs:subClassOf INFO missing_superclass CL:4033040 rdfs:subClassOf @@ -731,12 +834,14 @@ INFO missing_superclass CL:4033073 rdfs:subClassOf INFO missing_superclass CL:4033074 rdfs:subClassOf INFO missing_superclass CL:4033075 rdfs:subClassOf INFO missing_superclass CL:4033076 rdfs:subClassOf -INFO missing_superclass CL:4033077 rdfs:subClassOf INFO missing_superclass CL:4033078 rdfs:subClassOf INFO missing_superclass CL:4033079 rdfs:subClassOf -INFO missing_superclass CL:4033080 rdfs:subClassOf INFO missing_superclass CL:4033081 rdfs:subClassOf INFO missing_superclass CL:4033082 rdfs:subClassOf +INFO missing_superclass CL:4033087 rdfs:subClassOf +INFO missing_superclass CL:4033089 rdfs:subClassOf +INFO missing_superclass CL:4033091 rdfs:subClassOf +INFO missing_superclass CL:4033092 rdfs:subClassOf INFO missing_superclass CL:4040004 rdfs:subClassOf INFO missing_superclass CL:4047001 rdfs:subClassOf INFO missing_superclass CL:4047002 rdfs:subClassOf @@ -745,6 +850,19 @@ INFO missing_superclass CL:4047004 rdfs:subClassOf INFO missing_superclass CL:4047005 rdfs:subClassOf INFO missing_superclass CL:4047018 rdfs:subClassOf INFO missing_superclass CL:4047019 rdfs:subClassOf -INFO missing_superclass CL:4047051 rdfs:subClassOf +INFO missing_superclass CL:4047023 rdfs:subClassOf +INFO missing_superclass CL:4047025 rdfs:subClassOf INFO missing_superclass CL:4047052 rdfs:subClassOf +INFO missing_superclass CL:4047101 rdfs:subClassOf +INFO missing_superclass CL:4052001 rdfs:subClassOf INFO missing_superclass CL:4052002 rdfs:subClassOf +INFO missing_superclass CL:4052015 rdfs:subClassOf +INFO missing_superclass CL:4052018 rdfs:subClassOf +INFO missing_superclass CL:4052020 rdfs:subClassOf +INFO missing_superclass CL:4052021 rdfs:subClassOf +INFO missing_superclass CL:4052022 rdfs:subClassOf +INFO missing_superclass CL:4052023 rdfs:subClassOf +INFO missing_superclass CL:4052024 rdfs:subClassOf +INFO missing_superclass CL:4052025 rdfs:subClassOf +INFO missing_superclass CL:4052028 rdfs:subClassOf +INFO missing_superclass SO:0001260 rdfs:subClassOf diff --git a/src/ontology/subsets/blood_and_immune_upper_slim.json b/src/ontology/subsets/blood_and_immune_upper_slim.json index fdd02d37b..08f6e55c0 100644 --- a/src/ontology/subsets/blood_and_immune_upper_slim.json +++ b/src/ontology/subsets/blood_and_immune_upper_slim.json @@ -4,9 +4,9 @@ "meta" : { "basicPropertyValues" : [ { "pred" : "http://www.w3.org/2002/07/owl#versionInfo", - "val" : "2024-09-26" + "val" : "2025-01-08" } ], - "version" : "http://purl.obolibrary.org/obo/cl/releases/2024-09-26/subsets/blood_and_immune_upper_slim.owl" + "version" : "http://purl.obolibrary.org/obo/cl/releases/2025-01-08/subsets/blood_and_immune_upper_slim.owl" }, "nodes" : [ { "id" : "http://purl.obolibrary.org/obo/CL_0000000", @@ -18,7 +18,7 @@ "xrefs" : [ "CARO:mah" ] }, "comments" : [ "The definition of cell is intended to represent all cells, and thus a cell is defined as a material entity and not an anatomical structure, which implies that it is part of an organism (or the entirety of one)." ], - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/ubprop#_upper_level" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/ubprop#_upper_level" ], "xrefs" : [ { "val" : "CALOHA:TS-2035" }, { @@ -50,6 +50,7 @@ "val" : "A cell found in the embryo before the formation of all the gem layers is complete.", "xrefs" : [ "GOC:tfm" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "ZFA:0009002" } ] @@ -64,7 +65,7 @@ "xrefs" : [ "GOC:tfm", "MESH:D013234" ] }, "comments" : [ "This term applies to metazoan. For plant stem cells, consider using PO:0004011 ‘initial cell’ or its parent PO:0004010 ‘meristematic cell’." ], - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#general_cell_types_upper_slim", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#general_cell_types_upper_slim", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "animal stem cell" @@ -91,7 +92,7 @@ "xrefs" : [ "GOC:add", "GOC:dsd", "GOC:tfm", "PMID:19022770", "http://en.wikipedia.org/wiki/Hematopoietic_stem_cell" ] }, "comments" : [ "Markers differ between species, and two sets of markers have been described for mice. HSCs are reportedly CD34-positive, CD45-positive, CD48-negative, CD150-positive, CD133-positive, and CD244-negative." ], - "subsets" : [ "http://purl.obolibrary.org/obo/cl#blood_and_immune_upper_slim", "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#blood_and_immune_upper_slim", "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "blood forming stem cell" @@ -133,7 +134,7 @@ "val" : "A progenitor cell committed to the erythroid lineage.", "xrefs" : [ "GOC:add", "ISBN:0721601464" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#blood_and_immune_upper_slim", "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#blood_and_immune_upper_slim", "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003000", "pred" : "hasRelatedSynonym", @@ -171,6 +172,7 @@ "xrefs" : [ "GOC:add", "PMID:1104740", "http://en.wikipedia.org/wiki/Monoblast", "http://www.copewithcytokines.de" ] }, "comments" : [ "Morphology: mononuclear cell, diameter 12-20 _M, non-granular, N/C ratio 3/1 - 4/1; markers: CD11b (shared with many other myeloid cells); location: Adult: bone marrow; fetal: liver, Yolk Sac; role or process: hematopoiesis, monocyte development; lineage: hematopoietic, myeloid." ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003000", "pred" : "hasRelatedSynonym", @@ -202,6 +204,7 @@ "val" : "A stem cell that can give rise to multiple lineages of cells.", "xrefs" : [ "GOC:add" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "multi-fate stem cell" @@ -231,7 +234,7 @@ "xrefs" : [ "GOC:add", "ISBN:0878932437", "MESH:D023461" ] }, "comments" : [ "This cell type is intended to be compatible with any vertebrate common myeloid progenitor. For mammalian CMP known to be CD34-positive, please use the term 'common myeloid progenitor, CD34-positive' (CL_0001059)." ], - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "common myeloid precursor" @@ -287,7 +290,7 @@ "xrefs" : [ "GOC:add", "GOC:dsd", "GOC:tfm", "MESH:D055015", "PMID:16647566", "http://en.wikipedia.org/wiki/Megakaryocyte-erythroid_progenitor_cell" ] }, "comments" : [ "MEPs are reportedly CD19-negative, CD34-negative, CD45RA-negative, CD110-positive, CD117-positive, and SCA1-negative and reportedly express the transcription factors GATA-1 and NF-E2." ], - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "CFU-EM" @@ -328,7 +331,7 @@ "xrefs" : [ "GOC:add", "GOC:dsd", "GOC:tfm", "PMID:10407577", "PMID:16551251" ] }, "comments" : [ "CLP are CD7-positive, CD10-positive, CD19-negative, CD34-positive, CD45RA-positive, CD79a-negative, CD127-positive, AA4.1-positive, RAG-negative, Sca-1-low, sIgM-negative, sIgD-negative, TdT-negative, Vpre-B-negative, and pre-BCR-negative. Expression of transcription factors include E2A-positive, EBF-positive, Ikaros-negative, PU.1-negative, and Pax5-negative." ], - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "common lymphocyte precursor" @@ -376,6 +379,7 @@ "val" : "A stem cell from which all cells of the body can form.", "xrefs" : [ "GOC:add", "GOC:tfm" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "totipotential stem cell" @@ -398,7 +402,7 @@ "xrefs" : [ "SANBI:mhl" ] }, "comments" : [ "define using PATO mulit-potent or oligopotent?" ], - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "blast cell" @@ -418,6 +422,7 @@ "val" : "A cell that is commited to differentiating into a muscle cell. Embryonic myoblasts develop from the mesoderm. They undergo proliferation, migrate to their various sites, and then differentiate into the appropriate form of myocytes. Myoblasts also occur as transient populations of cells in muscles undergoing repair.", "xrefs" : [ "GOC:tfm", "MESH:D032446", "PMID:21849021" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "BTO:0000222" }, { @@ -442,7 +447,7 @@ "xrefs" : [ "ISBN:0517223651", "MESH:D005347", "http://en.wikipedia.org/wiki/Fibroblast" ] }, "comments" : [ "These cells may be vimentin-positive, fibronectin-positive, fsp1-positive, MMP-1-positive, collagen I-positive, collagen III-positive, and alpha-SMA-negative." ], - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#general_cell_types_upper_slim", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#general_cell_types_upper_slim", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "xrefs" : [ { "val" : "BTO:0000452" }, { @@ -470,7 +475,7 @@ "val" : "A cell that is usually found in a two-dimensional sheet with a free surface. The cell has a cytoskeleton that allows for tight cell to cell contact and for cell polarity where apical part is directed towards the lumen and the basal part to the basal lamina.", "xrefs" : [ "FB:ma", "GOC:tfm", "MESH:D004847" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#general_cell_types_upper_slim", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#general_cell_types_upper_slim", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "epitheliocyte" @@ -507,7 +512,7 @@ "val" : "An endothelial cell that lines the vasculature.", "xrefs" : [ "GOC:tfm" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "xrefs" : [ { "val" : "ZFA:0009036" } ], @@ -525,7 +530,7 @@ "val" : "Any epithelial cell that is part of some squamous epithelium.", "xrefs" : [ "FBC:Autogenerated" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "CALOHA:TS-1249" }, { @@ -541,6 +546,7 @@ "val" : "A cell which moves among different tissues of the body, via blood, lymph, or other medium.", "xrefs" : [ "GOC:add" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "ZFA:0009043" } ] @@ -554,7 +560,7 @@ "val" : "A cell found predominately in the blood.", "xrefs" : [ "GOC:add", "GOC:tfm" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#general_cell_types_upper_slim" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#general_cell_types_upper_slim", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "FMA:62844" }, { @@ -572,7 +578,7 @@ "val" : "A type of lymphocyte whose defining characteristic is the expression of a T cell receptor complex.", "xrefs" : [ "GOC:add", "GOC:tfm", "ISBN:0781735149" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#general_cell_types_upper_slim", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#general_cell_types_upper_slim", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "T lymphocyte" @@ -617,7 +623,7 @@ "xrefs" : [ "GOC:add", "GOC:tfm", "GO_REF:0000031", "ISBN:0781735149", "PMID:10428500", "PMID:15055519", "PMID:17380158" ] }, "comments" : [ "Morphology: Highly vesicular; markers: Surface: RANK, cFMS (MCSF receptor); Secreted: cathepsin K and TRAP (tartate resistant acid phosphatase); transcription factors: PU.1, cFOS, MITF, NFkB (p52); role or process: tissue remodelling: bone resorption; lineage: hematopoietic, myeloid." ], - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "pred" : "hasRelatedSynonym", "val" : "chondroclast" @@ -632,6 +638,12 @@ "val" : "MESH:D010010" }, { "val" : "ZFA:0009047" + }, { + "val" : "https://cellxgene.cziscience.com/cellguide/CL_0000092" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/description", + "val" : "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nOsteoclasts, derived from the monocyte/macrophage lineage, play a crucial role in bone remodeling through bone resorption. They are distinguished from other cells by their large size and their unique ability to secrete enzymes and acids that dissolve the calcium phosphate in bone. The formation of osteoclasts is influenced by two primary factors: macrophage colony-stimulating factor (M-CSF) and the ligand-activated receptor (RANKL) of nuclear factor kappa B (NF-κB).\nOsteoclasts also collaborate with osteoblasts, responsible for new bone formation, to maintain bone health and adapt bone structure. Their coordinated actions allow continuous remodeling while preserving overall bone strength and integrity. Imbalances in osteoclast activity can lead to pathological conditions. For example, excessive activity may contribute to diseases like osteoporosis, periprosthetic osteolysis, bone tumors, and Paget's disease. Other the other hand, osteoclast deficiency ca result in conditions like osteopetrosis." } ] } }, { @@ -643,7 +655,7 @@ "val" : "A leukocyte with abundant granules in the cytoplasm.", "xrefs" : [ "GOC:amm", "GOC:tfm", "MESH:D006098", "http://en.wikipedia.org/wiki/Granulocyte" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "granular leucocyte" @@ -680,7 +692,7 @@ "xrefs" : [ "GOC:add", "GOC:dsd", "GOC:tfm", "ISBN:068340007X", "MESH:D008407", "PMCID:PMC1312421", "PMCID:PMC2855166", "PMID:15153310", "PMID:16455980", "PMID:19671378", "PMID:212366338", "PMID:9354811" ] }, "comments" : [ "Mast cells are generally integrin beta-7-negative and positive for TLR2, TLR3, TLR4, TLR5, TLR7, TLR9, C3aR, C5aR, CR3, CR4, VEGF, FGF2, and renin. They can express MHC Class I and II on their surface. Activated murine mast cells (IgE+Antigen) were capable of expressing the following co-stimulatory molecules: CD95 (Fas), CD120b, CD137 (4-1BB), CD153 (CD30L), CD154 (CD40L), GITR, ICOSL, OX40L, PD-L1, and PD-L2. Note that there was some mouse strain variation. Mast cells have also been demonstrated to produce bFGF, CCL2, CCL4, CCL5, CCL11, CCL20, CXCL2, CXCL8, CXCL10, GM-CSF, IFN-gamma, IL-1, IL-2, IL-3, IL-8, IL-10, IL-11, IL-12, IL-13, IL-16, IL-25, IL-18, MIP-1, prostaglandin D2, SCF, TGF-beta, TNF-alpha, TSLP, VEGF, and XCL1. They express the transcription factors Transcription factors AP-1, GATA1, MITF, Notch2, PIAS3, PU.1, and STAT5." ], - "subsets" : [ "http://purl.obolibrary.org/obo/cl#blood_and_immune_upper_slim", "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#blood_and_immune_upper_slim", "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "histaminocyte" @@ -718,7 +730,7 @@ "val" : "A vertebrate phagocyte with a single nucleus.", "xrefs" : [ "GOC:add", "GOC:tfm", "ISBN:0781735149" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "xrefs" : [ { "val" : "BTO:0001433" }, { @@ -731,7 +743,7 @@ "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" }, { "pred" : "http://purl.org/dc/terms/description", - "val" : "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional.\n\nMononuclear phagocytes are immune cells that form a critical part of the body's innate immune system, the body's first line of defense against infections. Mononuclear phagocytes are characterized by the presence of a single, large nucleus. The ‘Mononuclear Phagocyte System’ nomenclature was introduced to distinguish mononuclear monocytes and macrophages from other cells with multiple nuclei. However, the cells within the mononuclear phagocyte system represent a highly heterogeneous group, all of which are able to perform highly efficient phagocytosis - engulfing and digesting microbes and cellular debris to fight infections and to maintain normal tissue homeostasis. \nIn addition to phagocytosis, mononuclear phagocytes also secrete chemical compounds to recruit other immune cells to a site of infection. These cells produce different types of signaling molecules, including cytokines, chemokines, and reactive oxygen species, triggering a cascade of responses to ensure rapid and efficient containment and neutralization of invading pathogens. These cells are also involved in antigen presentation, a process essential for stimulating an adaptive immune response. They can process and present antigens to T cells, thereby linking the innate and adaptive immune responses.\nMononuclear phagocytes play key roles in tissue repair and remodeling. After infection or injury, these cells help in the clearance of dead cells and debris, a crucial step in the initiation of tissue remodeling and the resolution of inflammation. Overall, mononuclear phagocytes are versatile cells that have tailored their functions to meet the unique challenges of different tissues within the body. They are pivotal in homeostasis, immunity, and inflammation, making them important aspects in a range of human diseases including infection, autoimmunity, and cancer." + "val" : "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nMononuclear phagocytes are immune cells that form a critical part of the body's innate immune system, the body's first line of defense against infections. Mononuclear phagocytes are characterized by the presence of a single, large nucleus. The ‘Mononuclear Phagocyte System’ nomenclature was introduced to distinguish mononuclear monocytes and macrophages from other cells with multiple nuclei. However, the cells within the mononuclear phagocyte system represent a highly heterogeneous group, all of which are able to perform highly efficient phagocytosis - engulfing and digesting microbes and cellular debris to fight infections and to maintain normal tissue homeostasis. \nIn addition to phagocytosis, mononuclear phagocytes also secrete chemical compounds to recruit other immune cells to a site of infection. These cells produce different types of signaling molecules, including cytokines, chemokines, and reactive oxygen species, triggering a cascade of responses to ensure rapid and efficient containment and neutralization of invading pathogens. These cells are also involved in antigen presentation, a process essential for stimulating an adaptive immune response. They can process and present antigens to T cells, thereby linking the innate and adaptive immune responses.\nMononuclear phagocytes play key roles in tissue repair and remodeling. After infection or injury, these cells help in the clearance of dead cells and debris, a crucial step in the initiation of tissue remodeling and the resolution of inflammation. Overall, mononuclear phagocytes are versatile cells that have tailored their functions to meet the unique challenges of different tissues within the body. They are pivotal in homeostasis, immunity, and inflammation, making them important aspects in a range of human diseases including infection, autoimmunity, and cancer." } ] } }, { @@ -744,7 +756,7 @@ "xrefs" : [ "GOC:tfm", "MESH:D042783", "PMID:21275341", "http://en.wikipedia.org/wiki/Endothelial_cell", "https://sourceforge.net/tracker/?func=detail&atid=440764&aid=3364936&group_id=36855" ] }, "comments" : [ "From FMA: 9.07.2001: Endothelial cell has always been classified as a kind of epithelial cell, specifically a squamous cell but that is not true. First, endothelial cell can either be squamous or cuboidal (e.g. high-endothelial cell) and secondly, it has different embryological derivation (mesodermal) than a true epithelial cell (ectodermal and endodermal). The basis for present classification is the fact that it comprises the outermost layer or lining of anatomical structures (location-based) but a better structural basis for the differentia is the cytoskeleton of the cell. Endothelial cell has vimentin filaments while an epithelial cell has keratin filaments. [Onard]." ], - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "endotheliocyte" @@ -772,6 +784,7 @@ "val" : "Ectoderm destined to be nervous tissue.", "xrefs" : [ "GOC:tfm", "ISBN:068340007X" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "neurectoderm cell" @@ -790,7 +803,7 @@ "xrefs" : [ "FB:ma", "GOC:dsd", "PMCID:PMC2613570", "PMID:10102814", "PMID:16923606", "PMID:17986482", "PMID:19960544", "http://en.wikipedia.org/wiki/Mesenchymal_stem_cell", "http://www.copewithcytokines.de/cope.cgi?key=mesenchymal%20stem%20cells" ] }, "comments" : [ "Many but not all mesenchymal cells derive from the mesoderm. MSCs are reportedly CD3-negative, CD4-negative, CD5-negative, CD8-negative, CD11a-negative, CD11b-negative, CD14-negative, CD19-negative, CD29-positive, CD31-negative, CD34-negative, CD38-negative, CD40-negative, CD44-positive, CD45-negative, CD49-positive, CD54-positive, CD66b-negative, CD79a-negative, CD80-negative, CD102-positive, CD106-positive, CD117-positive, CD121a-positive, CD121b-positive, CD123-positive, CD124-positive, CD133-negative, CD146-positive, CD166-positive, CD271-positive, B220-negative, Gr1-negative, MHCI-positive, MHCII-negative, SSEA4-negative, sca1-positive, Ter119-negative, and glycophorin A-negative. Cultured MSCs are capable of producing stem cell factor, IL7, IL8, IL11, TGF-beta, cofilin, galectin-1, laminin-receptor 1, cyclophilin A, and MMP-2." ], - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "pred" : "hasNarrowSynonym", "val" : "bone marrow stromal cells" @@ -862,7 +875,7 @@ "xrefs" : [ "GOC:add", "ISBN:0781735149" ] }, "comments" : [ "Note change of name; nearly all somatic cells can present antigens to T cells via MHC Class I complexes leading to effector responses, but professional antigen presenting cells constitutively express MHC Class II as well as costimulatory molecules, and thus can initiate immune responses via T cells." ], - "subsets" : [ "http://purl.obolibrary.org/obo/cl#blood_and_immune_upper_slim", "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#blood_and_immune_upper_slim", "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003000", "pred" : "hasRelatedSynonym", @@ -881,7 +894,7 @@ "val" : "A cell that specializes in controlled release of one or more substances.", "xrefs" : [ "GOC:tfm", "ISBN:0721662544" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "BTO:0003659" }, { @@ -897,7 +910,7 @@ "val" : "A cell whose primary function is to shorten.", "xrefs" : [ "FB:ma" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ] + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ] } }, { "id" : "http://purl.obolibrary.org/obo/CL_0000187", @@ -908,7 +921,7 @@ "val" : "A mature contractile cell, commonly known as a myocyte. This cell has as part of its cytoplasm myofibrils organized in various patterns.", "xrefs" : [ "MESH:D032342" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "muscle fiber" @@ -945,6 +958,7 @@ "val" : "A cell whose function is determined by the generation or the reception of an electric signal.", "xrefs" : [ "FB:ma" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "ZFA:0009128" } ] @@ -958,6 +972,7 @@ "val" : "A cell within an epithelial cell sheet whose main function is to act as an internal or external covering for a tissue or an organism.", "xrefs" : [ "JB:jb" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "boundary cell" @@ -975,6 +990,7 @@ "val" : "A cell whose primary function is to prevent the transport of stuff across compartments.", "xrefs" : [ "JB:jb" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "ZFA:0009132" } ] @@ -988,6 +1004,7 @@ "val" : "A cell that moves by its own activities.", "xrefs" : [ "FB:ma" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "ZFA:0009136" } ] @@ -1001,6 +1018,7 @@ "val" : "A cell of the outer of the three germ layers of the embryo.", "xrefs" : [ "MESH:D004475" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "ectoderm cell" @@ -1020,7 +1038,7 @@ "val" : "A cell of the middle germ layer of the embryo.", "xrefs" : [ "MESH:D008648" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "mesoblast" @@ -1032,6 +1050,12 @@ "val" : "FMA:72554" }, { "val" : "ZFA:0009138" + }, { + "val" : "https://cellxgene.cziscience.com/cellguide/CL_0000222" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/description", + "val" : "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nMesodermal cells are pluripotent and the most abundant in the human body. They contribute to the development of several structures such as the skeletal muscles, bones, heart and blood vessels, kidneys, gonads, connective tissues, and certain layers of the skin. Hence, the mesoderm is often regarded as an active and diverse layer due to its role in forming many bodily structures. \nIn embryonic development, these cells are instrumental, contributing to the body's structures through a carefully coordinated sequence of morphogenetic movements. This process forms the complex multicellular architecture of tissues and organs from a simple ball of cells. Without the function of mesodermal cells, the body's integral structures and systems would cease to form correctly, leading to developmental disorders such as axial mesodermal dysplasia complex" } ] } }, { @@ -1043,6 +1067,7 @@ "val" : "A cell of the inner of the three germ layers of the embryo.", "xrefs" : [ "MESH:D004707" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "endoderm cell" @@ -1062,6 +1087,7 @@ "val" : "A cell that lacks a nucleus.", "xrefs" : [ "FB:ma" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "non-nucleated cell" @@ -1078,7 +1104,8 @@ "definition" : { "val" : "A cell with a single nucleus.", "xrefs" : [ "FB:ma", "GOC:tfm" ] - } + }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ] } }, { "id" : "http://purl.obolibrary.org/obo/CL_0000228", @@ -1089,6 +1116,7 @@ "val" : "A cell with more than one nucleus.", "xrefs" : [ "FB:ma", "Wikipedia:Multinucleate" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "multinucleated cells", @@ -1108,7 +1136,7 @@ "val" : "A red blood cell. In mammals, mature erythrocytes are biconcave disks containing hemoglobin whose function is to transport oxygen.", "xrefs" : [ "GOC:tfm", "MESH:D004912" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#blood_and_immune_upper_slim", "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#blood_and_immune_upper_slim", "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "RBC" @@ -1138,7 +1166,7 @@ "xrefs" : [ "GOC:add", "GOC:dsd", "GOC:tfm", "MESH:D001792", "PMID:11110672", "PMID:16987572", "PMID:17204662", "PMID:17479180", "PMID:20414831", "http://en.wikipedia.org/wiki/Platelet" ] }, "comments" : [ "Platelets are reportedly CCR1-positive, CCR2-negative, CCR3-positive, CCR4-positive, CCR5-negative, CCR6-negative, CCR7-negative, CCR8-negative, CCR9-negative, CCR10-negative, CD16-positive, CD23-positive, CD32-positive, CD40-positive, CD41-positive CD42-positive, CD61-positive, CD62P-positive, CD64-positive, CD89-positive, CD102-positive, CD147-positive (activated platelets), CD154-positive (activated platelets), CD162-positive, CD209, CD282-positive, CD284-positive, CD289-positive, CD181-negative, CD182-negative, CD183-negative, CD184-positive, CLEC2-positive, GPVI-positive, JAMC-positive, PAR1-positive, PAR2-negative, PAR3-positive, PAR4-positive, TSP1-positive, and TXA2R-positive. Platelets can reportedly produce CCL2, CCL3, CCL5, CCL7, CCL17, CD40L, CXCL1, CXCL4, CXCL4L1, CXCL5, CXCL7, CXCL8, CXCL12, EGF, factor V, factor VII, factor XI, factor XIII, bFGF, histamine, IGF-1, IL-1beta, PAI-1, PDGF, plasminogen, protein S, serotonin, TGF-beta, TFPI, VEGF, and vWF." ], - "subsets" : [ "http://purl.obolibrary.org/obo/cl#blood_and_immune_upper_slim", "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#blood_and_immune_upper_slim", "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "anucleate thrombocyte" @@ -1170,7 +1198,7 @@ "val" : "Any cell capable of ingesting particulate matter via phagocytosis.", "xrefs" : [ "GOC:add", "ISBN:0721601464" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "BTO:0001044" }, { @@ -1191,7 +1219,7 @@ "xrefs" : [ "GOC:add", "GOC:tfm", "GO_REF:0000031", "PMID:16213494", "PMID:1919437" ] }, "comments" : [ "Morphology: Diameter 30_M-80 _M, abundant cytoplasm, low N/C ratio, eccentric nucleus. Irregular shape with pseudopods, highly adhesive. Contain vacuoles and phagosomes, may contain azurophilic granules; markers: Mouse & Human: CD68, in most cases CD11b. Mouse: in most cases F4/80+; role or process: immune, antigen presentation, & tissue remodelling; lineage: hematopoietic, myeloid." ], - "subsets" : [ "http://purl.obolibrary.org/obo/cl#blood_and_immune_upper_slim", "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#general_cell_types_upper_slim", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#blood_and_immune_upper_slim", "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#general_cell_types_upper_slim", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "histiocyte" @@ -1223,7 +1251,7 @@ "val" : "A lymphocyte of B lineage that is capable of B cell mediated immunity.", "xrefs" : [ "GOC:add", "GOC:tfm", "GO_REF:0000031", "ISBN:0781735149" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#blood_and_immune_upper_slim", "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#general_cell_types_upper_slim", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#blood_and_immune_upper_slim", "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#general_cell_types_upper_slim", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "B lymphocyte" @@ -1261,7 +1289,7 @@ "val" : "Any cell that in taxon some Eukaryota.", "xrefs" : [ "FBC:Autogenerated" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "MESH:D005057" } ] @@ -1275,7 +1303,7 @@ "val" : "A cell that is specialised to accumulate a particular substance(s).", "xrefs" : [ "FB:ma" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/ubprop#_upper_level" ] + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/ubprop#_upper_level" ] } }, { "id" : "http://purl.obolibrary.org/obo/CL_0000329", @@ -1286,6 +1314,7 @@ "val" : "Any cell that is capable of some oxygen transport.", "xrefs" : [ "FBC:Autogenerated" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "ZFA:0009164" } ] @@ -1299,6 +1328,7 @@ "val" : "A cell derived from the specialized ectoderm flanking each side of the embryonic neural plate, which after the closure of the neural tube, forms masses of cells that migrate out from the dorsal aspect of the neural tube to spread throughout the body.", "xrefs" : [ "doi:10.1016/j.stem.2015.02.017" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "FMA:86667" }, { @@ -1314,6 +1344,7 @@ "val" : "A mesenchymal cell in embryonic development found in a contracting mass and that gives rise to osteoprogenitors.", "xrefs" : [ "GOC:tfm", "PMID:5025404" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "ZFA:0009166" } ] @@ -1326,7 +1357,8 @@ "definition" : { "val" : "A cell of the outer layer of a blastula that gives rise to the ectoderm after gastrulation.", "xrefs" : [ "GOC:tfm", "ISBN:0618947256" ] - } + }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ] } }, { "id" : "http://purl.obolibrary.org/obo/CL_0000365", @@ -1337,6 +1369,7 @@ "val" : "Diploid cell produced by the fusion of sperm cell nucleus and egg cell.", "xrefs" : [ "ISBN:0471245208" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "pred" : "hasBroadSynonym", "val" : "zygote" @@ -1358,6 +1391,7 @@ "val" : "A cell whose function is determined by its response to an electric signal.", "xrefs" : [ "FB:ma" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "ZFA:0009190" } ] @@ -1371,6 +1405,7 @@ "val" : "A cell that initiates an electrical signal and passes that signal to another cell.", "xrefs" : [ "FB:ma" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "ZFA:0009193" } ] @@ -1384,7 +1419,7 @@ "val" : "A cell of hematopoietic origin, typically resident in particular tissues, specialized in the uptake, processing, and transport of antigens to lymph nodes for the purpose of stimulating an immune response via T cell activation. These cells are lineage negative (CD3-negative, CD19-negative, CD34-negative, and CD56-negative).", "xrefs" : [ "GOC:add", "ISBN:0781735149" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#general_cell_types_upper_slim", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#general_cell_types_upper_slim", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "synonyms" : [ { "pred" : "hasRelatedSynonym", "val" : "interdigitating cell" @@ -1413,6 +1448,7 @@ "lbl" : "biogenic amine secreting cell", "type" : "CLASS", "meta" : { + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "ZFA:0009212" } ] @@ -1426,6 +1462,7 @@ "val" : "A cell type that secretes 5-Hydroxytryptamine (serotonin).", "xrefs" : [ "GOC:tfm", "PMID:19630576" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "5-HT secreting cell" @@ -1445,7 +1482,30 @@ "definition" : { "val" : "A cell whose primary function is to protect the organism.", "xrefs" : [ "JB:jb" ] - } + }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/CL_0000499", + "lbl" : "stromal cell", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A connective tissue cell of an organ found in the loose connective tissue.", + "xrefs" : [ "GOC:tfm", "MESH:D017154" ] + }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#general_cell_types_upper_slim", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "xrefs" : [ { + "val" : "BTO:0002064" + }, { + "val" : "FMA:83624" + }, { + "val" : "ZFA:0009226" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/RO_0002175", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" + } ] } }, { "id" : "http://purl.obolibrary.org/obo/CL_0000518", @@ -1455,7 +1515,8 @@ "definition" : { "val" : "A phagocyte in vertebrates that is able to phagocytosis.", "xrefs" : [ "GOC:tfm" ] - } + }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ] } }, { "id" : "http://purl.obolibrary.org/obo/CL_0000540", @@ -1467,7 +1528,7 @@ "xrefs" : [ "MESH:D009474", "http://en.wikipedia.org/wiki/Neuron" ] }, "comments" : [ "These cells are also reportedly CD4-negative and CD200-positive. They are also capable of producing CD40L and IFN-gamma." ], - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#general_cell_types_upper_slim", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#general_cell_types_upper_slim", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "nerve cell" @@ -1505,7 +1566,7 @@ "xrefs" : [ "GOC:add", "ISBN:0683073696", "ISBN:0781735149" ] }, "comments" : [ "Editors note: consider adding taxon constraint to vertebrata (PMID:18025161)" ], - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "xrefs" : [ { "val" : "BTO:0000775" }, { @@ -1533,7 +1594,7 @@ "val" : "An immature, nucleated erythrocyte occupying the stage of erythropoeisis that follows formation of erythroid progenitor cells. This cell is CD71-positive, has both a nucleus and a nucleolus, and lacks hematopoeitic lineage markers.", "xrefs" : [ "ISBN:0721601464", "PMID:1638021" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#blood_and_immune_upper_slim", "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#blood_and_immune_upper_slim", "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "rubriblast", @@ -1555,6 +1616,7 @@ "val" : "A nucleated immature erythrocyte, having cytoplasm generally similar to that of the earlier proerythroblast but sometimes even more basophilic, and usually regular in outline. The nucleus is still relatively large, but the chromatin strands are thicker and more deeply staining, giving a coarser appearance; the nucleoli have disappeared. This cell is CD71-positive and lacks hematopoeitic lineage markers.", "xrefs" : [ "GOC:tfm", "ISBN:0721601464" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "basophilic normoblast", @@ -1587,6 +1649,7 @@ "val" : "A nucleated, immature erythrocyte in which the nucleus occupies a relatively smaller part of the cell than in its precursor, the basophilic erythroblast. The cytoplasm is beginning to acquire hemoglobin and thus is no longer a purely basophilic, but takes on acidophilic aspects, which becomes progressively more marked as the cell matures. The chromatin of the nucleus is arranged in coarse, deeply staining clumps. This cell is CD71-positive and lacks hematopoeitic lineage markers.", "xrefs" : [ "ISBN:0721601464" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "intermediate erythroblast", @@ -1627,6 +1690,7 @@ "val" : "The final stage of the nucleated, immature erythrocyte, before nuclear loss. Typically the cytoplasm is described as acidophilic, but it still shows a faint polychromatic tint. The nucleus is small and initially may still have coarse, clumped chromatin, as in its precursor, the polychromatophilic erythroblast, but ultimately it becomes pyknotic, and appears as a deeply staining, blue-black, homogeneous structureless mass. The nucleus is often eccentric and sometimes lobulated.", "xrefs" : [ "ISBN:0721601464" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "acidophilic erythroblast", @@ -1661,7 +1725,7 @@ "xrefs" : [ "GOC:dsd", "GOC:tfm", "ISBN:0721601464" ] }, "comments" : [ "Lineage negative is described here as CD2-negative, CD3-negative, CD4-negative, CD5-negative, CD8a-negative, CD14-negative, CD19-negative, CD20-negative, CD56-negative, Ly6g-negative, and Ter119-negative." ], - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "CFU-Meg", @@ -1721,7 +1785,7 @@ "xrefs" : [ "ISBN:0721601464", "MESH:D008533", "PMID:31043076", "http://en.wikipedia.org/wiki/Megakaryocyte" ] }, "comments" : [ "Megakaryocytes are reportedly CD181-positive and CD182-positive." ], - "subsets" : [ "http://purl.obolibrary.org/obo/cl#blood_and_immune_upper_slim", "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#blood_and_immune_upper_slim", "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "megacaryocyte" @@ -1754,7 +1818,7 @@ "xrefs" : [ "GOC:amm", "GOC:dsd", "GOC:tfm", "GO_REF:0000031", "ISBN:0721601464", "MESH:D055014", "PMCID:PMC2213186", "PMCID:PMC548021", "PMID:16551251", "PMID:16647566", "http://en.wikipedia.org/wiki/CFU-GM", "http://www.copewithcytokines.de" ] }, "comments" : [ "Originally described in the dendritic cell ontology (DC_CL:0000042)(PMID:19243617). GMPs are reportedly CD16-positive, CD32-positive, CD34-positive, CD38-positive, CD45RA-positive, CD110-negative, CD117-positive, CD123-positive, and SCA1-negative." ], - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "synonyms" : [ { "pred" : "hasBroadSynonym", "val" : "CFU-C , Colony forming unit in culture", @@ -1786,10 +1850,15 @@ } ], "xrefs" : [ { "val" : "ZFA:0009251" + }, { + "val" : "https://cellxgene.cziscience.com/cellguide/CL_0000557" } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" + }, { + "pred" : "http://purl.org/dc/terms/description", + "val" : "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nGranulocyte monocyte progenitor cells (GMP cells), originating from hematopoietic stem cells in the bone marrow, are a critical intermediate in myeloid cell development. Positioned at a key differentiation juncture, these cells exhibit bidirectional potential, giving rise to both granulocyte and monocyte lineages.\nTheir primary role is to generate mature granulocytes and monocytes, essential components of the body's innate immunity and inflammatory responses. Granulocytes, such as neutrophils, eosinophils, and basophils, contribute to the first line of defense against infections by migrating to the infection site and phagocytosing pathogens. Monocytes can differentiate into macrophages or dendritic cells, playing diverse roles in immune responses." } ] } }, { @@ -1801,7 +1870,7 @@ "val" : "An immature erythrocyte that changes the protein composition of its plasma membrane by exosome formation and extrusion. The types of protein removed differ between species though removal of the transferrin receptor is apparent in mammals and birds.", "xrefs" : [ "GOC:add", "GOC:tfm", "PMID:15946868", "PMID:2037622" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#blood_and_immune_upper_slim", "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#blood_and_immune_upper_slim", "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "BTO:0001173" }, { @@ -1822,7 +1891,7 @@ "xrefs" : [ "GOC:tfm", "ISBN:0721601464" ] }, "comments" : [ "Morphology: Mononuclear cell, diameter 14-18 _M, fine azurophilic granules; markers: CD11b (shared with many other myeloid cells); location: Adult: bone marrow; Fetal: Liver, Yolk Sac; role or process: hematopoiesis, monocyte development; lineage: hematopoietic, myeloid." ], - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "xrefs" : [ { "val" : "BTO:0004657" }, { @@ -1845,6 +1914,7 @@ "xrefs" : [ "GOC:dsd", "GOC:tfm", "PMID:12768659" ] }, "comments" : [ "These cells are reportedly CD31-positive, CD34-positive, CD144-positive, CD309-positive, and TAL1-positive." ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "angioblast" @@ -1866,7 +1936,7 @@ "xrefs" : [ "GO_REF:0000031", "MESH:D009000" ] }, "comments" : [ "Morphology: Mononuclear cell, diameter, 14 to 20 _M, N/C ratio 2:1-1:1. Nucleus may appear in variety of shapes: round, kidney, lobulated, or convoluted. Fine azurophilic granules present; markers: CD11b (shared with other myeloid cells), human: CD14, mouse: F4/80-mid,GR1-low; location: Blood, but can be recruited into tissues; role or process: immune & tissue remodelling; lineage: hematopoietic, myeloid." ], - "subsets" : [ "http://purl.obolibrary.org/obo/cl#blood_and_immune_upper_slim", "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#general_cell_types_upper_slim", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#blood_and_immune_upper_slim", "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#general_cell_types_upper_slim", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "xrefs" : [ { "val" : "BTO:0000876" }, { @@ -1891,7 +1961,7 @@ "xrefs" : [ "GOC:add", "GOC:tfm", "ISBN:0702022918", "ISBN:0702024783", "PMID:33348900", "Wikipedia:Giant_cell" ] }, "comments" : [ "Role or process: Chronic infection, granulomatous inflammation. Consider also megakaryocyte (CL:0000556) as sometimes multinucleated giant cell is used to refer to this." ], - "subsets" : [ "http://purl.obolibrary.org/obo/cl#blood_and_immune_upper_slim" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#blood_and_immune_upper_slim", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "Langerhans giant cell", @@ -1935,7 +2005,7 @@ "val" : "A non-terminally differentiated cell that is capable of developing into a muscle cell.", "xrefs" : [ "GOC:add" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "ZFA:0009291" } ] @@ -1949,6 +2019,7 @@ "val" : "A stem cell that can give rise to cell types of the body other than those of the germ-line.", "xrefs" : [ "GO:0048103" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "CALOHA:TS-2086" }, { @@ -1966,7 +2037,7 @@ "val" : "An achromatic cell of the myeloid or lymphoid lineages capable of ameboid movement, found in blood or other tissue.", "xrefs" : [ "GOC:add", "GOC:tfm", "ISBN:978-0-323-05290-0" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "leucocyte" @@ -2005,7 +2076,7 @@ "xrefs" : [ "GOC:add", "GOC:tfm", "PMID:16360205" ] }, "comments" : [ "Note that this is a non-mammalian cell type. Use platelet ; CL:0000233 for thrombocytes (platelets) in mammals." ], - "subsets" : [ "http://purl.obolibrary.org/obo/cl#blood_and_immune_upper_slim" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#blood_and_immune_upper_slim", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "ZFA:0009323" } ] @@ -2019,7 +2090,7 @@ "val" : "A cell of the monocyte, granulocyte, mast cell, megakaryocyte, or erythroid lineage.", "xrefs" : [ "GOC:add" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "BTO:0001441" }, { @@ -2040,7 +2111,7 @@ "xrefs" : [ "GOC:add", "GOC:tfm" ] }, "comments" : [ "Note that in FMA erythropoietic cells are types of nucleated erythrocytes and thus don't include erythrocytes." ], - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "erythropoietic cell" @@ -2068,7 +2139,7 @@ "val" : "A nucleated precursor of an erythrocyte that lacks hematopoietic lineage markers.", "xrefs" : [ "GOC:add", "ISBN:0721601464", "PMID:18174176" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#blood_and_immune_upper_slim", "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#blood_and_immune_upper_slim", "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "normoblast" @@ -2094,7 +2165,7 @@ "val" : "A cell of the monocyte, granulocyte, or mast cell lineage.", "xrefs" : [ "GOC:add" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "ZFA:0009326" } ] @@ -2109,7 +2180,7 @@ "xrefs" : [ "GOC:add", "GOC:amm", "GOC:dsd", "GOC:tfm", "ISBN:0721601464", "MESH:D001491", "PMCID:PMC2626675", "PMID:11927641", "PMID:19741522", "PMID:21236338", "PMID:9933081" ] }, "comments" : [ "Matures in the bone marrow and account for <1% of leukocytes in the peripheral blood, spleen, and bone marrow. Basophils are described as being CD11a-positive, CD11b-positive, CD13-positive, CD15-positive, CD18-positive, CD21-positive, CD25-positive, CD29-positive, CD35-positive, CD40-positive, CD40L-positive, CD44-positive, CD45R-negative, CD46-positive, CD49a-positive, CD49b-positive, CD49d-positive, CD55-positive, CD59-positive, CD62L-positive, CD63-positive, CD69-positive, CD90-negative, CD116-positive, CD117-negative, CD124-positive, CD125-positive, CD131-positive, CD161-positive, CD184-positive, CD191-positive, CD192-positive, CD197-positive, CD200R3-positive, CD218-positive, CD282-positive, CD284-positive, CD289-positive, CD290-positive, CD294-positive, natural killer cell receptor 2B4-positive, smad1-positive, CD3-negative, CD4-negative, CD7-negative, CD8-negative, CD14-negative, CD15-negative, CD16-negative, CD19-negative, CD20-negative, CD34-negative, CD36-negative, CD45R-negative, CD56-negative, CD57-negative, CD235a-negative, and GR1-negative. Transcription factors- GATA1-positive, PU.1-positive." ], - "subsets" : [ "http://purl.obolibrary.org/obo/cl#blood_and_immune_upper_slim", "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#blood_and_immune_upper_slim", "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "synonyms" : [ { "pred" : "hasBroadSynonym", "val" : "polymorphonuclear leucocyte" @@ -2145,7 +2216,7 @@ "xrefs" : [ "GOC:add", "GOC:amm", "GOC:dsd", "GOC:tfm", "ISBN:0721601464", "PMCID:PMC2626675", "PMID:10914487", "PMID:1662676" ] }, "comments" : [ "Eosinophils are also CD14-negative, CD32-positive, CD44-positive, CD48-positive, CD69-positive, CD192-negative, MBP1-positive, MBP2-positive, TLR2-negative, TLR4-negative, and lineage-negative (B220, CD2, CD14, CD19, CD56, CD71, CD117, CD123, CD235a (glycophorin A), and TER119). The cytokines IL-3, IL-5, and GM-CSF are involved in their development and differentiation. Usually considered CD16-negative, CD16 is observed on eosinophilic metamyelocyte." ], - "subsets" : [ "http://purl.obolibrary.org/obo/cl#blood_and_immune_upper_slim", "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#blood_and_immune_upper_slim", "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "synonyms" : [ { "pred" : "hasBroadSynonym", "val" : "polymorphonuclear leucocyte" @@ -2188,7 +2259,7 @@ "val" : "Any of the immature or mature forms of a granular leukocyte that in its mature form has a nucleus with three to five lobes connected by slender threads of chromatin, and cytoplasm containing fine inconspicuous granules and stainable by neutral dyes.", "xrefs" : [ "GOC:add", "GOC:amm", "GOC:tfm", "ISBN:0721601464" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#blood_and_immune_upper_slim", "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#blood_and_immune_upper_slim", "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "synonyms" : [ { "pred" : "hasBroadSynonym", "val" : "PMN" @@ -2252,7 +2323,7 @@ "xrefs" : [ "GOC:add", "PMID:10449155", "PMID:17332250", "PMID:9521319" ] }, "comments" : [ "These cells are CD1a-negative, CD1b-positive, CD11a-positive, CD11c-positive, CD13-positive, CD14-negative, CD20-negative, CD21-negative, CD33-positive, CD40-negative, CD50-positive, CD54-positive, CD58-positive, CD68-negative, CD80-negative, CD83-negative, CD85j-positive, CD86-positive, CD89-negative, CD95-positive, CD120a-negative, CD120b-positive, CD123-negative, CD178-negative, CD206-negative, CD207-negative, CD209-negative, and TNF-alpha-negative. Upon TLR stimulation, they are capable of producing high levels of TNF-alpha, IL-6, CXCL8 (IL-8)." ], - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "pred" : "hasBroadSynonym", "val" : "interdigitating cell" @@ -2279,7 +2350,7 @@ "val" : "A dendritic cell type of distinct morphology, localization, and surface marker expression (CD123-positive) from other dendritic cell types and associated with early stage immune responses, particularly the release of physiologically abundant amounts of type I interferons in response to infection.", "xrefs" : [ "GOC:add", "GOC:dsd", "PMCID:PMC2118448", "PMCID:PMC538703", "PMID:15549123", "PMID:17332250", "PMID:17850486", "PMID:20304825" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#blood_and_immune_upper_slim", "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#blood_and_immune_upper_slim", "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "DC2" @@ -2326,7 +2397,7 @@ "xrefs" : [ "GOC:add", "GOC:dsd", "ISBN:0781735149" ] }, "comments" : [ "Mature B cells are also reportedly CD10-negative, CD19-positive, CD22-positive, CD34-negative, CD48-positive, CD79a-positive, CD84-positive, CD127-negative, CD352-positive, RAG-negative, TdT-negative, Vpre-B-negative, and pre-BCR-negative. Transcription factors expressed: Pax5-positive." ], - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "mature B lymphocyte" @@ -2351,7 +2422,7 @@ "xrefs" : [ "GOC:add", "GOC:dsd", "GO_REF:0000031", "ISBN:0721601464", "ISBN:0781735149", "PMID:19447676", "PMID:20081059", "PMID:20839338", "PMID:20951740", "http://en.wikipedia.org/wiki/Plasma_cell" ] }, "comments" : [ "Plasma cells develop in the spleen and migrate to the bone marrow. Plasma cells are also reportedly CD5-negative, CD10-negative, CD19-positive, CD20-negative, CD21-negative, CD22-negative, CD23-negative, CD24-negative, CD25-negative, CD27-positive, CD34-negative, CD38-positive, CD40-positive, CD43-positive, CD45-positive, CD48-positive, CD53-low, CD80-negative, CD81-positive, CD86-positive, CD95-positive, CD196-negative, CD229-positive, CD270-positive, CD352-positive, CD361-positive, and IgD-negative. Transcription factors: BLIMP1-positive, IRF4-positive, PAX5-negative, SpiB-negative, Ets1-negative, and XBP1-positive." ], - "subsets" : [ "http://purl.obolibrary.org/obo/cl#blood_and_immune_upper_slim", "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#blood_and_immune_upper_slim", "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "plasma B cell" @@ -2394,7 +2465,7 @@ "val" : "A T cell that expresses an alpha-beta T cell receptor complex.", "xrefs" : [ "GOC:add", "GOC:tfm", "ISBN:0781735149" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#blood_and_immune_upper_slim", "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#blood_and_immune_upper_slim", "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "alpha-beta T lymphocyte" @@ -2419,7 +2490,7 @@ "xrefs" : [ "GOC:add", "GOC:tfm", "ISBN:0781735149" ] }, "comments" : [ "Note that gamma-delta T cells have both thymic and extrathymic differentiation pathways." ], - "subsets" : [ "http://purl.obolibrary.org/obo/cl#blood_and_immune_upper_slim", "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#blood_and_immune_upper_slim", "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "gamma-delta T lymphocyte" @@ -2455,7 +2526,7 @@ "xrefs" : [ "GOC:add", "GOC:dsd", "GOC:rhs", "GOC:tfm", "GO_REF:0000031", "ISBN:0781735149", "PMID:20081059", "PMID:20839338" ] }, "comments" : [ "Immature B cells are also reportedly CD5-positive, CD10-positive, CD19-positive, CD20-positive, CD21-positive, CD22-positive, CD24-positive, CD25-negative, CD27-negative, CD34-negative, CD38-positive, CD40-positive, CD43-negative, CD45-positive, CD48-positive, CD53-positive, CD79a-positive, CD80-negative, CD81-positive, CD86-negative, CD95-negative, CD127-negative, CD138-negative, CD185-positive, CD196-positive, MHCII/HLA-DR-positive, RAG-positive, TdT-negative, Vpre-B-negative, and preBCR-negative. Transcription factors expressed: Pax5-positive." ], - "subsets" : [ "http://purl.obolibrary.org/obo/cl#blood_and_immune_upper_slim", "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#blood_and_immune_upper_slim", "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "immature B lymphocyte" @@ -2487,7 +2558,7 @@ "val" : "A precursor B cell is a B cell with the phenotype CD10-positive.", "xrefs" : [ "GOC:rhs", "GOC:tfm", "GO_REF:0000031" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "synonyms" : [ { "pred" : "hasRelatedSynonym", "val" : "pre-B cell" @@ -2514,7 +2585,7 @@ "xrefs" : [ "GOC:add", "GO_REF:0000031", "ISBN:0781735149", "PMID:12810111", "PMID:22343568" ] }, "comments" : [ "This cell type is compatible with the HIPC Lyoplate markers for 'transitional B cell'." ], - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "transitional B cell", @@ -2556,7 +2627,7 @@ "xrefs" : [ "GOC:add", "GOC:dsd", "ISBN:0781735149", "PMID:12633665", "PMID:16551251", "PMID:18432934" ] }, "comments" : [ "Human pro-B cells are reportedly CD10-positive, CD22-positive, CD34-positive, CD38-positive, CD45-low, CD48-positive, CD79a-positive, CD127-positive, CD184-positive, RAG-positive, TdT-positive, Vpre-B-positive, pre-BCR-negative, IgD-negative, and IgM-negative. Transcription factors expressed: Pax5-positive, EBF-positive, E2A-negative, Ikaros-negative, and PU.1-negative." ], - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "synonyms" : [ { "pred" : "hasBroadSynonym", "val" : "pre-pro B cell", @@ -2606,7 +2677,7 @@ "val" : "A lymphoid progenitor cell of the T cell lineage, with some lineage specific marker expression, but not yet fully committed to the T cell lineage.", "xrefs" : [ "GOC:add", "ISBN:0781735149" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "pro-T lymphocyte" @@ -2637,6 +2708,7 @@ "xrefs" : [ "GOC:add", "GOC:tfm", "PMID:7758949" ] }, "comments" : [ "Note that this is a non-mammalian cell type." ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "ZFA:0009351" } ] @@ -2651,6 +2723,7 @@ "xrefs" : [ "GOC:add", "GOC:dsd", "PMCID:PMC1183570", "PMCID:PMC1312421", "PMID:8629001", "PMID:9354811", "http://www.copewithcytokines.de" ] }, "comments" : [ "MCP are CD16-positive, CD32-positive, CD34-positive, CD45-positive, integrin beta-7-positive, and lin-negative (CD2, CD3e, CD4, CD5, CD8a, CD14, CD19, CD20, CD27, integrin alpha-M, ly6c, ly6g, NCAM-1, and ter119). These cells also express the transcription factors GATA-1, GATA-2, and MITF, but not C/EBPa." ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "MCP" @@ -2675,7 +2748,7 @@ "xrefs" : [ "GOC:add", "GOC:tfm", "PMID:19022770" ] }, "comments" : [ "Markers differ between mouse and human." ], - "subsets" : [ "http://purl.obolibrary.org/obo/cl#blood_and_immune_upper_slim", "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#blood_and_immune_upper_slim", "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "MPP" @@ -2705,7 +2778,7 @@ "xrefs" : [ "GOC:add", "GOC:tfm" ] }, "comments" : [ "Note that this is a class of cell types, not an identified single cell type." ], - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "pred" : "hasBroadSynonym", "val" : "lymphoid progenitor cell" @@ -2730,7 +2803,7 @@ "xrefs" : [ "GOC:add", "GOC:tfm", "PMID:19022770" ] }, "comments" : [ "Note that this is a class of cell types, not an identified single cell type." ], - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "synonyms" : [ { "pred" : "hasBroadSynonym", "val" : "myeloid progenitor cell" @@ -2758,7 +2831,7 @@ "val" : "A leukocyte with a single non-segmented nucleus in the mature form.", "xrefs" : [ "GOC:add" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#blood_and_immune_upper_slim", "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#blood_and_immune_upper_slim", "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "mononuclear leukocyte" @@ -2786,7 +2859,7 @@ "xrefs" : [ "GOC:add", "GOC:ana", "GO_REF:0000031", "PMID:16168663", "PMID:17016554", "PMID:17016559" ] }, "comments" : [ "Markers: Mouse: CD11b+GR1+CD31+; Human: CD34+ CD33+CD15-CD13+. (According to some reports in humans these cells are iNOS+ARG1+IL13+IFNg+); location: In cancerous tissue; in the blood and lymphoid organs in sepsis." ], - "subsets" : [ "http://purl.obolibrary.org/obo/cl#blood_and_immune_upper_slim" ] + "subsets" : [ "http://purl.obolibrary.org/obo/cl#blood_and_immune_upper_slim", "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ] } }, { "id" : "http://purl.obolibrary.org/obo/CL_0000945", @@ -2798,7 +2871,7 @@ "xrefs" : [ "GOC:add", "GOC:rhs", "GOC:tfm", "GO_REF:0000031", "ISBN:0781735149" ] }, "comments" : [ "Types of B lineage lymphocytes include B cells and antibody secreting cells (plasmablasts and plasma cells). Lymphocytes of B cell lineage can be distinguished from those of T cell lineage by their lack of CD3e (as part of the T cell receptor complex)." ], - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" @@ -2812,7 +2885,8 @@ "definition" : { "val" : "A lymphocyte of B lineage that is devoted to secreting large amounts of immunoglobulin.", "xrefs" : [ "GOC:add", "GOC:tfm", "GO_REF:0000031", "ISBN:0721601464", "ISBN:0781735149" ] - } + }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ] } }, { "id" : "http://purl.obolibrary.org/obo/CL_0000954", @@ -2824,7 +2898,7 @@ "xrefs" : [ "GOC:dsd", "GOC:rhs", "GOC:tfm", "GO_REF:0000031", "PMID:16551251", "PMID:18432934", "PMID:9785673" ] }, "comments" : [ "Small pre-B-II cells are also reportedly CD10-positive, CD19-positive, CD34-negative, CD79a-positive, CD127-negative, TdT-negative, Vpre-B-negative, sIgM-negative, and sIgD-negative. Transcription factors: PU.1-positive, Ikaros-positive, E2A-positive, and PAX5-positive." ], - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "small pre-BII cell" @@ -2840,6 +2914,7 @@ "xrefs" : [ "GOC:dsd", "GOC:rhs", "GOC:tfm", "GO_REF:0000031", "PMID:9785673" ] }, "comments" : [ "pre-B-II cell are also reportedly CD19-positive, CD22-positive, CD38-positive, CD45-positive, and CD48-positive." ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "pre-B-lymphocyte" @@ -2863,7 +2938,7 @@ "xrefs" : [ "GOC:dsd", "GOC:msz", "GOC:tfm", "GO_REF:0000031", "PMCID:PMC2673126" ] }, "comments" : [ "This cell type is compatible with the HIPC Lyoplate markers for 'plasmablast'. Plasmablasts are also reportedly CD48-positive, CD63-positive, CD229-positive, CD270-positive, CD319-positive, CD352-positive, CD361-positive, and IgD-negative." ], - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "synonyms" : [ { "pred" : "hasBroadSynonym", "val" : "CD20-negative B cell" @@ -2888,7 +2963,7 @@ "val" : "A cell of a hematopoietic lineage.", "xrefs" : [ "GOC:add", "GO_REF:0000031" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "haematopoietic cell" @@ -2921,7 +2996,7 @@ "xrefs" : [ "GOC:amm", "GO_REF:0000031", "PMID:17850486" ] }, "comments" : [ "Originally described in the dendritic cell ontology (DC_CL:0000003)(PMID:19243617) These cells are also CD20-negative, MHCII-positive." ], - "subsets" : [ "http://purl.obolibrary.org/obo/cl#blood_and_immune_upper_slim", "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#blood_and_immune_upper_slim", "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "synonyms" : [ { "pred" : "hasBroadSynonym", "val" : "interdigitating cell" @@ -2954,7 +3029,8 @@ "lbl" : "CD7-negative lymphoid progenitor OR granulocyte monocyte progenitor", "type" : "CLASS", "meta" : { - "comments" : [ "Originally described in the dendritic cell ontology (DC_CL:1110000)(PMID:19243617)." ] + "comments" : [ "Originally described in the dendritic cell ontology (DC_CL:1110000)(PMID:19243617)." ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ] } }, { "id" : "http://purl.obolibrary.org/obo/CL_0001035", @@ -2965,13 +3041,19 @@ "val" : "A connective tissue cell found in bone.", "xrefs" : [ "GOC:add", "GO_REF:0000034" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#general_cell_types_upper_slim", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#general_cell_types_upper_slim", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "xrefs" : [ { + "val" : "https://cellxgene.cziscience.com/cellguide/CL_0001035" + } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" }, { "pred" : "http://purl.org/dc/terms/contributor", "val" : "https://orcid.org/0000-0001-9990-8331" + }, { + "pred" : "http://purl.org/dc/terms/description", + "val" : "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nBone cells, also known as osteocytes, form the building blocks of the skeletal system. They represent the most common type of bone cell, making up approximately 95% of the total bone cell population in mature adult bone tissue. Osteocytes are a stellate shape with numerous long, slender dendritic processes.\nThe formation of bone is a complex process involving the action of osteoclasts - cells that break down and reabsorb old bone, followed by osteoblasts that rebuild the bone. Osteocytes serve as coordinators for these two types of bone cells to ensure a balance in the bone remodeling process, contributing to maintaining both bone strength and mineral homeostasis.\nThe primary functions of osteocytes involve the creation, maintenance, and repair of bone tissue. They ensure that bone remodeling is performed by forming a network within the bone and communicating with other cells to help them respond to mechanical strain and damage.\nA remarkable aspect of osteocytes is their ability to perceive mechanical forces, translating them into biochemical signals that regulate bone remodeling and adaptation. Defects in osteocyte function, aside from other bone cells, have been associated with several bone disorders such as osteoporosis, renal osteodystrophy, and skeletal manifestations of diabetes." }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2011-11-16T04:28:16Z" @@ -2986,6 +3068,7 @@ "val" : "A hematopoietic oligopotent progenitor cell that has the ability to differentiate into limited cell types but lacks lineage cell markers and self renewal capabilities. Cell lacks hematopoeitic lineage markers.", "xrefs" : [ "GOC:tfm", "PMID:19022770" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "basicPropertyValues" : [ { "pred" : "http://purl.org/dc/terms/contributor", "val" : "https://orcid.org/0000-0003-1980-3228" @@ -3003,7 +3086,7 @@ "val" : "A lymphocyte that lacks characteristic T cell, B cell, myeloid cell, and dendritic cell markers, that functions as part of the innate immune response to produce cytokines and other effector responses.", "xrefs" : [ "GOC:add", "GOC:dsd", "PMID:23292121", "PMID:23348417" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#blood_and_immune_upper_slim", "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#blood_and_immune_upper_slim", "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" @@ -3025,6 +3108,7 @@ "xrefs" : [ "GOC:add" ] }, "comments" : [ "Types of B lineage lymphocytes include B cells and antibody secreting cells (plasmablasts and plasma cells). Lymphocytes of B cell lineage can be distinguished from those of T cell lineage by their lack of CD3e (as part of the T cell receptor complex)." ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "basicPropertyValues" : [ { "pred" : "http://purl.org/dc/terms/contributor", "val" : "https://orcid.org/0000-0001-9990-8331" @@ -3039,6 +3123,7 @@ "val" : "A B cell that is CD19-positive.", "xrefs" : [ "GOC:add" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "B lymphocyte, CD19-positive" @@ -3069,7 +3154,7 @@ "val" : "A progenitor cell that can give rise to plasmacytoid and myeloid dendritic cells, and to monocytes and macrophages.", "xrefs" : [ "GOC:tfm", "PMID:19273628" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "MDP" @@ -3092,7 +3177,7 @@ "xrefs" : [ "GOC:ak", "GOC:dsd", "GOC:tfm", "PMCID:PMC1312421" ] }, "comments" : [ "There may be an intermediate cell type. These cells also CD13-positive, CD16-positive, CD32-positive, and integrin beta 7-positive. Transcription factors: GATA1-positive, MCP-1-positive, mitf-positive, PU.1-positive, and CEBP/a-low." ], - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "BMCP" @@ -3114,7 +3199,7 @@ "val" : "A hematopoietic progenitor cell that is capable of developing into only one lineage of hematopoietic cells.", "xrefs" : [ "GOC:tfm", "PMID:19022770" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#blood_and_immune_upper_slim" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#blood_and_immune_upper_slim", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "basicPropertyValues" : [ { "pred" : "http://purl.org/dc/terms/contributor", "val" : "https://orcid.org/0000-0003-1980-3228" @@ -3133,7 +3218,7 @@ "xrefs" : [ "GOC:tfm", "PMID:19022770", "https://orcid.org/0000-0001-5208-3432" ] }, "comments" : [ "This cell type is intended to be compatible with any vertebrate hematopoietic oligopotent progenitor cell. For mammalian hematopoietic oligopotent progenitor cells known to be lineage-negative, please use the term 'hematopoietic oligopotent progenitor cell' (CL_0001060)." ], - "subsets" : [ "http://purl.obolibrary.org/obo/cl#blood_and_immune_upper_slim" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#blood_and_immune_upper_slim", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "basicPropertyValues" : [ { "pred" : "http://purl.org/dc/terms/contributor", "val" : "https://orcid.org/0000-0003-1980-3228" @@ -3151,6 +3236,7 @@ "val" : "An epithelial cell derived from ectoderm.", "xrefs" : [ "FMA:69074", "GOC:tfm" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "FMA:69074" }, { @@ -3173,7 +3259,7 @@ "val" : "A leukocyte that lacks granules.", "xrefs" : [ "GOC:tfm" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#blood_and_immune_upper_slim" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#blood_and_immune_upper_slim", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "agranular leukocyte" @@ -3199,7 +3285,7 @@ "xrefs" : [ "GOC:tfm", "ISBN:0618947256" ] }, "comments" : [ "MH consider whether bone marrow cells are bone cells in the structural sense vs. being part of bone organ sense." ], - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "BTO:0004850" }, { @@ -3225,7 +3311,7 @@ "xrefs" : [ "GOC:dsd", "GOC:tfm", "PMID:12768659" ] }, "comments" : [ "These cells are reportedly CD31-positive, CD34-positive, CD144-positive, TAL1-positive." ], - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "vascular endothelial cell" @@ -3239,10 +3325,15 @@ "val" : "CALOHA:TS-1106" }, { "val" : "FMA:67755" + }, { + "val" : "https://cellxgene.cziscience.com/cellguide/CL_0002139" } ], "basicPropertyValues" : [ { "pred" : "http://purl.org/dc/terms/contributor", "val" : "https://orcid.org/0000-0003-1980-3228" + }, { + "pred" : "http://purl.org/dc/terms/description", + "val" : "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nEndothelial cells of the vascular tree, commonly referred to as vascular endothelial cells, line the entire circulatory system, from the heart to the smallest capillaries. These cells have a unique, flattened shape, and are tightly bound together, forming a thin layer known as the endothelium. The endothelium is responsible for maintaining the interior surface of blood vessels, and plays a critical role in ensuring the smooth flow of blood. \nVascular endothelial cells act as a semi-permeable membrane, controlling the passage of materials and the transit of white blood cells into and out of the bloodstream. These cells are also involved in blood coagulation. When a blood vessel is damaged, endothelial cells promote clotting to prevent excessive bleeding and facilitate wound healing. Other functions include regulation of blood pressure and blood volume by releasing vasodilators and vasoconstrictors to either widen or constrict blood vessels, accordingly.\nFurthermore, the endothelial cells are crucial in the formation of new blood vessels, a process known as angiogenesis. This is particularly important in wound healing and the growth of new tissues during development or after injury. In the context of diseases such as cancer, angiogenesis helps facilitate tumor growth by providing nutrients and oxygen." }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2010-08-24T02:06:40Z" @@ -3257,7 +3348,7 @@ "val" : "A cell involved in the formation of a granulocyte.", "xrefs" : [ "GOC:tfm" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "FMA:83519" } ], @@ -3278,6 +3369,7 @@ "val" : "A cell involved in the formation of a monocyte (monopoiesis).", "xrefs" : [ "GOC:tfm" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "FMA:83552" } ], @@ -3298,6 +3390,7 @@ "val" : "A cell containing at least one nucleus.", "xrefs" : [ "GOC:tfm" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "FMA:67513" } ], @@ -3318,6 +3411,7 @@ "val" : "A cell type that secretes histamine.", "xrefs" : [ "GOC:tfm" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "basicPropertyValues" : [ { "pred" : "http://purl.org/dc/terms/contributor", "val" : "https://orcid.org/0000-0003-1980-3228" @@ -3335,7 +3429,7 @@ "val" : "A cell that is part of the nervous system.", "xrefs" : [ "GOC:tfm", "ISBN:0618947256" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "CALOHA:TS-2040" }, { @@ -3358,7 +3452,7 @@ "val" : "A cell of the supporting or framework tissue of the body, arising chiefly from the embryonic mesoderm and including adipose tissue, cartilage, and bone.", "xrefs" : [ "GOC:tfm", "ISBN:0618947256" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "CALOHA:TS-2096" }, { @@ -3385,6 +3479,7 @@ "val" : "A cell of the embryo.", "xrefs" : [ "FMA:0618947256" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "CALOHA:TS-0263" }, { @@ -3393,10 +3488,15 @@ "val" : "WBbt:0007028" }, { "val" : "ZFA:0007089" + }, { + "val" : "https://cellxgene.cziscience.com/cellguide/CL_0002321" } ], "basicPropertyValues" : [ { "pred" : "http://purl.org/dc/terms/contributor", "val" : "https://orcid.org/0000-0003-1980-3228" + }, { + "pred" : "http://purl.org/dc/terms/description", + "val" : "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nEmbryonic cells in metazoans, which include all multicellular animals, are biological units in their earliest developmental stages from conception until the organism is fully formed. \nThey are derived from a fertilized egg, which undergoes a series of cell divisions to produce a multicellular organism. During the early phases of embryonic development, these cells exhibit pluripotency, meaning they possess the potential to differentiate into a diverse array of specialized cell types that constitute different body tissues and structures. \nThe balance between cell proliferation and differentiation in embryonic cells is crucial for successful development. When cells continue to divide without differentiating, overgrowth may occur leading to conditions such as teratomas (tumors of embryonic cells). Conversely, if cell differentiation proceeds at the expense of cell proliferation, developmental anomalies could occur regarding size or mass of the organism or its parts." }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2010-09-15T03:39:21Z" @@ -3411,7 +3511,7 @@ "val" : "A T cell that has not completed T cell selection.", "xrefs" : [ "GOC:tfm" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#blood_and_immune_upper_slim", "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#blood_and_immune_upper_slim", "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "immature T-cell" @@ -3439,6 +3539,7 @@ "xrefs" : [ "GOC:tfm" ] }, "comments" : [ "From Onard of the FMA: Cardiac muscle cell or cardiac myocyte is a striated muscle cell. Cardiocyte on the other hand is any cell in the heart which includes cells other than muscle cells (e.g. endothelial cell of endocardium). Unless there is a consensus among anatomists that cardiocytes refer only to muscle cells, we will treat them as a general class of cells in the heart." ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "heart cell" @@ -3469,7 +3570,7 @@ "val" : "A lymphocyte found in adipose tissue that lacks lineage markers of other lymphocytes but is capable of mediating TH2 cytokine responses. This cell type is found in fat associated lymphoid clusters, proliferates in response to IL2 and produce large amounts of TH2 cytokines such as IL5, IL6 and IL13", "xrefs" : [ "GOC:tfm", "PMID:20023630" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#blood_and_immune_upper_slim" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#blood_and_immune_upper_slim", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "basicPropertyValues" : [ { "pred" : "http://purl.org/dc/terms/contributor", "val" : "https://orcid.org/0000-0003-1980-3228" @@ -3488,6 +3589,7 @@ "xrefs" : [ "GO_REF:0000034" ] }, "comments" : [ "Needs logical definition. Should be capable_of skeletal system morphogenesis? or skeletal tissue development? needs to be added to GO. NOTES:a cell type of the early embryo (see also: mesenchymal cells) that will give rise to mineralized connective tissue. Scleroblasts can differentiate into osteoblasts (bone-forming cells), chondroblasts (cartilage-forming cells), odontoblasts (dentin-forming cells), ameloblasts (enamel-forming cells). The mesenchymal cells developing into osteoblasts and chondroblasts are derived from the mesoderm. Those developing into odontoblasts are neural crest cells. Those developing into ameloblasts are derived from the ectoderm. (http://www.copewithcytokines.de/cope.cgi?key=scleroblasts)" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "scleroblast", @@ -3510,6 +3612,7 @@ "val" : "Cell that is part of the neural crest region of the neuroepithelium, prior to migration. Note that not all premigratory neural crest cells may become migratory neural crest cells.", "xrefs" : [ "UBERONREF:0000002" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "ZFA:0007084" } ], @@ -3530,7 +3633,7 @@ "val" : "Any hematopoietic cell that is a precursor of some other hematopoietic cell type.", "xrefs" : [ "GOC:dos" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ] + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ] } }, { "id" : "http://purl.obolibrary.org/obo/CL_0008019", @@ -3540,7 +3643,7 @@ "definition" : { "val" : "A non-polarised cell precursor cell that is part of some mesenchyme, is associated with the cell matrix but is not connected to other cells and is capable of migration." }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "mesenchyme cell" @@ -3558,6 +3661,7 @@ "definition" : { "val" : "A zygote in a plant or an animal." }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "MESH:D015053" } ], @@ -3575,13 +3679,13 @@ "val" : "A cell of the neural crest. Neural crest cells are multipotent. Premigratory neural crest cells are found at the neural plate boarder, some of which will undergo ectomesynchymal transition and delamination to form migratory neural crest cells.", "xrefs" : [ "https://orcid.org/0000-0001-5208-3432", "https://orcid.org/0000-0002-9900-7880" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "https://cellxgene.cziscience.com/cellguide/CL_0011012" } ], "basicPropertyValues" : [ { "pred" : "http://purl.org/dc/terms/description", - "val" : "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional.\n\nNeural crest cells are a group of transient and highly migratory cells that originate from the neuroectoderm during the early stages of embryonic development. They are multipotent cells with an exceptional degree of plasticity, capable of differentiating into various somatic cell types and therefore play a fundamental role in the formation of various organs and tissues, making them critical contributors to the developing embryo. \nAfter the initiation of neurulation (the formation of the neural tube) neural crest cells start to undergo epithelial-to-mesenchymal transition and delaminate and migrate from the dorsal neural tube to several regions throughout the embryo. They differentiate into a range of diverse cell types, such as neurons and glial cells of the peripheral nervous system, including sensory and autonomic neurons. They also contribute to the formation of adrenal glands, pigment cells in the skin (melanocytes), cardiac structures, including parts of the heart septum and major arteries, as well as bones and cartilage of the face and skull.\nDisorders or aberrations in the development or migration of the neural crest cells can lead to serious congenital malformations, such as neurocristopathies, including Hirschsprung disease, neuroblastoma, and neurofibromatosis." + "val" : "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nNeural crest cells are a group of transient and highly migratory cells that originate from the neuroectoderm during the early stages of embryonic development. They are multipotent cells with an exceptional degree of plasticity, capable of differentiating into various somatic cell types and therefore play a fundamental role in the formation of various organs and tissues, making them critical contributors to the developing embryo. \nAfter the initiation of neurulation (the formation of the neural tube) neural crest cells start to undergo epithelial-to-mesenchymal transition and delaminate and migrate from the dorsal neural tube to several regions throughout the embryo. They differentiate into a range of diverse cell types, such as neurons and glial cells of the peripheral nervous system, including sensory and autonomic neurons. They also contribute to the formation of adrenal glands, pigment cells in the skin (melanocytes), cardiac structures, including parts of the heart septum and major arteries, as well as bones and cartilage of the face and skull.\nDisorders or aberrations in the development or migration of the neural crest cells can lead to serious congenital malformations, such as neurocristopathies, including Hirschsprung disease, neuroblastoma, and neurofibromatosis." } ] } }, { @@ -3593,7 +3697,7 @@ "val" : "A precursor cell that has a tendency to differentiate into a specific type of cell. They are descendants of stem cells, only they are more constrained in their differentiation potential or capacity for self-renewal, and are often more limited in both senses.", "xrefs" : [ "ISBN:978-1-62808-994-3", "https://doi.org/10.1016/B978-0-12-409503-8.00002-0" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "basicPropertyValues" : [ { "pred" : "http://purl.org/dc/terms/contributor", "val" : "https://orcid.org/0000-0001-5208-3432" @@ -3609,7 +3713,7 @@ "xrefs" : [ "GOC:dos" ] }, "comments" : [ "Work is needed on GO 'cell differentiation' before it is clear whether the equivalent class definition 'native cell' that capable_of some 'cell differentiation' works. Also, may want to consider merging this with non-terminally differentiated cell." ], - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ] + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ] } }, { "id" : "http://purl.obolibrary.org/obo/CL_0017005", @@ -3620,7 +3724,7 @@ "val" : "A lymphocyte that has gotten larger after being stimulated by an antigen.", "xrefs" : [ "NCIT:C13013", "http://orcid.org/0000-0001-9990-8331" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#blood_and_immune_upper_slim" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#blood_and_immune_upper_slim", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "BTO:0000772" }, { @@ -3629,11 +3733,11 @@ "val" : "FMA:83030" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/date", - "val" : "2022-08-17T14:20:01Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "pred" : "http://purl.org/dc/terms/contributor", "val" : "http://orcid.org/0000-0003-2473-2313" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2022-08-17T14:20:01Z" } ] } }, { @@ -3645,18 +3749,18 @@ "val" : "A lymphocyte of B lineage that has gotten larger after being stimulated by an antigen.", "xrefs" : [ "EFO:0005293", "https://orcid.org/0000-0002-2825-0621" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#blood_and_immune_upper_slim" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#blood_and_immune_upper_slim", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "EFO:0005293" }, { "val" : "FMA:83031" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/date", - "val" : "2022-08-17T14:30:32Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "pred" : "http://purl.org/dc/terms/contributor", "val" : "http://orcid.org/0000-0003-2473-2313" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2022-08-17T14:30:32Z" } ] } }, { @@ -3757,6 +3861,7 @@ "val" : "Hematopoietic cells resident in the bone marrow. Include: hematopoietic stem cells (lymphoid stem cells and myeloid stem cells) and the precursor cells for thrombocytes, erythrocytes, basophils, neutrophils, eosinophils, monocytes and lymphocytes.", "xrefs" : [ "NPX:PDR" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "pred" : "hasRelatedSynonym", "val" : "bone marrow hematopoietic cells", @@ -3779,7 +3884,7 @@ "val" : "A leukocyte with a single non-segmented nucleus in the mature form found in the circulatory pool of blood.", "xrefs" : [ "GOC:TermGenie" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "basicPropertyValues" : [ { "pred" : "http://purl.org/dc/terms/contributor", "val" : "http://www.wikidata.org/entity/Q35563349" @@ -3797,7 +3902,7 @@ "val" : "A lymphocyte located in blood.", "xrefs" : [ "https://orcid.org/0000-0001-9990-8331" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#blood_and_immune_upper_slim" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#blood_and_immune_upper_slim", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "basicPropertyValues" : [ { "pred" : "http://purl.org/dc/terms/date", "val" : "2022-11-04T14:40:00Z" @@ -3812,6 +3917,7 @@ "val" : "A multinucleate cell formed by the fusion of multiple uninuclear cells through plasma membrane fusion. This process leads to a single large cell containing multiple nuclei within a shared cytoplasm.", "xrefs" : [ "PMID:20851884", "Wikipedia:Syncytium" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "syncytium", @@ -3849,9 +3955,6 @@ "val" : "Wikipedia:Mitosis" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0007067" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" } ] @@ -3933,15 +4036,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/geneontology/go-ontology/issues/28301" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0000789" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0000790" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0005717" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "cellular_component" @@ -3971,12 +4065,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/geneontology/go-ontology/issues/22355" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0005719" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0035327" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "cellular_component" @@ -4009,12 +4097,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/geneontology/go-ontology/issues/22355" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0005720" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0035328" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "cellular_component" @@ -4233,18 +4315,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/geneontology/go-ontology/issues/19116" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0042032" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0042089" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0042107" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0050663" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" @@ -4256,7 +4326,7 @@ "type" : "CLASS", "meta" : { "definition" : { - "val" : "The regulated release of serotonin by a cell. Serotonin (5-hydroxytryptamine, or 5-HT) is a monoamine synthesised in serotonergic neurons in the central nervous system, enterochromaffin cells in the gastrointestinal tract and some immune system cells.", + "val" : "The regulated release of serotonin by a cell. Serotonin (5-hydroxytryptamine, or 5-HT) is a monoamine synthesized in serotonergic neurons in the central nervous system, enterochromaffin cells in the gastrointestinal tract and some immune system cells.", "xrefs" : [ "GOC:ef", "ISBN:0198506732", "ISBN:0781735149" ] }, "synonyms" : [ { @@ -4324,9 +4394,6 @@ "val" : "Wikipedia:Neurulation" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0001679" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" } ] @@ -4708,12 +4775,6 @@ "val" : "immunoglobulin secretion" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0002378" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0048305" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" } ] @@ -4754,12 +4815,6 @@ "xrefs" : [ "GOC:dph" ] } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0002379" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0002380" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" } ] @@ -4830,12 +4885,6 @@ "val" : "cellular immune response" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0019723" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0042087" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" } ] @@ -5685,9 +5734,6 @@ "val" : "molecular function" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0005554" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "molecular_function" } ] @@ -5715,12 +5761,6 @@ "val" : "Reactome:R-HSA-193672" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0004926" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0099600" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "molecular_function" } ] @@ -5794,25 +5834,12 @@ "val" : "Reactome:R-HSA-114558" }, { "val" : "Reactome:R-HSA-167408" + }, { + "val" : "Reactome:R-HSA-381706" }, { "val" : "Wikipedia:GPCR" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0001622" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0001623" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0001624" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0001625" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0016526" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "molecular_function" } ] @@ -5845,9 +5872,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/geneontology/go-ontology/issues/17729" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0008372" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "cellular_component" @@ -5961,12 +5985,6 @@ "val" : "Wikipedia:Basement_membrane" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0005605" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0008003" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "cellular_component" } ] @@ -6252,9 +6270,6 @@ "val" : "Wikipedia:Ribosome" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0033279" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "cellular_component" } ] @@ -6308,12 +6323,6 @@ "val" : "Wikipedia:Cell_membrane" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0005887" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0005904" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "cellular_component" } ] @@ -6367,9 +6376,6 @@ "val" : "cellular DNA metabolism" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0055132" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" } ] @@ -6422,15 +6428,6 @@ "val" : "Wikipedia:Translation_(genetics)" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0006416" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0006453" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0043037" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" } ] @@ -6459,12 +6456,6 @@ "val" : "translation initiation" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0006440" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0006454" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" } ] @@ -6487,12 +6478,6 @@ "val" : "translation elongation" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0006442" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0006455" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" } ] @@ -6517,12 +6502,6 @@ "val" : "translational complex disassembly" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0006443" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0006456" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" } ] @@ -6545,21 +6524,9 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/geneontology/go-ontology/issues/20292" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "jl" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2012-12-13T16:25:32Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0015457" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0015460" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0044765" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" @@ -6619,12 +6586,6 @@ "val" : "Wikipedia:Exocytosis" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0016194" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0016195" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" } ] @@ -6661,15 +6622,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/geneontology/go-ontology/issues/25268" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0016193" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0016196" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0098701" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" @@ -6708,17 +6660,8 @@ "val" : "vesicle budding" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "jl" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2013-12-19T15:26:17Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0006902" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:1902591" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" @@ -6830,12 +6773,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002161", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_4896" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0006917" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0008632" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" @@ -6967,12 +6904,6 @@ "val" : "defense/immunity protein activity" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0002217" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0042829" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" } ] @@ -7043,15 +6974,9 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/geneontology/go-ontology/issues/27189" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "jl" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2013-12-19T15:25:51Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:1902589" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" @@ -7170,21 +7095,6 @@ "val" : "Wikipedia:Signal_transduction" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0023014" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0023015" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0023016" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0023033" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0023045" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" } ] @@ -7237,9 +7147,6 @@ "xrefs" : [ "GOC:mah" ] } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0038042" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" } ] @@ -7462,9 +7369,6 @@ "val" : "hemolymph circulation" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0070261" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" } ] @@ -7499,21 +7403,9 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/geneontology/go-ontology/issues/24968" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "jl" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2012-09-19T15:05:24Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0000004" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0007582" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0044699" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" @@ -7525,7 +7417,7 @@ "type" : "CLASS", "meta" : { "definition" : { - "val" : "The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.", + "val" : "A cellular process consisting of the biochemical pathways by which a living organism transforms chemical substances. This includes including anabolism (biosynthetic process) and catabolism (catabolic process). Metabolic processes includes the transformation of small molecules, as well macromolecular processes such as DNA repair and replication, protein synthesis and degradation.", "xrefs" : [ "GOC:go_curators", "ISBN:0198547684" ] }, "comments" : [ "Note that metabolic processes do not include single functions or processes such as protein-protein interactions, protein-nucleic acids, nor receptor-ligand interactions." ], @@ -7533,18 +7425,6 @@ "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "metabolism" - }, { - "pred" : "hasNarrowSynonym", - "val" : "metabolic process resulting in cell growth" - }, { - "pred" : "hasNarrowSynonym", - "val" : "metabolism resulting in cell growth" - }, { - "pred" : "hasNarrowSynonym", - "val" : "multicellular organism metabolic process" - }, { - "pred" : "hasRelatedSynonym", - "val" : "single-organism metabolic process" } ], "xrefs" : [ { "val" : "Wikipedia:Metabolism" @@ -7553,17 +7433,11 @@ "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/geneontology/go-ontology/issues/26424" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "jl" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/geneontology/go-ontology/issues/28932" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2012-10-17T15:46:40Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0044236" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0044710" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" @@ -7601,7 +7475,7 @@ "type" : "CLASS", "meta" : { "definition" : { - "val" : "The chemical reactions and pathways resulting in the formation of substances; typically the energy-requiring part of metabolism in which simpler substances are transformed into more complex ones.", + "val" : "A cellular process consisting of the biochemical pathways by which a living organism synthesizes chemical substances. This typically represents the energy-requiring part of metabolism in which simpler substances are transformed into more complex ones.", "xrefs" : [ "GOC:curators", "ISBN:0198547684" ] }, "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_chembl", "http://purl.obolibrary.org/obo/go#goslim_metagenomics", "http://purl.obolibrary.org/obo/go#goslim_plant", "http://purl.obolibrary.org/obo/go#goslim_plant_ribbon" ], @@ -7628,17 +7502,11 @@ "val" : "Wikipedia:Anabolism" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "jl" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/geneontology/go-ontology/issues/28932" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2012-10-17T15:52:18Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0044274" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0044711" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" @@ -7681,9 +7549,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/geneontology/go-ontology/issues/27189" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0043284" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" @@ -7743,9 +7608,6 @@ "val" : "physiological response to wounding" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0002245" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" } ] @@ -7801,9 +7663,6 @@ "val" : "Wikipedia:Embryogenesis" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0009795" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" } ] @@ -7905,20 +7764,8 @@ "val" : "single-organism cellular process" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "jl" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2012-12-11T16:56:55Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0008151" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0044763" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0050875" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" @@ -7962,14 +7809,8 @@ "val" : "single-organism membrane invagination" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "jl" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2013-12-02T13:58:34Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:1902534" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" @@ -8038,9 +7879,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/geneontology/go-ontology/issues/24835" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0016244" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" @@ -8148,15 +7986,6 @@ "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2014-03-06T11:37:54Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0016021" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0098589" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0098805" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "cellular_component" @@ -8195,12 +8024,6 @@ "xrefs" : [ "GOC:mah" ] } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0044235" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0071842" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" } ] @@ -8276,9 +8099,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/geneontology/go-ontology/issues/25421" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0006899" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" @@ -8462,15 +8282,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/geneontology/go-ontology/issues/27189" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0006411" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0044267" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0044268" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" @@ -8563,9 +8374,6 @@ "xrefs" : [ "GOC:mah" ] } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0042570" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "cellular_component" } ] @@ -8590,9 +8398,6 @@ "val" : "Wikipedia:Antigen_presentation" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0030333" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" } ] @@ -8647,9 +8452,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/geneontology/go-ontology/issues/27189" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0071845" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" @@ -8688,9 +8490,6 @@ "val" : "cellular component assembly at cellular level" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0071844" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" } ] @@ -8772,17 +8571,8 @@ "val" : "single organism signaling" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "jl" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2010-02-16T09:30:50Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0023046" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0044700" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" @@ -8938,9 +8728,6 @@ "xrefs" : [ "GOC:add" ] } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0046650" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" } ] @@ -9058,9 +8845,6 @@ "xrefs" : [ "GOC:add" ] } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0042115" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" } ] @@ -9141,12 +8925,6 @@ "xrefs" : [ "GOC:add" ] } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0042112" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0046652" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" } ] @@ -9279,9 +9057,6 @@ "xrefs" : [ "GOC:bf" ] } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0000068" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" } ] @@ -9468,9 +9243,6 @@ "val" : "Wikipedia:Extracellular_matrix" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0005578" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "cellular_component" } ] @@ -9600,9 +9372,6 @@ "val" : "NIF_Subcellular:sao180601769" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0016023" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "cellular_component" } ] @@ -9658,9 +9427,6 @@ "val" : "Wikipedia:Vesicle_(biology)" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0031988" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "cellular_component" } ] @@ -9803,18 +9569,9 @@ }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002161", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_4932" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "jl" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2012-09-19T16:07:47Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0044707" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0050874" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" @@ -9838,14 +9595,8 @@ "val" : "single-organism developmental process" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "jl" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2012-12-19T12:21:31Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0044767" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" @@ -9877,12 +9628,6 @@ "val" : "type I interferon secretion" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0045351" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0072641" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" } ] @@ -9933,15 +9678,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/geneontology/go-ontology/issues/22580" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0034623" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0043241" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0043624" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" @@ -9975,9 +9711,6 @@ "val" : "protein-protein complex" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0043234" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "cellular_component" } ] @@ -10098,9 +9831,6 @@ "val" : "ATP hydrolysis coupled ion transmembrane transport" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0099131" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" } ] @@ -10171,9 +9901,6 @@ "val" : "pre-BCR" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "bf" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2010-03-11T10:46:10Z" }, { @@ -10203,17 +9930,8 @@ "val" : "signalling receptor activity" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "bf" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2011-08-01T02:45:27Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0004872" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0019041" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "molecular_function" @@ -10239,9 +9957,6 @@ "xrefs" : [ "GOC:mah" ] } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0048590" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" } ] @@ -10649,15 +10364,6 @@ "val" : "regulation of homeostatic process" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0032844" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0032845" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0032846" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" } ] @@ -10774,15 +10480,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/geneontology/go-ontology/issues/26424" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0034960" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0043283" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0044259" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" @@ -10849,7 +10546,7 @@ } }, { "id" : "http://purl.obolibrary.org/obo/GO_0043228", - "lbl" : "non-membrane-bounded organelle", + "lbl" : "membraneless organelle", "type" : "CLASS", "meta" : { "definition" : { @@ -10858,6 +10555,12 @@ }, "subsets" : [ "http://purl.obolibrary.org/obo/go#gocheck_do_not_annotate", "http://purl.obolibrary.org/obo/go#goslim_mouse" ], "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "membrane-less organelle" + }, { + "pred" : "hasExactSynonym", + "val" : "non-membrane-bounded organelle" + }, { "pred" : "hasExactSynonym", "val" : "non-membrane-enclosed organelle" }, { @@ -10873,6 +10576,9 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/geneontology/go-ontology/issues/28153" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/geneontology/go-ontology/issues/29106" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "cellular_component" @@ -10932,7 +10638,7 @@ } }, { "id" : "http://purl.obolibrary.org/obo/GO_0043232", - "lbl" : "intracellular non-membrane-bounded organelle", + "lbl" : "intracellular membraneless organelle", "type" : "CLASS", "meta" : { "definition" : { @@ -10941,10 +10647,16 @@ }, "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_pir" ], "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "intracellular non-membrane-bounded organelle" + }, { "pred" : "hasExactSynonym", "val" : "intracellular non-membrane-enclosed organelle" } ], "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/geneontology/go-ontology/issues/29106" + }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "cellular_component" } ] @@ -11020,21 +10732,9 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/geneontology/go-ontology/issues/22580" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "mah" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2010-09-08T10:01:42Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0034600" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0034621" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0071822" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" @@ -11057,9 +10757,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/geneontology/go-ontology/issues/27194" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0071843" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" @@ -11082,9 +10779,6 @@ "val" : "Met-tRNA/eIF2.GTP ternary complex" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "jl" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2009-10-22T02:38:55Z" }, { @@ -11092,30 +10786,6 @@ "val" : "cellular_component" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/GO_0044237", - "lbl" : "cellular metabolic process", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "The chemical reactions and pathways by which individual cells transform chemical substances.", - "xrefs" : [ "GOC:go_curators" ] - }, - "comments" : [ "This term should not be used for direct annotation. It should be possible to make a more specific annotation to one of the children of this term." ], - "subsets" : [ "http://purl.obolibrary.org/obo/go#gocheck_do_not_annotate" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "cellular metabolism" - }, { - "pred" : "hasRelatedSynonym", - "val" : "intermediary metabolism", - "xrefs" : [ "GOC:mah" ] - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "biological_process" - } ] - } }, { "id" : "http://purl.obolibrary.org/obo/GO_0044238", "lbl" : "primary metabolic process", @@ -11141,38 +10811,6 @@ "val" : "biological_process" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/GO_0044249", - "lbl" : "cellular biosynthetic process", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "The chemical reactions and pathways resulting in the formation of substances, carried out by individual cells.", - "xrefs" : [ "GOC:jl" ] - }, - "comments" : [ "This term should not be used for direct annotation. It should be possible to make a more specific annotation to one of the children of this term." ], - "subsets" : [ "http://purl.obolibrary.org/obo/go#gocheck_do_not_annotate" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "cellular anabolism" - }, { - "pred" : "hasExactSynonym", - "val" : "cellular biosynthesis" - }, { - "pred" : "hasExactSynonym", - "val" : "cellular formation" - }, { - "pred" : "hasExactSynonym", - "val" : "cellular synthesis" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", - "val" : "https://github.com/geneontology/go-ontology/issues/27052" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "biological_process" - } ] - } }, { "id" : "http://purl.obolibrary.org/obo/GO_0044419", "lbl" : "biological process involved in interspecies interaction between organisms", @@ -11224,9 +10862,6 @@ "val" : "cell-cell fusion" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0006947" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" } ] @@ -11287,9 +10922,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002161", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_4751" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0002226" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" @@ -11651,9 +11283,6 @@ "val" : "stimulation of biological process" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0043119" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" } ] @@ -11685,9 +11314,6 @@ "val" : "inhibition of biological process" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0043118" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" } ] @@ -11722,9 +11348,6 @@ "val" : "stimulation of cellular process" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0051242" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" } ] @@ -11835,9 +11458,6 @@ "xrefs" : [ "GOC:dph", "GOC:tb" ] } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0048828" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" } ] @@ -12119,9 +11739,6 @@ "val" : "regulation of physiological process" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0050791" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" } ] @@ -12155,9 +11772,6 @@ "val" : "regulation of cellular physiological process" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0051244" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" } ] @@ -12281,9 +11895,6 @@ "val" : "physiological response to stimulus" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0051869" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" } ] @@ -12402,15 +12013,9 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/geneontology/go-ontology/issues/27052" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "jl" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2013-12-18T13:51:04Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:1902578" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" @@ -12533,15 +12138,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/geneontology/go-ontology/issues/4585" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0006323" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0007001" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0051277" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" @@ -12590,12 +12186,6 @@ "xrefs" : [ "GOC:ai" ] }, "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0009613" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0042828" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" } ] @@ -12635,14 +12225,8 @@ "val" : "ATP hydrolysis coupled transmembrane transport" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "tb" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2015-10-21T13:22:47Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0090662" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" @@ -12749,9 +12333,6 @@ "xrefs" : [ "GOC:dph" ] }, "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dph" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2009-04-28T09:33:36Z" }, { @@ -12788,17 +12369,8 @@ "val" : "single-organism membrane organization" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "jl" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2010-02-08T02:43:11Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0016044" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0044802" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" @@ -12825,17 +12397,8 @@ "val" : "Wikipedia:Lipid_bilayer_fusion" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "jl" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2010-02-08T02:48:06Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0006944" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0044801" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" @@ -12851,9 +12414,6 @@ "xrefs" : [ "GOC:dph" ] }, "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dph" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2010-05-25T09:05:34Z" }, { @@ -12871,9 +12431,6 @@ "xrefs" : [ "GOC:BHF", "GOC:rph", "PMID:21123617" ] }, "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dph" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2018-04-13T12:47:21Z" }, { @@ -12919,15 +12476,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/geneontology/go-ontology/issues/22580" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0006461" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0034622" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0043623" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" @@ -13060,9 +12608,6 @@ "comments" : [ "Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC." ], "subsets" : [ "http://purl.obolibrary.org/obo/go#gocheck_do_not_annotate" ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "mah" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2009-08-27T04:41:45Z" }, { @@ -13081,9 +12626,6 @@ }, "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_yeast" ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "mah" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2009-09-15T03:00:51Z" }, { @@ -13114,9 +12656,6 @@ "xrefs" : [ "GOC:add" ] } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "mah" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2010-03-09T04:20:31Z" }, { @@ -13147,9 +12686,6 @@ "xrefs" : [ "GOC:add" ] } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "mah" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2010-03-09T04:22:29Z" }, { @@ -13168,9 +12704,6 @@ }, "comments" : [ "Note that an IgD immunoglobulin complex has the function of antigen binding if a suitable antigen is available." ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "mah" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2010-03-24T01:44:53Z" }, { @@ -13189,9 +12722,6 @@ }, "comments" : [ "Note that an IgM immunoglobulin complex has the function of antigen binding if a suitable antigen is available." ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "mah" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2010-03-24T01:44:53Z" }, { @@ -13227,9 +12757,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/geneontology/go-ontology/issues/25143" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "mah" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2010-09-08T10:10:35Z" @@ -13264,15 +12791,9 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/geneontology/go-ontology/issues/27189" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "mah" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2010-09-10T01:39:16Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0071841" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" @@ -13289,9 +12810,6 @@ }, "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_flybase_ribbon" ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "mah" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2010-10-04T01:51:47Z" }, { @@ -13314,9 +12832,6 @@ "xrefs" : [ "GOC:vesicles" ] } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "mah" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2010-10-18T03:44:18Z" }, { @@ -13336,9 +12851,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/geneontology/go-ontology/issues/22302" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "mah" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2010-02-26T02:15:40Z" @@ -13357,9 +12869,6 @@ "xrefs" : [ "GOC:ascb_2009", "GOC:dph", "GOC:tb" ] }, "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "tb" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2009-12-11T11:44:58Z" }, { @@ -13378,9 +12887,6 @@ }, "comments" : [ "Note that immunologists typically use the word 'maturation' to refer to dendritic cells undergoing the process that GO describes as 'cell differentiation'." ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pr" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2011-04-01T10:08:42Z" }, { @@ -13407,14 +12913,8 @@ "val" : "induction of apoptosis by extracellular signals" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pr" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2011-11-23T09:30:23Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0008624" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" @@ -13437,9 +12937,6 @@ "val" : "apoptosis" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pr" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2011-11-23T09:45:24Z" }, { @@ -13457,9 +12954,6 @@ "xrefs" : [ "GOC:vesicles" ] }, "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pr" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2016-03-29T17:39:45Z" }, { @@ -13493,9 +12987,6 @@ "val" : "intraluminal vesicle assembly" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pr" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2016-10-03T14:35:25Z" }, { @@ -13529,15 +13020,9 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/geneontology/go-ontology/issues/22173" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dos" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2013-11-11T12:59:11Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0009814" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" @@ -13559,9 +13044,6 @@ "val" : "region of plasma membrane" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dos" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2014-03-06T11:55:32Z" }, { @@ -13834,14 +13316,18 @@ } }, { "id" : "http://purl.obolibrary.org/obo/GO_0110165", - "lbl" : "cellular anatomical entity", + "lbl" : "cellular anatomical structure", "type" : "CLASS", "meta" : { "definition" : { - "val" : "A part of a cellular organism that is either an immaterial entity or a material entity with granularity above the level of a protein complex but below that of an anatomical system. Or, a substance produced by a cellular organism with granularity above the level of a protein complex.", + "val" : "A part of a cellular organism consisting of a material entity with granularity above the level of a protein complex but below that of an anatomical system. Note that cellular organisms exclude viruses.", "xrefs" : [ "GOC:kmv" ] }, "subsets" : [ "http://purl.obolibrary.org/obo/go#gocheck_do_not_annotate", "http://purl.obolibrary.org/obo/go#goslim_pir" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "cellular anatomical entity" + } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/geneontology/go-ontology/issues/24200" @@ -13849,8 +13335,8 @@ "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/geneontology/go-ontology/issues/26424" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "kmv" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/geneontology/go-ontology/issues/28978" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2019-08-12T18:01:37Z" @@ -13871,9 +13357,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/geneontology/go-ontology/issues/13193" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "krc" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-03-21T17:26:07Z" @@ -13899,9 +13382,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/geneontology/go-ontology/issues/13298" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "krc" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-04-24T23:56:08Z" @@ -13922,9 +13402,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/geneontology/go-ontology/issues/13298" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "krc" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-04-26T16:07:02Z" @@ -13950,9 +13427,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/geneontology/go-ontology/issues/19910" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pg" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-03-23T14:44:23Z" @@ -13972,9 +13446,6 @@ }, "subsets" : [ "http://purl.obolibrary.org/obo/go#gocheck_do_not_annotate" ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pg" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-05-15T13:20:45Z" }, { @@ -13998,9 +13469,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/geneontology/go-ontology/issues/14256" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pg" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-10-23T11:53:42Z" @@ -14028,9 +13496,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/geneontology/go-ontology/issues/15939" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pg" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2018-08-13T18:38:18Z" @@ -14053,9 +13518,6 @@ "val" : "efflux" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pg" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2019-05-22T11:20:45Z" }, { @@ -14075,9 +13537,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/geneontology/go-ontology/issues/20261" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pg" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2020-11-11T17:19:06Z" @@ -14105,9 +13564,6 @@ "xrefs" : [ "GOC:TermGenie" ] } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pr" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2013-05-02T17:32:42Z" }, { @@ -14126,9 +13582,6 @@ }, "subsets" : [ "http://purl.obolibrary.org/obo/go#gocheck_do_not_annotate" ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "jl" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2014-05-22T14:22:34Z" }, { @@ -14146,9 +13599,6 @@ "xrefs" : [ "CL:0000842", "GOC:TermGenie", "GO_REF:0000086", "PMID:24759906" ] }, "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "cls" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2014-06-25T15:47:09Z" }, { @@ -14171,9 +13621,6 @@ "xrefs" : [ "GOC:vesicles" ] } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "jl" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2014-10-22T14:26:11Z" }, { @@ -14209,9 +13656,6 @@ "xrefs" : [ "GOC:TermGenie" ] } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pad" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2014-12-04T15:34:13Z" }, { @@ -14249,17 +13693,8 @@ "val" : "Wikipedia:Ribonucleoprotein" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pr" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2015-11-19T12:26:37Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0030529" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:1990903" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "cellular_component" @@ -14275,9 +13710,6 @@ "xrefs" : [ "GOC:obol" ] }, "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "tb" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2010-08-05T11:25:59Z" }, { @@ -14308,9 +13740,6 @@ "xrefs" : [ "GOC:obol" ] } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "mah" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2010-10-01T09:41:21Z" }, { @@ -14341,9 +13770,6 @@ "xrefs" : [ "GOC:obol" ] } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "mah" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2010-10-01T09:41:30Z" }, { @@ -14432,9 +13858,6 @@ "val" : "GC_ID:1" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "NCBITaxon:85055" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "ncbi_taxonomy" } ] @@ -14466,9 +13889,6 @@ "val" : "GC_ID:1" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "NCBITaxon:40673" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "ncbi_taxonomy" } ] @@ -14802,9 +14222,6 @@ "val" : "GC_ID:1" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "NCBITaxon:109679" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "ncbi_taxonomy" } ] @@ -15029,9 +14446,6 @@ "xrefs" : [ "PATOC:GVG" ] }, "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "PATO:0000072" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "quality" } ] @@ -15067,9 +14481,6 @@ "val" : "relational shape quality" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "PATO:0001647" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "quality" } ] @@ -15093,9 +14504,6 @@ "val" : "relational structural quality" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "PATO:0001452" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "quality" } ] @@ -15208,9 +14616,6 @@ "val" : "Wikipedia:Physical_property" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "PATO:0002079" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "quality" } ] @@ -15254,12 +14659,6 @@ "val" : "snap:Quality" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "PATO:0001237" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "PATO:0001238" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "quality" } ] @@ -15520,9 +14919,6 @@ "val" : "tubulate" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "PATO:0001203" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "quality" } ] @@ -15975,9 +15371,6 @@ "val" : "high N:C ratio" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "http://orcid.org/0000-0001-5208-3432" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "quality" } ] @@ -15991,9 +15384,6 @@ "val" : "A quality of continuant that exist at the anatomical level of organisation and anything under it. This includes, but is not limited to, cells , tissues, and components." }, "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "http://orcid.org/0000-0001-7258-9596" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "quality" } ] @@ -16007,9 +15397,6 @@ "val" : "A quality inhering in an anotomical structure by virtue of its capacity to be stained by specific histological dyes." }, "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "http://orcid.org/0000-0001-7258-9596" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "quality" } ] @@ -16024,9 +15411,6 @@ "xrefs" : [ "GOC:add" ] }, "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "http://orcid.org/0000-0001-7258-9596" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "quality" } ] @@ -16041,9 +15425,6 @@ "xrefs" : [ "GOC:add" ] }, "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "http://orcid.org/0000-0001-7258-9596" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "quality" } ] @@ -16057,7 +15438,7 @@ "val" : "An amino acid chain that is produced de novo by ribosome-mediated translation of a genetically-encoded mRNA, and any derivatives thereof.", "xrefs" : [ "PRO:DAN", "PRO:WCB" ] }, - "comments" : [ "The definition above excludes protein complexes, which some also consider a protein. Those who wish to refer to a class representing both senses of the word are directed to CHEBI:36080. Note that the definition allows for experimentally-manipulated genes, and allows for artifically-produced derivatives that mimic those found naturally. Proteins (in the sense defined here) that descended from a common ancestor can be classified into families and superfamilies composed of products of evolutionarily-related genes. The domain architecture of a protein is described by the order of its constituent domains. Proteins with the same domains in the same order are defined as homeomorphic [PRO:WCB]." ], + "comments" : [ "The definition above excludes protein complexes, which some also consider a protein. Those who wish to refer to a class representing both senses of the word are directed to CHEBI:36080. Note that the definition allows for experimentally-manipulated genes, and allows for artifically-produced derivatives that mimic those found naturally. Proteins (in the sense defined here) that descended from a common ancestor can be classified into families and superfamilies composed of products of evolutionarily-related genes. The domain architecture of a protein is described by the order of its constituent domains. Proteins with the same domains in the same order are defined as homeomorphic [PRO:WCB)." ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "natural protein", @@ -19091,15 +18472,15 @@ } ] } }, { - "id" : "http://purl.obolibrary.org/obo/PR_000050567", - "lbl" : "protein-containing material entity", + "id" : "http://purl.obolibrary.org/obo/PR_000064867", + "lbl" : "protein-containing molecular entity", "type" : "CLASS", "meta" : { "definition" : { - "val" : "A material entity that minimally consists of a protein.", + "val" : "A molecular entity that minimally consists of a protein.", "xrefs" : [ "PRO:DAN" ] }, - "comments" : [ "Note: This includes single proteins and derivatives thereof (PR:000000001), protein-containing complexes (GO:0032991), and protein aggregates (PR:000050566)." ], + "comments" : [ "Note: This includes single proteins and derivatives thereof (PR:000000001), protein-containing complexes (GO:0032991), and protein aggregates (PR:000050565)." ], "synonyms" : [ { "pred" : "hasNarrowSynonym", "val" : "protein", @@ -19219,9 +18600,6 @@ "val" : "galen:Wall" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "UBERON:0009915" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -19560,9 +18938,6 @@ "val" : "galen:ComplexSkeletalStructure" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "UBERON:0010322" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -20286,9 +19661,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "TODO - check relationship with epiblast. Note in FMA this is not a subclass of embryo, but in uberon embryo is the whole organism from zygote onwards and thus includes the blastula" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "UBERON:0007011" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -21764,9 +21136,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0002161", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_6040" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "UBERON:0003263" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -22110,7 +21479,7 @@ "val" : "Organ system that passes nutrients (such as amino acids and electrolytes), gases, hormones, blood cells, etc. to and from cells in the body to help fight diseases and help stabilize body temperature and pH to maintain homeostasis[WP].", "xrefs" : [ "Wikipedia:Circulatory_system" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#uberon_slim" ], "synonyms" : [ { "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003011", "pred" : "hasRelatedSynonym", @@ -22135,9 +21504,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002161", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_6157" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -23572,15 +22938,10 @@ "val" : "TAO:0001438" }, { "val" : "UMLS:C0333343" - }, { - "val" : "ZFA:0001438" }, { "val" : "galen:BodyCavity" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "UBERON:0000169" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -24735,9 +24096,6 @@ "val" : "ZFA:0000121" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "UBERON:0006258" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" }, { @@ -25634,9 +24992,6 @@ "val" : "Wikipedia:Trilaminar_blastocyst" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "UBERON:0007012" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -27225,9 +26580,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "consider adding new class (EMAPA:16097) for mesenchyme of embryo (some mesenchyme is extraembryonic - e.g. amnion mesoderm)" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "UBERON:0003313" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -27666,6 +27018,8 @@ "val" : "EHDAA2:0004731" }, { "val" : "Wikipedia:Coelom" + }, { + "val" : "ZFA:0001438" } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", @@ -28014,9 +27368,6 @@ "val" : "presumptive central nervous system" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "UBERON:3000469" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -28039,9 +27390,6 @@ "val" : "AAO:0000477" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "UBERON:3000477" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -28678,9 +28026,6 @@ "val" : "A relationship between a process and a barrier, where the process occurs in a region spanning the barrier. For cellular processes the barrier is typically a membrane. Examples include transport across a membrane and membrane depolarization." }, "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "https://orcid.org/0000-0002-7073-9172" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-07-20T17:19:37Z" } ] @@ -30962,9 +30307,6 @@ "val" : "RO:0004007" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2018-12-13T11:26:17Z" }, { @@ -30990,9 +30332,6 @@ "val" : "RO:0004008" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2018-12-13T11:26:32Z" }, { @@ -31018,9 +30357,6 @@ "val" : "RO:0004009" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2018-12-13T11:26:56Z" }, { @@ -31040,9 +30376,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0004050", "val" : "http://purl.obolibrary.org/obo/RO_0002418" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2018-03-13T23:55:05Z" @@ -31058,9 +30391,6 @@ "propertyType" : "OBJECT", "meta" : { "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2018-03-13T23:55:19Z" }, { @@ -31078,9 +30408,6 @@ "val" : "a relation between a process and a continuant, in which the process is regulated by the small molecule continuant" }, "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "https://orcid.org/0000-0003-1813-6857" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2020-04-22T20:27:26Z" } ] @@ -31098,9 +30425,6 @@ "val" : "RO:0012001" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "https://orcid.org/0000-0003-1813-6857" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2020-04-22T20:28:37Z" }, { @@ -31125,9 +30449,6 @@ "val" : "RO:0012003" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "https://orcid.org/0000-0003-1813-6857" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2020-06-08T17:21:33Z" }, { @@ -31148,9 +30469,6 @@ "val" : "a relation between a continuant and a process, in which the continuant is a small molecule that regulates the process" }, "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "https://orcid.org/0000-0003-1813-6857" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2020-06-24T13:15:17Z" } ] @@ -31165,9 +30483,6 @@ "val" : "a relation between a continuant and a process, in which the continuant is a small molecule that activates the process" }, "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "https://orcid.org/0000-0003-1813-6857" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2020-06-24T13:15:26Z" }, { @@ -31186,9 +30501,6 @@ "val" : "RO:0012008" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "https://orcid.org/0000-0003-1813-6857" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2021-02-26T07:28:29Z" }, { @@ -31213,9 +30525,6 @@ "val" : "has synaptic input or output in" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "https://orcid.org/0000-0002-1373-1705" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2020-07-17T09:26:52Z" } ] @@ -31240,13 +30549,34 @@ "val" : "has sensory terminal location" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "https://orcid.org/0000-0002-1373-1705" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2020-07-20T12:10:09Z" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0015004", + "lbl" : "has characterizing marker set", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "A relation that applies between a cell type and a set of markers that can be used to uniquely identify that cell type." + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "has marker gene combination" + }, { + "pred" : "hasExactSynonym", + "val" : "has marker signature set" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "C has_characterizing_marker_set y iff: C is a cell type and y is a collection of genes or proteins whose expression is sufficient to distinguish cell type C from most or all other cell types." + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0001-7258-9596" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/RO_0015006", "lbl" : "different in magnitude relative to", @@ -31372,9 +30702,6 @@ "val" : "RO:0040036" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2018-09-26T01:08:58Z" }, { @@ -32073,13 +31400,14 @@ "propertyType" : "ANNOTATION", "meta" : { "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2018-03-14T00:03:24Z" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/STATO_0000663", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" }, { "id" : "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "type" : "PROPERTY", @@ -32132,6 +31460,10 @@ "meta" : { "comments" : [ "a subset of general classes of cell types in the cell ontology." ] } + }, { + "id" : "http://purl.obolibrary.org/obo/cl#human_subset", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" }, { "id" : "http://purl.obolibrary.org/obo/cl#kidney_upper_slim", "lbl" : "kidney_upper_slim", @@ -32144,6 +31476,10 @@ "val" : "2023-11-22T11:18:57Z" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/cl#mouse_subset", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" }, { "id" : "http://purl.obolibrary.org/obo/go#gocheck_do_not_annotate", "type" : "PROPERTY", @@ -32466,10 +31802,6 @@ "id" : "http://purl.org/dc/elements/1.1/creator", "type" : "PROPERTY", "propertyType" : "ANNOTATION" - }, { - "id" : "http://purl.org/dc/elements/1.1/date", - "type" : "PROPERTY", - "propertyType" : "ANNOTATION" }, { "id" : "http://purl.org/dc/elements/1.1/description", "type" : "PROPERTY", @@ -32482,6 +31814,10 @@ "id" : "http://purl.org/dc/elements/1.1/title", "type" : "PROPERTY", "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.org/dc/elements/1.1/type", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" }, { "id" : "http://purl.org/dc/terms/contributor", "type" : "PROPERTY", @@ -32492,14 +31828,17 @@ "propertyType" : "ANNOTATION" }, { "id" : "http://purl.org/dc/terms/description", + "lbl" : "description", "type" : "PROPERTY", "propertyType" : "ANNOTATION" }, { "id" : "http://purl.org/dc/terms/license", + "lbl" : "license", "type" : "PROPERTY", "propertyType" : "ANNOTATION" }, { "id" : "http://purl.org/dc/terms/title", + "lbl" : "title", "type" : "PROPERTY", "propertyType" : "ANNOTATION" }, { @@ -32517,19 +31856,10 @@ "lbl" : "consider", "type" : "PROPERTY", "propertyType" : "ANNOTATION" - }, { - "id" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "type" : "PROPERTY", - "propertyType" : "ANNOTATION" }, { "id" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "type" : "PROPERTY", "propertyType" : "ANNOTATION" - }, { - "id" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "lbl" : "has_alternative_id", - "type" : "PROPERTY", - "propertyType" : "ANNOTATION" }, { "id" : "http://www.geneontology.org/formats/oboInOwl#hasBroadSynonym", "lbl" : "has_broad_synonym", @@ -32549,9 +31879,21 @@ } }, { "id" : "http://www.geneontology.org/formats/oboInOwl#hasDbXref", - "lbl" : "database_cross_reference", + "lbl" : "has cross-reference", "type" : "PROPERTY", - "propertyType" : "ANNOTATION" + "propertyType" : "ANNOTATION", + "meta" : { + "definition" : { + "val" : "An annotation property that links an ontology entity or a statement to a prefixed identifier or URI." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/information-artifact-ontology/ontology-metadata/issues/123" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0002-7356-1779" + } ] + } }, { "id" : "http://www.geneontology.org/formats/oboInOwl#hasExactSynonym", "lbl" : "has_exact_synonym", @@ -32630,10 +31972,6 @@ "id" : "http://www.geneontology.org/formats/oboInOwl#is_metadata_tag", "type" : "PROPERTY", "propertyType" : "ANNOTATION" - }, { - "id" : "http://www.geneontology.org/formats/oboInOwl#note", - "type" : "PROPERTY", - "propertyType" : "ANNOTATION" }, { "id" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "lbl" : "shorthand", @@ -32806,10 +32144,6 @@ "val" : "true" } ] } - }, { - "sub" : "http://purl.obolibrary.org/obo/CL_0000040", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000040", "pred" : "http://purl.obolibrary.org/obo/BFO_0000051", @@ -32907,11 +32241,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000057", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/CL_0002320" - }, { - "sub" : "http://purl.obolibrary.org/obo/CL_0000057", - "pred" : "http://purl.obolibrary.org/obo/RO_0002202", - "obj" : "http://purl.obolibrary.org/obo/CL_0000134" + "obj" : "http://purl.obolibrary.org/obo/CL_0000499" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000066", "pred" : "is_a", @@ -33000,10 +32330,6 @@ "val" : "true" } ] } - }, { - "sub" : "http://purl.obolibrary.org/obo/CL_0000092", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000092", "pred" : "http://purl.obolibrary.org/obo/BFO_0000051", @@ -33054,10 +32380,6 @@ "val" : "true" } ] } - }, { - "sub" : "http://purl.obolibrary.org/obo/CL_0000094", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000094", "pred" : "http://purl.obolibrary.org/obo/BFO_0000051", @@ -33104,10 +32426,6 @@ "sub" : "http://purl.obolibrary.org/obo/CL_0000097", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/CL_0002274" - }, { - "sub" : "http://purl.obolibrary.org/obo/CL_0000097", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000097", "pred" : "http://purl.obolibrary.org/obo/BFO_0000051", @@ -33528,10 +32846,6 @@ "sub" : "http://purl.obolibrary.org/obo/CL_0000451", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/CL_0000145" - }, { - "sub" : "http://purl.obolibrary.org/obo/CL_0000451", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000451", "pred" : "http://purl.obolibrary.org/obo/BFO_0000051", @@ -33580,6 +32894,14 @@ "sub" : "http://purl.obolibrary.org/obo/CL_0000473", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/CL_0000000" + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_0000499", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/CL_0002320" + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_0000499", + "pred" : "http://purl.obolibrary.org/obo/RO_0002202", + "obj" : "http://purl.obolibrary.org/obo/CL_0000134" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000518", "pred" : "is_a", @@ -33642,10 +32964,6 @@ "sub" : "http://purl.obolibrary.org/obo/CL_0000547", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/CL_0002242" - }, { - "sub" : "http://purl.obolibrary.org/obo/CL_0000547", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000547", "pred" : "http://purl.obolibrary.org/obo/BFO_0000051", @@ -33720,10 +33038,6 @@ "val" : "true" } ] } - }, { - "sub" : "http://purl.obolibrary.org/obo/CL_0000549", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000549", "pred" : "http://purl.obolibrary.org/obo/BFO_0000051", @@ -33746,10 +33060,6 @@ "val" : "true" } ] } - }, { - "sub" : "http://purl.obolibrary.org/obo/CL_0000550", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000550", "pred" : "http://purl.obolibrary.org/obo/BFO_0000051", @@ -33888,18 +33198,10 @@ "sub" : "http://purl.obolibrary.org/obo/CL_0000557", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/CL_0001012" - }, { - "sub" : "http://purl.obolibrary.org/obo/CL_0000557", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/CL_0011026" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000557", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/CL_1001610" - }, { - "sub" : "http://purl.obolibrary.org/obo/CL_0000557", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000557", "pred" : "http://purl.obolibrary.org/obo/BFO_0000051", @@ -33938,10 +33240,6 @@ "val" : "true" } ] } - }, { - "sub" : "http://purl.obolibrary.org/obo/CL_0000558", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000558", "pred" : "http://purl.obolibrary.org/obo/CL_4030046", @@ -34012,10 +33310,6 @@ "val" : "true" } ] } - }, { - "sub" : "http://purl.obolibrary.org/obo/CL_0000559", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000559", "pred" : "http://purl.obolibrary.org/obo/BFO_0000051", @@ -34042,10 +33336,6 @@ "sub" : "http://purl.obolibrary.org/obo/CL_0000566", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/CL_0011026" - }, { - "sub" : "http://purl.obolibrary.org/obo/CL_0000566", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000566", "pred" : "http://purl.obolibrary.org/obo/RO_0002104", @@ -34466,10 +33756,6 @@ "val" : "true" } ] } - }, { - "sub" : "http://purl.obolibrary.org/obo/CL_0000786", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000786", "pred" : "http://purl.obolibrary.org/obo/BFO_0000051", @@ -34508,10 +33794,6 @@ "val" : "true" } ] } - }, { - "sub" : "http://purl.obolibrary.org/obo/CL_0000789", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000789", "pred" : "http://purl.obolibrary.org/obo/RO_0002104", @@ -34526,10 +33808,6 @@ "val" : "true" } ] } - }, { - "sub" : "http://purl.obolibrary.org/obo/CL_0000798", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000798", "pred" : "http://purl.obolibrary.org/obo/RO_0002104", @@ -34620,10 +33898,6 @@ "val" : "true" } ] } - }, { - "sub" : "http://purl.obolibrary.org/obo/CL_0000826", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000826", "pred" : "http://purl.obolibrary.org/obo/BFO_0000051", @@ -34698,10 +33972,6 @@ "val" : "true" } ] } - }, { - "sub" : "http://purl.obolibrary.org/obo/CL_0000831", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000831", "pred" : "http://purl.obolibrary.org/obo/BFO_0000051", @@ -34810,10 +34080,6 @@ "sub" : "http://purl.obolibrary.org/obo/CL_0000837", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/CL_0008001" - }, { - "sub" : "http://purl.obolibrary.org/obo/CL_0000837", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000837", "pred" : "http://purl.obolibrary.org/obo/CL_4030046", @@ -34938,10 +34204,6 @@ "val" : "true" } ] } - }, { - "sub" : "http://purl.obolibrary.org/obo/CL_0000889", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000889", "pred" : "http://purl.obolibrary.org/obo/RO_0000053", @@ -35094,6 +34356,10 @@ "sub" : "http://purl.obolibrary.org/obo/CL_0001012", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/CL_0001060" + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_0001012", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/CL_0011026" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0001035", "pred" : "is_a", @@ -35178,10 +34444,6 @@ "sub" : "http://purl.obolibrary.org/obo/CL_0001200", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/CL_0000945" - }, { - "sub" : "http://purl.obolibrary.org/obo/CL_0001200", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0001200", "pred" : "http://purl.obolibrary.org/obo/CL_4030046", @@ -35240,10 +34502,6 @@ "sub" : "http://purl.obolibrary.org/obo/CL_0002028", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/CL_0002191" - }, { - "sub" : "http://purl.obolibrary.org/obo/CL_0002028", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0002028", "pred" : "http://purl.obolibrary.org/obo/BFO_0000051", @@ -35448,10 +34706,6 @@ "val" : "true" } ] } - }, { - "sub" : "http://purl.obolibrary.org/obo/CL_0002679", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0002679", "pred" : "http://purl.obolibrary.org/obo/CL_4030046", @@ -36520,8 +35774,8 @@ "obj" : "http://purl.obolibrary.org/obo/GO_0043232" }, { "sub" : "http://purl.obolibrary.org/obo/GO_0005840", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PR_000050567" + "pred" : "http://purl.obolibrary.org/obo/BFO_0000051", + "obj" : "http://purl.obolibrary.org/obo/PR_000000001" }, { "sub" : "http://purl.obolibrary.org/obo/GO_0005840", "pred" : "http://purl.obolibrary.org/obo/RO_0002216", @@ -36573,7 +35827,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/GO_0006413", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/GO_0044237" + "obj" : "http://purl.obolibrary.org/obo/GO_0008152" }, { "sub" : "http://purl.obolibrary.org/obo/GO_0006413", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", @@ -36921,7 +36175,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/GO_0008152", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/GO_0008150" + "obj" : "http://purl.obolibrary.org/obo/GO_0009987" }, { "sub" : "http://purl.obolibrary.org/obo/GO_0008219", "pred" : "is_a", @@ -36933,11 +36187,11 @@ }, { "sub" : "http://purl.obolibrary.org/obo/GO_0009059", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/GO_0043170" + "obj" : "http://purl.obolibrary.org/obo/GO_0009058" }, { "sub" : "http://purl.obolibrary.org/obo/GO_0009059", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/GO_0044249" + "obj" : "http://purl.obolibrary.org/obo/GO_0043170" }, { "sub" : "http://purl.obolibrary.org/obo/GO_0009605", "pred" : "is_a", @@ -37636,8 +36890,8 @@ "obj" : "http://purl.obolibrary.org/obo/GO_0005575" }, { "sub" : "http://purl.obolibrary.org/obo/GO_0032991", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PR_000050567" + "pred" : "http://purl.obolibrary.org/obo/BFO_0000051", + "obj" : "http://purl.obolibrary.org/obo/PR_000000001" }, { "sub" : "http://purl.obolibrary.org/obo/GO_0033151", "pred" : "is_a", @@ -37978,26 +37232,10 @@ "sub" : "http://purl.obolibrary.org/obo/GO_0044207", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", "obj" : "http://purl.obolibrary.org/obo/GO_0005737" - }, { - "sub" : "http://purl.obolibrary.org/obo/GO_0044237", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/GO_0008152" - }, { - "sub" : "http://purl.obolibrary.org/obo/GO_0044237", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/GO_0009987" }, { "sub" : "http://purl.obolibrary.org/obo/GO_0044238", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/GO_0008152" - }, { - "sub" : "http://purl.obolibrary.org/obo/GO_0044249", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/GO_0009058" - }, { - "sub" : "http://purl.obolibrary.org/obo/GO_0044249", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/GO_0044237" }, { "sub" : "http://purl.obolibrary.org/obo/GO_0044419", "pred" : "is_a", @@ -38870,10 +38108,6 @@ "sub" : "http://purl.obolibrary.org/obo/GO_0098644", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/GO_0099080" - }, { - "sub" : "http://purl.obolibrary.org/obo/GO_0098644", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/GO_0098644", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", @@ -39545,7 +38779,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/PR_000000001", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PR_000050567" + "obj" : "http://purl.obolibrary.org/obo/PR_000064867" }, { "sub" : "http://purl.obolibrary.org/obo/PR_000000001", "pred" : "http://purl.obolibrary.org/obo/RO_0002353", @@ -39762,10 +38996,6 @@ "sub" : "http://purl.obolibrary.org/obo/PR_000001969", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PR_000000001" - }, { - "sub" : "http://purl.obolibrary.org/obo/PR_000001971", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PR_000000001" }, { "sub" : "http://purl.obolibrary.org/obo/PR_000002062", "pred" : "is_a", @@ -39895,7 +39125,7 @@ "pred" : "http://purl.obolibrary.org/obo/RO_0002160", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_33208" }, { - "sub" : "http://purl.obolibrary.org/obo/PR_000050567", + "sub" : "http://purl.obolibrary.org/obo/PR_000064867", "pred" : "http://purl.obolibrary.org/obo/BFO_0000051", "obj" : "http://purl.obolibrary.org/obo/PR_000000001" }, { @@ -40173,7 +39403,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000178", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PR_000050567" + "obj" : "http://purl.obolibrary.org/obo/UBERON_0000061" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000178", "pred" : "is_a", @@ -40354,10 +39584,6 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0000481", "pred" : "http://purl.obolibrary.org/obo/BFO_0000051", "obj" : "http://purl.obolibrary.org/obo/UBERON_0000479" - }, { - "sub" : "http://purl.obolibrary.org/obo/UBERON_0000483", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000483", "pred" : "is_a", @@ -40787,10 +40013,6 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0001630", "pred" : "http://purl.obolibrary.org/obo/RO_0002473", "obj" : "http://purl.obolibrary.org/obo/UBERON_0002385" - }, { - "sub" : "http://purl.obolibrary.org/obo/UBERON_0001969", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0001969", "pred" : "is_a", @@ -40807,10 +40029,6 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0001969", "pred" : "http://purl.obolibrary.org/obo/RO_0002221", "obj" : "http://purl.obolibrary.org/obo/CL_0000232" - }, { - "sub" : "http://purl.obolibrary.org/obo/UBERON_0001981", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0001981", "pred" : "is_a", @@ -41342,6 +40560,10 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0002553", "pred" : "http://purl.obolibrary.org/obo/RO_0001015", "obj" : "http://purl.obolibrary.org/obo/UBERON_0000463" + }, { + "sub" : "http://purl.obolibrary.org/obo/UBERON_0003059", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/UBERON_0000061" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0003059", "pred" : "is_a", @@ -41785,10 +41007,6 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0004291", "pred" : "http://purl.obolibrary.org/obo/RO_0002202", "obj" : "http://purl.obolibrary.org/obo/UBERON_0004139" - }, { - "sub" : "http://purl.obolibrary.org/obo/UBERON_0004535", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0004535", "pred" : "is_a", @@ -41805,10 +41023,6 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0004535", "pred" : "http://purl.obolibrary.org/obo/BFO_0000051", "obj" : "http://purl.obolibrary.org/obo/UBERON_0001981" - }, { - "sub" : "http://purl.obolibrary.org/obo/UBERON_0004537", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0004537", "pred" : "is_a", @@ -42135,10 +41349,6 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0005764", "pred" : "http://purl.obolibrary.org/obo/RO_0002007", "obj" : "http://purl.obolibrary.org/obo/UBERON_0000061" - }, { - "sub" : "http://purl.obolibrary.org/obo/UBERON_0005769", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0005769", "pred" : "is_a", @@ -42345,10 +41555,6 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0006914", "pred" : "http://purl.obolibrary.org/obo/BFO_0000051", "obj" : "http://purl.obolibrary.org/obo/CL_0000076" - }, { - "sub" : "http://purl.obolibrary.org/obo/UBERON_0006965", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0006965", "pred" : "is_a", @@ -42662,10 +41868,6 @@ "val" : "CARO" } ] } - }, { - "sub" : "http://purl.obolibrary.org/obo/UBERON_0010210", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0010210", "pred" : "is_a", @@ -43920,10 +43122,6 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002590", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002592" - }, { - "sub" : "http://purl.obolibrary.org/obo/RO_0002592", - "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0000057" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002592", "pred" : "subPropertyOf", @@ -47886,6 +47084,9 @@ "predicateId" : "http://purl.obolibrary.org/obo/RO_0002576", "domainClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000061" ], "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000061" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0015004", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/CL_0000000" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0015006", "domainClassIds" : [ "http://purl.obolibrary.org/obo/PATO_0000001" ], diff --git a/src/ontology/subsets/blood_and_immune_upper_slim.obo b/src/ontology/subsets/blood_and_immune_upper_slim.obo index e723d3ceb..8b1dc648d 100644 --- a/src/ontology/subsets/blood_and_immune_upper_slim.obo +++ b/src/ontology/subsets/blood_and_immune_upper_slim.obo @@ -1,5 +1,5 @@ format-version: 1.2 -data-version: cl/releases/2024-09-26/subsets/blood_and_immune_upper_slim.owl +data-version: cl/releases/2025-01-08/subsets/blood_and_immune_upper_slim.owl subsetdef: abnormal_slim "" subsetdef: added_for_HCA "" subsetdef: attribute_slim "" @@ -44,10 +44,12 @@ subsetdef: http://purl.obolibrary.org/obo/valid_for_go_gp2term "" subsetdef: http://purl.obolibrary.org/obo/valid_for_go_ontology "" subsetdef: http://purl.obolibrary.org/obo/valid_for_gocam "" subsetdef: human_reference_atlas "" +subsetdef: human_subset "" subsetdef: inconsistent_with_fma "" subsetdef: kidney_upper_slim "a subset of general classes related to specific cell types in the kidney" subsetdef: location_grouping "" subsetdef: major_organ "" +subsetdef: mouse_subset "" subsetdef: mpath_slim "" subsetdef: non_informative "" subsetdef: organ_slim "" @@ -96,7 +98,7 @@ idspace: oboInOwl http://www.geneontology.org/formats/oboInOwl# idspace: sssom https://w3id.org/sssom/ idspace: terms http://purl.org/dc/terms/ ontology: cl/subsets/blood_and_immune_upper_slim -property_value: owl:versionInfo "2024-09-26" xsd:string +property_value: owl:versionInfo "2025-01-08" xsd:string [Term] id: CL:0000000 @@ -104,6 +106,8 @@ name: cell def: "A material entity of anatomical origin (part of or deriving from an organism) that has as its parts a maximally connected cell compartment surrounded by a plasma membrane." [CARO:mah] comment: The definition of cell is intended to represent all cells, and thus a cell is defined as a material entity and not an anatomical structure, which implies that it is part of an organism (or the entirety of one). subset: cellxgene_subset +subset: human_subset +subset: mouse_subset subset: ubprop:upper_level xref: CALOHA:TS-2035 xref: FBbt:00007002 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} @@ -125,6 +129,8 @@ relationship: RO:0002162 NCBITaxon:131567 ! in taxon cellular organisms id: CL:0000007 name: early embryonic cell (metazoa) def: "A cell found in the embryo before the formation of all the gem layers is complete." [GOC:tfm] +subset: human_subset +subset: mouse_subset xref: ZFA:0009002 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0002321 ! embryonic cell (metazoa) @@ -136,6 +142,8 @@ comment: This term applies to metazoan. For plant stem cells, consider using PO: subset: cellxgene_subset subset: general_cell_types_upper_slim subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "animal stem cell" EXACT [] xref: CALOHA:TS-2086 xref: FMA:63368 @@ -156,6 +164,8 @@ comment: Markers differ between species, and two sets of markers have been descr subset: blood_and_immune_upper_slim subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "blood forming stem cell" EXACT [] synonym: "colony forming unit hematopoietic" RELATED [] synonym: "hemopoietic stem cell" EXACT [] @@ -206,6 +216,8 @@ name: erythroid progenitor cell def: "A progenitor cell committed to the erythroid lineage." [GOC:add, ISBN:0721601464] subset: blood_and_immune_upper_slim subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "BFU-E" RELATED OMO:0003000 [] synonym: "blast forming unit erythroid" RELATED [] synonym: "burst forming unit erythroid" RELATED [] @@ -223,6 +235,8 @@ id: CL:0000040 name: monoblast def: "A myeloid progenitor cell committed to the monocyte lineage. This cell is CD11b-positive, has basophilic cytoplasm, euchromatin, and the presence of a nucleolus." [GOC:add, http://en.wikipedia.org/wiki/Monoblast, http://www.copewithcytokines.de, PMID:1104740] comment: Morphology: mononuclear cell, diameter 12-20 _M, non-granular, N/C ratio 3/1 - 4/1; markers: CD11b (shared with many other myeloid cells); location: Adult: bone marrow; fetal: liver, Yolk Sac; role or process: hematopoiesis, monocyte development; lineage: hematopoietic, myeloid. +subset: human_subset +subset: mouse_subset synonym: "CFU-M" RELATED OMO:0003000 [] synonym: "colony forming unit macrophage" RELATED [] synonym: "colony forming unit monocyte" RELATED [] @@ -232,7 +246,6 @@ xref: FMA:83553 xref: ZFA:0009017 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000763 ! myeloid cell is_a: CL:0002194 {is_inferred="true"} ! monopoietic cell -is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0002194 ! monopoietic cell intersection_of: capable_of GO:0030224 ! monocyte differentiation intersection_of: has_part CL:0017503 ! basophilic cytoplasm @@ -249,6 +262,8 @@ relationship: RO:0002202 CL:0002009 ! develops from macrophage dendritic cell pr id: CL:0000048 name: multi fate stem cell def: "A stem cell that can give rise to multiple lineages of cells." [GOC:add] +subset: human_subset +subset: mouse_subset synonym: "multi-fate stem cell" EXACT [] synonym: "multifate stem cell" EXACT [] synonym: "multipotent cell" EXACT [] @@ -268,6 +283,8 @@ def: "A progenitor cell committed to myeloid lineage, including the megakaryocyt comment: This cell type is intended to be compatible with any vertebrate common myeloid progenitor. For mammalian CMP known to be CD34-positive, please use the term 'common myeloid progenitor, CD34-positive' (CL_0001059). subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "CFU-GEMM" RELATED OMO:0003000 [ISBN:0878932437] synonym: "CFU-S" RELATED OMO:0003000 [ISBN:0878932437] synonym: "CMP" RELATED OMO:0003000 [ISBN:0878932437] @@ -291,6 +308,8 @@ def: "A progenitor cell committed to the megakaryocyte and erythroid lineages." comment: MEPs are reportedly CD19-negative, CD34-negative, CD45RA-negative, CD110-positive, CD117-positive, and SCA1-negative and reportedly express the transcription factors GATA-1 and NF-E2. subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "CFU-EM" EXACT [] synonym: "CFU-MegE" EXACT [] synonym: "colony forming unit erythroid megakaryocyte" EXACT [] @@ -318,6 +337,8 @@ def: "A oligopotent progenitor cell committed to the lymphoid lineage." [GOC:add comment: CLP are CD7-positive, CD10-positive, CD19-negative, CD34-positive, CD45RA-positive, CD79a-negative, CD127-positive, AA4.1-positive, RAG-negative, Sca-1-low, sIgM-negative, sIgD-negative, TdT-negative, Vpre-B-negative, and pre-BCR-negative. Expression of transcription factors include E2A-positive, EBF-positive, Ikaros-negative, PU.1-negative, and Pax5-negative. subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "CLP" RELATED OMO:0003000 [] synonym: "committed lymphopoietic stem cell" RELATED [] synonym: "common lymphocyte precursor" EXACT [] @@ -339,6 +360,8 @@ property_value: RO:0002175 NCBITaxon:9606 id: CL:0000052 name: totipotent stem cell def: "A stem cell from which all cells of the body can form." [GOC:add, GOC:tfm] +subset: human_subset +subset: mouse_subset synonym: "totipotential stem cell" EXACT [] xref: FMA:84790 xref: MESH:D039901 @@ -351,6 +374,8 @@ name: non-terminally differentiated cell def: "A precursor cell with a limited number of potential fates." [SANBI:mhl] comment: define using PATO mulit-potent or oligopotent? subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "blast cell" EXACT [] xref: BTO:0000125 xref: FMA:84782 @@ -360,6 +385,9 @@ is_a: CL:0011115 ! precursor cell id: CL:0000056 name: myoblast def: "A cell that is commited to differentiating into a muscle cell. Embryonic myoblasts develop from the mesoderm. They undergo proliferation, migrate to their various sites, and then differentiate into the appropriate form of myocytes. Myoblasts also occur as transient populations of cells in muscles undergoing repair." [GOC:tfm, MESH:D032446, PMID:21849021] +subset: cellxgene_subset +subset: human_subset +subset: mouse_subset xref: BTO:0000222 xref: CALOHA:TS-0650 xref: FBbt:00005083 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} @@ -376,14 +404,15 @@ comment: These cells may be vimentin-positive, fibronectin-positive, fsp1-positi subset: cellxgene_subset subset: general_cell_types_upper_slim subset: human_reference_atlas +subset: human_subset +subset: mouse_subset xref: BTO:0000452 xref: CALOHA:TS-0362 xref: FMA:63877 xref: NCIT:C12482 xref: VHOG:0001482 xref: ZFA:0009026 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} -is_a: CL:0002320 ! connective tissue cell -relationship: RO:0002202 CL:0000134 ! develops from mesenchymal stem cell +is_a: CL:0000499 ! stromal cell property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -393,6 +422,8 @@ def: "A cell that is usually found in a two-dimensional sheet with a free surfac subset: cellxgene_subset subset: general_cell_types_upper_slim subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "epitheliocyte" EXACT [] xref: BTO:0000414 xref: CALOHA:TS-2026 @@ -413,6 +444,8 @@ name: blood vessel endothelial cell def: "An endothelial cell that lines the vasculature." [GOC:tfm] subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset xref: ZFA:0009036 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0002139 ! endothelial cell of vascular tree intersection_of: CL:0000115 ! endothelial cell @@ -425,6 +458,8 @@ id: CL:0000076 name: squamous epithelial cell def: "Any epithelial cell that is part of some squamous epithelium." [FBC:Autogenerated] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset xref: CALOHA:TS-1249 xref: ZFA:0009039 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000066 ! epithelial cell @@ -436,6 +471,8 @@ relationship: part_of UBERON:0006914 ! squamous epithelium id: CL:0000080 name: circulating cell def: "A cell which moves among different tissues of the body, via blood, lymph, or other medium." [GOC:add] +subset: human_subset +subset: mouse_subset xref: ZFA:0009043 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000255 ! eukaryotic cell intersection_of: CL:0000000 ! cell @@ -448,6 +485,8 @@ name: blood cell def: "A cell found predominately in the blood." [GOC:add, GOC:tfm] subset: cellxgene_subset subset: general_cell_types_upper_slim +subset: human_subset +subset: mouse_subset xref: FMA:62844 xref: MESH:D001773 xref: ZFA:0009044 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} @@ -463,6 +502,8 @@ def: "A type of lymphocyte whose defining characteristic is the expression of a subset: cellxgene_subset subset: general_cell_types_upper_slim subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "immature T cell" RELATED [] synonym: "mature T cell" RELATED [] synonym: "T lymphocyte" EXACT [] @@ -488,16 +529,18 @@ name: osteoclast def: "A specialized phagocytic cell associated with the absorption and removal of the mineralized matrix of bone tissue, which typically differentiates from monocytes. This cell has the following markers: tartrate-resistant acid phosphatase type 5-positive, PU.1-positive, c-fos-positive, nuclear factor NF-kappa-B p100 subunit-positive, tumor necrosis factor receptor superfamily member 11A-positive and macrophage colony-stimulating factor 1 receptor-positive." [GO_REF:0000031, GOC:add, GOC:tfm, ISBN:0781735149, PMID:10428500, PMID:15055519, PMID:17380158] comment: Morphology: Highly vesicular; markers: Surface: RANK, cFMS (MCSF receptor); Secreted: cathepsin K and TRAP (tartate resistant acid phosphatase); transcription factors: PU.1, cFOS, MITF, NFkB (p52); role or process: tissue remodelling: bone resorption; lineage: hematopoietic, myeloid. subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "chondroclast" RELATED [] xref: BTO:0000968 xref: CALOHA:TS-0721 xref: FMA:66781 +xref: https://cellxgene.cziscience.com/cellguide/CL_0000092 xref: MESH:D010010 xref: ZFA:0009047 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000518 ! phagocyte (sensu Vertebrata) is_a: CL:0000766 {is_inferred="true"} ! myeloid leukocyte is_a: CL:0001035 {is_inferred="true"} ! bone cell -is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000766 ! myeloid leukocyte intersection_of: capable_of GO:0045453 ! bone resorption intersection_of: has_part PR:000001850 ! cathepsin K @@ -517,6 +560,7 @@ relationship: has_part PR:000011178 ! nuclear factor NF-kappa-B p100 subunit relationship: RO:0002104 PR:000001954 ! has plasma membrane part tumor necrosis factor receptor superfamily member 11A relationship: RO:0002104 PR:000002062 ! has plasma membrane part macrophage colony-stimulating factor 1 receptor relationship: RO:0002202 CL:0000576 ! develops from monocyte +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nOsteoclasts, derived from the monocyte/macrophage lineage, play a crucial role in bone remodeling through bone resorption. They are distinguished from other cells by their large size and their unique ability to secrete enzymes and acids that dissolve the calcium phosphate in bone. The formation of osteoclasts is influenced by two primary factors: macrophage colony-stimulating factor (M-CSF) and the ligand-activated receptor (RANKL) of nuclear factor kappa B (NF-κB).\nOsteoclasts also collaborate with osteoblasts, responsible for new bone formation, to maintain bone health and adapt bone structure. Their coordinated actions allow continuous remodeling while preserving overall bone strength and integrity. Imbalances in osteoclast activity can lead to pathological conditions. For example, excessive activity may contribute to diseases like osteoporosis, periprosthetic osteolysis, bone tumors, and Paget's disease. Other the other hand, osteoclast deficiency ca result in conditions like osteopetrosis." xsd:string {xref="DOI:10.3389/fmed.2017.00234", xref="DOI:10.37175/stemedicine.v1i4.57", xref="https://www.sciencedirect.com/topics/medicine-and-dentistry/osteoclast"} [Term] id: CL:0000094 @@ -524,6 +568,8 @@ name: granulocyte def: "A leukocyte with abundant granules in the cytoplasm." [GOC:amm, GOC:tfm, http://en.wikipedia.org/wiki/Granulocyte, MESH:D006098] subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "granular leucocyte" EXACT [] synonym: "granular leukocyte" EXACT [] synonym: "polymorphonuclear leukocyte" EXACT [] @@ -534,7 +580,6 @@ xref: FMA:62854 xref: ZFA:0009048 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000081 ! blood cell is_a: CL:0000766 {is_inferred="true"} ! myeloid leukocyte -is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000766 ! myeloid leukocyte intersection_of: capable_of GO:0008015 ! blood circulation intersection_of: CL:4030046 PR:000001002 ! lacks_plasma_membrane_part CD19 molecule @@ -563,6 +608,8 @@ comment: Mast cells are generally integrin beta-7-negative and positive for TLR2 subset: blood_and_immune_upper_slim subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "histaminocyte" EXACT [] synonym: "labrocyte" EXACT [ISBN:0721601464] synonym: "mastocyte" EXACT [ISBN:0721601464] @@ -572,7 +619,6 @@ xref: CALOHA:TS-0603 xref: FMA:66784 is_a: CL:0000766 {is_inferred="true"} ! myeloid leukocyte is_a: CL:0002274 ! histamine secreting cell -is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000766 ! myeloid leukocyte intersection_of: capable_of GO:0002349 ! histamine production involved in inflammatory response intersection_of: capable_of GO:0002539 ! prostaglandin production involved in inflammatory response @@ -607,6 +653,8 @@ name: mononuclear phagocyte def: "A vertebrate phagocyte with a single nucleus." [GOC:add, GOC:tfm, ISBN:0781735149] subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset xref: BTO:0001433 xref: https://cellxgene.cziscience.com/cellguide/CL_0000113 xref: ZFA:0009064 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} @@ -615,7 +663,7 @@ is_a: CL:0000842 ! mononuclear cell intersection_of: CL:0000518 ! phagocyte (sensu Vertebrata) intersection_of: bearer_of PATO:0001407 ! mononucleate property_value: RO:0002175 NCBITaxon:9606 -property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional.\n\nMononuclear phagocytes are immune cells that form a critical part of the body's innate immune system, the body's first line of defense against infections. Mononuclear phagocytes are characterized by the presence of a single, large nucleus. The ‘Mononuclear Phagocyte System’ nomenclature was introduced to distinguish mononuclear monocytes and macrophages from other cells with multiple nuclei. However, the cells within the mononuclear phagocyte system represent a highly heterogeneous group, all of which are able to perform highly efficient phagocytosis - engulfing and digesting microbes and cellular debris to fight infections and to maintain normal tissue homeostasis. \nIn addition to phagocytosis, mononuclear phagocytes also secrete chemical compounds to recruit other immune cells to a site of infection. These cells produce different types of signaling molecules, including cytokines, chemokines, and reactive oxygen species, triggering a cascade of responses to ensure rapid and efficient containment and neutralization of invading pathogens. These cells are also involved in antigen presentation, a process essential for stimulating an adaptive immune response. They can process and present antigens to T cells, thereby linking the innate and adaptive immune responses.\nMononuclear phagocytes play key roles in tissue repair and remodeling. After infection or injury, these cells help in the clearance of dead cells and debris, a crucial step in the initiation of tissue remodeling and the resolution of inflammation. Overall, mononuclear phagocytes are versatile cells that have tailored their functions to meet the unique challenges of different tissues within the body. They are pivotal in homeostasis, immunity, and inflammation, making them important aspects in a range of human diseases including infection, autoimmunity, and cancer." xsd:string {xref="DOI:10.1016/j.coi.2005.11.008", xref="DOI:10.1038/nri3087", xref="DOI:10.3389/fimmu.2019.01893"} +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nMononuclear phagocytes are immune cells that form a critical part of the body's innate immune system, the body's first line of defense against infections. Mononuclear phagocytes are characterized by the presence of a single, large nucleus. The ‘Mononuclear Phagocyte System’ nomenclature was introduced to distinguish mononuclear monocytes and macrophages from other cells with multiple nuclei. However, the cells within the mononuclear phagocyte system represent a highly heterogeneous group, all of which are able to perform highly efficient phagocytosis - engulfing and digesting microbes and cellular debris to fight infections and to maintain normal tissue homeostasis. \nIn addition to phagocytosis, mononuclear phagocytes also secrete chemical compounds to recruit other immune cells to a site of infection. These cells produce different types of signaling molecules, including cytokines, chemokines, and reactive oxygen species, triggering a cascade of responses to ensure rapid and efficient containment and neutralization of invading pathogens. These cells are also involved in antigen presentation, a process essential for stimulating an adaptive immune response. They can process and present antigens to T cells, thereby linking the innate and adaptive immune responses.\nMononuclear phagocytes play key roles in tissue repair and remodeling. After infection or injury, these cells help in the clearance of dead cells and debris, a crucial step in the initiation of tissue remodeling and the resolution of inflammation. Overall, mononuclear phagocytes are versatile cells that have tailored their functions to meet the unique challenges of different tissues within the body. They are pivotal in homeostasis, immunity, and inflammation, making them important aspects in a range of human diseases including infection, autoimmunity, and cancer." xsd:string {xref="DOI:10.1016/j.coi.2005.11.008", xref="DOI:10.1038/nri3087", xref="DOI:10.3389/fimmu.2019.01893"} [Term] id: CL:0000115 @@ -624,6 +672,8 @@ def: "An endothelial cell comprises the outermost layer or lining of anatomical comment: From FMA: 9.07.2001: Endothelial cell has always been classified as a kind of epithelial cell, specifically a squamous cell but that is not true. First, endothelial cell can either be squamous or cuboidal (e.g. high-endothelial cell) and secondly, it has different embryological derivation (mesodermal) than a true epithelial cell (ectodermal and endodermal). The basis for present classification is the fact that it comprises the outermost layer or lining of anatomical structures (location-based) but a better structural basis for the differentia is the cytoskeleton of the cell. Endothelial cell has vimentin filaments while an epithelial cell has keratin filaments. [Onard]. subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "endotheliocyte" EXACT [] xref: BTO:0001176 xref: CALOHA:TS-0278 @@ -638,6 +688,8 @@ property_value: RO:0002175 NCBITaxon:9606 id: CL:0000133 name: neurectodermal cell def: "Ectoderm destined to be nervous tissue." [GOC:tfm, ISBN:068340007X] +subset: human_subset +subset: mouse_subset synonym: "neurectoderm cell" EXACT [] xref: ZFA:0009080 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000221 ! ectodermal cell @@ -648,6 +700,8 @@ name: mesenchymal stem cell def: "A connective tissue cell that normally gives rise to other cells that are organized as three-dimensional masses. In humans, this cell type is CD73-positive, CD90-positive, CD105-positive, CD45-negative, CD34-negative, and MHCII-negative. They may further differentiate into osteoblasts, adipocytes, myocytes, neurons, or chondroblasts in vitro. Originally described as residing in the bone marrow, this cell type is now known to reside in many, if not all, adult organs." [FB:ma, GOC:dsd, http://en.wikipedia.org/wiki/Mesenchymal_stem_cell, http://www.copewithcytokines.de/cope.cgi?key=mesenchymal%20stem%20cells, PMCID:PMC2613570, PMID:10102814, PMID:16923606, PMID:17986482, PMID:19960544] comment: Many but not all mesenchymal cells derive from the mesoderm. MSCs are reportedly CD3-negative, CD4-negative, CD5-negative, CD8-negative, CD11a-negative, CD11b-negative, CD14-negative, CD19-negative, CD29-positive, CD31-negative, CD34-negative, CD38-negative, CD40-negative, CD44-positive, CD45-negative, CD49-positive, CD54-positive, CD66b-negative, CD79a-negative, CD80-negative, CD102-positive, CD106-positive, CD117-positive, CD121a-positive, CD121b-positive, CD123-positive, CD124-positive, CD133-negative, CD146-positive, CD166-positive, CD271-positive, B220-negative, Gr1-negative, MHCI-positive, MHCII-negative, SSEA4-negative, sca1-positive, Ter119-negative, and glycophorin A-negative. Cultured MSCs are capable of producing stem cell factor, IL7, IL8, IL11, TGF-beta, cofilin, galectin-1, laminin-receptor 1, cyclophilin A, and MMP-2. subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "BMSC" RELATED OMO:0003000 [] synonym: "bone marrow stromal cells" NARROW [] synonym: "CFU-F" RELATED OMO:0003000 [] @@ -675,6 +729,8 @@ def: "A cell capable of processing and presenting lipid and protein antigens to comment: Note change of name; nearly all somatic cells can present antigens to T cells via MHC Class I complexes leading to effector responses, but professional antigen presenting cells constitutively express MHC Class II as well as costimulatory molecules, and thus can initiate immune responses via T cells. subset: blood_and_immune_upper_slim subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "APC" RELATED OMO:0003000 [] xref: ZFA:0009088 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000738 ! leukocyte @@ -687,6 +743,8 @@ id: CL:0000151 name: secretory cell def: "A cell that specializes in controlled release of one or more substances." [GOC:tfm, ISBN:0721662544] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset xref: BTO:0003659 xref: FMA:86916 is_a: CL:0000000 ! cell @@ -699,6 +757,8 @@ id: CL:0000183 name: contractile cell def: "A cell whose primary function is to shorten." [FB:ma] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset is_a: CL:0000000 ! cell [Term] @@ -706,6 +766,8 @@ id: CL:0000187 name: muscle cell def: "A mature contractile cell, commonly known as a myocyte. This cell has as part of its cytoplasm myofibrils organized in various patterns." [MESH:D032342] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "muscle fiber" EXACT [] synonym: "myocyte" EXACT [] xref: BTO:0000888 @@ -725,6 +787,8 @@ property_value: foaf:depiction "https://www.swissbiopics.org/api/image/Muscle_ce id: CL:0000211 name: electrically active cell def: "A cell whose function is determined by the generation or the reception of an electric signal." [FB:ma] +subset: human_subset +subset: mouse_subset xref: ZFA:0009128 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000000 ! cell @@ -732,6 +796,8 @@ is_a: CL:0000000 ! cell id: CL:0000213 name: lining cell def: "A cell within an epithelial cell sheet whose main function is to act as an internal or external covering for a tissue or an organism." [JB:jb] +subset: human_subset +subset: mouse_subset synonym: "boundary cell" EXACT [] xref: ZFA:0009130 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000215 ! barrier cell @@ -740,6 +806,8 @@ is_a: CL:0000215 ! barrier cell id: CL:0000215 name: barrier cell def: "A cell whose primary function is to prevent the transport of stuff across compartments." [JB:jb] +subset: human_subset +subset: mouse_subset xref: ZFA:0009132 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000000 ! cell @@ -747,6 +815,8 @@ is_a: CL:0000000 ! cell id: CL:0000219 name: motile cell def: "A cell that moves by its own activities." [FB:ma] +subset: human_subset +subset: mouse_subset xref: ZFA:0009136 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000000 ! cell intersection_of: CL:0000000 ! cell @@ -757,6 +827,9 @@ relationship: capable_of GO:0048870 ! cell motility id: CL:0000221 name: ectodermal cell def: "A cell of the outer of the three germ layers of the embryo." [MESH:D004475] +subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "ectoderm cell" EXACT [] xref: FMA:72549 xref: ZFA:0009137 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} @@ -769,18 +842,24 @@ id: CL:0000222 name: mesodermal cell def: "A cell of the middle germ layer of the embryo." [MESH:D008648] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "mesoblast" EXACT [] synonym: "mesoderm cell" EXACT [] xref: FMA:72554 +xref: https://cellxgene.cziscience.com/cellguide/CL_0000222 xref: ZFA:0009138 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000255 ! eukaryotic cell is_a: CL:0002321 ! embryonic cell (metazoa) relationship: part_of UBERON:0000926 ! mesoderm +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nMesodermal cells are pluripotent and the most abundant in the human body. They contribute to the development of several structures such as the skeletal muscles, bones, heart and blood vessels, kidneys, gonads, connective tissues, and certain layers of the skin. Hence, the mesoderm is often regarded as an active and diverse layer due to its role in forming many bodily structures. \nIn embryonic development, these cells are instrumental, contributing to the body's structures through a carefully coordinated sequence of morphogenetic movements. This process forms the complex multicellular architecture of tissues and organs from a simple ball of cells. Without the function of mesodermal cells, the body's integral structures and systems would cease to form correctly, leading to developmental disorders such as axial mesodermal dysplasia complex" xsd:string {xref="DOI:10.1016/j.ceb.2019.07.012", xref="DOI:10.5535/arm.2016.40.1.162", xref="https://www.sciencedirect.com/topics/biochemistry-genetics-and-molecular-biology/mesoderm"} [Term] id: CL:0000223 name: endodermal cell def: "A cell of the inner of the three germ layers of the embryo." [MESH:D004707] +subset: human_subset +subset: mouse_subset synonym: "endoderm cell" EXACT [] xref: FMA:72555 xref: ZFA:0009139 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} @@ -792,6 +871,8 @@ relationship: part_of UBERON:0000925 ! endoderm id: CL:0000225 name: anucleate cell def: "A cell that lacks a nucleus." [FB:ma] +subset: human_subset +subset: mouse_subset synonym: "non-nucleated cell" EXACT [] xref: FMA:68647 is_a: CL:0000000 ! cell @@ -804,6 +885,8 @@ relationship: bearer_of PATO:0001405 ! anucleate id: CL:0000226 name: single nucleate cell def: "A cell with a single nucleus." [FB:ma, GOC:tfm] +subset: human_subset +subset: mouse_subset is_a: CL:0000255 ! eukaryotic cell is_a: CL:0002242 ! nucleate cell intersection_of: CL:0000000 ! cell @@ -814,6 +897,8 @@ relationship: bearer_of PATO:0001407 ! mononucleate id: CL:0000228 name: multinucleate cell def: "A cell with more than one nucleus." [FB:ma, Wikipedia:Multinucleate] +subset: human_subset +subset: mouse_subset synonym: "multinucleated cells" EXACT [Wikipedia:Multinucleate] synonym: "polynuclear cells" EXACT [Wikipedia:Multinucleate] is_a: CL:0000255 ! eukaryotic cell @@ -829,6 +914,8 @@ def: "A red blood cell. In mammals, mature erythrocytes are biconcave disks cont subset: blood_and_immune_upper_slim subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "RBC" EXACT [] synonym: "red blood cell" EXACT [] xref: BTO:0000424 @@ -857,6 +944,8 @@ comment: Platelets are reportedly CCR1-positive, CCR2-negative, CCR3-positive, C subset: blood_and_immune_upper_slim subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "anucleate thrombocyte" EXACT [] synonym: "blood platelet" EXACT [] synonym: "enucleate thrombocyte" EXACT [] @@ -876,7 +965,8 @@ property_value: RO:0002175 NCBITaxon:9606 id: CL:0000234 name: phagocyte def: "Any cell capable of ingesting particulate matter via phagocytosis." [GOC:add, ISBN:0721601464] -subset: cellxgene_subset +subset: human_subset +subset: mouse_subset xref: BTO:0001044 xref: FMA:83806 xref: MESH:D010586 @@ -897,6 +987,8 @@ subset: blood_and_immune_upper_slim subset: cellxgene_subset subset: general_cell_types_upper_slim subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "histiocyte" EXACT [] xref: BTO:0000801 xref: CALOHA:TS-0587 @@ -923,6 +1015,8 @@ subset: blood_and_immune_upper_slim subset: cellxgene_subset subset: general_cell_types_upper_slim subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "B lymphocyte" EXACT [] synonym: "B-cell" EXACT [] synonym: "B-lymphocyte" EXACT [] @@ -942,7 +1036,8 @@ property_value: RO:0002175 NCBITaxon:9606 id: CL:0000255 name: eukaryotic cell def: "Any cell that in taxon some Eukaryota." [FBC:Autogenerated] -subset: cellxgene_subset +subset: human_subset +subset: mouse_subset xref: MESH:D005057 is_a: CL:0000000 ! cell intersection_of: CL:0000000 ! cell @@ -953,6 +1048,8 @@ relationship: RO:0002162 NCBITaxon:2759 ! in taxon Eukaryota id: CL:0000325 name: stuff accumulating cell def: "A cell that is specialised to accumulate a particular substance(s)." [FB:ma] +subset: human_subset +subset: mouse_subset subset: ubprop:upper_level is_a: CL:0000000 ! cell @@ -960,6 +1057,8 @@ is_a: CL:0000000 ! cell id: CL:0000329 name: oxygen accumulating cell def: "Any cell that is capable of some oxygen transport." [FBC:Autogenerated] +subset: human_subset +subset: mouse_subset xref: ZFA:0009164 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000000 ! cell intersection_of: CL:0000000 ! cell @@ -970,6 +1069,8 @@ relationship: capable_of GO:0015671 ! oxygen transport id: CL:0000333 name: migratory neural crest cell def: "A cell derived from the specialized ectoderm flanking each side of the embryonic neural plate, which after the closure of the neural tube, forms masses of cells that migrate out from the dorsal aspect of the neural tube to spread throughout the body." [doi:10.1016/j.stem.2015.02.017] +subset: human_subset +subset: mouse_subset xref: FMA:86667 xref: ZFA:0007086 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000219 ! motile cell @@ -981,6 +1082,8 @@ relationship: RO:0002202 CL:0007004 ! develops from premigratory neural crest ce id: CL:0000335 name: mesenchyme condensation cell def: "A mesenchymal cell in embryonic development found in a contracting mass and that gives rise to osteoprogenitors." [GOC:tfm, PMID:5025404] +subset: human_subset +subset: mouse_subset xref: ZFA:0009166 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0008019 ! mesenchymal cell @@ -988,12 +1091,16 @@ is_a: CL:0008019 ! mesenchymal cell id: CL:0000352 name: epiblast cell def: "A cell of the outer layer of a blastula that gives rise to the ectoderm after gastrulation." [GOC:tfm, ISBN:0618947256] +subset: human_subset +subset: mouse_subset is_a: CL:0000052 ! totipotent stem cell [Term] id: CL:0000365 name: animal zygote def: "Diploid cell produced by the fusion of sperm cell nucleus and egg cell." [ISBN:0471245208] +subset: human_subset +subset: mouse_subset synonym: "zygote" BROAD [] xref: BTO:0000854 xref: EHDAA2:0004546 @@ -1009,6 +1116,8 @@ relationship: RO:0002162 NCBITaxon:33208 ! in taxon Metazoa id: CL:0000393 name: electrically responsive cell def: "A cell whose function is determined by its response to an electric signal." [FB:ma] +subset: human_subset +subset: mouse_subset xref: ZFA:0009190 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000211 ! electrically active cell @@ -1016,6 +1125,8 @@ is_a: CL:0000211 ! electrically active cell id: CL:0000404 name: electrically signaling cell def: "A cell that initiates an electrical signal and passes that signal to another cell." [FB:ma] +subset: human_subset +subset: mouse_subset xref: ZFA:0009193 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000211 ! electrically active cell @@ -1026,6 +1137,8 @@ def: "A cell of hematopoietic origin, typically resident in particular tissues, subset: cellxgene_subset subset: general_cell_types_upper_slim subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "interdigitating cell" RELATED [] synonym: "veiled cell" RELATED [] xref: BTO:0002042 @@ -1035,7 +1148,6 @@ xref: MESH:D003713 xref: ZFA:0009209 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000113 ! mononuclear phagocyte is_a: CL:0000145 ! professional antigen presenting cell -is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000738 ! leukocyte intersection_of: bearer_of PATO:0001407 ! mononucleate intersection_of: capable_of GO:0001816 ! cytokine production @@ -1062,6 +1174,8 @@ property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000457 name: biogenic amine secreting cell +subset: human_subset +subset: mouse_subset xref: ZFA:0009212 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000151 ! secretory cell @@ -1069,6 +1183,8 @@ is_a: CL:0000151 ! secretory cell id: CL:0000458 name: serotonin secreting cell def: "A cell type that secretes 5-Hydroxytryptamine (serotonin)." [GOC:tfm, PMID:19630576] +subset: human_subset +subset: mouse_subset synonym: "5-HT secreting cell" EXACT [] synonym: "5-Hydroxytryptamine secreting cell" EXACT [] xref: ZFA:0009213 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} @@ -1081,12 +1197,32 @@ relationship: capable_of GO:0001820 ! serotonin secretion id: CL:0000473 name: defensive cell def: "A cell whose primary function is to protect the organism." [JB:jb] +subset: human_subset +subset: mouse_subset is_a: CL:0000000 ! cell +[Term] +id: CL:0000499 +name: stromal cell +def: "A connective tissue cell of an organ found in the loose connective tissue." [GOC:tfm, MESH:D017154] +subset: cellxgene_subset +subset: general_cell_types_upper_slim +subset: human_reference_atlas +subset: human_subset +subset: mouse_subset +xref: BTO:0002064 +xref: FMA:83624 +xref: ZFA:0009226 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +is_a: CL:0002320 ! connective tissue cell +relationship: RO:0002202 CL:0000134 ! develops from mesenchymal stem cell +property_value: RO:0002175 NCBITaxon:9606 + [Term] id: CL:0000518 name: phagocyte (sensu Vertebrata) def: "A phagocyte in vertebrates that is able to phagocytosis." [GOC:tfm] +subset: human_subset +subset: mouse_subset is_a: CL:0000234 ! phagocyte is_a: CL:0000255 ! eukaryotic cell relationship: RO:0002162 NCBITaxon:7742 ! in taxon Vertebrata @@ -1099,6 +1235,8 @@ comment: These cells are also reportedly CD4-negative and CD200-positive. They a subset: cellxgene_subset subset: general_cell_types_upper_slim subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "nerve cell" EXACT [] xref: BTO:0000938 xref: CALOHA:TS-0683 @@ -1121,6 +1259,8 @@ def: "A lymphocyte is a leukocyte commonly found in the blood and lymph that has comment: Editors note: consider adding taxon constraint to vertebrata (PMID:18025161) subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset xref: BTO:0000775 xref: CALOHA:TS-0583 xref: FMA:62863 @@ -1146,12 +1286,13 @@ name: proerythroblast def: "An immature, nucleated erythrocyte occupying the stage of erythropoeisis that follows formation of erythroid progenitor cells. This cell is CD71-positive, has both a nucleus and a nucleolus, and lacks hematopoeitic lineage markers." [ISBN:0721601464, PMID:1638021] subset: blood_and_immune_upper_slim subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "pronormoblast" RELATED [] synonym: "rubriblast" EXACT [ISBN:0721601464] xref: FMA:83518 is_a: CL:0000764 {is_inferred="true"} ! erythroid lineage cell is_a: CL:0002242 ! nucleate cell -is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000764 ! erythroid lineage cell intersection_of: bearer_of PATO:0002505 ! nucleated intersection_of: bearer_of PATO:0040072 ! high nuclear/cytoplasmic ratio @@ -1190,6 +1331,8 @@ relationship: RO:0002202 CL:0000038 ! develops from erythroid progenitor cell id: CL:0000549 name: basophilic erythroblast def: "A nucleated immature erythrocyte, having cytoplasm generally similar to that of the earlier proerythroblast but sometimes even more basophilic, and usually regular in outline. The nucleus is still relatively large, but the chromatin strands are thicker and more deeply staining, giving a coarser appearance; the nucleoli have disappeared. This cell is CD71-positive and lacks hematopoeitic lineage markers." [GOC:tfm, ISBN:0721601464] +subset: human_subset +subset: mouse_subset synonym: "basophilic normoblast" EXACT [ISBN:0721601464] synonym: "early erythroblast" EXACT [ISBN:0721601464] synonym: "early normoblast" EXACT [ISBN:0721601464] @@ -1197,7 +1340,6 @@ synonym: "prorubricyte" EXACT [ISBN:0721601464] xref: FMA:83505 xref: ZFA:0005236 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000765 {is_inferred="true"} ! erythroblast -is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000765 ! erythroblast intersection_of: has_part CL:0017503 ! basophilic cytoplasm intersection_of: has_part GO:0000792 ! heterochromatin @@ -1210,6 +1352,8 @@ relationship: RO:0002104 PR:000001945 ! has plasma membrane part transferrin rec id: CL:0000550 name: polychromatophilic erythroblast def: "A nucleated, immature erythrocyte in which the nucleus occupies a relatively smaller part of the cell than in its precursor, the basophilic erythroblast. The cytoplasm is beginning to acquire hemoglobin and thus is no longer a purely basophilic, but takes on acidophilic aspects, which becomes progressively more marked as the cell matures. The chromatin of the nucleus is arranged in coarse, deeply staining clumps. This cell is CD71-positive and lacks hematopoeitic lineage markers." [ISBN:0721601464] +subset: human_subset +subset: mouse_subset synonym: "intermediate erythroblast" EXACT [ISBN:0721601464] synonym: "intermediate normoblast" EXACT [ISBN:0721601464] synonym: "polychromatic erythroblast" EXACT [ISBN:0721601464] @@ -1219,7 +1363,6 @@ synonym: "rubricyte" EXACT [ISBN:0721601464] xref: FMA:83506 xref: ZFA:0005241 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000765 {is_inferred="true"} ! erythroblast -is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000765 ! erythroblast intersection_of: has_part CL:0017504 ! polychromatophilic cytoplasm intersection_of: has_part GO:0000792 ! heterochromatin @@ -1233,6 +1376,8 @@ relationship: RO:0002202 CL:0000549 ! develops from basophilic erythroblast id: CL:0000552 name: orthochromatic erythroblast def: "The final stage of the nucleated, immature erythrocyte, before nuclear loss. Typically the cytoplasm is described as acidophilic, but it still shows a faint polychromatic tint. The nucleus is small and initially may still have coarse, clumped chromatin, as in its precursor, the polychromatophilic erythroblast, but ultimately it becomes pyknotic, and appears as a deeply staining, blue-black, homogeneous structureless mass. The nucleus is often eccentric and sometimes lobulated." [ISBN:0721601464] +subset: human_subset +subset: mouse_subset synonym: "acidophilic erythroblast" EXACT [ISBN:0721601464] synonym: "eosinophilic erythroblast" EXACT [ISBN:0721601464] synonym: "late erythoblast" EXACT [] @@ -1254,6 +1399,8 @@ def: "The earliest cytologically identifiable precursor in the thrombocytic seri comment: Lineage negative is described here as CD2-negative, CD3-negative, CD4-negative, CD5-negative, CD8a-negative, CD14-negative, CD19-negative, CD20-negative, CD56-negative, Ly6g-negative, and Ter119-negative. subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "CFU-Meg" EXACT [PMID:11722431, PMID:12482498] synonym: "colony-forming unit-megakaryocyte" EXACT [] synonym: "Meg-CFC" EXACT [PMCID:PMC1794060] @@ -1310,6 +1457,8 @@ comment: Megakaryocytes are reportedly CD181-positive and CD182-positive. subset: blood_and_immune_upper_slim subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "megacaryocyte" EXACT [] synonym: "megalocaryocyte" EXACT [] synonym: "megalokaryocyte" EXACT [] @@ -1329,6 +1478,8 @@ def: "A hematopoietic progenitor cell that is committed to the granulocyte and m comment: Originally described in the dendritic cell ontology (DC_CL:0000042)(PMID:19243617). GMPs are reportedly CD16-positive, CD32-positive, CD34-positive, CD38-positive, CD45RA-positive, CD110-negative, CD117-positive, CD123-positive, and SCA1-negative. subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "CFU-C , Colony forming unit in culture" BROAD [http://www.copewithcytokines.de] synonym: "CFU-GM" RELATED OMO:0003000 [ISBN:0721601464, PMCID:PMC2213186, PMCID:PMC548021] synonym: "colony forming unit granulocyte macrophage" EXACT [ISBN:0721601464, PMCID:PMC2213186, PMCID:PMC548021] @@ -1336,12 +1487,11 @@ synonym: "GMP" RELATED OMO:0003000 [ISBN:0721601464, PMCID:PMC2213186, PMCID:PMC synonym: "granulocyte-macrophage progenitor" EXACT [ISBN:0721601464, PMCID:PMC2213186, PMCID:PMC548021] synonym: "granulocyte/monocyte precursor" EXACT [] synonym: "granulocyte/monocyte progenitor" EXACT [] +xref: https://cellxgene.cziscience.com/cellguide/CL_0000557 xref: ZFA:0009251 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000763 ! myeloid cell is_a: CL:0001012 ! CD7-negative lymphoid progenitor OR granulocyte monocyte progenitor -is_a: CL:0011026 ! progenitor cell is_a: CL:1001610 ! bone marrow hematopoietic cell -is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0002032 ! hematopoietic oligopotent progenitor cell intersection_of: capable_of GO:0030225 ! macrophage differentiation intersection_of: capable_of GO:0030851 ! granulocyte differentiation @@ -1359,6 +1509,7 @@ relationship: has_part PR:000001944 ! transcription factor PU.1 relationship: has_part PR:000005307 ! CCAAT/enhancer-binding protein alpha relationship: RO:0002104 PR:000001865 ! has plasma membrane part interleukin-3 receptor class 2 alpha chain property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nGranulocyte monocyte progenitor cells (GMP cells), originating from hematopoietic stem cells in the bone marrow, are a critical intermediate in myeloid cell development. Positioned at a key differentiation juncture, these cells exhibit bidirectional potential, giving rise to both granulocyte and monocyte lineages.\nTheir primary role is to generate mature granulocytes and monocytes, essential components of the body's innate immunity and inflammatory responses. Granulocytes, such as neutrophils, eosinophils, and basophils, contribute to the first line of defense against infections by migrating to the infection site and phagocytosing pathogens. Monocytes can differentiate into macrophages or dendritic cells, playing diverse roles in immune responses." xsd:string {xref="DOI:10.1016/j.immuni.2017.10.021", xref="DOI:10.1146/annurev-immunol-081022113627", xref="DOI:10.1186/2050-7771-2-1"} [Term] id: CL:0000558 @@ -1366,12 +1517,13 @@ name: reticulocyte def: "An immature erythrocyte that changes the protein composition of its plasma membrane by exosome formation and extrusion. The types of protein removed differ between species though removal of the transferrin receptor is apparent in mammals and birds." [GOC:add, GOC:tfm, PMID:15946868, PMID:2037622] subset: blood_and_immune_upper_slim subset: cellxgene_subset +subset: human_subset +subset: mouse_subset xref: BTO:0001173 xref: CALOHA:TS-0864 xref: MESH:D012156 xref: ZFA:0009252 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000764 {is_inferred="true"} ! erythroid lineage cell -is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000764 ! erythroid lineage cell intersection_of: capable_of GO:0071971 ! extracellular exosome assembly intersection_of: CL:4030046 PR:000001002 ! lacks_plasma_membrane_part CD19 molecule @@ -1408,12 +1560,13 @@ def: "A precursor in the monocytic series, being a cell intermediate in developm comment: Morphology: Mononuclear cell, diameter 14-18 _M, fine azurophilic granules; markers: CD11b (shared with many other myeloid cells); location: Adult: bone marrow; Fetal: Liver, Yolk Sac; role or process: hematopoiesis, monocyte development; lineage: hematopoietic, myeloid. subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset xref: BTO:0004657 xref: FMA:83551 xref: ZFA:0009253 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000763 ! myeloid cell is_a: CL:0002194 {is_inferred="true"} ! monopoietic cell -is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0002194 ! monopoietic cell intersection_of: capable_of GO:0030224 ! monocyte differentiation intersection_of: has_part GO:0042582 ! azurophil granule @@ -1428,12 +1581,13 @@ id: CL:0000566 name: angioblastic mesenchymal cell def: "A mesenchymal stem cell capable of developing into blood vessel endothelium." [GOC:dsd, GOC:tfm, PMID:12768659] comment: These cells are reportedly CD31-positive, CD34-positive, CD144-positive, CD309-positive, and TAL1-positive. +subset: human_subset +subset: mouse_subset synonym: "angioblast" EXACT [] synonym: "chondroplast" EXACT [] xref: ZFA:0009258 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000134 {is_inferred="true"} ! mesenchymal stem cell is_a: CL:0011026 ! progenitor cell -is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000134 ! mesenchymal stem cell intersection_of: RO:0002104 PR:000001444 ! has plasma membrane part cadherin-5 intersection_of: RO:0002104 PR:000002112 ! has plasma membrane part vascular endothelial growth factor receptor 2 @@ -1452,6 +1606,8 @@ subset: blood_and_immune_upper_slim subset: cellxgene_subset subset: general_cell_types_upper_slim subset: human_reference_atlas +subset: human_subset +subset: mouse_subset xref: BTO:0000876 xref: CALOHA:TS-0638 xref: FMA:62864 @@ -1476,6 +1632,8 @@ name: multinucleated giant cell def: "A phagocytic syncytial cell formed by the fusion of macrophages, occurs in chronic inflammatory responses to persistent microorganism such as M.tuberculosis, component of granulomas. Sometimes used to refer to megakaryocytes." [GOC:add, GOC:tfm, ISBN:0702022918, ISBN:0702024783, PMID:33348900, Wikipedia:Giant_cell] comment: Role or process: Chronic infection, granulomatous inflammation. Consider also megakaryocyte (CL:0000556) as sometimes multinucleated giant cell is used to refer to this. subset: blood_and_immune_upper_slim +subset: human_subset +subset: mouse_subset synonym: "foreign body giant cell" EXACT [ISBN:0702022918, ISBN:0702024783] synonym: "Langerhans giant cell" EXACT [ISBN:0702022918, ISBN:0702024783] synonym: "macrophage polykaryon" EXACT [ISBN:0702022918, ISBN:0702024783] @@ -1500,6 +1658,8 @@ id: CL:0000680 name: muscle precursor cell def: "A non-terminally differentiated cell that is capable of developing into a muscle cell." [GOC:add] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset xref: ZFA:0009291 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000055 ! non-terminally differentiated cell is_a: CL:0000255 ! eukaryotic cell @@ -1512,6 +1672,8 @@ relationship: RO:0002203 CL:0000187 ! develops into muscle cell id: CL:0000723 name: somatic stem cell def: "A stem cell that can give rise to cell types of the body other than those of the germ-line." [GO:0048103] +subset: human_subset +subset: mouse_subset xref: CALOHA:TS-2086 xref: MESH:D053687 xref: ZFA:0009307 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} @@ -1526,6 +1688,8 @@ name: leukocyte def: "An achromatic cell of the myeloid or lymphoid lineages capable of ameboid movement, found in blood or other tissue." [GOC:add, GOC:tfm, ISBN:978-0-323-05290-0] subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "immune cell" RELATED [] synonym: "leucocyte" EXACT [] synonym: "white blood cell" EXACT [] @@ -1554,6 +1718,8 @@ name: nucleated thrombocyte def: "A nucleated blood cell involved in coagulation, typically seen in birds and other non-mammalian vertebrates." [GOC:add, GOC:tfm, PMID:16360205] comment: Note that this is a non-mammalian cell type. Use platelet ; CL:0000233 for thrombocytes (platelets) in mammals. subset: blood_and_immune_upper_slim +subset: human_subset +subset: mouse_subset xref: ZFA:0009323 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000226 ! single nucleate cell is_a: CL:0000763 {is_inferred="true"} ! myeloid cell @@ -1568,6 +1734,8 @@ id: CL:0000763 name: myeloid cell def: "A cell of the monocyte, granulocyte, mast cell, megakaryocyte, or erythroid lineage." [GOC:add] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset xref: BTO:0001441 xref: CALOHA:TS-0647 xref: MESH:D022423 @@ -1585,6 +1753,8 @@ def: "A immature or mature cell in the lineage leading to and including erythroc comment: Note that in FMA erythropoietic cells are types of nucleated erythrocytes and thus don't include erythrocytes. subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "erythropoietic cell" EXACT [] xref: CALOHA:TS-0290 xref: FMA:62845 @@ -1599,6 +1769,8 @@ name: erythroblast def: "A nucleated precursor of an erythrocyte that lacks hematopoietic lineage markers." [GOC:add, ISBN:0721601464, PMID:18174176] subset: blood_and_immune_upper_slim subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "normoblast" EXACT [] xref: BTO:0001571 xref: CALOHA:TS-0289 @@ -1643,6 +1815,8 @@ id: CL:0000766 name: myeloid leukocyte def: "A cell of the monocyte, granulocyte, or mast cell lineage." [GOC:add] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset xref: ZFA:0009326 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000738 {is_inferred="true"} ! leukocyte is_a: CL:0000763 ! myeloid cell @@ -1657,6 +1831,8 @@ comment: Matures in the bone marrow and account for <1% of leukocytes in the per subset: blood_and_immune_upper_slim subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "basophilic leucocyte" EXACT [] synonym: "basophilic leukocyte" EXACT [] synonym: "polymorphonuclear leucocyte" BROAD [] @@ -1686,6 +1862,8 @@ comment: Eosinophils are also CD14-negative, CD32-positive, CD44-positive, CD48- subset: blood_and_immune_upper_slim subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "eosinocyte" EXACT [] synonym: "eosinophilic granulocyte" EXACT [] synonym: "eosinophilic leucocyte" EXACT [] @@ -1717,6 +1895,8 @@ def: "Any of the immature or mature forms of a granular leukocyte that in its ma subset: blood_and_immune_upper_slim subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "neutrocyte" EXACT [] synonym: "neutrophil leucocyte" EXACT [] synonym: "neutrophil leukocyte" EXACT [] @@ -1748,6 +1928,8 @@ name: myeloid dendritic cell def: "A dendritic cell of the myeloid lineage." [GOC:add, PMID:10449155, PMID:17332250, PMID:9521319] comment: These cells are CD1a-negative, CD1b-positive, CD11a-positive, CD11c-positive, CD13-positive, CD14-negative, CD20-negative, CD21-negative, CD33-positive, CD40-negative, CD50-positive, CD54-positive, CD58-positive, CD68-negative, CD80-negative, CD83-negative, CD85j-positive, CD86-positive, CD89-negative, CD95-positive, CD120a-negative, CD120b-positive, CD123-negative, CD178-negative, CD206-negative, CD207-negative, CD209-negative, and TNF-alpha-negative. Upon TLR stimulation, they are capable of producing high levels of TNF-alpha, IL-6, CXCL8 (IL-8). subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "CD11c+CD123- DC" EXACT [] synonym: "interdigitating cell" BROAD [] synonym: "mDC" EXACT [] @@ -1768,6 +1950,8 @@ def: "A dendritic cell type of distinct morphology, localization, and surface ma subset: blood_and_immune_upper_slim subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "DC2" EXACT [] synonym: "interferon-producing cell" EXACT [] synonym: "IPC" EXACT [] @@ -1790,6 +1974,8 @@ name: mature B cell def: "A B cell that is mature, having left the bone marrow. Initially, these cells are IgM-positive and IgD-positive, and they can be activated by antigen." [GOC:add, GOC:dsd, ISBN:0781735149] comment: Mature B cells are also reportedly CD10-negative, CD19-positive, CD22-positive, CD34-negative, CD48-positive, CD79a-positive, CD84-positive, CD127-negative, CD352-positive, RAG-negative, TdT-negative, Vpre-B-negative, and pre-BCR-negative. Transcription factors expressed: Pax5-positive. subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "mature B lymphocyte" EXACT [] synonym: "mature B-cell" EXACT [] synonym: "mature B-lymphocyte" EXACT [] @@ -1815,6 +2001,8 @@ comment: Plasma cells develop in the spleen and migrate to the bone marrow. Plas subset: blood_and_immune_upper_slim subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "effector B cell" RELATED [] synonym: "effector B-cell" RELATED [] synonym: "plasma B cell" EXACT [] @@ -1826,7 +2014,6 @@ xref: FMA:70574 xref: MESH:D010950 xref: ZFA:0009332 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000946 {is_inferred="true"} ! antibody secreting cell -is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000946 ! antibody secreting cell intersection_of: CL:4030046 GO:0019814 ! lacks_plasma_membrane_part immunoglobulin complex intersection_of: CL:4030046 GO:0042613 ! lacks_plasma_membrane_part MHC class II protein complex @@ -1849,12 +2036,13 @@ name: alpha-beta T cell def: "A T cell that expresses an alpha-beta T cell receptor complex." [GOC:add, GOC:tfm, ISBN:0781735149] subset: blood_and_immune_upper_slim subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "alpha-beta T lymphocyte" EXACT [] synonym: "alpha-beta T-cell" EXACT [] synonym: "alpha-beta T-lymphocyte" EXACT [] xref: ZFA:0009335 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000084 {is_inferred="true"} ! T cell -is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000084 ! T cell intersection_of: RO:0002104 GO:0042105 ! has plasma membrane part alpha-beta T cell receptor complex disjoint_from: CL:0000798 ! gamma-delta T cell @@ -1868,6 +2056,8 @@ comment: Note that gamma-delta T cells have both thymic and extrathymic differen subset: blood_and_immune_upper_slim subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "gamma-delta T lymphocyte" EXACT [] synonym: "gamma-delta T-cell" EXACT [] synonym: "gamma-delta T-lymphocyte" EXACT [] @@ -1875,7 +2065,6 @@ synonym: "gammadelta T cell" EXACT [] synonym: "gd T cell" RELATED OMO:0003000 [] xref: ZFA:0009336 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000084 {is_inferred="true"} ! T cell -is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000084 ! T cell intersection_of: RO:0002104 GO:0042106 ! has plasma membrane part gamma-delta T cell receptor complex relationship: RO:0002104 GO:0042106 ! has plasma membrane part gamma-delta T cell receptor complex @@ -1889,6 +2078,8 @@ comment: Immature B cells are also reportedly CD5-positive, CD10-positive, CD19- subset: blood_and_immune_upper_slim subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "immature B lymphocyte" EXACT [] synonym: "immature B-cell" EXACT [] synonym: "immature B-lymphocyte" EXACT [] @@ -1913,6 +2104,8 @@ name: precursor B cell def: "A precursor B cell is a B cell with the phenotype CD10-positive." [GO_REF:0000031, GOC:rhs, GOC:tfm] subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "pre-B cell" RELATED [] xref: BTO:0001133 xref: CALOHA:TS-0819 @@ -1933,6 +2126,8 @@ def: "An immature B cell of an intermediate stage between the pre-B cell stage a comment: This cell type is compatible with the HIPC Lyoplate markers for 'transitional B cell'. subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "T1 B cell" NARROW [] synonym: "T2 B cell" NARROW [] synonym: "T3 B cell" NARROW [] @@ -1963,6 +2158,8 @@ def: "A progenitor cell of the B cell lineage, with some lineage specific activi comment: Human pro-B cells are reportedly CD10-positive, CD22-positive, CD34-positive, CD38-positive, CD45-low, CD48-positive, CD79a-positive, CD127-positive, CD184-positive, RAG-positive, TdT-positive, Vpre-B-positive, pre-BCR-negative, IgD-negative, and IgM-negative. Transcription factors expressed: Pax5-positive, EBF-positive, E2A-negative, Ikaros-negative, and PU.1-negative. subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "pre-B cell (Philadelphia nomenclature)" RELATED [PMID:11244048] synonym: "pre-pro B cell" BROAD [PMID:17582343] synonym: "pro-B lymphocyte" EXACT [] @@ -1975,7 +2172,6 @@ synonym: "progenitor B-lymphocyte" EXACT [] xref: BTO:0003104 xref: ZFA:0009349 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000838 {is_inferred="true"} ! lymphoid lineage restricted progenitor cell -is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000838 ! lymphoid lineage restricted progenitor cell intersection_of: has_part PR:000001903 ! paired box protein PAX-5 intersection_of: has_part PR:000006611 ! DNA nucleotidylexotransferase @@ -1991,6 +2187,8 @@ id: CL:0000827 name: pro-T cell def: "A lymphoid progenitor cell of the T cell lineage, with some lineage specific marker expression, but not yet fully committed to the T cell lineage." [GOC:add, ISBN:0781735149] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "DN1 cell" NARROW [] synonym: "DN1 thymocyte" NARROW [] synonym: "pro-T lymphocyte" EXACT [] @@ -2008,6 +2206,8 @@ id: CL:0000828 name: thromboblast def: "A progenitor cell of the thrombocyte, a nucleated blood cell involved in coagulation typically seen in birds and other non-mammalian vertebrates." [GOC:add, GOC:tfm, PMID:7758949] comment: Note that this is a non-mammalian cell type. +subset: human_subset +subset: mouse_subset xref: ZFA:0009351 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000226 ! single nucleate cell is_a: CL:0000763 ! myeloid cell @@ -2023,13 +2223,14 @@ id: CL:0000831 name: mast cell progenitor def: "A progenitor cell of the mast cell lineage. Markers for this cell are FceRIa-low, CD117-positive, CD9-positive, T1/ST2-positive, SCA1-negative, and lineage-negative." [GOC:add, GOC:dsd, http://www.copewithcytokines.de, PMCID:PMC1183570, PMCID:PMC1312421, PMID:8629001, PMID:9354811] comment: MCP are CD16-positive, CD32-positive, CD34-positive, CD45-positive, integrin beta-7-positive, and lin-negative (CD2, CD3e, CD4, CD5, CD8a, CD14, CD19, CD20, CD27, integrin alpha-M, ly6c, ly6g, NCAM-1, and ter119). These cells also express the transcription factors GATA-1, GATA-2, and MITF, but not C/EBPa. +subset: human_subset +subset: mouse_subset synonym: "CFU-Mast" RELATED [] synonym: "CFU-MC" RELATED [] synonym: "colony forming unit mast cell" RELATED [] synonym: "MCP" EXACT [] is_a: CL:0000763 ! myeloid cell is_a: CL:0000839 {is_inferred="true"} ! myeloid lineage restricted progenitor cell -is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000839 ! myeloid lineage restricted progenitor cell intersection_of: capable_of GO:0060374 ! mast cell differentiation intersection_of: CL:4030045 PR:000005307 ! lacks_part CCAAT/enhancer-binding protein alpha @@ -2089,6 +2290,8 @@ comment: Markers differ between mouse and human. subset: blood_and_immune_upper_slim subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "hemopoietic progenitor cell" EXACT [] synonym: "MPP" EXACT [] xref: BTO:0000725 @@ -2096,7 +2299,6 @@ xref: CALOHA:TS-0448 xref: ZFA:0009354 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000255 ! eukaryotic cell is_a: CL:0008001 ! hematopoietic precursor cell -is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000988 ! hematopoietic cell intersection_of: bearer_of PATO:0001402 ! multipotent intersection_of: CL:4030046 PR:000001002 ! lacks_plasma_membrane_part CD19 molecule @@ -2138,6 +2340,8 @@ name: lymphoid lineage restricted progenitor cell def: "A progenitor cell restricted to the lymphoid lineage." [GOC:add, GOC:tfm] comment: Note that this is a class of cell types, not an identified single cell type. subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "lymphoid progenitor cell" BROAD [] xref: BTO:0004731 xref: CALOHA:TS-2025 @@ -2157,6 +2361,8 @@ def: "A progenitor cell restricted to the myeloid lineage." [GOC:add, GOC:tfm, P comment: Note that this is a class of cell types, not an identified single cell type. subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "myeloid progenitor cell" BROAD [] xref: BTO:0004730 xref: CALOHA:TS-2099 @@ -2175,6 +2381,8 @@ name: mononuclear cell def: "A leukocyte with a single non-segmented nucleus in the mature form." [GOC:add] subset: blood_and_immune_upper_slim subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "mononuclear leukocyte" EXACT [] synonym: "peripheral blood mononuclear cell" NARROW [] xref: BTO:0000878 @@ -2192,8 +2400,10 @@ name: myeloid suppressor cell def: "An immature myeloid leukocyte of heterogeneous phenotype found particularly in cancer and sepsis patients that is capable of suppressing activity of T cells in ex vivo assays. This cell type is CD45-positive, CD11b-positive." [GO_REF:0000031, GOC:add, GOC:ana, PMID:16168663, PMID:17016554, PMID:17016559] comment: Markers: Mouse: CD11b+GR1+CD31+; Human: CD34+ CD33+CD15-CD13+. (According to some reports in humans these cells are iNOS+ARG1+IL13+IFNg+); location: In cancerous tissue; in the blood and lymphoid organs in sepsis. subset: blood_and_immune_upper_slim +subset: cellxgene_subset +subset: human_subset +subset: mouse_subset is_a: CL:0000766 {is_inferred="true"} ! myeloid leukocyte -is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000766 ! myeloid leukocyte intersection_of: bearer_of PATO:0001501 ! immature intersection_of: capable_of GO:0050777 ! negative regulation of immune response @@ -2209,7 +2419,10 @@ id: CL:0000945 name: lymphocyte of B lineage def: "A lymphocyte of B lineage with the commitment to express an immunoglobulin complex." [GO_REF:0000031, GOC:add, GOC:rhs, GOC:tfm, ISBN:0781735149] comment: Types of B lineage lymphocytes include B cells and antibody secreting cells (plasmablasts and plasma cells). Lymphocytes of B cell lineage can be distinguished from those of T cell lineage by their lack of CD3e (as part of the T cell receptor complex). +subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset is_a: CL:0000542 {is_inferred="true"} ! lymphocyte relationship: RO:0002202 CL:0000826 ! develops from pro-B cell property_value: RO:0002175 NCBITaxon:9606 @@ -2218,6 +2431,8 @@ property_value: RO:0002175 NCBITaxon:9606 id: CL:0000946 name: antibody secreting cell def: "A lymphocyte of B lineage that is devoted to secreting large amounts of immunoglobulin." [GO_REF:0000031, GOC:add, GOC:tfm, ISBN:0721601464, ISBN:0781735149] +subset: human_subset +subset: mouse_subset is_a: CL:0000945 {is_inferred="true"} ! lymphocyte of B lineage intersection_of: CL:0000945 ! lymphocyte of B lineage intersection_of: produces GO:0042571 ! immunoglobulin complex, circulating @@ -2229,6 +2444,8 @@ name: small pre-B-II cell def: "A small pre-B-II cell is a pre-B-II cell that is Rag1-positive, Rag2-positive, pre-BCR-negative, and BCR-negative, is not proliferating, and carries a DNA rearrangement of one or more immunoglobulin light chain genes." [GO_REF:0000031, GOC:dsd, GOC:rhs, GOC:tfm, PMID:16551251, PMID:18432934, PMID:9785673] comment: Small pre-B-II cells are also reportedly CD10-positive, CD19-positive, CD34-negative, CD79a-positive, CD127-negative, TdT-negative, Vpre-B-negative, sIgM-negative, and sIgD-negative. Transcription factors: PU.1-positive, Ikaros-positive, E2A-positive, and PAX5-positive. subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "small pre-BII cell" EXACT [] is_a: CL:0000955 {is_inferred="true"} ! pre-B-II cell intersection_of: CL:0000955 ! pre-B-II cell @@ -2248,6 +2465,8 @@ id: CL:0000955 name: pre-B-II cell def: "A pre-B-II cell is a precursor B cell that expresses immunoglobulin mu heavy chain (IgHmu+), and lack expression of CD34, TdT, immunoglobulin kappa light chain and immunoglobulin lambda light chain." [GO_REF:0000031, GOC:dsd, GOC:rhs, GOC:tfm, PMID:9785673] comment: pre-B-II cell are also reportedly CD19-positive, CD22-positive, CD38-positive, CD45-positive, and CD48-positive. +subset: human_subset +subset: mouse_subset synonym: "pre-B-lymphocyte" EXACT [] synonym: "pre-BII cell" EXACT [] xref: BTO:0001133 @@ -2268,6 +2487,8 @@ def: "An activated mature (naive or memory) B cell that is secreting immunoglobu comment: This cell type is compatible with the HIPC Lyoplate markers for 'plasmablast'. Plasmablasts are also reportedly CD48-positive, CD63-positive, CD229-positive, CD270-positive, CD319-positive, CD352-positive, CD361-positive, and IgD-negative. subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "CD20-negative B cell" BROAD [] synonym: "CD27-positive, CD38-positive, CD20-negative B cell" EXACT [] xref: FMA:84371 @@ -2291,6 +2512,8 @@ id: CL:0000988 name: hematopoietic cell def: "A cell of a hematopoietic lineage." [GO_REF:0000031, GOC:add] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "haematopoietic cell" EXACT [] synonym: "haemopoietic cell" EXACT [] synonym: "hemopoietic cell" EXACT [] @@ -2309,6 +2532,8 @@ comment: Originally described in the dendritic cell ontology (DC_CL:0000003)(PMI subset: blood_and_immune_upper_slim subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "cDC" EXACT [] synonym: "DC1" EXACT [] synonym: "dendritic reticular cell" EXACT [] @@ -2326,7 +2551,10 @@ property_value: RO:0002175 NCBITaxon:9606 id: CL:0001012 name: CD7-negative lymphoid progenitor OR granulocyte monocyte progenitor comment: Originally described in the dendritic cell ontology (DC_CL:1110000)(PMID:19243617). +subset: human_subset +subset: mouse_subset is_a: CL:0001060 ! hematopoietic oligopotent progenitor cell, lineage-negative +is_a: CL:0011026 ! progenitor cell [Term] id: CL:0001035 @@ -2334,18 +2562,24 @@ name: bone cell def: "A connective tissue cell found in bone." [GO_REF:0000034, GOC:add] subset: general_cell_types_upper_slim subset: human_reference_atlas +subset: human_subset +subset: mouse_subset +xref: https://cellxgene.cziscience.com/cellguide/CL_0001035 is_a: CL:0000255 ! eukaryotic cell intersection_of: CL:0000000 ! cell intersection_of: part_of UBERON:0001474 ! bone element relationship: part_of UBERON:0001474 ! bone element property_value: RO:0002175 NCBITaxon:9606 property_value: terms:contributor https://orcid.org/0000-0001-9990-8331 +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nBone cells, also known as osteocytes, form the building blocks of the skeletal system. They represent the most common type of bone cell, making up approximately 95% of the total bone cell population in mature adult bone tissue. Osteocytes are a stellate shape with numerous long, slender dendritic processes.\nThe formation of bone is a complex process involving the action of osteoclasts - cells that break down and reabsorb old bone, followed by osteoblasts that rebuild the bone. Osteocytes serve as coordinators for these two types of bone cells to ensure a balance in the bone remodeling process, contributing to maintaining both bone strength and mineral homeostasis.\nThe primary functions of osteocytes involve the creation, maintenance, and repair of bone tissue. They ensure that bone remodeling is performed by forming a network within the bone and communicating with other cells to help them respond to mechanical strain and damage.\nA remarkable aspect of osteocytes is their ability to perceive mechanical forces, translating them into biochemical signals that regulate bone remodeling and adaptation. Defects in osteocyte function, aside from other bone cells, have been associated with several bone disorders such as osteoporosis, renal osteodystrophy, and skeletal manifestations of diabetes." xsd:string {xref="DOI:10.1007/s00795-015-0099-y", xref="DOI:10.1007/s11914-012-0105-4", xref="DOI:10.1016/j.jot.2021.04.005", xref="DOI:10.1038/s41413-020-0099-y"} creation_date: 2011-11-16T04:28:16Z [Term] id: CL:0001060 name: hematopoietic oligopotent progenitor cell, lineage-negative def: "A hematopoietic oligopotent progenitor cell that has the ability to differentiate into limited cell types but lacks lineage cell markers and self renewal capabilities. Cell lacks hematopoeitic lineage markers." [GOC:tfm, PMID:19022770] +subset: human_subset +subset: mouse_subset is_a: CL:0002032 ! hematopoietic oligopotent progenitor cell intersection_of: CL:0002032 ! hematopoietic oligopotent progenitor cell intersection_of: bearer_of PATO:0001401 ! oligopotent @@ -2383,6 +2617,8 @@ def: "A lymphocyte that lacks characteristic T cell, B cell, myeloid cell, and d subset: blood_and_immune_upper_slim subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset is_a: CL:0000542 ! lymphocyte intersection_of: CL:0000542 ! lymphocyte intersection_of: capable_of GO:0001816 ! cytokine production @@ -2402,8 +2638,9 @@ id: CL:0001200 name: lymphocyte of B lineage, CD19-positive def: "A lymphocyte of B lineage that is CD19-positive." [GOC:add] comment: Types of B lineage lymphocytes include B cells and antibody secreting cells (plasmablasts and plasma cells). Lymphocytes of B cell lineage can be distinguished from those of T cell lineage by their lack of CD3e (as part of the T cell receptor complex). +subset: human_subset +subset: mouse_subset is_a: CL:0000945 ! lymphocyte of B lineage -is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000945 ! lymphocyte of B lineage intersection_of: CL:4030046 PR:000001020 ! lacks_plasma_membrane_part CD3 epsilon intersection_of: RO:0002104 PR:000001002 ! has plasma membrane part CD19 molecule @@ -2417,6 +2654,8 @@ property_value: terms:contributor https://orcid.org/0000-0001-9990-8331 id: CL:0001201 name: B cell, CD19-positive def: "A B cell that is CD19-positive." [GOC:add] +subset: human_subset +subset: mouse_subset synonym: "B lymphocyte, CD19-positive" EXACT [] synonym: "B-cell, CD19-positive" EXACT [] synonym: "B-lymphocyte, CD19-positive" EXACT [] @@ -2434,6 +2673,8 @@ id: CL:0002009 name: macrophage dendritic cell progenitor def: "A progenitor cell that can give rise to plasmacytoid and myeloid dendritic cells, and to monocytes and macrophages." [GOC:tfm, PMID:19273628] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "MDP" EXACT [] is_a: CL:0000763 ! myeloid cell is_a: CL:0002032 {is_inferred="true"} ! hematopoietic oligopotent progenitor cell @@ -2453,10 +2694,11 @@ name: basophil mast progenitor cell def: "A cell type that can give rise to basophil and mast cells. This cell is CD34-positive, CD117-positive, CD125-positive, FceRIa-negative, and T1/ST2-negative, and expresses Gata-1, Gata-2, C/EBPa" [GOC:ak, GOC:dsd, GOC:tfm, PMCID:PMC1312421] comment: There may be an intermediate cell type. These cells also CD13-positive, CD16-positive, CD32-positive, and integrin beta 7-positive. Transcription factors: GATA1-positive, MCP-1-positive, mitf-positive, PU.1-positive, and CEBP/a-low. subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "BMCP" EXACT [] is_a: CL:0000763 ! myeloid cell is_a: CL:0002191 ! granulocytopoietic cell -is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000839 ! myeloid lineage restricted progenitor cell intersection_of: capable_of GO:0030221 ! basophil differentiation intersection_of: capable_of GO:0060374 ! mast cell differentiation @@ -2483,6 +2725,8 @@ id: CL:0002031 name: hematopoietic lineage restricted progenitor cell def: "A hematopoietic progenitor cell that is capable of developing into only one lineage of hematopoietic cells." [GOC:tfm, PMID:19022770] subset: blood_and_immune_upper_slim +subset: human_subset +subset: mouse_subset is_a: CL:0000255 ! eukaryotic cell is_a: CL:0008001 ! hematopoietic precursor cell intersection_of: CL:0000988 ! hematopoietic cell @@ -2499,6 +2743,8 @@ name: hematopoietic oligopotent progenitor cell def: "A hematopoietic oligopotent progenitor cell that has the ability to differentiate into limited cell types but lacks lineage cell markers and self renewal capabilities." [GOC:tfm, https://orcid.org/0000-0001-5208-3432, PMID:19022770] comment: This cell type is intended to be compatible with any vertebrate hematopoietic oligopotent progenitor cell. For mammalian hematopoietic oligopotent progenitor cells known to be lineage-negative, please use the term 'hematopoietic oligopotent progenitor cell' (CL_0001060). subset: blood_and_immune_upper_slim +subset: human_subset +subset: mouse_subset is_a: CL:0000255 ! eukaryotic cell is_a: CL:0008001 ! hematopoietic precursor cell intersection_of: CL:0000988 ! hematopoietic cell @@ -2512,6 +2758,8 @@ creation_date: 2010-01-06T03:43:27Z id: CL:0002077 name: ecto-epithelial cell def: "An epithelial cell derived from ectoderm." [FMA:69074, GOC:tfm] +subset: human_subset +subset: mouse_subset xref: FMA:69074 xref: ZFA:0009385 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000066 ! epithelial cell @@ -2526,6 +2774,8 @@ id: CL:0002087 name: nongranular leukocyte def: "A leukocyte that lacks granules." [GOC:tfm] subset: blood_and_immune_upper_slim +subset: human_subset +subset: mouse_subset synonym: "agranular leukocyte" EXACT [] xref: FMA:62855 is_a: CL:0000738 {is_inferred="true"} ! leukocyte @@ -2541,6 +2791,8 @@ name: bone marrow cell def: "A cell found in the bone marrow. This can include fibroblasts, macrophages, adipocytes, osteoblasts, osteoclasts, endothelial cells and hematopoietic cells." [GOC:tfm, ISBN:0618947256] comment: MH consider whether bone marrow cells are bone cells in the structural sense vs. being part of bone organ sense. subset: cellxgene_subset +subset: human_subset +subset: mouse_subset xref: BTO:0004850 xref: FMA:83621 xref: MESH:D001854 @@ -2557,13 +2809,17 @@ name: endothelial cell of vascular tree def: "An endothelial cell of the vascular tree, which includes blood vessels and lymphatic vessels." [GOC:dsd, GOC:tfm, PMID:12768659] comment: These cells are reportedly CD31-positive, CD34-positive, CD144-positive, TAL1-positive. subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "cubodial endothelial cell of vascular tree" NARROW [] synonym: "vascular endothelial cell" EXACT [] xref: BTO:0001854 xref: CALOHA:TS-1106 xref: FMA:67755 +xref: https://cellxgene.cziscience.com/cellguide/CL_0002139 is_a: CL:0000115 ! endothelial cell property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nEndothelial cells of the vascular tree, commonly referred to as vascular endothelial cells, line the entire circulatory system, from the heart to the smallest capillaries. These cells have a unique, flattened shape, and are tightly bound together, forming a thin layer known as the endothelium. The endothelium is responsible for maintaining the interior surface of blood vessels, and plays a critical role in ensuring the smooth flow of blood. \nVascular endothelial cells act as a semi-permeable membrane, controlling the passage of materials and the transit of white blood cells into and out of the bloodstream. These cells are also involved in blood coagulation. When a blood vessel is damaged, endothelial cells promote clotting to prevent excessive bleeding and facilitate wound healing. Other functions include regulation of blood pressure and blood volume by releasing vasodilators and vasoconstrictors to either widen or constrict blood vessels, accordingly.\nFurthermore, the endothelial cells are crucial in the formation of new blood vessels, a process known as angiogenesis. This is particularly important in wound healing and the growth of new tissues during development or after injury. In the context of diseases such as cancer, angiogenesis helps facilitate tumor growth by providing nutrients and oxygen." xsd:string {xref="DOI:10.1038/s41569-022-00770-1", xref="DOI:10.1186/s12872-015-0124-z", xref="DOI:10.3389/fphys.2022.863265/full", xref="https://www.sciencedirect.com/topics/medicine-and-dentistry/vascular-endothelial-cell"} creation_date: 2010-08-24T02:06:40Z [Term] @@ -2571,6 +2827,8 @@ id: CL:0002191 name: granulocytopoietic cell def: "A cell involved in the formation of a granulocyte." [GOC:tfm] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset xref: FMA:83519 is_a: CL:0000839 {is_inferred="true"} ! myeloid lineage restricted progenitor cell intersection_of: CL:0000839 ! myeloid lineage restricted progenitor cell @@ -2583,6 +2841,8 @@ creation_date: 2010-08-30T12:54:27Z id: CL:0002194 name: monopoietic cell def: "A cell involved in the formation of a monocyte (monopoiesis)." [GOC:tfm] +subset: human_subset +subset: mouse_subset xref: FMA:83552 is_a: CL:0000839 {is_inferred="true"} ! myeloid lineage restricted progenitor cell intersection_of: CL:0000839 ! myeloid lineage restricted progenitor cell @@ -2595,6 +2855,8 @@ creation_date: 2010-08-30T01:27:48Z id: CL:0002242 name: nucleate cell def: "A cell containing at least one nucleus." [GOC:tfm] +subset: human_subset +subset: mouse_subset xref: FMA:67513 is_a: CL:0000000 ! cell intersection_of: CL:0000000 ! cell @@ -2607,6 +2869,8 @@ creation_date: 2010-09-07T03:32:33Z id: CL:0002274 name: histamine secreting cell def: "A cell type that secretes histamine." [GOC:tfm] +subset: human_subset +subset: mouse_subset is_a: CL:0000457 ! biogenic amine secreting cell intersection_of: CL:0000151 ! secretory cell intersection_of: capable_of GO:0001821 ! histamine secretion @@ -2619,6 +2883,8 @@ id: CL:0002319 name: neural cell def: "A cell that is part of the nervous system." [GOC:tfm, ISBN:0618947256] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset xref: CALOHA:TS-2040 xref: FMA:70333 is_a: CL:0000255 ! eukaryotic cell @@ -2633,6 +2899,8 @@ id: CL:0002320 name: connective tissue cell def: "A cell of the supporting or framework tissue of the body, arising chiefly from the embryonic mesoderm and including adipose tissue, cartilage, and bone." [GOC:tfm, ISBN:0618947256] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset xref: CALOHA:TS-2096 xref: FMA:63875 xref: MESH:D003239 @@ -2648,12 +2916,16 @@ creation_date: 2010-09-15T03:01:54Z id: CL:0002321 name: embryonic cell (metazoa) def: "A cell of the embryo." [FMA:0618947256] +subset: human_subset +subset: mouse_subset xref: CALOHA:TS-0263 xref: FMA:82840 +xref: https://cellxgene.cziscience.com/cellguide/CL_0002321 xref: WBbt:0007028 xref: ZFA:0007089 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000000 ! cell property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nEmbryonic cells in metazoans, which include all multicellular animals, are biological units in their earliest developmental stages from conception until the organism is fully formed. \nThey are derived from a fertilized egg, which undergoes a series of cell divisions to produce a multicellular organism. During the early phases of embryonic development, these cells exhibit pluripotency, meaning they possess the potential to differentiate into a diverse array of specialized cell types that constitute different body tissues and structures. \nThe balance between cell proliferation and differentiation in embryonic cells is crucial for successful development. When cells continue to divide without differentiating, overgrowth may occur leading to conditions such as teratomas (tumors of embryonic cells). Conversely, if cell differentiation proceeds at the expense of cell proliferation, developmental anomalies could occur regarding size or mass of the organism or its parts." xsd:string {xref="DOI:10.1002/iub.1404", xref="DOI:10.1093/molehr/gan048", xref="https://www.ncbi.nlm.nih.gov/books/NBK9906/"} creation_date: 2010-09-15T03:39:21Z [Term] @@ -2662,6 +2934,8 @@ name: immature T cell def: "A T cell that has not completed T cell selection." [GOC:tfm] subset: blood_and_immune_upper_slim subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "immature T-cell" EXACT [] xref: BTO:0001372 xref: CALOHA:TS-1042 @@ -2677,6 +2951,8 @@ id: CL:0002494 name: cardiocyte def: "A cell located in the heart, including both muscle and non muscle cells." [GOC:tfm] comment: From Onard of the FMA: Cardiac muscle cell or cardiac myocyte is a striated muscle cell. Cardiocyte on the other hand is any cell in the heart which includes cells other than muscle cells (e.g. endothelial cell of endocardium). Unless there is a consensus among anatomists that cardiocytes refer only to muscle cells, we will treat them as a general class of cells in the heart. +subset: human_subset +subset: mouse_subset synonym: "heart cell" EXACT [] xref: BTO:0001539 xref: CALOHA:TS-0115 @@ -2694,8 +2970,9 @@ id: CL:0002679 name: natural helper lymphocyte def: "A lymphocyte found in adipose tissue that lacks lineage markers of other lymphocytes but is capable of mediating TH2 cytokine responses. This cell type is found in fat associated lymphoid clusters, proliferates in response to IL2 and produce large amounts of TH2 cytokines such as IL5, IL6 and IL13" [GOC:tfm, PMID:20023630] subset: blood_and_immune_upper_slim +subset: human_subset +subset: mouse_subset is_a: CL:0000542 {is_inferred="true"} ! lymphocyte -is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000542 ! lymphocyte intersection_of: CL:4030046 GO:0042105 ! lacks_plasma_membrane_part alpha-beta T cell receptor complex intersection_of: CL:4030046 PR:000001002 ! lacks_plasma_membrane_part CD19 molecule @@ -2725,6 +3002,8 @@ id: CL:0007001 name: skeletogenic cell def: "Cell that has the potential to form a skeletal cell type (e.g. cells in periosteum, cells in marrow) and produce extracellular matrix (often mineralized) and skeletal tissue (often mineralized)." [GO_REF:0000034] comment: Needs logical definition. Should be capable_of skeletal system morphogenesis? or skeletal tissue development? needs to be added to GO. NOTES:a cell type of the early embryo (see also: mesenchymal cells) that will give rise to mineralized connective tissue. Scleroblasts can differentiate into osteoblasts (bone-forming cells), chondroblasts (cartilage-forming cells), odontoblasts (dentin-forming cells), ameloblasts (enamel-forming cells). The mesenchymal cells developing into osteoblasts and chondroblasts are derived from the mesoderm. Those developing into odontoblasts are neural crest cells. Those developing into ameloblasts are derived from the ectoderm. (http://www.copewithcytokines.de/cope.cgi?key=scleroblasts) +subset: human_subset +subset: mouse_subset synonym: "scleroblast" EXACT [GO_REF:0000034] is_a: CL:0000000 ! cell property_value: terms:contributor https://orcid.org/0000-0001-9114-8737 @@ -2734,6 +3013,8 @@ creation_date: 2012-06-15T02:51:27Z id: CL:0007004 name: premigratory neural crest cell def: "Cell that is part of the neural crest region of the neuroepithelium, prior to migration. Note that not all premigratory neural crest cells may become migratory neural crest cells." [UBERONREF:0000002] +subset: human_subset +subset: mouse_subset xref: ZFA:0007084 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0011012 ! neural crest cell relationship: part_of UBERON:0002342 ! neural crest @@ -2746,6 +3027,8 @@ id: CL:0008001 name: hematopoietic precursor cell def: "Any hematopoietic cell that is a precursor of some other hematopoietic cell type." [GOC:dos] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset is_a: CL:0000988 ! hematopoietic cell [Term] @@ -2754,6 +3037,8 @@ name: mesenchymal cell def: "A non-polarised cell precursor cell that is part of some mesenchyme, is associated with the cell matrix but is not connected to other cells and is capable of migration." [] subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "mesenchyme cell" EXACT [] is_a: CL:0000219 ! motile cell is_a: CL:0000255 ! eukaryotic cell @@ -2765,6 +3050,8 @@ property_value: RO:0002175 NCBITaxon:9606 id: CL:0010017 name: zygote def: "A zygote in a plant or an animal." [] +subset: human_subset +subset: mouse_subset xref: MESH:D015053 is_a: CL:0000000 ! cell property_value: seeAlso https://github.com/obophenotype/cell-ontology/issues/786 @@ -2774,16 +3061,20 @@ id: CL:0011012 name: neural crest cell def: "A cell of the neural crest. Neural crest cells are multipotent. Premigratory neural crest cells are found at the neural plate boarder, some of which will undergo ectomesynchymal transition and delamination to form migratory neural crest cells." [https://orcid.org/0000-0001-5208-3432, https://orcid.org/0000-0002-9900-7880] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset xref: https://cellxgene.cziscience.com/cellguide/CL_0011012 is_a: CL:0000048 ! multi fate stem cell is_a: CL:0002321 ! embryonic cell (metazoa) -property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional.\n\nNeural crest cells are a group of transient and highly migratory cells that originate from the neuroectoderm during the early stages of embryonic development. They are multipotent cells with an exceptional degree of plasticity, capable of differentiating into various somatic cell types and therefore play a fundamental role in the formation of various organs and tissues, making them critical contributors to the developing embryo. \nAfter the initiation of neurulation (the formation of the neural tube) neural crest cells start to undergo epithelial-to-mesenchymal transition and delaminate and migrate from the dorsal neural tube to several regions throughout the embryo. They differentiate into a range of diverse cell types, such as neurons and glial cells of the peripheral nervous system, including sensory and autonomic neurons. They also contribute to the formation of adrenal glands, pigment cells in the skin (melanocytes), cardiac structures, including parts of the heart septum and major arteries, as well as bones and cartilage of the face and skull.\nDisorders or aberrations in the development or migration of the neural crest cells can lead to serious congenital malformations, such as neurocristopathies, including Hirschsprung disease, neuroblastoma, and neurofibromatosis." xsd:string {xref="DOI:10.1002/dvg.23276", xref="DOI:10.1242/dev.193193", xref="DOI:10.3389/fcell.2020.00635/full", xref="https://doi.org/10.1016/j.ydbio.2011.12.042"} +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nNeural crest cells are a group of transient and highly migratory cells that originate from the neuroectoderm during the early stages of embryonic development. They are multipotent cells with an exceptional degree of plasticity, capable of differentiating into various somatic cell types and therefore play a fundamental role in the formation of various organs and tissues, making them critical contributors to the developing embryo. \nAfter the initiation of neurulation (the formation of the neural tube) neural crest cells start to undergo epithelial-to-mesenchymal transition and delaminate and migrate from the dorsal neural tube to several regions throughout the embryo. They differentiate into a range of diverse cell types, such as neurons and glial cells of the peripheral nervous system, including sensory and autonomic neurons. They also contribute to the formation of adrenal glands, pigment cells in the skin (melanocytes), cardiac structures, including parts of the heart septum and major arteries, as well as bones and cartilage of the face and skull.\nDisorders or aberrations in the development or migration of the neural crest cells can lead to serious congenital malformations, such as neurocristopathies, including Hirschsprung disease, neuroblastoma, and neurofibromatosis." xsd:string {xref="DOI:10.1002/dvg.23276", xref="DOI:10.1242/dev.193193", xref="DOI:10.3389/fcell.2020.00635/full", xref="https://doi.org/10.1016/j.ydbio.2011.12.042"} [Term] id: CL:0011026 name: progenitor cell def: "A precursor cell that has a tendency to differentiate into a specific type of cell. They are descendants of stem cells, only they are more constrained in their differentiation potential or capacity for self-renewal, and are often more limited in both senses." [https://doi.org/10.1016/B978-0-12-409503-8.00002-0, ISBN:978-1-62808-994-3] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset is_a: CL:0000255 ! eukaryotic cell is_a: CL:0011115 ! precursor cell intersection_of: CL:0011115 ! precursor cell @@ -2797,6 +3088,8 @@ name: precursor cell def: "A cell that, by division or terminal differentiation, can give rise to other cell types." [GOC:dos] comment: Work is needed on GO 'cell differentiation' before it is clear whether the equivalent class definition 'native cell' that capable_of some 'cell differentiation' works. Also, may want to consider merging this with non-terminally differentiated cell. subset: cellxgene_subset +subset: human_subset +subset: mouse_subset is_a: CL:0000000 ! cell intersection_of: CL:0000000 ! cell intersection_of: capable_of GO:0030154 ! cell differentiation @@ -2807,25 +3100,29 @@ id: CL:0017005 name: lymphoblast def: "A lymphocyte that has gotten larger after being stimulated by an antigen." [http://orcid.org/0000-0001-9990-8331, NCIT:C13013] subset: blood_and_immune_upper_slim +subset: human_subset +subset: mouse_subset xref: BTO:0000772 xref: EFO:0000572 xref: FMA:83030 is_a: CL:0000542 ! lymphocyte relationship: output_of GO:0046649 ! lymphocyte activation -property_value: dc:date "2022-08-17T14:20:01Z" xsd:string -created_by: http://orcid.org/0000-0003-2473-2313 +property_value: terms:contributor http://orcid.org/0000-0003-2473-2313 +property_value: terms:date "2022-08-17T14:20:01Z" xsd:dateTime [Term] id: CL:0017006 name: B-lymphoblast def: "A lymphocyte of B lineage that has gotten larger after being stimulated by an antigen." [EFO:0005293, https://orcid.org/0000-0002-2825-0621] subset: blood_and_immune_upper_slim +subset: human_subset +subset: mouse_subset xref: EFO:0005293 xref: FMA:83031 is_a: CL:0000945 ! lymphocyte of B lineage is_a: CL:0017005 ! lymphoblast -property_value: dc:date "2022-08-17T14:30:32Z" xsd:string -created_by: http://orcid.org/0000-0003-2473-2313 +property_value: terms:contributor http://orcid.org/0000-0003-2473-2313 +property_value: terms:date "2022-08-17T14:30:32Z" xsd:dateTime [Term] id: CL:0017500 @@ -2884,6 +3181,8 @@ creation_date: 2009-12-28T04:28:35Z id: CL:1001610 name: bone marrow hematopoietic cell def: "Hematopoietic cells resident in the bone marrow. Include: hematopoietic stem cells (lymphoid stem cells and myeloid stem cells) and the precursor cells for thrombocytes, erythrocytes, basophils, neutrophils, eosinophils, monocytes and lymphocytes." [NPX:PDR] +subset: human_subset +subset: mouse_subset synonym: "bone marrow hematopoietic cells" RELATED [CALOHA:TS-2109] synonym: "bone marrow poietic cells" RELATED [CALOHA:TS-2109] xref: CALOHA:TS-2109 @@ -2898,6 +3197,8 @@ id: CL:2000001 name: peripheral blood mononuclear cell def: "A leukocyte with a single non-segmented nucleus in the mature form found in the circulatory pool of blood." [GOC:TermGenie] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset is_a: CL:0000080 ! circulating cell is_a: CL:0000842 ! mononuclear cell intersection_of: CL:0000842 ! mononuclear cell @@ -2911,6 +3212,8 @@ id: CL:4030029 name: blood lymphocyte def: "A lymphocyte located in blood." [https://orcid.org/0000-0001-9990-8331] subset: blood_and_immune_upper_slim +subset: human_subset +subset: mouse_subset is_a: CL:0000542 ! lymphocyte is_a: CL:2000001 ! peripheral blood mononuclear cell intersection_of: CL:0000542 ! lymphocyte @@ -2921,6 +3224,8 @@ property_value: terms:date "2022-11-04T14:40:00Z" xsd:dateTime id: CL:4052002 name: syncytial cell def: "A multinucleate cell formed by the fusion of multiple uninuclear cells through plasma membrane fusion. This process leads to a single large cell containing multiple nuclei within a shared cytoplasm." [PMID:20851884, Wikipedia:Syncytium] +subset: human_subset +subset: mouse_subset synonym: "SC" RELATED OMO:0003000 [PMID:9067520] synonym: "syncytium" EXACT [WBbt:0008074] is_a: CL:0000228 ! multinucleate cell @@ -2935,7 +3240,6 @@ property_value: terms:date "2024-08-15T10:38:46Z" xsd:dateTime id: GO:0000278 name: mitotic cell cycle namespace: biological_process -alt_id: GO:0007067 def: "Progression through the phases of the mitotic cell cycle, the most common eukaryotic cell cycle, which canonically comprises four successive phases called G1, S, G2, and M and includes replication of the genome and the subsequent segregation of chromosomes into daughter cells. In some variant cell cycles nuclear replication or nuclear division may not be followed by cell division, or G1 and G2 phases may be absent." [GOC:mah, ISBN:0815316194] comment: Note that this term should not be confused with 'GO:0140014 ; mitotic nuclear division'. 'GO:0000278 ; mitotic cell cycle represents the entire mitotic cell cycle, while 'GO:0140014 ; mitotic nuclear division' specifically represents the actual nuclear division step of the mitotic cell cycle. subset: goslim_chembl @@ -2985,16 +3289,13 @@ intersection_of: has_part GO:0045026 ! plasma membrane fusion id: GO:0000785 name: chromatin namespace: cellular_component -alt_id: GO:0000789 -alt_id: GO:0000790 -alt_id: GO:0005717 def: "The ordered and organized complex of DNA, protein, and sometimes RNA, that forms the chromosome." [GOC:elh, PMID:20404130] comment: Chromosomes include parts that are not part of the chromatin. Examples include the kinetochore. synonym: "chromosome scaffold" RELATED [] synonym: "cytoplasmic chromatin" NARROW [] synonym: "nuclear chromatin" NARROW [] xref: NIF_Subcellular:sao1615953555 -is_a: GO:0110165 ! cellular anatomical entity +is_a: GO:0110165 ! cellular anatomical structure relationship: part_of GO:0005694 ! chromosome property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28301" xsd:anyURI @@ -3002,8 +3303,6 @@ property_value: term_tracker_item "https://github.com/geneontology/go-ontology/i id: GO:0000791 name: euchromatin namespace: cellular_component -alt_id: GO:0005719 -alt_id: GO:0035327 def: "A dispersed and relatively uncompacted form of chromatin that is in a transcription-competent conformation." [PMID:32017156] synonym: "nuclear euchromatin" RELATED [] synonym: "transcriptionally active chromatin" EXACT [] @@ -3016,8 +3315,6 @@ property_value: term_tracker_item "https://github.com/geneontology/go-ontology/i id: GO:0000792 name: heterochromatin namespace: cellular_component -alt_id: GO:0005720 -alt_id: GO:0035328 def: "A compact and highly condensed form of chromatin that is refractory to transcription." [PMID:32017156] synonym: "nuclear heterochromatin" NARROW [] synonym: "transcriptionally inactive chromatin" EXACT [] @@ -3139,10 +3436,6 @@ property_value: term_tracker_item "https://github.com/geneontology/go-ontology/i id: GO:0001816 name: cytokine production namespace: biological_process -alt_id: GO:0042032 -alt_id: GO:0042089 -alt_id: GO:0042107 -alt_id: GO:0050663 def: "The appearance of a cytokine due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels." [GOC:add, ISBN:0781735149] comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select one of the 'regulation' children terms. subset: gocheck_do_not_annotate @@ -3162,7 +3455,7 @@ property_value: term_tracker_item "https://github.com/geneontology/go-ontology/i id: GO:0001820 name: serotonin secretion namespace: biological_process -def: "The regulated release of serotonin by a cell. Serotonin (5-hydroxytryptamine, or 5-HT) is a monoamine synthesised in serotonergic neurons in the central nervous system, enterochromaffin cells in the gastrointestinal tract and some immune system cells." [GOC:ef, ISBN:0198506732, ISBN:0781735149] +def: "The regulated release of serotonin by a cell. Serotonin (5-hydroxytryptamine, or 5-HT) is a monoamine synthesized in serotonergic neurons in the central nervous system, enterochromaffin cells in the gastrointestinal tract and some immune system cells." [GOC:ef, ISBN:0198506732, ISBN:0781735149] synonym: "5-HT secretion" EXACT [] synonym: "5-hydroxytryptamine secretion" EXACT [] synonym: "serotonin release" RELATED [GOC:tb] @@ -3189,7 +3482,6 @@ relationship: part_of GO:0016331 ! morphogenesis of embryonic epithelium id: GO:0001841 name: neural tube formation namespace: biological_process -alt_id: GO:0001679 def: "The formation of a tube from the flat layer of ectodermal cells known as the neural plate. This will give rise to the central nervous system." [GOC:dph, ISBN:0878932437] synonym: "neural tube morphogenesis" EXACT [GOC:dph] synonym: "neurulation" EXACT [] @@ -3399,8 +3691,6 @@ property_value: RO:0002161 NCBITaxon:4895 id: GO:0002377 name: immunoglobulin production namespace: biological_process -alt_id: GO:0002378 -alt_id: GO:0048305 def: "The appearance of immunoglobulin due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels." [GOC:add, ISBN:0781735149] comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select one of the 'regulation' children terms. subset: gocheck_do_not_annotate @@ -3413,8 +3703,6 @@ is_a: GO:0002440 ! production of molecular mediator of immune response id: GO:0002381 name: immunoglobulin production involved in immunoglobulin-mediated immune response namespace: biological_process -alt_id: GO:0002379 -alt_id: GO:0002380 def: "The appearance of immunoglobulin due to biosynthesis or secretion following a cellular stimulus during an immune response, resulting in an increase in its intracellular or extracellular levels." [GOC:add, ISBN:0781735149, PMID:9185563] comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select one of the 'regulation' children terms. subset: gocheck_do_not_annotate @@ -3453,8 +3741,6 @@ is_a: GO:0010467 ! gene expression id: GO:0002443 name: leukocyte mediated immunity namespace: biological_process -alt_id: GO:0019723 -alt_id: GO:0042087 def: "Any process involved in the carrying out of an immune response by a leukocyte." [GO_REF:0000022, GOC:add, ISBN:0781735149] synonym: "cell-mediated immune response" RELATED [] synonym: "cellular immune response" RELATED [] @@ -3942,7 +4228,6 @@ is_a: GO:0003008 ! system process id: GO:0003674 name: molecular_function namespace: molecular_function -alt_id: GO:0005554 def: "A molecular process that can be carried out by the action of a single macromolecular machine, usually via direct physical interactions with other molecular entities. Function in this sense denotes an action, or activity, that a gene product (or a complex) performs." [GOC:pdt] comment: Note that, in addition to forming the root of the molecular function ontology, this term is recommended for the annotation of gene products whose molecular function is unknown. When this term is used for annotation, it indicates that no information was available about the molecular function of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this. Despite its name, this is not a type of 'function' in the sense typically defined by upper ontologies such as Basic Formal Ontology (BFO). It is instead a BFO:process carried out by a single gene product or complex. subset: goslim_candida @@ -3959,8 +4244,6 @@ disjoint_from: GO:0008150 ! biological_process id: GO:0004888 name: transmembrane signaling receptor activity namespace: molecular_function -alt_id: GO:0004926 -alt_id: GO:0099600 def: "Combining with an extracellular or intracellular signal and transmitting the signal from one side of the membrane to the other to initiate a change in cell activity or state as part of signal transduction." [GOC:go_curators, Wikipedia:Transmembrane_receptor] comment: This term includes intracellular membrane receptors, e.g. IP3 triggered release of Ca2+ from intracellular stores. synonym: "transmembrane receptor activity" BROAD [GOC:bf, GOC:signaling] @@ -3972,11 +4255,6 @@ is_a: GO:0038023 ! signaling receptor activity id: GO:0004930 name: G protein-coupled receptor activity namespace: molecular_function -alt_id: GO:0001622 -alt_id: GO:0001623 -alt_id: GO:0001624 -alt_id: GO:0001625 -alt_id: GO:0016526 def: "Combining with an extracellular signal and transmitting the signal across the membrane by activating an associated G-protein; promotes the exchange of GDP for GTP on the alpha subunit of a heterotrimeric G-protein complex." [GOC:bf, Wikipedia:GPCR] subset: goslim_chembl synonym: "EBV-induced receptor" NARROW [] @@ -3999,6 +4277,7 @@ synonym: "super conserved receptor expressed in brain receptor activity" NARROW xref: Reactome:R-HSA-114552 "Thrombin-activated PARs activate G12/13" xref: Reactome:R-HSA-114558 "Thrombin-activated PARs activate Gq" xref: Reactome:R-HSA-167408 "The high affinity receptor complex binds to G-protein" +xref: Reactome:R-HSA-381706 "GLP1R:GLP1 activates G(s)" xref: Wikipedia:GPCR is_a: GO:0004888 ! transmembrane signaling receptor activity relationship: part_of GO:0007186 ! G protein-coupled receptor signaling pathway @@ -4007,7 +4286,6 @@ relationship: part_of GO:0007186 ! G protein-coupled receptor signaling pathway id: GO:0005575 name: cellular_component namespace: cellular_component -alt_id: GO:0008372 def: "A location, relative to cellular compartments and structures, occupied by a macromolecular machine. There are three types of cellular components described in the gene ontology: (1) the cellular anatomical entity where a gene product carries out a molecular function (e.g., plasma membrane, cytoskeleton) or membrane-enclosed compartments (e.g., mitochondrion); (2) virion components, where viral proteins act, and (3) the stable macromolecular complexes of which gene product are parts (e.g., the clathrin complex)." [GOC:pdt] comment: Note that, in addition to forming the root of the cellular component ontology, this term is recommended for the annotation of gene products whose cellular component is unknown. When this term is used for annotation, it indicates that no information was available about the cellular component of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this. subset: goslim_candida @@ -4045,7 +4323,7 @@ subset: goslim_prokaryote_ribbon subset: goslim_yeast synonym: "extracellular" EXACT [] xref: Wikipedia:Extracellular -is_a: GO:0110165 ! cellular anatomical entity +is_a: GO:0110165 ! cellular anatomical structure [Term] id: GO:0005577 @@ -4082,8 +4360,6 @@ is_a: GO:0098651 ! basement membrane collagen trimer id: GO:0005604 name: basement membrane namespace: cellular_component -alt_id: GO:0005605 -alt_id: GO:0008003 def: "A collagen-containing extracellular matrix consisting of a thin layer of dense material found in various animal tissues interposed between the cells and the adjacent connective tissue. It consists of the basal lamina plus an associated layer of reticulin fibers." [ISBN:0198547684, PMID:22505934] comment: Note that this term has no relationship to 'membrane ; GO:0016020' because the basement membrane is not a lipid bilayer. synonym: "basal lamina" RELATED [] @@ -4103,7 +4379,7 @@ subset: goslim_drosophila subset: goslim_generic synonym: "intercellular space" RELATED [] xref: NIF_Subcellular:sao1425028079 -is_a: GO:0110165 ! cellular anatomical entity +is_a: GO:0110165 ! cellular anatomical structure relationship: part_of GO:0005576 ! extracellular region [Term] @@ -4121,7 +4397,7 @@ synonym: "nucleocytoplasm" RELATED [GOC:mah] synonym: "protoplasm" EXACT [] synonym: "protoplast" RELATED [GOC:mah] xref: Wikipedia:Intracellular -is_a: GO:0110165 ! cellular anatomical entity +is_a: GO:0110165 ! cellular anatomical structure relationship: part_of CL:0000000 ! cell property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/17776" xsd:anyURI @@ -4173,7 +4449,7 @@ synonym: "chromatid" RELATED [] synonym: "interphase chromosome" NARROW [] synonym: "prophase chromosome" NARROW [] xref: Wikipedia:Chromosome -is_a: GO:0043232 ! intracellular non-membrane-bounded organelle +is_a: GO:0043232 ! intracellular membraneless organelle [Term] id: GO:0005730 @@ -4189,7 +4465,7 @@ subset: goslim_plant subset: goslim_yeast xref: NIF_Subcellular:sao1820400233 xref: Wikipedia:Nucleolus -is_a: GO:0043232 ! intracellular non-membrane-bounded organelle +is_a: GO:0043232 ! intracellular membraneless organelle relationship: part_of GO:0031981 ! nuclear lumen [Term] @@ -4207,7 +4483,7 @@ subset: goslim_prokaryote subset: goslim_prokaryote_ribbon subset: goslim_yeast xref: Wikipedia:Cytoplasm -is_a: GO:0110165 ! cellular anatomical entity +is_a: GO:0110165 ! cellular anatomical structure relationship: part_of GO:0005622 ! intracellular anatomical structure property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/23023" xsd:anyURI @@ -4286,7 +4562,6 @@ relationship: RO:0002162 NCBITaxon:2759 {all_only="true"} ! in taxon Eukaryota id: GO:0005840 name: ribosome namespace: cellular_component -alt_id: GO:0033279 def: "An intracellular organelle, about 200 A in diameter, consisting of RNA and protein. It is the site of protein biosynthesis resulting from translation of messenger RNA (mRNA). It consists of two subunits, one large and one small, each containing only protein and RNA. Both the ribosome and its subunits are characterized by their sedimentation coefficients, expressed in Svedberg units (symbol: S). Hence, the prokaryotic ribosome (70S) comprises a large (50S) subunit and a small (30S) subunit, while the eukaryotic ribosome (80S) comprises a large (60S) subunit and a small (40S) subunit. Two sites on the ribosomal large subunit are involved in translation, namely the aminoacyl site (A site) and peptidyl site (P site). Ribosomes from prokaryotes, eukaryotes, mitochondria, and chloroplasts have characteristically distinct ribosomal proteins." [ISBN:0198506732] subset: goslim_candida subset: goslim_chembl @@ -4304,16 +4579,14 @@ synonym: "membrane bound ribosome" NARROW [NIF_Subcellular:sao1291545653] synonym: "ribosomal RNA" RELATED [] xref: NIF_Subcellular:sao1429207766 xref: Wikipedia:Ribosome -is_a: GO:0043232 ! intracellular non-membrane-bounded organelle -is_a: PR:000050567 ! protein-containing material entity +is_a: GO:0043232 ! intracellular membraneless organelle relationship: capable_of_part_of GO:0006412 ! translation +relationship: has_part PR:000000001 ! protein [Term] id: GO:0005886 name: plasma membrane namespace: cellular_component -alt_id: GO:0005887 -alt_id: GO:0005904 def: "The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins." [ISBN:0716731363] subset: goslim_agr subset: goslim_candida @@ -4359,7 +4632,6 @@ property_value: term_tracker_item "https://github.com/geneontology/go-ontology/i id: GO:0006259 name: DNA metabolic process namespace: biological_process -alt_id: GO:0055132 def: "Any cellular metabolic process involving deoxyribonucleic acid. This is one of the two main types of nucleic acid, consisting of a long, unbranched macromolecule formed from one, or more commonly, two, strands of linked deoxyribonucleotides." [ISBN:0198506732] subset: goslim_agr subset: goslim_candida @@ -4391,9 +4663,6 @@ is_a: GO:0006259 ! DNA metabolic process id: GO:0006412 name: translation namespace: biological_process -alt_id: GO:0006416 -alt_id: GO:0006453 -alt_id: GO:0043037 def: "The cellular metabolic process in which a protein is formed, using the sequence of a mature mRNA or circRNA molecule to specify the sequence of amino acids in a polypeptide chain. Translation is mediated by the ribosome, and begins with the formation of a ternary complex between aminoacylated initiator methionine tRNA, GTP, and initiation factor 2, which subsequently associates with the small subunit of the ribosome and an mRNA or circRNA. Translation ends with the release of a polypeptide chain from the ribosome." [GOC:go_curators] subset: goslim_candida subset: goslim_chembl @@ -4422,15 +4691,13 @@ relationship: starts_with GO:0006413 ! translational initiation id: GO:0006413 name: translational initiation namespace: biological_process -alt_id: GO:0006440 -alt_id: GO:0006454 def: "The process preceding formation of the peptide bond between the first two amino acids of a protein. This includes the formation of a complex of the ribosome, mRNA or circRNA, and an initiation complex that contains the first aminoacyl-tRNA." [ISBN:019879276X] subset: goslim_yeast synonym: "biopolymerisation" BROAD [] synonym: "biopolymerization" BROAD [] synonym: "protein synthesis initiation" BROAD [] synonym: "translation initiation" EXACT [] -is_a: GO:0044237 ! cellular metabolic process +is_a: GO:0008152 ! metabolic process relationship: part_of GO:0006412 ! translation relationship: starts_with GO:0001677 ! formation of translation initiation ternary complex @@ -4438,8 +4705,6 @@ relationship: starts_with GO:0001677 ! formation of translation initiation terna id: GO:0006414 name: translational elongation namespace: biological_process -alt_id: GO:0006442 -alt_id: GO:0006455 def: "The successive addition of amino acid residues to a nascent polypeptide chain during protein biosynthesis." [GOC:ems] subset: goslim_yeast synonym: "protein synthesis elongation" BROAD [] @@ -4451,8 +4716,6 @@ relationship: part_of GO:0006412 ! translation id: GO:0006415 name: translational termination namespace: biological_process -alt_id: GO:0006443 -alt_id: GO:0006456 def: "The process resulting in the release of a polypeptide chain from the ribosome, usually in response to a termination codon (UAA, UAG, or UGA in the universal genetic code)." [GOC:hjd, ISBN:019879276X] synonym: "protein synthesis termination" BROAD [] synonym: "translation termination" EXACT [] @@ -4464,9 +4727,6 @@ relationship: part_of GO:0006412 ! translation id: GO:0006810 name: transport namespace: biological_process -alt_id: GO:0015457 -alt_id: GO:0015460 -alt_id: GO:0044765 def: "The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter or a transporter complex, a pore or a motor protein." [GOC:dos, GOC:dph, GOC:jl, GOC:mah] comment: Note that this term should not be used for direct annotation. It should be possible to make a more specific annotation to one of the children of this term, for e.g. to transmembrane transport, to microtubule-based transport or to vesicle-mediated transport. subset: gocheck_do_not_annotate @@ -4481,7 +4741,6 @@ subset: goslim_prokaryote_ribbon synonym: "single-organism transport" RELATED [] is_a: GO:0051234 ! establishment of localization property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/20292" xsd:anyURI -created_by: jl creation_date: 2012-12-13T16:25:32Z [Term] @@ -4506,8 +4765,6 @@ is_a: GO:0006810 ! transport id: GO:0006887 name: exocytosis namespace: biological_process -alt_id: GO:0016194 -alt_id: GO:0016195 def: "A process of secretion by a cell that results in the release of intracellular molecules (e.g. hormones, matrix proteins) contained within a membrane-bounded vesicle. Exocytosis can occur either by full fusion, when the vesicle collapses into the plasma membrane, or by a kiss-and-run mechanism that involves the formation of a transient contact, a pore, between a granule (for example of chromaffin cells) and the plasma membrane. The latter process most of the time leads to only partial secretion of the granule content. Exocytosis begins with steps that prepare vesicles for fusion with the membrane (tethering and docking) and ends when molecules are secreted from the cell." [GOC:mah, ISBN:0716731363, PMID:22323285] subset: goslim_yeast synonym: "nonselective vesicle exocytosis" RELATED [] @@ -4524,9 +4781,6 @@ relationship: process_has_causal_agent GO:0070382 ! exocytic vesicle id: GO:0006897 name: endocytosis namespace: biological_process -alt_id: GO:0016193 -alt_id: GO:0016196 -alt_id: GO:0098701 def: "A vesicle-mediated transport process in which cells take up external materials or membrane constituents by the invagination of a part of the plasma membrane to form a new membrane-bounded vesicle." [GOC:mah, ISBN:0198506732, ISBN:0716731363, Wikipedia:Endocytosis] subset: goslim_yeast synonym: "endocytic import into cell" EXACT [] @@ -4546,8 +4800,6 @@ property_value: term_tracker_item "https://github.com/geneontology/go-ontology/i id: GO:0006900 name: vesicle budding from membrane namespace: biological_process -alt_id: GO:0006902 -alt_id: GO:1902591 def: "The evagination of a membrane, resulting in formation of a vesicle." [GOC:jid, GOC:tb] synonym: "membrane evagination" EXACT [] synonym: "nonselective vesicle assembly" RELATED [] @@ -4559,7 +4811,6 @@ synonym: "vesicle formation" EXACT [] is_a: GO:0016050 ! vesicle organization is_a: GO:0061024 ! membrane organization relationship: part_of GO:0016192 ! vesicle-mediated transport -created_by: jl creation_date: 2013-12-19T15:26:17Z [Term] @@ -4588,8 +4839,6 @@ property_value: term_tracker_item "https://github.com/geneontology/go-ontology/i id: GO:0006915 name: apoptotic process namespace: biological_process -alt_id: GO:0006917 -alt_id: GO:0008632 def: "A programmed cell death process which begins when a cell receives an internal (e.g. DNA damage) or external signal (e.g. an extracellular death ligand), and proceeds through a series of biochemical events (signaling pathway phase) which trigger an execution phase. The execution phase is the last step of an apoptotic process, and is typically characterized by rounding-up of the cell, retraction of pseudopodes, reduction of cellular volume (pyknosis), chromatin condensation, nuclear fragmentation (karyorrhexis), plasma membrane blebbing and fragmentation of the cell into apoptotic bodies. When the execution phase is completed, the cell has died." [GOC:cjm, GOC:dhl, GOC:ecd, GOC:go_curators, GOC:mtg_apoptosis, GOC:tb, ISBN:0198506732, PMID:18846107, PMID:21494263] synonym: "activation of apoptosis" NARROW [] synonym: "apoptosis" NARROW [] @@ -4681,8 +4930,6 @@ property_value: term_tracker_item "https://github.com/geneontology/go-ontology/i id: GO:0006952 name: defense response namespace: biological_process -alt_id: GO:0002217 -alt_id: GO:0042829 def: "Reactions, triggered in response to the presence of a foreign body or the occurrence of an injury, which result in restriction of damage to the organism attacked or prevention/recovery from the infection caused by the attack." [GOC:go_curators] synonym: "antimicrobial peptide activity" RELATED [] synonym: "defence response" EXACT [] @@ -4715,7 +4962,6 @@ is_a: GO:0050896 ! response to stimulus id: GO:0006996 name: organelle organization namespace: biological_process -alt_id: GO:1902589 def: "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of an organelle within a cell. An organelle is an organized structure of distinctive morphology and function. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton. Excludes the plasma membrane." [GOC:mah] comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. subset: gocheck_do_not_annotate @@ -4730,7 +4976,6 @@ intersection_of: GO:0016043 ! cellular component organization intersection_of: results_in_organization_of GO:0043226 ! organelle relationship: results_in_organization_of GO:0043226 ! organelle property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27189" xsd:anyURI -created_by: jl creation_date: 2013-12-19T15:25:51Z [Term] @@ -4788,11 +5033,6 @@ is_a: GO:0009987 ! cellular process id: GO:0007165 name: signal transduction namespace: biological_process -alt_id: GO:0023014 -alt_id: GO:0023015 -alt_id: GO:0023016 -alt_id: GO:0023033 -alt_id: GO:0023045 def: "The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell." [GOC:go_curators, GOC:mtg_signaling_feb11] comment: Note that signal transduction is defined broadly to include a ligand interacting with a receptor, downstream signaling steps and a response being triggered. A change in form of the signal in every step is not necessary. Note that in many cases the end of this process is regulation of the initiation of transcription. Note that specific transcription factors may be annotated to this term, but core/general transcription machinery such as RNA polymerase should not. subset: goslim_candida @@ -4815,7 +5055,6 @@ relationship: part_of GO:0051716 ! cellular response to stimulus id: GO:0007186 name: G protein-coupled receptor signaling pathway namespace: biological_process -alt_id: GO:0038042 def: "The series of molecular signals initiated by a ligand binding to its receptor, in which the activated receptor promotes the exchange of GDP for GTP on the alpha-subunit of an associated heterotrimeric G-protein complex. The GTP-bound activated alpha-G-protein then dissociates from the beta- and gamma-subunits to further transmit the signal within the cell. The pathway begins with receptor-ligand interaction, and ends with regulation of a downstream cellular process. The pathway can start from the plasma membrane, Golgi or nuclear membrane." [GOC:bf, GOC:mah, PMID:16902576, PMID:24568158, Wikipedia:G_protein-coupled_receptor] subset: goslim_drosophila synonym: "dimeric G-protein coupled receptor signaling pathway" NARROW [] @@ -4965,7 +5204,6 @@ is_a: GO:0050878 ! regulation of body fluid levels id: GO:0008015 name: blood circulation namespace: biological_process -alt_id: GO:0070261 def: "The flow of blood through the body of an animal, enabling the transport of nutrients to the tissues and the removal of waste products." [GOC:mtg_heart, ISBN:0192800825] subset: goslim_pir synonym: "hemolymph circulation" RELATED [] @@ -4975,9 +5213,6 @@ is_a: GO:0003013 ! circulatory system process id: GO:0008150 name: biological_process namespace: biological_process -alt_id: GO:0000004 -alt_id: GO:0007582 -alt_id: GO:0044699 def: "A biological process is the execution of a genetically-encoded biological module or program. It consists of all the steps required to achieve the specific biological objective of the module. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence." [GOC:pdt] comment: Note that, in addition to forming the root of the biological process ontology, this term is recommended for the annotation of gene products whose biological process is unknown. When this term is used for annotation, it indicates that no information was available about the biological process of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this. subset: goslim_candida @@ -4993,16 +5228,13 @@ synonym: "single organism process" RELATED [] synonym: "single-organism process" RELATED [] xref: Wikipedia:Biological_process property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/24968" xsd:anyURI -created_by: jl creation_date: 2012-09-19T15:05:24Z [Term] id: GO:0008152 name: metabolic process namespace: biological_process -alt_id: GO:0044236 -alt_id: GO:0044710 -def: "The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation." [GOC:go_curators, ISBN:0198547684] +def: "A cellular process consisting of the biochemical pathways by which a living organism transforms chemical substances. This includes including anabolism (biosynthetic process) and catabolism (catabolic process). Metabolic processes includes the transformation of small molecules, as well macromolecular processes such as DNA repair and replication, protein synthesis and degradation." [GOC:go_curators, ISBN:0198547684] comment: Note that metabolic processes do not include single functions or processes such as protein-protein interactions, protein-nucleic acids, nor receptor-ligand interactions. subset: gocheck_do_not_annotate subset: goslim_chembl @@ -5011,16 +5243,12 @@ subset: goslim_metagenomics subset: goslim_pir subset: goslim_plant subset: goslim_prokaryote_ribbon -synonym: "metabolic process resulting in cell growth" NARROW [] synonym: "metabolism" EXACT [] -synonym: "metabolism resulting in cell growth" NARROW [] -synonym: "multicellular organism metabolic process" NARROW [] -synonym: "single-organism metabolic process" RELATED [] xref: Wikipedia:Metabolism -is_a: GO:0008150 ! biological_process +is_a: GO:0009987 ! cellular process disjoint_from: GO:0051179 ! localization property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/26424" xsd:anyURI -created_by: jl +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28932" xsd:anyURI creation_date: 2012-10-17T15:46:40Z [Term] @@ -5039,9 +5267,7 @@ property_value: term_tracker_item "https://github.com/geneontology/go-ontology/i id: GO:0009058 name: biosynthetic process namespace: biological_process -alt_id: GO:0044274 -alt_id: GO:0044711 -def: "The chemical reactions and pathways resulting in the formation of substances; typically the energy-requiring part of metabolism in which simpler substances are transformed into more complex ones." [GOC:curators, ISBN:0198547684] +def: "A cellular process consisting of the biochemical pathways by which a living organism synthesizes chemical substances. This typically represents the energy-requiring part of metabolism in which simpler substances are transformed into more complex ones." [GOC:curators, ISBN:0198547684] subset: goslim_chembl subset: goslim_metagenomics subset: goslim_plant @@ -5054,14 +5280,13 @@ synonym: "single-organism biosynthetic process" RELATED [] synonym: "synthesis" EXACT [] xref: Wikipedia:Anabolism is_a: GO:0008152 ! metabolic process -created_by: jl +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28932" xsd:anyURI creation_date: 2012-10-17T15:52:18Z [Term] id: GO:0009059 name: macromolecule biosynthetic process namespace: biological_process -alt_id: GO:0043284 def: "The chemical reactions and pathways resulting in the formation of a macromolecule, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass." [GOC:mah] comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. subset: gocheck_do_not_annotate @@ -5071,8 +5296,8 @@ synonym: "macromolecule anabolism" EXACT [] synonym: "macromolecule biosynthesis" EXACT [] synonym: "macromolecule formation" EXACT [] synonym: "macromolecule synthesis" EXACT [] +is_a: GO:0009058 ! biosynthetic process is_a: GO:0043170 ! macromolecule metabolic process -is_a: GO:0044249 ! cellular biosynthetic process property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/15249" xsd:anyURI property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/25418" xsd:anyURI property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27189" xsd:anyURI @@ -5105,7 +5330,6 @@ is_a: GO:0050896 ! response to stimulus id: GO:0009611 name: response to wounding namespace: biological_process -alt_id: GO:0002245 def: "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to the organism." [GOC:go_curators] synonym: "physiological response to wounding" EXACT [] is_a: GO:0006950 ! response to stress @@ -5127,7 +5351,6 @@ relationship: part_of GO:0048856 ! anatomical structure development id: GO:0009790 name: embryo development namespace: biological_process -alt_id: GO:0009795 def: "The process whose specific outcome is the progression of an embryo from its formation until the end of its embryonic life stage. The end of the embryonic stage is organism-specific. For example, for mammals, the process would begin with zygote formation and end with birth. For insects, the process would begin at zygote formation and end with larval hatching. For plant zygotic embryos, this would be from zygote formation to the end of seed dormancy. For plant vegetative embryos, this would be from the initial determination of the cell or group of cells to form an embryo until the point when the embryo becomes independent of the parent plant." [GOC:go_curators, GOC:isa_complete, GOC:mtg_sensu] subset: gocheck_do_not_annotate subset: goslim_chembl @@ -5184,9 +5407,6 @@ property_value: RO:0002161 NCBITaxon:4891 id: GO:0009987 name: cellular process namespace: biological_process -alt_id: GO:0008151 -alt_id: GO:0044763 -alt_id: GO:0050875 def: "Any process that is carried out at the cellular level, but not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level." [GOC:go_curators, GOC:isa_complete] comment: This term should not be used for direct annotation. It should be possible to make a more specific annotation to one of the children of this term. subset: gocheck_do_not_annotate @@ -5196,7 +5416,6 @@ synonym: "cell physiology" EXACT [] synonym: "cellular physiological process" EXACT [] synonym: "single-organism cellular process" RELATED [] is_a: GO:0008150 ! biological_process -created_by: jl creation_date: 2012-12-11T16:56:55Z [Term] @@ -5216,12 +5435,10 @@ relationship: results_in_organization_of GO:0012505 ! endomembrane system id: GO:0010324 name: membrane invagination namespace: biological_process -alt_id: GO:1902534 def: "The infolding of a membrane." [GOC:tb] subset: goslim_yeast synonym: "single-organism membrane invagination" RELATED [] is_a: GO:0061024 ! membrane organization -created_by: jl creation_date: 2013-12-02T13:58:34Z [Term] @@ -5239,7 +5456,6 @@ property_value: term_tracker_item "https://github.com/geneontology/go-ontology/i id: GO:0012501 name: programmed cell death namespace: biological_process -alt_id: GO:0016244 def: "A process which begins when a cell receives an internal or external signal and activates a series of biochemical events (signaling pathway). The process ends with the death of the cell." [GOC:lr, GOC:mtg_apoptosis] comment: Note that this term should be used to annotate gene products in the organism undergoing the programmed cell death. To annotate genes in another organism whose products modulate programmed cell death in a host organism, consider the term 'modulation by symbiont of host programmed cell death ; GO:0052040'. Also, note that 'programmed cell death ; GO:0012501' should be used to refer to instances of caspase-independent cell death mechanisms, in the absence of further indications on the process taking place. At present, caspase-independent cell death is not yet represented in GO due to the lack of consensus and in-depth research on the topic. 'programmed cell death ; GO:0012501' may also be used to annotate gene products in taxa where apoptosis as defined in GO:0006915 does not occur, such as plants. You may also consider these specific children: GO:0097468 'programmed cell death in response to reactive oxygen species' (with descendants GO:0010421 'hydrogen peroxide-mediated programmed cell death' and GO:0010343 'singlet oxygen-mediated programmed cell death'), and GO:0009626 'plant-type hypersensitive response' and its children. subset: goslim_agr @@ -5274,7 +5490,7 @@ subset: goslim_candida subset: goslim_flybase_ribbon subset: goslim_yeast xref: Wikipedia:Endomembrane_system -is_a: GO:0110165 ! cellular anatomical entity +is_a: GO:0110165 ! cellular anatomical structure relationship: has_part GO:0005773 ! vacuole relationship: has_part GO:0005886 ! plasma membrane relationship: part_of CL:0000000 ! cell @@ -5309,9 +5525,6 @@ is_a: GO:0015669 ! gas transport id: GO:0016020 name: membrane namespace: cellular_component -alt_id: GO:0016021 -alt_id: GO:0098589 -alt_id: GO:0098805 def: "A lipid bilayer along with all the proteins and protein complexes embedded in it and attached to it." [GOC:dos, GOC:mah, ISBN:0815316194] subset: goslim_candida subset: goslim_chembl @@ -5328,7 +5541,7 @@ synonym: "transmembrane" RELATED [GOC:mah] synonym: "whole membrane" NARROW [] xref: Wikipedia:Biological_membrane xref: Wikipedia:Transmembrane_protein -is_a: GO:0110165 ! cellular anatomical entity +is_a: GO:0110165 ! cellular anatomical structure disjoint_from: GO:0031012 ! extracellular matrix creation_date: 2014-03-06T11:37:54Z @@ -5336,8 +5549,6 @@ creation_date: 2014-03-06T11:37:54Z id: GO:0016043 name: cellular component organization namespace: biological_process -alt_id: GO:0044235 -alt_id: GO:0071842 def: "A process that results in the assembly, arrangement of constituent parts, or disassembly of a cellular component." [GOC:ai, GOC:jl, GOC:mah] subset: gocheck_do_not_annotate subset: goslim_agr @@ -5382,7 +5593,6 @@ is_a: GO:0019724 ! B cell mediated immunity id: GO:0016192 name: vesicle-mediated transport namespace: biological_process -alt_id: GO:0006899 def: "A cellular transport process in which transported substances are moved in membrane-bounded vesicles; transported substances are enclosed in the vesicle lumen or located in the vesicle membrane. The process begins with a step that directs a substance to the forming vesicle, and includes vesicle budding and coating. Vesicles are then targeted to, and fuse with, an acceptor membrane." [GOC:ai, GOC:mah, ISBN:08789310662000] subset: goslim_candida subset: goslim_chembl @@ -5477,9 +5687,6 @@ relationship: part_of GO:0007154 ! cell communication id: GO:0019538 name: protein metabolic process namespace: biological_process -alt_id: GO:0006411 -alt_id: GO:0044267 -alt_id: GO:0044268 def: "The chemical reactions and pathways involving a protein. Includes protein modification." [GOC:ma] comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. subset: gocheck_do_not_annotate @@ -5534,7 +5741,6 @@ is_a: GO:0032991 ! protein-containing complex id: GO:0019815 name: B cell receptor complex namespace: cellular_component -alt_id: GO:0042570 def: "An immunoglobulin complex that is present in the plasma membrane of B cells and that in its canonical form is composed of two identical immunoglobulin heavy chains and two identical immunoglobulin light chains and a signaling subunit, a heterodimer of the Ig-alpha and Ig-beta proteins." [GOC:add, ISBN:0781735149] comment: Note that an immunoglobulin complex has the function of antigen binding if a suitable antigen is available. synonym: "antibody" RELATED [GOC:mah] @@ -5551,7 +5757,6 @@ is_a: GO:0098802 ! plasma membrane signaling receptor complex id: GO:0019882 name: antigen processing and presentation namespace: biological_process -alt_id: GO:0030333 def: "The process in which an antigen-presenting cell expresses antigen (peptide or lipid) on its cell surface in association with an MHC protein complex." [GO_REF:0000022, GOC:add, ISBN:0781735149, PMID:15771591, PMID:15928678] synonym: "antigen presentation" EXACT [] synonym: "antigen processing" EXACT [] @@ -5587,7 +5792,6 @@ relationship: part_of GO:0007049 ! cell cycle id: GO:0022411 name: cellular component disassembly namespace: biological_process -alt_id: GO:0071845 def: "A cellular process that results in the breakdown of a cellular component." [GOC:isa_complete] comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. subset: gocheck_do_not_annotate @@ -5616,7 +5820,6 @@ relationship: part_of GO:0007586 ! digestion id: GO:0022607 name: cellular component assembly namespace: biological_process -alt_id: GO:0071844 def: "The aggregation, arrangement and bonding together of a cellular component." [GOC:isa_complete] subset: goslim_chembl subset: goslim_euk_cellular_processes_ribbon @@ -5658,8 +5861,6 @@ relationship: results_in_assembly_of GO:1990904 ! ribonucleoprotein complex id: GO:0023052 name: signaling namespace: biological_process -alt_id: GO:0023046 -alt_id: GO:0044700 def: "The entirety of a process in which information is transmitted within a biological system. This process begins with an active signal and ends when a cellular response has been triggered." [GOC:mtg_signal, GOC:mtg_signaling_feb11, GOC:signaling] comment: Note that a signal is any variable property or parameter that serves to convey information, and may be a physical entity such as a gene product or small molecule, a photon, or a change in state such as movement or voltage change. subset: goslim_agr @@ -5677,7 +5878,6 @@ synonym: "signalling" EXACT [] synonym: "signalling process" RELATED [GOC:mah] synonym: "single organism signaling" RELATED [] is_a: GO:0050789 ! regulation of biological process -created_by: jl creation_date: 2010-02-16T09:30:50Z [Term] @@ -5729,7 +5929,7 @@ subset: goslim_agr subset: goslim_drosophila subset: goslim_flybase_ribbon xref: Wikipedia:Cell_junction -is_a: GO:0110165 ! cellular anatomical entity +is_a: GO:0110165 ! cellular anatomical structure property_value: RO:0002161 NCBITaxon:4751 [Term] @@ -5754,7 +5954,6 @@ property_value: term_tracker_item "https://github.com/geneontology/go-ontology/i id: GO:0030098 name: lymphocyte differentiation namespace: biological_process -alt_id: GO:0046650 def: "The process in which a relatively unspecialized precursor cell acquires specialized features of a lymphocyte. A lymphocyte is a leukocyte commonly found in the blood and lymph that has the characteristics of a large nucleus, a neutral staining cytoplasm, and prominent heterochromatin." [CL:0000542, GOC:go_curators] comment: Note that immunologists typically use the word 'development' to refer to cells of B or T cell lineages undergoing the process that GO describes as 'cell differentiation'. synonym: "lymphocyte cell differentiation" EXACT [] @@ -5825,7 +6024,6 @@ property_value: term_tracker_item "https://github.com/geneontology/go-ontology/i id: GO:0030183 name: B cell differentiation namespace: biological_process -alt_id: GO:0042115 def: "The process in which a precursor cell type acquires the specialized features of a B cell. A B cell is a lymphocyte of B lineage with the phenotype CD19-positive and capable of B cell mediated immunity." [GO_REF:0000022, GOC:mah] comment: Note that immunologists typically use the word 'development' to refer to cells of B or T cell lineages undergoing the process that GO describes as 'cell differentiation'. synonym: "B cell development" RELATED [GOC:add] @@ -5864,8 +6062,6 @@ is_a: GO:0030202 ! heparin metabolic process id: GO:0030217 name: T cell differentiation namespace: biological_process -alt_id: GO:0042112 -alt_id: GO:0046652 def: "The process in which a precursor cell type acquires characteristics of a more mature T-cell. A T cell is a type of lymphocyte whose definin characteristic is the expression of a T cell receptor complex." [GO_REF:0000022, GOC:jid, GOC:mah] comment: Note that the term 'thymocyte differentiation' was merged into this term because thymocytes are T cells, and thus the term was essentially redundant. Note that immunologists typically use the word 'development' to refer to cells of B or T cell lineages undergoing the process that GO describes as 'cell differentiation'. synonym: "T cell development" RELATED [GOC:add] @@ -5944,7 +6140,6 @@ relationship: results_in_acquisition_of_features_of CL:0000235 ! macrophage id: GO:0030261 name: chromosome condensation namespace: biological_process -alt_id: GO:0000068 def: "The progressive compaction of dispersed interphase chromatin into threadlike chromosomes prior to mitotic or meiotic nuclear division, or during apoptosis, in eukaryotic cells." [GOC:mah, ISBN:0815316194] synonym: "DNA condensation" BROAD [Wikipedia:DNA_condensation] synonym: "eukaryotic chromosome condensation" EXACT [GOC:bf] @@ -5980,7 +6175,7 @@ subset: goslim_drosophila subset: goslim_generic subset: goslim_pir subset: goslim_plant -is_a: GO:0110165 ! cellular anatomical entity +is_a: GO:0110165 ! cellular anatomical structure relationship: part_of CL:0000000 ! cell relationship: part_of GO:0071944 ! cell periphery @@ -6049,7 +6244,6 @@ relationship: results_in_acquisition_of_features_of CL:0000094 ! granulocyte id: GO:0031012 name: extracellular matrix namespace: cellular_component -alt_id: GO:0005578 def: "A structure lying external to one or more cells, which provides structural support, biochemical or biomechanical cues for cells or tissues." [GOC:BHF, GOC:mah, GOC:rph, NIF_Subcellular:nlx_subcell_20090513, PMID:21123617, PMID:28089324] subset: goslim_chembl subset: goslim_drosophila @@ -6117,7 +6311,6 @@ relationship: results_in_organization_of GO:0031143 ! pseudopodium id: GO:0031410 name: cytoplasmic vesicle namespace: cellular_component -alt_id: GO:0016023 def: "A vesicle found in the cytoplasm of a cell." [GOC:ai, GOC:mah, GOC:vesicles] subset: goslim_agr subset: goslim_candida @@ -6139,7 +6332,7 @@ id: GO:0031974 name: membrane-enclosed lumen namespace: cellular_component def: "The enclosed volume within a sealed membrane or between two sealed membranes. Encompasses the volume enclosed by the membranes of a particular organelle, e.g. endoplasmic reticulum lumen, or the space between the two lipid bilayers of a double membrane surrounding an organelle, e.g. nuclear envelope lumen." [GOC:add, GOC:mah] -is_a: GO:0110165 ! cellular anatomical entity +is_a: GO:0110165 ! cellular anatomical structure disjoint_from: GO:0045202 ! synapse [Term] @@ -6154,7 +6347,6 @@ relationship: part_of GO:0005634 ! nucleus id: GO:0031982 name: vesicle namespace: cellular_component -alt_id: GO:0031988 def: "Any small, fluid-filled, spherical organelle enclosed by membrane." [GOC:mah, GOC:pz, GOC:vesicles] subset: goslim_pir synonym: "membrane-bounded vesicle" RELATED [] @@ -6222,8 +6414,6 @@ relationship: positively_regulates GO:0009605 ! response to external stimulus id: GO:0032501 name: multicellular organismal process namespace: biological_process -alt_id: GO:0044707 -alt_id: GO:0050874 def: "Any biological process, occurring at the level of a multicellular organism, pertinent to its function." [GOC:curators, GOC:dph, GOC:isa_complete, GOC:tb] comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. subset: gocheck_do_not_annotate @@ -6236,14 +6426,12 @@ property_value: RO:0002161 NCBITaxon:2157 property_value: RO:0002161 NCBITaxon:4896 property_value: RO:0002161 NCBITaxon:4932 property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27189" xsd:anyURI -created_by: jl creation_date: 2012-09-19T16:07:47Z [Term] id: GO:0032502 name: developmental process namespace: biological_process -alt_id: GO:0044767 def: "A biological process whose specific outcome is the progression of an integrated living unit: an anatomical structure (which may be a subcellular structure, cell, tissue, or organ), or organism over time from an initial condition to a later condition." [GOC:isa_complete] subset: goslim_agr subset: goslim_flybase_ribbon @@ -6251,15 +6439,12 @@ subset: goslim_pir synonym: "development" NARROW [] synonym: "single-organism developmental process" RELATED [] is_a: GO:0008150 ! biological_process -created_by: jl creation_date: 2012-12-19T12:21:31Z [Term] id: GO:0032606 name: type I interferon production namespace: biological_process -alt_id: GO:0045351 -alt_id: GO:0072641 def: "The appearance of type I interferon due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. Type I interferons include the interferon-alpha, beta, delta, episilon, zeta, kappa, tau, and omega gene families." [GOC:add, ISBN:0126896631, PMID:15546383, PMID:16681834] comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select one of the 'regulation' children terms. subset: gocheck_do_not_annotate @@ -6283,9 +6468,6 @@ is_a: GO:0140352 ! export from cell id: GO:0032984 name: protein-containing complex disassembly namespace: biological_process -alt_id: GO:0034623 -alt_id: GO:0043241 -alt_id: GO:0043624 def: "The disaggregation of a protein-containing macromolecular complex into its constituent components." [GOC:mah] synonym: "cellular macromolecule complex disassembly" RELATED [] synonym: "cellular protein complex disassembly" RELATED [] @@ -6302,7 +6484,6 @@ property_value: term_tracker_item "https://github.com/geneontology/go-ontology/i id: GO:0032991 name: protein-containing complex namespace: cellular_component -alt_id: GO:0043234 def: "A stable assembly of two or more macromolecules, i.e. proteins, nucleic acids, carbohydrates or lipids, in which at least one component is a protein and the constituent parts function together." [GOC:dos, GOC:mah] comment: A protein complex in this context is meant as a stable set of interacting proteins which can be co-purified by an acceptable method, and where the complex has been shown to exist as an isolated, functional unit in vivo. Acceptable experimental methods include stringent protein purification followed by detection of protein interaction. The following methods should be considered non-acceptable: simple immunoprecipitation, pull-down experiments from cell extracts without further purification, colocalization and 2-hybrid screening. Interactions that should not be captured as protein complexes include: 1) enzyme/substrate, receptor/ligand or any similar transient interactions, unless these are a critical part of the complex assembly or are required e.g. for the receptor to be functional; 2) proteins associated in a pull-down/co-immunoprecipitation assay with no functional link or any evidence that this is a defined biological entity rather than a loose-affinity complex; 3) any complex where the only evidence is based on genetic interaction data; 4) partial complexes, where some subunits (e.g. transmembrane ones) cannot be expressed as recombinant proteins and are excluded from experiments (in this case, independent evidence is necessary to find out the composition of the full complex, if known). Interactions that may be captured as protein complexes include: 1) enzyme/substrate or receptor/ligand if the complex can only assemble and become functional in the presence of both classes of subunits; 2) complexes where one of the members has not been shown to be physically linked to the other(s), but is a homologue of, and has the same functionality as, a protein that has been experimentally demonstrated to form a complex with the other member(s); 3) complexes whose existence is accepted based on localization and pharmacological studies, but for which experimental evidence is not yet available for the complex as a whole. subset: goslim_agr @@ -6317,8 +6498,8 @@ synonym: "protein complex" NARROW [] synonym: "protein containing complex" EXACT [] synonym: "protein-protein complex" NARROW [] is_a: GO:0005575 ! cellular_component -is_a: PR:000050567 ! protein-containing material entity -disjoint_from: GO:0110165 ! cellular anatomical entity +disjoint_from: GO:0110165 ! cellular anatomical structure +relationship: has_part PR:000000001 ! protein [Term] id: GO:0033151 @@ -6362,7 +6543,6 @@ relationship: acts_on_population_of CL:0000232 ! erythrocyte id: GO:0034220 name: monoatomic ion transmembrane transport namespace: biological_process -alt_id: GO:0099131 def: "A process in which a monoatomic ion is transported across a membrane. Monatomic ions (also called simple ions) are ions consisting of exactly one atom." [GOC:mah] comment: Note that this term is not intended for use in annotating lateral movement within membranes. synonym: "ATP hydrolysis coupled ion transmembrane transport" NARROW [] @@ -6415,15 +6595,12 @@ def: "An immunoglobulin-like complex that is present in at least the plasma memb comment: Despite its name, the pre-BCR is not a receptor complex, as it appears to provide a low level of signal not dependent on a ligand, but rather simply on correct assembly of the complex as a measure for correct Ig heavy chain recombination and folding. A significant proportion of pre-BCR complexes fail to reach the cell surface, and in some cases may provide their signaling function from the trans-Golgi network or lysosome. synonym: "pre-BCR" EXACT [] is_a: GO:0098796 ! membrane protein complex -created_by: bf creation_date: 2010-03-11T10:46:10Z [Term] id: GO:0038023 name: signaling receptor activity namespace: molecular_function -alt_id: GO:0004872 -alt_id: GO:0019041 def: "Receiving a signal and transmitting it in the cell to initiate a change in cell activity. A signal is a physical entity or change in state that is used to transfer information in order to trigger a response." [GOC:bf, GOC:signaling] subset: goslim_agr subset: goslim_chembl @@ -6438,14 +6615,12 @@ synonym: "receptor activity" BROAD [] synonym: "receptor activity involved in signal transduction" EXACT [GOC:bf] synonym: "signalling receptor activity" EXACT [] is_a: GO:0060089 ! molecular transducer activity -created_by: bf creation_date: 2011-08-01T02:45:27Z [Term] id: GO:0040007 name: growth namespace: biological_process -alt_id: GO:0048590 def: "The increase in size or mass of an entire organism, a part of an organism or a cell." [GOC:bf, GOC:ma] comment: See also the biological process term 'cell growth ; GO:0016049'. subset: gocheck_do_not_annotate @@ -6656,9 +6831,6 @@ property_value: term_tracker_item "https://github.com/geneontology/go-ontology/i id: GO:0042592 name: homeostatic process namespace: biological_process -alt_id: GO:0032844 -alt_id: GO:0032845 -alt_id: GO:0032846 def: "Any biological process involved in the maintenance of an internal steady state." [GOC:jl, ISBN:0395825172] subset: goslim_agr subset: goslim_chembl @@ -6701,7 +6873,7 @@ subset: goslim_prokaryote_ribbon synonym: "cell process" BROAD [] synonym: "cellular process" BROAD [] synonym: "cellular projection" EXACT [] -is_a: GO:0110165 ! cellular anatomical entity +is_a: GO:0110165 ! cellular anatomical structure relationship: part_of CL:0000000 ! cell [Term] @@ -6730,9 +6902,6 @@ relationship: results_in_acquisition_of_features_of CL:0000782 ! myeloid dendrit id: GO:0043170 name: macromolecule metabolic process namespace: biological_process -alt_id: GO:0034960 -alt_id: GO:0043283 -alt_id: GO:0044259 def: "The chemical reactions and pathways involving macromolecules, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass." [GOC:mah] subset: gocheck_do_not_annotate subset: goslim_pir @@ -6763,7 +6932,7 @@ subset: goslim_prokaryote subset: goslim_prokaryote_ribbon xref: NIF_Subcellular:sao1539965131 xref: Wikipedia:Organelle -is_a: GO:0110165 ! cellular anatomical entity +is_a: GO:0110165 ! cellular anatomical structure [Term] id: GO:0043227 @@ -6776,23 +6945,26 @@ xref: NIF_Subcellular:sao414196390 is_a: GO:0043226 ! organelle intersection_of: GO:0043226 ! organelle intersection_of: has_part GO:0016020 ! membrane -disjoint_from: GO:0043228 ! non-membrane-bounded organelle +disjoint_from: GO:0043228 ! membraneless organelle relationship: has_part GO:0016020 ! membrane property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28153" xsd:anyURI [Term] id: GO:0043228 -name: non-membrane-bounded organelle +name: membraneless organelle namespace: cellular_component def: "Organized structure of distinctive morphology and function, not bounded by a lipid bilayer membrane. Includes ribosomes, the cytoskeleton and chromosomes." [GOC:go_curators] subset: gocheck_do_not_annotate subset: goslim_mouse synonym: "biological condensate" RELATED [] +synonym: "membrane-less organelle" EXACT [] +synonym: "non-membrane-bounded organelle" EXACT [] synonym: "non-membrane-enclosed organelle" EXACT [] xref: NIF_Subcellular:sao1456184038 is_a: GO:0043226 ! organelle property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/21881" xsd:anyURI property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28153" xsd:anyURI +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29106" xsd:anyURI [Term] id: GO:0043229 @@ -6833,15 +7005,17 @@ intersection_of: part_of GO:0005622 ! intracellular anatomical structure [Term] id: GO:0043232 -name: intracellular non-membrane-bounded organelle +name: intracellular membraneless organelle namespace: cellular_component def: "Organized structure of distinctive morphology and function, not bounded by a lipid bilayer membrane and occurring within the cell. Includes ribosomes, the cytoskeleton and chromosomes." [GOC:go_curators] subset: goslim_pir +synonym: "intracellular non-membrane-bounded organelle" EXACT [] synonym: "intracellular non-membrane-enclosed organelle" EXACT [] -is_a: GO:0043228 ! non-membrane-bounded organelle +is_a: GO:0043228 ! membraneless organelle is_a: GO:0043229 ! intracellular organelle -intersection_of: GO:0043228 ! non-membrane-bounded organelle +intersection_of: GO:0043228 ! membraneless organelle intersection_of: part_of GO:0005622 ! intracellular anatomical structure +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29106" xsd:anyURI [Term] id: GO:0043233 @@ -6869,9 +7043,6 @@ relationship: capable_of GO:0038023 ! signaling receptor activity id: GO:0043933 name: protein-containing complex organization namespace: biological_process -alt_id: GO:0034600 -alt_id: GO:0034621 -alt_id: GO:0071822 def: "Any process in which macromolecules aggregate, disaggregate, or are modified, resulting in the formation, disassembly, or alteration of a protein complex." [GOC:mah] synonym: "cellular macromolecular complex organization" RELATED [] synonym: "cellular macromolecular complex subunit organisation" RELATED [] @@ -6887,14 +7058,12 @@ intersection_of: GO:0016043 ! cellular component organization intersection_of: results_in_organization_of GO:0032991 ! protein-containing complex relationship: results_in_organization_of GO:0032991 ! protein-containing complex property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/22580" xsd:anyURI -created_by: mah creation_date: 2010-09-08T10:01:42Z [Term] id: GO:0044085 name: cellular component biogenesis namespace: biological_process -alt_id: GO:0071843 def: "A process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of a cellular component. Includes biosynthesis of constituent macromolecules, and those macromolecular modifications that are involved in synthesis or assembly of the cellular component." [GOC:jl, GOC:mah] subset: gocheck_do_not_annotate subset: goslim_pir @@ -6911,21 +7080,8 @@ synonym: "Met-tRNA/eIF2.GTP ternary complex" NARROW [] synonym: "translation initiation (ternary) complex" EXACT [] is_a: GO:1990904 ! ribonucleoprotein complex relationship: part_of GO:0005737 ! cytoplasm -created_by: jl creation_date: 2009-10-22T02:38:55Z -[Term] -id: GO:0044237 -name: cellular metabolic process -namespace: biological_process -def: "The chemical reactions and pathways by which individual cells transform chemical substances." [GOC:go_curators] -comment: This term should not be used for direct annotation. It should be possible to make a more specific annotation to one of the children of this term. -subset: gocheck_do_not_annotate -synonym: "cellular metabolism" EXACT [] -synonym: "intermediary metabolism" RELATED [GOC:mah] -is_a: GO:0008152 ! metabolic process -is_a: GO:0009987 ! cellular process - [Term] id: GO:0044238 name: primary metabolic process @@ -6941,21 +7097,6 @@ xref: Wikipedia:Primary_metabolite is_a: GO:0008152 ! metabolic process property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/26424" xsd:anyURI -[Term] -id: GO:0044249 -name: cellular biosynthetic process -namespace: biological_process -def: "The chemical reactions and pathways resulting in the formation of substances, carried out by individual cells." [GOC:jl] -comment: This term should not be used for direct annotation. It should be possible to make a more specific annotation to one of the children of this term. -subset: gocheck_do_not_annotate -synonym: "cellular anabolism" EXACT [] -synonym: "cellular biosynthesis" EXACT [] -synonym: "cellular formation" EXACT [] -synonym: "cellular synthesis" EXACT [] -is_a: GO:0009058 ! biosynthetic process -is_a: GO:0044237 ! cellular metabolic process -property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27052" xsd:anyURI - [Term] id: GO:0044419 name: biological process involved in interspecies interaction between organisms @@ -6976,7 +7117,6 @@ property_value: term_tracker_item "https://github.com/geneontology/go-ontology/i id: GO:0045026 name: plasma membrane fusion namespace: biological_process -alt_id: GO:0006947 def: "The joining of the lipid bilayer membrane that surround a cell with that of another cell, producing a single cell." [GOC:elh, GOC:mtg_muscle] synonym: "cell fusion" BROAD [] synonym: "cell-cell fusion" BROAD [] @@ -7003,7 +7143,6 @@ relationship: part_of GO:0030217 ! T cell differentiation id: GO:0045087 name: innate immune response namespace: biological_process -alt_id: GO:0002226 def: "Innate immune responses are defense responses mediated by germline encoded components that directly recognize components of potential pathogens." [GO_REF:0000022, GOC:add, GOC:ebc, GOC:mtg_sensu] synonym: "innate immunity" EXACT [GOC:pg] synonym: "nonspecific immune response" EXACT [] @@ -7216,7 +7355,6 @@ property_value: term_tracker_item "https://github.com/geneontology/go-ontology/i id: GO:0048518 name: positive regulation of biological process namespace: biological_process -alt_id: GO:0043119 def: "Any process that activates or increases the frequency, rate or extent of a biological process. Biological processes are regulated by many means; examples include the control of gene expression, protein modification or interaction with a protein or substrate molecule." [GOC:jid] subset: gocheck_do_not_annotate synonym: "activation of biological process" NARROW [] @@ -7234,7 +7372,6 @@ relationship: positively_regulates GO:0008150 ! biological_process id: GO:0048519 name: negative regulation of biological process namespace: biological_process -alt_id: GO:0043118 def: "Any process that stops, prevents, or reduces the frequency, rate or extent of a biological process. Biological processes are regulated by many means; examples include the control of gene expression, protein modification or interaction with a protein or substrate molecule." [GOC:jid] subset: gocheck_do_not_annotate synonym: "down regulation of biological process" EXACT [] @@ -7251,7 +7388,6 @@ relationship: negatively_regulates GO:0008150 ! biological_process id: GO:0048522 name: positive regulation of cellular process namespace: biological_process -alt_id: GO:0051242 def: "Any process that activates or increases the frequency, rate or extent of a cellular process, any of those that are carried out at the cellular level, but are not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level." [GOC:jid] subset: gocheck_do_not_annotate synonym: "activation of cellular process" NARROW [] @@ -7327,7 +7463,6 @@ relationship: part_of GO:0032502 ! developmental process id: GO:0048598 name: embryonic morphogenesis namespace: biological_process -alt_id: GO:0048828 def: "The process in which anatomical structures are generated and organized during the embryonic phase. The embryonic phase begins with zygote formation. The end of the embryonic phase is organism-specific. For example, it would be at birth for mammals, larval hatching for insects and seed dormancy in plants." [GOC:jid, GOC:mtg_sensu] synonym: "embryonic anatomical structure morphogenesis" EXACT [GOC:dph, GOC:tb] is_a: GO:0009653 ! anatomical structure morphogenesis @@ -7495,7 +7630,6 @@ relationship: positively_regulates GO:0006955 ! immune response id: GO:0050789 name: regulation of biological process namespace: biological_process -alt_id: GO:0050791 def: "Any process that modulates the frequency, rate or extent of a biological process. Biological processes are regulated by many means; examples include the control of gene expression, protein modification or interaction with a protein or substrate molecule." [GOC:ai, GOC:go_curators] subset: gocheck_do_not_annotate subset: goslim_candida @@ -7520,7 +7654,6 @@ relationship: regulates GO:0032502 ! developmental process id: GO:0050794 name: regulation of cellular process namespace: biological_process -alt_id: GO:0051244 def: "Any process that modulates the frequency, rate or extent of a cellular process, any of those that are carried out at the cellular level, but are not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level." [GOC:go_curators] subset: gocheck_do_not_annotate synonym: "regulation of cellular physiological process" EXACT [] @@ -7595,7 +7728,6 @@ subset: goslim_pir id: GO:0050896 name: response to stimulus namespace: biological_process -alt_id: GO:0051869 def: "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus. The process begins with detection of the stimulus and ends with a change in state or activity or the cell or organism." [GOC:ai, GOC:bf] comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. subset: gocheck_do_not_annotate @@ -7658,7 +7790,6 @@ relationship: positively_regulates GO:0006935 ! chemotaxis id: GO:0051179 name: localization namespace: biological_process -alt_id: GO:1902578 def: "Any process in which a cell, a substance, or a cellular entity, such as a protein complex or organelle, is transported, tethered to or otherwise maintained in a specific location. In the case of substances, localization may also be achieved via selective degradation." [GOC:ai, GOC:dos] subset: gocheck_do_not_annotate subset: goslim_pir @@ -7672,7 +7803,6 @@ synonym: "single organism localization" RELATED [GOC:TermGenie] synonym: "single-organism localization" RELATED [] is_a: GO:0008150 ! biological_process property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27052" xsd:anyURI -created_by: jl creation_date: 2013-12-18T13:51:04Z [Term] @@ -7729,9 +7859,6 @@ relationship: regulates GO:0046649 ! lymphocyte activation id: GO:0051276 name: chromosome organization namespace: biological_process -alt_id: GO:0006323 -alt_id: GO:0007001 -alt_id: GO:0051277 def: "A process that is carried out at the cellular level that results in the assembly, arrangement of constituent parts, or disassembly of chromosomes, structures composed of a very long molecule of DNA and associated proteins that carries hereditary information. This term covers covalent modifications at the molecular level as well as spatial relationships among the major components of a chromosome." [GOC:ai, GOC:dph, GOC:jl, GOC:mah] subset: goslim_chembl subset: goslim_drosophila @@ -7772,8 +7899,6 @@ is_a: GO:0006810 ! transport id: GO:0051707 name: response to other organism namespace: biological_process -alt_id: GO:0009613 -alt_id: GO:0042828 def: "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus from another living organism." [GOC:ai] is_a: GO:0043207 ! response to external biotic stimulus is_a: GO:0044419 ! biological process involved in interspecies interaction between organisms @@ -7792,7 +7917,6 @@ is_a: GO:0050896 ! response to stimulus id: GO:0055085 name: transmembrane transport namespace: biological_process -alt_id: GO:0090662 def: "The process in which a solute is transported across a lipid bilayer, from one side of a membrane to the other." [GOC:dph, GOC:jid] comment: Transmembrane transport is the transport of a solute across a lipid bilayer. Note that transport through the nuclear pore complex is not transmembrane because the nuclear membrane is a double membrane and is not traversed. For transport through the nuclear pore, consider instead the term 'nucleocytoplasmic transport ; GO:0006913' and its children. Note also that this term is not intended for use in annotating lateral movement within membranes. subset: goslim_chembl @@ -7808,7 +7932,6 @@ is_a: GO:0009987 ! cellular process intersection_of: GO:0006810 ! transport intersection_of: results_in_transport_across GO:0016020 ! membrane relationship: results_in_transport_across GO:0016020 ! membrane -created_by: tb creation_date: 2015-10-21T13:22:47Z [Term] @@ -7883,15 +8006,12 @@ is_a: GO:0035239 ! tube morphogenesis intersection_of: GO:0009653 ! anatomical structure morphogenesis intersection_of: results_in_morphogenesis_of UBERON:0003914 ! epithelial tube relationship: results_in_morphogenesis_of UBERON:0003914 ! epithelial tube -created_by: dph creation_date: 2009-04-28T09:33:36Z [Term] id: GO:0061024 name: membrane organization namespace: biological_process -alt_id: GO:0016044 -alt_id: GO:0044802 def: "A process which results in the assembly, arrangement of constituent parts, or disassembly of a membrane. A membrane is a double layer of lipid molecules that encloses all cells, and, in eukaryotes, many organelles; may be a single or double lipid bilayer; also includes associated proteins." [GOC:dph, GOC:tb] subset: goslim_chembl subset: goslim_drosophila @@ -7908,15 +8028,12 @@ is_a: GO:0016043 ! cellular component organization intersection_of: GO:0016043 ! cellular component organization intersection_of: results_in_organization_of GO:0016020 ! membrane relationship: results_in_organization_of GO:0016020 ! membrane -created_by: jl creation_date: 2010-02-08T02:43:11Z [Term] id: GO:0061025 name: membrane fusion namespace: biological_process -alt_id: GO:0006944 -alt_id: GO:0044801 def: "The membrane organization process that joins two lipid bilayers to form a single membrane." [GOC:dph, GOC:tb] subset: goslim_yeast synonym: "cellular membrane fusion" EXACT [] @@ -7926,7 +8043,6 @@ is_a: GO:0061024 ! membrane organization intersection_of: GO:0061024 ! membrane organization intersection_of: results_in_fusion_of GO:0016020 ! membrane relationship: results_in_fusion_of GO:0016020 ! membrane -created_by: jl creation_date: 2010-02-08T02:48:06Z [Term] @@ -7936,7 +8052,6 @@ namespace: biological_process def: "The process in which the anatomical structures of a branched epithelium are generated and organized." [GOC:dph] is_a: GO:0001763 ! morphogenesis of a branching structure is_a: GO:0002009 ! morphogenesis of an epithelium -created_by: dph creation_date: 2010-05-25T09:05:34Z [Term] @@ -7947,16 +8062,12 @@ def: "An extracellular matrix consisting mainly of proteins (especially collagen is_a: GO:0031012 ! extracellular matrix relationship: RO:0002160 NCBITaxon:33208 ! only in taxon Metazoa relationship: RO:0002162 NCBITaxon:33208 {all_only="true"} ! in taxon Metazoa -created_by: dph creation_date: 2018-04-13T12:47:21Z [Term] id: GO:0065003 name: protein-containing complex assembly namespace: biological_process -alt_id: GO:0006461 -alt_id: GO:0034622 -alt_id: GO:0043623 def: "The aggregation, arrangement and bonding together of a set of macromolecules to form a protein-containing complex." [GOC:jl] subset: goslim_chembl subset: goslim_drosophila @@ -8050,7 +8161,6 @@ comment: Note that this term is in the subset of terms that should not be used f subset: gocheck_do_not_annotate is_a: GO:0042221 ! response to chemical is_a: GO:0051716 ! cellular response to stimulus -created_by: mah creation_date: 2009-08-27T04:41:45Z [Term] @@ -8064,7 +8174,6 @@ is_a: GO:0022607 ! cellular component assembly intersection_of: GO:0022607 ! cellular component assembly intersection_of: results_in_assembly_of GO:0043226 ! organelle relationship: results_in_assembly_of GO:0043226 ! organelle -created_by: mah creation_date: 2009-09-15T03:00:51Z [Term] @@ -8076,7 +8185,6 @@ synonym: "immunoglobulin V(D)J joining" BROAD [GOC:add] synonym: "immunoglobulin V(D)J recombination" BROAD [GOC:add] synonym: "immunoglobulin V-D-J joining" EXACT [GOC:add] is_a: GO:0033152 ! immunoglobulin V(D)J recombination -created_by: mah creation_date: 2010-03-09T04:20:31Z [Term] @@ -8088,7 +8196,6 @@ synonym: "immunoglobulin V(D)J joining" BROAD [GOC:add] synonym: "immunoglobulin V(D)J recombination" BROAD [GOC:add] synonym: "immunoglobulin V-J joining" EXACT [GOC:add] is_a: GO:0033152 ! immunoglobulin V(D)J recombination -created_by: mah creation_date: 2010-03-09T04:22:29Z [Term] @@ -8098,7 +8205,6 @@ namespace: cellular_component def: "A protein complex composed of two identical immunoglobulin heavy chains of the IgD isotype and two identical immunoglobulin light chains, held together by disulfide bonds. An IgD immunoglobulin complex may be embedded in the plasma membrane or present in the extracellular space, in mucosal areas or other tissues, or circulating in the blood or lymph." [GOC:add, ISBN:0781765196, PMID:11282392] comment: Note that an IgD immunoglobulin complex has the function of antigen binding if a suitable antigen is available. is_a: GO:0019814 ! immunoglobulin complex -created_by: mah creation_date: 2010-03-24T01:44:53Z [Term] @@ -8108,7 +8214,6 @@ namespace: cellular_component def: "A protein complex composed of two identical immunoglobulin heavy chains of the IgM isotype and two identical immunoglobulin light chains, held together by disulfide bonds, and in its circulating form complexed with J chain in polymeric forms. An IgM immunoglobulin complex may be embedded in the plasma membrane or present in the extracellular space, in mucosal areas or other tissues, or circulating in the blood or lymph." [GOC:add, ISBN:0781765196, PMID:20176268] comment: Note that an IgM immunoglobulin complex has the function of antigen binding if a suitable antigen is available. is_a: GO:0019814 ! immunoglobulin complex -created_by: mah creation_date: 2010-03-24T01:44:53Z [Term] @@ -8125,14 +8230,12 @@ intersection_of: GO:0016043 ! cellular component organization intersection_of: results_in_organization_of GO:1990904 ! ribonucleoprotein complex relationship: results_in_organization_of GO:1990904 ! ribonucleoprotein complex property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/25143" xsd:anyURI -created_by: mah creation_date: 2010-09-08T10:10:35Z [Term] id: GO:0071840 name: cellular component organization or biogenesis namespace: biological_process -alt_id: GO:0071841 def: "A process that results in the biosynthesis of constituent macromolecules, assembly, arrangement of constituent parts, or disassembly of a cellular component." [GOC:mah] comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. subset: gocheck_do_not_annotate @@ -8143,7 +8246,6 @@ synonym: "cellular component organisation or biogenesis at cellular level" EXACT synonym: "cellular component organization or biogenesis at cellular level" EXACT [] is_a: GO:0009987 ! cellular process property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27189" xsd:anyURI -created_by: mah creation_date: 2010-09-10T01:39:16Z [Term] @@ -8152,8 +8254,7 @@ name: cell periphery namespace: cellular_component def: "The broad region around and including the plasma membrane of a cell, encompassing the cell cortex (inside the cell), the plasma membrane, and any external encapsulating structures." [GOC:pdt] subset: goslim_flybase_ribbon -is_a: GO:0110165 ! cellular anatomical entity -created_by: mah +is_a: GO:0110165 ! cellular anatomical structure creation_date: 2010-10-04T01:51:47Z [Term] @@ -8168,7 +8269,6 @@ intersection_of: GO:0022607 ! cellular component assembly intersection_of: results_in_assembly_of GO:0070062 ! extracellular exosome relationship: part_of GO:0097734 ! extracellular exosome biogenesis relationship: results_in_assembly_of GO:0070062 ! extracellular exosome -created_by: mah creation_date: 2010-10-18T03:44:18Z [Term] @@ -8182,7 +8282,6 @@ intersection_of: results_in_formation_of UBERON:0003914 ! epithelial tube relationship: part_of GO:0060562 ! epithelial tube morphogenesis relationship: results_in_formation_of UBERON:0003914 ! epithelial tube property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/22302" xsd:anyURI -created_by: mah creation_date: 2010-02-26T02:15:40Z [Term] @@ -8195,7 +8294,6 @@ is_a: GO:0061025 ! membrane fusion intersection_of: GO:0061025 ! membrane fusion intersection_of: results_in_fusion_of GO:0031090 ! organelle membrane relationship: results_in_fusion_of GO:0031090 ! organelle membrane -created_by: tb creation_date: 2009-12-11T11:44:58Z [Term] @@ -8208,21 +8306,18 @@ is_a: GO:1903131 ! mononuclear cell differentiation intersection_of: GO:0030154 ! cell differentiation intersection_of: results_in_acquisition_of_features_of CL:0000451 ! dendritic cell relationship: results_in_acquisition_of_features_of CL:0000451 ! dendritic cell -created_by: pr creation_date: 2011-04-01T10:08:42Z [Term] id: GO:0097190 name: apoptotic signaling pathway namespace: biological_process -alt_id: GO:0008624 def: "The series of molecular signals which triggers the apoptotic death of a cell. The pathway starts with reception of a signal, and ends when the execution phase of apoptosis is triggered." [GOC:mtg_apoptosis] comment: This term can be used to annotate gene products involved in apoptotic events happening downstream of the cross-talk point between the extrinsic and intrinsic apoptotic pathways. The cross-talk starts when caspase-8 cleaves Bid and truncated Bid interacts with mitochondria. From this point on it is not possible to distinguish between extrinsic and intrinsic pathways. synonym: "apoptotic signalling pathway" EXACT [GOC:mah] synonym: "induction of apoptosis by extracellular signals" EXACT [] is_a: GO:0007165 ! signal transduction relationship: part_of GO:0006915 ! apoptotic process -created_by: pr creation_date: 2011-11-23T09:30:23Z [Term] @@ -8235,7 +8330,6 @@ synonym: "execution phase of apoptotic process" EXACT [] is_a: GO:0009987 ! cellular process relationship: has_part GO:0032060 ! bleb assembly relationship: part_of GO:0006915 ! apoptotic process -created_by: pr creation_date: 2011-11-23T09:45:24Z [Term] @@ -8247,7 +8341,6 @@ is_a: GO:0031982 ! vesicle is_a: GO:0043231 ! intracellular membrane-bounded organelle intersection_of: GO:0031982 ! vesicle intersection_of: part_of GO:0005622 ! intracellular anatomical structure -created_by: pr creation_date: 2016-03-29T17:39:45Z [Term] @@ -8261,14 +8354,12 @@ synonym: "exosome production" EXACT [] synonym: "ILV assembly" RELATED [] synonym: "intraluminal vesicle assembly" RELATED [] is_a: GO:0140112 ! extracellular vesicle biogenesis -created_by: pr creation_date: 2016-10-03T14:35:25Z [Term] id: GO:0098542 name: defense response to other organism namespace: biological_process -alt_id: GO:0009814 def: "Reactions triggered in response to the presence of another organism that act to protect the cell or organism from damage caused by that organism." [GOC:dos] subset: goslim_generic subset: goslim_prokaryote @@ -8278,7 +8369,6 @@ synonym: "defense response, incompatible interaction" NARROW [] synonym: "resistance response to pathogen" NARROW [] is_a: GO:0051707 ! response to other organism property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/22173" xsd:anyURI -created_by: dos creation_date: 2013-11-11T12:59:11Z [Term] @@ -8293,7 +8383,6 @@ is_a: GO:0016020 ! membrane intersection_of: GO:0016020 ! membrane intersection_of: part_of GO:0005886 ! plasma membrane relationship: part_of GO:0005886 ! plasma membrane -created_by: dos creation_date: 2014-03-06T11:55:32Z [Term] @@ -8314,7 +8403,6 @@ def: "A complex of collagen trimers such as a fibril or collagen network." [GOC: synonym: "Supramolecular aggregate of collagen" EXACT [PMID:19693541] synonym: "Supramolecular collagen assembly" EXACT [PMID:21421911] is_a: GO:0099080 ! supramolecular complex -is_a: PR:000050567 ! protein-containing material entity relationship: has_part GO:0005581 ! collagen trimer relationship: part_of GO:0062023 ! collagen-containing extracellular matrix @@ -8353,7 +8441,7 @@ namespace: cellular_component def: "The part of a synapse that is part of the presynaptic cell." [GOC:dos] subset: goslim_synapse synonym: "presynaptic terminal" EXACT [] -is_a: GO:0110165 ! cellular anatomical entity +is_a: GO:0110165 ! cellular anatomical structure relationship: part_of CL:0000540 ! neuron relationship: part_of GO:0045202 ! synapse @@ -8363,7 +8451,7 @@ name: postsynapse namespace: cellular_component def: "The part of a synapse that is part of the post-synaptic cell." [GOC:dos] subset: goslim_synapse -is_a: GO:0110165 ! cellular anatomical entity +is_a: GO:0110165 ! cellular anatomical structure relationship: part_of CL:0000000 ! cell relationship: part_of GO:0045202 ! synapse @@ -8418,7 +8506,7 @@ id: GO:0099080 name: supramolecular complex namespace: cellular_component def: "A cellular component that consists of an indeterminate number of proteins or macromolecular complexes, organized into a regular, higher-order structure such as a polymer, sheet, network or a fiber." [GOC:dos] -is_a: GO:0110165 ! cellular anatomical entity +is_a: GO:0110165 ! cellular anatomical structure [Term] id: GO:0099081 @@ -8478,16 +8566,17 @@ is_a: GO:0099536 ! synaptic signaling [Term] id: GO:0110165 -name: cellular anatomical entity +name: cellular anatomical structure namespace: cellular_component -def: "A part of a cellular organism that is either an immaterial entity or a material entity with granularity above the level of a protein complex but below that of an anatomical system. Or, a substance produced by a cellular organism with granularity above the level of a protein complex." [GOC:kmv] +def: "A part of a cellular organism consisting of a material entity with granularity above the level of a protein complex but below that of an anatomical system. Note that cellular organisms exclude viruses." [GOC:kmv] subset: gocheck_do_not_annotate subset: goslim_pir +synonym: "cellular anatomical entity" EXACT [] is_a: GO:0005575 ! cellular_component is_a: UBERON:0000061 ! anatomical structure property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/24200" xsd:anyURI property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/26424" xsd:anyURI -created_by: kmv +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28978" xsd:anyURI creation_date: 2019-08-12T18:01:37Z [Term] @@ -8500,7 +8589,6 @@ intersection_of: GO:0042995 ! cell projection intersection_of: has_part GO:0098590 ! plasma membrane region relationship: has_part GO:0098590 ! plasma membrane region property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/13193" xsd:anyURI -created_by: krc creation_date: 2017-03-21T17:26:07Z [Term] @@ -8515,7 +8603,6 @@ intersection_of: GO:0022607 ! cellular component assembly intersection_of: results_in_assembly_of GO:0120025 ! plasma membrane bounded cell projection relationship: results_in_assembly_of GO:0120025 ! plasma membrane bounded cell projection property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/13298" xsd:anyURI -created_by: krc creation_date: 2017-04-24T23:56:08Z [Term] @@ -8528,7 +8615,6 @@ intersection_of: GO:0016043 ! cellular component organization intersection_of: results_in_organization_of GO:0120025 ! plasma membrane bounded cell projection relationship: results_in_organization_of GO:0120025 ! plasma membrane bounded cell projection property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/13298" xsd:anyURI -created_by: krc creation_date: 2017-04-26T16:07:02Z [Term] @@ -8544,7 +8630,6 @@ is_a: GO:1903047 ! mitotic cell cycle process intersection_of: GO:0000280 ! nuclear division intersection_of: part_of GO:0000278 ! mitotic cell cycle property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/19910" xsd:anyURI -created_by: pg creation_date: 2017-03-23T14:44:23Z [Term] @@ -8557,7 +8642,6 @@ is_a: GO:0009987 ! cellular process intersection_of: GO:0009987 ! cellular process intersection_of: part_of GO:0006887 ! exocytosis relationship: part_of GO:0006887 ! exocytosis -created_by: pg creation_date: 2017-05-15T13:20:45Z [Term] @@ -8568,7 +8652,6 @@ def: "The assembly and secretion a set of components to form an extracellular ve synonym: "extracellular vesicle assembly" EXACT [] is_a: GO:0044085 ! cellular component biogenesis property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/14256" xsd:anyURI -created_by: pg creation_date: 2017-10-23T11:53:42Z [Term] @@ -8581,7 +8664,6 @@ synonym: "cell fusion" BROAD [] is_a: GO:0009987 ! cellular process relationship: has_part GO:0045026 ! plasma membrane fusion property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/15939" xsd:anyURI -created_by: pg creation_date: 2018-08-13T18:38:18Z [Term] @@ -8597,7 +8679,6 @@ intersection_of: has_target_end_location GO:0005576 ! extracellular region intersection_of: has_target_start_location GO:0005622 ! intracellular anatomical structure relationship: has_target_end_location GO:0005576 ! extracellular region relationship: has_target_start_location GO:0005622 ! intracellular anatomical structure -created_by: pg creation_date: 2019-05-22T11:20:45Z [Term] @@ -8607,7 +8688,6 @@ namespace: biological_process def: "Reactions triggered in response to the presence of a symbiont that act to protect or prevent damage to the host." [GOC:pg] is_a: GO:0098542 ! defense response to other organism property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/20261" xsd:anyURI -created_by: pg creation_date: 2020-11-11T17:19:06Z [Term] @@ -8621,7 +8701,6 @@ is_a: GO:1903706 ! regulation of hemopoiesis intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0002521 ! leukocyte differentiation relationship: regulates GO:0002521 ! leukocyte differentiation -created_by: pr creation_date: 2013-05-02T17:32:42Z [Term] @@ -8634,7 +8713,6 @@ is_a: GO:0022402 ! cell cycle process intersection_of: GO:0009987 ! cellular process intersection_of: part_of GO:0000278 ! mitotic cell cycle relationship: part_of GO:0000278 ! mitotic cell cycle -created_by: jl creation_date: 2014-05-22T14:22:34Z [Term] @@ -8646,7 +8724,6 @@ is_a: GO:0002521 ! leukocyte differentiation intersection_of: GO:0030154 ! cell differentiation intersection_of: results_in_acquisition_of_features_of CL:0000842 ! mononuclear cell relationship: results_in_acquisition_of_features_of CL:0000842 ! mononuclear cell -created_by: cls creation_date: 2014-06-25T15:47:09Z [Term] @@ -8659,7 +8736,6 @@ is_a: GO:0031982 ! vesicle is_a: GO:0065010 ! extracellular membrane-bounded organelle intersection_of: GO:0031982 ! vesicle intersection_of: part_of GO:0005576 ! extracellular region -created_by: jl creation_date: 2014-10-22T14:26:11Z [Term] @@ -8678,15 +8754,12 @@ is_a: GO:2000026 ! regulation of multicellular organismal development intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0030097 ! hemopoiesis relationship: regulates GO:0030097 ! hemopoiesis -created_by: pad creation_date: 2014-12-04T15:34:13Z [Term] id: GO:1990904 name: ribonucleoprotein complex namespace: cellular_component -alt_id: GO:0030529 -alt_id: GO:1990903 def: "A macromolecular complex that contains both RNA and protein molecules." [GOC:krc, GOC:vesicles] subset: goslim_pir synonym: "extracellular ribonucleoprotein complex" NARROW [] @@ -8696,7 +8769,6 @@ synonym: "RNA-protein complex" EXACT [] synonym: "RNP" EXACT [] xref: Wikipedia:Ribonucleoprotein is_a: GO:0032991 ! protein-containing complex -created_by: pr creation_date: 2015-11-19T12:26:37Z [Term] @@ -8709,7 +8781,6 @@ is_a: GO:0051239 ! regulation of multicellular organismal process intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0007275 ! multicellular organism development relationship: regulates GO:0007275 ! multicellular organism development -created_by: tb creation_date: 2010-08-05T11:25:59Z [Term] @@ -8725,7 +8796,6 @@ is_a: GO:0050794 ! regulation of cellular process intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0048870 ! cell motility relationship: regulates GO:0048870 ! cell motility -created_by: mah creation_date: 2010-10-01T09:41:21Z [Term] @@ -8742,7 +8812,6 @@ is_a: GO:2000145 ! regulation of cell motility intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0048870 ! cell motility relationship: positively_regulates GO:0048870 ! cell motility -created_by: mah creation_date: 2010-10-01T09:41:30Z [Term] @@ -8776,7 +8845,6 @@ is_a: NCBITaxon:39107 ! Murinae id: NCBITaxon:10090 name: Mus musculus namespace: ncbi_taxonomy -alt_id: NCBITaxon:85055 synonym: "house mouse" EXACT genbank_common_name [] synonym: "mouse" EXACT OMO:0003003 [] xref: GC_ID:1 @@ -8793,7 +8861,6 @@ is_a: NCBITaxon:7776 ! Gnathostomata id: NCBITaxon:117571 name: Euteleostomi namespace: ncbi_taxonomy -alt_id: NCBITaxon:40673 synonym: "bony vertebrates" EXACT genbank_common_name [] xref: GC_ID:1 is_a: NCBITaxon:117570 ! Teleostomi @@ -8942,7 +9009,6 @@ is_a: NCBITaxon:1963758 ! Myomorpha id: NCBITaxon:39107 name: Murinae namespace: ncbi_taxonomy -alt_id: NCBITaxon:109679 xref: GC_ID:1 is_a: NCBITaxon:10066 ! Muridae @@ -9038,7 +9104,6 @@ is_a: NCBITaxon:314147 ! Glires id: PATO:0000001 name: quality namespace: quality -alt_id: PATO:0000072 def: "A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities" [PATOC:GVG] [Term] @@ -9053,7 +9118,6 @@ is_a: PATO:0001241 ! physical object quality id: PATO:0000052 name: shape namespace: quality -alt_id: PATO:0001647 def: "A morphological quality inhering in a bearer by virtue of the bearer's ratios of distances between its features (points, edges, surfaces and also holes etc)." [PATOC:GVG] comment: Shapes are invariant on size transformations. Shapes can be subdivided into 2D and 3D shapes, We can also make a distinction between shapes of complete self-connected objects, and shapes of parts of objects. subset: attribute_slim @@ -9064,7 +9128,6 @@ is_a: PATO:0000051 ! morphology id: PATO:0000141 name: structure namespace: quality -alt_id: PATO:0001452 def: "A morphology quality inhering in a bearer by virtue of the bearer's relative position, shape, arrangements and connectivity of an organism's various parts; the pattern underlying its form." [PATOC:GVG] subset: attribute_slim synonym: "conformation" BROAD [VT:1000738] @@ -9122,7 +9185,6 @@ is_a: PATO:0002318 ! superelliptic id: PATO:0001018 name: physical quality namespace: quality -alt_id: PATO:0002079 def: "A quality of a physical entity that exists through action of continuants at the physical level of organisation in relation to other entities." [PATOC:GVG] subset: attribute_slim synonym: "relational physical quality" EXACT [] @@ -9133,8 +9195,6 @@ is_a: PATO:0001241 ! physical object quality id: PATO:0001241 name: physical object quality namespace: quality -alt_id: PATO:0001237 -alt_id: PATO:0001238 def: "A quality which inheres in a continuant." [PATOC:GVG] comment: Relational qualities are qualities that hold between multiple entities. Normal (monadic) qualities such as the shape of a eyeball exist purely as a quality of that eyeball. A relational quality such as sensitivity to light is a quality of that eyeball (and connecting nervous system) as it relates to incoming light waves/particles. synonym: "monadic quality of a continuant" EXACT [] @@ -9292,7 +9352,6 @@ is_a: PATO:0002005 ! concavity id: PATO:0001873 name: cylindrical namespace: quality -alt_id: PATO:0001203 def: "A convex 3-D shape quality inhering in a bearer by virtue of the bearer's exhibiting a consistently-sized round cross section." [PATOC:MAH] subset: cell_quality subset: value_slim @@ -9527,7 +9586,6 @@ def: "A quality inhering in a cell by virtue of the cell having a high nuclear/c comment: A high nuclear/cytolasmic ratio is 70% or higher. synonym: "high N:C ratio" EXACT [] is_a: PATO:0001396 ! cellular quality -created_by: http://orcid.org/0000-0001-5208-3432 [Term] id: PATO:0070044 @@ -9535,7 +9593,6 @@ name: anatomical structure quality namespace: quality def: "A quality of continuant that exist at the anatomical level of organisation and anything under it. This includes, but is not limited to, cells , tissues, and components." [] is_a: PATO:0001241 ! physical object quality -created_by: http://orcid.org/0000-0001-7258-9596 [Term] id: PATO:0070045 @@ -9543,7 +9600,6 @@ name: anatomical histological quality namespace: quality def: "A quality inhering in an anotomical structure by virtue of its capacity to be stained by specific histological dyes." [] is_a: PATO:0070044 ! anatomical structure quality -created_by: http://orcid.org/0000-0001-7258-9596 [Term] id: PATO:0070046 @@ -9551,7 +9607,6 @@ name: neutrophillic namespace: quality def: "An affinity inhering in an anatomical structure by virtue of the bearer exhibiting a molecular interaction that stains and colors, pale-pink, with Wright-Giemsa stain." [GOC:add] is_a: PATO:0070045 ! anatomical histological quality -created_by: http://orcid.org/0000-0001-7258-9596 [Term] id: PATO:0070047 @@ -9559,18 +9614,17 @@ name: polychromatophilic namespace: quality def: "An affinity inhering in an anatomical structure by virtue of the bearer exhibiting a molecular interaction for both basic and acid stains under specific pH conditions." [GOC:add] is_a: PATO:0070045 ! anatomical histological quality -created_by: http://orcid.org/0000-0001-7258-9596 [Term] id: PR:000000001 name: protein namespace: protein def: "An amino acid chain that is produced de novo by ribosome-mediated translation of a genetically-encoded mRNA, and any derivatives thereof." [PRO:DAN, PRO:WCB] -comment: The definition above excludes protein complexes, which some also consider a protein. Those who wish to refer to a class representing both senses of the word are directed to CHEBI:36080. Note that the definition allows for experimentally-manipulated genes, and allows for artifically-produced derivatives that mimic those found naturally. Proteins (in the sense defined here) that descended from a common ancestor can be classified into families and superfamilies composed of products of evolutionarily-related genes. The domain architecture of a protein is described by the order of its constituent domains. Proteins with the same domains in the same order are defined as homeomorphic [PRO:WCB]. +comment: The definition above excludes protein complexes, which some also consider a protein. Those who wish to refer to a class representing both senses of the word are directed to CHEBI:36080. Note that the definition allows for experimentally-manipulated genes, and allows for artifically-produced derivatives that mimic those found naturally. Proteins (in the sense defined here) that descended from a common ancestor can be classified into families and superfamilies composed of products of evolutionarily-related genes. The domain architecture of a protein is described by the order of its constituent domains. Proteins with the same domains in the same order are defined as homeomorphic [PRO:WCB). synonym: "native protein" NARROW [IEDB:BP] synonym: "natural protein" EXACT [PRO:DAN] is_a: PR:000018263 ! amino acid chain -is_a: PR:000050567 ! protein-containing material entity +is_a: PR:000064867 ! protein-containing molecular entity relationship: output_of GO:0006412 ! translation [Term] @@ -10358,7 +10412,6 @@ namespace: protein def: "A protein with core architecture consisting of a signal sequence, followed by 7 Ig-like domains (Pfam:PF00047, Pfam:PF07679, or Pfam:PF07686), a transmembrane region, and a cytoplasmic Protein tyrosine kinase domain." [PRO:WCB] comment: Category=family. xref: PIRSF:PIRSF038502 -is_a: PR:000000001 ! protein [Term] id: PR:000002062 @@ -10746,11 +10799,11 @@ is_a: PR:000036194 ! eukaryotic protein relationship: RO:0002160 NCBITaxon:33208 ! only in taxon Metazoa [Term] -id: PR:000050567 -name: protein-containing material entity +id: PR:000064867 +name: protein-containing molecular entity namespace: protein -def: "A material entity that minimally consists of a protein." [PRO:DAN] -comment: Note: This includes single proteins and derivatives thereof (PR:000000001), protein-containing complexes (GO:0032991), and protein aggregates (PR:000050566). +def: "A molecular entity that minimally consists of a protein." [PRO:DAN] +comment: Note: This includes single proteins and derivatives thereof (PR:000000001), protein-containing complexes (GO:0032991), and protein aggregates (PR:000050565). synonym: "protein" NARROW [PRO:DAN] synonym: "protein aggregate" NARROW [PRO:DAN] synonym: "protein complex" NARROW [PRO:DAN] @@ -10800,7 +10853,6 @@ property_value: RO:0002175 NCBITaxon:9606 id: UBERON:0000060 name: anatomical wall namespace: uberon -alt_id: UBERON:0009915 def: "Organ component adjacent to an organ cavity and which consists of a maximal aggregate of organ component layers." [FMA:82482] subset: upper_level synonym: "organ wall" RELATED [FMA:82482] @@ -10968,7 +11020,6 @@ property_value: RO:0002175 NCBITaxon:4751 id: UBERON:0000075 name: subdivision of skeletal system namespace: uberon -alt_id: UBERON:0010322 def: "Anatomical cluster consisting of the skeletal elements and articular elements that are part of an individual subdivision of the organism." [https://orcid.org/0000-0002-6601-2165, UBERONREF:0000003] subset: non_informative synonym: "skeletal system part" RELATED [] @@ -11297,7 +11348,7 @@ xref: VHOG:0000224 xref: Wikipedia:Blood xref: XAO:0000124 xref: ZFA:0000007 -is_a: PR:000050567 ! protein-containing material entity +is_a: UBERON:0000061 ! anatomical structure is_a: UBERON:0000179 ! haemolymphatic fluid relationship: has_part CL:0000232 {source="CL:tm"} ! erythrocyte relationship: has_part UBERON:0001969 ! blood plasma @@ -11326,7 +11377,6 @@ creation_date: 2009-04-08T04:38:19Z id: UBERON:0000307 name: blastula namespace: uberon -alt_id: UBERON:0007011 def: "Organism at the blastula stage - an early stage of embryonic development in animals. It is produced by cleavage of a fertilized ovum and consists of a spherical layer of around 128 cells surrounding a central fluid-filled cavity called the blastocoel. The blastula follows the morula and precedes the gastrula in the developmental sequence." [Wikipedia:Blastula] subset: inconsistent_with_fma synonym: "blastosphere" RELATED [Wikipedia:Blastula] @@ -11790,7 +11840,6 @@ xref: VHOG:0000387 xref: Wikipedia:Epithelium xref: XAO:0003045 xref: ZFA:0001486 -is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0000479 ! tissue intersection_of: UBERON:0000479 ! tissue intersection_of: RO:0002473 CL:0000066 ! composed primarily of epithelial cell @@ -12035,7 +12084,6 @@ property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/d/ id: UBERON:0000926 name: mesoderm namespace: uberon -alt_id: UBERON:0003263 def: "The middle germ layer of the embryo, between the endoderm and ectoderm." [Wikipedia:Mesoderm] subset: efo_slim subset: pheno_slim @@ -12263,7 +12311,6 @@ id: UBERON:0001009 name: circulatory system namespace: uberon def: "Organ system that passes nutrients (such as amino acids and electrolytes), gases, hormones, blood cells, etc. to and from cells in the body to help fight diseases and help stabilize body temperature and pH to maintain homeostasis[WP]." [Wikipedia:Circulatory_system] -subset: human_reference_atlas subset: uberon_slim synonym: "systema cardiovasculare" RELATED OMO:0003011 [Wikipedia:Circulatory_system] xref: AAO:0000959 @@ -12283,7 +12330,6 @@ property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/2/ property_value: RO:0002161 NCBITaxon:147099 {source="Wikipedia:Acoelomorpha"} property_value: RO:0002161 NCBITaxon:6073 property_value: RO:0002161 NCBITaxon:6157 -property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001015 @@ -12703,7 +12749,6 @@ xref: MIAA:0000052 xref: NCIT:C13356 xref: UMLS:C0032105 {source="ncithesaurus:Plasma"} xref: Wikipedia:Blood_plasma -is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0000179 ! haemolymphatic fluid intersection_of: UBERON:0000463 ! organism substance intersection_of: has_part GO:0005577 ! fibrinogen complex @@ -12752,7 +12797,6 @@ xref: VHOG:0001250 xref: Wikipedia:Blood_vessel xref: XAO:0001011 xref: ZFA:0005314 -is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0000055 ! vessel is_a: UBERON:0004120 ! mesoderm-derived structure relationship: capable_of_part_of GO:0008015 ! blood circulation @@ -13033,7 +13077,6 @@ property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/e/ id: UBERON:0002323 name: coelemic cavity lumen namespace: uberon -alt_id: UBERON:0000169 def: "The cavity within the body of all animals higher than the coelenterates and certain primitive worms, formed by the splitting of the embryonic mesoderm into two layers. In mammals it forms the peritoneal, pleural, and pericardial cavities." [BTO:0001707] comment: EDITOR_NOTE check the FMA placement here; ncit placement of body cavity here probably not correct subset: uberon_slim @@ -13059,7 +13102,6 @@ xref: RETIRED_EHDAA2:0003186 xref: SCTID:361348008 xref: TAO:0001438 xref: UMLS:C0333343 {source="ncithesaurus:Cavity"} -xref: ZFA:0001438 is_a: UBERON:0002553 ! anatomical cavity relationship: RO:0002494 UBERON:0003886 ! transformation of future coelemic cavity lumen relationship: RO:0002572 UBERON:0011997 ! luminal space of coelom @@ -13515,6 +13557,7 @@ xref: TAO:0000279 xref: VHOG:0000559 xref: XAO:0000057 xref: ZFA:0000279 +is_a: UBERON:0000061 ! anatomical structure is_a: UBERON:0006598 ! presumptive structure intersection_of: UBERON:0005423 ! developing anatomical structure intersection_of: RO:0002387 UBERON:0002329 ! has potential to develop into somite @@ -13645,7 +13688,6 @@ property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/6/ id: UBERON:0003081 name: lateral plate mesoderm namespace: uberon -alt_id: UBERON:0006258 def: "Portion of the middle of the three primary germ layers of the embryo that resides on the periphery of the embryo, is continuous with the extra-embryonic mesoderm, splits into two layers enclosing the intra-embryonic coelom, and gives rise to body wall structures[MP]." [MP:0010117, Wikipedia:Lateral_plate_mesoderm] subset: pheno_slim subset: uberon_slim @@ -14035,7 +14077,6 @@ xref: WikipediaCategory:Cardiovascular_system xref: XAO:0000100 xref: XAO:0001010 xref: ZFA:0000010 -is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0000467 ! anatomical system intersection_of: UBERON:0000467 ! anatomical system intersection_of: has_part UBERON:0000948 ! heart @@ -14059,7 +14100,6 @@ synonym: "blood vessels" RELATED [TAO:0001079] synonym: "set of blood vessels" EXACT [] xref: TAO:0001079 xref: ZFA:0001079 -is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0002049 ! vasculature intersection_of: UBERON:0002049 ! vasculature intersection_of: RO:0002473 UBERON:0001981 ! composed primarily of blood vessel @@ -14116,7 +14156,6 @@ property_value: IAO:0000116 "EHDAA2 places this as a subtype of organism. This l id: UBERON:0004734 name: gastrula namespace: uberon -alt_id: UBERON:0007012 def: "Organism at the gastrula stage." [Wikipedia:Gastrula, Wikipedia:Trilaminar_blastocyst] subset: pheno_slim synonym: "blastocystis trilaminaris" RELATED [https://orcid.org/0000-0002-6601-2165] @@ -14533,7 +14572,6 @@ xref: NCIT:C13191 xref: SCTID:68989006 xref: UMLS:C0004799 {source="ncithesaurus:Basement_Membrane"} xref: Wikipedia:Basement_membrane -is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0005764 {source="FMA"} ! acellular membrane relationship: adjacent_to CL:0000066 ! epithelial cell relationship: has_part GO:0005587 ! collagen type IV trimer @@ -14752,7 +14790,6 @@ subset: efo_slim xref: EFO:0003709 xref: TAO:0005077 xref: ZFA:0005077 -is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0005423 ! developing anatomical structure relationship: has_part CL:0000115 ! endothelial cell relationship: has_part CL:0000566 ! angioblastic mesenchymal cell @@ -15007,7 +15044,6 @@ property_value: RO:0002175 NCBITaxon:9606 id: UBERON:0009142 name: entire embryonic mesenchyme namespace: uberon -alt_id: UBERON:0003313 def: "Sum total of mesenchyme in the embryo." [https://github.com/obophenotype/human-developmental-anatomy-ontology/issues/7] xref: EHDAA2:0001113 xref: EHDAA:177 @@ -15096,7 +15132,6 @@ synonym: "thrombus" EXACT [BTO:0000102] xref: BTO:0000102 xref: galen:BloodClot xref: Wikipedia:Thrombus -is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0000463 ! organism substance intersection_of: UBERON:0000463 ! organism substance intersection_of: output_of GO:0007596 ! blood coagulation @@ -15245,6 +15280,7 @@ synonym: "haemocoelom" NARROW [] synonym: "schizocoelom" NARROW [] xref: EHDAA2:0004731 xref: Wikipedia:Coelom +xref: ZFA:0001438 is_a: UBERON:0000481 {source="EHDAA2"} ! multi-tissue structure relationship: RO:0002162 NCBITaxon:33213 ! in taxon Bilateria property_value: IAO:0000116 "EHDAA2 distingsuishes between the lumen, the lining, and the 'coelomic cavity', which despire it's name, is not a space - it is the aggregate of space plus lining." xsd:string @@ -15422,7 +15458,6 @@ is_a: UBERON:0000479 {source="FMA"} ! tissue id: UBERON:0016879 name: future central nervous system namespace: uberon -alt_id: UBERON:3000469 def: "Primordium that develops into the central nervous system." [http://orcid.org/0000-0002-6601-2165] synonym: "future CNS" EXACT [] synonym: "presumptive central nervous system" EXACT [] @@ -15437,7 +15472,6 @@ relationship: RO:0002387 UBERON:0001017 ! has potential to develop into central id: UBERON:0016880 name: future nervous system namespace: uberon -alt_id: UBERON:3000477 def: "Primordium that develops into the nervous system." [http://orcid.org/0000-0002-6601-2165] synonym: "presumptive nervous system" EXACT [AAO:0000477] xref: AAO:0000477 @@ -15649,7 +15683,6 @@ id: RO:0002021 name: occurs across def: "A relationship between a process and a barrier, where the process occurs in a region spanning the barrier. For cellular processes the barrier is typically a membrane. Examples include transport across a membrane and membrane depolarization." [] is_a: RO:0002479 ! has part that occurs in -created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-07-20T17:19:37Z [Typedef] @@ -16505,7 +16538,6 @@ name: causally upstream of or within, negative effect property_value: RO:0004050 RO:0002418 property_value: seeAlso "https://wiki.geneontology.org/Causally_upstream_of_or_within,_negative_effect" xsd:anyURI is_a: causally_upstream_of_or_within ! causally upstream of or within -created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-03-13T23:55:05Z [Typedef] @@ -16513,7 +16545,6 @@ id: RO:0004047 name: causally upstream of or within, positive effect property_value: seeAlso https://wiki.geneontology.org/Causally_upstream_of_or_within,_positive_effect is_a: causally_upstream_of_or_within ! causally upstream of or within -created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-03-13T23:55:19Z [Typedef] @@ -16522,7 +16553,6 @@ name: has small molecule regulator def: "a relation between a process and a continuant, in which the process is regulated by the small molecule continuant" [] is_a: has_participant ! has participant inverse_of: RO:0012004 ! is small molecule regulator of -created_by: https://orcid.org/0000-0003-1813-6857 creation_date: 2020-04-22T20:27:26Z [Typedef] @@ -16530,7 +16560,6 @@ id: RO:0012004 name: is small molecule regulator of def: "a relation between a continuant and a process, in which the continuant is a small molecule that regulates the process" [] is_a: RO:0002596 ! capable of regulating -created_by: https://orcid.org/0000-0003-1813-6857 creation_date: 2020-06-24T13:15:17Z [Typedef] @@ -16540,7 +16569,6 @@ def: "a relation between a continuant and a process, in which the continuant is property_value: seeAlso "https://wiki.geneontology.org/Is_small_molecule_activator_of" xsd:anyURI is_a: RO:0002598 ! capable of positively regulating is_a: RO:0012004 ! is small molecule regulator of -created_by: https://orcid.org/0000-0003-1813-6857 creation_date: 2020-06-24T13:15:26Z [Typedef] @@ -16550,7 +16578,6 @@ def: "A relationship between a neuron and a region, where the neuron has a funct synonym: "has synaptic input or output in" EXACT [] is_a: RO:0002130 ! has synaptic terminal in transitive_over: part_of ! part of -created_by: https://orcid.org/0000-0002-1373-1705 creation_date: 2020-07-17T09:26:52Z [Typedef] @@ -16562,9 +16589,18 @@ synonym: "has sensory terminal in" EXACT [] synonym: "has sensory terminal location" EXACT [] is_a: RO:0002360 ! has dendrite location transitive_over: part_of ! part of -created_by: https://orcid.org/0000-0002-1373-1705 creation_date: 2020-07-20T12:10:09Z +[Typedef] +id: RO:0015004 +name: has characterizing marker set +def: "A relation that applies between a cell type and a set of markers that can be used to uniquely identify that cell type." [] +synonym: "has marker gene combination" EXACT [] +synonym: "has marker signature set" EXACT [] +property_value: IAO:0000116 "C has_characterizing_marker_set y iff: C is a cell type and y is a collection of genes or proteins whose expression is sufficient to distinguish cell type C from most or all other cell types." xsd:string +property_value: terms:contributor https://orcid.org/0000-0001-7258-9596 +domain: CL:0000000 ! cell + [Typedef] id: RO:0015006 name: different in magnitude relative to @@ -16638,7 +16674,6 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0012003 is_a: has_participant ! has participant -created_by: https://orcid.org/0000-0003-1813-6857 creation_date: 2020-06-08T17:21:33Z [Typedef] @@ -16934,7 +16969,6 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_ontology xref: RO:0004009 is_a: has_input ! has input is_a: has_primary_input_or_output ! has primary input or output -created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-12-13T11:26:56Z [Typedef] @@ -16945,7 +16979,6 @@ def: "p 'has primary input ot output' c iff either (a) p 'has primary input' c o subset: http://purl.obolibrary.org/obo/valid_for_go_ontology xref: RO:0004007 is_a: has_participant ! has participant -created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-12-13T11:26:17Z [Typedef] @@ -16957,7 +16990,6 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_ontology xref: RO:0004008 is_a: has_output ! has output is_a: has_primary_input_or_output ! has primary input or output -created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-12-13T11:26:32Z [Typedef] @@ -16968,7 +17000,6 @@ def: "a relation between a process and a continuant, in which the process is act xref: RO:0012001 is_a: RO:0012000 ! has small molecule regulator inverse_of: RO:0012005 ! is small molecule activator of -created_by: https://orcid.org/0000-0003-1813-6857 creation_date: 2020-04-22T20:28:37Z [Typedef] @@ -17293,7 +17324,6 @@ namespace: external def: "p has anatomical participant c iff p has participant c, and c is an anatomical entity" [] xref: RO:0040036 is_a: has_participant ! has participant -created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-09-26T01:08:58Z [Typedef] @@ -17365,7 +17395,6 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0012008 is_a: results_in_organization_of ! results in organization of -created_by: https://orcid.org/0000-0003-1813-6857 creation_date: 2021-02-26T07:28:29Z [Typedef] @@ -17417,7 +17446,6 @@ name: results in organization of namespace: external def: "p results in organization of c iff p results in the assembly, arrangement of constituent parts, or disassembly of c" [] xref: RO:0002592 -is_a: has_participant ! has participant is_a: results_in_changes_to_anatomical_or_cellular_structure ! results in changes to anatomical or cellular structure [Typedef] diff --git a/src/ontology/subsets/blood_and_immune_upper_slim.owl b/src/ontology/subsets/blood_and_immune_upper_slim.owl index 0fa546cf7..03661de11 100644 --- a/src/ontology/subsets/blood_and_immune_upper_slim.owl +++ b/src/ontology/subsets/blood_and_immune_upper_slim.owl @@ -22,8 +22,8 @@ xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#" xmlns:ncbitaxon="http://purl.obolibrary.org/obo/ncbitaxon#"> - - 2024-09-26 + + 2025-01-08 @@ -287,13 +287,18 @@ WHERE { - 2018-03-14T00:03:24Z is negative form of + + + + + + @@ -373,6 +378,14 @@ WHERE { + + + + + + + + @@ -384,6 +397,14 @@ WHERE { + + + + + + + + @@ -1010,12 +1031,6 @@ WHERE { - - - - - - @@ -1034,6 +1049,12 @@ WHERE { + + + + + + @@ -1048,19 +1069,25 @@ WHERE { - + + description + - + + license + - + + title + @@ -1088,26 +1115,12 @@ WHERE { - - - - - - - - - - has_alternative_id - - - - @@ -1123,7 +1136,11 @@ WHERE { + An annotation property that links an ontology entity or a statement to a prefixed identifier or URI. + + database_cross_reference + has cross-reference @@ -1206,12 +1223,6 @@ WHERE { - - - - - - @@ -1681,7 +1692,6 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 A relationship between a process and a barrier, where the process occurs in a region spanning the barrier. For cellular processes the barrier is typically a membrane. Examples include transport across a membrane and membrane depolarization. - 2017-07-20T17:19:37Z occurs across @@ -3966,7 +3976,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different - p results in organization of c iff p results in the assembly, arrangement of constituent parts, or disassembly of c RO:0002592 @@ -4088,7 +4097,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different p 'has primary input ot output' c iff either (a) p 'has primary input' c or (b) p 'has primary output' c. - 2018-12-13T11:26:17Z RO:0004007 external @@ -4106,7 +4114,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different p has primary output c if (a) p has output c and (b) the goal of process is to modify, produce, or transform c. - 2018-12-13T11:26:32Z RO:0004008 external @@ -4134,7 +4141,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different p has primary input c if (a) p has input c and (b) the goal of process is to modify, consume, or transform c. - 2018-12-13T11:26:56Z RO:0004009 external @@ -4161,7 +4167,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different - 2018-03-13T23:55:05Z causally upstream of or within, negative effect https://wiki.geneontology.org/Causally_upstream_of_or_within,_negative_effect @@ -4173,7 +4178,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different - 2018-03-13T23:55:19Z causally upstream of or within, positive effect @@ -4187,7 +4191,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different a relation between a process and a continuant, in which the process is regulated by the small molecule continuant - 2020-04-22T20:27:26Z has small molecule regulator @@ -4200,7 +4203,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different a relation between a process and a continuant, in which the process is activated by the small molecule continuant - 2020-04-22T20:28:37Z RO:0012001 external @@ -4217,7 +4219,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different p acts on population of c iff c' is a collection, has members of type c, and p has participant c - 2020-06-08T17:21:33Z RO:0012003 external @@ -4237,7 +4238,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different a relation between a continuant and a process, in which the continuant is a small molecule that regulates the process - 2020-06-24T13:15:17Z is small molecule regulator of @@ -4250,7 +4250,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different a relation between a continuant and a process, in which the continuant is a small molecule that activates the process - 2020-06-24T13:15:26Z is small molecule activator of https://wiki.geneontology.org/Is_small_molecule_activator_of @@ -4262,7 +4261,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different - 2021-02-26T07:28:29Z RO:0012008 external @@ -4286,7 +4284,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different A relationship between a neuron and a region, where the neuron has a functionally relevant number of input and/or output synapses in that region. - 2020-07-17T09:26:52Z has synaptic input or output in has synaptic IO in region @@ -4303,7 +4300,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different Relation between a sensory neuron and some structure in which it receives sensory input via a sensory dendrite. - 2020-07-20T12:10:09Z has sensory dendrite location has sensory terminal in @@ -4313,6 +4309,20 @@ Each of these 3 primitives can be composed to yield a cross-product of different + + + + + A relation that applies between a cell type and a set of markers that can be used to uniquely identify that cell type. + C has_characterizing_marker_set y iff: C is a cell type and y is a collection of genes or proteins whose expression is sufficient to distinguish cell type C from most or all other cell types. + + has marker gene combination + has marker signature set + has characterizing marker set + + + + @@ -4452,7 +4462,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different p has anatomical participant c iff p has participant c, and c is an anatomical entity - 2018-09-26T01:08:58Z RO:0040036 external @@ -4796,6 +4805,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different XAO:0003012 ZFA:0009000 + + The definition of cell is intended to represent all cells, and thus a cell is defined as a material entity and not an anatomical structure, which implies that it is part of an organism (or the entirety of one). cell @@ -4827,6 +4838,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different A cell found in the embryo before the formation of all the gem layers is complete. ZFA:0009002 + + early embryonic cell (metazoa) @@ -4880,6 +4893,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different animal stem cell + + This term applies to metazoan. For plant stem cells, consider using PO:0004011 ‘initial cell’ or its parent PO:0004010 ‘meristematic cell’. stem cell @@ -5067,6 +5082,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different colony forming unit hematopoietic + + Markers differ between species, and two sets of markers have been described for mice. HSCs are reportedly CD34-positive, CD45-positive, CD48-negative, CD150-positive, CD133-positive, and CD244-negative. hematopoietic stem cell @@ -5118,6 +5135,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different erythroid stem cell + + erythroid progenitor cell @@ -5186,7 +5205,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different - @@ -5225,6 +5243,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different colony forming unit macrophage colony forming unit monocyte monocyte stem cell + + Morphology: mononuclear cell, diameter 12-20 _M, non-granular, N/C ratio 3/1 - 4/1; markers: CD11b (shared with many other myeloid cells); location: Adult: bone marrow; fetal: liver, Yolk Sac; role or process: hematopoiesis, monocyte development; lineage: hematopoietic, myeloid. monoblast @@ -5290,6 +5310,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different multifate stem cell multipotent cell multipotent stem cell + + multi fate stem cell @@ -5327,6 +5349,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different myeloid stem cell pluripotent stem cell (bone marrow) + + This cell type is intended to be compatible with any vertebrate common myeloid progenitor. For mammalian CMP known to be CD34-positive, please use the term 'common myeloid progenitor, CD34-positive' (CL_0001059). common myeloid progenitor @@ -5445,6 +5469,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different megakaryocyte/erythrocyte progenitor megakaryocyte/erythroid progenitor cell + + MEPs are reportedly CD19-negative, CD34-negative, CD45RA-negative, CD110-positive, CD117-positive, and SCA1-negative and reportedly express the transcription factors GATA-1 and NF-E2. megakaryocyte-erythroid progenitor cell @@ -5510,6 +5536,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different lymphoid stem cell lymphopoietic stem cell + + CLP are CD7-positive, CD10-positive, CD19-negative, CD34-positive, CD45RA-positive, CD79a-negative, CD127-positive, AA4.1-positive, RAG-negative, Sca-1-low, sIgM-negative, sIgD-negative, TdT-negative, Vpre-B-negative, and pre-BCR-negative. Expression of transcription factors include E2A-positive, EBF-positive, Ikaros-negative, PU.1-negative, and Pax5-negative. common lymphoid progenitor @@ -5560,6 +5588,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different MESH:D039901 ZFA:0009024 totipotential stem cell + + totipotent stem cell @@ -5587,6 +5617,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different FMA:84782 blast cell + + define using PATO mulit-potent or oligopotent? non-terminally differentiated cell @@ -5610,6 +5642,9 @@ Each of these 3 primitives can be composed to yield a cross-product of different FMA:70335 VHOG:0001529 ZFA:0009025 + + + myoblast @@ -5638,13 +5673,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - - - - - - + A connective tissue cell which secretes an extracellular matrix rich in collagen and other macromolecules. Flattened and irregular in outline with branching processes; appear fusiform or spindle-shaped. BTO:0000452 @@ -5655,6 +5684,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different ZFA:0009026 + + These cells may be vimentin-positive, fibronectin-positive, fsp1-positive, MMP-1-positive, collagen I-positive, collagen III-positive, and alpha-SMA-negative. fibroblast @@ -5699,6 +5730,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different epitheliocyte + + epithelial cell https://www.swissbiopics.org/api/image/Epithelial_cells.svg @@ -5751,6 +5784,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different ZFA:0009036 + + blood vessel endothelial cell @@ -5794,6 +5829,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different CALOHA:TS-1249 ZFA:0009039 + + squamous epithelial cell @@ -5834,6 +5871,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different A cell which moves among different tissues of the body, via blood, lymph, or other medium. ZFA:0009043 + + circulating cell @@ -5878,6 +5917,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different ZFA:0009044 + + blood cell @@ -5945,6 +5986,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different mature T cell + + T cell @@ -6020,7 +6063,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different - @@ -6076,13 +6118,20 @@ Each of these 3 primitives can be composed to yield a cross-product of different A specialized phagocytic cell associated with the absorption and removal of the mineralized matrix of bone tissue, which typically differentiates from monocytes. This cell has the following markers: tartrate-resistant acid phosphatase type 5-positive, PU.1-positive, c-fos-positive, nuclear factor NF-kappa-B p100 subunit-positive, tumor necrosis factor receptor superfamily member 11A-positive and macrophage colony-stimulating factor 1 receptor-positive. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Osteoclasts, derived from the monocyte/macrophage lineage, play a crucial role in bone remodeling through bone resorption. They are distinguished from other cells by their large size and their unique ability to secrete enzymes and acids that dissolve the calcium phosphate in bone. The formation of osteoclasts is influenced by two primary factors: macrophage colony-stimulating factor (M-CSF) and the ligand-activated receptor (RANKL) of nuclear factor kappa B (NF-κB). +Osteoclasts also collaborate with osteoblasts, responsible for new bone formation, to maintain bone health and adapt bone structure. Their coordinated actions allow continuous remodeling while preserving overall bone strength and integrity. Imbalances in osteoclast activity can lead to pathological conditions. For example, excessive activity may contribute to diseases like osteoporosis, periprosthetic osteolysis, bone tumors, and Paget's disease. Other the other hand, osteoclast deficiency ca result in conditions like osteopetrosis. BTO:0000968 CALOHA:TS-0721 FMA:66781 MESH:D010010 ZFA:0009047 + https://cellxgene.cziscience.com/cellguide/CL_0000092 chondroclast + + Morphology: Highly vesicular; markers: Surface: RANK, cFMS (MCSF receptor); Secreted: cathepsin K and TRAP (tartate resistant acid phosphatase); transcription factors: PU.1, cFOS, MITF, NFkB (p52); role or process: tissue remodelling: bone resorption; lineage: hematopoietic, myeloid. osteoclast @@ -6110,6 +6159,17 @@ Each of these 3 primitives can be composed to yield a cross-product of different PMID:15055519 PMID:17380158 + + + + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Osteoclasts, derived from the monocyte/macrophage lineage, play a crucial role in bone remodeling through bone resorption. They are distinguished from other cells by their large size and their unique ability to secrete enzymes and acids that dissolve the calcium phosphate in bone. The formation of osteoclasts is influenced by two primary factors: macrophage colony-stimulating factor (M-CSF) and the ligand-activated receptor (RANKL) of nuclear factor kappa B (NF-κB). +Osteoclasts also collaborate with osteoblasts, responsible for new bone formation, to maintain bone health and adapt bone structure. Their coordinated actions allow continuous remodeling while preserving overall bone strength and integrity. Imbalances in osteoclast activity can lead to pathological conditions. For example, excessive activity may contribute to diseases like osteoporosis, periprosthetic osteolysis, bone tumors, and Paget's disease. Other the other hand, osteoclast deficiency ca result in conditions like osteopetrosis. + DOI:10.3389/fmed.2017.00234 + DOI:10.37175/stemedicine.v1i4.57 + https://www.sciencedirect.com/topics/medicine-and-dentistry/osteoclast + @@ -6167,7 +6227,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different - @@ -6227,6 +6286,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different granular leukocyte polymorphonuclear leukocyte + + granulocyte @@ -6314,7 +6375,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different - @@ -6404,6 +6464,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different tissue basophil + + Mast cells are generally integrin beta-7-negative and positive for TLR2, TLR3, TLR4, TLR5, TLR7, TLR9, C3aR, C5aR, CR3, CR4, VEGF, FGF2, and renin. They can express MHC Class I and II on their surface. Activated murine mast cells (IgE+Antigen) were capable of expressing the following co-stimulatory molecules: CD95 (Fas), CD120b, CD137 (4-1BB), CD153 (CD30L), CD154 (CD40L), GITR, ICOSL, OX40L, PD-L1, and PD-L2. Note that there was some mouse strain variation. Mast cells have also been demonstrated to produce bFGF, CCL2, CCL4, CCL5, CCL11, CCL20, CXCL2, CXCL8, CXCL10, GM-CSF, IFN-gamma, IL-1, IL-2, IL-3, IL-8, IL-10, IL-11, IL-12, IL-13, IL-16, IL-25, IL-18, MIP-1, prostaglandin D2, SCF, TGF-beta, TNF-alpha, TSLP, VEGF, and XCL1. They express the transcription factors Transcription factors AP-1, GATA1, MITF, Notch2, PIAS3, PU.1, and STAT5. mast cell @@ -6470,7 +6532,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different A vertebrate phagocyte with a single nucleus. - This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. Mononuclear phagocytes are immune cells that form a critical part of the body's innate immune system, the body's first line of defense against infections. Mononuclear phagocytes are characterized by the presence of a single, large nucleus. The ‘Mononuclear Phagocyte System’ nomenclature was introduced to distinguish mononuclear monocytes and macrophages from other cells with multiple nuclei. However, the cells within the mononuclear phagocyte system represent a highly heterogeneous group, all of which are able to perform highly efficient phagocytosis - engulfing and digesting microbes and cellular debris to fight infections and to maintain normal tissue homeostasis. In addition to phagocytosis, mononuclear phagocytes also secrete chemical compounds to recruit other immune cells to a site of infection. These cells produce different types of signaling molecules, including cytokines, chemokines, and reactive oxygen species, triggering a cascade of responses to ensure rapid and efficient containment and neutralization of invading pathogens. These cells are also involved in antigen presentation, a process essential for stimulating an adaptive immune response. They can process and present antigens to T cells, thereby linking the innate and adaptive immune responses. @@ -6479,6 +6541,8 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf ZFA:0009064 https://cellxgene.cziscience.com/cellguide/CL_0000113 + + mononuclear phagocyte @@ -6499,7 +6563,7 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf - This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. Mononuclear phagocytes are immune cells that form a critical part of the body's innate immune system, the body's first line of defense against infections. Mononuclear phagocytes are characterized by the presence of a single, large nucleus. The ‘Mononuclear Phagocyte System’ nomenclature was introduced to distinguish mononuclear monocytes and macrophages from other cells with multiple nuclei. However, the cells within the mononuclear phagocyte system represent a highly heterogeneous group, all of which are able to perform highly efficient phagocytosis - engulfing and digesting microbes and cellular debris to fight infections and to maintain normal tissue homeostasis. In addition to phagocytosis, mononuclear phagocytes also secrete chemical compounds to recruit other immune cells to a site of infection. These cells produce different types of signaling molecules, including cytokines, chemokines, and reactive oxygen species, triggering a cascade of responses to ensure rapid and efficient containment and neutralization of invading pathogens. These cells are also involved in antigen presentation, a process essential for stimulating an adaptive immune response. They can process and present antigens to T cells, thereby linking the innate and adaptive immune responses. @@ -6536,6 +6600,8 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf ZFA:0009065 endotheliocyte + + From FMA: 9.07.2001: Endothelial cell has always been classified as a kind of epithelial cell, specifically a squamous cell but that is not true. First, endothelial cell can either be squamous or cuboidal (e.g. high-endothelial cell) and secondly, it has different embryological derivation (mesodermal) than a true epithelial cell (ectodermal and endodermal). The basis for present classification is the fact that it comprises the outermost layer or lining of anatomical structures (location-based) but a better structural basis for the differentia is the cytoskeleton of the cell. Endothelial cell has vimentin filaments while an epithelial cell has keratin filaments. [Onard]. endothelial cell @@ -6566,6 +6632,8 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf Ectoderm destined to be nervous tissue. ZFA:0009080 neurectoderm cell + + neurectodermal cell @@ -6607,6 +6675,8 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf mesenchymal stromal cells stem cells, mesenchymal + + Many but not all mesenchymal cells derive from the mesoderm. MSCs are reportedly CD3-negative, CD4-negative, CD5-negative, CD8-negative, CD11a-negative, CD11b-negative, CD14-negative, CD19-negative, CD29-positive, CD31-negative, CD34-negative, CD38-negative, CD40-negative, CD44-positive, CD45-negative, CD49-positive, CD54-positive, CD66b-negative, CD79a-negative, CD80-negative, CD102-positive, CD106-positive, CD117-positive, CD121a-positive, CD121b-positive, CD123-positive, CD124-positive, CD133-negative, CD146-positive, CD166-positive, CD271-positive, B220-negative, Gr1-negative, MHCI-positive, MHCII-negative, SSEA4-negative, sca1-positive, Ter119-negative, and glycophorin A-negative. Cultured MSCs are capable of producing stem cell factor, IL7, IL8, IL11, TGF-beta, cofilin, galectin-1, laminin-receptor 1, cyclophilin A, and MMP-2. mesenchymal stem cell https://github.com/obophenotype/cell-ontology/issues/474 @@ -6711,6 +6781,8 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf APC + + Note change of name; nearly all somatic cells can present antigens to T cells via MHC Class I complexes leading to effector responses, but professional antigen presenting cells constitutively express MHC Class II as well as costimulatory molecules, and thus can initiate immune responses via T cells. professional antigen presenting cell @@ -6761,6 +6833,8 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf BTO:0003659 FMA:86916 + + secretory cell @@ -6779,6 +6853,8 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf A cell whose primary function is to shorten. + + contractile cell @@ -6813,6 +6889,8 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf muscle fiber myocyte + + muscle cell https://www.swissbiopics.org/api/image/Muscle_cells.svg @@ -6843,6 +6921,8 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf A cell whose function is determined by the generation or the reception of an electric signal. ZFA:0009128 + + electrically active cell @@ -6867,6 +6947,8 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf A cell within an epithelial cell sheet whose main function is to act as an internal or external covering for a tissue or an organism. ZFA:0009130 boundary cell + + lining cell @@ -6890,6 +6972,8 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf A cell whose primary function is to prevent the transport of stuff across compartments. ZFA:0009132 + + barrier cell @@ -6930,6 +7014,8 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf A cell that moves by its own activities. ZFA:0009136 + + motile cell @@ -6962,6 +7048,9 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf FMA:72549 ZFA:0009137 ectoderm cell + + + ectodermal cell @@ -6991,11 +7080,18 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf A cell of the middle germ layer of the embryo. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Mesodermal cells are pluripotent and the most abundant in the human body. They contribute to the development of several structures such as the skeletal muscles, bones, heart and blood vessels, kidneys, gonads, connective tissues, and certain layers of the skin. Hence, the mesoderm is often regarded as an active and diverse layer due to its role in forming many bodily structures. +In embryonic development, these cells are instrumental, contributing to the body's structures through a carefully coordinated sequence of morphogenetic movements. This process forms the complex multicellular architecture of tissues and organs from a simple ball of cells. Without the function of mesodermal cells, the body's integral structures and systems would cease to form correctly, leading to developmental disorders such as axial mesodermal dysplasia complex FMA:72554 ZFA:0009138 + https://cellxgene.cziscience.com/cellguide/CL_0000222 mesoblast mesoderm cell + + mesodermal cell @@ -7004,6 +7100,17 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf A cell of the middle germ layer of the embryo. MESH:D008648 + + + + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Mesodermal cells are pluripotent and the most abundant in the human body. They contribute to the development of several structures such as the skeletal muscles, bones, heart and blood vessels, kidneys, gonads, connective tissues, and certain layers of the skin. Hence, the mesoderm is often regarded as an active and diverse layer due to its role in forming many bodily structures. +In embryonic development, these cells are instrumental, contributing to the body's structures through a carefully coordinated sequence of morphogenetic movements. This process forms the complex multicellular architecture of tissues and organs from a simple ball of cells. Without the function of mesodermal cells, the body's integral structures and systems would cease to form correctly, leading to developmental disorders such as axial mesodermal dysplasia complex + DOI:10.1016/j.ceb.2019.07.012 + DOI:10.5535/arm.2016.40.1.162 + https://www.sciencedirect.com/topics/biochemistry-genetics-and-molecular-biology/mesoderm + @@ -7028,6 +7135,8 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf FMA:72555 ZFA:0009139 endoderm cell + + endodermal cell @@ -7070,6 +7179,8 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf A cell that lacks a nucleus. FMA:68647 non-nucleated cell + + anucleate cell @@ -7104,6 +7215,8 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf A cell with a single nucleus. + + single nucleate cell @@ -7141,6 +7254,8 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf A cell with more than one nucleus. multinucleated cells polynuclear cells + + multinucleate cell @@ -7231,6 +7346,8 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf red blood cell + + erythrocyte @@ -7285,6 +7402,8 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf enucleate thrombocyte + + Platelets are reportedly CCR1-positive, CCR2-negative, CCR3-positive, CCR4-positive, CCR5-negative, CCR6-negative, CCR7-negative, CCR8-negative, CCR9-negative, CCR10-negative, CD16-positive, CD23-positive, CD32-positive, CD40-positive, CD41-positive CD42-positive, CD61-positive, CD62P-positive, CD64-positive, CD89-positive, CD102-positive, CD147-positive (activated platelets), CD154-positive (activated platelets), CD162-positive, CD209, CD282-positive, CD284-positive, CD289-positive, CD181-negative, CD182-negative, CD183-negative, CD184-positive, CLEC2-positive, GPVI-positive, JAMC-positive, PAR1-positive, PAR2-negative, PAR3-positive, PAR4-positive, TSP1-positive, and TXA2R-positive. Platelets can reportedly produce CCL2, CCL3, CCL5, CCL7, CCL17, CD40L, CXCL1, CXCL4, CXCL4L1, CXCL5, CXCL7, CXCL8, CXCL12, EGF, factor V, factor VII, factor XI, factor XIII, bFGF, histamine, IGF-1, IL-1beta, PAI-1, PDGF, plasminogen, protein S, serotonin, TGF-beta, TFPI, VEGF, and vWF. platelet @@ -7341,7 +7460,8 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf FMA:83806 MESH:D010586 ZFA:0009140 - + + phagocyte @@ -7409,6 +7529,8 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf + + Morphology: Diameter 30_M-80 _M, abundant cytoplasm, low N/C ratio, eccentric nucleus. Irregular shape with pseudopods, highly adhesive. Contain vacuoles and phagosomes, may contain azurophilic granules; markers: Mouse & Human: CD68, in most cases CD11b. Mouse: in most cases F4/80+; role or process: immune, antigen presentation, & tissue remodelling; lineage: hematopoietic, myeloid. macrophage @@ -7473,6 +7595,8 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf + + B cell @@ -7523,7 +7647,8 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf Any cell that in taxon some Eukaryota. MESH:D005057 - + + eukaryotic cell @@ -7540,6 +7665,8 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf A cell that is specialised to accumulate a particular substance(s). + + stuff accumulating cell @@ -7575,6 +7702,8 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf Any cell that is capable of some oxygen transport. ZFA:0009164 + + oxygen accumulating cell @@ -7607,6 +7736,8 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf A cell derived from the specialized ectoderm flanking each side of the embryonic neural plate, which after the closure of the neural tube, forms masses of cells that migrate out from the dorsal aspect of the neural tube to spread throughout the body. FMA:86667 ZFA:0007086 + + migratory neural crest cell @@ -7630,6 +7761,8 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf A mesenchymal cell in embryonic development found in a contracting mass and that gives rise to osteoprogenitors. ZFA:0009166 + + mesenchyme condensation cell @@ -7653,6 +7786,8 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf A cell of the outer layer of a blastula that gives rise to the ectoderm after gastrulation. + + epiblast cell @@ -7693,6 +7828,8 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf BTO:0000854 EHDAA2:0004546 FMA:72395 + + animal zygote @@ -7710,6 +7847,8 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf A cell whose function is determined by its response to an electric signal. ZFA:0009190 + + electrically responsive cell @@ -7733,6 +7872,8 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf A cell that initiates an electrical signal and passes that signal to another cell. ZFA:0009193 + + electrically signaling cell @@ -7806,7 +7947,6 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf - @@ -7867,6 +8007,8 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf veiled cell + + dendritic cell @@ -7891,6 +8033,8 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf ZFA:0009212 + + biogenic amine secreting cell @@ -7927,6 +8071,8 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf ZFA:0009213 5-HT secreting cell 5-Hydroxytryptamine secreting cell + + serotonin secreting cell @@ -7950,6 +8096,8 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf A cell whose primary function is to protect the organism. + + defensive cell @@ -7961,6 +8109,44 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf + + + + + + + + + + + A connective tissue cell of an organ found in the loose connective tissue. + + BTO:0002064 + FMA:83624 + ZFA:0009226 + + + + + + stromal cell + + + + + A connective tissue cell of an organ found in the loose connective tissue. + GOC:tfm + MESH:D017154 + + + + + ZFA:0009226 + + + + + @@ -7973,6 +8159,8 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf A phagocyte in vertebrates that is able to phagocytosis. + + phagocyte (sensu Vertebrata) @@ -8008,6 +8196,8 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf nerve cell + + These cells are also reportedly CD4-negative and CD200-positive. They are also capable of producing CD40L and IFN-gamma. neuron @@ -8096,6 +8286,8 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf VHOG:0001535 ZFA:0009250 + + Editors note: consider adding taxon constraint to vertebrata (PMID:18025161) lymphocyte @@ -8193,7 +8385,6 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf - @@ -8296,6 +8487,8 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf pronormoblast + + proerythroblast @@ -8343,7 +8536,6 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf - @@ -8369,6 +8561,8 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf early erythroblast early normoblast prorubricyte + + basophilic erythroblast @@ -8440,7 +8634,6 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf - @@ -8474,6 +8667,8 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf polychromatic normoblast polychromatophilic normoblast rubricyte + + polychromatophilic erythroblast @@ -8577,6 +8772,8 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf late erythoblast orthochromatic normoblast pyknotic eto enrythroblast + + orthochromatic erythroblast @@ -8793,6 +8990,8 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf promegacaryocyte promegakaryocyte + + Lineage negative is described here as CD2-negative, CD3-negative, CD4-negative, CD5-negative, CD8a-negative, CD14-negative, CD19-negative, CD20-negative, CD56-negative, Ly6g-negative, and Ter119-negative. megakaryocyte progenitor cell @@ -8866,6 +9065,8 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf megalokaryocyte + + Megakaryocytes are reportedly CD181-positive and CD182-positive. megakaryocyte @@ -8932,9 +9133,7 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf - - @@ -8979,8 +9178,13 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf A hematopoietic progenitor cell that is committed to the granulocyte and monocyte lineages. These cells are CD123-positive, and do not express Gata1 or Gata2 but do express C/EBPa, and Pu.1. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Granulocyte monocyte progenitor cells (GMP cells), originating from hematopoietic stem cells in the bone marrow, are a critical intermediate in myeloid cell development. Positioned at a key differentiation juncture, these cells exhibit bidirectional potential, giving rise to both granulocyte and monocyte lineages. +Their primary role is to generate mature granulocytes and monocytes, essential components of the body's innate immunity and inflammatory responses. Granulocytes, such as neutrophils, eosinophils, and basophils, contribute to the first line of defense against infections by migrating to the infection site and phagocytosing pathogens. Monocytes can differentiate into macrophages or dendritic cells, playing diverse roles in immune responses. CFU-C , Colony forming unit in culture ZFA:0009251 + https://cellxgene.cziscience.com/cellguide/CL_0000557 colony forming unit granulocyte macrophage granulocyte-macrophage progenitor granulocyte/monocyte precursor @@ -8988,6 +9192,8 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf CFU-GM GMP + + Originally described in the dendritic cell ontology (DC_CL:0000042)(PMID:19243617). GMPs are reportedly CD16-positive, CD32-positive, CD34-positive, CD38-positive, CD45RA-positive, CD110-negative, CD117-positive, CD123-positive, and SCA1-negative. granulocyte monocyte progenitor cell @@ -9009,6 +9215,17 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf http://en.wikipedia.org/wiki/CFU-GM http://www.copewithcytokines.de + + + + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Granulocyte monocyte progenitor cells (GMP cells), originating from hematopoietic stem cells in the bone marrow, are a critical intermediate in myeloid cell development. Positioned at a key differentiation juncture, these cells exhibit bidirectional potential, giving rise to both granulocyte and monocyte lineages. +Their primary role is to generate mature granulocytes and monocytes, essential components of the body's innate immunity and inflammatory responses. Granulocytes, such as neutrophils, eosinophils, and basophils, contribute to the first line of defense against infections by migrating to the infection site and phagocytosing pathogens. Monocytes can differentiate into macrophages or dendritic cells, playing diverse roles in immune responses. + DOI:10.1016/j.immuni.2017.10.021 + DOI:10.1146/annurev-immunol-081022113627 + DOI:10.1186/2050-7771-2-1 + @@ -9121,7 +9338,6 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf - @@ -9213,6 +9429,8 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf ZFA:0009252 + + reticulocyte @@ -9263,7 +9481,6 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf - @@ -9288,6 +9505,8 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf FMA:83551 ZFA:0009253 + + Morphology: Mononuclear cell, diameter 14-18 _M, fine azurophilic granules; markers: CD11b (shared with many other myeloid cells); location: Adult: bone marrow; Fetal: Liver, Yolk Sac; role or process: hematopoiesis, monocyte development; lineage: hematopoietic, myeloid. promonocyte @@ -9338,7 +9557,6 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf - @@ -9367,6 +9585,8 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf ZFA:0009258 angioblast chondroplast + + These cells are reportedly CD31-positive, CD34-positive, CD144-positive, CD309-positive, and TAL1-positive. angioblastic mesenchymal cell @@ -9455,6 +9675,8 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf + + Morphology: Mononuclear cell, diameter, 14 to 20 _M, N/C ratio 2:1-1:1. Nucleus may appear in variety of shapes: round, kidney, lobulated, or convoluted. Fine azurophilic granules present; markers: CD11b (shared with other myeloid cells), human: CD14, mouse: F4/80-mid,GR1-low; location: Blood, but can be recruited into tissues; role or process: immune & tissue remodelling; lineage: hematopoietic, myeloid. monocyte @@ -9534,6 +9756,8 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf syncytial giant cell MGC + + Role or process: Chronic infection, granulomatous inflammation. Consider also megakaryocyte (CL:0000556) as sometimes multinucleated giant cell is used to refer to this. multinucleated giant cell @@ -9630,6 +9854,8 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf A non-terminally differentiated cell that is capable of developing into a muscle cell. ZFA:0009291 + + muscle precursor cell @@ -9672,6 +9898,8 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf CALOHA:TS-2086 MESH:D053687 ZFA:0009307 + + somatic stem cell @@ -9747,6 +9975,8 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf white blood cell immune cell + + leukocyte @@ -9808,6 +10038,8 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf A nucleated blood cell involved in coagulation, typically seen in birds and other non-mammalian vertebrates. ZFA:0009323 + + Note that this is a non-mammalian cell type. Use platelet ; CL:0000233 for thrombocytes (platelets) in mammals. nucleated thrombocyte @@ -9862,6 +10094,8 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf MESH:D022423 ZFA:0009324 + + myeloid cell @@ -9897,6 +10131,8 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf ZFA:0009325 erythropoietic cell + + Note that in FMA erythropoietic cells are types of nucleated erythrocytes and thus don't include erythrocytes. erythroid lineage cell @@ -10084,6 +10320,8 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf normoblast + + erythroblast @@ -10128,6 +10366,8 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf A cell of the monocyte, granulocyte, or mast cell lineage. ZFA:0009326 + + myeloid leukocyte @@ -10223,6 +10463,8 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf basophilic leukocyte + + Matures in the bone marrow and account for <1% of leukocytes in the peripheral blood, spleen, and bone marrow. Basophils are described as being CD11a-positive, CD11b-positive, CD13-positive, CD15-positive, CD18-positive, CD21-positive, CD25-positive, CD29-positive, CD35-positive, CD40-positive, CD40L-positive, CD44-positive, CD45R-negative, CD46-positive, CD49a-positive, CD49b-positive, CD49d-positive, CD55-positive, CD59-positive, CD62L-positive, CD63-positive, CD69-positive, CD90-negative, CD116-positive, CD117-negative, CD124-positive, CD125-positive, CD131-positive, CD161-positive, CD184-positive, CD191-positive, CD192-positive, CD197-positive, CD200R3-positive, CD218-positive, CD282-positive, CD284-positive, CD289-positive, CD290-positive, CD294-positive, natural killer cell receptor 2B4-positive, smad1-positive, CD3-negative, CD4-negative, CD7-negative, CD8-negative, CD14-negative, CD15-negative, CD16-negative, CD19-negative, CD20-negative, CD34-negative, CD36-negative, CD45R-negative, CD56-negative, CD57-negative, CD235a-negative, and GR1-negative. Transcription factors- GATA1-positive, PU.1-positive. basophil @@ -10327,6 +10569,8 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf eosinophilic leukocyte + + Eosinophils are also CD14-negative, CD32-positive, CD44-positive, CD48-positive, CD69-positive, CD192-negative, MBP1-positive, MBP2-positive, TLR2-negative, TLR4-negative, and lineage-negative (B220, CD2, CD14, CD19, CD56, CD71, CD117, CD123, CD235a (glycophorin A), and TER119). The cytokines IL-3, IL-5, and GM-CSF are involved in their development and differentiation. Usually considered CD16-negative, CD16 is observed on eosinophilic metamyelocyte. eosinophil @@ -10405,6 +10649,8 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf neutrophilic leukocyte + + neutrophil @@ -10471,6 +10717,8 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf CD11c+CD123- DC mDC + + These cells are CD1a-negative, CD1b-positive, CD11a-positive, CD11c-positive, CD13-positive, CD14-negative, CD20-negative, CD21-negative, CD33-positive, CD40-negative, CD50-positive, CD54-positive, CD58-positive, CD68-negative, CD80-negative, CD83-negative, CD85j-positive, CD86-positive, CD89-negative, CD95-positive, CD120a-negative, CD120b-positive, CD123-negative, CD178-negative, CD206-negative, CD207-negative, CD209-negative, and TNF-alpha-negative. Upon TLR stimulation, they are capable of producing high levels of TNF-alpha, IL-6, CXCL8 (IL-8). myeloid dendritic cell @@ -10527,6 +10775,8 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf type 2 DC + + plasmacytoid dendritic cell @@ -10603,6 +10853,8 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf mature B-cell mature B-lymphocyte + + Mature B cells are also reportedly CD10-negative, CD19-positive, CD22-positive, CD34-negative, CD48-positive, CD79a-positive, CD84-positive, CD127-negative, CD352-positive, RAG-negative, TdT-negative, Vpre-B-negative, and pre-BCR-negative. Transcription factors expressed: Pax5-positive. mature B cell @@ -10664,7 +10916,6 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf - @@ -10721,6 +10972,8 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf effector B-cell + + Plasma cells develop in the spleen and migrate to the bone marrow. Plasma cells are also reportedly CD5-negative, CD10-negative, CD19-positive, CD20-negative, CD21-negative, CD22-negative, CD23-negative, CD24-negative, CD25-negative, CD27-positive, CD34-negative, CD38-positive, CD40-positive, CD43-positive, CD45-positive, CD48-positive, CD53-low, CD80-negative, CD81-positive, CD86-positive, CD95-positive, CD196-negative, CD229-positive, CD270-positive, CD352-positive, CD361-positive, and IgD-negative. Transcription factors: BLIMP1-positive, IRF4-positive, PAX5-negative, SpiB-negative, Ets1-negative, and XBP1-positive. plasma cell @@ -10770,7 +11023,6 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf - @@ -10785,6 +11037,8 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf alpha-beta T-lymphocyte + + alpha-beta T cell @@ -10825,7 +11079,6 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf - @@ -10842,6 +11095,8 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf gd T cell + + Note that gamma-delta T cells have both thymic and extrathymic differentiation pathways. gamma-delta T cell @@ -10941,6 +11196,8 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf newly formed B cell + + Immature B cells are also reportedly CD5-positive, CD10-positive, CD19-positive, CD20-positive, CD21-positive, CD22-positive, CD24-positive, CD25-negative, CD27-negative, CD34-negative, CD38-positive, CD40-positive, CD43-negative, CD45-positive, CD48-positive, CD53-positive, CD79a-positive, CD80-negative, CD81-positive, CD86-negative, CD95-negative, CD127-negative, CD138-negative, CD185-positive, CD196-positive, MHCII/HLA-DR-positive, RAG-positive, TdT-negative, Vpre-B-negative, and preBCR-negative. Transcription factors expressed: Pax5-positive. immature B cell @@ -11012,6 +11269,8 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf ZFA:0009344 pre-B cell + + precursor B cell @@ -11116,6 +11375,8 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf T2 B cell T3 B cell + + This cell type is compatible with the HIPC Lyoplate markers for 'transitional B cell'. transitional stage B cell @@ -11174,7 +11435,6 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf - @@ -11213,6 +11473,8 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf progenitor B-lymphocyte pre-B cell (Philadelphia nomenclature) + + Human pro-B cells are reportedly CD10-positive, CD22-positive, CD34-positive, CD38-positive, CD45-low, CD48-positive, CD79a-positive, CD127-positive, CD184-positive, RAG-positive, TdT-positive, Vpre-B-positive, pre-BCR-negative, IgD-negative, and IgM-negative. Transcription factors expressed: Pax5-positive, EBF-positive, E2A-negative, Ikaros-negative, and PU.1-negative. pro-B cell @@ -11290,6 +11552,8 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf DN1 thymocyte TN1 cell + + pro-T cell @@ -11349,6 +11613,8 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf A progenitor cell of the thrombocyte, a nucleated blood cell involved in coagulation typically seen in birds and other non-mammalian vertebrates. ZFA:0009351 + + Note that this is a non-mammalian cell type. thromboblast @@ -11483,7 +11749,6 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf - @@ -11639,6 +11904,8 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf CFU-MC CFU-Mast colony forming unit mast cell + + MCP are CD16-positive, CD32-positive, CD34-positive, CD45-positive, integrin beta-7-positive, and lin-negative (CD2, CD3e, CD4, CD5, CD8a, CD14, CD19, CD20, CD27, integrin alpha-M, ly6c, ly6g, NCAM-1, and ter119). These cells also express the transcription factors GATA-1, GATA-2, and MITF, but not C/EBPa. mast cell progenitor @@ -11735,7 +12002,6 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf - @@ -11842,6 +12108,8 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf hemopoietic progenitor cell + + Markers differ between mouse and human. hematopoietic multipotent progenitor cell @@ -11893,6 +12161,8 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf FMA:70338 ZFA:0009355 + + Note that this is a class of cell types, not an identified single cell type. lymphoid lineage restricted progenitor cell @@ -11948,6 +12218,8 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf FMA:70339 ZFA:0009356 + + Note that this is a class of cell types, not an identified single cell type. myeloid lineage restricted progenitor cell @@ -12000,6 +12272,8 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf peripheral blood mononuclear cell + + mononuclear cell @@ -12050,7 +12324,6 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf - @@ -12077,6 +12350,9 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf An immature myeloid leukocyte of heterogeneous phenotype found particularly in cancer and sepsis patients that is capable of suppressing activity of T cells in ex vivo assays. This cell type is CD45-positive, CD11b-positive. + + + Markers: Mouse: CD11b+GR1+CD31+; Human: CD34+ CD33+CD15-CD13+. (According to some reports in humans these cells are iNOS+ARG1+IL13+IFNg+); location: In cancerous tissue; in the blood and lymphoid organs in sepsis. myeloid suppressor cell @@ -12112,6 +12388,9 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf A lymphocyte of B lineage with the commitment to express an immunoglobulin complex. + + + Types of B lineage lymphocytes include B cells and antibody secreting cells (plasmablasts and plasma cells). Lymphocytes of B cell lineage can be distinguished from those of T cell lineage by their lack of CD3e (as part of the T cell receptor complex). lymphocyte of B lineage @@ -12157,6 +12436,8 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf A lymphocyte of B lineage that is devoted to secreting large amounts of immunoglobulin. + + antibody secreting cell @@ -12242,6 +12523,8 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf A small pre-B-II cell is a pre-B-II cell that is Rag1-positive, Rag2-positive, pre-BCR-negative, and BCR-negative, is not proliferating, and carries a DNA rearrangement of one or more immunoglobulin light chain genes. small pre-BII cell + + Small pre-B-II cells are also reportedly CD10-positive, CD19-positive, CD34-negative, CD79a-positive, CD127-negative, TdT-negative, Vpre-B-negative, sIgM-negative, and sIgD-negative. Transcription factors: PU.1-positive, Ikaros-positive, E2A-positive, and PAX5-positive. small pre-B-II cell @@ -12312,6 +12595,8 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf CALOHA:TS-0819 pre-B-lymphocyte pre-BII cell + + pre-B-II cell are also reportedly CD19-positive, CD22-positive, CD38-positive, CD45-positive, and CD48-positive. pre-B-II cell @@ -12402,6 +12687,8 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf FMA:84371 CD27-positive, CD38-positive, CD20-negative B cell + + This cell type is compatible with the HIPC Lyoplate markers for 'plasmablast'. Plasmablasts are also reportedly CD48-positive, CD63-positive, CD229-positive, CD270-positive, CD319-positive, CD352-positive, CD361-positive, and IgD-negative. plasmablast @@ -12439,6 +12726,8 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf haemopoietic cell hemopoietic cell + + hematopoietic cell @@ -12489,6 +12778,8 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf type 1 DC + + Originally described in the dendritic cell ontology (DC_CL:0000003)(PMID:19243617) These cells are also CD20-negative, MHCII-positive. conventional dendritic cell @@ -12514,6 +12805,9 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf + + + Originally described in the dendritic cell ontology (DC_CL:1110000)(PMID:19243617). CD7-negative lymphoid progenitor OR granulocyte monocyte progenitor @@ -12544,8 +12838,17 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf A connective tissue cell found in bone. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Bone cells, also known as osteocytes, form the building blocks of the skeletal system. They represent the most common type of bone cell, making up approximately 95% of the total bone cell population in mature adult bone tissue. Osteocytes are a stellate shape with numerous long, slender dendritic processes. +The formation of bone is a complex process involving the action of osteoclasts - cells that break down and reabsorb old bone, followed by osteoblasts that rebuild the bone. Osteocytes serve as coordinators for these two types of bone cells to ensure a balance in the bone remodeling process, contributing to maintaining both bone strength and mineral homeostasis. +The primary functions of osteocytes involve the creation, maintenance, and repair of bone tissue. They ensure that bone remodeling is performed by forming a network within the bone and communicating with other cells to help them respond to mechanical strain and damage. +A remarkable aspect of osteocytes is their ability to perceive mechanical forces, translating them into biochemical signals that regulate bone remodeling and adaptation. Defects in osteocyte function, aside from other bone cells, have been associated with several bone disorders such as osteoporosis, renal osteodystrophy, and skeletal manifestations of diabetes. 2011-11-16T04:28:16Z + https://cellxgene.cziscience.com/cellguide/CL_0001035 + + bone cell @@ -12556,6 +12859,20 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf GOC:add GO_REF:0000034 + + + + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Bone cells, also known as osteocytes, form the building blocks of the skeletal system. They represent the most common type of bone cell, making up approximately 95% of the total bone cell population in mature adult bone tissue. Osteocytes are a stellate shape with numerous long, slender dendritic processes. +The formation of bone is a complex process involving the action of osteoclasts - cells that break down and reabsorb old bone, followed by osteoblasts that rebuild the bone. Osteocytes serve as coordinators for these two types of bone cells to ensure a balance in the bone remodeling process, contributing to maintaining both bone strength and mineral homeostasis. +The primary functions of osteocytes involve the creation, maintenance, and repair of bone tissue. They ensure that bone remodeling is performed by forming a network within the bone and communicating with other cells to help them respond to mechanical strain and damage. +A remarkable aspect of osteocytes is their ability to perceive mechanical forces, translating them into biochemical signals that regulate bone remodeling and adaptation. Defects in osteocyte function, aside from other bone cells, have been associated with several bone disorders such as osteoporosis, renal osteodystrophy, and skeletal manifestations of diabetes. + DOI:10.1007/s00795-015-0099-y + DOI:10.1007/s11914-012-0105-4 + DOI:10.1016/j.jot.2021.04.005 + DOI:10.1038/s41413-020-0099-y + @@ -12697,6 +13014,8 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf A hematopoietic oligopotent progenitor cell that has the ability to differentiate into limited cell types but lacks lineage cell markers and self renewal capabilities. Cell lacks hematopoeitic lineage markers. 2010-01-06T03:43:27Z + + hematopoietic oligopotent progenitor cell, lineage-negative @@ -12766,6 +13085,8 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf 2017-01-30T20:20:48Z + + innate lymphoid cell @@ -12804,7 +13125,6 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf - @@ -12825,6 +13145,8 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf A lymphocyte of B lineage that is CD19-positive. + + Types of B lineage lymphocytes include B cells and antibody secreting cells (plasmablasts and plasma cells). Lymphocytes of B cell lineage can be distinguished from those of T cell lineage by their lack of CD3e (as part of the T cell receptor complex). lymphocyte of B lineage, CD19-positive @@ -12864,6 +13186,8 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf B-lymphocyte, CD19-positive CD19+ B cell CD19-positive B cell + + B cell, CD19-positive @@ -12919,6 +13243,8 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf 2010-01-19T02:51:58Z MDP + + macrophage dendritic cell progenitor @@ -12981,7 +13307,6 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf - @@ -13041,6 +13366,8 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf 2010-04-27T12:46:33Z BMCP + + There may be an intermediate cell type. These cells also CD13-positive, CD16-positive, CD32-positive, and integrin beta 7-positive. Transcription factors: GATA1-positive, MCP-1-positive, mitf-positive, PU.1-positive, and CEBP/a-low. basophil mast progenitor cell @@ -13089,6 +13416,8 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf 2010-01-06T03:43:20Z + + hematopoietic lineage restricted progenitor cell @@ -13133,6 +13462,8 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf 2010-01-06T03:43:27Z + + This cell type is intended to be compatible with any vertebrate hematopoietic oligopotent progenitor cell. For mammalian hematopoietic oligopotent progenitor cells known to be lineage-negative, please use the term 'hematopoietic oligopotent progenitor cell' (CL_0001060). hematopoietic oligopotent progenitor cell @@ -13173,6 +13504,8 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf 2010-06-29T03:38:22Z FMA:69074 ZFA:0009385 + + ecto-epithelial cell @@ -13218,6 +13551,8 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf FMA:62855 agranular leukocyte + + nongranular leukocyte @@ -13263,6 +13598,8 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf FMA:83621 MESH:D001854 + + MH consider whether bone marrow cells are bone cells in the structural sense vs. being part of bone organ sense. bone marrow cell @@ -13288,13 +13625,21 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf An endothelial cell of the vascular tree, which includes blood vessels and lymphatic vessels. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Endothelial cells of the vascular tree, commonly referred to as vascular endothelial cells, line the entire circulatory system, from the heart to the smallest capillaries. These cells have a unique, flattened shape, and are tightly bound together, forming a thin layer known as the endothelium. The endothelium is responsible for maintaining the interior surface of blood vessels, and plays a critical role in ensuring the smooth flow of blood. +Vascular endothelial cells act as a semi-permeable membrane, controlling the passage of materials and the transit of white blood cells into and out of the bloodstream. These cells are also involved in blood coagulation. When a blood vessel is damaged, endothelial cells promote clotting to prevent excessive bleeding and facilitate wound healing. Other functions include regulation of blood pressure and blood volume by releasing vasodilators and vasoconstrictors to either widen or constrict blood vessels, accordingly. +Furthermore, the endothelial cells are crucial in the formation of new blood vessels, a process known as angiogenesis. This is particularly important in wound healing and the growth of new tissues during development or after injury. In the context of diseases such as cancer, angiogenesis helps facilitate tumor growth by providing nutrients and oxygen. 2010-08-24T02:06:40Z BTO:0001854 CALOHA:TS-1106 FMA:67755 + https://cellxgene.cziscience.com/cellguide/CL_0002139 vascular endothelial cell cubodial endothelial cell of vascular tree + + These cells are reportedly CD31-positive, CD34-positive, CD144-positive, TAL1-positive. endothelial cell of vascular tree @@ -13306,6 +13651,19 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf GOC:tfm PMID:12768659 + + + + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Endothelial cells of the vascular tree, commonly referred to as vascular endothelial cells, line the entire circulatory system, from the heart to the smallest capillaries. These cells have a unique, flattened shape, and are tightly bound together, forming a thin layer known as the endothelium. The endothelium is responsible for maintaining the interior surface of blood vessels, and plays a critical role in ensuring the smooth flow of blood. +Vascular endothelial cells act as a semi-permeable membrane, controlling the passage of materials and the transit of white blood cells into and out of the bloodstream. These cells are also involved in blood coagulation. When a blood vessel is damaged, endothelial cells promote clotting to prevent excessive bleeding and facilitate wound healing. Other functions include regulation of blood pressure and blood volume by releasing vasodilators and vasoconstrictors to either widen or constrict blood vessels, accordingly. +Furthermore, the endothelial cells are crucial in the formation of new blood vessels, a process known as angiogenesis. This is particularly important in wound healing and the growth of new tissues during development or after injury. In the context of diseases such as cancer, angiogenesis helps facilitate tumor growth by providing nutrients and oxygen. + DOI:10.1038/s41569-022-00770-1 + DOI:10.1186/s12872-015-0124-z + DOI:10.3389/fphys.2022.863265/full + https://www.sciencedirect.com/topics/medicine-and-dentistry/vascular-endothelial-cell + @@ -13335,6 +13693,8 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf 2010-08-30T12:54:27Z FMA:83519 + + granulocytopoietic cell @@ -13377,6 +13737,8 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf 2010-08-30T01:27:48Z FMA:83552 + + monopoietic cell @@ -13419,6 +13781,8 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf 2010-09-07T03:32:33Z FMA:67513 + + nucleate cell @@ -13454,6 +13818,8 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf A cell type that secretes histamine. 2010-09-10T03:04:42Z + + histamine secreting cell @@ -13492,6 +13858,8 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf CALOHA:TS-2040 FMA:70333 + + neural cell @@ -13533,6 +13901,8 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf MESH:D003239 ZFA:0009392 + + connective tissue cell @@ -13557,11 +13927,19 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf A cell of the embryo. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Embryonic cells in metazoans, which include all multicellular animals, are biological units in their earliest developmental stages from conception until the organism is fully formed. +They are derived from a fertilized egg, which undergoes a series of cell divisions to produce a multicellular organism. During the early phases of embryonic development, these cells exhibit pluripotency, meaning they possess the potential to differentiate into a diverse array of specialized cell types that constitute different body tissues and structures. +The balance between cell proliferation and differentiation in embryonic cells is crucial for successful development. When cells continue to divide without differentiating, overgrowth may occur leading to conditions such as teratomas (tumors of embryonic cells). Conversely, if cell differentiation proceeds at the expense of cell proliferation, developmental anomalies could occur regarding size or mass of the organism or its parts. 2010-09-15T03:39:21Z CALOHA:TS-0263 FMA:82840 WBbt:0007028 ZFA:0007089 + https://cellxgene.cziscience.com/cellguide/CL_0002321 + + embryonic cell (metazoa) @@ -13570,6 +13948,18 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf A cell of the embryo. FMA:0618947256 + + + + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Embryonic cells in metazoans, which include all multicellular animals, are biological units in their earliest developmental stages from conception until the organism is fully formed. +They are derived from a fertilized egg, which undergoes a series of cell divisions to produce a multicellular organism. During the early phases of embryonic development, these cells exhibit pluripotency, meaning they possess the potential to differentiate into a diverse array of specialized cell types that constitute different body tissues and structures. +The balance between cell proliferation and differentiation in embryonic cells is crucial for successful development. When cells continue to divide without differentiating, overgrowth may occur leading to conditions such as teratomas (tumors of embryonic cells). Conversely, if cell differentiation proceeds at the expense of cell proliferation, developmental anomalies could occur regarding size or mass of the organism or its parts. + DOI:10.1002/iub.1404 + DOI:10.1093/molehr/gan048 + https://www.ncbi.nlm.nih.gov/books/NBK9906/ + @@ -13608,6 +13998,8 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf immature T-cell + + immature T cell @@ -13654,6 +14046,8 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf FMA:83808 FMA:84791 heart cell + + From Onard of the FMA: Cardiac muscle cell or cardiac myocyte is a striated muscle cell. Cardiocyte on the other hand is any cell in the heart which includes cells other than muscle cells (e.g. endothelial cell of endocardium). Unless there is a consensus among anatomists that cardiocytes refer only to muscle cells, we will treat them as a general class of cells in the heart. cardiocyte @@ -13717,7 +14111,6 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf - @@ -13782,6 +14175,8 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf 2011-08-29T10:08:02Z + + natural helper lymphocyte @@ -13808,6 +14203,8 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf 2012-06-15T02:51:27Z scleroblast + + Needs logical definition. Should be capable_of skeletal system morphogenesis? or skeletal tissue development? needs to be added to GO. NOTES:a cell type of the early embryo (see also: mesenchymal cells) that will give rise to mineralized connective tissue. Scleroblasts can differentiate into osteoblasts (bone-forming cells), chondroblasts (cartilage-forming cells), odontoblasts (dentin-forming cells), ameloblasts (enamel-forming cells). The mesenchymal cells developing into osteoblasts and chondroblasts are derived from the mesoderm. Those developing into odontoblasts are neural crest cells. Those developing into ameloblasts are derived from the ectoderm. (http://www.copewithcytokines.de/cope.cgi?key=scleroblasts) skeletogenic cell @@ -13846,6 +14243,8 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf 2012-06-27T08:27:35Z ZFA:0007084 + + premigratory neural crest cell @@ -13869,6 +14268,8 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf Any hematopoietic cell that is a precursor of some other hematopoietic cell type. + + hematopoietic precursor cell @@ -13901,6 +14302,8 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf mesenchyme cell + + mesenchymal cell @@ -13913,6 +14316,8 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf A zygote in a plant or an animal. MESH:D015053 + + zygote @@ -13925,13 +14330,15 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf A cell of the neural crest. Neural crest cells are multipotent. Premigratory neural crest cells are found at the neural plate boarder, some of which will undergo ectomesynchymal transition and delamination to form migratory neural crest cells. - This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. Neural crest cells are a group of transient and highly migratory cells that originate from the neuroectoderm during the early stages of embryonic development. They are multipotent cells with an exceptional degree of plasticity, capable of differentiating into various somatic cell types and therefore play a fundamental role in the formation of various organs and tissues, making them critical contributors to the developing embryo. After the initiation of neurulation (the formation of the neural tube) neural crest cells start to undergo epithelial-to-mesenchymal transition and delaminate and migrate from the dorsal neural tube to several regions throughout the embryo. They differentiate into a range of diverse cell types, such as neurons and glial cells of the peripheral nervous system, including sensory and autonomic neurons. They also contribute to the formation of adrenal glands, pigment cells in the skin (melanocytes), cardiac structures, including parts of the heart septum and major arteries, as well as bones and cartilage of the face and skull. Disorders or aberrations in the development or migration of the neural crest cells can lead to serious congenital malformations, such as neurocristopathies, including Hirschsprung disease, neuroblastoma, and neurofibromatosis. https://cellxgene.cziscience.com/cellguide/CL_0011012 + + neural crest cell @@ -13944,7 +14351,7 @@ Disorders or aberrations in the development or migration of the neural crest cel - This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. Neural crest cells are a group of transient and highly migratory cells that originate from the neuroectoderm during the early stages of embryonic development. They are multipotent cells with an exceptional degree of plasticity, capable of differentiating into various somatic cell types and therefore play a fundamental role in the formation of various organs and tissues, making them critical contributors to the developing embryo. After the initiation of neurulation (the formation of the neural tube) neural crest cells start to undergo epithelial-to-mesenchymal transition and delaminate and migrate from the dorsal neural tube to several regions throughout the embryo. They differentiate into a range of diverse cell types, such as neurons and glial cells of the peripheral nervous system, including sensory and autonomic neurons. They also contribute to the formation of adrenal glands, pigment cells in the skin (melanocytes), cardiac structures, including parts of the heart septum and major arteries, as well as bones and cartilage of the face and skull. @@ -13982,6 +14389,8 @@ Disorders or aberrations in the development or migration of the neural crest cel A precursor cell that has a tendency to differentiate into a specific type of cell. They are descendants of stem cells, only they are more constrained in their differentiation potential or capacity for self-renewal, and are often more limited in both senses. + + progenitor cell @@ -14017,6 +14426,8 @@ Disorders or aberrations in the development or migration of the neural crest cel A cell that, by division or terminal differentiation, can give rise to other cell types. + + Work is needed on GO 'cell differentiation' before it is clear whether the equivalent class definition 'native cell' that capable_of some 'cell differentiation' works. Also, may want to consider merging this with non-terminally differentiated cell. precursor cell @@ -14040,12 +14451,14 @@ Disorders or aberrations in the development or migration of the neural crest cel A lymphocyte that has gotten larger after being stimulated by an antigen. - 2022-08-17T14:20:01Z - + + 2022-08-17T14:20:01Z BTO:0000772 EFO:0000572 FMA:83030 + + lymphoblast @@ -14064,11 +14477,13 @@ Disorders or aberrations in the development or migration of the neural crest cel A lymphocyte of B lineage that has gotten larger after being stimulated by an antigen. - 2022-08-17T14:30:32Z - + + 2022-08-17T14:30:32Z EFO:0005293 FMA:83031 + + B-lymphoblast @@ -14266,6 +14681,8 @@ Disorders or aberrations in the development or migration of the neural crest cel CALOHA:TS-2109 bone marrow hematopoietic cells bone marrow poietic cells + + bone marrow hematopoietic cell @@ -14316,6 +14733,8 @@ Disorders or aberrations in the development or migration of the neural crest cel 2014-02-11T17:29:04Z CL:2000001 + + peripheral blood mononuclear cell @@ -14346,6 +14765,8 @@ Disorders or aberrations in the development or migration of the neural crest cel A lymphocyte located in blood. 2022-11-04T14:40:00Z + + blood lymphocyte @@ -14387,6 +14808,8 @@ Disorders or aberrations in the development or migration of the neural crest cel 2024-08-15T10:38:46Z syncytium SC + + syncytial cell @@ -14446,7 +14869,6 @@ Disorders or aberrations in the development or migration of the neural crest cel Progression through the phases of the mitotic cell cycle, the most common eukaryotic cell cycle, which canonically comprises four successive phases called G1, S, G2, and M and includes replication of the genome and the subsequent segregation of chromosomes into daughter cells. In some variant cell cycles nuclear replication or nuclear division may not be followed by cell division, or G1 and G2 phases may be absent. - GO:0007067 Wikipedia:Mitosis biological_process mitosis @@ -14567,9 +14989,6 @@ Disorders or aberrations in the development or migration of the neural crest cel The ordered and organized complex of DNA, protein, and sometimes RNA, that forms the chromosome. https://github.com/geneontology/go-ontology/issues/28301 - GO:0000789 - GO:0000790 - GO:0005717 NIF_Subcellular:sao1615953555 cytoplasmic chromatin nuclear chromatin @@ -14595,8 +15014,6 @@ Disorders or aberrations in the development or migration of the neural crest cel A dispersed and relatively uncompacted form of chromatin that is in a transcription-competent conformation. https://github.com/geneontology/go-ontology/issues/22355 - GO:0005719 - GO:0035327 NIF_Subcellular:sao445485807 Wikipedia:Euchromatin transcriptionally active chromatin @@ -14620,8 +15037,6 @@ Disorders or aberrations in the development or migration of the neural crest cel A compact and highly condensed form of chromatin that is refractory to transcription. https://github.com/geneontology/go-ontology/issues/22355 - GO:0005720 - GO:0035328 NIF_Subcellular:sao581845896 Wikipedia:Heterochromatin transcriptionally inactive chromatin @@ -15002,10 +15417,6 @@ Disorders or aberrations in the development or migration of the neural crest cel The appearance of a cytokine due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. https://github.com/geneontology/go-ontology/issues/19116 - GO:0042032 - GO:0042089 - GO:0042107 - GO:0050663 cytokine biosynthetic process cytokine metabolic process cytokine secretion @@ -15065,7 +15476,7 @@ Disorders or aberrations in the development or migration of the neural crest cel - The regulated release of serotonin by a cell. Serotonin (5-hydroxytryptamine, or 5-HT) is a monoamine synthesised in serotonergic neurons in the central nervous system, enterochromaffin cells in the gastrointestinal tract and some immune system cells. + The regulated release of serotonin by a cell. Serotonin (5-hydroxytryptamine, or 5-HT) is a monoamine synthesized in serotonergic neurons in the central nervous system, enterochromaffin cells in the gastrointestinal tract and some immune system cells. 5-HT secretion 5-hydroxytryptamine secretion biological_process @@ -15076,7 +15487,7 @@ Disorders or aberrations in the development or migration of the neural crest cel - The regulated release of serotonin by a cell. Serotonin (5-hydroxytryptamine, or 5-HT) is a monoamine synthesised in serotonergic neurons in the central nervous system, enterochromaffin cells in the gastrointestinal tract and some immune system cells. + The regulated release of serotonin by a cell. Serotonin (5-hydroxytryptamine, or 5-HT) is a monoamine synthesized in serotonergic neurons in the central nervous system, enterochromaffin cells in the gastrointestinal tract and some immune system cells. GOC:ef ISBN:0198506732 ISBN:0781735149 @@ -15164,7 +15575,6 @@ Disorders or aberrations in the development or migration of the neural crest cel The formation of a tube from the flat layer of ectodermal cells known as the neural plate. This will give rise to the central nervous system. - GO:0001679 Wikipedia:Neurulation neural tube morphogenesis neurulation @@ -15808,8 +16218,6 @@ Disorders or aberrations in the development or migration of the neural crest cel The appearance of immunoglobulin due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. - GO:0002378 - GO:0048305 antibody production immunoglobulin biosynthetic process immunoglobulin secretion @@ -15851,8 +16259,6 @@ Disorders or aberrations in the development or migration of the neural crest cel The appearance of immunoglobulin due to biosynthesis or secretion following a cellular stimulus during an immune response, resulting in an increase in its intracellular or extracellular levels. - GO:0002379 - GO:0002380 immunoglobulin production involved in immunoglobulin mediated immune response immunoglobulin biosynthetic process involved in immune response immunoglobulin secretion involved in immune response @@ -15975,8 +16381,6 @@ Disorders or aberrations in the development or migration of the neural crest cel Any process involved in the carrying out of an immune response by a leukocyte. - GO:0019723 - GO:0042087 immune cell effector process immune cell mediated immunity leucocyte immune effector process @@ -17354,7 +17758,6 @@ Disorders or aberrations in the development or migration of the neural crest cel A molecular process that can be carried out by the action of a single macromolecular machine, usually via direct physical interactions with other molecular entities. Function in this sense denotes an action, or activity, that a gene product (or a complex) performs. - GO:0005554 molecular function molecular_function GO:0003674 @@ -17381,8 +17784,6 @@ Disorders or aberrations in the development or migration of the neural crest cel Combining with an extracellular or intracellular signal and transmitting the signal from one side of the membrane to the other to initiate a change in cell activity or state as part of signal transduction. - GO:0004926 - GO:0099600 transmembrane receptor activity Reactome:R-HSA-193672 transmembrane signalling receptor activity @@ -17431,14 +17832,10 @@ Disorders or aberrations in the development or migration of the neural crest cel Combining with an extracellular signal and transmitting the signal across the membrane by activating an associated G-protein; promotes the exchange of GDP for GTP on the alpha subunit of a heterotrimeric G-protein complex. - GO:0001622 - GO:0001623 - GO:0001624 - GO:0001625 - GO:0016526 Reactome:R-HSA-114552 Reactome:R-HSA-114558 Reactome:R-HSA-167408 + Reactome:R-HSA-381706 Wikipedia:GPCR G protein coupled receptor activity G protein linked receptor activity @@ -17487,6 +17884,12 @@ Disorders or aberrations in the development or migration of the neural crest cel Reactome:R-HSA-167408 The high affinity receptor complex binds to G-protein + + + + Reactome:R-HSA-381706 + GLP1R:GLP1 activates G(s) + @@ -17502,7 +17905,6 @@ Disorders or aberrations in the development or migration of the neural crest cel A location, relative to cellular compartments and structures, occupied by a macromolecular machine. There are three types of cellular components described in the gene ontology: (1) the cellular anatomical entity where a gene product carries out a molecular function (e.g., plasma membrane, cytoskeleton) or membrane-enclosed compartments (e.g., mitochondrion); (2) virion components, where viral proteins act, and (3) the stable macromolecular complexes of which gene product are parts (e.g., the clathrin complex). https://github.com/geneontology/go-ontology/issues/17729 - GO:0008372 NIF_Subcellular:sao1337158144 cell or subcellular entity cellular component @@ -17600,32 +18002,32 @@ Disorders or aberrations in the development or migration of the neural crest cel - - + + A protein complex consisting of three collagen chains assembled into a left-handed triple helix. These trimers typically assemble into higher order structures. Wikipedia:Collagen cellular_component GO:0005581 collagen trimer - + - + - + PMID:12382326 - + PMID:12382326 @@ -17668,8 +18070,6 @@ Disorders or aberrations in the development or migration of the neural crest cel A collagen-containing extracellular matrix consisting of a thin layer of dense material found in various animal tissues interposed between the cells and the adjacent connective tissue. It consists of the basal lamina plus an associated layer of reticulin fibers. - GO:0005605 - GO:0008003 Wikipedia:Basement_membrane cellular_component basal lamina @@ -18078,7 +18478,12 @@ Disorders or aberrations in the development or migration of the neural crest cel - + + + + + + @@ -18086,7 +18491,6 @@ Disorders or aberrations in the development or migration of the neural crest cel An intracellular organelle, about 200 A in diameter, consisting of RNA and protein. It is the site of protein biosynthesis resulting from translation of messenger RNA (mRNA). It consists of two subunits, one large and one small, each containing only protein and RNA. Both the ribosome and its subunits are characterized by their sedimentation coefficients, expressed in Svedberg units (symbol: S). Hence, the prokaryotic ribosome (70S) comprises a large (50S) subunit and a small (30S) subunit, while the eukaryotic ribosome (80S) comprises a large (60S) subunit and a small (40S) subunit. Two sites on the ribosomal large subunit are involved in translation, namely the aminoacyl site (A site) and peptidyl site (P site). Ribosomes from prokaryotes, eukaryotes, mitochondria, and chloroplasts have characteristically distinct ribosomal proteins. - GO:0033279 NIF_Subcellular:sao1429207766 Wikipedia:Ribosome free ribosome @@ -18139,8 +18543,6 @@ Disorders or aberrations in the development or migration of the neural crest cel The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins. - GO:0005887 - GO:0005904 juxtamembrane NIF_Subcellular:sao1663586795 Wikipedia:Cell_membrane @@ -18231,7 +18633,6 @@ Disorders or aberrations in the development or migration of the neural crest cel Any cellular metabolic process involving deoxyribonucleic acid. This is one of the two main types of nucleic acid, consisting of a long, unbranched macromolecule formed from one, or more commonly, two, strands of linked deoxyribonucleotides. - GO:0055132 DNA metabolism cellular DNA metabolism biological_process @@ -18310,9 +18711,6 @@ Disorders or aberrations in the development or migration of the neural crest cel The cellular metabolic process in which a protein is formed, using the sequence of a mature mRNA or circRNA molecule to specify the sequence of amino acids in a polypeptide chain. Translation is mediated by the ribosome, and begins with the formation of a ternary complex between aminoacylated initiator methionine tRNA, GTP, and initiation factor 2, which subsequently associates with the small subunit of the ribosome and an mRNA or circRNA. Translation ends with the release of a polypeptide chain from the ribosome. - GO:0006416 - GO:0006453 - GO:0043037 Wikipedia:Translation_(genetics) protein anabolism protein biosynthesis @@ -18345,7 +18743,7 @@ Disorders or aberrations in the development or migration of the neural crest cel - + @@ -18359,8 +18757,6 @@ Disorders or aberrations in the development or migration of the neural crest cel The process preceding formation of the peptide bond between the first two amino acids of a protein. This includes the formation of a complex of the ribosome, mRNA or circRNA, and an initiation complex that contains the first aminoacyl-tRNA. - GO:0006440 - GO:0006454 biopolymerisation biopolymerization protein synthesis initiation @@ -18390,8 +18786,6 @@ Disorders or aberrations in the development or migration of the neural crest cel The successive addition of amino acid residues to a nascent polypeptide chain during protein biosynthesis. - GO:0006442 - GO:0006455 protein synthesis elongation translation elongation biological_process @@ -18419,8 +18813,6 @@ Disorders or aberrations in the development or migration of the neural crest cel The process resulting in the release of a polypeptide chain from the ribosome, usually in response to a termination codon (UAA, UAG, or UGA in the universal genetic code). - GO:0006443 - GO:0006456 protein synthesis termination translation termination translational complex disassembly @@ -18444,11 +18836,7 @@ Disorders or aberrations in the development or migration of the neural crest cel The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter or a transporter complex, a pore or a motor protein. https://github.com/geneontology/go-ontology/issues/20292 - jl 2012-12-13T16:25:32Z - GO:0015457 - GO:0015460 - GO:0044765 biological_process single-organism transport GO:0006810 @@ -18545,8 +18933,6 @@ Disorders or aberrations in the development or migration of the neural crest cel A process of secretion by a cell that results in the release of intracellular molecules (e.g. hormones, matrix proteins) contained within a membrane-bounded vesicle. Exocytosis can occur either by full fusion, when the vesicle collapses into the plasma membrane, or by a kiss-and-run mechanism that involves the formation of a transient contact, a pore, between a granule (for example of chromaffin cells) and the plasma membrane. The latter process most of the time leads to only partial secretion of the granule content. Exocytosis begins with steps that prepare vesicles for fusion with the membrane (tethering and docking) and ends when molecules are secreted from the cell. - GO:0016194 - GO:0016195 Wikipedia:Exocytosis vesicle exocytosis biological_process @@ -18592,9 +18978,6 @@ Disorders or aberrations in the development or migration of the neural crest cel A vesicle-mediated transport process in which cells take up external materials or membrane constituents by the invagination of a part of the plasma membrane to form a new membrane-bounded vesicle. https://github.com/geneontology/go-ontology/issues/24907 https://github.com/geneontology/go-ontology/issues/25268 - GO:0016193 - GO:0016196 - GO:0098701 Wikipedia:Endocytosis endocytic import into cell vesicle endocytosis @@ -18629,10 +19012,7 @@ Disorders or aberrations in the development or migration of the neural crest cel The evagination of a membrane, resulting in formation of a vesicle. - jl 2013-12-19T15:26:17Z - GO:0006902 - GO:1902591 membrane evagination vesicle biosynthesis vesicle formation @@ -18754,8 +19134,6 @@ Disorders or aberrations in the development or migration of the neural crest cel A programmed cell death process which begins when a cell receives an internal (e.g. DNA damage) or external signal (e.g. an extracellular death ligand), and proceeds through a series of biochemical events (signaling pathway phase) which trigger an execution phase. The execution phase is the last step of an apoptotic process, and is typically characterized by rounding-up of the cell, retraction of pseudopodes, reduction of cellular volume (pyknosis), chromatin condensation, nuclear fragmentation (karyorrhexis), plasma membrane blebbing and fragmentation of the cell into apoptotic bodies. When the execution phase is completed, the cell has died. - GO:0006917 - GO:0008632 cell suicide cellular suicide Wikipedia:Apoptosis @@ -18970,8 +19348,6 @@ Disorders or aberrations in the development or migration of the neural crest cel Reactions, triggered in response to the presence of a foreign body or the occurrence of an injury, which result in restriction of damage to the organism attacked or prevention/recovery from the infection caused by the attack. - GO:0002217 - GO:0042829 defence response physiological defense response biological_process @@ -19067,9 +19443,7 @@ Disorders or aberrations in the development or migration of the neural crest cel A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of an organelle within a cell. An organelle is an organized structure of distinctive morphology and function. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton. Excludes the plasma membrane. https://github.com/geneontology/go-ontology/issues/27189 - jl 2013-12-19T15:25:51Z - GO:1902589 organelle organisation single organism organelle organization biological_process @@ -19254,11 +19628,6 @@ Disorders or aberrations in the development or migration of the neural crest cel The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell. - GO:0023014 - GO:0023015 - GO:0023016 - GO:0023033 - GO:0023045 Wikipedia:Signal_transduction signaling cascade signalling cascade @@ -19306,7 +19675,6 @@ Disorders or aberrations in the development or migration of the neural crest cel The series of molecular signals initiated by a ligand binding to its receptor, in which the activated receptor promotes the exchange of GDP for GTP on the alpha-subunit of an associated heterotrimeric G-protein complex. The GTP-bound activated alpha-G-protein then dissociates from the beta- and gamma-subunits to further transmit the signal within the cell. The pathway begins with receptor-ligand interaction, and ends with regulation of a downstream cellular process. The pathway can start from the plasma membrane, Golgi or nuclear membrane. - GO:0038042 G protein coupled receptor protein signaling pathway G protein coupled receptor protein signalling pathway G-protein coupled receptor protein signal transduction @@ -19732,7 +20100,6 @@ Disorders or aberrations in the development or migration of the neural crest cel The flow of blood through the body of an animal, enabling the transport of nutrients to the tissues and the removal of waste products. - GO:0070261 biological_process hemolymph circulation GO:0008015 @@ -19754,11 +20121,7 @@ Disorders or aberrations in the development or migration of the neural crest cel A biological process is the execution of a genetically-encoded biological module or program. It consists of all the steps required to achieve the specific biological objective of the module. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence. https://github.com/geneontology/go-ontology/issues/24968 - jl 2012-09-19T15:05:24Z - GO:0000004 - GO:0007582 - GO:0044699 Wikipedia:Biological_process biological process physiological process @@ -19788,21 +20151,15 @@ Disorders or aberrations in the development or migration of the neural crest cel - + - The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation. + A cellular process consisting of the biochemical pathways by which a living organism transforms chemical substances. This includes including anabolism (biosynthetic process) and catabolism (catabolic process). Metabolic processes includes the transformation of small molecules, as well macromolecular processes such as DNA repair and replication, protein synthesis and degradation. https://github.com/geneontology/go-ontology/issues/26424 - jl + https://github.com/geneontology/go-ontology/issues/28932 2012-10-17T15:46:40Z - GO:0044236 - GO:0044710 Wikipedia:Metabolism metabolism - metabolic process resulting in cell growth - metabolism resulting in cell growth - multicellular organism metabolic process biological_process - single-organism metabolic process GO:0008152 @@ -19817,7 +20174,7 @@ Disorders or aberrations in the development or migration of the neural crest cel - The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation. + A cellular process consisting of the biochemical pathways by which a living organism transforms chemical substances. This includes including anabolism (biosynthetic process) and catabolism (catabolic process). Metabolic processes includes the transformation of small molecules, as well macromolecular processes such as DNA repair and replication, protein synthesis and degradation. GOC:go_curators ISBN:0198547684 @@ -19853,11 +20210,9 @@ Disorders or aberrations in the development or migration of the neural crest cel - The chemical reactions and pathways resulting in the formation of substances; typically the energy-requiring part of metabolism in which simpler substances are transformed into more complex ones. - jl + A cellular process consisting of the biochemical pathways by which a living organism synthesizes chemical substances. This typically represents the energy-requiring part of metabolism in which simpler substances are transformed into more complex ones. + https://github.com/geneontology/go-ontology/issues/28932 2012-10-17T15:52:18Z - GO:0044274 - GO:0044711 formation Wikipedia:Anabolism anabolism @@ -19876,7 +20231,7 @@ Disorders or aberrations in the development or migration of the neural crest cel - The chemical reactions and pathways resulting in the formation of substances; typically the energy-requiring part of metabolism in which simpler substances are transformed into more complex ones. + A cellular process consisting of the biochemical pathways by which a living organism synthesizes chemical substances. This typically represents the energy-requiring part of metabolism in which simpler substances are transformed into more complex ones. GOC:curators ISBN:0198547684 @@ -19886,13 +20241,12 @@ Disorders or aberrations in the development or migration of the neural crest cel + - The chemical reactions and pathways resulting in the formation of a macromolecule, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass. https://github.com/geneontology/go-ontology/issues/15249 https://github.com/geneontology/go-ontology/issues/25418 https://github.com/geneontology/go-ontology/issues/27189 - GO:0043284 biopolymer biosynthetic process macromolecule anabolism macromolecule biosynthesis @@ -19971,7 +20325,6 @@ Disorders or aberrations in the development or migration of the neural crest cel Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to the organism. - GO:0002245 physiological response to wounding biological_process GO:0009611 @@ -20038,7 +20391,6 @@ Disorders or aberrations in the development or migration of the neural crest cel The process whose specific outcome is the progression of an embryo from its formation until the end of its embryonic life stage. The end of the embryonic stage is organism-specific. For example, for mammals, the process would begin with zygote formation and end with birth. For insects, the process would begin at zygote formation and end with larval hatching. For plant zygotic embryos, this would be from zygote formation to the end of seed dormancy. For plant vegetative embryos, this would be from the initial determination of the cell or group of cells to form an embryo until the point when the embryo becomes independent of the parent plant. - GO:0009795 embryogenesis and morphogenesis Wikipedia:Embryogenesis embryogenesis @@ -20179,11 +20531,7 @@ Disorders or aberrations in the development or migration of the neural crest cel Any process that is carried out at the cellular level, but not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level. - jl 2012-12-11T16:56:55Z - GO:0008151 - GO:0044763 - GO:0050875 cell physiology cellular physiological process cell growth and/or maintenance @@ -20255,9 +20603,7 @@ Disorders or aberrations in the development or migration of the neural crest cel The infolding of a membrane. - jl 2013-12-02T13:58:34Z - GO:1902534 biological_process single-organism membrane invagination GO:0010324 @@ -20320,7 +20666,6 @@ Disorders or aberrations in the development or migration of the neural crest cel A process which begins when a cell receives an internal or external signal and activates a series of biochemical events (signaling pathway). The process ends with the death of the cell. https://github.com/geneontology/go-ontology/issues/24835 - GO:0016244 regulated cell death Wikipedia:Programmed_cell_death caspase-independent cell death @@ -20474,9 +20819,6 @@ Disorders or aberrations in the development or migration of the neural crest cel A lipid bilayer along with all the proteins and protein complexes embedded in it and attached to it. 2014-03-06T11:37:54Z - GO:0016021 - GO:0098589 - GO:0098805 Wikipedia:Biological_membrane Wikipedia:Transmembrane_protein integral component of membrane @@ -20535,8 +20877,6 @@ Disorders or aberrations in the development or migration of the neural crest cel A process that results in the assembly, arrangement of constituent parts, or disassembly of a cellular component. - GO:0044235 - GO:0071842 cell organisation cellular component organisation at cellular level cellular component organisation in other organism @@ -20672,7 +21012,6 @@ Disorders or aberrations in the development or migration of the neural crest cel A cellular transport process in which transported substances are moved in membrane-bounded vesicles; transported substances are enclosed in the vesicle lumen or located in the vesicle membrane. The process begins with a step that directs a substance to the forming vesicle, and includes vesicle budding and coating. Vesicles are then targeted to, and fuse with, an acceptor membrane. https://github.com/geneontology/go-ontology/issues/25421 - GO:0006899 vesicle transport vesicular transport nonselective vesicle transport @@ -20926,9 +21265,6 @@ Disorders or aberrations in the development or migration of the neural crest cel The chemical reactions and pathways involving a protein. Includes protein modification. https://github.com/geneontology/go-ontology/issues/23112 https://github.com/geneontology/go-ontology/issues/27189 - GO:0006411 - GO:0044267 - GO:0044268 Wikipedia:Protein_metabolism cellular protein metabolic process cellular protein metabolism @@ -21030,7 +21366,6 @@ Disorders or aberrations in the development or migration of the neural crest cel An immunoglobulin complex that is present in the plasma membrane of B cells and that in its canonical form is composed of two identical immunoglobulin heavy chains and two identical immunoglobulin light chains and a signaling subunit, a heterodimer of the Ig-alpha and Ig-beta proteins. - GO:0042570 B lymphocyte receptor complex B-cell receptor complex B-lymphocyte receptor complex @@ -21064,7 +21399,6 @@ Disorders or aberrations in the development or migration of the neural crest cel The process in which an antigen-presenting cell expresses antigen (peptide or lipid) on its cell surface in association with an MHC protein complex. - GO:0030333 Wikipedia:Antigen_presentation antigen presentation antigen processing @@ -21199,7 +21533,6 @@ Disorders or aberrations in the development or migration of the neural crest cel A cellular process that results in the breakdown of a cellular component. https://github.com/geneontology/go-ontology/issues/27189 - GO:0071845 cell structure disassembly cellular component disassembly at cellular level biological_process @@ -21284,7 +21617,6 @@ Disorders or aberrations in the development or migration of the neural crest cel The aggregation, arrangement and bonding together of a cellular component. - GO:0071844 cell structure assembly cellular component assembly at cellular level biological_process @@ -21387,10 +21719,7 @@ Disorders or aberrations in the development or migration of the neural crest cel The entirety of a process in which information is transmitted within a biological system. This process begins with an active signal and ends when a cellular response has been triggered. - jl 2010-02-16T09:30:50Z - GO:0023046 - GO:0044700 biological signaling signaling process signalling @@ -21675,7 +22004,6 @@ Disorders or aberrations in the development or migration of the neural crest cel The process in which a relatively unspecialized precursor cell acquires specialized features of a lymphocyte. A lymphocyte is a leukocyte commonly found in the blood and lymph that has the characteristics of a large nucleus, a neutral staining cytoplasm, and prominent heterochromatin. - GO:0046650 lymphocyte cell differentiation lymphocytic blood cell differentiation biological_process @@ -21868,7 +22196,6 @@ Disorders or aberrations in the development or migration of the neural crest cel The process in which a precursor cell type acquires the specialized features of a B cell. A B cell is a lymphocyte of B lineage with the phenotype CD19-positive and capable of B cell mediated immunity. - GO:0042115 B lymphocyte differentiation B-cell differentiation B-lymphocyte differentiation @@ -21963,8 +22290,6 @@ Disorders or aberrations in the development or migration of the neural crest cel The process in which a precursor cell type acquires characteristics of a more mature T-cell. A T cell is a type of lymphocyte whose definin characteristic is the expression of a T cell receptor complex. - GO:0042112 - GO:0046652 T lymphocyte differentiation T-cell differentiation T-lymphocyte differentiation @@ -22209,7 +22534,6 @@ Disorders or aberrations in the development or migration of the neural crest cel The progressive compaction of dispersed interphase chromatin into threadlike chromosomes prior to mitotic or meiotic nuclear division, or during apoptosis, in eukaryotic cells. - GO:0000068 DNA condensation eukaryotic chromosome condensation nuclear chromosome condensation @@ -22520,7 +22844,6 @@ Disorders or aberrations in the development or migration of the neural crest cel A structure lying external to one or more cells, which provides structural support, biochemical or biomechanical cues for cells or tissues. - GO:0005578 NIF_Subcellular:nlx_subcell_20090513 Wikipedia:Extracellular_matrix proteinaceous extracellular matrix @@ -22705,7 +23028,6 @@ Disorders or aberrations in the development or migration of the neural crest cel A vesicle found in the cytoplasm of a cell. - GO:0016023 NIF_Subcellular:sao180601769 cellular_component cytoplasmic membrane bounded vesicle @@ -22781,7 +23103,6 @@ Disorders or aberrations in the development or migration of the neural crest cel Any small, fluid-filled, spherical organelle enclosed by membrane. - GO:0031988 NIF_Subcellular:sao221389602 Wikipedia:Vesicle_(biology) cellular_component @@ -22990,10 +23311,7 @@ Disorders or aberrations in the development or migration of the neural crest cel - jl 2012-09-19T16:07:47Z - GO:0044707 - GO:0050874 organismal physiological process biological_process single-multicellular organism process @@ -23020,9 +23338,7 @@ Disorders or aberrations in the development or migration of the neural crest cel A biological process whose specific outcome is the progression of an integrated living unit: an anatomical structure (which may be a subcellular structure, cell, tissue, or organ), or organism over time from an initial condition to a later condition. - jl 2012-12-19T12:21:31Z - GO:0044767 development biological_process single-organism developmental process @@ -23046,8 +23362,6 @@ Disorders or aberrations in the development or migration of the neural crest cel The appearance of type I interferon due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. Type I interferons include the interferon-alpha, beta, delta, episilon, zeta, kappa, tau, and omega gene families. - GO:0045351 - GO:0072641 interferon type I production type I IFN production type I interferon biosynthetic process @@ -23121,9 +23435,6 @@ Disorders or aberrations in the development or migration of the neural crest cel The disaggregation of a protein-containing macromolecular complex into its constituent components. https://github.com/geneontology/go-ontology/issues/22580 - GO:0034623 - GO:0043241 - GO:0043624 protein complex disassembly biological_process cellular macromolecule complex disassembly @@ -23145,10 +23456,14 @@ Disorders or aberrations in the development or migration of the neural crest cel - + + + + + + A stable assembly of two or more macromolecules, i.e. proteins, nucleic acids, carbohydrates or lipids, in which at least one component is a protein and the constituent parts function together. - GO:0043234 macromolecular complex macromolecule complex protein containing complex @@ -23313,7 +23628,6 @@ Disorders or aberrations in the development or migration of the neural crest cel A process in which a monoatomic ion is transported across a membrane. Monatomic ions (also called simple ions) are ions consisting of exactly one atom. - GO:0099131 ion transmembrane transport ion membrane transport transmembrane ion transport @@ -23484,7 +23798,6 @@ Disorders or aberrations in the development or migration of the neural crest cel An immunoglobulin-like complex that is present in at least the plasma membrane of pre-B cells, and that is composed of two identical immunoglobulin heavy chains and two surrogate light chains, each composed of the lambda-5 and VpreB proteins, and a signaling subunit, a heterodimer of the Ig-alpha and Ig-beta proteins. - bf 2010-03-11T10:46:10Z pre-BCR cellular_component @@ -23509,10 +23822,7 @@ Disorders or aberrations in the development or migration of the neural crest cel Receiving a signal and transmitting it in the cell to initiate a change in cell activity. A signal is a physical entity or change in state that is used to transfer information in order to trigger a response. - bf 2011-08-01T02:45:27Z - GO:0004872 - GO:0019041 receptor activity receptor activity involved in signal transduction signalling receptor activity @@ -23562,7 +23872,6 @@ Disorders or aberrations in the development or migration of the neural crest cel The increase in size or mass of an entire organism, a part of an organism or a cell. - GO:0048590 biological_process growth pattern non-developmental growth @@ -24136,9 +24445,6 @@ Disorders or aberrations in the development or migration of the neural crest cel Any biological process involved in the maintenance of an internal steady state. - GO:0032844 - GO:0032845 - GO:0032846 homeostasis activation of homeostatic process inhibition of homeostatic process @@ -24316,9 +24622,6 @@ Disorders or aberrations in the development or migration of the neural crest cel The chemical reactions and pathways involving macromolecules, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass. https://github.com/geneontology/go-ontology/issues/26424 - GO:0034960 - GO:0043283 - GO:0044259 biopolymer metabolic process macromolecule metabolism organismal macromolecule metabolism @@ -24435,14 +24738,17 @@ Disorders or aberrations in the development or migration of the neural crest cel Organized structure of distinctive morphology and function, not bounded by a lipid bilayer membrane. Includes ribosomes, the cytoskeleton and chromosomes. https://github.com/geneontology/go-ontology/issues/21881 https://github.com/geneontology/go-ontology/issues/28153 + https://github.com/geneontology/go-ontology/issues/29106 NIF_Subcellular:sao1456184038 + membrane-less organelle + non-membrane-bounded organelle non-membrane-enclosed organelle cellular_component biological condensate GO:0043228 - non-membrane-bounded organelle + membraneless organelle @@ -24578,11 +24884,13 @@ Disorders or aberrations in the development or migration of the neural crest cel Organized structure of distinctive morphology and function, not bounded by a lipid bilayer membrane and occurring within the cell. Includes ribosomes, the cytoskeleton and chromosomes. + https://github.com/geneontology/go-ontology/issues/29106 + intracellular non-membrane-bounded organelle intracellular non-membrane-enclosed organelle cellular_component GO:0043232 - intracellular non-membrane-bounded organelle + intracellular membraneless organelle @@ -24689,11 +24997,7 @@ Disorders or aberrations in the development or migration of the neural crest cel Any process in which macromolecules aggregate, disaggregate, or are modified, resulting in the formation, disassembly, or alteration of a protein complex. https://github.com/geneontology/go-ontology/issues/22580 - mah 2010-09-08T10:01:42Z - GO:0034600 - GO:0034621 - GO:0071822 protein complex subunit organisation protein complex subunit organization biological_process @@ -24728,7 +25032,6 @@ Disorders or aberrations in the development or migration of the neural crest cel A process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of a cellular component. Includes biosynthesis of constituent macromolecules, and those macromolecular modifications that are involved in synthesis or assembly of the cellular component. https://github.com/geneontology/go-ontology/issues/27194 - GO:0071843 cellular component biogenesis at cellular level biological_process GO:0044085 @@ -24757,7 +25060,6 @@ Disorders or aberrations in the development or migration of the neural crest cel A ribonucleoprotein complex that contains aminoacylated initiator methionine tRNA, GTP, and initiation factor 2 (either eIF2 in eukaryotes, or IF2 in prokaryotes). In prokaryotes, fMet-tRNA (initiator) is used rather than Met-tRNA (initiator). - jl 2009-10-22T02:38:55Z translation initiation (ternary) complex Met-tRNA/eIF2.GTP ternary complex @@ -24774,35 +25076,6 @@ Disorders or aberrations in the development or migration of the neural crest cel - - - - - - The chemical reactions and pathways by which individual cells transform chemical substances. - cellular metabolism - biological_process - intermediary metabolism - GO:0044237 - - This term should not be used for direct annotation. It should be possible to make a more specific annotation to one of the children of this term. - cellular metabolic process - - - - - The chemical reactions and pathways by which individual cells transform chemical substances. - GOC:go_curators - - - - - intermediary metabolism - GOC:mah - - - - @@ -24829,32 +25102,6 @@ Disorders or aberrations in the development or migration of the neural crest cel - - - - - - The chemical reactions and pathways resulting in the formation of substances, carried out by individual cells. - https://github.com/geneontology/go-ontology/issues/27052 - cellular anabolism - cellular biosynthesis - cellular formation - cellular synthesis - biological_process - GO:0044249 - - This term should not be used for direct annotation. It should be possible to make a more specific annotation to one of the children of this term. - cellular biosynthetic process - - - - - The chemical reactions and pathways resulting in the formation of substances, carried out by individual cells. - GOC:jl - - - - @@ -24905,7 +25152,6 @@ Disorders or aberrations in the development or migration of the neural crest cel The joining of the lipid bilayer membrane that surround a cell with that of another cell, producing a single cell. - GO:0006947 cell fusion cell-cell fusion biological_process @@ -24966,7 +25212,6 @@ Disorders or aberrations in the development or migration of the neural crest cel - GO:0002226 Wikipedia:Innate_immune_system innate immunity nonspecific immune response @@ -25602,7 +25847,6 @@ Disorders or aberrations in the development or migration of the neural crest cel Any process that activates or increases the frequency, rate or extent of a biological process. Biological processes are regulated by many means; examples include the control of gene expression, protein modification or interaction with a protein or substrate molecule. - GO:0043119 positive regulation of physiological process up regulation of biological process up-regulation of biological process @@ -25645,7 +25889,6 @@ Disorders or aberrations in the development or migration of the neural crest cel Any process that stops, prevents, or reduces the frequency, rate or extent of a biological process. Biological processes are regulated by many means; examples include the control of gene expression, protein modification or interaction with a protein or substrate molecule. - GO:0043118 down regulation of biological process down-regulation of biological process downregulation of biological process @@ -25688,7 +25931,6 @@ Disorders or aberrations in the development or migration of the neural crest cel Any process that activates or increases the frequency, rate or extent of a cellular process, any of those that are carried out at the cellular level, but are not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level. - GO:0051242 positive regulation of cellular physiological process up regulation of cellular process up-regulation of cellular process @@ -25877,7 +26119,6 @@ Disorders or aberrations in the development or migration of the neural crest cel The process in which anatomical structures are generated and organized during the embryonic phase. The embryonic phase begins with zygote formation. The end of the embryonic phase is organism-specific. For example, it would be at birth for mammals, larval hatching for insects and seed dormancy in plants. - GO:0048828 embryonic anatomical structure morphogenesis biological_process GO:0048598 @@ -26365,7 +26606,6 @@ Disorders or aberrations in the development or migration of the neural crest cel Any process that modulates the frequency, rate or extent of a biological process. Biological processes are regulated by many means; examples include the control of gene expression, protein modification or interaction with a protein or substrate molecule. - GO:0050791 regulation of physiological process biological_process GO:0050789 @@ -26441,7 +26681,6 @@ Disorders or aberrations in the development or migration of the neural crest cel Any process that modulates the frequency, rate or extent of a cellular process, any of those that are carried out at the cellular level, but are not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level. - GO:0051244 regulation of cellular physiological process biological_process GO:0050794 @@ -26634,7 +26873,6 @@ Disorders or aberrations in the development or migration of the neural crest cel Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus. The process begins with detection of the stimulus and ends with a change in state or activity or the cell or organism. - GO:0051869 physiological response to stimulus biological_process GO:0050896 @@ -26800,9 +27038,7 @@ Disorders or aberrations in the development or migration of the neural crest cel Any process in which a cell, a substance, or a cellular entity, such as a protein complex or organelle, is transported, tethered to or otherwise maintained in a specific location. In the case of substances, localization may also be achieved via selective degradation. https://github.com/geneontology/go-ontology/issues/27052 - jl 2013-12-18T13:51:04Z - GO:1902578 establishment and maintenance of localization establishment and maintenance of position localisation @@ -27008,9 +27244,6 @@ Disorders or aberrations in the development or migration of the neural crest cel A process that is carried out at the cellular level that results in the assembly, arrangement of constituent parts, or disassembly of chromosomes, structures composed of a very long molecule of DNA and associated proteins that carries hereditary information. This term covers covalent modifications at the molecular level as well as spatial relationships among the major components of a chromosome. https://github.com/geneontology/go-ontology/issues/22811 https://github.com/geneontology/go-ontology/issues/4585 - GO:0006323 - GO:0007001 - GO:0051277 DNA condensation chromosome organisation DNA packaging @@ -27091,8 +27324,6 @@ Disorders or aberrations in the development or migration of the neural crest cel Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus from another living organism. - GO:0009613 - GO:0042828 biological_process GO:0051707 response to other organism @@ -27151,9 +27382,7 @@ Disorders or aberrations in the development or migration of the neural crest cel The process in which a solute is transported across a lipid bilayer, from one side of a membrane to the other. - tb 2015-10-21T13:22:47Z - GO:0090662 membrane transport ATP hydrolysis coupled transmembrane transport biological_process @@ -27399,7 +27628,6 @@ Disorders or aberrations in the development or migration of the neural crest cel The process in which the anatomical structures of a tube are generated and organized from an epithelium. Epithelial tubes transport gases, liquids and cells from one site to another and form the basic structure of many organs and tissues, with tube shape and organization varying from the single-celled excretory organ in Caenorhabditis elegans to the branching trees of the mammalian kidney and insect tracheal system. - dph 2009-04-28T09:33:36Z biological_process GO:0060562 @@ -27436,10 +27664,7 @@ Disorders or aberrations in the development or migration of the neural crest cel A process which results in the assembly, arrangement of constituent parts, or disassembly of a membrane. A membrane is a double layer of lipid molecules that encloses all cells, and, in eukaryotes, many organelles; may be a single or double lipid bilayer; also includes associated proteins. - jl 2010-02-08T02:43:11Z - GO:0016044 - GO:0044802 cellular membrane organisation cellular membrane organization membrane organisation @@ -27499,10 +27724,7 @@ Disorders or aberrations in the development or migration of the neural crest cel The membrane organization process that joins two lipid bilayers to form a single membrane. - jl 2010-02-08T02:48:06Z - GO:0006944 - GO:0044801 Wikipedia:Lipid_bilayer_fusion cellular membrane fusion biological_process @@ -27527,7 +27749,6 @@ Disorders or aberrations in the development or migration of the neural crest cel The process in which the anatomical structures of a branched epithelium are generated and organized. - dph 2010-05-25T09:05:34Z biological_process GO:0061138 @@ -27559,7 +27780,6 @@ Disorders or aberrations in the development or migration of the neural crest cel An extracellular matrix consisting mainly of proteins (especially collagen) and glycosaminoglycans (mostly as proteoglycans) that provides not only essential physical scaffolding for the cellular constituents but can also initiate crucial biochemical and biomechanical cues required for tissue morphogenesis, differentiation and homeostasis. The components are secreted by cells in the vicinity and form a sheet underlying or overlying cells such as endothelial and epithelial cells. - dph 2018-04-13T12:47:21Z cellular_component GO:0062023 @@ -27600,9 +27820,6 @@ Disorders or aberrations in the development or migration of the neural crest cel The aggregation, arrangement and bonding together of a set of macromolecules to form a protein-containing complex. https://github.com/geneontology/go-ontology/issues/22580 - GO:0006461 - GO:0034622 - GO:0043623 cellular protein complex assembly biological_process cellular macromolecule complex assembly @@ -27838,7 +28055,6 @@ Disorders or aberrations in the development or migration of the neural crest cel Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a chemical stimulus. - mah 2009-08-27T04:41:45Z biological_process GO:0070887 @@ -27878,7 +28094,6 @@ Disorders or aberrations in the development or migration of the neural crest cel The aggregation, arrangement and bonding together of a set of components to form an organelle. An organelle is an organized structure of distinctive morphology and function. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton. Excludes the plasma membrane. - mah 2009-09-15T03:00:51Z biological_process GO:0070925 @@ -27899,7 +28114,6 @@ Disorders or aberrations in the development or migration of the neural crest cel The process in which immunoglobulin heavy chain V, D, and J gene segments are recombined within a single locus utilizing the conserved heptamer and nonomer recombination signal sequences (RSS). - mah 2010-03-09T04:20:31Z immunoglobulin V(D)J joining immunoglobulin V(D)J recombination @@ -27941,7 +28155,6 @@ Disorders or aberrations in the development or migration of the neural crest cel The process in which immunoglobulin light chain V and J gene segments are recombined within a single locus utilizing the conserved heptamer and nonomer recombination signal sequences (RSS). - mah 2010-03-09T04:22:29Z immunoglobulin V(D)J joining immunoglobulin V(D)J recombination @@ -27983,7 +28196,6 @@ Disorders or aberrations in the development or migration of the neural crest cel A protein complex composed of two identical immunoglobulin heavy chains of the IgD isotype and two identical immunoglobulin light chains, held together by disulfide bonds. An IgD immunoglobulin complex may be embedded in the plasma membrane or present in the extracellular space, in mucosal areas or other tissues, or circulating in the blood or lymph. - mah 2010-03-24T01:44:53Z cellular_component GO:0071738 @@ -28006,7 +28218,6 @@ Disorders or aberrations in the development or migration of the neural crest cel A protein complex composed of two identical immunoglobulin heavy chains of the IgM isotype and two identical immunoglobulin light chains, held together by disulfide bonds, and in its circulating form complexed with J chain in polymeric forms. An IgM immunoglobulin complex may be embedded in the plasma membrane or present in the extracellular space, in mucosal areas or other tissues, or circulating in the blood or lymph. - mah 2010-03-24T01:44:53Z cellular_component GO:0071753 @@ -28047,7 +28258,6 @@ Disorders or aberrations in the development or migration of the neural crest cel Any process in which macromolecules aggregate, disaggregate, or are modified, resulting in the formation, disassembly, or alteration of a ribonucleoprotein complex. https://github.com/geneontology/go-ontology/issues/25143 - mah 2010-09-08T10:10:35Z RNA-protein complex subunit organization protein-RNA complex subunit organization @@ -28090,9 +28300,7 @@ Disorders or aberrations in the development or migration of the neural crest cel A process that results in the biosynthesis of constituent macromolecules, assembly, arrangement of constituent parts, or disassembly of a cellular component. https://github.com/geneontology/go-ontology/issues/27189 - mah 2010-09-10T01:39:16Z - GO:0071841 cellular component organisation or biogenesis cellular component organisation or biogenesis at cellular level cellular component organization or biogenesis at cellular level @@ -28130,7 +28338,6 @@ Disorders or aberrations in the development or migration of the neural crest cel The broad region around and including the plasma membrane of a cell, encompassing the cell cortex (inside the cell), the plasma membrane, and any external encapsulating structures. - mah 2010-10-04T01:51:47Z cellular_component GO:0071944 @@ -28175,7 +28382,6 @@ Disorders or aberrations in the development or migration of the neural crest cel The aggregation, arrangement and bonding together of a set of components to form an extracellular vesicular exosome, a membrane-bounded vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Exosomes are defined by their size, which generally ranges from 30 nm to 100 nm. - mah 2010-10-18T03:44:18Z extracellular vesicular exosome assembly biological_process @@ -28229,7 +28435,6 @@ Disorders or aberrations in the development or migration of the neural crest cel The developmental process pertaining to the initial formation of an epithelial tube. https://github.com/geneontology/go-ontology/issues/22302 - mah 2010-02-26T02:15:40Z biological_process GO:0072175 @@ -28267,7 +28472,6 @@ Disorders or aberrations in the development or migration of the neural crest cel The joining of two lipid bilayers to form a single organelle membrane. - tb 2009-12-11T11:44:58Z biological_process GO:0090174 @@ -28306,7 +28510,6 @@ Disorders or aberrations in the development or migration of the neural crest cel The process in which a precursor cell type acquires the specialized features of a dendritic cell. A dendritic cell is a leukocyte of dendritic lineage specialized in the uptake, processing, and transport of antigens to lymph nodes for the purpose of stimulating an immune response via T cell activation. - pr 2011-04-01T10:08:42Z biological_process GO:0097028 @@ -28334,9 +28537,7 @@ Disorders or aberrations in the development or migration of the neural crest cel The series of molecular signals which triggers the apoptotic death of a cell. The pathway starts with reception of a signal, and ends when the execution phase of apoptosis is triggered. - pr 2011-11-23T09:30:23Z - GO:0008624 apoptotic signalling pathway induction of apoptosis by extracellular signals biological_process @@ -28376,7 +28577,6 @@ Disorders or aberrations in the development or migration of the neural crest cel A stage of the apoptotic process that starts with the controlled breakdown of the cell through the action of effector caspases or other effector molecules (e.g. cathepsins, calpains etc.). Key steps of the execution phase are rounding-up of the cell, retraction of pseudopodes, reduction of cellular volume (pyknosis), chromatin condensation, nuclear fragmentation (karyorrhexis), plasma membrane blebbing and fragmentation of the cell into apoptotic bodies. When the execution phase is completed, the cell has died. - pr 2011-11-23T09:45:24Z execution phase of apoptotic process apoptosis @@ -28411,7 +28611,6 @@ Disorders or aberrations in the development or migration of the neural crest cel Any vesicle that is part of the intracellular region. - pr 2016-03-29T17:39:45Z cellular_component GO:0097708 @@ -28431,7 +28630,6 @@ Disorders or aberrations in the development or migration of the neural crest cel The assembly and secretion of an extracellular exosome, a membrane-bounded vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. - pr 2016-10-03T14:35:25Z exosome assembly or secretion exosome biogenesis @@ -28460,9 +28658,7 @@ Disorders or aberrations in the development or migration of the neural crest cel Reactions triggered in response to the presence of another organism that act to protect the cell or organism from damage caused by that organism. https://github.com/geneontology/go-ontology/issues/22173 - dos 2013-11-11T12:59:11Z - GO:0009814 defence response incompatible interaction defence response to pathogen, incompatible interaction defense response, incompatible interaction @@ -28504,7 +28700,6 @@ Disorders or aberrations in the development or migration of the neural crest cel A membrane that is a (regional) part of the plasma membrane. - dos 2014-03-06T11:55:32Z region of plasma membrane cellular_component @@ -28561,7 +28756,6 @@ Disorders or aberrations in the development or migration of the neural crest cel - @@ -29113,21 +29307,22 @@ Disorders or aberrations in the development or migration of the neural crest cel - A part of a cellular organism that is either an immaterial entity or a material entity with granularity above the level of a protein complex but below that of an anatomical system. Or, a substance produced by a cellular organism with granularity above the level of a protein complex. + A part of a cellular organism consisting of a material entity with granularity above the level of a protein complex but below that of an anatomical system. Note that cellular organisms exclude viruses. https://github.com/geneontology/go-ontology/issues/24200 https://github.com/geneontology/go-ontology/issues/26424 - kmv + https://github.com/geneontology/go-ontology/issues/28978 2019-08-12T18:01:37Z + cellular anatomical entity cellular_component GO:0110165 - cellular anatomical entity + cellular anatomical structure - A part of a cellular organism that is either an immaterial entity or a material entity with granularity above the level of a protein complex but below that of an anatomical system. Or, a substance produced by a cellular organism with granularity above the level of a protein complex. + A part of a cellular organism consisting of a material entity with granularity above the level of a protein complex but below that of an anatomical system. Note that cellular organisms exclude viruses. GOC:kmv @@ -29156,7 +29351,6 @@ Disorders or aberrations in the development or migration of the neural crest cel A prolongation or process extending from a cell and that is bounded by plasma membrane, e.g. a cilium, lamellipodium, or axon. https://github.com/geneontology/go-ontology/issues/13193 - krc 2017-03-21T17:26:07Z cellular_component GO:0120025 @@ -29195,7 +29389,6 @@ Disorders or aberrations in the development or migration of the neural crest cel Formation of a prolongation or process extending and that is bounded by plasma membrane, e.g. a cilium, lamellipodium, or axon. https://github.com/geneontology/go-ontology/issues/13298 - krc 2017-04-24T23:56:08Z eupodium biological_process @@ -29243,7 +29436,6 @@ Disorders or aberrations in the development or migration of the neural crest cel A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a plasma membrane bounded prolongation or process extending from a cell, e.g. a cilium or axon. https://github.com/geneontology/go-ontology/issues/13298 - krc 2017-04-26T16:07:02Z biological_process GO:0120036 @@ -29276,7 +29468,6 @@ Disorders or aberrations in the development or migration of the neural crest cel A mitotic cell cycle process comprising the steps by which the nucleus of a eukaryotic cell divides; the process involves condensation of chromosomal DNA into a highly compacted form. Canonically, mitosis produces two daughter nuclei whose chromosome complement is identical to that of the mother cell. https://github.com/geneontology/go-ontology/issues/19910 - pg 2017-03-23T14:44:23Z mitosis biological_process @@ -29316,7 +29507,6 @@ Disorders or aberrations in the development or migration of the neural crest cel The cellular processes that contribute to exocytosis. - pg 2017-05-15T13:20:45Z biological_process GO:0140029 @@ -29338,7 +29528,6 @@ Disorders or aberrations in the development or migration of the neural crest cel The assembly and secretion a set of components to form an extracellular vesicule, a membrane-bounded vesicle that is released into the extracellular region. Extracellular vesicles include exosomes, microvesicles and apoptotic bodies, based on the mechanism by which they are released from cells and differentiated based on their size and content. https://github.com/geneontology/go-ontology/issues/14256 - pg 2017-10-23T11:53:42Z extracellular vesicle assembly biological_process @@ -29366,7 +29555,6 @@ Disorders or aberrations in the development or migration of the neural crest cel A cellular process in which two or more cells combine together, their plasma membrane fusing, producing a single cell. In some cases, nuclei fuse, producing a polyploid cell, while in other cases, nuclei remain separate, producing a syncytium. https://github.com/geneontology/go-ontology/issues/15939 - pg 2018-08-13T18:38:18Z cell fusion cell cell fusion @@ -29416,7 +29604,6 @@ Disorders or aberrations in the development or migration of the neural crest cel The directed movement of some substance from a cell, into the extracellular region. This may occur via transport across the plasma membrane or via exocytosis. - pg 2019-05-22T11:20:45Z efflux biological_process @@ -29438,7 +29625,6 @@ Disorders or aberrations in the development or migration of the neural crest cel Reactions triggered in response to the presence of a symbiont that act to protect or prevent damage to the host. https://github.com/geneontology/go-ontology/issues/20261 - pg 2020-11-11T17:19:06Z biological_process GO:0140546 @@ -29475,7 +29661,6 @@ Disorders or aberrations in the development or migration of the neural crest cel Any process that modulates the frequency, rate or extent of leukocyte differentiation. - pr 2013-05-02T17:32:42Z regulation of immune cell differentiation regulation of leucocyte differentiation @@ -29527,7 +29712,6 @@ Disorders or aberrations in the development or migration of the neural crest cel A process that is part of the mitotic cell cycle. - jl 2014-05-22T14:22:34Z biological_process GO:1903047 @@ -29567,7 +29751,6 @@ Disorders or aberrations in the development or migration of the neural crest cel The process in which a relatively unspecialized cell acquires the specialized features of a mononuclear cell. - cls 2014-06-25T15:47:09Z biological_process GO:1903131 @@ -29602,7 +29785,6 @@ Disorders or aberrations in the development or migration of the neural crest cel Any vesicle that is part of the extracellular region. - jl 2014-10-22T14:26:11Z cellular_component microparticle @@ -29651,7 +29833,6 @@ Disorders or aberrations in the development or migration of the neural crest cel Any process that modulates the frequency, rate or extent of hemopoiesis. - pad 2014-12-04T15:34:13Z regulation of blood cell biosynthesis regulation of blood cell formation @@ -29704,10 +29885,7 @@ Disorders or aberrations in the development or migration of the neural crest cel A macromolecular complex that contains both RNA and protein molecules. - pr 2015-11-19T12:26:37Z - GO:0030529 - GO:1990903 Wikipedia:Ribonucleoprotein RNA-protein complex RNP @@ -29752,7 +29930,6 @@ Disorders or aberrations in the development or migration of the neural crest cel Any process that modulates the frequency, rate or extent of multicellular organismal development. - tb 2010-08-05T11:25:59Z biological_process GO:2000026 @@ -29790,7 +29967,6 @@ Disorders or aberrations in the development or migration of the neural crest cel Any process that modulates the frequency, rate or extent of cell motility. - mah 2010-10-01T09:41:21Z regulation of cell locomotion regulation of movement of a cell @@ -29850,7 +30026,6 @@ Disorders or aberrations in the development or migration of the neural crest cel Any process that activates or increases the frequency, rate or extent of cell motility. - mah 2010-10-01T09:41:30Z positive regulation of cell locomotion positive regulation of movement of a cell @@ -29956,7 +30131,6 @@ Disorders or aberrations in the development or migration of the neural crest cel - NCBITaxon:85055 GC_ID:1 house mouse mouse @@ -29995,7 +30169,6 @@ Disorders or aberrations in the development or migration of the neural crest cel - NCBITaxon:40673 GC_ID:1 bony vertebrates ncbi_taxonomy @@ -30362,7 +30535,6 @@ Disorders or aberrations in the development or migration of the neural crest cel - NCBITaxon:109679 GC_ID:1 ncbi_taxonomy NCBITaxon:39107 @@ -30621,7 +30793,6 @@ Disorders or aberrations in the development or migration of the neural crest cel A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities - PATO:0000072 quality PATO:0000001 quality @@ -30659,7 +30830,6 @@ Disorders or aberrations in the development or migration of the neural crest cel A morphological quality inhering in a bearer by virtue of the bearer's ratios of distances between its features (points, edges, surfaces and also holes etc). - PATO:0001647 relational shape quality quality PATO:0000052 @@ -30681,7 +30851,6 @@ Disorders or aberrations in the development or migration of the neural crest cel A morphology quality inhering in a bearer by virtue of the bearer's relative position, shape, arrangements and connectivity of an organism's various parts; the pattern underlying its form. - PATO:0001452 conformation relational structural quality quality @@ -30800,7 +30969,6 @@ Disorders or aberrations in the development or migration of the neural crest cel A quality of a physical entity that exists through action of continuants at the physical level of organisation in relation to other entities. - PATO:0002079 Wikipedia:Physical_property relational physical quality quality @@ -30822,8 +30990,6 @@ Disorders or aberrations in the development or migration of the neural crest cel A quality which inheres in a continuant. - PATO:0001237 - PATO:0001238 snap:Quality monadic quality of a continuant multiply inhering quality of a physical entity @@ -31163,7 +31329,6 @@ Disorders or aberrations in the development or migration of the neural crest cel A convex 3-D shape quality inhering in a bearer by virtue of the bearer's exhibiting a consistently-sized round cross section. - PATO:0001203 rod-like rod-shaped tubulate @@ -31652,7 +31817,6 @@ Disorders or aberrations in the development or migration of the neural crest cel A quality inhering in a cell by virtue of the cell having a high nuclear/cytoplasmic ratio. - http://orcid.org/0000-0001-5208-3432 high N:C ratio quality PATO:0040072 @@ -31674,7 +31838,6 @@ Disorders or aberrations in the development or migration of the neural crest cel A quality of continuant that exist at the anatomical level of organisation and anything under it. This includes, but is not limited to, cells , tissues, and components. - http://orcid.org/0000-0001-7258-9596 quality PATO:0070044 anatomical structure quality @@ -31687,7 +31850,6 @@ Disorders or aberrations in the development or migration of the neural crest cel A quality inhering in an anotomical structure by virtue of its capacity to be stained by specific histological dyes. - http://orcid.org/0000-0001-7258-9596 quality PATO:0070045 anatomical histological quality @@ -31700,7 +31862,6 @@ Disorders or aberrations in the development or migration of the neural crest cel An affinity inhering in an anatomical structure by virtue of the bearer exhibiting a molecular interaction that stains and colors, pale-pink, with Wright-Giemsa stain. - http://orcid.org/0000-0001-7258-9596 quality PATO:0070046 neutrophillic @@ -31719,7 +31880,6 @@ Disorders or aberrations in the development or migration of the neural crest cel An affinity inhering in an anatomical structure by virtue of the bearer exhibiting a molecular interaction for both basic and acid stains under specific pH conditions. - http://orcid.org/0000-0001-7258-9596 quality PATO:0070047 polychromatophilic @@ -31737,7 +31897,7 @@ Disorders or aberrations in the development or migration of the neural crest cel - + @@ -31749,7 +31909,7 @@ Disorders or aberrations in the development or migration of the neural crest cel native protein protein PR:000000001 - The definition above excludes protein complexes, which some also consider a protein. Those who wish to refer to a class representing both senses of the word are directed to CHEBI:36080. Note that the definition allows for experimentally-manipulated genes, and allows for artifically-produced derivatives that mimic those found naturally. Proteins (in the sense defined here) that descended from a common ancestor can be classified into families and superfamilies composed of products of evolutionarily-related genes. The domain architecture of a protein is described by the order of its constituent domains. Proteins with the same domains in the same order are defined as homeomorphic [PRO:WCB]. + The definition above excludes protein complexes, which some also consider a protein. Those who wish to refer to a class representing both senses of the word are directed to CHEBI:36080. Note that the definition allows for experimentally-manipulated genes, and allows for artifically-produced derivatives that mimic those found naturally. Proteins (in the sense defined here) that descended from a common ancestor can be classified into families and superfamilies composed of products of evolutionarily-related genes. The domain architecture of a protein is described by the order of its constituent domains. Proteins with the same domains in the same order are defined as homeomorphic [PRO:WCB). protein @@ -33757,7 +33917,6 @@ Disorders or aberrations in the development or migration of the neural crest cel - A protein with core architecture consisting of a signal sequence, followed by 7 Ig-like domains (Pfam:PF00047, Pfam:PF07679, or Pfam:PF07686), a transmembrane region, and a cytoplasmic Protein tyrosine kinase domain. PIRSF:PIRSF038502 protein @@ -34896,51 +35055,51 @@ Disorders or aberrations in the development or migration of the neural crest cel - + - + - A material entity that minimally consists of a protein. + A molecular entity that minimally consists of a protein. protein protein aggregate protein complex protein-containing complex protein - PR:000050567 - Note: This includes single proteins and derivatives thereof (PR:000000001), protein-containing complexes (GO:0032991), and protein aggregates (PR:000050566). - protein-containing material entity + PR:000064867 + Note: This includes single proteins and derivatives thereof (PR:000000001), protein-containing complexes (GO:0032991), and protein aggregates (PR:000050565). + protein-containing molecular entity - + - A material entity that minimally consists of a protein. + A molecular entity that minimally consists of a protein. PRO:DAN - + protein PRO:DAN - + protein aggregate PRO:DAN - + protein complex PRO:DAN - + protein-containing complex PRO:DAN @@ -35061,7 +35220,6 @@ Disorders or aberrations in the development or migration of the neural crest cel Organ component adjacent to an organ cavity and which consists of a maximal aggregate of organ component layers. - UBERON:0009915 wall FMA:82482 galen:Wall @@ -35436,7 +35594,6 @@ Disorders or aberrations in the development or migration of the neural crest cel Anatomical cluster consisting of the skeletal elements and articular elements that are part of an individual subdivision of the organism. - UBERON:0010322 FMA:85544 NCIT:C34076 SCTID:118966000 @@ -35801,7 +35958,7 @@ Disorders or aberrations in the development or migration of the neural crest cel - + @@ -35837,14 +35994,14 @@ Disorders or aberrations in the development or migration of the neural crest cel gastrula stage - + - + BILS @@ -36153,7 +36310,7 @@ Disorders or aberrations in the development or migration of the neural crest cel - + @@ -36161,15 +36318,15 @@ Disorders or aberrations in the development or migration of the neural crest cel - + - - + + A fluid that is composed of blood plasma and erythrocytes. AAO:0000046 @@ -36206,34 +36363,34 @@ Disorders or aberrations in the development or migration of the neural crest cel blood - + - + - + - + CL:tm - + https://github.com/obophenotype/uberon/issues/1330 - + Bgee:AN @@ -36335,7 +36492,6 @@ Disorders or aberrations in the development or migration of the neural crest cel Organism at the blastula stage - an early stage of embryonic development in animals. It is produced by cleavage of a fertilized ovum and consists of a spherical layer of around 128 cells surrounding a central fluid-filled cavity called the blastocoel. The blastula follows the morula and precedes the gastrula in the developmental sequence. TODO - check relationship with epiblast. Note in FMA this is not a subclass of embryo, but in uberon embryo is the whole organism from zygote onwards and thus includes the blastula - UBERON:0007011 BILA:0000059 BTO:0000128 GAID:1294 @@ -37305,7 +37461,6 @@ Disorders or aberrations in the development or migration of the neural crest cel - @@ -37319,7 +37474,7 @@ Disorders or aberrations in the development or migration of the neural crest cel - + @@ -37361,14 +37516,14 @@ Disorders or aberrations in the development or migration of the neural crest cel epithelium https://upload.wikimedia.org/wikipedia/commons/8/8f/Illu_epithelium.jpg - + - + http://palaeos.com/metazoa/porifera/homoscleromorpha.html @@ -37788,7 +37943,7 @@ Disorders or aberrations in the development or migration of the neural crest cel - + Primary germ layer that is the outer of the embryo's three germ layers and gives rise to epidermis and neural tissue. AAO:0000137 BILA:0000036 @@ -37823,14 +37978,14 @@ Disorders or aberrations in the development or migration of the neural crest cel ectoderm http://upload.wikimedia.org/wikipedia/commons/1/19/Gray32.png - + - + Bgee:AN @@ -37870,7 +38025,7 @@ Disorders or aberrations in the development or migration of the neural crest cel - + Primary germ layer that lies remote from the surface of the embryo and gives rise to internal tissues such as gut. AAO:0000139 BILA:0000038 @@ -37905,14 +38060,14 @@ Disorders or aberrations in the development or migration of the neural crest cel http://upload.wikimedia.org/wikipedia/commons/c/c0/Endoderm2.png http://upload.wikimedia.org/wikipedia/commons/d/df/Gray10.png - + - + Bgee:AN @@ -37953,10 +38108,9 @@ Disorders or aberrations in the development or migration of the neural crest cel - + The middle germ layer of the embryo, between the endoderm and ectoderm. - UBERON:0003263 AAO:0000304 BILA:0000037 BTO:0000839 @@ -37994,14 +38148,14 @@ Disorders or aberrations in the development or migration of the neural crest cel mesoderm http://upload.wikimedia.org/wikipedia/commons/e/e8/Mesoderm.png - + - + Bgee:AN @@ -38175,7 +38329,7 @@ Disorders or aberrations in the development or migration of the neural crest cel - + @@ -38246,14 +38400,14 @@ Disorders or aberrations in the development or migration of the neural crest cel https://cdn.humanatlas.io/digital-objects/ref-organ/heart-female/v1.3/assets/3d-vh-f-heart.glb https://cdn.humanatlas.io/digital-objects/ref-organ/heart-male/v1.3/assets/3d-vh-m-heart.glb - + - + MA @@ -38504,7 +38658,6 @@ Disorders or aberrations in the development or migration of the neural crest cel - AAO:0000959 CALOHA:TS-2103 VHOG:0001248 @@ -38512,7 +38665,6 @@ Disorders or aberrations in the development or migration of the neural crest cel uberon systema cardiovasculare UBERON:0001009 - circulatory system http://upload.wikimedia.org/wikipedia/commons/2/29/Circulatory_System_en.svg @@ -38656,7 +38808,7 @@ Disorders or aberrations in the development or migration of the neural crest cel - + @@ -38704,14 +38856,14 @@ Disorders or aberrations in the development or migration of the neural crest cel http://upload.wikimedia.org/wikipedia/commons/b/b2/TE-Nervous_system_diagram.svg http://upload.wikimedia.org/wikipedia/commons/b/ba/Nervous_system_diagram.png - + - + Bgee:AN @@ -38777,7 +38929,7 @@ Disorders or aberrations in the development or migration of the neural crest cel - + The central nervous system is the core nervous system that serves an integrating and coordinating function. In vertebrates it consists of the neural tube derivatives: the brain and spinal cord. In invertebrates it includes central ganglia plus nerve cord. @@ -38822,7 +38974,7 @@ Disorders or aberrations in the development or migration of the neural crest cel central nervous system - + @@ -38836,7 +38988,7 @@ Disorders or aberrations in the development or migration of the neural crest cel - + Bgee:AN @@ -39224,7 +39376,7 @@ Disorders or aberrations in the development or migration of the neural crest cel - + Skeletal element that is composed of bone tissue. @@ -39266,14 +39418,14 @@ Disorders or aberrations in the development or migration of the neural crest cel bone element - + - + VSAO-modified @@ -39339,7 +39491,7 @@ Disorders or aberrations in the development or migration of the neural crest cel - + A tube extending from the mouth to the anus. @@ -39376,14 +39528,14 @@ Disorders or aberrations in the development or migration of the neural crest cel digestive tract - + - + NCBIBook:NBK10107 @@ -39528,7 +39680,6 @@ Disorders or aberrations in the development or migration of the neural crest cel - @@ -39603,7 +39754,6 @@ Disorders or aberrations in the development or migration of the neural crest cel - @@ -39612,8 +39762,8 @@ Disorders or aberrations in the development or migration of the neural crest cel - - + + @@ -39626,7 +39776,7 @@ Disorders or aberrations in the development or migration of the neural crest cel - + @@ -39680,34 +39830,34 @@ Disorders or aberrations in the development or migration of the neural crest cel blood vessel http://upload.wikimedia.org/wikipedia/commons/2/29/Circulatory_System_en.svg - + - + - + - + AEO - + EHDAA2 - + GO:0072360 @@ -40429,7 +40579,6 @@ Disorders or aberrations in the development or migration of the neural crest cel The cavity within the body of all animals higher than the coelenterates and certain primitive worms, formed by the splitting of the embryonic mesoderm into two layers. In mammals it forms the peritoneal, pleural, and pericardial cavities. - UBERON:0000169 body cavity AEO:0000186 BTO:0001707 @@ -40441,7 +40590,6 @@ Disorders or aberrations in the development or migration of the neural crest cel SCTID:361348008 TAO:0001438 UMLS:C0333343 - ZFA:0001438 galen:BodyCavity coelomic cavity coelomic cavity lumen @@ -40541,9 +40689,9 @@ Disorders or aberrations in the development or migration of the neural crest cel - - - + + + @@ -40591,15 +40739,15 @@ Disorders or aberrations in the development or migration of the neural crest cel notochord http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png - + - + - + @@ -40618,19 +40766,19 @@ Disorders or aberrations in the development or migration of the neural crest cel - + http://tolweb.org/Chordata/2499 - + ZFA - + EHDAA2 @@ -40670,8 +40818,8 @@ Disorders or aberrations in the development or migration of the neural crest cel - - + + Somites are spheres of epithelial cells that form sequentially along the anterior-posterior axis of the embryo through mesenchymal to epithelial transition of the presomitic mesoderm. mesodermal cluster @@ -40709,11 +40857,11 @@ Disorders or aberrations in the development or migration of the neural crest cel somite http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png - + - + @@ -40726,13 +40874,13 @@ Disorders or aberrations in the development or migration of the neural crest cel - + GOTAX:0000352 - + ZFA @@ -40794,22 +40942,22 @@ Disorders or aberrations in the development or migration of the neural crest cel - + - - + + - + A specialized region of ectoderm found between the neural ectoderm (neural plate) and non-neural ectoderm and composed of highly migratory pluripotent cells that delaminate in early embryonic development from the dorsal neural tube and give rise to an astounding variety of differentiated cell types[MP]. AAO:0010578 BTO:0001764 @@ -40842,45 +40990,45 @@ Disorders or aberrations in the development or migration of the neural crest cel http://upload.wikimedia.org/wikipedia/commons/5/5f/Gray644.png https://upload.wikimedia.org/wikipedia/commons/8/8f/Neural_Crest.png - + - + - + - + - + XAO https://github.com/obophenotype/uberon/wiki/The-neural-crest - + BTO - + PMID:11523831 - + PMID:11523831 @@ -41021,7 +41169,7 @@ Disorders or aberrations in the development or migration of the neural crest cel - + @@ -41077,14 +41225,14 @@ Disorders or aberrations in the development or migration of the neural crest cel bone marrow http://upload.wikimedia.org/wikipedia/commons/7/74/Gray72-en.svg - + - + FMA MA @@ -41296,7 +41444,7 @@ Disorders or aberrations in the development or migration of the neural crest cel - + @@ -41349,14 +41497,14 @@ Disorders or aberrations in the development or migration of the neural crest cel hematopoietic system - + - + FMA @@ -41656,6 +41804,7 @@ Disorders or aberrations in the development or migration of the neural crest cel + @@ -41669,7 +41818,7 @@ Disorders or aberrations in the development or migration of the neural crest cel - + Unsegmented field of paraxial mesoderm present posterior to the most recently formed somite pair, from which somites will form. AAO:0011086 EFO:0001982 @@ -41692,14 +41841,14 @@ Disorders or aberrations in the development or migration of the neural crest cel presomitic mesoderm - + - + Bgee:AN @@ -41853,9 +42002,9 @@ Disorders or aberrations in the development or migration of the neural crest cel - - - + + + A region of embryonic ectodermal cells that lie directly above the notochord. During neurulation, they change shape and produce an infolding of the neural plate (the neural fold) that then seals to form the neural tube[XAO]. The earliest recognizable dorsal ectodermal primordium of the central nervous system present near the end of gastrulation before infolding to form the neural keel; consists of a thickened pseudostratified epithelium[ZFA]. AAO:0011072 BTO:0001765 @@ -41884,34 +42033,34 @@ Disorders or aberrations in the development or migration of the neural crest cel neural plate https://upload.wikimedia.org/wikipedia/commons/8/8f/Neural_Crest.png - + - + - + - + GOTAX:0000352 - + Wikipedia - + Bgee:AN @@ -41951,7 +42100,7 @@ Disorders or aberrations in the development or migration of the neural crest cel - + The paraxial mesoderm is the mesoderm located bilaterally adjacent to the notochord and neural tube[GO]. AAO:0010568 EFO:0003515 @@ -41977,7 +42126,7 @@ Disorders or aberrations in the development or migration of the neural crest cel paraxial mesoderm http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png - + @@ -41990,7 +42139,7 @@ Disorders or aberrations in the development or migration of the neural crest cel - + Bgee:AN @@ -42037,7 +42186,7 @@ Disorders or aberrations in the development or migration of the neural crest cel - + @@ -42051,7 +42200,6 @@ Disorders or aberrations in the development or migration of the neural crest cel Portion of the middle of the three primary germ layers of the embryo that resides on the periphery of the embryo, is continuous with the extra-embryonic mesoderm, splits into two layers enclosing the intra-embryonic coelom, and gives rise to body wall structures[MP]. - UBERON:0006258 AAO:0010574 EHDAA2:0000919 EHDAA:379 @@ -42077,7 +42225,7 @@ Disorders or aberrations in the development or migration of the neural crest cel lateral plate mesoderm http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png - + @@ -42090,7 +42238,7 @@ Disorders or aberrations in the development or migration of the neural crest cel - + EHDAA2 VHOG @@ -42140,15 +42288,15 @@ Disorders or aberrations in the development or migration of the neural crest cel - - + + - + Bilateral groups of cells consisting of three rows: one row of endocardial precursors medially and two rows of myocardical precursors laterally. The two populations fuse at the midline to form the heart rudiment or cone. should probably be merged with heart rudiment. AAO:0011044 @@ -42165,15 +42313,15 @@ Disorders or aberrations in the development or migration of the neural crest cel heart primordium - + - + - + @@ -42186,19 +42334,19 @@ Disorders or aberrations in the development or migration of the neural crest cel - + ZFA - + ZFA - + XAO @@ -42227,8 +42375,8 @@ Disorders or aberrations in the development or migration of the neural crest cel - - + + Ventral somitic compartment that is a precursor of the axial skeleton[XAO]. Sclerotomes eventually differentiate into the vertebrae and most of the skull. The caudal (posterior) half of one sclerotome fuses with the rostral (anterior) half of the adjacent one to form each vertebra. From their initial location within the somite, the sclerotome cells migrate medially towards the notochord. These cells meet the sclerotome cells from the other side to form the vertebral body. From this vertebral body, sclerotome cells move dorsally and surround the developing spinal cord, forming the vertebral arch[WP]. AAO:0010571 AEO:0000212 @@ -42252,11 +42400,11 @@ Disorders or aberrations in the development or migration of the neural crest cel sclerotome http://upload.wikimedia.org/wikipedia/commons/9/96/Gray65.png - + - + @@ -42275,13 +42423,13 @@ Disorders or aberrations in the development or migration of the neural crest cel - + VHOG:0000680 - + ZFA @@ -42500,7 +42648,7 @@ Disorders or aberrations in the development or migration of the neural crest cel - + The part of the coelom in the embryo between the somatopleuric and splanchnopleuric mesoderm; the principal body cavities of the trunk (thoracic, abdominal, and pelvic) arise from this embryonic part of the coelom. consider merging with coelom. TODO - add spatial relationships to halves of LPM. Note the OG places XAO and ZFA coelem terms here. editor note: TODO check ZFA, which appears to be a structure present in adults EHDAA:251 @@ -42515,14 +42663,14 @@ Disorders or aberrations in the development or migration of the neural crest cel intraembryonic coelom - + - + Wikipedia @@ -42817,8 +42965,8 @@ Disorders or aberrations in the development or migration of the neural crest cel - - + + A specific region of the lateral mesoderm that will form the primary beating heart tube. In mammals the primary heart field gives rise to the left ventricle. XAO:0004185 first heart field @@ -42830,24 +42978,24 @@ Disorders or aberrations in the development or migration of the neural crest cel UBERON:0004140 primary heart field - + - + - + GO:0003128 - + https://orcid.org/0000-0003-3308-6245 @@ -42900,7 +43048,7 @@ Disorders or aberrations in the development or migration of the neural crest cel - + An epithelial tube that will give rise to the mature heart. AAO:0010411 EFO:0003526 @@ -42919,14 +43067,14 @@ Disorders or aberrations in the development or migration of the neural crest cel heart tube - + - + ZFA-modified @@ -43103,7 +43251,6 @@ Disorders or aberrations in the development or migration of the neural crest cel - @@ -43200,7 +43347,6 @@ Disorders or aberrations in the development or migration of the neural crest cel - @@ -43385,7 +43531,6 @@ Disorders or aberrations in the development or migration of the neural crest cel Organism at the gastrula stage. - UBERON:0007012 BILA:0000060 BTO:0001403 FBbt:00005317 @@ -43552,7 +43697,7 @@ Disorders or aberrations in the development or migration of the neural crest cel - + Organ consisting of skeletal tissue. Encompasses whole bones, fused bones, cartilaginious elements, teeth, dermal denticles. AAO:0011129 TAO:0001890 @@ -43566,14 +43711,14 @@ Disorders or aberrations in the development or migration of the neural crest cel skeletal element - + - + VSAO @@ -43600,7 +43745,7 @@ Disorders or aberrations in the development or migration of the neural crest cel - + @@ -43639,14 +43784,14 @@ Disorders or aberrations in the development or migration of the neural crest cel UBERON:0004770 articular system - + - + FMA @@ -44360,7 +44505,7 @@ Disorders or aberrations in the development or migration of the neural crest cel - + Mesenchyme that is part of a developing trunk. EFO:0003485 EHDAA2:0002092 @@ -44376,14 +44521,14 @@ Disorders or aberrations in the development or migration of the neural crest cel trunk mesenchyme - + - + EHDAA2 @@ -44500,7 +44645,7 @@ Disorders or aberrations in the development or migration of the neural crest cel - + Multi-tissue structure that arises from the heart rudiment and will become the heart tube. EHDAA2:0001512 EHDAA:424 @@ -44518,14 +44663,14 @@ Disorders or aberrations in the development or migration of the neural crest cel primitive heart tube - + - + ZFA @@ -44592,7 +44737,6 @@ Disorders or aberrations in the development or migration of the neural crest cel - @@ -44692,7 +44836,7 @@ Disorders or aberrations in the development or migration of the neural crest cel - + A delimited region of dense mesenchyme within looser mesenchyme. AEO:0000148 EHDAA2_RETIRED:0003148 @@ -44702,7 +44846,7 @@ Disorders or aberrations in the development or migration of the neural crest cel UBERON:0005856 developing mesenchymal condensation - + @@ -44721,7 +44865,7 @@ Disorders or aberrations in the development or migration of the neural crest cel - + AEO-modified-relation @@ -44815,7 +44959,7 @@ Disorders or aberrations in the development or migration of the neural crest cel - + The notochordal plate is the dorsal part of the notochordal process when the ventral portion breaks down. It is continuous laterally with the endoderm that composes the roof of the primitive foregut and is in contact dorsally with the neural tube. The folding off of the notochordal plate gives rise to the notochord. TODO - check ordering; awaiting confirmation from JB EHDAA2:0001278 @@ -44829,7 +44973,7 @@ Disorders or aberrations in the development or migration of the neural crest cel notochordal plate - + @@ -44842,7 +44986,7 @@ Disorders or aberrations in the development or migration of the neural crest cel - + EHDAA2 @@ -44870,7 +45014,7 @@ Disorders or aberrations in the development or migration of the neural crest cel - + A midline cellular cord formed from the migration of mesenchymal cells from the primitive knot. EHDAA2:0001279 EHDAA:224 @@ -44887,14 +45031,14 @@ Disorders or aberrations in the development or migration of the neural crest cel The notochordal process grows cranially until it reaches the prechordal plate, the future site of the mouth. In this area the ectoderm is attached directly to the endoderm without intervening mesoderm. This area is known as the oropharyngeal membrane, and it will break down to become the mouth. At the other end of the primitive streak the ectoderm is also fused directly to the endoderm; this is known as the cloacal membrane (proctodeum), or primordial anus. notochordal process - + - + EHDAA2 @@ -45282,7 +45426,6 @@ Disorders or aberrations in the development or migration of the neural crest cel - @@ -45784,7 +45927,7 @@ Disorders or aberrations in the development or migration of the neural crest cel - + @@ -45810,7 +45953,7 @@ Disorders or aberrations in the development or migration of the neural crest cel presumptive paraxial mesoderm - + @@ -45826,7 +45969,7 @@ Disorders or aberrations in the development or migration of the neural crest cel - + https://github.com/obophenotype/uberon/issues/1277 @@ -45902,7 +46045,7 @@ Disorders or aberrations in the development or migration of the neural crest cel - + Mesenchyme with little extracellular matrix. AEO:0000146 EHDAA2:0003146 @@ -45910,7 +46053,7 @@ Disorders or aberrations in the development or migration of the neural crest cel UBERON:0007524 dense mesenchyme tissue - + @@ -45923,7 +46066,7 @@ Disorders or aberrations in the development or migration of the neural crest cel - + AEO @@ -46026,7 +46169,7 @@ Disorders or aberrations in the development or migration of the neural crest cel - + Anatomical system that consists of all blood and lymph vessels. consider merging with vasculature @@ -46043,14 +46186,14 @@ Disorders or aberrations in the development or migration of the neural crest cel vascular system - + - + MA @@ -46078,7 +46221,7 @@ Disorders or aberrations in the development or migration of the neural crest cel - + @@ -46087,7 +46230,6 @@ Disorders or aberrations in the development or migration of the neural crest cel Sum total of mesenchyme in the embryo. consider adding new class (EMAPA:16097) for mesenchyme of embryo (some mesenchyme is extraembryonic - e.g. amnion mesoderm) - UBERON:0003313 EHDAA2:0001113 EHDAA:177 EMAPA:16097 @@ -46095,14 +46237,14 @@ Disorders or aberrations in the development or migration of the neural crest cel UBERON:0009142 entire embryonic mesenchyme - + - + EHDAA2 @@ -46158,7 +46300,7 @@ Disorders or aberrations in the development or migration of the neural crest cel - + EHDAA2:0002094 trunk and cervical paraxial mesenchyme uberon @@ -46166,14 +46308,14 @@ Disorders or aberrations in the development or migration of the neural crest cel UBERON:0009618 trunk paraxial mesoderm - + - + EHDAA2 @@ -46196,7 +46338,7 @@ Disorders or aberrations in the development or migration of the neural crest cel - + EFO:0003704 TAO:0005041 ZFA:0005041 @@ -46206,14 +46348,14 @@ Disorders or aberrations in the development or migration of the neural crest cel anterior lateral plate mesoderm - + - + ZFA @@ -46327,7 +46469,6 @@ Disorders or aberrations in the development or migration of the neural crest cel - @@ -46353,7 +46494,7 @@ Disorders or aberrations in the development or migration of the neural crest cel - + @@ -46373,14 +46514,14 @@ Disorders or aberrations in the development or migration of the neural crest cel UBERON:0010210 blood clot - + - + BTO @@ -46501,8 +46642,8 @@ Disorders or aberrations in the development or migration of the neural crest cel - - + + Anatomical cluster consisting of the skeletal elements (i.e. bone elements, cartilage elements, cartilage condensations) that are part of an individual subdivision of the organism. Excludes joints. FMA:23879 SCTID:129140006 @@ -46514,11 +46655,11 @@ Disorders or aberrations in the development or migration of the neural crest cel subdivision of skeleton - + - + @@ -46531,13 +46672,13 @@ Disorders or aberrations in the development or migration of the neural crest cel - + UBERONREF:0000003 - + VSAO @@ -46598,7 +46739,7 @@ Disorders or aberrations in the development or migration of the neural crest cel - + Subdivision of the skeletal system which consists of the postcranial axial skeleton plus associated joints. axial skeletal system FMA:302077 @@ -46608,7 +46749,7 @@ Disorders or aberrations in the development or migration of the neural crest cel postcranial axial skeletal system http://purl.obolibrary.org/obo/uberon/docs/The-axial-skeleton - + @@ -46621,7 +46762,7 @@ Disorders or aberrations in the development or migration of the neural crest cel - + cjm @@ -46801,6 +46942,7 @@ Disorders or aberrations in the development or migration of the neural crest cel EHDAA2:0004731 Wikipedia:Coelom + ZFA:0001438 enterocoelom haemocoelom schizocoelom @@ -46894,7 +47036,7 @@ Disorders or aberrations in the development or migration of the neural crest cel - + @@ -46915,7 +47057,7 @@ Disorders or aberrations in the development or migration of the neural crest cel UBERON:0012429 hematopoietic tissue - + @@ -46928,7 +47070,7 @@ Disorders or aberrations in the development or migration of the neural crest cel - + defitional @@ -47409,7 +47551,6 @@ Disorders or aberrations in the development or migration of the neural crest cel Primordium that develops into the central nervous system. - UBERON:3000469 future CNS presumptive central nervous system uberon @@ -47453,7 +47594,6 @@ Disorders or aberrations in the development or migration of the neural crest cel Primordium that develops into the nervous system. - UBERON:3000477 AAO:0000477 presumptive nervous system uberon @@ -47479,7 +47619,7 @@ Disorders or aberrations in the development or migration of the neural crest cel - + @@ -47502,7 +47642,7 @@ Disorders or aberrations in the development or migration of the neural crest cel UBERON:0016887 entire extraembryonic component - + @@ -47515,7 +47655,7 @@ Disorders or aberrations in the development or migration of the neural crest cel - + AEO diff --git a/src/ontology/subsets/blood_and_immune_upper_slim.tsv b/src/ontology/subsets/blood_and_immune_upper_slim.tsv index 0e404a0a9..8bf8e4124 100644 --- a/src/ontology/subsets/blood_and_immune_upper_slim.tsv +++ b/src/ontology/subsets/blood_and_immune_upper_slim.tsv @@ -1,419 +1,419 @@ ?x ?label -_:B219c8649X2Db5beX2D4319X2Dae80X2Db9cdc9e3289cgenid1003 -_:B219c8649X2Db5beX2D4319X2Dae80X2Db9cdc9e3289cgenid1010 -_:B219c8649X2Db5beX2D4319X2Dae80X2Db9cdc9e3289cgenid1023 -_:B219c8649X2Db5beX2D4319X2Dae80X2Db9cdc9e3289cgenid1034 -_:B219c8649X2Db5beX2D4319X2Dae80X2Db9cdc9e3289cgenid1044 -_:B219c8649X2Db5beX2D4319X2Dae80X2Db9cdc9e3289cgenid1092 -_:B219c8649X2Db5beX2D4319X2Dae80X2Db9cdc9e3289cgenid1099 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+_:Bd6eff882X2D6a0cX2D48b5X2D9088X2D564199da347cgenid5493 +_:Bd6eff882X2D6a0cX2D48b5X2D9088X2D564199da347cgenid5496 +_:Bd6eff882X2D6a0cX2D48b5X2D9088X2D564199da347cgenid569 +_:Bd6eff882X2D6a0cX2D48b5X2D9088X2D564199da347cgenid576 +_:Bd6eff882X2D6a0cX2D48b5X2D9088X2D564199da347cgenid589 +_:Bd6eff882X2D6a0cX2D48b5X2D9088X2D564199da347cgenid597 +_:Bd6eff882X2D6a0cX2D48b5X2D9088X2D564199da347cgenid604 +_:Bd6eff882X2D6a0cX2D48b5X2D9088X2D564199da347cgenid617 +_:Bd6eff882X2D6a0cX2D48b5X2D9088X2D564199da347cgenid627 +_:Bd6eff882X2D6a0cX2D48b5X2D9088X2D564199da347cgenid662 +_:Bd6eff882X2D6a0cX2D48b5X2D9088X2D564199da347cgenid679 +_:Bd6eff882X2D6a0cX2D48b5X2D9088X2D564199da347cgenid695 +_:Bd6eff882X2D6a0cX2D48b5X2D9088X2D564199da347cgenid70 +_:Bd6eff882X2D6a0cX2D48b5X2D9088X2D564199da347cgenid73 +_:Bd6eff882X2D6a0cX2D48b5X2D9088X2D564199da347cgenid748 +_:Bd6eff882X2D6a0cX2D48b5X2D9088X2D564199da347cgenid766 +_:Bd6eff882X2D6a0cX2D48b5X2D9088X2D564199da347cgenid787 +_:Bd6eff882X2D6a0cX2D48b5X2D9088X2D564199da347cgenid802 +_:Bd6eff882X2D6a0cX2D48b5X2D9088X2D564199da347cgenid857 +_:Bd6eff882X2D6a0cX2D48b5X2D9088X2D564199da347cgenid890 +_:Bd6eff882X2D6a0cX2D48b5X2D9088X2D564199da347cgenid935 +_:Bd6eff882X2D6a0cX2D48b5X2D9088X2D564199da347cgenid949 +_:Bd6eff882X2D6a0cX2D48b5X2D9088X2D564199da347cgenid964 +_:Bd6eff882X2D6a0cX2D48b5X2D9088X2D564199da347cgenid981 "cell" "early embryonic cell (metazoa)" "stem cell" @@ -473,6 +473,7 @@ _:B219c8649X2Db5beX2D4319X2Dae80X2Db9cdc9e3289cgenid995 "biogenic amine secreting cell" "serotonin secreting cell" "defensive cell" + "stromal cell" "phagocyte (sensu Vertebrata)" "neuron" "lymphocyte" @@ -845,19 +846,17 @@ _:B219c8649X2Db5beX2D4319X2Dae80X2Db9cdc9e3289cgenid995 "response to external biotic stimulus" "organelle" "membrane-bounded organelle" - "non-membrane-bounded organelle" + "membraneless organelle" "intracellular organelle" "extracellular organelle" "intracellular membrane-bounded organelle" - "intracellular non-membrane-bounded organelle" + "intracellular membraneless organelle" "organelle lumen" "receptor complex" "protein-containing complex organization" "cellular component biogenesis" "translation initiation ternary complex" - "cellular metabolic process" "primary metabolic process" - "cellular biosynthetic process" "biological process involved in interspecies interaction between organisms" "plasma membrane fusion" "T cell selection" @@ -976,7 +975,7 @@ _:B219c8649X2Db5beX2D4319X2Dae80X2Db9cdc9e3289cgenid995 "secretory vesicle" "synaptic signaling" "trans-synaptic signaling" - "cellular anatomical entity" + "cellular anatomical structure" "plasma membrane bounded cell projection" "plasma membrane bounded cell projection assembly" "plasma membrane bounded cell projection organization" @@ -1164,7 +1163,7 @@ _:B219c8649X2Db5beX2D4319X2Dae80X2Db9cdc9e3289cgenid995 "G-protein coupled receptor" "eukaryotic protein" "cathepsin-like protease" - "protein-containing material entity" + "protein-containing molecular entity" "processual entity" "tube" "vessel" diff --git a/src/ontology/subsets/eye_upper_slim.json b/src/ontology/subsets/eye_upper_slim.json index 27446ca77..dac5e56e0 100644 --- a/src/ontology/subsets/eye_upper_slim.json +++ b/src/ontology/subsets/eye_upper_slim.json @@ -4,9 +4,9 @@ "meta" : { "basicPropertyValues" : [ { "pred" : "http://www.w3.org/2002/07/owl#versionInfo", - "val" : "2024-09-26" + "val" : "2025-01-08" } ], - "version" : "http://purl.obolibrary.org/obo/cl/releases/2024-09-26/subsets/eye_upper_slim.owl" + "version" : "http://purl.obolibrary.org/obo/cl/releases/2025-01-08/subsets/eye_upper_slim.owl" }, "nodes" : [ { "id" : "http://purl.obolibrary.org/obo/CL_0000000", @@ -18,7 +18,7 @@ "xrefs" : [ "CARO:mah" ] }, "comments" : [ "The definition of cell is intended to represent all cells, and thus a cell is defined as a material entity and not an anatomical structure, which implies that it is part of an organism (or the entirety of one)." ], - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/ubprop#_upper_level" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/ubprop#_upper_level" ], "xrefs" : [ { "val" : "CALOHA:TS-2035" }, { @@ -50,6 +50,7 @@ "val" : "Any fibroblast that is derived from the neural crest.", "xrefs" : [ "https://orcid.org/0000-0001-5208-3432" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "fibroblast neural crest derived" @@ -64,7 +65,7 @@ "val" : "Any sensory receptor cell that is a(n) neuron and is capable of some detection of stimulus involved in sensory perception.", "xrefs" : [ "FBC:Autogenerated" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "neuronal receptor cell (sensu Animalia)" @@ -82,6 +83,7 @@ "val" : "A cell found in the embryo before the formation of all the gem layers is complete.", "xrefs" : [ "GOC:tfm" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "ZFA:0009002" } ] @@ -95,6 +97,7 @@ "val" : "Cell that is part of the migratory cranial neural crest population. Migratory cranial neural crest cells develop from premigratory cranial neural crest cells and have undergone epithelial to mesenchymal transition and delamination.", "xrefs" : [ "ZFA:0007091", "https://orcid.org/0000-0001-5208-3432" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "ZFA:0007091" } ] @@ -104,7 +107,11 @@ "lbl" : "glioblast", "type" : "CLASS", "meta" : { - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], + "definition" : { + "val" : "A non-terminally differentiated cell that develops form the neuroectoderm. Glioblast has the potential to differentiate into various types of glial cells, including astrocytes and oligodendrocytes.", + "xrefs" : [ "PMID:37824650", "Wikipedia:Glioblast" ] + }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "ZFA:0009010" } ] @@ -118,7 +125,7 @@ "val" : "A cell that will develop into a neuron often after a migration phase.", "xrefs" : [ "GOC:NV", "http://en.wikipedia.org/wiki/Neuroblast" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "neuroblast" @@ -141,7 +148,7 @@ "xrefs" : [ "GOC:tfm", "MESH:D013234" ] }, "comments" : [ "This term applies to metazoan. For plant stem cells, consider using PO:0004011 ‘initial cell’ or its parent PO:0004010 ‘meristematic cell’." ], - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#general_cell_types_upper_slim", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#general_cell_types_upper_slim", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "animal stem cell" @@ -168,7 +175,7 @@ "xrefs" : [ "GOC:add", "GOC:dsd", "GOC:tfm", "PMID:19022770", "http://en.wikipedia.org/wiki/Hematopoietic_stem_cell" ] }, "comments" : [ "Markers differ between species, and two sets of markers have been described for mice. HSCs are reportedly CD34-positive, CD45-positive, CD48-negative, CD150-positive, CD133-positive, and CD244-negative." ], - "subsets" : [ "http://purl.obolibrary.org/obo/cl#blood_and_immune_upper_slim", "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#blood_and_immune_upper_slim", "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "blood forming stem cell" @@ -210,7 +217,7 @@ "val" : "A progenitor cell committed to the erythroid lineage.", "xrefs" : [ "GOC:add", "ISBN:0721601464" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#blood_and_immune_upper_slim", "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#blood_and_immune_upper_slim", "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003000", "pred" : "hasRelatedSynonym", @@ -247,6 +254,7 @@ "val" : "A stem cell that can give rise to multiple lineages of cells.", "xrefs" : [ "GOC:add" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "multi-fate stem cell" @@ -276,7 +284,7 @@ "xrefs" : [ "GOC:add", "ISBN:0878932437", "MESH:D023461" ] }, "comments" : [ "This cell type is intended to be compatible with any vertebrate common myeloid progenitor. For mammalian CMP known to be CD34-positive, please use the term 'common myeloid progenitor, CD34-positive' (CL_0001059)." ], - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "common myeloid precursor" @@ -332,7 +340,7 @@ "xrefs" : [ "GOC:add", "GOC:dsd", "GOC:tfm", "MESH:D055015", "PMID:16647566", "http://en.wikipedia.org/wiki/Megakaryocyte-erythroid_progenitor_cell" ] }, "comments" : [ "MEPs are reportedly CD19-negative, CD34-negative, CD45RA-negative, CD110-positive, CD117-positive, and SCA1-negative and reportedly express the transcription factors GATA-1 and NF-E2." ], - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "CFU-EM" @@ -372,6 +380,7 @@ "val" : "A stem cell from which all cells of the body can form.", "xrefs" : [ "GOC:add", "GOC:tfm" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "totipotential stem cell" @@ -394,7 +403,7 @@ "xrefs" : [ "SANBI:mhl" ] }, "comments" : [ "define using PATO mulit-potent or oligopotent?" ], - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "blast cell" @@ -414,6 +423,7 @@ "val" : "A cell that is commited to differentiating into a muscle cell. Embryonic myoblasts develop from the mesoderm. They undergo proliferation, migrate to their various sites, and then differentiate into the appropriate form of myocytes. Myoblasts also occur as transient populations of cells in muscles undergoing repair.", "xrefs" : [ "GOC:tfm", "MESH:D032446", "PMID:21849021" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "BTO:0000222" }, { @@ -438,7 +448,7 @@ "xrefs" : [ "ISBN:0517223651", "MESH:D005347", "http://en.wikipedia.org/wiki/Fibroblast" ] }, "comments" : [ "These cells may be vimentin-positive, fibronectin-positive, fsp1-positive, MMP-1-positive, collagen I-positive, collagen III-positive, and alpha-SMA-negative." ], - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#general_cell_types_upper_slim", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#general_cell_types_upper_slim", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "xrefs" : [ { "val" : "BTO:0000452" }, { @@ -466,7 +476,7 @@ "val" : "A cell that is usually found in a two-dimensional sheet with a free surface. The cell has a cytoskeleton that allows for tight cell to cell contact and for cell polarity where apical part is directed towards the lumen and the basal part to the basal lamina.", "xrefs" : [ "FB:ma", "GOC:tfm", "MESH:D004847" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#general_cell_types_upper_slim", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#general_cell_types_upper_slim", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "epitheliocyte" @@ -503,7 +513,7 @@ "val" : "An endothelial cell that lines the vasculature.", "xrefs" : [ "GOC:tfm" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "xrefs" : [ { "val" : "ZFA:0009036" } ], @@ -521,7 +531,7 @@ "val" : "A columnar/cuboidal epithelial cell is a cell usually found in a two dimensional sheet with a free surface. Columnar/cuboidal epithelial cells take on the shape of a column or cube.", "xrefs" : [ "GO:0002065", "https://orcid.org/0000-0001-5208-3432" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "xrefs" : [ { "val" : "ZFA:0009038" } ], @@ -539,7 +549,7 @@ "val" : "Any epithelial cell that is part of some squamous epithelium.", "xrefs" : [ "FBC:Autogenerated" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "CALOHA:TS-1249" }, { @@ -556,7 +566,7 @@ "xrefs" : [ "GOC:tfm", "ISBN:0721662544", "PMID:26106328" ] }, "comments" : [ "Mesothelial cells, which morphologically resemble squamous epithelial cells, express both epithelial markers (cytokeratins) and mesenchymal markers (vimentin), reflecting their mesodermal origin. They feature surface microvilli and apical-basal polarity. Under certain conditions, they can undergo mesothelial-to-mesenchymal transition. These cells also produce extracellular matrix proteins, maintain serosal homeostasis, and facilitate fluid transport." ], - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "mesotheliocyte" @@ -580,7 +590,7 @@ "val" : "A cell found predominately in the blood.", "xrefs" : [ "GOC:add", "GOC:tfm" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#general_cell_types_upper_slim" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#general_cell_types_upper_slim", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "FMA:62844" }, { @@ -594,7 +604,7 @@ "lbl" : "neuron associated cell", "type" : "CLASS", "meta" : { - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ] + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ] } }, { "id" : "http://purl.obolibrary.org/obo/CL_0000099", @@ -605,7 +615,11 @@ "val" : "Most generally any neuron which is not motor or sensory. Interneurons may also refer to neurons whose axons remain within a particular brain region as contrasted with projection neurons which have axons projecting to other brain regions.", "xrefs" : [ "GOC:tfm", "MESH:D007395" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "synonyms" : [ { + "pred" : "hasRelatedSynonym", + "val" : "CNS interneuron" + } ], "xrefs" : [ { "val" : "BTO:0003811" }, { @@ -631,7 +645,7 @@ "val" : "Any neuron having a sensory function; an afferent neuron conveying sensory impulses.", "xrefs" : [ "ISBN:0721662544" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "xrefs" : [ { "val" : "BTO:0001037" }, { @@ -650,22 +664,6 @@ "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/CL_0000103", - "lbl" : "bipolar neuron", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A type of interneuron that has two neurites, usually an axon and a dendrite, extending from opposite poles of an ovoid cell body.", - "xrefs" : [ "GOC:tfm", "ISBN:0444009442" ] - }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#BDS_subset", "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], - "xrefs" : [ { - "val" : "FMA:67282" - }, { - "val" : "ZFA:0009055" - } ] - } }, { "id" : "http://purl.obolibrary.org/obo/CL_0000115", "lbl" : "endothelial cell", @@ -676,7 +674,7 @@ "xrefs" : [ "GOC:tfm", "MESH:D042783", "PMID:21275341", "http://en.wikipedia.org/wiki/Endothelial_cell", "https://sourceforge.net/tracker/?func=detail&atid=440764&aid=3364936&group_id=36855" ] }, "comments" : [ "From FMA: 9.07.2001: Endothelial cell has always been classified as a kind of epithelial cell, specifically a squamous cell but that is not true. First, endothelial cell can either be squamous or cuboidal (e.g. high-endothelial cell) and secondly, it has different embryological derivation (mesodermal) than a true epithelial cell (ectodermal and endodermal). The basis for present classification is the fact that it comprises the outermost layer or lining of anatomical structures (location-based) but a better structural basis for the differentia is the cytoskeleton of the cell. Endothelial cell has vimentin filaments while an epithelial cell has keratin filaments. [Onard]." ], - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "endotheliocyte" @@ -695,21 +693,12 @@ "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/CL_0000117", - "lbl" : "CNS neuron (sensu Vertebrata)", - "type" : "CLASS", - "meta" : { - "xrefs" : [ { - "val" : "ZFA:0009067" - } ] - } }, { "id" : "http://purl.obolibrary.org/obo/CL_0000123", "lbl" : "neuron associated cell (sensu Vertebrata)", "type" : "CLASS", "meta" : { - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ] + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ] } }, { "id" : "http://purl.obolibrary.org/obo/CL_0000125", @@ -721,7 +710,7 @@ "xrefs" : [ "MESH:D009457" ] }, "comments" : [ "Not all glial cells develop from glioblasts, with microglia developing from the mesoderm instead. See https://github.com/obophenotype/cell-ontology/issues/1571" ], - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#general_cell_types_upper_slim", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#general_cell_types_upper_slim", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "neuroglial cell" @@ -747,7 +736,7 @@ "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" }, { "pred" : "http://purl.org/dc/terms/description", - "val" : "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional.\n\nGlial cells, also known as neuroglia or simply glia, are non-neuronal cells in the central and peripheral nervous systems that provide support and protection for neurons. They constitute approximately half of the total cells in the human brain and more than half in other parts of the nervous system. Glial cells perform several key functions including, but not limited to, maintaining homeostasis, forming the myelin sheath around the neuron axons, and providing support and nutrition to neurons.\nThese different functions are performed by various glial cell types, including astrocytes, oligodendrocytes, microglia and other specialized types. Astrocytes, for example, are the most abundant glial cells and provide metabolic and nutrient support to neurons, help regulate the extracellular ion and neurotransmitter levels, and play a role in the formation and maintenance of the blood-brain barrier, contributing to the overall homeostasis and functioning of the nervous system. Additionally, astrocytes are involved in synaptic communication and participate in processes such as synaptogenesis and synaptic pruning.\nOligodendrocytes in the central nervous system function to insulate neurons by producing a fatty substance known as myelin. The myelin sheath enhances the speed and efficiency of nerve impulse conduction along the axons. \nMicroglia, the immune cells of the central nervous system, protect neurons from pathogens and clear away dead neurons through phagocytosis, a process also known as cellular eating. They also contribute to the regulation of inflammation in response to signals of tissue damage or infection in the central nervous system by releasing cytokines and other signaling molecules that modulate the immune response.\nDespite their overarching function in the support and protection of neurons, glial cells have also been shown to play significant roles in the pathophysiology of many psychiatric and neurodegenerative diseases, such as Alzheimer’s, Parkinson’s Disease and multiple sclerosis." + "val" : "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nGlial cells, also known as neuroglia or simply glia, are non-neuronal cells in the central and peripheral nervous systems that provide support and protection for neurons. They constitute approximately half of the total cells in the human brain and more than half in other parts of the nervous system. Glial cells perform several key functions including, but not limited to, maintaining homeostasis, forming the myelin sheath around the neuron axons, and providing support and nutrition to neurons.\nThese different functions are performed by various glial cell types, including astrocytes, oligodendrocytes, microglia and other specialized types. Astrocytes, for example, are the most abundant glial cells and provide metabolic and nutrient support to neurons, help regulate the extracellular ion and neurotransmitter levels, and play a role in the formation and maintenance of the blood-brain barrier, contributing to the overall homeostasis and functioning of the nervous system. Additionally, astrocytes are involved in synaptic communication and participate in processes such as synaptogenesis and synaptic pruning.\nOligodendrocytes in the central nervous system function to insulate neurons by producing a fatty substance known as myelin. The myelin sheath enhances the speed and efficiency of nerve impulse conduction along the axons. \nMicroglia, the immune cells of the central nervous system, protect neurons from pathogens and clear away dead neurons through phagocytosis, a process also known as cellular eating. They also contribute to the regulation of inflammation in response to signals of tissue damage or infection in the central nervous system by releasing cytokines and other signaling molecules that modulate the immune response.\nDespite their overarching function in the support and protection of neurons, glial cells have also been shown to play significant roles in the pathophysiology of many psychiatric and neurodegenerative diseases, such as Alzheimer’s, Parkinson’s Disease and multiple sclerosis." } ] } }, { @@ -759,7 +748,7 @@ "val" : "A neuroglial cell of ectodermal origin, i.e., the astrocytes and oligodendrocytes considered together.", "xrefs" : [ "GOC:tfm", "ISBN:0721662544" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "macrogliocyte" @@ -789,7 +778,7 @@ "xrefs" : [ "GOC:dsd", "GOC:tfm", "MESH:D001253", "PMID:11746784", "PMID:12162730", "PMID:12898703", "PMID:20942978", "http://en.wikipedia.org/wiki/Astrocyte" ] }, "comments" : [ "Astrocytes are reportedly CD68-negative, CD121a-positive, CD184-positive, CD192-positive, CRF-positive, EGFR-positive, GFAP-positive, GLUT1-positive, MBP-negative, and NGFR-positive." ], - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "astrocytic glia" @@ -817,7 +806,7 @@ "val" : "An hexagonal, flattened, mitochondria-rich endothelial cell that forms a monolayer on the posterior surface of the cornea (the corneal endothelium). Corneal endothelial cells are derived from the neural crest and are responsible for keeping the cornea transparent by maintaining the tissue in a semi-dry state through the action of their ionic pumps and tight junction barrier.", "xrefs" : [ "GOC:tfm", "PMID:21976958", "PMID:23284695", "PMID:34741068", "PMID:36769303" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#eye_upper_slim", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#eye_upper_slim", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "xrefs" : [ { "val" : "CALOHA:TS-0172" }, { @@ -839,6 +828,7 @@ "val" : "Ectoderm destined to be nervous tissue.", "xrefs" : [ "GOC:tfm", "ISBN:068340007X" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "neurectoderm cell" @@ -857,7 +847,7 @@ "xrefs" : [ "FB:ma", "GOC:dsd", "PMCID:PMC2613570", "PMID:10102814", "PMID:16923606", "PMID:17986482", "PMID:19960544", "http://en.wikipedia.org/wiki/Mesenchymal_stem_cell", "http://www.copewithcytokines.de/cope.cgi?key=mesenchymal%20stem%20cells" ] }, "comments" : [ "Many but not all mesenchymal cells derive from the mesoderm. MSCs are reportedly CD3-negative, CD4-negative, CD5-negative, CD8-negative, CD11a-negative, CD11b-negative, CD14-negative, CD19-negative, CD29-positive, CD31-negative, CD34-negative, CD38-negative, CD40-negative, CD44-positive, CD45-negative, CD49-positive, CD54-positive, CD66b-negative, CD79a-negative, CD80-negative, CD102-positive, CD106-positive, CD117-positive, CD121a-positive, CD121b-positive, CD123-positive, CD124-positive, CD133-negative, CD146-positive, CD166-positive, CD271-positive, B220-negative, Gr1-negative, MHCI-positive, MHCII-negative, SSEA4-negative, sca1-positive, Ter119-negative, and glycophorin A-negative. Cultured MSCs are capable of producing stem cell factor, IL7, IL8, IL11, TGF-beta, cofilin, galectin-1, laminin-receptor 1, cyclophilin A, and MMP-2." ], - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "pred" : "hasNarrowSynonym", "val" : "bone marrow stromal cells" @@ -928,6 +918,7 @@ "val" : "A pigment cell is a cell that contains pigment granules.", "xrefs" : [ "GOC:tfm" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "chromatocyte" @@ -950,7 +941,7 @@ "val" : "A pigment cell derived from the neural crest. Contains melanin-filled pigment granules, which gives a brown to black appearance.", "xrefs" : [ "SANBI:mhl" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#general_cell_types_upper_slim", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#general_cell_types_upper_slim", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "synonyms" : [ { "pred" : "hasNarrowSynonym", "val" : "melanophore" @@ -967,10 +958,15 @@ "val" : "VHOG:0001679" }, { "val" : "ZFA:0009091" + }, { + "val" : "https://cellxgene.cziscience.com/cellguide/CL_0000148" } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" + }, { + "pred" : "http://purl.org/dc/terms/description", + "val" : "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nMelanocytes are specialized cells prevalently found in the skin, but also present in the hair follicles, eyes, inner ear, bones, heart, and brain. Their primary function is the synthesis of melanin, a pigment responsible for coloration of skin, hair, and eyes. The presence and distribution of this pigment play a crucial role in the body's defense mechanism against harmful ultraviolet radiation.\nIn addition to melanin production, melanocytes also engage in a variety of other biological functions. They play a fundamental role in the immune response, owing to their ability to present antigens to T cells. Furthermore, they contribute to the maintenance of the skin's homeostasis by regulating processes such as extracellular matrix remodeling and cytokine production. A balance in melanocyte function is pivotal, as dysfunctions often result in dermatological disorders. For instance, the loss of melanocytes or reduction in their function may lead to hypopigmentation conditions such as vitiligo, whereas an abnormal increase could result in hyperpigmentation disorders or melanoma, a dangerous type of skin cancer." } ] } }, { @@ -978,6 +974,7 @@ "lbl" : "visual pigment cell", "type" : "CLASS", "meta" : { + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "pred" : "hasBroadSynonym", "val" : "pigment cell" @@ -992,7 +989,7 @@ "val" : "A cell that specializes in controlled release of one or more substances.", "xrefs" : [ "GOC:tfm", "ISBN:0721662544" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "BTO:0003659" }, { @@ -1008,7 +1005,7 @@ "val" : "A cell whose primary function is to shorten.", "xrefs" : [ "FB:ma" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ] + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ] } }, { "id" : "http://purl.obolibrary.org/obo/CL_0000187", @@ -1019,7 +1016,7 @@ "val" : "A mature contractile cell, commonly known as a myocyte. This cell has as part of its cytoplasm myofibrils organized in various patterns.", "xrefs" : [ "MESH:D032342" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "muscle fiber" @@ -1056,7 +1053,7 @@ "val" : "A non-striated, elongated, spindle-shaped cell found lining the digestive tract, uterus, and blood vessels. They develop from specialized myoblasts (smooth muscle myoblast).", "xrefs" : [ "MESH:D032389", "PMID:9315361", "http://en.wikipedia.org/wiki/Smooth_muscle_cell" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#general_cell_types_upper_slim", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#general_cell_types_upper_slim", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "synonyms" : [ { "pred" : "hasBroadSynonym", "val" : "non-striated muscle cell" @@ -1080,10 +1077,15 @@ "val" : "FMA:14072" }, { "val" : "ZFA:0009118" + }, { + "val" : "https://cellxgene.cziscience.com/cellguide/CL_0000192" } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" + }, { + "pred" : "http://purl.org/dc/terms/description", + "val" : "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nSmooth muscle cells are a specialized type of muscle cells that are primarily found within the walls of hollow organs such as the intestine, stomach, bladder, uterus, and blood vessels. These cells are an essential component of the autonomic nervous system controling involuntary movements within the body.\nSmooth muscle cells play a vital role in many physiological processes due to their unique functionality. They can contract and relax in a slow, sustained, and controlled manner to help modulate the size and shape of the lumens of the organs they surround. For example, in the digestive system, coordinated contraction and relaxation of smooth muscle cells propels food along the gastrointestinal tract - a process known as peristalsis. In the blood vessels, the smooth muscle cells, by contracting or relaxing, either constrict or dilate the vessels, which in turn, help regulate blood flow and pressure.\nOn a cellular level, smooth muscle cells possess a single, centrally located nucleus and contain an arranged network of actin and myosin filaments, which are the proteins responsible for muscle contraction. Unlike their counterparts in skeletal or cardiac muscles, these cells lack specific contact points for these filaments, hence the lack of visible striations. Furthermore, the contraction of smooth muscle cells is regulated by hormones and neurotransmitters, such as acetylcholine and norepinephrine, adding an additional layer of complex regulation to these highly specialized cells." } ] } }, { @@ -1094,6 +1096,7 @@ "definition" : { "val" : "A cell that is capable of detection of a stimulus involved in sensory perception." }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "receptor cell" @@ -1111,7 +1114,7 @@ "val" : "A cell specialized in detecting light stimuli that are involved in visual perception.", "xrefs" : [ "MESH:D010786" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "BTO:0001060" }, { @@ -1137,6 +1140,7 @@ "val" : "A cell whose function is determined by the generation or the reception of an electric signal.", "xrefs" : [ "FB:ma" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "ZFA:0009128" } ] @@ -1150,6 +1154,7 @@ "val" : "A cell within an epithelial cell sheet whose main function is to act as an internal or external covering for a tissue or an organism.", "xrefs" : [ "JB:jb" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "boundary cell" @@ -1167,6 +1172,7 @@ "val" : "A cell whose primary function is to prevent the transport of stuff across compartments.", "xrefs" : [ "JB:jb" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "ZFA:0009132" } ] @@ -1180,6 +1186,7 @@ "val" : "A cell that moves by its own activities.", "xrefs" : [ "FB:ma" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "ZFA:0009136" } ] @@ -1193,6 +1200,7 @@ "val" : "A cell of the outer of the three germ layers of the embryo.", "xrefs" : [ "MESH:D004475" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "ectoderm cell" @@ -1212,7 +1220,7 @@ "val" : "A cell of the middle germ layer of the embryo.", "xrefs" : [ "MESH:D008648" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "mesoblast" @@ -1224,6 +1232,12 @@ "val" : "FMA:72554" }, { "val" : "ZFA:0009138" + }, { + "val" : "https://cellxgene.cziscience.com/cellguide/CL_0000222" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/description", + "val" : "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nMesodermal cells are pluripotent and the most abundant in the human body. They contribute to the development of several structures such as the skeletal muscles, bones, heart and blood vessels, kidneys, gonads, connective tissues, and certain layers of the skin. Hence, the mesoderm is often regarded as an active and diverse layer due to its role in forming many bodily structures. \nIn embryonic development, these cells are instrumental, contributing to the body's structures through a carefully coordinated sequence of morphogenetic movements. This process forms the complex multicellular architecture of tissues and organs from a simple ball of cells. Without the function of mesodermal cells, the body's integral structures and systems would cease to form correctly, leading to developmental disorders such as axial mesodermal dysplasia complex" } ] } }, { @@ -1235,6 +1249,7 @@ "val" : "A cell of the inner of the three germ layers of the embryo.", "xrefs" : [ "MESH:D004707" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "endoderm cell" @@ -1254,7 +1269,7 @@ "val" : "A red blood cell. In mammals, mature erythrocytes are biconcave disks containing hemoglobin whose function is to transport oxygen.", "xrefs" : [ "GOC:tfm", "MESH:D004912" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#blood_and_immune_upper_slim", "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#blood_and_immune_upper_slim", "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "RBC" @@ -1283,7 +1298,7 @@ "val" : "Any cell that in taxon some Eukaryota.", "xrefs" : [ "FBC:Autogenerated" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "MESH:D005057" } ] @@ -1297,7 +1312,7 @@ "val" : "Any photoreceptor cell that is part of some eye.", "xrefs" : [ "FBC:Autogenerated" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#eye_upper_slim", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#eye_upper_slim", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "xrefs" : [ { "val" : "ZFA:0009154" } ], @@ -1315,6 +1330,7 @@ "val" : "A cell whose primary function is to provide structural support, to provide strength and physical integrity to the organism.", "xrefs" : [ "TAIR:sr" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "ZFA:0005745" } ] @@ -1324,7 +1340,7 @@ "lbl" : "crystallin accumulating cell", "type" : "CLASS", "meta" : { - "subsets" : [ "http://purl.obolibrary.org/obo/cl#eye_upper_slim" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#eye_upper_slim", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "lens cell" @@ -1339,7 +1355,7 @@ "val" : "A cell that is specialised to accumulate a particular substance(s).", "xrefs" : [ "FB:ma" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/ubprop#_upper_level" ] + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/ubprop#_upper_level" ] } }, { "id" : "http://purl.obolibrary.org/obo/CL_0000329", @@ -1350,6 +1366,7 @@ "val" : "Any cell that is capable of some oxygen transport.", "xrefs" : [ "FBC:Autogenerated" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "ZFA:0009164" } ] @@ -1363,6 +1380,7 @@ "val" : "A cell derived from the specialized ectoderm flanking each side of the embryonic neural plate, which after the closure of the neural tube, forms masses of cells that migrate out from the dorsal aspect of the neural tube to spread throughout the body.", "xrefs" : [ "doi:10.1016/j.stem.2015.02.017" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "FMA:86667" }, { @@ -1378,6 +1396,7 @@ "val" : "A mesenchymal cell in embryonic development found in a contracting mass and that gives rise to osteoprogenitors.", "xrefs" : [ "GOC:tfm", "PMID:5025404" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "ZFA:0009166" } ] @@ -1391,6 +1410,7 @@ "val" : "An early neural cell developing from the early ependymal cell of the neural tube.", "xrefs" : [ "GOC:tfm", "ISBN:0618947256" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "spongioblast" @@ -1410,6 +1430,7 @@ "val" : "Any animal cell containing pigment granules.", "xrefs" : [ "GOC:tfm", "ISBN:0721662544" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "ZFA:0009170" } ] @@ -1423,7 +1444,7 @@ "val" : "A cell of the sclera of the eye.", "xrefs" : [ "GOC:add" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#eye_upper_slim" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#eye_upper_slim", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "ZFA:0009174" } ] @@ -1437,7 +1458,7 @@ "val" : "A structural cell that is part of optic choroid.", "xrefs" : [ "GOC:add" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#eye_upper_slim" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#eye_upper_slim", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "ZFA:0009175" } ] @@ -1450,7 +1471,8 @@ "definition" : { "val" : "A cell of the outer layer of a blastula that gives rise to the ectoderm after gastrulation.", "xrefs" : [ "GOC:tfm", "ISBN:0618947256" ] - } + }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ] } }, { "id" : "http://purl.obolibrary.org/obo/CL_0000365", @@ -1461,6 +1483,7 @@ "val" : "Diploid cell produced by the fusion of sperm cell nucleus and egg cell.", "xrefs" : [ "ISBN:0471245208" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "pred" : "hasBroadSynonym", "val" : "zygote" @@ -1482,40 +1505,45 @@ "val" : "A cell whose function is determined by its response to an electric signal.", "xrefs" : [ "FB:ma" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "ZFA:0009190" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/CL_0000402", - "lbl" : "CNS interneuron", + "id" : "http://purl.obolibrary.org/obo/CL_0000404", + "lbl" : "electrically signaling cell", "type" : "CLASS", "meta" : { "definition" : { - "val" : "An interneuron that has its cell body in a central nervous system.", - "xrefs" : [ "doi:10.1016/B978-0-12-817424-1.00001-X" ] + "val" : "A cell that initiates an electrical signal and passes that signal to another cell.", + "xrefs" : [ "FB:ma" ] }, - "comments" : [ "Interneurons are commonly described as being only found in the central nervous system. However, in CL we define 'interneuron' more broadly as any neuron that is neither a motor neuron nor a sensory neuron, regardless of its location, so we need this term to refer strictly to interneurons of the central nervous system." ], - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { - "val" : "ZFA:0009191" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" + "val" : "ZFA:0009193" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/CL_0000404", - "lbl" : "electrically signaling cell", + "id" : "http://purl.obolibrary.org/obo/CL_0000499", + "lbl" : "stromal cell", "type" : "CLASS", "meta" : { "definition" : { - "val" : "A cell that initiates an electrical signal and passes that signal to another cell.", - "xrefs" : [ "FB:ma" ] + "val" : "A connective tissue cell of an organ found in the loose connective tissue.", + "xrefs" : [ "GOC:tfm", "MESH:D017154" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#general_cell_types_upper_slim", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "xrefs" : [ { - "val" : "ZFA:0009193" + "val" : "BTO:0002064" + }, { + "val" : "FMA:83624" + }, { + "val" : "ZFA:0009226" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/RO_0002175", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" } ] } }, { @@ -1527,7 +1555,7 @@ "val" : "A precursor cell destined to differentiate into smooth muscle myocytes.", "xrefs" : [ "GOC:tfm", "MESH:D032390" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "myoblast, smooth muscle", @@ -1540,6 +1568,12 @@ "val" : "FMA:84798" }, { "val" : "ZFA:0009235" + }, { + "val" : "https://cellxgene.cziscience.com/cellguide/CL_0000514" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/description", + "val" : "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nA precursor to the smooth muscle cell, the smooth muscle myoblast, is integral to various body systems, including the cardiovascular, gastrointestinal, and respiratory systems. Smooth muscle myoblasts arise from the differentiation of mesenchymal stem cells, a process tightly regulated by specific genetic factors and environmental signals. Their role extends to myogenesis, particularly in the formation of muscular tissue, especially during embryonic development.\nSmooth muscle myoblasts possess distinctive cellular characteristics. In contrast to skeletal muscle myoblasts, they do not fuse to create multinucleated fibers. Instead, they differentiate into individual, uninucleated smooth muscle cells. This differentiation unfolds in two distinct phases: proliferation, marked by rapid division to increase cell numbers, and differentiation, involving structural and functional transformation into mature smooth muscle cells. This intricate process is intricately mediated by various signaling molecules and transcription factors.\nFunctionally, smooth muscle myoblasts and the mature muscle cells they generate play pivotal roles in various physiological processes. Smooth muscle cells orchestrate involuntary muscle responses and are integral to body systems that regulate blood flow, propel food along the digestive tract, and control airflow in the respiratory tract. These diverse functions underscore the significance of smooth muscle myoblasts in the body's growth, maintenance, and overall function." } ] } }, { @@ -1551,7 +1585,7 @@ "val" : "A neuron which conveys sensory information centrally from the periphery.", "xrefs" : [ "GOC:tfm", "MESH:D009475" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "input neuron" @@ -1571,7 +1605,7 @@ "lbl" : "pigmented epithelial cell", "type" : "CLASS", "meta" : { - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "ZFA:0009241" } ] @@ -1586,7 +1620,7 @@ "xrefs" : [ "MESH:D009474", "http://en.wikipedia.org/wiki/Neuron" ] }, "comments" : [ "These cells are also reportedly CD4-negative and CD200-positive. They are also capable of producing CD40L and IFN-gamma." ], - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#general_cell_types_upper_slim", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#general_cell_types_upper_slim", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "nerve cell" @@ -1624,6 +1658,7 @@ "xrefs" : [ "GOC:tfm", "SANBI:mhl" ] }, "comments" : [ "Derived from UBERON:0002342 neural crest." ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "BTO:0003217" }, { @@ -1641,7 +1676,7 @@ "val" : "An immature, nucleated erythrocyte occupying the stage of erythropoeisis that follows formation of erythroid progenitor cells. This cell is CD71-positive, has both a nucleus and a nucleolus, and lacks hematopoeitic lineage markers.", "xrefs" : [ "ISBN:0721601464", "PMID:1638021" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#blood_and_immune_upper_slim", "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#blood_and_immune_upper_slim", "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "rubriblast", @@ -1663,6 +1698,7 @@ "val" : "A nucleated immature erythrocyte, having cytoplasm generally similar to that of the earlier proerythroblast but sometimes even more basophilic, and usually regular in outline. The nucleus is still relatively large, but the chromatin strands are thicker and more deeply staining, giving a coarser appearance; the nucleoli have disappeared. This cell is CD71-positive and lacks hematopoeitic lineage markers.", "xrefs" : [ "GOC:tfm", "ISBN:0721601464" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "basophilic normoblast", @@ -1695,6 +1731,7 @@ "val" : "A nucleated, immature erythrocyte in which the nucleus occupies a relatively smaller part of the cell than in its precursor, the basophilic erythroblast. The cytoplasm is beginning to acquire hemoglobin and thus is no longer a purely basophilic, but takes on acidophilic aspects, which becomes progressively more marked as the cell matures. The chromatin of the nucleus is arranged in coarse, deeply staining clumps. This cell is CD71-positive and lacks hematopoeitic lineage markers.", "xrefs" : [ "ISBN:0721601464" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "intermediate erythroblast", @@ -1735,6 +1772,7 @@ "val" : "The final stage of the nucleated, immature erythrocyte, before nuclear loss. Typically the cytoplasm is described as acidophilic, but it still shows a faint polychromatic tint. The nucleus is small and initially may still have coarse, clumped chromatin, as in its precursor, the polychromatophilic erythroblast, but ultimately it becomes pyknotic, and appears as a deeply staining, blue-black, homogeneous structureless mass. The nucleus is often eccentric and sometimes lobulated.", "xrefs" : [ "ISBN:0721601464" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "acidophilic erythroblast", @@ -1769,7 +1807,7 @@ "xrefs" : [ "GOC:dsd", "GOC:tfm", "ISBN:0721601464" ] }, "comments" : [ "Lineage negative is described here as CD2-negative, CD3-negative, CD4-negative, CD5-negative, CD8a-negative, CD14-negative, CD19-negative, CD20-negative, CD56-negative, Ly6g-negative, and Ter119-negative." ], - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "CFU-Meg", @@ -1829,7 +1867,7 @@ "xrefs" : [ "ISBN:0721601464", "MESH:D008533", "PMID:31043076", "http://en.wikipedia.org/wiki/Megakaryocyte" ] }, "comments" : [ "Megakaryocytes are reportedly CD181-positive and CD182-positive." ], - "subsets" : [ "http://purl.obolibrary.org/obo/cl#blood_and_immune_upper_slim", "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#blood_and_immune_upper_slim", "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "megacaryocyte" @@ -1861,7 +1899,7 @@ "val" : "An immature erythrocyte that changes the protein composition of its plasma membrane by exosome formation and extrusion. The types of protein removed differ between species though removal of the transferrin receptor is apparent in mammals and birds.", "xrefs" : [ "GOC:add", "GOC:tfm", "PMID:15946868", "PMID:2037622" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#blood_and_immune_upper_slim", "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#blood_and_immune_upper_slim", "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "BTO:0001173" }, { @@ -1881,7 +1919,7 @@ "val" : "Interneuron of the vertebrate retina. They integrate, modulate, and interpose a temporal domain in the visual message presented to the retinal ganglion cells, with which they synapse in the inner plexiform layer. They lack large axons.", "xrefs" : [ "GOC:tfm", "MESH:D025042", "WikipediaVersioned:Amacrine_cell&oldid=1023572246" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#eye_upper_slim", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#eye_upper_slim", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "amacrine neuron" @@ -1918,6 +1956,7 @@ "xrefs" : [ "GOC:dsd", "GOC:tfm", "PMID:12768659" ] }, "comments" : [ "These cells are reportedly CD31-positive, CD34-positive, CD144-positive, CD309-positive, and TAL1-positive." ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "angioblast" @@ -1938,7 +1977,7 @@ "val" : "One of the two photoreceptor cell types in the vertebrate retina. In cones the photopigment is in invaginations of the cell membrane of the outer segment. Cones are less sensitive to light than rods, but they provide vision with higher spatial and temporal acuity, and the combination of signals from cones with different pigments allows color vision.", "xrefs" : [ "MESH:D017949" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "synonyms" : [ { "pred" : "hasRelatedSynonym", "val" : "cone", @@ -1967,7 +2006,7 @@ "val" : "An epithelial cell of the cornea.", "xrefs" : [ "GOC:tfm" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#eye_upper_slim", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#eye_upper_slim", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "epithelial cell of cornea", @@ -1996,7 +2035,7 @@ "val" : "One of the two photoreceptor cell types of the vertebrate retina. In rods the photopigment is in stacks of membranous disks separate from the outer cell membrane. Rods are more sensitive to light than cones, but rod mediated vision has less spatial and temporal resolution than cone vision.", "xrefs" : [ "MESH:D017948" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "synonyms" : [ { "pred" : "hasRelatedSynonym", "val" : "rod", @@ -2025,7 +2064,7 @@ "val" : "Astrocyte-like radial glial cell that extends vertically throughout the retina, with the nucleus are usually in the middle of the inner nuclear layer.", "xrefs" : [ "GOC:NV", "PMID:21911394" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#eye_upper_slim", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#eye_upper_slim", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "synonyms" : [ { "synonymType" : "http://purl.obolibrary.org/obo/uberon/core#MISSPELLING", "pred" : "hasExactSynonym", @@ -2056,7 +2095,7 @@ "definition" : { "val" : "A neuron that is capable of some neurotansmission by glutamate secretion." }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "xrefs" : [ { "val" : "FBbt:00100291" }, { @@ -2078,7 +2117,7 @@ "val" : "A non-terminally differentiated cell that is capable of developing into a muscle cell.", "xrefs" : [ "GOC:add" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "ZFA:0009291" } ] @@ -2093,7 +2132,7 @@ "xrefs" : [ "GOC:dph" ] }, "comments" : [ "Unlike that of mammals, the brain of adult teleost fish exhibits an intense and widespread neurogenic activity as a result of the persistence of\nradial glial cells acting as neural progenitors throughout life." ], - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "pred" : "hasNarrowSynonym", "val" : "forebrain radial glial cell" @@ -2112,6 +2151,7 @@ "xrefs" : [ "GOC:tfm" ] }, "comments" : [ "The term \"neuroepithelial cell\" is used to describe both this cell type and sensory epithelial cell (CL:0000098)." ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "pred" : "hasBroadSynonym", "val" : "neuroepithelial cell" @@ -2131,6 +2171,7 @@ "val" : "A stem cell that can give rise to cell types of the body other than those of the germ-line.", "xrefs" : [ "GO:0048103" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "CALOHA:TS-2086" }, { @@ -2148,7 +2189,7 @@ "val" : "The set of neurons that receives neural inputs via bipolar, horizontal and amacrine cells. The axons of these cells make up the optic nerve.", "xrefs" : [ "GOC:dph" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#eye_upper_slim", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#eye_upper_slim", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "gangliocyte" @@ -2189,7 +2230,7 @@ "val" : "A neuron that laterally connects other neurons in the inner nuclear layer of the retina.", "xrefs" : [ "ISBN:0195088433" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#eye_upper_slim", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#eye_upper_slim", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "horizontal cell" @@ -2223,7 +2264,7 @@ "val" : "A bipolar neuron found in the retina and having connections with photoreceptors cells and neurons in the inner plexiform layer.", "xrefs" : [ "PMID:14689473" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#eye_upper_slim", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#eye_upper_slim", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "synonyms" : [ { "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003000", "pred" : "hasRelatedSynonym", @@ -2257,7 +2298,7 @@ "val" : "A cell of the monocyte, granulocyte, mast cell, megakaryocyte, or erythroid lineage.", "xrefs" : [ "GOC:add" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "BTO:0001441" }, { @@ -2278,7 +2319,7 @@ "xrefs" : [ "GOC:add", "GOC:tfm" ] }, "comments" : [ "Note that in FMA erythropoietic cells are types of nucleated erythrocytes and thus don't include erythrocytes." ], - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "erythropoietic cell" @@ -2306,7 +2347,7 @@ "val" : "A nucleated precursor of an erythrocyte that lacks hematopoietic lineage markers.", "xrefs" : [ "GOC:add", "ISBN:0721601464", "PMID:18174176" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#blood_and_immune_upper_slim", "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#blood_and_immune_upper_slim", "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "normoblast" @@ -2333,7 +2374,7 @@ "xrefs" : [ "GOC:add", "GOC:tfm", "PMID:19022770" ] }, "comments" : [ "Markers differ between mouse and human." ], - "subsets" : [ "http://purl.obolibrary.org/obo/cl#blood_and_immune_upper_slim", "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#blood_and_immune_upper_slim", "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "MPP" @@ -2363,7 +2404,7 @@ "xrefs" : [ "GOC:add", "GOC:tfm", "PMID:19022770" ] }, "comments" : [ "Note that this is a class of cell types, not an identified single cell type." ], - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "synonyms" : [ { "pred" : "hasBroadSynonym", "val" : "myeloid progenitor cell" @@ -2391,7 +2432,7 @@ "val" : "A cell of a hematopoietic lineage.", "xrefs" : [ "GOC:add", "GO_REF:0000031" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "haematopoietic cell" @@ -2423,7 +2464,7 @@ "val" : "A hematopoietic progenitor cell that is capable of developing into only one lineage of hematopoietic cells.", "xrefs" : [ "GOC:tfm", "PMID:19022770" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#blood_and_immune_upper_slim" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#blood_and_immune_upper_slim", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "basicPropertyValues" : [ { "pred" : "http://purl.org/dc/terms/contributor", "val" : "https://orcid.org/0000-0003-1980-3228" @@ -2442,7 +2483,7 @@ "xrefs" : [ "GOC:tfm", "PMID:19022770", "https://orcid.org/0000-0001-5208-3432" ] }, "comments" : [ "This cell type is intended to be compatible with any vertebrate hematopoietic oligopotent progenitor cell. For mammalian hematopoietic oligopotent progenitor cells known to be lineage-negative, please use the term 'hematopoietic oligopotent progenitor cell' (CL_0001060)." ], - "subsets" : [ "http://purl.obolibrary.org/obo/cl#blood_and_immune_upper_slim" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#blood_and_immune_upper_slim", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "basicPropertyValues" : [ { "pred" : "http://purl.org/dc/terms/contributor", "val" : "https://orcid.org/0000-0003-1980-3228" @@ -2460,6 +2501,7 @@ "val" : "An epithelial cell derived from ectoderm.", "xrefs" : [ "FMA:69074", "GOC:tfm" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "FMA:69074" }, { @@ -2482,6 +2524,7 @@ "val" : "Epithelial cell derived from mesoderm or mesenchyme.", "xrefs" : [ "FMA:69076", "GOC:tfm" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "epithelial mesenchymal cell" @@ -2509,7 +2552,7 @@ "xrefs" : [ "GOC:dsd", "GOC:tfm", "PMID:12768659" ] }, "comments" : [ "These cells are reportedly CD31-positive, CD34-positive, CD144-positive, TAL1-positive." ], - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "vascular endothelial cell" @@ -2523,10 +2566,15 @@ "val" : "CALOHA:TS-1106" }, { "val" : "FMA:67755" + }, { + "val" : "https://cellxgene.cziscience.com/cellguide/CL_0002139" } ], "basicPropertyValues" : [ { "pred" : "http://purl.org/dc/terms/contributor", "val" : "https://orcid.org/0000-0003-1980-3228" + }, { + "pred" : "http://purl.org/dc/terms/description", + "val" : "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nEndothelial cells of the vascular tree, commonly referred to as vascular endothelial cells, line the entire circulatory system, from the heart to the smallest capillaries. These cells have a unique, flattened shape, and are tightly bound together, forming a thin layer known as the endothelium. The endothelium is responsible for maintaining the interior surface of blood vessels, and plays a critical role in ensuring the smooth flow of blood. \nVascular endothelial cells act as a semi-permeable membrane, controlling the passage of materials and the transit of white blood cells into and out of the bloodstream. These cells are also involved in blood coagulation. When a blood vessel is damaged, endothelial cells promote clotting to prevent excessive bleeding and facilitate wound healing. Other functions include regulation of blood pressure and blood volume by releasing vasodilators and vasoconstrictors to either widen or constrict blood vessels, accordingly.\nFurthermore, the endothelial cells are crucial in the formation of new blood vessels, a process known as angiogenesis. This is particularly important in wound healing and the growth of new tissues during development or after injury. In the context of diseases such as cancer, angiogenesis helps facilitate tumor growth by providing nutrients and oxygen." }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2010-08-24T02:06:40Z" @@ -2541,6 +2589,7 @@ "val" : "Epithelial cells derived from general body ectoderm and ectoderm placodes.", "xrefs" : [ "GOC:tfm" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "FMA:70556" } ], @@ -2561,7 +2610,7 @@ "val" : "A cell comprising the transparent, biconvex body separating the posterior chamber and vitreous body, and constituting part of the refracting mechanism of the mammalian eye.", "xrefs" : [ "GOC:tfm", "ISBN:0721662544" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#eye_upper_slim" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#eye_upper_slim", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "FMA:70950" } ], @@ -2582,6 +2631,7 @@ "val" : "A cell containing at least one nucleus.", "xrefs" : [ "GOC:tfm" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "FMA:67513" } ], @@ -2603,7 +2653,7 @@ "xrefs" : [ "PMID:15106942" ] }, "comments" : [ "In a consensus model of unidirectional secretion, aqueous humour is formed by transferring solute, principally NaCl, from stroma to posterior chamber, with water passively following the osmotic gradient. Unidirectional secretion comprises three sequential steps. First, NaCl is transferred from the stromal interstitium into the pigmented ciliary epithelial (PE) cells. Second, solute passes from the PE into the non-pigmented ciliary epithelial (NPE) cells through gap junctions. Finally, NPE cells release Na+ and Cl− into the aqueous humour." ], - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#eye_upper_slim", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#eye_upper_slim", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "PE cell", @@ -2622,7 +2672,7 @@ "val" : "https://orcid.org/0000-0003-1980-3228" }, { "pred" : "http://purl.org/dc/terms/description", - "val" : "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional.\n\nPigmented ciliary epithelial cells, which are a type of pigment cell, have a crucial function within the eye's ciliary body. The ciliary body, located behind the iris, is one of the eye’s most vital structures and consists of two types of epithelial cells: the pigmented and the non-pigmented ciliary epithelial cells. The pigmented ciliary epithelial cells form the outer layer of the ciliary body and exhibit a black or brown pigmentation due to the melanin they contain.\nOne key function of pigmented ciliary epithelial cells is to aid in the formation of aqueous humor, an intraocular fluid that nourishes the cornea and lens, and maintains intraocular pressure which is essential for the eye’s shape and light refraction. These cells facilitate this function in conjunction with the non-pigmented ciliary epithelial cells. Together, the pigmented and non-pigmented ciliary epithelial cells form a bilayer epithelium that allows the secretion of aqueous humor through a bi-directional fluid transport mechanism.\nPigmented ciliary epithelial cells also contribute to the blood-aqueous barrier, a physiological frontier that controls the entry and exit of various substances from the blood to the aqueous humor and vice versa. The pigmentation in these cells, intensified by melanin, helps to absorb scattered light coming into the eye, reducing any potential damage and glare." + "val" : "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nPigmented ciliary epithelial cells, which are a type of pigment cell, have a crucial function within the eye's ciliary body. The ciliary body, located behind the iris, is one of the eye’s most vital structures and consists of two types of epithelial cells: the pigmented and the non-pigmented ciliary epithelial cells. The pigmented ciliary epithelial cells form the outer layer of the ciliary body and exhibit a black or brown pigmentation due to the melanin they contain.\nOne key function of pigmented ciliary epithelial cells is to aid in the formation of aqueous humor, an intraocular fluid that nourishes the cornea and lens, and maintains intraocular pressure which is essential for the eye’s shape and light refraction. These cells facilitate this function in conjunction with the non-pigmented ciliary epithelial cells. Together, the pigmented and non-pigmented ciliary epithelial cells form a bilayer epithelium that allows the secretion of aqueous humor through a bi-directional fluid transport mechanism.\nPigmented ciliary epithelial cells also contribute to the blood-aqueous barrier, a physiological frontier that controls the entry and exit of various substances from the blood to the aqueous humor and vice versa. The pigmentation in these cells, intensified by melanin, helps to absorb scattered light coming into the eye, reducing any potential damage and glare." }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2010-09-13T04:09:27Z" @@ -2638,7 +2688,7 @@ "xrefs" : [ "GOC:tfm", "PMID:15106942" ] }, "comments" : [ "In a consensus model of unidirectional secretion, aqueous humour is formed by transferring solute, principally NaCl, from stroma to posterior chamber, with water passively following the osmotic gradient. Unidirectional secretion comprises three sequential steps. First, NaCl is transferred from the stromal interstitium into the pigmented ciliary epithelial (PE) cells. Second, solute passes from the PE into the non-pigmented ciliary epithelial (NPE) cells through gap junctions. Finally, NPE cells release Na+ and Cl− into the aqueous humour." ], - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#eye_upper_slim", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#eye_upper_slim", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "NPE cell", @@ -2671,7 +2721,7 @@ "val" : "A cell that is part of the nervous system.", "xrefs" : [ "GOC:tfm", "ISBN:0618947256" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "CALOHA:TS-2040" }, { @@ -2694,7 +2744,7 @@ "val" : "A cell of the supporting or framework tissue of the body, arising chiefly from the embryonic mesoderm and including adipose tissue, cartilage, and bone.", "xrefs" : [ "GOC:tfm", "ISBN:0618947256" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "CALOHA:TS-2096" }, { @@ -2721,6 +2771,7 @@ "val" : "A cell of the embryo.", "xrefs" : [ "FMA:0618947256" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "CALOHA:TS-0263" }, { @@ -2729,10 +2780,15 @@ "val" : "WBbt:0007028" }, { "val" : "ZFA:0007089" + }, { + "val" : "https://cellxgene.cziscience.com/cellguide/CL_0002321" } ], "basicPropertyValues" : [ { "pred" : "http://purl.org/dc/terms/contributor", "val" : "https://orcid.org/0000-0003-1980-3228" + }, { + "pred" : "http://purl.org/dc/terms/description", + "val" : "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nEmbryonic cells in metazoans, which include all multicellular animals, are biological units in their earliest developmental stages from conception until the organism is fully formed. \nThey are derived from a fertilized egg, which undergoes a series of cell divisions to produce a multicellular organism. During the early phases of embryonic development, these cells exhibit pluripotency, meaning they possess the potential to differentiate into a diverse array of specialized cell types that constitute different body tissues and structures. \nThe balance between cell proliferation and differentiation in embryonic cells is crucial for successful development. When cells continue to divide without differentiating, overgrowth may occur leading to conditions such as teratomas (tumors of embryonic cells). Conversely, if cell differentiation proceeds at the expense of cell proliferation, developmental anomalies could occur regarding size or mass of the organism or its parts." }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2010-09-15T03:39:21Z" @@ -2747,7 +2803,7 @@ "val" : "A keratocyte is a specialized fibroblast residing in the cornea stroma that has a flattened, dendritic morphology; located between the lamellae with a large flattened nucleus, and lengthy processes which communicate with neighboring cells. This corneal layer, representing about 85-90% of corneal thickness, is built up from highly regular collagenous lamellae and extracellular matrix components. Keratocytes play the major role in keeping it transparent, healing its wounds, and synthesizing its components. This cell type secretes collagen I, V, VI, and keratan sulfate.", "xrefs" : [ "GOC:tfm", "ISBN:9780702029585" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#eye_upper_slim", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#eye_upper_slim", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "corneal fibroblast" @@ -2775,7 +2831,7 @@ "val" : "A melanocyte of the retina. This cell type is distinct from pigmented retinal epithelium.", "xrefs" : [ "GOC:tfm", "MP:0010190" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#eye_upper_slim" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#eye_upper_slim", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "basicPropertyValues" : [ { "pred" : "http://purl.org/dc/terms/contributor", "val" : "https://orcid.org/0000-0003-1980-3228" @@ -2794,6 +2850,7 @@ "xrefs" : [ "GOC:tfm" ] }, "comments" : [ "From Onard of the FMA: Cardiac muscle cell or cardiac myocyte is a striated muscle cell. Cardiocyte on the other hand is any cell in the heart which includes cells other than muscle cells (e.g. endothelial cell of endocardium). Unless there is a consensus among anatomists that cardiocytes refer only to muscle cells, we will treat them as a general class of cells in the heart." ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "heart cell" @@ -2824,7 +2881,7 @@ "val" : "A pigment cell located in the epithelium of the iris.", "xrefs" : [ "GOC:tfm" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#eye_upper_slim", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#eye_upper_slim", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" @@ -2845,7 +2902,7 @@ "val" : "A blood vessel endothelial cell that is part of the retina.", "xrefs" : [ "GOC:tfm" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#eye_upper_slim", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#eye_upper_slim", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "xrefs" : [ { "val" : "https://cellxgene.cziscience.com/cellguide/CL_0002585" } ], @@ -2857,7 +2914,7 @@ "val" : "https://orcid.org/0000-0003-1980-3228" }, { "pred" : "http://purl.org/dc/terms/description", - "val" : "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional.\n\nRetinal blood vessel endothelial cells constitute the innermost lining of the blood vessels found in the retina, the light-sensitive layer of tissue at the back of the eye. The primary role of these cells revolves around their location within the retinal vascular system, forming the structure of the blood-retinal barrier, a subset of the larger blood-ocular barrier system. \nThe endothelial cells are particularly involved in the growth of new retinal blood vessels from pre-existing ones (angiogenesis); this is critical in managing the amount of oxygen and essential nutrients delivered to the ocular tissues. They are crucial for maintaining homeostasis in the retinal environment by controlling the exchange of molecules between the blood and the retina. Furthermore, they mediate immune cell trafficking, supporting the immune privilege of the eye by preventing the unrestricted infiltration of inflammatory cells into the retina, thus maintaining ocular health and normal vision.\nThe malfunction or dysfunction of retinal blood vessel endothelial cells is implicated in numerous ocular pathologies, particularly diabetic retinopathy, which is one of the leading causes of blindness worldwide. In such conditions, the compromise in the integrity of the blood-retinal barrier and excess angiogenesis can lead to retinal edema and pathological neovascularization, resulting in vision loss." + "val" : "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nRetinal blood vessel endothelial cells constitute the innermost lining of the blood vessels found in the retina, the light-sensitive layer of tissue at the back of the eye. The primary role of these cells revolves around their location within the retinal vascular system, forming the structure of the blood-retinal barrier, a subset of the larger blood-ocular barrier system. \nThe endothelial cells are particularly involved in the growth of new retinal blood vessels from pre-existing ones (angiogenesis); this is critical in managing the amount of oxygen and essential nutrients delivered to the ocular tissues. They are crucial for maintaining homeostasis in the retinal environment by controlling the exchange of molecules between the blood and the retina. Furthermore, they mediate immune cell trafficking, supporting the immune privilege of the eye by preventing the unrestricted infiltration of inflammatory cells into the retina, thus maintaining ocular health and normal vision.\nThe malfunction or dysfunction of retinal blood vessel endothelial cells is implicated in numerous ocular pathologies, particularly diabetic retinopathy, which is one of the leading causes of blindness worldwide. In such conditions, the compromise in the integrity of the blood-retinal barrier and excess angiogenesis can lead to retinal edema and pathological neovascularization, resulting in vision loss." }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2011-03-06T03:28:27Z" @@ -2872,7 +2929,7 @@ "val" : "An epithelial cell of the retinal pigmented epithelium.", "xrefs" : [ "GOC:tfm" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#eye_upper_slim", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#eye_upper_slim", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "xrefs" : [ { "val" : "BTO:0004910" }, { @@ -2888,7 +2945,7 @@ "val" : "https://orcid.org/0000-0003-1980-3228" }, { "pred" : "http://purl.org/dc/terms/description", - "val" : "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional.\n\nRetinal pigment epithelial (RPE) cells form a single layer of cells at the back of the eye sandwiched between the neurosensory retina and the choroid, playing a significant role in maintaining vision health. These pigment-laden cells are highly specialized and perform an array of metabolic and transport functions essential for the maintenance of the photoreceptor cells (rods and cones) in the retina. The pigmentation of RPE cells actively aids in the absorption of excess light and the prevention of light scattering, thus enhancing the eye's optical properties.\nThe retinal pigment epithelium forms a key part of the blood/retina barrier. The cells have long sheet-like microvilli on their apical membrane that project into the light-sensitive outer segments of the photoreceptors, forming a close structural interaction. The basolateral membrane of the RPE interacts with the underlying Bruch’s membrane, which separates the RPE cells from fenestrated endothelium of the choriocapillaris. \nRPE cells support the photoreceptor by providing them with oxygen and nutrients (such as glucose, retinol and fatty acids) and removing waste products. They also recycle the visual pigment, in a process called the \"visual cycle\", where the RPE cells play a vital role in the regeneration of visual pigment (11-cis retinol) following the absorption of light. This is essential for the maintenance of photoreceptor excitability.\nBeyond this, RPE cells take part in the phagocytosis process, where they digest the shed ends of photoreceptor outer segments, thus, preventing the build-up of waste residue that could otherwise harm retinal health. They also secrete various factors, including growth factors required to maintain the structural integrity of choriocapillaris endothelium and photoreceptors, as well as immunosuppressive factors that play an important role in establishing the immune privilege of the eye." + "val" : "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nRetinal pigment epithelial (RPE) cells form a single layer of cells at the back of the eye sandwiched between the neurosensory retina and the choroid, playing a significant role in maintaining vision health. These pigment-laden cells are highly specialized and perform an array of metabolic and transport functions essential for the maintenance of the photoreceptor cells (rods and cones) in the retina. The pigmentation of RPE cells actively aids in the absorption of excess light and the prevention of light scattering, thus enhancing the eye's optical properties.\nThe retinal pigment epithelium forms a key part of the blood/retina barrier. The cells have long sheet-like microvilli on their apical membrane that project into the light-sensitive outer segments of the photoreceptors, forming a close structural interaction. The basolateral membrane of the RPE interacts with the underlying Bruch’s membrane, which separates the RPE cells from fenestrated endothelium of the choriocapillaris. \nRPE cells support the photoreceptor by providing them with oxygen and nutrients (such as glucose, retinol and fatty acids) and removing waste products. They also recycle the visual pigment, in a process called the \"visual cycle\", where the RPE cells play a vital role in the regeneration of visual pigment (11-cis retinol) following the absorption of light. This is essential for the maintenance of photoreceptor excitability.\nBeyond this, RPE cells take part in the phagocytosis process, where they digest the shed ends of photoreceptor outer segments, thus, preventing the build-up of waste residue that could otherwise harm retinal health. They also secrete various factors, including growth factors required to maintain the structural integrity of choriocapillaris endothelium and photoreceptors, as well as immunosuppressive factors that play an important role in establishing the immune privilege of the eye." }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2011-03-06T03:37:09Z" @@ -2903,6 +2960,7 @@ "val" : "A multi-fate stem cell that can give rise to different retinal cell types including rod and cone cells.", "xrefs" : [ "GOC:tfm", "PMID:20959166", "PMID:21148186" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "basicPropertyValues" : [ { "pred" : "http://purl.org/dc/terms/contributor", "val" : "https://orcid.org/0000-0003-1980-3228" @@ -2921,6 +2979,7 @@ "xrefs" : [ "CL:CVS" ] }, "comments" : [ "Is_a interneuron, part_of UBERON:0002240." ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "ZFA:0000778" } ] @@ -2934,6 +2993,7 @@ "val" : "Cell that is part of the neural crest region of the neuroepithelium, prior to migration. Note that not all premigratory neural crest cells may become migratory neural crest cells.", "xrefs" : [ "UBERONREF:0000002" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "ZFA:0007084" } ], @@ -2953,7 +3013,8 @@ "definition" : { "val" : "Any muscle cell in which the fibers are not organised into sarcomeres.", "xrefs" : [ "GOC:DOS" ] - } + }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ] } }, { "id" : "http://purl.obolibrary.org/obo/CL_0008001", @@ -2964,7 +3025,7 @@ "val" : "Any hematopoietic cell that is a precursor of some other hematopoietic cell type.", "xrefs" : [ "GOC:dos" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ] + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ] } }, { "id" : "http://purl.obolibrary.org/obo/CL_0008007", @@ -2975,6 +3036,7 @@ "val" : "A muscle cell that is part of some visceral muscle.", "xrefs" : [ "GOC:dos" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "FBbt:00005070" } ] @@ -2987,7 +3049,7 @@ "definition" : { "val" : "A non-polarised cell precursor cell that is part of some mesenchyme, is associated with the cell matrix but is not connected to other cells and is capable of migration." }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "mesenchyme cell" @@ -3006,6 +3068,7 @@ "val" : "Any neuron that is capable of part of some visual perception.", "xrefs" : [ "FBC:Autogenerated" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "basicPropertyValues" : [ { "pred" : "http://purl.org/dc/terms/contributor", "val" : "https://orcid.org/0000-0002-7073-9172" @@ -3023,7 +3086,7 @@ "val" : "Any cell in the retina, the innermost layer or coating at the back of the eyeball, which is sensitive to light and in which the optic nerve terminates.", "xrefs" : [ "GOC:pr" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#general_cell_types_upper_slim" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#general_cell_types_upper_slim", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "PMID:10702418" } ] @@ -3037,6 +3100,7 @@ "val" : "Any photoreceptor cell that is part of some camera-type eye.", "xrefs" : [ "FBC:Autogenerated" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "camera type eye photoreceptor cell" @@ -3050,6 +3114,7 @@ "definition" : { "val" : "A zygote in a plant or an animal." }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "MESH:D015053" } ], @@ -3067,13 +3132,13 @@ "val" : "A cell of the neural crest. Neural crest cells are multipotent. Premigratory neural crest cells are found at the neural plate boarder, some of which will undergo ectomesynchymal transition and delamination to form migratory neural crest cells.", "xrefs" : [ "https://orcid.org/0000-0001-5208-3432", "https://orcid.org/0000-0002-9900-7880" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "https://cellxgene.cziscience.com/cellguide/CL_0011012" } ], "basicPropertyValues" : [ { "pred" : "http://purl.org/dc/terms/description", - "val" : "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional.\n\nNeural crest cells are a group of transient and highly migratory cells that originate from the neuroectoderm during the early stages of embryonic development. They are multipotent cells with an exceptional degree of plasticity, capable of differentiating into various somatic cell types and therefore play a fundamental role in the formation of various organs and tissues, making them critical contributors to the developing embryo. \nAfter the initiation of neurulation (the formation of the neural tube) neural crest cells start to undergo epithelial-to-mesenchymal transition and delaminate and migrate from the dorsal neural tube to several regions throughout the embryo. They differentiate into a range of diverse cell types, such as neurons and glial cells of the peripheral nervous system, including sensory and autonomic neurons. They also contribute to the formation of adrenal glands, pigment cells in the skin (melanocytes), cardiac structures, including parts of the heart septum and major arteries, as well as bones and cartilage of the face and skull.\nDisorders or aberrations in the development or migration of the neural crest cells can lead to serious congenital malformations, such as neurocristopathies, including Hirschsprung disease, neuroblastoma, and neurofibromatosis." + "val" : "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nNeural crest cells are a group of transient and highly migratory cells that originate from the neuroectoderm during the early stages of embryonic development. They are multipotent cells with an exceptional degree of plasticity, capable of differentiating into various somatic cell types and therefore play a fundamental role in the formation of various organs and tissues, making them critical contributors to the developing embryo. \nAfter the initiation of neurulation (the formation of the neural tube) neural crest cells start to undergo epithelial-to-mesenchymal transition and delaminate and migrate from the dorsal neural tube to several regions throughout the embryo. They differentiate into a range of diverse cell types, such as neurons and glial cells of the peripheral nervous system, including sensory and autonomic neurons. They also contribute to the formation of adrenal glands, pigment cells in the skin (melanocytes), cardiac structures, including parts of the heart septum and major arteries, as well as bones and cartilage of the face and skull.\nDisorders or aberrations in the development or migration of the neural crest cells can lead to serious congenital malformations, such as neurocristopathies, including Hirschsprung disease, neuroblastoma, and neurofibromatosis." } ] } }, { @@ -3085,7 +3150,7 @@ "val" : "A precursor cell that has a tendency to differentiate into a specific type of cell. They are descendants of stem cells, only they are more constrained in their differentiation potential or capacity for self-renewal, and are often more limited in both senses.", "xrefs" : [ "ISBN:978-1-62808-994-3", "https://doi.org/10.1016/B978-0-12-409503-8.00002-0" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "basicPropertyValues" : [ { "pred" : "http://purl.org/dc/terms/contributor", "val" : "https://orcid.org/0000-0001-5208-3432" @@ -3101,7 +3166,7 @@ "xrefs" : [ "GOC:NV", "PMID:12771169" ] }, "comments" : [ "Need to MIREOT retinal inner nuclear layer (part of)" ], - "subsets" : [ "http://purl.obolibrary.org/obo/cl#eye_upper_slim" ] + "subsets" : [ "http://purl.obolibrary.org/obo/cl#eye_upper_slim", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ] } }, { "id" : "http://purl.obolibrary.org/obo/CL_0011115", @@ -3113,7 +3178,7 @@ "xrefs" : [ "GOC:dos" ] }, "comments" : [ "Work is needed on GO 'cell differentiation' before it is clear whether the equivalent class definition 'native cell' that capable_of some 'cell differentiation' works. Also, may want to consider merging this with non-terminally differentiated cell." ], - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ] + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ] } }, { "id" : "http://purl.obolibrary.org/obo/CL_0017502", @@ -3179,7 +3244,7 @@ "val" : "An epithelial cell that is part of the conjunctiva.", "xrefs" : [ "GOC:tfm" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#eye_upper_slim" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#eye_upper_slim", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "epithelial cell of conjunctiva", @@ -3198,7 +3263,7 @@ "val" : "A smooth muscle cell that is part of the ciliary body.", "xrefs" : [ "GOC:tfm" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#eye_upper_slim" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#eye_upper_slim", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "smooth muscle cell of ciliary body", @@ -3206,6 +3271,12 @@ } ], "xrefs" : [ { "val" : "FMA:70610" + }, { + "val" : "https://cellxgene.cziscience.com/cellguide/CL_1000443" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/description", + "val" : "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nCiliary muscle cells are specialized contractile cells that constitute the ciliary muscle, a component of the eye in vertebrates. These cells form a ring around the iris, the eye's colored part. Ciliary muscle cells fall into the category of smooth muscle cells, characterized by their lack of the striations typical of skeletal and cardiac muscle cells. Their shape is elongated and pointed at both ends, and they occur in multi-nucleated syncytia where many cells share the same cytoplasm.\nCiliary muscle cells primarily control the eye's accommodation, adjusting the thickness and curvature of the lens to fine-tune the focus of light on the retina. When ciliary muscle cells contract, tension on the zonular fibers holding the lens in place is reduced, allowing the lens to become thicker and increase its refractive power. Conversely, when the ciliary muscle cells relax, the tension on the zonular fibers increases, causing the lens to become flatter and decrease its refractive power. This adjustment facilitates clear vision at different distances, ranging from near to far objects.\nAdditionally, ciliary muscle cells play a role in draining the eye's aqueous humor, which is the clear fluid that fills the anterior chamber of the eye between the cornea and the lens. By controlling the shape of the surrounding trabecular meshwork through muscle contractions and relaxations, ciliary muscle cells indirectly regulate intraocular pressure, a factor critical for preventing ocular conditions like glaucoma." } ] } }, { @@ -3217,6 +3288,7 @@ "val" : "Any neuron that is part of a central nervous system.", "xrefs" : [ "GOC:TermGenie" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "basicPropertyValues" : [ { "pred" : "http://purl.org/dc/terms/contributor", "val" : "http://www.wikidata.org/entity/Q35563349" @@ -3234,7 +3306,7 @@ "val" : "A retinal cell that is immature or undifferentiated.", "xrefs" : [ "PMID:17565741" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#eye_upper_slim" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#eye_upper_slim", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "retinal stem cell", @@ -3258,7 +3330,7 @@ "xrefs" : [ "PMID:25236977", "PMID:33796062" ] }, "comments" : [ "In response to elevated intraocular pressure, a retinal astrocyte may modulate extracellular matrix remodeling. In the human retina, a retinal astrocyte is GFAP-positive, SOD3-positive and GYPC-positive." ], - "subsets" : [ "http://purl.obolibrary.org/obo/cl#eye_upper_slim" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#eye_upper_slim", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003004", "pred" : "hasRelatedSynonym", @@ -3292,9 +3364,6 @@ "val" : "Wikipedia:Mitosis" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0007067" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" } ] @@ -3344,15 +3413,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/geneontology/go-ontology/issues/28301" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0000789" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0000790" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0005717" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "cellular_component" @@ -3385,12 +3445,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/geneontology/go-ontology/issues/22355" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0005720" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0035328" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "cellular_component" @@ -3547,9 +3601,6 @@ "val" : "Wikipedia:Neurulation" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0001679" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" } ] @@ -3758,9 +3809,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/geneontology/go-ontology/issues/17729" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0008372" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "cellular_component" @@ -3874,12 +3922,6 @@ "val" : "Wikipedia:Basement_membrane" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0005605" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0008003" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "cellular_component" } ] @@ -4072,9 +4114,6 @@ "val" : "Wikipedia:Ribosome" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0033279" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "cellular_component" } ] @@ -4128,12 +4167,6 @@ "val" : "Wikipedia:Cell_membrane" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0005887" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0005904" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "cellular_component" } ] @@ -4202,15 +4235,6 @@ "val" : "Wikipedia:Translation_(genetics)" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0006416" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0006453" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0043037" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" } ] @@ -4239,12 +4263,6 @@ "val" : "translation initiation" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0006440" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0006454" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" } ] @@ -4267,12 +4285,6 @@ "val" : "translation elongation" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0006442" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0006455" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" } ] @@ -4297,12 +4309,6 @@ "val" : "translational complex disassembly" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0006443" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0006456" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" } ] @@ -4325,21 +4331,9 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/geneontology/go-ontology/issues/20292" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "jl" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2012-12-13T16:25:32Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0015457" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0015460" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0044765" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" @@ -4394,9 +4388,6 @@ }, "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_pir", "http://purl.obolibrary.org/obo/go#goslim_yeast" ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0006866" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" } ] @@ -4470,12 +4461,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002161", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_4896" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0006917" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0008632" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" @@ -4552,15 +4537,9 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/geneontology/go-ontology/issues/27189" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "jl" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2013-12-19T15:25:51Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:1902589" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" @@ -4656,21 +4635,6 @@ "val" : "Wikipedia:Signal_transduction" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0023014" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0023015" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0023016" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0023033" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0023045" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" } ] @@ -4769,9 +4733,6 @@ "val" : "neurotransmitter secretory pathway" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0010554" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" } ] @@ -4975,9 +4936,6 @@ "val" : "hemolymph circulation" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0070261" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" } ] @@ -5030,21 +4988,9 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/geneontology/go-ontology/issues/24968" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "jl" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2012-09-19T15:05:24Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0000004" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0007582" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0044699" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" @@ -5056,7 +5002,7 @@ "type" : "CLASS", "meta" : { "definition" : { - "val" : "The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.", + "val" : "A cellular process consisting of the biochemical pathways by which a living organism transforms chemical substances. This includes including anabolism (biosynthetic process) and catabolism (catabolic process). Metabolic processes includes the transformation of small molecules, as well macromolecular processes such as DNA repair and replication, protein synthesis and degradation.", "xrefs" : [ "GOC:go_curators", "ISBN:0198547684" ] }, "comments" : [ "Note that metabolic processes do not include single functions or processes such as protein-protein interactions, protein-nucleic acids, nor receptor-ligand interactions." ], @@ -5064,18 +5010,6 @@ "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "metabolism" - }, { - "pred" : "hasNarrowSynonym", - "val" : "metabolic process resulting in cell growth" - }, { - "pred" : "hasNarrowSynonym", - "val" : "metabolism resulting in cell growth" - }, { - "pred" : "hasNarrowSynonym", - "val" : "multicellular organism metabolic process" - }, { - "pred" : "hasRelatedSynonym", - "val" : "single-organism metabolic process" } ], "xrefs" : [ { "val" : "Wikipedia:Metabolism" @@ -5084,17 +5018,11 @@ "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/geneontology/go-ontology/issues/26424" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "jl" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/geneontology/go-ontology/issues/28932" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2012-10-17T15:46:40Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0044236" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0044710" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" @@ -5132,7 +5060,7 @@ "type" : "CLASS", "meta" : { "definition" : { - "val" : "The chemical reactions and pathways resulting in the formation of substances; typically the energy-requiring part of metabolism in which simpler substances are transformed into more complex ones.", + "val" : "A cellular process consisting of the biochemical pathways by which a living organism synthesizes chemical substances. This typically represents the energy-requiring part of metabolism in which simpler substances are transformed into more complex ones.", "xrefs" : [ "GOC:curators", "ISBN:0198547684" ] }, "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_chembl", "http://purl.obolibrary.org/obo/go#goslim_metagenomics", "http://purl.obolibrary.org/obo/go#goslim_plant", "http://purl.obolibrary.org/obo/go#goslim_plant_ribbon" ], @@ -5159,17 +5087,11 @@ "val" : "Wikipedia:Anabolism" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "jl" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/geneontology/go-ontology/issues/28932" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2012-10-17T15:52:18Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0044274" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0044711" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" @@ -5212,9 +5134,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/geneontology/go-ontology/issues/27189" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0043284" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" @@ -5426,9 +5345,6 @@ "val" : "Wikipedia:Embryogenesis" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0009795" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" } ] @@ -5530,20 +5446,8 @@ "val" : "single-organism cellular process" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "jl" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2012-12-11T16:56:55Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0008151" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0044763" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0050875" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" @@ -5612,9 +5516,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/geneontology/go-ontology/issues/24835" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0016244" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" @@ -5715,15 +5616,6 @@ "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2014-03-06T11:37:54Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0016021" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0098589" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0098805" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "cellular_component" @@ -5762,12 +5654,6 @@ "xrefs" : [ "GOC:mah" ] } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0044235" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0071842" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" } ] @@ -5920,15 +5806,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/geneontology/go-ontology/issues/27189" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0006411" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0044267" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0044268" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" @@ -5984,9 +5861,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/geneontology/go-ontology/issues/27189" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0071845" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" @@ -6025,9 +5899,6 @@ "val" : "cellular component assembly at cellular level" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0071844" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" } ] @@ -6109,17 +5980,8 @@ "val" : "single organism signaling" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "jl" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2010-02-16T09:30:50Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0023046" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0044700" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" @@ -6362,9 +6224,6 @@ "xrefs" : [ "GOC:bf" ] } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0000068" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" } ] @@ -6485,9 +6344,6 @@ "val" : "Wikipedia:Extracellular_matrix" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0005578" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "cellular_component" } ] @@ -6516,9 +6372,6 @@ "val" : "NIF_Subcellular:sao180601769" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0016023" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "cellular_component" } ] @@ -6574,9 +6427,6 @@ "val" : "Wikipedia:Vesicle_(biology)" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0031988" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "cellular_component" } ] @@ -6671,18 +6521,9 @@ }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002161", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_4932" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "jl" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2012-09-19T16:07:47Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0044707" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0050874" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" @@ -6706,14 +6547,8 @@ "val" : "single-organism developmental process" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "jl" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2012-12-19T12:21:31Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0044767" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" @@ -6765,15 +6600,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/geneontology/go-ontology/issues/22580" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0034623" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0043241" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0043624" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" @@ -6807,9 +6633,6 @@ "val" : "protein-protein complex" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0043234" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "cellular_component" } ] @@ -6862,9 +6685,6 @@ "val" : "ATP hydrolysis coupled ion transmembrane transport" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0099131" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" } ] @@ -6948,9 +6768,6 @@ "xrefs" : [ "GOC:PARL", "GOC:pad" ] }, "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "bf" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2014-07-24T10:06:19Z" }, { @@ -7057,15 +6874,6 @@ "val" : "regulation of homeostatic process" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0032844" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0032845" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0032846" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" } ] @@ -7203,15 +7011,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/geneontology/go-ontology/issues/26424" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0034960" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0043283" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0044259" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" @@ -7297,7 +7096,7 @@ } }, { "id" : "http://purl.obolibrary.org/obo/GO_0043228", - "lbl" : "non-membrane-bounded organelle", + "lbl" : "membraneless organelle", "type" : "CLASS", "meta" : { "definition" : { @@ -7306,6 +7105,12 @@ }, "subsets" : [ "http://purl.obolibrary.org/obo/go#gocheck_do_not_annotate", "http://purl.obolibrary.org/obo/go#goslim_mouse" ], "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "membrane-less organelle" + }, { + "pred" : "hasExactSynonym", + "val" : "non-membrane-bounded organelle" + }, { "pred" : "hasExactSynonym", "val" : "non-membrane-enclosed organelle" }, { @@ -7321,6 +7126,9 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/geneontology/go-ontology/issues/28153" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/geneontology/go-ontology/issues/29106" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "cellular_component" @@ -7380,7 +7188,7 @@ } }, { "id" : "http://purl.obolibrary.org/obo/GO_0043232", - "lbl" : "intracellular non-membrane-bounded organelle", + "lbl" : "intracellular membraneless organelle", "type" : "CLASS", "meta" : { "definition" : { @@ -7389,10 +7197,16 @@ }, "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_pir" ], "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "intracellular non-membrane-bounded organelle" + }, { "pred" : "hasExactSynonym", "val" : "intracellular non-membrane-enclosed organelle" } ], "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/geneontology/go-ontology/issues/29106" + }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "cellular_component" } ] @@ -7467,21 +7281,9 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/geneontology/go-ontology/issues/22580" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "mah" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2010-09-08T10:01:42Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0034600" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0034621" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0071822" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" @@ -7532,9 +7334,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/geneontology/go-ontology/issues/27194" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0071843" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" @@ -7557,9 +7356,6 @@ "val" : "Met-tRNA/eIF2.GTP ternary complex" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "jl" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2009-10-22T02:38:55Z" }, { @@ -7567,30 +7363,6 @@ "val" : "cellular_component" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/GO_0044237", - "lbl" : "cellular metabolic process", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "The chemical reactions and pathways by which individual cells transform chemical substances.", - "xrefs" : [ "GOC:go_curators" ] - }, - "comments" : [ "This term should not be used for direct annotation. It should be possible to make a more specific annotation to one of the children of this term." ], - "subsets" : [ "http://purl.obolibrary.org/obo/go#gocheck_do_not_annotate" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "cellular metabolism" - }, { - "pred" : "hasRelatedSynonym", - "val" : "intermediary metabolism", - "xrefs" : [ "GOC:mah" ] - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "biological_process" - } ] - } }, { "id" : "http://purl.obolibrary.org/obo/GO_0044238", "lbl" : "primary metabolic process", @@ -7616,38 +7388,6 @@ "val" : "biological_process" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/GO_0044249", - "lbl" : "cellular biosynthetic process", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "The chemical reactions and pathways resulting in the formation of substances, carried out by individual cells.", - "xrefs" : [ "GOC:jl" ] - }, - "comments" : [ "This term should not be used for direct annotation. It should be possible to make a more specific annotation to one of the children of this term." ], - "subsets" : [ "http://purl.obolibrary.org/obo/go#gocheck_do_not_annotate" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "cellular anabolism" - }, { - "pred" : "hasExactSynonym", - "val" : "cellular biosynthesis" - }, { - "pred" : "hasExactSynonym", - "val" : "cellular formation" - }, { - "pred" : "hasExactSynonym", - "val" : "cellular synthesis" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", - "val" : "https://github.com/geneontology/go-ontology/issues/27052" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "biological_process" - } ] - } }, { "id" : "http://purl.obolibrary.org/obo/GO_0044297", "lbl" : "cell body", @@ -7672,9 +7412,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0002161", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_4890" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "jl" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2010-02-05T10:37:16Z" @@ -7842,9 +7579,6 @@ "xrefs" : [ "GOC:dph", "GOC:tb" ] } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0048828" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" } ] @@ -8053,9 +7787,6 @@ "val" : "regulation of physiological process" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0050791" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" } ] @@ -8075,9 +7806,6 @@ "val" : "regulation of cellular physiological process" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0051244" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" } ] @@ -8126,9 +7854,6 @@ "val" : "physiological response to stimulus" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0051869" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" } ] @@ -8286,15 +8011,9 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/geneontology/go-ontology/issues/27052" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "jl" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2013-12-18T13:51:04Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:1902578" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" @@ -8373,15 +8092,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/geneontology/go-ontology/issues/4585" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0006323" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0007001" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0051277" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" @@ -8469,15 +8179,9 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/geneontology/go-ontology/issues/27189" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "jl" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2013-12-18T14:04:32Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:1902580" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" @@ -8569,14 +8273,8 @@ "val" : "ATP hydrolysis coupled transmembrane transport" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "tb" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2015-10-21T13:22:47Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0090662" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" @@ -8706,9 +8404,6 @@ "xrefs" : [ "GOC:dph" ] }, "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dph" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2009-04-28T09:33:36Z" }, { @@ -8726,9 +8421,6 @@ "xrefs" : [ "GOC:dph" ] }, "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dph" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2010-05-25T09:05:34Z" }, { @@ -8746,9 +8438,6 @@ "xrefs" : [ "GOC:dph" ] }, "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dph" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2013-06-21T16:14:47Z" }, { @@ -8766,9 +8455,6 @@ "xrefs" : [ "GOC:BHF", "GOC:rph", "PMID:21123617" ] }, "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dph" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2018-04-13T12:47:21Z" }, { @@ -8814,15 +8500,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/geneontology/go-ontology/issues/22580" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0006461" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0034622" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0043623" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" @@ -8932,9 +8609,6 @@ }, "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_yeast" ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "mah" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2009-09-15T03:00:51Z" }, { @@ -8970,9 +8644,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/geneontology/go-ontology/issues/25143" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "mah" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2010-09-08T10:10:35Z" @@ -9007,15 +8678,9 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/geneontology/go-ontology/issues/27189" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "mah" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2010-09-10T01:39:16Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0071841" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" @@ -9032,9 +8697,6 @@ }, "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_flybase_ribbon" ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "mah" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2010-10-04T01:51:47Z" }, { @@ -9061,9 +8723,6 @@ "xrefs" : [ "GOC:BHF" ] } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "mah" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2010-10-11T11:44:57Z" }, { @@ -9086,9 +8745,6 @@ "xrefs" : [ "GOC:vesicles" ] } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "mah" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2010-10-18T03:44:18Z" }, { @@ -9108,9 +8764,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/geneontology/go-ontology/issues/22302" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "mah" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2010-02-26T02:15:40Z" @@ -9138,14 +8791,8 @@ "val" : "induction of apoptosis by extracellular signals" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pr" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2011-11-23T09:30:23Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0008624" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" @@ -9168,9 +8815,6 @@ "val" : "apoptosis" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pr" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2011-11-23T09:45:24Z" }, { @@ -9191,9 +8835,6 @@ "val" : "NIF_Subcellular:sao172297168" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pr" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2012-12-17T12:31:49Z" }, { @@ -9211,9 +8852,6 @@ "xrefs" : [ "GOC:vesicles" ] }, "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pr" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2016-03-29T17:39:45Z" }, { @@ -9247,9 +8885,6 @@ "val" : "intraluminal vesicle assembly" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pr" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2016-10-03T14:35:25Z" }, { @@ -9273,9 +8908,6 @@ "val" : "region of plasma membrane" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dos" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2014-03-06T11:55:32Z" }, { @@ -9452,9 +9084,6 @@ "val" : "fibril" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0043205" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "cellular_component" } ] @@ -9526,14 +9155,18 @@ } }, { "id" : "http://purl.obolibrary.org/obo/GO_0110165", - "lbl" : "cellular anatomical entity", + "lbl" : "cellular anatomical structure", "type" : "CLASS", "meta" : { "definition" : { - "val" : "A part of a cellular organism that is either an immaterial entity or a material entity with granularity above the level of a protein complex but below that of an anatomical system. Or, a substance produced by a cellular organism with granularity above the level of a protein complex.", + "val" : "A part of a cellular organism consisting of a material entity with granularity above the level of a protein complex but below that of an anatomical system. Note that cellular organisms exclude viruses.", "xrefs" : [ "GOC:kmv" ] }, "subsets" : [ "http://purl.obolibrary.org/obo/go#gocheck_do_not_annotate", "http://purl.obolibrary.org/obo/go#goslim_pir" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "cellular anatomical entity" + } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/geneontology/go-ontology/issues/24200" @@ -9541,8 +9174,8 @@ "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/geneontology/go-ontology/issues/26424" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "kmv" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/geneontology/go-ontology/issues/28978" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2019-08-12T18:01:37Z" @@ -9563,9 +9196,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/geneontology/go-ontology/issues/13193" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "krc" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-03-21T17:26:07Z" @@ -9591,9 +9221,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/geneontology/go-ontology/issues/13298" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "krc" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-04-24T23:56:08Z" @@ -9614,9 +9241,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/geneontology/go-ontology/issues/13298" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "krc" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-04-26T16:07:02Z" @@ -9642,9 +9266,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/geneontology/go-ontology/issues/19910" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pg" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-03-23T14:44:23Z" @@ -9669,9 +9290,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/geneontology/go-ontology/issues/14256" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pg" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-10-23T11:53:42Z" @@ -9694,9 +9312,6 @@ "val" : "efflux" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pg" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2019-05-22T11:20:45Z" }, { @@ -9715,9 +9330,6 @@ }, "subsets" : [ "http://purl.obolibrary.org/obo/go#gocheck_do_not_annotate" ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "jl" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2014-05-22T14:22:34Z" }, { @@ -9740,9 +9352,6 @@ "xrefs" : [ "GOC:TermGenie" ] } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "mr" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2014-10-06T18:38:56Z" }, { @@ -9765,9 +9374,6 @@ "xrefs" : [ "GOC:vesicles" ] } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "jl" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2014-10-22T14:26:11Z" }, { @@ -9805,17 +9411,8 @@ "val" : "Wikipedia:Ribonucleoprotein" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pr" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2015-11-19T12:26:37Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0030529" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:1990903" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "cellular_component" @@ -9902,9 +9499,6 @@ "val" : "GC_ID:1" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "NCBITaxon:85055" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "ncbi_taxonomy" } ] @@ -9936,9 +9530,6 @@ "val" : "GC_ID:1" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "NCBITaxon:40673" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "ncbi_taxonomy" } ] @@ -10272,9 +9863,6 @@ "val" : "GC_ID:1" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "NCBITaxon:109679" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "ncbi_taxonomy" } ] @@ -10499,9 +10087,6 @@ "xrefs" : [ "PATOC:GVG" ] }, "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "PATO:0000072" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "quality" } ] @@ -10537,9 +10122,6 @@ "val" : "relational shape quality" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "PATO:0001647" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "quality" } ] @@ -10578,9 +10160,6 @@ "val" : "relational structural quality" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "PATO:0001452" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "quality" } ] @@ -10759,9 +10338,6 @@ "val" : "Wikipedia:Physical_property" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "PATO:0002079" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "quality" } ] @@ -10805,12 +10381,6 @@ "val" : "snap:Quality" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "PATO:0001237" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "PATO:0001238" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "quality" } ] @@ -11037,9 +10607,6 @@ "val" : "tubulate" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "PATO:0001203" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "quality" } ] @@ -11488,27 +11055,6 @@ "val" : "quality" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/PATO_0010006", - "lbl" : "cell morphology", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A quality of a single cell inhering in the bearer by virtue of the bearer's size or shape or structure.", - "xrefs" : [ "https://orcid.org/0000-0002-7073-9172" ] - }, - "comments" : [ "Use this term for morphologies that can *only* inhere in a cell, e.g. morphological qualities inhering in a cell by virtue of the presence, location or shape of one or more cell parts." ], - "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/terms/contributor", - "val" : "https://orcid.org/0000-0002-7073-9172" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2021-01-23T11:31:53Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "quality" - } ] - } }, { "id" : "http://purl.obolibrary.org/obo/PATO_0015006", "lbl" : "polymeric", @@ -11540,52 +11086,6 @@ "val" : "high N:C ratio" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "http://orcid.org/0000-0001-5208-3432" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "quality" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/PATO_0070006", - "lbl" : "cortical bipolar morphology", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A cell morphology that inheres in neurons which have two principal dendrites that emerge from the soma and begin to branch some distance from it, have few spines, and branch in narrow fields. This is in contrast to bitufted morphology where branching occurs close to the soma.", - "xrefs" : [ "PMID:18568015", "doi:10.1016/b978-0-12-369497-3.10004-4" ] - }, - "comments" : [ "This is specific to cortical bipolar cells and are distinguished from retinal bipolar cell morphology which has an axon and dendrite emerging from opposite ends of the soma." ], - "xrefs" : [ { - "val" : "ILX:0101312" - }, { - "val" : "ilxtr:BipolarPhenotype" - }, { - "val" : "nifext:2" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/terms/contributor", - "val" : "https://orcid.org/0000-0001-7258-9596" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "quality" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/PATO_0070027", - "lbl" : "bitufted dendrite cell morphology", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A cell morphology that inheres in neurons with dendrites that are bidirectional, emerging from opposite ends of the soma, with the two arbors extending in radial or tangential directions.", - "xrefs" : [ "PMID:18568015" ] - }, - "comments" : [ "This morphology type is distinct from bitufted cell morphology in that it refers to bitufted dendrite morphology rather than bitufted cell morphology." ], - "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/terms/contributor", - "val" : "https://orcid.org/0000-0001-7258-9596" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "quality" } ] @@ -11599,9 +11099,6 @@ "val" : "A quality of continuant that exist at the anatomical level of organisation and anything under it. This includes, but is not limited to, cells , tissues, and components." }, "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "http://orcid.org/0000-0001-7258-9596" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "quality" } ] @@ -11615,9 +11112,6 @@ "val" : "A quality inhering in an anotomical structure by virtue of its capacity to be stained by specific histological dyes." }, "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "http://orcid.org/0000-0001-7258-9596" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "quality" } ] @@ -11632,9 +11126,6 @@ "xrefs" : [ "GOC:add" ] }, "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "http://orcid.org/0000-0001-7258-9596" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "quality" } ] @@ -11663,7 +11154,7 @@ "val" : "An amino acid chain that is produced de novo by ribosome-mediated translation of a genetically-encoded mRNA, and any derivatives thereof.", "xrefs" : [ "PRO:DAN", "PRO:WCB" ] }, - "comments" : [ "The definition above excludes protein complexes, which some also consider a protein. Those who wish to refer to a class representing both senses of the word are directed to CHEBI:36080. Note that the definition allows for experimentally-manipulated genes, and allows for artifically-produced derivatives that mimic those found naturally. Proteins (in the sense defined here) that descended from a common ancestor can be classified into families and superfamilies composed of products of evolutionarily-related genes. The domain architecture of a protein is described by the order of its constituent domains. Proteins with the same domains in the same order are defined as homeomorphic [PRO:WCB]." ], + "comments" : [ "The definition above excludes protein complexes, which some also consider a protein. Those who wish to refer to a class representing both senses of the word are directed to CHEBI:36080. Note that the definition allows for experimentally-manipulated genes, and allows for artifically-produced derivatives that mimic those found naturally. Proteins (in the sense defined here) that descended from a common ancestor can be classified into families and superfamilies composed of products of evolutionarily-related genes. The domain architecture of a protein is described by the order of its constituent domains. Proteins with the same domains in the same order are defined as homeomorphic [PRO:WCB)." ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "natural protein", @@ -12642,15 +12133,15 @@ } ] } }, { - "id" : "http://purl.obolibrary.org/obo/PR_000050567", - "lbl" : "protein-containing material entity", + "id" : "http://purl.obolibrary.org/obo/PR_000064867", + "lbl" : "protein-containing molecular entity", "type" : "CLASS", "meta" : { "definition" : { - "val" : "A material entity that minimally consists of a protein.", + "val" : "A molecular entity that minimally consists of a protein.", "xrefs" : [ "PRO:DAN" ] }, - "comments" : [ "Note: This includes single proteins and derivatives thereof (PR:000000001), protein-containing complexes (GO:0032991), and protein aggregates (PR:000050566)." ], + "comments" : [ "Note: This includes single proteins and derivatives thereof (PR:000000001), protein-containing complexes (GO:0032991), and protein aggregates (PR:000050565)." ], "synonyms" : [ { "pred" : "hasNarrowSynonym", "val" : "protein", @@ -12967,8 +12458,6 @@ "val" : "Wikipedia:Head" }, { "val" : "XAO:0003024" - }, { - "val" : "ZFA:0001114" }, { "val" : "galen:Head" } ], @@ -13097,9 +12586,6 @@ "val" : "galen:Wall" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "UBERON:0009915" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -13507,9 +12993,6 @@ "val" : "galen:ComplexSkeletalStructure" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "UBERON:0010322" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -14039,9 +13522,6 @@ "val" : "NLX:147821" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "UBERON:0005163" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -14342,9 +13822,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "TODO - check relationship with epiblast. Note in FMA this is not a subclass of embryo, but in uberon embryo is the whole organism from zygote onwards and thus includes the blastula" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "UBERON:0007011" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -15915,9 +15392,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0002161", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_6040" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "UBERON:0003263" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -16958,7 +16432,7 @@ "val" : "Organ system that passes nutrients (such as amino acids and electrolytes), gases, hormones, blood cells, etc. to and from cells in the body to help fight diseases and help stabilize body temperature and pH to maintain homeostasis[WP].", "xrefs" : [ "Wikipedia:Circulatory_system" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#uberon_slim" ], "synonyms" : [ { "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003011", "pred" : "hasRelatedSynonym", @@ -16983,9 +16457,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002161", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_6157" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -19624,9 +19095,6 @@ "val" : "ZFA:0001619" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "UBERON:0005888" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -21572,9 +21040,6 @@ "val" : "http://uri.neuinfo.org/nif/nifstd/FMAID_7191" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "UBERON:0007036" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -22224,15 +21689,10 @@ "val" : "TAO:0001438" }, { "val" : "UMLS:C0333343" - }, { - "val" : "ZFA:0001438" }, { "val" : "galen:BodyCavity" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "UBERON:0000169" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -23356,9 +22816,6 @@ "val" : "ZFA:0000570" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "UBERON:0005060" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -23697,9 +23154,6 @@ "val" : "ZFA:0000121" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "UBERON:0006258" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" }, { @@ -24291,9 +23745,6 @@ "val" : "XAO:0000252" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "UBERON:0005713" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -24675,9 +24126,6 @@ "val" : "ZFA:0000338" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "UBERON:0023148" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -25792,9 +25240,6 @@ "val" : "Wikipedia:Trilaminar_blastocyst" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "UBERON:0007012" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -28567,6 +28012,8 @@ "val" : "UMLS:C0460004" }, { "val" : "WikipediaCategory:Head_and_neck" + }, { + "val" : "ZFA:0001114" }, { "val" : "galen:HeadAndNeck" } ], @@ -28594,9 +28041,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "consider adding new class (EMAPA:16097) for mesenchyme of embryo (some mesenchyme is extraembryonic - e.g. amnion mesoderm)" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "UBERON:0003313" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -29585,6 +29029,8 @@ "val" : "EHDAA2:0004731" }, { "val" : "Wikipedia:Coelom" + }, { + "val" : "ZFA:0001438" } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", @@ -29980,9 +29426,6 @@ "val" : "presumptive central nervous system" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "UBERON:3000469" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -30005,9 +29448,6 @@ "val" : "AAO:0000477" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "UBERON:3000477" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -30971,9 +30411,6 @@ "val" : "A relationship between a process and a barrier, where the process occurs in a region spanning the barrier. For cellular processes the barrier is typically a membrane. Examples include transport across a membrane and membrane depolarization." }, "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "https://orcid.org/0000-0002-7073-9172" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-07-20T17:19:37Z" } ] @@ -33255,9 +32692,6 @@ "val" : "RO:0004007" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2018-12-13T11:26:17Z" }, { @@ -33283,9 +32717,6 @@ "val" : "RO:0004008" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2018-12-13T11:26:32Z" }, { @@ -33311,9 +32742,6 @@ "val" : "RO:0004009" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2018-12-13T11:26:56Z" }, { @@ -33333,9 +32761,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0004050", "val" : "http://purl.obolibrary.org/obo/RO_0002418" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2018-03-13T23:55:05Z" @@ -33351,9 +32776,6 @@ "propertyType" : "OBJECT", "meta" : { "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2018-03-13T23:55:19Z" }, { @@ -33371,9 +32793,6 @@ "val" : "a relation between a process and a continuant, in which the process is regulated by the small molecule continuant" }, "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "https://orcid.org/0000-0003-1813-6857" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2020-04-22T20:27:26Z" } ] @@ -33391,9 +32810,6 @@ "val" : "RO:0012001" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "https://orcid.org/0000-0003-1813-6857" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2020-04-22T20:28:37Z" }, { @@ -33418,9 +32834,6 @@ "val" : "RO:0012003" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "https://orcid.org/0000-0003-1813-6857" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2020-06-08T17:21:33Z" }, { @@ -33441,9 +32854,6 @@ "val" : "a relation between a continuant and a process, in which the continuant is a small molecule that regulates the process" }, "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "https://orcid.org/0000-0003-1813-6857" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2020-06-24T13:15:17Z" } ] @@ -33458,9 +32868,6 @@ "val" : "a relation between a continuant and a process, in which the continuant is a small molecule that activates the process" }, "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "https://orcid.org/0000-0003-1813-6857" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2020-06-24T13:15:26Z" }, { @@ -33479,9 +32886,6 @@ "val" : "RO:0012008" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "https://orcid.org/0000-0003-1813-6857" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2021-02-26T07:28:29Z" }, { @@ -33506,9 +32910,6 @@ "val" : "has synaptic input or output in" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "https://orcid.org/0000-0002-1373-1705" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2020-07-17T09:26:52Z" } ] @@ -33533,13 +32934,34 @@ "val" : "has sensory terminal location" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "https://orcid.org/0000-0002-1373-1705" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2020-07-20T12:10:09Z" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0015004", + "lbl" : "has characterizing marker set", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "A relation that applies between a cell type and a set of markers that can be used to uniquely identify that cell type." + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "has marker gene combination" + }, { + "pred" : "hasExactSynonym", + "val" : "has marker signature set" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "C has_characterizing_marker_set y iff: C is a cell type and y is a collection of genes or proteins whose expression is sufficient to distinguish cell type C from most or all other cell types." + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0001-7258-9596" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/RO_0015006", "lbl" : "different in magnitude relative to", @@ -33665,9 +33087,6 @@ "val" : "RO:0040036" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2018-09-26T01:08:58Z" }, { @@ -34366,13 +33785,14 @@ "propertyType" : "ANNOTATION", "meta" : { "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2018-03-14T00:03:24Z" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/STATO_0000663", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" }, { "id" : "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "type" : "PROPERTY", @@ -34425,6 +33845,10 @@ "meta" : { "comments" : [ "a subset of general classes of cell types in the cell ontology." ] } + }, { + "id" : "http://purl.obolibrary.org/obo/cl#human_subset", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" }, { "id" : "http://purl.obolibrary.org/obo/cl#kidney_upper_slim", "lbl" : "kidney_upper_slim", @@ -34437,6 +33861,10 @@ "val" : "2023-11-22T11:18:57Z" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/cl#mouse_subset", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" }, { "id" : "http://purl.obolibrary.org/obo/go#gocheck_do_not_annotate", "type" : "PROPERTY", @@ -34759,10 +34187,6 @@ "id" : "http://purl.org/dc/elements/1.1/creator", "type" : "PROPERTY", "propertyType" : "ANNOTATION" - }, { - "id" : "http://purl.org/dc/elements/1.1/date", - "type" : "PROPERTY", - "propertyType" : "ANNOTATION" }, { "id" : "http://purl.org/dc/elements/1.1/description", "type" : "PROPERTY", @@ -34775,6 +34199,10 @@ "id" : "http://purl.org/dc/elements/1.1/title", "type" : "PROPERTY", "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.org/dc/elements/1.1/type", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" }, { "id" : "http://purl.org/dc/terms/contributor", "type" : "PROPERTY", @@ -34785,14 +34213,17 @@ "propertyType" : "ANNOTATION" }, { "id" : "http://purl.org/dc/terms/description", + "lbl" : "description", "type" : "PROPERTY", "propertyType" : "ANNOTATION" }, { "id" : "http://purl.org/dc/terms/license", + "lbl" : "license", "type" : "PROPERTY", "propertyType" : "ANNOTATION" }, { "id" : "http://purl.org/dc/terms/title", + "lbl" : "title", "type" : "PROPERTY", "propertyType" : "ANNOTATION" }, { @@ -34810,19 +34241,10 @@ "lbl" : "consider", "type" : "PROPERTY", "propertyType" : "ANNOTATION" - }, { - "id" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "type" : "PROPERTY", - "propertyType" : "ANNOTATION" }, { "id" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "type" : "PROPERTY", "propertyType" : "ANNOTATION" - }, { - "id" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "lbl" : "has_alternative_id", - "type" : "PROPERTY", - "propertyType" : "ANNOTATION" }, { "id" : "http://www.geneontology.org/formats/oboInOwl#hasBroadSynonym", "lbl" : "has_broad_synonym", @@ -34842,9 +34264,21 @@ } }, { "id" : "http://www.geneontology.org/formats/oboInOwl#hasDbXref", - "lbl" : "database_cross_reference", + "lbl" : "has cross-reference", "type" : "PROPERTY", - "propertyType" : "ANNOTATION" + "propertyType" : "ANNOTATION", + "meta" : { + "definition" : { + "val" : "An annotation property that links an ontology entity or a statement to a prefixed identifier or URI." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/information-artifact-ontology/ontology-metadata/issues/123" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0002-7356-1779" + } ] + } }, { "id" : "http://www.geneontology.org/formats/oboInOwl#hasExactSynonym", "lbl" : "has_exact_synonym", @@ -34923,10 +34357,6 @@ "id" : "http://www.geneontology.org/formats/oboInOwl#is_metadata_tag", "type" : "PROPERTY", "propertyType" : "ANNOTATION" - }, { - "id" : "http://www.geneontology.org/formats/oboInOwl#note", - "type" : "PROPERTY", - "propertyType" : "ANNOTATION" }, { "id" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "lbl" : "shorthand", @@ -35188,11 +34618,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000057", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/CL_0002320" - }, { - "sub" : "http://purl.obolibrary.org/obo/CL_0000057", - "pred" : "http://purl.obolibrary.org/obo/RO_0002202", - "obj" : "http://purl.obolibrary.org/obo/CL_0000134" + "obj" : "http://purl.obolibrary.org/obo/CL_0000499" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000066", "pred" : "is_a", @@ -35262,7 +34688,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000099", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/CL_0000540" + "obj" : "http://purl.obolibrary.org/obo/CL_2000029" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000101", "pred" : "is_a", @@ -35271,14 +34697,6 @@ "sub" : "http://purl.obolibrary.org/obo/CL_0000101", "pred" : "http://purl.obolibrary.org/obo/RO_0002215", "obj" : "http://purl.obolibrary.org/obo/GO_0050906" - }, { - "sub" : "http://purl.obolibrary.org/obo/CL_0000103", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/CL_0000099" - }, { - "sub" : "http://purl.obolibrary.org/obo/CL_0000103", - "pred" : "http://purl.obolibrary.org/obo/RO_0000053", - "obj" : "http://purl.obolibrary.org/obo/PATO_0070006" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000115", "pred" : "is_a", @@ -35291,18 +34709,6 @@ "sub" : "http://purl.obolibrary.org/obo/CL_0000115", "pred" : "http://purl.obolibrary.org/obo/RO_0002202", "obj" : "http://purl.obolibrary.org/obo/CL_0000222" - }, { - "sub" : "http://purl.obolibrary.org/obo/CL_0000117", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/CL_0000540" - }, { - "sub" : "http://purl.obolibrary.org/obo/CL_0000117", - "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", - "obj" : "http://purl.obolibrary.org/obo/UBERON_0001017" - }, { - "sub" : "http://purl.obolibrary.org/obo/CL_0000117", - "pred" : "http://purl.obolibrary.org/obo/RO_0002202", - "obj" : "http://purl.obolibrary.org/obo/CL_0000031" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000123", "pred" : "is_a", @@ -35680,17 +35086,17 @@ "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/CL_0000211" }, { - "sub" : "http://purl.obolibrary.org/obo/CL_0000402", + "sub" : "http://purl.obolibrary.org/obo/CL_0000404", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/CL_0000099" + "obj" : "http://purl.obolibrary.org/obo/CL_0000211" }, { - "sub" : "http://purl.obolibrary.org/obo/CL_0000402", + "sub" : "http://purl.obolibrary.org/obo/CL_0000499", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/CL_2000029" + "obj" : "http://purl.obolibrary.org/obo/CL_0002320" }, { - "sub" : "http://purl.obolibrary.org/obo/CL_0000404", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/CL_0000211" + "sub" : "http://purl.obolibrary.org/obo/CL_0000499", + "pred" : "http://purl.obolibrary.org/obo/RO_0002202", + "obj" : "http://purl.obolibrary.org/obo/CL_0000134" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000514", "pred" : "is_a", @@ -35749,10 +35155,6 @@ "sub" : "http://purl.obolibrary.org/obo/CL_0000547", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/CL_0002242" - }, { - "sub" : "http://purl.obolibrary.org/obo/CL_0000547", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000547", "pred" : "http://purl.obolibrary.org/obo/BFO_0000051", @@ -35827,10 +35229,6 @@ "val" : "true" } ] } - }, { - "sub" : "http://purl.obolibrary.org/obo/CL_0000549", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000549", "pred" : "http://purl.obolibrary.org/obo/BFO_0000051", @@ -35853,10 +35251,6 @@ "val" : "true" } ] } - }, { - "sub" : "http://purl.obolibrary.org/obo/CL_0000550", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000550", "pred" : "http://purl.obolibrary.org/obo/BFO_0000051", @@ -35997,10 +35391,6 @@ "val" : "true" } ] } - }, { - "sub" : "http://purl.obolibrary.org/obo/CL_0000558", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000558", "pred" : "http://purl.obolibrary.org/obo/CL_4030046", @@ -36091,10 +35481,6 @@ "sub" : "http://purl.obolibrary.org/obo/CL_0000566", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/CL_0011026" - }, { - "sub" : "http://purl.obolibrary.org/obo/CL_0000566", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000566", "pred" : "http://purl.obolibrary.org/obo/RO_0002104", @@ -36210,7 +35596,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000740", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/CL_0000117" + "obj" : "http://purl.obolibrary.org/obo/CL_0000540" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000740", "pred" : "http://purl.obolibrary.org/obo/RO_0002100", @@ -36223,10 +35609,6 @@ "sub" : "http://purl.obolibrary.org/obo/CL_0000745", "pred" : "http://purl.obolibrary.org/obo/RO_0002100", "obj" : "http://purl.obolibrary.org/obo/UBERON_0003902" - }, { - "sub" : "http://purl.obolibrary.org/obo/CL_0000748", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/CL_0000103" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000748", "pred" : "is_a", @@ -36347,10 +35729,6 @@ "sub" : "http://purl.obolibrary.org/obo/CL_0000837", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/CL_0008001" - }, { - "sub" : "http://purl.obolibrary.org/obo/CL_0000837", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000837", "pred" : "http://purl.obolibrary.org/obo/CL_4030046", @@ -36644,7 +36022,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/CL_0005000", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/CL_0000402", + "obj" : "http://purl.obolibrary.org/obo/CL_0000099", "meta" : { "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#is_inferred", @@ -37129,8 +36507,8 @@ "obj" : "http://purl.obolibrary.org/obo/GO_0043232" }, { "sub" : "http://purl.obolibrary.org/obo/GO_0005840", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PR_000050567" + "pred" : "http://purl.obolibrary.org/obo/BFO_0000051", + "obj" : "http://purl.obolibrary.org/obo/PR_000000001" }, { "sub" : "http://purl.obolibrary.org/obo/GO_0005840", "pred" : "http://purl.obolibrary.org/obo/RO_0002216", @@ -37174,7 +36552,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/GO_0006413", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/GO_0044237" + "obj" : "http://purl.obolibrary.org/obo/GO_0008152" }, { "sub" : "http://purl.obolibrary.org/obo/GO_0006413", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", @@ -37418,7 +36796,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/GO_0008152", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/GO_0008150" + "obj" : "http://purl.obolibrary.org/obo/GO_0009987" }, { "sub" : "http://purl.obolibrary.org/obo/GO_0008219", "pred" : "is_a", @@ -37430,11 +36808,11 @@ }, { "sub" : "http://purl.obolibrary.org/obo/GO_0009059", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/GO_0043170" + "obj" : "http://purl.obolibrary.org/obo/GO_0009058" }, { "sub" : "http://purl.obolibrary.org/obo/GO_0009059", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/GO_0044249" + "obj" : "http://purl.obolibrary.org/obo/GO_0043170" }, { "sub" : "http://purl.obolibrary.org/obo/GO_0009314", "pred" : "is_a", @@ -37905,8 +37283,8 @@ "obj" : "http://purl.obolibrary.org/obo/GO_0005575" }, { "sub" : "http://purl.obolibrary.org/obo/GO_0032991", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PR_000050567" + "pred" : "http://purl.obolibrary.org/obo/BFO_0000051", + "obj" : "http://purl.obolibrary.org/obo/PR_000000001" }, { "sub" : "http://purl.obolibrary.org/obo/GO_0034101", "pred" : "is_a", @@ -38151,26 +37529,10 @@ "sub" : "http://purl.obolibrary.org/obo/GO_0044207", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", "obj" : "http://purl.obolibrary.org/obo/GO_0005737" - }, { - "sub" : "http://purl.obolibrary.org/obo/GO_0044237", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/GO_0008152" - }, { - "sub" : "http://purl.obolibrary.org/obo/GO_0044237", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/GO_0009987" }, { "sub" : "http://purl.obolibrary.org/obo/GO_0044238", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/GO_0008152" - }, { - "sub" : "http://purl.obolibrary.org/obo/GO_0044249", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/GO_0009058" - }, { - "sub" : "http://purl.obolibrary.org/obo/GO_0044249", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/GO_0044237" }, { "sub" : "http://purl.obolibrary.org/obo/GO_0044297", "pred" : "is_a", @@ -38723,10 +38085,6 @@ "sub" : "http://purl.obolibrary.org/obo/GO_0098644", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/GO_0099080" - }, { - "sub" : "http://purl.obolibrary.org/obo/GO_0098644", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/GO_0098644", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", @@ -39287,10 +38645,6 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0010001", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0000141" - }, { - "sub" : "http://purl.obolibrary.org/obo/PATO_0010006", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PATO_0000051" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0015006", "pred" : "is_a", @@ -39299,14 +38653,6 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0040072", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0001396" - }, { - "sub" : "http://purl.obolibrary.org/obo/PATO_0070006", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PATO_0070027" - }, { - "sub" : "http://purl.obolibrary.org/obo/PATO_0070027", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PATO_0010006" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0070044", "pred" : "is_a", @@ -39330,7 +38676,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/PR_000000001", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PR_000050567" + "obj" : "http://purl.obolibrary.org/obo/PR_000064867" }, { "sub" : "http://purl.obolibrary.org/obo/PR_000000001", "pred" : "http://purl.obolibrary.org/obo/RO_0002353", @@ -39411,10 +38757,6 @@ "sub" : "http://purl.obolibrary.org/obo/PR_000001945", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PR_000000001" - }, { - "sub" : "http://purl.obolibrary.org/obo/PR_000001971", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PR_000000001" }, { "sub" : "http://purl.obolibrary.org/obo/PR_000002112", "pred" : "is_a", @@ -39460,7 +38802,7 @@ "pred" : "http://purl.obolibrary.org/obo/RO_0002160", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_2759" }, { - "sub" : "http://purl.obolibrary.org/obo/PR_000050567", + "sub" : "http://purl.obolibrary.org/obo/PR_000064867", "pred" : "http://purl.obolibrary.org/obo/BFO_0000051", "obj" : "http://purl.obolibrary.org/obo/PR_000000001" }, { @@ -39535,10 +38877,6 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0000033", "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_33213" - }, { - "sub" : "http://purl.obolibrary.org/obo/UBERON_0000042", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000042", "pred" : "is_a", @@ -39890,7 +39228,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000178", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PR_000050567" + "obj" : "http://purl.obolibrary.org/obo/UBERON_0000061" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000178", "pred" : "is_a", @@ -40071,10 +39409,6 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0000481", "pred" : "http://purl.obolibrary.org/obo/BFO_0000051", "obj" : "http://purl.obolibrary.org/obo/UBERON_0000479" - }, { - "sub" : "http://purl.obolibrary.org/obo/UBERON_0000483", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000483", "pred" : "is_a", @@ -40375,10 +39709,6 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0000959", "pred" : "http://purl.obolibrary.org/obo/uberon/core#extends_fibers_into", "obj" : "http://purl.obolibrary.org/obo/UBERON_0001908" - }, { - "sub" : "http://purl.obolibrary.org/obo/UBERON_0000964", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000964", "pred" : "is_a", @@ -41834,10 +41164,6 @@ "val" : "ZFA" } ] } - }, { - "sub" : "http://purl.obolibrary.org/obo/UBERON_0001969", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0001969", "pred" : "is_a", @@ -41854,10 +41180,6 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0001969", "pred" : "http://purl.obolibrary.org/obo/RO_0002221", "obj" : "http://purl.obolibrary.org/obo/CL_0000232" - }, { - "sub" : "http://purl.obolibrary.org/obo/UBERON_0001981", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0001981", "pred" : "is_a", @@ -42621,6 +41943,10 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0003057", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", "obj" : "http://purl.obolibrary.org/obo/UBERON_0003075" + }, { + "sub" : "http://purl.obolibrary.org/obo/UBERON_0003059", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/UBERON_0000061" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0003059", "pred" : "is_a", @@ -43695,10 +43021,6 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0004456", "pred" : "http://purl.obolibrary.org/obo/RO_0002492", "obj" : "http://purl.obolibrary.org/obo/UBERON_0000066" - }, { - "sub" : "http://purl.obolibrary.org/obo/UBERON_0004535", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0004535", "pred" : "is_a", @@ -43715,10 +43037,6 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0004535", "pred" : "http://purl.obolibrary.org/obo/BFO_0000051", "obj" : "http://purl.obolibrary.org/obo/UBERON_0001981" - }, { - "sub" : "http://purl.obolibrary.org/obo/UBERON_0004537", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0004537", "pred" : "is_a", @@ -44227,10 +43545,6 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0005764", "pred" : "http://purl.obolibrary.org/obo/RO_0002007", "obj" : "http://purl.obolibrary.org/obo/UBERON_0000061" - }, { - "sub" : "http://purl.obolibrary.org/obo/UBERON_0005769", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0005769", "pred" : "is_a", @@ -44291,10 +43605,6 @@ "val" : "AEO-modified-relation" } ] } - }, { - "sub" : "http://purl.obolibrary.org/obo/UBERON_0005906", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0005906", "pred" : "is_a", @@ -44623,10 +43933,6 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0006914", "pred" : "http://purl.obolibrary.org/obo/BFO_0000051", "obj" : "http://purl.obolibrary.org/obo/CL_0000076" - }, { - "sub" : "http://purl.obolibrary.org/obo/UBERON_0006965", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0006965", "pred" : "is_a", @@ -45066,6 +44372,10 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0009581", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", "obj" : "http://purl.obolibrary.org/obo/UBERON_0009616" + }, { + "sub" : "http://purl.obolibrary.org/obo/UBERON_0009615", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/UBERON_0004121" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0009615", "pred" : "is_a", @@ -45602,10 +44912,6 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0012275", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/UBERON_0004120" - }, { - "sub" : "http://purl.obolibrary.org/obo/UBERON_0012430", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0012430", "pred" : "is_a", @@ -46810,10 +46116,6 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002590", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002592" - }, { - "sub" : "http://purl.obolibrary.org/obo/RO_0002592", - "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0000057" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002592", "pred" : "subPropertyOf", @@ -47250,13 +46552,6 @@ "propertyId" : "http://purl.obolibrary.org/obo/RO_0002215", "fillerId" : "http://purl.obolibrary.org/obo/GO_0050906" } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/CL_0000103", - "genusIds" : [ "http://purl.obolibrary.org/obo/CL_0000099" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0000053", - "fillerId" : "http://purl.obolibrary.org/obo/PATO_0070006" - } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/CL_0000148", "genusIds" : [ "http://purl.obolibrary.org/obo/CL_0000147" ], @@ -47359,13 +46654,6 @@ "propertyId" : "http://purl.obolibrary.org/obo/RO_0002162", "fillerId" : "http://purl.obolibrary.org/obo/NCBITaxon_33208" } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/CL_0000402", - "genusIds" : [ "http://purl.obolibrary.org/obo/CL_0000099" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0002100", - "fillerId" : "http://purl.obolibrary.org/obo/UBERON_0001017" - } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/CL_0000514", "genusIds" : [ "http://purl.obolibrary.org/obo/CL_0000056" ], @@ -47600,7 +46888,7 @@ } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/CL_0000748", - "genusIds" : [ "http://purl.obolibrary.org/obo/CL_0000103" ], + "genusIds" : [ "http://purl.obolibrary.org/obo/CL_0000540" ], "restrictions" : [ { "propertyId" : "http://purl.obolibrary.org/obo/RO_0002100", "fillerId" : "http://purl.obolibrary.org/obo/UBERON_0001791" @@ -49827,6 +49115,9 @@ }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0013007", "domainClassIds" : [ "http://purl.obolibrary.org/obo/CL_0000101" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0015004", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/CL_0000000" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0015006", "domainClassIds" : [ "http://purl.obolibrary.org/obo/PATO_0000001" ], diff --git a/src/ontology/subsets/eye_upper_slim.obo b/src/ontology/subsets/eye_upper_slim.obo index 9b0a28e3c..32dfd32ca 100644 --- a/src/ontology/subsets/eye_upper_slim.obo +++ b/src/ontology/subsets/eye_upper_slim.obo @@ -1,5 +1,5 @@ format-version: 1.2 -data-version: cl/releases/2024-09-26/subsets/eye_upper_slim.owl +data-version: cl/releases/2025-01-08/subsets/eye_upper_slim.owl subsetdef: abnormal_slim "" subsetdef: added_for_HCA "" subsetdef: attribute_slim "" @@ -44,10 +44,12 @@ subsetdef: http://purl.obolibrary.org/obo/valid_for_go_gp2term "" subsetdef: http://purl.obolibrary.org/obo/valid_for_go_ontology "" subsetdef: http://purl.obolibrary.org/obo/valid_for_gocam "" subsetdef: human_reference_atlas "" +subsetdef: human_subset "" subsetdef: inconsistent_with_fma "" subsetdef: kidney_upper_slim "a subset of general classes related to specific cell types in the kidney" subsetdef: location_grouping "" subsetdef: major_organ "" +subsetdef: mouse_subset "" subsetdef: mpath_slim "" subsetdef: non_informative "" subsetdef: organ_slim "" @@ -96,7 +98,7 @@ idspace: oboInOwl http://www.geneontology.org/formats/oboInOwl# idspace: sssom https://w3id.org/sssom/ idspace: terms http://purl.org/dc/terms/ ontology: cl/subsets/eye_upper_slim -property_value: owl:versionInfo "2024-09-26" xsd:string +property_value: owl:versionInfo "2025-01-08" xsd:string [Term] id: CL:0000000 @@ -104,6 +106,8 @@ name: cell def: "A material entity of anatomical origin (part of or deriving from an organism) that has as its parts a maximally connected cell compartment surrounded by a plasma membrane." [CARO:mah] comment: The definition of cell is intended to represent all cells, and thus a cell is defined as a material entity and not an anatomical structure, which implies that it is part of an organism (or the entirety of one). subset: cellxgene_subset +subset: human_subset +subset: mouse_subset subset: ubprop:upper_level xref: CALOHA:TS-2035 xref: FBbt:00007002 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} @@ -125,6 +129,8 @@ relationship: RO:0002162 NCBITaxon:131567 ! in taxon cellular organisms id: CL:0000005 name: neural crest derived fibroblast def: "Any fibroblast that is derived from the neural crest." [https://orcid.org/0000-0001-5208-3432] +subset: human_subset +subset: mouse_subset synonym: "fibroblast neural crest derived" EXACT [] is_a: CL:0000057 ! fibroblast intersection_of: CL:0000057 ! fibroblast @@ -136,6 +142,8 @@ id: CL:0000006 name: neuronal receptor cell def: "Any sensory receptor cell that is a(n) neuron and is capable of some detection of stimulus involved in sensory perception." [FBC:Autogenerated] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "neuronal receptor cell (sensu Animalia)" EXACT [] xref: ZFA:0009001 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000101 ! sensory neuron @@ -148,6 +156,8 @@ intersection_of: capable_of GO:0050906 ! detection of stimulus involved in senso id: CL:0000007 name: early embryonic cell (metazoa) def: "A cell found in the embryo before the formation of all the gem layers is complete." [GOC:tfm] +subset: human_subset +subset: mouse_subset xref: ZFA:0009002 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0002321 ! embryonic cell (metazoa) @@ -155,13 +165,18 @@ is_a: CL:0002321 ! embryonic cell (metazoa) id: CL:0000008 name: migratory cranial neural crest cell def: "Cell that is part of the migratory cranial neural crest population. Migratory cranial neural crest cells develop from premigratory cranial neural crest cells and have undergone epithelial to mesenchymal transition and delamination." [https://orcid.org/0000-0001-5208-3432, ZFA:0007091] +subset: human_subset +subset: mouse_subset xref: ZFA:0007091 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000333 ! migratory neural crest cell [Term] id: CL:0000030 name: glioblast +def: "A non-terminally differentiated cell that develops form the neuroectoderm. Glioblast has the potential to differentiate into various types of glial cells, including astrocytes and oligodendrocytes." [PMID:37824650, Wikipedia:Glioblast] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset xref: ZFA:0009010 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000055 ! non-terminally differentiated cell is_a: CL:0000255 ! eukaryotic cell @@ -172,6 +187,8 @@ id: CL:0000031 name: neuroblast (sensu Vertebrata) def: "A cell that will develop into a neuron often after a migration phase." [GOC:NV, http://en.wikipedia.org/wiki/Neuroblast] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "neuroblast" EXACT [] xref: BTO:0000930 xref: FMA:70563 @@ -188,6 +205,8 @@ comment: This term applies to metazoan. For plant stem cells, consider using PO: subset: cellxgene_subset subset: general_cell_types_upper_slim subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "animal stem cell" EXACT [] xref: CALOHA:TS-2086 xref: FMA:63368 @@ -208,6 +227,8 @@ comment: Markers differ between species, and two sets of markers have been descr subset: blood_and_immune_upper_slim subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "blood forming stem cell" EXACT [] synonym: "colony forming unit hematopoietic" RELATED [] synonym: "hemopoietic stem cell" EXACT [] @@ -258,6 +279,8 @@ name: erythroid progenitor cell def: "A progenitor cell committed to the erythroid lineage." [GOC:add, ISBN:0721601464] subset: blood_and_immune_upper_slim subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "BFU-E" RELATED OMO:0003000 [] synonym: "blast forming unit erythroid" RELATED [] synonym: "burst forming unit erythroid" RELATED [] @@ -274,6 +297,8 @@ relationship: RO:0002202 CL:0000050 ! develops from megakaryocyte-erythroid prog id: CL:0000048 name: multi fate stem cell def: "A stem cell that can give rise to multiple lineages of cells." [GOC:add] +subset: human_subset +subset: mouse_subset synonym: "multi-fate stem cell" EXACT [] synonym: "multifate stem cell" EXACT [] synonym: "multipotent cell" EXACT [] @@ -293,6 +318,8 @@ def: "A progenitor cell committed to myeloid lineage, including the megakaryocyt comment: This cell type is intended to be compatible with any vertebrate common myeloid progenitor. For mammalian CMP known to be CD34-positive, please use the term 'common myeloid progenitor, CD34-positive' (CL_0001059). subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "CFU-GEMM" RELATED OMO:0003000 [ISBN:0878932437] synonym: "CFU-S" RELATED OMO:0003000 [ISBN:0878932437] synonym: "CMP" RELATED OMO:0003000 [ISBN:0878932437] @@ -314,6 +341,8 @@ def: "A progenitor cell committed to the megakaryocyte and erythroid lineages." comment: MEPs are reportedly CD19-negative, CD34-negative, CD45RA-negative, CD110-positive, CD117-positive, and SCA1-negative and reportedly express the transcription factors GATA-1 and NF-E2. subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "CFU-EM" EXACT [] synonym: "CFU-MegE" EXACT [] synonym: "colony forming unit erythroid megakaryocyte" EXACT [] @@ -336,6 +365,8 @@ property_value: RO:0002175 NCBITaxon:9606 id: CL:0000052 name: totipotent stem cell def: "A stem cell from which all cells of the body can form." [GOC:add, GOC:tfm] +subset: human_subset +subset: mouse_subset synonym: "totipotential stem cell" EXACT [] xref: FMA:84790 xref: MESH:D039901 @@ -348,6 +379,8 @@ name: non-terminally differentiated cell def: "A precursor cell with a limited number of potential fates." [SANBI:mhl] comment: define using PATO mulit-potent or oligopotent? subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "blast cell" EXACT [] xref: BTO:0000125 xref: FMA:84782 @@ -357,6 +390,9 @@ is_a: CL:0011115 ! precursor cell id: CL:0000056 name: myoblast def: "A cell that is commited to differentiating into a muscle cell. Embryonic myoblasts develop from the mesoderm. They undergo proliferation, migrate to their various sites, and then differentiate into the appropriate form of myocytes. Myoblasts also occur as transient populations of cells in muscles undergoing repair." [GOC:tfm, MESH:D032446, PMID:21849021] +subset: cellxgene_subset +subset: human_subset +subset: mouse_subset xref: BTO:0000222 xref: CALOHA:TS-0650 xref: FBbt:00005083 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} @@ -373,14 +409,15 @@ comment: These cells may be vimentin-positive, fibronectin-positive, fsp1-positi subset: cellxgene_subset subset: general_cell_types_upper_slim subset: human_reference_atlas +subset: human_subset +subset: mouse_subset xref: BTO:0000452 xref: CALOHA:TS-0362 xref: FMA:63877 xref: NCIT:C12482 xref: VHOG:0001482 xref: ZFA:0009026 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} -is_a: CL:0002320 ! connective tissue cell -relationship: RO:0002202 CL:0000134 ! develops from mesenchymal stem cell +is_a: CL:0000499 ! stromal cell property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -390,6 +427,8 @@ def: "A cell that is usually found in a two-dimensional sheet with a free surfac subset: cellxgene_subset subset: general_cell_types_upper_slim subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "epitheliocyte" EXACT [] xref: BTO:0000414 xref: CALOHA:TS-2026 @@ -409,6 +448,8 @@ name: blood vessel endothelial cell def: "An endothelial cell that lines the vasculature." [GOC:tfm] subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset xref: ZFA:0009036 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0002139 ! endothelial cell of vascular tree intersection_of: CL:0000115 ! endothelial cell @@ -422,6 +463,8 @@ name: columnar/cuboidal epithelial cell def: "A columnar/cuboidal epithelial cell is a cell usually found in a two dimensional sheet with a free surface. Columnar/cuboidal epithelial cells take on the shape of a column or cube." [GO:0002065, https://orcid.org/0000-0001-5208-3432] subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset xref: ZFA:0009038 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000066 ! epithelial cell property_value: RO:0002175 NCBITaxon:9606 @@ -431,6 +474,8 @@ id: CL:0000076 name: squamous epithelial cell def: "Any epithelial cell that is part of some squamous epithelium." [FBC:Autogenerated] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset xref: CALOHA:TS-1249 xref: ZFA:0009039 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000066 ! epithelial cell @@ -445,6 +490,8 @@ def: "A flat, squamous-like epithelial cell of mesodermal origin. It forms the m comment: Mesothelial cells, which morphologically resemble squamous epithelial cells, express both epithelial markers (cytokeratins) and mesenchymal markers (vimentin), reflecting their mesodermal origin. They feature surface microvilli and apical-basal polarity. Under certain conditions, they can undergo mesothelial-to-mesenchymal transition. These cells also produce extracellular matrix proteins, maintain serosal homeostasis, and facilitate fluid transport. {xref="PMID:26106328"} subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "mesotheliocyte" EXACT [] xref: FMA:66773 xref: ZFA:0009040 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} @@ -460,6 +507,8 @@ name: blood cell def: "A cell found predominately in the blood." [GOC:add, GOC:tfm] subset: cellxgene_subset subset: general_cell_types_upper_slim +subset: human_subset +subset: mouse_subset xref: FMA:62844 xref: MESH:D001773 xref: ZFA:0009044 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} @@ -472,6 +521,8 @@ relationship: capable_of GO:0008015 ! blood circulation id: CL:0000095 name: neuron associated cell subset: cellxgene_subset +subset: human_subset +subset: mouse_subset is_a: CL:0002319 ! neural cell relationship: RO:0002202 CL:0000133 ! develops from neurectodermal cell @@ -481,19 +532,25 @@ name: interneuron def: "Most generally any neuron which is not motor or sensory. Interneurons may also refer to neurons whose axons remain within a particular brain region as contrasted with projection neurons which have axons projecting to other brain regions." [GOC:tfm, MESH:D007395] subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset +synonym: "CNS interneuron" RELATED [] xref: BTO:0003811 xref: FBbt:00005125 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:67313 xref: WBbt:0005113 xref: ZFA:0009051 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} -is_a: CL:0000540 ! neuron +is_a: CL:2000029 ! central nervous system neuron property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000101 name: sensory neuron def: "Any neuron having a sensory function; an afferent neuron conveying sensory impulses." [ISBN:0721662544] +subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset xref: BTO:0001037 xref: FBbt:00005124 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:84649 @@ -506,19 +563,6 @@ intersection_of: capable_of GO:0050906 ! detection of stimulus involved in senso relationship: capable_of GO:0050906 ! detection of stimulus involved in sensory perception property_value: RO:0002175 NCBITaxon:9606 -[Term] -id: CL:0000103 -name: bipolar neuron -def: "A type of interneuron that has two neurites, usually an axon and a dendrite, extending from opposite poles of an ovoid cell body." [GOC:tfm, ISBN:0444009442] -subset: BDS_subset -subset: cellxgene_subset -xref: FMA:67282 -xref: ZFA:0009055 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} -is_a: CL:0000099 ! interneuron -intersection_of: CL:0000099 ! interneuron -intersection_of: bearer_of PATO:0070006 ! cortical bipolar morphology -relationship: bearer_of PATO:0070006 ! cortical bipolar morphology - [Term] id: CL:0000115 name: endothelial cell @@ -526,6 +570,8 @@ def: "An endothelial cell comprises the outermost layer or lining of anatomical comment: From FMA: 9.07.2001: Endothelial cell has always been classified as a kind of epithelial cell, specifically a squamous cell but that is not true. First, endothelial cell can either be squamous or cuboidal (e.g. high-endothelial cell) and secondly, it has different embryological derivation (mesodermal) than a true epithelial cell (ectodermal and endodermal). The basis for present classification is the fact that it comprises the outermost layer or lining of anatomical structures (location-based) but a better structural basis for the differentia is the cytoskeleton of the cell. Endothelial cell has vimentin filaments while an epithelial cell has keratin filaments. [Onard]. subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "endotheliocyte" EXACT [] xref: BTO:0001176 xref: CALOHA:TS-0278 @@ -536,18 +582,12 @@ is_a: CL:0000255 ! eukaryotic cell relationship: RO:0002202 CL:0000222 ! develops from mesodermal cell property_value: RO:0002175 NCBITaxon:9606 -[Term] -id: CL:0000117 -name: CNS neuron (sensu Vertebrata) -xref: ZFA:0009067 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} -is_a: CL:0000540 ! neuron -relationship: part_of UBERON:0001017 ! central nervous system -relationship: RO:0002202 CL:0000031 ! develops from neuroblast (sensu Vertebrata) - [Term] id: CL:0000123 name: neuron associated cell (sensu Vertebrata) subset: cellxgene_subset +subset: human_subset +subset: mouse_subset is_a: CL:0000095 ! neuron associated cell relationship: RO:0002162 NCBITaxon:7742 ! in taxon Vertebrata relationship: RO:0002202 CL:0000333 ! develops from migratory neural crest cell @@ -560,6 +600,8 @@ comment: Not all glial cells develop from glioblasts, with microglia developing subset: cellxgene_subset subset: general_cell_types_upper_slim subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "neuroglia" RELATED [] synonym: "neuroglial cell" EXACT [] xref: BTO:0002606 @@ -570,13 +612,15 @@ xref: https://cellxgene.cziscience.com/cellguide/CL_0000125 xref: ZFA:0009073 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000095 ! neuron associated cell property_value: RO:0002175 NCBITaxon:9606 -property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional.\n\nGlial cells, also known as neuroglia or simply glia, are non-neuronal cells in the central and peripheral nervous systems that provide support and protection for neurons. They constitute approximately half of the total cells in the human brain and more than half in other parts of the nervous system. Glial cells perform several key functions including, but not limited to, maintaining homeostasis, forming the myelin sheath around the neuron axons, and providing support and nutrition to neurons.\nThese different functions are performed by various glial cell types, including astrocytes, oligodendrocytes, microglia and other specialized types. Astrocytes, for example, are the most abundant glial cells and provide metabolic and nutrient support to neurons, help regulate the extracellular ion and neurotransmitter levels, and play a role in the formation and maintenance of the blood-brain barrier, contributing to the overall homeostasis and functioning of the nervous system. Additionally, astrocytes are involved in synaptic communication and participate in processes such as synaptogenesis and synaptic pruning.\nOligodendrocytes in the central nervous system function to insulate neurons by producing a fatty substance known as myelin. The myelin sheath enhances the speed and efficiency of nerve impulse conduction along the axons. \nMicroglia, the immune cells of the central nervous system, protect neurons from pathogens and clear away dead neurons through phagocytosis, a process also known as cellular eating. They also contribute to the regulation of inflammation in response to signals of tissue damage or infection in the central nervous system by releasing cytokines and other signaling molecules that modulate the immune response.\nDespite their overarching function in the support and protection of neurons, glial cells have also been shown to play significant roles in the pathophysiology of many psychiatric and neurodegenerative diseases, such as Alzheimer’s, Parkinson’s Disease and multiple sclerosis." xsd:string {xref="DOI:10.1002/glia.24343", xref="DOI:10.1038/nn1988", xref="DOI:10.1101/cshperspect.a020602", xref="DOI:10.1126/science.aat0473", xref="DOI:10.3389/fncel.2017.00024"} +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nGlial cells, also known as neuroglia or simply glia, are non-neuronal cells in the central and peripheral nervous systems that provide support and protection for neurons. They constitute approximately half of the total cells in the human brain and more than half in other parts of the nervous system. Glial cells perform several key functions including, but not limited to, maintaining homeostasis, forming the myelin sheath around the neuron axons, and providing support and nutrition to neurons.\nThese different functions are performed by various glial cell types, including astrocytes, oligodendrocytes, microglia and other specialized types. Astrocytes, for example, are the most abundant glial cells and provide metabolic and nutrient support to neurons, help regulate the extracellular ion and neurotransmitter levels, and play a role in the formation and maintenance of the blood-brain barrier, contributing to the overall homeostasis and functioning of the nervous system. Additionally, astrocytes are involved in synaptic communication and participate in processes such as synaptogenesis and synaptic pruning.\nOligodendrocytes in the central nervous system function to insulate neurons by producing a fatty substance known as myelin. The myelin sheath enhances the speed and efficiency of nerve impulse conduction along the axons. \nMicroglia, the immune cells of the central nervous system, protect neurons from pathogens and clear away dead neurons through phagocytosis, a process also known as cellular eating. They also contribute to the regulation of inflammation in response to signals of tissue damage or infection in the central nervous system by releasing cytokines and other signaling molecules that modulate the immune response.\nDespite their overarching function in the support and protection of neurons, glial cells have also been shown to play significant roles in the pathophysiology of many psychiatric and neurodegenerative diseases, such as Alzheimer’s, Parkinson’s Disease and multiple sclerosis." xsd:string {xref="DOI:10.1002/glia.24343", xref="DOI:10.1038/nn1988", xref="DOI:10.1101/cshperspect.a020602", xref="DOI:10.1126/science.aat0473", xref="DOI:10.3389/fncel.2017.00024"} [Term] id: CL:0000126 name: macroglial cell def: "A neuroglial cell of ectodermal origin, i.e., the astrocytes and oligodendrocytes considered together." [GOC:tfm, ISBN:0721662544] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "macroglia" RELATED OMO:0003004 [doi:10.1152/physrev.2001.81.2.871] synonym: "macrogliocyte" EXACT [] xref: BTO:0000771 @@ -593,6 +637,8 @@ def: "A class of large neuroglial (macroglial) cells in the central nervous syst comment: Astrocytes are reportedly CD68-negative, CD121a-positive, CD184-positive, CD192-positive, CRF-positive, EGFR-positive, GFAP-positive, GLUT1-positive, MBP-negative, and NGFR-positive. subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "astrocytic glia" EXACT [] xref: BTO:0000099 xref: CALOHA:TS-0060 @@ -608,6 +654,8 @@ def: "An hexagonal, flattened, mitochondria-rich endothelial cell that forms a m subset: cellxgene_subset subset: eye_upper_slim subset: human_reference_atlas +subset: human_subset +subset: mouse_subset xref: CALOHA:TS-0172 xref: FMA:70614 xref: ZFA:0009079 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} @@ -620,6 +668,8 @@ property_value: RO:0002175 NCBITaxon:9606 id: CL:0000133 name: neurectodermal cell def: "Ectoderm destined to be nervous tissue." [GOC:tfm, ISBN:068340007X] +subset: human_subset +subset: mouse_subset synonym: "neurectoderm cell" EXACT [] xref: ZFA:0009080 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000221 ! ectodermal cell @@ -630,6 +680,8 @@ name: mesenchymal stem cell def: "A connective tissue cell that normally gives rise to other cells that are organized as three-dimensional masses. In humans, this cell type is CD73-positive, CD90-positive, CD105-positive, CD45-negative, CD34-negative, and MHCII-negative. They may further differentiate into osteoblasts, adipocytes, myocytes, neurons, or chondroblasts in vitro. Originally described as residing in the bone marrow, this cell type is now known to reside in many, if not all, adult organs." [FB:ma, GOC:dsd, http://en.wikipedia.org/wiki/Mesenchymal_stem_cell, http://www.copewithcytokines.de/cope.cgi?key=mesenchymal%20stem%20cells, PMCID:PMC2613570, PMID:10102814, PMID:16923606, PMID:17986482, PMID:19960544] comment: Many but not all mesenchymal cells derive from the mesoderm. MSCs are reportedly CD3-negative, CD4-negative, CD5-negative, CD8-negative, CD11a-negative, CD11b-negative, CD14-negative, CD19-negative, CD29-positive, CD31-negative, CD34-negative, CD38-negative, CD40-negative, CD44-positive, CD45-negative, CD49-positive, CD54-positive, CD66b-negative, CD79a-negative, CD80-negative, CD102-positive, CD106-positive, CD117-positive, CD121a-positive, CD121b-positive, CD123-positive, CD124-positive, CD133-negative, CD146-positive, CD166-positive, CD271-positive, B220-negative, Gr1-negative, MHCI-positive, MHCII-negative, SSEA4-negative, sca1-positive, Ter119-negative, and glycophorin A-negative. Cultured MSCs are capable of producing stem cell factor, IL7, IL8, IL11, TGF-beta, cofilin, galectin-1, laminin-receptor 1, cyclophilin A, and MMP-2. subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "BMSC" RELATED OMO:0003000 [] synonym: "bone marrow stromal cells" NARROW [] synonym: "CFU-F" RELATED OMO:0003000 [] @@ -654,6 +706,8 @@ property_value: seeAlso "https://github.com/obophenotype/cell-ontology/issues/47 id: CL:0000147 name: pigment cell def: "A pigment cell is a cell that contains pigment granules." [GOC:tfm] +subset: human_subset +subset: mouse_subset synonym: "chromatocyte" EXACT [] synonym: "chromatophore" EXACT [] xref: VHOG:0001678 @@ -667,10 +721,13 @@ def: "A pigment cell derived from the neural crest. Contains melanin-filled pigm subset: cellxgene_subset subset: general_cell_types_upper_slim subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "melanophore" NARROW [] xref: BTO:0000847 xref: CALOHA:TS-0613 xref: FMA:70545 +xref: https://cellxgene.cziscience.com/cellguide/CL_0000148 xref: MESH:D008544 xref: VHOG:0001679 xref: ZFA:0009091 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} @@ -682,10 +739,13 @@ intersection_of: RO:0002202 CL:0000541 ! develops from melanoblast relationship: has_part GO:0042470 ! melanosome relationship: RO:0002202 CL:0000541 ! develops from melanoblast property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nMelanocytes are specialized cells prevalently found in the skin, but also present in the hair follicles, eyes, inner ear, bones, heart, and brain. Their primary function is the synthesis of melanin, a pigment responsible for coloration of skin, hair, and eyes. The presence and distribution of this pigment play a crucial role in the body's defense mechanism against harmful ultraviolet radiation.\nIn addition to melanin production, melanocytes also engage in a variety of other biological functions. They play a fundamental role in the immune response, owing to their ability to present antigens to T cells. Furthermore, they contribute to the maintenance of the skin's homeostasis by regulating processes such as extracellular matrix remodeling and cytokine production. A balance in melanocyte function is pivotal, as dysfunctions often result in dermatological disorders. For instance, the loss of melanocytes or reduction in their function may lead to hypopigmentation conditions such as vitiligo, whereas an abnormal increase could result in hyperpigmentation disorders or melanoma, a dangerous type of skin cancer." xsd:string {xref="DOI:10.1002/med.21754", xref="DOI:10.1038/nrc.2016.37", xref="DOI:10.1111/j.1751-1097.2007.00226.x", xref="DOI:10.3390/ijms21249769", xref="https://www.sciencedirect.com/topics/agricultural-and-biological-sciences/melanocyte"} [Term] id: CL:0000149 name: visual pigment cell +subset: human_subset +subset: mouse_subset synonym: "pigment cell" BROAD [] is_a: CL:0000147 ! pigment cell @@ -694,6 +754,8 @@ id: CL:0000151 name: secretory cell def: "A cell that specializes in controlled release of one or more substances." [GOC:tfm, ISBN:0721662544] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset xref: BTO:0003659 xref: FMA:86916 is_a: CL:0000000 ! cell @@ -706,6 +768,8 @@ id: CL:0000183 name: contractile cell def: "A cell whose primary function is to shorten." [FB:ma] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset is_a: CL:0000000 ! cell [Term] @@ -713,6 +777,8 @@ id: CL:0000187 name: muscle cell def: "A mature contractile cell, commonly known as a myocyte. This cell has as part of its cytoplasm myofibrils organized in various patterns." [MESH:D032342] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "muscle fiber" EXACT [] synonym: "myocyte" EXACT [] xref: BTO:0000888 @@ -735,6 +801,8 @@ def: "A non-striated, elongated, spindle-shaped cell found lining the digestive subset: cellxgene_subset subset: general_cell_types_upper_slim subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "myocytes, smooth muscle" EXACT [MESH:D032389] synonym: "non-striated muscle cell" BROAD [] synonym: "SMCs" EXACT [PMID:9315361] @@ -742,16 +810,20 @@ synonym: "smooth muscle fiber" EXACT [] xref: BTO:0004576 xref: CALOHA:TS-2159 xref: FMA:14072 +xref: https://cellxgene.cziscience.com/cellguide/CL_0000192 xref: ZFA:0009118 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0008000 ! non-striated muscle cell is_a: CL:0008007 ! visceral muscle cell relationship: RO:0002202 CL:0000514 ! develops from smooth muscle myoblast property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nSmooth muscle cells are a specialized type of muscle cells that are primarily found within the walls of hollow organs such as the intestine, stomach, bladder, uterus, and blood vessels. These cells are an essential component of the autonomic nervous system controling involuntary movements within the body.\nSmooth muscle cells play a vital role in many physiological processes due to their unique functionality. They can contract and relax in a slow, sustained, and controlled manner to help modulate the size and shape of the lumens of the organs they surround. For example, in the digestive system, coordinated contraction and relaxation of smooth muscle cells propels food along the gastrointestinal tract - a process known as peristalsis. In the blood vessels, the smooth muscle cells, by contracting or relaxing, either constrict or dilate the vessels, which in turn, help regulate blood flow and pressure.\nOn a cellular level, smooth muscle cells possess a single, centrally located nucleus and contain an arranged network of actin and myosin filaments, which are the proteins responsible for muscle contraction. Unlike their counterparts in skeletal or cardiac muscles, these cells lack specific contact points for these filaments, hence the lack of visible striations. Furthermore, the contraction of smooth muscle cells is regulated by hormones and neurotransmitters, such as acetylcholine and norepinephrine, adding an additional layer of complex regulation to these highly specialized cells." xsd:string {xref="DOI:10.1093/ptj/81.11.1810", xref="https://training.seer.cancer.gov/anatomy/muscular/types.html", xref="https://www.ncbi.nlm.nih.gov/books/NBK10854/", xref="https://www.ncbi.nlm.nih.gov/books/NBK526125", xref="https://www.ncbi.nlm.nih.gov/books/NBK556137/"} [Term] id: CL:0000197 name: sensory receptor cell def: "A cell that is capable of detection of a stimulus involved in sensory perception." [] +subset: human_subset +subset: mouse_subset synonym: "receptor cell" EXACT [] xref: MESH:D011984 is_a: CL:0000255 ! eukaryotic cell @@ -766,6 +838,8 @@ id: CL:0000210 name: photoreceptor cell def: "A cell specialized in detecting light stimuli that are involved in visual perception." [MESH:D010786] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset xref: BTO:0001060 xref: CALOHA:TS-0868 xref: FBbt:00004211 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} @@ -782,6 +856,8 @@ property_value: foaf:depiction "https://www.swissbiopics.org/api/image/Photorece id: CL:0000211 name: electrically active cell def: "A cell whose function is determined by the generation or the reception of an electric signal." [FB:ma] +subset: human_subset +subset: mouse_subset xref: ZFA:0009128 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000000 ! cell @@ -789,6 +865,8 @@ is_a: CL:0000000 ! cell id: CL:0000213 name: lining cell def: "A cell within an epithelial cell sheet whose main function is to act as an internal or external covering for a tissue or an organism." [JB:jb] +subset: human_subset +subset: mouse_subset synonym: "boundary cell" EXACT [] xref: ZFA:0009130 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000215 ! barrier cell @@ -797,6 +875,8 @@ is_a: CL:0000215 ! barrier cell id: CL:0000215 name: barrier cell def: "A cell whose primary function is to prevent the transport of stuff across compartments." [JB:jb] +subset: human_subset +subset: mouse_subset xref: ZFA:0009132 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000000 ! cell @@ -804,6 +884,8 @@ is_a: CL:0000000 ! cell id: CL:0000219 name: motile cell def: "A cell that moves by its own activities." [FB:ma] +subset: human_subset +subset: mouse_subset xref: ZFA:0009136 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000000 ! cell intersection_of: CL:0000000 ! cell @@ -814,6 +896,9 @@ relationship: capable_of GO:0048870 ! cell motility id: CL:0000221 name: ectodermal cell def: "A cell of the outer of the three germ layers of the embryo." [MESH:D004475] +subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "ectoderm cell" EXACT [] xref: FMA:72549 xref: ZFA:0009137 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} @@ -826,18 +911,24 @@ id: CL:0000222 name: mesodermal cell def: "A cell of the middle germ layer of the embryo." [MESH:D008648] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "mesoblast" EXACT [] synonym: "mesoderm cell" EXACT [] xref: FMA:72554 +xref: https://cellxgene.cziscience.com/cellguide/CL_0000222 xref: ZFA:0009138 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000255 ! eukaryotic cell is_a: CL:0002321 ! embryonic cell (metazoa) relationship: part_of UBERON:0000926 ! mesoderm +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nMesodermal cells are pluripotent and the most abundant in the human body. They contribute to the development of several structures such as the skeletal muscles, bones, heart and blood vessels, kidneys, gonads, connective tissues, and certain layers of the skin. Hence, the mesoderm is often regarded as an active and diverse layer due to its role in forming many bodily structures. \nIn embryonic development, these cells are instrumental, contributing to the body's structures through a carefully coordinated sequence of morphogenetic movements. This process forms the complex multicellular architecture of tissues and organs from a simple ball of cells. Without the function of mesodermal cells, the body's integral structures and systems would cease to form correctly, leading to developmental disorders such as axial mesodermal dysplasia complex" xsd:string {xref="DOI:10.1016/j.ceb.2019.07.012", xref="DOI:10.5535/arm.2016.40.1.162", xref="https://www.sciencedirect.com/topics/biochemistry-genetics-and-molecular-biology/mesoderm"} [Term] id: CL:0000223 name: endodermal cell def: "A cell of the inner of the three germ layers of the embryo." [MESH:D004707] +subset: human_subset +subset: mouse_subset synonym: "endoderm cell" EXACT [] xref: FMA:72555 xref: ZFA:0009139 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} @@ -852,6 +943,8 @@ def: "A red blood cell. In mammals, mature erythrocytes are biconcave disks cont subset: blood_and_immune_upper_slim subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "RBC" EXACT [] synonym: "red blood cell" EXACT [] xref: BTO:0000424 @@ -876,7 +969,8 @@ property_value: RO:0002175 NCBITaxon:9606 id: CL:0000255 name: eukaryotic cell def: "Any cell that in taxon some Eukaryota." [FBC:Autogenerated] -subset: cellxgene_subset +subset: human_subset +subset: mouse_subset xref: MESH:D005057 is_a: CL:0000000 ! cell intersection_of: CL:0000000 ! cell @@ -890,6 +984,8 @@ def: "Any photoreceptor cell that is part of some eye." [FBC:Autogenerated] subset: cellxgene_subset subset: eye_upper_slim subset: human_reference_atlas +subset: human_subset +subset: mouse_subset xref: ZFA:0009154 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000006 ! neuronal receptor cell is_a: CL:0000210 ! photoreceptor cell @@ -902,6 +998,8 @@ property_value: RO:0002175 NCBITaxon:9606 id: CL:0000293 name: structural cell def: "A cell whose primary function is to provide structural support, to provide strength and physical integrity to the organism." [TAIR:sr] +subset: human_subset +subset: mouse_subset xref: ZFA:0005745 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000000 ! cell @@ -909,6 +1007,8 @@ is_a: CL:0000000 ! cell id: CL:0000306 name: crystallin accumulating cell subset: eye_upper_slim +subset: human_subset +subset: mouse_subset synonym: "lens cell" EXACT [] is_a: CL:0000325 ! stuff accumulating cell @@ -916,6 +1016,8 @@ is_a: CL:0000325 ! stuff accumulating cell id: CL:0000325 name: stuff accumulating cell def: "A cell that is specialised to accumulate a particular substance(s)." [FB:ma] +subset: human_subset +subset: mouse_subset subset: ubprop:upper_level is_a: CL:0000000 ! cell @@ -923,6 +1025,8 @@ is_a: CL:0000000 ! cell id: CL:0000329 name: oxygen accumulating cell def: "Any cell that is capable of some oxygen transport." [FBC:Autogenerated] +subset: human_subset +subset: mouse_subset xref: ZFA:0009164 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000000 ! cell intersection_of: CL:0000000 ! cell @@ -933,6 +1037,8 @@ relationship: capable_of GO:0015671 ! oxygen transport id: CL:0000333 name: migratory neural crest cell def: "A cell derived from the specialized ectoderm flanking each side of the embryonic neural plate, which after the closure of the neural tube, forms masses of cells that migrate out from the dorsal aspect of the neural tube to spread throughout the body." [doi:10.1016/j.stem.2015.02.017] +subset: human_subset +subset: mouse_subset xref: FMA:86667 xref: ZFA:0007086 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000219 ! motile cell @@ -944,6 +1050,8 @@ relationship: RO:0002202 CL:0007004 ! develops from premigratory neural crest ce id: CL:0000335 name: mesenchyme condensation cell def: "A mesenchymal cell in embryonic development found in a contracting mass and that gives rise to osteoprogenitors." [GOC:tfm, PMID:5025404] +subset: human_subset +subset: mouse_subset xref: ZFA:0009166 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0008019 ! mesenchymal cell @@ -951,6 +1059,8 @@ is_a: CL:0008019 ! mesenchymal cell id: CL:0000339 name: glioblast (sensu Vertebrata) def: "An early neural cell developing from the early ependymal cell of the neural tube." [GOC:tfm, ISBN:0618947256] +subset: human_subset +subset: mouse_subset synonym: "spongioblast" EXACT [] xref: FMA:70564 xref: ZFA:0009169 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} @@ -962,6 +1072,8 @@ is_a: CL:0011026 ! progenitor cell id: CL:0000342 name: pigment cell (sensu Vertebrata) def: "Any animal cell containing pigment granules." [GOC:tfm, ISBN:0721662544] +subset: human_subset +subset: mouse_subset xref: ZFA:0009170 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000147 ! pigment cell is_a: CL:0000255 ! eukaryotic cell @@ -972,6 +1084,8 @@ id: CL:0000347 name: scleral cell def: "A cell of the sclera of the eye." [GOC:add] subset: eye_upper_slim +subset: human_subset +subset: mouse_subset xref: ZFA:0009174 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000255 ! eukaryotic cell is_a: CL:0000293 ! structural cell @@ -985,6 +1099,8 @@ id: CL:0000348 name: choroidal cell of the eye def: "A structural cell that is part of optic choroid." [GOC:add] subset: eye_upper_slim +subset: human_subset +subset: mouse_subset xref: ZFA:0009175 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000255 ! eukaryotic cell is_a: CL:0000293 ! structural cell @@ -997,12 +1113,16 @@ relationship: RO:0002202 CL:0000008 ! develops from migratory cranial neural cre id: CL:0000352 name: epiblast cell def: "A cell of the outer layer of a blastula that gives rise to the ectoderm after gastrulation." [GOC:tfm, ISBN:0618947256] +subset: human_subset +subset: mouse_subset is_a: CL:0000052 ! totipotent stem cell [Term] id: CL:0000365 name: animal zygote def: "Diploid cell produced by the fusion of sperm cell nucleus and egg cell." [ISBN:0471245208] +subset: human_subset +subset: mouse_subset synonym: "zygote" BROAD [] xref: BTO:0000854 xref: EHDAA2:0004546 @@ -1018,48 +1138,61 @@ relationship: RO:0002162 NCBITaxon:33208 ! in taxon Metazoa id: CL:0000393 name: electrically responsive cell def: "A cell whose function is determined by its response to an electric signal." [FB:ma] +subset: human_subset +subset: mouse_subset xref: ZFA:0009190 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000211 ! electrically active cell -[Term] -id: CL:0000402 -name: CNS interneuron -def: "An interneuron that has its cell body in a central nervous system." [doi:10.1016/B978-0-12-817424-1.00001-X] -comment: Interneurons are commonly described as being only found in the central nervous system. However, in CL we define 'interneuron' more broadly as any neuron that is neither a motor neuron nor a sensory neuron, regardless of its location, so we need this term to refer strictly to interneurons of the central nervous system. -subset: human_reference_atlas -xref: ZFA:0009191 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} -is_a: CL:0000099 ! interneuron -is_a: CL:2000029 ! central nervous system neuron -intersection_of: CL:0000099 ! interneuron -intersection_of: RO:0002100 UBERON:0001017 ! has soma location central nervous system -property_value: RO:0002175 NCBITaxon:9606 - [Term] id: CL:0000404 name: electrically signaling cell def: "A cell that initiates an electrical signal and passes that signal to another cell." [FB:ma] +subset: human_subset +subset: mouse_subset xref: ZFA:0009193 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000211 ! electrically active cell +[Term] +id: CL:0000499 +name: stromal cell +def: "A connective tissue cell of an organ found in the loose connective tissue." [GOC:tfm, MESH:D017154] +subset: cellxgene_subset +subset: general_cell_types_upper_slim +subset: human_reference_atlas +subset: human_subset +subset: mouse_subset +xref: BTO:0002064 +xref: FMA:83624 +xref: ZFA:0009226 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +is_a: CL:0002320 ! connective tissue cell +relationship: RO:0002202 CL:0000134 ! develops from mesenchymal stem cell +property_value: RO:0002175 NCBITaxon:9606 + [Term] id: CL:0000514 name: smooth muscle myoblast def: "A precursor cell destined to differentiate into smooth muscle myocytes." [GOC:tfm, MESH:D032390] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "myoblast, smooth muscle" EXACT [MESH:D032390] synonym: "satellite cell" RELATED [] xref: FMA:84798 +xref: https://cellxgene.cziscience.com/cellguide/CL_0000514 xref: ZFA:0009235 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000056 ! myoblast intersection_of: CL:0000056 ! myoblast intersection_of: RO:0002203 CL:0000192 ! develops into smooth muscle cell relationship: RO:0002203 CL:0000192 ! develops into smooth muscle cell +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nA precursor to the smooth muscle cell, the smooth muscle myoblast, is integral to various body systems, including the cardiovascular, gastrointestinal, and respiratory systems. Smooth muscle myoblasts arise from the differentiation of mesenchymal stem cells, a process tightly regulated by specific genetic factors and environmental signals. Their role extends to myogenesis, particularly in the formation of muscular tissue, especially during embryonic development.\nSmooth muscle myoblasts possess distinctive cellular characteristics. In contrast to skeletal muscle myoblasts, they do not fuse to create multinucleated fibers. Instead, they differentiate into individual, uninucleated smooth muscle cells. This differentiation unfolds in two distinct phases: proliferation, marked by rapid division to increase cell numbers, and differentiation, involving structural and functional transformation into mature smooth muscle cells. This intricate process is intricately mediated by various signaling molecules and transcription factors.\nFunctionally, smooth muscle myoblasts and the mature muscle cells they generate play pivotal roles in various physiological processes. Smooth muscle cells orchestrate involuntary muscle responses and are integral to body systems that regulate blood flow, propel food along the digestive tract, and control airflow in the respiratory tract. These diverse functions underscore the significance of smooth muscle myoblasts in the body's growth, maintenance, and overall function." xsd:string {xref="DOI:10.1074/jbc.RA118.001739", xref="https://www.ncbi.nlm.nih.gov/books/NBK544225/", xref="https://www.sciencedirect.com/topics/medicine-and-dentistry/smooth-muscle"} [Term] id: CL:0000526 name: afferent neuron def: "A neuron which conveys sensory information centrally from the periphery." [GOC:tfm, MESH:D009475] subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "input neuron" EXACT [] xref: FMA:87653 xref: ZFA:0009238 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} @@ -1070,6 +1203,8 @@ property_value: RO:0002175 NCBITaxon:9606 id: CL:0000529 name: pigmented epithelial cell subset: cellxgene_subset +subset: human_subset +subset: mouse_subset xref: ZFA:0009241 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000710 ! neurecto-epithelial cell @@ -1081,6 +1216,8 @@ comment: These cells are also reportedly CD4-negative and CD200-positive. They a subset: cellxgene_subset subset: general_cell_types_upper_slim subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "nerve cell" EXACT [] xref: BTO:0000938 xref: CALOHA:TS-0683 @@ -1101,6 +1238,8 @@ id: CL:0000541 name: melanoblast def: "A cell that originates from the neural crest and differentiates into a pigment cell." [GOC:tfm, SANBI:mhl] comment: Derived from UBERON:0002342 neural crest. +subset: human_subset +subset: mouse_subset xref: BTO:0003217 xref: FMA:83377 xref: ZFA:0009249 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} @@ -1114,12 +1253,13 @@ name: proerythroblast def: "An immature, nucleated erythrocyte occupying the stage of erythropoeisis that follows formation of erythroid progenitor cells. This cell is CD71-positive, has both a nucleus and a nucleolus, and lacks hematopoeitic lineage markers." [ISBN:0721601464, PMID:1638021] subset: blood_and_immune_upper_slim subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "pronormoblast" RELATED [] synonym: "rubriblast" EXACT [ISBN:0721601464] xref: FMA:83518 is_a: CL:0000764 {is_inferred="true"} ! erythroid lineage cell is_a: CL:0002242 ! nucleate cell -is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000764 ! erythroid lineage cell intersection_of: bearer_of PATO:0002505 ! nucleated intersection_of: bearer_of PATO:0040072 ! high nuclear/cytoplasmic ratio @@ -1158,6 +1298,8 @@ relationship: RO:0002202 CL:0000038 ! develops from erythroid progenitor cell id: CL:0000549 name: basophilic erythroblast def: "A nucleated immature erythrocyte, having cytoplasm generally similar to that of the earlier proerythroblast but sometimes even more basophilic, and usually regular in outline. The nucleus is still relatively large, but the chromatin strands are thicker and more deeply staining, giving a coarser appearance; the nucleoli have disappeared. This cell is CD71-positive and lacks hematopoeitic lineage markers." [GOC:tfm, ISBN:0721601464] +subset: human_subset +subset: mouse_subset synonym: "basophilic normoblast" EXACT [ISBN:0721601464] synonym: "early erythroblast" EXACT [ISBN:0721601464] synonym: "early normoblast" EXACT [ISBN:0721601464] @@ -1165,7 +1307,6 @@ synonym: "prorubricyte" EXACT [ISBN:0721601464] xref: FMA:83505 xref: ZFA:0005236 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000765 {is_inferred="true"} ! erythroblast -is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000765 ! erythroblast intersection_of: has_part CL:0017503 ! basophilic cytoplasm intersection_of: has_part GO:0000792 ! heterochromatin @@ -1178,6 +1319,8 @@ relationship: RO:0002104 PR:000001945 ! has plasma membrane part transferrin rec id: CL:0000550 name: polychromatophilic erythroblast def: "A nucleated, immature erythrocyte in which the nucleus occupies a relatively smaller part of the cell than in its precursor, the basophilic erythroblast. The cytoplasm is beginning to acquire hemoglobin and thus is no longer a purely basophilic, but takes on acidophilic aspects, which becomes progressively more marked as the cell matures. The chromatin of the nucleus is arranged in coarse, deeply staining clumps. This cell is CD71-positive and lacks hematopoeitic lineage markers." [ISBN:0721601464] +subset: human_subset +subset: mouse_subset synonym: "intermediate erythroblast" EXACT [ISBN:0721601464] synonym: "intermediate normoblast" EXACT [ISBN:0721601464] synonym: "polychromatic erythroblast" EXACT [ISBN:0721601464] @@ -1187,7 +1330,6 @@ synonym: "rubricyte" EXACT [ISBN:0721601464] xref: FMA:83506 xref: ZFA:0005241 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000765 {is_inferred="true"} ! erythroblast -is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000765 ! erythroblast intersection_of: has_part CL:0017504 ! polychromatophilic cytoplasm intersection_of: has_part GO:0000792 ! heterochromatin @@ -1201,6 +1343,8 @@ relationship: RO:0002202 CL:0000549 ! develops from basophilic erythroblast id: CL:0000552 name: orthochromatic erythroblast def: "The final stage of the nucleated, immature erythrocyte, before nuclear loss. Typically the cytoplasm is described as acidophilic, but it still shows a faint polychromatic tint. The nucleus is small and initially may still have coarse, clumped chromatin, as in its precursor, the polychromatophilic erythroblast, but ultimately it becomes pyknotic, and appears as a deeply staining, blue-black, homogeneous structureless mass. The nucleus is often eccentric and sometimes lobulated." [ISBN:0721601464] +subset: human_subset +subset: mouse_subset synonym: "acidophilic erythroblast" EXACT [ISBN:0721601464] synonym: "eosinophilic erythroblast" EXACT [ISBN:0721601464] synonym: "late erythoblast" EXACT [] @@ -1222,6 +1366,8 @@ def: "The earliest cytologically identifiable precursor in the thrombocytic seri comment: Lineage negative is described here as CD2-negative, CD3-negative, CD4-negative, CD5-negative, CD8a-negative, CD14-negative, CD19-negative, CD20-negative, CD56-negative, Ly6g-negative, and Ter119-negative. subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "CFU-Meg" EXACT [PMID:11722431, PMID:12482498] synonym: "colony-forming unit-megakaryocyte" EXACT [] synonym: "Meg-CFC" EXACT [PMCID:PMC1794060] @@ -1278,6 +1424,8 @@ comment: Megakaryocytes are reportedly CD181-positive and CD182-positive. subset: blood_and_immune_upper_slim subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "megacaryocyte" EXACT [] synonym: "megalocaryocyte" EXACT [] synonym: "megalokaryocyte" EXACT [] @@ -1296,12 +1444,13 @@ name: reticulocyte def: "An immature erythrocyte that changes the protein composition of its plasma membrane by exosome formation and extrusion. The types of protein removed differ between species though removal of the transferrin receptor is apparent in mammals and birds." [GOC:add, GOC:tfm, PMID:15946868, PMID:2037622] subset: blood_and_immune_upper_slim subset: cellxgene_subset +subset: human_subset +subset: mouse_subset xref: BTO:0001173 xref: CALOHA:TS-0864 xref: MESH:D012156 xref: ZFA:0009252 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000764 {is_inferred="true"} ! erythroid lineage cell -is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000764 ! erythroid lineage cell intersection_of: capable_of GO:0071971 ! extracellular exosome assembly intersection_of: CL:4030046 PR:000001002 ! lacks_plasma_membrane_part CD19 molecule @@ -1338,6 +1487,8 @@ def: "Interneuron of the vertebrate retina. They integrate, modulate, and interp subset: cellxgene_subset subset: eye_upper_slim subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "AC" RELATED OMO:0003000 [doi:10.1038/s41598-020-66092-9] synonym: "ACs" RELATED OMO:0003004 [doi:10.1038/s41598-020-66092-9] synonym: "amacrine neuron" EXACT [] @@ -1356,12 +1507,13 @@ id: CL:0000566 name: angioblastic mesenchymal cell def: "A mesenchymal stem cell capable of developing into blood vessel endothelium." [GOC:dsd, GOC:tfm, PMID:12768659] comment: These cells are reportedly CD31-positive, CD34-positive, CD144-positive, CD309-positive, and TAL1-positive. +subset: human_subset +subset: mouse_subset synonym: "angioblast" EXACT [] synonym: "chondroplast" EXACT [] xref: ZFA:0009258 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000134 {is_inferred="true"} ! mesenchymal stem cell is_a: CL:0011026 ! progenitor cell -is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000134 ! mesenchymal stem cell intersection_of: RO:0002104 PR:000001444 ! has plasma membrane part cadherin-5 intersection_of: RO:0002104 PR:000002112 ! has plasma membrane part vascular endothelial growth factor receptor 2 @@ -1377,6 +1529,8 @@ name: retinal cone cell def: "One of the two photoreceptor cell types in the vertebrate retina. In cones the photopigment is in invaginations of the cell membrane of the outer segment. Cones are less sensitive to light than rods, but they provide vision with higher spatial and temporal acuity, and the combination of signals from cones with different pigments allows color vision." [MESH:D017949] subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "cone" RELATED [doi:10.1038/s41598-020-66092-9] xref: BTO:0001036 xref: CALOHA:TS-0866 @@ -1393,6 +1547,8 @@ def: "An epithelial cell of the cornea." [GOC:tfm] subset: cellxgene_subset subset: eye_upper_slim subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "epithelial cell of cornea" EXACT [FMA:70551] xref: BTO:0004298 xref: CALOHA:TS-0173 @@ -1411,6 +1567,8 @@ name: retinal rod cell def: "One of the two photoreceptor cell types of the vertebrate retina. In rods the photopigment is in stacks of membranous disks separate from the outer cell membrane. Rods are more sensitive to light than cones, but rod mediated vision has less spatial and temporal resolution than cone vision." [MESH:D017948] subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "rod" RELATED [doi:10.1038/s41598-020-66092-9] xref: BTO:0001024 xref: CALOHA:TS-0870 @@ -1427,6 +1585,8 @@ def: "Astrocyte-like radial glial cell that extends vertically throughout the re subset: cellxgene_subset subset: eye_upper_slim subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "Muller cell" EXACT MISSPELLING [doi:10.21769/BioProtoc.4179] synonym: "Muller glia" EXACT [] synonym: "Müller cell" EXACT [] @@ -1443,6 +1603,8 @@ name: glutamatergic neuron def: "A neuron that is capable of some neurotansmission by glutamate secretion." [] subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset xref: FBbt:00100291 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: WBbt:0006829 xref: ZFA:0009290 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} @@ -1458,6 +1620,8 @@ id: CL:0000680 name: muscle precursor cell def: "A non-terminally differentiated cell that is capable of developing into a muscle cell." [GOC:add] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset xref: ZFA:0009291 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000055 ! non-terminally differentiated cell is_a: CL:0000255 ! eukaryotic cell @@ -1472,6 +1636,8 @@ name: radial glial cell def: "A cell present in the developing CNS. Functions as both a precursor cell and as a scaffold to support neuronal migration." [GOC:dph] comment: Unlike that of mammals, the brain of adult teleost fish exhibits an intense and widespread neurogenic activity as a result of the persistence of\nradial glial cells acting as neural progenitors throughout life. subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "forebrain radial glial cell" NARROW [] xref: ZFA:0009292 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000125 ! glial cell @@ -1482,6 +1648,8 @@ id: CL:0000710 name: neurecto-epithelial cell def: "Epithelial cells derived from neural plate and neural crest." [GOC:tfm] comment: The term "neuroepithelial cell" is used to describe both this cell type and sensory epithelial cell (CL:0000098). +subset: human_subset +subset: mouse_subset synonym: "neuroepithelial cell" BROAD [] xref: BTO:0004301 xref: FMA:70557 @@ -1495,6 +1663,8 @@ relationship: RO:0002202 CL:0000133 ! develops from neurectodermal cell id: CL:0000723 name: somatic stem cell def: "A stem cell that can give rise to cell types of the body other than those of the germ-line." [GO:0048103] +subset: human_subset +subset: mouse_subset xref: CALOHA:TS-2086 xref: MESH:D053687 xref: ZFA:0009307 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} @@ -1510,6 +1680,8 @@ def: "The set of neurons that receives neural inputs via bipolar, horizontal and subset: cellxgene_subset subset: eye_upper_slim subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "gangliocyte" EXACT [] synonym: "ganglion cell of retina" EXACT [] synonym: "RGC" RELATED OMO:0003000 [doi:10.1038/s41598-020-66092-9] @@ -1518,7 +1690,7 @@ xref: BTO:0001800 xref: FMA:67765 xref: MESH:D012165 xref: ZFA:0009310 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} -is_a: CL:0000117 ! CNS neuron (sensu Vertebrata) +is_a: CL:0000540 ! neuron relationship: RO:0002100 UBERON:0000966 ! has soma location retina property_value: RO:0002175 NCBITaxon:9606 @@ -1529,6 +1701,8 @@ def: "A neuron that laterally connects other neurons in the inner nuclear layer subset: cellxgene_subset subset: eye_upper_slim subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "HC" RELATED OMO:0003000 [doi:10.1038/s41598-020-66092-9] synonym: "HCs" RELATED OMO:0003004 [doi:10.1038/s41598-020-66092-9] synonym: "horizontal cell" EXACT [] @@ -1545,15 +1719,16 @@ def: "A bipolar neuron found in the retina and having connections with photorece subset: cellxgene_subset subset: eye_upper_slim subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "BC" RELATED OMO:0003000 [doi:10.1038/s41598-020-66092-9] synonym: "BCs" RELATED OMO:0003004 [doi:10.1038/s41598-020-66092-9] synonym: "BPs" RELATED OMO:0003004 [GSE137537] xref: ZFA:0009318 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} -is_a: CL:0000103 ! bipolar neuron is_a: CL:0000679 ! glutamatergic neuron is_a: CL:0008028 ! visual system neuron is_a: CL:0009004 ! retinal cell -intersection_of: CL:0000103 ! bipolar neuron +intersection_of: CL:0000540 ! neuron intersection_of: RO:0002100 UBERON:0001791 ! has soma location inner nuclear layer of retina relationship: RO:0002100 UBERON:0001791 ! has soma location inner nuclear layer of retina property_value: RO:0002175 NCBITaxon:9606 @@ -1563,6 +1738,8 @@ id: CL:0000763 name: myeloid cell def: "A cell of the monocyte, granulocyte, mast cell, megakaryocyte, or erythroid lineage." [GOC:add] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset xref: BTO:0001441 xref: CALOHA:TS-0647 xref: MESH:D022423 @@ -1580,6 +1757,8 @@ def: "A immature or mature cell in the lineage leading to and including erythroc comment: Note that in FMA erythropoietic cells are types of nucleated erythrocytes and thus don't include erythrocytes. subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "erythropoietic cell" EXACT [] xref: CALOHA:TS-0290 xref: FMA:62845 @@ -1594,6 +1773,8 @@ name: erythroblast def: "A nucleated precursor of an erythrocyte that lacks hematopoietic lineage markers." [GOC:add, ISBN:0721601464, PMID:18174176] subset: blood_and_immune_upper_slim subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "normoblast" EXACT [] xref: BTO:0001571 xref: CALOHA:TS-0289 @@ -1641,6 +1822,8 @@ comment: Markers differ between mouse and human. subset: blood_and_immune_upper_slim subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "hemopoietic progenitor cell" EXACT [] synonym: "MPP" EXACT [] xref: BTO:0000725 @@ -1648,7 +1831,6 @@ xref: CALOHA:TS-0448 xref: ZFA:0009354 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000255 ! eukaryotic cell is_a: CL:0008001 ! hematopoietic precursor cell -is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000988 ! hematopoietic cell intersection_of: bearer_of PATO:0001402 ! multipotent intersection_of: CL:4030046 PR:000001002 ! lacks_plasma_membrane_part CD19 molecule @@ -1691,6 +1873,8 @@ def: "A progenitor cell restricted to the myeloid lineage." [GOC:add, GOC:tfm, P comment: Note that this is a class of cell types, not an identified single cell type. subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "myeloid progenitor cell" BROAD [] xref: BTO:0004730 xref: CALOHA:TS-2099 @@ -1708,6 +1892,8 @@ id: CL:0000988 name: hematopoietic cell def: "A cell of a hematopoietic lineage." [GO_REF:0000031, GOC:add] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "haematopoietic cell" EXACT [] synonym: "haemopoietic cell" EXACT [] synonym: "hemopoietic cell" EXACT [] @@ -1723,6 +1909,8 @@ id: CL:0002031 name: hematopoietic lineage restricted progenitor cell def: "A hematopoietic progenitor cell that is capable of developing into only one lineage of hematopoietic cells." [GOC:tfm, PMID:19022770] subset: blood_and_immune_upper_slim +subset: human_subset +subset: mouse_subset is_a: CL:0000255 ! eukaryotic cell is_a: CL:0008001 ! hematopoietic precursor cell intersection_of: CL:0000988 ! hematopoietic cell @@ -1739,6 +1927,8 @@ name: hematopoietic oligopotent progenitor cell def: "A hematopoietic oligopotent progenitor cell that has the ability to differentiate into limited cell types but lacks lineage cell markers and self renewal capabilities." [GOC:tfm, https://orcid.org/0000-0001-5208-3432, PMID:19022770] comment: This cell type is intended to be compatible with any vertebrate hematopoietic oligopotent progenitor cell. For mammalian hematopoietic oligopotent progenitor cells known to be lineage-negative, please use the term 'hematopoietic oligopotent progenitor cell' (CL_0001060). subset: blood_and_immune_upper_slim +subset: human_subset +subset: mouse_subset is_a: CL:0000255 ! eukaryotic cell is_a: CL:0008001 ! hematopoietic precursor cell intersection_of: CL:0000988 ! hematopoietic cell @@ -1752,6 +1942,8 @@ creation_date: 2010-01-06T03:43:27Z id: CL:0002077 name: ecto-epithelial cell def: "An epithelial cell derived from ectoderm." [FMA:69074, GOC:tfm] +subset: human_subset +subset: mouse_subset xref: FMA:69074 xref: ZFA:0009385 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000066 ! epithelial cell @@ -1765,6 +1957,8 @@ creation_date: 2010-06-29T03:38:22Z id: CL:0002078 name: meso-epithelial cell def: "Epithelial cell derived from mesoderm or mesenchyme." [FMA:69076, GOC:tfm] +subset: human_subset +subset: mouse_subset synonym: "epithelial mesenchymal cell" EXACT [] xref: FMA:69076 xref: ZFA:0009388 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} @@ -1781,19 +1975,25 @@ name: endothelial cell of vascular tree def: "An endothelial cell of the vascular tree, which includes blood vessels and lymphatic vessels." [GOC:dsd, GOC:tfm, PMID:12768659] comment: These cells are reportedly CD31-positive, CD34-positive, CD144-positive, TAL1-positive. subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "cubodial endothelial cell of vascular tree" NARROW [] synonym: "vascular endothelial cell" EXACT [] xref: BTO:0001854 xref: CALOHA:TS-1106 xref: FMA:67755 +xref: https://cellxgene.cziscience.com/cellguide/CL_0002139 is_a: CL:0000115 ! endothelial cell property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nEndothelial cells of the vascular tree, commonly referred to as vascular endothelial cells, line the entire circulatory system, from the heart to the smallest capillaries. These cells have a unique, flattened shape, and are tightly bound together, forming a thin layer known as the endothelium. The endothelium is responsible for maintaining the interior surface of blood vessels, and plays a critical role in ensuring the smooth flow of blood. \nVascular endothelial cells act as a semi-permeable membrane, controlling the passage of materials and the transit of white blood cells into and out of the bloodstream. These cells are also involved in blood coagulation. When a blood vessel is damaged, endothelial cells promote clotting to prevent excessive bleeding and facilitate wound healing. Other functions include regulation of blood pressure and blood volume by releasing vasodilators and vasoconstrictors to either widen or constrict blood vessels, accordingly.\nFurthermore, the endothelial cells are crucial in the formation of new blood vessels, a process known as angiogenesis. This is particularly important in wound healing and the growth of new tissues during development or after injury. In the context of diseases such as cancer, angiogenesis helps facilitate tumor growth by providing nutrients and oxygen." xsd:string {xref="DOI:10.1038/s41569-022-00770-1", xref="DOI:10.1186/s12872-015-0124-z", xref="DOI:10.3389/fphys.2022.863265/full", xref="https://www.sciencedirect.com/topics/medicine-and-dentistry/vascular-endothelial-cell"} creation_date: 2010-08-24T02:06:40Z [Term] id: CL:0002159 name: general ecto-epithelial cell def: "Epithelial cells derived from general body ectoderm and ectoderm placodes." [GOC:tfm] +subset: human_subset +subset: mouse_subset xref: FMA:70556 is_a: CL:0002077 ! ecto-epithelial cell property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 @@ -1804,6 +2004,8 @@ id: CL:0002222 name: vertebrate lens cell def: "A cell comprising the transparent, biconvex body separating the posterior chamber and vitreous body, and constituting part of the refracting mechanism of the mammalian eye." [GOC:tfm, ISBN:0721662544] subset: eye_upper_slim +subset: human_subset +subset: mouse_subset xref: FMA:70950 is_a: CL:0000066 ! epithelial cell is_a: CL:0000306 ! crystallin accumulating cell @@ -1815,6 +2017,8 @@ creation_date: 2010-09-07T10:38:03Z id: CL:0002242 name: nucleate cell def: "A cell containing at least one nucleus." [GOC:tfm] +subset: human_subset +subset: mouse_subset xref: FMA:67513 is_a: CL:0000000 ! cell intersection_of: CL:0000000 ! cell @@ -1831,6 +2035,8 @@ comment: In a consensus model of unidirectional secretion, aqueous humour is for subset: cellxgene_subset subset: eye_upper_slim subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "PE cell" EXACT [https://doi.org/10.1016/j.exer.2003.09.021] xref: FMA:70606 xref: https://cellxgene.cziscience.com/cellguide/CL_0002303 @@ -1838,7 +2044,7 @@ is_a: CL:0000529 ! pigmented epithelial cell relationship: part_of UBERON:0001778 ! ciliary epithelium property_value: RO:0002175 NCBITaxon:9606 property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 -property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional.\n\nPigmented ciliary epithelial cells, which are a type of pigment cell, have a crucial function within the eye's ciliary body. The ciliary body, located behind the iris, is one of the eye’s most vital structures and consists of two types of epithelial cells: the pigmented and the non-pigmented ciliary epithelial cells. The pigmented ciliary epithelial cells form the outer layer of the ciliary body and exhibit a black or brown pigmentation due to the melanin they contain.\nOne key function of pigmented ciliary epithelial cells is to aid in the formation of aqueous humor, an intraocular fluid that nourishes the cornea and lens, and maintains intraocular pressure which is essential for the eye’s shape and light refraction. These cells facilitate this function in conjunction with the non-pigmented ciliary epithelial cells. Together, the pigmented and non-pigmented ciliary epithelial cells form a bilayer epithelium that allows the secretion of aqueous humor through a bi-directional fluid transport mechanism.\nPigmented ciliary epithelial cells also contribute to the blood-aqueous barrier, a physiological frontier that controls the entry and exit of various substances from the blood to the aqueous humor and vice versa. The pigmentation in these cells, intensified by melanin, helps to absorb scattered light coming into the eye, reducing any potential damage and glare." xsd:string {xref="DOI:10.1016/S1569-2590(05)10005-6", xref="DOI:10.1111/j.1444-0938.2002.tb02384.x"} +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nPigmented ciliary epithelial cells, which are a type of pigment cell, have a crucial function within the eye's ciliary body. The ciliary body, located behind the iris, is one of the eye’s most vital structures and consists of two types of epithelial cells: the pigmented and the non-pigmented ciliary epithelial cells. The pigmented ciliary epithelial cells form the outer layer of the ciliary body and exhibit a black or brown pigmentation due to the melanin they contain.\nOne key function of pigmented ciliary epithelial cells is to aid in the formation of aqueous humor, an intraocular fluid that nourishes the cornea and lens, and maintains intraocular pressure which is essential for the eye’s shape and light refraction. These cells facilitate this function in conjunction with the non-pigmented ciliary epithelial cells. Together, the pigmented and non-pigmented ciliary epithelial cells form a bilayer epithelium that allows the secretion of aqueous humor through a bi-directional fluid transport mechanism.\nPigmented ciliary epithelial cells also contribute to the blood-aqueous barrier, a physiological frontier that controls the entry and exit of various substances from the blood to the aqueous humor and vice versa. The pigmentation in these cells, intensified by melanin, helps to absorb scattered light coming into the eye, reducing any potential damage and glare." xsd:string {xref="DOI:10.1016/S1569-2590(05)10005-6", xref="DOI:10.1111/j.1444-0938.2002.tb02384.x"} creation_date: 2010-09-13T04:09:27Z [Term] @@ -1849,6 +2055,8 @@ comment: In a consensus model of unidirectional secretion, aqueous humour is for subset: cellxgene_subset subset: eye_upper_slim subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "nonpigmented ciliary epithelial cell" EXACT [PMID:10913011] synonym: "NPE cell" EXACT [https://doi.org/10.1016/j.exer.2003.09.021] xref: FMA:70607 @@ -1863,6 +2071,8 @@ id: CL:0002319 name: neural cell def: "A cell that is part of the nervous system." [GOC:tfm, ISBN:0618947256] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset xref: CALOHA:TS-2040 xref: FMA:70333 is_a: CL:0000255 ! eukaryotic cell @@ -1877,6 +2087,8 @@ id: CL:0002320 name: connective tissue cell def: "A cell of the supporting or framework tissue of the body, arising chiefly from the embryonic mesoderm and including adipose tissue, cartilage, and bone." [GOC:tfm, ISBN:0618947256] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset xref: CALOHA:TS-2096 xref: FMA:63875 xref: MESH:D003239 @@ -1892,12 +2104,16 @@ creation_date: 2010-09-15T03:01:54Z id: CL:0002321 name: embryonic cell (metazoa) def: "A cell of the embryo." [FMA:0618947256] +subset: human_subset +subset: mouse_subset xref: CALOHA:TS-0263 xref: FMA:82840 +xref: https://cellxgene.cziscience.com/cellguide/CL_0002321 xref: WBbt:0007028 xref: ZFA:0007089 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000000 ! cell property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nEmbryonic cells in metazoans, which include all multicellular animals, are biological units in their earliest developmental stages from conception until the organism is fully formed. \nThey are derived from a fertilized egg, which undergoes a series of cell divisions to produce a multicellular organism. During the early phases of embryonic development, these cells exhibit pluripotency, meaning they possess the potential to differentiate into a diverse array of specialized cell types that constitute different body tissues and structures. \nThe balance between cell proliferation and differentiation in embryonic cells is crucial for successful development. When cells continue to divide without differentiating, overgrowth may occur leading to conditions such as teratomas (tumors of embryonic cells). Conversely, if cell differentiation proceeds at the expense of cell proliferation, developmental anomalies could occur regarding size or mass of the organism or its parts." xsd:string {xref="DOI:10.1002/iub.1404", xref="DOI:10.1093/molehr/gan048", xref="https://www.ncbi.nlm.nih.gov/books/NBK9906/"} creation_date: 2010-09-15T03:39:21Z [Term] @@ -1907,6 +2123,8 @@ def: "A keratocyte is a specialized fibroblast residing in the cornea stroma th subset: cellxgene_subset subset: eye_upper_slim subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "corneal fibroblast" EXACT [] synonym: "corneal keratocyte" EXACT [] is_a: CL:0000005 ! neural crest derived fibroblast @@ -1922,6 +2140,8 @@ id: CL:0002485 name: retinal melanocyte def: "A melanocyte of the retina. This cell type is distinct from pigmented retinal epithelium." [GOC:tfm, MP:0010190] subset: eye_upper_slim +subset: human_subset +subset: mouse_subset is_a: CL:0000148 ! melanocyte is_a: CL:0009004 ! retinal cell intersection_of: CL:0000148 ! melanocyte @@ -1935,6 +2155,8 @@ id: CL:0002494 name: cardiocyte def: "A cell located in the heart, including both muscle and non muscle cells." [GOC:tfm] comment: From Onard of the FMA: Cardiac muscle cell or cardiac myocyte is a striated muscle cell. Cardiocyte on the other hand is any cell in the heart which includes cells other than muscle cells (e.g. endothelial cell of endocardium). Unless there is a consensus among anatomists that cardiocytes refer only to muscle cells, we will treat them as a general class of cells in the heart. +subset: human_subset +subset: mouse_subset synonym: "heart cell" EXACT [] xref: BTO:0001539 xref: CALOHA:TS-0115 @@ -1951,8 +2173,11 @@ creation_date: 2010-12-07T09:37:22Z id: CL:0002565 name: iris pigment epithelial cell def: "A pigment cell located in the epithelium of the iris." [GOC:tfm] +subset: cellxgene_subset subset: eye_upper_slim subset: human_reference_atlas +subset: human_subset +subset: mouse_subset is_a: CL:0000066 ! epithelial cell is_a: CL:0000342 {is_inferred="true"} ! pigment cell (sensu Vertebrata) intersection_of: CL:0000342 ! pigment cell (sensu Vertebrata) @@ -1969,6 +2194,8 @@ def: "A blood vessel endothelial cell that is part of the retina." [GOC:tfm] subset: cellxgene_subset subset: eye_upper_slim subset: human_reference_atlas +subset: human_subset +subset: mouse_subset xref: https://cellxgene.cziscience.com/cellguide/CL_0002585 is_a: CL:0000071 {is_inferred="true"} ! blood vessel endothelial cell is_a: CL:0009004 ! retinal cell @@ -1977,7 +2204,7 @@ intersection_of: part_of UBERON:0000966 ! retina relationship: part_of UBERON:0000966 ! retina property_value: RO:0002175 NCBITaxon:9606 property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 -property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional.\n\nRetinal blood vessel endothelial cells constitute the innermost lining of the blood vessels found in the retina, the light-sensitive layer of tissue at the back of the eye. The primary role of these cells revolves around their location within the retinal vascular system, forming the structure of the blood-retinal barrier, a subset of the larger blood-ocular barrier system. \nThe endothelial cells are particularly involved in the growth of new retinal blood vessels from pre-existing ones (angiogenesis); this is critical in managing the amount of oxygen and essential nutrients delivered to the ocular tissues. They are crucial for maintaining homeostasis in the retinal environment by controlling the exchange of molecules between the blood and the retina. Furthermore, they mediate immune cell trafficking, supporting the immune privilege of the eye by preventing the unrestricted infiltration of inflammatory cells into the retina, thus maintaining ocular health and normal vision.\nThe malfunction or dysfunction of retinal blood vessel endothelial cells is implicated in numerous ocular pathologies, particularly diabetic retinopathy, which is one of the leading causes of blindness worldwide. In such conditions, the compromise in the integrity of the blood-retinal barrier and excess angiogenesis can lead to retinal edema and pathological neovascularization, resulting in vision loss." xsd:string {xref="DOI:0.1016/j.preteyeres.2015.08.001", xref="DOI:10.1016/j.preteyeres.2012.08.004", xref="DOI:10.1038/nature04482", xref="DOI:10.5301/EJO.2010.6049"} +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nRetinal blood vessel endothelial cells constitute the innermost lining of the blood vessels found in the retina, the light-sensitive layer of tissue at the back of the eye. The primary role of these cells revolves around their location within the retinal vascular system, forming the structure of the blood-retinal barrier, a subset of the larger blood-ocular barrier system. \nThe endothelial cells are particularly involved in the growth of new retinal blood vessels from pre-existing ones (angiogenesis); this is critical in managing the amount of oxygen and essential nutrients delivered to the ocular tissues. They are crucial for maintaining homeostasis in the retinal environment by controlling the exchange of molecules between the blood and the retina. Furthermore, they mediate immune cell trafficking, supporting the immune privilege of the eye by preventing the unrestricted infiltration of inflammatory cells into the retina, thus maintaining ocular health and normal vision.\nThe malfunction or dysfunction of retinal blood vessel endothelial cells is implicated in numerous ocular pathologies, particularly diabetic retinopathy, which is one of the leading causes of blindness worldwide. In such conditions, the compromise in the integrity of the blood-retinal barrier and excess angiogenesis can lead to retinal edema and pathological neovascularization, resulting in vision loss." xsd:string {xref="DOI:0.1016/j.preteyeres.2015.08.001", xref="DOI:10.1016/j.preteyeres.2012.08.004", xref="DOI:10.1038/nature04482", xref="DOI:10.5301/EJO.2010.6049"} creation_date: 2011-03-06T03:28:27Z [Term] @@ -1987,6 +2214,8 @@ def: "An epithelial cell of the retinal pigmented epithelium." [GOC:tfm] subset: cellxgene_subset subset: eye_upper_slim subset: human_reference_atlas +subset: human_subset +subset: mouse_subset xref: BTO:0004910 xref: FMA:75802 xref: https://cellxgene.cziscience.com/cellguide/CL_0002586 @@ -1999,13 +2228,16 @@ relationship: has_part GO:0042470 ! melanosome relationship: part_of UBERON:0001782 ! pigmented layer of retina property_value: RO:0002175 NCBITaxon:9606 property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 -property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional.\n\nRetinal pigment epithelial (RPE) cells form a single layer of cells at the back of the eye sandwiched between the neurosensory retina and the choroid, playing a significant role in maintaining vision health. These pigment-laden cells are highly specialized and perform an array of metabolic and transport functions essential for the maintenance of the photoreceptor cells (rods and cones) in the retina. The pigmentation of RPE cells actively aids in the absorption of excess light and the prevention of light scattering, thus enhancing the eye's optical properties.\nThe retinal pigment epithelium forms a key part of the blood/retina barrier. The cells have long sheet-like microvilli on their apical membrane that project into the light-sensitive outer segments of the photoreceptors, forming a close structural interaction. The basolateral membrane of the RPE interacts with the underlying Bruch’s membrane, which separates the RPE cells from fenestrated endothelium of the choriocapillaris. \nRPE cells support the photoreceptor by providing them with oxygen and nutrients (such as glucose, retinol and fatty acids) and removing waste products. They also recycle the visual pigment, in a process called the \"visual cycle\", where the RPE cells play a vital role in the regeneration of visual pigment (11-cis retinol) following the absorption of light. This is essential for the maintenance of photoreceptor excitability.\nBeyond this, RPE cells take part in the phagocytosis process, where they digest the shed ends of photoreceptor outer segments, thus, preventing the build-up of waste residue that could otherwise harm retinal health. They also secrete various factors, including growth factors required to maintain the structural integrity of choriocapillaris endothelium and photoreceptors, as well as immunosuppressive factors that play an important role in establishing the immune privilege of the eye." xsd:string {xref="DOI:10.1111/febs.16018", xref="DOI:10.1152/physrev.00021.2004", xref="DOI:10.3389/fphar.2021.727870/full", xref="https://www.sciencedirect.com/topics/chemistry/retinal-pigment"} +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nRetinal pigment epithelial (RPE) cells form a single layer of cells at the back of the eye sandwiched between the neurosensory retina and the choroid, playing a significant role in maintaining vision health. These pigment-laden cells are highly specialized and perform an array of metabolic and transport functions essential for the maintenance of the photoreceptor cells (rods and cones) in the retina. The pigmentation of RPE cells actively aids in the absorption of excess light and the prevention of light scattering, thus enhancing the eye's optical properties.\nThe retinal pigment epithelium forms a key part of the blood/retina barrier. The cells have long sheet-like microvilli on their apical membrane that project into the light-sensitive outer segments of the photoreceptors, forming a close structural interaction. The basolateral membrane of the RPE interacts with the underlying Bruch’s membrane, which separates the RPE cells from fenestrated endothelium of the choriocapillaris. \nRPE cells support the photoreceptor by providing them with oxygen and nutrients (such as glucose, retinol and fatty acids) and removing waste products. They also recycle the visual pigment, in a process called the \"visual cycle\", where the RPE cells play a vital role in the regeneration of visual pigment (11-cis retinol) following the absorption of light. This is essential for the maintenance of photoreceptor excitability.\nBeyond this, RPE cells take part in the phagocytosis process, where they digest the shed ends of photoreceptor outer segments, thus, preventing the build-up of waste residue that could otherwise harm retinal health. They also secrete various factors, including growth factors required to maintain the structural integrity of choriocapillaris endothelium and photoreceptors, as well as immunosuppressive factors that play an important role in establishing the immune privilege of the eye." xsd:string {xref="DOI:10.1111/febs.16018", xref="DOI:10.1152/physrev.00021.2004", xref="DOI:10.3389/fphar.2021.727870/full", xref="https://www.sciencedirect.com/topics/chemistry/retinal-pigment"} creation_date: 2011-03-06T03:37:09Z [Term] id: CL:0002672 name: retinal progenitor cell def: "A multi-fate stem cell that can give rise to different retinal cell types including rod and cone cells." [GOC:tfm, PMID:20959166, PMID:21148186] +subset: cellxgene_subset +subset: human_subset +subset: mouse_subset is_a: CL:0000048 ! multi fate stem cell relationship: RO:0002202 CL:0000133 ! develops from neurectodermal cell property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 @@ -2016,8 +2248,10 @@ id: CL:0005000 name: spinal cord interneuron def: "A CNS interneuron located in the spinal cord." [CL:CVS] comment: Is_a interneuron, part_of UBERON:0002240. +subset: human_subset +subset: mouse_subset xref: ZFA:0000778 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} -is_a: CL:0000402 {is_inferred="true"} ! CNS interneuron +is_a: CL:0000099 {is_inferred="true"} ! interneuron intersection_of: CL:0000099 ! interneuron intersection_of: RO:0002100 UBERON:0002240 ! has soma location spinal cord relationship: RO:0002100 UBERON:0002240 ! has soma location spinal cord @@ -2026,6 +2260,8 @@ relationship: RO:0002100 UBERON:0002240 ! has soma location spinal cord id: CL:0007004 name: premigratory neural crest cell def: "Cell that is part of the neural crest region of the neuroepithelium, prior to migration. Note that not all premigratory neural crest cells may become migratory neural crest cells." [UBERONREF:0000002] +subset: human_subset +subset: mouse_subset xref: ZFA:0007084 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0011012 ! neural crest cell relationship: part_of UBERON:0002342 ! neural crest @@ -2037,6 +2273,8 @@ creation_date: 2012-06-27T08:27:35Z id: CL:0008000 name: non-striated muscle cell def: "Any muscle cell in which the fibers are not organised into sarcomeres." [GOC:DOS] +subset: human_subset +subset: mouse_subset is_a: CL:0000187 ! muscle cell [Term] @@ -2044,12 +2282,16 @@ id: CL:0008001 name: hematopoietic precursor cell def: "Any hematopoietic cell that is a precursor of some other hematopoietic cell type." [GOC:dos] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset is_a: CL:0000988 ! hematopoietic cell [Term] id: CL:0008007 name: visceral muscle cell def: "A muscle cell that is part of some visceral muscle." [GOC:dos] +subset: human_subset +subset: mouse_subset xref: FBbt:00005070 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} is_a: CL:0000187 ! muscle cell intersection_of: CL:0000187 ! muscle cell @@ -2062,6 +2304,8 @@ name: mesenchymal cell def: "A non-polarised cell precursor cell that is part of some mesenchyme, is associated with the cell matrix but is not connected to other cells and is capable of migration." [] subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "mesenchyme cell" EXACT [] is_a: CL:0000219 ! motile cell is_a: CL:0000255 ! eukaryotic cell @@ -2073,6 +2317,8 @@ property_value: RO:0002175 NCBITaxon:9606 id: CL:0008028 name: visual system neuron def: "Any neuron that is capable of part of some visual perception." [FBC:Autogenerated] +subset: human_subset +subset: mouse_subset is_a: CL:0000540 ! neuron intersection_of: CL:0000540 ! neuron intersection_of: capable_of_part_of GO:0007601 ! visual perception @@ -2085,6 +2331,8 @@ id: CL:0009004 name: retinal cell def: "Any cell in the retina, the innermost layer or coating at the back of the eyeball, which is sensitive to light and in which the optic nerve terminates." [GOC:pr] subset: general_cell_types_upper_slim +subset: human_subset +subset: mouse_subset xref: PMID:10702418 is_a: CL:0002319 ! neural cell intersection_of: CL:0002319 ! neural cell @@ -2095,6 +2343,8 @@ relationship: part_of UBERON:0005388 ! photoreceptor array id: CL:0010009 name: camera-type eye photoreceptor cell def: "Any photoreceptor cell that is part of some camera-type eye." [FBC:Autogenerated] +subset: human_subset +subset: mouse_subset synonym: "camera type eye photoreceptor cell" EXACT [] is_a: CL:0000287 ! eye photoreceptor cell is_a: CL:0009004 ! retinal cell @@ -2106,6 +2356,8 @@ relationship: part_of UBERON:0000966 {seeAlso="https://github.com/obophenotype/c id: CL:0010017 name: zygote def: "A zygote in a plant or an animal." [] +subset: human_subset +subset: mouse_subset xref: MESH:D015053 is_a: CL:0000000 ! cell property_value: seeAlso https://github.com/obophenotype/cell-ontology/issues/786 @@ -2115,16 +2367,20 @@ id: CL:0011012 name: neural crest cell def: "A cell of the neural crest. Neural crest cells are multipotent. Premigratory neural crest cells are found at the neural plate boarder, some of which will undergo ectomesynchymal transition and delamination to form migratory neural crest cells." [https://orcid.org/0000-0001-5208-3432, https://orcid.org/0000-0002-9900-7880] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset xref: https://cellxgene.cziscience.com/cellguide/CL_0011012 is_a: CL:0000048 ! multi fate stem cell is_a: CL:0002321 ! embryonic cell (metazoa) -property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional.\n\nNeural crest cells are a group of transient and highly migratory cells that originate from the neuroectoderm during the early stages of embryonic development. They are multipotent cells with an exceptional degree of plasticity, capable of differentiating into various somatic cell types and therefore play a fundamental role in the formation of various organs and tissues, making them critical contributors to the developing embryo. \nAfter the initiation of neurulation (the formation of the neural tube) neural crest cells start to undergo epithelial-to-mesenchymal transition and delaminate and migrate from the dorsal neural tube to several regions throughout the embryo. They differentiate into a range of diverse cell types, such as neurons and glial cells of the peripheral nervous system, including sensory and autonomic neurons. They also contribute to the formation of adrenal glands, pigment cells in the skin (melanocytes), cardiac structures, including parts of the heart septum and major arteries, as well as bones and cartilage of the face and skull.\nDisorders or aberrations in the development or migration of the neural crest cells can lead to serious congenital malformations, such as neurocristopathies, including Hirschsprung disease, neuroblastoma, and neurofibromatosis." xsd:string {xref="DOI:10.1002/dvg.23276", xref="DOI:10.1242/dev.193193", xref="DOI:10.3389/fcell.2020.00635/full", xref="https://doi.org/10.1016/j.ydbio.2011.12.042"} +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nNeural crest cells are a group of transient and highly migratory cells that originate from the neuroectoderm during the early stages of embryonic development. They are multipotent cells with an exceptional degree of plasticity, capable of differentiating into various somatic cell types and therefore play a fundamental role in the formation of various organs and tissues, making them critical contributors to the developing embryo. \nAfter the initiation of neurulation (the formation of the neural tube) neural crest cells start to undergo epithelial-to-mesenchymal transition and delaminate and migrate from the dorsal neural tube to several regions throughout the embryo. They differentiate into a range of diverse cell types, such as neurons and glial cells of the peripheral nervous system, including sensory and autonomic neurons. They also contribute to the formation of adrenal glands, pigment cells in the skin (melanocytes), cardiac structures, including parts of the heart septum and major arteries, as well as bones and cartilage of the face and skull.\nDisorders or aberrations in the development or migration of the neural crest cells can lead to serious congenital malformations, such as neurocristopathies, including Hirschsprung disease, neuroblastoma, and neurofibromatosis." xsd:string {xref="DOI:10.1002/dvg.23276", xref="DOI:10.1242/dev.193193", xref="DOI:10.3389/fcell.2020.00635/full", xref="https://doi.org/10.1016/j.ydbio.2011.12.042"} [Term] id: CL:0011026 name: progenitor cell def: "A precursor cell that has a tendency to differentiate into a specific type of cell. They are descendants of stem cells, only they are more constrained in their differentiation potential or capacity for self-renewal, and are often more limited in both senses." [https://doi.org/10.1016/B978-0-12-409503-8.00002-0, ISBN:978-1-62808-994-3] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset is_a: CL:0000255 ! eukaryotic cell is_a: CL:0011115 ! precursor cell intersection_of: CL:0011115 ! precursor cell @@ -2138,6 +2394,8 @@ name: interplexiform cell def: "A type of interneuron in the retinal inner nuclear layer which\ncarries information from the inner plexiform layer and the outer\nplexiform layer." [GOC:NV, PMID:12771169] comment: Need to MIREOT retinal inner nuclear layer (part of) subset: eye_upper_slim +subset: human_subset +subset: mouse_subset is_a: CL:0000099 ! interneuron is_a: CL:0009004 ! retinal cell relationship: part_of UBERON:0001791 ! inner nuclear layer of retina @@ -2148,6 +2406,8 @@ name: precursor cell def: "A cell that, by division or terminal differentiation, can give rise to other cell types." [GOC:dos] comment: Work is needed on GO 'cell differentiation' before it is clear whether the equivalent class definition 'native cell' that capable_of some 'cell differentiation' works. Also, may want to consider merging this with non-terminally differentiated cell. subset: cellxgene_subset +subset: human_subset +subset: mouse_subset is_a: CL:0000000 ! cell intersection_of: CL:0000000 ! cell intersection_of: capable_of GO:0030154 ! cell differentiation @@ -2193,6 +2453,8 @@ name: conjunctival epithelial cell def: "An epithelial cell that is part of the conjunctiva." [GOC:tfm] subset: cellxgene_subset subset: eye_upper_slim +subset: human_subset +subset: mouse_subset synonym: "epithelial cell of conjunctiva" EXACT [FMA:70552] xref: FMA:70552 is_a: CL:0000066 {is_inferred="true"} ! epithelial cell @@ -2206,17 +2468,23 @@ name: ciliary muscle cell def: "A smooth muscle cell that is part of the ciliary body." [GOC:tfm] subset: cellxgene_subset subset: eye_upper_slim +subset: human_subset +subset: mouse_subset synonym: "smooth muscle cell of ciliary body" EXACT [FMA:70610] xref: FMA:70610 +xref: https://cellxgene.cziscience.com/cellguide/CL_1000443 is_a: CL:0000192 {is_inferred="true"} ! smooth muscle cell intersection_of: CL:0000192 ! smooth muscle cell intersection_of: part_of UBERON:0001775 ! ciliary body relationship: part_of UBERON:0001775 ! ciliary body +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nCiliary muscle cells are specialized contractile cells that constitute the ciliary muscle, a component of the eye in vertebrates. These cells form a ring around the iris, the eye's colored part. Ciliary muscle cells fall into the category of smooth muscle cells, characterized by their lack of the striations typical of skeletal and cardiac muscle cells. Their shape is elongated and pointed at both ends, and they occur in multi-nucleated syncytia where many cells share the same cytoplasm.\nCiliary muscle cells primarily control the eye's accommodation, adjusting the thickness and curvature of the lens to fine-tune the focus of light on the retina. When ciliary muscle cells contract, tension on the zonular fibers holding the lens in place is reduced, allowing the lens to become thicker and increase its refractive power. Conversely, when the ciliary muscle cells relax, the tension on the zonular fibers increases, causing the lens to become flatter and decrease its refractive power. This adjustment facilitates clear vision at different distances, ranging from near to far objects.\nAdditionally, ciliary muscle cells play a role in draining the eye's aqueous humor, which is the clear fluid that fills the anterior chamber of the eye between the cornea and the lens. By controlling the shape of the surrounding trabecular meshwork through muscle contractions and relaxations, ciliary muscle cells indirectly regulate intraocular pressure, a factor critical for preventing ocular conditions like glaucoma." xsd:string {xref="DOI:10.1016/S1350-9462(98)00011-1", xref="DOI:10.1038/srep31171", xref="DOI:10.1111/j.1444-0938.2008.00260.x", xref="https://www.sciencedirect.com/topics/medicine-and-dentistry/ciliary-muscle"} [Term] id: CL:2000029 name: central nervous system neuron def: "Any neuron that is part of a central nervous system." [GOC:TermGenie] +subset: human_subset +subset: mouse_subset is_a: CL:0000540 ! neuron intersection_of: CL:0000540 ! neuron intersection_of: RO:0002100 UBERON:0001017 ! has soma location central nervous system @@ -2229,6 +2497,8 @@ id: CL:4023129 name: retinoblast def: "A retinal cell that is immature or undifferentiated." [PMID:17565741] subset: eye_upper_slim +subset: human_subset +subset: mouse_subset synonym: "retinal stem cell" EXACT [PMID:17565741] is_a: CL:0009004 ! retinal cell relationship: part_of UBERON:0000966 ! retina @@ -2240,7 +2510,10 @@ id: CL:4033015 name: retinal astrocyte def: "A star-shaped glial cell that is part of some retina. This cell links neurons to blood vessels and may provide structural and physiological support to optic nerve head axons." [PMID:25236977, PMID:33796062] comment: In response to elevated intraocular pressure, a retinal astrocyte may modulate extracellular matrix remodeling. In the human retina, a retinal astrocyte is GFAP-positive, SOD3-positive and GYPC-positive. {xref="PMID:33796062", xref="PMID:32555229"} +subset: cellxgene_subset subset: eye_upper_slim +subset: human_subset +subset: mouse_subset synonym: "retinal astroglia" RELATED OMO:0003004 [PMID:33796062] is_a: CL:0000127 ! astrocyte is_a: CL:0009004 ! retinal cell @@ -2254,7 +2527,6 @@ property_value: terms:date "2023-03-02T14:38:32Z" xsd:dateTime id: GO:0000278 name: mitotic cell cycle namespace: biological_process -alt_id: GO:0007067 def: "Progression through the phases of the mitotic cell cycle, the most common eukaryotic cell cycle, which canonically comprises four successive phases called G1, S, G2, and M and includes replication of the genome and the subsequent segregation of chromosomes into daughter cells. In some variant cell cycles nuclear replication or nuclear division may not be followed by cell division, or G1 and G2 phases may be absent." [GOC:mah, ISBN:0815316194] comment: Note that this term should not be confused with 'GO:0140014 ; mitotic nuclear division'. 'GO:0000278 ; mitotic cell cycle represents the entire mitotic cell cycle, while 'GO:0140014 ; mitotic nuclear division' specifically represents the actual nuclear division step of the mitotic cell cycle. subset: goslim_chembl @@ -2286,16 +2558,13 @@ relationship: results_in_fission_of GO:0005634 ! nucleus id: GO:0000785 name: chromatin namespace: cellular_component -alt_id: GO:0000789 -alt_id: GO:0000790 -alt_id: GO:0005717 def: "The ordered and organized complex of DNA, protein, and sometimes RNA, that forms the chromosome." [GOC:elh, PMID:20404130] comment: Chromosomes include parts that are not part of the chromatin. Examples include the kinetochore. synonym: "chromosome scaffold" RELATED [] synonym: "cytoplasmic chromatin" NARROW [] synonym: "nuclear chromatin" NARROW [] xref: NIF_Subcellular:sao1615953555 -is_a: GO:0110165 ! cellular anatomical entity +is_a: GO:0110165 ! cellular anatomical structure relationship: part_of GO:0005694 ! chromosome property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28301" xsd:anyURI @@ -2303,8 +2572,6 @@ property_value: term_tracker_item "https://github.com/geneontology/go-ontology/i id: GO:0000792 name: heterochromatin namespace: cellular_component -alt_id: GO:0005720 -alt_id: GO:0035328 def: "A compact and highly condensed form of chromatin that is refractory to transcription." [PMID:32017156] synonym: "nuclear heterochromatin" NARROW [] synonym: "transcriptionally inactive chromatin" EXACT [] @@ -2401,7 +2668,6 @@ relationship: part_of GO:0016331 ! morphogenesis of embryonic epithelium id: GO:0001841 name: neural tube formation namespace: biological_process -alt_id: GO:0001679 def: "The formation of a tube from the flat layer of ectodermal cells known as the neural plate. This will give rise to the central nervous system." [GOC:dph, ISBN:0878932437] synonym: "neural tube morphogenesis" EXACT [GOC:dph] synonym: "neurulation" EXACT [] @@ -2515,7 +2781,6 @@ is_a: GO:0003013 ! circulatory system process id: GO:0005575 name: cellular_component namespace: cellular_component -alt_id: GO:0008372 def: "A location, relative to cellular compartments and structures, occupied by a macromolecular machine. There are three types of cellular components described in the gene ontology: (1) the cellular anatomical entity where a gene product carries out a molecular function (e.g., plasma membrane, cytoskeleton) or membrane-enclosed compartments (e.g., mitochondrion); (2) virion components, where viral proteins act, and (3) the stable macromolecular complexes of which gene product are parts (e.g., the clathrin complex)." [GOC:pdt] comment: Note that, in addition to forming the root of the cellular component ontology, this term is recommended for the annotation of gene products whose cellular component is unknown. When this term is used for annotation, it indicates that no information was available about the cellular component of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this. subset: goslim_candida @@ -2553,7 +2818,7 @@ subset: goslim_prokaryote_ribbon subset: goslim_yeast synonym: "extracellular" EXACT [] xref: Wikipedia:Extracellular -is_a: GO:0110165 ! cellular anatomical entity +is_a: GO:0110165 ! cellular anatomical structure [Term] id: GO:0005577 @@ -2590,8 +2855,6 @@ is_a: GO:0098651 ! basement membrane collagen trimer id: GO:0005604 name: basement membrane namespace: cellular_component -alt_id: GO:0005605 -alt_id: GO:0008003 def: "A collagen-containing extracellular matrix consisting of a thin layer of dense material found in various animal tissues interposed between the cells and the adjacent connective tissue. It consists of the basal lamina plus an associated layer of reticulin fibers." [ISBN:0198547684, PMID:22505934] comment: Note that this term has no relationship to 'membrane ; GO:0016020' because the basement membrane is not a lipid bilayer. synonym: "basal lamina" RELATED [] @@ -2611,7 +2874,7 @@ subset: goslim_drosophila subset: goslim_generic synonym: "intercellular space" RELATED [] xref: NIF_Subcellular:sao1425028079 -is_a: GO:0110165 ! cellular anatomical entity +is_a: GO:0110165 ! cellular anatomical structure relationship: part_of GO:0005576 ! extracellular region [Term] @@ -2629,7 +2892,7 @@ synonym: "nucleocytoplasm" RELATED [GOC:mah] synonym: "protoplasm" EXACT [] synonym: "protoplast" RELATED [GOC:mah] xref: Wikipedia:Intracellular -is_a: GO:0110165 ! cellular anatomical entity +is_a: GO:0110165 ! cellular anatomical structure relationship: part_of CL:0000000 ! cell property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/17776" xsd:anyURI @@ -2681,7 +2944,7 @@ synonym: "chromatid" RELATED [] synonym: "interphase chromosome" NARROW [] synonym: "prophase chromosome" NARROW [] xref: Wikipedia:Chromosome -is_a: GO:0043232 ! intracellular non-membrane-bounded organelle +is_a: GO:0043232 ! intracellular membraneless organelle [Term] id: GO:0005730 @@ -2697,7 +2960,7 @@ subset: goslim_plant subset: goslim_yeast xref: NIF_Subcellular:sao1820400233 xref: Wikipedia:Nucleolus -is_a: GO:0043232 ! intracellular non-membrane-bounded organelle +is_a: GO:0043232 ! intracellular membraneless organelle relationship: part_of GO:0031981 ! nuclear lumen [Term] @@ -2715,7 +2978,7 @@ subset: goslim_prokaryote subset: goslim_prokaryote_ribbon subset: goslim_yeast xref: Wikipedia:Cytoplasm -is_a: GO:0110165 ! cellular anatomical entity +is_a: GO:0110165 ! cellular anatomical structure relationship: part_of GO:0005622 ! intracellular anatomical structure property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/23023" xsd:anyURI @@ -2723,7 +2986,6 @@ property_value: term_tracker_item "https://github.com/geneontology/go-ontology/i id: GO:0005840 name: ribosome namespace: cellular_component -alt_id: GO:0033279 def: "An intracellular organelle, about 200 A in diameter, consisting of RNA and protein. It is the site of protein biosynthesis resulting from translation of messenger RNA (mRNA). It consists of two subunits, one large and one small, each containing only protein and RNA. Both the ribosome and its subunits are characterized by their sedimentation coefficients, expressed in Svedberg units (symbol: S). Hence, the prokaryotic ribosome (70S) comprises a large (50S) subunit and a small (30S) subunit, while the eukaryotic ribosome (80S) comprises a large (60S) subunit and a small (40S) subunit. Two sites on the ribosomal large subunit are involved in translation, namely the aminoacyl site (A site) and peptidyl site (P site). Ribosomes from prokaryotes, eukaryotes, mitochondria, and chloroplasts have characteristically distinct ribosomal proteins." [ISBN:0198506732] subset: goslim_candida subset: goslim_chembl @@ -2741,16 +3003,14 @@ synonym: "membrane bound ribosome" NARROW [NIF_Subcellular:sao1291545653] synonym: "ribosomal RNA" RELATED [] xref: NIF_Subcellular:sao1429207766 xref: Wikipedia:Ribosome -is_a: GO:0043232 ! intracellular non-membrane-bounded organelle -is_a: PR:000050567 ! protein-containing material entity +is_a: GO:0043232 ! intracellular membraneless organelle relationship: capable_of_part_of GO:0006412 ! translation +relationship: has_part PR:000000001 ! protein [Term] id: GO:0005886 name: plasma membrane namespace: cellular_component -alt_id: GO:0005887 -alt_id: GO:0005904 def: "The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins." [ISBN:0716731363] subset: goslim_agr subset: goslim_candida @@ -2796,9 +3056,6 @@ property_value: term_tracker_item "https://github.com/geneontology/go-ontology/i id: GO:0006412 name: translation namespace: biological_process -alt_id: GO:0006416 -alt_id: GO:0006453 -alt_id: GO:0043037 def: "The cellular metabolic process in which a protein is formed, using the sequence of a mature mRNA or circRNA molecule to specify the sequence of amino acids in a polypeptide chain. Translation is mediated by the ribosome, and begins with the formation of a ternary complex between aminoacylated initiator methionine tRNA, GTP, and initiation factor 2, which subsequently associates with the small subunit of the ribosome and an mRNA or circRNA. Translation ends with the release of a polypeptide chain from the ribosome." [GOC:go_curators] subset: goslim_candida subset: goslim_chembl @@ -2827,15 +3084,13 @@ relationship: starts_with GO:0006413 ! translational initiation id: GO:0006413 name: translational initiation namespace: biological_process -alt_id: GO:0006440 -alt_id: GO:0006454 def: "The process preceding formation of the peptide bond between the first two amino acids of a protein. This includes the formation of a complex of the ribosome, mRNA or circRNA, and an initiation complex that contains the first aminoacyl-tRNA." [ISBN:019879276X] subset: goslim_yeast synonym: "biopolymerisation" BROAD [] synonym: "biopolymerization" BROAD [] synonym: "protein synthesis initiation" BROAD [] synonym: "translation initiation" EXACT [] -is_a: GO:0044237 ! cellular metabolic process +is_a: GO:0008152 ! metabolic process relationship: part_of GO:0006412 ! translation relationship: starts_with GO:0001677 ! formation of translation initiation ternary complex @@ -2843,8 +3098,6 @@ relationship: starts_with GO:0001677 ! formation of translation initiation terna id: GO:0006414 name: translational elongation namespace: biological_process -alt_id: GO:0006442 -alt_id: GO:0006455 def: "The successive addition of amino acid residues to a nascent polypeptide chain during protein biosynthesis." [GOC:ems] subset: goslim_yeast synonym: "protein synthesis elongation" BROAD [] @@ -2856,8 +3109,6 @@ relationship: part_of GO:0006412 ! translation id: GO:0006415 name: translational termination namespace: biological_process -alt_id: GO:0006443 -alt_id: GO:0006456 def: "The process resulting in the release of a polypeptide chain from the ribosome, usually in response to a termination codon (UAA, UAG, or UGA in the universal genetic code)." [GOC:hjd, ISBN:019879276X] synonym: "protein synthesis termination" BROAD [] synonym: "translation termination" EXACT [] @@ -2869,9 +3120,6 @@ relationship: part_of GO:0006412 ! translation id: GO:0006810 name: transport namespace: biological_process -alt_id: GO:0015457 -alt_id: GO:0015460 -alt_id: GO:0044765 def: "The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter or a transporter complex, a pore or a motor protein." [GOC:dos, GOC:dph, GOC:jl, GOC:mah] comment: Note that this term should not be used for direct annotation. It should be possible to make a more specific annotation to one of the children of this term, for e.g. to transmembrane transport, to microtubule-based transport or to vesicle-mediated transport. subset: gocheck_do_not_annotate @@ -2886,7 +3134,6 @@ subset: goslim_prokaryote_ribbon synonym: "single-organism transport" RELATED [] is_a: GO:0051234 ! establishment of localization property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/20292" xsd:anyURI -created_by: jl creation_date: 2012-12-13T16:25:32Z [Term] @@ -2915,7 +3162,6 @@ relationship: RO:0002162 NCBITaxon:33208 {all_only="true"} ! in taxon Metazoa id: GO:0006865 name: amino acid transport namespace: biological_process -alt_id: GO:0006866 def: "The directed movement of amino acids, organic acids containing one or more amino substituents, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:ai] subset: goslim_pir subset: goslim_yeast @@ -2925,8 +3171,6 @@ is_a: GO:0006810 ! transport id: GO:0006915 name: apoptotic process namespace: biological_process -alt_id: GO:0006917 -alt_id: GO:0008632 def: "A programmed cell death process which begins when a cell receives an internal (e.g. DNA damage) or external signal (e.g. an extracellular death ligand), and proceeds through a series of biochemical events (signaling pathway phase) which trigger an execution phase. The execution phase is the last step of an apoptotic process, and is typically characterized by rounding-up of the cell, retraction of pseudopodes, reduction of cellular volume (pyknosis), chromatin condensation, nuclear fragmentation (karyorrhexis), plasma membrane blebbing and fragmentation of the cell into apoptotic bodies. When the execution phase is completed, the cell has died." [GOC:cjm, GOC:dhl, GOC:ecd, GOC:go_curators, GOC:mtg_apoptosis, GOC:tb, ISBN:0198506732, PMID:18846107, PMID:21494263] synonym: "activation of apoptosis" NARROW [] synonym: "apoptosis" NARROW [] @@ -2980,7 +3224,6 @@ relationship: occurs_in UBERON:0002385 ! muscle tissue id: GO:0006996 name: organelle organization namespace: biological_process -alt_id: GO:1902589 def: "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of an organelle within a cell. An organelle is an organized structure of distinctive morphology and function. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton. Excludes the plasma membrane." [GOC:mah] comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. subset: gocheck_do_not_annotate @@ -2995,7 +3238,6 @@ intersection_of: GO:0016043 ! cellular component organization intersection_of: results_in_organization_of GO:0043226 ! organelle relationship: results_in_organization_of GO:0043226 ! organelle property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27189" xsd:anyURI -created_by: jl creation_date: 2013-12-19T15:25:51Z [Term] @@ -3039,11 +3281,6 @@ is_a: GO:0009987 ! cellular process id: GO:0007165 name: signal transduction namespace: biological_process -alt_id: GO:0023014 -alt_id: GO:0023015 -alt_id: GO:0023016 -alt_id: GO:0023033 -alt_id: GO:0023045 def: "The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell." [GOC:go_curators, GOC:mtg_signaling_feb11] comment: Note that signal transduction is defined broadly to include a ligand interacting with a receptor, downstream signaling steps and a response being triggered. A change in form of the signal in every step is not necessary. Note that in many cases the end of this process is regulation of the initiation of transcription. Note that specific transcription factors may be annotated to this term, but core/general transcription machinery such as RNA polymerase should not. subset: goslim_candida @@ -3101,7 +3338,6 @@ relationship: has_participant GO:0045202 ! synapse id: GO:0007269 name: neurotransmitter secretion namespace: biological_process -alt_id: GO:0010554 def: "The regulated release of neurotransmitter from the presynapse into the synaptic cleft via calcium-regulated exocytosis during synaptic transmission." [GOC:dph] comment: A neurotransmitter is any of a group of substances that are released on excitation from the axon terminal of a presynaptic neuron of the central or peripheral nervous system and travel across the synaptic cleft to either excite or inhibit the target cell. Among the many substances that have the properties of a neurotransmitter are acetylcholine, noradrenaline, adrenaline, dopamine, glycine, gamma-aminobutyrate, glutamic acid, substance P, enkephalins, endorphins and serotonin. subset: goslim_synapse @@ -3227,7 +3463,6 @@ is_a: GO:0050953 ! sensory perception of light stimulus id: GO:0008015 name: blood circulation namespace: biological_process -alt_id: GO:0070261 def: "The flow of blood through the body of an animal, enabling the transport of nutrients to the tissues and the removal of waste products." [GOC:mtg_heart, ISBN:0192800825] subset: goslim_pir synonym: "hemolymph circulation" RELATED [] @@ -3248,9 +3483,6 @@ relationship: regulates GO:0060047 ! heart contraction id: GO:0008150 name: biological_process namespace: biological_process -alt_id: GO:0000004 -alt_id: GO:0007582 -alt_id: GO:0044699 def: "A biological process is the execution of a genetically-encoded biological module or program. It consists of all the steps required to achieve the specific biological objective of the module. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence." [GOC:pdt] comment: Note that, in addition to forming the root of the biological process ontology, this term is recommended for the annotation of gene products whose biological process is unknown. When this term is used for annotation, it indicates that no information was available about the biological process of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this. subset: goslim_candida @@ -3266,16 +3498,13 @@ synonym: "single organism process" RELATED [] synonym: "single-organism process" RELATED [] xref: Wikipedia:Biological_process property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/24968" xsd:anyURI -created_by: jl creation_date: 2012-09-19T15:05:24Z [Term] id: GO:0008152 name: metabolic process namespace: biological_process -alt_id: GO:0044236 -alt_id: GO:0044710 -def: "The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation." [GOC:go_curators, ISBN:0198547684] +def: "A cellular process consisting of the biochemical pathways by which a living organism transforms chemical substances. This includes including anabolism (biosynthetic process) and catabolism (catabolic process). Metabolic processes includes the transformation of small molecules, as well macromolecular processes such as DNA repair and replication, protein synthesis and degradation." [GOC:go_curators, ISBN:0198547684] comment: Note that metabolic processes do not include single functions or processes such as protein-protein interactions, protein-nucleic acids, nor receptor-ligand interactions. subset: gocheck_do_not_annotate subset: goslim_chembl @@ -3284,16 +3513,12 @@ subset: goslim_metagenomics subset: goslim_pir subset: goslim_plant subset: goslim_prokaryote_ribbon -synonym: "metabolic process resulting in cell growth" NARROW [] synonym: "metabolism" EXACT [] -synonym: "metabolism resulting in cell growth" NARROW [] -synonym: "multicellular organism metabolic process" NARROW [] -synonym: "single-organism metabolic process" RELATED [] xref: Wikipedia:Metabolism -is_a: GO:0008150 ! biological_process +is_a: GO:0009987 ! cellular process disjoint_from: GO:0051179 ! localization property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/26424" xsd:anyURI -created_by: jl +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28932" xsd:anyURI creation_date: 2012-10-17T15:46:40Z [Term] @@ -3312,9 +3537,7 @@ property_value: term_tracker_item "https://github.com/geneontology/go-ontology/i id: GO:0009058 name: biosynthetic process namespace: biological_process -alt_id: GO:0044274 -alt_id: GO:0044711 -def: "The chemical reactions and pathways resulting in the formation of substances; typically the energy-requiring part of metabolism in which simpler substances are transformed into more complex ones." [GOC:curators, ISBN:0198547684] +def: "A cellular process consisting of the biochemical pathways by which a living organism synthesizes chemical substances. This typically represents the energy-requiring part of metabolism in which simpler substances are transformed into more complex ones." [GOC:curators, ISBN:0198547684] subset: goslim_chembl subset: goslim_metagenomics subset: goslim_plant @@ -3327,14 +3550,13 @@ synonym: "single-organism biosynthetic process" RELATED [] synonym: "synthesis" EXACT [] xref: Wikipedia:Anabolism is_a: GO:0008152 ! metabolic process -created_by: jl +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28932" xsd:anyURI creation_date: 2012-10-17T15:52:18Z [Term] id: GO:0009059 name: macromolecule biosynthetic process namespace: biological_process -alt_id: GO:0043284 def: "The chemical reactions and pathways resulting in the formation of a macromolecule, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass." [GOC:mah] comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. subset: gocheck_do_not_annotate @@ -3344,8 +3566,8 @@ synonym: "macromolecule anabolism" EXACT [] synonym: "macromolecule biosynthesis" EXACT [] synonym: "macromolecule formation" EXACT [] synonym: "macromolecule synthesis" EXACT [] +is_a: GO:0009058 ! biosynthetic process is_a: GO:0043170 ! macromolecule metabolic process -is_a: GO:0044249 ! cellular biosynthetic process property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/15249" xsd:anyURI property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/25418" xsd:anyURI property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27189" xsd:anyURI @@ -3447,7 +3669,6 @@ relationship: part_of GO:0048856 ! anatomical structure development id: GO:0009790 name: embryo development namespace: biological_process -alt_id: GO:0009795 def: "The process whose specific outcome is the progression of an embryo from its formation until the end of its embryonic life stage. The end of the embryonic stage is organism-specific. For example, for mammals, the process would begin with zygote formation and end with birth. For insects, the process would begin at zygote formation and end with larval hatching. For plant zygotic embryos, this would be from zygote formation to the end of seed dormancy. For plant vegetative embryos, this would be from the initial determination of the cell or group of cells to form an embryo until the point when the embryo becomes independent of the parent plant." [GOC:go_curators, GOC:isa_complete, GOC:mtg_sensu] subset: gocheck_do_not_annotate subset: goslim_chembl @@ -3504,9 +3725,6 @@ property_value: RO:0002161 NCBITaxon:4891 id: GO:0009987 name: cellular process namespace: biological_process -alt_id: GO:0008151 -alt_id: GO:0044763 -alt_id: GO:0050875 def: "Any process that is carried out at the cellular level, but not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level." [GOC:go_curators, GOC:isa_complete] comment: This term should not be used for direct annotation. It should be possible to make a more specific annotation to one of the children of this term. subset: gocheck_do_not_annotate @@ -3516,7 +3734,6 @@ synonym: "cell physiology" EXACT [] synonym: "cellular physiological process" EXACT [] synonym: "single-organism cellular process" RELATED [] is_a: GO:0008150 ! biological_process -created_by: jl creation_date: 2012-12-11T16:56:55Z [Term] @@ -3534,7 +3751,6 @@ property_value: term_tracker_item "https://github.com/geneontology/go-ontology/i id: GO:0012501 name: programmed cell death namespace: biological_process -alt_id: GO:0016244 def: "A process which begins when a cell receives an internal or external signal and activates a series of biochemical events (signaling pathway). The process ends with the death of the cell." [GOC:lr, GOC:mtg_apoptosis] comment: Note that this term should be used to annotate gene products in the organism undergoing the programmed cell death. To annotate genes in another organism whose products modulate programmed cell death in a host organism, consider the term 'modulation by symbiont of host programmed cell death ; GO:0052040'. Also, note that 'programmed cell death ; GO:0012501' should be used to refer to instances of caspase-independent cell death mechanisms, in the absence of further indications on the process taking place. At present, caspase-independent cell death is not yet represented in GO due to the lack of consensus and in-depth research on the topic. 'programmed cell death ; GO:0012501' may also be used to annotate gene products in taxa where apoptosis as defined in GO:0006915 does not occur, such as plants. You may also consider these specific children: GO:0097468 'programmed cell death in response to reactive oxygen species' (with descendants GO:0010421 'hydrogen peroxide-mediated programmed cell death' and GO:0010343 'singlet oxygen-mediated programmed cell death'), and GO:0009626 'plant-type hypersensitive response' and its children. subset: goslim_agr @@ -3594,9 +3810,6 @@ is_a: GO:0006865 ! amino acid transport id: GO:0016020 name: membrane namespace: cellular_component -alt_id: GO:0016021 -alt_id: GO:0098589 -alt_id: GO:0098805 def: "A lipid bilayer along with all the proteins and protein complexes embedded in it and attached to it." [GOC:dos, GOC:mah, ISBN:0815316194] subset: goslim_candida subset: goslim_chembl @@ -3613,7 +3826,7 @@ synonym: "transmembrane" RELATED [GOC:mah] synonym: "whole membrane" NARROW [] xref: Wikipedia:Biological_membrane xref: Wikipedia:Transmembrane_protein -is_a: GO:0110165 ! cellular anatomical entity +is_a: GO:0110165 ! cellular anatomical structure disjoint_from: GO:0031012 ! extracellular matrix creation_date: 2014-03-06T11:37:54Z @@ -3621,8 +3834,6 @@ creation_date: 2014-03-06T11:37:54Z id: GO:0016043 name: cellular component organization namespace: biological_process -alt_id: GO:0044235 -alt_id: GO:0071842 def: "A process that results in the assembly, arrangement of constituent parts, or disassembly of a cellular component." [GOC:ai, GOC:jl, GOC:mah] subset: gocheck_do_not_annotate subset: goslim_agr @@ -3703,9 +3914,6 @@ relationship: part_of GO:0007154 ! cell communication id: GO:0019538 name: protein metabolic process namespace: biological_process -alt_id: GO:0006411 -alt_id: GO:0044267 -alt_id: GO:0044268 def: "The chemical reactions and pathways involving a protein. Includes protein modification." [GOC:ma] comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. subset: gocheck_do_not_annotate @@ -3758,7 +3966,6 @@ relationship: part_of GO:0007049 ! cell cycle id: GO:0022411 name: cellular component disassembly namespace: biological_process -alt_id: GO:0071845 def: "A cellular process that results in the breakdown of a cellular component." [GOC:isa_complete] comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. subset: gocheck_do_not_annotate @@ -3787,7 +3994,6 @@ relationship: part_of GO:0007586 ! digestion id: GO:0022607 name: cellular component assembly namespace: biological_process -alt_id: GO:0071844 def: "The aggregation, arrangement and bonding together of a cellular component." [GOC:isa_complete] subset: goslim_chembl subset: goslim_euk_cellular_processes_ribbon @@ -3829,8 +4035,6 @@ relationship: results_in_assembly_of GO:1990904 ! ribonucleoprotein complex id: GO:0023052 name: signaling namespace: biological_process -alt_id: GO:0023046 -alt_id: GO:0044700 def: "The entirety of a process in which information is transmitted within a biological system. This process begins with an active signal and ends when a cellular response has been triggered." [GOC:mtg_signal, GOC:mtg_signaling_feb11, GOC:signaling] comment: Note that a signal is any variable property or parameter that serves to convey information, and may be a physical entity such as a gene product or small molecule, a photon, or a change in state such as movement or voltage change. subset: goslim_agr @@ -3848,7 +4052,6 @@ synonym: "signalling" EXACT [] synonym: "signalling process" RELATED [GOC:mah] synonym: "single organism signaling" RELATED [] is_a: GO:0050789 ! regulation of biological process -created_by: jl creation_date: 2010-02-16T09:30:50Z [Term] @@ -3900,7 +4103,7 @@ subset: goslim_agr subset: goslim_drosophila subset: goslim_flybase_ribbon xref: Wikipedia:Cell_junction -is_a: GO:0110165 ! cellular anatomical entity +is_a: GO:0110165 ! cellular anatomical structure property_value: RO:0002161 NCBITaxon:4751 [Term] @@ -3982,7 +4185,6 @@ relationship: results_in_acquisition_of_features_of CL:0000556 ! megakaryocyte id: GO:0030261 name: chromosome condensation namespace: biological_process -alt_id: GO:0000068 def: "The progressive compaction of dispersed interphase chromatin into threadlike chromosomes prior to mitotic or meiotic nuclear division, or during apoptosis, in eukaryotic cells." [GOC:mah, ISBN:0815316194] synonym: "DNA condensation" BROAD [Wikipedia:DNA_condensation] synonym: "eukaryotic chromosome condensation" EXACT [GOC:bf] @@ -4018,7 +4220,7 @@ subset: goslim_drosophila subset: goslim_generic subset: goslim_pir subset: goslim_plant -is_a: GO:0110165 ! cellular anatomical entity +is_a: GO:0110165 ! cellular anatomical structure relationship: part_of CL:0000000 ! cell relationship: part_of GO:0071944 ! cell periphery @@ -4045,7 +4247,6 @@ relationship: part_of GO:0097447 ! dendritic tree id: GO:0031012 name: extracellular matrix namespace: cellular_component -alt_id: GO:0005578 def: "A structure lying external to one or more cells, which provides structural support, biochemical or biomechanical cues for cells or tissues." [GOC:BHF, GOC:mah, GOC:rph, NIF_Subcellular:nlx_subcell_20090513, PMID:21123617, PMID:28089324] subset: goslim_chembl subset: goslim_drosophila @@ -4065,7 +4266,6 @@ disjoint_from: GO:0043226 ! organelle id: GO:0031410 name: cytoplasmic vesicle namespace: cellular_component -alt_id: GO:0016023 def: "A vesicle found in the cytoplasm of a cell." [GOC:ai, GOC:mah, GOC:vesicles] subset: goslim_agr subset: goslim_candida @@ -4087,7 +4287,7 @@ id: GO:0031974 name: membrane-enclosed lumen namespace: cellular_component def: "The enclosed volume within a sealed membrane or between two sealed membranes. Encompasses the volume enclosed by the membranes of a particular organelle, e.g. endoplasmic reticulum lumen, or the space between the two lipid bilayers of a double membrane surrounding an organelle, e.g. nuclear envelope lumen." [GOC:add, GOC:mah] -is_a: GO:0110165 ! cellular anatomical entity +is_a: GO:0110165 ! cellular anatomical structure disjoint_from: GO:0045202 ! synapse [Term] @@ -4102,7 +4302,6 @@ relationship: part_of GO:0005634 ! nucleus id: GO:0031982 name: vesicle namespace: cellular_component -alt_id: GO:0031988 def: "Any small, fluid-filled, spherical organelle enclosed by membrane." [GOC:mah, GOC:pz, GOC:vesicles] subset: goslim_pir synonym: "membrane-bounded vesicle" RELATED [] @@ -4140,8 +4339,6 @@ relationship: results_in_assembly_of GO:0032059 ! bleb id: GO:0032501 name: multicellular organismal process namespace: biological_process -alt_id: GO:0044707 -alt_id: GO:0050874 def: "Any biological process, occurring at the level of a multicellular organism, pertinent to its function." [GOC:curators, GOC:dph, GOC:isa_complete, GOC:tb] comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. subset: gocheck_do_not_annotate @@ -4154,14 +4351,12 @@ property_value: RO:0002161 NCBITaxon:2157 property_value: RO:0002161 NCBITaxon:4896 property_value: RO:0002161 NCBITaxon:4932 property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27189" xsd:anyURI -created_by: jl creation_date: 2012-09-19T16:07:47Z [Term] id: GO:0032502 name: developmental process namespace: biological_process -alt_id: GO:0044767 def: "A biological process whose specific outcome is the progression of an integrated living unit: an anatomical structure (which may be a subcellular structure, cell, tissue, or organ), or organism over time from an initial condition to a later condition." [GOC:isa_complete] subset: goslim_agr subset: goslim_flybase_ribbon @@ -4169,7 +4364,6 @@ subset: goslim_pir synonym: "development" NARROW [] synonym: "single-organism developmental process" RELATED [] is_a: GO:0008150 ! biological_process -created_by: jl creation_date: 2012-12-19T12:21:31Z [Term] @@ -4186,9 +4380,6 @@ is_a: GO:0140352 ! export from cell id: GO:0032984 name: protein-containing complex disassembly namespace: biological_process -alt_id: GO:0034623 -alt_id: GO:0043241 -alt_id: GO:0043624 def: "The disaggregation of a protein-containing macromolecular complex into its constituent components." [GOC:mah] synonym: "cellular macromolecule complex disassembly" RELATED [] synonym: "cellular protein complex disassembly" RELATED [] @@ -4205,7 +4396,6 @@ property_value: term_tracker_item "https://github.com/geneontology/go-ontology/i id: GO:0032991 name: protein-containing complex namespace: cellular_component -alt_id: GO:0043234 def: "A stable assembly of two or more macromolecules, i.e. proteins, nucleic acids, carbohydrates or lipids, in which at least one component is a protein and the constituent parts function together." [GOC:dos, GOC:mah] comment: A protein complex in this context is meant as a stable set of interacting proteins which can be co-purified by an acceptable method, and where the complex has been shown to exist as an isolated, functional unit in vivo. Acceptable experimental methods include stringent protein purification followed by detection of protein interaction. The following methods should be considered non-acceptable: simple immunoprecipitation, pull-down experiments from cell extracts without further purification, colocalization and 2-hybrid screening. Interactions that should not be captured as protein complexes include: 1) enzyme/substrate, receptor/ligand or any similar transient interactions, unless these are a critical part of the complex assembly or are required e.g. for the receptor to be functional; 2) proteins associated in a pull-down/co-immunoprecipitation assay with no functional link or any evidence that this is a defined biological entity rather than a loose-affinity complex; 3) any complex where the only evidence is based on genetic interaction data; 4) partial complexes, where some subunits (e.g. transmembrane ones) cannot be expressed as recombinant proteins and are excluded from experiments (in this case, independent evidence is necessary to find out the composition of the full complex, if known). Interactions that may be captured as protein complexes include: 1) enzyme/substrate or receptor/ligand if the complex can only assemble and become functional in the presence of both classes of subunits; 2) complexes where one of the members has not been shown to be physically linked to the other(s), but is a homologue of, and has the same functionality as, a protein that has been experimentally demonstrated to form a complex with the other member(s); 3) complexes whose existence is accepted based on localization and pharmacological studies, but for which experimental evidence is not yet available for the complex as a whole. subset: goslim_agr @@ -4220,8 +4410,8 @@ synonym: "protein complex" NARROW [] synonym: "protein containing complex" EXACT [] synonym: "protein-protein complex" NARROW [] is_a: GO:0005575 ! cellular_component -is_a: PR:000050567 ! protein-containing material entity -disjoint_from: GO:0110165 ! cellular anatomical entity +disjoint_from: GO:0110165 ! cellular anatomical structure +relationship: has_part PR:000000001 ! protein [Term] id: GO:0034101 @@ -4239,7 +4429,6 @@ relationship: acts_on_population_of CL:0000232 ! erythrocyte id: GO:0034220 name: monoatomic ion transmembrane transport namespace: biological_process -alt_id: GO:0099131 def: "A process in which a monoatomic ion is transported across a membrane. Monatomic ions (also called simple ions) are ions consisting of exactly one atom." [GOC:mah] comment: Note that this term is not intended for use in annotating lateral movement within membranes. synonym: "ATP hydrolysis coupled ion transmembrane transport" NARROW [] @@ -4297,9 +4486,8 @@ id: GO:0036477 name: somatodendritic compartment namespace: cellular_component def: "The region of a neuron that includes the cell body (cell soma) and dendrite(s), but excludes the axon." [GOC:pad, GOC:PARL] -is_a: GO:0110165 ! cellular anatomical entity +is_a: GO:0110165 ! cellular anatomical structure relationship: part_of CL:0000540 ! neuron -created_by: bf creation_date: 2014-07-24T10:06:19Z [Term] @@ -4344,9 +4532,6 @@ property_value: RO:0002161 NCBITaxon:6237 {source="GOC:kmv"} id: GO:0042592 name: homeostatic process namespace: biological_process -alt_id: GO:0032844 -alt_id: GO:0032845 -alt_id: GO:0032846 def: "Any biological process involved in the maintenance of an internal steady state." [GOC:jl, ISBN:0395825172] subset: goslim_agr subset: goslim_chembl @@ -4374,7 +4559,7 @@ subset: goslim_prokaryote_ribbon synonym: "cell process" BROAD [] synonym: "cellular process" BROAD [] synonym: "cellular projection" EXACT [] -is_a: GO:0110165 ! cellular anatomical entity +is_a: GO:0110165 ! cellular anatomical structure relationship: part_of CL:0000000 ! cell [Term] @@ -4424,9 +4609,6 @@ relationship: part_of GO:0036477 ! somatodendritic compartment id: GO:0043170 name: macromolecule metabolic process namespace: biological_process -alt_id: GO:0034960 -alt_id: GO:0043283 -alt_id: GO:0044259 def: "The chemical reactions and pathways involving macromolecules, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass." [GOC:mah] subset: gocheck_do_not_annotate subset: goslim_pir @@ -4448,7 +4630,7 @@ synonym: "Schwann cell myelin sheath" NARROW [] xref: FMA:62983 xref: NIF_Subcellular:sao593830697 xref: Wikipedia:Myelin -is_a: GO:0110165 ! cellular anatomical entity +is_a: GO:0110165 ! cellular anatomical structure relationship: part_of CL:0000125 ! glial cell relationship: RO:0002160 NCBITaxon:33208 ! only in taxon Metazoa relationship: RO:0002162 NCBITaxon:33208 {all_only="true"} ! in taxon Metazoa @@ -4465,7 +4647,7 @@ subset: goslim_prokaryote subset: goslim_prokaryote_ribbon xref: NIF_Subcellular:sao1539965131 xref: Wikipedia:Organelle -is_a: GO:0110165 ! cellular anatomical entity +is_a: GO:0110165 ! cellular anatomical structure [Term] id: GO:0043227 @@ -4478,23 +4660,26 @@ xref: NIF_Subcellular:sao414196390 is_a: GO:0043226 ! organelle intersection_of: GO:0043226 ! organelle intersection_of: has_part GO:0016020 ! membrane -disjoint_from: GO:0043228 ! non-membrane-bounded organelle +disjoint_from: GO:0043228 ! membraneless organelle relationship: has_part GO:0016020 ! membrane property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28153" xsd:anyURI [Term] id: GO:0043228 -name: non-membrane-bounded organelle +name: membraneless organelle namespace: cellular_component def: "Organized structure of distinctive morphology and function, not bounded by a lipid bilayer membrane. Includes ribosomes, the cytoskeleton and chromosomes." [GOC:go_curators] subset: gocheck_do_not_annotate subset: goslim_mouse synonym: "biological condensate" RELATED [] +synonym: "membrane-less organelle" EXACT [] +synonym: "non-membrane-bounded organelle" EXACT [] synonym: "non-membrane-enclosed organelle" EXACT [] xref: NIF_Subcellular:sao1456184038 is_a: GO:0043226 ! organelle property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/21881" xsd:anyURI property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28153" xsd:anyURI +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29106" xsd:anyURI [Term] id: GO:0043229 @@ -4535,15 +4720,17 @@ intersection_of: part_of GO:0005622 ! intracellular anatomical structure [Term] id: GO:0043232 -name: intracellular non-membrane-bounded organelle +name: intracellular membraneless organelle namespace: cellular_component def: "Organized structure of distinctive morphology and function, not bounded by a lipid bilayer membrane and occurring within the cell. Includes ribosomes, the cytoskeleton and chromosomes." [GOC:go_curators] subset: goslim_pir +synonym: "intracellular non-membrane-bounded organelle" EXACT [] synonym: "intracellular non-membrane-enclosed organelle" EXACT [] -is_a: GO:0043228 ! non-membrane-bounded organelle +is_a: GO:0043228 ! membraneless organelle is_a: GO:0043229 ! intracellular organelle -intersection_of: GO:0043228 ! non-membrane-bounded organelle +intersection_of: GO:0043228 ! membraneless organelle intersection_of: part_of GO:0005622 ! intracellular anatomical structure +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29106" xsd:anyURI [Term] id: GO:0043233 @@ -4570,9 +4757,6 @@ relationship: regulates GO:0007585 ! respiratory gaseous exchange by respiratory id: GO:0043933 name: protein-containing complex organization namespace: biological_process -alt_id: GO:0034600 -alt_id: GO:0034621 -alt_id: GO:0071822 def: "Any process in which macromolecules aggregate, disaggregate, or are modified, resulting in the formation, disassembly, or alteration of a protein complex." [GOC:mah] synonym: "cellular macromolecular complex organization" RELATED [] synonym: "cellular macromolecular complex subunit organisation" RELATED [] @@ -4588,7 +4772,6 @@ intersection_of: GO:0016043 ! cellular component organization intersection_of: results_in_organization_of GO:0032991 ! protein-containing complex relationship: results_in_organization_of GO:0032991 ! protein-containing complex property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/22580" xsd:anyURI -created_by: mah creation_date: 2010-09-08T10:01:42Z [Term] @@ -4615,7 +4798,6 @@ relationship: regulates GO:0022600 ! digestive system process id: GO:0044085 name: cellular component biogenesis namespace: biological_process -alt_id: GO:0071843 def: "A process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of a cellular component. Includes biosynthesis of constituent macromolecules, and those macromolecular modifications that are involved in synthesis or assembly of the cellular component." [GOC:jl, GOC:mah] subset: gocheck_do_not_annotate subset: goslim_pir @@ -4632,21 +4814,8 @@ synonym: "Met-tRNA/eIF2.GTP ternary complex" NARROW [] synonym: "translation initiation (ternary) complex" EXACT [] is_a: GO:1990904 ! ribonucleoprotein complex relationship: part_of GO:0005737 ! cytoplasm -created_by: jl creation_date: 2009-10-22T02:38:55Z -[Term] -id: GO:0044237 -name: cellular metabolic process -namespace: biological_process -def: "The chemical reactions and pathways by which individual cells transform chemical substances." [GOC:go_curators] -comment: This term should not be used for direct annotation. It should be possible to make a more specific annotation to one of the children of this term. -subset: gocheck_do_not_annotate -synonym: "cellular metabolism" EXACT [] -synonym: "intermediary metabolism" RELATED [GOC:mah] -is_a: GO:0008152 ! metabolic process -is_a: GO:0009987 ! cellular process - [Term] id: GO:0044238 name: primary metabolic process @@ -4662,21 +4831,6 @@ xref: Wikipedia:Primary_metabolite is_a: GO:0008152 ! metabolic process property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/26424" xsd:anyURI -[Term] -id: GO:0044249 -name: cellular biosynthetic process -namespace: biological_process -def: "The chemical reactions and pathways resulting in the formation of substances, carried out by individual cells." [GOC:jl] -comment: This term should not be used for direct annotation. It should be possible to make a more specific annotation to one of the children of this term. -subset: gocheck_do_not_annotate -synonym: "cellular anabolism" EXACT [] -synonym: "cellular biosynthesis" EXACT [] -synonym: "cellular formation" EXACT [] -synonym: "cellular synthesis" EXACT [] -is_a: GO:0009058 ! biosynthetic process -is_a: GO:0044237 ! cellular metabolic process -property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27052" xsd:anyURI - [Term] id: GO:0044297 name: cell body @@ -4687,10 +4841,9 @@ synonym: "cell soma" EXACT [] xref: FBbt:00005107 xref: FMA:67301 xref: Wikipedia:Cell_body -is_a: GO:0110165 ! cellular anatomical entity +is_a: GO:0110165 ! cellular anatomical structure relationship: part_of CL:0000000 ! cell property_value: RO:0002161 NCBITaxon:4890 -created_by: jl creation_date: 2010-02-05T10:37:16Z [Term] @@ -4786,7 +4939,6 @@ property_value: term_tracker_item "https://github.com/geneontology/go-ontology/i id: GO:0048598 name: embryonic morphogenesis namespace: biological_process -alt_id: GO:0048828 def: "The process in which anatomical structures are generated and organized during the embryonic phase. The embryonic phase begins with zygote formation. The end of the embryonic phase is organism-specific. For example, it would be at birth for mammals, larval hatching for insects and seed dormancy in plants." [GOC:jid, GOC:mtg_sensu] synonym: "embryonic anatomical structure morphogenesis" EXACT [GOC:dph, GOC:tb] is_a: GO:0009653 ! anatomical structure morphogenesis @@ -4909,7 +5061,6 @@ property_value: term_tracker_item "https://github.com/geneontology/go-ontology/i id: GO:0050789 name: regulation of biological process namespace: biological_process -alt_id: GO:0050791 def: "Any process that modulates the frequency, rate or extent of a biological process. Biological processes are regulated by many means; examples include the control of gene expression, protein modification or interaction with a protein or substrate molecule." [GOC:ai, GOC:go_curators] subset: gocheck_do_not_annotate subset: goslim_candida @@ -4924,7 +5075,6 @@ relationship: regulates GO:0008150 ! biological_process id: GO:0050794 name: regulation of cellular process namespace: biological_process -alt_id: GO:0051244 def: "Any process that modulates the frequency, rate or extent of a cellular process, any of those that are carried out at the cellular level, but are not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level." [GOC:go_curators] subset: gocheck_do_not_annotate synonym: "regulation of cellular physiological process" EXACT [] @@ -4958,7 +5108,6 @@ property_value: term_tracker_item "https://github.com/geneontology/go-ontology/i id: GO:0050896 name: response to stimulus namespace: biological_process -alt_id: GO:0051869 def: "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus. The process begins with detection of the stimulus and ends with a change in state or activity or the cell or organism." [GOC:ai, GOC:bf] comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. subset: gocheck_do_not_annotate @@ -5031,7 +5180,6 @@ relationship: part_of GO:0050953 ! sensory perception of light stimulus id: GO:0051179 name: localization namespace: biological_process -alt_id: GO:1902578 def: "Any process in which a cell, a substance, or a cellular entity, such as a protein complex or organelle, is transported, tethered to or otherwise maintained in a specific location. In the case of substances, localization may also be achieved via selective degradation." [GOC:ai, GOC:dos] subset: gocheck_do_not_annotate subset: goslim_pir @@ -5045,7 +5193,6 @@ synonym: "single organism localization" RELATED [GOC:TermGenie] synonym: "single-organism localization" RELATED [] is_a: GO:0008150 ! biological_process property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27052" xsd:anyURI -created_by: jl creation_date: 2013-12-18T13:51:04Z [Term] @@ -5076,9 +5223,6 @@ relationship: regulates GO:0032501 ! multicellular organismal process id: GO:0051276 name: chromosome organization namespace: biological_process -alt_id: GO:0006323 -alt_id: GO:0007001 -alt_id: GO:0051277 def: "A process that is carried out at the cellular level that results in the assembly, arrangement of constituent parts, or disassembly of chromosomes, structures composed of a very long molecule of DNA and associated proteins that carries hereditary information. This term covers covalent modifications at the molecular level as well as spatial relationships among the major components of a chromosome." [GOC:ai, GOC:dph, GOC:jl, GOC:mah] subset: goslim_chembl subset: goslim_drosophila @@ -5123,7 +5267,6 @@ is_a: GO:0050896 ! response to stimulus id: GO:0051641 name: cellular localization namespace: biological_process -alt_id: GO:1902580 def: "A cellular localization process whereby a substance or cellular entity, such as a protein complex or organelle, is transported to, and/or maintained in, a specific location within a cell including the localization of substances or cellular entities to the cell membrane." [GOC:tb, GOC:vw] comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. subset: gocheck_do_not_annotate @@ -5138,7 +5281,6 @@ synonym: "single-organism cellular localization" RELATED [] is_a: GO:0009987 ! cellular process is_a: GO:0051179 ! localization property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27189" xsd:anyURI -created_by: jl creation_date: 2013-12-18T14:04:32Z [Term] @@ -5181,7 +5323,6 @@ is_a: GO:0015800 ! acidic amino acid transport id: GO:0055085 name: transmembrane transport namespace: biological_process -alt_id: GO:0090662 def: "The process in which a solute is transported across a lipid bilayer, from one side of a membrane to the other." [GOC:dph, GOC:jid] comment: Transmembrane transport is the transport of a solute across a lipid bilayer. Note that transport through the nuclear pore complex is not transmembrane because the nuclear membrane is a double membrane and is not traversed. For transport through the nuclear pore, consider instead the term 'nucleocytoplasmic transport ; GO:0006913' and its children. Note also that this term is not intended for use in annotating lateral movement within membranes. subset: goslim_chembl @@ -5197,7 +5338,6 @@ is_a: GO:0009987 ! cellular process intersection_of: GO:0006810 ! transport intersection_of: results_in_transport_across GO:0016020 ! membrane relationship: results_in_transport_across GO:0016020 ! membrane -created_by: tb creation_date: 2015-10-21T13:22:47Z [Term] @@ -5267,7 +5407,6 @@ is_a: GO:0035239 ! tube morphogenesis intersection_of: GO:0009653 ! anatomical structure morphogenesis intersection_of: results_in_morphogenesis_of UBERON:0003914 ! epithelial tube relationship: results_in_morphogenesis_of UBERON:0003914 ! epithelial tube -created_by: dph creation_date: 2009-04-28T09:33:36Z [Term] @@ -5277,7 +5416,6 @@ namespace: biological_process def: "The process in which the anatomical structures of a branched epithelium are generated and organized." [GOC:dph] is_a: GO:0001763 ! morphogenesis of a branching structure is_a: GO:0002009 ! morphogenesis of an epithelium -created_by: dph creation_date: 2010-05-25T09:05:34Z [Term] @@ -5289,7 +5427,6 @@ is_a: GO:0007269 ! neurotransmitter secretion is_a: GO:0014047 ! glutamate secretion is_a: GO:0051938 ! L-glutamate import relationship: part_of GO:0035249 ! synaptic transmission, glutamatergic -created_by: dph creation_date: 2013-06-21T16:14:47Z [Term] @@ -5300,16 +5437,12 @@ def: "An extracellular matrix consisting mainly of proteins (especially collagen is_a: GO:0031012 ! extracellular matrix relationship: RO:0002160 NCBITaxon:33208 ! only in taxon Metazoa relationship: RO:0002162 NCBITaxon:33208 {all_only="true"} ! in taxon Metazoa -created_by: dph creation_date: 2018-04-13T12:47:21Z [Term] id: GO:0065003 name: protein-containing complex assembly namespace: biological_process -alt_id: GO:0006461 -alt_id: GO:0034622 -alt_id: GO:0043623 def: "The aggregation, arrangement and bonding together of a set of macromolecules to form a protein-containing complex." [GOC:jl] subset: goslim_chembl subset: goslim_drosophila @@ -5393,7 +5526,6 @@ is_a: GO:0022607 ! cellular component assembly intersection_of: GO:0022607 ! cellular component assembly intersection_of: results_in_assembly_of GO:0043226 ! organelle relationship: results_in_assembly_of GO:0043226 ! organelle -created_by: mah creation_date: 2009-09-15T03:00:51Z [Term] @@ -5410,14 +5542,12 @@ intersection_of: GO:0016043 ! cellular component organization intersection_of: results_in_organization_of GO:1990904 ! ribonucleoprotein complex relationship: results_in_organization_of GO:1990904 ! ribonucleoprotein complex property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/25143" xsd:anyURI -created_by: mah creation_date: 2010-09-08T10:10:35Z [Term] id: GO:0071840 name: cellular component organization or biogenesis namespace: biological_process -alt_id: GO:0071841 def: "A process that results in the biosynthesis of constituent macromolecules, assembly, arrangement of constituent parts, or disassembly of a cellular component." [GOC:mah] comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. subset: gocheck_do_not_annotate @@ -5428,7 +5558,6 @@ synonym: "cellular component organisation or biogenesis at cellular level" EXACT synonym: "cellular component organization or biogenesis at cellular level" EXACT [] is_a: GO:0009987 ! cellular process property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27189" xsd:anyURI -created_by: mah creation_date: 2010-09-10T01:39:16Z [Term] @@ -5437,8 +5566,7 @@ name: cell periphery namespace: cellular_component def: "The broad region around and including the plasma membrane of a cell, encompassing the cell cortex (inside the cell), the plasma membrane, and any external encapsulating structures." [GOC:pdt] subset: goslim_flybase_ribbon -is_a: GO:0110165 ! cellular anatomical entity -created_by: mah +is_a: GO:0110165 ! cellular anatomical structure creation_date: 2010-10-04T01:51:47Z [Term] @@ -5450,7 +5578,6 @@ synonym: "elastic fibre" EXACT [GOC:mah] synonym: "elastin fiber" EXACT [GOC:BHF] is_a: GO:0099512 ! supramolecular fiber relationship: part_of GO:0031012 ! extracellular matrix -created_by: mah creation_date: 2010-10-11T11:44:57Z [Term] @@ -5465,7 +5592,6 @@ intersection_of: GO:0022607 ! cellular component assembly intersection_of: results_in_assembly_of GO:0070062 ! extracellular exosome relationship: part_of GO:0097734 ! extracellular exosome biogenesis relationship: results_in_assembly_of GO:0070062 ! extracellular exosome -created_by: mah creation_date: 2010-10-18T03:44:18Z [Term] @@ -5479,21 +5605,18 @@ intersection_of: results_in_formation_of UBERON:0003914 ! epithelial tube relationship: part_of GO:0060562 ! epithelial tube morphogenesis relationship: results_in_formation_of UBERON:0003914 ! epithelial tube property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/22302" xsd:anyURI -created_by: mah creation_date: 2010-02-26T02:15:40Z [Term] id: GO:0097190 name: apoptotic signaling pathway namespace: biological_process -alt_id: GO:0008624 def: "The series of molecular signals which triggers the apoptotic death of a cell. The pathway starts with reception of a signal, and ends when the execution phase of apoptosis is triggered." [GOC:mtg_apoptosis] comment: This term can be used to annotate gene products involved in apoptotic events happening downstream of the cross-talk point between the extrinsic and intrinsic apoptotic pathways. The cross-talk starts when caspase-8 cleaves Bid and truncated Bid interacts with mitochondria. From this point on it is not possible to distinguish between extrinsic and intrinsic pathways. synonym: "apoptotic signalling pathway" EXACT [GOC:mah] synonym: "induction of apoptosis by extracellular signals" EXACT [] is_a: GO:0007165 ! signal transduction relationship: part_of GO:0006915 ! apoptotic process -created_by: pr creation_date: 2011-11-23T09:30:23Z [Term] @@ -5506,7 +5629,6 @@ synonym: "execution phase of apoptotic process" EXACT [] is_a: GO:0009987 ! cellular process relationship: has_part GO:0032060 ! bleb assembly relationship: part_of GO:0006915 ! apoptotic process -created_by: pr creation_date: 2011-11-23T09:45:24Z [Term] @@ -5518,7 +5640,6 @@ xref: NIF_Subcellular:sao172297168 is_a: GO:0043005 ! neuron projection relationship: has_part GO:0030425 ! dendrite relationship: part_of GO:0036477 ! somatodendritic compartment -created_by: pr creation_date: 2012-12-17T12:31:49Z [Term] @@ -5530,7 +5651,6 @@ is_a: GO:0031982 ! vesicle is_a: GO:0043231 ! intracellular membrane-bounded organelle intersection_of: GO:0031982 ! vesicle intersection_of: part_of GO:0005622 ! intracellular anatomical structure -created_by: pr creation_date: 2016-03-29T17:39:45Z [Term] @@ -5544,7 +5664,6 @@ synonym: "exosome production" EXACT [] synonym: "ILV assembly" RELATED [] synonym: "intraluminal vesicle assembly" RELATED [] is_a: GO:0140112 ! extracellular vesicle biogenesis -created_by: pr creation_date: 2016-10-03T14:35:25Z [Term] @@ -5559,7 +5678,6 @@ is_a: GO:0016020 ! membrane intersection_of: GO:0016020 ! membrane intersection_of: part_of GO:0005886 ! plasma membrane relationship: part_of GO:0005886 ! plasma membrane -created_by: dos creation_date: 2014-03-06T11:55:32Z [Term] @@ -5580,7 +5698,6 @@ def: "A complex of collagen trimers such as a fibril or collagen network." [GOC: synonym: "Supramolecular aggregate of collagen" EXACT [PMID:19693541] synonym: "Supramolecular collagen assembly" EXACT [PMID:21421911] is_a: GO:0099080 ! supramolecular complex -is_a: PR:000050567 ! protein-containing material entity relationship: has_part GO:0005581 ! collagen trimer relationship: part_of GO:0062023 ! collagen-containing extracellular matrix @@ -5609,7 +5726,7 @@ namespace: cellular_component def: "The part of a synapse that is part of the presynaptic cell." [GOC:dos] subset: goslim_synapse synonym: "presynaptic terminal" EXACT [] -is_a: GO:0110165 ! cellular anatomical entity +is_a: GO:0110165 ! cellular anatomical structure relationship: part_of CL:0000540 ! neuron relationship: part_of GO:0045202 ! synapse @@ -5619,7 +5736,7 @@ name: postsynapse namespace: cellular_component def: "The part of a synapse that is part of the post-synaptic cell." [GOC:dos] subset: goslim_synapse -is_a: GO:0110165 ! cellular anatomical entity +is_a: GO:0110165 ! cellular anatomical structure relationship: part_of CL:0000000 ! cell relationship: part_of GO:0045202 ! synapse @@ -5650,7 +5767,7 @@ id: GO:0099080 name: supramolecular complex namespace: cellular_component def: "A cellular component that consists of an indeterminate number of proteins or macromolecular complexes, organized into a regular, higher-order structure such as a polymer, sheet, network or a fiber." [GOC:dos] -is_a: GO:0110165 ! cellular anatomical entity +is_a: GO:0110165 ! cellular anatomical structure [Term] id: GO:0099081 @@ -5666,7 +5783,6 @@ relationship: bearer_of PATO:0015006 ! polymeric id: GO:0099512 name: supramolecular fiber namespace: cellular_component -alt_id: GO:0043205 def: "A polymer consisting of an indefinite number of protein or protein complex subunits that have polymerised to form a fiber-shaped structure." [GOC:dos] synonym: "fibril" RELATED [] is_a: GO:0099081 ! supramolecular polymer @@ -5728,16 +5844,17 @@ relationship: RO:0002162 NCBITaxon:33208 {all_only="true"} ! in taxon Metazoa [Term] id: GO:0110165 -name: cellular anatomical entity +name: cellular anatomical structure namespace: cellular_component -def: "A part of a cellular organism that is either an immaterial entity or a material entity with granularity above the level of a protein complex but below that of an anatomical system. Or, a substance produced by a cellular organism with granularity above the level of a protein complex." [GOC:kmv] +def: "A part of a cellular organism consisting of a material entity with granularity above the level of a protein complex but below that of an anatomical system. Note that cellular organisms exclude viruses." [GOC:kmv] subset: gocheck_do_not_annotate subset: goslim_pir +synonym: "cellular anatomical entity" EXACT [] is_a: GO:0005575 ! cellular_component is_a: UBERON:0000061 ! anatomical structure property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/24200" xsd:anyURI property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/26424" xsd:anyURI -created_by: kmv +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28978" xsd:anyURI creation_date: 2019-08-12T18:01:37Z [Term] @@ -5750,7 +5867,6 @@ intersection_of: GO:0042995 ! cell projection intersection_of: has_part GO:0098590 ! plasma membrane region relationship: has_part GO:0098590 ! plasma membrane region property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/13193" xsd:anyURI -created_by: krc creation_date: 2017-03-21T17:26:07Z [Term] @@ -5765,7 +5881,6 @@ intersection_of: GO:0022607 ! cellular component assembly intersection_of: results_in_assembly_of GO:0120025 ! plasma membrane bounded cell projection relationship: results_in_assembly_of GO:0120025 ! plasma membrane bounded cell projection property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/13298" xsd:anyURI -created_by: krc creation_date: 2017-04-24T23:56:08Z [Term] @@ -5778,7 +5893,6 @@ intersection_of: GO:0016043 ! cellular component organization intersection_of: results_in_organization_of GO:0120025 ! plasma membrane bounded cell projection relationship: results_in_organization_of GO:0120025 ! plasma membrane bounded cell projection property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/13298" xsd:anyURI -created_by: krc creation_date: 2017-04-26T16:07:02Z [Term] @@ -5794,7 +5908,6 @@ is_a: GO:1903047 ! mitotic cell cycle process intersection_of: GO:0000280 ! nuclear division intersection_of: part_of GO:0000278 ! mitotic cell cycle property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/19910" xsd:anyURI -created_by: pg creation_date: 2017-03-23T14:44:23Z [Term] @@ -5805,7 +5918,6 @@ def: "The assembly and secretion a set of components to form an extracellular ve synonym: "extracellular vesicle assembly" EXACT [] is_a: GO:0044085 ! cellular component biogenesis property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/14256" xsd:anyURI -created_by: pg creation_date: 2017-10-23T11:53:42Z [Term] @@ -5821,7 +5933,6 @@ intersection_of: has_target_end_location GO:0005576 ! extracellular region intersection_of: has_target_start_location GO:0005622 ! intracellular anatomical structure relationship: has_target_end_location GO:0005576 ! extracellular region relationship: has_target_start_location GO:0005622 ! intracellular anatomical structure -created_by: pg creation_date: 2019-05-22T11:20:45Z [Term] @@ -5834,7 +5945,6 @@ is_a: GO:0022402 ! cell cycle process intersection_of: GO:0009987 ! cellular process intersection_of: part_of GO:0000278 ! mitotic cell cycle relationship: part_of GO:0000278 ! mitotic cell cycle -created_by: jl creation_date: 2014-05-22T14:22:34Z [Term] @@ -5847,7 +5957,6 @@ is_a: GO:0044057 ! regulation of system process intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0008015 ! blood circulation relationship: regulates GO:0008015 ! blood circulation -created_by: mr creation_date: 2014-10-06T18:38:56Z [Term] @@ -5860,15 +5969,12 @@ is_a: GO:0031982 ! vesicle is_a: GO:0065010 ! extracellular membrane-bounded organelle intersection_of: GO:0031982 ! vesicle intersection_of: part_of GO:0005576 ! extracellular region -created_by: jl creation_date: 2014-10-22T14:26:11Z [Term] id: GO:1990904 name: ribonucleoprotein complex namespace: cellular_component -alt_id: GO:0030529 -alt_id: GO:1990903 def: "A macromolecular complex that contains both RNA and protein molecules." [GOC:krc, GOC:vesicles] subset: goslim_pir synonym: "extracellular ribonucleoprotein complex" NARROW [] @@ -5878,7 +5984,6 @@ synonym: "RNA-protein complex" EXACT [] synonym: "RNP" EXACT [] xref: Wikipedia:Ribonucleoprotein is_a: GO:0032991 ! protein-containing complex -created_by: pr creation_date: 2015-11-19T12:26:37Z [Term] @@ -5912,7 +6017,6 @@ is_a: NCBITaxon:39107 ! Murinae id: NCBITaxon:10090 name: Mus musculus namespace: ncbi_taxonomy -alt_id: NCBITaxon:85055 synonym: "house mouse" EXACT genbank_common_name [] synonym: "mouse" EXACT OMO:0003003 [] xref: GC_ID:1 @@ -5929,7 +6033,6 @@ is_a: NCBITaxon:7776 ! Gnathostomata id: NCBITaxon:117571 name: Euteleostomi namespace: ncbi_taxonomy -alt_id: NCBITaxon:40673 synonym: "bony vertebrates" EXACT genbank_common_name [] xref: GC_ID:1 is_a: NCBITaxon:117570 ! Teleostomi @@ -6078,7 +6181,6 @@ is_a: NCBITaxon:1963758 ! Myomorpha id: NCBITaxon:39107 name: Murinae namespace: ncbi_taxonomy -alt_id: NCBITaxon:109679 xref: GC_ID:1 is_a: NCBITaxon:10066 ! Muridae @@ -6174,7 +6276,6 @@ is_a: NCBITaxon:314147 ! Glires id: PATO:0000001 name: quality namespace: quality -alt_id: PATO:0000072 def: "A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities" [PATOC:GVG] [Term] @@ -6189,7 +6290,6 @@ is_a: PATO:0001241 ! physical object quality id: PATO:0000052 name: shape namespace: quality -alt_id: PATO:0001647 def: "A morphological quality inhering in a bearer by virtue of the bearer's ratios of distances between its features (points, edges, surfaces and also holes etc)." [PATOC:GVG] comment: Shapes are invariant on size transformations. Shapes can be subdivided into 2D and 3D shapes, We can also make a distinction between shapes of complete self-connected objects, and shapes of parts of objects. subset: attribute_slim @@ -6208,7 +6308,6 @@ is_a: PATO:0000051 ! morphology id: PATO:0000141 name: structure namespace: quality -alt_id: PATO:0001452 def: "A morphology quality inhering in a bearer by virtue of the bearer's relative position, shape, arrangements and connectivity of an organism's various parts; the pattern underlying its form." [PATOC:GVG] subset: attribute_slim synonym: "conformation" BROAD [VT:1000738] @@ -6298,7 +6397,6 @@ is_a: PATO:0000957 ! opacity id: PATO:0001018 name: physical quality namespace: quality -alt_id: PATO:0002079 def: "A quality of a physical entity that exists through action of continuants at the physical level of organisation in relation to other entities." [PATOC:GVG] subset: attribute_slim synonym: "relational physical quality" EXACT [] @@ -6309,8 +6407,6 @@ is_a: PATO:0001241 ! physical object quality id: PATO:0001241 name: physical object quality namespace: quality -alt_id: PATO:0001237 -alt_id: PATO:0001238 def: "A quality which inheres in a continuant." [PATOC:GVG] comment: Relational qualities are qualities that hold between multiple entities. Normal (monadic) qualities such as the shape of a eyeball exist purely as a quality of that eyeball. A relational quality such as sensitivity to light is a quality of that eyeball (and connecting nervous system) as it relates to incoming light waves/particles. synonym: "monadic quality of a continuant" EXACT [] @@ -6447,7 +6543,6 @@ is_a: PATO:0002005 ! concavity id: PATO:0001873 name: cylindrical namespace: quality -alt_id: PATO:0001203 def: "A convex 3-D shape quality inhering in a bearer by virtue of the bearer's exhibiting a consistently-sized round cross section." [PATOC:MAH] subset: cell_quality subset: value_slim @@ -6677,16 +6772,6 @@ is_a: PATO:0000141 ! structure property_value: terms:contributor https://orcid.org/0000-0002-7073-9172 creation_date: 2014-12-12T08:43:17Z -[Term] -id: PATO:0010006 -name: cell morphology -namespace: quality -def: "A quality of a single cell inhering in the bearer by virtue of the bearer's size or shape or structure." [https://orcid.org/0000-0002-7073-9172] -comment: Use this term for morphologies that can *only* inhere in a cell, e.g. morphological qualities inhering in a cell by virtue of the presence, location or shape of one or more cell parts. -is_a: PATO:0000051 ! morphology -property_value: terms:contributor https://orcid.org/0000-0002-7073-9172 -creation_date: 2021-01-23T11:31:53Z - [Term] id: PATO:0015006 name: polymeric @@ -6704,28 +6789,6 @@ def: "A quality inhering in a cell by virtue of the cell having a high nuclear/c comment: A high nuclear/cytolasmic ratio is 70% or higher. synonym: "high N:C ratio" EXACT [] is_a: PATO:0001396 ! cellular quality -created_by: http://orcid.org/0000-0001-5208-3432 - -[Term] -id: PATO:0070006 -name: cortical bipolar morphology -namespace: quality -def: "A cell morphology that inheres in neurons which have two principal dendrites that emerge from the soma and begin to branch some distance from it, have few spines, and branch in narrow fields. This is in contrast to bitufted morphology where branching occurs close to the soma." [doi:10.1016/b978-0-12-369497-3.10004-4, PMID:18568015] -comment: This is specific to cortical bipolar cells and are distinguished from retinal bipolar cell morphology which has an axon and dendrite emerging from opposite ends of the soma. -xref: ILX:0101312 -xref: ilxtr:BipolarPhenotype -xref: nifext:2 -is_a: PATO:0070027 ! bitufted dendrite cell morphology -property_value: terms:contributor https://orcid.org/0000-0001-7258-9596 - -[Term] -id: PATO:0070027 -name: bitufted dendrite cell morphology -namespace: quality -def: "A cell morphology that inheres in neurons with dendrites that are bidirectional, emerging from opposite ends of the soma, with the two arbors extending in radial or tangential directions." [PMID:18568015] -comment: This morphology type is distinct from bitufted cell morphology in that it refers to bitufted dendrite morphology rather than bitufted cell morphology. -is_a: PATO:0010006 ! cell morphology -property_value: terms:contributor https://orcid.org/0000-0001-7258-9596 [Term] id: PATO:0070044 @@ -6733,7 +6796,6 @@ name: anatomical structure quality namespace: quality def: "A quality of continuant that exist at the anatomical level of organisation and anything under it. This includes, but is not limited to, cells , tissues, and components." [] is_a: PATO:0001241 ! physical object quality -created_by: http://orcid.org/0000-0001-7258-9596 [Term] id: PATO:0070045 @@ -6741,7 +6803,6 @@ name: anatomical histological quality namespace: quality def: "A quality inhering in an anotomical structure by virtue of its capacity to be stained by specific histological dyes." [] is_a: PATO:0070044 ! anatomical structure quality -created_by: http://orcid.org/0000-0001-7258-9596 [Term] id: PATO:0070047 @@ -6749,7 +6810,6 @@ name: polychromatophilic namespace: quality def: "An affinity inhering in an anatomical structure by virtue of the bearer exhibiting a molecular interaction for both basic and acid stains under specific pH conditions." [GOC:add] is_a: PATO:0070045 ! anatomical histological quality -created_by: http://orcid.org/0000-0001-7258-9596 [Term] id: PATO:0070060 @@ -6764,11 +6824,11 @@ id: PR:000000001 name: protein namespace: protein def: "An amino acid chain that is produced de novo by ribosome-mediated translation of a genetically-encoded mRNA, and any derivatives thereof." [PRO:DAN, PRO:WCB] -comment: The definition above excludes protein complexes, which some also consider a protein. Those who wish to refer to a class representing both senses of the word are directed to CHEBI:36080. Note that the definition allows for experimentally-manipulated genes, and allows for artifically-produced derivatives that mimic those found naturally. Proteins (in the sense defined here) that descended from a common ancestor can be classified into families and superfamilies composed of products of evolutionarily-related genes. The domain architecture of a protein is described by the order of its constituent domains. Proteins with the same domains in the same order are defined as homeomorphic [PRO:WCB]. +comment: The definition above excludes protein complexes, which some also consider a protein. Those who wish to refer to a class representing both senses of the word are directed to CHEBI:36080. Note that the definition allows for experimentally-manipulated genes, and allows for artifically-produced derivatives that mimic those found naturally. Proteins (in the sense defined here) that descended from a common ancestor can be classified into families and superfamilies composed of products of evolutionarily-related genes. The domain architecture of a protein is described by the order of its constituent domains. Proteins with the same domains in the same order are defined as homeomorphic [PRO:WCB). synonym: "native protein" NARROW [IEDB:BP] synonym: "natural protein" EXACT [PRO:DAN] is_a: PR:000018263 ! amino acid chain -is_a: PR:000050567 ! protein-containing material entity +is_a: PR:000064867 ! protein-containing molecular entity relationship: output_of GO:0006412 ! translation [Term] @@ -7037,7 +7097,6 @@ namespace: protein def: "A protein with core architecture consisting of a signal sequence, followed by 7 Ig-like domains (Pfam:PF00047, Pfam:PF07679, or Pfam:PF07686), a transmembrane region, and a cytoplasmic Protein tyrosine kinase domain." [PRO:WCB] comment: Category=family. xref: PIRSF:PIRSF038502 -is_a: PR:000000001 ! protein [Term] id: PR:000002112 @@ -7159,11 +7218,11 @@ intersection_of: RO:0002160 NCBITaxon:2759 ! only in taxon Eukaryota relationship: RO:0002160 NCBITaxon:2759 ! only in taxon Eukaryota [Term] -id: PR:000050567 -name: protein-containing material entity +id: PR:000064867 +name: protein-containing molecular entity namespace: protein -def: "A material entity that minimally consists of a protein." [PRO:DAN] -comment: Note: This includes single proteins and derivatives thereof (PR:000000001), protein-containing complexes (GO:0032991), and protein aggregates (PR:000050566). +def: "A molecular entity that minimally consists of a protein." [PRO:DAN] +comment: Note: This includes single proteins and derivatives thereof (PR:000000001), protein-containing complexes (GO:0032991), and protein aggregates (PR:000050565). synonym: "protein" NARROW [PRO:DAN] synonym: "protein aggregate" NARROW [PRO:DAN] synonym: "protein complex" NARROW [PRO:DAN] @@ -7317,7 +7376,6 @@ xref: VHOG:0001644 xref: WBbt:0005739 xref: Wikipedia:Head xref: XAO:0003024 -xref: ZFA:0001114 is_a: UBERON:0011676 ! subdivision of organism along main body axis relationship: part_of UBERON:0007811 ! craniocervical region relationship: RO:0002162 NCBITaxon:33213 ! in taxon Bilateria @@ -7341,7 +7399,6 @@ xref: TAO:0005425 xref: UMLS:C0036760 {source="ncithesaurus:Serosa"} xref: Wikipedia:Serous_membrane xref: ZFA:0005425 -is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0000481 ! multi-tissue structure is_a: UBERON:0004120 ! mesoderm-derived structure relationship: has_part UBERON:0001136 ! mesothelium @@ -7377,7 +7434,6 @@ property_value: RO:0002175 NCBITaxon:9606 id: UBERON:0000060 name: anatomical wall namespace: uberon -alt_id: UBERON:0009915 def: "Organ component adjacent to an organ cavity and which consists of a maximal aggregate of organ component layers." [FMA:82482] subset: upper_level synonym: "organ wall" RELATED [FMA:82482] @@ -7577,7 +7633,6 @@ creation_date: 2009-06-18T09:00:04Z id: UBERON:0000075 name: subdivision of skeletal system namespace: uberon -alt_id: UBERON:0010322 def: "Anatomical cluster consisting of the skeletal elements and articular elements that are part of an individual subdivision of the organism." [https://orcid.org/0000-0002-6601-2165, UBERONREF:0000003] subset: non_informative synonym: "skeletal system part" RELATED [] @@ -7842,7 +7897,6 @@ property_value: seeAlso "https://github.com/obophenotype/uberon/issues/533" xsd: id: UBERON:0000122 name: neuron projection bundle namespace: uberon -alt_id: UBERON:0005163 def: "A fasciculated bundle of neuron projections (GO:0043005), largely or completely lacking synapses." [CARO:0001001, FBbt:00005099, FBC:DOS] synonym: "funiculus" EXACT [] synonym: "nerve fiber bundle" EXACT [FBbt:00005099] @@ -7963,7 +8017,7 @@ xref: VHOG:0000224 xref: Wikipedia:Blood xref: XAO:0000124 xref: ZFA:0000007 -is_a: PR:000050567 ! protein-containing material entity +is_a: UBERON:0000061 ! anatomical structure is_a: UBERON:0000179 ! haemolymphatic fluid relationship: has_part CL:0000232 {source="CL:tm"} ! erythrocyte relationship: has_part UBERON:0001969 ! blood plasma @@ -7992,7 +8046,6 @@ creation_date: 2009-04-08T04:38:19Z id: UBERON:0000307 name: blastula namespace: uberon -alt_id: UBERON:0007011 def: "Organism at the blastula stage - an early stage of embryonic development in animals. It is produced by cleavage of a fertilized ovum and consists of a spherical layer of around 128 cells surrounding a central fluid-filled cavity called the blastocoel. The blastula follows the morula and precedes the gastrula in the developmental sequence." [Wikipedia:Blastula] subset: inconsistent_with_fma synonym: "blastosphere" RELATED [Wikipedia:Blastula] @@ -8456,7 +8509,6 @@ xref: VHOG:0000387 xref: Wikipedia:Epithelium xref: XAO:0003045 xref: ZFA:0001486 -is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0000479 ! tissue intersection_of: UBERON:0000479 ! tissue intersection_of: RO:0002473 CL:0000066 ! composed primarily of epithelial cell @@ -8747,7 +8799,6 @@ property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/d/ id: UBERON:0000926 name: mesoderm namespace: uberon -alt_id: UBERON:0003263 def: "The middle germ layer of the embryo, between the endoderm and ectoderm." [Wikipedia:Mesoderm] subset: efo_slim subset: pheno_slim @@ -9109,7 +9160,6 @@ xref: VHOG:0000164 xref: Wikipedia:Cornea xref: XAO:0000180 xref: ZFA:0000640 -is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0010000 ! multicellular anatomical structure is_a: UBERON:0010313 ! neural crest-derived structure relationship: has_part UBERON:0001772 ! corneal epithelium @@ -9351,7 +9401,6 @@ id: UBERON:0001009 name: circulatory system namespace: uberon def: "Organ system that passes nutrients (such as amino acids and electrolytes), gases, hormones, blood cells, etc. to and from cells in the body to help fight diseases and help stabilize body temperature and pH to maintain homeostasis[WP]." [Wikipedia:Circulatory_system] -subset: human_reference_atlas subset: uberon_slim synonym: "systema cardiovasculare" RELATED OMO:0003011 [Wikipedia:Circulatory_system] xref: AAO:0000959 @@ -9371,7 +9420,6 @@ property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/2/ property_value: RO:0002161 NCBITaxon:147099 {source="Wikipedia:Acoelomorpha"} property_value: RO:0002161 NCBITaxon:6073 property_value: RO:0002161 NCBITaxon:6157 -property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001015 @@ -10652,7 +10700,6 @@ property_value: RO:0002175 NCBITaxon:9606 id: UBERON:0001793 name: nerve fiber layer of retina namespace: uberon -alt_id: UBERON:0005888 def: "Layer of the retina formed by expansion of the fibers of the optic nerve." [ISBN:0-914294-08-3, MGI:smb] subset: pheno_slim subset: vertebrate_core @@ -11306,7 +11353,6 @@ xref: MIAA:0000052 xref: NCIT:C13356 xref: UMLS:C0032105 {source="ncithesaurus:Plasma"} xref: Wikipedia:Blood_plasma -is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0000179 ! haemolymphatic fluid intersection_of: UBERON:0000463 ! organism substance intersection_of: has_part GO:0005577 ! fibrinogen complex @@ -11355,7 +11401,6 @@ xref: VHOG:0001250 xref: Wikipedia:Blood_vessel xref: XAO:0001011 xref: ZFA:0005314 -is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0000055 ! vessel is_a: UBERON:0004120 ! mesoderm-derived structure relationship: capable_of_part_of GO:0008015 ! blood circulation @@ -11675,7 +11720,6 @@ relationship: part_of UBERON:0013702 ! body proper id: UBERON:0002104 name: visual system namespace: uberon -alt_id: UBERON:0007036 def: "The sensory system subserving the sense of vision." [NIFSTD:FMAID_7191] subset: pheno_slim subset: uberon_slim @@ -11981,7 +12025,6 @@ property_value: foaf:depiction "https://upload.wikimedia.org/wikipedia/commons/d id: UBERON:0002323 name: coelemic cavity lumen namespace: uberon -alt_id: UBERON:0000169 def: "The cavity within the body of all animals higher than the coelenterates and certain primitive worms, formed by the splitting of the embryonic mesoderm into two layers. In mammals it forms the peritoneal, pleural, and pericardial cavities." [BTO:0001707] comment: EDITOR_NOTE check the FMA placement here; ncit placement of body cavity here probably not correct subset: uberon_slim @@ -12007,7 +12050,6 @@ xref: RETIRED_EHDAA2:0003186 xref: SCTID:361348008 xref: TAO:0001438 xref: UMLS:C0333343 {source="ncithesaurus:Cavity"} -xref: ZFA:0001438 is_a: UBERON:0002553 ! anatomical cavity relationship: RO:0002494 UBERON:0003886 ! transformation of future coelemic cavity lumen relationship: RO:0002572 UBERON:0011997 ! luminal space of coelom @@ -12494,6 +12536,7 @@ xref: TAO:0000279 xref: VHOG:0000559 xref: XAO:0000057 xref: ZFA:0000279 +is_a: UBERON:0000061 ! anatomical structure is_a: UBERON:0006598 ! presumptive structure intersection_of: UBERON:0005423 ! developing anatomical structure intersection_of: RO:0002387 UBERON:0002329 ! has potential to develop into somite @@ -12558,7 +12601,6 @@ property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/6/ id: UBERON:0003071 name: eye primordium namespace: uberon -alt_id: UBERON:0005060 def: "Portion of tissue that is part of the anterior neural keel and will form the optic vesicle[ZFA]. A paired ectodermal placode that becomes invaginated to form the embryonic lens vesicles." [GO:0046619, ZFA:0000570] subset: efo_slim synonym: "eye anlage" RELATED [XAO:0000227] @@ -12749,7 +12791,6 @@ property_value: IAO:0000116 "TODO - add grouping class for the anterior end of t id: UBERON:0003081 name: lateral plate mesoderm namespace: uberon -alt_id: UBERON:0006258 def: "Portion of the middle of the three primary germ layers of the embryo that resides on the periphery of the embryo, is continuous with the extra-embryonic mesoderm, splits into two layers enclosing the intra-embryonic coelom, and gives rise to body wall structures[MP]." [MP:0010117, Wikipedia:Lateral_plate_mesoderm] subset: pheno_slim subset: uberon_slim @@ -13053,7 +13094,6 @@ relationship: part_of UBERON:0001016 ! nervous system id: UBERON:0003842 name: neural tube lumen namespace: uberon -alt_id: UBERON:0005713 def: "An anatomical space that surrounded_by a neural tube." [OBOL:automatic] synonym: "cavity of neural tube" EXACT [https://orcid.org/0000-0002-6601-2165] synonym: "central lumen" RELATED [] @@ -13258,7 +13298,6 @@ intersection_of: RO:0000086 PATO:0002299 ! has quality tubular id: UBERON:0003931 name: diencephalic white matter namespace: uberon -alt_id: UBERON:0023148 def: "White matter that is part of a diencephalon [Automatically generated definition]." [OBOL:automatic] subset: vertebrate_core synonym: "diencephalic tract/commissure" EXACT [ZFA:0000338] @@ -13715,7 +13754,6 @@ xref: WikipediaCategory:Cardiovascular_system xref: XAO:0000100 xref: XAO:0001010 xref: ZFA:0000010 -is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0000467 ! anatomical system intersection_of: UBERON:0000467 ! anatomical system intersection_of: has_part UBERON:0000948 ! heart @@ -13739,7 +13777,6 @@ synonym: "blood vessels" RELATED [TAO:0001079] synonym: "set of blood vessels" EXACT [] xref: TAO:0001079 xref: ZFA:0001079 -is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0002049 ! vasculature intersection_of: UBERON:0002049 ! vasculature intersection_of: RO:0002473 UBERON:0001981 ! composed primarily of blood vessel @@ -13824,7 +13861,6 @@ relationship: part_of UBERON:0002028 ! hindbrain id: UBERON:0004734 name: gastrula namespace: uberon -alt_id: UBERON:0007012 def: "Organism at the gastrula stage." [Wikipedia:Gastrula, Wikipedia:Trilaminar_blastocyst] subset: pheno_slim synonym: "blastocystis trilaminaris" RELATED [https://orcid.org/0000-0002-6601-2165] @@ -14447,7 +14483,6 @@ xref: NCIT:C13191 xref: SCTID:68989006 xref: UMLS:C0004799 {source="ncithesaurus:Basement_Membrane"} xref: Wikipedia:Basement_membrane -is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0005764 {source="FMA"} ! acellular membrane relationship: adjacent_to CL:0000066 ! epithelial cell relationship: has_part GO:0005587 ! collagen type IV trimer @@ -14477,7 +14512,6 @@ def: "Organ with organ cavity, which has as parts a serous membrane and a serous comment: See notes for serous membrane xref: FMA:9689 xref: SCTID:362890006 -is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0000062 ! organ relationship: has_part UBERON:0000042 ! serous membrane relationship: has_part UBERON:0002553 ! anatomical cavity @@ -14898,7 +14932,6 @@ subset: efo_slim xref: EFO:0003709 xref: TAO:0005077 xref: ZFA:0005077 -is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0005423 ! developing anatomical structure relationship: has_part CL:0000115 ! endothelial cell relationship: has_part CL:0000566 ! angioblastic mesenchymal cell @@ -15326,6 +15359,7 @@ xref: NCIT:C12418 xref: SCTID:361355005 xref: UMLS:C0460004 {source="ncithesaurus:Head_and_Neck"} xref: WikipediaCategory:Head_and_neck +xref: ZFA:0001114 is_a: UBERON:0000475 {source="MA"} ! organism subdivision relationship: has_part UBERON:0000033 ! head relationship: has_part UBERON:0006562 ! pharynx @@ -15336,7 +15370,6 @@ relationship: part_of UBERON:0013702 ! body proper id: UBERON:0009142 name: entire embryonic mesenchyme namespace: uberon -alt_id: UBERON:0003313 def: "Sum total of mesenchyme in the embryo." [https://github.com/obophenotype/human-developmental-anatomy-ontology/issues/7] xref: EHDAA2:0001113 xref: EHDAA:177 @@ -15382,6 +15415,7 @@ synonym: "MHB neural plate" EXACT [https://orcid.org/0000-0002-6601-2165] synonym: "midbrain-hindbrain boundary neural plate" EXACT [ZFA:0007044] xref: TAO:0007044 xref: ZFA:0007044 +is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0006598 ! presumptive structure relationship: part_of UBERON:0003075 {source="ZFA"} ! neural plate relationship: RO:0002495 UBERON:0007281 ! immediate transformation of presumptive midbrain hindbrain boundary @@ -15847,6 +15881,7 @@ synonym: "haemocoelom" NARROW [] synonym: "schizocoelom" NARROW [] xref: EHDAA2:0004731 xref: Wikipedia:Coelom +xref: ZFA:0001438 is_a: UBERON:0000481 {source="EHDAA2"} ! multi-tissue structure relationship: RO:0002162 NCBITaxon:33213 ! in taxon Bilateria property_value: IAO:0000116 "EHDAA2 distingsuishes between the lumen, the lining, and the 'coelomic cavity', which despire it's name, is not a space - it is the aggregate of space plus lining." xsd:string @@ -15877,7 +15912,6 @@ synonym: "tunica fibrosa" BROAD [] xref: FMA:58102 xref: SCTID:361318005 xref: Wikipedia:Fibrous_tunic_of_eyeball -is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0004923 {source="FMA"} ! organ component layer is_a: UBERON:0010314 ! structure with developmental contribution from neural crest @@ -16056,7 +16090,6 @@ relationship: part_of UBERON:0000019 ! camera-type eye id: UBERON:0016879 name: future central nervous system namespace: uberon -alt_id: UBERON:3000469 def: "Primordium that develops into the central nervous system." [http://orcid.org/0000-0002-6601-2165] synonym: "future CNS" EXACT [] synonym: "presumptive central nervous system" EXACT [] @@ -16071,7 +16104,6 @@ relationship: RO:0002387 UBERON:0001017 ! has potential to develop into central id: UBERON:0016880 name: future nervous system namespace: uberon -alt_id: UBERON:3000477 def: "Primordium that develops into the nervous system." [http://orcid.org/0000-0002-6601-2165] synonym: "presumptive nervous system" EXACT [AAO:0000477] xref: AAO:0000477 @@ -16444,7 +16476,6 @@ id: RO:0002021 name: occurs across def: "A relationship between a process and a barrier, where the process occurs in a region spanning the barrier. For cellular processes the barrier is typically a membrane. Examples include transport across a membrane and membrane depolarization." [] is_a: RO:0002479 ! has part that occurs in -created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-07-20T17:19:37Z [Typedef] @@ -17303,7 +17334,6 @@ name: causally upstream of or within, negative effect property_value: RO:0004050 RO:0002418 property_value: seeAlso "https://wiki.geneontology.org/Causally_upstream_of_or_within,_negative_effect" xsd:anyURI is_a: causally_upstream_of_or_within ! causally upstream of or within -created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-03-13T23:55:05Z [Typedef] @@ -17311,7 +17341,6 @@ id: RO:0004047 name: causally upstream of or within, positive effect property_value: seeAlso https://wiki.geneontology.org/Causally_upstream_of_or_within,_positive_effect is_a: causally_upstream_of_or_within ! causally upstream of or within -created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-03-13T23:55:19Z [Typedef] @@ -17320,7 +17349,6 @@ name: has small molecule regulator def: "a relation between a process and a continuant, in which the process is regulated by the small molecule continuant" [] is_a: has_participant ! has participant inverse_of: RO:0012004 ! is small molecule regulator of -created_by: https://orcid.org/0000-0003-1813-6857 creation_date: 2020-04-22T20:27:26Z [Typedef] @@ -17328,7 +17356,6 @@ id: RO:0012004 name: is small molecule regulator of def: "a relation between a continuant and a process, in which the continuant is a small molecule that regulates the process" [] is_a: RO:0002596 ! capable of regulating -created_by: https://orcid.org/0000-0003-1813-6857 creation_date: 2020-06-24T13:15:17Z [Typedef] @@ -17338,7 +17365,6 @@ def: "a relation between a continuant and a process, in which the continuant is property_value: seeAlso "https://wiki.geneontology.org/Is_small_molecule_activator_of" xsd:anyURI is_a: RO:0002598 ! capable of positively regulating is_a: RO:0012004 ! is small molecule regulator of -created_by: https://orcid.org/0000-0003-1813-6857 creation_date: 2020-06-24T13:15:26Z [Typedef] @@ -17348,7 +17374,6 @@ def: "A relationship between a neuron and a region, where the neuron has a funct synonym: "has synaptic input or output in" EXACT [] is_a: RO:0002130 ! has synaptic terminal in transitive_over: part_of ! part of -created_by: https://orcid.org/0000-0002-1373-1705 creation_date: 2020-07-17T09:26:52Z [Typedef] @@ -17361,9 +17386,18 @@ synonym: "has sensory terminal location" EXACT [] domain: CL:0000101 ! sensory neuron is_a: RO:0002360 ! has dendrite location transitive_over: part_of ! part of -created_by: https://orcid.org/0000-0002-1373-1705 creation_date: 2020-07-20T12:10:09Z +[Typedef] +id: RO:0015004 +name: has characterizing marker set +def: "A relation that applies between a cell type and a set of markers that can be used to uniquely identify that cell type." [] +synonym: "has marker gene combination" EXACT [] +synonym: "has marker signature set" EXACT [] +property_value: IAO:0000116 "C has_characterizing_marker_set y iff: C is a cell type and y is a collection of genes or proteins whose expression is sufficient to distinguish cell type C from most or all other cell types." xsd:string +property_value: terms:contributor https://orcid.org/0000-0001-7258-9596 +domain: CL:0000000 ! cell + [Typedef] id: RO:0015006 name: different in magnitude relative to @@ -17437,7 +17471,6 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0012003 is_a: has_participant ! has participant -created_by: https://orcid.org/0000-0003-1813-6857 creation_date: 2020-06-08T17:21:33Z [Typedef] @@ -17733,7 +17766,6 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_ontology xref: RO:0004009 is_a: has_input ! has input is_a: has_primary_input_or_output ! has primary input or output -created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-12-13T11:26:56Z [Typedef] @@ -17744,7 +17776,6 @@ def: "p 'has primary input ot output' c iff either (a) p 'has primary input' c o subset: http://purl.obolibrary.org/obo/valid_for_go_ontology xref: RO:0004007 is_a: has_participant ! has participant -created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-12-13T11:26:17Z [Typedef] @@ -17756,7 +17787,6 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_ontology xref: RO:0004008 is_a: has_output ! has output is_a: has_primary_input_or_output ! has primary input or output -created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-12-13T11:26:32Z [Typedef] @@ -17767,7 +17797,6 @@ def: "a relation between a process and a continuant, in which the process is act xref: RO:0012001 is_a: RO:0012000 ! has small molecule regulator inverse_of: RO:0012005 ! is small molecule activator of -created_by: https://orcid.org/0000-0003-1813-6857 creation_date: 2020-04-22T20:28:37Z [Typedef] @@ -18092,7 +18121,6 @@ namespace: external def: "p has anatomical participant c iff p has participant c, and c is an anatomical entity" [] xref: RO:0040036 is_a: has_participant ! has participant -created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-09-26T01:08:58Z [Typedef] @@ -18164,7 +18192,6 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0012008 is_a: results_in_organization_of ! results in organization of -created_by: https://orcid.org/0000-0003-1813-6857 creation_date: 2021-02-26T07:28:29Z [Typedef] @@ -18216,7 +18243,6 @@ name: results in organization of namespace: external def: "p results in organization of c iff p results in the assembly, arrangement of constituent parts, or disassembly of c" [] xref: RO:0002592 -is_a: has_participant ! has participant is_a: results_in_changes_to_anatomical_or_cellular_structure ! results in changes to anatomical or cellular structure [Typedef] diff --git a/src/ontology/subsets/eye_upper_slim.owl b/src/ontology/subsets/eye_upper_slim.owl index 394d31707..8a7eb19b9 100644 --- a/src/ontology/subsets/eye_upper_slim.owl +++ b/src/ontology/subsets/eye_upper_slim.owl @@ -22,8 +22,8 @@ xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#" xmlns:ncbitaxon="http://purl.obolibrary.org/obo/ncbitaxon#"> - - 2024-09-26 + + 2025-01-08 @@ -287,13 +287,18 @@ WHERE { - 2018-03-14T00:03:24Z is negative form of + + + + + + @@ -373,6 +378,14 @@ WHERE { + + + + + + + + @@ -384,6 +397,14 @@ WHERE { + + + + + + + + @@ -1010,12 +1031,6 @@ WHERE { - - - - - - @@ -1034,6 +1049,12 @@ WHERE { + + + + + + @@ -1048,19 +1069,25 @@ WHERE { - + + description + - + + license + - + + title + @@ -1088,26 +1115,12 @@ WHERE { - - - - - - - - - - has_alternative_id - - - - @@ -1123,7 +1136,11 @@ WHERE { + An annotation property that links an ontology entity or a statement to a prefixed identifier or URI. + + database_cross_reference + has cross-reference @@ -1206,12 +1223,6 @@ WHERE { - - - - - - @@ -1682,7 +1693,6 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 A relationship between a process and a barrier, where the process occurs in a region spanning the barrier. For cellular processes the barrier is typically a membrane. Examples include transport across a membrane and membrane depolarization. - 2017-07-20T17:19:37Z occurs across @@ -3970,7 +3980,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different - p results in organization of c iff p results in the assembly, arrangement of constituent parts, or disassembly of c RO:0002592 @@ -4092,7 +4101,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different p 'has primary input ot output' c iff either (a) p 'has primary input' c or (b) p 'has primary output' c. - 2018-12-13T11:26:17Z RO:0004007 external @@ -4110,7 +4118,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different p has primary output c if (a) p has output c and (b) the goal of process is to modify, produce, or transform c. - 2018-12-13T11:26:32Z RO:0004008 external @@ -4138,7 +4145,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different p has primary input c if (a) p has input c and (b) the goal of process is to modify, consume, or transform c. - 2018-12-13T11:26:56Z RO:0004009 external @@ -4165,7 +4171,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different - 2018-03-13T23:55:05Z causally upstream of or within, negative effect https://wiki.geneontology.org/Causally_upstream_of_or_within,_negative_effect @@ -4177,7 +4182,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different - 2018-03-13T23:55:19Z causally upstream of or within, positive effect @@ -4191,7 +4195,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different a relation between a process and a continuant, in which the process is regulated by the small molecule continuant - 2020-04-22T20:27:26Z has small molecule regulator @@ -4204,7 +4207,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different a relation between a process and a continuant, in which the process is activated by the small molecule continuant - 2020-04-22T20:28:37Z RO:0012001 external @@ -4221,7 +4223,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different p acts on population of c iff c' is a collection, has members of type c, and p has participant c - 2020-06-08T17:21:33Z RO:0012003 external @@ -4241,7 +4242,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different a relation between a continuant and a process, in which the continuant is a small molecule that regulates the process - 2020-06-24T13:15:17Z is small molecule regulator of @@ -4254,7 +4254,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different a relation between a continuant and a process, in which the continuant is a small molecule that activates the process - 2020-06-24T13:15:26Z is small molecule activator of https://wiki.geneontology.org/Is_small_molecule_activator_of @@ -4266,7 +4265,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different - 2021-02-26T07:28:29Z RO:0012008 external @@ -4290,7 +4288,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different A relationship between a neuron and a region, where the neuron has a functionally relevant number of input and/or output synapses in that region. - 2020-07-17T09:26:52Z has synaptic input or output in has synaptic IO in region @@ -4308,7 +4305,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different Relation between a sensory neuron and some structure in which it receives sensory input via a sensory dendrite. - 2020-07-20T12:10:09Z has sensory dendrite location has sensory terminal in @@ -4318,6 +4314,20 @@ Each of these 3 primitives can be composed to yield a cross-product of different + + + + + A relation that applies between a cell type and a set of markers that can be used to uniquely identify that cell type. + C has_characterizing_marker_set y iff: C is a cell type and y is a collection of genes or proteins whose expression is sufficient to distinguish cell type C from most or all other cell types. + + has marker gene combination + has marker signature set + has characterizing marker set + + + + @@ -4457,7 +4467,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different p has anatomical participant c iff p has participant c, and c is an anatomical entity - 2018-09-26T01:08:58Z RO:0040036 external @@ -4801,6 +4810,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different XAO:0003012 ZFA:0009000 + + The definition of cell is intended to represent all cells, and thus a cell is defined as a material entity and not an anatomical structure, which implies that it is part of an organism (or the entirety of one). cell @@ -4849,6 +4860,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different Any fibroblast that is derived from the neural crest. fibroblast neural crest derived + + neural crest derived fibroblast @@ -4881,6 +4894,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different ZFA:0009001 neuronal receptor cell (sensu Animalia) + + neuronal receptor cell @@ -4904,6 +4919,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different A cell found in the embryo before the formation of all the gem layers is complete. ZFA:0009002 + + early embryonic cell (metazoa) @@ -4927,6 +4944,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different Cell that is part of the migratory cranial neural crest population. Migratory cranial neural crest cells develop from premigratory cranial neural crest cells and have undergone epithelial to mesenchymal transition and delamination. ZFA:0007091 + + migratory cranial neural crest cell @@ -4956,10 +4975,20 @@ Each of these 3 primitives can be composed to yield a cross-product of different + A non-terminally differentiated cell that develops form the neuroectoderm. Glioblast has the potential to differentiate into various types of glial cells, including astrocytes and oligodendrocytes. ZFA:0009010 + + glioblast + + + + A non-terminally differentiated cell that develops form the neuroectoderm. Glioblast has the potential to differentiate into various types of glial cells, including astrocytes and oligodendrocytes. + PMID:37824650 + Wikipedia:Glioblast + @@ -4986,6 +5015,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different ZFA:0009011 neuroblast + + neuroblast (sensu Vertebrata) @@ -5040,6 +5071,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different animal stem cell + + This term applies to metazoan. For plant stem cells, consider using PO:0004011 ‘initial cell’ or its parent PO:0004010 ‘meristematic cell’. stem cell @@ -5227,6 +5260,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different colony forming unit hematopoietic + + Markers differ between species, and two sets of markers have been described for mice. HSCs are reportedly CD34-positive, CD45-positive, CD48-negative, CD150-positive, CD133-positive, and CD244-negative. hematopoietic stem cell @@ -5278,6 +5313,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different erythroid stem cell + + erythroid progenitor cell @@ -5346,6 +5383,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different multifate stem cell multipotent cell multipotent stem cell + + multi fate stem cell @@ -5381,6 +5420,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different myeloid stem cell pluripotent stem cell (bone marrow) + + This cell type is intended to be compatible with any vertebrate common myeloid progenitor. For mammalian CMP known to be CD34-positive, please use the term 'common myeloid progenitor, CD34-positive' (CL_0001059). common myeloid progenitor @@ -5497,6 +5538,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different megakaryocyte/erythrocyte progenitor megakaryocyte/erythroid progenitor cell + + MEPs are reportedly CD19-negative, CD34-negative, CD45RA-negative, CD110-positive, CD117-positive, and SCA1-negative and reportedly express the transcription factors GATA-1 and NF-E2. megakaryocyte-erythroid progenitor cell @@ -5536,6 +5579,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different MESH:D039901 ZFA:0009024 totipotential stem cell + + totipotent stem cell @@ -5563,6 +5608,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different FMA:84782 blast cell + + define using PATO mulit-potent or oligopotent? non-terminally differentiated cell @@ -5586,6 +5633,9 @@ Each of these 3 primitives can be composed to yield a cross-product of different FMA:70335 VHOG:0001529 ZFA:0009025 + + + myoblast @@ -5614,13 +5664,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - - - - - - + A connective tissue cell which secretes an extracellular matrix rich in collagen and other macromolecules. Flattened and irregular in outline with branching processes; appear fusiform or spindle-shaped. BTO:0000452 @@ -5631,6 +5675,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different ZFA:0009026 + + These cells may be vimentin-positive, fibronectin-positive, fsp1-positive, MMP-1-positive, collagen I-positive, collagen III-positive, and alpha-SMA-negative. fibroblast @@ -5674,6 +5720,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different epitheliocyte + + epithelial cell https://www.swissbiopics.org/api/image/Epithelial_cells.svg @@ -5726,6 +5774,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different ZFA:0009036 + + blood vessel endothelial cell @@ -5752,6 +5802,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different ZFA:0009038 + + columnar/cuboidal epithelial cell @@ -5796,6 +5848,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different CALOHA:TS-1249 ZFA:0009039 + + squamous epithelial cell @@ -5831,6 +5885,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different ZFA:0009040 mesotheliocyte + + Mesothelial cells, which morphologically resemble squamous epithelial cells, express both epithelial markers (cytokeratins) and mesenchymal markers (vimentin), reflecting their mesodermal origin. They feature surface microvilli and apical-basal polarity. Under certain conditions, they can undergo mesothelial-to-mesenchymal transition. These cells also produce extracellular matrix proteins, maintain serosal homeostasis, and facilitate fluid transport. mesothelial cell @@ -5885,6 +5941,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different ZFA:0009044 + + blood cell @@ -5920,6 +5978,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different + + neuron associated cell @@ -5928,7 +5988,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + Most generally any neuron which is not motor or sensory. Interneurons may also refer to neurons whose axons remain within a particular brain region as contrasted with projection neurons which have axons projecting to other brain regions. BTO:0003811 @@ -5936,7 +5996,10 @@ Each of these 3 primitives can be composed to yield a cross-product of different FMA:67313 WBbt:0005113 ZFA:0009051 + CNS interneuron + + interneuron @@ -5991,6 +6054,9 @@ Each of these 3 primitives can be composed to yield a cross-product of different MESH:D011984 WBbt:0005759 ZFA:0009053 + + + sensory neuron @@ -6015,50 +6081,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - - - - - - - - - - - - - - - - - - - - - A type of interneuron that has two neurites, usually an axon and a dendrite, extending from opposite poles of an ovoid cell body. - FMA:67282 - ZFA:0009055 - - - bipolar neuron - - - - - A type of interneuron that has two neurites, usually an axon and a dendrite, extending from opposite poles of an ovoid cell body. - GOC:tfm - ISBN:0444009442 - - - - - ZFA:0009055 - - - - - @@ -6078,6 +6100,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different ZFA:0009065 endotheliocyte + + From FMA: 9.07.2001: Endothelial cell has always been classified as a kind of epithelial cell, specifically a squamous cell but that is not true. First, endothelial cell can either be squamous or cuboidal (e.g. high-endothelial cell) and secondly, it has different embryological derivation (mesodermal) than a true epithelial cell (ectodermal and endodermal). The basis for present classification is the fact that it comprises the outermost layer or lining of anatomical structures (location-based) but a better structural basis for the differentia is the cytoskeleton of the cell. Endothelial cell has vimentin filaments while an epithelial cell has keratin filaments. [Onard]. endothelial cell @@ -6101,34 +6125,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - - - - - - - - - - - - - - - - ZFA:0009067 - CNS neuron (sensu Vertebrata) - - - - - ZFA:0009067 - - - - - @@ -6146,6 +6142,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different + + neuron associated cell (sensu Vertebrata) @@ -6157,7 +6155,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different A non-neuronal cell of the nervous system. They not only provide physical support, but also respond to injury, regulate the ionic and chemical composition of the extracellular milieu. Guide neuronal migration during development, and exchange metabolites with neurons. - This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. Glial cells, also known as neuroglia or simply glia, are non-neuronal cells in the central and peripheral nervous systems that provide support and protection for neurons. They constitute approximately half of the total cells in the human brain and more than half in other parts of the nervous system. Glial cells perform several key functions including, but not limited to, maintaining homeostasis, forming the myelin sheath around the neuron axons, and providing support and nutrition to neurons. These different functions are performed by various glial cell types, including astrocytes, oligodendrocytes, microglia and other specialized types. Astrocytes, for example, are the most abundant glial cells and provide metabolic and nutrient support to neurons, help regulate the extracellular ion and neurotransmitter levels, and play a role in the formation and maintenance of the blood-brain barrier, contributing to the overall homeostasis and functioning of the nervous system. Additionally, astrocytes are involved in synaptic communication and participate in processes such as synaptogenesis and synaptic pruning. @@ -6174,6 +6172,8 @@ Despite their overarching function in the support and protection of neurons, gli neuroglia + + Not all glial cells develop from glioblasts, with microglia developing from the mesoderm instead. See https://github.com/obophenotype/cell-ontology/issues/1571 glial cell @@ -6187,7 +6187,7 @@ Despite their overarching function in the support and protection of neurons, gli - This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. Glial cells, also known as neuroglia or simply glia, are non-neuronal cells in the central and peripheral nervous systems that provide support and protection for neurons. They constitute approximately half of the total cells in the human brain and more than half in other parts of the nervous system. Glial cells perform several key functions including, but not limited to, maintaining homeostasis, forming the myelin sheath around the neuron axons, and providing support and nutrition to neurons. These different functions are performed by various glial cell types, including astrocytes, oligodendrocytes, microglia and other specialized types. Astrocytes, for example, are the most abundant glial cells and provide metabolic and nutrient support to neurons, help regulate the extracellular ion and neurotransmitter levels, and play a role in the formation and maintenance of the blood-brain barrier, contributing to the overall homeostasis and functioning of the nervous system. Additionally, astrocytes are involved in synaptic communication and participate in processes such as synaptogenesis and synaptic pruning. @@ -6233,6 +6233,8 @@ Despite their overarching function in the support and protection of neurons, gli macrogliocyte macroglia + + macroglial cell @@ -6270,6 +6272,8 @@ Despite their overarching function in the support and protection of neurons, gli ZFA:0009075 astrocytic glia + + Astrocytes are reportedly CD68-negative, CD121a-positive, CD184-positive, CD192-positive, CRF-positive, EGFR-positive, GFAP-positive, GLUT1-positive, MBP-negative, and NGFR-positive. astrocyte @@ -6319,6 +6323,8 @@ Despite their overarching function in the support and protection of neurons, gli ZFA:0009079 + + corneal endothelial cell @@ -6348,6 +6354,8 @@ Despite their overarching function in the support and protection of neurons, gli Ectoderm destined to be nervous tissue. ZFA:0009080 neurectoderm cell + + neurectodermal cell @@ -6389,6 +6397,8 @@ Despite their overarching function in the support and protection of neurons, gli mesenchymal stromal cells stem cells, mesenchymal + + Many but not all mesenchymal cells derive from the mesoderm. MSCs are reportedly CD3-negative, CD4-negative, CD5-negative, CD8-negative, CD11a-negative, CD11b-negative, CD14-negative, CD19-negative, CD29-positive, CD31-negative, CD34-negative, CD38-negative, CD40-negative, CD44-positive, CD45-negative, CD49-positive, CD54-positive, CD66b-negative, CD79a-negative, CD80-negative, CD102-positive, CD106-positive, CD117-positive, CD121a-positive, CD121b-positive, CD123-positive, CD124-positive, CD133-negative, CD146-positive, CD166-positive, CD271-positive, B220-negative, Gr1-negative, MHCI-positive, MHCII-negative, SSEA4-negative, sca1-positive, Ter119-negative, and glycophorin A-negative. Cultured MSCs are capable of producing stem cell factor, IL7, IL8, IL11, TGF-beta, cofilin, galectin-1, laminin-receptor 1, cyclophilin A, and MMP-2. mesenchymal stem cell https://github.com/obophenotype/cell-ontology/issues/474 @@ -6476,6 +6486,8 @@ Despite their overarching function in the support and protection of neurons, gli ZFA:0009090 chromatocyte chromatophore + + pigment cell @@ -6527,15 +6539,22 @@ Despite their overarching function in the support and protection of neurons, gli A pigment cell derived from the neural crest. Contains melanin-filled pigment granules, which gives a brown to black appearance. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Melanocytes are specialized cells prevalently found in the skin, but also present in the hair follicles, eyes, inner ear, bones, heart, and brain. Their primary function is the synthesis of melanin, a pigment responsible for coloration of skin, hair, and eyes. The presence and distribution of this pigment play a crucial role in the body's defense mechanism against harmful ultraviolet radiation. +In addition to melanin production, melanocytes also engage in a variety of other biological functions. They play a fundamental role in the immune response, owing to their ability to present antigens to T cells. Furthermore, they contribute to the maintenance of the skin's homeostasis by regulating processes such as extracellular matrix remodeling and cytokine production. A balance in melanocyte function is pivotal, as dysfunctions often result in dermatological disorders. For instance, the loss of melanocytes or reduction in their function may lead to hypopigmentation conditions such as vitiligo, whereas an abnormal increase could result in hyperpigmentation disorders or melanoma, a dangerous type of skin cancer. BTO:0000847 CALOHA:TS-0613 FMA:70545 MESH:D008544 VHOG:0001679 ZFA:0009091 + https://cellxgene.cziscience.com/cellguide/CL_0000148 melanophore + + melanocyte @@ -6545,6 +6564,19 @@ Despite their overarching function in the support and protection of neurons, gli A pigment cell derived from the neural crest. Contains melanin-filled pigment granules, which gives a brown to black appearance. SANBI:mhl + + + + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Melanocytes are specialized cells prevalently found in the skin, but also present in the hair follicles, eyes, inner ear, bones, heart, and brain. Their primary function is the synthesis of melanin, a pigment responsible for coloration of skin, hair, and eyes. The presence and distribution of this pigment play a crucial role in the body's defense mechanism against harmful ultraviolet radiation. +In addition to melanin production, melanocytes also engage in a variety of other biological functions. They play a fundamental role in the immune response, owing to their ability to present antigens to T cells. Furthermore, they contribute to the maintenance of the skin's homeostasis by regulating processes such as extracellular matrix remodeling and cytokine production. A balance in melanocyte function is pivotal, as dysfunctions often result in dermatological disorders. For instance, the loss of melanocytes or reduction in their function may lead to hypopigmentation conditions such as vitiligo, whereas an abnormal increase could result in hyperpigmentation disorders or melanoma, a dangerous type of skin cancer. + DOI:10.1002/med.21754 + DOI:10.1038/nrc.2016.37 + DOI:10.1111/j.1751-1097.2007.00226.x + DOI:10.3390/ijms21249769 + https://www.sciencedirect.com/topics/agricultural-and-biological-sciences/melanocyte + @@ -6559,6 +6591,8 @@ Despite their overarching function in the support and protection of neurons, gli pigment cell + + visual pigment cell @@ -6589,6 +6623,8 @@ Despite their overarching function in the support and protection of neurons, gli BTO:0003659 FMA:86916 + + secretory cell @@ -6607,6 +6643,8 @@ Despite their overarching function in the support and protection of neurons, gli A cell whose primary function is to shorten. + + contractile cell @@ -6641,6 +6679,8 @@ Despite their overarching function in the support and protection of neurons, gli muscle fiber myocyte + + muscle cell https://www.swissbiopics.org/api/image/Muscle_cells.svg @@ -6678,16 +6718,24 @@ Despite their overarching function in the support and protection of neurons, gli A non-striated, elongated, spindle-shaped cell found lining the digestive tract, uterus, and blood vessels. They develop from specialized myoblasts (smooth muscle myoblast). + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Smooth muscle cells are a specialized type of muscle cells that are primarily found within the walls of hollow organs such as the intestine, stomach, bladder, uterus, and blood vessels. These cells are an essential component of the autonomic nervous system controling involuntary movements within the body. +Smooth muscle cells play a vital role in many physiological processes due to their unique functionality. They can contract and relax in a slow, sustained, and controlled manner to help modulate the size and shape of the lumens of the organs they surround. For example, in the digestive system, coordinated contraction and relaxation of smooth muscle cells propels food along the gastrointestinal tract - a process known as peristalsis. In the blood vessels, the smooth muscle cells, by contracting or relaxing, either constrict or dilate the vessels, which in turn, help regulate blood flow and pressure. +On a cellular level, smooth muscle cells possess a single, centrally located nucleus and contain an arranged network of actin and myosin filaments, which are the proteins responsible for muscle contraction. Unlike their counterparts in skeletal or cardiac muscles, these cells lack specific contact points for these filaments, hence the lack of visible striations. Furthermore, the contraction of smooth muscle cells is regulated by hormones and neurotransmitters, such as acetylcholine and norepinephrine, adding an additional layer of complex regulation to these highly specialized cells. non-striated muscle cell BTO:0004576 CALOHA:TS-2159 FMA:14072 ZFA:0009118 + https://cellxgene.cziscience.com/cellguide/CL_0000192 SMCs myocytes, smooth muscle smooth muscle fiber + + smooth muscle cell @@ -6699,6 +6747,20 @@ Despite their overarching function in the support and protection of neurons, gli PMID:9315361 http://en.wikipedia.org/wiki/Smooth_muscle_cell + + + + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Smooth muscle cells are a specialized type of muscle cells that are primarily found within the walls of hollow organs such as the intestine, stomach, bladder, uterus, and blood vessels. These cells are an essential component of the autonomic nervous system controling involuntary movements within the body. +Smooth muscle cells play a vital role in many physiological processes due to their unique functionality. They can contract and relax in a slow, sustained, and controlled manner to help modulate the size and shape of the lumens of the organs they surround. For example, in the digestive system, coordinated contraction and relaxation of smooth muscle cells propels food along the gastrointestinal tract - a process known as peristalsis. In the blood vessels, the smooth muscle cells, by contracting or relaxing, either constrict or dilate the vessels, which in turn, help regulate blood flow and pressure. +On a cellular level, smooth muscle cells possess a single, centrally located nucleus and contain an arranged network of actin and myosin filaments, which are the proteins responsible for muscle contraction. Unlike their counterparts in skeletal or cardiac muscles, these cells lack specific contact points for these filaments, hence the lack of visible striations. Furthermore, the contraction of smooth muscle cells is regulated by hormones and neurotransmitters, such as acetylcholine and norepinephrine, adding an additional layer of complex regulation to these highly specialized cells. + DOI:10.1093/ptj/81.11.1810 + https://training.seer.cancer.gov/anatomy/muscular/types.html + https://www.ncbi.nlm.nih.gov/books/NBK10854/ + https://www.ncbi.nlm.nih.gov/books/NBK526125 + https://www.ncbi.nlm.nih.gov/books/NBK556137/ + @@ -6754,6 +6816,8 @@ Despite their overarching function in the support and protection of neurons, gli A cell that is capable of detection of a stimulus involved in sensory perception. MESH:D011984 receptor cell + + sensory receptor cell @@ -6788,6 +6852,8 @@ Despite their overarching function in the support and protection of neurons, gli FMA:86740 ZFA:0009127 + + photoreceptor cell https://www.swissbiopics.org/api/image/Photoreceptor_cell.svg @@ -6818,6 +6884,8 @@ Despite their overarching function in the support and protection of neurons, gli A cell whose function is determined by the generation or the reception of an electric signal. ZFA:0009128 + + electrically active cell @@ -6842,6 +6910,8 @@ Despite their overarching function in the support and protection of neurons, gli A cell within an epithelial cell sheet whose main function is to act as an internal or external covering for a tissue or an organism. ZFA:0009130 boundary cell + + lining cell @@ -6865,6 +6935,8 @@ Despite their overarching function in the support and protection of neurons, gli A cell whose primary function is to prevent the transport of stuff across compartments. ZFA:0009132 + + barrier cell @@ -6905,6 +6977,8 @@ Despite their overarching function in the support and protection of neurons, gli A cell that moves by its own activities. ZFA:0009136 + + motile cell @@ -6937,6 +7011,9 @@ Despite their overarching function in the support and protection of neurons, gli FMA:72549 ZFA:0009137 ectoderm cell + + + ectodermal cell @@ -6966,11 +7043,18 @@ Despite their overarching function in the support and protection of neurons, gli A cell of the middle germ layer of the embryo. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Mesodermal cells are pluripotent and the most abundant in the human body. They contribute to the development of several structures such as the skeletal muscles, bones, heart and blood vessels, kidneys, gonads, connective tissues, and certain layers of the skin. Hence, the mesoderm is often regarded as an active and diverse layer due to its role in forming many bodily structures. +In embryonic development, these cells are instrumental, contributing to the body's structures through a carefully coordinated sequence of morphogenetic movements. This process forms the complex multicellular architecture of tissues and organs from a simple ball of cells. Without the function of mesodermal cells, the body's integral structures and systems would cease to form correctly, leading to developmental disorders such as axial mesodermal dysplasia complex FMA:72554 ZFA:0009138 + https://cellxgene.cziscience.com/cellguide/CL_0000222 mesoblast mesoderm cell + + mesodermal cell @@ -6979,6 +7063,17 @@ Despite their overarching function in the support and protection of neurons, gli A cell of the middle germ layer of the embryo. MESH:D008648 + + + + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Mesodermal cells are pluripotent and the most abundant in the human body. They contribute to the development of several structures such as the skeletal muscles, bones, heart and blood vessels, kidneys, gonads, connective tissues, and certain layers of the skin. Hence, the mesoderm is often regarded as an active and diverse layer due to its role in forming many bodily structures. +In embryonic development, these cells are instrumental, contributing to the body's structures through a carefully coordinated sequence of morphogenetic movements. This process forms the complex multicellular architecture of tissues and organs from a simple ball of cells. Without the function of mesodermal cells, the body's integral structures and systems would cease to form correctly, leading to developmental disorders such as axial mesodermal dysplasia complex + DOI:10.1016/j.ceb.2019.07.012 + DOI:10.5535/arm.2016.40.1.162 + https://www.sciencedirect.com/topics/biochemistry-genetics-and-molecular-biology/mesoderm + @@ -7003,6 +7098,8 @@ Despite their overarching function in the support and protection of neurons, gli FMA:72555 ZFA:0009139 endoderm cell + + endodermal cell @@ -7086,6 +7183,8 @@ Despite their overarching function in the support and protection of neurons, gli red blood cell + + erythrocyte @@ -7128,7 +7227,8 @@ Despite their overarching function in the support and protection of neurons, gli Any cell that in taxon some Eukaryota. MESH:D005057 - + + eukaryotic cell @@ -7167,6 +7267,8 @@ Despite their overarching function in the support and protection of neurons, gli ZFA:0009154 + + eye photoreceptor cell @@ -7191,6 +7293,8 @@ Despite their overarching function in the support and protection of neurons, gli A cell whose primary function is to provide structural support, to provide strength and physical integrity to the organism. ZFA:0005745 + + structural cell @@ -7214,6 +7318,8 @@ Despite their overarching function in the support and protection of neurons, gli lens cell + + crystallin accumulating cell @@ -7224,6 +7330,8 @@ Despite their overarching function in the support and protection of neurons, gli A cell that is specialised to accumulate a particular substance(s). + + stuff accumulating cell @@ -7259,6 +7367,8 @@ Despite their overarching function in the support and protection of neurons, gli Any cell that is capable of some oxygen transport. ZFA:0009164 + + oxygen accumulating cell @@ -7291,6 +7401,8 @@ Despite their overarching function in the support and protection of neurons, gli A cell derived from the specialized ectoderm flanking each side of the embryonic neural plate, which after the closure of the neural tube, forms masses of cells that migrate out from the dorsal aspect of the neural tube to spread throughout the body. FMA:86667 ZFA:0007086 + + migratory neural crest cell @@ -7314,6 +7426,8 @@ Despite their overarching function in the support and protection of neurons, gli A mesenchymal cell in embryonic development found in a contracting mass and that gives rise to osteoprogenitors. ZFA:0009166 + + mesenchyme condensation cell @@ -7342,6 +7456,8 @@ Despite their overarching function in the support and protection of neurons, gli FMA:70564 ZFA:0009169 spongioblast + + glioblast (sensu Vertebrata) @@ -7373,6 +7489,8 @@ Despite their overarching function in the support and protection of neurons, gli Any animal cell containing pigment granules. ZFA:0009170 + + pigment cell (sensu Vertebrata) @@ -7422,6 +7540,8 @@ Despite their overarching function in the support and protection of neurons, gli A cell of the sclera of the eye. ZFA:0009174 + + scleral cell @@ -7470,6 +7590,8 @@ Despite their overarching function in the support and protection of neurons, gli A structural cell that is part of optic choroid. ZFA:0009175 + + choroidal cell of the eye @@ -7492,6 +7614,8 @@ Despite their overarching function in the support and protection of neurons, gli A cell of the outer layer of a blastula that gives rise to the ectoderm after gastrulation. + + epiblast cell @@ -7532,6 +7656,8 @@ Despite their overarching function in the support and protection of neurons, gli BTO:0000854 EHDAA2:0004546 FMA:72395 + + animal zygote @@ -7549,6 +7675,8 @@ Despite their overarching function in the support and protection of neurons, gli A cell whose function is determined by its response to an electric signal. ZFA:0009190 + + electrically responsive cell @@ -7566,62 +7694,64 @@ Despite their overarching function in the support and protection of neurons, gli - + - - - - - - - - - - - - - - - An interneuron that has its cell body in a central nervous system. - - ZFA:0009191 - - Interneurons are commonly described as being only found in the central nervous system. However, in CL we define 'interneuron' more broadly as any neuron that is neither a motor neuron nor a sensory neuron, regardless of its location, so we need this term to refer strictly to interneurons of the central nervous system. - CNS interneuron + + + A cell that initiates an electrical signal and passes that signal to another cell. + ZFA:0009193 + + + electrically signaling cell - + - An interneuron that has its cell body in a central nervous system. - doi:10.1016/B978-0-12-817424-1.00001-X + A cell that initiates an electrical signal and passes that signal to another cell. + FB:ma - + - ZFA:0009191 + ZFA:0009193 - + - - - A cell that initiates an electrical signal and passes that signal to another cell. - ZFA:0009193 - electrically signaling cell + + + + + + + + + A connective tissue cell of an organ found in the loose connective tissue. + + BTO:0002064 + FMA:83624 + ZFA:0009226 + + + + + + stromal cell - + - A cell that initiates an electrical signal and passes that signal to another cell. - FB:ma + A connective tissue cell of an organ found in the loose connective tissue. + GOC:tfm + MESH:D017154 - + - ZFA:0009193 + ZFA:0009226 @@ -7649,11 +7779,19 @@ Despite their overarching function in the support and protection of neurons, gli A precursor cell destined to differentiate into smooth muscle myocytes. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +A precursor to the smooth muscle cell, the smooth muscle myoblast, is integral to various body systems, including the cardiovascular, gastrointestinal, and respiratory systems. Smooth muscle myoblasts arise from the differentiation of mesenchymal stem cells, a process tightly regulated by specific genetic factors and environmental signals. Their role extends to myogenesis, particularly in the formation of muscular tissue, especially during embryonic development. +Smooth muscle myoblasts possess distinctive cellular characteristics. In contrast to skeletal muscle myoblasts, they do not fuse to create multinucleated fibers. Instead, they differentiate into individual, uninucleated smooth muscle cells. This differentiation unfolds in two distinct phases: proliferation, marked by rapid division to increase cell numbers, and differentiation, involving structural and functional transformation into mature smooth muscle cells. This intricate process is intricately mediated by various signaling molecules and transcription factors. +Functionally, smooth muscle myoblasts and the mature muscle cells they generate play pivotal roles in various physiological processes. Smooth muscle cells orchestrate involuntary muscle responses and are integral to body systems that regulate blood flow, propel food along the digestive tract, and control airflow in the respiratory tract. These diverse functions underscore the significance of smooth muscle myoblasts in the body's growth, maintenance, and overall function. FMA:84798 ZFA:0009235 + https://cellxgene.cziscience.com/cellguide/CL_0000514 myoblast, smooth muscle satellite cell + + smooth muscle myoblast @@ -7663,6 +7801,18 @@ Despite their overarching function in the support and protection of neurons, gli GOC:tfm MESH:D032390 + + + + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +A precursor to the smooth muscle cell, the smooth muscle myoblast, is integral to various body systems, including the cardiovascular, gastrointestinal, and respiratory systems. Smooth muscle myoblasts arise from the differentiation of mesenchymal stem cells, a process tightly regulated by specific genetic factors and environmental signals. Their role extends to myogenesis, particularly in the formation of muscular tissue, especially during embryonic development. +Smooth muscle myoblasts possess distinctive cellular characteristics. In contrast to skeletal muscle myoblasts, they do not fuse to create multinucleated fibers. Instead, they differentiate into individual, uninucleated smooth muscle cells. This differentiation unfolds in two distinct phases: proliferation, marked by rapid division to increase cell numbers, and differentiation, involving structural and functional transformation into mature smooth muscle cells. This intricate process is intricately mediated by various signaling molecules and transcription factors. +Functionally, smooth muscle myoblasts and the mature muscle cells they generate play pivotal roles in various physiological processes. Smooth muscle cells orchestrate involuntary muscle responses and are integral to body systems that regulate blood flow, propel food along the digestive tract, and control airflow in the respiratory tract. These diverse functions underscore the significance of smooth muscle myoblasts in the body's growth, maintenance, and overall function. + DOI:10.1074/jbc.RA118.001739 + https://www.ncbi.nlm.nih.gov/books/NBK544225/ + https://www.sciencedirect.com/topics/medicine-and-dentistry/smooth-muscle + @@ -7687,6 +7837,8 @@ Despite their overarching function in the support and protection of neurons, gli FMA:87653 ZFA:0009238 input neuron + + afferent neuron @@ -7712,6 +7864,8 @@ Despite their overarching function in the support and protection of neurons, gli ZFA:0009241 + + pigmented epithelial cell @@ -7747,6 +7901,8 @@ Despite their overarching function in the support and protection of neurons, gli nerve cell + + These cells are also reportedly CD4-negative and CD200-positive. They are also capable of producing CD40L and IFN-gamma. neuron @@ -7789,6 +7945,8 @@ Despite their overarching function in the support and protection of neurons, gli BTO:0003217 FMA:83377 ZFA:0009249 + + Derived from UBERON:0002342 neural crest. melanoblast @@ -7884,7 +8042,6 @@ Despite their overarching function in the support and protection of neurons, gli - @@ -7987,6 +8144,8 @@ Despite their overarching function in the support and protection of neurons, gli pronormoblast + + proerythroblast @@ -8034,7 +8193,6 @@ Despite their overarching function in the support and protection of neurons, gli - @@ -8060,6 +8218,8 @@ Despite their overarching function in the support and protection of neurons, gli early erythroblast early normoblast prorubricyte + + basophilic erythroblast @@ -8131,7 +8291,6 @@ Despite their overarching function in the support and protection of neurons, gli - @@ -8165,6 +8324,8 @@ Despite their overarching function in the support and protection of neurons, gli polychromatic normoblast polychromatophilic normoblast rubricyte + + polychromatophilic erythroblast @@ -8268,6 +8429,8 @@ Despite their overarching function in the support and protection of neurons, gli late erythoblast orthochromatic normoblast pyknotic eto enrythroblast + + orthochromatic erythroblast @@ -8484,6 +8647,8 @@ Despite their overarching function in the support and protection of neurons, gli promegacaryocyte promegakaryocyte + + Lineage negative is described here as CD2-negative, CD3-negative, CD4-negative, CD5-negative, CD8a-negative, CD14-negative, CD19-negative, CD20-negative, CD56-negative, Ly6g-negative, and Ter119-negative. megakaryocyte progenitor cell @@ -8557,6 +8722,8 @@ Despite their overarching function in the support and protection of neurons, gli megalokaryocyte + + Megakaryocytes are reportedly CD181-positive and CD182-positive. megakaryocyte @@ -8642,7 +8809,6 @@ Despite their overarching function in the support and protection of neurons, gli - @@ -8734,6 +8900,8 @@ Despite their overarching function in the support and protection of neurons, gli ZFA:0009252 + + reticulocyte @@ -8793,6 +8961,8 @@ Despite their overarching function in the support and protection of neurons, gli ACs + + amacrine cell @@ -8852,7 +9022,6 @@ Despite their overarching function in the support and protection of neurons, gli - @@ -8881,6 +9050,8 @@ Despite their overarching function in the support and protection of neurons, gli ZFA:0009258 angioblast chondroplast + + These cells are reportedly CD31-positive, CD34-positive, CD144-positive, CD309-positive, and TAL1-positive. angioblastic mesenchymal cell @@ -8925,6 +9096,8 @@ Despite their overarching function in the support and protection of neurons, gli ZFA:0009262 cone + + retinal cone cell @@ -8980,6 +9153,8 @@ Despite their overarching function in the support and protection of neurons, gli epithelial cell of cornea + + corneal epithelial cell @@ -9022,6 +9197,8 @@ Despite their overarching function in the support and protection of neurons, gli ZFA:0009275 rod + + retinal rod cell @@ -9066,6 +9243,8 @@ Despite their overarching function in the support and protection of neurons, gli Müller cell + + Mueller cell @@ -9120,6 +9299,8 @@ Despite their overarching function in the support and protection of neurons, gli WBbt:0006829 ZFA:0009290 + + glutamatergic neuron @@ -9169,6 +9350,8 @@ Despite their overarching function in the support and protection of neurons, gli A non-terminally differentiated cell that is capable of developing into a muscle cell. ZFA:0009291 + + muscle precursor cell @@ -9200,6 +9383,8 @@ Despite their overarching function in the support and protection of neurons, gli ZFA:0009292 forebrain radial glial cell + + Unlike that of mammals, the brain of adult teleost fish exhibits an intense and widespread neurogenic activity as a result of the persistence of radial glial cells acting as neural progenitors throughout life. radial glial cell @@ -9245,6 +9430,8 @@ radial glial cells acting as neural progenitors throughout life. neuroepithelial cell BTO:0004301 FMA:70557 + + The term "neuroepithelial cell" is used to describe both this cell type and sensory epithelial cell (CL:0000098). neurecto-epithelial cell @@ -9282,6 +9469,8 @@ radial glial cells acting as neural progenitors throughout life. CALOHA:TS-2086 MESH:D053687 ZFA:0009307 + + somatic stem cell @@ -9302,7 +9491,7 @@ radial glial cells acting as neural progenitors throughout life. - + @@ -9321,6 +9510,8 @@ radial glial cells acting as neural progenitors throughout life. RGCs + + retinal ganglion cell @@ -9373,6 +9564,8 @@ radial glial cells acting as neural progenitors throughout life. HCs + + retina horizontal cell @@ -9412,7 +9605,7 @@ radial glial cells acting as neural progenitors throughout life. - + @@ -9420,7 +9613,6 @@ radial glial cells acting as neural progenitors throughout life. - @@ -9454,6 +9646,8 @@ radial glial cells acting as neural progenitors throughout life. BPs + + retinal bipolar neuron @@ -9523,6 +9717,8 @@ radial glial cells acting as neural progenitors throughout life. MESH:D022423 ZFA:0009324 + + myeloid cell @@ -9558,6 +9754,8 @@ radial glial cells acting as neural progenitors throughout life. ZFA:0009325 erythropoietic cell + + Note that in FMA erythropoietic cells are types of nucleated erythrocytes and thus don't include erythrocytes. erythroid lineage cell @@ -9745,6 +9943,8 @@ radial glial cells acting as neural progenitors throughout life. normoblast + + erythroblast @@ -9842,7 +10042,6 @@ radial glial cells acting as neural progenitors throughout life. - @@ -9949,6 +10148,8 @@ radial glial cells acting as neural progenitors throughout life. hemopoietic progenitor cell + + Markers differ between mouse and human. hematopoietic multipotent progenitor cell @@ -10000,6 +10201,8 @@ radial glial cells acting as neural progenitors throughout life. FMA:70339 ZFA:0009356 + + Note that this is a class of cell types, not an identified single cell type. myeloid lineage restricted progenitor cell @@ -10041,6 +10244,8 @@ radial glial cells acting as neural progenitors throughout life. haemopoietic cell hemopoietic cell + + hematopoietic cell @@ -10092,6 +10297,8 @@ radial glial cells acting as neural progenitors throughout life. 2010-01-06T03:43:20Z + + hematopoietic lineage restricted progenitor cell @@ -10136,6 +10343,8 @@ radial glial cells acting as neural progenitors throughout life. 2010-01-06T03:43:27Z + + This cell type is intended to be compatible with any vertebrate hematopoietic oligopotent progenitor cell. For mammalian hematopoietic oligopotent progenitor cells known to be lineage-negative, please use the term 'hematopoietic oligopotent progenitor cell' (CL_0001060). hematopoietic oligopotent progenitor cell @@ -10176,6 +10385,8 @@ radial glial cells acting as neural progenitors throughout life. 2010-06-29T03:38:22Z FMA:69074 ZFA:0009385 + + ecto-epithelial cell @@ -10221,6 +10432,8 @@ radial glial cells acting as neural progenitors throughout life. FMA:69076 ZFA:0009388 epithelial mesenchymal cell + + meso-epithelial cell @@ -10245,13 +10458,21 @@ radial glial cells acting as neural progenitors throughout life. An endothelial cell of the vascular tree, which includes blood vessels and lymphatic vessels. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Endothelial cells of the vascular tree, commonly referred to as vascular endothelial cells, line the entire circulatory system, from the heart to the smallest capillaries. These cells have a unique, flattened shape, and are tightly bound together, forming a thin layer known as the endothelium. The endothelium is responsible for maintaining the interior surface of blood vessels, and plays a critical role in ensuring the smooth flow of blood. +Vascular endothelial cells act as a semi-permeable membrane, controlling the passage of materials and the transit of white blood cells into and out of the bloodstream. These cells are also involved in blood coagulation. When a blood vessel is damaged, endothelial cells promote clotting to prevent excessive bleeding and facilitate wound healing. Other functions include regulation of blood pressure and blood volume by releasing vasodilators and vasoconstrictors to either widen or constrict blood vessels, accordingly. +Furthermore, the endothelial cells are crucial in the formation of new blood vessels, a process known as angiogenesis. This is particularly important in wound healing and the growth of new tissues during development or after injury. In the context of diseases such as cancer, angiogenesis helps facilitate tumor growth by providing nutrients and oxygen. 2010-08-24T02:06:40Z BTO:0001854 CALOHA:TS-1106 FMA:67755 + https://cellxgene.cziscience.com/cellguide/CL_0002139 vascular endothelial cell cubodial endothelial cell of vascular tree + + These cells are reportedly CD31-positive, CD34-positive, CD144-positive, TAL1-positive. endothelial cell of vascular tree @@ -10263,6 +10484,19 @@ radial glial cells acting as neural progenitors throughout life. GOC:tfm PMID:12768659 + + + + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Endothelial cells of the vascular tree, commonly referred to as vascular endothelial cells, line the entire circulatory system, from the heart to the smallest capillaries. These cells have a unique, flattened shape, and are tightly bound together, forming a thin layer known as the endothelium. The endothelium is responsible for maintaining the interior surface of blood vessels, and plays a critical role in ensuring the smooth flow of blood. +Vascular endothelial cells act as a semi-permeable membrane, controlling the passage of materials and the transit of white blood cells into and out of the bloodstream. These cells are also involved in blood coagulation. When a blood vessel is damaged, endothelial cells promote clotting to prevent excessive bleeding and facilitate wound healing. Other functions include regulation of blood pressure and blood volume by releasing vasodilators and vasoconstrictors to either widen or constrict blood vessels, accordingly. +Furthermore, the endothelial cells are crucial in the formation of new blood vessels, a process known as angiogenesis. This is particularly important in wound healing and the growth of new tissues during development or after injury. In the context of diseases such as cancer, angiogenesis helps facilitate tumor growth by providing nutrients and oxygen. + DOI:10.1038/s41569-022-00770-1 + DOI:10.1186/s12872-015-0124-z + DOI:10.3389/fphys.2022.863265/full + https://www.sciencedirect.com/topics/medicine-and-dentistry/vascular-endothelial-cell + @@ -10274,6 +10508,8 @@ radial glial cells acting as neural progenitors throughout life. 2010-08-26T08:31:08Z FMA:70556 + + general ecto-epithelial cell @@ -10301,6 +10537,8 @@ radial glial cells acting as neural progenitors throughout life. 2010-09-07T10:38:03Z FMA:70950 + + vertebrate lens cell @@ -10338,6 +10576,8 @@ radial glial cells acting as neural progenitors throughout life. 2010-09-07T03:32:33Z FMA:67513 + + nucleate cell @@ -10362,7 +10602,7 @@ radial glial cells acting as neural progenitors throughout life. A cell that is part of pigmented ciliary epithelium. This cell type uptakes sodium and chloride ions from stromal interstitium and passes the ions to non-pigmented ciliary epithelial cells via gap junctions. - This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. Pigmented ciliary epithelial cells, which are a type of pigment cell, have a crucial function within the eye's ciliary body. The ciliary body, located behind the iris, is one of the eye’s most vital structures and consists of two types of epithelial cells: the pigmented and the non-pigmented ciliary epithelial cells. The pigmented ciliary epithelial cells form the outer layer of the ciliary body and exhibit a black or brown pigmentation due to the melanin they contain. One key function of pigmented ciliary epithelial cells is to aid in the formation of aqueous humor, an intraocular fluid that nourishes the cornea and lens, and maintains intraocular pressure which is essential for the eye’s shape and light refraction. These cells facilitate this function in conjunction with the non-pigmented ciliary epithelial cells. Together, the pigmented and non-pigmented ciliary epithelial cells form a bilayer epithelium that allows the secretion of aqueous humor through a bi-directional fluid transport mechanism. @@ -10373,6 +10613,8 @@ Pigmented ciliary epithelial cells also contribute to the blood-aqueous barrier, PE cell + + In a consensus model of unidirectional secretion, aqueous humour is formed by transferring solute, principally NaCl, from stroma to posterior chamber, with water passively following the osmotic gradient. Unidirectional secretion comprises three sequential steps. First, NaCl is transferred from the stromal interstitium into the pigmented ciliary epithelial (PE) cells. Second, solute passes from the PE into the non-pigmented ciliary epithelial (NPE) cells through gap junctions. Finally, NPE cells release Na+ and Cl− into the aqueous humour. pigmented ciliary epithelial cell @@ -10386,7 +10628,7 @@ Pigmented ciliary epithelial cells also contribute to the blood-aqueous barrier, - This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. Pigmented ciliary epithelial cells, which are a type of pigment cell, have a crucial function within the eye's ciliary body. The ciliary body, located behind the iris, is one of the eye’s most vital structures and consists of two types of epithelial cells: the pigmented and the non-pigmented ciliary epithelial cells. The pigmented ciliary epithelial cells form the outer layer of the ciliary body and exhibit a black or brown pigmentation due to the melanin they contain. One key function of pigmented ciliary epithelial cells is to aid in the formation of aqueous humor, an intraocular fluid that nourishes the cornea and lens, and maintains intraocular pressure which is essential for the eye’s shape and light refraction. These cells facilitate this function in conjunction with the non-pigmented ciliary epithelial cells. Together, the pigmented and non-pigmented ciliary epithelial cells form a bilayer epithelium that allows the secretion of aqueous humor through a bi-directional fluid transport mechanism. @@ -10428,6 +10670,8 @@ Pigmented ciliary epithelial cells also contribute to the blood-aqueous barrier, nonpigmented ciliary epithelial cell + + In a consensus model of unidirectional secretion, aqueous humour is formed by transferring solute, principally NaCl, from stroma to posterior chamber, with water passively following the osmotic gradient. Unidirectional secretion comprises three sequential steps. First, NaCl is transferred from the stromal interstitium into the pigmented ciliary epithelial (PE) cells. Second, solute passes from the PE into the non-pigmented ciliary epithelial (NPE) cells through gap junctions. Finally, NPE cells release Na+ and Cl− into the aqueous humour. non-pigmented ciliary epithelial cell @@ -10487,6 +10731,8 @@ Pigmented ciliary epithelial cells also contribute to the blood-aqueous barrier, CALOHA:TS-2040 FMA:70333 + + neural cell @@ -10528,6 +10774,8 @@ Pigmented ciliary epithelial cells also contribute to the blood-aqueous barrier, MESH:D003239 ZFA:0009392 + + connective tissue cell @@ -10552,11 +10800,19 @@ Pigmented ciliary epithelial cells also contribute to the blood-aqueous barrier, A cell of the embryo. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Embryonic cells in metazoans, which include all multicellular animals, are biological units in their earliest developmental stages from conception until the organism is fully formed. +They are derived from a fertilized egg, which undergoes a series of cell divisions to produce a multicellular organism. During the early phases of embryonic development, these cells exhibit pluripotency, meaning they possess the potential to differentiate into a diverse array of specialized cell types that constitute different body tissues and structures. +The balance between cell proliferation and differentiation in embryonic cells is crucial for successful development. When cells continue to divide without differentiating, overgrowth may occur leading to conditions such as teratomas (tumors of embryonic cells). Conversely, if cell differentiation proceeds at the expense of cell proliferation, developmental anomalies could occur regarding size or mass of the organism or its parts. 2010-09-15T03:39:21Z CALOHA:TS-0263 FMA:82840 WBbt:0007028 ZFA:0007089 + https://cellxgene.cziscience.com/cellguide/CL_0002321 + + embryonic cell (metazoa) @@ -10565,6 +10821,18 @@ Pigmented ciliary epithelial cells also contribute to the blood-aqueous barrier, A cell of the embryo. FMA:0618947256 + + + + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Embryonic cells in metazoans, which include all multicellular animals, are biological units in their earliest developmental stages from conception until the organism is fully formed. +They are derived from a fertilized egg, which undergoes a series of cell divisions to produce a multicellular organism. During the early phases of embryonic development, these cells exhibit pluripotency, meaning they possess the potential to differentiate into a diverse array of specialized cell types that constitute different body tissues and structures. +The balance between cell proliferation and differentiation in embryonic cells is crucial for successful development. When cells continue to divide without differentiating, overgrowth may occur leading to conditions such as teratomas (tumors of embryonic cells). Conversely, if cell differentiation proceeds at the expense of cell proliferation, developmental anomalies could occur regarding size or mass of the organism or its parts. + DOI:10.1002/iub.1404 + DOI:10.1093/molehr/gan048 + https://www.ncbi.nlm.nih.gov/books/NBK9906/ + @@ -10603,6 +10871,8 @@ Pigmented ciliary epithelial cells also contribute to the blood-aqueous barrier, corneal keratocyte + + keratocyte @@ -10642,6 +10912,8 @@ Pigmented ciliary epithelial cells also contribute to the blood-aqueous barrier, 2010-12-03T03:25:32Z + + retinal melanocyte @@ -10683,6 +10955,8 @@ Pigmented ciliary epithelial cells also contribute to the blood-aqueous barrier, FMA:83808 FMA:84791 heart cell + + From Onard of the FMA: Cardiac muscle cell or cardiac myocyte is a striated muscle cell. Cardiocyte on the other hand is any cell in the heart which includes cells other than muscle cells (e.g. endothelial cell of endocardium). Unless there is a consensus among anatomists that cardiocytes refer only to muscle cells, we will treat them as a general class of cells in the heart. cardiocyte @@ -10721,7 +10995,10 @@ Pigmented ciliary epithelial cells also contribute to the blood-aqueous barrier, 2011-03-01T05:28:52Z + + + iris pigment epithelial cell @@ -10765,7 +11042,7 @@ Pigmented ciliary epithelial cells also contribute to the blood-aqueous barrier, A blood vessel endothelial cell that is part of the retina. - This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. Retinal blood vessel endothelial cells constitute the innermost lining of the blood vessels found in the retina, the light-sensitive layer of tissue at the back of the eye. The primary role of these cells revolves around their location within the retinal vascular system, forming the structure of the blood-retinal barrier, a subset of the larger blood-ocular barrier system. The endothelial cells are particularly involved in the growth of new retinal blood vessels from pre-existing ones (angiogenesis); this is critical in managing the amount of oxygen and essential nutrients delivered to the ocular tissues. They are crucial for maintaining homeostasis in the retinal environment by controlling the exchange of molecules between the blood and the retina. Furthermore, they mediate immune cell trafficking, supporting the immune privilege of the eye by preventing the unrestricted infiltration of inflammatory cells into the retina, thus maintaining ocular health and normal vision. @@ -10774,6 +11051,8 @@ The malfunction or dysfunction of retinal blood vessel endothelial cells is impl https://cellxgene.cziscience.com/cellguide/CL_0002585 + + retinal blood vessel endothelial cell @@ -10792,7 +11071,7 @@ The malfunction or dysfunction of retinal blood vessel endothelial cells is impl - This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. Retinal blood vessel endothelial cells constitute the innermost lining of the blood vessels found in the retina, the light-sensitive layer of tissue at the back of the eye. The primary role of these cells revolves around their location within the retinal vascular system, forming the structure of the blood-retinal barrier, a subset of the larger blood-ocular barrier system. The endothelial cells are particularly involved in the growth of new retinal blood vessels from pre-existing ones (angiogenesis); this is critical in managing the amount of oxygen and essential nutrients delivered to the ocular tissues. They are crucial for maintaining homeostasis in the retinal environment by controlling the exchange of molecules between the blood and the retina. Furthermore, they mediate immune cell trafficking, supporting the immune privilege of the eye by preventing the unrestricted infiltration of inflammatory cells into the retina, thus maintaining ocular health and normal vision. @@ -10837,7 +11116,7 @@ The malfunction or dysfunction of retinal blood vessel endothelial cells is impl An epithelial cell of the retinal pigmented epithelium. - This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. Retinal pigment epithelial (RPE) cells form a single layer of cells at the back of the eye sandwiched between the neurosensory retina and the choroid, playing a significant role in maintaining vision health. These pigment-laden cells are highly specialized and perform an array of metabolic and transport functions essential for the maintenance of the photoreceptor cells (rods and cones) in the retina. The pigmentation of RPE cells actively aids in the absorption of excess light and the prevention of light scattering, thus enhancing the eye's optical properties. The retinal pigment epithelium forms a key part of the blood/retina barrier. The cells have long sheet-like microvilli on their apical membrane that project into the light-sensitive outer segments of the photoreceptors, forming a close structural interaction. The basolateral membrane of the RPE interacts with the underlying Bruch’s membrane, which separates the RPE cells from fenestrated endothelium of the choriocapillaris. @@ -10849,6 +11128,8 @@ Beyond this, RPE cells take part in the phagocytosis process, where they digest https://cellxgene.cziscience.com/cellguide/CL_0002586 + + retinal pigment epithelial cell @@ -10861,7 +11142,7 @@ Beyond this, RPE cells take part in the phagocytosis process, where they digest - This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. Retinal pigment epithelial (RPE) cells form a single layer of cells at the back of the eye sandwiched between the neurosensory retina and the choroid, playing a significant role in maintaining vision health. These pigment-laden cells are highly specialized and perform an array of metabolic and transport functions essential for the maintenance of the photoreceptor cells (rods and cones) in the retina. The pigmentation of RPE cells actively aids in the absorption of excess light and the prevention of light scattering, thus enhancing the eye's optical properties. The retinal pigment epithelium forms a key part of the blood/retina barrier. The cells have long sheet-like microvilli on their apical membrane that project into the light-sensitive outer segments of the photoreceptors, forming a close structural interaction. The basolateral membrane of the RPE interacts with the underlying Bruch’s membrane, which separates the RPE cells from fenestrated endothelium of the choriocapillaris. @@ -10888,6 +11169,9 @@ Beyond this, RPE cells take part in the phagocytosis process, where they digest A multi-fate stem cell that can give rise to different retinal cell types including rod and cone cells. 2011-08-16T02:38:01Z + + + retinal progenitor cell @@ -10915,7 +11199,7 @@ Beyond this, RPE cells take part in the phagocytosis process, where they digest - + @@ -10924,13 +11208,15 @@ Beyond this, RPE cells take part in the phagocytosis process, where they digest A CNS interneuron located in the spinal cord. ZFA:0000778 + + Is_a interneuron, part_of UBERON:0002240. spinal cord interneuron - + true @@ -10968,6 +11254,8 @@ Beyond this, RPE cells take part in the phagocytosis process, where they digest 2012-06-27T08:27:35Z ZFA:0007084 + + premigratory neural crest cell @@ -10990,6 +11278,8 @@ Beyond this, RPE cells take part in the phagocytosis process, where they digest Any muscle cell in which the fibers are not organised into sarcomeres. + + non-striated muscle cell @@ -11007,6 +11297,8 @@ Beyond this, RPE cells take part in the phagocytosis process, where they digest Any hematopoietic cell that is a precursor of some other hematopoietic cell type. + + hematopoietic precursor cell @@ -11041,6 +11333,8 @@ Beyond this, RPE cells take part in the phagocytosis process, where they digest A muscle cell that is part of some visceral muscle. FBbt:00005070 + + visceral muscle cell @@ -11079,6 +11373,8 @@ Beyond this, RPE cells take part in the phagocytosis process, where they digest mesenchyme cell + + mesenchymal cell @@ -11109,6 +11405,8 @@ Beyond this, RPE cells take part in the phagocytosis process, where they digest Any neuron that is capable of part of some visual perception. 2017-07-09T19:12:36Z + + visual system neuron @@ -11144,6 +11442,8 @@ Beyond this, RPE cells take part in the phagocytosis process, where they digest Any cell in the retina, the innermost layer or coating at the back of the eyeball, which is sensitive to light and in which the optic nerve terminates. PMID:10702418 + + retinal cell @@ -11171,19 +11471,21 @@ Beyond this, RPE cells take part in the phagocytosis process, where they digest - + Any photoreceptor cell that is part of some camera-type eye. camera type eye photoreceptor cell + + camera-type eye photoreceptor cell - + - + https://github.com/obophenotype/cell-ontology/issues/2245 @@ -11201,6 +11503,8 @@ Beyond this, RPE cells take part in the phagocytosis process, where they digest A zygote in a plant or an animal. MESH:D015053 + + zygote @@ -11213,13 +11517,15 @@ Beyond this, RPE cells take part in the phagocytosis process, where they digest A cell of the neural crest. Neural crest cells are multipotent. Premigratory neural crest cells are found at the neural plate boarder, some of which will undergo ectomesynchymal transition and delamination to form migratory neural crest cells. - This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. Neural crest cells are a group of transient and highly migratory cells that originate from the neuroectoderm during the early stages of embryonic development. They are multipotent cells with an exceptional degree of plasticity, capable of differentiating into various somatic cell types and therefore play a fundamental role in the formation of various organs and tissues, making them critical contributors to the developing embryo. After the initiation of neurulation (the formation of the neural tube) neural crest cells start to undergo epithelial-to-mesenchymal transition and delaminate and migrate from the dorsal neural tube to several regions throughout the embryo. They differentiate into a range of diverse cell types, such as neurons and glial cells of the peripheral nervous system, including sensory and autonomic neurons. They also contribute to the formation of adrenal glands, pigment cells in the skin (melanocytes), cardiac structures, including parts of the heart septum and major arteries, as well as bones and cartilage of the face and skull. Disorders or aberrations in the development or migration of the neural crest cells can lead to serious congenital malformations, such as neurocristopathies, including Hirschsprung disease, neuroblastoma, and neurofibromatosis. https://cellxgene.cziscience.com/cellguide/CL_0011012 + + neural crest cell @@ -11232,7 +11538,7 @@ Disorders or aberrations in the development or migration of the neural crest cel - This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. Neural crest cells are a group of transient and highly migratory cells that originate from the neuroectoderm during the early stages of embryonic development. They are multipotent cells with an exceptional degree of plasticity, capable of differentiating into various somatic cell types and therefore play a fundamental role in the formation of various organs and tissues, making them critical contributors to the developing embryo. After the initiation of neurulation (the formation of the neural tube) neural crest cells start to undergo epithelial-to-mesenchymal transition and delaminate and migrate from the dorsal neural tube to several regions throughout the embryo. They differentiate into a range of diverse cell types, such as neurons and glial cells of the peripheral nervous system, including sensory and autonomic neurons. They also contribute to the formation of adrenal glands, pigment cells in the skin (melanocytes), cardiac structures, including parts of the heart septum and major arteries, as well as bones and cartilage of the face and skull. @@ -11270,6 +11576,8 @@ Disorders or aberrations in the development or migration of the neural crest cel A precursor cell that has a tendency to differentiate into a specific type of cell. They are descendants of stem cells, only they are more constrained in their differentiation potential or capacity for self-renewal, and are often more limited in both senses. + + progenitor cell @@ -11297,6 +11605,8 @@ Disorders or aberrations in the development or migration of the neural crest cel carries information from the inner plexiform layer and the outer plexiform layer. + + Need to MIREOT retinal inner nuclear layer (part of) interplexiform cell @@ -11335,6 +11645,8 @@ plexiform layer. A cell that, by division or terminal differentiation, can give rise to other cell types. + + Work is needed on GO 'cell differentiation' before it is clear whether the equivalent class definition 'native cell' that capable_of some 'cell differentiation' works. Also, may want to consider merging this with non-terminally differentiated cell. precursor cell @@ -11479,6 +11791,8 @@ plexiform layer. epithelial cell of conjunctiva + + conjunctival epithelial cell @@ -11524,10 +11838,18 @@ plexiform layer. A smooth muscle cell that is part of the ciliary body. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Ciliary muscle cells are specialized contractile cells that constitute the ciliary muscle, a component of the eye in vertebrates. These cells form a ring around the iris, the eye's colored part. Ciliary muscle cells fall into the category of smooth muscle cells, characterized by their lack of the striations typical of skeletal and cardiac muscle cells. Their shape is elongated and pointed at both ends, and they occur in multi-nucleated syncytia where many cells share the same cytoplasm. +Ciliary muscle cells primarily control the eye's accommodation, adjusting the thickness and curvature of the lens to fine-tune the focus of light on the retina. When ciliary muscle cells contract, tension on the zonular fibers holding the lens in place is reduced, allowing the lens to become thicker and increase its refractive power. Conversely, when the ciliary muscle cells relax, the tension on the zonular fibers increases, causing the lens to become flatter and decrease its refractive power. This adjustment facilitates clear vision at different distances, ranging from near to far objects. +Additionally, ciliary muscle cells play a role in draining the eye's aqueous humor, which is the clear fluid that fills the anterior chamber of the eye between the cornea and the lens. By controlling the shape of the surrounding trabecular meshwork through muscle contractions and relaxations, ciliary muscle cells indirectly regulate intraocular pressure, a factor critical for preventing ocular conditions like glaucoma. FMA:70610 + https://cellxgene.cziscience.com/cellguide/CL_1000443 smooth muscle cell of ciliary body + + ciliary muscle cell @@ -11542,6 +11864,19 @@ plexiform layer. A smooth muscle cell that is part of the ciliary body. GOC:tfm + + + + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Ciliary muscle cells are specialized contractile cells that constitute the ciliary muscle, a component of the eye in vertebrates. These cells form a ring around the iris, the eye's colored part. Ciliary muscle cells fall into the category of smooth muscle cells, characterized by their lack of the striations typical of skeletal and cardiac muscle cells. Their shape is elongated and pointed at both ends, and they occur in multi-nucleated syncytia where many cells share the same cytoplasm. +Ciliary muscle cells primarily control the eye's accommodation, adjusting the thickness and curvature of the lens to fine-tune the focus of light on the retina. When ciliary muscle cells contract, tension on the zonular fibers holding the lens in place is reduced, allowing the lens to become thicker and increase its refractive power. Conversely, when the ciliary muscle cells relax, the tension on the zonular fibers increases, causing the lens to become flatter and decrease its refractive power. This adjustment facilitates clear vision at different distances, ranging from near to far objects. +Additionally, ciliary muscle cells play a role in draining the eye's aqueous humor, which is the clear fluid that fills the anterior chamber of the eye between the cornea and the lens. By controlling the shape of the surrounding trabecular meshwork through muscle contractions and relaxations, ciliary muscle cells indirectly regulate intraocular pressure, a factor critical for preventing ocular conditions like glaucoma. + DOI:10.1016/S1350-9462(98)00011-1 + DOI:10.1038/srep31171 + DOI:10.1111/j.1444-0938.2008.00260.x + https://www.sciencedirect.com/topics/medicine-and-dentistry/ciliary-muscle + @@ -11576,6 +11911,8 @@ plexiform layer. 2014-06-25T01:17:43Z CL:2000029 + + central nervous system neuron @@ -11602,6 +11939,8 @@ plexiform layer. retinal stem cell + + retinoblast @@ -11645,7 +11984,10 @@ plexiform layer. 2023-03-02T14:38:32Z retinal astroglia + + + In response to elevated intraocular pressure, a retinal astrocyte may modulate extracellular matrix remodeling. In the human retina, a retinal astrocyte is GFAP-positive, SOD3-positive and GYPC-positive. retinal astrocyte @@ -11707,7 +12049,6 @@ plexiform layer. Progression through the phases of the mitotic cell cycle, the most common eukaryotic cell cycle, which canonically comprises four successive phases called G1, S, G2, and M and includes replication of the genome and the subsequent segregation of chromosomes into daughter cells. In some variant cell cycles nuclear replication or nuclear division may not be followed by cell division, or G1 and G2 phases may be absent. - GO:0007067 Wikipedia:Mitosis biological_process mitosis @@ -11778,9 +12119,6 @@ plexiform layer. The ordered and organized complex of DNA, protein, and sometimes RNA, that forms the chromosome. https://github.com/geneontology/go-ontology/issues/28301 - GO:0000789 - GO:0000790 - GO:0005717 NIF_Subcellular:sao1615953555 cytoplasmic chromatin nuclear chromatin @@ -11806,8 +12144,6 @@ plexiform layer. A compact and highly condensed form of chromatin that is refractory to transcription. https://github.com/geneontology/go-ontology/issues/22355 - GO:0005720 - GO:0035328 NIF_Subcellular:sao581845896 Wikipedia:Heterochromatin transcriptionally inactive chromatin @@ -12143,7 +12479,6 @@ plexiform layer. The formation of a tube from the flat layer of ectodermal cells known as the neural plate. This will give rise to the central nervous system. - GO:0001679 Wikipedia:Neurulation neural tube morphogenesis neurulation @@ -12440,7 +12775,6 @@ plexiform layer. A location, relative to cellular compartments and structures, occupied by a macromolecular machine. There are three types of cellular components described in the gene ontology: (1) the cellular anatomical entity where a gene product carries out a molecular function (e.g., plasma membrane, cytoskeleton) or membrane-enclosed compartments (e.g., mitochondrion); (2) virion components, where viral proteins act, and (3) the stable macromolecular complexes of which gene product are parts (e.g., the clathrin complex). https://github.com/geneontology/go-ontology/issues/17729 - GO:0008372 NIF_Subcellular:sao1337158144 cell or subcellular entity cellular component @@ -12538,32 +12872,32 @@ plexiform layer. - - + + A protein complex consisting of three collagen chains assembled into a left-handed triple helix. These trimers typically assemble into higher order structures. Wikipedia:Collagen cellular_component GO:0005581 collagen trimer - + - + - + PMID:12382326 - + PMID:12382326 @@ -12606,8 +12940,6 @@ plexiform layer. A collagen-containing extracellular matrix consisting of a thin layer of dense material found in various animal tissues interposed between the cells and the adjacent connective tissue. It consists of the basal lamina plus an associated layer of reticulin fibers. - GO:0005605 - GO:0008003 Wikipedia:Basement_membrane cellular_component basal lamina @@ -12873,7 +13205,12 @@ plexiform layer. - + + + + + + @@ -12881,7 +13218,6 @@ plexiform layer. An intracellular organelle, about 200 A in diameter, consisting of RNA and protein. It is the site of protein biosynthesis resulting from translation of messenger RNA (mRNA). It consists of two subunits, one large and one small, each containing only protein and RNA. Both the ribosome and its subunits are characterized by their sedimentation coefficients, expressed in Svedberg units (symbol: S). Hence, the prokaryotic ribosome (70S) comprises a large (50S) subunit and a small (30S) subunit, while the eukaryotic ribosome (80S) comprises a large (60S) subunit and a small (40S) subunit. Two sites on the ribosomal large subunit are involved in translation, namely the aminoacyl site (A site) and peptidyl site (P site). Ribosomes from prokaryotes, eukaryotes, mitochondria, and chloroplasts have characteristically distinct ribosomal proteins. - GO:0033279 NIF_Subcellular:sao1429207766 Wikipedia:Ribosome free ribosome @@ -12934,8 +13270,6 @@ plexiform layer. The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins. - GO:0005887 - GO:0005904 juxtamembrane NIF_Subcellular:sao1663586795 Wikipedia:Cell_membrane @@ -13051,9 +13385,6 @@ plexiform layer. The cellular metabolic process in which a protein is formed, using the sequence of a mature mRNA or circRNA molecule to specify the sequence of amino acids in a polypeptide chain. Translation is mediated by the ribosome, and begins with the formation of a ternary complex between aminoacylated initiator methionine tRNA, GTP, and initiation factor 2, which subsequently associates with the small subunit of the ribosome and an mRNA or circRNA. Translation ends with the release of a polypeptide chain from the ribosome. - GO:0006416 - GO:0006453 - GO:0043037 Wikipedia:Translation_(genetics) protein anabolism protein biosynthesis @@ -13086,7 +13417,7 @@ plexiform layer. - + @@ -13100,8 +13431,6 @@ plexiform layer. The process preceding formation of the peptide bond between the first two amino acids of a protein. This includes the formation of a complex of the ribosome, mRNA or circRNA, and an initiation complex that contains the first aminoacyl-tRNA. - GO:0006440 - GO:0006454 biopolymerisation biopolymerization protein synthesis initiation @@ -13131,8 +13460,6 @@ plexiform layer. The successive addition of amino acid residues to a nascent polypeptide chain during protein biosynthesis. - GO:0006442 - GO:0006455 protein synthesis elongation translation elongation biological_process @@ -13160,8 +13487,6 @@ plexiform layer. The process resulting in the release of a polypeptide chain from the ribosome, usually in response to a termination codon (UAA, UAG, or UGA in the universal genetic code). - GO:0006443 - GO:0006456 protein synthesis termination translation termination translational complex disassembly @@ -13185,11 +13510,7 @@ plexiform layer. The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter or a transporter complex, a pore or a motor protein. https://github.com/geneontology/go-ontology/issues/20292 - jl 2012-12-13T16:25:32Z - GO:0015457 - GO:0015460 - GO:0044765 biological_process single-organism transport GO:0006810 @@ -13276,7 +13597,6 @@ plexiform layer. The directed movement of amino acids, organic acids containing one or more amino substituents, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. - GO:0006866 biological_process GO:0006865 @@ -13323,8 +13643,6 @@ plexiform layer. A programmed cell death process which begins when a cell receives an internal (e.g. DNA damage) or external signal (e.g. an extracellular death ligand), and proceeds through a series of biochemical events (signaling pathway phase) which trigger an execution phase. The execution phase is the last step of an apoptotic process, and is typically characterized by rounding-up of the cell, retraction of pseudopodes, reduction of cellular volume (pyknosis), chromatin condensation, nuclear fragmentation (karyorrhexis), plasma membrane blebbing and fragmentation of the cell into apoptotic bodies. When the execution phase is completed, the cell has died. - GO:0006917 - GO:0008632 cell suicide cellular suicide Wikipedia:Apoptosis @@ -13467,9 +13785,7 @@ plexiform layer. A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of an organelle within a cell. An organelle is an organized structure of distinctive morphology and function. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton. Excludes the plasma membrane. https://github.com/geneontology/go-ontology/issues/27189 - jl 2013-12-19T15:25:51Z - GO:1902589 organelle organisation single organism organelle organization biological_process @@ -13602,11 +13918,6 @@ plexiform layer. The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell. - GO:0023014 - GO:0023015 - GO:0023016 - GO:0023033 - GO:0023045 Wikipedia:Signal_transduction signaling cascade signalling cascade @@ -13738,7 +14049,6 @@ plexiform layer. The regulated release of neurotransmitter from the presynapse into the synaptic cleft via calcium-regulated exocytosis during synaptic transmission. - GO:0010554 neurotransmitter release neurotransmitter secretory pathway biological_process @@ -14076,7 +14386,6 @@ plexiform layer. The flow of blood through the body of an animal, enabling the transport of nutrients to the tissues and the removal of waste products. - GO:0070261 biological_process hemolymph circulation GO:0008015 @@ -14136,11 +14445,7 @@ plexiform layer. A biological process is the execution of a genetically-encoded biological module or program. It consists of all the steps required to achieve the specific biological objective of the module. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence. https://github.com/geneontology/go-ontology/issues/24968 - jl 2012-09-19T15:05:24Z - GO:0000004 - GO:0007582 - GO:0044699 Wikipedia:Biological_process biological process physiological process @@ -14170,21 +14475,15 @@ plexiform layer. - + - The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation. + A cellular process consisting of the biochemical pathways by which a living organism transforms chemical substances. This includes including anabolism (biosynthetic process) and catabolism (catabolic process). Metabolic processes includes the transformation of small molecules, as well macromolecular processes such as DNA repair and replication, protein synthesis and degradation. https://github.com/geneontology/go-ontology/issues/26424 - jl + https://github.com/geneontology/go-ontology/issues/28932 2012-10-17T15:46:40Z - GO:0044236 - GO:0044710 Wikipedia:Metabolism metabolism - metabolic process resulting in cell growth - metabolism resulting in cell growth - multicellular organism metabolic process biological_process - single-organism metabolic process GO:0008152 @@ -14199,7 +14498,7 @@ plexiform layer. - The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation. + A cellular process consisting of the biochemical pathways by which a living organism transforms chemical substances. This includes including anabolism (biosynthetic process) and catabolism (catabolic process). Metabolic processes includes the transformation of small molecules, as well macromolecular processes such as DNA repair and replication, protein synthesis and degradation. GOC:go_curators ISBN:0198547684 @@ -14235,11 +14534,9 @@ plexiform layer. - The chemical reactions and pathways resulting in the formation of substances; typically the energy-requiring part of metabolism in which simpler substances are transformed into more complex ones. - jl + A cellular process consisting of the biochemical pathways by which a living organism synthesizes chemical substances. This typically represents the energy-requiring part of metabolism in which simpler substances are transformed into more complex ones. + https://github.com/geneontology/go-ontology/issues/28932 2012-10-17T15:52:18Z - GO:0044274 - GO:0044711 formation Wikipedia:Anabolism anabolism @@ -14258,7 +14555,7 @@ plexiform layer. - The chemical reactions and pathways resulting in the formation of substances; typically the energy-requiring part of metabolism in which simpler substances are transformed into more complex ones. + A cellular process consisting of the biochemical pathways by which a living organism synthesizes chemical substances. This typically represents the energy-requiring part of metabolism in which simpler substances are transformed into more complex ones. GOC:curators ISBN:0198547684 @@ -14268,13 +14565,12 @@ plexiform layer. + - The chemical reactions and pathways resulting in the formation of a macromolecule, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass. https://github.com/geneontology/go-ontology/issues/15249 https://github.com/geneontology/go-ontology/issues/25418 https://github.com/geneontology/go-ontology/issues/27189 - GO:0043284 biopolymer biosynthetic process macromolecule anabolism macromolecule biosynthesis @@ -14525,7 +14821,6 @@ plexiform layer. The process whose specific outcome is the progression of an embryo from its formation until the end of its embryonic life stage. The end of the embryonic stage is organism-specific. For example, for mammals, the process would begin with zygote formation and end with birth. For insects, the process would begin at zygote formation and end with larval hatching. For plant zygotic embryos, this would be from zygote formation to the end of seed dormancy. For plant vegetative embryos, this would be from the initial determination of the cell or group of cells to form an embryo until the point when the embryo becomes independent of the parent plant. - GO:0009795 embryogenesis and morphogenesis Wikipedia:Embryogenesis embryogenesis @@ -14666,11 +14961,7 @@ plexiform layer. Any process that is carried out at the cellular level, but not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level. - jl 2012-12-11T16:56:55Z - GO:0008151 - GO:0044763 - GO:0050875 cell physiology cellular physiological process cell growth and/or maintenance @@ -14739,7 +15030,6 @@ plexiform layer. A process which begins when a cell receives an internal or external signal and activates a series of biochemical events (signaling pathway). The process ends with the death of the cell. https://github.com/geneontology/go-ontology/issues/24835 - GO:0016244 regulated cell death Wikipedia:Programmed_cell_death caspase-independent cell death @@ -14853,9 +15143,6 @@ plexiform layer. A lipid bilayer along with all the proteins and protein complexes embedded in it and attached to it. 2014-03-06T11:37:54Z - GO:0016021 - GO:0098589 - GO:0098805 Wikipedia:Biological_membrane Wikipedia:Transmembrane_protein integral component of membrane @@ -14914,8 +15201,6 @@ plexiform layer. A process that results in the assembly, arrangement of constituent parts, or disassembly of a cellular component. - GO:0044235 - GO:0071842 cell organisation cellular component organisation at cellular level cellular component organisation in other organism @@ -15159,9 +15444,6 @@ plexiform layer. The chemical reactions and pathways involving a protein. Includes protein modification. https://github.com/geneontology/go-ontology/issues/23112 https://github.com/geneontology/go-ontology/issues/27189 - GO:0006411 - GO:0044267 - GO:0044268 Wikipedia:Protein_metabolism cellular protein metabolic process cellular protein metabolism @@ -15304,7 +15586,6 @@ plexiform layer. A cellular process that results in the breakdown of a cellular component. https://github.com/geneontology/go-ontology/issues/27189 - GO:0071845 cell structure disassembly cellular component disassembly at cellular level biological_process @@ -15389,7 +15670,6 @@ plexiform layer. The aggregation, arrangement and bonding together of a cellular component. - GO:0071844 cell structure assembly cellular component assembly at cellular level biological_process @@ -15492,10 +15772,7 @@ plexiform layer. The entirety of a process in which information is transmitted within a biological system. This process begins with an active signal and ends when a cellular response has been triggered. - jl 2010-02-16T09:30:50Z - GO:0023046 - GO:0044700 biological signaling signaling process signalling @@ -15949,7 +16226,6 @@ plexiform layer. The progressive compaction of dispersed interphase chromatin into threadlike chromosomes prior to mitotic or meiotic nuclear division, or during apoptosis, in eukaryotic cells. - GO:0000068 DNA condensation eukaryotic chromosome condensation nuclear chromosome condensation @@ -16126,7 +16402,6 @@ plexiform layer. A structure lying external to one or more cells, which provides structural support, biochemical or biomechanical cues for cells or tissues. - GO:0005578 NIF_Subcellular:nlx_subcell_20090513 Wikipedia:Extracellular_matrix proteinaceous extracellular matrix @@ -16177,7 +16452,6 @@ plexiform layer. A vesicle found in the cytoplasm of a cell. - GO:0016023 NIF_Subcellular:sao180601769 cellular_component cytoplasmic membrane bounded vesicle @@ -16253,7 +16527,6 @@ plexiform layer. Any small, fluid-filled, spherical organelle enclosed by membrane. - GO:0031988 NIF_Subcellular:sao221389602 Wikipedia:Vesicle_(biology) cellular_component @@ -16382,10 +16655,7 @@ plexiform layer. - jl 2012-09-19T16:07:47Z - GO:0044707 - GO:0050874 organismal physiological process biological_process single-multicellular organism process @@ -16412,9 +16682,7 @@ plexiform layer. A biological process whose specific outcome is the progression of an integrated living unit: an anatomical structure (which may be a subcellular structure, cell, tissue, or organ), or organism over time from an initial condition to a later condition. - jl 2012-12-19T12:21:31Z - GO:0044767 development biological_process single-organism developmental process @@ -16478,9 +16746,6 @@ plexiform layer. The disaggregation of a protein-containing macromolecular complex into its constituent components. https://github.com/geneontology/go-ontology/issues/22580 - GO:0034623 - GO:0043241 - GO:0043624 protein complex disassembly biological_process cellular macromolecule complex disassembly @@ -16502,10 +16767,14 @@ plexiform layer. - + + + + + + A stable assembly of two or more macromolecules, i.e. proteins, nucleic acids, carbohydrates or lipids, in which at least one component is a protein and the constituent parts function together. - GO:0043234 macromolecular complex macromolecule complex protein containing complex @@ -16589,7 +16858,6 @@ plexiform layer. A process in which a monoatomic ion is transported across a membrane. Monatomic ions (also called simple ions) are ions consisting of exactly one atom. - GO:0099131 ion transmembrane transport ion membrane transport transmembrane ion transport @@ -16785,7 +17053,6 @@ plexiform layer. The region of a neuron that includes the cell body (cell soma) and dendrite(s), but excludes the axon. - bf 2014-07-24T10:06:19Z cellular_component GO:0036477 @@ -16924,9 +17191,6 @@ plexiform layer. Any biological process involved in the maintenance of an internal steady state. - GO:0032844 - GO:0032845 - GO:0032846 homeostasis activation of homeostatic process inhibition of homeostatic process @@ -17118,9 +17382,6 @@ plexiform layer. The chemical reactions and pathways involving macromolecules, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass. https://github.com/geneontology/go-ontology/issues/26424 - GO:0034960 - GO:0043283 - GO:0044259 biopolymer metabolic process macromolecule metabolism organismal macromolecule metabolism @@ -17275,14 +17536,17 @@ plexiform layer. Organized structure of distinctive morphology and function, not bounded by a lipid bilayer membrane. Includes ribosomes, the cytoskeleton and chromosomes. https://github.com/geneontology/go-ontology/issues/21881 https://github.com/geneontology/go-ontology/issues/28153 + https://github.com/geneontology/go-ontology/issues/29106 NIF_Subcellular:sao1456184038 + membrane-less organelle + non-membrane-bounded organelle non-membrane-enclosed organelle cellular_component biological condensate GO:0043228 - non-membrane-bounded organelle + membraneless organelle @@ -17418,11 +17682,13 @@ plexiform layer. Organized structure of distinctive morphology and function, not bounded by a lipid bilayer membrane and occurring within the cell. Includes ribosomes, the cytoskeleton and chromosomes. + https://github.com/geneontology/go-ontology/issues/29106 + intracellular non-membrane-bounded organelle intracellular non-membrane-enclosed organelle cellular_component GO:0043232 - intracellular non-membrane-bounded organelle + intracellular membraneless organelle @@ -17528,11 +17794,7 @@ plexiform layer. Any process in which macromolecules aggregate, disaggregate, or are modified, resulting in the formation, disassembly, or alteration of a protein complex. https://github.com/geneontology/go-ontology/issues/22580 - mah 2010-09-08T10:01:42Z - GO:0034600 - GO:0034621 - GO:0071822 protein complex subunit organisation protein complex subunit organization biological_process @@ -17637,7 +17899,6 @@ plexiform layer. A process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of a cellular component. Includes biosynthesis of constituent macromolecules, and those macromolecular modifications that are involved in synthesis or assembly of the cellular component. https://github.com/geneontology/go-ontology/issues/27194 - GO:0071843 cellular component biogenesis at cellular level biological_process GO:0044085 @@ -17666,7 +17927,6 @@ plexiform layer. A ribonucleoprotein complex that contains aminoacylated initiator methionine tRNA, GTP, and initiation factor 2 (either eIF2 in eukaryotes, or IF2 in prokaryotes). In prokaryotes, fMet-tRNA (initiator) is used rather than Met-tRNA (initiator). - jl 2009-10-22T02:38:55Z translation initiation (ternary) complex Met-tRNA/eIF2.GTP ternary complex @@ -17683,35 +17943,6 @@ plexiform layer. - - - - - - The chemical reactions and pathways by which individual cells transform chemical substances. - cellular metabolism - biological_process - intermediary metabolism - GO:0044237 - - This term should not be used for direct annotation. It should be possible to make a more specific annotation to one of the children of this term. - cellular metabolic process - - - - - The chemical reactions and pathways by which individual cells transform chemical substances. - GOC:go_curators - - - - - intermediary metabolism - GOC:mah - - - - @@ -17738,32 +17969,6 @@ plexiform layer. - - - - - - The chemical reactions and pathways resulting in the formation of substances, carried out by individual cells. - https://github.com/geneontology/go-ontology/issues/27052 - cellular anabolism - cellular biosynthesis - cellular formation - cellular synthesis - biological_process - GO:0044249 - - This term should not be used for direct annotation. It should be possible to make a more specific annotation to one of the children of this term. - cellular biosynthetic process - - - - - The chemical reactions and pathways resulting in the formation of substances, carried out by individual cells. - GOC:jl - - - - @@ -17776,7 +17981,6 @@ plexiform layer. The portion of a cell bearing surface projections such as axons, dendrites, cilia, or flagella that includes the nucleus, but excludes all cell projections. - jl 2010-02-05T10:37:16Z FBbt:00005107 FMA:67301 @@ -18074,7 +18278,6 @@ plexiform layer. The process in which anatomical structures are generated and organized during the embryonic phase. The embryonic phase begins with zygote formation. The end of the embryonic phase is organism-specific. For example, it would be at birth for mammals, larval hatching for insects and seed dormancy in plants. - GO:0048828 embryonic anatomical structure morphogenesis biological_process GO:0048598 @@ -18443,7 +18646,6 @@ plexiform layer. Any process that modulates the frequency, rate or extent of a biological process. Biological processes are regulated by many means; examples include the control of gene expression, protein modification or interaction with a protein or substrate molecule. - GO:0050791 regulation of physiological process biological_process GO:0050789 @@ -18484,7 +18686,6 @@ plexiform layer. Any process that modulates the frequency, rate or extent of a cellular process, any of those that are carried out at the cellular level, but are not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level. - GO:0051244 regulation of cellular physiological process biological_process GO:0050794 @@ -18562,7 +18763,6 @@ plexiform layer. Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus. The process begins with detection of the stimulus and ends with a change in state or activity or the cell or organism. - GO:0051869 physiological response to stimulus biological_process GO:0050896 @@ -18738,9 +18938,7 @@ plexiform layer. Any process in which a cell, a substance, or a cellular entity, such as a protein complex or organelle, is transported, tethered to or otherwise maintained in a specific location. In the case of substances, localization may also be achieved via selective degradation. https://github.com/geneontology/go-ontology/issues/27052 - jl 2013-12-18T13:51:04Z - GO:1902578 establishment and maintenance of localization establishment and maintenance of position localisation @@ -18870,9 +19068,6 @@ plexiform layer. A process that is carried out at the cellular level that results in the assembly, arrangement of constituent parts, or disassembly of chromosomes, structures composed of a very long molecule of DNA and associated proteins that carries hereditary information. This term covers covalent modifications at the molecular level as well as spatial relationships among the major components of a chromosome. https://github.com/geneontology/go-ontology/issues/22811 https://github.com/geneontology/go-ontology/issues/4585 - GO:0006323 - GO:0007001 - GO:0051277 DNA condensation chromosome organisation DNA packaging @@ -18961,9 +19156,7 @@ plexiform layer. A cellular localization process whereby a substance or cellular entity, such as a protein complex or organelle, is transported to, and/or maintained in, a specific location within a cell including the localization of substances or cellular entities to the cell membrane. https://github.com/geneontology/go-ontology/issues/27189 - jl 2013-12-18T14:04:32Z - GO:1902580 cellular localisation establishment and maintenance of cellular localization establishment and maintenance of localization in cell or cell membrane @@ -19147,9 +19340,7 @@ plexiform layer. The process in which a solute is transported across a lipid bilayer, from one side of a membrane to the other. - tb 2015-10-21T13:22:47Z - GO:0090662 membrane transport ATP hydrolysis coupled transmembrane transport biological_process @@ -19348,7 +19539,6 @@ plexiform layer. The process in which the anatomical structures of a tube are generated and organized from an epithelium. Epithelial tubes transport gases, liquids and cells from one site to another and form the basic structure of many organs and tissues, with tube shape and organization varying from the single-celled excretory organ in Caenorhabditis elegans to the branching trees of the mammalian kidney and insect tracheal system. - dph 2009-04-28T09:33:36Z biological_process GO:0060562 @@ -19369,7 +19559,6 @@ plexiform layer. The process in which the anatomical structures of a branched epithelium are generated and organized. - dph 2010-05-25T09:05:34Z biological_process GO:0061138 @@ -19397,7 +19586,6 @@ plexiform layer. The controlled release of glutamate by a cell, in which the glutamate acts as a neurotransmitter. - dph 2013-06-21T16:14:47Z biological_process GO:0061535 @@ -19429,7 +19617,6 @@ plexiform layer. An extracellular matrix consisting mainly of proteins (especially collagen) and glycosaminoglycans (mostly as proteoglycans) that provides not only essential physical scaffolding for the cellular constituents but can also initiate crucial biochemical and biomechanical cues required for tissue morphogenesis, differentiation and homeostasis. The components are secreted by cells in the vicinity and form a sheet underlying or overlying cells such as endothelial and epithelial cells. - dph 2018-04-13T12:47:21Z cellular_component GO:0062023 @@ -19470,9 +19657,6 @@ plexiform layer. The aggregation, arrangement and bonding together of a set of macromolecules to form a protein-containing complex. https://github.com/geneontology/go-ontology/issues/22580 - GO:0006461 - GO:0034622 - GO:0043623 cellular protein complex assembly biological_process cellular macromolecule complex assembly @@ -19686,7 +19870,6 @@ plexiform layer. The aggregation, arrangement and bonding together of a set of components to form an organelle. An organelle is an organized structure of distinctive morphology and function. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton. Excludes the plasma membrane. - mah 2009-09-15T03:00:51Z biological_process GO:0070925 @@ -19725,7 +19908,6 @@ plexiform layer. Any process in which macromolecules aggregate, disaggregate, or are modified, resulting in the formation, disassembly, or alteration of a ribonucleoprotein complex. https://github.com/geneontology/go-ontology/issues/25143 - mah 2010-09-08T10:10:35Z RNA-protein complex subunit organization protein-RNA complex subunit organization @@ -19768,9 +19950,7 @@ plexiform layer. A process that results in the biosynthesis of constituent macromolecules, assembly, arrangement of constituent parts, or disassembly of a cellular component. https://github.com/geneontology/go-ontology/issues/27189 - mah 2010-09-10T01:39:16Z - GO:0071841 cellular component organisation or biogenesis cellular component organisation or biogenesis at cellular level cellular component organization or biogenesis at cellular level @@ -19808,7 +19988,6 @@ plexiform layer. The broad region around and including the plasma membrane of a cell, encompassing the cell cortex (inside the cell), the plasma membrane, and any external encapsulating structures. - mah 2010-10-04T01:51:47Z cellular_component GO:0071944 @@ -19835,7 +20014,6 @@ plexiform layer. An supramolecular fiber that consists of an insoluble core of polymerized tropoelastin monomers and a surrounding mantle of microfibrils. Elastic fibers provide elasticity and recoiling to tissues and organs, and maintain structural integrity against mechanical strain. - mah 2010-10-11T11:44:57Z elastic fibre elastin fiber @@ -19895,7 +20073,6 @@ plexiform layer. The aggregation, arrangement and bonding together of a set of components to form an extracellular vesicular exosome, a membrane-bounded vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Exosomes are defined by their size, which generally ranges from 30 nm to 100 nm. - mah 2010-10-18T03:44:18Z extracellular vesicular exosome assembly biological_process @@ -19949,7 +20126,6 @@ plexiform layer. The developmental process pertaining to the initial formation of an epithelial tube. https://github.com/geneontology/go-ontology/issues/22302 - mah 2010-02-26T02:15:40Z biological_process GO:0072175 @@ -19975,9 +20151,7 @@ plexiform layer. The series of molecular signals which triggers the apoptotic death of a cell. The pathway starts with reception of a signal, and ends when the execution phase of apoptosis is triggered. - pr 2011-11-23T09:30:23Z - GO:0008624 apoptotic signalling pathway induction of apoptosis by extracellular signals biological_process @@ -20017,7 +20191,6 @@ plexiform layer. A stage of the apoptotic process that starts with the controlled breakdown of the cell through the action of effector caspases or other effector molecules (e.g. cathepsins, calpains etc.). Key steps of the execution phase are rounding-up of the cell, retraction of pseudopodes, reduction of cellular volume (pyknosis), chromatin condensation, nuclear fragmentation (karyorrhexis), plasma membrane blebbing and fragmentation of the cell into apoptotic bodies. When the execution phase is completed, the cell has died. - pr 2011-11-23T09:45:24Z execution phase of apoptotic process apoptosis @@ -20052,7 +20225,6 @@ plexiform layer. The entire complement of dendrites for a neuron, consisting of each primary dendrite and all its branches. - pr 2012-12-17T12:31:49Z NIF_Subcellular:sao172297168 cellular_component @@ -20087,7 +20259,6 @@ plexiform layer. Any vesicle that is part of the intracellular region. - pr 2016-03-29T17:39:45Z cellular_component GO:0097708 @@ -20107,7 +20278,6 @@ plexiform layer. The assembly and secretion of an extracellular exosome, a membrane-bounded vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. - pr 2016-10-03T14:35:25Z exosome assembly or secretion exosome biogenesis @@ -20152,7 +20322,6 @@ plexiform layer. A membrane that is a (regional) part of the plasma membrane. - dos 2014-03-06T11:55:32Z region of plasma membrane cellular_component @@ -20209,7 +20378,6 @@ plexiform layer. - @@ -20528,7 +20696,6 @@ plexiform layer. A polymer consisting of an indefinite number of protein or protein complex subunits that have polymerised to form a fiber-shaped structure. - GO:0043205 cellular_component fibril GO:0099512 @@ -20724,21 +20891,22 @@ plexiform layer. - A part of a cellular organism that is either an immaterial entity or a material entity with granularity above the level of a protein complex but below that of an anatomical system. Or, a substance produced by a cellular organism with granularity above the level of a protein complex. + A part of a cellular organism consisting of a material entity with granularity above the level of a protein complex but below that of an anatomical system. Note that cellular organisms exclude viruses. https://github.com/geneontology/go-ontology/issues/24200 https://github.com/geneontology/go-ontology/issues/26424 - kmv + https://github.com/geneontology/go-ontology/issues/28978 2019-08-12T18:01:37Z + cellular anatomical entity cellular_component GO:0110165 - cellular anatomical entity + cellular anatomical structure - A part of a cellular organism that is either an immaterial entity or a material entity with granularity above the level of a protein complex but below that of an anatomical system. Or, a substance produced by a cellular organism with granularity above the level of a protein complex. + A part of a cellular organism consisting of a material entity with granularity above the level of a protein complex but below that of an anatomical system. Note that cellular organisms exclude viruses. GOC:kmv @@ -20767,7 +20935,6 @@ plexiform layer. A prolongation or process extending from a cell and that is bounded by plasma membrane, e.g. a cilium, lamellipodium, or axon. https://github.com/geneontology/go-ontology/issues/13193 - krc 2017-03-21T17:26:07Z cellular_component GO:0120025 @@ -20806,7 +20973,6 @@ plexiform layer. Formation of a prolongation or process extending and that is bounded by plasma membrane, e.g. a cilium, lamellipodium, or axon. https://github.com/geneontology/go-ontology/issues/13298 - krc 2017-04-24T23:56:08Z eupodium biological_process @@ -20854,7 +21020,6 @@ plexiform layer. A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a plasma membrane bounded prolongation or process extending from a cell, e.g. a cilium or axon. https://github.com/geneontology/go-ontology/issues/13298 - krc 2017-04-26T16:07:02Z biological_process GO:0120036 @@ -20887,7 +21052,6 @@ plexiform layer. A mitotic cell cycle process comprising the steps by which the nucleus of a eukaryotic cell divides; the process involves condensation of chromosomal DNA into a highly compacted form. Canonically, mitosis produces two daughter nuclei whose chromosome complement is identical to that of the mother cell. https://github.com/geneontology/go-ontology/issues/19910 - pg 2017-03-23T14:44:23Z mitosis biological_process @@ -20911,7 +21075,6 @@ plexiform layer. The assembly and secretion a set of components to form an extracellular vesicule, a membrane-bounded vesicle that is released into the extracellular region. Extracellular vesicles include exosomes, microvesicles and apoptotic bodies, based on the mechanism by which they are released from cells and differentiated based on their size and content. https://github.com/geneontology/go-ontology/issues/14256 - pg 2017-10-23T11:53:42Z extracellular vesicle assembly biological_process @@ -20960,7 +21123,6 @@ plexiform layer. The directed movement of some substance from a cell, into the extracellular region. This may occur via transport across the plasma membrane or via exocytosis. - pg 2019-05-22T11:20:45Z efflux biological_process @@ -20998,7 +21160,6 @@ plexiform layer. A process that is part of the mitotic cell cycle. - jl 2014-05-22T14:22:34Z biological_process GO:1903047 @@ -21038,7 +21199,6 @@ plexiform layer. Any process that modulates the frequency, rate or extent of blood circulation. - mr 2014-10-06T18:38:56Z biological_process regulation of hemolymph circulation @@ -21080,7 +21240,6 @@ plexiform layer. Any vesicle that is part of the extracellular region. - jl 2014-10-22T14:26:11Z cellular_component microparticle @@ -21110,10 +21269,7 @@ plexiform layer. A macromolecular complex that contains both RNA and protein molecules. - pr 2015-11-19T12:26:37Z - GO:0030529 - GO:1990903 Wikipedia:Ribonucleoprotein RNA-protein complex RNP @@ -21205,7 +21361,6 @@ plexiform layer. - NCBITaxon:85055 GC_ID:1 house mouse mouse @@ -21244,7 +21399,6 @@ plexiform layer. - NCBITaxon:40673 GC_ID:1 bony vertebrates ncbi_taxonomy @@ -21611,7 +21765,6 @@ plexiform layer. - NCBITaxon:109679 GC_ID:1 ncbi_taxonomy NCBITaxon:39107 @@ -21870,7 +22023,6 @@ plexiform layer. A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities - PATO:0000072 quality PATO:0000001 quality @@ -21908,7 +22060,6 @@ plexiform layer. A morphological quality inhering in a bearer by virtue of the bearer's ratios of distances between its features (points, edges, surfaces and also holes etc). - PATO:0001647 relational shape quality quality PATO:0000052 @@ -21950,7 +22101,6 @@ plexiform layer. A morphology quality inhering in a bearer by virtue of the bearer's relative position, shape, arrangements and connectivity of an organism's various parts; the pattern underlying its form. - PATO:0001452 conformation relational structural quality quality @@ -22134,7 +22284,6 @@ plexiform layer. A quality of a physical entity that exists through action of continuants at the physical level of organisation in relation to other entities. - PATO:0002079 Wikipedia:Physical_property relational physical quality quality @@ -22156,8 +22305,6 @@ plexiform layer. A quality which inheres in a continuant. - PATO:0001237 - PATO:0001238 snap:Quality monadic quality of a continuant multiply inhering quality of a physical entity @@ -22454,7 +22601,6 @@ plexiform layer. A convex 3-D shape quality inhering in a bearer by virtue of the bearer's exhibiting a consistently-sized round cross section. - PATO:0001203 rod-like rod-shaped tubulate @@ -22940,27 +23086,6 @@ plexiform layer. - - - - - A quality of a single cell inhering in the bearer by virtue of the bearer's size or shape or structure. - - 2021-01-23T11:31:53Z - quality - PATO:0010006 - Use this term for morphologies that can *only* inhere in a cell, e.g. morphological qualities inhering in a cell by virtue of the presence, location or shape of one or more cell parts. - cell morphology - - - - - A quality of a single cell inhering in the bearer by virtue of the bearer's size or shape or structure. - https://orcid.org/0000-0002-7073-9172 - - - - @@ -22987,7 +23112,6 @@ plexiform layer. A quality inhering in a cell by virtue of the cell having a high nuclear/cytoplasmic ratio. - http://orcid.org/0000-0001-5208-3432 high N:C ratio quality PATO:0040072 @@ -23004,56 +23128,11 @@ plexiform layer. - - - - - A cell morphology that inheres in neurons which have two principal dendrites that emerge from the soma and begin to branch some distance from it, have few spines, and branch in narrow fields. This is in contrast to bitufted morphology where branching occurs close to the soma. - - ILX:0101312 - ilxtr:BipolarPhenotype - nifext:2 - quality - PATO:0070006 - This is specific to cortical bipolar cells and are distinguished from retinal bipolar cell morphology which has an axon and dendrite emerging from opposite ends of the soma. - cortical bipolar morphology - - - - - A cell morphology that inheres in neurons which have two principal dendrites that emerge from the soma and begin to branch some distance from it, have few spines, and branch in narrow fields. This is in contrast to bitufted morphology where branching occurs close to the soma. - PMID:18568015 - doi:10.1016/b978-0-12-369497-3.10004-4 - - - - - - - - - A cell morphology that inheres in neurons with dendrites that are bidirectional, emerging from opposite ends of the soma, with the two arbors extending in radial or tangential directions. - - quality - PATO:0070027 - This morphology type is distinct from bitufted cell morphology in that it refers to bitufted dendrite morphology rather than bitufted cell morphology. - bitufted dendrite cell morphology - - - - - A cell morphology that inheres in neurons with dendrites that are bidirectional, emerging from opposite ends of the soma, with the two arbors extending in radial or tangential directions. - PMID:18568015 - - - - A quality of continuant that exist at the anatomical level of organisation and anything under it. This includes, but is not limited to, cells , tissues, and components. - http://orcid.org/0000-0001-7258-9596 quality PATO:0070044 anatomical structure quality @@ -23066,7 +23145,6 @@ plexiform layer. A quality inhering in an anotomical structure by virtue of its capacity to be stained by specific histological dyes. - http://orcid.org/0000-0001-7258-9596 quality PATO:0070045 anatomical histological quality @@ -23079,7 +23157,6 @@ plexiform layer. An affinity inhering in an anatomical structure by virtue of the bearer exhibiting a molecular interaction for both basic and acid stains under specific pH conditions. - http://orcid.org/0000-0001-7258-9596 quality PATO:0070047 polychromatophilic @@ -23116,7 +23193,7 @@ plexiform layer. - + @@ -23128,7 +23205,7 @@ plexiform layer. native protein protein PR:000000001 - The definition above excludes protein complexes, which some also consider a protein. Those who wish to refer to a class representing both senses of the word are directed to CHEBI:36080. Note that the definition allows for experimentally-manipulated genes, and allows for artifically-produced derivatives that mimic those found naturally. Proteins (in the sense defined here) that descended from a common ancestor can be classified into families and superfamilies composed of products of evolutionarily-related genes. The domain architecture of a protein is described by the order of its constituent domains. Proteins with the same domains in the same order are defined as homeomorphic [PRO:WCB]. + The definition above excludes protein complexes, which some also consider a protein. Those who wish to refer to a class representing both senses of the word are directed to CHEBI:36080. Note that the definition allows for experimentally-manipulated genes, and allows for artifically-produced derivatives that mimic those found naturally. Proteins (in the sense defined here) that descended from a common ancestor can be classified into families and superfamilies composed of products of evolutionarily-related genes. The domain architecture of a protein is described by the order of its constituent domains. Proteins with the same domains in the same order are defined as homeomorphic [PRO:WCB). protein @@ -23810,7 +23887,6 @@ plexiform layer. - A protein with core architecture consisting of a signal sequence, followed by 7 Ig-like domains (Pfam:PF00047, Pfam:PF07679, or Pfam:PF07686), a transmembrane region, and a cytoplasmic Protein tyrosine kinase domain. PIRSF:PIRSF038502 protein @@ -24182,51 +24258,51 @@ plexiform layer. - + - + - A material entity that minimally consists of a protein. + A molecular entity that minimally consists of a protein. protein protein aggregate protein complex protein-containing complex protein - PR:000050567 - Note: This includes single proteins and derivatives thereof (PR:000000001), protein-containing complexes (GO:0032991), and protein aggregates (PR:000050566). - protein-containing material entity + PR:000064867 + Note: This includes single proteins and derivatives thereof (PR:000000001), protein-containing complexes (GO:0032991), and protein aggregates (PR:000050565). + protein-containing molecular entity - + - A material entity that minimally consists of a protein. + A molecular entity that minimally consists of a protein. PRO:DAN - + protein PRO:DAN - + protein aggregate PRO:DAN - + protein complex PRO:DAN - + protein-containing complex PRO:DAN @@ -24600,7 +24676,6 @@ plexiform layer. WBbt:0005739 Wikipedia:Head XAO:0003024 - ZFA:0001114 galen:Head head (volume) adult head @@ -24645,7 +24720,6 @@ plexiform layer. - @@ -24789,7 +24863,6 @@ plexiform layer. Organ component adjacent to an organ cavity and which consists of a maximal aggregate of organ component layers. - UBERON:0009915 wall FMA:82482 galen:Wall @@ -25262,7 +25335,6 @@ plexiform layer. Anatomical cluster consisting of the skeletal elements and articular elements that are part of an individual subdivision of the organism. - UBERON:0010322 FMA:85544 NCIT:C34076 SCTID:118966000 @@ -25308,7 +25380,7 @@ plexiform layer. - + The surface (external) layer of ectoderm which begins to proliferate shortly after separation from the neuroectoderm. merge with non-neural. In vertebrates, the ectoderm has three parts: external ectoderm (also known as surface ectoderm), the neurectoderm (neural crest, and neural tube) EHDAA2:0001968 @@ -25331,7 +25403,7 @@ plexiform layer. external ectoderm http://upload.wikimedia.org/wikipedia/commons/1/1d/Ectoderm.png - + @@ -25344,7 +25416,7 @@ plexiform layer. - + EHDAA2 @@ -25693,7 +25765,7 @@ plexiform layer. - + @@ -25729,14 +25801,14 @@ plexiform layer. gastrula stage - + - + BILS @@ -25896,7 +25968,6 @@ plexiform layer. A fasciculated bundle of neuron projections (GO:0043005), largely or completely lacking synapses. - UBERON:0005163 CARO:0001001 FBbt:00005099 NLX:147821 @@ -26137,7 +26208,7 @@ plexiform layer. - + @@ -26145,15 +26216,15 @@ plexiform layer. - + - - + + A fluid that is composed of blood plasma and erythrocytes. AAO:0000046 @@ -26190,34 +26261,34 @@ plexiform layer. blood - + - + - + - + CL:tm - + https://github.com/obophenotype/uberon/issues/1330 - + Bgee:AN @@ -26319,7 +26390,6 @@ plexiform layer. Organism at the blastula stage - an early stage of embryonic development in animals. It is produced by cleavage of a fertilized ovum and consists of a spherical layer of around 128 cells surrounding a central fluid-filled cavity called the blastocoel. The blastula follows the morula and precedes the gastrula in the developmental sequence. TODO - check relationship with epiblast. Note in FMA this is not a subclass of embryo, but in uberon embryo is the whole organism from zygote onwards and thus includes the blastula - UBERON:0007011 BILA:0000059 BTO:0000128 GAID:1294 @@ -27289,7 +27359,6 @@ plexiform layer. - @@ -27303,7 +27372,7 @@ plexiform layer. - + @@ -27345,14 +27414,14 @@ plexiform layer. epithelium https://upload.wikimedia.org/wikipedia/commons/8/8f/Illu_epithelium.jpg - + - + http://palaeos.com/metazoa/porifera/homoscleromorpha.html @@ -27874,7 +27943,7 @@ plexiform layer. - + Primary germ layer that is the outer of the embryo's three germ layers and gives rise to epidermis and neural tissue. AAO:0000137 BILA:0000036 @@ -27909,14 +27978,14 @@ plexiform layer. ectoderm http://upload.wikimedia.org/wikipedia/commons/1/19/Gray32.png - + - + Bgee:AN @@ -27956,7 +28025,7 @@ plexiform layer. - + Primary germ layer that lies remote from the surface of the embryo and gives rise to internal tissues such as gut. AAO:0000139 BILA:0000038 @@ -27991,14 +28060,14 @@ plexiform layer. http://upload.wikimedia.org/wikipedia/commons/c/c0/Endoderm2.png http://upload.wikimedia.org/wikipedia/commons/d/df/Gray10.png - + - + Bgee:AN @@ -28039,10 +28108,9 @@ plexiform layer. - + The middle germ layer of the embryo, between the endoderm and ectoderm. - UBERON:0003263 AAO:0000304 BILA:0000037 BTO:0000839 @@ -28080,14 +28148,14 @@ plexiform layer. mesoderm http://upload.wikimedia.org/wikipedia/commons/e/e8/Mesoderm.png - + - + Bgee:AN @@ -28275,7 +28343,7 @@ plexiform layer. - + @@ -28337,14 +28405,14 @@ plexiform layer. cranial nerve II - + - + EHDAA2 @@ -28454,7 +28522,7 @@ plexiform layer. - + @@ -28525,14 +28593,14 @@ plexiform layer. https://cdn.humanatlas.io/digital-objects/ref-organ/heart-female/v1.3/assets/3d-vh-f-heart.glb https://cdn.humanatlas.io/digital-objects/ref-organ/heart-male/v1.3/assets/3d-vh-m-heart.glb - + - + MA @@ -28574,7 +28642,7 @@ plexiform layer. - + @@ -28593,7 +28661,7 @@ plexiform layer. - + The brain is the center of the nervous system in all vertebrate, and most invertebrate, animals. Some primitive animals such as jellyfish and starfish have a decentralized nervous system without a brain, while sponges lack any nervous system at all. In vertebrates, the brain is located in the head, protected by the skull and close to the primary sensory apparatus of vision, hearing, balance, taste, and smell[WP]. requires review for applicability to invertebrate structures, e.g. synganglion @@ -28652,11 +28720,11 @@ plexiform layer. https://cdn.humanatlas.io/digital-objects/ref-organ/brain-female/v1.4/assets/3d-allen-f-brain.glb https://cdn.humanatlas.io/digital-objects/ref-organ/brain-male/v1.4/assets/3d-allen-m-brain.glb - + - + @@ -28669,13 +28737,13 @@ plexiform layer. - + FMA - + Bgee:AN @@ -28925,12 +28993,11 @@ plexiform layer. - - - - + + + @@ -29014,34 +29081,34 @@ plexiform layer. cornea http://upload.wikimedia.org/wikipedia/commons/1/1e/Schematic_diagram_of_the_human_eye_en.svg - + - + - + - + MA - + MA - + FMA-isa @@ -29218,10 +29285,10 @@ plexiform layer. - - - - + + + + The retina is the innermost layer or coating at the back of the eyeball, which is sensitive to light and in which the optic nerve terminates. @@ -29269,44 +29336,44 @@ plexiform layer. retina http://upload.wikimedia.org/wikipedia/commons/e/ed/Human_eye_cross-sectional_view_grayscale.png - + - + - + - + - + FMA - + FMA - + FMA - + EHDAA2 @@ -29361,8 +29428,8 @@ plexiform layer. - - + + @@ -29394,24 +29461,24 @@ plexiform layer. eye - + - + - + PMID:21062451 - + PMID:21062451 @@ -29648,7 +29715,6 @@ plexiform layer. - AAO:0000959 CALOHA:TS-2103 VHOG:0001248 @@ -29656,7 +29722,6 @@ plexiform layer. uberon systema cardiovasculare UBERON:0001009 - circulatory system http://upload.wikimedia.org/wikipedia/commons/2/29/Circulatory_System_en.svg @@ -29800,7 +29865,7 @@ plexiform layer. - + @@ -29848,14 +29913,14 @@ plexiform layer. http://upload.wikimedia.org/wikipedia/commons/b/b2/TE-Nervous_system_diagram.svg http://upload.wikimedia.org/wikipedia/commons/b/ba/Nervous_system_diagram.png - + - + Bgee:AN @@ -29921,7 +29986,7 @@ plexiform layer. - + The central nervous system is the core nervous system that serves an integrating and coordinating function. In vertebrates it consists of the neural tube derivatives: the brain and spinal cord. In invertebrates it includes central ganglia plus nerve cord. @@ -29966,7 +30031,7 @@ plexiform layer. central nervous system - + @@ -29980,7 +30045,7 @@ plexiform layer. - + Bgee:AN @@ -30633,7 +30698,7 @@ plexiform layer. - + Simple squamous epithelium of mesodermal origin which lines serous membranes. Examples: mesothelium of pleura, mesothelium of peritoneum[FMA]. Wikipedia: The mesothelium is a membrane that forms the lining of several body cavities: the pleura (thoracal cavity), peritoneum (abdominal cavity including the mesentery) and pericardium (heart sac). Mesothelial tissue also surrounds the male internal reproductive organs (the tunica vaginalis testis) and covers the internal reproductive organs of women (the tunica serosa uteri). AEO:0000111 BTO:0002422 @@ -30658,14 +30723,14 @@ plexiform layer. mesothelium http://upload.wikimedia.org/wikipedia/commons/2/25/Mesothelium_peritoneal_wash_high_mag.jpg - + - + FMA @@ -30955,7 +31020,7 @@ plexiform layer. - + A tube extending from the mouth to the anus. @@ -30992,14 +31057,14 @@ plexiform layer. digestive tract - + - + NCBIBook:NBK10107 @@ -31054,7 +31119,7 @@ plexiform layer. - + The ciliary muscle is a ring of smooth muscle in the middle layer of the eye that controls the eye's accommodation for viewing objects at varying distances and regulates the flow of aqueous humour through Schlemm's canal. [WP,unvetted]. BTO:0000654 @@ -31077,7 +31142,7 @@ plexiform layer. ciliary muscle http://upload.wikimedia.org/wikipedia/commons/2/28/Gray872.png - + @@ -31096,7 +31161,7 @@ plexiform layer. - + FMA @@ -31214,7 +31279,7 @@ plexiform layer. - + @@ -31260,14 +31325,14 @@ plexiform layer. eyelid https://upload.wikimedia.org/wikipedia/commons/8/84/Eye_makeup.jpg - + - + multiple @@ -31533,7 +31598,7 @@ plexiform layer. - + @@ -31572,14 +31637,14 @@ plexiform layer. iris - + - + XAO @@ -31633,7 +31698,7 @@ plexiform layer. - + @@ -31682,14 +31747,14 @@ plexiform layer. corneal epithelium http://upload.wikimedia.org/wikipedia/commons/6/66/Gray871.png - + - + ISBN:0781772214 @@ -31777,15 +31842,15 @@ plexiform layer. - - + + - + @@ -31820,34 +31885,34 @@ plexiform layer. sclera http://upload.wikimedia.org/wikipedia/commons/1/1e/Schematic_diagram_of_the_human_eye_en.svg - + - + - + - + FMA - + ZFA - + ISBN:0781772214 @@ -31889,7 +31954,7 @@ plexiform layer. - + @@ -31927,14 +31992,14 @@ plexiform layer. ciliary body http://upload.wikimedia.org/wikipedia/commons/1/1e/Schematic_diagram_of_the_human_eye_en.svg - + - + ISBN:0781772214 @@ -31972,14 +32037,14 @@ plexiform layer. - + - + @@ -32040,24 +32105,24 @@ plexiform layer. optic choroid http://upload.wikimedia.org/wikipedia/commons/1/1e/Schematic_diagram_of_the_human_eye_en.svg - + - + - + MA - + Wikipedia @@ -32250,9 +32315,9 @@ plexiform layer. - - - + + + A double layer covering the ciliary body that produces aqueous humor. BTO:0001770 @@ -32272,15 +32337,15 @@ plexiform layer. ciliary epithelium - + - + - + @@ -32293,19 +32358,19 @@ plexiform layer. - + MA - + MP - + Wikipedia @@ -32421,7 +32486,7 @@ plexiform layer. - + @@ -32479,14 +32544,14 @@ plexiform layer. pigmented layer of retina http://upload.wikimedia.org/wikipedia/commons/5/55/Gray881.png - + - + Wikipedia @@ -32562,7 +32627,7 @@ plexiform layer. - + @@ -32594,14 +32659,14 @@ plexiform layer. photoreceptor layer of retina http://upload.wikimedia.org/wikipedia/commons/5/55/Gray881.png - + - + ZFA @@ -33094,7 +33159,7 @@ plexiform layer. - + @@ -33150,7 +33215,7 @@ plexiform layer. ganglionic layer of retina http://upload.wikimedia.org/wikipedia/commons/5/55/Gray881.png - + @@ -33163,7 +33228,7 @@ plexiform layer. - + FMA @@ -33217,7 +33282,7 @@ plexiform layer. - + @@ -33243,7 +33308,6 @@ plexiform layer. Layer of the retina formed by expansion of the fibers of the optic nerve. - UBERON:0005888 nerve fiber layer DMBA:15652 EMAPA:18591 @@ -33272,14 +33336,14 @@ plexiform layer. nerve fiber layer of retina - + - + FMA @@ -33969,7 +34033,7 @@ plexiform layer. - + @@ -34001,14 +34065,14 @@ plexiform layer. anterior segment of eyeball http://upload.wikimedia.org/wikipedia/commons/b/ba/Cataract_in_human_eye.png - + - + FMA @@ -34052,7 +34116,7 @@ plexiform layer. - + @@ -34082,14 +34146,14 @@ plexiform layer. posterior segment of eyeball http://upload.wikimedia.org/wikipedia/commons/1/1e/Schematic_diagram_of_the_human_eye_en.svg - + - + FMA @@ -34126,9 +34190,9 @@ plexiform layer. - - - + + + @@ -34176,15 +34240,15 @@ plexiform layer. conjunctiva http://upload.wikimedia.org/wikipedia/commons/5/55/Gray883.png - + - + - + @@ -34197,19 +34261,19 @@ plexiform layer. - + cjm - + MA - + ISBN:0781772214 @@ -34367,7 +34431,7 @@ plexiform layer. - + The midbrain is the middle division of the three primary divisions of the developing chordate brain or the corresponding part of the adult brain (in vertebrates, includes a ventral part containing the cerebral peduncles and a dorsal tectum containing the corpora quadrigemina and that surrounds the aqueduct of Sylvius connecting the third and fourth ventricles)[GO]. developmental relationships need revised @@ -34413,14 +34477,14 @@ plexiform layer. midbrain http://upload.wikimedia.org/wikipedia/commons/f/f9/Human_brain_inferior_view_description.JPG - + - + Bgee:AN @@ -34891,7 +34955,7 @@ plexiform layer. - + Ventral part of the midbrain, separated from the hindbrain by the isthmus[ISBN:0471888893]. Subdivision of the midbrain lying anterior to the tectum and posterior to the substantia nigra and cerebral peduncle[FMA] The part of the midbrain extending from the substantia nigra to the cerebral aqueduct in a horizontal section of the midbrain. It forms the floor of the midbrain that surrounds the cerebral aqueduct[WP]. MTg @@ -34930,14 +34994,14 @@ plexiform layer. midbrain tegmentum http://upload.wikimedia.org/wikipedia/commons/b/b6/Gray712.png - + - + ZFA @@ -35023,7 +35087,6 @@ plexiform layer. - @@ -35098,7 +35161,6 @@ plexiform layer. - @@ -35107,8 +35169,8 @@ plexiform layer. - - + + @@ -35121,7 +35183,7 @@ plexiform layer. - + @@ -35175,34 +35237,34 @@ plexiform layer. blood vessel http://upload.wikimedia.org/wikipedia/commons/2/29/Circulatory_System_en.svg - + - + - + - + AEO - + EHDAA2 - + GO:0072360 @@ -35531,7 +35593,7 @@ plexiform layer. - + The most posterior of the three principal regions of the brain. In mammals and birds the hindbrain is divided into a rostral metencephalon and a caudal myelencephalon. In zebrafish, with the exception of the cerebellum, the ventral remainder of the metencephalon can be separated only arbitrarily from the more caudal myelencephalic portion of the medulla oblongata (From: Neuroanatomy of the Zebrafish Brain)[ZFA]. Organ component of neuraxis that has as its parts the pons, cerebellum and medulla oblongata[FMA]. @@ -35574,14 +35636,14 @@ plexiform layer. hindbrain http://upload.wikimedia.org/wikipedia/commons/5/54/EmbryonicBrain.svg - + - + Bgee:AN @@ -36022,7 +36084,6 @@ plexiform layer. The sensory system subserving the sense of vision. - UBERON:0007036 AAO:0000632 BILA:0000140 EMAPA:36003 @@ -36212,7 +36273,7 @@ plexiform layer. - + Vasculature that is part of the eye region. FMA:74743 @@ -36234,14 +36295,14 @@ plexiform layer. https://cdn.humanatlas.io/digital-objects/ref-organ/blood-vasculature-female/v1.3/assets/3d-vh-f-blood-vasculature.glb https://cdn.humanatlas.io/digital-objects/ref-organ/blood-vasculature-male/v1.3/assets/3d-vh-m-blood-vasculature.glb - + - + ISBN:0781772214 @@ -36445,7 +36506,7 @@ plexiform layer. - + @@ -36519,14 +36580,14 @@ plexiform layer. https://cdn.humanatlas.io/digital-objects/ref-organ/spinal-cord-female/v1.1/assets/3d-vh-f-spinal-cord.glb https://cdn.humanatlas.io/digital-objects/ref-organ/spinal-cord-male/v1.1/assets/3d-vh-m-spinal-cord.glb - + - + ZFA @@ -36869,7 +36930,6 @@ plexiform layer. The cavity within the body of all animals higher than the coelenterates and certain primitive worms, formed by the splitting of the embryonic mesoderm into two layers. In mammals it forms the peritoneal, pleural, and pericardial cavities. - UBERON:0000169 body cavity AEO:0000186 BTO:0001707 @@ -36881,7 +36941,6 @@ plexiform layer. SCTID:361348008 TAO:0001438 UMLS:C0333343 - ZFA:0001438 galen:BodyCavity coelomic cavity coelomic cavity lumen @@ -36981,9 +37040,9 @@ plexiform layer. - - - + + + @@ -37031,15 +37090,15 @@ plexiform layer. notochord http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png - + - + - + @@ -37058,19 +37117,19 @@ plexiform layer. - + http://tolweb.org/Chordata/2499 - + ZFA - + EHDAA2 @@ -37110,8 +37169,8 @@ plexiform layer. - - + + Somites are spheres of epithelial cells that form sequentially along the anterior-posterior axis of the embryo through mesenchymal to epithelial transition of the presomitic mesoderm. mesodermal cluster @@ -37149,11 +37208,11 @@ plexiform layer. somite http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png - + - + @@ -37166,13 +37225,13 @@ plexiform layer. - + GOTAX:0000352 - + ZFA @@ -37234,22 +37293,22 @@ plexiform layer. - + - - + + - + A specialized region of ectoderm found between the neural ectoderm (neural plate) and non-neural ectoderm and composed of highly migratory pluripotent cells that delaminate in early embryonic development from the dorsal neural tube and give rise to an astounding variety of differentiated cell types[MP]. AAO:0010578 BTO:0001764 @@ -37282,45 +37341,45 @@ plexiform layer. http://upload.wikimedia.org/wikipedia/commons/5/5f/Gray644.png https://upload.wikimedia.org/wikipedia/commons/8/8f/Neural_Crest.png - + - + - + - + - + XAO https://github.com/obophenotype/uberon/wiki/The-neural-crest - + BTO - + PMID:11523831 - + PMID:11523831 @@ -37606,7 +37665,7 @@ plexiform layer. - + @@ -37659,14 +37718,14 @@ plexiform layer. hematopoietic system - + - + FMA @@ -37706,8 +37765,8 @@ plexiform layer. - - + + @@ -37733,11 +37792,11 @@ plexiform layer. iris epithelium - + - + @@ -37750,13 +37809,13 @@ plexiform layer. - + MA - + MP @@ -37895,7 +37954,7 @@ plexiform layer. - + Ectodermal placode that develops in the head into a part of the sensory nervous system. With a few exceptions (lens, adenohypophyseal), cranial placodes are neurogenic. Do not merge with neurogenic placode ectodermal placode @@ -37912,7 +37971,7 @@ plexiform layer. cranial placode - + @@ -37925,7 +37984,7 @@ plexiform layer. - + PMID:11523831 PMID:22512454 @@ -38125,7 +38184,7 @@ plexiform layer. - + @@ -38138,7 +38197,7 @@ plexiform layer. - + The part of the brain that is the morphological boundary between the midbrain and hindbrain and that is the location of an organizing center which patterns the midbrain and hindbrain primordia of the neural plate. consider adding class for organizer. Consider adding separate class for isthmus as a structure AAO:0011064 @@ -38167,24 +38226,24 @@ plexiform layer. midbrain-hindbrain boundary - + - + - + ZFA - + ZFA @@ -38293,6 +38352,7 @@ plexiform layer. + @@ -38306,7 +38366,7 @@ plexiform layer. - + Unsegmented field of paraxial mesoderm present posterior to the most recently formed somite pair, from which somites will form. AAO:0011086 EFO:0001982 @@ -38329,14 +38389,14 @@ plexiform layer. presomitic mesoderm - + - + Bgee:AN @@ -38503,7 +38563,7 @@ plexiform layer. - + @@ -38517,7 +38577,6 @@ plexiform layer. Portion of tissue that is part of the anterior neural keel and will form the optic vesicle[ZFA]. A paired ectodermal placode that becomes invaginated to form the embryonic lens vesicles. - UBERON:0005060 AAO:0011038 EFO:0003541 EHDAA2:0004431 @@ -38540,7 +38599,7 @@ plexiform layer. eye primordium - + @@ -38553,7 +38612,7 @@ plexiform layer. - + PMID:16496288 XAO @@ -38603,8 +38662,8 @@ plexiform layer. - - + + @@ -38632,24 +38691,24 @@ plexiform layer. optic cup - + - + - + ZFA - + ZFA @@ -38705,7 +38764,7 @@ plexiform layer. - + @@ -38743,7 +38802,7 @@ plexiform layer. lens placode http://upload.wikimedia.org/wikipedia/commons/2/2f/Gray864.png - + @@ -38756,7 +38815,7 @@ plexiform layer. - + ZFA @@ -38795,9 +38854,9 @@ plexiform layer. - - - + + + A region of embryonic ectodermal cells that lie directly above the notochord. During neurulation, they change shape and produce an infolding of the neural plate (the neural fold) that then seals to form the neural tube[XAO]. The earliest recognizable dorsal ectodermal primordium of the central nervous system present near the end of gastrulation before infolding to form the neural keel; consists of a thickened pseudostratified epithelium[ZFA]. AAO:0011072 BTO:0001765 @@ -38826,34 +38885,34 @@ plexiform layer. neural plate https://upload.wikimedia.org/wikipedia/commons/8/8f/Neural_Crest.png - + - + - + - + GOTAX:0000352 - + Wikipedia - + Bgee:AN @@ -38928,7 +38987,7 @@ plexiform layer. - + The paraxial mesoderm is the mesoderm located bilaterally adjacent to the notochord and neural tube[GO]. AAO:0010568 EFO:0003515 @@ -38954,7 +39013,7 @@ plexiform layer. paraxial mesoderm http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png - + @@ -38967,7 +39026,7 @@ plexiform layer. - + Bgee:AN @@ -39043,7 +39102,7 @@ plexiform layer. - + @@ -39057,7 +39116,6 @@ plexiform layer. Portion of the middle of the three primary germ layers of the embryo that resides on the periphery of the embryo, is continuous with the extra-embryonic mesoderm, splits into two layers enclosing the intra-embryonic coelom, and gives rise to body wall structures[MP]. - UBERON:0006258 AAO:0010574 EHDAA2:0000919 EHDAA:379 @@ -39083,7 +39141,7 @@ plexiform layer. lateral plate mesoderm http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png - + @@ -39096,7 +39154,7 @@ plexiform layer. - + EHDAA2 VHOG @@ -39146,15 +39204,15 @@ plexiform layer. - - + + - + Bilateral groups of cells consisting of three rows: one row of endocardial precursors medially and two rows of myocardical precursors laterally. The two populations fuse at the midline to form the heart rudiment or cone. should probably be merged with heart rudiment. AAO:0011044 @@ -39171,15 +39229,15 @@ plexiform layer. heart primordium - + - + - + @@ -39192,19 +39250,19 @@ plexiform layer. - + ZFA - + ZFA - + XAO @@ -39233,8 +39291,8 @@ plexiform layer. - - + + Ventral somitic compartment that is a precursor of the axial skeleton[XAO]. Sclerotomes eventually differentiate into the vertebrae and most of the skull. The caudal (posterior) half of one sclerotome fuses with the rostral (anterior) half of the adjacent one to form each vertebra. From their initial location within the somite, the sclerotome cells migrate medially towards the notochord. These cells meet the sclerotome cells from the other side to form the vertebral body. From this vertebral body, sclerotome cells move dorsally and surround the developing spinal cord, forming the vertebral arch[WP]. AAO:0010571 AEO:0000212 @@ -39258,11 +39316,11 @@ plexiform layer. sclerotome http://upload.wikimedia.org/wikipedia/commons/9/96/Gray65.png - + - + @@ -39281,13 +39339,13 @@ plexiform layer. - + VHOG:0000680 - + ZFA @@ -39608,7 +39666,7 @@ plexiform layer. - + Mesenchyme that is part of a developing camera-type eye. TODO - change mesenchyme relationships to precursor_of EHDAA2:0000485 @@ -39620,14 +39678,14 @@ plexiform layer. UBERON:0003314 eye mesenchyme - + - + EHDAA2 @@ -40020,7 +40078,6 @@ plexiform layer. An anatomical space that surrounded_by a neural tube. - UBERON:0005713 AAO:0011073 EHDAA2:0001269 EHDAA:2889 @@ -40402,7 +40459,7 @@ plexiform layer. - + The part of the coelom in the embryo between the somatopleuric and splanchnopleuric mesoderm; the principal body cavities of the trunk (thoracic, abdominal, and pelvic) arise from this embryonic part of the coelom. consider merging with coelom. TODO - add spatial relationships to halves of LPM. Note the OG places XAO and ZFA coelem terms here. editor note: TODO check ZFA, which appears to be a structure present in adults EHDAA:251 @@ -40417,14 +40474,14 @@ plexiform layer. intraembryonic coelom - + - + Wikipedia @@ -40517,7 +40574,7 @@ plexiform layer. - + The part of the retina that contains neurons and photoreceptor cells[GO]. AAO:0011095 @@ -40548,14 +40605,14 @@ plexiform layer. retinal neural layer - + - + Bgee:AN @@ -40675,7 +40732,6 @@ plexiform layer. White matter that is part of a diencephalon [Automatically generated definition]. - UBERON:0023148 BIRNLEX:1678 FMA:83931 TAO:0000338 @@ -40808,7 +40864,7 @@ plexiform layer. - + The layer of undifferentiated, proliferating cells that line the neural tube lumen that is the immediate transformation of the germinal neuroepithelium. consider merging with 'ventricular zone'; note that the MA class probably does not belong here, as this is an embryonic structure ependymal layer @@ -40825,7 +40881,7 @@ plexiform layer. neural tube ventricular layer - + @@ -40838,7 +40894,7 @@ plexiform layer. - + NCBIBook:NBK10047 @@ -41240,9 +41296,9 @@ plexiform layer. - - - + + + @@ -41274,34 +41330,34 @@ plexiform layer. optic vesicle http://upload.wikimedia.org/wikipedia/commons/e/e0/Gray863.png - + - + - + - + ZFA - + GO-def - + ZFA @@ -41397,8 +41453,8 @@ plexiform layer. - - + + A specific region of the lateral mesoderm that will form the primary beating heart tube. In mammals the primary heart field gives rise to the left ventricle. XAO:0004185 first heart field @@ -41410,24 +41466,24 @@ plexiform layer. UBERON:0004140 primary heart field - + - + - + GO:0003128 - + https://orcid.org/0000-0003-3308-6245 @@ -41480,7 +41536,7 @@ plexiform layer. - + An epithelial tube that will give rise to the mature heart. AAO:0010411 EFO:0003526 @@ -41499,14 +41555,14 @@ plexiform layer. heart tube - + - + ZFA-modified @@ -41583,7 +41639,7 @@ plexiform layer. - + @@ -41599,14 +41655,14 @@ plexiform layer. eye muscle - + - + MA @@ -41789,7 +41845,7 @@ plexiform layer. - + A transparent homogeneous acellular layer found between the substantia propria and the endothelial layer of the cornea[MP]. EMAPA:18804 @@ -41818,14 +41874,14 @@ plexiform layer. Descemet's membrane https://github.com/obophenotype/uberon/issues/15 - + - + Cline et al @@ -42084,7 +42140,6 @@ plexiform layer. - @@ -42181,7 +42236,6 @@ plexiform layer. - @@ -42463,7 +42517,6 @@ plexiform layer. Organism at the gastrula stage. - UBERON:0007012 BILA:0000060 BTO:0001403 FBbt:00005317 @@ -42577,7 +42630,7 @@ plexiform layer. - + Organ consisting of skeletal tissue. Encompasses whole bones, fused bones, cartilaginious elements, teeth, dermal denticles. AAO:0011129 TAO:0001890 @@ -42591,14 +42644,14 @@ plexiform layer. skeletal element - + - + VSAO @@ -42625,7 +42678,7 @@ plexiform layer. - + @@ -42664,14 +42717,14 @@ plexiform layer. UBERON:0004770 articular system - + - + FMA @@ -43523,7 +43576,7 @@ plexiform layer. - + Portion of primordial embryonic connective tissue of the developing head, consisting of mesenchymal cells supported in interlaminar jelly, that derive mostly from the mesoderm and contribute to head connective tissue, bone and musculature in conjunction with cranial neural crest cells. EFO:0003492 EHDAA2:0000732 @@ -43544,14 +43597,14 @@ plexiform layer. head mesenchyme - + - + EHDAA2 @@ -43609,7 +43662,7 @@ plexiform layer. - + Mesenchyme that is part of a developing trunk. EFO:0003485 EHDAA2:0002092 @@ -43625,14 +43678,14 @@ plexiform layer. trunk mesenchyme - + - + EHDAA2 @@ -44147,7 +44200,7 @@ plexiform layer. - + Portion of tissue that is part of the eye and gives rise to the mature, fully layered cornea. TAO:0002188 ZFA:0001688 @@ -44155,7 +44208,7 @@ plexiform layer. UBERON:0005427 corneal primordium - + @@ -44174,7 +44227,7 @@ plexiform layer. - + ZFA @@ -44197,7 +44250,7 @@ plexiform layer. - + Multi-tissue structure that arises from the heart rudiment and will become the heart tube. EHDAA2:0001512 EHDAA:424 @@ -44215,14 +44268,14 @@ plexiform layer. primitive heart tube - + - + ZFA @@ -44313,7 +44366,6 @@ plexiform layer. - @@ -44413,7 +44465,7 @@ plexiform layer. - + A delimited region of dense mesenchyme within looser mesenchyme. AEO:0000148 EHDAA2_RETIRED:0003148 @@ -44423,7 +44475,7 @@ plexiform layer. UBERON:0005856 developing mesenchymal condensation - + @@ -44442,7 +44494,7 @@ plexiform layer. - + AEO-modified-relation @@ -44463,7 +44515,6 @@ plexiform layer. - @@ -44500,8 +44551,8 @@ plexiform layer. - - + + @@ -44518,11 +44569,11 @@ plexiform layer. UBERON:0005908 conjunctival sac - + - + @@ -44535,13 +44586,13 @@ plexiform layer. - + FMA - + HPO:pr @@ -44783,7 +44834,7 @@ plexiform layer. - + @@ -44806,14 +44857,14 @@ plexiform layer. future diencephalon - + - + EHDAA2 @@ -44989,7 +45040,7 @@ plexiform layer. - + @@ -45013,14 +45064,14 @@ plexiform layer. future spinal cord - + - + EHDAA2 @@ -45057,7 +45108,7 @@ plexiform layer. - + The notochordal plate is the dorsal part of the notochordal process when the ventral portion breaks down. It is continuous laterally with the endoderm that composes the roof of the primitive foregut and is in contact dorsally with the neural tube. The folding off of the notochordal plate gives rise to the notochord. TODO - check ordering; awaiting confirmation from JB EHDAA2:0001278 @@ -45071,7 +45122,7 @@ plexiform layer. notochordal plate - + @@ -45084,7 +45135,7 @@ plexiform layer. - + EHDAA2 @@ -45112,7 +45163,7 @@ plexiform layer. - + A midline cellular cord formed from the migration of mesenchymal cells from the primitive knot. EHDAA2:0001279 EHDAA:224 @@ -45129,14 +45180,14 @@ plexiform layer. The notochordal process grows cranially until it reaches the prechordal plate, the future site of the mouth. In this area the ectoderm is attached directly to the endoderm without intervening mesoderm. This area is known as the oropharyngeal membrane, and it will break down to become the mouth. At the other end of the primitive streak the ectoderm is also fused directly to the endoderm; this is known as the cloacal membrane (proctodeum), or primordial anus. notochordal process - + - + EHDAA2 @@ -45717,7 +45768,6 @@ plexiform layer. - @@ -46178,8 +46228,8 @@ plexiform layer. - - + + @@ -46205,24 +46255,24 @@ plexiform layer. presumptive hindbrain - + - + - + XAO-abduced - + cjm @@ -46273,7 +46323,7 @@ plexiform layer. - + @@ -46292,14 +46342,14 @@ plexiform layer. presumptive midbrain hindbrain boundary - + - + ZFA @@ -46445,7 +46495,7 @@ plexiform layer. - + @@ -46471,7 +46521,7 @@ plexiform layer. presumptive paraxial mesoderm - + @@ -46487,7 +46537,7 @@ plexiform layer. - + https://github.com/obophenotype/uberon/issues/1277 @@ -46569,7 +46619,7 @@ plexiform layer. - + A neural decussation that is part of a diencephalon. FMA:62446 diencephalon decussation @@ -46577,7 +46627,7 @@ plexiform layer. UBERON:0007425 decussation of diencephalon - + @@ -46590,7 +46640,7 @@ plexiform layer. - + Obol @@ -46665,7 +46715,7 @@ plexiform layer. - + Mesenchyme with little extracellular matrix. AEO:0000146 EHDAA2:0003146 @@ -46673,7 +46723,7 @@ plexiform layer. UBERON:0007524 dense mesenchyme tissue - + @@ -46686,7 +46736,7 @@ plexiform layer. - + AEO @@ -46925,7 +46975,7 @@ plexiform layer. - + An axon tract that is part of a brain. the NIFSTD class 'nerve tract' is classified under 'regional part of brain', so it may seem like it belongs here, but actually includes spinal cord tracts FMA:83848 @@ -46935,14 +46985,14 @@ plexiform layer. UBERON:0007702 tract of brain - + - + cjm @@ -46970,7 +47020,7 @@ plexiform layer. - + Anatomical system that consists of all blood and lymph vessels. consider merging with vasculature @@ -46987,14 +47037,14 @@ plexiform layer. vascular system - + - + MA @@ -47049,6 +47099,7 @@ plexiform layer. SCTID:361355005 UMLS:C0460004 WikipediaCategory:Head_and_neck + ZFA:0001114 galen:HeadAndNeck uberon cephalic area @@ -47115,7 +47166,7 @@ plexiform layer. - + @@ -47124,7 +47175,6 @@ plexiform layer. Sum total of mesenchyme in the embryo. consider adding new class (EMAPA:16097) for mesenchyme of embryo (some mesenchyme is extraembryonic - e.g. amnion mesoderm) - UBERON:0003313 EHDAA2:0001113 EHDAA:177 EMAPA:16097 @@ -47132,14 +47182,14 @@ plexiform layer. UBERON:0009142 entire embryonic mesenchyme - + - + EHDAA2 @@ -47234,8 +47284,9 @@ plexiform layer. + - + @@ -47251,14 +47302,14 @@ plexiform layer. UBERON:0009615 midbrain hindbrain boundary neural plate - + - + ZFA @@ -47291,14 +47342,14 @@ plexiform layer. - + - + @@ -47323,24 +47374,24 @@ plexiform layer. presumptive midbrain - + - + - + ZFA - + ZFA @@ -47386,7 +47437,7 @@ plexiform layer. - + EHDAA2:0002094 trunk and cervical paraxial mesenchyme uberon @@ -47394,14 +47445,14 @@ plexiform layer. UBERON:0009618 trunk paraxial mesoderm - + - + EHDAA2 @@ -47424,7 +47475,7 @@ plexiform layer. - + EFO:0003704 TAO:0005041 ZFA:0005041 @@ -47434,14 +47485,14 @@ plexiform layer. anterior lateral plate mesoderm - + - + ZFA @@ -47497,14 +47548,14 @@ plexiform layer. - + EHDAA2:0001315 EHDAA:1122 uberon UBERON:0009920 optic neural crest - + @@ -47517,7 +47568,7 @@ plexiform layer. - + EHDAA2 @@ -47658,7 +47709,7 @@ plexiform layer. - + @@ -47681,14 +47732,14 @@ plexiform layer. eyeball of camera-type eye - + - + FMA @@ -47729,8 +47780,8 @@ plexiform layer. - - + + Portion of tissue that is dorsolateral to the floor plate and part of the midbrain. DHBA:12322 EFO:0003567 @@ -47744,11 +47795,11 @@ plexiform layer. midbrain basal plate - + - + @@ -47761,13 +47812,13 @@ plexiform layer. - + EHDAA2 - + ZFA @@ -47796,7 +47847,7 @@ plexiform layer. - + Portion of neural tube that gives rise to the midbrain. we follow ZFA in temporally dividing midbrain NT from presumptive midbrain, but in future this may be collapsed TAO:0007039 @@ -47805,14 +47856,14 @@ plexiform layer. UBERON:0010286 midbrain neural tube - + - + ZFA @@ -48115,8 +48166,8 @@ plexiform layer. - - + + Anatomical cluster consisting of the skeletal elements (i.e. bone elements, cartilage elements, cartilage condensations) that are part of an individual subdivision of the organism. Excludes joints. FMA:23879 SCTID:129140006 @@ -48128,11 +48179,11 @@ plexiform layer. subdivision of skeleton - + - + @@ -48145,13 +48196,13 @@ plexiform layer. - + UBERONREF:0000003 - + VSAO @@ -48212,7 +48263,7 @@ plexiform layer. - + Subdivision of the skeletal system which consists of the postcranial axial skeleton plus associated joints. axial skeletal system FMA:302077 @@ -48222,7 +48273,7 @@ plexiform layer. postcranial axial skeletal system http://purl.obolibrary.org/obo/uberon/docs/The-axial-skeleton - + @@ -48235,7 +48286,7 @@ plexiform layer. - + cjm @@ -48357,7 +48408,7 @@ plexiform layer. - + AAO:0010038 EMAPA:18808 FMA:49150 @@ -48367,14 +48418,14 @@ plexiform layer. UBERON:0011222 intra-ocular muscle - + - + EMAPA @@ -48636,7 +48687,7 @@ plexiform layer. - + @@ -48678,7 +48729,7 @@ plexiform layer. anterior uvea - + @@ -48691,7 +48742,7 @@ plexiform layer. - + MP @@ -48742,6 +48793,7 @@ plexiform layer. EHDAA2:0004731 Wikipedia:Coelom + ZFA:0001438 enterocoelom haemocoelom schizocoelom @@ -48822,7 +48874,6 @@ plexiform layer. - @@ -49415,7 +49466,6 @@ plexiform layer. Primordium that develops into the central nervous system. - UBERON:3000469 future CNS presumptive central nervous system uberon @@ -49459,7 +49509,6 @@ plexiform layer. Primordium that develops into the nervous system. - UBERON:3000477 AAO:0000477 presumptive nervous system uberon @@ -49485,7 +49534,7 @@ plexiform layer. - + @@ -49508,7 +49557,7 @@ plexiform layer. UBERON:0016887 entire extraembryonic component - + @@ -49521,7 +49570,7 @@ plexiform layer. - + AEO diff --git a/src/ontology/subsets/eye_upper_slim.tsv b/src/ontology/subsets/eye_upper_slim.tsv index 114a1bbfa..ad42fdc40 100644 --- a/src/ontology/subsets/eye_upper_slim.tsv +++ b/src/ontology/subsets/eye_upper_slim.tsv @@ -1,349 +1,347 @@ ?x ?label -_:B53189381X2D873cX2D4ec4X2Daff8X2D63fc38c8481egenid1008 -_:B53189381X2D873cX2D4ec4X2Daff8X2D63fc38c8481egenid1024 -_:B53189381X2D873cX2D4ec4X2Daff8X2D63fc38c8481egenid1030 -_:B53189381X2D873cX2D4ec4X2Daff8X2D63fc38c8481egenid1039 -_:B53189381X2D873cX2D4ec4X2Daff8X2D63fc38c8481egenid1045 -_:B53189381X2D873cX2D4ec4X2Daff8X2D63fc38c8481egenid1051 -_:B53189381X2D873cX2D4ec4X2Daff8X2D63fc38c8481egenid1057 -_:B53189381X2D873cX2D4ec4X2Daff8X2D63fc38c8481egenid1064 -_:B53189381X2D873cX2D4ec4X2Daff8X2D63fc38c8481egenid1072 -_:B53189381X2D873cX2D4ec4X2Daff8X2D63fc38c8481egenid1082 -_:B53189381X2D873cX2D4ec4X2Daff8X2D63fc38c8481egenid1096 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+_:B931103c1X2D84a8X2D48d8X2D8209X2Db7596f243407genid793 +_:B931103c1X2D84a8X2D48d8X2D8209X2Db7596f243407genid800 +_:B931103c1X2D84a8X2D48d8X2D8209X2Db7596f243407genid811 +_:B931103c1X2D84a8X2D48d8X2D8209X2Db7596f243407genid817 +_:B931103c1X2D84a8X2D48d8X2D8209X2Db7596f243407genid834 +_:B931103c1X2D84a8X2D48d8X2D8209X2Db7596f243407genid840 +_:B931103c1X2D84a8X2D48d8X2D8209X2Db7596f243407genid849 +_:B931103c1X2D84a8X2D48d8X2D8209X2Db7596f243407genid859 +_:B931103c1X2D84a8X2D48d8X2D8209X2Db7596f243407genid907 +_:B931103c1X2D84a8X2D48d8X2D8209X2Db7596f243407genid957 +_:B931103c1X2D84a8X2D48d8X2D8209X2Db7596f243407genid967 +_:B931103c1X2D84a8X2D48d8X2D8209X2Db7596f243407genid974 +_:B931103c1X2D84a8X2D48d8X2D8209X2Db7596f243407genid981 +_:B931103c1X2D84a8X2D48d8X2D8209X2Db7596f243407genid988 "cell" "neural crest derived fibroblast" "neuronal receptor cell" @@ -370,9 +368,7 @@ _:B53189381X2D873cX2D4ec4X2Daff8X2D63fc38c8481egenid997 "neuron associated cell" "interneuron" "sensory neuron" - "bipolar neuron" "endothelial cell" - "CNS neuron (sensu Vertebrata)" "neuron associated cell (sensu Vertebrata)" "glial cell" "macroglial cell" @@ -412,8 +408,8 @@ _:B53189381X2D873cX2D4ec4X2Daff8X2D63fc38c8481egenid997 "epiblast cell" "animal zygote" "electrically responsive cell" - "CNS interneuron" "electrically signaling cell" + "stromal cell" "smooth muscle myoblast" "afferent neuron" "pigmented epithelial cell" @@ -645,11 +641,11 @@ _:B53189381X2D873cX2D4ec4X2Daff8X2D63fc38c8481egenid997 "myelin sheath" "organelle" "membrane-bounded organelle" - "non-membrane-bounded organelle" + "membraneless organelle" "intracellular organelle" "extracellular organelle" "intracellular membrane-bounded organelle" - "intracellular non-membrane-bounded organelle" + "intracellular membraneless organelle" "organelle lumen" "regulation of respiratory gaseous exchange" "protein-containing complex organization" @@ -657,9 +653,7 @@ _:B53189381X2D873cX2D4ec4X2Daff8X2D63fc38c8481egenid997 "regulation of digestive system process" "cellular component biogenesis" "translation initiation ternary complex" - "cellular metabolic process" "primary metabolic process" - "cellular biosynthetic process" "cell body" "synapse" "secretion" @@ -742,7 +736,7 @@ _:B53189381X2D873cX2D4ec4X2Daff8X2D63fc38c8481egenid997 "trans-synaptic signaling" "chemical synaptic transmission, postsynaptic" "signal release from synapse" - "cellular anatomical entity" + "cellular anatomical structure" "plasma membrane bounded cell projection" "plasma membrane bounded cell projection assembly" "plasma membrane bounded cell projection organization" @@ -835,11 +829,8 @@ _:B53189381X2D873cX2D4ec4X2Daff8X2D63fc38c8481egenid997 "acidophilic" "nucleated" "disconnected" - "cell morphology" "polymeric" "high nuclear/cytoplasmic ratio" - "cortical bipolar morphology" - "bitufted dendrite cell morphology" "anatomical structure quality" "anatomical histological quality" "polychromatophilic" @@ -875,7 +866,7 @@ _:B53189381X2D873cX2D4ec4X2Daff8X2D63fc38c8481egenid997 "integrin alpha" "Mus musculus protein" "eukaryotic protein" - "protein-containing material entity" + "protein-containing molecular entity" "processual entity" "camera-type eye" "sense organ" diff --git a/src/ontology/subsets/general_cell_types_upper_slim.json b/src/ontology/subsets/general_cell_types_upper_slim.json index 6a4f6cb9e..54b3f06d6 100644 --- a/src/ontology/subsets/general_cell_types_upper_slim.json +++ b/src/ontology/subsets/general_cell_types_upper_slim.json @@ -4,9 +4,9 @@ "meta" : { "basicPropertyValues" : [ { "pred" : "http://www.w3.org/2002/07/owl#versionInfo", - "val" : "2024-09-26" + "val" : "2025-01-08" } ], - "version" : "http://purl.obolibrary.org/obo/cl/releases/2024-09-26/subsets/general_cell_types_upper_slim.owl" + "version" : "http://purl.obolibrary.org/obo/cl/releases/2025-01-08/subsets/general_cell_types_upper_slim.owl" }, "nodes" : [ { "id" : "http://purl.obolibrary.org/obo/CL_0000000", @@ -18,7 +18,7 @@ "xrefs" : [ "CARO:mah" ] }, "comments" : [ "The definition of cell is intended to represent all cells, and thus a cell is defined as a material entity and not an anatomical structure, which implies that it is part of an organism (or the entirety of one)." ], - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/ubprop#_upper_level" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/ubprop#_upper_level" ], "xrefs" : [ { "val" : "CALOHA:TS-2035" }, { @@ -50,6 +50,7 @@ "val" : "A cell found in the embryo before the formation of all the gem layers is complete.", "xrefs" : [ "GOC:tfm" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "ZFA:0009002" } ] @@ -64,7 +65,7 @@ "xrefs" : [ "GOC:tfm", "MESH:D013234" ] }, "comments" : [ "This term applies to metazoan. For plant stem cells, consider using PO:0004011 ‘initial cell’ or its parent PO:0004010 ‘meristematic cell’." ], - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#general_cell_types_upper_slim", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#general_cell_types_upper_slim", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "animal stem cell" @@ -91,7 +92,7 @@ "xrefs" : [ "GOC:add", "GOC:dsd", "GOC:tfm", "PMID:19022770", "http://en.wikipedia.org/wiki/Hematopoietic_stem_cell" ] }, "comments" : [ "Markers differ between species, and two sets of markers have been described for mice. HSCs are reportedly CD34-positive, CD45-positive, CD48-negative, CD150-positive, CD133-positive, and CD244-negative." ], - "subsets" : [ "http://purl.obolibrary.org/obo/cl#blood_and_immune_upper_slim", "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#blood_and_immune_upper_slim", "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "blood forming stem cell" @@ -134,7 +135,7 @@ "xrefs" : [ "GOC:tfm", "ISBN:0721662544" ] }, "comments" : [ "Originally this term had some plant germ line cell children." ], - "subsets" : [ "http://purl.obolibrary.org/obo/cl#general_cell_types_upper_slim", "http://purl.obolibrary.org/obo/ubprop#_upper_level" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#general_cell_types_upper_slim", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/ubprop#_upper_level" ], "xrefs" : [ { "val" : "ZFA:0009016" } ] @@ -149,6 +150,7 @@ "xrefs" : [ "GOC:add", "PMID:1104740", "http://en.wikipedia.org/wiki/Monoblast", "http://www.copewithcytokines.de" ] }, "comments" : [ "Morphology: mononuclear cell, diameter 12-20 _M, non-granular, N/C ratio 3/1 - 4/1; markers: CD11b (shared with many other myeloid cells); location: Adult: bone marrow; fetal: liver, Yolk Sac; role or process: hematopoiesis, monocyte development; lineage: hematopoietic, myeloid." ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003000", "pred" : "hasRelatedSynonym", @@ -180,6 +182,7 @@ "val" : "A stem cell that can give rise to multiple lineages of cells.", "xrefs" : [ "GOC:add" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "multi-fate stem cell" @@ -209,7 +212,7 @@ "xrefs" : [ "GOC:add", "ISBN:0878932437", "MESH:D023461" ] }, "comments" : [ "This cell type is intended to be compatible with any vertebrate common myeloid progenitor. For mammalian CMP known to be CD34-positive, please use the term 'common myeloid progenitor, CD34-positive' (CL_0001059)." ], - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "common myeloid precursor" @@ -265,7 +268,7 @@ "xrefs" : [ "GOC:add", "GOC:dsd", "GOC:tfm", "PMID:10407577", "PMID:16551251" ] }, "comments" : [ "CLP are CD7-positive, CD10-positive, CD19-negative, CD34-positive, CD45RA-positive, CD79a-negative, CD127-positive, AA4.1-positive, RAG-negative, Sca-1-low, sIgM-negative, sIgD-negative, TdT-negative, Vpre-B-negative, and pre-BCR-negative. Expression of transcription factors include E2A-positive, EBF-positive, Ikaros-negative, PU.1-negative, and Pax5-negative." ], - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "common lymphocyte precursor" @@ -313,6 +316,7 @@ "val" : "A stem cell from which all cells of the body can form.", "xrefs" : [ "GOC:add", "GOC:tfm" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "totipotential stem cell" @@ -335,7 +339,7 @@ "xrefs" : [ "SANBI:mhl" ] }, "comments" : [ "define using PATO mulit-potent or oligopotent?" ], - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "blast cell" @@ -355,6 +359,7 @@ "val" : "A cell that is commited to differentiating into a muscle cell. Embryonic myoblasts develop from the mesoderm. They undergo proliferation, migrate to their various sites, and then differentiate into the appropriate form of myocytes. Myoblasts also occur as transient populations of cells in muscles undergoing repair.", "xrefs" : [ "GOC:tfm", "MESH:D032446", "PMID:21849021" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "BTO:0000222" }, { @@ -379,7 +384,7 @@ "xrefs" : [ "ISBN:0517223651", "MESH:D005347", "http://en.wikipedia.org/wiki/Fibroblast" ] }, "comments" : [ "These cells may be vimentin-positive, fibronectin-positive, fsp1-positive, MMP-1-positive, collagen I-positive, collagen III-positive, and alpha-SMA-negative." ], - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#general_cell_types_upper_slim", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#general_cell_types_upper_slim", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "xrefs" : [ { "val" : "BTO:0000452" }, { @@ -407,7 +412,7 @@ "val" : "A cell that is usually found in a two-dimensional sheet with a free surface. The cell has a cytoskeleton that allows for tight cell to cell contact and for cell polarity where apical part is directed towards the lumen and the basal part to the basal lamina.", "xrefs" : [ "FB:ma", "GOC:tfm", "MESH:D004847" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#general_cell_types_upper_slim", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#general_cell_types_upper_slim", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "epitheliocyte" @@ -444,7 +449,7 @@ "val" : "A columnar/cuboidal epithelial cell is a cell usually found in a two dimensional sheet with a free surface. Columnar/cuboidal epithelial cells take on the shape of a column or cube.", "xrefs" : [ "GO:0002065", "https://orcid.org/0000-0001-5208-3432" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "xrefs" : [ { "val" : "ZFA:0009038" } ], @@ -462,7 +467,7 @@ "val" : "A cell found predominately in the blood.", "xrefs" : [ "GOC:add", "GOC:tfm" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#general_cell_types_upper_slim" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#general_cell_types_upper_slim", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "FMA:62844" }, { @@ -480,7 +485,7 @@ "val" : "A type of lymphocyte whose defining characteristic is the expression of a T cell receptor complex.", "xrefs" : [ "GOC:add", "GOC:tfm", "ISBN:0781735149" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#general_cell_types_upper_slim", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#general_cell_types_upper_slim", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "T lymphocyte" @@ -525,7 +530,7 @@ "xrefs" : [ "GOC:add", "GOC:tfm", "GO_REF:0000031", "ISBN:0781735149", "PMID:10428500", "PMID:15055519", "PMID:17380158" ] }, "comments" : [ "Morphology: Highly vesicular; markers: Surface: RANK, cFMS (MCSF receptor); Secreted: cathepsin K and TRAP (tartate resistant acid phosphatase); transcription factors: PU.1, cFOS, MITF, NFkB (p52); role or process: tissue remodelling: bone resorption; lineage: hematopoietic, myeloid." ], - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "pred" : "hasRelatedSynonym", "val" : "chondroclast" @@ -540,6 +545,12 @@ "val" : "MESH:D010010" }, { "val" : "ZFA:0009047" + }, { + "val" : "https://cellxgene.cziscience.com/cellguide/CL_0000092" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/description", + "val" : "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nOsteoclasts, derived from the monocyte/macrophage lineage, play a crucial role in bone remodeling through bone resorption. They are distinguished from other cells by their large size and their unique ability to secrete enzymes and acids that dissolve the calcium phosphate in bone. The formation of osteoclasts is influenced by two primary factors: macrophage colony-stimulating factor (M-CSF) and the ligand-activated receptor (RANKL) of nuclear factor kappa B (NF-κB).\nOsteoclasts also collaborate with osteoblasts, responsible for new bone formation, to maintain bone health and adapt bone structure. Their coordinated actions allow continuous remodeling while preserving overall bone strength and integrity. Imbalances in osteoclast activity can lead to pathological conditions. For example, excessive activity may contribute to diseases like osteoporosis, periprosthetic osteolysis, bone tumors, and Paget's disease. Other the other hand, osteoclast deficiency ca result in conditions like osteopetrosis." } ] } }, { @@ -551,7 +562,7 @@ "val" : "A leukocyte with abundant granules in the cytoplasm.", "xrefs" : [ "GOC:amm", "GOC:tfm", "MESH:D006098", "http://en.wikipedia.org/wiki/Granulocyte" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "granular leucocyte" @@ -583,7 +594,7 @@ "lbl" : "neuron associated cell", "type" : "CLASS", "meta" : { - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ] + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ] } }, { "id" : "http://purl.obolibrary.org/obo/CL_0000100", @@ -594,7 +605,7 @@ "val" : "An efferent neuron that passes from the central nervous system or a ganglion toward or to a muscle and conducts an impulse that causes or inhibits movement.", "xrefs" : [ "MESH:D009046", "PMID:16875686" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "motoneuron" @@ -624,7 +635,7 @@ "val" : "Any neuron having a sensory function; an afferent neuron conveying sensory impulses.", "xrefs" : [ "ISBN:0721662544" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "xrefs" : [ { "val" : "BTO:0001037" }, { @@ -652,7 +663,7 @@ "val" : "A vertebrate phagocyte with a single nucleus.", "xrefs" : [ "GOC:add", "GOC:tfm", "ISBN:0781735149" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "xrefs" : [ { "val" : "BTO:0001433" }, { @@ -665,7 +676,7 @@ "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" }, { "pred" : "http://purl.org/dc/terms/description", - "val" : "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional.\n\nMononuclear phagocytes are immune cells that form a critical part of the body's innate immune system, the body's first line of defense against infections. Mononuclear phagocytes are characterized by the presence of a single, large nucleus. The ‘Mononuclear Phagocyte System’ nomenclature was introduced to distinguish mononuclear monocytes and macrophages from other cells with multiple nuclei. However, the cells within the mononuclear phagocyte system represent a highly heterogeneous group, all of which are able to perform highly efficient phagocytosis - engulfing and digesting microbes and cellular debris to fight infections and to maintain normal tissue homeostasis. \nIn addition to phagocytosis, mononuclear phagocytes also secrete chemical compounds to recruit other immune cells to a site of infection. These cells produce different types of signaling molecules, including cytokines, chemokines, and reactive oxygen species, triggering a cascade of responses to ensure rapid and efficient containment and neutralization of invading pathogens. These cells are also involved in antigen presentation, a process essential for stimulating an adaptive immune response. They can process and present antigens to T cells, thereby linking the innate and adaptive immune responses.\nMononuclear phagocytes play key roles in tissue repair and remodeling. After infection or injury, these cells help in the clearance of dead cells and debris, a crucial step in the initiation of tissue remodeling and the resolution of inflammation. Overall, mononuclear phagocytes are versatile cells that have tailored their functions to meet the unique challenges of different tissues within the body. They are pivotal in homeostasis, immunity, and inflammation, making them important aspects in a range of human diseases including infection, autoimmunity, and cancer." + "val" : "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nMononuclear phagocytes are immune cells that form a critical part of the body's innate immune system, the body's first line of defense against infections. Mononuclear phagocytes are characterized by the presence of a single, large nucleus. The ‘Mononuclear Phagocyte System’ nomenclature was introduced to distinguish mononuclear monocytes and macrophages from other cells with multiple nuclei. However, the cells within the mononuclear phagocyte system represent a highly heterogeneous group, all of which are able to perform highly efficient phagocytosis - engulfing and digesting microbes and cellular debris to fight infections and to maintain normal tissue homeostasis. \nIn addition to phagocytosis, mononuclear phagocytes also secrete chemical compounds to recruit other immune cells to a site of infection. These cells produce different types of signaling molecules, including cytokines, chemokines, and reactive oxygen species, triggering a cascade of responses to ensure rapid and efficient containment and neutralization of invading pathogens. These cells are also involved in antigen presentation, a process essential for stimulating an adaptive immune response. They can process and present antigens to T cells, thereby linking the innate and adaptive immune responses.\nMononuclear phagocytes play key roles in tissue repair and remodeling. After infection or injury, these cells help in the clearance of dead cells and debris, a crucial step in the initiation of tissue remodeling and the resolution of inflammation. Overall, mononuclear phagocytes are versatile cells that have tailored their functions to meet the unique challenges of different tissues within the body. They are pivotal in homeostasis, immunity, and inflammation, making them important aspects in a range of human diseases including infection, autoimmunity, and cancer." } ] } }, { @@ -678,7 +689,7 @@ "xrefs" : [ "MESH:D009457" ] }, "comments" : [ "Not all glial cells develop from glioblasts, with microglia developing from the mesoderm instead. See https://github.com/obophenotype/cell-ontology/issues/1571" ], - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#general_cell_types_upper_slim", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#general_cell_types_upper_slim", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "neuroglial cell" @@ -704,7 +715,7 @@ "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" }, { "pred" : "http://purl.org/dc/terms/description", - "val" : "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional.\n\nGlial cells, also known as neuroglia or simply glia, are non-neuronal cells in the central and peripheral nervous systems that provide support and protection for neurons. They constitute approximately half of the total cells in the human brain and more than half in other parts of the nervous system. Glial cells perform several key functions including, but not limited to, maintaining homeostasis, forming the myelin sheath around the neuron axons, and providing support and nutrition to neurons.\nThese different functions are performed by various glial cell types, including astrocytes, oligodendrocytes, microglia and other specialized types. Astrocytes, for example, are the most abundant glial cells and provide metabolic and nutrient support to neurons, help regulate the extracellular ion and neurotransmitter levels, and play a role in the formation and maintenance of the blood-brain barrier, contributing to the overall homeostasis and functioning of the nervous system. Additionally, astrocytes are involved in synaptic communication and participate in processes such as synaptogenesis and synaptic pruning.\nOligodendrocytes in the central nervous system function to insulate neurons by producing a fatty substance known as myelin. The myelin sheath enhances the speed and efficiency of nerve impulse conduction along the axons. \nMicroglia, the immune cells of the central nervous system, protect neurons from pathogens and clear away dead neurons through phagocytosis, a process also known as cellular eating. They also contribute to the regulation of inflammation in response to signals of tissue damage or infection in the central nervous system by releasing cytokines and other signaling molecules that modulate the immune response.\nDespite their overarching function in the support and protection of neurons, glial cells have also been shown to play significant roles in the pathophysiology of many psychiatric and neurodegenerative diseases, such as Alzheimer’s, Parkinson’s Disease and multiple sclerosis." + "val" : "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nGlial cells, also known as neuroglia or simply glia, are non-neuronal cells in the central and peripheral nervous systems that provide support and protection for neurons. They constitute approximately half of the total cells in the human brain and more than half in other parts of the nervous system. Glial cells perform several key functions including, but not limited to, maintaining homeostasis, forming the myelin sheath around the neuron axons, and providing support and nutrition to neurons.\nThese different functions are performed by various glial cell types, including astrocytes, oligodendrocytes, microglia and other specialized types. Astrocytes, for example, are the most abundant glial cells and provide metabolic and nutrient support to neurons, help regulate the extracellular ion and neurotransmitter levels, and play a role in the formation and maintenance of the blood-brain barrier, contributing to the overall homeostasis and functioning of the nervous system. Additionally, astrocytes are involved in synaptic communication and participate in processes such as synaptogenesis and synaptic pruning.\nOligodendrocytes in the central nervous system function to insulate neurons by producing a fatty substance known as myelin. The myelin sheath enhances the speed and efficiency of nerve impulse conduction along the axons. \nMicroglia, the immune cells of the central nervous system, protect neurons from pathogens and clear away dead neurons through phagocytosis, a process also known as cellular eating. They also contribute to the regulation of inflammation in response to signals of tissue damage or infection in the central nervous system by releasing cytokines and other signaling molecules that modulate the immune response.\nDespite their overarching function in the support and protection of neurons, glial cells have also been shown to play significant roles in the pathophysiology of many psychiatric and neurodegenerative diseases, such as Alzheimer’s, Parkinson’s Disease and multiple sclerosis." } ] } }, { @@ -716,6 +727,7 @@ "val" : "Ectoderm destined to be nervous tissue.", "xrefs" : [ "GOC:tfm", "ISBN:068340007X" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "neurectoderm cell" @@ -734,7 +746,7 @@ "xrefs" : [ "FB:ma", "GOC:dsd", "PMCID:PMC2613570", "PMID:10102814", "PMID:16923606", "PMID:17986482", "PMID:19960544", "http://en.wikipedia.org/wiki/Mesenchymal_stem_cell", "http://www.copewithcytokines.de/cope.cgi?key=mesenchymal%20stem%20cells" ] }, "comments" : [ "Many but not all mesenchymal cells derive from the mesoderm. MSCs are reportedly CD3-negative, CD4-negative, CD5-negative, CD8-negative, CD11a-negative, CD11b-negative, CD14-negative, CD19-negative, CD29-positive, CD31-negative, CD34-negative, CD38-negative, CD40-negative, CD44-positive, CD45-negative, CD49-positive, CD54-positive, CD66b-negative, CD79a-negative, CD80-negative, CD102-positive, CD106-positive, CD117-positive, CD121a-positive, CD121b-positive, CD123-positive, CD124-positive, CD133-negative, CD146-positive, CD166-positive, CD271-positive, B220-negative, Gr1-negative, MHCI-positive, MHCII-negative, SSEA4-negative, sca1-positive, Ter119-negative, and glycophorin A-negative. Cultured MSCs are capable of producing stem cell factor, IL7, IL8, IL11, TGF-beta, cofilin, galectin-1, laminin-receptor 1, cyclophilin A, and MMP-2." ], - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "pred" : "hasNarrowSynonym", "val" : "bone marrow stromal cells" @@ -805,7 +817,7 @@ "val" : "A fat-storing cell found mostly in the abdominal cavity and subcutaneous tissue of mammals. Fat is usually stored in the form of triglycerides.", "xrefs" : [ "MESH:D017667" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#general_cell_types_upper_slim", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#general_cell_types_upper_slim", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "adipose cell" @@ -837,7 +849,7 @@ "xrefs" : [ "GOC:add", "ISBN:0781735149" ] }, "comments" : [ "Note change of name; nearly all somatic cells can present antigens to T cells via MHC Class I complexes leading to effector responses, but professional antigen presenting cells constitutively express MHC Class II as well as costimulatory molecules, and thus can initiate immune responses via T cells." ], - "subsets" : [ "http://purl.obolibrary.org/obo/cl#blood_and_immune_upper_slim", "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#blood_and_immune_upper_slim", "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003000", "pred" : "hasRelatedSynonym", @@ -856,6 +868,7 @@ "val" : "A pigment cell is a cell that contains pigment granules.", "xrefs" : [ "GOC:tfm" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "chromatocyte" @@ -878,7 +891,7 @@ "val" : "A pigment cell derived from the neural crest. Contains melanin-filled pigment granules, which gives a brown to black appearance.", "xrefs" : [ "SANBI:mhl" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#general_cell_types_upper_slim", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#general_cell_types_upper_slim", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "synonyms" : [ { "pred" : "hasNarrowSynonym", "val" : "melanophore" @@ -895,10 +908,15 @@ "val" : "VHOG:0001679" }, { "val" : "ZFA:0009091" + }, { + "val" : "https://cellxgene.cziscience.com/cellguide/CL_0000148" } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" + }, { + "pred" : "http://purl.org/dc/terms/description", + "val" : "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nMelanocytes are specialized cells prevalently found in the skin, but also present in the hair follicles, eyes, inner ear, bones, heart, and brain. Their primary function is the synthesis of melanin, a pigment responsible for coloration of skin, hair, and eyes. The presence and distribution of this pigment play a crucial role in the body's defense mechanism against harmful ultraviolet radiation.\nIn addition to melanin production, melanocytes also engage in a variety of other biological functions. They play a fundamental role in the immune response, owing to their ability to present antigens to T cells. Furthermore, they contribute to the maintenance of the skin's homeostasis by regulating processes such as extracellular matrix remodeling and cytokine production. A balance in melanocyte function is pivotal, as dysfunctions often result in dermatological disorders. For instance, the loss of melanocytes or reduction in their function may lead to hypopigmentation conditions such as vitiligo, whereas an abnormal increase could result in hyperpigmentation disorders or melanoma, a dangerous type of skin cancer." } ] } }, { @@ -906,6 +924,7 @@ "lbl" : "visual pigment cell", "type" : "CLASS", "meta" : { + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "pred" : "hasBroadSynonym", "val" : "pigment cell" @@ -920,7 +939,7 @@ "val" : "A cell that specializes in controlled release of one or more substances.", "xrefs" : [ "GOC:tfm", "ISBN:0721662544" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "BTO:0003659" }, { @@ -936,7 +955,7 @@ "val" : "A cell of an exocrine gland; i.e. a gland that discharges its secretion via a duct.", "xrefs" : [ "ISBN:0198547684" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#general_cell_types_upper_slim" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#general_cell_types_upper_slim", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "FMA:16014" }, { @@ -952,7 +971,7 @@ "val" : "A cell of an endocrine gland, ductless glands that secrete substances which are released directly into the circulation and which influence metabolism and other body functions.", "xrefs" : [ "MESH:D055098" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#general_cell_types_upper_slim", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#general_cell_types_upper_slim", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "endocrinocyte" @@ -976,7 +995,7 @@ "val" : "A cell whose primary function is to shorten.", "xrefs" : [ "FB:ma" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ] + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ] } }, { "id" : "http://purl.obolibrary.org/obo/CL_0000187", @@ -987,7 +1006,7 @@ "val" : "A mature contractile cell, commonly known as a myocyte. This cell has as part of its cytoplasm myofibrils organized in various patterns.", "xrefs" : [ "MESH:D032342" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "muscle fiber" @@ -1024,7 +1043,7 @@ "val" : "A somatic cell located in skeletal muscle.", "xrefs" : [ "GOC:tfm" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#general_cell_types_upper_slim", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#general_cell_types_upper_slim", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "skeletal muscle cell" @@ -1037,10 +1056,15 @@ "val" : "FMA:9727" }, { "val" : "ZFA:0009115" + }, { + "val" : "https://cellxgene.cziscience.com/cellguide/CL_0000188" } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" + }, { + "pred" : "http://purl.org/dc/terms/description", + "val" : "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nSkeletal muscle cells, or myocytes, are essential for the musculoskeletal system, featuring a striated appearance from tightly packed sarcomeres. These elongated, multi-nucleated cells convert ATP into mechanical energ and are key for voluntary movement and posture. They also are responsible for maintaining body temperature, storing nutrients, and stabilizing joints.\nSkeletal muscle cells organize themselves tightly into bundles to form muscle fibers. Embedded within each of these cells are thousands of myofibrils, which are made up of the contractile proteins, actin (the thin filament), and myosin (the thick filament). Contraction of a skeletal muscle cell occurs when these myofibrils shorten, a process driven by the sliding of actin and myosin filaments over each other in a mechanism famously known as the sliding filament theory.\nAdditionally, skeletal muscle cells exhibit a high degree of plasticity, which allows for their adaptation in response to alterations in functional demands or damages. They have an innate regenerative capacity due to the presence of satellite cells—quiescent muscle stem cells that reside within the muscle fibers. Upon muscle injury, these satellite cells become activated, proliferate, and differentiate into new muscle cells, thereby contributing to the repair and growth of injured skeletal muscle. With this, skeletal muscle cells serve not only a pivotal biomechanical function but also possess a great capacity for self-healing and regeneration." } ] } }, { @@ -1052,7 +1076,7 @@ "val" : "A non-striated, elongated, spindle-shaped cell found lining the digestive tract, uterus, and blood vessels. They develop from specialized myoblasts (smooth muscle myoblast).", "xrefs" : [ "MESH:D032389", "PMID:9315361", "http://en.wikipedia.org/wiki/Smooth_muscle_cell" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#general_cell_types_upper_slim", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#general_cell_types_upper_slim", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "synonyms" : [ { "pred" : "hasBroadSynonym", "val" : "non-striated muscle cell" @@ -1076,10 +1100,15 @@ "val" : "FMA:14072" }, { "val" : "ZFA:0009118" + }, { + "val" : "https://cellxgene.cziscience.com/cellguide/CL_0000192" } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" + }, { + "pred" : "http://purl.org/dc/terms/description", + "val" : "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nSmooth muscle cells are a specialized type of muscle cells that are primarily found within the walls of hollow organs such as the intestine, stomach, bladder, uterus, and blood vessels. These cells are an essential component of the autonomic nervous system controling involuntary movements within the body.\nSmooth muscle cells play a vital role in many physiological processes due to their unique functionality. They can contract and relax in a slow, sustained, and controlled manner to help modulate the size and shape of the lumens of the organs they surround. For example, in the digestive system, coordinated contraction and relaxation of smooth muscle cells propels food along the gastrointestinal tract - a process known as peristalsis. In the blood vessels, the smooth muscle cells, by contracting or relaxing, either constrict or dilate the vessels, which in turn, help regulate blood flow and pressure.\nOn a cellular level, smooth muscle cells possess a single, centrally located nucleus and contain an arranged network of actin and myosin filaments, which are the proteins responsible for muscle contraction. Unlike their counterparts in skeletal or cardiac muscles, these cells lack specific contact points for these filaments, hence the lack of visible striations. Furthermore, the contraction of smooth muscle cells is regulated by hormones and neurotransmitters, such as acetylcholine and norepinephrine, adding an additional layer of complex regulation to these highly specialized cells." } ] } }, { @@ -1091,7 +1120,7 @@ "val" : "A cell specialized in detecting light stimuli that are involved in visual perception.", "xrefs" : [ "MESH:D010786" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "BTO:0001060" }, { @@ -1117,6 +1146,7 @@ "val" : "A cell whose function is determined by the generation or the reception of an electric signal.", "xrefs" : [ "FB:ma" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "ZFA:0009128" } ] @@ -1130,6 +1160,7 @@ "val" : "A cell that moves by its own activities.", "xrefs" : [ "FB:ma" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "ZFA:0009136" } ] @@ -1143,6 +1174,7 @@ "val" : "A cell of the outer of the three germ layers of the embryo.", "xrefs" : [ "MESH:D004475" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "ectoderm cell" @@ -1162,7 +1194,7 @@ "val" : "A cell of the middle germ layer of the embryo.", "xrefs" : [ "MESH:D008648" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "mesoblast" @@ -1174,6 +1206,12 @@ "val" : "FMA:72554" }, { "val" : "ZFA:0009138" + }, { + "val" : "https://cellxgene.cziscience.com/cellguide/CL_0000222" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/description", + "val" : "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nMesodermal cells are pluripotent and the most abundant in the human body. They contribute to the development of several structures such as the skeletal muscles, bones, heart and blood vessels, kidneys, gonads, connective tissues, and certain layers of the skin. Hence, the mesoderm is often regarded as an active and diverse layer due to its role in forming many bodily structures. \nIn embryonic development, these cells are instrumental, contributing to the body's structures through a carefully coordinated sequence of morphogenetic movements. This process forms the complex multicellular architecture of tissues and organs from a simple ball of cells. Without the function of mesodermal cells, the body's integral structures and systems would cease to form correctly, leading to developmental disorders such as axial mesodermal dysplasia complex" } ] } }, { @@ -1185,6 +1223,7 @@ "val" : "A cell of the inner of the three germ layers of the embryo.", "xrefs" : [ "MESH:D004707" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "endoderm cell" @@ -1203,7 +1242,8 @@ "definition" : { "val" : "A cell with a single nucleus.", "xrefs" : [ "FB:ma", "GOC:tfm" ] - } + }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ] } }, { "id" : "http://purl.obolibrary.org/obo/CL_0000228", @@ -1214,6 +1254,7 @@ "val" : "A cell with more than one nucleus.", "xrefs" : [ "FB:ma", "Wikipedia:Multinucleate" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "multinucleated cells", @@ -1233,7 +1274,7 @@ "val" : "Any cell capable of ingesting particulate matter via phagocytosis.", "xrefs" : [ "GOC:add", "ISBN:0721601464" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "BTO:0001044" }, { @@ -1254,7 +1295,7 @@ "xrefs" : [ "GOC:add", "GOC:tfm", "GO_REF:0000031", "PMID:16213494", "PMID:1919437" ] }, "comments" : [ "Morphology: Diameter 30_M-80 _M, abundant cytoplasm, low N/C ratio, eccentric nucleus. Irregular shape with pseudopods, highly adhesive. Contain vacuoles and phagosomes, may contain azurophilic granules; markers: Mouse & Human: CD68, in most cases CD11b. Mouse: in most cases F4/80+; role or process: immune, antigen presentation, & tissue remodelling; lineage: hematopoietic, myeloid." ], - "subsets" : [ "http://purl.obolibrary.org/obo/cl#blood_and_immune_upper_slim", "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#general_cell_types_upper_slim", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#blood_and_immune_upper_slim", "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#general_cell_types_upper_slim", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "histiocyte" @@ -1286,7 +1327,7 @@ "val" : "A lymphocyte of B lineage that is capable of B cell mediated immunity.", "xrefs" : [ "GOC:add", "GOC:tfm", "GO_REF:0000031", "ISBN:0781735149" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#blood_and_immune_upper_slim", "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#general_cell_types_upper_slim", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#blood_and_immune_upper_slim", "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#general_cell_types_upper_slim", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "B lymphocyte" @@ -1324,7 +1365,7 @@ "val" : "Any cell that in taxon some Eukaryota.", "xrefs" : [ "FBC:Autogenerated" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "MESH:D005057" } ] @@ -1338,13 +1379,14 @@ "val" : "A cell that is specialised to accumulate a particular substance(s).", "xrefs" : [ "FB:ma" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/ubprop#_upper_level" ] + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/ubprop#_upper_level" ] } }, { "id" : "http://purl.obolibrary.org/obo/CL_0000327", "lbl" : "extracellular matrix secreting cell", "type" : "CLASS", "meta" : { + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "ZFA:0009162" } ] @@ -1358,6 +1400,7 @@ "val" : "A cell derived from the specialized ectoderm flanking each side of the embryonic neural plate, which after the closure of the neural tube, forms masses of cells that migrate out from the dorsal aspect of the neural tube to spread throughout the body.", "xrefs" : [ "doi:10.1016/j.stem.2015.02.017" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "FMA:86667" }, { @@ -1373,7 +1416,7 @@ "val" : "Any cell that is part of some extraembryonic structure.", "xrefs" : [ "FBC:Autogenerated" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#general_cell_types_upper_slim" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#general_cell_types_upper_slim", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "ZFA:0009176" } ] @@ -1386,7 +1429,8 @@ "definition" : { "val" : "A cell of the outer layer of a blastula that gives rise to the ectoderm after gastrulation.", "xrefs" : [ "GOC:tfm", "ISBN:0618947256" ] - } + }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ] } }, { "id" : "http://purl.obolibrary.org/obo/CL_0000355", @@ -1398,6 +1442,7 @@ "xrefs" : [ "PMID:18282570" ] }, "comments" : [ "Multi-potency demonstrated ex vivo. At the time of writing, it is unclear whether the endogenous population differentiates into multiple cell types in vivo." ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "FMA:86767" }, { @@ -1413,6 +1458,7 @@ "val" : "Diploid cell produced by the fusion of sperm cell nucleus and egg cell.", "xrefs" : [ "ISBN:0471245208" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "pred" : "hasBroadSynonym", "val" : "zygote" @@ -1434,6 +1480,7 @@ "val" : "A cell whose function is determined by its response to an electric signal.", "xrefs" : [ "FB:ma" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "ZFA:0009190" } ] @@ -1447,6 +1494,7 @@ "val" : "A cell that initiates an electrical signal and passes that signal to another cell.", "xrefs" : [ "FB:ma" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "ZFA:0009193" } ] @@ -1460,7 +1508,7 @@ "val" : "A cell of hematopoietic origin, typically resident in particular tissues, specialized in the uptake, processing, and transport of antigens to lymph nodes for the purpose of stimulating an immune response via T cell activation. These cells are lineage negative (CD3-negative, CD19-negative, CD34-negative, and CD56-negative).", "xrefs" : [ "GOC:add", "ISBN:0781735149" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#general_cell_types_upper_slim", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#general_cell_types_upper_slim", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "synonyms" : [ { "pred" : "hasRelatedSynonym", "val" : "interdigitating cell" @@ -1492,7 +1540,8 @@ "definition" : { "val" : "A cell whose primary function is to protect the organism.", "xrefs" : [ "JB:jb" ] - } + }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ] } }, { "id" : "http://purl.obolibrary.org/obo/CL_0000499", @@ -1500,10 +1549,10 @@ "type" : "CLASS", "meta" : { "definition" : { - "val" : "A connective tissue cell of an organ found in the loose connective tissue. These are most often associated with the uterine mucosa and the ovary as well as the hematopoietic system and elsewhere.", + "val" : "A connective tissue cell of an organ found in the loose connective tissue.", "xrefs" : [ "GOC:tfm", "MESH:D017154" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#general_cell_types_upper_slim", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#general_cell_types_upper_slim", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "xrefs" : [ { "val" : "BTO:0002064" }, { @@ -1525,7 +1574,7 @@ "val" : "A precursor cell destined to differentiate into cardiac muscle cell.", "xrefs" : [ "GOC:tfm", "MESH:D032386" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "cardiac muscle progenitor cell" @@ -1548,7 +1597,7 @@ "val" : "A precursor cell destined to differentiate into smooth muscle myocytes.", "xrefs" : [ "GOC:tfm", "MESH:D032390" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "myoblast, smooth muscle", @@ -1561,6 +1610,12 @@ "val" : "FMA:84798" }, { "val" : "ZFA:0009235" + }, { + "val" : "https://cellxgene.cziscience.com/cellguide/CL_0000514" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/description", + "val" : "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nA precursor to the smooth muscle cell, the smooth muscle myoblast, is integral to various body systems, including the cardiovascular, gastrointestinal, and respiratory systems. Smooth muscle myoblasts arise from the differentiation of mesenchymal stem cells, a process tightly regulated by specific genetic factors and environmental signals. Their role extends to myogenesis, particularly in the formation of muscular tissue, especially during embryonic development.\nSmooth muscle myoblasts possess distinctive cellular characteristics. In contrast to skeletal muscle myoblasts, they do not fuse to create multinucleated fibers. Instead, they differentiate into individual, uninucleated smooth muscle cells. This differentiation unfolds in two distinct phases: proliferation, marked by rapid division to increase cell numbers, and differentiation, involving structural and functional transformation into mature smooth muscle cells. This intricate process is intricately mediated by various signaling molecules and transcription factors.\nFunctionally, smooth muscle myoblasts and the mature muscle cells they generate play pivotal roles in various physiological processes. Smooth muscle cells orchestrate involuntary muscle responses and are integral to body systems that regulate blood flow, propel food along the digestive tract, and control airflow in the respiratory tract. These diverse functions underscore the significance of smooth muscle myoblasts in the body's growth, maintenance, and overall function." } ] } }, { @@ -1572,6 +1627,7 @@ "val" : "A myoblast that differentiates into skeletal muscle fibers.", "xrefs" : [ "SANBI:mhl" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "skeletal myoblast" @@ -1590,7 +1646,8 @@ "definition" : { "val" : "A phagocyte in vertebrates that is able to phagocytosis.", "xrefs" : [ "GOC:tfm" ] - } + }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ] } }, { "id" : "http://purl.obolibrary.org/obo/CL_0000526", @@ -1601,7 +1658,7 @@ "val" : "A neuron which conveys sensory information centrally from the periphery.", "xrefs" : [ "GOC:tfm", "MESH:D009475" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "input neuron" @@ -1625,6 +1682,7 @@ "val" : "A neuron which sends impulses peripherally to activate muscles or secretory cells.", "xrefs" : [ "MESH:D009476" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "output neuron" @@ -1643,7 +1701,7 @@ "xrefs" : [ "MESH:D009474", "http://en.wikipedia.org/wiki/Neuron" ] }, "comments" : [ "These cells are also reportedly CD4-negative and CD200-positive. They are also capable of producing CD40L and IFN-gamma." ], - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#general_cell_types_upper_slim", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#general_cell_types_upper_slim", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "nerve cell" @@ -1681,6 +1739,7 @@ "xrefs" : [ "GOC:tfm", "SANBI:mhl" ] }, "comments" : [ "Derived from UBERON:0002342 neural crest." ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "BTO:0003217" }, { @@ -1699,7 +1758,7 @@ "xrefs" : [ "GOC:add", "ISBN:0683073696", "ISBN:0781735149" ] }, "comments" : [ "Editors note: consider adding taxon constraint to vertebrata (PMID:18025161)" ], - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "xrefs" : [ { "val" : "BTO:0000775" }, { @@ -1728,7 +1787,7 @@ "xrefs" : [ "GOC:amm", "GOC:dsd", "GOC:tfm", "GO_REF:0000031", "ISBN:0721601464", "MESH:D055014", "PMCID:PMC2213186", "PMCID:PMC548021", "PMID:16551251", "PMID:16647566", "http://en.wikipedia.org/wiki/CFU-GM", "http://www.copewithcytokines.de" ] }, "comments" : [ "Originally described in the dendritic cell ontology (DC_CL:0000042)(PMID:19243617). GMPs are reportedly CD16-positive, CD32-positive, CD34-positive, CD38-positive, CD45RA-positive, CD110-negative, CD117-positive, CD123-positive, and SCA1-negative." ], - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "synonyms" : [ { "pred" : "hasBroadSynonym", "val" : "CFU-C , Colony forming unit in culture", @@ -1760,10 +1819,15 @@ } ], "xrefs" : [ { "val" : "ZFA:0009251" + }, { + "val" : "https://cellxgene.cziscience.com/cellguide/CL_0000557" } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" + }, { + "pred" : "http://purl.org/dc/terms/description", + "val" : "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nGranulocyte monocyte progenitor cells (GMP cells), originating from hematopoietic stem cells in the bone marrow, are a critical intermediate in myeloid cell development. Positioned at a key differentiation juncture, these cells exhibit bidirectional potential, giving rise to both granulocyte and monocyte lineages.\nTheir primary role is to generate mature granulocytes and monocytes, essential components of the body's innate immunity and inflammatory responses. Granulocytes, such as neutrophils, eosinophils, and basophils, contribute to the first line of defense against infections by migrating to the infection site and phagocytosing pathogens. Monocytes can differentiate into macrophages or dendritic cells, playing diverse roles in immune responses." } ] } }, { @@ -1776,7 +1840,7 @@ "xrefs" : [ "GOC:tfm", "ISBN:0721601464" ] }, "comments" : [ "Morphology: Mononuclear cell, diameter 14-18 _M, fine azurophilic granules; markers: CD11b (shared with many other myeloid cells); location: Adult: bone marrow; Fetal: Liver, Yolk Sac; role or process: hematopoiesis, monocyte development; lineage: hematopoietic, myeloid." ], - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "xrefs" : [ { "val" : "BTO:0004657" }, { @@ -1799,6 +1863,7 @@ "xrefs" : [ "GOC:dsd", "GOC:tfm", "PMID:12768659" ] }, "comments" : [ "These cells are reportedly CD31-positive, CD34-positive, CD144-positive, CD309-positive, and TAL1-positive." ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "angioblast" @@ -1820,7 +1885,7 @@ "xrefs" : [ "GO_REF:0000031", "MESH:D009000" ] }, "comments" : [ "Morphology: Mononuclear cell, diameter, 14 to 20 _M, N/C ratio 2:1-1:1. Nucleus may appear in variety of shapes: round, kidney, lobulated, or convoluted. Fine azurophilic granules present; markers: CD11b (shared with other myeloid cells), human: CD14, mouse: F4/80-mid,GR1-low; location: Blood, but can be recruited into tissues; role or process: immune & tissue remodelling; lineage: hematopoietic, myeloid." ], - "subsets" : [ "http://purl.obolibrary.org/obo/cl#blood_and_immune_upper_slim", "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#general_cell_types_upper_slim", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#blood_and_immune_upper_slim", "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#general_cell_types_upper_slim", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "xrefs" : [ { "val" : "BTO:0000876" }, { @@ -1844,7 +1909,7 @@ "val" : "A lymphocyte that can spontaneously kill a variety of target cells without prior antigenic activation via germline encoded activation receptors and also regulate immune responses via cytokine release and direct contact with other cells.", "xrefs" : [ "GOC:add", "ISBN:0781735149", "PMID:15771571" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#general_cell_types_upper_slim", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#general_cell_types_upper_slim", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "synonyms" : [ { "pred" : "hasBroadSynonym", "val" : "large granular lymphocyte" @@ -1886,7 +1951,7 @@ "val" : "A non-terminally differentiated cell that is capable of developing into a muscle cell.", "xrefs" : [ "GOC:add" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "ZFA:0009291" } ] @@ -1900,6 +1965,7 @@ "val" : "A stem cell that can give rise to cell types of the body other than those of the germ-line.", "xrefs" : [ "GO:0048103" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "CALOHA:TS-2086" }, { @@ -1917,6 +1983,7 @@ "val" : "Muscle cell which has as its direct parts myofilaments organized into sarcomeres.", "xrefs" : [ "GOC:tfm", "ISBN:0721662544" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "BTO:0002916" }, { @@ -1936,7 +2003,7 @@ "val" : "An achromatic cell of the myeloid or lymphoid lineages capable of ameboid movement, found in blood or other tissue.", "xrefs" : [ "GOC:add", "GOC:tfm", "ISBN:978-0-323-05290-0" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "leucocyte" @@ -1975,7 +2042,7 @@ "xrefs" : [ "GOC:mtg_cardiacconduct_nov11", "GOC:tfm", "ISBN:0323052908", "PMID:22426062", "PMID:4711263" ] }, "comments" : [ "This class encompasses the muscle cells responsible for heart* contraction in both vertebrates and arthropods. The ultrastucture of a wide range of arthropod heart cells has been examined including spiders, horseshoe crabs, crustaceans (see Sherman, 1973 and refs therein) and insects (see Lehmacher et al (2012) and refs therein). According to these refs, the cells participating in heart contraction in all cases are transversely striated. Insects hearts additionally contain ostial cells, also transversely striated muscle cells, but which do not participate in heart contraction." ], - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#general_cell_types_upper_slim", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#general_cell_types_upper_slim", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "synonyms" : [ { "pred" : "hasBroadSynonym", "val" : "cardiocyte" @@ -2003,13 +2070,15 @@ "val" : "MESH:D032383" }, { "val" : "ZFA:0009316" + }, { + "val" : "https://cellxgene.cziscience.com/cellguide/CL_0000746" } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "FMA:83808" + "pred" : "http://purl.org/dc/terms/description", + "val" : "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nCardiac muscle cells, also known as cardiomyocytes or cardiac myocytes, are specialized cells that form the heart tissue. These cells are elongated, branched, and contain a single centrally located nucleus. Their anatomy is composed primarily of densely packed myofibrils, which are protein structures that consist of sarcomeres - the fundamental units of muscle contraction. Cardiac muscle cells are united at their ends through specialized junctions known as intercalated discs, which allow the heart to contract in a unified, powerful and rhythmic way.\nFunctionally, cardiac muscle cells are responsible for the heart's consistent pumping action that circulates blood throughout the body. Unlike most cells in the body, cardiac muscle cells spontaneously depolarize and generate action potentials without external stimulation. This unique trait stems from the presence of ion channels in the cells' membrane that allow a cyclic flow of ions across the membrane, which create the electrical impulses necessary for heart contraction. The spread of these electrical signals from one cardiac muscle cell to another - facilitated by the interconnected network made by the intercalated disks - results in a synchronized contraction of the heart muscle.\nUnlike skeletal muscle cells which can tire and need rest, cardiac muscle cells have to work ceaselessly throughout the entire lifespan, without the opportunity for rest, to ensure continuous circulation of blood. This is made possible through the high volume of mitochondria and a constant supply of oxygen from coronary circulation. In conclusion, cardiac muscle cells, through their unique structure and vital functionality, play a pivotal role in sustaining life by providing the means for blood to reach every cell in the body." } ] } }, { @@ -2021,7 +2090,7 @@ "val" : "A cell of the monocyte, granulocyte, mast cell, megakaryocyte, or erythroid lineage.", "xrefs" : [ "GOC:add" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "BTO:0001441" }, { @@ -2041,7 +2110,7 @@ "val" : "A cell of the monocyte, granulocyte, or mast cell lineage.", "xrefs" : [ "GOC:add" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "ZFA:0009326" } ] @@ -2056,7 +2125,7 @@ "xrefs" : [ "GOC:add", "PMID:10449155", "PMID:17332250", "PMID:9521319" ] }, "comments" : [ "These cells are CD1a-negative, CD1b-positive, CD11a-positive, CD11c-positive, CD13-positive, CD14-negative, CD20-negative, CD21-negative, CD33-positive, CD40-negative, CD50-positive, CD54-positive, CD58-positive, CD68-negative, CD80-negative, CD83-negative, CD85j-positive, CD86-positive, CD89-negative, CD95-positive, CD120a-negative, CD120b-positive, CD123-negative, CD178-negative, CD206-negative, CD207-negative, CD209-negative, and TNF-alpha-negative. Upon TLR stimulation, they are capable of producing high levels of TNF-alpha, IL-6, CXCL8 (IL-8)." ], - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "pred" : "hasBroadSynonym", "val" : "interdigitating cell" @@ -2084,6 +2153,7 @@ "xrefs" : [ "GOC:add", "GOC:pam", "GO_REF:0000031", "PMID:11532393", "PMID:12457618", "PMID:15032583", "PMID:15766674" ] }, "comments" : [ "Most markers only described for human pro NK cells." ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "NKP", @@ -2117,7 +2187,7 @@ "xrefs" : [ "GOC:add", "GOC:dsd", "ISBN:0781735149", "PMID:12633665", "PMID:16551251", "PMID:18432934" ] }, "comments" : [ "Human pro-B cells are reportedly CD10-positive, CD22-positive, CD34-positive, CD38-positive, CD45-low, CD48-positive, CD79a-positive, CD127-positive, CD184-positive, RAG-positive, TdT-positive, Vpre-B-positive, pre-BCR-negative, IgD-negative, and IgM-negative. Transcription factors expressed: Pax5-positive, EBF-positive, E2A-negative, Ikaros-negative, and PU.1-negative." ], - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "synonyms" : [ { "pred" : "hasBroadSynonym", "val" : "pre-pro B cell", @@ -2167,7 +2237,7 @@ "val" : "A lymphoid progenitor cell of the T cell lineage, with some lineage specific marker expression, but not yet fully committed to the T cell lineage.", "xrefs" : [ "GOC:add", "ISBN:0781735149" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "pro-T lymphocyte" @@ -2198,7 +2268,7 @@ "xrefs" : [ "GOC:add", "GOC:tfm", "PMID:19022770" ] }, "comments" : [ "Markers differ between mouse and human." ], - "subsets" : [ "http://purl.obolibrary.org/obo/cl#blood_and_immune_upper_slim", "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#blood_and_immune_upper_slim", "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "MPP" @@ -2228,7 +2298,7 @@ "xrefs" : [ "GOC:add", "GOC:tfm" ] }, "comments" : [ "Note that this is a class of cell types, not an identified single cell type." ], - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "pred" : "hasBroadSynonym", "val" : "lymphoid progenitor cell" @@ -2253,7 +2323,7 @@ "xrefs" : [ "GOC:add", "GOC:tfm", "PMID:19022770" ] }, "comments" : [ "Note that this is a class of cell types, not an identified single cell type." ], - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "synonyms" : [ { "pred" : "hasBroadSynonym", "val" : "myeloid progenitor cell" @@ -2281,7 +2351,7 @@ "val" : "A leukocyte with a single non-segmented nucleus in the mature form.", "xrefs" : [ "GOC:add" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#blood_and_immune_upper_slim", "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#blood_and_immune_upper_slim", "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "mononuclear leukocyte" @@ -2309,7 +2379,7 @@ "xrefs" : [ "GOC:add", "GOC:rhs", "GOC:tfm", "GO_REF:0000031", "ISBN:0781735149" ] }, "comments" : [ "Types of B lineage lymphocytes include B cells and antibody secreting cells (plasmablasts and plasma cells). Lymphocytes of B cell lineage can be distinguished from those of T cell lineage by their lack of CD3e (as part of the T cell receptor complex)." ], - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" @@ -2324,7 +2394,7 @@ "val" : "A cell of a hematopoietic lineage.", "xrefs" : [ "GOC:add", "GO_REF:0000031" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "haematopoietic cell" @@ -2357,7 +2427,7 @@ "xrefs" : [ "GOC:amm", "GO_REF:0000031", "PMID:17850486" ] }, "comments" : [ "Originally described in the dendritic cell ontology (DC_CL:0000003)(PMID:19243617) These cells are also CD20-negative, MHCII-positive." ], - "subsets" : [ "http://purl.obolibrary.org/obo/cl#blood_and_immune_upper_slim", "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#blood_and_immune_upper_slim", "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "synonyms" : [ { "pred" : "hasBroadSynonym", "val" : "interdigitating cell" @@ -2390,7 +2460,8 @@ "lbl" : "CD7-negative lymphoid progenitor OR granulocyte monocyte progenitor", "type" : "CLASS", "meta" : { - "comments" : [ "Originally described in the dendritic cell ontology (DC_CL:1110000)(PMID:19243617)." ] + "comments" : [ "Originally described in the dendritic cell ontology (DC_CL:1110000)(PMID:19243617)." ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ] } }, { "id" : "http://purl.obolibrary.org/obo/CL_0001035", @@ -2401,13 +2472,19 @@ "val" : "A connective tissue cell found in bone.", "xrefs" : [ "GOC:add", "GO_REF:0000034" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#general_cell_types_upper_slim", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#general_cell_types_upper_slim", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "xrefs" : [ { + "val" : "https://cellxgene.cziscience.com/cellguide/CL_0001035" + } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" }, { "pred" : "http://purl.org/dc/terms/contributor", "val" : "https://orcid.org/0000-0001-9990-8331" + }, { + "pred" : "http://purl.org/dc/terms/description", + "val" : "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nBone cells, also known as osteocytes, form the building blocks of the skeletal system. They represent the most common type of bone cell, making up approximately 95% of the total bone cell population in mature adult bone tissue. Osteocytes are a stellate shape with numerous long, slender dendritic processes.\nThe formation of bone is a complex process involving the action of osteoclasts - cells that break down and reabsorb old bone, followed by osteoblasts that rebuild the bone. Osteocytes serve as coordinators for these two types of bone cells to ensure a balance in the bone remodeling process, contributing to maintaining both bone strength and mineral homeostasis.\nThe primary functions of osteocytes involve the creation, maintenance, and repair of bone tissue. They ensure that bone remodeling is performed by forming a network within the bone and communicating with other cells to help them respond to mechanical strain and damage.\nA remarkable aspect of osteocytes is their ability to perceive mechanical forces, translating them into biochemical signals that regulate bone remodeling and adaptation. Defects in osteocyte function, aside from other bone cells, have been associated with several bone disorders such as osteoporosis, renal osteodystrophy, and skeletal manifestations of diabetes." }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2011-11-16T04:28:16Z" @@ -2422,6 +2499,7 @@ "val" : "A hematopoietic oligopotent progenitor cell that has the ability to differentiate into limited cell types but lacks lineage cell markers and self renewal capabilities. Cell lacks hematopoeitic lineage markers.", "xrefs" : [ "GOC:tfm", "PMID:19022770" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "basicPropertyValues" : [ { "pred" : "http://purl.org/dc/terms/contributor", "val" : "https://orcid.org/0000-0003-1980-3228" @@ -2439,7 +2517,7 @@ "val" : "A lymphocyte that lacks characteristic T cell, B cell, myeloid cell, and dendritic cell markers, that functions as part of the innate immune response to produce cytokines and other effector responses.", "xrefs" : [ "GOC:add", "GOC:dsd", "PMID:23292121", "PMID:23348417" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#blood_and_immune_upper_slim", "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#blood_and_immune_upper_slim", "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" @@ -2460,7 +2538,7 @@ "val" : "An innate lymphoid cell that is capable of producing the type 1 cytokine IFN-gamma, but not Th2 or Th17 cell-associated cytokines.", "xrefs" : [ "GOC:add", "GOC:dsd", "PMID:23348417" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" @@ -2481,7 +2559,7 @@ "val" : "A progenitor cell that can give rise to plasmacytoid and myeloid dendritic cells, and to monocytes and macrophages.", "xrefs" : [ "GOC:tfm", "PMID:19273628" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "MDP" @@ -2503,7 +2581,7 @@ "val" : "A hematopoietic progenitor cell that is capable of developing into only one lineage of hematopoietic cells.", "xrefs" : [ "GOC:tfm", "PMID:19022770" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#blood_and_immune_upper_slim" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#blood_and_immune_upper_slim", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "basicPropertyValues" : [ { "pred" : "http://purl.org/dc/terms/contributor", "val" : "https://orcid.org/0000-0003-1980-3228" @@ -2522,7 +2600,7 @@ "xrefs" : [ "GOC:tfm", "PMID:19022770", "https://orcid.org/0000-0001-5208-3432" ] }, "comments" : [ "This cell type is intended to be compatible with any vertebrate hematopoietic oligopotent progenitor cell. For mammalian hematopoietic oligopotent progenitor cells known to be lineage-negative, please use the term 'hematopoietic oligopotent progenitor cell' (CL_0001060)." ], - "subsets" : [ "http://purl.obolibrary.org/obo/cl#blood_and_immune_upper_slim" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#blood_and_immune_upper_slim", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "basicPropertyValues" : [ { "pred" : "http://purl.org/dc/terms/contributor", "val" : "https://orcid.org/0000-0003-1980-3228" @@ -2540,6 +2618,7 @@ "val" : "An epithelial cell derived from ectoderm.", "xrefs" : [ "FMA:69074", "GOC:tfm" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "FMA:69074" }, { @@ -2563,7 +2642,7 @@ "xrefs" : [ "GOC:tfm", "ISBN:0618947256" ] }, "comments" : [ "MH consider whether bone marrow cells are bone cells in the structural sense vs. being part of bone organ sense." ], - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "BTO:0004850" }, { @@ -2588,6 +2667,7 @@ "val" : "A cell involved in the formation of a monocyte (monopoiesis).", "xrefs" : [ "GOC:tfm" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "FMA:83552" } ], @@ -2608,6 +2688,7 @@ "val" : "A cell containing at least one nucleus.", "xrefs" : [ "GOC:tfm" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "FMA:67513" } ], @@ -2628,7 +2709,7 @@ "val" : "A cell that is part of the nervous system.", "xrefs" : [ "GOC:tfm", "ISBN:0618947256" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "CALOHA:TS-2040" }, { @@ -2651,7 +2732,7 @@ "val" : "A cell of the supporting or framework tissue of the body, arising chiefly from the embryonic mesoderm and including adipose tissue, cartilage, and bone.", "xrefs" : [ "GOC:tfm", "ISBN:0618947256" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "CALOHA:TS-2096" }, { @@ -2678,6 +2759,7 @@ "val" : "A cell of the embryo.", "xrefs" : [ "FMA:0618947256" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "CALOHA:TS-0263" }, { @@ -2686,10 +2768,15 @@ "val" : "WBbt:0007028" }, { "val" : "ZFA:0007089" + }, { + "val" : "https://cellxgene.cziscience.com/cellguide/CL_0002321" } ], "basicPropertyValues" : [ { "pred" : "http://purl.org/dc/terms/contributor", "val" : "https://orcid.org/0000-0003-1980-3228" + }, { + "pred" : "http://purl.org/dc/terms/description", + "val" : "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nEmbryonic cells in metazoans, which include all multicellular animals, are biological units in their earliest developmental stages from conception until the organism is fully formed. \nThey are derived from a fertilized egg, which undergoes a series of cell divisions to produce a multicellular organism. During the early phases of embryonic development, these cells exhibit pluripotency, meaning they possess the potential to differentiate into a diverse array of specialized cell types that constitute different body tissues and structures. \nThe balance between cell proliferation and differentiation in embryonic cells is crucial for successful development. When cells continue to divide without differentiating, overgrowth may occur leading to conditions such as teratomas (tumors of embryonic cells). Conversely, if cell differentiation proceeds at the expense of cell proliferation, developmental anomalies could occur regarding size or mass of the organism or its parts." }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2010-09-15T03:39:21Z" @@ -2704,6 +2791,7 @@ "val" : "A transversely striated, multinucleated syncytial muscle cell, formed by the fusion of myoblasts during muscle development.", "xrefs" : [ "GOC:dos", "GOC:tfm", "ISBN:0323052908", "PMID:22274696" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "myofiber", @@ -2734,6 +2822,7 @@ "xrefs" : [ "GOC:tfm" ] }, "comments" : [ "From Onard of the FMA: Cardiac muscle cell or cardiac myocyte is a striated muscle cell. Cardiocyte on the other hand is any cell in the heart which includes cells other than muscle cells (e.g. endothelial cell of endocardium). Unless there is a consensus among anatomists that cardiocytes refer only to muscle cells, we will treat them as a general class of cells in the heart." ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "heart cell" @@ -2765,6 +2854,7 @@ "xrefs" : [ "GO_REF:0000034" ] }, "comments" : [ "Needs logical definition. Should be capable_of skeletal system morphogenesis? or skeletal tissue development? needs to be added to GO. NOTES:a cell type of the early embryo (see also: mesenchymal cells) that will give rise to mineralized connective tissue. Scleroblasts can differentiate into osteoblasts (bone-forming cells), chondroblasts (cartilage-forming cells), odontoblasts (dentin-forming cells), ameloblasts (enamel-forming cells). The mesenchymal cells developing into osteoblasts and chondroblasts are derived from the mesoderm. Those developing into odontoblasts are neural crest cells. Those developing into ameloblasts are derived from the ectoderm. (http://www.copewithcytokines.de/cope.cgi?key=scleroblasts)" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "scleroblast", @@ -2787,6 +2877,7 @@ "val" : "Cell that is part of the neural crest region of the neuroepithelium, prior to migration. Note that not all premigratory neural crest cells may become migratory neural crest cells.", "xrefs" : [ "UBERONREF:0000002" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "ZFA:0007084" } ], @@ -2806,7 +2897,8 @@ "definition" : { "val" : "Any muscle cell in which the fibers are not organised into sarcomeres.", "xrefs" : [ "GOC:DOS" ] - } + }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ] } }, { "id" : "http://purl.obolibrary.org/obo/CL_0008001", @@ -2817,7 +2909,7 @@ "val" : "Any hematopoietic cell that is a precursor of some other hematopoietic cell type.", "xrefs" : [ "GOC:dos" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ] + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ] } }, { "id" : "http://purl.obolibrary.org/obo/CL_0008002", @@ -2828,7 +2920,7 @@ "val" : "A transversely striated, synctial cell of skeletal muscle. It is formed when proliferating myoblasts exit the cell cycle, differentiate and fuse.", "xrefs" : [ "GOC:tfm", "ISBN:0323052908" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "MESH:D018485" } ] @@ -2842,6 +2934,7 @@ "val" : "A muscle cell that is part of some visceral muscle.", "xrefs" : [ "GOC:dos" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "FBbt:00005070" } ] @@ -2854,7 +2947,7 @@ "definition" : { "val" : "A non-polarised cell precursor cell that is part of some mesenchyme, is associated with the cell matrix but is not connected to other cells and is capable of migration." }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "mesenchyme cell" @@ -2873,6 +2966,7 @@ "val" : "Any neuron that is capable of part of some visual perception.", "xrefs" : [ "FBC:Autogenerated" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "basicPropertyValues" : [ { "pred" : "http://purl.org/dc/terms/contributor", "val" : "https://orcid.org/0000-0002-7073-9172" @@ -2890,7 +2984,7 @@ "val" : "Any cell in the retina, the innermost layer or coating at the back of the eyeball, which is sensitive to light and in which the optic nerve terminates.", "xrefs" : [ "GOC:pr" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#general_cell_types_upper_slim" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#general_cell_types_upper_slim", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "PMID:10702418" } ] @@ -2903,6 +2997,7 @@ "definition" : { "val" : "A zygote in a plant or an animal." }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "MESH:D015053" } ], @@ -2920,6 +3015,7 @@ "val" : "Any myoblast that develops into some cardiac muscle cell.", "xrefs" : [ "FBC:Autogenerated" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "MESH:D032386" } ] @@ -2933,13 +3029,13 @@ "val" : "A cell of the neural crest. Neural crest cells are multipotent. Premigratory neural crest cells are found at the neural plate boarder, some of which will undergo ectomesynchymal transition and delamination to form migratory neural crest cells.", "xrefs" : [ "https://orcid.org/0000-0001-5208-3432", "https://orcid.org/0000-0002-9900-7880" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "https://cellxgene.cziscience.com/cellguide/CL_0011012" } ], "basicPropertyValues" : [ { "pred" : "http://purl.org/dc/terms/description", - "val" : "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional.\n\nNeural crest cells are a group of transient and highly migratory cells that originate from the neuroectoderm during the early stages of embryonic development. They are multipotent cells with an exceptional degree of plasticity, capable of differentiating into various somatic cell types and therefore play a fundamental role in the formation of various organs and tissues, making them critical contributors to the developing embryo. \nAfter the initiation of neurulation (the formation of the neural tube) neural crest cells start to undergo epithelial-to-mesenchymal transition and delaminate and migrate from the dorsal neural tube to several regions throughout the embryo. They differentiate into a range of diverse cell types, such as neurons and glial cells of the peripheral nervous system, including sensory and autonomic neurons. They also contribute to the formation of adrenal glands, pigment cells in the skin (melanocytes), cardiac structures, including parts of the heart septum and major arteries, as well as bones and cartilage of the face and skull.\nDisorders or aberrations in the development or migration of the neural crest cells can lead to serious congenital malformations, such as neurocristopathies, including Hirschsprung disease, neuroblastoma, and neurofibromatosis." + "val" : "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nNeural crest cells are a group of transient and highly migratory cells that originate from the neuroectoderm during the early stages of embryonic development. They are multipotent cells with an exceptional degree of plasticity, capable of differentiating into various somatic cell types and therefore play a fundamental role in the formation of various organs and tissues, making them critical contributors to the developing embryo. \nAfter the initiation of neurulation (the formation of the neural tube) neural crest cells start to undergo epithelial-to-mesenchymal transition and delaminate and migrate from the dorsal neural tube to several regions throughout the embryo. They differentiate into a range of diverse cell types, such as neurons and glial cells of the peripheral nervous system, including sensory and autonomic neurons. They also contribute to the formation of adrenal glands, pigment cells in the skin (melanocytes), cardiac structures, including parts of the heart septum and major arteries, as well as bones and cartilage of the face and skull.\nDisorders or aberrations in the development or migration of the neural crest cells can lead to serious congenital malformations, such as neurocristopathies, including Hirschsprung disease, neuroblastoma, and neurofibromatosis." } ] } }, { @@ -2951,7 +3047,7 @@ "val" : "A precursor cell that has a tendency to differentiate into a specific type of cell. They are descendants of stem cells, only they are more constrained in their differentiation potential or capacity for self-renewal, and are often more limited in both senses.", "xrefs" : [ "ISBN:978-1-62808-994-3", "https://doi.org/10.1016/B978-0-12-409503-8.00002-0" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "basicPropertyValues" : [ { "pred" : "http://purl.org/dc/terms/contributor", "val" : "https://orcid.org/0000-0001-5208-3432" @@ -2967,7 +3063,7 @@ "xrefs" : [ "GOC:dos" ] }, "comments" : [ "Work is needed on GO 'cell differentiation' before it is clear whether the equivalent class definition 'native cell' that capable_of some 'cell differentiation' works. Also, may want to consider merging this with non-terminally differentiated cell." ], - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ] + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ] } }, { "id" : "http://purl.obolibrary.org/obo/CL_0017500", @@ -3012,6 +3108,7 @@ "val" : "Hematopoietic cells resident in the bone marrow. Include: hematopoietic stem cells (lymphoid stem cells and myeloid stem cells) and the precursor cells for thrombocytes, erythrocytes, basophils, neutrophils, eosinophils, monocytes and lymphocytes.", "xrefs" : [ "NPX:PDR" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "pred" : "hasRelatedSynonym", "val" : "bone marrow hematopoietic cells", @@ -3034,6 +3131,7 @@ "val" : "A multinucleate cell formed by the fusion of multiple uninuclear cells through plasma membrane fusion. This process leads to a single large cell containing multiple nuclei within a shared cytoplasm.", "xrefs" : [ "PMID:20851884", "Wikipedia:Syncytium" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "syncytium", @@ -3110,15 +3208,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/geneontology/go-ontology/issues/28301" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0000789" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0000790" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0005717" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "cellular_component" @@ -3148,12 +3237,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/geneontology/go-ontology/issues/22355" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0005719" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0035327" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "cellular_component" @@ -3186,12 +3269,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/geneontology/go-ontology/issues/22355" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0005720" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0035328" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "cellular_component" @@ -3391,18 +3468,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/geneontology/go-ontology/issues/19116" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0042032" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0042089" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0042107" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0050663" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" @@ -3443,9 +3508,6 @@ "val" : "Wikipedia:Neurulation" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0001679" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" } ] @@ -3649,12 +3711,6 @@ "val" : "immunoglobulin secretion" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0002378" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0048305" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" } ] @@ -3711,12 +3767,6 @@ "val" : "cellular immune response" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0019723" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0042087" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" } ] @@ -4008,9 +4058,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/geneontology/go-ontology/issues/17729" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0008372" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "cellular_component" @@ -4097,12 +4144,6 @@ "val" : "Wikipedia:Basement_membrane" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0005605" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0008003" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "cellular_component" } ] @@ -4355,12 +4396,6 @@ "val" : "Wikipedia:Cell_membrane" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0005887" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0005904" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "cellular_component" } ] @@ -4414,9 +4449,6 @@ "val" : "cellular DNA metabolism" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0055132" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" } ] @@ -4469,15 +4501,6 @@ "val" : "Wikipedia:Translation_(genetics)" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0006416" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0006453" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0043037" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" } ] @@ -4506,12 +4529,6 @@ "val" : "translation initiation" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0006440" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0006454" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" } ] @@ -4534,12 +4551,6 @@ "val" : "translation elongation" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0006442" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0006455" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" } ] @@ -4564,12 +4575,6 @@ "val" : "translational complex disassembly" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0006443" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0006456" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" } ] @@ -4592,21 +4597,9 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/geneontology/go-ontology/issues/20292" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "jl" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2012-12-13T16:25:32Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0015457" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0015460" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0044765" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" @@ -4652,12 +4645,6 @@ "val" : "Wikipedia:Exocytosis" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0016194" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0016195" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" } ] @@ -4694,15 +4681,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/geneontology/go-ontology/issues/25268" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0016193" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0016196" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0098701" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" @@ -4741,17 +4719,8 @@ "val" : "vesicle budding" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "jl" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2013-12-19T15:26:17Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0006902" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:1902591" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" @@ -4871,15 +4840,9 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/geneontology/go-ontology/issues/27189" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "jl" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2013-12-19T15:25:51Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:1902589" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" @@ -5151,9 +5114,6 @@ "val" : "hemolymph circulation" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0070261" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" } ] @@ -5188,21 +5148,9 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/geneontology/go-ontology/issues/24968" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "jl" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2012-09-19T15:05:24Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0000004" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0007582" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0044699" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" @@ -5214,7 +5162,7 @@ "type" : "CLASS", "meta" : { "definition" : { - "val" : "The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.", + "val" : "A cellular process consisting of the biochemical pathways by which a living organism transforms chemical substances. This includes including anabolism (biosynthetic process) and catabolism (catabolic process). Metabolic processes includes the transformation of small molecules, as well macromolecular processes such as DNA repair and replication, protein synthesis and degradation.", "xrefs" : [ "GOC:go_curators", "ISBN:0198547684" ] }, "comments" : [ "Note that metabolic processes do not include single functions or processes such as protein-protein interactions, protein-nucleic acids, nor receptor-ligand interactions." ], @@ -5222,18 +5170,6 @@ "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "metabolism" - }, { - "pred" : "hasNarrowSynonym", - "val" : "metabolic process resulting in cell growth" - }, { - "pred" : "hasNarrowSynonym", - "val" : "metabolism resulting in cell growth" - }, { - "pred" : "hasNarrowSynonym", - "val" : "multicellular organism metabolic process" - }, { - "pred" : "hasRelatedSynonym", - "val" : "single-organism metabolic process" } ], "xrefs" : [ { "val" : "Wikipedia:Metabolism" @@ -5242,17 +5178,11 @@ "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/geneontology/go-ontology/issues/26424" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "jl" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/geneontology/go-ontology/issues/28932" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2012-10-17T15:46:40Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0044236" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0044710" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" @@ -5264,7 +5194,7 @@ "type" : "CLASS", "meta" : { "definition" : { - "val" : "The chemical reactions and pathways resulting in the formation of substances; typically the energy-requiring part of metabolism in which simpler substances are transformed into more complex ones.", + "val" : "A cellular process consisting of the biochemical pathways by which a living organism synthesizes chemical substances. This typically represents the energy-requiring part of metabolism in which simpler substances are transformed into more complex ones.", "xrefs" : [ "GOC:curators", "ISBN:0198547684" ] }, "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_chembl", "http://purl.obolibrary.org/obo/go#goslim_metagenomics", "http://purl.obolibrary.org/obo/go#goslim_plant", "http://purl.obolibrary.org/obo/go#goslim_plant_ribbon" ], @@ -5291,17 +5221,11 @@ "val" : "Wikipedia:Anabolism" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "jl" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/geneontology/go-ontology/issues/28932" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2012-10-17T15:52:18Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0044274" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0044711" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" @@ -5344,9 +5268,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/geneontology/go-ontology/issues/27189" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0043284" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" @@ -5578,9 +5499,6 @@ "val" : "Wikipedia:Embryogenesis" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0009795" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" } ] @@ -5697,20 +5615,8 @@ "val" : "single-organism cellular process" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "jl" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2012-12-11T16:56:55Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0008151" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0044763" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0050875" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" @@ -5754,14 +5660,8 @@ "val" : "single-organism membrane invagination" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "jl" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2013-12-02T13:58:34Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:1902534" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" @@ -5878,15 +5778,6 @@ "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2014-03-06T11:37:54Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0016021" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0098589" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0098805" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "cellular_component" @@ -5925,12 +5816,6 @@ "xrefs" : [ "GOC:mah" ] } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0044235" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0071842" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" } ] @@ -5988,9 +5873,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/geneontology/go-ontology/issues/25421" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0006899" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" @@ -6174,15 +6056,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/geneontology/go-ontology/issues/27189" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0006411" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0044267" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0044268" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" @@ -6241,9 +6114,6 @@ "val" : "Wikipedia:Antigen_presentation" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0030333" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" } ] @@ -6283,9 +6153,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/geneontology/go-ontology/issues/27189" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0071845" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" @@ -6311,15 +6178,9 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/geneontology/go-ontology/issues/27054" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "jl" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2012-09-19T15:56:06Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0044702" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" @@ -6358,9 +6219,6 @@ "val" : "cellular component assembly at cellular level" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0071844" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" } ] @@ -6442,17 +6300,8 @@ "val" : "single organism signaling" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "jl" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2010-02-16T09:30:50Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0023046" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0044700" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" @@ -6620,9 +6469,6 @@ "xrefs" : [ "GOC:add" ] } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0046650" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" } ] @@ -6740,12 +6586,6 @@ "xrefs" : [ "GOC:add" ] } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0042112" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0046652" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" } ] @@ -6861,9 +6701,6 @@ "val" : "Wikipedia:Extracellular_matrix" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0005578" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "cellular_component" } ] @@ -6976,9 +6813,6 @@ "val" : "NIF_Subcellular:sao180601769" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0016023" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "cellular_component" } ] @@ -7034,9 +6868,6 @@ "val" : "Wikipedia:Vesicle_(biology)" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0031988" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "cellular_component" } ] @@ -7074,18 +6905,9 @@ }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002161", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_4932" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "jl" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2012-09-19T16:07:47Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0044707" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0050874" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" @@ -7109,14 +6931,8 @@ "val" : "single-organism developmental process" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "jl" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2012-12-19T12:21:31Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0044767" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" @@ -7151,12 +6967,6 @@ "val" : "interferon-gamma secretion" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0042095" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0072643" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" } ] @@ -7207,15 +7017,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/geneontology/go-ontology/issues/22580" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0034623" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0043241" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0043624" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" @@ -7249,9 +7050,6 @@ "val" : "protein-protein complex" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0043234" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "cellular_component" } ] @@ -7349,9 +7147,6 @@ "val" : "ATP hydrolysis coupled ion transmembrane transport" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0099131" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" } ] @@ -7551,15 +7346,6 @@ "val" : "regulation of homeostatic process" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0032844" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0032845" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0032846" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" } ] @@ -7676,15 +7462,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/geneontology/go-ontology/issues/26424" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0034960" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0043283" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0044259" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" @@ -7751,7 +7528,7 @@ } }, { "id" : "http://purl.obolibrary.org/obo/GO_0043228", - "lbl" : "non-membrane-bounded organelle", + "lbl" : "membraneless organelle", "type" : "CLASS", "meta" : { "definition" : { @@ -7760,6 +7537,12 @@ }, "subsets" : [ "http://purl.obolibrary.org/obo/go#gocheck_do_not_annotate", "http://purl.obolibrary.org/obo/go#goslim_mouse" ], "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "membrane-less organelle" + }, { + "pred" : "hasExactSynonym", + "val" : "non-membrane-bounded organelle" + }, { "pred" : "hasExactSynonym", "val" : "non-membrane-enclosed organelle" }, { @@ -7775,6 +7558,9 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/geneontology/go-ontology/issues/28153" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/geneontology/go-ontology/issues/29106" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "cellular_component" @@ -7819,7 +7605,7 @@ } }, { "id" : "http://purl.obolibrary.org/obo/GO_0043232", - "lbl" : "intracellular non-membrane-bounded organelle", + "lbl" : "intracellular membraneless organelle", "type" : "CLASS", "meta" : { "definition" : { @@ -7828,10 +7614,16 @@ }, "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_pir" ], "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "intracellular non-membrane-bounded organelle" + }, { "pred" : "hasExactSynonym", "val" : "intracellular non-membrane-enclosed organelle" } ], "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/geneontology/go-ontology/issues/29106" + }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "cellular_component" } ] @@ -7913,21 +7705,9 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/geneontology/go-ontology/issues/22580" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "mah" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2010-09-08T10:01:42Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0034600" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0034621" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0071822" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" @@ -7950,9 +7730,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/geneontology/go-ontology/issues/27194" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0071843" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" @@ -7975,9 +7752,6 @@ "val" : "Met-tRNA/eIF2.GTP ternary complex" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "jl" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2009-10-22T02:38:55Z" }, { @@ -7985,30 +7759,6 @@ "val" : "cellular_component" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/GO_0044237", - "lbl" : "cellular metabolic process", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "The chemical reactions and pathways by which individual cells transform chemical substances.", - "xrefs" : [ "GOC:go_curators" ] - }, - "comments" : [ "This term should not be used for direct annotation. It should be possible to make a more specific annotation to one of the children of this term." ], - "subsets" : [ "http://purl.obolibrary.org/obo/go#gocheck_do_not_annotate" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "cellular metabolism" - }, { - "pred" : "hasRelatedSynonym", - "val" : "intermediary metabolism", - "xrefs" : [ "GOC:mah" ] - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "biological_process" - } ] - } }, { "id" : "http://purl.obolibrary.org/obo/GO_0044238", "lbl" : "primary metabolic process", @@ -8034,38 +7784,6 @@ "val" : "biological_process" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/GO_0044249", - "lbl" : "cellular biosynthetic process", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "The chemical reactions and pathways resulting in the formation of substances, carried out by individual cells.", - "xrefs" : [ "GOC:jl" ] - }, - "comments" : [ "This term should not be used for direct annotation. It should be possible to make a more specific annotation to one of the children of this term." ], - "subsets" : [ "http://purl.obolibrary.org/obo/go#gocheck_do_not_annotate" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "cellular anabolism" - }, { - "pred" : "hasExactSynonym", - "val" : "cellular biosynthesis" - }, { - "pred" : "hasExactSynonym", - "val" : "cellular formation" - }, { - "pred" : "hasExactSynonym", - "val" : "cellular synthesis" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", - "val" : "https://github.com/geneontology/go-ontology/issues/27052" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "biological_process" - } ] - } }, { "id" : "http://purl.obolibrary.org/obo/GO_0044419", "lbl" : "biological process involved in interspecies interaction between organisms", @@ -8117,9 +7835,6 @@ "val" : "cell-cell fusion" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0006947" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" } ] @@ -8153,9 +7868,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002161", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_4751" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0002226" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" @@ -8489,9 +8201,6 @@ "xrefs" : [ "GOC:dph", "GOC:tb" ] } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0048828" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" } ] @@ -8689,9 +8398,6 @@ "val" : "regulation of physiological process" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0050791" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" } ] @@ -8725,9 +8431,6 @@ "val" : "regulation of cellular physiological process" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0051244" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" } ] @@ -8817,9 +8520,6 @@ "val" : "physiological response to stimulus" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0051869" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" } ] @@ -8977,15 +8677,9 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/geneontology/go-ontology/issues/27052" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "jl" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2013-12-18T13:51:04Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:1902578" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" @@ -9096,12 +8790,6 @@ "xrefs" : [ "GOC:ai" ] }, "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0009613" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0042828" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" } ] @@ -9125,14 +8813,8 @@ "val" : "ATP hydrolysis coupled transmembrane transport" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "tb" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2015-10-21T13:22:47Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0090662" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" @@ -9220,9 +8902,6 @@ "xrefs" : [ "GOC:dph" ] }, "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dph" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2009-04-28T09:33:36Z" }, { @@ -9259,17 +8938,8 @@ "val" : "single-organism membrane organization" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "jl" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2010-02-08T02:43:11Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0016044" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0044802" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" @@ -9296,17 +8966,8 @@ "val" : "Wikipedia:Lipid_bilayer_fusion" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "jl" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2010-02-08T02:48:06Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0006944" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0044801" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" @@ -9322,9 +8983,6 @@ "xrefs" : [ "GOC:BHF", "GOC:rph", "PMID:21123617" ] }, "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dph" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2018-04-13T12:47:21Z" }, { @@ -9370,15 +9028,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/geneontology/go-ontology/issues/22580" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0006461" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0034622" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0043623" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" @@ -9486,9 +9135,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/geneontology/go-ontology/issues/25143" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "mah" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2010-09-08T10:10:35Z" @@ -9523,15 +9169,9 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/geneontology/go-ontology/issues/27189" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "mah" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2010-09-10T01:39:16Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0071841" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" @@ -9548,9 +9188,6 @@ }, "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_flybase_ribbon" ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "mah" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2010-10-04T01:51:47Z" }, { @@ -9577,9 +9214,6 @@ "xrefs" : [ "GOC:BHF" ] } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "mah" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2010-10-11T11:44:57Z" }, { @@ -9599,9 +9233,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/geneontology/go-ontology/issues/22302" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "mah" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2010-02-26T02:15:40Z" @@ -9620,9 +9251,6 @@ "xrefs" : [ "GOC:ascb_2009", "GOC:dph", "GOC:tb" ] }, "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "tb" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2009-12-11T11:44:58Z" }, { @@ -9641,9 +9269,6 @@ }, "comments" : [ "Note that immunologists typically use the word 'maturation' to refer to dendritic cells undergoing the process that GO describes as 'cell differentiation'." ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pr" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2011-04-01T10:08:42Z" }, { @@ -9661,9 +9286,6 @@ "xrefs" : [ "GOC:vesicles" ] }, "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pr" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2016-03-29T17:39:45Z" }, { @@ -9697,15 +9319,9 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/geneontology/go-ontology/issues/22173" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dos" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2013-11-11T12:59:11Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0009814" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" @@ -9727,9 +9343,6 @@ "val" : "region of plasma membrane" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dos" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2014-03-06T11:55:32Z" }, { @@ -9982,9 +9595,6 @@ "val" : "fibril" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0043205" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "cellular_component" } ] @@ -10021,14 +9631,18 @@ } }, { "id" : "http://purl.obolibrary.org/obo/GO_0110165", - "lbl" : "cellular anatomical entity", + "lbl" : "cellular anatomical structure", "type" : "CLASS", "meta" : { "definition" : { - "val" : "A part of a cellular organism that is either an immaterial entity or a material entity with granularity above the level of a protein complex but below that of an anatomical system. Or, a substance produced by a cellular organism with granularity above the level of a protein complex.", + "val" : "A part of a cellular organism consisting of a material entity with granularity above the level of a protein complex but below that of an anatomical system. Note that cellular organisms exclude viruses.", "xrefs" : [ "GOC:kmv" ] }, "subsets" : [ "http://purl.obolibrary.org/obo/go#gocheck_do_not_annotate", "http://purl.obolibrary.org/obo/go#goslim_pir" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "cellular anatomical entity" + } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/geneontology/go-ontology/issues/24200" @@ -10036,8 +9650,8 @@ "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/geneontology/go-ontology/issues/26424" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "kmv" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/geneontology/go-ontology/issues/28978" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2019-08-12T18:01:37Z" @@ -10058,9 +9672,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/geneontology/go-ontology/issues/13193" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "krc" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-03-21T17:26:07Z" @@ -10081,9 +9692,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/geneontology/go-ontology/issues/13298" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "krc" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-04-26T16:07:02Z" @@ -10103,9 +9711,6 @@ }, "subsets" : [ "http://purl.obolibrary.org/obo/go#gocheck_do_not_annotate" ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pg" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-05-15T13:20:45Z" }, { @@ -10132,9 +9737,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/geneontology/go-ontology/issues/15939" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pg" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2018-08-13T18:38:18Z" @@ -10157,9 +9759,6 @@ "val" : "efflux" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pg" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2019-05-22T11:20:45Z" }, { @@ -10179,9 +9778,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/geneontology/go-ontology/issues/20261" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pg" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2020-11-11T17:19:06Z" @@ -10209,9 +9805,6 @@ "xrefs" : [ "GOC:TermGenie" ] } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pr" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2013-05-02T17:32:42Z" }, { @@ -10229,9 +9822,6 @@ "xrefs" : [ "CL:0000842", "GOC:TermGenie", "GO_REF:0000086", "PMID:24759906" ] }, "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "cls" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2014-06-25T15:47:09Z" }, { @@ -10267,9 +9857,6 @@ "xrefs" : [ "GOC:TermGenie" ] } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pad" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2014-12-04T15:34:13Z" }, { @@ -10307,17 +9894,8 @@ "val" : "Wikipedia:Ribonucleoprotein" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pr" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2015-11-19T12:26:37Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0030529" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:1990903" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "cellular_component" @@ -10333,9 +9911,6 @@ "xrefs" : [ "GOC:obol" ] }, "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "tb" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2010-08-05T11:25:59Z" }, { @@ -10424,9 +9999,6 @@ "val" : "GC_ID:1" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "NCBITaxon:85055" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "ncbi_taxonomy" } ] @@ -10458,9 +10030,6 @@ "val" : "GC_ID:1" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "NCBITaxon:40673" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "ncbi_taxonomy" } ] @@ -10794,9 +10363,6 @@ "val" : "GC_ID:1" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "NCBITaxon:109679" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "ncbi_taxonomy" } ] @@ -11021,9 +10587,6 @@ "xrefs" : [ "PATOC:GVG" ] }, "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "PATO:0000072" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "quality" } ] @@ -11059,9 +10622,6 @@ "val" : "relational shape quality" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "PATO:0001647" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "quality" } ] @@ -11085,9 +10645,6 @@ "val" : "relational structural quality" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "PATO:0001452" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "quality" } ] @@ -11163,9 +10720,6 @@ "val" : "Wikipedia:Physical_property" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "PATO:0002079" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "quality" } ] @@ -11209,12 +10763,6 @@ "val" : "snap:Quality" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "PATO:0001237" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "PATO:0001238" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "quality" } ] @@ -11392,9 +10940,6 @@ "val" : "tubulate" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "PATO:0001203" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "quality" } ] @@ -11787,9 +11332,6 @@ "val" : "high N:C ratio" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "http://orcid.org/0000-0001-5208-3432" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "quality" } ] @@ -11803,9 +11345,6 @@ "val" : "A quality of continuant that exist at the anatomical level of organisation and anything under it. This includes, but is not limited to, cells , tissues, and components." }, "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "http://orcid.org/0000-0001-7258-9596" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "quality" } ] @@ -11819,9 +11358,6 @@ "val" : "A quality inhering in an anotomical structure by virtue of its capacity to be stained by specific histological dyes." }, "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "http://orcid.org/0000-0001-7258-9596" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "quality" } ] @@ -11836,9 +11372,6 @@ "xrefs" : [ "GOC:add" ] }, "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "http://orcid.org/0000-0001-7258-9596" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "quality" } ] @@ -11852,7 +11385,7 @@ "val" : "An amino acid chain that is produced de novo by ribosome-mediated translation of a genetically-encoded mRNA, and any derivatives thereof.", "xrefs" : [ "PRO:DAN", "PRO:WCB" ] }, - "comments" : [ "The definition above excludes protein complexes, which some also consider a protein. Those who wish to refer to a class representing both senses of the word are directed to CHEBI:36080. Note that the definition allows for experimentally-manipulated genes, and allows for artifically-produced derivatives that mimic those found naturally. Proteins (in the sense defined here) that descended from a common ancestor can be classified into families and superfamilies composed of products of evolutionarily-related genes. The domain architecture of a protein is described by the order of its constituent domains. Proteins with the same domains in the same order are defined as homeomorphic [PRO:WCB]." ], + "comments" : [ "The definition above excludes protein complexes, which some also consider a protein. Those who wish to refer to a class representing both senses of the word are directed to CHEBI:36080. Note that the definition allows for experimentally-manipulated genes, and allows for artifically-produced derivatives that mimic those found naturally. Proteins (in the sense defined here) that descended from a common ancestor can be classified into families and superfamilies composed of products of evolutionarily-related genes. The domain architecture of a protein is described by the order of its constituent domains. Proteins with the same domains in the same order are defined as homeomorphic [PRO:WCB)." ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "natural protein", @@ -13746,15 +13279,15 @@ } ] } }, { - "id" : "http://purl.obolibrary.org/obo/PR_000050567", - "lbl" : "protein-containing material entity", + "id" : "http://purl.obolibrary.org/obo/PR_000064867", + "lbl" : "protein-containing molecular entity", "type" : "CLASS", "meta" : { "definition" : { - "val" : "A material entity that minimally consists of a protein.", + "val" : "A molecular entity that minimally consists of a protein.", "xrefs" : [ "PRO:DAN" ] }, - "comments" : [ "Note: This includes single proteins and derivatives thereof (PR:000000001), protein-containing complexes (GO:0032991), and protein aggregates (PR:000050566)." ], + "comments" : [ "Note: This includes single proteins and derivatives thereof (PR:000000001), protein-containing complexes (GO:0032991), and protein aggregates (PR:000050565)." ], "synonyms" : [ { "pred" : "hasNarrowSynonym", "val" : "protein", @@ -14068,9 +13601,6 @@ "val" : "galen:Wall" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "UBERON:0009915" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -14443,9 +13973,6 @@ "val" : "galen:ComplexSkeletalStructure" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "UBERON:0010322" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -15065,9 +14592,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "TODO - check relationship with epiblast. Note in FMA this is not a subclass of embryo, but in uberon embryo is the whole organism from zygote onwards and thus includes the blastula" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "UBERON:0007011" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -16565,9 +16089,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0002161", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_6040" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "UBERON:0003263" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -16929,7 +16450,7 @@ "val" : "Organ system that passes nutrients (such as amino acids and electrolytes), gases, hormones, blood cells, etc. to and from cells in the body to help fight diseases and help stabilize body temperature and pH to maintain homeostasis[WP].", "xrefs" : [ "Wikipedia:Circulatory_system" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#uberon_slim" ], "synonyms" : [ { "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003011", "pred" : "hasRelatedSynonym", @@ -16954,9 +16475,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002161", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_6157" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -17581,9 +17099,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "check relationship with myocardium. part_of in MA - but we also have a more specific class 'cardiac muscle tissue of myocardium'. Check ncit" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "UBERON:0007096" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -18136,9 +17651,6 @@ "val" : "http://uri.neuinfo.org/nif/nifstd/FMAID_7191" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "UBERON:0007036" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -19607,9 +19119,6 @@ "val" : "ZFA:0000121" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "UBERON:0006258" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" }, { @@ -20204,9 +19713,6 @@ "val" : "Wikipedia:Trilaminar_blastocyst" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "UBERON:0007012" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -21316,9 +20822,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "consider adding new class (EMAPA:16097) for mesenchyme of embryo (some mesenchyme is extraembryonic - e.g. amnion mesoderm)" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "UBERON:0003313" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -21687,6 +21190,8 @@ "val" : "EHDAA2:0004731" }, { "val" : "Wikipedia:Coelom" + }, { + "val" : "ZFA:0001438" } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", @@ -22008,9 +21513,6 @@ "val" : "presumptive central nervous system" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "UBERON:3000469" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -22033,9 +21535,6 @@ "val" : "AAO:0000477" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "UBERON:3000477" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -22785,9 +22284,6 @@ "val" : "A relationship between a process and a barrier, where the process occurs in a region spanning the barrier. For cellular processes the barrier is typically a membrane. Examples include transport across a membrane and membrane depolarization." }, "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "https://orcid.org/0000-0002-7073-9172" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-07-20T17:19:37Z" } ] @@ -25069,9 +24565,6 @@ "val" : "RO:0004007" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2018-12-13T11:26:17Z" }, { @@ -25097,9 +24590,6 @@ "val" : "RO:0004008" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2018-12-13T11:26:32Z" }, { @@ -25125,9 +24615,6 @@ "val" : "RO:0004009" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2018-12-13T11:26:56Z" }, { @@ -25147,9 +24634,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0004050", "val" : "http://purl.obolibrary.org/obo/RO_0002418" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2018-03-13T23:55:05Z" @@ -25165,9 +24649,6 @@ "propertyType" : "OBJECT", "meta" : { "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2018-03-13T23:55:19Z" }, { @@ -25185,9 +24666,6 @@ "val" : "a relation between a process and a continuant, in which the process is regulated by the small molecule continuant" }, "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "https://orcid.org/0000-0003-1813-6857" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2020-04-22T20:27:26Z" } ] @@ -25205,9 +24683,6 @@ "val" : "RO:0012001" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "https://orcid.org/0000-0003-1813-6857" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2020-04-22T20:28:37Z" }, { @@ -25232,9 +24707,6 @@ "val" : "RO:0012003" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "https://orcid.org/0000-0003-1813-6857" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2020-06-08T17:21:33Z" }, { @@ -25255,9 +24727,6 @@ "val" : "a relation between a continuant and a process, in which the continuant is a small molecule that regulates the process" }, "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "https://orcid.org/0000-0003-1813-6857" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2020-06-24T13:15:17Z" } ] @@ -25272,9 +24741,6 @@ "val" : "a relation between a continuant and a process, in which the continuant is a small molecule that activates the process" }, "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "https://orcid.org/0000-0003-1813-6857" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2020-06-24T13:15:26Z" }, { @@ -25293,9 +24759,6 @@ "val" : "RO:0012008" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "https://orcid.org/0000-0003-1813-6857" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2021-02-26T07:28:29Z" }, { @@ -25320,9 +24783,6 @@ "val" : "has synaptic input or output in" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "https://orcid.org/0000-0002-1373-1705" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2020-07-17T09:26:52Z" } ] @@ -25347,13 +24807,34 @@ "val" : "has sensory terminal location" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "https://orcid.org/0000-0002-1373-1705" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2020-07-20T12:10:09Z" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0015004", + "lbl" : "has characterizing marker set", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "A relation that applies between a cell type and a set of markers that can be used to uniquely identify that cell type." + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "has marker gene combination" + }, { + "pred" : "hasExactSynonym", + "val" : "has marker signature set" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "C has_characterizing_marker_set y iff: C is a cell type and y is a collection of genes or proteins whose expression is sufficient to distinguish cell type C from most or all other cell types." + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0001-7258-9596" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/RO_0015006", "lbl" : "different in magnitude relative to", @@ -25479,9 +24960,6 @@ "val" : "RO:0040036" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2018-09-26T01:08:58Z" }, { @@ -26180,13 +25658,14 @@ "propertyType" : "ANNOTATION", "meta" : { "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2018-03-14T00:03:24Z" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/STATO_0000663", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" }, { "id" : "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "type" : "PROPERTY", @@ -26239,6 +25718,10 @@ "meta" : { "comments" : [ "a subset of general classes of cell types in the cell ontology." ] } + }, { + "id" : "http://purl.obolibrary.org/obo/cl#human_subset", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" }, { "id" : "http://purl.obolibrary.org/obo/cl#kidney_upper_slim", "lbl" : "kidney_upper_slim", @@ -26251,6 +25734,10 @@ "val" : "2023-11-22T11:18:57Z" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/cl#mouse_subset", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" }, { "id" : "http://purl.obolibrary.org/obo/go#gocheck_do_not_annotate", "type" : "PROPERTY", @@ -26573,10 +26060,6 @@ "id" : "http://purl.org/dc/elements/1.1/creator", "type" : "PROPERTY", "propertyType" : "ANNOTATION" - }, { - "id" : "http://purl.org/dc/elements/1.1/date", - "type" : "PROPERTY", - "propertyType" : "ANNOTATION" }, { "id" : "http://purl.org/dc/elements/1.1/description", "type" : "PROPERTY", @@ -26589,6 +26072,10 @@ "id" : "http://purl.org/dc/elements/1.1/title", "type" : "PROPERTY", "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.org/dc/elements/1.1/type", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" }, { "id" : "http://purl.org/dc/terms/contributor", "type" : "PROPERTY", @@ -26599,14 +26086,17 @@ "propertyType" : "ANNOTATION" }, { "id" : "http://purl.org/dc/terms/description", + "lbl" : "description", "type" : "PROPERTY", "propertyType" : "ANNOTATION" }, { "id" : "http://purl.org/dc/terms/license", + "lbl" : "license", "type" : "PROPERTY", "propertyType" : "ANNOTATION" }, { "id" : "http://purl.org/dc/terms/title", + "lbl" : "title", "type" : "PROPERTY", "propertyType" : "ANNOTATION" }, { @@ -26624,19 +26114,10 @@ "lbl" : "consider", "type" : "PROPERTY", "propertyType" : "ANNOTATION" - }, { - "id" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "type" : "PROPERTY", - "propertyType" : "ANNOTATION" }, { "id" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "type" : "PROPERTY", "propertyType" : "ANNOTATION" - }, { - "id" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "lbl" : "has_alternative_id", - "type" : "PROPERTY", - "propertyType" : "ANNOTATION" }, { "id" : "http://www.geneontology.org/formats/oboInOwl#hasBroadSynonym", "lbl" : "has_broad_synonym", @@ -26656,9 +26137,21 @@ } }, { "id" : "http://www.geneontology.org/formats/oboInOwl#hasDbXref", - "lbl" : "database_cross_reference", + "lbl" : "has cross-reference", "type" : "PROPERTY", - "propertyType" : "ANNOTATION" + "propertyType" : "ANNOTATION", + "meta" : { + "definition" : { + "val" : "An annotation property that links an ontology entity or a statement to a prefixed identifier or URI." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/information-artifact-ontology/ontology-metadata/issues/123" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0002-7356-1779" + } ] + } }, { "id" : "http://www.geneontology.org/formats/oboInOwl#hasExactSynonym", "lbl" : "has_exact_synonym", @@ -26737,10 +26230,6 @@ "id" : "http://www.geneontology.org/formats/oboInOwl#is_metadata_tag", "type" : "PROPERTY", "propertyType" : "ANNOTATION" - }, { - "id" : "http://www.geneontology.org/formats/oboInOwl#note", - "type" : "PROPERTY", - "propertyType" : "ANNOTATION" }, { "id" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "lbl" : "shorthand", @@ -26903,10 +26392,6 @@ "val" : "true" } ] } - }, { - "sub" : "http://purl.obolibrary.org/obo/CL_0000040", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000040", "pred" : "http://purl.obolibrary.org/obo/BFO_0000051", @@ -26978,11 +26463,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000057", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/CL_0002320" - }, { - "sub" : "http://purl.obolibrary.org/obo/CL_0000057", - "pred" : "http://purl.obolibrary.org/obo/RO_0002202", - "obj" : "http://purl.obolibrary.org/obo/CL_0000134" + "obj" : "http://purl.obolibrary.org/obo/CL_0000499" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000066", "pred" : "is_a", @@ -27051,10 +26532,6 @@ "val" : "true" } ] } - }, { - "sub" : "http://purl.obolibrary.org/obo/CL_0000092", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000092", "pred" : "http://purl.obolibrary.org/obo/BFO_0000051", @@ -27105,10 +26582,6 @@ "val" : "true" } ] } - }, { - "sub" : "http://purl.obolibrary.org/obo/CL_0000094", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000094", "pred" : "http://purl.obolibrary.org/obo/BFO_0000051", @@ -27543,10 +27016,6 @@ "sub" : "http://purl.obolibrary.org/obo/CL_0000451", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/CL_0000145" - }, { - "sub" : "http://purl.obolibrary.org/obo/CL_0000451", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000451", "pred" : "http://purl.obolibrary.org/obo/BFO_0000051", @@ -27703,18 +27172,10 @@ "sub" : "http://purl.obolibrary.org/obo/CL_0000557", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/CL_0001012" - }, { - "sub" : "http://purl.obolibrary.org/obo/CL_0000557", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/CL_0011026" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000557", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/CL_1001610" - }, { - "sub" : "http://purl.obolibrary.org/obo/CL_0000557", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000557", "pred" : "http://purl.obolibrary.org/obo/BFO_0000051", @@ -27757,10 +27218,6 @@ "val" : "true" } ] } - }, { - "sub" : "http://purl.obolibrary.org/obo/CL_0000559", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000559", "pred" : "http://purl.obolibrary.org/obo/BFO_0000051", @@ -27787,10 +27244,6 @@ "sub" : "http://purl.obolibrary.org/obo/CL_0000566", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/CL_0011026" - }, { - "sub" : "http://purl.obolibrary.org/obo/CL_0000566", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000566", "pred" : "http://purl.obolibrary.org/obo/RO_0002104", @@ -28023,10 +27476,6 @@ "val" : "true" } ] } - }, { - "sub" : "http://purl.obolibrary.org/obo/CL_0000825", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000825", "pred" : "http://purl.obolibrary.org/obo/CL_4030046", @@ -28065,10 +27514,6 @@ "val" : "true" } ] } - }, { - "sub" : "http://purl.obolibrary.org/obo/CL_0000826", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000826", "pred" : "http://purl.obolibrary.org/obo/BFO_0000051", @@ -28111,10 +27556,6 @@ "sub" : "http://purl.obolibrary.org/obo/CL_0000837", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/CL_0008001" - }, { - "sub" : "http://purl.obolibrary.org/obo/CL_0000837", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000837", "pred" : "http://purl.obolibrary.org/obo/CL_4030046", @@ -28265,6 +27706,10 @@ "sub" : "http://purl.obolibrary.org/obo/CL_0001012", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/CL_0001060" + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_0001012", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/CL_0011026" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0001035", "pred" : "is_a", @@ -29132,7 +28577,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/GO_0006413", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/GO_0044237" + "obj" : "http://purl.obolibrary.org/obo/GO_0008152" }, { "sub" : "http://purl.obolibrary.org/obo/GO_0006413", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", @@ -29380,7 +28825,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/GO_0008152", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/GO_0008150" + "obj" : "http://purl.obolibrary.org/obo/GO_0009987" }, { "sub" : "http://purl.obolibrary.org/obo/GO_0009058", "pred" : "is_a", @@ -29388,11 +28833,11 @@ }, { "sub" : "http://purl.obolibrary.org/obo/GO_0009059", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/GO_0043170" + "obj" : "http://purl.obolibrary.org/obo/GO_0009058" }, { "sub" : "http://purl.obolibrary.org/obo/GO_0009059", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/GO_0044249" + "obj" : "http://purl.obolibrary.org/obo/GO_0043170" }, { "sub" : "http://purl.obolibrary.org/obo/GO_0009314", "pred" : "is_a", @@ -29975,8 +29420,8 @@ "obj" : "http://purl.obolibrary.org/obo/GO_0005575" }, { "sub" : "http://purl.obolibrary.org/obo/GO_0032991", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PR_000050567" + "pred" : "http://purl.obolibrary.org/obo/BFO_0000051", + "obj" : "http://purl.obolibrary.org/obo/PR_000000001" }, { "sub" : "http://purl.obolibrary.org/obo/GO_0033151", "pred" : "is_a", @@ -30221,26 +29666,10 @@ "sub" : "http://purl.obolibrary.org/obo/GO_0044207", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", "obj" : "http://purl.obolibrary.org/obo/GO_0005737" - }, { - "sub" : "http://purl.obolibrary.org/obo/GO_0044237", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/GO_0008152" - }, { - "sub" : "http://purl.obolibrary.org/obo/GO_0044237", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/GO_0009987" }, { "sub" : "http://purl.obolibrary.org/obo/GO_0044238", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/GO_0008152" - }, { - "sub" : "http://purl.obolibrary.org/obo/GO_0044249", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/GO_0009058" - }, { - "sub" : "http://purl.obolibrary.org/obo/GO_0044249", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/GO_0044237" }, { "sub" : "http://purl.obolibrary.org/obo/GO_0044419", "pred" : "is_a", @@ -30841,10 +30270,6 @@ "sub" : "http://purl.obolibrary.org/obo/GO_0098644", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/GO_0099080" - }, { - "sub" : "http://purl.obolibrary.org/obo/GO_0098644", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/GO_0098644", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", @@ -31404,7 +30829,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/PR_000000001", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PR_000050567" + "obj" : "http://purl.obolibrary.org/obo/PR_000064867" }, { "sub" : "http://purl.obolibrary.org/obo/PR_000000001", "pred" : "http://purl.obolibrary.org/obo/RO_0002353", @@ -31545,10 +30970,6 @@ "sub" : "http://purl.obolibrary.org/obo/PR_000001969", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PR_000000001" - }, { - "sub" : "http://purl.obolibrary.org/obo/PR_000001971", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PR_000000001" }, { "sub" : "http://purl.obolibrary.org/obo/PR_000002062", "pred" : "is_a", @@ -31638,7 +31059,7 @@ "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PR_000001006" }, { - "sub" : "http://purl.obolibrary.org/obo/PR_000050567", + "sub" : "http://purl.obolibrary.org/obo/PR_000064867", "pred" : "http://purl.obolibrary.org/obo/BFO_0000051", "obj" : "http://purl.obolibrary.org/obo/PR_000000001" }, { @@ -31707,10 +31128,6 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0000043", "pred" : "http://purl.obolibrary.org/obo/RO_0002176", "obj" : "http://purl.obolibrary.org/obo/UBERON_0001630" - }, { - "sub" : "http://purl.obolibrary.org/obo/UBERON_0000058", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000058", "pred" : "is_a", @@ -32117,10 +31534,6 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0000481", "pred" : "http://purl.obolibrary.org/obo/BFO_0000051", "obj" : "http://purl.obolibrary.org/obo/UBERON_0000479" - }, { - "sub" : "http://purl.obolibrary.org/obo/UBERON_0000483", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000483", "pred" : "is_a", @@ -32742,10 +32155,6 @@ "val" : "ZFA" } ] } - }, { - "sub" : "http://purl.obolibrary.org/obo/UBERON_0002330", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0002330", "pred" : "is_a", @@ -32837,10 +32246,6 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0002346", "pred" : "http://purl.obolibrary.org/obo/BFO_0000051", "obj" : "http://purl.obolibrary.org/obo/CL_0000133" - }, { - "sub" : "http://purl.obolibrary.org/obo/UBERON_0002365", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0002365", "pred" : "is_a", @@ -33026,6 +32431,10 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0002553", "pred" : "http://purl.obolibrary.org/obo/RO_0001015", "obj" : "http://purl.obolibrary.org/obo/UBERON_0000463" + }, { + "sub" : "http://purl.obolibrary.org/obo/UBERON_0003059", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/UBERON_0000061" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0003059", "pred" : "is_a", @@ -33612,10 +33021,6 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0005764", "pred" : "http://purl.obolibrary.org/obo/RO_0002007", "obj" : "http://purl.obolibrary.org/obo/UBERON_0000061" - }, { - "sub" : "http://purl.obolibrary.org/obo/UBERON_0005769", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0005769", "pred" : "is_a", @@ -33878,10 +33283,6 @@ "val" : "AEO" } ] } - }, { - "sub" : "http://purl.obolibrary.org/obo/UBERON_0007845", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0007845", "pred" : "is_a", @@ -34082,10 +33483,6 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0011822", "pred" : "http://purl.obolibrary.org/obo/BFO_0000051", "obj" : "http://purl.obolibrary.org/obo/GO_0071953" - }, { - "sub" : "http://purl.obolibrary.org/obo/UBERON_0011823", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0011823", "pred" : "is_a", @@ -34094,10 +33491,6 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0011823", "pred" : "http://purl.obolibrary.org/obo/RO_0002473", "obj" : "http://purl.obolibrary.org/obo/UBERON_0011860" - }, { - "sub" : "http://purl.obolibrary.org/obo/UBERON_0011860", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0011860", "pred" : "is_a", @@ -35266,10 +34659,6 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002590", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002592" - }, { - "sub" : "http://purl.obolibrary.org/obo/RO_0002592", - "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0000057" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002592", "pred" : "subPropertyOf", @@ -38040,6 +37429,9 @@ }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0013007", "domainClassIds" : [ "http://purl.obolibrary.org/obo/CL_0000101" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0015004", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/CL_0000000" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0015006", "domainClassIds" : [ "http://purl.obolibrary.org/obo/PATO_0000001" ], diff --git a/src/ontology/subsets/general_cell_types_upper_slim.obo b/src/ontology/subsets/general_cell_types_upper_slim.obo index 9c6b81e98..d9315920d 100644 --- a/src/ontology/subsets/general_cell_types_upper_slim.obo +++ b/src/ontology/subsets/general_cell_types_upper_slim.obo @@ -1,5 +1,5 @@ format-version: 1.2 -data-version: cl/releases/2024-09-26/subsets/general_cell_types_upper_slim.owl +data-version: cl/releases/2025-01-08/subsets/general_cell_types_upper_slim.owl subsetdef: abnormal_slim "" subsetdef: added_for_HCA "" subsetdef: attribute_slim "" @@ -44,10 +44,12 @@ subsetdef: http://purl.obolibrary.org/obo/valid_for_go_gp2term "" subsetdef: http://purl.obolibrary.org/obo/valid_for_go_ontology "" subsetdef: http://purl.obolibrary.org/obo/valid_for_gocam "" subsetdef: human_reference_atlas "" +subsetdef: human_subset "" subsetdef: inconsistent_with_fma "" subsetdef: kidney_upper_slim "a subset of general classes related to specific cell types in the kidney" subsetdef: location_grouping "" subsetdef: major_organ "" +subsetdef: mouse_subset "" subsetdef: mpath_slim "" subsetdef: non_informative "" subsetdef: organ_slim "" @@ -96,7 +98,7 @@ idspace: oboInOwl http://www.geneontology.org/formats/oboInOwl# idspace: sssom https://w3id.org/sssom/ idspace: terms http://purl.org/dc/terms/ ontology: cl/subsets/general_cell_types_upper_slim -property_value: owl:versionInfo "2024-09-26" xsd:string +property_value: owl:versionInfo "2025-01-08" xsd:string [Term] id: CL:0000000 @@ -104,6 +106,8 @@ name: cell def: "A material entity of anatomical origin (part of or deriving from an organism) that has as its parts a maximally connected cell compartment surrounded by a plasma membrane." [CARO:mah] comment: The definition of cell is intended to represent all cells, and thus a cell is defined as a material entity and not an anatomical structure, which implies that it is part of an organism (or the entirety of one). subset: cellxgene_subset +subset: human_subset +subset: mouse_subset subset: ubprop:upper_level xref: CALOHA:TS-2035 xref: FBbt:00007002 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} @@ -125,6 +129,8 @@ relationship: RO:0002162 NCBITaxon:131567 ! in taxon cellular organisms id: CL:0000007 name: early embryonic cell (metazoa) def: "A cell found in the embryo before the formation of all the gem layers is complete." [GOC:tfm] +subset: human_subset +subset: mouse_subset xref: ZFA:0009002 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0002321 ! embryonic cell (metazoa) @@ -136,6 +142,8 @@ comment: This term applies to metazoan. For plant stem cells, consider using PO: subset: cellxgene_subset subset: general_cell_types_upper_slim subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "animal stem cell" EXACT [] xref: CALOHA:TS-2086 xref: FMA:63368 @@ -156,6 +164,8 @@ comment: Markers differ between species, and two sets of markers have been descr subset: blood_and_immune_upper_slim subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "blood forming stem cell" EXACT [] synonym: "colony forming unit hematopoietic" RELATED [] synonym: "hemopoietic stem cell" EXACT [] @@ -206,6 +216,8 @@ name: germ line cell def: "A cell that is within the developmental lineage of gametes and is able to pass along its genetic material to offspring." [GOC:tfm, ISBN:0721662544] comment: Originally this term had some plant germ line cell children. subset: general_cell_types_upper_slim +subset: human_subset +subset: mouse_subset subset: ubprop:upper_level xref: ZFA:0009016 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000000 ! cell @@ -216,6 +228,8 @@ id: CL:0000040 name: monoblast def: "A myeloid progenitor cell committed to the monocyte lineage. This cell is CD11b-positive, has basophilic cytoplasm, euchromatin, and the presence of a nucleolus." [GOC:add, http://en.wikipedia.org/wiki/Monoblast, http://www.copewithcytokines.de, PMID:1104740] comment: Morphology: mononuclear cell, diameter 12-20 _M, non-granular, N/C ratio 3/1 - 4/1; markers: CD11b (shared with many other myeloid cells); location: Adult: bone marrow; fetal: liver, Yolk Sac; role or process: hematopoiesis, monocyte development; lineage: hematopoietic, myeloid. +subset: human_subset +subset: mouse_subset synonym: "CFU-M" RELATED OMO:0003000 [] synonym: "colony forming unit macrophage" RELATED [] synonym: "colony forming unit monocyte" RELATED [] @@ -225,7 +239,6 @@ xref: FMA:83553 xref: ZFA:0009017 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000763 ! myeloid cell is_a: CL:0002194 {is_inferred="true"} ! monopoietic cell -is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0002194 ! monopoietic cell intersection_of: capable_of GO:0030224 ! monocyte differentiation intersection_of: has_part CL:0017503 ! basophilic cytoplasm @@ -242,6 +255,8 @@ relationship: RO:0002202 CL:0002009 ! develops from macrophage dendritic cell pr id: CL:0000048 name: multi fate stem cell def: "A stem cell that can give rise to multiple lineages of cells." [GOC:add] +subset: human_subset +subset: mouse_subset synonym: "multi-fate stem cell" EXACT [] synonym: "multifate stem cell" EXACT [] synonym: "multipotent cell" EXACT [] @@ -261,6 +276,8 @@ def: "A progenitor cell committed to myeloid lineage, including the megakaryocyt comment: This cell type is intended to be compatible with any vertebrate common myeloid progenitor. For mammalian CMP known to be CD34-positive, please use the term 'common myeloid progenitor, CD34-positive' (CL_0001059). subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "CFU-GEMM" RELATED OMO:0003000 [ISBN:0878932437] synonym: "CFU-S" RELATED OMO:0003000 [ISBN:0878932437] synonym: "CMP" RELATED OMO:0003000 [ISBN:0878932437] @@ -283,6 +300,8 @@ def: "A oligopotent progenitor cell committed to the lymphoid lineage." [GOC:add comment: CLP are CD7-positive, CD10-positive, CD19-negative, CD34-positive, CD45RA-positive, CD79a-negative, CD127-positive, AA4.1-positive, RAG-negative, Sca-1-low, sIgM-negative, sIgD-negative, TdT-negative, Vpre-B-negative, and pre-BCR-negative. Expression of transcription factors include E2A-positive, EBF-positive, Ikaros-negative, PU.1-negative, and Pax5-negative. subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "CLP" RELATED OMO:0003000 [] synonym: "committed lymphopoietic stem cell" RELATED [] synonym: "common lymphocyte precursor" EXACT [] @@ -304,6 +323,8 @@ property_value: RO:0002175 NCBITaxon:9606 id: CL:0000052 name: totipotent stem cell def: "A stem cell from which all cells of the body can form." [GOC:add, GOC:tfm] +subset: human_subset +subset: mouse_subset synonym: "totipotential stem cell" EXACT [] xref: FMA:84790 xref: MESH:D039901 @@ -316,6 +337,8 @@ name: non-terminally differentiated cell def: "A precursor cell with a limited number of potential fates." [SANBI:mhl] comment: define using PATO mulit-potent or oligopotent? subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "blast cell" EXACT [] xref: BTO:0000125 xref: FMA:84782 @@ -325,6 +348,9 @@ is_a: CL:0011115 ! precursor cell id: CL:0000056 name: myoblast def: "A cell that is commited to differentiating into a muscle cell. Embryonic myoblasts develop from the mesoderm. They undergo proliferation, migrate to their various sites, and then differentiate into the appropriate form of myocytes. Myoblasts also occur as transient populations of cells in muscles undergoing repair." [GOC:tfm, MESH:D032446, PMID:21849021] +subset: cellxgene_subset +subset: human_subset +subset: mouse_subset xref: BTO:0000222 xref: CALOHA:TS-0650 xref: FBbt:00005083 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} @@ -341,14 +367,15 @@ comment: These cells may be vimentin-positive, fibronectin-positive, fsp1-positi subset: cellxgene_subset subset: general_cell_types_upper_slim subset: human_reference_atlas +subset: human_subset +subset: mouse_subset xref: BTO:0000452 xref: CALOHA:TS-0362 xref: FMA:63877 xref: NCIT:C12482 xref: VHOG:0001482 xref: ZFA:0009026 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} -is_a: CL:0002320 ! connective tissue cell -relationship: RO:0002202 CL:0000134 ! develops from mesenchymal stem cell +is_a: CL:0000499 ! stromal cell property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -358,6 +385,8 @@ def: "A cell that is usually found in a two-dimensional sheet with a free surfac subset: cellxgene_subset subset: general_cell_types_upper_slim subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "epitheliocyte" EXACT [] xref: BTO:0000414 xref: CALOHA:TS-2026 @@ -378,6 +407,8 @@ name: columnar/cuboidal epithelial cell def: "A columnar/cuboidal epithelial cell is a cell usually found in a two dimensional sheet with a free surface. Columnar/cuboidal epithelial cells take on the shape of a column or cube." [GO:0002065, https://orcid.org/0000-0001-5208-3432] subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset xref: ZFA:0009038 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000066 ! epithelial cell property_value: RO:0002175 NCBITaxon:9606 @@ -388,6 +419,8 @@ name: blood cell def: "A cell found predominately in the blood." [GOC:add, GOC:tfm] subset: cellxgene_subset subset: general_cell_types_upper_slim +subset: human_subset +subset: mouse_subset xref: FMA:62844 xref: MESH:D001773 xref: ZFA:0009044 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} @@ -403,6 +436,8 @@ def: "A type of lymphocyte whose defining characteristic is the expression of a subset: cellxgene_subset subset: general_cell_types_upper_slim subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "immature T cell" RELATED [] synonym: "mature T cell" RELATED [] synonym: "T lymphocyte" EXACT [] @@ -428,16 +463,18 @@ name: osteoclast def: "A specialized phagocytic cell associated with the absorption and removal of the mineralized matrix of bone tissue, which typically differentiates from monocytes. This cell has the following markers: tartrate-resistant acid phosphatase type 5-positive, PU.1-positive, c-fos-positive, nuclear factor NF-kappa-B p100 subunit-positive, tumor necrosis factor receptor superfamily member 11A-positive and macrophage colony-stimulating factor 1 receptor-positive." [GO_REF:0000031, GOC:add, GOC:tfm, ISBN:0781735149, PMID:10428500, PMID:15055519, PMID:17380158] comment: Morphology: Highly vesicular; markers: Surface: RANK, cFMS (MCSF receptor); Secreted: cathepsin K and TRAP (tartate resistant acid phosphatase); transcription factors: PU.1, cFOS, MITF, NFkB (p52); role or process: tissue remodelling: bone resorption; lineage: hematopoietic, myeloid. subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "chondroclast" RELATED [] xref: BTO:0000968 xref: CALOHA:TS-0721 xref: FMA:66781 +xref: https://cellxgene.cziscience.com/cellguide/CL_0000092 xref: MESH:D010010 xref: ZFA:0009047 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000518 ! phagocyte (sensu Vertebrata) is_a: CL:0000766 {is_inferred="true"} ! myeloid leukocyte is_a: CL:0001035 {is_inferred="true"} ! bone cell -is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000766 ! myeloid leukocyte intersection_of: capable_of GO:0045453 ! bone resorption intersection_of: has_part PR:000001850 ! cathepsin K @@ -457,6 +494,7 @@ relationship: has_part PR:000011178 ! nuclear factor NF-kappa-B p100 subunit relationship: RO:0002104 PR:000001954 ! has plasma membrane part tumor necrosis factor receptor superfamily member 11A relationship: RO:0002104 PR:000002062 ! has plasma membrane part macrophage colony-stimulating factor 1 receptor relationship: RO:0002202 CL:0000576 ! develops from monocyte +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nOsteoclasts, derived from the monocyte/macrophage lineage, play a crucial role in bone remodeling through bone resorption. They are distinguished from other cells by their large size and their unique ability to secrete enzymes and acids that dissolve the calcium phosphate in bone. The formation of osteoclasts is influenced by two primary factors: macrophage colony-stimulating factor (M-CSF) and the ligand-activated receptor (RANKL) of nuclear factor kappa B (NF-κB).\nOsteoclasts also collaborate with osteoblasts, responsible for new bone formation, to maintain bone health and adapt bone structure. Their coordinated actions allow continuous remodeling while preserving overall bone strength and integrity. Imbalances in osteoclast activity can lead to pathological conditions. For example, excessive activity may contribute to diseases like osteoporosis, periprosthetic osteolysis, bone tumors, and Paget's disease. Other the other hand, osteoclast deficiency ca result in conditions like osteopetrosis." xsd:string {xref="DOI:10.3389/fmed.2017.00234", xref="DOI:10.37175/stemedicine.v1i4.57", xref="https://www.sciencedirect.com/topics/medicine-and-dentistry/osteoclast"} [Term] id: CL:0000094 @@ -464,6 +502,8 @@ name: granulocyte def: "A leukocyte with abundant granules in the cytoplasm." [GOC:amm, GOC:tfm, http://en.wikipedia.org/wiki/Granulocyte, MESH:D006098] subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "granular leucocyte" EXACT [] synonym: "granular leukocyte" EXACT [] synonym: "polymorphonuclear leukocyte" EXACT [] @@ -474,7 +514,6 @@ xref: FMA:62854 xref: ZFA:0009048 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000081 ! blood cell is_a: CL:0000766 {is_inferred="true"} ! myeloid leukocyte -is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000766 ! myeloid leukocyte intersection_of: capable_of GO:0008015 ! blood circulation intersection_of: CL:4030046 PR:000001002 ! lacks_plasma_membrane_part CD19 molecule @@ -499,6 +538,8 @@ property_value: RO:0002175 NCBITaxon:9606 id: CL:0000095 name: neuron associated cell subset: cellxgene_subset +subset: human_subset +subset: mouse_subset is_a: CL:0002319 ! neural cell relationship: RO:0002202 CL:0000133 ! develops from neurectodermal cell @@ -508,6 +549,8 @@ name: motor neuron def: "An efferent neuron that passes from the central nervous system or a ganglion toward or to a muscle and conducts an impulse that causes or inhibits movement." [MESH:D009046, PMID:16875686] subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "motoneuron" EXACT [] xref: BTO:0000312 xref: FBbt:00005123 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} @@ -521,7 +564,10 @@ property_value: RO:0002175 NCBITaxon:9606 id: CL:0000101 name: sensory neuron def: "Any neuron having a sensory function; an afferent neuron conveying sensory impulses." [ISBN:0721662544] +subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset xref: BTO:0001037 xref: FBbt:00005124 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:84649 @@ -540,6 +586,8 @@ name: mononuclear phagocyte def: "A vertebrate phagocyte with a single nucleus." [GOC:add, GOC:tfm, ISBN:0781735149] subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset xref: BTO:0001433 xref: https://cellxgene.cziscience.com/cellguide/CL_0000113 xref: ZFA:0009064 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} @@ -548,7 +596,7 @@ is_a: CL:0000842 ! mononuclear cell intersection_of: CL:0000518 ! phagocyte (sensu Vertebrata) intersection_of: bearer_of PATO:0001407 ! mononucleate property_value: RO:0002175 NCBITaxon:9606 -property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional.\n\nMononuclear phagocytes are immune cells that form a critical part of the body's innate immune system, the body's first line of defense against infections. Mononuclear phagocytes are characterized by the presence of a single, large nucleus. The ‘Mononuclear Phagocyte System’ nomenclature was introduced to distinguish mononuclear monocytes and macrophages from other cells with multiple nuclei. However, the cells within the mononuclear phagocyte system represent a highly heterogeneous group, all of which are able to perform highly efficient phagocytosis - engulfing and digesting microbes and cellular debris to fight infections and to maintain normal tissue homeostasis. \nIn addition to phagocytosis, mononuclear phagocytes also secrete chemical compounds to recruit other immune cells to a site of infection. These cells produce different types of signaling molecules, including cytokines, chemokines, and reactive oxygen species, triggering a cascade of responses to ensure rapid and efficient containment and neutralization of invading pathogens. These cells are also involved in antigen presentation, a process essential for stimulating an adaptive immune response. They can process and present antigens to T cells, thereby linking the innate and adaptive immune responses.\nMononuclear phagocytes play key roles in tissue repair and remodeling. After infection or injury, these cells help in the clearance of dead cells and debris, a crucial step in the initiation of tissue remodeling and the resolution of inflammation. Overall, mononuclear phagocytes are versatile cells that have tailored their functions to meet the unique challenges of different tissues within the body. They are pivotal in homeostasis, immunity, and inflammation, making them important aspects in a range of human diseases including infection, autoimmunity, and cancer." xsd:string {xref="DOI:10.1016/j.coi.2005.11.008", xref="DOI:10.1038/nri3087", xref="DOI:10.3389/fimmu.2019.01893"} +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nMononuclear phagocytes are immune cells that form a critical part of the body's innate immune system, the body's first line of defense against infections. Mononuclear phagocytes are characterized by the presence of a single, large nucleus. The ‘Mononuclear Phagocyte System’ nomenclature was introduced to distinguish mononuclear monocytes and macrophages from other cells with multiple nuclei. However, the cells within the mononuclear phagocyte system represent a highly heterogeneous group, all of which are able to perform highly efficient phagocytosis - engulfing and digesting microbes and cellular debris to fight infections and to maintain normal tissue homeostasis. \nIn addition to phagocytosis, mononuclear phagocytes also secrete chemical compounds to recruit other immune cells to a site of infection. These cells produce different types of signaling molecules, including cytokines, chemokines, and reactive oxygen species, triggering a cascade of responses to ensure rapid and efficient containment and neutralization of invading pathogens. These cells are also involved in antigen presentation, a process essential for stimulating an adaptive immune response. They can process and present antigens to T cells, thereby linking the innate and adaptive immune responses.\nMononuclear phagocytes play key roles in tissue repair and remodeling. After infection or injury, these cells help in the clearance of dead cells and debris, a crucial step in the initiation of tissue remodeling and the resolution of inflammation. Overall, mononuclear phagocytes are versatile cells that have tailored their functions to meet the unique challenges of different tissues within the body. They are pivotal in homeostasis, immunity, and inflammation, making them important aspects in a range of human diseases including infection, autoimmunity, and cancer." xsd:string {xref="DOI:10.1016/j.coi.2005.11.008", xref="DOI:10.1038/nri3087", xref="DOI:10.3389/fimmu.2019.01893"} [Term] id: CL:0000125 @@ -558,6 +606,8 @@ comment: Not all glial cells develop from glioblasts, with microglia developing subset: cellxgene_subset subset: general_cell_types_upper_slim subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "neuroglia" RELATED [] synonym: "neuroglial cell" EXACT [] xref: BTO:0002606 @@ -568,12 +618,14 @@ xref: https://cellxgene.cziscience.com/cellguide/CL_0000125 xref: ZFA:0009073 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000095 ! neuron associated cell property_value: RO:0002175 NCBITaxon:9606 -property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional.\n\nGlial cells, also known as neuroglia or simply glia, are non-neuronal cells in the central and peripheral nervous systems that provide support and protection for neurons. They constitute approximately half of the total cells in the human brain and more than half in other parts of the nervous system. Glial cells perform several key functions including, but not limited to, maintaining homeostasis, forming the myelin sheath around the neuron axons, and providing support and nutrition to neurons.\nThese different functions are performed by various glial cell types, including astrocytes, oligodendrocytes, microglia and other specialized types. Astrocytes, for example, are the most abundant glial cells and provide metabolic and nutrient support to neurons, help regulate the extracellular ion and neurotransmitter levels, and play a role in the formation and maintenance of the blood-brain barrier, contributing to the overall homeostasis and functioning of the nervous system. Additionally, astrocytes are involved in synaptic communication and participate in processes such as synaptogenesis and synaptic pruning.\nOligodendrocytes in the central nervous system function to insulate neurons by producing a fatty substance known as myelin. The myelin sheath enhances the speed and efficiency of nerve impulse conduction along the axons. \nMicroglia, the immune cells of the central nervous system, protect neurons from pathogens and clear away dead neurons through phagocytosis, a process also known as cellular eating. They also contribute to the regulation of inflammation in response to signals of tissue damage or infection in the central nervous system by releasing cytokines and other signaling molecules that modulate the immune response.\nDespite their overarching function in the support and protection of neurons, glial cells have also been shown to play significant roles in the pathophysiology of many psychiatric and neurodegenerative diseases, such as Alzheimer’s, Parkinson’s Disease and multiple sclerosis." xsd:string {xref="DOI:10.1002/glia.24343", xref="DOI:10.1038/nn1988", xref="DOI:10.1101/cshperspect.a020602", xref="DOI:10.1126/science.aat0473", xref="DOI:10.3389/fncel.2017.00024"} +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nGlial cells, also known as neuroglia or simply glia, are non-neuronal cells in the central and peripheral nervous systems that provide support and protection for neurons. They constitute approximately half of the total cells in the human brain and more than half in other parts of the nervous system. Glial cells perform several key functions including, but not limited to, maintaining homeostasis, forming the myelin sheath around the neuron axons, and providing support and nutrition to neurons.\nThese different functions are performed by various glial cell types, including astrocytes, oligodendrocytes, microglia and other specialized types. Astrocytes, for example, are the most abundant glial cells and provide metabolic and nutrient support to neurons, help regulate the extracellular ion and neurotransmitter levels, and play a role in the formation and maintenance of the blood-brain barrier, contributing to the overall homeostasis and functioning of the nervous system. Additionally, astrocytes are involved in synaptic communication and participate in processes such as synaptogenesis and synaptic pruning.\nOligodendrocytes in the central nervous system function to insulate neurons by producing a fatty substance known as myelin. The myelin sheath enhances the speed and efficiency of nerve impulse conduction along the axons. \nMicroglia, the immune cells of the central nervous system, protect neurons from pathogens and clear away dead neurons through phagocytosis, a process also known as cellular eating. They also contribute to the regulation of inflammation in response to signals of tissue damage or infection in the central nervous system by releasing cytokines and other signaling molecules that modulate the immune response.\nDespite their overarching function in the support and protection of neurons, glial cells have also been shown to play significant roles in the pathophysiology of many psychiatric and neurodegenerative diseases, such as Alzheimer’s, Parkinson’s Disease and multiple sclerosis." xsd:string {xref="DOI:10.1002/glia.24343", xref="DOI:10.1038/nn1988", xref="DOI:10.1101/cshperspect.a020602", xref="DOI:10.1126/science.aat0473", xref="DOI:10.3389/fncel.2017.00024"} [Term] id: CL:0000133 name: neurectodermal cell def: "Ectoderm destined to be nervous tissue." [GOC:tfm, ISBN:068340007X] +subset: human_subset +subset: mouse_subset synonym: "neurectoderm cell" EXACT [] xref: ZFA:0009080 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000221 ! ectodermal cell @@ -584,6 +636,8 @@ name: mesenchymal stem cell def: "A connective tissue cell that normally gives rise to other cells that are organized as three-dimensional masses. In humans, this cell type is CD73-positive, CD90-positive, CD105-positive, CD45-negative, CD34-negative, and MHCII-negative. They may further differentiate into osteoblasts, adipocytes, myocytes, neurons, or chondroblasts in vitro. Originally described as residing in the bone marrow, this cell type is now known to reside in many, if not all, adult organs." [FB:ma, GOC:dsd, http://en.wikipedia.org/wiki/Mesenchymal_stem_cell, http://www.copewithcytokines.de/cope.cgi?key=mesenchymal%20stem%20cells, PMCID:PMC2613570, PMID:10102814, PMID:16923606, PMID:17986482, PMID:19960544] comment: Many but not all mesenchymal cells derive from the mesoderm. MSCs are reportedly CD3-negative, CD4-negative, CD5-negative, CD8-negative, CD11a-negative, CD11b-negative, CD14-negative, CD19-negative, CD29-positive, CD31-negative, CD34-negative, CD38-negative, CD40-negative, CD44-positive, CD45-negative, CD49-positive, CD54-positive, CD66b-negative, CD79a-negative, CD80-negative, CD102-positive, CD106-positive, CD117-positive, CD121a-positive, CD121b-positive, CD123-positive, CD124-positive, CD133-negative, CD146-positive, CD166-positive, CD271-positive, B220-negative, Gr1-negative, MHCI-positive, MHCII-negative, SSEA4-negative, sca1-positive, Ter119-negative, and glycophorin A-negative. Cultured MSCs are capable of producing stem cell factor, IL7, IL8, IL11, TGF-beta, cofilin, galectin-1, laminin-receptor 1, cyclophilin A, and MMP-2. subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "BMSC" RELATED OMO:0003000 [] synonym: "bone marrow stromal cells" NARROW [] synonym: "CFU-F" RELATED OMO:0003000 [] @@ -611,6 +665,8 @@ def: "A fat-storing cell found mostly in the abdominal cavity and subcutaneous t subset: cellxgene_subset subset: general_cell_types_upper_slim subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "adipose cell" EXACT [] synonym: "fat cell" EXACT [] xref: BTO:0000443 @@ -629,6 +685,8 @@ def: "A cell capable of processing and presenting lipid and protein antigens to comment: Note change of name; nearly all somatic cells can present antigens to T cells via MHC Class I complexes leading to effector responses, but professional antigen presenting cells constitutively express MHC Class II as well as costimulatory molecules, and thus can initiate immune responses via T cells. subset: blood_and_immune_upper_slim subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "APC" RELATED OMO:0003000 [] xref: ZFA:0009088 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000738 ! leukocyte @@ -640,6 +698,8 @@ relationship: capable_of GO:0002504 ! antigen processing and presentation of pep id: CL:0000147 name: pigment cell def: "A pigment cell is a cell that contains pigment granules." [GOC:tfm] +subset: human_subset +subset: mouse_subset synonym: "chromatocyte" EXACT [] synonym: "chromatophore" EXACT [] xref: VHOG:0001678 @@ -653,10 +713,13 @@ def: "A pigment cell derived from the neural crest. Contains melanin-filled pigm subset: cellxgene_subset subset: general_cell_types_upper_slim subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "melanophore" NARROW [] xref: BTO:0000847 xref: CALOHA:TS-0613 xref: FMA:70545 +xref: https://cellxgene.cziscience.com/cellguide/CL_0000148 xref: MESH:D008544 xref: VHOG:0001679 xref: ZFA:0009091 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} @@ -668,10 +731,13 @@ intersection_of: RO:0002202 CL:0000541 ! develops from melanoblast relationship: has_part GO:0042470 ! melanosome relationship: RO:0002202 CL:0000541 ! develops from melanoblast property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nMelanocytes are specialized cells prevalently found in the skin, but also present in the hair follicles, eyes, inner ear, bones, heart, and brain. Their primary function is the synthesis of melanin, a pigment responsible for coloration of skin, hair, and eyes. The presence and distribution of this pigment play a crucial role in the body's defense mechanism against harmful ultraviolet radiation.\nIn addition to melanin production, melanocytes also engage in a variety of other biological functions. They play a fundamental role in the immune response, owing to their ability to present antigens to T cells. Furthermore, they contribute to the maintenance of the skin's homeostasis by regulating processes such as extracellular matrix remodeling and cytokine production. A balance in melanocyte function is pivotal, as dysfunctions often result in dermatological disorders. For instance, the loss of melanocytes or reduction in their function may lead to hypopigmentation conditions such as vitiligo, whereas an abnormal increase could result in hyperpigmentation disorders or melanoma, a dangerous type of skin cancer." xsd:string {xref="DOI:10.1002/med.21754", xref="DOI:10.1038/nrc.2016.37", xref="DOI:10.1111/j.1751-1097.2007.00226.x", xref="DOI:10.3390/ijms21249769", xref="https://www.sciencedirect.com/topics/agricultural-and-biological-sciences/melanocyte"} [Term] id: CL:0000149 name: visual pigment cell +subset: human_subset +subset: mouse_subset synonym: "pigment cell" BROAD [] is_a: CL:0000147 ! pigment cell @@ -680,6 +746,8 @@ id: CL:0000151 name: secretory cell def: "A cell that specializes in controlled release of one or more substances." [GOC:tfm, ISBN:0721662544] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset xref: BTO:0003659 xref: FMA:86916 is_a: CL:0000000 ! cell @@ -692,6 +760,8 @@ id: CL:0000152 name: exocrine cell def: "A cell of an exocrine gland; i.e. a gland that discharges its secretion via a duct." [ISBN:0198547684] subset: general_cell_types_upper_slim +subset: human_subset +subset: mouse_subset xref: FMA:16014 xref: ZFA:0009092 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000151 ! secretory cell @@ -707,6 +777,8 @@ def: "A cell of an endocrine gland, ductless glands that secrete substances whic subset: cellxgene_subset subset: general_cell_types_upper_slim subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "endocrinocyte" EXACT [] xref: FMA:83809 xref: ZFA:0009096 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} @@ -720,6 +792,8 @@ id: CL:0000183 name: contractile cell def: "A cell whose primary function is to shorten." [FB:ma] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset is_a: CL:0000000 ! cell [Term] @@ -727,6 +801,8 @@ id: CL:0000187 name: muscle cell def: "A mature contractile cell, commonly known as a myocyte. This cell has as part of its cytoplasm myofibrils organized in various patterns." [MESH:D032342] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "muscle fiber" EXACT [] synonym: "myocyte" EXACT [] xref: BTO:0000888 @@ -749,16 +825,20 @@ def: "A somatic cell located in skeletal muscle." [GOC:tfm] subset: cellxgene_subset subset: general_cell_types_upper_slim subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "skeletal muscle cell" EXACT [] xref: BTO:0004392 xref: CALOHA:TS-2158 xref: FMA:9727 +xref: https://cellxgene.cziscience.com/cellguide/CL_0000188 xref: ZFA:0009115 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000255 ! eukaryotic cell intersection_of: CL:0000000 ! cell intersection_of: part_of UBERON:0001134 ! skeletal muscle tissue relationship: part_of UBERON:0001134 ! skeletal muscle tissue property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nSkeletal muscle cells, or myocytes, are essential for the musculoskeletal system, featuring a striated appearance from tightly packed sarcomeres. These elongated, multi-nucleated cells convert ATP into mechanical energ and are key for voluntary movement and posture. They also are responsible for maintaining body temperature, storing nutrients, and stabilizing joints.\nSkeletal muscle cells organize themselves tightly into bundles to form muscle fibers. Embedded within each of these cells are thousands of myofibrils, which are made up of the contractile proteins, actin (the thin filament), and myosin (the thick filament). Contraction of a skeletal muscle cell occurs when these myofibrils shorten, a process driven by the sliding of actin and myosin filaments over each other in a mechanism famously known as the sliding filament theory.\nAdditionally, skeletal muscle cells exhibit a high degree of plasticity, which allows for their adaptation in response to alterations in functional demands or damages. They have an innate regenerative capacity due to the presence of satellite cells—quiescent muscle stem cells that reside within the muscle fibers. Upon muscle injury, these satellite cells become activated, proliferate, and differentiate into new muscle cells, thereby contributing to the repair and growth of injured skeletal muscle. With this, skeletal muscle cells serve not only a pivotal biomechanical function but also possess a great capacity for self-healing and regeneration." xsd:string {xref="DOI:10.1002/cphy.c160033", xref="DOI:10.3390/biology10101056", xref="https://www.nature.com/scitable/topicpage/the-sliding-filament-theory-of-muscle-contraction-14567666/", xref="https://www.ncbi.nlm.nih.gov/books/NBK537139", xref="https://www.ncbi.nlm.nih.gov/books/NBK9961/"} [Term] id: CL:0000192 @@ -767,6 +847,8 @@ def: "A non-striated, elongated, spindle-shaped cell found lining the digestive subset: cellxgene_subset subset: general_cell_types_upper_slim subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "myocytes, smooth muscle" EXACT [MESH:D032389] synonym: "non-striated muscle cell" BROAD [] synonym: "SMCs" EXACT [PMID:9315361] @@ -774,17 +856,21 @@ synonym: "smooth muscle fiber" EXACT [] xref: BTO:0004576 xref: CALOHA:TS-2159 xref: FMA:14072 +xref: https://cellxgene.cziscience.com/cellguide/CL_0000192 xref: ZFA:0009118 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0008000 ! non-striated muscle cell is_a: CL:0008007 ! visceral muscle cell relationship: RO:0002202 CL:0000514 ! develops from smooth muscle myoblast property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nSmooth muscle cells are a specialized type of muscle cells that are primarily found within the walls of hollow organs such as the intestine, stomach, bladder, uterus, and blood vessels. These cells are an essential component of the autonomic nervous system controling involuntary movements within the body.\nSmooth muscle cells play a vital role in many physiological processes due to their unique functionality. They can contract and relax in a slow, sustained, and controlled manner to help modulate the size and shape of the lumens of the organs they surround. For example, in the digestive system, coordinated contraction and relaxation of smooth muscle cells propels food along the gastrointestinal tract - a process known as peristalsis. In the blood vessels, the smooth muscle cells, by contracting or relaxing, either constrict or dilate the vessels, which in turn, help regulate blood flow and pressure.\nOn a cellular level, smooth muscle cells possess a single, centrally located nucleus and contain an arranged network of actin and myosin filaments, which are the proteins responsible for muscle contraction. Unlike their counterparts in skeletal or cardiac muscles, these cells lack specific contact points for these filaments, hence the lack of visible striations. Furthermore, the contraction of smooth muscle cells is regulated by hormones and neurotransmitters, such as acetylcholine and norepinephrine, adding an additional layer of complex regulation to these highly specialized cells." xsd:string {xref="DOI:10.1093/ptj/81.11.1810", xref="https://training.seer.cancer.gov/anatomy/muscular/types.html", xref="https://www.ncbi.nlm.nih.gov/books/NBK10854/", xref="https://www.ncbi.nlm.nih.gov/books/NBK526125", xref="https://www.ncbi.nlm.nih.gov/books/NBK556137/"} [Term] id: CL:0000210 name: photoreceptor cell def: "A cell specialized in detecting light stimuli that are involved in visual perception." [MESH:D010786] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset xref: BTO:0001060 xref: CALOHA:TS-0868 xref: FBbt:00004211 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} @@ -801,6 +887,8 @@ property_value: foaf:depiction "https://www.swissbiopics.org/api/image/Photorece id: CL:0000211 name: electrically active cell def: "A cell whose function is determined by the generation or the reception of an electric signal." [FB:ma] +subset: human_subset +subset: mouse_subset xref: ZFA:0009128 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000000 ! cell @@ -808,6 +896,8 @@ is_a: CL:0000000 ! cell id: CL:0000219 name: motile cell def: "A cell that moves by its own activities." [FB:ma] +subset: human_subset +subset: mouse_subset xref: ZFA:0009136 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000000 ! cell intersection_of: CL:0000000 ! cell @@ -818,6 +908,9 @@ relationship: capable_of GO:0048870 ! cell motility id: CL:0000221 name: ectodermal cell def: "A cell of the outer of the three germ layers of the embryo." [MESH:D004475] +subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "ectoderm cell" EXACT [] xref: FMA:72549 xref: ZFA:0009137 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} @@ -830,18 +923,24 @@ id: CL:0000222 name: mesodermal cell def: "A cell of the middle germ layer of the embryo." [MESH:D008648] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "mesoblast" EXACT [] synonym: "mesoderm cell" EXACT [] xref: FMA:72554 +xref: https://cellxgene.cziscience.com/cellguide/CL_0000222 xref: ZFA:0009138 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000255 ! eukaryotic cell is_a: CL:0002321 ! embryonic cell (metazoa) relationship: part_of UBERON:0000926 ! mesoderm +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nMesodermal cells are pluripotent and the most abundant in the human body. They contribute to the development of several structures such as the skeletal muscles, bones, heart and blood vessels, kidneys, gonads, connective tissues, and certain layers of the skin. Hence, the mesoderm is often regarded as an active and diverse layer due to its role in forming many bodily structures. \nIn embryonic development, these cells are instrumental, contributing to the body's structures through a carefully coordinated sequence of morphogenetic movements. This process forms the complex multicellular architecture of tissues and organs from a simple ball of cells. Without the function of mesodermal cells, the body's integral structures and systems would cease to form correctly, leading to developmental disorders such as axial mesodermal dysplasia complex" xsd:string {xref="DOI:10.1016/j.ceb.2019.07.012", xref="DOI:10.5535/arm.2016.40.1.162", xref="https://www.sciencedirect.com/topics/biochemistry-genetics-and-molecular-biology/mesoderm"} [Term] id: CL:0000223 name: endodermal cell def: "A cell of the inner of the three germ layers of the embryo." [MESH:D004707] +subset: human_subset +subset: mouse_subset synonym: "endoderm cell" EXACT [] xref: FMA:72555 xref: ZFA:0009139 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} @@ -853,6 +952,8 @@ relationship: part_of UBERON:0000925 ! endoderm id: CL:0000226 name: single nucleate cell def: "A cell with a single nucleus." [FB:ma, GOC:tfm] +subset: human_subset +subset: mouse_subset is_a: CL:0000255 ! eukaryotic cell is_a: CL:0002242 ! nucleate cell intersection_of: CL:0000000 ! cell @@ -863,6 +964,8 @@ relationship: bearer_of PATO:0001407 ! mononucleate id: CL:0000228 name: multinucleate cell def: "A cell with more than one nucleus." [FB:ma, Wikipedia:Multinucleate] +subset: human_subset +subset: mouse_subset synonym: "multinucleated cells" EXACT [Wikipedia:Multinucleate] synonym: "polynuclear cells" EXACT [Wikipedia:Multinucleate] is_a: CL:0000255 ! eukaryotic cell @@ -875,7 +978,8 @@ relationship: bearer_of PATO:0001908 ! multinucleate id: CL:0000234 name: phagocyte def: "Any cell capable of ingesting particulate matter via phagocytosis." [GOC:add, ISBN:0721601464] -subset: cellxgene_subset +subset: human_subset +subset: mouse_subset xref: BTO:0001044 xref: FMA:83806 xref: MESH:D010586 @@ -896,6 +1000,8 @@ subset: blood_and_immune_upper_slim subset: cellxgene_subset subset: general_cell_types_upper_slim subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "histiocyte" EXACT [] xref: BTO:0000801 xref: CALOHA:TS-0587 @@ -922,6 +1028,8 @@ subset: blood_and_immune_upper_slim subset: cellxgene_subset subset: general_cell_types_upper_slim subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "B lymphocyte" EXACT [] synonym: "B-cell" EXACT [] synonym: "B-lymphocyte" EXACT [] @@ -941,7 +1049,8 @@ property_value: RO:0002175 NCBITaxon:9606 id: CL:0000255 name: eukaryotic cell def: "Any cell that in taxon some Eukaryota." [FBC:Autogenerated] -subset: cellxgene_subset +subset: human_subset +subset: mouse_subset xref: MESH:D005057 is_a: CL:0000000 ! cell intersection_of: CL:0000000 ! cell @@ -952,12 +1061,16 @@ relationship: RO:0002162 NCBITaxon:2759 ! in taxon Eukaryota id: CL:0000325 name: stuff accumulating cell def: "A cell that is specialised to accumulate a particular substance(s)." [FB:ma] +subset: human_subset +subset: mouse_subset subset: ubprop:upper_level is_a: CL:0000000 ! cell [Term] id: CL:0000327 name: extracellular matrix secreting cell +subset: human_subset +subset: mouse_subset xref: ZFA:0009162 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000499 ! stromal cell @@ -965,6 +1078,8 @@ is_a: CL:0000499 ! stromal cell id: CL:0000333 name: migratory neural crest cell def: "A cell derived from the specialized ectoderm flanking each side of the embryonic neural plate, which after the closure of the neural tube, forms masses of cells that migrate out from the dorsal aspect of the neural tube to spread throughout the body." [doi:10.1016/j.stem.2015.02.017] +subset: human_subset +subset: mouse_subset xref: FMA:86667 xref: ZFA:0007086 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000219 ! motile cell @@ -976,7 +1091,10 @@ relationship: RO:0002202 CL:0007004 ! develops from premigratory neural crest ce id: CL:0000349 name: extraembryonic cell def: "Any cell that is part of some extraembryonic structure." [FBC:Autogenerated] +subset: cellxgene_subset subset: general_cell_types_upper_slim +subset: human_subset +subset: mouse_subset xref: ZFA:0009176 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000255 ! eukaryotic cell intersection_of: CL:0000000 ! cell @@ -987,6 +1105,8 @@ relationship: part_of UBERON:0000478 ! extraembryonic structure id: CL:0000352 name: epiblast cell def: "A cell of the outer layer of a blastula that gives rise to the ectoderm after gastrulation." [GOC:tfm, ISBN:0618947256] +subset: human_subset +subset: mouse_subset is_a: CL:0000052 ! totipotent stem cell [Term] @@ -994,6 +1114,8 @@ id: CL:0000355 name: multi-potent skeletal muscle stem cell def: "A multifate stem cell found in skeletal muscle than can differentiate into many different cell types, including muscle. Distinct cell type from satellite cell." [PMID:18282570] comment: Multi-potency demonstrated ex vivo. At the time of writing, it is unclear whether the endogenous population differentiates into multiple cell types in vivo. +subset: human_subset +subset: mouse_subset xref: FMA:86767 xref: ZFA:0009179 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000048 {is_inferred="true"} ! multi fate stem cell @@ -1005,6 +1127,8 @@ intersection_of: part_of UBERON:0001134 ! skeletal muscle tissue id: CL:0000365 name: animal zygote def: "Diploid cell produced by the fusion of sperm cell nucleus and egg cell." [ISBN:0471245208] +subset: human_subset +subset: mouse_subset synonym: "zygote" BROAD [] xref: BTO:0000854 xref: EHDAA2:0004546 @@ -1020,6 +1144,8 @@ relationship: RO:0002162 NCBITaxon:33208 ! in taxon Metazoa id: CL:0000393 name: electrically responsive cell def: "A cell whose function is determined by its response to an electric signal." [FB:ma] +subset: human_subset +subset: mouse_subset xref: ZFA:0009190 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000211 ! electrically active cell @@ -1027,6 +1153,8 @@ is_a: CL:0000211 ! electrically active cell id: CL:0000404 name: electrically signaling cell def: "A cell that initiates an electrical signal and passes that signal to another cell." [FB:ma] +subset: human_subset +subset: mouse_subset xref: ZFA:0009193 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000211 ! electrically active cell @@ -1037,6 +1165,8 @@ def: "A cell of hematopoietic origin, typically resident in particular tissues, subset: cellxgene_subset subset: general_cell_types_upper_slim subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "interdigitating cell" RELATED [] synonym: "veiled cell" RELATED [] xref: BTO:0002042 @@ -1046,7 +1176,6 @@ xref: MESH:D003713 xref: ZFA:0009209 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000113 ! mononuclear phagocyte is_a: CL:0000145 ! professional antigen presenting cell -is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000738 ! leukocyte intersection_of: bearer_of PATO:0001407 ! mononucleate intersection_of: capable_of GO:0001816 ! cytokine production @@ -1074,15 +1203,19 @@ property_value: RO:0002175 NCBITaxon:9606 id: CL:0000473 name: defensive cell def: "A cell whose primary function is to protect the organism." [JB:jb] +subset: human_subset +subset: mouse_subset is_a: CL:0000000 ! cell [Term] id: CL:0000499 name: stromal cell -def: "A connective tissue cell of an organ found in the loose connective tissue. These are most often associated with the uterine mucosa and the ovary as well as the hematopoietic system and elsewhere." [GOC:tfm, MESH:D017154] +def: "A connective tissue cell of an organ found in the loose connective tissue." [GOC:tfm, MESH:D017154] subset: cellxgene_subset subset: general_cell_types_upper_slim subset: human_reference_atlas +subset: human_subset +subset: mouse_subset xref: BTO:0002064 xref: FMA:83624 xref: ZFA:0009226 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} @@ -1095,6 +1228,8 @@ id: CL:0000513 name: cardiac muscle myoblast def: "A precursor cell destined to differentiate into cardiac muscle cell." [GOC:tfm, MESH:D032386] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "cardiac muscle progenitor cell" EXACT [] synonym: "cardiomyocyte progenitor cell" EXACT [] xref: FMA:84797 @@ -1111,19 +1246,25 @@ id: CL:0000514 name: smooth muscle myoblast def: "A precursor cell destined to differentiate into smooth muscle myocytes." [GOC:tfm, MESH:D032390] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "myoblast, smooth muscle" EXACT [MESH:D032390] synonym: "satellite cell" RELATED [] xref: FMA:84798 +xref: https://cellxgene.cziscience.com/cellguide/CL_0000514 xref: ZFA:0009235 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000056 ! myoblast intersection_of: CL:0000056 ! myoblast intersection_of: RO:0002203 CL:0000192 ! develops into smooth muscle cell relationship: RO:0002203 CL:0000192 ! develops into smooth muscle cell +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nA precursor to the smooth muscle cell, the smooth muscle myoblast, is integral to various body systems, including the cardiovascular, gastrointestinal, and respiratory systems. Smooth muscle myoblasts arise from the differentiation of mesenchymal stem cells, a process tightly regulated by specific genetic factors and environmental signals. Their role extends to myogenesis, particularly in the formation of muscular tissue, especially during embryonic development.\nSmooth muscle myoblasts possess distinctive cellular characteristics. In contrast to skeletal muscle myoblasts, they do not fuse to create multinucleated fibers. Instead, they differentiate into individual, uninucleated smooth muscle cells. This differentiation unfolds in two distinct phases: proliferation, marked by rapid division to increase cell numbers, and differentiation, involving structural and functional transformation into mature smooth muscle cells. This intricate process is intricately mediated by various signaling molecules and transcription factors.\nFunctionally, smooth muscle myoblasts and the mature muscle cells they generate play pivotal roles in various physiological processes. Smooth muscle cells orchestrate involuntary muscle responses and are integral to body systems that regulate blood flow, propel food along the digestive tract, and control airflow in the respiratory tract. These diverse functions underscore the significance of smooth muscle myoblasts in the body's growth, maintenance, and overall function." xsd:string {xref="DOI:10.1074/jbc.RA118.001739", xref="https://www.ncbi.nlm.nih.gov/books/NBK544225/", xref="https://www.sciencedirect.com/topics/medicine-and-dentistry/smooth-muscle"} [Term] id: CL:0000515 name: skeletal muscle myoblast def: "A myoblast that differentiates into skeletal muscle fibers." [SANBI:mhl] +subset: human_subset +subset: mouse_subset synonym: "skeletal myoblast" EXACT [] xref: FMA:84799 xref: ZFA:0009236 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} @@ -1138,6 +1279,8 @@ relationship: RO:0002203 CL:0008002 ! develops into skeletal muscle fiber id: CL:0000518 name: phagocyte (sensu Vertebrata) def: "A phagocyte in vertebrates that is able to phagocytosis." [GOC:tfm] +subset: human_subset +subset: mouse_subset is_a: CL:0000234 ! phagocyte is_a: CL:0000255 ! eukaryotic cell relationship: RO:0002162 NCBITaxon:7742 ! in taxon Vertebrata @@ -1147,6 +1290,8 @@ id: CL:0000526 name: afferent neuron def: "A neuron which conveys sensory information centrally from the periphery." [GOC:tfm, MESH:D009475] subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "input neuron" EXACT [] xref: FMA:87653 xref: ZFA:0009238 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} @@ -1157,6 +1302,9 @@ property_value: RO:0002175 NCBITaxon:9606 id: CL:0000527 name: efferent neuron def: "A neuron which sends impulses peripherally to activate muscles or secretory cells." [MESH:D009476] +subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "output neuron" EXACT [] xref: ZFA:0009239 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000540 ! neuron @@ -1169,6 +1317,8 @@ comment: These cells are also reportedly CD4-negative and CD200-positive. They a subset: cellxgene_subset subset: general_cell_types_upper_slim subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "nerve cell" EXACT [] xref: BTO:0000938 xref: CALOHA:TS-0683 @@ -1189,6 +1339,8 @@ id: CL:0000541 name: melanoblast def: "A cell that originates from the neural crest and differentiates into a pigment cell." [GOC:tfm, SANBI:mhl] comment: Derived from UBERON:0002342 neural crest. +subset: human_subset +subset: mouse_subset xref: BTO:0003217 xref: FMA:83377 xref: ZFA:0009249 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} @@ -1203,6 +1355,8 @@ def: "A lymphocyte is a leukocyte commonly found in the blood and lymph that has comment: Editors note: consider adding taxon constraint to vertebrata (PMID:18025161) subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset xref: BTO:0000775 xref: CALOHA:TS-0583 xref: FMA:62863 @@ -1229,6 +1383,8 @@ def: "A hematopoietic progenitor cell that is committed to the granulocyte and m comment: Originally described in the dendritic cell ontology (DC_CL:0000042)(PMID:19243617). GMPs are reportedly CD16-positive, CD32-positive, CD34-positive, CD38-positive, CD45RA-positive, CD110-negative, CD117-positive, CD123-positive, and SCA1-negative. subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "CFU-C , Colony forming unit in culture" BROAD [http://www.copewithcytokines.de] synonym: "CFU-GM" RELATED OMO:0003000 [ISBN:0721601464, PMCID:PMC2213186, PMCID:PMC548021] synonym: "colony forming unit granulocyte macrophage" EXACT [ISBN:0721601464, PMCID:PMC2213186, PMCID:PMC548021] @@ -1236,12 +1392,11 @@ synonym: "GMP" RELATED OMO:0003000 [ISBN:0721601464, PMCID:PMC2213186, PMCID:PMC synonym: "granulocyte-macrophage progenitor" EXACT [ISBN:0721601464, PMCID:PMC2213186, PMCID:PMC548021] synonym: "granulocyte/monocyte precursor" EXACT [] synonym: "granulocyte/monocyte progenitor" EXACT [] +xref: https://cellxgene.cziscience.com/cellguide/CL_0000557 xref: ZFA:0009251 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000763 ! myeloid cell is_a: CL:0001012 ! CD7-negative lymphoid progenitor OR granulocyte monocyte progenitor -is_a: CL:0011026 ! progenitor cell is_a: CL:1001610 ! bone marrow hematopoietic cell -is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0002032 ! hematopoietic oligopotent progenitor cell intersection_of: capable_of GO:0030225 ! macrophage differentiation intersection_of: capable_of GO:0030851 ! granulocyte differentiation @@ -1259,6 +1414,7 @@ relationship: has_part PR:000001944 ! transcription factor PU.1 relationship: has_part PR:000005307 ! CCAAT/enhancer-binding protein alpha relationship: RO:0002104 PR:000001865 ! has plasma membrane part interleukin-3 receptor class 2 alpha chain property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nGranulocyte monocyte progenitor cells (GMP cells), originating from hematopoietic stem cells in the bone marrow, are a critical intermediate in myeloid cell development. Positioned at a key differentiation juncture, these cells exhibit bidirectional potential, giving rise to both granulocyte and monocyte lineages.\nTheir primary role is to generate mature granulocytes and monocytes, essential components of the body's innate immunity and inflammatory responses. Granulocytes, such as neutrophils, eosinophils, and basophils, contribute to the first line of defense against infections by migrating to the infection site and phagocytosing pathogens. Monocytes can differentiate into macrophages or dendritic cells, playing diverse roles in immune responses." xsd:string {xref="DOI:10.1016/j.immuni.2017.10.021", xref="DOI:10.1146/annurev-immunol-081022113627", xref="DOI:10.1186/2050-7771-2-1"} [Term] id: CL:0000559 @@ -1267,12 +1423,13 @@ def: "A precursor in the monocytic series, being a cell intermediate in developm comment: Morphology: Mononuclear cell, diameter 14-18 _M, fine azurophilic granules; markers: CD11b (shared with many other myeloid cells); location: Adult: bone marrow; Fetal: Liver, Yolk Sac; role or process: hematopoiesis, monocyte development; lineage: hematopoietic, myeloid. subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset xref: BTO:0004657 xref: FMA:83551 xref: ZFA:0009253 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000763 ! myeloid cell is_a: CL:0002194 {is_inferred="true"} ! monopoietic cell -is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0002194 ! monopoietic cell intersection_of: capable_of GO:0030224 ! monocyte differentiation intersection_of: has_part GO:0042582 ! azurophil granule @@ -1287,12 +1444,13 @@ id: CL:0000566 name: angioblastic mesenchymal cell def: "A mesenchymal stem cell capable of developing into blood vessel endothelium." [GOC:dsd, GOC:tfm, PMID:12768659] comment: These cells are reportedly CD31-positive, CD34-positive, CD144-positive, CD309-positive, and TAL1-positive. +subset: human_subset +subset: mouse_subset synonym: "angioblast" EXACT [] synonym: "chondroplast" EXACT [] xref: ZFA:0009258 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000134 {is_inferred="true"} ! mesenchymal stem cell is_a: CL:0011026 ! progenitor cell -is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000134 ! mesenchymal stem cell intersection_of: RO:0002104 PR:000001444 ! has plasma membrane part cadherin-5 intersection_of: RO:0002104 PR:000002112 ! has plasma membrane part vascular endothelial growth factor receptor 2 @@ -1311,6 +1469,8 @@ subset: blood_and_immune_upper_slim subset: cellxgene_subset subset: general_cell_types_upper_slim subset: human_reference_atlas +subset: human_subset +subset: mouse_subset xref: BTO:0000876 xref: CALOHA:TS-0638 xref: FMA:62864 @@ -1336,6 +1496,8 @@ def: "A lymphocyte that can spontaneously kill a variety of target cells without subset: cellxgene_subset subset: general_cell_types_upper_slim subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "large granular lymphocyte" BROAD [] synonym: "NK cell" EXACT [] synonym: "null cell" BROAD [] @@ -1367,6 +1529,8 @@ id: CL:0000680 name: muscle precursor cell def: "A non-terminally differentiated cell that is capable of developing into a muscle cell." [GOC:add] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset xref: ZFA:0009291 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000055 ! non-terminally differentiated cell is_a: CL:0000255 ! eukaryotic cell @@ -1379,6 +1543,8 @@ relationship: RO:0002203 CL:0000187 ! develops into muscle cell id: CL:0000723 name: somatic stem cell def: "A stem cell that can give rise to cell types of the body other than those of the germ-line." [GO:0048103] +subset: human_subset +subset: mouse_subset xref: CALOHA:TS-2086 xref: MESH:D053687 xref: ZFA:0009307 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} @@ -1391,6 +1557,8 @@ relationship: capable_of GO:0048103 ! somatic stem cell division id: CL:0000737 name: striated muscle cell def: "Muscle cell which has as its direct parts myofilaments organized into sarcomeres." [GOC:tfm, ISBN:0721662544] +subset: human_subset +subset: mouse_subset xref: BTO:0002916 xref: CALOHA:TS-2157 xref: FMA:86936 @@ -1409,6 +1577,8 @@ name: leukocyte def: "An achromatic cell of the myeloid or lymphoid lineages capable of ameboid movement, found in blood or other tissue." [GOC:add, GOC:tfm, ISBN:978-0-323-05290-0] subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "immune cell" RELATED [] synonym: "leucocyte" EXACT [] synonym: "white blood cell" EXACT [] @@ -1434,12 +1604,13 @@ property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000746 name: cardiac muscle cell -alt_id: FMA:83808 def: "Cardiac muscle cells are striated muscle cells that are responsible for heart contraction. In mammals, the contractile fiber resembles those of skeletal muscle but are only one third as large in diameter, are richer in sarcoplasm, and contain centrally located instead of peripheral nuclei." [GOC:mtg_cardiacconduct_nov11, GOC:tfm, ISBN:0323052908, PMID:22426062, PMID:4711263] comment: This class encompasses the muscle cells responsible for heart* contraction in both vertebrates and arthropods. The ultrastucture of a wide range of arthropod heart cells has been examined including spiders, horseshoe crabs, crustaceans (see Sherman, 1973 and refs therein) and insects (see Lehmacher et al (2012) and refs therein). According to these refs, the cells participating in heart contraction in all cases are transversely striated. Insects hearts additionally contain ostial cells, also transversely striated muscle cells, but which do not participate in heart contraction. subset: cellxgene_subset subset: general_cell_types_upper_slim subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "cardiac muscle fiber" EXACT [GO:0048739] synonym: "cardiac myocyte" EXACT [] synonym: "cardiocyte" BROAD [] @@ -1448,6 +1619,7 @@ synonym: "heart muscle cell" EXACT [] xref: BTO:0001539 xref: CALOHA:TS-0115 xref: FMA:14067 +xref: https://cellxgene.cziscience.com/cellguide/CL_0000746 xref: MESH:D032383 xref: ZFA:0009316 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000737 ! striated muscle cell @@ -1461,12 +1633,15 @@ relationship: bearer_of PATO:0002478 ! transversely striated relationship: participates_in GO:0060047 ! heart contraction relationship: RO:0002202 CL:0000513 ! develops from cardiac muscle myoblast property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nCardiac muscle cells, also known as cardiomyocytes or cardiac myocytes, are specialized cells that form the heart tissue. These cells are elongated, branched, and contain a single centrally located nucleus. Their anatomy is composed primarily of densely packed myofibrils, which are protein structures that consist of sarcomeres - the fundamental units of muscle contraction. Cardiac muscle cells are united at their ends through specialized junctions known as intercalated discs, which allow the heart to contract in a unified, powerful and rhythmic way.\nFunctionally, cardiac muscle cells are responsible for the heart's consistent pumping action that circulates blood throughout the body. Unlike most cells in the body, cardiac muscle cells spontaneously depolarize and generate action potentials without external stimulation. This unique trait stems from the presence of ion channels in the cells' membrane that allow a cyclic flow of ions across the membrane, which create the electrical impulses necessary for heart contraction. The spread of these electrical signals from one cardiac muscle cell to another - facilitated by the interconnected network made by the intercalated disks - results in a synchronized contraction of the heart muscle.\nUnlike skeletal muscle cells which can tire and need rest, cardiac muscle cells have to work ceaselessly throughout the entire lifespan, without the opportunity for rest, to ensure continuous circulation of blood. This is made possible through the high volume of mitochondria and a constant supply of oxygen from coronary circulation. In conclusion, cardiac muscle cells, through their unique structure and vital functionality, play a pivotal role in sustaining life by providing the means for blood to reach every cell in the body." xsd:string {xref="DOI:10.1016/j.ccep.2010.10.012", xref="DOI:10.1038/nrcardio.2016.203", xref="https://www.ncbi.nlm.nih.gov/books/NBK572070", xref="https://www.sciencedirect.com/topics/agricultural-and-biological-sciences/cardiac-muscle"} [Term] id: CL:0000763 name: myeloid cell def: "A cell of the monocyte, granulocyte, mast cell, megakaryocyte, or erythroid lineage." [GOC:add] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset xref: BTO:0001441 xref: CALOHA:TS-0647 xref: MESH:D022423 @@ -1482,6 +1657,8 @@ id: CL:0000766 name: myeloid leukocyte def: "A cell of the monocyte, granulocyte, or mast cell lineage." [GOC:add] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset xref: ZFA:0009326 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000738 {is_inferred="true"} ! leukocyte is_a: CL:0000763 ! myeloid cell @@ -1494,6 +1671,8 @@ name: myeloid dendritic cell def: "A dendritic cell of the myeloid lineage." [GOC:add, PMID:10449155, PMID:17332250, PMID:9521319] comment: These cells are CD1a-negative, CD1b-positive, CD11a-positive, CD11c-positive, CD13-positive, CD14-negative, CD20-negative, CD21-negative, CD33-positive, CD40-negative, CD50-positive, CD54-positive, CD58-positive, CD68-negative, CD80-negative, CD83-negative, CD85j-positive, CD86-positive, CD89-negative, CD95-positive, CD120a-negative, CD120b-positive, CD123-negative, CD178-negative, CD206-negative, CD207-negative, CD209-negative, and TNF-alpha-negative. Upon TLR stimulation, they are capable of producing high levels of TNF-alpha, IL-6, CXCL8 (IL-8). subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "CD11c+CD123- DC" EXACT [] synonym: "interdigitating cell" BROAD [] synonym: "mDC" EXACT [] @@ -1512,6 +1691,8 @@ id: CL:0000825 name: pro-NK cell def: "A lymphoid progenitor cell that is committed to the natural killer cell lineage, expressing CD122 (IL-15) receptor, but lacking many of the phenotypic characteristics of later stages of natural killer cell development such as expression of NK activating and inhibitory molecules. In human this cell has the phenotype CD34-positive, CD45RA-positive, CD10-positive, CD117-negative, and CD161 negative." [GO_REF:0000031, GOC:add, GOC:pam, PMID:11532393, PMID:12457618, PMID:15032583, PMID:15766674] comment: Most markers only described for human pro NK cells. +subset: human_subset +subset: mouse_subset synonym: "natural killer cell progenitor" EXACT [] synonym: "NKP" EXACT [PMID:12457618, PMID:15032583, PMID:15766674] synonym: "null cell" RELATED [PMID:11532393] @@ -1519,7 +1700,6 @@ synonym: "preNK cell" RELATED [PMID:11532393] synonym: "pro-natural killer cell" EXACT [] xref: ZFA:0009348 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000838 {is_inferred="true"} ! lymphoid lineage restricted progenitor cell -is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000838 ! lymphoid lineage restricted progenitor cell intersection_of: CL:4030046 PR:000001874 ! lacks_plasma_membrane_part KLRB1-like protein intersection_of: CL:4030046 PR:000002065 ! lacks_plasma_membrane_part mast/stem cell growth factor receptor @@ -1542,6 +1722,8 @@ def: "A progenitor cell of the B cell lineage, with some lineage specific activi comment: Human pro-B cells are reportedly CD10-positive, CD22-positive, CD34-positive, CD38-positive, CD45-low, CD48-positive, CD79a-positive, CD127-positive, CD184-positive, RAG-positive, TdT-positive, Vpre-B-positive, pre-BCR-negative, IgD-negative, and IgM-negative. Transcription factors expressed: Pax5-positive, EBF-positive, E2A-negative, Ikaros-negative, and PU.1-negative. subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "pre-B cell (Philadelphia nomenclature)" RELATED [PMID:11244048] synonym: "pre-pro B cell" BROAD [PMID:17582343] synonym: "pro-B lymphocyte" EXACT [] @@ -1554,7 +1736,6 @@ synonym: "progenitor B-lymphocyte" EXACT [] xref: BTO:0003104 xref: ZFA:0009349 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000838 {is_inferred="true"} ! lymphoid lineage restricted progenitor cell -is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000838 ! lymphoid lineage restricted progenitor cell intersection_of: has_part PR:000001903 ! paired box protein PAX-5 intersection_of: has_part PR:000006611 ! DNA nucleotidylexotransferase @@ -1570,6 +1751,8 @@ id: CL:0000827 name: pro-T cell def: "A lymphoid progenitor cell of the T cell lineage, with some lineage specific marker expression, but not yet fully committed to the T cell lineage." [GOC:add, ISBN:0781735149] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "DN1 cell" NARROW [] synonym: "DN1 thymocyte" NARROW [] synonym: "pro-T lymphocyte" EXACT [] @@ -1590,6 +1773,8 @@ comment: Markers differ between mouse and human. subset: blood_and_immune_upper_slim subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "hemopoietic progenitor cell" EXACT [] synonym: "MPP" EXACT [] xref: BTO:0000725 @@ -1597,7 +1782,6 @@ xref: CALOHA:TS-0448 xref: ZFA:0009354 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000255 ! eukaryotic cell is_a: CL:0008001 ! hematopoietic precursor cell -is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000988 ! hematopoietic cell intersection_of: bearer_of PATO:0001402 ! multipotent intersection_of: CL:4030046 PR:000001002 ! lacks_plasma_membrane_part CD19 molecule @@ -1639,6 +1823,8 @@ name: lymphoid lineage restricted progenitor cell def: "A progenitor cell restricted to the lymphoid lineage." [GOC:add, GOC:tfm] comment: Note that this is a class of cell types, not an identified single cell type. subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "lymphoid progenitor cell" BROAD [] xref: BTO:0004731 xref: CALOHA:TS-2025 @@ -1658,6 +1844,8 @@ def: "A progenitor cell restricted to the myeloid lineage." [GOC:add, GOC:tfm, P comment: Note that this is a class of cell types, not an identified single cell type. subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "myeloid progenitor cell" BROAD [] xref: BTO:0004730 xref: CALOHA:TS-2099 @@ -1676,6 +1864,8 @@ name: mononuclear cell def: "A leukocyte with a single non-segmented nucleus in the mature form." [GOC:add] subset: blood_and_immune_upper_slim subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "mononuclear leukocyte" EXACT [] synonym: "peripheral blood mononuclear cell" NARROW [] xref: BTO:0000878 @@ -1692,7 +1882,10 @@ id: CL:0000945 name: lymphocyte of B lineage def: "A lymphocyte of B lineage with the commitment to express an immunoglobulin complex." [GO_REF:0000031, GOC:add, GOC:rhs, GOC:tfm, ISBN:0781735149] comment: Types of B lineage lymphocytes include B cells and antibody secreting cells (plasmablasts and plasma cells). Lymphocytes of B cell lineage can be distinguished from those of T cell lineage by their lack of CD3e (as part of the T cell receptor complex). +subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset is_a: CL:0000542 {is_inferred="true"} ! lymphocyte relationship: RO:0002202 CL:0000826 ! develops from pro-B cell property_value: RO:0002175 NCBITaxon:9606 @@ -1702,6 +1895,8 @@ id: CL:0000988 name: hematopoietic cell def: "A cell of a hematopoietic lineage." [GO_REF:0000031, GOC:add] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "haematopoietic cell" EXACT [] synonym: "haemopoietic cell" EXACT [] synonym: "hemopoietic cell" EXACT [] @@ -1720,6 +1915,8 @@ comment: Originally described in the dendritic cell ontology (DC_CL:0000003)(PMI subset: blood_and_immune_upper_slim subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "cDC" EXACT [] synonym: "DC1" EXACT [] synonym: "dendritic reticular cell" EXACT [] @@ -1737,7 +1934,10 @@ property_value: RO:0002175 NCBITaxon:9606 id: CL:0001012 name: CD7-negative lymphoid progenitor OR granulocyte monocyte progenitor comment: Originally described in the dendritic cell ontology (DC_CL:1110000)(PMID:19243617). +subset: human_subset +subset: mouse_subset is_a: CL:0001060 ! hematopoietic oligopotent progenitor cell, lineage-negative +is_a: CL:0011026 ! progenitor cell [Term] id: CL:0001035 @@ -1745,18 +1945,24 @@ name: bone cell def: "A connective tissue cell found in bone." [GO_REF:0000034, GOC:add] subset: general_cell_types_upper_slim subset: human_reference_atlas +subset: human_subset +subset: mouse_subset +xref: https://cellxgene.cziscience.com/cellguide/CL_0001035 is_a: CL:0000255 ! eukaryotic cell intersection_of: CL:0000000 ! cell intersection_of: part_of UBERON:0001474 ! bone element relationship: part_of UBERON:0001474 ! bone element property_value: RO:0002175 NCBITaxon:9606 property_value: terms:contributor https://orcid.org/0000-0001-9990-8331 +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nBone cells, also known as osteocytes, form the building blocks of the skeletal system. They represent the most common type of bone cell, making up approximately 95% of the total bone cell population in mature adult bone tissue. Osteocytes are a stellate shape with numerous long, slender dendritic processes.\nThe formation of bone is a complex process involving the action of osteoclasts - cells that break down and reabsorb old bone, followed by osteoblasts that rebuild the bone. Osteocytes serve as coordinators for these two types of bone cells to ensure a balance in the bone remodeling process, contributing to maintaining both bone strength and mineral homeostasis.\nThe primary functions of osteocytes involve the creation, maintenance, and repair of bone tissue. They ensure that bone remodeling is performed by forming a network within the bone and communicating with other cells to help them respond to mechanical strain and damage.\nA remarkable aspect of osteocytes is their ability to perceive mechanical forces, translating them into biochemical signals that regulate bone remodeling and adaptation. Defects in osteocyte function, aside from other bone cells, have been associated with several bone disorders such as osteoporosis, renal osteodystrophy, and skeletal manifestations of diabetes." xsd:string {xref="DOI:10.1007/s00795-015-0099-y", xref="DOI:10.1007/s11914-012-0105-4", xref="DOI:10.1016/j.jot.2021.04.005", xref="DOI:10.1038/s41413-020-0099-y"} creation_date: 2011-11-16T04:28:16Z [Term] id: CL:0001060 name: hematopoietic oligopotent progenitor cell, lineage-negative def: "A hematopoietic oligopotent progenitor cell that has the ability to differentiate into limited cell types but lacks lineage cell markers and self renewal capabilities. Cell lacks hematopoeitic lineage markers." [GOC:tfm, PMID:19022770] +subset: human_subset +subset: mouse_subset is_a: CL:0002032 ! hematopoietic oligopotent progenitor cell intersection_of: CL:0002032 ! hematopoietic oligopotent progenitor cell intersection_of: bearer_of PATO:0001401 ! oligopotent @@ -1794,6 +2000,8 @@ def: "A lymphocyte that lacks characteristic T cell, B cell, myeloid cell, and d subset: blood_and_immune_upper_slim subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset is_a: CL:0000542 ! lymphocyte intersection_of: CL:0000542 ! lymphocyte intersection_of: capable_of GO:0001816 ! cytokine production @@ -1813,6 +2021,8 @@ id: CL:0001067 name: group 1 innate lymphoid cell def: "An innate lymphoid cell that is capable of producing the type 1 cytokine IFN-gamma, but not Th2 or Th17 cell-associated cytokines." [GOC:add, GOC:dsd, PMID:23348417] subset: human_reference_atlas +subset: human_subset +subset: mouse_subset is_a: CL:0001065 ! innate lymphoid cell intersection_of: CL:0001065 ! innate lymphoid cell intersection_of: capable_of GO:0032609 ! type II interferon production @@ -1826,6 +2036,8 @@ id: CL:0002009 name: macrophage dendritic cell progenitor def: "A progenitor cell that can give rise to plasmacytoid and myeloid dendritic cells, and to monocytes and macrophages." [GOC:tfm, PMID:19273628] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "MDP" EXACT [] is_a: CL:0000763 ! myeloid cell is_a: CL:0002032 {is_inferred="true"} ! hematopoietic oligopotent progenitor cell @@ -1844,6 +2056,8 @@ id: CL:0002031 name: hematopoietic lineage restricted progenitor cell def: "A hematopoietic progenitor cell that is capable of developing into only one lineage of hematopoietic cells." [GOC:tfm, PMID:19022770] subset: blood_and_immune_upper_slim +subset: human_subset +subset: mouse_subset is_a: CL:0000255 ! eukaryotic cell is_a: CL:0008001 ! hematopoietic precursor cell intersection_of: CL:0000988 ! hematopoietic cell @@ -1860,6 +2074,8 @@ name: hematopoietic oligopotent progenitor cell def: "A hematopoietic oligopotent progenitor cell that has the ability to differentiate into limited cell types but lacks lineage cell markers and self renewal capabilities." [GOC:tfm, https://orcid.org/0000-0001-5208-3432, PMID:19022770] comment: This cell type is intended to be compatible with any vertebrate hematopoietic oligopotent progenitor cell. For mammalian hematopoietic oligopotent progenitor cells known to be lineage-negative, please use the term 'hematopoietic oligopotent progenitor cell' (CL_0001060). subset: blood_and_immune_upper_slim +subset: human_subset +subset: mouse_subset is_a: CL:0000255 ! eukaryotic cell is_a: CL:0008001 ! hematopoietic precursor cell intersection_of: CL:0000988 ! hematopoietic cell @@ -1873,6 +2089,8 @@ creation_date: 2010-01-06T03:43:27Z id: CL:0002077 name: ecto-epithelial cell def: "An epithelial cell derived from ectoderm." [FMA:69074, GOC:tfm] +subset: human_subset +subset: mouse_subset xref: FMA:69074 xref: ZFA:0009385 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000066 ! epithelial cell @@ -1888,6 +2106,8 @@ name: bone marrow cell def: "A cell found in the bone marrow. This can include fibroblasts, macrophages, adipocytes, osteoblasts, osteoclasts, endothelial cells and hematopoietic cells." [GOC:tfm, ISBN:0618947256] comment: MH consider whether bone marrow cells are bone cells in the structural sense vs. being part of bone organ sense. subset: cellxgene_subset +subset: human_subset +subset: mouse_subset xref: BTO:0004850 xref: FMA:83621 xref: MESH:D001854 @@ -1902,6 +2122,8 @@ creation_date: 2010-07-22T04:48:15Z id: CL:0002194 name: monopoietic cell def: "A cell involved in the formation of a monocyte (monopoiesis)." [GOC:tfm] +subset: human_subset +subset: mouse_subset xref: FMA:83552 is_a: CL:0000839 {is_inferred="true"} ! myeloid lineage restricted progenitor cell intersection_of: CL:0000839 ! myeloid lineage restricted progenitor cell @@ -1914,6 +2136,8 @@ creation_date: 2010-08-30T01:27:48Z id: CL:0002242 name: nucleate cell def: "A cell containing at least one nucleus." [GOC:tfm] +subset: human_subset +subset: mouse_subset xref: FMA:67513 is_a: CL:0000000 ! cell intersection_of: CL:0000000 ! cell @@ -1927,6 +2151,8 @@ id: CL:0002319 name: neural cell def: "A cell that is part of the nervous system." [GOC:tfm, ISBN:0618947256] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset xref: CALOHA:TS-2040 xref: FMA:70333 is_a: CL:0000255 ! eukaryotic cell @@ -1941,6 +2167,8 @@ id: CL:0002320 name: connective tissue cell def: "A cell of the supporting or framework tissue of the body, arising chiefly from the embryonic mesoderm and including adipose tissue, cartilage, and bone." [GOC:tfm, ISBN:0618947256] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset xref: CALOHA:TS-2096 xref: FMA:63875 xref: MESH:D003239 @@ -1956,18 +2184,25 @@ creation_date: 2010-09-15T03:01:54Z id: CL:0002321 name: embryonic cell (metazoa) def: "A cell of the embryo." [FMA:0618947256] +subset: human_subset +subset: mouse_subset xref: CALOHA:TS-0263 xref: FMA:82840 +xref: https://cellxgene.cziscience.com/cellguide/CL_0002321 xref: WBbt:0007028 xref: ZFA:0007089 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000000 ! cell property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nEmbryonic cells in metazoans, which include all multicellular animals, are biological units in their earliest developmental stages from conception until the organism is fully formed. \nThey are derived from a fertilized egg, which undergoes a series of cell divisions to produce a multicellular organism. During the early phases of embryonic development, these cells exhibit pluripotency, meaning they possess the potential to differentiate into a diverse array of specialized cell types that constitute different body tissues and structures. \nThe balance between cell proliferation and differentiation in embryonic cells is crucial for successful development. When cells continue to divide without differentiating, overgrowth may occur leading to conditions such as teratomas (tumors of embryonic cells). Conversely, if cell differentiation proceeds at the expense of cell proliferation, developmental anomalies could occur regarding size or mass of the organism or its parts." xsd:string {xref="DOI:10.1002/iub.1404", xref="DOI:10.1093/molehr/gan048", xref="https://www.ncbi.nlm.nih.gov/books/NBK9906/"} creation_date: 2010-09-15T03:39:21Z [Term] id: CL:0002372 name: myotube def: "A transversely striated, multinucleated syncytial muscle cell, formed by the fusion of myoblasts during muscle development." [GOC:dos, GOC:tfm, ISBN:0323052908, PMID:22274696] +subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "myofiber" EXACT [FBbt:00005812] synonym: "myofibril" EXACT [FBbt:00005812] xref: FBbt:00005812 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} @@ -1986,6 +2221,8 @@ id: CL:0002494 name: cardiocyte def: "A cell located in the heart, including both muscle and non muscle cells." [GOC:tfm] comment: From Onard of the FMA: Cardiac muscle cell or cardiac myocyte is a striated muscle cell. Cardiocyte on the other hand is any cell in the heart which includes cells other than muscle cells (e.g. endothelial cell of endocardium). Unless there is a consensus among anatomists that cardiocytes refer only to muscle cells, we will treat them as a general class of cells in the heart. +subset: human_subset +subset: mouse_subset synonym: "heart cell" EXACT [] xref: BTO:0001539 xref: CALOHA:TS-0115 @@ -2003,6 +2240,8 @@ id: CL:0007001 name: skeletogenic cell def: "Cell that has the potential to form a skeletal cell type (e.g. cells in periosteum, cells in marrow) and produce extracellular matrix (often mineralized) and skeletal tissue (often mineralized)." [GO_REF:0000034] comment: Needs logical definition. Should be capable_of skeletal system morphogenesis? or skeletal tissue development? needs to be added to GO. NOTES:a cell type of the early embryo (see also: mesenchymal cells) that will give rise to mineralized connective tissue. Scleroblasts can differentiate into osteoblasts (bone-forming cells), chondroblasts (cartilage-forming cells), odontoblasts (dentin-forming cells), ameloblasts (enamel-forming cells). The mesenchymal cells developing into osteoblasts and chondroblasts are derived from the mesoderm. Those developing into odontoblasts are neural crest cells. Those developing into ameloblasts are derived from the ectoderm. (http://www.copewithcytokines.de/cope.cgi?key=scleroblasts) +subset: human_subset +subset: mouse_subset synonym: "scleroblast" EXACT [GO_REF:0000034] is_a: CL:0000000 ! cell property_value: terms:contributor https://orcid.org/0000-0001-9114-8737 @@ -2012,6 +2251,8 @@ creation_date: 2012-06-15T02:51:27Z id: CL:0007004 name: premigratory neural crest cell def: "Cell that is part of the neural crest region of the neuroepithelium, prior to migration. Note that not all premigratory neural crest cells may become migratory neural crest cells." [UBERONREF:0000002] +subset: human_subset +subset: mouse_subset xref: ZFA:0007084 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0011012 ! neural crest cell relationship: part_of UBERON:0002342 ! neural crest @@ -2023,6 +2264,8 @@ creation_date: 2012-06-27T08:27:35Z id: CL:0008000 name: non-striated muscle cell def: "Any muscle cell in which the fibers are not organised into sarcomeres." [GOC:DOS] +subset: human_subset +subset: mouse_subset is_a: CL:0000187 ! muscle cell [Term] @@ -2030,6 +2273,8 @@ id: CL:0008001 name: hematopoietic precursor cell def: "Any hematopoietic cell that is a precursor of some other hematopoietic cell type." [GOC:dos] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset is_a: CL:0000988 ! hematopoietic cell [Term] @@ -2037,6 +2282,8 @@ id: CL:0008002 name: skeletal muscle fiber def: "A transversely striated, synctial cell of skeletal muscle. It is formed when proliferating myoblasts exit the cell cycle, differentiate and fuse." [GOC:tfm, ISBN:0323052908] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset xref: MESH:D018485 is_a: CL:0000188 ! cell of skeletal muscle is_a: CL:0002372 ! myotube @@ -2051,6 +2298,8 @@ relationship: RO:0002202 CL:0000515 ! develops from skeletal muscle myoblast id: CL:0008007 name: visceral muscle cell def: "A muscle cell that is part of some visceral muscle." [GOC:dos] +subset: human_subset +subset: mouse_subset xref: FBbt:00005070 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} is_a: CL:0000187 ! muscle cell intersection_of: CL:0000187 ! muscle cell @@ -2063,6 +2312,8 @@ name: mesenchymal cell def: "A non-polarised cell precursor cell that is part of some mesenchyme, is associated with the cell matrix but is not connected to other cells and is capable of migration." [] subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "mesenchyme cell" EXACT [] is_a: CL:0000219 ! motile cell is_a: CL:0000255 ! eukaryotic cell @@ -2074,6 +2325,8 @@ property_value: RO:0002175 NCBITaxon:9606 id: CL:0008028 name: visual system neuron def: "Any neuron that is capable of part of some visual perception." [FBC:Autogenerated] +subset: human_subset +subset: mouse_subset is_a: CL:0000540 ! neuron intersection_of: CL:0000540 ! neuron intersection_of: capable_of_part_of GO:0007601 ! visual perception @@ -2086,6 +2339,8 @@ id: CL:0009004 name: retinal cell def: "Any cell in the retina, the innermost layer or coating at the back of the eyeball, which is sensitive to light and in which the optic nerve terminates." [GOC:pr] subset: general_cell_types_upper_slim +subset: human_subset +subset: mouse_subset xref: PMID:10702418 is_a: CL:0002319 ! neural cell intersection_of: CL:0002319 ! neural cell @@ -2096,6 +2351,8 @@ relationship: part_of UBERON:0005388 ! photoreceptor array id: CL:0010017 name: zygote def: "A zygote in a plant or an animal." [] +subset: human_subset +subset: mouse_subset xref: MESH:D015053 is_a: CL:0000000 ! cell property_value: seeAlso https://github.com/obophenotype/cell-ontology/issues/786 @@ -2104,6 +2361,8 @@ property_value: seeAlso https://github.com/obophenotype/cell-ontology/issues/786 id: CL:0010021 name: cardiac myoblast def: "Any myoblast that develops into some cardiac muscle cell." [FBC:Autogenerated] +subset: human_subset +subset: mouse_subset xref: MESH:D032386 is_a: CL:0000056 ! myoblast intersection_of: CL:0000056 ! myoblast @@ -2115,16 +2374,20 @@ id: CL:0011012 name: neural crest cell def: "A cell of the neural crest. Neural crest cells are multipotent. Premigratory neural crest cells are found at the neural plate boarder, some of which will undergo ectomesynchymal transition and delamination to form migratory neural crest cells." [https://orcid.org/0000-0001-5208-3432, https://orcid.org/0000-0002-9900-7880] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset xref: https://cellxgene.cziscience.com/cellguide/CL_0011012 is_a: CL:0000048 ! multi fate stem cell is_a: CL:0002321 ! embryonic cell (metazoa) -property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional.\n\nNeural crest cells are a group of transient and highly migratory cells that originate from the neuroectoderm during the early stages of embryonic development. They are multipotent cells with an exceptional degree of plasticity, capable of differentiating into various somatic cell types and therefore play a fundamental role in the formation of various organs and tissues, making them critical contributors to the developing embryo. \nAfter the initiation of neurulation (the formation of the neural tube) neural crest cells start to undergo epithelial-to-mesenchymal transition and delaminate and migrate from the dorsal neural tube to several regions throughout the embryo. They differentiate into a range of diverse cell types, such as neurons and glial cells of the peripheral nervous system, including sensory and autonomic neurons. They also contribute to the formation of adrenal glands, pigment cells in the skin (melanocytes), cardiac structures, including parts of the heart septum and major arteries, as well as bones and cartilage of the face and skull.\nDisorders or aberrations in the development or migration of the neural crest cells can lead to serious congenital malformations, such as neurocristopathies, including Hirschsprung disease, neuroblastoma, and neurofibromatosis." xsd:string {xref="DOI:10.1002/dvg.23276", xref="DOI:10.1242/dev.193193", xref="DOI:10.3389/fcell.2020.00635/full", xref="https://doi.org/10.1016/j.ydbio.2011.12.042"} +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nNeural crest cells are a group of transient and highly migratory cells that originate from the neuroectoderm during the early stages of embryonic development. They are multipotent cells with an exceptional degree of plasticity, capable of differentiating into various somatic cell types and therefore play a fundamental role in the formation of various organs and tissues, making them critical contributors to the developing embryo. \nAfter the initiation of neurulation (the formation of the neural tube) neural crest cells start to undergo epithelial-to-mesenchymal transition and delaminate and migrate from the dorsal neural tube to several regions throughout the embryo. They differentiate into a range of diverse cell types, such as neurons and glial cells of the peripheral nervous system, including sensory and autonomic neurons. They also contribute to the formation of adrenal glands, pigment cells in the skin (melanocytes), cardiac structures, including parts of the heart septum and major arteries, as well as bones and cartilage of the face and skull.\nDisorders or aberrations in the development or migration of the neural crest cells can lead to serious congenital malformations, such as neurocristopathies, including Hirschsprung disease, neuroblastoma, and neurofibromatosis." xsd:string {xref="DOI:10.1002/dvg.23276", xref="DOI:10.1242/dev.193193", xref="DOI:10.3389/fcell.2020.00635/full", xref="https://doi.org/10.1016/j.ydbio.2011.12.042"} [Term] id: CL:0011026 name: progenitor cell def: "A precursor cell that has a tendency to differentiate into a specific type of cell. They are descendants of stem cells, only they are more constrained in their differentiation potential or capacity for self-renewal, and are often more limited in both senses." [https://doi.org/10.1016/B978-0-12-409503-8.00002-0, ISBN:978-1-62808-994-3] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset is_a: CL:0000255 ! eukaryotic cell is_a: CL:0011115 ! precursor cell intersection_of: CL:0011115 ! precursor cell @@ -2138,6 +2401,8 @@ name: precursor cell def: "A cell that, by division or terminal differentiation, can give rise to other cell types." [GOC:dos] comment: Work is needed on GO 'cell differentiation' before it is clear whether the equivalent class definition 'native cell' that capable_of some 'cell differentiation' works. Also, may want to consider merging this with non-terminally differentiated cell. subset: cellxgene_subset +subset: human_subset +subset: mouse_subset is_a: CL:0000000 ! cell intersection_of: CL:0000000 ! cell intersection_of: capable_of GO:0030154 ! cell differentiation @@ -2169,6 +2434,8 @@ creation_date: 2009-12-22T04:24:54Z id: CL:1001610 name: bone marrow hematopoietic cell def: "Hematopoietic cells resident in the bone marrow. Include: hematopoietic stem cells (lymphoid stem cells and myeloid stem cells) and the precursor cells for thrombocytes, erythrocytes, basophils, neutrophils, eosinophils, monocytes and lymphocytes." [NPX:PDR] +subset: human_subset +subset: mouse_subset synonym: "bone marrow hematopoietic cells" RELATED [CALOHA:TS-2109] synonym: "bone marrow poietic cells" RELATED [CALOHA:TS-2109] xref: CALOHA:TS-2109 @@ -2182,6 +2449,8 @@ relationship: part_of UBERON:0012429 ! hematopoietic tissue id: CL:4052002 name: syncytial cell def: "A multinucleate cell formed by the fusion of multiple uninuclear cells through plasma membrane fusion. This process leads to a single large cell containing multiple nuclei within a shared cytoplasm." [PMID:20851884, Wikipedia:Syncytium] +subset: human_subset +subset: mouse_subset synonym: "SC" RELATED OMO:0003000 [PMID:9067520] synonym: "syncytium" EXACT [WBbt:0008074] is_a: CL:0000228 ! multinucleate cell @@ -2214,16 +2483,13 @@ intersection_of: has_part GO:0045026 ! plasma membrane fusion id: GO:0000785 name: chromatin namespace: cellular_component -alt_id: GO:0000789 -alt_id: GO:0000790 -alt_id: GO:0005717 def: "The ordered and organized complex of DNA, protein, and sometimes RNA, that forms the chromosome." [GOC:elh, PMID:20404130] comment: Chromosomes include parts that are not part of the chromatin. Examples include the kinetochore. synonym: "chromosome scaffold" RELATED [] synonym: "cytoplasmic chromatin" NARROW [] synonym: "nuclear chromatin" NARROW [] xref: NIF_Subcellular:sao1615953555 -is_a: GO:0110165 ! cellular anatomical entity +is_a: GO:0110165 ! cellular anatomical structure relationship: part_of GO:0005694 ! chromosome property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28301" xsd:anyURI @@ -2231,8 +2497,6 @@ property_value: term_tracker_item "https://github.com/geneontology/go-ontology/i id: GO:0000791 name: euchromatin namespace: cellular_component -alt_id: GO:0005719 -alt_id: GO:0035327 def: "A dispersed and relatively uncompacted form of chromatin that is in a transcription-competent conformation." [PMID:32017156] synonym: "nuclear euchromatin" RELATED [] synonym: "transcriptionally active chromatin" EXACT [] @@ -2245,8 +2509,6 @@ property_value: term_tracker_item "https://github.com/geneontology/go-ontology/i id: GO:0000792 name: heterochromatin namespace: cellular_component -alt_id: GO:0005720 -alt_id: GO:0035328 def: "A compact and highly condensed form of chromatin that is refractory to transcription." [PMID:32017156] synonym: "nuclear heterochromatin" NARROW [] synonym: "transcriptionally inactive chromatin" EXACT [] @@ -2359,10 +2621,6 @@ property_value: term_tracker_item "https://github.com/geneontology/go-ontology/i id: GO:0001816 name: cytokine production namespace: biological_process -alt_id: GO:0042032 -alt_id: GO:0042089 -alt_id: GO:0042107 -alt_id: GO:0050663 def: "The appearance of a cytokine due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels." [GOC:add, ISBN:0781735149] comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select one of the 'regulation' children terms. subset: gocheck_do_not_annotate @@ -2390,7 +2648,6 @@ relationship: part_of GO:0016331 ! morphogenesis of embryonic epithelium id: GO:0001841 name: neural tube formation namespace: biological_process -alt_id: GO:0001679 def: "The formation of a tube from the flat layer of ectodermal cells known as the neural plate. This will give rise to the central nervous system." [GOC:dph, ISBN:0878932437] synonym: "neural tube morphogenesis" EXACT [GOC:dph] synonym: "neurulation" EXACT [] @@ -2508,8 +2765,6 @@ property_value: RO:0002161 NCBITaxon:4895 id: GO:0002377 name: immunoglobulin production namespace: biological_process -alt_id: GO:0002378 -alt_id: GO:0048305 def: "The appearance of immunoglobulin due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels." [GOC:add, ISBN:0781735149] comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select one of the 'regulation' children terms. subset: gocheck_do_not_annotate @@ -2533,8 +2788,6 @@ is_a: GO:0010467 ! gene expression id: GO:0002443 name: leukocyte mediated immunity namespace: biological_process -alt_id: GO:0019723 -alt_id: GO:0042087 def: "Any process involved in the carrying out of an immune response by a leukocyte." [GO_REF:0000022, GOC:add, ISBN:0781735149] synonym: "cell-mediated immune response" RELATED [] synonym: "cellular immune response" RELATED [] @@ -2701,7 +2954,6 @@ is_a: GO:0003013 ! circulatory system process id: GO:0005575 name: cellular_component namespace: cellular_component -alt_id: GO:0008372 def: "A location, relative to cellular compartments and structures, occupied by a macromolecular machine. There are three types of cellular components described in the gene ontology: (1) the cellular anatomical entity where a gene product carries out a molecular function (e.g., plasma membrane, cytoskeleton) or membrane-enclosed compartments (e.g., mitochondrion); (2) virion components, where viral proteins act, and (3) the stable macromolecular complexes of which gene product are parts (e.g., the clathrin complex)." [GOC:pdt] comment: Note that, in addition to forming the root of the cellular component ontology, this term is recommended for the annotation of gene products whose cellular component is unknown. When this term is used for annotation, it indicates that no information was available about the cellular component of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this. subset: goslim_candida @@ -2739,7 +2991,7 @@ subset: goslim_prokaryote_ribbon subset: goslim_yeast synonym: "extracellular" EXACT [] xref: Wikipedia:Extracellular -is_a: GO:0110165 ! cellular anatomical entity +is_a: GO:0110165 ! cellular anatomical structure [Term] id: GO:0005581 @@ -2764,8 +3016,6 @@ is_a: GO:0098651 ! basement membrane collagen trimer id: GO:0005604 name: basement membrane namespace: cellular_component -alt_id: GO:0005605 -alt_id: GO:0008003 def: "A collagen-containing extracellular matrix consisting of a thin layer of dense material found in various animal tissues interposed between the cells and the adjacent connective tissue. It consists of the basal lamina plus an associated layer of reticulin fibers." [ISBN:0198547684, PMID:22505934] comment: Note that this term has no relationship to 'membrane ; GO:0016020' because the basement membrane is not a lipid bilayer. synonym: "basal lamina" RELATED [] @@ -2789,7 +3039,7 @@ synonym: "nucleocytoplasm" RELATED [GOC:mah] synonym: "protoplasm" EXACT [] synonym: "protoplast" RELATED [GOC:mah] xref: Wikipedia:Intracellular -is_a: GO:0110165 ! cellular anatomical entity +is_a: GO:0110165 ! cellular anatomical structure relationship: part_of CL:0000000 ! cell property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/17776" xsd:anyURI @@ -2841,7 +3091,7 @@ synonym: "chromatid" RELATED [] synonym: "interphase chromosome" NARROW [] synonym: "prophase chromosome" NARROW [] xref: Wikipedia:Chromosome -is_a: GO:0043232 ! intracellular non-membrane-bounded organelle +is_a: GO:0043232 ! intracellular membraneless organelle [Term] id: GO:0005730 @@ -2857,7 +3107,7 @@ subset: goslim_plant subset: goslim_yeast xref: NIF_Subcellular:sao1820400233 xref: Wikipedia:Nucleolus -is_a: GO:0043232 ! intracellular non-membrane-bounded organelle +is_a: GO:0043232 ! intracellular membraneless organelle relationship: part_of GO:0031981 ! nuclear lumen [Term] @@ -2875,7 +3125,7 @@ subset: goslim_prokaryote subset: goslim_prokaryote_ribbon subset: goslim_yeast xref: Wikipedia:Cytoplasm -is_a: GO:0110165 ! cellular anatomical entity +is_a: GO:0110165 ! cellular anatomical structure relationship: part_of GO:0005622 ! intracellular anatomical structure property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/23023" xsd:anyURI @@ -2926,8 +3176,6 @@ relationship: part_of GO:0005737 ! cytoplasm id: GO:0005886 name: plasma membrane namespace: cellular_component -alt_id: GO:0005887 -alt_id: GO:0005904 def: "The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins." [ISBN:0716731363] subset: goslim_agr subset: goslim_candida @@ -2973,7 +3221,6 @@ property_value: term_tracker_item "https://github.com/geneontology/go-ontology/i id: GO:0006259 name: DNA metabolic process namespace: biological_process -alt_id: GO:0055132 def: "Any cellular metabolic process involving deoxyribonucleic acid. This is one of the two main types of nucleic acid, consisting of a long, unbranched macromolecule formed from one, or more commonly, two, strands of linked deoxyribonucleotides." [ISBN:0198506732] subset: goslim_agr subset: goslim_candida @@ -3005,9 +3252,6 @@ is_a: GO:0006259 ! DNA metabolic process id: GO:0006412 name: translation namespace: biological_process -alt_id: GO:0006416 -alt_id: GO:0006453 -alt_id: GO:0043037 def: "The cellular metabolic process in which a protein is formed, using the sequence of a mature mRNA or circRNA molecule to specify the sequence of amino acids in a polypeptide chain. Translation is mediated by the ribosome, and begins with the formation of a ternary complex between aminoacylated initiator methionine tRNA, GTP, and initiation factor 2, which subsequently associates with the small subunit of the ribosome and an mRNA or circRNA. Translation ends with the release of a polypeptide chain from the ribosome." [GOC:go_curators] subset: goslim_candida subset: goslim_chembl @@ -3036,15 +3280,13 @@ relationship: starts_with GO:0006413 ! translational initiation id: GO:0006413 name: translational initiation namespace: biological_process -alt_id: GO:0006440 -alt_id: GO:0006454 def: "The process preceding formation of the peptide bond between the first two amino acids of a protein. This includes the formation of a complex of the ribosome, mRNA or circRNA, and an initiation complex that contains the first aminoacyl-tRNA." [ISBN:019879276X] subset: goslim_yeast synonym: "biopolymerisation" BROAD [] synonym: "biopolymerization" BROAD [] synonym: "protein synthesis initiation" BROAD [] synonym: "translation initiation" EXACT [] -is_a: GO:0044237 ! cellular metabolic process +is_a: GO:0008152 ! metabolic process relationship: part_of GO:0006412 ! translation relationship: starts_with GO:0001677 ! formation of translation initiation ternary complex @@ -3052,8 +3294,6 @@ relationship: starts_with GO:0001677 ! formation of translation initiation terna id: GO:0006414 name: translational elongation namespace: biological_process -alt_id: GO:0006442 -alt_id: GO:0006455 def: "The successive addition of amino acid residues to a nascent polypeptide chain during protein biosynthesis." [GOC:ems] subset: goslim_yeast synonym: "protein synthesis elongation" BROAD [] @@ -3065,8 +3305,6 @@ relationship: part_of GO:0006412 ! translation id: GO:0006415 name: translational termination namespace: biological_process -alt_id: GO:0006443 -alt_id: GO:0006456 def: "The process resulting in the release of a polypeptide chain from the ribosome, usually in response to a termination codon (UAA, UAG, or UGA in the universal genetic code)." [GOC:hjd, ISBN:019879276X] synonym: "protein synthesis termination" BROAD [] synonym: "translation termination" EXACT [] @@ -3078,9 +3316,6 @@ relationship: part_of GO:0006412 ! translation id: GO:0006810 name: transport namespace: biological_process -alt_id: GO:0015457 -alt_id: GO:0015460 -alt_id: GO:0044765 def: "The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter or a transporter complex, a pore or a motor protein." [GOC:dos, GOC:dph, GOC:jl, GOC:mah] comment: Note that this term should not be used for direct annotation. It should be possible to make a more specific annotation to one of the children of this term, for e.g. to transmembrane transport, to microtubule-based transport or to vesicle-mediated transport. subset: gocheck_do_not_annotate @@ -3095,7 +3330,6 @@ subset: goslim_prokaryote_ribbon synonym: "single-organism transport" RELATED [] is_a: GO:0051234 ! establishment of localization property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/20292" xsd:anyURI -created_by: jl creation_date: 2012-12-13T16:25:32Z [Term] @@ -3113,8 +3347,6 @@ is_a: GO:0006810 ! transport id: GO:0006887 name: exocytosis namespace: biological_process -alt_id: GO:0016194 -alt_id: GO:0016195 def: "A process of secretion by a cell that results in the release of intracellular molecules (e.g. hormones, matrix proteins) contained within a membrane-bounded vesicle. Exocytosis can occur either by full fusion, when the vesicle collapses into the plasma membrane, or by a kiss-and-run mechanism that involves the formation of a transient contact, a pore, between a granule (for example of chromaffin cells) and the plasma membrane. The latter process most of the time leads to only partial secretion of the granule content. Exocytosis begins with steps that prepare vesicles for fusion with the membrane (tethering and docking) and ends when molecules are secreted from the cell." [GOC:mah, ISBN:0716731363, PMID:22323285] subset: goslim_yeast synonym: "nonselective vesicle exocytosis" RELATED [] @@ -3131,9 +3363,6 @@ relationship: process_has_causal_agent GO:0070382 ! exocytic vesicle id: GO:0006897 name: endocytosis namespace: biological_process -alt_id: GO:0016193 -alt_id: GO:0016196 -alt_id: GO:0098701 def: "A vesicle-mediated transport process in which cells take up external materials or membrane constituents by the invagination of a part of the plasma membrane to form a new membrane-bounded vesicle." [GOC:mah, ISBN:0198506732, ISBN:0716731363, Wikipedia:Endocytosis] subset: goslim_yeast synonym: "endocytic import into cell" EXACT [] @@ -3153,8 +3382,6 @@ property_value: term_tracker_item "https://github.com/geneontology/go-ontology/i id: GO:0006900 name: vesicle budding from membrane namespace: biological_process -alt_id: GO:0006902 -alt_id: GO:1902591 def: "The evagination of a membrane, resulting in formation of a vesicle." [GOC:jid, GOC:tb] synonym: "membrane evagination" EXACT [] synonym: "nonselective vesicle assembly" RELATED [] @@ -3166,7 +3393,6 @@ synonym: "vesicle formation" EXACT [] is_a: GO:0016050 ! vesicle organization is_a: GO:0061024 ! membrane organization relationship: part_of GO:0016192 ! vesicle-mediated transport -created_by: jl creation_date: 2013-12-19T15:26:17Z [Term] @@ -3226,7 +3452,6 @@ is_a: GO:0050896 ! response to stimulus id: GO:0006996 name: organelle organization namespace: biological_process -alt_id: GO:1902589 def: "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of an organelle within a cell. An organelle is an organized structure of distinctive morphology and function. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton. Excludes the plasma membrane." [GOC:mah] comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. subset: gocheck_do_not_annotate @@ -3241,7 +3466,6 @@ intersection_of: GO:0016043 ! cellular component organization intersection_of: results_in_organization_of GO:0043226 ! organelle relationship: results_in_organization_of GO:0043226 ! organelle property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27189" xsd:anyURI -created_by: jl creation_date: 2013-12-19T15:25:51Z [Term] @@ -3397,7 +3621,6 @@ is_a: GO:0050953 ! sensory perception of light stimulus id: GO:0008015 name: blood circulation namespace: biological_process -alt_id: GO:0070261 def: "The flow of blood through the body of an animal, enabling the transport of nutrients to the tissues and the removal of waste products." [GOC:mtg_heart, ISBN:0192800825] subset: goslim_pir synonym: "hemolymph circulation" RELATED [] @@ -3407,9 +3630,6 @@ is_a: GO:0003013 ! circulatory system process id: GO:0008150 name: biological_process namespace: biological_process -alt_id: GO:0000004 -alt_id: GO:0007582 -alt_id: GO:0044699 def: "A biological process is the execution of a genetically-encoded biological module or program. It consists of all the steps required to achieve the specific biological objective of the module. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence." [GOC:pdt] comment: Note that, in addition to forming the root of the biological process ontology, this term is recommended for the annotation of gene products whose biological process is unknown. When this term is used for annotation, it indicates that no information was available about the biological process of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this. subset: goslim_candida @@ -3425,16 +3645,13 @@ synonym: "single organism process" RELATED [] synonym: "single-organism process" RELATED [] xref: Wikipedia:Biological_process property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/24968" xsd:anyURI -created_by: jl creation_date: 2012-09-19T15:05:24Z [Term] id: GO:0008152 name: metabolic process namespace: biological_process -alt_id: GO:0044236 -alt_id: GO:0044710 -def: "The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation." [GOC:go_curators, ISBN:0198547684] +def: "A cellular process consisting of the biochemical pathways by which a living organism transforms chemical substances. This includes including anabolism (biosynthetic process) and catabolism (catabolic process). Metabolic processes includes the transformation of small molecules, as well macromolecular processes such as DNA repair and replication, protein synthesis and degradation." [GOC:go_curators, ISBN:0198547684] comment: Note that metabolic processes do not include single functions or processes such as protein-protein interactions, protein-nucleic acids, nor receptor-ligand interactions. subset: gocheck_do_not_annotate subset: goslim_chembl @@ -3443,25 +3660,19 @@ subset: goslim_metagenomics subset: goslim_pir subset: goslim_plant subset: goslim_prokaryote_ribbon -synonym: "metabolic process resulting in cell growth" NARROW [] synonym: "metabolism" EXACT [] -synonym: "metabolism resulting in cell growth" NARROW [] -synonym: "multicellular organism metabolic process" NARROW [] -synonym: "single-organism metabolic process" RELATED [] xref: Wikipedia:Metabolism -is_a: GO:0008150 ! biological_process +is_a: GO:0009987 ! cellular process disjoint_from: GO:0051179 ! localization property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/26424" xsd:anyURI -created_by: jl +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28932" xsd:anyURI creation_date: 2012-10-17T15:46:40Z [Term] id: GO:0009058 name: biosynthetic process namespace: biological_process -alt_id: GO:0044274 -alt_id: GO:0044711 -def: "The chemical reactions and pathways resulting in the formation of substances; typically the energy-requiring part of metabolism in which simpler substances are transformed into more complex ones." [GOC:curators, ISBN:0198547684] +def: "A cellular process consisting of the biochemical pathways by which a living organism synthesizes chemical substances. This typically represents the energy-requiring part of metabolism in which simpler substances are transformed into more complex ones." [GOC:curators, ISBN:0198547684] subset: goslim_chembl subset: goslim_metagenomics subset: goslim_plant @@ -3474,14 +3685,13 @@ synonym: "single-organism biosynthetic process" RELATED [] synonym: "synthesis" EXACT [] xref: Wikipedia:Anabolism is_a: GO:0008152 ! metabolic process -created_by: jl +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28932" xsd:anyURI creation_date: 2012-10-17T15:52:18Z [Term] id: GO:0009059 name: macromolecule biosynthetic process namespace: biological_process -alt_id: GO:0043284 def: "The chemical reactions and pathways resulting in the formation of a macromolecule, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass." [GOC:mah] comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. subset: gocheck_do_not_annotate @@ -3491,8 +3701,8 @@ synonym: "macromolecule anabolism" EXACT [] synonym: "macromolecule biosynthesis" EXACT [] synonym: "macromolecule formation" EXACT [] synonym: "macromolecule synthesis" EXACT [] +is_a: GO:0009058 ! biosynthetic process is_a: GO:0043170 ! macromolecule metabolic process -is_a: GO:0044249 ! cellular biosynthetic process property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/15249" xsd:anyURI property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/25418" xsd:anyURI property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27189" xsd:anyURI @@ -3606,7 +3816,6 @@ relationship: part_of GO:0048856 ! anatomical structure development id: GO:0009790 name: embryo development namespace: biological_process -alt_id: GO:0009795 def: "The process whose specific outcome is the progression of an embryo from its formation until the end of its embryonic life stage. The end of the embryonic stage is organism-specific. For example, for mammals, the process would begin with zygote formation and end with birth. For insects, the process would begin at zygote formation and end with larval hatching. For plant zygotic embryos, this would be from zygote formation to the end of seed dormancy. For plant vegetative embryos, this would be from the initial determination of the cell or group of cells to form an embryo until the point when the embryo becomes independent of the parent plant." [GOC:go_curators, GOC:isa_complete, GOC:mtg_sensu] subset: gocheck_do_not_annotate subset: goslim_chembl @@ -3672,9 +3881,6 @@ is_a: GO:0010817 ! regulation of hormone levels id: GO:0009987 name: cellular process namespace: biological_process -alt_id: GO:0008151 -alt_id: GO:0044763 -alt_id: GO:0050875 def: "Any process that is carried out at the cellular level, but not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level." [GOC:go_curators, GOC:isa_complete] comment: This term should not be used for direct annotation. It should be possible to make a more specific annotation to one of the children of this term. subset: gocheck_do_not_annotate @@ -3684,7 +3890,6 @@ synonym: "cell physiology" EXACT [] synonym: "cellular physiological process" EXACT [] synonym: "single-organism cellular process" RELATED [] is_a: GO:0008150 ! biological_process -created_by: jl creation_date: 2012-12-11T16:56:55Z [Term] @@ -3704,12 +3909,10 @@ relationship: results_in_organization_of GO:0012505 ! endomembrane system id: GO:0010324 name: membrane invagination namespace: biological_process -alt_id: GO:1902534 def: "The infolding of a membrane." [GOC:tb] subset: goslim_yeast synonym: "single-organism membrane invagination" RELATED [] is_a: GO:0061024 ! membrane organization -created_by: jl creation_date: 2013-12-02T13:58:34Z [Term] @@ -3738,7 +3941,7 @@ subset: goslim_candida subset: goslim_flybase_ribbon subset: goslim_yeast xref: Wikipedia:Endomembrane_system -is_a: GO:0110165 ! cellular anatomical entity +is_a: GO:0110165 ! cellular anatomical structure relationship: has_part GO:0005773 ! vacuole relationship: has_part GO:0005886 ! plasma membrane relationship: part_of CL:0000000 ! cell @@ -3758,9 +3961,6 @@ relationship: part_of GO:0031982 ! vesicle id: GO:0016020 name: membrane namespace: cellular_component -alt_id: GO:0016021 -alt_id: GO:0098589 -alt_id: GO:0098805 def: "A lipid bilayer along with all the proteins and protein complexes embedded in it and attached to it." [GOC:dos, GOC:mah, ISBN:0815316194] subset: goslim_candida subset: goslim_chembl @@ -3777,7 +3977,7 @@ synonym: "transmembrane" RELATED [GOC:mah] synonym: "whole membrane" NARROW [] xref: Wikipedia:Biological_membrane xref: Wikipedia:Transmembrane_protein -is_a: GO:0110165 ! cellular anatomical entity +is_a: GO:0110165 ! cellular anatomical structure disjoint_from: GO:0031012 ! extracellular matrix creation_date: 2014-03-06T11:37:54Z @@ -3785,8 +3985,6 @@ creation_date: 2014-03-06T11:37:54Z id: GO:0016043 name: cellular component organization namespace: biological_process -alt_id: GO:0044235 -alt_id: GO:0071842 def: "A process that results in the assembly, arrangement of constituent parts, or disassembly of a cellular component." [GOC:ai, GOC:jl, GOC:mah] subset: gocheck_do_not_annotate subset: goslim_agr @@ -3823,7 +4021,6 @@ relationship: results_in_organization_of GO:0031982 ! vesicle id: GO:0016192 name: vesicle-mediated transport namespace: biological_process -alt_id: GO:0006899 def: "A cellular transport process in which transported substances are moved in membrane-bounded vesicles; transported substances are enclosed in the vesicle lumen or located in the vesicle membrane. The process begins with a step that directs a substance to the forming vesicle, and includes vesicle budding and coating. Vesicles are then targeted to, and fuse with, an acceptor membrane." [GOC:ai, GOC:mah, ISBN:08789310662000] subset: goslim_candida subset: goslim_chembl @@ -3918,9 +4115,6 @@ relationship: part_of GO:0007154 ! cell communication id: GO:0019538 name: protein metabolic process namespace: biological_process -alt_id: GO:0006411 -alt_id: GO:0044267 -alt_id: GO:0044268 def: "The chemical reactions and pathways involving a protein. Includes protein modification." [GOC:ma] comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. subset: gocheck_do_not_annotate @@ -3965,7 +4159,6 @@ relationship: process_has_causal_agent CL:0000236 ! B cell id: GO:0019882 name: antigen processing and presentation namespace: biological_process -alt_id: GO:0030333 def: "The process in which an antigen-presenting cell expresses antigen (peptide or lipid) on its cell surface in association with an MHC protein complex." [GO_REF:0000022, GOC:add, ISBN:0781735149, PMID:15771591, PMID:15928678] synonym: "antigen presentation" EXACT [] synonym: "antigen processing" EXACT [] @@ -3989,7 +4182,6 @@ relationship: results_in_development_of UBERON:0001049 ! neural tube id: GO:0022411 name: cellular component disassembly namespace: biological_process -alt_id: GO:0071845 def: "A cellular process that results in the breakdown of a cellular component." [GOC:isa_complete] comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. subset: gocheck_do_not_annotate @@ -4007,7 +4199,6 @@ property_value: term_tracker_item "https://github.com/geneontology/go-ontology/i id: GO:0022414 name: reproductive process namespace: biological_process -alt_id: GO:0044702 def: "A biological process that directly contributes to the process of producing new individuals by one or two organisms. The new individuals inherit some proportion of their genetic material from the parent or parents." [GOC:dph, GOC:isa_complete] subset: gocheck_do_not_annotate subset: goslim_agr @@ -4021,7 +4212,6 @@ synonym: "single organism reproductive process" RELATED [] xref: Wikipedia:Reproduction is_a: GO:0008150 ! biological_process property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27054" xsd:anyURI -created_by: jl creation_date: 2012-09-19T15:56:06Z [Term] @@ -4039,7 +4229,6 @@ relationship: part_of GO:0007586 ! digestion id: GO:0022607 name: cellular component assembly namespace: biological_process -alt_id: GO:0071844 def: "The aggregation, arrangement and bonding together of a cellular component." [GOC:isa_complete] subset: goslim_chembl subset: goslim_euk_cellular_processes_ribbon @@ -4081,8 +4270,6 @@ relationship: results_in_assembly_of GO:1990904 ! ribonucleoprotein complex id: GO:0023052 name: signaling namespace: biological_process -alt_id: GO:0023046 -alt_id: GO:0044700 def: "The entirety of a process in which information is transmitted within a biological system. This process begins with an active signal and ends when a cellular response has been triggered." [GOC:mtg_signal, GOC:mtg_signaling_feb11, GOC:signaling] comment: Note that a signal is any variable property or parameter that serves to convey information, and may be a physical entity such as a gene product or small molecule, a photon, or a change in state such as movement or voltage change. subset: goslim_agr @@ -4100,7 +4287,6 @@ synonym: "signalling" EXACT [] synonym: "signalling process" RELATED [GOC:mah] synonym: "single organism signaling" RELATED [] is_a: GO:0050789 ! regulation of biological process -created_by: jl creation_date: 2010-02-16T09:30:50Z [Term] @@ -4132,7 +4318,7 @@ name: sarcomere namespace: cellular_component def: "The repeating unit of a myofibril in a muscle cell, composed of an array of overlapping thick and thin filaments between two adjacent Z discs." [ISBN:0815316194] xref: Wikipedia:Sarcomere -is_a: GO:0110165 ! cellular anatomical entity +is_a: GO:0110165 ! cellular anatomical structure relationship: part_of GO:0030016 ! myofibril [Term] @@ -4159,7 +4345,7 @@ subset: goslim_agr subset: goslim_drosophila subset: goslim_flybase_ribbon xref: Wikipedia:Cell_junction -is_a: GO:0110165 ! cellular anatomical entity +is_a: GO:0110165 ! cellular anatomical structure property_value: RO:0002161 NCBITaxon:4751 [Term] @@ -4184,7 +4370,6 @@ property_value: term_tracker_item "https://github.com/geneontology/go-ontology/i id: GO:0030098 name: lymphocyte differentiation namespace: biological_process -alt_id: GO:0046650 def: "The process in which a relatively unspecialized precursor cell acquires specialized features of a lymphocyte. A lymphocyte is a leukocyte commonly found in the blood and lymph that has the characteristics of a large nucleus, a neutral staining cytoplasm, and prominent heterochromatin." [CL:0000542, GOC:go_curators] comment: Note that immunologists typically use the word 'development' to refer to cells of B or T cell lineages undergoing the process that GO describes as 'cell differentiation'. synonym: "lymphocyte cell differentiation" EXACT [] @@ -4255,8 +4440,6 @@ property_value: term_tracker_item "https://github.com/geneontology/go-ontology/i id: GO:0030217 name: T cell differentiation namespace: biological_process -alt_id: GO:0042112 -alt_id: GO:0046652 def: "The process in which a precursor cell type acquires characteristics of a more mature T-cell. A T cell is a type of lymphocyte whose definin characteristic is the expression of a T cell receptor complex." [GO_REF:0000022, GOC:jid, GOC:mah] comment: Note that the term 'thymocyte differentiation' was merged into this term because thymocytes are T cells, and thus the term was essentially redundant. Note that immunologists typically use the word 'development' to refer to cells of B or T cell lineages undergoing the process that GO describes as 'cell differentiation'. synonym: "T cell development" RELATED [GOC:add] @@ -4304,7 +4487,7 @@ subset: goslim_drosophila subset: goslim_generic subset: goslim_pir subset: goslim_plant -is_a: GO:0110165 ! cellular anatomical entity +is_a: GO:0110165 ! cellular anatomical structure relationship: part_of CL:0000000 ! cell relationship: part_of GO:0071944 ! cell periphery @@ -4334,7 +4517,6 @@ relationship: results_in_acquisition_of_features_of CL:0000094 ! granulocyte id: GO:0031012 name: extracellular matrix namespace: cellular_component -alt_id: GO:0005578 def: "A structure lying external to one or more cells, which provides structural support, biochemical or biomechanical cues for cells or tissues." [GOC:BHF, GOC:mah, GOC:rph, NIF_Subcellular:nlx_subcell_20090513, PMID:21123617, PMID:28089324] subset: goslim_chembl subset: goslim_drosophila @@ -4394,7 +4576,6 @@ relationship: results_in_organization_of GO:0031143 ! pseudopodium id: GO:0031410 name: cytoplasmic vesicle namespace: cellular_component -alt_id: GO:0016023 def: "A vesicle found in the cytoplasm of a cell." [GOC:ai, GOC:mah, GOC:vesicles] subset: goslim_agr subset: goslim_candida @@ -4416,7 +4597,7 @@ id: GO:0031974 name: membrane-enclosed lumen namespace: cellular_component def: "The enclosed volume within a sealed membrane or between two sealed membranes. Encompasses the volume enclosed by the membranes of a particular organelle, e.g. endoplasmic reticulum lumen, or the space between the two lipid bilayers of a double membrane surrounding an organelle, e.g. nuclear envelope lumen." [GOC:add, GOC:mah] -is_a: GO:0110165 ! cellular anatomical entity +is_a: GO:0110165 ! cellular anatomical structure disjoint_from: GO:0045202 ! synapse [Term] @@ -4431,7 +4612,6 @@ relationship: part_of GO:0005634 ! nucleus id: GO:0031982 name: vesicle namespace: cellular_component -alt_id: GO:0031988 def: "Any small, fluid-filled, spherical organelle enclosed by membrane." [GOC:mah, GOC:pz, GOC:vesicles] subset: goslim_pir synonym: "membrane-bounded vesicle" RELATED [] @@ -4444,8 +4624,6 @@ is_a: GO:0043227 ! membrane-bounded organelle id: GO:0032501 name: multicellular organismal process namespace: biological_process -alt_id: GO:0044707 -alt_id: GO:0050874 def: "Any biological process, occurring at the level of a multicellular organism, pertinent to its function." [GOC:curators, GOC:dph, GOC:isa_complete, GOC:tb] comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. subset: gocheck_do_not_annotate @@ -4458,14 +4636,12 @@ property_value: RO:0002161 NCBITaxon:2157 property_value: RO:0002161 NCBITaxon:4896 property_value: RO:0002161 NCBITaxon:4932 property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27189" xsd:anyURI -created_by: jl creation_date: 2012-09-19T16:07:47Z [Term] id: GO:0032502 name: developmental process namespace: biological_process -alt_id: GO:0044767 def: "A biological process whose specific outcome is the progression of an integrated living unit: an anatomical structure (which may be a subcellular structure, cell, tissue, or organ), or organism over time from an initial condition to a later condition." [GOC:isa_complete] subset: goslim_agr subset: goslim_flybase_ribbon @@ -4473,15 +4649,12 @@ subset: goslim_pir synonym: "development" NARROW [] synonym: "single-organism developmental process" RELATED [] is_a: GO:0008150 ! biological_process -created_by: jl creation_date: 2012-12-19T12:21:31Z [Term] id: GO:0032609 name: type II interferon production namespace: biological_process -alt_id: GO:0042095 -alt_id: GO:0072643 def: "The appearance of interferon-gamma due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. Interferon-gamma is also known as type II interferon." [GOC:add, GOC:mah, PMID:15546383] subset: gocheck_do_not_annotate synonym: "IFNG production" EXACT [GOC:mah] @@ -4505,9 +4678,6 @@ is_a: GO:0140352 ! export from cell id: GO:0032984 name: protein-containing complex disassembly namespace: biological_process -alt_id: GO:0034623 -alt_id: GO:0043241 -alt_id: GO:0043624 def: "The disaggregation of a protein-containing macromolecular complex into its constituent components." [GOC:mah] synonym: "cellular macromolecule complex disassembly" RELATED [] synonym: "cellular protein complex disassembly" RELATED [] @@ -4524,7 +4694,6 @@ property_value: term_tracker_item "https://github.com/geneontology/go-ontology/i id: GO:0032991 name: protein-containing complex namespace: cellular_component -alt_id: GO:0043234 def: "A stable assembly of two or more macromolecules, i.e. proteins, nucleic acids, carbohydrates or lipids, in which at least one component is a protein and the constituent parts function together." [GOC:dos, GOC:mah] comment: A protein complex in this context is meant as a stable set of interacting proteins which can be co-purified by an acceptable method, and where the complex has been shown to exist as an isolated, functional unit in vivo. Acceptable experimental methods include stringent protein purification followed by detection of protein interaction. The following methods should be considered non-acceptable: simple immunoprecipitation, pull-down experiments from cell extracts without further purification, colocalization and 2-hybrid screening. Interactions that should not be captured as protein complexes include: 1) enzyme/substrate, receptor/ligand or any similar transient interactions, unless these are a critical part of the complex assembly or are required e.g. for the receptor to be functional; 2) proteins associated in a pull-down/co-immunoprecipitation assay with no functional link or any evidence that this is a defined biological entity rather than a loose-affinity complex; 3) any complex where the only evidence is based on genetic interaction data; 4) partial complexes, where some subunits (e.g. transmembrane ones) cannot be expressed as recombinant proteins and are excluded from experiments (in this case, independent evidence is necessary to find out the composition of the full complex, if known). Interactions that may be captured as protein complexes include: 1) enzyme/substrate or receptor/ligand if the complex can only assemble and become functional in the presence of both classes of subunits; 2) complexes where one of the members has not been shown to be physically linked to the other(s), but is a homologue of, and has the same functionality as, a protein that has been experimentally demonstrated to form a complex with the other member(s); 3) complexes whose existence is accepted based on localization and pharmacological studies, but for which experimental evidence is not yet available for the complex as a whole. subset: goslim_agr @@ -4539,8 +4708,8 @@ synonym: "protein complex" NARROW [] synonym: "protein containing complex" EXACT [] synonym: "protein-protein complex" NARROW [] is_a: GO:0005575 ! cellular_component -is_a: PR:000050567 ! protein-containing material entity -disjoint_from: GO:0110165 ! cellular anatomical entity +disjoint_from: GO:0110165 ! cellular anatomical structure +relationship: has_part PR:000000001 ! protein [Term] id: GO:0033151 @@ -4572,7 +4741,6 @@ is_a: GO:0033151 ! V(D)J recombination id: GO:0034220 name: monoatomic ion transmembrane transport namespace: biological_process -alt_id: GO:0099131 def: "A process in which a monoatomic ion is transported across a membrane. Monatomic ions (also called simple ions) are ions consisting of exactly one atom." [GOC:mah] comment: Note that this term is not intended for use in annotating lateral movement within membranes. synonym: "ATP hydrolysis coupled ion transmembrane transport" NARROW [] @@ -4682,9 +4850,6 @@ property_value: term_tracker_item "https://github.com/geneontology/go-ontology/i id: GO:0042592 name: homeostatic process namespace: biological_process -alt_id: GO:0032844 -alt_id: GO:0032845 -alt_id: GO:0032846 def: "Any biological process involved in the maintenance of an internal steady state." [GOC:jl, ISBN:0395825172] subset: goslim_agr subset: goslim_chembl @@ -4727,7 +4892,7 @@ subset: goslim_prokaryote_ribbon synonym: "cell process" BROAD [] synonym: "cellular process" BROAD [] synonym: "cellular projection" EXACT [] -is_a: GO:0110165 ! cellular anatomical entity +is_a: GO:0110165 ! cellular anatomical structure relationship: part_of CL:0000000 ! cell [Term] @@ -4756,9 +4921,6 @@ relationship: results_in_acquisition_of_features_of CL:0000782 ! myeloid dendrit id: GO:0043170 name: macromolecule metabolic process namespace: biological_process -alt_id: GO:0034960 -alt_id: GO:0043283 -alt_id: GO:0044259 def: "The chemical reactions and pathways involving macromolecules, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass." [GOC:mah] subset: gocheck_do_not_annotate subset: goslim_pir @@ -4789,7 +4951,7 @@ subset: goslim_prokaryote subset: goslim_prokaryote_ribbon xref: NIF_Subcellular:sao1539965131 xref: Wikipedia:Organelle -is_a: GO:0110165 ! cellular anatomical entity +is_a: GO:0110165 ! cellular anatomical structure [Term] id: GO:0043227 @@ -4802,23 +4964,26 @@ xref: NIF_Subcellular:sao414196390 is_a: GO:0043226 ! organelle intersection_of: GO:0043226 ! organelle intersection_of: has_part GO:0016020 ! membrane -disjoint_from: GO:0043228 ! non-membrane-bounded organelle +disjoint_from: GO:0043228 ! membraneless organelle relationship: has_part GO:0016020 ! membrane property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28153" xsd:anyURI [Term] id: GO:0043228 -name: non-membrane-bounded organelle +name: membraneless organelle namespace: cellular_component def: "Organized structure of distinctive morphology and function, not bounded by a lipid bilayer membrane. Includes ribosomes, the cytoskeleton and chromosomes." [GOC:go_curators] subset: gocheck_do_not_annotate subset: goslim_mouse synonym: "biological condensate" RELATED [] +synonym: "membrane-less organelle" EXACT [] +synonym: "non-membrane-bounded organelle" EXACT [] synonym: "non-membrane-enclosed organelle" EXACT [] xref: NIF_Subcellular:sao1456184038 is_a: GO:0043226 ! organelle property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/21881" xsd:anyURI property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28153" xsd:anyURI +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29106" xsd:anyURI [Term] id: GO:0043229 @@ -4847,15 +5012,17 @@ intersection_of: part_of GO:0005622 ! intracellular anatomical structure [Term] id: GO:0043232 -name: intracellular non-membrane-bounded organelle +name: intracellular membraneless organelle namespace: cellular_component def: "Organized structure of distinctive morphology and function, not bounded by a lipid bilayer membrane and occurring within the cell. Includes ribosomes, the cytoskeleton and chromosomes." [GOC:go_curators] subset: goslim_pir +synonym: "intracellular non-membrane-bounded organelle" EXACT [] synonym: "intracellular non-membrane-enclosed organelle" EXACT [] -is_a: GO:0043228 ! non-membrane-bounded organelle +is_a: GO:0043228 ! membraneless organelle is_a: GO:0043229 ! intracellular organelle -intersection_of: GO:0043228 ! non-membrane-bounded organelle +intersection_of: GO:0043228 ! membraneless organelle intersection_of: part_of GO:0005622 ! intracellular anatomical structure +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29106" xsd:anyURI [Term] id: GO:0043233 @@ -4874,7 +5041,7 @@ name: contractile muscle fiber namespace: cellular_component def: "Fibers, composed of actin, myosin, and associated proteins, found in cells of smooth or striated muscle." [GOC:go_curators, ISBN:0815316194] synonym: "contractile fibre" EXACT [] -is_a: GO:0043232 ! intracellular non-membrane-bounded organelle +is_a: GO:0043232 ! intracellular membraneless organelle is_a: GO:0099512 ! supramolecular fiber relationship: part_of CL:0000187 ! muscle cell relationship: part_of GO:0005737 ! cytoplasm @@ -4886,9 +5053,6 @@ property_value: term_tracker_item "https://github.com/geneontology/go-ontology/i id: GO:0043933 name: protein-containing complex organization namespace: biological_process -alt_id: GO:0034600 -alt_id: GO:0034621 -alt_id: GO:0071822 def: "Any process in which macromolecules aggregate, disaggregate, or are modified, resulting in the formation, disassembly, or alteration of a protein complex." [GOC:mah] synonym: "cellular macromolecular complex organization" RELATED [] synonym: "cellular macromolecular complex subunit organisation" RELATED [] @@ -4904,14 +5068,12 @@ intersection_of: GO:0016043 ! cellular component organization intersection_of: results_in_organization_of GO:0032991 ! protein-containing complex relationship: results_in_organization_of GO:0032991 ! protein-containing complex property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/22580" xsd:anyURI -created_by: mah creation_date: 2010-09-08T10:01:42Z [Term] id: GO:0044085 name: cellular component biogenesis namespace: biological_process -alt_id: GO:0071843 def: "A process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of a cellular component. Includes biosynthesis of constituent macromolecules, and those macromolecular modifications that are involved in synthesis or assembly of the cellular component." [GOC:jl, GOC:mah] subset: gocheck_do_not_annotate subset: goslim_pir @@ -4928,21 +5090,8 @@ synonym: "Met-tRNA/eIF2.GTP ternary complex" NARROW [] synonym: "translation initiation (ternary) complex" EXACT [] is_a: GO:1990904 ! ribonucleoprotein complex relationship: part_of GO:0005737 ! cytoplasm -created_by: jl creation_date: 2009-10-22T02:38:55Z -[Term] -id: GO:0044237 -name: cellular metabolic process -namespace: biological_process -def: "The chemical reactions and pathways by which individual cells transform chemical substances." [GOC:go_curators] -comment: This term should not be used for direct annotation. It should be possible to make a more specific annotation to one of the children of this term. -subset: gocheck_do_not_annotate -synonym: "cellular metabolism" EXACT [] -synonym: "intermediary metabolism" RELATED [GOC:mah] -is_a: GO:0008152 ! metabolic process -is_a: GO:0009987 ! cellular process - [Term] id: GO:0044238 name: primary metabolic process @@ -4958,21 +5107,6 @@ xref: Wikipedia:Primary_metabolite is_a: GO:0008152 ! metabolic process property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/26424" xsd:anyURI -[Term] -id: GO:0044249 -name: cellular biosynthetic process -namespace: biological_process -def: "The chemical reactions and pathways resulting in the formation of substances, carried out by individual cells." [GOC:jl] -comment: This term should not be used for direct annotation. It should be possible to make a more specific annotation to one of the children of this term. -subset: gocheck_do_not_annotate -synonym: "cellular anabolism" EXACT [] -synonym: "cellular biosynthesis" EXACT [] -synonym: "cellular formation" EXACT [] -synonym: "cellular synthesis" EXACT [] -is_a: GO:0009058 ! biosynthetic process -is_a: GO:0044237 ! cellular metabolic process -property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27052" xsd:anyURI - [Term] id: GO:0044419 name: biological process involved in interspecies interaction between organisms @@ -4993,7 +5127,6 @@ property_value: term_tracker_item "https://github.com/geneontology/go-ontology/i id: GO:0045026 name: plasma membrane fusion namespace: biological_process -alt_id: GO:0006947 def: "The joining of the lipid bilayer membrane that surround a cell with that of another cell, producing a single cell." [GOC:elh, GOC:mtg_muscle] synonym: "cell fusion" BROAD [] synonym: "cell-cell fusion" BROAD [] @@ -5007,7 +5140,6 @@ relationship: results_in_fusion_of GO:0005886 ! plasma membrane id: GO:0045087 name: innate immune response namespace: biological_process -alt_id: GO:0002226 def: "Innate immune responses are defense responses mediated by germline encoded components that directly recognize components of potential pathogens." [GO_REF:0000022, GOC:add, GOC:ebc, GOC:mtg_sensu] synonym: "innate immunity" EXACT [GOC:pg] synonym: "nonspecific immune response" EXACT [] @@ -5215,7 +5347,6 @@ relationship: regulates GO:0050896 ! response to stimulus id: GO:0048598 name: embryonic morphogenesis namespace: biological_process -alt_id: GO:0048828 def: "The process in which anatomical structures are generated and organized during the embryonic phase. The embryonic phase begins with zygote formation. The end of the embryonic phase is organism-specific. For example, it would be at birth for mammals, larval hatching for insects and seed dormancy in plants." [GOC:jid, GOC:mtg_sensu] synonym: "embryonic anatomical structure morphogenesis" EXACT [GOC:dph, GOC:tb] is_a: GO:0009653 ! anatomical structure morphogenesis @@ -5336,7 +5467,6 @@ relationship: regulates GO:0006955 ! immune response id: GO:0050789 name: regulation of biological process namespace: biological_process -alt_id: GO:0050791 def: "Any process that modulates the frequency, rate or extent of a biological process. Biological processes are regulated by many means; examples include the control of gene expression, protein modification or interaction with a protein or substrate molecule." [GOC:ai, GOC:go_curators] subset: gocheck_do_not_annotate subset: goslim_candida @@ -5361,7 +5491,6 @@ relationship: regulates GO:0032502 ! developmental process id: GO:0050794 name: regulation of cellular process namespace: biological_process -alt_id: GO:0051244 def: "Any process that modulates the frequency, rate or extent of a cellular process, any of those that are carried out at the cellular level, but are not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level." [GOC:go_curators] subset: gocheck_do_not_annotate synonym: "regulation of cellular physiological process" EXACT [] @@ -5420,7 +5549,6 @@ property_value: term_tracker_item "https://github.com/geneontology/go-ontology/i id: GO:0050896 name: response to stimulus namespace: biological_process -alt_id: GO:0051869 def: "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus. The process begins with detection of the stimulus and ends with a change in state or activity or the cell or organism." [GOC:ai, GOC:bf] comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. subset: gocheck_do_not_annotate @@ -5493,7 +5621,6 @@ relationship: part_of GO:0050953 ! sensory perception of light stimulus id: GO:0051179 name: localization namespace: biological_process -alt_id: GO:1902578 def: "Any process in which a cell, a substance, or a cellular entity, such as a protein complex or organelle, is transported, tethered to or otherwise maintained in a specific location. In the case of substances, localization may also be achieved via selective degradation." [GOC:ai, GOC:dos] subset: gocheck_do_not_annotate subset: goslim_pir @@ -5507,7 +5634,6 @@ synonym: "single organism localization" RELATED [GOC:TermGenie] synonym: "single-organism localization" RELATED [] is_a: GO:0008150 ! biological_process property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27052" xsd:anyURI -created_by: jl creation_date: 2013-12-18T13:51:04Z [Term] @@ -5571,8 +5697,6 @@ is_a: GO:0050896 ! response to stimulus id: GO:0051707 name: response to other organism namespace: biological_process -alt_id: GO:0009613 -alt_id: GO:0042828 def: "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus from another living organism." [GOC:ai] is_a: GO:0043207 ! response to external biotic stimulus is_a: GO:0044419 ! biological process involved in interspecies interaction between organisms @@ -5581,7 +5705,6 @@ is_a: GO:0044419 ! biological process involved in interspecies interaction betwe id: GO:0055085 name: transmembrane transport namespace: biological_process -alt_id: GO:0090662 def: "The process in which a solute is transported across a lipid bilayer, from one side of a membrane to the other." [GOC:dph, GOC:jid] comment: Transmembrane transport is the transport of a solute across a lipid bilayer. Note that transport through the nuclear pore complex is not transmembrane because the nuclear membrane is a double membrane and is not traversed. For transport through the nuclear pore, consider instead the term 'nucleocytoplasmic transport ; GO:0006913' and its children. Note also that this term is not intended for use in annotating lateral movement within membranes. subset: goslim_chembl @@ -5597,7 +5720,6 @@ is_a: GO:0009987 ! cellular process intersection_of: GO:0006810 ! transport intersection_of: results_in_transport_across GO:0016020 ! membrane relationship: results_in_transport_across GO:0016020 ! membrane -created_by: tb creation_date: 2015-10-21T13:22:47Z [Term] @@ -5650,15 +5772,12 @@ is_a: GO:0035239 ! tube morphogenesis intersection_of: GO:0009653 ! anatomical structure morphogenesis intersection_of: results_in_morphogenesis_of UBERON:0003914 ! epithelial tube relationship: results_in_morphogenesis_of UBERON:0003914 ! epithelial tube -created_by: dph creation_date: 2009-04-28T09:33:36Z [Term] id: GO:0061024 name: membrane organization namespace: biological_process -alt_id: GO:0016044 -alt_id: GO:0044802 def: "A process which results in the assembly, arrangement of constituent parts, or disassembly of a membrane. A membrane is a double layer of lipid molecules that encloses all cells, and, in eukaryotes, many organelles; may be a single or double lipid bilayer; also includes associated proteins." [GOC:dph, GOC:tb] subset: goslim_chembl subset: goslim_drosophila @@ -5675,15 +5794,12 @@ is_a: GO:0016043 ! cellular component organization intersection_of: GO:0016043 ! cellular component organization intersection_of: results_in_organization_of GO:0016020 ! membrane relationship: results_in_organization_of GO:0016020 ! membrane -created_by: jl creation_date: 2010-02-08T02:43:11Z [Term] id: GO:0061025 name: membrane fusion namespace: biological_process -alt_id: GO:0006944 -alt_id: GO:0044801 def: "The membrane organization process that joins two lipid bilayers to form a single membrane." [GOC:dph, GOC:tb] subset: goslim_yeast synonym: "cellular membrane fusion" EXACT [] @@ -5693,7 +5809,6 @@ is_a: GO:0061024 ! membrane organization intersection_of: GO:0061024 ! membrane organization intersection_of: results_in_fusion_of GO:0016020 ! membrane relationship: results_in_fusion_of GO:0016020 ! membrane -created_by: jl creation_date: 2010-02-08T02:48:06Z [Term] @@ -5704,16 +5819,12 @@ def: "An extracellular matrix consisting mainly of proteins (especially collagen is_a: GO:0031012 ! extracellular matrix relationship: RO:0002160 NCBITaxon:33208 ! only in taxon Metazoa relationship: RO:0002162 NCBITaxon:33208 {all_only="true"} ! in taxon Metazoa -created_by: dph creation_date: 2018-04-13T12:47:21Z [Term] id: GO:0065003 name: protein-containing complex assembly namespace: biological_process -alt_id: GO:0006461 -alt_id: GO:0034622 -alt_id: GO:0043623 def: "The aggregation, arrangement and bonding together of a set of macromolecules to form a protein-containing complex." [GOC:jl] subset: goslim_chembl subset: goslim_drosophila @@ -5791,14 +5902,12 @@ intersection_of: GO:0016043 ! cellular component organization intersection_of: results_in_organization_of GO:1990904 ! ribonucleoprotein complex relationship: results_in_organization_of GO:1990904 ! ribonucleoprotein complex property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/25143" xsd:anyURI -created_by: mah creation_date: 2010-09-08T10:10:35Z [Term] id: GO:0071840 name: cellular component organization or biogenesis namespace: biological_process -alt_id: GO:0071841 def: "A process that results in the biosynthesis of constituent macromolecules, assembly, arrangement of constituent parts, or disassembly of a cellular component." [GOC:mah] comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. subset: gocheck_do_not_annotate @@ -5809,7 +5918,6 @@ synonym: "cellular component organisation or biogenesis at cellular level" EXACT synonym: "cellular component organization or biogenesis at cellular level" EXACT [] is_a: GO:0009987 ! cellular process property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27189" xsd:anyURI -created_by: mah creation_date: 2010-09-10T01:39:16Z [Term] @@ -5818,8 +5926,7 @@ name: cell periphery namespace: cellular_component def: "The broad region around and including the plasma membrane of a cell, encompassing the cell cortex (inside the cell), the plasma membrane, and any external encapsulating structures." [GOC:pdt] subset: goslim_flybase_ribbon -is_a: GO:0110165 ! cellular anatomical entity -created_by: mah +is_a: GO:0110165 ! cellular anatomical structure creation_date: 2010-10-04T01:51:47Z [Term] @@ -5831,7 +5938,6 @@ synonym: "elastic fibre" EXACT [GOC:mah] synonym: "elastin fiber" EXACT [GOC:BHF] is_a: GO:0099512 ! supramolecular fiber relationship: part_of GO:0031012 ! extracellular matrix -created_by: mah creation_date: 2010-10-11T11:44:57Z [Term] @@ -5845,7 +5951,6 @@ intersection_of: results_in_formation_of UBERON:0003914 ! epithelial tube relationship: part_of GO:0060562 ! epithelial tube morphogenesis relationship: results_in_formation_of UBERON:0003914 ! epithelial tube property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/22302" xsd:anyURI -created_by: mah creation_date: 2010-02-26T02:15:40Z [Term] @@ -5858,7 +5963,6 @@ is_a: GO:0061025 ! membrane fusion intersection_of: GO:0061025 ! membrane fusion intersection_of: results_in_fusion_of GO:0031090 ! organelle membrane relationship: results_in_fusion_of GO:0031090 ! organelle membrane -created_by: tb creation_date: 2009-12-11T11:44:58Z [Term] @@ -5871,7 +5975,6 @@ is_a: GO:1903131 ! mononuclear cell differentiation intersection_of: GO:0030154 ! cell differentiation intersection_of: results_in_acquisition_of_features_of CL:0000451 ! dendritic cell relationship: results_in_acquisition_of_features_of CL:0000451 ! dendritic cell -created_by: pr creation_date: 2011-04-01T10:08:42Z [Term] @@ -5883,14 +5986,12 @@ is_a: GO:0031982 ! vesicle is_a: GO:0043231 ! intracellular membrane-bounded organelle intersection_of: GO:0031982 ! vesicle intersection_of: part_of GO:0005622 ! intracellular anatomical structure -created_by: pr creation_date: 2016-03-29T17:39:45Z [Term] id: GO:0098542 name: defense response to other organism namespace: biological_process -alt_id: GO:0009814 def: "Reactions triggered in response to the presence of another organism that act to protect the cell or organism from damage caused by that organism." [GOC:dos] subset: goslim_generic subset: goslim_prokaryote @@ -5900,7 +6001,6 @@ synonym: "defense response, incompatible interaction" NARROW [] synonym: "resistance response to pathogen" NARROW [] is_a: GO:0051707 ! response to other organism property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/22173" xsd:anyURI -created_by: dos creation_date: 2013-11-11T12:59:11Z [Term] @@ -5915,7 +6015,6 @@ is_a: GO:0016020 ! membrane intersection_of: GO:0016020 ! membrane intersection_of: part_of GO:0005886 ! plasma membrane relationship: part_of GO:0005886 ! plasma membrane -created_by: dos creation_date: 2014-03-06T11:55:32Z [Term] @@ -5944,7 +6043,6 @@ def: "A complex of collagen trimers such as a fibril or collagen network." [GOC: synonym: "Supramolecular aggregate of collagen" EXACT [PMID:19693541] synonym: "Supramolecular collagen assembly" EXACT [PMID:21421911] is_a: GO:0099080 ! supramolecular complex -is_a: PR:000050567 ! protein-containing material entity relationship: has_part GO:0005581 ! collagen trimer relationship: part_of GO:0062023 ! collagen-containing extracellular matrix @@ -5983,7 +6081,7 @@ namespace: cellular_component def: "The part of a synapse that is part of the presynaptic cell." [GOC:dos] subset: goslim_synapse synonym: "presynaptic terminal" EXACT [] -is_a: GO:0110165 ! cellular anatomical entity +is_a: GO:0110165 ! cellular anatomical structure relationship: part_of CL:0000540 ! neuron relationship: part_of GO:0045202 ! synapse @@ -5993,7 +6091,7 @@ name: postsynapse namespace: cellular_component def: "The part of a synapse that is part of the post-synaptic cell." [GOC:dos] subset: goslim_synapse -is_a: GO:0110165 ! cellular anatomical entity +is_a: GO:0110165 ! cellular anatomical structure relationship: part_of CL:0000000 ! cell relationship: part_of GO:0045202 ! synapse @@ -6035,7 +6133,7 @@ id: GO:0099080 name: supramolecular complex namespace: cellular_component def: "A cellular component that consists of an indeterminate number of proteins or macromolecular complexes, organized into a regular, higher-order structure such as a polymer, sheet, network or a fiber." [GOC:dos] -is_a: GO:0110165 ! cellular anatomical entity +is_a: GO:0110165 ! cellular anatomical structure [Term] id: GO:0099081 @@ -6075,7 +6173,6 @@ relationship: capable_of GO:0099500 ! vesicle fusion to plasma membrane id: GO:0099512 name: supramolecular fiber namespace: cellular_component -alt_id: GO:0043205 def: "A polymer consisting of an indefinite number of protein or protein complex subunits that have polymerised to form a fiber-shaped structure." [GOC:dos] synonym: "fibril" RELATED [] is_a: GO:0099081 ! supramolecular polymer @@ -6108,16 +6205,17 @@ is_a: GO:0099536 ! synaptic signaling [Term] id: GO:0110165 -name: cellular anatomical entity +name: cellular anatomical structure namespace: cellular_component -def: "A part of a cellular organism that is either an immaterial entity or a material entity with granularity above the level of a protein complex but below that of an anatomical system. Or, a substance produced by a cellular organism with granularity above the level of a protein complex." [GOC:kmv] +def: "A part of a cellular organism consisting of a material entity with granularity above the level of a protein complex but below that of an anatomical system. Note that cellular organisms exclude viruses." [GOC:kmv] subset: gocheck_do_not_annotate subset: goslim_pir +synonym: "cellular anatomical entity" EXACT [] is_a: GO:0005575 ! cellular_component is_a: UBERON:0000061 ! anatomical structure property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/24200" xsd:anyURI property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/26424" xsd:anyURI -created_by: kmv +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28978" xsd:anyURI creation_date: 2019-08-12T18:01:37Z [Term] @@ -6130,7 +6228,6 @@ intersection_of: GO:0042995 ! cell projection intersection_of: has_part GO:0098590 ! plasma membrane region relationship: has_part GO:0098590 ! plasma membrane region property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/13193" xsd:anyURI -created_by: krc creation_date: 2017-03-21T17:26:07Z [Term] @@ -6143,7 +6240,6 @@ intersection_of: GO:0016043 ! cellular component organization intersection_of: results_in_organization_of GO:0120025 ! plasma membrane bounded cell projection relationship: results_in_organization_of GO:0120025 ! plasma membrane bounded cell projection property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/13298" xsd:anyURI -created_by: krc creation_date: 2017-04-26T16:07:02Z [Term] @@ -6156,7 +6252,6 @@ is_a: GO:0009987 ! cellular process intersection_of: GO:0009987 ! cellular process intersection_of: part_of GO:0006887 ! exocytosis relationship: part_of GO:0006887 ! exocytosis -created_by: pg creation_date: 2017-05-15T13:20:45Z [Term] @@ -6169,7 +6264,6 @@ synonym: "cell fusion" BROAD [] is_a: GO:0009987 ! cellular process relationship: has_part GO:0045026 ! plasma membrane fusion property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/15939" xsd:anyURI -created_by: pg creation_date: 2018-08-13T18:38:18Z [Term] @@ -6185,7 +6279,6 @@ intersection_of: has_target_end_location GO:0005576 ! extracellular region intersection_of: has_target_start_location GO:0005622 ! intracellular anatomical structure relationship: has_target_end_location GO:0005576 ! extracellular region relationship: has_target_start_location GO:0005622 ! intracellular anatomical structure -created_by: pg creation_date: 2019-05-22T11:20:45Z [Term] @@ -6195,7 +6288,6 @@ namespace: biological_process def: "Reactions triggered in response to the presence of a symbiont that act to protect or prevent damage to the host." [GOC:pg] is_a: GO:0098542 ! defense response to other organism property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/20261" xsd:anyURI -created_by: pg creation_date: 2020-11-11T17:19:06Z [Term] @@ -6209,7 +6301,6 @@ is_a: GO:1903706 ! regulation of hemopoiesis intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0002521 ! leukocyte differentiation relationship: regulates GO:0002521 ! leukocyte differentiation -created_by: pr creation_date: 2013-05-02T17:32:42Z [Term] @@ -6221,7 +6312,6 @@ is_a: GO:0002521 ! leukocyte differentiation intersection_of: GO:0030154 ! cell differentiation intersection_of: results_in_acquisition_of_features_of CL:0000842 ! mononuclear cell relationship: results_in_acquisition_of_features_of CL:0000842 ! mononuclear cell -created_by: cls creation_date: 2014-06-25T15:47:09Z [Term] @@ -6240,15 +6330,12 @@ is_a: GO:2000026 ! regulation of multicellular organismal development intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0030097 ! hemopoiesis relationship: regulates GO:0030097 ! hemopoiesis -created_by: pad creation_date: 2014-12-04T15:34:13Z [Term] id: GO:1990904 name: ribonucleoprotein complex namespace: cellular_component -alt_id: GO:0030529 -alt_id: GO:1990903 def: "A macromolecular complex that contains both RNA and protein molecules." [GOC:krc, GOC:vesicles] subset: goslim_pir synonym: "extracellular ribonucleoprotein complex" NARROW [] @@ -6258,7 +6345,6 @@ synonym: "RNA-protein complex" EXACT [] synonym: "RNP" EXACT [] xref: Wikipedia:Ribonucleoprotein is_a: GO:0032991 ! protein-containing complex -created_by: pr creation_date: 2015-11-19T12:26:37Z [Term] @@ -6271,7 +6357,6 @@ is_a: GO:0051239 ! regulation of multicellular organismal process intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0007275 ! multicellular organism development relationship: regulates GO:0007275 ! multicellular organism development -created_by: tb creation_date: 2010-08-05T11:25:59Z [Term] @@ -6305,7 +6390,6 @@ is_a: NCBITaxon:39107 ! Murinae id: NCBITaxon:10090 name: Mus musculus namespace: ncbi_taxonomy -alt_id: NCBITaxon:85055 synonym: "house mouse" EXACT genbank_common_name [] synonym: "mouse" EXACT OMO:0003003 [] xref: GC_ID:1 @@ -6322,7 +6406,6 @@ is_a: NCBITaxon:7776 ! Gnathostomata id: NCBITaxon:117571 name: Euteleostomi namespace: ncbi_taxonomy -alt_id: NCBITaxon:40673 synonym: "bony vertebrates" EXACT genbank_common_name [] xref: GC_ID:1 is_a: NCBITaxon:117570 ! Teleostomi @@ -6471,7 +6554,6 @@ is_a: NCBITaxon:1963758 ! Myomorpha id: NCBITaxon:39107 name: Murinae namespace: ncbi_taxonomy -alt_id: NCBITaxon:109679 xref: GC_ID:1 is_a: NCBITaxon:10066 ! Muridae @@ -6567,7 +6649,6 @@ is_a: NCBITaxon:314147 ! Glires id: PATO:0000001 name: quality namespace: quality -alt_id: PATO:0000072 def: "A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities" [PATOC:GVG] [Term] @@ -6582,7 +6663,6 @@ is_a: PATO:0001241 ! physical object quality id: PATO:0000052 name: shape namespace: quality -alt_id: PATO:0001647 def: "A morphological quality inhering in a bearer by virtue of the bearer's ratios of distances between its features (points, edges, surfaces and also holes etc)." [PATOC:GVG] comment: Shapes are invariant on size transformations. Shapes can be subdivided into 2D and 3D shapes, We can also make a distinction between shapes of complete self-connected objects, and shapes of parts of objects. subset: attribute_slim @@ -6593,7 +6673,6 @@ is_a: PATO:0000051 ! morphology id: PATO:0000141 name: structure namespace: quality -alt_id: PATO:0001452 def: "A morphology quality inhering in a bearer by virtue of the bearer's relative position, shape, arrangements and connectivity of an organism's various parts; the pattern underlying its form." [PATOC:GVG] subset: attribute_slim synonym: "conformation" BROAD [VT:1000738] @@ -6631,7 +6710,6 @@ is_a: PATO:0002318 ! superelliptic id: PATO:0001018 name: physical quality namespace: quality -alt_id: PATO:0002079 def: "A quality of a physical entity that exists through action of continuants at the physical level of organisation in relation to other entities." [PATOC:GVG] subset: attribute_slim synonym: "relational physical quality" EXACT [] @@ -6642,8 +6720,6 @@ is_a: PATO:0001241 ! physical object quality id: PATO:0001241 name: physical object quality namespace: quality -alt_id: PATO:0001237 -alt_id: PATO:0001238 def: "A quality which inheres in a continuant." [PATOC:GVG] comment: Relational qualities are qualities that hold between multiple entities. Normal (monadic) qualities such as the shape of a eyeball exist purely as a quality of that eyeball. A relational quality such as sensitivity to light is a quality of that eyeball (and connecting nervous system) as it relates to incoming light waves/particles. synonym: "monadic quality of a continuant" EXACT [] @@ -6757,7 +6833,6 @@ is_a: PATO:0001579 ! contractility id: PATO:0001873 name: cylindrical namespace: quality -alt_id: PATO:0001203 def: "A convex 3-D shape quality inhering in a bearer by virtue of the bearer's exhibiting a consistently-sized round cross section." [PATOC:MAH] subset: cell_quality subset: value_slim @@ -6963,7 +7038,6 @@ def: "A quality inhering in a cell by virtue of the cell having a high nuclear/c comment: A high nuclear/cytolasmic ratio is 70% or higher. synonym: "high N:C ratio" EXACT [] is_a: PATO:0001396 ! cellular quality -created_by: http://orcid.org/0000-0001-5208-3432 [Term] id: PATO:0070044 @@ -6971,7 +7045,6 @@ name: anatomical structure quality namespace: quality def: "A quality of continuant that exist at the anatomical level of organisation and anything under it. This includes, but is not limited to, cells , tissues, and components." [] is_a: PATO:0001241 ! physical object quality -created_by: http://orcid.org/0000-0001-7258-9596 [Term] id: PATO:0070045 @@ -6979,7 +7052,6 @@ name: anatomical histological quality namespace: quality def: "A quality inhering in an anotomical structure by virtue of its capacity to be stained by specific histological dyes." [] is_a: PATO:0070044 ! anatomical structure quality -created_by: http://orcid.org/0000-0001-7258-9596 [Term] id: PATO:0070046 @@ -6987,18 +7059,17 @@ name: neutrophillic namespace: quality def: "An affinity inhering in an anatomical structure by virtue of the bearer exhibiting a molecular interaction that stains and colors, pale-pink, with Wright-Giemsa stain." [GOC:add] is_a: PATO:0070045 ! anatomical histological quality -created_by: http://orcid.org/0000-0001-7258-9596 [Term] id: PR:000000001 name: protein namespace: protein def: "An amino acid chain that is produced de novo by ribosome-mediated translation of a genetically-encoded mRNA, and any derivatives thereof." [PRO:DAN, PRO:WCB] -comment: The definition above excludes protein complexes, which some also consider a protein. Those who wish to refer to a class representing both senses of the word are directed to CHEBI:36080. Note that the definition allows for experimentally-manipulated genes, and allows for artifically-produced derivatives that mimic those found naturally. Proteins (in the sense defined here) that descended from a common ancestor can be classified into families and superfamilies composed of products of evolutionarily-related genes. The domain architecture of a protein is described by the order of its constituent domains. Proteins with the same domains in the same order are defined as homeomorphic [PRO:WCB]. +comment: The definition above excludes protein complexes, which some also consider a protein. Those who wish to refer to a class representing both senses of the word are directed to CHEBI:36080. Note that the definition allows for experimentally-manipulated genes, and allows for artifically-produced derivatives that mimic those found naturally. Proteins (in the sense defined here) that descended from a common ancestor can be classified into families and superfamilies composed of products of evolutionarily-related genes. The domain architecture of a protein is described by the order of its constituent domains. Proteins with the same domains in the same order are defined as homeomorphic [PRO:WCB). synonym: "native protein" NARROW [IEDB:BP] synonym: "natural protein" EXACT [PRO:DAN] is_a: PR:000018263 ! amino acid chain -is_a: PR:000050567 ! protein-containing material entity +is_a: PR:000064867 ! protein-containing molecular entity relationship: output_of GO:0006412 ! translation [Term] @@ -7482,7 +7553,6 @@ namespace: protein def: "A protein with core architecture consisting of a signal sequence, followed by 7 Ig-like domains (Pfam:PF00047, Pfam:PF07679, or Pfam:PF07686), a transmembrane region, and a cytoplasmic Protein tyrosine kinase domain." [PRO:WCB] comment: Category=family. xref: PIRSF:PIRSF038502 -is_a: PR:000000001 ! protein [Term] id: PR:000002062 @@ -7740,11 +7810,11 @@ synonym: "PTPRC/iso:CD45R" EXACT PRO-short-label [PRO:DNx] is_a: PR:000001006 ! receptor-type tyrosine-protein phosphatase C [Term] -id: PR:000050567 -name: protein-containing material entity +id: PR:000064867 +name: protein-containing molecular entity namespace: protein -def: "A material entity that minimally consists of a protein." [PRO:DAN] -comment: Note: This includes single proteins and derivatives thereof (PR:000000001), protein-containing complexes (GO:0032991), and protein aggregates (PR:000050566). +def: "A molecular entity that minimally consists of a protein." [PRO:DAN] +comment: Note: This includes single proteins and derivatives thereof (PR:000000001), protein-containing complexes (GO:0032991), and protein aggregates (PR:000050565). synonym: "protein" NARROW [PRO:DAN] synonym: "protein aggregate" NARROW [PRO:DAN] synonym: "protein complex" NARROW [PRO:DAN] @@ -7875,7 +7945,6 @@ xref: UMLS:C0687028 {source="ncithesaurus:Duct"} xref: Wikipedia:Duct_(anatomy) xref: XAO:0004000 xref: ZFA:0005171 -is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0000063 ! organ subunit relationship: has_part UBERON:0034969 ! epithelial layer of duct relationship: RO:0000086 PATO:0002299 ! has quality tubular @@ -7885,7 +7954,6 @@ relationship: RO:0002570 UBERON:0000463 ! conduit for organism substance id: UBERON:0000060 name: anatomical wall namespace: uberon -alt_id: UBERON:0009915 def: "Organ component adjacent to an organ cavity and which consists of a maximal aggregate of organ component layers." [FMA:82482] subset: upper_level synonym: "organ wall" RELATED [FMA:82482] @@ -8066,7 +8134,6 @@ property_value: RO:0002175 NCBITaxon:4751 id: UBERON:0000075 name: subdivision of skeletal system namespace: uberon -alt_id: UBERON:0010322 def: "Anatomical cluster consisting of the skeletal elements and articular elements that are part of an individual subdivision of the organism." [https://orcid.org/0000-0002-6601-2165, UBERONREF:0000003] subset: non_informative synonym: "skeletal system part" RELATED [] @@ -8364,7 +8431,6 @@ property_value: seeAlso "https://github.com/obophenotype/uberon/issues/661" xsd: id: UBERON:0000307 name: blastula namespace: uberon -alt_id: UBERON:0007011 def: "Organism at the blastula stage - an early stage of embryonic development in animals. It is produced by cleavage of a fertilized ovum and consists of a spherical layer of around 128 cells surrounding a central fluid-filled cavity called the blastocoel. The blastula follows the morula and precedes the gastrula in the developmental sequence." [Wikipedia:Blastula] subset: inconsistent_with_fma synonym: "blastosphere" RELATED [Wikipedia:Blastula] @@ -8863,7 +8929,6 @@ xref: VHOG:0000387 xref: Wikipedia:Epithelium xref: XAO:0003045 xref: ZFA:0001486 -is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0000479 ! tissue intersection_of: UBERON:0000479 ! tissue intersection_of: RO:0002473 CL:0000066 ! composed primarily of epithelial cell @@ -9086,7 +9151,6 @@ property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/d/ id: UBERON:0000926 name: mesoderm namespace: uberon -alt_id: UBERON:0003263 def: "The middle germ layer of the embryo, between the endoderm and ectoderm." [Wikipedia:Mesoderm] subset: efo_slim subset: pheno_slim @@ -9334,7 +9398,6 @@ id: UBERON:0001009 name: circulatory system namespace: uberon def: "Organ system that passes nutrients (such as amino acids and electrolytes), gases, hormones, blood cells, etc. to and from cells in the body to help fight diseases and help stabilize body temperature and pH to maintain homeostasis[WP]." [Wikipedia:Circulatory_system] -subset: human_reference_atlas subset: uberon_slim synonym: "systema cardiovasculare" RELATED OMO:0003011 [Wikipedia:Circulatory_system] xref: AAO:0000959 @@ -9356,7 +9419,6 @@ property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/2/ property_value: RO:0002161 NCBITaxon:147099 {source="Wikipedia:Acoelomorpha"} property_value: RO:0002161 NCBITaxon:6073 property_value: RO:0002161 NCBITaxon:6157 -property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001015 @@ -9612,7 +9674,6 @@ property_value: RO:0002175 NCBITaxon:4751 id: UBERON:0001133 name: cardiac muscle tissue namespace: uberon -alt_id: UBERON:0007096 def: "Muscle tissue composed of cardiac muscle cells, forming the muscles of the heart[ZFA,modified]." [ZFA:0005280] subset: pheno_slim subset: uberon_slim @@ -9948,7 +10009,6 @@ relationship: part_of UBERON:0013702 ! body proper id: UBERON:0002104 name: visual system namespace: uberon -alt_id: UBERON:0007036 def: "The sensory system subserving the sense of vision." [NIFSTD:FMAID_7191] subset: pheno_slim subset: uberon_slim @@ -10125,7 +10185,6 @@ xref: NCIT:C12957 xref: UMLS:C1516995 {source="ncithesaurus:Exocrine_System"} xref: Wikipedia:Exocrine_gland xref: WikipediaCategory:Exocrine_system -is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0000467 ! anatomical system disjoint_from: UBERON:0002390 ! hematopoietic system disjoint_from: UBERON:0002405 ! immune system @@ -10235,7 +10294,6 @@ xref: NCIT:C12712 xref: SCTID:115976003 xref: UMLS:C0015282 {source="ncithesaurus:Exocrine_Gland"} xref: Wikipedia:Exocrine_gland -is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0002530 ! gland intersection_of: UBERON:0002530 ! gland intersection_of: part_of UBERON:0002330 ! exocrine system @@ -10599,6 +10657,7 @@ xref: TAO:0000279 xref: VHOG:0000559 xref: XAO:0000057 xref: ZFA:0000279 +is_a: UBERON:0000061 ! anatomical structure is_a: UBERON:0006598 ! presumptive structure intersection_of: UBERON:0005423 ! developing anatomical structure intersection_of: RO:0002387 UBERON:0002329 ! has potential to develop into somite @@ -10729,7 +10788,6 @@ property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/6/ id: UBERON:0003081 name: lateral plate mesoderm namespace: uberon -alt_id: UBERON:0006258 def: "Portion of the middle of the three primary germ layers of the embryo that resides on the periphery of the embryo, is continuous with the extra-embryonic mesoderm, splits into two layers enclosing the intra-embryonic coelom, and gives rise to body wall structures[MP]." [MP:0010117, Wikipedia:Lateral_plate_mesoderm] subset: pheno_slim subset: uberon_slim @@ -11031,7 +11089,6 @@ property_value: IAO:0000116 "EHDAA2 places this as a subtype of organism. This l id: UBERON:0004734 name: gastrula namespace: uberon -alt_id: UBERON:0007012 def: "Organism at the gastrula stage." [Wikipedia:Gastrula, Wikipedia:Trilaminar_blastocyst] subset: pheno_slim synonym: "blastocystis trilaminaris" RELATED [https://orcid.org/0000-0002-6601-2165] @@ -11354,7 +11411,6 @@ xref: NCIT:C13191 xref: SCTID:68989006 xref: UMLS:C0004799 {source="ncithesaurus:Basement_Membrane"} xref: Wikipedia:Basement_membrane -is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0005764 {source="FMA"} ! acellular membrane relationship: adjacent_to CL:0000066 ! epithelial cell relationship: has_part GO:0005587 ! collagen type IV trimer @@ -11636,7 +11692,6 @@ name: regular connective tissue namespace: uberon def: "Connective tissue, which consists of fibroblasts, the intercellular matrix of which contains a regular network of collagen and elastic fiber bundles. Examples: bone (tissue), cartilage (tissue), dense regular connective tissue." [FMA:20103] xref: FMA:20103 -is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0002384 {source="FMA"} ! connective tissue disjoint_from: UBERON:0011821 ! irregular connective tissue relationship: has_part CL:0000057 ! fibroblast @@ -11671,7 +11726,6 @@ intersection_of: RO:0002473 UBERON:0011860 ! composed primarily of collection of id: UBERON:0009142 name: entire embryonic mesenchyme namespace: uberon -alt_id: UBERON:0003313 def: "Sum total of mesenchyme in the embryo." [https://github.com/obophenotype/human-developmental-anatomy-ontology/issues/7] xref: EHDAA2:0001113 xref: EHDAA:177 @@ -11830,7 +11884,6 @@ xref: AAO:0000121 xref: NCIT:C32450 xref: UMLS:C1511770 {source="ncithesaurus:Dense_Connective_Tissue"} xref: Wikipedia:Dense_connective_tissue -is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0002384 ! connective tissue intersection_of: UBERON:0002384 ! connective tissue intersection_of: RO:0002473 UBERON:0011860 ! composed primarily of collection of collagen fibrils @@ -11845,7 +11898,6 @@ xref: FMA:63212 xref: MESH:D024022 xref: NCIT:C32339 xref: NIF_Subcellular:sao7547390221 -is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0000476 {source="ZFA"} ! acellular anatomical structure relationship: RO:0002473 GO:0005581 ! composed primarily of collagen trimer relationship: RO:0002473 GO:0098643 ! composed primarily of banded collagen fibril @@ -11880,6 +11932,7 @@ synonym: "haemocoelom" NARROW [] synonym: "schizocoelom" NARROW [] xref: EHDAA2:0004731 xref: Wikipedia:Coelom +xref: ZFA:0001438 is_a: UBERON:0000481 {source="EHDAA2"} ! multi-tissue structure relationship: RO:0002162 NCBITaxon:33213 ! in taxon Bilateria property_value: IAO:0000116 "EHDAA2 distingsuishes between the lumen, the lining, and the 'coelomic cavity', which despire it's name, is not a space - it is the aggregate of space plus lining." xsd:string @@ -12051,7 +12104,6 @@ is_a: UBERON:0000479 {source="FMA"} ! tissue id: UBERON:0016879 name: future central nervous system namespace: uberon -alt_id: UBERON:3000469 def: "Primordium that develops into the central nervous system." [http://orcid.org/0000-0002-6601-2165] synonym: "future CNS" EXACT [] synonym: "presumptive central nervous system" EXACT [] @@ -12066,7 +12118,6 @@ relationship: RO:0002387 UBERON:0001017 ! has potential to develop into central id: UBERON:0016880 name: future nervous system namespace: uberon -alt_id: UBERON:3000477 def: "Primordium that develops into the nervous system." [http://orcid.org/0000-0002-6601-2165] synonym: "presumptive nervous system" EXACT [AAO:0000477] xref: AAO:0000477 @@ -12337,7 +12388,6 @@ id: RO:0002021 name: occurs across def: "A relationship between a process and a barrier, where the process occurs in a region spanning the barrier. For cellular processes the barrier is typically a membrane. Examples include transport across a membrane and membrane depolarization." [] is_a: RO:0002479 ! has part that occurs in -created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-07-20T17:19:37Z [Typedef] @@ -13193,7 +13243,6 @@ name: causally upstream of or within, negative effect property_value: RO:0004050 RO:0002418 property_value: seeAlso "https://wiki.geneontology.org/Causally_upstream_of_or_within,_negative_effect" xsd:anyURI is_a: causally_upstream_of_or_within ! causally upstream of or within -created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-03-13T23:55:05Z [Typedef] @@ -13201,7 +13250,6 @@ id: RO:0004047 name: causally upstream of or within, positive effect property_value: seeAlso https://wiki.geneontology.org/Causally_upstream_of_or_within,_positive_effect is_a: causally_upstream_of_or_within ! causally upstream of or within -created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-03-13T23:55:19Z [Typedef] @@ -13210,7 +13258,6 @@ name: has small molecule regulator def: "a relation between a process and a continuant, in which the process is regulated by the small molecule continuant" [] is_a: has_participant ! has participant inverse_of: RO:0012004 ! is small molecule regulator of -created_by: https://orcid.org/0000-0003-1813-6857 creation_date: 2020-04-22T20:27:26Z [Typedef] @@ -13218,7 +13265,6 @@ id: RO:0012004 name: is small molecule regulator of def: "a relation between a continuant and a process, in which the continuant is a small molecule that regulates the process" [] is_a: RO:0002596 ! capable of regulating -created_by: https://orcid.org/0000-0003-1813-6857 creation_date: 2020-06-24T13:15:17Z [Typedef] @@ -13228,7 +13274,6 @@ def: "a relation between a continuant and a process, in which the continuant is property_value: seeAlso "https://wiki.geneontology.org/Is_small_molecule_activator_of" xsd:anyURI is_a: RO:0002598 ! capable of positively regulating is_a: RO:0012004 ! is small molecule regulator of -created_by: https://orcid.org/0000-0003-1813-6857 creation_date: 2020-06-24T13:15:26Z [Typedef] @@ -13238,7 +13283,6 @@ def: "A relationship between a neuron and a region, where the neuron has a funct synonym: "has synaptic input or output in" EXACT [] is_a: RO:0002130 ! has synaptic terminal in transitive_over: part_of ! part of -created_by: https://orcid.org/0000-0002-1373-1705 creation_date: 2020-07-17T09:26:52Z [Typedef] @@ -13251,9 +13295,18 @@ synonym: "has sensory terminal location" EXACT [] domain: CL:0000101 ! sensory neuron is_a: RO:0002360 ! has dendrite location transitive_over: part_of ! part of -created_by: https://orcid.org/0000-0002-1373-1705 creation_date: 2020-07-20T12:10:09Z +[Typedef] +id: RO:0015004 +name: has characterizing marker set +def: "A relation that applies between a cell type and a set of markers that can be used to uniquely identify that cell type." [] +synonym: "has marker gene combination" EXACT [] +synonym: "has marker signature set" EXACT [] +property_value: IAO:0000116 "C has_characterizing_marker_set y iff: C is a cell type and y is a collection of genes or proteins whose expression is sufficient to distinguish cell type C from most or all other cell types." xsd:string +property_value: terms:contributor https://orcid.org/0000-0001-7258-9596 +domain: CL:0000000 ! cell + [Typedef] id: RO:0015006 name: different in magnitude relative to @@ -13327,7 +13380,6 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0012003 is_a: has_participant ! has participant -created_by: https://orcid.org/0000-0003-1813-6857 creation_date: 2020-06-08T17:21:33Z [Typedef] @@ -13623,7 +13675,6 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_ontology xref: RO:0004009 is_a: has_input ! has input is_a: has_primary_input_or_output ! has primary input or output -created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-12-13T11:26:56Z [Typedef] @@ -13634,7 +13685,6 @@ def: "p 'has primary input ot output' c iff either (a) p 'has primary input' c o subset: http://purl.obolibrary.org/obo/valid_for_go_ontology xref: RO:0004007 is_a: has_participant ! has participant -created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-12-13T11:26:17Z [Typedef] @@ -13646,7 +13696,6 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_ontology xref: RO:0004008 is_a: has_output ! has output is_a: has_primary_input_or_output ! has primary input or output -created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-12-13T11:26:32Z [Typedef] @@ -13657,7 +13706,6 @@ def: "a relation between a process and a continuant, in which the process is act xref: RO:0012001 is_a: RO:0012000 ! has small molecule regulator inverse_of: RO:0012005 ! is small molecule activator of -created_by: https://orcid.org/0000-0003-1813-6857 creation_date: 2020-04-22T20:28:37Z [Typedef] @@ -13982,7 +14030,6 @@ namespace: external def: "p has anatomical participant c iff p has participant c, and c is an anatomical entity" [] xref: RO:0040036 is_a: has_participant ! has participant -created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-09-26T01:08:58Z [Typedef] @@ -14054,7 +14101,6 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0012008 is_a: results_in_organization_of ! results in organization of -created_by: https://orcid.org/0000-0003-1813-6857 creation_date: 2021-02-26T07:28:29Z [Typedef] @@ -14106,7 +14152,6 @@ name: results in organization of namespace: external def: "p results in organization of c iff p results in the assembly, arrangement of constituent parts, or disassembly of c" [] xref: RO:0002592 -is_a: has_participant ! has participant is_a: results_in_changes_to_anatomical_or_cellular_structure ! results in changes to anatomical or cellular structure [Typedef] diff --git a/src/ontology/subsets/general_cell_types_upper_slim.owl b/src/ontology/subsets/general_cell_types_upper_slim.owl index 8065f3828..bbfd7cd75 100644 --- a/src/ontology/subsets/general_cell_types_upper_slim.owl +++ b/src/ontology/subsets/general_cell_types_upper_slim.owl @@ -22,8 +22,8 @@ xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#" xmlns:ncbitaxon="http://purl.obolibrary.org/obo/ncbitaxon#"> - - 2024-09-26 + + 2025-01-08 @@ -287,13 +287,18 @@ WHERE { - 2018-03-14T00:03:24Z is negative form of + + + + + + @@ -373,6 +378,14 @@ WHERE { + + + + + + + + @@ -384,6 +397,14 @@ WHERE { + + + + + + + + @@ -1010,12 +1031,6 @@ WHERE { - - - - - - @@ -1034,6 +1049,12 @@ WHERE { + + + + + + @@ -1048,19 +1069,25 @@ WHERE { - + + description + - + + license + - + + title + @@ -1088,26 +1115,12 @@ WHERE { - - - - - - - - - - has_alternative_id - - - - @@ -1123,7 +1136,11 @@ WHERE { + An annotation property that links an ontology entity or a statement to a prefixed identifier or URI. + + database_cross_reference + has cross-reference @@ -1206,12 +1223,6 @@ WHERE { - - - - - - @@ -1681,7 +1692,6 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 A relationship between a process and a barrier, where the process occurs in a region spanning the barrier. For cellular processes the barrier is typically a membrane. Examples include transport across a membrane and membrane depolarization. - 2017-07-20T17:19:37Z occurs across @@ -3960,7 +3970,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different - p results in organization of c iff p results in the assembly, arrangement of constituent parts, or disassembly of c RO:0002592 @@ -4082,7 +4091,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different p 'has primary input ot output' c iff either (a) p 'has primary input' c or (b) p 'has primary output' c. - 2018-12-13T11:26:17Z RO:0004007 external @@ -4100,7 +4108,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different p has primary output c if (a) p has output c and (b) the goal of process is to modify, produce, or transform c. - 2018-12-13T11:26:32Z RO:0004008 external @@ -4128,7 +4135,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different p has primary input c if (a) p has input c and (b) the goal of process is to modify, consume, or transform c. - 2018-12-13T11:26:56Z RO:0004009 external @@ -4155,7 +4161,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different - 2018-03-13T23:55:05Z causally upstream of or within, negative effect https://wiki.geneontology.org/Causally_upstream_of_or_within,_negative_effect @@ -4167,7 +4172,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different - 2018-03-13T23:55:19Z causally upstream of or within, positive effect @@ -4181,7 +4185,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different a relation between a process and a continuant, in which the process is regulated by the small molecule continuant - 2020-04-22T20:27:26Z has small molecule regulator @@ -4194,7 +4197,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different a relation between a process and a continuant, in which the process is activated by the small molecule continuant - 2020-04-22T20:28:37Z RO:0012001 external @@ -4211,7 +4213,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different p acts on population of c iff c' is a collection, has members of type c, and p has participant c - 2020-06-08T17:21:33Z RO:0012003 external @@ -4231,7 +4232,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different a relation between a continuant and a process, in which the continuant is a small molecule that regulates the process - 2020-06-24T13:15:17Z is small molecule regulator of @@ -4244,7 +4244,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different a relation between a continuant and a process, in which the continuant is a small molecule that activates the process - 2020-06-24T13:15:26Z is small molecule activator of https://wiki.geneontology.org/Is_small_molecule_activator_of @@ -4256,7 +4255,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different - 2021-02-26T07:28:29Z RO:0012008 external @@ -4280,7 +4278,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different A relationship between a neuron and a region, where the neuron has a functionally relevant number of input and/or output synapses in that region. - 2020-07-17T09:26:52Z has synaptic input or output in has synaptic IO in region @@ -4298,7 +4295,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different Relation between a sensory neuron and some structure in which it receives sensory input via a sensory dendrite. - 2020-07-20T12:10:09Z has sensory dendrite location has sensory terminal in @@ -4308,6 +4304,20 @@ Each of these 3 primitives can be composed to yield a cross-product of different + + + + + A relation that applies between a cell type and a set of markers that can be used to uniquely identify that cell type. + C has_characterizing_marker_set y iff: C is a cell type and y is a collection of genes or proteins whose expression is sufficient to distinguish cell type C from most or all other cell types. + + has marker gene combination + has marker signature set + has characterizing marker set + + + + @@ -4447,7 +4457,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different p has anatomical participant c iff p has participant c, and c is an anatomical entity - 2018-09-26T01:08:58Z RO:0040036 external @@ -4791,6 +4800,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different XAO:0003012 ZFA:0009000 + + The definition of cell is intended to represent all cells, and thus a cell is defined as a material entity and not an anatomical structure, which implies that it is part of an organism (or the entirety of one). cell @@ -4822,6 +4833,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different A cell found in the embryo before the formation of all the gem layers is complete. ZFA:0009002 + + early embryonic cell (metazoa) @@ -4875,6 +4888,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different animal stem cell + + This term applies to metazoan. For plant stem cells, consider using PO:0004011 ‘initial cell’ or its parent PO:0004010 ‘meristematic cell’. stem cell @@ -5062,6 +5077,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different colony forming unit hematopoietic + + Markers differ between species, and two sets of markers have been described for mice. HSCs are reportedly CD34-positive, CD45-positive, CD48-negative, CD150-positive, CD133-positive, and CD244-negative. hematopoietic stem cell @@ -5104,6 +5121,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different A cell that is within the developmental lineage of gametes and is able to pass along its genetic material to offspring. ZFA:0009016 + + Originally this term had some plant germ line cell children. germ line cell @@ -5156,7 +5175,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different - @@ -5195,6 +5213,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different colony forming unit macrophage colony forming unit monocyte monocyte stem cell + + Morphology: mononuclear cell, diameter 12-20 _M, non-granular, N/C ratio 3/1 - 4/1; markers: CD11b (shared with many other myeloid cells); location: Adult: bone marrow; fetal: liver, Yolk Sac; role or process: hematopoiesis, monocyte development; lineage: hematopoietic, myeloid. monoblast @@ -5260,6 +5280,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different multifate stem cell multipotent cell multipotent stem cell + + multi fate stem cell @@ -5296,6 +5318,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different myeloid stem cell pluripotent stem cell (bone marrow) + + This cell type is intended to be compatible with any vertebrate common myeloid progenitor. For mammalian CMP known to be CD34-positive, please use the term 'common myeloid progenitor, CD34-positive' (CL_0001059). common myeloid progenitor @@ -5403,6 +5427,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different lymphoid stem cell lymphopoietic stem cell + + CLP are CD7-positive, CD10-positive, CD19-negative, CD34-positive, CD45RA-positive, CD79a-negative, CD127-positive, AA4.1-positive, RAG-negative, Sca-1-low, sIgM-negative, sIgD-negative, TdT-negative, Vpre-B-negative, and pre-BCR-negative. Expression of transcription factors include E2A-positive, EBF-positive, Ikaros-negative, PU.1-negative, and Pax5-negative. common lymphoid progenitor @@ -5453,6 +5479,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different MESH:D039901 ZFA:0009024 totipotential stem cell + + totipotent stem cell @@ -5480,6 +5508,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different FMA:84782 blast cell + + define using PATO mulit-potent or oligopotent? non-terminally differentiated cell @@ -5503,6 +5533,9 @@ Each of these 3 primitives can be composed to yield a cross-product of different FMA:70335 VHOG:0001529 ZFA:0009025 + + + myoblast @@ -5531,13 +5564,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - - - - - - + A connective tissue cell which secretes an extracellular matrix rich in collagen and other macromolecules. Flattened and irregular in outline with branching processes; appear fusiform or spindle-shaped. BTO:0000452 @@ -5548,6 +5575,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different ZFA:0009026 + + These cells may be vimentin-positive, fibronectin-positive, fsp1-positive, MMP-1-positive, collagen I-positive, collagen III-positive, and alpha-SMA-negative. fibroblast @@ -5592,6 +5621,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different epitheliocyte + + epithelial cell https://www.swissbiopics.org/api/image/Epithelial_cells.svg @@ -5627,6 +5658,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different ZFA:0009038 + + columnar/cuboidal epithelial cell @@ -5673,6 +5706,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different ZFA:0009044 + + blood cell @@ -5740,6 +5775,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different mature T cell + + T cell @@ -5815,7 +5852,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different - @@ -5871,13 +5907,20 @@ Each of these 3 primitives can be composed to yield a cross-product of different A specialized phagocytic cell associated with the absorption and removal of the mineralized matrix of bone tissue, which typically differentiates from monocytes. This cell has the following markers: tartrate-resistant acid phosphatase type 5-positive, PU.1-positive, c-fos-positive, nuclear factor NF-kappa-B p100 subunit-positive, tumor necrosis factor receptor superfamily member 11A-positive and macrophage colony-stimulating factor 1 receptor-positive. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Osteoclasts, derived from the monocyte/macrophage lineage, play a crucial role in bone remodeling through bone resorption. They are distinguished from other cells by their large size and their unique ability to secrete enzymes and acids that dissolve the calcium phosphate in bone. The formation of osteoclasts is influenced by two primary factors: macrophage colony-stimulating factor (M-CSF) and the ligand-activated receptor (RANKL) of nuclear factor kappa B (NF-κB). +Osteoclasts also collaborate with osteoblasts, responsible for new bone formation, to maintain bone health and adapt bone structure. Their coordinated actions allow continuous remodeling while preserving overall bone strength and integrity. Imbalances in osteoclast activity can lead to pathological conditions. For example, excessive activity may contribute to diseases like osteoporosis, periprosthetic osteolysis, bone tumors, and Paget's disease. Other the other hand, osteoclast deficiency ca result in conditions like osteopetrosis. BTO:0000968 CALOHA:TS-0721 FMA:66781 MESH:D010010 ZFA:0009047 + https://cellxgene.cziscience.com/cellguide/CL_0000092 chondroclast + + Morphology: Highly vesicular; markers: Surface: RANK, cFMS (MCSF receptor); Secreted: cathepsin K and TRAP (tartate resistant acid phosphatase); transcription factors: PU.1, cFOS, MITF, NFkB (p52); role or process: tissue remodelling: bone resorption; lineage: hematopoietic, myeloid. osteoclast @@ -5905,6 +5948,17 @@ Each of these 3 primitives can be composed to yield a cross-product of different PMID:15055519 PMID:17380158 + + + + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Osteoclasts, derived from the monocyte/macrophage lineage, play a crucial role in bone remodeling through bone resorption. They are distinguished from other cells by their large size and their unique ability to secrete enzymes and acids that dissolve the calcium phosphate in bone. The formation of osteoclasts is influenced by two primary factors: macrophage colony-stimulating factor (M-CSF) and the ligand-activated receptor (RANKL) of nuclear factor kappa B (NF-κB). +Osteoclasts also collaborate with osteoblasts, responsible for new bone formation, to maintain bone health and adapt bone structure. Their coordinated actions allow continuous remodeling while preserving overall bone strength and integrity. Imbalances in osteoclast activity can lead to pathological conditions. For example, excessive activity may contribute to diseases like osteoporosis, periprosthetic osteolysis, bone tumors, and Paget's disease. Other the other hand, osteoclast deficiency ca result in conditions like osteopetrosis. + DOI:10.3389/fmed.2017.00234 + DOI:10.37175/stemedicine.v1i4.57 + https://www.sciencedirect.com/topics/medicine-and-dentistry/osteoclast + @@ -5962,7 +6016,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different - @@ -6022,6 +6075,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different granular leukocyte polymorphonuclear leukocyte + + granulocyte @@ -6060,6 +6115,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different + + neuron associated cell @@ -6078,6 +6135,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different ZFA:0009052 motoneuron + + motor neuron @@ -6132,6 +6191,9 @@ Each of these 3 primitives can be composed to yield a cross-product of different MESH:D011984 WBbt:0005759 ZFA:0009053 + + + sensory neuron @@ -6174,7 +6236,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different A vertebrate phagocyte with a single nucleus. - This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. Mononuclear phagocytes are immune cells that form a critical part of the body's innate immune system, the body's first line of defense against infections. Mononuclear phagocytes are characterized by the presence of a single, large nucleus. The ‘Mononuclear Phagocyte System’ nomenclature was introduced to distinguish mononuclear monocytes and macrophages from other cells with multiple nuclei. However, the cells within the mononuclear phagocyte system represent a highly heterogeneous group, all of which are able to perform highly efficient phagocytosis - engulfing and digesting microbes and cellular debris to fight infections and to maintain normal tissue homeostasis. In addition to phagocytosis, mononuclear phagocytes also secrete chemical compounds to recruit other immune cells to a site of infection. These cells produce different types of signaling molecules, including cytokines, chemokines, and reactive oxygen species, triggering a cascade of responses to ensure rapid and efficient containment and neutralization of invading pathogens. These cells are also involved in antigen presentation, a process essential for stimulating an adaptive immune response. They can process and present antigens to T cells, thereby linking the innate and adaptive immune responses. @@ -6183,6 +6245,8 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf ZFA:0009064 https://cellxgene.cziscience.com/cellguide/CL_0000113 + + mononuclear phagocyte @@ -6203,7 +6267,7 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf - This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. Mononuclear phagocytes are immune cells that form a critical part of the body's innate immune system, the body's first line of defense against infections. Mononuclear phagocytes are characterized by the presence of a single, large nucleus. The ‘Mononuclear Phagocyte System’ nomenclature was introduced to distinguish mononuclear monocytes and macrophages from other cells with multiple nuclei. However, the cells within the mononuclear phagocyte system represent a highly heterogeneous group, all of which are able to perform highly efficient phagocytosis - engulfing and digesting microbes and cellular debris to fight infections and to maintain normal tissue homeostasis. In addition to phagocytosis, mononuclear phagocytes also secrete chemical compounds to recruit other immune cells to a site of infection. These cells produce different types of signaling molecules, including cytokines, chemokines, and reactive oxygen species, triggering a cascade of responses to ensure rapid and efficient containment and neutralization of invading pathogens. These cells are also involved in antigen presentation, a process essential for stimulating an adaptive immune response. They can process and present antigens to T cells, thereby linking the innate and adaptive immune responses. @@ -6227,7 +6291,7 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf A non-neuronal cell of the nervous system. They not only provide physical support, but also respond to injury, regulate the ionic and chemical composition of the extracellular milieu. Guide neuronal migration during development, and exchange metabolites with neurons. - This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. Glial cells, also known as neuroglia or simply glia, are non-neuronal cells in the central and peripheral nervous systems that provide support and protection for neurons. They constitute approximately half of the total cells in the human brain and more than half in other parts of the nervous system. Glial cells perform several key functions including, but not limited to, maintaining homeostasis, forming the myelin sheath around the neuron axons, and providing support and nutrition to neurons. These different functions are performed by various glial cell types, including astrocytes, oligodendrocytes, microglia and other specialized types. Astrocytes, for example, are the most abundant glial cells and provide metabolic and nutrient support to neurons, help regulate the extracellular ion and neurotransmitter levels, and play a role in the formation and maintenance of the blood-brain barrier, contributing to the overall homeostasis and functioning of the nervous system. Additionally, astrocytes are involved in synaptic communication and participate in processes such as synaptogenesis and synaptic pruning. @@ -6244,6 +6308,8 @@ Despite their overarching function in the support and protection of neurons, gli neuroglia + + Not all glial cells develop from glioblasts, with microglia developing from the mesoderm instead. See https://github.com/obophenotype/cell-ontology/issues/1571 glial cell @@ -6257,7 +6323,7 @@ Despite their overarching function in the support and protection of neurons, gli - This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. Glial cells, also known as neuroglia or simply glia, are non-neuronal cells in the central and peripheral nervous systems that provide support and protection for neurons. They constitute approximately half of the total cells in the human brain and more than half in other parts of the nervous system. Glial cells perform several key functions including, but not limited to, maintaining homeostasis, forming the myelin sheath around the neuron axons, and providing support and nutrition to neurons. These different functions are performed by various glial cell types, including astrocytes, oligodendrocytes, microglia and other specialized types. Astrocytes, for example, are the most abundant glial cells and provide metabolic and nutrient support to neurons, help regulate the extracellular ion and neurotransmitter levels, and play a role in the formation and maintenance of the blood-brain barrier, contributing to the overall homeostasis and functioning of the nervous system. Additionally, astrocytes are involved in synaptic communication and participate in processes such as synaptogenesis and synaptic pruning. @@ -6292,6 +6358,8 @@ Despite their overarching function in the support and protection of neurons, gli Ectoderm destined to be nervous tissue. ZFA:0009080 neurectoderm cell + + neurectodermal cell @@ -6333,6 +6401,8 @@ Despite their overarching function in the support and protection of neurons, gli mesenchymal stromal cells stem cells, mesenchymal + + Many but not all mesenchymal cells derive from the mesoderm. MSCs are reportedly CD3-negative, CD4-negative, CD5-negative, CD8-negative, CD11a-negative, CD11b-negative, CD14-negative, CD19-negative, CD29-positive, CD31-negative, CD34-negative, CD38-negative, CD40-negative, CD44-positive, CD45-negative, CD49-positive, CD54-positive, CD66b-negative, CD79a-negative, CD80-negative, CD102-positive, CD106-positive, CD117-positive, CD121a-positive, CD121b-positive, CD123-positive, CD124-positive, CD133-negative, CD146-positive, CD166-positive, CD271-positive, B220-negative, Gr1-negative, MHCI-positive, MHCII-negative, SSEA4-negative, sca1-positive, Ter119-negative, and glycophorin A-negative. Cultured MSCs are capable of producing stem cell factor, IL7, IL8, IL11, TGF-beta, cofilin, galectin-1, laminin-receptor 1, cyclophilin A, and MMP-2. mesenchymal stem cell https://github.com/obophenotype/cell-ontology/issues/474 @@ -6432,6 +6502,8 @@ Despite their overarching function in the support and protection of neurons, gli fat cell + + adipocyte @@ -6476,6 +6548,8 @@ Despite their overarching function in the support and protection of neurons, gli APC + + Note change of name; nearly all somatic cells can present antigens to T cells via MHC Class I complexes leading to effector responses, but professional antigen presenting cells constitutively express MHC Class II as well as costimulatory molecules, and thus can initiate immune responses via T cells. professional antigen presenting cell @@ -6510,6 +6584,8 @@ Despite their overarching function in the support and protection of neurons, gli ZFA:0009090 chromatocyte chromatophore + + pigment cell @@ -6561,15 +6637,22 @@ Despite their overarching function in the support and protection of neurons, gli A pigment cell derived from the neural crest. Contains melanin-filled pigment granules, which gives a brown to black appearance. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Melanocytes are specialized cells prevalently found in the skin, but also present in the hair follicles, eyes, inner ear, bones, heart, and brain. Their primary function is the synthesis of melanin, a pigment responsible for coloration of skin, hair, and eyes. The presence and distribution of this pigment play a crucial role in the body's defense mechanism against harmful ultraviolet radiation. +In addition to melanin production, melanocytes also engage in a variety of other biological functions. They play a fundamental role in the immune response, owing to their ability to present antigens to T cells. Furthermore, they contribute to the maintenance of the skin's homeostasis by regulating processes such as extracellular matrix remodeling and cytokine production. A balance in melanocyte function is pivotal, as dysfunctions often result in dermatological disorders. For instance, the loss of melanocytes or reduction in their function may lead to hypopigmentation conditions such as vitiligo, whereas an abnormal increase could result in hyperpigmentation disorders or melanoma, a dangerous type of skin cancer. BTO:0000847 CALOHA:TS-0613 FMA:70545 MESH:D008544 VHOG:0001679 ZFA:0009091 + https://cellxgene.cziscience.com/cellguide/CL_0000148 melanophore + + melanocyte @@ -6579,6 +6662,19 @@ Despite their overarching function in the support and protection of neurons, gli A pigment cell derived from the neural crest. Contains melanin-filled pigment granules, which gives a brown to black appearance. SANBI:mhl + + + + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Melanocytes are specialized cells prevalently found in the skin, but also present in the hair follicles, eyes, inner ear, bones, heart, and brain. Their primary function is the synthesis of melanin, a pigment responsible for coloration of skin, hair, and eyes. The presence and distribution of this pigment play a crucial role in the body's defense mechanism against harmful ultraviolet radiation. +In addition to melanin production, melanocytes also engage in a variety of other biological functions. They play a fundamental role in the immune response, owing to their ability to present antigens to T cells. Furthermore, they contribute to the maintenance of the skin's homeostasis by regulating processes such as extracellular matrix remodeling and cytokine production. A balance in melanocyte function is pivotal, as dysfunctions often result in dermatological disorders. For instance, the loss of melanocytes or reduction in their function may lead to hypopigmentation conditions such as vitiligo, whereas an abnormal increase could result in hyperpigmentation disorders or melanoma, a dangerous type of skin cancer. + DOI:10.1002/med.21754 + DOI:10.1038/nrc.2016.37 + DOI:10.1111/j.1751-1097.2007.00226.x + DOI:10.3390/ijms21249769 + https://www.sciencedirect.com/topics/agricultural-and-biological-sciences/melanocyte + @@ -6593,6 +6689,8 @@ Despite their overarching function in the support and protection of neurons, gli pigment cell + + visual pigment cell @@ -6623,6 +6721,8 @@ Despite their overarching function in the support and protection of neurons, gli BTO:0003659 FMA:86916 + + secretory cell @@ -6661,6 +6761,8 @@ Despite their overarching function in the support and protection of neurons, gli FMA:16014 ZFA:0009092 + + exocrine cell @@ -6733,6 +6835,8 @@ Despite their overarching function in the support and protection of neurons, gli endocrinocyte + + endocrine cell @@ -6757,6 +6861,8 @@ Despite their overarching function in the support and protection of neurons, gli A cell whose primary function is to shorten. + + contractile cell @@ -6791,6 +6897,8 @@ Despite their overarching function in the support and protection of neurons, gli muscle fiber myocyte + + muscle cell https://www.swissbiopics.org/api/image/Muscle_cells.svg @@ -6838,13 +6946,21 @@ Despite their overarching function in the support and protection of neurons, gli A somatic cell located in skeletal muscle. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Skeletal muscle cells, or myocytes, are essential for the musculoskeletal system, featuring a striated appearance from tightly packed sarcomeres. These elongated, multi-nucleated cells convert ATP into mechanical energ and are key for voluntary movement and posture. They also are responsible for maintaining body temperature, storing nutrients, and stabilizing joints. +Skeletal muscle cells organize themselves tightly into bundles to form muscle fibers. Embedded within each of these cells are thousands of myofibrils, which are made up of the contractile proteins, actin (the thin filament), and myosin (the thick filament). Contraction of a skeletal muscle cell occurs when these myofibrils shorten, a process driven by the sliding of actin and myosin filaments over each other in a mechanism famously known as the sliding filament theory. +Additionally, skeletal muscle cells exhibit a high degree of plasticity, which allows for their adaptation in response to alterations in functional demands or damages. They have an innate regenerative capacity due to the presence of satellite cells—quiescent muscle stem cells that reside within the muscle fibers. Upon muscle injury, these satellite cells become activated, proliferate, and differentiate into new muscle cells, thereby contributing to the repair and growth of injured skeletal muscle. With this, skeletal muscle cells serve not only a pivotal biomechanical function but also possess a great capacity for self-healing and regeneration. BTO:0004392 CALOHA:TS-2158 FMA:9727 ZFA:0009115 + https://cellxgene.cziscience.com/cellguide/CL_0000188 skeletal muscle cell + + cell of skeletal muscle @@ -6854,6 +6970,20 @@ Despite their overarching function in the support and protection of neurons, gli A somatic cell located in skeletal muscle. GOC:tfm + + + + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Skeletal muscle cells, or myocytes, are essential for the musculoskeletal system, featuring a striated appearance from tightly packed sarcomeres. These elongated, multi-nucleated cells convert ATP into mechanical energ and are key for voluntary movement and posture. They also are responsible for maintaining body temperature, storing nutrients, and stabilizing joints. +Skeletal muscle cells organize themselves tightly into bundles to form muscle fibers. Embedded within each of these cells are thousands of myofibrils, which are made up of the contractile proteins, actin (the thin filament), and myosin (the thick filament). Contraction of a skeletal muscle cell occurs when these myofibrils shorten, a process driven by the sliding of actin and myosin filaments over each other in a mechanism famously known as the sliding filament theory. +Additionally, skeletal muscle cells exhibit a high degree of plasticity, which allows for their adaptation in response to alterations in functional demands or damages. They have an innate regenerative capacity due to the presence of satellite cells—quiescent muscle stem cells that reside within the muscle fibers. Upon muscle injury, these satellite cells become activated, proliferate, and differentiate into new muscle cells, thereby contributing to the repair and growth of injured skeletal muscle. With this, skeletal muscle cells serve not only a pivotal biomechanical function but also possess a great capacity for self-healing and regeneration. + DOI:10.1002/cphy.c160033 + DOI:10.3390/biology10101056 + https://www.nature.com/scitable/topicpage/the-sliding-filament-theory-of-muscle-contraction-14567666/ + https://www.ncbi.nlm.nih.gov/books/NBK537139 + https://www.ncbi.nlm.nih.gov/books/NBK9961/ + @@ -6876,16 +7006,24 @@ Despite their overarching function in the support and protection of neurons, gli A non-striated, elongated, spindle-shaped cell found lining the digestive tract, uterus, and blood vessels. They develop from specialized myoblasts (smooth muscle myoblast). + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Smooth muscle cells are a specialized type of muscle cells that are primarily found within the walls of hollow organs such as the intestine, stomach, bladder, uterus, and blood vessels. These cells are an essential component of the autonomic nervous system controling involuntary movements within the body. +Smooth muscle cells play a vital role in many physiological processes due to their unique functionality. They can contract and relax in a slow, sustained, and controlled manner to help modulate the size and shape of the lumens of the organs they surround. For example, in the digestive system, coordinated contraction and relaxation of smooth muscle cells propels food along the gastrointestinal tract - a process known as peristalsis. In the blood vessels, the smooth muscle cells, by contracting or relaxing, either constrict or dilate the vessels, which in turn, help regulate blood flow and pressure. +On a cellular level, smooth muscle cells possess a single, centrally located nucleus and contain an arranged network of actin and myosin filaments, which are the proteins responsible for muscle contraction. Unlike their counterparts in skeletal or cardiac muscles, these cells lack specific contact points for these filaments, hence the lack of visible striations. Furthermore, the contraction of smooth muscle cells is regulated by hormones and neurotransmitters, such as acetylcholine and norepinephrine, adding an additional layer of complex regulation to these highly specialized cells. non-striated muscle cell BTO:0004576 CALOHA:TS-2159 FMA:14072 ZFA:0009118 + https://cellxgene.cziscience.com/cellguide/CL_0000192 SMCs myocytes, smooth muscle smooth muscle fiber + + smooth muscle cell @@ -6897,6 +7035,20 @@ Despite their overarching function in the support and protection of neurons, gli PMID:9315361 http://en.wikipedia.org/wiki/Smooth_muscle_cell + + + + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Smooth muscle cells are a specialized type of muscle cells that are primarily found within the walls of hollow organs such as the intestine, stomach, bladder, uterus, and blood vessels. These cells are an essential component of the autonomic nervous system controling involuntary movements within the body. +Smooth muscle cells play a vital role in many physiological processes due to their unique functionality. They can contract and relax in a slow, sustained, and controlled manner to help modulate the size and shape of the lumens of the organs they surround. For example, in the digestive system, coordinated contraction and relaxation of smooth muscle cells propels food along the gastrointestinal tract - a process known as peristalsis. In the blood vessels, the smooth muscle cells, by contracting or relaxing, either constrict or dilate the vessels, which in turn, help regulate blood flow and pressure. +On a cellular level, smooth muscle cells possess a single, centrally located nucleus and contain an arranged network of actin and myosin filaments, which are the proteins responsible for muscle contraction. Unlike their counterparts in skeletal or cardiac muscles, these cells lack specific contact points for these filaments, hence the lack of visible striations. Furthermore, the contraction of smooth muscle cells is regulated by hormones and neurotransmitters, such as acetylcholine and norepinephrine, adding an additional layer of complex regulation to these highly specialized cells. + DOI:10.1093/ptj/81.11.1810 + https://training.seer.cancer.gov/anatomy/muscular/types.html + https://www.ncbi.nlm.nih.gov/books/NBK10854/ + https://www.ncbi.nlm.nih.gov/books/NBK526125 + https://www.ncbi.nlm.nih.gov/books/NBK556137/ + @@ -6947,6 +7099,8 @@ Despite their overarching function in the support and protection of neurons, gli FMA:86740 ZFA:0009127 + + photoreceptor cell https://www.swissbiopics.org/api/image/Photoreceptor_cell.svg @@ -6977,6 +7131,8 @@ Despite their overarching function in the support and protection of neurons, gli A cell whose function is determined by the generation or the reception of an electric signal. ZFA:0009128 + + electrically active cell @@ -7017,6 +7173,8 @@ Despite their overarching function in the support and protection of neurons, gli A cell that moves by its own activities. ZFA:0009136 + + motile cell @@ -7049,6 +7207,9 @@ Despite their overarching function in the support and protection of neurons, gli FMA:72549 ZFA:0009137 ectoderm cell + + + ectodermal cell @@ -7078,11 +7239,18 @@ Despite their overarching function in the support and protection of neurons, gli A cell of the middle germ layer of the embryo. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Mesodermal cells are pluripotent and the most abundant in the human body. They contribute to the development of several structures such as the skeletal muscles, bones, heart and blood vessels, kidneys, gonads, connective tissues, and certain layers of the skin. Hence, the mesoderm is often regarded as an active and diverse layer due to its role in forming many bodily structures. +In embryonic development, these cells are instrumental, contributing to the body's structures through a carefully coordinated sequence of morphogenetic movements. This process forms the complex multicellular architecture of tissues and organs from a simple ball of cells. Without the function of mesodermal cells, the body's integral structures and systems would cease to form correctly, leading to developmental disorders such as axial mesodermal dysplasia complex FMA:72554 ZFA:0009138 + https://cellxgene.cziscience.com/cellguide/CL_0000222 mesoblast mesoderm cell + + mesodermal cell @@ -7091,6 +7259,17 @@ Despite their overarching function in the support and protection of neurons, gli A cell of the middle germ layer of the embryo. MESH:D008648 + + + + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Mesodermal cells are pluripotent and the most abundant in the human body. They contribute to the development of several structures such as the skeletal muscles, bones, heart and blood vessels, kidneys, gonads, connective tissues, and certain layers of the skin. Hence, the mesoderm is often regarded as an active and diverse layer due to its role in forming many bodily structures. +In embryonic development, these cells are instrumental, contributing to the body's structures through a carefully coordinated sequence of morphogenetic movements. This process forms the complex multicellular architecture of tissues and organs from a simple ball of cells. Without the function of mesodermal cells, the body's integral structures and systems would cease to form correctly, leading to developmental disorders such as axial mesodermal dysplasia complex + DOI:10.1016/j.ceb.2019.07.012 + DOI:10.5535/arm.2016.40.1.162 + https://www.sciencedirect.com/topics/biochemistry-genetics-and-molecular-biology/mesoderm + @@ -7115,6 +7294,8 @@ Despite their overarching function in the support and protection of neurons, gli FMA:72555 ZFA:0009139 endoderm cell + + endodermal cell @@ -7155,6 +7336,8 @@ Despite their overarching function in the support and protection of neurons, gli A cell with a single nucleus. + + single nucleate cell @@ -7192,6 +7375,8 @@ Despite their overarching function in the support and protection of neurons, gli A cell with more than one nucleus. multinucleated cells polynuclear cells + + multinucleate cell @@ -7244,7 +7429,8 @@ Despite their overarching function in the support and protection of neurons, gli FMA:83806 MESH:D010586 ZFA:0009140 - + + phagocyte @@ -7312,6 +7498,8 @@ Despite their overarching function in the support and protection of neurons, gli + + Morphology: Diameter 30_M-80 _M, abundant cytoplasm, low N/C ratio, eccentric nucleus. Irregular shape with pseudopods, highly adhesive. Contain vacuoles and phagosomes, may contain azurophilic granules; markers: Mouse & Human: CD68, in most cases CD11b. Mouse: in most cases F4/80+; role or process: immune, antigen presentation, & tissue remodelling; lineage: hematopoietic, myeloid. macrophage @@ -7376,6 +7564,8 @@ Despite their overarching function in the support and protection of neurons, gli + + B cell @@ -7426,7 +7616,8 @@ Despite their overarching function in the support and protection of neurons, gli Any cell that in taxon some Eukaryota. MESH:D005057 - + + eukaryotic cell @@ -7443,6 +7634,8 @@ Despite their overarching function in the support and protection of neurons, gli A cell that is specialised to accumulate a particular substance(s). + + stuff accumulating cell @@ -7460,6 +7653,8 @@ Despite their overarching function in the support and protection of neurons, gli ZFA:0009162 + + extracellular matrix secreting cell @@ -7486,6 +7681,8 @@ Despite their overarching function in the support and protection of neurons, gli A cell derived from the specialized ectoderm flanking each side of the embryonic neural plate, which after the closure of the neural tube, forms masses of cells that migrate out from the dorsal aspect of the neural tube to spread throughout the body. FMA:86667 ZFA:0007086 + + migratory neural crest cell @@ -7526,7 +7723,10 @@ Despite their overarching function in the support and protection of neurons, gli Any cell that is part of some extraembryonic structure. ZFA:0009176 + + + extraembryonic cell @@ -7549,6 +7749,8 @@ Despite their overarching function in the support and protection of neurons, gli A cell of the outer layer of a blastula that gives rise to the ectoderm after gastrulation. + + epiblast cell @@ -7580,6 +7782,8 @@ Despite their overarching function in the support and protection of neurons, gli A multifate stem cell found in skeletal muscle than can differentiate into many different cell types, including muscle. Distinct cell type from satellite cell. FMA:86767 ZFA:0009179 + + Multi-potency demonstrated ex vivo. At the time of writing, it is unclear whether the endogenous population differentiates into multiple cell types in vivo. multi-potent skeletal muscle stem cell @@ -7632,6 +7836,8 @@ Despite their overarching function in the support and protection of neurons, gli BTO:0000854 EHDAA2:0004546 FMA:72395 + + animal zygote @@ -7649,6 +7855,8 @@ Despite their overarching function in the support and protection of neurons, gli A cell whose function is determined by its response to an electric signal. ZFA:0009190 + + electrically responsive cell @@ -7672,6 +7880,8 @@ Despite their overarching function in the support and protection of neurons, gli A cell that initiates an electrical signal and passes that signal to another cell. ZFA:0009193 + + electrically signaling cell @@ -7745,7 +7955,6 @@ Despite their overarching function in the support and protection of neurons, gli - @@ -7806,6 +8015,8 @@ Despite their overarching function in the support and protection of neurons, gli veiled cell + + dendritic cell @@ -7830,6 +8041,8 @@ Despite their overarching function in the support and protection of neurons, gli A cell whose primary function is to protect the organism. + + defensive cell @@ -7851,20 +8064,22 @@ Despite their overarching function in the support and protection of neurons, gli - A connective tissue cell of an organ found in the loose connective tissue. These are most often associated with the uterine mucosa and the ovary as well as the hematopoietic system and elsewhere. + A connective tissue cell of an organ found in the loose connective tissue. BTO:0002064 FMA:83624 ZFA:0009226 + + stromal cell - A connective tissue cell of an organ found in the loose connective tissue. These are most often associated with the uterine mucosa and the ovary as well as the hematopoietic system and elsewhere. + A connective tissue cell of an organ found in the loose connective tissue. GOC:tfm MESH:D017154 @@ -7909,6 +8124,8 @@ Despite their overarching function in the support and protection of neurons, gli cardiac muscle progenitor cell cardiomyocyte progenitor cell + + cardiac muscle myoblast @@ -7949,11 +8166,19 @@ Despite their overarching function in the support and protection of neurons, gli A precursor cell destined to differentiate into smooth muscle myocytes. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +A precursor to the smooth muscle cell, the smooth muscle myoblast, is integral to various body systems, including the cardiovascular, gastrointestinal, and respiratory systems. Smooth muscle myoblasts arise from the differentiation of mesenchymal stem cells, a process tightly regulated by specific genetic factors and environmental signals. Their role extends to myogenesis, particularly in the formation of muscular tissue, especially during embryonic development. +Smooth muscle myoblasts possess distinctive cellular characteristics. In contrast to skeletal muscle myoblasts, they do not fuse to create multinucleated fibers. Instead, they differentiate into individual, uninucleated smooth muscle cells. This differentiation unfolds in two distinct phases: proliferation, marked by rapid division to increase cell numbers, and differentiation, involving structural and functional transformation into mature smooth muscle cells. This intricate process is intricately mediated by various signaling molecules and transcription factors. +Functionally, smooth muscle myoblasts and the mature muscle cells they generate play pivotal roles in various physiological processes. Smooth muscle cells orchestrate involuntary muscle responses and are integral to body systems that regulate blood flow, propel food along the digestive tract, and control airflow in the respiratory tract. These diverse functions underscore the significance of smooth muscle myoblasts in the body's growth, maintenance, and overall function. FMA:84798 ZFA:0009235 + https://cellxgene.cziscience.com/cellguide/CL_0000514 myoblast, smooth muscle satellite cell + + smooth muscle myoblast @@ -7963,6 +8188,18 @@ Despite their overarching function in the support and protection of neurons, gli GOC:tfm MESH:D032390 + + + + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +A precursor to the smooth muscle cell, the smooth muscle myoblast, is integral to various body systems, including the cardiovascular, gastrointestinal, and respiratory systems. Smooth muscle myoblasts arise from the differentiation of mesenchymal stem cells, a process tightly regulated by specific genetic factors and environmental signals. Their role extends to myogenesis, particularly in the formation of muscular tissue, especially during embryonic development. +Smooth muscle myoblasts possess distinctive cellular characteristics. In contrast to skeletal muscle myoblasts, they do not fuse to create multinucleated fibers. Instead, they differentiate into individual, uninucleated smooth muscle cells. This differentiation unfolds in two distinct phases: proliferation, marked by rapid division to increase cell numbers, and differentiation, involving structural and functional transformation into mature smooth muscle cells. This intricate process is intricately mediated by various signaling molecules and transcription factors. +Functionally, smooth muscle myoblasts and the mature muscle cells they generate play pivotal roles in various physiological processes. Smooth muscle cells orchestrate involuntary muscle responses and are integral to body systems that regulate blood flow, propel food along the digestive tract, and control airflow in the respiratory tract. These diverse functions underscore the significance of smooth muscle myoblasts in the body's growth, maintenance, and overall function. + DOI:10.1074/jbc.RA118.001739 + https://www.ncbi.nlm.nih.gov/books/NBK544225/ + https://www.sciencedirect.com/topics/medicine-and-dentistry/smooth-muscle + @@ -8010,6 +8247,8 @@ Despite their overarching function in the support and protection of neurons, gli FMA:84799 ZFA:0009236 skeletal myoblast + + skeletal muscle myoblast @@ -8039,6 +8278,8 @@ Despite their overarching function in the support and protection of neurons, gli A phagocyte in vertebrates that is able to phagocytosis. + + phagocyte (sensu Vertebrata) @@ -8059,6 +8300,8 @@ Despite their overarching function in the support and protection of neurons, gli FMA:87653 ZFA:0009238 input neuron + + afferent neuron @@ -8085,6 +8328,9 @@ Despite their overarching function in the support and protection of neurons, gli A neuron which sends impulses peripherally to activate muscles or secretory cells. ZFA:0009239 output neuron + + + efferent neuron @@ -8126,6 +8372,8 @@ Despite their overarching function in the support and protection of neurons, gli nerve cell + + These cells are also reportedly CD4-negative and CD200-positive. They are also capable of producing CD40L and IFN-gamma. neuron @@ -8168,6 +8416,8 @@ Despite their overarching function in the support and protection of neurons, gli BTO:0003217 FMA:83377 ZFA:0009249 + + Derived from UBERON:0002342 neural crest. melanoblast @@ -8248,6 +8498,8 @@ Despite their overarching function in the support and protection of neurons, gli VHOG:0001535 ZFA:0009250 + + Editors note: consider adding taxon constraint to vertebrata (PMID:18025161) lymphocyte @@ -8313,9 +8565,7 @@ Despite their overarching function in the support and protection of neurons, gli - - @@ -8360,8 +8610,13 @@ Despite their overarching function in the support and protection of neurons, gli A hematopoietic progenitor cell that is committed to the granulocyte and monocyte lineages. These cells are CD123-positive, and do not express Gata1 or Gata2 but do express C/EBPa, and Pu.1. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Granulocyte monocyte progenitor cells (GMP cells), originating from hematopoietic stem cells in the bone marrow, are a critical intermediate in myeloid cell development. Positioned at a key differentiation juncture, these cells exhibit bidirectional potential, giving rise to both granulocyte and monocyte lineages. +Their primary role is to generate mature granulocytes and monocytes, essential components of the body's innate immunity and inflammatory responses. Granulocytes, such as neutrophils, eosinophils, and basophils, contribute to the first line of defense against infections by migrating to the infection site and phagocytosing pathogens. Monocytes can differentiate into macrophages or dendritic cells, playing diverse roles in immune responses. CFU-C , Colony forming unit in culture ZFA:0009251 + https://cellxgene.cziscience.com/cellguide/CL_0000557 colony forming unit granulocyte macrophage granulocyte-macrophage progenitor granulocyte/monocyte precursor @@ -8369,6 +8624,8 @@ Despite their overarching function in the support and protection of neurons, gli CFU-GM GMP + + Originally described in the dendritic cell ontology (DC_CL:0000042)(PMID:19243617). GMPs are reportedly CD16-positive, CD32-positive, CD34-positive, CD38-positive, CD45RA-positive, CD110-negative, CD117-positive, CD123-positive, and SCA1-negative. granulocyte monocyte progenitor cell @@ -8390,6 +8647,17 @@ Despite their overarching function in the support and protection of neurons, gli http://en.wikipedia.org/wiki/CFU-GM http://www.copewithcytokines.de + + + + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Granulocyte monocyte progenitor cells (GMP cells), originating from hematopoietic stem cells in the bone marrow, are a critical intermediate in myeloid cell development. Positioned at a key differentiation juncture, these cells exhibit bidirectional potential, giving rise to both granulocyte and monocyte lineages. +Their primary role is to generate mature granulocytes and monocytes, essential components of the body's innate immunity and inflammatory responses. Granulocytes, such as neutrophils, eosinophils, and basophils, contribute to the first line of defense against infections by migrating to the infection site and phagocytosing pathogens. Monocytes can differentiate into macrophages or dendritic cells, playing diverse roles in immune responses. + DOI:10.1016/j.immuni.2017.10.021 + DOI:10.1146/annurev-immunol-081022113627 + DOI:10.1186/2050-7771-2-1 + @@ -8463,7 +8731,6 @@ Despite their overarching function in the support and protection of neurons, gli - @@ -8488,6 +8755,8 @@ Despite their overarching function in the support and protection of neurons, gli FMA:83551 ZFA:0009253 + + Morphology: Mononuclear cell, diameter 14-18 _M, fine azurophilic granules; markers: CD11b (shared with many other myeloid cells); location: Adult: bone marrow; Fetal: Liver, Yolk Sac; role or process: hematopoiesis, monocyte development; lineage: hematopoietic, myeloid. promonocyte @@ -8538,7 +8807,6 @@ Despite their overarching function in the support and protection of neurons, gli - @@ -8567,6 +8835,8 @@ Despite their overarching function in the support and protection of neurons, gli ZFA:0009258 angioblast chondroplast + + These cells are reportedly CD31-positive, CD34-positive, CD144-positive, CD309-positive, and TAL1-positive. angioblastic mesenchymal cell @@ -8655,6 +8925,8 @@ Despite their overarching function in the support and protection of neurons, gli + + Morphology: Mononuclear cell, diameter, 14 to 20 _M, N/C ratio 2:1-1:1. Nucleus may appear in variety of shapes: round, kidney, lobulated, or convoluted. Fine azurophilic granules present; markers: CD11b (shared with other myeloid cells), human: CD14, mouse: F4/80-mid,GR1-low; location: Blood, but can be recruited into tissues; role or process: immune & tissue remodelling; lineage: hematopoietic, myeloid. monocyte @@ -8761,6 +9033,8 @@ Despite their overarching function in the support and protection of neurons, gli NK cell + + natural killer cell @@ -8812,6 +9086,8 @@ Despite their overarching function in the support and protection of neurons, gli A non-terminally differentiated cell that is capable of developing into a muscle cell. ZFA:0009291 + + muscle precursor cell @@ -8854,6 +9130,8 @@ Despite their overarching function in the support and protection of neurons, gli CALOHA:TS-2086 MESH:D053687 ZFA:0009307 + + somatic stem cell @@ -8908,6 +9186,8 @@ Despite their overarching function in the support and protection of neurons, gli CALOHA:TS-2157 FMA:86936 ZFA:0005784 + + striated muscle cell @@ -8984,6 +9264,8 @@ Despite their overarching function in the support and protection of neurons, gli white blood cell immune cell + + leukocyte @@ -9058,19 +9340,26 @@ Despite their overarching function in the support and protection of neurons, gli Cardiac muscle cells are striated muscle cells that are responsible for heart contraction. In mammals, the contractile fiber resembles those of skeletal muscle but are only one third as large in diameter, are richer in sarcoplasm, and contain centrally located instead of peripheral nuclei. - FMA:83808 + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Cardiac muscle cells, also known as cardiomyocytes or cardiac myocytes, are specialized cells that form the heart tissue. These cells are elongated, branched, and contain a single centrally located nucleus. Their anatomy is composed primarily of densely packed myofibrils, which are protein structures that consist of sarcomeres - the fundamental units of muscle contraction. Cardiac muscle cells are united at their ends through specialized junctions known as intercalated discs, which allow the heart to contract in a unified, powerful and rhythmic way. +Functionally, cardiac muscle cells are responsible for the heart's consistent pumping action that circulates blood throughout the body. Unlike most cells in the body, cardiac muscle cells spontaneously depolarize and generate action potentials without external stimulation. This unique trait stems from the presence of ion channels in the cells' membrane that allow a cyclic flow of ions across the membrane, which create the electrical impulses necessary for heart contraction. The spread of these electrical signals from one cardiac muscle cell to another - facilitated by the interconnected network made by the intercalated disks - results in a synchronized contraction of the heart muscle. +Unlike skeletal muscle cells which can tire and need rest, cardiac muscle cells have to work ceaselessly throughout the entire lifespan, without the opportunity for rest, to ensure continuous circulation of blood. This is made possible through the high volume of mitochondria and a constant supply of oxygen from coronary circulation. In conclusion, cardiac muscle cells, through their unique structure and vital functionality, play a pivotal role in sustaining life by providing the means for blood to reach every cell in the body. cardiocyte BTO:0001539 CALOHA:TS-0115 FMA:14067 MESH:D032383 ZFA:0009316 + https://cellxgene.cziscience.com/cellguide/CL_0000746 cardiac muscle fiber cardiac myocyte cardiomyocyte heart muscle cell + + This class encompasses the muscle cells responsible for heart* contraction in both vertebrates and arthropods. The ultrastucture of a wide range of arthropod heart cells has been examined including spiders, horseshoe crabs, crustaceans (see Sherman, 1973 and refs therein) and insects (see Lehmacher et al (2012) and refs therein). According to these refs, the cells participating in heart contraction in all cases are transversely striated. Insects hearts additionally contain ostial cells, also transversely striated muscle cells, but which do not participate in heart contraction. cardiac muscle cell @@ -9085,6 +9374,19 @@ Despite their overarching function in the support and protection of neurons, gli PMID:22426062 PMID:4711263 + + + + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Cardiac muscle cells, also known as cardiomyocytes or cardiac myocytes, are specialized cells that form the heart tissue. These cells are elongated, branched, and contain a single centrally located nucleus. Their anatomy is composed primarily of densely packed myofibrils, which are protein structures that consist of sarcomeres - the fundamental units of muscle contraction. Cardiac muscle cells are united at their ends through specialized junctions known as intercalated discs, which allow the heart to contract in a unified, powerful and rhythmic way. +Functionally, cardiac muscle cells are responsible for the heart's consistent pumping action that circulates blood throughout the body. Unlike most cells in the body, cardiac muscle cells spontaneously depolarize and generate action potentials without external stimulation. This unique trait stems from the presence of ion channels in the cells' membrane that allow a cyclic flow of ions across the membrane, which create the electrical impulses necessary for heart contraction. The spread of these electrical signals from one cardiac muscle cell to another - facilitated by the interconnected network made by the intercalated disks - results in a synchronized contraction of the heart muscle. +Unlike skeletal muscle cells which can tire and need rest, cardiac muscle cells have to work ceaselessly throughout the entire lifespan, without the opportunity for rest, to ensure continuous circulation of blood. This is made possible through the high volume of mitochondria and a constant supply of oxygen from coronary circulation. In conclusion, cardiac muscle cells, through their unique structure and vital functionality, play a pivotal role in sustaining life by providing the means for blood to reach every cell in the body. + DOI:10.1016/j.ccep.2010.10.012 + DOI:10.1038/nrcardio.2016.203 + https://www.ncbi.nlm.nih.gov/books/NBK572070 + https://www.sciencedirect.com/topics/agricultural-and-biological-sciences/cardiac-muscle + @@ -9128,6 +9430,8 @@ Despite their overarching function in the support and protection of neurons, gli MESH:D022423 ZFA:0009324 + + myeloid cell @@ -9170,6 +9474,8 @@ Despite their overarching function in the support and protection of neurons, gli A cell of the monocyte, granulocyte, or mast cell lineage. ZFA:0009326 + + myeloid leukocyte @@ -9232,6 +9538,8 @@ Despite their overarching function in the support and protection of neurons, gli CD11c+CD123- DC mDC + + These cells are CD1a-negative, CD1b-positive, CD11a-positive, CD11c-positive, CD13-positive, CD14-negative, CD20-negative, CD21-negative, CD33-positive, CD40-negative, CD50-positive, CD54-positive, CD58-positive, CD68-negative, CD80-negative, CD83-negative, CD85j-positive, CD86-positive, CD89-negative, CD95-positive, CD120a-negative, CD120b-positive, CD123-negative, CD178-negative, CD206-negative, CD207-negative, CD209-negative, and TNF-alpha-negative. Upon TLR stimulation, they are capable of producing high levels of TNF-alpha, IL-6, CXCL8 (IL-8). myeloid dendritic cell @@ -9288,7 +9596,6 @@ Despite their overarching function in the support and protection of neurons, gli - @@ -9338,6 +9645,8 @@ Despite their overarching function in the support and protection of neurons, gli pro-natural killer cell null cell preNK cell + + Most markers only described for human pro NK cells. pro-NK cell @@ -9411,7 +9720,6 @@ Despite their overarching function in the support and protection of neurons, gli - @@ -9450,6 +9758,8 @@ Despite their overarching function in the support and protection of neurons, gli progenitor B-lymphocyte pre-B cell (Philadelphia nomenclature) + + Human pro-B cells are reportedly CD10-positive, CD22-positive, CD34-positive, CD38-positive, CD45-low, CD48-positive, CD79a-positive, CD127-positive, CD184-positive, RAG-positive, TdT-positive, Vpre-B-positive, pre-BCR-negative, IgD-negative, and IgM-negative. Transcription factors expressed: Pax5-positive, EBF-positive, E2A-negative, Ikaros-negative, and PU.1-negative. pro-B cell @@ -9527,6 +9837,8 @@ Despite their overarching function in the support and protection of neurons, gli DN1 thymocyte TN1 cell + + pro-T cell @@ -9623,7 +9935,6 @@ Despite their overarching function in the support and protection of neurons, gli - @@ -9730,6 +10041,8 @@ Despite their overarching function in the support and protection of neurons, gli hemopoietic progenitor cell + + Markers differ between mouse and human. hematopoietic multipotent progenitor cell @@ -9781,6 +10094,8 @@ Despite their overarching function in the support and protection of neurons, gli FMA:70338 ZFA:0009355 + + Note that this is a class of cell types, not an identified single cell type. lymphoid lineage restricted progenitor cell @@ -9836,6 +10151,8 @@ Despite their overarching function in the support and protection of neurons, gli FMA:70339 ZFA:0009356 + + Note that this is a class of cell types, not an identified single cell type. myeloid lineage restricted progenitor cell @@ -9888,6 +10205,8 @@ Despite their overarching function in the support and protection of neurons, gli peripheral blood mononuclear cell + + mononuclear cell @@ -9923,6 +10242,9 @@ Despite their overarching function in the support and protection of neurons, gli A lymphocyte of B lineage with the commitment to express an immunoglobulin complex. + + + Types of B lineage lymphocytes include B cells and antibody secreting cells (plasmablasts and plasma cells). Lymphocytes of B cell lineage can be distinguished from those of T cell lineage by their lack of CD3e (as part of the T cell receptor complex). lymphocyte of B lineage @@ -9960,6 +10282,8 @@ Despite their overarching function in the support and protection of neurons, gli haemopoietic cell hemopoietic cell + + hematopoietic cell @@ -10010,6 +10334,8 @@ Despite their overarching function in the support and protection of neurons, gli type 1 DC + + Originally described in the dendritic cell ontology (DC_CL:0000003)(PMID:19243617) These cells are also CD20-negative, MHCII-positive. conventional dendritic cell @@ -10035,6 +10361,9 @@ Despite their overarching function in the support and protection of neurons, gli + + + Originally described in the dendritic cell ontology (DC_CL:1110000)(PMID:19243617). CD7-negative lymphoid progenitor OR granulocyte monocyte progenitor @@ -10065,8 +10394,17 @@ Despite their overarching function in the support and protection of neurons, gli A connective tissue cell found in bone. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Bone cells, also known as osteocytes, form the building blocks of the skeletal system. They represent the most common type of bone cell, making up approximately 95% of the total bone cell population in mature adult bone tissue. Osteocytes are a stellate shape with numerous long, slender dendritic processes. +The formation of bone is a complex process involving the action of osteoclasts - cells that break down and reabsorb old bone, followed by osteoblasts that rebuild the bone. Osteocytes serve as coordinators for these two types of bone cells to ensure a balance in the bone remodeling process, contributing to maintaining both bone strength and mineral homeostasis. +The primary functions of osteocytes involve the creation, maintenance, and repair of bone tissue. They ensure that bone remodeling is performed by forming a network within the bone and communicating with other cells to help them respond to mechanical strain and damage. +A remarkable aspect of osteocytes is their ability to perceive mechanical forces, translating them into biochemical signals that regulate bone remodeling and adaptation. Defects in osteocyte function, aside from other bone cells, have been associated with several bone disorders such as osteoporosis, renal osteodystrophy, and skeletal manifestations of diabetes. 2011-11-16T04:28:16Z + https://cellxgene.cziscience.com/cellguide/CL_0001035 + + bone cell @@ -10077,6 +10415,20 @@ Despite their overarching function in the support and protection of neurons, gli GOC:add GO_REF:0000034 + + + + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Bone cells, also known as osteocytes, form the building blocks of the skeletal system. They represent the most common type of bone cell, making up approximately 95% of the total bone cell population in mature adult bone tissue. Osteocytes are a stellate shape with numerous long, slender dendritic processes. +The formation of bone is a complex process involving the action of osteoclasts - cells that break down and reabsorb old bone, followed by osteoblasts that rebuild the bone. Osteocytes serve as coordinators for these two types of bone cells to ensure a balance in the bone remodeling process, contributing to maintaining both bone strength and mineral homeostasis. +The primary functions of osteocytes involve the creation, maintenance, and repair of bone tissue. They ensure that bone remodeling is performed by forming a network within the bone and communicating with other cells to help them respond to mechanical strain and damage. +A remarkable aspect of osteocytes is their ability to perceive mechanical forces, translating them into biochemical signals that regulate bone remodeling and adaptation. Defects in osteocyte function, aside from other bone cells, have been associated with several bone disorders such as osteoporosis, renal osteodystrophy, and skeletal manifestations of diabetes. + DOI:10.1007/s00795-015-0099-y + DOI:10.1007/s11914-012-0105-4 + DOI:10.1016/j.jot.2021.04.005 + DOI:10.1038/s41413-020-0099-y + @@ -10218,6 +10570,8 @@ Despite their overarching function in the support and protection of neurons, gli A hematopoietic oligopotent progenitor cell that has the ability to differentiate into limited cell types but lacks lineage cell markers and self renewal capabilities. Cell lacks hematopoeitic lineage markers. 2010-01-06T03:43:27Z + + hematopoietic oligopotent progenitor cell, lineage-negative @@ -10287,6 +10641,8 @@ Despite their overarching function in the support and protection of neurons, gli 2017-01-30T20:20:48Z + + innate lymphoid cell @@ -10327,6 +10683,8 @@ Despite their overarching function in the support and protection of neurons, gli 2017-01-30T20:42:44Z + + group 1 innate lymphoid cell @@ -10385,6 +10743,8 @@ Despite their overarching function in the support and protection of neurons, gli 2010-01-19T02:51:58Z MDP + + macrophage dendritic cell progenitor @@ -10436,6 +10796,8 @@ Despite their overarching function in the support and protection of neurons, gli 2010-01-06T03:43:20Z + + hematopoietic lineage restricted progenitor cell @@ -10480,6 +10842,8 @@ Despite their overarching function in the support and protection of neurons, gli 2010-01-06T03:43:27Z + + This cell type is intended to be compatible with any vertebrate hematopoietic oligopotent progenitor cell. For mammalian hematopoietic oligopotent progenitor cells known to be lineage-negative, please use the term 'hematopoietic oligopotent progenitor cell' (CL_0001060). hematopoietic oligopotent progenitor cell @@ -10520,6 +10884,8 @@ Despite their overarching function in the support and protection of neurons, gli 2010-06-29T03:38:22Z FMA:69074 ZFA:0009385 + + ecto-epithelial cell @@ -10566,6 +10932,8 @@ Despite their overarching function in the support and protection of neurons, gli FMA:83621 MESH:D001854 + + MH consider whether bone marrow cells are bone cells in the structural sense vs. being part of bone organ sense. bone marrow cell @@ -10610,6 +10978,8 @@ Despite their overarching function in the support and protection of neurons, gli 2010-08-30T01:27:48Z FMA:83552 + + monopoietic cell @@ -10652,6 +11022,8 @@ Despite their overarching function in the support and protection of neurons, gli 2010-09-07T03:32:33Z FMA:67513 + + nucleate cell @@ -10690,6 +11062,8 @@ Despite their overarching function in the support and protection of neurons, gli CALOHA:TS-2040 FMA:70333 + + neural cell @@ -10731,6 +11105,8 @@ Despite their overarching function in the support and protection of neurons, gli MESH:D003239 ZFA:0009392 + + connective tissue cell @@ -10755,11 +11131,19 @@ Despite their overarching function in the support and protection of neurons, gli A cell of the embryo. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Embryonic cells in metazoans, which include all multicellular animals, are biological units in their earliest developmental stages from conception until the organism is fully formed. +They are derived from a fertilized egg, which undergoes a series of cell divisions to produce a multicellular organism. During the early phases of embryonic development, these cells exhibit pluripotency, meaning they possess the potential to differentiate into a diverse array of specialized cell types that constitute different body tissues and structures. +The balance between cell proliferation and differentiation in embryonic cells is crucial for successful development. When cells continue to divide without differentiating, overgrowth may occur leading to conditions such as teratomas (tumors of embryonic cells). Conversely, if cell differentiation proceeds at the expense of cell proliferation, developmental anomalies could occur regarding size or mass of the organism or its parts. 2010-09-15T03:39:21Z CALOHA:TS-0263 FMA:82840 WBbt:0007028 ZFA:0007089 + https://cellxgene.cziscience.com/cellguide/CL_0002321 + + embryonic cell (metazoa) @@ -10768,6 +11152,18 @@ Despite their overarching function in the support and protection of neurons, gli A cell of the embryo. FMA:0618947256 + + + + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Embryonic cells in metazoans, which include all multicellular animals, are biological units in their earliest developmental stages from conception until the organism is fully formed. +They are derived from a fertilized egg, which undergoes a series of cell divisions to produce a multicellular organism. During the early phases of embryonic development, these cells exhibit pluripotency, meaning they possess the potential to differentiate into a diverse array of specialized cell types that constitute different body tissues and structures. +The balance between cell proliferation and differentiation in embryonic cells is crucial for successful development. When cells continue to divide without differentiating, overgrowth may occur leading to conditions such as teratomas (tumors of embryonic cells). Conversely, if cell differentiation proceeds at the expense of cell proliferation, developmental anomalies could occur regarding size or mass of the organism or its parts. + DOI:10.1002/iub.1404 + DOI:10.1093/molehr/gan048 + https://www.ncbi.nlm.nih.gov/books/NBK9906/ + @@ -10813,6 +11209,9 @@ Despite their overarching function in the support and protection of neurons, gli FBbt:00005812 myofiber myofibril + + + myotube @@ -10874,6 +11273,8 @@ Despite their overarching function in the support and protection of neurons, gli FMA:83808 FMA:84791 heart cell + + From Onard of the FMA: Cardiac muscle cell or cardiac myocyte is a striated muscle cell. Cardiocyte on the other hand is any cell in the heart which includes cells other than muscle cells (e.g. endothelial cell of endocardium). Unless there is a consensus among anatomists that cardiocytes refer only to muscle cells, we will treat them as a general class of cells in the heart. cardiocyte @@ -10894,6 +11295,8 @@ Despite their overarching function in the support and protection of neurons, gli 2012-06-15T02:51:27Z scleroblast + + Needs logical definition. Should be capable_of skeletal system morphogenesis? or skeletal tissue development? needs to be added to GO. NOTES:a cell type of the early embryo (see also: mesenchymal cells) that will give rise to mineralized connective tissue. Scleroblasts can differentiate into osteoblasts (bone-forming cells), chondroblasts (cartilage-forming cells), odontoblasts (dentin-forming cells), ameloblasts (enamel-forming cells). The mesenchymal cells developing into osteoblasts and chondroblasts are derived from the mesoderm. Those developing into odontoblasts are neural crest cells. Those developing into ameloblasts are derived from the ectoderm. (http://www.copewithcytokines.de/cope.cgi?key=scleroblasts) skeletogenic cell @@ -10932,6 +11335,8 @@ Despite their overarching function in the support and protection of neurons, gli 2012-06-27T08:27:35Z ZFA:0007084 + + premigratory neural crest cell @@ -10954,6 +11359,8 @@ Despite their overarching function in the support and protection of neurons, gli Any muscle cell in which the fibers are not organised into sarcomeres. + + non-striated muscle cell @@ -10971,6 +11378,8 @@ Despite their overarching function in the support and protection of neurons, gli Any hematopoietic cell that is a precursor of some other hematopoietic cell type. + + hematopoietic precursor cell @@ -11019,6 +11428,8 @@ Despite their overarching function in the support and protection of neurons, gli A transversely striated, synctial cell of skeletal muscle. It is formed when proliferating myoblasts exit the cell cycle, differentiate and fuse. MESH:D018485 + + skeletal muscle fiber @@ -11054,6 +11465,8 @@ Despite their overarching function in the support and protection of neurons, gli A muscle cell that is part of some visceral muscle. FBbt:00005070 + + visceral muscle cell @@ -11092,6 +11505,8 @@ Despite their overarching function in the support and protection of neurons, gli mesenchyme cell + + mesenchymal cell @@ -11122,6 +11537,8 @@ Despite their overarching function in the support and protection of neurons, gli Any neuron that is capable of part of some visual perception. 2017-07-09T19:12:36Z + + visual system neuron @@ -11157,6 +11574,8 @@ Despite their overarching function in the support and protection of neurons, gli Any cell in the retina, the innermost layer or coating at the back of the eyeball, which is sensitive to light and in which the optic nerve terminates. PMID:10702418 + + retinal cell @@ -11174,6 +11593,8 @@ Despite their overarching function in the support and protection of neurons, gli A zygote in a plant or an animal. MESH:D015053 + + zygote @@ -11203,6 +11624,8 @@ Despite their overarching function in the support and protection of neurons, gli Any myoblast that develops into some cardiac muscle cell. MESH:D032386 + + cardiac myoblast @@ -11220,13 +11643,15 @@ Despite their overarching function in the support and protection of neurons, gli A cell of the neural crest. Neural crest cells are multipotent. Premigratory neural crest cells are found at the neural plate boarder, some of which will undergo ectomesynchymal transition and delamination to form migratory neural crest cells. - This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. Neural crest cells are a group of transient and highly migratory cells that originate from the neuroectoderm during the early stages of embryonic development. They are multipotent cells with an exceptional degree of plasticity, capable of differentiating into various somatic cell types and therefore play a fundamental role in the formation of various organs and tissues, making them critical contributors to the developing embryo. After the initiation of neurulation (the formation of the neural tube) neural crest cells start to undergo epithelial-to-mesenchymal transition and delaminate and migrate from the dorsal neural tube to several regions throughout the embryo. They differentiate into a range of diverse cell types, such as neurons and glial cells of the peripheral nervous system, including sensory and autonomic neurons. They also contribute to the formation of adrenal glands, pigment cells in the skin (melanocytes), cardiac structures, including parts of the heart septum and major arteries, as well as bones and cartilage of the face and skull. Disorders or aberrations in the development or migration of the neural crest cells can lead to serious congenital malformations, such as neurocristopathies, including Hirschsprung disease, neuroblastoma, and neurofibromatosis. https://cellxgene.cziscience.com/cellguide/CL_0011012 + + neural crest cell @@ -11239,7 +11664,7 @@ Disorders or aberrations in the development or migration of the neural crest cel - This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. Neural crest cells are a group of transient and highly migratory cells that originate from the neuroectoderm during the early stages of embryonic development. They are multipotent cells with an exceptional degree of plasticity, capable of differentiating into various somatic cell types and therefore play a fundamental role in the formation of various organs and tissues, making them critical contributors to the developing embryo. After the initiation of neurulation (the formation of the neural tube) neural crest cells start to undergo epithelial-to-mesenchymal transition and delaminate and migrate from the dorsal neural tube to several regions throughout the embryo. They differentiate into a range of diverse cell types, such as neurons and glial cells of the peripheral nervous system, including sensory and autonomic neurons. They also contribute to the formation of adrenal glands, pigment cells in the skin (melanocytes), cardiac structures, including parts of the heart septum and major arteries, as well as bones and cartilage of the face and skull. @@ -11277,6 +11702,8 @@ Disorders or aberrations in the development or migration of the neural crest cel A precursor cell that has a tendency to differentiate into a specific type of cell. They are descendants of stem cells, only they are more constrained in their differentiation potential or capacity for self-renewal, and are often more limited in both senses. + + progenitor cell @@ -11312,6 +11739,8 @@ Disorders or aberrations in the development or migration of the neural crest cel A cell that, by division or terminal differentiation, can give rise to other cell types. + + Work is needed on GO 'cell differentiation' before it is clear whether the equivalent class definition 'native cell' that capable_of some 'cell differentiation' works. Also, may want to consider merging this with non-terminally differentiated cell. precursor cell @@ -11420,6 +11849,8 @@ Disorders or aberrations in the development or migration of the neural crest cel CALOHA:TS-2109 bone marrow hematopoietic cells bone marrow poietic cells + + bone marrow hematopoietic cell @@ -11473,6 +11904,8 @@ Disorders or aberrations in the development or migration of the neural crest cel 2024-08-15T10:38:46Z syncytium SC + + syncytial cell @@ -11560,9 +11993,6 @@ Disorders or aberrations in the development or migration of the neural crest cel The ordered and organized complex of DNA, protein, and sometimes RNA, that forms the chromosome. https://github.com/geneontology/go-ontology/issues/28301 - GO:0000789 - GO:0000790 - GO:0005717 NIF_Subcellular:sao1615953555 cytoplasmic chromatin nuclear chromatin @@ -11588,8 +12018,6 @@ Disorders or aberrations in the development or migration of the neural crest cel A dispersed and relatively uncompacted form of chromatin that is in a transcription-competent conformation. https://github.com/geneontology/go-ontology/issues/22355 - GO:0005719 - GO:0035327 NIF_Subcellular:sao445485807 Wikipedia:Euchromatin transcriptionally active chromatin @@ -11613,8 +12041,6 @@ Disorders or aberrations in the development or migration of the neural crest cel A compact and highly condensed form of chromatin that is refractory to transcription. https://github.com/geneontology/go-ontology/issues/22355 - GO:0005720 - GO:0035328 NIF_Subcellular:sao581845896 Wikipedia:Heterochromatin transcriptionally inactive chromatin @@ -11969,10 +12395,6 @@ Disorders or aberrations in the development or migration of the neural crest cel The appearance of a cytokine due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. https://github.com/geneontology/go-ontology/issues/19116 - GO:0042032 - GO:0042089 - GO:0042107 - GO:0050663 cytokine biosynthetic process cytokine metabolic process cytokine secretion @@ -12080,7 +12502,6 @@ Disorders or aberrations in the development or migration of the neural crest cel The formation of a tube from the flat layer of ectodermal cells known as the neural plate. This will give rise to the central nervous system. - GO:0001679 Wikipedia:Neurulation neural tube morphogenesis neurulation @@ -12433,8 +12854,6 @@ Disorders or aberrations in the development or migration of the neural crest cel The appearance of immunoglobulin due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. - GO:0002378 - GO:0048305 antibody production immunoglobulin biosynthetic process immunoglobulin secretion @@ -12512,8 +12931,6 @@ Disorders or aberrations in the development or migration of the neural crest cel Any process involved in the carrying out of an immune response by a leukocyte. - GO:0019723 - GO:0042087 immune cell effector process immune cell mediated immunity leucocyte immune effector process @@ -12964,7 +13381,6 @@ Disorders or aberrations in the development or migration of the neural crest cel A location, relative to cellular compartments and structures, occupied by a macromolecular machine. There are three types of cellular components described in the gene ontology: (1) the cellular anatomical entity where a gene product carries out a molecular function (e.g., plasma membrane, cytoskeleton) or membrane-enclosed compartments (e.g., mitochondrion); (2) virion components, where viral proteins act, and (3) the stable macromolecular complexes of which gene product are parts (e.g., the clathrin complex). https://github.com/geneontology/go-ontology/issues/17729 - GO:0008372 NIF_Subcellular:sao1337158144 cell or subcellular entity cellular component @@ -13034,32 +13450,32 @@ Disorders or aberrations in the development or migration of the neural crest cel - - + + A protein complex consisting of three collagen chains assembled into a left-handed triple helix. These trimers typically assemble into higher order structures. Wikipedia:Collagen cellular_component GO:0005581 collagen trimer - + - + - + PMID:12382326 - + PMID:12382326 @@ -13102,8 +13518,6 @@ Disorders or aberrations in the development or migration of the neural crest cel A collagen-containing extracellular matrix consisting of a thin layer of dense material found in various animal tissues interposed between the cells and the adjacent connective tissue. It consists of the basal lamina plus an associated layer of reticulin fibers. - GO:0005605 - GO:0008003 Wikipedia:Basement_membrane cellular_component basal lamina @@ -13430,8 +13844,6 @@ Disorders or aberrations in the development or migration of the neural crest cel The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins. - GO:0005887 - GO:0005904 juxtamembrane NIF_Subcellular:sao1663586795 Wikipedia:Cell_membrane @@ -13522,7 +13934,6 @@ Disorders or aberrations in the development or migration of the neural crest cel Any cellular metabolic process involving deoxyribonucleic acid. This is one of the two main types of nucleic acid, consisting of a long, unbranched macromolecule formed from one, or more commonly, two, strands of linked deoxyribonucleotides. - GO:0055132 DNA metabolism cellular DNA metabolism biological_process @@ -13601,9 +14012,6 @@ Disorders or aberrations in the development or migration of the neural crest cel The cellular metabolic process in which a protein is formed, using the sequence of a mature mRNA or circRNA molecule to specify the sequence of amino acids in a polypeptide chain. Translation is mediated by the ribosome, and begins with the formation of a ternary complex between aminoacylated initiator methionine tRNA, GTP, and initiation factor 2, which subsequently associates with the small subunit of the ribosome and an mRNA or circRNA. Translation ends with the release of a polypeptide chain from the ribosome. - GO:0006416 - GO:0006453 - GO:0043037 Wikipedia:Translation_(genetics) protein anabolism protein biosynthesis @@ -13636,7 +14044,7 @@ Disorders or aberrations in the development or migration of the neural crest cel - + @@ -13650,8 +14058,6 @@ Disorders or aberrations in the development or migration of the neural crest cel The process preceding formation of the peptide bond between the first two amino acids of a protein. This includes the formation of a complex of the ribosome, mRNA or circRNA, and an initiation complex that contains the first aminoacyl-tRNA. - GO:0006440 - GO:0006454 biopolymerisation biopolymerization protein synthesis initiation @@ -13681,8 +14087,6 @@ Disorders or aberrations in the development or migration of the neural crest cel The successive addition of amino acid residues to a nascent polypeptide chain during protein biosynthesis. - GO:0006442 - GO:0006455 protein synthesis elongation translation elongation biological_process @@ -13710,8 +14114,6 @@ Disorders or aberrations in the development or migration of the neural crest cel The process resulting in the release of a polypeptide chain from the ribosome, usually in response to a termination codon (UAA, UAG, or UGA in the universal genetic code). - GO:0006443 - GO:0006456 protein synthesis termination translation termination translational complex disassembly @@ -13735,11 +14137,7 @@ Disorders or aberrations in the development or migration of the neural crest cel The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter or a transporter complex, a pore or a motor protein. https://github.com/geneontology/go-ontology/issues/20292 - jl 2012-12-13T16:25:32Z - GO:0015457 - GO:0015460 - GO:0044765 biological_process single-organism transport GO:0006810 @@ -13818,8 +14216,6 @@ Disorders or aberrations in the development or migration of the neural crest cel A process of secretion by a cell that results in the release of intracellular molecules (e.g. hormones, matrix proteins) contained within a membrane-bounded vesicle. Exocytosis can occur either by full fusion, when the vesicle collapses into the plasma membrane, or by a kiss-and-run mechanism that involves the formation of a transient contact, a pore, between a granule (for example of chromaffin cells) and the plasma membrane. The latter process most of the time leads to only partial secretion of the granule content. Exocytosis begins with steps that prepare vesicles for fusion with the membrane (tethering and docking) and ends when molecules are secreted from the cell. - GO:0016194 - GO:0016195 Wikipedia:Exocytosis vesicle exocytosis biological_process @@ -13865,9 +14261,6 @@ Disorders or aberrations in the development or migration of the neural crest cel A vesicle-mediated transport process in which cells take up external materials or membrane constituents by the invagination of a part of the plasma membrane to form a new membrane-bounded vesicle. https://github.com/geneontology/go-ontology/issues/24907 https://github.com/geneontology/go-ontology/issues/25268 - GO:0016193 - GO:0016196 - GO:0098701 Wikipedia:Endocytosis endocytic import into cell vesicle endocytosis @@ -13902,10 +14295,7 @@ Disorders or aberrations in the development or migration of the neural crest cel The evagination of a membrane, resulting in formation of a vesicle. - jl 2013-12-19T15:26:17Z - GO:0006902 - GO:1902591 membrane evagination vesicle biosynthesis vesicle formation @@ -14105,9 +14495,7 @@ Disorders or aberrations in the development or migration of the neural crest cel A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of an organelle within a cell. An organelle is an organized structure of distinctive morphology and function. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton. Excludes the plasma membrane. https://github.com/geneontology/go-ontology/issues/27189 - jl 2013-12-19T15:25:51Z - GO:1902589 organelle organisation single organism organelle organization biological_process @@ -14574,7 +14962,6 @@ Disorders or aberrations in the development or migration of the neural crest cel The flow of blood through the body of an animal, enabling the transport of nutrients to the tissues and the removal of waste products. - GO:0070261 biological_process hemolymph circulation GO:0008015 @@ -14596,11 +14983,7 @@ Disorders or aberrations in the development or migration of the neural crest cel A biological process is the execution of a genetically-encoded biological module or program. It consists of all the steps required to achieve the specific biological objective of the module. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence. https://github.com/geneontology/go-ontology/issues/24968 - jl 2012-09-19T15:05:24Z - GO:0000004 - GO:0007582 - GO:0044699 Wikipedia:Biological_process biological process physiological process @@ -14630,21 +15013,15 @@ Disorders or aberrations in the development or migration of the neural crest cel - + - The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation. + A cellular process consisting of the biochemical pathways by which a living organism transforms chemical substances. This includes including anabolism (biosynthetic process) and catabolism (catabolic process). Metabolic processes includes the transformation of small molecules, as well macromolecular processes such as DNA repair and replication, protein synthesis and degradation. https://github.com/geneontology/go-ontology/issues/26424 - jl + https://github.com/geneontology/go-ontology/issues/28932 2012-10-17T15:46:40Z - GO:0044236 - GO:0044710 Wikipedia:Metabolism metabolism - metabolic process resulting in cell growth - metabolism resulting in cell growth - multicellular organism metabolic process biological_process - single-organism metabolic process GO:0008152 @@ -14659,7 +15036,7 @@ Disorders or aberrations in the development or migration of the neural crest cel - The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation. + A cellular process consisting of the biochemical pathways by which a living organism transforms chemical substances. This includes including anabolism (biosynthetic process) and catabolism (catabolic process). Metabolic processes includes the transformation of small molecules, as well macromolecular processes such as DNA repair and replication, protein synthesis and degradation. GOC:go_curators ISBN:0198547684 @@ -14670,11 +15047,9 @@ Disorders or aberrations in the development or migration of the neural crest cel - The chemical reactions and pathways resulting in the formation of substances; typically the energy-requiring part of metabolism in which simpler substances are transformed into more complex ones. - jl + A cellular process consisting of the biochemical pathways by which a living organism synthesizes chemical substances. This typically represents the energy-requiring part of metabolism in which simpler substances are transformed into more complex ones. + https://github.com/geneontology/go-ontology/issues/28932 2012-10-17T15:52:18Z - GO:0044274 - GO:0044711 formation Wikipedia:Anabolism anabolism @@ -14693,7 +15068,7 @@ Disorders or aberrations in the development or migration of the neural crest cel - The chemical reactions and pathways resulting in the formation of substances; typically the energy-requiring part of metabolism in which simpler substances are transformed into more complex ones. + A cellular process consisting of the biochemical pathways by which a living organism synthesizes chemical substances. This typically represents the energy-requiring part of metabolism in which simpler substances are transformed into more complex ones. GOC:curators ISBN:0198547684 @@ -14703,13 +15078,12 @@ Disorders or aberrations in the development or migration of the neural crest cel + - The chemical reactions and pathways resulting in the formation of a macromolecule, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass. https://github.com/geneontology/go-ontology/issues/15249 https://github.com/geneontology/go-ontology/issues/25418 https://github.com/geneontology/go-ontology/issues/27189 - GO:0043284 biopolymer biosynthetic process macromolecule anabolism macromolecule biosynthesis @@ -14983,7 +15357,6 @@ Disorders or aberrations in the development or migration of the neural crest cel The process whose specific outcome is the progression of an embryo from its formation until the end of its embryonic life stage. The end of the embryonic stage is organism-specific. For example, for mammals, the process would begin with zygote formation and end with birth. For insects, the process would begin at zygote formation and end with larval hatching. For plant zygotic embryos, this would be from zygote formation to the end of seed dormancy. For plant vegetative embryos, this would be from the initial determination of the cell or group of cells to form an embryo until the point when the embryo becomes independent of the parent plant. - GO:0009795 embryogenesis and morphogenesis Wikipedia:Embryogenesis embryogenesis @@ -15144,11 +15517,7 @@ Disorders or aberrations in the development or migration of the neural crest cel Any process that is carried out at the cellular level, but not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level. - jl 2012-12-11T16:56:55Z - GO:0008151 - GO:0044763 - GO:0050875 cell physiology cellular physiological process cell growth and/or maintenance @@ -15220,9 +15589,7 @@ Disorders or aberrations in the development or migration of the neural crest cel The infolding of a membrane. - jl 2013-12-02T13:58:34Z - GO:1902534 biological_process single-organism membrane invagination GO:0010324 @@ -15365,9 +15732,6 @@ Disorders or aberrations in the development or migration of the neural crest cel A lipid bilayer along with all the proteins and protein complexes embedded in it and attached to it. 2014-03-06T11:37:54Z - GO:0016021 - GO:0098589 - GO:0098805 Wikipedia:Biological_membrane Wikipedia:Transmembrane_protein integral component of membrane @@ -15426,8 +15790,6 @@ Disorders or aberrations in the development or migration of the neural crest cel A process that results in the assembly, arrangement of constituent parts, or disassembly of a cellular component. - GO:0044235 - GO:0071842 cell organisation cellular component organisation at cellular level cellular component organisation in other organism @@ -15542,7 +15904,6 @@ Disorders or aberrations in the development or migration of the neural crest cel A cellular transport process in which transported substances are moved in membrane-bounded vesicles; transported substances are enclosed in the vesicle lumen or located in the vesicle membrane. The process begins with a step that directs a substance to the forming vesicle, and includes vesicle budding and coating. Vesicles are then targeted to, and fuse with, an acceptor membrane. https://github.com/geneontology/go-ontology/issues/25421 - GO:0006899 vesicle transport vesicular transport nonselective vesicle transport @@ -15796,9 +16157,6 @@ Disorders or aberrations in the development or migration of the neural crest cel The chemical reactions and pathways involving a protein. Includes protein modification. https://github.com/geneontology/go-ontology/issues/23112 https://github.com/geneontology/go-ontology/issues/27189 - GO:0006411 - GO:0044267 - GO:0044268 Wikipedia:Protein_metabolism cellular protein metabolic process cellular protein metabolism @@ -15876,7 +16234,6 @@ Disorders or aberrations in the development or migration of the neural crest cel The process in which an antigen-presenting cell expresses antigen (peptide or lipid) on its cell surface in association with an MHC protein complex. - GO:0030333 Wikipedia:Antigen_presentation antigen presentation antigen processing @@ -15973,7 +16330,6 @@ Disorders or aberrations in the development or migration of the neural crest cel A cellular process that results in the breakdown of a cellular component. https://github.com/geneontology/go-ontology/issues/27189 - GO:0071845 cell structure disassembly cellular component disassembly at cellular level biological_process @@ -15998,9 +16354,7 @@ Disorders or aberrations in the development or migration of the neural crest cel A biological process that directly contributes to the process of producing new individuals by one or two organisms. The new individuals inherit some proportion of their genetic material from the parent or parents. https://github.com/geneontology/go-ontology/issues/27054 - jl 2012-09-19T15:56:06Z - GO:0044702 Wikipedia:Reproduction biological_process single organism reproductive process @@ -16091,7 +16445,6 @@ Disorders or aberrations in the development or migration of the neural crest cel The aggregation, arrangement and bonding together of a cellular component. - GO:0071844 cell structure assembly cellular component assembly at cellular level biological_process @@ -16194,10 +16547,7 @@ Disorders or aberrations in the development or migration of the neural crest cel The entirety of a process in which information is transmitted within a biological system. This process begins with an active signal and ends when a cellular response has been triggered. - jl 2010-02-16T09:30:50Z - GO:0023046 - GO:0044700 biological signaling signaling process signalling @@ -16497,7 +16847,6 @@ Disorders or aberrations in the development or migration of the neural crest cel The process in which a relatively unspecialized precursor cell acquires specialized features of a lymphocyte. A lymphocyte is a leukocyte commonly found in the blood and lymph that has the characteristics of a large nucleus, a neutral staining cytoplasm, and prominent heterochromatin. - GO:0046650 lymphocyte cell differentiation lymphocytic blood cell differentiation biological_process @@ -16690,8 +17039,6 @@ Disorders or aberrations in the development or migration of the neural crest cel The process in which a precursor cell type acquires characteristics of a more mature T-cell. A T cell is a type of lymphocyte whose definin characteristic is the expression of a T cell receptor complex. - GO:0042112 - GO:0046652 T lymphocyte differentiation T-cell differentiation T-lymphocyte differentiation @@ -16912,7 +17259,6 @@ Disorders or aberrations in the development or migration of the neural crest cel A structure lying external to one or more cells, which provides structural support, biochemical or biomechanical cues for cells or tissues. - GO:0005578 NIF_Subcellular:nlx_subcell_20090513 Wikipedia:Extracellular_matrix proteinaceous extracellular matrix @@ -17077,7 +17423,6 @@ Disorders or aberrations in the development or migration of the neural crest cel A vesicle found in the cytoplasm of a cell. - GO:0016023 NIF_Subcellular:sao180601769 cellular_component cytoplasmic membrane bounded vesicle @@ -17153,7 +17498,6 @@ Disorders or aberrations in the development or migration of the neural crest cel Any small, fluid-filled, spherical organelle enclosed by membrane. - GO:0031988 NIF_Subcellular:sao221389602 Wikipedia:Vesicle_(biology) cellular_component @@ -17184,10 +17528,7 @@ Disorders or aberrations in the development or migration of the neural crest cel - jl 2012-09-19T16:07:47Z - GO:0044707 - GO:0050874 organismal physiological process biological_process single-multicellular organism process @@ -17214,9 +17555,7 @@ Disorders or aberrations in the development or migration of the neural crest cel A biological process whose specific outcome is the progression of an integrated living unit: an anatomical structure (which may be a subcellular structure, cell, tissue, or organ), or organism over time from an initial condition to a later condition. - jl 2012-12-19T12:21:31Z - GO:0044767 development biological_process single-organism developmental process @@ -17240,8 +17579,6 @@ Disorders or aberrations in the development or migration of the neural crest cel The appearance of interferon-gamma due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. Interferon-gamma is also known as type II interferon. - GO:0042095 - GO:0072643 IFNG production interferon-gamma production type II IFN production @@ -17320,9 +17657,6 @@ Disorders or aberrations in the development or migration of the neural crest cel The disaggregation of a protein-containing macromolecular complex into its constituent components. https://github.com/geneontology/go-ontology/issues/22580 - GO:0034623 - GO:0043241 - GO:0043624 protein complex disassembly biological_process cellular macromolecule complex disassembly @@ -17344,10 +17678,14 @@ Disorders or aberrations in the development or migration of the neural crest cel - + + + + + + A stable assembly of two or more macromolecules, i.e. proteins, nucleic acids, carbohydrates or lipids, in which at least one component is a protein and the constituent parts function together. - GO:0043234 macromolecular complex macromolecule complex protein containing complex @@ -17461,7 +17799,6 @@ Disorders or aberrations in the development or migration of the neural crest cel A process in which a monoatomic ion is transported across a membrane. Monatomic ions (also called simple ions) are ions consisting of exactly one atom. - GO:0099131 ion transmembrane transport ion membrane transport transmembrane ion transport @@ -17814,9 +18151,6 @@ Disorders or aberrations in the development or migration of the neural crest cel Any biological process involved in the maintenance of an internal steady state. - GO:0032844 - GO:0032845 - GO:0032846 homeostasis activation of homeostatic process inhibition of homeostatic process @@ -17994,9 +18328,6 @@ Disorders or aberrations in the development or migration of the neural crest cel The chemical reactions and pathways involving macromolecules, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass. https://github.com/geneontology/go-ontology/issues/26424 - GO:0034960 - GO:0043283 - GO:0044259 biopolymer metabolic process macromolecule metabolism organismal macromolecule metabolism @@ -18113,14 +18444,17 @@ Disorders or aberrations in the development or migration of the neural crest cel Organized structure of distinctive morphology and function, not bounded by a lipid bilayer membrane. Includes ribosomes, the cytoskeleton and chromosomes. https://github.com/geneontology/go-ontology/issues/21881 https://github.com/geneontology/go-ontology/issues/28153 + https://github.com/geneontology/go-ontology/issues/29106 NIF_Subcellular:sao1456184038 + membrane-less organelle + non-membrane-bounded organelle non-membrane-enclosed organelle cellular_component biological condensate GO:0043228 - non-membrane-bounded organelle + membraneless organelle @@ -18218,11 +18552,13 @@ Disorders or aberrations in the development or migration of the neural crest cel Organized structure of distinctive morphology and function, not bounded by a lipid bilayer membrane and occurring within the cell. Includes ribosomes, the cytoskeleton and chromosomes. + https://github.com/geneontology/go-ontology/issues/29106 + intracellular non-membrane-bounded organelle intracellular non-membrane-enclosed organelle cellular_component GO:0043232 - intracellular non-membrane-bounded organelle + intracellular membraneless organelle @@ -18339,11 +18675,7 @@ Disorders or aberrations in the development or migration of the neural crest cel Any process in which macromolecules aggregate, disaggregate, or are modified, resulting in the formation, disassembly, or alteration of a protein complex. https://github.com/geneontology/go-ontology/issues/22580 - mah 2010-09-08T10:01:42Z - GO:0034600 - GO:0034621 - GO:0071822 protein complex subunit organisation protein complex subunit organization biological_process @@ -18378,7 +18710,6 @@ Disorders or aberrations in the development or migration of the neural crest cel A process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of a cellular component. Includes biosynthesis of constituent macromolecules, and those macromolecular modifications that are involved in synthesis or assembly of the cellular component. https://github.com/geneontology/go-ontology/issues/27194 - GO:0071843 cellular component biogenesis at cellular level biological_process GO:0044085 @@ -18407,7 +18738,6 @@ Disorders or aberrations in the development or migration of the neural crest cel A ribonucleoprotein complex that contains aminoacylated initiator methionine tRNA, GTP, and initiation factor 2 (either eIF2 in eukaryotes, or IF2 in prokaryotes). In prokaryotes, fMet-tRNA (initiator) is used rather than Met-tRNA (initiator). - jl 2009-10-22T02:38:55Z translation initiation (ternary) complex Met-tRNA/eIF2.GTP ternary complex @@ -18424,35 +18754,6 @@ Disorders or aberrations in the development or migration of the neural crest cel - - - - - - The chemical reactions and pathways by which individual cells transform chemical substances. - cellular metabolism - biological_process - intermediary metabolism - GO:0044237 - - This term should not be used for direct annotation. It should be possible to make a more specific annotation to one of the children of this term. - cellular metabolic process - - - - - The chemical reactions and pathways by which individual cells transform chemical substances. - GOC:go_curators - - - - - intermediary metabolism - GOC:mah - - - - @@ -18479,32 +18780,6 @@ Disorders or aberrations in the development or migration of the neural crest cel - - - - - - The chemical reactions and pathways resulting in the formation of substances, carried out by individual cells. - https://github.com/geneontology/go-ontology/issues/27052 - cellular anabolism - cellular biosynthesis - cellular formation - cellular synthesis - biological_process - GO:0044249 - - This term should not be used for direct annotation. It should be possible to make a more specific annotation to one of the children of this term. - cellular biosynthetic process - - - - - The chemical reactions and pathways resulting in the formation of substances, carried out by individual cells. - GOC:jl - - - - @@ -18555,7 +18830,6 @@ Disorders or aberrations in the development or migration of the neural crest cel The joining of the lipid bilayer membrane that surround a cell with that of another cell, producing a single cell. - GO:0006947 cell fusion cell-cell fusion biological_process @@ -18581,7 +18855,6 @@ Disorders or aberrations in the development or migration of the neural crest cel - GO:0002226 Wikipedia:Innate_immune_system innate immunity nonspecific immune response @@ -19201,7 +19474,6 @@ Disorders or aberrations in the development or migration of the neural crest cel The process in which anatomical structures are generated and organized during the embryonic phase. The embryonic phase begins with zygote formation. The end of the embryonic phase is organism-specific. For example, it would be at birth for mammals, larval hatching for insects and seed dormancy in plants. - GO:0048828 embryonic anatomical structure morphogenesis biological_process GO:0048598 @@ -19553,7 +19825,6 @@ Disorders or aberrations in the development or migration of the neural crest cel Any process that modulates the frequency, rate or extent of a biological process. Biological processes are regulated by many means; examples include the control of gene expression, protein modification or interaction with a protein or substrate molecule. - GO:0050791 regulation of physiological process biological_process GO:0050789 @@ -19629,7 +19900,6 @@ Disorders or aberrations in the development or migration of the neural crest cel Any process that modulates the frequency, rate or extent of a cellular process, any of those that are carried out at the cellular level, but are not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level. - GO:0051244 regulation of cellular physiological process biological_process GO:0050794 @@ -19782,7 +20052,6 @@ Disorders or aberrations in the development or migration of the neural crest cel Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus. The process begins with detection of the stimulus and ends with a change in state or activity or the cell or organism. - GO:0051869 physiological response to stimulus biological_process GO:0050896 @@ -19958,9 +20227,7 @@ Disorders or aberrations in the development or migration of the neural crest cel Any process in which a cell, a substance, or a cellular entity, such as a protein complex or organelle, is transported, tethered to or otherwise maintained in a specific location. In the case of substances, localization may also be achieved via selective degradation. https://github.com/geneontology/go-ontology/issues/27052 - jl 2013-12-18T13:51:04Z - GO:1902578 establishment and maintenance of localization establishment and maintenance of position localisation @@ -20157,8 +20424,6 @@ Disorders or aberrations in the development or migration of the neural crest cel Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus from another living organism. - GO:0009613 - GO:0042828 biological_process GO:0051707 response to other organism @@ -20195,9 +20460,7 @@ Disorders or aberrations in the development or migration of the neural crest cel The process in which a solute is transported across a lipid bilayer, from one side of a membrane to the other. - tb 2015-10-21T13:22:47Z - GO:0090662 membrane transport ATP hydrolysis coupled transmembrane transport biological_process @@ -20369,7 +20632,6 @@ Disorders or aberrations in the development or migration of the neural crest cel The process in which the anatomical structures of a tube are generated and organized from an epithelium. Epithelial tubes transport gases, liquids and cells from one site to another and form the basic structure of many organs and tissues, with tube shape and organization varying from the single-celled excretory organ in Caenorhabditis elegans to the branching trees of the mammalian kidney and insect tracheal system. - dph 2009-04-28T09:33:36Z biological_process GO:0060562 @@ -20406,10 +20668,7 @@ Disorders or aberrations in the development or migration of the neural crest cel A process which results in the assembly, arrangement of constituent parts, or disassembly of a membrane. A membrane is a double layer of lipid molecules that encloses all cells, and, in eukaryotes, many organelles; may be a single or double lipid bilayer; also includes associated proteins. - jl 2010-02-08T02:43:11Z - GO:0016044 - GO:0044802 cellular membrane organisation cellular membrane organization membrane organisation @@ -20469,10 +20728,7 @@ Disorders or aberrations in the development or migration of the neural crest cel The membrane organization process that joins two lipid bilayers to form a single membrane. - jl 2010-02-08T02:48:06Z - GO:0006944 - GO:0044801 Wikipedia:Lipid_bilayer_fusion cellular membrane fusion biological_process @@ -20508,7 +20764,6 @@ Disorders or aberrations in the development or migration of the neural crest cel An extracellular matrix consisting mainly of proteins (especially collagen) and glycosaminoglycans (mostly as proteoglycans) that provides not only essential physical scaffolding for the cellular constituents but can also initiate crucial biochemical and biomechanical cues required for tissue morphogenesis, differentiation and homeostasis. The components are secreted by cells in the vicinity and form a sheet underlying or overlying cells such as endothelial and epithelial cells. - dph 2018-04-13T12:47:21Z cellular_component GO:0062023 @@ -20549,9 +20804,6 @@ Disorders or aberrations in the development or migration of the neural crest cel The aggregation, arrangement and bonding together of a set of macromolecules to form a protein-containing complex. https://github.com/geneontology/go-ontology/issues/22580 - GO:0006461 - GO:0034622 - GO:0043623 cellular protein complex assembly biological_process cellular macromolecule complex assembly @@ -20727,7 +20979,6 @@ Disorders or aberrations in the development or migration of the neural crest cel Any process in which macromolecules aggregate, disaggregate, or are modified, resulting in the formation, disassembly, or alteration of a ribonucleoprotein complex. https://github.com/geneontology/go-ontology/issues/25143 - mah 2010-09-08T10:10:35Z RNA-protein complex subunit organization protein-RNA complex subunit organization @@ -20770,9 +21021,7 @@ Disorders or aberrations in the development or migration of the neural crest cel A process that results in the biosynthesis of constituent macromolecules, assembly, arrangement of constituent parts, or disassembly of a cellular component. https://github.com/geneontology/go-ontology/issues/27189 - mah 2010-09-10T01:39:16Z - GO:0071841 cellular component organisation or biogenesis cellular component organisation or biogenesis at cellular level cellular component organization or biogenesis at cellular level @@ -20810,7 +21059,6 @@ Disorders or aberrations in the development or migration of the neural crest cel The broad region around and including the plasma membrane of a cell, encompassing the cell cortex (inside the cell), the plasma membrane, and any external encapsulating structures. - mah 2010-10-04T01:51:47Z cellular_component GO:0071944 @@ -20837,7 +21085,6 @@ Disorders or aberrations in the development or migration of the neural crest cel An supramolecular fiber that consists of an insoluble core of polymerized tropoelastin monomers and a surrounding mantle of microfibrils. Elastic fibers provide elasticity and recoiling to tissues and organs, and maintain structural integrity against mechanical strain. - mah 2010-10-11T11:44:57Z elastic fibre elastin fiber @@ -20897,7 +21144,6 @@ Disorders or aberrations in the development or migration of the neural crest cel The developmental process pertaining to the initial formation of an epithelial tube. https://github.com/geneontology/go-ontology/issues/22302 - mah 2010-02-26T02:15:40Z biological_process GO:0072175 @@ -20935,7 +21181,6 @@ Disorders or aberrations in the development or migration of the neural crest cel The joining of two lipid bilayers to form a single organelle membrane. - tb 2009-12-11T11:44:58Z biological_process GO:0090174 @@ -20974,7 +21219,6 @@ Disorders or aberrations in the development or migration of the neural crest cel The process in which a precursor cell type acquires the specialized features of a dendritic cell. A dendritic cell is a leukocyte of dendritic lineage specialized in the uptake, processing, and transport of antigens to lymph nodes for the purpose of stimulating an immune response via T cell activation. - pr 2011-04-01T10:08:42Z biological_process GO:0097028 @@ -21008,7 +21252,6 @@ Disorders or aberrations in the development or migration of the neural crest cel Any vesicle that is part of the intracellular region. - pr 2016-03-29T17:39:45Z cellular_component GO:0097708 @@ -21029,9 +21272,7 @@ Disorders or aberrations in the development or migration of the neural crest cel Reactions triggered in response to the presence of another organism that act to protect the cell or organism from damage caused by that organism. https://github.com/geneontology/go-ontology/issues/22173 - dos 2013-11-11T12:59:11Z - GO:0009814 defence response incompatible interaction defence response to pathogen, incompatible interaction defense response, incompatible interaction @@ -21073,7 +21314,6 @@ Disorders or aberrations in the development or migration of the neural crest cel A membrane that is a (regional) part of the plasma membrane. - dos 2014-03-06T11:55:32Z region of plasma membrane cellular_component @@ -21150,7 +21390,6 @@ Disorders or aberrations in the development or migration of the neural crest cel - @@ -21619,7 +21858,6 @@ Disorders or aberrations in the development or migration of the neural crest cel A polymer consisting of an indefinite number of protein or protein complex subunits that have polymerised to form a fiber-shaped structure. - GO:0043205 cellular_component fibril GO:0099512 @@ -21707,21 +21945,22 @@ Disorders or aberrations in the development or migration of the neural crest cel - A part of a cellular organism that is either an immaterial entity or a material entity with granularity above the level of a protein complex but below that of an anatomical system. Or, a substance produced by a cellular organism with granularity above the level of a protein complex. + A part of a cellular organism consisting of a material entity with granularity above the level of a protein complex but below that of an anatomical system. Note that cellular organisms exclude viruses. https://github.com/geneontology/go-ontology/issues/24200 https://github.com/geneontology/go-ontology/issues/26424 - kmv + https://github.com/geneontology/go-ontology/issues/28978 2019-08-12T18:01:37Z + cellular anatomical entity cellular_component GO:0110165 - cellular anatomical entity + cellular anatomical structure - A part of a cellular organism that is either an immaterial entity or a material entity with granularity above the level of a protein complex but below that of an anatomical system. Or, a substance produced by a cellular organism with granularity above the level of a protein complex. + A part of a cellular organism consisting of a material entity with granularity above the level of a protein complex but below that of an anatomical system. Note that cellular organisms exclude viruses. GOC:kmv @@ -21750,7 +21989,6 @@ Disorders or aberrations in the development or migration of the neural crest cel A prolongation or process extending from a cell and that is bounded by plasma membrane, e.g. a cilium, lamellipodium, or axon. https://github.com/geneontology/go-ontology/issues/13193 - krc 2017-03-21T17:26:07Z cellular_component GO:0120025 @@ -21788,7 +22026,6 @@ Disorders or aberrations in the development or migration of the neural crest cel A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a plasma membrane bounded prolongation or process extending from a cell, e.g. a cilium or axon. https://github.com/geneontology/go-ontology/issues/13298 - krc 2017-04-26T16:07:02Z biological_process GO:0120036 @@ -21825,7 +22062,6 @@ Disorders or aberrations in the development or migration of the neural crest cel The cellular processes that contribute to exocytosis. - pg 2017-05-15T13:20:45Z biological_process GO:0140029 @@ -21853,7 +22089,6 @@ Disorders or aberrations in the development or migration of the neural crest cel A cellular process in which two or more cells combine together, their plasma membrane fusing, producing a single cell. In some cases, nuclei fuse, producing a polyploid cell, while in other cases, nuclei remain separate, producing a syncytium. https://github.com/geneontology/go-ontology/issues/15939 - pg 2018-08-13T18:38:18Z cell fusion cell cell fusion @@ -21903,7 +22138,6 @@ Disorders or aberrations in the development or migration of the neural crest cel The directed movement of some substance from a cell, into the extracellular region. This may occur via transport across the plasma membrane or via exocytosis. - pg 2019-05-22T11:20:45Z efflux biological_process @@ -21925,7 +22159,6 @@ Disorders or aberrations in the development or migration of the neural crest cel Reactions triggered in response to the presence of a symbiont that act to protect or prevent damage to the host. https://github.com/geneontology/go-ontology/issues/20261 - pg 2020-11-11T17:19:06Z biological_process GO:0140546 @@ -21962,7 +22195,6 @@ Disorders or aberrations in the development or migration of the neural crest cel Any process that modulates the frequency, rate or extent of leukocyte differentiation. - pr 2013-05-02T17:32:42Z regulation of immune cell differentiation regulation of leucocyte differentiation @@ -22014,7 +22246,6 @@ Disorders or aberrations in the development or migration of the neural crest cel The process in which a relatively unspecialized cell acquires the specialized features of a mononuclear cell. - cls 2014-06-25T15:47:09Z biological_process GO:1903131 @@ -22056,7 +22287,6 @@ Disorders or aberrations in the development or migration of the neural crest cel Any process that modulates the frequency, rate or extent of hemopoiesis. - pad 2014-12-04T15:34:13Z regulation of blood cell biosynthesis regulation of blood cell formation @@ -22109,10 +22339,7 @@ Disorders or aberrations in the development or migration of the neural crest cel A macromolecular complex that contains both RNA and protein molecules. - pr 2015-11-19T12:26:37Z - GO:0030529 - GO:1990903 Wikipedia:Ribonucleoprotein RNA-protein complex RNP @@ -22157,7 +22384,6 @@ Disorders or aberrations in the development or migration of the neural crest cel Any process that modulates the frequency, rate or extent of multicellular organismal development. - tb 2010-08-05T11:25:59Z biological_process GO:2000026 @@ -22242,7 +22468,6 @@ Disorders or aberrations in the development or migration of the neural crest cel - NCBITaxon:85055 GC_ID:1 house mouse mouse @@ -22281,7 +22506,6 @@ Disorders or aberrations in the development or migration of the neural crest cel - NCBITaxon:40673 GC_ID:1 bony vertebrates ncbi_taxonomy @@ -22648,7 +22872,6 @@ Disorders or aberrations in the development or migration of the neural crest cel - NCBITaxon:109679 GC_ID:1 ncbi_taxonomy NCBITaxon:39107 @@ -22907,7 +23130,6 @@ Disorders or aberrations in the development or migration of the neural crest cel A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities - PATO:0000072 quality PATO:0000001 quality @@ -22945,7 +23167,6 @@ Disorders or aberrations in the development or migration of the neural crest cel A morphological quality inhering in a bearer by virtue of the bearer's ratios of distances between its features (points, edges, surfaces and also holes etc). - PATO:0001647 relational shape quality quality PATO:0000052 @@ -22967,7 +23188,6 @@ Disorders or aberrations in the development or migration of the neural crest cel A morphology quality inhering in a bearer by virtue of the bearer's relative position, shape, arrangements and connectivity of an organism's various parts; the pattern underlying its form. - PATO:0001452 conformation relational structural quality quality @@ -23044,7 +23264,6 @@ Disorders or aberrations in the development or migration of the neural crest cel A quality of a physical entity that exists through action of continuants at the physical level of organisation in relation to other entities. - PATO:0002079 Wikipedia:Physical_property relational physical quality quality @@ -23066,8 +23285,6 @@ Disorders or aberrations in the development or migration of the neural crest cel A quality which inheres in a continuant. - PATO:0001237 - PATO:0001238 snap:Quality monadic quality of a continuant multiply inhering quality of a physical entity @@ -23308,7 +23525,6 @@ Disorders or aberrations in the development or migration of the neural crest cel A convex 3-D shape quality inhering in a bearer by virtue of the bearer's exhibiting a consistently-sized round cross section. - PATO:0001203 rod-like rod-shaped tubulate @@ -23735,7 +23951,6 @@ Disorders or aberrations in the development or migration of the neural crest cel A quality inhering in a cell by virtue of the cell having a high nuclear/cytoplasmic ratio. - http://orcid.org/0000-0001-5208-3432 high N:C ratio quality PATO:0040072 @@ -23757,7 +23972,6 @@ Disorders or aberrations in the development or migration of the neural crest cel A quality of continuant that exist at the anatomical level of organisation and anything under it. This includes, but is not limited to, cells , tissues, and components. - http://orcid.org/0000-0001-7258-9596 quality PATO:0070044 anatomical structure quality @@ -23770,7 +23984,6 @@ Disorders or aberrations in the development or migration of the neural crest cel A quality inhering in an anotomical structure by virtue of its capacity to be stained by specific histological dyes. - http://orcid.org/0000-0001-7258-9596 quality PATO:0070045 anatomical histological quality @@ -23783,7 +23996,6 @@ Disorders or aberrations in the development or migration of the neural crest cel An affinity inhering in an anatomical structure by virtue of the bearer exhibiting a molecular interaction that stains and colors, pale-pink, with Wright-Giemsa stain. - http://orcid.org/0000-0001-7258-9596 quality PATO:0070046 neutrophillic @@ -23801,7 +24013,7 @@ Disorders or aberrations in the development or migration of the neural crest cel - + @@ -23813,7 +24025,7 @@ Disorders or aberrations in the development or migration of the neural crest cel native protein protein PR:000000001 - The definition above excludes protein complexes, which some also consider a protein. Those who wish to refer to a class representing both senses of the word are directed to CHEBI:36080. Note that the definition allows for experimentally-manipulated genes, and allows for artifically-produced derivatives that mimic those found naturally. Proteins (in the sense defined here) that descended from a common ancestor can be classified into families and superfamilies composed of products of evolutionarily-related genes. The domain architecture of a protein is described by the order of its constituent domains. Proteins with the same domains in the same order are defined as homeomorphic [PRO:WCB]. + The definition above excludes protein complexes, which some also consider a protein. Those who wish to refer to a class representing both senses of the word are directed to CHEBI:36080. Note that the definition allows for experimentally-manipulated genes, and allows for artifically-produced derivatives that mimic those found naturally. Proteins (in the sense defined here) that descended from a common ancestor can be classified into families and superfamilies composed of products of evolutionarily-related genes. The domain architecture of a protein is described by the order of its constituent domains. Proteins with the same domains in the same order are defined as homeomorphic [PRO:WCB). protein @@ -25065,7 +25277,6 @@ Disorders or aberrations in the development or migration of the neural crest cel - A protein with core architecture consisting of a signal sequence, followed by 7 Ig-like domains (Pfam:PF00047, Pfam:PF07679, or Pfam:PF07686), a transmembrane region, and a cytoplasmic Protein tyrosine kinase domain. PIRSF:PIRSF038502 protein @@ -25826,51 +26037,51 @@ Disorders or aberrations in the development or migration of the neural crest cel - + - + - A material entity that minimally consists of a protein. + A molecular entity that minimally consists of a protein. protein protein aggregate protein complex protein-containing complex protein - PR:000050567 - Note: This includes single proteins and derivatives thereof (PR:000000001), protein-containing complexes (GO:0032991), and protein aggregates (PR:000050566). - protein-containing material entity + PR:000064867 + Note: This includes single proteins and derivatives thereof (PR:000000001), protein-containing complexes (GO:0032991), and protein aggregates (PR:000050565). + protein-containing molecular entity - + - A material entity that minimally consists of a protein. + A molecular entity that minimally consists of a protein. PRO:DAN - + protein PRO:DAN - + protein aggregate PRO:DAN - + protein complex PRO:DAN - + protein-containing complex PRO:DAN @@ -26081,8 +26292,8 @@ Disorders or aberrations in the development or migration of the neural crest cel - - + + @@ -26130,11 +26341,11 @@ Disorders or aberrations in the development or migration of the neural crest cel tendon http://upload.wikimedia.org/wikipedia/commons/3/3c/Achilles-tendon.jpg - + - + @@ -26147,13 +26358,13 @@ Disorders or aberrations in the development or migration of the neural crest cel - + OG - + AEO @@ -26190,7 +26401,6 @@ Disorders or aberrations in the development or migration of the neural crest cel - @@ -26277,7 +26487,6 @@ Disorders or aberrations in the development or migration of the neural crest cel Organ component adjacent to an organ cavity and which consists of a maximal aggregate of organ component layers. - UBERON:0009915 wall FMA:82482 galen:Wall @@ -26694,7 +26903,6 @@ Disorders or aberrations in the development or migration of the neural crest cel Anatomical cluster consisting of the skeletal elements and articular elements that are part of an individual subdivision of the organism. - UBERON:0010322 FMA:85544 NCIT:C34076 SCTID:118966000 @@ -27059,7 +27267,7 @@ Disorders or aberrations in the development or migration of the neural crest cel - + @@ -27095,14 +27303,14 @@ Disorders or aberrations in the development or migration of the neural crest cel gastrula stage - + - + BILS @@ -27437,7 +27645,6 @@ Disorders or aberrations in the development or migration of the neural crest cel Organism at the blastula stage - an early stage of embryonic development in animals. It is produced by cleavage of a fertilized ovum and consists of a spherical layer of around 128 cells surrounding a central fluid-filled cavity called the blastocoel. The blastula follows the morula and precedes the gastrula in the developmental sequence. TODO - check relationship with epiblast. Note in FMA this is not a subclass of embryo, but in uberon embryo is the whole organism from zygote onwards and thus includes the blastula - UBERON:0007011 BILA:0000059 BTO:0000128 GAID:1294 @@ -28496,7 +28703,6 @@ Disorders or aberrations in the development or migration of the neural crest cel - @@ -28510,7 +28716,7 @@ Disorders or aberrations in the development or migration of the neural crest cel - + @@ -28552,14 +28758,14 @@ Disorders or aberrations in the development or migration of the neural crest cel epithelium https://upload.wikimedia.org/wikipedia/commons/8/8f/Illu_epithelium.jpg - + - + http://palaeos.com/metazoa/porifera/homoscleromorpha.html @@ -28902,7 +29108,7 @@ Disorders or aberrations in the development or migration of the neural crest cel - + Primary germ layer that is the outer of the embryo's three germ layers and gives rise to epidermis and neural tissue. AAO:0000137 BILA:0000036 @@ -28937,14 +29143,14 @@ Disorders or aberrations in the development or migration of the neural crest cel ectoderm http://upload.wikimedia.org/wikipedia/commons/1/19/Gray32.png - + - + Bgee:AN @@ -28984,7 +29190,7 @@ Disorders or aberrations in the development or migration of the neural crest cel - + Primary germ layer that lies remote from the surface of the embryo and gives rise to internal tissues such as gut. AAO:0000139 BILA:0000038 @@ -29019,14 +29225,14 @@ Disorders or aberrations in the development or migration of the neural crest cel http://upload.wikimedia.org/wikipedia/commons/c/c0/Endoderm2.png http://upload.wikimedia.org/wikipedia/commons/d/df/Gray10.png - + - + Bgee:AN @@ -29067,10 +29273,9 @@ Disorders or aberrations in the development or migration of the neural crest cel - + The middle germ layer of the embryo, between the endoderm and ectoderm. - UBERON:0003263 AAO:0000304 BILA:0000037 BTO:0000839 @@ -29108,14 +29313,14 @@ Disorders or aberrations in the development or migration of the neural crest cel mesoderm http://upload.wikimedia.org/wikipedia/commons/e/e8/Mesoderm.png - + - + Bgee:AN @@ -29371,8 +29576,8 @@ Disorders or aberrations in the development or migration of the neural crest cel - - + + @@ -29404,24 +29609,24 @@ Disorders or aberrations in the development or migration of the neural crest cel eye - + - + - + PMID:21062451 - + PMID:21062451 @@ -29663,7 +29868,6 @@ Disorders or aberrations in the development or migration of the neural crest cel - AAO:0000959 CALOHA:TS-2103 VHOG:0001248 @@ -29671,7 +29875,6 @@ Disorders or aberrations in the development or migration of the neural crest cel uberon systema cardiovasculare UBERON:0001009 - circulatory system http://upload.wikimedia.org/wikipedia/commons/2/29/Circulatory_System_en.svg @@ -29815,7 +30018,7 @@ Disorders or aberrations in the development or migration of the neural crest cel - + @@ -29865,14 +30068,14 @@ Disorders or aberrations in the development or migration of the neural crest cel http://upload.wikimedia.org/wikipedia/commons/b/b2/TE-Nervous_system_diagram.svg http://upload.wikimedia.org/wikipedia/commons/b/ba/Nervous_system_diagram.png - + - + Bgee:AN @@ -29938,7 +30141,7 @@ Disorders or aberrations in the development or migration of the neural crest cel - + The central nervous system is the core nervous system that serves an integrating and coordinating function. In vertebrates it consists of the neural tube derivatives: the brain and spinal cord. In invertebrates it includes central ganglia plus nerve cord. @@ -29983,7 +30186,7 @@ Disorders or aberrations in the development or migration of the neural crest cel central nervous system - + @@ -29997,7 +30200,7 @@ Disorders or aberrations in the development or migration of the neural crest cel - + Bgee:AN @@ -30331,7 +30534,6 @@ Disorders or aberrations in the development or migration of the neural crest cel Muscle tissue composed of cardiac muscle cells, forming the muscles of the heart[ZFA,modified]. check relationship with myocardium. part_of in MA - but we also have a more specific class 'cardiac muscle tissue of myocardium'. Check ncit - UBERON:0007096 AAO:0010245 AEO:0000142 BILA:0000134 @@ -30717,7 +30919,7 @@ Disorders or aberrations in the development or migration of the neural crest cel - + Skeletal element that is composed of bone tissue. @@ -30759,14 +30961,14 @@ Disorders or aberrations in the development or migration of the neural crest cel bone element - + - + VSAO-modified @@ -30832,7 +31034,7 @@ Disorders or aberrations in the development or migration of the neural crest cel - + A tube extending from the mouth to the anus. @@ -30869,14 +31071,14 @@ Disorders or aberrations in the development or migration of the neural crest cel digestive tract - + - + NCBIBook:NBK10107 @@ -31233,7 +31435,6 @@ Disorders or aberrations in the development or migration of the neural crest cel The sensory system subserving the sense of vision. - UBERON:0007036 AAO:0000632 BILA:0000140 EMAPA:36003 @@ -31405,9 +31606,9 @@ Disorders or aberrations in the development or migration of the neural crest cel - - - + + + @@ -31455,15 +31656,15 @@ Disorders or aberrations in the development or migration of the neural crest cel notochord http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png - + - + - + @@ -31482,19 +31683,19 @@ Disorders or aberrations in the development or migration of the neural crest cel - + http://tolweb.org/Chordata/2499 - + ZFA - + EHDAA2 @@ -31534,8 +31735,8 @@ Disorders or aberrations in the development or migration of the neural crest cel - - + + Somites are spheres of epithelial cells that form sequentially along the anterior-posterior axis of the embryo through mesenchymal to epithelial transition of the presomitic mesoderm. mesodermal cluster @@ -31573,11 +31774,11 @@ Disorders or aberrations in the development or migration of the neural crest cel somite http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png - + - + @@ -31590,13 +31791,13 @@ Disorders or aberrations in the development or migration of the neural crest cel - + GOTAX:0000352 - + ZFA @@ -31655,7 +31856,6 @@ Disorders or aberrations in the development or migration of the neural crest cel - @@ -31722,22 +31922,22 @@ Disorders or aberrations in the development or migration of the neural crest cel - + - - + + - + A specialized region of ectoderm found between the neural ectoderm (neural plate) and non-neural ectoderm and composed of highly migratory pluripotent cells that delaminate in early embryonic development from the dorsal neural tube and give rise to an astounding variety of differentiated cell types[MP]. AAO:0010578 BTO:0001764 @@ -31770,45 +31970,45 @@ Disorders or aberrations in the development or migration of the neural crest cel http://upload.wikimedia.org/wikipedia/commons/5/5f/Gray644.png https://upload.wikimedia.org/wikipedia/commons/8/8f/Neural_Crest.png - + - + - + - + - + XAO https://github.com/obophenotype/uberon/wiki/The-neural-crest - + BTO - + PMID:11523831 - + PMID:11523831 @@ -31937,7 +32137,6 @@ Disorders or aberrations in the development or migration of the neural crest cel - @@ -32116,7 +32315,7 @@ Disorders or aberrations in the development or migration of the neural crest cel - + @@ -32172,14 +32371,14 @@ Disorders or aberrations in the development or migration of the neural crest cel bone marrow http://upload.wikimedia.org/wikipedia/commons/7/74/Gray72-en.svg - + - + FMA MA @@ -32391,7 +32590,7 @@ Disorders or aberrations in the development or migration of the neural crest cel - + @@ -32445,14 +32644,14 @@ Disorders or aberrations in the development or migration of the neural crest cel hematopoietic system - + - + FMA @@ -32849,6 +33048,7 @@ Disorders or aberrations in the development or migration of the neural crest cel + @@ -32862,7 +33062,7 @@ Disorders or aberrations in the development or migration of the neural crest cel - + Unsegmented field of paraxial mesoderm present posterior to the most recently formed somite pair, from which somites will form. AAO:0011086 EFO:0001982 @@ -32885,14 +33085,14 @@ Disorders or aberrations in the development or migration of the neural crest cel presomitic mesoderm - + - + Bgee:AN @@ -33046,9 +33246,9 @@ Disorders or aberrations in the development or migration of the neural crest cel - - - + + + A region of embryonic ectodermal cells that lie directly above the notochord. During neurulation, they change shape and produce an infolding of the neural plate (the neural fold) that then seals to form the neural tube[XAO]. The earliest recognizable dorsal ectodermal primordium of the central nervous system present near the end of gastrulation before infolding to form the neural keel; consists of a thickened pseudostratified epithelium[ZFA]. AAO:0011072 BTO:0001765 @@ -33077,34 +33277,34 @@ Disorders or aberrations in the development or migration of the neural crest cel neural plate https://upload.wikimedia.org/wikipedia/commons/8/8f/Neural_Crest.png - + - + - + - + GOTAX:0000352 - + Wikipedia - + Bgee:AN @@ -33144,7 +33344,7 @@ Disorders or aberrations in the development or migration of the neural crest cel - + The paraxial mesoderm is the mesoderm located bilaterally adjacent to the notochord and neural tube[GO]. AAO:0010568 EFO:0003515 @@ -33170,7 +33370,7 @@ Disorders or aberrations in the development or migration of the neural crest cel paraxial mesoderm http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png - + @@ -33183,7 +33383,7 @@ Disorders or aberrations in the development or migration of the neural crest cel - + Bgee:AN @@ -33230,7 +33430,7 @@ Disorders or aberrations in the development or migration of the neural crest cel - + @@ -33244,7 +33444,6 @@ Disorders or aberrations in the development or migration of the neural crest cel Portion of the middle of the three primary germ layers of the embryo that resides on the periphery of the embryo, is continuous with the extra-embryonic mesoderm, splits into two layers enclosing the intra-embryonic coelom, and gives rise to body wall structures[MP]. - UBERON:0006258 AAO:0010574 EHDAA2:0000919 EHDAA:379 @@ -33270,7 +33469,7 @@ Disorders or aberrations in the development or migration of the neural crest cel lateral plate mesoderm http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png - + @@ -33283,7 +33482,7 @@ Disorders or aberrations in the development or migration of the neural crest cel - + EHDAA2 VHOG @@ -33333,7 +33532,7 @@ Disorders or aberrations in the development or migration of the neural crest cel - + @@ -33374,7 +33573,7 @@ Disorders or aberrations in the development or migration of the neural crest cel myotome http://upload.wikimedia.org/wikipedia/commons/9/96/Gray65.png - + @@ -33387,7 +33586,7 @@ Disorders or aberrations in the development or migration of the neural crest cel - + EHDAA2-abduced @@ -33547,7 +33746,7 @@ Disorders or aberrations in the development or migration of the neural crest cel - + The part of the coelom in the embryo between the somatopleuric and splanchnopleuric mesoderm; the principal body cavities of the trunk (thoracic, abdominal, and pelvic) arise from this embryonic part of the coelom. consider merging with coelom. TODO - add spatial relationships to halves of LPM. Note the OG places XAO and ZFA coelem terms here. editor note: TODO check ZFA, which appears to be a structure present in adults EHDAA:251 @@ -33562,14 +33761,14 @@ Disorders or aberrations in the development or migration of the neural crest cel intraembryonic coelom - + - + Wikipedia @@ -33871,7 +34070,7 @@ Disorders or aberrations in the development or migration of the neural crest cel - + The bilaminar epithelium formed from the myotome and dermatome. AAO:0010572 AEO:0000214 @@ -33889,7 +34088,7 @@ Disorders or aberrations in the development or migration of the neural crest cel UBERON:0004290 dermomyotome - + @@ -33908,7 +34107,7 @@ Disorders or aberrations in the development or migration of the neural crest cel - + EHDAA2 ZFA @@ -34072,7 +34271,6 @@ Disorders or aberrations in the development or migration of the neural crest cel Organism at the gastrula stage. - UBERON:0007012 BILA:0000060 BTO:0001403 FBbt:00005317 @@ -34239,7 +34437,7 @@ Disorders or aberrations in the development or migration of the neural crest cel - + Organ consisting of skeletal tissue. Encompasses whole bones, fused bones, cartilaginious elements, teeth, dermal denticles. AAO:0011129 TAO:0001890 @@ -34253,14 +34451,14 @@ Disorders or aberrations in the development or migration of the neural crest cel skeletal element - + - + VSAO @@ -34287,7 +34485,7 @@ Disorders or aberrations in the development or migration of the neural crest cel - + @@ -34326,14 +34524,14 @@ Disorders or aberrations in the development or migration of the neural crest cel UBERON:0004770 articular system - + - + FMA @@ -34774,7 +34972,7 @@ Disorders or aberrations in the development or migration of the neural crest cel - + Mesenchyme that is part of a developing trunk. EFO:0003485 EHDAA2:0002092 @@ -34790,14 +34988,14 @@ Disorders or aberrations in the development or migration of the neural crest cel trunk mesenchyme - + - + EHDAA2 @@ -35005,7 +35203,6 @@ Disorders or aberrations in the development or migration of the neural crest cel - @@ -35107,7 +35304,7 @@ Disorders or aberrations in the development or migration of the neural crest cel - + The notochordal plate is the dorsal part of the notochordal process when the ventral portion breaks down. It is continuous laterally with the endoderm that composes the roof of the primitive foregut and is in contact dorsally with the neural tube. The folding off of the notochordal plate gives rise to the notochord. TODO - check ordering; awaiting confirmation from JB EHDAA2:0001278 @@ -35121,7 +35318,7 @@ Disorders or aberrations in the development or migration of the neural crest cel notochordal plate - + @@ -35134,7 +35331,7 @@ Disorders or aberrations in the development or migration of the neural crest cel - + EHDAA2 @@ -35162,7 +35359,7 @@ Disorders or aberrations in the development or migration of the neural crest cel - + A midline cellular cord formed from the migration of mesenchymal cells from the primitive knot. EHDAA2:0001279 EHDAA:224 @@ -35179,14 +35376,14 @@ Disorders or aberrations in the development or migration of the neural crest cel The notochordal process grows cranially until it reaches the prechordal plate, the future site of the mouth. In this area the ectoderm is attached directly to the endoderm without intervening mesoderm. This area is known as the oropharyngeal membrane, and it will break down to become the mouth. At the other end of the primitive streak the ectoderm is also fused directly to the endoderm; this is known as the cloacal membrane (proctodeum), or primordial anus. notochordal process - + - + EHDAA2 @@ -35797,7 +35994,7 @@ Disorders or aberrations in the development or migration of the neural crest cel - + @@ -35823,7 +36020,7 @@ Disorders or aberrations in the development or migration of the neural crest cel presumptive paraxial mesoderm - + @@ -35839,7 +36036,7 @@ Disorders or aberrations in the development or migration of the neural crest cel - + https://github.com/obophenotype/uberon/issues/1277 @@ -35888,7 +36085,7 @@ Disorders or aberrations in the development or migration of the neural crest cel - + Mesenchyme with little extracellular matrix. AEO:0000146 EHDAA2:0003146 @@ -35896,7 +36093,7 @@ Disorders or aberrations in the development or migration of the neural crest cel UBERON:0007524 dense mesenchyme tissue - + @@ -35909,7 +36106,7 @@ Disorders or aberrations in the development or migration of the neural crest cel - + AEO @@ -35924,7 +36121,6 @@ Disorders or aberrations in the development or migration of the neural crest cel - @@ -36068,7 +36264,7 @@ Disorders or aberrations in the development or migration of the neural crest cel - + @@ -36077,7 +36273,6 @@ Disorders or aberrations in the development or migration of the neural crest cel Sum total of mesenchyme in the embryo. consider adding new class (EMAPA:16097) for mesenchyme of embryo (some mesenchyme is extraembryonic - e.g. amnion mesoderm) - UBERON:0003313 EHDAA2:0001113 EHDAA:177 EMAPA:16097 @@ -36085,14 +36280,14 @@ Disorders or aberrations in the development or migration of the neural crest cel UBERON:0009142 entire embryonic mesenchyme - + - + EHDAA2 @@ -36114,7 +36309,7 @@ Disorders or aberrations in the development or migration of the neural crest cel - + EHDAA2:0002094 trunk and cervical paraxial mesenchyme uberon @@ -36122,14 +36317,14 @@ Disorders or aberrations in the development or migration of the neural crest cel UBERON:0009618 trunk paraxial mesoderm - + - + EHDAA2 @@ -36538,7 +36733,6 @@ Disorders or aberrations in the development or migration of the neural crest cel - @@ -36574,7 +36768,6 @@ Disorders or aberrations in the development or migration of the neural crest cel - @@ -36611,7 +36804,7 @@ Disorders or aberrations in the development or migration of the neural crest cel - + @@ -36635,7 +36828,7 @@ Disorders or aberrations in the development or migration of the neural crest cel UBERON:0011899 epimysium - + @@ -36648,7 +36841,7 @@ Disorders or aberrations in the development or migration of the neural crest cel - + FMA @@ -36694,6 +36887,7 @@ Disorders or aberrations in the development or migration of the neural crest cel EHDAA2:0004731 Wikipedia:Coelom + ZFA:0001438 enterocoelom haemocoelom schizocoelom @@ -36754,7 +36948,7 @@ Disorders or aberrations in the development or migration of the neural crest cel - + @@ -36775,7 +36969,7 @@ Disorders or aberrations in the development or migration of the neural crest cel UBERON:0012429 hematopoietic tissue - + @@ -36788,7 +36982,7 @@ Disorders or aberrations in the development or migration of the neural crest cel - + defitional @@ -37273,7 +37467,6 @@ Disorders or aberrations in the development or migration of the neural crest cel Primordium that develops into the central nervous system. - UBERON:3000469 future CNS presumptive central nervous system uberon @@ -37317,7 +37510,6 @@ Disorders or aberrations in the development or migration of the neural crest cel Primordium that develops into the nervous system. - UBERON:3000477 AAO:0000477 presumptive nervous system uberon @@ -37343,7 +37535,7 @@ Disorders or aberrations in the development or migration of the neural crest cel - + @@ -37366,7 +37558,7 @@ Disorders or aberrations in the development or migration of the neural crest cel UBERON:0016887 entire extraembryonic component - + @@ -37379,7 +37571,7 @@ Disorders or aberrations in the development or migration of the neural crest cel - + AEO @@ -37465,7 +37657,7 @@ Disorders or aberrations in the development or migration of the neural crest cel - + @@ -37482,14 +37674,14 @@ Disorders or aberrations in the development or migration of the neural crest cel skeletal musculature - + - + MA diff --git a/src/ontology/subsets/general_cell_types_upper_slim.tsv b/src/ontology/subsets/general_cell_types_upper_slim.tsv index 2bc1ed24c..0fd23a842 100644 --- a/src/ontology/subsets/general_cell_types_upper_slim.tsv +++ b/src/ontology/subsets/general_cell_types_upper_slim.tsv @@ -1,313 +1,313 @@ ?x ?label -_:B0be79aadX2D3b9dX2D4de8X2D9b61X2Dad49ee9a54c2genid1000 -_:B0be79aadX2D3b9dX2D4de8X2D9b61X2Dad49ee9a54c2genid1006 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+_:Be724617aX2D7808X2D41ddX2D87c4X2D66795569b4e8genid70 +_:Be724617aX2D7808X2D41ddX2D87c4X2D66795569b4e8genid722 +_:Be724617aX2D7808X2D41ddX2D87c4X2D66795569b4e8genid73 +_:Be724617aX2D7808X2D41ddX2D87c4X2D66795569b4e8genid736 +_:Be724617aX2D7808X2D41ddX2D87c4X2D66795569b4e8genid751 +_:Be724617aX2D7808X2D41ddX2D87c4X2D66795569b4e8genid768 +_:Be724617aX2D7808X2D41ddX2D87c4X2D66795569b4e8genid789 +_:Be724617aX2D7808X2D41ddX2D87c4X2D66795569b4e8genid797 +_:Be724617aX2D7808X2D41ddX2D87c4X2D66795569b4e8genid804 +_:Be724617aX2D7808X2D41ddX2D87c4X2D66795569b4e8genid814 +_:Be724617aX2D7808X2D41ddX2D87c4X2D66795569b4e8genid827 +_:Be724617aX2D7808X2D41ddX2D87c4X2D66795569b4e8genid844 +_:Be724617aX2D7808X2D41ddX2D87c4X2D66795569b4e8genid852 +_:Be724617aX2D7808X2D41ddX2D87c4X2D66795569b4e8genid859 +_:Be724617aX2D7808X2D41ddX2D87c4X2D66795569b4e8genid869 +_:Be724617aX2D7808X2D41ddX2D87c4X2D66795569b4e8genid896 +_:Be724617aX2D7808X2D41ddX2D87c4X2D66795569b4e8genid913 +_:Be724617aX2D7808X2D41ddX2D87c4X2D66795569b4e8genid922 +_:Be724617aX2D7808X2D41ddX2D87c4X2D66795569b4e8genid972 +_:Be724617aX2D7808X2D41ddX2D87c4X2D66795569b4e8genid980 +_:Be724617aX2D7808X2D41ddX2D87c4X2D66795569b4e8genid988 "cell" "early embryonic cell (metazoa)" "stem cell" @@ -627,18 +627,16 @@ _:B0be79aadX2D3b9dX2D4de8X2D9b61X2Dad49ee9a54c2genid993 "response to external biotic stimulus" "organelle" "membrane-bounded organelle" - "non-membrane-bounded organelle" + "membraneless organelle" "intracellular organelle" "intracellular membrane-bounded organelle" - "intracellular non-membrane-bounded organelle" + "intracellular membraneless organelle" "organelle lumen" "contractile muscle fiber" "protein-containing complex organization" "cellular component biogenesis" "translation initiation ternary complex" - "cellular metabolic process" "primary metabolic process" - "cellular biosynthetic process" "biological process involved in interspecies interaction between organisms" "plasma membrane fusion" "innate immune response" @@ -729,7 +727,7 @@ _:B0be79aadX2D3b9dX2D4de8X2D9b61X2Dad49ee9a54c2genid993 "supramolecular fiber" "synaptic signaling" "trans-synaptic signaling" - "cellular anatomical entity" + "cellular anatomical structure" "plasma membrane bounded cell projection" "plasma membrane bounded cell projection organization" "exocytic process" @@ -871,7 +869,7 @@ _:B0be79aadX2D3b9dX2D4de8X2D9b61X2Dad49ee9a54c2genid993 "eukaryotic protein" "cathepsin-like protease" "receptor-type tyrosine-protein phosphatase C isoform CD45R" - "protein-containing material entity" + "protein-containing molecular entity" "processual entity" "sense organ" "tube" diff --git a/src/ontology/subsets/kidney_upper_slim.json b/src/ontology/subsets/kidney_upper_slim.json index ddee7b988..891a1d186 100644 --- a/src/ontology/subsets/kidney_upper_slim.json +++ b/src/ontology/subsets/kidney_upper_slim.json @@ -4,9 +4,9 @@ "meta" : { "basicPropertyValues" : [ { "pred" : "http://www.w3.org/2002/07/owl#versionInfo", - "val" : "2024-09-26" + "val" : "2025-01-08" } ], - "version" : "http://purl.obolibrary.org/obo/cl/releases/2024-09-26/subsets/kidney_upper_slim.owl" + "version" : "http://purl.obolibrary.org/obo/cl/releases/2025-01-08/subsets/kidney_upper_slim.owl" }, "nodes" : [ { "id" : "http://purl.obolibrary.org/obo/CL_0000000", @@ -18,7 +18,7 @@ "xrefs" : [ "CARO:mah" ] }, "comments" : [ "The definition of cell is intended to represent all cells, and thus a cell is defined as a material entity and not an anatomical structure, which implies that it is part of an organism (or the entirety of one)." ], - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/ubprop#_upper_level" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/ubprop#_upper_level" ], "xrefs" : [ { "val" : "CALOHA:TS-2035" }, { @@ -50,6 +50,7 @@ "val" : "A cell found in the embryo before the formation of all the gem layers is complete.", "xrefs" : [ "GOC:tfm" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "ZFA:0009002" } ] @@ -64,7 +65,7 @@ "xrefs" : [ "GOC:tfm", "MESH:D013234" ] }, "comments" : [ "This term applies to metazoan. For plant stem cells, consider using PO:0004011 ‘initial cell’ or its parent PO:0004010 ‘meristematic cell’." ], - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#general_cell_types_upper_slim", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#general_cell_types_upper_slim", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "animal stem cell" @@ -91,7 +92,7 @@ "xrefs" : [ "GOC:add", "GOC:dsd", "GOC:tfm", "PMID:19022770", "http://en.wikipedia.org/wiki/Hematopoietic_stem_cell" ] }, "comments" : [ "Markers differ between species, and two sets of markers have been described for mice. HSCs are reportedly CD34-positive, CD45-positive, CD48-negative, CD150-positive, CD133-positive, and CD244-negative." ], - "subsets" : [ "http://purl.obolibrary.org/obo/cl#blood_and_immune_upper_slim", "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#blood_and_immune_upper_slim", "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "blood forming stem cell" @@ -133,7 +134,7 @@ "val" : "A progenitor cell committed to the erythroid lineage.", "xrefs" : [ "GOC:add", "ISBN:0721601464" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#blood_and_immune_upper_slim", "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#blood_and_immune_upper_slim", "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003000", "pred" : "hasRelatedSynonym", @@ -171,7 +172,7 @@ "xrefs" : [ "GOC:tfm", "ISBN:0721662544" ] }, "comments" : [ "Originally this term had some plant germ line cell children." ], - "subsets" : [ "http://purl.obolibrary.org/obo/cl#general_cell_types_upper_slim", "http://purl.obolibrary.org/obo/ubprop#_upper_level" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#general_cell_types_upper_slim", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/ubprop#_upper_level" ], "xrefs" : [ { "val" : "ZFA:0009016" } ] @@ -185,6 +186,7 @@ "val" : "A stem cell that can give rise to multiple lineages of cells.", "xrefs" : [ "GOC:add" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "multi-fate stem cell" @@ -214,7 +216,7 @@ "xrefs" : [ "GOC:add", "ISBN:0878932437", "MESH:D023461" ] }, "comments" : [ "This cell type is intended to be compatible with any vertebrate common myeloid progenitor. For mammalian CMP known to be CD34-positive, please use the term 'common myeloid progenitor, CD34-positive' (CL_0001059)." ], - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "common myeloid precursor" @@ -270,7 +272,7 @@ "xrefs" : [ "GOC:add", "GOC:dsd", "GOC:tfm", "MESH:D055015", "PMID:16647566", "http://en.wikipedia.org/wiki/Megakaryocyte-erythroid_progenitor_cell" ] }, "comments" : [ "MEPs are reportedly CD19-negative, CD34-negative, CD45RA-negative, CD110-positive, CD117-positive, and SCA1-negative and reportedly express the transcription factors GATA-1 and NF-E2." ], - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "CFU-EM" @@ -310,6 +312,7 @@ "val" : "A stem cell from which all cells of the body can form.", "xrefs" : [ "GOC:add", "GOC:tfm" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "totipotential stem cell" @@ -332,7 +335,7 @@ "xrefs" : [ "SANBI:mhl" ] }, "comments" : [ "define using PATO mulit-potent or oligopotent?" ], - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "blast cell" @@ -352,6 +355,7 @@ "val" : "A cell that is commited to differentiating into a muscle cell. Embryonic myoblasts develop from the mesoderm. They undergo proliferation, migrate to their various sites, and then differentiate into the appropriate form of myocytes. Myoblasts also occur as transient populations of cells in muscles undergoing repair.", "xrefs" : [ "GOC:tfm", "MESH:D032446", "PMID:21849021" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "BTO:0000222" }, { @@ -376,7 +380,7 @@ "xrefs" : [ "ISBN:0517223651", "MESH:D005347", "http://en.wikipedia.org/wiki/Fibroblast" ] }, "comments" : [ "These cells may be vimentin-positive, fibronectin-positive, fsp1-positive, MMP-1-positive, collagen I-positive, collagen III-positive, and alpha-SMA-negative." ], - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#general_cell_types_upper_slim", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#general_cell_types_upper_slim", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "xrefs" : [ { "val" : "BTO:0000452" }, { @@ -404,7 +408,7 @@ "val" : "A cell that is usually found in a two-dimensional sheet with a free surface. The cell has a cytoskeleton that allows for tight cell to cell contact and for cell polarity where apical part is directed towards the lumen and the basal part to the basal lamina.", "xrefs" : [ "FB:ma", "GOC:tfm", "MESH:D004847" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#general_cell_types_upper_slim", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#general_cell_types_upper_slim", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "epitheliocyte" @@ -441,7 +445,7 @@ "val" : "An epithelial cell that is part of a duct.", "xrefs" : [ "https://orcid.org/0000-0001-5208-3432" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "ZFA:0009372" } ] @@ -455,7 +459,7 @@ "val" : "An endothelial cell that lines the vasculature.", "xrefs" : [ "GOC:tfm" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "xrefs" : [ { "val" : "ZFA:0009036" } ], @@ -467,7 +471,10 @@ }, { "id" : "http://purl.obolibrary.org/obo/CL_0000072", "lbl" : "non-branched duct epithelial cell", - "type" : "CLASS" + "type" : "CLASS", + "meta" : { + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ] + } }, { "id" : "http://purl.obolibrary.org/obo/CL_0000075", "lbl" : "columnar/cuboidal epithelial cell", @@ -477,7 +484,7 @@ "val" : "A columnar/cuboidal epithelial cell is a cell usually found in a two dimensional sheet with a free surface. Columnar/cuboidal epithelial cells take on the shape of a column or cube.", "xrefs" : [ "GO:0002065", "https://orcid.org/0000-0001-5208-3432" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "xrefs" : [ { "val" : "ZFA:0009038" } ], @@ -495,7 +502,7 @@ "val" : "Any epithelial cell that is part of some squamous epithelium.", "xrefs" : [ "FBC:Autogenerated" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "CALOHA:TS-1249" }, { @@ -511,7 +518,7 @@ "val" : "A cell found predominately in the blood.", "xrefs" : [ "GOC:add", "GOC:tfm" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#general_cell_types_upper_slim" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#general_cell_types_upper_slim", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "FMA:62844" }, { @@ -530,7 +537,7 @@ "xrefs" : [ "GOC:tfm", "MESH:D042783", "PMID:21275341", "http://en.wikipedia.org/wiki/Endothelial_cell", "https://sourceforge.net/tracker/?func=detail&atid=440764&aid=3364936&group_id=36855" ] }, "comments" : [ "From FMA: 9.07.2001: Endothelial cell has always been classified as a kind of epithelial cell, specifically a squamous cell but that is not true. First, endothelial cell can either be squamous or cuboidal (e.g. high-endothelial cell) and secondly, it has different embryological derivation (mesodermal) than a true epithelial cell (ectodermal and endodermal). The basis for present classification is the fact that it comprises the outermost layer or lining of anatomical structures (location-based) but a better structural basis for the differentia is the cytoskeleton of the cell. Endothelial cell has vimentin filaments while an epithelial cell has keratin filaments. [Onard]." ], - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "endotheliocyte" @@ -558,6 +565,7 @@ "val" : "Ectoderm destined to be nervous tissue.", "xrefs" : [ "GOC:tfm", "ISBN:068340007X" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "neurectoderm cell" @@ -576,7 +584,7 @@ "xrefs" : [ "FB:ma", "GOC:dsd", "PMCID:PMC2613570", "PMID:10102814", "PMID:16923606", "PMID:17986482", "PMID:19960544", "http://en.wikipedia.org/wiki/Mesenchymal_stem_cell", "http://www.copewithcytokines.de/cope.cgi?key=mesenchymal%20stem%20cells" ] }, "comments" : [ "Many but not all mesenchymal cells derive from the mesoderm. MSCs are reportedly CD3-negative, CD4-negative, CD5-negative, CD8-negative, CD11a-negative, CD11b-negative, CD14-negative, CD19-negative, CD29-positive, CD31-negative, CD34-negative, CD38-negative, CD40-negative, CD44-positive, CD45-negative, CD49-positive, CD54-positive, CD66b-negative, CD79a-negative, CD80-negative, CD102-positive, CD106-positive, CD117-positive, CD121a-positive, CD121b-positive, CD123-positive, CD124-positive, CD133-negative, CD146-positive, CD166-positive, CD271-positive, B220-negative, Gr1-negative, MHCI-positive, MHCII-negative, SSEA4-negative, sca1-positive, Ter119-negative, and glycophorin A-negative. Cultured MSCs are capable of producing stem cell factor, IL7, IL8, IL11, TGF-beta, cofilin, galectin-1, laminin-receptor 1, cyclophilin A, and MMP-2." ], - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "pred" : "hasNarrowSynonym", "val" : "bone marrow stromal cells" @@ -647,7 +655,7 @@ "val" : "A cell that specializes in controlled release of one or more substances.", "xrefs" : [ "GOC:tfm", "ISBN:0721662544" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "BTO:0003659" }, { @@ -662,7 +670,8 @@ "definition" : { "val" : "Any secretory cell that is capable of some protein secretion.", "xrefs" : [ "FBC:Autogenerated" ] - } + }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ] } }, { "id" : "http://purl.obolibrary.org/obo/CL_0000183", @@ -673,7 +682,7 @@ "val" : "A cell whose primary function is to shorten.", "xrefs" : [ "FB:ma" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ] + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ] } }, { "id" : "http://purl.obolibrary.org/obo/CL_0000187", @@ -684,7 +693,7 @@ "val" : "A mature contractile cell, commonly known as a myocyte. This cell has as part of its cytoplasm myofibrils organized in various patterns.", "xrefs" : [ "MESH:D032342" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "muscle fiber" @@ -721,7 +730,7 @@ "val" : "A non-striated, elongated, spindle-shaped cell found lining the digestive tract, uterus, and blood vessels. They develop from specialized myoblasts (smooth muscle myoblast).", "xrefs" : [ "MESH:D032389", "PMID:9315361", "http://en.wikipedia.org/wiki/Smooth_muscle_cell" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#general_cell_types_upper_slim", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#general_cell_types_upper_slim", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "synonyms" : [ { "pred" : "hasBroadSynonym", "val" : "non-striated muscle cell" @@ -745,10 +754,15 @@ "val" : "FMA:14072" }, { "val" : "ZFA:0009118" + }, { + "val" : "https://cellxgene.cziscience.com/cellguide/CL_0000192" } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" + }, { + "pred" : "http://purl.org/dc/terms/description", + "val" : "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nSmooth muscle cells are a specialized type of muscle cells that are primarily found within the walls of hollow organs such as the intestine, stomach, bladder, uterus, and blood vessels. These cells are an essential component of the autonomic nervous system controling involuntary movements within the body.\nSmooth muscle cells play a vital role in many physiological processes due to their unique functionality. They can contract and relax in a slow, sustained, and controlled manner to help modulate the size and shape of the lumens of the organs they surround. For example, in the digestive system, coordinated contraction and relaxation of smooth muscle cells propels food along the gastrointestinal tract - a process known as peristalsis. In the blood vessels, the smooth muscle cells, by contracting or relaxing, either constrict or dilate the vessels, which in turn, help regulate blood flow and pressure.\nOn a cellular level, smooth muscle cells possess a single, centrally located nucleus and contain an arranged network of actin and myosin filaments, which are the proteins responsible for muscle contraction. Unlike their counterparts in skeletal or cardiac muscles, these cells lack specific contact points for these filaments, hence the lack of visible striations. Furthermore, the contraction of smooth muscle cells is regulated by hormones and neurotransmitters, such as acetylcholine and norepinephrine, adding an additional layer of complex regulation to these highly specialized cells." } ] } }, { @@ -760,6 +774,7 @@ "val" : "A cell whose function is determined by the generation or the reception of an electric signal.", "xrefs" : [ "FB:ma" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "ZFA:0009128" } ] @@ -773,6 +788,7 @@ "val" : "A cell within an epithelial cell sheet whose main function is to act as an internal or external covering for a tissue or an organism.", "xrefs" : [ "JB:jb" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "boundary cell" @@ -790,6 +806,7 @@ "val" : "A cell whose primary function is to prevent the transport of stuff across compartments.", "xrefs" : [ "JB:jb" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "ZFA:0009132" } ] @@ -803,6 +820,7 @@ "val" : "A cell that moves by its own activities.", "xrefs" : [ "FB:ma" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "ZFA:0009136" } ] @@ -816,6 +834,7 @@ "val" : "A cell of the outer of the three germ layers of the embryo.", "xrefs" : [ "MESH:D004475" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "ectoderm cell" @@ -835,7 +854,7 @@ "val" : "A cell of the middle germ layer of the embryo.", "xrefs" : [ "MESH:D008648" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "mesoblast" @@ -847,6 +866,12 @@ "val" : "FMA:72554" }, { "val" : "ZFA:0009138" + }, { + "val" : "https://cellxgene.cziscience.com/cellguide/CL_0000222" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/description", + "val" : "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nMesodermal cells are pluripotent and the most abundant in the human body. They contribute to the development of several structures such as the skeletal muscles, bones, heart and blood vessels, kidneys, gonads, connective tissues, and certain layers of the skin. Hence, the mesoderm is often regarded as an active and diverse layer due to its role in forming many bodily structures. \nIn embryonic development, these cells are instrumental, contributing to the body's structures through a carefully coordinated sequence of morphogenetic movements. This process forms the complex multicellular architecture of tissues and organs from a simple ball of cells. Without the function of mesodermal cells, the body's integral structures and systems would cease to form correctly, leading to developmental disorders such as axial mesodermal dysplasia complex" } ] } }, { @@ -858,6 +883,7 @@ "val" : "A cell of the inner of the three germ layers of the embryo.", "xrefs" : [ "MESH:D004707" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "endoderm cell" @@ -877,7 +903,7 @@ "val" : "A red blood cell. In mammals, mature erythrocytes are biconcave disks containing hemoglobin whose function is to transport oxygen.", "xrefs" : [ "GOC:tfm", "MESH:D004912" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#blood_and_immune_upper_slim", "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#blood_and_immune_upper_slim", "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "RBC" @@ -906,7 +932,7 @@ "val" : "Any cell that in taxon some Eukaryota.", "xrefs" : [ "FBC:Autogenerated" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "MESH:D005057" } ] @@ -920,6 +946,7 @@ "val" : "Any cell that is capable of some oxygen transport.", "xrefs" : [ "FBC:Autogenerated" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "ZFA:0009164" } ] @@ -933,6 +960,7 @@ "val" : "A cell derived from the specialized ectoderm flanking each side of the embryonic neural plate, which after the closure of the neural tube, forms masses of cells that migrate out from the dorsal aspect of the neural tube to spread throughout the body.", "xrefs" : [ "doi:10.1016/j.stem.2015.02.017" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "FMA:86667" }, { @@ -948,6 +976,7 @@ "val" : "A mesenchymal cell in embryonic development found in a contracting mass and that gives rise to osteoprogenitors.", "xrefs" : [ "GOC:tfm", "PMID:5025404" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "ZFA:0009166" } ] @@ -960,7 +989,8 @@ "definition" : { "val" : "A cell of the outer layer of a blastula that gives rise to the ectoderm after gastrulation.", "xrefs" : [ "GOC:tfm", "ISBN:0618947256" ] - } + }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ] } }, { "id" : "http://purl.obolibrary.org/obo/CL_0000365", @@ -971,6 +1001,7 @@ "val" : "Diploid cell produced by the fusion of sperm cell nucleus and egg cell.", "xrefs" : [ "ISBN:0471245208" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "pred" : "hasBroadSynonym", "val" : "zygote" @@ -992,6 +1023,7 @@ "val" : "A cell whose function is determined by its response to an electric signal.", "xrefs" : [ "FB:ma" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "ZFA:0009190" } ] @@ -1005,10 +1037,33 @@ "val" : "A cell that initiates an electrical signal and passes that signal to another cell.", "xrefs" : [ "FB:ma" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "ZFA:0009193" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/CL_0000499", + "lbl" : "stromal cell", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A connective tissue cell of an organ found in the loose connective tissue.", + "xrefs" : [ "GOC:tfm", "MESH:D017154" ] + }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#general_cell_types_upper_slim", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "xrefs" : [ { + "val" : "BTO:0002064" + }, { + "val" : "FMA:83624" + }, { + "val" : "ZFA:0009226" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/RO_0002175", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/CL_0000514", "lbl" : "smooth muscle myoblast", @@ -1018,7 +1073,7 @@ "val" : "A precursor cell destined to differentiate into smooth muscle myocytes.", "xrefs" : [ "GOC:tfm", "MESH:D032390" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "myoblast, smooth muscle", @@ -1031,6 +1086,12 @@ "val" : "FMA:84798" }, { "val" : "ZFA:0009235" + }, { + "val" : "https://cellxgene.cziscience.com/cellguide/CL_0000514" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/description", + "val" : "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nA precursor to the smooth muscle cell, the smooth muscle myoblast, is integral to various body systems, including the cardiovascular, gastrointestinal, and respiratory systems. Smooth muscle myoblasts arise from the differentiation of mesenchymal stem cells, a process tightly regulated by specific genetic factors and environmental signals. Their role extends to myogenesis, particularly in the formation of muscular tissue, especially during embryonic development.\nSmooth muscle myoblasts possess distinctive cellular characteristics. In contrast to skeletal muscle myoblasts, they do not fuse to create multinucleated fibers. Instead, they differentiate into individual, uninucleated smooth muscle cells. This differentiation unfolds in two distinct phases: proliferation, marked by rapid division to increase cell numbers, and differentiation, involving structural and functional transformation into mature smooth muscle cells. This intricate process is intricately mediated by various signaling molecules and transcription factors.\nFunctionally, smooth muscle myoblasts and the mature muscle cells they generate play pivotal roles in various physiological processes. Smooth muscle cells orchestrate involuntary muscle responses and are integral to body systems that regulate blood flow, propel food along the digestive tract, and control airflow in the respiratory tract. These diverse functions underscore the significance of smooth muscle myoblasts in the body's growth, maintenance, and overall function." } ] } }, { @@ -1043,7 +1104,7 @@ "xrefs" : [ "MESH:D009474", "http://en.wikipedia.org/wiki/Neuron" ] }, "comments" : [ "These cells are also reportedly CD4-negative and CD200-positive. They are also capable of producing CD40L and IFN-gamma." ], - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#general_cell_types_upper_slim", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#general_cell_types_upper_slim", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "nerve cell" @@ -1080,7 +1141,7 @@ "val" : "An immature, nucleated erythrocyte occupying the stage of erythropoeisis that follows formation of erythroid progenitor cells. This cell is CD71-positive, has both a nucleus and a nucleolus, and lacks hematopoeitic lineage markers.", "xrefs" : [ "ISBN:0721601464", "PMID:1638021" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#blood_and_immune_upper_slim", "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#blood_and_immune_upper_slim", "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "rubriblast", @@ -1102,6 +1163,7 @@ "val" : "A nucleated immature erythrocyte, having cytoplasm generally similar to that of the earlier proerythroblast but sometimes even more basophilic, and usually regular in outline. The nucleus is still relatively large, but the chromatin strands are thicker and more deeply staining, giving a coarser appearance; the nucleoli have disappeared. This cell is CD71-positive and lacks hematopoeitic lineage markers.", "xrefs" : [ "GOC:tfm", "ISBN:0721601464" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "basophilic normoblast", @@ -1134,6 +1196,7 @@ "val" : "A nucleated, immature erythrocyte in which the nucleus occupies a relatively smaller part of the cell than in its precursor, the basophilic erythroblast. The cytoplasm is beginning to acquire hemoglobin and thus is no longer a purely basophilic, but takes on acidophilic aspects, which becomes progressively more marked as the cell matures. The chromatin of the nucleus is arranged in coarse, deeply staining clumps. This cell is CD71-positive and lacks hematopoeitic lineage markers.", "xrefs" : [ "ISBN:0721601464" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "intermediate erythroblast", @@ -1174,6 +1237,7 @@ "val" : "The final stage of the nucleated, immature erythrocyte, before nuclear loss. Typically the cytoplasm is described as acidophilic, but it still shows a faint polychromatic tint. The nucleus is small and initially may still have coarse, clumped chromatin, as in its precursor, the polychromatophilic erythroblast, but ultimately it becomes pyknotic, and appears as a deeply staining, blue-black, homogeneous structureless mass. The nucleus is often eccentric and sometimes lobulated.", "xrefs" : [ "ISBN:0721601464" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "acidophilic erythroblast", @@ -1208,7 +1272,7 @@ "xrefs" : [ "GOC:dsd", "GOC:tfm", "ISBN:0721601464" ] }, "comments" : [ "Lineage negative is described here as CD2-negative, CD3-negative, CD4-negative, CD5-negative, CD8a-negative, CD14-negative, CD19-negative, CD20-negative, CD56-negative, Ly6g-negative, and Ter119-negative." ], - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "CFU-Meg", @@ -1268,7 +1332,7 @@ "xrefs" : [ "ISBN:0721601464", "MESH:D008533", "PMID:31043076", "http://en.wikipedia.org/wiki/Megakaryocyte" ] }, "comments" : [ "Megakaryocytes are reportedly CD181-positive and CD182-positive." ], - "subsets" : [ "http://purl.obolibrary.org/obo/cl#blood_and_immune_upper_slim", "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#blood_and_immune_upper_slim", "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "megacaryocyte" @@ -1300,7 +1364,7 @@ "val" : "An immature erythrocyte that changes the protein composition of its plasma membrane by exosome formation and extrusion. The types of protein removed differ between species though removal of the transferrin receptor is apparent in mammals and birds.", "xrefs" : [ "GOC:add", "GOC:tfm", "PMID:15946868", "PMID:2037622" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#blood_and_immune_upper_slim", "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#blood_and_immune_upper_slim", "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "BTO:0001173" }, { @@ -1321,6 +1385,7 @@ "xrefs" : [ "GOC:dsd", "GOC:tfm", "PMID:12768659" ] }, "comments" : [ "These cells are reportedly CD31-positive, CD34-positive, CD144-positive, CD309-positive, and TAL1-positive." ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "angioblast" @@ -1341,7 +1406,7 @@ "val" : "The reproductive cell in multicellular organisms.", "xrefs" : [ "MESH:D005854" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "BTO:0000535" }, { @@ -1361,7 +1426,7 @@ "val" : "A cell whose primary function is to support other cell types.", "xrefs" : [ "FB:ma", "GOC:tfm" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "supportive cell" @@ -1381,7 +1446,7 @@ "val" : "A smooth muscle cell that synthesizes, stores, and secretes the enzyme renin. This cell type are located in the wall of the afferent arteriole at the entrance to the glomerulus. While having a different origin than other kidney smooth muscle cells, this cell type expresses smooth muscle actin upon maturation.", "xrefs" : [ "GOC:cvs", "GOC:tfm", "PMID:11457727" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "synonyms" : [ { "pred" : "hasBroadSynonym", "val" : "juxtaglomerular cell" @@ -1412,7 +1477,7 @@ "xrefs" : [ "GOC:tfm", "http://www.copewithcytokines.de/cope.cgi?key=mesangial%20cells" ] }, "comments" : [ "Do all of these cells really develop from some mesenchymal stem cell?" ], - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "kidney mesangial cell" @@ -1438,7 +1503,7 @@ "val" : "An endothelial cell that has small pores, or fenestrations, which allow for the efficient exchange of substances between the blood and surrounding tissues.", "xrefs" : [ "DOI:10.1007/978-3-211-99390-3_133" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "window cell" @@ -1450,7 +1515,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://purl.org/dc/terms/description", - "val" : "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional.\n\nFenestrated cells are specialized epithelial cells that are characterized by a distinctive structural feature, fenestrations or tiny pores, which allow an exchange of substances such as fluids, nutrients, and waste between blood vessels and the surrounding tissue environments. These cells are present in various types of epithelial tissues in the human body, including the intestinal tract, endocrine glands, and certain parts of the renal system. \nThere are multiple types of endothelial cell fenestrations. The most common type is found in systemic capillaries of the endocrine tissue (e.g., pancreatic islets), gastrointestinal mucosa, and renal peritubular capillaries. Here, the fenestrated cells have fenestrations in their peripheral cytoplasm with a unique thin and permeable diaphragm that provides a high degree of selectivity, blocking the passage of larger molecules while allowing the free movement of smaller ones. In contrast, other types of fenestrations, such as the discontinuous epithelium of the liver sinusoidal endothelial cells, do not have diaphragms. \nCharacteristically, fenestrated cells play a vital role in the filtering process of body systems. They are a key part of the glomeruli in the kidneys where blood is filtered under high pressure. The fenestrations present in the endothelial cells lining the capillaries of the glomerulus allow the free passage of water and small solute molecules towards the Bowman's capsule, leaving behind larger proteins and cells in the blood, thereby aiding in the filtration and waste removal process. \nIn the endocrine system, fenestrated cells in glandular capillaries allow the prompt release of hormones into the bloodstream. These cells have tightly clustered fenestrations which increase the surface area available for passive diffusion, improving the efficiency of hormone secretion. In villi of the small intestine, these cells increase absorption efficiency, permitting the exchange of water, electrolytes, and nutrients.\nOverall, fenestrated cells contribute immensely to important physiological processes of filtration, absorption, and secretion, primarily connecting our body's circulation system with the surrounding tissues and organs." + "val" : "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nFenestrated cells are specialized epithelial cells that are characterized by a distinctive structural feature, fenestrations or tiny pores, which allow an exchange of substances such as fluids, nutrients, and waste between blood vessels and the surrounding tissue environments. These cells are present in various types of epithelial tissues in the human body, including the intestinal tract, endocrine glands, and certain parts of the renal system. \nThere are multiple types of endothelial cell fenestrations. The most common type is found in systemic capillaries of the endocrine tissue (e.g., pancreatic islets), gastrointestinal mucosa, and renal peritubular capillaries. Here, the fenestrated cells have fenestrations in their peripheral cytoplasm with a unique thin and permeable diaphragm that provides a high degree of selectivity, blocking the passage of larger molecules while allowing the free movement of smaller ones. In contrast, other types of fenestrations, such as the discontinuous epithelium of the liver sinusoidal endothelial cells, do not have diaphragms. \nCharacteristically, fenestrated cells play a vital role in the filtering process of body systems. They are a key part of the glomeruli in the kidneys where blood is filtered under high pressure. The fenestrations present in the endothelial cells lining the capillaries of the glomerulus allow the free passage of water and small solute molecules towards the Bowman's capsule, leaving behind larger proteins and cells in the blood, thereby aiding in the filtration and waste removal process. \nIn the endocrine system, fenestrated cells in glandular capillaries allow the prompt release of hormones into the bloodstream. These cells have tightly clustered fenestrations which increase the surface area available for passive diffusion, improving the efficiency of hormone secretion. In villi of the small intestine, these cells increase absorption efficiency, permitting the exchange of water, electrolytes, and nutrients.\nOverall, fenestrated cells contribute immensely to important physiological processes of filtration, absorption, and secretion, primarily connecting our body's circulation system with the surrounding tissues and organs." } ] } }, { @@ -1463,7 +1528,7 @@ "xrefs" : [ "GOC:dsd", "GOC:tfm", "ISBN:0721662544", "MESH:D020286", "PMID:16807374", "PMID:17986482", "PMID:20024907" ] }, "comments" : [ "Pericytes are CD10-positive, CD13-positive, CD31-negative, CD45-negative, CD106-positive, CD117-negative, CD140-positive, CD144-negative, CD146-positive, CD271-positive, CD325-positive, NG2-positive, RGS5-positive, SMA-positive, and desmin-positive. A subpopulation is CD248-positive. They are also capable of producing angiopoietin 1, CXCL12, TGF-beta, and VEGF-A." ], - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "ARC", @@ -1505,7 +1570,7 @@ "val" : "A non-terminally differentiated cell that is capable of developing into a muscle cell.", "xrefs" : [ "GOC:add" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "ZFA:0009291" } ] @@ -1519,6 +1584,7 @@ "val" : "A stem cell that can give rise to cell types of the body other than those of the germ-line.", "xrefs" : [ "GO:0048103" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "CALOHA:TS-2086" }, { @@ -1536,7 +1602,7 @@ "val" : "A cell of the monocyte, granulocyte, mast cell, megakaryocyte, or erythroid lineage.", "xrefs" : [ "GOC:add" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "BTO:0001441" }, { @@ -1557,7 +1623,7 @@ "xrefs" : [ "GOC:add", "GOC:tfm" ] }, "comments" : [ "Note that in FMA erythropoietic cells are types of nucleated erythrocytes and thus don't include erythrocytes." ], - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "erythropoietic cell" @@ -1585,7 +1651,7 @@ "val" : "A nucleated precursor of an erythrocyte that lacks hematopoietic lineage markers.", "xrefs" : [ "GOC:add", "ISBN:0721601464", "PMID:18174176" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#blood_and_immune_upper_slim", "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#blood_and_immune_upper_slim", "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "normoblast" @@ -1612,7 +1678,7 @@ "xrefs" : [ "GOC:add", "GOC:tfm", "PMID:19022770" ] }, "comments" : [ "Markers differ between mouse and human." ], - "subsets" : [ "http://purl.obolibrary.org/obo/cl#blood_and_immune_upper_slim", "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#blood_and_immune_upper_slim", "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "MPP" @@ -1642,7 +1708,7 @@ "xrefs" : [ "GOC:add", "GOC:tfm", "PMID:19022770" ] }, "comments" : [ "Note that this is a class of cell types, not an identified single cell type." ], - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "synonyms" : [ { "pred" : "hasBroadSynonym", "val" : "myeloid progenitor cell" @@ -1670,7 +1736,7 @@ "val" : "A cell of a hematopoietic lineage.", "xrefs" : [ "GOC:add", "GO_REF:0000031" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "haematopoietic cell" @@ -1702,7 +1768,7 @@ "val" : "A hematopoietic progenitor cell that is capable of developing into only one lineage of hematopoietic cells.", "xrefs" : [ "GOC:tfm", "PMID:19022770" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#blood_and_immune_upper_slim" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#blood_and_immune_upper_slim", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "basicPropertyValues" : [ { "pred" : "http://purl.org/dc/terms/contributor", "val" : "https://orcid.org/0000-0003-1980-3228" @@ -1721,7 +1787,7 @@ "xrefs" : [ "GOC:tfm", "PMID:19022770", "https://orcid.org/0000-0001-5208-3432" ] }, "comments" : [ "This cell type is intended to be compatible with any vertebrate hematopoietic oligopotent progenitor cell. For mammalian hematopoietic oligopotent progenitor cells known to be lineage-negative, please use the term 'hematopoietic oligopotent progenitor cell' (CL_0001060)." ], - "subsets" : [ "http://purl.obolibrary.org/obo/cl#blood_and_immune_upper_slim" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#blood_and_immune_upper_slim", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "basicPropertyValues" : [ { "pred" : "http://purl.org/dc/terms/contributor", "val" : "https://orcid.org/0000-0003-1980-3228" @@ -1739,6 +1805,7 @@ "val" : "An epithelial cell derived from ectoderm.", "xrefs" : [ "FMA:69074", "GOC:tfm" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "FMA:69074" }, { @@ -1761,6 +1828,7 @@ "val" : "Epithelial cell derived from mesoderm or mesenchyme.", "xrefs" : [ "FMA:69076", "GOC:tfm" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "epithelial mesenchymal cell" @@ -1788,7 +1856,7 @@ "xrefs" : [ "GOC:dsd", "GOC:tfm", "PMID:12768659" ] }, "comments" : [ "These cells are reportedly CD31-positive, CD34-positive, CD144-positive, TAL1-positive." ], - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "vascular endothelial cell" @@ -1802,10 +1870,15 @@ "val" : "CALOHA:TS-1106" }, { "val" : "FMA:67755" + }, { + "val" : "https://cellxgene.cziscience.com/cellguide/CL_0002139" } ], "basicPropertyValues" : [ { "pred" : "http://purl.org/dc/terms/contributor", "val" : "https://orcid.org/0000-0003-1980-3228" + }, { + "pred" : "http://purl.org/dc/terms/description", + "val" : "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nEndothelial cells of the vascular tree, commonly referred to as vascular endothelial cells, line the entire circulatory system, from the heart to the smallest capillaries. These cells have a unique, flattened shape, and are tightly bound together, forming a thin layer known as the endothelium. The endothelium is responsible for maintaining the interior surface of blood vessels, and plays a critical role in ensuring the smooth flow of blood. \nVascular endothelial cells act as a semi-permeable membrane, controlling the passage of materials and the transit of white blood cells into and out of the bloodstream. These cells are also involved in blood coagulation. When a blood vessel is damaged, endothelial cells promote clotting to prevent excessive bleeding and facilitate wound healing. Other functions include regulation of blood pressure and blood volume by releasing vasodilators and vasoconstrictors to either widen or constrict blood vessels, accordingly.\nFurthermore, the endothelial cells are crucial in the formation of new blood vessels, a process known as angiogenesis. This is particularly important in wound healing and the growth of new tissues during development or after injury. In the context of diseases such as cancer, angiogenesis helps facilitate tumor growth by providing nutrients and oxygen." }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2010-08-24T02:06:40Z" @@ -1820,7 +1893,7 @@ "val" : "An endothelial cell found in capillaries.", "xrefs" : [ "GOC:tfm" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "xrefs" : [ { "val" : "BTO:0004956" }, { @@ -1848,6 +1921,7 @@ "val" : "A cell that is a specialized type of pericyte providing structural support for the capillary loops of kidney. A flat, elongated cell with extensive fine cytoplasmic processes found outside the kidney glomerulus near the macula densa and bound laterally by afferent and efferent arterioles. Being phagocytic, this cell participates in the continuous turnover of the basal lamina by removing its outer portion containing residues of filtration, while the lamina is renewed on its inner surface by the endothelial cells.", "xrefs" : [ "GOC:tfm", "ISBN:0412046911", "http:/www.copewithcytokines.de/cope.cgi?key=Lacis%20cells" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "Goormaghtigh cell" @@ -1881,7 +1955,7 @@ "xrefs" : [ "GOC:tfm", "PMID:15840009" ] }, "comments" : [ "Glomerular endothelial cells have 60-80 nm fenestrations typically lacking diaphragms in adults but present during embryonic development. Some studies found diaphragms in 2-6% of mature rat glomerular capillaries. Their presence may depend on fixation techniques, developmental stage, or dynamic cell changes. Additionally, these cells help maintain the structural integrity of glomerular capillaries through interactions with the basement membrane and podocytes." ], - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#kidney_upper_slim" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#kidney_upper_slim", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "BTO:0004632" }, { @@ -1904,6 +1978,7 @@ "val" : "A cell containing at least one nucleus.", "xrefs" : [ "GOC:tfm" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "FMA:67513" } ], @@ -1924,7 +1999,7 @@ "val" : "An epithelial cell of the distal convoluted tubule of the kidney that helps regulate systemic levels of potassium, sodium, calcium, and pH.", "xrefs" : [ "GOC:tfm", "ISBN:0517223651" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#kidney_upper_slim" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#kidney_upper_slim", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "kidney distal tubule epithelial cell" @@ -1945,7 +2020,7 @@ "xrefs" : [ "GOC:tfm", "ISBN:1-4160-2328-3" ] }, "comments" : [ "The vast majority of proximal tubule epithelial cells have a brush border, but there are rare exceptions." ], - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#kidney_upper_slim", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#kidney_upper_slim", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "kidney proximal tubule epithelial cell" @@ -1969,7 +2044,7 @@ "val" : "A cell that is part of the nervous system.", "xrefs" : [ "GOC:tfm", "ISBN:0618947256" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "CALOHA:TS-2040" }, { @@ -1992,7 +2067,7 @@ "val" : "A cell of the supporting or framework tissue of the body, arising chiefly from the embryonic mesoderm and including adipose tissue, cartilage, and bone.", "xrefs" : [ "GOC:tfm", "ISBN:0618947256" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "CALOHA:TS-2096" }, { @@ -2019,6 +2094,7 @@ "val" : "A cell of the embryo.", "xrefs" : [ "FMA:0618947256" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "CALOHA:TS-0263" }, { @@ -2027,10 +2103,15 @@ "val" : "WBbt:0007028" }, { "val" : "ZFA:0007089" + }, { + "val" : "https://cellxgene.cziscience.com/cellguide/CL_0002321" } ], "basicPropertyValues" : [ { "pred" : "http://purl.org/dc/terms/contributor", "val" : "https://orcid.org/0000-0003-1980-3228" + }, { + "pred" : "http://purl.org/dc/terms/description", + "val" : "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nEmbryonic cells in metazoans, which include all multicellular animals, are biological units in their earliest developmental stages from conception until the organism is fully formed. \nThey are derived from a fertilized egg, which undergoes a series of cell divisions to produce a multicellular organism. During the early phases of embryonic development, these cells exhibit pluripotency, meaning they possess the potential to differentiate into a diverse array of specialized cell types that constitute different body tissues and structures. \nThe balance between cell proliferation and differentiation in embryonic cells is crucial for successful development. When cells continue to divide without differentiating, overgrowth may occur leading to conditions such as teratomas (tumors of embryonic cells). Conversely, if cell differentiation proceeds at the expense of cell proliferation, developmental anomalies could occur regarding size or mass of the organism or its parts." }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2010-09-15T03:39:21Z" @@ -2046,6 +2127,7 @@ "xrefs" : [ "GOC:tfm" ] }, "comments" : [ "From Onard of the FMA: Cardiac muscle cell or cardiac myocyte is a striated muscle cell. Cardiocyte on the other hand is any cell in the heart which includes cells other than muscle cells (e.g. endothelial cell of endocardium). Unless there is a consensus among anatomists that cardiocytes refer only to muscle cells, we will treat them as a general class of cells in the heart." ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "heart cell" @@ -2076,7 +2158,7 @@ "val" : "An epithelial cell of the kidney.", "xrefs" : [ "GOC:tfm", "KUPO:SJ" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "KUPO:0001019" }, { @@ -2099,6 +2181,7 @@ "val" : "An epithelial cell of the kidney cortex.", "xrefs" : [ "GOC:tfm" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "KUPO:0001016" } ] @@ -2112,6 +2195,7 @@ "val" : "A squamous shaped endothelial cell.", "xrefs" : [ "GOC:dos" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "basicPropertyValues" : [ { "pred" : "http://purl.org/dc/terms/contributor", "val" : "https://orcid.org/0000-0003-1980-3228" @@ -2128,6 +2212,7 @@ "definition" : { "val" : "A cell that is part of a cortex of kidney." }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "basicPropertyValues" : [ { "pred" : "http://purl.org/dc/terms/contributor", "val" : "https://orcid.org/0000-0002-0956-8634" @@ -2145,7 +2230,7 @@ "val" : "A cuboidal epithelial cell of the kidney which regulates sodium and potassium balance. The activity of sodium and potassium channels on the apical membrane of the cell is regulated by aldosterone and vasopressin. In mammals this cell type is located in the renal collecting duct system.", "xrefs" : [ "CL:CVS" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "ZFA:0005322" }, { @@ -2153,7 +2238,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://purl.org/dc/terms/description", - "val" : "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional.\n\nRenal principal cells are the major cell type in the initial collecting tubule and the cortical and outer medullary collecting ducts, as well as the connecting tubule, in the nephrons of the kidneys.\nA key function of renal principal cells is the regulation of water balance in the body. These cells express aquaporin-2 (AQP2) water channels, which facilitate the reabsorption of water from the fluid within the renal tubule lumen back into the blood. The translocation of AQP2 to the cell membrane is controlled by the hormone vasopressin: In response to high vasopressin levels, AQP2 moves to the cell membrane, allowing water to pass through effectively and be reabsorbed, therefore concentrating the urine. Conversely, in low vasopressin conditions, AQP2 is removed from the membrane, reducing water reabsorption and diluting the urine. \nRenal principal cells are also involved in the regulation of sodium and potassium levels in the body. They have sodium channels (ENaC) in their luminal membranes which permit the reabsorption of sodium ions from the tubule fluid back into the blood, resulting in a net reabsorption of sodium ions into the systemic circulation. This process is controlled, in part, by the hormone aldosterone. Additionally, renal principal cells contain potassium channels that facilitate the secretion of potassium ions into the urine. The activities of these channels, in coordination with other cell types in the nephron, are critical for maintaining electrolyte balance and overall body homeostasis." + "val" : "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nRenal principal cells are the major cell type in the initial collecting tubule and the cortical and outer medullary collecting ducts, as well as the connecting tubule, in the nephrons of the kidneys.\nA key function of renal principal cells is the regulation of water balance in the body. These cells express aquaporin-2 (AQP2) water channels, which facilitate the reabsorption of water from the fluid within the renal tubule lumen back into the blood. The translocation of AQP2 to the cell membrane is controlled by the hormone vasopressin: In response to high vasopressin levels, AQP2 moves to the cell membrane, allowing water to pass through effectively and be reabsorbed, therefore concentrating the urine. Conversely, in low vasopressin conditions, AQP2 is removed from the membrane, reducing water reabsorption and diluting the urine. \nRenal principal cells are also involved in the regulation of sodium and potassium levels in the body. They have sodium channels (ENaC) in their luminal membranes which permit the reabsorption of sodium ions from the tubule fluid back into the blood, resulting in a net reabsorption of sodium ions into the systemic circulation. This process is controlled, in part, by the hormone aldosterone. Additionally, renal principal cells contain potassium channels that facilitate the secretion of potassium ions into the urine. The activities of these channels, in coordination with other cell types in the nephron, are critical for maintaining electrolyte balance and overall body homeostasis." } ] } }, { @@ -2165,6 +2250,7 @@ "val" : "Cell that is part of the neural crest region of the neuroepithelium, prior to migration. Note that not all premigratory neural crest cells may become migratory neural crest cells.", "xrefs" : [ "UBERONREF:0000002" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "ZFA:0007084" } ], @@ -2184,7 +2270,8 @@ "definition" : { "val" : "Any muscle cell in which the fibers are not organised into sarcomeres.", "xrefs" : [ "GOC:DOS" ] - } + }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ] } }, { "id" : "http://purl.obolibrary.org/obo/CL_0008001", @@ -2195,7 +2282,7 @@ "val" : "Any hematopoietic cell that is a precursor of some other hematopoietic cell type.", "xrefs" : [ "GOC:dos" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ] + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ] } }, { "id" : "http://purl.obolibrary.org/obo/CL_0008007", @@ -2206,6 +2293,7 @@ "val" : "A muscle cell that is part of some visceral muscle.", "xrefs" : [ "GOC:dos" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "FBbt:00005070" } ] @@ -2218,7 +2306,7 @@ "definition" : { "val" : "A non-polarised cell precursor cell that is part of some mesenchyme, is associated with the cell matrix but is not connected to other cells and is capable of migration." }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "mesenchyme cell" @@ -2237,7 +2325,7 @@ "val" : "Mural cells are pericytes and the vascular smooth muscle cells (vSMCs) of the microcirculation.", "xrefs" : [ "Wiki:Mural_cell&oldid=930603194" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#added_for_HCA", "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#added_for_HCA", "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "xrefs" : [ { "val" : "ZFA:0005944" } ], @@ -2260,6 +2348,7 @@ "definition" : { "val" : "A zygote in a plant or an animal." }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "MESH:D015053" } ], @@ -2277,13 +2366,13 @@ "val" : "A cell of the neural crest. Neural crest cells are multipotent. Premigratory neural crest cells are found at the neural plate boarder, some of which will undergo ectomesynchymal transition and delamination to form migratory neural crest cells.", "xrefs" : [ "https://orcid.org/0000-0001-5208-3432", "https://orcid.org/0000-0002-9900-7880" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "https://cellxgene.cziscience.com/cellguide/CL_0011012" } ], "basicPropertyValues" : [ { "pred" : "http://purl.org/dc/terms/description", - "val" : "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional.\n\nNeural crest cells are a group of transient and highly migratory cells that originate from the neuroectoderm during the early stages of embryonic development. They are multipotent cells with an exceptional degree of plasticity, capable of differentiating into various somatic cell types and therefore play a fundamental role in the formation of various organs and tissues, making them critical contributors to the developing embryo. \nAfter the initiation of neurulation (the formation of the neural tube) neural crest cells start to undergo epithelial-to-mesenchymal transition and delaminate and migrate from the dorsal neural tube to several regions throughout the embryo. They differentiate into a range of diverse cell types, such as neurons and glial cells of the peripheral nervous system, including sensory and autonomic neurons. They also contribute to the formation of adrenal glands, pigment cells in the skin (melanocytes), cardiac structures, including parts of the heart septum and major arteries, as well as bones and cartilage of the face and skull.\nDisorders or aberrations in the development or migration of the neural crest cells can lead to serious congenital malformations, such as neurocristopathies, including Hirschsprung disease, neuroblastoma, and neurofibromatosis." + "val" : "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nNeural crest cells are a group of transient and highly migratory cells that originate from the neuroectoderm during the early stages of embryonic development. They are multipotent cells with an exceptional degree of plasticity, capable of differentiating into various somatic cell types and therefore play a fundamental role in the formation of various organs and tissues, making them critical contributors to the developing embryo. \nAfter the initiation of neurulation (the formation of the neural tube) neural crest cells start to undergo epithelial-to-mesenchymal transition and delaminate and migrate from the dorsal neural tube to several regions throughout the embryo. They differentiate into a range of diverse cell types, such as neurons and glial cells of the peripheral nervous system, including sensory and autonomic neurons. They also contribute to the formation of adrenal glands, pigment cells in the skin (melanocytes), cardiac structures, including parts of the heart septum and major arteries, as well as bones and cartilage of the face and skull.\nDisorders or aberrations in the development or migration of the neural crest cells can lead to serious congenital malformations, such as neurocristopathies, including Hirschsprung disease, neuroblastoma, and neurofibromatosis." } ] } }, { @@ -2295,7 +2384,7 @@ "val" : "A precursor cell that has a tendency to differentiate into a specific type of cell. They are descendants of stem cells, only they are more constrained in their differentiation potential or capacity for self-renewal, and are often more limited in both senses.", "xrefs" : [ "ISBN:978-1-62808-994-3", "https://doi.org/10.1016/B978-0-12-409503-8.00002-0" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "basicPropertyValues" : [ { "pred" : "http://purl.org/dc/terms/contributor", "val" : "https://orcid.org/0000-0001-5208-3432" @@ -2311,7 +2400,7 @@ "xrefs" : [ "GOC:dos" ] }, "comments" : [ "Work is needed on GO 'cell differentiation' before it is clear whether the equivalent class definition 'native cell' that capable_of some 'cell differentiation' works. Also, may want to consider merging this with non-terminally differentiated cell." ], - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ] + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ] } }, { "id" : "http://purl.obolibrary.org/obo/CL_0017502", @@ -2377,9 +2466,15 @@ "val" : "An epithelial cell that is part of the nephron.", "xrefs" : [ "GOC:tfm" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "FMA:70965" + }, { + "val" : "https://cellxgene.cziscience.com/cellguide/CL_1000449" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/description", + "val" : "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nEpithelial cells of the nephron form the epithelial lining of the nephron, the functional unit of the kidney that filters the blood to produce urine. Each kidney holds approximately one million nephrons, each of which is composed of several distinct parts, including the renal corpuscle, the proximal tubule, the loop of Henle, and the distal tubule. All sections are lined with highly specialized epithelial cells adapted to perform different functions within the sections of the nephron. \nThe different epithelial cells of the nephron play crucial roles in the process of filtration, reabsorption, secretion, and excretion, essential tasks for the regulation of body fluid composition and volume. During filtration, the blood is forced through the walls of glomerular capillaries into the Bowman's capsule, where waste products, electrolytes, and water are separated from the blood cells and proteins. As the filtrate then passes through the nephron, epithelial cells of the tubular portion reabsorb useful substances such as glucose, amino acids, and electrolytes, along with most of the water back into the bloodstream. Waste products like urea and creatinine, as well as excess ions and water, remain in the tubule for elimination.\nIn addition, epithelial cells of the nephron also play a vital part in maintaining the body's acid-base balance by actively secreting hydrogen ions into the urine while reabsorbing bicarbonate from the urine back into the blood. They are also involved in the regulation of blood pressure through the renin-angiotensin-aldosterone system and contribute to erythrocyte production by releasing the hormone erythropoietin in response to low oxygen levels in the blood. Abnormalities or damage in renal epithelial cells often result in impaired kidney function, leading to various renal diseases." } ] } }, { @@ -2391,7 +2486,7 @@ "val" : "An epithelial cell that is part of the glomerular capsule.", "xrefs" : [ "GOC:tfm" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#kidney_upper_slim" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#kidney_upper_slim", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "Bowmans capsule epithelial cell" @@ -2415,7 +2510,7 @@ "val" : "An epithelial cell that is part of the collecting duct of renal tubule.", "xrefs" : [ "GOC:tfm" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#kidney_upper_slim", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#kidney_upper_slim", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "epithelial cell of renal collecting tubule", @@ -2433,7 +2528,7 @@ "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" }, { "pred" : "http://purl.org/dc/terms/description", - "val" : "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional.\n\nKidney collecting duct epithelial cells are a specialized type of cells that form an integral part of the renal system. Located in the collecting duct system of the kidneys, these cells are responsible for one of the final steps in the process of urine formation, and they are instrumental in the fine tuning of the volume and composition of urine by reabsorbing water and certain solutes back into the bloodstream.\nThese cells express specific channels and carriers that actively and passively transport ions and water. They also have channels on their membranes, such as sodium channels and potassium channels, involved in reabsorbing or secreting these electrolytes depending upon the body's needs. The function of renal collecting duct epithelial cells can be regulated by a variety of hormones, including vasopressin (antidiuretic hormone), which can modulate the ion channels and carriers and hence indirectly influence body fluid homeostasis.\nAside from their function in ion and water balance, kidney collecting duct epithelial cells also aid in maintaining the body's acid-base balance. They have specialized functionality to secret hydrogen ions into the tubular lumen, which contributes to acid excretion. Any dysfunction may have serious implications and lead to various renal or systemic diseases, exemplifying the importance of these cells in maintaining overall body homeostasis." + "val" : "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nKidney collecting duct epithelial cells are a specialized type of cells that form an integral part of the renal system. Located in the collecting duct system of the kidneys, these cells are responsible for one of the final steps in the process of urine formation, and they are instrumental in the fine tuning of the volume and composition of urine by reabsorbing water and certain solutes back into the bloodstream.\nThese cells express specific channels and carriers that actively and passively transport ions and water. They also have channels on their membranes, such as sodium channels and potassium channels, involved in reabsorbing or secreting these electrolytes depending upon the body's needs. The function of renal collecting duct epithelial cells can be regulated by a variety of hormones, including vasopressin (antidiuretic hormone), which can modulate the ion channels and carriers and hence indirectly influence body fluid homeostasis.\nAside from their function in ion and water balance, kidney collecting duct epithelial cells also aid in maintaining the body's acid-base balance. They have specialized functionality to secret hydrogen ions into the tubular lumen, which contributes to acid excretion. Any dysfunction may have serious implications and lead to various renal or systemic diseases, exemplifying the importance of these cells in maintaining overall body homeostasis." } ] } }, { @@ -2446,7 +2541,7 @@ "xrefs" : [ "GOC:tfm" ] }, "comments" : [ "This needs to be further defined as a juxtamedullary nephron. Will request the juxtamedullary nephron tubule class from UBERON." ], - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "kidney tubule epithelial cell" @@ -2465,7 +2560,7 @@ "definition" : { "val" : "A cell that is part of a kidney." }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "KUPO:0001010" }, { @@ -2480,7 +2575,7 @@ "definition" : { "val" : "A cell that is part of kidney interstitium." }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#kidney_upper_slim" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#kidney_upper_slim", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "KUPO:0001013" }, { @@ -2496,6 +2591,7 @@ "val" : "A cell that is part of a renal medulla.", "xrefs" : [ "PMID:22343825" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "KUPO:0001017" }, { @@ -2510,7 +2606,7 @@ "definition" : { "val" : "A cell that is part of a renal pelvis." }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#kidney_upper_slim" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#kidney_upper_slim", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "KUPO:0001018" } ] @@ -2523,7 +2619,7 @@ "definition" : { "val" : "A cell that is part of a nephron tubule." }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#kidney_upper_slim" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#kidney_upper_slim", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "KUPO:0001020" } ] @@ -2537,7 +2633,7 @@ "val" : "Any kidney epithelial cell that is part of some glomerular epithelium.", "xrefs" : [ "FBC:Autogenerated" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "KUPO:0001023" } ] @@ -2550,7 +2646,7 @@ "definition" : { "val" : "An epithelial cell that is part of a renal medulla collecting duct." }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#kidney_upper_slim" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#kidney_upper_slim", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "KUPO:0001060" } ] @@ -2564,7 +2660,7 @@ "val" : "Any kidney cell that is part of some papillary duct.", "xrefs" : [ "FBC:Autogenerated" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#kidney_upper_slim" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#kidney_upper_slim", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "KUPO:0001064" } ] @@ -2578,7 +2674,7 @@ "val" : "Any renal cortical epithelial cell that is part of some renal corpuscle.", "xrefs" : [ "FBC:Autogenerated" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#kidney_upper_slim" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#kidney_upper_slim", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "KUPO:0001021" } ] @@ -2592,7 +2688,7 @@ "val" : "Any kidney tubule cell that is part of some renal cortex tubule.", "xrefs" : [ "FBC:Autogenerated" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "KUPO:0001024" } ] @@ -2606,7 +2702,7 @@ "val" : "Any kidney cortical cell that is part of some juxtaglomerular apparatus.", "xrefs" : [ "FBC:Autogenerated" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#kidney_upper_slim" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#kidney_upper_slim", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "juxtaglomerulus cell", @@ -2625,7 +2721,7 @@ "val" : "A fibroblast that is part of an interstitial compartment of a kidney.", "xrefs" : [ "PMID:10559635" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "xrefs" : [ { "val" : "KUPO:0001102" } ], @@ -2643,6 +2739,7 @@ "val" : "Any kidney corpuscule cell that is part of some renal glomerulus.", "xrefs" : [ "FBC:Autogenerated" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "KUPO:0001036" } ] @@ -2656,13 +2753,18 @@ "val" : "Any nephron tubule epithelial cell that is part of some renal connecting tubule.", "xrefs" : [ "FBC:Autogenerated" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#kidney_upper_slim", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#kidney_upper_slim", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "xrefs" : [ { "val" : "KUPO:0001058" + }, { + "val" : "https://cellxgene.cziscience.com/cellguide/CL_1000768" } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" + }, { + "pred" : "http://purl.org/dc/terms/description", + "val" : "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nKidney connecting tubule epithelial cells are found in collecting duct system of the kidney, specifically in at the interconnection segment between the nephron and the collecting ducts. The epithelial cells lining the connecting tubule are crucial for the journey of filtrate before it empties into urine-collecting ducts and therefore play a critical role in maintaining the body’s fluid and electrolyte balance.\nOne of the principal functions of connecting tubule epithelial cells involves the selective reabsorption and secretion of various solutes. This reabsorption process includes critical regulatory electrolytes such as sodium ions (Na+), chloride ions (Cl-), and bicarbonate ions (HCO3-), thus playing a role in the regulation of the acid-base homeostasis. Their function also involves the secretion of potassium ions (K+) into the renal tubular fluid.\nThe connecting tubule epithelial cells are primarily intercalated cells, which can be categorized into two types according to their specific functions: type A intercalated cells, which secrete acid, and the type B intercalated cells, which secrete base (bicarbonate) and reabsorb chloride. By regulating the concentrations of these ions, as well as reabsorption of water, connecting tubule epithelial cells contribute substantively to maintaining the body's electrolyte levels, pH balance, and overall homeostasis.\nIn addition to intercalating cells, the collecting duct system also has principal cells, which are characterized by the expression of the water channel AQP2. AQP2-expressing cells have also been identified in connecting tubules, but there is some controversy whether these represent a unique cell type as there are some morphologic differences compared with principal cells." } ] } }, { @@ -2674,13 +2776,18 @@ "val" : "Any epithelial cell of distal tubule that is part of some distal convoluted tubule.", "xrefs" : [ "FBC:Autogenerated" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#kidney_upper_slim", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#kidney_upper_slim", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "xrefs" : [ { "val" : "KUPO:0001056" + }, { + "val" : "https://cellxgene.cziscience.com/cellguide/CL_1000849" } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" + }, { + "pred" : "http://purl.org/dc/terms/description", + "val" : "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nKidney distal convoluted tubule epithelial cells, often referred to simply as distal convoluted tubule (DCT) cells, constitute a significant portion of the nephron -- the functional building unit of the kidney involved in filtration and reabsorption of substances from blood. The DCT epithelial cells form lining of the distal convoluted tubule, a segment of the nephron located after the loop of Henle and before the collecting tubule. These cells are characterized by unique morphological features such as small size, low height and fewer microvilli compared to proximal convoluted tubule epithelial cells. \nThese cells perform a host of vital functions contributing to the regulation of extracellular fluid volume and electrolyte balance, blood pressure and pH. While the DCT is less prominent in water and sodium reabsorption compared to the proximal tubule and the loop of Henle, it plays a crucial role in fine-tuning the process. DCT epithelial cells are responsible for the final adjustments of sodium, potassium and calcium reabsorption, thereby affecting overall fluid and electrolyte balance, blood pressure regulation and bone health. The reabsorption process is regulated by hormones including aldosterone and parathyroid hormone.\nThe distal convoluted tubule (DCT) also plays a significant role in acid-base homeostasis by secreting protons (H+) into the tubular fluid and reabsorbing bicarbonate ions (HCO3-), thus regulating the pH of the blood. The ability of DCT cells to adjust urine concentration plays a part in maintaining the body’s pH balance and preventing conditions like acidosis or alkalosis. In summary, kidney distal convoluted tubule epithelial cells perform functions that are crucial to maintaining body's homeostasis." } ] } }, { @@ -2692,6 +2799,7 @@ "val" : "A blood vessel cell that is part of a kidney.", "xrefs" : [ "PMID:34843404" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "KUPO:0001014" } ] @@ -2705,7 +2813,7 @@ "val" : "Any kidney blood vessel cell that is part of some kidney arterial blood vessel.", "xrefs" : [ "FBC:Autogenerated" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#kidney_upper_slim" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#kidney_upper_slim", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "KUPO:0001029" } ] @@ -2718,7 +2826,7 @@ "definition" : { "val" : "An endothelial cell that is part of the capillary of the kidney." }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#kidney_upper_slim" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#kidney_upper_slim", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "KUPO:0001030" } ] @@ -2732,7 +2840,7 @@ "val" : "Any kidney blood vessel cell that is part of some renal vein.", "xrefs" : [ "FBC:Autogenerated" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#kidney_upper_slim" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#kidney_upper_slim", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "KUPO:0001031" } ] @@ -2746,7 +2854,7 @@ "val" : "Any nephron tubule epithelial cell that is part of some loop of Henle.", "xrefs" : [ "FBC:Autogenerated" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "KUPO:0001047" } ] @@ -2760,7 +2868,7 @@ "val" : "Any kidney loop of Henle epithelial cell that is part of some ascending limb of loop of Henle.", "xrefs" : [ "FBC:Autogenerated" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#kidney_upper_slim" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#kidney_upper_slim", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "KUPO:0001048" } ] @@ -2774,9 +2882,15 @@ "val" : "Any kidney loop of Henle epithelial cell that is part of some descending limb of loop of Henle.", "xrefs" : [ "FBC:Autogenerated" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#kidney_upper_slim" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#kidney_upper_slim", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "KUPO:0001053" + }, { + "val" : "https://cellxgene.cziscience.com/cellguide/CL_1001021" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/description", + "val" : "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nThe kidney loop of Henle descending limb epithelial cells are highly specialized cells that play a crucial role in maintaining the body's salt and water balance. These cells line the descending limb of the loop of Henle, which is a portion of the renal tubule located in the kidneys, an organ responsible for filtering waste products, ions and extra water from the blood and converting them into urine. However, the descending limb epithelial cells are specifically involved in the countercurrent multiplication system, a mechanism to concentrate urine that involves both active and passive transport processes. \nThese cells are notably permeable to water but relatively impermeable to solutes, a characteristic that dramatically influences the osmotic gradient in the renal medulla. As filtrate initially descends down the loop of Henle, water gets drawn out due to the increasing osmotic gradient, thereby concentrating the filtrate. Additionally, these epithelial cells are exceptionally thin walled, allowing water to freely diffuse across the membrane.\nFurthermore, the kidney loop of Henle descending limb epithelial cells are inextricably linked to the functioning of numerous diuretic drugs, which work by blocking the reabsorption of water and certain electrolytes in the kidneys, leading to increased urine production to rid the body of excess fluids." } ] } }, { @@ -2787,7 +2901,7 @@ "definition" : { "val" : "A cell that is part of a collecting duct of renal tubule." }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "KUPO:0001012" }, { @@ -2802,7 +2916,7 @@ "definition" : { "val" : "A pericyte cell located in the kidney interstitium." }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "xrefs" : [ { "val" : "KUPO:0001104" } ], @@ -2820,6 +2934,7 @@ "val" : "Any blood vessel endothelial cell that is part of a microvascular endothelium.", "xrefs" : [ "GOC:TermGenie" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "basicPropertyValues" : [ { "pred" : "http://purl.org/dc/terms/contributor", "val" : "http://www.wikidata.org/entity/Q35563349" @@ -2837,6 +2952,7 @@ "val" : "Any cell that is located within the interstitium between the cells most prominent in defining a given tissue. \"Interstitial cell\" is a morphological term and refers to a variety of cells with differing origins and phenotypes.", "xrefs" : [ "PMID:24987007" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "basicPropertyValues" : [ { "pred" : "http://purl.org/dc/terms/date", "val" : "2022-11-30T14:35:08Z" @@ -2851,6 +2967,7 @@ "val" : "A cell that is adjacent to a vessel. A perivascular cell plays a crucial role in maintaining vascular function and tissue homeostasis. This cell type regulates vessel integrity and flow dynamics.", "xrefs" : [ "PMID:24928499", "PMID:27889329" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "basicPropertyValues" : [ { "pred" : "http://purl.org/dc/terms/contributor", "val" : "https://orcid.org/0000-0001-6677-8489" @@ -2878,9 +2995,6 @@ "val" : "Wikipedia:Mitosis" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0007067" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" } ] @@ -2930,15 +3044,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/geneontology/go-ontology/issues/28301" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0000789" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0000790" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0005717" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "cellular_component" @@ -2971,12 +3076,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/geneontology/go-ontology/issues/22355" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0005720" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0035328" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "cellular_component" @@ -3133,9 +3232,6 @@ "val" : "Wikipedia:Neurulation" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0001679" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" } ] @@ -3568,9 +3664,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/geneontology/go-ontology/issues/17729" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0008372" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "cellular_component" @@ -3684,12 +3777,6 @@ "val" : "Wikipedia:Basement_membrane" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0005605" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0008003" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "cellular_component" } ] @@ -3882,9 +3969,6 @@ "val" : "Wikipedia:Ribosome" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0033279" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "cellular_component" } ] @@ -3938,12 +4022,6 @@ "val" : "Wikipedia:Cell_membrane" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0005887" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0005904" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "cellular_component" } ] @@ -4012,15 +4090,6 @@ "val" : "Wikipedia:Translation_(genetics)" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0006416" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0006453" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0043037" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" } ] @@ -4049,12 +4118,6 @@ "val" : "translation initiation" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0006440" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0006454" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" } ] @@ -4077,12 +4140,6 @@ "val" : "translation elongation" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0006442" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0006455" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" } ] @@ -4107,12 +4164,6 @@ "val" : "translational complex disassembly" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0006443" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0006456" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" } ] @@ -4135,21 +4186,9 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/geneontology/go-ontology/issues/20292" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "jl" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2012-12-13T16:25:32Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0015457" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0015460" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0044765" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" @@ -4257,12 +4296,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002161", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_4896" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0006917" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0008632" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" @@ -4339,15 +4372,9 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/geneontology/go-ontology/issues/27189" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "jl" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2013-12-19T15:25:51Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:1902589" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" @@ -4443,21 +4470,6 @@ "val" : "Wikipedia:Signal_transduction" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0023014" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0023015" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0023016" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0023033" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0023045" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" } ] @@ -4551,9 +4563,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002161", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_4751" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0009552" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" @@ -4693,9 +4702,6 @@ "val" : "hemolymph circulation" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0070261" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" } ] @@ -4742,15 +4748,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/geneontology/go-ontology/issues/23112" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0008105" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0016249" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0034613" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" @@ -4786,21 +4783,9 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/geneontology/go-ontology/issues/24968" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "jl" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2012-09-19T15:05:24Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0000004" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0007582" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0044699" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" @@ -4812,7 +4797,7 @@ "type" : "CLASS", "meta" : { "definition" : { - "val" : "The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.", + "val" : "A cellular process consisting of the biochemical pathways by which a living organism transforms chemical substances. This includes including anabolism (biosynthetic process) and catabolism (catabolic process). Metabolic processes includes the transformation of small molecules, as well macromolecular processes such as DNA repair and replication, protein synthesis and degradation.", "xrefs" : [ "GOC:go_curators", "ISBN:0198547684" ] }, "comments" : [ "Note that metabolic processes do not include single functions or processes such as protein-protein interactions, protein-nucleic acids, nor receptor-ligand interactions." ], @@ -4820,18 +4805,6 @@ "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "metabolism" - }, { - "pred" : "hasNarrowSynonym", - "val" : "metabolic process resulting in cell growth" - }, { - "pred" : "hasNarrowSynonym", - "val" : "metabolism resulting in cell growth" - }, { - "pred" : "hasNarrowSynonym", - "val" : "multicellular organism metabolic process" - }, { - "pred" : "hasRelatedSynonym", - "val" : "single-organism metabolic process" } ], "xrefs" : [ { "val" : "Wikipedia:Metabolism" @@ -4840,17 +4813,11 @@ "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/geneontology/go-ontology/issues/26424" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "jl" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/geneontology/go-ontology/issues/28932" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2012-10-17T15:46:40Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0044236" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0044710" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" @@ -4915,7 +4882,7 @@ "type" : "CLASS", "meta" : { "definition" : { - "val" : "The chemical reactions and pathways resulting in the formation of substances; typically the energy-requiring part of metabolism in which simpler substances are transformed into more complex ones.", + "val" : "A cellular process consisting of the biochemical pathways by which a living organism synthesizes chemical substances. This typically represents the energy-requiring part of metabolism in which simpler substances are transformed into more complex ones.", "xrefs" : [ "GOC:curators", "ISBN:0198547684" ] }, "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_chembl", "http://purl.obolibrary.org/obo/go#goslim_metagenomics", "http://purl.obolibrary.org/obo/go#goslim_plant", "http://purl.obolibrary.org/obo/go#goslim_plant_ribbon" ], @@ -4942,17 +4909,11 @@ "val" : "Wikipedia:Anabolism" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "jl" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/geneontology/go-ontology/issues/28932" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2012-10-17T15:52:18Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0044274" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0044711" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" @@ -4995,9 +4956,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/geneontology/go-ontology/issues/27189" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0043284" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" @@ -5023,12 +4981,6 @@ "val" : "protein secretion resulting in cell fate commitment" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0045166" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0045731" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" } ] @@ -5108,9 +5060,6 @@ "val" : "Wikipedia:Embryogenesis" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0009795" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" } ] @@ -5212,20 +5161,8 @@ "val" : "single-organism cellular process" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "jl" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2012-12-11T16:56:55Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0008151" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0044763" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0050875" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" @@ -5294,9 +5231,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/geneontology/go-ontology/issues/24835" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0016244" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" @@ -5317,9 +5251,6 @@ "val" : "enzyme transport" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0015831" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" } ] @@ -5391,15 +5322,6 @@ "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2014-03-06T11:37:54Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0016021" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0098589" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0098805" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "cellular_component" @@ -5438,12 +5360,6 @@ "xrefs" : [ "GOC:mah" ] } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0044235" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0071842" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" } ] @@ -5596,15 +5512,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/geneontology/go-ontology/issues/27189" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0006411" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0044267" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0044268" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" @@ -5681,9 +5588,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/geneontology/go-ontology/issues/27189" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0071845" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" @@ -5709,15 +5613,9 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/geneontology/go-ontology/issues/27054" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "jl" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2012-09-19T15:56:06Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0044702" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" @@ -5756,9 +5654,6 @@ "val" : "cellular component assembly at cellular level" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0071844" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" } ] @@ -5840,17 +5735,8 @@ "val" : "single organism signaling" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "jl" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2010-02-16T09:30:50Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0023046" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0044700" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" @@ -6093,9 +5979,6 @@ "xrefs" : [ "GOC:bf" ] } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0000068" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" } ] @@ -6178,9 +6061,6 @@ "val" : "Wikipedia:Extracellular_matrix" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0005578" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "cellular_component" } ] @@ -6236,9 +6116,6 @@ "val" : "Wikipedia:Vesicle_(biology)" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0031988" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "cellular_component" } ] @@ -6333,18 +6210,9 @@ }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002161", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_4932" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "jl" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2012-09-19T16:07:47Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0044707" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0050874" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" @@ -6368,14 +6236,8 @@ "val" : "single-organism developmental process" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "jl" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2012-12-19T12:21:31Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0044767" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" @@ -6427,15 +6289,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/geneontology/go-ontology/issues/22580" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0034623" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0043241" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0043624" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" @@ -6469,9 +6322,6 @@ "val" : "protein-protein complex" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0043234" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "cellular_component" } ] @@ -6544,9 +6394,6 @@ "val" : "ATP hydrolysis coupled ion transmembrane transport" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0099131" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" } ] @@ -6620,9 +6467,6 @@ "val" : "establishment of protein localization in extracellular region" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "bf" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2010-11-09T10:25:08Z" }, { @@ -6657,9 +6501,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002161", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_4751" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "bf" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2011-12-12T10:53:24Z" @@ -6759,15 +6600,6 @@ "val" : "regulation of homeostatic process" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0032844" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0032845" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0032846" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" } ] @@ -6856,15 +6688,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/geneontology/go-ontology/issues/26424" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0034960" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0043283" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0044259" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" @@ -6917,7 +6740,7 @@ } }, { "id" : "http://purl.obolibrary.org/obo/GO_0043228", - "lbl" : "non-membrane-bounded organelle", + "lbl" : "membraneless organelle", "type" : "CLASS", "meta" : { "definition" : { @@ -6926,6 +6749,12 @@ }, "subsets" : [ "http://purl.obolibrary.org/obo/go#gocheck_do_not_annotate", "http://purl.obolibrary.org/obo/go#goslim_mouse" ], "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "membrane-less organelle" + }, { + "pred" : "hasExactSynonym", + "val" : "non-membrane-bounded organelle" + }, { "pred" : "hasExactSynonym", "val" : "non-membrane-enclosed organelle" }, { @@ -6941,6 +6770,9 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/geneontology/go-ontology/issues/28153" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/geneontology/go-ontology/issues/29106" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "cellular_component" @@ -7000,7 +6832,7 @@ } }, { "id" : "http://purl.obolibrary.org/obo/GO_0043232", - "lbl" : "intracellular non-membrane-bounded organelle", + "lbl" : "intracellular membraneless organelle", "type" : "CLASS", "meta" : { "definition" : { @@ -7009,10 +6841,16 @@ }, "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_pir" ], "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "intracellular non-membrane-bounded organelle" + }, { "pred" : "hasExactSynonym", "val" : "intracellular non-membrane-enclosed organelle" } ], "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/geneontology/go-ontology/issues/29106" + }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "cellular_component" } ] @@ -7073,21 +6911,9 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/geneontology/go-ontology/issues/22580" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "mah" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2010-09-08T10:01:42Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0034600" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0034621" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0071822" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" @@ -7124,9 +6950,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/geneontology/go-ontology/issues/27194" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0071843" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" @@ -7149,9 +6972,6 @@ "val" : "Met-tRNA/eIF2.GTP ternary complex" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "jl" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2009-10-22T02:38:55Z" }, { @@ -7159,30 +6979,6 @@ "val" : "cellular_component" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/GO_0044237", - "lbl" : "cellular metabolic process", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "The chemical reactions and pathways by which individual cells transform chemical substances.", - "xrefs" : [ "GOC:go_curators" ] - }, - "comments" : [ "This term should not be used for direct annotation. It should be possible to make a more specific annotation to one of the children of this term." ], - "subsets" : [ "http://purl.obolibrary.org/obo/go#gocheck_do_not_annotate" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "cellular metabolism" - }, { - "pred" : "hasRelatedSynonym", - "val" : "intermediary metabolism", - "xrefs" : [ "GOC:mah" ] - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "biological_process" - } ] - } }, { "id" : "http://purl.obolibrary.org/obo/GO_0044238", "lbl" : "primary metabolic process", @@ -7208,38 +7004,6 @@ "val" : "biological_process" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/GO_0044249", - "lbl" : "cellular biosynthetic process", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "The chemical reactions and pathways resulting in the formation of substances, carried out by individual cells.", - "xrefs" : [ "GOC:jl" ] - }, - "comments" : [ "This term should not be used for direct annotation. It should be possible to make a more specific annotation to one of the children of this term." ], - "subsets" : [ "http://purl.obolibrary.org/obo/go#gocheck_do_not_annotate" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "cellular anabolism" - }, { - "pred" : "hasExactSynonym", - "val" : "cellular biosynthesis" - }, { - "pred" : "hasExactSynonym", - "val" : "cellular formation" - }, { - "pred" : "hasExactSynonym", - "val" : "cellular synthesis" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", - "val" : "https://github.com/geneontology/go-ontology/issues/27052" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "biological_process" - } ] - } }, { "id" : "http://purl.obolibrary.org/obo/GO_0045184", "lbl" : "establishment of protein localization", @@ -7451,9 +7215,6 @@ "xrefs" : [ "GOC:dph", "GOC:tb" ] } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0048828" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" } ] @@ -7673,9 +7434,6 @@ "val" : "regulation of physiological process" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0050791" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" } ] @@ -7695,9 +7453,6 @@ "val" : "regulation of cellular physiological process" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0051244" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" } ] @@ -7808,9 +7563,6 @@ "val" : "physiological response to stimulus" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0051869" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" } ] @@ -7855,15 +7607,9 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/geneontology/go-ontology/issues/27052" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "jl" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2013-12-18T13:51:04Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:1902578" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" @@ -7942,15 +7688,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/geneontology/go-ontology/issues/4585" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0006323" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0007001" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0051277" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" @@ -8013,15 +7750,9 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/geneontology/go-ontology/issues/27189" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "jl" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2013-12-18T14:04:32Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:1902580" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" @@ -8062,14 +7793,8 @@ "val" : "ATP hydrolysis coupled transmembrane transport" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "tb" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2015-10-21T13:22:47Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0090662" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" @@ -8124,9 +7849,6 @@ "xrefs" : [ "GOC:dph" ] }, "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dph" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2009-04-28T09:33:36Z" }, { @@ -8144,9 +7866,6 @@ "xrefs" : [ "GOC:dph" ] }, "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dph" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2010-05-25T09:05:34Z" }, { @@ -8164,9 +7883,6 @@ "xrefs" : [ "GOC:BHF", "GOC:rph", "PMID:21123617" ] }, "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dph" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2018-04-13T12:47:21Z" }, { @@ -8212,15 +7928,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/geneontology/go-ontology/issues/22580" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0006461" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0034622" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0043623" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" @@ -8402,9 +8109,6 @@ "xrefs" : [ "GOC:mah" ] } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "mah" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2009-06-16T04:08:29Z" }, { @@ -8423,9 +8127,6 @@ }, "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_yeast" ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "mah" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2009-09-15T03:00:51Z" }, { @@ -8451,9 +8152,6 @@ "val" : "protein localization in extracellular region" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "mah" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2010-02-25T04:00:13Z" }, { @@ -8489,9 +8187,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/geneontology/go-ontology/issues/25143" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "mah" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2010-09-08T10:10:35Z" @@ -8526,15 +8221,9 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/geneontology/go-ontology/issues/27189" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "mah" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2010-09-10T01:39:16Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0071841" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" @@ -8551,9 +8240,6 @@ }, "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_flybase_ribbon" ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "mah" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2010-10-04T01:51:47Z" }, { @@ -8576,9 +8262,6 @@ "xrefs" : [ "GOC:vesicles" ] } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "mah" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2010-10-18T03:44:18Z" }, { @@ -8598,9 +8281,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/geneontology/go-ontology/issues/22302" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "mah" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2010-02-26T02:15:40Z" @@ -8628,14 +8308,8 @@ "val" : "induction of apoptosis by extracellular signals" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pr" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2011-11-23T09:30:23Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0008624" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" @@ -8658,9 +8332,6 @@ "val" : "apoptosis" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pr" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2011-11-23T09:45:24Z" }, { @@ -8678,9 +8349,6 @@ "xrefs" : [ "GOC:pr", "GOC:sart" ] }, "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pr" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2012-01-03T03:10:17Z" }, { @@ -8700,9 +8368,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/geneontology/go-ontology/issues/22368" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pr" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2012-03-05T02:03:58Z" @@ -8737,9 +8402,6 @@ "val" : "intraluminal vesicle assembly" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pr" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2016-10-03T14:35:25Z" }, { @@ -8763,9 +8425,6 @@ "val" : "region of plasma membrane" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dos" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2014-03-06T11:55:32Z" }, { @@ -8975,14 +8634,18 @@ } }, { "id" : "http://purl.obolibrary.org/obo/GO_0110165", - "lbl" : "cellular anatomical entity", + "lbl" : "cellular anatomical structure", "type" : "CLASS", "meta" : { "definition" : { - "val" : "A part of a cellular organism that is either an immaterial entity or a material entity with granularity above the level of a protein complex but below that of an anatomical system. Or, a substance produced by a cellular organism with granularity above the level of a protein complex.", + "val" : "A part of a cellular organism consisting of a material entity with granularity above the level of a protein complex but below that of an anatomical system. Note that cellular organisms exclude viruses.", "xrefs" : [ "GOC:kmv" ] }, "subsets" : [ "http://purl.obolibrary.org/obo/go#gocheck_do_not_annotate", "http://purl.obolibrary.org/obo/go#goslim_pir" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "cellular anatomical entity" + } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/geneontology/go-ontology/issues/24200" @@ -8990,8 +8653,8 @@ "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/geneontology/go-ontology/issues/26424" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "kmv" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/geneontology/go-ontology/issues/28978" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2019-08-12T18:01:37Z" @@ -9012,9 +8675,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/geneontology/go-ontology/issues/13193" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "krc" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-03-21T17:26:07Z" @@ -9040,9 +8700,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/geneontology/go-ontology/issues/13298" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "krc" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-04-24T23:56:08Z" @@ -9063,9 +8720,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/geneontology/go-ontology/issues/13298" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "krc" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-04-26T16:07:02Z" @@ -9091,9 +8745,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/geneontology/go-ontology/issues/19910" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pg" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-03-23T14:44:23Z" @@ -9118,9 +8769,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/geneontology/go-ontology/issues/14256" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pg" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-10-23T11:53:42Z" @@ -9143,9 +8791,6 @@ "val" : "efflux" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pg" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2019-05-22T11:20:45Z" }, { @@ -9164,9 +8809,6 @@ }, "subsets" : [ "http://purl.obolibrary.org/obo/go#gocheck_do_not_annotate" ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "jl" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2014-05-22T14:22:34Z" }, { @@ -9189,9 +8831,6 @@ "xrefs" : [ "GOC:vesicles" ] } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "jl" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2014-10-22T14:26:11Z" }, { @@ -9229,17 +8868,8 @@ "val" : "Wikipedia:Ribonucleoprotein" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pr" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2015-11-19T12:26:37Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0030529" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:1990903" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "cellular_component" @@ -9326,9 +8956,6 @@ "val" : "GC_ID:1" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "NCBITaxon:85055" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "ncbi_taxonomy" } ] @@ -9360,9 +8987,6 @@ "val" : "GC_ID:1" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "NCBITaxon:40673" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "ncbi_taxonomy" } ] @@ -9696,9 +9320,6 @@ "val" : "GC_ID:1" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "NCBITaxon:109679" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "ncbi_taxonomy" } ] @@ -9923,9 +9544,6 @@ "xrefs" : [ "PATOC:GVG" ] }, "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "PATO:0000072" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "quality" } ] @@ -9961,9 +9579,6 @@ "val" : "relational shape quality" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "PATO:0001647" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "quality" } ] @@ -9987,9 +9602,6 @@ "val" : "relational structural quality" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "PATO:0001452" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "quality" } ] @@ -10087,9 +9699,6 @@ "val" : "Wikipedia:Physical_property" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "PATO:0002079" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "quality" } ] @@ -10133,12 +9742,6 @@ "val" : "snap:Quality" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "PATO:0001237" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "PATO:0001238" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "quality" } ] @@ -10350,9 +9953,6 @@ "val" : "tubulate" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "PATO:0001203" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "quality" } ] @@ -10865,9 +10465,6 @@ "val" : "high N:C ratio" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "http://orcid.org/0000-0001-5208-3432" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "quality" } ] @@ -10881,9 +10478,6 @@ "val" : "A quality of continuant that exist at the anatomical level of organisation and anything under it. This includes, but is not limited to, cells , tissues, and components." }, "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "http://orcid.org/0000-0001-7258-9596" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "quality" } ] @@ -10897,9 +10491,6 @@ "val" : "A quality inhering in an anotomical structure by virtue of its capacity to be stained by specific histological dyes." }, "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "http://orcid.org/0000-0001-7258-9596" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "quality" } ] @@ -10914,9 +10505,6 @@ "xrefs" : [ "GOC:add" ] }, "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "http://orcid.org/0000-0001-7258-9596" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "quality" } ] @@ -10930,7 +10518,7 @@ "val" : "An amino acid chain that is produced de novo by ribosome-mediated translation of a genetically-encoded mRNA, and any derivatives thereof.", "xrefs" : [ "PRO:DAN", "PRO:WCB" ] }, - "comments" : [ "The definition above excludes protein complexes, which some also consider a protein. Those who wish to refer to a class representing both senses of the word are directed to CHEBI:36080. Note that the definition allows for experimentally-manipulated genes, and allows for artifically-produced derivatives that mimic those found naturally. Proteins (in the sense defined here) that descended from a common ancestor can be classified into families and superfamilies composed of products of evolutionarily-related genes. The domain architecture of a protein is described by the order of its constituent domains. Proteins with the same domains in the same order are defined as homeomorphic [PRO:WCB]." ], + "comments" : [ "The definition above excludes protein complexes, which some also consider a protein. Those who wish to refer to a class representing both senses of the word are directed to CHEBI:36080. Note that the definition allows for experimentally-manipulated genes, and allows for artifically-produced derivatives that mimic those found naturally. Proteins (in the sense defined here) that descended from a common ancestor can be classified into families and superfamilies composed of products of evolutionarily-related genes. The domain architecture of a protein is described by the order of its constituent domains. Proteins with the same domains in the same order are defined as homeomorphic [PRO:WCB)." ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "natural protein", @@ -11957,15 +11545,15 @@ } ] } }, { - "id" : "http://purl.obolibrary.org/obo/PR_000050567", - "lbl" : "protein-containing material entity", + "id" : "http://purl.obolibrary.org/obo/PR_000064867", + "lbl" : "protein-containing molecular entity", "type" : "CLASS", "meta" : { "definition" : { - "val" : "A material entity that minimally consists of a protein.", + "val" : "A molecular entity that minimally consists of a protein.", "xrefs" : [ "PRO:DAN" ] }, - "comments" : [ "Note: This includes single proteins and derivatives thereof (PR:000000001), protein-containing complexes (GO:0032991), and protein aggregates (PR:000050566)." ], + "comments" : [ "Note: This includes single proteins and derivatives thereof (PR:000000001), protein-containing complexes (GO:0032991), and protein aggregates (PR:000050565)." ], "synonyms" : [ { "pred" : "hasNarrowSynonym", "val" : "protein", @@ -12331,9 +11919,6 @@ "val" : "galen:Wall" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "UBERON:0009915" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -12803,9 +12388,6 @@ "val" : "galen:ComplexSkeletalStructure" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "UBERON:0010322" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -13932,12 +13514,6 @@ "val" : "galen:Excretion" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "UBERON:0000324" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "UBERON:0007550" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -14081,9 +13657,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "TODO - check relationship with epiblast. Note in FMA this is not a subclass of embryo, but in uberon embryo is the whole organism from zygote onwards and thus includes the blastula" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "UBERON:0007011" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -15937,9 +15510,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0002161", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_6040" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "UBERON:0003263" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -16682,7 +16252,7 @@ "val" : "Organ system that passes nutrients (such as amino acids and electrolytes), gases, hormones, blood cells, etc. to and from cells in the body to help fight diseases and help stabilize body temperature and pH to maintain homeostasis[WP].", "xrefs" : [ "Wikipedia:Circulatory_system" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#uberon_slim" ], "synonyms" : [ { "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003011", "pred" : "hasRelatedSynonym", @@ -16707,9 +16277,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002161", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_6157" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -17909,9 +17476,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "UBERON:0004210" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -18504,9 +18068,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "UBERON:0005166" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -20191,9 +19752,6 @@ "val" : "ZFA:0000151" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "UBERON:0005794" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -20572,15 +20130,10 @@ "val" : "TAO:0001438" }, { "val" : "UMLS:C0333343" - }, { - "val" : "ZFA:0001438" }, { "val" : "galen:BodyCavity" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "UBERON:0000169" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -21856,9 +21409,6 @@ "val" : "ZFA:0000121" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "UBERON:0006258" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" }, { @@ -23433,12 +22983,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "UBERON:0002449" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "UBERON:0005098" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -23909,7 +23453,7 @@ "val" : "The part of the cardiovascular system consisting of all arteries.", "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#pheno_slim" ], "xrefs" : [ { "val" : "BTO:0004690" }, { @@ -23928,9 +23472,6 @@ "val" : "VHOG:0000273" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -23944,7 +23485,6 @@ "val" : "The part of the cardiovascular system consisting of all venous vessels. In vertebrates with a double circulation, this can be divided into systemic and pulmonary portions.", "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "vein system" @@ -23969,9 +23509,6 @@ "val" : "VHOG:0000277" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -24256,9 +23793,6 @@ "val" : "Wikipedia:Trilaminar_blastocyst" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "UBERON:0007012" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -24958,9 +24492,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "UBERON:0005165" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -27119,9 +26650,6 @@ "val" : "VSAO:0000303" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "UBERON:0007824" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -27298,9 +26826,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "consider adding new class (EMAPA:16097) for mesenchyme of embryo (some mesenchyme is extraembryonic - e.g. amnion mesoderm)" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "UBERON:0003313" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -28209,6 +27734,8 @@ "val" : "EHDAA2:0004731" }, { "val" : "Wikipedia:Coelom" + }, { + "val" : "ZFA:0001438" } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", @@ -28694,9 +28221,6 @@ "val" : "presumptive central nervous system" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "UBERON:3000469" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -28719,9 +28243,6 @@ "val" : "AAO:0000477" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "UBERON:3000477" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -29058,9 +28579,6 @@ "val" : "microvessel" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "http://orcid.org/0000-0002-2825-0621" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" }, { @@ -29081,9 +28599,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "http://orcid.org/0000-0002-6095-8718" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2022-05-25T18:21:29Z" @@ -29578,9 +29093,6 @@ "val" : "A relationship between a process and a barrier, where the process occurs in a region spanning the barrier. For cellular processes the barrier is typically a membrane. Examples include transport across a membrane and membrane depolarization." }, "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "https://orcid.org/0000-0002-7073-9172" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-07-20T17:19:37Z" } ] @@ -31862,9 +31374,6 @@ "val" : "RO:0004007" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2018-12-13T11:26:17Z" }, { @@ -31890,9 +31399,6 @@ "val" : "RO:0004008" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2018-12-13T11:26:32Z" }, { @@ -31918,9 +31424,6 @@ "val" : "RO:0004009" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2018-12-13T11:26:56Z" }, { @@ -31940,9 +31443,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0004050", "val" : "http://purl.obolibrary.org/obo/RO_0002418" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2018-03-13T23:55:05Z" @@ -31958,9 +31458,6 @@ "propertyType" : "OBJECT", "meta" : { "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2018-03-13T23:55:19Z" }, { @@ -31978,9 +31475,6 @@ "val" : "a relation between a process and a continuant, in which the process is regulated by the small molecule continuant" }, "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "https://orcid.org/0000-0003-1813-6857" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2020-04-22T20:27:26Z" } ] @@ -31998,9 +31492,6 @@ "val" : "RO:0012001" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "https://orcid.org/0000-0003-1813-6857" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2020-04-22T20:28:37Z" }, { @@ -32025,9 +31516,6 @@ "val" : "RO:0012003" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "https://orcid.org/0000-0003-1813-6857" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2020-06-08T17:21:33Z" }, { @@ -32048,9 +31536,6 @@ "val" : "a relation between a continuant and a process, in which the continuant is a small molecule that regulates the process" }, "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "https://orcid.org/0000-0003-1813-6857" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2020-06-24T13:15:17Z" } ] @@ -32065,9 +31550,6 @@ "val" : "a relation between a continuant and a process, in which the continuant is a small molecule that activates the process" }, "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "https://orcid.org/0000-0003-1813-6857" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2020-06-24T13:15:26Z" }, { @@ -32086,9 +31568,6 @@ "val" : "RO:0012008" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "https://orcid.org/0000-0003-1813-6857" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2021-02-26T07:28:29Z" }, { @@ -32113,9 +31592,6 @@ "val" : "has synaptic input or output in" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "https://orcid.org/0000-0002-1373-1705" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2020-07-17T09:26:52Z" } ] @@ -32140,13 +31616,34 @@ "val" : "has sensory terminal location" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "https://orcid.org/0000-0002-1373-1705" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2020-07-20T12:10:09Z" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0015004", + "lbl" : "has characterizing marker set", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "A relation that applies between a cell type and a set of markers that can be used to uniquely identify that cell type." + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "has marker gene combination" + }, { + "pred" : "hasExactSynonym", + "val" : "has marker signature set" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "C has_characterizing_marker_set y iff: C is a cell type and y is a collection of genes or proteins whose expression is sufficient to distinguish cell type C from most or all other cell types." + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0001-7258-9596" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/RO_0015006", "lbl" : "different in magnitude relative to", @@ -32272,9 +31769,6 @@ "val" : "RO:0040036" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2018-09-26T01:08:58Z" }, { @@ -32973,13 +32467,14 @@ "propertyType" : "ANNOTATION", "meta" : { "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2018-03-14T00:03:24Z" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/STATO_0000663", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" }, { "id" : "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "type" : "PROPERTY", @@ -33032,6 +32527,10 @@ "meta" : { "comments" : [ "a subset of general classes of cell types in the cell ontology." ] } + }, { + "id" : "http://purl.obolibrary.org/obo/cl#human_subset", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" }, { "id" : "http://purl.obolibrary.org/obo/cl#kidney_upper_slim", "lbl" : "kidney_upper_slim", @@ -33044,6 +32543,10 @@ "val" : "2023-11-22T11:18:57Z" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/cl#mouse_subset", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" }, { "id" : "http://purl.obolibrary.org/obo/go#gocheck_do_not_annotate", "type" : "PROPERTY", @@ -33366,10 +32869,6 @@ "id" : "http://purl.org/dc/elements/1.1/creator", "type" : "PROPERTY", "propertyType" : "ANNOTATION" - }, { - "id" : "http://purl.org/dc/elements/1.1/date", - "type" : "PROPERTY", - "propertyType" : "ANNOTATION" }, { "id" : "http://purl.org/dc/elements/1.1/description", "type" : "PROPERTY", @@ -33382,6 +32881,10 @@ "id" : "http://purl.org/dc/elements/1.1/title", "type" : "PROPERTY", "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.org/dc/elements/1.1/type", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" }, { "id" : "http://purl.org/dc/terms/contributor", "type" : "PROPERTY", @@ -33392,14 +32895,17 @@ "propertyType" : "ANNOTATION" }, { "id" : "http://purl.org/dc/terms/description", + "lbl" : "description", "type" : "PROPERTY", "propertyType" : "ANNOTATION" }, { "id" : "http://purl.org/dc/terms/license", + "lbl" : "license", "type" : "PROPERTY", "propertyType" : "ANNOTATION" }, { "id" : "http://purl.org/dc/terms/title", + "lbl" : "title", "type" : "PROPERTY", "propertyType" : "ANNOTATION" }, { @@ -33417,19 +32923,10 @@ "lbl" : "consider", "type" : "PROPERTY", "propertyType" : "ANNOTATION" - }, { - "id" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "type" : "PROPERTY", - "propertyType" : "ANNOTATION" }, { "id" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "type" : "PROPERTY", "propertyType" : "ANNOTATION" - }, { - "id" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "lbl" : "has_alternative_id", - "type" : "PROPERTY", - "propertyType" : "ANNOTATION" }, { "id" : "http://www.geneontology.org/formats/oboInOwl#hasBroadSynonym", "lbl" : "has_broad_synonym", @@ -33449,9 +32946,21 @@ } }, { "id" : "http://www.geneontology.org/formats/oboInOwl#hasDbXref", - "lbl" : "database_cross_reference", + "lbl" : "has cross-reference", "type" : "PROPERTY", - "propertyType" : "ANNOTATION" + "propertyType" : "ANNOTATION", + "meta" : { + "definition" : { + "val" : "An annotation property that links an ontology entity or a statement to a prefixed identifier or URI." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/information-artifact-ontology/ontology-metadata/issues/123" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0002-7356-1779" + } ] + } }, { "id" : "http://www.geneontology.org/formats/oboInOwl#hasExactSynonym", "lbl" : "has_exact_synonym", @@ -33530,10 +33039,6 @@ "id" : "http://www.geneontology.org/formats/oboInOwl#is_metadata_tag", "type" : "PROPERTY", "propertyType" : "ANNOTATION" - }, { - "id" : "http://www.geneontology.org/formats/oboInOwl#note", - "type" : "PROPERTY", - "propertyType" : "ANNOTATION" }, { "id" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "lbl" : "shorthand", @@ -33759,11 +33264,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000057", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/CL_0002320" - }, { - "sub" : "http://purl.obolibrary.org/obo/CL_0000057", - "pred" : "http://purl.obolibrary.org/obo/RO_0002202", - "obj" : "http://purl.obolibrary.org/obo/CL_0000134" + "obj" : "http://purl.obolibrary.org/obo/CL_0000499" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000066", "pred" : "is_a", @@ -34054,6 +33555,14 @@ "sub" : "http://purl.obolibrary.org/obo/CL_0000404", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/CL_0000211" + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_0000499", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/CL_0002320" + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_0000499", + "pred" : "http://purl.obolibrary.org/obo/RO_0002202", + "obj" : "http://purl.obolibrary.org/obo/CL_0000134" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000514", "pred" : "is_a", @@ -34092,10 +33601,6 @@ "sub" : "http://purl.obolibrary.org/obo/CL_0000547", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/CL_0002242" - }, { - "sub" : "http://purl.obolibrary.org/obo/CL_0000547", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000547", "pred" : "http://purl.obolibrary.org/obo/BFO_0000051", @@ -34170,10 +33675,6 @@ "val" : "true" } ] } - }, { - "sub" : "http://purl.obolibrary.org/obo/CL_0000549", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000549", "pred" : "http://purl.obolibrary.org/obo/BFO_0000051", @@ -34196,10 +33697,6 @@ "val" : "true" } ] } - }, { - "sub" : "http://purl.obolibrary.org/obo/CL_0000550", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000550", "pred" : "http://purl.obolibrary.org/obo/BFO_0000051", @@ -34340,10 +33837,6 @@ "val" : "true" } ] } - }, { - "sub" : "http://purl.obolibrary.org/obo/CL_0000558", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000558", "pred" : "http://purl.obolibrary.org/obo/CL_4030046", @@ -34414,10 +33907,6 @@ "sub" : "http://purl.obolibrary.org/obo/CL_0000566", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/CL_0011026" - }, { - "sub" : "http://purl.obolibrary.org/obo/CL_0000566", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000566", "pred" : "http://purl.obolibrary.org/obo/RO_0002104", @@ -34628,10 +34117,6 @@ "sub" : "http://purl.obolibrary.org/obo/CL_0000837", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/CL_0008001" - }, { - "sub" : "http://purl.obolibrary.org/obo/CL_0000837", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000837", "pred" : "http://purl.obolibrary.org/obo/CL_4030046", @@ -34812,10 +34297,6 @@ "sub" : "http://purl.obolibrary.org/obo/CL_0002188", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/CL_0002681" - }, { - "sub" : "http://purl.obolibrary.org/obo/CL_0002188", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0002188", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", @@ -35808,8 +35289,8 @@ "obj" : "http://purl.obolibrary.org/obo/GO_0043232" }, { "sub" : "http://purl.obolibrary.org/obo/GO_0005840", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PR_000050567" + "pred" : "http://purl.obolibrary.org/obo/BFO_0000051", + "obj" : "http://purl.obolibrary.org/obo/PR_000000001" }, { "sub" : "http://purl.obolibrary.org/obo/GO_0005840", "pred" : "http://purl.obolibrary.org/obo/RO_0002216", @@ -35853,7 +35334,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/GO_0006413", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/GO_0044237" + "obj" : "http://purl.obolibrary.org/obo/GO_0008152" }, { "sub" : "http://purl.obolibrary.org/obo/GO_0006413", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", @@ -36069,7 +35550,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/GO_0008152", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/GO_0008150" + "obj" : "http://purl.obolibrary.org/obo/GO_0009987" }, { "sub" : "http://purl.obolibrary.org/obo/GO_0008217", "pred" : "is_a", @@ -36089,11 +35570,11 @@ }, { "sub" : "http://purl.obolibrary.org/obo/GO_0009059", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/GO_0043170" + "obj" : "http://purl.obolibrary.org/obo/GO_0009058" }, { "sub" : "http://purl.obolibrary.org/obo/GO_0009059", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/GO_0044249" + "obj" : "http://purl.obolibrary.org/obo/GO_0043170" }, { "sub" : "http://purl.obolibrary.org/obo/GO_0009306", "pred" : "is_a", @@ -36528,8 +36009,8 @@ "obj" : "http://purl.obolibrary.org/obo/GO_0005575" }, { "sub" : "http://purl.obolibrary.org/obo/GO_0032991", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PR_000050567" + "pred" : "http://purl.obolibrary.org/obo/BFO_0000051", + "obj" : "http://purl.obolibrary.org/obo/PR_000000001" }, { "sub" : "http://purl.obolibrary.org/obo/GO_0033036", "pred" : "is_a", @@ -36734,26 +36215,10 @@ "sub" : "http://purl.obolibrary.org/obo/GO_0044207", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", "obj" : "http://purl.obolibrary.org/obo/GO_0005737" - }, { - "sub" : "http://purl.obolibrary.org/obo/GO_0044237", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/GO_0008152" - }, { - "sub" : "http://purl.obolibrary.org/obo/GO_0044237", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/GO_0009987" }, { "sub" : "http://purl.obolibrary.org/obo/GO_0044238", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/GO_0008152" - }, { - "sub" : "http://purl.obolibrary.org/obo/GO_0044249", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/GO_0009058" - }, { - "sub" : "http://purl.obolibrary.org/obo/GO_0044249", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/GO_0044237" }, { "sub" : "http://purl.obolibrary.org/obo/GO_0045184", "pred" : "is_a", @@ -37246,10 +36711,6 @@ "sub" : "http://purl.obolibrary.org/obo/GO_0098644", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/GO_0099080" - }, { - "sub" : "http://purl.obolibrary.org/obo/GO_0098644", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/GO_0098644", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", @@ -37781,7 +37242,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/PR_000000001", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PR_000050567" + "obj" : "http://purl.obolibrary.org/obo/PR_000064867" }, { "sub" : "http://purl.obolibrary.org/obo/PR_000000001", "pred" : "http://purl.obolibrary.org/obo/RO_0002353", @@ -37862,10 +37323,6 @@ "sub" : "http://purl.obolibrary.org/obo/PR_000001945", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PR_000000001" - }, { - "sub" : "http://purl.obolibrary.org/obo/PR_000001971", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PR_000000001" }, { "sub" : "http://purl.obolibrary.org/obo/PR_000002112", "pred" : "is_a", @@ -37919,7 +37376,7 @@ "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PR_000000001" }, { - "sub" : "http://purl.obolibrary.org/obo/PR_000050567", + "sub" : "http://purl.obolibrary.org/obo/PR_000064867", "pred" : "http://purl.obolibrary.org/obo/BFO_0000051", "obj" : "http://purl.obolibrary.org/obo/PR_000000001" }, { @@ -38038,10 +37495,6 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0000057", "pred" : "http://purl.obolibrary.org/obo/uberon/core#channels_from", "obj" : "http://purl.obolibrary.org/obo/UBERON_0001255" - }, { - "sub" : "http://purl.obolibrary.org/obo/UBERON_0000058", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000058", "pred" : "is_a", @@ -38570,7 +38023,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000178", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PR_000050567" + "obj" : "http://purl.obolibrary.org/obo/UBERON_0000061" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000178", "pred" : "is_a", @@ -38791,10 +38244,6 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0000481", "pred" : "http://purl.obolibrary.org/obo/BFO_0000051", "obj" : "http://purl.obolibrary.org/obo/UBERON_0000479" - }, { - "sub" : "http://purl.obolibrary.org/obo/UBERON_0000483", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000483", "pred" : "is_a", @@ -39955,10 +39404,6 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0001915", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", "obj" : "http://purl.obolibrary.org/obo/UBERON_0001982" - }, { - "sub" : "http://purl.obolibrary.org/obo/UBERON_0001969", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0001969", "pred" : "is_a", @@ -40017,10 +39462,6 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0001980", "pred" : "http://purl.obolibrary.org/obo/RO_0002433", "obj" : "http://purl.obolibrary.org/obo/UBERON_0001637" - }, { - "sub" : "http://purl.obolibrary.org/obo/UBERON_0001981", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0001981", "pred" : "is_a", @@ -40360,10 +39801,6 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0002224", "pred" : "http://purl.obolibrary.org/obo/RO_0002572", "obj" : "http://purl.obolibrary.org/obo/UBERON_0000915" - }, { - "sub" : "http://purl.obolibrary.org/obo/UBERON_0002303", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0002303", "pred" : "is_a", @@ -40775,6 +40212,10 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0002553", "pred" : "http://purl.obolibrary.org/obo/RO_0001015", "obj" : "http://purl.obolibrary.org/obo/UBERON_0000463" + }, { + "sub" : "http://purl.obolibrary.org/obo/UBERON_0003059", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/UBERON_0000061" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0003059", "pred" : "is_a", @@ -40807,10 +40248,6 @@ "val" : "GO" } ] } - }, { - "sub" : "http://purl.obolibrary.org/obo/UBERON_0003060", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/UBERON_0012275" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0003060", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", @@ -41728,10 +41165,6 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0004341", "pred" : "http://purl.obolibrary.org/obo/RO_0002387", "obj" : "http://purl.obolibrary.org/obo/UBERON_0000926" - }, { - "sub" : "http://purl.obolibrary.org/obo/UBERON_0004535", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0004535", "pred" : "is_a", @@ -41748,10 +41181,6 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0004535", "pred" : "http://purl.obolibrary.org/obo/BFO_0000051", "obj" : "http://purl.obolibrary.org/obo/UBERON_0001981" - }, { - "sub" : "http://purl.obolibrary.org/obo/UBERON_0004537", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0004537", "pred" : "is_a", @@ -41760,10 +41189,6 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0004537", "pred" : "http://purl.obolibrary.org/obo/RO_0002473", "obj" : "http://purl.obolibrary.org/obo/UBERON_0001981" - }, { - "sub" : "http://purl.obolibrary.org/obo/UBERON_0004572", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0004572", "pred" : "is_a", @@ -41778,10 +41203,6 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0004572", "pred" : "http://purl.obolibrary.org/obo/RO_0002351", "obj" : "http://purl.obolibrary.org/obo/UBERON_0001637" - }, { - "sub" : "http://purl.obolibrary.org/obo/UBERON_0004582", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0004582", "pred" : "is_a", @@ -42494,10 +41915,6 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0005764", "pred" : "http://purl.obolibrary.org/obo/RO_0002007", "obj" : "http://purl.obolibrary.org/obo/UBERON_0000061" - }, { - "sub" : "http://purl.obolibrary.org/obo/UBERON_0005769", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0005769", "pred" : "is_a", @@ -42845,10 +42262,6 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0006914", "pred" : "http://purl.obolibrary.org/obo/BFO_0000051", "obj" : "http://purl.obolibrary.org/obo/CL_0000076" - }, { - "sub" : "http://purl.obolibrary.org/obo/UBERON_0006965", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0006965", "pred" : "is_a", @@ -43276,6 +42689,10 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0009201", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/UBERON_0006555" + }, { + "sub" : "http://purl.obolibrary.org/obo/UBERON_0009201", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/UBERON_0012275" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0009569", "pred" : "is_a", @@ -44974,10 +44391,6 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002590", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002592" - }, { - "sub" : "http://purl.obolibrary.org/obo/RO_0002592", - "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0000057" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002592", "pred" : "subPropertyOf", @@ -48089,6 +47502,9 @@ "predicateId" : "http://purl.obolibrary.org/obo/RO_0002576", "domainClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000061" ], "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000061" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0015004", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/CL_0000000" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0015006", "domainClassIds" : [ "http://purl.obolibrary.org/obo/PATO_0000001" ], diff --git a/src/ontology/subsets/kidney_upper_slim.obo b/src/ontology/subsets/kidney_upper_slim.obo index abc4ba250..13d794cca 100644 --- a/src/ontology/subsets/kidney_upper_slim.obo +++ b/src/ontology/subsets/kidney_upper_slim.obo @@ -1,5 +1,5 @@ format-version: 1.2 -data-version: cl/releases/2024-09-26/subsets/kidney_upper_slim.owl +data-version: cl/releases/2025-01-08/subsets/kidney_upper_slim.owl subsetdef: abnormal_slim "" subsetdef: added_for_HCA "" subsetdef: attribute_slim "" @@ -44,10 +44,12 @@ subsetdef: http://purl.obolibrary.org/obo/valid_for_go_gp2term "" subsetdef: http://purl.obolibrary.org/obo/valid_for_go_ontology "" subsetdef: http://purl.obolibrary.org/obo/valid_for_gocam "" subsetdef: human_reference_atlas "" +subsetdef: human_subset "" subsetdef: inconsistent_with_fma "" subsetdef: kidney_upper_slim "a subset of general classes related to specific cell types in the kidney" subsetdef: location_grouping "" subsetdef: major_organ "" +subsetdef: mouse_subset "" subsetdef: mpath_slim "" subsetdef: non_informative "" subsetdef: organ_slim "" @@ -96,7 +98,7 @@ idspace: oboInOwl http://www.geneontology.org/formats/oboInOwl# idspace: sssom https://w3id.org/sssom/ idspace: terms http://purl.org/dc/terms/ ontology: cl/subsets/kidney_upper_slim -property_value: owl:versionInfo "2024-09-26" xsd:string +property_value: owl:versionInfo "2025-01-08" xsd:string [Term] id: CL:0000000 @@ -104,6 +106,8 @@ name: cell def: "A material entity of anatomical origin (part of or deriving from an organism) that has as its parts a maximally connected cell compartment surrounded by a plasma membrane." [CARO:mah] comment: The definition of cell is intended to represent all cells, and thus a cell is defined as a material entity and not an anatomical structure, which implies that it is part of an organism (or the entirety of one). subset: cellxgene_subset +subset: human_subset +subset: mouse_subset subset: ubprop:upper_level xref: CALOHA:TS-2035 xref: FBbt:00007002 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} @@ -125,6 +129,8 @@ relationship: RO:0002162 NCBITaxon:131567 ! in taxon cellular organisms id: CL:0000007 name: early embryonic cell (metazoa) def: "A cell found in the embryo before the formation of all the gem layers is complete." [GOC:tfm] +subset: human_subset +subset: mouse_subset xref: ZFA:0009002 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0002321 ! embryonic cell (metazoa) @@ -136,6 +142,8 @@ comment: This term applies to metazoan. For plant stem cells, consider using PO: subset: cellxgene_subset subset: general_cell_types_upper_slim subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "animal stem cell" EXACT [] xref: CALOHA:TS-2086 xref: FMA:63368 @@ -156,6 +164,8 @@ comment: Markers differ between species, and two sets of markers have been descr subset: blood_and_immune_upper_slim subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "blood forming stem cell" EXACT [] synonym: "colony forming unit hematopoietic" RELATED [] synonym: "hemopoietic stem cell" EXACT [] @@ -206,6 +216,8 @@ name: erythroid progenitor cell def: "A progenitor cell committed to the erythroid lineage." [GOC:add, ISBN:0721601464] subset: blood_and_immune_upper_slim subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "BFU-E" RELATED OMO:0003000 [] synonym: "blast forming unit erythroid" RELATED [] synonym: "burst forming unit erythroid" RELATED [] @@ -224,6 +236,8 @@ name: germ line cell def: "A cell that is within the developmental lineage of gametes and is able to pass along its genetic material to offspring." [GOC:tfm, ISBN:0721662544] comment: Originally this term had some plant germ line cell children. subset: general_cell_types_upper_slim +subset: human_subset +subset: mouse_subset subset: ubprop:upper_level xref: ZFA:0009016 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000000 ! cell @@ -233,6 +247,8 @@ relationship: capable_of GO:0022414 ! reproductive process id: CL:0000048 name: multi fate stem cell def: "A stem cell that can give rise to multiple lineages of cells." [GOC:add] +subset: human_subset +subset: mouse_subset synonym: "multi-fate stem cell" EXACT [] synonym: "multifate stem cell" EXACT [] synonym: "multipotent cell" EXACT [] @@ -252,6 +268,8 @@ def: "A progenitor cell committed to myeloid lineage, including the megakaryocyt comment: This cell type is intended to be compatible with any vertebrate common myeloid progenitor. For mammalian CMP known to be CD34-positive, please use the term 'common myeloid progenitor, CD34-positive' (CL_0001059). subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "CFU-GEMM" RELATED OMO:0003000 [ISBN:0878932437] synonym: "CFU-S" RELATED OMO:0003000 [ISBN:0878932437] synonym: "CMP" RELATED OMO:0003000 [ISBN:0878932437] @@ -273,6 +291,8 @@ def: "A progenitor cell committed to the megakaryocyte and erythroid lineages." comment: MEPs are reportedly CD19-negative, CD34-negative, CD45RA-negative, CD110-positive, CD117-positive, and SCA1-negative and reportedly express the transcription factors GATA-1 and NF-E2. subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "CFU-EM" EXACT [] synonym: "CFU-MegE" EXACT [] synonym: "colony forming unit erythroid megakaryocyte" EXACT [] @@ -295,6 +315,8 @@ property_value: RO:0002175 NCBITaxon:9606 id: CL:0000052 name: totipotent stem cell def: "A stem cell from which all cells of the body can form." [GOC:add, GOC:tfm] +subset: human_subset +subset: mouse_subset synonym: "totipotential stem cell" EXACT [] xref: FMA:84790 xref: MESH:D039901 @@ -307,6 +329,8 @@ name: non-terminally differentiated cell def: "A precursor cell with a limited number of potential fates." [SANBI:mhl] comment: define using PATO mulit-potent or oligopotent? subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "blast cell" EXACT [] xref: BTO:0000125 xref: FMA:84782 @@ -316,6 +340,9 @@ is_a: CL:0011115 ! precursor cell id: CL:0000056 name: myoblast def: "A cell that is commited to differentiating into a muscle cell. Embryonic myoblasts develop from the mesoderm. They undergo proliferation, migrate to their various sites, and then differentiate into the appropriate form of myocytes. Myoblasts also occur as transient populations of cells in muscles undergoing repair." [GOC:tfm, MESH:D032446, PMID:21849021] +subset: cellxgene_subset +subset: human_subset +subset: mouse_subset xref: BTO:0000222 xref: CALOHA:TS-0650 xref: FBbt:00005083 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} @@ -332,14 +359,15 @@ comment: These cells may be vimentin-positive, fibronectin-positive, fsp1-positi subset: cellxgene_subset subset: general_cell_types_upper_slim subset: human_reference_atlas +subset: human_subset +subset: mouse_subset xref: BTO:0000452 xref: CALOHA:TS-0362 xref: FMA:63877 xref: NCIT:C12482 xref: VHOG:0001482 xref: ZFA:0009026 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} -is_a: CL:0002320 ! connective tissue cell -relationship: RO:0002202 CL:0000134 ! develops from mesenchymal stem cell +is_a: CL:0000499 ! stromal cell property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -349,6 +377,8 @@ def: "A cell that is usually found in a two-dimensional sheet with a free surfac subset: cellxgene_subset subset: general_cell_types_upper_slim subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "epitheliocyte" EXACT [] xref: BTO:0000414 xref: CALOHA:TS-2026 @@ -367,6 +397,8 @@ id: CL:0000068 name: duct epithelial cell def: "An epithelial cell that is part of a duct." [https://orcid.org/0000-0001-5208-3432] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset xref: ZFA:0009372 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000066 ! epithelial cell intersection_of: CL:0000066 ! epithelial cell @@ -379,6 +411,8 @@ name: blood vessel endothelial cell def: "An endothelial cell that lines the vasculature." [GOC:tfm] subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset xref: ZFA:0009036 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0002139 ! endothelial cell of vascular tree intersection_of: CL:0000115 ! endothelial cell @@ -389,6 +423,8 @@ property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000072 name: non-branched duct epithelial cell +subset: human_subset +subset: mouse_subset is_a: CL:0000068 ! duct epithelial cell is_a: CL:0002078 ! meso-epithelial cell @@ -398,6 +434,8 @@ name: columnar/cuboidal epithelial cell def: "A columnar/cuboidal epithelial cell is a cell usually found in a two dimensional sheet with a free surface. Columnar/cuboidal epithelial cells take on the shape of a column or cube." [GO:0002065, https://orcid.org/0000-0001-5208-3432] subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset xref: ZFA:0009038 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000066 ! epithelial cell property_value: RO:0002175 NCBITaxon:9606 @@ -407,6 +445,8 @@ id: CL:0000076 name: squamous epithelial cell def: "Any epithelial cell that is part of some squamous epithelium." [FBC:Autogenerated] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset xref: CALOHA:TS-1249 xref: ZFA:0009039 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000066 ! epithelial cell @@ -420,6 +460,8 @@ name: blood cell def: "A cell found predominately in the blood." [GOC:add, GOC:tfm] subset: cellxgene_subset subset: general_cell_types_upper_slim +subset: human_subset +subset: mouse_subset xref: FMA:62844 xref: MESH:D001773 xref: ZFA:0009044 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} @@ -435,6 +477,8 @@ def: "An endothelial cell comprises the outermost layer or lining of anatomical comment: From FMA: 9.07.2001: Endothelial cell has always been classified as a kind of epithelial cell, specifically a squamous cell but that is not true. First, endothelial cell can either be squamous or cuboidal (e.g. high-endothelial cell) and secondly, it has different embryological derivation (mesodermal) than a true epithelial cell (ectodermal and endodermal). The basis for present classification is the fact that it comprises the outermost layer or lining of anatomical structures (location-based) but a better structural basis for the differentia is the cytoskeleton of the cell. Endothelial cell has vimentin filaments while an epithelial cell has keratin filaments. [Onard]. subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "endotheliocyte" EXACT [] xref: BTO:0001176 xref: CALOHA:TS-0278 @@ -449,6 +493,8 @@ property_value: RO:0002175 NCBITaxon:9606 id: CL:0000133 name: neurectodermal cell def: "Ectoderm destined to be nervous tissue." [GOC:tfm, ISBN:068340007X] +subset: human_subset +subset: mouse_subset synonym: "neurectoderm cell" EXACT [] xref: ZFA:0009080 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000221 ! ectodermal cell @@ -459,6 +505,8 @@ name: mesenchymal stem cell def: "A connective tissue cell that normally gives rise to other cells that are organized as three-dimensional masses. In humans, this cell type is CD73-positive, CD90-positive, CD105-positive, CD45-negative, CD34-negative, and MHCII-negative. They may further differentiate into osteoblasts, adipocytes, myocytes, neurons, or chondroblasts in vitro. Originally described as residing in the bone marrow, this cell type is now known to reside in many, if not all, adult organs." [FB:ma, GOC:dsd, http://en.wikipedia.org/wiki/Mesenchymal_stem_cell, http://www.copewithcytokines.de/cope.cgi?key=mesenchymal%20stem%20cells, PMCID:PMC2613570, PMID:10102814, PMID:16923606, PMID:17986482, PMID:19960544] comment: Many but not all mesenchymal cells derive from the mesoderm. MSCs are reportedly CD3-negative, CD4-negative, CD5-negative, CD8-negative, CD11a-negative, CD11b-negative, CD14-negative, CD19-negative, CD29-positive, CD31-negative, CD34-negative, CD38-negative, CD40-negative, CD44-positive, CD45-negative, CD49-positive, CD54-positive, CD66b-negative, CD79a-negative, CD80-negative, CD102-positive, CD106-positive, CD117-positive, CD121a-positive, CD121b-positive, CD123-positive, CD124-positive, CD133-negative, CD146-positive, CD166-positive, CD271-positive, B220-negative, Gr1-negative, MHCI-positive, MHCII-negative, SSEA4-negative, sca1-positive, Ter119-negative, and glycophorin A-negative. Cultured MSCs are capable of producing stem cell factor, IL7, IL8, IL11, TGF-beta, cofilin, galectin-1, laminin-receptor 1, cyclophilin A, and MMP-2. subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "BMSC" RELATED OMO:0003000 [] synonym: "bone marrow stromal cells" NARROW [] synonym: "CFU-F" RELATED OMO:0003000 [] @@ -484,6 +532,8 @@ id: CL:0000151 name: secretory cell def: "A cell that specializes in controlled release of one or more substances." [GOC:tfm, ISBN:0721662544] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset xref: BTO:0003659 xref: FMA:86916 is_a: CL:0000000 ! cell @@ -495,6 +545,8 @@ relationship: capable_of GO:0032940 ! secretion by cell id: CL:0000154 name: protein secreting cell def: "Any secretory cell that is capable of some protein secretion." [FBC:Autogenerated] +subset: human_subset +subset: mouse_subset is_a: CL:0000151 ! secretory cell intersection_of: CL:0000151 ! secretory cell intersection_of: capable_of GO:0009306 ! protein secretion @@ -505,6 +557,8 @@ id: CL:0000183 name: contractile cell def: "A cell whose primary function is to shorten." [FB:ma] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset is_a: CL:0000000 ! cell [Term] @@ -512,6 +566,8 @@ id: CL:0000187 name: muscle cell def: "A mature contractile cell, commonly known as a myocyte. This cell has as part of its cytoplasm myofibrils organized in various patterns." [MESH:D032342] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "muscle fiber" EXACT [] synonym: "myocyte" EXACT [] xref: BTO:0000888 @@ -534,6 +590,8 @@ def: "A non-striated, elongated, spindle-shaped cell found lining the digestive subset: cellxgene_subset subset: general_cell_types_upper_slim subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "myocytes, smooth muscle" EXACT [MESH:D032389] synonym: "non-striated muscle cell" BROAD [] synonym: "SMCs" EXACT [PMID:9315361] @@ -541,16 +599,20 @@ synonym: "smooth muscle fiber" EXACT [] xref: BTO:0004576 xref: CALOHA:TS-2159 xref: FMA:14072 +xref: https://cellxgene.cziscience.com/cellguide/CL_0000192 xref: ZFA:0009118 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0008000 ! non-striated muscle cell is_a: CL:0008007 ! visceral muscle cell relationship: RO:0002202 CL:0000514 ! develops from smooth muscle myoblast property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nSmooth muscle cells are a specialized type of muscle cells that are primarily found within the walls of hollow organs such as the intestine, stomach, bladder, uterus, and blood vessels. These cells are an essential component of the autonomic nervous system controling involuntary movements within the body.\nSmooth muscle cells play a vital role in many physiological processes due to their unique functionality. They can contract and relax in a slow, sustained, and controlled manner to help modulate the size and shape of the lumens of the organs they surround. For example, in the digestive system, coordinated contraction and relaxation of smooth muscle cells propels food along the gastrointestinal tract - a process known as peristalsis. In the blood vessels, the smooth muscle cells, by contracting or relaxing, either constrict or dilate the vessels, which in turn, help regulate blood flow and pressure.\nOn a cellular level, smooth muscle cells possess a single, centrally located nucleus and contain an arranged network of actin and myosin filaments, which are the proteins responsible for muscle contraction. Unlike their counterparts in skeletal or cardiac muscles, these cells lack specific contact points for these filaments, hence the lack of visible striations. Furthermore, the contraction of smooth muscle cells is regulated by hormones and neurotransmitters, such as acetylcholine and norepinephrine, adding an additional layer of complex regulation to these highly specialized cells." xsd:string {xref="DOI:10.1093/ptj/81.11.1810", xref="https://training.seer.cancer.gov/anatomy/muscular/types.html", xref="https://www.ncbi.nlm.nih.gov/books/NBK10854/", xref="https://www.ncbi.nlm.nih.gov/books/NBK526125", xref="https://www.ncbi.nlm.nih.gov/books/NBK556137/"} [Term] id: CL:0000211 name: electrically active cell def: "A cell whose function is determined by the generation or the reception of an electric signal." [FB:ma] +subset: human_subset +subset: mouse_subset xref: ZFA:0009128 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000000 ! cell @@ -558,6 +620,8 @@ is_a: CL:0000000 ! cell id: CL:0000213 name: lining cell def: "A cell within an epithelial cell sheet whose main function is to act as an internal or external covering for a tissue or an organism." [JB:jb] +subset: human_subset +subset: mouse_subset synonym: "boundary cell" EXACT [] xref: ZFA:0009130 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000215 ! barrier cell @@ -566,6 +630,8 @@ is_a: CL:0000215 ! barrier cell id: CL:0000215 name: barrier cell def: "A cell whose primary function is to prevent the transport of stuff across compartments." [JB:jb] +subset: human_subset +subset: mouse_subset xref: ZFA:0009132 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000000 ! cell @@ -573,6 +639,8 @@ is_a: CL:0000000 ! cell id: CL:0000219 name: motile cell def: "A cell that moves by its own activities." [FB:ma] +subset: human_subset +subset: mouse_subset xref: ZFA:0009136 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000000 ! cell intersection_of: CL:0000000 ! cell @@ -583,6 +651,9 @@ relationship: capable_of GO:0048870 ! cell motility id: CL:0000221 name: ectodermal cell def: "A cell of the outer of the three germ layers of the embryo." [MESH:D004475] +subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "ectoderm cell" EXACT [] xref: FMA:72549 xref: ZFA:0009137 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} @@ -595,18 +666,24 @@ id: CL:0000222 name: mesodermal cell def: "A cell of the middle germ layer of the embryo." [MESH:D008648] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "mesoblast" EXACT [] synonym: "mesoderm cell" EXACT [] xref: FMA:72554 +xref: https://cellxgene.cziscience.com/cellguide/CL_0000222 xref: ZFA:0009138 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000255 ! eukaryotic cell is_a: CL:0002321 ! embryonic cell (metazoa) relationship: part_of UBERON:0000926 ! mesoderm +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nMesodermal cells are pluripotent and the most abundant in the human body. They contribute to the development of several structures such as the skeletal muscles, bones, heart and blood vessels, kidneys, gonads, connective tissues, and certain layers of the skin. Hence, the mesoderm is often regarded as an active and diverse layer due to its role in forming many bodily structures. \nIn embryonic development, these cells are instrumental, contributing to the body's structures through a carefully coordinated sequence of morphogenetic movements. This process forms the complex multicellular architecture of tissues and organs from a simple ball of cells. Without the function of mesodermal cells, the body's integral structures and systems would cease to form correctly, leading to developmental disorders such as axial mesodermal dysplasia complex" xsd:string {xref="DOI:10.1016/j.ceb.2019.07.012", xref="DOI:10.5535/arm.2016.40.1.162", xref="https://www.sciencedirect.com/topics/biochemistry-genetics-and-molecular-biology/mesoderm"} [Term] id: CL:0000223 name: endodermal cell def: "A cell of the inner of the three germ layers of the embryo." [MESH:D004707] +subset: human_subset +subset: mouse_subset synonym: "endoderm cell" EXACT [] xref: FMA:72555 xref: ZFA:0009139 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} @@ -621,6 +698,8 @@ def: "A red blood cell. In mammals, mature erythrocytes are biconcave disks cont subset: blood_and_immune_upper_slim subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "RBC" EXACT [] synonym: "red blood cell" EXACT [] xref: BTO:0000424 @@ -645,7 +724,8 @@ property_value: RO:0002175 NCBITaxon:9606 id: CL:0000255 name: eukaryotic cell def: "Any cell that in taxon some Eukaryota." [FBC:Autogenerated] -subset: cellxgene_subset +subset: human_subset +subset: mouse_subset xref: MESH:D005057 is_a: CL:0000000 ! cell intersection_of: CL:0000000 ! cell @@ -656,6 +736,8 @@ relationship: RO:0002162 NCBITaxon:2759 ! in taxon Eukaryota id: CL:0000329 name: oxygen accumulating cell def: "Any cell that is capable of some oxygen transport." [FBC:Autogenerated] +subset: human_subset +subset: mouse_subset xref: ZFA:0009164 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000000 ! cell intersection_of: CL:0000000 ! cell @@ -666,6 +748,8 @@ relationship: capable_of GO:0015671 ! oxygen transport id: CL:0000333 name: migratory neural crest cell def: "A cell derived from the specialized ectoderm flanking each side of the embryonic neural plate, which after the closure of the neural tube, forms masses of cells that migrate out from the dorsal aspect of the neural tube to spread throughout the body." [doi:10.1016/j.stem.2015.02.017] +subset: human_subset +subset: mouse_subset xref: FMA:86667 xref: ZFA:0007086 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000219 ! motile cell @@ -677,6 +761,8 @@ relationship: RO:0002202 CL:0007004 ! develops from premigratory neural crest ce id: CL:0000335 name: mesenchyme condensation cell def: "A mesenchymal cell in embryonic development found in a contracting mass and that gives rise to osteoprogenitors." [GOC:tfm, PMID:5025404] +subset: human_subset +subset: mouse_subset xref: ZFA:0009166 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0008019 ! mesenchymal cell @@ -684,12 +770,16 @@ is_a: CL:0008019 ! mesenchymal cell id: CL:0000352 name: epiblast cell def: "A cell of the outer layer of a blastula that gives rise to the ectoderm after gastrulation." [GOC:tfm, ISBN:0618947256] +subset: human_subset +subset: mouse_subset is_a: CL:0000052 ! totipotent stem cell [Term] id: CL:0000365 name: animal zygote def: "Diploid cell produced by the fusion of sperm cell nucleus and egg cell." [ISBN:0471245208] +subset: human_subset +subset: mouse_subset synonym: "zygote" BROAD [] xref: BTO:0000854 xref: EHDAA2:0004546 @@ -705,6 +795,8 @@ relationship: RO:0002162 NCBITaxon:33208 ! in taxon Metazoa id: CL:0000393 name: electrically responsive cell def: "A cell whose function is determined by its response to an electric signal." [FB:ma] +subset: human_subset +subset: mouse_subset xref: ZFA:0009190 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000211 ! electrically active cell @@ -712,22 +804,44 @@ is_a: CL:0000211 ! electrically active cell id: CL:0000404 name: electrically signaling cell def: "A cell that initiates an electrical signal and passes that signal to another cell." [FB:ma] +subset: human_subset +subset: mouse_subset xref: ZFA:0009193 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000211 ! electrically active cell +[Term] +id: CL:0000499 +name: stromal cell +def: "A connective tissue cell of an organ found in the loose connective tissue." [GOC:tfm, MESH:D017154] +subset: cellxgene_subset +subset: general_cell_types_upper_slim +subset: human_reference_atlas +subset: human_subset +subset: mouse_subset +xref: BTO:0002064 +xref: FMA:83624 +xref: ZFA:0009226 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +is_a: CL:0002320 ! connective tissue cell +relationship: RO:0002202 CL:0000134 ! develops from mesenchymal stem cell +property_value: RO:0002175 NCBITaxon:9606 + [Term] id: CL:0000514 name: smooth muscle myoblast def: "A precursor cell destined to differentiate into smooth muscle myocytes." [GOC:tfm, MESH:D032390] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "myoblast, smooth muscle" EXACT [MESH:D032390] synonym: "satellite cell" RELATED [] xref: FMA:84798 +xref: https://cellxgene.cziscience.com/cellguide/CL_0000514 xref: ZFA:0009235 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000056 ! myoblast intersection_of: CL:0000056 ! myoblast intersection_of: RO:0002203 CL:0000192 ! develops into smooth muscle cell relationship: RO:0002203 CL:0000192 ! develops into smooth muscle cell +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nA precursor to the smooth muscle cell, the smooth muscle myoblast, is integral to various body systems, including the cardiovascular, gastrointestinal, and respiratory systems. Smooth muscle myoblasts arise from the differentiation of mesenchymal stem cells, a process tightly regulated by specific genetic factors and environmental signals. Their role extends to myogenesis, particularly in the formation of muscular tissue, especially during embryonic development.\nSmooth muscle myoblasts possess distinctive cellular characteristics. In contrast to skeletal muscle myoblasts, they do not fuse to create multinucleated fibers. Instead, they differentiate into individual, uninucleated smooth muscle cells. This differentiation unfolds in two distinct phases: proliferation, marked by rapid division to increase cell numbers, and differentiation, involving structural and functional transformation into mature smooth muscle cells. This intricate process is intricately mediated by various signaling molecules and transcription factors.\nFunctionally, smooth muscle myoblasts and the mature muscle cells they generate play pivotal roles in various physiological processes. Smooth muscle cells orchestrate involuntary muscle responses and are integral to body systems that regulate blood flow, propel food along the digestive tract, and control airflow in the respiratory tract. These diverse functions underscore the significance of smooth muscle myoblasts in the body's growth, maintenance, and overall function." xsd:string {xref="DOI:10.1074/jbc.RA118.001739", xref="https://www.ncbi.nlm.nih.gov/books/NBK544225/", xref="https://www.sciencedirect.com/topics/medicine-and-dentistry/smooth-muscle"} [Term] id: CL:0000540 @@ -737,6 +851,8 @@ comment: These cells are also reportedly CD4-negative and CD200-positive. They a subset: cellxgene_subset subset: general_cell_types_upper_slim subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "nerve cell" EXACT [] xref: BTO:0000938 xref: CALOHA:TS-0683 @@ -758,12 +874,13 @@ name: proerythroblast def: "An immature, nucleated erythrocyte occupying the stage of erythropoeisis that follows formation of erythroid progenitor cells. This cell is CD71-positive, has both a nucleus and a nucleolus, and lacks hematopoeitic lineage markers." [ISBN:0721601464, PMID:1638021] subset: blood_and_immune_upper_slim subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "pronormoblast" RELATED [] synonym: "rubriblast" EXACT [ISBN:0721601464] xref: FMA:83518 is_a: CL:0000764 {is_inferred="true"} ! erythroid lineage cell is_a: CL:0002242 ! nucleate cell -is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000764 ! erythroid lineage cell intersection_of: bearer_of PATO:0002505 ! nucleated intersection_of: bearer_of PATO:0040072 ! high nuclear/cytoplasmic ratio @@ -802,6 +919,8 @@ relationship: RO:0002202 CL:0000038 ! develops from erythroid progenitor cell id: CL:0000549 name: basophilic erythroblast def: "A nucleated immature erythrocyte, having cytoplasm generally similar to that of the earlier proerythroblast but sometimes even more basophilic, and usually regular in outline. The nucleus is still relatively large, but the chromatin strands are thicker and more deeply staining, giving a coarser appearance; the nucleoli have disappeared. This cell is CD71-positive and lacks hematopoeitic lineage markers." [GOC:tfm, ISBN:0721601464] +subset: human_subset +subset: mouse_subset synonym: "basophilic normoblast" EXACT [ISBN:0721601464] synonym: "early erythroblast" EXACT [ISBN:0721601464] synonym: "early normoblast" EXACT [ISBN:0721601464] @@ -809,7 +928,6 @@ synonym: "prorubricyte" EXACT [ISBN:0721601464] xref: FMA:83505 xref: ZFA:0005236 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000765 {is_inferred="true"} ! erythroblast -is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000765 ! erythroblast intersection_of: has_part CL:0017503 ! basophilic cytoplasm intersection_of: has_part GO:0000792 ! heterochromatin @@ -822,6 +940,8 @@ relationship: RO:0002104 PR:000001945 ! has plasma membrane part transferrin rec id: CL:0000550 name: polychromatophilic erythroblast def: "A nucleated, immature erythrocyte in which the nucleus occupies a relatively smaller part of the cell than in its precursor, the basophilic erythroblast. The cytoplasm is beginning to acquire hemoglobin and thus is no longer a purely basophilic, but takes on acidophilic aspects, which becomes progressively more marked as the cell matures. The chromatin of the nucleus is arranged in coarse, deeply staining clumps. This cell is CD71-positive and lacks hematopoeitic lineage markers." [ISBN:0721601464] +subset: human_subset +subset: mouse_subset synonym: "intermediate erythroblast" EXACT [ISBN:0721601464] synonym: "intermediate normoblast" EXACT [ISBN:0721601464] synonym: "polychromatic erythroblast" EXACT [ISBN:0721601464] @@ -831,7 +951,6 @@ synonym: "rubricyte" EXACT [ISBN:0721601464] xref: FMA:83506 xref: ZFA:0005241 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000765 {is_inferred="true"} ! erythroblast -is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000765 ! erythroblast intersection_of: has_part CL:0017504 ! polychromatophilic cytoplasm intersection_of: has_part GO:0000792 ! heterochromatin @@ -845,6 +964,8 @@ relationship: RO:0002202 CL:0000549 ! develops from basophilic erythroblast id: CL:0000552 name: orthochromatic erythroblast def: "The final stage of the nucleated, immature erythrocyte, before nuclear loss. Typically the cytoplasm is described as acidophilic, but it still shows a faint polychromatic tint. The nucleus is small and initially may still have coarse, clumped chromatin, as in its precursor, the polychromatophilic erythroblast, but ultimately it becomes pyknotic, and appears as a deeply staining, blue-black, homogeneous structureless mass. The nucleus is often eccentric and sometimes lobulated." [ISBN:0721601464] +subset: human_subset +subset: mouse_subset synonym: "acidophilic erythroblast" EXACT [ISBN:0721601464] synonym: "eosinophilic erythroblast" EXACT [ISBN:0721601464] synonym: "late erythoblast" EXACT [] @@ -866,6 +987,8 @@ def: "The earliest cytologically identifiable precursor in the thrombocytic seri comment: Lineage negative is described here as CD2-negative, CD3-negative, CD4-negative, CD5-negative, CD8a-negative, CD14-negative, CD19-negative, CD20-negative, CD56-negative, Ly6g-negative, and Ter119-negative. subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "CFU-Meg" EXACT [PMID:11722431, PMID:12482498] synonym: "colony-forming unit-megakaryocyte" EXACT [] synonym: "Meg-CFC" EXACT [PMCID:PMC1794060] @@ -922,6 +1045,8 @@ comment: Megakaryocytes are reportedly CD181-positive and CD182-positive. subset: blood_and_immune_upper_slim subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "megacaryocyte" EXACT [] synonym: "megalocaryocyte" EXACT [] synonym: "megalokaryocyte" EXACT [] @@ -940,12 +1065,13 @@ name: reticulocyte def: "An immature erythrocyte that changes the protein composition of its plasma membrane by exosome formation and extrusion. The types of protein removed differ between species though removal of the transferrin receptor is apparent in mammals and birds." [GOC:add, GOC:tfm, PMID:15946868, PMID:2037622] subset: blood_and_immune_upper_slim subset: cellxgene_subset +subset: human_subset +subset: mouse_subset xref: BTO:0001173 xref: CALOHA:TS-0864 xref: MESH:D012156 xref: ZFA:0009252 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000764 {is_inferred="true"} ! erythroid lineage cell -is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000764 ! erythroid lineage cell intersection_of: capable_of GO:0071971 ! extracellular exosome assembly intersection_of: CL:4030046 PR:000001002 ! lacks_plasma_membrane_part CD19 molecule @@ -980,12 +1106,13 @@ id: CL:0000566 name: angioblastic mesenchymal cell def: "A mesenchymal stem cell capable of developing into blood vessel endothelium." [GOC:dsd, GOC:tfm, PMID:12768659] comment: These cells are reportedly CD31-positive, CD34-positive, CD144-positive, CD309-positive, and TAL1-positive. +subset: human_subset +subset: mouse_subset synonym: "angioblast" EXACT [] synonym: "chondroplast" EXACT [] xref: ZFA:0009258 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000134 {is_inferred="true"} ! mesenchymal stem cell is_a: CL:0011026 ! progenitor cell -is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000134 ! mesenchymal stem cell intersection_of: RO:0002104 PR:000001444 ! has plasma membrane part cadherin-5 intersection_of: RO:0002104 PR:000002112 ! has plasma membrane part vascular endothelial growth factor receptor 2 @@ -1000,6 +1127,8 @@ id: CL:0000586 name: germ cell def: "The reproductive cell in multicellular organisms." [MESH:D005854] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset xref: BTO:0000535 xref: NCIT:C12597 xref: VHOG:0001534 @@ -1012,6 +1141,8 @@ id: CL:0000630 name: supporting cell def: "A cell whose primary function is to support other cell types." [FB:ma, GOC:tfm] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "supportive cell" EXACT [] xref: BTO:0002315 xref: ZFA:0009387 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} @@ -1022,6 +1153,8 @@ id: CL:0000648 name: kidney granular cell def: "A smooth muscle cell that synthesizes, stores, and secretes the enzyme renin. This cell type are located in the wall of the afferent arteriole at the entrance to the glomerulus. While having a different origin than other kidney smooth muscle cells, this cell type expresses smooth muscle actin upon maturation." [GOC:cvs, GOC:tfm, PMID:11457727] subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "JG cell" EXACT [] synonym: "juxtaglomerular cell" BROAD [] synonym: "renin secreting cell" EXACT [] @@ -1042,6 +1175,8 @@ name: mesangial cell def: "A cell type that encapsulates the capillaries and venules in the kidney. This cell secretes mesangial matrix that provides the structural support for the capillaries." [GOC:tfm, http://www.copewithcytokines.de/cope.cgi?key=mesangial%20cells] comment: Do all of these cells really develop from some mesenchymal stem cell? subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "kidney mesangial cell" EXACT [] xref: BTO:0000853 xref: CALOHA:TS-0617 @@ -1056,6 +1191,8 @@ id: CL:0000666 name: fenestrated endothelial cell def: "An endothelial cell that has small pores, or fenestrations, which allow for the efficient exchange of substances between the blood and surrounding tissues." [DOI:10.1007/978-3-211-99390-3_133] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "window cell" EXACT [] xref: https://cellxgene.cziscience.com/cellguide/CL_0000666 xref: ZFA:0009286 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} @@ -1063,7 +1200,7 @@ is_a: CL:0000115 ! endothelial cell intersection_of: CL:0000115 ! endothelial cell intersection_of: bearer_of PATO:0002064 ! fenestrated relationship: bearer_of PATO:0002064 ! fenestrated -property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional.\n\nFenestrated cells are specialized epithelial cells that are characterized by a distinctive structural feature, fenestrations or tiny pores, which allow an exchange of substances such as fluids, nutrients, and waste between blood vessels and the surrounding tissue environments. These cells are present in various types of epithelial tissues in the human body, including the intestinal tract, endocrine glands, and certain parts of the renal system. \nThere are multiple types of endothelial cell fenestrations. The most common type is found in systemic capillaries of the endocrine tissue (e.g., pancreatic islets), gastrointestinal mucosa, and renal peritubular capillaries. Here, the fenestrated cells have fenestrations in their peripheral cytoplasm with a unique thin and permeable diaphragm that provides a high degree of selectivity, blocking the passage of larger molecules while allowing the free movement of smaller ones. In contrast, other types of fenestrations, such as the discontinuous epithelium of the liver sinusoidal endothelial cells, do not have diaphragms. \nCharacteristically, fenestrated cells play a vital role in the filtering process of body systems. They are a key part of the glomeruli in the kidneys where blood is filtered under high pressure. The fenestrations present in the endothelial cells lining the capillaries of the glomerulus allow the free passage of water and small solute molecules towards the Bowman's capsule, leaving behind larger proteins and cells in the blood, thereby aiding in the filtration and waste removal process. \nIn the endocrine system, fenestrated cells in glandular capillaries allow the prompt release of hormones into the bloodstream. These cells have tightly clustered fenestrations which increase the surface area available for passive diffusion, improving the efficiency of hormone secretion. In villi of the small intestine, these cells increase absorption efficiency, permitting the exchange of water, electrolytes, and nutrients.\nOverall, fenestrated cells contribute immensely to important physiological processes of filtration, absorption, and secretion, primarily connecting our body's circulation system with the surrounding tissues and organs." xsd:string {xref="DOI:10.1002/ar.1092200109", xref="DOI:10.1016/0306-4522(86)90162-4", xref="DOI:10.1016/j.devcel.2012.11.003", xref="DOI:10.1038/s41467-022-31571-2", xref="DOI:10.1152/ajprenal.90601.2008"} +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nFenestrated cells are specialized epithelial cells that are characterized by a distinctive structural feature, fenestrations or tiny pores, which allow an exchange of substances such as fluids, nutrients, and waste between blood vessels and the surrounding tissue environments. These cells are present in various types of epithelial tissues in the human body, including the intestinal tract, endocrine glands, and certain parts of the renal system. \nThere are multiple types of endothelial cell fenestrations. The most common type is found in systemic capillaries of the endocrine tissue (e.g., pancreatic islets), gastrointestinal mucosa, and renal peritubular capillaries. Here, the fenestrated cells have fenestrations in their peripheral cytoplasm with a unique thin and permeable diaphragm that provides a high degree of selectivity, blocking the passage of larger molecules while allowing the free movement of smaller ones. In contrast, other types of fenestrations, such as the discontinuous epithelium of the liver sinusoidal endothelial cells, do not have diaphragms. \nCharacteristically, fenestrated cells play a vital role in the filtering process of body systems. They are a key part of the glomeruli in the kidneys where blood is filtered under high pressure. The fenestrations present in the endothelial cells lining the capillaries of the glomerulus allow the free passage of water and small solute molecules towards the Bowman's capsule, leaving behind larger proteins and cells in the blood, thereby aiding in the filtration and waste removal process. \nIn the endocrine system, fenestrated cells in glandular capillaries allow the prompt release of hormones into the bloodstream. These cells have tightly clustered fenestrations which increase the surface area available for passive diffusion, improving the efficiency of hormone secretion. In villi of the small intestine, these cells increase absorption efficiency, permitting the exchange of water, electrolytes, and nutrients.\nOverall, fenestrated cells contribute immensely to important physiological processes of filtration, absorption, and secretion, primarily connecting our body's circulation system with the surrounding tissues and organs." xsd:string {xref="DOI:10.1002/ar.1092200109", xref="DOI:10.1016/0306-4522(86)90162-4", xref="DOI:10.1016/j.devcel.2012.11.003", xref="DOI:10.1038/s41467-022-31571-2", xref="DOI:10.1152/ajprenal.90601.2008"} [Term] id: CL:0000669 @@ -1072,6 +1209,8 @@ def: "An elongated, contractile cell found wrapped about precapillary arterioles comment: Pericytes are CD10-positive, CD13-positive, CD31-negative, CD45-negative, CD106-positive, CD117-negative, CD140-positive, CD144-negative, CD146-positive, CD271-positive, CD325-positive, NG2-positive, RGS5-positive, SMA-positive, and desmin-positive. A subpopulation is CD248-positive. They are also capable of producing angiopoietin 1, CXCL12, TGF-beta, and VEGF-A. subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "adventitial cell" RELATED [] synonym: "adventitial reticular cell" EXACT [] synonym: "ARC" EXACT [PMID:17986482] @@ -1092,6 +1231,8 @@ id: CL:0000680 name: muscle precursor cell def: "A non-terminally differentiated cell that is capable of developing into a muscle cell." [GOC:add] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset xref: ZFA:0009291 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000055 ! non-terminally differentiated cell is_a: CL:0000255 ! eukaryotic cell @@ -1104,6 +1245,8 @@ relationship: RO:0002203 CL:0000187 ! develops into muscle cell id: CL:0000723 name: somatic stem cell def: "A stem cell that can give rise to cell types of the body other than those of the germ-line." [GO:0048103] +subset: human_subset +subset: mouse_subset xref: CALOHA:TS-2086 xref: MESH:D053687 xref: ZFA:0009307 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} @@ -1117,6 +1260,8 @@ id: CL:0000763 name: myeloid cell def: "A cell of the monocyte, granulocyte, mast cell, megakaryocyte, or erythroid lineage." [GOC:add] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset xref: BTO:0001441 xref: CALOHA:TS-0647 xref: MESH:D022423 @@ -1134,6 +1279,8 @@ def: "A immature or mature cell in the lineage leading to and including erythroc comment: Note that in FMA erythropoietic cells are types of nucleated erythrocytes and thus don't include erythrocytes. subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "erythropoietic cell" EXACT [] xref: CALOHA:TS-0290 xref: FMA:62845 @@ -1148,6 +1295,8 @@ name: erythroblast def: "A nucleated precursor of an erythrocyte that lacks hematopoietic lineage markers." [GOC:add, ISBN:0721601464, PMID:18174176] subset: blood_and_immune_upper_slim subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "normoblast" EXACT [] xref: BTO:0001571 xref: CALOHA:TS-0289 @@ -1195,6 +1344,8 @@ comment: Markers differ between mouse and human. subset: blood_and_immune_upper_slim subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "hemopoietic progenitor cell" EXACT [] synonym: "MPP" EXACT [] xref: BTO:0000725 @@ -1202,7 +1353,6 @@ xref: CALOHA:TS-0448 xref: ZFA:0009354 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000255 ! eukaryotic cell is_a: CL:0008001 ! hematopoietic precursor cell -is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000988 ! hematopoietic cell intersection_of: bearer_of PATO:0001402 ! multipotent intersection_of: CL:4030046 PR:000001002 ! lacks_plasma_membrane_part CD19 molecule @@ -1245,6 +1395,8 @@ def: "A progenitor cell restricted to the myeloid lineage." [GOC:add, GOC:tfm, P comment: Note that this is a class of cell types, not an identified single cell type. subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "myeloid progenitor cell" BROAD [] xref: BTO:0004730 xref: CALOHA:TS-2099 @@ -1262,6 +1414,8 @@ id: CL:0000988 name: hematopoietic cell def: "A cell of a hematopoietic lineage." [GO_REF:0000031, GOC:add] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "haematopoietic cell" EXACT [] synonym: "haemopoietic cell" EXACT [] synonym: "hemopoietic cell" EXACT [] @@ -1277,6 +1431,8 @@ id: CL:0002031 name: hematopoietic lineage restricted progenitor cell def: "A hematopoietic progenitor cell that is capable of developing into only one lineage of hematopoietic cells." [GOC:tfm, PMID:19022770] subset: blood_and_immune_upper_slim +subset: human_subset +subset: mouse_subset is_a: CL:0000255 ! eukaryotic cell is_a: CL:0008001 ! hematopoietic precursor cell intersection_of: CL:0000988 ! hematopoietic cell @@ -1293,6 +1449,8 @@ name: hematopoietic oligopotent progenitor cell def: "A hematopoietic oligopotent progenitor cell that has the ability to differentiate into limited cell types but lacks lineage cell markers and self renewal capabilities." [GOC:tfm, https://orcid.org/0000-0001-5208-3432, PMID:19022770] comment: This cell type is intended to be compatible with any vertebrate hematopoietic oligopotent progenitor cell. For mammalian hematopoietic oligopotent progenitor cells known to be lineage-negative, please use the term 'hematopoietic oligopotent progenitor cell' (CL_0001060). subset: blood_and_immune_upper_slim +subset: human_subset +subset: mouse_subset is_a: CL:0000255 ! eukaryotic cell is_a: CL:0008001 ! hematopoietic precursor cell intersection_of: CL:0000988 ! hematopoietic cell @@ -1306,6 +1464,8 @@ creation_date: 2010-01-06T03:43:27Z id: CL:0002077 name: ecto-epithelial cell def: "An epithelial cell derived from ectoderm." [FMA:69074, GOC:tfm] +subset: human_subset +subset: mouse_subset xref: FMA:69074 xref: ZFA:0009385 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000066 ! epithelial cell @@ -1319,6 +1479,8 @@ creation_date: 2010-06-29T03:38:22Z id: CL:0002078 name: meso-epithelial cell def: "Epithelial cell derived from mesoderm or mesenchyme." [FMA:69076, GOC:tfm] +subset: human_subset +subset: mouse_subset synonym: "epithelial mesenchymal cell" EXACT [] xref: FMA:69076 xref: ZFA:0009388 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} @@ -1335,13 +1497,17 @@ name: endothelial cell of vascular tree def: "An endothelial cell of the vascular tree, which includes blood vessels and lymphatic vessels." [GOC:dsd, GOC:tfm, PMID:12768659] comment: These cells are reportedly CD31-positive, CD34-positive, CD144-positive, TAL1-positive. subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "cubodial endothelial cell of vascular tree" NARROW [] synonym: "vascular endothelial cell" EXACT [] xref: BTO:0001854 xref: CALOHA:TS-1106 xref: FMA:67755 +xref: https://cellxgene.cziscience.com/cellguide/CL_0002139 is_a: CL:0000115 ! endothelial cell property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nEndothelial cells of the vascular tree, commonly referred to as vascular endothelial cells, line the entire circulatory system, from the heart to the smallest capillaries. These cells have a unique, flattened shape, and are tightly bound together, forming a thin layer known as the endothelium. The endothelium is responsible for maintaining the interior surface of blood vessels, and plays a critical role in ensuring the smooth flow of blood. \nVascular endothelial cells act as a semi-permeable membrane, controlling the passage of materials and the transit of white blood cells into and out of the bloodstream. These cells are also involved in blood coagulation. When a blood vessel is damaged, endothelial cells promote clotting to prevent excessive bleeding and facilitate wound healing. Other functions include regulation of blood pressure and blood volume by releasing vasodilators and vasoconstrictors to either widen or constrict blood vessels, accordingly.\nFurthermore, the endothelial cells are crucial in the formation of new blood vessels, a process known as angiogenesis. This is particularly important in wound healing and the growth of new tissues during development or after injury. In the context of diseases such as cancer, angiogenesis helps facilitate tumor growth by providing nutrients and oxygen." xsd:string {xref="DOI:10.1038/s41569-022-00770-1", xref="DOI:10.1186/s12872-015-0124-z", xref="DOI:10.3389/fphys.2022.863265/full", xref="https://www.sciencedirect.com/topics/medicine-and-dentistry/vascular-endothelial-cell"} creation_date: 2010-08-24T02:06:40Z [Term] @@ -1350,6 +1516,8 @@ name: capillary endothelial cell def: "An endothelial cell found in capillaries." [GOC:tfm] subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset xref: BTO:0004956 xref: CALOHA:TS-0112 xref: FMA:67756 @@ -1366,6 +1534,8 @@ creation_date: 2010-08-24T10:15:00Z id: CL:0002173 name: extraglomerular mesangial cell def: "A cell that is a specialized type of pericyte providing structural support for the capillary loops of kidney. A flat, elongated cell with extensive fine cytoplasmic processes found outside the kidney glomerulus near the macula densa and bound laterally by afferent and efferent arterioles. Being phagocytic, this cell participates in the continuous turnover of the basal lamina by removing its outer portion containing residues of filtration, while the lamina is renewed on its inner surface by the endothelial cells." [GOC:tfm, http:/www.copewithcytokines.de/cope.cgi?key=Lacis%20cells, ISBN:0412046911] +subset: human_subset +subset: mouse_subset synonym: "Goormaghtigh cell" EXACT [] synonym: "lacis cell" RELATED [] synonym: "polar cushion cells" EXACT [] @@ -1386,12 +1556,13 @@ name: glomerular endothelial cell def: "An endothelial cell that is part of the glomerulus of the kidney. This cell is flattened, highly fenestrated, and plays a vital role in the formation of glomerular ultrafiltrate." [GOC:tfm, PMID:15840009] comment: Glomerular endothelial cells have 60-80 nm fenestrations typically lacking diaphragms in adults but present during embryonic development. Some studies found diaphragms in 2-6% of mature rat glomerular capillaries. Their presence may depend on fixation techniques, developmental stage, or dynamic cell changes. Additionally, these cells help maintain the structural integrity of glomerular capillaries through interactions with the basement membrane and podocytes. {xref="PMID:33123011", xref="PMID:18480313", xref="PMID:19129259"} subset: cellxgene_subset +subset: human_subset subset: kidney_upper_slim +subset: mouse_subset xref: BTO:0004632 xref: FMA:70970 is_a: CL:0000666 ! fenestrated endothelial cell is_a: CL:0002681 ! kidney cortical cell -is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000115 ! endothelial cell intersection_of: part_of UBERON:0000074 ! renal glomerulus relationship: has_part GO:0036053 ! glomerular endothelium fenestra @@ -1403,6 +1574,8 @@ creation_date: 2010-08-26T10:59:44Z id: CL:0002242 name: nucleate cell def: "A cell containing at least one nucleus." [GOC:tfm] +subset: human_subset +subset: mouse_subset xref: FMA:67513 is_a: CL:0000000 ! cell intersection_of: CL:0000000 ! cell @@ -1415,7 +1588,9 @@ creation_date: 2010-09-07T03:32:33Z id: CL:0002305 name: epithelial cell of distal tubule def: "An epithelial cell of the distal convoluted tubule of the kidney that helps regulate systemic levels of potassium, sodium, calcium, and pH." [GOC:tfm, ISBN:0517223651] +subset: human_subset subset: kidney_upper_slim +subset: mouse_subset synonym: "kidney distal tubule epithelial cell" EXACT [] xref: FMA:70981 xref: KUPO:0001055 @@ -1433,7 +1608,9 @@ def: "An epithelial cell of the proximal tubule of the kidney." [GOC:tfm, ISBN:1 comment: The vast majority of proximal tubule epithelial cells have a brush border, but there are rare exceptions. subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset subset: kidney_upper_slim +subset: mouse_subset synonym: "kidney proximal tubule epithelial cell" EXACT [] xref: FMA:70973 xref: KUPO:0001044 @@ -1450,6 +1627,8 @@ id: CL:0002319 name: neural cell def: "A cell that is part of the nervous system." [GOC:tfm, ISBN:0618947256] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset xref: CALOHA:TS-2040 xref: FMA:70333 is_a: CL:0000255 ! eukaryotic cell @@ -1464,6 +1643,8 @@ id: CL:0002320 name: connective tissue cell def: "A cell of the supporting or framework tissue of the body, arising chiefly from the embryonic mesoderm and including adipose tissue, cartilage, and bone." [GOC:tfm, ISBN:0618947256] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset xref: CALOHA:TS-2096 xref: FMA:63875 xref: MESH:D003239 @@ -1479,12 +1660,16 @@ creation_date: 2010-09-15T03:01:54Z id: CL:0002321 name: embryonic cell (metazoa) def: "A cell of the embryo." [FMA:0618947256] +subset: human_subset +subset: mouse_subset xref: CALOHA:TS-0263 xref: FMA:82840 +xref: https://cellxgene.cziscience.com/cellguide/CL_0002321 xref: WBbt:0007028 xref: ZFA:0007089 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000000 ! cell property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nEmbryonic cells in metazoans, which include all multicellular animals, are biological units in their earliest developmental stages from conception until the organism is fully formed. \nThey are derived from a fertilized egg, which undergoes a series of cell divisions to produce a multicellular organism. During the early phases of embryonic development, these cells exhibit pluripotency, meaning they possess the potential to differentiate into a diverse array of specialized cell types that constitute different body tissues and structures. \nThe balance between cell proliferation and differentiation in embryonic cells is crucial for successful development. When cells continue to divide without differentiating, overgrowth may occur leading to conditions such as teratomas (tumors of embryonic cells). Conversely, if cell differentiation proceeds at the expense of cell proliferation, developmental anomalies could occur regarding size or mass of the organism or its parts." xsd:string {xref="DOI:10.1002/iub.1404", xref="DOI:10.1093/molehr/gan048", xref="https://www.ncbi.nlm.nih.gov/books/NBK9906/"} creation_date: 2010-09-15T03:39:21Z [Term] @@ -1492,6 +1677,8 @@ id: CL:0002494 name: cardiocyte def: "A cell located in the heart, including both muscle and non muscle cells." [GOC:tfm] comment: From Onard of the FMA: Cardiac muscle cell or cardiac myocyte is a striated muscle cell. Cardiocyte on the other hand is any cell in the heart which includes cells other than muscle cells (e.g. endothelial cell of endocardium). Unless there is a consensus among anatomists that cardiocytes refer only to muscle cells, we will treat them as a general class of cells in the heart. +subset: human_subset +subset: mouse_subset synonym: "heart cell" EXACT [] xref: BTO:0001539 xref: CALOHA:TS-0115 @@ -1509,6 +1696,8 @@ id: CL:0002518 name: kidney epithelial cell def: "An epithelial cell of the kidney." [GOC:tfm, KUPO:SJ] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset xref: KUPO:0001019 xref: ZFA:0009374 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000066 ! epithelial cell @@ -1522,6 +1711,8 @@ creation_date: 2011-02-08T10:46:34Z id: CL:0002584 name: renal cortical epithelial cell def: "An epithelial cell of the kidney cortex." [GOC:tfm] +subset: human_subset +subset: mouse_subset xref: KUPO:0001016 is_a: CL:0002518 {is_inferred="true"} ! kidney epithelial cell is_a: CL:0002681 {is_inferred="true"} ! kidney cortical cell @@ -1532,6 +1723,8 @@ intersection_of: part_of UBERON:0001225 ! cortex of kidney id: CL:0002653 name: squamous endothelial cell def: "A squamous shaped endothelial cell." [GOC:dos] +subset: human_subset +subset: mouse_subset is_a: CL:0000115 ! endothelial cell property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-07-08T03:31:25Z @@ -1540,6 +1733,8 @@ creation_date: 2011-07-08T03:31:25Z id: CL:0002681 name: kidney cortical cell def: "A cell that is part of a cortex of kidney." [] +subset: human_subset +subset: mouse_subset is_a: CL:1000497 ! kidney cell intersection_of: CL:1000497 ! kidney cell intersection_of: part_of UBERON:0001225 ! cortex of kidney @@ -1552,16 +1747,20 @@ id: CL:0005009 name: renal principal cell def: "A cuboidal epithelial cell of the kidney which regulates sodium and potassium balance. The activity of sodium and potassium channels on the apical membrane of the cell is regulated by aldosterone and vasopressin. In mammals this cell type is located in the renal collecting duct system." [CL:CVS] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset xref: https://cellxgene.cziscience.com/cellguide/CL_0005009 xref: ZFA:0005322 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000075 ! columnar/cuboidal epithelial cell is_a: CL:0002518 ! kidney epithelial cell -property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional.\n\nRenal principal cells are the major cell type in the initial collecting tubule and the cortical and outer medullary collecting ducts, as well as the connecting tubule, in the nephrons of the kidneys.\nA key function of renal principal cells is the regulation of water balance in the body. These cells express aquaporin-2 (AQP2) water channels, which facilitate the reabsorption of water from the fluid within the renal tubule lumen back into the blood. The translocation of AQP2 to the cell membrane is controlled by the hormone vasopressin: In response to high vasopressin levels, AQP2 moves to the cell membrane, allowing water to pass through effectively and be reabsorbed, therefore concentrating the urine. Conversely, in low vasopressin conditions, AQP2 is removed from the membrane, reducing water reabsorption and diluting the urine. \nRenal principal cells are also involved in the regulation of sodium and potassium levels in the body. They have sodium channels (ENaC) in their luminal membranes which permit the reabsorption of sodium ions from the tubule fluid back into the blood, resulting in a net reabsorption of sodium ions into the systemic circulation. This process is controlled, in part, by the hormone aldosterone. Additionally, renal principal cells contain potassium channels that facilitate the secretion of potassium ions into the urine. The activities of these channels, in coordination with other cell types in the nephron, are critical for maintaining electrolyte balance and overall body homeostasis." xsd:string {xref="DOI:10.1016/j.krcp.2013.07.005", xref="DOI:10.2215/CJN.05760513", xref="DOI:10.2215/CJN.08580813"} +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nRenal principal cells are the major cell type in the initial collecting tubule and the cortical and outer medullary collecting ducts, as well as the connecting tubule, in the nephrons of the kidneys.\nA key function of renal principal cells is the regulation of water balance in the body. These cells express aquaporin-2 (AQP2) water channels, which facilitate the reabsorption of water from the fluid within the renal tubule lumen back into the blood. The translocation of AQP2 to the cell membrane is controlled by the hormone vasopressin: In response to high vasopressin levels, AQP2 moves to the cell membrane, allowing water to pass through effectively and be reabsorbed, therefore concentrating the urine. Conversely, in low vasopressin conditions, AQP2 is removed from the membrane, reducing water reabsorption and diluting the urine. \nRenal principal cells are also involved in the regulation of sodium and potassium levels in the body. They have sodium channels (ENaC) in their luminal membranes which permit the reabsorption of sodium ions from the tubule fluid back into the blood, resulting in a net reabsorption of sodium ions into the systemic circulation. This process is controlled, in part, by the hormone aldosterone. Additionally, renal principal cells contain potassium channels that facilitate the secretion of potassium ions into the urine. The activities of these channels, in coordination with other cell types in the nephron, are critical for maintaining electrolyte balance and overall body homeostasis." xsd:string {xref="DOI:10.1016/j.krcp.2013.07.005", xref="DOI:10.2215/CJN.05760513", xref="DOI:10.2215/CJN.08580813"} [Term] id: CL:0007004 name: premigratory neural crest cell def: "Cell that is part of the neural crest region of the neuroepithelium, prior to migration. Note that not all premigratory neural crest cells may become migratory neural crest cells." [UBERONREF:0000002] +subset: human_subset +subset: mouse_subset xref: ZFA:0007084 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0011012 ! neural crest cell relationship: part_of UBERON:0002342 ! neural crest @@ -1573,6 +1772,8 @@ creation_date: 2012-06-27T08:27:35Z id: CL:0008000 name: non-striated muscle cell def: "Any muscle cell in which the fibers are not organised into sarcomeres." [GOC:DOS] +subset: human_subset +subset: mouse_subset is_a: CL:0000187 ! muscle cell [Term] @@ -1580,12 +1781,16 @@ id: CL:0008001 name: hematopoietic precursor cell def: "Any hematopoietic cell that is a precursor of some other hematopoietic cell type." [GOC:dos] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset is_a: CL:0000988 ! hematopoietic cell [Term] id: CL:0008007 name: visceral muscle cell def: "A muscle cell that is part of some visceral muscle." [GOC:dos] +subset: human_subset +subset: mouse_subset xref: FBbt:00005070 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} is_a: CL:0000187 ! muscle cell intersection_of: CL:0000187 ! muscle cell @@ -1598,6 +1803,8 @@ name: mesenchymal cell def: "A non-polarised cell precursor cell that is part of some mesenchyme, is associated with the cell matrix but is not connected to other cells and is capable of migration." [] subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "mesenchyme cell" EXACT [] is_a: CL:0000219 ! motile cell is_a: CL:0000255 ! eukaryotic cell @@ -1612,6 +1819,8 @@ def: "Mural cells are pericytes and the vascular smooth muscle cells (vSMCs) of subset: added_for_HCA subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset xref: ZFA:0005944 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:4033054 ! perivascular cell property_value: RO:0002175 NCBITaxon:9606 @@ -1622,6 +1831,8 @@ creation_date: 2020-02-29T17:33:55Z id: CL:0010017 name: zygote def: "A zygote in a plant or an animal." [] +subset: human_subset +subset: mouse_subset xref: MESH:D015053 is_a: CL:0000000 ! cell property_value: seeAlso https://github.com/obophenotype/cell-ontology/issues/786 @@ -1631,16 +1842,20 @@ id: CL:0011012 name: neural crest cell def: "A cell of the neural crest. Neural crest cells are multipotent. Premigratory neural crest cells are found at the neural plate boarder, some of which will undergo ectomesynchymal transition and delamination to form migratory neural crest cells." [https://orcid.org/0000-0001-5208-3432, https://orcid.org/0000-0002-9900-7880] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset xref: https://cellxgene.cziscience.com/cellguide/CL_0011012 is_a: CL:0000048 ! multi fate stem cell is_a: CL:0002321 ! embryonic cell (metazoa) -property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional.\n\nNeural crest cells are a group of transient and highly migratory cells that originate from the neuroectoderm during the early stages of embryonic development. They are multipotent cells with an exceptional degree of plasticity, capable of differentiating into various somatic cell types and therefore play a fundamental role in the formation of various organs and tissues, making them critical contributors to the developing embryo. \nAfter the initiation of neurulation (the formation of the neural tube) neural crest cells start to undergo epithelial-to-mesenchymal transition and delaminate and migrate from the dorsal neural tube to several regions throughout the embryo. They differentiate into a range of diverse cell types, such as neurons and glial cells of the peripheral nervous system, including sensory and autonomic neurons. They also contribute to the formation of adrenal glands, pigment cells in the skin (melanocytes), cardiac structures, including parts of the heart septum and major arteries, as well as bones and cartilage of the face and skull.\nDisorders or aberrations in the development or migration of the neural crest cells can lead to serious congenital malformations, such as neurocristopathies, including Hirschsprung disease, neuroblastoma, and neurofibromatosis." xsd:string {xref="DOI:10.1002/dvg.23276", xref="DOI:10.1242/dev.193193", xref="DOI:10.3389/fcell.2020.00635/full", xref="https://doi.org/10.1016/j.ydbio.2011.12.042"} +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nNeural crest cells are a group of transient and highly migratory cells that originate from the neuroectoderm during the early stages of embryonic development. They are multipotent cells with an exceptional degree of plasticity, capable of differentiating into various somatic cell types and therefore play a fundamental role in the formation of various organs and tissues, making them critical contributors to the developing embryo. \nAfter the initiation of neurulation (the formation of the neural tube) neural crest cells start to undergo epithelial-to-mesenchymal transition and delaminate and migrate from the dorsal neural tube to several regions throughout the embryo. They differentiate into a range of diverse cell types, such as neurons and glial cells of the peripheral nervous system, including sensory and autonomic neurons. They also contribute to the formation of adrenal glands, pigment cells in the skin (melanocytes), cardiac structures, including parts of the heart septum and major arteries, as well as bones and cartilage of the face and skull.\nDisorders or aberrations in the development or migration of the neural crest cells can lead to serious congenital malformations, such as neurocristopathies, including Hirschsprung disease, neuroblastoma, and neurofibromatosis." xsd:string {xref="DOI:10.1002/dvg.23276", xref="DOI:10.1242/dev.193193", xref="DOI:10.3389/fcell.2020.00635/full", xref="https://doi.org/10.1016/j.ydbio.2011.12.042"} [Term] id: CL:0011026 name: progenitor cell def: "A precursor cell that has a tendency to differentiate into a specific type of cell. They are descendants of stem cells, only they are more constrained in their differentiation potential or capacity for self-renewal, and are often more limited in both senses." [https://doi.org/10.1016/B978-0-12-409503-8.00002-0, ISBN:978-1-62808-994-3] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset is_a: CL:0000255 ! eukaryotic cell is_a: CL:0011115 ! precursor cell intersection_of: CL:0011115 ! precursor cell @@ -1654,6 +1869,8 @@ name: precursor cell def: "A cell that, by division or terminal differentiation, can give rise to other cell types." [GOC:dos] comment: Work is needed on GO 'cell differentiation' before it is clear whether the equivalent class definition 'native cell' that capable_of some 'cell differentiation' works. Also, may want to consider merging this with non-terminally differentiated cell. subset: cellxgene_subset +subset: human_subset +subset: mouse_subset is_a: CL:0000000 ! cell intersection_of: CL:0000000 ! cell intersection_of: capable_of GO:0030154 ! cell differentiation @@ -1698,18 +1915,24 @@ id: CL:1000449 name: epithelial cell of nephron def: "An epithelial cell that is part of the nephron." [GOC:tfm] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset xref: FMA:70965 +xref: https://cellxgene.cziscience.com/cellguide/CL_1000449 is_a: CL:0002518 ! kidney epithelial cell intersection_of: CL:0000066 ! epithelial cell intersection_of: part_of UBERON:0001285 ! nephron relationship: part_of UBERON:0001285 ! nephron +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nEpithelial cells of the nephron form the epithelial lining of the nephron, the functional unit of the kidney that filters the blood to produce urine. Each kidney holds approximately one million nephrons, each of which is composed of several distinct parts, including the renal corpuscle, the proximal tubule, the loop of Henle, and the distal tubule. All sections are lined with highly specialized epithelial cells adapted to perform different functions within the sections of the nephron. \nThe different epithelial cells of the nephron play crucial roles in the process of filtration, reabsorption, secretion, and excretion, essential tasks for the regulation of body fluid composition and volume. During filtration, the blood is forced through the walls of glomerular capillaries into the Bowman's capsule, where waste products, electrolytes, and water are separated from the blood cells and proteins. As the filtrate then passes through the nephron, epithelial cells of the tubular portion reabsorb useful substances such as glucose, amino acids, and electrolytes, along with most of the water back into the bloodstream. Waste products like urea and creatinine, as well as excess ions and water, remain in the tubule for elimination.\nIn addition, epithelial cells of the nephron also play a vital part in maintaining the body's acid-base balance by actively secreting hydrogen ions into the urine while reabsorbing bicarbonate from the urine back into the blood. They are also involved in the regulation of blood pressure through the renin-angiotensin-aldosterone system and contribute to erythrocyte production by releasing the hormone erythropoietin in response to low oxygen levels in the blood. Abnormalities or damage in renal epithelial cells often result in impaired kidney function, leading to various renal diseases." xsd:string {xref="DOI:10.1007/978-94-011-2354-9_6", xref="DOI:10.1007/s004670050586", xref="DOI:10.1016/B978-0-323-35775-3.00011-4", xref="DOI:10.1146/annurev-physiol-052521-121841", xref="DOI:10.1681/ASN.2012010029"} [Term] id: CL:1000450 name: epithelial cell of glomerular capsule def: "An epithelial cell that is part of the glomerular capsule." [GOC:tfm] subset: cellxgene_subset +subset: human_subset subset: kidney_upper_slim +subset: mouse_subset synonym: "Bowmans capsule epithelial cell" EXACT [] synonym: "epithelial cell of Bowman's capsule" EXACT [FMA:70966] xref: FMA:70966 @@ -1725,7 +1948,9 @@ name: kidney collecting duct epithelial cell def: "An epithelial cell that is part of the collecting duct of renal tubule." [GOC:tfm] subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset subset: kidney_upper_slim +subset: mouse_subset synonym: "epithelial cell of renal collecting tubule" EXACT [FMA:70982] xref: FMA:70982 xref: https://cellxgene.cziscience.com/cellguide/CL_1000454 @@ -1736,7 +1961,7 @@ is_a: CL:1001225 {is_inferred="true"} ! kidney collecting duct cell intersection_of: CL:0000066 ! epithelial cell intersection_of: part_of UBERON:0001232 ! collecting duct of renal tubule property_value: RO:0002175 NCBITaxon:9606 -property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional.\n\nKidney collecting duct epithelial cells are a specialized type of cells that form an integral part of the renal system. Located in the collecting duct system of the kidneys, these cells are responsible for one of the final steps in the process of urine formation, and they are instrumental in the fine tuning of the volume and composition of urine by reabsorbing water and certain solutes back into the bloodstream.\nThese cells express specific channels and carriers that actively and passively transport ions and water. They also have channels on their membranes, such as sodium channels and potassium channels, involved in reabsorbing or secreting these electrolytes depending upon the body's needs. The function of renal collecting duct epithelial cells can be regulated by a variety of hormones, including vasopressin (antidiuretic hormone), which can modulate the ion channels and carriers and hence indirectly influence body fluid homeostasis.\nAside from their function in ion and water balance, kidney collecting duct epithelial cells also aid in maintaining the body's acid-base balance. They have specialized functionality to secret hydrogen ions into the tubular lumen, which contributes to acid excretion. Any dysfunction may have serious implications and lead to various renal or systemic diseases, exemplifying the importance of these cells in maintaining overall body homeostasis." xsd:string {xref="DOI:10.1016/j.ajpath.2014.01.014", xref="DOI:10.1016/j.semnephrol.2019.04.005", xref="DOI:10.2215/CJN.05760513", xref="DOI:10.2215/CJN.08880914"} +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nKidney collecting duct epithelial cells are a specialized type of cells that form an integral part of the renal system. Located in the collecting duct system of the kidneys, these cells are responsible for one of the final steps in the process of urine formation, and they are instrumental in the fine tuning of the volume and composition of urine by reabsorbing water and certain solutes back into the bloodstream.\nThese cells express specific channels and carriers that actively and passively transport ions and water. They also have channels on their membranes, such as sodium channels and potassium channels, involved in reabsorbing or secreting these electrolytes depending upon the body's needs. The function of renal collecting duct epithelial cells can be regulated by a variety of hormones, including vasopressin (antidiuretic hormone), which can modulate the ion channels and carriers and hence indirectly influence body fluid homeostasis.\nAside from their function in ion and water balance, kidney collecting duct epithelial cells also aid in maintaining the body's acid-base balance. They have specialized functionality to secret hydrogen ions into the tubular lumen, which contributes to acid excretion. Any dysfunction may have serious implications and lead to various renal or systemic diseases, exemplifying the importance of these cells in maintaining overall body homeostasis." xsd:string {xref="DOI:10.1016/j.ajpath.2014.01.014", xref="DOI:10.1016/j.semnephrol.2019.04.005", xref="DOI:10.2215/CJN.05760513", xref="DOI:10.2215/CJN.08880914"} [Term] id: CL:1000494 @@ -1744,6 +1969,8 @@ name: nephron tubule epithelial cell def: "An epithelial cell that is part of a nephron tubule." [GOC:tfm] comment: This needs to be further defined as a juxtamedullary nephron. Will request the juxtamedullary nephron tubule class from UBERON. subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "kidney tubule epithelial cell" EXACT [] xref: FMA:86785 xref: KUPO:0001022 @@ -1758,6 +1985,8 @@ id: CL:1000497 name: kidney cell def: "A cell that is part of a kidney." [] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset xref: KUPO:0001010 xref: ZFA:0009389 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000255 ! eukaryotic cell @@ -1770,7 +1999,9 @@ id: CL:1000500 name: kidney interstitial cell def: "A cell that is part of kidney interstitium." [] subset: cellxgene_subset +subset: human_subset subset: kidney_upper_slim +subset: mouse_subset xref: KUPO:0001013 xref: ZFA:0009390 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:1000497 ! kidney cell @@ -1783,6 +2014,8 @@ relationship: part_of UBERON:0005215 ! kidney interstitium id: CL:1000504 name: kidney medulla cell def: "A cell that is part of a renal medulla." [PMID:22343825] +subset: human_subset +subset: mouse_subset xref: KUPO:0001017 xref: ZFA:0009391 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:1000497 ! kidney cell @@ -1794,7 +2027,9 @@ relationship: part_of UBERON:0000362 ! renal medulla id: CL:1000505 name: kidney pelvis cell def: "A cell that is part of a renal pelvis." [] +subset: human_subset subset: kidney_upper_slim +subset: mouse_subset xref: KUPO:0001018 is_a: CL:1000497 ! kidney cell intersection_of: CL:1000497 ! kidney cell @@ -1805,7 +2040,9 @@ relationship: part_of UBERON:0001224 ! renal pelvis id: CL:1000507 name: kidney tubule cell def: "A cell that is part of a nephron tubule." [] +subset: human_subset subset: kidney_upper_slim +subset: mouse_subset xref: KUPO:0001020 is_a: CL:1000497 ! kidney cell intersection_of: CL:1000497 ! kidney cell @@ -1817,6 +2054,8 @@ id: CL:1000510 name: kidney glomerular epithelial cell def: "Any kidney epithelial cell that is part of some glomerular epithelium." [FBC:Autogenerated] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset xref: KUPO:0001023 is_a: CL:1000746 ! glomerular cell intersection_of: CL:0002518 ! kidney epithelial cell @@ -1827,7 +2066,9 @@ relationship: part_of UBERON:0004188 ! glomerular epithelium id: CL:1000546 name: kidney medulla collecting duct epithelial cell def: "An epithelial cell that is part of a renal medulla collecting duct." [] +subset: human_subset subset: kidney_upper_slim +subset: mouse_subset xref: KUPO:0001060 is_a: CL:1000454 ! kidney collecting duct epithelial cell is_a: CL:1000504 ! kidney medulla cell @@ -1839,7 +2080,9 @@ relationship: part_of UBERON:0005185 ! renal medulla collecting duct id: CL:1000550 name: kidney papillary duct principal epithelial cell def: "Any kidney cell that is part of some papillary duct." [FBC:Autogenerated] +subset: human_subset subset: kidney_upper_slim +subset: mouse_subset xref: KUPO:0001064 is_a: CL:1001225 ! kidney collecting duct cell intersection_of: CL:1000497 ! kidney cell @@ -1850,7 +2093,9 @@ relationship: part_of UBERON:0005167 ! papillary duct id: CL:1000612 name: kidney corpuscule cell def: "Any renal cortical epithelial cell that is part of some renal corpuscle." [FBC:Autogenerated] +subset: human_subset subset: kidney_upper_slim +subset: mouse_subset xref: KUPO:0001021 is_a: CL:0002584 ! renal cortical epithelial cell is_a: CL:1000449 ! epithelial cell of nephron @@ -1863,6 +2108,8 @@ id: CL:1000615 name: kidney cortex tubule cell def: "Any kidney tubule cell that is part of some renal cortex tubule." [FBC:Autogenerated] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset xref: KUPO:0001024 is_a: CL:0002584 ! renal cortical epithelial cell is_a: CL:1000449 ! epithelial cell of nephron @@ -1875,7 +2122,9 @@ relationship: part_of UBERON:0006853 ! renal cortex tubule id: CL:1000618 name: juxtaglomerular complex cell def: "Any kidney cortical cell that is part of some juxtaglomerular apparatus." [FBC:Autogenerated] +subset: human_subset subset: kidney_upper_slim +subset: mouse_subset synonym: "juxtaglomerulus cell" EXACT [GO:0072052] xref: KUPO:0001028 is_a: CL:0002681 {is_inferred="true"} ! kidney cortical cell @@ -1889,6 +2138,8 @@ name: kidney interstitial fibroblast def: "A fibroblast that is part of an interstitial compartment of a kidney." [PMID:10559635] subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset xref: KUPO:0001102 is_a: CL:0000057 ! fibroblast is_a: CL:1000500 ! kidney interstitial cell @@ -1900,6 +2151,8 @@ property_value: RO:0002175 NCBITaxon:9606 id: CL:1000746 name: glomerular cell def: "Any kidney corpuscule cell that is part of some renal glomerulus." [FBC:Autogenerated] +subset: human_subset +subset: mouse_subset xref: KUPO:0001036 is_a: CL:1000612 ! kidney corpuscule cell intersection_of: CL:1000612 ! kidney corpuscule cell @@ -1912,7 +2165,10 @@ name: kidney connecting tubule epithelial cell def: "Any nephron tubule epithelial cell that is part of some renal connecting tubule." [FBC:Autogenerated] subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset subset: kidney_upper_slim +subset: mouse_subset +xref: https://cellxgene.cziscience.com/cellguide/CL_1000768 xref: KUPO:0001058 is_a: CL:1000494 {is_inferred="true"} ! nephron tubule epithelial cell is_a: CL:1000615 ! kidney cortex tubule cell @@ -1920,6 +2176,7 @@ intersection_of: CL:1000494 ! nephron tubule epithelial cell intersection_of: part_of UBERON:0005097 ! renal connecting tubule relationship: part_of UBERON:0005097 ! renal connecting tubule property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nKidney connecting tubule epithelial cells are found in collecting duct system of the kidney, specifically in at the interconnection segment between the nephron and the collecting ducts. The epithelial cells lining the connecting tubule are crucial for the journey of filtrate before it empties into urine-collecting ducts and therefore play a critical role in maintaining the body’s fluid and electrolyte balance.\nOne of the principal functions of connecting tubule epithelial cells involves the selective reabsorption and secretion of various solutes. This reabsorption process includes critical regulatory electrolytes such as sodium ions (Na+), chloride ions (Cl-), and bicarbonate ions (HCO3-), thus playing a role in the regulation of the acid-base homeostasis. Their function also involves the secretion of potassium ions (K+) into the renal tubular fluid.\nThe connecting tubule epithelial cells are primarily intercalated cells, which can be categorized into two types according to their specific functions: type A intercalated cells, which secrete acid, and the type B intercalated cells, which secrete base (bicarbonate) and reabsorb chloride. By regulating the concentrations of these ions, as well as reabsorption of water, connecting tubule epithelial cells contribute substantively to maintaining the body's electrolyte levels, pH balance, and overall homeostasis.\nIn addition to intercalating cells, the collecting duct system also has principal cells, which are characterized by the expression of the water channel AQP2. AQP2-expressing cells have also been identified in connecting tubules, but there is some controversy whether these represent a unique cell type as there are some morphologic differences compared with principal cells." xsd:string {xref="DOI:10.1002/cphy.c110052", xref="DOI:10.1007/s00418-021-02033-5", xref="DOI:10.1097/MNH.0b013e32820ac850", xref="DOI:10.1681/ASN.2019040415", xref="DOI:10.23876/j.krcp.2017.36.4.305"} [Term] id: CL:1000849 @@ -1927,18 +2184,24 @@ name: kidney distal convoluted tubule epithelial cell def: "Any epithelial cell of distal tubule that is part of some distal convoluted tubule." [FBC:Autogenerated] subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset subset: kidney_upper_slim +subset: mouse_subset +xref: https://cellxgene.cziscience.com/cellguide/CL_1000849 xref: KUPO:0001056 is_a: CL:0002305 {is_inferred="true"} ! epithelial cell of distal tubule intersection_of: CL:0002305 ! epithelial cell of distal tubule intersection_of: part_of UBERON:0001292 ! distal convoluted tubule relationship: part_of UBERON:0001292 ! distal convoluted tubule property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nKidney distal convoluted tubule epithelial cells, often referred to simply as distal convoluted tubule (DCT) cells, constitute a significant portion of the nephron -- the functional building unit of the kidney involved in filtration and reabsorption of substances from blood. The DCT epithelial cells form lining of the distal convoluted tubule, a segment of the nephron located after the loop of Henle and before the collecting tubule. These cells are characterized by unique morphological features such as small size, low height and fewer microvilli compared to proximal convoluted tubule epithelial cells. \nThese cells perform a host of vital functions contributing to the regulation of extracellular fluid volume and electrolyte balance, blood pressure and pH. While the DCT is less prominent in water and sodium reabsorption compared to the proximal tubule and the loop of Henle, it plays a crucial role in fine-tuning the process. DCT epithelial cells are responsible for the final adjustments of sodium, potassium and calcium reabsorption, thereby affecting overall fluid and electrolyte balance, blood pressure regulation and bone health. The reabsorption process is regulated by hormones including aldosterone and parathyroid hormone.\nThe distal convoluted tubule (DCT) also plays a significant role in acid-base homeostasis by secreting protons (H+) into the tubular fluid and reabsorbing bicarbonate ions (HCO3-), thus regulating the pH of the blood. The ability of DCT cells to adjust urine concentration plays a part in maintaining the body’s pH balance and preventing conditions like acidosis or alkalosis. In summary, kidney distal convoluted tubule epithelial cells perform functions that are crucial to maintaining body's homeostasis." xsd:string {xref="DOI:10.1002/cphy.c140002", xref="DOI:10.1007/s40620-021-01032-y", xref="DOI:10.1152/physrev.2000.80.1.277", xref="DOI:10.1681/ASN.2019040415", xref="DOI:10.2215/CJN.05920613"} [Term] id: CL:1000854 name: kidney blood vessel cell def: "A blood vessel cell that is part of a kidney." [PMID:34843404] +subset: human_subset +subset: mouse_subset xref: KUPO:0001014 is_a: CL:1000504 {is_inferred="true"} ! kidney medulla cell intersection_of: CL:0000000 ! cell @@ -1950,7 +2213,9 @@ relationship: participates_in GO:0008015 ! blood circulation id: CL:1000891 name: kidney arterial blood vessel cell def: "Any kidney blood vessel cell that is part of some kidney arterial blood vessel." [FBC:Autogenerated] +subset: human_subset subset: kidney_upper_slim +subset: mouse_subset xref: KUPO:0001029 is_a: CL:1000854 {is_inferred="true"} ! kidney blood vessel cell intersection_of: CL:1000854 ! kidney blood vessel cell @@ -1962,7 +2227,9 @@ id: CL:1000892 name: kidney capillary endothelial cell def: "An endothelial cell that is part of the capillary of the kidney." [] subset: cellxgene_subset +subset: human_subset subset: kidney_upper_slim +subset: mouse_subset xref: KUPO:0001030 is_a: CL:0002144 ! capillary endothelial cell is_a: CL:1000854 ! kidney blood vessel cell @@ -1974,7 +2241,9 @@ relationship: part_of UBERON:0003527 ! kidney capillary id: CL:1000893 name: kidney venous blood vessel cell def: "Any kidney blood vessel cell that is part of some renal vein." [FBC:Autogenerated] +subset: human_subset subset: kidney_upper_slim +subset: mouse_subset xref: KUPO:0001031 is_a: CL:1000854 {is_inferred="true"} ! kidney blood vessel cell intersection_of: CL:1000854 ! kidney blood vessel cell @@ -1986,6 +2255,8 @@ id: CL:1000909 name: kidney loop of Henle epithelial cell def: "Any nephron tubule epithelial cell that is part of some loop of Henle." [FBC:Autogenerated] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset xref: KUPO:0001047 is_a: CL:1000494 {is_inferred="true"} ! nephron tubule epithelial cell intersection_of: CL:1000494 ! nephron tubule epithelial cell @@ -1997,7 +2268,9 @@ id: CL:1001016 name: kidney loop of Henle ascending limb epithelial cell def: "Any kidney loop of Henle epithelial cell that is part of some ascending limb of loop of Henle." [FBC:Autogenerated] subset: cellxgene_subset +subset: human_subset subset: kidney_upper_slim +subset: mouse_subset xref: KUPO:0001048 is_a: CL:0002305 ! epithelial cell of distal tubule is_a: CL:1000909 {is_inferred="true"} ! kidney loop of Henle epithelial cell @@ -2009,18 +2282,24 @@ relationship: part_of UBERON:0005164 ! ascending limb of loop of Henle id: CL:1001021 name: kidney loop of Henle descending limb epithelial cell def: "Any kidney loop of Henle epithelial cell that is part of some descending limb of loop of Henle." [FBC:Autogenerated] +subset: human_subset subset: kidney_upper_slim +subset: mouse_subset +xref: https://cellxgene.cziscience.com/cellguide/CL_1001021 xref: KUPO:0001053 is_a: CL:1000909 {is_inferred="true"} ! kidney loop of Henle epithelial cell intersection_of: CL:1000909 ! kidney loop of Henle epithelial cell intersection_of: part_of UBERON:0001289 ! descending limb of loop of Henle relationship: part_of UBERON:0001289 ! descending limb of loop of Henle +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nThe kidney loop of Henle descending limb epithelial cells are highly specialized cells that play a crucial role in maintaining the body's salt and water balance. These cells line the descending limb of the loop of Henle, which is a portion of the renal tubule located in the kidneys, an organ responsible for filtering waste products, ions and extra water from the blood and converting them into urine. However, the descending limb epithelial cells are specifically involved in the countercurrent multiplication system, a mechanism to concentrate urine that involves both active and passive transport processes. \nThese cells are notably permeable to water but relatively impermeable to solutes, a characteristic that dramatically influences the osmotic gradient in the renal medulla. As filtrate initially descends down the loop of Henle, water gets drawn out due to the increasing osmotic gradient, thereby concentrating the filtrate. Additionally, these epithelial cells are exceptionally thin walled, allowing water to freely diffuse across the membrane.\nFurthermore, the kidney loop of Henle descending limb epithelial cells are inextricably linked to the functioning of numerous diuretic drugs, which work by blocking the reabsorption of water and certain electrolytes in the kidneys, leading to increased urine production to rid the body of excess fluids." xsd:string {xref="DOI:10.1007/s00360-018-1164-3", xref="DOI:10.1146/annurev-physiol-021113-170350", xref="DOI:10.1152/advan.00227.2022"} [Term] id: CL:1001225 name: kidney collecting duct cell def: "A cell that is part of a collecting duct of renal tubule." [] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset xref: KUPO:0001012 xref: Wikipedia:Kidney_collecting_duct_cell is_a: CL:1000497 ! kidney cell @@ -2034,6 +2313,8 @@ name: renal interstitial pericyte def: "A pericyte cell located in the kidney interstitium." [] subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset xref: KUPO:0001104 is_a: CL:0000669 {is_inferred="true"} ! pericyte is_a: CL:1000500 ! kidney interstitial cell @@ -2045,6 +2326,9 @@ property_value: RO:0002175 NCBITaxon:9606 id: CL:2000008 name: microvascular endothelial cell def: "Any blood vessel endothelial cell that is part of a microvascular endothelium." [GOC:TermGenie] +subset: cellxgene_subset +subset: human_subset +subset: mouse_subset is_a: CL:0000071 ! blood vessel endothelial cell intersection_of: CL:0000071 ! blood vessel endothelial cell intersection_of: part_of UBERON:0008339 ! microvascular endothelium @@ -2056,6 +2340,8 @@ creation_date: 2014-06-04T15:07:42Z id: CL:4030031 name: interstitial cell def: "Any cell that is located within the interstitium between the cells most prominent in defining a given tissue. \"Interstitial cell\" is a morphological term and refers to a variety of cells with differing origins and phenotypes." [PMID:24987007] +subset: human_subset +subset: mouse_subset is_a: CL:0000255 ! eukaryotic cell intersection_of: CL:0000000 ! cell intersection_of: part_of UBERON:0005169 ! interstitial tissue @@ -2066,6 +2352,9 @@ property_value: terms:date "2022-11-30T14:35:08Z" xsd:dateTime id: CL:4033054 name: perivascular cell def: "A cell that is adjacent to a vessel. A perivascular cell plays a crucial role in maintaining vascular function and tissue homeostasis. This cell type regulates vessel integrity and flow dynamics." [PMID:24928499, PMID:27889329] +subset: cellxgene_subset +subset: human_subset +subset: mouse_subset is_a: CL:0000000 ! cell intersection_of: CL:0000000 ! cell intersection_of: adjacent_to UBERON:0002049 ! vasculature @@ -2077,7 +2366,6 @@ property_value: terms:date "2023-08-22T13:40:28Z" xsd:dateTime id: GO:0000278 name: mitotic cell cycle namespace: biological_process -alt_id: GO:0007067 def: "Progression through the phases of the mitotic cell cycle, the most common eukaryotic cell cycle, which canonically comprises four successive phases called G1, S, G2, and M and includes replication of the genome and the subsequent segregation of chromosomes into daughter cells. In some variant cell cycles nuclear replication or nuclear division may not be followed by cell division, or G1 and G2 phases may be absent." [GOC:mah, ISBN:0815316194] comment: Note that this term should not be confused with 'GO:0140014 ; mitotic nuclear division'. 'GO:0000278 ; mitotic cell cycle represents the entire mitotic cell cycle, while 'GO:0140014 ; mitotic nuclear division' specifically represents the actual nuclear division step of the mitotic cell cycle. subset: goslim_chembl @@ -2109,16 +2397,13 @@ relationship: results_in_fission_of GO:0005634 ! nucleus id: GO:0000785 name: chromatin namespace: cellular_component -alt_id: GO:0000789 -alt_id: GO:0000790 -alt_id: GO:0005717 def: "The ordered and organized complex of DNA, protein, and sometimes RNA, that forms the chromosome." [GOC:elh, PMID:20404130] comment: Chromosomes include parts that are not part of the chromatin. Examples include the kinetochore. synonym: "chromosome scaffold" RELATED [] synonym: "cytoplasmic chromatin" NARROW [] synonym: "nuclear chromatin" NARROW [] xref: NIF_Subcellular:sao1615953555 -is_a: GO:0110165 ! cellular anatomical entity +is_a: GO:0110165 ! cellular anatomical structure relationship: part_of GO:0005694 ! chromosome property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28301" xsd:anyURI @@ -2126,8 +2411,6 @@ property_value: term_tracker_item "https://github.com/geneontology/go-ontology/i id: GO:0000792 name: heterochromatin namespace: cellular_component -alt_id: GO:0005720 -alt_id: GO:0035328 def: "A compact and highly condensed form of chromatin that is refractory to transcription." [PMID:32017156] synonym: "nuclear heterochromatin" NARROW [] synonym: "transcriptionally inactive chromatin" EXACT [] @@ -2224,7 +2507,6 @@ relationship: part_of GO:0016331 ! morphogenesis of embryonic epithelium id: GO:0001841 name: neural tube formation namespace: biological_process -alt_id: GO:0001679 def: "The formation of a tube from the flat layer of ectodermal cells known as the neural plate. This will give rise to the central nervous system." [GOC:dph, ISBN:0878932437] synonym: "neural tube morphogenesis" EXACT [GOC:dph] synonym: "neurulation" EXACT [] @@ -2463,7 +2745,6 @@ relationship: part_of GO:0003091 ! renal water homeostasis id: GO:0005575 name: cellular_component namespace: cellular_component -alt_id: GO:0008372 def: "A location, relative to cellular compartments and structures, occupied by a macromolecular machine. There are three types of cellular components described in the gene ontology: (1) the cellular anatomical entity where a gene product carries out a molecular function (e.g., plasma membrane, cytoskeleton) or membrane-enclosed compartments (e.g., mitochondrion); (2) virion components, where viral proteins act, and (3) the stable macromolecular complexes of which gene product are parts (e.g., the clathrin complex)." [GOC:pdt] comment: Note that, in addition to forming the root of the cellular component ontology, this term is recommended for the annotation of gene products whose cellular component is unknown. When this term is used for annotation, it indicates that no information was available about the cellular component of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this. subset: goslim_candida @@ -2501,7 +2782,7 @@ subset: goslim_prokaryote_ribbon subset: goslim_yeast synonym: "extracellular" EXACT [] xref: Wikipedia:Extracellular -is_a: GO:0110165 ! cellular anatomical entity +is_a: GO:0110165 ! cellular anatomical structure [Term] id: GO:0005577 @@ -2538,8 +2819,6 @@ is_a: GO:0098651 ! basement membrane collagen trimer id: GO:0005604 name: basement membrane namespace: cellular_component -alt_id: GO:0005605 -alt_id: GO:0008003 def: "A collagen-containing extracellular matrix consisting of a thin layer of dense material found in various animal tissues interposed between the cells and the adjacent connective tissue. It consists of the basal lamina plus an associated layer of reticulin fibers." [ISBN:0198547684, PMID:22505934] comment: Note that this term has no relationship to 'membrane ; GO:0016020' because the basement membrane is not a lipid bilayer. synonym: "basal lamina" RELATED [] @@ -2559,7 +2838,7 @@ subset: goslim_drosophila subset: goslim_generic synonym: "intercellular space" RELATED [] xref: NIF_Subcellular:sao1425028079 -is_a: GO:0110165 ! cellular anatomical entity +is_a: GO:0110165 ! cellular anatomical structure relationship: part_of GO:0005576 ! extracellular region [Term] @@ -2577,7 +2856,7 @@ synonym: "nucleocytoplasm" RELATED [GOC:mah] synonym: "protoplasm" EXACT [] synonym: "protoplast" RELATED [GOC:mah] xref: Wikipedia:Intracellular -is_a: GO:0110165 ! cellular anatomical entity +is_a: GO:0110165 ! cellular anatomical structure relationship: part_of CL:0000000 ! cell property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/17776" xsd:anyURI @@ -2629,7 +2908,7 @@ synonym: "chromatid" RELATED [] synonym: "interphase chromosome" NARROW [] synonym: "prophase chromosome" NARROW [] xref: Wikipedia:Chromosome -is_a: GO:0043232 ! intracellular non-membrane-bounded organelle +is_a: GO:0043232 ! intracellular membraneless organelle [Term] id: GO:0005730 @@ -2645,7 +2924,7 @@ subset: goslim_plant subset: goslim_yeast xref: NIF_Subcellular:sao1820400233 xref: Wikipedia:Nucleolus -is_a: GO:0043232 ! intracellular non-membrane-bounded organelle +is_a: GO:0043232 ! intracellular membraneless organelle relationship: part_of GO:0031981 ! nuclear lumen [Term] @@ -2663,7 +2942,7 @@ subset: goslim_prokaryote subset: goslim_prokaryote_ribbon subset: goslim_yeast xref: Wikipedia:Cytoplasm -is_a: GO:0110165 ! cellular anatomical entity +is_a: GO:0110165 ! cellular anatomical structure relationship: part_of GO:0005622 ! intracellular anatomical structure property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/23023" xsd:anyURI @@ -2671,7 +2950,6 @@ property_value: term_tracker_item "https://github.com/geneontology/go-ontology/i id: GO:0005840 name: ribosome namespace: cellular_component -alt_id: GO:0033279 def: "An intracellular organelle, about 200 A in diameter, consisting of RNA and protein. It is the site of protein biosynthesis resulting from translation of messenger RNA (mRNA). It consists of two subunits, one large and one small, each containing only protein and RNA. Both the ribosome and its subunits are characterized by their sedimentation coefficients, expressed in Svedberg units (symbol: S). Hence, the prokaryotic ribosome (70S) comprises a large (50S) subunit and a small (30S) subunit, while the eukaryotic ribosome (80S) comprises a large (60S) subunit and a small (40S) subunit. Two sites on the ribosomal large subunit are involved in translation, namely the aminoacyl site (A site) and peptidyl site (P site). Ribosomes from prokaryotes, eukaryotes, mitochondria, and chloroplasts have characteristically distinct ribosomal proteins." [ISBN:0198506732] subset: goslim_candida subset: goslim_chembl @@ -2689,16 +2967,14 @@ synonym: "membrane bound ribosome" NARROW [NIF_Subcellular:sao1291545653] synonym: "ribosomal RNA" RELATED [] xref: NIF_Subcellular:sao1429207766 xref: Wikipedia:Ribosome -is_a: GO:0043232 ! intracellular non-membrane-bounded organelle -is_a: PR:000050567 ! protein-containing material entity +is_a: GO:0043232 ! intracellular membraneless organelle relationship: capable_of_part_of GO:0006412 ! translation +relationship: has_part PR:000000001 ! protein [Term] id: GO:0005886 name: plasma membrane namespace: cellular_component -alt_id: GO:0005887 -alt_id: GO:0005904 def: "The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins." [ISBN:0716731363] subset: goslim_agr subset: goslim_candida @@ -2744,9 +3020,6 @@ property_value: term_tracker_item "https://github.com/geneontology/go-ontology/i id: GO:0006412 name: translation namespace: biological_process -alt_id: GO:0006416 -alt_id: GO:0006453 -alt_id: GO:0043037 def: "The cellular metabolic process in which a protein is formed, using the sequence of a mature mRNA or circRNA molecule to specify the sequence of amino acids in a polypeptide chain. Translation is mediated by the ribosome, and begins with the formation of a ternary complex between aminoacylated initiator methionine tRNA, GTP, and initiation factor 2, which subsequently associates with the small subunit of the ribosome and an mRNA or circRNA. Translation ends with the release of a polypeptide chain from the ribosome." [GOC:go_curators] subset: goslim_candida subset: goslim_chembl @@ -2775,15 +3048,13 @@ relationship: starts_with GO:0006413 ! translational initiation id: GO:0006413 name: translational initiation namespace: biological_process -alt_id: GO:0006440 -alt_id: GO:0006454 def: "The process preceding formation of the peptide bond between the first two amino acids of a protein. This includes the formation of a complex of the ribosome, mRNA or circRNA, and an initiation complex that contains the first aminoacyl-tRNA." [ISBN:019879276X] subset: goslim_yeast synonym: "biopolymerisation" BROAD [] synonym: "biopolymerization" BROAD [] synonym: "protein synthesis initiation" BROAD [] synonym: "translation initiation" EXACT [] -is_a: GO:0044237 ! cellular metabolic process +is_a: GO:0008152 ! metabolic process relationship: part_of GO:0006412 ! translation relationship: starts_with GO:0001677 ! formation of translation initiation ternary complex @@ -2791,8 +3062,6 @@ relationship: starts_with GO:0001677 ! formation of translation initiation terna id: GO:0006414 name: translational elongation namespace: biological_process -alt_id: GO:0006442 -alt_id: GO:0006455 def: "The successive addition of amino acid residues to a nascent polypeptide chain during protein biosynthesis." [GOC:ems] subset: goslim_yeast synonym: "protein synthesis elongation" BROAD [] @@ -2804,8 +3073,6 @@ relationship: part_of GO:0006412 ! translation id: GO:0006415 name: translational termination namespace: biological_process -alt_id: GO:0006443 -alt_id: GO:0006456 def: "The process resulting in the release of a polypeptide chain from the ribosome, usually in response to a termination codon (UAA, UAG, or UGA in the universal genetic code)." [GOC:hjd, ISBN:019879276X] synonym: "protein synthesis termination" BROAD [] synonym: "translation termination" EXACT [] @@ -2817,9 +3084,6 @@ relationship: part_of GO:0006412 ! translation id: GO:0006810 name: transport namespace: biological_process -alt_id: GO:0015457 -alt_id: GO:0015460 -alt_id: GO:0044765 def: "The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter or a transporter complex, a pore or a motor protein." [GOC:dos, GOC:dph, GOC:jl, GOC:mah] comment: Note that this term should not be used for direct annotation. It should be possible to make a more specific annotation to one of the children of this term, for e.g. to transmembrane transport, to microtubule-based transport or to vesicle-mediated transport. subset: gocheck_do_not_annotate @@ -2834,7 +3098,6 @@ subset: goslim_prokaryote_ribbon synonym: "single-organism transport" RELATED [] is_a: GO:0051234 ! establishment of localization property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/20292" xsd:anyURI -created_by: jl creation_date: 2012-12-13T16:25:32Z [Term] @@ -2859,8 +3122,6 @@ is_a: GO:0042044 ! fluid transport id: GO:0006915 name: apoptotic process namespace: biological_process -alt_id: GO:0006917 -alt_id: GO:0008632 def: "A programmed cell death process which begins when a cell receives an internal (e.g. DNA damage) or external signal (e.g. an extracellular death ligand), and proceeds through a series of biochemical events (signaling pathway phase) which trigger an execution phase. The execution phase is the last step of an apoptotic process, and is typically characterized by rounding-up of the cell, retraction of pseudopodes, reduction of cellular volume (pyknosis), chromatin condensation, nuclear fragmentation (karyorrhexis), plasma membrane blebbing and fragmentation of the cell into apoptotic bodies. When the execution phase is completed, the cell has died." [GOC:cjm, GOC:dhl, GOC:ecd, GOC:go_curators, GOC:mtg_apoptosis, GOC:tb, ISBN:0198506732, PMID:18846107, PMID:21494263] synonym: "activation of apoptosis" NARROW [] synonym: "apoptosis" NARROW [] @@ -2914,7 +3175,6 @@ relationship: occurs_in UBERON:0002385 ! muscle tissue id: GO:0006996 name: organelle organization namespace: biological_process -alt_id: GO:1902589 def: "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of an organelle within a cell. An organelle is an organized structure of distinctive morphology and function. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton. Excludes the plasma membrane." [GOC:mah] comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. subset: gocheck_do_not_annotate @@ -2929,7 +3189,6 @@ intersection_of: GO:0016043 ! cellular component organization intersection_of: results_in_organization_of GO:0043226 ! organelle relationship: results_in_organization_of GO:0043226 ! organelle property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27189" xsd:anyURI -created_by: jl creation_date: 2013-12-19T15:25:51Z [Term] @@ -2973,11 +3232,6 @@ is_a: GO:0009987 ! cellular process id: GO:0007165 name: signal transduction namespace: biological_process -alt_id: GO:0023014 -alt_id: GO:0023015 -alt_id: GO:0023016 -alt_id: GO:0023033 -alt_id: GO:0023045 def: "The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell." [GOC:go_curators, GOC:mtg_signaling_feb11] comment: Note that signal transduction is defined broadly to include a ligand interacting with a receptor, downstream signaling steps and a response being triggered. A change in form of the signal in every step is not necessary. Note that in many cases the end of this process is regulation of the initiation of transcription. Note that specific transcription factors may be annotated to this term, but core/general transcription machinery such as RNA polymerase should not. subset: goslim_candida @@ -3040,7 +3294,6 @@ property_value: term_tracker_item "https://github.com/geneontology/go-ontology/i id: GO:0007276 name: gamete generation namespace: biological_process -alt_id: GO:0009552 def: "The generation and maintenance of gametes in a multicellular organism. A gamete is a haploid reproductive cell." [GOC:ems, GOC:mtg_sensu] synonym: "gametogenesis" RELATED [] is_a: GO:0048609 ! multicellular organismal reproductive process @@ -3129,7 +3382,6 @@ property_value: term_tracker_item "https://github.com/geneontology/go-ontology/i id: GO:0008015 name: blood circulation namespace: biological_process -alt_id: GO:0070261 def: "The flow of blood through the body of an animal, enabling the transport of nutrients to the tissues and the removal of waste products." [GOC:mtg_heart, ISBN:0192800825] subset: goslim_pir synonym: "hemolymph circulation" RELATED [] @@ -3139,9 +3391,6 @@ is_a: GO:0003013 ! circulatory system process id: GO:0008104 name: protein localization namespace: biological_process -alt_id: GO:0008105 -alt_id: GO:0016249 -alt_id: GO:0034613 def: "Any process in which a protein is transported to, or maintained in, a specific location." [GOC:ai] subset: goslim_drosophila synonym: "asymmetric protein localisation" RELATED [GOC:mah] @@ -3162,9 +3411,6 @@ property_value: term_tracker_item "https://github.com/geneontology/go-ontology/i id: GO:0008150 name: biological_process namespace: biological_process -alt_id: GO:0000004 -alt_id: GO:0007582 -alt_id: GO:0044699 def: "A biological process is the execution of a genetically-encoded biological module or program. It consists of all the steps required to achieve the specific biological objective of the module. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence." [GOC:pdt] comment: Note that, in addition to forming the root of the biological process ontology, this term is recommended for the annotation of gene products whose biological process is unknown. When this term is used for annotation, it indicates that no information was available about the biological process of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this. subset: goslim_candida @@ -3180,16 +3426,13 @@ synonym: "single organism process" RELATED [] synonym: "single-organism process" RELATED [] xref: Wikipedia:Biological_process property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/24968" xsd:anyURI -created_by: jl creation_date: 2012-09-19T15:05:24Z [Term] id: GO:0008152 name: metabolic process namespace: biological_process -alt_id: GO:0044236 -alt_id: GO:0044710 -def: "The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation." [GOC:go_curators, ISBN:0198547684] +def: "A cellular process consisting of the biochemical pathways by which a living organism transforms chemical substances. This includes including anabolism (biosynthetic process) and catabolism (catabolic process). Metabolic processes includes the transformation of small molecules, as well macromolecular processes such as DNA repair and replication, protein synthesis and degradation." [GOC:go_curators, ISBN:0198547684] comment: Note that metabolic processes do not include single functions or processes such as protein-protein interactions, protein-nucleic acids, nor receptor-ligand interactions. subset: gocheck_do_not_annotate subset: goslim_chembl @@ -3198,16 +3441,12 @@ subset: goslim_metagenomics subset: goslim_pir subset: goslim_plant subset: goslim_prokaryote_ribbon -synonym: "metabolic process resulting in cell growth" NARROW [] synonym: "metabolism" EXACT [] -synonym: "metabolism resulting in cell growth" NARROW [] -synonym: "multicellular organism metabolic process" NARROW [] -synonym: "single-organism metabolic process" RELATED [] xref: Wikipedia:Metabolism -is_a: GO:0008150 ! biological_process +is_a: GO:0009987 ! cellular process disjoint_from: GO:0051179 ! localization property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/26424" xsd:anyURI -created_by: jl +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28932" xsd:anyURI creation_date: 2012-10-17T15:46:40Z [Term] @@ -3238,9 +3477,7 @@ property_value: term_tracker_item "https://github.com/geneontology/go-ontology/i id: GO:0009058 name: biosynthetic process namespace: biological_process -alt_id: GO:0044274 -alt_id: GO:0044711 -def: "The chemical reactions and pathways resulting in the formation of substances; typically the energy-requiring part of metabolism in which simpler substances are transformed into more complex ones." [GOC:curators, ISBN:0198547684] +def: "A cellular process consisting of the biochemical pathways by which a living organism synthesizes chemical substances. This typically represents the energy-requiring part of metabolism in which simpler substances are transformed into more complex ones." [GOC:curators, ISBN:0198547684] subset: goslim_chembl subset: goslim_metagenomics subset: goslim_plant @@ -3253,14 +3490,13 @@ synonym: "single-organism biosynthetic process" RELATED [] synonym: "synthesis" EXACT [] xref: Wikipedia:Anabolism is_a: GO:0008152 ! metabolic process -created_by: jl +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28932" xsd:anyURI creation_date: 2012-10-17T15:52:18Z [Term] id: GO:0009059 name: macromolecule biosynthetic process namespace: biological_process -alt_id: GO:0043284 def: "The chemical reactions and pathways resulting in the formation of a macromolecule, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass." [GOC:mah] comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. subset: gocheck_do_not_annotate @@ -3270,8 +3506,8 @@ synonym: "macromolecule anabolism" EXACT [] synonym: "macromolecule biosynthesis" EXACT [] synonym: "macromolecule formation" EXACT [] synonym: "macromolecule synthesis" EXACT [] +is_a: GO:0009058 ! biosynthetic process is_a: GO:0043170 ! macromolecule metabolic process -is_a: GO:0044249 ! cellular biosynthetic process property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/15249" xsd:anyURI property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/25418" xsd:anyURI property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27189" xsd:anyURI @@ -3280,8 +3516,6 @@ property_value: term_tracker_item "https://github.com/geneontology/go-ontology/i id: GO:0009306 name: protein secretion namespace: biological_process -alt_id: GO:0045166 -alt_id: GO:0045731 def: "The controlled release of proteins from a cell." [GOC:ai] synonym: "glycoprotein secretion" NARROW [] synonym: "protein secretion during cell fate commitment" NARROW [] @@ -3325,7 +3559,6 @@ relationship: part_of GO:0048856 ! anatomical structure development id: GO:0009790 name: embryo development namespace: biological_process -alt_id: GO:0009795 def: "The process whose specific outcome is the progression of an embryo from its formation until the end of its embryonic life stage. The end of the embryonic stage is organism-specific. For example, for mammals, the process would begin with zygote formation and end with birth. For insects, the process would begin at zygote formation and end with larval hatching. For plant zygotic embryos, this would be from zygote formation to the end of seed dormancy. For plant vegetative embryos, this would be from the initial determination of the cell or group of cells to form an embryo until the point when the embryo becomes independent of the parent plant." [GOC:go_curators, GOC:isa_complete, GOC:mtg_sensu] subset: gocheck_do_not_annotate subset: goslim_chembl @@ -3382,9 +3615,6 @@ property_value: RO:0002161 NCBITaxon:4891 id: GO:0009987 name: cellular process namespace: biological_process -alt_id: GO:0008151 -alt_id: GO:0044763 -alt_id: GO:0050875 def: "Any process that is carried out at the cellular level, but not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level." [GOC:go_curators, GOC:isa_complete] comment: This term should not be used for direct annotation. It should be possible to make a more specific annotation to one of the children of this term. subset: gocheck_do_not_annotate @@ -3394,7 +3624,6 @@ synonym: "cell physiology" EXACT [] synonym: "cellular physiological process" EXACT [] synonym: "single-organism cellular process" RELATED [] is_a: GO:0008150 ! biological_process -created_by: jl creation_date: 2012-12-11T16:56:55Z [Term] @@ -3412,7 +3641,6 @@ property_value: term_tracker_item "https://github.com/geneontology/go-ontology/i id: GO:0012501 name: programmed cell death namespace: biological_process -alt_id: GO:0016244 def: "A process which begins when a cell receives an internal or external signal and activates a series of biochemical events (signaling pathway). The process ends with the death of the cell." [GOC:lr, GOC:mtg_apoptosis] comment: Note that this term should be used to annotate gene products in the organism undergoing the programmed cell death. To annotate genes in another organism whose products modulate programmed cell death in a host organism, consider the term 'modulation by symbiont of host programmed cell death ; GO:0052040'. Also, note that 'programmed cell death ; GO:0012501' should be used to refer to instances of caspase-independent cell death mechanisms, in the absence of further indications on the process taking place. At present, caspase-independent cell death is not yet represented in GO due to the lack of consensus and in-depth research on the topic. 'programmed cell death ; GO:0012501' may also be used to annotate gene products in taxa where apoptosis as defined in GO:0006915 does not occur, such as plants. You may also consider these specific children: GO:0097468 'programmed cell death in response to reactive oxygen species' (with descendants GO:0010421 'hydrogen peroxide-mediated programmed cell death' and GO:0010343 'singlet oxygen-mediated programmed cell death'), and GO:0009626 'plant-type hypersensitive response' and its children. subset: goslim_agr @@ -3442,7 +3670,6 @@ property_value: term_tracker_item "https://github.com/geneontology/go-ontology/i id: GO:0015031 name: protein transport namespace: biological_process -alt_id: GO:0015831 def: "The directed movement of proteins into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:ai] subset: goslim_chembl subset: goslim_pir @@ -3472,9 +3699,6 @@ is_a: GO:0015669 ! gas transport id: GO:0016020 name: membrane namespace: cellular_component -alt_id: GO:0016021 -alt_id: GO:0098589 -alt_id: GO:0098805 def: "A lipid bilayer along with all the proteins and protein complexes embedded in it and attached to it." [GOC:dos, GOC:mah, ISBN:0815316194] subset: goslim_candida subset: goslim_chembl @@ -3491,7 +3715,7 @@ synonym: "transmembrane" RELATED [GOC:mah] synonym: "whole membrane" NARROW [] xref: Wikipedia:Biological_membrane xref: Wikipedia:Transmembrane_protein -is_a: GO:0110165 ! cellular anatomical entity +is_a: GO:0110165 ! cellular anatomical structure disjoint_from: GO:0031012 ! extracellular matrix creation_date: 2014-03-06T11:37:54Z @@ -3499,8 +3723,6 @@ creation_date: 2014-03-06T11:37:54Z id: GO:0016043 name: cellular component organization namespace: biological_process -alt_id: GO:0044235 -alt_id: GO:0071842 def: "A process that results in the assembly, arrangement of constituent parts, or disassembly of a cellular component." [GOC:ai, GOC:jl, GOC:mah] subset: gocheck_do_not_annotate subset: goslim_agr @@ -3581,9 +3803,6 @@ relationship: part_of GO:0007154 ! cell communication id: GO:0019538 name: protein metabolic process namespace: biological_process -alt_id: GO:0006411 -alt_id: GO:0044267 -alt_id: GO:0044268 def: "The chemical reactions and pathways involving a protein. Includes protein modification." [GOC:ma] comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. subset: gocheck_do_not_annotate @@ -3646,7 +3865,6 @@ relationship: part_of GO:0007049 ! cell cycle id: GO:0022411 name: cellular component disassembly namespace: biological_process -alt_id: GO:0071845 def: "A cellular process that results in the breakdown of a cellular component." [GOC:isa_complete] comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. subset: gocheck_do_not_annotate @@ -3664,7 +3882,6 @@ property_value: term_tracker_item "https://github.com/geneontology/go-ontology/i id: GO:0022414 name: reproductive process namespace: biological_process -alt_id: GO:0044702 def: "A biological process that directly contributes to the process of producing new individuals by one or two organisms. The new individuals inherit some proportion of their genetic material from the parent or parents." [GOC:dph, GOC:isa_complete] subset: gocheck_do_not_annotate subset: goslim_agr @@ -3678,7 +3895,6 @@ synonym: "single organism reproductive process" RELATED [] xref: Wikipedia:Reproduction is_a: GO:0008150 ! biological_process property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27054" xsd:anyURI -created_by: jl creation_date: 2012-09-19T15:56:06Z [Term] @@ -3696,7 +3912,6 @@ relationship: part_of GO:0007586 ! digestion id: GO:0022607 name: cellular component assembly namespace: biological_process -alt_id: GO:0071844 def: "The aggregation, arrangement and bonding together of a cellular component." [GOC:isa_complete] subset: goslim_chembl subset: goslim_euk_cellular_processes_ribbon @@ -3738,8 +3953,6 @@ relationship: results_in_assembly_of GO:1990904 ! ribonucleoprotein complex id: GO:0023052 name: signaling namespace: biological_process -alt_id: GO:0023046 -alt_id: GO:0044700 def: "The entirety of a process in which information is transmitted within a biological system. This process begins with an active signal and ends when a cellular response has been triggered." [GOC:mtg_signal, GOC:mtg_signaling_feb11, GOC:signaling] comment: Note that a signal is any variable property or parameter that serves to convey information, and may be a physical entity such as a gene product or small molecule, a photon, or a change in state such as movement or voltage change. subset: goslim_agr @@ -3757,7 +3970,6 @@ synonym: "signalling" EXACT [] synonym: "signalling process" RELATED [GOC:mah] synonym: "single organism signaling" RELATED [] is_a: GO:0050789 ! regulation of biological process -created_by: jl creation_date: 2010-02-16T09:30:50Z [Term] @@ -3809,7 +4021,7 @@ subset: goslim_agr subset: goslim_drosophila subset: goslim_flybase_ribbon xref: Wikipedia:Cell_junction -is_a: GO:0110165 ! cellular anatomical entity +is_a: GO:0110165 ! cellular anatomical structure property_value: RO:0002161 NCBITaxon:4751 [Term] @@ -3891,7 +4103,6 @@ relationship: results_in_acquisition_of_features_of CL:0000556 ! megakaryocyte id: GO:0030261 name: chromosome condensation namespace: biological_process -alt_id: GO:0000068 def: "The progressive compaction of dispersed interphase chromatin into threadlike chromosomes prior to mitotic or meiotic nuclear division, or during apoptosis, in eukaryotic cells." [GOC:mah, ISBN:0815316194] synonym: "DNA condensation" BROAD [Wikipedia:DNA_condensation] synonym: "eukaryotic chromosome condensation" EXACT [GOC:bf] @@ -3927,7 +4138,7 @@ subset: goslim_drosophila subset: goslim_generic subset: goslim_pir subset: goslim_plant -is_a: GO:0110165 ! cellular anatomical entity +is_a: GO:0110165 ! cellular anatomical structure relationship: part_of CL:0000000 ! cell relationship: part_of GO:0071944 ! cell periphery @@ -3935,7 +4146,6 @@ relationship: part_of GO:0071944 ! cell periphery id: GO:0031012 name: extracellular matrix namespace: cellular_component -alt_id: GO:0005578 def: "A structure lying external to one or more cells, which provides structural support, biochemical or biomechanical cues for cells or tissues." [GOC:BHF, GOC:mah, GOC:rph, NIF_Subcellular:nlx_subcell_20090513, PMID:21123617, PMID:28089324] subset: goslim_chembl subset: goslim_drosophila @@ -3956,7 +4166,7 @@ id: GO:0031974 name: membrane-enclosed lumen namespace: cellular_component def: "The enclosed volume within a sealed membrane or between two sealed membranes. Encompasses the volume enclosed by the membranes of a particular organelle, e.g. endoplasmic reticulum lumen, or the space between the two lipid bilayers of a double membrane surrounding an organelle, e.g. nuclear envelope lumen." [GOC:add, GOC:mah] -is_a: GO:0110165 ! cellular anatomical entity +is_a: GO:0110165 ! cellular anatomical structure disjoint_from: GO:0045202 ! synapse [Term] @@ -3971,7 +4181,6 @@ relationship: part_of GO:0005634 ! nucleus id: GO:0031982 name: vesicle namespace: cellular_component -alt_id: GO:0031988 def: "Any small, fluid-filled, spherical organelle enclosed by membrane." [GOC:mah, GOC:pz, GOC:vesicles] subset: goslim_pir synonym: "membrane-bounded vesicle" RELATED [] @@ -4009,8 +4218,6 @@ relationship: results_in_assembly_of GO:0032059 ! bleb id: GO:0032501 name: multicellular organismal process namespace: biological_process -alt_id: GO:0044707 -alt_id: GO:0050874 def: "Any biological process, occurring at the level of a multicellular organism, pertinent to its function." [GOC:curators, GOC:dph, GOC:isa_complete, GOC:tb] comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. subset: gocheck_do_not_annotate @@ -4023,14 +4230,12 @@ property_value: RO:0002161 NCBITaxon:2157 property_value: RO:0002161 NCBITaxon:4896 property_value: RO:0002161 NCBITaxon:4932 property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27189" xsd:anyURI -created_by: jl creation_date: 2012-09-19T16:07:47Z [Term] id: GO:0032502 name: developmental process namespace: biological_process -alt_id: GO:0044767 def: "A biological process whose specific outcome is the progression of an integrated living unit: an anatomical structure (which may be a subcellular structure, cell, tissue, or organ), or organism over time from an initial condition to a later condition." [GOC:isa_complete] subset: goslim_agr subset: goslim_flybase_ribbon @@ -4038,7 +4243,6 @@ subset: goslim_pir synonym: "development" NARROW [] synonym: "single-organism developmental process" RELATED [] is_a: GO:0008150 ! biological_process -created_by: jl creation_date: 2012-12-19T12:21:31Z [Term] @@ -4055,9 +4259,6 @@ is_a: GO:0140352 ! export from cell id: GO:0032984 name: protein-containing complex disassembly namespace: biological_process -alt_id: GO:0034623 -alt_id: GO:0043241 -alt_id: GO:0043624 def: "The disaggregation of a protein-containing macromolecular complex into its constituent components." [GOC:mah] synonym: "cellular macromolecule complex disassembly" RELATED [] synonym: "cellular protein complex disassembly" RELATED [] @@ -4074,7 +4275,6 @@ property_value: term_tracker_item "https://github.com/geneontology/go-ontology/i id: GO:0032991 name: protein-containing complex namespace: cellular_component -alt_id: GO:0043234 def: "A stable assembly of two or more macromolecules, i.e. proteins, nucleic acids, carbohydrates or lipids, in which at least one component is a protein and the constituent parts function together." [GOC:dos, GOC:mah] comment: A protein complex in this context is meant as a stable set of interacting proteins which can be co-purified by an acceptable method, and where the complex has been shown to exist as an isolated, functional unit in vivo. Acceptable experimental methods include stringent protein purification followed by detection of protein interaction. The following methods should be considered non-acceptable: simple immunoprecipitation, pull-down experiments from cell extracts without further purification, colocalization and 2-hybrid screening. Interactions that should not be captured as protein complexes include: 1) enzyme/substrate, receptor/ligand or any similar transient interactions, unless these are a critical part of the complex assembly or are required e.g. for the receptor to be functional; 2) proteins associated in a pull-down/co-immunoprecipitation assay with no functional link or any evidence that this is a defined biological entity rather than a loose-affinity complex; 3) any complex where the only evidence is based on genetic interaction data; 4) partial complexes, where some subunits (e.g. transmembrane ones) cannot be expressed as recombinant proteins and are excluded from experiments (in this case, independent evidence is necessary to find out the composition of the full complex, if known). Interactions that may be captured as protein complexes include: 1) enzyme/substrate or receptor/ligand if the complex can only assemble and become functional in the presence of both classes of subunits; 2) complexes where one of the members has not been shown to be physically linked to the other(s), but is a homologue of, and has the same functionality as, a protein that has been experimentally demonstrated to form a complex with the other member(s); 3) complexes whose existence is accepted based on localization and pharmacological studies, but for which experimental evidence is not yet available for the complex as a whole. subset: goslim_agr @@ -4089,8 +4289,8 @@ synonym: "protein complex" NARROW [] synonym: "protein containing complex" EXACT [] synonym: "protein-protein complex" NARROW [] is_a: GO:0005575 ! cellular_component -is_a: PR:000050567 ! protein-containing material entity -disjoint_from: GO:0110165 ! cellular anatomical entity +disjoint_from: GO:0110165 ! cellular anatomical structure +relationship: has_part PR:000000001 ! protein [Term] id: GO:0033036 @@ -4117,7 +4317,6 @@ relationship: acts_on_population_of CL:0000232 ! erythrocyte id: GO:0034220 name: monoatomic ion transmembrane transport namespace: biological_process -alt_id: GO:0099131 def: "A process in which a monoatomic ion is transported across a membrane. Monatomic ions (also called simple ions) are ions consisting of exactly one atom." [GOC:mah] comment: Note that this term is not intended for use in annotating lateral movement within membranes. synonym: "ATP hydrolysis coupled ion transmembrane transport" NARROW [] @@ -4173,7 +4372,6 @@ is_a: GO:0045184 ! establishment of protein localization is_a: GO:0071692 ! protein localization to extracellular region intersection_of: GO:0045184 ! establishment of protein localization intersection_of: has_target_end_location GO:0005576 ! extracellular region -created_by: bf creation_date: 2010-11-09T10:25:08Z [Term] @@ -4187,7 +4385,6 @@ is_a: GO:0046930 ! pore complex property_value: RO:0002161 NCBITaxon:2 property_value: RO:0002161 NCBITaxon:2157 property_value: RO:0002161 NCBITaxon:4751 -created_by: bf creation_date: 2011-12-12T10:53:24Z [Term] @@ -4227,9 +4424,6 @@ relationship: has_part GO:0034220 ! monoatomic ion transmembrane transport id: GO:0042592 name: homeostatic process namespace: biological_process -alt_id: GO:0032844 -alt_id: GO:0032845 -alt_id: GO:0032846 def: "Any biological process involved in the maintenance of an internal steady state." [GOC:jl, ISBN:0395825172] subset: goslim_agr subset: goslim_chembl @@ -4257,7 +4451,7 @@ subset: goslim_prokaryote_ribbon synonym: "cell process" BROAD [] synonym: "cellular process" BROAD [] synonym: "cellular projection" EXACT [] -is_a: GO:0110165 ! cellular anatomical entity +is_a: GO:0110165 ! cellular anatomical structure relationship: part_of CL:0000000 ! cell [Term] @@ -4284,9 +4478,6 @@ relationship: part_of CL:0000586 ! germ cell id: GO:0043170 name: macromolecule metabolic process namespace: biological_process -alt_id: GO:0034960 -alt_id: GO:0043283 -alt_id: GO:0044259 def: "The chemical reactions and pathways involving macromolecules, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass." [GOC:mah] subset: gocheck_do_not_annotate subset: goslim_pir @@ -4309,7 +4500,7 @@ subset: goslim_prokaryote subset: goslim_prokaryote_ribbon xref: NIF_Subcellular:sao1539965131 xref: Wikipedia:Organelle -is_a: GO:0110165 ! cellular anatomical entity +is_a: GO:0110165 ! cellular anatomical structure [Term] id: GO:0043227 @@ -4322,23 +4513,26 @@ xref: NIF_Subcellular:sao414196390 is_a: GO:0043226 ! organelle intersection_of: GO:0043226 ! organelle intersection_of: has_part GO:0016020 ! membrane -disjoint_from: GO:0043228 ! non-membrane-bounded organelle +disjoint_from: GO:0043228 ! membraneless organelle relationship: has_part GO:0016020 ! membrane property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28153" xsd:anyURI [Term] id: GO:0043228 -name: non-membrane-bounded organelle +name: membraneless organelle namespace: cellular_component def: "Organized structure of distinctive morphology and function, not bounded by a lipid bilayer membrane. Includes ribosomes, the cytoskeleton and chromosomes." [GOC:go_curators] subset: gocheck_do_not_annotate subset: goslim_mouse synonym: "biological condensate" RELATED [] +synonym: "membrane-less organelle" EXACT [] +synonym: "non-membrane-bounded organelle" EXACT [] synonym: "non-membrane-enclosed organelle" EXACT [] xref: NIF_Subcellular:sao1456184038 is_a: GO:0043226 ! organelle property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/21881" xsd:anyURI property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28153" xsd:anyURI +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29106" xsd:anyURI [Term] id: GO:0043229 @@ -4379,15 +4573,17 @@ intersection_of: part_of GO:0005622 ! intracellular anatomical structure [Term] id: GO:0043232 -name: intracellular non-membrane-bounded organelle +name: intracellular membraneless organelle namespace: cellular_component def: "Organized structure of distinctive morphology and function, not bounded by a lipid bilayer membrane and occurring within the cell. Includes ribosomes, the cytoskeleton and chromosomes." [GOC:go_curators] subset: goslim_pir +synonym: "intracellular non-membrane-bounded organelle" EXACT [] synonym: "intracellular non-membrane-enclosed organelle" EXACT [] -is_a: GO:0043228 ! non-membrane-bounded organelle +is_a: GO:0043228 ! membraneless organelle is_a: GO:0043229 ! intracellular organelle -intersection_of: GO:0043228 ! non-membrane-bounded organelle +intersection_of: GO:0043228 ! membraneless organelle intersection_of: part_of GO:0005622 ! intracellular anatomical structure +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29106" xsd:anyURI [Term] id: GO:0043233 @@ -4404,9 +4600,6 @@ relationship: part_of GO:0043226 ! organelle id: GO:0043933 name: protein-containing complex organization namespace: biological_process -alt_id: GO:0034600 -alt_id: GO:0034621 -alt_id: GO:0071822 def: "Any process in which macromolecules aggregate, disaggregate, or are modified, resulting in the formation, disassembly, or alteration of a protein complex." [GOC:mah] synonym: "cellular macromolecular complex organization" RELATED [] synonym: "cellular macromolecular complex subunit organisation" RELATED [] @@ -4422,7 +4615,6 @@ intersection_of: GO:0016043 ! cellular component organization intersection_of: results_in_organization_of GO:0032991 ! protein-containing complex relationship: results_in_organization_of GO:0032991 ! protein-containing complex property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/22580" xsd:anyURI -created_by: mah creation_date: 2010-09-08T10:01:42Z [Term] @@ -4439,7 +4631,6 @@ relationship: regulates GO:0003008 ! system process id: GO:0044085 name: cellular component biogenesis namespace: biological_process -alt_id: GO:0071843 def: "A process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of a cellular component. Includes biosynthesis of constituent macromolecules, and those macromolecular modifications that are involved in synthesis or assembly of the cellular component." [GOC:jl, GOC:mah] subset: gocheck_do_not_annotate subset: goslim_pir @@ -4456,21 +4647,8 @@ synonym: "Met-tRNA/eIF2.GTP ternary complex" NARROW [] synonym: "translation initiation (ternary) complex" EXACT [] is_a: GO:1990904 ! ribonucleoprotein complex relationship: part_of GO:0005737 ! cytoplasm -created_by: jl creation_date: 2009-10-22T02:38:55Z -[Term] -id: GO:0044237 -name: cellular metabolic process -namespace: biological_process -def: "The chemical reactions and pathways by which individual cells transform chemical substances." [GOC:go_curators] -comment: This term should not be used for direct annotation. It should be possible to make a more specific annotation to one of the children of this term. -subset: gocheck_do_not_annotate -synonym: "cellular metabolism" EXACT [] -synonym: "intermediary metabolism" RELATED [GOC:mah] -is_a: GO:0008152 ! metabolic process -is_a: GO:0009987 ! cellular process - [Term] id: GO:0044238 name: primary metabolic process @@ -4486,21 +4664,6 @@ xref: Wikipedia:Primary_metabolite is_a: GO:0008152 ! metabolic process property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/26424" xsd:anyURI -[Term] -id: GO:0044249 -name: cellular biosynthetic process -namespace: biological_process -def: "The chemical reactions and pathways resulting in the formation of substances, carried out by individual cells." [GOC:jl] -comment: This term should not be used for direct annotation. It should be possible to make a more specific annotation to one of the children of this term. -subset: gocheck_do_not_annotate -synonym: "cellular anabolism" EXACT [] -synonym: "cellular biosynthesis" EXACT [] -synonym: "cellular formation" EXACT [] -synonym: "cellular synthesis" EXACT [] -is_a: GO:0009058 ! biosynthetic process -is_a: GO:0044237 ! cellular metabolic process -property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27052" xsd:anyURI - [Term] id: GO:0045184 name: establishment of protein localization @@ -4616,7 +4779,6 @@ property_value: term_tracker_item "https://github.com/geneontology/go-ontology/i id: GO:0048598 name: embryonic morphogenesis namespace: biological_process -alt_id: GO:0048828 def: "The process in which anatomical structures are generated and organized during the embryonic phase. The embryonic phase begins with zygote formation. The end of the embryonic phase is organism-specific. For example, it would be at birth for mammals, larval hatching for insects and seed dormancy in plants." [GOC:jid, GOC:mtg_sensu] synonym: "embryonic anatomical structure morphogenesis" EXACT [GOC:dph, GOC:tb] is_a: GO:0009653 ! anatomical structure morphogenesis @@ -4744,7 +4906,6 @@ property_value: term_tracker_item "https://github.com/geneontology/go-ontology/i id: GO:0050789 name: regulation of biological process namespace: biological_process -alt_id: GO:0050791 def: "Any process that modulates the frequency, rate or extent of a biological process. Biological processes are regulated by many means; examples include the control of gene expression, protein modification or interaction with a protein or substrate molecule." [GOC:ai, GOC:go_curators] subset: gocheck_do_not_annotate subset: goslim_candida @@ -4759,7 +4920,6 @@ relationship: regulates GO:0008150 ! biological_process id: GO:0050794 name: regulation of cellular process namespace: biological_process -alt_id: GO:0051244 def: "Any process that modulates the frequency, rate or extent of a cellular process, any of those that are carried out at the cellular level, but are not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level." [GOC:go_curators] subset: gocheck_do_not_annotate synonym: "regulation of cellular physiological process" EXACT [] @@ -4822,7 +4982,6 @@ property_value: term_tracker_item "https://github.com/geneontology/go-ontology/i id: GO:0050896 name: response to stimulus namespace: biological_process -alt_id: GO:0051869 def: "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus. The process begins with detection of the stimulus and ends with a change in state or activity or the cell or organism." [GOC:ai, GOC:bf] comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. subset: gocheck_do_not_annotate @@ -4839,7 +4998,6 @@ is_a: GO:0008150 ! biological_process id: GO:0051179 name: localization namespace: biological_process -alt_id: GO:1902578 def: "Any process in which a cell, a substance, or a cellular entity, such as a protein complex or organelle, is transported, tethered to or otherwise maintained in a specific location. In the case of substances, localization may also be achieved via selective degradation." [GOC:ai, GOC:dos] subset: gocheck_do_not_annotate subset: goslim_pir @@ -4853,7 +5011,6 @@ synonym: "single organism localization" RELATED [GOC:TermGenie] synonym: "single-organism localization" RELATED [] is_a: GO:0008150 ! biological_process property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27052" xsd:anyURI -created_by: jl creation_date: 2013-12-18T13:51:04Z [Term] @@ -4884,9 +5041,6 @@ relationship: regulates GO:0032501 ! multicellular organismal process id: GO:0051276 name: chromosome organization namespace: biological_process -alt_id: GO:0006323 -alt_id: GO:0007001 -alt_id: GO:0051277 def: "A process that is carried out at the cellular level that results in the assembly, arrangement of constituent parts, or disassembly of chromosomes, structures composed of a very long molecule of DNA and associated proteins that carries hereditary information. This term covers covalent modifications at the molecular level as well as spatial relationships among the major components of a chromosome." [GOC:ai, GOC:dph, GOC:jl, GOC:mah] subset: goslim_chembl subset: goslim_drosophila @@ -4920,7 +5074,6 @@ is_a: GO:0009987 ! cellular process id: GO:0051641 name: cellular localization namespace: biological_process -alt_id: GO:1902580 def: "A cellular localization process whereby a substance or cellular entity, such as a protein complex or organelle, is transported to, and/or maintained in, a specific location within a cell including the localization of substances or cellular entities to the cell membrane." [GOC:tb, GOC:vw] comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. subset: gocheck_do_not_annotate @@ -4935,7 +5088,6 @@ synonym: "single-organism cellular localization" RELATED [] is_a: GO:0009987 ! cellular process is_a: GO:0051179 ! localization property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27189" xsd:anyURI -created_by: jl creation_date: 2013-12-18T14:04:32Z [Term] @@ -4952,7 +5104,6 @@ is_a: GO:0050896 ! response to stimulus id: GO:0055085 name: transmembrane transport namespace: biological_process -alt_id: GO:0090662 def: "The process in which a solute is transported across a lipid bilayer, from one side of a membrane to the other." [GOC:dph, GOC:jid] comment: Transmembrane transport is the transport of a solute across a lipid bilayer. Note that transport through the nuclear pore complex is not transmembrane because the nuclear membrane is a double membrane and is not traversed. For transport through the nuclear pore, consider instead the term 'nucleocytoplasmic transport ; GO:0006913' and its children. Note also that this term is not intended for use in annotating lateral movement within membranes. subset: goslim_chembl @@ -4968,7 +5119,6 @@ is_a: GO:0009987 ! cellular process intersection_of: GO:0006810 ! transport intersection_of: results_in_transport_across GO:0016020 ! membrane relationship: results_in_transport_across GO:0016020 ! membrane -created_by: tb creation_date: 2015-10-21T13:22:47Z [Term] @@ -5003,7 +5153,6 @@ is_a: GO:0035239 ! tube morphogenesis intersection_of: GO:0009653 ! anatomical structure morphogenesis intersection_of: results_in_morphogenesis_of UBERON:0003914 ! epithelial tube relationship: results_in_morphogenesis_of UBERON:0003914 ! epithelial tube -created_by: dph creation_date: 2009-04-28T09:33:36Z [Term] @@ -5013,7 +5162,6 @@ namespace: biological_process def: "The process in which the anatomical structures of a branched epithelium are generated and organized." [GOC:dph] is_a: GO:0001763 ! morphogenesis of a branching structure is_a: GO:0002009 ! morphogenesis of an epithelium -created_by: dph creation_date: 2010-05-25T09:05:34Z [Term] @@ -5024,16 +5172,12 @@ def: "An extracellular matrix consisting mainly of proteins (especially collagen is_a: GO:0031012 ! extracellular matrix relationship: RO:0002160 NCBITaxon:33208 ! only in taxon Metazoa relationship: RO:0002162 NCBITaxon:33208 {all_only="true"} ! in taxon Metazoa -created_by: dph creation_date: 2018-04-13T12:47:21Z [Term] id: GO:0065003 name: protein-containing complex assembly namespace: biological_process -alt_id: GO:0006461 -alt_id: GO:0034622 -alt_id: GO:0043623 def: "The aggregation, arrangement and bonding together of a set of macromolecules to form a protein-containing complex." [GOC:jl] subset: goslim_chembl subset: goslim_drosophila @@ -5143,7 +5287,6 @@ def: "Any process in which a macromolecule is transported to, and/or maintained synonym: "cellular macromolecule localisation" EXACT [GOC:mah] is_a: GO:0033036 ! macromolecule localization is_a: GO:0051641 ! cellular localization -created_by: mah creation_date: 2009-06-16T04:08:29Z [Term] @@ -5157,7 +5300,6 @@ is_a: GO:0022607 ! cellular component assembly intersection_of: GO:0022607 ! cellular component assembly intersection_of: results_in_assembly_of GO:0043226 ! organelle relationship: results_in_assembly_of GO:0043226 ! organelle -created_by: mah creation_date: 2009-09-15T03:00:51Z [Term] @@ -5171,7 +5313,6 @@ is_a: GO:0008104 ! protein localization intersection_of: GO:0008104 ! protein localization intersection_of: has_target_end_location GO:0005576 ! extracellular region relationship: has_target_end_location GO:0005576 ! extracellular region -created_by: mah creation_date: 2010-02-25T04:00:13Z [Term] @@ -5188,14 +5329,12 @@ intersection_of: GO:0016043 ! cellular component organization intersection_of: results_in_organization_of GO:1990904 ! ribonucleoprotein complex relationship: results_in_organization_of GO:1990904 ! ribonucleoprotein complex property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/25143" xsd:anyURI -created_by: mah creation_date: 2010-09-08T10:10:35Z [Term] id: GO:0071840 name: cellular component organization or biogenesis namespace: biological_process -alt_id: GO:0071841 def: "A process that results in the biosynthesis of constituent macromolecules, assembly, arrangement of constituent parts, or disassembly of a cellular component." [GOC:mah] comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. subset: gocheck_do_not_annotate @@ -5206,7 +5345,6 @@ synonym: "cellular component organisation or biogenesis at cellular level" EXACT synonym: "cellular component organization or biogenesis at cellular level" EXACT [] is_a: GO:0009987 ! cellular process property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27189" xsd:anyURI -created_by: mah creation_date: 2010-09-10T01:39:16Z [Term] @@ -5215,8 +5353,7 @@ name: cell periphery namespace: cellular_component def: "The broad region around and including the plasma membrane of a cell, encompassing the cell cortex (inside the cell), the plasma membrane, and any external encapsulating structures." [GOC:pdt] subset: goslim_flybase_ribbon -is_a: GO:0110165 ! cellular anatomical entity -created_by: mah +is_a: GO:0110165 ! cellular anatomical structure creation_date: 2010-10-04T01:51:47Z [Term] @@ -5231,7 +5368,6 @@ intersection_of: GO:0022607 ! cellular component assembly intersection_of: results_in_assembly_of GO:0070062 ! extracellular exosome relationship: part_of GO:0097734 ! extracellular exosome biogenesis relationship: results_in_assembly_of GO:0070062 ! extracellular exosome -created_by: mah creation_date: 2010-10-18T03:44:18Z [Term] @@ -5245,21 +5381,18 @@ intersection_of: results_in_formation_of UBERON:0003914 ! epithelial tube relationship: part_of GO:0060562 ! epithelial tube morphogenesis relationship: results_in_formation_of UBERON:0003914 ! epithelial tube property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/22302" xsd:anyURI -created_by: mah creation_date: 2010-02-26T02:15:40Z [Term] id: GO:0097190 name: apoptotic signaling pathway namespace: biological_process -alt_id: GO:0008624 def: "The series of molecular signals which triggers the apoptotic death of a cell. The pathway starts with reception of a signal, and ends when the execution phase of apoptosis is triggered." [GOC:mtg_apoptosis] comment: This term can be used to annotate gene products involved in apoptotic events happening downstream of the cross-talk point between the extrinsic and intrinsic apoptotic pathways. The cross-talk starts when caspase-8 cleaves Bid and truncated Bid interacts with mitochondria. From this point on it is not possible to distinguish between extrinsic and intrinsic pathways. synonym: "apoptotic signalling pathway" EXACT [GOC:mah] synonym: "induction of apoptosis by extracellular signals" EXACT [] is_a: GO:0007165 ! signal transduction relationship: part_of GO:0006915 ! apoptotic process -created_by: pr creation_date: 2011-11-23T09:30:23Z [Term] @@ -5272,7 +5405,6 @@ synonym: "execution phase of apoptotic process" EXACT [] is_a: GO:0009987 ! cellular process relationship: has_part GO:0032060 ! bleb assembly relationship: part_of GO:0006915 ! apoptotic process -created_by: pr creation_date: 2011-11-23T09:45:24Z [Term] @@ -5281,7 +5413,6 @@ name: renal filtration namespace: biological_process def: "A renal system process in which fluid circulating through the body is filtered through a barrier system." [GOC:pr, GOC:sart] is_a: GO:0003014 ! renal system process -created_by: pr creation_date: 2012-01-03T03:10:17Z [Term] @@ -5292,7 +5423,6 @@ def: "The elimination of substances from peritubular capillaries (or surrounding is_a: GO:0003014 ! renal system process is_a: GO:0007588 ! excretion property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/22368" xsd:anyURI -created_by: pr creation_date: 2012-03-05T02:03:58Z [Term] @@ -5306,7 +5436,6 @@ synonym: "exosome production" EXACT [] synonym: "ILV assembly" RELATED [] synonym: "intraluminal vesicle assembly" RELATED [] is_a: GO:0140112 ! extracellular vesicle biogenesis -created_by: pr creation_date: 2016-10-03T14:35:25Z [Term] @@ -5321,7 +5450,6 @@ is_a: GO:0016020 ! membrane intersection_of: GO:0016020 ! membrane intersection_of: part_of GO:0005886 ! plasma membrane relationship: part_of GO:0005886 ! plasma membrane -created_by: dos creation_date: 2014-03-06T11:55:32Z [Term] @@ -5342,7 +5470,6 @@ def: "A complex of collagen trimers such as a fibril or collagen network." [GOC: synonym: "Supramolecular aggregate of collagen" EXACT [PMID:19693541] synonym: "Supramolecular collagen assembly" EXACT [PMID:21421911] is_a: GO:0099080 ! supramolecular complex -is_a: PR:000050567 ! protein-containing material entity relationship: has_part GO:0005581 ! collagen trimer relationship: part_of GO:0062023 ! collagen-containing extracellular matrix @@ -5371,7 +5498,7 @@ namespace: cellular_component def: "The part of a synapse that is part of the presynaptic cell." [GOC:dos] subset: goslim_synapse synonym: "presynaptic terminal" EXACT [] -is_a: GO:0110165 ! cellular anatomical entity +is_a: GO:0110165 ! cellular anatomical structure relationship: part_of CL:0000540 ! neuron relationship: part_of GO:0045202 ! synapse @@ -5381,7 +5508,7 @@ name: postsynapse namespace: cellular_component def: "The part of a synapse that is part of the post-synaptic cell." [GOC:dos] subset: goslim_synapse -is_a: GO:0110165 ! cellular anatomical entity +is_a: GO:0110165 ! cellular anatomical structure relationship: part_of CL:0000000 ! cell relationship: part_of GO:0045202 ! synapse @@ -5423,7 +5550,7 @@ id: GO:0099080 name: supramolecular complex namespace: cellular_component def: "A cellular component that consists of an indeterminate number of proteins or macromolecular complexes, organized into a regular, higher-order structure such as a polymer, sheet, network or a fiber." [GOC:dos] -is_a: GO:0110165 ! cellular anatomical entity +is_a: GO:0110165 ! cellular anatomical structure [Term] id: GO:0099081 @@ -5459,16 +5586,17 @@ is_a: GO:0099536 ! synaptic signaling [Term] id: GO:0110165 -name: cellular anatomical entity +name: cellular anatomical structure namespace: cellular_component -def: "A part of a cellular organism that is either an immaterial entity or a material entity with granularity above the level of a protein complex but below that of an anatomical system. Or, a substance produced by a cellular organism with granularity above the level of a protein complex." [GOC:kmv] +def: "A part of a cellular organism consisting of a material entity with granularity above the level of a protein complex but below that of an anatomical system. Note that cellular organisms exclude viruses." [GOC:kmv] subset: gocheck_do_not_annotate subset: goslim_pir +synonym: "cellular anatomical entity" EXACT [] is_a: GO:0005575 ! cellular_component is_a: UBERON:0000061 ! anatomical structure property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/24200" xsd:anyURI property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/26424" xsd:anyURI -created_by: kmv +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28978" xsd:anyURI creation_date: 2019-08-12T18:01:37Z [Term] @@ -5481,7 +5609,6 @@ intersection_of: GO:0042995 ! cell projection intersection_of: has_part GO:0098590 ! plasma membrane region relationship: has_part GO:0098590 ! plasma membrane region property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/13193" xsd:anyURI -created_by: krc creation_date: 2017-03-21T17:26:07Z [Term] @@ -5496,7 +5623,6 @@ intersection_of: GO:0022607 ! cellular component assembly intersection_of: results_in_assembly_of GO:0120025 ! plasma membrane bounded cell projection relationship: results_in_assembly_of GO:0120025 ! plasma membrane bounded cell projection property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/13298" xsd:anyURI -created_by: krc creation_date: 2017-04-24T23:56:08Z [Term] @@ -5509,7 +5635,6 @@ intersection_of: GO:0016043 ! cellular component organization intersection_of: results_in_organization_of GO:0120025 ! plasma membrane bounded cell projection relationship: results_in_organization_of GO:0120025 ! plasma membrane bounded cell projection property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/13298" xsd:anyURI -created_by: krc creation_date: 2017-04-26T16:07:02Z [Term] @@ -5525,7 +5650,6 @@ is_a: GO:1903047 ! mitotic cell cycle process intersection_of: GO:0000280 ! nuclear division intersection_of: part_of GO:0000278 ! mitotic cell cycle property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/19910" xsd:anyURI -created_by: pg creation_date: 2017-03-23T14:44:23Z [Term] @@ -5536,7 +5660,6 @@ def: "The assembly and secretion a set of components to form an extracellular ve synonym: "extracellular vesicle assembly" EXACT [] is_a: GO:0044085 ! cellular component biogenesis property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/14256" xsd:anyURI -created_by: pg creation_date: 2017-10-23T11:53:42Z [Term] @@ -5552,7 +5675,6 @@ intersection_of: has_target_end_location GO:0005576 ! extracellular region intersection_of: has_target_start_location GO:0005622 ! intracellular anatomical structure relationship: has_target_end_location GO:0005576 ! extracellular region relationship: has_target_start_location GO:0005622 ! intracellular anatomical structure -created_by: pg creation_date: 2019-05-22T11:20:45Z [Term] @@ -5565,7 +5687,6 @@ is_a: GO:0022402 ! cell cycle process intersection_of: GO:0009987 ! cellular process intersection_of: part_of GO:0000278 ! mitotic cell cycle relationship: part_of GO:0000278 ! mitotic cell cycle -created_by: jl creation_date: 2014-05-22T14:22:34Z [Term] @@ -5578,15 +5699,12 @@ is_a: GO:0031982 ! vesicle is_a: GO:0065010 ! extracellular membrane-bounded organelle intersection_of: GO:0031982 ! vesicle intersection_of: part_of GO:0005576 ! extracellular region -created_by: jl creation_date: 2014-10-22T14:26:11Z [Term] id: GO:1990904 name: ribonucleoprotein complex namespace: cellular_component -alt_id: GO:0030529 -alt_id: GO:1990903 def: "A macromolecular complex that contains both RNA and protein molecules." [GOC:krc, GOC:vesicles] subset: goslim_pir synonym: "extracellular ribonucleoprotein complex" NARROW [] @@ -5596,7 +5714,6 @@ synonym: "RNA-protein complex" EXACT [] synonym: "RNP" EXACT [] xref: Wikipedia:Ribonucleoprotein is_a: GO:0032991 ! protein-containing complex -created_by: pr creation_date: 2015-11-19T12:26:37Z [Term] @@ -5630,7 +5747,6 @@ is_a: NCBITaxon:39107 ! Murinae id: NCBITaxon:10090 name: Mus musculus namespace: ncbi_taxonomy -alt_id: NCBITaxon:85055 synonym: "house mouse" EXACT genbank_common_name [] synonym: "mouse" EXACT OMO:0003003 [] xref: GC_ID:1 @@ -5647,7 +5763,6 @@ is_a: NCBITaxon:7776 ! Gnathostomata id: NCBITaxon:117571 name: Euteleostomi namespace: ncbi_taxonomy -alt_id: NCBITaxon:40673 synonym: "bony vertebrates" EXACT genbank_common_name [] xref: GC_ID:1 is_a: NCBITaxon:117570 ! Teleostomi @@ -5796,7 +5911,6 @@ is_a: NCBITaxon:1963758 ! Myomorpha id: NCBITaxon:39107 name: Murinae namespace: ncbi_taxonomy -alt_id: NCBITaxon:109679 xref: GC_ID:1 is_a: NCBITaxon:10066 ! Muridae @@ -5892,7 +6006,6 @@ is_a: NCBITaxon:314147 ! Glires id: PATO:0000001 name: quality namespace: quality -alt_id: PATO:0000072 def: "A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities" [PATOC:GVG] [Term] @@ -5907,7 +6020,6 @@ is_a: PATO:0001241 ! physical object quality id: PATO:0000052 name: shape namespace: quality -alt_id: PATO:0001647 def: "A morphological quality inhering in a bearer by virtue of the bearer's ratios of distances between its features (points, edges, surfaces and also holes etc)." [PATOC:GVG] comment: Shapes are invariant on size transformations. Shapes can be subdivided into 2D and 3D shapes, We can also make a distinction between shapes of complete self-connected objects, and shapes of parts of objects. subset: attribute_slim @@ -5918,7 +6030,6 @@ is_a: PATO:0000051 ! morphology id: PATO:0000141 name: structure namespace: quality -alt_id: PATO:0001452 def: "A morphology quality inhering in a bearer by virtue of the bearer's relative position, shape, arrangements and connectivity of an organism's various parts; the pattern underlying its form." [PATOC:GVG] subset: attribute_slim synonym: "conformation" BROAD [VT:1000738] @@ -5968,7 +6079,6 @@ is_a: PATO:0002318 ! superelliptic id: PATO:0001018 name: physical quality namespace: quality -alt_id: PATO:0002079 def: "A quality of a physical entity that exists through action of continuants at the physical level of organisation in relation to other entities." [PATOC:GVG] subset: attribute_slim synonym: "relational physical quality" EXACT [] @@ -5979,8 +6089,6 @@ is_a: PATO:0001241 ! physical object quality id: PATO:0001241 name: physical object quality namespace: quality -alt_id: PATO:0001237 -alt_id: PATO:0001238 def: "A quality which inheres in a continuant." [PATOC:GVG] comment: Relational qualities are qualities that hold between multiple entities. Normal (monadic) qualities such as the shape of a eyeball exist purely as a quality of that eyeball. A relational quality such as sensitivity to light is a quality of that eyeball (and connecting nervous system) as it relates to incoming light waves/particles. synonym: "monadic quality of a continuant" EXACT [] @@ -6109,7 +6217,6 @@ is_a: PATO:0002005 ! concavity id: PATO:0001873 name: cylindrical namespace: quality -alt_id: PATO:0001203 def: "A convex 3-D shape quality inhering in a bearer by virtue of the bearer's exhibiting a consistently-sized round cross section." [PATOC:MAH] subset: cell_quality subset: value_slim @@ -6374,7 +6481,6 @@ def: "A quality inhering in a cell by virtue of the cell having a high nuclear/c comment: A high nuclear/cytolasmic ratio is 70% or higher. synonym: "high N:C ratio" EXACT [] is_a: PATO:0001396 ! cellular quality -created_by: http://orcid.org/0000-0001-5208-3432 [Term] id: PATO:0070044 @@ -6382,7 +6488,6 @@ name: anatomical structure quality namespace: quality def: "A quality of continuant that exist at the anatomical level of organisation and anything under it. This includes, but is not limited to, cells , tissues, and components." [] is_a: PATO:0001241 ! physical object quality -created_by: http://orcid.org/0000-0001-7258-9596 [Term] id: PATO:0070045 @@ -6390,7 +6495,6 @@ name: anatomical histological quality namespace: quality def: "A quality inhering in an anotomical structure by virtue of its capacity to be stained by specific histological dyes." [] is_a: PATO:0070044 ! anatomical structure quality -created_by: http://orcid.org/0000-0001-7258-9596 [Term] id: PATO:0070047 @@ -6398,18 +6502,17 @@ name: polychromatophilic namespace: quality def: "An affinity inhering in an anatomical structure by virtue of the bearer exhibiting a molecular interaction for both basic and acid stains under specific pH conditions." [GOC:add] is_a: PATO:0070045 ! anatomical histological quality -created_by: http://orcid.org/0000-0001-7258-9596 [Term] id: PR:000000001 name: protein namespace: protein def: "An amino acid chain that is produced de novo by ribosome-mediated translation of a genetically-encoded mRNA, and any derivatives thereof." [PRO:DAN, PRO:WCB] -comment: The definition above excludes protein complexes, which some also consider a protein. Those who wish to refer to a class representing both senses of the word are directed to CHEBI:36080. Note that the definition allows for experimentally-manipulated genes, and allows for artifically-produced derivatives that mimic those found naturally. Proteins (in the sense defined here) that descended from a common ancestor can be classified into families and superfamilies composed of products of evolutionarily-related genes. The domain architecture of a protein is described by the order of its constituent domains. Proteins with the same domains in the same order are defined as homeomorphic [PRO:WCB]. +comment: The definition above excludes protein complexes, which some also consider a protein. Those who wish to refer to a class representing both senses of the word are directed to CHEBI:36080. Note that the definition allows for experimentally-manipulated genes, and allows for artifically-produced derivatives that mimic those found naturally. Proteins (in the sense defined here) that descended from a common ancestor can be classified into families and superfamilies composed of products of evolutionarily-related genes. The domain architecture of a protein is described by the order of its constituent domains. Proteins with the same domains in the same order are defined as homeomorphic [PRO:WCB). synonym: "native protein" NARROW [IEDB:BP] synonym: "natural protein" EXACT [PRO:DAN] is_a: PR:000018263 ! amino acid chain -is_a: PR:000050567 ! protein-containing material entity +is_a: PR:000064867 ! protein-containing molecular entity relationship: output_of GO:0006412 ! translation [Term] @@ -6678,7 +6781,6 @@ namespace: protein def: "A protein with core architecture consisting of a signal sequence, followed by 7 Ig-like domains (Pfam:PF00047, Pfam:PF07679, or Pfam:PF07686), a transmembrane region, and a cytoplasmic Protein tyrosine kinase domain." [PRO:WCB] comment: Category=family. xref: PIRSF:PIRSF038502 -is_a: PR:000000001 ! protein [Term] id: PR:000002112 @@ -6820,11 +6922,11 @@ synonym: "fam:angiotensinogenase" EXACT PRO-short-label [PRO:DAN] is_a: PR:000000001 ! protein [Term] -id: PR:000050567 -name: protein-containing material entity +id: PR:000064867 +name: protein-containing molecular entity namespace: protein -def: "A material entity that minimally consists of a protein." [PRO:DAN] -comment: Note: This includes single proteins and derivatives thereof (PR:000000001), protein-containing complexes (GO:0032991), and protein aggregates (PR:000050566). +def: "A molecular entity that minimally consists of a protein." [PRO:DAN] +comment: Note: This includes single proteins and derivatives thereof (PR:000000001), protein-containing complexes (GO:0032991), and protein aggregates (PR:000050565). synonym: "protein" NARROW [PRO:DAN] synonym: "protein aggregate" NARROW [PRO:DAN] synonym: "protein complex" NARROW [PRO:DAN] @@ -7009,7 +7111,6 @@ xref: UMLS:C0687028 {source="ncithesaurus:Duct"} xref: Wikipedia:Duct_(anatomy) xref: XAO:0004000 xref: ZFA:0005171 -is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0000063 ! organ subunit relationship: has_part UBERON:0034969 ! epithelial layer of duct relationship: RO:0000086 PATO:0002299 ! has quality tubular @@ -7019,7 +7120,6 @@ relationship: RO:0002570 UBERON:0000463 ! conduit for organism substance id: UBERON:0000060 name: anatomical wall namespace: uberon -alt_id: UBERON:0009915 def: "Organ component adjacent to an organ cavity and which consists of a maximal aggregate of organ component layers." [FMA:82482] subset: upper_level synonym: "organ wall" RELATED [FMA:82482] @@ -7243,7 +7343,6 @@ creation_date: 2009-06-18T09:26:37Z id: UBERON:0000075 name: subdivision of skeletal system namespace: uberon -alt_id: UBERON:0010322 def: "Anatomical cluster consisting of the skeletal elements and articular elements that are part of an individual subdivision of the organism." [https://orcid.org/0000-0002-6601-2165, UBERONREF:0000003] subset: non_informative synonym: "skeletal system part" RELATED [] @@ -7780,8 +7879,6 @@ property_value: seeAlso "https://github.com/obophenotype/uberon/issues/661" xsd: id: UBERON:0000174 name: excreta namespace: uberon -alt_id: UBERON:0000324 -alt_id: UBERON:0007550 def: "A portion of organism substance that is the product of an excretion process that will be eliminated from the body. An excretion process is elimination by an organism of the waste products that arise as a result of metabolic activity." [GO:0007588, http://orcid.org/0000-0002-6601-2165] synonym: "excreted substance" EXACT [] synonym: "excretion" RELATED [BTO:0000491] @@ -7833,7 +7930,7 @@ xref: VHOG:0000224 xref: Wikipedia:Blood xref: XAO:0000124 xref: ZFA:0000007 -is_a: PR:000050567 ! protein-containing material entity +is_a: UBERON:0000061 ! anatomical structure is_a: UBERON:0000179 ! haemolymphatic fluid relationship: has_part CL:0000232 {source="CL:tm"} ! erythrocyte relationship: has_part UBERON:0001969 ! blood plasma @@ -7862,7 +7959,6 @@ creation_date: 2009-04-08T04:38:19Z id: UBERON:0000307 name: blastula namespace: uberon -alt_id: UBERON:0007011 def: "Organism at the blastula stage - an early stage of embryonic development in animals. It is produced by cleavage of a fertilized ovum and consists of a spherical layer of around 128 cells surrounding a central fluid-filled cavity called the blastocoel. The blastula follows the morula and precedes the gastrula in the developmental sequence." [Wikipedia:Blastula] subset: inconsistent_with_fma synonym: "blastosphere" RELATED [Wikipedia:Blastula] @@ -8415,7 +8511,6 @@ xref: VHOG:0000387 xref: Wikipedia:Epithelium xref: XAO:0003045 xref: ZFA:0001486 -is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0000479 ! tissue intersection_of: UBERON:0000479 ! tissue intersection_of: RO:0002473 CL:0000066 ! composed primarily of epithelial cell @@ -8749,7 +8844,6 @@ property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/d/ id: UBERON:0000926 name: mesoderm namespace: uberon -alt_id: UBERON:0003263 def: "The middle germ layer of the embryo, between the endoderm and ectoderm." [Wikipedia:Mesoderm] subset: efo_slim subset: pheno_slim @@ -9194,7 +9288,6 @@ id: UBERON:0001009 name: circulatory system namespace: uberon def: "Organ system that passes nutrients (such as amino acids and electrolytes), gases, hormones, blood cells, etc. to and from cells in the body to help fight diseases and help stabilize body temperature and pH to maintain homeostasis[WP]." [Wikipedia:Circulatory_system] -subset: human_reference_atlas subset: uberon_slim synonym: "systema cardiovasculare" RELATED OMO:0003011 [Wikipedia:Circulatory_system] xref: AAO:0000959 @@ -9214,7 +9307,6 @@ property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/2/ property_value: RO:0002161 NCBITaxon:147099 {source="Wikipedia:Acoelomorpha"} property_value: RO:0002161 NCBITaxon:6073 property_value: RO:0002161 NCBITaxon:6157 -property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001015 @@ -9797,7 +9889,6 @@ property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/3/ id: UBERON:0001231 name: nephron tubule namespace: uberon -alt_id: UBERON:0004210 def: "An epithelial tube that is part of the nephron, the functional part of the kidney." [GO:0072078, Wikipedia:Renal_tubule] subset: efo_slim subset: human_reference_atlas @@ -10110,7 +10201,6 @@ property_value: RO:0002175 NCBITaxon:9606 id: UBERON:0001290 name: proximal straight tubule namespace: uberon -alt_id: UBERON:0005166 def: "The proximal straight tubule is the part of the descending limb that extends from the proximal convoluted tubule to the descending thin tubule." [GO:0072020] subset: human_reference_atlas subset: uberon_slim @@ -10523,7 +10613,6 @@ xref: MIAA:0000052 xref: NCIT:C13356 xref: UMLS:C0032105 {source="ncithesaurus:Plasma"} xref: Wikipedia:Blood_plasma -is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0000179 ! haemolymphatic fluid intersection_of: UBERON:0000463 ! organism substance intersection_of: has_part GO:0005577 ! fibrinogen complex @@ -10633,7 +10722,6 @@ xref: VHOG:0001250 xref: Wikipedia:Blood_vessel xref: XAO:0001011 xref: ZFA:0005314 -is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0000055 ! vessel is_a: UBERON:0004120 ! mesoderm-derived structure relationship: capable_of_part_of GO:0008015 ! blood circulation @@ -11022,7 +11110,6 @@ property_value: terms:contributor https://orcid.org/0000-0003-2804-127X id: UBERON:0002120 name: pronephros namespace: uberon -alt_id: UBERON:0005794 def: "In mammals, the pronephros is the first of the three embryonic kidneys to be established and exists only transiently. In lower vertebrates such as fish and amphibia, the pronephros is the fully functional embryonic kidney and is indispensible for larval life[GO]." [GO:0048793, Wikipedia:Pronephros] comment: Once the more complex mesonephros forms the pronephros undergoes apoptosis in amphibians. In fishes the nephron degenerates but the organ remains and becomes a component of the immune system[Wikipedia:Pronephros]. // TODO - check developmental relationships. Note that we previously include the ZFA/XAO terms under the more specific 'pronephric kidney', but these are now merged. TODO GCI: relationship: capable_of GO:0030104 subset: efo_slim @@ -11176,7 +11263,6 @@ xref: NCIT:C32891 xref: SCTID:362219002 xref: UMLS:C0022445 {source="ncithesaurus:Juxtaglomerular_Apparatus"} xref: Wikipedia:Juxtaglomerular_apparatus -is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0000061 ! anatomical structure relationship: capable_of GO:0003093 {source="GO"} ! regulation of glomerular filtration relationship: has_part CL:0000648 ! kidney granular cell @@ -11232,7 +11318,6 @@ relationship: part_of UBERON:0002319 {source="MA"} ! mesangium id: UBERON:0002323 name: coelemic cavity lumen namespace: uberon -alt_id: UBERON:0000169 def: "The cavity within the body of all animals higher than the coelenterates and certain primitive worms, formed by the splitting of the embryonic mesoderm into two layers. In mammals it forms the peritoneal, pleural, and pericardial cavities." [BTO:0001707] comment: EDITOR_NOTE check the FMA placement here; ncit placement of body cavity here probably not correct subset: uberon_slim @@ -11258,7 +11343,6 @@ xref: RETIRED_EHDAA2:0003186 xref: SCTID:361348008 xref: TAO:0001438 xref: UMLS:C0333343 {source="ncithesaurus:Cavity"} -xref: ZFA:0001438 is_a: UBERON:0002553 ! anatomical cavity relationship: RO:0002494 UBERON:0003886 ! transformation of future coelemic cavity lumen relationship: RO:0002572 UBERON:0011997 ! luminal space of coelom @@ -11674,6 +11758,7 @@ xref: TAO:0000279 xref: VHOG:0000559 xref: XAO:0000057 xref: ZFA:0000279 +is_a: UBERON:0000061 ! anatomical structure is_a: UBERON:0006598 ! presumptive structure intersection_of: UBERON:0005423 ! developing anatomical structure intersection_of: RO:0002387 UBERON:0002329 ! has potential to develop into somite @@ -11701,7 +11786,6 @@ xref: Wikipedia:Pronephric_duct xref: XAO:0000063 xref: ZFA:0000150 is_a: UBERON:0009201 {source="GO"} ! nephric duct -is_a: UBERON:0012275 ! meso-epithelium relationship: part_of UBERON:0002120 ! pronephros relationship: RO:0002202 UBERON:0003064 {source="Wikipedia"} ! develops from intermediate mesoderm relationship: RO:0002202 UBERON:0005721 {source="XAO"} ! develops from pronephric mesoderm @@ -11894,7 +11978,6 @@ property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/6/ id: UBERON:0003081 name: lateral plate mesoderm namespace: uberon -alt_id: UBERON:0006258 def: "Portion of the middle of the three primary germ layers of the embryo that resides on the periphery of the embryo, is continuous with the extra-embryonic mesoderm, splits into two layers enclosing the intra-embryonic coelom, and gives rise to body wall structures[MP]." [MP:0010117, Wikipedia:Lateral_plate_mesoderm] subset: pheno_slim subset: uberon_slim @@ -12670,8 +12753,6 @@ property_value: IAO:0000116 "TODO" xsd:string id: UBERON:0004200 name: kidney pyramid namespace: uberon -alt_id: UBERON:0002449 -alt_id: UBERON:0005098 def: "Kidney pyramids are the conical arrangements of tubules that constitute the renal medulla in a multi-lobed mammalian kidney; they contain the loops of Henle and the medullary collecting ducts." [GO:0072056, http://anatomy.uams.edu/anatomyhtml/kidney.html] subset: human_reference_atlas subset: pheno_slim @@ -12900,7 +12981,6 @@ xref: WikipediaCategory:Cardiovascular_system xref: XAO:0000100 xref: XAO:0001010 xref: ZFA:0000010 -is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0000467 ! anatomical system intersection_of: UBERON:0000467 ! anatomical system intersection_of: has_part UBERON:0000948 ! heart @@ -12924,7 +13004,6 @@ synonym: "blood vessels" RELATED [TAO:0001079] synonym: "set of blood vessels" EXACT [] xref: TAO:0001079 xref: ZFA:0001079 -is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0002049 ! vasculature intersection_of: UBERON:0002049 ! vasculature intersection_of: RO:0002473 UBERON:0001981 ! composed primarily of blood vessel @@ -12938,7 +13017,6 @@ id: UBERON:0004572 name: arterial system namespace: uberon def: "The part of the cardiovascular system consisting of all arteries." [https://orcid.org/0000-0002-6601-2165] -subset: human_reference_atlas subset: pheno_slim xref: BTO:0004690 xref: EHDAA2:0000143 @@ -12948,17 +13026,14 @@ xref: EMAPA:16371 xref: MA:0002719 xref: SCTID:362030008 xref: VHOG:0000273 -is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0007798 {source="MA"} ! vascular system relationship: RO:0002351 UBERON:0001637 ! has member artery -property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0004582 name: venous system namespace: uberon def: "The part of the cardiovascular system consisting of all venous vessels. In vertebrates with a double circulation, this can be divided into systemic and pulmonary portions." [https://orcid.org/0000-0002-6601-2165] -subset: human_reference_atlas synonym: "vein system" EXACT [] xref: BTO:0004692 xref: EHDAA2:0002171 @@ -12969,10 +13044,8 @@ xref: NCIT:C33858 xref: SCTID:362060003 xref: UMLS:C1267406 {source="ncithesaurus:Venous_System"} xref: VHOG:0000277 -is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0007798 {source="MA"} ! vascular system relationship: RO:0002473 UBERON:0001638 ! composed primarily of vein -property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0004638 @@ -13082,7 +13155,6 @@ property_value: RO:0002175 NCBITaxon:9606 id: UBERON:0004734 name: gastrula namespace: uberon -alt_id: UBERON:0007012 def: "Organism at the gastrula stage." [Wikipedia:Gastrula, Wikipedia:Trilaminar_blastocyst] subset: pheno_slim synonym: "blastocystis trilaminaris" RELATED [https://orcid.org/0000-0002-6601-2165] @@ -13448,7 +13520,6 @@ property_value: IAO:0000116 "class added for consistency with GO - consider merg id: UBERON:0005096 name: descending thin limb namespace: uberon -alt_id: UBERON:0005165 def: "The descending thin limb is a part of the loop of Henle situated just after the proximal straight tubule (S3). It extends to the tip of the loop of Henle[GO]." [GO:0072022, Wikipedia:Descending_limb_of_loop_of_Henle] subset: human_reference_atlas subset: uberon_slim @@ -13912,7 +13983,6 @@ xref: NCIT:C13191 xref: SCTID:68989006 xref: UMLS:C0004799 {source="ncithesaurus:Basement_Membrane"} xref: Wikipedia:Basement_membrane -is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0005764 {source="FMA"} ! acellular membrane relationship: adjacent_to CL:0000066 ! epithelial cell relationship: has_part GO:0005587 ! collagen type IV trimer @@ -14310,7 +14380,6 @@ subset: efo_slim xref: EFO:0003709 xref: TAO:0005077 xref: ZFA:0005077 -is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0005423 ! developing anatomical structure relationship: has_part CL:0000115 ! endothelial cell relationship: has_part CL:0000566 ! angioblastic mesenchymal cell @@ -14627,7 +14696,6 @@ property_value: RO:0002175 NCBITaxon:9606 id: UBERON:0007823 name: appendage girdle region namespace: uberon -alt_id: UBERON:0007824 def: "An organism subdivision that encompasses the region containing the pectoral or pelvic girdle. Note that this includes both the skeletal elements and associated tissues (integument, muscle, etc)." [https://orcid.org/0000-0002-6601-2165, UBERONREF:0000003] synonym: "fin girdle" RELATED SENSU [] synonym: "fin girdle region" RELATED SENSU [] @@ -14729,7 +14797,6 @@ is_a: UBERON:0007685 ! region of nephron tubule id: UBERON:0009142 name: entire embryonic mesenchyme namespace: uberon -alt_id: UBERON:0003313 def: "Sum total of mesenchyme in the embryo." [https://github.com/obophenotype/human-developmental-anatomy-ontology/issues/7] xref: EHDAA2:0001113 xref: EHDAA:177 @@ -14761,6 +14828,7 @@ is_a: UBERON:0003914 {source="EHDAA2"} ! epithelial tube is_a: UBERON:0004819 ! kidney epithelium is_a: UBERON:0006553 ! renal duct is_a: UBERON:0006555 ! excretory tube +is_a: UBERON:0012275 ! meso-epithelium union_of: UBERON:0003060 ! pronephric duct union_of: UBERON:0003074 ! mesonephric duct @@ -15208,6 +15276,7 @@ synonym: "haemocoelom" NARROW [] synonym: "schizocoelom" NARROW [] xref: EHDAA2:0004731 xref: Wikipedia:Coelom +xref: ZFA:0001438 is_a: UBERON:0000481 {source="EHDAA2"} ! multi-tissue structure relationship: RO:0002162 NCBITaxon:33213 ! in taxon Bilateria property_value: IAO:0000116 "EHDAA2 distingsuishes between the lumen, the lining, and the 'coelomic cavity', which despire it's name, is not a space - it is the aggregate of space plus lining." xsd:string @@ -15455,7 +15524,6 @@ is_a: UBERON:0036215 ! anatomical surface region id: UBERON:0016879 name: future central nervous system namespace: uberon -alt_id: UBERON:3000469 def: "Primordium that develops into the central nervous system." [http://orcid.org/0000-0002-6601-2165] synonym: "future CNS" EXACT [] synonym: "presumptive central nervous system" EXACT [] @@ -15470,7 +15538,6 @@ relationship: RO:0002387 UBERON:0001017 ! has potential to develop into central id: UBERON:0016880 name: future nervous system namespace: uberon -alt_id: UBERON:3000477 def: "Primordium that develops into the nervous system." [http://orcid.org/0000-0002-6601-2165] synonym: "presumptive nervous system" EXACT [AAO:0000477] xref: AAO:0000477 @@ -15656,7 +15723,6 @@ synonym: "microvessel" BROAD [] is_a: UBERON:0001981 ! blood vessel is_a: UBERON:0010523 ! microcirculatory vessel property_value: seeAlso "https://github.com/obophenotype/uberon/issues/2186" xsd:string -created_by: http://orcid.org/0000-0002-2825-0621 [Term] id: UBERON:8450002 @@ -15669,7 +15735,6 @@ intersection_of: UBERON:0000467 ! anatomical system intersection_of: capable_of GO:0046903 ! secretion relationship: capable_of GO:0046903 ! secretion property_value: RO:0002175 NCBITaxon:9606 -created_by: http://orcid.org/0000-0002-6095-8718 creation_date: 2022-05-25T18:21:29Z [Term] @@ -15797,7 +15862,6 @@ id: RO:0002021 name: occurs across def: "A relationship between a process and a barrier, where the process occurs in a region spanning the barrier. For cellular processes the barrier is typically a membrane. Examples include transport across a membrane and membrane depolarization." [] is_a: RO:0002479 ! has part that occurs in -created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-07-20T17:19:37Z [Typedef] @@ -16653,7 +16717,6 @@ name: causally upstream of or within, negative effect property_value: RO:0004050 RO:0002418 property_value: seeAlso "https://wiki.geneontology.org/Causally_upstream_of_or_within,_negative_effect" xsd:anyURI is_a: causally_upstream_of_or_within ! causally upstream of or within -created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-03-13T23:55:05Z [Typedef] @@ -16661,7 +16724,6 @@ id: RO:0004047 name: causally upstream of or within, positive effect property_value: seeAlso https://wiki.geneontology.org/Causally_upstream_of_or_within,_positive_effect is_a: causally_upstream_of_or_within ! causally upstream of or within -created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-03-13T23:55:19Z [Typedef] @@ -16670,7 +16732,6 @@ name: has small molecule regulator def: "a relation between a process and a continuant, in which the process is regulated by the small molecule continuant" [] is_a: has_participant ! has participant inverse_of: RO:0012004 ! is small molecule regulator of -created_by: https://orcid.org/0000-0003-1813-6857 creation_date: 2020-04-22T20:27:26Z [Typedef] @@ -16678,7 +16739,6 @@ id: RO:0012004 name: is small molecule regulator of def: "a relation between a continuant and a process, in which the continuant is a small molecule that regulates the process" [] is_a: RO:0002596 ! capable of regulating -created_by: https://orcid.org/0000-0003-1813-6857 creation_date: 2020-06-24T13:15:17Z [Typedef] @@ -16688,7 +16748,6 @@ def: "a relation between a continuant and a process, in which the continuant is property_value: seeAlso "https://wiki.geneontology.org/Is_small_molecule_activator_of" xsd:anyURI is_a: RO:0002598 ! capable of positively regulating is_a: RO:0012004 ! is small molecule regulator of -created_by: https://orcid.org/0000-0003-1813-6857 creation_date: 2020-06-24T13:15:26Z [Typedef] @@ -16698,7 +16757,6 @@ def: "A relationship between a neuron and a region, where the neuron has a funct synonym: "has synaptic input or output in" EXACT [] is_a: RO:0002130 ! has synaptic terminal in transitive_over: part_of ! part of -created_by: https://orcid.org/0000-0002-1373-1705 creation_date: 2020-07-17T09:26:52Z [Typedef] @@ -16710,9 +16768,18 @@ synonym: "has sensory terminal in" EXACT [] synonym: "has sensory terminal location" EXACT [] is_a: RO:0002360 ! has dendrite location transitive_over: part_of ! part of -created_by: https://orcid.org/0000-0002-1373-1705 creation_date: 2020-07-20T12:10:09Z +[Typedef] +id: RO:0015004 +name: has characterizing marker set +def: "A relation that applies between a cell type and a set of markers that can be used to uniquely identify that cell type." [] +synonym: "has marker gene combination" EXACT [] +synonym: "has marker signature set" EXACT [] +property_value: IAO:0000116 "C has_characterizing_marker_set y iff: C is a cell type and y is a collection of genes or proteins whose expression is sufficient to distinguish cell type C from most or all other cell types." xsd:string +property_value: terms:contributor https://orcid.org/0000-0001-7258-9596 +domain: CL:0000000 ! cell + [Typedef] id: RO:0015006 name: different in magnitude relative to @@ -16786,7 +16853,6 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0012003 is_a: has_participant ! has participant -created_by: https://orcid.org/0000-0003-1813-6857 creation_date: 2020-06-08T17:21:33Z [Typedef] @@ -17082,7 +17148,6 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_ontology xref: RO:0004009 is_a: has_input ! has input is_a: has_primary_input_or_output ! has primary input or output -created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-12-13T11:26:56Z [Typedef] @@ -17093,7 +17158,6 @@ def: "p 'has primary input ot output' c iff either (a) p 'has primary input' c o subset: http://purl.obolibrary.org/obo/valid_for_go_ontology xref: RO:0004007 is_a: has_participant ! has participant -created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-12-13T11:26:17Z [Typedef] @@ -17105,7 +17169,6 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_ontology xref: RO:0004008 is_a: has_output ! has output is_a: has_primary_input_or_output ! has primary input or output -created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-12-13T11:26:32Z [Typedef] @@ -17116,7 +17179,6 @@ def: "a relation between a process and a continuant, in which the process is act xref: RO:0012001 is_a: RO:0012000 ! has small molecule regulator inverse_of: RO:0012005 ! is small molecule activator of -created_by: https://orcid.org/0000-0003-1813-6857 creation_date: 2020-04-22T20:28:37Z [Typedef] @@ -17441,7 +17503,6 @@ namespace: external def: "p has anatomical participant c iff p has participant c, and c is an anatomical entity" [] xref: RO:0040036 is_a: has_participant ! has participant -created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-09-26T01:08:58Z [Typedef] @@ -17513,7 +17574,6 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0012008 is_a: results_in_organization_of ! results in organization of -created_by: https://orcid.org/0000-0003-1813-6857 creation_date: 2021-02-26T07:28:29Z [Typedef] @@ -17565,7 +17625,6 @@ name: results in organization of namespace: external def: "p results in organization of c iff p results in the assembly, arrangement of constituent parts, or disassembly of c" [] xref: RO:0002592 -is_a: has_participant ! has participant is_a: results_in_changes_to_anatomical_or_cellular_structure ! results in changes to anatomical or cellular structure [Typedef] diff --git a/src/ontology/subsets/kidney_upper_slim.owl b/src/ontology/subsets/kidney_upper_slim.owl index ae3211d54..f79961ee4 100644 --- a/src/ontology/subsets/kidney_upper_slim.owl +++ b/src/ontology/subsets/kidney_upper_slim.owl @@ -22,8 +22,8 @@ xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#" xmlns:ncbitaxon="http://purl.obolibrary.org/obo/ncbitaxon#"> - - 2024-09-26 + + 2025-01-08 @@ -287,13 +287,18 @@ WHERE { - 2018-03-14T00:03:24Z is negative form of + + + + + + @@ -373,6 +378,14 @@ WHERE { + + + + + + + + @@ -384,6 +397,14 @@ WHERE { + + + + + + + + @@ -1010,12 +1031,6 @@ WHERE { - - - - - - @@ -1034,6 +1049,12 @@ WHERE { + + + + + + @@ -1048,19 +1069,25 @@ WHERE { - + + description + - + + license + - + + title + @@ -1088,26 +1115,12 @@ WHERE { - - - - - - - - - - has_alternative_id - - - - @@ -1123,7 +1136,11 @@ WHERE { + An annotation property that links an ontology entity or a statement to a prefixed identifier or URI. + + database_cross_reference + has cross-reference @@ -1206,12 +1223,6 @@ WHERE { - - - - - - @@ -1681,7 +1692,6 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 A relationship between a process and a barrier, where the process occurs in a region spanning the barrier. For cellular processes the barrier is typically a membrane. Examples include transport across a membrane and membrane depolarization. - 2017-07-20T17:19:37Z occurs across @@ -3966,7 +3976,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different - p results in organization of c iff p results in the assembly, arrangement of constituent parts, or disassembly of c RO:0002592 @@ -4088,7 +4097,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different p 'has primary input ot output' c iff either (a) p 'has primary input' c or (b) p 'has primary output' c. - 2018-12-13T11:26:17Z RO:0004007 external @@ -4106,7 +4114,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different p has primary output c if (a) p has output c and (b) the goal of process is to modify, produce, or transform c. - 2018-12-13T11:26:32Z RO:0004008 external @@ -4134,7 +4141,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different p has primary input c if (a) p has input c and (b) the goal of process is to modify, consume, or transform c. - 2018-12-13T11:26:56Z RO:0004009 external @@ -4161,7 +4167,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different - 2018-03-13T23:55:05Z causally upstream of or within, negative effect https://wiki.geneontology.org/Causally_upstream_of_or_within,_negative_effect @@ -4173,7 +4178,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different - 2018-03-13T23:55:19Z causally upstream of or within, positive effect @@ -4187,7 +4191,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different a relation between a process and a continuant, in which the process is regulated by the small molecule continuant - 2020-04-22T20:27:26Z has small molecule regulator @@ -4200,7 +4203,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different a relation between a process and a continuant, in which the process is activated by the small molecule continuant - 2020-04-22T20:28:37Z RO:0012001 external @@ -4217,7 +4219,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different p acts on population of c iff c' is a collection, has members of type c, and p has participant c - 2020-06-08T17:21:33Z RO:0012003 external @@ -4237,7 +4238,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different a relation between a continuant and a process, in which the continuant is a small molecule that regulates the process - 2020-06-24T13:15:17Z is small molecule regulator of @@ -4250,7 +4250,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different a relation between a continuant and a process, in which the continuant is a small molecule that activates the process - 2020-06-24T13:15:26Z is small molecule activator of https://wiki.geneontology.org/Is_small_molecule_activator_of @@ -4262,7 +4261,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different - 2021-02-26T07:28:29Z RO:0012008 external @@ -4286,7 +4284,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different A relationship between a neuron and a region, where the neuron has a functionally relevant number of input and/or output synapses in that region. - 2020-07-17T09:26:52Z has synaptic input or output in has synaptic IO in region @@ -4303,7 +4300,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different Relation between a sensory neuron and some structure in which it receives sensory input via a sensory dendrite. - 2020-07-20T12:10:09Z has sensory dendrite location has sensory terminal in @@ -4313,6 +4309,20 @@ Each of these 3 primitives can be composed to yield a cross-product of different + + + + + A relation that applies between a cell type and a set of markers that can be used to uniquely identify that cell type. + C has_characterizing_marker_set y iff: C is a cell type and y is a collection of genes or proteins whose expression is sufficient to distinguish cell type C from most or all other cell types. + + has marker gene combination + has marker signature set + has characterizing marker set + + + + @@ -4452,7 +4462,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different p has anatomical participant c iff p has participant c, and c is an anatomical entity - 2018-09-26T01:08:58Z RO:0040036 external @@ -4796,6 +4805,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different XAO:0003012 ZFA:0009000 + + The definition of cell is intended to represent all cells, and thus a cell is defined as a material entity and not an anatomical structure, which implies that it is part of an organism (or the entirety of one). cell @@ -4827,6 +4838,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different A cell found in the embryo before the formation of all the gem layers is complete. ZFA:0009002 + + early embryonic cell (metazoa) @@ -4880,6 +4893,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different animal stem cell + + This term applies to metazoan. For plant stem cells, consider using PO:0004011 ‘initial cell’ or its parent PO:0004010 ‘meristematic cell’. stem cell @@ -5067,6 +5082,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different colony forming unit hematopoietic + + Markers differ between species, and two sets of markers have been described for mice. HSCs are reportedly CD34-positive, CD45-positive, CD48-negative, CD150-positive, CD133-positive, and CD244-negative. hematopoietic stem cell @@ -5118,6 +5135,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different erythroid stem cell + + erythroid progenitor cell @@ -5167,6 +5186,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different A cell that is within the developmental lineage of gametes and is able to pass along its genetic material to offspring. ZFA:0009016 + + Originally this term had some plant germ line cell children. germ line cell @@ -5219,6 +5240,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different multifate stem cell multipotent cell multipotent stem cell + + multi fate stem cell @@ -5254,6 +5277,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different myeloid stem cell pluripotent stem cell (bone marrow) + + This cell type is intended to be compatible with any vertebrate common myeloid progenitor. For mammalian CMP known to be CD34-positive, please use the term 'common myeloid progenitor, CD34-positive' (CL_0001059). common myeloid progenitor @@ -5370,6 +5395,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different megakaryocyte/erythrocyte progenitor megakaryocyte/erythroid progenitor cell + + MEPs are reportedly CD19-negative, CD34-negative, CD45RA-negative, CD110-positive, CD117-positive, and SCA1-negative and reportedly express the transcription factors GATA-1 and NF-E2. megakaryocyte-erythroid progenitor cell @@ -5409,6 +5436,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different MESH:D039901 ZFA:0009024 totipotential stem cell + + totipotent stem cell @@ -5436,6 +5465,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different FMA:84782 blast cell + + define using PATO mulit-potent or oligopotent? non-terminally differentiated cell @@ -5459,6 +5490,9 @@ Each of these 3 primitives can be composed to yield a cross-product of different FMA:70335 VHOG:0001529 ZFA:0009025 + + + myoblast @@ -5487,13 +5521,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - - - - - - + A connective tissue cell which secretes an extracellular matrix rich in collagen and other macromolecules. Flattened and irregular in outline with branching processes; appear fusiform or spindle-shaped. BTO:0000452 @@ -5504,6 +5532,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different ZFA:0009026 + + These cells may be vimentin-positive, fibronectin-positive, fsp1-positive, MMP-1-positive, collagen I-positive, collagen III-positive, and alpha-SMA-negative. fibroblast @@ -5547,6 +5577,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different epitheliocyte + + epithelial cell https://www.swissbiopics.org/api/image/Epithelial_cells.svg @@ -5598,6 +5630,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different An epithelial cell that is part of a duct. ZFA:0009372 + + duct epithelial cell @@ -5640,6 +5674,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different ZFA:0009036 + + blood vessel endothelial cell @@ -5663,6 +5699,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different + + non-branched duct epithelial cell @@ -5676,6 +5714,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different ZFA:0009038 + + columnar/cuboidal epithelial cell @@ -5720,6 +5760,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different CALOHA:TS-1249 ZFA:0009039 + + squamous epithelial cell @@ -5764,6 +5806,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different ZFA:0009044 + + blood cell @@ -5807,6 +5851,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different ZFA:0009065 endotheliocyte + + From FMA: 9.07.2001: Endothelial cell has always been classified as a kind of epithelial cell, specifically a squamous cell but that is not true. First, endothelial cell can either be squamous or cuboidal (e.g. high-endothelial cell) and secondly, it has different embryological derivation (mesodermal) than a true epithelial cell (ectodermal and endodermal). The basis for present classification is the fact that it comprises the outermost layer or lining of anatomical structures (location-based) but a better structural basis for the differentia is the cytoskeleton of the cell. Endothelial cell has vimentin filaments while an epithelial cell has keratin filaments. [Onard]. endothelial cell @@ -5837,6 +5883,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different Ectoderm destined to be nervous tissue. ZFA:0009080 neurectoderm cell + + neurectodermal cell @@ -5878,6 +5926,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different mesenchymal stromal cells stem cells, mesenchymal + + Many but not all mesenchymal cells derive from the mesoderm. MSCs are reportedly CD3-negative, CD4-negative, CD5-negative, CD8-negative, CD11a-negative, CD11b-negative, CD14-negative, CD19-negative, CD29-positive, CD31-negative, CD34-negative, CD38-negative, CD40-negative, CD44-positive, CD45-negative, CD49-positive, CD54-positive, CD66b-negative, CD79a-negative, CD80-negative, CD102-positive, CD106-positive, CD117-positive, CD121a-positive, CD121b-positive, CD123-positive, CD124-positive, CD133-negative, CD146-positive, CD166-positive, CD271-positive, B220-negative, Gr1-negative, MHCI-positive, MHCII-negative, SSEA4-negative, sca1-positive, Ter119-negative, and glycophorin A-negative. Cultured MSCs are capable of producing stem cell factor, IL7, IL8, IL11, TGF-beta, cofilin, galectin-1, laminin-receptor 1, cyclophilin A, and MMP-2. mesenchymal stem cell https://github.com/obophenotype/cell-ontology/issues/474 @@ -5981,6 +6031,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different BTO:0003659 FMA:86916 + + secretory cell @@ -6015,6 +6067,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different Any secretory cell that is capable of some protein secretion. + + protein secreting cell @@ -6032,6 +6086,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different A cell whose primary function is to shorten. + + contractile cell @@ -6066,6 +6122,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different muscle fiber myocyte + + muscle cell https://www.swissbiopics.org/api/image/Muscle_cells.svg @@ -6103,16 +6161,24 @@ Each of these 3 primitives can be composed to yield a cross-product of different A non-striated, elongated, spindle-shaped cell found lining the digestive tract, uterus, and blood vessels. They develop from specialized myoblasts (smooth muscle myoblast). + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Smooth muscle cells are a specialized type of muscle cells that are primarily found within the walls of hollow organs such as the intestine, stomach, bladder, uterus, and blood vessels. These cells are an essential component of the autonomic nervous system controling involuntary movements within the body. +Smooth muscle cells play a vital role in many physiological processes due to their unique functionality. They can contract and relax in a slow, sustained, and controlled manner to help modulate the size and shape of the lumens of the organs they surround. For example, in the digestive system, coordinated contraction and relaxation of smooth muscle cells propels food along the gastrointestinal tract - a process known as peristalsis. In the blood vessels, the smooth muscle cells, by contracting or relaxing, either constrict or dilate the vessels, which in turn, help regulate blood flow and pressure. +On a cellular level, smooth muscle cells possess a single, centrally located nucleus and contain an arranged network of actin and myosin filaments, which are the proteins responsible for muscle contraction. Unlike their counterparts in skeletal or cardiac muscles, these cells lack specific contact points for these filaments, hence the lack of visible striations. Furthermore, the contraction of smooth muscle cells is regulated by hormones and neurotransmitters, such as acetylcholine and norepinephrine, adding an additional layer of complex regulation to these highly specialized cells. non-striated muscle cell BTO:0004576 CALOHA:TS-2159 FMA:14072 ZFA:0009118 + https://cellxgene.cziscience.com/cellguide/CL_0000192 SMCs myocytes, smooth muscle smooth muscle fiber + + smooth muscle cell @@ -6124,6 +6190,20 @@ Each of these 3 primitives can be composed to yield a cross-product of different PMID:9315361 http://en.wikipedia.org/wiki/Smooth_muscle_cell + + + + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Smooth muscle cells are a specialized type of muscle cells that are primarily found within the walls of hollow organs such as the intestine, stomach, bladder, uterus, and blood vessels. These cells are an essential component of the autonomic nervous system controling involuntary movements within the body. +Smooth muscle cells play a vital role in many physiological processes due to their unique functionality. They can contract and relax in a slow, sustained, and controlled manner to help modulate the size and shape of the lumens of the organs they surround. For example, in the digestive system, coordinated contraction and relaxation of smooth muscle cells propels food along the gastrointestinal tract - a process known as peristalsis. In the blood vessels, the smooth muscle cells, by contracting or relaxing, either constrict or dilate the vessels, which in turn, help regulate blood flow and pressure. +On a cellular level, smooth muscle cells possess a single, centrally located nucleus and contain an arranged network of actin and myosin filaments, which are the proteins responsible for muscle contraction. Unlike their counterparts in skeletal or cardiac muscles, these cells lack specific contact points for these filaments, hence the lack of visible striations. Furthermore, the contraction of smooth muscle cells is regulated by hormones and neurotransmitters, such as acetylcholine and norepinephrine, adding an additional layer of complex regulation to these highly specialized cells. + DOI:10.1093/ptj/81.11.1810 + https://training.seer.cancer.gov/anatomy/muscular/types.html + https://www.ncbi.nlm.nih.gov/books/NBK10854/ + https://www.ncbi.nlm.nih.gov/books/NBK526125 + https://www.ncbi.nlm.nih.gov/books/NBK556137/ + @@ -6151,6 +6231,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different A cell whose function is determined by the generation or the reception of an electric signal. ZFA:0009128 + + electrically active cell @@ -6175,6 +6257,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different A cell within an epithelial cell sheet whose main function is to act as an internal or external covering for a tissue or an organism. ZFA:0009130 boundary cell + + lining cell @@ -6198,6 +6282,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different A cell whose primary function is to prevent the transport of stuff across compartments. ZFA:0009132 + + barrier cell @@ -6238,6 +6324,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different A cell that moves by its own activities. ZFA:0009136 + + motile cell @@ -6270,6 +6358,9 @@ Each of these 3 primitives can be composed to yield a cross-product of different FMA:72549 ZFA:0009137 ectoderm cell + + + ectodermal cell @@ -6299,11 +6390,18 @@ Each of these 3 primitives can be composed to yield a cross-product of different A cell of the middle germ layer of the embryo. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Mesodermal cells are pluripotent and the most abundant in the human body. They contribute to the development of several structures such as the skeletal muscles, bones, heart and blood vessels, kidneys, gonads, connective tissues, and certain layers of the skin. Hence, the mesoderm is often regarded as an active and diverse layer due to its role in forming many bodily structures. +In embryonic development, these cells are instrumental, contributing to the body's structures through a carefully coordinated sequence of morphogenetic movements. This process forms the complex multicellular architecture of tissues and organs from a simple ball of cells. Without the function of mesodermal cells, the body's integral structures and systems would cease to form correctly, leading to developmental disorders such as axial mesodermal dysplasia complex FMA:72554 ZFA:0009138 + https://cellxgene.cziscience.com/cellguide/CL_0000222 mesoblast mesoderm cell + + mesodermal cell @@ -6312,6 +6410,17 @@ Each of these 3 primitives can be composed to yield a cross-product of different A cell of the middle germ layer of the embryo. MESH:D008648 + + + + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Mesodermal cells are pluripotent and the most abundant in the human body. They contribute to the development of several structures such as the skeletal muscles, bones, heart and blood vessels, kidneys, gonads, connective tissues, and certain layers of the skin. Hence, the mesoderm is often regarded as an active and diverse layer due to its role in forming many bodily structures. +In embryonic development, these cells are instrumental, contributing to the body's structures through a carefully coordinated sequence of morphogenetic movements. This process forms the complex multicellular architecture of tissues and organs from a simple ball of cells. Without the function of mesodermal cells, the body's integral structures and systems would cease to form correctly, leading to developmental disorders such as axial mesodermal dysplasia complex + DOI:10.1016/j.ceb.2019.07.012 + DOI:10.5535/arm.2016.40.1.162 + https://www.sciencedirect.com/topics/biochemistry-genetics-and-molecular-biology/mesoderm + @@ -6336,6 +6445,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different FMA:72555 ZFA:0009139 endoderm cell + + endodermal cell @@ -6419,6 +6530,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different red blood cell + + erythrocyte @@ -6461,7 +6574,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different Any cell that in taxon some Eukaryota. MESH:D005057 - + + eukaryotic cell @@ -6496,6 +6610,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different Any cell that is capable of some oxygen transport. ZFA:0009164 + + oxygen accumulating cell @@ -6528,6 +6644,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different A cell derived from the specialized ectoderm flanking each side of the embryonic neural plate, which after the closure of the neural tube, forms masses of cells that migrate out from the dorsal aspect of the neural tube to spread throughout the body. FMA:86667 ZFA:0007086 + + migratory neural crest cell @@ -6551,6 +6669,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different A mesenchymal cell in embryonic development found in a contracting mass and that gives rise to osteoprogenitors. ZFA:0009166 + + mesenchyme condensation cell @@ -6574,6 +6694,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different A cell of the outer layer of a blastula that gives rise to the ectoderm after gastrulation. + + epiblast cell @@ -6614,6 +6736,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different BTO:0000854 EHDAA2:0004546 FMA:72395 + + animal zygote @@ -6631,6 +6755,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different A cell whose function is determined by its response to an electric signal. ZFA:0009190 + + electrically responsive cell @@ -6654,6 +6780,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different A cell that initiates an electrical signal and passes that signal to another cell. ZFA:0009193 + + electrically signaling cell @@ -6671,6 +6799,44 @@ Each of these 3 primitives can be composed to yield a cross-product of different + + + + + + + + + + + A connective tissue cell of an organ found in the loose connective tissue. + + BTO:0002064 + FMA:83624 + ZFA:0009226 + + + + + + stromal cell + + + + + A connective tissue cell of an organ found in the loose connective tissue. + GOC:tfm + MESH:D017154 + + + + + ZFA:0009226 + + + + + @@ -6693,11 +6859,19 @@ Each of these 3 primitives can be composed to yield a cross-product of different A precursor cell destined to differentiate into smooth muscle myocytes. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +A precursor to the smooth muscle cell, the smooth muscle myoblast, is integral to various body systems, including the cardiovascular, gastrointestinal, and respiratory systems. Smooth muscle myoblasts arise from the differentiation of mesenchymal stem cells, a process tightly regulated by specific genetic factors and environmental signals. Their role extends to myogenesis, particularly in the formation of muscular tissue, especially during embryonic development. +Smooth muscle myoblasts possess distinctive cellular characteristics. In contrast to skeletal muscle myoblasts, they do not fuse to create multinucleated fibers. Instead, they differentiate into individual, uninucleated smooth muscle cells. This differentiation unfolds in two distinct phases: proliferation, marked by rapid division to increase cell numbers, and differentiation, involving structural and functional transformation into mature smooth muscle cells. This intricate process is intricately mediated by various signaling molecules and transcription factors. +Functionally, smooth muscle myoblasts and the mature muscle cells they generate play pivotal roles in various physiological processes. Smooth muscle cells orchestrate involuntary muscle responses and are integral to body systems that regulate blood flow, propel food along the digestive tract, and control airflow in the respiratory tract. These diverse functions underscore the significance of smooth muscle myoblasts in the body's growth, maintenance, and overall function. FMA:84798 ZFA:0009235 + https://cellxgene.cziscience.com/cellguide/CL_0000514 myoblast, smooth muscle satellite cell + + smooth muscle myoblast @@ -6707,6 +6881,18 @@ Each of these 3 primitives can be composed to yield a cross-product of different GOC:tfm MESH:D032390 + + + + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +A precursor to the smooth muscle cell, the smooth muscle myoblast, is integral to various body systems, including the cardiovascular, gastrointestinal, and respiratory systems. Smooth muscle myoblasts arise from the differentiation of mesenchymal stem cells, a process tightly regulated by specific genetic factors and environmental signals. Their role extends to myogenesis, particularly in the formation of muscular tissue, especially during embryonic development. +Smooth muscle myoblasts possess distinctive cellular characteristics. In contrast to skeletal muscle myoblasts, they do not fuse to create multinucleated fibers. Instead, they differentiate into individual, uninucleated smooth muscle cells. This differentiation unfolds in two distinct phases: proliferation, marked by rapid division to increase cell numbers, and differentiation, involving structural and functional transformation into mature smooth muscle cells. This intricate process is intricately mediated by various signaling molecules and transcription factors. +Functionally, smooth muscle myoblasts and the mature muscle cells they generate play pivotal roles in various physiological processes. Smooth muscle cells orchestrate involuntary muscle responses and are integral to body systems that regulate blood flow, propel food along the digestive tract, and control airflow in the respiratory tract. These diverse functions underscore the significance of smooth muscle myoblasts in the body's growth, maintenance, and overall function. + DOI:10.1074/jbc.RA118.001739 + https://www.ncbi.nlm.nih.gov/books/NBK544225/ + https://www.sciencedirect.com/topics/medicine-and-dentistry/smooth-muscle + @@ -6746,6 +6932,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different nerve cell + + These cells are also reportedly CD4-negative and CD200-positive. They are also capable of producing CD40L and IFN-gamma. neuron @@ -6849,7 +7037,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different - @@ -6952,6 +7139,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different pronormoblast + + proerythroblast @@ -6999,7 +7188,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different - @@ -7025,6 +7213,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different early erythroblast early normoblast prorubricyte + + basophilic erythroblast @@ -7096,7 +7286,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different - @@ -7130,6 +7319,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different polychromatic normoblast polychromatophilic normoblast rubricyte + + polychromatophilic erythroblast @@ -7233,6 +7424,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different late erythoblast orthochromatic normoblast pyknotic eto enrythroblast + + orthochromatic erythroblast @@ -7449,6 +7642,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different promegacaryocyte promegakaryocyte + + Lineage negative is described here as CD2-negative, CD3-negative, CD4-negative, CD5-negative, CD8a-negative, CD14-negative, CD19-negative, CD20-negative, CD56-negative, Ly6g-negative, and Ter119-negative. megakaryocyte progenitor cell @@ -7522,6 +7717,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different megalokaryocyte + + Megakaryocytes are reportedly CD181-positive and CD182-positive. megakaryocyte @@ -7607,7 +7804,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different - @@ -7699,6 +7895,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different ZFA:0009252 + + reticulocyte @@ -7749,7 +7947,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different - @@ -7778,6 +7975,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different ZFA:0009258 angioblast chondroplast + + These cells are reportedly CD31-positive, CD34-positive, CD144-positive, CD309-positive, and TAL1-positive. angioblastic mesenchymal cell @@ -7820,6 +8019,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different VHOG:0001534 WBbt:0006796 + + germ cell @@ -7846,6 +8047,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different ZFA:0009387 supportive cell + + supporting cell @@ -7898,6 +8101,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different ZFA:0005238 JG cell renin secreting cell + + kidney granular cell @@ -7936,6 +8141,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different ZFA:0009283 kidney mesangial cell + + Do all of these cells really develop from some mesenchymal stem cell? mesangial cell @@ -7977,7 +8184,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different An endothelial cell that has small pores, or fenestrations, which allow for the efficient exchange of substances between the blood and surrounding tissues. - This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. Fenestrated cells are specialized epithelial cells that are characterized by a distinctive structural feature, fenestrations or tiny pores, which allow an exchange of substances such as fluids, nutrients, and waste between blood vessels and the surrounding tissue environments. These cells are present in various types of epithelial tissues in the human body, including the intestinal tract, endocrine glands, and certain parts of the renal system. There are multiple types of endothelial cell fenestrations. The most common type is found in systemic capillaries of the endocrine tissue (e.g., pancreatic islets), gastrointestinal mucosa, and renal peritubular capillaries. Here, the fenestrated cells have fenestrations in their peripheral cytoplasm with a unique thin and permeable diaphragm that provides a high degree of selectivity, blocking the passage of larger molecules while allowing the free movement of smaller ones. In contrast, other types of fenestrations, such as the discontinuous epithelium of the liver sinusoidal endothelial cells, do not have diaphragms. @@ -7988,6 +8195,8 @@ Overall, fenestrated cells contribute immensely to important physiological proce https://cellxgene.cziscience.com/cellguide/CL_0000666 window cell + + fenestrated endothelial cell @@ -7999,7 +8208,7 @@ Overall, fenestrated cells contribute immensely to important physiological proce - This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. Fenestrated cells are specialized epithelial cells that are characterized by a distinctive structural feature, fenestrations or tiny pores, which allow an exchange of substances such as fluids, nutrients, and waste between blood vessels and the surrounding tissue environments. These cells are present in various types of epithelial tissues in the human body, including the intestinal tract, endocrine glands, and certain parts of the renal system. There are multiple types of endothelial cell fenestrations. The most common type is found in systemic capillaries of the endocrine tissue (e.g., pancreatic islets), gastrointestinal mucosa, and renal peritubular capillaries. Here, the fenestrated cells have fenestrations in their peripheral cytoplasm with a unique thin and permeable diaphragm that provides a high degree of selectivity, blocking the passage of larger molecules while allowing the free movement of smaller ones. In contrast, other types of fenestrations, such as the discontinuous epithelium of the liver sinusoidal endothelial cells, do not have diaphragms. @@ -8040,6 +8249,8 @@ Overall, fenestrated cells contribute immensely to important physiological proce pericyte of Rouget adventitial cell + + Pericytes are CD10-positive, CD13-positive, CD31-negative, CD45-negative, CD106-positive, CD117-negative, CD140-positive, CD144-negative, CD146-positive, CD271-positive, CD325-positive, NG2-positive, RGS5-positive, SMA-positive, and desmin-positive. A subpopulation is CD248-positive. They are also capable of producing angiopoietin 1, CXCL12, TGF-beta, and VEGF-A. pericyte @@ -8102,6 +8313,8 @@ Overall, fenestrated cells contribute immensely to important physiological proce A non-terminally differentiated cell that is capable of developing into a muscle cell. ZFA:0009291 + + muscle precursor cell @@ -8144,6 +8357,8 @@ Overall, fenestrated cells contribute immensely to important physiological proce CALOHA:TS-2086 MESH:D053687 ZFA:0009307 + + somatic stem cell @@ -8189,6 +8404,8 @@ Overall, fenestrated cells contribute immensely to important physiological proce MESH:D022423 ZFA:0009324 + + myeloid cell @@ -8224,6 +8441,8 @@ Overall, fenestrated cells contribute immensely to important physiological proce ZFA:0009325 erythropoietic cell + + Note that in FMA erythropoietic cells are types of nucleated erythrocytes and thus don't include erythrocytes. erythroid lineage cell @@ -8411,6 +8630,8 @@ Overall, fenestrated cells contribute immensely to important physiological proce normoblast + + erythroblast @@ -8508,7 +8729,6 @@ Overall, fenestrated cells contribute immensely to important physiological proce - @@ -8615,6 +8835,8 @@ Overall, fenestrated cells contribute immensely to important physiological proce hemopoietic progenitor cell + + Markers differ between mouse and human. hematopoietic multipotent progenitor cell @@ -8666,6 +8888,8 @@ Overall, fenestrated cells contribute immensely to important physiological proce FMA:70339 ZFA:0009356 + + Note that this is a class of cell types, not an identified single cell type. myeloid lineage restricted progenitor cell @@ -8707,6 +8931,8 @@ Overall, fenestrated cells contribute immensely to important physiological proce haemopoietic cell hemopoietic cell + + hematopoietic cell @@ -8758,6 +8984,8 @@ Overall, fenestrated cells contribute immensely to important physiological proce 2010-01-06T03:43:20Z + + hematopoietic lineage restricted progenitor cell @@ -8802,6 +9030,8 @@ Overall, fenestrated cells contribute immensely to important physiological proce 2010-01-06T03:43:27Z + + This cell type is intended to be compatible with any vertebrate hematopoietic oligopotent progenitor cell. For mammalian hematopoietic oligopotent progenitor cells known to be lineage-negative, please use the term 'hematopoietic oligopotent progenitor cell' (CL_0001060). hematopoietic oligopotent progenitor cell @@ -8842,6 +9072,8 @@ Overall, fenestrated cells contribute immensely to important physiological proce 2010-06-29T03:38:22Z FMA:69074 ZFA:0009385 + + ecto-epithelial cell @@ -8887,6 +9119,8 @@ Overall, fenestrated cells contribute immensely to important physiological proce FMA:69076 ZFA:0009388 epithelial mesenchymal cell + + meso-epithelial cell @@ -8911,13 +9145,21 @@ Overall, fenestrated cells contribute immensely to important physiological proce An endothelial cell of the vascular tree, which includes blood vessels and lymphatic vessels. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Endothelial cells of the vascular tree, commonly referred to as vascular endothelial cells, line the entire circulatory system, from the heart to the smallest capillaries. These cells have a unique, flattened shape, and are tightly bound together, forming a thin layer known as the endothelium. The endothelium is responsible for maintaining the interior surface of blood vessels, and plays a critical role in ensuring the smooth flow of blood. +Vascular endothelial cells act as a semi-permeable membrane, controlling the passage of materials and the transit of white blood cells into and out of the bloodstream. These cells are also involved in blood coagulation. When a blood vessel is damaged, endothelial cells promote clotting to prevent excessive bleeding and facilitate wound healing. Other functions include regulation of blood pressure and blood volume by releasing vasodilators and vasoconstrictors to either widen or constrict blood vessels, accordingly. +Furthermore, the endothelial cells are crucial in the formation of new blood vessels, a process known as angiogenesis. This is particularly important in wound healing and the growth of new tissues during development or after injury. In the context of diseases such as cancer, angiogenesis helps facilitate tumor growth by providing nutrients and oxygen. 2010-08-24T02:06:40Z BTO:0001854 CALOHA:TS-1106 FMA:67755 + https://cellxgene.cziscience.com/cellguide/CL_0002139 vascular endothelial cell cubodial endothelial cell of vascular tree + + These cells are reportedly CD31-positive, CD34-positive, CD144-positive, TAL1-positive. endothelial cell of vascular tree @@ -8929,6 +9171,19 @@ Overall, fenestrated cells contribute immensely to important physiological proce GOC:tfm PMID:12768659 + + + + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Endothelial cells of the vascular tree, commonly referred to as vascular endothelial cells, line the entire circulatory system, from the heart to the smallest capillaries. These cells have a unique, flattened shape, and are tightly bound together, forming a thin layer known as the endothelium. The endothelium is responsible for maintaining the interior surface of blood vessels, and plays a critical role in ensuring the smooth flow of blood. +Vascular endothelial cells act as a semi-permeable membrane, controlling the passage of materials and the transit of white blood cells into and out of the bloodstream. These cells are also involved in blood coagulation. When a blood vessel is damaged, endothelial cells promote clotting to prevent excessive bleeding and facilitate wound healing. Other functions include regulation of blood pressure and blood volume by releasing vasodilators and vasoconstrictors to either widen or constrict blood vessels, accordingly. +Furthermore, the endothelial cells are crucial in the formation of new blood vessels, a process known as angiogenesis. This is particularly important in wound healing and the growth of new tissues during development or after injury. In the context of diseases such as cancer, angiogenesis helps facilitate tumor growth by providing nutrients and oxygen. + DOI:10.1038/s41569-022-00770-1 + DOI:10.1186/s12872-015-0124-z + DOI:10.3389/fphys.2022.863265/full + https://www.sciencedirect.com/topics/medicine-and-dentistry/vascular-endothelial-cell + @@ -8962,6 +9217,8 @@ Overall, fenestrated cells contribute immensely to important physiological proce CALOHA:TS-0112 FMA:67756 + + capillary endothelial cell @@ -9005,6 +9262,8 @@ Overall, fenestrated cells contribute immensely to important physiological proce Goormaghtigh cell polar cushion cells lacis cell + + extraglomerular mesangial cell @@ -9040,7 +9299,6 @@ Overall, fenestrated cells contribute immensely to important physiological proce - @@ -9059,7 +9317,9 @@ Overall, fenestrated cells contribute immensely to important physiological proce BTO:0004632 FMA:70970 + + Glomerular endothelial cells have 60-80 nm fenestrations typically lacking diaphragms in adults but present during embryonic development. Some studies found diaphragms in 2-6% of mature rat glomerular capillaries. Their presence may depend on fixation techniques, developmental stage, or dynamic cell changes. Additionally, these cells help maintain the structural integrity of glomerular capillaries through interactions with the basement membrane and podocytes. glomerular endothelial cell @@ -9106,6 +9366,8 @@ Overall, fenestrated cells contribute immensely to important physiological proce 2010-09-07T03:32:33Z FMA:67513 + + nucleate cell @@ -9144,7 +9406,9 @@ Overall, fenestrated cells contribute immensely to important physiological proce FMA:70981 KUPO:0001055 kidney distal tubule epithelial cell + + epithelial cell of distal tubule @@ -9192,7 +9456,9 @@ Overall, fenestrated cells contribute immensely to important physiological proce KUPO:0001044 kidney proximal tubule epithelial cell + + The vast majority of proximal tubule epithelial cells have a brush border, but there are rare exceptions. epithelial cell of proximal tubule @@ -9240,6 +9506,8 @@ Overall, fenestrated cells contribute immensely to important physiological proce CALOHA:TS-2040 FMA:70333 + + neural cell @@ -9281,6 +9549,8 @@ Overall, fenestrated cells contribute immensely to important physiological proce MESH:D003239 ZFA:0009392 + + connective tissue cell @@ -9305,11 +9575,19 @@ Overall, fenestrated cells contribute immensely to important physiological proce A cell of the embryo. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Embryonic cells in metazoans, which include all multicellular animals, are biological units in their earliest developmental stages from conception until the organism is fully formed. +They are derived from a fertilized egg, which undergoes a series of cell divisions to produce a multicellular organism. During the early phases of embryonic development, these cells exhibit pluripotency, meaning they possess the potential to differentiate into a diverse array of specialized cell types that constitute different body tissues and structures. +The balance between cell proliferation and differentiation in embryonic cells is crucial for successful development. When cells continue to divide without differentiating, overgrowth may occur leading to conditions such as teratomas (tumors of embryonic cells). Conversely, if cell differentiation proceeds at the expense of cell proliferation, developmental anomalies could occur regarding size or mass of the organism or its parts. 2010-09-15T03:39:21Z CALOHA:TS-0263 FMA:82840 WBbt:0007028 ZFA:0007089 + https://cellxgene.cziscience.com/cellguide/CL_0002321 + + embryonic cell (metazoa) @@ -9318,6 +9596,18 @@ Overall, fenestrated cells contribute immensely to important physiological proce A cell of the embryo. FMA:0618947256 + + + + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Embryonic cells in metazoans, which include all multicellular animals, are biological units in their earliest developmental stages from conception until the organism is fully formed. +They are derived from a fertilized egg, which undergoes a series of cell divisions to produce a multicellular organism. During the early phases of embryonic development, these cells exhibit pluripotency, meaning they possess the potential to differentiate into a diverse array of specialized cell types that constitute different body tissues and structures. +The balance between cell proliferation and differentiation in embryonic cells is crucial for successful development. When cells continue to divide without differentiating, overgrowth may occur leading to conditions such as teratomas (tumors of embryonic cells). Conversely, if cell differentiation proceeds at the expense of cell proliferation, developmental anomalies could occur regarding size or mass of the organism or its parts. + DOI:10.1002/iub.1404 + DOI:10.1093/molehr/gan048 + https://www.ncbi.nlm.nih.gov/books/NBK9906/ + @@ -9356,6 +9646,8 @@ Overall, fenestrated cells contribute immensely to important physiological proce FMA:83808 FMA:84791 heart cell + + From Onard of the FMA: Cardiac muscle cell or cardiac myocyte is a striated muscle cell. Cardiocyte on the other hand is any cell in the heart which includes cells other than muscle cells (e.g. endothelial cell of endocardium). Unless there is a consensus among anatomists that cardiocytes refer only to muscle cells, we will treat them as a general class of cells in the heart. cardiocyte @@ -9390,6 +9682,8 @@ Overall, fenestrated cells contribute immensely to important physiological proce KUPO:0001019 ZFA:0009374 + + kidney epithelial cell @@ -9432,6 +9726,8 @@ Overall, fenestrated cells contribute immensely to important physiological proce An epithelial cell of the kidney cortex. KUPO:0001016 + + renal cortical epithelial cell @@ -9462,6 +9758,8 @@ Overall, fenestrated cells contribute immensely to important physiological proce A squamous shaped endothelial cell. 2011-07-08T03:31:25Z + + squamous endothelial cell @@ -9497,6 +9795,8 @@ Overall, fenestrated cells contribute immensely to important physiological proce A cell that is part of a cortex of kidney. 2011-10-25T03:49:41Z + + kidney cortical cell @@ -9508,7 +9808,7 @@ Overall, fenestrated cells contribute immensely to important physiological proce A cuboidal epithelial cell of the kidney which regulates sodium and potassium balance. The activity of sodium and potassium channels on the apical membrane of the cell is regulated by aldosterone and vasopressin. In mammals this cell type is located in the renal collecting duct system. - This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. Renal principal cells are the major cell type in the initial collecting tubule and the cortical and outer medullary collecting ducts, as well as the connecting tubule, in the nephrons of the kidneys. A key function of renal principal cells is the regulation of water balance in the body. These cells express aquaporin-2 (AQP2) water channels, which facilitate the reabsorption of water from the fluid within the renal tubule lumen back into the blood. The translocation of AQP2 to the cell membrane is controlled by the hormone vasopressin: In response to high vasopressin levels, AQP2 moves to the cell membrane, allowing water to pass through effectively and be reabsorbed, therefore concentrating the urine. Conversely, in low vasopressin conditions, AQP2 is removed from the membrane, reducing water reabsorption and diluting the urine. @@ -9516,6 +9816,8 @@ Renal principal cells are also involved in the regulation of sodium and potassiu ZFA:0005322 https://cellxgene.cziscience.com/cellguide/CL_0005009 + + renal principal cell @@ -9527,7 +9829,7 @@ Renal principal cells are also involved in the regulation of sodium and potassiu - This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. Renal principal cells are the major cell type in the initial collecting tubule and the cortical and outer medullary collecting ducts, as well as the connecting tubule, in the nephrons of the kidneys. A key function of renal principal cells is the regulation of water balance in the body. These cells express aquaporin-2 (AQP2) water channels, which facilitate the reabsorption of water from the fluid within the renal tubule lumen back into the blood. The translocation of AQP2 to the cell membrane is controlled by the hormone vasopressin: In response to high vasopressin levels, AQP2 moves to the cell membrane, allowing water to pass through effectively and be reabsorbed, therefore concentrating the urine. Conversely, in low vasopressin conditions, AQP2 is removed from the membrane, reducing water reabsorption and diluting the urine. @@ -9565,6 +9867,8 @@ Renal principal cells are also involved in the regulation of sodium and potassiu 2012-06-27T08:27:35Z ZFA:0007084 + + premigratory neural crest cell @@ -9587,6 +9891,8 @@ Renal principal cells are also involved in the regulation of sodium and potassiu Any muscle cell in which the fibers are not organised into sarcomeres. + + non-striated muscle cell @@ -9604,6 +9910,8 @@ Renal principal cells are also involved in the regulation of sodium and potassiu Any hematopoietic cell that is a precursor of some other hematopoietic cell type. + + hematopoietic precursor cell @@ -9638,6 +9946,8 @@ Renal principal cells are also involved in the regulation of sodium and potassiu A muscle cell that is part of some visceral muscle. FBbt:00005070 + + visceral muscle cell @@ -9676,6 +9986,8 @@ Renal principal cells are also involved in the regulation of sodium and potassiu mesenchyme cell + + mesenchymal cell @@ -9693,6 +10005,8 @@ Renal principal cells are also involved in the regulation of sodium and potassiu ZFA:0005944 + + mural cell @@ -9717,6 +10031,8 @@ Renal principal cells are also involved in the regulation of sodium and potassiu A zygote in a plant or an animal. MESH:D015053 + + zygote @@ -9729,13 +10045,15 @@ Renal principal cells are also involved in the regulation of sodium and potassiu A cell of the neural crest. Neural crest cells are multipotent. Premigratory neural crest cells are found at the neural plate boarder, some of which will undergo ectomesynchymal transition and delamination to form migratory neural crest cells. - This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. Neural crest cells are a group of transient and highly migratory cells that originate from the neuroectoderm during the early stages of embryonic development. They are multipotent cells with an exceptional degree of plasticity, capable of differentiating into various somatic cell types and therefore play a fundamental role in the formation of various organs and tissues, making them critical contributors to the developing embryo. After the initiation of neurulation (the formation of the neural tube) neural crest cells start to undergo epithelial-to-mesenchymal transition and delaminate and migrate from the dorsal neural tube to several regions throughout the embryo. They differentiate into a range of diverse cell types, such as neurons and glial cells of the peripheral nervous system, including sensory and autonomic neurons. They also contribute to the formation of adrenal glands, pigment cells in the skin (melanocytes), cardiac structures, including parts of the heart septum and major arteries, as well as bones and cartilage of the face and skull. Disorders or aberrations in the development or migration of the neural crest cells can lead to serious congenital malformations, such as neurocristopathies, including Hirschsprung disease, neuroblastoma, and neurofibromatosis. https://cellxgene.cziscience.com/cellguide/CL_0011012 + + neural crest cell @@ -9748,7 +10066,7 @@ Disorders or aberrations in the development or migration of the neural crest cel - This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. Neural crest cells are a group of transient and highly migratory cells that originate from the neuroectoderm during the early stages of embryonic development. They are multipotent cells with an exceptional degree of plasticity, capable of differentiating into various somatic cell types and therefore play a fundamental role in the formation of various organs and tissues, making them critical contributors to the developing embryo. After the initiation of neurulation (the formation of the neural tube) neural crest cells start to undergo epithelial-to-mesenchymal transition and delaminate and migrate from the dorsal neural tube to several regions throughout the embryo. They differentiate into a range of diverse cell types, such as neurons and glial cells of the peripheral nervous system, including sensory and autonomic neurons. They also contribute to the formation of adrenal glands, pigment cells in the skin (melanocytes), cardiac structures, including parts of the heart septum and major arteries, as well as bones and cartilage of the face and skull. @@ -9786,6 +10104,8 @@ Disorders or aberrations in the development or migration of the neural crest cel A precursor cell that has a tendency to differentiate into a specific type of cell. They are descendants of stem cells, only they are more constrained in their differentiation potential or capacity for self-renewal, and are often more limited in both senses. + + progenitor cell @@ -9821,6 +10141,8 @@ Disorders or aberrations in the development or migration of the neural crest cel A cell that, by division or terminal differentiation, can give rise to other cell types. + + Work is needed on GO 'cell differentiation' before it is clear whether the equivalent class definition 'native cell' that capable_of some 'cell differentiation' works. Also, may want to consider merging this with non-terminally differentiated cell. precursor cell @@ -9961,8 +10283,16 @@ Disorders or aberrations in the development or migration of the neural crest cel An epithelial cell that is part of the nephron. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Epithelial cells of the nephron form the epithelial lining of the nephron, the functional unit of the kidney that filters the blood to produce urine. Each kidney holds approximately one million nephrons, each of which is composed of several distinct parts, including the renal corpuscle, the proximal tubule, the loop of Henle, and the distal tubule. All sections are lined with highly specialized epithelial cells adapted to perform different functions within the sections of the nephron. +The different epithelial cells of the nephron play crucial roles in the process of filtration, reabsorption, secretion, and excretion, essential tasks for the regulation of body fluid composition and volume. During filtration, the blood is forced through the walls of glomerular capillaries into the Bowman's capsule, where waste products, electrolytes, and water are separated from the blood cells and proteins. As the filtrate then passes through the nephron, epithelial cells of the tubular portion reabsorb useful substances such as glucose, amino acids, and electrolytes, along with most of the water back into the bloodstream. Waste products like urea and creatinine, as well as excess ions and water, remain in the tubule for elimination. +In addition, epithelial cells of the nephron also play a vital part in maintaining the body's acid-base balance by actively secreting hydrogen ions into the urine while reabsorbing bicarbonate from the urine back into the blood. They are also involved in the regulation of blood pressure through the renin-angiotensin-aldosterone system and contribute to erythrocyte production by releasing the hormone erythropoietin in response to low oxygen levels in the blood. Abnormalities or damage in renal epithelial cells often result in impaired kidney function, leading to various renal diseases. FMA:70965 + https://cellxgene.cziscience.com/cellguide/CL_1000449 + + epithelial cell of nephron @@ -9971,6 +10301,20 @@ Disorders or aberrations in the development or migration of the neural crest cel An epithelial cell that is part of the nephron. GOC:tfm + + + + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Epithelial cells of the nephron form the epithelial lining of the nephron, the functional unit of the kidney that filters the blood to produce urine. Each kidney holds approximately one million nephrons, each of which is composed of several distinct parts, including the renal corpuscle, the proximal tubule, the loop of Henle, and the distal tubule. All sections are lined with highly specialized epithelial cells adapted to perform different functions within the sections of the nephron. +The different epithelial cells of the nephron play crucial roles in the process of filtration, reabsorption, secretion, and excretion, essential tasks for the regulation of body fluid composition and volume. During filtration, the blood is forced through the walls of glomerular capillaries into the Bowman's capsule, where waste products, electrolytes, and water are separated from the blood cells and proteins. As the filtrate then passes through the nephron, epithelial cells of the tubular portion reabsorb useful substances such as glucose, amino acids, and electrolytes, along with most of the water back into the bloodstream. Waste products like urea and creatinine, as well as excess ions and water, remain in the tubule for elimination. +In addition, epithelial cells of the nephron also play a vital part in maintaining the body's acid-base balance by actively secreting hydrogen ions into the urine while reabsorbing bicarbonate from the urine back into the blood. They are also involved in the regulation of blood pressure through the renin-angiotensin-aldosterone system and contribute to erythrocyte production by releasing the hormone erythropoietin in response to low oxygen levels in the blood. Abnormalities or damage in renal epithelial cells often result in impaired kidney function, leading to various renal diseases. + DOI:10.1007/978-94-011-2354-9_6 + DOI:10.1007/s004670050586 + DOI:10.1016/B978-0-323-35775-3.00011-4 + DOI:10.1146/annurev-physiol-052521-121841 + DOI:10.1681/ASN.2012010029 + @@ -10001,7 +10345,9 @@ Disorders or aberrations in the development or migration of the neural crest cel Bowmans capsule epithelial cell epithelial cell of Bowman's capsule + + epithelial cell of glomerular capsule @@ -10038,7 +10384,7 @@ Disorders or aberrations in the development or migration of the neural crest cel An epithelial cell that is part of the collecting duct of renal tubule. - This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. Kidney collecting duct epithelial cells are a specialized type of cells that form an integral part of the renal system. Located in the collecting duct system of the kidneys, these cells are responsible for one of the final steps in the process of urine formation, and they are instrumental in the fine tuning of the volume and composition of urine by reabsorbing water and certain solutes back into the bloodstream. These cells express specific channels and carriers that actively and passively transport ions and water. They also have channels on their membranes, such as sodium channels and potassium channels, involved in reabsorbing or secreting these electrolytes depending upon the body's needs. The function of renal collecting duct epithelial cells can be regulated by a variety of hormones, including vasopressin (antidiuretic hormone), which can modulate the ion channels and carriers and hence indirectly influence body fluid homeostasis. @@ -10048,10 +10394,18 @@ Aside from their function in ion and water balance, kidney collecting duct epith https://cellxgene.cziscience.com/cellguide/CL_1000454 epithelial cell of renal collecting tubule + + kidney collecting duct epithelial cell + + + + + true + @@ -10067,7 +10421,7 @@ Aside from their function in ion and water balance, kidney collecting duct epith - This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. Kidney collecting duct epithelial cells are a specialized type of cells that form an integral part of the renal system. Located in the collecting duct system of the kidneys, these cells are responsible for one of the final steps in the process of urine formation, and they are instrumental in the fine tuning of the volume and composition of urine by reabsorbing water and certain solutes back into the bloodstream. These cells express specific channels and carriers that actively and passively transport ions and water. They also have channels on their membranes, such as sodium channels and potassium channels, involved in reabsorbing or secreting these electrolytes depending upon the body's needs. The function of renal collecting duct epithelial cells can be regulated by a variety of hormones, including vasopressin (antidiuretic hormone), which can modulate the ion channels and carriers and hence indirectly influence body fluid homeostasis. @@ -10083,12 +10437,6 @@ Aside from their function in ion and water balance, kidney collecting duct epith epithelial cell of renal collecting tubule FMA:70982 - - - - - true - @@ -10119,6 +10467,8 @@ Aside from their function in ion and water balance, kidney collecting duct epith KUPO:0001022 kidney tubule epithelial cell + + This needs to be further defined as a juxtamedullary nephron. Will request the juxtamedullary nephron tubule class from UBERON. nephron tubule epithelial cell @@ -10156,6 +10506,8 @@ Aside from their function in ion and water balance, kidney collecting duct epith KUPO:0001010 ZFA:0009389 + + kidney cell @@ -10193,7 +10545,9 @@ Aside from their function in ion and water balance, kidney collecting duct epith KUPO:0001013 ZFA:0009390 + + kidney interstitial cell @@ -10229,6 +10583,8 @@ Aside from their function in ion and water balance, kidney collecting duct epith A cell that is part of a renal medulla. KUPO:0001017 ZFA:0009391 + + kidney medulla cell @@ -10269,7 +10625,9 @@ Aside from their function in ion and water balance, kidney collecting duct epith A cell that is part of a renal pelvis. KUPO:0001018 + + kidney pelvis cell @@ -10298,7 +10656,9 @@ Aside from their function in ion and water balance, kidney collecting duct epith A cell that is part of a nephron tubule. KUPO:0001020 + + kidney tubule cell @@ -10328,6 +10688,8 @@ Aside from their function in ion and water balance, kidney collecting duct epith Any kidney epithelial cell that is part of some glomerular epithelium. KUPO:0001023 + + kidney glomerular epithelial cell @@ -10363,7 +10725,9 @@ Aside from their function in ion and water balance, kidney collecting duct epith An epithelial cell that is part of a renal medulla collecting duct. KUPO:0001060 + + kidney medulla collecting duct epithelial cell @@ -10392,7 +10756,9 @@ Aside from their function in ion and water balance, kidney collecting duct epith Any kidney cell that is part of some papillary duct. KUPO:0001064 + + kidney papillary duct principal epithelial cell @@ -10428,7 +10794,9 @@ Aside from their function in ion and water balance, kidney collecting duct epith Any renal cortical epithelial cell that is part of some renal corpuscle. KUPO:0001021 + + kidney corpuscule cell @@ -10466,6 +10834,8 @@ Aside from their function in ion and water balance, kidney collecting duct epith Any kidney tubule cell that is part of some renal cortex tubule. KUPO:0001024 + + kidney cortex tubule cell @@ -10507,7 +10877,9 @@ Aside from their function in ion and water balance, kidney collecting duct epith Any kidney cortical cell that is part of some juxtaglomerular apparatus. KUPO:0001028 juxtaglomerulus cell + + juxtaglomerular complex cell @@ -10551,6 +10923,8 @@ Aside from their function in ion and water balance, kidney collecting duct epith KUPO:0001102 + + kidney interstitial fibroblast @@ -10586,6 +10960,8 @@ Aside from their function in ion and water balance, kidney collecting duct epith Any kidney corpuscule cell that is part of some renal glomerulus. KUPO:0001036 + + glomerular cell @@ -10621,9 +10997,18 @@ Aside from their function in ion and water balance, kidney collecting duct epith Any nephron tubule epithelial cell that is part of some renal connecting tubule. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Kidney connecting tubule epithelial cells are found in collecting duct system of the kidney, specifically in at the interconnection segment between the nephron and the collecting ducts. The epithelial cells lining the connecting tubule are crucial for the journey of filtrate before it empties into urine-collecting ducts and therefore play a critical role in maintaining the body’s fluid and electrolyte balance. +One of the principal functions of connecting tubule epithelial cells involves the selective reabsorption and secretion of various solutes. This reabsorption process includes critical regulatory electrolytes such as sodium ions (Na+), chloride ions (Cl-), and bicarbonate ions (HCO3-), thus playing a role in the regulation of the acid-base homeostasis. Their function also involves the secretion of potassium ions (K+) into the renal tubular fluid. +The connecting tubule epithelial cells are primarily intercalated cells, which can be categorized into two types according to their specific functions: type A intercalated cells, which secrete acid, and the type B intercalated cells, which secrete base (bicarbonate) and reabsorb chloride. By regulating the concentrations of these ions, as well as reabsorption of water, connecting tubule epithelial cells contribute substantively to maintaining the body's electrolyte levels, pH balance, and overall homeostasis. +In addition to intercalating cells, the collecting duct system also has principal cells, which are characterized by the expression of the water channel AQP2. AQP2-expressing cells have also been identified in connecting tubules, but there is some controversy whether these represent a unique cell type as there are some morphologic differences compared with principal cells. KUPO:0001058 + https://cellxgene.cziscience.com/cellguide/CL_1000768 + + kidney connecting tubule epithelial cell @@ -10639,6 +11024,21 @@ Aside from their function in ion and water balance, kidney collecting duct epith Any nephron tubule epithelial cell that is part of some renal connecting tubule. FBC:Autogenerated + + + + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Kidney connecting tubule epithelial cells are found in collecting duct system of the kidney, specifically in at the interconnection segment between the nephron and the collecting ducts. The epithelial cells lining the connecting tubule are crucial for the journey of filtrate before it empties into urine-collecting ducts and therefore play a critical role in maintaining the body’s fluid and electrolyte balance. +One of the principal functions of connecting tubule epithelial cells involves the selective reabsorption and secretion of various solutes. This reabsorption process includes critical regulatory electrolytes such as sodium ions (Na+), chloride ions (Cl-), and bicarbonate ions (HCO3-), thus playing a role in the regulation of the acid-base homeostasis. Their function also involves the secretion of potassium ions (K+) into the renal tubular fluid. +The connecting tubule epithelial cells are primarily intercalated cells, which can be categorized into two types according to their specific functions: type A intercalated cells, which secrete acid, and the type B intercalated cells, which secrete base (bicarbonate) and reabsorb chloride. By regulating the concentrations of these ions, as well as reabsorption of water, connecting tubule epithelial cells contribute substantively to maintaining the body's electrolyte levels, pH balance, and overall homeostasis. +In addition to intercalating cells, the collecting duct system also has principal cells, which are characterized by the expression of the water channel AQP2. AQP2-expressing cells have also been identified in connecting tubules, but there is some controversy whether these represent a unique cell type as there are some morphologic differences compared with principal cells. + DOI:10.1002/cphy.c110052 + DOI:10.1007/s00418-021-02033-5 + DOI:10.1097/MNH.0b013e32820ac850 + DOI:10.1681/ASN.2019040415 + DOI:10.23876/j.krcp.2017.36.4.305 + @@ -10665,9 +11065,17 @@ Aside from their function in ion and water balance, kidney collecting duct epith Any epithelial cell of distal tubule that is part of some distal convoluted tubule. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Kidney distal convoluted tubule epithelial cells, often referred to simply as distal convoluted tubule (DCT) cells, constitute a significant portion of the nephron -- the functional building unit of the kidney involved in filtration and reabsorption of substances from blood. The DCT epithelial cells form lining of the distal convoluted tubule, a segment of the nephron located after the loop of Henle and before the collecting tubule. These cells are characterized by unique morphological features such as small size, low height and fewer microvilli compared to proximal convoluted tubule epithelial cells. +These cells perform a host of vital functions contributing to the regulation of extracellular fluid volume and electrolyte balance, blood pressure and pH. While the DCT is less prominent in water and sodium reabsorption compared to the proximal tubule and the loop of Henle, it plays a crucial role in fine-tuning the process. DCT epithelial cells are responsible for the final adjustments of sodium, potassium and calcium reabsorption, thereby affecting overall fluid and electrolyte balance, blood pressure regulation and bone health. The reabsorption process is regulated by hormones including aldosterone and parathyroid hormone. +The distal convoluted tubule (DCT) also plays a significant role in acid-base homeostasis by secreting protons (H+) into the tubular fluid and reabsorbing bicarbonate ions (HCO3-), thus regulating the pH of the blood. The ability of DCT cells to adjust urine concentration plays a part in maintaining the body’s pH balance and preventing conditions like acidosis or alkalosis. In summary, kidney distal convoluted tubule epithelial cells perform functions that are crucial to maintaining body's homeostasis. KUPO:0001056 + https://cellxgene.cziscience.com/cellguide/CL_1000849 + + kidney distal convoluted tubule epithelial cell @@ -10683,6 +11091,20 @@ Aside from their function in ion and water balance, kidney collecting duct epith Any epithelial cell of distal tubule that is part of some distal convoluted tubule. FBC:Autogenerated + + + + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Kidney distal convoluted tubule epithelial cells, often referred to simply as distal convoluted tubule (DCT) cells, constitute a significant portion of the nephron -- the functional building unit of the kidney involved in filtration and reabsorption of substances from blood. The DCT epithelial cells form lining of the distal convoluted tubule, a segment of the nephron located after the loop of Henle and before the collecting tubule. These cells are characterized by unique morphological features such as small size, low height and fewer microvilli compared to proximal convoluted tubule epithelial cells. +These cells perform a host of vital functions contributing to the regulation of extracellular fluid volume and electrolyte balance, blood pressure and pH. While the DCT is less prominent in water and sodium reabsorption compared to the proximal tubule and the loop of Henle, it plays a crucial role in fine-tuning the process. DCT epithelial cells are responsible for the final adjustments of sodium, potassium and calcium reabsorption, thereby affecting overall fluid and electrolyte balance, blood pressure regulation and bone health. The reabsorption process is regulated by hormones including aldosterone and parathyroid hormone. +The distal convoluted tubule (DCT) also plays a significant role in acid-base homeostasis by secreting protons (H+) into the tubular fluid and reabsorbing bicarbonate ions (HCO3-), thus regulating the pH of the blood. The ability of DCT cells to adjust urine concentration plays a part in maintaining the body’s pH balance and preventing conditions like acidosis or alkalosis. In summary, kidney distal convoluted tubule epithelial cells perform functions that are crucial to maintaining body's homeostasis. + DOI:10.1002/cphy.c140002 + DOI:10.1007/s40620-021-01032-y + DOI:10.1152/physrev.2000.80.1.277 + DOI:10.1681/ASN.2019040415 + DOI:10.2215/CJN.05920613 + @@ -10715,6 +11137,8 @@ Aside from their function in ion and water balance, kidney collecting duct epith A blood vessel cell that is part of a kidney. KUPO:0001014 + + kidney blood vessel cell @@ -10755,7 +11179,9 @@ Aside from their function in ion and water balance, kidney collecting duct epith Any kidney blood vessel cell that is part of some kidney arterial blood vessel. KUPO:0001029 + + kidney arterial blood vessel cell @@ -10798,7 +11224,9 @@ Aside from their function in ion and water balance, kidney collecting duct epith An endothelial cell that is part of the capillary of the kidney. KUPO:0001030 + + kidney capillary endothelial cell @@ -10827,7 +11255,9 @@ Aside from their function in ion and water balance, kidney collecting duct epith Any kidney blood vessel cell that is part of some renal vein. KUPO:0001031 + + kidney venous blood vessel cell @@ -10869,6 +11299,8 @@ Aside from their function in ion and water balance, kidney collecting duct epith Any nephron tubule epithelial cell that is part of some loop of Henle. KUPO:0001047 + + kidney loop of Henle epithelial cell @@ -10911,7 +11343,9 @@ Aside from their function in ion and water balance, kidney collecting duct epith Any kidney loop of Henle epithelial cell that is part of some ascending limb of loop of Henle. KUPO:0001048 + + kidney loop of Henle ascending limb epithelial cell @@ -10951,8 +11385,16 @@ Aside from their function in ion and water balance, kidney collecting duct epith Any kidney loop of Henle epithelial cell that is part of some descending limb of loop of Henle. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +The kidney loop of Henle descending limb epithelial cells are highly specialized cells that play a crucial role in maintaining the body's salt and water balance. These cells line the descending limb of the loop of Henle, which is a portion of the renal tubule located in the kidneys, an organ responsible for filtering waste products, ions and extra water from the blood and converting them into urine. However, the descending limb epithelial cells are specifically involved in the countercurrent multiplication system, a mechanism to concentrate urine that involves both active and passive transport processes. +These cells are notably permeable to water but relatively impermeable to solutes, a characteristic that dramatically influences the osmotic gradient in the renal medulla. As filtrate initially descends down the loop of Henle, water gets drawn out due to the increasing osmotic gradient, thereby concentrating the filtrate. Additionally, these epithelial cells are exceptionally thin walled, allowing water to freely diffuse across the membrane. +Furthermore, the kidney loop of Henle descending limb epithelial cells are inextricably linked to the functioning of numerous diuretic drugs, which work by blocking the reabsorption of water and certain electrolytes in the kidneys, leading to increased urine production to rid the body of excess fluids. KUPO:0001053 + https://cellxgene.cziscience.com/cellguide/CL_1001021 + + kidney loop of Henle descending limb epithelial cell @@ -10967,6 +11409,18 @@ Aside from their function in ion and water balance, kidney collecting duct epith Any kidney loop of Henle epithelial cell that is part of some descending limb of loop of Henle. FBC:Autogenerated + + + + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +The kidney loop of Henle descending limb epithelial cells are highly specialized cells that play a crucial role in maintaining the body's salt and water balance. These cells line the descending limb of the loop of Henle, which is a portion of the renal tubule located in the kidneys, an organ responsible for filtering waste products, ions and extra water from the blood and converting them into urine. However, the descending limb epithelial cells are specifically involved in the countercurrent multiplication system, a mechanism to concentrate urine that involves both active and passive transport processes. +These cells are notably permeable to water but relatively impermeable to solutes, a characteristic that dramatically influences the osmotic gradient in the renal medulla. As filtrate initially descends down the loop of Henle, water gets drawn out due to the increasing osmotic gradient, thereby concentrating the filtrate. Additionally, these epithelial cells are exceptionally thin walled, allowing water to freely diffuse across the membrane. +Furthermore, the kidney loop of Henle descending limb epithelial cells are inextricably linked to the functioning of numerous diuretic drugs, which work by blocking the reabsorption of water and certain electrolytes in the kidneys, leading to increased urine production to rid the body of excess fluids. + DOI:10.1007/s00360-018-1164-3 + DOI:10.1146/annurev-physiol-021113-170350 + DOI:10.1152/advan.00227.2022 + @@ -10995,6 +11449,8 @@ Aside from their function in ion and water balance, kidney collecting duct epith KUPO:0001012 Wikipedia:Kidney_collecting_duct_cell + + kidney collecting duct cell @@ -11020,6 +11476,8 @@ Aside from their function in ion and water balance, kidney collecting duct epith KUPO:0001104 + + renal interstitial pericyte @@ -11057,6 +11515,9 @@ Aside from their function in ion and water balance, kidney collecting duct epith 2014-06-04T15:07:42Z CL:2000008 + + + microvascular endothelial cell @@ -11091,6 +11552,8 @@ Aside from their function in ion and water balance, kidney collecting duct epith Any cell that is located within the interstitium between the cells most prominent in defining a given tissue. "Interstitial cell" is a morphological term and refers to a variety of cells with differing origins and phenotypes. 2022-11-30T14:35:08Z + + interstitial cell @@ -11126,6 +11589,9 @@ Aside from their function in ion and water balance, kidney collecting duct epith A cell that is adjacent to a vessel. A perivascular cell plays a crucial role in maintaining vascular function and tissue homeostasis. This cell type regulates vessel integrity and flow dynamics. 2023-08-22T13:40:28Z + + + perivascular cell @@ -11172,7 +11638,6 @@ Aside from their function in ion and water balance, kidney collecting duct epith Progression through the phases of the mitotic cell cycle, the most common eukaryotic cell cycle, which canonically comprises four successive phases called G1, S, G2, and M and includes replication of the genome and the subsequent segregation of chromosomes into daughter cells. In some variant cell cycles nuclear replication or nuclear division may not be followed by cell division, or G1 and G2 phases may be absent. - GO:0007067 Wikipedia:Mitosis biological_process mitosis @@ -11243,9 +11708,6 @@ Aside from their function in ion and water balance, kidney collecting duct epith The ordered and organized complex of DNA, protein, and sometimes RNA, that forms the chromosome. https://github.com/geneontology/go-ontology/issues/28301 - GO:0000789 - GO:0000790 - GO:0005717 NIF_Subcellular:sao1615953555 cytoplasmic chromatin nuclear chromatin @@ -11271,8 +11733,6 @@ Aside from their function in ion and water balance, kidney collecting duct epith A compact and highly condensed form of chromatin that is refractory to transcription. https://github.com/geneontology/go-ontology/issues/22355 - GO:0005720 - GO:0035328 NIF_Subcellular:sao581845896 Wikipedia:Heterochromatin transcriptionally inactive chromatin @@ -11608,7 +12068,6 @@ Aside from their function in ion and water balance, kidney collecting duct epith The formation of a tube from the flat layer of ectodermal cells known as the neural plate. This will give rise to the central nervous system. - GO:0001679 Wikipedia:Neurulation neural tube morphogenesis neurulation @@ -12266,7 +12725,6 @@ Aside from their function in ion and water balance, kidney collecting duct epith A location, relative to cellular compartments and structures, occupied by a macromolecular machine. There are three types of cellular components described in the gene ontology: (1) the cellular anatomical entity where a gene product carries out a molecular function (e.g., plasma membrane, cytoskeleton) or membrane-enclosed compartments (e.g., mitochondrion); (2) virion components, where viral proteins act, and (3) the stable macromolecular complexes of which gene product are parts (e.g., the clathrin complex). https://github.com/geneontology/go-ontology/issues/17729 - GO:0008372 NIF_Subcellular:sao1337158144 cell or subcellular entity cellular component @@ -12364,32 +12822,32 @@ Aside from their function in ion and water balance, kidney collecting duct epith - - + + A protein complex consisting of three collagen chains assembled into a left-handed triple helix. These trimers typically assemble into higher order structures. Wikipedia:Collagen cellular_component GO:0005581 collagen trimer - + - + - + PMID:12382326 - + PMID:12382326 @@ -12432,8 +12890,6 @@ Aside from their function in ion and water balance, kidney collecting duct epith A collagen-containing extracellular matrix consisting of a thin layer of dense material found in various animal tissues interposed between the cells and the adjacent connective tissue. It consists of the basal lamina plus an associated layer of reticulin fibers. - GO:0005605 - GO:0008003 Wikipedia:Basement_membrane cellular_component basal lamina @@ -12699,7 +13155,12 @@ Aside from their function in ion and water balance, kidney collecting duct epith - + + + + + + @@ -12707,7 +13168,6 @@ Aside from their function in ion and water balance, kidney collecting duct epith An intracellular organelle, about 200 A in diameter, consisting of RNA and protein. It is the site of protein biosynthesis resulting from translation of messenger RNA (mRNA). It consists of two subunits, one large and one small, each containing only protein and RNA. Both the ribosome and its subunits are characterized by their sedimentation coefficients, expressed in Svedberg units (symbol: S). Hence, the prokaryotic ribosome (70S) comprises a large (50S) subunit and a small (30S) subunit, while the eukaryotic ribosome (80S) comprises a large (60S) subunit and a small (40S) subunit. Two sites on the ribosomal large subunit are involved in translation, namely the aminoacyl site (A site) and peptidyl site (P site). Ribosomes from prokaryotes, eukaryotes, mitochondria, and chloroplasts have characteristically distinct ribosomal proteins. - GO:0033279 NIF_Subcellular:sao1429207766 Wikipedia:Ribosome free ribosome @@ -12760,8 +13220,6 @@ Aside from their function in ion and water balance, kidney collecting duct epith The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins. - GO:0005887 - GO:0005904 juxtamembrane NIF_Subcellular:sao1663586795 Wikipedia:Cell_membrane @@ -12877,9 +13335,6 @@ Aside from their function in ion and water balance, kidney collecting duct epith The cellular metabolic process in which a protein is formed, using the sequence of a mature mRNA or circRNA molecule to specify the sequence of amino acids in a polypeptide chain. Translation is mediated by the ribosome, and begins with the formation of a ternary complex between aminoacylated initiator methionine tRNA, GTP, and initiation factor 2, which subsequently associates with the small subunit of the ribosome and an mRNA or circRNA. Translation ends with the release of a polypeptide chain from the ribosome. - GO:0006416 - GO:0006453 - GO:0043037 Wikipedia:Translation_(genetics) protein anabolism protein biosynthesis @@ -12912,7 +13367,7 @@ Aside from their function in ion and water balance, kidney collecting duct epith - + @@ -12926,8 +13381,6 @@ Aside from their function in ion and water balance, kidney collecting duct epith The process preceding formation of the peptide bond between the first two amino acids of a protein. This includes the formation of a complex of the ribosome, mRNA or circRNA, and an initiation complex that contains the first aminoacyl-tRNA. - GO:0006440 - GO:0006454 biopolymerisation biopolymerization protein synthesis initiation @@ -12957,8 +13410,6 @@ Aside from their function in ion and water balance, kidney collecting duct epith The successive addition of amino acid residues to a nascent polypeptide chain during protein biosynthesis. - GO:0006442 - GO:0006455 protein synthesis elongation translation elongation biological_process @@ -12986,8 +13437,6 @@ Aside from their function in ion and water balance, kidney collecting duct epith The process resulting in the release of a polypeptide chain from the ribosome, usually in response to a termination codon (UAA, UAG, or UGA in the universal genetic code). - GO:0006443 - GO:0006456 protein synthesis termination translation termination translational complex disassembly @@ -13011,11 +13460,7 @@ Aside from their function in ion and water balance, kidney collecting duct epith The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter or a transporter complex, a pore or a motor protein. https://github.com/geneontology/go-ontology/issues/20292 - jl 2012-12-13T16:25:32Z - GO:0015457 - GO:0015460 - GO:0044765 biological_process single-organism transport GO:0006810 @@ -13114,8 +13559,6 @@ Aside from their function in ion and water balance, kidney collecting duct epith A programmed cell death process which begins when a cell receives an internal (e.g. DNA damage) or external signal (e.g. an extracellular death ligand), and proceeds through a series of biochemical events (signaling pathway phase) which trigger an execution phase. The execution phase is the last step of an apoptotic process, and is typically characterized by rounding-up of the cell, retraction of pseudopodes, reduction of cellular volume (pyknosis), chromatin condensation, nuclear fragmentation (karyorrhexis), plasma membrane blebbing and fragmentation of the cell into apoptotic bodies. When the execution phase is completed, the cell has died. - GO:0006917 - GO:0008632 cell suicide cellular suicide Wikipedia:Apoptosis @@ -13258,9 +13701,7 @@ Aside from their function in ion and water balance, kidney collecting duct epith A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of an organelle within a cell. An organelle is an organized structure of distinctive morphology and function. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton. Excludes the plasma membrane. https://github.com/geneontology/go-ontology/issues/27189 - jl 2013-12-19T15:25:51Z - GO:1902589 organelle organisation single organism organelle organization biological_process @@ -13393,11 +13834,6 @@ Aside from their function in ion and water balance, kidney collecting duct epith The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell. - GO:0023014 - GO:0023015 - GO:0023016 - GO:0023033 - GO:0023045 Wikipedia:Signal_transduction signaling cascade signalling cascade @@ -13540,7 +13976,6 @@ Aside from their function in ion and water balance, kidney collecting duct epith - GO:0009552 biological_process gametogenesis GO:0007276 @@ -13790,7 +14225,6 @@ Aside from their function in ion and water balance, kidney collecting duct epith The flow of blood through the body of an animal, enabling the transport of nutrients to the tissues and the removal of waste products. - GO:0070261 biological_process hemolymph circulation GO:0008015 @@ -13830,9 +14264,6 @@ Aside from their function in ion and water balance, kidney collecting duct epith Any process in which a protein is transported to, or maintained in, a specific location. https://github.com/geneontology/go-ontology/issues/23112 - GO:0008105 - GO:0016249 - GO:0034613 cellular protein localisation cellular protein localization protein localisation @@ -13884,11 +14315,7 @@ Aside from their function in ion and water balance, kidney collecting duct epith A biological process is the execution of a genetically-encoded biological module or program. It consists of all the steps required to achieve the specific biological objective of the module. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence. https://github.com/geneontology/go-ontology/issues/24968 - jl 2012-09-19T15:05:24Z - GO:0000004 - GO:0007582 - GO:0044699 Wikipedia:Biological_process biological process physiological process @@ -13918,21 +14345,15 @@ Aside from their function in ion and water balance, kidney collecting duct epith - + - The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation. + A cellular process consisting of the biochemical pathways by which a living organism transforms chemical substances. This includes including anabolism (biosynthetic process) and catabolism (catabolic process). Metabolic processes includes the transformation of small molecules, as well macromolecular processes such as DNA repair and replication, protein synthesis and degradation. https://github.com/geneontology/go-ontology/issues/26424 - jl + https://github.com/geneontology/go-ontology/issues/28932 2012-10-17T15:46:40Z - GO:0044236 - GO:0044710 Wikipedia:Metabolism metabolism - metabolic process resulting in cell growth - metabolism resulting in cell growth - multicellular organism metabolic process biological_process - single-organism metabolic process GO:0008152 @@ -13947,7 +14368,7 @@ Aside from their function in ion and water balance, kidney collecting duct epith - The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation. + A cellular process consisting of the biochemical pathways by which a living organism transforms chemical substances. This includes including anabolism (biosynthetic process) and catabolism (catabolic process). Metabolic processes includes the transformation of small molecules, as well macromolecular processes such as DNA repair and replication, protein synthesis and degradation. GOC:go_curators ISBN:0198547684 @@ -14013,11 +14434,9 @@ Aside from their function in ion and water balance, kidney collecting duct epith - The chemical reactions and pathways resulting in the formation of substances; typically the energy-requiring part of metabolism in which simpler substances are transformed into more complex ones. - jl + A cellular process consisting of the biochemical pathways by which a living organism synthesizes chemical substances. This typically represents the energy-requiring part of metabolism in which simpler substances are transformed into more complex ones. + https://github.com/geneontology/go-ontology/issues/28932 2012-10-17T15:52:18Z - GO:0044274 - GO:0044711 formation Wikipedia:Anabolism anabolism @@ -14036,7 +14455,7 @@ Aside from their function in ion and water balance, kidney collecting duct epith - The chemical reactions and pathways resulting in the formation of substances; typically the energy-requiring part of metabolism in which simpler substances are transformed into more complex ones. + A cellular process consisting of the biochemical pathways by which a living organism synthesizes chemical substances. This typically represents the energy-requiring part of metabolism in which simpler substances are transformed into more complex ones. GOC:curators ISBN:0198547684 @@ -14046,13 +14465,12 @@ Aside from their function in ion and water balance, kidney collecting duct epith + - The chemical reactions and pathways resulting in the formation of a macromolecule, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass. https://github.com/geneontology/go-ontology/issues/15249 https://github.com/geneontology/go-ontology/issues/25418 https://github.com/geneontology/go-ontology/issues/27189 - GO:0043284 biopolymer biosynthetic process macromolecule anabolism macromolecule biosynthesis @@ -14098,8 +14516,6 @@ Aside from their function in ion and water balance, kidney collecting duct epith The controlled release of proteins from a cell. - GO:0045166 - GO:0045731 glycoprotein secretion protein secretion during cell fate commitment protein secretion resulting in cell fate commitment @@ -14223,7 +14639,6 @@ Aside from their function in ion and water balance, kidney collecting duct epith The process whose specific outcome is the progression of an embryo from its formation until the end of its embryonic life stage. The end of the embryonic stage is organism-specific. For example, for mammals, the process would begin with zygote formation and end with birth. For insects, the process would begin at zygote formation and end with larval hatching. For plant zygotic embryos, this would be from zygote formation to the end of seed dormancy. For plant vegetative embryos, this would be from the initial determination of the cell or group of cells to form an embryo until the point when the embryo becomes independent of the parent plant. - GO:0009795 embryogenesis and morphogenesis Wikipedia:Embryogenesis embryogenesis @@ -14364,11 +14779,7 @@ Aside from their function in ion and water balance, kidney collecting duct epith Any process that is carried out at the cellular level, but not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level. - jl 2012-12-11T16:56:55Z - GO:0008151 - GO:0044763 - GO:0050875 cell physiology cellular physiological process cell growth and/or maintenance @@ -14437,7 +14848,6 @@ Aside from their function in ion and water balance, kidney collecting duct epith A process which begins when a cell receives an internal or external signal and activates a series of biochemical events (signaling pathway). The process ends with the death of the cell. https://github.com/geneontology/go-ontology/issues/24835 - GO:0016244 regulated cell death Wikipedia:Programmed_cell_death caspase-independent cell death @@ -14487,7 +14897,6 @@ Aside from their function in ion and water balance, kidney collecting duct epith The directed movement of proteins into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. - GO:0015831 enzyme transport biological_process GO:0015031 @@ -14549,9 +14958,6 @@ Aside from their function in ion and water balance, kidney collecting duct epith A lipid bilayer along with all the proteins and protein complexes embedded in it and attached to it. 2014-03-06T11:37:54Z - GO:0016021 - GO:0098589 - GO:0098805 Wikipedia:Biological_membrane Wikipedia:Transmembrane_protein integral component of membrane @@ -14610,8 +15016,6 @@ Aside from their function in ion and water balance, kidney collecting duct epith A process that results in the assembly, arrangement of constituent parts, or disassembly of a cellular component. - GO:0044235 - GO:0071842 cell organisation cellular component organisation at cellular level cellular component organisation in other organism @@ -14855,9 +15259,6 @@ Aside from their function in ion and water balance, kidney collecting duct epith The chemical reactions and pathways involving a protein. Includes protein modification. https://github.com/geneontology/go-ontology/issues/23112 https://github.com/geneontology/go-ontology/issues/27189 - GO:0006411 - GO:0044267 - GO:0044268 Wikipedia:Protein_metabolism cellular protein metabolic process cellular protein metabolism @@ -15021,7 +15422,6 @@ Aside from their function in ion and water balance, kidney collecting duct epith A cellular process that results in the breakdown of a cellular component. https://github.com/geneontology/go-ontology/issues/27189 - GO:0071845 cell structure disassembly cellular component disassembly at cellular level biological_process @@ -15046,9 +15446,7 @@ Aside from their function in ion and water balance, kidney collecting duct epith A biological process that directly contributes to the process of producing new individuals by one or two organisms. The new individuals inherit some proportion of their genetic material from the parent or parents. https://github.com/geneontology/go-ontology/issues/27054 - jl 2012-09-19T15:56:06Z - GO:0044702 Wikipedia:Reproduction biological_process single organism reproductive process @@ -15139,7 +15537,6 @@ Aside from their function in ion and water balance, kidney collecting duct epith The aggregation, arrangement and bonding together of a cellular component. - GO:0071844 cell structure assembly cellular component assembly at cellular level biological_process @@ -15242,10 +15639,7 @@ Aside from their function in ion and water balance, kidney collecting duct epith The entirety of a process in which information is transmitted within a biological system. This process begins with an active signal and ends when a cellular response has been triggered. - jl 2010-02-16T09:30:50Z - GO:0023046 - GO:0044700 biological signaling signaling process signalling @@ -15699,7 +16093,6 @@ Aside from their function in ion and water balance, kidney collecting duct epith The progressive compaction of dispersed interphase chromatin into threadlike chromosomes prior to mitotic or meiotic nuclear division, or during apoptosis, in eukaryotic cells. - GO:0000068 DNA condensation eukaryotic chromosome condensation nuclear chromosome condensation @@ -15824,7 +16217,6 @@ Aside from their function in ion and water balance, kidney collecting duct epith A structure lying external to one or more cells, which provides structural support, biochemical or biomechanical cues for cells or tissues. - GO:0005578 NIF_Subcellular:nlx_subcell_20090513 Wikipedia:Extracellular_matrix proteinaceous extracellular matrix @@ -15903,7 +16295,6 @@ Aside from their function in ion and water balance, kidney collecting duct epith Any small, fluid-filled, spherical organelle enclosed by membrane. - GO:0031988 NIF_Subcellular:sao221389602 Wikipedia:Vesicle_(biology) cellular_component @@ -16032,10 +16423,7 @@ Aside from their function in ion and water balance, kidney collecting duct epith - jl 2012-09-19T16:07:47Z - GO:0044707 - GO:0050874 organismal physiological process biological_process single-multicellular organism process @@ -16062,9 +16450,7 @@ Aside from their function in ion and water balance, kidney collecting duct epith A biological process whose specific outcome is the progression of an integrated living unit: an anatomical structure (which may be a subcellular structure, cell, tissue, or organ), or organism over time from an initial condition to a later condition. - jl 2012-12-19T12:21:31Z - GO:0044767 development biological_process single-organism developmental process @@ -16128,9 +16514,6 @@ Aside from their function in ion and water balance, kidney collecting duct epith The disaggregation of a protein-containing macromolecular complex into its constituent components. https://github.com/geneontology/go-ontology/issues/22580 - GO:0034623 - GO:0043241 - GO:0043624 protein complex disassembly biological_process cellular macromolecule complex disassembly @@ -16152,10 +16535,14 @@ Aside from their function in ion and water balance, kidney collecting duct epith - + + + + + + A stable assembly of two or more macromolecules, i.e. proteins, nucleic acids, carbohydrates or lipids, in which at least one component is a protein and the constituent parts function together. - GO:0043234 macromolecular complex macromolecule complex protein containing complex @@ -16265,7 +16652,6 @@ Aside from their function in ion and water balance, kidney collecting duct epith A process in which a monoatomic ion is transported across a membrane. Monatomic ions (also called simple ions) are ions consisting of exactly one atom. - GO:0099131 ion transmembrane transport ion membrane transport transmembrane ion transport @@ -16448,7 +16834,6 @@ Aside from their function in ion and water balance, kidney collecting duct epith The directed movement of a protein to a specific location within the extracellular region. - bf 2010-11-09T10:25:08Z establishment of protein localisation in extracellular region establishment of protein localization in extracellular region @@ -16480,7 +16865,6 @@ Aside from their function in ion and water balance, kidney collecting duct epith - bf 2011-12-12T10:53:24Z GEnC fenestration glomerular endothelial cell fenestration @@ -16607,9 +16991,6 @@ Aside from their function in ion and water balance, kidney collecting duct epith Any biological process involved in the maintenance of an internal steady state. - GO:0032844 - GO:0032845 - GO:0032846 homeostasis activation of homeostatic process inhibition of homeostatic process @@ -16741,9 +17122,6 @@ Aside from their function in ion and water balance, kidney collecting duct epith The chemical reactions and pathways involving macromolecules, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass. https://github.com/geneontology/go-ontology/issues/26424 - GO:0034960 - GO:0043283 - GO:0044259 biopolymer metabolic process macromolecule metabolism organismal macromolecule metabolism @@ -16841,14 +17219,17 @@ Aside from their function in ion and water balance, kidney collecting duct epith Organized structure of distinctive morphology and function, not bounded by a lipid bilayer membrane. Includes ribosomes, the cytoskeleton and chromosomes. https://github.com/geneontology/go-ontology/issues/21881 https://github.com/geneontology/go-ontology/issues/28153 + https://github.com/geneontology/go-ontology/issues/29106 NIF_Subcellular:sao1456184038 + membrane-less organelle + non-membrane-bounded organelle non-membrane-enclosed organelle cellular_component biological condensate GO:0043228 - non-membrane-bounded organelle + membraneless organelle @@ -16984,11 +17365,13 @@ Aside from their function in ion and water balance, kidney collecting duct epith Organized structure of distinctive morphology and function, not bounded by a lipid bilayer membrane and occurring within the cell. Includes ribosomes, the cytoskeleton and chromosomes. + https://github.com/geneontology/go-ontology/issues/29106 + intracellular non-membrane-bounded organelle intracellular non-membrane-enclosed organelle cellular_component GO:0043232 - intracellular non-membrane-bounded organelle + intracellular membraneless organelle @@ -17059,11 +17442,7 @@ Aside from their function in ion and water balance, kidney collecting duct epith Any process in which macromolecules aggregate, disaggregate, or are modified, resulting in the formation, disassembly, or alteration of a protein complex. https://github.com/geneontology/go-ontology/issues/22580 - mah 2010-09-08T10:01:42Z - GO:0034600 - GO:0034621 - GO:0071822 protein complex subunit organisation protein complex subunit organization biological_process @@ -17133,7 +17512,6 @@ Aside from their function in ion and water balance, kidney collecting duct epith A process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of a cellular component. Includes biosynthesis of constituent macromolecules, and those macromolecular modifications that are involved in synthesis or assembly of the cellular component. https://github.com/geneontology/go-ontology/issues/27194 - GO:0071843 cellular component biogenesis at cellular level biological_process GO:0044085 @@ -17162,7 +17540,6 @@ Aside from their function in ion and water balance, kidney collecting duct epith A ribonucleoprotein complex that contains aminoacylated initiator methionine tRNA, GTP, and initiation factor 2 (either eIF2 in eukaryotes, or IF2 in prokaryotes). In prokaryotes, fMet-tRNA (initiator) is used rather than Met-tRNA (initiator). - jl 2009-10-22T02:38:55Z translation initiation (ternary) complex Met-tRNA/eIF2.GTP ternary complex @@ -17179,35 +17556,6 @@ Aside from their function in ion and water balance, kidney collecting duct epith - - - - - - The chemical reactions and pathways by which individual cells transform chemical substances. - cellular metabolism - biological_process - intermediary metabolism - GO:0044237 - - This term should not be used for direct annotation. It should be possible to make a more specific annotation to one of the children of this term. - cellular metabolic process - - - - - The chemical reactions and pathways by which individual cells transform chemical substances. - GOC:go_curators - - - - - intermediary metabolism - GOC:mah - - - - @@ -17234,32 +17582,6 @@ Aside from their function in ion and water balance, kidney collecting duct epith - - - - - - The chemical reactions and pathways resulting in the formation of substances, carried out by individual cells. - https://github.com/geneontology/go-ontology/issues/27052 - cellular anabolism - cellular biosynthesis - cellular formation - cellular synthesis - biological_process - GO:0044249 - - This term should not be used for direct annotation. It should be possible to make a more specific annotation to one of the children of this term. - cellular biosynthetic process - - - - - The chemical reactions and pathways resulting in the formation of substances, carried out by individual cells. - GOC:jl - - - - @@ -17588,7 +17910,6 @@ Aside from their function in ion and water balance, kidney collecting duct epith The process in which anatomical structures are generated and organized during the embryonic phase. The embryonic phase begins with zygote formation. The end of the embryonic phase is organism-specific. For example, it would be at birth for mammals, larval hatching for insects and seed dormancy in plants. - GO:0048828 embryonic anatomical structure morphogenesis biological_process GO:0048598 @@ -17963,7 +18284,6 @@ Aside from their function in ion and water balance, kidney collecting duct epith Any process that modulates the frequency, rate or extent of a biological process. Biological processes are regulated by many means; examples include the control of gene expression, protein modification or interaction with a protein or substrate molecule. - GO:0050791 regulation of physiological process biological_process GO:0050789 @@ -18004,7 +18324,6 @@ Aside from their function in ion and water balance, kidney collecting duct epith Any process that modulates the frequency, rate or extent of a cellular process, any of those that are carried out at the cellular level, but are not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level. - GO:0051244 regulation of cellular physiological process biological_process GO:0050794 @@ -18154,7 +18473,6 @@ Aside from their function in ion and water balance, kidney collecting duct epith Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus. The process begins with detection of the stimulus and ends with a change in state or activity or the cell or organism. - GO:0051869 physiological response to stimulus biological_process GO:0050896 @@ -18184,9 +18502,7 @@ Aside from their function in ion and water balance, kidney collecting duct epith Any process in which a cell, a substance, or a cellular entity, such as a protein complex or organelle, is transported, tethered to or otherwise maintained in a specific location. In the case of substances, localization may also be achieved via selective degradation. https://github.com/geneontology/go-ontology/issues/27052 - jl 2013-12-18T13:51:04Z - GO:1902578 establishment and maintenance of localization establishment and maintenance of position localisation @@ -18316,9 +18632,6 @@ Aside from their function in ion and water balance, kidney collecting duct epith A process that is carried out at the cellular level that results in the assembly, arrangement of constituent parts, or disassembly of chromosomes, structures composed of a very long molecule of DNA and associated proteins that carries hereditary information. This term covers covalent modifications at the molecular level as well as spatial relationships among the major components of a chromosome. https://github.com/geneontology/go-ontology/issues/22811 https://github.com/geneontology/go-ontology/issues/4585 - GO:0006323 - GO:0007001 - GO:0051277 DNA condensation chromosome organisation DNA packaging @@ -18382,9 +18695,7 @@ Aside from their function in ion and water balance, kidney collecting duct epith A cellular localization process whereby a substance or cellular entity, such as a protein complex or organelle, is transported to, and/or maintained in, a specific location within a cell including the localization of substances or cellular entities to the cell membrane. https://github.com/geneontology/go-ontology/issues/27189 - jl 2013-12-18T14:04:32Z - GO:1902580 cellular localisation establishment and maintenance of cellular localization establishment and maintenance of localization in cell or cell membrane @@ -18466,9 +18777,7 @@ Aside from their function in ion and water balance, kidney collecting duct epith The process in which a solute is transported across a lipid bilayer, from one side of a membrane to the other. - tb 2015-10-21T13:22:47Z - GO:0090662 membrane transport ATP hydrolysis coupled transmembrane transport biological_process @@ -18574,7 +18883,6 @@ Aside from their function in ion and water balance, kidney collecting duct epith The process in which the anatomical structures of a tube are generated and organized from an epithelium. Epithelial tubes transport gases, liquids and cells from one site to another and form the basic structure of many organs and tissues, with tube shape and organization varying from the single-celled excretory organ in Caenorhabditis elegans to the branching trees of the mammalian kidney and insect tracheal system. - dph 2009-04-28T09:33:36Z biological_process GO:0060562 @@ -18595,7 +18903,6 @@ Aside from their function in ion and water balance, kidney collecting duct epith The process in which the anatomical structures of a branched epithelium are generated and organized. - dph 2010-05-25T09:05:34Z biological_process GO:0061138 @@ -18627,7 +18934,6 @@ Aside from their function in ion and water balance, kidney collecting duct epith An extracellular matrix consisting mainly of proteins (especially collagen) and glycosaminoglycans (mostly as proteoglycans) that provides not only essential physical scaffolding for the cellular constituents but can also initiate crucial biochemical and biomechanical cues required for tissue morphogenesis, differentiation and homeostasis. The components are secreted by cells in the vicinity and form a sheet underlying or overlying cells such as endothelial and epithelial cells. - dph 2018-04-13T12:47:21Z cellular_component GO:0062023 @@ -18668,9 +18974,6 @@ Aside from their function in ion and water balance, kidney collecting duct epith The aggregation, arrangement and bonding together of a set of macromolecules to form a protein-containing complex. https://github.com/geneontology/go-ontology/issues/22580 - GO:0006461 - GO:0034622 - GO:0043623 cellular protein complex assembly biological_process cellular macromolecule complex assembly @@ -18960,7 +19263,6 @@ Aside from their function in ion and water balance, kidney collecting duct epith Any process in which a macromolecule is transported to, and/or maintained in, a specific location at the level of a cell. Localization at the cellular level encompasses movement within the cell, from within the cell to the cell surface, or from one location to another at the surface of a cell. - mah 2009-06-16T04:08:29Z cellular macromolecule localisation biological_process @@ -19005,7 +19307,6 @@ Aside from their function in ion and water balance, kidney collecting duct epith The aggregation, arrangement and bonding together of a set of components to form an organelle. An organelle is an organized structure of distinctive morphology and function. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton. Excludes the plasma membrane. - mah 2009-09-15T03:00:51Z biological_process GO:0070925 @@ -19043,7 +19344,6 @@ Aside from their function in ion and water balance, kidney collecting duct epith Any process in which a protein is transported from one specific location in the extracellular region to another, or maintained in a specific extracellular location. - mah 2010-02-25T04:00:13Z protein localisation in extracellular region protein localization in extracellular region @@ -19089,7 +19389,6 @@ Aside from their function in ion and water balance, kidney collecting duct epith Any process in which macromolecules aggregate, disaggregate, or are modified, resulting in the formation, disassembly, or alteration of a ribonucleoprotein complex. https://github.com/geneontology/go-ontology/issues/25143 - mah 2010-09-08T10:10:35Z RNA-protein complex subunit organization protein-RNA complex subunit organization @@ -19132,9 +19431,7 @@ Aside from their function in ion and water balance, kidney collecting duct epith A process that results in the biosynthesis of constituent macromolecules, assembly, arrangement of constituent parts, or disassembly of a cellular component. https://github.com/geneontology/go-ontology/issues/27189 - mah 2010-09-10T01:39:16Z - GO:0071841 cellular component organisation or biogenesis cellular component organisation or biogenesis at cellular level cellular component organization or biogenesis at cellular level @@ -19172,7 +19469,6 @@ Aside from their function in ion and water balance, kidney collecting duct epith The broad region around and including the plasma membrane of a cell, encompassing the cell cortex (inside the cell), the plasma membrane, and any external encapsulating structures. - mah 2010-10-04T01:51:47Z cellular_component GO:0071944 @@ -19217,7 +19513,6 @@ Aside from their function in ion and water balance, kidney collecting duct epith The aggregation, arrangement and bonding together of a set of components to form an extracellular vesicular exosome, a membrane-bounded vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Exosomes are defined by their size, which generally ranges from 30 nm to 100 nm. - mah 2010-10-18T03:44:18Z extracellular vesicular exosome assembly biological_process @@ -19271,7 +19566,6 @@ Aside from their function in ion and water balance, kidney collecting duct epith The developmental process pertaining to the initial formation of an epithelial tube. https://github.com/geneontology/go-ontology/issues/22302 - mah 2010-02-26T02:15:40Z biological_process GO:0072175 @@ -19297,9 +19591,7 @@ Aside from their function in ion and water balance, kidney collecting duct epith The series of molecular signals which triggers the apoptotic death of a cell. The pathway starts with reception of a signal, and ends when the execution phase of apoptosis is triggered. - pr 2011-11-23T09:30:23Z - GO:0008624 apoptotic signalling pathway induction of apoptosis by extracellular signals biological_process @@ -19339,7 +19631,6 @@ Aside from their function in ion and water balance, kidney collecting duct epith A stage of the apoptotic process that starts with the controlled breakdown of the cell through the action of effector caspases or other effector molecules (e.g. cathepsins, calpains etc.). Key steps of the execution phase are rounding-up of the cell, retraction of pseudopodes, reduction of cellular volume (pyknosis), chromatin condensation, nuclear fragmentation (karyorrhexis), plasma membrane blebbing and fragmentation of the cell into apoptotic bodies. When the execution phase is completed, the cell has died. - pr 2011-11-23T09:45:24Z execution phase of apoptotic process apoptosis @@ -19362,7 +19653,6 @@ Aside from their function in ion and water balance, kidney collecting duct epith A renal system process in which fluid circulating through the body is filtered through a barrier system. - pr 2012-01-03T03:10:17Z biological_process GO:0097205 @@ -19385,7 +19675,6 @@ Aside from their function in ion and water balance, kidney collecting duct epith The elimination of substances from peritubular capillaries (or surrounding hemolymph in invertebrates) into the renal tubules to be incorporated subsequently into the urine. Substances that are secreted include organic anions, ammonia, potassium and drugs. https://github.com/geneontology/go-ontology/issues/22368 - pr 2012-03-05T02:03:58Z biological_process GO:0097254 @@ -19407,7 +19696,6 @@ Aside from their function in ion and water balance, kidney collecting duct epith The assembly and secretion of an extracellular exosome, a membrane-bounded vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. - pr 2016-10-03T14:35:25Z exosome assembly or secretion exosome biogenesis @@ -19452,7 +19740,6 @@ Aside from their function in ion and water balance, kidney collecting duct epith A membrane that is a (regional) part of the plasma membrane. - dos 2014-03-06T11:55:32Z region of plasma membrane cellular_component @@ -19509,7 +19796,6 @@ Aside from their function in ion and water balance, kidney collecting duct epith - @@ -19911,21 +20197,22 @@ Aside from their function in ion and water balance, kidney collecting duct epith - A part of a cellular organism that is either an immaterial entity or a material entity with granularity above the level of a protein complex but below that of an anatomical system. Or, a substance produced by a cellular organism with granularity above the level of a protein complex. + A part of a cellular organism consisting of a material entity with granularity above the level of a protein complex but below that of an anatomical system. Note that cellular organisms exclude viruses. https://github.com/geneontology/go-ontology/issues/24200 https://github.com/geneontology/go-ontology/issues/26424 - kmv + https://github.com/geneontology/go-ontology/issues/28978 2019-08-12T18:01:37Z + cellular anatomical entity cellular_component GO:0110165 - cellular anatomical entity + cellular anatomical structure - A part of a cellular organism that is either an immaterial entity or a material entity with granularity above the level of a protein complex but below that of an anatomical system. Or, a substance produced by a cellular organism with granularity above the level of a protein complex. + A part of a cellular organism consisting of a material entity with granularity above the level of a protein complex but below that of an anatomical system. Note that cellular organisms exclude viruses. GOC:kmv @@ -19954,7 +20241,6 @@ Aside from their function in ion and water balance, kidney collecting duct epith A prolongation or process extending from a cell and that is bounded by plasma membrane, e.g. a cilium, lamellipodium, or axon. https://github.com/geneontology/go-ontology/issues/13193 - krc 2017-03-21T17:26:07Z cellular_component GO:0120025 @@ -19993,7 +20279,6 @@ Aside from their function in ion and water balance, kidney collecting duct epith Formation of a prolongation or process extending and that is bounded by plasma membrane, e.g. a cilium, lamellipodium, or axon. https://github.com/geneontology/go-ontology/issues/13298 - krc 2017-04-24T23:56:08Z eupodium biological_process @@ -20041,7 +20326,6 @@ Aside from their function in ion and water balance, kidney collecting duct epith A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a plasma membrane bounded prolongation or process extending from a cell, e.g. a cilium or axon. https://github.com/geneontology/go-ontology/issues/13298 - krc 2017-04-26T16:07:02Z biological_process GO:0120036 @@ -20074,7 +20358,6 @@ Aside from their function in ion and water balance, kidney collecting duct epith A mitotic cell cycle process comprising the steps by which the nucleus of a eukaryotic cell divides; the process involves condensation of chromosomal DNA into a highly compacted form. Canonically, mitosis produces two daughter nuclei whose chromosome complement is identical to that of the mother cell. https://github.com/geneontology/go-ontology/issues/19910 - pg 2017-03-23T14:44:23Z mitosis biological_process @@ -20098,7 +20381,6 @@ Aside from their function in ion and water balance, kidney collecting duct epith The assembly and secretion a set of components to form an extracellular vesicule, a membrane-bounded vesicle that is released into the extracellular region. Extracellular vesicles include exosomes, microvesicles and apoptotic bodies, based on the mechanism by which they are released from cells and differentiated based on their size and content. https://github.com/geneontology/go-ontology/issues/14256 - pg 2017-10-23T11:53:42Z extracellular vesicle assembly biological_process @@ -20147,7 +20429,6 @@ Aside from their function in ion and water balance, kidney collecting duct epith The directed movement of some substance from a cell, into the extracellular region. This may occur via transport across the plasma membrane or via exocytosis. - pg 2019-05-22T11:20:45Z efflux biological_process @@ -20185,7 +20466,6 @@ Aside from their function in ion and water balance, kidney collecting duct epith A process that is part of the mitotic cell cycle. - jl 2014-05-22T14:22:34Z biological_process GO:1903047 @@ -20220,7 +20500,6 @@ Aside from their function in ion and water balance, kidney collecting duct epith Any vesicle that is part of the extracellular region. - jl 2014-10-22T14:26:11Z cellular_component microparticle @@ -20250,10 +20529,7 @@ Aside from their function in ion and water balance, kidney collecting duct epith A macromolecular complex that contains both RNA and protein molecules. - pr 2015-11-19T12:26:37Z - GO:0030529 - GO:1990903 Wikipedia:Ribonucleoprotein RNA-protein complex RNP @@ -20345,7 +20621,6 @@ Aside from their function in ion and water balance, kidney collecting duct epith - NCBITaxon:85055 GC_ID:1 house mouse mouse @@ -20384,7 +20659,6 @@ Aside from their function in ion and water balance, kidney collecting duct epith - NCBITaxon:40673 GC_ID:1 bony vertebrates ncbi_taxonomy @@ -20751,7 +21025,6 @@ Aside from their function in ion and water balance, kidney collecting duct epith - NCBITaxon:109679 GC_ID:1 ncbi_taxonomy NCBITaxon:39107 @@ -21010,7 +21283,6 @@ Aside from their function in ion and water balance, kidney collecting duct epith A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities - PATO:0000072 quality PATO:0000001 quality @@ -21048,7 +21320,6 @@ Aside from their function in ion and water balance, kidney collecting duct epith A morphological quality inhering in a bearer by virtue of the bearer's ratios of distances between its features (points, edges, surfaces and also holes etc). - PATO:0001647 relational shape quality quality PATO:0000052 @@ -21070,7 +21341,6 @@ Aside from their function in ion and water balance, kidney collecting duct epith A morphology quality inhering in a bearer by virtue of the bearer's relative position, shape, arrangements and connectivity of an organism's various parts; the pattern underlying its form. - PATO:0001452 conformation relational structural quality quality @@ -21170,7 +21440,6 @@ Aside from their function in ion and water balance, kidney collecting duct epith A quality of a physical entity that exists through action of continuants at the physical level of organisation in relation to other entities. - PATO:0002079 Wikipedia:Physical_property relational physical quality quality @@ -21192,8 +21461,6 @@ Aside from their function in ion and water balance, kidney collecting duct epith A quality which inheres in a continuant. - PATO:0001237 - PATO:0001238 snap:Quality monadic quality of a continuant multiply inhering quality of a physical entity @@ -21471,7 +21738,6 @@ Aside from their function in ion and water balance, kidney collecting duct epith A convex 3-D shape quality inhering in a bearer by virtue of the bearer's exhibiting a consistently-sized round cross section. - PATO:0001203 rod-like rod-shaped tubulate @@ -22023,7 +22289,6 @@ Aside from their function in ion and water balance, kidney collecting duct epith A quality inhering in a cell by virtue of the cell having a high nuclear/cytoplasmic ratio. - http://orcid.org/0000-0001-5208-3432 high N:C ratio quality PATO:0040072 @@ -22045,7 +22310,6 @@ Aside from their function in ion and water balance, kidney collecting duct epith A quality of continuant that exist at the anatomical level of organisation and anything under it. This includes, but is not limited to, cells , tissues, and components. - http://orcid.org/0000-0001-7258-9596 quality PATO:0070044 anatomical structure quality @@ -22058,7 +22322,6 @@ Aside from their function in ion and water balance, kidney collecting duct epith A quality inhering in an anotomical structure by virtue of its capacity to be stained by specific histological dyes. - http://orcid.org/0000-0001-7258-9596 quality PATO:0070045 anatomical histological quality @@ -22071,7 +22334,6 @@ Aside from their function in ion and water balance, kidney collecting duct epith An affinity inhering in an anatomical structure by virtue of the bearer exhibiting a molecular interaction for both basic and acid stains under specific pH conditions. - http://orcid.org/0000-0001-7258-9596 quality PATO:0070047 polychromatophilic @@ -22089,7 +22351,7 @@ Aside from their function in ion and water balance, kidney collecting duct epith - + @@ -22101,7 +22363,7 @@ Aside from their function in ion and water balance, kidney collecting duct epith native protein protein PR:000000001 - The definition above excludes protein complexes, which some also consider a protein. Those who wish to refer to a class representing both senses of the word are directed to CHEBI:36080. Note that the definition allows for experimentally-manipulated genes, and allows for artifically-produced derivatives that mimic those found naturally. Proteins (in the sense defined here) that descended from a common ancestor can be classified into families and superfamilies composed of products of evolutionarily-related genes. The domain architecture of a protein is described by the order of its constituent domains. Proteins with the same domains in the same order are defined as homeomorphic [PRO:WCB]. + The definition above excludes protein complexes, which some also consider a protein. Those who wish to refer to a class representing both senses of the word are directed to CHEBI:36080. Note that the definition allows for experimentally-manipulated genes, and allows for artifically-produced derivatives that mimic those found naturally. Proteins (in the sense defined here) that descended from a common ancestor can be classified into families and superfamilies composed of products of evolutionarily-related genes. The domain architecture of a protein is described by the order of its constituent domains. Proteins with the same domains in the same order are defined as homeomorphic [PRO:WCB). protein @@ -22783,7 +23045,6 @@ Aside from their function in ion and water balance, kidney collecting duct epith - A protein with core architecture consisting of a signal sequence, followed by 7 Ig-like domains (Pfam:PF00047, Pfam:PF07679, or Pfam:PF07686), a transmembrane region, and a cytoplasmic Protein tyrosine kinase domain. PIRSF:PIRSF038502 protein @@ -23211,51 +23472,51 @@ Aside from their function in ion and water balance, kidney collecting duct epith - + - + - A material entity that minimally consists of a protein. + A molecular entity that minimally consists of a protein. protein protein aggregate protein complex protein-containing complex protein - PR:000050567 - Note: This includes single proteins and derivatives thereof (PR:000000001), protein-containing complexes (GO:0032991), and protein aggregates (PR:000050566). - protein-containing material entity + PR:000064867 + Note: This includes single proteins and derivatives thereof (PR:000000001), protein-containing complexes (GO:0032991), and protein aggregates (PR:000050565). + protein-containing molecular entity - + - A material entity that minimally consists of a protein. + A molecular entity that minimally consists of a protein. PRO:DAN - + protein PRO:DAN - + protein aggregate PRO:DAN - + protein complex PRO:DAN - + protein-containing complex PRO:DAN @@ -23458,7 +23719,7 @@ Aside from their function in ion and water balance, kidney collecting duct epith - + @@ -23512,14 +23773,14 @@ Aside from their function in ion and water balance, kidney collecting duct epith ureter https://upload.wikimedia.org/wikipedia/commons/3/30/Urinary_system.svg - + - + GO @@ -23569,7 +23830,7 @@ Aside from their function in ion and water balance, kidney collecting duct epith - + @@ -23617,14 +23878,14 @@ Aside from their function in ion and water balance, kidney collecting duct epith urethra https://upload.wikimedia.org/wikipedia/commons/c/cb/Female_anatomy.png - + - + Wikipedia @@ -23646,7 +23907,6 @@ Aside from their function in ion and water balance, kidney collecting duct epith - @@ -23733,7 +23993,6 @@ Aside from their function in ion and water balance, kidney collecting duct epith Organ component adjacent to an organ cavity and which consists of a maximal aggregate of organ component layers. - UBERON:0009915 wall FMA:82482 galen:Wall @@ -24132,7 +24391,7 @@ Aside from their function in ion and water balance, kidney collecting duct epith - + @@ -24182,14 +24441,14 @@ Aside from their function in ion and water balance, kidney collecting duct epith http://upload.wikimedia.org/wikipedia/commons/3/30/Gray1130.svg https://upload.wikimedia.org/wikipedia/commons/2/22/Renal_corpuscle.svg - + - + FMA MA @@ -24282,7 +24541,6 @@ Aside from their function in ion and water balance, kidney collecting duct epith Anatomical cluster consisting of the skeletal elements and articular elements that are part of an individual subdivision of the organism. - UBERON:0010322 FMA:85544 NCIT:C34076 SCTID:118966000 @@ -24452,14 +24710,14 @@ Aside from their function in ion and water balance, kidney collecting duct epith - + - + @@ -24491,24 +24749,24 @@ Aside from their function in ion and water balance, kidney collecting duct epith metanephros - + - + - + GO - + ISBN:9780878932504 @@ -24623,8 +24881,8 @@ Aside from their function in ion and water balance, kidney collecting duct epith - - + + An epithelial swelling on the Wolffian duct that elongates to invade the adjacent metanephric mesenchyme[MP]. BTO:0001646 EHDAA2:0002140 @@ -24648,11 +24906,11 @@ Aside from their function in ion and water balance, kidney collecting duct epith ureteric bud - + - + @@ -24665,13 +24923,13 @@ Aside from their function in ion and water balance, kidney collecting duct epith - + EHDAA2 - + ISBN:9780878932504 @@ -25052,7 +25310,7 @@ Aside from their function in ion and water balance, kidney collecting duct epith - + @@ -25088,14 +25346,14 @@ Aside from their function in ion and water balance, kidney collecting duct epith gastrula stage - + - + BILS @@ -25355,8 +25613,8 @@ Aside from their function in ion and water balance, kidney collecting duct epith - - + + @@ -25382,24 +25640,24 @@ Aside from their function in ion and water balance, kidney collecting duct epith UBERON:0000162 cloaca - + - + - + ZFA - + AAO @@ -25440,8 +25698,8 @@ Aside from their function in ion and water balance, kidney collecting duct epith - - + + @@ -25459,24 +25717,24 @@ Aside from their function in ion and water balance, kidney collecting duct epith embryonic cloaca - + - + - + EHDAA2 - + EHDAA2 @@ -25499,7 +25757,7 @@ Aside from their function in ion and water balance, kidney collecting duct epith - + @@ -25538,14 +25796,14 @@ Aside from their function in ion and water balance, kidney collecting duct epith primitive urogenital sinus http://upload.wikimedia.org/wikipedia/commons/6/6d/Gray1109.png - + - + MP-def @@ -25773,8 +26031,6 @@ Aside from their function in ion and water balance, kidney collecting duct epith A portion of organism substance that is the product of an excretion process that will be eliminated from the body. An excretion process is elimination by an organism of the waste products that arise as a result of metabolic activity. - UBERON:0000324 - UBERON:0007550 AEO:0000184 BTO:0000491 EHDAA2_RETIRED:0003184 @@ -25820,7 +26076,7 @@ Aside from their function in ion and water balance, kidney collecting duct epith - + @@ -25828,15 +26084,15 @@ Aside from their function in ion and water balance, kidney collecting duct epith - + - - + + A fluid that is composed of blood plasma and erythrocytes. AAO:0000046 @@ -25873,34 +26129,34 @@ Aside from their function in ion and water balance, kidney collecting duct epith blood - + - + - + - + CL:tm - + https://github.com/obophenotype/uberon/issues/1330 - + Bgee:AN @@ -26002,7 +26258,6 @@ Aside from their function in ion and water balance, kidney collecting duct epith Organism at the blastula stage - an early stage of embryonic development in animals. It is produced by cleavage of a fertilized ovum and consists of a spherical layer of around 128 cells surrounding a central fluid-filled cavity called the blastocoel. The blastula follows the morula and precedes the gastrula in the developmental sequence. TODO - check relationship with epiblast. Note in FMA this is not a subclass of embryo, but in uberon embryo is the whole organism from zygote onwards and thus includes the blastula - UBERON:0007011 BILA:0000059 BTO:0000128 GAID:1294 @@ -27229,7 +27484,6 @@ Aside from their function in ion and water balance, kidney collecting duct epith - @@ -27243,7 +27497,7 @@ Aside from their function in ion and water balance, kidney collecting duct epith - + @@ -27285,14 +27539,14 @@ Aside from their function in ion and water balance, kidney collecting duct epith epithelium https://upload.wikimedia.org/wikipedia/commons/8/8f/Illu_epithelium.jpg - + - + http://palaeos.com/metazoa/porifera/homoscleromorpha.html @@ -27650,7 +27904,7 @@ Aside from their function in ion and water balance, kidney collecting duct epith - + @@ -27685,14 +27939,14 @@ Aside from their function in ion and water balance, kidney collecting duct epith abdomen - + - + MA @@ -27921,7 +28175,7 @@ Aside from their function in ion and water balance, kidney collecting duct epith - + Primary germ layer that is the outer of the embryo's three germ layers and gives rise to epidermis and neural tissue. AAO:0000137 BILA:0000036 @@ -27956,14 +28210,14 @@ Aside from their function in ion and water balance, kidney collecting duct epith ectoderm http://upload.wikimedia.org/wikipedia/commons/1/19/Gray32.png - + - + Bgee:AN @@ -28003,7 +28257,7 @@ Aside from their function in ion and water balance, kidney collecting duct epith - + Primary germ layer that lies remote from the surface of the embryo and gives rise to internal tissues such as gut. AAO:0000139 BILA:0000038 @@ -28038,14 +28292,14 @@ Aside from their function in ion and water balance, kidney collecting duct epith http://upload.wikimedia.org/wikipedia/commons/c/c0/Endoderm2.png http://upload.wikimedia.org/wikipedia/commons/d/df/Gray10.png - + - + Bgee:AN @@ -28086,10 +28340,9 @@ Aside from their function in ion and water balance, kidney collecting duct epith - + The middle germ layer of the embryo, between the endoderm and ectoderm. - UBERON:0003263 AAO:0000304 BILA:0000037 BTO:0000839 @@ -28127,14 +28380,14 @@ Aside from their function in ion and water balance, kidney collecting duct epith mesoderm http://upload.wikimedia.org/wikipedia/commons/e/e8/Mesoderm.png - + - + Bgee:AN @@ -28300,7 +28553,7 @@ Aside from their function in ion and water balance, kidney collecting duct epith - + @@ -28343,7 +28596,7 @@ Aside from their function in ion and water balance, kidney collecting duct epith proctodeum https://github.com/obophenotype/uberon/issues/685 - + @@ -28356,7 +28609,7 @@ Aside from their function in ion and water balance, kidney collecting duct epith - + EHDAA2 @@ -28418,7 +28671,7 @@ Aside from their function in ion and water balance, kidney collecting duct epith - + @@ -28489,14 +28742,14 @@ Aside from their function in ion and water balance, kidney collecting duct epith https://cdn.humanatlas.io/digital-objects/ref-organ/heart-female/v1.3/assets/3d-vh-f-heart.glb https://cdn.humanatlas.io/digital-objects/ref-organ/heart-male/v1.3/assets/3d-vh-m-heart.glb - + - + MA @@ -29198,7 +29451,6 @@ Aside from their function in ion and water balance, kidney collecting duct epith - AAO:0000959 CALOHA:TS-2103 VHOG:0001248 @@ -29206,7 +29458,6 @@ Aside from their function in ion and water balance, kidney collecting duct epith uberon systema cardiovasculare UBERON:0001009 - circulatory system http://upload.wikimedia.org/wikipedia/commons/2/29/Circulatory_System_en.svg @@ -29350,7 +29601,7 @@ Aside from their function in ion and water balance, kidney collecting duct epith - + @@ -29398,14 +29649,14 @@ Aside from their function in ion and water balance, kidney collecting duct epith http://upload.wikimedia.org/wikipedia/commons/b/b2/TE-Nervous_system_diagram.svg http://upload.wikimedia.org/wikipedia/commons/b/ba/Nervous_system_diagram.png - + - + Bgee:AN @@ -29471,7 +29722,7 @@ Aside from their function in ion and water balance, kidney collecting duct epith - + The central nervous system is the core nervous system that serves an integrating and coordinating function. In vertebrates it consists of the neural tube derivatives: the brain and spinal cord. In invertebrates it includes central ganglia plus nerve cord. @@ -29516,7 +29767,7 @@ Aside from their function in ion and water balance, kidney collecting duct epith central nervous system - + @@ -29530,7 +29781,7 @@ Aside from their function in ion and water balance, kidney collecting duct epith - + Bgee:AN @@ -29727,7 +29978,7 @@ Aside from their function in ion and water balance, kidney collecting duct epith - + @@ -29761,14 +30012,14 @@ Aside from their function in ion and water balance, kidney collecting duct epith hindgut http://upload.wikimedia.org/wikipedia/commons/f/f7/Gray472.png - + - + Wikipedia @@ -30259,14 +30510,14 @@ Aside from their function in ion and water balance, kidney collecting duct epith - + - + @@ -30318,24 +30569,24 @@ Aside from their function in ion and water balance, kidney collecting duct epith renal pelvis https://upload.wikimedia.org/wikipedia/commons/c/c0/Illu_kidney2.jpg - + - + - + MA - + FMA @@ -30381,7 +30632,7 @@ Aside from their function in ion and water balance, kidney collecting duct epith - + @@ -30417,14 +30668,14 @@ Aside from their function in ion and water balance, kidney collecting duct epith https://cdn.humanatlas.io/digital-objects/ref-organ/kidney-male-right/v1.3/assets/3d-vh-m-kidney-r.glb https://upload.wikimedia.org/wikipedia/commons/6/69/Illu_kidney.jpg - + - + FMA @@ -30460,7 +30711,7 @@ Aside from their function in ion and water balance, kidney collecting duct epith - + @@ -30505,14 +30756,14 @@ Aside from their function in ion and water balance, kidney collecting duct epith renal corpuscle https://upload.wikimedia.org/wikipedia/commons/2/22/Renal_corpuscle.svg - + - + MA ZFA @@ -30586,7 +30837,7 @@ Aside from their function in ion and water balance, kidney collecting duct epith - + @@ -30628,14 +30879,14 @@ Aside from their function in ion and water balance, kidney collecting duct epith glomerular capsule http://upload.wikimedia.org/wikipedia/commons/3/30/Gray1130.svg - + - + Wikipedia @@ -30725,10 +30976,10 @@ Aside from their function in ion and water balance, kidney collecting duct epith - + - + @@ -30743,7 +30994,6 @@ Aside from their function in ion and water balance, kidney collecting duct epith An epithelial tube that is part of the nephron, the functional part of the kidney. - UBERON:0004210 renal tubule BTO:0000343 CALOHA:TS-1262 @@ -30772,7 +31022,7 @@ Aside from their function in ion and water balance, kidney collecting duct epith nephron tubule - + @@ -30781,14 +31031,14 @@ Aside from their function in ion and water balance, kidney collecting duct epith - + - + GO MA ZFA @@ -30802,7 +31052,7 @@ Aside from their function in ion and water balance, kidney collecting duct epith - + ZFA @@ -31016,7 +31266,7 @@ Aside from their function in ion and water balance, kidney collecting duct epith - + @@ -31063,7 +31313,7 @@ Aside from their function in ion and water balance, kidney collecting duct epith https://cdn.humanatlas.io/digital-objects/ref-organ/urinary-bladder-male/v1.2/assets/3d-vh-m-urinary-bladder.glb https://upload.wikimedia.org/wikipedia/commons/3/30/Urinary_system.svg - + @@ -31076,7 +31326,7 @@ Aside from their function in ion and water balance, kidney collecting duct epith - + FMA @@ -31206,7 +31456,7 @@ Aside from their function in ion and water balance, kidney collecting duct epith - + @@ -31219,7 +31469,7 @@ Aside from their function in ion and water balance, kidney collecting duct epith - + The basic functional unit of the kidney. its chief function is to regulate the concentration of water and soluble substances like sodium salts by filtering the blood, reabsorbing what is needed and excreting the rest as urine. A nephron eliminates wastes from the body, regulates blood volume and blood pressure, controls levels of electrolytes and metabolites, and regulates blood pH. Its functions are vital to life and are regulated by the endocrine system by hormones such as antidiuretic hormone, aldosterone, and parathyroid hormone.[WP]. kidney terms require review for cross-vertebrate compatibility and developmental relationships. @@ -31250,24 +31500,24 @@ Aside from their function in ion and water balance, kidney collecting duct epith nephron http://upload.wikimedia.org/wikipedia/commons/0/02/Gray1128.png - + - + - + FMA - + Bgee:AN @@ -31318,14 +31568,14 @@ Aside from their function in ion and water balance, kidney collecting duct epith - + - + @@ -31361,11 +31611,11 @@ Aside from their function in ion and water balance, kidney collecting duct epith proximal convoluted tubule http://upload.wikimedia.org/wikipedia/commons/0/02/Gray1128.png - + - + @@ -31378,13 +31628,13 @@ Aside from their function in ion and water balance, kidney collecting duct epith - + GO - + Wikipedia @@ -31516,7 +31766,7 @@ Aside from their function in ion and water balance, kidney collecting duct epith - + @@ -31543,7 +31793,7 @@ Aside from their function in ion and water balance, kidney collecting duct epith descending limb of loop of Henle http://upload.wikimedia.org/wikipedia/commons/0/02/Gray1128.png - + @@ -31556,7 +31806,7 @@ Aside from their function in ion and water balance, kidney collecting duct epith - + FMA @@ -31580,14 +31830,14 @@ Aside from their function in ion and water balance, kidney collecting duct epith - + - + @@ -31609,7 +31859,6 @@ Aside from their function in ion and water balance, kidney collecting duct epith The proximal straight tubule is the part of the descending limb that extends from the proximal convoluted tubule to the descending thin tubule. TODO - is S3 exactly coincident with PST? todo - ensure relationships work across species (loop of Henle) - UBERON:0005166 BTO:0000055 EMAPA:29661 EMAPA:29669 @@ -31632,11 +31881,11 @@ Aside from their function in ion and water balance, kidney collecting duct epith proximal straight tubule - + - + @@ -31649,13 +31898,13 @@ Aside from their function in ion and water balance, kidney collecting duct epith - + MA - + MA @@ -31697,7 +31946,7 @@ Aside from their function in ion and water balance, kidney collecting duct epith - + @@ -31733,7 +31982,7 @@ Aside from their function in ion and water balance, kidney collecting duct epith distal convoluted tubule https://upload.wikimedia.org/wikipedia/commons/2/21/Kidney_nephron.png - + @@ -31746,7 +31995,7 @@ Aside from their function in ion and water balance, kidney collecting duct epith - + EMAPA GO MA-modified-from-isa @@ -32021,7 +32270,7 @@ Aside from their function in ion and water balance, kidney collecting duct epith - + @@ -32044,14 +32293,14 @@ Aside from their function in ion and water balance, kidney collecting duct epith kidney arcuate artery https://upload.wikimedia.org/wikipedia/commons/8/87/2610_The_Kidney.jpg - + - + MA @@ -32092,7 +32341,7 @@ Aside from their function in ion and water balance, kidney collecting duct epith - + A tube extending from the mouth to the anus. @@ -32129,14 +32378,14 @@ Aside from their function in ion and water balance, kidney collecting duct epith digestive tract - + - + NCBIBook:NBK10107 @@ -32614,7 +32863,6 @@ Aside from their function in ion and water balance, kidney collecting duct epith - @@ -32842,7 +33090,6 @@ Aside from their function in ion and water balance, kidney collecting duct epith - @@ -32851,8 +33098,8 @@ Aside from their function in ion and water balance, kidney collecting duct epith - - + + @@ -32865,7 +33112,7 @@ Aside from their function in ion and water balance, kidney collecting duct epith - + @@ -32919,34 +33166,34 @@ Aside from their function in ion and water balance, kidney collecting duct epith blood vessel http://upload.wikimedia.org/wikipedia/commons/2/29/Circulatory_System_en.svg - + - + - + - + AEO - + EHDAA2 - + GO:0072360 @@ -33803,7 +34050,7 @@ Aside from their function in ion and water balance, kidney collecting duct epith - + @@ -33855,14 +34102,14 @@ Aside from their function in ion and water balance, kidney collecting duct epith kidney - + - + FMA @@ -33897,8 +34144,8 @@ Aside from their function in ion and water balance, kidney collecting duct epith - - + + @@ -33906,7 +34153,6 @@ Aside from their function in ion and water balance, kidney collecting duct epith In mammals, the pronephros is the first of the three embryonic kidneys to be established and exists only transiently. In lower vertebrates such as fish and amphibia, the pronephros is the fully functional embryonic kidney and is indispensible for larval life[GO]. - UBERON:0005794 AAO:0011089 BTO:0001541 EFO:0000927 @@ -33936,11 +34182,11 @@ Aside from their function in ion and water balance, kidney collecting duct epith Once the more complex mesonephros forms the pronephros undergoes apoptosis in amphibians. In fishes the nephron degenerates but the organ remains and becomes a component of the immune system[Wikipedia:Pronephros]. // TODO - check developmental relationships. Note that we previously include the ZFA/XAO terms under the more specific 'pronephric kidney', but these are now merged. TODO GCI: relationship: capable_of GO:0030104 pronephros - + - + @@ -33953,13 +34199,13 @@ Aside from their function in ion and water balance, kidney collecting duct epith - + OG - + ZFA @@ -34285,9 +34531,8 @@ Aside from their function in ion and water balance, kidney collecting duct epith - - + @@ -34306,7 +34551,7 @@ Aside from their function in ion and water balance, kidney collecting duct epith - + An anatomical structure which consists of juxtaglomerular cells, extraglomerular mesangial cells and the macula densa. The juxtaglomerular apparatus lies adjacent to the glomerulus and regulates kidney function by maintaining the blood flow to the kidney and the filtration rate[GO]. a microscopic structure in the kidney, which regulates the function of each nephron. The juxtaglomerular apparatus is named for its proximity to the glomerulus: it is found between the vascular pole of the renal corpuscle and the returning distal convoluted tubule of the same nephron. This location is critical to its function in regulating renal blood flow and glomerular filtration rate. The three cellular components of the apparatus are the macula densa, extraglomerular mesangial cells, and juxtaglomerular cells (also known as granular cells)[WP]. BTO:0005157 @@ -34328,24 +34573,24 @@ Aside from their function in ion and water balance, kidney collecting duct epith juxtaglomerular apparatus - + - + - + MA - + GO @@ -34469,8 +34714,8 @@ Aside from their function in ion and water balance, kidney collecting duct epith - - + + @@ -34487,24 +34732,24 @@ Aside from their function in ion and water balance, kidney collecting duct epith EDITOR_NOTE check MA part_ofs - should be spatially disjoint from renal glomerulus? extraglomerular mesangium - + - + - + MA - + MA @@ -34534,7 +34779,6 @@ Aside from their function in ion and water balance, kidney collecting duct epith The cavity within the body of all animals higher than the coelenterates and certain primitive worms, formed by the splitting of the embryonic mesoderm into two layers. In mammals it forms the peritoneal, pleural, and pericardial cavities. - UBERON:0000169 body cavity AEO:0000186 BTO:0001707 @@ -34546,7 +34790,6 @@ Aside from their function in ion and water balance, kidney collecting duct epith SCTID:361348008 TAO:0001438 UMLS:C0333343 - ZFA:0001438 galen:BodyCavity coelomic cavity coelomic cavity lumen @@ -34646,9 +34889,9 @@ Aside from their function in ion and water balance, kidney collecting duct epith - - - + + + @@ -34696,15 +34939,15 @@ Aside from their function in ion and water balance, kidney collecting duct epith notochord http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png - + - + - + @@ -34723,19 +34966,19 @@ Aside from their function in ion and water balance, kidney collecting duct epith - + http://tolweb.org/Chordata/2499 - + ZFA - + EHDAA2 @@ -34775,8 +35018,8 @@ Aside from their function in ion and water balance, kidney collecting duct epith - - + + Somites are spheres of epithelial cells that form sequentially along the anterior-posterior axis of the embryo through mesenchymal to epithelial transition of the presomitic mesoderm. mesodermal cluster @@ -34814,11 +35057,11 @@ Aside from their function in ion and water balance, kidney collecting duct epith somite http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png - + - + @@ -34831,13 +35074,13 @@ Aside from their function in ion and water balance, kidney collecting duct epith - + GOTAX:0000352 - + ZFA @@ -34897,8 +35140,8 @@ Aside from their function in ion and water balance, kidney collecting duct epith - - + + The macula densa is an area of specialized cells in the distal tubule that makes contact with the vascular pole of the glomerulus[GO]. BTO:0003940 @@ -34916,24 +35159,24 @@ Aside from their function in ion and water balance, kidney collecting duct epith macula densa - + - + - + MA - + GO @@ -34958,22 +35201,22 @@ Aside from their function in ion and water balance, kidney collecting duct epith - + - - + + - + A specialized region of ectoderm found between the neural ectoderm (neural plate) and non-neural ectoderm and composed of highly migratory pluripotent cells that delaminate in early embryonic development from the dorsal neural tube and give rise to an astounding variety of differentiated cell types[MP]. AAO:0010578 BTO:0001764 @@ -35006,45 +35249,45 @@ Aside from their function in ion and water balance, kidney collecting duct epith http://upload.wikimedia.org/wikipedia/commons/5/5f/Gray644.png https://upload.wikimedia.org/wikipedia/commons/8/8f/Neural_Crest.png - + - + - + - + - + XAO https://github.com/obophenotype/uberon/wiki/The-neural-crest - + BTO - + PMID:11523831 - + PMID:11523831 @@ -35408,7 +35651,7 @@ Aside from their function in ion and water balance, kidney collecting duct epith - + @@ -35461,14 +35704,14 @@ Aside from their function in ion and water balance, kidney collecting duct epith hematopoietic system - + - + FMA @@ -35673,6 +35916,7 @@ Aside from their function in ion and water balance, kidney collecting duct epith + @@ -35686,7 +35930,7 @@ Aside from their function in ion and water balance, kidney collecting duct epith - + Unsegmented field of paraxial mesoderm present posterior to the most recently formed somite pair, from which somites will form. AAO:0011086 EFO:0001982 @@ -35709,14 +35953,14 @@ Aside from their function in ion and water balance, kidney collecting duct epith presomitic mesoderm - + - + Bgee:AN @@ -35750,15 +35994,14 @@ Aside from their function in ion and water balance, kidney collecting duct epith - - - + + In mammals, the pronephric duct is the predecessor of the Wolffian duct[WP]. AAO:0011088 NCIT:C34279 @@ -35777,11 +36020,11 @@ Aside from their function in ion and water balance, kidney collecting duct epith The pronephric duct collects the filtrate from the pronephric tubules and opens to the exterior of the pronephric kidney[GOC:mtg_kidney_jan10, PMID:15647339, XAO:0000063, ZFA:0000150] pronephric duct - + - + @@ -35794,13 +36037,13 @@ Aside from their function in ion and water balance, kidney collecting duct epith - + Wikipedia - + XAO @@ -35906,9 +36149,9 @@ Aside from their function in ion and water balance, kidney collecting duct epith - - - + + + @@ -35947,34 +36190,34 @@ Aside from their function in ion and water balance, kidney collecting duct epith intermediate mesoderm http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png - + - + - + - + AAO - + EMAPA - + XAO @@ -36083,7 +36326,7 @@ Aside from their function in ion and water balance, kidney collecting duct epith - + Paired organ that connects the primitive kidney Wolffian body (or mesonephros) to the cloaca and serves as the anlage for certain male reproductive organs. the Wolffian duct is what remains of the pronephric duct after the atrophy of the pronephros[WP]. In Zebrafish: Duct of the adult kidney (mesonephros), present bilaterally ventral to the somites and leading to the cloacal chamber[ZFA]. Consider adding subclasses for male and female specific variants TODO - mesonephric portion of the nephric duct @@ -36112,7 +36355,7 @@ Aside from their function in ion and water balance, kidney collecting duct epith mesonephric duct http://upload.wikimedia.org/wikipedia/commons/6/6d/Gray1109.png - + @@ -36125,7 +36368,7 @@ Aside from their function in ion and water balance, kidney collecting duct epith - + EHDAA2 @@ -36179,9 +36422,9 @@ Aside from their function in ion and water balance, kidney collecting duct epith - - - + + + A region of embryonic ectodermal cells that lie directly above the notochord. During neurulation, they change shape and produce an infolding of the neural plate (the neural fold) that then seals to form the neural tube[XAO]. The earliest recognizable dorsal ectodermal primordium of the central nervous system present near the end of gastrulation before infolding to form the neural keel; consists of a thickened pseudostratified epithelium[ZFA]. AAO:0011072 BTO:0001765 @@ -36210,34 +36453,34 @@ Aside from their function in ion and water balance, kidney collecting duct epith neural plate https://upload.wikimedia.org/wikipedia/commons/8/8f/Neural_Crest.png - + - + - + - + GOTAX:0000352 - + Wikipedia - + Bgee:AN @@ -36277,7 +36520,7 @@ Aside from their function in ion and water balance, kidney collecting duct epith - + The paraxial mesoderm is the mesoderm located bilaterally adjacent to the notochord and neural tube[GO]. AAO:0010568 EFO:0003515 @@ -36303,7 +36546,7 @@ Aside from their function in ion and water balance, kidney collecting duct epith paraxial mesoderm http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png - + @@ -36316,7 +36559,7 @@ Aside from their function in ion and water balance, kidney collecting duct epith - + Bgee:AN @@ -36363,7 +36606,7 @@ Aside from their function in ion and water balance, kidney collecting duct epith - + @@ -36377,7 +36620,6 @@ Aside from their function in ion and water balance, kidney collecting duct epith Portion of the middle of the three primary germ layers of the embryo that resides on the periphery of the embryo, is continuous with the extra-embryonic mesoderm, splits into two layers enclosing the intra-embryonic coelom, and gives rise to body wall structures[MP]. - UBERON:0006258 AAO:0010574 EHDAA2:0000919 EHDAA:379 @@ -36403,7 +36645,7 @@ Aside from their function in ion and water balance, kidney collecting duct epith lateral plate mesoderm http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png - + @@ -36416,7 +36658,7 @@ Aside from their function in ion and water balance, kidney collecting duct epith - + EHDAA2 VHOG @@ -36466,15 +36708,15 @@ Aside from their function in ion and water balance, kidney collecting duct epith - - + + - + Bilateral groups of cells consisting of three rows: one row of endocardial precursors medially and two rows of myocardical precursors laterally. The two populations fuse at the midline to form the heart rudiment or cone. should probably be merged with heart rudiment. AAO:0011044 @@ -36491,15 +36733,15 @@ Aside from their function in ion and water balance, kidney collecting duct epith heart primordium - + - + - + @@ -36512,19 +36754,19 @@ Aside from their function in ion and water balance, kidney collecting duct epith - + ZFA - + ZFA - + XAO @@ -36553,8 +36795,8 @@ Aside from their function in ion and water balance, kidney collecting duct epith - - + + Ventral somitic compartment that is a precursor of the axial skeleton[XAO]. Sclerotomes eventually differentiate into the vertebrae and most of the skull. The caudal (posterior) half of one sclerotome fuses with the rostral (anterior) half of the adjacent one to form each vertebra. From their initial location within the somite, the sclerotome cells migrate medially towards the notochord. These cells meet the sclerotome cells from the other side to form the vertebral body. From this vertebral body, sclerotome cells move dorsally and surround the developing spinal cord, forming the vertebral arch[WP]. AAO:0010571 AEO:0000212 @@ -36578,11 +36820,11 @@ Aside from their function in ion and water balance, kidney collecting duct epith sclerotome http://upload.wikimedia.org/wikipedia/commons/9/96/Gray65.png - + - + @@ -36601,13 +36843,13 @@ Aside from their function in ion and water balance, kidney collecting duct epith - + VHOG:0000680 - + ZFA @@ -36852,7 +37094,7 @@ Aside from their function in ion and water balance, kidney collecting duct epith - + @@ -36878,14 +37120,14 @@ Aside from their function in ion and water balance, kidney collecting duct epith Genes: The positional specification of the metanephrogenic mesenchyme is negatively regulated by Foxc1 and Foxc2. Next the permanent kidney forming metanephrogenic mesenchyme is specified by Hox11 genes. The competence to respond to ureteric bud inducers is regulated by WT1. GDNF secretion restricted to posterior region by Robo2 and Sprouty1. The receptors for GDNF are synthesized in the nephric ducts and later in ureteric buds [ISBN:9780878932504 "Developmental Biology"] metanephric mesenchyme - + - + ISBN:9780878932504 @@ -37573,7 +37815,7 @@ Aside from their function in ion and water balance, kidney collecting duct epith - + The part of the coelom in the embryo between the somatopleuric and splanchnopleuric mesoderm; the principal body cavities of the trunk (thoracic, abdominal, and pelvic) arise from this embryonic part of the coelom. consider merging with coelom. TODO - add spatial relationships to halves of LPM. Note the OG places XAO and ZFA coelem terms here. editor note: TODO check ZFA, which appears to be a structure present in adults EHDAA:251 @@ -37588,14 +37830,14 @@ Aside from their function in ion and water balance, kidney collecting duct epith intraembryonic coelom - + - + Wikipedia @@ -38175,8 +38417,8 @@ Aside from their function in ion and water balance, kidney collecting duct epith - - + + In mammals, the proximal tubule is a nephron tubule that connects Bowman's capsule to the loop of Henle. It has a brush border epithelial morphology[GO]. TODO - ensure definition works across species. @@ -38193,24 +38435,24 @@ Aside from their function in ion and water balance, kidney collecting duct epith proximal tubule - + - + - + GO - + GO @@ -38269,7 +38511,7 @@ Aside from their function in ion and water balance, kidney collecting duct epith - + The intermediate tubule is a nephron tubule that lies between the proximal and distal tubules. TODO - check for applicability across species FMA:17718 @@ -38279,14 +38521,14 @@ Aside from their function in ion and water balance, kidney collecting duct epith UBERON:0004136 intermediate tubule - + - + FMA @@ -38362,8 +38604,8 @@ Aside from their function in ion and water balance, kidney collecting duct epith - - + + A specific region of the lateral mesoderm that will form the primary beating heart tube. In mammals the primary heart field gives rise to the left ventricle. XAO:0004185 first heart field @@ -38375,24 +38617,24 @@ Aside from their function in ion and water balance, kidney collecting duct epith UBERON:0004140 primary heart field - + - + - + GO:0003128 - + https://orcid.org/0000-0003-3308-6245 @@ -38445,7 +38687,7 @@ Aside from their function in ion and water balance, kidney collecting duct epith - + An epithelial tube that will give rise to the mature heart. AAO:0010411 EFO:0003526 @@ -38464,14 +38706,14 @@ Aside from their function in ion and water balance, kidney collecting duct epith heart tube - + - + ZFA-modified @@ -38693,8 +38935,8 @@ Aside from their function in ion and water balance, kidney collecting duct epith - - + + The comma-shaped body is the precursor structure to the S-shaped body that contributes to the morphogenesis of the nephron. EMAPA:27681 ZFA:0005588 @@ -38704,24 +38946,24 @@ Aside from their function in ion and water balance, kidney collecting duct epith comma-shaped body - + - + - + cjm - + ZFA @@ -38743,8 +38985,8 @@ Aside from their function in ion and water balance, kidney collecting duct epith - - + + The S-shaped body is the successor of the comma-shaped body that contributes to the morphogenesis of the nephron. TODO EMAPA:27756 @@ -38756,24 +38998,24 @@ Aside from their function in ion and water balance, kidney collecting duct epith S-shaped body - + - + - + cjm - + GO @@ -38815,8 +39057,6 @@ Aside from their function in ion and water balance, kidney collecting duct epith Kidney pyramids are the conical arrangements of tubules that constitute the renal medulla in a multi-lobed mammalian kidney; they contain the loops of Henle and the medullary collecting ducts. - UBERON:0002449 - UBERON:0005098 pyramid BTO:0003926 FMA:258870 @@ -39185,7 +39425,7 @@ Aside from their function in ion and water balance, kidney collecting duct epith - + @@ -39223,14 +39463,14 @@ Aside from their function in ion and water balance, kidney collecting duct epith glomerular capillary - + - + https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships @@ -39476,7 +39716,6 @@ Aside from their function in ion and water balance, kidney collecting duct epith - @@ -39573,7 +39812,6 @@ Aside from their function in ion and water balance, kidney collecting duct epith - @@ -39615,7 +39853,6 @@ Aside from their function in ion and water balance, kidney collecting duct epith - @@ -39624,7 +39861,6 @@ Aside from their function in ion and water balance, kidney collecting duct epith The part of the cardiovascular system consisting of all arteries. - BTO:0004690 EHDAA2:0000143 EHDAA:396 @@ -39635,7 +39871,6 @@ Aside from their function in ion and water balance, kidney collecting duct epith VHOG:0000273 uberon UBERON:0004572 - arterial system @@ -39657,7 +39892,6 @@ Aside from their function in ion and water balance, kidney collecting duct epith - @@ -39666,7 +39900,6 @@ Aside from their function in ion and water balance, kidney collecting duct epith The part of the cardiovascular system consisting of all venous vessels. In vertebrates with a double circulation, this can be divided into systemic and pulmonary portions. - BTO:0004692 EHDAA2:0002171 EHDAA:486 @@ -39679,7 +39912,6 @@ Aside from their function in ion and water balance, kidney collecting duct epith vein system uberon UBERON:0004582 - venous system @@ -39774,7 +40006,7 @@ Aside from their function in ion and water balance, kidney collecting duct epith - + @@ -39811,14 +40043,14 @@ Aside from their function in ion and water balance, kidney collecting duct epith renal afferent arteriole http://upload.wikimedia.org/wikipedia/commons/0/02/Gray1128.png - + - + Wikipedia @@ -40064,7 +40296,6 @@ Aside from their function in ion and water balance, kidney collecting duct epith Organism at the gastrula stage. - UBERON:0007012 BILA:0000060 BTO:0001403 FBbt:00005317 @@ -40178,7 +40409,7 @@ Aside from their function in ion and water balance, kidney collecting duct epith - + Organ consisting of skeletal tissue. Encompasses whole bones, fused bones, cartilaginious elements, teeth, dermal denticles. AAO:0011129 TAO:0001890 @@ -40192,14 +40423,14 @@ Aside from their function in ion and water balance, kidney collecting duct epith skeletal element - + - + VSAO @@ -40226,7 +40457,7 @@ Aside from their function in ion and water balance, kidney collecting duct epith - + @@ -40265,14 +40496,14 @@ Aside from their function in ion and water balance, kidney collecting duct epith UBERON:0004770 articular system - + - + FMA @@ -40570,7 +40801,7 @@ Aside from their function in ion and water balance, kidney collecting duct epith - + @@ -40591,14 +40822,14 @@ Aside from their function in ion and water balance, kidney collecting duct epith somatopleure http://upload.wikimedia.org/wikipedia/commons/2/28/Gray16.png - + - + EHDAA2 @@ -40664,9 +40895,9 @@ Aside from their function in ion and water balance, kidney collecting duct epith - - - + + + @@ -40686,34 +40917,34 @@ Aside from their function in ion and water balance, kidney collecting duct epith urogenital fold - + - + - + - + EHDAA2 - + Wikipedia - + EHDAA2 @@ -41188,7 +41419,7 @@ Aside from their function in ion and water balance, kidney collecting duct epith - + Missing definition for term UBERON:0005095. Please replace it using linked reference. class added for consistency with GO - consider merging with kidney mesenchyme. uberon @@ -41196,14 +41427,14 @@ Aside from their function in ion and water balance, kidney collecting duct epith UBERON:0005095 kidney rudiment - + - + GO @@ -41239,7 +41470,6 @@ Aside from their function in ion and water balance, kidney collecting duct epith The descending thin limb is a part of the loop of Henle situated just after the proximal straight tubule (S3). It extends to the tip of the loop of Henle[GO]. - UBERON:0005165 EMAPA:35514 FMA:17719 MA:0002625 @@ -41319,7 +41549,7 @@ Aside from their function in ion and water balance, kidney collecting duct epith - + The connecting tubule is a tubular segment of the nephron; it connects the distal convoluted tubule to the collecting duct[GO]. BTO:0004539 @@ -41337,14 +41567,14 @@ Aside from their function in ion and water balance, kidney collecting duct epith renal connecting tubule http://upload.wikimedia.org/wikipedia/commons/0/02/Gray1128.png - + - + Wikipedia @@ -42075,7 +42305,7 @@ Aside from their function in ion and water balance, kidney collecting duct epith - + Mesenchyme that is part of a developing trunk. EFO:0003485 EHDAA2:0002092 @@ -42091,14 +42321,14 @@ Aside from their function in ion and water balance, kidney collecting duct epith trunk mesenchyme - + - + EHDAA2 @@ -42215,7 +42445,7 @@ Aside from their function in ion and water balance, kidney collecting duct epith - + Multi-tissue structure that arises from the heart rudiment and will become the heart tube. EHDAA2:0001512 EHDAA:424 @@ -42233,14 +42463,14 @@ Aside from their function in ion and water balance, kidney collecting duct epith primitive heart tube - + - + ZFA @@ -42268,7 +42498,7 @@ Aside from their function in ion and water balance, kidney collecting duct epith - + @@ -42295,7 +42525,7 @@ Aside from their function in ion and water balance, kidney collecting duct epith gonad primordium - + @@ -42308,7 +42538,7 @@ Aside from their function in ion and water balance, kidney collecting duct epith - + ZFA @@ -42367,14 +42597,14 @@ Aside from their function in ion and water balance, kidney collecting duct epith - + - + A mesoderm that has the potential to develop into a pronephros. AAO:0011090 EFO:0003479 @@ -42392,24 +42622,24 @@ Aside from their function in ion and water balance, kidney collecting duct epith the intermediate mesoderm of the chick embryo acquires its ability to form kidneys through its interactions with the paraxial mesoderm [ISBN:9780878932504 "Developmental Biology", PMID:10720431 "Signals from trunk paraxial mesoderm induce pronephros formation in chick intermediate mesoderm"]. These interactions induce the expression of TFs including Lim1, Pax2 and Pax6 that cause the intermediate mesoderm to form the kidney pronephric mesoderm - + - + - + ZFA - + Bgee:AN @@ -42456,7 +42686,7 @@ Aside from their function in ion and water balance, kidney collecting duct epith - + @@ -42473,14 +42703,14 @@ Aside from their function in ion and water balance, kidney collecting duct epith glomerular tuft - + - + Wikipedia @@ -42620,7 +42850,6 @@ Aside from their function in ion and water balance, kidney collecting duct epith - @@ -42731,7 +42960,7 @@ Aside from their function in ion and water balance, kidney collecting duct epith - + @@ -42759,14 +42988,14 @@ Aside from their function in ion and water balance, kidney collecting duct epith glomerular basement membrane http://upload.wikimedia.org/wikipedia/commons/d/de/PhysiologieGlom%C3%A9rulaire.png - + - + true https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships @@ -42851,7 +43080,7 @@ Aside from their function in ion and water balance, kidney collecting duct epith - + A delimited region of dense mesenchyme within looser mesenchyme. AEO:0000148 EHDAA2_RETIRED:0003148 @@ -42861,7 +43090,7 @@ Aside from their function in ion and water balance, kidney collecting duct epith UBERON:0005856 developing mesenchymal condensation - + @@ -42880,7 +43109,7 @@ Aside from their function in ion and water balance, kidney collecting duct epith - + AEO-modified-relation @@ -42977,7 +43206,7 @@ Aside from their function in ion and water balance, kidney collecting duct epith - + @@ -43016,14 +43245,14 @@ Aside from their function in ion and water balance, kidney collecting duct epith cloacal membrane http://upload.wikimedia.org/wikipedia/commons/d/d2/Gray991.png - + - + Wikipedia @@ -43057,7 +43286,7 @@ Aside from their function in ion and water balance, kidney collecting duct epith - + The notochordal plate is the dorsal part of the notochordal process when the ventral portion breaks down. It is continuous laterally with the endoderm that composes the roof of the primitive foregut and is in contact dorsally with the neural tube. The folding off of the notochordal plate gives rise to the notochord. TODO - check ordering; awaiting confirmation from JB EHDAA2:0001278 @@ -43071,7 +43300,7 @@ Aside from their function in ion and water balance, kidney collecting duct epith notochordal plate - + @@ -43084,7 +43313,7 @@ Aside from their function in ion and water balance, kidney collecting duct epith - + EHDAA2 @@ -43112,7 +43341,7 @@ Aside from their function in ion and water balance, kidney collecting duct epith - + A midline cellular cord formed from the migration of mesenchymal cells from the primitive knot. EHDAA2:0001279 EHDAA:224 @@ -43129,14 +43358,14 @@ Aside from their function in ion and water balance, kidney collecting duct epith The notochordal process grows cranially until it reaches the prechordal plate, the future site of the mouth. In this area the ectoderm is attached directly to the endoderm without intervening mesoderm. This area is known as the oropharyngeal membrane, and it will break down to become the mouth. At the other end of the primitive streak the ectoderm is also fused directly to the endoderm; this is known as the cloacal membrane (proctodeum), or primordial anus. notochordal process - + - + EHDAA2 @@ -43680,7 +43909,7 @@ Aside from their function in ion and water balance, kidney collecting duct epith - + A region of nephron tubule that is part of a cortex of kidney. EMAPA:18976 MA:0002609 @@ -43690,14 +43919,14 @@ Aside from their function in ion and water balance, kidney collecting duct epith UBERON:0006853 renal cortex tubule - + - + MA @@ -43868,7 +44097,6 @@ Aside from their function in ion and water balance, kidney collecting duct epith - @@ -44370,7 +44598,7 @@ Aside from their function in ion and water balance, kidney collecting duct epith - + @@ -44396,7 +44624,7 @@ Aside from their function in ion and water balance, kidney collecting duct epith presumptive paraxial mesoderm - + @@ -44412,7 +44640,7 @@ Aside from their function in ion and water balance, kidney collecting duct epith - + https://github.com/obophenotype/uberon/issues/1277 @@ -44573,7 +44801,7 @@ Aside from their function in ion and water balance, kidney collecting duct epith - + Mesenchyme with little extracellular matrix. AEO:0000146 EHDAA2:0003146 @@ -44581,7 +44809,7 @@ Aside from their function in ion and water balance, kidney collecting duct epith UBERON:0007524 dense mesenchyme tissue - + @@ -44594,7 +44822,7 @@ Aside from their function in ion and water balance, kidney collecting duct epith - + AEO @@ -44808,7 +45036,7 @@ Aside from their function in ion and water balance, kidney collecting duct epith - + Anatomical system that consists of all blood and lymph vessels. consider merging with vasculature @@ -44825,14 +45053,14 @@ Aside from their function in ion and water balance, kidney collecting duct epith vascular system - + - + MA @@ -44884,7 +45112,6 @@ Aside from their function in ion and water balance, kidney collecting duct epith An organism subdivision that encompasses the region containing the pectoral or pelvic girdle. Note that this includes both the skeletal elements and associated tissues (integument, muscle, etc). - UBERON:0007824 girdle girdle region EMAPA:37854 @@ -44970,7 +45197,7 @@ Aside from their function in ion and water balance, kidney collecting duct epith - + @@ -45008,14 +45235,14 @@ Aside from their function in ion and water balance, kidney collecting duct epith pelvic girdle skeleton http://upload.wikimedia.org/wikipedia/commons/f/fe/Gray242.png - + - + PMID:21455939 @@ -45098,7 +45325,7 @@ Aside from their function in ion and water balance, kidney collecting duct epith - + The functional tissue of the kidney, consisting of the nephrons. BTO:0003604 FMA:15574 @@ -45109,7 +45336,7 @@ Aside from their function in ion and water balance, kidney collecting duct epith UBERON:0008987 renal parenchyma - + @@ -45122,7 +45349,7 @@ Aside from their function in ion and water balance, kidney collecting duct epith - + FMA @@ -45192,7 +45419,7 @@ Aside from their function in ion and water balance, kidney collecting duct epith - + @@ -45201,7 +45428,6 @@ Aside from their function in ion and water balance, kidney collecting duct epith Sum total of mesenchyme in the embryo. consider adding new class (EMAPA:16097) for mesenchyme of embryo (some mesenchyme is extraembryonic - e.g. amnion mesoderm) - UBERON:0003313 EHDAA2:0001113 EHDAA:177 EMAPA:16097 @@ -45209,14 +45435,14 @@ Aside from their function in ion and water balance, kidney collecting duct epith UBERON:0009142 entire embryonic mesenchyme - + - + EHDAA2 @@ -45268,6 +45494,7 @@ Aside from their function in ion and water balance, kidney collecting duct epith + A nephric duct is a tube that drains a primitive kidney[GO]. EMAPA:16577 Wikipedia:Wolffian_duct @@ -45335,7 +45562,7 @@ Aside from their function in ion and water balance, kidney collecting duct epith - + EHDAA2:0002094 trunk and cervical paraxial mesenchyme uberon @@ -45343,14 +45570,14 @@ Aside from their function in ion and water balance, kidney collecting duct epith UBERON:0009618 trunk paraxial mesoderm - + - + EHDAA2 @@ -45449,7 +45676,7 @@ Aside from their function in ion and water balance, kidney collecting duct epith - + EFO:0003704 TAO:0005041 ZFA:0005041 @@ -45459,14 +45686,14 @@ Aside from their function in ion and water balance, kidney collecting duct epith anterior lateral plate mesoderm - + - + ZFA @@ -45787,7 +46014,7 @@ Aside from their function in ion and water balance, kidney collecting duct epith - + @@ -45805,14 +46032,14 @@ Aside from their function in ion and water balance, kidney collecting duct epith UBERON:0010227 future cardiac atrium - + - + ZFA @@ -45955,7 +46182,7 @@ Aside from their function in ion and water balance, kidney collecting duct epith - + @@ -45969,7 +46196,7 @@ Aside from their function in ion and water balance, kidney collecting duct epith UBERON:0010377 mesenchyme from somatopleure - + @@ -45982,7 +46209,7 @@ Aside from their function in ion and water balance, kidney collecting duct epith - + EHDAA2 @@ -45998,7 +46225,7 @@ Aside from their function in ion and water balance, kidney collecting duct epith - + A vessel of the microcirculature, lying between the arterioles and venules; includes capillaries (blood and lymphatic), metarterioles and arteriovenous anastomoses. MESH:D055806 TAO:0005251 @@ -46008,14 +46235,14 @@ Aside from their function in ion and water balance, kidney collecting duct epith UBERON:0010523 microcirculatory vessel - + - + ZFA @@ -46048,7 +46275,7 @@ Aside from their function in ion and water balance, kidney collecting duct epith - + @@ -46064,7 +46291,7 @@ Aside from their function in ion and water balance, kidney collecting duct epith UBERON:0010532 primitive nephron - + @@ -46077,7 +46304,7 @@ Aside from their function in ion and water balance, kidney collecting duct epith - + EHDAA2 @@ -46093,7 +46320,7 @@ Aside from their function in ion and water balance, kidney collecting duct epith - + @@ -46104,7 +46331,7 @@ Aside from their function in ion and water balance, kidney collecting duct epith UBERON:0010536 nephron progenitor - + @@ -46117,7 +46344,7 @@ Aside from their function in ion and water balance, kidney collecting duct epith - + cjm @@ -46360,8 +46587,8 @@ Aside from their function in ion and water balance, kidney collecting duct epith - - + + Anatomical cluster consisting of the skeletal elements (i.e. bone elements, cartilage elements, cartilage condensations) that are part of an individual subdivision of the organism. Excludes joints. FMA:23879 SCTID:129140006 @@ -46373,11 +46600,11 @@ Aside from their function in ion and water balance, kidney collecting duct epith subdivision of skeleton - + - + @@ -46390,13 +46617,13 @@ Aside from their function in ion and water balance, kidney collecting duct epith - + UBERONREF:0000003 - + VSAO @@ -46457,7 +46684,7 @@ Aside from their function in ion and water balance, kidney collecting duct epith - + Subdivision of the skeletal system which consists of the postcranial axial skeleton plus associated joints. axial skeletal system FMA:302077 @@ -46467,7 +46694,7 @@ Aside from their function in ion and water balance, kidney collecting duct epith postcranial axial skeletal system http://purl.obolibrary.org/obo/uberon/docs/The-axial-skeleton - + @@ -46480,7 +46707,7 @@ Aside from their function in ion and water balance, kidney collecting duct epith - + cjm @@ -46504,7 +46731,7 @@ Aside from their function in ion and water balance, kidney collecting duct epith - + @@ -46529,14 +46756,14 @@ Aside from their function in ion and water balance, kidney collecting duct epith upper urinary tract - + - + FMA @@ -46742,6 +46969,7 @@ Aside from their function in ion and water balance, kidney collecting duct epith EHDAA2:0004731 Wikipedia:Coelom + ZFA:0001438 enterocoelom haemocoelom schizocoelom @@ -46854,7 +47082,7 @@ Aside from their function in ion and water balance, kidney collecting duct epith - + @@ -46869,14 +47097,14 @@ Aside from their function in ion and water balance, kidney collecting duct epith We presume this is distinct from AAO:0001003, an external integumentary structure - check with amphibian anatomy ontology developers. AO notes: the text def states mesenchymal swelling, EHDAA2 splits into mesenchymal and epithelial parts embryonic cloacal fold - + - + EHDAA2 @@ -46899,20 +47127,20 @@ Aside from their function in ion and water balance, kidney collecting duct epith - + EHDAA2:0004588 uberon UBERON:0012361 internal anal region - + - + EHDAA2 @@ -46922,20 +47150,20 @@ Aside from their function in ion and water balance, kidney collecting duct epith - + EHDAA2:0004589 uberon UBERON:0012469 external anal region - + - + EHDAA2 @@ -46962,7 +47190,7 @@ Aside from their function in ion and water balance, kidney collecting duct epith - + @@ -46982,14 +47210,14 @@ Aside from their function in ion and water balance, kidney collecting duct epith skeleton of pelvic complex - + - + FMA @@ -47041,7 +47269,7 @@ Aside from their function in ion and water balance, kidney collecting duct epith - + The precursor of the urethra. SCTID:361531004 Wikipedia:Urethral_groove @@ -47052,14 +47280,14 @@ Aside from their function in ion and water balance, kidney collecting duct epith UBERON:0013241 embryonic urethral groove - + - + Wikipedia @@ -47560,7 +47788,6 @@ Aside from their function in ion and water balance, kidney collecting duct epith Primordium that develops into the central nervous system. - UBERON:3000469 future CNS presumptive central nervous system uberon @@ -47604,7 +47831,6 @@ Aside from their function in ion and water balance, kidney collecting duct epith Primordium that develops into the nervous system. - UBERON:3000477 AAO:0000477 presumptive nervous system uberon @@ -47630,7 +47856,7 @@ Aside from their function in ion and water balance, kidney collecting duct epith - + @@ -47653,7 +47879,7 @@ Aside from their function in ion and water balance, kidney collecting duct epith UBERON:0016887 entire extraembryonic component - + @@ -47666,7 +47892,7 @@ Aside from their function in ion and water balance, kidney collecting duct epith - + AEO @@ -48077,7 +48303,7 @@ Aside from their function in ion and water balance, kidney collecting duct epith - + The upper tract of the renal system. The renal pelvis is the large cavity in the middle of each kidney. Urine drains from each kidney through a long tube called the ureter, into the bladder, where it is stored until it is passed from the body through the urethra. NCIT:C54419 @@ -48088,14 +48314,14 @@ Aside from their function in ion and water balance, kidney collecting duct epith renal pelvis/ureter - + - + NCIT @@ -48113,7 +48339,6 @@ Aside from their function in ion and water balance, kidney collecting duct epith Any of the smallest blood vessels where blood circulates within organ tissues. Microvessels include terminal arterioles, metarterioles, capillaries, and venules (but exclude lymphatic capillaries). Arterioles carry oxygenated blood to the capillaries, and blood flows out of the capillaries through venules into veins. - http://orcid.org/0000-0002-2825-0621 microvasculature microvessel uberon @@ -48154,7 +48379,6 @@ Aside from their function in ion and water balance, kidney collecting duct epith An anatomical system that eliminates waste products that arise as a result of metabolic activity. - http://orcid.org/0000-0002-6095-8718 2022-05-25T18:21:29Z uberon UBERON:8450002 diff --git a/src/ontology/subsets/kidney_upper_slim.tsv b/src/ontology/subsets/kidney_upper_slim.tsv index a90c4c556..79926a968 100644 --- a/src/ontology/subsets/kidney_upper_slim.tsv +++ b/src/ontology/subsets/kidney_upper_slim.tsv @@ -1,370 +1,370 @@ ?x ?label -_:B869127b4X2D9725X2D463eX2Dbe79X2D2d475f23f3cfgenid1004 -_:B869127b4X2D9725X2D463eX2Dbe79X2D2d475f23f3cfgenid1010 -_:B869127b4X2D9725X2D463eX2Dbe79X2D2d475f23f3cfgenid1016 -_:B869127b4X2D9725X2D463eX2Dbe79X2D2d475f23f3cfgenid1022 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+_:B88db9545X2D0e81X2D47a4X2Dbb18X2D2eb39c1c66ebgenid895 +_:B88db9545X2D0e81X2D47a4X2Dbb18X2D2eb39c1c66ebgenid901 +_:B88db9545X2D0e81X2D47a4X2Dbb18X2D2eb39c1c66ebgenid911 +_:B88db9545X2D0e81X2D47a4X2Dbb18X2D2eb39c1c66ebgenid917 +_:B88db9545X2D0e81X2D47a4X2Dbb18X2D2eb39c1c66ebgenid924 +_:B88db9545X2D0e81X2D47a4X2Dbb18X2D2eb39c1c66ebgenid932 +_:B88db9545X2D0e81X2D47a4X2Dbb18X2D2eb39c1c66ebgenid946 +_:B88db9545X2D0e81X2D47a4X2Dbb18X2D2eb39c1c66ebgenid959 +_:B88db9545X2D0e81X2D47a4X2Dbb18X2D2eb39c1c66ebgenid965 +_:B88db9545X2D0e81X2D47a4X2Dbb18X2D2eb39c1c66ebgenid971 +_:B88db9545X2D0e81X2D47a4X2Dbb18X2D2eb39c1c66ebgenid977 +_:B88db9545X2D0e81X2D47a4X2Dbb18X2D2eb39c1c66ebgenid983 +_:B88db9545X2D0e81X2D47a4X2Dbb18X2D2eb39c1c66ebgenid989 +_:B88db9545X2D0e81X2D47a4X2Dbb18X2D2eb39c1c66ebgenid996 "cell" "early embryonic cell (metazoa)" "stem cell" @@ -409,6 +409,7 @@ _:B869127b4X2D9725X2D463eX2Dbe79X2D2d475f23f3cfgenid995 "animal zygote" "electrically responsive cell" "electrically signaling cell" + "stromal cell" "smooth muscle myoblast" "neuron" "proerythroblast" @@ -654,19 +655,17 @@ _:B869127b4X2D9725X2D463eX2Dbe79X2D2d475f23f3cfgenid995 "macromolecule metabolic process" "organelle" "membrane-bounded organelle" - "non-membrane-bounded organelle" + "membraneless organelle" "intracellular organelle" "extracellular organelle" "intracellular membrane-bounded organelle" - "intracellular non-membrane-bounded organelle" + "intracellular membraneless organelle" "organelle lumen" "protein-containing complex organization" "regulation of system process" "cellular component biogenesis" "translation initiation ternary complex" - "cellular metabolic process" "primary metabolic process" - "cellular biosynthetic process" "establishment of protein localization" "synapse" "secretion" @@ -743,7 +742,7 @@ _:B869127b4X2D9725X2D463eX2Dbe79X2D2d475f23f3cfgenid995 "supramolecular polymer" "synaptic signaling" "trans-synaptic signaling" - "cellular anatomical entity" + "cellular anatomical structure" "plasma membrane bounded cell projection" "plasma membrane bounded cell projection assembly" "plasma membrane bounded cell projection organization" @@ -869,7 +868,7 @@ _:B869127b4X2D9725X2D463eX2Dbe79X2D2d475f23f3cfgenid995 "Mus musculus protein" "eukaryotic protein" "angiotensinogenase" - "protein-containing material entity" + "protein-containing molecular entity" "processual entity" "tube" "appendage" diff --git a/src/ontology/tmp/README.md b/src/ontology/tmp/README.md deleted file mode 100644 index 128805c29..000000000 --- a/src/ontology/tmp/README.md +++ /dev/null @@ -1 +0,0 @@ -# README for temp files \ No newline at end of file diff --git a/subsets/blood_and_immune_upper_slim.json b/subsets/blood_and_immune_upper_slim.json index fdd02d37b..08f6e55c0 100644 --- a/subsets/blood_and_immune_upper_slim.json +++ b/subsets/blood_and_immune_upper_slim.json @@ -4,9 +4,9 @@ "meta" : { "basicPropertyValues" : [ { "pred" : "http://www.w3.org/2002/07/owl#versionInfo", - "val" : "2024-09-26" + "val" : "2025-01-08" } ], - "version" : "http://purl.obolibrary.org/obo/cl/releases/2024-09-26/subsets/blood_and_immune_upper_slim.owl" + "version" : "http://purl.obolibrary.org/obo/cl/releases/2025-01-08/subsets/blood_and_immune_upper_slim.owl" }, "nodes" : [ { "id" : "http://purl.obolibrary.org/obo/CL_0000000", @@ -18,7 +18,7 @@ "xrefs" : [ "CARO:mah" ] }, "comments" : [ "The definition of cell is intended to represent all cells, and thus a cell is defined as a material entity and not an anatomical structure, which implies that it is part of an organism (or the entirety of one)." ], - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/ubprop#_upper_level" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/ubprop#_upper_level" ], "xrefs" : [ { "val" : "CALOHA:TS-2035" }, { @@ -50,6 +50,7 @@ "val" : "A cell found in the embryo before the formation of all the gem layers is complete.", "xrefs" : [ "GOC:tfm" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "ZFA:0009002" } ] @@ -64,7 +65,7 @@ "xrefs" : [ "GOC:tfm", "MESH:D013234" ] }, "comments" : [ "This term applies to metazoan. For plant stem cells, consider using PO:0004011 ‘initial cell’ or its parent PO:0004010 ‘meristematic cell’." ], - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#general_cell_types_upper_slim", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#general_cell_types_upper_slim", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "animal stem cell" @@ -91,7 +92,7 @@ "xrefs" : [ "GOC:add", "GOC:dsd", "GOC:tfm", "PMID:19022770", "http://en.wikipedia.org/wiki/Hematopoietic_stem_cell" ] }, "comments" : [ "Markers differ between species, and two sets of markers have been described for mice. HSCs are reportedly CD34-positive, CD45-positive, CD48-negative, CD150-positive, CD133-positive, and CD244-negative." ], - "subsets" : [ "http://purl.obolibrary.org/obo/cl#blood_and_immune_upper_slim", "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#blood_and_immune_upper_slim", "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "blood forming stem cell" @@ -133,7 +134,7 @@ "val" : "A progenitor cell committed to the erythroid lineage.", "xrefs" : [ "GOC:add", "ISBN:0721601464" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#blood_and_immune_upper_slim", "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#blood_and_immune_upper_slim", "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003000", "pred" : "hasRelatedSynonym", @@ -171,6 +172,7 @@ "xrefs" : [ "GOC:add", "PMID:1104740", "http://en.wikipedia.org/wiki/Monoblast", "http://www.copewithcytokines.de" ] }, "comments" : [ "Morphology: mononuclear cell, diameter 12-20 _M, non-granular, N/C ratio 3/1 - 4/1; markers: CD11b (shared with many other myeloid cells); location: Adult: bone marrow; fetal: liver, Yolk Sac; role or process: hematopoiesis, monocyte development; lineage: hematopoietic, myeloid." ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003000", "pred" : "hasRelatedSynonym", @@ -202,6 +204,7 @@ "val" : "A stem cell that can give rise to multiple lineages of cells.", "xrefs" : [ "GOC:add" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "multi-fate stem cell" @@ -231,7 +234,7 @@ "xrefs" : [ "GOC:add", "ISBN:0878932437", "MESH:D023461" ] }, "comments" : [ "This cell type is intended to be compatible with any vertebrate common myeloid progenitor. For mammalian CMP known to be CD34-positive, please use the term 'common myeloid progenitor, CD34-positive' (CL_0001059)." ], - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "common myeloid precursor" @@ -287,7 +290,7 @@ "xrefs" : [ "GOC:add", "GOC:dsd", "GOC:tfm", "MESH:D055015", "PMID:16647566", "http://en.wikipedia.org/wiki/Megakaryocyte-erythroid_progenitor_cell" ] }, "comments" : [ "MEPs are reportedly CD19-negative, CD34-negative, CD45RA-negative, CD110-positive, CD117-positive, and SCA1-negative and reportedly express the transcription factors GATA-1 and NF-E2." ], - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "CFU-EM" @@ -328,7 +331,7 @@ "xrefs" : [ "GOC:add", "GOC:dsd", "GOC:tfm", "PMID:10407577", "PMID:16551251" ] }, "comments" : [ "CLP are CD7-positive, CD10-positive, CD19-negative, CD34-positive, CD45RA-positive, CD79a-negative, CD127-positive, AA4.1-positive, RAG-negative, Sca-1-low, sIgM-negative, sIgD-negative, TdT-negative, Vpre-B-negative, and pre-BCR-negative. Expression of transcription factors include E2A-positive, EBF-positive, Ikaros-negative, PU.1-negative, and Pax5-negative." ], - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "common lymphocyte precursor" @@ -376,6 +379,7 @@ "val" : "A stem cell from which all cells of the body can form.", "xrefs" : [ "GOC:add", "GOC:tfm" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "totipotential stem cell" @@ -398,7 +402,7 @@ "xrefs" : [ "SANBI:mhl" ] }, "comments" : [ "define using PATO mulit-potent or oligopotent?" ], - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "blast cell" @@ -418,6 +422,7 @@ "val" : "A cell that is commited to differentiating into a muscle cell. Embryonic myoblasts develop from the mesoderm. They undergo proliferation, migrate to their various sites, and then differentiate into the appropriate form of myocytes. Myoblasts also occur as transient populations of cells in muscles undergoing repair.", "xrefs" : [ "GOC:tfm", "MESH:D032446", "PMID:21849021" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "BTO:0000222" }, { @@ -442,7 +447,7 @@ "xrefs" : [ "ISBN:0517223651", "MESH:D005347", "http://en.wikipedia.org/wiki/Fibroblast" ] }, "comments" : [ "These cells may be vimentin-positive, fibronectin-positive, fsp1-positive, MMP-1-positive, collagen I-positive, collagen III-positive, and alpha-SMA-negative." ], - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#general_cell_types_upper_slim", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#general_cell_types_upper_slim", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "xrefs" : [ { "val" : "BTO:0000452" }, { @@ -470,7 +475,7 @@ "val" : "A cell that is usually found in a two-dimensional sheet with a free surface. The cell has a cytoskeleton that allows for tight cell to cell contact and for cell polarity where apical part is directed towards the lumen and the basal part to the basal lamina.", "xrefs" : [ "FB:ma", "GOC:tfm", "MESH:D004847" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#general_cell_types_upper_slim", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#general_cell_types_upper_slim", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "epitheliocyte" @@ -507,7 +512,7 @@ "val" : "An endothelial cell that lines the vasculature.", "xrefs" : [ "GOC:tfm" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "xrefs" : [ { "val" : "ZFA:0009036" } ], @@ -525,7 +530,7 @@ "val" : "Any epithelial cell that is part of some squamous epithelium.", "xrefs" : [ "FBC:Autogenerated" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "CALOHA:TS-1249" }, { @@ -541,6 +546,7 @@ "val" : "A cell which moves among different tissues of the body, via blood, lymph, or other medium.", "xrefs" : [ "GOC:add" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "ZFA:0009043" } ] @@ -554,7 +560,7 @@ "val" : "A cell found predominately in the blood.", "xrefs" : [ "GOC:add", "GOC:tfm" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#general_cell_types_upper_slim" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#general_cell_types_upper_slim", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "FMA:62844" }, { @@ -572,7 +578,7 @@ "val" : "A type of lymphocyte whose defining characteristic is the expression of a T cell receptor complex.", "xrefs" : [ "GOC:add", "GOC:tfm", "ISBN:0781735149" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#general_cell_types_upper_slim", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#general_cell_types_upper_slim", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "T lymphocyte" @@ -617,7 +623,7 @@ "xrefs" : [ "GOC:add", "GOC:tfm", "GO_REF:0000031", "ISBN:0781735149", "PMID:10428500", "PMID:15055519", "PMID:17380158" ] }, "comments" : [ "Morphology: Highly vesicular; markers: Surface: RANK, cFMS (MCSF receptor); Secreted: cathepsin K and TRAP (tartate resistant acid phosphatase); transcription factors: PU.1, cFOS, MITF, NFkB (p52); role or process: tissue remodelling: bone resorption; lineage: hematopoietic, myeloid." ], - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "pred" : "hasRelatedSynonym", "val" : "chondroclast" @@ -632,6 +638,12 @@ "val" : "MESH:D010010" }, { "val" : "ZFA:0009047" + }, { + "val" : "https://cellxgene.cziscience.com/cellguide/CL_0000092" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/description", + "val" : "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nOsteoclasts, derived from the monocyte/macrophage lineage, play a crucial role in bone remodeling through bone resorption. They are distinguished from other cells by their large size and their unique ability to secrete enzymes and acids that dissolve the calcium phosphate in bone. The formation of osteoclasts is influenced by two primary factors: macrophage colony-stimulating factor (M-CSF) and the ligand-activated receptor (RANKL) of nuclear factor kappa B (NF-κB).\nOsteoclasts also collaborate with osteoblasts, responsible for new bone formation, to maintain bone health and adapt bone structure. Their coordinated actions allow continuous remodeling while preserving overall bone strength and integrity. Imbalances in osteoclast activity can lead to pathological conditions. For example, excessive activity may contribute to diseases like osteoporosis, periprosthetic osteolysis, bone tumors, and Paget's disease. Other the other hand, osteoclast deficiency ca result in conditions like osteopetrosis." } ] } }, { @@ -643,7 +655,7 @@ "val" : "A leukocyte with abundant granules in the cytoplasm.", "xrefs" : [ "GOC:amm", "GOC:tfm", "MESH:D006098", "http://en.wikipedia.org/wiki/Granulocyte" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "granular leucocyte" @@ -680,7 +692,7 @@ "xrefs" : [ "GOC:add", "GOC:dsd", "GOC:tfm", "ISBN:068340007X", "MESH:D008407", "PMCID:PMC1312421", "PMCID:PMC2855166", "PMID:15153310", "PMID:16455980", "PMID:19671378", "PMID:212366338", "PMID:9354811" ] }, "comments" : [ "Mast cells are generally integrin beta-7-negative and positive for TLR2, TLR3, TLR4, TLR5, TLR7, TLR9, C3aR, C5aR, CR3, CR4, VEGF, FGF2, and renin. They can express MHC Class I and II on their surface. Activated murine mast cells (IgE+Antigen) were capable of expressing the following co-stimulatory molecules: CD95 (Fas), CD120b, CD137 (4-1BB), CD153 (CD30L), CD154 (CD40L), GITR, ICOSL, OX40L, PD-L1, and PD-L2. Note that there was some mouse strain variation. Mast cells have also been demonstrated to produce bFGF, CCL2, CCL4, CCL5, CCL11, CCL20, CXCL2, CXCL8, CXCL10, GM-CSF, IFN-gamma, IL-1, IL-2, IL-3, IL-8, IL-10, IL-11, IL-12, IL-13, IL-16, IL-25, IL-18, MIP-1, prostaglandin D2, SCF, TGF-beta, TNF-alpha, TSLP, VEGF, and XCL1. They express the transcription factors Transcription factors AP-1, GATA1, MITF, Notch2, PIAS3, PU.1, and STAT5." ], - "subsets" : [ "http://purl.obolibrary.org/obo/cl#blood_and_immune_upper_slim", "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#blood_and_immune_upper_slim", "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "histaminocyte" @@ -718,7 +730,7 @@ "val" : "A vertebrate phagocyte with a single nucleus.", "xrefs" : [ "GOC:add", "GOC:tfm", "ISBN:0781735149" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "xrefs" : [ { "val" : "BTO:0001433" }, { @@ -731,7 +743,7 @@ "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" }, { "pred" : "http://purl.org/dc/terms/description", - "val" : "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional.\n\nMononuclear phagocytes are immune cells that form a critical part of the body's innate immune system, the body's first line of defense against infections. Mononuclear phagocytes are characterized by the presence of a single, large nucleus. The ‘Mononuclear Phagocyte System’ nomenclature was introduced to distinguish mononuclear monocytes and macrophages from other cells with multiple nuclei. However, the cells within the mononuclear phagocyte system represent a highly heterogeneous group, all of which are able to perform highly efficient phagocytosis - engulfing and digesting microbes and cellular debris to fight infections and to maintain normal tissue homeostasis. \nIn addition to phagocytosis, mononuclear phagocytes also secrete chemical compounds to recruit other immune cells to a site of infection. These cells produce different types of signaling molecules, including cytokines, chemokines, and reactive oxygen species, triggering a cascade of responses to ensure rapid and efficient containment and neutralization of invading pathogens. These cells are also involved in antigen presentation, a process essential for stimulating an adaptive immune response. They can process and present antigens to T cells, thereby linking the innate and adaptive immune responses.\nMononuclear phagocytes play key roles in tissue repair and remodeling. After infection or injury, these cells help in the clearance of dead cells and debris, a crucial step in the initiation of tissue remodeling and the resolution of inflammation. Overall, mononuclear phagocytes are versatile cells that have tailored their functions to meet the unique challenges of different tissues within the body. They are pivotal in homeostasis, immunity, and inflammation, making them important aspects in a range of human diseases including infection, autoimmunity, and cancer." + "val" : "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nMononuclear phagocytes are immune cells that form a critical part of the body's innate immune system, the body's first line of defense against infections. Mononuclear phagocytes are characterized by the presence of a single, large nucleus. The ‘Mononuclear Phagocyte System’ nomenclature was introduced to distinguish mononuclear monocytes and macrophages from other cells with multiple nuclei. However, the cells within the mononuclear phagocyte system represent a highly heterogeneous group, all of which are able to perform highly efficient phagocytosis - engulfing and digesting microbes and cellular debris to fight infections and to maintain normal tissue homeostasis. \nIn addition to phagocytosis, mononuclear phagocytes also secrete chemical compounds to recruit other immune cells to a site of infection. These cells produce different types of signaling molecules, including cytokines, chemokines, and reactive oxygen species, triggering a cascade of responses to ensure rapid and efficient containment and neutralization of invading pathogens. These cells are also involved in antigen presentation, a process essential for stimulating an adaptive immune response. They can process and present antigens to T cells, thereby linking the innate and adaptive immune responses.\nMononuclear phagocytes play key roles in tissue repair and remodeling. After infection or injury, these cells help in the clearance of dead cells and debris, a crucial step in the initiation of tissue remodeling and the resolution of inflammation. Overall, mononuclear phagocytes are versatile cells that have tailored their functions to meet the unique challenges of different tissues within the body. They are pivotal in homeostasis, immunity, and inflammation, making them important aspects in a range of human diseases including infection, autoimmunity, and cancer." } ] } }, { @@ -744,7 +756,7 @@ "xrefs" : [ "GOC:tfm", "MESH:D042783", "PMID:21275341", "http://en.wikipedia.org/wiki/Endothelial_cell", "https://sourceforge.net/tracker/?func=detail&atid=440764&aid=3364936&group_id=36855" ] }, "comments" : [ "From FMA: 9.07.2001: Endothelial cell has always been classified as a kind of epithelial cell, specifically a squamous cell but that is not true. First, endothelial cell can either be squamous or cuboidal (e.g. high-endothelial cell) and secondly, it has different embryological derivation (mesodermal) than a true epithelial cell (ectodermal and endodermal). The basis for present classification is the fact that it comprises the outermost layer or lining of anatomical structures (location-based) but a better structural basis for the differentia is the cytoskeleton of the cell. Endothelial cell has vimentin filaments while an epithelial cell has keratin filaments. [Onard]." ], - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "endotheliocyte" @@ -772,6 +784,7 @@ "val" : "Ectoderm destined to be nervous tissue.", "xrefs" : [ "GOC:tfm", "ISBN:068340007X" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "neurectoderm cell" @@ -790,7 +803,7 @@ "xrefs" : [ "FB:ma", "GOC:dsd", "PMCID:PMC2613570", "PMID:10102814", "PMID:16923606", "PMID:17986482", "PMID:19960544", "http://en.wikipedia.org/wiki/Mesenchymal_stem_cell", "http://www.copewithcytokines.de/cope.cgi?key=mesenchymal%20stem%20cells" ] }, "comments" : [ "Many but not all mesenchymal cells derive from the mesoderm. MSCs are reportedly CD3-negative, CD4-negative, CD5-negative, CD8-negative, CD11a-negative, CD11b-negative, CD14-negative, CD19-negative, CD29-positive, CD31-negative, CD34-negative, CD38-negative, CD40-negative, CD44-positive, CD45-negative, CD49-positive, CD54-positive, CD66b-negative, CD79a-negative, CD80-negative, CD102-positive, CD106-positive, CD117-positive, CD121a-positive, CD121b-positive, CD123-positive, CD124-positive, CD133-negative, CD146-positive, CD166-positive, CD271-positive, B220-negative, Gr1-negative, MHCI-positive, MHCII-negative, SSEA4-negative, sca1-positive, Ter119-negative, and glycophorin A-negative. Cultured MSCs are capable of producing stem cell factor, IL7, IL8, IL11, TGF-beta, cofilin, galectin-1, laminin-receptor 1, cyclophilin A, and MMP-2." ], - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "pred" : "hasNarrowSynonym", "val" : "bone marrow stromal cells" @@ -862,7 +875,7 @@ "xrefs" : [ "GOC:add", "ISBN:0781735149" ] }, "comments" : [ "Note change of name; nearly all somatic cells can present antigens to T cells via MHC Class I complexes leading to effector responses, but professional antigen presenting cells constitutively express MHC Class II as well as costimulatory molecules, and thus can initiate immune responses via T cells." ], - "subsets" : [ "http://purl.obolibrary.org/obo/cl#blood_and_immune_upper_slim", "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#blood_and_immune_upper_slim", "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003000", "pred" : "hasRelatedSynonym", @@ -881,7 +894,7 @@ "val" : "A cell that specializes in controlled release of one or more substances.", "xrefs" : [ "GOC:tfm", "ISBN:0721662544" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "BTO:0003659" }, { @@ -897,7 +910,7 @@ "val" : "A cell whose primary function is to shorten.", "xrefs" : [ "FB:ma" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ] + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ] } }, { "id" : "http://purl.obolibrary.org/obo/CL_0000187", @@ -908,7 +921,7 @@ "val" : "A mature contractile cell, commonly known as a myocyte. This cell has as part of its cytoplasm myofibrils organized in various patterns.", "xrefs" : [ "MESH:D032342" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "muscle fiber" @@ -945,6 +958,7 @@ "val" : "A cell whose function is determined by the generation or the reception of an electric signal.", "xrefs" : [ "FB:ma" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "ZFA:0009128" } ] @@ -958,6 +972,7 @@ "val" : "A cell within an epithelial cell sheet whose main function is to act as an internal or external covering for a tissue or an organism.", "xrefs" : [ "JB:jb" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "boundary cell" @@ -975,6 +990,7 @@ "val" : "A cell whose primary function is to prevent the transport of stuff across compartments.", "xrefs" : [ "JB:jb" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "ZFA:0009132" } ] @@ -988,6 +1004,7 @@ "val" : "A cell that moves by its own activities.", "xrefs" : [ "FB:ma" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "ZFA:0009136" } ] @@ -1001,6 +1018,7 @@ "val" : "A cell of the outer of the three germ layers of the embryo.", "xrefs" : [ "MESH:D004475" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "ectoderm cell" @@ -1020,7 +1038,7 @@ "val" : "A cell of the middle germ layer of the embryo.", "xrefs" : [ "MESH:D008648" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "mesoblast" @@ -1032,6 +1050,12 @@ "val" : "FMA:72554" }, { "val" : "ZFA:0009138" + }, { + "val" : "https://cellxgene.cziscience.com/cellguide/CL_0000222" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/description", + "val" : "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nMesodermal cells are pluripotent and the most abundant in the human body. They contribute to the development of several structures such as the skeletal muscles, bones, heart and blood vessels, kidneys, gonads, connective tissues, and certain layers of the skin. Hence, the mesoderm is often regarded as an active and diverse layer due to its role in forming many bodily structures. \nIn embryonic development, these cells are instrumental, contributing to the body's structures through a carefully coordinated sequence of morphogenetic movements. This process forms the complex multicellular architecture of tissues and organs from a simple ball of cells. Without the function of mesodermal cells, the body's integral structures and systems would cease to form correctly, leading to developmental disorders such as axial mesodermal dysplasia complex" } ] } }, { @@ -1043,6 +1067,7 @@ "val" : "A cell of the inner of the three germ layers of the embryo.", "xrefs" : [ "MESH:D004707" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "endoderm cell" @@ -1062,6 +1087,7 @@ "val" : "A cell that lacks a nucleus.", "xrefs" : [ "FB:ma" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "non-nucleated cell" @@ -1078,7 +1104,8 @@ "definition" : { "val" : "A cell with a single nucleus.", "xrefs" : [ "FB:ma", "GOC:tfm" ] - } + }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ] } }, { "id" : "http://purl.obolibrary.org/obo/CL_0000228", @@ -1089,6 +1116,7 @@ "val" : "A cell with more than one nucleus.", "xrefs" : [ "FB:ma", "Wikipedia:Multinucleate" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "multinucleated cells", @@ -1108,7 +1136,7 @@ "val" : "A red blood cell. In mammals, mature erythrocytes are biconcave disks containing hemoglobin whose function is to transport oxygen.", "xrefs" : [ "GOC:tfm", "MESH:D004912" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#blood_and_immune_upper_slim", "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#blood_and_immune_upper_slim", "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "RBC" @@ -1138,7 +1166,7 @@ "xrefs" : [ "GOC:add", "GOC:dsd", "GOC:tfm", "MESH:D001792", "PMID:11110672", "PMID:16987572", "PMID:17204662", "PMID:17479180", "PMID:20414831", "http://en.wikipedia.org/wiki/Platelet" ] }, "comments" : [ "Platelets are reportedly CCR1-positive, CCR2-negative, CCR3-positive, CCR4-positive, CCR5-negative, CCR6-negative, CCR7-negative, CCR8-negative, CCR9-negative, CCR10-negative, CD16-positive, CD23-positive, CD32-positive, CD40-positive, CD41-positive CD42-positive, CD61-positive, CD62P-positive, CD64-positive, CD89-positive, CD102-positive, CD147-positive (activated platelets), CD154-positive (activated platelets), CD162-positive, CD209, CD282-positive, CD284-positive, CD289-positive, CD181-negative, CD182-negative, CD183-negative, CD184-positive, CLEC2-positive, GPVI-positive, JAMC-positive, PAR1-positive, PAR2-negative, PAR3-positive, PAR4-positive, TSP1-positive, and TXA2R-positive. Platelets can reportedly produce CCL2, CCL3, CCL5, CCL7, CCL17, CD40L, CXCL1, CXCL4, CXCL4L1, CXCL5, CXCL7, CXCL8, CXCL12, EGF, factor V, factor VII, factor XI, factor XIII, bFGF, histamine, IGF-1, IL-1beta, PAI-1, PDGF, plasminogen, protein S, serotonin, TGF-beta, TFPI, VEGF, and vWF." ], - "subsets" : [ "http://purl.obolibrary.org/obo/cl#blood_and_immune_upper_slim", "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#blood_and_immune_upper_slim", "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "anucleate thrombocyte" @@ -1170,7 +1198,7 @@ "val" : "Any cell capable of ingesting particulate matter via phagocytosis.", "xrefs" : [ "GOC:add", "ISBN:0721601464" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "BTO:0001044" }, { @@ -1191,7 +1219,7 @@ "xrefs" : [ "GOC:add", "GOC:tfm", "GO_REF:0000031", "PMID:16213494", "PMID:1919437" ] }, "comments" : [ "Morphology: Diameter 30_M-80 _M, abundant cytoplasm, low N/C ratio, eccentric nucleus. Irregular shape with pseudopods, highly adhesive. Contain vacuoles and phagosomes, may contain azurophilic granules; markers: Mouse & Human: CD68, in most cases CD11b. Mouse: in most cases F4/80+; role or process: immune, antigen presentation, & tissue remodelling; lineage: hematopoietic, myeloid." ], - "subsets" : [ "http://purl.obolibrary.org/obo/cl#blood_and_immune_upper_slim", "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#general_cell_types_upper_slim", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#blood_and_immune_upper_slim", "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#general_cell_types_upper_slim", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "histiocyte" @@ -1223,7 +1251,7 @@ "val" : "A lymphocyte of B lineage that is capable of B cell mediated immunity.", "xrefs" : [ "GOC:add", "GOC:tfm", "GO_REF:0000031", "ISBN:0781735149" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#blood_and_immune_upper_slim", "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#general_cell_types_upper_slim", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#blood_and_immune_upper_slim", "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#general_cell_types_upper_slim", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "B lymphocyte" @@ -1261,7 +1289,7 @@ "val" : "Any cell that in taxon some Eukaryota.", "xrefs" : [ "FBC:Autogenerated" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "MESH:D005057" } ] @@ -1275,7 +1303,7 @@ "val" : "A cell that is specialised to accumulate a particular substance(s).", "xrefs" : [ "FB:ma" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/ubprop#_upper_level" ] + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/ubprop#_upper_level" ] } }, { "id" : "http://purl.obolibrary.org/obo/CL_0000329", @@ -1286,6 +1314,7 @@ "val" : "Any cell that is capable of some oxygen transport.", "xrefs" : [ "FBC:Autogenerated" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "ZFA:0009164" } ] @@ -1299,6 +1328,7 @@ "val" : "A cell derived from the specialized ectoderm flanking each side of the embryonic neural plate, which after the closure of the neural tube, forms masses of cells that migrate out from the dorsal aspect of the neural tube to spread throughout the body.", "xrefs" : [ "doi:10.1016/j.stem.2015.02.017" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "FMA:86667" }, { @@ -1314,6 +1344,7 @@ "val" : "A mesenchymal cell in embryonic development found in a contracting mass and that gives rise to osteoprogenitors.", "xrefs" : [ "GOC:tfm", "PMID:5025404" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "ZFA:0009166" } ] @@ -1326,7 +1357,8 @@ "definition" : { "val" : "A cell of the outer layer of a blastula that gives rise to the ectoderm after gastrulation.", "xrefs" : [ "GOC:tfm", "ISBN:0618947256" ] - } + }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ] } }, { "id" : "http://purl.obolibrary.org/obo/CL_0000365", @@ -1337,6 +1369,7 @@ "val" : "Diploid cell produced by the fusion of sperm cell nucleus and egg cell.", "xrefs" : [ "ISBN:0471245208" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "pred" : "hasBroadSynonym", "val" : "zygote" @@ -1358,6 +1391,7 @@ "val" : "A cell whose function is determined by its response to an electric signal.", "xrefs" : [ "FB:ma" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "ZFA:0009190" } ] @@ -1371,6 +1405,7 @@ "val" : "A cell that initiates an electrical signal and passes that signal to another cell.", "xrefs" : [ "FB:ma" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "ZFA:0009193" } ] @@ -1384,7 +1419,7 @@ "val" : "A cell of hematopoietic origin, typically resident in particular tissues, specialized in the uptake, processing, and transport of antigens to lymph nodes for the purpose of stimulating an immune response via T cell activation. These cells are lineage negative (CD3-negative, CD19-negative, CD34-negative, and CD56-negative).", "xrefs" : [ "GOC:add", "ISBN:0781735149" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#general_cell_types_upper_slim", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#general_cell_types_upper_slim", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "synonyms" : [ { "pred" : "hasRelatedSynonym", "val" : "interdigitating cell" @@ -1413,6 +1448,7 @@ "lbl" : "biogenic amine secreting cell", "type" : "CLASS", "meta" : { + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "ZFA:0009212" } ] @@ -1426,6 +1462,7 @@ "val" : "A cell type that secretes 5-Hydroxytryptamine (serotonin).", "xrefs" : [ "GOC:tfm", "PMID:19630576" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "5-HT secreting cell" @@ -1445,7 +1482,30 @@ "definition" : { "val" : "A cell whose primary function is to protect the organism.", "xrefs" : [ "JB:jb" ] - } + }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/CL_0000499", + "lbl" : "stromal cell", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A connective tissue cell of an organ found in the loose connective tissue.", + "xrefs" : [ "GOC:tfm", "MESH:D017154" ] + }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#general_cell_types_upper_slim", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "xrefs" : [ { + "val" : "BTO:0002064" + }, { + "val" : "FMA:83624" + }, { + "val" : "ZFA:0009226" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/RO_0002175", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" + } ] } }, { "id" : "http://purl.obolibrary.org/obo/CL_0000518", @@ -1455,7 +1515,8 @@ "definition" : { "val" : "A phagocyte in vertebrates that is able to phagocytosis.", "xrefs" : [ "GOC:tfm" ] - } + }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ] } }, { "id" : "http://purl.obolibrary.org/obo/CL_0000540", @@ -1467,7 +1528,7 @@ "xrefs" : [ "MESH:D009474", "http://en.wikipedia.org/wiki/Neuron" ] }, "comments" : [ "These cells are also reportedly CD4-negative and CD200-positive. They are also capable of producing CD40L and IFN-gamma." ], - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#general_cell_types_upper_slim", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#general_cell_types_upper_slim", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "nerve cell" @@ -1505,7 +1566,7 @@ "xrefs" : [ "GOC:add", "ISBN:0683073696", "ISBN:0781735149" ] }, "comments" : [ "Editors note: consider adding taxon constraint to vertebrata (PMID:18025161)" ], - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "xrefs" : [ { "val" : "BTO:0000775" }, { @@ -1533,7 +1594,7 @@ "val" : "An immature, nucleated erythrocyte occupying the stage of erythropoeisis that follows formation of erythroid progenitor cells. This cell is CD71-positive, has both a nucleus and a nucleolus, and lacks hematopoeitic lineage markers.", "xrefs" : [ "ISBN:0721601464", "PMID:1638021" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#blood_and_immune_upper_slim", "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#blood_and_immune_upper_slim", "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "rubriblast", @@ -1555,6 +1616,7 @@ "val" : "A nucleated immature erythrocyte, having cytoplasm generally similar to that of the earlier proerythroblast but sometimes even more basophilic, and usually regular in outline. The nucleus is still relatively large, but the chromatin strands are thicker and more deeply staining, giving a coarser appearance; the nucleoli have disappeared. This cell is CD71-positive and lacks hematopoeitic lineage markers.", "xrefs" : [ "GOC:tfm", "ISBN:0721601464" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "basophilic normoblast", @@ -1587,6 +1649,7 @@ "val" : "A nucleated, immature erythrocyte in which the nucleus occupies a relatively smaller part of the cell than in its precursor, the basophilic erythroblast. The cytoplasm is beginning to acquire hemoglobin and thus is no longer a purely basophilic, but takes on acidophilic aspects, which becomes progressively more marked as the cell matures. The chromatin of the nucleus is arranged in coarse, deeply staining clumps. This cell is CD71-positive and lacks hematopoeitic lineage markers.", "xrefs" : [ "ISBN:0721601464" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "intermediate erythroblast", @@ -1627,6 +1690,7 @@ "val" : "The final stage of the nucleated, immature erythrocyte, before nuclear loss. Typically the cytoplasm is described as acidophilic, but it still shows a faint polychromatic tint. The nucleus is small and initially may still have coarse, clumped chromatin, as in its precursor, the polychromatophilic erythroblast, but ultimately it becomes pyknotic, and appears as a deeply staining, blue-black, homogeneous structureless mass. The nucleus is often eccentric and sometimes lobulated.", "xrefs" : [ "ISBN:0721601464" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "acidophilic erythroblast", @@ -1661,7 +1725,7 @@ "xrefs" : [ "GOC:dsd", "GOC:tfm", "ISBN:0721601464" ] }, "comments" : [ "Lineage negative is described here as CD2-negative, CD3-negative, CD4-negative, CD5-negative, CD8a-negative, CD14-negative, CD19-negative, CD20-negative, CD56-negative, Ly6g-negative, and Ter119-negative." ], - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "CFU-Meg", @@ -1721,7 +1785,7 @@ "xrefs" : [ "ISBN:0721601464", "MESH:D008533", "PMID:31043076", "http://en.wikipedia.org/wiki/Megakaryocyte" ] }, "comments" : [ "Megakaryocytes are reportedly CD181-positive and CD182-positive." ], - "subsets" : [ "http://purl.obolibrary.org/obo/cl#blood_and_immune_upper_slim", "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#blood_and_immune_upper_slim", "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "megacaryocyte" @@ -1754,7 +1818,7 @@ "xrefs" : [ "GOC:amm", "GOC:dsd", "GOC:tfm", "GO_REF:0000031", "ISBN:0721601464", "MESH:D055014", "PMCID:PMC2213186", "PMCID:PMC548021", "PMID:16551251", "PMID:16647566", "http://en.wikipedia.org/wiki/CFU-GM", "http://www.copewithcytokines.de" ] }, "comments" : [ "Originally described in the dendritic cell ontology (DC_CL:0000042)(PMID:19243617). GMPs are reportedly CD16-positive, CD32-positive, CD34-positive, CD38-positive, CD45RA-positive, CD110-negative, CD117-positive, CD123-positive, and SCA1-negative." ], - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "synonyms" : [ { "pred" : "hasBroadSynonym", "val" : "CFU-C , Colony forming unit in culture", @@ -1786,10 +1850,15 @@ } ], "xrefs" : [ { "val" : "ZFA:0009251" + }, { + "val" : "https://cellxgene.cziscience.com/cellguide/CL_0000557" } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" + }, { + "pred" : "http://purl.org/dc/terms/description", + "val" : "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nGranulocyte monocyte progenitor cells (GMP cells), originating from hematopoietic stem cells in the bone marrow, are a critical intermediate in myeloid cell development. Positioned at a key differentiation juncture, these cells exhibit bidirectional potential, giving rise to both granulocyte and monocyte lineages.\nTheir primary role is to generate mature granulocytes and monocytes, essential components of the body's innate immunity and inflammatory responses. Granulocytes, such as neutrophils, eosinophils, and basophils, contribute to the first line of defense against infections by migrating to the infection site and phagocytosing pathogens. Monocytes can differentiate into macrophages or dendritic cells, playing diverse roles in immune responses." } ] } }, { @@ -1801,7 +1870,7 @@ "val" : "An immature erythrocyte that changes the protein composition of its plasma membrane by exosome formation and extrusion. The types of protein removed differ between species though removal of the transferrin receptor is apparent in mammals and birds.", "xrefs" : [ "GOC:add", "GOC:tfm", "PMID:15946868", "PMID:2037622" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#blood_and_immune_upper_slim", "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#blood_and_immune_upper_slim", "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "BTO:0001173" }, { @@ -1822,7 +1891,7 @@ "xrefs" : [ "GOC:tfm", "ISBN:0721601464" ] }, "comments" : [ "Morphology: Mononuclear cell, diameter 14-18 _M, fine azurophilic granules; markers: CD11b (shared with many other myeloid cells); location: Adult: bone marrow; Fetal: Liver, Yolk Sac; role or process: hematopoiesis, monocyte development; lineage: hematopoietic, myeloid." ], - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "xrefs" : [ { "val" : "BTO:0004657" }, { @@ -1845,6 +1914,7 @@ "xrefs" : [ "GOC:dsd", "GOC:tfm", "PMID:12768659" ] }, "comments" : [ "These cells are reportedly CD31-positive, CD34-positive, CD144-positive, CD309-positive, and TAL1-positive." ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "angioblast" @@ -1866,7 +1936,7 @@ "xrefs" : [ "GO_REF:0000031", "MESH:D009000" ] }, "comments" : [ "Morphology: Mononuclear cell, diameter, 14 to 20 _M, N/C ratio 2:1-1:1. Nucleus may appear in variety of shapes: round, kidney, lobulated, or convoluted. Fine azurophilic granules present; markers: CD11b (shared with other myeloid cells), human: CD14, mouse: F4/80-mid,GR1-low; location: Blood, but can be recruited into tissues; role or process: immune & tissue remodelling; lineage: hematopoietic, myeloid." ], - "subsets" : [ "http://purl.obolibrary.org/obo/cl#blood_and_immune_upper_slim", "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#general_cell_types_upper_slim", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#blood_and_immune_upper_slim", "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#general_cell_types_upper_slim", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "xrefs" : [ { "val" : "BTO:0000876" }, { @@ -1891,7 +1961,7 @@ "xrefs" : [ "GOC:add", "GOC:tfm", "ISBN:0702022918", "ISBN:0702024783", "PMID:33348900", "Wikipedia:Giant_cell" ] }, "comments" : [ "Role or process: Chronic infection, granulomatous inflammation. Consider also megakaryocyte (CL:0000556) as sometimes multinucleated giant cell is used to refer to this." ], - "subsets" : [ "http://purl.obolibrary.org/obo/cl#blood_and_immune_upper_slim" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#blood_and_immune_upper_slim", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "Langerhans giant cell", @@ -1935,7 +2005,7 @@ "val" : "A non-terminally differentiated cell that is capable of developing into a muscle cell.", "xrefs" : [ "GOC:add" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "ZFA:0009291" } ] @@ -1949,6 +2019,7 @@ "val" : "A stem cell that can give rise to cell types of the body other than those of the germ-line.", "xrefs" : [ "GO:0048103" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "CALOHA:TS-2086" }, { @@ -1966,7 +2037,7 @@ "val" : "An achromatic cell of the myeloid or lymphoid lineages capable of ameboid movement, found in blood or other tissue.", "xrefs" : [ "GOC:add", "GOC:tfm", "ISBN:978-0-323-05290-0" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "leucocyte" @@ -2005,7 +2076,7 @@ "xrefs" : [ "GOC:add", "GOC:tfm", "PMID:16360205" ] }, "comments" : [ "Note that this is a non-mammalian cell type. Use platelet ; CL:0000233 for thrombocytes (platelets) in mammals." ], - "subsets" : [ "http://purl.obolibrary.org/obo/cl#blood_and_immune_upper_slim" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#blood_and_immune_upper_slim", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "ZFA:0009323" } ] @@ -2019,7 +2090,7 @@ "val" : "A cell of the monocyte, granulocyte, mast cell, megakaryocyte, or erythroid lineage.", "xrefs" : [ "GOC:add" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "BTO:0001441" }, { @@ -2040,7 +2111,7 @@ "xrefs" : [ "GOC:add", "GOC:tfm" ] }, "comments" : [ "Note that in FMA erythropoietic cells are types of nucleated erythrocytes and thus don't include erythrocytes." ], - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "erythropoietic cell" @@ -2068,7 +2139,7 @@ "val" : "A nucleated precursor of an erythrocyte that lacks hematopoietic lineage markers.", "xrefs" : [ "GOC:add", "ISBN:0721601464", "PMID:18174176" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#blood_and_immune_upper_slim", "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#blood_and_immune_upper_slim", "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "normoblast" @@ -2094,7 +2165,7 @@ "val" : "A cell of the monocyte, granulocyte, or mast cell lineage.", "xrefs" : [ "GOC:add" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "ZFA:0009326" } ] @@ -2109,7 +2180,7 @@ "xrefs" : [ "GOC:add", "GOC:amm", "GOC:dsd", "GOC:tfm", "ISBN:0721601464", "MESH:D001491", "PMCID:PMC2626675", "PMID:11927641", "PMID:19741522", "PMID:21236338", "PMID:9933081" ] }, "comments" : [ "Matures in the bone marrow and account for <1% of leukocytes in the peripheral blood, spleen, and bone marrow. Basophils are described as being CD11a-positive, CD11b-positive, CD13-positive, CD15-positive, CD18-positive, CD21-positive, CD25-positive, CD29-positive, CD35-positive, CD40-positive, CD40L-positive, CD44-positive, CD45R-negative, CD46-positive, CD49a-positive, CD49b-positive, CD49d-positive, CD55-positive, CD59-positive, CD62L-positive, CD63-positive, CD69-positive, CD90-negative, CD116-positive, CD117-negative, CD124-positive, CD125-positive, CD131-positive, CD161-positive, CD184-positive, CD191-positive, CD192-positive, CD197-positive, CD200R3-positive, CD218-positive, CD282-positive, CD284-positive, CD289-positive, CD290-positive, CD294-positive, natural killer cell receptor 2B4-positive, smad1-positive, CD3-negative, CD4-negative, CD7-negative, CD8-negative, CD14-negative, CD15-negative, CD16-negative, CD19-negative, CD20-negative, CD34-negative, CD36-negative, CD45R-negative, CD56-negative, CD57-negative, CD235a-negative, and GR1-negative. Transcription factors- GATA1-positive, PU.1-positive." ], - "subsets" : [ "http://purl.obolibrary.org/obo/cl#blood_and_immune_upper_slim", "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#blood_and_immune_upper_slim", "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "synonyms" : [ { "pred" : "hasBroadSynonym", "val" : "polymorphonuclear leucocyte" @@ -2145,7 +2216,7 @@ "xrefs" : [ "GOC:add", "GOC:amm", "GOC:dsd", "GOC:tfm", "ISBN:0721601464", "PMCID:PMC2626675", "PMID:10914487", "PMID:1662676" ] }, "comments" : [ "Eosinophils are also CD14-negative, CD32-positive, CD44-positive, CD48-positive, CD69-positive, CD192-negative, MBP1-positive, MBP2-positive, TLR2-negative, TLR4-negative, and lineage-negative (B220, CD2, CD14, CD19, CD56, CD71, CD117, CD123, CD235a (glycophorin A), and TER119). The cytokines IL-3, IL-5, and GM-CSF are involved in their development and differentiation. Usually considered CD16-negative, CD16 is observed on eosinophilic metamyelocyte." ], - "subsets" : [ "http://purl.obolibrary.org/obo/cl#blood_and_immune_upper_slim", "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#blood_and_immune_upper_slim", "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "synonyms" : [ { "pred" : "hasBroadSynonym", "val" : "polymorphonuclear leucocyte" @@ -2188,7 +2259,7 @@ "val" : "Any of the immature or mature forms of a granular leukocyte that in its mature form has a nucleus with three to five lobes connected by slender threads of chromatin, and cytoplasm containing fine inconspicuous granules and stainable by neutral dyes.", "xrefs" : [ "GOC:add", "GOC:amm", "GOC:tfm", "ISBN:0721601464" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#blood_and_immune_upper_slim", "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#blood_and_immune_upper_slim", "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "synonyms" : [ { "pred" : "hasBroadSynonym", "val" : "PMN" @@ -2252,7 +2323,7 @@ "xrefs" : [ "GOC:add", "PMID:10449155", "PMID:17332250", "PMID:9521319" ] }, "comments" : [ "These cells are CD1a-negative, CD1b-positive, CD11a-positive, CD11c-positive, CD13-positive, CD14-negative, CD20-negative, CD21-negative, CD33-positive, CD40-negative, CD50-positive, CD54-positive, CD58-positive, CD68-negative, CD80-negative, CD83-negative, CD85j-positive, CD86-positive, CD89-negative, CD95-positive, CD120a-negative, CD120b-positive, CD123-negative, CD178-negative, CD206-negative, CD207-negative, CD209-negative, and TNF-alpha-negative. Upon TLR stimulation, they are capable of producing high levels of TNF-alpha, IL-6, CXCL8 (IL-8)." ], - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "pred" : "hasBroadSynonym", "val" : "interdigitating cell" @@ -2279,7 +2350,7 @@ "val" : "A dendritic cell type of distinct morphology, localization, and surface marker expression (CD123-positive) from other dendritic cell types and associated with early stage immune responses, particularly the release of physiologically abundant amounts of type I interferons in response to infection.", "xrefs" : [ "GOC:add", "GOC:dsd", "PMCID:PMC2118448", "PMCID:PMC538703", "PMID:15549123", "PMID:17332250", "PMID:17850486", "PMID:20304825" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#blood_and_immune_upper_slim", "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#blood_and_immune_upper_slim", "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "DC2" @@ -2326,7 +2397,7 @@ "xrefs" : [ "GOC:add", "GOC:dsd", "ISBN:0781735149" ] }, "comments" : [ "Mature B cells are also reportedly CD10-negative, CD19-positive, CD22-positive, CD34-negative, CD48-positive, CD79a-positive, CD84-positive, CD127-negative, CD352-positive, RAG-negative, TdT-negative, Vpre-B-negative, and pre-BCR-negative. Transcription factors expressed: Pax5-positive." ], - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "mature B lymphocyte" @@ -2351,7 +2422,7 @@ "xrefs" : [ "GOC:add", "GOC:dsd", "GO_REF:0000031", "ISBN:0721601464", "ISBN:0781735149", "PMID:19447676", "PMID:20081059", "PMID:20839338", "PMID:20951740", "http://en.wikipedia.org/wiki/Plasma_cell" ] }, "comments" : [ "Plasma cells develop in the spleen and migrate to the bone marrow. Plasma cells are also reportedly CD5-negative, CD10-negative, CD19-positive, CD20-negative, CD21-negative, CD22-negative, CD23-negative, CD24-negative, CD25-negative, CD27-positive, CD34-negative, CD38-positive, CD40-positive, CD43-positive, CD45-positive, CD48-positive, CD53-low, CD80-negative, CD81-positive, CD86-positive, CD95-positive, CD196-negative, CD229-positive, CD270-positive, CD352-positive, CD361-positive, and IgD-negative. Transcription factors: BLIMP1-positive, IRF4-positive, PAX5-negative, SpiB-negative, Ets1-negative, and XBP1-positive." ], - "subsets" : [ "http://purl.obolibrary.org/obo/cl#blood_and_immune_upper_slim", "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#blood_and_immune_upper_slim", "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "plasma B cell" @@ -2394,7 +2465,7 @@ "val" : "A T cell that expresses an alpha-beta T cell receptor complex.", "xrefs" : [ "GOC:add", "GOC:tfm", "ISBN:0781735149" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#blood_and_immune_upper_slim", "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#blood_and_immune_upper_slim", "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "alpha-beta T lymphocyte" @@ -2419,7 +2490,7 @@ "xrefs" : [ "GOC:add", "GOC:tfm", "ISBN:0781735149" ] }, "comments" : [ "Note that gamma-delta T cells have both thymic and extrathymic differentiation pathways." ], - "subsets" : [ "http://purl.obolibrary.org/obo/cl#blood_and_immune_upper_slim", "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#blood_and_immune_upper_slim", "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "gamma-delta T lymphocyte" @@ -2455,7 +2526,7 @@ "xrefs" : [ "GOC:add", "GOC:dsd", "GOC:rhs", "GOC:tfm", "GO_REF:0000031", "ISBN:0781735149", "PMID:20081059", "PMID:20839338" ] }, "comments" : [ "Immature B cells are also reportedly CD5-positive, CD10-positive, CD19-positive, CD20-positive, CD21-positive, CD22-positive, CD24-positive, CD25-negative, CD27-negative, CD34-negative, CD38-positive, CD40-positive, CD43-negative, CD45-positive, CD48-positive, CD53-positive, CD79a-positive, CD80-negative, CD81-positive, CD86-negative, CD95-negative, CD127-negative, CD138-negative, CD185-positive, CD196-positive, MHCII/HLA-DR-positive, RAG-positive, TdT-negative, Vpre-B-negative, and preBCR-negative. Transcription factors expressed: Pax5-positive." ], - "subsets" : [ "http://purl.obolibrary.org/obo/cl#blood_and_immune_upper_slim", "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#blood_and_immune_upper_slim", "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "immature B lymphocyte" @@ -2487,7 +2558,7 @@ "val" : "A precursor B cell is a B cell with the phenotype CD10-positive.", "xrefs" : [ "GOC:rhs", "GOC:tfm", "GO_REF:0000031" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "synonyms" : [ { "pred" : "hasRelatedSynonym", "val" : "pre-B cell" @@ -2514,7 +2585,7 @@ "xrefs" : [ "GOC:add", "GO_REF:0000031", "ISBN:0781735149", "PMID:12810111", "PMID:22343568" ] }, "comments" : [ "This cell type is compatible with the HIPC Lyoplate markers for 'transitional B cell'." ], - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "transitional B cell", @@ -2556,7 +2627,7 @@ "xrefs" : [ "GOC:add", "GOC:dsd", "ISBN:0781735149", "PMID:12633665", "PMID:16551251", "PMID:18432934" ] }, "comments" : [ "Human pro-B cells are reportedly CD10-positive, CD22-positive, CD34-positive, CD38-positive, CD45-low, CD48-positive, CD79a-positive, CD127-positive, CD184-positive, RAG-positive, TdT-positive, Vpre-B-positive, pre-BCR-negative, IgD-negative, and IgM-negative. Transcription factors expressed: Pax5-positive, EBF-positive, E2A-negative, Ikaros-negative, and PU.1-negative." ], - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "synonyms" : [ { "pred" : "hasBroadSynonym", "val" : "pre-pro B cell", @@ -2606,7 +2677,7 @@ "val" : "A lymphoid progenitor cell of the T cell lineage, with some lineage specific marker expression, but not yet fully committed to the T cell lineage.", "xrefs" : [ "GOC:add", "ISBN:0781735149" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "pro-T lymphocyte" @@ -2637,6 +2708,7 @@ "xrefs" : [ "GOC:add", "GOC:tfm", "PMID:7758949" ] }, "comments" : [ "Note that this is a non-mammalian cell type." ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "ZFA:0009351" } ] @@ -2651,6 +2723,7 @@ "xrefs" : [ "GOC:add", "GOC:dsd", "PMCID:PMC1183570", "PMCID:PMC1312421", "PMID:8629001", "PMID:9354811", "http://www.copewithcytokines.de" ] }, "comments" : [ "MCP are CD16-positive, CD32-positive, CD34-positive, CD45-positive, integrin beta-7-positive, and lin-negative (CD2, CD3e, CD4, CD5, CD8a, CD14, CD19, CD20, CD27, integrin alpha-M, ly6c, ly6g, NCAM-1, and ter119). These cells also express the transcription factors GATA-1, GATA-2, and MITF, but not C/EBPa." ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "MCP" @@ -2675,7 +2748,7 @@ "xrefs" : [ "GOC:add", "GOC:tfm", "PMID:19022770" ] }, "comments" : [ "Markers differ between mouse and human." ], - "subsets" : [ "http://purl.obolibrary.org/obo/cl#blood_and_immune_upper_slim", "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#blood_and_immune_upper_slim", "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "MPP" @@ -2705,7 +2778,7 @@ "xrefs" : [ "GOC:add", "GOC:tfm" ] }, "comments" : [ "Note that this is a class of cell types, not an identified single cell type." ], - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "pred" : "hasBroadSynonym", "val" : "lymphoid progenitor cell" @@ -2730,7 +2803,7 @@ "xrefs" : [ "GOC:add", "GOC:tfm", "PMID:19022770" ] }, "comments" : [ "Note that this is a class of cell types, not an identified single cell type." ], - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "synonyms" : [ { "pred" : "hasBroadSynonym", "val" : "myeloid progenitor cell" @@ -2758,7 +2831,7 @@ "val" : "A leukocyte with a single non-segmented nucleus in the mature form.", "xrefs" : [ "GOC:add" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#blood_and_immune_upper_slim", "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#blood_and_immune_upper_slim", "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "mononuclear leukocyte" @@ -2786,7 +2859,7 @@ "xrefs" : [ "GOC:add", "GOC:ana", "GO_REF:0000031", "PMID:16168663", "PMID:17016554", "PMID:17016559" ] }, "comments" : [ "Markers: Mouse: CD11b+GR1+CD31+; Human: CD34+ CD33+CD15-CD13+. (According to some reports in humans these cells are iNOS+ARG1+IL13+IFNg+); location: In cancerous tissue; in the blood and lymphoid organs in sepsis." ], - "subsets" : [ "http://purl.obolibrary.org/obo/cl#blood_and_immune_upper_slim" ] + "subsets" : [ "http://purl.obolibrary.org/obo/cl#blood_and_immune_upper_slim", "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ] } }, { "id" : "http://purl.obolibrary.org/obo/CL_0000945", @@ -2798,7 +2871,7 @@ "xrefs" : [ "GOC:add", "GOC:rhs", "GOC:tfm", "GO_REF:0000031", "ISBN:0781735149" ] }, "comments" : [ "Types of B lineage lymphocytes include B cells and antibody secreting cells (plasmablasts and plasma cells). Lymphocytes of B cell lineage can be distinguished from those of T cell lineage by their lack of CD3e (as part of the T cell receptor complex)." ], - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" @@ -2812,7 +2885,8 @@ "definition" : { "val" : "A lymphocyte of B lineage that is devoted to secreting large amounts of immunoglobulin.", "xrefs" : [ "GOC:add", "GOC:tfm", "GO_REF:0000031", "ISBN:0721601464", "ISBN:0781735149" ] - } + }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ] } }, { "id" : "http://purl.obolibrary.org/obo/CL_0000954", @@ -2824,7 +2898,7 @@ "xrefs" : [ "GOC:dsd", "GOC:rhs", "GOC:tfm", "GO_REF:0000031", "PMID:16551251", "PMID:18432934", "PMID:9785673" ] }, "comments" : [ "Small pre-B-II cells are also reportedly CD10-positive, CD19-positive, CD34-negative, CD79a-positive, CD127-negative, TdT-negative, Vpre-B-negative, sIgM-negative, and sIgD-negative. Transcription factors: PU.1-positive, Ikaros-positive, E2A-positive, and PAX5-positive." ], - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "small pre-BII cell" @@ -2840,6 +2914,7 @@ "xrefs" : [ "GOC:dsd", "GOC:rhs", "GOC:tfm", "GO_REF:0000031", "PMID:9785673" ] }, "comments" : [ "pre-B-II cell are also reportedly CD19-positive, CD22-positive, CD38-positive, CD45-positive, and CD48-positive." ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "pre-B-lymphocyte" @@ -2863,7 +2938,7 @@ "xrefs" : [ "GOC:dsd", "GOC:msz", "GOC:tfm", "GO_REF:0000031", "PMCID:PMC2673126" ] }, "comments" : [ "This cell type is compatible with the HIPC Lyoplate markers for 'plasmablast'. Plasmablasts are also reportedly CD48-positive, CD63-positive, CD229-positive, CD270-positive, CD319-positive, CD352-positive, CD361-positive, and IgD-negative." ], - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "synonyms" : [ { "pred" : "hasBroadSynonym", "val" : "CD20-negative B cell" @@ -2888,7 +2963,7 @@ "val" : "A cell of a hematopoietic lineage.", "xrefs" : [ "GOC:add", "GO_REF:0000031" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "haematopoietic cell" @@ -2921,7 +2996,7 @@ "xrefs" : [ "GOC:amm", "GO_REF:0000031", "PMID:17850486" ] }, "comments" : [ "Originally described in the dendritic cell ontology (DC_CL:0000003)(PMID:19243617) These cells are also CD20-negative, MHCII-positive." ], - "subsets" : [ "http://purl.obolibrary.org/obo/cl#blood_and_immune_upper_slim", "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#blood_and_immune_upper_slim", "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "synonyms" : [ { "pred" : "hasBroadSynonym", "val" : "interdigitating cell" @@ -2954,7 +3029,8 @@ "lbl" : "CD7-negative lymphoid progenitor OR granulocyte monocyte progenitor", "type" : "CLASS", "meta" : { - "comments" : [ "Originally described in the dendritic cell ontology (DC_CL:1110000)(PMID:19243617)." ] + "comments" : [ "Originally described in the dendritic cell ontology (DC_CL:1110000)(PMID:19243617)." ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ] } }, { "id" : "http://purl.obolibrary.org/obo/CL_0001035", @@ -2965,13 +3041,19 @@ "val" : "A connective tissue cell found in bone.", "xrefs" : [ "GOC:add", "GO_REF:0000034" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#general_cell_types_upper_slim", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#general_cell_types_upper_slim", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "xrefs" : [ { + "val" : "https://cellxgene.cziscience.com/cellguide/CL_0001035" + } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" }, { "pred" : "http://purl.org/dc/terms/contributor", "val" : "https://orcid.org/0000-0001-9990-8331" + }, { + "pred" : "http://purl.org/dc/terms/description", + "val" : "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nBone cells, also known as osteocytes, form the building blocks of the skeletal system. They represent the most common type of bone cell, making up approximately 95% of the total bone cell population in mature adult bone tissue. Osteocytes are a stellate shape with numerous long, slender dendritic processes.\nThe formation of bone is a complex process involving the action of osteoclasts - cells that break down and reabsorb old bone, followed by osteoblasts that rebuild the bone. Osteocytes serve as coordinators for these two types of bone cells to ensure a balance in the bone remodeling process, contributing to maintaining both bone strength and mineral homeostasis.\nThe primary functions of osteocytes involve the creation, maintenance, and repair of bone tissue. They ensure that bone remodeling is performed by forming a network within the bone and communicating with other cells to help them respond to mechanical strain and damage.\nA remarkable aspect of osteocytes is their ability to perceive mechanical forces, translating them into biochemical signals that regulate bone remodeling and adaptation. Defects in osteocyte function, aside from other bone cells, have been associated with several bone disorders such as osteoporosis, renal osteodystrophy, and skeletal manifestations of diabetes." }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2011-11-16T04:28:16Z" @@ -2986,6 +3068,7 @@ "val" : "A hematopoietic oligopotent progenitor cell that has the ability to differentiate into limited cell types but lacks lineage cell markers and self renewal capabilities. Cell lacks hematopoeitic lineage markers.", "xrefs" : [ "GOC:tfm", "PMID:19022770" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "basicPropertyValues" : [ { "pred" : "http://purl.org/dc/terms/contributor", "val" : "https://orcid.org/0000-0003-1980-3228" @@ -3003,7 +3086,7 @@ "val" : "A lymphocyte that lacks characteristic T cell, B cell, myeloid cell, and dendritic cell markers, that functions as part of the innate immune response to produce cytokines and other effector responses.", "xrefs" : [ "GOC:add", "GOC:dsd", "PMID:23292121", "PMID:23348417" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#blood_and_immune_upper_slim", "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#blood_and_immune_upper_slim", "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" @@ -3025,6 +3108,7 @@ "xrefs" : [ "GOC:add" ] }, "comments" : [ "Types of B lineage lymphocytes include B cells and antibody secreting cells (plasmablasts and plasma cells). Lymphocytes of B cell lineage can be distinguished from those of T cell lineage by their lack of CD3e (as part of the T cell receptor complex)." ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "basicPropertyValues" : [ { "pred" : "http://purl.org/dc/terms/contributor", "val" : "https://orcid.org/0000-0001-9990-8331" @@ -3039,6 +3123,7 @@ "val" : "A B cell that is CD19-positive.", "xrefs" : [ "GOC:add" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "B lymphocyte, CD19-positive" @@ -3069,7 +3154,7 @@ "val" : "A progenitor cell that can give rise to plasmacytoid and myeloid dendritic cells, and to monocytes and macrophages.", "xrefs" : [ "GOC:tfm", "PMID:19273628" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "MDP" @@ -3092,7 +3177,7 @@ "xrefs" : [ "GOC:ak", "GOC:dsd", "GOC:tfm", "PMCID:PMC1312421" ] }, "comments" : [ "There may be an intermediate cell type. These cells also CD13-positive, CD16-positive, CD32-positive, and integrin beta 7-positive. Transcription factors: GATA1-positive, MCP-1-positive, mitf-positive, PU.1-positive, and CEBP/a-low." ], - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "BMCP" @@ -3114,7 +3199,7 @@ "val" : "A hematopoietic progenitor cell that is capable of developing into only one lineage of hematopoietic cells.", "xrefs" : [ "GOC:tfm", "PMID:19022770" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#blood_and_immune_upper_slim" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#blood_and_immune_upper_slim", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "basicPropertyValues" : [ { "pred" : "http://purl.org/dc/terms/contributor", "val" : "https://orcid.org/0000-0003-1980-3228" @@ -3133,7 +3218,7 @@ "xrefs" : [ "GOC:tfm", "PMID:19022770", "https://orcid.org/0000-0001-5208-3432" ] }, "comments" : [ "This cell type is intended to be compatible with any vertebrate hematopoietic oligopotent progenitor cell. For mammalian hematopoietic oligopotent progenitor cells known to be lineage-negative, please use the term 'hematopoietic oligopotent progenitor cell' (CL_0001060)." ], - "subsets" : [ "http://purl.obolibrary.org/obo/cl#blood_and_immune_upper_slim" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#blood_and_immune_upper_slim", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "basicPropertyValues" : [ { "pred" : "http://purl.org/dc/terms/contributor", "val" : "https://orcid.org/0000-0003-1980-3228" @@ -3151,6 +3236,7 @@ "val" : "An epithelial cell derived from ectoderm.", "xrefs" : [ "FMA:69074", "GOC:tfm" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "FMA:69074" }, { @@ -3173,7 +3259,7 @@ "val" : "A leukocyte that lacks granules.", "xrefs" : [ "GOC:tfm" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#blood_and_immune_upper_slim" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#blood_and_immune_upper_slim", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "agranular leukocyte" @@ -3199,7 +3285,7 @@ "xrefs" : [ "GOC:tfm", "ISBN:0618947256" ] }, "comments" : [ "MH consider whether bone marrow cells are bone cells in the structural sense vs. being part of bone organ sense." ], - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "BTO:0004850" }, { @@ -3225,7 +3311,7 @@ "xrefs" : [ "GOC:dsd", "GOC:tfm", "PMID:12768659" ] }, "comments" : [ "These cells are reportedly CD31-positive, CD34-positive, CD144-positive, TAL1-positive." ], - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "vascular endothelial cell" @@ -3239,10 +3325,15 @@ "val" : "CALOHA:TS-1106" }, { "val" : "FMA:67755" + }, { + "val" : "https://cellxgene.cziscience.com/cellguide/CL_0002139" } ], "basicPropertyValues" : [ { "pred" : "http://purl.org/dc/terms/contributor", "val" : "https://orcid.org/0000-0003-1980-3228" + }, { + "pred" : "http://purl.org/dc/terms/description", + "val" : "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nEndothelial cells of the vascular tree, commonly referred to as vascular endothelial cells, line the entire circulatory system, from the heart to the smallest capillaries. These cells have a unique, flattened shape, and are tightly bound together, forming a thin layer known as the endothelium. The endothelium is responsible for maintaining the interior surface of blood vessels, and plays a critical role in ensuring the smooth flow of blood. \nVascular endothelial cells act as a semi-permeable membrane, controlling the passage of materials and the transit of white blood cells into and out of the bloodstream. These cells are also involved in blood coagulation. When a blood vessel is damaged, endothelial cells promote clotting to prevent excessive bleeding and facilitate wound healing. Other functions include regulation of blood pressure and blood volume by releasing vasodilators and vasoconstrictors to either widen or constrict blood vessels, accordingly.\nFurthermore, the endothelial cells are crucial in the formation of new blood vessels, a process known as angiogenesis. This is particularly important in wound healing and the growth of new tissues during development or after injury. In the context of diseases such as cancer, angiogenesis helps facilitate tumor growth by providing nutrients and oxygen." }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2010-08-24T02:06:40Z" @@ -3257,7 +3348,7 @@ "val" : "A cell involved in the formation of a granulocyte.", "xrefs" : [ "GOC:tfm" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "FMA:83519" } ], @@ -3278,6 +3369,7 @@ "val" : "A cell involved in the formation of a monocyte (monopoiesis).", "xrefs" : [ "GOC:tfm" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "FMA:83552" } ], @@ -3298,6 +3390,7 @@ "val" : "A cell containing at least one nucleus.", "xrefs" : [ "GOC:tfm" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "FMA:67513" } ], @@ -3318,6 +3411,7 @@ "val" : "A cell type that secretes histamine.", "xrefs" : [ "GOC:tfm" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "basicPropertyValues" : [ { "pred" : "http://purl.org/dc/terms/contributor", "val" : "https://orcid.org/0000-0003-1980-3228" @@ -3335,7 +3429,7 @@ "val" : "A cell that is part of the nervous system.", "xrefs" : [ "GOC:tfm", "ISBN:0618947256" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "CALOHA:TS-2040" }, { @@ -3358,7 +3452,7 @@ "val" : "A cell of the supporting or framework tissue of the body, arising chiefly from the embryonic mesoderm and including adipose tissue, cartilage, and bone.", "xrefs" : [ "GOC:tfm", "ISBN:0618947256" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "CALOHA:TS-2096" }, { @@ -3385,6 +3479,7 @@ "val" : "A cell of the embryo.", "xrefs" : [ "FMA:0618947256" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "CALOHA:TS-0263" }, { @@ -3393,10 +3488,15 @@ "val" : "WBbt:0007028" }, { "val" : "ZFA:0007089" + }, { + "val" : "https://cellxgene.cziscience.com/cellguide/CL_0002321" } ], "basicPropertyValues" : [ { "pred" : "http://purl.org/dc/terms/contributor", "val" : "https://orcid.org/0000-0003-1980-3228" + }, { + "pred" : "http://purl.org/dc/terms/description", + "val" : "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nEmbryonic cells in metazoans, which include all multicellular animals, are biological units in their earliest developmental stages from conception until the organism is fully formed. \nThey are derived from a fertilized egg, which undergoes a series of cell divisions to produce a multicellular organism. During the early phases of embryonic development, these cells exhibit pluripotency, meaning they possess the potential to differentiate into a diverse array of specialized cell types that constitute different body tissues and structures. \nThe balance between cell proliferation and differentiation in embryonic cells is crucial for successful development. When cells continue to divide without differentiating, overgrowth may occur leading to conditions such as teratomas (tumors of embryonic cells). Conversely, if cell differentiation proceeds at the expense of cell proliferation, developmental anomalies could occur regarding size or mass of the organism or its parts." }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2010-09-15T03:39:21Z" @@ -3411,7 +3511,7 @@ "val" : "A T cell that has not completed T cell selection.", "xrefs" : [ "GOC:tfm" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#blood_and_immune_upper_slim", "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#blood_and_immune_upper_slim", "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "immature T-cell" @@ -3439,6 +3539,7 @@ "xrefs" : [ "GOC:tfm" ] }, "comments" : [ "From Onard of the FMA: Cardiac muscle cell or cardiac myocyte is a striated muscle cell. Cardiocyte on the other hand is any cell in the heart which includes cells other than muscle cells (e.g. endothelial cell of endocardium). Unless there is a consensus among anatomists that cardiocytes refer only to muscle cells, we will treat them as a general class of cells in the heart." ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "heart cell" @@ -3469,7 +3570,7 @@ "val" : "A lymphocyte found in adipose tissue that lacks lineage markers of other lymphocytes but is capable of mediating TH2 cytokine responses. This cell type is found in fat associated lymphoid clusters, proliferates in response to IL2 and produce large amounts of TH2 cytokines such as IL5, IL6 and IL13", "xrefs" : [ "GOC:tfm", "PMID:20023630" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#blood_and_immune_upper_slim" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#blood_and_immune_upper_slim", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "basicPropertyValues" : [ { "pred" : "http://purl.org/dc/terms/contributor", "val" : "https://orcid.org/0000-0003-1980-3228" @@ -3488,6 +3589,7 @@ "xrefs" : [ "GO_REF:0000034" ] }, "comments" : [ "Needs logical definition. Should be capable_of skeletal system morphogenesis? or skeletal tissue development? needs to be added to GO. NOTES:a cell type of the early embryo (see also: mesenchymal cells) that will give rise to mineralized connective tissue. Scleroblasts can differentiate into osteoblasts (bone-forming cells), chondroblasts (cartilage-forming cells), odontoblasts (dentin-forming cells), ameloblasts (enamel-forming cells). The mesenchymal cells developing into osteoblasts and chondroblasts are derived from the mesoderm. Those developing into odontoblasts are neural crest cells. Those developing into ameloblasts are derived from the ectoderm. (http://www.copewithcytokines.de/cope.cgi?key=scleroblasts)" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "scleroblast", @@ -3510,6 +3612,7 @@ "val" : "Cell that is part of the neural crest region of the neuroepithelium, prior to migration. Note that not all premigratory neural crest cells may become migratory neural crest cells.", "xrefs" : [ "UBERONREF:0000002" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "ZFA:0007084" } ], @@ -3530,7 +3633,7 @@ "val" : "Any hematopoietic cell that is a precursor of some other hematopoietic cell type.", "xrefs" : [ "GOC:dos" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ] + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ] } }, { "id" : "http://purl.obolibrary.org/obo/CL_0008019", @@ -3540,7 +3643,7 @@ "definition" : { "val" : "A non-polarised cell precursor cell that is part of some mesenchyme, is associated with the cell matrix but is not connected to other cells and is capable of migration." }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "mesenchyme cell" @@ -3558,6 +3661,7 @@ "definition" : { "val" : "A zygote in a plant or an animal." }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "MESH:D015053" } ], @@ -3575,13 +3679,13 @@ "val" : "A cell of the neural crest. Neural crest cells are multipotent. Premigratory neural crest cells are found at the neural plate boarder, some of which will undergo ectomesynchymal transition and delamination to form migratory neural crest cells.", "xrefs" : [ "https://orcid.org/0000-0001-5208-3432", "https://orcid.org/0000-0002-9900-7880" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "https://cellxgene.cziscience.com/cellguide/CL_0011012" } ], "basicPropertyValues" : [ { "pred" : "http://purl.org/dc/terms/description", - "val" : "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional.\n\nNeural crest cells are a group of transient and highly migratory cells that originate from the neuroectoderm during the early stages of embryonic development. They are multipotent cells with an exceptional degree of plasticity, capable of differentiating into various somatic cell types and therefore play a fundamental role in the formation of various organs and tissues, making them critical contributors to the developing embryo. \nAfter the initiation of neurulation (the formation of the neural tube) neural crest cells start to undergo epithelial-to-mesenchymal transition and delaminate and migrate from the dorsal neural tube to several regions throughout the embryo. They differentiate into a range of diverse cell types, such as neurons and glial cells of the peripheral nervous system, including sensory and autonomic neurons. They also contribute to the formation of adrenal glands, pigment cells in the skin (melanocytes), cardiac structures, including parts of the heart septum and major arteries, as well as bones and cartilage of the face and skull.\nDisorders or aberrations in the development or migration of the neural crest cells can lead to serious congenital malformations, such as neurocristopathies, including Hirschsprung disease, neuroblastoma, and neurofibromatosis." + "val" : "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nNeural crest cells are a group of transient and highly migratory cells that originate from the neuroectoderm during the early stages of embryonic development. They are multipotent cells with an exceptional degree of plasticity, capable of differentiating into various somatic cell types and therefore play a fundamental role in the formation of various organs and tissues, making them critical contributors to the developing embryo. \nAfter the initiation of neurulation (the formation of the neural tube) neural crest cells start to undergo epithelial-to-mesenchymal transition and delaminate and migrate from the dorsal neural tube to several regions throughout the embryo. They differentiate into a range of diverse cell types, such as neurons and glial cells of the peripheral nervous system, including sensory and autonomic neurons. They also contribute to the formation of adrenal glands, pigment cells in the skin (melanocytes), cardiac structures, including parts of the heart septum and major arteries, as well as bones and cartilage of the face and skull.\nDisorders or aberrations in the development or migration of the neural crest cells can lead to serious congenital malformations, such as neurocristopathies, including Hirschsprung disease, neuroblastoma, and neurofibromatosis." } ] } }, { @@ -3593,7 +3697,7 @@ "val" : "A precursor cell that has a tendency to differentiate into a specific type of cell. They are descendants of stem cells, only they are more constrained in their differentiation potential or capacity for self-renewal, and are often more limited in both senses.", "xrefs" : [ "ISBN:978-1-62808-994-3", "https://doi.org/10.1016/B978-0-12-409503-8.00002-0" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "basicPropertyValues" : [ { "pred" : "http://purl.org/dc/terms/contributor", "val" : "https://orcid.org/0000-0001-5208-3432" @@ -3609,7 +3713,7 @@ "xrefs" : [ "GOC:dos" ] }, "comments" : [ "Work is needed on GO 'cell differentiation' before it is clear whether the equivalent class definition 'native cell' that capable_of some 'cell differentiation' works. Also, may want to consider merging this with non-terminally differentiated cell." ], - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ] + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ] } }, { "id" : "http://purl.obolibrary.org/obo/CL_0017005", @@ -3620,7 +3724,7 @@ "val" : "A lymphocyte that has gotten larger after being stimulated by an antigen.", "xrefs" : [ "NCIT:C13013", "http://orcid.org/0000-0001-9990-8331" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#blood_and_immune_upper_slim" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#blood_and_immune_upper_slim", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "BTO:0000772" }, { @@ -3629,11 +3733,11 @@ "val" : "FMA:83030" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/date", - "val" : "2022-08-17T14:20:01Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "pred" : "http://purl.org/dc/terms/contributor", "val" : "http://orcid.org/0000-0003-2473-2313" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2022-08-17T14:20:01Z" } ] } }, { @@ -3645,18 +3749,18 @@ "val" : "A lymphocyte of B lineage that has gotten larger after being stimulated by an antigen.", "xrefs" : [ "EFO:0005293", "https://orcid.org/0000-0002-2825-0621" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#blood_and_immune_upper_slim" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#blood_and_immune_upper_slim", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "EFO:0005293" }, { "val" : "FMA:83031" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/date", - "val" : "2022-08-17T14:30:32Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "pred" : "http://purl.org/dc/terms/contributor", "val" : "http://orcid.org/0000-0003-2473-2313" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2022-08-17T14:30:32Z" } ] } }, { @@ -3757,6 +3861,7 @@ "val" : "Hematopoietic cells resident in the bone marrow. Include: hematopoietic stem cells (lymphoid stem cells and myeloid stem cells) and the precursor cells for thrombocytes, erythrocytes, basophils, neutrophils, eosinophils, monocytes and lymphocytes.", "xrefs" : [ "NPX:PDR" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "pred" : "hasRelatedSynonym", "val" : "bone marrow hematopoietic cells", @@ -3779,7 +3884,7 @@ "val" : "A leukocyte with a single non-segmented nucleus in the mature form found in the circulatory pool of blood.", "xrefs" : [ "GOC:TermGenie" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "basicPropertyValues" : [ { "pred" : "http://purl.org/dc/terms/contributor", "val" : "http://www.wikidata.org/entity/Q35563349" @@ -3797,7 +3902,7 @@ "val" : "A lymphocyte located in blood.", "xrefs" : [ "https://orcid.org/0000-0001-9990-8331" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#blood_and_immune_upper_slim" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#blood_and_immune_upper_slim", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "basicPropertyValues" : [ { "pred" : "http://purl.org/dc/terms/date", "val" : "2022-11-04T14:40:00Z" @@ -3812,6 +3917,7 @@ "val" : "A multinucleate cell formed by the fusion of multiple uninuclear cells through plasma membrane fusion. This process leads to a single large cell containing multiple nuclei within a shared cytoplasm.", "xrefs" : [ "PMID:20851884", "Wikipedia:Syncytium" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "syncytium", @@ -3849,9 +3955,6 @@ "val" : "Wikipedia:Mitosis" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0007067" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" } ] @@ -3933,15 +4036,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/geneontology/go-ontology/issues/28301" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0000789" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0000790" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0005717" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "cellular_component" @@ -3971,12 +4065,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/geneontology/go-ontology/issues/22355" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0005719" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0035327" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "cellular_component" @@ -4009,12 +4097,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/geneontology/go-ontology/issues/22355" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0005720" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0035328" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "cellular_component" @@ -4233,18 +4315,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/geneontology/go-ontology/issues/19116" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0042032" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0042089" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0042107" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0050663" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" @@ -4256,7 +4326,7 @@ "type" : "CLASS", "meta" : { "definition" : { - "val" : "The regulated release of serotonin by a cell. Serotonin (5-hydroxytryptamine, or 5-HT) is a monoamine synthesised in serotonergic neurons in the central nervous system, enterochromaffin cells in the gastrointestinal tract and some immune system cells.", + "val" : "The regulated release of serotonin by a cell. Serotonin (5-hydroxytryptamine, or 5-HT) is a monoamine synthesized in serotonergic neurons in the central nervous system, enterochromaffin cells in the gastrointestinal tract and some immune system cells.", "xrefs" : [ "GOC:ef", "ISBN:0198506732", "ISBN:0781735149" ] }, "synonyms" : [ { @@ -4324,9 +4394,6 @@ "val" : "Wikipedia:Neurulation" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0001679" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" } ] @@ -4708,12 +4775,6 @@ "val" : "immunoglobulin secretion" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0002378" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0048305" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" } ] @@ -4754,12 +4815,6 @@ "xrefs" : [ "GOC:dph" ] } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0002379" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0002380" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" } ] @@ -4830,12 +4885,6 @@ "val" : "cellular immune response" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0019723" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0042087" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" } ] @@ -5685,9 +5734,6 @@ "val" : "molecular function" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0005554" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "molecular_function" } ] @@ -5715,12 +5761,6 @@ "val" : "Reactome:R-HSA-193672" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0004926" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0099600" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "molecular_function" } ] @@ -5794,25 +5834,12 @@ "val" : "Reactome:R-HSA-114558" }, { "val" : "Reactome:R-HSA-167408" + }, { + "val" : "Reactome:R-HSA-381706" }, { "val" : "Wikipedia:GPCR" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0001622" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0001623" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0001624" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0001625" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0016526" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "molecular_function" } ] @@ -5845,9 +5872,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/geneontology/go-ontology/issues/17729" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0008372" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "cellular_component" @@ -5961,12 +5985,6 @@ "val" : "Wikipedia:Basement_membrane" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0005605" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0008003" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "cellular_component" } ] @@ -6252,9 +6270,6 @@ "val" : "Wikipedia:Ribosome" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0033279" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "cellular_component" } ] @@ -6308,12 +6323,6 @@ "val" : "Wikipedia:Cell_membrane" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0005887" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0005904" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "cellular_component" } ] @@ -6367,9 +6376,6 @@ "val" : "cellular DNA metabolism" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0055132" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" } ] @@ -6422,15 +6428,6 @@ "val" : "Wikipedia:Translation_(genetics)" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0006416" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0006453" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0043037" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" } ] @@ -6459,12 +6456,6 @@ "val" : "translation initiation" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0006440" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0006454" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" } ] @@ -6487,12 +6478,6 @@ "val" : "translation elongation" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0006442" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0006455" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" } ] @@ -6517,12 +6502,6 @@ "val" : "translational complex disassembly" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0006443" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0006456" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" } ] @@ -6545,21 +6524,9 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/geneontology/go-ontology/issues/20292" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "jl" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2012-12-13T16:25:32Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0015457" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0015460" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0044765" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" @@ -6619,12 +6586,6 @@ "val" : "Wikipedia:Exocytosis" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0016194" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0016195" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" } ] @@ -6661,15 +6622,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/geneontology/go-ontology/issues/25268" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0016193" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0016196" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0098701" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" @@ -6708,17 +6660,8 @@ "val" : "vesicle budding" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "jl" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2013-12-19T15:26:17Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0006902" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:1902591" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" @@ -6830,12 +6773,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002161", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_4896" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0006917" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0008632" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" @@ -6967,12 +6904,6 @@ "val" : "defense/immunity protein activity" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0002217" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0042829" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" } ] @@ -7043,15 +6974,9 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/geneontology/go-ontology/issues/27189" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "jl" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2013-12-19T15:25:51Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:1902589" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" @@ -7170,21 +7095,6 @@ "val" : "Wikipedia:Signal_transduction" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0023014" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0023015" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0023016" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0023033" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0023045" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" } ] @@ -7237,9 +7147,6 @@ "xrefs" : [ "GOC:mah" ] } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0038042" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" } ] @@ -7462,9 +7369,6 @@ "val" : "hemolymph circulation" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0070261" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" } ] @@ -7499,21 +7403,9 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/geneontology/go-ontology/issues/24968" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "jl" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2012-09-19T15:05:24Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0000004" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0007582" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0044699" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" @@ -7525,7 +7417,7 @@ "type" : "CLASS", "meta" : { "definition" : { - "val" : "The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.", + "val" : "A cellular process consisting of the biochemical pathways by which a living organism transforms chemical substances. This includes including anabolism (biosynthetic process) and catabolism (catabolic process). Metabolic processes includes the transformation of small molecules, as well macromolecular processes such as DNA repair and replication, protein synthesis and degradation.", "xrefs" : [ "GOC:go_curators", "ISBN:0198547684" ] }, "comments" : [ "Note that metabolic processes do not include single functions or processes such as protein-protein interactions, protein-nucleic acids, nor receptor-ligand interactions." ], @@ -7533,18 +7425,6 @@ "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "metabolism" - }, { - "pred" : "hasNarrowSynonym", - "val" : "metabolic process resulting in cell growth" - }, { - "pred" : "hasNarrowSynonym", - "val" : "metabolism resulting in cell growth" - }, { - "pred" : "hasNarrowSynonym", - "val" : "multicellular organism metabolic process" - }, { - "pred" : "hasRelatedSynonym", - "val" : "single-organism metabolic process" } ], "xrefs" : [ { "val" : "Wikipedia:Metabolism" @@ -7553,17 +7433,11 @@ "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/geneontology/go-ontology/issues/26424" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "jl" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/geneontology/go-ontology/issues/28932" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2012-10-17T15:46:40Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0044236" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0044710" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" @@ -7601,7 +7475,7 @@ "type" : "CLASS", "meta" : { "definition" : { - "val" : "The chemical reactions and pathways resulting in the formation of substances; typically the energy-requiring part of metabolism in which simpler substances are transformed into more complex ones.", + "val" : "A cellular process consisting of the biochemical pathways by which a living organism synthesizes chemical substances. This typically represents the energy-requiring part of metabolism in which simpler substances are transformed into more complex ones.", "xrefs" : [ "GOC:curators", "ISBN:0198547684" ] }, "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_chembl", "http://purl.obolibrary.org/obo/go#goslim_metagenomics", "http://purl.obolibrary.org/obo/go#goslim_plant", "http://purl.obolibrary.org/obo/go#goslim_plant_ribbon" ], @@ -7628,17 +7502,11 @@ "val" : "Wikipedia:Anabolism" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "jl" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/geneontology/go-ontology/issues/28932" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2012-10-17T15:52:18Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0044274" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0044711" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" @@ -7681,9 +7549,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/geneontology/go-ontology/issues/27189" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0043284" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" @@ -7743,9 +7608,6 @@ "val" : "physiological response to wounding" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0002245" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" } ] @@ -7801,9 +7663,6 @@ "val" : "Wikipedia:Embryogenesis" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0009795" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" } ] @@ -7905,20 +7764,8 @@ "val" : "single-organism cellular process" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "jl" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2012-12-11T16:56:55Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0008151" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0044763" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0050875" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" @@ -7962,14 +7809,8 @@ "val" : "single-organism membrane invagination" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "jl" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2013-12-02T13:58:34Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:1902534" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" @@ -8038,9 +7879,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/geneontology/go-ontology/issues/24835" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0016244" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" @@ -8148,15 +7986,6 @@ "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2014-03-06T11:37:54Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0016021" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0098589" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0098805" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "cellular_component" @@ -8195,12 +8024,6 @@ "xrefs" : [ "GOC:mah" ] } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0044235" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0071842" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" } ] @@ -8276,9 +8099,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/geneontology/go-ontology/issues/25421" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0006899" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" @@ -8462,15 +8282,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/geneontology/go-ontology/issues/27189" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0006411" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0044267" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0044268" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" @@ -8563,9 +8374,6 @@ "xrefs" : [ "GOC:mah" ] } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0042570" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "cellular_component" } ] @@ -8590,9 +8398,6 @@ "val" : "Wikipedia:Antigen_presentation" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0030333" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" } ] @@ -8647,9 +8452,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/geneontology/go-ontology/issues/27189" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0071845" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" @@ -8688,9 +8490,6 @@ "val" : "cellular component assembly at cellular level" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0071844" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" } ] @@ -8772,17 +8571,8 @@ "val" : "single organism signaling" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "jl" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2010-02-16T09:30:50Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0023046" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0044700" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" @@ -8938,9 +8728,6 @@ "xrefs" : [ "GOC:add" ] } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0046650" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" } ] @@ -9058,9 +8845,6 @@ "xrefs" : [ "GOC:add" ] } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0042115" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" } ] @@ -9141,12 +8925,6 @@ "xrefs" : [ "GOC:add" ] } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0042112" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0046652" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" } ] @@ -9279,9 +9057,6 @@ "xrefs" : [ "GOC:bf" ] } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0000068" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" } ] @@ -9468,9 +9243,6 @@ "val" : "Wikipedia:Extracellular_matrix" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0005578" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "cellular_component" } ] @@ -9600,9 +9372,6 @@ "val" : "NIF_Subcellular:sao180601769" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0016023" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "cellular_component" } ] @@ -9658,9 +9427,6 @@ "val" : "Wikipedia:Vesicle_(biology)" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0031988" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "cellular_component" } ] @@ -9803,18 +9569,9 @@ }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002161", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_4932" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "jl" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2012-09-19T16:07:47Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0044707" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0050874" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" @@ -9838,14 +9595,8 @@ "val" : "single-organism developmental process" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "jl" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2012-12-19T12:21:31Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0044767" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" @@ -9877,12 +9628,6 @@ "val" : "type I interferon secretion" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0045351" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0072641" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" } ] @@ -9933,15 +9678,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/geneontology/go-ontology/issues/22580" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0034623" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0043241" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0043624" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" @@ -9975,9 +9711,6 @@ "val" : "protein-protein complex" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0043234" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "cellular_component" } ] @@ -10098,9 +9831,6 @@ "val" : "ATP hydrolysis coupled ion transmembrane transport" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0099131" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" } ] @@ -10171,9 +9901,6 @@ "val" : "pre-BCR" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "bf" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2010-03-11T10:46:10Z" }, { @@ -10203,17 +9930,8 @@ "val" : "signalling receptor activity" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "bf" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2011-08-01T02:45:27Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0004872" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0019041" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "molecular_function" @@ -10239,9 +9957,6 @@ "xrefs" : [ "GOC:mah" ] } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0048590" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" } ] @@ -10649,15 +10364,6 @@ "val" : "regulation of homeostatic process" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0032844" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0032845" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0032846" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" } ] @@ -10774,15 +10480,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/geneontology/go-ontology/issues/26424" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0034960" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0043283" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0044259" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" @@ -10849,7 +10546,7 @@ } }, { "id" : "http://purl.obolibrary.org/obo/GO_0043228", - "lbl" : "non-membrane-bounded organelle", + "lbl" : "membraneless organelle", "type" : "CLASS", "meta" : { "definition" : { @@ -10858,6 +10555,12 @@ }, "subsets" : [ "http://purl.obolibrary.org/obo/go#gocheck_do_not_annotate", "http://purl.obolibrary.org/obo/go#goslim_mouse" ], "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "membrane-less organelle" + }, { + "pred" : "hasExactSynonym", + "val" : "non-membrane-bounded organelle" + }, { "pred" : "hasExactSynonym", "val" : "non-membrane-enclosed organelle" }, { @@ -10873,6 +10576,9 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/geneontology/go-ontology/issues/28153" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/geneontology/go-ontology/issues/29106" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "cellular_component" @@ -10932,7 +10638,7 @@ } }, { "id" : "http://purl.obolibrary.org/obo/GO_0043232", - "lbl" : "intracellular non-membrane-bounded organelle", + "lbl" : "intracellular membraneless organelle", "type" : "CLASS", "meta" : { "definition" : { @@ -10941,10 +10647,16 @@ }, "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_pir" ], "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "intracellular non-membrane-bounded organelle" + }, { "pred" : "hasExactSynonym", "val" : "intracellular non-membrane-enclosed organelle" } ], "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/geneontology/go-ontology/issues/29106" + }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "cellular_component" } ] @@ -11020,21 +10732,9 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/geneontology/go-ontology/issues/22580" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "mah" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2010-09-08T10:01:42Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0034600" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0034621" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0071822" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" @@ -11057,9 +10757,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/geneontology/go-ontology/issues/27194" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0071843" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" @@ -11082,9 +10779,6 @@ "val" : "Met-tRNA/eIF2.GTP ternary complex" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "jl" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2009-10-22T02:38:55Z" }, { @@ -11092,30 +10786,6 @@ "val" : "cellular_component" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/GO_0044237", - "lbl" : "cellular metabolic process", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "The chemical reactions and pathways by which individual cells transform chemical substances.", - "xrefs" : [ "GOC:go_curators" ] - }, - "comments" : [ "This term should not be used for direct annotation. It should be possible to make a more specific annotation to one of the children of this term." ], - "subsets" : [ "http://purl.obolibrary.org/obo/go#gocheck_do_not_annotate" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "cellular metabolism" - }, { - "pred" : "hasRelatedSynonym", - "val" : "intermediary metabolism", - "xrefs" : [ "GOC:mah" ] - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "biological_process" - } ] - } }, { "id" : "http://purl.obolibrary.org/obo/GO_0044238", "lbl" : "primary metabolic process", @@ -11141,38 +10811,6 @@ "val" : "biological_process" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/GO_0044249", - "lbl" : "cellular biosynthetic process", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "The chemical reactions and pathways resulting in the formation of substances, carried out by individual cells.", - "xrefs" : [ "GOC:jl" ] - }, - "comments" : [ "This term should not be used for direct annotation. It should be possible to make a more specific annotation to one of the children of this term." ], - "subsets" : [ "http://purl.obolibrary.org/obo/go#gocheck_do_not_annotate" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "cellular anabolism" - }, { - "pred" : "hasExactSynonym", - "val" : "cellular biosynthesis" - }, { - "pred" : "hasExactSynonym", - "val" : "cellular formation" - }, { - "pred" : "hasExactSynonym", - "val" : "cellular synthesis" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", - "val" : "https://github.com/geneontology/go-ontology/issues/27052" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "biological_process" - } ] - } }, { "id" : "http://purl.obolibrary.org/obo/GO_0044419", "lbl" : "biological process involved in interspecies interaction between organisms", @@ -11224,9 +10862,6 @@ "val" : "cell-cell fusion" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0006947" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" } ] @@ -11287,9 +10922,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002161", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_4751" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0002226" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" @@ -11651,9 +11283,6 @@ "val" : "stimulation of biological process" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0043119" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" } ] @@ -11685,9 +11314,6 @@ "val" : "inhibition of biological process" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0043118" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" } ] @@ -11722,9 +11348,6 @@ "val" : "stimulation of cellular process" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0051242" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" } ] @@ -11835,9 +11458,6 @@ "xrefs" : [ "GOC:dph", "GOC:tb" ] } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0048828" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" } ] @@ -12119,9 +11739,6 @@ "val" : "regulation of physiological process" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0050791" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" } ] @@ -12155,9 +11772,6 @@ "val" : "regulation of cellular physiological process" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0051244" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" } ] @@ -12281,9 +11895,6 @@ "val" : "physiological response to stimulus" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0051869" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" } ] @@ -12402,15 +12013,9 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/geneontology/go-ontology/issues/27052" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "jl" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2013-12-18T13:51:04Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:1902578" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" @@ -12533,15 +12138,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/geneontology/go-ontology/issues/4585" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0006323" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0007001" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0051277" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" @@ -12590,12 +12186,6 @@ "xrefs" : [ "GOC:ai" ] }, "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0009613" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0042828" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" } ] @@ -12635,14 +12225,8 @@ "val" : "ATP hydrolysis coupled transmembrane transport" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "tb" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2015-10-21T13:22:47Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0090662" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" @@ -12749,9 +12333,6 @@ "xrefs" : [ "GOC:dph" ] }, "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dph" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2009-04-28T09:33:36Z" }, { @@ -12788,17 +12369,8 @@ "val" : "single-organism membrane organization" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "jl" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2010-02-08T02:43:11Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0016044" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0044802" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" @@ -12825,17 +12397,8 @@ "val" : "Wikipedia:Lipid_bilayer_fusion" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "jl" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2010-02-08T02:48:06Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0006944" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0044801" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" @@ -12851,9 +12414,6 @@ "xrefs" : [ "GOC:dph" ] }, "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dph" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2010-05-25T09:05:34Z" }, { @@ -12871,9 +12431,6 @@ "xrefs" : [ "GOC:BHF", "GOC:rph", "PMID:21123617" ] }, "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dph" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2018-04-13T12:47:21Z" }, { @@ -12919,15 +12476,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/geneontology/go-ontology/issues/22580" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0006461" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0034622" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0043623" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" @@ -13060,9 +12608,6 @@ "comments" : [ "Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC." ], "subsets" : [ "http://purl.obolibrary.org/obo/go#gocheck_do_not_annotate" ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "mah" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2009-08-27T04:41:45Z" }, { @@ -13081,9 +12626,6 @@ }, "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_yeast" ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "mah" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2009-09-15T03:00:51Z" }, { @@ -13114,9 +12656,6 @@ "xrefs" : [ "GOC:add" ] } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "mah" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2010-03-09T04:20:31Z" }, { @@ -13147,9 +12686,6 @@ "xrefs" : [ "GOC:add" ] } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "mah" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2010-03-09T04:22:29Z" }, { @@ -13168,9 +12704,6 @@ }, "comments" : [ "Note that an IgD immunoglobulin complex has the function of antigen binding if a suitable antigen is available." ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "mah" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2010-03-24T01:44:53Z" }, { @@ -13189,9 +12722,6 @@ }, "comments" : [ "Note that an IgM immunoglobulin complex has the function of antigen binding if a suitable antigen is available." ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "mah" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2010-03-24T01:44:53Z" }, { @@ -13227,9 +12757,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/geneontology/go-ontology/issues/25143" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "mah" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2010-09-08T10:10:35Z" @@ -13264,15 +12791,9 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/geneontology/go-ontology/issues/27189" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "mah" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2010-09-10T01:39:16Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0071841" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" @@ -13289,9 +12810,6 @@ }, "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_flybase_ribbon" ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "mah" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2010-10-04T01:51:47Z" }, { @@ -13314,9 +12832,6 @@ "xrefs" : [ "GOC:vesicles" ] } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "mah" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2010-10-18T03:44:18Z" }, { @@ -13336,9 +12851,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/geneontology/go-ontology/issues/22302" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "mah" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2010-02-26T02:15:40Z" @@ -13357,9 +12869,6 @@ "xrefs" : [ "GOC:ascb_2009", "GOC:dph", "GOC:tb" ] }, "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "tb" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2009-12-11T11:44:58Z" }, { @@ -13378,9 +12887,6 @@ }, "comments" : [ "Note that immunologists typically use the word 'maturation' to refer to dendritic cells undergoing the process that GO describes as 'cell differentiation'." ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pr" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2011-04-01T10:08:42Z" }, { @@ -13407,14 +12913,8 @@ "val" : "induction of apoptosis by extracellular signals" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pr" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2011-11-23T09:30:23Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0008624" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" @@ -13437,9 +12937,6 @@ "val" : "apoptosis" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pr" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2011-11-23T09:45:24Z" }, { @@ -13457,9 +12954,6 @@ "xrefs" : [ "GOC:vesicles" ] }, "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pr" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2016-03-29T17:39:45Z" }, { @@ -13493,9 +12987,6 @@ "val" : "intraluminal vesicle assembly" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pr" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2016-10-03T14:35:25Z" }, { @@ -13529,15 +13020,9 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/geneontology/go-ontology/issues/22173" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dos" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2013-11-11T12:59:11Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0009814" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" @@ -13559,9 +13044,6 @@ "val" : "region of plasma membrane" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dos" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2014-03-06T11:55:32Z" }, { @@ -13834,14 +13316,18 @@ } }, { "id" : "http://purl.obolibrary.org/obo/GO_0110165", - "lbl" : "cellular anatomical entity", + "lbl" : "cellular anatomical structure", "type" : "CLASS", "meta" : { "definition" : { - "val" : "A part of a cellular organism that is either an immaterial entity or a material entity with granularity above the level of a protein complex but below that of an anatomical system. Or, a substance produced by a cellular organism with granularity above the level of a protein complex.", + "val" : "A part of a cellular organism consisting of a material entity with granularity above the level of a protein complex but below that of an anatomical system. Note that cellular organisms exclude viruses.", "xrefs" : [ "GOC:kmv" ] }, "subsets" : [ "http://purl.obolibrary.org/obo/go#gocheck_do_not_annotate", "http://purl.obolibrary.org/obo/go#goslim_pir" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "cellular anatomical entity" + } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/geneontology/go-ontology/issues/24200" @@ -13849,8 +13335,8 @@ "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/geneontology/go-ontology/issues/26424" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "kmv" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/geneontology/go-ontology/issues/28978" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2019-08-12T18:01:37Z" @@ -13871,9 +13357,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/geneontology/go-ontology/issues/13193" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "krc" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-03-21T17:26:07Z" @@ -13899,9 +13382,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/geneontology/go-ontology/issues/13298" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "krc" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-04-24T23:56:08Z" @@ -13922,9 +13402,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/geneontology/go-ontology/issues/13298" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "krc" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-04-26T16:07:02Z" @@ -13950,9 +13427,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/geneontology/go-ontology/issues/19910" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pg" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-03-23T14:44:23Z" @@ -13972,9 +13446,6 @@ }, "subsets" : [ "http://purl.obolibrary.org/obo/go#gocheck_do_not_annotate" ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pg" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-05-15T13:20:45Z" }, { @@ -13998,9 +13469,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/geneontology/go-ontology/issues/14256" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pg" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-10-23T11:53:42Z" @@ -14028,9 +13496,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/geneontology/go-ontology/issues/15939" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pg" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2018-08-13T18:38:18Z" @@ -14053,9 +13518,6 @@ "val" : "efflux" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pg" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2019-05-22T11:20:45Z" }, { @@ -14075,9 +13537,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/geneontology/go-ontology/issues/20261" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pg" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2020-11-11T17:19:06Z" @@ -14105,9 +13564,6 @@ "xrefs" : [ "GOC:TermGenie" ] } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pr" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2013-05-02T17:32:42Z" }, { @@ -14126,9 +13582,6 @@ }, "subsets" : [ "http://purl.obolibrary.org/obo/go#gocheck_do_not_annotate" ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "jl" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2014-05-22T14:22:34Z" }, { @@ -14146,9 +13599,6 @@ "xrefs" : [ "CL:0000842", "GOC:TermGenie", "GO_REF:0000086", "PMID:24759906" ] }, "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "cls" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2014-06-25T15:47:09Z" }, { @@ -14171,9 +13621,6 @@ "xrefs" : [ "GOC:vesicles" ] } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "jl" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2014-10-22T14:26:11Z" }, { @@ -14209,9 +13656,6 @@ "xrefs" : [ "GOC:TermGenie" ] } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pad" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2014-12-04T15:34:13Z" }, { @@ -14249,17 +13693,8 @@ "val" : "Wikipedia:Ribonucleoprotein" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pr" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2015-11-19T12:26:37Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0030529" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:1990903" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "cellular_component" @@ -14275,9 +13710,6 @@ "xrefs" : [ "GOC:obol" ] }, "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "tb" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2010-08-05T11:25:59Z" }, { @@ -14308,9 +13740,6 @@ "xrefs" : [ "GOC:obol" ] } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "mah" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2010-10-01T09:41:21Z" }, { @@ -14341,9 +13770,6 @@ "xrefs" : [ "GOC:obol" ] } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "mah" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2010-10-01T09:41:30Z" }, { @@ -14432,9 +13858,6 @@ "val" : "GC_ID:1" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "NCBITaxon:85055" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "ncbi_taxonomy" } ] @@ -14466,9 +13889,6 @@ "val" : "GC_ID:1" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "NCBITaxon:40673" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "ncbi_taxonomy" } ] @@ -14802,9 +14222,6 @@ "val" : "GC_ID:1" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "NCBITaxon:109679" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "ncbi_taxonomy" } ] @@ -15029,9 +14446,6 @@ "xrefs" : [ "PATOC:GVG" ] }, "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "PATO:0000072" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "quality" } ] @@ -15067,9 +14481,6 @@ "val" : "relational shape quality" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "PATO:0001647" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "quality" } ] @@ -15093,9 +14504,6 @@ "val" : "relational structural quality" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "PATO:0001452" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "quality" } ] @@ -15208,9 +14616,6 @@ "val" : "Wikipedia:Physical_property" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "PATO:0002079" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "quality" } ] @@ -15254,12 +14659,6 @@ "val" : "snap:Quality" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "PATO:0001237" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "PATO:0001238" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "quality" } ] @@ -15520,9 +14919,6 @@ "val" : "tubulate" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "PATO:0001203" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "quality" } ] @@ -15975,9 +15371,6 @@ "val" : "high N:C ratio" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "http://orcid.org/0000-0001-5208-3432" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "quality" } ] @@ -15991,9 +15384,6 @@ "val" : "A quality of continuant that exist at the anatomical level of organisation and anything under it. This includes, but is not limited to, cells , tissues, and components." }, "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "http://orcid.org/0000-0001-7258-9596" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "quality" } ] @@ -16007,9 +15397,6 @@ "val" : "A quality inhering in an anotomical structure by virtue of its capacity to be stained by specific histological dyes." }, "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "http://orcid.org/0000-0001-7258-9596" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "quality" } ] @@ -16024,9 +15411,6 @@ "xrefs" : [ "GOC:add" ] }, "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "http://orcid.org/0000-0001-7258-9596" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "quality" } ] @@ -16041,9 +15425,6 @@ "xrefs" : [ "GOC:add" ] }, "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "http://orcid.org/0000-0001-7258-9596" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "quality" } ] @@ -16057,7 +15438,7 @@ "val" : "An amino acid chain that is produced de novo by ribosome-mediated translation of a genetically-encoded mRNA, and any derivatives thereof.", "xrefs" : [ "PRO:DAN", "PRO:WCB" ] }, - "comments" : [ "The definition above excludes protein complexes, which some also consider a protein. Those who wish to refer to a class representing both senses of the word are directed to CHEBI:36080. Note that the definition allows for experimentally-manipulated genes, and allows for artifically-produced derivatives that mimic those found naturally. Proteins (in the sense defined here) that descended from a common ancestor can be classified into families and superfamilies composed of products of evolutionarily-related genes. The domain architecture of a protein is described by the order of its constituent domains. Proteins with the same domains in the same order are defined as homeomorphic [PRO:WCB]." ], + "comments" : [ "The definition above excludes protein complexes, which some also consider a protein. Those who wish to refer to a class representing both senses of the word are directed to CHEBI:36080. Note that the definition allows for experimentally-manipulated genes, and allows for artifically-produced derivatives that mimic those found naturally. Proteins (in the sense defined here) that descended from a common ancestor can be classified into families and superfamilies composed of products of evolutionarily-related genes. The domain architecture of a protein is described by the order of its constituent domains. Proteins with the same domains in the same order are defined as homeomorphic [PRO:WCB)." ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "natural protein", @@ -19091,15 +18472,15 @@ } ] } }, { - "id" : "http://purl.obolibrary.org/obo/PR_000050567", - "lbl" : "protein-containing material entity", + "id" : "http://purl.obolibrary.org/obo/PR_000064867", + "lbl" : "protein-containing molecular entity", "type" : "CLASS", "meta" : { "definition" : { - "val" : "A material entity that minimally consists of a protein.", + "val" : "A molecular entity that minimally consists of a protein.", "xrefs" : [ "PRO:DAN" ] }, - "comments" : [ "Note: This includes single proteins and derivatives thereof (PR:000000001), protein-containing complexes (GO:0032991), and protein aggregates (PR:000050566)." ], + "comments" : [ "Note: This includes single proteins and derivatives thereof (PR:000000001), protein-containing complexes (GO:0032991), and protein aggregates (PR:000050565)." ], "synonyms" : [ { "pred" : "hasNarrowSynonym", "val" : "protein", @@ -19219,9 +18600,6 @@ "val" : "galen:Wall" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "UBERON:0009915" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -19560,9 +18938,6 @@ "val" : "galen:ComplexSkeletalStructure" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "UBERON:0010322" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -20286,9 +19661,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "TODO - check relationship with epiblast. Note in FMA this is not a subclass of embryo, but in uberon embryo is the whole organism from zygote onwards and thus includes the blastula" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "UBERON:0007011" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -21764,9 +21136,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0002161", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_6040" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "UBERON:0003263" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -22110,7 +21479,7 @@ "val" : "Organ system that passes nutrients (such as amino acids and electrolytes), gases, hormones, blood cells, etc. to and from cells in the body to help fight diseases and help stabilize body temperature and pH to maintain homeostasis[WP].", "xrefs" : [ "Wikipedia:Circulatory_system" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#uberon_slim" ], "synonyms" : [ { "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003011", "pred" : "hasRelatedSynonym", @@ -22135,9 +21504,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002161", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_6157" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -23572,15 +22938,10 @@ "val" : "TAO:0001438" }, { "val" : "UMLS:C0333343" - }, { - "val" : "ZFA:0001438" }, { "val" : "galen:BodyCavity" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "UBERON:0000169" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -24735,9 +24096,6 @@ "val" : "ZFA:0000121" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "UBERON:0006258" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" }, { @@ -25634,9 +24992,6 @@ "val" : "Wikipedia:Trilaminar_blastocyst" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "UBERON:0007012" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -27225,9 +26580,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "consider adding new class (EMAPA:16097) for mesenchyme of embryo (some mesenchyme is extraembryonic - e.g. amnion mesoderm)" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "UBERON:0003313" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -27666,6 +27018,8 @@ "val" : "EHDAA2:0004731" }, { "val" : "Wikipedia:Coelom" + }, { + "val" : "ZFA:0001438" } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", @@ -28014,9 +27368,6 @@ "val" : "presumptive central nervous system" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "UBERON:3000469" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -28039,9 +27390,6 @@ "val" : "AAO:0000477" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "UBERON:3000477" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -28678,9 +28026,6 @@ "val" : "A relationship between a process and a barrier, where the process occurs in a region spanning the barrier. For cellular processes the barrier is typically a membrane. Examples include transport across a membrane and membrane depolarization." }, "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "https://orcid.org/0000-0002-7073-9172" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-07-20T17:19:37Z" } ] @@ -30962,9 +30307,6 @@ "val" : "RO:0004007" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2018-12-13T11:26:17Z" }, { @@ -30990,9 +30332,6 @@ "val" : "RO:0004008" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2018-12-13T11:26:32Z" }, { @@ -31018,9 +30357,6 @@ "val" : "RO:0004009" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2018-12-13T11:26:56Z" }, { @@ -31040,9 +30376,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0004050", "val" : "http://purl.obolibrary.org/obo/RO_0002418" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2018-03-13T23:55:05Z" @@ -31058,9 +30391,6 @@ "propertyType" : "OBJECT", "meta" : { "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2018-03-13T23:55:19Z" }, { @@ -31078,9 +30408,6 @@ "val" : "a relation between a process and a continuant, in which the process is regulated by the small molecule continuant" }, "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "https://orcid.org/0000-0003-1813-6857" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2020-04-22T20:27:26Z" } ] @@ -31098,9 +30425,6 @@ "val" : "RO:0012001" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "https://orcid.org/0000-0003-1813-6857" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2020-04-22T20:28:37Z" }, { @@ -31125,9 +30449,6 @@ "val" : "RO:0012003" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "https://orcid.org/0000-0003-1813-6857" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2020-06-08T17:21:33Z" }, { @@ -31148,9 +30469,6 @@ "val" : "a relation between a continuant and a process, in which the continuant is a small molecule that regulates the process" }, "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "https://orcid.org/0000-0003-1813-6857" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2020-06-24T13:15:17Z" } ] @@ -31165,9 +30483,6 @@ "val" : "a relation between a continuant and a process, in which the continuant is a small molecule that activates the process" }, "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "https://orcid.org/0000-0003-1813-6857" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2020-06-24T13:15:26Z" }, { @@ -31186,9 +30501,6 @@ "val" : "RO:0012008" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "https://orcid.org/0000-0003-1813-6857" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2021-02-26T07:28:29Z" }, { @@ -31213,9 +30525,6 @@ "val" : "has synaptic input or output in" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "https://orcid.org/0000-0002-1373-1705" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2020-07-17T09:26:52Z" } ] @@ -31240,13 +30549,34 @@ "val" : "has sensory terminal location" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "https://orcid.org/0000-0002-1373-1705" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2020-07-20T12:10:09Z" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0015004", + "lbl" : "has characterizing marker set", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "A relation that applies between a cell type and a set of markers that can be used to uniquely identify that cell type." + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "has marker gene combination" + }, { + "pred" : "hasExactSynonym", + "val" : "has marker signature set" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "C has_characterizing_marker_set y iff: C is a cell type and y is a collection of genes or proteins whose expression is sufficient to distinguish cell type C from most or all other cell types." + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0001-7258-9596" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/RO_0015006", "lbl" : "different in magnitude relative to", @@ -31372,9 +30702,6 @@ "val" : "RO:0040036" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2018-09-26T01:08:58Z" }, { @@ -32073,13 +31400,14 @@ "propertyType" : "ANNOTATION", "meta" : { "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2018-03-14T00:03:24Z" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/STATO_0000663", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" }, { "id" : "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "type" : "PROPERTY", @@ -32132,6 +31460,10 @@ "meta" : { "comments" : [ "a subset of general classes of cell types in the cell ontology." ] } + }, { + "id" : "http://purl.obolibrary.org/obo/cl#human_subset", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" }, { "id" : "http://purl.obolibrary.org/obo/cl#kidney_upper_slim", "lbl" : "kidney_upper_slim", @@ -32144,6 +31476,10 @@ "val" : "2023-11-22T11:18:57Z" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/cl#mouse_subset", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" }, { "id" : "http://purl.obolibrary.org/obo/go#gocheck_do_not_annotate", "type" : "PROPERTY", @@ -32466,10 +31802,6 @@ "id" : "http://purl.org/dc/elements/1.1/creator", "type" : "PROPERTY", "propertyType" : "ANNOTATION" - }, { - "id" : "http://purl.org/dc/elements/1.1/date", - "type" : "PROPERTY", - "propertyType" : "ANNOTATION" }, { "id" : "http://purl.org/dc/elements/1.1/description", "type" : "PROPERTY", @@ -32482,6 +31814,10 @@ "id" : "http://purl.org/dc/elements/1.1/title", "type" : "PROPERTY", "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.org/dc/elements/1.1/type", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" }, { "id" : "http://purl.org/dc/terms/contributor", "type" : "PROPERTY", @@ -32492,14 +31828,17 @@ "propertyType" : "ANNOTATION" }, { "id" : "http://purl.org/dc/terms/description", + "lbl" : "description", "type" : "PROPERTY", "propertyType" : "ANNOTATION" }, { "id" : "http://purl.org/dc/terms/license", + "lbl" : "license", "type" : "PROPERTY", "propertyType" : "ANNOTATION" }, { "id" : "http://purl.org/dc/terms/title", + "lbl" : "title", "type" : "PROPERTY", "propertyType" : "ANNOTATION" }, { @@ -32517,19 +31856,10 @@ "lbl" : "consider", "type" : "PROPERTY", "propertyType" : "ANNOTATION" - }, { - "id" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "type" : "PROPERTY", - "propertyType" : "ANNOTATION" }, { "id" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "type" : "PROPERTY", "propertyType" : "ANNOTATION" - }, { - "id" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "lbl" : "has_alternative_id", - "type" : "PROPERTY", - "propertyType" : "ANNOTATION" }, { "id" : "http://www.geneontology.org/formats/oboInOwl#hasBroadSynonym", "lbl" : "has_broad_synonym", @@ -32549,9 +31879,21 @@ } }, { "id" : "http://www.geneontology.org/formats/oboInOwl#hasDbXref", - "lbl" : "database_cross_reference", + "lbl" : "has cross-reference", "type" : "PROPERTY", - "propertyType" : "ANNOTATION" + "propertyType" : "ANNOTATION", + "meta" : { + "definition" : { + "val" : "An annotation property that links an ontology entity or a statement to a prefixed identifier or URI." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/information-artifact-ontology/ontology-metadata/issues/123" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0002-7356-1779" + } ] + } }, { "id" : "http://www.geneontology.org/formats/oboInOwl#hasExactSynonym", "lbl" : "has_exact_synonym", @@ -32630,10 +31972,6 @@ "id" : "http://www.geneontology.org/formats/oboInOwl#is_metadata_tag", "type" : "PROPERTY", "propertyType" : "ANNOTATION" - }, { - "id" : "http://www.geneontology.org/formats/oboInOwl#note", - "type" : "PROPERTY", - "propertyType" : "ANNOTATION" }, { "id" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "lbl" : "shorthand", @@ -32806,10 +32144,6 @@ "val" : "true" } ] } - }, { - "sub" : "http://purl.obolibrary.org/obo/CL_0000040", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000040", "pred" : "http://purl.obolibrary.org/obo/BFO_0000051", @@ -32907,11 +32241,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000057", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/CL_0002320" - }, { - "sub" : "http://purl.obolibrary.org/obo/CL_0000057", - "pred" : "http://purl.obolibrary.org/obo/RO_0002202", - "obj" : "http://purl.obolibrary.org/obo/CL_0000134" + "obj" : "http://purl.obolibrary.org/obo/CL_0000499" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000066", "pred" : "is_a", @@ -33000,10 +32330,6 @@ "val" : "true" } ] } - }, { - "sub" : "http://purl.obolibrary.org/obo/CL_0000092", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000092", "pred" : "http://purl.obolibrary.org/obo/BFO_0000051", @@ -33054,10 +32380,6 @@ "val" : "true" } ] } - }, { - "sub" : "http://purl.obolibrary.org/obo/CL_0000094", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000094", "pred" : "http://purl.obolibrary.org/obo/BFO_0000051", @@ -33104,10 +32426,6 @@ "sub" : "http://purl.obolibrary.org/obo/CL_0000097", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/CL_0002274" - }, { - "sub" : "http://purl.obolibrary.org/obo/CL_0000097", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000097", "pred" : "http://purl.obolibrary.org/obo/BFO_0000051", @@ -33528,10 +32846,6 @@ "sub" : "http://purl.obolibrary.org/obo/CL_0000451", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/CL_0000145" - }, { - "sub" : "http://purl.obolibrary.org/obo/CL_0000451", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000451", "pred" : "http://purl.obolibrary.org/obo/BFO_0000051", @@ -33580,6 +32894,14 @@ "sub" : "http://purl.obolibrary.org/obo/CL_0000473", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/CL_0000000" + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_0000499", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/CL_0002320" + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_0000499", + "pred" : "http://purl.obolibrary.org/obo/RO_0002202", + "obj" : "http://purl.obolibrary.org/obo/CL_0000134" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000518", "pred" : "is_a", @@ -33642,10 +32964,6 @@ "sub" : "http://purl.obolibrary.org/obo/CL_0000547", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/CL_0002242" - }, { - "sub" : "http://purl.obolibrary.org/obo/CL_0000547", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000547", "pred" : "http://purl.obolibrary.org/obo/BFO_0000051", @@ -33720,10 +33038,6 @@ "val" : "true" } ] } - }, { - "sub" : "http://purl.obolibrary.org/obo/CL_0000549", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000549", "pred" : "http://purl.obolibrary.org/obo/BFO_0000051", @@ -33746,10 +33060,6 @@ "val" : "true" } ] } - }, { - "sub" : "http://purl.obolibrary.org/obo/CL_0000550", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000550", "pred" : "http://purl.obolibrary.org/obo/BFO_0000051", @@ -33888,18 +33198,10 @@ "sub" : "http://purl.obolibrary.org/obo/CL_0000557", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/CL_0001012" - }, { - "sub" : "http://purl.obolibrary.org/obo/CL_0000557", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/CL_0011026" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000557", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/CL_1001610" - }, { - "sub" : "http://purl.obolibrary.org/obo/CL_0000557", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000557", "pred" : "http://purl.obolibrary.org/obo/BFO_0000051", @@ -33938,10 +33240,6 @@ "val" : "true" } ] } - }, { - "sub" : "http://purl.obolibrary.org/obo/CL_0000558", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000558", "pred" : "http://purl.obolibrary.org/obo/CL_4030046", @@ -34012,10 +33310,6 @@ "val" : "true" } ] } - }, { - "sub" : "http://purl.obolibrary.org/obo/CL_0000559", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000559", "pred" : "http://purl.obolibrary.org/obo/BFO_0000051", @@ -34042,10 +33336,6 @@ "sub" : "http://purl.obolibrary.org/obo/CL_0000566", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/CL_0011026" - }, { - "sub" : "http://purl.obolibrary.org/obo/CL_0000566", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000566", "pred" : "http://purl.obolibrary.org/obo/RO_0002104", @@ -34466,10 +33756,6 @@ "val" : "true" } ] } - }, { - "sub" : "http://purl.obolibrary.org/obo/CL_0000786", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000786", "pred" : "http://purl.obolibrary.org/obo/BFO_0000051", @@ -34508,10 +33794,6 @@ "val" : "true" } ] } - }, { - "sub" : "http://purl.obolibrary.org/obo/CL_0000789", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000789", "pred" : "http://purl.obolibrary.org/obo/RO_0002104", @@ -34526,10 +33808,6 @@ "val" : "true" } ] } - }, { - "sub" : "http://purl.obolibrary.org/obo/CL_0000798", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000798", "pred" : "http://purl.obolibrary.org/obo/RO_0002104", @@ -34620,10 +33898,6 @@ "val" : "true" } ] } - }, { - "sub" : "http://purl.obolibrary.org/obo/CL_0000826", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000826", "pred" : "http://purl.obolibrary.org/obo/BFO_0000051", @@ -34698,10 +33972,6 @@ "val" : "true" } ] } - }, { - "sub" : "http://purl.obolibrary.org/obo/CL_0000831", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000831", "pred" : "http://purl.obolibrary.org/obo/BFO_0000051", @@ -34810,10 +34080,6 @@ "sub" : "http://purl.obolibrary.org/obo/CL_0000837", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/CL_0008001" - }, { - "sub" : "http://purl.obolibrary.org/obo/CL_0000837", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000837", "pred" : "http://purl.obolibrary.org/obo/CL_4030046", @@ -34938,10 +34204,6 @@ "val" : "true" } ] } - }, { - "sub" : "http://purl.obolibrary.org/obo/CL_0000889", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000889", "pred" : "http://purl.obolibrary.org/obo/RO_0000053", @@ -35094,6 +34356,10 @@ "sub" : "http://purl.obolibrary.org/obo/CL_0001012", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/CL_0001060" + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_0001012", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/CL_0011026" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0001035", "pred" : "is_a", @@ -35178,10 +34444,6 @@ "sub" : "http://purl.obolibrary.org/obo/CL_0001200", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/CL_0000945" - }, { - "sub" : "http://purl.obolibrary.org/obo/CL_0001200", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0001200", "pred" : "http://purl.obolibrary.org/obo/CL_4030046", @@ -35240,10 +34502,6 @@ "sub" : "http://purl.obolibrary.org/obo/CL_0002028", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/CL_0002191" - }, { - "sub" : "http://purl.obolibrary.org/obo/CL_0002028", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0002028", "pred" : "http://purl.obolibrary.org/obo/BFO_0000051", @@ -35448,10 +34706,6 @@ "val" : "true" } ] } - }, { - "sub" : "http://purl.obolibrary.org/obo/CL_0002679", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0002679", "pred" : "http://purl.obolibrary.org/obo/CL_4030046", @@ -36520,8 +35774,8 @@ "obj" : "http://purl.obolibrary.org/obo/GO_0043232" }, { "sub" : "http://purl.obolibrary.org/obo/GO_0005840", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PR_000050567" + "pred" : "http://purl.obolibrary.org/obo/BFO_0000051", + "obj" : "http://purl.obolibrary.org/obo/PR_000000001" }, { "sub" : "http://purl.obolibrary.org/obo/GO_0005840", "pred" : "http://purl.obolibrary.org/obo/RO_0002216", @@ -36573,7 +35827,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/GO_0006413", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/GO_0044237" + "obj" : "http://purl.obolibrary.org/obo/GO_0008152" }, { "sub" : "http://purl.obolibrary.org/obo/GO_0006413", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", @@ -36921,7 +36175,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/GO_0008152", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/GO_0008150" + "obj" : "http://purl.obolibrary.org/obo/GO_0009987" }, { "sub" : "http://purl.obolibrary.org/obo/GO_0008219", "pred" : "is_a", @@ -36933,11 +36187,11 @@ }, { "sub" : "http://purl.obolibrary.org/obo/GO_0009059", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/GO_0043170" + "obj" : "http://purl.obolibrary.org/obo/GO_0009058" }, { "sub" : "http://purl.obolibrary.org/obo/GO_0009059", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/GO_0044249" + "obj" : "http://purl.obolibrary.org/obo/GO_0043170" }, { "sub" : "http://purl.obolibrary.org/obo/GO_0009605", "pred" : "is_a", @@ -37636,8 +36890,8 @@ "obj" : "http://purl.obolibrary.org/obo/GO_0005575" }, { "sub" : "http://purl.obolibrary.org/obo/GO_0032991", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PR_000050567" + "pred" : "http://purl.obolibrary.org/obo/BFO_0000051", + "obj" : "http://purl.obolibrary.org/obo/PR_000000001" }, { "sub" : "http://purl.obolibrary.org/obo/GO_0033151", "pred" : "is_a", @@ -37978,26 +37232,10 @@ "sub" : "http://purl.obolibrary.org/obo/GO_0044207", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", "obj" : "http://purl.obolibrary.org/obo/GO_0005737" - }, { - "sub" : "http://purl.obolibrary.org/obo/GO_0044237", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/GO_0008152" - }, { - "sub" : "http://purl.obolibrary.org/obo/GO_0044237", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/GO_0009987" }, { "sub" : "http://purl.obolibrary.org/obo/GO_0044238", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/GO_0008152" - }, { - "sub" : "http://purl.obolibrary.org/obo/GO_0044249", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/GO_0009058" - }, { - "sub" : "http://purl.obolibrary.org/obo/GO_0044249", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/GO_0044237" }, { "sub" : "http://purl.obolibrary.org/obo/GO_0044419", "pred" : "is_a", @@ -38870,10 +38108,6 @@ "sub" : "http://purl.obolibrary.org/obo/GO_0098644", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/GO_0099080" - }, { - "sub" : "http://purl.obolibrary.org/obo/GO_0098644", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/GO_0098644", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", @@ -39545,7 +38779,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/PR_000000001", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PR_000050567" + "obj" : "http://purl.obolibrary.org/obo/PR_000064867" }, { "sub" : "http://purl.obolibrary.org/obo/PR_000000001", "pred" : "http://purl.obolibrary.org/obo/RO_0002353", @@ -39762,10 +38996,6 @@ "sub" : "http://purl.obolibrary.org/obo/PR_000001969", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PR_000000001" - }, { - "sub" : "http://purl.obolibrary.org/obo/PR_000001971", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PR_000000001" }, { "sub" : "http://purl.obolibrary.org/obo/PR_000002062", "pred" : "is_a", @@ -39895,7 +39125,7 @@ "pred" : "http://purl.obolibrary.org/obo/RO_0002160", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_33208" }, { - "sub" : "http://purl.obolibrary.org/obo/PR_000050567", + "sub" : "http://purl.obolibrary.org/obo/PR_000064867", "pred" : "http://purl.obolibrary.org/obo/BFO_0000051", "obj" : "http://purl.obolibrary.org/obo/PR_000000001" }, { @@ -40173,7 +39403,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000178", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PR_000050567" + "obj" : "http://purl.obolibrary.org/obo/UBERON_0000061" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000178", "pred" : "is_a", @@ -40354,10 +39584,6 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0000481", "pred" : "http://purl.obolibrary.org/obo/BFO_0000051", "obj" : "http://purl.obolibrary.org/obo/UBERON_0000479" - }, { - "sub" : "http://purl.obolibrary.org/obo/UBERON_0000483", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000483", "pred" : "is_a", @@ -40787,10 +40013,6 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0001630", "pred" : "http://purl.obolibrary.org/obo/RO_0002473", "obj" : "http://purl.obolibrary.org/obo/UBERON_0002385" - }, { - "sub" : "http://purl.obolibrary.org/obo/UBERON_0001969", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0001969", "pred" : "is_a", @@ -40807,10 +40029,6 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0001969", "pred" : "http://purl.obolibrary.org/obo/RO_0002221", "obj" : "http://purl.obolibrary.org/obo/CL_0000232" - }, { - "sub" : "http://purl.obolibrary.org/obo/UBERON_0001981", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0001981", "pred" : "is_a", @@ -41342,6 +40560,10 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0002553", "pred" : "http://purl.obolibrary.org/obo/RO_0001015", "obj" : "http://purl.obolibrary.org/obo/UBERON_0000463" + }, { + "sub" : "http://purl.obolibrary.org/obo/UBERON_0003059", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/UBERON_0000061" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0003059", "pred" : "is_a", @@ -41785,10 +41007,6 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0004291", "pred" : "http://purl.obolibrary.org/obo/RO_0002202", "obj" : "http://purl.obolibrary.org/obo/UBERON_0004139" - }, { - "sub" : "http://purl.obolibrary.org/obo/UBERON_0004535", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0004535", "pred" : "is_a", @@ -41805,10 +41023,6 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0004535", "pred" : "http://purl.obolibrary.org/obo/BFO_0000051", "obj" : "http://purl.obolibrary.org/obo/UBERON_0001981" - }, { - "sub" : "http://purl.obolibrary.org/obo/UBERON_0004537", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0004537", "pred" : "is_a", @@ -42135,10 +41349,6 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0005764", "pred" : "http://purl.obolibrary.org/obo/RO_0002007", "obj" : "http://purl.obolibrary.org/obo/UBERON_0000061" - }, { - "sub" : "http://purl.obolibrary.org/obo/UBERON_0005769", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0005769", "pred" : "is_a", @@ -42345,10 +41555,6 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0006914", "pred" : "http://purl.obolibrary.org/obo/BFO_0000051", "obj" : "http://purl.obolibrary.org/obo/CL_0000076" - }, { - "sub" : "http://purl.obolibrary.org/obo/UBERON_0006965", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0006965", "pred" : "is_a", @@ -42662,10 +41868,6 @@ "val" : "CARO" } ] } - }, { - "sub" : "http://purl.obolibrary.org/obo/UBERON_0010210", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0010210", "pred" : "is_a", @@ -43920,10 +43122,6 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002590", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002592" - }, { - "sub" : "http://purl.obolibrary.org/obo/RO_0002592", - "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0000057" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002592", "pred" : "subPropertyOf", @@ -47886,6 +47084,9 @@ "predicateId" : "http://purl.obolibrary.org/obo/RO_0002576", "domainClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000061" ], "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000061" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0015004", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/CL_0000000" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0015006", "domainClassIds" : [ "http://purl.obolibrary.org/obo/PATO_0000001" ], diff --git a/subsets/blood_and_immune_upper_slim.obo b/subsets/blood_and_immune_upper_slim.obo index e723d3ceb..8b1dc648d 100644 --- a/subsets/blood_and_immune_upper_slim.obo +++ b/subsets/blood_and_immune_upper_slim.obo @@ -1,5 +1,5 @@ format-version: 1.2 -data-version: cl/releases/2024-09-26/subsets/blood_and_immune_upper_slim.owl +data-version: cl/releases/2025-01-08/subsets/blood_and_immune_upper_slim.owl subsetdef: abnormal_slim "" subsetdef: added_for_HCA "" subsetdef: attribute_slim "" @@ -44,10 +44,12 @@ subsetdef: http://purl.obolibrary.org/obo/valid_for_go_gp2term "" subsetdef: http://purl.obolibrary.org/obo/valid_for_go_ontology "" subsetdef: http://purl.obolibrary.org/obo/valid_for_gocam "" subsetdef: human_reference_atlas "" +subsetdef: human_subset "" subsetdef: inconsistent_with_fma "" subsetdef: kidney_upper_slim "a subset of general classes related to specific cell types in the kidney" subsetdef: location_grouping "" subsetdef: major_organ "" +subsetdef: mouse_subset "" subsetdef: mpath_slim "" subsetdef: non_informative "" subsetdef: organ_slim "" @@ -96,7 +98,7 @@ idspace: oboInOwl http://www.geneontology.org/formats/oboInOwl# idspace: sssom https://w3id.org/sssom/ idspace: terms http://purl.org/dc/terms/ ontology: cl/subsets/blood_and_immune_upper_slim -property_value: owl:versionInfo "2024-09-26" xsd:string +property_value: owl:versionInfo "2025-01-08" xsd:string [Term] id: CL:0000000 @@ -104,6 +106,8 @@ name: cell def: "A material entity of anatomical origin (part of or deriving from an organism) that has as its parts a maximally connected cell compartment surrounded by a plasma membrane." [CARO:mah] comment: The definition of cell is intended to represent all cells, and thus a cell is defined as a material entity and not an anatomical structure, which implies that it is part of an organism (or the entirety of one). subset: cellxgene_subset +subset: human_subset +subset: mouse_subset subset: ubprop:upper_level xref: CALOHA:TS-2035 xref: FBbt:00007002 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} @@ -125,6 +129,8 @@ relationship: RO:0002162 NCBITaxon:131567 ! in taxon cellular organisms id: CL:0000007 name: early embryonic cell (metazoa) def: "A cell found in the embryo before the formation of all the gem layers is complete." [GOC:tfm] +subset: human_subset +subset: mouse_subset xref: ZFA:0009002 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0002321 ! embryonic cell (metazoa) @@ -136,6 +142,8 @@ comment: This term applies to metazoan. For plant stem cells, consider using PO: subset: cellxgene_subset subset: general_cell_types_upper_slim subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "animal stem cell" EXACT [] xref: CALOHA:TS-2086 xref: FMA:63368 @@ -156,6 +164,8 @@ comment: Markers differ between species, and two sets of markers have been descr subset: blood_and_immune_upper_slim subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "blood forming stem cell" EXACT [] synonym: "colony forming unit hematopoietic" RELATED [] synonym: "hemopoietic stem cell" EXACT [] @@ -206,6 +216,8 @@ name: erythroid progenitor cell def: "A progenitor cell committed to the erythroid lineage." [GOC:add, ISBN:0721601464] subset: blood_and_immune_upper_slim subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "BFU-E" RELATED OMO:0003000 [] synonym: "blast forming unit erythroid" RELATED [] synonym: "burst forming unit erythroid" RELATED [] @@ -223,6 +235,8 @@ id: CL:0000040 name: monoblast def: "A myeloid progenitor cell committed to the monocyte lineage. This cell is CD11b-positive, has basophilic cytoplasm, euchromatin, and the presence of a nucleolus." [GOC:add, http://en.wikipedia.org/wiki/Monoblast, http://www.copewithcytokines.de, PMID:1104740] comment: Morphology: mononuclear cell, diameter 12-20 _M, non-granular, N/C ratio 3/1 - 4/1; markers: CD11b (shared with many other myeloid cells); location: Adult: bone marrow; fetal: liver, Yolk Sac; role or process: hematopoiesis, monocyte development; lineage: hematopoietic, myeloid. +subset: human_subset +subset: mouse_subset synonym: "CFU-M" RELATED OMO:0003000 [] synonym: "colony forming unit macrophage" RELATED [] synonym: "colony forming unit monocyte" RELATED [] @@ -232,7 +246,6 @@ xref: FMA:83553 xref: ZFA:0009017 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000763 ! myeloid cell is_a: CL:0002194 {is_inferred="true"} ! monopoietic cell -is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0002194 ! monopoietic cell intersection_of: capable_of GO:0030224 ! monocyte differentiation intersection_of: has_part CL:0017503 ! basophilic cytoplasm @@ -249,6 +262,8 @@ relationship: RO:0002202 CL:0002009 ! develops from macrophage dendritic cell pr id: CL:0000048 name: multi fate stem cell def: "A stem cell that can give rise to multiple lineages of cells." [GOC:add] +subset: human_subset +subset: mouse_subset synonym: "multi-fate stem cell" EXACT [] synonym: "multifate stem cell" EXACT [] synonym: "multipotent cell" EXACT [] @@ -268,6 +283,8 @@ def: "A progenitor cell committed to myeloid lineage, including the megakaryocyt comment: This cell type is intended to be compatible with any vertebrate common myeloid progenitor. For mammalian CMP known to be CD34-positive, please use the term 'common myeloid progenitor, CD34-positive' (CL_0001059). subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "CFU-GEMM" RELATED OMO:0003000 [ISBN:0878932437] synonym: "CFU-S" RELATED OMO:0003000 [ISBN:0878932437] synonym: "CMP" RELATED OMO:0003000 [ISBN:0878932437] @@ -291,6 +308,8 @@ def: "A progenitor cell committed to the megakaryocyte and erythroid lineages." comment: MEPs are reportedly CD19-negative, CD34-negative, CD45RA-negative, CD110-positive, CD117-positive, and SCA1-negative and reportedly express the transcription factors GATA-1 and NF-E2. subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "CFU-EM" EXACT [] synonym: "CFU-MegE" EXACT [] synonym: "colony forming unit erythroid megakaryocyte" EXACT [] @@ -318,6 +337,8 @@ def: "A oligopotent progenitor cell committed to the lymphoid lineage." [GOC:add comment: CLP are CD7-positive, CD10-positive, CD19-negative, CD34-positive, CD45RA-positive, CD79a-negative, CD127-positive, AA4.1-positive, RAG-negative, Sca-1-low, sIgM-negative, sIgD-negative, TdT-negative, Vpre-B-negative, and pre-BCR-negative. Expression of transcription factors include E2A-positive, EBF-positive, Ikaros-negative, PU.1-negative, and Pax5-negative. subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "CLP" RELATED OMO:0003000 [] synonym: "committed lymphopoietic stem cell" RELATED [] synonym: "common lymphocyte precursor" EXACT [] @@ -339,6 +360,8 @@ property_value: RO:0002175 NCBITaxon:9606 id: CL:0000052 name: totipotent stem cell def: "A stem cell from which all cells of the body can form." [GOC:add, GOC:tfm] +subset: human_subset +subset: mouse_subset synonym: "totipotential stem cell" EXACT [] xref: FMA:84790 xref: MESH:D039901 @@ -351,6 +374,8 @@ name: non-terminally differentiated cell def: "A precursor cell with a limited number of potential fates." [SANBI:mhl] comment: define using PATO mulit-potent or oligopotent? subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "blast cell" EXACT [] xref: BTO:0000125 xref: FMA:84782 @@ -360,6 +385,9 @@ is_a: CL:0011115 ! precursor cell id: CL:0000056 name: myoblast def: "A cell that is commited to differentiating into a muscle cell. Embryonic myoblasts develop from the mesoderm. They undergo proliferation, migrate to their various sites, and then differentiate into the appropriate form of myocytes. Myoblasts also occur as transient populations of cells in muscles undergoing repair." [GOC:tfm, MESH:D032446, PMID:21849021] +subset: cellxgene_subset +subset: human_subset +subset: mouse_subset xref: BTO:0000222 xref: CALOHA:TS-0650 xref: FBbt:00005083 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} @@ -376,14 +404,15 @@ comment: These cells may be vimentin-positive, fibronectin-positive, fsp1-positi subset: cellxgene_subset subset: general_cell_types_upper_slim subset: human_reference_atlas +subset: human_subset +subset: mouse_subset xref: BTO:0000452 xref: CALOHA:TS-0362 xref: FMA:63877 xref: NCIT:C12482 xref: VHOG:0001482 xref: ZFA:0009026 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} -is_a: CL:0002320 ! connective tissue cell -relationship: RO:0002202 CL:0000134 ! develops from mesenchymal stem cell +is_a: CL:0000499 ! stromal cell property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -393,6 +422,8 @@ def: "A cell that is usually found in a two-dimensional sheet with a free surfac subset: cellxgene_subset subset: general_cell_types_upper_slim subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "epitheliocyte" EXACT [] xref: BTO:0000414 xref: CALOHA:TS-2026 @@ -413,6 +444,8 @@ name: blood vessel endothelial cell def: "An endothelial cell that lines the vasculature." [GOC:tfm] subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset xref: ZFA:0009036 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0002139 ! endothelial cell of vascular tree intersection_of: CL:0000115 ! endothelial cell @@ -425,6 +458,8 @@ id: CL:0000076 name: squamous epithelial cell def: "Any epithelial cell that is part of some squamous epithelium." [FBC:Autogenerated] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset xref: CALOHA:TS-1249 xref: ZFA:0009039 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000066 ! epithelial cell @@ -436,6 +471,8 @@ relationship: part_of UBERON:0006914 ! squamous epithelium id: CL:0000080 name: circulating cell def: "A cell which moves among different tissues of the body, via blood, lymph, or other medium." [GOC:add] +subset: human_subset +subset: mouse_subset xref: ZFA:0009043 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000255 ! eukaryotic cell intersection_of: CL:0000000 ! cell @@ -448,6 +485,8 @@ name: blood cell def: "A cell found predominately in the blood." [GOC:add, GOC:tfm] subset: cellxgene_subset subset: general_cell_types_upper_slim +subset: human_subset +subset: mouse_subset xref: FMA:62844 xref: MESH:D001773 xref: ZFA:0009044 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} @@ -463,6 +502,8 @@ def: "A type of lymphocyte whose defining characteristic is the expression of a subset: cellxgene_subset subset: general_cell_types_upper_slim subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "immature T cell" RELATED [] synonym: "mature T cell" RELATED [] synonym: "T lymphocyte" EXACT [] @@ -488,16 +529,18 @@ name: osteoclast def: "A specialized phagocytic cell associated with the absorption and removal of the mineralized matrix of bone tissue, which typically differentiates from monocytes. This cell has the following markers: tartrate-resistant acid phosphatase type 5-positive, PU.1-positive, c-fos-positive, nuclear factor NF-kappa-B p100 subunit-positive, tumor necrosis factor receptor superfamily member 11A-positive and macrophage colony-stimulating factor 1 receptor-positive." [GO_REF:0000031, GOC:add, GOC:tfm, ISBN:0781735149, PMID:10428500, PMID:15055519, PMID:17380158] comment: Morphology: Highly vesicular; markers: Surface: RANK, cFMS (MCSF receptor); Secreted: cathepsin K and TRAP (tartate resistant acid phosphatase); transcription factors: PU.1, cFOS, MITF, NFkB (p52); role or process: tissue remodelling: bone resorption; lineage: hematopoietic, myeloid. subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "chondroclast" RELATED [] xref: BTO:0000968 xref: CALOHA:TS-0721 xref: FMA:66781 +xref: https://cellxgene.cziscience.com/cellguide/CL_0000092 xref: MESH:D010010 xref: ZFA:0009047 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000518 ! phagocyte (sensu Vertebrata) is_a: CL:0000766 {is_inferred="true"} ! myeloid leukocyte is_a: CL:0001035 {is_inferred="true"} ! bone cell -is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000766 ! myeloid leukocyte intersection_of: capable_of GO:0045453 ! bone resorption intersection_of: has_part PR:000001850 ! cathepsin K @@ -517,6 +560,7 @@ relationship: has_part PR:000011178 ! nuclear factor NF-kappa-B p100 subunit relationship: RO:0002104 PR:000001954 ! has plasma membrane part tumor necrosis factor receptor superfamily member 11A relationship: RO:0002104 PR:000002062 ! has plasma membrane part macrophage colony-stimulating factor 1 receptor relationship: RO:0002202 CL:0000576 ! develops from monocyte +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nOsteoclasts, derived from the monocyte/macrophage lineage, play a crucial role in bone remodeling through bone resorption. They are distinguished from other cells by their large size and their unique ability to secrete enzymes and acids that dissolve the calcium phosphate in bone. The formation of osteoclasts is influenced by two primary factors: macrophage colony-stimulating factor (M-CSF) and the ligand-activated receptor (RANKL) of nuclear factor kappa B (NF-κB).\nOsteoclasts also collaborate with osteoblasts, responsible for new bone formation, to maintain bone health and adapt bone structure. Their coordinated actions allow continuous remodeling while preserving overall bone strength and integrity. Imbalances in osteoclast activity can lead to pathological conditions. For example, excessive activity may contribute to diseases like osteoporosis, periprosthetic osteolysis, bone tumors, and Paget's disease. Other the other hand, osteoclast deficiency ca result in conditions like osteopetrosis." xsd:string {xref="DOI:10.3389/fmed.2017.00234", xref="DOI:10.37175/stemedicine.v1i4.57", xref="https://www.sciencedirect.com/topics/medicine-and-dentistry/osteoclast"} [Term] id: CL:0000094 @@ -524,6 +568,8 @@ name: granulocyte def: "A leukocyte with abundant granules in the cytoplasm." [GOC:amm, GOC:tfm, http://en.wikipedia.org/wiki/Granulocyte, MESH:D006098] subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "granular leucocyte" EXACT [] synonym: "granular leukocyte" EXACT [] synonym: "polymorphonuclear leukocyte" EXACT [] @@ -534,7 +580,6 @@ xref: FMA:62854 xref: ZFA:0009048 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000081 ! blood cell is_a: CL:0000766 {is_inferred="true"} ! myeloid leukocyte -is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000766 ! myeloid leukocyte intersection_of: capable_of GO:0008015 ! blood circulation intersection_of: CL:4030046 PR:000001002 ! lacks_plasma_membrane_part CD19 molecule @@ -563,6 +608,8 @@ comment: Mast cells are generally integrin beta-7-negative and positive for TLR2 subset: blood_and_immune_upper_slim subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "histaminocyte" EXACT [] synonym: "labrocyte" EXACT [ISBN:0721601464] synonym: "mastocyte" EXACT [ISBN:0721601464] @@ -572,7 +619,6 @@ xref: CALOHA:TS-0603 xref: FMA:66784 is_a: CL:0000766 {is_inferred="true"} ! myeloid leukocyte is_a: CL:0002274 ! histamine secreting cell -is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000766 ! myeloid leukocyte intersection_of: capable_of GO:0002349 ! histamine production involved in inflammatory response intersection_of: capable_of GO:0002539 ! prostaglandin production involved in inflammatory response @@ -607,6 +653,8 @@ name: mononuclear phagocyte def: "A vertebrate phagocyte with a single nucleus." [GOC:add, GOC:tfm, ISBN:0781735149] subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset xref: BTO:0001433 xref: https://cellxgene.cziscience.com/cellguide/CL_0000113 xref: ZFA:0009064 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} @@ -615,7 +663,7 @@ is_a: CL:0000842 ! mononuclear cell intersection_of: CL:0000518 ! phagocyte (sensu Vertebrata) intersection_of: bearer_of PATO:0001407 ! mononucleate property_value: RO:0002175 NCBITaxon:9606 -property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional.\n\nMononuclear phagocytes are immune cells that form a critical part of the body's innate immune system, the body's first line of defense against infections. Mononuclear phagocytes are characterized by the presence of a single, large nucleus. The ‘Mononuclear Phagocyte System’ nomenclature was introduced to distinguish mononuclear monocytes and macrophages from other cells with multiple nuclei. However, the cells within the mononuclear phagocyte system represent a highly heterogeneous group, all of which are able to perform highly efficient phagocytosis - engulfing and digesting microbes and cellular debris to fight infections and to maintain normal tissue homeostasis. \nIn addition to phagocytosis, mononuclear phagocytes also secrete chemical compounds to recruit other immune cells to a site of infection. These cells produce different types of signaling molecules, including cytokines, chemokines, and reactive oxygen species, triggering a cascade of responses to ensure rapid and efficient containment and neutralization of invading pathogens. These cells are also involved in antigen presentation, a process essential for stimulating an adaptive immune response. They can process and present antigens to T cells, thereby linking the innate and adaptive immune responses.\nMononuclear phagocytes play key roles in tissue repair and remodeling. After infection or injury, these cells help in the clearance of dead cells and debris, a crucial step in the initiation of tissue remodeling and the resolution of inflammation. Overall, mononuclear phagocytes are versatile cells that have tailored their functions to meet the unique challenges of different tissues within the body. They are pivotal in homeostasis, immunity, and inflammation, making them important aspects in a range of human diseases including infection, autoimmunity, and cancer." xsd:string {xref="DOI:10.1016/j.coi.2005.11.008", xref="DOI:10.1038/nri3087", xref="DOI:10.3389/fimmu.2019.01893"} +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nMononuclear phagocytes are immune cells that form a critical part of the body's innate immune system, the body's first line of defense against infections. Mononuclear phagocytes are characterized by the presence of a single, large nucleus. The ‘Mononuclear Phagocyte System’ nomenclature was introduced to distinguish mononuclear monocytes and macrophages from other cells with multiple nuclei. However, the cells within the mononuclear phagocyte system represent a highly heterogeneous group, all of which are able to perform highly efficient phagocytosis - engulfing and digesting microbes and cellular debris to fight infections and to maintain normal tissue homeostasis. \nIn addition to phagocytosis, mononuclear phagocytes also secrete chemical compounds to recruit other immune cells to a site of infection. These cells produce different types of signaling molecules, including cytokines, chemokines, and reactive oxygen species, triggering a cascade of responses to ensure rapid and efficient containment and neutralization of invading pathogens. These cells are also involved in antigen presentation, a process essential for stimulating an adaptive immune response. They can process and present antigens to T cells, thereby linking the innate and adaptive immune responses.\nMononuclear phagocytes play key roles in tissue repair and remodeling. After infection or injury, these cells help in the clearance of dead cells and debris, a crucial step in the initiation of tissue remodeling and the resolution of inflammation. Overall, mononuclear phagocytes are versatile cells that have tailored their functions to meet the unique challenges of different tissues within the body. They are pivotal in homeostasis, immunity, and inflammation, making them important aspects in a range of human diseases including infection, autoimmunity, and cancer." xsd:string {xref="DOI:10.1016/j.coi.2005.11.008", xref="DOI:10.1038/nri3087", xref="DOI:10.3389/fimmu.2019.01893"} [Term] id: CL:0000115 @@ -624,6 +672,8 @@ def: "An endothelial cell comprises the outermost layer or lining of anatomical comment: From FMA: 9.07.2001: Endothelial cell has always been classified as a kind of epithelial cell, specifically a squamous cell but that is not true. First, endothelial cell can either be squamous or cuboidal (e.g. high-endothelial cell) and secondly, it has different embryological derivation (mesodermal) than a true epithelial cell (ectodermal and endodermal). The basis for present classification is the fact that it comprises the outermost layer or lining of anatomical structures (location-based) but a better structural basis for the differentia is the cytoskeleton of the cell. Endothelial cell has vimentin filaments while an epithelial cell has keratin filaments. [Onard]. subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "endotheliocyte" EXACT [] xref: BTO:0001176 xref: CALOHA:TS-0278 @@ -638,6 +688,8 @@ property_value: RO:0002175 NCBITaxon:9606 id: CL:0000133 name: neurectodermal cell def: "Ectoderm destined to be nervous tissue." [GOC:tfm, ISBN:068340007X] +subset: human_subset +subset: mouse_subset synonym: "neurectoderm cell" EXACT [] xref: ZFA:0009080 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000221 ! ectodermal cell @@ -648,6 +700,8 @@ name: mesenchymal stem cell def: "A connective tissue cell that normally gives rise to other cells that are organized as three-dimensional masses. In humans, this cell type is CD73-positive, CD90-positive, CD105-positive, CD45-negative, CD34-negative, and MHCII-negative. They may further differentiate into osteoblasts, adipocytes, myocytes, neurons, or chondroblasts in vitro. Originally described as residing in the bone marrow, this cell type is now known to reside in many, if not all, adult organs." [FB:ma, GOC:dsd, http://en.wikipedia.org/wiki/Mesenchymal_stem_cell, http://www.copewithcytokines.de/cope.cgi?key=mesenchymal%20stem%20cells, PMCID:PMC2613570, PMID:10102814, PMID:16923606, PMID:17986482, PMID:19960544] comment: Many but not all mesenchymal cells derive from the mesoderm. MSCs are reportedly CD3-negative, CD4-negative, CD5-negative, CD8-negative, CD11a-negative, CD11b-negative, CD14-negative, CD19-negative, CD29-positive, CD31-negative, CD34-negative, CD38-negative, CD40-negative, CD44-positive, CD45-negative, CD49-positive, CD54-positive, CD66b-negative, CD79a-negative, CD80-negative, CD102-positive, CD106-positive, CD117-positive, CD121a-positive, CD121b-positive, CD123-positive, CD124-positive, CD133-negative, CD146-positive, CD166-positive, CD271-positive, B220-negative, Gr1-negative, MHCI-positive, MHCII-negative, SSEA4-negative, sca1-positive, Ter119-negative, and glycophorin A-negative. Cultured MSCs are capable of producing stem cell factor, IL7, IL8, IL11, TGF-beta, cofilin, galectin-1, laminin-receptor 1, cyclophilin A, and MMP-2. subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "BMSC" RELATED OMO:0003000 [] synonym: "bone marrow stromal cells" NARROW [] synonym: "CFU-F" RELATED OMO:0003000 [] @@ -675,6 +729,8 @@ def: "A cell capable of processing and presenting lipid and protein antigens to comment: Note change of name; nearly all somatic cells can present antigens to T cells via MHC Class I complexes leading to effector responses, but professional antigen presenting cells constitutively express MHC Class II as well as costimulatory molecules, and thus can initiate immune responses via T cells. subset: blood_and_immune_upper_slim subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "APC" RELATED OMO:0003000 [] xref: ZFA:0009088 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000738 ! leukocyte @@ -687,6 +743,8 @@ id: CL:0000151 name: secretory cell def: "A cell that specializes in controlled release of one or more substances." [GOC:tfm, ISBN:0721662544] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset xref: BTO:0003659 xref: FMA:86916 is_a: CL:0000000 ! cell @@ -699,6 +757,8 @@ id: CL:0000183 name: contractile cell def: "A cell whose primary function is to shorten." [FB:ma] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset is_a: CL:0000000 ! cell [Term] @@ -706,6 +766,8 @@ id: CL:0000187 name: muscle cell def: "A mature contractile cell, commonly known as a myocyte. This cell has as part of its cytoplasm myofibrils organized in various patterns." [MESH:D032342] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "muscle fiber" EXACT [] synonym: "myocyte" EXACT [] xref: BTO:0000888 @@ -725,6 +787,8 @@ property_value: foaf:depiction "https://www.swissbiopics.org/api/image/Muscle_ce id: CL:0000211 name: electrically active cell def: "A cell whose function is determined by the generation or the reception of an electric signal." [FB:ma] +subset: human_subset +subset: mouse_subset xref: ZFA:0009128 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000000 ! cell @@ -732,6 +796,8 @@ is_a: CL:0000000 ! cell id: CL:0000213 name: lining cell def: "A cell within an epithelial cell sheet whose main function is to act as an internal or external covering for a tissue or an organism." [JB:jb] +subset: human_subset +subset: mouse_subset synonym: "boundary cell" EXACT [] xref: ZFA:0009130 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000215 ! barrier cell @@ -740,6 +806,8 @@ is_a: CL:0000215 ! barrier cell id: CL:0000215 name: barrier cell def: "A cell whose primary function is to prevent the transport of stuff across compartments." [JB:jb] +subset: human_subset +subset: mouse_subset xref: ZFA:0009132 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000000 ! cell @@ -747,6 +815,8 @@ is_a: CL:0000000 ! cell id: CL:0000219 name: motile cell def: "A cell that moves by its own activities." [FB:ma] +subset: human_subset +subset: mouse_subset xref: ZFA:0009136 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000000 ! cell intersection_of: CL:0000000 ! cell @@ -757,6 +827,9 @@ relationship: capable_of GO:0048870 ! cell motility id: CL:0000221 name: ectodermal cell def: "A cell of the outer of the three germ layers of the embryo." [MESH:D004475] +subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "ectoderm cell" EXACT [] xref: FMA:72549 xref: ZFA:0009137 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} @@ -769,18 +842,24 @@ id: CL:0000222 name: mesodermal cell def: "A cell of the middle germ layer of the embryo." [MESH:D008648] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "mesoblast" EXACT [] synonym: "mesoderm cell" EXACT [] xref: FMA:72554 +xref: https://cellxgene.cziscience.com/cellguide/CL_0000222 xref: ZFA:0009138 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000255 ! eukaryotic cell is_a: CL:0002321 ! embryonic cell (metazoa) relationship: part_of UBERON:0000926 ! mesoderm +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nMesodermal cells are pluripotent and the most abundant in the human body. They contribute to the development of several structures such as the skeletal muscles, bones, heart and blood vessels, kidneys, gonads, connective tissues, and certain layers of the skin. Hence, the mesoderm is often regarded as an active and diverse layer due to its role in forming many bodily structures. \nIn embryonic development, these cells are instrumental, contributing to the body's structures through a carefully coordinated sequence of morphogenetic movements. This process forms the complex multicellular architecture of tissues and organs from a simple ball of cells. Without the function of mesodermal cells, the body's integral structures and systems would cease to form correctly, leading to developmental disorders such as axial mesodermal dysplasia complex" xsd:string {xref="DOI:10.1016/j.ceb.2019.07.012", xref="DOI:10.5535/arm.2016.40.1.162", xref="https://www.sciencedirect.com/topics/biochemistry-genetics-and-molecular-biology/mesoderm"} [Term] id: CL:0000223 name: endodermal cell def: "A cell of the inner of the three germ layers of the embryo." [MESH:D004707] +subset: human_subset +subset: mouse_subset synonym: "endoderm cell" EXACT [] xref: FMA:72555 xref: ZFA:0009139 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} @@ -792,6 +871,8 @@ relationship: part_of UBERON:0000925 ! endoderm id: CL:0000225 name: anucleate cell def: "A cell that lacks a nucleus." [FB:ma] +subset: human_subset +subset: mouse_subset synonym: "non-nucleated cell" EXACT [] xref: FMA:68647 is_a: CL:0000000 ! cell @@ -804,6 +885,8 @@ relationship: bearer_of PATO:0001405 ! anucleate id: CL:0000226 name: single nucleate cell def: "A cell with a single nucleus." [FB:ma, GOC:tfm] +subset: human_subset +subset: mouse_subset is_a: CL:0000255 ! eukaryotic cell is_a: CL:0002242 ! nucleate cell intersection_of: CL:0000000 ! cell @@ -814,6 +897,8 @@ relationship: bearer_of PATO:0001407 ! mononucleate id: CL:0000228 name: multinucleate cell def: "A cell with more than one nucleus." [FB:ma, Wikipedia:Multinucleate] +subset: human_subset +subset: mouse_subset synonym: "multinucleated cells" EXACT [Wikipedia:Multinucleate] synonym: "polynuclear cells" EXACT [Wikipedia:Multinucleate] is_a: CL:0000255 ! eukaryotic cell @@ -829,6 +914,8 @@ def: "A red blood cell. In mammals, mature erythrocytes are biconcave disks cont subset: blood_and_immune_upper_slim subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "RBC" EXACT [] synonym: "red blood cell" EXACT [] xref: BTO:0000424 @@ -857,6 +944,8 @@ comment: Platelets are reportedly CCR1-positive, CCR2-negative, CCR3-positive, C subset: blood_and_immune_upper_slim subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "anucleate thrombocyte" EXACT [] synonym: "blood platelet" EXACT [] synonym: "enucleate thrombocyte" EXACT [] @@ -876,7 +965,8 @@ property_value: RO:0002175 NCBITaxon:9606 id: CL:0000234 name: phagocyte def: "Any cell capable of ingesting particulate matter via phagocytosis." [GOC:add, ISBN:0721601464] -subset: cellxgene_subset +subset: human_subset +subset: mouse_subset xref: BTO:0001044 xref: FMA:83806 xref: MESH:D010586 @@ -897,6 +987,8 @@ subset: blood_and_immune_upper_slim subset: cellxgene_subset subset: general_cell_types_upper_slim subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "histiocyte" EXACT [] xref: BTO:0000801 xref: CALOHA:TS-0587 @@ -923,6 +1015,8 @@ subset: blood_and_immune_upper_slim subset: cellxgene_subset subset: general_cell_types_upper_slim subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "B lymphocyte" EXACT [] synonym: "B-cell" EXACT [] synonym: "B-lymphocyte" EXACT [] @@ -942,7 +1036,8 @@ property_value: RO:0002175 NCBITaxon:9606 id: CL:0000255 name: eukaryotic cell def: "Any cell that in taxon some Eukaryota." [FBC:Autogenerated] -subset: cellxgene_subset +subset: human_subset +subset: mouse_subset xref: MESH:D005057 is_a: CL:0000000 ! cell intersection_of: CL:0000000 ! cell @@ -953,6 +1048,8 @@ relationship: RO:0002162 NCBITaxon:2759 ! in taxon Eukaryota id: CL:0000325 name: stuff accumulating cell def: "A cell that is specialised to accumulate a particular substance(s)." [FB:ma] +subset: human_subset +subset: mouse_subset subset: ubprop:upper_level is_a: CL:0000000 ! cell @@ -960,6 +1057,8 @@ is_a: CL:0000000 ! cell id: CL:0000329 name: oxygen accumulating cell def: "Any cell that is capable of some oxygen transport." [FBC:Autogenerated] +subset: human_subset +subset: mouse_subset xref: ZFA:0009164 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000000 ! cell intersection_of: CL:0000000 ! cell @@ -970,6 +1069,8 @@ relationship: capable_of GO:0015671 ! oxygen transport id: CL:0000333 name: migratory neural crest cell def: "A cell derived from the specialized ectoderm flanking each side of the embryonic neural plate, which after the closure of the neural tube, forms masses of cells that migrate out from the dorsal aspect of the neural tube to spread throughout the body." [doi:10.1016/j.stem.2015.02.017] +subset: human_subset +subset: mouse_subset xref: FMA:86667 xref: ZFA:0007086 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000219 ! motile cell @@ -981,6 +1082,8 @@ relationship: RO:0002202 CL:0007004 ! develops from premigratory neural crest ce id: CL:0000335 name: mesenchyme condensation cell def: "A mesenchymal cell in embryonic development found in a contracting mass and that gives rise to osteoprogenitors." [GOC:tfm, PMID:5025404] +subset: human_subset +subset: mouse_subset xref: ZFA:0009166 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0008019 ! mesenchymal cell @@ -988,12 +1091,16 @@ is_a: CL:0008019 ! mesenchymal cell id: CL:0000352 name: epiblast cell def: "A cell of the outer layer of a blastula that gives rise to the ectoderm after gastrulation." [GOC:tfm, ISBN:0618947256] +subset: human_subset +subset: mouse_subset is_a: CL:0000052 ! totipotent stem cell [Term] id: CL:0000365 name: animal zygote def: "Diploid cell produced by the fusion of sperm cell nucleus and egg cell." [ISBN:0471245208] +subset: human_subset +subset: mouse_subset synonym: "zygote" BROAD [] xref: BTO:0000854 xref: EHDAA2:0004546 @@ -1009,6 +1116,8 @@ relationship: RO:0002162 NCBITaxon:33208 ! in taxon Metazoa id: CL:0000393 name: electrically responsive cell def: "A cell whose function is determined by its response to an electric signal." [FB:ma] +subset: human_subset +subset: mouse_subset xref: ZFA:0009190 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000211 ! electrically active cell @@ -1016,6 +1125,8 @@ is_a: CL:0000211 ! electrically active cell id: CL:0000404 name: electrically signaling cell def: "A cell that initiates an electrical signal and passes that signal to another cell." [FB:ma] +subset: human_subset +subset: mouse_subset xref: ZFA:0009193 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000211 ! electrically active cell @@ -1026,6 +1137,8 @@ def: "A cell of hematopoietic origin, typically resident in particular tissues, subset: cellxgene_subset subset: general_cell_types_upper_slim subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "interdigitating cell" RELATED [] synonym: "veiled cell" RELATED [] xref: BTO:0002042 @@ -1035,7 +1148,6 @@ xref: MESH:D003713 xref: ZFA:0009209 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000113 ! mononuclear phagocyte is_a: CL:0000145 ! professional antigen presenting cell -is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000738 ! leukocyte intersection_of: bearer_of PATO:0001407 ! mononucleate intersection_of: capable_of GO:0001816 ! cytokine production @@ -1062,6 +1174,8 @@ property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000457 name: biogenic amine secreting cell +subset: human_subset +subset: mouse_subset xref: ZFA:0009212 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000151 ! secretory cell @@ -1069,6 +1183,8 @@ is_a: CL:0000151 ! secretory cell id: CL:0000458 name: serotonin secreting cell def: "A cell type that secretes 5-Hydroxytryptamine (serotonin)." [GOC:tfm, PMID:19630576] +subset: human_subset +subset: mouse_subset synonym: "5-HT secreting cell" EXACT [] synonym: "5-Hydroxytryptamine secreting cell" EXACT [] xref: ZFA:0009213 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} @@ -1081,12 +1197,32 @@ relationship: capable_of GO:0001820 ! serotonin secretion id: CL:0000473 name: defensive cell def: "A cell whose primary function is to protect the organism." [JB:jb] +subset: human_subset +subset: mouse_subset is_a: CL:0000000 ! cell +[Term] +id: CL:0000499 +name: stromal cell +def: "A connective tissue cell of an organ found in the loose connective tissue." [GOC:tfm, MESH:D017154] +subset: cellxgene_subset +subset: general_cell_types_upper_slim +subset: human_reference_atlas +subset: human_subset +subset: mouse_subset +xref: BTO:0002064 +xref: FMA:83624 +xref: ZFA:0009226 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +is_a: CL:0002320 ! connective tissue cell +relationship: RO:0002202 CL:0000134 ! develops from mesenchymal stem cell +property_value: RO:0002175 NCBITaxon:9606 + [Term] id: CL:0000518 name: phagocyte (sensu Vertebrata) def: "A phagocyte in vertebrates that is able to phagocytosis." [GOC:tfm] +subset: human_subset +subset: mouse_subset is_a: CL:0000234 ! phagocyte is_a: CL:0000255 ! eukaryotic cell relationship: RO:0002162 NCBITaxon:7742 ! in taxon Vertebrata @@ -1099,6 +1235,8 @@ comment: These cells are also reportedly CD4-negative and CD200-positive. They a subset: cellxgene_subset subset: general_cell_types_upper_slim subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "nerve cell" EXACT [] xref: BTO:0000938 xref: CALOHA:TS-0683 @@ -1121,6 +1259,8 @@ def: "A lymphocyte is a leukocyte commonly found in the blood and lymph that has comment: Editors note: consider adding taxon constraint to vertebrata (PMID:18025161) subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset xref: BTO:0000775 xref: CALOHA:TS-0583 xref: FMA:62863 @@ -1146,12 +1286,13 @@ name: proerythroblast def: "An immature, nucleated erythrocyte occupying the stage of erythropoeisis that follows formation of erythroid progenitor cells. This cell is CD71-positive, has both a nucleus and a nucleolus, and lacks hematopoeitic lineage markers." [ISBN:0721601464, PMID:1638021] subset: blood_and_immune_upper_slim subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "pronormoblast" RELATED [] synonym: "rubriblast" EXACT [ISBN:0721601464] xref: FMA:83518 is_a: CL:0000764 {is_inferred="true"} ! erythroid lineage cell is_a: CL:0002242 ! nucleate cell -is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000764 ! erythroid lineage cell intersection_of: bearer_of PATO:0002505 ! nucleated intersection_of: bearer_of PATO:0040072 ! high nuclear/cytoplasmic ratio @@ -1190,6 +1331,8 @@ relationship: RO:0002202 CL:0000038 ! develops from erythroid progenitor cell id: CL:0000549 name: basophilic erythroblast def: "A nucleated immature erythrocyte, having cytoplasm generally similar to that of the earlier proerythroblast but sometimes even more basophilic, and usually regular in outline. The nucleus is still relatively large, but the chromatin strands are thicker and more deeply staining, giving a coarser appearance; the nucleoli have disappeared. This cell is CD71-positive and lacks hematopoeitic lineage markers." [GOC:tfm, ISBN:0721601464] +subset: human_subset +subset: mouse_subset synonym: "basophilic normoblast" EXACT [ISBN:0721601464] synonym: "early erythroblast" EXACT [ISBN:0721601464] synonym: "early normoblast" EXACT [ISBN:0721601464] @@ -1197,7 +1340,6 @@ synonym: "prorubricyte" EXACT [ISBN:0721601464] xref: FMA:83505 xref: ZFA:0005236 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000765 {is_inferred="true"} ! erythroblast -is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000765 ! erythroblast intersection_of: has_part CL:0017503 ! basophilic cytoplasm intersection_of: has_part GO:0000792 ! heterochromatin @@ -1210,6 +1352,8 @@ relationship: RO:0002104 PR:000001945 ! has plasma membrane part transferrin rec id: CL:0000550 name: polychromatophilic erythroblast def: "A nucleated, immature erythrocyte in which the nucleus occupies a relatively smaller part of the cell than in its precursor, the basophilic erythroblast. The cytoplasm is beginning to acquire hemoglobin and thus is no longer a purely basophilic, but takes on acidophilic aspects, which becomes progressively more marked as the cell matures. The chromatin of the nucleus is arranged in coarse, deeply staining clumps. This cell is CD71-positive and lacks hematopoeitic lineage markers." [ISBN:0721601464] +subset: human_subset +subset: mouse_subset synonym: "intermediate erythroblast" EXACT [ISBN:0721601464] synonym: "intermediate normoblast" EXACT [ISBN:0721601464] synonym: "polychromatic erythroblast" EXACT [ISBN:0721601464] @@ -1219,7 +1363,6 @@ synonym: "rubricyte" EXACT [ISBN:0721601464] xref: FMA:83506 xref: ZFA:0005241 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000765 {is_inferred="true"} ! erythroblast -is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000765 ! erythroblast intersection_of: has_part CL:0017504 ! polychromatophilic cytoplasm intersection_of: has_part GO:0000792 ! heterochromatin @@ -1233,6 +1376,8 @@ relationship: RO:0002202 CL:0000549 ! develops from basophilic erythroblast id: CL:0000552 name: orthochromatic erythroblast def: "The final stage of the nucleated, immature erythrocyte, before nuclear loss. Typically the cytoplasm is described as acidophilic, but it still shows a faint polychromatic tint. The nucleus is small and initially may still have coarse, clumped chromatin, as in its precursor, the polychromatophilic erythroblast, but ultimately it becomes pyknotic, and appears as a deeply staining, blue-black, homogeneous structureless mass. The nucleus is often eccentric and sometimes lobulated." [ISBN:0721601464] +subset: human_subset +subset: mouse_subset synonym: "acidophilic erythroblast" EXACT [ISBN:0721601464] synonym: "eosinophilic erythroblast" EXACT [ISBN:0721601464] synonym: "late erythoblast" EXACT [] @@ -1254,6 +1399,8 @@ def: "The earliest cytologically identifiable precursor in the thrombocytic seri comment: Lineage negative is described here as CD2-negative, CD3-negative, CD4-negative, CD5-negative, CD8a-negative, CD14-negative, CD19-negative, CD20-negative, CD56-negative, Ly6g-negative, and Ter119-negative. subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "CFU-Meg" EXACT [PMID:11722431, PMID:12482498] synonym: "colony-forming unit-megakaryocyte" EXACT [] synonym: "Meg-CFC" EXACT [PMCID:PMC1794060] @@ -1310,6 +1457,8 @@ comment: Megakaryocytes are reportedly CD181-positive and CD182-positive. subset: blood_and_immune_upper_slim subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "megacaryocyte" EXACT [] synonym: "megalocaryocyte" EXACT [] synonym: "megalokaryocyte" EXACT [] @@ -1329,6 +1478,8 @@ def: "A hematopoietic progenitor cell that is committed to the granulocyte and m comment: Originally described in the dendritic cell ontology (DC_CL:0000042)(PMID:19243617). GMPs are reportedly CD16-positive, CD32-positive, CD34-positive, CD38-positive, CD45RA-positive, CD110-negative, CD117-positive, CD123-positive, and SCA1-negative. subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "CFU-C , Colony forming unit in culture" BROAD [http://www.copewithcytokines.de] synonym: "CFU-GM" RELATED OMO:0003000 [ISBN:0721601464, PMCID:PMC2213186, PMCID:PMC548021] synonym: "colony forming unit granulocyte macrophage" EXACT [ISBN:0721601464, PMCID:PMC2213186, PMCID:PMC548021] @@ -1336,12 +1487,11 @@ synonym: "GMP" RELATED OMO:0003000 [ISBN:0721601464, PMCID:PMC2213186, PMCID:PMC synonym: "granulocyte-macrophage progenitor" EXACT [ISBN:0721601464, PMCID:PMC2213186, PMCID:PMC548021] synonym: "granulocyte/monocyte precursor" EXACT [] synonym: "granulocyte/monocyte progenitor" EXACT [] +xref: https://cellxgene.cziscience.com/cellguide/CL_0000557 xref: ZFA:0009251 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000763 ! myeloid cell is_a: CL:0001012 ! CD7-negative lymphoid progenitor OR granulocyte monocyte progenitor -is_a: CL:0011026 ! progenitor cell is_a: CL:1001610 ! bone marrow hematopoietic cell -is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0002032 ! hematopoietic oligopotent progenitor cell intersection_of: capable_of GO:0030225 ! macrophage differentiation intersection_of: capable_of GO:0030851 ! granulocyte differentiation @@ -1359,6 +1509,7 @@ relationship: has_part PR:000001944 ! transcription factor PU.1 relationship: has_part PR:000005307 ! CCAAT/enhancer-binding protein alpha relationship: RO:0002104 PR:000001865 ! has plasma membrane part interleukin-3 receptor class 2 alpha chain property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nGranulocyte monocyte progenitor cells (GMP cells), originating from hematopoietic stem cells in the bone marrow, are a critical intermediate in myeloid cell development. Positioned at a key differentiation juncture, these cells exhibit bidirectional potential, giving rise to both granulocyte and monocyte lineages.\nTheir primary role is to generate mature granulocytes and monocytes, essential components of the body's innate immunity and inflammatory responses. Granulocytes, such as neutrophils, eosinophils, and basophils, contribute to the first line of defense against infections by migrating to the infection site and phagocytosing pathogens. Monocytes can differentiate into macrophages or dendritic cells, playing diverse roles in immune responses." xsd:string {xref="DOI:10.1016/j.immuni.2017.10.021", xref="DOI:10.1146/annurev-immunol-081022113627", xref="DOI:10.1186/2050-7771-2-1"} [Term] id: CL:0000558 @@ -1366,12 +1517,13 @@ name: reticulocyte def: "An immature erythrocyte that changes the protein composition of its plasma membrane by exosome formation and extrusion. The types of protein removed differ between species though removal of the transferrin receptor is apparent in mammals and birds." [GOC:add, GOC:tfm, PMID:15946868, PMID:2037622] subset: blood_and_immune_upper_slim subset: cellxgene_subset +subset: human_subset +subset: mouse_subset xref: BTO:0001173 xref: CALOHA:TS-0864 xref: MESH:D012156 xref: ZFA:0009252 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000764 {is_inferred="true"} ! erythroid lineage cell -is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000764 ! erythroid lineage cell intersection_of: capable_of GO:0071971 ! extracellular exosome assembly intersection_of: CL:4030046 PR:000001002 ! lacks_plasma_membrane_part CD19 molecule @@ -1408,12 +1560,13 @@ def: "A precursor in the monocytic series, being a cell intermediate in developm comment: Morphology: Mononuclear cell, diameter 14-18 _M, fine azurophilic granules; markers: CD11b (shared with many other myeloid cells); location: Adult: bone marrow; Fetal: Liver, Yolk Sac; role or process: hematopoiesis, monocyte development; lineage: hematopoietic, myeloid. subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset xref: BTO:0004657 xref: FMA:83551 xref: ZFA:0009253 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000763 ! myeloid cell is_a: CL:0002194 {is_inferred="true"} ! monopoietic cell -is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0002194 ! monopoietic cell intersection_of: capable_of GO:0030224 ! monocyte differentiation intersection_of: has_part GO:0042582 ! azurophil granule @@ -1428,12 +1581,13 @@ id: CL:0000566 name: angioblastic mesenchymal cell def: "A mesenchymal stem cell capable of developing into blood vessel endothelium." [GOC:dsd, GOC:tfm, PMID:12768659] comment: These cells are reportedly CD31-positive, CD34-positive, CD144-positive, CD309-positive, and TAL1-positive. +subset: human_subset +subset: mouse_subset synonym: "angioblast" EXACT [] synonym: "chondroplast" EXACT [] xref: ZFA:0009258 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000134 {is_inferred="true"} ! mesenchymal stem cell is_a: CL:0011026 ! progenitor cell -is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000134 ! mesenchymal stem cell intersection_of: RO:0002104 PR:000001444 ! has plasma membrane part cadherin-5 intersection_of: RO:0002104 PR:000002112 ! has plasma membrane part vascular endothelial growth factor receptor 2 @@ -1452,6 +1606,8 @@ subset: blood_and_immune_upper_slim subset: cellxgene_subset subset: general_cell_types_upper_slim subset: human_reference_atlas +subset: human_subset +subset: mouse_subset xref: BTO:0000876 xref: CALOHA:TS-0638 xref: FMA:62864 @@ -1476,6 +1632,8 @@ name: multinucleated giant cell def: "A phagocytic syncytial cell formed by the fusion of macrophages, occurs in chronic inflammatory responses to persistent microorganism such as M.tuberculosis, component of granulomas. Sometimes used to refer to megakaryocytes." [GOC:add, GOC:tfm, ISBN:0702022918, ISBN:0702024783, PMID:33348900, Wikipedia:Giant_cell] comment: Role or process: Chronic infection, granulomatous inflammation. Consider also megakaryocyte (CL:0000556) as sometimes multinucleated giant cell is used to refer to this. subset: blood_and_immune_upper_slim +subset: human_subset +subset: mouse_subset synonym: "foreign body giant cell" EXACT [ISBN:0702022918, ISBN:0702024783] synonym: "Langerhans giant cell" EXACT [ISBN:0702022918, ISBN:0702024783] synonym: "macrophage polykaryon" EXACT [ISBN:0702022918, ISBN:0702024783] @@ -1500,6 +1658,8 @@ id: CL:0000680 name: muscle precursor cell def: "A non-terminally differentiated cell that is capable of developing into a muscle cell." [GOC:add] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset xref: ZFA:0009291 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000055 ! non-terminally differentiated cell is_a: CL:0000255 ! eukaryotic cell @@ -1512,6 +1672,8 @@ relationship: RO:0002203 CL:0000187 ! develops into muscle cell id: CL:0000723 name: somatic stem cell def: "A stem cell that can give rise to cell types of the body other than those of the germ-line." [GO:0048103] +subset: human_subset +subset: mouse_subset xref: CALOHA:TS-2086 xref: MESH:D053687 xref: ZFA:0009307 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} @@ -1526,6 +1688,8 @@ name: leukocyte def: "An achromatic cell of the myeloid or lymphoid lineages capable of ameboid movement, found in blood or other tissue." [GOC:add, GOC:tfm, ISBN:978-0-323-05290-0] subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "immune cell" RELATED [] synonym: "leucocyte" EXACT [] synonym: "white blood cell" EXACT [] @@ -1554,6 +1718,8 @@ name: nucleated thrombocyte def: "A nucleated blood cell involved in coagulation, typically seen in birds and other non-mammalian vertebrates." [GOC:add, GOC:tfm, PMID:16360205] comment: Note that this is a non-mammalian cell type. Use platelet ; CL:0000233 for thrombocytes (platelets) in mammals. subset: blood_and_immune_upper_slim +subset: human_subset +subset: mouse_subset xref: ZFA:0009323 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000226 ! single nucleate cell is_a: CL:0000763 {is_inferred="true"} ! myeloid cell @@ -1568,6 +1734,8 @@ id: CL:0000763 name: myeloid cell def: "A cell of the monocyte, granulocyte, mast cell, megakaryocyte, or erythroid lineage." [GOC:add] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset xref: BTO:0001441 xref: CALOHA:TS-0647 xref: MESH:D022423 @@ -1585,6 +1753,8 @@ def: "A immature or mature cell in the lineage leading to and including erythroc comment: Note that in FMA erythropoietic cells are types of nucleated erythrocytes and thus don't include erythrocytes. subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "erythropoietic cell" EXACT [] xref: CALOHA:TS-0290 xref: FMA:62845 @@ -1599,6 +1769,8 @@ name: erythroblast def: "A nucleated precursor of an erythrocyte that lacks hematopoietic lineage markers." [GOC:add, ISBN:0721601464, PMID:18174176] subset: blood_and_immune_upper_slim subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "normoblast" EXACT [] xref: BTO:0001571 xref: CALOHA:TS-0289 @@ -1643,6 +1815,8 @@ id: CL:0000766 name: myeloid leukocyte def: "A cell of the monocyte, granulocyte, or mast cell lineage." [GOC:add] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset xref: ZFA:0009326 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000738 {is_inferred="true"} ! leukocyte is_a: CL:0000763 ! myeloid cell @@ -1657,6 +1831,8 @@ comment: Matures in the bone marrow and account for <1% of leukocytes in the per subset: blood_and_immune_upper_slim subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "basophilic leucocyte" EXACT [] synonym: "basophilic leukocyte" EXACT [] synonym: "polymorphonuclear leucocyte" BROAD [] @@ -1686,6 +1862,8 @@ comment: Eosinophils are also CD14-negative, CD32-positive, CD44-positive, CD48- subset: blood_and_immune_upper_slim subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "eosinocyte" EXACT [] synonym: "eosinophilic granulocyte" EXACT [] synonym: "eosinophilic leucocyte" EXACT [] @@ -1717,6 +1895,8 @@ def: "Any of the immature or mature forms of a granular leukocyte that in its ma subset: blood_and_immune_upper_slim subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "neutrocyte" EXACT [] synonym: "neutrophil leucocyte" EXACT [] synonym: "neutrophil leukocyte" EXACT [] @@ -1748,6 +1928,8 @@ name: myeloid dendritic cell def: "A dendritic cell of the myeloid lineage." [GOC:add, PMID:10449155, PMID:17332250, PMID:9521319] comment: These cells are CD1a-negative, CD1b-positive, CD11a-positive, CD11c-positive, CD13-positive, CD14-negative, CD20-negative, CD21-negative, CD33-positive, CD40-negative, CD50-positive, CD54-positive, CD58-positive, CD68-negative, CD80-negative, CD83-negative, CD85j-positive, CD86-positive, CD89-negative, CD95-positive, CD120a-negative, CD120b-positive, CD123-negative, CD178-negative, CD206-negative, CD207-negative, CD209-negative, and TNF-alpha-negative. Upon TLR stimulation, they are capable of producing high levels of TNF-alpha, IL-6, CXCL8 (IL-8). subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "CD11c+CD123- DC" EXACT [] synonym: "interdigitating cell" BROAD [] synonym: "mDC" EXACT [] @@ -1768,6 +1950,8 @@ def: "A dendritic cell type of distinct morphology, localization, and surface ma subset: blood_and_immune_upper_slim subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "DC2" EXACT [] synonym: "interferon-producing cell" EXACT [] synonym: "IPC" EXACT [] @@ -1790,6 +1974,8 @@ name: mature B cell def: "A B cell that is mature, having left the bone marrow. Initially, these cells are IgM-positive and IgD-positive, and they can be activated by antigen." [GOC:add, GOC:dsd, ISBN:0781735149] comment: Mature B cells are also reportedly CD10-negative, CD19-positive, CD22-positive, CD34-negative, CD48-positive, CD79a-positive, CD84-positive, CD127-negative, CD352-positive, RAG-negative, TdT-negative, Vpre-B-negative, and pre-BCR-negative. Transcription factors expressed: Pax5-positive. subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "mature B lymphocyte" EXACT [] synonym: "mature B-cell" EXACT [] synonym: "mature B-lymphocyte" EXACT [] @@ -1815,6 +2001,8 @@ comment: Plasma cells develop in the spleen and migrate to the bone marrow. Plas subset: blood_and_immune_upper_slim subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "effector B cell" RELATED [] synonym: "effector B-cell" RELATED [] synonym: "plasma B cell" EXACT [] @@ -1826,7 +2014,6 @@ xref: FMA:70574 xref: MESH:D010950 xref: ZFA:0009332 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000946 {is_inferred="true"} ! antibody secreting cell -is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000946 ! antibody secreting cell intersection_of: CL:4030046 GO:0019814 ! lacks_plasma_membrane_part immunoglobulin complex intersection_of: CL:4030046 GO:0042613 ! lacks_plasma_membrane_part MHC class II protein complex @@ -1849,12 +2036,13 @@ name: alpha-beta T cell def: "A T cell that expresses an alpha-beta T cell receptor complex." [GOC:add, GOC:tfm, ISBN:0781735149] subset: blood_and_immune_upper_slim subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "alpha-beta T lymphocyte" EXACT [] synonym: "alpha-beta T-cell" EXACT [] synonym: "alpha-beta T-lymphocyte" EXACT [] xref: ZFA:0009335 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000084 {is_inferred="true"} ! T cell -is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000084 ! T cell intersection_of: RO:0002104 GO:0042105 ! has plasma membrane part alpha-beta T cell receptor complex disjoint_from: CL:0000798 ! gamma-delta T cell @@ -1868,6 +2056,8 @@ comment: Note that gamma-delta T cells have both thymic and extrathymic differen subset: blood_and_immune_upper_slim subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "gamma-delta T lymphocyte" EXACT [] synonym: "gamma-delta T-cell" EXACT [] synonym: "gamma-delta T-lymphocyte" EXACT [] @@ -1875,7 +2065,6 @@ synonym: "gammadelta T cell" EXACT [] synonym: "gd T cell" RELATED OMO:0003000 [] xref: ZFA:0009336 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000084 {is_inferred="true"} ! T cell -is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000084 ! T cell intersection_of: RO:0002104 GO:0042106 ! has plasma membrane part gamma-delta T cell receptor complex relationship: RO:0002104 GO:0042106 ! has plasma membrane part gamma-delta T cell receptor complex @@ -1889,6 +2078,8 @@ comment: Immature B cells are also reportedly CD5-positive, CD10-positive, CD19- subset: blood_and_immune_upper_slim subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "immature B lymphocyte" EXACT [] synonym: "immature B-cell" EXACT [] synonym: "immature B-lymphocyte" EXACT [] @@ -1913,6 +2104,8 @@ name: precursor B cell def: "A precursor B cell is a B cell with the phenotype CD10-positive." [GO_REF:0000031, GOC:rhs, GOC:tfm] subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "pre-B cell" RELATED [] xref: BTO:0001133 xref: CALOHA:TS-0819 @@ -1933,6 +2126,8 @@ def: "An immature B cell of an intermediate stage between the pre-B cell stage a comment: This cell type is compatible with the HIPC Lyoplate markers for 'transitional B cell'. subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "T1 B cell" NARROW [] synonym: "T2 B cell" NARROW [] synonym: "T3 B cell" NARROW [] @@ -1963,6 +2158,8 @@ def: "A progenitor cell of the B cell lineage, with some lineage specific activi comment: Human pro-B cells are reportedly CD10-positive, CD22-positive, CD34-positive, CD38-positive, CD45-low, CD48-positive, CD79a-positive, CD127-positive, CD184-positive, RAG-positive, TdT-positive, Vpre-B-positive, pre-BCR-negative, IgD-negative, and IgM-negative. Transcription factors expressed: Pax5-positive, EBF-positive, E2A-negative, Ikaros-negative, and PU.1-negative. subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "pre-B cell (Philadelphia nomenclature)" RELATED [PMID:11244048] synonym: "pre-pro B cell" BROAD [PMID:17582343] synonym: "pro-B lymphocyte" EXACT [] @@ -1975,7 +2172,6 @@ synonym: "progenitor B-lymphocyte" EXACT [] xref: BTO:0003104 xref: ZFA:0009349 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000838 {is_inferred="true"} ! lymphoid lineage restricted progenitor cell -is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000838 ! lymphoid lineage restricted progenitor cell intersection_of: has_part PR:000001903 ! paired box protein PAX-5 intersection_of: has_part PR:000006611 ! DNA nucleotidylexotransferase @@ -1991,6 +2187,8 @@ id: CL:0000827 name: pro-T cell def: "A lymphoid progenitor cell of the T cell lineage, with some lineage specific marker expression, but not yet fully committed to the T cell lineage." [GOC:add, ISBN:0781735149] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "DN1 cell" NARROW [] synonym: "DN1 thymocyte" NARROW [] synonym: "pro-T lymphocyte" EXACT [] @@ -2008,6 +2206,8 @@ id: CL:0000828 name: thromboblast def: "A progenitor cell of the thrombocyte, a nucleated blood cell involved in coagulation typically seen in birds and other non-mammalian vertebrates." [GOC:add, GOC:tfm, PMID:7758949] comment: Note that this is a non-mammalian cell type. +subset: human_subset +subset: mouse_subset xref: ZFA:0009351 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000226 ! single nucleate cell is_a: CL:0000763 ! myeloid cell @@ -2023,13 +2223,14 @@ id: CL:0000831 name: mast cell progenitor def: "A progenitor cell of the mast cell lineage. Markers for this cell are FceRIa-low, CD117-positive, CD9-positive, T1/ST2-positive, SCA1-negative, and lineage-negative." [GOC:add, GOC:dsd, http://www.copewithcytokines.de, PMCID:PMC1183570, PMCID:PMC1312421, PMID:8629001, PMID:9354811] comment: MCP are CD16-positive, CD32-positive, CD34-positive, CD45-positive, integrin beta-7-positive, and lin-negative (CD2, CD3e, CD4, CD5, CD8a, CD14, CD19, CD20, CD27, integrin alpha-M, ly6c, ly6g, NCAM-1, and ter119). These cells also express the transcription factors GATA-1, GATA-2, and MITF, but not C/EBPa. +subset: human_subset +subset: mouse_subset synonym: "CFU-Mast" RELATED [] synonym: "CFU-MC" RELATED [] synonym: "colony forming unit mast cell" RELATED [] synonym: "MCP" EXACT [] is_a: CL:0000763 ! myeloid cell is_a: CL:0000839 {is_inferred="true"} ! myeloid lineage restricted progenitor cell -is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000839 ! myeloid lineage restricted progenitor cell intersection_of: capable_of GO:0060374 ! mast cell differentiation intersection_of: CL:4030045 PR:000005307 ! lacks_part CCAAT/enhancer-binding protein alpha @@ -2089,6 +2290,8 @@ comment: Markers differ between mouse and human. subset: blood_and_immune_upper_slim subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "hemopoietic progenitor cell" EXACT [] synonym: "MPP" EXACT [] xref: BTO:0000725 @@ -2096,7 +2299,6 @@ xref: CALOHA:TS-0448 xref: ZFA:0009354 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000255 ! eukaryotic cell is_a: CL:0008001 ! hematopoietic precursor cell -is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000988 ! hematopoietic cell intersection_of: bearer_of PATO:0001402 ! multipotent intersection_of: CL:4030046 PR:000001002 ! lacks_plasma_membrane_part CD19 molecule @@ -2138,6 +2340,8 @@ name: lymphoid lineage restricted progenitor cell def: "A progenitor cell restricted to the lymphoid lineage." [GOC:add, GOC:tfm] comment: Note that this is a class of cell types, not an identified single cell type. subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "lymphoid progenitor cell" BROAD [] xref: BTO:0004731 xref: CALOHA:TS-2025 @@ -2157,6 +2361,8 @@ def: "A progenitor cell restricted to the myeloid lineage." [GOC:add, GOC:tfm, P comment: Note that this is a class of cell types, not an identified single cell type. subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "myeloid progenitor cell" BROAD [] xref: BTO:0004730 xref: CALOHA:TS-2099 @@ -2175,6 +2381,8 @@ name: mononuclear cell def: "A leukocyte with a single non-segmented nucleus in the mature form." [GOC:add] subset: blood_and_immune_upper_slim subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "mononuclear leukocyte" EXACT [] synonym: "peripheral blood mononuclear cell" NARROW [] xref: BTO:0000878 @@ -2192,8 +2400,10 @@ name: myeloid suppressor cell def: "An immature myeloid leukocyte of heterogeneous phenotype found particularly in cancer and sepsis patients that is capable of suppressing activity of T cells in ex vivo assays. This cell type is CD45-positive, CD11b-positive." [GO_REF:0000031, GOC:add, GOC:ana, PMID:16168663, PMID:17016554, PMID:17016559] comment: Markers: Mouse: CD11b+GR1+CD31+; Human: CD34+ CD33+CD15-CD13+. (According to some reports in humans these cells are iNOS+ARG1+IL13+IFNg+); location: In cancerous tissue; in the blood and lymphoid organs in sepsis. subset: blood_and_immune_upper_slim +subset: cellxgene_subset +subset: human_subset +subset: mouse_subset is_a: CL:0000766 {is_inferred="true"} ! myeloid leukocyte -is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000766 ! myeloid leukocyte intersection_of: bearer_of PATO:0001501 ! immature intersection_of: capable_of GO:0050777 ! negative regulation of immune response @@ -2209,7 +2419,10 @@ id: CL:0000945 name: lymphocyte of B lineage def: "A lymphocyte of B lineage with the commitment to express an immunoglobulin complex." [GO_REF:0000031, GOC:add, GOC:rhs, GOC:tfm, ISBN:0781735149] comment: Types of B lineage lymphocytes include B cells and antibody secreting cells (plasmablasts and plasma cells). Lymphocytes of B cell lineage can be distinguished from those of T cell lineage by their lack of CD3e (as part of the T cell receptor complex). +subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset is_a: CL:0000542 {is_inferred="true"} ! lymphocyte relationship: RO:0002202 CL:0000826 ! develops from pro-B cell property_value: RO:0002175 NCBITaxon:9606 @@ -2218,6 +2431,8 @@ property_value: RO:0002175 NCBITaxon:9606 id: CL:0000946 name: antibody secreting cell def: "A lymphocyte of B lineage that is devoted to secreting large amounts of immunoglobulin." [GO_REF:0000031, GOC:add, GOC:tfm, ISBN:0721601464, ISBN:0781735149] +subset: human_subset +subset: mouse_subset is_a: CL:0000945 {is_inferred="true"} ! lymphocyte of B lineage intersection_of: CL:0000945 ! lymphocyte of B lineage intersection_of: produces GO:0042571 ! immunoglobulin complex, circulating @@ -2229,6 +2444,8 @@ name: small pre-B-II cell def: "A small pre-B-II cell is a pre-B-II cell that is Rag1-positive, Rag2-positive, pre-BCR-negative, and BCR-negative, is not proliferating, and carries a DNA rearrangement of one or more immunoglobulin light chain genes." [GO_REF:0000031, GOC:dsd, GOC:rhs, GOC:tfm, PMID:16551251, PMID:18432934, PMID:9785673] comment: Small pre-B-II cells are also reportedly CD10-positive, CD19-positive, CD34-negative, CD79a-positive, CD127-negative, TdT-negative, Vpre-B-negative, sIgM-negative, and sIgD-negative. Transcription factors: PU.1-positive, Ikaros-positive, E2A-positive, and PAX5-positive. subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "small pre-BII cell" EXACT [] is_a: CL:0000955 {is_inferred="true"} ! pre-B-II cell intersection_of: CL:0000955 ! pre-B-II cell @@ -2248,6 +2465,8 @@ id: CL:0000955 name: pre-B-II cell def: "A pre-B-II cell is a precursor B cell that expresses immunoglobulin mu heavy chain (IgHmu+), and lack expression of CD34, TdT, immunoglobulin kappa light chain and immunoglobulin lambda light chain." [GO_REF:0000031, GOC:dsd, GOC:rhs, GOC:tfm, PMID:9785673] comment: pre-B-II cell are also reportedly CD19-positive, CD22-positive, CD38-positive, CD45-positive, and CD48-positive. +subset: human_subset +subset: mouse_subset synonym: "pre-B-lymphocyte" EXACT [] synonym: "pre-BII cell" EXACT [] xref: BTO:0001133 @@ -2268,6 +2487,8 @@ def: "An activated mature (naive or memory) B cell that is secreting immunoglobu comment: This cell type is compatible with the HIPC Lyoplate markers for 'plasmablast'. Plasmablasts are also reportedly CD48-positive, CD63-positive, CD229-positive, CD270-positive, CD319-positive, CD352-positive, CD361-positive, and IgD-negative. subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "CD20-negative B cell" BROAD [] synonym: "CD27-positive, CD38-positive, CD20-negative B cell" EXACT [] xref: FMA:84371 @@ -2291,6 +2512,8 @@ id: CL:0000988 name: hematopoietic cell def: "A cell of a hematopoietic lineage." [GO_REF:0000031, GOC:add] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "haematopoietic cell" EXACT [] synonym: "haemopoietic cell" EXACT [] synonym: "hemopoietic cell" EXACT [] @@ -2309,6 +2532,8 @@ comment: Originally described in the dendritic cell ontology (DC_CL:0000003)(PMI subset: blood_and_immune_upper_slim subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "cDC" EXACT [] synonym: "DC1" EXACT [] synonym: "dendritic reticular cell" EXACT [] @@ -2326,7 +2551,10 @@ property_value: RO:0002175 NCBITaxon:9606 id: CL:0001012 name: CD7-negative lymphoid progenitor OR granulocyte monocyte progenitor comment: Originally described in the dendritic cell ontology (DC_CL:1110000)(PMID:19243617). +subset: human_subset +subset: mouse_subset is_a: CL:0001060 ! hematopoietic oligopotent progenitor cell, lineage-negative +is_a: CL:0011026 ! progenitor cell [Term] id: CL:0001035 @@ -2334,18 +2562,24 @@ name: bone cell def: "A connective tissue cell found in bone." [GO_REF:0000034, GOC:add] subset: general_cell_types_upper_slim subset: human_reference_atlas +subset: human_subset +subset: mouse_subset +xref: https://cellxgene.cziscience.com/cellguide/CL_0001035 is_a: CL:0000255 ! eukaryotic cell intersection_of: CL:0000000 ! cell intersection_of: part_of UBERON:0001474 ! bone element relationship: part_of UBERON:0001474 ! bone element property_value: RO:0002175 NCBITaxon:9606 property_value: terms:contributor https://orcid.org/0000-0001-9990-8331 +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nBone cells, also known as osteocytes, form the building blocks of the skeletal system. They represent the most common type of bone cell, making up approximately 95% of the total bone cell population in mature adult bone tissue. Osteocytes are a stellate shape with numerous long, slender dendritic processes.\nThe formation of bone is a complex process involving the action of osteoclasts - cells that break down and reabsorb old bone, followed by osteoblasts that rebuild the bone. Osteocytes serve as coordinators for these two types of bone cells to ensure a balance in the bone remodeling process, contributing to maintaining both bone strength and mineral homeostasis.\nThe primary functions of osteocytes involve the creation, maintenance, and repair of bone tissue. They ensure that bone remodeling is performed by forming a network within the bone and communicating with other cells to help them respond to mechanical strain and damage.\nA remarkable aspect of osteocytes is their ability to perceive mechanical forces, translating them into biochemical signals that regulate bone remodeling and adaptation. Defects in osteocyte function, aside from other bone cells, have been associated with several bone disorders such as osteoporosis, renal osteodystrophy, and skeletal manifestations of diabetes." xsd:string {xref="DOI:10.1007/s00795-015-0099-y", xref="DOI:10.1007/s11914-012-0105-4", xref="DOI:10.1016/j.jot.2021.04.005", xref="DOI:10.1038/s41413-020-0099-y"} creation_date: 2011-11-16T04:28:16Z [Term] id: CL:0001060 name: hematopoietic oligopotent progenitor cell, lineage-negative def: "A hematopoietic oligopotent progenitor cell that has the ability to differentiate into limited cell types but lacks lineage cell markers and self renewal capabilities. Cell lacks hematopoeitic lineage markers." [GOC:tfm, PMID:19022770] +subset: human_subset +subset: mouse_subset is_a: CL:0002032 ! hematopoietic oligopotent progenitor cell intersection_of: CL:0002032 ! hematopoietic oligopotent progenitor cell intersection_of: bearer_of PATO:0001401 ! oligopotent @@ -2383,6 +2617,8 @@ def: "A lymphocyte that lacks characteristic T cell, B cell, myeloid cell, and d subset: blood_and_immune_upper_slim subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset is_a: CL:0000542 ! lymphocyte intersection_of: CL:0000542 ! lymphocyte intersection_of: capable_of GO:0001816 ! cytokine production @@ -2402,8 +2638,9 @@ id: CL:0001200 name: lymphocyte of B lineage, CD19-positive def: "A lymphocyte of B lineage that is CD19-positive." [GOC:add] comment: Types of B lineage lymphocytes include B cells and antibody secreting cells (plasmablasts and plasma cells). Lymphocytes of B cell lineage can be distinguished from those of T cell lineage by their lack of CD3e (as part of the T cell receptor complex). +subset: human_subset +subset: mouse_subset is_a: CL:0000945 ! lymphocyte of B lineage -is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000945 ! lymphocyte of B lineage intersection_of: CL:4030046 PR:000001020 ! lacks_plasma_membrane_part CD3 epsilon intersection_of: RO:0002104 PR:000001002 ! has plasma membrane part CD19 molecule @@ -2417,6 +2654,8 @@ property_value: terms:contributor https://orcid.org/0000-0001-9990-8331 id: CL:0001201 name: B cell, CD19-positive def: "A B cell that is CD19-positive." [GOC:add] +subset: human_subset +subset: mouse_subset synonym: "B lymphocyte, CD19-positive" EXACT [] synonym: "B-cell, CD19-positive" EXACT [] synonym: "B-lymphocyte, CD19-positive" EXACT [] @@ -2434,6 +2673,8 @@ id: CL:0002009 name: macrophage dendritic cell progenitor def: "A progenitor cell that can give rise to plasmacytoid and myeloid dendritic cells, and to monocytes and macrophages." [GOC:tfm, PMID:19273628] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "MDP" EXACT [] is_a: CL:0000763 ! myeloid cell is_a: CL:0002032 {is_inferred="true"} ! hematopoietic oligopotent progenitor cell @@ -2453,10 +2694,11 @@ name: basophil mast progenitor cell def: "A cell type that can give rise to basophil and mast cells. This cell is CD34-positive, CD117-positive, CD125-positive, FceRIa-negative, and T1/ST2-negative, and expresses Gata-1, Gata-2, C/EBPa" [GOC:ak, GOC:dsd, GOC:tfm, PMCID:PMC1312421] comment: There may be an intermediate cell type. These cells also CD13-positive, CD16-positive, CD32-positive, and integrin beta 7-positive. Transcription factors: GATA1-positive, MCP-1-positive, mitf-positive, PU.1-positive, and CEBP/a-low. subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "BMCP" EXACT [] is_a: CL:0000763 ! myeloid cell is_a: CL:0002191 ! granulocytopoietic cell -is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000839 ! myeloid lineage restricted progenitor cell intersection_of: capable_of GO:0030221 ! basophil differentiation intersection_of: capable_of GO:0060374 ! mast cell differentiation @@ -2483,6 +2725,8 @@ id: CL:0002031 name: hematopoietic lineage restricted progenitor cell def: "A hematopoietic progenitor cell that is capable of developing into only one lineage of hematopoietic cells." [GOC:tfm, PMID:19022770] subset: blood_and_immune_upper_slim +subset: human_subset +subset: mouse_subset is_a: CL:0000255 ! eukaryotic cell is_a: CL:0008001 ! hematopoietic precursor cell intersection_of: CL:0000988 ! hematopoietic cell @@ -2499,6 +2743,8 @@ name: hematopoietic oligopotent progenitor cell def: "A hematopoietic oligopotent progenitor cell that has the ability to differentiate into limited cell types but lacks lineage cell markers and self renewal capabilities." [GOC:tfm, https://orcid.org/0000-0001-5208-3432, PMID:19022770] comment: This cell type is intended to be compatible with any vertebrate hematopoietic oligopotent progenitor cell. For mammalian hematopoietic oligopotent progenitor cells known to be lineage-negative, please use the term 'hematopoietic oligopotent progenitor cell' (CL_0001060). subset: blood_and_immune_upper_slim +subset: human_subset +subset: mouse_subset is_a: CL:0000255 ! eukaryotic cell is_a: CL:0008001 ! hematopoietic precursor cell intersection_of: CL:0000988 ! hematopoietic cell @@ -2512,6 +2758,8 @@ creation_date: 2010-01-06T03:43:27Z id: CL:0002077 name: ecto-epithelial cell def: "An epithelial cell derived from ectoderm." [FMA:69074, GOC:tfm] +subset: human_subset +subset: mouse_subset xref: FMA:69074 xref: ZFA:0009385 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000066 ! epithelial cell @@ -2526,6 +2774,8 @@ id: CL:0002087 name: nongranular leukocyte def: "A leukocyte that lacks granules." [GOC:tfm] subset: blood_and_immune_upper_slim +subset: human_subset +subset: mouse_subset synonym: "agranular leukocyte" EXACT [] xref: FMA:62855 is_a: CL:0000738 {is_inferred="true"} ! leukocyte @@ -2541,6 +2791,8 @@ name: bone marrow cell def: "A cell found in the bone marrow. This can include fibroblasts, macrophages, adipocytes, osteoblasts, osteoclasts, endothelial cells and hematopoietic cells." [GOC:tfm, ISBN:0618947256] comment: MH consider whether bone marrow cells are bone cells in the structural sense vs. being part of bone organ sense. subset: cellxgene_subset +subset: human_subset +subset: mouse_subset xref: BTO:0004850 xref: FMA:83621 xref: MESH:D001854 @@ -2557,13 +2809,17 @@ name: endothelial cell of vascular tree def: "An endothelial cell of the vascular tree, which includes blood vessels and lymphatic vessels." [GOC:dsd, GOC:tfm, PMID:12768659] comment: These cells are reportedly CD31-positive, CD34-positive, CD144-positive, TAL1-positive. subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "cubodial endothelial cell of vascular tree" NARROW [] synonym: "vascular endothelial cell" EXACT [] xref: BTO:0001854 xref: CALOHA:TS-1106 xref: FMA:67755 +xref: https://cellxgene.cziscience.com/cellguide/CL_0002139 is_a: CL:0000115 ! endothelial cell property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nEndothelial cells of the vascular tree, commonly referred to as vascular endothelial cells, line the entire circulatory system, from the heart to the smallest capillaries. These cells have a unique, flattened shape, and are tightly bound together, forming a thin layer known as the endothelium. The endothelium is responsible for maintaining the interior surface of blood vessels, and plays a critical role in ensuring the smooth flow of blood. \nVascular endothelial cells act as a semi-permeable membrane, controlling the passage of materials and the transit of white blood cells into and out of the bloodstream. These cells are also involved in blood coagulation. When a blood vessel is damaged, endothelial cells promote clotting to prevent excessive bleeding and facilitate wound healing. Other functions include regulation of blood pressure and blood volume by releasing vasodilators and vasoconstrictors to either widen or constrict blood vessels, accordingly.\nFurthermore, the endothelial cells are crucial in the formation of new blood vessels, a process known as angiogenesis. This is particularly important in wound healing and the growth of new tissues during development or after injury. In the context of diseases such as cancer, angiogenesis helps facilitate tumor growth by providing nutrients and oxygen." xsd:string {xref="DOI:10.1038/s41569-022-00770-1", xref="DOI:10.1186/s12872-015-0124-z", xref="DOI:10.3389/fphys.2022.863265/full", xref="https://www.sciencedirect.com/topics/medicine-and-dentistry/vascular-endothelial-cell"} creation_date: 2010-08-24T02:06:40Z [Term] @@ -2571,6 +2827,8 @@ id: CL:0002191 name: granulocytopoietic cell def: "A cell involved in the formation of a granulocyte." [GOC:tfm] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset xref: FMA:83519 is_a: CL:0000839 {is_inferred="true"} ! myeloid lineage restricted progenitor cell intersection_of: CL:0000839 ! myeloid lineage restricted progenitor cell @@ -2583,6 +2841,8 @@ creation_date: 2010-08-30T12:54:27Z id: CL:0002194 name: monopoietic cell def: "A cell involved in the formation of a monocyte (monopoiesis)." [GOC:tfm] +subset: human_subset +subset: mouse_subset xref: FMA:83552 is_a: CL:0000839 {is_inferred="true"} ! myeloid lineage restricted progenitor cell intersection_of: CL:0000839 ! myeloid lineage restricted progenitor cell @@ -2595,6 +2855,8 @@ creation_date: 2010-08-30T01:27:48Z id: CL:0002242 name: nucleate cell def: "A cell containing at least one nucleus." [GOC:tfm] +subset: human_subset +subset: mouse_subset xref: FMA:67513 is_a: CL:0000000 ! cell intersection_of: CL:0000000 ! cell @@ -2607,6 +2869,8 @@ creation_date: 2010-09-07T03:32:33Z id: CL:0002274 name: histamine secreting cell def: "A cell type that secretes histamine." [GOC:tfm] +subset: human_subset +subset: mouse_subset is_a: CL:0000457 ! biogenic amine secreting cell intersection_of: CL:0000151 ! secretory cell intersection_of: capable_of GO:0001821 ! histamine secretion @@ -2619,6 +2883,8 @@ id: CL:0002319 name: neural cell def: "A cell that is part of the nervous system." [GOC:tfm, ISBN:0618947256] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset xref: CALOHA:TS-2040 xref: FMA:70333 is_a: CL:0000255 ! eukaryotic cell @@ -2633,6 +2899,8 @@ id: CL:0002320 name: connective tissue cell def: "A cell of the supporting or framework tissue of the body, arising chiefly from the embryonic mesoderm and including adipose tissue, cartilage, and bone." [GOC:tfm, ISBN:0618947256] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset xref: CALOHA:TS-2096 xref: FMA:63875 xref: MESH:D003239 @@ -2648,12 +2916,16 @@ creation_date: 2010-09-15T03:01:54Z id: CL:0002321 name: embryonic cell (metazoa) def: "A cell of the embryo." [FMA:0618947256] +subset: human_subset +subset: mouse_subset xref: CALOHA:TS-0263 xref: FMA:82840 +xref: https://cellxgene.cziscience.com/cellguide/CL_0002321 xref: WBbt:0007028 xref: ZFA:0007089 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000000 ! cell property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nEmbryonic cells in metazoans, which include all multicellular animals, are biological units in their earliest developmental stages from conception until the organism is fully formed. \nThey are derived from a fertilized egg, which undergoes a series of cell divisions to produce a multicellular organism. During the early phases of embryonic development, these cells exhibit pluripotency, meaning they possess the potential to differentiate into a diverse array of specialized cell types that constitute different body tissues and structures. \nThe balance between cell proliferation and differentiation in embryonic cells is crucial for successful development. When cells continue to divide without differentiating, overgrowth may occur leading to conditions such as teratomas (tumors of embryonic cells). Conversely, if cell differentiation proceeds at the expense of cell proliferation, developmental anomalies could occur regarding size or mass of the organism or its parts." xsd:string {xref="DOI:10.1002/iub.1404", xref="DOI:10.1093/molehr/gan048", xref="https://www.ncbi.nlm.nih.gov/books/NBK9906/"} creation_date: 2010-09-15T03:39:21Z [Term] @@ -2662,6 +2934,8 @@ name: immature T cell def: "A T cell that has not completed T cell selection." [GOC:tfm] subset: blood_and_immune_upper_slim subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "immature T-cell" EXACT [] xref: BTO:0001372 xref: CALOHA:TS-1042 @@ -2677,6 +2951,8 @@ id: CL:0002494 name: cardiocyte def: "A cell located in the heart, including both muscle and non muscle cells." [GOC:tfm] comment: From Onard of the FMA: Cardiac muscle cell or cardiac myocyte is a striated muscle cell. Cardiocyte on the other hand is any cell in the heart which includes cells other than muscle cells (e.g. endothelial cell of endocardium). Unless there is a consensus among anatomists that cardiocytes refer only to muscle cells, we will treat them as a general class of cells in the heart. +subset: human_subset +subset: mouse_subset synonym: "heart cell" EXACT [] xref: BTO:0001539 xref: CALOHA:TS-0115 @@ -2694,8 +2970,9 @@ id: CL:0002679 name: natural helper lymphocyte def: "A lymphocyte found in adipose tissue that lacks lineage markers of other lymphocytes but is capable of mediating TH2 cytokine responses. This cell type is found in fat associated lymphoid clusters, proliferates in response to IL2 and produce large amounts of TH2 cytokines such as IL5, IL6 and IL13" [GOC:tfm, PMID:20023630] subset: blood_and_immune_upper_slim +subset: human_subset +subset: mouse_subset is_a: CL:0000542 {is_inferred="true"} ! lymphocyte -is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000542 ! lymphocyte intersection_of: CL:4030046 GO:0042105 ! lacks_plasma_membrane_part alpha-beta T cell receptor complex intersection_of: CL:4030046 PR:000001002 ! lacks_plasma_membrane_part CD19 molecule @@ -2725,6 +3002,8 @@ id: CL:0007001 name: skeletogenic cell def: "Cell that has the potential to form a skeletal cell type (e.g. cells in periosteum, cells in marrow) and produce extracellular matrix (often mineralized) and skeletal tissue (often mineralized)." [GO_REF:0000034] comment: Needs logical definition. Should be capable_of skeletal system morphogenesis? or skeletal tissue development? needs to be added to GO. NOTES:a cell type of the early embryo (see also: mesenchymal cells) that will give rise to mineralized connective tissue. Scleroblasts can differentiate into osteoblasts (bone-forming cells), chondroblasts (cartilage-forming cells), odontoblasts (dentin-forming cells), ameloblasts (enamel-forming cells). The mesenchymal cells developing into osteoblasts and chondroblasts are derived from the mesoderm. Those developing into odontoblasts are neural crest cells. Those developing into ameloblasts are derived from the ectoderm. (http://www.copewithcytokines.de/cope.cgi?key=scleroblasts) +subset: human_subset +subset: mouse_subset synonym: "scleroblast" EXACT [GO_REF:0000034] is_a: CL:0000000 ! cell property_value: terms:contributor https://orcid.org/0000-0001-9114-8737 @@ -2734,6 +3013,8 @@ creation_date: 2012-06-15T02:51:27Z id: CL:0007004 name: premigratory neural crest cell def: "Cell that is part of the neural crest region of the neuroepithelium, prior to migration. Note that not all premigratory neural crest cells may become migratory neural crest cells." [UBERONREF:0000002] +subset: human_subset +subset: mouse_subset xref: ZFA:0007084 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0011012 ! neural crest cell relationship: part_of UBERON:0002342 ! neural crest @@ -2746,6 +3027,8 @@ id: CL:0008001 name: hematopoietic precursor cell def: "Any hematopoietic cell that is a precursor of some other hematopoietic cell type." [GOC:dos] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset is_a: CL:0000988 ! hematopoietic cell [Term] @@ -2754,6 +3037,8 @@ name: mesenchymal cell def: "A non-polarised cell precursor cell that is part of some mesenchyme, is associated with the cell matrix but is not connected to other cells and is capable of migration." [] subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "mesenchyme cell" EXACT [] is_a: CL:0000219 ! motile cell is_a: CL:0000255 ! eukaryotic cell @@ -2765,6 +3050,8 @@ property_value: RO:0002175 NCBITaxon:9606 id: CL:0010017 name: zygote def: "A zygote in a plant or an animal." [] +subset: human_subset +subset: mouse_subset xref: MESH:D015053 is_a: CL:0000000 ! cell property_value: seeAlso https://github.com/obophenotype/cell-ontology/issues/786 @@ -2774,16 +3061,20 @@ id: CL:0011012 name: neural crest cell def: "A cell of the neural crest. Neural crest cells are multipotent. Premigratory neural crest cells are found at the neural plate boarder, some of which will undergo ectomesynchymal transition and delamination to form migratory neural crest cells." [https://orcid.org/0000-0001-5208-3432, https://orcid.org/0000-0002-9900-7880] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset xref: https://cellxgene.cziscience.com/cellguide/CL_0011012 is_a: CL:0000048 ! multi fate stem cell is_a: CL:0002321 ! embryonic cell (metazoa) -property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional.\n\nNeural crest cells are a group of transient and highly migratory cells that originate from the neuroectoderm during the early stages of embryonic development. They are multipotent cells with an exceptional degree of plasticity, capable of differentiating into various somatic cell types and therefore play a fundamental role in the formation of various organs and tissues, making them critical contributors to the developing embryo. \nAfter the initiation of neurulation (the formation of the neural tube) neural crest cells start to undergo epithelial-to-mesenchymal transition and delaminate and migrate from the dorsal neural tube to several regions throughout the embryo. They differentiate into a range of diverse cell types, such as neurons and glial cells of the peripheral nervous system, including sensory and autonomic neurons. They also contribute to the formation of adrenal glands, pigment cells in the skin (melanocytes), cardiac structures, including parts of the heart septum and major arteries, as well as bones and cartilage of the face and skull.\nDisorders or aberrations in the development or migration of the neural crest cells can lead to serious congenital malformations, such as neurocristopathies, including Hirschsprung disease, neuroblastoma, and neurofibromatosis." xsd:string {xref="DOI:10.1002/dvg.23276", xref="DOI:10.1242/dev.193193", xref="DOI:10.3389/fcell.2020.00635/full", xref="https://doi.org/10.1016/j.ydbio.2011.12.042"} +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nNeural crest cells are a group of transient and highly migratory cells that originate from the neuroectoderm during the early stages of embryonic development. They are multipotent cells with an exceptional degree of plasticity, capable of differentiating into various somatic cell types and therefore play a fundamental role in the formation of various organs and tissues, making them critical contributors to the developing embryo. \nAfter the initiation of neurulation (the formation of the neural tube) neural crest cells start to undergo epithelial-to-mesenchymal transition and delaminate and migrate from the dorsal neural tube to several regions throughout the embryo. They differentiate into a range of diverse cell types, such as neurons and glial cells of the peripheral nervous system, including sensory and autonomic neurons. They also contribute to the formation of adrenal glands, pigment cells in the skin (melanocytes), cardiac structures, including parts of the heart septum and major arteries, as well as bones and cartilage of the face and skull.\nDisorders or aberrations in the development or migration of the neural crest cells can lead to serious congenital malformations, such as neurocristopathies, including Hirschsprung disease, neuroblastoma, and neurofibromatosis." xsd:string {xref="DOI:10.1002/dvg.23276", xref="DOI:10.1242/dev.193193", xref="DOI:10.3389/fcell.2020.00635/full", xref="https://doi.org/10.1016/j.ydbio.2011.12.042"} [Term] id: CL:0011026 name: progenitor cell def: "A precursor cell that has a tendency to differentiate into a specific type of cell. They are descendants of stem cells, only they are more constrained in their differentiation potential or capacity for self-renewal, and are often more limited in both senses." [https://doi.org/10.1016/B978-0-12-409503-8.00002-0, ISBN:978-1-62808-994-3] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset is_a: CL:0000255 ! eukaryotic cell is_a: CL:0011115 ! precursor cell intersection_of: CL:0011115 ! precursor cell @@ -2797,6 +3088,8 @@ name: precursor cell def: "A cell that, by division or terminal differentiation, can give rise to other cell types." [GOC:dos] comment: Work is needed on GO 'cell differentiation' before it is clear whether the equivalent class definition 'native cell' that capable_of some 'cell differentiation' works. Also, may want to consider merging this with non-terminally differentiated cell. subset: cellxgene_subset +subset: human_subset +subset: mouse_subset is_a: CL:0000000 ! cell intersection_of: CL:0000000 ! cell intersection_of: capable_of GO:0030154 ! cell differentiation @@ -2807,25 +3100,29 @@ id: CL:0017005 name: lymphoblast def: "A lymphocyte that has gotten larger after being stimulated by an antigen." [http://orcid.org/0000-0001-9990-8331, NCIT:C13013] subset: blood_and_immune_upper_slim +subset: human_subset +subset: mouse_subset xref: BTO:0000772 xref: EFO:0000572 xref: FMA:83030 is_a: CL:0000542 ! lymphocyte relationship: output_of GO:0046649 ! lymphocyte activation -property_value: dc:date "2022-08-17T14:20:01Z" xsd:string -created_by: http://orcid.org/0000-0003-2473-2313 +property_value: terms:contributor http://orcid.org/0000-0003-2473-2313 +property_value: terms:date "2022-08-17T14:20:01Z" xsd:dateTime [Term] id: CL:0017006 name: B-lymphoblast def: "A lymphocyte of B lineage that has gotten larger after being stimulated by an antigen." [EFO:0005293, https://orcid.org/0000-0002-2825-0621] subset: blood_and_immune_upper_slim +subset: human_subset +subset: mouse_subset xref: EFO:0005293 xref: FMA:83031 is_a: CL:0000945 ! lymphocyte of B lineage is_a: CL:0017005 ! lymphoblast -property_value: dc:date "2022-08-17T14:30:32Z" xsd:string -created_by: http://orcid.org/0000-0003-2473-2313 +property_value: terms:contributor http://orcid.org/0000-0003-2473-2313 +property_value: terms:date "2022-08-17T14:30:32Z" xsd:dateTime [Term] id: CL:0017500 @@ -2884,6 +3181,8 @@ creation_date: 2009-12-28T04:28:35Z id: CL:1001610 name: bone marrow hematopoietic cell def: "Hematopoietic cells resident in the bone marrow. Include: hematopoietic stem cells (lymphoid stem cells and myeloid stem cells) and the precursor cells for thrombocytes, erythrocytes, basophils, neutrophils, eosinophils, monocytes and lymphocytes." [NPX:PDR] +subset: human_subset +subset: mouse_subset synonym: "bone marrow hematopoietic cells" RELATED [CALOHA:TS-2109] synonym: "bone marrow poietic cells" RELATED [CALOHA:TS-2109] xref: CALOHA:TS-2109 @@ -2898,6 +3197,8 @@ id: CL:2000001 name: peripheral blood mononuclear cell def: "A leukocyte with a single non-segmented nucleus in the mature form found in the circulatory pool of blood." [GOC:TermGenie] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset is_a: CL:0000080 ! circulating cell is_a: CL:0000842 ! mononuclear cell intersection_of: CL:0000842 ! mononuclear cell @@ -2911,6 +3212,8 @@ id: CL:4030029 name: blood lymphocyte def: "A lymphocyte located in blood." [https://orcid.org/0000-0001-9990-8331] subset: blood_and_immune_upper_slim +subset: human_subset +subset: mouse_subset is_a: CL:0000542 ! lymphocyte is_a: CL:2000001 ! peripheral blood mononuclear cell intersection_of: CL:0000542 ! lymphocyte @@ -2921,6 +3224,8 @@ property_value: terms:date "2022-11-04T14:40:00Z" xsd:dateTime id: CL:4052002 name: syncytial cell def: "A multinucleate cell formed by the fusion of multiple uninuclear cells through plasma membrane fusion. This process leads to a single large cell containing multiple nuclei within a shared cytoplasm." [PMID:20851884, Wikipedia:Syncytium] +subset: human_subset +subset: mouse_subset synonym: "SC" RELATED OMO:0003000 [PMID:9067520] synonym: "syncytium" EXACT [WBbt:0008074] is_a: CL:0000228 ! multinucleate cell @@ -2935,7 +3240,6 @@ property_value: terms:date "2024-08-15T10:38:46Z" xsd:dateTime id: GO:0000278 name: mitotic cell cycle namespace: biological_process -alt_id: GO:0007067 def: "Progression through the phases of the mitotic cell cycle, the most common eukaryotic cell cycle, which canonically comprises four successive phases called G1, S, G2, and M and includes replication of the genome and the subsequent segregation of chromosomes into daughter cells. In some variant cell cycles nuclear replication or nuclear division may not be followed by cell division, or G1 and G2 phases may be absent." [GOC:mah, ISBN:0815316194] comment: Note that this term should not be confused with 'GO:0140014 ; mitotic nuclear division'. 'GO:0000278 ; mitotic cell cycle represents the entire mitotic cell cycle, while 'GO:0140014 ; mitotic nuclear division' specifically represents the actual nuclear division step of the mitotic cell cycle. subset: goslim_chembl @@ -2985,16 +3289,13 @@ intersection_of: has_part GO:0045026 ! plasma membrane fusion id: GO:0000785 name: chromatin namespace: cellular_component -alt_id: GO:0000789 -alt_id: GO:0000790 -alt_id: GO:0005717 def: "The ordered and organized complex of DNA, protein, and sometimes RNA, that forms the chromosome." [GOC:elh, PMID:20404130] comment: Chromosomes include parts that are not part of the chromatin. Examples include the kinetochore. synonym: "chromosome scaffold" RELATED [] synonym: "cytoplasmic chromatin" NARROW [] synonym: "nuclear chromatin" NARROW [] xref: NIF_Subcellular:sao1615953555 -is_a: GO:0110165 ! cellular anatomical entity +is_a: GO:0110165 ! cellular anatomical structure relationship: part_of GO:0005694 ! chromosome property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28301" xsd:anyURI @@ -3002,8 +3303,6 @@ property_value: term_tracker_item "https://github.com/geneontology/go-ontology/i id: GO:0000791 name: euchromatin namespace: cellular_component -alt_id: GO:0005719 -alt_id: GO:0035327 def: "A dispersed and relatively uncompacted form of chromatin that is in a transcription-competent conformation." [PMID:32017156] synonym: "nuclear euchromatin" RELATED [] synonym: "transcriptionally active chromatin" EXACT [] @@ -3016,8 +3315,6 @@ property_value: term_tracker_item "https://github.com/geneontology/go-ontology/i id: GO:0000792 name: heterochromatin namespace: cellular_component -alt_id: GO:0005720 -alt_id: GO:0035328 def: "A compact and highly condensed form of chromatin that is refractory to transcription." [PMID:32017156] synonym: "nuclear heterochromatin" NARROW [] synonym: "transcriptionally inactive chromatin" EXACT [] @@ -3139,10 +3436,6 @@ property_value: term_tracker_item "https://github.com/geneontology/go-ontology/i id: GO:0001816 name: cytokine production namespace: biological_process -alt_id: GO:0042032 -alt_id: GO:0042089 -alt_id: GO:0042107 -alt_id: GO:0050663 def: "The appearance of a cytokine due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels." [GOC:add, ISBN:0781735149] comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select one of the 'regulation' children terms. subset: gocheck_do_not_annotate @@ -3162,7 +3455,7 @@ property_value: term_tracker_item "https://github.com/geneontology/go-ontology/i id: GO:0001820 name: serotonin secretion namespace: biological_process -def: "The regulated release of serotonin by a cell. Serotonin (5-hydroxytryptamine, or 5-HT) is a monoamine synthesised in serotonergic neurons in the central nervous system, enterochromaffin cells in the gastrointestinal tract and some immune system cells." [GOC:ef, ISBN:0198506732, ISBN:0781735149] +def: "The regulated release of serotonin by a cell. Serotonin (5-hydroxytryptamine, or 5-HT) is a monoamine synthesized in serotonergic neurons in the central nervous system, enterochromaffin cells in the gastrointestinal tract and some immune system cells." [GOC:ef, ISBN:0198506732, ISBN:0781735149] synonym: "5-HT secretion" EXACT [] synonym: "5-hydroxytryptamine secretion" EXACT [] synonym: "serotonin release" RELATED [GOC:tb] @@ -3189,7 +3482,6 @@ relationship: part_of GO:0016331 ! morphogenesis of embryonic epithelium id: GO:0001841 name: neural tube formation namespace: biological_process -alt_id: GO:0001679 def: "The formation of a tube from the flat layer of ectodermal cells known as the neural plate. This will give rise to the central nervous system." [GOC:dph, ISBN:0878932437] synonym: "neural tube morphogenesis" EXACT [GOC:dph] synonym: "neurulation" EXACT [] @@ -3399,8 +3691,6 @@ property_value: RO:0002161 NCBITaxon:4895 id: GO:0002377 name: immunoglobulin production namespace: biological_process -alt_id: GO:0002378 -alt_id: GO:0048305 def: "The appearance of immunoglobulin due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels." [GOC:add, ISBN:0781735149] comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select one of the 'regulation' children terms. subset: gocheck_do_not_annotate @@ -3413,8 +3703,6 @@ is_a: GO:0002440 ! production of molecular mediator of immune response id: GO:0002381 name: immunoglobulin production involved in immunoglobulin-mediated immune response namespace: biological_process -alt_id: GO:0002379 -alt_id: GO:0002380 def: "The appearance of immunoglobulin due to biosynthesis or secretion following a cellular stimulus during an immune response, resulting in an increase in its intracellular or extracellular levels." [GOC:add, ISBN:0781735149, PMID:9185563] comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select one of the 'regulation' children terms. subset: gocheck_do_not_annotate @@ -3453,8 +3741,6 @@ is_a: GO:0010467 ! gene expression id: GO:0002443 name: leukocyte mediated immunity namespace: biological_process -alt_id: GO:0019723 -alt_id: GO:0042087 def: "Any process involved in the carrying out of an immune response by a leukocyte." [GO_REF:0000022, GOC:add, ISBN:0781735149] synonym: "cell-mediated immune response" RELATED [] synonym: "cellular immune response" RELATED [] @@ -3942,7 +4228,6 @@ is_a: GO:0003008 ! system process id: GO:0003674 name: molecular_function namespace: molecular_function -alt_id: GO:0005554 def: "A molecular process that can be carried out by the action of a single macromolecular machine, usually via direct physical interactions with other molecular entities. Function in this sense denotes an action, or activity, that a gene product (or a complex) performs." [GOC:pdt] comment: Note that, in addition to forming the root of the molecular function ontology, this term is recommended for the annotation of gene products whose molecular function is unknown. When this term is used for annotation, it indicates that no information was available about the molecular function of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this. Despite its name, this is not a type of 'function' in the sense typically defined by upper ontologies such as Basic Formal Ontology (BFO). It is instead a BFO:process carried out by a single gene product or complex. subset: goslim_candida @@ -3959,8 +4244,6 @@ disjoint_from: GO:0008150 ! biological_process id: GO:0004888 name: transmembrane signaling receptor activity namespace: molecular_function -alt_id: GO:0004926 -alt_id: GO:0099600 def: "Combining with an extracellular or intracellular signal and transmitting the signal from one side of the membrane to the other to initiate a change in cell activity or state as part of signal transduction." [GOC:go_curators, Wikipedia:Transmembrane_receptor] comment: This term includes intracellular membrane receptors, e.g. IP3 triggered release of Ca2+ from intracellular stores. synonym: "transmembrane receptor activity" BROAD [GOC:bf, GOC:signaling] @@ -3972,11 +4255,6 @@ is_a: GO:0038023 ! signaling receptor activity id: GO:0004930 name: G protein-coupled receptor activity namespace: molecular_function -alt_id: GO:0001622 -alt_id: GO:0001623 -alt_id: GO:0001624 -alt_id: GO:0001625 -alt_id: GO:0016526 def: "Combining with an extracellular signal and transmitting the signal across the membrane by activating an associated G-protein; promotes the exchange of GDP for GTP on the alpha subunit of a heterotrimeric G-protein complex." [GOC:bf, Wikipedia:GPCR] subset: goslim_chembl synonym: "EBV-induced receptor" NARROW [] @@ -3999,6 +4277,7 @@ synonym: "super conserved receptor expressed in brain receptor activity" NARROW xref: Reactome:R-HSA-114552 "Thrombin-activated PARs activate G12/13" xref: Reactome:R-HSA-114558 "Thrombin-activated PARs activate Gq" xref: Reactome:R-HSA-167408 "The high affinity receptor complex binds to G-protein" +xref: Reactome:R-HSA-381706 "GLP1R:GLP1 activates G(s)" xref: Wikipedia:GPCR is_a: GO:0004888 ! transmembrane signaling receptor activity relationship: part_of GO:0007186 ! G protein-coupled receptor signaling pathway @@ -4007,7 +4286,6 @@ relationship: part_of GO:0007186 ! G protein-coupled receptor signaling pathway id: GO:0005575 name: cellular_component namespace: cellular_component -alt_id: GO:0008372 def: "A location, relative to cellular compartments and structures, occupied by a macromolecular machine. There are three types of cellular components described in the gene ontology: (1) the cellular anatomical entity where a gene product carries out a molecular function (e.g., plasma membrane, cytoskeleton) or membrane-enclosed compartments (e.g., mitochondrion); (2) virion components, where viral proteins act, and (3) the stable macromolecular complexes of which gene product are parts (e.g., the clathrin complex)." [GOC:pdt] comment: Note that, in addition to forming the root of the cellular component ontology, this term is recommended for the annotation of gene products whose cellular component is unknown. When this term is used for annotation, it indicates that no information was available about the cellular component of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this. subset: goslim_candida @@ -4045,7 +4323,7 @@ subset: goslim_prokaryote_ribbon subset: goslim_yeast synonym: "extracellular" EXACT [] xref: Wikipedia:Extracellular -is_a: GO:0110165 ! cellular anatomical entity +is_a: GO:0110165 ! cellular anatomical structure [Term] id: GO:0005577 @@ -4082,8 +4360,6 @@ is_a: GO:0098651 ! basement membrane collagen trimer id: GO:0005604 name: basement membrane namespace: cellular_component -alt_id: GO:0005605 -alt_id: GO:0008003 def: "A collagen-containing extracellular matrix consisting of a thin layer of dense material found in various animal tissues interposed between the cells and the adjacent connective tissue. It consists of the basal lamina plus an associated layer of reticulin fibers." [ISBN:0198547684, PMID:22505934] comment: Note that this term has no relationship to 'membrane ; GO:0016020' because the basement membrane is not a lipid bilayer. synonym: "basal lamina" RELATED [] @@ -4103,7 +4379,7 @@ subset: goslim_drosophila subset: goslim_generic synonym: "intercellular space" RELATED [] xref: NIF_Subcellular:sao1425028079 -is_a: GO:0110165 ! cellular anatomical entity +is_a: GO:0110165 ! cellular anatomical structure relationship: part_of GO:0005576 ! extracellular region [Term] @@ -4121,7 +4397,7 @@ synonym: "nucleocytoplasm" RELATED [GOC:mah] synonym: "protoplasm" EXACT [] synonym: "protoplast" RELATED [GOC:mah] xref: Wikipedia:Intracellular -is_a: GO:0110165 ! cellular anatomical entity +is_a: GO:0110165 ! cellular anatomical structure relationship: part_of CL:0000000 ! cell property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/17776" xsd:anyURI @@ -4173,7 +4449,7 @@ synonym: "chromatid" RELATED [] synonym: "interphase chromosome" NARROW [] synonym: "prophase chromosome" NARROW [] xref: Wikipedia:Chromosome -is_a: GO:0043232 ! intracellular non-membrane-bounded organelle +is_a: GO:0043232 ! intracellular membraneless organelle [Term] id: GO:0005730 @@ -4189,7 +4465,7 @@ subset: goslim_plant subset: goslim_yeast xref: NIF_Subcellular:sao1820400233 xref: Wikipedia:Nucleolus -is_a: GO:0043232 ! intracellular non-membrane-bounded organelle +is_a: GO:0043232 ! intracellular membraneless organelle relationship: part_of GO:0031981 ! nuclear lumen [Term] @@ -4207,7 +4483,7 @@ subset: goslim_prokaryote subset: goslim_prokaryote_ribbon subset: goslim_yeast xref: Wikipedia:Cytoplasm -is_a: GO:0110165 ! cellular anatomical entity +is_a: GO:0110165 ! cellular anatomical structure relationship: part_of GO:0005622 ! intracellular anatomical structure property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/23023" xsd:anyURI @@ -4286,7 +4562,6 @@ relationship: RO:0002162 NCBITaxon:2759 {all_only="true"} ! in taxon Eukaryota id: GO:0005840 name: ribosome namespace: cellular_component -alt_id: GO:0033279 def: "An intracellular organelle, about 200 A in diameter, consisting of RNA and protein. It is the site of protein biosynthesis resulting from translation of messenger RNA (mRNA). It consists of two subunits, one large and one small, each containing only protein and RNA. Both the ribosome and its subunits are characterized by their sedimentation coefficients, expressed in Svedberg units (symbol: S). Hence, the prokaryotic ribosome (70S) comprises a large (50S) subunit and a small (30S) subunit, while the eukaryotic ribosome (80S) comprises a large (60S) subunit and a small (40S) subunit. Two sites on the ribosomal large subunit are involved in translation, namely the aminoacyl site (A site) and peptidyl site (P site). Ribosomes from prokaryotes, eukaryotes, mitochondria, and chloroplasts have characteristically distinct ribosomal proteins." [ISBN:0198506732] subset: goslim_candida subset: goslim_chembl @@ -4304,16 +4579,14 @@ synonym: "membrane bound ribosome" NARROW [NIF_Subcellular:sao1291545653] synonym: "ribosomal RNA" RELATED [] xref: NIF_Subcellular:sao1429207766 xref: Wikipedia:Ribosome -is_a: GO:0043232 ! intracellular non-membrane-bounded organelle -is_a: PR:000050567 ! protein-containing material entity +is_a: GO:0043232 ! intracellular membraneless organelle relationship: capable_of_part_of GO:0006412 ! translation +relationship: has_part PR:000000001 ! protein [Term] id: GO:0005886 name: plasma membrane namespace: cellular_component -alt_id: GO:0005887 -alt_id: GO:0005904 def: "The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins." [ISBN:0716731363] subset: goslim_agr subset: goslim_candida @@ -4359,7 +4632,6 @@ property_value: term_tracker_item "https://github.com/geneontology/go-ontology/i id: GO:0006259 name: DNA metabolic process namespace: biological_process -alt_id: GO:0055132 def: "Any cellular metabolic process involving deoxyribonucleic acid. This is one of the two main types of nucleic acid, consisting of a long, unbranched macromolecule formed from one, or more commonly, two, strands of linked deoxyribonucleotides." [ISBN:0198506732] subset: goslim_agr subset: goslim_candida @@ -4391,9 +4663,6 @@ is_a: GO:0006259 ! DNA metabolic process id: GO:0006412 name: translation namespace: biological_process -alt_id: GO:0006416 -alt_id: GO:0006453 -alt_id: GO:0043037 def: "The cellular metabolic process in which a protein is formed, using the sequence of a mature mRNA or circRNA molecule to specify the sequence of amino acids in a polypeptide chain. Translation is mediated by the ribosome, and begins with the formation of a ternary complex between aminoacylated initiator methionine tRNA, GTP, and initiation factor 2, which subsequently associates with the small subunit of the ribosome and an mRNA or circRNA. Translation ends with the release of a polypeptide chain from the ribosome." [GOC:go_curators] subset: goslim_candida subset: goslim_chembl @@ -4422,15 +4691,13 @@ relationship: starts_with GO:0006413 ! translational initiation id: GO:0006413 name: translational initiation namespace: biological_process -alt_id: GO:0006440 -alt_id: GO:0006454 def: "The process preceding formation of the peptide bond between the first two amino acids of a protein. This includes the formation of a complex of the ribosome, mRNA or circRNA, and an initiation complex that contains the first aminoacyl-tRNA." [ISBN:019879276X] subset: goslim_yeast synonym: "biopolymerisation" BROAD [] synonym: "biopolymerization" BROAD [] synonym: "protein synthesis initiation" BROAD [] synonym: "translation initiation" EXACT [] -is_a: GO:0044237 ! cellular metabolic process +is_a: GO:0008152 ! metabolic process relationship: part_of GO:0006412 ! translation relationship: starts_with GO:0001677 ! formation of translation initiation ternary complex @@ -4438,8 +4705,6 @@ relationship: starts_with GO:0001677 ! formation of translation initiation terna id: GO:0006414 name: translational elongation namespace: biological_process -alt_id: GO:0006442 -alt_id: GO:0006455 def: "The successive addition of amino acid residues to a nascent polypeptide chain during protein biosynthesis." [GOC:ems] subset: goslim_yeast synonym: "protein synthesis elongation" BROAD [] @@ -4451,8 +4716,6 @@ relationship: part_of GO:0006412 ! translation id: GO:0006415 name: translational termination namespace: biological_process -alt_id: GO:0006443 -alt_id: GO:0006456 def: "The process resulting in the release of a polypeptide chain from the ribosome, usually in response to a termination codon (UAA, UAG, or UGA in the universal genetic code)." [GOC:hjd, ISBN:019879276X] synonym: "protein synthesis termination" BROAD [] synonym: "translation termination" EXACT [] @@ -4464,9 +4727,6 @@ relationship: part_of GO:0006412 ! translation id: GO:0006810 name: transport namespace: biological_process -alt_id: GO:0015457 -alt_id: GO:0015460 -alt_id: GO:0044765 def: "The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter or a transporter complex, a pore or a motor protein." [GOC:dos, GOC:dph, GOC:jl, GOC:mah] comment: Note that this term should not be used for direct annotation. It should be possible to make a more specific annotation to one of the children of this term, for e.g. to transmembrane transport, to microtubule-based transport or to vesicle-mediated transport. subset: gocheck_do_not_annotate @@ -4481,7 +4741,6 @@ subset: goslim_prokaryote_ribbon synonym: "single-organism transport" RELATED [] is_a: GO:0051234 ! establishment of localization property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/20292" xsd:anyURI -created_by: jl creation_date: 2012-12-13T16:25:32Z [Term] @@ -4506,8 +4765,6 @@ is_a: GO:0006810 ! transport id: GO:0006887 name: exocytosis namespace: biological_process -alt_id: GO:0016194 -alt_id: GO:0016195 def: "A process of secretion by a cell that results in the release of intracellular molecules (e.g. hormones, matrix proteins) contained within a membrane-bounded vesicle. Exocytosis can occur either by full fusion, when the vesicle collapses into the plasma membrane, or by a kiss-and-run mechanism that involves the formation of a transient contact, a pore, between a granule (for example of chromaffin cells) and the plasma membrane. The latter process most of the time leads to only partial secretion of the granule content. Exocytosis begins with steps that prepare vesicles for fusion with the membrane (tethering and docking) and ends when molecules are secreted from the cell." [GOC:mah, ISBN:0716731363, PMID:22323285] subset: goslim_yeast synonym: "nonselective vesicle exocytosis" RELATED [] @@ -4524,9 +4781,6 @@ relationship: process_has_causal_agent GO:0070382 ! exocytic vesicle id: GO:0006897 name: endocytosis namespace: biological_process -alt_id: GO:0016193 -alt_id: GO:0016196 -alt_id: GO:0098701 def: "A vesicle-mediated transport process in which cells take up external materials or membrane constituents by the invagination of a part of the plasma membrane to form a new membrane-bounded vesicle." [GOC:mah, ISBN:0198506732, ISBN:0716731363, Wikipedia:Endocytosis] subset: goslim_yeast synonym: "endocytic import into cell" EXACT [] @@ -4546,8 +4800,6 @@ property_value: term_tracker_item "https://github.com/geneontology/go-ontology/i id: GO:0006900 name: vesicle budding from membrane namespace: biological_process -alt_id: GO:0006902 -alt_id: GO:1902591 def: "The evagination of a membrane, resulting in formation of a vesicle." [GOC:jid, GOC:tb] synonym: "membrane evagination" EXACT [] synonym: "nonselective vesicle assembly" RELATED [] @@ -4559,7 +4811,6 @@ synonym: "vesicle formation" EXACT [] is_a: GO:0016050 ! vesicle organization is_a: GO:0061024 ! membrane organization relationship: part_of GO:0016192 ! vesicle-mediated transport -created_by: jl creation_date: 2013-12-19T15:26:17Z [Term] @@ -4588,8 +4839,6 @@ property_value: term_tracker_item "https://github.com/geneontology/go-ontology/i id: GO:0006915 name: apoptotic process namespace: biological_process -alt_id: GO:0006917 -alt_id: GO:0008632 def: "A programmed cell death process which begins when a cell receives an internal (e.g. DNA damage) or external signal (e.g. an extracellular death ligand), and proceeds through a series of biochemical events (signaling pathway phase) which trigger an execution phase. The execution phase is the last step of an apoptotic process, and is typically characterized by rounding-up of the cell, retraction of pseudopodes, reduction of cellular volume (pyknosis), chromatin condensation, nuclear fragmentation (karyorrhexis), plasma membrane blebbing and fragmentation of the cell into apoptotic bodies. When the execution phase is completed, the cell has died." [GOC:cjm, GOC:dhl, GOC:ecd, GOC:go_curators, GOC:mtg_apoptosis, GOC:tb, ISBN:0198506732, PMID:18846107, PMID:21494263] synonym: "activation of apoptosis" NARROW [] synonym: "apoptosis" NARROW [] @@ -4681,8 +4930,6 @@ property_value: term_tracker_item "https://github.com/geneontology/go-ontology/i id: GO:0006952 name: defense response namespace: biological_process -alt_id: GO:0002217 -alt_id: GO:0042829 def: "Reactions, triggered in response to the presence of a foreign body or the occurrence of an injury, which result in restriction of damage to the organism attacked or prevention/recovery from the infection caused by the attack." [GOC:go_curators] synonym: "antimicrobial peptide activity" RELATED [] synonym: "defence response" EXACT [] @@ -4715,7 +4962,6 @@ is_a: GO:0050896 ! response to stimulus id: GO:0006996 name: organelle organization namespace: biological_process -alt_id: GO:1902589 def: "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of an organelle within a cell. An organelle is an organized structure of distinctive morphology and function. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton. Excludes the plasma membrane." [GOC:mah] comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. subset: gocheck_do_not_annotate @@ -4730,7 +4976,6 @@ intersection_of: GO:0016043 ! cellular component organization intersection_of: results_in_organization_of GO:0043226 ! organelle relationship: results_in_organization_of GO:0043226 ! organelle property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27189" xsd:anyURI -created_by: jl creation_date: 2013-12-19T15:25:51Z [Term] @@ -4788,11 +5033,6 @@ is_a: GO:0009987 ! cellular process id: GO:0007165 name: signal transduction namespace: biological_process -alt_id: GO:0023014 -alt_id: GO:0023015 -alt_id: GO:0023016 -alt_id: GO:0023033 -alt_id: GO:0023045 def: "The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell." [GOC:go_curators, GOC:mtg_signaling_feb11] comment: Note that signal transduction is defined broadly to include a ligand interacting with a receptor, downstream signaling steps and a response being triggered. A change in form of the signal in every step is not necessary. Note that in many cases the end of this process is regulation of the initiation of transcription. Note that specific transcription factors may be annotated to this term, but core/general transcription machinery such as RNA polymerase should not. subset: goslim_candida @@ -4815,7 +5055,6 @@ relationship: part_of GO:0051716 ! cellular response to stimulus id: GO:0007186 name: G protein-coupled receptor signaling pathway namespace: biological_process -alt_id: GO:0038042 def: "The series of molecular signals initiated by a ligand binding to its receptor, in which the activated receptor promotes the exchange of GDP for GTP on the alpha-subunit of an associated heterotrimeric G-protein complex. The GTP-bound activated alpha-G-protein then dissociates from the beta- and gamma-subunits to further transmit the signal within the cell. The pathway begins with receptor-ligand interaction, and ends with regulation of a downstream cellular process. The pathway can start from the plasma membrane, Golgi or nuclear membrane." [GOC:bf, GOC:mah, PMID:16902576, PMID:24568158, Wikipedia:G_protein-coupled_receptor] subset: goslim_drosophila synonym: "dimeric G-protein coupled receptor signaling pathway" NARROW [] @@ -4965,7 +5204,6 @@ is_a: GO:0050878 ! regulation of body fluid levels id: GO:0008015 name: blood circulation namespace: biological_process -alt_id: GO:0070261 def: "The flow of blood through the body of an animal, enabling the transport of nutrients to the tissues and the removal of waste products." [GOC:mtg_heart, ISBN:0192800825] subset: goslim_pir synonym: "hemolymph circulation" RELATED [] @@ -4975,9 +5213,6 @@ is_a: GO:0003013 ! circulatory system process id: GO:0008150 name: biological_process namespace: biological_process -alt_id: GO:0000004 -alt_id: GO:0007582 -alt_id: GO:0044699 def: "A biological process is the execution of a genetically-encoded biological module or program. It consists of all the steps required to achieve the specific biological objective of the module. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence." [GOC:pdt] comment: Note that, in addition to forming the root of the biological process ontology, this term is recommended for the annotation of gene products whose biological process is unknown. When this term is used for annotation, it indicates that no information was available about the biological process of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this. subset: goslim_candida @@ -4993,16 +5228,13 @@ synonym: "single organism process" RELATED [] synonym: "single-organism process" RELATED [] xref: Wikipedia:Biological_process property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/24968" xsd:anyURI -created_by: jl creation_date: 2012-09-19T15:05:24Z [Term] id: GO:0008152 name: metabolic process namespace: biological_process -alt_id: GO:0044236 -alt_id: GO:0044710 -def: "The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation." [GOC:go_curators, ISBN:0198547684] +def: "A cellular process consisting of the biochemical pathways by which a living organism transforms chemical substances. This includes including anabolism (biosynthetic process) and catabolism (catabolic process). Metabolic processes includes the transformation of small molecules, as well macromolecular processes such as DNA repair and replication, protein synthesis and degradation." [GOC:go_curators, ISBN:0198547684] comment: Note that metabolic processes do not include single functions or processes such as protein-protein interactions, protein-nucleic acids, nor receptor-ligand interactions. subset: gocheck_do_not_annotate subset: goslim_chembl @@ -5011,16 +5243,12 @@ subset: goslim_metagenomics subset: goslim_pir subset: goslim_plant subset: goslim_prokaryote_ribbon -synonym: "metabolic process resulting in cell growth" NARROW [] synonym: "metabolism" EXACT [] -synonym: "metabolism resulting in cell growth" NARROW [] -synonym: "multicellular organism metabolic process" NARROW [] -synonym: "single-organism metabolic process" RELATED [] xref: Wikipedia:Metabolism -is_a: GO:0008150 ! biological_process +is_a: GO:0009987 ! cellular process disjoint_from: GO:0051179 ! localization property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/26424" xsd:anyURI -created_by: jl +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28932" xsd:anyURI creation_date: 2012-10-17T15:46:40Z [Term] @@ -5039,9 +5267,7 @@ property_value: term_tracker_item "https://github.com/geneontology/go-ontology/i id: GO:0009058 name: biosynthetic process namespace: biological_process -alt_id: GO:0044274 -alt_id: GO:0044711 -def: "The chemical reactions and pathways resulting in the formation of substances; typically the energy-requiring part of metabolism in which simpler substances are transformed into more complex ones." [GOC:curators, ISBN:0198547684] +def: "A cellular process consisting of the biochemical pathways by which a living organism synthesizes chemical substances. This typically represents the energy-requiring part of metabolism in which simpler substances are transformed into more complex ones." [GOC:curators, ISBN:0198547684] subset: goslim_chembl subset: goslim_metagenomics subset: goslim_plant @@ -5054,14 +5280,13 @@ synonym: "single-organism biosynthetic process" RELATED [] synonym: "synthesis" EXACT [] xref: Wikipedia:Anabolism is_a: GO:0008152 ! metabolic process -created_by: jl +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28932" xsd:anyURI creation_date: 2012-10-17T15:52:18Z [Term] id: GO:0009059 name: macromolecule biosynthetic process namespace: biological_process -alt_id: GO:0043284 def: "The chemical reactions and pathways resulting in the formation of a macromolecule, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass." [GOC:mah] comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. subset: gocheck_do_not_annotate @@ -5071,8 +5296,8 @@ synonym: "macromolecule anabolism" EXACT [] synonym: "macromolecule biosynthesis" EXACT [] synonym: "macromolecule formation" EXACT [] synonym: "macromolecule synthesis" EXACT [] +is_a: GO:0009058 ! biosynthetic process is_a: GO:0043170 ! macromolecule metabolic process -is_a: GO:0044249 ! cellular biosynthetic process property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/15249" xsd:anyURI property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/25418" xsd:anyURI property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27189" xsd:anyURI @@ -5105,7 +5330,6 @@ is_a: GO:0050896 ! response to stimulus id: GO:0009611 name: response to wounding namespace: biological_process -alt_id: GO:0002245 def: "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to the organism." [GOC:go_curators] synonym: "physiological response to wounding" EXACT [] is_a: GO:0006950 ! response to stress @@ -5127,7 +5351,6 @@ relationship: part_of GO:0048856 ! anatomical structure development id: GO:0009790 name: embryo development namespace: biological_process -alt_id: GO:0009795 def: "The process whose specific outcome is the progression of an embryo from its formation until the end of its embryonic life stage. The end of the embryonic stage is organism-specific. For example, for mammals, the process would begin with zygote formation and end with birth. For insects, the process would begin at zygote formation and end with larval hatching. For plant zygotic embryos, this would be from zygote formation to the end of seed dormancy. For plant vegetative embryos, this would be from the initial determination of the cell or group of cells to form an embryo until the point when the embryo becomes independent of the parent plant." [GOC:go_curators, GOC:isa_complete, GOC:mtg_sensu] subset: gocheck_do_not_annotate subset: goslim_chembl @@ -5184,9 +5407,6 @@ property_value: RO:0002161 NCBITaxon:4891 id: GO:0009987 name: cellular process namespace: biological_process -alt_id: GO:0008151 -alt_id: GO:0044763 -alt_id: GO:0050875 def: "Any process that is carried out at the cellular level, but not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level." [GOC:go_curators, GOC:isa_complete] comment: This term should not be used for direct annotation. It should be possible to make a more specific annotation to one of the children of this term. subset: gocheck_do_not_annotate @@ -5196,7 +5416,6 @@ synonym: "cell physiology" EXACT [] synonym: "cellular physiological process" EXACT [] synonym: "single-organism cellular process" RELATED [] is_a: GO:0008150 ! biological_process -created_by: jl creation_date: 2012-12-11T16:56:55Z [Term] @@ -5216,12 +5435,10 @@ relationship: results_in_organization_of GO:0012505 ! endomembrane system id: GO:0010324 name: membrane invagination namespace: biological_process -alt_id: GO:1902534 def: "The infolding of a membrane." [GOC:tb] subset: goslim_yeast synonym: "single-organism membrane invagination" RELATED [] is_a: GO:0061024 ! membrane organization -created_by: jl creation_date: 2013-12-02T13:58:34Z [Term] @@ -5239,7 +5456,6 @@ property_value: term_tracker_item "https://github.com/geneontology/go-ontology/i id: GO:0012501 name: programmed cell death namespace: biological_process -alt_id: GO:0016244 def: "A process which begins when a cell receives an internal or external signal and activates a series of biochemical events (signaling pathway). The process ends with the death of the cell." [GOC:lr, GOC:mtg_apoptosis] comment: Note that this term should be used to annotate gene products in the organism undergoing the programmed cell death. To annotate genes in another organism whose products modulate programmed cell death in a host organism, consider the term 'modulation by symbiont of host programmed cell death ; GO:0052040'. Also, note that 'programmed cell death ; GO:0012501' should be used to refer to instances of caspase-independent cell death mechanisms, in the absence of further indications on the process taking place. At present, caspase-independent cell death is not yet represented in GO due to the lack of consensus and in-depth research on the topic. 'programmed cell death ; GO:0012501' may also be used to annotate gene products in taxa where apoptosis as defined in GO:0006915 does not occur, such as plants. You may also consider these specific children: GO:0097468 'programmed cell death in response to reactive oxygen species' (with descendants GO:0010421 'hydrogen peroxide-mediated programmed cell death' and GO:0010343 'singlet oxygen-mediated programmed cell death'), and GO:0009626 'plant-type hypersensitive response' and its children. subset: goslim_agr @@ -5274,7 +5490,7 @@ subset: goslim_candida subset: goslim_flybase_ribbon subset: goslim_yeast xref: Wikipedia:Endomembrane_system -is_a: GO:0110165 ! cellular anatomical entity +is_a: GO:0110165 ! cellular anatomical structure relationship: has_part GO:0005773 ! vacuole relationship: has_part GO:0005886 ! plasma membrane relationship: part_of CL:0000000 ! cell @@ -5309,9 +5525,6 @@ is_a: GO:0015669 ! gas transport id: GO:0016020 name: membrane namespace: cellular_component -alt_id: GO:0016021 -alt_id: GO:0098589 -alt_id: GO:0098805 def: "A lipid bilayer along with all the proteins and protein complexes embedded in it and attached to it." [GOC:dos, GOC:mah, ISBN:0815316194] subset: goslim_candida subset: goslim_chembl @@ -5328,7 +5541,7 @@ synonym: "transmembrane" RELATED [GOC:mah] synonym: "whole membrane" NARROW [] xref: Wikipedia:Biological_membrane xref: Wikipedia:Transmembrane_protein -is_a: GO:0110165 ! cellular anatomical entity +is_a: GO:0110165 ! cellular anatomical structure disjoint_from: GO:0031012 ! extracellular matrix creation_date: 2014-03-06T11:37:54Z @@ -5336,8 +5549,6 @@ creation_date: 2014-03-06T11:37:54Z id: GO:0016043 name: cellular component organization namespace: biological_process -alt_id: GO:0044235 -alt_id: GO:0071842 def: "A process that results in the assembly, arrangement of constituent parts, or disassembly of a cellular component." [GOC:ai, GOC:jl, GOC:mah] subset: gocheck_do_not_annotate subset: goslim_agr @@ -5382,7 +5593,6 @@ is_a: GO:0019724 ! B cell mediated immunity id: GO:0016192 name: vesicle-mediated transport namespace: biological_process -alt_id: GO:0006899 def: "A cellular transport process in which transported substances are moved in membrane-bounded vesicles; transported substances are enclosed in the vesicle lumen or located in the vesicle membrane. The process begins with a step that directs a substance to the forming vesicle, and includes vesicle budding and coating. Vesicles are then targeted to, and fuse with, an acceptor membrane." [GOC:ai, GOC:mah, ISBN:08789310662000] subset: goslim_candida subset: goslim_chembl @@ -5477,9 +5687,6 @@ relationship: part_of GO:0007154 ! cell communication id: GO:0019538 name: protein metabolic process namespace: biological_process -alt_id: GO:0006411 -alt_id: GO:0044267 -alt_id: GO:0044268 def: "The chemical reactions and pathways involving a protein. Includes protein modification." [GOC:ma] comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. subset: gocheck_do_not_annotate @@ -5534,7 +5741,6 @@ is_a: GO:0032991 ! protein-containing complex id: GO:0019815 name: B cell receptor complex namespace: cellular_component -alt_id: GO:0042570 def: "An immunoglobulin complex that is present in the plasma membrane of B cells and that in its canonical form is composed of two identical immunoglobulin heavy chains and two identical immunoglobulin light chains and a signaling subunit, a heterodimer of the Ig-alpha and Ig-beta proteins." [GOC:add, ISBN:0781735149] comment: Note that an immunoglobulin complex has the function of antigen binding if a suitable antigen is available. synonym: "antibody" RELATED [GOC:mah] @@ -5551,7 +5757,6 @@ is_a: GO:0098802 ! plasma membrane signaling receptor complex id: GO:0019882 name: antigen processing and presentation namespace: biological_process -alt_id: GO:0030333 def: "The process in which an antigen-presenting cell expresses antigen (peptide or lipid) on its cell surface in association with an MHC protein complex." [GO_REF:0000022, GOC:add, ISBN:0781735149, PMID:15771591, PMID:15928678] synonym: "antigen presentation" EXACT [] synonym: "antigen processing" EXACT [] @@ -5587,7 +5792,6 @@ relationship: part_of GO:0007049 ! cell cycle id: GO:0022411 name: cellular component disassembly namespace: biological_process -alt_id: GO:0071845 def: "A cellular process that results in the breakdown of a cellular component." [GOC:isa_complete] comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. subset: gocheck_do_not_annotate @@ -5616,7 +5820,6 @@ relationship: part_of GO:0007586 ! digestion id: GO:0022607 name: cellular component assembly namespace: biological_process -alt_id: GO:0071844 def: "The aggregation, arrangement and bonding together of a cellular component." [GOC:isa_complete] subset: goslim_chembl subset: goslim_euk_cellular_processes_ribbon @@ -5658,8 +5861,6 @@ relationship: results_in_assembly_of GO:1990904 ! ribonucleoprotein complex id: GO:0023052 name: signaling namespace: biological_process -alt_id: GO:0023046 -alt_id: GO:0044700 def: "The entirety of a process in which information is transmitted within a biological system. This process begins with an active signal and ends when a cellular response has been triggered." [GOC:mtg_signal, GOC:mtg_signaling_feb11, GOC:signaling] comment: Note that a signal is any variable property or parameter that serves to convey information, and may be a physical entity such as a gene product or small molecule, a photon, or a change in state such as movement or voltage change. subset: goslim_agr @@ -5677,7 +5878,6 @@ synonym: "signalling" EXACT [] synonym: "signalling process" RELATED [GOC:mah] synonym: "single organism signaling" RELATED [] is_a: GO:0050789 ! regulation of biological process -created_by: jl creation_date: 2010-02-16T09:30:50Z [Term] @@ -5729,7 +5929,7 @@ subset: goslim_agr subset: goslim_drosophila subset: goslim_flybase_ribbon xref: Wikipedia:Cell_junction -is_a: GO:0110165 ! cellular anatomical entity +is_a: GO:0110165 ! cellular anatomical structure property_value: RO:0002161 NCBITaxon:4751 [Term] @@ -5754,7 +5954,6 @@ property_value: term_tracker_item "https://github.com/geneontology/go-ontology/i id: GO:0030098 name: lymphocyte differentiation namespace: biological_process -alt_id: GO:0046650 def: "The process in which a relatively unspecialized precursor cell acquires specialized features of a lymphocyte. A lymphocyte is a leukocyte commonly found in the blood and lymph that has the characteristics of a large nucleus, a neutral staining cytoplasm, and prominent heterochromatin." [CL:0000542, GOC:go_curators] comment: Note that immunologists typically use the word 'development' to refer to cells of B or T cell lineages undergoing the process that GO describes as 'cell differentiation'. synonym: "lymphocyte cell differentiation" EXACT [] @@ -5825,7 +6024,6 @@ property_value: term_tracker_item "https://github.com/geneontology/go-ontology/i id: GO:0030183 name: B cell differentiation namespace: biological_process -alt_id: GO:0042115 def: "The process in which a precursor cell type acquires the specialized features of a B cell. A B cell is a lymphocyte of B lineage with the phenotype CD19-positive and capable of B cell mediated immunity." [GO_REF:0000022, GOC:mah] comment: Note that immunologists typically use the word 'development' to refer to cells of B or T cell lineages undergoing the process that GO describes as 'cell differentiation'. synonym: "B cell development" RELATED [GOC:add] @@ -5864,8 +6062,6 @@ is_a: GO:0030202 ! heparin metabolic process id: GO:0030217 name: T cell differentiation namespace: biological_process -alt_id: GO:0042112 -alt_id: GO:0046652 def: "The process in which a precursor cell type acquires characteristics of a more mature T-cell. A T cell is a type of lymphocyte whose definin characteristic is the expression of a T cell receptor complex." [GO_REF:0000022, GOC:jid, GOC:mah] comment: Note that the term 'thymocyte differentiation' was merged into this term because thymocytes are T cells, and thus the term was essentially redundant. Note that immunologists typically use the word 'development' to refer to cells of B or T cell lineages undergoing the process that GO describes as 'cell differentiation'. synonym: "T cell development" RELATED [GOC:add] @@ -5944,7 +6140,6 @@ relationship: results_in_acquisition_of_features_of CL:0000235 ! macrophage id: GO:0030261 name: chromosome condensation namespace: biological_process -alt_id: GO:0000068 def: "The progressive compaction of dispersed interphase chromatin into threadlike chromosomes prior to mitotic or meiotic nuclear division, or during apoptosis, in eukaryotic cells." [GOC:mah, ISBN:0815316194] synonym: "DNA condensation" BROAD [Wikipedia:DNA_condensation] synonym: "eukaryotic chromosome condensation" EXACT [GOC:bf] @@ -5980,7 +6175,7 @@ subset: goslim_drosophila subset: goslim_generic subset: goslim_pir subset: goslim_plant -is_a: GO:0110165 ! cellular anatomical entity +is_a: GO:0110165 ! cellular anatomical structure relationship: part_of CL:0000000 ! cell relationship: part_of GO:0071944 ! cell periphery @@ -6049,7 +6244,6 @@ relationship: results_in_acquisition_of_features_of CL:0000094 ! granulocyte id: GO:0031012 name: extracellular matrix namespace: cellular_component -alt_id: GO:0005578 def: "A structure lying external to one or more cells, which provides structural support, biochemical or biomechanical cues for cells or tissues." [GOC:BHF, GOC:mah, GOC:rph, NIF_Subcellular:nlx_subcell_20090513, PMID:21123617, PMID:28089324] subset: goslim_chembl subset: goslim_drosophila @@ -6117,7 +6311,6 @@ relationship: results_in_organization_of GO:0031143 ! pseudopodium id: GO:0031410 name: cytoplasmic vesicle namespace: cellular_component -alt_id: GO:0016023 def: "A vesicle found in the cytoplasm of a cell." [GOC:ai, GOC:mah, GOC:vesicles] subset: goslim_agr subset: goslim_candida @@ -6139,7 +6332,7 @@ id: GO:0031974 name: membrane-enclosed lumen namespace: cellular_component def: "The enclosed volume within a sealed membrane or between two sealed membranes. Encompasses the volume enclosed by the membranes of a particular organelle, e.g. endoplasmic reticulum lumen, or the space between the two lipid bilayers of a double membrane surrounding an organelle, e.g. nuclear envelope lumen." [GOC:add, GOC:mah] -is_a: GO:0110165 ! cellular anatomical entity +is_a: GO:0110165 ! cellular anatomical structure disjoint_from: GO:0045202 ! synapse [Term] @@ -6154,7 +6347,6 @@ relationship: part_of GO:0005634 ! nucleus id: GO:0031982 name: vesicle namespace: cellular_component -alt_id: GO:0031988 def: "Any small, fluid-filled, spherical organelle enclosed by membrane." [GOC:mah, GOC:pz, GOC:vesicles] subset: goslim_pir synonym: "membrane-bounded vesicle" RELATED [] @@ -6222,8 +6414,6 @@ relationship: positively_regulates GO:0009605 ! response to external stimulus id: GO:0032501 name: multicellular organismal process namespace: biological_process -alt_id: GO:0044707 -alt_id: GO:0050874 def: "Any biological process, occurring at the level of a multicellular organism, pertinent to its function." [GOC:curators, GOC:dph, GOC:isa_complete, GOC:tb] comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. subset: gocheck_do_not_annotate @@ -6236,14 +6426,12 @@ property_value: RO:0002161 NCBITaxon:2157 property_value: RO:0002161 NCBITaxon:4896 property_value: RO:0002161 NCBITaxon:4932 property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27189" xsd:anyURI -created_by: jl creation_date: 2012-09-19T16:07:47Z [Term] id: GO:0032502 name: developmental process namespace: biological_process -alt_id: GO:0044767 def: "A biological process whose specific outcome is the progression of an integrated living unit: an anatomical structure (which may be a subcellular structure, cell, tissue, or organ), or organism over time from an initial condition to a later condition." [GOC:isa_complete] subset: goslim_agr subset: goslim_flybase_ribbon @@ -6251,15 +6439,12 @@ subset: goslim_pir synonym: "development" NARROW [] synonym: "single-organism developmental process" RELATED [] is_a: GO:0008150 ! biological_process -created_by: jl creation_date: 2012-12-19T12:21:31Z [Term] id: GO:0032606 name: type I interferon production namespace: biological_process -alt_id: GO:0045351 -alt_id: GO:0072641 def: "The appearance of type I interferon due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. Type I interferons include the interferon-alpha, beta, delta, episilon, zeta, kappa, tau, and omega gene families." [GOC:add, ISBN:0126896631, PMID:15546383, PMID:16681834] comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select one of the 'regulation' children terms. subset: gocheck_do_not_annotate @@ -6283,9 +6468,6 @@ is_a: GO:0140352 ! export from cell id: GO:0032984 name: protein-containing complex disassembly namespace: biological_process -alt_id: GO:0034623 -alt_id: GO:0043241 -alt_id: GO:0043624 def: "The disaggregation of a protein-containing macromolecular complex into its constituent components." [GOC:mah] synonym: "cellular macromolecule complex disassembly" RELATED [] synonym: "cellular protein complex disassembly" RELATED [] @@ -6302,7 +6484,6 @@ property_value: term_tracker_item "https://github.com/geneontology/go-ontology/i id: GO:0032991 name: protein-containing complex namespace: cellular_component -alt_id: GO:0043234 def: "A stable assembly of two or more macromolecules, i.e. proteins, nucleic acids, carbohydrates or lipids, in which at least one component is a protein and the constituent parts function together." [GOC:dos, GOC:mah] comment: A protein complex in this context is meant as a stable set of interacting proteins which can be co-purified by an acceptable method, and where the complex has been shown to exist as an isolated, functional unit in vivo. Acceptable experimental methods include stringent protein purification followed by detection of protein interaction. The following methods should be considered non-acceptable: simple immunoprecipitation, pull-down experiments from cell extracts without further purification, colocalization and 2-hybrid screening. Interactions that should not be captured as protein complexes include: 1) enzyme/substrate, receptor/ligand or any similar transient interactions, unless these are a critical part of the complex assembly or are required e.g. for the receptor to be functional; 2) proteins associated in a pull-down/co-immunoprecipitation assay with no functional link or any evidence that this is a defined biological entity rather than a loose-affinity complex; 3) any complex where the only evidence is based on genetic interaction data; 4) partial complexes, where some subunits (e.g. transmembrane ones) cannot be expressed as recombinant proteins and are excluded from experiments (in this case, independent evidence is necessary to find out the composition of the full complex, if known). Interactions that may be captured as protein complexes include: 1) enzyme/substrate or receptor/ligand if the complex can only assemble and become functional in the presence of both classes of subunits; 2) complexes where one of the members has not been shown to be physically linked to the other(s), but is a homologue of, and has the same functionality as, a protein that has been experimentally demonstrated to form a complex with the other member(s); 3) complexes whose existence is accepted based on localization and pharmacological studies, but for which experimental evidence is not yet available for the complex as a whole. subset: goslim_agr @@ -6317,8 +6498,8 @@ synonym: "protein complex" NARROW [] synonym: "protein containing complex" EXACT [] synonym: "protein-protein complex" NARROW [] is_a: GO:0005575 ! cellular_component -is_a: PR:000050567 ! protein-containing material entity -disjoint_from: GO:0110165 ! cellular anatomical entity +disjoint_from: GO:0110165 ! cellular anatomical structure +relationship: has_part PR:000000001 ! protein [Term] id: GO:0033151 @@ -6362,7 +6543,6 @@ relationship: acts_on_population_of CL:0000232 ! erythrocyte id: GO:0034220 name: monoatomic ion transmembrane transport namespace: biological_process -alt_id: GO:0099131 def: "A process in which a monoatomic ion is transported across a membrane. Monatomic ions (also called simple ions) are ions consisting of exactly one atom." [GOC:mah] comment: Note that this term is not intended for use in annotating lateral movement within membranes. synonym: "ATP hydrolysis coupled ion transmembrane transport" NARROW [] @@ -6415,15 +6595,12 @@ def: "An immunoglobulin-like complex that is present in at least the plasma memb comment: Despite its name, the pre-BCR is not a receptor complex, as it appears to provide a low level of signal not dependent on a ligand, but rather simply on correct assembly of the complex as a measure for correct Ig heavy chain recombination and folding. A significant proportion of pre-BCR complexes fail to reach the cell surface, and in some cases may provide their signaling function from the trans-Golgi network or lysosome. synonym: "pre-BCR" EXACT [] is_a: GO:0098796 ! membrane protein complex -created_by: bf creation_date: 2010-03-11T10:46:10Z [Term] id: GO:0038023 name: signaling receptor activity namespace: molecular_function -alt_id: GO:0004872 -alt_id: GO:0019041 def: "Receiving a signal and transmitting it in the cell to initiate a change in cell activity. A signal is a physical entity or change in state that is used to transfer information in order to trigger a response." [GOC:bf, GOC:signaling] subset: goslim_agr subset: goslim_chembl @@ -6438,14 +6615,12 @@ synonym: "receptor activity" BROAD [] synonym: "receptor activity involved in signal transduction" EXACT [GOC:bf] synonym: "signalling receptor activity" EXACT [] is_a: GO:0060089 ! molecular transducer activity -created_by: bf creation_date: 2011-08-01T02:45:27Z [Term] id: GO:0040007 name: growth namespace: biological_process -alt_id: GO:0048590 def: "The increase in size or mass of an entire organism, a part of an organism or a cell." [GOC:bf, GOC:ma] comment: See also the biological process term 'cell growth ; GO:0016049'. subset: gocheck_do_not_annotate @@ -6656,9 +6831,6 @@ property_value: term_tracker_item "https://github.com/geneontology/go-ontology/i id: GO:0042592 name: homeostatic process namespace: biological_process -alt_id: GO:0032844 -alt_id: GO:0032845 -alt_id: GO:0032846 def: "Any biological process involved in the maintenance of an internal steady state." [GOC:jl, ISBN:0395825172] subset: goslim_agr subset: goslim_chembl @@ -6701,7 +6873,7 @@ subset: goslim_prokaryote_ribbon synonym: "cell process" BROAD [] synonym: "cellular process" BROAD [] synonym: "cellular projection" EXACT [] -is_a: GO:0110165 ! cellular anatomical entity +is_a: GO:0110165 ! cellular anatomical structure relationship: part_of CL:0000000 ! cell [Term] @@ -6730,9 +6902,6 @@ relationship: results_in_acquisition_of_features_of CL:0000782 ! myeloid dendrit id: GO:0043170 name: macromolecule metabolic process namespace: biological_process -alt_id: GO:0034960 -alt_id: GO:0043283 -alt_id: GO:0044259 def: "The chemical reactions and pathways involving macromolecules, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass." [GOC:mah] subset: gocheck_do_not_annotate subset: goslim_pir @@ -6763,7 +6932,7 @@ subset: goslim_prokaryote subset: goslim_prokaryote_ribbon xref: NIF_Subcellular:sao1539965131 xref: Wikipedia:Organelle -is_a: GO:0110165 ! cellular anatomical entity +is_a: GO:0110165 ! cellular anatomical structure [Term] id: GO:0043227 @@ -6776,23 +6945,26 @@ xref: NIF_Subcellular:sao414196390 is_a: GO:0043226 ! organelle intersection_of: GO:0043226 ! organelle intersection_of: has_part GO:0016020 ! membrane -disjoint_from: GO:0043228 ! non-membrane-bounded organelle +disjoint_from: GO:0043228 ! membraneless organelle relationship: has_part GO:0016020 ! membrane property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28153" xsd:anyURI [Term] id: GO:0043228 -name: non-membrane-bounded organelle +name: membraneless organelle namespace: cellular_component def: "Organized structure of distinctive morphology and function, not bounded by a lipid bilayer membrane. Includes ribosomes, the cytoskeleton and chromosomes." [GOC:go_curators] subset: gocheck_do_not_annotate subset: goslim_mouse synonym: "biological condensate" RELATED [] +synonym: "membrane-less organelle" EXACT [] +synonym: "non-membrane-bounded organelle" EXACT [] synonym: "non-membrane-enclosed organelle" EXACT [] xref: NIF_Subcellular:sao1456184038 is_a: GO:0043226 ! organelle property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/21881" xsd:anyURI property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28153" xsd:anyURI +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29106" xsd:anyURI [Term] id: GO:0043229 @@ -6833,15 +7005,17 @@ intersection_of: part_of GO:0005622 ! intracellular anatomical structure [Term] id: GO:0043232 -name: intracellular non-membrane-bounded organelle +name: intracellular membraneless organelle namespace: cellular_component def: "Organized structure of distinctive morphology and function, not bounded by a lipid bilayer membrane and occurring within the cell. Includes ribosomes, the cytoskeleton and chromosomes." [GOC:go_curators] subset: goslim_pir +synonym: "intracellular non-membrane-bounded organelle" EXACT [] synonym: "intracellular non-membrane-enclosed organelle" EXACT [] -is_a: GO:0043228 ! non-membrane-bounded organelle +is_a: GO:0043228 ! membraneless organelle is_a: GO:0043229 ! intracellular organelle -intersection_of: GO:0043228 ! non-membrane-bounded organelle +intersection_of: GO:0043228 ! membraneless organelle intersection_of: part_of GO:0005622 ! intracellular anatomical structure +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29106" xsd:anyURI [Term] id: GO:0043233 @@ -6869,9 +7043,6 @@ relationship: capable_of GO:0038023 ! signaling receptor activity id: GO:0043933 name: protein-containing complex organization namespace: biological_process -alt_id: GO:0034600 -alt_id: GO:0034621 -alt_id: GO:0071822 def: "Any process in which macromolecules aggregate, disaggregate, or are modified, resulting in the formation, disassembly, or alteration of a protein complex." [GOC:mah] synonym: "cellular macromolecular complex organization" RELATED [] synonym: "cellular macromolecular complex subunit organisation" RELATED [] @@ -6887,14 +7058,12 @@ intersection_of: GO:0016043 ! cellular component organization intersection_of: results_in_organization_of GO:0032991 ! protein-containing complex relationship: results_in_organization_of GO:0032991 ! protein-containing complex property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/22580" xsd:anyURI -created_by: mah creation_date: 2010-09-08T10:01:42Z [Term] id: GO:0044085 name: cellular component biogenesis namespace: biological_process -alt_id: GO:0071843 def: "A process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of a cellular component. Includes biosynthesis of constituent macromolecules, and those macromolecular modifications that are involved in synthesis or assembly of the cellular component." [GOC:jl, GOC:mah] subset: gocheck_do_not_annotate subset: goslim_pir @@ -6911,21 +7080,8 @@ synonym: "Met-tRNA/eIF2.GTP ternary complex" NARROW [] synonym: "translation initiation (ternary) complex" EXACT [] is_a: GO:1990904 ! ribonucleoprotein complex relationship: part_of GO:0005737 ! cytoplasm -created_by: jl creation_date: 2009-10-22T02:38:55Z -[Term] -id: GO:0044237 -name: cellular metabolic process -namespace: biological_process -def: "The chemical reactions and pathways by which individual cells transform chemical substances." [GOC:go_curators] -comment: This term should not be used for direct annotation. It should be possible to make a more specific annotation to one of the children of this term. -subset: gocheck_do_not_annotate -synonym: "cellular metabolism" EXACT [] -synonym: "intermediary metabolism" RELATED [GOC:mah] -is_a: GO:0008152 ! metabolic process -is_a: GO:0009987 ! cellular process - [Term] id: GO:0044238 name: primary metabolic process @@ -6941,21 +7097,6 @@ xref: Wikipedia:Primary_metabolite is_a: GO:0008152 ! metabolic process property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/26424" xsd:anyURI -[Term] -id: GO:0044249 -name: cellular biosynthetic process -namespace: biological_process -def: "The chemical reactions and pathways resulting in the formation of substances, carried out by individual cells." [GOC:jl] -comment: This term should not be used for direct annotation. It should be possible to make a more specific annotation to one of the children of this term. -subset: gocheck_do_not_annotate -synonym: "cellular anabolism" EXACT [] -synonym: "cellular biosynthesis" EXACT [] -synonym: "cellular formation" EXACT [] -synonym: "cellular synthesis" EXACT [] -is_a: GO:0009058 ! biosynthetic process -is_a: GO:0044237 ! cellular metabolic process -property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27052" xsd:anyURI - [Term] id: GO:0044419 name: biological process involved in interspecies interaction between organisms @@ -6976,7 +7117,6 @@ property_value: term_tracker_item "https://github.com/geneontology/go-ontology/i id: GO:0045026 name: plasma membrane fusion namespace: biological_process -alt_id: GO:0006947 def: "The joining of the lipid bilayer membrane that surround a cell with that of another cell, producing a single cell." [GOC:elh, GOC:mtg_muscle] synonym: "cell fusion" BROAD [] synonym: "cell-cell fusion" BROAD [] @@ -7003,7 +7143,6 @@ relationship: part_of GO:0030217 ! T cell differentiation id: GO:0045087 name: innate immune response namespace: biological_process -alt_id: GO:0002226 def: "Innate immune responses are defense responses mediated by germline encoded components that directly recognize components of potential pathogens." [GO_REF:0000022, GOC:add, GOC:ebc, GOC:mtg_sensu] synonym: "innate immunity" EXACT [GOC:pg] synonym: "nonspecific immune response" EXACT [] @@ -7216,7 +7355,6 @@ property_value: term_tracker_item "https://github.com/geneontology/go-ontology/i id: GO:0048518 name: positive regulation of biological process namespace: biological_process -alt_id: GO:0043119 def: "Any process that activates or increases the frequency, rate or extent of a biological process. Biological processes are regulated by many means; examples include the control of gene expression, protein modification or interaction with a protein or substrate molecule." [GOC:jid] subset: gocheck_do_not_annotate synonym: "activation of biological process" NARROW [] @@ -7234,7 +7372,6 @@ relationship: positively_regulates GO:0008150 ! biological_process id: GO:0048519 name: negative regulation of biological process namespace: biological_process -alt_id: GO:0043118 def: "Any process that stops, prevents, or reduces the frequency, rate or extent of a biological process. Biological processes are regulated by many means; examples include the control of gene expression, protein modification or interaction with a protein or substrate molecule." [GOC:jid] subset: gocheck_do_not_annotate synonym: "down regulation of biological process" EXACT [] @@ -7251,7 +7388,6 @@ relationship: negatively_regulates GO:0008150 ! biological_process id: GO:0048522 name: positive regulation of cellular process namespace: biological_process -alt_id: GO:0051242 def: "Any process that activates or increases the frequency, rate or extent of a cellular process, any of those that are carried out at the cellular level, but are not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level." [GOC:jid] subset: gocheck_do_not_annotate synonym: "activation of cellular process" NARROW [] @@ -7327,7 +7463,6 @@ relationship: part_of GO:0032502 ! developmental process id: GO:0048598 name: embryonic morphogenesis namespace: biological_process -alt_id: GO:0048828 def: "The process in which anatomical structures are generated and organized during the embryonic phase. The embryonic phase begins with zygote formation. The end of the embryonic phase is organism-specific. For example, it would be at birth for mammals, larval hatching for insects and seed dormancy in plants." [GOC:jid, GOC:mtg_sensu] synonym: "embryonic anatomical structure morphogenesis" EXACT [GOC:dph, GOC:tb] is_a: GO:0009653 ! anatomical structure morphogenesis @@ -7495,7 +7630,6 @@ relationship: positively_regulates GO:0006955 ! immune response id: GO:0050789 name: regulation of biological process namespace: biological_process -alt_id: GO:0050791 def: "Any process that modulates the frequency, rate or extent of a biological process. Biological processes are regulated by many means; examples include the control of gene expression, protein modification or interaction with a protein or substrate molecule." [GOC:ai, GOC:go_curators] subset: gocheck_do_not_annotate subset: goslim_candida @@ -7520,7 +7654,6 @@ relationship: regulates GO:0032502 ! developmental process id: GO:0050794 name: regulation of cellular process namespace: biological_process -alt_id: GO:0051244 def: "Any process that modulates the frequency, rate or extent of a cellular process, any of those that are carried out at the cellular level, but are not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level." [GOC:go_curators] subset: gocheck_do_not_annotate synonym: "regulation of cellular physiological process" EXACT [] @@ -7595,7 +7728,6 @@ subset: goslim_pir id: GO:0050896 name: response to stimulus namespace: biological_process -alt_id: GO:0051869 def: "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus. The process begins with detection of the stimulus and ends with a change in state or activity or the cell or organism." [GOC:ai, GOC:bf] comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. subset: gocheck_do_not_annotate @@ -7658,7 +7790,6 @@ relationship: positively_regulates GO:0006935 ! chemotaxis id: GO:0051179 name: localization namespace: biological_process -alt_id: GO:1902578 def: "Any process in which a cell, a substance, or a cellular entity, such as a protein complex or organelle, is transported, tethered to or otherwise maintained in a specific location. In the case of substances, localization may also be achieved via selective degradation." [GOC:ai, GOC:dos] subset: gocheck_do_not_annotate subset: goslim_pir @@ -7672,7 +7803,6 @@ synonym: "single organism localization" RELATED [GOC:TermGenie] synonym: "single-organism localization" RELATED [] is_a: GO:0008150 ! biological_process property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27052" xsd:anyURI -created_by: jl creation_date: 2013-12-18T13:51:04Z [Term] @@ -7729,9 +7859,6 @@ relationship: regulates GO:0046649 ! lymphocyte activation id: GO:0051276 name: chromosome organization namespace: biological_process -alt_id: GO:0006323 -alt_id: GO:0007001 -alt_id: GO:0051277 def: "A process that is carried out at the cellular level that results in the assembly, arrangement of constituent parts, or disassembly of chromosomes, structures composed of a very long molecule of DNA and associated proteins that carries hereditary information. This term covers covalent modifications at the molecular level as well as spatial relationships among the major components of a chromosome." [GOC:ai, GOC:dph, GOC:jl, GOC:mah] subset: goslim_chembl subset: goslim_drosophila @@ -7772,8 +7899,6 @@ is_a: GO:0006810 ! transport id: GO:0051707 name: response to other organism namespace: biological_process -alt_id: GO:0009613 -alt_id: GO:0042828 def: "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus from another living organism." [GOC:ai] is_a: GO:0043207 ! response to external biotic stimulus is_a: GO:0044419 ! biological process involved in interspecies interaction between organisms @@ -7792,7 +7917,6 @@ is_a: GO:0050896 ! response to stimulus id: GO:0055085 name: transmembrane transport namespace: biological_process -alt_id: GO:0090662 def: "The process in which a solute is transported across a lipid bilayer, from one side of a membrane to the other." [GOC:dph, GOC:jid] comment: Transmembrane transport is the transport of a solute across a lipid bilayer. Note that transport through the nuclear pore complex is not transmembrane because the nuclear membrane is a double membrane and is not traversed. For transport through the nuclear pore, consider instead the term 'nucleocytoplasmic transport ; GO:0006913' and its children. Note also that this term is not intended for use in annotating lateral movement within membranes. subset: goslim_chembl @@ -7808,7 +7932,6 @@ is_a: GO:0009987 ! cellular process intersection_of: GO:0006810 ! transport intersection_of: results_in_transport_across GO:0016020 ! membrane relationship: results_in_transport_across GO:0016020 ! membrane -created_by: tb creation_date: 2015-10-21T13:22:47Z [Term] @@ -7883,15 +8006,12 @@ is_a: GO:0035239 ! tube morphogenesis intersection_of: GO:0009653 ! anatomical structure morphogenesis intersection_of: results_in_morphogenesis_of UBERON:0003914 ! epithelial tube relationship: results_in_morphogenesis_of UBERON:0003914 ! epithelial tube -created_by: dph creation_date: 2009-04-28T09:33:36Z [Term] id: GO:0061024 name: membrane organization namespace: biological_process -alt_id: GO:0016044 -alt_id: GO:0044802 def: "A process which results in the assembly, arrangement of constituent parts, or disassembly of a membrane. A membrane is a double layer of lipid molecules that encloses all cells, and, in eukaryotes, many organelles; may be a single or double lipid bilayer; also includes associated proteins." [GOC:dph, GOC:tb] subset: goslim_chembl subset: goslim_drosophila @@ -7908,15 +8028,12 @@ is_a: GO:0016043 ! cellular component organization intersection_of: GO:0016043 ! cellular component organization intersection_of: results_in_organization_of GO:0016020 ! membrane relationship: results_in_organization_of GO:0016020 ! membrane -created_by: jl creation_date: 2010-02-08T02:43:11Z [Term] id: GO:0061025 name: membrane fusion namespace: biological_process -alt_id: GO:0006944 -alt_id: GO:0044801 def: "The membrane organization process that joins two lipid bilayers to form a single membrane." [GOC:dph, GOC:tb] subset: goslim_yeast synonym: "cellular membrane fusion" EXACT [] @@ -7926,7 +8043,6 @@ is_a: GO:0061024 ! membrane organization intersection_of: GO:0061024 ! membrane organization intersection_of: results_in_fusion_of GO:0016020 ! membrane relationship: results_in_fusion_of GO:0016020 ! membrane -created_by: jl creation_date: 2010-02-08T02:48:06Z [Term] @@ -7936,7 +8052,6 @@ namespace: biological_process def: "The process in which the anatomical structures of a branched epithelium are generated and organized." [GOC:dph] is_a: GO:0001763 ! morphogenesis of a branching structure is_a: GO:0002009 ! morphogenesis of an epithelium -created_by: dph creation_date: 2010-05-25T09:05:34Z [Term] @@ -7947,16 +8062,12 @@ def: "An extracellular matrix consisting mainly of proteins (especially collagen is_a: GO:0031012 ! extracellular matrix relationship: RO:0002160 NCBITaxon:33208 ! only in taxon Metazoa relationship: RO:0002162 NCBITaxon:33208 {all_only="true"} ! in taxon Metazoa -created_by: dph creation_date: 2018-04-13T12:47:21Z [Term] id: GO:0065003 name: protein-containing complex assembly namespace: biological_process -alt_id: GO:0006461 -alt_id: GO:0034622 -alt_id: GO:0043623 def: "The aggregation, arrangement and bonding together of a set of macromolecules to form a protein-containing complex." [GOC:jl] subset: goslim_chembl subset: goslim_drosophila @@ -8050,7 +8161,6 @@ comment: Note that this term is in the subset of terms that should not be used f subset: gocheck_do_not_annotate is_a: GO:0042221 ! response to chemical is_a: GO:0051716 ! cellular response to stimulus -created_by: mah creation_date: 2009-08-27T04:41:45Z [Term] @@ -8064,7 +8174,6 @@ is_a: GO:0022607 ! cellular component assembly intersection_of: GO:0022607 ! cellular component assembly intersection_of: results_in_assembly_of GO:0043226 ! organelle relationship: results_in_assembly_of GO:0043226 ! organelle -created_by: mah creation_date: 2009-09-15T03:00:51Z [Term] @@ -8076,7 +8185,6 @@ synonym: "immunoglobulin V(D)J joining" BROAD [GOC:add] synonym: "immunoglobulin V(D)J recombination" BROAD [GOC:add] synonym: "immunoglobulin V-D-J joining" EXACT [GOC:add] is_a: GO:0033152 ! immunoglobulin V(D)J recombination -created_by: mah creation_date: 2010-03-09T04:20:31Z [Term] @@ -8088,7 +8196,6 @@ synonym: "immunoglobulin V(D)J joining" BROAD [GOC:add] synonym: "immunoglobulin V(D)J recombination" BROAD [GOC:add] synonym: "immunoglobulin V-J joining" EXACT [GOC:add] is_a: GO:0033152 ! immunoglobulin V(D)J recombination -created_by: mah creation_date: 2010-03-09T04:22:29Z [Term] @@ -8098,7 +8205,6 @@ namespace: cellular_component def: "A protein complex composed of two identical immunoglobulin heavy chains of the IgD isotype and two identical immunoglobulin light chains, held together by disulfide bonds. An IgD immunoglobulin complex may be embedded in the plasma membrane or present in the extracellular space, in mucosal areas or other tissues, or circulating in the blood or lymph." [GOC:add, ISBN:0781765196, PMID:11282392] comment: Note that an IgD immunoglobulin complex has the function of antigen binding if a suitable antigen is available. is_a: GO:0019814 ! immunoglobulin complex -created_by: mah creation_date: 2010-03-24T01:44:53Z [Term] @@ -8108,7 +8214,6 @@ namespace: cellular_component def: "A protein complex composed of two identical immunoglobulin heavy chains of the IgM isotype and two identical immunoglobulin light chains, held together by disulfide bonds, and in its circulating form complexed with J chain in polymeric forms. An IgM immunoglobulin complex may be embedded in the plasma membrane or present in the extracellular space, in mucosal areas or other tissues, or circulating in the blood or lymph." [GOC:add, ISBN:0781765196, PMID:20176268] comment: Note that an IgM immunoglobulin complex has the function of antigen binding if a suitable antigen is available. is_a: GO:0019814 ! immunoglobulin complex -created_by: mah creation_date: 2010-03-24T01:44:53Z [Term] @@ -8125,14 +8230,12 @@ intersection_of: GO:0016043 ! cellular component organization intersection_of: results_in_organization_of GO:1990904 ! ribonucleoprotein complex relationship: results_in_organization_of GO:1990904 ! ribonucleoprotein complex property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/25143" xsd:anyURI -created_by: mah creation_date: 2010-09-08T10:10:35Z [Term] id: GO:0071840 name: cellular component organization or biogenesis namespace: biological_process -alt_id: GO:0071841 def: "A process that results in the biosynthesis of constituent macromolecules, assembly, arrangement of constituent parts, or disassembly of a cellular component." [GOC:mah] comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. subset: gocheck_do_not_annotate @@ -8143,7 +8246,6 @@ synonym: "cellular component organisation or biogenesis at cellular level" EXACT synonym: "cellular component organization or biogenesis at cellular level" EXACT [] is_a: GO:0009987 ! cellular process property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27189" xsd:anyURI -created_by: mah creation_date: 2010-09-10T01:39:16Z [Term] @@ -8152,8 +8254,7 @@ name: cell periphery namespace: cellular_component def: "The broad region around and including the plasma membrane of a cell, encompassing the cell cortex (inside the cell), the plasma membrane, and any external encapsulating structures." [GOC:pdt] subset: goslim_flybase_ribbon -is_a: GO:0110165 ! cellular anatomical entity -created_by: mah +is_a: GO:0110165 ! cellular anatomical structure creation_date: 2010-10-04T01:51:47Z [Term] @@ -8168,7 +8269,6 @@ intersection_of: GO:0022607 ! cellular component assembly intersection_of: results_in_assembly_of GO:0070062 ! extracellular exosome relationship: part_of GO:0097734 ! extracellular exosome biogenesis relationship: results_in_assembly_of GO:0070062 ! extracellular exosome -created_by: mah creation_date: 2010-10-18T03:44:18Z [Term] @@ -8182,7 +8282,6 @@ intersection_of: results_in_formation_of UBERON:0003914 ! epithelial tube relationship: part_of GO:0060562 ! epithelial tube morphogenesis relationship: results_in_formation_of UBERON:0003914 ! epithelial tube property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/22302" xsd:anyURI -created_by: mah creation_date: 2010-02-26T02:15:40Z [Term] @@ -8195,7 +8294,6 @@ is_a: GO:0061025 ! membrane fusion intersection_of: GO:0061025 ! membrane fusion intersection_of: results_in_fusion_of GO:0031090 ! organelle membrane relationship: results_in_fusion_of GO:0031090 ! organelle membrane -created_by: tb creation_date: 2009-12-11T11:44:58Z [Term] @@ -8208,21 +8306,18 @@ is_a: GO:1903131 ! mononuclear cell differentiation intersection_of: GO:0030154 ! cell differentiation intersection_of: results_in_acquisition_of_features_of CL:0000451 ! dendritic cell relationship: results_in_acquisition_of_features_of CL:0000451 ! dendritic cell -created_by: pr creation_date: 2011-04-01T10:08:42Z [Term] id: GO:0097190 name: apoptotic signaling pathway namespace: biological_process -alt_id: GO:0008624 def: "The series of molecular signals which triggers the apoptotic death of a cell. The pathway starts with reception of a signal, and ends when the execution phase of apoptosis is triggered." [GOC:mtg_apoptosis] comment: This term can be used to annotate gene products involved in apoptotic events happening downstream of the cross-talk point between the extrinsic and intrinsic apoptotic pathways. The cross-talk starts when caspase-8 cleaves Bid and truncated Bid interacts with mitochondria. From this point on it is not possible to distinguish between extrinsic and intrinsic pathways. synonym: "apoptotic signalling pathway" EXACT [GOC:mah] synonym: "induction of apoptosis by extracellular signals" EXACT [] is_a: GO:0007165 ! signal transduction relationship: part_of GO:0006915 ! apoptotic process -created_by: pr creation_date: 2011-11-23T09:30:23Z [Term] @@ -8235,7 +8330,6 @@ synonym: "execution phase of apoptotic process" EXACT [] is_a: GO:0009987 ! cellular process relationship: has_part GO:0032060 ! bleb assembly relationship: part_of GO:0006915 ! apoptotic process -created_by: pr creation_date: 2011-11-23T09:45:24Z [Term] @@ -8247,7 +8341,6 @@ is_a: GO:0031982 ! vesicle is_a: GO:0043231 ! intracellular membrane-bounded organelle intersection_of: GO:0031982 ! vesicle intersection_of: part_of GO:0005622 ! intracellular anatomical structure -created_by: pr creation_date: 2016-03-29T17:39:45Z [Term] @@ -8261,14 +8354,12 @@ synonym: "exosome production" EXACT [] synonym: "ILV assembly" RELATED [] synonym: "intraluminal vesicle assembly" RELATED [] is_a: GO:0140112 ! extracellular vesicle biogenesis -created_by: pr creation_date: 2016-10-03T14:35:25Z [Term] id: GO:0098542 name: defense response to other organism namespace: biological_process -alt_id: GO:0009814 def: "Reactions triggered in response to the presence of another organism that act to protect the cell or organism from damage caused by that organism." [GOC:dos] subset: goslim_generic subset: goslim_prokaryote @@ -8278,7 +8369,6 @@ synonym: "defense response, incompatible interaction" NARROW [] synonym: "resistance response to pathogen" NARROW [] is_a: GO:0051707 ! response to other organism property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/22173" xsd:anyURI -created_by: dos creation_date: 2013-11-11T12:59:11Z [Term] @@ -8293,7 +8383,6 @@ is_a: GO:0016020 ! membrane intersection_of: GO:0016020 ! membrane intersection_of: part_of GO:0005886 ! plasma membrane relationship: part_of GO:0005886 ! plasma membrane -created_by: dos creation_date: 2014-03-06T11:55:32Z [Term] @@ -8314,7 +8403,6 @@ def: "A complex of collagen trimers such as a fibril or collagen network." [GOC: synonym: "Supramolecular aggregate of collagen" EXACT [PMID:19693541] synonym: "Supramolecular collagen assembly" EXACT [PMID:21421911] is_a: GO:0099080 ! supramolecular complex -is_a: PR:000050567 ! protein-containing material entity relationship: has_part GO:0005581 ! collagen trimer relationship: part_of GO:0062023 ! collagen-containing extracellular matrix @@ -8353,7 +8441,7 @@ namespace: cellular_component def: "The part of a synapse that is part of the presynaptic cell." [GOC:dos] subset: goslim_synapse synonym: "presynaptic terminal" EXACT [] -is_a: GO:0110165 ! cellular anatomical entity +is_a: GO:0110165 ! cellular anatomical structure relationship: part_of CL:0000540 ! neuron relationship: part_of GO:0045202 ! synapse @@ -8363,7 +8451,7 @@ name: postsynapse namespace: cellular_component def: "The part of a synapse that is part of the post-synaptic cell." [GOC:dos] subset: goslim_synapse -is_a: GO:0110165 ! cellular anatomical entity +is_a: GO:0110165 ! cellular anatomical structure relationship: part_of CL:0000000 ! cell relationship: part_of GO:0045202 ! synapse @@ -8418,7 +8506,7 @@ id: GO:0099080 name: supramolecular complex namespace: cellular_component def: "A cellular component that consists of an indeterminate number of proteins or macromolecular complexes, organized into a regular, higher-order structure such as a polymer, sheet, network or a fiber." [GOC:dos] -is_a: GO:0110165 ! cellular anatomical entity +is_a: GO:0110165 ! cellular anatomical structure [Term] id: GO:0099081 @@ -8478,16 +8566,17 @@ is_a: GO:0099536 ! synaptic signaling [Term] id: GO:0110165 -name: cellular anatomical entity +name: cellular anatomical structure namespace: cellular_component -def: "A part of a cellular organism that is either an immaterial entity or a material entity with granularity above the level of a protein complex but below that of an anatomical system. Or, a substance produced by a cellular organism with granularity above the level of a protein complex." [GOC:kmv] +def: "A part of a cellular organism consisting of a material entity with granularity above the level of a protein complex but below that of an anatomical system. Note that cellular organisms exclude viruses." [GOC:kmv] subset: gocheck_do_not_annotate subset: goslim_pir +synonym: "cellular anatomical entity" EXACT [] is_a: GO:0005575 ! cellular_component is_a: UBERON:0000061 ! anatomical structure property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/24200" xsd:anyURI property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/26424" xsd:anyURI -created_by: kmv +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28978" xsd:anyURI creation_date: 2019-08-12T18:01:37Z [Term] @@ -8500,7 +8589,6 @@ intersection_of: GO:0042995 ! cell projection intersection_of: has_part GO:0098590 ! plasma membrane region relationship: has_part GO:0098590 ! plasma membrane region property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/13193" xsd:anyURI -created_by: krc creation_date: 2017-03-21T17:26:07Z [Term] @@ -8515,7 +8603,6 @@ intersection_of: GO:0022607 ! cellular component assembly intersection_of: results_in_assembly_of GO:0120025 ! plasma membrane bounded cell projection relationship: results_in_assembly_of GO:0120025 ! plasma membrane bounded cell projection property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/13298" xsd:anyURI -created_by: krc creation_date: 2017-04-24T23:56:08Z [Term] @@ -8528,7 +8615,6 @@ intersection_of: GO:0016043 ! cellular component organization intersection_of: results_in_organization_of GO:0120025 ! plasma membrane bounded cell projection relationship: results_in_organization_of GO:0120025 ! plasma membrane bounded cell projection property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/13298" xsd:anyURI -created_by: krc creation_date: 2017-04-26T16:07:02Z [Term] @@ -8544,7 +8630,6 @@ is_a: GO:1903047 ! mitotic cell cycle process intersection_of: GO:0000280 ! nuclear division intersection_of: part_of GO:0000278 ! mitotic cell cycle property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/19910" xsd:anyURI -created_by: pg creation_date: 2017-03-23T14:44:23Z [Term] @@ -8557,7 +8642,6 @@ is_a: GO:0009987 ! cellular process intersection_of: GO:0009987 ! cellular process intersection_of: part_of GO:0006887 ! exocytosis relationship: part_of GO:0006887 ! exocytosis -created_by: pg creation_date: 2017-05-15T13:20:45Z [Term] @@ -8568,7 +8652,6 @@ def: "The assembly and secretion a set of components to form an extracellular ve synonym: "extracellular vesicle assembly" EXACT [] is_a: GO:0044085 ! cellular component biogenesis property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/14256" xsd:anyURI -created_by: pg creation_date: 2017-10-23T11:53:42Z [Term] @@ -8581,7 +8664,6 @@ synonym: "cell fusion" BROAD [] is_a: GO:0009987 ! cellular process relationship: has_part GO:0045026 ! plasma membrane fusion property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/15939" xsd:anyURI -created_by: pg creation_date: 2018-08-13T18:38:18Z [Term] @@ -8597,7 +8679,6 @@ intersection_of: has_target_end_location GO:0005576 ! extracellular region intersection_of: has_target_start_location GO:0005622 ! intracellular anatomical structure relationship: has_target_end_location GO:0005576 ! extracellular region relationship: has_target_start_location GO:0005622 ! intracellular anatomical structure -created_by: pg creation_date: 2019-05-22T11:20:45Z [Term] @@ -8607,7 +8688,6 @@ namespace: biological_process def: "Reactions triggered in response to the presence of a symbiont that act to protect or prevent damage to the host." [GOC:pg] is_a: GO:0098542 ! defense response to other organism property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/20261" xsd:anyURI -created_by: pg creation_date: 2020-11-11T17:19:06Z [Term] @@ -8621,7 +8701,6 @@ is_a: GO:1903706 ! regulation of hemopoiesis intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0002521 ! leukocyte differentiation relationship: regulates GO:0002521 ! leukocyte differentiation -created_by: pr creation_date: 2013-05-02T17:32:42Z [Term] @@ -8634,7 +8713,6 @@ is_a: GO:0022402 ! cell cycle process intersection_of: GO:0009987 ! cellular process intersection_of: part_of GO:0000278 ! mitotic cell cycle relationship: part_of GO:0000278 ! mitotic cell cycle -created_by: jl creation_date: 2014-05-22T14:22:34Z [Term] @@ -8646,7 +8724,6 @@ is_a: GO:0002521 ! leukocyte differentiation intersection_of: GO:0030154 ! cell differentiation intersection_of: results_in_acquisition_of_features_of CL:0000842 ! mononuclear cell relationship: results_in_acquisition_of_features_of CL:0000842 ! mononuclear cell -created_by: cls creation_date: 2014-06-25T15:47:09Z [Term] @@ -8659,7 +8736,6 @@ is_a: GO:0031982 ! vesicle is_a: GO:0065010 ! extracellular membrane-bounded organelle intersection_of: GO:0031982 ! vesicle intersection_of: part_of GO:0005576 ! extracellular region -created_by: jl creation_date: 2014-10-22T14:26:11Z [Term] @@ -8678,15 +8754,12 @@ is_a: GO:2000026 ! regulation of multicellular organismal development intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0030097 ! hemopoiesis relationship: regulates GO:0030097 ! hemopoiesis -created_by: pad creation_date: 2014-12-04T15:34:13Z [Term] id: GO:1990904 name: ribonucleoprotein complex namespace: cellular_component -alt_id: GO:0030529 -alt_id: GO:1990903 def: "A macromolecular complex that contains both RNA and protein molecules." [GOC:krc, GOC:vesicles] subset: goslim_pir synonym: "extracellular ribonucleoprotein complex" NARROW [] @@ -8696,7 +8769,6 @@ synonym: "RNA-protein complex" EXACT [] synonym: "RNP" EXACT [] xref: Wikipedia:Ribonucleoprotein is_a: GO:0032991 ! protein-containing complex -created_by: pr creation_date: 2015-11-19T12:26:37Z [Term] @@ -8709,7 +8781,6 @@ is_a: GO:0051239 ! regulation of multicellular organismal process intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0007275 ! multicellular organism development relationship: regulates GO:0007275 ! multicellular organism development -created_by: tb creation_date: 2010-08-05T11:25:59Z [Term] @@ -8725,7 +8796,6 @@ is_a: GO:0050794 ! regulation of cellular process intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0048870 ! cell motility relationship: regulates GO:0048870 ! cell motility -created_by: mah creation_date: 2010-10-01T09:41:21Z [Term] @@ -8742,7 +8812,6 @@ is_a: GO:2000145 ! regulation of cell motility intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0048870 ! cell motility relationship: positively_regulates GO:0048870 ! cell motility -created_by: mah creation_date: 2010-10-01T09:41:30Z [Term] @@ -8776,7 +8845,6 @@ is_a: NCBITaxon:39107 ! Murinae id: NCBITaxon:10090 name: Mus musculus namespace: ncbi_taxonomy -alt_id: NCBITaxon:85055 synonym: "house mouse" EXACT genbank_common_name [] synonym: "mouse" EXACT OMO:0003003 [] xref: GC_ID:1 @@ -8793,7 +8861,6 @@ is_a: NCBITaxon:7776 ! Gnathostomata id: NCBITaxon:117571 name: Euteleostomi namespace: ncbi_taxonomy -alt_id: NCBITaxon:40673 synonym: "bony vertebrates" EXACT genbank_common_name [] xref: GC_ID:1 is_a: NCBITaxon:117570 ! Teleostomi @@ -8942,7 +9009,6 @@ is_a: NCBITaxon:1963758 ! Myomorpha id: NCBITaxon:39107 name: Murinae namespace: ncbi_taxonomy -alt_id: NCBITaxon:109679 xref: GC_ID:1 is_a: NCBITaxon:10066 ! Muridae @@ -9038,7 +9104,6 @@ is_a: NCBITaxon:314147 ! Glires id: PATO:0000001 name: quality namespace: quality -alt_id: PATO:0000072 def: "A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities" [PATOC:GVG] [Term] @@ -9053,7 +9118,6 @@ is_a: PATO:0001241 ! physical object quality id: PATO:0000052 name: shape namespace: quality -alt_id: PATO:0001647 def: "A morphological quality inhering in a bearer by virtue of the bearer's ratios of distances between its features (points, edges, surfaces and also holes etc)." [PATOC:GVG] comment: Shapes are invariant on size transformations. Shapes can be subdivided into 2D and 3D shapes, We can also make a distinction between shapes of complete self-connected objects, and shapes of parts of objects. subset: attribute_slim @@ -9064,7 +9128,6 @@ is_a: PATO:0000051 ! morphology id: PATO:0000141 name: structure namespace: quality -alt_id: PATO:0001452 def: "A morphology quality inhering in a bearer by virtue of the bearer's relative position, shape, arrangements and connectivity of an organism's various parts; the pattern underlying its form." [PATOC:GVG] subset: attribute_slim synonym: "conformation" BROAD [VT:1000738] @@ -9122,7 +9185,6 @@ is_a: PATO:0002318 ! superelliptic id: PATO:0001018 name: physical quality namespace: quality -alt_id: PATO:0002079 def: "A quality of a physical entity that exists through action of continuants at the physical level of organisation in relation to other entities." [PATOC:GVG] subset: attribute_slim synonym: "relational physical quality" EXACT [] @@ -9133,8 +9195,6 @@ is_a: PATO:0001241 ! physical object quality id: PATO:0001241 name: physical object quality namespace: quality -alt_id: PATO:0001237 -alt_id: PATO:0001238 def: "A quality which inheres in a continuant." [PATOC:GVG] comment: Relational qualities are qualities that hold between multiple entities. Normal (monadic) qualities such as the shape of a eyeball exist purely as a quality of that eyeball. A relational quality such as sensitivity to light is a quality of that eyeball (and connecting nervous system) as it relates to incoming light waves/particles. synonym: "monadic quality of a continuant" EXACT [] @@ -9292,7 +9352,6 @@ is_a: PATO:0002005 ! concavity id: PATO:0001873 name: cylindrical namespace: quality -alt_id: PATO:0001203 def: "A convex 3-D shape quality inhering in a bearer by virtue of the bearer's exhibiting a consistently-sized round cross section." [PATOC:MAH] subset: cell_quality subset: value_slim @@ -9527,7 +9586,6 @@ def: "A quality inhering in a cell by virtue of the cell having a high nuclear/c comment: A high nuclear/cytolasmic ratio is 70% or higher. synonym: "high N:C ratio" EXACT [] is_a: PATO:0001396 ! cellular quality -created_by: http://orcid.org/0000-0001-5208-3432 [Term] id: PATO:0070044 @@ -9535,7 +9593,6 @@ name: anatomical structure quality namespace: quality def: "A quality of continuant that exist at the anatomical level of organisation and anything under it. This includes, but is not limited to, cells , tissues, and components." [] is_a: PATO:0001241 ! physical object quality -created_by: http://orcid.org/0000-0001-7258-9596 [Term] id: PATO:0070045 @@ -9543,7 +9600,6 @@ name: anatomical histological quality namespace: quality def: "A quality inhering in an anotomical structure by virtue of its capacity to be stained by specific histological dyes." [] is_a: PATO:0070044 ! anatomical structure quality -created_by: http://orcid.org/0000-0001-7258-9596 [Term] id: PATO:0070046 @@ -9551,7 +9607,6 @@ name: neutrophillic namespace: quality def: "An affinity inhering in an anatomical structure by virtue of the bearer exhibiting a molecular interaction that stains and colors, pale-pink, with Wright-Giemsa stain." [GOC:add] is_a: PATO:0070045 ! anatomical histological quality -created_by: http://orcid.org/0000-0001-7258-9596 [Term] id: PATO:0070047 @@ -9559,18 +9614,17 @@ name: polychromatophilic namespace: quality def: "An affinity inhering in an anatomical structure by virtue of the bearer exhibiting a molecular interaction for both basic and acid stains under specific pH conditions." [GOC:add] is_a: PATO:0070045 ! anatomical histological quality -created_by: http://orcid.org/0000-0001-7258-9596 [Term] id: PR:000000001 name: protein namespace: protein def: "An amino acid chain that is produced de novo by ribosome-mediated translation of a genetically-encoded mRNA, and any derivatives thereof." [PRO:DAN, PRO:WCB] -comment: The definition above excludes protein complexes, which some also consider a protein. Those who wish to refer to a class representing both senses of the word are directed to CHEBI:36080. Note that the definition allows for experimentally-manipulated genes, and allows for artifically-produced derivatives that mimic those found naturally. Proteins (in the sense defined here) that descended from a common ancestor can be classified into families and superfamilies composed of products of evolutionarily-related genes. The domain architecture of a protein is described by the order of its constituent domains. Proteins with the same domains in the same order are defined as homeomorphic [PRO:WCB]. +comment: The definition above excludes protein complexes, which some also consider a protein. Those who wish to refer to a class representing both senses of the word are directed to CHEBI:36080. Note that the definition allows for experimentally-manipulated genes, and allows for artifically-produced derivatives that mimic those found naturally. Proteins (in the sense defined here) that descended from a common ancestor can be classified into families and superfamilies composed of products of evolutionarily-related genes. The domain architecture of a protein is described by the order of its constituent domains. Proteins with the same domains in the same order are defined as homeomorphic [PRO:WCB). synonym: "native protein" NARROW [IEDB:BP] synonym: "natural protein" EXACT [PRO:DAN] is_a: PR:000018263 ! amino acid chain -is_a: PR:000050567 ! protein-containing material entity +is_a: PR:000064867 ! protein-containing molecular entity relationship: output_of GO:0006412 ! translation [Term] @@ -10358,7 +10412,6 @@ namespace: protein def: "A protein with core architecture consisting of a signal sequence, followed by 7 Ig-like domains (Pfam:PF00047, Pfam:PF07679, or Pfam:PF07686), a transmembrane region, and a cytoplasmic Protein tyrosine kinase domain." [PRO:WCB] comment: Category=family. xref: PIRSF:PIRSF038502 -is_a: PR:000000001 ! protein [Term] id: PR:000002062 @@ -10746,11 +10799,11 @@ is_a: PR:000036194 ! eukaryotic protein relationship: RO:0002160 NCBITaxon:33208 ! only in taxon Metazoa [Term] -id: PR:000050567 -name: protein-containing material entity +id: PR:000064867 +name: protein-containing molecular entity namespace: protein -def: "A material entity that minimally consists of a protein." [PRO:DAN] -comment: Note: This includes single proteins and derivatives thereof (PR:000000001), protein-containing complexes (GO:0032991), and protein aggregates (PR:000050566). +def: "A molecular entity that minimally consists of a protein." [PRO:DAN] +comment: Note: This includes single proteins and derivatives thereof (PR:000000001), protein-containing complexes (GO:0032991), and protein aggregates (PR:000050565). synonym: "protein" NARROW [PRO:DAN] synonym: "protein aggregate" NARROW [PRO:DAN] synonym: "protein complex" NARROW [PRO:DAN] @@ -10800,7 +10853,6 @@ property_value: RO:0002175 NCBITaxon:9606 id: UBERON:0000060 name: anatomical wall namespace: uberon -alt_id: UBERON:0009915 def: "Organ component adjacent to an organ cavity and which consists of a maximal aggregate of organ component layers." [FMA:82482] subset: upper_level synonym: "organ wall" RELATED [FMA:82482] @@ -10968,7 +11020,6 @@ property_value: RO:0002175 NCBITaxon:4751 id: UBERON:0000075 name: subdivision of skeletal system namespace: uberon -alt_id: UBERON:0010322 def: "Anatomical cluster consisting of the skeletal elements and articular elements that are part of an individual subdivision of the organism." [https://orcid.org/0000-0002-6601-2165, UBERONREF:0000003] subset: non_informative synonym: "skeletal system part" RELATED [] @@ -11297,7 +11348,7 @@ xref: VHOG:0000224 xref: Wikipedia:Blood xref: XAO:0000124 xref: ZFA:0000007 -is_a: PR:000050567 ! protein-containing material entity +is_a: UBERON:0000061 ! anatomical structure is_a: UBERON:0000179 ! haemolymphatic fluid relationship: has_part CL:0000232 {source="CL:tm"} ! erythrocyte relationship: has_part UBERON:0001969 ! blood plasma @@ -11326,7 +11377,6 @@ creation_date: 2009-04-08T04:38:19Z id: UBERON:0000307 name: blastula namespace: uberon -alt_id: UBERON:0007011 def: "Organism at the blastula stage - an early stage of embryonic development in animals. It is produced by cleavage of a fertilized ovum and consists of a spherical layer of around 128 cells surrounding a central fluid-filled cavity called the blastocoel. The blastula follows the morula and precedes the gastrula in the developmental sequence." [Wikipedia:Blastula] subset: inconsistent_with_fma synonym: "blastosphere" RELATED [Wikipedia:Blastula] @@ -11790,7 +11840,6 @@ xref: VHOG:0000387 xref: Wikipedia:Epithelium xref: XAO:0003045 xref: ZFA:0001486 -is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0000479 ! tissue intersection_of: UBERON:0000479 ! tissue intersection_of: RO:0002473 CL:0000066 ! composed primarily of epithelial cell @@ -12035,7 +12084,6 @@ property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/d/ id: UBERON:0000926 name: mesoderm namespace: uberon -alt_id: UBERON:0003263 def: "The middle germ layer of the embryo, between the endoderm and ectoderm." [Wikipedia:Mesoderm] subset: efo_slim subset: pheno_slim @@ -12263,7 +12311,6 @@ id: UBERON:0001009 name: circulatory system namespace: uberon def: "Organ system that passes nutrients (such as amino acids and electrolytes), gases, hormones, blood cells, etc. to and from cells in the body to help fight diseases and help stabilize body temperature and pH to maintain homeostasis[WP]." [Wikipedia:Circulatory_system] -subset: human_reference_atlas subset: uberon_slim synonym: "systema cardiovasculare" RELATED OMO:0003011 [Wikipedia:Circulatory_system] xref: AAO:0000959 @@ -12283,7 +12330,6 @@ property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/2/ property_value: RO:0002161 NCBITaxon:147099 {source="Wikipedia:Acoelomorpha"} property_value: RO:0002161 NCBITaxon:6073 property_value: RO:0002161 NCBITaxon:6157 -property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001015 @@ -12703,7 +12749,6 @@ xref: MIAA:0000052 xref: NCIT:C13356 xref: UMLS:C0032105 {source="ncithesaurus:Plasma"} xref: Wikipedia:Blood_plasma -is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0000179 ! haemolymphatic fluid intersection_of: UBERON:0000463 ! organism substance intersection_of: has_part GO:0005577 ! fibrinogen complex @@ -12752,7 +12797,6 @@ xref: VHOG:0001250 xref: Wikipedia:Blood_vessel xref: XAO:0001011 xref: ZFA:0005314 -is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0000055 ! vessel is_a: UBERON:0004120 ! mesoderm-derived structure relationship: capable_of_part_of GO:0008015 ! blood circulation @@ -13033,7 +13077,6 @@ property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/e/ id: UBERON:0002323 name: coelemic cavity lumen namespace: uberon -alt_id: UBERON:0000169 def: "The cavity within the body of all animals higher than the coelenterates and certain primitive worms, formed by the splitting of the embryonic mesoderm into two layers. In mammals it forms the peritoneal, pleural, and pericardial cavities." [BTO:0001707] comment: EDITOR_NOTE check the FMA placement here; ncit placement of body cavity here probably not correct subset: uberon_slim @@ -13059,7 +13102,6 @@ xref: RETIRED_EHDAA2:0003186 xref: SCTID:361348008 xref: TAO:0001438 xref: UMLS:C0333343 {source="ncithesaurus:Cavity"} -xref: ZFA:0001438 is_a: UBERON:0002553 ! anatomical cavity relationship: RO:0002494 UBERON:0003886 ! transformation of future coelemic cavity lumen relationship: RO:0002572 UBERON:0011997 ! luminal space of coelom @@ -13515,6 +13557,7 @@ xref: TAO:0000279 xref: VHOG:0000559 xref: XAO:0000057 xref: ZFA:0000279 +is_a: UBERON:0000061 ! anatomical structure is_a: UBERON:0006598 ! presumptive structure intersection_of: UBERON:0005423 ! developing anatomical structure intersection_of: RO:0002387 UBERON:0002329 ! has potential to develop into somite @@ -13645,7 +13688,6 @@ property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/6/ id: UBERON:0003081 name: lateral plate mesoderm namespace: uberon -alt_id: UBERON:0006258 def: "Portion of the middle of the three primary germ layers of the embryo that resides on the periphery of the embryo, is continuous with the extra-embryonic mesoderm, splits into two layers enclosing the intra-embryonic coelom, and gives rise to body wall structures[MP]." [MP:0010117, Wikipedia:Lateral_plate_mesoderm] subset: pheno_slim subset: uberon_slim @@ -14035,7 +14077,6 @@ xref: WikipediaCategory:Cardiovascular_system xref: XAO:0000100 xref: XAO:0001010 xref: ZFA:0000010 -is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0000467 ! anatomical system intersection_of: UBERON:0000467 ! anatomical system intersection_of: has_part UBERON:0000948 ! heart @@ -14059,7 +14100,6 @@ synonym: "blood vessels" RELATED [TAO:0001079] synonym: "set of blood vessels" EXACT [] xref: TAO:0001079 xref: ZFA:0001079 -is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0002049 ! vasculature intersection_of: UBERON:0002049 ! vasculature intersection_of: RO:0002473 UBERON:0001981 ! composed primarily of blood vessel @@ -14116,7 +14156,6 @@ property_value: IAO:0000116 "EHDAA2 places this as a subtype of organism. This l id: UBERON:0004734 name: gastrula namespace: uberon -alt_id: UBERON:0007012 def: "Organism at the gastrula stage." [Wikipedia:Gastrula, Wikipedia:Trilaminar_blastocyst] subset: pheno_slim synonym: "blastocystis trilaminaris" RELATED [https://orcid.org/0000-0002-6601-2165] @@ -14533,7 +14572,6 @@ xref: NCIT:C13191 xref: SCTID:68989006 xref: UMLS:C0004799 {source="ncithesaurus:Basement_Membrane"} xref: Wikipedia:Basement_membrane -is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0005764 {source="FMA"} ! acellular membrane relationship: adjacent_to CL:0000066 ! epithelial cell relationship: has_part GO:0005587 ! collagen type IV trimer @@ -14752,7 +14790,6 @@ subset: efo_slim xref: EFO:0003709 xref: TAO:0005077 xref: ZFA:0005077 -is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0005423 ! developing anatomical structure relationship: has_part CL:0000115 ! endothelial cell relationship: has_part CL:0000566 ! angioblastic mesenchymal cell @@ -15007,7 +15044,6 @@ property_value: RO:0002175 NCBITaxon:9606 id: UBERON:0009142 name: entire embryonic mesenchyme namespace: uberon -alt_id: UBERON:0003313 def: "Sum total of mesenchyme in the embryo." [https://github.com/obophenotype/human-developmental-anatomy-ontology/issues/7] xref: EHDAA2:0001113 xref: EHDAA:177 @@ -15096,7 +15132,6 @@ synonym: "thrombus" EXACT [BTO:0000102] xref: BTO:0000102 xref: galen:BloodClot xref: Wikipedia:Thrombus -is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0000463 ! organism substance intersection_of: UBERON:0000463 ! organism substance intersection_of: output_of GO:0007596 ! blood coagulation @@ -15245,6 +15280,7 @@ synonym: "haemocoelom" NARROW [] synonym: "schizocoelom" NARROW [] xref: EHDAA2:0004731 xref: Wikipedia:Coelom +xref: ZFA:0001438 is_a: UBERON:0000481 {source="EHDAA2"} ! multi-tissue structure relationship: RO:0002162 NCBITaxon:33213 ! in taxon Bilateria property_value: IAO:0000116 "EHDAA2 distingsuishes between the lumen, the lining, and the 'coelomic cavity', which despire it's name, is not a space - it is the aggregate of space plus lining." xsd:string @@ -15422,7 +15458,6 @@ is_a: UBERON:0000479 {source="FMA"} ! tissue id: UBERON:0016879 name: future central nervous system namespace: uberon -alt_id: UBERON:3000469 def: "Primordium that develops into the central nervous system." [http://orcid.org/0000-0002-6601-2165] synonym: "future CNS" EXACT [] synonym: "presumptive central nervous system" EXACT [] @@ -15437,7 +15472,6 @@ relationship: RO:0002387 UBERON:0001017 ! has potential to develop into central id: UBERON:0016880 name: future nervous system namespace: uberon -alt_id: UBERON:3000477 def: "Primordium that develops into the nervous system." [http://orcid.org/0000-0002-6601-2165] synonym: "presumptive nervous system" EXACT [AAO:0000477] xref: AAO:0000477 @@ -15649,7 +15683,6 @@ id: RO:0002021 name: occurs across def: "A relationship between a process and a barrier, where the process occurs in a region spanning the barrier. For cellular processes the barrier is typically a membrane. Examples include transport across a membrane and membrane depolarization." [] is_a: RO:0002479 ! has part that occurs in -created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-07-20T17:19:37Z [Typedef] @@ -16505,7 +16538,6 @@ name: causally upstream of or within, negative effect property_value: RO:0004050 RO:0002418 property_value: seeAlso "https://wiki.geneontology.org/Causally_upstream_of_or_within,_negative_effect" xsd:anyURI is_a: causally_upstream_of_or_within ! causally upstream of or within -created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-03-13T23:55:05Z [Typedef] @@ -16513,7 +16545,6 @@ id: RO:0004047 name: causally upstream of or within, positive effect property_value: seeAlso https://wiki.geneontology.org/Causally_upstream_of_or_within,_positive_effect is_a: causally_upstream_of_or_within ! causally upstream of or within -created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-03-13T23:55:19Z [Typedef] @@ -16522,7 +16553,6 @@ name: has small molecule regulator def: "a relation between a process and a continuant, in which the process is regulated by the small molecule continuant" [] is_a: has_participant ! has participant inverse_of: RO:0012004 ! is small molecule regulator of -created_by: https://orcid.org/0000-0003-1813-6857 creation_date: 2020-04-22T20:27:26Z [Typedef] @@ -16530,7 +16560,6 @@ id: RO:0012004 name: is small molecule regulator of def: "a relation between a continuant and a process, in which the continuant is a small molecule that regulates the process" [] is_a: RO:0002596 ! capable of regulating -created_by: https://orcid.org/0000-0003-1813-6857 creation_date: 2020-06-24T13:15:17Z [Typedef] @@ -16540,7 +16569,6 @@ def: "a relation between a continuant and a process, in which the continuant is property_value: seeAlso "https://wiki.geneontology.org/Is_small_molecule_activator_of" xsd:anyURI is_a: RO:0002598 ! capable of positively regulating is_a: RO:0012004 ! is small molecule regulator of -created_by: https://orcid.org/0000-0003-1813-6857 creation_date: 2020-06-24T13:15:26Z [Typedef] @@ -16550,7 +16578,6 @@ def: "A relationship between a neuron and a region, where the neuron has a funct synonym: "has synaptic input or output in" EXACT [] is_a: RO:0002130 ! has synaptic terminal in transitive_over: part_of ! part of -created_by: https://orcid.org/0000-0002-1373-1705 creation_date: 2020-07-17T09:26:52Z [Typedef] @@ -16562,9 +16589,18 @@ synonym: "has sensory terminal in" EXACT [] synonym: "has sensory terminal location" EXACT [] is_a: RO:0002360 ! has dendrite location transitive_over: part_of ! part of -created_by: https://orcid.org/0000-0002-1373-1705 creation_date: 2020-07-20T12:10:09Z +[Typedef] +id: RO:0015004 +name: has characterizing marker set +def: "A relation that applies between a cell type and a set of markers that can be used to uniquely identify that cell type." [] +synonym: "has marker gene combination" EXACT [] +synonym: "has marker signature set" EXACT [] +property_value: IAO:0000116 "C has_characterizing_marker_set y iff: C is a cell type and y is a collection of genes or proteins whose expression is sufficient to distinguish cell type C from most or all other cell types." xsd:string +property_value: terms:contributor https://orcid.org/0000-0001-7258-9596 +domain: CL:0000000 ! cell + [Typedef] id: RO:0015006 name: different in magnitude relative to @@ -16638,7 +16674,6 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0012003 is_a: has_participant ! has participant -created_by: https://orcid.org/0000-0003-1813-6857 creation_date: 2020-06-08T17:21:33Z [Typedef] @@ -16934,7 +16969,6 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_ontology xref: RO:0004009 is_a: has_input ! has input is_a: has_primary_input_or_output ! has primary input or output -created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-12-13T11:26:56Z [Typedef] @@ -16945,7 +16979,6 @@ def: "p 'has primary input ot output' c iff either (a) p 'has primary input' c o subset: http://purl.obolibrary.org/obo/valid_for_go_ontology xref: RO:0004007 is_a: has_participant ! has participant -created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-12-13T11:26:17Z [Typedef] @@ -16957,7 +16990,6 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_ontology xref: RO:0004008 is_a: has_output ! has output is_a: has_primary_input_or_output ! has primary input or output -created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-12-13T11:26:32Z [Typedef] @@ -16968,7 +17000,6 @@ def: "a relation between a process and a continuant, in which the process is act xref: RO:0012001 is_a: RO:0012000 ! has small molecule regulator inverse_of: RO:0012005 ! is small molecule activator of -created_by: https://orcid.org/0000-0003-1813-6857 creation_date: 2020-04-22T20:28:37Z [Typedef] @@ -17293,7 +17324,6 @@ namespace: external def: "p has anatomical participant c iff p has participant c, and c is an anatomical entity" [] xref: RO:0040036 is_a: has_participant ! has participant -created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-09-26T01:08:58Z [Typedef] @@ -17365,7 +17395,6 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0012008 is_a: results_in_organization_of ! results in organization of -created_by: https://orcid.org/0000-0003-1813-6857 creation_date: 2021-02-26T07:28:29Z [Typedef] @@ -17417,7 +17446,6 @@ name: results in organization of namespace: external def: "p results in organization of c iff p results in the assembly, arrangement of constituent parts, or disassembly of c" [] xref: RO:0002592 -is_a: has_participant ! has participant is_a: results_in_changes_to_anatomical_or_cellular_structure ! results in changes to anatomical or cellular structure [Typedef] diff --git a/subsets/blood_and_immune_upper_slim.owl b/subsets/blood_and_immune_upper_slim.owl index 0fa546cf7..03661de11 100644 --- a/subsets/blood_and_immune_upper_slim.owl +++ b/subsets/blood_and_immune_upper_slim.owl @@ -22,8 +22,8 @@ xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#" xmlns:ncbitaxon="http://purl.obolibrary.org/obo/ncbitaxon#"> - - 2024-09-26 + + 2025-01-08 @@ -287,13 +287,18 @@ WHERE { - 2018-03-14T00:03:24Z is negative form of + + + + + + @@ -373,6 +378,14 @@ WHERE { + + + + + + + + @@ -384,6 +397,14 @@ WHERE { + + + + + + + + @@ -1010,12 +1031,6 @@ WHERE { - - - - - - @@ -1034,6 +1049,12 @@ WHERE { + + + + + + @@ -1048,19 +1069,25 @@ WHERE { - + + description + - + + license + - + + title + @@ -1088,26 +1115,12 @@ WHERE { - - - - - - - - - - has_alternative_id - - - - @@ -1123,7 +1136,11 @@ WHERE { + An annotation property that links an ontology entity or a statement to a prefixed identifier or URI. + + database_cross_reference + has cross-reference @@ -1206,12 +1223,6 @@ WHERE { - - - - - - @@ -1681,7 +1692,6 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 A relationship between a process and a barrier, where the process occurs in a region spanning the barrier. For cellular processes the barrier is typically a membrane. Examples include transport across a membrane and membrane depolarization. - 2017-07-20T17:19:37Z occurs across @@ -3966,7 +3976,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different - p results in organization of c iff p results in the assembly, arrangement of constituent parts, or disassembly of c RO:0002592 @@ -4088,7 +4097,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different p 'has primary input ot output' c iff either (a) p 'has primary input' c or (b) p 'has primary output' c. - 2018-12-13T11:26:17Z RO:0004007 external @@ -4106,7 +4114,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different p has primary output c if (a) p has output c and (b) the goal of process is to modify, produce, or transform c. - 2018-12-13T11:26:32Z RO:0004008 external @@ -4134,7 +4141,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different p has primary input c if (a) p has input c and (b) the goal of process is to modify, consume, or transform c. - 2018-12-13T11:26:56Z RO:0004009 external @@ -4161,7 +4167,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different - 2018-03-13T23:55:05Z causally upstream of or within, negative effect https://wiki.geneontology.org/Causally_upstream_of_or_within,_negative_effect @@ -4173,7 +4178,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different - 2018-03-13T23:55:19Z causally upstream of or within, positive effect @@ -4187,7 +4191,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different a relation between a process and a continuant, in which the process is regulated by the small molecule continuant - 2020-04-22T20:27:26Z has small molecule regulator @@ -4200,7 +4203,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different a relation between a process and a continuant, in which the process is activated by the small molecule continuant - 2020-04-22T20:28:37Z RO:0012001 external @@ -4217,7 +4219,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different p acts on population of c iff c' is a collection, has members of type c, and p has participant c - 2020-06-08T17:21:33Z RO:0012003 external @@ -4237,7 +4238,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different a relation between a continuant and a process, in which the continuant is a small molecule that regulates the process - 2020-06-24T13:15:17Z is small molecule regulator of @@ -4250,7 +4250,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different a relation between a continuant and a process, in which the continuant is a small molecule that activates the process - 2020-06-24T13:15:26Z is small molecule activator of https://wiki.geneontology.org/Is_small_molecule_activator_of @@ -4262,7 +4261,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different - 2021-02-26T07:28:29Z RO:0012008 external @@ -4286,7 +4284,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different A relationship between a neuron and a region, where the neuron has a functionally relevant number of input and/or output synapses in that region. - 2020-07-17T09:26:52Z has synaptic input or output in has synaptic IO in region @@ -4303,7 +4300,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different Relation between a sensory neuron and some structure in which it receives sensory input via a sensory dendrite. - 2020-07-20T12:10:09Z has sensory dendrite location has sensory terminal in @@ -4313,6 +4309,20 @@ Each of these 3 primitives can be composed to yield a cross-product of different + + + + + A relation that applies between a cell type and a set of markers that can be used to uniquely identify that cell type. + C has_characterizing_marker_set y iff: C is a cell type and y is a collection of genes or proteins whose expression is sufficient to distinguish cell type C from most or all other cell types. + + has marker gene combination + has marker signature set + has characterizing marker set + + + + @@ -4452,7 +4462,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different p has anatomical participant c iff p has participant c, and c is an anatomical entity - 2018-09-26T01:08:58Z RO:0040036 external @@ -4796,6 +4805,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different XAO:0003012 ZFA:0009000 + + The definition of cell is intended to represent all cells, and thus a cell is defined as a material entity and not an anatomical structure, which implies that it is part of an organism (or the entirety of one). cell @@ -4827,6 +4838,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different A cell found in the embryo before the formation of all the gem layers is complete. ZFA:0009002 + + early embryonic cell (metazoa) @@ -4880,6 +4893,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different animal stem cell + + This term applies to metazoan. For plant stem cells, consider using PO:0004011 ‘initial cell’ or its parent PO:0004010 ‘meristematic cell’. stem cell @@ -5067,6 +5082,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different colony forming unit hematopoietic + + Markers differ between species, and two sets of markers have been described for mice. HSCs are reportedly CD34-positive, CD45-positive, CD48-negative, CD150-positive, CD133-positive, and CD244-negative. hematopoietic stem cell @@ -5118,6 +5135,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different erythroid stem cell + + erythroid progenitor cell @@ -5186,7 +5205,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different - @@ -5225,6 +5243,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different colony forming unit macrophage colony forming unit monocyte monocyte stem cell + + Morphology: mononuclear cell, diameter 12-20 _M, non-granular, N/C ratio 3/1 - 4/1; markers: CD11b (shared with many other myeloid cells); location: Adult: bone marrow; fetal: liver, Yolk Sac; role or process: hematopoiesis, monocyte development; lineage: hematopoietic, myeloid. monoblast @@ -5290,6 +5310,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different multifate stem cell multipotent cell multipotent stem cell + + multi fate stem cell @@ -5327,6 +5349,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different myeloid stem cell pluripotent stem cell (bone marrow) + + This cell type is intended to be compatible with any vertebrate common myeloid progenitor. For mammalian CMP known to be CD34-positive, please use the term 'common myeloid progenitor, CD34-positive' (CL_0001059). common myeloid progenitor @@ -5445,6 +5469,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different megakaryocyte/erythrocyte progenitor megakaryocyte/erythroid progenitor cell + + MEPs are reportedly CD19-negative, CD34-negative, CD45RA-negative, CD110-positive, CD117-positive, and SCA1-negative and reportedly express the transcription factors GATA-1 and NF-E2. megakaryocyte-erythroid progenitor cell @@ -5510,6 +5536,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different lymphoid stem cell lymphopoietic stem cell + + CLP are CD7-positive, CD10-positive, CD19-negative, CD34-positive, CD45RA-positive, CD79a-negative, CD127-positive, AA4.1-positive, RAG-negative, Sca-1-low, sIgM-negative, sIgD-negative, TdT-negative, Vpre-B-negative, and pre-BCR-negative. Expression of transcription factors include E2A-positive, EBF-positive, Ikaros-negative, PU.1-negative, and Pax5-negative. common lymphoid progenitor @@ -5560,6 +5588,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different MESH:D039901 ZFA:0009024 totipotential stem cell + + totipotent stem cell @@ -5587,6 +5617,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different FMA:84782 blast cell + + define using PATO mulit-potent or oligopotent? non-terminally differentiated cell @@ -5610,6 +5642,9 @@ Each of these 3 primitives can be composed to yield a cross-product of different FMA:70335 VHOG:0001529 ZFA:0009025 + + + myoblast @@ -5638,13 +5673,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - - - - - - + A connective tissue cell which secretes an extracellular matrix rich in collagen and other macromolecules. Flattened and irregular in outline with branching processes; appear fusiform or spindle-shaped. BTO:0000452 @@ -5655,6 +5684,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different ZFA:0009026 + + These cells may be vimentin-positive, fibronectin-positive, fsp1-positive, MMP-1-positive, collagen I-positive, collagen III-positive, and alpha-SMA-negative. fibroblast @@ -5699,6 +5730,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different epitheliocyte + + epithelial cell https://www.swissbiopics.org/api/image/Epithelial_cells.svg @@ -5751,6 +5784,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different ZFA:0009036 + + blood vessel endothelial cell @@ -5794,6 +5829,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different CALOHA:TS-1249 ZFA:0009039 + + squamous epithelial cell @@ -5834,6 +5871,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different A cell which moves among different tissues of the body, via blood, lymph, or other medium. ZFA:0009043 + + circulating cell @@ -5878,6 +5917,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different ZFA:0009044 + + blood cell @@ -5945,6 +5986,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different mature T cell + + T cell @@ -6020,7 +6063,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different - @@ -6076,13 +6118,20 @@ Each of these 3 primitives can be composed to yield a cross-product of different A specialized phagocytic cell associated with the absorption and removal of the mineralized matrix of bone tissue, which typically differentiates from monocytes. This cell has the following markers: tartrate-resistant acid phosphatase type 5-positive, PU.1-positive, c-fos-positive, nuclear factor NF-kappa-B p100 subunit-positive, tumor necrosis factor receptor superfamily member 11A-positive and macrophage colony-stimulating factor 1 receptor-positive. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Osteoclasts, derived from the monocyte/macrophage lineage, play a crucial role in bone remodeling through bone resorption. They are distinguished from other cells by their large size and their unique ability to secrete enzymes and acids that dissolve the calcium phosphate in bone. The formation of osteoclasts is influenced by two primary factors: macrophage colony-stimulating factor (M-CSF) and the ligand-activated receptor (RANKL) of nuclear factor kappa B (NF-κB). +Osteoclasts also collaborate with osteoblasts, responsible for new bone formation, to maintain bone health and adapt bone structure. Their coordinated actions allow continuous remodeling while preserving overall bone strength and integrity. Imbalances in osteoclast activity can lead to pathological conditions. For example, excessive activity may contribute to diseases like osteoporosis, periprosthetic osteolysis, bone tumors, and Paget's disease. Other the other hand, osteoclast deficiency ca result in conditions like osteopetrosis. BTO:0000968 CALOHA:TS-0721 FMA:66781 MESH:D010010 ZFA:0009047 + https://cellxgene.cziscience.com/cellguide/CL_0000092 chondroclast + + Morphology: Highly vesicular; markers: Surface: RANK, cFMS (MCSF receptor); Secreted: cathepsin K and TRAP (tartate resistant acid phosphatase); transcription factors: PU.1, cFOS, MITF, NFkB (p52); role or process: tissue remodelling: bone resorption; lineage: hematopoietic, myeloid. osteoclast @@ -6110,6 +6159,17 @@ Each of these 3 primitives can be composed to yield a cross-product of different PMID:15055519 PMID:17380158 + + + + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Osteoclasts, derived from the monocyte/macrophage lineage, play a crucial role in bone remodeling through bone resorption. They are distinguished from other cells by their large size and their unique ability to secrete enzymes and acids that dissolve the calcium phosphate in bone. The formation of osteoclasts is influenced by two primary factors: macrophage colony-stimulating factor (M-CSF) and the ligand-activated receptor (RANKL) of nuclear factor kappa B (NF-κB). +Osteoclasts also collaborate with osteoblasts, responsible for new bone formation, to maintain bone health and adapt bone structure. Their coordinated actions allow continuous remodeling while preserving overall bone strength and integrity. Imbalances in osteoclast activity can lead to pathological conditions. For example, excessive activity may contribute to diseases like osteoporosis, periprosthetic osteolysis, bone tumors, and Paget's disease. Other the other hand, osteoclast deficiency ca result in conditions like osteopetrosis. + DOI:10.3389/fmed.2017.00234 + DOI:10.37175/stemedicine.v1i4.57 + https://www.sciencedirect.com/topics/medicine-and-dentistry/osteoclast + @@ -6167,7 +6227,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different - @@ -6227,6 +6286,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different granular leukocyte polymorphonuclear leukocyte + + granulocyte @@ -6314,7 +6375,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different - @@ -6404,6 +6464,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different tissue basophil + + Mast cells are generally integrin beta-7-negative and positive for TLR2, TLR3, TLR4, TLR5, TLR7, TLR9, C3aR, C5aR, CR3, CR4, VEGF, FGF2, and renin. They can express MHC Class I and II on their surface. Activated murine mast cells (IgE+Antigen) were capable of expressing the following co-stimulatory molecules: CD95 (Fas), CD120b, CD137 (4-1BB), CD153 (CD30L), CD154 (CD40L), GITR, ICOSL, OX40L, PD-L1, and PD-L2. Note that there was some mouse strain variation. Mast cells have also been demonstrated to produce bFGF, CCL2, CCL4, CCL5, CCL11, CCL20, CXCL2, CXCL8, CXCL10, GM-CSF, IFN-gamma, IL-1, IL-2, IL-3, IL-8, IL-10, IL-11, IL-12, IL-13, IL-16, IL-25, IL-18, MIP-1, prostaglandin D2, SCF, TGF-beta, TNF-alpha, TSLP, VEGF, and XCL1. They express the transcription factors Transcription factors AP-1, GATA1, MITF, Notch2, PIAS3, PU.1, and STAT5. mast cell @@ -6470,7 +6532,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different A vertebrate phagocyte with a single nucleus. - This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. Mononuclear phagocytes are immune cells that form a critical part of the body's innate immune system, the body's first line of defense against infections. Mononuclear phagocytes are characterized by the presence of a single, large nucleus. The ‘Mononuclear Phagocyte System’ nomenclature was introduced to distinguish mononuclear monocytes and macrophages from other cells with multiple nuclei. However, the cells within the mononuclear phagocyte system represent a highly heterogeneous group, all of which are able to perform highly efficient phagocytosis - engulfing and digesting microbes and cellular debris to fight infections and to maintain normal tissue homeostasis. In addition to phagocytosis, mononuclear phagocytes also secrete chemical compounds to recruit other immune cells to a site of infection. These cells produce different types of signaling molecules, including cytokines, chemokines, and reactive oxygen species, triggering a cascade of responses to ensure rapid and efficient containment and neutralization of invading pathogens. These cells are also involved in antigen presentation, a process essential for stimulating an adaptive immune response. They can process and present antigens to T cells, thereby linking the innate and adaptive immune responses. @@ -6479,6 +6541,8 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf ZFA:0009064 https://cellxgene.cziscience.com/cellguide/CL_0000113 + + mononuclear phagocyte @@ -6499,7 +6563,7 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf - This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. Mononuclear phagocytes are immune cells that form a critical part of the body's innate immune system, the body's first line of defense against infections. Mononuclear phagocytes are characterized by the presence of a single, large nucleus. The ‘Mononuclear Phagocyte System’ nomenclature was introduced to distinguish mononuclear monocytes and macrophages from other cells with multiple nuclei. However, the cells within the mononuclear phagocyte system represent a highly heterogeneous group, all of which are able to perform highly efficient phagocytosis - engulfing and digesting microbes and cellular debris to fight infections and to maintain normal tissue homeostasis. In addition to phagocytosis, mononuclear phagocytes also secrete chemical compounds to recruit other immune cells to a site of infection. These cells produce different types of signaling molecules, including cytokines, chemokines, and reactive oxygen species, triggering a cascade of responses to ensure rapid and efficient containment and neutralization of invading pathogens. These cells are also involved in antigen presentation, a process essential for stimulating an adaptive immune response. They can process and present antigens to T cells, thereby linking the innate and adaptive immune responses. @@ -6536,6 +6600,8 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf ZFA:0009065 endotheliocyte + + From FMA: 9.07.2001: Endothelial cell has always been classified as a kind of epithelial cell, specifically a squamous cell but that is not true. First, endothelial cell can either be squamous or cuboidal (e.g. high-endothelial cell) and secondly, it has different embryological derivation (mesodermal) than a true epithelial cell (ectodermal and endodermal). The basis for present classification is the fact that it comprises the outermost layer or lining of anatomical structures (location-based) but a better structural basis for the differentia is the cytoskeleton of the cell. Endothelial cell has vimentin filaments while an epithelial cell has keratin filaments. [Onard]. endothelial cell @@ -6566,6 +6632,8 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf Ectoderm destined to be nervous tissue. ZFA:0009080 neurectoderm cell + + neurectodermal cell @@ -6607,6 +6675,8 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf mesenchymal stromal cells stem cells, mesenchymal + + Many but not all mesenchymal cells derive from the mesoderm. MSCs are reportedly CD3-negative, CD4-negative, CD5-negative, CD8-negative, CD11a-negative, CD11b-negative, CD14-negative, CD19-negative, CD29-positive, CD31-negative, CD34-negative, CD38-negative, CD40-negative, CD44-positive, CD45-negative, CD49-positive, CD54-positive, CD66b-negative, CD79a-negative, CD80-negative, CD102-positive, CD106-positive, CD117-positive, CD121a-positive, CD121b-positive, CD123-positive, CD124-positive, CD133-negative, CD146-positive, CD166-positive, CD271-positive, B220-negative, Gr1-negative, MHCI-positive, MHCII-negative, SSEA4-negative, sca1-positive, Ter119-negative, and glycophorin A-negative. Cultured MSCs are capable of producing stem cell factor, IL7, IL8, IL11, TGF-beta, cofilin, galectin-1, laminin-receptor 1, cyclophilin A, and MMP-2. mesenchymal stem cell https://github.com/obophenotype/cell-ontology/issues/474 @@ -6711,6 +6781,8 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf APC + + Note change of name; nearly all somatic cells can present antigens to T cells via MHC Class I complexes leading to effector responses, but professional antigen presenting cells constitutively express MHC Class II as well as costimulatory molecules, and thus can initiate immune responses via T cells. professional antigen presenting cell @@ -6761,6 +6833,8 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf BTO:0003659 FMA:86916 + + secretory cell @@ -6779,6 +6853,8 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf A cell whose primary function is to shorten. + + contractile cell @@ -6813,6 +6889,8 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf muscle fiber myocyte + + muscle cell https://www.swissbiopics.org/api/image/Muscle_cells.svg @@ -6843,6 +6921,8 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf A cell whose function is determined by the generation or the reception of an electric signal. ZFA:0009128 + + electrically active cell @@ -6867,6 +6947,8 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf A cell within an epithelial cell sheet whose main function is to act as an internal or external covering for a tissue or an organism. ZFA:0009130 boundary cell + + lining cell @@ -6890,6 +6972,8 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf A cell whose primary function is to prevent the transport of stuff across compartments. ZFA:0009132 + + barrier cell @@ -6930,6 +7014,8 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf A cell that moves by its own activities. ZFA:0009136 + + motile cell @@ -6962,6 +7048,9 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf FMA:72549 ZFA:0009137 ectoderm cell + + + ectodermal cell @@ -6991,11 +7080,18 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf A cell of the middle germ layer of the embryo. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Mesodermal cells are pluripotent and the most abundant in the human body. They contribute to the development of several structures such as the skeletal muscles, bones, heart and blood vessels, kidneys, gonads, connective tissues, and certain layers of the skin. Hence, the mesoderm is often regarded as an active and diverse layer due to its role in forming many bodily structures. +In embryonic development, these cells are instrumental, contributing to the body's structures through a carefully coordinated sequence of morphogenetic movements. This process forms the complex multicellular architecture of tissues and organs from a simple ball of cells. Without the function of mesodermal cells, the body's integral structures and systems would cease to form correctly, leading to developmental disorders such as axial mesodermal dysplasia complex FMA:72554 ZFA:0009138 + https://cellxgene.cziscience.com/cellguide/CL_0000222 mesoblast mesoderm cell + + mesodermal cell @@ -7004,6 +7100,17 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf A cell of the middle germ layer of the embryo. MESH:D008648 + + + + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Mesodermal cells are pluripotent and the most abundant in the human body. They contribute to the development of several structures such as the skeletal muscles, bones, heart and blood vessels, kidneys, gonads, connective tissues, and certain layers of the skin. Hence, the mesoderm is often regarded as an active and diverse layer due to its role in forming many bodily structures. +In embryonic development, these cells are instrumental, contributing to the body's structures through a carefully coordinated sequence of morphogenetic movements. This process forms the complex multicellular architecture of tissues and organs from a simple ball of cells. Without the function of mesodermal cells, the body's integral structures and systems would cease to form correctly, leading to developmental disorders such as axial mesodermal dysplasia complex + DOI:10.1016/j.ceb.2019.07.012 + DOI:10.5535/arm.2016.40.1.162 + https://www.sciencedirect.com/topics/biochemistry-genetics-and-molecular-biology/mesoderm + @@ -7028,6 +7135,8 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf FMA:72555 ZFA:0009139 endoderm cell + + endodermal cell @@ -7070,6 +7179,8 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf A cell that lacks a nucleus. FMA:68647 non-nucleated cell + + anucleate cell @@ -7104,6 +7215,8 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf A cell with a single nucleus. + + single nucleate cell @@ -7141,6 +7254,8 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf A cell with more than one nucleus. multinucleated cells polynuclear cells + + multinucleate cell @@ -7231,6 +7346,8 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf red blood cell + + erythrocyte @@ -7285,6 +7402,8 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf enucleate thrombocyte + + Platelets are reportedly CCR1-positive, CCR2-negative, CCR3-positive, CCR4-positive, CCR5-negative, CCR6-negative, CCR7-negative, CCR8-negative, CCR9-negative, CCR10-negative, CD16-positive, CD23-positive, CD32-positive, CD40-positive, CD41-positive CD42-positive, CD61-positive, CD62P-positive, CD64-positive, CD89-positive, CD102-positive, CD147-positive (activated platelets), CD154-positive (activated platelets), CD162-positive, CD209, CD282-positive, CD284-positive, CD289-positive, CD181-negative, CD182-negative, CD183-negative, CD184-positive, CLEC2-positive, GPVI-positive, JAMC-positive, PAR1-positive, PAR2-negative, PAR3-positive, PAR4-positive, TSP1-positive, and TXA2R-positive. Platelets can reportedly produce CCL2, CCL3, CCL5, CCL7, CCL17, CD40L, CXCL1, CXCL4, CXCL4L1, CXCL5, CXCL7, CXCL8, CXCL12, EGF, factor V, factor VII, factor XI, factor XIII, bFGF, histamine, IGF-1, IL-1beta, PAI-1, PDGF, plasminogen, protein S, serotonin, TGF-beta, TFPI, VEGF, and vWF. platelet @@ -7341,7 +7460,8 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf FMA:83806 MESH:D010586 ZFA:0009140 - + + phagocyte @@ -7409,6 +7529,8 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf + + Morphology: Diameter 30_M-80 _M, abundant cytoplasm, low N/C ratio, eccentric nucleus. Irregular shape with pseudopods, highly adhesive. Contain vacuoles and phagosomes, may contain azurophilic granules; markers: Mouse & Human: CD68, in most cases CD11b. Mouse: in most cases F4/80+; role or process: immune, antigen presentation, & tissue remodelling; lineage: hematopoietic, myeloid. macrophage @@ -7473,6 +7595,8 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf + + B cell @@ -7523,7 +7647,8 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf Any cell that in taxon some Eukaryota. MESH:D005057 - + + eukaryotic cell @@ -7540,6 +7665,8 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf A cell that is specialised to accumulate a particular substance(s). + + stuff accumulating cell @@ -7575,6 +7702,8 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf Any cell that is capable of some oxygen transport. ZFA:0009164 + + oxygen accumulating cell @@ -7607,6 +7736,8 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf A cell derived from the specialized ectoderm flanking each side of the embryonic neural plate, which after the closure of the neural tube, forms masses of cells that migrate out from the dorsal aspect of the neural tube to spread throughout the body. FMA:86667 ZFA:0007086 + + migratory neural crest cell @@ -7630,6 +7761,8 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf A mesenchymal cell in embryonic development found in a contracting mass and that gives rise to osteoprogenitors. ZFA:0009166 + + mesenchyme condensation cell @@ -7653,6 +7786,8 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf A cell of the outer layer of a blastula that gives rise to the ectoderm after gastrulation. + + epiblast cell @@ -7693,6 +7828,8 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf BTO:0000854 EHDAA2:0004546 FMA:72395 + + animal zygote @@ -7710,6 +7847,8 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf A cell whose function is determined by its response to an electric signal. ZFA:0009190 + + electrically responsive cell @@ -7733,6 +7872,8 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf A cell that initiates an electrical signal and passes that signal to another cell. ZFA:0009193 + + electrically signaling cell @@ -7806,7 +7947,6 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf - @@ -7867,6 +8007,8 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf veiled cell + + dendritic cell @@ -7891,6 +8033,8 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf ZFA:0009212 + + biogenic amine secreting cell @@ -7927,6 +8071,8 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf ZFA:0009213 5-HT secreting cell 5-Hydroxytryptamine secreting cell + + serotonin secreting cell @@ -7950,6 +8096,8 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf A cell whose primary function is to protect the organism. + + defensive cell @@ -7961,6 +8109,44 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf + + + + + + + + + + + A connective tissue cell of an organ found in the loose connective tissue. + + BTO:0002064 + FMA:83624 + ZFA:0009226 + + + + + + stromal cell + + + + + A connective tissue cell of an organ found in the loose connective tissue. + GOC:tfm + MESH:D017154 + + + + + ZFA:0009226 + + + + + @@ -7973,6 +8159,8 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf A phagocyte in vertebrates that is able to phagocytosis. + + phagocyte (sensu Vertebrata) @@ -8008,6 +8196,8 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf nerve cell + + These cells are also reportedly CD4-negative and CD200-positive. They are also capable of producing CD40L and IFN-gamma. neuron @@ -8096,6 +8286,8 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf VHOG:0001535 ZFA:0009250 + + Editors note: consider adding taxon constraint to vertebrata (PMID:18025161) lymphocyte @@ -8193,7 +8385,6 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf - @@ -8296,6 +8487,8 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf pronormoblast + + proerythroblast @@ -8343,7 +8536,6 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf - @@ -8369,6 +8561,8 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf early erythroblast early normoblast prorubricyte + + basophilic erythroblast @@ -8440,7 +8634,6 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf - @@ -8474,6 +8667,8 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf polychromatic normoblast polychromatophilic normoblast rubricyte + + polychromatophilic erythroblast @@ -8577,6 +8772,8 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf late erythoblast orthochromatic normoblast pyknotic eto enrythroblast + + orthochromatic erythroblast @@ -8793,6 +8990,8 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf promegacaryocyte promegakaryocyte + + Lineage negative is described here as CD2-negative, CD3-negative, CD4-negative, CD5-negative, CD8a-negative, CD14-negative, CD19-negative, CD20-negative, CD56-negative, Ly6g-negative, and Ter119-negative. megakaryocyte progenitor cell @@ -8866,6 +9065,8 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf megalokaryocyte + + Megakaryocytes are reportedly CD181-positive and CD182-positive. megakaryocyte @@ -8932,9 +9133,7 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf - - @@ -8979,8 +9178,13 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf A hematopoietic progenitor cell that is committed to the granulocyte and monocyte lineages. These cells are CD123-positive, and do not express Gata1 or Gata2 but do express C/EBPa, and Pu.1. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Granulocyte monocyte progenitor cells (GMP cells), originating from hematopoietic stem cells in the bone marrow, are a critical intermediate in myeloid cell development. Positioned at a key differentiation juncture, these cells exhibit bidirectional potential, giving rise to both granulocyte and monocyte lineages. +Their primary role is to generate mature granulocytes and monocytes, essential components of the body's innate immunity and inflammatory responses. Granulocytes, such as neutrophils, eosinophils, and basophils, contribute to the first line of defense against infections by migrating to the infection site and phagocytosing pathogens. Monocytes can differentiate into macrophages or dendritic cells, playing diverse roles in immune responses. CFU-C , Colony forming unit in culture ZFA:0009251 + https://cellxgene.cziscience.com/cellguide/CL_0000557 colony forming unit granulocyte macrophage granulocyte-macrophage progenitor granulocyte/monocyte precursor @@ -8988,6 +9192,8 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf CFU-GM GMP + + Originally described in the dendritic cell ontology (DC_CL:0000042)(PMID:19243617). GMPs are reportedly CD16-positive, CD32-positive, CD34-positive, CD38-positive, CD45RA-positive, CD110-negative, CD117-positive, CD123-positive, and SCA1-negative. granulocyte monocyte progenitor cell @@ -9009,6 +9215,17 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf http://en.wikipedia.org/wiki/CFU-GM http://www.copewithcytokines.de + + + + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Granulocyte monocyte progenitor cells (GMP cells), originating from hematopoietic stem cells in the bone marrow, are a critical intermediate in myeloid cell development. Positioned at a key differentiation juncture, these cells exhibit bidirectional potential, giving rise to both granulocyte and monocyte lineages. +Their primary role is to generate mature granulocytes and monocytes, essential components of the body's innate immunity and inflammatory responses. Granulocytes, such as neutrophils, eosinophils, and basophils, contribute to the first line of defense against infections by migrating to the infection site and phagocytosing pathogens. Monocytes can differentiate into macrophages or dendritic cells, playing diverse roles in immune responses. + DOI:10.1016/j.immuni.2017.10.021 + DOI:10.1146/annurev-immunol-081022113627 + DOI:10.1186/2050-7771-2-1 + @@ -9121,7 +9338,6 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf - @@ -9213,6 +9429,8 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf ZFA:0009252 + + reticulocyte @@ -9263,7 +9481,6 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf - @@ -9288,6 +9505,8 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf FMA:83551 ZFA:0009253 + + Morphology: Mononuclear cell, diameter 14-18 _M, fine azurophilic granules; markers: CD11b (shared with many other myeloid cells); location: Adult: bone marrow; Fetal: Liver, Yolk Sac; role or process: hematopoiesis, monocyte development; lineage: hematopoietic, myeloid. promonocyte @@ -9338,7 +9557,6 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf - @@ -9367,6 +9585,8 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf ZFA:0009258 angioblast chondroplast + + These cells are reportedly CD31-positive, CD34-positive, CD144-positive, CD309-positive, and TAL1-positive. angioblastic mesenchymal cell @@ -9455,6 +9675,8 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf + + Morphology: Mononuclear cell, diameter, 14 to 20 _M, N/C ratio 2:1-1:1. Nucleus may appear in variety of shapes: round, kidney, lobulated, or convoluted. Fine azurophilic granules present; markers: CD11b (shared with other myeloid cells), human: CD14, mouse: F4/80-mid,GR1-low; location: Blood, but can be recruited into tissues; role or process: immune & tissue remodelling; lineage: hematopoietic, myeloid. monocyte @@ -9534,6 +9756,8 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf syncytial giant cell MGC + + Role or process: Chronic infection, granulomatous inflammation. Consider also megakaryocyte (CL:0000556) as sometimes multinucleated giant cell is used to refer to this. multinucleated giant cell @@ -9630,6 +9854,8 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf A non-terminally differentiated cell that is capable of developing into a muscle cell. ZFA:0009291 + + muscle precursor cell @@ -9672,6 +9898,8 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf CALOHA:TS-2086 MESH:D053687 ZFA:0009307 + + somatic stem cell @@ -9747,6 +9975,8 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf white blood cell immune cell + + leukocyte @@ -9808,6 +10038,8 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf A nucleated blood cell involved in coagulation, typically seen in birds and other non-mammalian vertebrates. ZFA:0009323 + + Note that this is a non-mammalian cell type. Use platelet ; CL:0000233 for thrombocytes (platelets) in mammals. nucleated thrombocyte @@ -9862,6 +10094,8 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf MESH:D022423 ZFA:0009324 + + myeloid cell @@ -9897,6 +10131,8 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf ZFA:0009325 erythropoietic cell + + Note that in FMA erythropoietic cells are types of nucleated erythrocytes and thus don't include erythrocytes. erythroid lineage cell @@ -10084,6 +10320,8 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf normoblast + + erythroblast @@ -10128,6 +10366,8 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf A cell of the monocyte, granulocyte, or mast cell lineage. ZFA:0009326 + + myeloid leukocyte @@ -10223,6 +10463,8 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf basophilic leukocyte + + Matures in the bone marrow and account for <1% of leukocytes in the peripheral blood, spleen, and bone marrow. Basophils are described as being CD11a-positive, CD11b-positive, CD13-positive, CD15-positive, CD18-positive, CD21-positive, CD25-positive, CD29-positive, CD35-positive, CD40-positive, CD40L-positive, CD44-positive, CD45R-negative, CD46-positive, CD49a-positive, CD49b-positive, CD49d-positive, CD55-positive, CD59-positive, CD62L-positive, CD63-positive, CD69-positive, CD90-negative, CD116-positive, CD117-negative, CD124-positive, CD125-positive, CD131-positive, CD161-positive, CD184-positive, CD191-positive, CD192-positive, CD197-positive, CD200R3-positive, CD218-positive, CD282-positive, CD284-positive, CD289-positive, CD290-positive, CD294-positive, natural killer cell receptor 2B4-positive, smad1-positive, CD3-negative, CD4-negative, CD7-negative, CD8-negative, CD14-negative, CD15-negative, CD16-negative, CD19-negative, CD20-negative, CD34-negative, CD36-negative, CD45R-negative, CD56-negative, CD57-negative, CD235a-negative, and GR1-negative. Transcription factors- GATA1-positive, PU.1-positive. basophil @@ -10327,6 +10569,8 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf eosinophilic leukocyte + + Eosinophils are also CD14-negative, CD32-positive, CD44-positive, CD48-positive, CD69-positive, CD192-negative, MBP1-positive, MBP2-positive, TLR2-negative, TLR4-negative, and lineage-negative (B220, CD2, CD14, CD19, CD56, CD71, CD117, CD123, CD235a (glycophorin A), and TER119). The cytokines IL-3, IL-5, and GM-CSF are involved in their development and differentiation. Usually considered CD16-negative, CD16 is observed on eosinophilic metamyelocyte. eosinophil @@ -10405,6 +10649,8 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf neutrophilic leukocyte + + neutrophil @@ -10471,6 +10717,8 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf CD11c+CD123- DC mDC + + These cells are CD1a-negative, CD1b-positive, CD11a-positive, CD11c-positive, CD13-positive, CD14-negative, CD20-negative, CD21-negative, CD33-positive, CD40-negative, CD50-positive, CD54-positive, CD58-positive, CD68-negative, CD80-negative, CD83-negative, CD85j-positive, CD86-positive, CD89-negative, CD95-positive, CD120a-negative, CD120b-positive, CD123-negative, CD178-negative, CD206-negative, CD207-negative, CD209-negative, and TNF-alpha-negative. Upon TLR stimulation, they are capable of producing high levels of TNF-alpha, IL-6, CXCL8 (IL-8). myeloid dendritic cell @@ -10527,6 +10775,8 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf type 2 DC + + plasmacytoid dendritic cell @@ -10603,6 +10853,8 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf mature B-cell mature B-lymphocyte + + Mature B cells are also reportedly CD10-negative, CD19-positive, CD22-positive, CD34-negative, CD48-positive, CD79a-positive, CD84-positive, CD127-negative, CD352-positive, RAG-negative, TdT-negative, Vpre-B-negative, and pre-BCR-negative. Transcription factors expressed: Pax5-positive. mature B cell @@ -10664,7 +10916,6 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf - @@ -10721,6 +10972,8 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf effector B-cell + + Plasma cells develop in the spleen and migrate to the bone marrow. Plasma cells are also reportedly CD5-negative, CD10-negative, CD19-positive, CD20-negative, CD21-negative, CD22-negative, CD23-negative, CD24-negative, CD25-negative, CD27-positive, CD34-negative, CD38-positive, CD40-positive, CD43-positive, CD45-positive, CD48-positive, CD53-low, CD80-negative, CD81-positive, CD86-positive, CD95-positive, CD196-negative, CD229-positive, CD270-positive, CD352-positive, CD361-positive, and IgD-negative. Transcription factors: BLIMP1-positive, IRF4-positive, PAX5-negative, SpiB-negative, Ets1-negative, and XBP1-positive. plasma cell @@ -10770,7 +11023,6 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf - @@ -10785,6 +11037,8 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf alpha-beta T-lymphocyte + + alpha-beta T cell @@ -10825,7 +11079,6 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf - @@ -10842,6 +11095,8 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf gd T cell + + Note that gamma-delta T cells have both thymic and extrathymic differentiation pathways. gamma-delta T cell @@ -10941,6 +11196,8 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf newly formed B cell + + Immature B cells are also reportedly CD5-positive, CD10-positive, CD19-positive, CD20-positive, CD21-positive, CD22-positive, CD24-positive, CD25-negative, CD27-negative, CD34-negative, CD38-positive, CD40-positive, CD43-negative, CD45-positive, CD48-positive, CD53-positive, CD79a-positive, CD80-negative, CD81-positive, CD86-negative, CD95-negative, CD127-negative, CD138-negative, CD185-positive, CD196-positive, MHCII/HLA-DR-positive, RAG-positive, TdT-negative, Vpre-B-negative, and preBCR-negative. Transcription factors expressed: Pax5-positive. immature B cell @@ -11012,6 +11269,8 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf ZFA:0009344 pre-B cell + + precursor B cell @@ -11116,6 +11375,8 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf T2 B cell T3 B cell + + This cell type is compatible with the HIPC Lyoplate markers for 'transitional B cell'. transitional stage B cell @@ -11174,7 +11435,6 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf - @@ -11213,6 +11473,8 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf progenitor B-lymphocyte pre-B cell (Philadelphia nomenclature) + + Human pro-B cells are reportedly CD10-positive, CD22-positive, CD34-positive, CD38-positive, CD45-low, CD48-positive, CD79a-positive, CD127-positive, CD184-positive, RAG-positive, TdT-positive, Vpre-B-positive, pre-BCR-negative, IgD-negative, and IgM-negative. Transcription factors expressed: Pax5-positive, EBF-positive, E2A-negative, Ikaros-negative, and PU.1-negative. pro-B cell @@ -11290,6 +11552,8 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf DN1 thymocyte TN1 cell + + pro-T cell @@ -11349,6 +11613,8 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf A progenitor cell of the thrombocyte, a nucleated blood cell involved in coagulation typically seen in birds and other non-mammalian vertebrates. ZFA:0009351 + + Note that this is a non-mammalian cell type. thromboblast @@ -11483,7 +11749,6 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf - @@ -11639,6 +11904,8 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf CFU-MC CFU-Mast colony forming unit mast cell + + MCP are CD16-positive, CD32-positive, CD34-positive, CD45-positive, integrin beta-7-positive, and lin-negative (CD2, CD3e, CD4, CD5, CD8a, CD14, CD19, CD20, CD27, integrin alpha-M, ly6c, ly6g, NCAM-1, and ter119). These cells also express the transcription factors GATA-1, GATA-2, and MITF, but not C/EBPa. mast cell progenitor @@ -11735,7 +12002,6 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf - @@ -11842,6 +12108,8 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf hemopoietic progenitor cell + + Markers differ between mouse and human. hematopoietic multipotent progenitor cell @@ -11893,6 +12161,8 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf FMA:70338 ZFA:0009355 + + Note that this is a class of cell types, not an identified single cell type. lymphoid lineage restricted progenitor cell @@ -11948,6 +12218,8 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf FMA:70339 ZFA:0009356 + + Note that this is a class of cell types, not an identified single cell type. myeloid lineage restricted progenitor cell @@ -12000,6 +12272,8 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf peripheral blood mononuclear cell + + mononuclear cell @@ -12050,7 +12324,6 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf - @@ -12077,6 +12350,9 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf An immature myeloid leukocyte of heterogeneous phenotype found particularly in cancer and sepsis patients that is capable of suppressing activity of T cells in ex vivo assays. This cell type is CD45-positive, CD11b-positive. + + + Markers: Mouse: CD11b+GR1+CD31+; Human: CD34+ CD33+CD15-CD13+. (According to some reports in humans these cells are iNOS+ARG1+IL13+IFNg+); location: In cancerous tissue; in the blood and lymphoid organs in sepsis. myeloid suppressor cell @@ -12112,6 +12388,9 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf A lymphocyte of B lineage with the commitment to express an immunoglobulin complex. + + + Types of B lineage lymphocytes include B cells and antibody secreting cells (plasmablasts and plasma cells). Lymphocytes of B cell lineage can be distinguished from those of T cell lineage by their lack of CD3e (as part of the T cell receptor complex). lymphocyte of B lineage @@ -12157,6 +12436,8 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf A lymphocyte of B lineage that is devoted to secreting large amounts of immunoglobulin. + + antibody secreting cell @@ -12242,6 +12523,8 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf A small pre-B-II cell is a pre-B-II cell that is Rag1-positive, Rag2-positive, pre-BCR-negative, and BCR-negative, is not proliferating, and carries a DNA rearrangement of one or more immunoglobulin light chain genes. small pre-BII cell + + Small pre-B-II cells are also reportedly CD10-positive, CD19-positive, CD34-negative, CD79a-positive, CD127-negative, TdT-negative, Vpre-B-negative, sIgM-negative, and sIgD-negative. Transcription factors: PU.1-positive, Ikaros-positive, E2A-positive, and PAX5-positive. small pre-B-II cell @@ -12312,6 +12595,8 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf CALOHA:TS-0819 pre-B-lymphocyte pre-BII cell + + pre-B-II cell are also reportedly CD19-positive, CD22-positive, CD38-positive, CD45-positive, and CD48-positive. pre-B-II cell @@ -12402,6 +12687,8 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf FMA:84371 CD27-positive, CD38-positive, CD20-negative B cell + + This cell type is compatible with the HIPC Lyoplate markers for 'plasmablast'. Plasmablasts are also reportedly CD48-positive, CD63-positive, CD229-positive, CD270-positive, CD319-positive, CD352-positive, CD361-positive, and IgD-negative. plasmablast @@ -12439,6 +12726,8 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf haemopoietic cell hemopoietic cell + + hematopoietic cell @@ -12489,6 +12778,8 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf type 1 DC + + Originally described in the dendritic cell ontology (DC_CL:0000003)(PMID:19243617) These cells are also CD20-negative, MHCII-positive. conventional dendritic cell @@ -12514,6 +12805,9 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf + + + Originally described in the dendritic cell ontology (DC_CL:1110000)(PMID:19243617). CD7-negative lymphoid progenitor OR granulocyte monocyte progenitor @@ -12544,8 +12838,17 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf A connective tissue cell found in bone. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Bone cells, also known as osteocytes, form the building blocks of the skeletal system. They represent the most common type of bone cell, making up approximately 95% of the total bone cell population in mature adult bone tissue. Osteocytes are a stellate shape with numerous long, slender dendritic processes. +The formation of bone is a complex process involving the action of osteoclasts - cells that break down and reabsorb old bone, followed by osteoblasts that rebuild the bone. Osteocytes serve as coordinators for these two types of bone cells to ensure a balance in the bone remodeling process, contributing to maintaining both bone strength and mineral homeostasis. +The primary functions of osteocytes involve the creation, maintenance, and repair of bone tissue. They ensure that bone remodeling is performed by forming a network within the bone and communicating with other cells to help them respond to mechanical strain and damage. +A remarkable aspect of osteocytes is their ability to perceive mechanical forces, translating them into biochemical signals that regulate bone remodeling and adaptation. Defects in osteocyte function, aside from other bone cells, have been associated with several bone disorders such as osteoporosis, renal osteodystrophy, and skeletal manifestations of diabetes. 2011-11-16T04:28:16Z + https://cellxgene.cziscience.com/cellguide/CL_0001035 + + bone cell @@ -12556,6 +12859,20 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf GOC:add GO_REF:0000034 + + + + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Bone cells, also known as osteocytes, form the building blocks of the skeletal system. They represent the most common type of bone cell, making up approximately 95% of the total bone cell population in mature adult bone tissue. Osteocytes are a stellate shape with numerous long, slender dendritic processes. +The formation of bone is a complex process involving the action of osteoclasts - cells that break down and reabsorb old bone, followed by osteoblasts that rebuild the bone. Osteocytes serve as coordinators for these two types of bone cells to ensure a balance in the bone remodeling process, contributing to maintaining both bone strength and mineral homeostasis. +The primary functions of osteocytes involve the creation, maintenance, and repair of bone tissue. They ensure that bone remodeling is performed by forming a network within the bone and communicating with other cells to help them respond to mechanical strain and damage. +A remarkable aspect of osteocytes is their ability to perceive mechanical forces, translating them into biochemical signals that regulate bone remodeling and adaptation. Defects in osteocyte function, aside from other bone cells, have been associated with several bone disorders such as osteoporosis, renal osteodystrophy, and skeletal manifestations of diabetes. + DOI:10.1007/s00795-015-0099-y + DOI:10.1007/s11914-012-0105-4 + DOI:10.1016/j.jot.2021.04.005 + DOI:10.1038/s41413-020-0099-y + @@ -12697,6 +13014,8 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf A hematopoietic oligopotent progenitor cell that has the ability to differentiate into limited cell types but lacks lineage cell markers and self renewal capabilities. Cell lacks hematopoeitic lineage markers. 2010-01-06T03:43:27Z + + hematopoietic oligopotent progenitor cell, lineage-negative @@ -12766,6 +13085,8 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf 2017-01-30T20:20:48Z + + innate lymphoid cell @@ -12804,7 +13125,6 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf - @@ -12825,6 +13145,8 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf A lymphocyte of B lineage that is CD19-positive. + + Types of B lineage lymphocytes include B cells and antibody secreting cells (plasmablasts and plasma cells). Lymphocytes of B cell lineage can be distinguished from those of T cell lineage by their lack of CD3e (as part of the T cell receptor complex). lymphocyte of B lineage, CD19-positive @@ -12864,6 +13186,8 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf B-lymphocyte, CD19-positive CD19+ B cell CD19-positive B cell + + B cell, CD19-positive @@ -12919,6 +13243,8 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf 2010-01-19T02:51:58Z MDP + + macrophage dendritic cell progenitor @@ -12981,7 +13307,6 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf - @@ -13041,6 +13366,8 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf 2010-04-27T12:46:33Z BMCP + + There may be an intermediate cell type. These cells also CD13-positive, CD16-positive, CD32-positive, and integrin beta 7-positive. Transcription factors: GATA1-positive, MCP-1-positive, mitf-positive, PU.1-positive, and CEBP/a-low. basophil mast progenitor cell @@ -13089,6 +13416,8 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf 2010-01-06T03:43:20Z + + hematopoietic lineage restricted progenitor cell @@ -13133,6 +13462,8 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf 2010-01-06T03:43:27Z + + This cell type is intended to be compatible with any vertebrate hematopoietic oligopotent progenitor cell. For mammalian hematopoietic oligopotent progenitor cells known to be lineage-negative, please use the term 'hematopoietic oligopotent progenitor cell' (CL_0001060). hematopoietic oligopotent progenitor cell @@ -13173,6 +13504,8 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf 2010-06-29T03:38:22Z FMA:69074 ZFA:0009385 + + ecto-epithelial cell @@ -13218,6 +13551,8 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf FMA:62855 agranular leukocyte + + nongranular leukocyte @@ -13263,6 +13598,8 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf FMA:83621 MESH:D001854 + + MH consider whether bone marrow cells are bone cells in the structural sense vs. being part of bone organ sense. bone marrow cell @@ -13288,13 +13625,21 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf An endothelial cell of the vascular tree, which includes blood vessels and lymphatic vessels. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Endothelial cells of the vascular tree, commonly referred to as vascular endothelial cells, line the entire circulatory system, from the heart to the smallest capillaries. These cells have a unique, flattened shape, and are tightly bound together, forming a thin layer known as the endothelium. The endothelium is responsible for maintaining the interior surface of blood vessels, and plays a critical role in ensuring the smooth flow of blood. +Vascular endothelial cells act as a semi-permeable membrane, controlling the passage of materials and the transit of white blood cells into and out of the bloodstream. These cells are also involved in blood coagulation. When a blood vessel is damaged, endothelial cells promote clotting to prevent excessive bleeding and facilitate wound healing. Other functions include regulation of blood pressure and blood volume by releasing vasodilators and vasoconstrictors to either widen or constrict blood vessels, accordingly. +Furthermore, the endothelial cells are crucial in the formation of new blood vessels, a process known as angiogenesis. This is particularly important in wound healing and the growth of new tissues during development or after injury. In the context of diseases such as cancer, angiogenesis helps facilitate tumor growth by providing nutrients and oxygen. 2010-08-24T02:06:40Z BTO:0001854 CALOHA:TS-1106 FMA:67755 + https://cellxgene.cziscience.com/cellguide/CL_0002139 vascular endothelial cell cubodial endothelial cell of vascular tree + + These cells are reportedly CD31-positive, CD34-positive, CD144-positive, TAL1-positive. endothelial cell of vascular tree @@ -13306,6 +13651,19 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf GOC:tfm PMID:12768659 + + + + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Endothelial cells of the vascular tree, commonly referred to as vascular endothelial cells, line the entire circulatory system, from the heart to the smallest capillaries. These cells have a unique, flattened shape, and are tightly bound together, forming a thin layer known as the endothelium. The endothelium is responsible for maintaining the interior surface of blood vessels, and plays a critical role in ensuring the smooth flow of blood. +Vascular endothelial cells act as a semi-permeable membrane, controlling the passage of materials and the transit of white blood cells into and out of the bloodstream. These cells are also involved in blood coagulation. When a blood vessel is damaged, endothelial cells promote clotting to prevent excessive bleeding and facilitate wound healing. Other functions include regulation of blood pressure and blood volume by releasing vasodilators and vasoconstrictors to either widen or constrict blood vessels, accordingly. +Furthermore, the endothelial cells are crucial in the formation of new blood vessels, a process known as angiogenesis. This is particularly important in wound healing and the growth of new tissues during development or after injury. In the context of diseases such as cancer, angiogenesis helps facilitate tumor growth by providing nutrients and oxygen. + DOI:10.1038/s41569-022-00770-1 + DOI:10.1186/s12872-015-0124-z + DOI:10.3389/fphys.2022.863265/full + https://www.sciencedirect.com/topics/medicine-and-dentistry/vascular-endothelial-cell + @@ -13335,6 +13693,8 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf 2010-08-30T12:54:27Z FMA:83519 + + granulocytopoietic cell @@ -13377,6 +13737,8 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf 2010-08-30T01:27:48Z FMA:83552 + + monopoietic cell @@ -13419,6 +13781,8 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf 2010-09-07T03:32:33Z FMA:67513 + + nucleate cell @@ -13454,6 +13818,8 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf A cell type that secretes histamine. 2010-09-10T03:04:42Z + + histamine secreting cell @@ -13492,6 +13858,8 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf CALOHA:TS-2040 FMA:70333 + + neural cell @@ -13533,6 +13901,8 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf MESH:D003239 ZFA:0009392 + + connective tissue cell @@ -13557,11 +13927,19 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf A cell of the embryo. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Embryonic cells in metazoans, which include all multicellular animals, are biological units in their earliest developmental stages from conception until the organism is fully formed. +They are derived from a fertilized egg, which undergoes a series of cell divisions to produce a multicellular organism. During the early phases of embryonic development, these cells exhibit pluripotency, meaning they possess the potential to differentiate into a diverse array of specialized cell types that constitute different body tissues and structures. +The balance between cell proliferation and differentiation in embryonic cells is crucial for successful development. When cells continue to divide without differentiating, overgrowth may occur leading to conditions such as teratomas (tumors of embryonic cells). Conversely, if cell differentiation proceeds at the expense of cell proliferation, developmental anomalies could occur regarding size or mass of the organism or its parts. 2010-09-15T03:39:21Z CALOHA:TS-0263 FMA:82840 WBbt:0007028 ZFA:0007089 + https://cellxgene.cziscience.com/cellguide/CL_0002321 + + embryonic cell (metazoa) @@ -13570,6 +13948,18 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf A cell of the embryo. FMA:0618947256 + + + + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Embryonic cells in metazoans, which include all multicellular animals, are biological units in their earliest developmental stages from conception until the organism is fully formed. +They are derived from a fertilized egg, which undergoes a series of cell divisions to produce a multicellular organism. During the early phases of embryonic development, these cells exhibit pluripotency, meaning they possess the potential to differentiate into a diverse array of specialized cell types that constitute different body tissues and structures. +The balance between cell proliferation and differentiation in embryonic cells is crucial for successful development. When cells continue to divide without differentiating, overgrowth may occur leading to conditions such as teratomas (tumors of embryonic cells). Conversely, if cell differentiation proceeds at the expense of cell proliferation, developmental anomalies could occur regarding size or mass of the organism or its parts. + DOI:10.1002/iub.1404 + DOI:10.1093/molehr/gan048 + https://www.ncbi.nlm.nih.gov/books/NBK9906/ + @@ -13608,6 +13998,8 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf immature T-cell + + immature T cell @@ -13654,6 +14046,8 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf FMA:83808 FMA:84791 heart cell + + From Onard of the FMA: Cardiac muscle cell or cardiac myocyte is a striated muscle cell. Cardiocyte on the other hand is any cell in the heart which includes cells other than muscle cells (e.g. endothelial cell of endocardium). Unless there is a consensus among anatomists that cardiocytes refer only to muscle cells, we will treat them as a general class of cells in the heart. cardiocyte @@ -13717,7 +14111,6 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf - @@ -13782,6 +14175,8 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf 2011-08-29T10:08:02Z + + natural helper lymphocyte @@ -13808,6 +14203,8 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf 2012-06-15T02:51:27Z scleroblast + + Needs logical definition. Should be capable_of skeletal system morphogenesis? or skeletal tissue development? needs to be added to GO. NOTES:a cell type of the early embryo (see also: mesenchymal cells) that will give rise to mineralized connective tissue. Scleroblasts can differentiate into osteoblasts (bone-forming cells), chondroblasts (cartilage-forming cells), odontoblasts (dentin-forming cells), ameloblasts (enamel-forming cells). The mesenchymal cells developing into osteoblasts and chondroblasts are derived from the mesoderm. Those developing into odontoblasts are neural crest cells. Those developing into ameloblasts are derived from the ectoderm. (http://www.copewithcytokines.de/cope.cgi?key=scleroblasts) skeletogenic cell @@ -13846,6 +14243,8 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf 2012-06-27T08:27:35Z ZFA:0007084 + + premigratory neural crest cell @@ -13869,6 +14268,8 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf Any hematopoietic cell that is a precursor of some other hematopoietic cell type. + + hematopoietic precursor cell @@ -13901,6 +14302,8 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf mesenchyme cell + + mesenchymal cell @@ -13913,6 +14316,8 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf A zygote in a plant or an animal. MESH:D015053 + + zygote @@ -13925,13 +14330,15 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf A cell of the neural crest. Neural crest cells are multipotent. Premigratory neural crest cells are found at the neural plate boarder, some of which will undergo ectomesynchymal transition and delamination to form migratory neural crest cells. - This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. Neural crest cells are a group of transient and highly migratory cells that originate from the neuroectoderm during the early stages of embryonic development. They are multipotent cells with an exceptional degree of plasticity, capable of differentiating into various somatic cell types and therefore play a fundamental role in the formation of various organs and tissues, making them critical contributors to the developing embryo. After the initiation of neurulation (the formation of the neural tube) neural crest cells start to undergo epithelial-to-mesenchymal transition and delaminate and migrate from the dorsal neural tube to several regions throughout the embryo. They differentiate into a range of diverse cell types, such as neurons and glial cells of the peripheral nervous system, including sensory and autonomic neurons. They also contribute to the formation of adrenal glands, pigment cells in the skin (melanocytes), cardiac structures, including parts of the heart septum and major arteries, as well as bones and cartilage of the face and skull. Disorders or aberrations in the development or migration of the neural crest cells can lead to serious congenital malformations, such as neurocristopathies, including Hirschsprung disease, neuroblastoma, and neurofibromatosis. https://cellxgene.cziscience.com/cellguide/CL_0011012 + + neural crest cell @@ -13944,7 +14351,7 @@ Disorders or aberrations in the development or migration of the neural crest cel - This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. Neural crest cells are a group of transient and highly migratory cells that originate from the neuroectoderm during the early stages of embryonic development. They are multipotent cells with an exceptional degree of plasticity, capable of differentiating into various somatic cell types and therefore play a fundamental role in the formation of various organs and tissues, making them critical contributors to the developing embryo. After the initiation of neurulation (the formation of the neural tube) neural crest cells start to undergo epithelial-to-mesenchymal transition and delaminate and migrate from the dorsal neural tube to several regions throughout the embryo. They differentiate into a range of diverse cell types, such as neurons and glial cells of the peripheral nervous system, including sensory and autonomic neurons. They also contribute to the formation of adrenal glands, pigment cells in the skin (melanocytes), cardiac structures, including parts of the heart septum and major arteries, as well as bones and cartilage of the face and skull. @@ -13982,6 +14389,8 @@ Disorders or aberrations in the development or migration of the neural crest cel A precursor cell that has a tendency to differentiate into a specific type of cell. They are descendants of stem cells, only they are more constrained in their differentiation potential or capacity for self-renewal, and are often more limited in both senses. + + progenitor cell @@ -14017,6 +14426,8 @@ Disorders or aberrations in the development or migration of the neural crest cel A cell that, by division or terminal differentiation, can give rise to other cell types. + + Work is needed on GO 'cell differentiation' before it is clear whether the equivalent class definition 'native cell' that capable_of some 'cell differentiation' works. Also, may want to consider merging this with non-terminally differentiated cell. precursor cell @@ -14040,12 +14451,14 @@ Disorders or aberrations in the development or migration of the neural crest cel A lymphocyte that has gotten larger after being stimulated by an antigen. - 2022-08-17T14:20:01Z - + + 2022-08-17T14:20:01Z BTO:0000772 EFO:0000572 FMA:83030 + + lymphoblast @@ -14064,11 +14477,13 @@ Disorders or aberrations in the development or migration of the neural crest cel A lymphocyte of B lineage that has gotten larger after being stimulated by an antigen. - 2022-08-17T14:30:32Z - + + 2022-08-17T14:30:32Z EFO:0005293 FMA:83031 + + B-lymphoblast @@ -14266,6 +14681,8 @@ Disorders or aberrations in the development or migration of the neural crest cel CALOHA:TS-2109 bone marrow hematopoietic cells bone marrow poietic cells + + bone marrow hematopoietic cell @@ -14316,6 +14733,8 @@ Disorders or aberrations in the development or migration of the neural crest cel 2014-02-11T17:29:04Z CL:2000001 + + peripheral blood mononuclear cell @@ -14346,6 +14765,8 @@ Disorders or aberrations in the development or migration of the neural crest cel A lymphocyte located in blood. 2022-11-04T14:40:00Z + + blood lymphocyte @@ -14387,6 +14808,8 @@ Disorders or aberrations in the development or migration of the neural crest cel 2024-08-15T10:38:46Z syncytium SC + + syncytial cell @@ -14446,7 +14869,6 @@ Disorders or aberrations in the development or migration of the neural crest cel Progression through the phases of the mitotic cell cycle, the most common eukaryotic cell cycle, which canonically comprises four successive phases called G1, S, G2, and M and includes replication of the genome and the subsequent segregation of chromosomes into daughter cells. In some variant cell cycles nuclear replication or nuclear division may not be followed by cell division, or G1 and G2 phases may be absent. - GO:0007067 Wikipedia:Mitosis biological_process mitosis @@ -14567,9 +14989,6 @@ Disorders or aberrations in the development or migration of the neural crest cel The ordered and organized complex of DNA, protein, and sometimes RNA, that forms the chromosome. https://github.com/geneontology/go-ontology/issues/28301 - GO:0000789 - GO:0000790 - GO:0005717 NIF_Subcellular:sao1615953555 cytoplasmic chromatin nuclear chromatin @@ -14595,8 +15014,6 @@ Disorders or aberrations in the development or migration of the neural crest cel A dispersed and relatively uncompacted form of chromatin that is in a transcription-competent conformation. https://github.com/geneontology/go-ontology/issues/22355 - GO:0005719 - GO:0035327 NIF_Subcellular:sao445485807 Wikipedia:Euchromatin transcriptionally active chromatin @@ -14620,8 +15037,6 @@ Disorders or aberrations in the development or migration of the neural crest cel A compact and highly condensed form of chromatin that is refractory to transcription. https://github.com/geneontology/go-ontology/issues/22355 - GO:0005720 - GO:0035328 NIF_Subcellular:sao581845896 Wikipedia:Heterochromatin transcriptionally inactive chromatin @@ -15002,10 +15417,6 @@ Disorders or aberrations in the development or migration of the neural crest cel The appearance of a cytokine due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. https://github.com/geneontology/go-ontology/issues/19116 - GO:0042032 - GO:0042089 - GO:0042107 - GO:0050663 cytokine biosynthetic process cytokine metabolic process cytokine secretion @@ -15065,7 +15476,7 @@ Disorders or aberrations in the development or migration of the neural crest cel - The regulated release of serotonin by a cell. Serotonin (5-hydroxytryptamine, or 5-HT) is a monoamine synthesised in serotonergic neurons in the central nervous system, enterochromaffin cells in the gastrointestinal tract and some immune system cells. + The regulated release of serotonin by a cell. Serotonin (5-hydroxytryptamine, or 5-HT) is a monoamine synthesized in serotonergic neurons in the central nervous system, enterochromaffin cells in the gastrointestinal tract and some immune system cells. 5-HT secretion 5-hydroxytryptamine secretion biological_process @@ -15076,7 +15487,7 @@ Disorders or aberrations in the development or migration of the neural crest cel - The regulated release of serotonin by a cell. Serotonin (5-hydroxytryptamine, or 5-HT) is a monoamine synthesised in serotonergic neurons in the central nervous system, enterochromaffin cells in the gastrointestinal tract and some immune system cells. + The regulated release of serotonin by a cell. Serotonin (5-hydroxytryptamine, or 5-HT) is a monoamine synthesized in serotonergic neurons in the central nervous system, enterochromaffin cells in the gastrointestinal tract and some immune system cells. GOC:ef ISBN:0198506732 ISBN:0781735149 @@ -15164,7 +15575,6 @@ Disorders or aberrations in the development or migration of the neural crest cel The formation of a tube from the flat layer of ectodermal cells known as the neural plate. This will give rise to the central nervous system. - GO:0001679 Wikipedia:Neurulation neural tube morphogenesis neurulation @@ -15808,8 +16218,6 @@ Disorders or aberrations in the development or migration of the neural crest cel The appearance of immunoglobulin due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. - GO:0002378 - GO:0048305 antibody production immunoglobulin biosynthetic process immunoglobulin secretion @@ -15851,8 +16259,6 @@ Disorders or aberrations in the development or migration of the neural crest cel The appearance of immunoglobulin due to biosynthesis or secretion following a cellular stimulus during an immune response, resulting in an increase in its intracellular or extracellular levels. - GO:0002379 - GO:0002380 immunoglobulin production involved in immunoglobulin mediated immune response immunoglobulin biosynthetic process involved in immune response immunoglobulin secretion involved in immune response @@ -15975,8 +16381,6 @@ Disorders or aberrations in the development or migration of the neural crest cel Any process involved in the carrying out of an immune response by a leukocyte. - GO:0019723 - GO:0042087 immune cell effector process immune cell mediated immunity leucocyte immune effector process @@ -17354,7 +17758,6 @@ Disorders or aberrations in the development or migration of the neural crest cel A molecular process that can be carried out by the action of a single macromolecular machine, usually via direct physical interactions with other molecular entities. Function in this sense denotes an action, or activity, that a gene product (or a complex) performs. - GO:0005554 molecular function molecular_function GO:0003674 @@ -17381,8 +17784,6 @@ Disorders or aberrations in the development or migration of the neural crest cel Combining with an extracellular or intracellular signal and transmitting the signal from one side of the membrane to the other to initiate a change in cell activity or state as part of signal transduction. - GO:0004926 - GO:0099600 transmembrane receptor activity Reactome:R-HSA-193672 transmembrane signalling receptor activity @@ -17431,14 +17832,10 @@ Disorders or aberrations in the development or migration of the neural crest cel Combining with an extracellular signal and transmitting the signal across the membrane by activating an associated G-protein; promotes the exchange of GDP for GTP on the alpha subunit of a heterotrimeric G-protein complex. - GO:0001622 - GO:0001623 - GO:0001624 - GO:0001625 - GO:0016526 Reactome:R-HSA-114552 Reactome:R-HSA-114558 Reactome:R-HSA-167408 + Reactome:R-HSA-381706 Wikipedia:GPCR G protein coupled receptor activity G protein linked receptor activity @@ -17487,6 +17884,12 @@ Disorders or aberrations in the development or migration of the neural crest cel Reactome:R-HSA-167408 The high affinity receptor complex binds to G-protein + + + + Reactome:R-HSA-381706 + GLP1R:GLP1 activates G(s) + @@ -17502,7 +17905,6 @@ Disorders or aberrations in the development or migration of the neural crest cel A location, relative to cellular compartments and structures, occupied by a macromolecular machine. There are three types of cellular components described in the gene ontology: (1) the cellular anatomical entity where a gene product carries out a molecular function (e.g., plasma membrane, cytoskeleton) or membrane-enclosed compartments (e.g., mitochondrion); (2) virion components, where viral proteins act, and (3) the stable macromolecular complexes of which gene product are parts (e.g., the clathrin complex). https://github.com/geneontology/go-ontology/issues/17729 - GO:0008372 NIF_Subcellular:sao1337158144 cell or subcellular entity cellular component @@ -17600,32 +18002,32 @@ Disorders or aberrations in the development or migration of the neural crest cel - - + + A protein complex consisting of three collagen chains assembled into a left-handed triple helix. These trimers typically assemble into higher order structures. Wikipedia:Collagen cellular_component GO:0005581 collagen trimer - + - + - + PMID:12382326 - + PMID:12382326 @@ -17668,8 +18070,6 @@ Disorders or aberrations in the development or migration of the neural crest cel A collagen-containing extracellular matrix consisting of a thin layer of dense material found in various animal tissues interposed between the cells and the adjacent connective tissue. It consists of the basal lamina plus an associated layer of reticulin fibers. - GO:0005605 - GO:0008003 Wikipedia:Basement_membrane cellular_component basal lamina @@ -18078,7 +18478,12 @@ Disorders or aberrations in the development or migration of the neural crest cel - + + + + + + @@ -18086,7 +18491,6 @@ Disorders or aberrations in the development or migration of the neural crest cel An intracellular organelle, about 200 A in diameter, consisting of RNA and protein. It is the site of protein biosynthesis resulting from translation of messenger RNA (mRNA). It consists of two subunits, one large and one small, each containing only protein and RNA. Both the ribosome and its subunits are characterized by their sedimentation coefficients, expressed in Svedberg units (symbol: S). Hence, the prokaryotic ribosome (70S) comprises a large (50S) subunit and a small (30S) subunit, while the eukaryotic ribosome (80S) comprises a large (60S) subunit and a small (40S) subunit. Two sites on the ribosomal large subunit are involved in translation, namely the aminoacyl site (A site) and peptidyl site (P site). Ribosomes from prokaryotes, eukaryotes, mitochondria, and chloroplasts have characteristically distinct ribosomal proteins. - GO:0033279 NIF_Subcellular:sao1429207766 Wikipedia:Ribosome free ribosome @@ -18139,8 +18543,6 @@ Disorders or aberrations in the development or migration of the neural crest cel The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins. - GO:0005887 - GO:0005904 juxtamembrane NIF_Subcellular:sao1663586795 Wikipedia:Cell_membrane @@ -18231,7 +18633,6 @@ Disorders or aberrations in the development or migration of the neural crest cel Any cellular metabolic process involving deoxyribonucleic acid. This is one of the two main types of nucleic acid, consisting of a long, unbranched macromolecule formed from one, or more commonly, two, strands of linked deoxyribonucleotides. - GO:0055132 DNA metabolism cellular DNA metabolism biological_process @@ -18310,9 +18711,6 @@ Disorders or aberrations in the development or migration of the neural crest cel The cellular metabolic process in which a protein is formed, using the sequence of a mature mRNA or circRNA molecule to specify the sequence of amino acids in a polypeptide chain. Translation is mediated by the ribosome, and begins with the formation of a ternary complex between aminoacylated initiator methionine tRNA, GTP, and initiation factor 2, which subsequently associates with the small subunit of the ribosome and an mRNA or circRNA. Translation ends with the release of a polypeptide chain from the ribosome. - GO:0006416 - GO:0006453 - GO:0043037 Wikipedia:Translation_(genetics) protein anabolism protein biosynthesis @@ -18345,7 +18743,7 @@ Disorders or aberrations in the development or migration of the neural crest cel - + @@ -18359,8 +18757,6 @@ Disorders or aberrations in the development or migration of the neural crest cel The process preceding formation of the peptide bond between the first two amino acids of a protein. This includes the formation of a complex of the ribosome, mRNA or circRNA, and an initiation complex that contains the first aminoacyl-tRNA. - GO:0006440 - GO:0006454 biopolymerisation biopolymerization protein synthesis initiation @@ -18390,8 +18786,6 @@ Disorders or aberrations in the development or migration of the neural crest cel The successive addition of amino acid residues to a nascent polypeptide chain during protein biosynthesis. - GO:0006442 - GO:0006455 protein synthesis elongation translation elongation biological_process @@ -18419,8 +18813,6 @@ Disorders or aberrations in the development or migration of the neural crest cel The process resulting in the release of a polypeptide chain from the ribosome, usually in response to a termination codon (UAA, UAG, or UGA in the universal genetic code). - GO:0006443 - GO:0006456 protein synthesis termination translation termination translational complex disassembly @@ -18444,11 +18836,7 @@ Disorders or aberrations in the development or migration of the neural crest cel The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter or a transporter complex, a pore or a motor protein. https://github.com/geneontology/go-ontology/issues/20292 - jl 2012-12-13T16:25:32Z - GO:0015457 - GO:0015460 - GO:0044765 biological_process single-organism transport GO:0006810 @@ -18545,8 +18933,6 @@ Disorders or aberrations in the development or migration of the neural crest cel A process of secretion by a cell that results in the release of intracellular molecules (e.g. hormones, matrix proteins) contained within a membrane-bounded vesicle. Exocytosis can occur either by full fusion, when the vesicle collapses into the plasma membrane, or by a kiss-and-run mechanism that involves the formation of a transient contact, a pore, between a granule (for example of chromaffin cells) and the plasma membrane. The latter process most of the time leads to only partial secretion of the granule content. Exocytosis begins with steps that prepare vesicles for fusion with the membrane (tethering and docking) and ends when molecules are secreted from the cell. - GO:0016194 - GO:0016195 Wikipedia:Exocytosis vesicle exocytosis biological_process @@ -18592,9 +18978,6 @@ Disorders or aberrations in the development or migration of the neural crest cel A vesicle-mediated transport process in which cells take up external materials or membrane constituents by the invagination of a part of the plasma membrane to form a new membrane-bounded vesicle. https://github.com/geneontology/go-ontology/issues/24907 https://github.com/geneontology/go-ontology/issues/25268 - GO:0016193 - GO:0016196 - GO:0098701 Wikipedia:Endocytosis endocytic import into cell vesicle endocytosis @@ -18629,10 +19012,7 @@ Disorders or aberrations in the development or migration of the neural crest cel The evagination of a membrane, resulting in formation of a vesicle. - jl 2013-12-19T15:26:17Z - GO:0006902 - GO:1902591 membrane evagination vesicle biosynthesis vesicle formation @@ -18754,8 +19134,6 @@ Disorders or aberrations in the development or migration of the neural crest cel A programmed cell death process which begins when a cell receives an internal (e.g. DNA damage) or external signal (e.g. an extracellular death ligand), and proceeds through a series of biochemical events (signaling pathway phase) which trigger an execution phase. The execution phase is the last step of an apoptotic process, and is typically characterized by rounding-up of the cell, retraction of pseudopodes, reduction of cellular volume (pyknosis), chromatin condensation, nuclear fragmentation (karyorrhexis), plasma membrane blebbing and fragmentation of the cell into apoptotic bodies. When the execution phase is completed, the cell has died. - GO:0006917 - GO:0008632 cell suicide cellular suicide Wikipedia:Apoptosis @@ -18970,8 +19348,6 @@ Disorders or aberrations in the development or migration of the neural crest cel Reactions, triggered in response to the presence of a foreign body or the occurrence of an injury, which result in restriction of damage to the organism attacked or prevention/recovery from the infection caused by the attack. - GO:0002217 - GO:0042829 defence response physiological defense response biological_process @@ -19067,9 +19443,7 @@ Disorders or aberrations in the development or migration of the neural crest cel A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of an organelle within a cell. An organelle is an organized structure of distinctive morphology and function. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton. Excludes the plasma membrane. https://github.com/geneontology/go-ontology/issues/27189 - jl 2013-12-19T15:25:51Z - GO:1902589 organelle organisation single organism organelle organization biological_process @@ -19254,11 +19628,6 @@ Disorders or aberrations in the development or migration of the neural crest cel The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell. - GO:0023014 - GO:0023015 - GO:0023016 - GO:0023033 - GO:0023045 Wikipedia:Signal_transduction signaling cascade signalling cascade @@ -19306,7 +19675,6 @@ Disorders or aberrations in the development or migration of the neural crest cel The series of molecular signals initiated by a ligand binding to its receptor, in which the activated receptor promotes the exchange of GDP for GTP on the alpha-subunit of an associated heterotrimeric G-protein complex. The GTP-bound activated alpha-G-protein then dissociates from the beta- and gamma-subunits to further transmit the signal within the cell. The pathway begins with receptor-ligand interaction, and ends with regulation of a downstream cellular process. The pathway can start from the plasma membrane, Golgi or nuclear membrane. - GO:0038042 G protein coupled receptor protein signaling pathway G protein coupled receptor protein signalling pathway G-protein coupled receptor protein signal transduction @@ -19732,7 +20100,6 @@ Disorders or aberrations in the development or migration of the neural crest cel The flow of blood through the body of an animal, enabling the transport of nutrients to the tissues and the removal of waste products. - GO:0070261 biological_process hemolymph circulation GO:0008015 @@ -19754,11 +20121,7 @@ Disorders or aberrations in the development or migration of the neural crest cel A biological process is the execution of a genetically-encoded biological module or program. It consists of all the steps required to achieve the specific biological objective of the module. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence. https://github.com/geneontology/go-ontology/issues/24968 - jl 2012-09-19T15:05:24Z - GO:0000004 - GO:0007582 - GO:0044699 Wikipedia:Biological_process biological process physiological process @@ -19788,21 +20151,15 @@ Disorders or aberrations in the development or migration of the neural crest cel - + - The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation. + A cellular process consisting of the biochemical pathways by which a living organism transforms chemical substances. This includes including anabolism (biosynthetic process) and catabolism (catabolic process). Metabolic processes includes the transformation of small molecules, as well macromolecular processes such as DNA repair and replication, protein synthesis and degradation. https://github.com/geneontology/go-ontology/issues/26424 - jl + https://github.com/geneontology/go-ontology/issues/28932 2012-10-17T15:46:40Z - GO:0044236 - GO:0044710 Wikipedia:Metabolism metabolism - metabolic process resulting in cell growth - metabolism resulting in cell growth - multicellular organism metabolic process biological_process - single-organism metabolic process GO:0008152 @@ -19817,7 +20174,7 @@ Disorders or aberrations in the development or migration of the neural crest cel - The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation. + A cellular process consisting of the biochemical pathways by which a living organism transforms chemical substances. This includes including anabolism (biosynthetic process) and catabolism (catabolic process). Metabolic processes includes the transformation of small molecules, as well macromolecular processes such as DNA repair and replication, protein synthesis and degradation. GOC:go_curators ISBN:0198547684 @@ -19853,11 +20210,9 @@ Disorders or aberrations in the development or migration of the neural crest cel - The chemical reactions and pathways resulting in the formation of substances; typically the energy-requiring part of metabolism in which simpler substances are transformed into more complex ones. - jl + A cellular process consisting of the biochemical pathways by which a living organism synthesizes chemical substances. This typically represents the energy-requiring part of metabolism in which simpler substances are transformed into more complex ones. + https://github.com/geneontology/go-ontology/issues/28932 2012-10-17T15:52:18Z - GO:0044274 - GO:0044711 formation Wikipedia:Anabolism anabolism @@ -19876,7 +20231,7 @@ Disorders or aberrations in the development or migration of the neural crest cel - The chemical reactions and pathways resulting in the formation of substances; typically the energy-requiring part of metabolism in which simpler substances are transformed into more complex ones. + A cellular process consisting of the biochemical pathways by which a living organism synthesizes chemical substances. This typically represents the energy-requiring part of metabolism in which simpler substances are transformed into more complex ones. GOC:curators ISBN:0198547684 @@ -19886,13 +20241,12 @@ Disorders or aberrations in the development or migration of the neural crest cel + - The chemical reactions and pathways resulting in the formation of a macromolecule, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass. https://github.com/geneontology/go-ontology/issues/15249 https://github.com/geneontology/go-ontology/issues/25418 https://github.com/geneontology/go-ontology/issues/27189 - GO:0043284 biopolymer biosynthetic process macromolecule anabolism macromolecule biosynthesis @@ -19971,7 +20325,6 @@ Disorders or aberrations in the development or migration of the neural crest cel Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to the organism. - GO:0002245 physiological response to wounding biological_process GO:0009611 @@ -20038,7 +20391,6 @@ Disorders or aberrations in the development or migration of the neural crest cel The process whose specific outcome is the progression of an embryo from its formation until the end of its embryonic life stage. The end of the embryonic stage is organism-specific. For example, for mammals, the process would begin with zygote formation and end with birth. For insects, the process would begin at zygote formation and end with larval hatching. For plant zygotic embryos, this would be from zygote formation to the end of seed dormancy. For plant vegetative embryos, this would be from the initial determination of the cell or group of cells to form an embryo until the point when the embryo becomes independent of the parent plant. - GO:0009795 embryogenesis and morphogenesis Wikipedia:Embryogenesis embryogenesis @@ -20179,11 +20531,7 @@ Disorders or aberrations in the development or migration of the neural crest cel Any process that is carried out at the cellular level, but not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level. - jl 2012-12-11T16:56:55Z - GO:0008151 - GO:0044763 - GO:0050875 cell physiology cellular physiological process cell growth and/or maintenance @@ -20255,9 +20603,7 @@ Disorders or aberrations in the development or migration of the neural crest cel The infolding of a membrane. - jl 2013-12-02T13:58:34Z - GO:1902534 biological_process single-organism membrane invagination GO:0010324 @@ -20320,7 +20666,6 @@ Disorders or aberrations in the development or migration of the neural crest cel A process which begins when a cell receives an internal or external signal and activates a series of biochemical events (signaling pathway). The process ends with the death of the cell. https://github.com/geneontology/go-ontology/issues/24835 - GO:0016244 regulated cell death Wikipedia:Programmed_cell_death caspase-independent cell death @@ -20474,9 +20819,6 @@ Disorders or aberrations in the development or migration of the neural crest cel A lipid bilayer along with all the proteins and protein complexes embedded in it and attached to it. 2014-03-06T11:37:54Z - GO:0016021 - GO:0098589 - GO:0098805 Wikipedia:Biological_membrane Wikipedia:Transmembrane_protein integral component of membrane @@ -20535,8 +20877,6 @@ Disorders or aberrations in the development or migration of the neural crest cel A process that results in the assembly, arrangement of constituent parts, or disassembly of a cellular component. - GO:0044235 - GO:0071842 cell organisation cellular component organisation at cellular level cellular component organisation in other organism @@ -20672,7 +21012,6 @@ Disorders or aberrations in the development or migration of the neural crest cel A cellular transport process in which transported substances are moved in membrane-bounded vesicles; transported substances are enclosed in the vesicle lumen or located in the vesicle membrane. The process begins with a step that directs a substance to the forming vesicle, and includes vesicle budding and coating. Vesicles are then targeted to, and fuse with, an acceptor membrane. https://github.com/geneontology/go-ontology/issues/25421 - GO:0006899 vesicle transport vesicular transport nonselective vesicle transport @@ -20926,9 +21265,6 @@ Disorders or aberrations in the development or migration of the neural crest cel The chemical reactions and pathways involving a protein. Includes protein modification. https://github.com/geneontology/go-ontology/issues/23112 https://github.com/geneontology/go-ontology/issues/27189 - GO:0006411 - GO:0044267 - GO:0044268 Wikipedia:Protein_metabolism cellular protein metabolic process cellular protein metabolism @@ -21030,7 +21366,6 @@ Disorders or aberrations in the development or migration of the neural crest cel An immunoglobulin complex that is present in the plasma membrane of B cells and that in its canonical form is composed of two identical immunoglobulin heavy chains and two identical immunoglobulin light chains and a signaling subunit, a heterodimer of the Ig-alpha and Ig-beta proteins. - GO:0042570 B lymphocyte receptor complex B-cell receptor complex B-lymphocyte receptor complex @@ -21064,7 +21399,6 @@ Disorders or aberrations in the development or migration of the neural crest cel The process in which an antigen-presenting cell expresses antigen (peptide or lipid) on its cell surface in association with an MHC protein complex. - GO:0030333 Wikipedia:Antigen_presentation antigen presentation antigen processing @@ -21199,7 +21533,6 @@ Disorders or aberrations in the development or migration of the neural crest cel A cellular process that results in the breakdown of a cellular component. https://github.com/geneontology/go-ontology/issues/27189 - GO:0071845 cell structure disassembly cellular component disassembly at cellular level biological_process @@ -21284,7 +21617,6 @@ Disorders or aberrations in the development or migration of the neural crest cel The aggregation, arrangement and bonding together of a cellular component. - GO:0071844 cell structure assembly cellular component assembly at cellular level biological_process @@ -21387,10 +21719,7 @@ Disorders or aberrations in the development or migration of the neural crest cel The entirety of a process in which information is transmitted within a biological system. This process begins with an active signal and ends when a cellular response has been triggered. - jl 2010-02-16T09:30:50Z - GO:0023046 - GO:0044700 biological signaling signaling process signalling @@ -21675,7 +22004,6 @@ Disorders or aberrations in the development or migration of the neural crest cel The process in which a relatively unspecialized precursor cell acquires specialized features of a lymphocyte. A lymphocyte is a leukocyte commonly found in the blood and lymph that has the characteristics of a large nucleus, a neutral staining cytoplasm, and prominent heterochromatin. - GO:0046650 lymphocyte cell differentiation lymphocytic blood cell differentiation biological_process @@ -21868,7 +22196,6 @@ Disorders or aberrations in the development or migration of the neural crest cel The process in which a precursor cell type acquires the specialized features of a B cell. A B cell is a lymphocyte of B lineage with the phenotype CD19-positive and capable of B cell mediated immunity. - GO:0042115 B lymphocyte differentiation B-cell differentiation B-lymphocyte differentiation @@ -21963,8 +22290,6 @@ Disorders or aberrations in the development or migration of the neural crest cel The process in which a precursor cell type acquires characteristics of a more mature T-cell. A T cell is a type of lymphocyte whose definin characteristic is the expression of a T cell receptor complex. - GO:0042112 - GO:0046652 T lymphocyte differentiation T-cell differentiation T-lymphocyte differentiation @@ -22209,7 +22534,6 @@ Disorders or aberrations in the development or migration of the neural crest cel The progressive compaction of dispersed interphase chromatin into threadlike chromosomes prior to mitotic or meiotic nuclear division, or during apoptosis, in eukaryotic cells. - GO:0000068 DNA condensation eukaryotic chromosome condensation nuclear chromosome condensation @@ -22520,7 +22844,6 @@ Disorders or aberrations in the development or migration of the neural crest cel A structure lying external to one or more cells, which provides structural support, biochemical or biomechanical cues for cells or tissues. - GO:0005578 NIF_Subcellular:nlx_subcell_20090513 Wikipedia:Extracellular_matrix proteinaceous extracellular matrix @@ -22705,7 +23028,6 @@ Disorders or aberrations in the development or migration of the neural crest cel A vesicle found in the cytoplasm of a cell. - GO:0016023 NIF_Subcellular:sao180601769 cellular_component cytoplasmic membrane bounded vesicle @@ -22781,7 +23103,6 @@ Disorders or aberrations in the development or migration of the neural crest cel Any small, fluid-filled, spherical organelle enclosed by membrane. - GO:0031988 NIF_Subcellular:sao221389602 Wikipedia:Vesicle_(biology) cellular_component @@ -22990,10 +23311,7 @@ Disorders or aberrations in the development or migration of the neural crest cel - jl 2012-09-19T16:07:47Z - GO:0044707 - GO:0050874 organismal physiological process biological_process single-multicellular organism process @@ -23020,9 +23338,7 @@ Disorders or aberrations in the development or migration of the neural crest cel A biological process whose specific outcome is the progression of an integrated living unit: an anatomical structure (which may be a subcellular structure, cell, tissue, or organ), or organism over time from an initial condition to a later condition. - jl 2012-12-19T12:21:31Z - GO:0044767 development biological_process single-organism developmental process @@ -23046,8 +23362,6 @@ Disorders or aberrations in the development or migration of the neural crest cel The appearance of type I interferon due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. Type I interferons include the interferon-alpha, beta, delta, episilon, zeta, kappa, tau, and omega gene families. - GO:0045351 - GO:0072641 interferon type I production type I IFN production type I interferon biosynthetic process @@ -23121,9 +23435,6 @@ Disorders or aberrations in the development or migration of the neural crest cel The disaggregation of a protein-containing macromolecular complex into its constituent components. https://github.com/geneontology/go-ontology/issues/22580 - GO:0034623 - GO:0043241 - GO:0043624 protein complex disassembly biological_process cellular macromolecule complex disassembly @@ -23145,10 +23456,14 @@ Disorders or aberrations in the development or migration of the neural crest cel - + + + + + + A stable assembly of two or more macromolecules, i.e. proteins, nucleic acids, carbohydrates or lipids, in which at least one component is a protein and the constituent parts function together. - GO:0043234 macromolecular complex macromolecule complex protein containing complex @@ -23313,7 +23628,6 @@ Disorders or aberrations in the development or migration of the neural crest cel A process in which a monoatomic ion is transported across a membrane. Monatomic ions (also called simple ions) are ions consisting of exactly one atom. - GO:0099131 ion transmembrane transport ion membrane transport transmembrane ion transport @@ -23484,7 +23798,6 @@ Disorders or aberrations in the development or migration of the neural crest cel An immunoglobulin-like complex that is present in at least the plasma membrane of pre-B cells, and that is composed of two identical immunoglobulin heavy chains and two surrogate light chains, each composed of the lambda-5 and VpreB proteins, and a signaling subunit, a heterodimer of the Ig-alpha and Ig-beta proteins. - bf 2010-03-11T10:46:10Z pre-BCR cellular_component @@ -23509,10 +23822,7 @@ Disorders or aberrations in the development or migration of the neural crest cel Receiving a signal and transmitting it in the cell to initiate a change in cell activity. A signal is a physical entity or change in state that is used to transfer information in order to trigger a response. - bf 2011-08-01T02:45:27Z - GO:0004872 - GO:0019041 receptor activity receptor activity involved in signal transduction signalling receptor activity @@ -23562,7 +23872,6 @@ Disorders or aberrations in the development or migration of the neural crest cel The increase in size or mass of an entire organism, a part of an organism or a cell. - GO:0048590 biological_process growth pattern non-developmental growth @@ -24136,9 +24445,6 @@ Disorders or aberrations in the development or migration of the neural crest cel Any biological process involved in the maintenance of an internal steady state. - GO:0032844 - GO:0032845 - GO:0032846 homeostasis activation of homeostatic process inhibition of homeostatic process @@ -24316,9 +24622,6 @@ Disorders or aberrations in the development or migration of the neural crest cel The chemical reactions and pathways involving macromolecules, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass. https://github.com/geneontology/go-ontology/issues/26424 - GO:0034960 - GO:0043283 - GO:0044259 biopolymer metabolic process macromolecule metabolism organismal macromolecule metabolism @@ -24435,14 +24738,17 @@ Disorders or aberrations in the development or migration of the neural crest cel Organized structure of distinctive morphology and function, not bounded by a lipid bilayer membrane. Includes ribosomes, the cytoskeleton and chromosomes. https://github.com/geneontology/go-ontology/issues/21881 https://github.com/geneontology/go-ontology/issues/28153 + https://github.com/geneontology/go-ontology/issues/29106 NIF_Subcellular:sao1456184038 + membrane-less organelle + non-membrane-bounded organelle non-membrane-enclosed organelle cellular_component biological condensate GO:0043228 - non-membrane-bounded organelle + membraneless organelle @@ -24578,11 +24884,13 @@ Disorders or aberrations in the development or migration of the neural crest cel Organized structure of distinctive morphology and function, not bounded by a lipid bilayer membrane and occurring within the cell. Includes ribosomes, the cytoskeleton and chromosomes. + https://github.com/geneontology/go-ontology/issues/29106 + intracellular non-membrane-bounded organelle intracellular non-membrane-enclosed organelle cellular_component GO:0043232 - intracellular non-membrane-bounded organelle + intracellular membraneless organelle @@ -24689,11 +24997,7 @@ Disorders or aberrations in the development or migration of the neural crest cel Any process in which macromolecules aggregate, disaggregate, or are modified, resulting in the formation, disassembly, or alteration of a protein complex. https://github.com/geneontology/go-ontology/issues/22580 - mah 2010-09-08T10:01:42Z - GO:0034600 - GO:0034621 - GO:0071822 protein complex subunit organisation protein complex subunit organization biological_process @@ -24728,7 +25032,6 @@ Disorders or aberrations in the development or migration of the neural crest cel A process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of a cellular component. Includes biosynthesis of constituent macromolecules, and those macromolecular modifications that are involved in synthesis or assembly of the cellular component. https://github.com/geneontology/go-ontology/issues/27194 - GO:0071843 cellular component biogenesis at cellular level biological_process GO:0044085 @@ -24757,7 +25060,6 @@ Disorders or aberrations in the development or migration of the neural crest cel A ribonucleoprotein complex that contains aminoacylated initiator methionine tRNA, GTP, and initiation factor 2 (either eIF2 in eukaryotes, or IF2 in prokaryotes). In prokaryotes, fMet-tRNA (initiator) is used rather than Met-tRNA (initiator). - jl 2009-10-22T02:38:55Z translation initiation (ternary) complex Met-tRNA/eIF2.GTP ternary complex @@ -24774,35 +25076,6 @@ Disorders or aberrations in the development or migration of the neural crest cel - - - - - - The chemical reactions and pathways by which individual cells transform chemical substances. - cellular metabolism - biological_process - intermediary metabolism - GO:0044237 - - This term should not be used for direct annotation. It should be possible to make a more specific annotation to one of the children of this term. - cellular metabolic process - - - - - The chemical reactions and pathways by which individual cells transform chemical substances. - GOC:go_curators - - - - - intermediary metabolism - GOC:mah - - - - @@ -24829,32 +25102,6 @@ Disorders or aberrations in the development or migration of the neural crest cel - - - - - - The chemical reactions and pathways resulting in the formation of substances, carried out by individual cells. - https://github.com/geneontology/go-ontology/issues/27052 - cellular anabolism - cellular biosynthesis - cellular formation - cellular synthesis - biological_process - GO:0044249 - - This term should not be used for direct annotation. It should be possible to make a more specific annotation to one of the children of this term. - cellular biosynthetic process - - - - - The chemical reactions and pathways resulting in the formation of substances, carried out by individual cells. - GOC:jl - - - - @@ -24905,7 +25152,6 @@ Disorders or aberrations in the development or migration of the neural crest cel The joining of the lipid bilayer membrane that surround a cell with that of another cell, producing a single cell. - GO:0006947 cell fusion cell-cell fusion biological_process @@ -24966,7 +25212,6 @@ Disorders or aberrations in the development or migration of the neural crest cel - GO:0002226 Wikipedia:Innate_immune_system innate immunity nonspecific immune response @@ -25602,7 +25847,6 @@ Disorders or aberrations in the development or migration of the neural crest cel Any process that activates or increases the frequency, rate or extent of a biological process. Biological processes are regulated by many means; examples include the control of gene expression, protein modification or interaction with a protein or substrate molecule. - GO:0043119 positive regulation of physiological process up regulation of biological process up-regulation of biological process @@ -25645,7 +25889,6 @@ Disorders or aberrations in the development or migration of the neural crest cel Any process that stops, prevents, or reduces the frequency, rate or extent of a biological process. Biological processes are regulated by many means; examples include the control of gene expression, protein modification or interaction with a protein or substrate molecule. - GO:0043118 down regulation of biological process down-regulation of biological process downregulation of biological process @@ -25688,7 +25931,6 @@ Disorders or aberrations in the development or migration of the neural crest cel Any process that activates or increases the frequency, rate or extent of a cellular process, any of those that are carried out at the cellular level, but are not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level. - GO:0051242 positive regulation of cellular physiological process up regulation of cellular process up-regulation of cellular process @@ -25877,7 +26119,6 @@ Disorders or aberrations in the development or migration of the neural crest cel The process in which anatomical structures are generated and organized during the embryonic phase. The embryonic phase begins with zygote formation. The end of the embryonic phase is organism-specific. For example, it would be at birth for mammals, larval hatching for insects and seed dormancy in plants. - GO:0048828 embryonic anatomical structure morphogenesis biological_process GO:0048598 @@ -26365,7 +26606,6 @@ Disorders or aberrations in the development or migration of the neural crest cel Any process that modulates the frequency, rate or extent of a biological process. Biological processes are regulated by many means; examples include the control of gene expression, protein modification or interaction with a protein or substrate molecule. - GO:0050791 regulation of physiological process biological_process GO:0050789 @@ -26441,7 +26681,6 @@ Disorders or aberrations in the development or migration of the neural crest cel Any process that modulates the frequency, rate or extent of a cellular process, any of those that are carried out at the cellular level, but are not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level. - GO:0051244 regulation of cellular physiological process biological_process GO:0050794 @@ -26634,7 +26873,6 @@ Disorders or aberrations in the development or migration of the neural crest cel Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus. The process begins with detection of the stimulus and ends with a change in state or activity or the cell or organism. - GO:0051869 physiological response to stimulus biological_process GO:0050896 @@ -26800,9 +27038,7 @@ Disorders or aberrations in the development or migration of the neural crest cel Any process in which a cell, a substance, or a cellular entity, such as a protein complex or organelle, is transported, tethered to or otherwise maintained in a specific location. In the case of substances, localization may also be achieved via selective degradation. https://github.com/geneontology/go-ontology/issues/27052 - jl 2013-12-18T13:51:04Z - GO:1902578 establishment and maintenance of localization establishment and maintenance of position localisation @@ -27008,9 +27244,6 @@ Disorders or aberrations in the development or migration of the neural crest cel A process that is carried out at the cellular level that results in the assembly, arrangement of constituent parts, or disassembly of chromosomes, structures composed of a very long molecule of DNA and associated proteins that carries hereditary information. This term covers covalent modifications at the molecular level as well as spatial relationships among the major components of a chromosome. https://github.com/geneontology/go-ontology/issues/22811 https://github.com/geneontology/go-ontology/issues/4585 - GO:0006323 - GO:0007001 - GO:0051277 DNA condensation chromosome organisation DNA packaging @@ -27091,8 +27324,6 @@ Disorders or aberrations in the development or migration of the neural crest cel Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus from another living organism. - GO:0009613 - GO:0042828 biological_process GO:0051707 response to other organism @@ -27151,9 +27382,7 @@ Disorders or aberrations in the development or migration of the neural crest cel The process in which a solute is transported across a lipid bilayer, from one side of a membrane to the other. - tb 2015-10-21T13:22:47Z - GO:0090662 membrane transport ATP hydrolysis coupled transmembrane transport biological_process @@ -27399,7 +27628,6 @@ Disorders or aberrations in the development or migration of the neural crest cel The process in which the anatomical structures of a tube are generated and organized from an epithelium. Epithelial tubes transport gases, liquids and cells from one site to another and form the basic structure of many organs and tissues, with tube shape and organization varying from the single-celled excretory organ in Caenorhabditis elegans to the branching trees of the mammalian kidney and insect tracheal system. - dph 2009-04-28T09:33:36Z biological_process GO:0060562 @@ -27436,10 +27664,7 @@ Disorders or aberrations in the development or migration of the neural crest cel A process which results in the assembly, arrangement of constituent parts, or disassembly of a membrane. A membrane is a double layer of lipid molecules that encloses all cells, and, in eukaryotes, many organelles; may be a single or double lipid bilayer; also includes associated proteins. - jl 2010-02-08T02:43:11Z - GO:0016044 - GO:0044802 cellular membrane organisation cellular membrane organization membrane organisation @@ -27499,10 +27724,7 @@ Disorders or aberrations in the development or migration of the neural crest cel The membrane organization process that joins two lipid bilayers to form a single membrane. - jl 2010-02-08T02:48:06Z - GO:0006944 - GO:0044801 Wikipedia:Lipid_bilayer_fusion cellular membrane fusion biological_process @@ -27527,7 +27749,6 @@ Disorders or aberrations in the development or migration of the neural crest cel The process in which the anatomical structures of a branched epithelium are generated and organized. - dph 2010-05-25T09:05:34Z biological_process GO:0061138 @@ -27559,7 +27780,6 @@ Disorders or aberrations in the development or migration of the neural crest cel An extracellular matrix consisting mainly of proteins (especially collagen) and glycosaminoglycans (mostly as proteoglycans) that provides not only essential physical scaffolding for the cellular constituents but can also initiate crucial biochemical and biomechanical cues required for tissue morphogenesis, differentiation and homeostasis. The components are secreted by cells in the vicinity and form a sheet underlying or overlying cells such as endothelial and epithelial cells. - dph 2018-04-13T12:47:21Z cellular_component GO:0062023 @@ -27600,9 +27820,6 @@ Disorders or aberrations in the development or migration of the neural crest cel The aggregation, arrangement and bonding together of a set of macromolecules to form a protein-containing complex. https://github.com/geneontology/go-ontology/issues/22580 - GO:0006461 - GO:0034622 - GO:0043623 cellular protein complex assembly biological_process cellular macromolecule complex assembly @@ -27838,7 +28055,6 @@ Disorders or aberrations in the development or migration of the neural crest cel Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a chemical stimulus. - mah 2009-08-27T04:41:45Z biological_process GO:0070887 @@ -27878,7 +28094,6 @@ Disorders or aberrations in the development or migration of the neural crest cel The aggregation, arrangement and bonding together of a set of components to form an organelle. An organelle is an organized structure of distinctive morphology and function. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton. Excludes the plasma membrane. - mah 2009-09-15T03:00:51Z biological_process GO:0070925 @@ -27899,7 +28114,6 @@ Disorders or aberrations in the development or migration of the neural crest cel The process in which immunoglobulin heavy chain V, D, and J gene segments are recombined within a single locus utilizing the conserved heptamer and nonomer recombination signal sequences (RSS). - mah 2010-03-09T04:20:31Z immunoglobulin V(D)J joining immunoglobulin V(D)J recombination @@ -27941,7 +28155,6 @@ Disorders or aberrations in the development or migration of the neural crest cel The process in which immunoglobulin light chain V and J gene segments are recombined within a single locus utilizing the conserved heptamer and nonomer recombination signal sequences (RSS). - mah 2010-03-09T04:22:29Z immunoglobulin V(D)J joining immunoglobulin V(D)J recombination @@ -27983,7 +28196,6 @@ Disorders or aberrations in the development or migration of the neural crest cel A protein complex composed of two identical immunoglobulin heavy chains of the IgD isotype and two identical immunoglobulin light chains, held together by disulfide bonds. An IgD immunoglobulin complex may be embedded in the plasma membrane or present in the extracellular space, in mucosal areas or other tissues, or circulating in the blood or lymph. - mah 2010-03-24T01:44:53Z cellular_component GO:0071738 @@ -28006,7 +28218,6 @@ Disorders or aberrations in the development or migration of the neural crest cel A protein complex composed of two identical immunoglobulin heavy chains of the IgM isotype and two identical immunoglobulin light chains, held together by disulfide bonds, and in its circulating form complexed with J chain in polymeric forms. An IgM immunoglobulin complex may be embedded in the plasma membrane or present in the extracellular space, in mucosal areas or other tissues, or circulating in the blood or lymph. - mah 2010-03-24T01:44:53Z cellular_component GO:0071753 @@ -28047,7 +28258,6 @@ Disorders or aberrations in the development or migration of the neural crest cel Any process in which macromolecules aggregate, disaggregate, or are modified, resulting in the formation, disassembly, or alteration of a ribonucleoprotein complex. https://github.com/geneontology/go-ontology/issues/25143 - mah 2010-09-08T10:10:35Z RNA-protein complex subunit organization protein-RNA complex subunit organization @@ -28090,9 +28300,7 @@ Disorders or aberrations in the development or migration of the neural crest cel A process that results in the biosynthesis of constituent macromolecules, assembly, arrangement of constituent parts, or disassembly of a cellular component. https://github.com/geneontology/go-ontology/issues/27189 - mah 2010-09-10T01:39:16Z - GO:0071841 cellular component organisation or biogenesis cellular component organisation or biogenesis at cellular level cellular component organization or biogenesis at cellular level @@ -28130,7 +28338,6 @@ Disorders or aberrations in the development or migration of the neural crest cel The broad region around and including the plasma membrane of a cell, encompassing the cell cortex (inside the cell), the plasma membrane, and any external encapsulating structures. - mah 2010-10-04T01:51:47Z cellular_component GO:0071944 @@ -28175,7 +28382,6 @@ Disorders or aberrations in the development or migration of the neural crest cel The aggregation, arrangement and bonding together of a set of components to form an extracellular vesicular exosome, a membrane-bounded vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Exosomes are defined by their size, which generally ranges from 30 nm to 100 nm. - mah 2010-10-18T03:44:18Z extracellular vesicular exosome assembly biological_process @@ -28229,7 +28435,6 @@ Disorders or aberrations in the development or migration of the neural crest cel The developmental process pertaining to the initial formation of an epithelial tube. https://github.com/geneontology/go-ontology/issues/22302 - mah 2010-02-26T02:15:40Z biological_process GO:0072175 @@ -28267,7 +28472,6 @@ Disorders or aberrations in the development or migration of the neural crest cel The joining of two lipid bilayers to form a single organelle membrane. - tb 2009-12-11T11:44:58Z biological_process GO:0090174 @@ -28306,7 +28510,6 @@ Disorders or aberrations in the development or migration of the neural crest cel The process in which a precursor cell type acquires the specialized features of a dendritic cell. A dendritic cell is a leukocyte of dendritic lineage specialized in the uptake, processing, and transport of antigens to lymph nodes for the purpose of stimulating an immune response via T cell activation. - pr 2011-04-01T10:08:42Z biological_process GO:0097028 @@ -28334,9 +28537,7 @@ Disorders or aberrations in the development or migration of the neural crest cel The series of molecular signals which triggers the apoptotic death of a cell. The pathway starts with reception of a signal, and ends when the execution phase of apoptosis is triggered. - pr 2011-11-23T09:30:23Z - GO:0008624 apoptotic signalling pathway induction of apoptosis by extracellular signals biological_process @@ -28376,7 +28577,6 @@ Disorders or aberrations in the development or migration of the neural crest cel A stage of the apoptotic process that starts with the controlled breakdown of the cell through the action of effector caspases or other effector molecules (e.g. cathepsins, calpains etc.). Key steps of the execution phase are rounding-up of the cell, retraction of pseudopodes, reduction of cellular volume (pyknosis), chromatin condensation, nuclear fragmentation (karyorrhexis), plasma membrane blebbing and fragmentation of the cell into apoptotic bodies. When the execution phase is completed, the cell has died. - pr 2011-11-23T09:45:24Z execution phase of apoptotic process apoptosis @@ -28411,7 +28611,6 @@ Disorders or aberrations in the development or migration of the neural crest cel Any vesicle that is part of the intracellular region. - pr 2016-03-29T17:39:45Z cellular_component GO:0097708 @@ -28431,7 +28630,6 @@ Disorders or aberrations in the development or migration of the neural crest cel The assembly and secretion of an extracellular exosome, a membrane-bounded vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. - pr 2016-10-03T14:35:25Z exosome assembly or secretion exosome biogenesis @@ -28460,9 +28658,7 @@ Disorders or aberrations in the development or migration of the neural crest cel Reactions triggered in response to the presence of another organism that act to protect the cell or organism from damage caused by that organism. https://github.com/geneontology/go-ontology/issues/22173 - dos 2013-11-11T12:59:11Z - GO:0009814 defence response incompatible interaction defence response to pathogen, incompatible interaction defense response, incompatible interaction @@ -28504,7 +28700,6 @@ Disorders or aberrations in the development or migration of the neural crest cel A membrane that is a (regional) part of the plasma membrane. - dos 2014-03-06T11:55:32Z region of plasma membrane cellular_component @@ -28561,7 +28756,6 @@ Disorders or aberrations in the development or migration of the neural crest cel - @@ -29113,21 +29307,22 @@ Disorders or aberrations in the development or migration of the neural crest cel - A part of a cellular organism that is either an immaterial entity or a material entity with granularity above the level of a protein complex but below that of an anatomical system. Or, a substance produced by a cellular organism with granularity above the level of a protein complex. + A part of a cellular organism consisting of a material entity with granularity above the level of a protein complex but below that of an anatomical system. Note that cellular organisms exclude viruses. https://github.com/geneontology/go-ontology/issues/24200 https://github.com/geneontology/go-ontology/issues/26424 - kmv + https://github.com/geneontology/go-ontology/issues/28978 2019-08-12T18:01:37Z + cellular anatomical entity cellular_component GO:0110165 - cellular anatomical entity + cellular anatomical structure - A part of a cellular organism that is either an immaterial entity or a material entity with granularity above the level of a protein complex but below that of an anatomical system. Or, a substance produced by a cellular organism with granularity above the level of a protein complex. + A part of a cellular organism consisting of a material entity with granularity above the level of a protein complex but below that of an anatomical system. Note that cellular organisms exclude viruses. GOC:kmv @@ -29156,7 +29351,6 @@ Disorders or aberrations in the development or migration of the neural crest cel A prolongation or process extending from a cell and that is bounded by plasma membrane, e.g. a cilium, lamellipodium, or axon. https://github.com/geneontology/go-ontology/issues/13193 - krc 2017-03-21T17:26:07Z cellular_component GO:0120025 @@ -29195,7 +29389,6 @@ Disorders or aberrations in the development or migration of the neural crest cel Formation of a prolongation or process extending and that is bounded by plasma membrane, e.g. a cilium, lamellipodium, or axon. https://github.com/geneontology/go-ontology/issues/13298 - krc 2017-04-24T23:56:08Z eupodium biological_process @@ -29243,7 +29436,6 @@ Disorders or aberrations in the development or migration of the neural crest cel A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a plasma membrane bounded prolongation or process extending from a cell, e.g. a cilium or axon. https://github.com/geneontology/go-ontology/issues/13298 - krc 2017-04-26T16:07:02Z biological_process GO:0120036 @@ -29276,7 +29468,6 @@ Disorders or aberrations in the development or migration of the neural crest cel A mitotic cell cycle process comprising the steps by which the nucleus of a eukaryotic cell divides; the process involves condensation of chromosomal DNA into a highly compacted form. Canonically, mitosis produces two daughter nuclei whose chromosome complement is identical to that of the mother cell. https://github.com/geneontology/go-ontology/issues/19910 - pg 2017-03-23T14:44:23Z mitosis biological_process @@ -29316,7 +29507,6 @@ Disorders or aberrations in the development or migration of the neural crest cel The cellular processes that contribute to exocytosis. - pg 2017-05-15T13:20:45Z biological_process GO:0140029 @@ -29338,7 +29528,6 @@ Disorders or aberrations in the development or migration of the neural crest cel The assembly and secretion a set of components to form an extracellular vesicule, a membrane-bounded vesicle that is released into the extracellular region. Extracellular vesicles include exosomes, microvesicles and apoptotic bodies, based on the mechanism by which they are released from cells and differentiated based on their size and content. https://github.com/geneontology/go-ontology/issues/14256 - pg 2017-10-23T11:53:42Z extracellular vesicle assembly biological_process @@ -29366,7 +29555,6 @@ Disorders or aberrations in the development or migration of the neural crest cel A cellular process in which two or more cells combine together, their plasma membrane fusing, producing a single cell. In some cases, nuclei fuse, producing a polyploid cell, while in other cases, nuclei remain separate, producing a syncytium. https://github.com/geneontology/go-ontology/issues/15939 - pg 2018-08-13T18:38:18Z cell fusion cell cell fusion @@ -29416,7 +29604,6 @@ Disorders or aberrations in the development or migration of the neural crest cel The directed movement of some substance from a cell, into the extracellular region. This may occur via transport across the plasma membrane or via exocytosis. - pg 2019-05-22T11:20:45Z efflux biological_process @@ -29438,7 +29625,6 @@ Disorders or aberrations in the development or migration of the neural crest cel Reactions triggered in response to the presence of a symbiont that act to protect or prevent damage to the host. https://github.com/geneontology/go-ontology/issues/20261 - pg 2020-11-11T17:19:06Z biological_process GO:0140546 @@ -29475,7 +29661,6 @@ Disorders or aberrations in the development or migration of the neural crest cel Any process that modulates the frequency, rate or extent of leukocyte differentiation. - pr 2013-05-02T17:32:42Z regulation of immune cell differentiation regulation of leucocyte differentiation @@ -29527,7 +29712,6 @@ Disorders or aberrations in the development or migration of the neural crest cel A process that is part of the mitotic cell cycle. - jl 2014-05-22T14:22:34Z biological_process GO:1903047 @@ -29567,7 +29751,6 @@ Disorders or aberrations in the development or migration of the neural crest cel The process in which a relatively unspecialized cell acquires the specialized features of a mononuclear cell. - cls 2014-06-25T15:47:09Z biological_process GO:1903131 @@ -29602,7 +29785,6 @@ Disorders or aberrations in the development or migration of the neural crest cel Any vesicle that is part of the extracellular region. - jl 2014-10-22T14:26:11Z cellular_component microparticle @@ -29651,7 +29833,6 @@ Disorders or aberrations in the development or migration of the neural crest cel Any process that modulates the frequency, rate or extent of hemopoiesis. - pad 2014-12-04T15:34:13Z regulation of blood cell biosynthesis regulation of blood cell formation @@ -29704,10 +29885,7 @@ Disorders or aberrations in the development or migration of the neural crest cel A macromolecular complex that contains both RNA and protein molecules. - pr 2015-11-19T12:26:37Z - GO:0030529 - GO:1990903 Wikipedia:Ribonucleoprotein RNA-protein complex RNP @@ -29752,7 +29930,6 @@ Disorders or aberrations in the development or migration of the neural crest cel Any process that modulates the frequency, rate or extent of multicellular organismal development. - tb 2010-08-05T11:25:59Z biological_process GO:2000026 @@ -29790,7 +29967,6 @@ Disorders or aberrations in the development or migration of the neural crest cel Any process that modulates the frequency, rate or extent of cell motility. - mah 2010-10-01T09:41:21Z regulation of cell locomotion regulation of movement of a cell @@ -29850,7 +30026,6 @@ Disorders or aberrations in the development or migration of the neural crest cel Any process that activates or increases the frequency, rate or extent of cell motility. - mah 2010-10-01T09:41:30Z positive regulation of cell locomotion positive regulation of movement of a cell @@ -29956,7 +30131,6 @@ Disorders or aberrations in the development or migration of the neural crest cel - NCBITaxon:85055 GC_ID:1 house mouse mouse @@ -29995,7 +30169,6 @@ Disorders or aberrations in the development or migration of the neural crest cel - NCBITaxon:40673 GC_ID:1 bony vertebrates ncbi_taxonomy @@ -30362,7 +30535,6 @@ Disorders or aberrations in the development or migration of the neural crest cel - NCBITaxon:109679 GC_ID:1 ncbi_taxonomy NCBITaxon:39107 @@ -30621,7 +30793,6 @@ Disorders or aberrations in the development or migration of the neural crest cel A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities - PATO:0000072 quality PATO:0000001 quality @@ -30659,7 +30830,6 @@ Disorders or aberrations in the development or migration of the neural crest cel A morphological quality inhering in a bearer by virtue of the bearer's ratios of distances between its features (points, edges, surfaces and also holes etc). - PATO:0001647 relational shape quality quality PATO:0000052 @@ -30681,7 +30851,6 @@ Disorders or aberrations in the development or migration of the neural crest cel A morphology quality inhering in a bearer by virtue of the bearer's relative position, shape, arrangements and connectivity of an organism's various parts; the pattern underlying its form. - PATO:0001452 conformation relational structural quality quality @@ -30800,7 +30969,6 @@ Disorders or aberrations in the development or migration of the neural crest cel A quality of a physical entity that exists through action of continuants at the physical level of organisation in relation to other entities. - PATO:0002079 Wikipedia:Physical_property relational physical quality quality @@ -30822,8 +30990,6 @@ Disorders or aberrations in the development or migration of the neural crest cel A quality which inheres in a continuant. - PATO:0001237 - PATO:0001238 snap:Quality monadic quality of a continuant multiply inhering quality of a physical entity @@ -31163,7 +31329,6 @@ Disorders or aberrations in the development or migration of the neural crest cel A convex 3-D shape quality inhering in a bearer by virtue of the bearer's exhibiting a consistently-sized round cross section. - PATO:0001203 rod-like rod-shaped tubulate @@ -31652,7 +31817,6 @@ Disorders or aberrations in the development or migration of the neural crest cel A quality inhering in a cell by virtue of the cell having a high nuclear/cytoplasmic ratio. - http://orcid.org/0000-0001-5208-3432 high N:C ratio quality PATO:0040072 @@ -31674,7 +31838,6 @@ Disorders or aberrations in the development or migration of the neural crest cel A quality of continuant that exist at the anatomical level of organisation and anything under it. This includes, but is not limited to, cells , tissues, and components. - http://orcid.org/0000-0001-7258-9596 quality PATO:0070044 anatomical structure quality @@ -31687,7 +31850,6 @@ Disorders or aberrations in the development or migration of the neural crest cel A quality inhering in an anotomical structure by virtue of its capacity to be stained by specific histological dyes. - http://orcid.org/0000-0001-7258-9596 quality PATO:0070045 anatomical histological quality @@ -31700,7 +31862,6 @@ Disorders or aberrations in the development or migration of the neural crest cel An affinity inhering in an anatomical structure by virtue of the bearer exhibiting a molecular interaction that stains and colors, pale-pink, with Wright-Giemsa stain. - http://orcid.org/0000-0001-7258-9596 quality PATO:0070046 neutrophillic @@ -31719,7 +31880,6 @@ Disorders or aberrations in the development or migration of the neural crest cel An affinity inhering in an anatomical structure by virtue of the bearer exhibiting a molecular interaction for both basic and acid stains under specific pH conditions. - http://orcid.org/0000-0001-7258-9596 quality PATO:0070047 polychromatophilic @@ -31737,7 +31897,7 @@ Disorders or aberrations in the development or migration of the neural crest cel - + @@ -31749,7 +31909,7 @@ Disorders or aberrations in the development or migration of the neural crest cel native protein protein PR:000000001 - The definition above excludes protein complexes, which some also consider a protein. Those who wish to refer to a class representing both senses of the word are directed to CHEBI:36080. Note that the definition allows for experimentally-manipulated genes, and allows for artifically-produced derivatives that mimic those found naturally. Proteins (in the sense defined here) that descended from a common ancestor can be classified into families and superfamilies composed of products of evolutionarily-related genes. The domain architecture of a protein is described by the order of its constituent domains. Proteins with the same domains in the same order are defined as homeomorphic [PRO:WCB]. + The definition above excludes protein complexes, which some also consider a protein. Those who wish to refer to a class representing both senses of the word are directed to CHEBI:36080. Note that the definition allows for experimentally-manipulated genes, and allows for artifically-produced derivatives that mimic those found naturally. Proteins (in the sense defined here) that descended from a common ancestor can be classified into families and superfamilies composed of products of evolutionarily-related genes. The domain architecture of a protein is described by the order of its constituent domains. Proteins with the same domains in the same order are defined as homeomorphic [PRO:WCB). protein @@ -33757,7 +33917,6 @@ Disorders or aberrations in the development or migration of the neural crest cel - A protein with core architecture consisting of a signal sequence, followed by 7 Ig-like domains (Pfam:PF00047, Pfam:PF07679, or Pfam:PF07686), a transmembrane region, and a cytoplasmic Protein tyrosine kinase domain. PIRSF:PIRSF038502 protein @@ -34896,51 +35055,51 @@ Disorders or aberrations in the development or migration of the neural crest cel - + - + - A material entity that minimally consists of a protein. + A molecular entity that minimally consists of a protein. protein protein aggregate protein complex protein-containing complex protein - PR:000050567 - Note: This includes single proteins and derivatives thereof (PR:000000001), protein-containing complexes (GO:0032991), and protein aggregates (PR:000050566). - protein-containing material entity + PR:000064867 + Note: This includes single proteins and derivatives thereof (PR:000000001), protein-containing complexes (GO:0032991), and protein aggregates (PR:000050565). + protein-containing molecular entity - + - A material entity that minimally consists of a protein. + A molecular entity that minimally consists of a protein. PRO:DAN - + protein PRO:DAN - + protein aggregate PRO:DAN - + protein complex PRO:DAN - + protein-containing complex PRO:DAN @@ -35061,7 +35220,6 @@ Disorders or aberrations in the development or migration of the neural crest cel Organ component adjacent to an organ cavity and which consists of a maximal aggregate of organ component layers. - UBERON:0009915 wall FMA:82482 galen:Wall @@ -35436,7 +35594,6 @@ Disorders or aberrations in the development or migration of the neural crest cel Anatomical cluster consisting of the skeletal elements and articular elements that are part of an individual subdivision of the organism. - UBERON:0010322 FMA:85544 NCIT:C34076 SCTID:118966000 @@ -35801,7 +35958,7 @@ Disorders or aberrations in the development or migration of the neural crest cel - + @@ -35837,14 +35994,14 @@ Disorders or aberrations in the development or migration of the neural crest cel gastrula stage - + - + BILS @@ -36153,7 +36310,7 @@ Disorders or aberrations in the development or migration of the neural crest cel - + @@ -36161,15 +36318,15 @@ Disorders or aberrations in the development or migration of the neural crest cel - + - - + + A fluid that is composed of blood plasma and erythrocytes. AAO:0000046 @@ -36206,34 +36363,34 @@ Disorders or aberrations in the development or migration of the neural crest cel blood - + - + - + - + CL:tm - + https://github.com/obophenotype/uberon/issues/1330 - + Bgee:AN @@ -36335,7 +36492,6 @@ Disorders or aberrations in the development or migration of the neural crest cel Organism at the blastula stage - an early stage of embryonic development in animals. It is produced by cleavage of a fertilized ovum and consists of a spherical layer of around 128 cells surrounding a central fluid-filled cavity called the blastocoel. The blastula follows the morula and precedes the gastrula in the developmental sequence. TODO - check relationship with epiblast. Note in FMA this is not a subclass of embryo, but in uberon embryo is the whole organism from zygote onwards and thus includes the blastula - UBERON:0007011 BILA:0000059 BTO:0000128 GAID:1294 @@ -37305,7 +37461,6 @@ Disorders or aberrations in the development or migration of the neural crest cel - @@ -37319,7 +37474,7 @@ Disorders or aberrations in the development or migration of the neural crest cel - + @@ -37361,14 +37516,14 @@ Disorders or aberrations in the development or migration of the neural crest cel epithelium https://upload.wikimedia.org/wikipedia/commons/8/8f/Illu_epithelium.jpg - + - + http://palaeos.com/metazoa/porifera/homoscleromorpha.html @@ -37788,7 +37943,7 @@ Disorders or aberrations in the development or migration of the neural crest cel - + Primary germ layer that is the outer of the embryo's three germ layers and gives rise to epidermis and neural tissue. AAO:0000137 BILA:0000036 @@ -37823,14 +37978,14 @@ Disorders or aberrations in the development or migration of the neural crest cel ectoderm http://upload.wikimedia.org/wikipedia/commons/1/19/Gray32.png - + - + Bgee:AN @@ -37870,7 +38025,7 @@ Disorders or aberrations in the development or migration of the neural crest cel - + Primary germ layer that lies remote from the surface of the embryo and gives rise to internal tissues such as gut. AAO:0000139 BILA:0000038 @@ -37905,14 +38060,14 @@ Disorders or aberrations in the development or migration of the neural crest cel http://upload.wikimedia.org/wikipedia/commons/c/c0/Endoderm2.png http://upload.wikimedia.org/wikipedia/commons/d/df/Gray10.png - + - + Bgee:AN @@ -37953,10 +38108,9 @@ Disorders or aberrations in the development or migration of the neural crest cel - + The middle germ layer of the embryo, between the endoderm and ectoderm. - UBERON:0003263 AAO:0000304 BILA:0000037 BTO:0000839 @@ -37994,14 +38148,14 @@ Disorders or aberrations in the development or migration of the neural crest cel mesoderm http://upload.wikimedia.org/wikipedia/commons/e/e8/Mesoderm.png - + - + Bgee:AN @@ -38175,7 +38329,7 @@ Disorders or aberrations in the development or migration of the neural crest cel - + @@ -38246,14 +38400,14 @@ Disorders or aberrations in the development or migration of the neural crest cel https://cdn.humanatlas.io/digital-objects/ref-organ/heart-female/v1.3/assets/3d-vh-f-heart.glb https://cdn.humanatlas.io/digital-objects/ref-organ/heart-male/v1.3/assets/3d-vh-m-heart.glb - + - + MA @@ -38504,7 +38658,6 @@ Disorders or aberrations in the development or migration of the neural crest cel - AAO:0000959 CALOHA:TS-2103 VHOG:0001248 @@ -38512,7 +38665,6 @@ Disorders or aberrations in the development or migration of the neural crest cel uberon systema cardiovasculare UBERON:0001009 - circulatory system http://upload.wikimedia.org/wikipedia/commons/2/29/Circulatory_System_en.svg @@ -38656,7 +38808,7 @@ Disorders or aberrations in the development or migration of the neural crest cel - + @@ -38704,14 +38856,14 @@ Disorders or aberrations in the development or migration of the neural crest cel http://upload.wikimedia.org/wikipedia/commons/b/b2/TE-Nervous_system_diagram.svg http://upload.wikimedia.org/wikipedia/commons/b/ba/Nervous_system_diagram.png - + - + Bgee:AN @@ -38777,7 +38929,7 @@ Disorders or aberrations in the development or migration of the neural crest cel - + The central nervous system is the core nervous system that serves an integrating and coordinating function. In vertebrates it consists of the neural tube derivatives: the brain and spinal cord. In invertebrates it includes central ganglia plus nerve cord. @@ -38822,7 +38974,7 @@ Disorders or aberrations in the development or migration of the neural crest cel central nervous system - + @@ -38836,7 +38988,7 @@ Disorders or aberrations in the development or migration of the neural crest cel - + Bgee:AN @@ -39224,7 +39376,7 @@ Disorders or aberrations in the development or migration of the neural crest cel - + Skeletal element that is composed of bone tissue. @@ -39266,14 +39418,14 @@ Disorders or aberrations in the development or migration of the neural crest cel bone element - + - + VSAO-modified @@ -39339,7 +39491,7 @@ Disorders or aberrations in the development or migration of the neural crest cel - + A tube extending from the mouth to the anus. @@ -39376,14 +39528,14 @@ Disorders or aberrations in the development or migration of the neural crest cel digestive tract - + - + NCBIBook:NBK10107 @@ -39528,7 +39680,6 @@ Disorders or aberrations in the development or migration of the neural crest cel - @@ -39603,7 +39754,6 @@ Disorders or aberrations in the development or migration of the neural crest cel - @@ -39612,8 +39762,8 @@ Disorders or aberrations in the development or migration of the neural crest cel - - + + @@ -39626,7 +39776,7 @@ Disorders or aberrations in the development or migration of the neural crest cel - + @@ -39680,34 +39830,34 @@ Disorders or aberrations in the development or migration of the neural crest cel blood vessel http://upload.wikimedia.org/wikipedia/commons/2/29/Circulatory_System_en.svg - + - + - + - + AEO - + EHDAA2 - + GO:0072360 @@ -40429,7 +40579,6 @@ Disorders or aberrations in the development or migration of the neural crest cel The cavity within the body of all animals higher than the coelenterates and certain primitive worms, formed by the splitting of the embryonic mesoderm into two layers. In mammals it forms the peritoneal, pleural, and pericardial cavities. - UBERON:0000169 body cavity AEO:0000186 BTO:0001707 @@ -40441,7 +40590,6 @@ Disorders or aberrations in the development or migration of the neural crest cel SCTID:361348008 TAO:0001438 UMLS:C0333343 - ZFA:0001438 galen:BodyCavity coelomic cavity coelomic cavity lumen @@ -40541,9 +40689,9 @@ Disorders or aberrations in the development or migration of the neural crest cel - - - + + + @@ -40591,15 +40739,15 @@ Disorders or aberrations in the development or migration of the neural crest cel notochord http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png - + - + - + @@ -40618,19 +40766,19 @@ Disorders or aberrations in the development or migration of the neural crest cel - + http://tolweb.org/Chordata/2499 - + ZFA - + EHDAA2 @@ -40670,8 +40818,8 @@ Disorders or aberrations in the development or migration of the neural crest cel - - + + Somites are spheres of epithelial cells that form sequentially along the anterior-posterior axis of the embryo through mesenchymal to epithelial transition of the presomitic mesoderm. mesodermal cluster @@ -40709,11 +40857,11 @@ Disorders or aberrations in the development or migration of the neural crest cel somite http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png - + - + @@ -40726,13 +40874,13 @@ Disorders or aberrations in the development or migration of the neural crest cel - + GOTAX:0000352 - + ZFA @@ -40794,22 +40942,22 @@ Disorders or aberrations in the development or migration of the neural crest cel - + - - + + - + A specialized region of ectoderm found between the neural ectoderm (neural plate) and non-neural ectoderm and composed of highly migratory pluripotent cells that delaminate in early embryonic development from the dorsal neural tube and give rise to an astounding variety of differentiated cell types[MP]. AAO:0010578 BTO:0001764 @@ -40842,45 +40990,45 @@ Disorders or aberrations in the development or migration of the neural crest cel http://upload.wikimedia.org/wikipedia/commons/5/5f/Gray644.png https://upload.wikimedia.org/wikipedia/commons/8/8f/Neural_Crest.png - + - + - + - + - + XAO https://github.com/obophenotype/uberon/wiki/The-neural-crest - + BTO - + PMID:11523831 - + PMID:11523831 @@ -41021,7 +41169,7 @@ Disorders or aberrations in the development or migration of the neural crest cel - + @@ -41077,14 +41225,14 @@ Disorders or aberrations in the development or migration of the neural crest cel bone marrow http://upload.wikimedia.org/wikipedia/commons/7/74/Gray72-en.svg - + - + FMA MA @@ -41296,7 +41444,7 @@ Disorders or aberrations in the development or migration of the neural crest cel - + @@ -41349,14 +41497,14 @@ Disorders or aberrations in the development or migration of the neural crest cel hematopoietic system - + - + FMA @@ -41656,6 +41804,7 @@ Disorders or aberrations in the development or migration of the neural crest cel + @@ -41669,7 +41818,7 @@ Disorders or aberrations in the development or migration of the neural crest cel - + Unsegmented field of paraxial mesoderm present posterior to the most recently formed somite pair, from which somites will form. AAO:0011086 EFO:0001982 @@ -41692,14 +41841,14 @@ Disorders or aberrations in the development or migration of the neural crest cel presomitic mesoderm - + - + Bgee:AN @@ -41853,9 +42002,9 @@ Disorders or aberrations in the development or migration of the neural crest cel - - - + + + A region of embryonic ectodermal cells that lie directly above the notochord. During neurulation, they change shape and produce an infolding of the neural plate (the neural fold) that then seals to form the neural tube[XAO]. The earliest recognizable dorsal ectodermal primordium of the central nervous system present near the end of gastrulation before infolding to form the neural keel; consists of a thickened pseudostratified epithelium[ZFA]. AAO:0011072 BTO:0001765 @@ -41884,34 +42033,34 @@ Disorders or aberrations in the development or migration of the neural crest cel neural plate https://upload.wikimedia.org/wikipedia/commons/8/8f/Neural_Crest.png - + - + - + - + GOTAX:0000352 - + Wikipedia - + Bgee:AN @@ -41951,7 +42100,7 @@ Disorders or aberrations in the development or migration of the neural crest cel - + The paraxial mesoderm is the mesoderm located bilaterally adjacent to the notochord and neural tube[GO]. AAO:0010568 EFO:0003515 @@ -41977,7 +42126,7 @@ Disorders or aberrations in the development or migration of the neural crest cel paraxial mesoderm http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png - + @@ -41990,7 +42139,7 @@ Disorders or aberrations in the development or migration of the neural crest cel - + Bgee:AN @@ -42037,7 +42186,7 @@ Disorders or aberrations in the development or migration of the neural crest cel - + @@ -42051,7 +42200,6 @@ Disorders or aberrations in the development or migration of the neural crest cel Portion of the middle of the three primary germ layers of the embryo that resides on the periphery of the embryo, is continuous with the extra-embryonic mesoderm, splits into two layers enclosing the intra-embryonic coelom, and gives rise to body wall structures[MP]. - UBERON:0006258 AAO:0010574 EHDAA2:0000919 EHDAA:379 @@ -42077,7 +42225,7 @@ Disorders or aberrations in the development or migration of the neural crest cel lateral plate mesoderm http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png - + @@ -42090,7 +42238,7 @@ Disorders or aberrations in the development or migration of the neural crest cel - + EHDAA2 VHOG @@ -42140,15 +42288,15 @@ Disorders or aberrations in the development or migration of the neural crest cel - - + + - + Bilateral groups of cells consisting of three rows: one row of endocardial precursors medially and two rows of myocardical precursors laterally. The two populations fuse at the midline to form the heart rudiment or cone. should probably be merged with heart rudiment. AAO:0011044 @@ -42165,15 +42313,15 @@ Disorders or aberrations in the development or migration of the neural crest cel heart primordium - + - + - + @@ -42186,19 +42334,19 @@ Disorders or aberrations in the development or migration of the neural crest cel - + ZFA - + ZFA - + XAO @@ -42227,8 +42375,8 @@ Disorders or aberrations in the development or migration of the neural crest cel - - + + Ventral somitic compartment that is a precursor of the axial skeleton[XAO]. Sclerotomes eventually differentiate into the vertebrae and most of the skull. The caudal (posterior) half of one sclerotome fuses with the rostral (anterior) half of the adjacent one to form each vertebra. From their initial location within the somite, the sclerotome cells migrate medially towards the notochord. These cells meet the sclerotome cells from the other side to form the vertebral body. From this vertebral body, sclerotome cells move dorsally and surround the developing spinal cord, forming the vertebral arch[WP]. AAO:0010571 AEO:0000212 @@ -42252,11 +42400,11 @@ Disorders or aberrations in the development or migration of the neural crest cel sclerotome http://upload.wikimedia.org/wikipedia/commons/9/96/Gray65.png - + - + @@ -42275,13 +42423,13 @@ Disorders or aberrations in the development or migration of the neural crest cel - + VHOG:0000680 - + ZFA @@ -42500,7 +42648,7 @@ Disorders or aberrations in the development or migration of the neural crest cel - + The part of the coelom in the embryo between the somatopleuric and splanchnopleuric mesoderm; the principal body cavities of the trunk (thoracic, abdominal, and pelvic) arise from this embryonic part of the coelom. consider merging with coelom. TODO - add spatial relationships to halves of LPM. Note the OG places XAO and ZFA coelem terms here. editor note: TODO check ZFA, which appears to be a structure present in adults EHDAA:251 @@ -42515,14 +42663,14 @@ Disorders or aberrations in the development or migration of the neural crest cel intraembryonic coelom - + - + Wikipedia @@ -42817,8 +42965,8 @@ Disorders or aberrations in the development or migration of the neural crest cel - - + + A specific region of the lateral mesoderm that will form the primary beating heart tube. In mammals the primary heart field gives rise to the left ventricle. XAO:0004185 first heart field @@ -42830,24 +42978,24 @@ Disorders or aberrations in the development or migration of the neural crest cel UBERON:0004140 primary heart field - + - + - + GO:0003128 - + https://orcid.org/0000-0003-3308-6245 @@ -42900,7 +43048,7 @@ Disorders or aberrations in the development or migration of the neural crest cel - + An epithelial tube that will give rise to the mature heart. AAO:0010411 EFO:0003526 @@ -42919,14 +43067,14 @@ Disorders or aberrations in the development or migration of the neural crest cel heart tube - + - + ZFA-modified @@ -43103,7 +43251,6 @@ Disorders or aberrations in the development or migration of the neural crest cel - @@ -43200,7 +43347,6 @@ Disorders or aberrations in the development or migration of the neural crest cel - @@ -43385,7 +43531,6 @@ Disorders or aberrations in the development or migration of the neural crest cel Organism at the gastrula stage. - UBERON:0007012 BILA:0000060 BTO:0001403 FBbt:00005317 @@ -43552,7 +43697,7 @@ Disorders or aberrations in the development or migration of the neural crest cel - + Organ consisting of skeletal tissue. Encompasses whole bones, fused bones, cartilaginious elements, teeth, dermal denticles. AAO:0011129 TAO:0001890 @@ -43566,14 +43711,14 @@ Disorders or aberrations in the development or migration of the neural crest cel skeletal element - + - + VSAO @@ -43600,7 +43745,7 @@ Disorders or aberrations in the development or migration of the neural crest cel - + @@ -43639,14 +43784,14 @@ Disorders or aberrations in the development or migration of the neural crest cel UBERON:0004770 articular system - + - + FMA @@ -44360,7 +44505,7 @@ Disorders or aberrations in the development or migration of the neural crest cel - + Mesenchyme that is part of a developing trunk. EFO:0003485 EHDAA2:0002092 @@ -44376,14 +44521,14 @@ Disorders or aberrations in the development or migration of the neural crest cel trunk mesenchyme - + - + EHDAA2 @@ -44500,7 +44645,7 @@ Disorders or aberrations in the development or migration of the neural crest cel - + Multi-tissue structure that arises from the heart rudiment and will become the heart tube. EHDAA2:0001512 EHDAA:424 @@ -44518,14 +44663,14 @@ Disorders or aberrations in the development or migration of the neural crest cel primitive heart tube - + - + ZFA @@ -44592,7 +44737,6 @@ Disorders or aberrations in the development or migration of the neural crest cel - @@ -44692,7 +44836,7 @@ Disorders or aberrations in the development or migration of the neural crest cel - + A delimited region of dense mesenchyme within looser mesenchyme. AEO:0000148 EHDAA2_RETIRED:0003148 @@ -44702,7 +44846,7 @@ Disorders or aberrations in the development or migration of the neural crest cel UBERON:0005856 developing mesenchymal condensation - + @@ -44721,7 +44865,7 @@ Disorders or aberrations in the development or migration of the neural crest cel - + AEO-modified-relation @@ -44815,7 +44959,7 @@ Disorders or aberrations in the development or migration of the neural crest cel - + The notochordal plate is the dorsal part of the notochordal process when the ventral portion breaks down. It is continuous laterally with the endoderm that composes the roof of the primitive foregut and is in contact dorsally with the neural tube. The folding off of the notochordal plate gives rise to the notochord. TODO - check ordering; awaiting confirmation from JB EHDAA2:0001278 @@ -44829,7 +44973,7 @@ Disorders or aberrations in the development or migration of the neural crest cel notochordal plate - + @@ -44842,7 +44986,7 @@ Disorders or aberrations in the development or migration of the neural crest cel - + EHDAA2 @@ -44870,7 +45014,7 @@ Disorders or aberrations in the development or migration of the neural crest cel - + A midline cellular cord formed from the migration of mesenchymal cells from the primitive knot. EHDAA2:0001279 EHDAA:224 @@ -44887,14 +45031,14 @@ Disorders or aberrations in the development or migration of the neural crest cel The notochordal process grows cranially until it reaches the prechordal plate, the future site of the mouth. In this area the ectoderm is attached directly to the endoderm without intervening mesoderm. This area is known as the oropharyngeal membrane, and it will break down to become the mouth. At the other end of the primitive streak the ectoderm is also fused directly to the endoderm; this is known as the cloacal membrane (proctodeum), or primordial anus. notochordal process - + - + EHDAA2 @@ -45282,7 +45426,6 @@ Disorders or aberrations in the development or migration of the neural crest cel - @@ -45784,7 +45927,7 @@ Disorders or aberrations in the development or migration of the neural crest cel - + @@ -45810,7 +45953,7 @@ Disorders or aberrations in the development or migration of the neural crest cel presumptive paraxial mesoderm - + @@ -45826,7 +45969,7 @@ Disorders or aberrations in the development or migration of the neural crest cel - + https://github.com/obophenotype/uberon/issues/1277 @@ -45902,7 +46045,7 @@ Disorders or aberrations in the development or migration of the neural crest cel - + Mesenchyme with little extracellular matrix. AEO:0000146 EHDAA2:0003146 @@ -45910,7 +46053,7 @@ Disorders or aberrations in the development or migration of the neural crest cel UBERON:0007524 dense mesenchyme tissue - + @@ -45923,7 +46066,7 @@ Disorders or aberrations in the development or migration of the neural crest cel - + AEO @@ -46026,7 +46169,7 @@ Disorders or aberrations in the development or migration of the neural crest cel - + Anatomical system that consists of all blood and lymph vessels. consider merging with vasculature @@ -46043,14 +46186,14 @@ Disorders or aberrations in the development or migration of the neural crest cel vascular system - + - + MA @@ -46078,7 +46221,7 @@ Disorders or aberrations in the development or migration of the neural crest cel - + @@ -46087,7 +46230,6 @@ Disorders or aberrations in the development or migration of the neural crest cel Sum total of mesenchyme in the embryo. consider adding new class (EMAPA:16097) for mesenchyme of embryo (some mesenchyme is extraembryonic - e.g. amnion mesoderm) - UBERON:0003313 EHDAA2:0001113 EHDAA:177 EMAPA:16097 @@ -46095,14 +46237,14 @@ Disorders or aberrations in the development or migration of the neural crest cel UBERON:0009142 entire embryonic mesenchyme - + - + EHDAA2 @@ -46158,7 +46300,7 @@ Disorders or aberrations in the development or migration of the neural crest cel - + EHDAA2:0002094 trunk and cervical paraxial mesenchyme uberon @@ -46166,14 +46308,14 @@ Disorders or aberrations in the development or migration of the neural crest cel UBERON:0009618 trunk paraxial mesoderm - + - + EHDAA2 @@ -46196,7 +46338,7 @@ Disorders or aberrations in the development or migration of the neural crest cel - + EFO:0003704 TAO:0005041 ZFA:0005041 @@ -46206,14 +46348,14 @@ Disorders or aberrations in the development or migration of the neural crest cel anterior lateral plate mesoderm - + - + ZFA @@ -46327,7 +46469,6 @@ Disorders or aberrations in the development or migration of the neural crest cel - @@ -46353,7 +46494,7 @@ Disorders or aberrations in the development or migration of the neural crest cel - + @@ -46373,14 +46514,14 @@ Disorders or aberrations in the development or migration of the neural crest cel UBERON:0010210 blood clot - + - + BTO @@ -46501,8 +46642,8 @@ Disorders or aberrations in the development or migration of the neural crest cel - - + + Anatomical cluster consisting of the skeletal elements (i.e. bone elements, cartilage elements, cartilage condensations) that are part of an individual subdivision of the organism. Excludes joints. FMA:23879 SCTID:129140006 @@ -46514,11 +46655,11 @@ Disorders or aberrations in the development or migration of the neural crest cel subdivision of skeleton - + - + @@ -46531,13 +46672,13 @@ Disorders or aberrations in the development or migration of the neural crest cel - + UBERONREF:0000003 - + VSAO @@ -46598,7 +46739,7 @@ Disorders or aberrations in the development or migration of the neural crest cel - + Subdivision of the skeletal system which consists of the postcranial axial skeleton plus associated joints. axial skeletal system FMA:302077 @@ -46608,7 +46749,7 @@ Disorders or aberrations in the development or migration of the neural crest cel postcranial axial skeletal system http://purl.obolibrary.org/obo/uberon/docs/The-axial-skeleton - + @@ -46621,7 +46762,7 @@ Disorders or aberrations in the development or migration of the neural crest cel - + cjm @@ -46801,6 +46942,7 @@ Disorders or aberrations in the development or migration of the neural crest cel EHDAA2:0004731 Wikipedia:Coelom + ZFA:0001438 enterocoelom haemocoelom schizocoelom @@ -46894,7 +47036,7 @@ Disorders or aberrations in the development or migration of the neural crest cel - + @@ -46915,7 +47057,7 @@ Disorders or aberrations in the development or migration of the neural crest cel UBERON:0012429 hematopoietic tissue - + @@ -46928,7 +47070,7 @@ Disorders or aberrations in the development or migration of the neural crest cel - + defitional @@ -47409,7 +47551,6 @@ Disorders or aberrations in the development or migration of the neural crest cel Primordium that develops into the central nervous system. - UBERON:3000469 future CNS presumptive central nervous system uberon @@ -47453,7 +47594,6 @@ Disorders or aberrations in the development or migration of the neural crest cel Primordium that develops into the nervous system. - UBERON:3000477 AAO:0000477 presumptive nervous system uberon @@ -47479,7 +47619,7 @@ Disorders or aberrations in the development or migration of the neural crest cel - + @@ -47502,7 +47642,7 @@ Disorders or aberrations in the development or migration of the neural crest cel UBERON:0016887 entire extraembryonic component - + @@ -47515,7 +47655,7 @@ Disorders or aberrations in the development or migration of the neural crest cel - + AEO diff --git a/subsets/blood_and_immune_upper_slim.tsv b/subsets/blood_and_immune_upper_slim.tsv index 0e404a0a9..8bf8e4124 100644 --- a/subsets/blood_and_immune_upper_slim.tsv +++ b/subsets/blood_and_immune_upper_slim.tsv @@ -1,419 +1,419 @@ ?x ?label -_:B219c8649X2Db5beX2D4319X2Dae80X2Db9cdc9e3289cgenid1003 -_:B219c8649X2Db5beX2D4319X2Dae80X2Db9cdc9e3289cgenid1010 -_:B219c8649X2Db5beX2D4319X2Dae80X2Db9cdc9e3289cgenid1023 -_:B219c8649X2Db5beX2D4319X2Dae80X2Db9cdc9e3289cgenid1034 -_:B219c8649X2Db5beX2D4319X2Dae80X2Db9cdc9e3289cgenid1044 -_:B219c8649X2Db5beX2D4319X2Dae80X2Db9cdc9e3289cgenid1092 -_:B219c8649X2Db5beX2D4319X2Dae80X2Db9cdc9e3289cgenid1099 -_:B219c8649X2Db5beX2D4319X2Dae80X2Db9cdc9e3289cgenid1118 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+_:Bd6eff882X2D6a0cX2D48b5X2D9088X2D564199da347cgenid5496 +_:Bd6eff882X2D6a0cX2D48b5X2D9088X2D564199da347cgenid569 +_:Bd6eff882X2D6a0cX2D48b5X2D9088X2D564199da347cgenid576 +_:Bd6eff882X2D6a0cX2D48b5X2D9088X2D564199da347cgenid589 +_:Bd6eff882X2D6a0cX2D48b5X2D9088X2D564199da347cgenid597 +_:Bd6eff882X2D6a0cX2D48b5X2D9088X2D564199da347cgenid604 +_:Bd6eff882X2D6a0cX2D48b5X2D9088X2D564199da347cgenid617 +_:Bd6eff882X2D6a0cX2D48b5X2D9088X2D564199da347cgenid627 +_:Bd6eff882X2D6a0cX2D48b5X2D9088X2D564199da347cgenid662 +_:Bd6eff882X2D6a0cX2D48b5X2D9088X2D564199da347cgenid679 +_:Bd6eff882X2D6a0cX2D48b5X2D9088X2D564199da347cgenid695 +_:Bd6eff882X2D6a0cX2D48b5X2D9088X2D564199da347cgenid70 +_:Bd6eff882X2D6a0cX2D48b5X2D9088X2D564199da347cgenid73 +_:Bd6eff882X2D6a0cX2D48b5X2D9088X2D564199da347cgenid748 +_:Bd6eff882X2D6a0cX2D48b5X2D9088X2D564199da347cgenid766 +_:Bd6eff882X2D6a0cX2D48b5X2D9088X2D564199da347cgenid787 +_:Bd6eff882X2D6a0cX2D48b5X2D9088X2D564199da347cgenid802 +_:Bd6eff882X2D6a0cX2D48b5X2D9088X2D564199da347cgenid857 +_:Bd6eff882X2D6a0cX2D48b5X2D9088X2D564199da347cgenid890 +_:Bd6eff882X2D6a0cX2D48b5X2D9088X2D564199da347cgenid935 +_:Bd6eff882X2D6a0cX2D48b5X2D9088X2D564199da347cgenid949 +_:Bd6eff882X2D6a0cX2D48b5X2D9088X2D564199da347cgenid964 +_:Bd6eff882X2D6a0cX2D48b5X2D9088X2D564199da347cgenid981 "cell" "early embryonic cell (metazoa)" "stem cell" @@ -473,6 +473,7 @@ _:B219c8649X2Db5beX2D4319X2Dae80X2Db9cdc9e3289cgenid995 "biogenic amine secreting cell" "serotonin secreting cell" "defensive cell" + "stromal cell" "phagocyte (sensu Vertebrata)" "neuron" "lymphocyte" @@ -845,19 +846,17 @@ _:B219c8649X2Db5beX2D4319X2Dae80X2Db9cdc9e3289cgenid995 "response to external biotic stimulus" "organelle" "membrane-bounded organelle" - "non-membrane-bounded organelle" + "membraneless organelle" "intracellular organelle" "extracellular organelle" "intracellular membrane-bounded organelle" - "intracellular non-membrane-bounded organelle" + "intracellular membraneless organelle" "organelle lumen" "receptor complex" "protein-containing complex organization" "cellular component biogenesis" "translation initiation ternary complex" - "cellular metabolic process" "primary metabolic process" - "cellular biosynthetic process" "biological process involved in interspecies interaction between organisms" "plasma membrane fusion" "T cell selection" @@ -976,7 +975,7 @@ _:B219c8649X2Db5beX2D4319X2Dae80X2Db9cdc9e3289cgenid995 "secretory vesicle" "synaptic signaling" "trans-synaptic signaling" - "cellular anatomical entity" + "cellular anatomical structure" "plasma membrane bounded cell projection" "plasma membrane bounded cell projection assembly" "plasma membrane bounded cell projection organization" @@ -1164,7 +1163,7 @@ _:B219c8649X2Db5beX2D4319X2Dae80X2Db9cdc9e3289cgenid995 "G-protein coupled receptor" "eukaryotic protein" "cathepsin-like protease" - "protein-containing material entity" + "protein-containing molecular entity" "processual entity" "tube" "vessel" diff --git a/subsets/eye_upper_slim.json b/subsets/eye_upper_slim.json index 27446ca77..dac5e56e0 100644 --- a/subsets/eye_upper_slim.json +++ b/subsets/eye_upper_slim.json @@ -4,9 +4,9 @@ "meta" : { "basicPropertyValues" : [ { "pred" : "http://www.w3.org/2002/07/owl#versionInfo", - "val" : "2024-09-26" + "val" : "2025-01-08" } ], - "version" : "http://purl.obolibrary.org/obo/cl/releases/2024-09-26/subsets/eye_upper_slim.owl" + "version" : "http://purl.obolibrary.org/obo/cl/releases/2025-01-08/subsets/eye_upper_slim.owl" }, "nodes" : [ { "id" : "http://purl.obolibrary.org/obo/CL_0000000", @@ -18,7 +18,7 @@ "xrefs" : [ "CARO:mah" ] }, "comments" : [ "The definition of cell is intended to represent all cells, and thus a cell is defined as a material entity and not an anatomical structure, which implies that it is part of an organism (or the entirety of one)." ], - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/ubprop#_upper_level" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/ubprop#_upper_level" ], "xrefs" : [ { "val" : "CALOHA:TS-2035" }, { @@ -50,6 +50,7 @@ "val" : "Any fibroblast that is derived from the neural crest.", "xrefs" : [ "https://orcid.org/0000-0001-5208-3432" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "fibroblast neural crest derived" @@ -64,7 +65,7 @@ "val" : "Any sensory receptor cell that is a(n) neuron and is capable of some detection of stimulus involved in sensory perception.", "xrefs" : [ "FBC:Autogenerated" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "neuronal receptor cell (sensu Animalia)" @@ -82,6 +83,7 @@ "val" : "A cell found in the embryo before the formation of all the gem layers is complete.", "xrefs" : [ "GOC:tfm" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "ZFA:0009002" } ] @@ -95,6 +97,7 @@ "val" : "Cell that is part of the migratory cranial neural crest population. Migratory cranial neural crest cells develop from premigratory cranial neural crest cells and have undergone epithelial to mesenchymal transition and delamination.", "xrefs" : [ "ZFA:0007091", "https://orcid.org/0000-0001-5208-3432" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "ZFA:0007091" } ] @@ -104,7 +107,11 @@ "lbl" : "glioblast", "type" : "CLASS", "meta" : { - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], + "definition" : { + "val" : "A non-terminally differentiated cell that develops form the neuroectoderm. Glioblast has the potential to differentiate into various types of glial cells, including astrocytes and oligodendrocytes.", + "xrefs" : [ "PMID:37824650", "Wikipedia:Glioblast" ] + }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "ZFA:0009010" } ] @@ -118,7 +125,7 @@ "val" : "A cell that will develop into a neuron often after a migration phase.", "xrefs" : [ "GOC:NV", "http://en.wikipedia.org/wiki/Neuroblast" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "neuroblast" @@ -141,7 +148,7 @@ "xrefs" : [ "GOC:tfm", "MESH:D013234" ] }, "comments" : [ "This term applies to metazoan. For plant stem cells, consider using PO:0004011 ‘initial cell’ or its parent PO:0004010 ‘meristematic cell’." ], - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#general_cell_types_upper_slim", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#general_cell_types_upper_slim", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "animal stem cell" @@ -168,7 +175,7 @@ "xrefs" : [ "GOC:add", "GOC:dsd", "GOC:tfm", "PMID:19022770", "http://en.wikipedia.org/wiki/Hematopoietic_stem_cell" ] }, "comments" : [ "Markers differ between species, and two sets of markers have been described for mice. HSCs are reportedly CD34-positive, CD45-positive, CD48-negative, CD150-positive, CD133-positive, and CD244-negative." ], - "subsets" : [ "http://purl.obolibrary.org/obo/cl#blood_and_immune_upper_slim", "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#blood_and_immune_upper_slim", "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "blood forming stem cell" @@ -210,7 +217,7 @@ "val" : "A progenitor cell committed to the erythroid lineage.", "xrefs" : [ "GOC:add", "ISBN:0721601464" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#blood_and_immune_upper_slim", "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#blood_and_immune_upper_slim", "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003000", "pred" : "hasRelatedSynonym", @@ -247,6 +254,7 @@ "val" : "A stem cell that can give rise to multiple lineages of cells.", "xrefs" : [ "GOC:add" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "multi-fate stem cell" @@ -276,7 +284,7 @@ "xrefs" : [ "GOC:add", "ISBN:0878932437", "MESH:D023461" ] }, "comments" : [ "This cell type is intended to be compatible with any vertebrate common myeloid progenitor. For mammalian CMP known to be CD34-positive, please use the term 'common myeloid progenitor, CD34-positive' (CL_0001059)." ], - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "common myeloid precursor" @@ -332,7 +340,7 @@ "xrefs" : [ "GOC:add", "GOC:dsd", "GOC:tfm", "MESH:D055015", "PMID:16647566", "http://en.wikipedia.org/wiki/Megakaryocyte-erythroid_progenitor_cell" ] }, "comments" : [ "MEPs are reportedly CD19-negative, CD34-negative, CD45RA-negative, CD110-positive, CD117-positive, and SCA1-negative and reportedly express the transcription factors GATA-1 and NF-E2." ], - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "CFU-EM" @@ -372,6 +380,7 @@ "val" : "A stem cell from which all cells of the body can form.", "xrefs" : [ "GOC:add", "GOC:tfm" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "totipotential stem cell" @@ -394,7 +403,7 @@ "xrefs" : [ "SANBI:mhl" ] }, "comments" : [ "define using PATO mulit-potent or oligopotent?" ], - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "blast cell" @@ -414,6 +423,7 @@ "val" : "A cell that is commited to differentiating into a muscle cell. Embryonic myoblasts develop from the mesoderm. They undergo proliferation, migrate to their various sites, and then differentiate into the appropriate form of myocytes. Myoblasts also occur as transient populations of cells in muscles undergoing repair.", "xrefs" : [ "GOC:tfm", "MESH:D032446", "PMID:21849021" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "BTO:0000222" }, { @@ -438,7 +448,7 @@ "xrefs" : [ "ISBN:0517223651", "MESH:D005347", "http://en.wikipedia.org/wiki/Fibroblast" ] }, "comments" : [ "These cells may be vimentin-positive, fibronectin-positive, fsp1-positive, MMP-1-positive, collagen I-positive, collagen III-positive, and alpha-SMA-negative." ], - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#general_cell_types_upper_slim", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#general_cell_types_upper_slim", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "xrefs" : [ { "val" : "BTO:0000452" }, { @@ -466,7 +476,7 @@ "val" : "A cell that is usually found in a two-dimensional sheet with a free surface. The cell has a cytoskeleton that allows for tight cell to cell contact and for cell polarity where apical part is directed towards the lumen and the basal part to the basal lamina.", "xrefs" : [ "FB:ma", "GOC:tfm", "MESH:D004847" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#general_cell_types_upper_slim", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#general_cell_types_upper_slim", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "epitheliocyte" @@ -503,7 +513,7 @@ "val" : "An endothelial cell that lines the vasculature.", "xrefs" : [ "GOC:tfm" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "xrefs" : [ { "val" : "ZFA:0009036" } ], @@ -521,7 +531,7 @@ "val" : "A columnar/cuboidal epithelial cell is a cell usually found in a two dimensional sheet with a free surface. Columnar/cuboidal epithelial cells take on the shape of a column or cube.", "xrefs" : [ "GO:0002065", "https://orcid.org/0000-0001-5208-3432" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "xrefs" : [ { "val" : "ZFA:0009038" } ], @@ -539,7 +549,7 @@ "val" : "Any epithelial cell that is part of some squamous epithelium.", "xrefs" : [ "FBC:Autogenerated" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "CALOHA:TS-1249" }, { @@ -556,7 +566,7 @@ "xrefs" : [ "GOC:tfm", "ISBN:0721662544", "PMID:26106328" ] }, "comments" : [ "Mesothelial cells, which morphologically resemble squamous epithelial cells, express both epithelial markers (cytokeratins) and mesenchymal markers (vimentin), reflecting their mesodermal origin. They feature surface microvilli and apical-basal polarity. Under certain conditions, they can undergo mesothelial-to-mesenchymal transition. These cells also produce extracellular matrix proteins, maintain serosal homeostasis, and facilitate fluid transport." ], - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "mesotheliocyte" @@ -580,7 +590,7 @@ "val" : "A cell found predominately in the blood.", "xrefs" : [ "GOC:add", "GOC:tfm" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#general_cell_types_upper_slim" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#general_cell_types_upper_slim", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "FMA:62844" }, { @@ -594,7 +604,7 @@ "lbl" : "neuron associated cell", "type" : "CLASS", "meta" : { - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ] + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ] } }, { "id" : "http://purl.obolibrary.org/obo/CL_0000099", @@ -605,7 +615,11 @@ "val" : "Most generally any neuron which is not motor or sensory. Interneurons may also refer to neurons whose axons remain within a particular brain region as contrasted with projection neurons which have axons projecting to other brain regions.", "xrefs" : [ "GOC:tfm", "MESH:D007395" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "synonyms" : [ { + "pred" : "hasRelatedSynonym", + "val" : "CNS interneuron" + } ], "xrefs" : [ { "val" : "BTO:0003811" }, { @@ -631,7 +645,7 @@ "val" : "Any neuron having a sensory function; an afferent neuron conveying sensory impulses.", "xrefs" : [ "ISBN:0721662544" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "xrefs" : [ { "val" : "BTO:0001037" }, { @@ -650,22 +664,6 @@ "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/CL_0000103", - "lbl" : "bipolar neuron", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A type of interneuron that has two neurites, usually an axon and a dendrite, extending from opposite poles of an ovoid cell body.", - "xrefs" : [ "GOC:tfm", "ISBN:0444009442" ] - }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#BDS_subset", "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], - "xrefs" : [ { - "val" : "FMA:67282" - }, { - "val" : "ZFA:0009055" - } ] - } }, { "id" : "http://purl.obolibrary.org/obo/CL_0000115", "lbl" : "endothelial cell", @@ -676,7 +674,7 @@ "xrefs" : [ "GOC:tfm", "MESH:D042783", "PMID:21275341", "http://en.wikipedia.org/wiki/Endothelial_cell", "https://sourceforge.net/tracker/?func=detail&atid=440764&aid=3364936&group_id=36855" ] }, "comments" : [ "From FMA: 9.07.2001: Endothelial cell has always been classified as a kind of epithelial cell, specifically a squamous cell but that is not true. First, endothelial cell can either be squamous or cuboidal (e.g. high-endothelial cell) and secondly, it has different embryological derivation (mesodermal) than a true epithelial cell (ectodermal and endodermal). The basis for present classification is the fact that it comprises the outermost layer or lining of anatomical structures (location-based) but a better structural basis for the differentia is the cytoskeleton of the cell. Endothelial cell has vimentin filaments while an epithelial cell has keratin filaments. [Onard]." ], - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "endotheliocyte" @@ -695,21 +693,12 @@ "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/CL_0000117", - "lbl" : "CNS neuron (sensu Vertebrata)", - "type" : "CLASS", - "meta" : { - "xrefs" : [ { - "val" : "ZFA:0009067" - } ] - } }, { "id" : "http://purl.obolibrary.org/obo/CL_0000123", "lbl" : "neuron associated cell (sensu Vertebrata)", "type" : "CLASS", "meta" : { - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ] + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ] } }, { "id" : "http://purl.obolibrary.org/obo/CL_0000125", @@ -721,7 +710,7 @@ "xrefs" : [ "MESH:D009457" ] }, "comments" : [ "Not all glial cells develop from glioblasts, with microglia developing from the mesoderm instead. See https://github.com/obophenotype/cell-ontology/issues/1571" ], - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#general_cell_types_upper_slim", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#general_cell_types_upper_slim", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "neuroglial cell" @@ -747,7 +736,7 @@ "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" }, { "pred" : "http://purl.org/dc/terms/description", - "val" : "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional.\n\nGlial cells, also known as neuroglia or simply glia, are non-neuronal cells in the central and peripheral nervous systems that provide support and protection for neurons. They constitute approximately half of the total cells in the human brain and more than half in other parts of the nervous system. Glial cells perform several key functions including, but not limited to, maintaining homeostasis, forming the myelin sheath around the neuron axons, and providing support and nutrition to neurons.\nThese different functions are performed by various glial cell types, including astrocytes, oligodendrocytes, microglia and other specialized types. Astrocytes, for example, are the most abundant glial cells and provide metabolic and nutrient support to neurons, help regulate the extracellular ion and neurotransmitter levels, and play a role in the formation and maintenance of the blood-brain barrier, contributing to the overall homeostasis and functioning of the nervous system. Additionally, astrocytes are involved in synaptic communication and participate in processes such as synaptogenesis and synaptic pruning.\nOligodendrocytes in the central nervous system function to insulate neurons by producing a fatty substance known as myelin. The myelin sheath enhances the speed and efficiency of nerve impulse conduction along the axons. \nMicroglia, the immune cells of the central nervous system, protect neurons from pathogens and clear away dead neurons through phagocytosis, a process also known as cellular eating. They also contribute to the regulation of inflammation in response to signals of tissue damage or infection in the central nervous system by releasing cytokines and other signaling molecules that modulate the immune response.\nDespite their overarching function in the support and protection of neurons, glial cells have also been shown to play significant roles in the pathophysiology of many psychiatric and neurodegenerative diseases, such as Alzheimer’s, Parkinson’s Disease and multiple sclerosis." + "val" : "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nGlial cells, also known as neuroglia or simply glia, are non-neuronal cells in the central and peripheral nervous systems that provide support and protection for neurons. They constitute approximately half of the total cells in the human brain and more than half in other parts of the nervous system. Glial cells perform several key functions including, but not limited to, maintaining homeostasis, forming the myelin sheath around the neuron axons, and providing support and nutrition to neurons.\nThese different functions are performed by various glial cell types, including astrocytes, oligodendrocytes, microglia and other specialized types. Astrocytes, for example, are the most abundant glial cells and provide metabolic and nutrient support to neurons, help regulate the extracellular ion and neurotransmitter levels, and play a role in the formation and maintenance of the blood-brain barrier, contributing to the overall homeostasis and functioning of the nervous system. Additionally, astrocytes are involved in synaptic communication and participate in processes such as synaptogenesis and synaptic pruning.\nOligodendrocytes in the central nervous system function to insulate neurons by producing a fatty substance known as myelin. The myelin sheath enhances the speed and efficiency of nerve impulse conduction along the axons. \nMicroglia, the immune cells of the central nervous system, protect neurons from pathogens and clear away dead neurons through phagocytosis, a process also known as cellular eating. They also contribute to the regulation of inflammation in response to signals of tissue damage or infection in the central nervous system by releasing cytokines and other signaling molecules that modulate the immune response.\nDespite their overarching function in the support and protection of neurons, glial cells have also been shown to play significant roles in the pathophysiology of many psychiatric and neurodegenerative diseases, such as Alzheimer’s, Parkinson’s Disease and multiple sclerosis." } ] } }, { @@ -759,7 +748,7 @@ "val" : "A neuroglial cell of ectodermal origin, i.e., the astrocytes and oligodendrocytes considered together.", "xrefs" : [ "GOC:tfm", "ISBN:0721662544" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "macrogliocyte" @@ -789,7 +778,7 @@ "xrefs" : [ "GOC:dsd", "GOC:tfm", "MESH:D001253", "PMID:11746784", "PMID:12162730", "PMID:12898703", "PMID:20942978", "http://en.wikipedia.org/wiki/Astrocyte" ] }, "comments" : [ "Astrocytes are reportedly CD68-negative, CD121a-positive, CD184-positive, CD192-positive, CRF-positive, EGFR-positive, GFAP-positive, GLUT1-positive, MBP-negative, and NGFR-positive." ], - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "astrocytic glia" @@ -817,7 +806,7 @@ "val" : "An hexagonal, flattened, mitochondria-rich endothelial cell that forms a monolayer on the posterior surface of the cornea (the corneal endothelium). Corneal endothelial cells are derived from the neural crest and are responsible for keeping the cornea transparent by maintaining the tissue in a semi-dry state through the action of their ionic pumps and tight junction barrier.", "xrefs" : [ "GOC:tfm", "PMID:21976958", "PMID:23284695", "PMID:34741068", "PMID:36769303" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#eye_upper_slim", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#eye_upper_slim", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "xrefs" : [ { "val" : "CALOHA:TS-0172" }, { @@ -839,6 +828,7 @@ "val" : "Ectoderm destined to be nervous tissue.", "xrefs" : [ "GOC:tfm", "ISBN:068340007X" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "neurectoderm cell" @@ -857,7 +847,7 @@ "xrefs" : [ "FB:ma", "GOC:dsd", "PMCID:PMC2613570", "PMID:10102814", "PMID:16923606", "PMID:17986482", "PMID:19960544", "http://en.wikipedia.org/wiki/Mesenchymal_stem_cell", "http://www.copewithcytokines.de/cope.cgi?key=mesenchymal%20stem%20cells" ] }, "comments" : [ "Many but not all mesenchymal cells derive from the mesoderm. MSCs are reportedly CD3-negative, CD4-negative, CD5-negative, CD8-negative, CD11a-negative, CD11b-negative, CD14-negative, CD19-negative, CD29-positive, CD31-negative, CD34-negative, CD38-negative, CD40-negative, CD44-positive, CD45-negative, CD49-positive, CD54-positive, CD66b-negative, CD79a-negative, CD80-negative, CD102-positive, CD106-positive, CD117-positive, CD121a-positive, CD121b-positive, CD123-positive, CD124-positive, CD133-negative, CD146-positive, CD166-positive, CD271-positive, B220-negative, Gr1-negative, MHCI-positive, MHCII-negative, SSEA4-negative, sca1-positive, Ter119-negative, and glycophorin A-negative. Cultured MSCs are capable of producing stem cell factor, IL7, IL8, IL11, TGF-beta, cofilin, galectin-1, laminin-receptor 1, cyclophilin A, and MMP-2." ], - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "pred" : "hasNarrowSynonym", "val" : "bone marrow stromal cells" @@ -928,6 +918,7 @@ "val" : "A pigment cell is a cell that contains pigment granules.", "xrefs" : [ "GOC:tfm" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "chromatocyte" @@ -950,7 +941,7 @@ "val" : "A pigment cell derived from the neural crest. Contains melanin-filled pigment granules, which gives a brown to black appearance.", "xrefs" : [ "SANBI:mhl" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#general_cell_types_upper_slim", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#general_cell_types_upper_slim", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "synonyms" : [ { "pred" : "hasNarrowSynonym", "val" : "melanophore" @@ -967,10 +958,15 @@ "val" : "VHOG:0001679" }, { "val" : "ZFA:0009091" + }, { + "val" : "https://cellxgene.cziscience.com/cellguide/CL_0000148" } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" + }, { + "pred" : "http://purl.org/dc/terms/description", + "val" : "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nMelanocytes are specialized cells prevalently found in the skin, but also present in the hair follicles, eyes, inner ear, bones, heart, and brain. Their primary function is the synthesis of melanin, a pigment responsible for coloration of skin, hair, and eyes. The presence and distribution of this pigment play a crucial role in the body's defense mechanism against harmful ultraviolet radiation.\nIn addition to melanin production, melanocytes also engage in a variety of other biological functions. They play a fundamental role in the immune response, owing to their ability to present antigens to T cells. Furthermore, they contribute to the maintenance of the skin's homeostasis by regulating processes such as extracellular matrix remodeling and cytokine production. A balance in melanocyte function is pivotal, as dysfunctions often result in dermatological disorders. For instance, the loss of melanocytes or reduction in their function may lead to hypopigmentation conditions such as vitiligo, whereas an abnormal increase could result in hyperpigmentation disorders or melanoma, a dangerous type of skin cancer." } ] } }, { @@ -978,6 +974,7 @@ "lbl" : "visual pigment cell", "type" : "CLASS", "meta" : { + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "pred" : "hasBroadSynonym", "val" : "pigment cell" @@ -992,7 +989,7 @@ "val" : "A cell that specializes in controlled release of one or more substances.", "xrefs" : [ "GOC:tfm", "ISBN:0721662544" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "BTO:0003659" }, { @@ -1008,7 +1005,7 @@ "val" : "A cell whose primary function is to shorten.", "xrefs" : [ "FB:ma" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ] + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ] } }, { "id" : "http://purl.obolibrary.org/obo/CL_0000187", @@ -1019,7 +1016,7 @@ "val" : "A mature contractile cell, commonly known as a myocyte. This cell has as part of its cytoplasm myofibrils organized in various patterns.", "xrefs" : [ "MESH:D032342" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "muscle fiber" @@ -1056,7 +1053,7 @@ "val" : "A non-striated, elongated, spindle-shaped cell found lining the digestive tract, uterus, and blood vessels. They develop from specialized myoblasts (smooth muscle myoblast).", "xrefs" : [ "MESH:D032389", "PMID:9315361", "http://en.wikipedia.org/wiki/Smooth_muscle_cell" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#general_cell_types_upper_slim", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#general_cell_types_upper_slim", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "synonyms" : [ { "pred" : "hasBroadSynonym", "val" : "non-striated muscle cell" @@ -1080,10 +1077,15 @@ "val" : "FMA:14072" }, { "val" : "ZFA:0009118" + }, { + "val" : "https://cellxgene.cziscience.com/cellguide/CL_0000192" } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" + }, { + "pred" : "http://purl.org/dc/terms/description", + "val" : "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nSmooth muscle cells are a specialized type of muscle cells that are primarily found within the walls of hollow organs such as the intestine, stomach, bladder, uterus, and blood vessels. These cells are an essential component of the autonomic nervous system controling involuntary movements within the body.\nSmooth muscle cells play a vital role in many physiological processes due to their unique functionality. They can contract and relax in a slow, sustained, and controlled manner to help modulate the size and shape of the lumens of the organs they surround. For example, in the digestive system, coordinated contraction and relaxation of smooth muscle cells propels food along the gastrointestinal tract - a process known as peristalsis. In the blood vessels, the smooth muscle cells, by contracting or relaxing, either constrict or dilate the vessels, which in turn, help regulate blood flow and pressure.\nOn a cellular level, smooth muscle cells possess a single, centrally located nucleus and contain an arranged network of actin and myosin filaments, which are the proteins responsible for muscle contraction. Unlike their counterparts in skeletal or cardiac muscles, these cells lack specific contact points for these filaments, hence the lack of visible striations. Furthermore, the contraction of smooth muscle cells is regulated by hormones and neurotransmitters, such as acetylcholine and norepinephrine, adding an additional layer of complex regulation to these highly specialized cells." } ] } }, { @@ -1094,6 +1096,7 @@ "definition" : { "val" : "A cell that is capable of detection of a stimulus involved in sensory perception." }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "receptor cell" @@ -1111,7 +1114,7 @@ "val" : "A cell specialized in detecting light stimuli that are involved in visual perception.", "xrefs" : [ "MESH:D010786" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "BTO:0001060" }, { @@ -1137,6 +1140,7 @@ "val" : "A cell whose function is determined by the generation or the reception of an electric signal.", "xrefs" : [ "FB:ma" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "ZFA:0009128" } ] @@ -1150,6 +1154,7 @@ "val" : "A cell within an epithelial cell sheet whose main function is to act as an internal or external covering for a tissue or an organism.", "xrefs" : [ "JB:jb" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "boundary cell" @@ -1167,6 +1172,7 @@ "val" : "A cell whose primary function is to prevent the transport of stuff across compartments.", "xrefs" : [ "JB:jb" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "ZFA:0009132" } ] @@ -1180,6 +1186,7 @@ "val" : "A cell that moves by its own activities.", "xrefs" : [ "FB:ma" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "ZFA:0009136" } ] @@ -1193,6 +1200,7 @@ "val" : "A cell of the outer of the three germ layers of the embryo.", "xrefs" : [ "MESH:D004475" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "ectoderm cell" @@ -1212,7 +1220,7 @@ "val" : "A cell of the middle germ layer of the embryo.", "xrefs" : [ "MESH:D008648" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "mesoblast" @@ -1224,6 +1232,12 @@ "val" : "FMA:72554" }, { "val" : "ZFA:0009138" + }, { + "val" : "https://cellxgene.cziscience.com/cellguide/CL_0000222" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/description", + "val" : "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nMesodermal cells are pluripotent and the most abundant in the human body. They contribute to the development of several structures such as the skeletal muscles, bones, heart and blood vessels, kidneys, gonads, connective tissues, and certain layers of the skin. Hence, the mesoderm is often regarded as an active and diverse layer due to its role in forming many bodily structures. \nIn embryonic development, these cells are instrumental, contributing to the body's structures through a carefully coordinated sequence of morphogenetic movements. This process forms the complex multicellular architecture of tissues and organs from a simple ball of cells. Without the function of mesodermal cells, the body's integral structures and systems would cease to form correctly, leading to developmental disorders such as axial mesodermal dysplasia complex" } ] } }, { @@ -1235,6 +1249,7 @@ "val" : "A cell of the inner of the three germ layers of the embryo.", "xrefs" : [ "MESH:D004707" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "endoderm cell" @@ -1254,7 +1269,7 @@ "val" : "A red blood cell. In mammals, mature erythrocytes are biconcave disks containing hemoglobin whose function is to transport oxygen.", "xrefs" : [ "GOC:tfm", "MESH:D004912" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#blood_and_immune_upper_slim", "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#blood_and_immune_upper_slim", "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "RBC" @@ -1283,7 +1298,7 @@ "val" : "Any cell that in taxon some Eukaryota.", "xrefs" : [ "FBC:Autogenerated" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "MESH:D005057" } ] @@ -1297,7 +1312,7 @@ "val" : "Any photoreceptor cell that is part of some eye.", "xrefs" : [ "FBC:Autogenerated" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#eye_upper_slim", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#eye_upper_slim", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "xrefs" : [ { "val" : "ZFA:0009154" } ], @@ -1315,6 +1330,7 @@ "val" : "A cell whose primary function is to provide structural support, to provide strength and physical integrity to the organism.", "xrefs" : [ "TAIR:sr" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "ZFA:0005745" } ] @@ -1324,7 +1340,7 @@ "lbl" : "crystallin accumulating cell", "type" : "CLASS", "meta" : { - "subsets" : [ "http://purl.obolibrary.org/obo/cl#eye_upper_slim" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#eye_upper_slim", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "lens cell" @@ -1339,7 +1355,7 @@ "val" : "A cell that is specialised to accumulate a particular substance(s).", "xrefs" : [ "FB:ma" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/ubprop#_upper_level" ] + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/ubprop#_upper_level" ] } }, { "id" : "http://purl.obolibrary.org/obo/CL_0000329", @@ -1350,6 +1366,7 @@ "val" : "Any cell that is capable of some oxygen transport.", "xrefs" : [ "FBC:Autogenerated" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "ZFA:0009164" } ] @@ -1363,6 +1380,7 @@ "val" : "A cell derived from the specialized ectoderm flanking each side of the embryonic neural plate, which after the closure of the neural tube, forms masses of cells that migrate out from the dorsal aspect of the neural tube to spread throughout the body.", "xrefs" : [ "doi:10.1016/j.stem.2015.02.017" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "FMA:86667" }, { @@ -1378,6 +1396,7 @@ "val" : "A mesenchymal cell in embryonic development found in a contracting mass and that gives rise to osteoprogenitors.", "xrefs" : [ "GOC:tfm", "PMID:5025404" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "ZFA:0009166" } ] @@ -1391,6 +1410,7 @@ "val" : "An early neural cell developing from the early ependymal cell of the neural tube.", "xrefs" : [ "GOC:tfm", "ISBN:0618947256" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "spongioblast" @@ -1410,6 +1430,7 @@ "val" : "Any animal cell containing pigment granules.", "xrefs" : [ "GOC:tfm", "ISBN:0721662544" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "ZFA:0009170" } ] @@ -1423,7 +1444,7 @@ "val" : "A cell of the sclera of the eye.", "xrefs" : [ "GOC:add" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#eye_upper_slim" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#eye_upper_slim", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "ZFA:0009174" } ] @@ -1437,7 +1458,7 @@ "val" : "A structural cell that is part of optic choroid.", "xrefs" : [ "GOC:add" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#eye_upper_slim" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#eye_upper_slim", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "ZFA:0009175" } ] @@ -1450,7 +1471,8 @@ "definition" : { "val" : "A cell of the outer layer of a blastula that gives rise to the ectoderm after gastrulation.", "xrefs" : [ "GOC:tfm", "ISBN:0618947256" ] - } + }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ] } }, { "id" : "http://purl.obolibrary.org/obo/CL_0000365", @@ -1461,6 +1483,7 @@ "val" : "Diploid cell produced by the fusion of sperm cell nucleus and egg cell.", "xrefs" : [ "ISBN:0471245208" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "pred" : "hasBroadSynonym", "val" : "zygote" @@ -1482,40 +1505,45 @@ "val" : "A cell whose function is determined by its response to an electric signal.", "xrefs" : [ "FB:ma" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "ZFA:0009190" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/CL_0000402", - "lbl" : "CNS interneuron", + "id" : "http://purl.obolibrary.org/obo/CL_0000404", + "lbl" : "electrically signaling cell", "type" : "CLASS", "meta" : { "definition" : { - "val" : "An interneuron that has its cell body in a central nervous system.", - "xrefs" : [ "doi:10.1016/B978-0-12-817424-1.00001-X" ] + "val" : "A cell that initiates an electrical signal and passes that signal to another cell.", + "xrefs" : [ "FB:ma" ] }, - "comments" : [ "Interneurons are commonly described as being only found in the central nervous system. However, in CL we define 'interneuron' more broadly as any neuron that is neither a motor neuron nor a sensory neuron, regardless of its location, so we need this term to refer strictly to interneurons of the central nervous system." ], - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { - "val" : "ZFA:0009191" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" + "val" : "ZFA:0009193" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/CL_0000404", - "lbl" : "electrically signaling cell", + "id" : "http://purl.obolibrary.org/obo/CL_0000499", + "lbl" : "stromal cell", "type" : "CLASS", "meta" : { "definition" : { - "val" : "A cell that initiates an electrical signal and passes that signal to another cell.", - "xrefs" : [ "FB:ma" ] + "val" : "A connective tissue cell of an organ found in the loose connective tissue.", + "xrefs" : [ "GOC:tfm", "MESH:D017154" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#general_cell_types_upper_slim", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "xrefs" : [ { - "val" : "ZFA:0009193" + "val" : "BTO:0002064" + }, { + "val" : "FMA:83624" + }, { + "val" : "ZFA:0009226" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/RO_0002175", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" } ] } }, { @@ -1527,7 +1555,7 @@ "val" : "A precursor cell destined to differentiate into smooth muscle myocytes.", "xrefs" : [ "GOC:tfm", "MESH:D032390" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "myoblast, smooth muscle", @@ -1540,6 +1568,12 @@ "val" : "FMA:84798" }, { "val" : "ZFA:0009235" + }, { + "val" : "https://cellxgene.cziscience.com/cellguide/CL_0000514" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/description", + "val" : "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nA precursor to the smooth muscle cell, the smooth muscle myoblast, is integral to various body systems, including the cardiovascular, gastrointestinal, and respiratory systems. Smooth muscle myoblasts arise from the differentiation of mesenchymal stem cells, a process tightly regulated by specific genetic factors and environmental signals. Their role extends to myogenesis, particularly in the formation of muscular tissue, especially during embryonic development.\nSmooth muscle myoblasts possess distinctive cellular characteristics. In contrast to skeletal muscle myoblasts, they do not fuse to create multinucleated fibers. Instead, they differentiate into individual, uninucleated smooth muscle cells. This differentiation unfolds in two distinct phases: proliferation, marked by rapid division to increase cell numbers, and differentiation, involving structural and functional transformation into mature smooth muscle cells. This intricate process is intricately mediated by various signaling molecules and transcription factors.\nFunctionally, smooth muscle myoblasts and the mature muscle cells they generate play pivotal roles in various physiological processes. Smooth muscle cells orchestrate involuntary muscle responses and are integral to body systems that regulate blood flow, propel food along the digestive tract, and control airflow in the respiratory tract. These diverse functions underscore the significance of smooth muscle myoblasts in the body's growth, maintenance, and overall function." } ] } }, { @@ -1551,7 +1585,7 @@ "val" : "A neuron which conveys sensory information centrally from the periphery.", "xrefs" : [ "GOC:tfm", "MESH:D009475" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "input neuron" @@ -1571,7 +1605,7 @@ "lbl" : "pigmented epithelial cell", "type" : "CLASS", "meta" : { - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "ZFA:0009241" } ] @@ -1586,7 +1620,7 @@ "xrefs" : [ "MESH:D009474", "http://en.wikipedia.org/wiki/Neuron" ] }, "comments" : [ "These cells are also reportedly CD4-negative and CD200-positive. They are also capable of producing CD40L and IFN-gamma." ], - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#general_cell_types_upper_slim", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#general_cell_types_upper_slim", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "nerve cell" @@ -1624,6 +1658,7 @@ "xrefs" : [ "GOC:tfm", "SANBI:mhl" ] }, "comments" : [ "Derived from UBERON:0002342 neural crest." ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "BTO:0003217" }, { @@ -1641,7 +1676,7 @@ "val" : "An immature, nucleated erythrocyte occupying the stage of erythropoeisis that follows formation of erythroid progenitor cells. This cell is CD71-positive, has both a nucleus and a nucleolus, and lacks hematopoeitic lineage markers.", "xrefs" : [ "ISBN:0721601464", "PMID:1638021" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#blood_and_immune_upper_slim", "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#blood_and_immune_upper_slim", "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "rubriblast", @@ -1663,6 +1698,7 @@ "val" : "A nucleated immature erythrocyte, having cytoplasm generally similar to that of the earlier proerythroblast but sometimes even more basophilic, and usually regular in outline. The nucleus is still relatively large, but the chromatin strands are thicker and more deeply staining, giving a coarser appearance; the nucleoli have disappeared. This cell is CD71-positive and lacks hematopoeitic lineage markers.", "xrefs" : [ "GOC:tfm", "ISBN:0721601464" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "basophilic normoblast", @@ -1695,6 +1731,7 @@ "val" : "A nucleated, immature erythrocyte in which the nucleus occupies a relatively smaller part of the cell than in its precursor, the basophilic erythroblast. The cytoplasm is beginning to acquire hemoglobin and thus is no longer a purely basophilic, but takes on acidophilic aspects, which becomes progressively more marked as the cell matures. The chromatin of the nucleus is arranged in coarse, deeply staining clumps. This cell is CD71-positive and lacks hematopoeitic lineage markers.", "xrefs" : [ "ISBN:0721601464" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "intermediate erythroblast", @@ -1735,6 +1772,7 @@ "val" : "The final stage of the nucleated, immature erythrocyte, before nuclear loss. Typically the cytoplasm is described as acidophilic, but it still shows a faint polychromatic tint. The nucleus is small and initially may still have coarse, clumped chromatin, as in its precursor, the polychromatophilic erythroblast, but ultimately it becomes pyknotic, and appears as a deeply staining, blue-black, homogeneous structureless mass. The nucleus is often eccentric and sometimes lobulated.", "xrefs" : [ "ISBN:0721601464" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "acidophilic erythroblast", @@ -1769,7 +1807,7 @@ "xrefs" : [ "GOC:dsd", "GOC:tfm", "ISBN:0721601464" ] }, "comments" : [ "Lineage negative is described here as CD2-negative, CD3-negative, CD4-negative, CD5-negative, CD8a-negative, CD14-negative, CD19-negative, CD20-negative, CD56-negative, Ly6g-negative, and Ter119-negative." ], - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "CFU-Meg", @@ -1829,7 +1867,7 @@ "xrefs" : [ "ISBN:0721601464", "MESH:D008533", "PMID:31043076", "http://en.wikipedia.org/wiki/Megakaryocyte" ] }, "comments" : [ "Megakaryocytes are reportedly CD181-positive and CD182-positive." ], - "subsets" : [ "http://purl.obolibrary.org/obo/cl#blood_and_immune_upper_slim", "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#blood_and_immune_upper_slim", "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "megacaryocyte" @@ -1861,7 +1899,7 @@ "val" : "An immature erythrocyte that changes the protein composition of its plasma membrane by exosome formation and extrusion. The types of protein removed differ between species though removal of the transferrin receptor is apparent in mammals and birds.", "xrefs" : [ "GOC:add", "GOC:tfm", "PMID:15946868", "PMID:2037622" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#blood_and_immune_upper_slim", "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#blood_and_immune_upper_slim", "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "BTO:0001173" }, { @@ -1881,7 +1919,7 @@ "val" : "Interneuron of the vertebrate retina. They integrate, modulate, and interpose a temporal domain in the visual message presented to the retinal ganglion cells, with which they synapse in the inner plexiform layer. They lack large axons.", "xrefs" : [ "GOC:tfm", "MESH:D025042", "WikipediaVersioned:Amacrine_cell&oldid=1023572246" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#eye_upper_slim", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#eye_upper_slim", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "amacrine neuron" @@ -1918,6 +1956,7 @@ "xrefs" : [ "GOC:dsd", "GOC:tfm", "PMID:12768659" ] }, "comments" : [ "These cells are reportedly CD31-positive, CD34-positive, CD144-positive, CD309-positive, and TAL1-positive." ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "angioblast" @@ -1938,7 +1977,7 @@ "val" : "One of the two photoreceptor cell types in the vertebrate retina. In cones the photopigment is in invaginations of the cell membrane of the outer segment. Cones are less sensitive to light than rods, but they provide vision with higher spatial and temporal acuity, and the combination of signals from cones with different pigments allows color vision.", "xrefs" : [ "MESH:D017949" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "synonyms" : [ { "pred" : "hasRelatedSynonym", "val" : "cone", @@ -1967,7 +2006,7 @@ "val" : "An epithelial cell of the cornea.", "xrefs" : [ "GOC:tfm" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#eye_upper_slim", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#eye_upper_slim", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "epithelial cell of cornea", @@ -1996,7 +2035,7 @@ "val" : "One of the two photoreceptor cell types of the vertebrate retina. In rods the photopigment is in stacks of membranous disks separate from the outer cell membrane. Rods are more sensitive to light than cones, but rod mediated vision has less spatial and temporal resolution than cone vision.", "xrefs" : [ "MESH:D017948" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "synonyms" : [ { "pred" : "hasRelatedSynonym", "val" : "rod", @@ -2025,7 +2064,7 @@ "val" : "Astrocyte-like radial glial cell that extends vertically throughout the retina, with the nucleus are usually in the middle of the inner nuclear layer.", "xrefs" : [ "GOC:NV", "PMID:21911394" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#eye_upper_slim", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#eye_upper_slim", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "synonyms" : [ { "synonymType" : "http://purl.obolibrary.org/obo/uberon/core#MISSPELLING", "pred" : "hasExactSynonym", @@ -2056,7 +2095,7 @@ "definition" : { "val" : "A neuron that is capable of some neurotansmission by glutamate secretion." }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "xrefs" : [ { "val" : "FBbt:00100291" }, { @@ -2078,7 +2117,7 @@ "val" : "A non-terminally differentiated cell that is capable of developing into a muscle cell.", "xrefs" : [ "GOC:add" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "ZFA:0009291" } ] @@ -2093,7 +2132,7 @@ "xrefs" : [ "GOC:dph" ] }, "comments" : [ "Unlike that of mammals, the brain of adult teleost fish exhibits an intense and widespread neurogenic activity as a result of the persistence of\nradial glial cells acting as neural progenitors throughout life." ], - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "pred" : "hasNarrowSynonym", "val" : "forebrain radial glial cell" @@ -2112,6 +2151,7 @@ "xrefs" : [ "GOC:tfm" ] }, "comments" : [ "The term \"neuroepithelial cell\" is used to describe both this cell type and sensory epithelial cell (CL:0000098)." ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "pred" : "hasBroadSynonym", "val" : "neuroepithelial cell" @@ -2131,6 +2171,7 @@ "val" : "A stem cell that can give rise to cell types of the body other than those of the germ-line.", "xrefs" : [ "GO:0048103" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "CALOHA:TS-2086" }, { @@ -2148,7 +2189,7 @@ "val" : "The set of neurons that receives neural inputs via bipolar, horizontal and amacrine cells. The axons of these cells make up the optic nerve.", "xrefs" : [ "GOC:dph" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#eye_upper_slim", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#eye_upper_slim", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "gangliocyte" @@ -2189,7 +2230,7 @@ "val" : "A neuron that laterally connects other neurons in the inner nuclear layer of the retina.", "xrefs" : [ "ISBN:0195088433" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#eye_upper_slim", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#eye_upper_slim", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "horizontal cell" @@ -2223,7 +2264,7 @@ "val" : "A bipolar neuron found in the retina and having connections with photoreceptors cells and neurons in the inner plexiform layer.", "xrefs" : [ "PMID:14689473" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#eye_upper_slim", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#eye_upper_slim", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "synonyms" : [ { "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003000", "pred" : "hasRelatedSynonym", @@ -2257,7 +2298,7 @@ "val" : "A cell of the monocyte, granulocyte, mast cell, megakaryocyte, or erythroid lineage.", "xrefs" : [ "GOC:add" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "BTO:0001441" }, { @@ -2278,7 +2319,7 @@ "xrefs" : [ "GOC:add", "GOC:tfm" ] }, "comments" : [ "Note that in FMA erythropoietic cells are types of nucleated erythrocytes and thus don't include erythrocytes." ], - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "erythropoietic cell" @@ -2306,7 +2347,7 @@ "val" : "A nucleated precursor of an erythrocyte that lacks hematopoietic lineage markers.", "xrefs" : [ "GOC:add", "ISBN:0721601464", "PMID:18174176" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#blood_and_immune_upper_slim", "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#blood_and_immune_upper_slim", "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "normoblast" @@ -2333,7 +2374,7 @@ "xrefs" : [ "GOC:add", "GOC:tfm", "PMID:19022770" ] }, "comments" : [ "Markers differ between mouse and human." ], - "subsets" : [ "http://purl.obolibrary.org/obo/cl#blood_and_immune_upper_slim", "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#blood_and_immune_upper_slim", "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "MPP" @@ -2363,7 +2404,7 @@ "xrefs" : [ "GOC:add", "GOC:tfm", "PMID:19022770" ] }, "comments" : [ "Note that this is a class of cell types, not an identified single cell type." ], - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "synonyms" : [ { "pred" : "hasBroadSynonym", "val" : "myeloid progenitor cell" @@ -2391,7 +2432,7 @@ "val" : "A cell of a hematopoietic lineage.", "xrefs" : [ "GOC:add", "GO_REF:0000031" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "haematopoietic cell" @@ -2423,7 +2464,7 @@ "val" : "A hematopoietic progenitor cell that is capable of developing into only one lineage of hematopoietic cells.", "xrefs" : [ "GOC:tfm", "PMID:19022770" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#blood_and_immune_upper_slim" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#blood_and_immune_upper_slim", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "basicPropertyValues" : [ { "pred" : "http://purl.org/dc/terms/contributor", "val" : "https://orcid.org/0000-0003-1980-3228" @@ -2442,7 +2483,7 @@ "xrefs" : [ "GOC:tfm", "PMID:19022770", "https://orcid.org/0000-0001-5208-3432" ] }, "comments" : [ "This cell type is intended to be compatible with any vertebrate hematopoietic oligopotent progenitor cell. For mammalian hematopoietic oligopotent progenitor cells known to be lineage-negative, please use the term 'hematopoietic oligopotent progenitor cell' (CL_0001060)." ], - "subsets" : [ "http://purl.obolibrary.org/obo/cl#blood_and_immune_upper_slim" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#blood_and_immune_upper_slim", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "basicPropertyValues" : [ { "pred" : "http://purl.org/dc/terms/contributor", "val" : "https://orcid.org/0000-0003-1980-3228" @@ -2460,6 +2501,7 @@ "val" : "An epithelial cell derived from ectoderm.", "xrefs" : [ "FMA:69074", "GOC:tfm" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "FMA:69074" }, { @@ -2482,6 +2524,7 @@ "val" : "Epithelial cell derived from mesoderm or mesenchyme.", "xrefs" : [ "FMA:69076", "GOC:tfm" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "epithelial mesenchymal cell" @@ -2509,7 +2552,7 @@ "xrefs" : [ "GOC:dsd", "GOC:tfm", "PMID:12768659" ] }, "comments" : [ "These cells are reportedly CD31-positive, CD34-positive, CD144-positive, TAL1-positive." ], - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "vascular endothelial cell" @@ -2523,10 +2566,15 @@ "val" : "CALOHA:TS-1106" }, { "val" : "FMA:67755" + }, { + "val" : "https://cellxgene.cziscience.com/cellguide/CL_0002139" } ], "basicPropertyValues" : [ { "pred" : "http://purl.org/dc/terms/contributor", "val" : "https://orcid.org/0000-0003-1980-3228" + }, { + "pred" : "http://purl.org/dc/terms/description", + "val" : "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nEndothelial cells of the vascular tree, commonly referred to as vascular endothelial cells, line the entire circulatory system, from the heart to the smallest capillaries. These cells have a unique, flattened shape, and are tightly bound together, forming a thin layer known as the endothelium. The endothelium is responsible for maintaining the interior surface of blood vessels, and plays a critical role in ensuring the smooth flow of blood. \nVascular endothelial cells act as a semi-permeable membrane, controlling the passage of materials and the transit of white blood cells into and out of the bloodstream. These cells are also involved in blood coagulation. When a blood vessel is damaged, endothelial cells promote clotting to prevent excessive bleeding and facilitate wound healing. Other functions include regulation of blood pressure and blood volume by releasing vasodilators and vasoconstrictors to either widen or constrict blood vessels, accordingly.\nFurthermore, the endothelial cells are crucial in the formation of new blood vessels, a process known as angiogenesis. This is particularly important in wound healing and the growth of new tissues during development or after injury. In the context of diseases such as cancer, angiogenesis helps facilitate tumor growth by providing nutrients and oxygen." }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2010-08-24T02:06:40Z" @@ -2541,6 +2589,7 @@ "val" : "Epithelial cells derived from general body ectoderm and ectoderm placodes.", "xrefs" : [ "GOC:tfm" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "FMA:70556" } ], @@ -2561,7 +2610,7 @@ "val" : "A cell comprising the transparent, biconvex body separating the posterior chamber and vitreous body, and constituting part of the refracting mechanism of the mammalian eye.", "xrefs" : [ "GOC:tfm", "ISBN:0721662544" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#eye_upper_slim" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#eye_upper_slim", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "FMA:70950" } ], @@ -2582,6 +2631,7 @@ "val" : "A cell containing at least one nucleus.", "xrefs" : [ "GOC:tfm" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "FMA:67513" } ], @@ -2603,7 +2653,7 @@ "xrefs" : [ "PMID:15106942" ] }, "comments" : [ "In a consensus model of unidirectional secretion, aqueous humour is formed by transferring solute, principally NaCl, from stroma to posterior chamber, with water passively following the osmotic gradient. Unidirectional secretion comprises three sequential steps. First, NaCl is transferred from the stromal interstitium into the pigmented ciliary epithelial (PE) cells. Second, solute passes from the PE into the non-pigmented ciliary epithelial (NPE) cells through gap junctions. Finally, NPE cells release Na+ and Cl− into the aqueous humour." ], - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#eye_upper_slim", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#eye_upper_slim", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "PE cell", @@ -2622,7 +2672,7 @@ "val" : "https://orcid.org/0000-0003-1980-3228" }, { "pred" : "http://purl.org/dc/terms/description", - "val" : "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional.\n\nPigmented ciliary epithelial cells, which are a type of pigment cell, have a crucial function within the eye's ciliary body. The ciliary body, located behind the iris, is one of the eye’s most vital structures and consists of two types of epithelial cells: the pigmented and the non-pigmented ciliary epithelial cells. The pigmented ciliary epithelial cells form the outer layer of the ciliary body and exhibit a black or brown pigmentation due to the melanin they contain.\nOne key function of pigmented ciliary epithelial cells is to aid in the formation of aqueous humor, an intraocular fluid that nourishes the cornea and lens, and maintains intraocular pressure which is essential for the eye’s shape and light refraction. These cells facilitate this function in conjunction with the non-pigmented ciliary epithelial cells. Together, the pigmented and non-pigmented ciliary epithelial cells form a bilayer epithelium that allows the secretion of aqueous humor through a bi-directional fluid transport mechanism.\nPigmented ciliary epithelial cells also contribute to the blood-aqueous barrier, a physiological frontier that controls the entry and exit of various substances from the blood to the aqueous humor and vice versa. The pigmentation in these cells, intensified by melanin, helps to absorb scattered light coming into the eye, reducing any potential damage and glare." + "val" : "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nPigmented ciliary epithelial cells, which are a type of pigment cell, have a crucial function within the eye's ciliary body. The ciliary body, located behind the iris, is one of the eye’s most vital structures and consists of two types of epithelial cells: the pigmented and the non-pigmented ciliary epithelial cells. The pigmented ciliary epithelial cells form the outer layer of the ciliary body and exhibit a black or brown pigmentation due to the melanin they contain.\nOne key function of pigmented ciliary epithelial cells is to aid in the formation of aqueous humor, an intraocular fluid that nourishes the cornea and lens, and maintains intraocular pressure which is essential for the eye’s shape and light refraction. These cells facilitate this function in conjunction with the non-pigmented ciliary epithelial cells. Together, the pigmented and non-pigmented ciliary epithelial cells form a bilayer epithelium that allows the secretion of aqueous humor through a bi-directional fluid transport mechanism.\nPigmented ciliary epithelial cells also contribute to the blood-aqueous barrier, a physiological frontier that controls the entry and exit of various substances from the blood to the aqueous humor and vice versa. The pigmentation in these cells, intensified by melanin, helps to absorb scattered light coming into the eye, reducing any potential damage and glare." }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2010-09-13T04:09:27Z" @@ -2638,7 +2688,7 @@ "xrefs" : [ "GOC:tfm", "PMID:15106942" ] }, "comments" : [ "In a consensus model of unidirectional secretion, aqueous humour is formed by transferring solute, principally NaCl, from stroma to posterior chamber, with water passively following the osmotic gradient. Unidirectional secretion comprises three sequential steps. First, NaCl is transferred from the stromal interstitium into the pigmented ciliary epithelial (PE) cells. Second, solute passes from the PE into the non-pigmented ciliary epithelial (NPE) cells through gap junctions. Finally, NPE cells release Na+ and Cl− into the aqueous humour." ], - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#eye_upper_slim", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#eye_upper_slim", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "NPE cell", @@ -2671,7 +2721,7 @@ "val" : "A cell that is part of the nervous system.", "xrefs" : [ "GOC:tfm", "ISBN:0618947256" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "CALOHA:TS-2040" }, { @@ -2694,7 +2744,7 @@ "val" : "A cell of the supporting or framework tissue of the body, arising chiefly from the embryonic mesoderm and including adipose tissue, cartilage, and bone.", "xrefs" : [ "GOC:tfm", "ISBN:0618947256" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "CALOHA:TS-2096" }, { @@ -2721,6 +2771,7 @@ "val" : "A cell of the embryo.", "xrefs" : [ "FMA:0618947256" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "CALOHA:TS-0263" }, { @@ -2729,10 +2780,15 @@ "val" : "WBbt:0007028" }, { "val" : "ZFA:0007089" + }, { + "val" : "https://cellxgene.cziscience.com/cellguide/CL_0002321" } ], "basicPropertyValues" : [ { "pred" : "http://purl.org/dc/terms/contributor", "val" : "https://orcid.org/0000-0003-1980-3228" + }, { + "pred" : "http://purl.org/dc/terms/description", + "val" : "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nEmbryonic cells in metazoans, which include all multicellular animals, are biological units in their earliest developmental stages from conception until the organism is fully formed. \nThey are derived from a fertilized egg, which undergoes a series of cell divisions to produce a multicellular organism. During the early phases of embryonic development, these cells exhibit pluripotency, meaning they possess the potential to differentiate into a diverse array of specialized cell types that constitute different body tissues and structures. \nThe balance between cell proliferation and differentiation in embryonic cells is crucial for successful development. When cells continue to divide without differentiating, overgrowth may occur leading to conditions such as teratomas (tumors of embryonic cells). Conversely, if cell differentiation proceeds at the expense of cell proliferation, developmental anomalies could occur regarding size or mass of the organism or its parts." }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2010-09-15T03:39:21Z" @@ -2747,7 +2803,7 @@ "val" : "A keratocyte is a specialized fibroblast residing in the cornea stroma that has a flattened, dendritic morphology; located between the lamellae with a large flattened nucleus, and lengthy processes which communicate with neighboring cells. This corneal layer, representing about 85-90% of corneal thickness, is built up from highly regular collagenous lamellae and extracellular matrix components. Keratocytes play the major role in keeping it transparent, healing its wounds, and synthesizing its components. This cell type secretes collagen I, V, VI, and keratan sulfate.", "xrefs" : [ "GOC:tfm", "ISBN:9780702029585" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#eye_upper_slim", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#eye_upper_slim", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "corneal fibroblast" @@ -2775,7 +2831,7 @@ "val" : "A melanocyte of the retina. This cell type is distinct from pigmented retinal epithelium.", "xrefs" : [ "GOC:tfm", "MP:0010190" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#eye_upper_slim" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#eye_upper_slim", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "basicPropertyValues" : [ { "pred" : "http://purl.org/dc/terms/contributor", "val" : "https://orcid.org/0000-0003-1980-3228" @@ -2794,6 +2850,7 @@ "xrefs" : [ "GOC:tfm" ] }, "comments" : [ "From Onard of the FMA: Cardiac muscle cell or cardiac myocyte is a striated muscle cell. Cardiocyte on the other hand is any cell in the heart which includes cells other than muscle cells (e.g. endothelial cell of endocardium). Unless there is a consensus among anatomists that cardiocytes refer only to muscle cells, we will treat them as a general class of cells in the heart." ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "heart cell" @@ -2824,7 +2881,7 @@ "val" : "A pigment cell located in the epithelium of the iris.", "xrefs" : [ "GOC:tfm" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#eye_upper_slim", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#eye_upper_slim", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" @@ -2845,7 +2902,7 @@ "val" : "A blood vessel endothelial cell that is part of the retina.", "xrefs" : [ "GOC:tfm" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#eye_upper_slim", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#eye_upper_slim", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "xrefs" : [ { "val" : "https://cellxgene.cziscience.com/cellguide/CL_0002585" } ], @@ -2857,7 +2914,7 @@ "val" : "https://orcid.org/0000-0003-1980-3228" }, { "pred" : "http://purl.org/dc/terms/description", - "val" : "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional.\n\nRetinal blood vessel endothelial cells constitute the innermost lining of the blood vessels found in the retina, the light-sensitive layer of tissue at the back of the eye. The primary role of these cells revolves around their location within the retinal vascular system, forming the structure of the blood-retinal barrier, a subset of the larger blood-ocular barrier system. \nThe endothelial cells are particularly involved in the growth of new retinal blood vessels from pre-existing ones (angiogenesis); this is critical in managing the amount of oxygen and essential nutrients delivered to the ocular tissues. They are crucial for maintaining homeostasis in the retinal environment by controlling the exchange of molecules between the blood and the retina. Furthermore, they mediate immune cell trafficking, supporting the immune privilege of the eye by preventing the unrestricted infiltration of inflammatory cells into the retina, thus maintaining ocular health and normal vision.\nThe malfunction or dysfunction of retinal blood vessel endothelial cells is implicated in numerous ocular pathologies, particularly diabetic retinopathy, which is one of the leading causes of blindness worldwide. In such conditions, the compromise in the integrity of the blood-retinal barrier and excess angiogenesis can lead to retinal edema and pathological neovascularization, resulting in vision loss." + "val" : "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nRetinal blood vessel endothelial cells constitute the innermost lining of the blood vessels found in the retina, the light-sensitive layer of tissue at the back of the eye. The primary role of these cells revolves around their location within the retinal vascular system, forming the structure of the blood-retinal barrier, a subset of the larger blood-ocular barrier system. \nThe endothelial cells are particularly involved in the growth of new retinal blood vessels from pre-existing ones (angiogenesis); this is critical in managing the amount of oxygen and essential nutrients delivered to the ocular tissues. They are crucial for maintaining homeostasis in the retinal environment by controlling the exchange of molecules between the blood and the retina. Furthermore, they mediate immune cell trafficking, supporting the immune privilege of the eye by preventing the unrestricted infiltration of inflammatory cells into the retina, thus maintaining ocular health and normal vision.\nThe malfunction or dysfunction of retinal blood vessel endothelial cells is implicated in numerous ocular pathologies, particularly diabetic retinopathy, which is one of the leading causes of blindness worldwide. In such conditions, the compromise in the integrity of the blood-retinal barrier and excess angiogenesis can lead to retinal edema and pathological neovascularization, resulting in vision loss." }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2011-03-06T03:28:27Z" @@ -2872,7 +2929,7 @@ "val" : "An epithelial cell of the retinal pigmented epithelium.", "xrefs" : [ "GOC:tfm" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#eye_upper_slim", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#eye_upper_slim", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "xrefs" : [ { "val" : "BTO:0004910" }, { @@ -2888,7 +2945,7 @@ "val" : "https://orcid.org/0000-0003-1980-3228" }, { "pred" : "http://purl.org/dc/terms/description", - "val" : "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional.\n\nRetinal pigment epithelial (RPE) cells form a single layer of cells at the back of the eye sandwiched between the neurosensory retina and the choroid, playing a significant role in maintaining vision health. These pigment-laden cells are highly specialized and perform an array of metabolic and transport functions essential for the maintenance of the photoreceptor cells (rods and cones) in the retina. The pigmentation of RPE cells actively aids in the absorption of excess light and the prevention of light scattering, thus enhancing the eye's optical properties.\nThe retinal pigment epithelium forms a key part of the blood/retina barrier. The cells have long sheet-like microvilli on their apical membrane that project into the light-sensitive outer segments of the photoreceptors, forming a close structural interaction. The basolateral membrane of the RPE interacts with the underlying Bruch’s membrane, which separates the RPE cells from fenestrated endothelium of the choriocapillaris. \nRPE cells support the photoreceptor by providing them with oxygen and nutrients (such as glucose, retinol and fatty acids) and removing waste products. They also recycle the visual pigment, in a process called the \"visual cycle\", where the RPE cells play a vital role in the regeneration of visual pigment (11-cis retinol) following the absorption of light. This is essential for the maintenance of photoreceptor excitability.\nBeyond this, RPE cells take part in the phagocytosis process, where they digest the shed ends of photoreceptor outer segments, thus, preventing the build-up of waste residue that could otherwise harm retinal health. They also secrete various factors, including growth factors required to maintain the structural integrity of choriocapillaris endothelium and photoreceptors, as well as immunosuppressive factors that play an important role in establishing the immune privilege of the eye." + "val" : "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nRetinal pigment epithelial (RPE) cells form a single layer of cells at the back of the eye sandwiched between the neurosensory retina and the choroid, playing a significant role in maintaining vision health. These pigment-laden cells are highly specialized and perform an array of metabolic and transport functions essential for the maintenance of the photoreceptor cells (rods and cones) in the retina. The pigmentation of RPE cells actively aids in the absorption of excess light and the prevention of light scattering, thus enhancing the eye's optical properties.\nThe retinal pigment epithelium forms a key part of the blood/retina barrier. The cells have long sheet-like microvilli on their apical membrane that project into the light-sensitive outer segments of the photoreceptors, forming a close structural interaction. The basolateral membrane of the RPE interacts with the underlying Bruch’s membrane, which separates the RPE cells from fenestrated endothelium of the choriocapillaris. \nRPE cells support the photoreceptor by providing them with oxygen and nutrients (such as glucose, retinol and fatty acids) and removing waste products. They also recycle the visual pigment, in a process called the \"visual cycle\", where the RPE cells play a vital role in the regeneration of visual pigment (11-cis retinol) following the absorption of light. This is essential for the maintenance of photoreceptor excitability.\nBeyond this, RPE cells take part in the phagocytosis process, where they digest the shed ends of photoreceptor outer segments, thus, preventing the build-up of waste residue that could otherwise harm retinal health. They also secrete various factors, including growth factors required to maintain the structural integrity of choriocapillaris endothelium and photoreceptors, as well as immunosuppressive factors that play an important role in establishing the immune privilege of the eye." }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2011-03-06T03:37:09Z" @@ -2903,6 +2960,7 @@ "val" : "A multi-fate stem cell that can give rise to different retinal cell types including rod and cone cells.", "xrefs" : [ "GOC:tfm", "PMID:20959166", "PMID:21148186" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "basicPropertyValues" : [ { "pred" : "http://purl.org/dc/terms/contributor", "val" : "https://orcid.org/0000-0003-1980-3228" @@ -2921,6 +2979,7 @@ "xrefs" : [ "CL:CVS" ] }, "comments" : [ "Is_a interneuron, part_of UBERON:0002240." ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "ZFA:0000778" } ] @@ -2934,6 +2993,7 @@ "val" : "Cell that is part of the neural crest region of the neuroepithelium, prior to migration. Note that not all premigratory neural crest cells may become migratory neural crest cells.", "xrefs" : [ "UBERONREF:0000002" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "ZFA:0007084" } ], @@ -2953,7 +3013,8 @@ "definition" : { "val" : "Any muscle cell in which the fibers are not organised into sarcomeres.", "xrefs" : [ "GOC:DOS" ] - } + }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ] } }, { "id" : "http://purl.obolibrary.org/obo/CL_0008001", @@ -2964,7 +3025,7 @@ "val" : "Any hematopoietic cell that is a precursor of some other hematopoietic cell type.", "xrefs" : [ "GOC:dos" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ] + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ] } }, { "id" : "http://purl.obolibrary.org/obo/CL_0008007", @@ -2975,6 +3036,7 @@ "val" : "A muscle cell that is part of some visceral muscle.", "xrefs" : [ "GOC:dos" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "FBbt:00005070" } ] @@ -2987,7 +3049,7 @@ "definition" : { "val" : "A non-polarised cell precursor cell that is part of some mesenchyme, is associated with the cell matrix but is not connected to other cells and is capable of migration." }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "mesenchyme cell" @@ -3006,6 +3068,7 @@ "val" : "Any neuron that is capable of part of some visual perception.", "xrefs" : [ "FBC:Autogenerated" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "basicPropertyValues" : [ { "pred" : "http://purl.org/dc/terms/contributor", "val" : "https://orcid.org/0000-0002-7073-9172" @@ -3023,7 +3086,7 @@ "val" : "Any cell in the retina, the innermost layer or coating at the back of the eyeball, which is sensitive to light and in which the optic nerve terminates.", "xrefs" : [ "GOC:pr" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#general_cell_types_upper_slim" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#general_cell_types_upper_slim", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "PMID:10702418" } ] @@ -3037,6 +3100,7 @@ "val" : "Any photoreceptor cell that is part of some camera-type eye.", "xrefs" : [ "FBC:Autogenerated" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "camera type eye photoreceptor cell" @@ -3050,6 +3114,7 @@ "definition" : { "val" : "A zygote in a plant or an animal." }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "MESH:D015053" } ], @@ -3067,13 +3132,13 @@ "val" : "A cell of the neural crest. Neural crest cells are multipotent. Premigratory neural crest cells are found at the neural plate boarder, some of which will undergo ectomesynchymal transition and delamination to form migratory neural crest cells.", "xrefs" : [ "https://orcid.org/0000-0001-5208-3432", "https://orcid.org/0000-0002-9900-7880" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "https://cellxgene.cziscience.com/cellguide/CL_0011012" } ], "basicPropertyValues" : [ { "pred" : "http://purl.org/dc/terms/description", - "val" : "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional.\n\nNeural crest cells are a group of transient and highly migratory cells that originate from the neuroectoderm during the early stages of embryonic development. They are multipotent cells with an exceptional degree of plasticity, capable of differentiating into various somatic cell types and therefore play a fundamental role in the formation of various organs and tissues, making them critical contributors to the developing embryo. \nAfter the initiation of neurulation (the formation of the neural tube) neural crest cells start to undergo epithelial-to-mesenchymal transition and delaminate and migrate from the dorsal neural tube to several regions throughout the embryo. They differentiate into a range of diverse cell types, such as neurons and glial cells of the peripheral nervous system, including sensory and autonomic neurons. They also contribute to the formation of adrenal glands, pigment cells in the skin (melanocytes), cardiac structures, including parts of the heart septum and major arteries, as well as bones and cartilage of the face and skull.\nDisorders or aberrations in the development or migration of the neural crest cells can lead to serious congenital malformations, such as neurocristopathies, including Hirschsprung disease, neuroblastoma, and neurofibromatosis." + "val" : "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nNeural crest cells are a group of transient and highly migratory cells that originate from the neuroectoderm during the early stages of embryonic development. They are multipotent cells with an exceptional degree of plasticity, capable of differentiating into various somatic cell types and therefore play a fundamental role in the formation of various organs and tissues, making them critical contributors to the developing embryo. \nAfter the initiation of neurulation (the formation of the neural tube) neural crest cells start to undergo epithelial-to-mesenchymal transition and delaminate and migrate from the dorsal neural tube to several regions throughout the embryo. They differentiate into a range of diverse cell types, such as neurons and glial cells of the peripheral nervous system, including sensory and autonomic neurons. They also contribute to the formation of adrenal glands, pigment cells in the skin (melanocytes), cardiac structures, including parts of the heart septum and major arteries, as well as bones and cartilage of the face and skull.\nDisorders or aberrations in the development or migration of the neural crest cells can lead to serious congenital malformations, such as neurocristopathies, including Hirschsprung disease, neuroblastoma, and neurofibromatosis." } ] } }, { @@ -3085,7 +3150,7 @@ "val" : "A precursor cell that has a tendency to differentiate into a specific type of cell. They are descendants of stem cells, only they are more constrained in their differentiation potential or capacity for self-renewal, and are often more limited in both senses.", "xrefs" : [ "ISBN:978-1-62808-994-3", "https://doi.org/10.1016/B978-0-12-409503-8.00002-0" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "basicPropertyValues" : [ { "pred" : "http://purl.org/dc/terms/contributor", "val" : "https://orcid.org/0000-0001-5208-3432" @@ -3101,7 +3166,7 @@ "xrefs" : [ "GOC:NV", "PMID:12771169" ] }, "comments" : [ "Need to MIREOT retinal inner nuclear layer (part of)" ], - "subsets" : [ "http://purl.obolibrary.org/obo/cl#eye_upper_slim" ] + "subsets" : [ "http://purl.obolibrary.org/obo/cl#eye_upper_slim", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ] } }, { "id" : "http://purl.obolibrary.org/obo/CL_0011115", @@ -3113,7 +3178,7 @@ "xrefs" : [ "GOC:dos" ] }, "comments" : [ "Work is needed on GO 'cell differentiation' before it is clear whether the equivalent class definition 'native cell' that capable_of some 'cell differentiation' works. Also, may want to consider merging this with non-terminally differentiated cell." ], - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ] + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ] } }, { "id" : "http://purl.obolibrary.org/obo/CL_0017502", @@ -3179,7 +3244,7 @@ "val" : "An epithelial cell that is part of the conjunctiva.", "xrefs" : [ "GOC:tfm" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#eye_upper_slim" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#eye_upper_slim", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "epithelial cell of conjunctiva", @@ -3198,7 +3263,7 @@ "val" : "A smooth muscle cell that is part of the ciliary body.", "xrefs" : [ "GOC:tfm" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#eye_upper_slim" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#eye_upper_slim", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "smooth muscle cell of ciliary body", @@ -3206,6 +3271,12 @@ } ], "xrefs" : [ { "val" : "FMA:70610" + }, { + "val" : "https://cellxgene.cziscience.com/cellguide/CL_1000443" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/description", + "val" : "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nCiliary muscle cells are specialized contractile cells that constitute the ciliary muscle, a component of the eye in vertebrates. These cells form a ring around the iris, the eye's colored part. Ciliary muscle cells fall into the category of smooth muscle cells, characterized by their lack of the striations typical of skeletal and cardiac muscle cells. Their shape is elongated and pointed at both ends, and they occur in multi-nucleated syncytia where many cells share the same cytoplasm.\nCiliary muscle cells primarily control the eye's accommodation, adjusting the thickness and curvature of the lens to fine-tune the focus of light on the retina. When ciliary muscle cells contract, tension on the zonular fibers holding the lens in place is reduced, allowing the lens to become thicker and increase its refractive power. Conversely, when the ciliary muscle cells relax, the tension on the zonular fibers increases, causing the lens to become flatter and decrease its refractive power. This adjustment facilitates clear vision at different distances, ranging from near to far objects.\nAdditionally, ciliary muscle cells play a role in draining the eye's aqueous humor, which is the clear fluid that fills the anterior chamber of the eye between the cornea and the lens. By controlling the shape of the surrounding trabecular meshwork through muscle contractions and relaxations, ciliary muscle cells indirectly regulate intraocular pressure, a factor critical for preventing ocular conditions like glaucoma." } ] } }, { @@ -3217,6 +3288,7 @@ "val" : "Any neuron that is part of a central nervous system.", "xrefs" : [ "GOC:TermGenie" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "basicPropertyValues" : [ { "pred" : "http://purl.org/dc/terms/contributor", "val" : "http://www.wikidata.org/entity/Q35563349" @@ -3234,7 +3306,7 @@ "val" : "A retinal cell that is immature or undifferentiated.", "xrefs" : [ "PMID:17565741" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#eye_upper_slim" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#eye_upper_slim", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "retinal stem cell", @@ -3258,7 +3330,7 @@ "xrefs" : [ "PMID:25236977", "PMID:33796062" ] }, "comments" : [ "In response to elevated intraocular pressure, a retinal astrocyte may modulate extracellular matrix remodeling. In the human retina, a retinal astrocyte is GFAP-positive, SOD3-positive and GYPC-positive." ], - "subsets" : [ "http://purl.obolibrary.org/obo/cl#eye_upper_slim" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#eye_upper_slim", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003004", "pred" : "hasRelatedSynonym", @@ -3292,9 +3364,6 @@ "val" : "Wikipedia:Mitosis" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0007067" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" } ] @@ -3344,15 +3413,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/geneontology/go-ontology/issues/28301" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0000789" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0000790" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0005717" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "cellular_component" @@ -3385,12 +3445,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/geneontology/go-ontology/issues/22355" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0005720" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0035328" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "cellular_component" @@ -3547,9 +3601,6 @@ "val" : "Wikipedia:Neurulation" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0001679" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" } ] @@ -3758,9 +3809,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/geneontology/go-ontology/issues/17729" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0008372" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "cellular_component" @@ -3874,12 +3922,6 @@ "val" : "Wikipedia:Basement_membrane" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0005605" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0008003" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "cellular_component" } ] @@ -4072,9 +4114,6 @@ "val" : "Wikipedia:Ribosome" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0033279" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "cellular_component" } ] @@ -4128,12 +4167,6 @@ "val" : "Wikipedia:Cell_membrane" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0005887" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0005904" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "cellular_component" } ] @@ -4202,15 +4235,6 @@ "val" : "Wikipedia:Translation_(genetics)" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0006416" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0006453" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0043037" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" } ] @@ -4239,12 +4263,6 @@ "val" : "translation initiation" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0006440" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0006454" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" } ] @@ -4267,12 +4285,6 @@ "val" : "translation elongation" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0006442" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0006455" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" } ] @@ -4297,12 +4309,6 @@ "val" : "translational complex disassembly" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0006443" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0006456" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" } ] @@ -4325,21 +4331,9 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/geneontology/go-ontology/issues/20292" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "jl" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2012-12-13T16:25:32Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0015457" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0015460" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0044765" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" @@ -4394,9 +4388,6 @@ }, "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_pir", "http://purl.obolibrary.org/obo/go#goslim_yeast" ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0006866" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" } ] @@ -4470,12 +4461,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002161", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_4896" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0006917" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0008632" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" @@ -4552,15 +4537,9 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/geneontology/go-ontology/issues/27189" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "jl" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2013-12-19T15:25:51Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:1902589" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" @@ -4656,21 +4635,6 @@ "val" : "Wikipedia:Signal_transduction" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0023014" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0023015" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0023016" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0023033" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0023045" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" } ] @@ -4769,9 +4733,6 @@ "val" : "neurotransmitter secretory pathway" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0010554" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" } ] @@ -4975,9 +4936,6 @@ "val" : "hemolymph circulation" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0070261" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" } ] @@ -5030,21 +4988,9 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/geneontology/go-ontology/issues/24968" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "jl" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2012-09-19T15:05:24Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0000004" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0007582" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0044699" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" @@ -5056,7 +5002,7 @@ "type" : "CLASS", "meta" : { "definition" : { - "val" : "The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.", + "val" : "A cellular process consisting of the biochemical pathways by which a living organism transforms chemical substances. This includes including anabolism (biosynthetic process) and catabolism (catabolic process). Metabolic processes includes the transformation of small molecules, as well macromolecular processes such as DNA repair and replication, protein synthesis and degradation.", "xrefs" : [ "GOC:go_curators", "ISBN:0198547684" ] }, "comments" : [ "Note that metabolic processes do not include single functions or processes such as protein-protein interactions, protein-nucleic acids, nor receptor-ligand interactions." ], @@ -5064,18 +5010,6 @@ "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "metabolism" - }, { - "pred" : "hasNarrowSynonym", - "val" : "metabolic process resulting in cell growth" - }, { - "pred" : "hasNarrowSynonym", - "val" : "metabolism resulting in cell growth" - }, { - "pred" : "hasNarrowSynonym", - "val" : "multicellular organism metabolic process" - }, { - "pred" : "hasRelatedSynonym", - "val" : "single-organism metabolic process" } ], "xrefs" : [ { "val" : "Wikipedia:Metabolism" @@ -5084,17 +5018,11 @@ "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/geneontology/go-ontology/issues/26424" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "jl" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/geneontology/go-ontology/issues/28932" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2012-10-17T15:46:40Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0044236" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0044710" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" @@ -5132,7 +5060,7 @@ "type" : "CLASS", "meta" : { "definition" : { - "val" : "The chemical reactions and pathways resulting in the formation of substances; typically the energy-requiring part of metabolism in which simpler substances are transformed into more complex ones.", + "val" : "A cellular process consisting of the biochemical pathways by which a living organism synthesizes chemical substances. This typically represents the energy-requiring part of metabolism in which simpler substances are transformed into more complex ones.", "xrefs" : [ "GOC:curators", "ISBN:0198547684" ] }, "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_chembl", "http://purl.obolibrary.org/obo/go#goslim_metagenomics", "http://purl.obolibrary.org/obo/go#goslim_plant", "http://purl.obolibrary.org/obo/go#goslim_plant_ribbon" ], @@ -5159,17 +5087,11 @@ "val" : "Wikipedia:Anabolism" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "jl" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/geneontology/go-ontology/issues/28932" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2012-10-17T15:52:18Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0044274" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0044711" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" @@ -5212,9 +5134,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/geneontology/go-ontology/issues/27189" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0043284" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" @@ -5426,9 +5345,6 @@ "val" : "Wikipedia:Embryogenesis" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0009795" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" } ] @@ -5530,20 +5446,8 @@ "val" : "single-organism cellular process" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "jl" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2012-12-11T16:56:55Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0008151" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0044763" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0050875" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" @@ -5612,9 +5516,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/geneontology/go-ontology/issues/24835" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0016244" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" @@ -5715,15 +5616,6 @@ "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2014-03-06T11:37:54Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0016021" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0098589" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0098805" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "cellular_component" @@ -5762,12 +5654,6 @@ "xrefs" : [ "GOC:mah" ] } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0044235" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0071842" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" } ] @@ -5920,15 +5806,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/geneontology/go-ontology/issues/27189" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0006411" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0044267" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0044268" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" @@ -5984,9 +5861,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/geneontology/go-ontology/issues/27189" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0071845" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" @@ -6025,9 +5899,6 @@ "val" : "cellular component assembly at cellular level" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0071844" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" } ] @@ -6109,17 +5980,8 @@ "val" : "single organism signaling" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "jl" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2010-02-16T09:30:50Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0023046" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0044700" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" @@ -6362,9 +6224,6 @@ "xrefs" : [ "GOC:bf" ] } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0000068" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" } ] @@ -6485,9 +6344,6 @@ "val" : "Wikipedia:Extracellular_matrix" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0005578" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "cellular_component" } ] @@ -6516,9 +6372,6 @@ "val" : "NIF_Subcellular:sao180601769" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0016023" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "cellular_component" } ] @@ -6574,9 +6427,6 @@ "val" : "Wikipedia:Vesicle_(biology)" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0031988" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "cellular_component" } ] @@ -6671,18 +6521,9 @@ }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002161", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_4932" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "jl" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2012-09-19T16:07:47Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0044707" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0050874" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" @@ -6706,14 +6547,8 @@ "val" : "single-organism developmental process" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "jl" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2012-12-19T12:21:31Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0044767" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" @@ -6765,15 +6600,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/geneontology/go-ontology/issues/22580" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0034623" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0043241" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0043624" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" @@ -6807,9 +6633,6 @@ "val" : "protein-protein complex" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0043234" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "cellular_component" } ] @@ -6862,9 +6685,6 @@ "val" : "ATP hydrolysis coupled ion transmembrane transport" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0099131" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" } ] @@ -6948,9 +6768,6 @@ "xrefs" : [ "GOC:PARL", "GOC:pad" ] }, "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "bf" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2014-07-24T10:06:19Z" }, { @@ -7057,15 +6874,6 @@ "val" : "regulation of homeostatic process" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0032844" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0032845" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0032846" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" } ] @@ -7203,15 +7011,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/geneontology/go-ontology/issues/26424" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0034960" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0043283" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0044259" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" @@ -7297,7 +7096,7 @@ } }, { "id" : "http://purl.obolibrary.org/obo/GO_0043228", - "lbl" : "non-membrane-bounded organelle", + "lbl" : "membraneless organelle", "type" : "CLASS", "meta" : { "definition" : { @@ -7306,6 +7105,12 @@ }, "subsets" : [ "http://purl.obolibrary.org/obo/go#gocheck_do_not_annotate", "http://purl.obolibrary.org/obo/go#goslim_mouse" ], "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "membrane-less organelle" + }, { + "pred" : "hasExactSynonym", + "val" : "non-membrane-bounded organelle" + }, { "pred" : "hasExactSynonym", "val" : "non-membrane-enclosed organelle" }, { @@ -7321,6 +7126,9 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/geneontology/go-ontology/issues/28153" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/geneontology/go-ontology/issues/29106" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "cellular_component" @@ -7380,7 +7188,7 @@ } }, { "id" : "http://purl.obolibrary.org/obo/GO_0043232", - "lbl" : "intracellular non-membrane-bounded organelle", + "lbl" : "intracellular membraneless organelle", "type" : "CLASS", "meta" : { "definition" : { @@ -7389,10 +7197,16 @@ }, "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_pir" ], "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "intracellular non-membrane-bounded organelle" + }, { "pred" : "hasExactSynonym", "val" : "intracellular non-membrane-enclosed organelle" } ], "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/geneontology/go-ontology/issues/29106" + }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "cellular_component" } ] @@ -7467,21 +7281,9 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/geneontology/go-ontology/issues/22580" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "mah" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2010-09-08T10:01:42Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0034600" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0034621" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0071822" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" @@ -7532,9 +7334,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/geneontology/go-ontology/issues/27194" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0071843" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" @@ -7557,9 +7356,6 @@ "val" : "Met-tRNA/eIF2.GTP ternary complex" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "jl" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2009-10-22T02:38:55Z" }, { @@ -7567,30 +7363,6 @@ "val" : "cellular_component" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/GO_0044237", - "lbl" : "cellular metabolic process", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "The chemical reactions and pathways by which individual cells transform chemical substances.", - "xrefs" : [ "GOC:go_curators" ] - }, - "comments" : [ "This term should not be used for direct annotation. It should be possible to make a more specific annotation to one of the children of this term." ], - "subsets" : [ "http://purl.obolibrary.org/obo/go#gocheck_do_not_annotate" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "cellular metabolism" - }, { - "pred" : "hasRelatedSynonym", - "val" : "intermediary metabolism", - "xrefs" : [ "GOC:mah" ] - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "biological_process" - } ] - } }, { "id" : "http://purl.obolibrary.org/obo/GO_0044238", "lbl" : "primary metabolic process", @@ -7616,38 +7388,6 @@ "val" : "biological_process" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/GO_0044249", - "lbl" : "cellular biosynthetic process", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "The chemical reactions and pathways resulting in the formation of substances, carried out by individual cells.", - "xrefs" : [ "GOC:jl" ] - }, - "comments" : [ "This term should not be used for direct annotation. It should be possible to make a more specific annotation to one of the children of this term." ], - "subsets" : [ "http://purl.obolibrary.org/obo/go#gocheck_do_not_annotate" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "cellular anabolism" - }, { - "pred" : "hasExactSynonym", - "val" : "cellular biosynthesis" - }, { - "pred" : "hasExactSynonym", - "val" : "cellular formation" - }, { - "pred" : "hasExactSynonym", - "val" : "cellular synthesis" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", - "val" : "https://github.com/geneontology/go-ontology/issues/27052" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "biological_process" - } ] - } }, { "id" : "http://purl.obolibrary.org/obo/GO_0044297", "lbl" : "cell body", @@ -7672,9 +7412,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0002161", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_4890" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "jl" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2010-02-05T10:37:16Z" @@ -7842,9 +7579,6 @@ "xrefs" : [ "GOC:dph", "GOC:tb" ] } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0048828" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" } ] @@ -8053,9 +7787,6 @@ "val" : "regulation of physiological process" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0050791" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" } ] @@ -8075,9 +7806,6 @@ "val" : "regulation of cellular physiological process" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0051244" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" } ] @@ -8126,9 +7854,6 @@ "val" : "physiological response to stimulus" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0051869" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" } ] @@ -8286,15 +8011,9 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/geneontology/go-ontology/issues/27052" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "jl" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2013-12-18T13:51:04Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:1902578" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" @@ -8373,15 +8092,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/geneontology/go-ontology/issues/4585" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0006323" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0007001" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0051277" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" @@ -8469,15 +8179,9 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/geneontology/go-ontology/issues/27189" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "jl" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2013-12-18T14:04:32Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:1902580" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" @@ -8569,14 +8273,8 @@ "val" : "ATP hydrolysis coupled transmembrane transport" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "tb" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2015-10-21T13:22:47Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0090662" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" @@ -8706,9 +8404,6 @@ "xrefs" : [ "GOC:dph" ] }, "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dph" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2009-04-28T09:33:36Z" }, { @@ -8726,9 +8421,6 @@ "xrefs" : [ "GOC:dph" ] }, "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dph" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2010-05-25T09:05:34Z" }, { @@ -8746,9 +8438,6 @@ "xrefs" : [ "GOC:dph" ] }, "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dph" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2013-06-21T16:14:47Z" }, { @@ -8766,9 +8455,6 @@ "xrefs" : [ "GOC:BHF", "GOC:rph", "PMID:21123617" ] }, "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dph" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2018-04-13T12:47:21Z" }, { @@ -8814,15 +8500,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/geneontology/go-ontology/issues/22580" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0006461" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0034622" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0043623" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" @@ -8932,9 +8609,6 @@ }, "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_yeast" ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "mah" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2009-09-15T03:00:51Z" }, { @@ -8970,9 +8644,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/geneontology/go-ontology/issues/25143" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "mah" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2010-09-08T10:10:35Z" @@ -9007,15 +8678,9 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/geneontology/go-ontology/issues/27189" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "mah" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2010-09-10T01:39:16Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0071841" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" @@ -9032,9 +8697,6 @@ }, "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_flybase_ribbon" ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "mah" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2010-10-04T01:51:47Z" }, { @@ -9061,9 +8723,6 @@ "xrefs" : [ "GOC:BHF" ] } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "mah" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2010-10-11T11:44:57Z" }, { @@ -9086,9 +8745,6 @@ "xrefs" : [ "GOC:vesicles" ] } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "mah" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2010-10-18T03:44:18Z" }, { @@ -9108,9 +8764,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/geneontology/go-ontology/issues/22302" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "mah" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2010-02-26T02:15:40Z" @@ -9138,14 +8791,8 @@ "val" : "induction of apoptosis by extracellular signals" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pr" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2011-11-23T09:30:23Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0008624" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" @@ -9168,9 +8815,6 @@ "val" : "apoptosis" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pr" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2011-11-23T09:45:24Z" }, { @@ -9191,9 +8835,6 @@ "val" : "NIF_Subcellular:sao172297168" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pr" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2012-12-17T12:31:49Z" }, { @@ -9211,9 +8852,6 @@ "xrefs" : [ "GOC:vesicles" ] }, "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pr" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2016-03-29T17:39:45Z" }, { @@ -9247,9 +8885,6 @@ "val" : "intraluminal vesicle assembly" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pr" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2016-10-03T14:35:25Z" }, { @@ -9273,9 +8908,6 @@ "val" : "region of plasma membrane" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dos" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2014-03-06T11:55:32Z" }, { @@ -9452,9 +9084,6 @@ "val" : "fibril" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0043205" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "cellular_component" } ] @@ -9526,14 +9155,18 @@ } }, { "id" : "http://purl.obolibrary.org/obo/GO_0110165", - "lbl" : "cellular anatomical entity", + "lbl" : "cellular anatomical structure", "type" : "CLASS", "meta" : { "definition" : { - "val" : "A part of a cellular organism that is either an immaterial entity or a material entity with granularity above the level of a protein complex but below that of an anatomical system. Or, a substance produced by a cellular organism with granularity above the level of a protein complex.", + "val" : "A part of a cellular organism consisting of a material entity with granularity above the level of a protein complex but below that of an anatomical system. Note that cellular organisms exclude viruses.", "xrefs" : [ "GOC:kmv" ] }, "subsets" : [ "http://purl.obolibrary.org/obo/go#gocheck_do_not_annotate", "http://purl.obolibrary.org/obo/go#goslim_pir" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "cellular anatomical entity" + } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/geneontology/go-ontology/issues/24200" @@ -9541,8 +9174,8 @@ "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/geneontology/go-ontology/issues/26424" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "kmv" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/geneontology/go-ontology/issues/28978" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2019-08-12T18:01:37Z" @@ -9563,9 +9196,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/geneontology/go-ontology/issues/13193" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "krc" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-03-21T17:26:07Z" @@ -9591,9 +9221,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/geneontology/go-ontology/issues/13298" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "krc" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-04-24T23:56:08Z" @@ -9614,9 +9241,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/geneontology/go-ontology/issues/13298" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "krc" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-04-26T16:07:02Z" @@ -9642,9 +9266,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/geneontology/go-ontology/issues/19910" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pg" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-03-23T14:44:23Z" @@ -9669,9 +9290,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/geneontology/go-ontology/issues/14256" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pg" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-10-23T11:53:42Z" @@ -9694,9 +9312,6 @@ "val" : "efflux" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pg" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2019-05-22T11:20:45Z" }, { @@ -9715,9 +9330,6 @@ }, "subsets" : [ "http://purl.obolibrary.org/obo/go#gocheck_do_not_annotate" ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "jl" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2014-05-22T14:22:34Z" }, { @@ -9740,9 +9352,6 @@ "xrefs" : [ "GOC:TermGenie" ] } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "mr" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2014-10-06T18:38:56Z" }, { @@ -9765,9 +9374,6 @@ "xrefs" : [ "GOC:vesicles" ] } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "jl" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2014-10-22T14:26:11Z" }, { @@ -9805,17 +9411,8 @@ "val" : "Wikipedia:Ribonucleoprotein" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pr" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2015-11-19T12:26:37Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0030529" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:1990903" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "cellular_component" @@ -9902,9 +9499,6 @@ "val" : "GC_ID:1" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "NCBITaxon:85055" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "ncbi_taxonomy" } ] @@ -9936,9 +9530,6 @@ "val" : "GC_ID:1" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "NCBITaxon:40673" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "ncbi_taxonomy" } ] @@ -10272,9 +9863,6 @@ "val" : "GC_ID:1" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "NCBITaxon:109679" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "ncbi_taxonomy" } ] @@ -10499,9 +10087,6 @@ "xrefs" : [ "PATOC:GVG" ] }, "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "PATO:0000072" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "quality" } ] @@ -10537,9 +10122,6 @@ "val" : "relational shape quality" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "PATO:0001647" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "quality" } ] @@ -10578,9 +10160,6 @@ "val" : "relational structural quality" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "PATO:0001452" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "quality" } ] @@ -10759,9 +10338,6 @@ "val" : "Wikipedia:Physical_property" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "PATO:0002079" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "quality" } ] @@ -10805,12 +10381,6 @@ "val" : "snap:Quality" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "PATO:0001237" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "PATO:0001238" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "quality" } ] @@ -11037,9 +10607,6 @@ "val" : "tubulate" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "PATO:0001203" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "quality" } ] @@ -11488,27 +11055,6 @@ "val" : "quality" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/PATO_0010006", - "lbl" : "cell morphology", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A quality of a single cell inhering in the bearer by virtue of the bearer's size or shape or structure.", - "xrefs" : [ "https://orcid.org/0000-0002-7073-9172" ] - }, - "comments" : [ "Use this term for morphologies that can *only* inhere in a cell, e.g. morphological qualities inhering in a cell by virtue of the presence, location or shape of one or more cell parts." ], - "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/terms/contributor", - "val" : "https://orcid.org/0000-0002-7073-9172" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2021-01-23T11:31:53Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "quality" - } ] - } }, { "id" : "http://purl.obolibrary.org/obo/PATO_0015006", "lbl" : "polymeric", @@ -11540,52 +11086,6 @@ "val" : "high N:C ratio" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "http://orcid.org/0000-0001-5208-3432" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "quality" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/PATO_0070006", - "lbl" : "cortical bipolar morphology", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A cell morphology that inheres in neurons which have two principal dendrites that emerge from the soma and begin to branch some distance from it, have few spines, and branch in narrow fields. This is in contrast to bitufted morphology where branching occurs close to the soma.", - "xrefs" : [ "PMID:18568015", "doi:10.1016/b978-0-12-369497-3.10004-4" ] - }, - "comments" : [ "This is specific to cortical bipolar cells and are distinguished from retinal bipolar cell morphology which has an axon and dendrite emerging from opposite ends of the soma." ], - "xrefs" : [ { - "val" : "ILX:0101312" - }, { - "val" : "ilxtr:BipolarPhenotype" - }, { - "val" : "nifext:2" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/terms/contributor", - "val" : "https://orcid.org/0000-0001-7258-9596" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "quality" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/PATO_0070027", - "lbl" : "bitufted dendrite cell morphology", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A cell morphology that inheres in neurons with dendrites that are bidirectional, emerging from opposite ends of the soma, with the two arbors extending in radial or tangential directions.", - "xrefs" : [ "PMID:18568015" ] - }, - "comments" : [ "This morphology type is distinct from bitufted cell morphology in that it refers to bitufted dendrite morphology rather than bitufted cell morphology." ], - "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/terms/contributor", - "val" : "https://orcid.org/0000-0001-7258-9596" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "quality" } ] @@ -11599,9 +11099,6 @@ "val" : "A quality of continuant that exist at the anatomical level of organisation and anything under it. This includes, but is not limited to, cells , tissues, and components." }, "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "http://orcid.org/0000-0001-7258-9596" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "quality" } ] @@ -11615,9 +11112,6 @@ "val" : "A quality inhering in an anotomical structure by virtue of its capacity to be stained by specific histological dyes." }, "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "http://orcid.org/0000-0001-7258-9596" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "quality" } ] @@ -11632,9 +11126,6 @@ "xrefs" : [ "GOC:add" ] }, "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "http://orcid.org/0000-0001-7258-9596" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "quality" } ] @@ -11663,7 +11154,7 @@ "val" : "An amino acid chain that is produced de novo by ribosome-mediated translation of a genetically-encoded mRNA, and any derivatives thereof.", "xrefs" : [ "PRO:DAN", "PRO:WCB" ] }, - "comments" : [ "The definition above excludes protein complexes, which some also consider a protein. Those who wish to refer to a class representing both senses of the word are directed to CHEBI:36080. Note that the definition allows for experimentally-manipulated genes, and allows for artifically-produced derivatives that mimic those found naturally. Proteins (in the sense defined here) that descended from a common ancestor can be classified into families and superfamilies composed of products of evolutionarily-related genes. The domain architecture of a protein is described by the order of its constituent domains. Proteins with the same domains in the same order are defined as homeomorphic [PRO:WCB]." ], + "comments" : [ "The definition above excludes protein complexes, which some also consider a protein. Those who wish to refer to a class representing both senses of the word are directed to CHEBI:36080. Note that the definition allows for experimentally-manipulated genes, and allows for artifically-produced derivatives that mimic those found naturally. Proteins (in the sense defined here) that descended from a common ancestor can be classified into families and superfamilies composed of products of evolutionarily-related genes. The domain architecture of a protein is described by the order of its constituent domains. Proteins with the same domains in the same order are defined as homeomorphic [PRO:WCB)." ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "natural protein", @@ -12642,15 +12133,15 @@ } ] } }, { - "id" : "http://purl.obolibrary.org/obo/PR_000050567", - "lbl" : "protein-containing material entity", + "id" : "http://purl.obolibrary.org/obo/PR_000064867", + "lbl" : "protein-containing molecular entity", "type" : "CLASS", "meta" : { "definition" : { - "val" : "A material entity that minimally consists of a protein.", + "val" : "A molecular entity that minimally consists of a protein.", "xrefs" : [ "PRO:DAN" ] }, - "comments" : [ "Note: This includes single proteins and derivatives thereof (PR:000000001), protein-containing complexes (GO:0032991), and protein aggregates (PR:000050566)." ], + "comments" : [ "Note: This includes single proteins and derivatives thereof (PR:000000001), protein-containing complexes (GO:0032991), and protein aggregates (PR:000050565)." ], "synonyms" : [ { "pred" : "hasNarrowSynonym", "val" : "protein", @@ -12967,8 +12458,6 @@ "val" : "Wikipedia:Head" }, { "val" : "XAO:0003024" - }, { - "val" : "ZFA:0001114" }, { "val" : "galen:Head" } ], @@ -13097,9 +12586,6 @@ "val" : "galen:Wall" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "UBERON:0009915" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -13507,9 +12993,6 @@ "val" : "galen:ComplexSkeletalStructure" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "UBERON:0010322" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -14039,9 +13522,6 @@ "val" : "NLX:147821" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "UBERON:0005163" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -14342,9 +13822,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "TODO - check relationship with epiblast. Note in FMA this is not a subclass of embryo, but in uberon embryo is the whole organism from zygote onwards and thus includes the blastula" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "UBERON:0007011" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -15915,9 +15392,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0002161", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_6040" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "UBERON:0003263" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -16958,7 +16432,7 @@ "val" : "Organ system that passes nutrients (such as amino acids and electrolytes), gases, hormones, blood cells, etc. to and from cells in the body to help fight diseases and help stabilize body temperature and pH to maintain homeostasis[WP].", "xrefs" : [ "Wikipedia:Circulatory_system" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#uberon_slim" ], "synonyms" : [ { "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003011", "pred" : "hasRelatedSynonym", @@ -16983,9 +16457,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002161", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_6157" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -19624,9 +19095,6 @@ "val" : "ZFA:0001619" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "UBERON:0005888" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -21572,9 +21040,6 @@ "val" : "http://uri.neuinfo.org/nif/nifstd/FMAID_7191" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "UBERON:0007036" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -22224,15 +21689,10 @@ "val" : "TAO:0001438" }, { "val" : "UMLS:C0333343" - }, { - "val" : "ZFA:0001438" }, { "val" : "galen:BodyCavity" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "UBERON:0000169" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -23356,9 +22816,6 @@ "val" : "ZFA:0000570" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "UBERON:0005060" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -23697,9 +23154,6 @@ "val" : "ZFA:0000121" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "UBERON:0006258" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" }, { @@ -24291,9 +23745,6 @@ "val" : "XAO:0000252" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "UBERON:0005713" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -24675,9 +24126,6 @@ "val" : "ZFA:0000338" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "UBERON:0023148" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -25792,9 +25240,6 @@ "val" : "Wikipedia:Trilaminar_blastocyst" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "UBERON:0007012" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -28567,6 +28012,8 @@ "val" : "UMLS:C0460004" }, { "val" : "WikipediaCategory:Head_and_neck" + }, { + "val" : "ZFA:0001114" }, { "val" : "galen:HeadAndNeck" } ], @@ -28594,9 +28041,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "consider adding new class (EMAPA:16097) for mesenchyme of embryo (some mesenchyme is extraembryonic - e.g. amnion mesoderm)" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "UBERON:0003313" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -29585,6 +29029,8 @@ "val" : "EHDAA2:0004731" }, { "val" : "Wikipedia:Coelom" + }, { + "val" : "ZFA:0001438" } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", @@ -29980,9 +29426,6 @@ "val" : "presumptive central nervous system" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "UBERON:3000469" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -30005,9 +29448,6 @@ "val" : "AAO:0000477" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "UBERON:3000477" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -30971,9 +30411,6 @@ "val" : "A relationship between a process and a barrier, where the process occurs in a region spanning the barrier. For cellular processes the barrier is typically a membrane. Examples include transport across a membrane and membrane depolarization." }, "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "https://orcid.org/0000-0002-7073-9172" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-07-20T17:19:37Z" } ] @@ -33255,9 +32692,6 @@ "val" : "RO:0004007" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2018-12-13T11:26:17Z" }, { @@ -33283,9 +32717,6 @@ "val" : "RO:0004008" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2018-12-13T11:26:32Z" }, { @@ -33311,9 +32742,6 @@ "val" : "RO:0004009" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2018-12-13T11:26:56Z" }, { @@ -33333,9 +32761,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0004050", "val" : "http://purl.obolibrary.org/obo/RO_0002418" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2018-03-13T23:55:05Z" @@ -33351,9 +32776,6 @@ "propertyType" : "OBJECT", "meta" : { "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2018-03-13T23:55:19Z" }, { @@ -33371,9 +32793,6 @@ "val" : "a relation between a process and a continuant, in which the process is regulated by the small molecule continuant" }, "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "https://orcid.org/0000-0003-1813-6857" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2020-04-22T20:27:26Z" } ] @@ -33391,9 +32810,6 @@ "val" : "RO:0012001" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "https://orcid.org/0000-0003-1813-6857" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2020-04-22T20:28:37Z" }, { @@ -33418,9 +32834,6 @@ "val" : "RO:0012003" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "https://orcid.org/0000-0003-1813-6857" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2020-06-08T17:21:33Z" }, { @@ -33441,9 +32854,6 @@ "val" : "a relation between a continuant and a process, in which the continuant is a small molecule that regulates the process" }, "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "https://orcid.org/0000-0003-1813-6857" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2020-06-24T13:15:17Z" } ] @@ -33458,9 +32868,6 @@ "val" : "a relation between a continuant and a process, in which the continuant is a small molecule that activates the process" }, "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "https://orcid.org/0000-0003-1813-6857" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2020-06-24T13:15:26Z" }, { @@ -33479,9 +32886,6 @@ "val" : "RO:0012008" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "https://orcid.org/0000-0003-1813-6857" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2021-02-26T07:28:29Z" }, { @@ -33506,9 +32910,6 @@ "val" : "has synaptic input or output in" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "https://orcid.org/0000-0002-1373-1705" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2020-07-17T09:26:52Z" } ] @@ -33533,13 +32934,34 @@ "val" : "has sensory terminal location" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "https://orcid.org/0000-0002-1373-1705" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2020-07-20T12:10:09Z" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0015004", + "lbl" : "has characterizing marker set", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "A relation that applies between a cell type and a set of markers that can be used to uniquely identify that cell type." + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "has marker gene combination" + }, { + "pred" : "hasExactSynonym", + "val" : "has marker signature set" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "C has_characterizing_marker_set y iff: C is a cell type and y is a collection of genes or proteins whose expression is sufficient to distinguish cell type C from most or all other cell types." + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0001-7258-9596" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/RO_0015006", "lbl" : "different in magnitude relative to", @@ -33665,9 +33087,6 @@ "val" : "RO:0040036" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2018-09-26T01:08:58Z" }, { @@ -34366,13 +33785,14 @@ "propertyType" : "ANNOTATION", "meta" : { "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2018-03-14T00:03:24Z" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/STATO_0000663", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" }, { "id" : "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "type" : "PROPERTY", @@ -34425,6 +33845,10 @@ "meta" : { "comments" : [ "a subset of general classes of cell types in the cell ontology." ] } + }, { + "id" : "http://purl.obolibrary.org/obo/cl#human_subset", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" }, { "id" : "http://purl.obolibrary.org/obo/cl#kidney_upper_slim", "lbl" : "kidney_upper_slim", @@ -34437,6 +33861,10 @@ "val" : "2023-11-22T11:18:57Z" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/cl#mouse_subset", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" }, { "id" : "http://purl.obolibrary.org/obo/go#gocheck_do_not_annotate", "type" : "PROPERTY", @@ -34759,10 +34187,6 @@ "id" : "http://purl.org/dc/elements/1.1/creator", "type" : "PROPERTY", "propertyType" : "ANNOTATION" - }, { - "id" : "http://purl.org/dc/elements/1.1/date", - "type" : "PROPERTY", - "propertyType" : "ANNOTATION" }, { "id" : "http://purl.org/dc/elements/1.1/description", "type" : "PROPERTY", @@ -34775,6 +34199,10 @@ "id" : "http://purl.org/dc/elements/1.1/title", "type" : "PROPERTY", "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.org/dc/elements/1.1/type", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" }, { "id" : "http://purl.org/dc/terms/contributor", "type" : "PROPERTY", @@ -34785,14 +34213,17 @@ "propertyType" : "ANNOTATION" }, { "id" : "http://purl.org/dc/terms/description", + "lbl" : "description", "type" : "PROPERTY", "propertyType" : "ANNOTATION" }, { "id" : "http://purl.org/dc/terms/license", + "lbl" : "license", "type" : "PROPERTY", "propertyType" : "ANNOTATION" }, { "id" : "http://purl.org/dc/terms/title", + "lbl" : "title", "type" : "PROPERTY", "propertyType" : "ANNOTATION" }, { @@ -34810,19 +34241,10 @@ "lbl" : "consider", "type" : "PROPERTY", "propertyType" : "ANNOTATION" - }, { - "id" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "type" : "PROPERTY", - "propertyType" : "ANNOTATION" }, { "id" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "type" : "PROPERTY", "propertyType" : "ANNOTATION" - }, { - "id" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "lbl" : "has_alternative_id", - "type" : "PROPERTY", - "propertyType" : "ANNOTATION" }, { "id" : "http://www.geneontology.org/formats/oboInOwl#hasBroadSynonym", "lbl" : "has_broad_synonym", @@ -34842,9 +34264,21 @@ } }, { "id" : "http://www.geneontology.org/formats/oboInOwl#hasDbXref", - "lbl" : "database_cross_reference", + "lbl" : "has cross-reference", "type" : "PROPERTY", - "propertyType" : "ANNOTATION" + "propertyType" : "ANNOTATION", + "meta" : { + "definition" : { + "val" : "An annotation property that links an ontology entity or a statement to a prefixed identifier or URI." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/information-artifact-ontology/ontology-metadata/issues/123" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0002-7356-1779" + } ] + } }, { "id" : "http://www.geneontology.org/formats/oboInOwl#hasExactSynonym", "lbl" : "has_exact_synonym", @@ -34923,10 +34357,6 @@ "id" : "http://www.geneontology.org/formats/oboInOwl#is_metadata_tag", "type" : "PROPERTY", "propertyType" : "ANNOTATION" - }, { - "id" : "http://www.geneontology.org/formats/oboInOwl#note", - "type" : "PROPERTY", - "propertyType" : "ANNOTATION" }, { "id" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "lbl" : "shorthand", @@ -35188,11 +34618,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000057", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/CL_0002320" - }, { - "sub" : "http://purl.obolibrary.org/obo/CL_0000057", - "pred" : "http://purl.obolibrary.org/obo/RO_0002202", - "obj" : "http://purl.obolibrary.org/obo/CL_0000134" + "obj" : "http://purl.obolibrary.org/obo/CL_0000499" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000066", "pred" : "is_a", @@ -35262,7 +34688,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000099", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/CL_0000540" + "obj" : "http://purl.obolibrary.org/obo/CL_2000029" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000101", "pred" : "is_a", @@ -35271,14 +34697,6 @@ "sub" : "http://purl.obolibrary.org/obo/CL_0000101", "pred" : "http://purl.obolibrary.org/obo/RO_0002215", "obj" : "http://purl.obolibrary.org/obo/GO_0050906" - }, { - "sub" : "http://purl.obolibrary.org/obo/CL_0000103", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/CL_0000099" - }, { - "sub" : "http://purl.obolibrary.org/obo/CL_0000103", - "pred" : "http://purl.obolibrary.org/obo/RO_0000053", - "obj" : "http://purl.obolibrary.org/obo/PATO_0070006" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000115", "pred" : "is_a", @@ -35291,18 +34709,6 @@ "sub" : "http://purl.obolibrary.org/obo/CL_0000115", "pred" : "http://purl.obolibrary.org/obo/RO_0002202", "obj" : "http://purl.obolibrary.org/obo/CL_0000222" - }, { - "sub" : "http://purl.obolibrary.org/obo/CL_0000117", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/CL_0000540" - }, { - "sub" : "http://purl.obolibrary.org/obo/CL_0000117", - "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", - "obj" : "http://purl.obolibrary.org/obo/UBERON_0001017" - }, { - "sub" : "http://purl.obolibrary.org/obo/CL_0000117", - "pred" : "http://purl.obolibrary.org/obo/RO_0002202", - "obj" : "http://purl.obolibrary.org/obo/CL_0000031" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000123", "pred" : "is_a", @@ -35680,17 +35086,17 @@ "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/CL_0000211" }, { - "sub" : "http://purl.obolibrary.org/obo/CL_0000402", + "sub" : "http://purl.obolibrary.org/obo/CL_0000404", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/CL_0000099" + "obj" : "http://purl.obolibrary.org/obo/CL_0000211" }, { - "sub" : "http://purl.obolibrary.org/obo/CL_0000402", + "sub" : "http://purl.obolibrary.org/obo/CL_0000499", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/CL_2000029" + "obj" : "http://purl.obolibrary.org/obo/CL_0002320" }, { - "sub" : "http://purl.obolibrary.org/obo/CL_0000404", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/CL_0000211" + "sub" : "http://purl.obolibrary.org/obo/CL_0000499", + "pred" : "http://purl.obolibrary.org/obo/RO_0002202", + "obj" : "http://purl.obolibrary.org/obo/CL_0000134" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000514", "pred" : "is_a", @@ -35749,10 +35155,6 @@ "sub" : "http://purl.obolibrary.org/obo/CL_0000547", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/CL_0002242" - }, { - "sub" : "http://purl.obolibrary.org/obo/CL_0000547", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000547", "pred" : "http://purl.obolibrary.org/obo/BFO_0000051", @@ -35827,10 +35229,6 @@ "val" : "true" } ] } - }, { - "sub" : "http://purl.obolibrary.org/obo/CL_0000549", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000549", "pred" : "http://purl.obolibrary.org/obo/BFO_0000051", @@ -35853,10 +35251,6 @@ "val" : "true" } ] } - }, { - "sub" : "http://purl.obolibrary.org/obo/CL_0000550", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000550", "pred" : "http://purl.obolibrary.org/obo/BFO_0000051", @@ -35997,10 +35391,6 @@ "val" : "true" } ] } - }, { - "sub" : "http://purl.obolibrary.org/obo/CL_0000558", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000558", "pred" : "http://purl.obolibrary.org/obo/CL_4030046", @@ -36091,10 +35481,6 @@ "sub" : "http://purl.obolibrary.org/obo/CL_0000566", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/CL_0011026" - }, { - "sub" : "http://purl.obolibrary.org/obo/CL_0000566", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000566", "pred" : "http://purl.obolibrary.org/obo/RO_0002104", @@ -36210,7 +35596,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000740", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/CL_0000117" + "obj" : "http://purl.obolibrary.org/obo/CL_0000540" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000740", "pred" : "http://purl.obolibrary.org/obo/RO_0002100", @@ -36223,10 +35609,6 @@ "sub" : "http://purl.obolibrary.org/obo/CL_0000745", "pred" : "http://purl.obolibrary.org/obo/RO_0002100", "obj" : "http://purl.obolibrary.org/obo/UBERON_0003902" - }, { - "sub" : "http://purl.obolibrary.org/obo/CL_0000748", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/CL_0000103" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000748", "pred" : "is_a", @@ -36347,10 +35729,6 @@ "sub" : "http://purl.obolibrary.org/obo/CL_0000837", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/CL_0008001" - }, { - "sub" : "http://purl.obolibrary.org/obo/CL_0000837", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000837", "pred" : "http://purl.obolibrary.org/obo/CL_4030046", @@ -36644,7 +36022,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/CL_0005000", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/CL_0000402", + "obj" : "http://purl.obolibrary.org/obo/CL_0000099", "meta" : { "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#is_inferred", @@ -37129,8 +36507,8 @@ "obj" : "http://purl.obolibrary.org/obo/GO_0043232" }, { "sub" : "http://purl.obolibrary.org/obo/GO_0005840", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PR_000050567" + "pred" : "http://purl.obolibrary.org/obo/BFO_0000051", + "obj" : "http://purl.obolibrary.org/obo/PR_000000001" }, { "sub" : "http://purl.obolibrary.org/obo/GO_0005840", "pred" : "http://purl.obolibrary.org/obo/RO_0002216", @@ -37174,7 +36552,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/GO_0006413", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/GO_0044237" + "obj" : "http://purl.obolibrary.org/obo/GO_0008152" }, { "sub" : "http://purl.obolibrary.org/obo/GO_0006413", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", @@ -37418,7 +36796,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/GO_0008152", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/GO_0008150" + "obj" : "http://purl.obolibrary.org/obo/GO_0009987" }, { "sub" : "http://purl.obolibrary.org/obo/GO_0008219", "pred" : "is_a", @@ -37430,11 +36808,11 @@ }, { "sub" : "http://purl.obolibrary.org/obo/GO_0009059", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/GO_0043170" + "obj" : "http://purl.obolibrary.org/obo/GO_0009058" }, { "sub" : "http://purl.obolibrary.org/obo/GO_0009059", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/GO_0044249" + "obj" : "http://purl.obolibrary.org/obo/GO_0043170" }, { "sub" : "http://purl.obolibrary.org/obo/GO_0009314", "pred" : "is_a", @@ -37905,8 +37283,8 @@ "obj" : "http://purl.obolibrary.org/obo/GO_0005575" }, { "sub" : "http://purl.obolibrary.org/obo/GO_0032991", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PR_000050567" + "pred" : "http://purl.obolibrary.org/obo/BFO_0000051", + "obj" : "http://purl.obolibrary.org/obo/PR_000000001" }, { "sub" : "http://purl.obolibrary.org/obo/GO_0034101", "pred" : "is_a", @@ -38151,26 +37529,10 @@ "sub" : "http://purl.obolibrary.org/obo/GO_0044207", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", "obj" : "http://purl.obolibrary.org/obo/GO_0005737" - }, { - "sub" : "http://purl.obolibrary.org/obo/GO_0044237", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/GO_0008152" - }, { - "sub" : "http://purl.obolibrary.org/obo/GO_0044237", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/GO_0009987" }, { "sub" : "http://purl.obolibrary.org/obo/GO_0044238", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/GO_0008152" - }, { - "sub" : "http://purl.obolibrary.org/obo/GO_0044249", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/GO_0009058" - }, { - "sub" : "http://purl.obolibrary.org/obo/GO_0044249", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/GO_0044237" }, { "sub" : "http://purl.obolibrary.org/obo/GO_0044297", "pred" : "is_a", @@ -38723,10 +38085,6 @@ "sub" : "http://purl.obolibrary.org/obo/GO_0098644", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/GO_0099080" - }, { - "sub" : "http://purl.obolibrary.org/obo/GO_0098644", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/GO_0098644", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", @@ -39287,10 +38645,6 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0010001", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0000141" - }, { - "sub" : "http://purl.obolibrary.org/obo/PATO_0010006", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PATO_0000051" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0015006", "pred" : "is_a", @@ -39299,14 +38653,6 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0040072", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0001396" - }, { - "sub" : "http://purl.obolibrary.org/obo/PATO_0070006", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PATO_0070027" - }, { - "sub" : "http://purl.obolibrary.org/obo/PATO_0070027", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PATO_0010006" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0070044", "pred" : "is_a", @@ -39330,7 +38676,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/PR_000000001", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PR_000050567" + "obj" : "http://purl.obolibrary.org/obo/PR_000064867" }, { "sub" : "http://purl.obolibrary.org/obo/PR_000000001", "pred" : "http://purl.obolibrary.org/obo/RO_0002353", @@ -39411,10 +38757,6 @@ "sub" : "http://purl.obolibrary.org/obo/PR_000001945", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PR_000000001" - }, { - "sub" : "http://purl.obolibrary.org/obo/PR_000001971", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PR_000000001" }, { "sub" : "http://purl.obolibrary.org/obo/PR_000002112", "pred" : "is_a", @@ -39460,7 +38802,7 @@ "pred" : "http://purl.obolibrary.org/obo/RO_0002160", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_2759" }, { - "sub" : "http://purl.obolibrary.org/obo/PR_000050567", + "sub" : "http://purl.obolibrary.org/obo/PR_000064867", "pred" : "http://purl.obolibrary.org/obo/BFO_0000051", "obj" : "http://purl.obolibrary.org/obo/PR_000000001" }, { @@ -39535,10 +38877,6 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0000033", "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_33213" - }, { - "sub" : "http://purl.obolibrary.org/obo/UBERON_0000042", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000042", "pred" : "is_a", @@ -39890,7 +39228,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000178", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PR_000050567" + "obj" : "http://purl.obolibrary.org/obo/UBERON_0000061" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000178", "pred" : "is_a", @@ -40071,10 +39409,6 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0000481", "pred" : "http://purl.obolibrary.org/obo/BFO_0000051", "obj" : "http://purl.obolibrary.org/obo/UBERON_0000479" - }, { - "sub" : "http://purl.obolibrary.org/obo/UBERON_0000483", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000483", "pred" : "is_a", @@ -40375,10 +39709,6 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0000959", "pred" : "http://purl.obolibrary.org/obo/uberon/core#extends_fibers_into", "obj" : "http://purl.obolibrary.org/obo/UBERON_0001908" - }, { - "sub" : "http://purl.obolibrary.org/obo/UBERON_0000964", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000964", "pred" : "is_a", @@ -41834,10 +41164,6 @@ "val" : "ZFA" } ] } - }, { - "sub" : "http://purl.obolibrary.org/obo/UBERON_0001969", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0001969", "pred" : "is_a", @@ -41854,10 +41180,6 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0001969", "pred" : "http://purl.obolibrary.org/obo/RO_0002221", "obj" : "http://purl.obolibrary.org/obo/CL_0000232" - }, { - "sub" : "http://purl.obolibrary.org/obo/UBERON_0001981", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0001981", "pred" : "is_a", @@ -42621,6 +41943,10 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0003057", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", "obj" : "http://purl.obolibrary.org/obo/UBERON_0003075" + }, { + "sub" : "http://purl.obolibrary.org/obo/UBERON_0003059", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/UBERON_0000061" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0003059", "pred" : "is_a", @@ -43695,10 +43021,6 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0004456", "pred" : "http://purl.obolibrary.org/obo/RO_0002492", "obj" : "http://purl.obolibrary.org/obo/UBERON_0000066" - }, { - "sub" : "http://purl.obolibrary.org/obo/UBERON_0004535", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0004535", "pred" : "is_a", @@ -43715,10 +43037,6 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0004535", "pred" : "http://purl.obolibrary.org/obo/BFO_0000051", "obj" : "http://purl.obolibrary.org/obo/UBERON_0001981" - }, { - "sub" : "http://purl.obolibrary.org/obo/UBERON_0004537", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0004537", "pred" : "is_a", @@ -44227,10 +43545,6 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0005764", "pred" : "http://purl.obolibrary.org/obo/RO_0002007", "obj" : "http://purl.obolibrary.org/obo/UBERON_0000061" - }, { - "sub" : "http://purl.obolibrary.org/obo/UBERON_0005769", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0005769", "pred" : "is_a", @@ -44291,10 +43605,6 @@ "val" : "AEO-modified-relation" } ] } - }, { - "sub" : "http://purl.obolibrary.org/obo/UBERON_0005906", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0005906", "pred" : "is_a", @@ -44623,10 +43933,6 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0006914", "pred" : "http://purl.obolibrary.org/obo/BFO_0000051", "obj" : "http://purl.obolibrary.org/obo/CL_0000076" - }, { - "sub" : "http://purl.obolibrary.org/obo/UBERON_0006965", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0006965", "pred" : "is_a", @@ -45066,6 +44372,10 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0009581", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", "obj" : "http://purl.obolibrary.org/obo/UBERON_0009616" + }, { + "sub" : "http://purl.obolibrary.org/obo/UBERON_0009615", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/UBERON_0004121" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0009615", "pred" : "is_a", @@ -45602,10 +44912,6 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0012275", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/UBERON_0004120" - }, { - "sub" : "http://purl.obolibrary.org/obo/UBERON_0012430", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0012430", "pred" : "is_a", @@ -46810,10 +46116,6 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002590", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002592" - }, { - "sub" : "http://purl.obolibrary.org/obo/RO_0002592", - "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0000057" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002592", "pred" : "subPropertyOf", @@ -47250,13 +46552,6 @@ "propertyId" : "http://purl.obolibrary.org/obo/RO_0002215", "fillerId" : "http://purl.obolibrary.org/obo/GO_0050906" } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/CL_0000103", - "genusIds" : [ "http://purl.obolibrary.org/obo/CL_0000099" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0000053", - "fillerId" : "http://purl.obolibrary.org/obo/PATO_0070006" - } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/CL_0000148", "genusIds" : [ "http://purl.obolibrary.org/obo/CL_0000147" ], @@ -47359,13 +46654,6 @@ "propertyId" : "http://purl.obolibrary.org/obo/RO_0002162", "fillerId" : "http://purl.obolibrary.org/obo/NCBITaxon_33208" } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/CL_0000402", - "genusIds" : [ "http://purl.obolibrary.org/obo/CL_0000099" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0002100", - "fillerId" : "http://purl.obolibrary.org/obo/UBERON_0001017" - } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/CL_0000514", "genusIds" : [ "http://purl.obolibrary.org/obo/CL_0000056" ], @@ -47600,7 +46888,7 @@ } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/CL_0000748", - "genusIds" : [ "http://purl.obolibrary.org/obo/CL_0000103" ], + "genusIds" : [ "http://purl.obolibrary.org/obo/CL_0000540" ], "restrictions" : [ { "propertyId" : "http://purl.obolibrary.org/obo/RO_0002100", "fillerId" : "http://purl.obolibrary.org/obo/UBERON_0001791" @@ -49827,6 +49115,9 @@ }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0013007", "domainClassIds" : [ "http://purl.obolibrary.org/obo/CL_0000101" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0015004", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/CL_0000000" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0015006", "domainClassIds" : [ "http://purl.obolibrary.org/obo/PATO_0000001" ], diff --git a/subsets/eye_upper_slim.obo b/subsets/eye_upper_slim.obo index 9b0a28e3c..32dfd32ca 100644 --- a/subsets/eye_upper_slim.obo +++ b/subsets/eye_upper_slim.obo @@ -1,5 +1,5 @@ format-version: 1.2 -data-version: cl/releases/2024-09-26/subsets/eye_upper_slim.owl +data-version: cl/releases/2025-01-08/subsets/eye_upper_slim.owl subsetdef: abnormal_slim "" subsetdef: added_for_HCA "" subsetdef: attribute_slim "" @@ -44,10 +44,12 @@ subsetdef: http://purl.obolibrary.org/obo/valid_for_go_gp2term "" subsetdef: http://purl.obolibrary.org/obo/valid_for_go_ontology "" subsetdef: http://purl.obolibrary.org/obo/valid_for_gocam "" subsetdef: human_reference_atlas "" +subsetdef: human_subset "" subsetdef: inconsistent_with_fma "" subsetdef: kidney_upper_slim "a subset of general classes related to specific cell types in the kidney" subsetdef: location_grouping "" subsetdef: major_organ "" +subsetdef: mouse_subset "" subsetdef: mpath_slim "" subsetdef: non_informative "" subsetdef: organ_slim "" @@ -96,7 +98,7 @@ idspace: oboInOwl http://www.geneontology.org/formats/oboInOwl# idspace: sssom https://w3id.org/sssom/ idspace: terms http://purl.org/dc/terms/ ontology: cl/subsets/eye_upper_slim -property_value: owl:versionInfo "2024-09-26" xsd:string +property_value: owl:versionInfo "2025-01-08" xsd:string [Term] id: CL:0000000 @@ -104,6 +106,8 @@ name: cell def: "A material entity of anatomical origin (part of or deriving from an organism) that has as its parts a maximally connected cell compartment surrounded by a plasma membrane." [CARO:mah] comment: The definition of cell is intended to represent all cells, and thus a cell is defined as a material entity and not an anatomical structure, which implies that it is part of an organism (or the entirety of one). subset: cellxgene_subset +subset: human_subset +subset: mouse_subset subset: ubprop:upper_level xref: CALOHA:TS-2035 xref: FBbt:00007002 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} @@ -125,6 +129,8 @@ relationship: RO:0002162 NCBITaxon:131567 ! in taxon cellular organisms id: CL:0000005 name: neural crest derived fibroblast def: "Any fibroblast that is derived from the neural crest." [https://orcid.org/0000-0001-5208-3432] +subset: human_subset +subset: mouse_subset synonym: "fibroblast neural crest derived" EXACT [] is_a: CL:0000057 ! fibroblast intersection_of: CL:0000057 ! fibroblast @@ -136,6 +142,8 @@ id: CL:0000006 name: neuronal receptor cell def: "Any sensory receptor cell that is a(n) neuron and is capable of some detection of stimulus involved in sensory perception." [FBC:Autogenerated] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "neuronal receptor cell (sensu Animalia)" EXACT [] xref: ZFA:0009001 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000101 ! sensory neuron @@ -148,6 +156,8 @@ intersection_of: capable_of GO:0050906 ! detection of stimulus involved in senso id: CL:0000007 name: early embryonic cell (metazoa) def: "A cell found in the embryo before the formation of all the gem layers is complete." [GOC:tfm] +subset: human_subset +subset: mouse_subset xref: ZFA:0009002 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0002321 ! embryonic cell (metazoa) @@ -155,13 +165,18 @@ is_a: CL:0002321 ! embryonic cell (metazoa) id: CL:0000008 name: migratory cranial neural crest cell def: "Cell that is part of the migratory cranial neural crest population. Migratory cranial neural crest cells develop from premigratory cranial neural crest cells and have undergone epithelial to mesenchymal transition and delamination." [https://orcid.org/0000-0001-5208-3432, ZFA:0007091] +subset: human_subset +subset: mouse_subset xref: ZFA:0007091 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000333 ! migratory neural crest cell [Term] id: CL:0000030 name: glioblast +def: "A non-terminally differentiated cell that develops form the neuroectoderm. Glioblast has the potential to differentiate into various types of glial cells, including astrocytes and oligodendrocytes." [PMID:37824650, Wikipedia:Glioblast] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset xref: ZFA:0009010 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000055 ! non-terminally differentiated cell is_a: CL:0000255 ! eukaryotic cell @@ -172,6 +187,8 @@ id: CL:0000031 name: neuroblast (sensu Vertebrata) def: "A cell that will develop into a neuron often after a migration phase." [GOC:NV, http://en.wikipedia.org/wiki/Neuroblast] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "neuroblast" EXACT [] xref: BTO:0000930 xref: FMA:70563 @@ -188,6 +205,8 @@ comment: This term applies to metazoan. For plant stem cells, consider using PO: subset: cellxgene_subset subset: general_cell_types_upper_slim subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "animal stem cell" EXACT [] xref: CALOHA:TS-2086 xref: FMA:63368 @@ -208,6 +227,8 @@ comment: Markers differ between species, and two sets of markers have been descr subset: blood_and_immune_upper_slim subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "blood forming stem cell" EXACT [] synonym: "colony forming unit hematopoietic" RELATED [] synonym: "hemopoietic stem cell" EXACT [] @@ -258,6 +279,8 @@ name: erythroid progenitor cell def: "A progenitor cell committed to the erythroid lineage." [GOC:add, ISBN:0721601464] subset: blood_and_immune_upper_slim subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "BFU-E" RELATED OMO:0003000 [] synonym: "blast forming unit erythroid" RELATED [] synonym: "burst forming unit erythroid" RELATED [] @@ -274,6 +297,8 @@ relationship: RO:0002202 CL:0000050 ! develops from megakaryocyte-erythroid prog id: CL:0000048 name: multi fate stem cell def: "A stem cell that can give rise to multiple lineages of cells." [GOC:add] +subset: human_subset +subset: mouse_subset synonym: "multi-fate stem cell" EXACT [] synonym: "multifate stem cell" EXACT [] synonym: "multipotent cell" EXACT [] @@ -293,6 +318,8 @@ def: "A progenitor cell committed to myeloid lineage, including the megakaryocyt comment: This cell type is intended to be compatible with any vertebrate common myeloid progenitor. For mammalian CMP known to be CD34-positive, please use the term 'common myeloid progenitor, CD34-positive' (CL_0001059). subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "CFU-GEMM" RELATED OMO:0003000 [ISBN:0878932437] synonym: "CFU-S" RELATED OMO:0003000 [ISBN:0878932437] synonym: "CMP" RELATED OMO:0003000 [ISBN:0878932437] @@ -314,6 +341,8 @@ def: "A progenitor cell committed to the megakaryocyte and erythroid lineages." comment: MEPs are reportedly CD19-negative, CD34-negative, CD45RA-negative, CD110-positive, CD117-positive, and SCA1-negative and reportedly express the transcription factors GATA-1 and NF-E2. subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "CFU-EM" EXACT [] synonym: "CFU-MegE" EXACT [] synonym: "colony forming unit erythroid megakaryocyte" EXACT [] @@ -336,6 +365,8 @@ property_value: RO:0002175 NCBITaxon:9606 id: CL:0000052 name: totipotent stem cell def: "A stem cell from which all cells of the body can form." [GOC:add, GOC:tfm] +subset: human_subset +subset: mouse_subset synonym: "totipotential stem cell" EXACT [] xref: FMA:84790 xref: MESH:D039901 @@ -348,6 +379,8 @@ name: non-terminally differentiated cell def: "A precursor cell with a limited number of potential fates." [SANBI:mhl] comment: define using PATO mulit-potent or oligopotent? subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "blast cell" EXACT [] xref: BTO:0000125 xref: FMA:84782 @@ -357,6 +390,9 @@ is_a: CL:0011115 ! precursor cell id: CL:0000056 name: myoblast def: "A cell that is commited to differentiating into a muscle cell. Embryonic myoblasts develop from the mesoderm. They undergo proliferation, migrate to their various sites, and then differentiate into the appropriate form of myocytes. Myoblasts also occur as transient populations of cells in muscles undergoing repair." [GOC:tfm, MESH:D032446, PMID:21849021] +subset: cellxgene_subset +subset: human_subset +subset: mouse_subset xref: BTO:0000222 xref: CALOHA:TS-0650 xref: FBbt:00005083 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} @@ -373,14 +409,15 @@ comment: These cells may be vimentin-positive, fibronectin-positive, fsp1-positi subset: cellxgene_subset subset: general_cell_types_upper_slim subset: human_reference_atlas +subset: human_subset +subset: mouse_subset xref: BTO:0000452 xref: CALOHA:TS-0362 xref: FMA:63877 xref: NCIT:C12482 xref: VHOG:0001482 xref: ZFA:0009026 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} -is_a: CL:0002320 ! connective tissue cell -relationship: RO:0002202 CL:0000134 ! develops from mesenchymal stem cell +is_a: CL:0000499 ! stromal cell property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -390,6 +427,8 @@ def: "A cell that is usually found in a two-dimensional sheet with a free surfac subset: cellxgene_subset subset: general_cell_types_upper_slim subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "epitheliocyte" EXACT [] xref: BTO:0000414 xref: CALOHA:TS-2026 @@ -409,6 +448,8 @@ name: blood vessel endothelial cell def: "An endothelial cell that lines the vasculature." [GOC:tfm] subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset xref: ZFA:0009036 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0002139 ! endothelial cell of vascular tree intersection_of: CL:0000115 ! endothelial cell @@ -422,6 +463,8 @@ name: columnar/cuboidal epithelial cell def: "A columnar/cuboidal epithelial cell is a cell usually found in a two dimensional sheet with a free surface. Columnar/cuboidal epithelial cells take on the shape of a column or cube." [GO:0002065, https://orcid.org/0000-0001-5208-3432] subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset xref: ZFA:0009038 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000066 ! epithelial cell property_value: RO:0002175 NCBITaxon:9606 @@ -431,6 +474,8 @@ id: CL:0000076 name: squamous epithelial cell def: "Any epithelial cell that is part of some squamous epithelium." [FBC:Autogenerated] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset xref: CALOHA:TS-1249 xref: ZFA:0009039 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000066 ! epithelial cell @@ -445,6 +490,8 @@ def: "A flat, squamous-like epithelial cell of mesodermal origin. It forms the m comment: Mesothelial cells, which morphologically resemble squamous epithelial cells, express both epithelial markers (cytokeratins) and mesenchymal markers (vimentin), reflecting their mesodermal origin. They feature surface microvilli and apical-basal polarity. Under certain conditions, they can undergo mesothelial-to-mesenchymal transition. These cells also produce extracellular matrix proteins, maintain serosal homeostasis, and facilitate fluid transport. {xref="PMID:26106328"} subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "mesotheliocyte" EXACT [] xref: FMA:66773 xref: ZFA:0009040 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} @@ -460,6 +507,8 @@ name: blood cell def: "A cell found predominately in the blood." [GOC:add, GOC:tfm] subset: cellxgene_subset subset: general_cell_types_upper_slim +subset: human_subset +subset: mouse_subset xref: FMA:62844 xref: MESH:D001773 xref: ZFA:0009044 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} @@ -472,6 +521,8 @@ relationship: capable_of GO:0008015 ! blood circulation id: CL:0000095 name: neuron associated cell subset: cellxgene_subset +subset: human_subset +subset: mouse_subset is_a: CL:0002319 ! neural cell relationship: RO:0002202 CL:0000133 ! develops from neurectodermal cell @@ -481,19 +532,25 @@ name: interneuron def: "Most generally any neuron which is not motor or sensory. Interneurons may also refer to neurons whose axons remain within a particular brain region as contrasted with projection neurons which have axons projecting to other brain regions." [GOC:tfm, MESH:D007395] subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset +synonym: "CNS interneuron" RELATED [] xref: BTO:0003811 xref: FBbt:00005125 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:67313 xref: WBbt:0005113 xref: ZFA:0009051 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} -is_a: CL:0000540 ! neuron +is_a: CL:2000029 ! central nervous system neuron property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000101 name: sensory neuron def: "Any neuron having a sensory function; an afferent neuron conveying sensory impulses." [ISBN:0721662544] +subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset xref: BTO:0001037 xref: FBbt:00005124 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:84649 @@ -506,19 +563,6 @@ intersection_of: capable_of GO:0050906 ! detection of stimulus involved in senso relationship: capable_of GO:0050906 ! detection of stimulus involved in sensory perception property_value: RO:0002175 NCBITaxon:9606 -[Term] -id: CL:0000103 -name: bipolar neuron -def: "A type of interneuron that has two neurites, usually an axon and a dendrite, extending from opposite poles of an ovoid cell body." [GOC:tfm, ISBN:0444009442] -subset: BDS_subset -subset: cellxgene_subset -xref: FMA:67282 -xref: ZFA:0009055 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} -is_a: CL:0000099 ! interneuron -intersection_of: CL:0000099 ! interneuron -intersection_of: bearer_of PATO:0070006 ! cortical bipolar morphology -relationship: bearer_of PATO:0070006 ! cortical bipolar morphology - [Term] id: CL:0000115 name: endothelial cell @@ -526,6 +570,8 @@ def: "An endothelial cell comprises the outermost layer or lining of anatomical comment: From FMA: 9.07.2001: Endothelial cell has always been classified as a kind of epithelial cell, specifically a squamous cell but that is not true. First, endothelial cell can either be squamous or cuboidal (e.g. high-endothelial cell) and secondly, it has different embryological derivation (mesodermal) than a true epithelial cell (ectodermal and endodermal). The basis for present classification is the fact that it comprises the outermost layer or lining of anatomical structures (location-based) but a better structural basis for the differentia is the cytoskeleton of the cell. Endothelial cell has vimentin filaments while an epithelial cell has keratin filaments. [Onard]. subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "endotheliocyte" EXACT [] xref: BTO:0001176 xref: CALOHA:TS-0278 @@ -536,18 +582,12 @@ is_a: CL:0000255 ! eukaryotic cell relationship: RO:0002202 CL:0000222 ! develops from mesodermal cell property_value: RO:0002175 NCBITaxon:9606 -[Term] -id: CL:0000117 -name: CNS neuron (sensu Vertebrata) -xref: ZFA:0009067 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} -is_a: CL:0000540 ! neuron -relationship: part_of UBERON:0001017 ! central nervous system -relationship: RO:0002202 CL:0000031 ! develops from neuroblast (sensu Vertebrata) - [Term] id: CL:0000123 name: neuron associated cell (sensu Vertebrata) subset: cellxgene_subset +subset: human_subset +subset: mouse_subset is_a: CL:0000095 ! neuron associated cell relationship: RO:0002162 NCBITaxon:7742 ! in taxon Vertebrata relationship: RO:0002202 CL:0000333 ! develops from migratory neural crest cell @@ -560,6 +600,8 @@ comment: Not all glial cells develop from glioblasts, with microglia developing subset: cellxgene_subset subset: general_cell_types_upper_slim subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "neuroglia" RELATED [] synonym: "neuroglial cell" EXACT [] xref: BTO:0002606 @@ -570,13 +612,15 @@ xref: https://cellxgene.cziscience.com/cellguide/CL_0000125 xref: ZFA:0009073 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000095 ! neuron associated cell property_value: RO:0002175 NCBITaxon:9606 -property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional.\n\nGlial cells, also known as neuroglia or simply glia, are non-neuronal cells in the central and peripheral nervous systems that provide support and protection for neurons. They constitute approximately half of the total cells in the human brain and more than half in other parts of the nervous system. Glial cells perform several key functions including, but not limited to, maintaining homeostasis, forming the myelin sheath around the neuron axons, and providing support and nutrition to neurons.\nThese different functions are performed by various glial cell types, including astrocytes, oligodendrocytes, microglia and other specialized types. Astrocytes, for example, are the most abundant glial cells and provide metabolic and nutrient support to neurons, help regulate the extracellular ion and neurotransmitter levels, and play a role in the formation and maintenance of the blood-brain barrier, contributing to the overall homeostasis and functioning of the nervous system. Additionally, astrocytes are involved in synaptic communication and participate in processes such as synaptogenesis and synaptic pruning.\nOligodendrocytes in the central nervous system function to insulate neurons by producing a fatty substance known as myelin. The myelin sheath enhances the speed and efficiency of nerve impulse conduction along the axons. \nMicroglia, the immune cells of the central nervous system, protect neurons from pathogens and clear away dead neurons through phagocytosis, a process also known as cellular eating. They also contribute to the regulation of inflammation in response to signals of tissue damage or infection in the central nervous system by releasing cytokines and other signaling molecules that modulate the immune response.\nDespite their overarching function in the support and protection of neurons, glial cells have also been shown to play significant roles in the pathophysiology of many psychiatric and neurodegenerative diseases, such as Alzheimer’s, Parkinson’s Disease and multiple sclerosis." xsd:string {xref="DOI:10.1002/glia.24343", xref="DOI:10.1038/nn1988", xref="DOI:10.1101/cshperspect.a020602", xref="DOI:10.1126/science.aat0473", xref="DOI:10.3389/fncel.2017.00024"} +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nGlial cells, also known as neuroglia or simply glia, are non-neuronal cells in the central and peripheral nervous systems that provide support and protection for neurons. They constitute approximately half of the total cells in the human brain and more than half in other parts of the nervous system. Glial cells perform several key functions including, but not limited to, maintaining homeostasis, forming the myelin sheath around the neuron axons, and providing support and nutrition to neurons.\nThese different functions are performed by various glial cell types, including astrocytes, oligodendrocytes, microglia and other specialized types. Astrocytes, for example, are the most abundant glial cells and provide metabolic and nutrient support to neurons, help regulate the extracellular ion and neurotransmitter levels, and play a role in the formation and maintenance of the blood-brain barrier, contributing to the overall homeostasis and functioning of the nervous system. Additionally, astrocytes are involved in synaptic communication and participate in processes such as synaptogenesis and synaptic pruning.\nOligodendrocytes in the central nervous system function to insulate neurons by producing a fatty substance known as myelin. The myelin sheath enhances the speed and efficiency of nerve impulse conduction along the axons. \nMicroglia, the immune cells of the central nervous system, protect neurons from pathogens and clear away dead neurons through phagocytosis, a process also known as cellular eating. They also contribute to the regulation of inflammation in response to signals of tissue damage or infection in the central nervous system by releasing cytokines and other signaling molecules that modulate the immune response.\nDespite their overarching function in the support and protection of neurons, glial cells have also been shown to play significant roles in the pathophysiology of many psychiatric and neurodegenerative diseases, such as Alzheimer’s, Parkinson’s Disease and multiple sclerosis." xsd:string {xref="DOI:10.1002/glia.24343", xref="DOI:10.1038/nn1988", xref="DOI:10.1101/cshperspect.a020602", xref="DOI:10.1126/science.aat0473", xref="DOI:10.3389/fncel.2017.00024"} [Term] id: CL:0000126 name: macroglial cell def: "A neuroglial cell of ectodermal origin, i.e., the astrocytes and oligodendrocytes considered together." [GOC:tfm, ISBN:0721662544] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "macroglia" RELATED OMO:0003004 [doi:10.1152/physrev.2001.81.2.871] synonym: "macrogliocyte" EXACT [] xref: BTO:0000771 @@ -593,6 +637,8 @@ def: "A class of large neuroglial (macroglial) cells in the central nervous syst comment: Astrocytes are reportedly CD68-negative, CD121a-positive, CD184-positive, CD192-positive, CRF-positive, EGFR-positive, GFAP-positive, GLUT1-positive, MBP-negative, and NGFR-positive. subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "astrocytic glia" EXACT [] xref: BTO:0000099 xref: CALOHA:TS-0060 @@ -608,6 +654,8 @@ def: "An hexagonal, flattened, mitochondria-rich endothelial cell that forms a m subset: cellxgene_subset subset: eye_upper_slim subset: human_reference_atlas +subset: human_subset +subset: mouse_subset xref: CALOHA:TS-0172 xref: FMA:70614 xref: ZFA:0009079 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} @@ -620,6 +668,8 @@ property_value: RO:0002175 NCBITaxon:9606 id: CL:0000133 name: neurectodermal cell def: "Ectoderm destined to be nervous tissue." [GOC:tfm, ISBN:068340007X] +subset: human_subset +subset: mouse_subset synonym: "neurectoderm cell" EXACT [] xref: ZFA:0009080 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000221 ! ectodermal cell @@ -630,6 +680,8 @@ name: mesenchymal stem cell def: "A connective tissue cell that normally gives rise to other cells that are organized as three-dimensional masses. In humans, this cell type is CD73-positive, CD90-positive, CD105-positive, CD45-negative, CD34-negative, and MHCII-negative. They may further differentiate into osteoblasts, adipocytes, myocytes, neurons, or chondroblasts in vitro. Originally described as residing in the bone marrow, this cell type is now known to reside in many, if not all, adult organs." [FB:ma, GOC:dsd, http://en.wikipedia.org/wiki/Mesenchymal_stem_cell, http://www.copewithcytokines.de/cope.cgi?key=mesenchymal%20stem%20cells, PMCID:PMC2613570, PMID:10102814, PMID:16923606, PMID:17986482, PMID:19960544] comment: Many but not all mesenchymal cells derive from the mesoderm. MSCs are reportedly CD3-negative, CD4-negative, CD5-negative, CD8-negative, CD11a-negative, CD11b-negative, CD14-negative, CD19-negative, CD29-positive, CD31-negative, CD34-negative, CD38-negative, CD40-negative, CD44-positive, CD45-negative, CD49-positive, CD54-positive, CD66b-negative, CD79a-negative, CD80-negative, CD102-positive, CD106-positive, CD117-positive, CD121a-positive, CD121b-positive, CD123-positive, CD124-positive, CD133-negative, CD146-positive, CD166-positive, CD271-positive, B220-negative, Gr1-negative, MHCI-positive, MHCII-negative, SSEA4-negative, sca1-positive, Ter119-negative, and glycophorin A-negative. Cultured MSCs are capable of producing stem cell factor, IL7, IL8, IL11, TGF-beta, cofilin, galectin-1, laminin-receptor 1, cyclophilin A, and MMP-2. subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "BMSC" RELATED OMO:0003000 [] synonym: "bone marrow stromal cells" NARROW [] synonym: "CFU-F" RELATED OMO:0003000 [] @@ -654,6 +706,8 @@ property_value: seeAlso "https://github.com/obophenotype/cell-ontology/issues/47 id: CL:0000147 name: pigment cell def: "A pigment cell is a cell that contains pigment granules." [GOC:tfm] +subset: human_subset +subset: mouse_subset synonym: "chromatocyte" EXACT [] synonym: "chromatophore" EXACT [] xref: VHOG:0001678 @@ -667,10 +721,13 @@ def: "A pigment cell derived from the neural crest. Contains melanin-filled pigm subset: cellxgene_subset subset: general_cell_types_upper_slim subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "melanophore" NARROW [] xref: BTO:0000847 xref: CALOHA:TS-0613 xref: FMA:70545 +xref: https://cellxgene.cziscience.com/cellguide/CL_0000148 xref: MESH:D008544 xref: VHOG:0001679 xref: ZFA:0009091 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} @@ -682,10 +739,13 @@ intersection_of: RO:0002202 CL:0000541 ! develops from melanoblast relationship: has_part GO:0042470 ! melanosome relationship: RO:0002202 CL:0000541 ! develops from melanoblast property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nMelanocytes are specialized cells prevalently found in the skin, but also present in the hair follicles, eyes, inner ear, bones, heart, and brain. Their primary function is the synthesis of melanin, a pigment responsible for coloration of skin, hair, and eyes. The presence and distribution of this pigment play a crucial role in the body's defense mechanism against harmful ultraviolet radiation.\nIn addition to melanin production, melanocytes also engage in a variety of other biological functions. They play a fundamental role in the immune response, owing to their ability to present antigens to T cells. Furthermore, they contribute to the maintenance of the skin's homeostasis by regulating processes such as extracellular matrix remodeling and cytokine production. A balance in melanocyte function is pivotal, as dysfunctions often result in dermatological disorders. For instance, the loss of melanocytes or reduction in their function may lead to hypopigmentation conditions such as vitiligo, whereas an abnormal increase could result in hyperpigmentation disorders or melanoma, a dangerous type of skin cancer." xsd:string {xref="DOI:10.1002/med.21754", xref="DOI:10.1038/nrc.2016.37", xref="DOI:10.1111/j.1751-1097.2007.00226.x", xref="DOI:10.3390/ijms21249769", xref="https://www.sciencedirect.com/topics/agricultural-and-biological-sciences/melanocyte"} [Term] id: CL:0000149 name: visual pigment cell +subset: human_subset +subset: mouse_subset synonym: "pigment cell" BROAD [] is_a: CL:0000147 ! pigment cell @@ -694,6 +754,8 @@ id: CL:0000151 name: secretory cell def: "A cell that specializes in controlled release of one or more substances." [GOC:tfm, ISBN:0721662544] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset xref: BTO:0003659 xref: FMA:86916 is_a: CL:0000000 ! cell @@ -706,6 +768,8 @@ id: CL:0000183 name: contractile cell def: "A cell whose primary function is to shorten." [FB:ma] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset is_a: CL:0000000 ! cell [Term] @@ -713,6 +777,8 @@ id: CL:0000187 name: muscle cell def: "A mature contractile cell, commonly known as a myocyte. This cell has as part of its cytoplasm myofibrils organized in various patterns." [MESH:D032342] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "muscle fiber" EXACT [] synonym: "myocyte" EXACT [] xref: BTO:0000888 @@ -735,6 +801,8 @@ def: "A non-striated, elongated, spindle-shaped cell found lining the digestive subset: cellxgene_subset subset: general_cell_types_upper_slim subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "myocytes, smooth muscle" EXACT [MESH:D032389] synonym: "non-striated muscle cell" BROAD [] synonym: "SMCs" EXACT [PMID:9315361] @@ -742,16 +810,20 @@ synonym: "smooth muscle fiber" EXACT [] xref: BTO:0004576 xref: CALOHA:TS-2159 xref: FMA:14072 +xref: https://cellxgene.cziscience.com/cellguide/CL_0000192 xref: ZFA:0009118 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0008000 ! non-striated muscle cell is_a: CL:0008007 ! visceral muscle cell relationship: RO:0002202 CL:0000514 ! develops from smooth muscle myoblast property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nSmooth muscle cells are a specialized type of muscle cells that are primarily found within the walls of hollow organs such as the intestine, stomach, bladder, uterus, and blood vessels. These cells are an essential component of the autonomic nervous system controling involuntary movements within the body.\nSmooth muscle cells play a vital role in many physiological processes due to their unique functionality. They can contract and relax in a slow, sustained, and controlled manner to help modulate the size and shape of the lumens of the organs they surround. For example, in the digestive system, coordinated contraction and relaxation of smooth muscle cells propels food along the gastrointestinal tract - a process known as peristalsis. In the blood vessels, the smooth muscle cells, by contracting or relaxing, either constrict or dilate the vessels, which in turn, help regulate blood flow and pressure.\nOn a cellular level, smooth muscle cells possess a single, centrally located nucleus and contain an arranged network of actin and myosin filaments, which are the proteins responsible for muscle contraction. Unlike their counterparts in skeletal or cardiac muscles, these cells lack specific contact points for these filaments, hence the lack of visible striations. Furthermore, the contraction of smooth muscle cells is regulated by hormones and neurotransmitters, such as acetylcholine and norepinephrine, adding an additional layer of complex regulation to these highly specialized cells." xsd:string {xref="DOI:10.1093/ptj/81.11.1810", xref="https://training.seer.cancer.gov/anatomy/muscular/types.html", xref="https://www.ncbi.nlm.nih.gov/books/NBK10854/", xref="https://www.ncbi.nlm.nih.gov/books/NBK526125", xref="https://www.ncbi.nlm.nih.gov/books/NBK556137/"} [Term] id: CL:0000197 name: sensory receptor cell def: "A cell that is capable of detection of a stimulus involved in sensory perception." [] +subset: human_subset +subset: mouse_subset synonym: "receptor cell" EXACT [] xref: MESH:D011984 is_a: CL:0000255 ! eukaryotic cell @@ -766,6 +838,8 @@ id: CL:0000210 name: photoreceptor cell def: "A cell specialized in detecting light stimuli that are involved in visual perception." [MESH:D010786] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset xref: BTO:0001060 xref: CALOHA:TS-0868 xref: FBbt:00004211 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} @@ -782,6 +856,8 @@ property_value: foaf:depiction "https://www.swissbiopics.org/api/image/Photorece id: CL:0000211 name: electrically active cell def: "A cell whose function is determined by the generation or the reception of an electric signal." [FB:ma] +subset: human_subset +subset: mouse_subset xref: ZFA:0009128 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000000 ! cell @@ -789,6 +865,8 @@ is_a: CL:0000000 ! cell id: CL:0000213 name: lining cell def: "A cell within an epithelial cell sheet whose main function is to act as an internal or external covering for a tissue or an organism." [JB:jb] +subset: human_subset +subset: mouse_subset synonym: "boundary cell" EXACT [] xref: ZFA:0009130 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000215 ! barrier cell @@ -797,6 +875,8 @@ is_a: CL:0000215 ! barrier cell id: CL:0000215 name: barrier cell def: "A cell whose primary function is to prevent the transport of stuff across compartments." [JB:jb] +subset: human_subset +subset: mouse_subset xref: ZFA:0009132 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000000 ! cell @@ -804,6 +884,8 @@ is_a: CL:0000000 ! cell id: CL:0000219 name: motile cell def: "A cell that moves by its own activities." [FB:ma] +subset: human_subset +subset: mouse_subset xref: ZFA:0009136 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000000 ! cell intersection_of: CL:0000000 ! cell @@ -814,6 +896,9 @@ relationship: capable_of GO:0048870 ! cell motility id: CL:0000221 name: ectodermal cell def: "A cell of the outer of the three germ layers of the embryo." [MESH:D004475] +subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "ectoderm cell" EXACT [] xref: FMA:72549 xref: ZFA:0009137 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} @@ -826,18 +911,24 @@ id: CL:0000222 name: mesodermal cell def: "A cell of the middle germ layer of the embryo." [MESH:D008648] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "mesoblast" EXACT [] synonym: "mesoderm cell" EXACT [] xref: FMA:72554 +xref: https://cellxgene.cziscience.com/cellguide/CL_0000222 xref: ZFA:0009138 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000255 ! eukaryotic cell is_a: CL:0002321 ! embryonic cell (metazoa) relationship: part_of UBERON:0000926 ! mesoderm +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nMesodermal cells are pluripotent and the most abundant in the human body. They contribute to the development of several structures such as the skeletal muscles, bones, heart and blood vessels, kidneys, gonads, connective tissues, and certain layers of the skin. Hence, the mesoderm is often regarded as an active and diverse layer due to its role in forming many bodily structures. \nIn embryonic development, these cells are instrumental, contributing to the body's structures through a carefully coordinated sequence of morphogenetic movements. This process forms the complex multicellular architecture of tissues and organs from a simple ball of cells. Without the function of mesodermal cells, the body's integral structures and systems would cease to form correctly, leading to developmental disorders such as axial mesodermal dysplasia complex" xsd:string {xref="DOI:10.1016/j.ceb.2019.07.012", xref="DOI:10.5535/arm.2016.40.1.162", xref="https://www.sciencedirect.com/topics/biochemistry-genetics-and-molecular-biology/mesoderm"} [Term] id: CL:0000223 name: endodermal cell def: "A cell of the inner of the three germ layers of the embryo." [MESH:D004707] +subset: human_subset +subset: mouse_subset synonym: "endoderm cell" EXACT [] xref: FMA:72555 xref: ZFA:0009139 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} @@ -852,6 +943,8 @@ def: "A red blood cell. In mammals, mature erythrocytes are biconcave disks cont subset: blood_and_immune_upper_slim subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "RBC" EXACT [] synonym: "red blood cell" EXACT [] xref: BTO:0000424 @@ -876,7 +969,8 @@ property_value: RO:0002175 NCBITaxon:9606 id: CL:0000255 name: eukaryotic cell def: "Any cell that in taxon some Eukaryota." [FBC:Autogenerated] -subset: cellxgene_subset +subset: human_subset +subset: mouse_subset xref: MESH:D005057 is_a: CL:0000000 ! cell intersection_of: CL:0000000 ! cell @@ -890,6 +984,8 @@ def: "Any photoreceptor cell that is part of some eye." [FBC:Autogenerated] subset: cellxgene_subset subset: eye_upper_slim subset: human_reference_atlas +subset: human_subset +subset: mouse_subset xref: ZFA:0009154 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000006 ! neuronal receptor cell is_a: CL:0000210 ! photoreceptor cell @@ -902,6 +998,8 @@ property_value: RO:0002175 NCBITaxon:9606 id: CL:0000293 name: structural cell def: "A cell whose primary function is to provide structural support, to provide strength and physical integrity to the organism." [TAIR:sr] +subset: human_subset +subset: mouse_subset xref: ZFA:0005745 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000000 ! cell @@ -909,6 +1007,8 @@ is_a: CL:0000000 ! cell id: CL:0000306 name: crystallin accumulating cell subset: eye_upper_slim +subset: human_subset +subset: mouse_subset synonym: "lens cell" EXACT [] is_a: CL:0000325 ! stuff accumulating cell @@ -916,6 +1016,8 @@ is_a: CL:0000325 ! stuff accumulating cell id: CL:0000325 name: stuff accumulating cell def: "A cell that is specialised to accumulate a particular substance(s)." [FB:ma] +subset: human_subset +subset: mouse_subset subset: ubprop:upper_level is_a: CL:0000000 ! cell @@ -923,6 +1025,8 @@ is_a: CL:0000000 ! cell id: CL:0000329 name: oxygen accumulating cell def: "Any cell that is capable of some oxygen transport." [FBC:Autogenerated] +subset: human_subset +subset: mouse_subset xref: ZFA:0009164 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000000 ! cell intersection_of: CL:0000000 ! cell @@ -933,6 +1037,8 @@ relationship: capable_of GO:0015671 ! oxygen transport id: CL:0000333 name: migratory neural crest cell def: "A cell derived from the specialized ectoderm flanking each side of the embryonic neural plate, which after the closure of the neural tube, forms masses of cells that migrate out from the dorsal aspect of the neural tube to spread throughout the body." [doi:10.1016/j.stem.2015.02.017] +subset: human_subset +subset: mouse_subset xref: FMA:86667 xref: ZFA:0007086 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000219 ! motile cell @@ -944,6 +1050,8 @@ relationship: RO:0002202 CL:0007004 ! develops from premigratory neural crest ce id: CL:0000335 name: mesenchyme condensation cell def: "A mesenchymal cell in embryonic development found in a contracting mass and that gives rise to osteoprogenitors." [GOC:tfm, PMID:5025404] +subset: human_subset +subset: mouse_subset xref: ZFA:0009166 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0008019 ! mesenchymal cell @@ -951,6 +1059,8 @@ is_a: CL:0008019 ! mesenchymal cell id: CL:0000339 name: glioblast (sensu Vertebrata) def: "An early neural cell developing from the early ependymal cell of the neural tube." [GOC:tfm, ISBN:0618947256] +subset: human_subset +subset: mouse_subset synonym: "spongioblast" EXACT [] xref: FMA:70564 xref: ZFA:0009169 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} @@ -962,6 +1072,8 @@ is_a: CL:0011026 ! progenitor cell id: CL:0000342 name: pigment cell (sensu Vertebrata) def: "Any animal cell containing pigment granules." [GOC:tfm, ISBN:0721662544] +subset: human_subset +subset: mouse_subset xref: ZFA:0009170 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000147 ! pigment cell is_a: CL:0000255 ! eukaryotic cell @@ -972,6 +1084,8 @@ id: CL:0000347 name: scleral cell def: "A cell of the sclera of the eye." [GOC:add] subset: eye_upper_slim +subset: human_subset +subset: mouse_subset xref: ZFA:0009174 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000255 ! eukaryotic cell is_a: CL:0000293 ! structural cell @@ -985,6 +1099,8 @@ id: CL:0000348 name: choroidal cell of the eye def: "A structural cell that is part of optic choroid." [GOC:add] subset: eye_upper_slim +subset: human_subset +subset: mouse_subset xref: ZFA:0009175 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000255 ! eukaryotic cell is_a: CL:0000293 ! structural cell @@ -997,12 +1113,16 @@ relationship: RO:0002202 CL:0000008 ! develops from migratory cranial neural cre id: CL:0000352 name: epiblast cell def: "A cell of the outer layer of a blastula that gives rise to the ectoderm after gastrulation." [GOC:tfm, ISBN:0618947256] +subset: human_subset +subset: mouse_subset is_a: CL:0000052 ! totipotent stem cell [Term] id: CL:0000365 name: animal zygote def: "Diploid cell produced by the fusion of sperm cell nucleus and egg cell." [ISBN:0471245208] +subset: human_subset +subset: mouse_subset synonym: "zygote" BROAD [] xref: BTO:0000854 xref: EHDAA2:0004546 @@ -1018,48 +1138,61 @@ relationship: RO:0002162 NCBITaxon:33208 ! in taxon Metazoa id: CL:0000393 name: electrically responsive cell def: "A cell whose function is determined by its response to an electric signal." [FB:ma] +subset: human_subset +subset: mouse_subset xref: ZFA:0009190 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000211 ! electrically active cell -[Term] -id: CL:0000402 -name: CNS interneuron -def: "An interneuron that has its cell body in a central nervous system." [doi:10.1016/B978-0-12-817424-1.00001-X] -comment: Interneurons are commonly described as being only found in the central nervous system. However, in CL we define 'interneuron' more broadly as any neuron that is neither a motor neuron nor a sensory neuron, regardless of its location, so we need this term to refer strictly to interneurons of the central nervous system. -subset: human_reference_atlas -xref: ZFA:0009191 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} -is_a: CL:0000099 ! interneuron -is_a: CL:2000029 ! central nervous system neuron -intersection_of: CL:0000099 ! interneuron -intersection_of: RO:0002100 UBERON:0001017 ! has soma location central nervous system -property_value: RO:0002175 NCBITaxon:9606 - [Term] id: CL:0000404 name: electrically signaling cell def: "A cell that initiates an electrical signal and passes that signal to another cell." [FB:ma] +subset: human_subset +subset: mouse_subset xref: ZFA:0009193 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000211 ! electrically active cell +[Term] +id: CL:0000499 +name: stromal cell +def: "A connective tissue cell of an organ found in the loose connective tissue." [GOC:tfm, MESH:D017154] +subset: cellxgene_subset +subset: general_cell_types_upper_slim +subset: human_reference_atlas +subset: human_subset +subset: mouse_subset +xref: BTO:0002064 +xref: FMA:83624 +xref: ZFA:0009226 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +is_a: CL:0002320 ! connective tissue cell +relationship: RO:0002202 CL:0000134 ! develops from mesenchymal stem cell +property_value: RO:0002175 NCBITaxon:9606 + [Term] id: CL:0000514 name: smooth muscle myoblast def: "A precursor cell destined to differentiate into smooth muscle myocytes." [GOC:tfm, MESH:D032390] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "myoblast, smooth muscle" EXACT [MESH:D032390] synonym: "satellite cell" RELATED [] xref: FMA:84798 +xref: https://cellxgene.cziscience.com/cellguide/CL_0000514 xref: ZFA:0009235 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000056 ! myoblast intersection_of: CL:0000056 ! myoblast intersection_of: RO:0002203 CL:0000192 ! develops into smooth muscle cell relationship: RO:0002203 CL:0000192 ! develops into smooth muscle cell +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nA precursor to the smooth muscle cell, the smooth muscle myoblast, is integral to various body systems, including the cardiovascular, gastrointestinal, and respiratory systems. Smooth muscle myoblasts arise from the differentiation of mesenchymal stem cells, a process tightly regulated by specific genetic factors and environmental signals. Their role extends to myogenesis, particularly in the formation of muscular tissue, especially during embryonic development.\nSmooth muscle myoblasts possess distinctive cellular characteristics. In contrast to skeletal muscle myoblasts, they do not fuse to create multinucleated fibers. Instead, they differentiate into individual, uninucleated smooth muscle cells. This differentiation unfolds in two distinct phases: proliferation, marked by rapid division to increase cell numbers, and differentiation, involving structural and functional transformation into mature smooth muscle cells. This intricate process is intricately mediated by various signaling molecules and transcription factors.\nFunctionally, smooth muscle myoblasts and the mature muscle cells they generate play pivotal roles in various physiological processes. Smooth muscle cells orchestrate involuntary muscle responses and are integral to body systems that regulate blood flow, propel food along the digestive tract, and control airflow in the respiratory tract. These diverse functions underscore the significance of smooth muscle myoblasts in the body's growth, maintenance, and overall function." xsd:string {xref="DOI:10.1074/jbc.RA118.001739", xref="https://www.ncbi.nlm.nih.gov/books/NBK544225/", xref="https://www.sciencedirect.com/topics/medicine-and-dentistry/smooth-muscle"} [Term] id: CL:0000526 name: afferent neuron def: "A neuron which conveys sensory information centrally from the periphery." [GOC:tfm, MESH:D009475] subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "input neuron" EXACT [] xref: FMA:87653 xref: ZFA:0009238 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} @@ -1070,6 +1203,8 @@ property_value: RO:0002175 NCBITaxon:9606 id: CL:0000529 name: pigmented epithelial cell subset: cellxgene_subset +subset: human_subset +subset: mouse_subset xref: ZFA:0009241 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000710 ! neurecto-epithelial cell @@ -1081,6 +1216,8 @@ comment: These cells are also reportedly CD4-negative and CD200-positive. They a subset: cellxgene_subset subset: general_cell_types_upper_slim subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "nerve cell" EXACT [] xref: BTO:0000938 xref: CALOHA:TS-0683 @@ -1101,6 +1238,8 @@ id: CL:0000541 name: melanoblast def: "A cell that originates from the neural crest and differentiates into a pigment cell." [GOC:tfm, SANBI:mhl] comment: Derived from UBERON:0002342 neural crest. +subset: human_subset +subset: mouse_subset xref: BTO:0003217 xref: FMA:83377 xref: ZFA:0009249 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} @@ -1114,12 +1253,13 @@ name: proerythroblast def: "An immature, nucleated erythrocyte occupying the stage of erythropoeisis that follows formation of erythroid progenitor cells. This cell is CD71-positive, has both a nucleus and a nucleolus, and lacks hematopoeitic lineage markers." [ISBN:0721601464, PMID:1638021] subset: blood_and_immune_upper_slim subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "pronormoblast" RELATED [] synonym: "rubriblast" EXACT [ISBN:0721601464] xref: FMA:83518 is_a: CL:0000764 {is_inferred="true"} ! erythroid lineage cell is_a: CL:0002242 ! nucleate cell -is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000764 ! erythroid lineage cell intersection_of: bearer_of PATO:0002505 ! nucleated intersection_of: bearer_of PATO:0040072 ! high nuclear/cytoplasmic ratio @@ -1158,6 +1298,8 @@ relationship: RO:0002202 CL:0000038 ! develops from erythroid progenitor cell id: CL:0000549 name: basophilic erythroblast def: "A nucleated immature erythrocyte, having cytoplasm generally similar to that of the earlier proerythroblast but sometimes even more basophilic, and usually regular in outline. The nucleus is still relatively large, but the chromatin strands are thicker and more deeply staining, giving a coarser appearance; the nucleoli have disappeared. This cell is CD71-positive and lacks hematopoeitic lineage markers." [GOC:tfm, ISBN:0721601464] +subset: human_subset +subset: mouse_subset synonym: "basophilic normoblast" EXACT [ISBN:0721601464] synonym: "early erythroblast" EXACT [ISBN:0721601464] synonym: "early normoblast" EXACT [ISBN:0721601464] @@ -1165,7 +1307,6 @@ synonym: "prorubricyte" EXACT [ISBN:0721601464] xref: FMA:83505 xref: ZFA:0005236 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000765 {is_inferred="true"} ! erythroblast -is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000765 ! erythroblast intersection_of: has_part CL:0017503 ! basophilic cytoplasm intersection_of: has_part GO:0000792 ! heterochromatin @@ -1178,6 +1319,8 @@ relationship: RO:0002104 PR:000001945 ! has plasma membrane part transferrin rec id: CL:0000550 name: polychromatophilic erythroblast def: "A nucleated, immature erythrocyte in which the nucleus occupies a relatively smaller part of the cell than in its precursor, the basophilic erythroblast. The cytoplasm is beginning to acquire hemoglobin and thus is no longer a purely basophilic, but takes on acidophilic aspects, which becomes progressively more marked as the cell matures. The chromatin of the nucleus is arranged in coarse, deeply staining clumps. This cell is CD71-positive and lacks hematopoeitic lineage markers." [ISBN:0721601464] +subset: human_subset +subset: mouse_subset synonym: "intermediate erythroblast" EXACT [ISBN:0721601464] synonym: "intermediate normoblast" EXACT [ISBN:0721601464] synonym: "polychromatic erythroblast" EXACT [ISBN:0721601464] @@ -1187,7 +1330,6 @@ synonym: "rubricyte" EXACT [ISBN:0721601464] xref: FMA:83506 xref: ZFA:0005241 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000765 {is_inferred="true"} ! erythroblast -is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000765 ! erythroblast intersection_of: has_part CL:0017504 ! polychromatophilic cytoplasm intersection_of: has_part GO:0000792 ! heterochromatin @@ -1201,6 +1343,8 @@ relationship: RO:0002202 CL:0000549 ! develops from basophilic erythroblast id: CL:0000552 name: orthochromatic erythroblast def: "The final stage of the nucleated, immature erythrocyte, before nuclear loss. Typically the cytoplasm is described as acidophilic, but it still shows a faint polychromatic tint. The nucleus is small and initially may still have coarse, clumped chromatin, as in its precursor, the polychromatophilic erythroblast, but ultimately it becomes pyknotic, and appears as a deeply staining, blue-black, homogeneous structureless mass. The nucleus is often eccentric and sometimes lobulated." [ISBN:0721601464] +subset: human_subset +subset: mouse_subset synonym: "acidophilic erythroblast" EXACT [ISBN:0721601464] synonym: "eosinophilic erythroblast" EXACT [ISBN:0721601464] synonym: "late erythoblast" EXACT [] @@ -1222,6 +1366,8 @@ def: "The earliest cytologically identifiable precursor in the thrombocytic seri comment: Lineage negative is described here as CD2-negative, CD3-negative, CD4-negative, CD5-negative, CD8a-negative, CD14-negative, CD19-negative, CD20-negative, CD56-negative, Ly6g-negative, and Ter119-negative. subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "CFU-Meg" EXACT [PMID:11722431, PMID:12482498] synonym: "colony-forming unit-megakaryocyte" EXACT [] synonym: "Meg-CFC" EXACT [PMCID:PMC1794060] @@ -1278,6 +1424,8 @@ comment: Megakaryocytes are reportedly CD181-positive and CD182-positive. subset: blood_and_immune_upper_slim subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "megacaryocyte" EXACT [] synonym: "megalocaryocyte" EXACT [] synonym: "megalokaryocyte" EXACT [] @@ -1296,12 +1444,13 @@ name: reticulocyte def: "An immature erythrocyte that changes the protein composition of its plasma membrane by exosome formation and extrusion. The types of protein removed differ between species though removal of the transferrin receptor is apparent in mammals and birds." [GOC:add, GOC:tfm, PMID:15946868, PMID:2037622] subset: blood_and_immune_upper_slim subset: cellxgene_subset +subset: human_subset +subset: mouse_subset xref: BTO:0001173 xref: CALOHA:TS-0864 xref: MESH:D012156 xref: ZFA:0009252 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000764 {is_inferred="true"} ! erythroid lineage cell -is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000764 ! erythroid lineage cell intersection_of: capable_of GO:0071971 ! extracellular exosome assembly intersection_of: CL:4030046 PR:000001002 ! lacks_plasma_membrane_part CD19 molecule @@ -1338,6 +1487,8 @@ def: "Interneuron of the vertebrate retina. They integrate, modulate, and interp subset: cellxgene_subset subset: eye_upper_slim subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "AC" RELATED OMO:0003000 [doi:10.1038/s41598-020-66092-9] synonym: "ACs" RELATED OMO:0003004 [doi:10.1038/s41598-020-66092-9] synonym: "amacrine neuron" EXACT [] @@ -1356,12 +1507,13 @@ id: CL:0000566 name: angioblastic mesenchymal cell def: "A mesenchymal stem cell capable of developing into blood vessel endothelium." [GOC:dsd, GOC:tfm, PMID:12768659] comment: These cells are reportedly CD31-positive, CD34-positive, CD144-positive, CD309-positive, and TAL1-positive. +subset: human_subset +subset: mouse_subset synonym: "angioblast" EXACT [] synonym: "chondroplast" EXACT [] xref: ZFA:0009258 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000134 {is_inferred="true"} ! mesenchymal stem cell is_a: CL:0011026 ! progenitor cell -is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000134 ! mesenchymal stem cell intersection_of: RO:0002104 PR:000001444 ! has plasma membrane part cadherin-5 intersection_of: RO:0002104 PR:000002112 ! has plasma membrane part vascular endothelial growth factor receptor 2 @@ -1377,6 +1529,8 @@ name: retinal cone cell def: "One of the two photoreceptor cell types in the vertebrate retina. In cones the photopigment is in invaginations of the cell membrane of the outer segment. Cones are less sensitive to light than rods, but they provide vision with higher spatial and temporal acuity, and the combination of signals from cones with different pigments allows color vision." [MESH:D017949] subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "cone" RELATED [doi:10.1038/s41598-020-66092-9] xref: BTO:0001036 xref: CALOHA:TS-0866 @@ -1393,6 +1547,8 @@ def: "An epithelial cell of the cornea." [GOC:tfm] subset: cellxgene_subset subset: eye_upper_slim subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "epithelial cell of cornea" EXACT [FMA:70551] xref: BTO:0004298 xref: CALOHA:TS-0173 @@ -1411,6 +1567,8 @@ name: retinal rod cell def: "One of the two photoreceptor cell types of the vertebrate retina. In rods the photopigment is in stacks of membranous disks separate from the outer cell membrane. Rods are more sensitive to light than cones, but rod mediated vision has less spatial and temporal resolution than cone vision." [MESH:D017948] subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "rod" RELATED [doi:10.1038/s41598-020-66092-9] xref: BTO:0001024 xref: CALOHA:TS-0870 @@ -1427,6 +1585,8 @@ def: "Astrocyte-like radial glial cell that extends vertically throughout the re subset: cellxgene_subset subset: eye_upper_slim subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "Muller cell" EXACT MISSPELLING [doi:10.21769/BioProtoc.4179] synonym: "Muller glia" EXACT [] synonym: "Müller cell" EXACT [] @@ -1443,6 +1603,8 @@ name: glutamatergic neuron def: "A neuron that is capable of some neurotansmission by glutamate secretion." [] subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset xref: FBbt:00100291 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: WBbt:0006829 xref: ZFA:0009290 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} @@ -1458,6 +1620,8 @@ id: CL:0000680 name: muscle precursor cell def: "A non-terminally differentiated cell that is capable of developing into a muscle cell." [GOC:add] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset xref: ZFA:0009291 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000055 ! non-terminally differentiated cell is_a: CL:0000255 ! eukaryotic cell @@ -1472,6 +1636,8 @@ name: radial glial cell def: "A cell present in the developing CNS. Functions as both a precursor cell and as a scaffold to support neuronal migration." [GOC:dph] comment: Unlike that of mammals, the brain of adult teleost fish exhibits an intense and widespread neurogenic activity as a result of the persistence of\nradial glial cells acting as neural progenitors throughout life. subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "forebrain radial glial cell" NARROW [] xref: ZFA:0009292 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000125 ! glial cell @@ -1482,6 +1648,8 @@ id: CL:0000710 name: neurecto-epithelial cell def: "Epithelial cells derived from neural plate and neural crest." [GOC:tfm] comment: The term "neuroepithelial cell" is used to describe both this cell type and sensory epithelial cell (CL:0000098). +subset: human_subset +subset: mouse_subset synonym: "neuroepithelial cell" BROAD [] xref: BTO:0004301 xref: FMA:70557 @@ -1495,6 +1663,8 @@ relationship: RO:0002202 CL:0000133 ! develops from neurectodermal cell id: CL:0000723 name: somatic stem cell def: "A stem cell that can give rise to cell types of the body other than those of the germ-line." [GO:0048103] +subset: human_subset +subset: mouse_subset xref: CALOHA:TS-2086 xref: MESH:D053687 xref: ZFA:0009307 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} @@ -1510,6 +1680,8 @@ def: "The set of neurons that receives neural inputs via bipolar, horizontal and subset: cellxgene_subset subset: eye_upper_slim subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "gangliocyte" EXACT [] synonym: "ganglion cell of retina" EXACT [] synonym: "RGC" RELATED OMO:0003000 [doi:10.1038/s41598-020-66092-9] @@ -1518,7 +1690,7 @@ xref: BTO:0001800 xref: FMA:67765 xref: MESH:D012165 xref: ZFA:0009310 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} -is_a: CL:0000117 ! CNS neuron (sensu Vertebrata) +is_a: CL:0000540 ! neuron relationship: RO:0002100 UBERON:0000966 ! has soma location retina property_value: RO:0002175 NCBITaxon:9606 @@ -1529,6 +1701,8 @@ def: "A neuron that laterally connects other neurons in the inner nuclear layer subset: cellxgene_subset subset: eye_upper_slim subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "HC" RELATED OMO:0003000 [doi:10.1038/s41598-020-66092-9] synonym: "HCs" RELATED OMO:0003004 [doi:10.1038/s41598-020-66092-9] synonym: "horizontal cell" EXACT [] @@ -1545,15 +1719,16 @@ def: "A bipolar neuron found in the retina and having connections with photorece subset: cellxgene_subset subset: eye_upper_slim subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "BC" RELATED OMO:0003000 [doi:10.1038/s41598-020-66092-9] synonym: "BCs" RELATED OMO:0003004 [doi:10.1038/s41598-020-66092-9] synonym: "BPs" RELATED OMO:0003004 [GSE137537] xref: ZFA:0009318 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} -is_a: CL:0000103 ! bipolar neuron is_a: CL:0000679 ! glutamatergic neuron is_a: CL:0008028 ! visual system neuron is_a: CL:0009004 ! retinal cell -intersection_of: CL:0000103 ! bipolar neuron +intersection_of: CL:0000540 ! neuron intersection_of: RO:0002100 UBERON:0001791 ! has soma location inner nuclear layer of retina relationship: RO:0002100 UBERON:0001791 ! has soma location inner nuclear layer of retina property_value: RO:0002175 NCBITaxon:9606 @@ -1563,6 +1738,8 @@ id: CL:0000763 name: myeloid cell def: "A cell of the monocyte, granulocyte, mast cell, megakaryocyte, or erythroid lineage." [GOC:add] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset xref: BTO:0001441 xref: CALOHA:TS-0647 xref: MESH:D022423 @@ -1580,6 +1757,8 @@ def: "A immature or mature cell in the lineage leading to and including erythroc comment: Note that in FMA erythropoietic cells are types of nucleated erythrocytes and thus don't include erythrocytes. subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "erythropoietic cell" EXACT [] xref: CALOHA:TS-0290 xref: FMA:62845 @@ -1594,6 +1773,8 @@ name: erythroblast def: "A nucleated precursor of an erythrocyte that lacks hematopoietic lineage markers." [GOC:add, ISBN:0721601464, PMID:18174176] subset: blood_and_immune_upper_slim subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "normoblast" EXACT [] xref: BTO:0001571 xref: CALOHA:TS-0289 @@ -1641,6 +1822,8 @@ comment: Markers differ between mouse and human. subset: blood_and_immune_upper_slim subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "hemopoietic progenitor cell" EXACT [] synonym: "MPP" EXACT [] xref: BTO:0000725 @@ -1648,7 +1831,6 @@ xref: CALOHA:TS-0448 xref: ZFA:0009354 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000255 ! eukaryotic cell is_a: CL:0008001 ! hematopoietic precursor cell -is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000988 ! hematopoietic cell intersection_of: bearer_of PATO:0001402 ! multipotent intersection_of: CL:4030046 PR:000001002 ! lacks_plasma_membrane_part CD19 molecule @@ -1691,6 +1873,8 @@ def: "A progenitor cell restricted to the myeloid lineage." [GOC:add, GOC:tfm, P comment: Note that this is a class of cell types, not an identified single cell type. subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "myeloid progenitor cell" BROAD [] xref: BTO:0004730 xref: CALOHA:TS-2099 @@ -1708,6 +1892,8 @@ id: CL:0000988 name: hematopoietic cell def: "A cell of a hematopoietic lineage." [GO_REF:0000031, GOC:add] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "haematopoietic cell" EXACT [] synonym: "haemopoietic cell" EXACT [] synonym: "hemopoietic cell" EXACT [] @@ -1723,6 +1909,8 @@ id: CL:0002031 name: hematopoietic lineage restricted progenitor cell def: "A hematopoietic progenitor cell that is capable of developing into only one lineage of hematopoietic cells." [GOC:tfm, PMID:19022770] subset: blood_and_immune_upper_slim +subset: human_subset +subset: mouse_subset is_a: CL:0000255 ! eukaryotic cell is_a: CL:0008001 ! hematopoietic precursor cell intersection_of: CL:0000988 ! hematopoietic cell @@ -1739,6 +1927,8 @@ name: hematopoietic oligopotent progenitor cell def: "A hematopoietic oligopotent progenitor cell that has the ability to differentiate into limited cell types but lacks lineage cell markers and self renewal capabilities." [GOC:tfm, https://orcid.org/0000-0001-5208-3432, PMID:19022770] comment: This cell type is intended to be compatible with any vertebrate hematopoietic oligopotent progenitor cell. For mammalian hematopoietic oligopotent progenitor cells known to be lineage-negative, please use the term 'hematopoietic oligopotent progenitor cell' (CL_0001060). subset: blood_and_immune_upper_slim +subset: human_subset +subset: mouse_subset is_a: CL:0000255 ! eukaryotic cell is_a: CL:0008001 ! hematopoietic precursor cell intersection_of: CL:0000988 ! hematopoietic cell @@ -1752,6 +1942,8 @@ creation_date: 2010-01-06T03:43:27Z id: CL:0002077 name: ecto-epithelial cell def: "An epithelial cell derived from ectoderm." [FMA:69074, GOC:tfm] +subset: human_subset +subset: mouse_subset xref: FMA:69074 xref: ZFA:0009385 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000066 ! epithelial cell @@ -1765,6 +1957,8 @@ creation_date: 2010-06-29T03:38:22Z id: CL:0002078 name: meso-epithelial cell def: "Epithelial cell derived from mesoderm or mesenchyme." [FMA:69076, GOC:tfm] +subset: human_subset +subset: mouse_subset synonym: "epithelial mesenchymal cell" EXACT [] xref: FMA:69076 xref: ZFA:0009388 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} @@ -1781,19 +1975,25 @@ name: endothelial cell of vascular tree def: "An endothelial cell of the vascular tree, which includes blood vessels and lymphatic vessels." [GOC:dsd, GOC:tfm, PMID:12768659] comment: These cells are reportedly CD31-positive, CD34-positive, CD144-positive, TAL1-positive. subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "cubodial endothelial cell of vascular tree" NARROW [] synonym: "vascular endothelial cell" EXACT [] xref: BTO:0001854 xref: CALOHA:TS-1106 xref: FMA:67755 +xref: https://cellxgene.cziscience.com/cellguide/CL_0002139 is_a: CL:0000115 ! endothelial cell property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nEndothelial cells of the vascular tree, commonly referred to as vascular endothelial cells, line the entire circulatory system, from the heart to the smallest capillaries. These cells have a unique, flattened shape, and are tightly bound together, forming a thin layer known as the endothelium. The endothelium is responsible for maintaining the interior surface of blood vessels, and plays a critical role in ensuring the smooth flow of blood. \nVascular endothelial cells act as a semi-permeable membrane, controlling the passage of materials and the transit of white blood cells into and out of the bloodstream. These cells are also involved in blood coagulation. When a blood vessel is damaged, endothelial cells promote clotting to prevent excessive bleeding and facilitate wound healing. Other functions include regulation of blood pressure and blood volume by releasing vasodilators and vasoconstrictors to either widen or constrict blood vessels, accordingly.\nFurthermore, the endothelial cells are crucial in the formation of new blood vessels, a process known as angiogenesis. This is particularly important in wound healing and the growth of new tissues during development or after injury. In the context of diseases such as cancer, angiogenesis helps facilitate tumor growth by providing nutrients and oxygen." xsd:string {xref="DOI:10.1038/s41569-022-00770-1", xref="DOI:10.1186/s12872-015-0124-z", xref="DOI:10.3389/fphys.2022.863265/full", xref="https://www.sciencedirect.com/topics/medicine-and-dentistry/vascular-endothelial-cell"} creation_date: 2010-08-24T02:06:40Z [Term] id: CL:0002159 name: general ecto-epithelial cell def: "Epithelial cells derived from general body ectoderm and ectoderm placodes." [GOC:tfm] +subset: human_subset +subset: mouse_subset xref: FMA:70556 is_a: CL:0002077 ! ecto-epithelial cell property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 @@ -1804,6 +2004,8 @@ id: CL:0002222 name: vertebrate lens cell def: "A cell comprising the transparent, biconvex body separating the posterior chamber and vitreous body, and constituting part of the refracting mechanism of the mammalian eye." [GOC:tfm, ISBN:0721662544] subset: eye_upper_slim +subset: human_subset +subset: mouse_subset xref: FMA:70950 is_a: CL:0000066 ! epithelial cell is_a: CL:0000306 ! crystallin accumulating cell @@ -1815,6 +2017,8 @@ creation_date: 2010-09-07T10:38:03Z id: CL:0002242 name: nucleate cell def: "A cell containing at least one nucleus." [GOC:tfm] +subset: human_subset +subset: mouse_subset xref: FMA:67513 is_a: CL:0000000 ! cell intersection_of: CL:0000000 ! cell @@ -1831,6 +2035,8 @@ comment: In a consensus model of unidirectional secretion, aqueous humour is for subset: cellxgene_subset subset: eye_upper_slim subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "PE cell" EXACT [https://doi.org/10.1016/j.exer.2003.09.021] xref: FMA:70606 xref: https://cellxgene.cziscience.com/cellguide/CL_0002303 @@ -1838,7 +2044,7 @@ is_a: CL:0000529 ! pigmented epithelial cell relationship: part_of UBERON:0001778 ! ciliary epithelium property_value: RO:0002175 NCBITaxon:9606 property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 -property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional.\n\nPigmented ciliary epithelial cells, which are a type of pigment cell, have a crucial function within the eye's ciliary body. The ciliary body, located behind the iris, is one of the eye’s most vital structures and consists of two types of epithelial cells: the pigmented and the non-pigmented ciliary epithelial cells. The pigmented ciliary epithelial cells form the outer layer of the ciliary body and exhibit a black or brown pigmentation due to the melanin they contain.\nOne key function of pigmented ciliary epithelial cells is to aid in the formation of aqueous humor, an intraocular fluid that nourishes the cornea and lens, and maintains intraocular pressure which is essential for the eye’s shape and light refraction. These cells facilitate this function in conjunction with the non-pigmented ciliary epithelial cells. Together, the pigmented and non-pigmented ciliary epithelial cells form a bilayer epithelium that allows the secretion of aqueous humor through a bi-directional fluid transport mechanism.\nPigmented ciliary epithelial cells also contribute to the blood-aqueous barrier, a physiological frontier that controls the entry and exit of various substances from the blood to the aqueous humor and vice versa. The pigmentation in these cells, intensified by melanin, helps to absorb scattered light coming into the eye, reducing any potential damage and glare." xsd:string {xref="DOI:10.1016/S1569-2590(05)10005-6", xref="DOI:10.1111/j.1444-0938.2002.tb02384.x"} +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nPigmented ciliary epithelial cells, which are a type of pigment cell, have a crucial function within the eye's ciliary body. The ciliary body, located behind the iris, is one of the eye’s most vital structures and consists of two types of epithelial cells: the pigmented and the non-pigmented ciliary epithelial cells. The pigmented ciliary epithelial cells form the outer layer of the ciliary body and exhibit a black or brown pigmentation due to the melanin they contain.\nOne key function of pigmented ciliary epithelial cells is to aid in the formation of aqueous humor, an intraocular fluid that nourishes the cornea and lens, and maintains intraocular pressure which is essential for the eye’s shape and light refraction. These cells facilitate this function in conjunction with the non-pigmented ciliary epithelial cells. Together, the pigmented and non-pigmented ciliary epithelial cells form a bilayer epithelium that allows the secretion of aqueous humor through a bi-directional fluid transport mechanism.\nPigmented ciliary epithelial cells also contribute to the blood-aqueous barrier, a physiological frontier that controls the entry and exit of various substances from the blood to the aqueous humor and vice versa. The pigmentation in these cells, intensified by melanin, helps to absorb scattered light coming into the eye, reducing any potential damage and glare." xsd:string {xref="DOI:10.1016/S1569-2590(05)10005-6", xref="DOI:10.1111/j.1444-0938.2002.tb02384.x"} creation_date: 2010-09-13T04:09:27Z [Term] @@ -1849,6 +2055,8 @@ comment: In a consensus model of unidirectional secretion, aqueous humour is for subset: cellxgene_subset subset: eye_upper_slim subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "nonpigmented ciliary epithelial cell" EXACT [PMID:10913011] synonym: "NPE cell" EXACT [https://doi.org/10.1016/j.exer.2003.09.021] xref: FMA:70607 @@ -1863,6 +2071,8 @@ id: CL:0002319 name: neural cell def: "A cell that is part of the nervous system." [GOC:tfm, ISBN:0618947256] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset xref: CALOHA:TS-2040 xref: FMA:70333 is_a: CL:0000255 ! eukaryotic cell @@ -1877,6 +2087,8 @@ id: CL:0002320 name: connective tissue cell def: "A cell of the supporting or framework tissue of the body, arising chiefly from the embryonic mesoderm and including adipose tissue, cartilage, and bone." [GOC:tfm, ISBN:0618947256] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset xref: CALOHA:TS-2096 xref: FMA:63875 xref: MESH:D003239 @@ -1892,12 +2104,16 @@ creation_date: 2010-09-15T03:01:54Z id: CL:0002321 name: embryonic cell (metazoa) def: "A cell of the embryo." [FMA:0618947256] +subset: human_subset +subset: mouse_subset xref: CALOHA:TS-0263 xref: FMA:82840 +xref: https://cellxgene.cziscience.com/cellguide/CL_0002321 xref: WBbt:0007028 xref: ZFA:0007089 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000000 ! cell property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nEmbryonic cells in metazoans, which include all multicellular animals, are biological units in their earliest developmental stages from conception until the organism is fully formed. \nThey are derived from a fertilized egg, which undergoes a series of cell divisions to produce a multicellular organism. During the early phases of embryonic development, these cells exhibit pluripotency, meaning they possess the potential to differentiate into a diverse array of specialized cell types that constitute different body tissues and structures. \nThe balance between cell proliferation and differentiation in embryonic cells is crucial for successful development. When cells continue to divide without differentiating, overgrowth may occur leading to conditions such as teratomas (tumors of embryonic cells). Conversely, if cell differentiation proceeds at the expense of cell proliferation, developmental anomalies could occur regarding size or mass of the organism or its parts." xsd:string {xref="DOI:10.1002/iub.1404", xref="DOI:10.1093/molehr/gan048", xref="https://www.ncbi.nlm.nih.gov/books/NBK9906/"} creation_date: 2010-09-15T03:39:21Z [Term] @@ -1907,6 +2123,8 @@ def: "A keratocyte is a specialized fibroblast residing in the cornea stroma th subset: cellxgene_subset subset: eye_upper_slim subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "corneal fibroblast" EXACT [] synonym: "corneal keratocyte" EXACT [] is_a: CL:0000005 ! neural crest derived fibroblast @@ -1922,6 +2140,8 @@ id: CL:0002485 name: retinal melanocyte def: "A melanocyte of the retina. This cell type is distinct from pigmented retinal epithelium." [GOC:tfm, MP:0010190] subset: eye_upper_slim +subset: human_subset +subset: mouse_subset is_a: CL:0000148 ! melanocyte is_a: CL:0009004 ! retinal cell intersection_of: CL:0000148 ! melanocyte @@ -1935,6 +2155,8 @@ id: CL:0002494 name: cardiocyte def: "A cell located in the heart, including both muscle and non muscle cells." [GOC:tfm] comment: From Onard of the FMA: Cardiac muscle cell or cardiac myocyte is a striated muscle cell. Cardiocyte on the other hand is any cell in the heart which includes cells other than muscle cells (e.g. endothelial cell of endocardium). Unless there is a consensus among anatomists that cardiocytes refer only to muscle cells, we will treat them as a general class of cells in the heart. +subset: human_subset +subset: mouse_subset synonym: "heart cell" EXACT [] xref: BTO:0001539 xref: CALOHA:TS-0115 @@ -1951,8 +2173,11 @@ creation_date: 2010-12-07T09:37:22Z id: CL:0002565 name: iris pigment epithelial cell def: "A pigment cell located in the epithelium of the iris." [GOC:tfm] +subset: cellxgene_subset subset: eye_upper_slim subset: human_reference_atlas +subset: human_subset +subset: mouse_subset is_a: CL:0000066 ! epithelial cell is_a: CL:0000342 {is_inferred="true"} ! pigment cell (sensu Vertebrata) intersection_of: CL:0000342 ! pigment cell (sensu Vertebrata) @@ -1969,6 +2194,8 @@ def: "A blood vessel endothelial cell that is part of the retina." [GOC:tfm] subset: cellxgene_subset subset: eye_upper_slim subset: human_reference_atlas +subset: human_subset +subset: mouse_subset xref: https://cellxgene.cziscience.com/cellguide/CL_0002585 is_a: CL:0000071 {is_inferred="true"} ! blood vessel endothelial cell is_a: CL:0009004 ! retinal cell @@ -1977,7 +2204,7 @@ intersection_of: part_of UBERON:0000966 ! retina relationship: part_of UBERON:0000966 ! retina property_value: RO:0002175 NCBITaxon:9606 property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 -property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional.\n\nRetinal blood vessel endothelial cells constitute the innermost lining of the blood vessels found in the retina, the light-sensitive layer of tissue at the back of the eye. The primary role of these cells revolves around their location within the retinal vascular system, forming the structure of the blood-retinal barrier, a subset of the larger blood-ocular barrier system. \nThe endothelial cells are particularly involved in the growth of new retinal blood vessels from pre-existing ones (angiogenesis); this is critical in managing the amount of oxygen and essential nutrients delivered to the ocular tissues. They are crucial for maintaining homeostasis in the retinal environment by controlling the exchange of molecules between the blood and the retina. Furthermore, they mediate immune cell trafficking, supporting the immune privilege of the eye by preventing the unrestricted infiltration of inflammatory cells into the retina, thus maintaining ocular health and normal vision.\nThe malfunction or dysfunction of retinal blood vessel endothelial cells is implicated in numerous ocular pathologies, particularly diabetic retinopathy, which is one of the leading causes of blindness worldwide. In such conditions, the compromise in the integrity of the blood-retinal barrier and excess angiogenesis can lead to retinal edema and pathological neovascularization, resulting in vision loss." xsd:string {xref="DOI:0.1016/j.preteyeres.2015.08.001", xref="DOI:10.1016/j.preteyeres.2012.08.004", xref="DOI:10.1038/nature04482", xref="DOI:10.5301/EJO.2010.6049"} +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nRetinal blood vessel endothelial cells constitute the innermost lining of the blood vessels found in the retina, the light-sensitive layer of tissue at the back of the eye. The primary role of these cells revolves around their location within the retinal vascular system, forming the structure of the blood-retinal barrier, a subset of the larger blood-ocular barrier system. \nThe endothelial cells are particularly involved in the growth of new retinal blood vessels from pre-existing ones (angiogenesis); this is critical in managing the amount of oxygen and essential nutrients delivered to the ocular tissues. They are crucial for maintaining homeostasis in the retinal environment by controlling the exchange of molecules between the blood and the retina. Furthermore, they mediate immune cell trafficking, supporting the immune privilege of the eye by preventing the unrestricted infiltration of inflammatory cells into the retina, thus maintaining ocular health and normal vision.\nThe malfunction or dysfunction of retinal blood vessel endothelial cells is implicated in numerous ocular pathologies, particularly diabetic retinopathy, which is one of the leading causes of blindness worldwide. In such conditions, the compromise in the integrity of the blood-retinal barrier and excess angiogenesis can lead to retinal edema and pathological neovascularization, resulting in vision loss." xsd:string {xref="DOI:0.1016/j.preteyeres.2015.08.001", xref="DOI:10.1016/j.preteyeres.2012.08.004", xref="DOI:10.1038/nature04482", xref="DOI:10.5301/EJO.2010.6049"} creation_date: 2011-03-06T03:28:27Z [Term] @@ -1987,6 +2214,8 @@ def: "An epithelial cell of the retinal pigmented epithelium." [GOC:tfm] subset: cellxgene_subset subset: eye_upper_slim subset: human_reference_atlas +subset: human_subset +subset: mouse_subset xref: BTO:0004910 xref: FMA:75802 xref: https://cellxgene.cziscience.com/cellguide/CL_0002586 @@ -1999,13 +2228,16 @@ relationship: has_part GO:0042470 ! melanosome relationship: part_of UBERON:0001782 ! pigmented layer of retina property_value: RO:0002175 NCBITaxon:9606 property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 -property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional.\n\nRetinal pigment epithelial (RPE) cells form a single layer of cells at the back of the eye sandwiched between the neurosensory retina and the choroid, playing a significant role in maintaining vision health. These pigment-laden cells are highly specialized and perform an array of metabolic and transport functions essential for the maintenance of the photoreceptor cells (rods and cones) in the retina. The pigmentation of RPE cells actively aids in the absorption of excess light and the prevention of light scattering, thus enhancing the eye's optical properties.\nThe retinal pigment epithelium forms a key part of the blood/retina barrier. The cells have long sheet-like microvilli on their apical membrane that project into the light-sensitive outer segments of the photoreceptors, forming a close structural interaction. The basolateral membrane of the RPE interacts with the underlying Bruch’s membrane, which separates the RPE cells from fenestrated endothelium of the choriocapillaris. \nRPE cells support the photoreceptor by providing them with oxygen and nutrients (such as glucose, retinol and fatty acids) and removing waste products. They also recycle the visual pigment, in a process called the \"visual cycle\", where the RPE cells play a vital role in the regeneration of visual pigment (11-cis retinol) following the absorption of light. This is essential for the maintenance of photoreceptor excitability.\nBeyond this, RPE cells take part in the phagocytosis process, where they digest the shed ends of photoreceptor outer segments, thus, preventing the build-up of waste residue that could otherwise harm retinal health. They also secrete various factors, including growth factors required to maintain the structural integrity of choriocapillaris endothelium and photoreceptors, as well as immunosuppressive factors that play an important role in establishing the immune privilege of the eye." xsd:string {xref="DOI:10.1111/febs.16018", xref="DOI:10.1152/physrev.00021.2004", xref="DOI:10.3389/fphar.2021.727870/full", xref="https://www.sciencedirect.com/topics/chemistry/retinal-pigment"} +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nRetinal pigment epithelial (RPE) cells form a single layer of cells at the back of the eye sandwiched between the neurosensory retina and the choroid, playing a significant role in maintaining vision health. These pigment-laden cells are highly specialized and perform an array of metabolic and transport functions essential for the maintenance of the photoreceptor cells (rods and cones) in the retina. The pigmentation of RPE cells actively aids in the absorption of excess light and the prevention of light scattering, thus enhancing the eye's optical properties.\nThe retinal pigment epithelium forms a key part of the blood/retina barrier. The cells have long sheet-like microvilli on their apical membrane that project into the light-sensitive outer segments of the photoreceptors, forming a close structural interaction. The basolateral membrane of the RPE interacts with the underlying Bruch’s membrane, which separates the RPE cells from fenestrated endothelium of the choriocapillaris. \nRPE cells support the photoreceptor by providing them with oxygen and nutrients (such as glucose, retinol and fatty acids) and removing waste products. They also recycle the visual pigment, in a process called the \"visual cycle\", where the RPE cells play a vital role in the regeneration of visual pigment (11-cis retinol) following the absorption of light. This is essential for the maintenance of photoreceptor excitability.\nBeyond this, RPE cells take part in the phagocytosis process, where they digest the shed ends of photoreceptor outer segments, thus, preventing the build-up of waste residue that could otherwise harm retinal health. They also secrete various factors, including growth factors required to maintain the structural integrity of choriocapillaris endothelium and photoreceptors, as well as immunosuppressive factors that play an important role in establishing the immune privilege of the eye." xsd:string {xref="DOI:10.1111/febs.16018", xref="DOI:10.1152/physrev.00021.2004", xref="DOI:10.3389/fphar.2021.727870/full", xref="https://www.sciencedirect.com/topics/chemistry/retinal-pigment"} creation_date: 2011-03-06T03:37:09Z [Term] id: CL:0002672 name: retinal progenitor cell def: "A multi-fate stem cell that can give rise to different retinal cell types including rod and cone cells." [GOC:tfm, PMID:20959166, PMID:21148186] +subset: cellxgene_subset +subset: human_subset +subset: mouse_subset is_a: CL:0000048 ! multi fate stem cell relationship: RO:0002202 CL:0000133 ! develops from neurectodermal cell property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 @@ -2016,8 +2248,10 @@ id: CL:0005000 name: spinal cord interneuron def: "A CNS interneuron located in the spinal cord." [CL:CVS] comment: Is_a interneuron, part_of UBERON:0002240. +subset: human_subset +subset: mouse_subset xref: ZFA:0000778 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} -is_a: CL:0000402 {is_inferred="true"} ! CNS interneuron +is_a: CL:0000099 {is_inferred="true"} ! interneuron intersection_of: CL:0000099 ! interneuron intersection_of: RO:0002100 UBERON:0002240 ! has soma location spinal cord relationship: RO:0002100 UBERON:0002240 ! has soma location spinal cord @@ -2026,6 +2260,8 @@ relationship: RO:0002100 UBERON:0002240 ! has soma location spinal cord id: CL:0007004 name: premigratory neural crest cell def: "Cell that is part of the neural crest region of the neuroepithelium, prior to migration. Note that not all premigratory neural crest cells may become migratory neural crest cells." [UBERONREF:0000002] +subset: human_subset +subset: mouse_subset xref: ZFA:0007084 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0011012 ! neural crest cell relationship: part_of UBERON:0002342 ! neural crest @@ -2037,6 +2273,8 @@ creation_date: 2012-06-27T08:27:35Z id: CL:0008000 name: non-striated muscle cell def: "Any muscle cell in which the fibers are not organised into sarcomeres." [GOC:DOS] +subset: human_subset +subset: mouse_subset is_a: CL:0000187 ! muscle cell [Term] @@ -2044,12 +2282,16 @@ id: CL:0008001 name: hematopoietic precursor cell def: "Any hematopoietic cell that is a precursor of some other hematopoietic cell type." [GOC:dos] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset is_a: CL:0000988 ! hematopoietic cell [Term] id: CL:0008007 name: visceral muscle cell def: "A muscle cell that is part of some visceral muscle." [GOC:dos] +subset: human_subset +subset: mouse_subset xref: FBbt:00005070 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} is_a: CL:0000187 ! muscle cell intersection_of: CL:0000187 ! muscle cell @@ -2062,6 +2304,8 @@ name: mesenchymal cell def: "A non-polarised cell precursor cell that is part of some mesenchyme, is associated with the cell matrix but is not connected to other cells and is capable of migration." [] subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "mesenchyme cell" EXACT [] is_a: CL:0000219 ! motile cell is_a: CL:0000255 ! eukaryotic cell @@ -2073,6 +2317,8 @@ property_value: RO:0002175 NCBITaxon:9606 id: CL:0008028 name: visual system neuron def: "Any neuron that is capable of part of some visual perception." [FBC:Autogenerated] +subset: human_subset +subset: mouse_subset is_a: CL:0000540 ! neuron intersection_of: CL:0000540 ! neuron intersection_of: capable_of_part_of GO:0007601 ! visual perception @@ -2085,6 +2331,8 @@ id: CL:0009004 name: retinal cell def: "Any cell in the retina, the innermost layer or coating at the back of the eyeball, which is sensitive to light and in which the optic nerve terminates." [GOC:pr] subset: general_cell_types_upper_slim +subset: human_subset +subset: mouse_subset xref: PMID:10702418 is_a: CL:0002319 ! neural cell intersection_of: CL:0002319 ! neural cell @@ -2095,6 +2343,8 @@ relationship: part_of UBERON:0005388 ! photoreceptor array id: CL:0010009 name: camera-type eye photoreceptor cell def: "Any photoreceptor cell that is part of some camera-type eye." [FBC:Autogenerated] +subset: human_subset +subset: mouse_subset synonym: "camera type eye photoreceptor cell" EXACT [] is_a: CL:0000287 ! eye photoreceptor cell is_a: CL:0009004 ! retinal cell @@ -2106,6 +2356,8 @@ relationship: part_of UBERON:0000966 {seeAlso="https://github.com/obophenotype/c id: CL:0010017 name: zygote def: "A zygote in a plant or an animal." [] +subset: human_subset +subset: mouse_subset xref: MESH:D015053 is_a: CL:0000000 ! cell property_value: seeAlso https://github.com/obophenotype/cell-ontology/issues/786 @@ -2115,16 +2367,20 @@ id: CL:0011012 name: neural crest cell def: "A cell of the neural crest. Neural crest cells are multipotent. Premigratory neural crest cells are found at the neural plate boarder, some of which will undergo ectomesynchymal transition and delamination to form migratory neural crest cells." [https://orcid.org/0000-0001-5208-3432, https://orcid.org/0000-0002-9900-7880] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset xref: https://cellxgene.cziscience.com/cellguide/CL_0011012 is_a: CL:0000048 ! multi fate stem cell is_a: CL:0002321 ! embryonic cell (metazoa) -property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional.\n\nNeural crest cells are a group of transient and highly migratory cells that originate from the neuroectoderm during the early stages of embryonic development. They are multipotent cells with an exceptional degree of plasticity, capable of differentiating into various somatic cell types and therefore play a fundamental role in the formation of various organs and tissues, making them critical contributors to the developing embryo. \nAfter the initiation of neurulation (the formation of the neural tube) neural crest cells start to undergo epithelial-to-mesenchymal transition and delaminate and migrate from the dorsal neural tube to several regions throughout the embryo. They differentiate into a range of diverse cell types, such as neurons and glial cells of the peripheral nervous system, including sensory and autonomic neurons. They also contribute to the formation of adrenal glands, pigment cells in the skin (melanocytes), cardiac structures, including parts of the heart septum and major arteries, as well as bones and cartilage of the face and skull.\nDisorders or aberrations in the development or migration of the neural crest cells can lead to serious congenital malformations, such as neurocristopathies, including Hirschsprung disease, neuroblastoma, and neurofibromatosis." xsd:string {xref="DOI:10.1002/dvg.23276", xref="DOI:10.1242/dev.193193", xref="DOI:10.3389/fcell.2020.00635/full", xref="https://doi.org/10.1016/j.ydbio.2011.12.042"} +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nNeural crest cells are a group of transient and highly migratory cells that originate from the neuroectoderm during the early stages of embryonic development. They are multipotent cells with an exceptional degree of plasticity, capable of differentiating into various somatic cell types and therefore play a fundamental role in the formation of various organs and tissues, making them critical contributors to the developing embryo. \nAfter the initiation of neurulation (the formation of the neural tube) neural crest cells start to undergo epithelial-to-mesenchymal transition and delaminate and migrate from the dorsal neural tube to several regions throughout the embryo. They differentiate into a range of diverse cell types, such as neurons and glial cells of the peripheral nervous system, including sensory and autonomic neurons. They also contribute to the formation of adrenal glands, pigment cells in the skin (melanocytes), cardiac structures, including parts of the heart septum and major arteries, as well as bones and cartilage of the face and skull.\nDisorders or aberrations in the development or migration of the neural crest cells can lead to serious congenital malformations, such as neurocristopathies, including Hirschsprung disease, neuroblastoma, and neurofibromatosis." xsd:string {xref="DOI:10.1002/dvg.23276", xref="DOI:10.1242/dev.193193", xref="DOI:10.3389/fcell.2020.00635/full", xref="https://doi.org/10.1016/j.ydbio.2011.12.042"} [Term] id: CL:0011026 name: progenitor cell def: "A precursor cell that has a tendency to differentiate into a specific type of cell. They are descendants of stem cells, only they are more constrained in their differentiation potential or capacity for self-renewal, and are often more limited in both senses." [https://doi.org/10.1016/B978-0-12-409503-8.00002-0, ISBN:978-1-62808-994-3] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset is_a: CL:0000255 ! eukaryotic cell is_a: CL:0011115 ! precursor cell intersection_of: CL:0011115 ! precursor cell @@ -2138,6 +2394,8 @@ name: interplexiform cell def: "A type of interneuron in the retinal inner nuclear layer which\ncarries information from the inner plexiform layer and the outer\nplexiform layer." [GOC:NV, PMID:12771169] comment: Need to MIREOT retinal inner nuclear layer (part of) subset: eye_upper_slim +subset: human_subset +subset: mouse_subset is_a: CL:0000099 ! interneuron is_a: CL:0009004 ! retinal cell relationship: part_of UBERON:0001791 ! inner nuclear layer of retina @@ -2148,6 +2406,8 @@ name: precursor cell def: "A cell that, by division or terminal differentiation, can give rise to other cell types." [GOC:dos] comment: Work is needed on GO 'cell differentiation' before it is clear whether the equivalent class definition 'native cell' that capable_of some 'cell differentiation' works. Also, may want to consider merging this with non-terminally differentiated cell. subset: cellxgene_subset +subset: human_subset +subset: mouse_subset is_a: CL:0000000 ! cell intersection_of: CL:0000000 ! cell intersection_of: capable_of GO:0030154 ! cell differentiation @@ -2193,6 +2453,8 @@ name: conjunctival epithelial cell def: "An epithelial cell that is part of the conjunctiva." [GOC:tfm] subset: cellxgene_subset subset: eye_upper_slim +subset: human_subset +subset: mouse_subset synonym: "epithelial cell of conjunctiva" EXACT [FMA:70552] xref: FMA:70552 is_a: CL:0000066 {is_inferred="true"} ! epithelial cell @@ -2206,17 +2468,23 @@ name: ciliary muscle cell def: "A smooth muscle cell that is part of the ciliary body." [GOC:tfm] subset: cellxgene_subset subset: eye_upper_slim +subset: human_subset +subset: mouse_subset synonym: "smooth muscle cell of ciliary body" EXACT [FMA:70610] xref: FMA:70610 +xref: https://cellxgene.cziscience.com/cellguide/CL_1000443 is_a: CL:0000192 {is_inferred="true"} ! smooth muscle cell intersection_of: CL:0000192 ! smooth muscle cell intersection_of: part_of UBERON:0001775 ! ciliary body relationship: part_of UBERON:0001775 ! ciliary body +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nCiliary muscle cells are specialized contractile cells that constitute the ciliary muscle, a component of the eye in vertebrates. These cells form a ring around the iris, the eye's colored part. Ciliary muscle cells fall into the category of smooth muscle cells, characterized by their lack of the striations typical of skeletal and cardiac muscle cells. Their shape is elongated and pointed at both ends, and they occur in multi-nucleated syncytia where many cells share the same cytoplasm.\nCiliary muscle cells primarily control the eye's accommodation, adjusting the thickness and curvature of the lens to fine-tune the focus of light on the retina. When ciliary muscle cells contract, tension on the zonular fibers holding the lens in place is reduced, allowing the lens to become thicker and increase its refractive power. Conversely, when the ciliary muscle cells relax, the tension on the zonular fibers increases, causing the lens to become flatter and decrease its refractive power. This adjustment facilitates clear vision at different distances, ranging from near to far objects.\nAdditionally, ciliary muscle cells play a role in draining the eye's aqueous humor, which is the clear fluid that fills the anterior chamber of the eye between the cornea and the lens. By controlling the shape of the surrounding trabecular meshwork through muscle contractions and relaxations, ciliary muscle cells indirectly regulate intraocular pressure, a factor critical for preventing ocular conditions like glaucoma." xsd:string {xref="DOI:10.1016/S1350-9462(98)00011-1", xref="DOI:10.1038/srep31171", xref="DOI:10.1111/j.1444-0938.2008.00260.x", xref="https://www.sciencedirect.com/topics/medicine-and-dentistry/ciliary-muscle"} [Term] id: CL:2000029 name: central nervous system neuron def: "Any neuron that is part of a central nervous system." [GOC:TermGenie] +subset: human_subset +subset: mouse_subset is_a: CL:0000540 ! neuron intersection_of: CL:0000540 ! neuron intersection_of: RO:0002100 UBERON:0001017 ! has soma location central nervous system @@ -2229,6 +2497,8 @@ id: CL:4023129 name: retinoblast def: "A retinal cell that is immature or undifferentiated." [PMID:17565741] subset: eye_upper_slim +subset: human_subset +subset: mouse_subset synonym: "retinal stem cell" EXACT [PMID:17565741] is_a: CL:0009004 ! retinal cell relationship: part_of UBERON:0000966 ! retina @@ -2240,7 +2510,10 @@ id: CL:4033015 name: retinal astrocyte def: "A star-shaped glial cell that is part of some retina. This cell links neurons to blood vessels and may provide structural and physiological support to optic nerve head axons." [PMID:25236977, PMID:33796062] comment: In response to elevated intraocular pressure, a retinal astrocyte may modulate extracellular matrix remodeling. In the human retina, a retinal astrocyte is GFAP-positive, SOD3-positive and GYPC-positive. {xref="PMID:33796062", xref="PMID:32555229"} +subset: cellxgene_subset subset: eye_upper_slim +subset: human_subset +subset: mouse_subset synonym: "retinal astroglia" RELATED OMO:0003004 [PMID:33796062] is_a: CL:0000127 ! astrocyte is_a: CL:0009004 ! retinal cell @@ -2254,7 +2527,6 @@ property_value: terms:date "2023-03-02T14:38:32Z" xsd:dateTime id: GO:0000278 name: mitotic cell cycle namespace: biological_process -alt_id: GO:0007067 def: "Progression through the phases of the mitotic cell cycle, the most common eukaryotic cell cycle, which canonically comprises four successive phases called G1, S, G2, and M and includes replication of the genome and the subsequent segregation of chromosomes into daughter cells. In some variant cell cycles nuclear replication or nuclear division may not be followed by cell division, or G1 and G2 phases may be absent." [GOC:mah, ISBN:0815316194] comment: Note that this term should not be confused with 'GO:0140014 ; mitotic nuclear division'. 'GO:0000278 ; mitotic cell cycle represents the entire mitotic cell cycle, while 'GO:0140014 ; mitotic nuclear division' specifically represents the actual nuclear division step of the mitotic cell cycle. subset: goslim_chembl @@ -2286,16 +2558,13 @@ relationship: results_in_fission_of GO:0005634 ! nucleus id: GO:0000785 name: chromatin namespace: cellular_component -alt_id: GO:0000789 -alt_id: GO:0000790 -alt_id: GO:0005717 def: "The ordered and organized complex of DNA, protein, and sometimes RNA, that forms the chromosome." [GOC:elh, PMID:20404130] comment: Chromosomes include parts that are not part of the chromatin. Examples include the kinetochore. synonym: "chromosome scaffold" RELATED [] synonym: "cytoplasmic chromatin" NARROW [] synonym: "nuclear chromatin" NARROW [] xref: NIF_Subcellular:sao1615953555 -is_a: GO:0110165 ! cellular anatomical entity +is_a: GO:0110165 ! cellular anatomical structure relationship: part_of GO:0005694 ! chromosome property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28301" xsd:anyURI @@ -2303,8 +2572,6 @@ property_value: term_tracker_item "https://github.com/geneontology/go-ontology/i id: GO:0000792 name: heterochromatin namespace: cellular_component -alt_id: GO:0005720 -alt_id: GO:0035328 def: "A compact and highly condensed form of chromatin that is refractory to transcription." [PMID:32017156] synonym: "nuclear heterochromatin" NARROW [] synonym: "transcriptionally inactive chromatin" EXACT [] @@ -2401,7 +2668,6 @@ relationship: part_of GO:0016331 ! morphogenesis of embryonic epithelium id: GO:0001841 name: neural tube formation namespace: biological_process -alt_id: GO:0001679 def: "The formation of a tube from the flat layer of ectodermal cells known as the neural plate. This will give rise to the central nervous system." [GOC:dph, ISBN:0878932437] synonym: "neural tube morphogenesis" EXACT [GOC:dph] synonym: "neurulation" EXACT [] @@ -2515,7 +2781,6 @@ is_a: GO:0003013 ! circulatory system process id: GO:0005575 name: cellular_component namespace: cellular_component -alt_id: GO:0008372 def: "A location, relative to cellular compartments and structures, occupied by a macromolecular machine. There are three types of cellular components described in the gene ontology: (1) the cellular anatomical entity where a gene product carries out a molecular function (e.g., plasma membrane, cytoskeleton) or membrane-enclosed compartments (e.g., mitochondrion); (2) virion components, where viral proteins act, and (3) the stable macromolecular complexes of which gene product are parts (e.g., the clathrin complex)." [GOC:pdt] comment: Note that, in addition to forming the root of the cellular component ontology, this term is recommended for the annotation of gene products whose cellular component is unknown. When this term is used for annotation, it indicates that no information was available about the cellular component of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this. subset: goslim_candida @@ -2553,7 +2818,7 @@ subset: goslim_prokaryote_ribbon subset: goslim_yeast synonym: "extracellular" EXACT [] xref: Wikipedia:Extracellular -is_a: GO:0110165 ! cellular anatomical entity +is_a: GO:0110165 ! cellular anatomical structure [Term] id: GO:0005577 @@ -2590,8 +2855,6 @@ is_a: GO:0098651 ! basement membrane collagen trimer id: GO:0005604 name: basement membrane namespace: cellular_component -alt_id: GO:0005605 -alt_id: GO:0008003 def: "A collagen-containing extracellular matrix consisting of a thin layer of dense material found in various animal tissues interposed between the cells and the adjacent connective tissue. It consists of the basal lamina plus an associated layer of reticulin fibers." [ISBN:0198547684, PMID:22505934] comment: Note that this term has no relationship to 'membrane ; GO:0016020' because the basement membrane is not a lipid bilayer. synonym: "basal lamina" RELATED [] @@ -2611,7 +2874,7 @@ subset: goslim_drosophila subset: goslim_generic synonym: "intercellular space" RELATED [] xref: NIF_Subcellular:sao1425028079 -is_a: GO:0110165 ! cellular anatomical entity +is_a: GO:0110165 ! cellular anatomical structure relationship: part_of GO:0005576 ! extracellular region [Term] @@ -2629,7 +2892,7 @@ synonym: "nucleocytoplasm" RELATED [GOC:mah] synonym: "protoplasm" EXACT [] synonym: "protoplast" RELATED [GOC:mah] xref: Wikipedia:Intracellular -is_a: GO:0110165 ! cellular anatomical entity +is_a: GO:0110165 ! cellular anatomical structure relationship: part_of CL:0000000 ! cell property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/17776" xsd:anyURI @@ -2681,7 +2944,7 @@ synonym: "chromatid" RELATED [] synonym: "interphase chromosome" NARROW [] synonym: "prophase chromosome" NARROW [] xref: Wikipedia:Chromosome -is_a: GO:0043232 ! intracellular non-membrane-bounded organelle +is_a: GO:0043232 ! intracellular membraneless organelle [Term] id: GO:0005730 @@ -2697,7 +2960,7 @@ subset: goslim_plant subset: goslim_yeast xref: NIF_Subcellular:sao1820400233 xref: Wikipedia:Nucleolus -is_a: GO:0043232 ! intracellular non-membrane-bounded organelle +is_a: GO:0043232 ! intracellular membraneless organelle relationship: part_of GO:0031981 ! nuclear lumen [Term] @@ -2715,7 +2978,7 @@ subset: goslim_prokaryote subset: goslim_prokaryote_ribbon subset: goslim_yeast xref: Wikipedia:Cytoplasm -is_a: GO:0110165 ! cellular anatomical entity +is_a: GO:0110165 ! cellular anatomical structure relationship: part_of GO:0005622 ! intracellular anatomical structure property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/23023" xsd:anyURI @@ -2723,7 +2986,6 @@ property_value: term_tracker_item "https://github.com/geneontology/go-ontology/i id: GO:0005840 name: ribosome namespace: cellular_component -alt_id: GO:0033279 def: "An intracellular organelle, about 200 A in diameter, consisting of RNA and protein. It is the site of protein biosynthesis resulting from translation of messenger RNA (mRNA). It consists of two subunits, one large and one small, each containing only protein and RNA. Both the ribosome and its subunits are characterized by their sedimentation coefficients, expressed in Svedberg units (symbol: S). Hence, the prokaryotic ribosome (70S) comprises a large (50S) subunit and a small (30S) subunit, while the eukaryotic ribosome (80S) comprises a large (60S) subunit and a small (40S) subunit. Two sites on the ribosomal large subunit are involved in translation, namely the aminoacyl site (A site) and peptidyl site (P site). Ribosomes from prokaryotes, eukaryotes, mitochondria, and chloroplasts have characteristically distinct ribosomal proteins." [ISBN:0198506732] subset: goslim_candida subset: goslim_chembl @@ -2741,16 +3003,14 @@ synonym: "membrane bound ribosome" NARROW [NIF_Subcellular:sao1291545653] synonym: "ribosomal RNA" RELATED [] xref: NIF_Subcellular:sao1429207766 xref: Wikipedia:Ribosome -is_a: GO:0043232 ! intracellular non-membrane-bounded organelle -is_a: PR:000050567 ! protein-containing material entity +is_a: GO:0043232 ! intracellular membraneless organelle relationship: capable_of_part_of GO:0006412 ! translation +relationship: has_part PR:000000001 ! protein [Term] id: GO:0005886 name: plasma membrane namespace: cellular_component -alt_id: GO:0005887 -alt_id: GO:0005904 def: "The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins." [ISBN:0716731363] subset: goslim_agr subset: goslim_candida @@ -2796,9 +3056,6 @@ property_value: term_tracker_item "https://github.com/geneontology/go-ontology/i id: GO:0006412 name: translation namespace: biological_process -alt_id: GO:0006416 -alt_id: GO:0006453 -alt_id: GO:0043037 def: "The cellular metabolic process in which a protein is formed, using the sequence of a mature mRNA or circRNA molecule to specify the sequence of amino acids in a polypeptide chain. Translation is mediated by the ribosome, and begins with the formation of a ternary complex between aminoacylated initiator methionine tRNA, GTP, and initiation factor 2, which subsequently associates with the small subunit of the ribosome and an mRNA or circRNA. Translation ends with the release of a polypeptide chain from the ribosome." [GOC:go_curators] subset: goslim_candida subset: goslim_chembl @@ -2827,15 +3084,13 @@ relationship: starts_with GO:0006413 ! translational initiation id: GO:0006413 name: translational initiation namespace: biological_process -alt_id: GO:0006440 -alt_id: GO:0006454 def: "The process preceding formation of the peptide bond between the first two amino acids of a protein. This includes the formation of a complex of the ribosome, mRNA or circRNA, and an initiation complex that contains the first aminoacyl-tRNA." [ISBN:019879276X] subset: goslim_yeast synonym: "biopolymerisation" BROAD [] synonym: "biopolymerization" BROAD [] synonym: "protein synthesis initiation" BROAD [] synonym: "translation initiation" EXACT [] -is_a: GO:0044237 ! cellular metabolic process +is_a: GO:0008152 ! metabolic process relationship: part_of GO:0006412 ! translation relationship: starts_with GO:0001677 ! formation of translation initiation ternary complex @@ -2843,8 +3098,6 @@ relationship: starts_with GO:0001677 ! formation of translation initiation terna id: GO:0006414 name: translational elongation namespace: biological_process -alt_id: GO:0006442 -alt_id: GO:0006455 def: "The successive addition of amino acid residues to a nascent polypeptide chain during protein biosynthesis." [GOC:ems] subset: goslim_yeast synonym: "protein synthesis elongation" BROAD [] @@ -2856,8 +3109,6 @@ relationship: part_of GO:0006412 ! translation id: GO:0006415 name: translational termination namespace: biological_process -alt_id: GO:0006443 -alt_id: GO:0006456 def: "The process resulting in the release of a polypeptide chain from the ribosome, usually in response to a termination codon (UAA, UAG, or UGA in the universal genetic code)." [GOC:hjd, ISBN:019879276X] synonym: "protein synthesis termination" BROAD [] synonym: "translation termination" EXACT [] @@ -2869,9 +3120,6 @@ relationship: part_of GO:0006412 ! translation id: GO:0006810 name: transport namespace: biological_process -alt_id: GO:0015457 -alt_id: GO:0015460 -alt_id: GO:0044765 def: "The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter or a transporter complex, a pore or a motor protein." [GOC:dos, GOC:dph, GOC:jl, GOC:mah] comment: Note that this term should not be used for direct annotation. It should be possible to make a more specific annotation to one of the children of this term, for e.g. to transmembrane transport, to microtubule-based transport or to vesicle-mediated transport. subset: gocheck_do_not_annotate @@ -2886,7 +3134,6 @@ subset: goslim_prokaryote_ribbon synonym: "single-organism transport" RELATED [] is_a: GO:0051234 ! establishment of localization property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/20292" xsd:anyURI -created_by: jl creation_date: 2012-12-13T16:25:32Z [Term] @@ -2915,7 +3162,6 @@ relationship: RO:0002162 NCBITaxon:33208 {all_only="true"} ! in taxon Metazoa id: GO:0006865 name: amino acid transport namespace: biological_process -alt_id: GO:0006866 def: "The directed movement of amino acids, organic acids containing one or more amino substituents, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:ai] subset: goslim_pir subset: goslim_yeast @@ -2925,8 +3171,6 @@ is_a: GO:0006810 ! transport id: GO:0006915 name: apoptotic process namespace: biological_process -alt_id: GO:0006917 -alt_id: GO:0008632 def: "A programmed cell death process which begins when a cell receives an internal (e.g. DNA damage) or external signal (e.g. an extracellular death ligand), and proceeds through a series of biochemical events (signaling pathway phase) which trigger an execution phase. The execution phase is the last step of an apoptotic process, and is typically characterized by rounding-up of the cell, retraction of pseudopodes, reduction of cellular volume (pyknosis), chromatin condensation, nuclear fragmentation (karyorrhexis), plasma membrane blebbing and fragmentation of the cell into apoptotic bodies. When the execution phase is completed, the cell has died." [GOC:cjm, GOC:dhl, GOC:ecd, GOC:go_curators, GOC:mtg_apoptosis, GOC:tb, ISBN:0198506732, PMID:18846107, PMID:21494263] synonym: "activation of apoptosis" NARROW [] synonym: "apoptosis" NARROW [] @@ -2980,7 +3224,6 @@ relationship: occurs_in UBERON:0002385 ! muscle tissue id: GO:0006996 name: organelle organization namespace: biological_process -alt_id: GO:1902589 def: "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of an organelle within a cell. An organelle is an organized structure of distinctive morphology and function. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton. Excludes the plasma membrane." [GOC:mah] comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. subset: gocheck_do_not_annotate @@ -2995,7 +3238,6 @@ intersection_of: GO:0016043 ! cellular component organization intersection_of: results_in_organization_of GO:0043226 ! organelle relationship: results_in_organization_of GO:0043226 ! organelle property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27189" xsd:anyURI -created_by: jl creation_date: 2013-12-19T15:25:51Z [Term] @@ -3039,11 +3281,6 @@ is_a: GO:0009987 ! cellular process id: GO:0007165 name: signal transduction namespace: biological_process -alt_id: GO:0023014 -alt_id: GO:0023015 -alt_id: GO:0023016 -alt_id: GO:0023033 -alt_id: GO:0023045 def: "The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell." [GOC:go_curators, GOC:mtg_signaling_feb11] comment: Note that signal transduction is defined broadly to include a ligand interacting with a receptor, downstream signaling steps and a response being triggered. A change in form of the signal in every step is not necessary. Note that in many cases the end of this process is regulation of the initiation of transcription. Note that specific transcription factors may be annotated to this term, but core/general transcription machinery such as RNA polymerase should not. subset: goslim_candida @@ -3101,7 +3338,6 @@ relationship: has_participant GO:0045202 ! synapse id: GO:0007269 name: neurotransmitter secretion namespace: biological_process -alt_id: GO:0010554 def: "The regulated release of neurotransmitter from the presynapse into the synaptic cleft via calcium-regulated exocytosis during synaptic transmission." [GOC:dph] comment: A neurotransmitter is any of a group of substances that are released on excitation from the axon terminal of a presynaptic neuron of the central or peripheral nervous system and travel across the synaptic cleft to either excite or inhibit the target cell. Among the many substances that have the properties of a neurotransmitter are acetylcholine, noradrenaline, adrenaline, dopamine, glycine, gamma-aminobutyrate, glutamic acid, substance P, enkephalins, endorphins and serotonin. subset: goslim_synapse @@ -3227,7 +3463,6 @@ is_a: GO:0050953 ! sensory perception of light stimulus id: GO:0008015 name: blood circulation namespace: biological_process -alt_id: GO:0070261 def: "The flow of blood through the body of an animal, enabling the transport of nutrients to the tissues and the removal of waste products." [GOC:mtg_heart, ISBN:0192800825] subset: goslim_pir synonym: "hemolymph circulation" RELATED [] @@ -3248,9 +3483,6 @@ relationship: regulates GO:0060047 ! heart contraction id: GO:0008150 name: biological_process namespace: biological_process -alt_id: GO:0000004 -alt_id: GO:0007582 -alt_id: GO:0044699 def: "A biological process is the execution of a genetically-encoded biological module or program. It consists of all the steps required to achieve the specific biological objective of the module. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence." [GOC:pdt] comment: Note that, in addition to forming the root of the biological process ontology, this term is recommended for the annotation of gene products whose biological process is unknown. When this term is used for annotation, it indicates that no information was available about the biological process of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this. subset: goslim_candida @@ -3266,16 +3498,13 @@ synonym: "single organism process" RELATED [] synonym: "single-organism process" RELATED [] xref: Wikipedia:Biological_process property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/24968" xsd:anyURI -created_by: jl creation_date: 2012-09-19T15:05:24Z [Term] id: GO:0008152 name: metabolic process namespace: biological_process -alt_id: GO:0044236 -alt_id: GO:0044710 -def: "The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation." [GOC:go_curators, ISBN:0198547684] +def: "A cellular process consisting of the biochemical pathways by which a living organism transforms chemical substances. This includes including anabolism (biosynthetic process) and catabolism (catabolic process). Metabolic processes includes the transformation of small molecules, as well macromolecular processes such as DNA repair and replication, protein synthesis and degradation." [GOC:go_curators, ISBN:0198547684] comment: Note that metabolic processes do not include single functions or processes such as protein-protein interactions, protein-nucleic acids, nor receptor-ligand interactions. subset: gocheck_do_not_annotate subset: goslim_chembl @@ -3284,16 +3513,12 @@ subset: goslim_metagenomics subset: goslim_pir subset: goslim_plant subset: goslim_prokaryote_ribbon -synonym: "metabolic process resulting in cell growth" NARROW [] synonym: "metabolism" EXACT [] -synonym: "metabolism resulting in cell growth" NARROW [] -synonym: "multicellular organism metabolic process" NARROW [] -synonym: "single-organism metabolic process" RELATED [] xref: Wikipedia:Metabolism -is_a: GO:0008150 ! biological_process +is_a: GO:0009987 ! cellular process disjoint_from: GO:0051179 ! localization property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/26424" xsd:anyURI -created_by: jl +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28932" xsd:anyURI creation_date: 2012-10-17T15:46:40Z [Term] @@ -3312,9 +3537,7 @@ property_value: term_tracker_item "https://github.com/geneontology/go-ontology/i id: GO:0009058 name: biosynthetic process namespace: biological_process -alt_id: GO:0044274 -alt_id: GO:0044711 -def: "The chemical reactions and pathways resulting in the formation of substances; typically the energy-requiring part of metabolism in which simpler substances are transformed into more complex ones." [GOC:curators, ISBN:0198547684] +def: "A cellular process consisting of the biochemical pathways by which a living organism synthesizes chemical substances. This typically represents the energy-requiring part of metabolism in which simpler substances are transformed into more complex ones." [GOC:curators, ISBN:0198547684] subset: goslim_chembl subset: goslim_metagenomics subset: goslim_plant @@ -3327,14 +3550,13 @@ synonym: "single-organism biosynthetic process" RELATED [] synonym: "synthesis" EXACT [] xref: Wikipedia:Anabolism is_a: GO:0008152 ! metabolic process -created_by: jl +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28932" xsd:anyURI creation_date: 2012-10-17T15:52:18Z [Term] id: GO:0009059 name: macromolecule biosynthetic process namespace: biological_process -alt_id: GO:0043284 def: "The chemical reactions and pathways resulting in the formation of a macromolecule, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass." [GOC:mah] comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. subset: gocheck_do_not_annotate @@ -3344,8 +3566,8 @@ synonym: "macromolecule anabolism" EXACT [] synonym: "macromolecule biosynthesis" EXACT [] synonym: "macromolecule formation" EXACT [] synonym: "macromolecule synthesis" EXACT [] +is_a: GO:0009058 ! biosynthetic process is_a: GO:0043170 ! macromolecule metabolic process -is_a: GO:0044249 ! cellular biosynthetic process property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/15249" xsd:anyURI property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/25418" xsd:anyURI property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27189" xsd:anyURI @@ -3447,7 +3669,6 @@ relationship: part_of GO:0048856 ! anatomical structure development id: GO:0009790 name: embryo development namespace: biological_process -alt_id: GO:0009795 def: "The process whose specific outcome is the progression of an embryo from its formation until the end of its embryonic life stage. The end of the embryonic stage is organism-specific. For example, for mammals, the process would begin with zygote formation and end with birth. For insects, the process would begin at zygote formation and end with larval hatching. For plant zygotic embryos, this would be from zygote formation to the end of seed dormancy. For plant vegetative embryos, this would be from the initial determination of the cell or group of cells to form an embryo until the point when the embryo becomes independent of the parent plant." [GOC:go_curators, GOC:isa_complete, GOC:mtg_sensu] subset: gocheck_do_not_annotate subset: goslim_chembl @@ -3504,9 +3725,6 @@ property_value: RO:0002161 NCBITaxon:4891 id: GO:0009987 name: cellular process namespace: biological_process -alt_id: GO:0008151 -alt_id: GO:0044763 -alt_id: GO:0050875 def: "Any process that is carried out at the cellular level, but not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level." [GOC:go_curators, GOC:isa_complete] comment: This term should not be used for direct annotation. It should be possible to make a more specific annotation to one of the children of this term. subset: gocheck_do_not_annotate @@ -3516,7 +3734,6 @@ synonym: "cell physiology" EXACT [] synonym: "cellular physiological process" EXACT [] synonym: "single-organism cellular process" RELATED [] is_a: GO:0008150 ! biological_process -created_by: jl creation_date: 2012-12-11T16:56:55Z [Term] @@ -3534,7 +3751,6 @@ property_value: term_tracker_item "https://github.com/geneontology/go-ontology/i id: GO:0012501 name: programmed cell death namespace: biological_process -alt_id: GO:0016244 def: "A process which begins when a cell receives an internal or external signal and activates a series of biochemical events (signaling pathway). The process ends with the death of the cell." [GOC:lr, GOC:mtg_apoptosis] comment: Note that this term should be used to annotate gene products in the organism undergoing the programmed cell death. To annotate genes in another organism whose products modulate programmed cell death in a host organism, consider the term 'modulation by symbiont of host programmed cell death ; GO:0052040'. Also, note that 'programmed cell death ; GO:0012501' should be used to refer to instances of caspase-independent cell death mechanisms, in the absence of further indications on the process taking place. At present, caspase-independent cell death is not yet represented in GO due to the lack of consensus and in-depth research on the topic. 'programmed cell death ; GO:0012501' may also be used to annotate gene products in taxa where apoptosis as defined in GO:0006915 does not occur, such as plants. You may also consider these specific children: GO:0097468 'programmed cell death in response to reactive oxygen species' (with descendants GO:0010421 'hydrogen peroxide-mediated programmed cell death' and GO:0010343 'singlet oxygen-mediated programmed cell death'), and GO:0009626 'plant-type hypersensitive response' and its children. subset: goslim_agr @@ -3594,9 +3810,6 @@ is_a: GO:0006865 ! amino acid transport id: GO:0016020 name: membrane namespace: cellular_component -alt_id: GO:0016021 -alt_id: GO:0098589 -alt_id: GO:0098805 def: "A lipid bilayer along with all the proteins and protein complexes embedded in it and attached to it." [GOC:dos, GOC:mah, ISBN:0815316194] subset: goslim_candida subset: goslim_chembl @@ -3613,7 +3826,7 @@ synonym: "transmembrane" RELATED [GOC:mah] synonym: "whole membrane" NARROW [] xref: Wikipedia:Biological_membrane xref: Wikipedia:Transmembrane_protein -is_a: GO:0110165 ! cellular anatomical entity +is_a: GO:0110165 ! cellular anatomical structure disjoint_from: GO:0031012 ! extracellular matrix creation_date: 2014-03-06T11:37:54Z @@ -3621,8 +3834,6 @@ creation_date: 2014-03-06T11:37:54Z id: GO:0016043 name: cellular component organization namespace: biological_process -alt_id: GO:0044235 -alt_id: GO:0071842 def: "A process that results in the assembly, arrangement of constituent parts, or disassembly of a cellular component." [GOC:ai, GOC:jl, GOC:mah] subset: gocheck_do_not_annotate subset: goslim_agr @@ -3703,9 +3914,6 @@ relationship: part_of GO:0007154 ! cell communication id: GO:0019538 name: protein metabolic process namespace: biological_process -alt_id: GO:0006411 -alt_id: GO:0044267 -alt_id: GO:0044268 def: "The chemical reactions and pathways involving a protein. Includes protein modification." [GOC:ma] comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. subset: gocheck_do_not_annotate @@ -3758,7 +3966,6 @@ relationship: part_of GO:0007049 ! cell cycle id: GO:0022411 name: cellular component disassembly namespace: biological_process -alt_id: GO:0071845 def: "A cellular process that results in the breakdown of a cellular component." [GOC:isa_complete] comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. subset: gocheck_do_not_annotate @@ -3787,7 +3994,6 @@ relationship: part_of GO:0007586 ! digestion id: GO:0022607 name: cellular component assembly namespace: biological_process -alt_id: GO:0071844 def: "The aggregation, arrangement and bonding together of a cellular component." [GOC:isa_complete] subset: goslim_chembl subset: goslim_euk_cellular_processes_ribbon @@ -3829,8 +4035,6 @@ relationship: results_in_assembly_of GO:1990904 ! ribonucleoprotein complex id: GO:0023052 name: signaling namespace: biological_process -alt_id: GO:0023046 -alt_id: GO:0044700 def: "The entirety of a process in which information is transmitted within a biological system. This process begins with an active signal and ends when a cellular response has been triggered." [GOC:mtg_signal, GOC:mtg_signaling_feb11, GOC:signaling] comment: Note that a signal is any variable property or parameter that serves to convey information, and may be a physical entity such as a gene product or small molecule, a photon, or a change in state such as movement or voltage change. subset: goslim_agr @@ -3848,7 +4052,6 @@ synonym: "signalling" EXACT [] synonym: "signalling process" RELATED [GOC:mah] synonym: "single organism signaling" RELATED [] is_a: GO:0050789 ! regulation of biological process -created_by: jl creation_date: 2010-02-16T09:30:50Z [Term] @@ -3900,7 +4103,7 @@ subset: goslim_agr subset: goslim_drosophila subset: goslim_flybase_ribbon xref: Wikipedia:Cell_junction -is_a: GO:0110165 ! cellular anatomical entity +is_a: GO:0110165 ! cellular anatomical structure property_value: RO:0002161 NCBITaxon:4751 [Term] @@ -3982,7 +4185,6 @@ relationship: results_in_acquisition_of_features_of CL:0000556 ! megakaryocyte id: GO:0030261 name: chromosome condensation namespace: biological_process -alt_id: GO:0000068 def: "The progressive compaction of dispersed interphase chromatin into threadlike chromosomes prior to mitotic or meiotic nuclear division, or during apoptosis, in eukaryotic cells." [GOC:mah, ISBN:0815316194] synonym: "DNA condensation" BROAD [Wikipedia:DNA_condensation] synonym: "eukaryotic chromosome condensation" EXACT [GOC:bf] @@ -4018,7 +4220,7 @@ subset: goslim_drosophila subset: goslim_generic subset: goslim_pir subset: goslim_plant -is_a: GO:0110165 ! cellular anatomical entity +is_a: GO:0110165 ! cellular anatomical structure relationship: part_of CL:0000000 ! cell relationship: part_of GO:0071944 ! cell periphery @@ -4045,7 +4247,6 @@ relationship: part_of GO:0097447 ! dendritic tree id: GO:0031012 name: extracellular matrix namespace: cellular_component -alt_id: GO:0005578 def: "A structure lying external to one or more cells, which provides structural support, biochemical or biomechanical cues for cells or tissues." [GOC:BHF, GOC:mah, GOC:rph, NIF_Subcellular:nlx_subcell_20090513, PMID:21123617, PMID:28089324] subset: goslim_chembl subset: goslim_drosophila @@ -4065,7 +4266,6 @@ disjoint_from: GO:0043226 ! organelle id: GO:0031410 name: cytoplasmic vesicle namespace: cellular_component -alt_id: GO:0016023 def: "A vesicle found in the cytoplasm of a cell." [GOC:ai, GOC:mah, GOC:vesicles] subset: goslim_agr subset: goslim_candida @@ -4087,7 +4287,7 @@ id: GO:0031974 name: membrane-enclosed lumen namespace: cellular_component def: "The enclosed volume within a sealed membrane or between two sealed membranes. Encompasses the volume enclosed by the membranes of a particular organelle, e.g. endoplasmic reticulum lumen, or the space between the two lipid bilayers of a double membrane surrounding an organelle, e.g. nuclear envelope lumen." [GOC:add, GOC:mah] -is_a: GO:0110165 ! cellular anatomical entity +is_a: GO:0110165 ! cellular anatomical structure disjoint_from: GO:0045202 ! synapse [Term] @@ -4102,7 +4302,6 @@ relationship: part_of GO:0005634 ! nucleus id: GO:0031982 name: vesicle namespace: cellular_component -alt_id: GO:0031988 def: "Any small, fluid-filled, spherical organelle enclosed by membrane." [GOC:mah, GOC:pz, GOC:vesicles] subset: goslim_pir synonym: "membrane-bounded vesicle" RELATED [] @@ -4140,8 +4339,6 @@ relationship: results_in_assembly_of GO:0032059 ! bleb id: GO:0032501 name: multicellular organismal process namespace: biological_process -alt_id: GO:0044707 -alt_id: GO:0050874 def: "Any biological process, occurring at the level of a multicellular organism, pertinent to its function." [GOC:curators, GOC:dph, GOC:isa_complete, GOC:tb] comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. subset: gocheck_do_not_annotate @@ -4154,14 +4351,12 @@ property_value: RO:0002161 NCBITaxon:2157 property_value: RO:0002161 NCBITaxon:4896 property_value: RO:0002161 NCBITaxon:4932 property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27189" xsd:anyURI -created_by: jl creation_date: 2012-09-19T16:07:47Z [Term] id: GO:0032502 name: developmental process namespace: biological_process -alt_id: GO:0044767 def: "A biological process whose specific outcome is the progression of an integrated living unit: an anatomical structure (which may be a subcellular structure, cell, tissue, or organ), or organism over time from an initial condition to a later condition." [GOC:isa_complete] subset: goslim_agr subset: goslim_flybase_ribbon @@ -4169,7 +4364,6 @@ subset: goslim_pir synonym: "development" NARROW [] synonym: "single-organism developmental process" RELATED [] is_a: GO:0008150 ! biological_process -created_by: jl creation_date: 2012-12-19T12:21:31Z [Term] @@ -4186,9 +4380,6 @@ is_a: GO:0140352 ! export from cell id: GO:0032984 name: protein-containing complex disassembly namespace: biological_process -alt_id: GO:0034623 -alt_id: GO:0043241 -alt_id: GO:0043624 def: "The disaggregation of a protein-containing macromolecular complex into its constituent components." [GOC:mah] synonym: "cellular macromolecule complex disassembly" RELATED [] synonym: "cellular protein complex disassembly" RELATED [] @@ -4205,7 +4396,6 @@ property_value: term_tracker_item "https://github.com/geneontology/go-ontology/i id: GO:0032991 name: protein-containing complex namespace: cellular_component -alt_id: GO:0043234 def: "A stable assembly of two or more macromolecules, i.e. proteins, nucleic acids, carbohydrates or lipids, in which at least one component is a protein and the constituent parts function together." [GOC:dos, GOC:mah] comment: A protein complex in this context is meant as a stable set of interacting proteins which can be co-purified by an acceptable method, and where the complex has been shown to exist as an isolated, functional unit in vivo. Acceptable experimental methods include stringent protein purification followed by detection of protein interaction. The following methods should be considered non-acceptable: simple immunoprecipitation, pull-down experiments from cell extracts without further purification, colocalization and 2-hybrid screening. Interactions that should not be captured as protein complexes include: 1) enzyme/substrate, receptor/ligand or any similar transient interactions, unless these are a critical part of the complex assembly or are required e.g. for the receptor to be functional; 2) proteins associated in a pull-down/co-immunoprecipitation assay with no functional link or any evidence that this is a defined biological entity rather than a loose-affinity complex; 3) any complex where the only evidence is based on genetic interaction data; 4) partial complexes, where some subunits (e.g. transmembrane ones) cannot be expressed as recombinant proteins and are excluded from experiments (in this case, independent evidence is necessary to find out the composition of the full complex, if known). Interactions that may be captured as protein complexes include: 1) enzyme/substrate or receptor/ligand if the complex can only assemble and become functional in the presence of both classes of subunits; 2) complexes where one of the members has not been shown to be physically linked to the other(s), but is a homologue of, and has the same functionality as, a protein that has been experimentally demonstrated to form a complex with the other member(s); 3) complexes whose existence is accepted based on localization and pharmacological studies, but for which experimental evidence is not yet available for the complex as a whole. subset: goslim_agr @@ -4220,8 +4410,8 @@ synonym: "protein complex" NARROW [] synonym: "protein containing complex" EXACT [] synonym: "protein-protein complex" NARROW [] is_a: GO:0005575 ! cellular_component -is_a: PR:000050567 ! protein-containing material entity -disjoint_from: GO:0110165 ! cellular anatomical entity +disjoint_from: GO:0110165 ! cellular anatomical structure +relationship: has_part PR:000000001 ! protein [Term] id: GO:0034101 @@ -4239,7 +4429,6 @@ relationship: acts_on_population_of CL:0000232 ! erythrocyte id: GO:0034220 name: monoatomic ion transmembrane transport namespace: biological_process -alt_id: GO:0099131 def: "A process in which a monoatomic ion is transported across a membrane. Monatomic ions (also called simple ions) are ions consisting of exactly one atom." [GOC:mah] comment: Note that this term is not intended for use in annotating lateral movement within membranes. synonym: "ATP hydrolysis coupled ion transmembrane transport" NARROW [] @@ -4297,9 +4486,8 @@ id: GO:0036477 name: somatodendritic compartment namespace: cellular_component def: "The region of a neuron that includes the cell body (cell soma) and dendrite(s), but excludes the axon." [GOC:pad, GOC:PARL] -is_a: GO:0110165 ! cellular anatomical entity +is_a: GO:0110165 ! cellular anatomical structure relationship: part_of CL:0000540 ! neuron -created_by: bf creation_date: 2014-07-24T10:06:19Z [Term] @@ -4344,9 +4532,6 @@ property_value: RO:0002161 NCBITaxon:6237 {source="GOC:kmv"} id: GO:0042592 name: homeostatic process namespace: biological_process -alt_id: GO:0032844 -alt_id: GO:0032845 -alt_id: GO:0032846 def: "Any biological process involved in the maintenance of an internal steady state." [GOC:jl, ISBN:0395825172] subset: goslim_agr subset: goslim_chembl @@ -4374,7 +4559,7 @@ subset: goslim_prokaryote_ribbon synonym: "cell process" BROAD [] synonym: "cellular process" BROAD [] synonym: "cellular projection" EXACT [] -is_a: GO:0110165 ! cellular anatomical entity +is_a: GO:0110165 ! cellular anatomical structure relationship: part_of CL:0000000 ! cell [Term] @@ -4424,9 +4609,6 @@ relationship: part_of GO:0036477 ! somatodendritic compartment id: GO:0043170 name: macromolecule metabolic process namespace: biological_process -alt_id: GO:0034960 -alt_id: GO:0043283 -alt_id: GO:0044259 def: "The chemical reactions and pathways involving macromolecules, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass." [GOC:mah] subset: gocheck_do_not_annotate subset: goslim_pir @@ -4448,7 +4630,7 @@ synonym: "Schwann cell myelin sheath" NARROW [] xref: FMA:62983 xref: NIF_Subcellular:sao593830697 xref: Wikipedia:Myelin -is_a: GO:0110165 ! cellular anatomical entity +is_a: GO:0110165 ! cellular anatomical structure relationship: part_of CL:0000125 ! glial cell relationship: RO:0002160 NCBITaxon:33208 ! only in taxon Metazoa relationship: RO:0002162 NCBITaxon:33208 {all_only="true"} ! in taxon Metazoa @@ -4465,7 +4647,7 @@ subset: goslim_prokaryote subset: goslim_prokaryote_ribbon xref: NIF_Subcellular:sao1539965131 xref: Wikipedia:Organelle -is_a: GO:0110165 ! cellular anatomical entity +is_a: GO:0110165 ! cellular anatomical structure [Term] id: GO:0043227 @@ -4478,23 +4660,26 @@ xref: NIF_Subcellular:sao414196390 is_a: GO:0043226 ! organelle intersection_of: GO:0043226 ! organelle intersection_of: has_part GO:0016020 ! membrane -disjoint_from: GO:0043228 ! non-membrane-bounded organelle +disjoint_from: GO:0043228 ! membraneless organelle relationship: has_part GO:0016020 ! membrane property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28153" xsd:anyURI [Term] id: GO:0043228 -name: non-membrane-bounded organelle +name: membraneless organelle namespace: cellular_component def: "Organized structure of distinctive morphology and function, not bounded by a lipid bilayer membrane. Includes ribosomes, the cytoskeleton and chromosomes." [GOC:go_curators] subset: gocheck_do_not_annotate subset: goslim_mouse synonym: "biological condensate" RELATED [] +synonym: "membrane-less organelle" EXACT [] +synonym: "non-membrane-bounded organelle" EXACT [] synonym: "non-membrane-enclosed organelle" EXACT [] xref: NIF_Subcellular:sao1456184038 is_a: GO:0043226 ! organelle property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/21881" xsd:anyURI property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28153" xsd:anyURI +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29106" xsd:anyURI [Term] id: GO:0043229 @@ -4535,15 +4720,17 @@ intersection_of: part_of GO:0005622 ! intracellular anatomical structure [Term] id: GO:0043232 -name: intracellular non-membrane-bounded organelle +name: intracellular membraneless organelle namespace: cellular_component def: "Organized structure of distinctive morphology and function, not bounded by a lipid bilayer membrane and occurring within the cell. Includes ribosomes, the cytoskeleton and chromosomes." [GOC:go_curators] subset: goslim_pir +synonym: "intracellular non-membrane-bounded organelle" EXACT [] synonym: "intracellular non-membrane-enclosed organelle" EXACT [] -is_a: GO:0043228 ! non-membrane-bounded organelle +is_a: GO:0043228 ! membraneless organelle is_a: GO:0043229 ! intracellular organelle -intersection_of: GO:0043228 ! non-membrane-bounded organelle +intersection_of: GO:0043228 ! membraneless organelle intersection_of: part_of GO:0005622 ! intracellular anatomical structure +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29106" xsd:anyURI [Term] id: GO:0043233 @@ -4570,9 +4757,6 @@ relationship: regulates GO:0007585 ! respiratory gaseous exchange by respiratory id: GO:0043933 name: protein-containing complex organization namespace: biological_process -alt_id: GO:0034600 -alt_id: GO:0034621 -alt_id: GO:0071822 def: "Any process in which macromolecules aggregate, disaggregate, or are modified, resulting in the formation, disassembly, or alteration of a protein complex." [GOC:mah] synonym: "cellular macromolecular complex organization" RELATED [] synonym: "cellular macromolecular complex subunit organisation" RELATED [] @@ -4588,7 +4772,6 @@ intersection_of: GO:0016043 ! cellular component organization intersection_of: results_in_organization_of GO:0032991 ! protein-containing complex relationship: results_in_organization_of GO:0032991 ! protein-containing complex property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/22580" xsd:anyURI -created_by: mah creation_date: 2010-09-08T10:01:42Z [Term] @@ -4615,7 +4798,6 @@ relationship: regulates GO:0022600 ! digestive system process id: GO:0044085 name: cellular component biogenesis namespace: biological_process -alt_id: GO:0071843 def: "A process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of a cellular component. Includes biosynthesis of constituent macromolecules, and those macromolecular modifications that are involved in synthesis or assembly of the cellular component." [GOC:jl, GOC:mah] subset: gocheck_do_not_annotate subset: goslim_pir @@ -4632,21 +4814,8 @@ synonym: "Met-tRNA/eIF2.GTP ternary complex" NARROW [] synonym: "translation initiation (ternary) complex" EXACT [] is_a: GO:1990904 ! ribonucleoprotein complex relationship: part_of GO:0005737 ! cytoplasm -created_by: jl creation_date: 2009-10-22T02:38:55Z -[Term] -id: GO:0044237 -name: cellular metabolic process -namespace: biological_process -def: "The chemical reactions and pathways by which individual cells transform chemical substances." [GOC:go_curators] -comment: This term should not be used for direct annotation. It should be possible to make a more specific annotation to one of the children of this term. -subset: gocheck_do_not_annotate -synonym: "cellular metabolism" EXACT [] -synonym: "intermediary metabolism" RELATED [GOC:mah] -is_a: GO:0008152 ! metabolic process -is_a: GO:0009987 ! cellular process - [Term] id: GO:0044238 name: primary metabolic process @@ -4662,21 +4831,6 @@ xref: Wikipedia:Primary_metabolite is_a: GO:0008152 ! metabolic process property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/26424" xsd:anyURI -[Term] -id: GO:0044249 -name: cellular biosynthetic process -namespace: biological_process -def: "The chemical reactions and pathways resulting in the formation of substances, carried out by individual cells." [GOC:jl] -comment: This term should not be used for direct annotation. It should be possible to make a more specific annotation to one of the children of this term. -subset: gocheck_do_not_annotate -synonym: "cellular anabolism" EXACT [] -synonym: "cellular biosynthesis" EXACT [] -synonym: "cellular formation" EXACT [] -synonym: "cellular synthesis" EXACT [] -is_a: GO:0009058 ! biosynthetic process -is_a: GO:0044237 ! cellular metabolic process -property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27052" xsd:anyURI - [Term] id: GO:0044297 name: cell body @@ -4687,10 +4841,9 @@ synonym: "cell soma" EXACT [] xref: FBbt:00005107 xref: FMA:67301 xref: Wikipedia:Cell_body -is_a: GO:0110165 ! cellular anatomical entity +is_a: GO:0110165 ! cellular anatomical structure relationship: part_of CL:0000000 ! cell property_value: RO:0002161 NCBITaxon:4890 -created_by: jl creation_date: 2010-02-05T10:37:16Z [Term] @@ -4786,7 +4939,6 @@ property_value: term_tracker_item "https://github.com/geneontology/go-ontology/i id: GO:0048598 name: embryonic morphogenesis namespace: biological_process -alt_id: GO:0048828 def: "The process in which anatomical structures are generated and organized during the embryonic phase. The embryonic phase begins with zygote formation. The end of the embryonic phase is organism-specific. For example, it would be at birth for mammals, larval hatching for insects and seed dormancy in plants." [GOC:jid, GOC:mtg_sensu] synonym: "embryonic anatomical structure morphogenesis" EXACT [GOC:dph, GOC:tb] is_a: GO:0009653 ! anatomical structure morphogenesis @@ -4909,7 +5061,6 @@ property_value: term_tracker_item "https://github.com/geneontology/go-ontology/i id: GO:0050789 name: regulation of biological process namespace: biological_process -alt_id: GO:0050791 def: "Any process that modulates the frequency, rate or extent of a biological process. Biological processes are regulated by many means; examples include the control of gene expression, protein modification or interaction with a protein or substrate molecule." [GOC:ai, GOC:go_curators] subset: gocheck_do_not_annotate subset: goslim_candida @@ -4924,7 +5075,6 @@ relationship: regulates GO:0008150 ! biological_process id: GO:0050794 name: regulation of cellular process namespace: biological_process -alt_id: GO:0051244 def: "Any process that modulates the frequency, rate or extent of a cellular process, any of those that are carried out at the cellular level, but are not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level." [GOC:go_curators] subset: gocheck_do_not_annotate synonym: "regulation of cellular physiological process" EXACT [] @@ -4958,7 +5108,6 @@ property_value: term_tracker_item "https://github.com/geneontology/go-ontology/i id: GO:0050896 name: response to stimulus namespace: biological_process -alt_id: GO:0051869 def: "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus. The process begins with detection of the stimulus and ends with a change in state or activity or the cell or organism." [GOC:ai, GOC:bf] comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. subset: gocheck_do_not_annotate @@ -5031,7 +5180,6 @@ relationship: part_of GO:0050953 ! sensory perception of light stimulus id: GO:0051179 name: localization namespace: biological_process -alt_id: GO:1902578 def: "Any process in which a cell, a substance, or a cellular entity, such as a protein complex or organelle, is transported, tethered to or otherwise maintained in a specific location. In the case of substances, localization may also be achieved via selective degradation." [GOC:ai, GOC:dos] subset: gocheck_do_not_annotate subset: goslim_pir @@ -5045,7 +5193,6 @@ synonym: "single organism localization" RELATED [GOC:TermGenie] synonym: "single-organism localization" RELATED [] is_a: GO:0008150 ! biological_process property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27052" xsd:anyURI -created_by: jl creation_date: 2013-12-18T13:51:04Z [Term] @@ -5076,9 +5223,6 @@ relationship: regulates GO:0032501 ! multicellular organismal process id: GO:0051276 name: chromosome organization namespace: biological_process -alt_id: GO:0006323 -alt_id: GO:0007001 -alt_id: GO:0051277 def: "A process that is carried out at the cellular level that results in the assembly, arrangement of constituent parts, or disassembly of chromosomes, structures composed of a very long molecule of DNA and associated proteins that carries hereditary information. This term covers covalent modifications at the molecular level as well as spatial relationships among the major components of a chromosome." [GOC:ai, GOC:dph, GOC:jl, GOC:mah] subset: goslim_chembl subset: goslim_drosophila @@ -5123,7 +5267,6 @@ is_a: GO:0050896 ! response to stimulus id: GO:0051641 name: cellular localization namespace: biological_process -alt_id: GO:1902580 def: "A cellular localization process whereby a substance or cellular entity, such as a protein complex or organelle, is transported to, and/or maintained in, a specific location within a cell including the localization of substances or cellular entities to the cell membrane." [GOC:tb, GOC:vw] comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. subset: gocheck_do_not_annotate @@ -5138,7 +5281,6 @@ synonym: "single-organism cellular localization" RELATED [] is_a: GO:0009987 ! cellular process is_a: GO:0051179 ! localization property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27189" xsd:anyURI -created_by: jl creation_date: 2013-12-18T14:04:32Z [Term] @@ -5181,7 +5323,6 @@ is_a: GO:0015800 ! acidic amino acid transport id: GO:0055085 name: transmembrane transport namespace: biological_process -alt_id: GO:0090662 def: "The process in which a solute is transported across a lipid bilayer, from one side of a membrane to the other." [GOC:dph, GOC:jid] comment: Transmembrane transport is the transport of a solute across a lipid bilayer. Note that transport through the nuclear pore complex is not transmembrane because the nuclear membrane is a double membrane and is not traversed. For transport through the nuclear pore, consider instead the term 'nucleocytoplasmic transport ; GO:0006913' and its children. Note also that this term is not intended for use in annotating lateral movement within membranes. subset: goslim_chembl @@ -5197,7 +5338,6 @@ is_a: GO:0009987 ! cellular process intersection_of: GO:0006810 ! transport intersection_of: results_in_transport_across GO:0016020 ! membrane relationship: results_in_transport_across GO:0016020 ! membrane -created_by: tb creation_date: 2015-10-21T13:22:47Z [Term] @@ -5267,7 +5407,6 @@ is_a: GO:0035239 ! tube morphogenesis intersection_of: GO:0009653 ! anatomical structure morphogenesis intersection_of: results_in_morphogenesis_of UBERON:0003914 ! epithelial tube relationship: results_in_morphogenesis_of UBERON:0003914 ! epithelial tube -created_by: dph creation_date: 2009-04-28T09:33:36Z [Term] @@ -5277,7 +5416,6 @@ namespace: biological_process def: "The process in which the anatomical structures of a branched epithelium are generated and organized." [GOC:dph] is_a: GO:0001763 ! morphogenesis of a branching structure is_a: GO:0002009 ! morphogenesis of an epithelium -created_by: dph creation_date: 2010-05-25T09:05:34Z [Term] @@ -5289,7 +5427,6 @@ is_a: GO:0007269 ! neurotransmitter secretion is_a: GO:0014047 ! glutamate secretion is_a: GO:0051938 ! L-glutamate import relationship: part_of GO:0035249 ! synaptic transmission, glutamatergic -created_by: dph creation_date: 2013-06-21T16:14:47Z [Term] @@ -5300,16 +5437,12 @@ def: "An extracellular matrix consisting mainly of proteins (especially collagen is_a: GO:0031012 ! extracellular matrix relationship: RO:0002160 NCBITaxon:33208 ! only in taxon Metazoa relationship: RO:0002162 NCBITaxon:33208 {all_only="true"} ! in taxon Metazoa -created_by: dph creation_date: 2018-04-13T12:47:21Z [Term] id: GO:0065003 name: protein-containing complex assembly namespace: biological_process -alt_id: GO:0006461 -alt_id: GO:0034622 -alt_id: GO:0043623 def: "The aggregation, arrangement and bonding together of a set of macromolecules to form a protein-containing complex." [GOC:jl] subset: goslim_chembl subset: goslim_drosophila @@ -5393,7 +5526,6 @@ is_a: GO:0022607 ! cellular component assembly intersection_of: GO:0022607 ! cellular component assembly intersection_of: results_in_assembly_of GO:0043226 ! organelle relationship: results_in_assembly_of GO:0043226 ! organelle -created_by: mah creation_date: 2009-09-15T03:00:51Z [Term] @@ -5410,14 +5542,12 @@ intersection_of: GO:0016043 ! cellular component organization intersection_of: results_in_organization_of GO:1990904 ! ribonucleoprotein complex relationship: results_in_organization_of GO:1990904 ! ribonucleoprotein complex property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/25143" xsd:anyURI -created_by: mah creation_date: 2010-09-08T10:10:35Z [Term] id: GO:0071840 name: cellular component organization or biogenesis namespace: biological_process -alt_id: GO:0071841 def: "A process that results in the biosynthesis of constituent macromolecules, assembly, arrangement of constituent parts, or disassembly of a cellular component." [GOC:mah] comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. subset: gocheck_do_not_annotate @@ -5428,7 +5558,6 @@ synonym: "cellular component organisation or biogenesis at cellular level" EXACT synonym: "cellular component organization or biogenesis at cellular level" EXACT [] is_a: GO:0009987 ! cellular process property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27189" xsd:anyURI -created_by: mah creation_date: 2010-09-10T01:39:16Z [Term] @@ -5437,8 +5566,7 @@ name: cell periphery namespace: cellular_component def: "The broad region around and including the plasma membrane of a cell, encompassing the cell cortex (inside the cell), the plasma membrane, and any external encapsulating structures." [GOC:pdt] subset: goslim_flybase_ribbon -is_a: GO:0110165 ! cellular anatomical entity -created_by: mah +is_a: GO:0110165 ! cellular anatomical structure creation_date: 2010-10-04T01:51:47Z [Term] @@ -5450,7 +5578,6 @@ synonym: "elastic fibre" EXACT [GOC:mah] synonym: "elastin fiber" EXACT [GOC:BHF] is_a: GO:0099512 ! supramolecular fiber relationship: part_of GO:0031012 ! extracellular matrix -created_by: mah creation_date: 2010-10-11T11:44:57Z [Term] @@ -5465,7 +5592,6 @@ intersection_of: GO:0022607 ! cellular component assembly intersection_of: results_in_assembly_of GO:0070062 ! extracellular exosome relationship: part_of GO:0097734 ! extracellular exosome biogenesis relationship: results_in_assembly_of GO:0070062 ! extracellular exosome -created_by: mah creation_date: 2010-10-18T03:44:18Z [Term] @@ -5479,21 +5605,18 @@ intersection_of: results_in_formation_of UBERON:0003914 ! epithelial tube relationship: part_of GO:0060562 ! epithelial tube morphogenesis relationship: results_in_formation_of UBERON:0003914 ! epithelial tube property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/22302" xsd:anyURI -created_by: mah creation_date: 2010-02-26T02:15:40Z [Term] id: GO:0097190 name: apoptotic signaling pathway namespace: biological_process -alt_id: GO:0008624 def: "The series of molecular signals which triggers the apoptotic death of a cell. The pathway starts with reception of a signal, and ends when the execution phase of apoptosis is triggered." [GOC:mtg_apoptosis] comment: This term can be used to annotate gene products involved in apoptotic events happening downstream of the cross-talk point between the extrinsic and intrinsic apoptotic pathways. The cross-talk starts when caspase-8 cleaves Bid and truncated Bid interacts with mitochondria. From this point on it is not possible to distinguish between extrinsic and intrinsic pathways. synonym: "apoptotic signalling pathway" EXACT [GOC:mah] synonym: "induction of apoptosis by extracellular signals" EXACT [] is_a: GO:0007165 ! signal transduction relationship: part_of GO:0006915 ! apoptotic process -created_by: pr creation_date: 2011-11-23T09:30:23Z [Term] @@ -5506,7 +5629,6 @@ synonym: "execution phase of apoptotic process" EXACT [] is_a: GO:0009987 ! cellular process relationship: has_part GO:0032060 ! bleb assembly relationship: part_of GO:0006915 ! apoptotic process -created_by: pr creation_date: 2011-11-23T09:45:24Z [Term] @@ -5518,7 +5640,6 @@ xref: NIF_Subcellular:sao172297168 is_a: GO:0043005 ! neuron projection relationship: has_part GO:0030425 ! dendrite relationship: part_of GO:0036477 ! somatodendritic compartment -created_by: pr creation_date: 2012-12-17T12:31:49Z [Term] @@ -5530,7 +5651,6 @@ is_a: GO:0031982 ! vesicle is_a: GO:0043231 ! intracellular membrane-bounded organelle intersection_of: GO:0031982 ! vesicle intersection_of: part_of GO:0005622 ! intracellular anatomical structure -created_by: pr creation_date: 2016-03-29T17:39:45Z [Term] @@ -5544,7 +5664,6 @@ synonym: "exosome production" EXACT [] synonym: "ILV assembly" RELATED [] synonym: "intraluminal vesicle assembly" RELATED [] is_a: GO:0140112 ! extracellular vesicle biogenesis -created_by: pr creation_date: 2016-10-03T14:35:25Z [Term] @@ -5559,7 +5678,6 @@ is_a: GO:0016020 ! membrane intersection_of: GO:0016020 ! membrane intersection_of: part_of GO:0005886 ! plasma membrane relationship: part_of GO:0005886 ! plasma membrane -created_by: dos creation_date: 2014-03-06T11:55:32Z [Term] @@ -5580,7 +5698,6 @@ def: "A complex of collagen trimers such as a fibril or collagen network." [GOC: synonym: "Supramolecular aggregate of collagen" EXACT [PMID:19693541] synonym: "Supramolecular collagen assembly" EXACT [PMID:21421911] is_a: GO:0099080 ! supramolecular complex -is_a: PR:000050567 ! protein-containing material entity relationship: has_part GO:0005581 ! collagen trimer relationship: part_of GO:0062023 ! collagen-containing extracellular matrix @@ -5609,7 +5726,7 @@ namespace: cellular_component def: "The part of a synapse that is part of the presynaptic cell." [GOC:dos] subset: goslim_synapse synonym: "presynaptic terminal" EXACT [] -is_a: GO:0110165 ! cellular anatomical entity +is_a: GO:0110165 ! cellular anatomical structure relationship: part_of CL:0000540 ! neuron relationship: part_of GO:0045202 ! synapse @@ -5619,7 +5736,7 @@ name: postsynapse namespace: cellular_component def: "The part of a synapse that is part of the post-synaptic cell." [GOC:dos] subset: goslim_synapse -is_a: GO:0110165 ! cellular anatomical entity +is_a: GO:0110165 ! cellular anatomical structure relationship: part_of CL:0000000 ! cell relationship: part_of GO:0045202 ! synapse @@ -5650,7 +5767,7 @@ id: GO:0099080 name: supramolecular complex namespace: cellular_component def: "A cellular component that consists of an indeterminate number of proteins or macromolecular complexes, organized into a regular, higher-order structure such as a polymer, sheet, network or a fiber." [GOC:dos] -is_a: GO:0110165 ! cellular anatomical entity +is_a: GO:0110165 ! cellular anatomical structure [Term] id: GO:0099081 @@ -5666,7 +5783,6 @@ relationship: bearer_of PATO:0015006 ! polymeric id: GO:0099512 name: supramolecular fiber namespace: cellular_component -alt_id: GO:0043205 def: "A polymer consisting of an indefinite number of protein or protein complex subunits that have polymerised to form a fiber-shaped structure." [GOC:dos] synonym: "fibril" RELATED [] is_a: GO:0099081 ! supramolecular polymer @@ -5728,16 +5844,17 @@ relationship: RO:0002162 NCBITaxon:33208 {all_only="true"} ! in taxon Metazoa [Term] id: GO:0110165 -name: cellular anatomical entity +name: cellular anatomical structure namespace: cellular_component -def: "A part of a cellular organism that is either an immaterial entity or a material entity with granularity above the level of a protein complex but below that of an anatomical system. Or, a substance produced by a cellular organism with granularity above the level of a protein complex." [GOC:kmv] +def: "A part of a cellular organism consisting of a material entity with granularity above the level of a protein complex but below that of an anatomical system. Note that cellular organisms exclude viruses." [GOC:kmv] subset: gocheck_do_not_annotate subset: goslim_pir +synonym: "cellular anatomical entity" EXACT [] is_a: GO:0005575 ! cellular_component is_a: UBERON:0000061 ! anatomical structure property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/24200" xsd:anyURI property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/26424" xsd:anyURI -created_by: kmv +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28978" xsd:anyURI creation_date: 2019-08-12T18:01:37Z [Term] @@ -5750,7 +5867,6 @@ intersection_of: GO:0042995 ! cell projection intersection_of: has_part GO:0098590 ! plasma membrane region relationship: has_part GO:0098590 ! plasma membrane region property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/13193" xsd:anyURI -created_by: krc creation_date: 2017-03-21T17:26:07Z [Term] @@ -5765,7 +5881,6 @@ intersection_of: GO:0022607 ! cellular component assembly intersection_of: results_in_assembly_of GO:0120025 ! plasma membrane bounded cell projection relationship: results_in_assembly_of GO:0120025 ! plasma membrane bounded cell projection property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/13298" xsd:anyURI -created_by: krc creation_date: 2017-04-24T23:56:08Z [Term] @@ -5778,7 +5893,6 @@ intersection_of: GO:0016043 ! cellular component organization intersection_of: results_in_organization_of GO:0120025 ! plasma membrane bounded cell projection relationship: results_in_organization_of GO:0120025 ! plasma membrane bounded cell projection property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/13298" xsd:anyURI -created_by: krc creation_date: 2017-04-26T16:07:02Z [Term] @@ -5794,7 +5908,6 @@ is_a: GO:1903047 ! mitotic cell cycle process intersection_of: GO:0000280 ! nuclear division intersection_of: part_of GO:0000278 ! mitotic cell cycle property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/19910" xsd:anyURI -created_by: pg creation_date: 2017-03-23T14:44:23Z [Term] @@ -5805,7 +5918,6 @@ def: "The assembly and secretion a set of components to form an extracellular ve synonym: "extracellular vesicle assembly" EXACT [] is_a: GO:0044085 ! cellular component biogenesis property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/14256" xsd:anyURI -created_by: pg creation_date: 2017-10-23T11:53:42Z [Term] @@ -5821,7 +5933,6 @@ intersection_of: has_target_end_location GO:0005576 ! extracellular region intersection_of: has_target_start_location GO:0005622 ! intracellular anatomical structure relationship: has_target_end_location GO:0005576 ! extracellular region relationship: has_target_start_location GO:0005622 ! intracellular anatomical structure -created_by: pg creation_date: 2019-05-22T11:20:45Z [Term] @@ -5834,7 +5945,6 @@ is_a: GO:0022402 ! cell cycle process intersection_of: GO:0009987 ! cellular process intersection_of: part_of GO:0000278 ! mitotic cell cycle relationship: part_of GO:0000278 ! mitotic cell cycle -created_by: jl creation_date: 2014-05-22T14:22:34Z [Term] @@ -5847,7 +5957,6 @@ is_a: GO:0044057 ! regulation of system process intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0008015 ! blood circulation relationship: regulates GO:0008015 ! blood circulation -created_by: mr creation_date: 2014-10-06T18:38:56Z [Term] @@ -5860,15 +5969,12 @@ is_a: GO:0031982 ! vesicle is_a: GO:0065010 ! extracellular membrane-bounded organelle intersection_of: GO:0031982 ! vesicle intersection_of: part_of GO:0005576 ! extracellular region -created_by: jl creation_date: 2014-10-22T14:26:11Z [Term] id: GO:1990904 name: ribonucleoprotein complex namespace: cellular_component -alt_id: GO:0030529 -alt_id: GO:1990903 def: "A macromolecular complex that contains both RNA and protein molecules." [GOC:krc, GOC:vesicles] subset: goslim_pir synonym: "extracellular ribonucleoprotein complex" NARROW [] @@ -5878,7 +5984,6 @@ synonym: "RNA-protein complex" EXACT [] synonym: "RNP" EXACT [] xref: Wikipedia:Ribonucleoprotein is_a: GO:0032991 ! protein-containing complex -created_by: pr creation_date: 2015-11-19T12:26:37Z [Term] @@ -5912,7 +6017,6 @@ is_a: NCBITaxon:39107 ! Murinae id: NCBITaxon:10090 name: Mus musculus namespace: ncbi_taxonomy -alt_id: NCBITaxon:85055 synonym: "house mouse" EXACT genbank_common_name [] synonym: "mouse" EXACT OMO:0003003 [] xref: GC_ID:1 @@ -5929,7 +6033,6 @@ is_a: NCBITaxon:7776 ! Gnathostomata id: NCBITaxon:117571 name: Euteleostomi namespace: ncbi_taxonomy -alt_id: NCBITaxon:40673 synonym: "bony vertebrates" EXACT genbank_common_name [] xref: GC_ID:1 is_a: NCBITaxon:117570 ! Teleostomi @@ -6078,7 +6181,6 @@ is_a: NCBITaxon:1963758 ! Myomorpha id: NCBITaxon:39107 name: Murinae namespace: ncbi_taxonomy -alt_id: NCBITaxon:109679 xref: GC_ID:1 is_a: NCBITaxon:10066 ! Muridae @@ -6174,7 +6276,6 @@ is_a: NCBITaxon:314147 ! Glires id: PATO:0000001 name: quality namespace: quality -alt_id: PATO:0000072 def: "A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities" [PATOC:GVG] [Term] @@ -6189,7 +6290,6 @@ is_a: PATO:0001241 ! physical object quality id: PATO:0000052 name: shape namespace: quality -alt_id: PATO:0001647 def: "A morphological quality inhering in a bearer by virtue of the bearer's ratios of distances between its features (points, edges, surfaces and also holes etc)." [PATOC:GVG] comment: Shapes are invariant on size transformations. Shapes can be subdivided into 2D and 3D shapes, We can also make a distinction between shapes of complete self-connected objects, and shapes of parts of objects. subset: attribute_slim @@ -6208,7 +6308,6 @@ is_a: PATO:0000051 ! morphology id: PATO:0000141 name: structure namespace: quality -alt_id: PATO:0001452 def: "A morphology quality inhering in a bearer by virtue of the bearer's relative position, shape, arrangements and connectivity of an organism's various parts; the pattern underlying its form." [PATOC:GVG] subset: attribute_slim synonym: "conformation" BROAD [VT:1000738] @@ -6298,7 +6397,6 @@ is_a: PATO:0000957 ! opacity id: PATO:0001018 name: physical quality namespace: quality -alt_id: PATO:0002079 def: "A quality of a physical entity that exists through action of continuants at the physical level of organisation in relation to other entities." [PATOC:GVG] subset: attribute_slim synonym: "relational physical quality" EXACT [] @@ -6309,8 +6407,6 @@ is_a: PATO:0001241 ! physical object quality id: PATO:0001241 name: physical object quality namespace: quality -alt_id: PATO:0001237 -alt_id: PATO:0001238 def: "A quality which inheres in a continuant." [PATOC:GVG] comment: Relational qualities are qualities that hold between multiple entities. Normal (monadic) qualities such as the shape of a eyeball exist purely as a quality of that eyeball. A relational quality such as sensitivity to light is a quality of that eyeball (and connecting nervous system) as it relates to incoming light waves/particles. synonym: "monadic quality of a continuant" EXACT [] @@ -6447,7 +6543,6 @@ is_a: PATO:0002005 ! concavity id: PATO:0001873 name: cylindrical namespace: quality -alt_id: PATO:0001203 def: "A convex 3-D shape quality inhering in a bearer by virtue of the bearer's exhibiting a consistently-sized round cross section." [PATOC:MAH] subset: cell_quality subset: value_slim @@ -6677,16 +6772,6 @@ is_a: PATO:0000141 ! structure property_value: terms:contributor https://orcid.org/0000-0002-7073-9172 creation_date: 2014-12-12T08:43:17Z -[Term] -id: PATO:0010006 -name: cell morphology -namespace: quality -def: "A quality of a single cell inhering in the bearer by virtue of the bearer's size or shape or structure." [https://orcid.org/0000-0002-7073-9172] -comment: Use this term for morphologies that can *only* inhere in a cell, e.g. morphological qualities inhering in a cell by virtue of the presence, location or shape of one or more cell parts. -is_a: PATO:0000051 ! morphology -property_value: terms:contributor https://orcid.org/0000-0002-7073-9172 -creation_date: 2021-01-23T11:31:53Z - [Term] id: PATO:0015006 name: polymeric @@ -6704,28 +6789,6 @@ def: "A quality inhering in a cell by virtue of the cell having a high nuclear/c comment: A high nuclear/cytolasmic ratio is 70% or higher. synonym: "high N:C ratio" EXACT [] is_a: PATO:0001396 ! cellular quality -created_by: http://orcid.org/0000-0001-5208-3432 - -[Term] -id: PATO:0070006 -name: cortical bipolar morphology -namespace: quality -def: "A cell morphology that inheres in neurons which have two principal dendrites that emerge from the soma and begin to branch some distance from it, have few spines, and branch in narrow fields. This is in contrast to bitufted morphology where branching occurs close to the soma." [doi:10.1016/b978-0-12-369497-3.10004-4, PMID:18568015] -comment: This is specific to cortical bipolar cells and are distinguished from retinal bipolar cell morphology which has an axon and dendrite emerging from opposite ends of the soma. -xref: ILX:0101312 -xref: ilxtr:BipolarPhenotype -xref: nifext:2 -is_a: PATO:0070027 ! bitufted dendrite cell morphology -property_value: terms:contributor https://orcid.org/0000-0001-7258-9596 - -[Term] -id: PATO:0070027 -name: bitufted dendrite cell morphology -namespace: quality -def: "A cell morphology that inheres in neurons with dendrites that are bidirectional, emerging from opposite ends of the soma, with the two arbors extending in radial or tangential directions." [PMID:18568015] -comment: This morphology type is distinct from bitufted cell morphology in that it refers to bitufted dendrite morphology rather than bitufted cell morphology. -is_a: PATO:0010006 ! cell morphology -property_value: terms:contributor https://orcid.org/0000-0001-7258-9596 [Term] id: PATO:0070044 @@ -6733,7 +6796,6 @@ name: anatomical structure quality namespace: quality def: "A quality of continuant that exist at the anatomical level of organisation and anything under it. This includes, but is not limited to, cells , tissues, and components." [] is_a: PATO:0001241 ! physical object quality -created_by: http://orcid.org/0000-0001-7258-9596 [Term] id: PATO:0070045 @@ -6741,7 +6803,6 @@ name: anatomical histological quality namespace: quality def: "A quality inhering in an anotomical structure by virtue of its capacity to be stained by specific histological dyes." [] is_a: PATO:0070044 ! anatomical structure quality -created_by: http://orcid.org/0000-0001-7258-9596 [Term] id: PATO:0070047 @@ -6749,7 +6810,6 @@ name: polychromatophilic namespace: quality def: "An affinity inhering in an anatomical structure by virtue of the bearer exhibiting a molecular interaction for both basic and acid stains under specific pH conditions." [GOC:add] is_a: PATO:0070045 ! anatomical histological quality -created_by: http://orcid.org/0000-0001-7258-9596 [Term] id: PATO:0070060 @@ -6764,11 +6824,11 @@ id: PR:000000001 name: protein namespace: protein def: "An amino acid chain that is produced de novo by ribosome-mediated translation of a genetically-encoded mRNA, and any derivatives thereof." [PRO:DAN, PRO:WCB] -comment: The definition above excludes protein complexes, which some also consider a protein. Those who wish to refer to a class representing both senses of the word are directed to CHEBI:36080. Note that the definition allows for experimentally-manipulated genes, and allows for artifically-produced derivatives that mimic those found naturally. Proteins (in the sense defined here) that descended from a common ancestor can be classified into families and superfamilies composed of products of evolutionarily-related genes. The domain architecture of a protein is described by the order of its constituent domains. Proteins with the same domains in the same order are defined as homeomorphic [PRO:WCB]. +comment: The definition above excludes protein complexes, which some also consider a protein. Those who wish to refer to a class representing both senses of the word are directed to CHEBI:36080. Note that the definition allows for experimentally-manipulated genes, and allows for artifically-produced derivatives that mimic those found naturally. Proteins (in the sense defined here) that descended from a common ancestor can be classified into families and superfamilies composed of products of evolutionarily-related genes. The domain architecture of a protein is described by the order of its constituent domains. Proteins with the same domains in the same order are defined as homeomorphic [PRO:WCB). synonym: "native protein" NARROW [IEDB:BP] synonym: "natural protein" EXACT [PRO:DAN] is_a: PR:000018263 ! amino acid chain -is_a: PR:000050567 ! protein-containing material entity +is_a: PR:000064867 ! protein-containing molecular entity relationship: output_of GO:0006412 ! translation [Term] @@ -7037,7 +7097,6 @@ namespace: protein def: "A protein with core architecture consisting of a signal sequence, followed by 7 Ig-like domains (Pfam:PF00047, Pfam:PF07679, or Pfam:PF07686), a transmembrane region, and a cytoplasmic Protein tyrosine kinase domain." [PRO:WCB] comment: Category=family. xref: PIRSF:PIRSF038502 -is_a: PR:000000001 ! protein [Term] id: PR:000002112 @@ -7159,11 +7218,11 @@ intersection_of: RO:0002160 NCBITaxon:2759 ! only in taxon Eukaryota relationship: RO:0002160 NCBITaxon:2759 ! only in taxon Eukaryota [Term] -id: PR:000050567 -name: protein-containing material entity +id: PR:000064867 +name: protein-containing molecular entity namespace: protein -def: "A material entity that minimally consists of a protein." [PRO:DAN] -comment: Note: This includes single proteins and derivatives thereof (PR:000000001), protein-containing complexes (GO:0032991), and protein aggregates (PR:000050566). +def: "A molecular entity that minimally consists of a protein." [PRO:DAN] +comment: Note: This includes single proteins and derivatives thereof (PR:000000001), protein-containing complexes (GO:0032991), and protein aggregates (PR:000050565). synonym: "protein" NARROW [PRO:DAN] synonym: "protein aggregate" NARROW [PRO:DAN] synonym: "protein complex" NARROW [PRO:DAN] @@ -7317,7 +7376,6 @@ xref: VHOG:0001644 xref: WBbt:0005739 xref: Wikipedia:Head xref: XAO:0003024 -xref: ZFA:0001114 is_a: UBERON:0011676 ! subdivision of organism along main body axis relationship: part_of UBERON:0007811 ! craniocervical region relationship: RO:0002162 NCBITaxon:33213 ! in taxon Bilateria @@ -7341,7 +7399,6 @@ xref: TAO:0005425 xref: UMLS:C0036760 {source="ncithesaurus:Serosa"} xref: Wikipedia:Serous_membrane xref: ZFA:0005425 -is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0000481 ! multi-tissue structure is_a: UBERON:0004120 ! mesoderm-derived structure relationship: has_part UBERON:0001136 ! mesothelium @@ -7377,7 +7434,6 @@ property_value: RO:0002175 NCBITaxon:9606 id: UBERON:0000060 name: anatomical wall namespace: uberon -alt_id: UBERON:0009915 def: "Organ component adjacent to an organ cavity and which consists of a maximal aggregate of organ component layers." [FMA:82482] subset: upper_level synonym: "organ wall" RELATED [FMA:82482] @@ -7577,7 +7633,6 @@ creation_date: 2009-06-18T09:00:04Z id: UBERON:0000075 name: subdivision of skeletal system namespace: uberon -alt_id: UBERON:0010322 def: "Anatomical cluster consisting of the skeletal elements and articular elements that are part of an individual subdivision of the organism." [https://orcid.org/0000-0002-6601-2165, UBERONREF:0000003] subset: non_informative synonym: "skeletal system part" RELATED [] @@ -7842,7 +7897,6 @@ property_value: seeAlso "https://github.com/obophenotype/uberon/issues/533" xsd: id: UBERON:0000122 name: neuron projection bundle namespace: uberon -alt_id: UBERON:0005163 def: "A fasciculated bundle of neuron projections (GO:0043005), largely or completely lacking synapses." [CARO:0001001, FBbt:00005099, FBC:DOS] synonym: "funiculus" EXACT [] synonym: "nerve fiber bundle" EXACT [FBbt:00005099] @@ -7963,7 +8017,7 @@ xref: VHOG:0000224 xref: Wikipedia:Blood xref: XAO:0000124 xref: ZFA:0000007 -is_a: PR:000050567 ! protein-containing material entity +is_a: UBERON:0000061 ! anatomical structure is_a: UBERON:0000179 ! haemolymphatic fluid relationship: has_part CL:0000232 {source="CL:tm"} ! erythrocyte relationship: has_part UBERON:0001969 ! blood plasma @@ -7992,7 +8046,6 @@ creation_date: 2009-04-08T04:38:19Z id: UBERON:0000307 name: blastula namespace: uberon -alt_id: UBERON:0007011 def: "Organism at the blastula stage - an early stage of embryonic development in animals. It is produced by cleavage of a fertilized ovum and consists of a spherical layer of around 128 cells surrounding a central fluid-filled cavity called the blastocoel. The blastula follows the morula and precedes the gastrula in the developmental sequence." [Wikipedia:Blastula] subset: inconsistent_with_fma synonym: "blastosphere" RELATED [Wikipedia:Blastula] @@ -8456,7 +8509,6 @@ xref: VHOG:0000387 xref: Wikipedia:Epithelium xref: XAO:0003045 xref: ZFA:0001486 -is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0000479 ! tissue intersection_of: UBERON:0000479 ! tissue intersection_of: RO:0002473 CL:0000066 ! composed primarily of epithelial cell @@ -8747,7 +8799,6 @@ property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/d/ id: UBERON:0000926 name: mesoderm namespace: uberon -alt_id: UBERON:0003263 def: "The middle germ layer of the embryo, between the endoderm and ectoderm." [Wikipedia:Mesoderm] subset: efo_slim subset: pheno_slim @@ -9109,7 +9160,6 @@ xref: VHOG:0000164 xref: Wikipedia:Cornea xref: XAO:0000180 xref: ZFA:0000640 -is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0010000 ! multicellular anatomical structure is_a: UBERON:0010313 ! neural crest-derived structure relationship: has_part UBERON:0001772 ! corneal epithelium @@ -9351,7 +9401,6 @@ id: UBERON:0001009 name: circulatory system namespace: uberon def: "Organ system that passes nutrients (such as amino acids and electrolytes), gases, hormones, blood cells, etc. to and from cells in the body to help fight diseases and help stabilize body temperature and pH to maintain homeostasis[WP]." [Wikipedia:Circulatory_system] -subset: human_reference_atlas subset: uberon_slim synonym: "systema cardiovasculare" RELATED OMO:0003011 [Wikipedia:Circulatory_system] xref: AAO:0000959 @@ -9371,7 +9420,6 @@ property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/2/ property_value: RO:0002161 NCBITaxon:147099 {source="Wikipedia:Acoelomorpha"} property_value: RO:0002161 NCBITaxon:6073 property_value: RO:0002161 NCBITaxon:6157 -property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001015 @@ -10652,7 +10700,6 @@ property_value: RO:0002175 NCBITaxon:9606 id: UBERON:0001793 name: nerve fiber layer of retina namespace: uberon -alt_id: UBERON:0005888 def: "Layer of the retina formed by expansion of the fibers of the optic nerve." [ISBN:0-914294-08-3, MGI:smb] subset: pheno_slim subset: vertebrate_core @@ -11306,7 +11353,6 @@ xref: MIAA:0000052 xref: NCIT:C13356 xref: UMLS:C0032105 {source="ncithesaurus:Plasma"} xref: Wikipedia:Blood_plasma -is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0000179 ! haemolymphatic fluid intersection_of: UBERON:0000463 ! organism substance intersection_of: has_part GO:0005577 ! fibrinogen complex @@ -11355,7 +11401,6 @@ xref: VHOG:0001250 xref: Wikipedia:Blood_vessel xref: XAO:0001011 xref: ZFA:0005314 -is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0000055 ! vessel is_a: UBERON:0004120 ! mesoderm-derived structure relationship: capable_of_part_of GO:0008015 ! blood circulation @@ -11675,7 +11720,6 @@ relationship: part_of UBERON:0013702 ! body proper id: UBERON:0002104 name: visual system namespace: uberon -alt_id: UBERON:0007036 def: "The sensory system subserving the sense of vision." [NIFSTD:FMAID_7191] subset: pheno_slim subset: uberon_slim @@ -11981,7 +12025,6 @@ property_value: foaf:depiction "https://upload.wikimedia.org/wikipedia/commons/d id: UBERON:0002323 name: coelemic cavity lumen namespace: uberon -alt_id: UBERON:0000169 def: "The cavity within the body of all animals higher than the coelenterates and certain primitive worms, formed by the splitting of the embryonic mesoderm into two layers. In mammals it forms the peritoneal, pleural, and pericardial cavities." [BTO:0001707] comment: EDITOR_NOTE check the FMA placement here; ncit placement of body cavity here probably not correct subset: uberon_slim @@ -12007,7 +12050,6 @@ xref: RETIRED_EHDAA2:0003186 xref: SCTID:361348008 xref: TAO:0001438 xref: UMLS:C0333343 {source="ncithesaurus:Cavity"} -xref: ZFA:0001438 is_a: UBERON:0002553 ! anatomical cavity relationship: RO:0002494 UBERON:0003886 ! transformation of future coelemic cavity lumen relationship: RO:0002572 UBERON:0011997 ! luminal space of coelom @@ -12494,6 +12536,7 @@ xref: TAO:0000279 xref: VHOG:0000559 xref: XAO:0000057 xref: ZFA:0000279 +is_a: UBERON:0000061 ! anatomical structure is_a: UBERON:0006598 ! presumptive structure intersection_of: UBERON:0005423 ! developing anatomical structure intersection_of: RO:0002387 UBERON:0002329 ! has potential to develop into somite @@ -12558,7 +12601,6 @@ property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/6/ id: UBERON:0003071 name: eye primordium namespace: uberon -alt_id: UBERON:0005060 def: "Portion of tissue that is part of the anterior neural keel and will form the optic vesicle[ZFA]. A paired ectodermal placode that becomes invaginated to form the embryonic lens vesicles." [GO:0046619, ZFA:0000570] subset: efo_slim synonym: "eye anlage" RELATED [XAO:0000227] @@ -12749,7 +12791,6 @@ property_value: IAO:0000116 "TODO - add grouping class for the anterior end of t id: UBERON:0003081 name: lateral plate mesoderm namespace: uberon -alt_id: UBERON:0006258 def: "Portion of the middle of the three primary germ layers of the embryo that resides on the periphery of the embryo, is continuous with the extra-embryonic mesoderm, splits into two layers enclosing the intra-embryonic coelom, and gives rise to body wall structures[MP]." [MP:0010117, Wikipedia:Lateral_plate_mesoderm] subset: pheno_slim subset: uberon_slim @@ -13053,7 +13094,6 @@ relationship: part_of UBERON:0001016 ! nervous system id: UBERON:0003842 name: neural tube lumen namespace: uberon -alt_id: UBERON:0005713 def: "An anatomical space that surrounded_by a neural tube." [OBOL:automatic] synonym: "cavity of neural tube" EXACT [https://orcid.org/0000-0002-6601-2165] synonym: "central lumen" RELATED [] @@ -13258,7 +13298,6 @@ intersection_of: RO:0000086 PATO:0002299 ! has quality tubular id: UBERON:0003931 name: diencephalic white matter namespace: uberon -alt_id: UBERON:0023148 def: "White matter that is part of a diencephalon [Automatically generated definition]." [OBOL:automatic] subset: vertebrate_core synonym: "diencephalic tract/commissure" EXACT [ZFA:0000338] @@ -13715,7 +13754,6 @@ xref: WikipediaCategory:Cardiovascular_system xref: XAO:0000100 xref: XAO:0001010 xref: ZFA:0000010 -is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0000467 ! anatomical system intersection_of: UBERON:0000467 ! anatomical system intersection_of: has_part UBERON:0000948 ! heart @@ -13739,7 +13777,6 @@ synonym: "blood vessels" RELATED [TAO:0001079] synonym: "set of blood vessels" EXACT [] xref: TAO:0001079 xref: ZFA:0001079 -is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0002049 ! vasculature intersection_of: UBERON:0002049 ! vasculature intersection_of: RO:0002473 UBERON:0001981 ! composed primarily of blood vessel @@ -13824,7 +13861,6 @@ relationship: part_of UBERON:0002028 ! hindbrain id: UBERON:0004734 name: gastrula namespace: uberon -alt_id: UBERON:0007012 def: "Organism at the gastrula stage." [Wikipedia:Gastrula, Wikipedia:Trilaminar_blastocyst] subset: pheno_slim synonym: "blastocystis trilaminaris" RELATED [https://orcid.org/0000-0002-6601-2165] @@ -14447,7 +14483,6 @@ xref: NCIT:C13191 xref: SCTID:68989006 xref: UMLS:C0004799 {source="ncithesaurus:Basement_Membrane"} xref: Wikipedia:Basement_membrane -is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0005764 {source="FMA"} ! acellular membrane relationship: adjacent_to CL:0000066 ! epithelial cell relationship: has_part GO:0005587 ! collagen type IV trimer @@ -14477,7 +14512,6 @@ def: "Organ with organ cavity, which has as parts a serous membrane and a serous comment: See notes for serous membrane xref: FMA:9689 xref: SCTID:362890006 -is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0000062 ! organ relationship: has_part UBERON:0000042 ! serous membrane relationship: has_part UBERON:0002553 ! anatomical cavity @@ -14898,7 +14932,6 @@ subset: efo_slim xref: EFO:0003709 xref: TAO:0005077 xref: ZFA:0005077 -is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0005423 ! developing anatomical structure relationship: has_part CL:0000115 ! endothelial cell relationship: has_part CL:0000566 ! angioblastic mesenchymal cell @@ -15326,6 +15359,7 @@ xref: NCIT:C12418 xref: SCTID:361355005 xref: UMLS:C0460004 {source="ncithesaurus:Head_and_Neck"} xref: WikipediaCategory:Head_and_neck +xref: ZFA:0001114 is_a: UBERON:0000475 {source="MA"} ! organism subdivision relationship: has_part UBERON:0000033 ! head relationship: has_part UBERON:0006562 ! pharynx @@ -15336,7 +15370,6 @@ relationship: part_of UBERON:0013702 ! body proper id: UBERON:0009142 name: entire embryonic mesenchyme namespace: uberon -alt_id: UBERON:0003313 def: "Sum total of mesenchyme in the embryo." [https://github.com/obophenotype/human-developmental-anatomy-ontology/issues/7] xref: EHDAA2:0001113 xref: EHDAA:177 @@ -15382,6 +15415,7 @@ synonym: "MHB neural plate" EXACT [https://orcid.org/0000-0002-6601-2165] synonym: "midbrain-hindbrain boundary neural plate" EXACT [ZFA:0007044] xref: TAO:0007044 xref: ZFA:0007044 +is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0006598 ! presumptive structure relationship: part_of UBERON:0003075 {source="ZFA"} ! neural plate relationship: RO:0002495 UBERON:0007281 ! immediate transformation of presumptive midbrain hindbrain boundary @@ -15847,6 +15881,7 @@ synonym: "haemocoelom" NARROW [] synonym: "schizocoelom" NARROW [] xref: EHDAA2:0004731 xref: Wikipedia:Coelom +xref: ZFA:0001438 is_a: UBERON:0000481 {source="EHDAA2"} ! multi-tissue structure relationship: RO:0002162 NCBITaxon:33213 ! in taxon Bilateria property_value: IAO:0000116 "EHDAA2 distingsuishes between the lumen, the lining, and the 'coelomic cavity', which despire it's name, is not a space - it is the aggregate of space plus lining." xsd:string @@ -15877,7 +15912,6 @@ synonym: "tunica fibrosa" BROAD [] xref: FMA:58102 xref: SCTID:361318005 xref: Wikipedia:Fibrous_tunic_of_eyeball -is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0004923 {source="FMA"} ! organ component layer is_a: UBERON:0010314 ! structure with developmental contribution from neural crest @@ -16056,7 +16090,6 @@ relationship: part_of UBERON:0000019 ! camera-type eye id: UBERON:0016879 name: future central nervous system namespace: uberon -alt_id: UBERON:3000469 def: "Primordium that develops into the central nervous system." [http://orcid.org/0000-0002-6601-2165] synonym: "future CNS" EXACT [] synonym: "presumptive central nervous system" EXACT [] @@ -16071,7 +16104,6 @@ relationship: RO:0002387 UBERON:0001017 ! has potential to develop into central id: UBERON:0016880 name: future nervous system namespace: uberon -alt_id: UBERON:3000477 def: "Primordium that develops into the nervous system." [http://orcid.org/0000-0002-6601-2165] synonym: "presumptive nervous system" EXACT [AAO:0000477] xref: AAO:0000477 @@ -16444,7 +16476,6 @@ id: RO:0002021 name: occurs across def: "A relationship between a process and a barrier, where the process occurs in a region spanning the barrier. For cellular processes the barrier is typically a membrane. Examples include transport across a membrane and membrane depolarization." [] is_a: RO:0002479 ! has part that occurs in -created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-07-20T17:19:37Z [Typedef] @@ -17303,7 +17334,6 @@ name: causally upstream of or within, negative effect property_value: RO:0004050 RO:0002418 property_value: seeAlso "https://wiki.geneontology.org/Causally_upstream_of_or_within,_negative_effect" xsd:anyURI is_a: causally_upstream_of_or_within ! causally upstream of or within -created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-03-13T23:55:05Z [Typedef] @@ -17311,7 +17341,6 @@ id: RO:0004047 name: causally upstream of or within, positive effect property_value: seeAlso https://wiki.geneontology.org/Causally_upstream_of_or_within,_positive_effect is_a: causally_upstream_of_or_within ! causally upstream of or within -created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-03-13T23:55:19Z [Typedef] @@ -17320,7 +17349,6 @@ name: has small molecule regulator def: "a relation between a process and a continuant, in which the process is regulated by the small molecule continuant" [] is_a: has_participant ! has participant inverse_of: RO:0012004 ! is small molecule regulator of -created_by: https://orcid.org/0000-0003-1813-6857 creation_date: 2020-04-22T20:27:26Z [Typedef] @@ -17328,7 +17356,6 @@ id: RO:0012004 name: is small molecule regulator of def: "a relation between a continuant and a process, in which the continuant is a small molecule that regulates the process" [] is_a: RO:0002596 ! capable of regulating -created_by: https://orcid.org/0000-0003-1813-6857 creation_date: 2020-06-24T13:15:17Z [Typedef] @@ -17338,7 +17365,6 @@ def: "a relation between a continuant and a process, in which the continuant is property_value: seeAlso "https://wiki.geneontology.org/Is_small_molecule_activator_of" xsd:anyURI is_a: RO:0002598 ! capable of positively regulating is_a: RO:0012004 ! is small molecule regulator of -created_by: https://orcid.org/0000-0003-1813-6857 creation_date: 2020-06-24T13:15:26Z [Typedef] @@ -17348,7 +17374,6 @@ def: "A relationship between a neuron and a region, where the neuron has a funct synonym: "has synaptic input or output in" EXACT [] is_a: RO:0002130 ! has synaptic terminal in transitive_over: part_of ! part of -created_by: https://orcid.org/0000-0002-1373-1705 creation_date: 2020-07-17T09:26:52Z [Typedef] @@ -17361,9 +17386,18 @@ synonym: "has sensory terminal location" EXACT [] domain: CL:0000101 ! sensory neuron is_a: RO:0002360 ! has dendrite location transitive_over: part_of ! part of -created_by: https://orcid.org/0000-0002-1373-1705 creation_date: 2020-07-20T12:10:09Z +[Typedef] +id: RO:0015004 +name: has characterizing marker set +def: "A relation that applies between a cell type and a set of markers that can be used to uniquely identify that cell type." [] +synonym: "has marker gene combination" EXACT [] +synonym: "has marker signature set" EXACT [] +property_value: IAO:0000116 "C has_characterizing_marker_set y iff: C is a cell type and y is a collection of genes or proteins whose expression is sufficient to distinguish cell type C from most or all other cell types." xsd:string +property_value: terms:contributor https://orcid.org/0000-0001-7258-9596 +domain: CL:0000000 ! cell + [Typedef] id: RO:0015006 name: different in magnitude relative to @@ -17437,7 +17471,6 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0012003 is_a: has_participant ! has participant -created_by: https://orcid.org/0000-0003-1813-6857 creation_date: 2020-06-08T17:21:33Z [Typedef] @@ -17733,7 +17766,6 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_ontology xref: RO:0004009 is_a: has_input ! has input is_a: has_primary_input_or_output ! has primary input or output -created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-12-13T11:26:56Z [Typedef] @@ -17744,7 +17776,6 @@ def: "p 'has primary input ot output' c iff either (a) p 'has primary input' c o subset: http://purl.obolibrary.org/obo/valid_for_go_ontology xref: RO:0004007 is_a: has_participant ! has participant -created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-12-13T11:26:17Z [Typedef] @@ -17756,7 +17787,6 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_ontology xref: RO:0004008 is_a: has_output ! has output is_a: has_primary_input_or_output ! has primary input or output -created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-12-13T11:26:32Z [Typedef] @@ -17767,7 +17797,6 @@ def: "a relation between a process and a continuant, in which the process is act xref: RO:0012001 is_a: RO:0012000 ! has small molecule regulator inverse_of: RO:0012005 ! is small molecule activator of -created_by: https://orcid.org/0000-0003-1813-6857 creation_date: 2020-04-22T20:28:37Z [Typedef] @@ -18092,7 +18121,6 @@ namespace: external def: "p has anatomical participant c iff p has participant c, and c is an anatomical entity" [] xref: RO:0040036 is_a: has_participant ! has participant -created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-09-26T01:08:58Z [Typedef] @@ -18164,7 +18192,6 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0012008 is_a: results_in_organization_of ! results in organization of -created_by: https://orcid.org/0000-0003-1813-6857 creation_date: 2021-02-26T07:28:29Z [Typedef] @@ -18216,7 +18243,6 @@ name: results in organization of namespace: external def: "p results in organization of c iff p results in the assembly, arrangement of constituent parts, or disassembly of c" [] xref: RO:0002592 -is_a: has_participant ! has participant is_a: results_in_changes_to_anatomical_or_cellular_structure ! results in changes to anatomical or cellular structure [Typedef] diff --git a/subsets/eye_upper_slim.owl b/subsets/eye_upper_slim.owl index 394d31707..8a7eb19b9 100644 --- a/subsets/eye_upper_slim.owl +++ b/subsets/eye_upper_slim.owl @@ -22,8 +22,8 @@ xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#" xmlns:ncbitaxon="http://purl.obolibrary.org/obo/ncbitaxon#"> - - 2024-09-26 + + 2025-01-08 @@ -287,13 +287,18 @@ WHERE { - 2018-03-14T00:03:24Z is negative form of + + + + + + @@ -373,6 +378,14 @@ WHERE { + + + + + + + + @@ -384,6 +397,14 @@ WHERE { + + + + + + + + @@ -1010,12 +1031,6 @@ WHERE { - - - - - - @@ -1034,6 +1049,12 @@ WHERE { + + + + + + @@ -1048,19 +1069,25 @@ WHERE { - + + description + - + + license + - + + title + @@ -1088,26 +1115,12 @@ WHERE { - - - - - - - - - - has_alternative_id - - - - @@ -1123,7 +1136,11 @@ WHERE { + An annotation property that links an ontology entity or a statement to a prefixed identifier or URI. + + database_cross_reference + has cross-reference @@ -1206,12 +1223,6 @@ WHERE { - - - - - - @@ -1682,7 +1693,6 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 A relationship between a process and a barrier, where the process occurs in a region spanning the barrier. For cellular processes the barrier is typically a membrane. Examples include transport across a membrane and membrane depolarization. - 2017-07-20T17:19:37Z occurs across @@ -3970,7 +3980,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different - p results in organization of c iff p results in the assembly, arrangement of constituent parts, or disassembly of c RO:0002592 @@ -4092,7 +4101,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different p 'has primary input ot output' c iff either (a) p 'has primary input' c or (b) p 'has primary output' c. - 2018-12-13T11:26:17Z RO:0004007 external @@ -4110,7 +4118,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different p has primary output c if (a) p has output c and (b) the goal of process is to modify, produce, or transform c. - 2018-12-13T11:26:32Z RO:0004008 external @@ -4138,7 +4145,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different p has primary input c if (a) p has input c and (b) the goal of process is to modify, consume, or transform c. - 2018-12-13T11:26:56Z RO:0004009 external @@ -4165,7 +4171,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different - 2018-03-13T23:55:05Z causally upstream of or within, negative effect https://wiki.geneontology.org/Causally_upstream_of_or_within,_negative_effect @@ -4177,7 +4182,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different - 2018-03-13T23:55:19Z causally upstream of or within, positive effect @@ -4191,7 +4195,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different a relation between a process and a continuant, in which the process is regulated by the small molecule continuant - 2020-04-22T20:27:26Z has small molecule regulator @@ -4204,7 +4207,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different a relation between a process and a continuant, in which the process is activated by the small molecule continuant - 2020-04-22T20:28:37Z RO:0012001 external @@ -4221,7 +4223,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different p acts on population of c iff c' is a collection, has members of type c, and p has participant c - 2020-06-08T17:21:33Z RO:0012003 external @@ -4241,7 +4242,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different a relation between a continuant and a process, in which the continuant is a small molecule that regulates the process - 2020-06-24T13:15:17Z is small molecule regulator of @@ -4254,7 +4254,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different a relation between a continuant and a process, in which the continuant is a small molecule that activates the process - 2020-06-24T13:15:26Z is small molecule activator of https://wiki.geneontology.org/Is_small_molecule_activator_of @@ -4266,7 +4265,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different - 2021-02-26T07:28:29Z RO:0012008 external @@ -4290,7 +4288,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different A relationship between a neuron and a region, where the neuron has a functionally relevant number of input and/or output synapses in that region. - 2020-07-17T09:26:52Z has synaptic input or output in has synaptic IO in region @@ -4308,7 +4305,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different Relation between a sensory neuron and some structure in which it receives sensory input via a sensory dendrite. - 2020-07-20T12:10:09Z has sensory dendrite location has sensory terminal in @@ -4318,6 +4314,20 @@ Each of these 3 primitives can be composed to yield a cross-product of different + + + + + A relation that applies between a cell type and a set of markers that can be used to uniquely identify that cell type. + C has_characterizing_marker_set y iff: C is a cell type and y is a collection of genes or proteins whose expression is sufficient to distinguish cell type C from most or all other cell types. + + has marker gene combination + has marker signature set + has characterizing marker set + + + + @@ -4457,7 +4467,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different p has anatomical participant c iff p has participant c, and c is an anatomical entity - 2018-09-26T01:08:58Z RO:0040036 external @@ -4801,6 +4810,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different XAO:0003012 ZFA:0009000 + + The definition of cell is intended to represent all cells, and thus a cell is defined as a material entity and not an anatomical structure, which implies that it is part of an organism (or the entirety of one). cell @@ -4849,6 +4860,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different Any fibroblast that is derived from the neural crest. fibroblast neural crest derived + + neural crest derived fibroblast @@ -4881,6 +4894,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different ZFA:0009001 neuronal receptor cell (sensu Animalia) + + neuronal receptor cell @@ -4904,6 +4919,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different A cell found in the embryo before the formation of all the gem layers is complete. ZFA:0009002 + + early embryonic cell (metazoa) @@ -4927,6 +4944,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different Cell that is part of the migratory cranial neural crest population. Migratory cranial neural crest cells develop from premigratory cranial neural crest cells and have undergone epithelial to mesenchymal transition and delamination. ZFA:0007091 + + migratory cranial neural crest cell @@ -4956,10 +4975,20 @@ Each of these 3 primitives can be composed to yield a cross-product of different + A non-terminally differentiated cell that develops form the neuroectoderm. Glioblast has the potential to differentiate into various types of glial cells, including astrocytes and oligodendrocytes. ZFA:0009010 + + glioblast + + + + A non-terminally differentiated cell that develops form the neuroectoderm. Glioblast has the potential to differentiate into various types of glial cells, including astrocytes and oligodendrocytes. + PMID:37824650 + Wikipedia:Glioblast + @@ -4986,6 +5015,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different ZFA:0009011 neuroblast + + neuroblast (sensu Vertebrata) @@ -5040,6 +5071,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different animal stem cell + + This term applies to metazoan. For plant stem cells, consider using PO:0004011 ‘initial cell’ or its parent PO:0004010 ‘meristematic cell’. stem cell @@ -5227,6 +5260,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different colony forming unit hematopoietic + + Markers differ between species, and two sets of markers have been described for mice. HSCs are reportedly CD34-positive, CD45-positive, CD48-negative, CD150-positive, CD133-positive, and CD244-negative. hematopoietic stem cell @@ -5278,6 +5313,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different erythroid stem cell + + erythroid progenitor cell @@ -5346,6 +5383,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different multifate stem cell multipotent cell multipotent stem cell + + multi fate stem cell @@ -5381,6 +5420,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different myeloid stem cell pluripotent stem cell (bone marrow) + + This cell type is intended to be compatible with any vertebrate common myeloid progenitor. For mammalian CMP known to be CD34-positive, please use the term 'common myeloid progenitor, CD34-positive' (CL_0001059). common myeloid progenitor @@ -5497,6 +5538,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different megakaryocyte/erythrocyte progenitor megakaryocyte/erythroid progenitor cell + + MEPs are reportedly CD19-negative, CD34-negative, CD45RA-negative, CD110-positive, CD117-positive, and SCA1-negative and reportedly express the transcription factors GATA-1 and NF-E2. megakaryocyte-erythroid progenitor cell @@ -5536,6 +5579,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different MESH:D039901 ZFA:0009024 totipotential stem cell + + totipotent stem cell @@ -5563,6 +5608,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different FMA:84782 blast cell + + define using PATO mulit-potent or oligopotent? non-terminally differentiated cell @@ -5586,6 +5633,9 @@ Each of these 3 primitives can be composed to yield a cross-product of different FMA:70335 VHOG:0001529 ZFA:0009025 + + + myoblast @@ -5614,13 +5664,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - - - - - - + A connective tissue cell which secretes an extracellular matrix rich in collagen and other macromolecules. Flattened and irregular in outline with branching processes; appear fusiform or spindle-shaped. BTO:0000452 @@ -5631,6 +5675,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different ZFA:0009026 + + These cells may be vimentin-positive, fibronectin-positive, fsp1-positive, MMP-1-positive, collagen I-positive, collagen III-positive, and alpha-SMA-negative. fibroblast @@ -5674,6 +5720,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different epitheliocyte + + epithelial cell https://www.swissbiopics.org/api/image/Epithelial_cells.svg @@ -5726,6 +5774,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different ZFA:0009036 + + blood vessel endothelial cell @@ -5752,6 +5802,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different ZFA:0009038 + + columnar/cuboidal epithelial cell @@ -5796,6 +5848,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different CALOHA:TS-1249 ZFA:0009039 + + squamous epithelial cell @@ -5831,6 +5885,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different ZFA:0009040 mesotheliocyte + + Mesothelial cells, which morphologically resemble squamous epithelial cells, express both epithelial markers (cytokeratins) and mesenchymal markers (vimentin), reflecting their mesodermal origin. They feature surface microvilli and apical-basal polarity. Under certain conditions, they can undergo mesothelial-to-mesenchymal transition. These cells also produce extracellular matrix proteins, maintain serosal homeostasis, and facilitate fluid transport. mesothelial cell @@ -5885,6 +5941,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different ZFA:0009044 + + blood cell @@ -5920,6 +5978,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different + + neuron associated cell @@ -5928,7 +5988,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + Most generally any neuron which is not motor or sensory. Interneurons may also refer to neurons whose axons remain within a particular brain region as contrasted with projection neurons which have axons projecting to other brain regions. BTO:0003811 @@ -5936,7 +5996,10 @@ Each of these 3 primitives can be composed to yield a cross-product of different FMA:67313 WBbt:0005113 ZFA:0009051 + CNS interneuron + + interneuron @@ -5991,6 +6054,9 @@ Each of these 3 primitives can be composed to yield a cross-product of different MESH:D011984 WBbt:0005759 ZFA:0009053 + + + sensory neuron @@ -6015,50 +6081,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - - - - - - - - - - - - - - - - - - - - - A type of interneuron that has two neurites, usually an axon and a dendrite, extending from opposite poles of an ovoid cell body. - FMA:67282 - ZFA:0009055 - - - bipolar neuron - - - - - A type of interneuron that has two neurites, usually an axon and a dendrite, extending from opposite poles of an ovoid cell body. - GOC:tfm - ISBN:0444009442 - - - - - ZFA:0009055 - - - - - @@ -6078,6 +6100,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different ZFA:0009065 endotheliocyte + + From FMA: 9.07.2001: Endothelial cell has always been classified as a kind of epithelial cell, specifically a squamous cell but that is not true. First, endothelial cell can either be squamous or cuboidal (e.g. high-endothelial cell) and secondly, it has different embryological derivation (mesodermal) than a true epithelial cell (ectodermal and endodermal). The basis for present classification is the fact that it comprises the outermost layer or lining of anatomical structures (location-based) but a better structural basis for the differentia is the cytoskeleton of the cell. Endothelial cell has vimentin filaments while an epithelial cell has keratin filaments. [Onard]. endothelial cell @@ -6101,34 +6125,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - - - - - - - - - - - - - - - - ZFA:0009067 - CNS neuron (sensu Vertebrata) - - - - - ZFA:0009067 - - - - - @@ -6146,6 +6142,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different + + neuron associated cell (sensu Vertebrata) @@ -6157,7 +6155,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different A non-neuronal cell of the nervous system. They not only provide physical support, but also respond to injury, regulate the ionic and chemical composition of the extracellular milieu. Guide neuronal migration during development, and exchange metabolites with neurons. - This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. Glial cells, also known as neuroglia or simply glia, are non-neuronal cells in the central and peripheral nervous systems that provide support and protection for neurons. They constitute approximately half of the total cells in the human brain and more than half in other parts of the nervous system. Glial cells perform several key functions including, but not limited to, maintaining homeostasis, forming the myelin sheath around the neuron axons, and providing support and nutrition to neurons. These different functions are performed by various glial cell types, including astrocytes, oligodendrocytes, microglia and other specialized types. Astrocytes, for example, are the most abundant glial cells and provide metabolic and nutrient support to neurons, help regulate the extracellular ion and neurotransmitter levels, and play a role in the formation and maintenance of the blood-brain barrier, contributing to the overall homeostasis and functioning of the nervous system. Additionally, astrocytes are involved in synaptic communication and participate in processes such as synaptogenesis and synaptic pruning. @@ -6174,6 +6172,8 @@ Despite their overarching function in the support and protection of neurons, gli neuroglia + + Not all glial cells develop from glioblasts, with microglia developing from the mesoderm instead. See https://github.com/obophenotype/cell-ontology/issues/1571 glial cell @@ -6187,7 +6187,7 @@ Despite their overarching function in the support and protection of neurons, gli - This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. Glial cells, also known as neuroglia or simply glia, are non-neuronal cells in the central and peripheral nervous systems that provide support and protection for neurons. They constitute approximately half of the total cells in the human brain and more than half in other parts of the nervous system. Glial cells perform several key functions including, but not limited to, maintaining homeostasis, forming the myelin sheath around the neuron axons, and providing support and nutrition to neurons. These different functions are performed by various glial cell types, including astrocytes, oligodendrocytes, microglia and other specialized types. Astrocytes, for example, are the most abundant glial cells and provide metabolic and nutrient support to neurons, help regulate the extracellular ion and neurotransmitter levels, and play a role in the formation and maintenance of the blood-brain barrier, contributing to the overall homeostasis and functioning of the nervous system. Additionally, astrocytes are involved in synaptic communication and participate in processes such as synaptogenesis and synaptic pruning. @@ -6233,6 +6233,8 @@ Despite their overarching function in the support and protection of neurons, gli macrogliocyte macroglia + + macroglial cell @@ -6270,6 +6272,8 @@ Despite their overarching function in the support and protection of neurons, gli ZFA:0009075 astrocytic glia + + Astrocytes are reportedly CD68-negative, CD121a-positive, CD184-positive, CD192-positive, CRF-positive, EGFR-positive, GFAP-positive, GLUT1-positive, MBP-negative, and NGFR-positive. astrocyte @@ -6319,6 +6323,8 @@ Despite their overarching function in the support and protection of neurons, gli ZFA:0009079 + + corneal endothelial cell @@ -6348,6 +6354,8 @@ Despite their overarching function in the support and protection of neurons, gli Ectoderm destined to be nervous tissue. ZFA:0009080 neurectoderm cell + + neurectodermal cell @@ -6389,6 +6397,8 @@ Despite their overarching function in the support and protection of neurons, gli mesenchymal stromal cells stem cells, mesenchymal + + Many but not all mesenchymal cells derive from the mesoderm. MSCs are reportedly CD3-negative, CD4-negative, CD5-negative, CD8-negative, CD11a-negative, CD11b-negative, CD14-negative, CD19-negative, CD29-positive, CD31-negative, CD34-negative, CD38-negative, CD40-negative, CD44-positive, CD45-negative, CD49-positive, CD54-positive, CD66b-negative, CD79a-negative, CD80-negative, CD102-positive, CD106-positive, CD117-positive, CD121a-positive, CD121b-positive, CD123-positive, CD124-positive, CD133-negative, CD146-positive, CD166-positive, CD271-positive, B220-negative, Gr1-negative, MHCI-positive, MHCII-negative, SSEA4-negative, sca1-positive, Ter119-negative, and glycophorin A-negative. Cultured MSCs are capable of producing stem cell factor, IL7, IL8, IL11, TGF-beta, cofilin, galectin-1, laminin-receptor 1, cyclophilin A, and MMP-2. mesenchymal stem cell https://github.com/obophenotype/cell-ontology/issues/474 @@ -6476,6 +6486,8 @@ Despite their overarching function in the support and protection of neurons, gli ZFA:0009090 chromatocyte chromatophore + + pigment cell @@ -6527,15 +6539,22 @@ Despite their overarching function in the support and protection of neurons, gli A pigment cell derived from the neural crest. Contains melanin-filled pigment granules, which gives a brown to black appearance. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Melanocytes are specialized cells prevalently found in the skin, but also present in the hair follicles, eyes, inner ear, bones, heart, and brain. Their primary function is the synthesis of melanin, a pigment responsible for coloration of skin, hair, and eyes. The presence and distribution of this pigment play a crucial role in the body's defense mechanism against harmful ultraviolet radiation. +In addition to melanin production, melanocytes also engage in a variety of other biological functions. They play a fundamental role in the immune response, owing to their ability to present antigens to T cells. Furthermore, they contribute to the maintenance of the skin's homeostasis by regulating processes such as extracellular matrix remodeling and cytokine production. A balance in melanocyte function is pivotal, as dysfunctions often result in dermatological disorders. For instance, the loss of melanocytes or reduction in their function may lead to hypopigmentation conditions such as vitiligo, whereas an abnormal increase could result in hyperpigmentation disorders or melanoma, a dangerous type of skin cancer. BTO:0000847 CALOHA:TS-0613 FMA:70545 MESH:D008544 VHOG:0001679 ZFA:0009091 + https://cellxgene.cziscience.com/cellguide/CL_0000148 melanophore + + melanocyte @@ -6545,6 +6564,19 @@ Despite their overarching function in the support and protection of neurons, gli A pigment cell derived from the neural crest. Contains melanin-filled pigment granules, which gives a brown to black appearance. SANBI:mhl + + + + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Melanocytes are specialized cells prevalently found in the skin, but also present in the hair follicles, eyes, inner ear, bones, heart, and brain. Their primary function is the synthesis of melanin, a pigment responsible for coloration of skin, hair, and eyes. The presence and distribution of this pigment play a crucial role in the body's defense mechanism against harmful ultraviolet radiation. +In addition to melanin production, melanocytes also engage in a variety of other biological functions. They play a fundamental role in the immune response, owing to their ability to present antigens to T cells. Furthermore, they contribute to the maintenance of the skin's homeostasis by regulating processes such as extracellular matrix remodeling and cytokine production. A balance in melanocyte function is pivotal, as dysfunctions often result in dermatological disorders. For instance, the loss of melanocytes or reduction in their function may lead to hypopigmentation conditions such as vitiligo, whereas an abnormal increase could result in hyperpigmentation disorders or melanoma, a dangerous type of skin cancer. + DOI:10.1002/med.21754 + DOI:10.1038/nrc.2016.37 + DOI:10.1111/j.1751-1097.2007.00226.x + DOI:10.3390/ijms21249769 + https://www.sciencedirect.com/topics/agricultural-and-biological-sciences/melanocyte + @@ -6559,6 +6591,8 @@ Despite their overarching function in the support and protection of neurons, gli pigment cell + + visual pigment cell @@ -6589,6 +6623,8 @@ Despite their overarching function in the support and protection of neurons, gli BTO:0003659 FMA:86916 + + secretory cell @@ -6607,6 +6643,8 @@ Despite their overarching function in the support and protection of neurons, gli A cell whose primary function is to shorten. + + contractile cell @@ -6641,6 +6679,8 @@ Despite their overarching function in the support and protection of neurons, gli muscle fiber myocyte + + muscle cell https://www.swissbiopics.org/api/image/Muscle_cells.svg @@ -6678,16 +6718,24 @@ Despite their overarching function in the support and protection of neurons, gli A non-striated, elongated, spindle-shaped cell found lining the digestive tract, uterus, and blood vessels. They develop from specialized myoblasts (smooth muscle myoblast). + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Smooth muscle cells are a specialized type of muscle cells that are primarily found within the walls of hollow organs such as the intestine, stomach, bladder, uterus, and blood vessels. These cells are an essential component of the autonomic nervous system controling involuntary movements within the body. +Smooth muscle cells play a vital role in many physiological processes due to their unique functionality. They can contract and relax in a slow, sustained, and controlled manner to help modulate the size and shape of the lumens of the organs they surround. For example, in the digestive system, coordinated contraction and relaxation of smooth muscle cells propels food along the gastrointestinal tract - a process known as peristalsis. In the blood vessels, the smooth muscle cells, by contracting or relaxing, either constrict or dilate the vessels, which in turn, help regulate blood flow and pressure. +On a cellular level, smooth muscle cells possess a single, centrally located nucleus and contain an arranged network of actin and myosin filaments, which are the proteins responsible for muscle contraction. Unlike their counterparts in skeletal or cardiac muscles, these cells lack specific contact points for these filaments, hence the lack of visible striations. Furthermore, the contraction of smooth muscle cells is regulated by hormones and neurotransmitters, such as acetylcholine and norepinephrine, adding an additional layer of complex regulation to these highly specialized cells. non-striated muscle cell BTO:0004576 CALOHA:TS-2159 FMA:14072 ZFA:0009118 + https://cellxgene.cziscience.com/cellguide/CL_0000192 SMCs myocytes, smooth muscle smooth muscle fiber + + smooth muscle cell @@ -6699,6 +6747,20 @@ Despite their overarching function in the support and protection of neurons, gli PMID:9315361 http://en.wikipedia.org/wiki/Smooth_muscle_cell + + + + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Smooth muscle cells are a specialized type of muscle cells that are primarily found within the walls of hollow organs such as the intestine, stomach, bladder, uterus, and blood vessels. These cells are an essential component of the autonomic nervous system controling involuntary movements within the body. +Smooth muscle cells play a vital role in many physiological processes due to their unique functionality. They can contract and relax in a slow, sustained, and controlled manner to help modulate the size and shape of the lumens of the organs they surround. For example, in the digestive system, coordinated contraction and relaxation of smooth muscle cells propels food along the gastrointestinal tract - a process known as peristalsis. In the blood vessels, the smooth muscle cells, by contracting or relaxing, either constrict or dilate the vessels, which in turn, help regulate blood flow and pressure. +On a cellular level, smooth muscle cells possess a single, centrally located nucleus and contain an arranged network of actin and myosin filaments, which are the proteins responsible for muscle contraction. Unlike their counterparts in skeletal or cardiac muscles, these cells lack specific contact points for these filaments, hence the lack of visible striations. Furthermore, the contraction of smooth muscle cells is regulated by hormones and neurotransmitters, such as acetylcholine and norepinephrine, adding an additional layer of complex regulation to these highly specialized cells. + DOI:10.1093/ptj/81.11.1810 + https://training.seer.cancer.gov/anatomy/muscular/types.html + https://www.ncbi.nlm.nih.gov/books/NBK10854/ + https://www.ncbi.nlm.nih.gov/books/NBK526125 + https://www.ncbi.nlm.nih.gov/books/NBK556137/ + @@ -6754,6 +6816,8 @@ Despite their overarching function in the support and protection of neurons, gli A cell that is capable of detection of a stimulus involved in sensory perception. MESH:D011984 receptor cell + + sensory receptor cell @@ -6788,6 +6852,8 @@ Despite their overarching function in the support and protection of neurons, gli FMA:86740 ZFA:0009127 + + photoreceptor cell https://www.swissbiopics.org/api/image/Photoreceptor_cell.svg @@ -6818,6 +6884,8 @@ Despite their overarching function in the support and protection of neurons, gli A cell whose function is determined by the generation or the reception of an electric signal. ZFA:0009128 + + electrically active cell @@ -6842,6 +6910,8 @@ Despite their overarching function in the support and protection of neurons, gli A cell within an epithelial cell sheet whose main function is to act as an internal or external covering for a tissue or an organism. ZFA:0009130 boundary cell + + lining cell @@ -6865,6 +6935,8 @@ Despite their overarching function in the support and protection of neurons, gli A cell whose primary function is to prevent the transport of stuff across compartments. ZFA:0009132 + + barrier cell @@ -6905,6 +6977,8 @@ Despite their overarching function in the support and protection of neurons, gli A cell that moves by its own activities. ZFA:0009136 + + motile cell @@ -6937,6 +7011,9 @@ Despite their overarching function in the support and protection of neurons, gli FMA:72549 ZFA:0009137 ectoderm cell + + + ectodermal cell @@ -6966,11 +7043,18 @@ Despite their overarching function in the support and protection of neurons, gli A cell of the middle germ layer of the embryo. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Mesodermal cells are pluripotent and the most abundant in the human body. They contribute to the development of several structures such as the skeletal muscles, bones, heart and blood vessels, kidneys, gonads, connective tissues, and certain layers of the skin. Hence, the mesoderm is often regarded as an active and diverse layer due to its role in forming many bodily structures. +In embryonic development, these cells are instrumental, contributing to the body's structures through a carefully coordinated sequence of morphogenetic movements. This process forms the complex multicellular architecture of tissues and organs from a simple ball of cells. Without the function of mesodermal cells, the body's integral structures and systems would cease to form correctly, leading to developmental disorders such as axial mesodermal dysplasia complex FMA:72554 ZFA:0009138 + https://cellxgene.cziscience.com/cellguide/CL_0000222 mesoblast mesoderm cell + + mesodermal cell @@ -6979,6 +7063,17 @@ Despite their overarching function in the support and protection of neurons, gli A cell of the middle germ layer of the embryo. MESH:D008648 + + + + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Mesodermal cells are pluripotent and the most abundant in the human body. They contribute to the development of several structures such as the skeletal muscles, bones, heart and blood vessels, kidneys, gonads, connective tissues, and certain layers of the skin. Hence, the mesoderm is often regarded as an active and diverse layer due to its role in forming many bodily structures. +In embryonic development, these cells are instrumental, contributing to the body's structures through a carefully coordinated sequence of morphogenetic movements. This process forms the complex multicellular architecture of tissues and organs from a simple ball of cells. Without the function of mesodermal cells, the body's integral structures and systems would cease to form correctly, leading to developmental disorders such as axial mesodermal dysplasia complex + DOI:10.1016/j.ceb.2019.07.012 + DOI:10.5535/arm.2016.40.1.162 + https://www.sciencedirect.com/topics/biochemistry-genetics-and-molecular-biology/mesoderm + @@ -7003,6 +7098,8 @@ Despite their overarching function in the support and protection of neurons, gli FMA:72555 ZFA:0009139 endoderm cell + + endodermal cell @@ -7086,6 +7183,8 @@ Despite their overarching function in the support and protection of neurons, gli red blood cell + + erythrocyte @@ -7128,7 +7227,8 @@ Despite their overarching function in the support and protection of neurons, gli Any cell that in taxon some Eukaryota. MESH:D005057 - + + eukaryotic cell @@ -7167,6 +7267,8 @@ Despite their overarching function in the support and protection of neurons, gli ZFA:0009154 + + eye photoreceptor cell @@ -7191,6 +7293,8 @@ Despite their overarching function in the support and protection of neurons, gli A cell whose primary function is to provide structural support, to provide strength and physical integrity to the organism. ZFA:0005745 + + structural cell @@ -7214,6 +7318,8 @@ Despite their overarching function in the support and protection of neurons, gli lens cell + + crystallin accumulating cell @@ -7224,6 +7330,8 @@ Despite their overarching function in the support and protection of neurons, gli A cell that is specialised to accumulate a particular substance(s). + + stuff accumulating cell @@ -7259,6 +7367,8 @@ Despite their overarching function in the support and protection of neurons, gli Any cell that is capable of some oxygen transport. ZFA:0009164 + + oxygen accumulating cell @@ -7291,6 +7401,8 @@ Despite their overarching function in the support and protection of neurons, gli A cell derived from the specialized ectoderm flanking each side of the embryonic neural plate, which after the closure of the neural tube, forms masses of cells that migrate out from the dorsal aspect of the neural tube to spread throughout the body. FMA:86667 ZFA:0007086 + + migratory neural crest cell @@ -7314,6 +7426,8 @@ Despite their overarching function in the support and protection of neurons, gli A mesenchymal cell in embryonic development found in a contracting mass and that gives rise to osteoprogenitors. ZFA:0009166 + + mesenchyme condensation cell @@ -7342,6 +7456,8 @@ Despite their overarching function in the support and protection of neurons, gli FMA:70564 ZFA:0009169 spongioblast + + glioblast (sensu Vertebrata) @@ -7373,6 +7489,8 @@ Despite their overarching function in the support and protection of neurons, gli Any animal cell containing pigment granules. ZFA:0009170 + + pigment cell (sensu Vertebrata) @@ -7422,6 +7540,8 @@ Despite their overarching function in the support and protection of neurons, gli A cell of the sclera of the eye. ZFA:0009174 + + scleral cell @@ -7470,6 +7590,8 @@ Despite their overarching function in the support and protection of neurons, gli A structural cell that is part of optic choroid. ZFA:0009175 + + choroidal cell of the eye @@ -7492,6 +7614,8 @@ Despite their overarching function in the support and protection of neurons, gli A cell of the outer layer of a blastula that gives rise to the ectoderm after gastrulation. + + epiblast cell @@ -7532,6 +7656,8 @@ Despite their overarching function in the support and protection of neurons, gli BTO:0000854 EHDAA2:0004546 FMA:72395 + + animal zygote @@ -7549,6 +7675,8 @@ Despite their overarching function in the support and protection of neurons, gli A cell whose function is determined by its response to an electric signal. ZFA:0009190 + + electrically responsive cell @@ -7566,62 +7694,64 @@ Despite their overarching function in the support and protection of neurons, gli - + - - - - - - - - - - - - - - - An interneuron that has its cell body in a central nervous system. - - ZFA:0009191 - - Interneurons are commonly described as being only found in the central nervous system. However, in CL we define 'interneuron' more broadly as any neuron that is neither a motor neuron nor a sensory neuron, regardless of its location, so we need this term to refer strictly to interneurons of the central nervous system. - CNS interneuron + + + A cell that initiates an electrical signal and passes that signal to another cell. + ZFA:0009193 + + + electrically signaling cell - + - An interneuron that has its cell body in a central nervous system. - doi:10.1016/B978-0-12-817424-1.00001-X + A cell that initiates an electrical signal and passes that signal to another cell. + FB:ma - + - ZFA:0009191 + ZFA:0009193 - + - - - A cell that initiates an electrical signal and passes that signal to another cell. - ZFA:0009193 - electrically signaling cell + + + + + + + + + A connective tissue cell of an organ found in the loose connective tissue. + + BTO:0002064 + FMA:83624 + ZFA:0009226 + + + + + + stromal cell - + - A cell that initiates an electrical signal and passes that signal to another cell. - FB:ma + A connective tissue cell of an organ found in the loose connective tissue. + GOC:tfm + MESH:D017154 - + - ZFA:0009193 + ZFA:0009226 @@ -7649,11 +7779,19 @@ Despite their overarching function in the support and protection of neurons, gli A precursor cell destined to differentiate into smooth muscle myocytes. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +A precursor to the smooth muscle cell, the smooth muscle myoblast, is integral to various body systems, including the cardiovascular, gastrointestinal, and respiratory systems. Smooth muscle myoblasts arise from the differentiation of mesenchymal stem cells, a process tightly regulated by specific genetic factors and environmental signals. Their role extends to myogenesis, particularly in the formation of muscular tissue, especially during embryonic development. +Smooth muscle myoblasts possess distinctive cellular characteristics. In contrast to skeletal muscle myoblasts, they do not fuse to create multinucleated fibers. Instead, they differentiate into individual, uninucleated smooth muscle cells. This differentiation unfolds in two distinct phases: proliferation, marked by rapid division to increase cell numbers, and differentiation, involving structural and functional transformation into mature smooth muscle cells. This intricate process is intricately mediated by various signaling molecules and transcription factors. +Functionally, smooth muscle myoblasts and the mature muscle cells they generate play pivotal roles in various physiological processes. Smooth muscle cells orchestrate involuntary muscle responses and are integral to body systems that regulate blood flow, propel food along the digestive tract, and control airflow in the respiratory tract. These diverse functions underscore the significance of smooth muscle myoblasts in the body's growth, maintenance, and overall function. FMA:84798 ZFA:0009235 + https://cellxgene.cziscience.com/cellguide/CL_0000514 myoblast, smooth muscle satellite cell + + smooth muscle myoblast @@ -7663,6 +7801,18 @@ Despite their overarching function in the support and protection of neurons, gli GOC:tfm MESH:D032390 + + + + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +A precursor to the smooth muscle cell, the smooth muscle myoblast, is integral to various body systems, including the cardiovascular, gastrointestinal, and respiratory systems. Smooth muscle myoblasts arise from the differentiation of mesenchymal stem cells, a process tightly regulated by specific genetic factors and environmental signals. Their role extends to myogenesis, particularly in the formation of muscular tissue, especially during embryonic development. +Smooth muscle myoblasts possess distinctive cellular characteristics. In contrast to skeletal muscle myoblasts, they do not fuse to create multinucleated fibers. Instead, they differentiate into individual, uninucleated smooth muscle cells. This differentiation unfolds in two distinct phases: proliferation, marked by rapid division to increase cell numbers, and differentiation, involving structural and functional transformation into mature smooth muscle cells. This intricate process is intricately mediated by various signaling molecules and transcription factors. +Functionally, smooth muscle myoblasts and the mature muscle cells they generate play pivotal roles in various physiological processes. Smooth muscle cells orchestrate involuntary muscle responses and are integral to body systems that regulate blood flow, propel food along the digestive tract, and control airflow in the respiratory tract. These diverse functions underscore the significance of smooth muscle myoblasts in the body's growth, maintenance, and overall function. + DOI:10.1074/jbc.RA118.001739 + https://www.ncbi.nlm.nih.gov/books/NBK544225/ + https://www.sciencedirect.com/topics/medicine-and-dentistry/smooth-muscle + @@ -7687,6 +7837,8 @@ Despite their overarching function in the support and protection of neurons, gli FMA:87653 ZFA:0009238 input neuron + + afferent neuron @@ -7712,6 +7864,8 @@ Despite their overarching function in the support and protection of neurons, gli ZFA:0009241 + + pigmented epithelial cell @@ -7747,6 +7901,8 @@ Despite their overarching function in the support and protection of neurons, gli nerve cell + + These cells are also reportedly CD4-negative and CD200-positive. They are also capable of producing CD40L and IFN-gamma. neuron @@ -7789,6 +7945,8 @@ Despite their overarching function in the support and protection of neurons, gli BTO:0003217 FMA:83377 ZFA:0009249 + + Derived from UBERON:0002342 neural crest. melanoblast @@ -7884,7 +8042,6 @@ Despite their overarching function in the support and protection of neurons, gli - @@ -7987,6 +8144,8 @@ Despite their overarching function in the support and protection of neurons, gli pronormoblast + + proerythroblast @@ -8034,7 +8193,6 @@ Despite their overarching function in the support and protection of neurons, gli - @@ -8060,6 +8218,8 @@ Despite their overarching function in the support and protection of neurons, gli early erythroblast early normoblast prorubricyte + + basophilic erythroblast @@ -8131,7 +8291,6 @@ Despite their overarching function in the support and protection of neurons, gli - @@ -8165,6 +8324,8 @@ Despite their overarching function in the support and protection of neurons, gli polychromatic normoblast polychromatophilic normoblast rubricyte + + polychromatophilic erythroblast @@ -8268,6 +8429,8 @@ Despite their overarching function in the support and protection of neurons, gli late erythoblast orthochromatic normoblast pyknotic eto enrythroblast + + orthochromatic erythroblast @@ -8484,6 +8647,8 @@ Despite their overarching function in the support and protection of neurons, gli promegacaryocyte promegakaryocyte + + Lineage negative is described here as CD2-negative, CD3-negative, CD4-negative, CD5-negative, CD8a-negative, CD14-negative, CD19-negative, CD20-negative, CD56-negative, Ly6g-negative, and Ter119-negative. megakaryocyte progenitor cell @@ -8557,6 +8722,8 @@ Despite their overarching function in the support and protection of neurons, gli megalokaryocyte + + Megakaryocytes are reportedly CD181-positive and CD182-positive. megakaryocyte @@ -8642,7 +8809,6 @@ Despite their overarching function in the support and protection of neurons, gli - @@ -8734,6 +8900,8 @@ Despite their overarching function in the support and protection of neurons, gli ZFA:0009252 + + reticulocyte @@ -8793,6 +8961,8 @@ Despite their overarching function in the support and protection of neurons, gli ACs + + amacrine cell @@ -8852,7 +9022,6 @@ Despite their overarching function in the support and protection of neurons, gli - @@ -8881,6 +9050,8 @@ Despite their overarching function in the support and protection of neurons, gli ZFA:0009258 angioblast chondroplast + + These cells are reportedly CD31-positive, CD34-positive, CD144-positive, CD309-positive, and TAL1-positive. angioblastic mesenchymal cell @@ -8925,6 +9096,8 @@ Despite their overarching function in the support and protection of neurons, gli ZFA:0009262 cone + + retinal cone cell @@ -8980,6 +9153,8 @@ Despite their overarching function in the support and protection of neurons, gli epithelial cell of cornea + + corneal epithelial cell @@ -9022,6 +9197,8 @@ Despite their overarching function in the support and protection of neurons, gli ZFA:0009275 rod + + retinal rod cell @@ -9066,6 +9243,8 @@ Despite their overarching function in the support and protection of neurons, gli Müller cell + + Mueller cell @@ -9120,6 +9299,8 @@ Despite their overarching function in the support and protection of neurons, gli WBbt:0006829 ZFA:0009290 + + glutamatergic neuron @@ -9169,6 +9350,8 @@ Despite their overarching function in the support and protection of neurons, gli A non-terminally differentiated cell that is capable of developing into a muscle cell. ZFA:0009291 + + muscle precursor cell @@ -9200,6 +9383,8 @@ Despite their overarching function in the support and protection of neurons, gli ZFA:0009292 forebrain radial glial cell + + Unlike that of mammals, the brain of adult teleost fish exhibits an intense and widespread neurogenic activity as a result of the persistence of radial glial cells acting as neural progenitors throughout life. radial glial cell @@ -9245,6 +9430,8 @@ radial glial cells acting as neural progenitors throughout life. neuroepithelial cell BTO:0004301 FMA:70557 + + The term "neuroepithelial cell" is used to describe both this cell type and sensory epithelial cell (CL:0000098). neurecto-epithelial cell @@ -9282,6 +9469,8 @@ radial glial cells acting as neural progenitors throughout life. CALOHA:TS-2086 MESH:D053687 ZFA:0009307 + + somatic stem cell @@ -9302,7 +9491,7 @@ radial glial cells acting as neural progenitors throughout life. - + @@ -9321,6 +9510,8 @@ radial glial cells acting as neural progenitors throughout life. RGCs + + retinal ganglion cell @@ -9373,6 +9564,8 @@ radial glial cells acting as neural progenitors throughout life. HCs + + retina horizontal cell @@ -9412,7 +9605,7 @@ radial glial cells acting as neural progenitors throughout life. - + @@ -9420,7 +9613,6 @@ radial glial cells acting as neural progenitors throughout life. - @@ -9454,6 +9646,8 @@ radial glial cells acting as neural progenitors throughout life. BPs + + retinal bipolar neuron @@ -9523,6 +9717,8 @@ radial glial cells acting as neural progenitors throughout life. MESH:D022423 ZFA:0009324 + + myeloid cell @@ -9558,6 +9754,8 @@ radial glial cells acting as neural progenitors throughout life. ZFA:0009325 erythropoietic cell + + Note that in FMA erythropoietic cells are types of nucleated erythrocytes and thus don't include erythrocytes. erythroid lineage cell @@ -9745,6 +9943,8 @@ radial glial cells acting as neural progenitors throughout life. normoblast + + erythroblast @@ -9842,7 +10042,6 @@ radial glial cells acting as neural progenitors throughout life. - @@ -9949,6 +10148,8 @@ radial glial cells acting as neural progenitors throughout life. hemopoietic progenitor cell + + Markers differ between mouse and human. hematopoietic multipotent progenitor cell @@ -10000,6 +10201,8 @@ radial glial cells acting as neural progenitors throughout life. FMA:70339 ZFA:0009356 + + Note that this is a class of cell types, not an identified single cell type. myeloid lineage restricted progenitor cell @@ -10041,6 +10244,8 @@ radial glial cells acting as neural progenitors throughout life. haemopoietic cell hemopoietic cell + + hematopoietic cell @@ -10092,6 +10297,8 @@ radial glial cells acting as neural progenitors throughout life. 2010-01-06T03:43:20Z + + hematopoietic lineage restricted progenitor cell @@ -10136,6 +10343,8 @@ radial glial cells acting as neural progenitors throughout life. 2010-01-06T03:43:27Z + + This cell type is intended to be compatible with any vertebrate hematopoietic oligopotent progenitor cell. For mammalian hematopoietic oligopotent progenitor cells known to be lineage-negative, please use the term 'hematopoietic oligopotent progenitor cell' (CL_0001060). hematopoietic oligopotent progenitor cell @@ -10176,6 +10385,8 @@ radial glial cells acting as neural progenitors throughout life. 2010-06-29T03:38:22Z FMA:69074 ZFA:0009385 + + ecto-epithelial cell @@ -10221,6 +10432,8 @@ radial glial cells acting as neural progenitors throughout life. FMA:69076 ZFA:0009388 epithelial mesenchymal cell + + meso-epithelial cell @@ -10245,13 +10458,21 @@ radial glial cells acting as neural progenitors throughout life. An endothelial cell of the vascular tree, which includes blood vessels and lymphatic vessels. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Endothelial cells of the vascular tree, commonly referred to as vascular endothelial cells, line the entire circulatory system, from the heart to the smallest capillaries. These cells have a unique, flattened shape, and are tightly bound together, forming a thin layer known as the endothelium. The endothelium is responsible for maintaining the interior surface of blood vessels, and plays a critical role in ensuring the smooth flow of blood. +Vascular endothelial cells act as a semi-permeable membrane, controlling the passage of materials and the transit of white blood cells into and out of the bloodstream. These cells are also involved in blood coagulation. When a blood vessel is damaged, endothelial cells promote clotting to prevent excessive bleeding and facilitate wound healing. Other functions include regulation of blood pressure and blood volume by releasing vasodilators and vasoconstrictors to either widen or constrict blood vessels, accordingly. +Furthermore, the endothelial cells are crucial in the formation of new blood vessels, a process known as angiogenesis. This is particularly important in wound healing and the growth of new tissues during development or after injury. In the context of diseases such as cancer, angiogenesis helps facilitate tumor growth by providing nutrients and oxygen. 2010-08-24T02:06:40Z BTO:0001854 CALOHA:TS-1106 FMA:67755 + https://cellxgene.cziscience.com/cellguide/CL_0002139 vascular endothelial cell cubodial endothelial cell of vascular tree + + These cells are reportedly CD31-positive, CD34-positive, CD144-positive, TAL1-positive. endothelial cell of vascular tree @@ -10263,6 +10484,19 @@ radial glial cells acting as neural progenitors throughout life. GOC:tfm PMID:12768659 + + + + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Endothelial cells of the vascular tree, commonly referred to as vascular endothelial cells, line the entire circulatory system, from the heart to the smallest capillaries. These cells have a unique, flattened shape, and are tightly bound together, forming a thin layer known as the endothelium. The endothelium is responsible for maintaining the interior surface of blood vessels, and plays a critical role in ensuring the smooth flow of blood. +Vascular endothelial cells act as a semi-permeable membrane, controlling the passage of materials and the transit of white blood cells into and out of the bloodstream. These cells are also involved in blood coagulation. When a blood vessel is damaged, endothelial cells promote clotting to prevent excessive bleeding and facilitate wound healing. Other functions include regulation of blood pressure and blood volume by releasing vasodilators and vasoconstrictors to either widen or constrict blood vessels, accordingly. +Furthermore, the endothelial cells are crucial in the formation of new blood vessels, a process known as angiogenesis. This is particularly important in wound healing and the growth of new tissues during development or after injury. In the context of diseases such as cancer, angiogenesis helps facilitate tumor growth by providing nutrients and oxygen. + DOI:10.1038/s41569-022-00770-1 + DOI:10.1186/s12872-015-0124-z + DOI:10.3389/fphys.2022.863265/full + https://www.sciencedirect.com/topics/medicine-and-dentistry/vascular-endothelial-cell + @@ -10274,6 +10508,8 @@ radial glial cells acting as neural progenitors throughout life. 2010-08-26T08:31:08Z FMA:70556 + + general ecto-epithelial cell @@ -10301,6 +10537,8 @@ radial glial cells acting as neural progenitors throughout life. 2010-09-07T10:38:03Z FMA:70950 + + vertebrate lens cell @@ -10338,6 +10576,8 @@ radial glial cells acting as neural progenitors throughout life. 2010-09-07T03:32:33Z FMA:67513 + + nucleate cell @@ -10362,7 +10602,7 @@ radial glial cells acting as neural progenitors throughout life. A cell that is part of pigmented ciliary epithelium. This cell type uptakes sodium and chloride ions from stromal interstitium and passes the ions to non-pigmented ciliary epithelial cells via gap junctions. - This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. Pigmented ciliary epithelial cells, which are a type of pigment cell, have a crucial function within the eye's ciliary body. The ciliary body, located behind the iris, is one of the eye’s most vital structures and consists of two types of epithelial cells: the pigmented and the non-pigmented ciliary epithelial cells. The pigmented ciliary epithelial cells form the outer layer of the ciliary body and exhibit a black or brown pigmentation due to the melanin they contain. One key function of pigmented ciliary epithelial cells is to aid in the formation of aqueous humor, an intraocular fluid that nourishes the cornea and lens, and maintains intraocular pressure which is essential for the eye’s shape and light refraction. These cells facilitate this function in conjunction with the non-pigmented ciliary epithelial cells. Together, the pigmented and non-pigmented ciliary epithelial cells form a bilayer epithelium that allows the secretion of aqueous humor through a bi-directional fluid transport mechanism. @@ -10373,6 +10613,8 @@ Pigmented ciliary epithelial cells also contribute to the blood-aqueous barrier, PE cell + + In a consensus model of unidirectional secretion, aqueous humour is formed by transferring solute, principally NaCl, from stroma to posterior chamber, with water passively following the osmotic gradient. Unidirectional secretion comprises three sequential steps. First, NaCl is transferred from the stromal interstitium into the pigmented ciliary epithelial (PE) cells. Second, solute passes from the PE into the non-pigmented ciliary epithelial (NPE) cells through gap junctions. Finally, NPE cells release Na+ and Cl− into the aqueous humour. pigmented ciliary epithelial cell @@ -10386,7 +10628,7 @@ Pigmented ciliary epithelial cells also contribute to the blood-aqueous barrier, - This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. Pigmented ciliary epithelial cells, which are a type of pigment cell, have a crucial function within the eye's ciliary body. The ciliary body, located behind the iris, is one of the eye’s most vital structures and consists of two types of epithelial cells: the pigmented and the non-pigmented ciliary epithelial cells. The pigmented ciliary epithelial cells form the outer layer of the ciliary body and exhibit a black or brown pigmentation due to the melanin they contain. One key function of pigmented ciliary epithelial cells is to aid in the formation of aqueous humor, an intraocular fluid that nourishes the cornea and lens, and maintains intraocular pressure which is essential for the eye’s shape and light refraction. These cells facilitate this function in conjunction with the non-pigmented ciliary epithelial cells. Together, the pigmented and non-pigmented ciliary epithelial cells form a bilayer epithelium that allows the secretion of aqueous humor through a bi-directional fluid transport mechanism. @@ -10428,6 +10670,8 @@ Pigmented ciliary epithelial cells also contribute to the blood-aqueous barrier, nonpigmented ciliary epithelial cell + + In a consensus model of unidirectional secretion, aqueous humour is formed by transferring solute, principally NaCl, from stroma to posterior chamber, with water passively following the osmotic gradient. Unidirectional secretion comprises three sequential steps. First, NaCl is transferred from the stromal interstitium into the pigmented ciliary epithelial (PE) cells. Second, solute passes from the PE into the non-pigmented ciliary epithelial (NPE) cells through gap junctions. Finally, NPE cells release Na+ and Cl− into the aqueous humour. non-pigmented ciliary epithelial cell @@ -10487,6 +10731,8 @@ Pigmented ciliary epithelial cells also contribute to the blood-aqueous barrier, CALOHA:TS-2040 FMA:70333 + + neural cell @@ -10528,6 +10774,8 @@ Pigmented ciliary epithelial cells also contribute to the blood-aqueous barrier, MESH:D003239 ZFA:0009392 + + connective tissue cell @@ -10552,11 +10800,19 @@ Pigmented ciliary epithelial cells also contribute to the blood-aqueous barrier, A cell of the embryo. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Embryonic cells in metazoans, which include all multicellular animals, are biological units in their earliest developmental stages from conception until the organism is fully formed. +They are derived from a fertilized egg, which undergoes a series of cell divisions to produce a multicellular organism. During the early phases of embryonic development, these cells exhibit pluripotency, meaning they possess the potential to differentiate into a diverse array of specialized cell types that constitute different body tissues and structures. +The balance between cell proliferation and differentiation in embryonic cells is crucial for successful development. When cells continue to divide without differentiating, overgrowth may occur leading to conditions such as teratomas (tumors of embryonic cells). Conversely, if cell differentiation proceeds at the expense of cell proliferation, developmental anomalies could occur regarding size or mass of the organism or its parts. 2010-09-15T03:39:21Z CALOHA:TS-0263 FMA:82840 WBbt:0007028 ZFA:0007089 + https://cellxgene.cziscience.com/cellguide/CL_0002321 + + embryonic cell (metazoa) @@ -10565,6 +10821,18 @@ Pigmented ciliary epithelial cells also contribute to the blood-aqueous barrier, A cell of the embryo. FMA:0618947256 + + + + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Embryonic cells in metazoans, which include all multicellular animals, are biological units in their earliest developmental stages from conception until the organism is fully formed. +They are derived from a fertilized egg, which undergoes a series of cell divisions to produce a multicellular organism. During the early phases of embryonic development, these cells exhibit pluripotency, meaning they possess the potential to differentiate into a diverse array of specialized cell types that constitute different body tissues and structures. +The balance between cell proliferation and differentiation in embryonic cells is crucial for successful development. When cells continue to divide without differentiating, overgrowth may occur leading to conditions such as teratomas (tumors of embryonic cells). Conversely, if cell differentiation proceeds at the expense of cell proliferation, developmental anomalies could occur regarding size or mass of the organism or its parts. + DOI:10.1002/iub.1404 + DOI:10.1093/molehr/gan048 + https://www.ncbi.nlm.nih.gov/books/NBK9906/ + @@ -10603,6 +10871,8 @@ Pigmented ciliary epithelial cells also contribute to the blood-aqueous barrier, corneal keratocyte + + keratocyte @@ -10642,6 +10912,8 @@ Pigmented ciliary epithelial cells also contribute to the blood-aqueous barrier, 2010-12-03T03:25:32Z + + retinal melanocyte @@ -10683,6 +10955,8 @@ Pigmented ciliary epithelial cells also contribute to the blood-aqueous barrier, FMA:83808 FMA:84791 heart cell + + From Onard of the FMA: Cardiac muscle cell or cardiac myocyte is a striated muscle cell. Cardiocyte on the other hand is any cell in the heart which includes cells other than muscle cells (e.g. endothelial cell of endocardium). Unless there is a consensus among anatomists that cardiocytes refer only to muscle cells, we will treat them as a general class of cells in the heart. cardiocyte @@ -10721,7 +10995,10 @@ Pigmented ciliary epithelial cells also contribute to the blood-aqueous barrier, 2011-03-01T05:28:52Z + + + iris pigment epithelial cell @@ -10765,7 +11042,7 @@ Pigmented ciliary epithelial cells also contribute to the blood-aqueous barrier, A blood vessel endothelial cell that is part of the retina. - This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. Retinal blood vessel endothelial cells constitute the innermost lining of the blood vessels found in the retina, the light-sensitive layer of tissue at the back of the eye. The primary role of these cells revolves around their location within the retinal vascular system, forming the structure of the blood-retinal barrier, a subset of the larger blood-ocular barrier system. The endothelial cells are particularly involved in the growth of new retinal blood vessels from pre-existing ones (angiogenesis); this is critical in managing the amount of oxygen and essential nutrients delivered to the ocular tissues. They are crucial for maintaining homeostasis in the retinal environment by controlling the exchange of molecules between the blood and the retina. Furthermore, they mediate immune cell trafficking, supporting the immune privilege of the eye by preventing the unrestricted infiltration of inflammatory cells into the retina, thus maintaining ocular health and normal vision. @@ -10774,6 +11051,8 @@ The malfunction or dysfunction of retinal blood vessel endothelial cells is impl https://cellxgene.cziscience.com/cellguide/CL_0002585 + + retinal blood vessel endothelial cell @@ -10792,7 +11071,7 @@ The malfunction or dysfunction of retinal blood vessel endothelial cells is impl - This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. Retinal blood vessel endothelial cells constitute the innermost lining of the blood vessels found in the retina, the light-sensitive layer of tissue at the back of the eye. The primary role of these cells revolves around their location within the retinal vascular system, forming the structure of the blood-retinal barrier, a subset of the larger blood-ocular barrier system. The endothelial cells are particularly involved in the growth of new retinal blood vessels from pre-existing ones (angiogenesis); this is critical in managing the amount of oxygen and essential nutrients delivered to the ocular tissues. They are crucial for maintaining homeostasis in the retinal environment by controlling the exchange of molecules between the blood and the retina. Furthermore, they mediate immune cell trafficking, supporting the immune privilege of the eye by preventing the unrestricted infiltration of inflammatory cells into the retina, thus maintaining ocular health and normal vision. @@ -10837,7 +11116,7 @@ The malfunction or dysfunction of retinal blood vessel endothelial cells is impl An epithelial cell of the retinal pigmented epithelium. - This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. Retinal pigment epithelial (RPE) cells form a single layer of cells at the back of the eye sandwiched between the neurosensory retina and the choroid, playing a significant role in maintaining vision health. These pigment-laden cells are highly specialized and perform an array of metabolic and transport functions essential for the maintenance of the photoreceptor cells (rods and cones) in the retina. The pigmentation of RPE cells actively aids in the absorption of excess light and the prevention of light scattering, thus enhancing the eye's optical properties. The retinal pigment epithelium forms a key part of the blood/retina barrier. The cells have long sheet-like microvilli on their apical membrane that project into the light-sensitive outer segments of the photoreceptors, forming a close structural interaction. The basolateral membrane of the RPE interacts with the underlying Bruch’s membrane, which separates the RPE cells from fenestrated endothelium of the choriocapillaris. @@ -10849,6 +11128,8 @@ Beyond this, RPE cells take part in the phagocytosis process, where they digest https://cellxgene.cziscience.com/cellguide/CL_0002586 + + retinal pigment epithelial cell @@ -10861,7 +11142,7 @@ Beyond this, RPE cells take part in the phagocytosis process, where they digest - This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. Retinal pigment epithelial (RPE) cells form a single layer of cells at the back of the eye sandwiched between the neurosensory retina and the choroid, playing a significant role in maintaining vision health. These pigment-laden cells are highly specialized and perform an array of metabolic and transport functions essential for the maintenance of the photoreceptor cells (rods and cones) in the retina. The pigmentation of RPE cells actively aids in the absorption of excess light and the prevention of light scattering, thus enhancing the eye's optical properties. The retinal pigment epithelium forms a key part of the blood/retina barrier. The cells have long sheet-like microvilli on their apical membrane that project into the light-sensitive outer segments of the photoreceptors, forming a close structural interaction. The basolateral membrane of the RPE interacts with the underlying Bruch’s membrane, which separates the RPE cells from fenestrated endothelium of the choriocapillaris. @@ -10888,6 +11169,9 @@ Beyond this, RPE cells take part in the phagocytosis process, where they digest A multi-fate stem cell that can give rise to different retinal cell types including rod and cone cells. 2011-08-16T02:38:01Z + + + retinal progenitor cell @@ -10915,7 +11199,7 @@ Beyond this, RPE cells take part in the phagocytosis process, where they digest - + @@ -10924,13 +11208,15 @@ Beyond this, RPE cells take part in the phagocytosis process, where they digest A CNS interneuron located in the spinal cord. ZFA:0000778 + + Is_a interneuron, part_of UBERON:0002240. spinal cord interneuron - + true @@ -10968,6 +11254,8 @@ Beyond this, RPE cells take part in the phagocytosis process, where they digest 2012-06-27T08:27:35Z ZFA:0007084 + + premigratory neural crest cell @@ -10990,6 +11278,8 @@ Beyond this, RPE cells take part in the phagocytosis process, where they digest Any muscle cell in which the fibers are not organised into sarcomeres. + + non-striated muscle cell @@ -11007,6 +11297,8 @@ Beyond this, RPE cells take part in the phagocytosis process, where they digest Any hematopoietic cell that is a precursor of some other hematopoietic cell type. + + hematopoietic precursor cell @@ -11041,6 +11333,8 @@ Beyond this, RPE cells take part in the phagocytosis process, where they digest A muscle cell that is part of some visceral muscle. FBbt:00005070 + + visceral muscle cell @@ -11079,6 +11373,8 @@ Beyond this, RPE cells take part in the phagocytosis process, where they digest mesenchyme cell + + mesenchymal cell @@ -11109,6 +11405,8 @@ Beyond this, RPE cells take part in the phagocytosis process, where they digest Any neuron that is capable of part of some visual perception. 2017-07-09T19:12:36Z + + visual system neuron @@ -11144,6 +11442,8 @@ Beyond this, RPE cells take part in the phagocytosis process, where they digest Any cell in the retina, the innermost layer or coating at the back of the eyeball, which is sensitive to light and in which the optic nerve terminates. PMID:10702418 + + retinal cell @@ -11171,19 +11471,21 @@ Beyond this, RPE cells take part in the phagocytosis process, where they digest - + Any photoreceptor cell that is part of some camera-type eye. camera type eye photoreceptor cell + + camera-type eye photoreceptor cell - + - + https://github.com/obophenotype/cell-ontology/issues/2245 @@ -11201,6 +11503,8 @@ Beyond this, RPE cells take part in the phagocytosis process, where they digest A zygote in a plant or an animal. MESH:D015053 + + zygote @@ -11213,13 +11517,15 @@ Beyond this, RPE cells take part in the phagocytosis process, where they digest A cell of the neural crest. Neural crest cells are multipotent. Premigratory neural crest cells are found at the neural plate boarder, some of which will undergo ectomesynchymal transition and delamination to form migratory neural crest cells. - This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. Neural crest cells are a group of transient and highly migratory cells that originate from the neuroectoderm during the early stages of embryonic development. They are multipotent cells with an exceptional degree of plasticity, capable of differentiating into various somatic cell types and therefore play a fundamental role in the formation of various organs and tissues, making them critical contributors to the developing embryo. After the initiation of neurulation (the formation of the neural tube) neural crest cells start to undergo epithelial-to-mesenchymal transition and delaminate and migrate from the dorsal neural tube to several regions throughout the embryo. They differentiate into a range of diverse cell types, such as neurons and glial cells of the peripheral nervous system, including sensory and autonomic neurons. They also contribute to the formation of adrenal glands, pigment cells in the skin (melanocytes), cardiac structures, including parts of the heart septum and major arteries, as well as bones and cartilage of the face and skull. Disorders or aberrations in the development or migration of the neural crest cells can lead to serious congenital malformations, such as neurocristopathies, including Hirschsprung disease, neuroblastoma, and neurofibromatosis. https://cellxgene.cziscience.com/cellguide/CL_0011012 + + neural crest cell @@ -11232,7 +11538,7 @@ Disorders or aberrations in the development or migration of the neural crest cel - This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. Neural crest cells are a group of transient and highly migratory cells that originate from the neuroectoderm during the early stages of embryonic development. They are multipotent cells with an exceptional degree of plasticity, capable of differentiating into various somatic cell types and therefore play a fundamental role in the formation of various organs and tissues, making them critical contributors to the developing embryo. After the initiation of neurulation (the formation of the neural tube) neural crest cells start to undergo epithelial-to-mesenchymal transition and delaminate and migrate from the dorsal neural tube to several regions throughout the embryo. They differentiate into a range of diverse cell types, such as neurons and glial cells of the peripheral nervous system, including sensory and autonomic neurons. They also contribute to the formation of adrenal glands, pigment cells in the skin (melanocytes), cardiac structures, including parts of the heart septum and major arteries, as well as bones and cartilage of the face and skull. @@ -11270,6 +11576,8 @@ Disorders or aberrations in the development or migration of the neural crest cel A precursor cell that has a tendency to differentiate into a specific type of cell. They are descendants of stem cells, only they are more constrained in their differentiation potential or capacity for self-renewal, and are often more limited in both senses. + + progenitor cell @@ -11297,6 +11605,8 @@ Disorders or aberrations in the development or migration of the neural crest cel carries information from the inner plexiform layer and the outer plexiform layer. + + Need to MIREOT retinal inner nuclear layer (part of) interplexiform cell @@ -11335,6 +11645,8 @@ plexiform layer. A cell that, by division or terminal differentiation, can give rise to other cell types. + + Work is needed on GO 'cell differentiation' before it is clear whether the equivalent class definition 'native cell' that capable_of some 'cell differentiation' works. Also, may want to consider merging this with non-terminally differentiated cell. precursor cell @@ -11479,6 +11791,8 @@ plexiform layer. epithelial cell of conjunctiva + + conjunctival epithelial cell @@ -11524,10 +11838,18 @@ plexiform layer. A smooth muscle cell that is part of the ciliary body. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Ciliary muscle cells are specialized contractile cells that constitute the ciliary muscle, a component of the eye in vertebrates. These cells form a ring around the iris, the eye's colored part. Ciliary muscle cells fall into the category of smooth muscle cells, characterized by their lack of the striations typical of skeletal and cardiac muscle cells. Their shape is elongated and pointed at both ends, and they occur in multi-nucleated syncytia where many cells share the same cytoplasm. +Ciliary muscle cells primarily control the eye's accommodation, adjusting the thickness and curvature of the lens to fine-tune the focus of light on the retina. When ciliary muscle cells contract, tension on the zonular fibers holding the lens in place is reduced, allowing the lens to become thicker and increase its refractive power. Conversely, when the ciliary muscle cells relax, the tension on the zonular fibers increases, causing the lens to become flatter and decrease its refractive power. This adjustment facilitates clear vision at different distances, ranging from near to far objects. +Additionally, ciliary muscle cells play a role in draining the eye's aqueous humor, which is the clear fluid that fills the anterior chamber of the eye between the cornea and the lens. By controlling the shape of the surrounding trabecular meshwork through muscle contractions and relaxations, ciliary muscle cells indirectly regulate intraocular pressure, a factor critical for preventing ocular conditions like glaucoma. FMA:70610 + https://cellxgene.cziscience.com/cellguide/CL_1000443 smooth muscle cell of ciliary body + + ciliary muscle cell @@ -11542,6 +11864,19 @@ plexiform layer. A smooth muscle cell that is part of the ciliary body. GOC:tfm + + + + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Ciliary muscle cells are specialized contractile cells that constitute the ciliary muscle, a component of the eye in vertebrates. These cells form a ring around the iris, the eye's colored part. Ciliary muscle cells fall into the category of smooth muscle cells, characterized by their lack of the striations typical of skeletal and cardiac muscle cells. Their shape is elongated and pointed at both ends, and they occur in multi-nucleated syncytia where many cells share the same cytoplasm. +Ciliary muscle cells primarily control the eye's accommodation, adjusting the thickness and curvature of the lens to fine-tune the focus of light on the retina. When ciliary muscle cells contract, tension on the zonular fibers holding the lens in place is reduced, allowing the lens to become thicker and increase its refractive power. Conversely, when the ciliary muscle cells relax, the tension on the zonular fibers increases, causing the lens to become flatter and decrease its refractive power. This adjustment facilitates clear vision at different distances, ranging from near to far objects. +Additionally, ciliary muscle cells play a role in draining the eye's aqueous humor, which is the clear fluid that fills the anterior chamber of the eye between the cornea and the lens. By controlling the shape of the surrounding trabecular meshwork through muscle contractions and relaxations, ciliary muscle cells indirectly regulate intraocular pressure, a factor critical for preventing ocular conditions like glaucoma. + DOI:10.1016/S1350-9462(98)00011-1 + DOI:10.1038/srep31171 + DOI:10.1111/j.1444-0938.2008.00260.x + https://www.sciencedirect.com/topics/medicine-and-dentistry/ciliary-muscle + @@ -11576,6 +11911,8 @@ plexiform layer. 2014-06-25T01:17:43Z CL:2000029 + + central nervous system neuron @@ -11602,6 +11939,8 @@ plexiform layer. retinal stem cell + + retinoblast @@ -11645,7 +11984,10 @@ plexiform layer. 2023-03-02T14:38:32Z retinal astroglia + + + In response to elevated intraocular pressure, a retinal astrocyte may modulate extracellular matrix remodeling. In the human retina, a retinal astrocyte is GFAP-positive, SOD3-positive and GYPC-positive. retinal astrocyte @@ -11707,7 +12049,6 @@ plexiform layer. Progression through the phases of the mitotic cell cycle, the most common eukaryotic cell cycle, which canonically comprises four successive phases called G1, S, G2, and M and includes replication of the genome and the subsequent segregation of chromosomes into daughter cells. In some variant cell cycles nuclear replication or nuclear division may not be followed by cell division, or G1 and G2 phases may be absent. - GO:0007067 Wikipedia:Mitosis biological_process mitosis @@ -11778,9 +12119,6 @@ plexiform layer. The ordered and organized complex of DNA, protein, and sometimes RNA, that forms the chromosome. https://github.com/geneontology/go-ontology/issues/28301 - GO:0000789 - GO:0000790 - GO:0005717 NIF_Subcellular:sao1615953555 cytoplasmic chromatin nuclear chromatin @@ -11806,8 +12144,6 @@ plexiform layer. A compact and highly condensed form of chromatin that is refractory to transcription. https://github.com/geneontology/go-ontology/issues/22355 - GO:0005720 - GO:0035328 NIF_Subcellular:sao581845896 Wikipedia:Heterochromatin transcriptionally inactive chromatin @@ -12143,7 +12479,6 @@ plexiform layer. The formation of a tube from the flat layer of ectodermal cells known as the neural plate. This will give rise to the central nervous system. - GO:0001679 Wikipedia:Neurulation neural tube morphogenesis neurulation @@ -12440,7 +12775,6 @@ plexiform layer. A location, relative to cellular compartments and structures, occupied by a macromolecular machine. There are three types of cellular components described in the gene ontology: (1) the cellular anatomical entity where a gene product carries out a molecular function (e.g., plasma membrane, cytoskeleton) or membrane-enclosed compartments (e.g., mitochondrion); (2) virion components, where viral proteins act, and (3) the stable macromolecular complexes of which gene product are parts (e.g., the clathrin complex). https://github.com/geneontology/go-ontology/issues/17729 - GO:0008372 NIF_Subcellular:sao1337158144 cell or subcellular entity cellular component @@ -12538,32 +12872,32 @@ plexiform layer. - - + + A protein complex consisting of three collagen chains assembled into a left-handed triple helix. These trimers typically assemble into higher order structures. Wikipedia:Collagen cellular_component GO:0005581 collagen trimer - + - + - + PMID:12382326 - + PMID:12382326 @@ -12606,8 +12940,6 @@ plexiform layer. A collagen-containing extracellular matrix consisting of a thin layer of dense material found in various animal tissues interposed between the cells and the adjacent connective tissue. It consists of the basal lamina plus an associated layer of reticulin fibers. - GO:0005605 - GO:0008003 Wikipedia:Basement_membrane cellular_component basal lamina @@ -12873,7 +13205,12 @@ plexiform layer. - + + + + + + @@ -12881,7 +13218,6 @@ plexiform layer. An intracellular organelle, about 200 A in diameter, consisting of RNA and protein. It is the site of protein biosynthesis resulting from translation of messenger RNA (mRNA). It consists of two subunits, one large and one small, each containing only protein and RNA. Both the ribosome and its subunits are characterized by their sedimentation coefficients, expressed in Svedberg units (symbol: S). Hence, the prokaryotic ribosome (70S) comprises a large (50S) subunit and a small (30S) subunit, while the eukaryotic ribosome (80S) comprises a large (60S) subunit and a small (40S) subunit. Two sites on the ribosomal large subunit are involved in translation, namely the aminoacyl site (A site) and peptidyl site (P site). Ribosomes from prokaryotes, eukaryotes, mitochondria, and chloroplasts have characteristically distinct ribosomal proteins. - GO:0033279 NIF_Subcellular:sao1429207766 Wikipedia:Ribosome free ribosome @@ -12934,8 +13270,6 @@ plexiform layer. The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins. - GO:0005887 - GO:0005904 juxtamembrane NIF_Subcellular:sao1663586795 Wikipedia:Cell_membrane @@ -13051,9 +13385,6 @@ plexiform layer. The cellular metabolic process in which a protein is formed, using the sequence of a mature mRNA or circRNA molecule to specify the sequence of amino acids in a polypeptide chain. Translation is mediated by the ribosome, and begins with the formation of a ternary complex between aminoacylated initiator methionine tRNA, GTP, and initiation factor 2, which subsequently associates with the small subunit of the ribosome and an mRNA or circRNA. Translation ends with the release of a polypeptide chain from the ribosome. - GO:0006416 - GO:0006453 - GO:0043037 Wikipedia:Translation_(genetics) protein anabolism protein biosynthesis @@ -13086,7 +13417,7 @@ plexiform layer. - + @@ -13100,8 +13431,6 @@ plexiform layer. The process preceding formation of the peptide bond between the first two amino acids of a protein. This includes the formation of a complex of the ribosome, mRNA or circRNA, and an initiation complex that contains the first aminoacyl-tRNA. - GO:0006440 - GO:0006454 biopolymerisation biopolymerization protein synthesis initiation @@ -13131,8 +13460,6 @@ plexiform layer. The successive addition of amino acid residues to a nascent polypeptide chain during protein biosynthesis. - GO:0006442 - GO:0006455 protein synthesis elongation translation elongation biological_process @@ -13160,8 +13487,6 @@ plexiform layer. The process resulting in the release of a polypeptide chain from the ribosome, usually in response to a termination codon (UAA, UAG, or UGA in the universal genetic code). - GO:0006443 - GO:0006456 protein synthesis termination translation termination translational complex disassembly @@ -13185,11 +13510,7 @@ plexiform layer. The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter or a transporter complex, a pore or a motor protein. https://github.com/geneontology/go-ontology/issues/20292 - jl 2012-12-13T16:25:32Z - GO:0015457 - GO:0015460 - GO:0044765 biological_process single-organism transport GO:0006810 @@ -13276,7 +13597,6 @@ plexiform layer. The directed movement of amino acids, organic acids containing one or more amino substituents, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. - GO:0006866 biological_process GO:0006865 @@ -13323,8 +13643,6 @@ plexiform layer. A programmed cell death process which begins when a cell receives an internal (e.g. DNA damage) or external signal (e.g. an extracellular death ligand), and proceeds through a series of biochemical events (signaling pathway phase) which trigger an execution phase. The execution phase is the last step of an apoptotic process, and is typically characterized by rounding-up of the cell, retraction of pseudopodes, reduction of cellular volume (pyknosis), chromatin condensation, nuclear fragmentation (karyorrhexis), plasma membrane blebbing and fragmentation of the cell into apoptotic bodies. When the execution phase is completed, the cell has died. - GO:0006917 - GO:0008632 cell suicide cellular suicide Wikipedia:Apoptosis @@ -13467,9 +13785,7 @@ plexiform layer. A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of an organelle within a cell. An organelle is an organized structure of distinctive morphology and function. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton. Excludes the plasma membrane. https://github.com/geneontology/go-ontology/issues/27189 - jl 2013-12-19T15:25:51Z - GO:1902589 organelle organisation single organism organelle organization biological_process @@ -13602,11 +13918,6 @@ plexiform layer. The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell. - GO:0023014 - GO:0023015 - GO:0023016 - GO:0023033 - GO:0023045 Wikipedia:Signal_transduction signaling cascade signalling cascade @@ -13738,7 +14049,6 @@ plexiform layer. The regulated release of neurotransmitter from the presynapse into the synaptic cleft via calcium-regulated exocytosis during synaptic transmission. - GO:0010554 neurotransmitter release neurotransmitter secretory pathway biological_process @@ -14076,7 +14386,6 @@ plexiform layer. The flow of blood through the body of an animal, enabling the transport of nutrients to the tissues and the removal of waste products. - GO:0070261 biological_process hemolymph circulation GO:0008015 @@ -14136,11 +14445,7 @@ plexiform layer. A biological process is the execution of a genetically-encoded biological module or program. It consists of all the steps required to achieve the specific biological objective of the module. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence. https://github.com/geneontology/go-ontology/issues/24968 - jl 2012-09-19T15:05:24Z - GO:0000004 - GO:0007582 - GO:0044699 Wikipedia:Biological_process biological process physiological process @@ -14170,21 +14475,15 @@ plexiform layer. - + - The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation. + A cellular process consisting of the biochemical pathways by which a living organism transforms chemical substances. This includes including anabolism (biosynthetic process) and catabolism (catabolic process). Metabolic processes includes the transformation of small molecules, as well macromolecular processes such as DNA repair and replication, protein synthesis and degradation. https://github.com/geneontology/go-ontology/issues/26424 - jl + https://github.com/geneontology/go-ontology/issues/28932 2012-10-17T15:46:40Z - GO:0044236 - GO:0044710 Wikipedia:Metabolism metabolism - metabolic process resulting in cell growth - metabolism resulting in cell growth - multicellular organism metabolic process biological_process - single-organism metabolic process GO:0008152 @@ -14199,7 +14498,7 @@ plexiform layer. - The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation. + A cellular process consisting of the biochemical pathways by which a living organism transforms chemical substances. This includes including anabolism (biosynthetic process) and catabolism (catabolic process). Metabolic processes includes the transformation of small molecules, as well macromolecular processes such as DNA repair and replication, protein synthesis and degradation. GOC:go_curators ISBN:0198547684 @@ -14235,11 +14534,9 @@ plexiform layer. - The chemical reactions and pathways resulting in the formation of substances; typically the energy-requiring part of metabolism in which simpler substances are transformed into more complex ones. - jl + A cellular process consisting of the biochemical pathways by which a living organism synthesizes chemical substances. This typically represents the energy-requiring part of metabolism in which simpler substances are transformed into more complex ones. + https://github.com/geneontology/go-ontology/issues/28932 2012-10-17T15:52:18Z - GO:0044274 - GO:0044711 formation Wikipedia:Anabolism anabolism @@ -14258,7 +14555,7 @@ plexiform layer. - The chemical reactions and pathways resulting in the formation of substances; typically the energy-requiring part of metabolism in which simpler substances are transformed into more complex ones. + A cellular process consisting of the biochemical pathways by which a living organism synthesizes chemical substances. This typically represents the energy-requiring part of metabolism in which simpler substances are transformed into more complex ones. GOC:curators ISBN:0198547684 @@ -14268,13 +14565,12 @@ plexiform layer. + - The chemical reactions and pathways resulting in the formation of a macromolecule, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass. https://github.com/geneontology/go-ontology/issues/15249 https://github.com/geneontology/go-ontology/issues/25418 https://github.com/geneontology/go-ontology/issues/27189 - GO:0043284 biopolymer biosynthetic process macromolecule anabolism macromolecule biosynthesis @@ -14525,7 +14821,6 @@ plexiform layer. The process whose specific outcome is the progression of an embryo from its formation until the end of its embryonic life stage. The end of the embryonic stage is organism-specific. For example, for mammals, the process would begin with zygote formation and end with birth. For insects, the process would begin at zygote formation and end with larval hatching. For plant zygotic embryos, this would be from zygote formation to the end of seed dormancy. For plant vegetative embryos, this would be from the initial determination of the cell or group of cells to form an embryo until the point when the embryo becomes independent of the parent plant. - GO:0009795 embryogenesis and morphogenesis Wikipedia:Embryogenesis embryogenesis @@ -14666,11 +14961,7 @@ plexiform layer. Any process that is carried out at the cellular level, but not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level. - jl 2012-12-11T16:56:55Z - GO:0008151 - GO:0044763 - GO:0050875 cell physiology cellular physiological process cell growth and/or maintenance @@ -14739,7 +15030,6 @@ plexiform layer. A process which begins when a cell receives an internal or external signal and activates a series of biochemical events (signaling pathway). The process ends with the death of the cell. https://github.com/geneontology/go-ontology/issues/24835 - GO:0016244 regulated cell death Wikipedia:Programmed_cell_death caspase-independent cell death @@ -14853,9 +15143,6 @@ plexiform layer. A lipid bilayer along with all the proteins and protein complexes embedded in it and attached to it. 2014-03-06T11:37:54Z - GO:0016021 - GO:0098589 - GO:0098805 Wikipedia:Biological_membrane Wikipedia:Transmembrane_protein integral component of membrane @@ -14914,8 +15201,6 @@ plexiform layer. A process that results in the assembly, arrangement of constituent parts, or disassembly of a cellular component. - GO:0044235 - GO:0071842 cell organisation cellular component organisation at cellular level cellular component organisation in other organism @@ -15159,9 +15444,6 @@ plexiform layer. The chemical reactions and pathways involving a protein. Includes protein modification. https://github.com/geneontology/go-ontology/issues/23112 https://github.com/geneontology/go-ontology/issues/27189 - GO:0006411 - GO:0044267 - GO:0044268 Wikipedia:Protein_metabolism cellular protein metabolic process cellular protein metabolism @@ -15304,7 +15586,6 @@ plexiform layer. A cellular process that results in the breakdown of a cellular component. https://github.com/geneontology/go-ontology/issues/27189 - GO:0071845 cell structure disassembly cellular component disassembly at cellular level biological_process @@ -15389,7 +15670,6 @@ plexiform layer. The aggregation, arrangement and bonding together of a cellular component. - GO:0071844 cell structure assembly cellular component assembly at cellular level biological_process @@ -15492,10 +15772,7 @@ plexiform layer. The entirety of a process in which information is transmitted within a biological system. This process begins with an active signal and ends when a cellular response has been triggered. - jl 2010-02-16T09:30:50Z - GO:0023046 - GO:0044700 biological signaling signaling process signalling @@ -15949,7 +16226,6 @@ plexiform layer. The progressive compaction of dispersed interphase chromatin into threadlike chromosomes prior to mitotic or meiotic nuclear division, or during apoptosis, in eukaryotic cells. - GO:0000068 DNA condensation eukaryotic chromosome condensation nuclear chromosome condensation @@ -16126,7 +16402,6 @@ plexiform layer. A structure lying external to one or more cells, which provides structural support, biochemical or biomechanical cues for cells or tissues. - GO:0005578 NIF_Subcellular:nlx_subcell_20090513 Wikipedia:Extracellular_matrix proteinaceous extracellular matrix @@ -16177,7 +16452,6 @@ plexiform layer. A vesicle found in the cytoplasm of a cell. - GO:0016023 NIF_Subcellular:sao180601769 cellular_component cytoplasmic membrane bounded vesicle @@ -16253,7 +16527,6 @@ plexiform layer. Any small, fluid-filled, spherical organelle enclosed by membrane. - GO:0031988 NIF_Subcellular:sao221389602 Wikipedia:Vesicle_(biology) cellular_component @@ -16382,10 +16655,7 @@ plexiform layer. - jl 2012-09-19T16:07:47Z - GO:0044707 - GO:0050874 organismal physiological process biological_process single-multicellular organism process @@ -16412,9 +16682,7 @@ plexiform layer. A biological process whose specific outcome is the progression of an integrated living unit: an anatomical structure (which may be a subcellular structure, cell, tissue, or organ), or organism over time from an initial condition to a later condition. - jl 2012-12-19T12:21:31Z - GO:0044767 development biological_process single-organism developmental process @@ -16478,9 +16746,6 @@ plexiform layer. The disaggregation of a protein-containing macromolecular complex into its constituent components. https://github.com/geneontology/go-ontology/issues/22580 - GO:0034623 - GO:0043241 - GO:0043624 protein complex disassembly biological_process cellular macromolecule complex disassembly @@ -16502,10 +16767,14 @@ plexiform layer. - + + + + + + A stable assembly of two or more macromolecules, i.e. proteins, nucleic acids, carbohydrates or lipids, in which at least one component is a protein and the constituent parts function together. - GO:0043234 macromolecular complex macromolecule complex protein containing complex @@ -16589,7 +16858,6 @@ plexiform layer. A process in which a monoatomic ion is transported across a membrane. Monatomic ions (also called simple ions) are ions consisting of exactly one atom. - GO:0099131 ion transmembrane transport ion membrane transport transmembrane ion transport @@ -16785,7 +17053,6 @@ plexiform layer. The region of a neuron that includes the cell body (cell soma) and dendrite(s), but excludes the axon. - bf 2014-07-24T10:06:19Z cellular_component GO:0036477 @@ -16924,9 +17191,6 @@ plexiform layer. Any biological process involved in the maintenance of an internal steady state. - GO:0032844 - GO:0032845 - GO:0032846 homeostasis activation of homeostatic process inhibition of homeostatic process @@ -17118,9 +17382,6 @@ plexiform layer. The chemical reactions and pathways involving macromolecules, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass. https://github.com/geneontology/go-ontology/issues/26424 - GO:0034960 - GO:0043283 - GO:0044259 biopolymer metabolic process macromolecule metabolism organismal macromolecule metabolism @@ -17275,14 +17536,17 @@ plexiform layer. Organized structure of distinctive morphology and function, not bounded by a lipid bilayer membrane. Includes ribosomes, the cytoskeleton and chromosomes. https://github.com/geneontology/go-ontology/issues/21881 https://github.com/geneontology/go-ontology/issues/28153 + https://github.com/geneontology/go-ontology/issues/29106 NIF_Subcellular:sao1456184038 + membrane-less organelle + non-membrane-bounded organelle non-membrane-enclosed organelle cellular_component biological condensate GO:0043228 - non-membrane-bounded organelle + membraneless organelle @@ -17418,11 +17682,13 @@ plexiform layer. Organized structure of distinctive morphology and function, not bounded by a lipid bilayer membrane and occurring within the cell. Includes ribosomes, the cytoskeleton and chromosomes. + https://github.com/geneontology/go-ontology/issues/29106 + intracellular non-membrane-bounded organelle intracellular non-membrane-enclosed organelle cellular_component GO:0043232 - intracellular non-membrane-bounded organelle + intracellular membraneless organelle @@ -17528,11 +17794,7 @@ plexiform layer. Any process in which macromolecules aggregate, disaggregate, or are modified, resulting in the formation, disassembly, or alteration of a protein complex. https://github.com/geneontology/go-ontology/issues/22580 - mah 2010-09-08T10:01:42Z - GO:0034600 - GO:0034621 - GO:0071822 protein complex subunit organisation protein complex subunit organization biological_process @@ -17637,7 +17899,6 @@ plexiform layer. A process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of a cellular component. Includes biosynthesis of constituent macromolecules, and those macromolecular modifications that are involved in synthesis or assembly of the cellular component. https://github.com/geneontology/go-ontology/issues/27194 - GO:0071843 cellular component biogenesis at cellular level biological_process GO:0044085 @@ -17666,7 +17927,6 @@ plexiform layer. A ribonucleoprotein complex that contains aminoacylated initiator methionine tRNA, GTP, and initiation factor 2 (either eIF2 in eukaryotes, or IF2 in prokaryotes). In prokaryotes, fMet-tRNA (initiator) is used rather than Met-tRNA (initiator). - jl 2009-10-22T02:38:55Z translation initiation (ternary) complex Met-tRNA/eIF2.GTP ternary complex @@ -17683,35 +17943,6 @@ plexiform layer. - - - - - - The chemical reactions and pathways by which individual cells transform chemical substances. - cellular metabolism - biological_process - intermediary metabolism - GO:0044237 - - This term should not be used for direct annotation. It should be possible to make a more specific annotation to one of the children of this term. - cellular metabolic process - - - - - The chemical reactions and pathways by which individual cells transform chemical substances. - GOC:go_curators - - - - - intermediary metabolism - GOC:mah - - - - @@ -17738,32 +17969,6 @@ plexiform layer. - - - - - - The chemical reactions and pathways resulting in the formation of substances, carried out by individual cells. - https://github.com/geneontology/go-ontology/issues/27052 - cellular anabolism - cellular biosynthesis - cellular formation - cellular synthesis - biological_process - GO:0044249 - - This term should not be used for direct annotation. It should be possible to make a more specific annotation to one of the children of this term. - cellular biosynthetic process - - - - - The chemical reactions and pathways resulting in the formation of substances, carried out by individual cells. - GOC:jl - - - - @@ -17776,7 +17981,6 @@ plexiform layer. The portion of a cell bearing surface projections such as axons, dendrites, cilia, or flagella that includes the nucleus, but excludes all cell projections. - jl 2010-02-05T10:37:16Z FBbt:00005107 FMA:67301 @@ -18074,7 +18278,6 @@ plexiform layer. The process in which anatomical structures are generated and organized during the embryonic phase. The embryonic phase begins with zygote formation. The end of the embryonic phase is organism-specific. For example, it would be at birth for mammals, larval hatching for insects and seed dormancy in plants. - GO:0048828 embryonic anatomical structure morphogenesis biological_process GO:0048598 @@ -18443,7 +18646,6 @@ plexiform layer. Any process that modulates the frequency, rate or extent of a biological process. Biological processes are regulated by many means; examples include the control of gene expression, protein modification or interaction with a protein or substrate molecule. - GO:0050791 regulation of physiological process biological_process GO:0050789 @@ -18484,7 +18686,6 @@ plexiform layer. Any process that modulates the frequency, rate or extent of a cellular process, any of those that are carried out at the cellular level, but are not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level. - GO:0051244 regulation of cellular physiological process biological_process GO:0050794 @@ -18562,7 +18763,6 @@ plexiform layer. Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus. The process begins with detection of the stimulus and ends with a change in state or activity or the cell or organism. - GO:0051869 physiological response to stimulus biological_process GO:0050896 @@ -18738,9 +18938,7 @@ plexiform layer. Any process in which a cell, a substance, or a cellular entity, such as a protein complex or organelle, is transported, tethered to or otherwise maintained in a specific location. In the case of substances, localization may also be achieved via selective degradation. https://github.com/geneontology/go-ontology/issues/27052 - jl 2013-12-18T13:51:04Z - GO:1902578 establishment and maintenance of localization establishment and maintenance of position localisation @@ -18870,9 +19068,6 @@ plexiform layer. A process that is carried out at the cellular level that results in the assembly, arrangement of constituent parts, or disassembly of chromosomes, structures composed of a very long molecule of DNA and associated proteins that carries hereditary information. This term covers covalent modifications at the molecular level as well as spatial relationships among the major components of a chromosome. https://github.com/geneontology/go-ontology/issues/22811 https://github.com/geneontology/go-ontology/issues/4585 - GO:0006323 - GO:0007001 - GO:0051277 DNA condensation chromosome organisation DNA packaging @@ -18961,9 +19156,7 @@ plexiform layer. A cellular localization process whereby a substance or cellular entity, such as a protein complex or organelle, is transported to, and/or maintained in, a specific location within a cell including the localization of substances or cellular entities to the cell membrane. https://github.com/geneontology/go-ontology/issues/27189 - jl 2013-12-18T14:04:32Z - GO:1902580 cellular localisation establishment and maintenance of cellular localization establishment and maintenance of localization in cell or cell membrane @@ -19147,9 +19340,7 @@ plexiform layer. The process in which a solute is transported across a lipid bilayer, from one side of a membrane to the other. - tb 2015-10-21T13:22:47Z - GO:0090662 membrane transport ATP hydrolysis coupled transmembrane transport biological_process @@ -19348,7 +19539,6 @@ plexiform layer. The process in which the anatomical structures of a tube are generated and organized from an epithelium. Epithelial tubes transport gases, liquids and cells from one site to another and form the basic structure of many organs and tissues, with tube shape and organization varying from the single-celled excretory organ in Caenorhabditis elegans to the branching trees of the mammalian kidney and insect tracheal system. - dph 2009-04-28T09:33:36Z biological_process GO:0060562 @@ -19369,7 +19559,6 @@ plexiform layer. The process in which the anatomical structures of a branched epithelium are generated and organized. - dph 2010-05-25T09:05:34Z biological_process GO:0061138 @@ -19397,7 +19586,6 @@ plexiform layer. The controlled release of glutamate by a cell, in which the glutamate acts as a neurotransmitter. - dph 2013-06-21T16:14:47Z biological_process GO:0061535 @@ -19429,7 +19617,6 @@ plexiform layer. An extracellular matrix consisting mainly of proteins (especially collagen) and glycosaminoglycans (mostly as proteoglycans) that provides not only essential physical scaffolding for the cellular constituents but can also initiate crucial biochemical and biomechanical cues required for tissue morphogenesis, differentiation and homeostasis. The components are secreted by cells in the vicinity and form a sheet underlying or overlying cells such as endothelial and epithelial cells. - dph 2018-04-13T12:47:21Z cellular_component GO:0062023 @@ -19470,9 +19657,6 @@ plexiform layer. The aggregation, arrangement and bonding together of a set of macromolecules to form a protein-containing complex. https://github.com/geneontology/go-ontology/issues/22580 - GO:0006461 - GO:0034622 - GO:0043623 cellular protein complex assembly biological_process cellular macromolecule complex assembly @@ -19686,7 +19870,6 @@ plexiform layer. The aggregation, arrangement and bonding together of a set of components to form an organelle. An organelle is an organized structure of distinctive morphology and function. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton. Excludes the plasma membrane. - mah 2009-09-15T03:00:51Z biological_process GO:0070925 @@ -19725,7 +19908,6 @@ plexiform layer. Any process in which macromolecules aggregate, disaggregate, or are modified, resulting in the formation, disassembly, or alteration of a ribonucleoprotein complex. https://github.com/geneontology/go-ontology/issues/25143 - mah 2010-09-08T10:10:35Z RNA-protein complex subunit organization protein-RNA complex subunit organization @@ -19768,9 +19950,7 @@ plexiform layer. A process that results in the biosynthesis of constituent macromolecules, assembly, arrangement of constituent parts, or disassembly of a cellular component. https://github.com/geneontology/go-ontology/issues/27189 - mah 2010-09-10T01:39:16Z - GO:0071841 cellular component organisation or biogenesis cellular component organisation or biogenesis at cellular level cellular component organization or biogenesis at cellular level @@ -19808,7 +19988,6 @@ plexiform layer. The broad region around and including the plasma membrane of a cell, encompassing the cell cortex (inside the cell), the plasma membrane, and any external encapsulating structures. - mah 2010-10-04T01:51:47Z cellular_component GO:0071944 @@ -19835,7 +20014,6 @@ plexiform layer. An supramolecular fiber that consists of an insoluble core of polymerized tropoelastin monomers and a surrounding mantle of microfibrils. Elastic fibers provide elasticity and recoiling to tissues and organs, and maintain structural integrity against mechanical strain. - mah 2010-10-11T11:44:57Z elastic fibre elastin fiber @@ -19895,7 +20073,6 @@ plexiform layer. The aggregation, arrangement and bonding together of a set of components to form an extracellular vesicular exosome, a membrane-bounded vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Exosomes are defined by their size, which generally ranges from 30 nm to 100 nm. - mah 2010-10-18T03:44:18Z extracellular vesicular exosome assembly biological_process @@ -19949,7 +20126,6 @@ plexiform layer. The developmental process pertaining to the initial formation of an epithelial tube. https://github.com/geneontology/go-ontology/issues/22302 - mah 2010-02-26T02:15:40Z biological_process GO:0072175 @@ -19975,9 +20151,7 @@ plexiform layer. The series of molecular signals which triggers the apoptotic death of a cell. The pathway starts with reception of a signal, and ends when the execution phase of apoptosis is triggered. - pr 2011-11-23T09:30:23Z - GO:0008624 apoptotic signalling pathway induction of apoptosis by extracellular signals biological_process @@ -20017,7 +20191,6 @@ plexiform layer. A stage of the apoptotic process that starts with the controlled breakdown of the cell through the action of effector caspases or other effector molecules (e.g. cathepsins, calpains etc.). Key steps of the execution phase are rounding-up of the cell, retraction of pseudopodes, reduction of cellular volume (pyknosis), chromatin condensation, nuclear fragmentation (karyorrhexis), plasma membrane blebbing and fragmentation of the cell into apoptotic bodies. When the execution phase is completed, the cell has died. - pr 2011-11-23T09:45:24Z execution phase of apoptotic process apoptosis @@ -20052,7 +20225,6 @@ plexiform layer. The entire complement of dendrites for a neuron, consisting of each primary dendrite and all its branches. - pr 2012-12-17T12:31:49Z NIF_Subcellular:sao172297168 cellular_component @@ -20087,7 +20259,6 @@ plexiform layer. Any vesicle that is part of the intracellular region. - pr 2016-03-29T17:39:45Z cellular_component GO:0097708 @@ -20107,7 +20278,6 @@ plexiform layer. The assembly and secretion of an extracellular exosome, a membrane-bounded vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. - pr 2016-10-03T14:35:25Z exosome assembly or secretion exosome biogenesis @@ -20152,7 +20322,6 @@ plexiform layer. A membrane that is a (regional) part of the plasma membrane. - dos 2014-03-06T11:55:32Z region of plasma membrane cellular_component @@ -20209,7 +20378,6 @@ plexiform layer. - @@ -20528,7 +20696,6 @@ plexiform layer. A polymer consisting of an indefinite number of protein or protein complex subunits that have polymerised to form a fiber-shaped structure. - GO:0043205 cellular_component fibril GO:0099512 @@ -20724,21 +20891,22 @@ plexiform layer. - A part of a cellular organism that is either an immaterial entity or a material entity with granularity above the level of a protein complex but below that of an anatomical system. Or, a substance produced by a cellular organism with granularity above the level of a protein complex. + A part of a cellular organism consisting of a material entity with granularity above the level of a protein complex but below that of an anatomical system. Note that cellular organisms exclude viruses. https://github.com/geneontology/go-ontology/issues/24200 https://github.com/geneontology/go-ontology/issues/26424 - kmv + https://github.com/geneontology/go-ontology/issues/28978 2019-08-12T18:01:37Z + cellular anatomical entity cellular_component GO:0110165 - cellular anatomical entity + cellular anatomical structure - A part of a cellular organism that is either an immaterial entity or a material entity with granularity above the level of a protein complex but below that of an anatomical system. Or, a substance produced by a cellular organism with granularity above the level of a protein complex. + A part of a cellular organism consisting of a material entity with granularity above the level of a protein complex but below that of an anatomical system. Note that cellular organisms exclude viruses. GOC:kmv @@ -20767,7 +20935,6 @@ plexiform layer. A prolongation or process extending from a cell and that is bounded by plasma membrane, e.g. a cilium, lamellipodium, or axon. https://github.com/geneontology/go-ontology/issues/13193 - krc 2017-03-21T17:26:07Z cellular_component GO:0120025 @@ -20806,7 +20973,6 @@ plexiform layer. Formation of a prolongation or process extending and that is bounded by plasma membrane, e.g. a cilium, lamellipodium, or axon. https://github.com/geneontology/go-ontology/issues/13298 - krc 2017-04-24T23:56:08Z eupodium biological_process @@ -20854,7 +21020,6 @@ plexiform layer. A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a plasma membrane bounded prolongation or process extending from a cell, e.g. a cilium or axon. https://github.com/geneontology/go-ontology/issues/13298 - krc 2017-04-26T16:07:02Z biological_process GO:0120036 @@ -20887,7 +21052,6 @@ plexiform layer. A mitotic cell cycle process comprising the steps by which the nucleus of a eukaryotic cell divides; the process involves condensation of chromosomal DNA into a highly compacted form. Canonically, mitosis produces two daughter nuclei whose chromosome complement is identical to that of the mother cell. https://github.com/geneontology/go-ontology/issues/19910 - pg 2017-03-23T14:44:23Z mitosis biological_process @@ -20911,7 +21075,6 @@ plexiform layer. The assembly and secretion a set of components to form an extracellular vesicule, a membrane-bounded vesicle that is released into the extracellular region. Extracellular vesicles include exosomes, microvesicles and apoptotic bodies, based on the mechanism by which they are released from cells and differentiated based on their size and content. https://github.com/geneontology/go-ontology/issues/14256 - pg 2017-10-23T11:53:42Z extracellular vesicle assembly biological_process @@ -20960,7 +21123,6 @@ plexiform layer. The directed movement of some substance from a cell, into the extracellular region. This may occur via transport across the plasma membrane or via exocytosis. - pg 2019-05-22T11:20:45Z efflux biological_process @@ -20998,7 +21160,6 @@ plexiform layer. A process that is part of the mitotic cell cycle. - jl 2014-05-22T14:22:34Z biological_process GO:1903047 @@ -21038,7 +21199,6 @@ plexiform layer. Any process that modulates the frequency, rate or extent of blood circulation. - mr 2014-10-06T18:38:56Z biological_process regulation of hemolymph circulation @@ -21080,7 +21240,6 @@ plexiform layer. Any vesicle that is part of the extracellular region. - jl 2014-10-22T14:26:11Z cellular_component microparticle @@ -21110,10 +21269,7 @@ plexiform layer. A macromolecular complex that contains both RNA and protein molecules. - pr 2015-11-19T12:26:37Z - GO:0030529 - GO:1990903 Wikipedia:Ribonucleoprotein RNA-protein complex RNP @@ -21205,7 +21361,6 @@ plexiform layer. - NCBITaxon:85055 GC_ID:1 house mouse mouse @@ -21244,7 +21399,6 @@ plexiform layer. - NCBITaxon:40673 GC_ID:1 bony vertebrates ncbi_taxonomy @@ -21611,7 +21765,6 @@ plexiform layer. - NCBITaxon:109679 GC_ID:1 ncbi_taxonomy NCBITaxon:39107 @@ -21870,7 +22023,6 @@ plexiform layer. A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities - PATO:0000072 quality PATO:0000001 quality @@ -21908,7 +22060,6 @@ plexiform layer. A morphological quality inhering in a bearer by virtue of the bearer's ratios of distances between its features (points, edges, surfaces and also holes etc). - PATO:0001647 relational shape quality quality PATO:0000052 @@ -21950,7 +22101,6 @@ plexiform layer. A morphology quality inhering in a bearer by virtue of the bearer's relative position, shape, arrangements and connectivity of an organism's various parts; the pattern underlying its form. - PATO:0001452 conformation relational structural quality quality @@ -22134,7 +22284,6 @@ plexiform layer. A quality of a physical entity that exists through action of continuants at the physical level of organisation in relation to other entities. - PATO:0002079 Wikipedia:Physical_property relational physical quality quality @@ -22156,8 +22305,6 @@ plexiform layer. A quality which inheres in a continuant. - PATO:0001237 - PATO:0001238 snap:Quality monadic quality of a continuant multiply inhering quality of a physical entity @@ -22454,7 +22601,6 @@ plexiform layer. A convex 3-D shape quality inhering in a bearer by virtue of the bearer's exhibiting a consistently-sized round cross section. - PATO:0001203 rod-like rod-shaped tubulate @@ -22940,27 +23086,6 @@ plexiform layer. - - - - - A quality of a single cell inhering in the bearer by virtue of the bearer's size or shape or structure. - - 2021-01-23T11:31:53Z - quality - PATO:0010006 - Use this term for morphologies that can *only* inhere in a cell, e.g. morphological qualities inhering in a cell by virtue of the presence, location or shape of one or more cell parts. - cell morphology - - - - - A quality of a single cell inhering in the bearer by virtue of the bearer's size or shape or structure. - https://orcid.org/0000-0002-7073-9172 - - - - @@ -22987,7 +23112,6 @@ plexiform layer. A quality inhering in a cell by virtue of the cell having a high nuclear/cytoplasmic ratio. - http://orcid.org/0000-0001-5208-3432 high N:C ratio quality PATO:0040072 @@ -23004,56 +23128,11 @@ plexiform layer. - - - - - A cell morphology that inheres in neurons which have two principal dendrites that emerge from the soma and begin to branch some distance from it, have few spines, and branch in narrow fields. This is in contrast to bitufted morphology where branching occurs close to the soma. - - ILX:0101312 - ilxtr:BipolarPhenotype - nifext:2 - quality - PATO:0070006 - This is specific to cortical bipolar cells and are distinguished from retinal bipolar cell morphology which has an axon and dendrite emerging from opposite ends of the soma. - cortical bipolar morphology - - - - - A cell morphology that inheres in neurons which have two principal dendrites that emerge from the soma and begin to branch some distance from it, have few spines, and branch in narrow fields. This is in contrast to bitufted morphology where branching occurs close to the soma. - PMID:18568015 - doi:10.1016/b978-0-12-369497-3.10004-4 - - - - - - - - - A cell morphology that inheres in neurons with dendrites that are bidirectional, emerging from opposite ends of the soma, with the two arbors extending in radial or tangential directions. - - quality - PATO:0070027 - This morphology type is distinct from bitufted cell morphology in that it refers to bitufted dendrite morphology rather than bitufted cell morphology. - bitufted dendrite cell morphology - - - - - A cell morphology that inheres in neurons with dendrites that are bidirectional, emerging from opposite ends of the soma, with the two arbors extending in radial or tangential directions. - PMID:18568015 - - - - A quality of continuant that exist at the anatomical level of organisation and anything under it. This includes, but is not limited to, cells , tissues, and components. - http://orcid.org/0000-0001-7258-9596 quality PATO:0070044 anatomical structure quality @@ -23066,7 +23145,6 @@ plexiform layer. A quality inhering in an anotomical structure by virtue of its capacity to be stained by specific histological dyes. - http://orcid.org/0000-0001-7258-9596 quality PATO:0070045 anatomical histological quality @@ -23079,7 +23157,6 @@ plexiform layer. An affinity inhering in an anatomical structure by virtue of the bearer exhibiting a molecular interaction for both basic and acid stains under specific pH conditions. - http://orcid.org/0000-0001-7258-9596 quality PATO:0070047 polychromatophilic @@ -23116,7 +23193,7 @@ plexiform layer. - + @@ -23128,7 +23205,7 @@ plexiform layer. native protein protein PR:000000001 - The definition above excludes protein complexes, which some also consider a protein. Those who wish to refer to a class representing both senses of the word are directed to CHEBI:36080. Note that the definition allows for experimentally-manipulated genes, and allows for artifically-produced derivatives that mimic those found naturally. Proteins (in the sense defined here) that descended from a common ancestor can be classified into families and superfamilies composed of products of evolutionarily-related genes. The domain architecture of a protein is described by the order of its constituent domains. Proteins with the same domains in the same order are defined as homeomorphic [PRO:WCB]. + The definition above excludes protein complexes, which some also consider a protein. Those who wish to refer to a class representing both senses of the word are directed to CHEBI:36080. Note that the definition allows for experimentally-manipulated genes, and allows for artifically-produced derivatives that mimic those found naturally. Proteins (in the sense defined here) that descended from a common ancestor can be classified into families and superfamilies composed of products of evolutionarily-related genes. The domain architecture of a protein is described by the order of its constituent domains. Proteins with the same domains in the same order are defined as homeomorphic [PRO:WCB). protein @@ -23810,7 +23887,6 @@ plexiform layer. - A protein with core architecture consisting of a signal sequence, followed by 7 Ig-like domains (Pfam:PF00047, Pfam:PF07679, or Pfam:PF07686), a transmembrane region, and a cytoplasmic Protein tyrosine kinase domain. PIRSF:PIRSF038502 protein @@ -24182,51 +24258,51 @@ plexiform layer. - + - + - A material entity that minimally consists of a protein. + A molecular entity that minimally consists of a protein. protein protein aggregate protein complex protein-containing complex protein - PR:000050567 - Note: This includes single proteins and derivatives thereof (PR:000000001), protein-containing complexes (GO:0032991), and protein aggregates (PR:000050566). - protein-containing material entity + PR:000064867 + Note: This includes single proteins and derivatives thereof (PR:000000001), protein-containing complexes (GO:0032991), and protein aggregates (PR:000050565). + protein-containing molecular entity - + - A material entity that minimally consists of a protein. + A molecular entity that minimally consists of a protein. PRO:DAN - + protein PRO:DAN - + protein aggregate PRO:DAN - + protein complex PRO:DAN - + protein-containing complex PRO:DAN @@ -24600,7 +24676,6 @@ plexiform layer. WBbt:0005739 Wikipedia:Head XAO:0003024 - ZFA:0001114 galen:Head head (volume) adult head @@ -24645,7 +24720,6 @@ plexiform layer. - @@ -24789,7 +24863,6 @@ plexiform layer. Organ component adjacent to an organ cavity and which consists of a maximal aggregate of organ component layers. - UBERON:0009915 wall FMA:82482 galen:Wall @@ -25262,7 +25335,6 @@ plexiform layer. Anatomical cluster consisting of the skeletal elements and articular elements that are part of an individual subdivision of the organism. - UBERON:0010322 FMA:85544 NCIT:C34076 SCTID:118966000 @@ -25308,7 +25380,7 @@ plexiform layer. - + The surface (external) layer of ectoderm which begins to proliferate shortly after separation from the neuroectoderm. merge with non-neural. In vertebrates, the ectoderm has three parts: external ectoderm (also known as surface ectoderm), the neurectoderm (neural crest, and neural tube) EHDAA2:0001968 @@ -25331,7 +25403,7 @@ plexiform layer. external ectoderm http://upload.wikimedia.org/wikipedia/commons/1/1d/Ectoderm.png - + @@ -25344,7 +25416,7 @@ plexiform layer. - + EHDAA2 @@ -25693,7 +25765,7 @@ plexiform layer. - + @@ -25729,14 +25801,14 @@ plexiform layer. gastrula stage - + - + BILS @@ -25896,7 +25968,6 @@ plexiform layer. A fasciculated bundle of neuron projections (GO:0043005), largely or completely lacking synapses. - UBERON:0005163 CARO:0001001 FBbt:00005099 NLX:147821 @@ -26137,7 +26208,7 @@ plexiform layer. - + @@ -26145,15 +26216,15 @@ plexiform layer. - + - - + + A fluid that is composed of blood plasma and erythrocytes. AAO:0000046 @@ -26190,34 +26261,34 @@ plexiform layer. blood - + - + - + - + CL:tm - + https://github.com/obophenotype/uberon/issues/1330 - + Bgee:AN @@ -26319,7 +26390,6 @@ plexiform layer. Organism at the blastula stage - an early stage of embryonic development in animals. It is produced by cleavage of a fertilized ovum and consists of a spherical layer of around 128 cells surrounding a central fluid-filled cavity called the blastocoel. The blastula follows the morula and precedes the gastrula in the developmental sequence. TODO - check relationship with epiblast. Note in FMA this is not a subclass of embryo, but in uberon embryo is the whole organism from zygote onwards and thus includes the blastula - UBERON:0007011 BILA:0000059 BTO:0000128 GAID:1294 @@ -27289,7 +27359,6 @@ plexiform layer. - @@ -27303,7 +27372,7 @@ plexiform layer. - + @@ -27345,14 +27414,14 @@ plexiform layer. epithelium https://upload.wikimedia.org/wikipedia/commons/8/8f/Illu_epithelium.jpg - + - + http://palaeos.com/metazoa/porifera/homoscleromorpha.html @@ -27874,7 +27943,7 @@ plexiform layer. - + Primary germ layer that is the outer of the embryo's three germ layers and gives rise to epidermis and neural tissue. AAO:0000137 BILA:0000036 @@ -27909,14 +27978,14 @@ plexiform layer. ectoderm http://upload.wikimedia.org/wikipedia/commons/1/19/Gray32.png - + - + Bgee:AN @@ -27956,7 +28025,7 @@ plexiform layer. - + Primary germ layer that lies remote from the surface of the embryo and gives rise to internal tissues such as gut. AAO:0000139 BILA:0000038 @@ -27991,14 +28060,14 @@ plexiform layer. http://upload.wikimedia.org/wikipedia/commons/c/c0/Endoderm2.png http://upload.wikimedia.org/wikipedia/commons/d/df/Gray10.png - + - + Bgee:AN @@ -28039,10 +28108,9 @@ plexiform layer. - + The middle germ layer of the embryo, between the endoderm and ectoderm. - UBERON:0003263 AAO:0000304 BILA:0000037 BTO:0000839 @@ -28080,14 +28148,14 @@ plexiform layer. mesoderm http://upload.wikimedia.org/wikipedia/commons/e/e8/Mesoderm.png - + - + Bgee:AN @@ -28275,7 +28343,7 @@ plexiform layer. - + @@ -28337,14 +28405,14 @@ plexiform layer. cranial nerve II - + - + EHDAA2 @@ -28454,7 +28522,7 @@ plexiform layer. - + @@ -28525,14 +28593,14 @@ plexiform layer. https://cdn.humanatlas.io/digital-objects/ref-organ/heart-female/v1.3/assets/3d-vh-f-heart.glb https://cdn.humanatlas.io/digital-objects/ref-organ/heart-male/v1.3/assets/3d-vh-m-heart.glb - + - + MA @@ -28574,7 +28642,7 @@ plexiform layer. - + @@ -28593,7 +28661,7 @@ plexiform layer. - + The brain is the center of the nervous system in all vertebrate, and most invertebrate, animals. Some primitive animals such as jellyfish and starfish have a decentralized nervous system without a brain, while sponges lack any nervous system at all. In vertebrates, the brain is located in the head, protected by the skull and close to the primary sensory apparatus of vision, hearing, balance, taste, and smell[WP]. requires review for applicability to invertebrate structures, e.g. synganglion @@ -28652,11 +28720,11 @@ plexiform layer. https://cdn.humanatlas.io/digital-objects/ref-organ/brain-female/v1.4/assets/3d-allen-f-brain.glb https://cdn.humanatlas.io/digital-objects/ref-organ/brain-male/v1.4/assets/3d-allen-m-brain.glb - + - + @@ -28669,13 +28737,13 @@ plexiform layer. - + FMA - + Bgee:AN @@ -28925,12 +28993,11 @@ plexiform layer. - - - - + + + @@ -29014,34 +29081,34 @@ plexiform layer. cornea http://upload.wikimedia.org/wikipedia/commons/1/1e/Schematic_diagram_of_the_human_eye_en.svg - + - + - + - + MA - + MA - + FMA-isa @@ -29218,10 +29285,10 @@ plexiform layer. - - - - + + + + The retina is the innermost layer or coating at the back of the eyeball, which is sensitive to light and in which the optic nerve terminates. @@ -29269,44 +29336,44 @@ plexiform layer. retina http://upload.wikimedia.org/wikipedia/commons/e/ed/Human_eye_cross-sectional_view_grayscale.png - + - + - + - + - + FMA - + FMA - + FMA - + EHDAA2 @@ -29361,8 +29428,8 @@ plexiform layer. - - + + @@ -29394,24 +29461,24 @@ plexiform layer. eye - + - + - + PMID:21062451 - + PMID:21062451 @@ -29648,7 +29715,6 @@ plexiform layer. - AAO:0000959 CALOHA:TS-2103 VHOG:0001248 @@ -29656,7 +29722,6 @@ plexiform layer. uberon systema cardiovasculare UBERON:0001009 - circulatory system http://upload.wikimedia.org/wikipedia/commons/2/29/Circulatory_System_en.svg @@ -29800,7 +29865,7 @@ plexiform layer. - + @@ -29848,14 +29913,14 @@ plexiform layer. http://upload.wikimedia.org/wikipedia/commons/b/b2/TE-Nervous_system_diagram.svg http://upload.wikimedia.org/wikipedia/commons/b/ba/Nervous_system_diagram.png - + - + Bgee:AN @@ -29921,7 +29986,7 @@ plexiform layer. - + The central nervous system is the core nervous system that serves an integrating and coordinating function. In vertebrates it consists of the neural tube derivatives: the brain and spinal cord. In invertebrates it includes central ganglia plus nerve cord. @@ -29966,7 +30031,7 @@ plexiform layer. central nervous system - + @@ -29980,7 +30045,7 @@ plexiform layer. - + Bgee:AN @@ -30633,7 +30698,7 @@ plexiform layer. - + Simple squamous epithelium of mesodermal origin which lines serous membranes. Examples: mesothelium of pleura, mesothelium of peritoneum[FMA]. Wikipedia: The mesothelium is a membrane that forms the lining of several body cavities: the pleura (thoracal cavity), peritoneum (abdominal cavity including the mesentery) and pericardium (heart sac). Mesothelial tissue also surrounds the male internal reproductive organs (the tunica vaginalis testis) and covers the internal reproductive organs of women (the tunica serosa uteri). AEO:0000111 BTO:0002422 @@ -30658,14 +30723,14 @@ plexiform layer. mesothelium http://upload.wikimedia.org/wikipedia/commons/2/25/Mesothelium_peritoneal_wash_high_mag.jpg - + - + FMA @@ -30955,7 +31020,7 @@ plexiform layer. - + A tube extending from the mouth to the anus. @@ -30992,14 +31057,14 @@ plexiform layer. digestive tract - + - + NCBIBook:NBK10107 @@ -31054,7 +31119,7 @@ plexiform layer. - + The ciliary muscle is a ring of smooth muscle in the middle layer of the eye that controls the eye's accommodation for viewing objects at varying distances and regulates the flow of aqueous humour through Schlemm's canal. [WP,unvetted]. BTO:0000654 @@ -31077,7 +31142,7 @@ plexiform layer. ciliary muscle http://upload.wikimedia.org/wikipedia/commons/2/28/Gray872.png - + @@ -31096,7 +31161,7 @@ plexiform layer. - + FMA @@ -31214,7 +31279,7 @@ plexiform layer. - + @@ -31260,14 +31325,14 @@ plexiform layer. eyelid https://upload.wikimedia.org/wikipedia/commons/8/84/Eye_makeup.jpg - + - + multiple @@ -31533,7 +31598,7 @@ plexiform layer. - + @@ -31572,14 +31637,14 @@ plexiform layer. iris - + - + XAO @@ -31633,7 +31698,7 @@ plexiform layer. - + @@ -31682,14 +31747,14 @@ plexiform layer. corneal epithelium http://upload.wikimedia.org/wikipedia/commons/6/66/Gray871.png - + - + ISBN:0781772214 @@ -31777,15 +31842,15 @@ plexiform layer. - - + + - + @@ -31820,34 +31885,34 @@ plexiform layer. sclera http://upload.wikimedia.org/wikipedia/commons/1/1e/Schematic_diagram_of_the_human_eye_en.svg - + - + - + - + FMA - + ZFA - + ISBN:0781772214 @@ -31889,7 +31954,7 @@ plexiform layer. - + @@ -31927,14 +31992,14 @@ plexiform layer. ciliary body http://upload.wikimedia.org/wikipedia/commons/1/1e/Schematic_diagram_of_the_human_eye_en.svg - + - + ISBN:0781772214 @@ -31972,14 +32037,14 @@ plexiform layer. - + - + @@ -32040,24 +32105,24 @@ plexiform layer. optic choroid http://upload.wikimedia.org/wikipedia/commons/1/1e/Schematic_diagram_of_the_human_eye_en.svg - + - + - + MA - + Wikipedia @@ -32250,9 +32315,9 @@ plexiform layer. - - - + + + A double layer covering the ciliary body that produces aqueous humor. BTO:0001770 @@ -32272,15 +32337,15 @@ plexiform layer. ciliary epithelium - + - + - + @@ -32293,19 +32358,19 @@ plexiform layer. - + MA - + MP - + Wikipedia @@ -32421,7 +32486,7 @@ plexiform layer. - + @@ -32479,14 +32544,14 @@ plexiform layer. pigmented layer of retina http://upload.wikimedia.org/wikipedia/commons/5/55/Gray881.png - + - + Wikipedia @@ -32562,7 +32627,7 @@ plexiform layer. - + @@ -32594,14 +32659,14 @@ plexiform layer. photoreceptor layer of retina http://upload.wikimedia.org/wikipedia/commons/5/55/Gray881.png - + - + ZFA @@ -33094,7 +33159,7 @@ plexiform layer. - + @@ -33150,7 +33215,7 @@ plexiform layer. ganglionic layer of retina http://upload.wikimedia.org/wikipedia/commons/5/55/Gray881.png - + @@ -33163,7 +33228,7 @@ plexiform layer. - + FMA @@ -33217,7 +33282,7 @@ plexiform layer. - + @@ -33243,7 +33308,6 @@ plexiform layer. Layer of the retina formed by expansion of the fibers of the optic nerve. - UBERON:0005888 nerve fiber layer DMBA:15652 EMAPA:18591 @@ -33272,14 +33336,14 @@ plexiform layer. nerve fiber layer of retina - + - + FMA @@ -33969,7 +34033,7 @@ plexiform layer. - + @@ -34001,14 +34065,14 @@ plexiform layer. anterior segment of eyeball http://upload.wikimedia.org/wikipedia/commons/b/ba/Cataract_in_human_eye.png - + - + FMA @@ -34052,7 +34116,7 @@ plexiform layer. - + @@ -34082,14 +34146,14 @@ plexiform layer. posterior segment of eyeball http://upload.wikimedia.org/wikipedia/commons/1/1e/Schematic_diagram_of_the_human_eye_en.svg - + - + FMA @@ -34126,9 +34190,9 @@ plexiform layer. - - - + + + @@ -34176,15 +34240,15 @@ plexiform layer. conjunctiva http://upload.wikimedia.org/wikipedia/commons/5/55/Gray883.png - + - + - + @@ -34197,19 +34261,19 @@ plexiform layer. - + cjm - + MA - + ISBN:0781772214 @@ -34367,7 +34431,7 @@ plexiform layer. - + The midbrain is the middle division of the three primary divisions of the developing chordate brain or the corresponding part of the adult brain (in vertebrates, includes a ventral part containing the cerebral peduncles and a dorsal tectum containing the corpora quadrigemina and that surrounds the aqueduct of Sylvius connecting the third and fourth ventricles)[GO]. developmental relationships need revised @@ -34413,14 +34477,14 @@ plexiform layer. midbrain http://upload.wikimedia.org/wikipedia/commons/f/f9/Human_brain_inferior_view_description.JPG - + - + Bgee:AN @@ -34891,7 +34955,7 @@ plexiform layer. - + Ventral part of the midbrain, separated from the hindbrain by the isthmus[ISBN:0471888893]. Subdivision of the midbrain lying anterior to the tectum and posterior to the substantia nigra and cerebral peduncle[FMA] The part of the midbrain extending from the substantia nigra to the cerebral aqueduct in a horizontal section of the midbrain. It forms the floor of the midbrain that surrounds the cerebral aqueduct[WP]. MTg @@ -34930,14 +34994,14 @@ plexiform layer. midbrain tegmentum http://upload.wikimedia.org/wikipedia/commons/b/b6/Gray712.png - + - + ZFA @@ -35023,7 +35087,6 @@ plexiform layer. - @@ -35098,7 +35161,6 @@ plexiform layer. - @@ -35107,8 +35169,8 @@ plexiform layer. - - + + @@ -35121,7 +35183,7 @@ plexiform layer. - + @@ -35175,34 +35237,34 @@ plexiform layer. blood vessel http://upload.wikimedia.org/wikipedia/commons/2/29/Circulatory_System_en.svg - + - + - + - + AEO - + EHDAA2 - + GO:0072360 @@ -35531,7 +35593,7 @@ plexiform layer. - + The most posterior of the three principal regions of the brain. In mammals and birds the hindbrain is divided into a rostral metencephalon and a caudal myelencephalon. In zebrafish, with the exception of the cerebellum, the ventral remainder of the metencephalon can be separated only arbitrarily from the more caudal myelencephalic portion of the medulla oblongata (From: Neuroanatomy of the Zebrafish Brain)[ZFA]. Organ component of neuraxis that has as its parts the pons, cerebellum and medulla oblongata[FMA]. @@ -35574,14 +35636,14 @@ plexiform layer. hindbrain http://upload.wikimedia.org/wikipedia/commons/5/54/EmbryonicBrain.svg - + - + Bgee:AN @@ -36022,7 +36084,6 @@ plexiform layer. The sensory system subserving the sense of vision. - UBERON:0007036 AAO:0000632 BILA:0000140 EMAPA:36003 @@ -36212,7 +36273,7 @@ plexiform layer. - + Vasculature that is part of the eye region. FMA:74743 @@ -36234,14 +36295,14 @@ plexiform layer. https://cdn.humanatlas.io/digital-objects/ref-organ/blood-vasculature-female/v1.3/assets/3d-vh-f-blood-vasculature.glb https://cdn.humanatlas.io/digital-objects/ref-organ/blood-vasculature-male/v1.3/assets/3d-vh-m-blood-vasculature.glb - + - + ISBN:0781772214 @@ -36445,7 +36506,7 @@ plexiform layer. - + @@ -36519,14 +36580,14 @@ plexiform layer. https://cdn.humanatlas.io/digital-objects/ref-organ/spinal-cord-female/v1.1/assets/3d-vh-f-spinal-cord.glb https://cdn.humanatlas.io/digital-objects/ref-organ/spinal-cord-male/v1.1/assets/3d-vh-m-spinal-cord.glb - + - + ZFA @@ -36869,7 +36930,6 @@ plexiform layer. The cavity within the body of all animals higher than the coelenterates and certain primitive worms, formed by the splitting of the embryonic mesoderm into two layers. In mammals it forms the peritoneal, pleural, and pericardial cavities. - UBERON:0000169 body cavity AEO:0000186 BTO:0001707 @@ -36881,7 +36941,6 @@ plexiform layer. SCTID:361348008 TAO:0001438 UMLS:C0333343 - ZFA:0001438 galen:BodyCavity coelomic cavity coelomic cavity lumen @@ -36981,9 +37040,9 @@ plexiform layer. - - - + + + @@ -37031,15 +37090,15 @@ plexiform layer. notochord http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png - + - + - + @@ -37058,19 +37117,19 @@ plexiform layer. - + http://tolweb.org/Chordata/2499 - + ZFA - + EHDAA2 @@ -37110,8 +37169,8 @@ plexiform layer. - - + + Somites are spheres of epithelial cells that form sequentially along the anterior-posterior axis of the embryo through mesenchymal to epithelial transition of the presomitic mesoderm. mesodermal cluster @@ -37149,11 +37208,11 @@ plexiform layer. somite http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png - + - + @@ -37166,13 +37225,13 @@ plexiform layer. - + GOTAX:0000352 - + ZFA @@ -37234,22 +37293,22 @@ plexiform layer. - + - - + + - + A specialized region of ectoderm found between the neural ectoderm (neural plate) and non-neural ectoderm and composed of highly migratory pluripotent cells that delaminate in early embryonic development from the dorsal neural tube and give rise to an astounding variety of differentiated cell types[MP]. AAO:0010578 BTO:0001764 @@ -37282,45 +37341,45 @@ plexiform layer. http://upload.wikimedia.org/wikipedia/commons/5/5f/Gray644.png https://upload.wikimedia.org/wikipedia/commons/8/8f/Neural_Crest.png - + - + - + - + - + XAO https://github.com/obophenotype/uberon/wiki/The-neural-crest - + BTO - + PMID:11523831 - + PMID:11523831 @@ -37606,7 +37665,7 @@ plexiform layer. - + @@ -37659,14 +37718,14 @@ plexiform layer. hematopoietic system - + - + FMA @@ -37706,8 +37765,8 @@ plexiform layer. - - + + @@ -37733,11 +37792,11 @@ plexiform layer. iris epithelium - + - + @@ -37750,13 +37809,13 @@ plexiform layer. - + MA - + MP @@ -37895,7 +37954,7 @@ plexiform layer. - + Ectodermal placode that develops in the head into a part of the sensory nervous system. With a few exceptions (lens, adenohypophyseal), cranial placodes are neurogenic. Do not merge with neurogenic placode ectodermal placode @@ -37912,7 +37971,7 @@ plexiform layer. cranial placode - + @@ -37925,7 +37984,7 @@ plexiform layer. - + PMID:11523831 PMID:22512454 @@ -38125,7 +38184,7 @@ plexiform layer. - + @@ -38138,7 +38197,7 @@ plexiform layer. - + The part of the brain that is the morphological boundary between the midbrain and hindbrain and that is the location of an organizing center which patterns the midbrain and hindbrain primordia of the neural plate. consider adding class for organizer. Consider adding separate class for isthmus as a structure AAO:0011064 @@ -38167,24 +38226,24 @@ plexiform layer. midbrain-hindbrain boundary - + - + - + ZFA - + ZFA @@ -38293,6 +38352,7 @@ plexiform layer. + @@ -38306,7 +38366,7 @@ plexiform layer. - + Unsegmented field of paraxial mesoderm present posterior to the most recently formed somite pair, from which somites will form. AAO:0011086 EFO:0001982 @@ -38329,14 +38389,14 @@ plexiform layer. presomitic mesoderm - + - + Bgee:AN @@ -38503,7 +38563,7 @@ plexiform layer. - + @@ -38517,7 +38577,6 @@ plexiform layer. Portion of tissue that is part of the anterior neural keel and will form the optic vesicle[ZFA]. A paired ectodermal placode that becomes invaginated to form the embryonic lens vesicles. - UBERON:0005060 AAO:0011038 EFO:0003541 EHDAA2:0004431 @@ -38540,7 +38599,7 @@ plexiform layer. eye primordium - + @@ -38553,7 +38612,7 @@ plexiform layer. - + PMID:16496288 XAO @@ -38603,8 +38662,8 @@ plexiform layer. - - + + @@ -38632,24 +38691,24 @@ plexiform layer. optic cup - + - + - + ZFA - + ZFA @@ -38705,7 +38764,7 @@ plexiform layer. - + @@ -38743,7 +38802,7 @@ plexiform layer. lens placode http://upload.wikimedia.org/wikipedia/commons/2/2f/Gray864.png - + @@ -38756,7 +38815,7 @@ plexiform layer. - + ZFA @@ -38795,9 +38854,9 @@ plexiform layer. - - - + + + A region of embryonic ectodermal cells that lie directly above the notochord. During neurulation, they change shape and produce an infolding of the neural plate (the neural fold) that then seals to form the neural tube[XAO]. The earliest recognizable dorsal ectodermal primordium of the central nervous system present near the end of gastrulation before infolding to form the neural keel; consists of a thickened pseudostratified epithelium[ZFA]. AAO:0011072 BTO:0001765 @@ -38826,34 +38885,34 @@ plexiform layer. neural plate https://upload.wikimedia.org/wikipedia/commons/8/8f/Neural_Crest.png - + - + - + - + GOTAX:0000352 - + Wikipedia - + Bgee:AN @@ -38928,7 +38987,7 @@ plexiform layer. - + The paraxial mesoderm is the mesoderm located bilaterally adjacent to the notochord and neural tube[GO]. AAO:0010568 EFO:0003515 @@ -38954,7 +39013,7 @@ plexiform layer. paraxial mesoderm http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png - + @@ -38967,7 +39026,7 @@ plexiform layer. - + Bgee:AN @@ -39043,7 +39102,7 @@ plexiform layer. - + @@ -39057,7 +39116,6 @@ plexiform layer. Portion of the middle of the three primary germ layers of the embryo that resides on the periphery of the embryo, is continuous with the extra-embryonic mesoderm, splits into two layers enclosing the intra-embryonic coelom, and gives rise to body wall structures[MP]. - UBERON:0006258 AAO:0010574 EHDAA2:0000919 EHDAA:379 @@ -39083,7 +39141,7 @@ plexiform layer. lateral plate mesoderm http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png - + @@ -39096,7 +39154,7 @@ plexiform layer. - + EHDAA2 VHOG @@ -39146,15 +39204,15 @@ plexiform layer. - - + + - + Bilateral groups of cells consisting of three rows: one row of endocardial precursors medially and two rows of myocardical precursors laterally. The two populations fuse at the midline to form the heart rudiment or cone. should probably be merged with heart rudiment. AAO:0011044 @@ -39171,15 +39229,15 @@ plexiform layer. heart primordium - + - + - + @@ -39192,19 +39250,19 @@ plexiform layer. - + ZFA - + ZFA - + XAO @@ -39233,8 +39291,8 @@ plexiform layer. - - + + Ventral somitic compartment that is a precursor of the axial skeleton[XAO]. Sclerotomes eventually differentiate into the vertebrae and most of the skull. The caudal (posterior) half of one sclerotome fuses with the rostral (anterior) half of the adjacent one to form each vertebra. From their initial location within the somite, the sclerotome cells migrate medially towards the notochord. These cells meet the sclerotome cells from the other side to form the vertebral body. From this vertebral body, sclerotome cells move dorsally and surround the developing spinal cord, forming the vertebral arch[WP]. AAO:0010571 AEO:0000212 @@ -39258,11 +39316,11 @@ plexiform layer. sclerotome http://upload.wikimedia.org/wikipedia/commons/9/96/Gray65.png - + - + @@ -39281,13 +39339,13 @@ plexiform layer. - + VHOG:0000680 - + ZFA @@ -39608,7 +39666,7 @@ plexiform layer. - + Mesenchyme that is part of a developing camera-type eye. TODO - change mesenchyme relationships to precursor_of EHDAA2:0000485 @@ -39620,14 +39678,14 @@ plexiform layer. UBERON:0003314 eye mesenchyme - + - + EHDAA2 @@ -40020,7 +40078,6 @@ plexiform layer. An anatomical space that surrounded_by a neural tube. - UBERON:0005713 AAO:0011073 EHDAA2:0001269 EHDAA:2889 @@ -40402,7 +40459,7 @@ plexiform layer. - + The part of the coelom in the embryo between the somatopleuric and splanchnopleuric mesoderm; the principal body cavities of the trunk (thoracic, abdominal, and pelvic) arise from this embryonic part of the coelom. consider merging with coelom. TODO - add spatial relationships to halves of LPM. Note the OG places XAO and ZFA coelem terms here. editor note: TODO check ZFA, which appears to be a structure present in adults EHDAA:251 @@ -40417,14 +40474,14 @@ plexiform layer. intraembryonic coelom - + - + Wikipedia @@ -40517,7 +40574,7 @@ plexiform layer. - + The part of the retina that contains neurons and photoreceptor cells[GO]. AAO:0011095 @@ -40548,14 +40605,14 @@ plexiform layer. retinal neural layer - + - + Bgee:AN @@ -40675,7 +40732,6 @@ plexiform layer. White matter that is part of a diencephalon [Automatically generated definition]. - UBERON:0023148 BIRNLEX:1678 FMA:83931 TAO:0000338 @@ -40808,7 +40864,7 @@ plexiform layer. - + The layer of undifferentiated, proliferating cells that line the neural tube lumen that is the immediate transformation of the germinal neuroepithelium. consider merging with 'ventricular zone'; note that the MA class probably does not belong here, as this is an embryonic structure ependymal layer @@ -40825,7 +40881,7 @@ plexiform layer. neural tube ventricular layer - + @@ -40838,7 +40894,7 @@ plexiform layer. - + NCBIBook:NBK10047 @@ -41240,9 +41296,9 @@ plexiform layer. - - - + + + @@ -41274,34 +41330,34 @@ plexiform layer. optic vesicle http://upload.wikimedia.org/wikipedia/commons/e/e0/Gray863.png - + - + - + - + ZFA - + GO-def - + ZFA @@ -41397,8 +41453,8 @@ plexiform layer. - - + + A specific region of the lateral mesoderm that will form the primary beating heart tube. In mammals the primary heart field gives rise to the left ventricle. XAO:0004185 first heart field @@ -41410,24 +41466,24 @@ plexiform layer. UBERON:0004140 primary heart field - + - + - + GO:0003128 - + https://orcid.org/0000-0003-3308-6245 @@ -41480,7 +41536,7 @@ plexiform layer. - + An epithelial tube that will give rise to the mature heart. AAO:0010411 EFO:0003526 @@ -41499,14 +41555,14 @@ plexiform layer. heart tube - + - + ZFA-modified @@ -41583,7 +41639,7 @@ plexiform layer. - + @@ -41599,14 +41655,14 @@ plexiform layer. eye muscle - + - + MA @@ -41789,7 +41845,7 @@ plexiform layer. - + A transparent homogeneous acellular layer found between the substantia propria and the endothelial layer of the cornea[MP]. EMAPA:18804 @@ -41818,14 +41874,14 @@ plexiform layer. Descemet's membrane https://github.com/obophenotype/uberon/issues/15 - + - + Cline et al @@ -42084,7 +42140,6 @@ plexiform layer. - @@ -42181,7 +42236,6 @@ plexiform layer. - @@ -42463,7 +42517,6 @@ plexiform layer. Organism at the gastrula stage. - UBERON:0007012 BILA:0000060 BTO:0001403 FBbt:00005317 @@ -42577,7 +42630,7 @@ plexiform layer. - + Organ consisting of skeletal tissue. Encompasses whole bones, fused bones, cartilaginious elements, teeth, dermal denticles. AAO:0011129 TAO:0001890 @@ -42591,14 +42644,14 @@ plexiform layer. skeletal element - + - + VSAO @@ -42625,7 +42678,7 @@ plexiform layer. - + @@ -42664,14 +42717,14 @@ plexiform layer. UBERON:0004770 articular system - + - + FMA @@ -43523,7 +43576,7 @@ plexiform layer. - + Portion of primordial embryonic connective tissue of the developing head, consisting of mesenchymal cells supported in interlaminar jelly, that derive mostly from the mesoderm and contribute to head connective tissue, bone and musculature in conjunction with cranial neural crest cells. EFO:0003492 EHDAA2:0000732 @@ -43544,14 +43597,14 @@ plexiform layer. head mesenchyme - + - + EHDAA2 @@ -43609,7 +43662,7 @@ plexiform layer. - + Mesenchyme that is part of a developing trunk. EFO:0003485 EHDAA2:0002092 @@ -43625,14 +43678,14 @@ plexiform layer. trunk mesenchyme - + - + EHDAA2 @@ -44147,7 +44200,7 @@ plexiform layer. - + Portion of tissue that is part of the eye and gives rise to the mature, fully layered cornea. TAO:0002188 ZFA:0001688 @@ -44155,7 +44208,7 @@ plexiform layer. UBERON:0005427 corneal primordium - + @@ -44174,7 +44227,7 @@ plexiform layer. - + ZFA @@ -44197,7 +44250,7 @@ plexiform layer. - + Multi-tissue structure that arises from the heart rudiment and will become the heart tube. EHDAA2:0001512 EHDAA:424 @@ -44215,14 +44268,14 @@ plexiform layer. primitive heart tube - + - + ZFA @@ -44313,7 +44366,6 @@ plexiform layer. - @@ -44413,7 +44465,7 @@ plexiform layer. - + A delimited region of dense mesenchyme within looser mesenchyme. AEO:0000148 EHDAA2_RETIRED:0003148 @@ -44423,7 +44475,7 @@ plexiform layer. UBERON:0005856 developing mesenchymal condensation - + @@ -44442,7 +44494,7 @@ plexiform layer. - + AEO-modified-relation @@ -44463,7 +44515,6 @@ plexiform layer. - @@ -44500,8 +44551,8 @@ plexiform layer. - - + + @@ -44518,11 +44569,11 @@ plexiform layer. UBERON:0005908 conjunctival sac - + - + @@ -44535,13 +44586,13 @@ plexiform layer. - + FMA - + HPO:pr @@ -44783,7 +44834,7 @@ plexiform layer. - + @@ -44806,14 +44857,14 @@ plexiform layer. future diencephalon - + - + EHDAA2 @@ -44989,7 +45040,7 @@ plexiform layer. - + @@ -45013,14 +45064,14 @@ plexiform layer. future spinal cord - + - + EHDAA2 @@ -45057,7 +45108,7 @@ plexiform layer. - + The notochordal plate is the dorsal part of the notochordal process when the ventral portion breaks down. It is continuous laterally with the endoderm that composes the roof of the primitive foregut and is in contact dorsally with the neural tube. The folding off of the notochordal plate gives rise to the notochord. TODO - check ordering; awaiting confirmation from JB EHDAA2:0001278 @@ -45071,7 +45122,7 @@ plexiform layer. notochordal plate - + @@ -45084,7 +45135,7 @@ plexiform layer. - + EHDAA2 @@ -45112,7 +45163,7 @@ plexiform layer. - + A midline cellular cord formed from the migration of mesenchymal cells from the primitive knot. EHDAA2:0001279 EHDAA:224 @@ -45129,14 +45180,14 @@ plexiform layer. The notochordal process grows cranially until it reaches the prechordal plate, the future site of the mouth. In this area the ectoderm is attached directly to the endoderm without intervening mesoderm. This area is known as the oropharyngeal membrane, and it will break down to become the mouth. At the other end of the primitive streak the ectoderm is also fused directly to the endoderm; this is known as the cloacal membrane (proctodeum), or primordial anus. notochordal process - + - + EHDAA2 @@ -45717,7 +45768,6 @@ plexiform layer. - @@ -46178,8 +46228,8 @@ plexiform layer. - - + + @@ -46205,24 +46255,24 @@ plexiform layer. presumptive hindbrain - + - + - + XAO-abduced - + cjm @@ -46273,7 +46323,7 @@ plexiform layer. - + @@ -46292,14 +46342,14 @@ plexiform layer. presumptive midbrain hindbrain boundary - + - + ZFA @@ -46445,7 +46495,7 @@ plexiform layer. - + @@ -46471,7 +46521,7 @@ plexiform layer. presumptive paraxial mesoderm - + @@ -46487,7 +46537,7 @@ plexiform layer. - + https://github.com/obophenotype/uberon/issues/1277 @@ -46569,7 +46619,7 @@ plexiform layer. - + A neural decussation that is part of a diencephalon. FMA:62446 diencephalon decussation @@ -46577,7 +46627,7 @@ plexiform layer. UBERON:0007425 decussation of diencephalon - + @@ -46590,7 +46640,7 @@ plexiform layer. - + Obol @@ -46665,7 +46715,7 @@ plexiform layer. - + Mesenchyme with little extracellular matrix. AEO:0000146 EHDAA2:0003146 @@ -46673,7 +46723,7 @@ plexiform layer. UBERON:0007524 dense mesenchyme tissue - + @@ -46686,7 +46736,7 @@ plexiform layer. - + AEO @@ -46925,7 +46975,7 @@ plexiform layer. - + An axon tract that is part of a brain. the NIFSTD class 'nerve tract' is classified under 'regional part of brain', so it may seem like it belongs here, but actually includes spinal cord tracts FMA:83848 @@ -46935,14 +46985,14 @@ plexiform layer. UBERON:0007702 tract of brain - + - + cjm @@ -46970,7 +47020,7 @@ plexiform layer. - + Anatomical system that consists of all blood and lymph vessels. consider merging with vasculature @@ -46987,14 +47037,14 @@ plexiform layer. vascular system - + - + MA @@ -47049,6 +47099,7 @@ plexiform layer. SCTID:361355005 UMLS:C0460004 WikipediaCategory:Head_and_neck + ZFA:0001114 galen:HeadAndNeck uberon cephalic area @@ -47115,7 +47166,7 @@ plexiform layer. - + @@ -47124,7 +47175,6 @@ plexiform layer. Sum total of mesenchyme in the embryo. consider adding new class (EMAPA:16097) for mesenchyme of embryo (some mesenchyme is extraembryonic - e.g. amnion mesoderm) - UBERON:0003313 EHDAA2:0001113 EHDAA:177 EMAPA:16097 @@ -47132,14 +47182,14 @@ plexiform layer. UBERON:0009142 entire embryonic mesenchyme - + - + EHDAA2 @@ -47234,8 +47284,9 @@ plexiform layer. + - + @@ -47251,14 +47302,14 @@ plexiform layer. UBERON:0009615 midbrain hindbrain boundary neural plate - + - + ZFA @@ -47291,14 +47342,14 @@ plexiform layer. - + - + @@ -47323,24 +47374,24 @@ plexiform layer. presumptive midbrain - + - + - + ZFA - + ZFA @@ -47386,7 +47437,7 @@ plexiform layer. - + EHDAA2:0002094 trunk and cervical paraxial mesenchyme uberon @@ -47394,14 +47445,14 @@ plexiform layer. UBERON:0009618 trunk paraxial mesoderm - + - + EHDAA2 @@ -47424,7 +47475,7 @@ plexiform layer. - + EFO:0003704 TAO:0005041 ZFA:0005041 @@ -47434,14 +47485,14 @@ plexiform layer. anterior lateral plate mesoderm - + - + ZFA @@ -47497,14 +47548,14 @@ plexiform layer. - + EHDAA2:0001315 EHDAA:1122 uberon UBERON:0009920 optic neural crest - + @@ -47517,7 +47568,7 @@ plexiform layer. - + EHDAA2 @@ -47658,7 +47709,7 @@ plexiform layer. - + @@ -47681,14 +47732,14 @@ plexiform layer. eyeball of camera-type eye - + - + FMA @@ -47729,8 +47780,8 @@ plexiform layer. - - + + Portion of tissue that is dorsolateral to the floor plate and part of the midbrain. DHBA:12322 EFO:0003567 @@ -47744,11 +47795,11 @@ plexiform layer. midbrain basal plate - + - + @@ -47761,13 +47812,13 @@ plexiform layer. - + EHDAA2 - + ZFA @@ -47796,7 +47847,7 @@ plexiform layer. - + Portion of neural tube that gives rise to the midbrain. we follow ZFA in temporally dividing midbrain NT from presumptive midbrain, but in future this may be collapsed TAO:0007039 @@ -47805,14 +47856,14 @@ plexiform layer. UBERON:0010286 midbrain neural tube - + - + ZFA @@ -48115,8 +48166,8 @@ plexiform layer. - - + + Anatomical cluster consisting of the skeletal elements (i.e. bone elements, cartilage elements, cartilage condensations) that are part of an individual subdivision of the organism. Excludes joints. FMA:23879 SCTID:129140006 @@ -48128,11 +48179,11 @@ plexiform layer. subdivision of skeleton - + - + @@ -48145,13 +48196,13 @@ plexiform layer. - + UBERONREF:0000003 - + VSAO @@ -48212,7 +48263,7 @@ plexiform layer. - + Subdivision of the skeletal system which consists of the postcranial axial skeleton plus associated joints. axial skeletal system FMA:302077 @@ -48222,7 +48273,7 @@ plexiform layer. postcranial axial skeletal system http://purl.obolibrary.org/obo/uberon/docs/The-axial-skeleton - + @@ -48235,7 +48286,7 @@ plexiform layer. - + cjm @@ -48357,7 +48408,7 @@ plexiform layer. - + AAO:0010038 EMAPA:18808 FMA:49150 @@ -48367,14 +48418,14 @@ plexiform layer. UBERON:0011222 intra-ocular muscle - + - + EMAPA @@ -48636,7 +48687,7 @@ plexiform layer. - + @@ -48678,7 +48729,7 @@ plexiform layer. anterior uvea - + @@ -48691,7 +48742,7 @@ plexiform layer. - + MP @@ -48742,6 +48793,7 @@ plexiform layer. EHDAA2:0004731 Wikipedia:Coelom + ZFA:0001438 enterocoelom haemocoelom schizocoelom @@ -48822,7 +48874,6 @@ plexiform layer. - @@ -49415,7 +49466,6 @@ plexiform layer. Primordium that develops into the central nervous system. - UBERON:3000469 future CNS presumptive central nervous system uberon @@ -49459,7 +49509,6 @@ plexiform layer. Primordium that develops into the nervous system. - UBERON:3000477 AAO:0000477 presumptive nervous system uberon @@ -49485,7 +49534,7 @@ plexiform layer. - + @@ -49508,7 +49557,7 @@ plexiform layer. UBERON:0016887 entire extraembryonic component - + @@ -49521,7 +49570,7 @@ plexiform layer. - + AEO diff --git a/subsets/eye_upper_slim.tsv b/subsets/eye_upper_slim.tsv index 114a1bbfa..ad42fdc40 100644 --- a/subsets/eye_upper_slim.tsv +++ b/subsets/eye_upper_slim.tsv @@ -1,349 +1,347 @@ ?x ?label -_:B53189381X2D873cX2D4ec4X2Daff8X2D63fc38c8481egenid1008 -_:B53189381X2D873cX2D4ec4X2Daff8X2D63fc38c8481egenid1024 -_:B53189381X2D873cX2D4ec4X2Daff8X2D63fc38c8481egenid1030 -_:B53189381X2D873cX2D4ec4X2Daff8X2D63fc38c8481egenid1039 -_:B53189381X2D873cX2D4ec4X2Daff8X2D63fc38c8481egenid1045 -_:B53189381X2D873cX2D4ec4X2Daff8X2D63fc38c8481egenid1051 -_:B53189381X2D873cX2D4ec4X2Daff8X2D63fc38c8481egenid1057 -_:B53189381X2D873cX2D4ec4X2Daff8X2D63fc38c8481egenid1064 -_:B53189381X2D873cX2D4ec4X2Daff8X2D63fc38c8481egenid1072 -_:B53189381X2D873cX2D4ec4X2Daff8X2D63fc38c8481egenid1082 -_:B53189381X2D873cX2D4ec4X2Daff8X2D63fc38c8481egenid1096 -_:B53189381X2D873cX2D4ec4X2Daff8X2D63fc38c8481egenid1105 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+_:B931103c1X2D84a8X2D48d8X2D8209X2Db7596f243407genid800 +_:B931103c1X2D84a8X2D48d8X2D8209X2Db7596f243407genid811 +_:B931103c1X2D84a8X2D48d8X2D8209X2Db7596f243407genid817 +_:B931103c1X2D84a8X2D48d8X2D8209X2Db7596f243407genid834 +_:B931103c1X2D84a8X2D48d8X2D8209X2Db7596f243407genid840 +_:B931103c1X2D84a8X2D48d8X2D8209X2Db7596f243407genid849 +_:B931103c1X2D84a8X2D48d8X2D8209X2Db7596f243407genid859 +_:B931103c1X2D84a8X2D48d8X2D8209X2Db7596f243407genid907 +_:B931103c1X2D84a8X2D48d8X2D8209X2Db7596f243407genid957 +_:B931103c1X2D84a8X2D48d8X2D8209X2Db7596f243407genid967 +_:B931103c1X2D84a8X2D48d8X2D8209X2Db7596f243407genid974 +_:B931103c1X2D84a8X2D48d8X2D8209X2Db7596f243407genid981 +_:B931103c1X2D84a8X2D48d8X2D8209X2Db7596f243407genid988 "cell" "neural crest derived fibroblast" "neuronal receptor cell" @@ -370,9 +368,7 @@ _:B53189381X2D873cX2D4ec4X2Daff8X2D63fc38c8481egenid997 "neuron associated cell" "interneuron" "sensory neuron" - "bipolar neuron" "endothelial cell" - "CNS neuron (sensu Vertebrata)" "neuron associated cell (sensu Vertebrata)" "glial cell" "macroglial cell" @@ -412,8 +408,8 @@ _:B53189381X2D873cX2D4ec4X2Daff8X2D63fc38c8481egenid997 "epiblast cell" "animal zygote" "electrically responsive cell" - "CNS interneuron" "electrically signaling cell" + "stromal cell" "smooth muscle myoblast" "afferent neuron" "pigmented epithelial cell" @@ -645,11 +641,11 @@ _:B53189381X2D873cX2D4ec4X2Daff8X2D63fc38c8481egenid997 "myelin sheath" "organelle" "membrane-bounded organelle" - "non-membrane-bounded organelle" + "membraneless organelle" "intracellular organelle" "extracellular organelle" "intracellular membrane-bounded organelle" - "intracellular non-membrane-bounded organelle" + "intracellular membraneless organelle" "organelle lumen" "regulation of respiratory gaseous exchange" "protein-containing complex organization" @@ -657,9 +653,7 @@ _:B53189381X2D873cX2D4ec4X2Daff8X2D63fc38c8481egenid997 "regulation of digestive system process" "cellular component biogenesis" "translation initiation ternary complex" - "cellular metabolic process" "primary metabolic process" - "cellular biosynthetic process" "cell body" "synapse" "secretion" @@ -742,7 +736,7 @@ _:B53189381X2D873cX2D4ec4X2Daff8X2D63fc38c8481egenid997 "trans-synaptic signaling" "chemical synaptic transmission, postsynaptic" "signal release from synapse" - "cellular anatomical entity" + "cellular anatomical structure" "plasma membrane bounded cell projection" "plasma membrane bounded cell projection assembly" "plasma membrane bounded cell projection organization" @@ -835,11 +829,8 @@ _:B53189381X2D873cX2D4ec4X2Daff8X2D63fc38c8481egenid997 "acidophilic" "nucleated" "disconnected" - "cell morphology" "polymeric" "high nuclear/cytoplasmic ratio" - "cortical bipolar morphology" - "bitufted dendrite cell morphology" "anatomical structure quality" "anatomical histological quality" "polychromatophilic" @@ -875,7 +866,7 @@ _:B53189381X2D873cX2D4ec4X2Daff8X2D63fc38c8481egenid997 "integrin alpha" "Mus musculus protein" "eukaryotic protein" - "protein-containing material entity" + "protein-containing molecular entity" "processual entity" "camera-type eye" "sense organ" diff --git a/subsets/general_cell_types_upper_slim.json b/subsets/general_cell_types_upper_slim.json index 6a4f6cb9e..54b3f06d6 100644 --- a/subsets/general_cell_types_upper_slim.json +++ b/subsets/general_cell_types_upper_slim.json @@ -4,9 +4,9 @@ "meta" : { "basicPropertyValues" : [ { "pred" : "http://www.w3.org/2002/07/owl#versionInfo", - "val" : "2024-09-26" + "val" : "2025-01-08" } ], - "version" : "http://purl.obolibrary.org/obo/cl/releases/2024-09-26/subsets/general_cell_types_upper_slim.owl" + "version" : "http://purl.obolibrary.org/obo/cl/releases/2025-01-08/subsets/general_cell_types_upper_slim.owl" }, "nodes" : [ { "id" : "http://purl.obolibrary.org/obo/CL_0000000", @@ -18,7 +18,7 @@ "xrefs" : [ "CARO:mah" ] }, "comments" : [ "The definition of cell is intended to represent all cells, and thus a cell is defined as a material entity and not an anatomical structure, which implies that it is part of an organism (or the entirety of one)." ], - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/ubprop#_upper_level" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/ubprop#_upper_level" ], "xrefs" : [ { "val" : "CALOHA:TS-2035" }, { @@ -50,6 +50,7 @@ "val" : "A cell found in the embryo before the formation of all the gem layers is complete.", "xrefs" : [ "GOC:tfm" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "ZFA:0009002" } ] @@ -64,7 +65,7 @@ "xrefs" : [ "GOC:tfm", "MESH:D013234" ] }, "comments" : [ "This term applies to metazoan. For plant stem cells, consider using PO:0004011 ‘initial cell’ or its parent PO:0004010 ‘meristematic cell’." ], - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#general_cell_types_upper_slim", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#general_cell_types_upper_slim", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "animal stem cell" @@ -91,7 +92,7 @@ "xrefs" : [ "GOC:add", "GOC:dsd", "GOC:tfm", "PMID:19022770", "http://en.wikipedia.org/wiki/Hematopoietic_stem_cell" ] }, "comments" : [ "Markers differ between species, and two sets of markers have been described for mice. HSCs are reportedly CD34-positive, CD45-positive, CD48-negative, CD150-positive, CD133-positive, and CD244-negative." ], - "subsets" : [ "http://purl.obolibrary.org/obo/cl#blood_and_immune_upper_slim", "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#blood_and_immune_upper_slim", "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "blood forming stem cell" @@ -134,7 +135,7 @@ "xrefs" : [ "GOC:tfm", "ISBN:0721662544" ] }, "comments" : [ "Originally this term had some plant germ line cell children." ], - "subsets" : [ "http://purl.obolibrary.org/obo/cl#general_cell_types_upper_slim", "http://purl.obolibrary.org/obo/ubprop#_upper_level" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#general_cell_types_upper_slim", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/ubprop#_upper_level" ], "xrefs" : [ { "val" : "ZFA:0009016" } ] @@ -149,6 +150,7 @@ "xrefs" : [ "GOC:add", "PMID:1104740", "http://en.wikipedia.org/wiki/Monoblast", "http://www.copewithcytokines.de" ] }, "comments" : [ "Morphology: mononuclear cell, diameter 12-20 _M, non-granular, N/C ratio 3/1 - 4/1; markers: CD11b (shared with many other myeloid cells); location: Adult: bone marrow; fetal: liver, Yolk Sac; role or process: hematopoiesis, monocyte development; lineage: hematopoietic, myeloid." ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003000", "pred" : "hasRelatedSynonym", @@ -180,6 +182,7 @@ "val" : "A stem cell that can give rise to multiple lineages of cells.", "xrefs" : [ "GOC:add" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "multi-fate stem cell" @@ -209,7 +212,7 @@ "xrefs" : [ "GOC:add", "ISBN:0878932437", "MESH:D023461" ] }, "comments" : [ "This cell type is intended to be compatible with any vertebrate common myeloid progenitor. For mammalian CMP known to be CD34-positive, please use the term 'common myeloid progenitor, CD34-positive' (CL_0001059)." ], - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "common myeloid precursor" @@ -265,7 +268,7 @@ "xrefs" : [ "GOC:add", "GOC:dsd", "GOC:tfm", "PMID:10407577", "PMID:16551251" ] }, "comments" : [ "CLP are CD7-positive, CD10-positive, CD19-negative, CD34-positive, CD45RA-positive, CD79a-negative, CD127-positive, AA4.1-positive, RAG-negative, Sca-1-low, sIgM-negative, sIgD-negative, TdT-negative, Vpre-B-negative, and pre-BCR-negative. Expression of transcription factors include E2A-positive, EBF-positive, Ikaros-negative, PU.1-negative, and Pax5-negative." ], - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "common lymphocyte precursor" @@ -313,6 +316,7 @@ "val" : "A stem cell from which all cells of the body can form.", "xrefs" : [ "GOC:add", "GOC:tfm" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "totipotential stem cell" @@ -335,7 +339,7 @@ "xrefs" : [ "SANBI:mhl" ] }, "comments" : [ "define using PATO mulit-potent or oligopotent?" ], - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "blast cell" @@ -355,6 +359,7 @@ "val" : "A cell that is commited to differentiating into a muscle cell. Embryonic myoblasts develop from the mesoderm. They undergo proliferation, migrate to their various sites, and then differentiate into the appropriate form of myocytes. Myoblasts also occur as transient populations of cells in muscles undergoing repair.", "xrefs" : [ "GOC:tfm", "MESH:D032446", "PMID:21849021" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "BTO:0000222" }, { @@ -379,7 +384,7 @@ "xrefs" : [ "ISBN:0517223651", "MESH:D005347", "http://en.wikipedia.org/wiki/Fibroblast" ] }, "comments" : [ "These cells may be vimentin-positive, fibronectin-positive, fsp1-positive, MMP-1-positive, collagen I-positive, collagen III-positive, and alpha-SMA-negative." ], - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#general_cell_types_upper_slim", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#general_cell_types_upper_slim", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "xrefs" : [ { "val" : "BTO:0000452" }, { @@ -407,7 +412,7 @@ "val" : "A cell that is usually found in a two-dimensional sheet with a free surface. The cell has a cytoskeleton that allows for tight cell to cell contact and for cell polarity where apical part is directed towards the lumen and the basal part to the basal lamina.", "xrefs" : [ "FB:ma", "GOC:tfm", "MESH:D004847" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#general_cell_types_upper_slim", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#general_cell_types_upper_slim", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "epitheliocyte" @@ -444,7 +449,7 @@ "val" : "A columnar/cuboidal epithelial cell is a cell usually found in a two dimensional sheet with a free surface. Columnar/cuboidal epithelial cells take on the shape of a column or cube.", "xrefs" : [ "GO:0002065", "https://orcid.org/0000-0001-5208-3432" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "xrefs" : [ { "val" : "ZFA:0009038" } ], @@ -462,7 +467,7 @@ "val" : "A cell found predominately in the blood.", "xrefs" : [ "GOC:add", "GOC:tfm" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#general_cell_types_upper_slim" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#general_cell_types_upper_slim", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "FMA:62844" }, { @@ -480,7 +485,7 @@ "val" : "A type of lymphocyte whose defining characteristic is the expression of a T cell receptor complex.", "xrefs" : [ "GOC:add", "GOC:tfm", "ISBN:0781735149" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#general_cell_types_upper_slim", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#general_cell_types_upper_slim", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "T lymphocyte" @@ -525,7 +530,7 @@ "xrefs" : [ "GOC:add", "GOC:tfm", "GO_REF:0000031", "ISBN:0781735149", "PMID:10428500", "PMID:15055519", "PMID:17380158" ] }, "comments" : [ "Morphology: Highly vesicular; markers: Surface: RANK, cFMS (MCSF receptor); Secreted: cathepsin K and TRAP (tartate resistant acid phosphatase); transcription factors: PU.1, cFOS, MITF, NFkB (p52); role or process: tissue remodelling: bone resorption; lineage: hematopoietic, myeloid." ], - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "pred" : "hasRelatedSynonym", "val" : "chondroclast" @@ -540,6 +545,12 @@ "val" : "MESH:D010010" }, { "val" : "ZFA:0009047" + }, { + "val" : "https://cellxgene.cziscience.com/cellguide/CL_0000092" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/description", + "val" : "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nOsteoclasts, derived from the monocyte/macrophage lineage, play a crucial role in bone remodeling through bone resorption. They are distinguished from other cells by their large size and their unique ability to secrete enzymes and acids that dissolve the calcium phosphate in bone. The formation of osteoclasts is influenced by two primary factors: macrophage colony-stimulating factor (M-CSF) and the ligand-activated receptor (RANKL) of nuclear factor kappa B (NF-κB).\nOsteoclasts also collaborate with osteoblasts, responsible for new bone formation, to maintain bone health and adapt bone structure. Their coordinated actions allow continuous remodeling while preserving overall bone strength and integrity. Imbalances in osteoclast activity can lead to pathological conditions. For example, excessive activity may contribute to diseases like osteoporosis, periprosthetic osteolysis, bone tumors, and Paget's disease. Other the other hand, osteoclast deficiency ca result in conditions like osteopetrosis." } ] } }, { @@ -551,7 +562,7 @@ "val" : "A leukocyte with abundant granules in the cytoplasm.", "xrefs" : [ "GOC:amm", "GOC:tfm", "MESH:D006098", "http://en.wikipedia.org/wiki/Granulocyte" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "granular leucocyte" @@ -583,7 +594,7 @@ "lbl" : "neuron associated cell", "type" : "CLASS", "meta" : { - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ] + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ] } }, { "id" : "http://purl.obolibrary.org/obo/CL_0000100", @@ -594,7 +605,7 @@ "val" : "An efferent neuron that passes from the central nervous system or a ganglion toward or to a muscle and conducts an impulse that causes or inhibits movement.", "xrefs" : [ "MESH:D009046", "PMID:16875686" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "motoneuron" @@ -624,7 +635,7 @@ "val" : "Any neuron having a sensory function; an afferent neuron conveying sensory impulses.", "xrefs" : [ "ISBN:0721662544" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "xrefs" : [ { "val" : "BTO:0001037" }, { @@ -652,7 +663,7 @@ "val" : "A vertebrate phagocyte with a single nucleus.", "xrefs" : [ "GOC:add", "GOC:tfm", "ISBN:0781735149" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "xrefs" : [ { "val" : "BTO:0001433" }, { @@ -665,7 +676,7 @@ "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" }, { "pred" : "http://purl.org/dc/terms/description", - "val" : "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional.\n\nMononuclear phagocytes are immune cells that form a critical part of the body's innate immune system, the body's first line of defense against infections. Mononuclear phagocytes are characterized by the presence of a single, large nucleus. The ‘Mononuclear Phagocyte System’ nomenclature was introduced to distinguish mononuclear monocytes and macrophages from other cells with multiple nuclei. However, the cells within the mononuclear phagocyte system represent a highly heterogeneous group, all of which are able to perform highly efficient phagocytosis - engulfing and digesting microbes and cellular debris to fight infections and to maintain normal tissue homeostasis. \nIn addition to phagocytosis, mononuclear phagocytes also secrete chemical compounds to recruit other immune cells to a site of infection. These cells produce different types of signaling molecules, including cytokines, chemokines, and reactive oxygen species, triggering a cascade of responses to ensure rapid and efficient containment and neutralization of invading pathogens. These cells are also involved in antigen presentation, a process essential for stimulating an adaptive immune response. They can process and present antigens to T cells, thereby linking the innate and adaptive immune responses.\nMononuclear phagocytes play key roles in tissue repair and remodeling. After infection or injury, these cells help in the clearance of dead cells and debris, a crucial step in the initiation of tissue remodeling and the resolution of inflammation. Overall, mononuclear phagocytes are versatile cells that have tailored their functions to meet the unique challenges of different tissues within the body. They are pivotal in homeostasis, immunity, and inflammation, making them important aspects in a range of human diseases including infection, autoimmunity, and cancer." + "val" : "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nMononuclear phagocytes are immune cells that form a critical part of the body's innate immune system, the body's first line of defense against infections. Mononuclear phagocytes are characterized by the presence of a single, large nucleus. The ‘Mononuclear Phagocyte System’ nomenclature was introduced to distinguish mononuclear monocytes and macrophages from other cells with multiple nuclei. However, the cells within the mononuclear phagocyte system represent a highly heterogeneous group, all of which are able to perform highly efficient phagocytosis - engulfing and digesting microbes and cellular debris to fight infections and to maintain normal tissue homeostasis. \nIn addition to phagocytosis, mononuclear phagocytes also secrete chemical compounds to recruit other immune cells to a site of infection. These cells produce different types of signaling molecules, including cytokines, chemokines, and reactive oxygen species, triggering a cascade of responses to ensure rapid and efficient containment and neutralization of invading pathogens. These cells are also involved in antigen presentation, a process essential for stimulating an adaptive immune response. They can process and present antigens to T cells, thereby linking the innate and adaptive immune responses.\nMononuclear phagocytes play key roles in tissue repair and remodeling. After infection or injury, these cells help in the clearance of dead cells and debris, a crucial step in the initiation of tissue remodeling and the resolution of inflammation. Overall, mononuclear phagocytes are versatile cells that have tailored their functions to meet the unique challenges of different tissues within the body. They are pivotal in homeostasis, immunity, and inflammation, making them important aspects in a range of human diseases including infection, autoimmunity, and cancer." } ] } }, { @@ -678,7 +689,7 @@ "xrefs" : [ "MESH:D009457" ] }, "comments" : [ "Not all glial cells develop from glioblasts, with microglia developing from the mesoderm instead. See https://github.com/obophenotype/cell-ontology/issues/1571" ], - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#general_cell_types_upper_slim", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#general_cell_types_upper_slim", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "neuroglial cell" @@ -704,7 +715,7 @@ "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" }, { "pred" : "http://purl.org/dc/terms/description", - "val" : "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional.\n\nGlial cells, also known as neuroglia or simply glia, are non-neuronal cells in the central and peripheral nervous systems that provide support and protection for neurons. They constitute approximately half of the total cells in the human brain and more than half in other parts of the nervous system. Glial cells perform several key functions including, but not limited to, maintaining homeostasis, forming the myelin sheath around the neuron axons, and providing support and nutrition to neurons.\nThese different functions are performed by various glial cell types, including astrocytes, oligodendrocytes, microglia and other specialized types. Astrocytes, for example, are the most abundant glial cells and provide metabolic and nutrient support to neurons, help regulate the extracellular ion and neurotransmitter levels, and play a role in the formation and maintenance of the blood-brain barrier, contributing to the overall homeostasis and functioning of the nervous system. Additionally, astrocytes are involved in synaptic communication and participate in processes such as synaptogenesis and synaptic pruning.\nOligodendrocytes in the central nervous system function to insulate neurons by producing a fatty substance known as myelin. The myelin sheath enhances the speed and efficiency of nerve impulse conduction along the axons. \nMicroglia, the immune cells of the central nervous system, protect neurons from pathogens and clear away dead neurons through phagocytosis, a process also known as cellular eating. They also contribute to the regulation of inflammation in response to signals of tissue damage or infection in the central nervous system by releasing cytokines and other signaling molecules that modulate the immune response.\nDespite their overarching function in the support and protection of neurons, glial cells have also been shown to play significant roles in the pathophysiology of many psychiatric and neurodegenerative diseases, such as Alzheimer’s, Parkinson’s Disease and multiple sclerosis." + "val" : "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nGlial cells, also known as neuroglia or simply glia, are non-neuronal cells in the central and peripheral nervous systems that provide support and protection for neurons. They constitute approximately half of the total cells in the human brain and more than half in other parts of the nervous system. Glial cells perform several key functions including, but not limited to, maintaining homeostasis, forming the myelin sheath around the neuron axons, and providing support and nutrition to neurons.\nThese different functions are performed by various glial cell types, including astrocytes, oligodendrocytes, microglia and other specialized types. Astrocytes, for example, are the most abundant glial cells and provide metabolic and nutrient support to neurons, help regulate the extracellular ion and neurotransmitter levels, and play a role in the formation and maintenance of the blood-brain barrier, contributing to the overall homeostasis and functioning of the nervous system. Additionally, astrocytes are involved in synaptic communication and participate in processes such as synaptogenesis and synaptic pruning.\nOligodendrocytes in the central nervous system function to insulate neurons by producing a fatty substance known as myelin. The myelin sheath enhances the speed and efficiency of nerve impulse conduction along the axons. \nMicroglia, the immune cells of the central nervous system, protect neurons from pathogens and clear away dead neurons through phagocytosis, a process also known as cellular eating. They also contribute to the regulation of inflammation in response to signals of tissue damage or infection in the central nervous system by releasing cytokines and other signaling molecules that modulate the immune response.\nDespite their overarching function in the support and protection of neurons, glial cells have also been shown to play significant roles in the pathophysiology of many psychiatric and neurodegenerative diseases, such as Alzheimer’s, Parkinson’s Disease and multiple sclerosis." } ] } }, { @@ -716,6 +727,7 @@ "val" : "Ectoderm destined to be nervous tissue.", "xrefs" : [ "GOC:tfm", "ISBN:068340007X" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "neurectoderm cell" @@ -734,7 +746,7 @@ "xrefs" : [ "FB:ma", "GOC:dsd", "PMCID:PMC2613570", "PMID:10102814", "PMID:16923606", "PMID:17986482", "PMID:19960544", "http://en.wikipedia.org/wiki/Mesenchymal_stem_cell", "http://www.copewithcytokines.de/cope.cgi?key=mesenchymal%20stem%20cells" ] }, "comments" : [ "Many but not all mesenchymal cells derive from the mesoderm. MSCs are reportedly CD3-negative, CD4-negative, CD5-negative, CD8-negative, CD11a-negative, CD11b-negative, CD14-negative, CD19-negative, CD29-positive, CD31-negative, CD34-negative, CD38-negative, CD40-negative, CD44-positive, CD45-negative, CD49-positive, CD54-positive, CD66b-negative, CD79a-negative, CD80-negative, CD102-positive, CD106-positive, CD117-positive, CD121a-positive, CD121b-positive, CD123-positive, CD124-positive, CD133-negative, CD146-positive, CD166-positive, CD271-positive, B220-negative, Gr1-negative, MHCI-positive, MHCII-negative, SSEA4-negative, sca1-positive, Ter119-negative, and glycophorin A-negative. Cultured MSCs are capable of producing stem cell factor, IL7, IL8, IL11, TGF-beta, cofilin, galectin-1, laminin-receptor 1, cyclophilin A, and MMP-2." ], - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "pred" : "hasNarrowSynonym", "val" : "bone marrow stromal cells" @@ -805,7 +817,7 @@ "val" : "A fat-storing cell found mostly in the abdominal cavity and subcutaneous tissue of mammals. Fat is usually stored in the form of triglycerides.", "xrefs" : [ "MESH:D017667" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#general_cell_types_upper_slim", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#general_cell_types_upper_slim", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "adipose cell" @@ -837,7 +849,7 @@ "xrefs" : [ "GOC:add", "ISBN:0781735149" ] }, "comments" : [ "Note change of name; nearly all somatic cells can present antigens to T cells via MHC Class I complexes leading to effector responses, but professional antigen presenting cells constitutively express MHC Class II as well as costimulatory molecules, and thus can initiate immune responses via T cells." ], - "subsets" : [ "http://purl.obolibrary.org/obo/cl#blood_and_immune_upper_slim", "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#blood_and_immune_upper_slim", "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003000", "pred" : "hasRelatedSynonym", @@ -856,6 +868,7 @@ "val" : "A pigment cell is a cell that contains pigment granules.", "xrefs" : [ "GOC:tfm" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "chromatocyte" @@ -878,7 +891,7 @@ "val" : "A pigment cell derived from the neural crest. Contains melanin-filled pigment granules, which gives a brown to black appearance.", "xrefs" : [ "SANBI:mhl" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#general_cell_types_upper_slim", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#general_cell_types_upper_slim", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "synonyms" : [ { "pred" : "hasNarrowSynonym", "val" : "melanophore" @@ -895,10 +908,15 @@ "val" : "VHOG:0001679" }, { "val" : "ZFA:0009091" + }, { + "val" : "https://cellxgene.cziscience.com/cellguide/CL_0000148" } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" + }, { + "pred" : "http://purl.org/dc/terms/description", + "val" : "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nMelanocytes are specialized cells prevalently found in the skin, but also present in the hair follicles, eyes, inner ear, bones, heart, and brain. Their primary function is the synthesis of melanin, a pigment responsible for coloration of skin, hair, and eyes. The presence and distribution of this pigment play a crucial role in the body's defense mechanism against harmful ultraviolet radiation.\nIn addition to melanin production, melanocytes also engage in a variety of other biological functions. They play a fundamental role in the immune response, owing to their ability to present antigens to T cells. Furthermore, they contribute to the maintenance of the skin's homeostasis by regulating processes such as extracellular matrix remodeling and cytokine production. A balance in melanocyte function is pivotal, as dysfunctions often result in dermatological disorders. For instance, the loss of melanocytes or reduction in their function may lead to hypopigmentation conditions such as vitiligo, whereas an abnormal increase could result in hyperpigmentation disorders or melanoma, a dangerous type of skin cancer." } ] } }, { @@ -906,6 +924,7 @@ "lbl" : "visual pigment cell", "type" : "CLASS", "meta" : { + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "pred" : "hasBroadSynonym", "val" : "pigment cell" @@ -920,7 +939,7 @@ "val" : "A cell that specializes in controlled release of one or more substances.", "xrefs" : [ "GOC:tfm", "ISBN:0721662544" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "BTO:0003659" }, { @@ -936,7 +955,7 @@ "val" : "A cell of an exocrine gland; i.e. a gland that discharges its secretion via a duct.", "xrefs" : [ "ISBN:0198547684" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#general_cell_types_upper_slim" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#general_cell_types_upper_slim", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "FMA:16014" }, { @@ -952,7 +971,7 @@ "val" : "A cell of an endocrine gland, ductless glands that secrete substances which are released directly into the circulation and which influence metabolism and other body functions.", "xrefs" : [ "MESH:D055098" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#general_cell_types_upper_slim", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#general_cell_types_upper_slim", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "endocrinocyte" @@ -976,7 +995,7 @@ "val" : "A cell whose primary function is to shorten.", "xrefs" : [ "FB:ma" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ] + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ] } }, { "id" : "http://purl.obolibrary.org/obo/CL_0000187", @@ -987,7 +1006,7 @@ "val" : "A mature contractile cell, commonly known as a myocyte. This cell has as part of its cytoplasm myofibrils organized in various patterns.", "xrefs" : [ "MESH:D032342" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "muscle fiber" @@ -1024,7 +1043,7 @@ "val" : "A somatic cell located in skeletal muscle.", "xrefs" : [ "GOC:tfm" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#general_cell_types_upper_slim", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#general_cell_types_upper_slim", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "skeletal muscle cell" @@ -1037,10 +1056,15 @@ "val" : "FMA:9727" }, { "val" : "ZFA:0009115" + }, { + "val" : "https://cellxgene.cziscience.com/cellguide/CL_0000188" } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" + }, { + "pred" : "http://purl.org/dc/terms/description", + "val" : "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nSkeletal muscle cells, or myocytes, are essential for the musculoskeletal system, featuring a striated appearance from tightly packed sarcomeres. These elongated, multi-nucleated cells convert ATP into mechanical energ and are key for voluntary movement and posture. They also are responsible for maintaining body temperature, storing nutrients, and stabilizing joints.\nSkeletal muscle cells organize themselves tightly into bundles to form muscle fibers. Embedded within each of these cells are thousands of myofibrils, which are made up of the contractile proteins, actin (the thin filament), and myosin (the thick filament). Contraction of a skeletal muscle cell occurs when these myofibrils shorten, a process driven by the sliding of actin and myosin filaments over each other in a mechanism famously known as the sliding filament theory.\nAdditionally, skeletal muscle cells exhibit a high degree of plasticity, which allows for their adaptation in response to alterations in functional demands or damages. They have an innate regenerative capacity due to the presence of satellite cells—quiescent muscle stem cells that reside within the muscle fibers. Upon muscle injury, these satellite cells become activated, proliferate, and differentiate into new muscle cells, thereby contributing to the repair and growth of injured skeletal muscle. With this, skeletal muscle cells serve not only a pivotal biomechanical function but also possess a great capacity for self-healing and regeneration." } ] } }, { @@ -1052,7 +1076,7 @@ "val" : "A non-striated, elongated, spindle-shaped cell found lining the digestive tract, uterus, and blood vessels. They develop from specialized myoblasts (smooth muscle myoblast).", "xrefs" : [ "MESH:D032389", "PMID:9315361", "http://en.wikipedia.org/wiki/Smooth_muscle_cell" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#general_cell_types_upper_slim", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#general_cell_types_upper_slim", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "synonyms" : [ { "pred" : "hasBroadSynonym", "val" : "non-striated muscle cell" @@ -1076,10 +1100,15 @@ "val" : "FMA:14072" }, { "val" : "ZFA:0009118" + }, { + "val" : "https://cellxgene.cziscience.com/cellguide/CL_0000192" } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" + }, { + "pred" : "http://purl.org/dc/terms/description", + "val" : "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nSmooth muscle cells are a specialized type of muscle cells that are primarily found within the walls of hollow organs such as the intestine, stomach, bladder, uterus, and blood vessels. These cells are an essential component of the autonomic nervous system controling involuntary movements within the body.\nSmooth muscle cells play a vital role in many physiological processes due to their unique functionality. They can contract and relax in a slow, sustained, and controlled manner to help modulate the size and shape of the lumens of the organs they surround. For example, in the digestive system, coordinated contraction and relaxation of smooth muscle cells propels food along the gastrointestinal tract - a process known as peristalsis. In the blood vessels, the smooth muscle cells, by contracting or relaxing, either constrict or dilate the vessels, which in turn, help regulate blood flow and pressure.\nOn a cellular level, smooth muscle cells possess a single, centrally located nucleus and contain an arranged network of actin and myosin filaments, which are the proteins responsible for muscle contraction. Unlike their counterparts in skeletal or cardiac muscles, these cells lack specific contact points for these filaments, hence the lack of visible striations. Furthermore, the contraction of smooth muscle cells is regulated by hormones and neurotransmitters, such as acetylcholine and norepinephrine, adding an additional layer of complex regulation to these highly specialized cells." } ] } }, { @@ -1091,7 +1120,7 @@ "val" : "A cell specialized in detecting light stimuli that are involved in visual perception.", "xrefs" : [ "MESH:D010786" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "BTO:0001060" }, { @@ -1117,6 +1146,7 @@ "val" : "A cell whose function is determined by the generation or the reception of an electric signal.", "xrefs" : [ "FB:ma" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "ZFA:0009128" } ] @@ -1130,6 +1160,7 @@ "val" : "A cell that moves by its own activities.", "xrefs" : [ "FB:ma" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "ZFA:0009136" } ] @@ -1143,6 +1174,7 @@ "val" : "A cell of the outer of the three germ layers of the embryo.", "xrefs" : [ "MESH:D004475" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "ectoderm cell" @@ -1162,7 +1194,7 @@ "val" : "A cell of the middle germ layer of the embryo.", "xrefs" : [ "MESH:D008648" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "mesoblast" @@ -1174,6 +1206,12 @@ "val" : "FMA:72554" }, { "val" : "ZFA:0009138" + }, { + "val" : "https://cellxgene.cziscience.com/cellguide/CL_0000222" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/description", + "val" : "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nMesodermal cells are pluripotent and the most abundant in the human body. They contribute to the development of several structures such as the skeletal muscles, bones, heart and blood vessels, kidneys, gonads, connective tissues, and certain layers of the skin. Hence, the mesoderm is often regarded as an active and diverse layer due to its role in forming many bodily structures. \nIn embryonic development, these cells are instrumental, contributing to the body's structures through a carefully coordinated sequence of morphogenetic movements. This process forms the complex multicellular architecture of tissues and organs from a simple ball of cells. Without the function of mesodermal cells, the body's integral structures and systems would cease to form correctly, leading to developmental disorders such as axial mesodermal dysplasia complex" } ] } }, { @@ -1185,6 +1223,7 @@ "val" : "A cell of the inner of the three germ layers of the embryo.", "xrefs" : [ "MESH:D004707" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "endoderm cell" @@ -1203,7 +1242,8 @@ "definition" : { "val" : "A cell with a single nucleus.", "xrefs" : [ "FB:ma", "GOC:tfm" ] - } + }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ] } }, { "id" : "http://purl.obolibrary.org/obo/CL_0000228", @@ -1214,6 +1254,7 @@ "val" : "A cell with more than one nucleus.", "xrefs" : [ "FB:ma", "Wikipedia:Multinucleate" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "multinucleated cells", @@ -1233,7 +1274,7 @@ "val" : "Any cell capable of ingesting particulate matter via phagocytosis.", "xrefs" : [ "GOC:add", "ISBN:0721601464" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "BTO:0001044" }, { @@ -1254,7 +1295,7 @@ "xrefs" : [ "GOC:add", "GOC:tfm", "GO_REF:0000031", "PMID:16213494", "PMID:1919437" ] }, "comments" : [ "Morphology: Diameter 30_M-80 _M, abundant cytoplasm, low N/C ratio, eccentric nucleus. Irregular shape with pseudopods, highly adhesive. Contain vacuoles and phagosomes, may contain azurophilic granules; markers: Mouse & Human: CD68, in most cases CD11b. Mouse: in most cases F4/80+; role or process: immune, antigen presentation, & tissue remodelling; lineage: hematopoietic, myeloid." ], - "subsets" : [ "http://purl.obolibrary.org/obo/cl#blood_and_immune_upper_slim", "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#general_cell_types_upper_slim", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#blood_and_immune_upper_slim", "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#general_cell_types_upper_slim", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "histiocyte" @@ -1286,7 +1327,7 @@ "val" : "A lymphocyte of B lineage that is capable of B cell mediated immunity.", "xrefs" : [ "GOC:add", "GOC:tfm", "GO_REF:0000031", "ISBN:0781735149" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#blood_and_immune_upper_slim", "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#general_cell_types_upper_slim", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#blood_and_immune_upper_slim", "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#general_cell_types_upper_slim", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "B lymphocyte" @@ -1324,7 +1365,7 @@ "val" : "Any cell that in taxon some Eukaryota.", "xrefs" : [ "FBC:Autogenerated" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "MESH:D005057" } ] @@ -1338,13 +1379,14 @@ "val" : "A cell that is specialised to accumulate a particular substance(s).", "xrefs" : [ "FB:ma" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/ubprop#_upper_level" ] + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/ubprop#_upper_level" ] } }, { "id" : "http://purl.obolibrary.org/obo/CL_0000327", "lbl" : "extracellular matrix secreting cell", "type" : "CLASS", "meta" : { + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "ZFA:0009162" } ] @@ -1358,6 +1400,7 @@ "val" : "A cell derived from the specialized ectoderm flanking each side of the embryonic neural plate, which after the closure of the neural tube, forms masses of cells that migrate out from the dorsal aspect of the neural tube to spread throughout the body.", "xrefs" : [ "doi:10.1016/j.stem.2015.02.017" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "FMA:86667" }, { @@ -1373,7 +1416,7 @@ "val" : "Any cell that is part of some extraembryonic structure.", "xrefs" : [ "FBC:Autogenerated" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#general_cell_types_upper_slim" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#general_cell_types_upper_slim", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "ZFA:0009176" } ] @@ -1386,7 +1429,8 @@ "definition" : { "val" : "A cell of the outer layer of a blastula that gives rise to the ectoderm after gastrulation.", "xrefs" : [ "GOC:tfm", "ISBN:0618947256" ] - } + }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ] } }, { "id" : "http://purl.obolibrary.org/obo/CL_0000355", @@ -1398,6 +1442,7 @@ "xrefs" : [ "PMID:18282570" ] }, "comments" : [ "Multi-potency demonstrated ex vivo. At the time of writing, it is unclear whether the endogenous population differentiates into multiple cell types in vivo." ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "FMA:86767" }, { @@ -1413,6 +1458,7 @@ "val" : "Diploid cell produced by the fusion of sperm cell nucleus and egg cell.", "xrefs" : [ "ISBN:0471245208" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "pred" : "hasBroadSynonym", "val" : "zygote" @@ -1434,6 +1480,7 @@ "val" : "A cell whose function is determined by its response to an electric signal.", "xrefs" : [ "FB:ma" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "ZFA:0009190" } ] @@ -1447,6 +1494,7 @@ "val" : "A cell that initiates an electrical signal and passes that signal to another cell.", "xrefs" : [ "FB:ma" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "ZFA:0009193" } ] @@ -1460,7 +1508,7 @@ "val" : "A cell of hematopoietic origin, typically resident in particular tissues, specialized in the uptake, processing, and transport of antigens to lymph nodes for the purpose of stimulating an immune response via T cell activation. These cells are lineage negative (CD3-negative, CD19-negative, CD34-negative, and CD56-negative).", "xrefs" : [ "GOC:add", "ISBN:0781735149" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#general_cell_types_upper_slim", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#general_cell_types_upper_slim", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "synonyms" : [ { "pred" : "hasRelatedSynonym", "val" : "interdigitating cell" @@ -1492,7 +1540,8 @@ "definition" : { "val" : "A cell whose primary function is to protect the organism.", "xrefs" : [ "JB:jb" ] - } + }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ] } }, { "id" : "http://purl.obolibrary.org/obo/CL_0000499", @@ -1500,10 +1549,10 @@ "type" : "CLASS", "meta" : { "definition" : { - "val" : "A connective tissue cell of an organ found in the loose connective tissue. These are most often associated with the uterine mucosa and the ovary as well as the hematopoietic system and elsewhere.", + "val" : "A connective tissue cell of an organ found in the loose connective tissue.", "xrefs" : [ "GOC:tfm", "MESH:D017154" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#general_cell_types_upper_slim", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#general_cell_types_upper_slim", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "xrefs" : [ { "val" : "BTO:0002064" }, { @@ -1525,7 +1574,7 @@ "val" : "A precursor cell destined to differentiate into cardiac muscle cell.", "xrefs" : [ "GOC:tfm", "MESH:D032386" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "cardiac muscle progenitor cell" @@ -1548,7 +1597,7 @@ "val" : "A precursor cell destined to differentiate into smooth muscle myocytes.", "xrefs" : [ "GOC:tfm", "MESH:D032390" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "myoblast, smooth muscle", @@ -1561,6 +1610,12 @@ "val" : "FMA:84798" }, { "val" : "ZFA:0009235" + }, { + "val" : "https://cellxgene.cziscience.com/cellguide/CL_0000514" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/description", + "val" : "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nA precursor to the smooth muscle cell, the smooth muscle myoblast, is integral to various body systems, including the cardiovascular, gastrointestinal, and respiratory systems. Smooth muscle myoblasts arise from the differentiation of mesenchymal stem cells, a process tightly regulated by specific genetic factors and environmental signals. Their role extends to myogenesis, particularly in the formation of muscular tissue, especially during embryonic development.\nSmooth muscle myoblasts possess distinctive cellular characteristics. In contrast to skeletal muscle myoblasts, they do not fuse to create multinucleated fibers. Instead, they differentiate into individual, uninucleated smooth muscle cells. This differentiation unfolds in two distinct phases: proliferation, marked by rapid division to increase cell numbers, and differentiation, involving structural and functional transformation into mature smooth muscle cells. This intricate process is intricately mediated by various signaling molecules and transcription factors.\nFunctionally, smooth muscle myoblasts and the mature muscle cells they generate play pivotal roles in various physiological processes. Smooth muscle cells orchestrate involuntary muscle responses and are integral to body systems that regulate blood flow, propel food along the digestive tract, and control airflow in the respiratory tract. These diverse functions underscore the significance of smooth muscle myoblasts in the body's growth, maintenance, and overall function." } ] } }, { @@ -1572,6 +1627,7 @@ "val" : "A myoblast that differentiates into skeletal muscle fibers.", "xrefs" : [ "SANBI:mhl" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "skeletal myoblast" @@ -1590,7 +1646,8 @@ "definition" : { "val" : "A phagocyte in vertebrates that is able to phagocytosis.", "xrefs" : [ "GOC:tfm" ] - } + }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ] } }, { "id" : "http://purl.obolibrary.org/obo/CL_0000526", @@ -1601,7 +1658,7 @@ "val" : "A neuron which conveys sensory information centrally from the periphery.", "xrefs" : [ "GOC:tfm", "MESH:D009475" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "input neuron" @@ -1625,6 +1682,7 @@ "val" : "A neuron which sends impulses peripherally to activate muscles or secretory cells.", "xrefs" : [ "MESH:D009476" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "output neuron" @@ -1643,7 +1701,7 @@ "xrefs" : [ "MESH:D009474", "http://en.wikipedia.org/wiki/Neuron" ] }, "comments" : [ "These cells are also reportedly CD4-negative and CD200-positive. They are also capable of producing CD40L and IFN-gamma." ], - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#general_cell_types_upper_slim", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#general_cell_types_upper_slim", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "nerve cell" @@ -1681,6 +1739,7 @@ "xrefs" : [ "GOC:tfm", "SANBI:mhl" ] }, "comments" : [ "Derived from UBERON:0002342 neural crest." ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "BTO:0003217" }, { @@ -1699,7 +1758,7 @@ "xrefs" : [ "GOC:add", "ISBN:0683073696", "ISBN:0781735149" ] }, "comments" : [ "Editors note: consider adding taxon constraint to vertebrata (PMID:18025161)" ], - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "xrefs" : [ { "val" : "BTO:0000775" }, { @@ -1728,7 +1787,7 @@ "xrefs" : [ "GOC:amm", "GOC:dsd", "GOC:tfm", "GO_REF:0000031", "ISBN:0721601464", "MESH:D055014", "PMCID:PMC2213186", "PMCID:PMC548021", "PMID:16551251", "PMID:16647566", "http://en.wikipedia.org/wiki/CFU-GM", "http://www.copewithcytokines.de" ] }, "comments" : [ "Originally described in the dendritic cell ontology (DC_CL:0000042)(PMID:19243617). GMPs are reportedly CD16-positive, CD32-positive, CD34-positive, CD38-positive, CD45RA-positive, CD110-negative, CD117-positive, CD123-positive, and SCA1-negative." ], - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "synonyms" : [ { "pred" : "hasBroadSynonym", "val" : "CFU-C , Colony forming unit in culture", @@ -1760,10 +1819,15 @@ } ], "xrefs" : [ { "val" : "ZFA:0009251" + }, { + "val" : "https://cellxgene.cziscience.com/cellguide/CL_0000557" } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" + }, { + "pred" : "http://purl.org/dc/terms/description", + "val" : "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nGranulocyte monocyte progenitor cells (GMP cells), originating from hematopoietic stem cells in the bone marrow, are a critical intermediate in myeloid cell development. Positioned at a key differentiation juncture, these cells exhibit bidirectional potential, giving rise to both granulocyte and monocyte lineages.\nTheir primary role is to generate mature granulocytes and monocytes, essential components of the body's innate immunity and inflammatory responses. Granulocytes, such as neutrophils, eosinophils, and basophils, contribute to the first line of defense against infections by migrating to the infection site and phagocytosing pathogens. Monocytes can differentiate into macrophages or dendritic cells, playing diverse roles in immune responses." } ] } }, { @@ -1776,7 +1840,7 @@ "xrefs" : [ "GOC:tfm", "ISBN:0721601464" ] }, "comments" : [ "Morphology: Mononuclear cell, diameter 14-18 _M, fine azurophilic granules; markers: CD11b (shared with many other myeloid cells); location: Adult: bone marrow; Fetal: Liver, Yolk Sac; role or process: hematopoiesis, monocyte development; lineage: hematopoietic, myeloid." ], - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "xrefs" : [ { "val" : "BTO:0004657" }, { @@ -1799,6 +1863,7 @@ "xrefs" : [ "GOC:dsd", "GOC:tfm", "PMID:12768659" ] }, "comments" : [ "These cells are reportedly CD31-positive, CD34-positive, CD144-positive, CD309-positive, and TAL1-positive." ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "angioblast" @@ -1820,7 +1885,7 @@ "xrefs" : [ "GO_REF:0000031", "MESH:D009000" ] }, "comments" : [ "Morphology: Mononuclear cell, diameter, 14 to 20 _M, N/C ratio 2:1-1:1. Nucleus may appear in variety of shapes: round, kidney, lobulated, or convoluted. Fine azurophilic granules present; markers: CD11b (shared with other myeloid cells), human: CD14, mouse: F4/80-mid,GR1-low; location: Blood, but can be recruited into tissues; role or process: immune & tissue remodelling; lineage: hematopoietic, myeloid." ], - "subsets" : [ "http://purl.obolibrary.org/obo/cl#blood_and_immune_upper_slim", "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#general_cell_types_upper_slim", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#blood_and_immune_upper_slim", "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#general_cell_types_upper_slim", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "xrefs" : [ { "val" : "BTO:0000876" }, { @@ -1844,7 +1909,7 @@ "val" : "A lymphocyte that can spontaneously kill a variety of target cells without prior antigenic activation via germline encoded activation receptors and also regulate immune responses via cytokine release and direct contact with other cells.", "xrefs" : [ "GOC:add", "ISBN:0781735149", "PMID:15771571" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#general_cell_types_upper_slim", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#general_cell_types_upper_slim", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "synonyms" : [ { "pred" : "hasBroadSynonym", "val" : "large granular lymphocyte" @@ -1886,7 +1951,7 @@ "val" : "A non-terminally differentiated cell that is capable of developing into a muscle cell.", "xrefs" : [ "GOC:add" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "ZFA:0009291" } ] @@ -1900,6 +1965,7 @@ "val" : "A stem cell that can give rise to cell types of the body other than those of the germ-line.", "xrefs" : [ "GO:0048103" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "CALOHA:TS-2086" }, { @@ -1917,6 +1983,7 @@ "val" : "Muscle cell which has as its direct parts myofilaments organized into sarcomeres.", "xrefs" : [ "GOC:tfm", "ISBN:0721662544" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "BTO:0002916" }, { @@ -1936,7 +2003,7 @@ "val" : "An achromatic cell of the myeloid or lymphoid lineages capable of ameboid movement, found in blood or other tissue.", "xrefs" : [ "GOC:add", "GOC:tfm", "ISBN:978-0-323-05290-0" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "leucocyte" @@ -1975,7 +2042,7 @@ "xrefs" : [ "GOC:mtg_cardiacconduct_nov11", "GOC:tfm", "ISBN:0323052908", "PMID:22426062", "PMID:4711263" ] }, "comments" : [ "This class encompasses the muscle cells responsible for heart* contraction in both vertebrates and arthropods. The ultrastucture of a wide range of arthropod heart cells has been examined including spiders, horseshoe crabs, crustaceans (see Sherman, 1973 and refs therein) and insects (see Lehmacher et al (2012) and refs therein). According to these refs, the cells participating in heart contraction in all cases are transversely striated. Insects hearts additionally contain ostial cells, also transversely striated muscle cells, but which do not participate in heart contraction." ], - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#general_cell_types_upper_slim", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#general_cell_types_upper_slim", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "synonyms" : [ { "pred" : "hasBroadSynonym", "val" : "cardiocyte" @@ -2003,13 +2070,15 @@ "val" : "MESH:D032383" }, { "val" : "ZFA:0009316" + }, { + "val" : "https://cellxgene.cziscience.com/cellguide/CL_0000746" } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "FMA:83808" + "pred" : "http://purl.org/dc/terms/description", + "val" : "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nCardiac muscle cells, also known as cardiomyocytes or cardiac myocytes, are specialized cells that form the heart tissue. These cells are elongated, branched, and contain a single centrally located nucleus. Their anatomy is composed primarily of densely packed myofibrils, which are protein structures that consist of sarcomeres - the fundamental units of muscle contraction. Cardiac muscle cells are united at their ends through specialized junctions known as intercalated discs, which allow the heart to contract in a unified, powerful and rhythmic way.\nFunctionally, cardiac muscle cells are responsible for the heart's consistent pumping action that circulates blood throughout the body. Unlike most cells in the body, cardiac muscle cells spontaneously depolarize and generate action potentials without external stimulation. This unique trait stems from the presence of ion channels in the cells' membrane that allow a cyclic flow of ions across the membrane, which create the electrical impulses necessary for heart contraction. The spread of these electrical signals from one cardiac muscle cell to another - facilitated by the interconnected network made by the intercalated disks - results in a synchronized contraction of the heart muscle.\nUnlike skeletal muscle cells which can tire and need rest, cardiac muscle cells have to work ceaselessly throughout the entire lifespan, without the opportunity for rest, to ensure continuous circulation of blood. This is made possible through the high volume of mitochondria and a constant supply of oxygen from coronary circulation. In conclusion, cardiac muscle cells, through their unique structure and vital functionality, play a pivotal role in sustaining life by providing the means for blood to reach every cell in the body." } ] } }, { @@ -2021,7 +2090,7 @@ "val" : "A cell of the monocyte, granulocyte, mast cell, megakaryocyte, or erythroid lineage.", "xrefs" : [ "GOC:add" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "BTO:0001441" }, { @@ -2041,7 +2110,7 @@ "val" : "A cell of the monocyte, granulocyte, or mast cell lineage.", "xrefs" : [ "GOC:add" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "ZFA:0009326" } ] @@ -2056,7 +2125,7 @@ "xrefs" : [ "GOC:add", "PMID:10449155", "PMID:17332250", "PMID:9521319" ] }, "comments" : [ "These cells are CD1a-negative, CD1b-positive, CD11a-positive, CD11c-positive, CD13-positive, CD14-negative, CD20-negative, CD21-negative, CD33-positive, CD40-negative, CD50-positive, CD54-positive, CD58-positive, CD68-negative, CD80-negative, CD83-negative, CD85j-positive, CD86-positive, CD89-negative, CD95-positive, CD120a-negative, CD120b-positive, CD123-negative, CD178-negative, CD206-negative, CD207-negative, CD209-negative, and TNF-alpha-negative. Upon TLR stimulation, they are capable of producing high levels of TNF-alpha, IL-6, CXCL8 (IL-8)." ], - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "pred" : "hasBroadSynonym", "val" : "interdigitating cell" @@ -2084,6 +2153,7 @@ "xrefs" : [ "GOC:add", "GOC:pam", "GO_REF:0000031", "PMID:11532393", "PMID:12457618", "PMID:15032583", "PMID:15766674" ] }, "comments" : [ "Most markers only described for human pro NK cells." ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "NKP", @@ -2117,7 +2187,7 @@ "xrefs" : [ "GOC:add", "GOC:dsd", "ISBN:0781735149", "PMID:12633665", "PMID:16551251", "PMID:18432934" ] }, "comments" : [ "Human pro-B cells are reportedly CD10-positive, CD22-positive, CD34-positive, CD38-positive, CD45-low, CD48-positive, CD79a-positive, CD127-positive, CD184-positive, RAG-positive, TdT-positive, Vpre-B-positive, pre-BCR-negative, IgD-negative, and IgM-negative. Transcription factors expressed: Pax5-positive, EBF-positive, E2A-negative, Ikaros-negative, and PU.1-negative." ], - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "synonyms" : [ { "pred" : "hasBroadSynonym", "val" : "pre-pro B cell", @@ -2167,7 +2237,7 @@ "val" : "A lymphoid progenitor cell of the T cell lineage, with some lineage specific marker expression, but not yet fully committed to the T cell lineage.", "xrefs" : [ "GOC:add", "ISBN:0781735149" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "pro-T lymphocyte" @@ -2198,7 +2268,7 @@ "xrefs" : [ "GOC:add", "GOC:tfm", "PMID:19022770" ] }, "comments" : [ "Markers differ between mouse and human." ], - "subsets" : [ "http://purl.obolibrary.org/obo/cl#blood_and_immune_upper_slim", "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#blood_and_immune_upper_slim", "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "MPP" @@ -2228,7 +2298,7 @@ "xrefs" : [ "GOC:add", "GOC:tfm" ] }, "comments" : [ "Note that this is a class of cell types, not an identified single cell type." ], - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "pred" : "hasBroadSynonym", "val" : "lymphoid progenitor cell" @@ -2253,7 +2323,7 @@ "xrefs" : [ "GOC:add", "GOC:tfm", "PMID:19022770" ] }, "comments" : [ "Note that this is a class of cell types, not an identified single cell type." ], - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "synonyms" : [ { "pred" : "hasBroadSynonym", "val" : "myeloid progenitor cell" @@ -2281,7 +2351,7 @@ "val" : "A leukocyte with a single non-segmented nucleus in the mature form.", "xrefs" : [ "GOC:add" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#blood_and_immune_upper_slim", "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#blood_and_immune_upper_slim", "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "mononuclear leukocyte" @@ -2309,7 +2379,7 @@ "xrefs" : [ "GOC:add", "GOC:rhs", "GOC:tfm", "GO_REF:0000031", "ISBN:0781735149" ] }, "comments" : [ "Types of B lineage lymphocytes include B cells and antibody secreting cells (plasmablasts and plasma cells). Lymphocytes of B cell lineage can be distinguished from those of T cell lineage by their lack of CD3e (as part of the T cell receptor complex)." ], - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" @@ -2324,7 +2394,7 @@ "val" : "A cell of a hematopoietic lineage.", "xrefs" : [ "GOC:add", "GO_REF:0000031" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "haematopoietic cell" @@ -2357,7 +2427,7 @@ "xrefs" : [ "GOC:amm", "GO_REF:0000031", "PMID:17850486" ] }, "comments" : [ "Originally described in the dendritic cell ontology (DC_CL:0000003)(PMID:19243617) These cells are also CD20-negative, MHCII-positive." ], - "subsets" : [ "http://purl.obolibrary.org/obo/cl#blood_and_immune_upper_slim", "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#blood_and_immune_upper_slim", "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "synonyms" : [ { "pred" : "hasBroadSynonym", "val" : "interdigitating cell" @@ -2390,7 +2460,8 @@ "lbl" : "CD7-negative lymphoid progenitor OR granulocyte monocyte progenitor", "type" : "CLASS", "meta" : { - "comments" : [ "Originally described in the dendritic cell ontology (DC_CL:1110000)(PMID:19243617)." ] + "comments" : [ "Originally described in the dendritic cell ontology (DC_CL:1110000)(PMID:19243617)." ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ] } }, { "id" : "http://purl.obolibrary.org/obo/CL_0001035", @@ -2401,13 +2472,19 @@ "val" : "A connective tissue cell found in bone.", "xrefs" : [ "GOC:add", "GO_REF:0000034" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#general_cell_types_upper_slim", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#general_cell_types_upper_slim", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "xrefs" : [ { + "val" : "https://cellxgene.cziscience.com/cellguide/CL_0001035" + } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" }, { "pred" : "http://purl.org/dc/terms/contributor", "val" : "https://orcid.org/0000-0001-9990-8331" + }, { + "pred" : "http://purl.org/dc/terms/description", + "val" : "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nBone cells, also known as osteocytes, form the building blocks of the skeletal system. They represent the most common type of bone cell, making up approximately 95% of the total bone cell population in mature adult bone tissue. Osteocytes are a stellate shape with numerous long, slender dendritic processes.\nThe formation of bone is a complex process involving the action of osteoclasts - cells that break down and reabsorb old bone, followed by osteoblasts that rebuild the bone. Osteocytes serve as coordinators for these two types of bone cells to ensure a balance in the bone remodeling process, contributing to maintaining both bone strength and mineral homeostasis.\nThe primary functions of osteocytes involve the creation, maintenance, and repair of bone tissue. They ensure that bone remodeling is performed by forming a network within the bone and communicating with other cells to help them respond to mechanical strain and damage.\nA remarkable aspect of osteocytes is their ability to perceive mechanical forces, translating them into biochemical signals that regulate bone remodeling and adaptation. Defects in osteocyte function, aside from other bone cells, have been associated with several bone disorders such as osteoporosis, renal osteodystrophy, and skeletal manifestations of diabetes." }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2011-11-16T04:28:16Z" @@ -2422,6 +2499,7 @@ "val" : "A hematopoietic oligopotent progenitor cell that has the ability to differentiate into limited cell types but lacks lineage cell markers and self renewal capabilities. Cell lacks hematopoeitic lineage markers.", "xrefs" : [ "GOC:tfm", "PMID:19022770" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "basicPropertyValues" : [ { "pred" : "http://purl.org/dc/terms/contributor", "val" : "https://orcid.org/0000-0003-1980-3228" @@ -2439,7 +2517,7 @@ "val" : "A lymphocyte that lacks characteristic T cell, B cell, myeloid cell, and dendritic cell markers, that functions as part of the innate immune response to produce cytokines and other effector responses.", "xrefs" : [ "GOC:add", "GOC:dsd", "PMID:23292121", "PMID:23348417" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#blood_and_immune_upper_slim", "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#blood_and_immune_upper_slim", "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" @@ -2460,7 +2538,7 @@ "val" : "An innate lymphoid cell that is capable of producing the type 1 cytokine IFN-gamma, but not Th2 or Th17 cell-associated cytokines.", "xrefs" : [ "GOC:add", "GOC:dsd", "PMID:23348417" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" @@ -2481,7 +2559,7 @@ "val" : "A progenitor cell that can give rise to plasmacytoid and myeloid dendritic cells, and to monocytes and macrophages.", "xrefs" : [ "GOC:tfm", "PMID:19273628" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "MDP" @@ -2503,7 +2581,7 @@ "val" : "A hematopoietic progenitor cell that is capable of developing into only one lineage of hematopoietic cells.", "xrefs" : [ "GOC:tfm", "PMID:19022770" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#blood_and_immune_upper_slim" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#blood_and_immune_upper_slim", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "basicPropertyValues" : [ { "pred" : "http://purl.org/dc/terms/contributor", "val" : "https://orcid.org/0000-0003-1980-3228" @@ -2522,7 +2600,7 @@ "xrefs" : [ "GOC:tfm", "PMID:19022770", "https://orcid.org/0000-0001-5208-3432" ] }, "comments" : [ "This cell type is intended to be compatible with any vertebrate hematopoietic oligopotent progenitor cell. For mammalian hematopoietic oligopotent progenitor cells known to be lineage-negative, please use the term 'hematopoietic oligopotent progenitor cell' (CL_0001060)." ], - "subsets" : [ "http://purl.obolibrary.org/obo/cl#blood_and_immune_upper_slim" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#blood_and_immune_upper_slim", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "basicPropertyValues" : [ { "pred" : "http://purl.org/dc/terms/contributor", "val" : "https://orcid.org/0000-0003-1980-3228" @@ -2540,6 +2618,7 @@ "val" : "An epithelial cell derived from ectoderm.", "xrefs" : [ "FMA:69074", "GOC:tfm" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "FMA:69074" }, { @@ -2563,7 +2642,7 @@ "xrefs" : [ "GOC:tfm", "ISBN:0618947256" ] }, "comments" : [ "MH consider whether bone marrow cells are bone cells in the structural sense vs. being part of bone organ sense." ], - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "BTO:0004850" }, { @@ -2588,6 +2667,7 @@ "val" : "A cell involved in the formation of a monocyte (monopoiesis).", "xrefs" : [ "GOC:tfm" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "FMA:83552" } ], @@ -2608,6 +2688,7 @@ "val" : "A cell containing at least one nucleus.", "xrefs" : [ "GOC:tfm" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "FMA:67513" } ], @@ -2628,7 +2709,7 @@ "val" : "A cell that is part of the nervous system.", "xrefs" : [ "GOC:tfm", "ISBN:0618947256" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "CALOHA:TS-2040" }, { @@ -2651,7 +2732,7 @@ "val" : "A cell of the supporting or framework tissue of the body, arising chiefly from the embryonic mesoderm and including adipose tissue, cartilage, and bone.", "xrefs" : [ "GOC:tfm", "ISBN:0618947256" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "CALOHA:TS-2096" }, { @@ -2678,6 +2759,7 @@ "val" : "A cell of the embryo.", "xrefs" : [ "FMA:0618947256" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "CALOHA:TS-0263" }, { @@ -2686,10 +2768,15 @@ "val" : "WBbt:0007028" }, { "val" : "ZFA:0007089" + }, { + "val" : "https://cellxgene.cziscience.com/cellguide/CL_0002321" } ], "basicPropertyValues" : [ { "pred" : "http://purl.org/dc/terms/contributor", "val" : "https://orcid.org/0000-0003-1980-3228" + }, { + "pred" : "http://purl.org/dc/terms/description", + "val" : "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nEmbryonic cells in metazoans, which include all multicellular animals, are biological units in their earliest developmental stages from conception until the organism is fully formed. \nThey are derived from a fertilized egg, which undergoes a series of cell divisions to produce a multicellular organism. During the early phases of embryonic development, these cells exhibit pluripotency, meaning they possess the potential to differentiate into a diverse array of specialized cell types that constitute different body tissues and structures. \nThe balance between cell proliferation and differentiation in embryonic cells is crucial for successful development. When cells continue to divide without differentiating, overgrowth may occur leading to conditions such as teratomas (tumors of embryonic cells). Conversely, if cell differentiation proceeds at the expense of cell proliferation, developmental anomalies could occur regarding size or mass of the organism or its parts." }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2010-09-15T03:39:21Z" @@ -2704,6 +2791,7 @@ "val" : "A transversely striated, multinucleated syncytial muscle cell, formed by the fusion of myoblasts during muscle development.", "xrefs" : [ "GOC:dos", "GOC:tfm", "ISBN:0323052908", "PMID:22274696" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "myofiber", @@ -2734,6 +2822,7 @@ "xrefs" : [ "GOC:tfm" ] }, "comments" : [ "From Onard of the FMA: Cardiac muscle cell or cardiac myocyte is a striated muscle cell. Cardiocyte on the other hand is any cell in the heart which includes cells other than muscle cells (e.g. endothelial cell of endocardium). Unless there is a consensus among anatomists that cardiocytes refer only to muscle cells, we will treat them as a general class of cells in the heart." ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "heart cell" @@ -2765,6 +2854,7 @@ "xrefs" : [ "GO_REF:0000034" ] }, "comments" : [ "Needs logical definition. Should be capable_of skeletal system morphogenesis? or skeletal tissue development? needs to be added to GO. NOTES:a cell type of the early embryo (see also: mesenchymal cells) that will give rise to mineralized connective tissue. Scleroblasts can differentiate into osteoblasts (bone-forming cells), chondroblasts (cartilage-forming cells), odontoblasts (dentin-forming cells), ameloblasts (enamel-forming cells). The mesenchymal cells developing into osteoblasts and chondroblasts are derived from the mesoderm. Those developing into odontoblasts are neural crest cells. Those developing into ameloblasts are derived from the ectoderm. (http://www.copewithcytokines.de/cope.cgi?key=scleroblasts)" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "scleroblast", @@ -2787,6 +2877,7 @@ "val" : "Cell that is part of the neural crest region of the neuroepithelium, prior to migration. Note that not all premigratory neural crest cells may become migratory neural crest cells.", "xrefs" : [ "UBERONREF:0000002" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "ZFA:0007084" } ], @@ -2806,7 +2897,8 @@ "definition" : { "val" : "Any muscle cell in which the fibers are not organised into sarcomeres.", "xrefs" : [ "GOC:DOS" ] - } + }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ] } }, { "id" : "http://purl.obolibrary.org/obo/CL_0008001", @@ -2817,7 +2909,7 @@ "val" : "Any hematopoietic cell that is a precursor of some other hematopoietic cell type.", "xrefs" : [ "GOC:dos" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ] + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ] } }, { "id" : "http://purl.obolibrary.org/obo/CL_0008002", @@ -2828,7 +2920,7 @@ "val" : "A transversely striated, synctial cell of skeletal muscle. It is formed when proliferating myoblasts exit the cell cycle, differentiate and fuse.", "xrefs" : [ "GOC:tfm", "ISBN:0323052908" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "MESH:D018485" } ] @@ -2842,6 +2934,7 @@ "val" : "A muscle cell that is part of some visceral muscle.", "xrefs" : [ "GOC:dos" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "FBbt:00005070" } ] @@ -2854,7 +2947,7 @@ "definition" : { "val" : "A non-polarised cell precursor cell that is part of some mesenchyme, is associated with the cell matrix but is not connected to other cells and is capable of migration." }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "mesenchyme cell" @@ -2873,6 +2966,7 @@ "val" : "Any neuron that is capable of part of some visual perception.", "xrefs" : [ "FBC:Autogenerated" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "basicPropertyValues" : [ { "pred" : "http://purl.org/dc/terms/contributor", "val" : "https://orcid.org/0000-0002-7073-9172" @@ -2890,7 +2984,7 @@ "val" : "Any cell in the retina, the innermost layer or coating at the back of the eyeball, which is sensitive to light and in which the optic nerve terminates.", "xrefs" : [ "GOC:pr" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#general_cell_types_upper_slim" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#general_cell_types_upper_slim", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "PMID:10702418" } ] @@ -2903,6 +2997,7 @@ "definition" : { "val" : "A zygote in a plant or an animal." }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "MESH:D015053" } ], @@ -2920,6 +3015,7 @@ "val" : "Any myoblast that develops into some cardiac muscle cell.", "xrefs" : [ "FBC:Autogenerated" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "MESH:D032386" } ] @@ -2933,13 +3029,13 @@ "val" : "A cell of the neural crest. Neural crest cells are multipotent. Premigratory neural crest cells are found at the neural plate boarder, some of which will undergo ectomesynchymal transition and delamination to form migratory neural crest cells.", "xrefs" : [ "https://orcid.org/0000-0001-5208-3432", "https://orcid.org/0000-0002-9900-7880" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "https://cellxgene.cziscience.com/cellguide/CL_0011012" } ], "basicPropertyValues" : [ { "pred" : "http://purl.org/dc/terms/description", - "val" : "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional.\n\nNeural crest cells are a group of transient and highly migratory cells that originate from the neuroectoderm during the early stages of embryonic development. They are multipotent cells with an exceptional degree of plasticity, capable of differentiating into various somatic cell types and therefore play a fundamental role in the formation of various organs and tissues, making them critical contributors to the developing embryo. \nAfter the initiation of neurulation (the formation of the neural tube) neural crest cells start to undergo epithelial-to-mesenchymal transition and delaminate and migrate from the dorsal neural tube to several regions throughout the embryo. They differentiate into a range of diverse cell types, such as neurons and glial cells of the peripheral nervous system, including sensory and autonomic neurons. They also contribute to the formation of adrenal glands, pigment cells in the skin (melanocytes), cardiac structures, including parts of the heart septum and major arteries, as well as bones and cartilage of the face and skull.\nDisorders or aberrations in the development or migration of the neural crest cells can lead to serious congenital malformations, such as neurocristopathies, including Hirschsprung disease, neuroblastoma, and neurofibromatosis." + "val" : "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nNeural crest cells are a group of transient and highly migratory cells that originate from the neuroectoderm during the early stages of embryonic development. They are multipotent cells with an exceptional degree of plasticity, capable of differentiating into various somatic cell types and therefore play a fundamental role in the formation of various organs and tissues, making them critical contributors to the developing embryo. \nAfter the initiation of neurulation (the formation of the neural tube) neural crest cells start to undergo epithelial-to-mesenchymal transition and delaminate and migrate from the dorsal neural tube to several regions throughout the embryo. They differentiate into a range of diverse cell types, such as neurons and glial cells of the peripheral nervous system, including sensory and autonomic neurons. They also contribute to the formation of adrenal glands, pigment cells in the skin (melanocytes), cardiac structures, including parts of the heart septum and major arteries, as well as bones and cartilage of the face and skull.\nDisorders or aberrations in the development or migration of the neural crest cells can lead to serious congenital malformations, such as neurocristopathies, including Hirschsprung disease, neuroblastoma, and neurofibromatosis." } ] } }, { @@ -2951,7 +3047,7 @@ "val" : "A precursor cell that has a tendency to differentiate into a specific type of cell. They are descendants of stem cells, only they are more constrained in their differentiation potential or capacity for self-renewal, and are often more limited in both senses.", "xrefs" : [ "ISBN:978-1-62808-994-3", "https://doi.org/10.1016/B978-0-12-409503-8.00002-0" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "basicPropertyValues" : [ { "pred" : "http://purl.org/dc/terms/contributor", "val" : "https://orcid.org/0000-0001-5208-3432" @@ -2967,7 +3063,7 @@ "xrefs" : [ "GOC:dos" ] }, "comments" : [ "Work is needed on GO 'cell differentiation' before it is clear whether the equivalent class definition 'native cell' that capable_of some 'cell differentiation' works. Also, may want to consider merging this with non-terminally differentiated cell." ], - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ] + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ] } }, { "id" : "http://purl.obolibrary.org/obo/CL_0017500", @@ -3012,6 +3108,7 @@ "val" : "Hematopoietic cells resident in the bone marrow. Include: hematopoietic stem cells (lymphoid stem cells and myeloid stem cells) and the precursor cells for thrombocytes, erythrocytes, basophils, neutrophils, eosinophils, monocytes and lymphocytes.", "xrefs" : [ "NPX:PDR" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "pred" : "hasRelatedSynonym", "val" : "bone marrow hematopoietic cells", @@ -3034,6 +3131,7 @@ "val" : "A multinucleate cell formed by the fusion of multiple uninuclear cells through plasma membrane fusion. This process leads to a single large cell containing multiple nuclei within a shared cytoplasm.", "xrefs" : [ "PMID:20851884", "Wikipedia:Syncytium" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "syncytium", @@ -3110,15 +3208,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/geneontology/go-ontology/issues/28301" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0000789" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0000790" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0005717" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "cellular_component" @@ -3148,12 +3237,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/geneontology/go-ontology/issues/22355" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0005719" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0035327" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "cellular_component" @@ -3186,12 +3269,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/geneontology/go-ontology/issues/22355" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0005720" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0035328" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "cellular_component" @@ -3391,18 +3468,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/geneontology/go-ontology/issues/19116" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0042032" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0042089" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0042107" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0050663" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" @@ -3443,9 +3508,6 @@ "val" : "Wikipedia:Neurulation" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0001679" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" } ] @@ -3649,12 +3711,6 @@ "val" : "immunoglobulin secretion" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0002378" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0048305" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" } ] @@ -3711,12 +3767,6 @@ "val" : "cellular immune response" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0019723" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0042087" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" } ] @@ -4008,9 +4058,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/geneontology/go-ontology/issues/17729" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0008372" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "cellular_component" @@ -4097,12 +4144,6 @@ "val" : "Wikipedia:Basement_membrane" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0005605" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0008003" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "cellular_component" } ] @@ -4355,12 +4396,6 @@ "val" : "Wikipedia:Cell_membrane" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0005887" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0005904" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "cellular_component" } ] @@ -4414,9 +4449,6 @@ "val" : "cellular DNA metabolism" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0055132" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" } ] @@ -4469,15 +4501,6 @@ "val" : "Wikipedia:Translation_(genetics)" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0006416" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0006453" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0043037" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" } ] @@ -4506,12 +4529,6 @@ "val" : "translation initiation" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0006440" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0006454" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" } ] @@ -4534,12 +4551,6 @@ "val" : "translation elongation" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0006442" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0006455" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" } ] @@ -4564,12 +4575,6 @@ "val" : "translational complex disassembly" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0006443" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0006456" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" } ] @@ -4592,21 +4597,9 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/geneontology/go-ontology/issues/20292" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "jl" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2012-12-13T16:25:32Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0015457" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0015460" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0044765" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" @@ -4652,12 +4645,6 @@ "val" : "Wikipedia:Exocytosis" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0016194" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0016195" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" } ] @@ -4694,15 +4681,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/geneontology/go-ontology/issues/25268" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0016193" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0016196" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0098701" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" @@ -4741,17 +4719,8 @@ "val" : "vesicle budding" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "jl" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2013-12-19T15:26:17Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0006902" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:1902591" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" @@ -4871,15 +4840,9 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/geneontology/go-ontology/issues/27189" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "jl" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2013-12-19T15:25:51Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:1902589" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" @@ -5151,9 +5114,6 @@ "val" : "hemolymph circulation" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0070261" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" } ] @@ -5188,21 +5148,9 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/geneontology/go-ontology/issues/24968" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "jl" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2012-09-19T15:05:24Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0000004" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0007582" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0044699" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" @@ -5214,7 +5162,7 @@ "type" : "CLASS", "meta" : { "definition" : { - "val" : "The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.", + "val" : "A cellular process consisting of the biochemical pathways by which a living organism transforms chemical substances. This includes including anabolism (biosynthetic process) and catabolism (catabolic process). Metabolic processes includes the transformation of small molecules, as well macromolecular processes such as DNA repair and replication, protein synthesis and degradation.", "xrefs" : [ "GOC:go_curators", "ISBN:0198547684" ] }, "comments" : [ "Note that metabolic processes do not include single functions or processes such as protein-protein interactions, protein-nucleic acids, nor receptor-ligand interactions." ], @@ -5222,18 +5170,6 @@ "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "metabolism" - }, { - "pred" : "hasNarrowSynonym", - "val" : "metabolic process resulting in cell growth" - }, { - "pred" : "hasNarrowSynonym", - "val" : "metabolism resulting in cell growth" - }, { - "pred" : "hasNarrowSynonym", - "val" : "multicellular organism metabolic process" - }, { - "pred" : "hasRelatedSynonym", - "val" : "single-organism metabolic process" } ], "xrefs" : [ { "val" : "Wikipedia:Metabolism" @@ -5242,17 +5178,11 @@ "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/geneontology/go-ontology/issues/26424" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "jl" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/geneontology/go-ontology/issues/28932" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2012-10-17T15:46:40Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0044236" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0044710" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" @@ -5264,7 +5194,7 @@ "type" : "CLASS", "meta" : { "definition" : { - "val" : "The chemical reactions and pathways resulting in the formation of substances; typically the energy-requiring part of metabolism in which simpler substances are transformed into more complex ones.", + "val" : "A cellular process consisting of the biochemical pathways by which a living organism synthesizes chemical substances. This typically represents the energy-requiring part of metabolism in which simpler substances are transformed into more complex ones.", "xrefs" : [ "GOC:curators", "ISBN:0198547684" ] }, "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_chembl", "http://purl.obolibrary.org/obo/go#goslim_metagenomics", "http://purl.obolibrary.org/obo/go#goslim_plant", "http://purl.obolibrary.org/obo/go#goslim_plant_ribbon" ], @@ -5291,17 +5221,11 @@ "val" : "Wikipedia:Anabolism" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "jl" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/geneontology/go-ontology/issues/28932" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2012-10-17T15:52:18Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0044274" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0044711" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" @@ -5344,9 +5268,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/geneontology/go-ontology/issues/27189" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0043284" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" @@ -5578,9 +5499,6 @@ "val" : "Wikipedia:Embryogenesis" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0009795" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" } ] @@ -5697,20 +5615,8 @@ "val" : "single-organism cellular process" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "jl" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2012-12-11T16:56:55Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0008151" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0044763" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0050875" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" @@ -5754,14 +5660,8 @@ "val" : "single-organism membrane invagination" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "jl" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2013-12-02T13:58:34Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:1902534" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" @@ -5878,15 +5778,6 @@ "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2014-03-06T11:37:54Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0016021" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0098589" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0098805" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "cellular_component" @@ -5925,12 +5816,6 @@ "xrefs" : [ "GOC:mah" ] } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0044235" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0071842" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" } ] @@ -5988,9 +5873,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/geneontology/go-ontology/issues/25421" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0006899" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" @@ -6174,15 +6056,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/geneontology/go-ontology/issues/27189" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0006411" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0044267" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0044268" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" @@ -6241,9 +6114,6 @@ "val" : "Wikipedia:Antigen_presentation" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0030333" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" } ] @@ -6283,9 +6153,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/geneontology/go-ontology/issues/27189" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0071845" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" @@ -6311,15 +6178,9 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/geneontology/go-ontology/issues/27054" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "jl" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2012-09-19T15:56:06Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0044702" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" @@ -6358,9 +6219,6 @@ "val" : "cellular component assembly at cellular level" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0071844" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" } ] @@ -6442,17 +6300,8 @@ "val" : "single organism signaling" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "jl" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2010-02-16T09:30:50Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0023046" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0044700" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" @@ -6620,9 +6469,6 @@ "xrefs" : [ "GOC:add" ] } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0046650" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" } ] @@ -6740,12 +6586,6 @@ "xrefs" : [ "GOC:add" ] } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0042112" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0046652" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" } ] @@ -6861,9 +6701,6 @@ "val" : "Wikipedia:Extracellular_matrix" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0005578" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "cellular_component" } ] @@ -6976,9 +6813,6 @@ "val" : "NIF_Subcellular:sao180601769" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0016023" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "cellular_component" } ] @@ -7034,9 +6868,6 @@ "val" : "Wikipedia:Vesicle_(biology)" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0031988" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "cellular_component" } ] @@ -7074,18 +6905,9 @@ }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002161", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_4932" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "jl" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2012-09-19T16:07:47Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0044707" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0050874" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" @@ -7109,14 +6931,8 @@ "val" : "single-organism developmental process" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "jl" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2012-12-19T12:21:31Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0044767" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" @@ -7151,12 +6967,6 @@ "val" : "interferon-gamma secretion" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0042095" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0072643" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" } ] @@ -7207,15 +7017,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/geneontology/go-ontology/issues/22580" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0034623" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0043241" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0043624" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" @@ -7249,9 +7050,6 @@ "val" : "protein-protein complex" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0043234" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "cellular_component" } ] @@ -7349,9 +7147,6 @@ "val" : "ATP hydrolysis coupled ion transmembrane transport" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0099131" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" } ] @@ -7551,15 +7346,6 @@ "val" : "regulation of homeostatic process" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0032844" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0032845" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0032846" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" } ] @@ -7676,15 +7462,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/geneontology/go-ontology/issues/26424" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0034960" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0043283" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0044259" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" @@ -7751,7 +7528,7 @@ } }, { "id" : "http://purl.obolibrary.org/obo/GO_0043228", - "lbl" : "non-membrane-bounded organelle", + "lbl" : "membraneless organelle", "type" : "CLASS", "meta" : { "definition" : { @@ -7760,6 +7537,12 @@ }, "subsets" : [ "http://purl.obolibrary.org/obo/go#gocheck_do_not_annotate", "http://purl.obolibrary.org/obo/go#goslim_mouse" ], "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "membrane-less organelle" + }, { + "pred" : "hasExactSynonym", + "val" : "non-membrane-bounded organelle" + }, { "pred" : "hasExactSynonym", "val" : "non-membrane-enclosed organelle" }, { @@ -7775,6 +7558,9 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/geneontology/go-ontology/issues/28153" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/geneontology/go-ontology/issues/29106" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "cellular_component" @@ -7819,7 +7605,7 @@ } }, { "id" : "http://purl.obolibrary.org/obo/GO_0043232", - "lbl" : "intracellular non-membrane-bounded organelle", + "lbl" : "intracellular membraneless organelle", "type" : "CLASS", "meta" : { "definition" : { @@ -7828,10 +7614,16 @@ }, "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_pir" ], "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "intracellular non-membrane-bounded organelle" + }, { "pred" : "hasExactSynonym", "val" : "intracellular non-membrane-enclosed organelle" } ], "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/geneontology/go-ontology/issues/29106" + }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "cellular_component" } ] @@ -7913,21 +7705,9 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/geneontology/go-ontology/issues/22580" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "mah" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2010-09-08T10:01:42Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0034600" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0034621" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0071822" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" @@ -7950,9 +7730,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/geneontology/go-ontology/issues/27194" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0071843" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" @@ -7975,9 +7752,6 @@ "val" : "Met-tRNA/eIF2.GTP ternary complex" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "jl" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2009-10-22T02:38:55Z" }, { @@ -7985,30 +7759,6 @@ "val" : "cellular_component" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/GO_0044237", - "lbl" : "cellular metabolic process", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "The chemical reactions and pathways by which individual cells transform chemical substances.", - "xrefs" : [ "GOC:go_curators" ] - }, - "comments" : [ "This term should not be used for direct annotation. It should be possible to make a more specific annotation to one of the children of this term." ], - "subsets" : [ "http://purl.obolibrary.org/obo/go#gocheck_do_not_annotate" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "cellular metabolism" - }, { - "pred" : "hasRelatedSynonym", - "val" : "intermediary metabolism", - "xrefs" : [ "GOC:mah" ] - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "biological_process" - } ] - } }, { "id" : "http://purl.obolibrary.org/obo/GO_0044238", "lbl" : "primary metabolic process", @@ -8034,38 +7784,6 @@ "val" : "biological_process" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/GO_0044249", - "lbl" : "cellular biosynthetic process", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "The chemical reactions and pathways resulting in the formation of substances, carried out by individual cells.", - "xrefs" : [ "GOC:jl" ] - }, - "comments" : [ "This term should not be used for direct annotation. It should be possible to make a more specific annotation to one of the children of this term." ], - "subsets" : [ "http://purl.obolibrary.org/obo/go#gocheck_do_not_annotate" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "cellular anabolism" - }, { - "pred" : "hasExactSynonym", - "val" : "cellular biosynthesis" - }, { - "pred" : "hasExactSynonym", - "val" : "cellular formation" - }, { - "pred" : "hasExactSynonym", - "val" : "cellular synthesis" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", - "val" : "https://github.com/geneontology/go-ontology/issues/27052" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "biological_process" - } ] - } }, { "id" : "http://purl.obolibrary.org/obo/GO_0044419", "lbl" : "biological process involved in interspecies interaction between organisms", @@ -8117,9 +7835,6 @@ "val" : "cell-cell fusion" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0006947" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" } ] @@ -8153,9 +7868,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002161", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_4751" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0002226" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" @@ -8489,9 +8201,6 @@ "xrefs" : [ "GOC:dph", "GOC:tb" ] } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0048828" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" } ] @@ -8689,9 +8398,6 @@ "val" : "regulation of physiological process" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0050791" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" } ] @@ -8725,9 +8431,6 @@ "val" : "regulation of cellular physiological process" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0051244" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" } ] @@ -8817,9 +8520,6 @@ "val" : "physiological response to stimulus" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0051869" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" } ] @@ -8977,15 +8677,9 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/geneontology/go-ontology/issues/27052" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "jl" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2013-12-18T13:51:04Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:1902578" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" @@ -9096,12 +8790,6 @@ "xrefs" : [ "GOC:ai" ] }, "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0009613" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0042828" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" } ] @@ -9125,14 +8813,8 @@ "val" : "ATP hydrolysis coupled transmembrane transport" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "tb" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2015-10-21T13:22:47Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0090662" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" @@ -9220,9 +8902,6 @@ "xrefs" : [ "GOC:dph" ] }, "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dph" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2009-04-28T09:33:36Z" }, { @@ -9259,17 +8938,8 @@ "val" : "single-organism membrane organization" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "jl" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2010-02-08T02:43:11Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0016044" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0044802" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" @@ -9296,17 +8966,8 @@ "val" : "Wikipedia:Lipid_bilayer_fusion" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "jl" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2010-02-08T02:48:06Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0006944" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0044801" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" @@ -9322,9 +8983,6 @@ "xrefs" : [ "GOC:BHF", "GOC:rph", "PMID:21123617" ] }, "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dph" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2018-04-13T12:47:21Z" }, { @@ -9370,15 +9028,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/geneontology/go-ontology/issues/22580" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0006461" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0034622" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0043623" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" @@ -9486,9 +9135,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/geneontology/go-ontology/issues/25143" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "mah" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2010-09-08T10:10:35Z" @@ -9523,15 +9169,9 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/geneontology/go-ontology/issues/27189" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "mah" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2010-09-10T01:39:16Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0071841" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" @@ -9548,9 +9188,6 @@ }, "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_flybase_ribbon" ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "mah" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2010-10-04T01:51:47Z" }, { @@ -9577,9 +9214,6 @@ "xrefs" : [ "GOC:BHF" ] } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "mah" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2010-10-11T11:44:57Z" }, { @@ -9599,9 +9233,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/geneontology/go-ontology/issues/22302" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "mah" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2010-02-26T02:15:40Z" @@ -9620,9 +9251,6 @@ "xrefs" : [ "GOC:ascb_2009", "GOC:dph", "GOC:tb" ] }, "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "tb" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2009-12-11T11:44:58Z" }, { @@ -9641,9 +9269,6 @@ }, "comments" : [ "Note that immunologists typically use the word 'maturation' to refer to dendritic cells undergoing the process that GO describes as 'cell differentiation'." ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pr" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2011-04-01T10:08:42Z" }, { @@ -9661,9 +9286,6 @@ "xrefs" : [ "GOC:vesicles" ] }, "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pr" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2016-03-29T17:39:45Z" }, { @@ -9697,15 +9319,9 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/geneontology/go-ontology/issues/22173" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dos" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2013-11-11T12:59:11Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0009814" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" @@ -9727,9 +9343,6 @@ "val" : "region of plasma membrane" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dos" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2014-03-06T11:55:32Z" }, { @@ -9982,9 +9595,6 @@ "val" : "fibril" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0043205" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "cellular_component" } ] @@ -10021,14 +9631,18 @@ } }, { "id" : "http://purl.obolibrary.org/obo/GO_0110165", - "lbl" : "cellular anatomical entity", + "lbl" : "cellular anatomical structure", "type" : "CLASS", "meta" : { "definition" : { - "val" : "A part of a cellular organism that is either an immaterial entity or a material entity with granularity above the level of a protein complex but below that of an anatomical system. Or, a substance produced by a cellular organism with granularity above the level of a protein complex.", + "val" : "A part of a cellular organism consisting of a material entity with granularity above the level of a protein complex but below that of an anatomical system. Note that cellular organisms exclude viruses.", "xrefs" : [ "GOC:kmv" ] }, "subsets" : [ "http://purl.obolibrary.org/obo/go#gocheck_do_not_annotate", "http://purl.obolibrary.org/obo/go#goslim_pir" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "cellular anatomical entity" + } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/geneontology/go-ontology/issues/24200" @@ -10036,8 +9650,8 @@ "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/geneontology/go-ontology/issues/26424" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "kmv" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/geneontology/go-ontology/issues/28978" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2019-08-12T18:01:37Z" @@ -10058,9 +9672,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/geneontology/go-ontology/issues/13193" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "krc" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-03-21T17:26:07Z" @@ -10081,9 +9692,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/geneontology/go-ontology/issues/13298" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "krc" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-04-26T16:07:02Z" @@ -10103,9 +9711,6 @@ }, "subsets" : [ "http://purl.obolibrary.org/obo/go#gocheck_do_not_annotate" ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pg" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-05-15T13:20:45Z" }, { @@ -10132,9 +9737,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/geneontology/go-ontology/issues/15939" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pg" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2018-08-13T18:38:18Z" @@ -10157,9 +9759,6 @@ "val" : "efflux" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pg" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2019-05-22T11:20:45Z" }, { @@ -10179,9 +9778,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/geneontology/go-ontology/issues/20261" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pg" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2020-11-11T17:19:06Z" @@ -10209,9 +9805,6 @@ "xrefs" : [ "GOC:TermGenie" ] } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pr" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2013-05-02T17:32:42Z" }, { @@ -10229,9 +9822,6 @@ "xrefs" : [ "CL:0000842", "GOC:TermGenie", "GO_REF:0000086", "PMID:24759906" ] }, "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "cls" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2014-06-25T15:47:09Z" }, { @@ -10267,9 +9857,6 @@ "xrefs" : [ "GOC:TermGenie" ] } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pad" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2014-12-04T15:34:13Z" }, { @@ -10307,17 +9894,8 @@ "val" : "Wikipedia:Ribonucleoprotein" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pr" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2015-11-19T12:26:37Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0030529" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:1990903" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "cellular_component" @@ -10333,9 +9911,6 @@ "xrefs" : [ "GOC:obol" ] }, "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "tb" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2010-08-05T11:25:59Z" }, { @@ -10424,9 +9999,6 @@ "val" : "GC_ID:1" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "NCBITaxon:85055" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "ncbi_taxonomy" } ] @@ -10458,9 +10030,6 @@ "val" : "GC_ID:1" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "NCBITaxon:40673" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "ncbi_taxonomy" } ] @@ -10794,9 +10363,6 @@ "val" : "GC_ID:1" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "NCBITaxon:109679" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "ncbi_taxonomy" } ] @@ -11021,9 +10587,6 @@ "xrefs" : [ "PATOC:GVG" ] }, "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "PATO:0000072" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "quality" } ] @@ -11059,9 +10622,6 @@ "val" : "relational shape quality" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "PATO:0001647" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "quality" } ] @@ -11085,9 +10645,6 @@ "val" : "relational structural quality" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "PATO:0001452" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "quality" } ] @@ -11163,9 +10720,6 @@ "val" : "Wikipedia:Physical_property" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "PATO:0002079" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "quality" } ] @@ -11209,12 +10763,6 @@ "val" : "snap:Quality" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "PATO:0001237" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "PATO:0001238" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "quality" } ] @@ -11392,9 +10940,6 @@ "val" : "tubulate" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "PATO:0001203" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "quality" } ] @@ -11787,9 +11332,6 @@ "val" : "high N:C ratio" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "http://orcid.org/0000-0001-5208-3432" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "quality" } ] @@ -11803,9 +11345,6 @@ "val" : "A quality of continuant that exist at the anatomical level of organisation and anything under it. This includes, but is not limited to, cells , tissues, and components." }, "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "http://orcid.org/0000-0001-7258-9596" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "quality" } ] @@ -11819,9 +11358,6 @@ "val" : "A quality inhering in an anotomical structure by virtue of its capacity to be stained by specific histological dyes." }, "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "http://orcid.org/0000-0001-7258-9596" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "quality" } ] @@ -11836,9 +11372,6 @@ "xrefs" : [ "GOC:add" ] }, "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "http://orcid.org/0000-0001-7258-9596" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "quality" } ] @@ -11852,7 +11385,7 @@ "val" : "An amino acid chain that is produced de novo by ribosome-mediated translation of a genetically-encoded mRNA, and any derivatives thereof.", "xrefs" : [ "PRO:DAN", "PRO:WCB" ] }, - "comments" : [ "The definition above excludes protein complexes, which some also consider a protein. Those who wish to refer to a class representing both senses of the word are directed to CHEBI:36080. Note that the definition allows for experimentally-manipulated genes, and allows for artifically-produced derivatives that mimic those found naturally. Proteins (in the sense defined here) that descended from a common ancestor can be classified into families and superfamilies composed of products of evolutionarily-related genes. The domain architecture of a protein is described by the order of its constituent domains. Proteins with the same domains in the same order are defined as homeomorphic [PRO:WCB]." ], + "comments" : [ "The definition above excludes protein complexes, which some also consider a protein. Those who wish to refer to a class representing both senses of the word are directed to CHEBI:36080. Note that the definition allows for experimentally-manipulated genes, and allows for artifically-produced derivatives that mimic those found naturally. Proteins (in the sense defined here) that descended from a common ancestor can be classified into families and superfamilies composed of products of evolutionarily-related genes. The domain architecture of a protein is described by the order of its constituent domains. Proteins with the same domains in the same order are defined as homeomorphic [PRO:WCB)." ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "natural protein", @@ -13746,15 +13279,15 @@ } ] } }, { - "id" : "http://purl.obolibrary.org/obo/PR_000050567", - "lbl" : "protein-containing material entity", + "id" : "http://purl.obolibrary.org/obo/PR_000064867", + "lbl" : "protein-containing molecular entity", "type" : "CLASS", "meta" : { "definition" : { - "val" : "A material entity that minimally consists of a protein.", + "val" : "A molecular entity that minimally consists of a protein.", "xrefs" : [ "PRO:DAN" ] }, - "comments" : [ "Note: This includes single proteins and derivatives thereof (PR:000000001), protein-containing complexes (GO:0032991), and protein aggregates (PR:000050566)." ], + "comments" : [ "Note: This includes single proteins and derivatives thereof (PR:000000001), protein-containing complexes (GO:0032991), and protein aggregates (PR:000050565)." ], "synonyms" : [ { "pred" : "hasNarrowSynonym", "val" : "protein", @@ -14068,9 +13601,6 @@ "val" : "galen:Wall" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "UBERON:0009915" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -14443,9 +13973,6 @@ "val" : "galen:ComplexSkeletalStructure" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "UBERON:0010322" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -15065,9 +14592,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "TODO - check relationship with epiblast. Note in FMA this is not a subclass of embryo, but in uberon embryo is the whole organism from zygote onwards and thus includes the blastula" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "UBERON:0007011" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -16565,9 +16089,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0002161", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_6040" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "UBERON:0003263" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -16929,7 +16450,7 @@ "val" : "Organ system that passes nutrients (such as amino acids and electrolytes), gases, hormones, blood cells, etc. to and from cells in the body to help fight diseases and help stabilize body temperature and pH to maintain homeostasis[WP].", "xrefs" : [ "Wikipedia:Circulatory_system" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#uberon_slim" ], "synonyms" : [ { "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003011", "pred" : "hasRelatedSynonym", @@ -16954,9 +16475,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002161", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_6157" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -17581,9 +17099,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "check relationship with myocardium. part_of in MA - but we also have a more specific class 'cardiac muscle tissue of myocardium'. Check ncit" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "UBERON:0007096" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -18136,9 +17651,6 @@ "val" : "http://uri.neuinfo.org/nif/nifstd/FMAID_7191" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "UBERON:0007036" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -19607,9 +19119,6 @@ "val" : "ZFA:0000121" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "UBERON:0006258" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" }, { @@ -20204,9 +19713,6 @@ "val" : "Wikipedia:Trilaminar_blastocyst" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "UBERON:0007012" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -21316,9 +20822,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "consider adding new class (EMAPA:16097) for mesenchyme of embryo (some mesenchyme is extraembryonic - e.g. amnion mesoderm)" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "UBERON:0003313" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -21687,6 +21190,8 @@ "val" : "EHDAA2:0004731" }, { "val" : "Wikipedia:Coelom" + }, { + "val" : "ZFA:0001438" } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", @@ -22008,9 +21513,6 @@ "val" : "presumptive central nervous system" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "UBERON:3000469" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -22033,9 +21535,6 @@ "val" : "AAO:0000477" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "UBERON:3000477" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -22785,9 +22284,6 @@ "val" : "A relationship between a process and a barrier, where the process occurs in a region spanning the barrier. For cellular processes the barrier is typically a membrane. Examples include transport across a membrane and membrane depolarization." }, "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "https://orcid.org/0000-0002-7073-9172" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-07-20T17:19:37Z" } ] @@ -25069,9 +24565,6 @@ "val" : "RO:0004007" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2018-12-13T11:26:17Z" }, { @@ -25097,9 +24590,6 @@ "val" : "RO:0004008" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2018-12-13T11:26:32Z" }, { @@ -25125,9 +24615,6 @@ "val" : "RO:0004009" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2018-12-13T11:26:56Z" }, { @@ -25147,9 +24634,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0004050", "val" : "http://purl.obolibrary.org/obo/RO_0002418" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2018-03-13T23:55:05Z" @@ -25165,9 +24649,6 @@ "propertyType" : "OBJECT", "meta" : { "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2018-03-13T23:55:19Z" }, { @@ -25185,9 +24666,6 @@ "val" : "a relation between a process and a continuant, in which the process is regulated by the small molecule continuant" }, "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "https://orcid.org/0000-0003-1813-6857" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2020-04-22T20:27:26Z" } ] @@ -25205,9 +24683,6 @@ "val" : "RO:0012001" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "https://orcid.org/0000-0003-1813-6857" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2020-04-22T20:28:37Z" }, { @@ -25232,9 +24707,6 @@ "val" : "RO:0012003" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "https://orcid.org/0000-0003-1813-6857" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2020-06-08T17:21:33Z" }, { @@ -25255,9 +24727,6 @@ "val" : "a relation between a continuant and a process, in which the continuant is a small molecule that regulates the process" }, "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "https://orcid.org/0000-0003-1813-6857" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2020-06-24T13:15:17Z" } ] @@ -25272,9 +24741,6 @@ "val" : "a relation between a continuant and a process, in which the continuant is a small molecule that activates the process" }, "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "https://orcid.org/0000-0003-1813-6857" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2020-06-24T13:15:26Z" }, { @@ -25293,9 +24759,6 @@ "val" : "RO:0012008" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "https://orcid.org/0000-0003-1813-6857" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2021-02-26T07:28:29Z" }, { @@ -25320,9 +24783,6 @@ "val" : "has synaptic input or output in" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "https://orcid.org/0000-0002-1373-1705" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2020-07-17T09:26:52Z" } ] @@ -25347,13 +24807,34 @@ "val" : "has sensory terminal location" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "https://orcid.org/0000-0002-1373-1705" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2020-07-20T12:10:09Z" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0015004", + "lbl" : "has characterizing marker set", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "A relation that applies between a cell type and a set of markers that can be used to uniquely identify that cell type." + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "has marker gene combination" + }, { + "pred" : "hasExactSynonym", + "val" : "has marker signature set" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "C has_characterizing_marker_set y iff: C is a cell type and y is a collection of genes or proteins whose expression is sufficient to distinguish cell type C from most or all other cell types." + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0001-7258-9596" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/RO_0015006", "lbl" : "different in magnitude relative to", @@ -25479,9 +24960,6 @@ "val" : "RO:0040036" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2018-09-26T01:08:58Z" }, { @@ -26180,13 +25658,14 @@ "propertyType" : "ANNOTATION", "meta" : { "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2018-03-14T00:03:24Z" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/STATO_0000663", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" }, { "id" : "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "type" : "PROPERTY", @@ -26239,6 +25718,10 @@ "meta" : { "comments" : [ "a subset of general classes of cell types in the cell ontology." ] } + }, { + "id" : "http://purl.obolibrary.org/obo/cl#human_subset", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" }, { "id" : "http://purl.obolibrary.org/obo/cl#kidney_upper_slim", "lbl" : "kidney_upper_slim", @@ -26251,6 +25734,10 @@ "val" : "2023-11-22T11:18:57Z" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/cl#mouse_subset", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" }, { "id" : "http://purl.obolibrary.org/obo/go#gocheck_do_not_annotate", "type" : "PROPERTY", @@ -26573,10 +26060,6 @@ "id" : "http://purl.org/dc/elements/1.1/creator", "type" : "PROPERTY", "propertyType" : "ANNOTATION" - }, { - "id" : "http://purl.org/dc/elements/1.1/date", - "type" : "PROPERTY", - "propertyType" : "ANNOTATION" }, { "id" : "http://purl.org/dc/elements/1.1/description", "type" : "PROPERTY", @@ -26589,6 +26072,10 @@ "id" : "http://purl.org/dc/elements/1.1/title", "type" : "PROPERTY", "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.org/dc/elements/1.1/type", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" }, { "id" : "http://purl.org/dc/terms/contributor", "type" : "PROPERTY", @@ -26599,14 +26086,17 @@ "propertyType" : "ANNOTATION" }, { "id" : "http://purl.org/dc/terms/description", + "lbl" : "description", "type" : "PROPERTY", "propertyType" : "ANNOTATION" }, { "id" : "http://purl.org/dc/terms/license", + "lbl" : "license", "type" : "PROPERTY", "propertyType" : "ANNOTATION" }, { "id" : "http://purl.org/dc/terms/title", + "lbl" : "title", "type" : "PROPERTY", "propertyType" : "ANNOTATION" }, { @@ -26624,19 +26114,10 @@ "lbl" : "consider", "type" : "PROPERTY", "propertyType" : "ANNOTATION" - }, { - "id" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "type" : "PROPERTY", - "propertyType" : "ANNOTATION" }, { "id" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "type" : "PROPERTY", "propertyType" : "ANNOTATION" - }, { - "id" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "lbl" : "has_alternative_id", - "type" : "PROPERTY", - "propertyType" : "ANNOTATION" }, { "id" : "http://www.geneontology.org/formats/oboInOwl#hasBroadSynonym", "lbl" : "has_broad_synonym", @@ -26656,9 +26137,21 @@ } }, { "id" : "http://www.geneontology.org/formats/oboInOwl#hasDbXref", - "lbl" : "database_cross_reference", + "lbl" : "has cross-reference", "type" : "PROPERTY", - "propertyType" : "ANNOTATION" + "propertyType" : "ANNOTATION", + "meta" : { + "definition" : { + "val" : "An annotation property that links an ontology entity or a statement to a prefixed identifier or URI." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/information-artifact-ontology/ontology-metadata/issues/123" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0002-7356-1779" + } ] + } }, { "id" : "http://www.geneontology.org/formats/oboInOwl#hasExactSynonym", "lbl" : "has_exact_synonym", @@ -26737,10 +26230,6 @@ "id" : "http://www.geneontology.org/formats/oboInOwl#is_metadata_tag", "type" : "PROPERTY", "propertyType" : "ANNOTATION" - }, { - "id" : "http://www.geneontology.org/formats/oboInOwl#note", - "type" : "PROPERTY", - "propertyType" : "ANNOTATION" }, { "id" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "lbl" : "shorthand", @@ -26903,10 +26392,6 @@ "val" : "true" } ] } - }, { - "sub" : "http://purl.obolibrary.org/obo/CL_0000040", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000040", "pred" : "http://purl.obolibrary.org/obo/BFO_0000051", @@ -26978,11 +26463,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000057", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/CL_0002320" - }, { - "sub" : "http://purl.obolibrary.org/obo/CL_0000057", - "pred" : "http://purl.obolibrary.org/obo/RO_0002202", - "obj" : "http://purl.obolibrary.org/obo/CL_0000134" + "obj" : "http://purl.obolibrary.org/obo/CL_0000499" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000066", "pred" : "is_a", @@ -27051,10 +26532,6 @@ "val" : "true" } ] } - }, { - "sub" : "http://purl.obolibrary.org/obo/CL_0000092", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000092", "pred" : "http://purl.obolibrary.org/obo/BFO_0000051", @@ -27105,10 +26582,6 @@ "val" : "true" } ] } - }, { - "sub" : "http://purl.obolibrary.org/obo/CL_0000094", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000094", "pred" : "http://purl.obolibrary.org/obo/BFO_0000051", @@ -27543,10 +27016,6 @@ "sub" : "http://purl.obolibrary.org/obo/CL_0000451", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/CL_0000145" - }, { - "sub" : "http://purl.obolibrary.org/obo/CL_0000451", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000451", "pred" : "http://purl.obolibrary.org/obo/BFO_0000051", @@ -27703,18 +27172,10 @@ "sub" : "http://purl.obolibrary.org/obo/CL_0000557", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/CL_0001012" - }, { - "sub" : "http://purl.obolibrary.org/obo/CL_0000557", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/CL_0011026" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000557", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/CL_1001610" - }, { - "sub" : "http://purl.obolibrary.org/obo/CL_0000557", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000557", "pred" : "http://purl.obolibrary.org/obo/BFO_0000051", @@ -27757,10 +27218,6 @@ "val" : "true" } ] } - }, { - "sub" : "http://purl.obolibrary.org/obo/CL_0000559", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000559", "pred" : "http://purl.obolibrary.org/obo/BFO_0000051", @@ -27787,10 +27244,6 @@ "sub" : "http://purl.obolibrary.org/obo/CL_0000566", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/CL_0011026" - }, { - "sub" : "http://purl.obolibrary.org/obo/CL_0000566", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000566", "pred" : "http://purl.obolibrary.org/obo/RO_0002104", @@ -28023,10 +27476,6 @@ "val" : "true" } ] } - }, { - "sub" : "http://purl.obolibrary.org/obo/CL_0000825", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000825", "pred" : "http://purl.obolibrary.org/obo/CL_4030046", @@ -28065,10 +27514,6 @@ "val" : "true" } ] } - }, { - "sub" : "http://purl.obolibrary.org/obo/CL_0000826", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000826", "pred" : "http://purl.obolibrary.org/obo/BFO_0000051", @@ -28111,10 +27556,6 @@ "sub" : "http://purl.obolibrary.org/obo/CL_0000837", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/CL_0008001" - }, { - "sub" : "http://purl.obolibrary.org/obo/CL_0000837", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000837", "pred" : "http://purl.obolibrary.org/obo/CL_4030046", @@ -28265,6 +27706,10 @@ "sub" : "http://purl.obolibrary.org/obo/CL_0001012", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/CL_0001060" + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_0001012", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/CL_0011026" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0001035", "pred" : "is_a", @@ -29132,7 +28577,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/GO_0006413", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/GO_0044237" + "obj" : "http://purl.obolibrary.org/obo/GO_0008152" }, { "sub" : "http://purl.obolibrary.org/obo/GO_0006413", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", @@ -29380,7 +28825,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/GO_0008152", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/GO_0008150" + "obj" : "http://purl.obolibrary.org/obo/GO_0009987" }, { "sub" : "http://purl.obolibrary.org/obo/GO_0009058", "pred" : "is_a", @@ -29388,11 +28833,11 @@ }, { "sub" : "http://purl.obolibrary.org/obo/GO_0009059", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/GO_0043170" + "obj" : "http://purl.obolibrary.org/obo/GO_0009058" }, { "sub" : "http://purl.obolibrary.org/obo/GO_0009059", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/GO_0044249" + "obj" : "http://purl.obolibrary.org/obo/GO_0043170" }, { "sub" : "http://purl.obolibrary.org/obo/GO_0009314", "pred" : "is_a", @@ -29975,8 +29420,8 @@ "obj" : "http://purl.obolibrary.org/obo/GO_0005575" }, { "sub" : "http://purl.obolibrary.org/obo/GO_0032991", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PR_000050567" + "pred" : "http://purl.obolibrary.org/obo/BFO_0000051", + "obj" : "http://purl.obolibrary.org/obo/PR_000000001" }, { "sub" : "http://purl.obolibrary.org/obo/GO_0033151", "pred" : "is_a", @@ -30221,26 +29666,10 @@ "sub" : "http://purl.obolibrary.org/obo/GO_0044207", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", "obj" : "http://purl.obolibrary.org/obo/GO_0005737" - }, { - "sub" : "http://purl.obolibrary.org/obo/GO_0044237", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/GO_0008152" - }, { - "sub" : "http://purl.obolibrary.org/obo/GO_0044237", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/GO_0009987" }, { "sub" : "http://purl.obolibrary.org/obo/GO_0044238", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/GO_0008152" - }, { - "sub" : "http://purl.obolibrary.org/obo/GO_0044249", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/GO_0009058" - }, { - "sub" : "http://purl.obolibrary.org/obo/GO_0044249", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/GO_0044237" }, { "sub" : "http://purl.obolibrary.org/obo/GO_0044419", "pred" : "is_a", @@ -30841,10 +30270,6 @@ "sub" : "http://purl.obolibrary.org/obo/GO_0098644", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/GO_0099080" - }, { - "sub" : "http://purl.obolibrary.org/obo/GO_0098644", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/GO_0098644", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", @@ -31404,7 +30829,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/PR_000000001", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PR_000050567" + "obj" : "http://purl.obolibrary.org/obo/PR_000064867" }, { "sub" : "http://purl.obolibrary.org/obo/PR_000000001", "pred" : "http://purl.obolibrary.org/obo/RO_0002353", @@ -31545,10 +30970,6 @@ "sub" : "http://purl.obolibrary.org/obo/PR_000001969", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PR_000000001" - }, { - "sub" : "http://purl.obolibrary.org/obo/PR_000001971", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PR_000000001" }, { "sub" : "http://purl.obolibrary.org/obo/PR_000002062", "pred" : "is_a", @@ -31638,7 +31059,7 @@ "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PR_000001006" }, { - "sub" : "http://purl.obolibrary.org/obo/PR_000050567", + "sub" : "http://purl.obolibrary.org/obo/PR_000064867", "pred" : "http://purl.obolibrary.org/obo/BFO_0000051", "obj" : "http://purl.obolibrary.org/obo/PR_000000001" }, { @@ -31707,10 +31128,6 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0000043", "pred" : "http://purl.obolibrary.org/obo/RO_0002176", "obj" : "http://purl.obolibrary.org/obo/UBERON_0001630" - }, { - "sub" : "http://purl.obolibrary.org/obo/UBERON_0000058", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000058", "pred" : "is_a", @@ -32117,10 +31534,6 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0000481", "pred" : "http://purl.obolibrary.org/obo/BFO_0000051", "obj" : "http://purl.obolibrary.org/obo/UBERON_0000479" - }, { - "sub" : "http://purl.obolibrary.org/obo/UBERON_0000483", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000483", "pred" : "is_a", @@ -32742,10 +32155,6 @@ "val" : "ZFA" } ] } - }, { - "sub" : "http://purl.obolibrary.org/obo/UBERON_0002330", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0002330", "pred" : "is_a", @@ -32837,10 +32246,6 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0002346", "pred" : "http://purl.obolibrary.org/obo/BFO_0000051", "obj" : "http://purl.obolibrary.org/obo/CL_0000133" - }, { - "sub" : "http://purl.obolibrary.org/obo/UBERON_0002365", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0002365", "pred" : "is_a", @@ -33026,6 +32431,10 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0002553", "pred" : "http://purl.obolibrary.org/obo/RO_0001015", "obj" : "http://purl.obolibrary.org/obo/UBERON_0000463" + }, { + "sub" : "http://purl.obolibrary.org/obo/UBERON_0003059", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/UBERON_0000061" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0003059", "pred" : "is_a", @@ -33612,10 +33021,6 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0005764", "pred" : "http://purl.obolibrary.org/obo/RO_0002007", "obj" : "http://purl.obolibrary.org/obo/UBERON_0000061" - }, { - "sub" : "http://purl.obolibrary.org/obo/UBERON_0005769", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0005769", "pred" : "is_a", @@ -33878,10 +33283,6 @@ "val" : "AEO" } ] } - }, { - "sub" : "http://purl.obolibrary.org/obo/UBERON_0007845", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0007845", "pred" : "is_a", @@ -34082,10 +33483,6 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0011822", "pred" : "http://purl.obolibrary.org/obo/BFO_0000051", "obj" : "http://purl.obolibrary.org/obo/GO_0071953" - }, { - "sub" : "http://purl.obolibrary.org/obo/UBERON_0011823", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0011823", "pred" : "is_a", @@ -34094,10 +33491,6 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0011823", "pred" : "http://purl.obolibrary.org/obo/RO_0002473", "obj" : "http://purl.obolibrary.org/obo/UBERON_0011860" - }, { - "sub" : "http://purl.obolibrary.org/obo/UBERON_0011860", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0011860", "pred" : "is_a", @@ -35266,10 +34659,6 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002590", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002592" - }, { - "sub" : "http://purl.obolibrary.org/obo/RO_0002592", - "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0000057" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002592", "pred" : "subPropertyOf", @@ -38040,6 +37429,9 @@ }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0013007", "domainClassIds" : [ "http://purl.obolibrary.org/obo/CL_0000101" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0015004", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/CL_0000000" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0015006", "domainClassIds" : [ "http://purl.obolibrary.org/obo/PATO_0000001" ], diff --git a/subsets/general_cell_types_upper_slim.obo b/subsets/general_cell_types_upper_slim.obo index 9c6b81e98..d9315920d 100644 --- a/subsets/general_cell_types_upper_slim.obo +++ b/subsets/general_cell_types_upper_slim.obo @@ -1,5 +1,5 @@ format-version: 1.2 -data-version: cl/releases/2024-09-26/subsets/general_cell_types_upper_slim.owl +data-version: cl/releases/2025-01-08/subsets/general_cell_types_upper_slim.owl subsetdef: abnormal_slim "" subsetdef: added_for_HCA "" subsetdef: attribute_slim "" @@ -44,10 +44,12 @@ subsetdef: http://purl.obolibrary.org/obo/valid_for_go_gp2term "" subsetdef: http://purl.obolibrary.org/obo/valid_for_go_ontology "" subsetdef: http://purl.obolibrary.org/obo/valid_for_gocam "" subsetdef: human_reference_atlas "" +subsetdef: human_subset "" subsetdef: inconsistent_with_fma "" subsetdef: kidney_upper_slim "a subset of general classes related to specific cell types in the kidney" subsetdef: location_grouping "" subsetdef: major_organ "" +subsetdef: mouse_subset "" subsetdef: mpath_slim "" subsetdef: non_informative "" subsetdef: organ_slim "" @@ -96,7 +98,7 @@ idspace: oboInOwl http://www.geneontology.org/formats/oboInOwl# idspace: sssom https://w3id.org/sssom/ idspace: terms http://purl.org/dc/terms/ ontology: cl/subsets/general_cell_types_upper_slim -property_value: owl:versionInfo "2024-09-26" xsd:string +property_value: owl:versionInfo "2025-01-08" xsd:string [Term] id: CL:0000000 @@ -104,6 +106,8 @@ name: cell def: "A material entity of anatomical origin (part of or deriving from an organism) that has as its parts a maximally connected cell compartment surrounded by a plasma membrane." [CARO:mah] comment: The definition of cell is intended to represent all cells, and thus a cell is defined as a material entity and not an anatomical structure, which implies that it is part of an organism (or the entirety of one). subset: cellxgene_subset +subset: human_subset +subset: mouse_subset subset: ubprop:upper_level xref: CALOHA:TS-2035 xref: FBbt:00007002 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} @@ -125,6 +129,8 @@ relationship: RO:0002162 NCBITaxon:131567 ! in taxon cellular organisms id: CL:0000007 name: early embryonic cell (metazoa) def: "A cell found in the embryo before the formation of all the gem layers is complete." [GOC:tfm] +subset: human_subset +subset: mouse_subset xref: ZFA:0009002 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0002321 ! embryonic cell (metazoa) @@ -136,6 +142,8 @@ comment: This term applies to metazoan. For plant stem cells, consider using PO: subset: cellxgene_subset subset: general_cell_types_upper_slim subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "animal stem cell" EXACT [] xref: CALOHA:TS-2086 xref: FMA:63368 @@ -156,6 +164,8 @@ comment: Markers differ between species, and two sets of markers have been descr subset: blood_and_immune_upper_slim subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "blood forming stem cell" EXACT [] synonym: "colony forming unit hematopoietic" RELATED [] synonym: "hemopoietic stem cell" EXACT [] @@ -206,6 +216,8 @@ name: germ line cell def: "A cell that is within the developmental lineage of gametes and is able to pass along its genetic material to offspring." [GOC:tfm, ISBN:0721662544] comment: Originally this term had some plant germ line cell children. subset: general_cell_types_upper_slim +subset: human_subset +subset: mouse_subset subset: ubprop:upper_level xref: ZFA:0009016 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000000 ! cell @@ -216,6 +228,8 @@ id: CL:0000040 name: monoblast def: "A myeloid progenitor cell committed to the monocyte lineage. This cell is CD11b-positive, has basophilic cytoplasm, euchromatin, and the presence of a nucleolus." [GOC:add, http://en.wikipedia.org/wiki/Monoblast, http://www.copewithcytokines.de, PMID:1104740] comment: Morphology: mononuclear cell, diameter 12-20 _M, non-granular, N/C ratio 3/1 - 4/1; markers: CD11b (shared with many other myeloid cells); location: Adult: bone marrow; fetal: liver, Yolk Sac; role or process: hematopoiesis, monocyte development; lineage: hematopoietic, myeloid. +subset: human_subset +subset: mouse_subset synonym: "CFU-M" RELATED OMO:0003000 [] synonym: "colony forming unit macrophage" RELATED [] synonym: "colony forming unit monocyte" RELATED [] @@ -225,7 +239,6 @@ xref: FMA:83553 xref: ZFA:0009017 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000763 ! myeloid cell is_a: CL:0002194 {is_inferred="true"} ! monopoietic cell -is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0002194 ! monopoietic cell intersection_of: capable_of GO:0030224 ! monocyte differentiation intersection_of: has_part CL:0017503 ! basophilic cytoplasm @@ -242,6 +255,8 @@ relationship: RO:0002202 CL:0002009 ! develops from macrophage dendritic cell pr id: CL:0000048 name: multi fate stem cell def: "A stem cell that can give rise to multiple lineages of cells." [GOC:add] +subset: human_subset +subset: mouse_subset synonym: "multi-fate stem cell" EXACT [] synonym: "multifate stem cell" EXACT [] synonym: "multipotent cell" EXACT [] @@ -261,6 +276,8 @@ def: "A progenitor cell committed to myeloid lineage, including the megakaryocyt comment: This cell type is intended to be compatible with any vertebrate common myeloid progenitor. For mammalian CMP known to be CD34-positive, please use the term 'common myeloid progenitor, CD34-positive' (CL_0001059). subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "CFU-GEMM" RELATED OMO:0003000 [ISBN:0878932437] synonym: "CFU-S" RELATED OMO:0003000 [ISBN:0878932437] synonym: "CMP" RELATED OMO:0003000 [ISBN:0878932437] @@ -283,6 +300,8 @@ def: "A oligopotent progenitor cell committed to the lymphoid lineage." [GOC:add comment: CLP are CD7-positive, CD10-positive, CD19-negative, CD34-positive, CD45RA-positive, CD79a-negative, CD127-positive, AA4.1-positive, RAG-negative, Sca-1-low, sIgM-negative, sIgD-negative, TdT-negative, Vpre-B-negative, and pre-BCR-negative. Expression of transcription factors include E2A-positive, EBF-positive, Ikaros-negative, PU.1-negative, and Pax5-negative. subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "CLP" RELATED OMO:0003000 [] synonym: "committed lymphopoietic stem cell" RELATED [] synonym: "common lymphocyte precursor" EXACT [] @@ -304,6 +323,8 @@ property_value: RO:0002175 NCBITaxon:9606 id: CL:0000052 name: totipotent stem cell def: "A stem cell from which all cells of the body can form." [GOC:add, GOC:tfm] +subset: human_subset +subset: mouse_subset synonym: "totipotential stem cell" EXACT [] xref: FMA:84790 xref: MESH:D039901 @@ -316,6 +337,8 @@ name: non-terminally differentiated cell def: "A precursor cell with a limited number of potential fates." [SANBI:mhl] comment: define using PATO mulit-potent or oligopotent? subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "blast cell" EXACT [] xref: BTO:0000125 xref: FMA:84782 @@ -325,6 +348,9 @@ is_a: CL:0011115 ! precursor cell id: CL:0000056 name: myoblast def: "A cell that is commited to differentiating into a muscle cell. Embryonic myoblasts develop from the mesoderm. They undergo proliferation, migrate to their various sites, and then differentiate into the appropriate form of myocytes. Myoblasts also occur as transient populations of cells in muscles undergoing repair." [GOC:tfm, MESH:D032446, PMID:21849021] +subset: cellxgene_subset +subset: human_subset +subset: mouse_subset xref: BTO:0000222 xref: CALOHA:TS-0650 xref: FBbt:00005083 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} @@ -341,14 +367,15 @@ comment: These cells may be vimentin-positive, fibronectin-positive, fsp1-positi subset: cellxgene_subset subset: general_cell_types_upper_slim subset: human_reference_atlas +subset: human_subset +subset: mouse_subset xref: BTO:0000452 xref: CALOHA:TS-0362 xref: FMA:63877 xref: NCIT:C12482 xref: VHOG:0001482 xref: ZFA:0009026 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} -is_a: CL:0002320 ! connective tissue cell -relationship: RO:0002202 CL:0000134 ! develops from mesenchymal stem cell +is_a: CL:0000499 ! stromal cell property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -358,6 +385,8 @@ def: "A cell that is usually found in a two-dimensional sheet with a free surfac subset: cellxgene_subset subset: general_cell_types_upper_slim subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "epitheliocyte" EXACT [] xref: BTO:0000414 xref: CALOHA:TS-2026 @@ -378,6 +407,8 @@ name: columnar/cuboidal epithelial cell def: "A columnar/cuboidal epithelial cell is a cell usually found in a two dimensional sheet with a free surface. Columnar/cuboidal epithelial cells take on the shape of a column or cube." [GO:0002065, https://orcid.org/0000-0001-5208-3432] subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset xref: ZFA:0009038 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000066 ! epithelial cell property_value: RO:0002175 NCBITaxon:9606 @@ -388,6 +419,8 @@ name: blood cell def: "A cell found predominately in the blood." [GOC:add, GOC:tfm] subset: cellxgene_subset subset: general_cell_types_upper_slim +subset: human_subset +subset: mouse_subset xref: FMA:62844 xref: MESH:D001773 xref: ZFA:0009044 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} @@ -403,6 +436,8 @@ def: "A type of lymphocyte whose defining characteristic is the expression of a subset: cellxgene_subset subset: general_cell_types_upper_slim subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "immature T cell" RELATED [] synonym: "mature T cell" RELATED [] synonym: "T lymphocyte" EXACT [] @@ -428,16 +463,18 @@ name: osteoclast def: "A specialized phagocytic cell associated with the absorption and removal of the mineralized matrix of bone tissue, which typically differentiates from monocytes. This cell has the following markers: tartrate-resistant acid phosphatase type 5-positive, PU.1-positive, c-fos-positive, nuclear factor NF-kappa-B p100 subunit-positive, tumor necrosis factor receptor superfamily member 11A-positive and macrophage colony-stimulating factor 1 receptor-positive." [GO_REF:0000031, GOC:add, GOC:tfm, ISBN:0781735149, PMID:10428500, PMID:15055519, PMID:17380158] comment: Morphology: Highly vesicular; markers: Surface: RANK, cFMS (MCSF receptor); Secreted: cathepsin K and TRAP (tartate resistant acid phosphatase); transcription factors: PU.1, cFOS, MITF, NFkB (p52); role or process: tissue remodelling: bone resorption; lineage: hematopoietic, myeloid. subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "chondroclast" RELATED [] xref: BTO:0000968 xref: CALOHA:TS-0721 xref: FMA:66781 +xref: https://cellxgene.cziscience.com/cellguide/CL_0000092 xref: MESH:D010010 xref: ZFA:0009047 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000518 ! phagocyte (sensu Vertebrata) is_a: CL:0000766 {is_inferred="true"} ! myeloid leukocyte is_a: CL:0001035 {is_inferred="true"} ! bone cell -is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000766 ! myeloid leukocyte intersection_of: capable_of GO:0045453 ! bone resorption intersection_of: has_part PR:000001850 ! cathepsin K @@ -457,6 +494,7 @@ relationship: has_part PR:000011178 ! nuclear factor NF-kappa-B p100 subunit relationship: RO:0002104 PR:000001954 ! has plasma membrane part tumor necrosis factor receptor superfamily member 11A relationship: RO:0002104 PR:000002062 ! has plasma membrane part macrophage colony-stimulating factor 1 receptor relationship: RO:0002202 CL:0000576 ! develops from monocyte +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nOsteoclasts, derived from the monocyte/macrophage lineage, play a crucial role in bone remodeling through bone resorption. They are distinguished from other cells by their large size and their unique ability to secrete enzymes and acids that dissolve the calcium phosphate in bone. The formation of osteoclasts is influenced by two primary factors: macrophage colony-stimulating factor (M-CSF) and the ligand-activated receptor (RANKL) of nuclear factor kappa B (NF-κB).\nOsteoclasts also collaborate with osteoblasts, responsible for new bone formation, to maintain bone health and adapt bone structure. Their coordinated actions allow continuous remodeling while preserving overall bone strength and integrity. Imbalances in osteoclast activity can lead to pathological conditions. For example, excessive activity may contribute to diseases like osteoporosis, periprosthetic osteolysis, bone tumors, and Paget's disease. Other the other hand, osteoclast deficiency ca result in conditions like osteopetrosis." xsd:string {xref="DOI:10.3389/fmed.2017.00234", xref="DOI:10.37175/stemedicine.v1i4.57", xref="https://www.sciencedirect.com/topics/medicine-and-dentistry/osteoclast"} [Term] id: CL:0000094 @@ -464,6 +502,8 @@ name: granulocyte def: "A leukocyte with abundant granules in the cytoplasm." [GOC:amm, GOC:tfm, http://en.wikipedia.org/wiki/Granulocyte, MESH:D006098] subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "granular leucocyte" EXACT [] synonym: "granular leukocyte" EXACT [] synonym: "polymorphonuclear leukocyte" EXACT [] @@ -474,7 +514,6 @@ xref: FMA:62854 xref: ZFA:0009048 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000081 ! blood cell is_a: CL:0000766 {is_inferred="true"} ! myeloid leukocyte -is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000766 ! myeloid leukocyte intersection_of: capable_of GO:0008015 ! blood circulation intersection_of: CL:4030046 PR:000001002 ! lacks_plasma_membrane_part CD19 molecule @@ -499,6 +538,8 @@ property_value: RO:0002175 NCBITaxon:9606 id: CL:0000095 name: neuron associated cell subset: cellxgene_subset +subset: human_subset +subset: mouse_subset is_a: CL:0002319 ! neural cell relationship: RO:0002202 CL:0000133 ! develops from neurectodermal cell @@ -508,6 +549,8 @@ name: motor neuron def: "An efferent neuron that passes from the central nervous system or a ganglion toward or to a muscle and conducts an impulse that causes or inhibits movement." [MESH:D009046, PMID:16875686] subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "motoneuron" EXACT [] xref: BTO:0000312 xref: FBbt:00005123 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} @@ -521,7 +564,10 @@ property_value: RO:0002175 NCBITaxon:9606 id: CL:0000101 name: sensory neuron def: "Any neuron having a sensory function; an afferent neuron conveying sensory impulses." [ISBN:0721662544] +subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset xref: BTO:0001037 xref: FBbt:00005124 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:84649 @@ -540,6 +586,8 @@ name: mononuclear phagocyte def: "A vertebrate phagocyte with a single nucleus." [GOC:add, GOC:tfm, ISBN:0781735149] subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset xref: BTO:0001433 xref: https://cellxgene.cziscience.com/cellguide/CL_0000113 xref: ZFA:0009064 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} @@ -548,7 +596,7 @@ is_a: CL:0000842 ! mononuclear cell intersection_of: CL:0000518 ! phagocyte (sensu Vertebrata) intersection_of: bearer_of PATO:0001407 ! mononucleate property_value: RO:0002175 NCBITaxon:9606 -property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional.\n\nMononuclear phagocytes are immune cells that form a critical part of the body's innate immune system, the body's first line of defense against infections. Mononuclear phagocytes are characterized by the presence of a single, large nucleus. The ‘Mononuclear Phagocyte System’ nomenclature was introduced to distinguish mononuclear monocytes and macrophages from other cells with multiple nuclei. However, the cells within the mononuclear phagocyte system represent a highly heterogeneous group, all of which are able to perform highly efficient phagocytosis - engulfing and digesting microbes and cellular debris to fight infections and to maintain normal tissue homeostasis. \nIn addition to phagocytosis, mononuclear phagocytes also secrete chemical compounds to recruit other immune cells to a site of infection. These cells produce different types of signaling molecules, including cytokines, chemokines, and reactive oxygen species, triggering a cascade of responses to ensure rapid and efficient containment and neutralization of invading pathogens. These cells are also involved in antigen presentation, a process essential for stimulating an adaptive immune response. They can process and present antigens to T cells, thereby linking the innate and adaptive immune responses.\nMononuclear phagocytes play key roles in tissue repair and remodeling. After infection or injury, these cells help in the clearance of dead cells and debris, a crucial step in the initiation of tissue remodeling and the resolution of inflammation. Overall, mononuclear phagocytes are versatile cells that have tailored their functions to meet the unique challenges of different tissues within the body. They are pivotal in homeostasis, immunity, and inflammation, making them important aspects in a range of human diseases including infection, autoimmunity, and cancer." xsd:string {xref="DOI:10.1016/j.coi.2005.11.008", xref="DOI:10.1038/nri3087", xref="DOI:10.3389/fimmu.2019.01893"} +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nMononuclear phagocytes are immune cells that form a critical part of the body's innate immune system, the body's first line of defense against infections. Mononuclear phagocytes are characterized by the presence of a single, large nucleus. The ‘Mononuclear Phagocyte System’ nomenclature was introduced to distinguish mononuclear monocytes and macrophages from other cells with multiple nuclei. However, the cells within the mononuclear phagocyte system represent a highly heterogeneous group, all of which are able to perform highly efficient phagocytosis - engulfing and digesting microbes and cellular debris to fight infections and to maintain normal tissue homeostasis. \nIn addition to phagocytosis, mononuclear phagocytes also secrete chemical compounds to recruit other immune cells to a site of infection. These cells produce different types of signaling molecules, including cytokines, chemokines, and reactive oxygen species, triggering a cascade of responses to ensure rapid and efficient containment and neutralization of invading pathogens. These cells are also involved in antigen presentation, a process essential for stimulating an adaptive immune response. They can process and present antigens to T cells, thereby linking the innate and adaptive immune responses.\nMononuclear phagocytes play key roles in tissue repair and remodeling. After infection or injury, these cells help in the clearance of dead cells and debris, a crucial step in the initiation of tissue remodeling and the resolution of inflammation. Overall, mononuclear phagocytes are versatile cells that have tailored their functions to meet the unique challenges of different tissues within the body. They are pivotal in homeostasis, immunity, and inflammation, making them important aspects in a range of human diseases including infection, autoimmunity, and cancer." xsd:string {xref="DOI:10.1016/j.coi.2005.11.008", xref="DOI:10.1038/nri3087", xref="DOI:10.3389/fimmu.2019.01893"} [Term] id: CL:0000125 @@ -558,6 +606,8 @@ comment: Not all glial cells develop from glioblasts, with microglia developing subset: cellxgene_subset subset: general_cell_types_upper_slim subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "neuroglia" RELATED [] synonym: "neuroglial cell" EXACT [] xref: BTO:0002606 @@ -568,12 +618,14 @@ xref: https://cellxgene.cziscience.com/cellguide/CL_0000125 xref: ZFA:0009073 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000095 ! neuron associated cell property_value: RO:0002175 NCBITaxon:9606 -property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional.\n\nGlial cells, also known as neuroglia or simply glia, are non-neuronal cells in the central and peripheral nervous systems that provide support and protection for neurons. They constitute approximately half of the total cells in the human brain and more than half in other parts of the nervous system. Glial cells perform several key functions including, but not limited to, maintaining homeostasis, forming the myelin sheath around the neuron axons, and providing support and nutrition to neurons.\nThese different functions are performed by various glial cell types, including astrocytes, oligodendrocytes, microglia and other specialized types. Astrocytes, for example, are the most abundant glial cells and provide metabolic and nutrient support to neurons, help regulate the extracellular ion and neurotransmitter levels, and play a role in the formation and maintenance of the blood-brain barrier, contributing to the overall homeostasis and functioning of the nervous system. Additionally, astrocytes are involved in synaptic communication and participate in processes such as synaptogenesis and synaptic pruning.\nOligodendrocytes in the central nervous system function to insulate neurons by producing a fatty substance known as myelin. The myelin sheath enhances the speed and efficiency of nerve impulse conduction along the axons. \nMicroglia, the immune cells of the central nervous system, protect neurons from pathogens and clear away dead neurons through phagocytosis, a process also known as cellular eating. They also contribute to the regulation of inflammation in response to signals of tissue damage or infection in the central nervous system by releasing cytokines and other signaling molecules that modulate the immune response.\nDespite their overarching function in the support and protection of neurons, glial cells have also been shown to play significant roles in the pathophysiology of many psychiatric and neurodegenerative diseases, such as Alzheimer’s, Parkinson’s Disease and multiple sclerosis." xsd:string {xref="DOI:10.1002/glia.24343", xref="DOI:10.1038/nn1988", xref="DOI:10.1101/cshperspect.a020602", xref="DOI:10.1126/science.aat0473", xref="DOI:10.3389/fncel.2017.00024"} +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nGlial cells, also known as neuroglia or simply glia, are non-neuronal cells in the central and peripheral nervous systems that provide support and protection for neurons. They constitute approximately half of the total cells in the human brain and more than half in other parts of the nervous system. Glial cells perform several key functions including, but not limited to, maintaining homeostasis, forming the myelin sheath around the neuron axons, and providing support and nutrition to neurons.\nThese different functions are performed by various glial cell types, including astrocytes, oligodendrocytes, microglia and other specialized types. Astrocytes, for example, are the most abundant glial cells and provide metabolic and nutrient support to neurons, help regulate the extracellular ion and neurotransmitter levels, and play a role in the formation and maintenance of the blood-brain barrier, contributing to the overall homeostasis and functioning of the nervous system. Additionally, astrocytes are involved in synaptic communication and participate in processes such as synaptogenesis and synaptic pruning.\nOligodendrocytes in the central nervous system function to insulate neurons by producing a fatty substance known as myelin. The myelin sheath enhances the speed and efficiency of nerve impulse conduction along the axons. \nMicroglia, the immune cells of the central nervous system, protect neurons from pathogens and clear away dead neurons through phagocytosis, a process also known as cellular eating. They also contribute to the regulation of inflammation in response to signals of tissue damage or infection in the central nervous system by releasing cytokines and other signaling molecules that modulate the immune response.\nDespite their overarching function in the support and protection of neurons, glial cells have also been shown to play significant roles in the pathophysiology of many psychiatric and neurodegenerative diseases, such as Alzheimer’s, Parkinson’s Disease and multiple sclerosis." xsd:string {xref="DOI:10.1002/glia.24343", xref="DOI:10.1038/nn1988", xref="DOI:10.1101/cshperspect.a020602", xref="DOI:10.1126/science.aat0473", xref="DOI:10.3389/fncel.2017.00024"} [Term] id: CL:0000133 name: neurectodermal cell def: "Ectoderm destined to be nervous tissue." [GOC:tfm, ISBN:068340007X] +subset: human_subset +subset: mouse_subset synonym: "neurectoderm cell" EXACT [] xref: ZFA:0009080 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000221 ! ectodermal cell @@ -584,6 +636,8 @@ name: mesenchymal stem cell def: "A connective tissue cell that normally gives rise to other cells that are organized as three-dimensional masses. In humans, this cell type is CD73-positive, CD90-positive, CD105-positive, CD45-negative, CD34-negative, and MHCII-negative. They may further differentiate into osteoblasts, adipocytes, myocytes, neurons, or chondroblasts in vitro. Originally described as residing in the bone marrow, this cell type is now known to reside in many, if not all, adult organs." [FB:ma, GOC:dsd, http://en.wikipedia.org/wiki/Mesenchymal_stem_cell, http://www.copewithcytokines.de/cope.cgi?key=mesenchymal%20stem%20cells, PMCID:PMC2613570, PMID:10102814, PMID:16923606, PMID:17986482, PMID:19960544] comment: Many but not all mesenchymal cells derive from the mesoderm. MSCs are reportedly CD3-negative, CD4-negative, CD5-negative, CD8-negative, CD11a-negative, CD11b-negative, CD14-negative, CD19-negative, CD29-positive, CD31-negative, CD34-negative, CD38-negative, CD40-negative, CD44-positive, CD45-negative, CD49-positive, CD54-positive, CD66b-negative, CD79a-negative, CD80-negative, CD102-positive, CD106-positive, CD117-positive, CD121a-positive, CD121b-positive, CD123-positive, CD124-positive, CD133-negative, CD146-positive, CD166-positive, CD271-positive, B220-negative, Gr1-negative, MHCI-positive, MHCII-negative, SSEA4-negative, sca1-positive, Ter119-negative, and glycophorin A-negative. Cultured MSCs are capable of producing stem cell factor, IL7, IL8, IL11, TGF-beta, cofilin, galectin-1, laminin-receptor 1, cyclophilin A, and MMP-2. subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "BMSC" RELATED OMO:0003000 [] synonym: "bone marrow stromal cells" NARROW [] synonym: "CFU-F" RELATED OMO:0003000 [] @@ -611,6 +665,8 @@ def: "A fat-storing cell found mostly in the abdominal cavity and subcutaneous t subset: cellxgene_subset subset: general_cell_types_upper_slim subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "adipose cell" EXACT [] synonym: "fat cell" EXACT [] xref: BTO:0000443 @@ -629,6 +685,8 @@ def: "A cell capable of processing and presenting lipid and protein antigens to comment: Note change of name; nearly all somatic cells can present antigens to T cells via MHC Class I complexes leading to effector responses, but professional antigen presenting cells constitutively express MHC Class II as well as costimulatory molecules, and thus can initiate immune responses via T cells. subset: blood_and_immune_upper_slim subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "APC" RELATED OMO:0003000 [] xref: ZFA:0009088 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000738 ! leukocyte @@ -640,6 +698,8 @@ relationship: capable_of GO:0002504 ! antigen processing and presentation of pep id: CL:0000147 name: pigment cell def: "A pigment cell is a cell that contains pigment granules." [GOC:tfm] +subset: human_subset +subset: mouse_subset synonym: "chromatocyte" EXACT [] synonym: "chromatophore" EXACT [] xref: VHOG:0001678 @@ -653,10 +713,13 @@ def: "A pigment cell derived from the neural crest. Contains melanin-filled pigm subset: cellxgene_subset subset: general_cell_types_upper_slim subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "melanophore" NARROW [] xref: BTO:0000847 xref: CALOHA:TS-0613 xref: FMA:70545 +xref: https://cellxgene.cziscience.com/cellguide/CL_0000148 xref: MESH:D008544 xref: VHOG:0001679 xref: ZFA:0009091 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} @@ -668,10 +731,13 @@ intersection_of: RO:0002202 CL:0000541 ! develops from melanoblast relationship: has_part GO:0042470 ! melanosome relationship: RO:0002202 CL:0000541 ! develops from melanoblast property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nMelanocytes are specialized cells prevalently found in the skin, but also present in the hair follicles, eyes, inner ear, bones, heart, and brain. Their primary function is the synthesis of melanin, a pigment responsible for coloration of skin, hair, and eyes. The presence and distribution of this pigment play a crucial role in the body's defense mechanism against harmful ultraviolet radiation.\nIn addition to melanin production, melanocytes also engage in a variety of other biological functions. They play a fundamental role in the immune response, owing to their ability to present antigens to T cells. Furthermore, they contribute to the maintenance of the skin's homeostasis by regulating processes such as extracellular matrix remodeling and cytokine production. A balance in melanocyte function is pivotal, as dysfunctions often result in dermatological disorders. For instance, the loss of melanocytes or reduction in their function may lead to hypopigmentation conditions such as vitiligo, whereas an abnormal increase could result in hyperpigmentation disorders or melanoma, a dangerous type of skin cancer." xsd:string {xref="DOI:10.1002/med.21754", xref="DOI:10.1038/nrc.2016.37", xref="DOI:10.1111/j.1751-1097.2007.00226.x", xref="DOI:10.3390/ijms21249769", xref="https://www.sciencedirect.com/topics/agricultural-and-biological-sciences/melanocyte"} [Term] id: CL:0000149 name: visual pigment cell +subset: human_subset +subset: mouse_subset synonym: "pigment cell" BROAD [] is_a: CL:0000147 ! pigment cell @@ -680,6 +746,8 @@ id: CL:0000151 name: secretory cell def: "A cell that specializes in controlled release of one or more substances." [GOC:tfm, ISBN:0721662544] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset xref: BTO:0003659 xref: FMA:86916 is_a: CL:0000000 ! cell @@ -692,6 +760,8 @@ id: CL:0000152 name: exocrine cell def: "A cell of an exocrine gland; i.e. a gland that discharges its secretion via a duct." [ISBN:0198547684] subset: general_cell_types_upper_slim +subset: human_subset +subset: mouse_subset xref: FMA:16014 xref: ZFA:0009092 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000151 ! secretory cell @@ -707,6 +777,8 @@ def: "A cell of an endocrine gland, ductless glands that secrete substances whic subset: cellxgene_subset subset: general_cell_types_upper_slim subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "endocrinocyte" EXACT [] xref: FMA:83809 xref: ZFA:0009096 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} @@ -720,6 +792,8 @@ id: CL:0000183 name: contractile cell def: "A cell whose primary function is to shorten." [FB:ma] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset is_a: CL:0000000 ! cell [Term] @@ -727,6 +801,8 @@ id: CL:0000187 name: muscle cell def: "A mature contractile cell, commonly known as a myocyte. This cell has as part of its cytoplasm myofibrils organized in various patterns." [MESH:D032342] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "muscle fiber" EXACT [] synonym: "myocyte" EXACT [] xref: BTO:0000888 @@ -749,16 +825,20 @@ def: "A somatic cell located in skeletal muscle." [GOC:tfm] subset: cellxgene_subset subset: general_cell_types_upper_slim subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "skeletal muscle cell" EXACT [] xref: BTO:0004392 xref: CALOHA:TS-2158 xref: FMA:9727 +xref: https://cellxgene.cziscience.com/cellguide/CL_0000188 xref: ZFA:0009115 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000255 ! eukaryotic cell intersection_of: CL:0000000 ! cell intersection_of: part_of UBERON:0001134 ! skeletal muscle tissue relationship: part_of UBERON:0001134 ! skeletal muscle tissue property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nSkeletal muscle cells, or myocytes, are essential for the musculoskeletal system, featuring a striated appearance from tightly packed sarcomeres. These elongated, multi-nucleated cells convert ATP into mechanical energ and are key for voluntary movement and posture. They also are responsible for maintaining body temperature, storing nutrients, and stabilizing joints.\nSkeletal muscle cells organize themselves tightly into bundles to form muscle fibers. Embedded within each of these cells are thousands of myofibrils, which are made up of the contractile proteins, actin (the thin filament), and myosin (the thick filament). Contraction of a skeletal muscle cell occurs when these myofibrils shorten, a process driven by the sliding of actin and myosin filaments over each other in a mechanism famously known as the sliding filament theory.\nAdditionally, skeletal muscle cells exhibit a high degree of plasticity, which allows for their adaptation in response to alterations in functional demands or damages. They have an innate regenerative capacity due to the presence of satellite cells—quiescent muscle stem cells that reside within the muscle fibers. Upon muscle injury, these satellite cells become activated, proliferate, and differentiate into new muscle cells, thereby contributing to the repair and growth of injured skeletal muscle. With this, skeletal muscle cells serve not only a pivotal biomechanical function but also possess a great capacity for self-healing and regeneration." xsd:string {xref="DOI:10.1002/cphy.c160033", xref="DOI:10.3390/biology10101056", xref="https://www.nature.com/scitable/topicpage/the-sliding-filament-theory-of-muscle-contraction-14567666/", xref="https://www.ncbi.nlm.nih.gov/books/NBK537139", xref="https://www.ncbi.nlm.nih.gov/books/NBK9961/"} [Term] id: CL:0000192 @@ -767,6 +847,8 @@ def: "A non-striated, elongated, spindle-shaped cell found lining the digestive subset: cellxgene_subset subset: general_cell_types_upper_slim subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "myocytes, smooth muscle" EXACT [MESH:D032389] synonym: "non-striated muscle cell" BROAD [] synonym: "SMCs" EXACT [PMID:9315361] @@ -774,17 +856,21 @@ synonym: "smooth muscle fiber" EXACT [] xref: BTO:0004576 xref: CALOHA:TS-2159 xref: FMA:14072 +xref: https://cellxgene.cziscience.com/cellguide/CL_0000192 xref: ZFA:0009118 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0008000 ! non-striated muscle cell is_a: CL:0008007 ! visceral muscle cell relationship: RO:0002202 CL:0000514 ! develops from smooth muscle myoblast property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nSmooth muscle cells are a specialized type of muscle cells that are primarily found within the walls of hollow organs such as the intestine, stomach, bladder, uterus, and blood vessels. These cells are an essential component of the autonomic nervous system controling involuntary movements within the body.\nSmooth muscle cells play a vital role in many physiological processes due to their unique functionality. They can contract and relax in a slow, sustained, and controlled manner to help modulate the size and shape of the lumens of the organs they surround. For example, in the digestive system, coordinated contraction and relaxation of smooth muscle cells propels food along the gastrointestinal tract - a process known as peristalsis. In the blood vessels, the smooth muscle cells, by contracting or relaxing, either constrict or dilate the vessels, which in turn, help regulate blood flow and pressure.\nOn a cellular level, smooth muscle cells possess a single, centrally located nucleus and contain an arranged network of actin and myosin filaments, which are the proteins responsible for muscle contraction. Unlike their counterparts in skeletal or cardiac muscles, these cells lack specific contact points for these filaments, hence the lack of visible striations. Furthermore, the contraction of smooth muscle cells is regulated by hormones and neurotransmitters, such as acetylcholine and norepinephrine, adding an additional layer of complex regulation to these highly specialized cells." xsd:string {xref="DOI:10.1093/ptj/81.11.1810", xref="https://training.seer.cancer.gov/anatomy/muscular/types.html", xref="https://www.ncbi.nlm.nih.gov/books/NBK10854/", xref="https://www.ncbi.nlm.nih.gov/books/NBK526125", xref="https://www.ncbi.nlm.nih.gov/books/NBK556137/"} [Term] id: CL:0000210 name: photoreceptor cell def: "A cell specialized in detecting light stimuli that are involved in visual perception." [MESH:D010786] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset xref: BTO:0001060 xref: CALOHA:TS-0868 xref: FBbt:00004211 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} @@ -801,6 +887,8 @@ property_value: foaf:depiction "https://www.swissbiopics.org/api/image/Photorece id: CL:0000211 name: electrically active cell def: "A cell whose function is determined by the generation or the reception of an electric signal." [FB:ma] +subset: human_subset +subset: mouse_subset xref: ZFA:0009128 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000000 ! cell @@ -808,6 +896,8 @@ is_a: CL:0000000 ! cell id: CL:0000219 name: motile cell def: "A cell that moves by its own activities." [FB:ma] +subset: human_subset +subset: mouse_subset xref: ZFA:0009136 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000000 ! cell intersection_of: CL:0000000 ! cell @@ -818,6 +908,9 @@ relationship: capable_of GO:0048870 ! cell motility id: CL:0000221 name: ectodermal cell def: "A cell of the outer of the three germ layers of the embryo." [MESH:D004475] +subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "ectoderm cell" EXACT [] xref: FMA:72549 xref: ZFA:0009137 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} @@ -830,18 +923,24 @@ id: CL:0000222 name: mesodermal cell def: "A cell of the middle germ layer of the embryo." [MESH:D008648] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "mesoblast" EXACT [] synonym: "mesoderm cell" EXACT [] xref: FMA:72554 +xref: https://cellxgene.cziscience.com/cellguide/CL_0000222 xref: ZFA:0009138 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000255 ! eukaryotic cell is_a: CL:0002321 ! embryonic cell (metazoa) relationship: part_of UBERON:0000926 ! mesoderm +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nMesodermal cells are pluripotent and the most abundant in the human body. They contribute to the development of several structures such as the skeletal muscles, bones, heart and blood vessels, kidneys, gonads, connective tissues, and certain layers of the skin. Hence, the mesoderm is often regarded as an active and diverse layer due to its role in forming many bodily structures. \nIn embryonic development, these cells are instrumental, contributing to the body's structures through a carefully coordinated sequence of morphogenetic movements. This process forms the complex multicellular architecture of tissues and organs from a simple ball of cells. Without the function of mesodermal cells, the body's integral structures and systems would cease to form correctly, leading to developmental disorders such as axial mesodermal dysplasia complex" xsd:string {xref="DOI:10.1016/j.ceb.2019.07.012", xref="DOI:10.5535/arm.2016.40.1.162", xref="https://www.sciencedirect.com/topics/biochemistry-genetics-and-molecular-biology/mesoderm"} [Term] id: CL:0000223 name: endodermal cell def: "A cell of the inner of the three germ layers of the embryo." [MESH:D004707] +subset: human_subset +subset: mouse_subset synonym: "endoderm cell" EXACT [] xref: FMA:72555 xref: ZFA:0009139 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} @@ -853,6 +952,8 @@ relationship: part_of UBERON:0000925 ! endoderm id: CL:0000226 name: single nucleate cell def: "A cell with a single nucleus." [FB:ma, GOC:tfm] +subset: human_subset +subset: mouse_subset is_a: CL:0000255 ! eukaryotic cell is_a: CL:0002242 ! nucleate cell intersection_of: CL:0000000 ! cell @@ -863,6 +964,8 @@ relationship: bearer_of PATO:0001407 ! mononucleate id: CL:0000228 name: multinucleate cell def: "A cell with more than one nucleus." [FB:ma, Wikipedia:Multinucleate] +subset: human_subset +subset: mouse_subset synonym: "multinucleated cells" EXACT [Wikipedia:Multinucleate] synonym: "polynuclear cells" EXACT [Wikipedia:Multinucleate] is_a: CL:0000255 ! eukaryotic cell @@ -875,7 +978,8 @@ relationship: bearer_of PATO:0001908 ! multinucleate id: CL:0000234 name: phagocyte def: "Any cell capable of ingesting particulate matter via phagocytosis." [GOC:add, ISBN:0721601464] -subset: cellxgene_subset +subset: human_subset +subset: mouse_subset xref: BTO:0001044 xref: FMA:83806 xref: MESH:D010586 @@ -896,6 +1000,8 @@ subset: blood_and_immune_upper_slim subset: cellxgene_subset subset: general_cell_types_upper_slim subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "histiocyte" EXACT [] xref: BTO:0000801 xref: CALOHA:TS-0587 @@ -922,6 +1028,8 @@ subset: blood_and_immune_upper_slim subset: cellxgene_subset subset: general_cell_types_upper_slim subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "B lymphocyte" EXACT [] synonym: "B-cell" EXACT [] synonym: "B-lymphocyte" EXACT [] @@ -941,7 +1049,8 @@ property_value: RO:0002175 NCBITaxon:9606 id: CL:0000255 name: eukaryotic cell def: "Any cell that in taxon some Eukaryota." [FBC:Autogenerated] -subset: cellxgene_subset +subset: human_subset +subset: mouse_subset xref: MESH:D005057 is_a: CL:0000000 ! cell intersection_of: CL:0000000 ! cell @@ -952,12 +1061,16 @@ relationship: RO:0002162 NCBITaxon:2759 ! in taxon Eukaryota id: CL:0000325 name: stuff accumulating cell def: "A cell that is specialised to accumulate a particular substance(s)." [FB:ma] +subset: human_subset +subset: mouse_subset subset: ubprop:upper_level is_a: CL:0000000 ! cell [Term] id: CL:0000327 name: extracellular matrix secreting cell +subset: human_subset +subset: mouse_subset xref: ZFA:0009162 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000499 ! stromal cell @@ -965,6 +1078,8 @@ is_a: CL:0000499 ! stromal cell id: CL:0000333 name: migratory neural crest cell def: "A cell derived from the specialized ectoderm flanking each side of the embryonic neural plate, which after the closure of the neural tube, forms masses of cells that migrate out from the dorsal aspect of the neural tube to spread throughout the body." [doi:10.1016/j.stem.2015.02.017] +subset: human_subset +subset: mouse_subset xref: FMA:86667 xref: ZFA:0007086 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000219 ! motile cell @@ -976,7 +1091,10 @@ relationship: RO:0002202 CL:0007004 ! develops from premigratory neural crest ce id: CL:0000349 name: extraembryonic cell def: "Any cell that is part of some extraembryonic structure." [FBC:Autogenerated] +subset: cellxgene_subset subset: general_cell_types_upper_slim +subset: human_subset +subset: mouse_subset xref: ZFA:0009176 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000255 ! eukaryotic cell intersection_of: CL:0000000 ! cell @@ -987,6 +1105,8 @@ relationship: part_of UBERON:0000478 ! extraembryonic structure id: CL:0000352 name: epiblast cell def: "A cell of the outer layer of a blastula that gives rise to the ectoderm after gastrulation." [GOC:tfm, ISBN:0618947256] +subset: human_subset +subset: mouse_subset is_a: CL:0000052 ! totipotent stem cell [Term] @@ -994,6 +1114,8 @@ id: CL:0000355 name: multi-potent skeletal muscle stem cell def: "A multifate stem cell found in skeletal muscle than can differentiate into many different cell types, including muscle. Distinct cell type from satellite cell." [PMID:18282570] comment: Multi-potency demonstrated ex vivo. At the time of writing, it is unclear whether the endogenous population differentiates into multiple cell types in vivo. +subset: human_subset +subset: mouse_subset xref: FMA:86767 xref: ZFA:0009179 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000048 {is_inferred="true"} ! multi fate stem cell @@ -1005,6 +1127,8 @@ intersection_of: part_of UBERON:0001134 ! skeletal muscle tissue id: CL:0000365 name: animal zygote def: "Diploid cell produced by the fusion of sperm cell nucleus and egg cell." [ISBN:0471245208] +subset: human_subset +subset: mouse_subset synonym: "zygote" BROAD [] xref: BTO:0000854 xref: EHDAA2:0004546 @@ -1020,6 +1144,8 @@ relationship: RO:0002162 NCBITaxon:33208 ! in taxon Metazoa id: CL:0000393 name: electrically responsive cell def: "A cell whose function is determined by its response to an electric signal." [FB:ma] +subset: human_subset +subset: mouse_subset xref: ZFA:0009190 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000211 ! electrically active cell @@ -1027,6 +1153,8 @@ is_a: CL:0000211 ! electrically active cell id: CL:0000404 name: electrically signaling cell def: "A cell that initiates an electrical signal and passes that signal to another cell." [FB:ma] +subset: human_subset +subset: mouse_subset xref: ZFA:0009193 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000211 ! electrically active cell @@ -1037,6 +1165,8 @@ def: "A cell of hematopoietic origin, typically resident in particular tissues, subset: cellxgene_subset subset: general_cell_types_upper_slim subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "interdigitating cell" RELATED [] synonym: "veiled cell" RELATED [] xref: BTO:0002042 @@ -1046,7 +1176,6 @@ xref: MESH:D003713 xref: ZFA:0009209 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000113 ! mononuclear phagocyte is_a: CL:0000145 ! professional antigen presenting cell -is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000738 ! leukocyte intersection_of: bearer_of PATO:0001407 ! mononucleate intersection_of: capable_of GO:0001816 ! cytokine production @@ -1074,15 +1203,19 @@ property_value: RO:0002175 NCBITaxon:9606 id: CL:0000473 name: defensive cell def: "A cell whose primary function is to protect the organism." [JB:jb] +subset: human_subset +subset: mouse_subset is_a: CL:0000000 ! cell [Term] id: CL:0000499 name: stromal cell -def: "A connective tissue cell of an organ found in the loose connective tissue. These are most often associated with the uterine mucosa and the ovary as well as the hematopoietic system and elsewhere." [GOC:tfm, MESH:D017154] +def: "A connective tissue cell of an organ found in the loose connective tissue." [GOC:tfm, MESH:D017154] subset: cellxgene_subset subset: general_cell_types_upper_slim subset: human_reference_atlas +subset: human_subset +subset: mouse_subset xref: BTO:0002064 xref: FMA:83624 xref: ZFA:0009226 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} @@ -1095,6 +1228,8 @@ id: CL:0000513 name: cardiac muscle myoblast def: "A precursor cell destined to differentiate into cardiac muscle cell." [GOC:tfm, MESH:D032386] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "cardiac muscle progenitor cell" EXACT [] synonym: "cardiomyocyte progenitor cell" EXACT [] xref: FMA:84797 @@ -1111,19 +1246,25 @@ id: CL:0000514 name: smooth muscle myoblast def: "A precursor cell destined to differentiate into smooth muscle myocytes." [GOC:tfm, MESH:D032390] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "myoblast, smooth muscle" EXACT [MESH:D032390] synonym: "satellite cell" RELATED [] xref: FMA:84798 +xref: https://cellxgene.cziscience.com/cellguide/CL_0000514 xref: ZFA:0009235 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000056 ! myoblast intersection_of: CL:0000056 ! myoblast intersection_of: RO:0002203 CL:0000192 ! develops into smooth muscle cell relationship: RO:0002203 CL:0000192 ! develops into smooth muscle cell +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nA precursor to the smooth muscle cell, the smooth muscle myoblast, is integral to various body systems, including the cardiovascular, gastrointestinal, and respiratory systems. Smooth muscle myoblasts arise from the differentiation of mesenchymal stem cells, a process tightly regulated by specific genetic factors and environmental signals. Their role extends to myogenesis, particularly in the formation of muscular tissue, especially during embryonic development.\nSmooth muscle myoblasts possess distinctive cellular characteristics. In contrast to skeletal muscle myoblasts, they do not fuse to create multinucleated fibers. Instead, they differentiate into individual, uninucleated smooth muscle cells. This differentiation unfolds in two distinct phases: proliferation, marked by rapid division to increase cell numbers, and differentiation, involving structural and functional transformation into mature smooth muscle cells. This intricate process is intricately mediated by various signaling molecules and transcription factors.\nFunctionally, smooth muscle myoblasts and the mature muscle cells they generate play pivotal roles in various physiological processes. Smooth muscle cells orchestrate involuntary muscle responses and are integral to body systems that regulate blood flow, propel food along the digestive tract, and control airflow in the respiratory tract. These diverse functions underscore the significance of smooth muscle myoblasts in the body's growth, maintenance, and overall function." xsd:string {xref="DOI:10.1074/jbc.RA118.001739", xref="https://www.ncbi.nlm.nih.gov/books/NBK544225/", xref="https://www.sciencedirect.com/topics/medicine-and-dentistry/smooth-muscle"} [Term] id: CL:0000515 name: skeletal muscle myoblast def: "A myoblast that differentiates into skeletal muscle fibers." [SANBI:mhl] +subset: human_subset +subset: mouse_subset synonym: "skeletal myoblast" EXACT [] xref: FMA:84799 xref: ZFA:0009236 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} @@ -1138,6 +1279,8 @@ relationship: RO:0002203 CL:0008002 ! develops into skeletal muscle fiber id: CL:0000518 name: phagocyte (sensu Vertebrata) def: "A phagocyte in vertebrates that is able to phagocytosis." [GOC:tfm] +subset: human_subset +subset: mouse_subset is_a: CL:0000234 ! phagocyte is_a: CL:0000255 ! eukaryotic cell relationship: RO:0002162 NCBITaxon:7742 ! in taxon Vertebrata @@ -1147,6 +1290,8 @@ id: CL:0000526 name: afferent neuron def: "A neuron which conveys sensory information centrally from the periphery." [GOC:tfm, MESH:D009475] subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "input neuron" EXACT [] xref: FMA:87653 xref: ZFA:0009238 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} @@ -1157,6 +1302,9 @@ property_value: RO:0002175 NCBITaxon:9606 id: CL:0000527 name: efferent neuron def: "A neuron which sends impulses peripherally to activate muscles or secretory cells." [MESH:D009476] +subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "output neuron" EXACT [] xref: ZFA:0009239 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000540 ! neuron @@ -1169,6 +1317,8 @@ comment: These cells are also reportedly CD4-negative and CD200-positive. They a subset: cellxgene_subset subset: general_cell_types_upper_slim subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "nerve cell" EXACT [] xref: BTO:0000938 xref: CALOHA:TS-0683 @@ -1189,6 +1339,8 @@ id: CL:0000541 name: melanoblast def: "A cell that originates from the neural crest and differentiates into a pigment cell." [GOC:tfm, SANBI:mhl] comment: Derived from UBERON:0002342 neural crest. +subset: human_subset +subset: mouse_subset xref: BTO:0003217 xref: FMA:83377 xref: ZFA:0009249 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} @@ -1203,6 +1355,8 @@ def: "A lymphocyte is a leukocyte commonly found in the blood and lymph that has comment: Editors note: consider adding taxon constraint to vertebrata (PMID:18025161) subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset xref: BTO:0000775 xref: CALOHA:TS-0583 xref: FMA:62863 @@ -1229,6 +1383,8 @@ def: "A hematopoietic progenitor cell that is committed to the granulocyte and m comment: Originally described in the dendritic cell ontology (DC_CL:0000042)(PMID:19243617). GMPs are reportedly CD16-positive, CD32-positive, CD34-positive, CD38-positive, CD45RA-positive, CD110-negative, CD117-positive, CD123-positive, and SCA1-negative. subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "CFU-C , Colony forming unit in culture" BROAD [http://www.copewithcytokines.de] synonym: "CFU-GM" RELATED OMO:0003000 [ISBN:0721601464, PMCID:PMC2213186, PMCID:PMC548021] synonym: "colony forming unit granulocyte macrophage" EXACT [ISBN:0721601464, PMCID:PMC2213186, PMCID:PMC548021] @@ -1236,12 +1392,11 @@ synonym: "GMP" RELATED OMO:0003000 [ISBN:0721601464, PMCID:PMC2213186, PMCID:PMC synonym: "granulocyte-macrophage progenitor" EXACT [ISBN:0721601464, PMCID:PMC2213186, PMCID:PMC548021] synonym: "granulocyte/monocyte precursor" EXACT [] synonym: "granulocyte/monocyte progenitor" EXACT [] +xref: https://cellxgene.cziscience.com/cellguide/CL_0000557 xref: ZFA:0009251 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000763 ! myeloid cell is_a: CL:0001012 ! CD7-negative lymphoid progenitor OR granulocyte monocyte progenitor -is_a: CL:0011026 ! progenitor cell is_a: CL:1001610 ! bone marrow hematopoietic cell -is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0002032 ! hematopoietic oligopotent progenitor cell intersection_of: capable_of GO:0030225 ! macrophage differentiation intersection_of: capable_of GO:0030851 ! granulocyte differentiation @@ -1259,6 +1414,7 @@ relationship: has_part PR:000001944 ! transcription factor PU.1 relationship: has_part PR:000005307 ! CCAAT/enhancer-binding protein alpha relationship: RO:0002104 PR:000001865 ! has plasma membrane part interleukin-3 receptor class 2 alpha chain property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nGranulocyte monocyte progenitor cells (GMP cells), originating from hematopoietic stem cells in the bone marrow, are a critical intermediate in myeloid cell development. Positioned at a key differentiation juncture, these cells exhibit bidirectional potential, giving rise to both granulocyte and monocyte lineages.\nTheir primary role is to generate mature granulocytes and monocytes, essential components of the body's innate immunity and inflammatory responses. Granulocytes, such as neutrophils, eosinophils, and basophils, contribute to the first line of defense against infections by migrating to the infection site and phagocytosing pathogens. Monocytes can differentiate into macrophages or dendritic cells, playing diverse roles in immune responses." xsd:string {xref="DOI:10.1016/j.immuni.2017.10.021", xref="DOI:10.1146/annurev-immunol-081022113627", xref="DOI:10.1186/2050-7771-2-1"} [Term] id: CL:0000559 @@ -1267,12 +1423,13 @@ def: "A precursor in the monocytic series, being a cell intermediate in developm comment: Morphology: Mononuclear cell, diameter 14-18 _M, fine azurophilic granules; markers: CD11b (shared with many other myeloid cells); location: Adult: bone marrow; Fetal: Liver, Yolk Sac; role or process: hematopoiesis, monocyte development; lineage: hematopoietic, myeloid. subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset xref: BTO:0004657 xref: FMA:83551 xref: ZFA:0009253 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000763 ! myeloid cell is_a: CL:0002194 {is_inferred="true"} ! monopoietic cell -is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0002194 ! monopoietic cell intersection_of: capable_of GO:0030224 ! monocyte differentiation intersection_of: has_part GO:0042582 ! azurophil granule @@ -1287,12 +1444,13 @@ id: CL:0000566 name: angioblastic mesenchymal cell def: "A mesenchymal stem cell capable of developing into blood vessel endothelium." [GOC:dsd, GOC:tfm, PMID:12768659] comment: These cells are reportedly CD31-positive, CD34-positive, CD144-positive, CD309-positive, and TAL1-positive. +subset: human_subset +subset: mouse_subset synonym: "angioblast" EXACT [] synonym: "chondroplast" EXACT [] xref: ZFA:0009258 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000134 {is_inferred="true"} ! mesenchymal stem cell is_a: CL:0011026 ! progenitor cell -is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000134 ! mesenchymal stem cell intersection_of: RO:0002104 PR:000001444 ! has plasma membrane part cadherin-5 intersection_of: RO:0002104 PR:000002112 ! has plasma membrane part vascular endothelial growth factor receptor 2 @@ -1311,6 +1469,8 @@ subset: blood_and_immune_upper_slim subset: cellxgene_subset subset: general_cell_types_upper_slim subset: human_reference_atlas +subset: human_subset +subset: mouse_subset xref: BTO:0000876 xref: CALOHA:TS-0638 xref: FMA:62864 @@ -1336,6 +1496,8 @@ def: "A lymphocyte that can spontaneously kill a variety of target cells without subset: cellxgene_subset subset: general_cell_types_upper_slim subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "large granular lymphocyte" BROAD [] synonym: "NK cell" EXACT [] synonym: "null cell" BROAD [] @@ -1367,6 +1529,8 @@ id: CL:0000680 name: muscle precursor cell def: "A non-terminally differentiated cell that is capable of developing into a muscle cell." [GOC:add] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset xref: ZFA:0009291 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000055 ! non-terminally differentiated cell is_a: CL:0000255 ! eukaryotic cell @@ -1379,6 +1543,8 @@ relationship: RO:0002203 CL:0000187 ! develops into muscle cell id: CL:0000723 name: somatic stem cell def: "A stem cell that can give rise to cell types of the body other than those of the germ-line." [GO:0048103] +subset: human_subset +subset: mouse_subset xref: CALOHA:TS-2086 xref: MESH:D053687 xref: ZFA:0009307 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} @@ -1391,6 +1557,8 @@ relationship: capable_of GO:0048103 ! somatic stem cell division id: CL:0000737 name: striated muscle cell def: "Muscle cell which has as its direct parts myofilaments organized into sarcomeres." [GOC:tfm, ISBN:0721662544] +subset: human_subset +subset: mouse_subset xref: BTO:0002916 xref: CALOHA:TS-2157 xref: FMA:86936 @@ -1409,6 +1577,8 @@ name: leukocyte def: "An achromatic cell of the myeloid or lymphoid lineages capable of ameboid movement, found in blood or other tissue." [GOC:add, GOC:tfm, ISBN:978-0-323-05290-0] subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "immune cell" RELATED [] synonym: "leucocyte" EXACT [] synonym: "white blood cell" EXACT [] @@ -1434,12 +1604,13 @@ property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000746 name: cardiac muscle cell -alt_id: FMA:83808 def: "Cardiac muscle cells are striated muscle cells that are responsible for heart contraction. In mammals, the contractile fiber resembles those of skeletal muscle but are only one third as large in diameter, are richer in sarcoplasm, and contain centrally located instead of peripheral nuclei." [GOC:mtg_cardiacconduct_nov11, GOC:tfm, ISBN:0323052908, PMID:22426062, PMID:4711263] comment: This class encompasses the muscle cells responsible for heart* contraction in both vertebrates and arthropods. The ultrastucture of a wide range of arthropod heart cells has been examined including spiders, horseshoe crabs, crustaceans (see Sherman, 1973 and refs therein) and insects (see Lehmacher et al (2012) and refs therein). According to these refs, the cells participating in heart contraction in all cases are transversely striated. Insects hearts additionally contain ostial cells, also transversely striated muscle cells, but which do not participate in heart contraction. subset: cellxgene_subset subset: general_cell_types_upper_slim subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "cardiac muscle fiber" EXACT [GO:0048739] synonym: "cardiac myocyte" EXACT [] synonym: "cardiocyte" BROAD [] @@ -1448,6 +1619,7 @@ synonym: "heart muscle cell" EXACT [] xref: BTO:0001539 xref: CALOHA:TS-0115 xref: FMA:14067 +xref: https://cellxgene.cziscience.com/cellguide/CL_0000746 xref: MESH:D032383 xref: ZFA:0009316 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000737 ! striated muscle cell @@ -1461,12 +1633,15 @@ relationship: bearer_of PATO:0002478 ! transversely striated relationship: participates_in GO:0060047 ! heart contraction relationship: RO:0002202 CL:0000513 ! develops from cardiac muscle myoblast property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nCardiac muscle cells, also known as cardiomyocytes or cardiac myocytes, are specialized cells that form the heart tissue. These cells are elongated, branched, and contain a single centrally located nucleus. Their anatomy is composed primarily of densely packed myofibrils, which are protein structures that consist of sarcomeres - the fundamental units of muscle contraction. Cardiac muscle cells are united at their ends through specialized junctions known as intercalated discs, which allow the heart to contract in a unified, powerful and rhythmic way.\nFunctionally, cardiac muscle cells are responsible for the heart's consistent pumping action that circulates blood throughout the body. Unlike most cells in the body, cardiac muscle cells spontaneously depolarize and generate action potentials without external stimulation. This unique trait stems from the presence of ion channels in the cells' membrane that allow a cyclic flow of ions across the membrane, which create the electrical impulses necessary for heart contraction. The spread of these electrical signals from one cardiac muscle cell to another - facilitated by the interconnected network made by the intercalated disks - results in a synchronized contraction of the heart muscle.\nUnlike skeletal muscle cells which can tire and need rest, cardiac muscle cells have to work ceaselessly throughout the entire lifespan, without the opportunity for rest, to ensure continuous circulation of blood. This is made possible through the high volume of mitochondria and a constant supply of oxygen from coronary circulation. In conclusion, cardiac muscle cells, through their unique structure and vital functionality, play a pivotal role in sustaining life by providing the means for blood to reach every cell in the body." xsd:string {xref="DOI:10.1016/j.ccep.2010.10.012", xref="DOI:10.1038/nrcardio.2016.203", xref="https://www.ncbi.nlm.nih.gov/books/NBK572070", xref="https://www.sciencedirect.com/topics/agricultural-and-biological-sciences/cardiac-muscle"} [Term] id: CL:0000763 name: myeloid cell def: "A cell of the monocyte, granulocyte, mast cell, megakaryocyte, or erythroid lineage." [GOC:add] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset xref: BTO:0001441 xref: CALOHA:TS-0647 xref: MESH:D022423 @@ -1482,6 +1657,8 @@ id: CL:0000766 name: myeloid leukocyte def: "A cell of the monocyte, granulocyte, or mast cell lineage." [GOC:add] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset xref: ZFA:0009326 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000738 {is_inferred="true"} ! leukocyte is_a: CL:0000763 ! myeloid cell @@ -1494,6 +1671,8 @@ name: myeloid dendritic cell def: "A dendritic cell of the myeloid lineage." [GOC:add, PMID:10449155, PMID:17332250, PMID:9521319] comment: These cells are CD1a-negative, CD1b-positive, CD11a-positive, CD11c-positive, CD13-positive, CD14-negative, CD20-negative, CD21-negative, CD33-positive, CD40-negative, CD50-positive, CD54-positive, CD58-positive, CD68-negative, CD80-negative, CD83-negative, CD85j-positive, CD86-positive, CD89-negative, CD95-positive, CD120a-negative, CD120b-positive, CD123-negative, CD178-negative, CD206-negative, CD207-negative, CD209-negative, and TNF-alpha-negative. Upon TLR stimulation, they are capable of producing high levels of TNF-alpha, IL-6, CXCL8 (IL-8). subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "CD11c+CD123- DC" EXACT [] synonym: "interdigitating cell" BROAD [] synonym: "mDC" EXACT [] @@ -1512,6 +1691,8 @@ id: CL:0000825 name: pro-NK cell def: "A lymphoid progenitor cell that is committed to the natural killer cell lineage, expressing CD122 (IL-15) receptor, but lacking many of the phenotypic characteristics of later stages of natural killer cell development such as expression of NK activating and inhibitory molecules. In human this cell has the phenotype CD34-positive, CD45RA-positive, CD10-positive, CD117-negative, and CD161 negative." [GO_REF:0000031, GOC:add, GOC:pam, PMID:11532393, PMID:12457618, PMID:15032583, PMID:15766674] comment: Most markers only described for human pro NK cells. +subset: human_subset +subset: mouse_subset synonym: "natural killer cell progenitor" EXACT [] synonym: "NKP" EXACT [PMID:12457618, PMID:15032583, PMID:15766674] synonym: "null cell" RELATED [PMID:11532393] @@ -1519,7 +1700,6 @@ synonym: "preNK cell" RELATED [PMID:11532393] synonym: "pro-natural killer cell" EXACT [] xref: ZFA:0009348 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000838 {is_inferred="true"} ! lymphoid lineage restricted progenitor cell -is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000838 ! lymphoid lineage restricted progenitor cell intersection_of: CL:4030046 PR:000001874 ! lacks_plasma_membrane_part KLRB1-like protein intersection_of: CL:4030046 PR:000002065 ! lacks_plasma_membrane_part mast/stem cell growth factor receptor @@ -1542,6 +1722,8 @@ def: "A progenitor cell of the B cell lineage, with some lineage specific activi comment: Human pro-B cells are reportedly CD10-positive, CD22-positive, CD34-positive, CD38-positive, CD45-low, CD48-positive, CD79a-positive, CD127-positive, CD184-positive, RAG-positive, TdT-positive, Vpre-B-positive, pre-BCR-negative, IgD-negative, and IgM-negative. Transcription factors expressed: Pax5-positive, EBF-positive, E2A-negative, Ikaros-negative, and PU.1-negative. subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "pre-B cell (Philadelphia nomenclature)" RELATED [PMID:11244048] synonym: "pre-pro B cell" BROAD [PMID:17582343] synonym: "pro-B lymphocyte" EXACT [] @@ -1554,7 +1736,6 @@ synonym: "progenitor B-lymphocyte" EXACT [] xref: BTO:0003104 xref: ZFA:0009349 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000838 {is_inferred="true"} ! lymphoid lineage restricted progenitor cell -is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000838 ! lymphoid lineage restricted progenitor cell intersection_of: has_part PR:000001903 ! paired box protein PAX-5 intersection_of: has_part PR:000006611 ! DNA nucleotidylexotransferase @@ -1570,6 +1751,8 @@ id: CL:0000827 name: pro-T cell def: "A lymphoid progenitor cell of the T cell lineage, with some lineage specific marker expression, but not yet fully committed to the T cell lineage." [GOC:add, ISBN:0781735149] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "DN1 cell" NARROW [] synonym: "DN1 thymocyte" NARROW [] synonym: "pro-T lymphocyte" EXACT [] @@ -1590,6 +1773,8 @@ comment: Markers differ between mouse and human. subset: blood_and_immune_upper_slim subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "hemopoietic progenitor cell" EXACT [] synonym: "MPP" EXACT [] xref: BTO:0000725 @@ -1597,7 +1782,6 @@ xref: CALOHA:TS-0448 xref: ZFA:0009354 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000255 ! eukaryotic cell is_a: CL:0008001 ! hematopoietic precursor cell -is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000988 ! hematopoietic cell intersection_of: bearer_of PATO:0001402 ! multipotent intersection_of: CL:4030046 PR:000001002 ! lacks_plasma_membrane_part CD19 molecule @@ -1639,6 +1823,8 @@ name: lymphoid lineage restricted progenitor cell def: "A progenitor cell restricted to the lymphoid lineage." [GOC:add, GOC:tfm] comment: Note that this is a class of cell types, not an identified single cell type. subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "lymphoid progenitor cell" BROAD [] xref: BTO:0004731 xref: CALOHA:TS-2025 @@ -1658,6 +1844,8 @@ def: "A progenitor cell restricted to the myeloid lineage." [GOC:add, GOC:tfm, P comment: Note that this is a class of cell types, not an identified single cell type. subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "myeloid progenitor cell" BROAD [] xref: BTO:0004730 xref: CALOHA:TS-2099 @@ -1676,6 +1864,8 @@ name: mononuclear cell def: "A leukocyte with a single non-segmented nucleus in the mature form." [GOC:add] subset: blood_and_immune_upper_slim subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "mononuclear leukocyte" EXACT [] synonym: "peripheral blood mononuclear cell" NARROW [] xref: BTO:0000878 @@ -1692,7 +1882,10 @@ id: CL:0000945 name: lymphocyte of B lineage def: "A lymphocyte of B lineage with the commitment to express an immunoglobulin complex." [GO_REF:0000031, GOC:add, GOC:rhs, GOC:tfm, ISBN:0781735149] comment: Types of B lineage lymphocytes include B cells and antibody secreting cells (plasmablasts and plasma cells). Lymphocytes of B cell lineage can be distinguished from those of T cell lineage by their lack of CD3e (as part of the T cell receptor complex). +subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset is_a: CL:0000542 {is_inferred="true"} ! lymphocyte relationship: RO:0002202 CL:0000826 ! develops from pro-B cell property_value: RO:0002175 NCBITaxon:9606 @@ -1702,6 +1895,8 @@ id: CL:0000988 name: hematopoietic cell def: "A cell of a hematopoietic lineage." [GO_REF:0000031, GOC:add] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "haematopoietic cell" EXACT [] synonym: "haemopoietic cell" EXACT [] synonym: "hemopoietic cell" EXACT [] @@ -1720,6 +1915,8 @@ comment: Originally described in the dendritic cell ontology (DC_CL:0000003)(PMI subset: blood_and_immune_upper_slim subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "cDC" EXACT [] synonym: "DC1" EXACT [] synonym: "dendritic reticular cell" EXACT [] @@ -1737,7 +1934,10 @@ property_value: RO:0002175 NCBITaxon:9606 id: CL:0001012 name: CD7-negative lymphoid progenitor OR granulocyte monocyte progenitor comment: Originally described in the dendritic cell ontology (DC_CL:1110000)(PMID:19243617). +subset: human_subset +subset: mouse_subset is_a: CL:0001060 ! hematopoietic oligopotent progenitor cell, lineage-negative +is_a: CL:0011026 ! progenitor cell [Term] id: CL:0001035 @@ -1745,18 +1945,24 @@ name: bone cell def: "A connective tissue cell found in bone." [GO_REF:0000034, GOC:add] subset: general_cell_types_upper_slim subset: human_reference_atlas +subset: human_subset +subset: mouse_subset +xref: https://cellxgene.cziscience.com/cellguide/CL_0001035 is_a: CL:0000255 ! eukaryotic cell intersection_of: CL:0000000 ! cell intersection_of: part_of UBERON:0001474 ! bone element relationship: part_of UBERON:0001474 ! bone element property_value: RO:0002175 NCBITaxon:9606 property_value: terms:contributor https://orcid.org/0000-0001-9990-8331 +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nBone cells, also known as osteocytes, form the building blocks of the skeletal system. They represent the most common type of bone cell, making up approximately 95% of the total bone cell population in mature adult bone tissue. Osteocytes are a stellate shape with numerous long, slender dendritic processes.\nThe formation of bone is a complex process involving the action of osteoclasts - cells that break down and reabsorb old bone, followed by osteoblasts that rebuild the bone. Osteocytes serve as coordinators for these two types of bone cells to ensure a balance in the bone remodeling process, contributing to maintaining both bone strength and mineral homeostasis.\nThe primary functions of osteocytes involve the creation, maintenance, and repair of bone tissue. They ensure that bone remodeling is performed by forming a network within the bone and communicating with other cells to help them respond to mechanical strain and damage.\nA remarkable aspect of osteocytes is their ability to perceive mechanical forces, translating them into biochemical signals that regulate bone remodeling and adaptation. Defects in osteocyte function, aside from other bone cells, have been associated with several bone disorders such as osteoporosis, renal osteodystrophy, and skeletal manifestations of diabetes." xsd:string {xref="DOI:10.1007/s00795-015-0099-y", xref="DOI:10.1007/s11914-012-0105-4", xref="DOI:10.1016/j.jot.2021.04.005", xref="DOI:10.1038/s41413-020-0099-y"} creation_date: 2011-11-16T04:28:16Z [Term] id: CL:0001060 name: hematopoietic oligopotent progenitor cell, lineage-negative def: "A hematopoietic oligopotent progenitor cell that has the ability to differentiate into limited cell types but lacks lineage cell markers and self renewal capabilities. Cell lacks hematopoeitic lineage markers." [GOC:tfm, PMID:19022770] +subset: human_subset +subset: mouse_subset is_a: CL:0002032 ! hematopoietic oligopotent progenitor cell intersection_of: CL:0002032 ! hematopoietic oligopotent progenitor cell intersection_of: bearer_of PATO:0001401 ! oligopotent @@ -1794,6 +2000,8 @@ def: "A lymphocyte that lacks characteristic T cell, B cell, myeloid cell, and d subset: blood_and_immune_upper_slim subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset is_a: CL:0000542 ! lymphocyte intersection_of: CL:0000542 ! lymphocyte intersection_of: capable_of GO:0001816 ! cytokine production @@ -1813,6 +2021,8 @@ id: CL:0001067 name: group 1 innate lymphoid cell def: "An innate lymphoid cell that is capable of producing the type 1 cytokine IFN-gamma, but not Th2 or Th17 cell-associated cytokines." [GOC:add, GOC:dsd, PMID:23348417] subset: human_reference_atlas +subset: human_subset +subset: mouse_subset is_a: CL:0001065 ! innate lymphoid cell intersection_of: CL:0001065 ! innate lymphoid cell intersection_of: capable_of GO:0032609 ! type II interferon production @@ -1826,6 +2036,8 @@ id: CL:0002009 name: macrophage dendritic cell progenitor def: "A progenitor cell that can give rise to plasmacytoid and myeloid dendritic cells, and to monocytes and macrophages." [GOC:tfm, PMID:19273628] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "MDP" EXACT [] is_a: CL:0000763 ! myeloid cell is_a: CL:0002032 {is_inferred="true"} ! hematopoietic oligopotent progenitor cell @@ -1844,6 +2056,8 @@ id: CL:0002031 name: hematopoietic lineage restricted progenitor cell def: "A hematopoietic progenitor cell that is capable of developing into only one lineage of hematopoietic cells." [GOC:tfm, PMID:19022770] subset: blood_and_immune_upper_slim +subset: human_subset +subset: mouse_subset is_a: CL:0000255 ! eukaryotic cell is_a: CL:0008001 ! hematopoietic precursor cell intersection_of: CL:0000988 ! hematopoietic cell @@ -1860,6 +2074,8 @@ name: hematopoietic oligopotent progenitor cell def: "A hematopoietic oligopotent progenitor cell that has the ability to differentiate into limited cell types but lacks lineage cell markers and self renewal capabilities." [GOC:tfm, https://orcid.org/0000-0001-5208-3432, PMID:19022770] comment: This cell type is intended to be compatible with any vertebrate hematopoietic oligopotent progenitor cell. For mammalian hematopoietic oligopotent progenitor cells known to be lineage-negative, please use the term 'hematopoietic oligopotent progenitor cell' (CL_0001060). subset: blood_and_immune_upper_slim +subset: human_subset +subset: mouse_subset is_a: CL:0000255 ! eukaryotic cell is_a: CL:0008001 ! hematopoietic precursor cell intersection_of: CL:0000988 ! hematopoietic cell @@ -1873,6 +2089,8 @@ creation_date: 2010-01-06T03:43:27Z id: CL:0002077 name: ecto-epithelial cell def: "An epithelial cell derived from ectoderm." [FMA:69074, GOC:tfm] +subset: human_subset +subset: mouse_subset xref: FMA:69074 xref: ZFA:0009385 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000066 ! epithelial cell @@ -1888,6 +2106,8 @@ name: bone marrow cell def: "A cell found in the bone marrow. This can include fibroblasts, macrophages, adipocytes, osteoblasts, osteoclasts, endothelial cells and hematopoietic cells." [GOC:tfm, ISBN:0618947256] comment: MH consider whether bone marrow cells are bone cells in the structural sense vs. being part of bone organ sense. subset: cellxgene_subset +subset: human_subset +subset: mouse_subset xref: BTO:0004850 xref: FMA:83621 xref: MESH:D001854 @@ -1902,6 +2122,8 @@ creation_date: 2010-07-22T04:48:15Z id: CL:0002194 name: monopoietic cell def: "A cell involved in the formation of a monocyte (monopoiesis)." [GOC:tfm] +subset: human_subset +subset: mouse_subset xref: FMA:83552 is_a: CL:0000839 {is_inferred="true"} ! myeloid lineage restricted progenitor cell intersection_of: CL:0000839 ! myeloid lineage restricted progenitor cell @@ -1914,6 +2136,8 @@ creation_date: 2010-08-30T01:27:48Z id: CL:0002242 name: nucleate cell def: "A cell containing at least one nucleus." [GOC:tfm] +subset: human_subset +subset: mouse_subset xref: FMA:67513 is_a: CL:0000000 ! cell intersection_of: CL:0000000 ! cell @@ -1927,6 +2151,8 @@ id: CL:0002319 name: neural cell def: "A cell that is part of the nervous system." [GOC:tfm, ISBN:0618947256] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset xref: CALOHA:TS-2040 xref: FMA:70333 is_a: CL:0000255 ! eukaryotic cell @@ -1941,6 +2167,8 @@ id: CL:0002320 name: connective tissue cell def: "A cell of the supporting or framework tissue of the body, arising chiefly from the embryonic mesoderm and including adipose tissue, cartilage, and bone." [GOC:tfm, ISBN:0618947256] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset xref: CALOHA:TS-2096 xref: FMA:63875 xref: MESH:D003239 @@ -1956,18 +2184,25 @@ creation_date: 2010-09-15T03:01:54Z id: CL:0002321 name: embryonic cell (metazoa) def: "A cell of the embryo." [FMA:0618947256] +subset: human_subset +subset: mouse_subset xref: CALOHA:TS-0263 xref: FMA:82840 +xref: https://cellxgene.cziscience.com/cellguide/CL_0002321 xref: WBbt:0007028 xref: ZFA:0007089 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000000 ! cell property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nEmbryonic cells in metazoans, which include all multicellular animals, are biological units in their earliest developmental stages from conception until the organism is fully formed. \nThey are derived from a fertilized egg, which undergoes a series of cell divisions to produce a multicellular organism. During the early phases of embryonic development, these cells exhibit pluripotency, meaning they possess the potential to differentiate into a diverse array of specialized cell types that constitute different body tissues and structures. \nThe balance between cell proliferation and differentiation in embryonic cells is crucial for successful development. When cells continue to divide without differentiating, overgrowth may occur leading to conditions such as teratomas (tumors of embryonic cells). Conversely, if cell differentiation proceeds at the expense of cell proliferation, developmental anomalies could occur regarding size or mass of the organism or its parts." xsd:string {xref="DOI:10.1002/iub.1404", xref="DOI:10.1093/molehr/gan048", xref="https://www.ncbi.nlm.nih.gov/books/NBK9906/"} creation_date: 2010-09-15T03:39:21Z [Term] id: CL:0002372 name: myotube def: "A transversely striated, multinucleated syncytial muscle cell, formed by the fusion of myoblasts during muscle development." [GOC:dos, GOC:tfm, ISBN:0323052908, PMID:22274696] +subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "myofiber" EXACT [FBbt:00005812] synonym: "myofibril" EXACT [FBbt:00005812] xref: FBbt:00005812 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} @@ -1986,6 +2221,8 @@ id: CL:0002494 name: cardiocyte def: "A cell located in the heart, including both muscle and non muscle cells." [GOC:tfm] comment: From Onard of the FMA: Cardiac muscle cell or cardiac myocyte is a striated muscle cell. Cardiocyte on the other hand is any cell in the heart which includes cells other than muscle cells (e.g. endothelial cell of endocardium). Unless there is a consensus among anatomists that cardiocytes refer only to muscle cells, we will treat them as a general class of cells in the heart. +subset: human_subset +subset: mouse_subset synonym: "heart cell" EXACT [] xref: BTO:0001539 xref: CALOHA:TS-0115 @@ -2003,6 +2240,8 @@ id: CL:0007001 name: skeletogenic cell def: "Cell that has the potential to form a skeletal cell type (e.g. cells in periosteum, cells in marrow) and produce extracellular matrix (often mineralized) and skeletal tissue (often mineralized)." [GO_REF:0000034] comment: Needs logical definition. Should be capable_of skeletal system morphogenesis? or skeletal tissue development? needs to be added to GO. NOTES:a cell type of the early embryo (see also: mesenchymal cells) that will give rise to mineralized connective tissue. Scleroblasts can differentiate into osteoblasts (bone-forming cells), chondroblasts (cartilage-forming cells), odontoblasts (dentin-forming cells), ameloblasts (enamel-forming cells). The mesenchymal cells developing into osteoblasts and chondroblasts are derived from the mesoderm. Those developing into odontoblasts are neural crest cells. Those developing into ameloblasts are derived from the ectoderm. (http://www.copewithcytokines.de/cope.cgi?key=scleroblasts) +subset: human_subset +subset: mouse_subset synonym: "scleroblast" EXACT [GO_REF:0000034] is_a: CL:0000000 ! cell property_value: terms:contributor https://orcid.org/0000-0001-9114-8737 @@ -2012,6 +2251,8 @@ creation_date: 2012-06-15T02:51:27Z id: CL:0007004 name: premigratory neural crest cell def: "Cell that is part of the neural crest region of the neuroepithelium, prior to migration. Note that not all premigratory neural crest cells may become migratory neural crest cells." [UBERONREF:0000002] +subset: human_subset +subset: mouse_subset xref: ZFA:0007084 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0011012 ! neural crest cell relationship: part_of UBERON:0002342 ! neural crest @@ -2023,6 +2264,8 @@ creation_date: 2012-06-27T08:27:35Z id: CL:0008000 name: non-striated muscle cell def: "Any muscle cell in which the fibers are not organised into sarcomeres." [GOC:DOS] +subset: human_subset +subset: mouse_subset is_a: CL:0000187 ! muscle cell [Term] @@ -2030,6 +2273,8 @@ id: CL:0008001 name: hematopoietic precursor cell def: "Any hematopoietic cell that is a precursor of some other hematopoietic cell type." [GOC:dos] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset is_a: CL:0000988 ! hematopoietic cell [Term] @@ -2037,6 +2282,8 @@ id: CL:0008002 name: skeletal muscle fiber def: "A transversely striated, synctial cell of skeletal muscle. It is formed when proliferating myoblasts exit the cell cycle, differentiate and fuse." [GOC:tfm, ISBN:0323052908] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset xref: MESH:D018485 is_a: CL:0000188 ! cell of skeletal muscle is_a: CL:0002372 ! myotube @@ -2051,6 +2298,8 @@ relationship: RO:0002202 CL:0000515 ! develops from skeletal muscle myoblast id: CL:0008007 name: visceral muscle cell def: "A muscle cell that is part of some visceral muscle." [GOC:dos] +subset: human_subset +subset: mouse_subset xref: FBbt:00005070 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} is_a: CL:0000187 ! muscle cell intersection_of: CL:0000187 ! muscle cell @@ -2063,6 +2312,8 @@ name: mesenchymal cell def: "A non-polarised cell precursor cell that is part of some mesenchyme, is associated with the cell matrix but is not connected to other cells and is capable of migration." [] subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "mesenchyme cell" EXACT [] is_a: CL:0000219 ! motile cell is_a: CL:0000255 ! eukaryotic cell @@ -2074,6 +2325,8 @@ property_value: RO:0002175 NCBITaxon:9606 id: CL:0008028 name: visual system neuron def: "Any neuron that is capable of part of some visual perception." [FBC:Autogenerated] +subset: human_subset +subset: mouse_subset is_a: CL:0000540 ! neuron intersection_of: CL:0000540 ! neuron intersection_of: capable_of_part_of GO:0007601 ! visual perception @@ -2086,6 +2339,8 @@ id: CL:0009004 name: retinal cell def: "Any cell in the retina, the innermost layer or coating at the back of the eyeball, which is sensitive to light and in which the optic nerve terminates." [GOC:pr] subset: general_cell_types_upper_slim +subset: human_subset +subset: mouse_subset xref: PMID:10702418 is_a: CL:0002319 ! neural cell intersection_of: CL:0002319 ! neural cell @@ -2096,6 +2351,8 @@ relationship: part_of UBERON:0005388 ! photoreceptor array id: CL:0010017 name: zygote def: "A zygote in a plant or an animal." [] +subset: human_subset +subset: mouse_subset xref: MESH:D015053 is_a: CL:0000000 ! cell property_value: seeAlso https://github.com/obophenotype/cell-ontology/issues/786 @@ -2104,6 +2361,8 @@ property_value: seeAlso https://github.com/obophenotype/cell-ontology/issues/786 id: CL:0010021 name: cardiac myoblast def: "Any myoblast that develops into some cardiac muscle cell." [FBC:Autogenerated] +subset: human_subset +subset: mouse_subset xref: MESH:D032386 is_a: CL:0000056 ! myoblast intersection_of: CL:0000056 ! myoblast @@ -2115,16 +2374,20 @@ id: CL:0011012 name: neural crest cell def: "A cell of the neural crest. Neural crest cells are multipotent. Premigratory neural crest cells are found at the neural plate boarder, some of which will undergo ectomesynchymal transition and delamination to form migratory neural crest cells." [https://orcid.org/0000-0001-5208-3432, https://orcid.org/0000-0002-9900-7880] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset xref: https://cellxgene.cziscience.com/cellguide/CL_0011012 is_a: CL:0000048 ! multi fate stem cell is_a: CL:0002321 ! embryonic cell (metazoa) -property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional.\n\nNeural crest cells are a group of transient and highly migratory cells that originate from the neuroectoderm during the early stages of embryonic development. They are multipotent cells with an exceptional degree of plasticity, capable of differentiating into various somatic cell types and therefore play a fundamental role in the formation of various organs and tissues, making them critical contributors to the developing embryo. \nAfter the initiation of neurulation (the formation of the neural tube) neural crest cells start to undergo epithelial-to-mesenchymal transition and delaminate and migrate from the dorsal neural tube to several regions throughout the embryo. They differentiate into a range of diverse cell types, such as neurons and glial cells of the peripheral nervous system, including sensory and autonomic neurons. They also contribute to the formation of adrenal glands, pigment cells in the skin (melanocytes), cardiac structures, including parts of the heart septum and major arteries, as well as bones and cartilage of the face and skull.\nDisorders or aberrations in the development or migration of the neural crest cells can lead to serious congenital malformations, such as neurocristopathies, including Hirschsprung disease, neuroblastoma, and neurofibromatosis." xsd:string {xref="DOI:10.1002/dvg.23276", xref="DOI:10.1242/dev.193193", xref="DOI:10.3389/fcell.2020.00635/full", xref="https://doi.org/10.1016/j.ydbio.2011.12.042"} +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nNeural crest cells are a group of transient and highly migratory cells that originate from the neuroectoderm during the early stages of embryonic development. They are multipotent cells with an exceptional degree of plasticity, capable of differentiating into various somatic cell types and therefore play a fundamental role in the formation of various organs and tissues, making them critical contributors to the developing embryo. \nAfter the initiation of neurulation (the formation of the neural tube) neural crest cells start to undergo epithelial-to-mesenchymal transition and delaminate and migrate from the dorsal neural tube to several regions throughout the embryo. They differentiate into a range of diverse cell types, such as neurons and glial cells of the peripheral nervous system, including sensory and autonomic neurons. They also contribute to the formation of adrenal glands, pigment cells in the skin (melanocytes), cardiac structures, including parts of the heart septum and major arteries, as well as bones and cartilage of the face and skull.\nDisorders or aberrations in the development or migration of the neural crest cells can lead to serious congenital malformations, such as neurocristopathies, including Hirschsprung disease, neuroblastoma, and neurofibromatosis." xsd:string {xref="DOI:10.1002/dvg.23276", xref="DOI:10.1242/dev.193193", xref="DOI:10.3389/fcell.2020.00635/full", xref="https://doi.org/10.1016/j.ydbio.2011.12.042"} [Term] id: CL:0011026 name: progenitor cell def: "A precursor cell that has a tendency to differentiate into a specific type of cell. They are descendants of stem cells, only they are more constrained in their differentiation potential or capacity for self-renewal, and are often more limited in both senses." [https://doi.org/10.1016/B978-0-12-409503-8.00002-0, ISBN:978-1-62808-994-3] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset is_a: CL:0000255 ! eukaryotic cell is_a: CL:0011115 ! precursor cell intersection_of: CL:0011115 ! precursor cell @@ -2138,6 +2401,8 @@ name: precursor cell def: "A cell that, by division or terminal differentiation, can give rise to other cell types." [GOC:dos] comment: Work is needed on GO 'cell differentiation' before it is clear whether the equivalent class definition 'native cell' that capable_of some 'cell differentiation' works. Also, may want to consider merging this with non-terminally differentiated cell. subset: cellxgene_subset +subset: human_subset +subset: mouse_subset is_a: CL:0000000 ! cell intersection_of: CL:0000000 ! cell intersection_of: capable_of GO:0030154 ! cell differentiation @@ -2169,6 +2434,8 @@ creation_date: 2009-12-22T04:24:54Z id: CL:1001610 name: bone marrow hematopoietic cell def: "Hematopoietic cells resident in the bone marrow. Include: hematopoietic stem cells (lymphoid stem cells and myeloid stem cells) and the precursor cells for thrombocytes, erythrocytes, basophils, neutrophils, eosinophils, monocytes and lymphocytes." [NPX:PDR] +subset: human_subset +subset: mouse_subset synonym: "bone marrow hematopoietic cells" RELATED [CALOHA:TS-2109] synonym: "bone marrow poietic cells" RELATED [CALOHA:TS-2109] xref: CALOHA:TS-2109 @@ -2182,6 +2449,8 @@ relationship: part_of UBERON:0012429 ! hematopoietic tissue id: CL:4052002 name: syncytial cell def: "A multinucleate cell formed by the fusion of multiple uninuclear cells through plasma membrane fusion. This process leads to a single large cell containing multiple nuclei within a shared cytoplasm." [PMID:20851884, Wikipedia:Syncytium] +subset: human_subset +subset: mouse_subset synonym: "SC" RELATED OMO:0003000 [PMID:9067520] synonym: "syncytium" EXACT [WBbt:0008074] is_a: CL:0000228 ! multinucleate cell @@ -2214,16 +2483,13 @@ intersection_of: has_part GO:0045026 ! plasma membrane fusion id: GO:0000785 name: chromatin namespace: cellular_component -alt_id: GO:0000789 -alt_id: GO:0000790 -alt_id: GO:0005717 def: "The ordered and organized complex of DNA, protein, and sometimes RNA, that forms the chromosome." [GOC:elh, PMID:20404130] comment: Chromosomes include parts that are not part of the chromatin. Examples include the kinetochore. synonym: "chromosome scaffold" RELATED [] synonym: "cytoplasmic chromatin" NARROW [] synonym: "nuclear chromatin" NARROW [] xref: NIF_Subcellular:sao1615953555 -is_a: GO:0110165 ! cellular anatomical entity +is_a: GO:0110165 ! cellular anatomical structure relationship: part_of GO:0005694 ! chromosome property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28301" xsd:anyURI @@ -2231,8 +2497,6 @@ property_value: term_tracker_item "https://github.com/geneontology/go-ontology/i id: GO:0000791 name: euchromatin namespace: cellular_component -alt_id: GO:0005719 -alt_id: GO:0035327 def: "A dispersed and relatively uncompacted form of chromatin that is in a transcription-competent conformation." [PMID:32017156] synonym: "nuclear euchromatin" RELATED [] synonym: "transcriptionally active chromatin" EXACT [] @@ -2245,8 +2509,6 @@ property_value: term_tracker_item "https://github.com/geneontology/go-ontology/i id: GO:0000792 name: heterochromatin namespace: cellular_component -alt_id: GO:0005720 -alt_id: GO:0035328 def: "A compact and highly condensed form of chromatin that is refractory to transcription." [PMID:32017156] synonym: "nuclear heterochromatin" NARROW [] synonym: "transcriptionally inactive chromatin" EXACT [] @@ -2359,10 +2621,6 @@ property_value: term_tracker_item "https://github.com/geneontology/go-ontology/i id: GO:0001816 name: cytokine production namespace: biological_process -alt_id: GO:0042032 -alt_id: GO:0042089 -alt_id: GO:0042107 -alt_id: GO:0050663 def: "The appearance of a cytokine due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels." [GOC:add, ISBN:0781735149] comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select one of the 'regulation' children terms. subset: gocheck_do_not_annotate @@ -2390,7 +2648,6 @@ relationship: part_of GO:0016331 ! morphogenesis of embryonic epithelium id: GO:0001841 name: neural tube formation namespace: biological_process -alt_id: GO:0001679 def: "The formation of a tube from the flat layer of ectodermal cells known as the neural plate. This will give rise to the central nervous system." [GOC:dph, ISBN:0878932437] synonym: "neural tube morphogenesis" EXACT [GOC:dph] synonym: "neurulation" EXACT [] @@ -2508,8 +2765,6 @@ property_value: RO:0002161 NCBITaxon:4895 id: GO:0002377 name: immunoglobulin production namespace: biological_process -alt_id: GO:0002378 -alt_id: GO:0048305 def: "The appearance of immunoglobulin due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels." [GOC:add, ISBN:0781735149] comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select one of the 'regulation' children terms. subset: gocheck_do_not_annotate @@ -2533,8 +2788,6 @@ is_a: GO:0010467 ! gene expression id: GO:0002443 name: leukocyte mediated immunity namespace: biological_process -alt_id: GO:0019723 -alt_id: GO:0042087 def: "Any process involved in the carrying out of an immune response by a leukocyte." [GO_REF:0000022, GOC:add, ISBN:0781735149] synonym: "cell-mediated immune response" RELATED [] synonym: "cellular immune response" RELATED [] @@ -2701,7 +2954,6 @@ is_a: GO:0003013 ! circulatory system process id: GO:0005575 name: cellular_component namespace: cellular_component -alt_id: GO:0008372 def: "A location, relative to cellular compartments and structures, occupied by a macromolecular machine. There are three types of cellular components described in the gene ontology: (1) the cellular anatomical entity where a gene product carries out a molecular function (e.g., plasma membrane, cytoskeleton) or membrane-enclosed compartments (e.g., mitochondrion); (2) virion components, where viral proteins act, and (3) the stable macromolecular complexes of which gene product are parts (e.g., the clathrin complex)." [GOC:pdt] comment: Note that, in addition to forming the root of the cellular component ontology, this term is recommended for the annotation of gene products whose cellular component is unknown. When this term is used for annotation, it indicates that no information was available about the cellular component of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this. subset: goslim_candida @@ -2739,7 +2991,7 @@ subset: goslim_prokaryote_ribbon subset: goslim_yeast synonym: "extracellular" EXACT [] xref: Wikipedia:Extracellular -is_a: GO:0110165 ! cellular anatomical entity +is_a: GO:0110165 ! cellular anatomical structure [Term] id: GO:0005581 @@ -2764,8 +3016,6 @@ is_a: GO:0098651 ! basement membrane collagen trimer id: GO:0005604 name: basement membrane namespace: cellular_component -alt_id: GO:0005605 -alt_id: GO:0008003 def: "A collagen-containing extracellular matrix consisting of a thin layer of dense material found in various animal tissues interposed between the cells and the adjacent connective tissue. It consists of the basal lamina plus an associated layer of reticulin fibers." [ISBN:0198547684, PMID:22505934] comment: Note that this term has no relationship to 'membrane ; GO:0016020' because the basement membrane is not a lipid bilayer. synonym: "basal lamina" RELATED [] @@ -2789,7 +3039,7 @@ synonym: "nucleocytoplasm" RELATED [GOC:mah] synonym: "protoplasm" EXACT [] synonym: "protoplast" RELATED [GOC:mah] xref: Wikipedia:Intracellular -is_a: GO:0110165 ! cellular anatomical entity +is_a: GO:0110165 ! cellular anatomical structure relationship: part_of CL:0000000 ! cell property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/17776" xsd:anyURI @@ -2841,7 +3091,7 @@ synonym: "chromatid" RELATED [] synonym: "interphase chromosome" NARROW [] synonym: "prophase chromosome" NARROW [] xref: Wikipedia:Chromosome -is_a: GO:0043232 ! intracellular non-membrane-bounded organelle +is_a: GO:0043232 ! intracellular membraneless organelle [Term] id: GO:0005730 @@ -2857,7 +3107,7 @@ subset: goslim_plant subset: goslim_yeast xref: NIF_Subcellular:sao1820400233 xref: Wikipedia:Nucleolus -is_a: GO:0043232 ! intracellular non-membrane-bounded organelle +is_a: GO:0043232 ! intracellular membraneless organelle relationship: part_of GO:0031981 ! nuclear lumen [Term] @@ -2875,7 +3125,7 @@ subset: goslim_prokaryote subset: goslim_prokaryote_ribbon subset: goslim_yeast xref: Wikipedia:Cytoplasm -is_a: GO:0110165 ! cellular anatomical entity +is_a: GO:0110165 ! cellular anatomical structure relationship: part_of GO:0005622 ! intracellular anatomical structure property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/23023" xsd:anyURI @@ -2926,8 +3176,6 @@ relationship: part_of GO:0005737 ! cytoplasm id: GO:0005886 name: plasma membrane namespace: cellular_component -alt_id: GO:0005887 -alt_id: GO:0005904 def: "The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins." [ISBN:0716731363] subset: goslim_agr subset: goslim_candida @@ -2973,7 +3221,6 @@ property_value: term_tracker_item "https://github.com/geneontology/go-ontology/i id: GO:0006259 name: DNA metabolic process namespace: biological_process -alt_id: GO:0055132 def: "Any cellular metabolic process involving deoxyribonucleic acid. This is one of the two main types of nucleic acid, consisting of a long, unbranched macromolecule formed from one, or more commonly, two, strands of linked deoxyribonucleotides." [ISBN:0198506732] subset: goslim_agr subset: goslim_candida @@ -3005,9 +3252,6 @@ is_a: GO:0006259 ! DNA metabolic process id: GO:0006412 name: translation namespace: biological_process -alt_id: GO:0006416 -alt_id: GO:0006453 -alt_id: GO:0043037 def: "The cellular metabolic process in which a protein is formed, using the sequence of a mature mRNA or circRNA molecule to specify the sequence of amino acids in a polypeptide chain. Translation is mediated by the ribosome, and begins with the formation of a ternary complex between aminoacylated initiator methionine tRNA, GTP, and initiation factor 2, which subsequently associates with the small subunit of the ribosome and an mRNA or circRNA. Translation ends with the release of a polypeptide chain from the ribosome." [GOC:go_curators] subset: goslim_candida subset: goslim_chembl @@ -3036,15 +3280,13 @@ relationship: starts_with GO:0006413 ! translational initiation id: GO:0006413 name: translational initiation namespace: biological_process -alt_id: GO:0006440 -alt_id: GO:0006454 def: "The process preceding formation of the peptide bond between the first two amino acids of a protein. This includes the formation of a complex of the ribosome, mRNA or circRNA, and an initiation complex that contains the first aminoacyl-tRNA." [ISBN:019879276X] subset: goslim_yeast synonym: "biopolymerisation" BROAD [] synonym: "biopolymerization" BROAD [] synonym: "protein synthesis initiation" BROAD [] synonym: "translation initiation" EXACT [] -is_a: GO:0044237 ! cellular metabolic process +is_a: GO:0008152 ! metabolic process relationship: part_of GO:0006412 ! translation relationship: starts_with GO:0001677 ! formation of translation initiation ternary complex @@ -3052,8 +3294,6 @@ relationship: starts_with GO:0001677 ! formation of translation initiation terna id: GO:0006414 name: translational elongation namespace: biological_process -alt_id: GO:0006442 -alt_id: GO:0006455 def: "The successive addition of amino acid residues to a nascent polypeptide chain during protein biosynthesis." [GOC:ems] subset: goslim_yeast synonym: "protein synthesis elongation" BROAD [] @@ -3065,8 +3305,6 @@ relationship: part_of GO:0006412 ! translation id: GO:0006415 name: translational termination namespace: biological_process -alt_id: GO:0006443 -alt_id: GO:0006456 def: "The process resulting in the release of a polypeptide chain from the ribosome, usually in response to a termination codon (UAA, UAG, or UGA in the universal genetic code)." [GOC:hjd, ISBN:019879276X] synonym: "protein synthesis termination" BROAD [] synonym: "translation termination" EXACT [] @@ -3078,9 +3316,6 @@ relationship: part_of GO:0006412 ! translation id: GO:0006810 name: transport namespace: biological_process -alt_id: GO:0015457 -alt_id: GO:0015460 -alt_id: GO:0044765 def: "The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter or a transporter complex, a pore or a motor protein." [GOC:dos, GOC:dph, GOC:jl, GOC:mah] comment: Note that this term should not be used for direct annotation. It should be possible to make a more specific annotation to one of the children of this term, for e.g. to transmembrane transport, to microtubule-based transport or to vesicle-mediated transport. subset: gocheck_do_not_annotate @@ -3095,7 +3330,6 @@ subset: goslim_prokaryote_ribbon synonym: "single-organism transport" RELATED [] is_a: GO:0051234 ! establishment of localization property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/20292" xsd:anyURI -created_by: jl creation_date: 2012-12-13T16:25:32Z [Term] @@ -3113,8 +3347,6 @@ is_a: GO:0006810 ! transport id: GO:0006887 name: exocytosis namespace: biological_process -alt_id: GO:0016194 -alt_id: GO:0016195 def: "A process of secretion by a cell that results in the release of intracellular molecules (e.g. hormones, matrix proteins) contained within a membrane-bounded vesicle. Exocytosis can occur either by full fusion, when the vesicle collapses into the plasma membrane, or by a kiss-and-run mechanism that involves the formation of a transient contact, a pore, between a granule (for example of chromaffin cells) and the plasma membrane. The latter process most of the time leads to only partial secretion of the granule content. Exocytosis begins with steps that prepare vesicles for fusion with the membrane (tethering and docking) and ends when molecules are secreted from the cell." [GOC:mah, ISBN:0716731363, PMID:22323285] subset: goslim_yeast synonym: "nonselective vesicle exocytosis" RELATED [] @@ -3131,9 +3363,6 @@ relationship: process_has_causal_agent GO:0070382 ! exocytic vesicle id: GO:0006897 name: endocytosis namespace: biological_process -alt_id: GO:0016193 -alt_id: GO:0016196 -alt_id: GO:0098701 def: "A vesicle-mediated transport process in which cells take up external materials or membrane constituents by the invagination of a part of the plasma membrane to form a new membrane-bounded vesicle." [GOC:mah, ISBN:0198506732, ISBN:0716731363, Wikipedia:Endocytosis] subset: goslim_yeast synonym: "endocytic import into cell" EXACT [] @@ -3153,8 +3382,6 @@ property_value: term_tracker_item "https://github.com/geneontology/go-ontology/i id: GO:0006900 name: vesicle budding from membrane namespace: biological_process -alt_id: GO:0006902 -alt_id: GO:1902591 def: "The evagination of a membrane, resulting in formation of a vesicle." [GOC:jid, GOC:tb] synonym: "membrane evagination" EXACT [] synonym: "nonselective vesicle assembly" RELATED [] @@ -3166,7 +3393,6 @@ synonym: "vesicle formation" EXACT [] is_a: GO:0016050 ! vesicle organization is_a: GO:0061024 ! membrane organization relationship: part_of GO:0016192 ! vesicle-mediated transport -created_by: jl creation_date: 2013-12-19T15:26:17Z [Term] @@ -3226,7 +3452,6 @@ is_a: GO:0050896 ! response to stimulus id: GO:0006996 name: organelle organization namespace: biological_process -alt_id: GO:1902589 def: "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of an organelle within a cell. An organelle is an organized structure of distinctive morphology and function. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton. Excludes the plasma membrane." [GOC:mah] comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. subset: gocheck_do_not_annotate @@ -3241,7 +3466,6 @@ intersection_of: GO:0016043 ! cellular component organization intersection_of: results_in_organization_of GO:0043226 ! organelle relationship: results_in_organization_of GO:0043226 ! organelle property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27189" xsd:anyURI -created_by: jl creation_date: 2013-12-19T15:25:51Z [Term] @@ -3397,7 +3621,6 @@ is_a: GO:0050953 ! sensory perception of light stimulus id: GO:0008015 name: blood circulation namespace: biological_process -alt_id: GO:0070261 def: "The flow of blood through the body of an animal, enabling the transport of nutrients to the tissues and the removal of waste products." [GOC:mtg_heart, ISBN:0192800825] subset: goslim_pir synonym: "hemolymph circulation" RELATED [] @@ -3407,9 +3630,6 @@ is_a: GO:0003013 ! circulatory system process id: GO:0008150 name: biological_process namespace: biological_process -alt_id: GO:0000004 -alt_id: GO:0007582 -alt_id: GO:0044699 def: "A biological process is the execution of a genetically-encoded biological module or program. It consists of all the steps required to achieve the specific biological objective of the module. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence." [GOC:pdt] comment: Note that, in addition to forming the root of the biological process ontology, this term is recommended for the annotation of gene products whose biological process is unknown. When this term is used for annotation, it indicates that no information was available about the biological process of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this. subset: goslim_candida @@ -3425,16 +3645,13 @@ synonym: "single organism process" RELATED [] synonym: "single-organism process" RELATED [] xref: Wikipedia:Biological_process property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/24968" xsd:anyURI -created_by: jl creation_date: 2012-09-19T15:05:24Z [Term] id: GO:0008152 name: metabolic process namespace: biological_process -alt_id: GO:0044236 -alt_id: GO:0044710 -def: "The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation." [GOC:go_curators, ISBN:0198547684] +def: "A cellular process consisting of the biochemical pathways by which a living organism transforms chemical substances. This includes including anabolism (biosynthetic process) and catabolism (catabolic process). Metabolic processes includes the transformation of small molecules, as well macromolecular processes such as DNA repair and replication, protein synthesis and degradation." [GOC:go_curators, ISBN:0198547684] comment: Note that metabolic processes do not include single functions or processes such as protein-protein interactions, protein-nucleic acids, nor receptor-ligand interactions. subset: gocheck_do_not_annotate subset: goslim_chembl @@ -3443,25 +3660,19 @@ subset: goslim_metagenomics subset: goslim_pir subset: goslim_plant subset: goslim_prokaryote_ribbon -synonym: "metabolic process resulting in cell growth" NARROW [] synonym: "metabolism" EXACT [] -synonym: "metabolism resulting in cell growth" NARROW [] -synonym: "multicellular organism metabolic process" NARROW [] -synonym: "single-organism metabolic process" RELATED [] xref: Wikipedia:Metabolism -is_a: GO:0008150 ! biological_process +is_a: GO:0009987 ! cellular process disjoint_from: GO:0051179 ! localization property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/26424" xsd:anyURI -created_by: jl +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28932" xsd:anyURI creation_date: 2012-10-17T15:46:40Z [Term] id: GO:0009058 name: biosynthetic process namespace: biological_process -alt_id: GO:0044274 -alt_id: GO:0044711 -def: "The chemical reactions and pathways resulting in the formation of substances; typically the energy-requiring part of metabolism in which simpler substances are transformed into more complex ones." [GOC:curators, ISBN:0198547684] +def: "A cellular process consisting of the biochemical pathways by which a living organism synthesizes chemical substances. This typically represents the energy-requiring part of metabolism in which simpler substances are transformed into more complex ones." [GOC:curators, ISBN:0198547684] subset: goslim_chembl subset: goslim_metagenomics subset: goslim_plant @@ -3474,14 +3685,13 @@ synonym: "single-organism biosynthetic process" RELATED [] synonym: "synthesis" EXACT [] xref: Wikipedia:Anabolism is_a: GO:0008152 ! metabolic process -created_by: jl +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28932" xsd:anyURI creation_date: 2012-10-17T15:52:18Z [Term] id: GO:0009059 name: macromolecule biosynthetic process namespace: biological_process -alt_id: GO:0043284 def: "The chemical reactions and pathways resulting in the formation of a macromolecule, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass." [GOC:mah] comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. subset: gocheck_do_not_annotate @@ -3491,8 +3701,8 @@ synonym: "macromolecule anabolism" EXACT [] synonym: "macromolecule biosynthesis" EXACT [] synonym: "macromolecule formation" EXACT [] synonym: "macromolecule synthesis" EXACT [] +is_a: GO:0009058 ! biosynthetic process is_a: GO:0043170 ! macromolecule metabolic process -is_a: GO:0044249 ! cellular biosynthetic process property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/15249" xsd:anyURI property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/25418" xsd:anyURI property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27189" xsd:anyURI @@ -3606,7 +3816,6 @@ relationship: part_of GO:0048856 ! anatomical structure development id: GO:0009790 name: embryo development namespace: biological_process -alt_id: GO:0009795 def: "The process whose specific outcome is the progression of an embryo from its formation until the end of its embryonic life stage. The end of the embryonic stage is organism-specific. For example, for mammals, the process would begin with zygote formation and end with birth. For insects, the process would begin at zygote formation and end with larval hatching. For plant zygotic embryos, this would be from zygote formation to the end of seed dormancy. For plant vegetative embryos, this would be from the initial determination of the cell or group of cells to form an embryo until the point when the embryo becomes independent of the parent plant." [GOC:go_curators, GOC:isa_complete, GOC:mtg_sensu] subset: gocheck_do_not_annotate subset: goslim_chembl @@ -3672,9 +3881,6 @@ is_a: GO:0010817 ! regulation of hormone levels id: GO:0009987 name: cellular process namespace: biological_process -alt_id: GO:0008151 -alt_id: GO:0044763 -alt_id: GO:0050875 def: "Any process that is carried out at the cellular level, but not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level." [GOC:go_curators, GOC:isa_complete] comment: This term should not be used for direct annotation. It should be possible to make a more specific annotation to one of the children of this term. subset: gocheck_do_not_annotate @@ -3684,7 +3890,6 @@ synonym: "cell physiology" EXACT [] synonym: "cellular physiological process" EXACT [] synonym: "single-organism cellular process" RELATED [] is_a: GO:0008150 ! biological_process -created_by: jl creation_date: 2012-12-11T16:56:55Z [Term] @@ -3704,12 +3909,10 @@ relationship: results_in_organization_of GO:0012505 ! endomembrane system id: GO:0010324 name: membrane invagination namespace: biological_process -alt_id: GO:1902534 def: "The infolding of a membrane." [GOC:tb] subset: goslim_yeast synonym: "single-organism membrane invagination" RELATED [] is_a: GO:0061024 ! membrane organization -created_by: jl creation_date: 2013-12-02T13:58:34Z [Term] @@ -3738,7 +3941,7 @@ subset: goslim_candida subset: goslim_flybase_ribbon subset: goslim_yeast xref: Wikipedia:Endomembrane_system -is_a: GO:0110165 ! cellular anatomical entity +is_a: GO:0110165 ! cellular anatomical structure relationship: has_part GO:0005773 ! vacuole relationship: has_part GO:0005886 ! plasma membrane relationship: part_of CL:0000000 ! cell @@ -3758,9 +3961,6 @@ relationship: part_of GO:0031982 ! vesicle id: GO:0016020 name: membrane namespace: cellular_component -alt_id: GO:0016021 -alt_id: GO:0098589 -alt_id: GO:0098805 def: "A lipid bilayer along with all the proteins and protein complexes embedded in it and attached to it." [GOC:dos, GOC:mah, ISBN:0815316194] subset: goslim_candida subset: goslim_chembl @@ -3777,7 +3977,7 @@ synonym: "transmembrane" RELATED [GOC:mah] synonym: "whole membrane" NARROW [] xref: Wikipedia:Biological_membrane xref: Wikipedia:Transmembrane_protein -is_a: GO:0110165 ! cellular anatomical entity +is_a: GO:0110165 ! cellular anatomical structure disjoint_from: GO:0031012 ! extracellular matrix creation_date: 2014-03-06T11:37:54Z @@ -3785,8 +3985,6 @@ creation_date: 2014-03-06T11:37:54Z id: GO:0016043 name: cellular component organization namespace: biological_process -alt_id: GO:0044235 -alt_id: GO:0071842 def: "A process that results in the assembly, arrangement of constituent parts, or disassembly of a cellular component." [GOC:ai, GOC:jl, GOC:mah] subset: gocheck_do_not_annotate subset: goslim_agr @@ -3823,7 +4021,6 @@ relationship: results_in_organization_of GO:0031982 ! vesicle id: GO:0016192 name: vesicle-mediated transport namespace: biological_process -alt_id: GO:0006899 def: "A cellular transport process in which transported substances are moved in membrane-bounded vesicles; transported substances are enclosed in the vesicle lumen or located in the vesicle membrane. The process begins with a step that directs a substance to the forming vesicle, and includes vesicle budding and coating. Vesicles are then targeted to, and fuse with, an acceptor membrane." [GOC:ai, GOC:mah, ISBN:08789310662000] subset: goslim_candida subset: goslim_chembl @@ -3918,9 +4115,6 @@ relationship: part_of GO:0007154 ! cell communication id: GO:0019538 name: protein metabolic process namespace: biological_process -alt_id: GO:0006411 -alt_id: GO:0044267 -alt_id: GO:0044268 def: "The chemical reactions and pathways involving a protein. Includes protein modification." [GOC:ma] comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. subset: gocheck_do_not_annotate @@ -3965,7 +4159,6 @@ relationship: process_has_causal_agent CL:0000236 ! B cell id: GO:0019882 name: antigen processing and presentation namespace: biological_process -alt_id: GO:0030333 def: "The process in which an antigen-presenting cell expresses antigen (peptide or lipid) on its cell surface in association with an MHC protein complex." [GO_REF:0000022, GOC:add, ISBN:0781735149, PMID:15771591, PMID:15928678] synonym: "antigen presentation" EXACT [] synonym: "antigen processing" EXACT [] @@ -3989,7 +4182,6 @@ relationship: results_in_development_of UBERON:0001049 ! neural tube id: GO:0022411 name: cellular component disassembly namespace: biological_process -alt_id: GO:0071845 def: "A cellular process that results in the breakdown of a cellular component." [GOC:isa_complete] comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. subset: gocheck_do_not_annotate @@ -4007,7 +4199,6 @@ property_value: term_tracker_item "https://github.com/geneontology/go-ontology/i id: GO:0022414 name: reproductive process namespace: biological_process -alt_id: GO:0044702 def: "A biological process that directly contributes to the process of producing new individuals by one or two organisms. The new individuals inherit some proportion of their genetic material from the parent or parents." [GOC:dph, GOC:isa_complete] subset: gocheck_do_not_annotate subset: goslim_agr @@ -4021,7 +4212,6 @@ synonym: "single organism reproductive process" RELATED [] xref: Wikipedia:Reproduction is_a: GO:0008150 ! biological_process property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27054" xsd:anyURI -created_by: jl creation_date: 2012-09-19T15:56:06Z [Term] @@ -4039,7 +4229,6 @@ relationship: part_of GO:0007586 ! digestion id: GO:0022607 name: cellular component assembly namespace: biological_process -alt_id: GO:0071844 def: "The aggregation, arrangement and bonding together of a cellular component." [GOC:isa_complete] subset: goslim_chembl subset: goslim_euk_cellular_processes_ribbon @@ -4081,8 +4270,6 @@ relationship: results_in_assembly_of GO:1990904 ! ribonucleoprotein complex id: GO:0023052 name: signaling namespace: biological_process -alt_id: GO:0023046 -alt_id: GO:0044700 def: "The entirety of a process in which information is transmitted within a biological system. This process begins with an active signal and ends when a cellular response has been triggered." [GOC:mtg_signal, GOC:mtg_signaling_feb11, GOC:signaling] comment: Note that a signal is any variable property or parameter that serves to convey information, and may be a physical entity such as a gene product or small molecule, a photon, or a change in state such as movement or voltage change. subset: goslim_agr @@ -4100,7 +4287,6 @@ synonym: "signalling" EXACT [] synonym: "signalling process" RELATED [GOC:mah] synonym: "single organism signaling" RELATED [] is_a: GO:0050789 ! regulation of biological process -created_by: jl creation_date: 2010-02-16T09:30:50Z [Term] @@ -4132,7 +4318,7 @@ name: sarcomere namespace: cellular_component def: "The repeating unit of a myofibril in a muscle cell, composed of an array of overlapping thick and thin filaments between two adjacent Z discs." [ISBN:0815316194] xref: Wikipedia:Sarcomere -is_a: GO:0110165 ! cellular anatomical entity +is_a: GO:0110165 ! cellular anatomical structure relationship: part_of GO:0030016 ! myofibril [Term] @@ -4159,7 +4345,7 @@ subset: goslim_agr subset: goslim_drosophila subset: goslim_flybase_ribbon xref: Wikipedia:Cell_junction -is_a: GO:0110165 ! cellular anatomical entity +is_a: GO:0110165 ! cellular anatomical structure property_value: RO:0002161 NCBITaxon:4751 [Term] @@ -4184,7 +4370,6 @@ property_value: term_tracker_item "https://github.com/geneontology/go-ontology/i id: GO:0030098 name: lymphocyte differentiation namespace: biological_process -alt_id: GO:0046650 def: "The process in which a relatively unspecialized precursor cell acquires specialized features of a lymphocyte. A lymphocyte is a leukocyte commonly found in the blood and lymph that has the characteristics of a large nucleus, a neutral staining cytoplasm, and prominent heterochromatin." [CL:0000542, GOC:go_curators] comment: Note that immunologists typically use the word 'development' to refer to cells of B or T cell lineages undergoing the process that GO describes as 'cell differentiation'. synonym: "lymphocyte cell differentiation" EXACT [] @@ -4255,8 +4440,6 @@ property_value: term_tracker_item "https://github.com/geneontology/go-ontology/i id: GO:0030217 name: T cell differentiation namespace: biological_process -alt_id: GO:0042112 -alt_id: GO:0046652 def: "The process in which a precursor cell type acquires characteristics of a more mature T-cell. A T cell is a type of lymphocyte whose definin characteristic is the expression of a T cell receptor complex." [GO_REF:0000022, GOC:jid, GOC:mah] comment: Note that the term 'thymocyte differentiation' was merged into this term because thymocytes are T cells, and thus the term was essentially redundant. Note that immunologists typically use the word 'development' to refer to cells of B or T cell lineages undergoing the process that GO describes as 'cell differentiation'. synonym: "T cell development" RELATED [GOC:add] @@ -4304,7 +4487,7 @@ subset: goslim_drosophila subset: goslim_generic subset: goslim_pir subset: goslim_plant -is_a: GO:0110165 ! cellular anatomical entity +is_a: GO:0110165 ! cellular anatomical structure relationship: part_of CL:0000000 ! cell relationship: part_of GO:0071944 ! cell periphery @@ -4334,7 +4517,6 @@ relationship: results_in_acquisition_of_features_of CL:0000094 ! granulocyte id: GO:0031012 name: extracellular matrix namespace: cellular_component -alt_id: GO:0005578 def: "A structure lying external to one or more cells, which provides structural support, biochemical or biomechanical cues for cells or tissues." [GOC:BHF, GOC:mah, GOC:rph, NIF_Subcellular:nlx_subcell_20090513, PMID:21123617, PMID:28089324] subset: goslim_chembl subset: goslim_drosophila @@ -4394,7 +4576,6 @@ relationship: results_in_organization_of GO:0031143 ! pseudopodium id: GO:0031410 name: cytoplasmic vesicle namespace: cellular_component -alt_id: GO:0016023 def: "A vesicle found in the cytoplasm of a cell." [GOC:ai, GOC:mah, GOC:vesicles] subset: goslim_agr subset: goslim_candida @@ -4416,7 +4597,7 @@ id: GO:0031974 name: membrane-enclosed lumen namespace: cellular_component def: "The enclosed volume within a sealed membrane or between two sealed membranes. Encompasses the volume enclosed by the membranes of a particular organelle, e.g. endoplasmic reticulum lumen, or the space between the two lipid bilayers of a double membrane surrounding an organelle, e.g. nuclear envelope lumen." [GOC:add, GOC:mah] -is_a: GO:0110165 ! cellular anatomical entity +is_a: GO:0110165 ! cellular anatomical structure disjoint_from: GO:0045202 ! synapse [Term] @@ -4431,7 +4612,6 @@ relationship: part_of GO:0005634 ! nucleus id: GO:0031982 name: vesicle namespace: cellular_component -alt_id: GO:0031988 def: "Any small, fluid-filled, spherical organelle enclosed by membrane." [GOC:mah, GOC:pz, GOC:vesicles] subset: goslim_pir synonym: "membrane-bounded vesicle" RELATED [] @@ -4444,8 +4624,6 @@ is_a: GO:0043227 ! membrane-bounded organelle id: GO:0032501 name: multicellular organismal process namespace: biological_process -alt_id: GO:0044707 -alt_id: GO:0050874 def: "Any biological process, occurring at the level of a multicellular organism, pertinent to its function." [GOC:curators, GOC:dph, GOC:isa_complete, GOC:tb] comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. subset: gocheck_do_not_annotate @@ -4458,14 +4636,12 @@ property_value: RO:0002161 NCBITaxon:2157 property_value: RO:0002161 NCBITaxon:4896 property_value: RO:0002161 NCBITaxon:4932 property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27189" xsd:anyURI -created_by: jl creation_date: 2012-09-19T16:07:47Z [Term] id: GO:0032502 name: developmental process namespace: biological_process -alt_id: GO:0044767 def: "A biological process whose specific outcome is the progression of an integrated living unit: an anatomical structure (which may be a subcellular structure, cell, tissue, or organ), or organism over time from an initial condition to a later condition." [GOC:isa_complete] subset: goslim_agr subset: goslim_flybase_ribbon @@ -4473,15 +4649,12 @@ subset: goslim_pir synonym: "development" NARROW [] synonym: "single-organism developmental process" RELATED [] is_a: GO:0008150 ! biological_process -created_by: jl creation_date: 2012-12-19T12:21:31Z [Term] id: GO:0032609 name: type II interferon production namespace: biological_process -alt_id: GO:0042095 -alt_id: GO:0072643 def: "The appearance of interferon-gamma due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. Interferon-gamma is also known as type II interferon." [GOC:add, GOC:mah, PMID:15546383] subset: gocheck_do_not_annotate synonym: "IFNG production" EXACT [GOC:mah] @@ -4505,9 +4678,6 @@ is_a: GO:0140352 ! export from cell id: GO:0032984 name: protein-containing complex disassembly namespace: biological_process -alt_id: GO:0034623 -alt_id: GO:0043241 -alt_id: GO:0043624 def: "The disaggregation of a protein-containing macromolecular complex into its constituent components." [GOC:mah] synonym: "cellular macromolecule complex disassembly" RELATED [] synonym: "cellular protein complex disassembly" RELATED [] @@ -4524,7 +4694,6 @@ property_value: term_tracker_item "https://github.com/geneontology/go-ontology/i id: GO:0032991 name: protein-containing complex namespace: cellular_component -alt_id: GO:0043234 def: "A stable assembly of two or more macromolecules, i.e. proteins, nucleic acids, carbohydrates or lipids, in which at least one component is a protein and the constituent parts function together." [GOC:dos, GOC:mah] comment: A protein complex in this context is meant as a stable set of interacting proteins which can be co-purified by an acceptable method, and where the complex has been shown to exist as an isolated, functional unit in vivo. Acceptable experimental methods include stringent protein purification followed by detection of protein interaction. The following methods should be considered non-acceptable: simple immunoprecipitation, pull-down experiments from cell extracts without further purification, colocalization and 2-hybrid screening. Interactions that should not be captured as protein complexes include: 1) enzyme/substrate, receptor/ligand or any similar transient interactions, unless these are a critical part of the complex assembly or are required e.g. for the receptor to be functional; 2) proteins associated in a pull-down/co-immunoprecipitation assay with no functional link or any evidence that this is a defined biological entity rather than a loose-affinity complex; 3) any complex where the only evidence is based on genetic interaction data; 4) partial complexes, where some subunits (e.g. transmembrane ones) cannot be expressed as recombinant proteins and are excluded from experiments (in this case, independent evidence is necessary to find out the composition of the full complex, if known). Interactions that may be captured as protein complexes include: 1) enzyme/substrate or receptor/ligand if the complex can only assemble and become functional in the presence of both classes of subunits; 2) complexes where one of the members has not been shown to be physically linked to the other(s), but is a homologue of, and has the same functionality as, a protein that has been experimentally demonstrated to form a complex with the other member(s); 3) complexes whose existence is accepted based on localization and pharmacological studies, but for which experimental evidence is not yet available for the complex as a whole. subset: goslim_agr @@ -4539,8 +4708,8 @@ synonym: "protein complex" NARROW [] synonym: "protein containing complex" EXACT [] synonym: "protein-protein complex" NARROW [] is_a: GO:0005575 ! cellular_component -is_a: PR:000050567 ! protein-containing material entity -disjoint_from: GO:0110165 ! cellular anatomical entity +disjoint_from: GO:0110165 ! cellular anatomical structure +relationship: has_part PR:000000001 ! protein [Term] id: GO:0033151 @@ -4572,7 +4741,6 @@ is_a: GO:0033151 ! V(D)J recombination id: GO:0034220 name: monoatomic ion transmembrane transport namespace: biological_process -alt_id: GO:0099131 def: "A process in which a monoatomic ion is transported across a membrane. Monatomic ions (also called simple ions) are ions consisting of exactly one atom." [GOC:mah] comment: Note that this term is not intended for use in annotating lateral movement within membranes. synonym: "ATP hydrolysis coupled ion transmembrane transport" NARROW [] @@ -4682,9 +4850,6 @@ property_value: term_tracker_item "https://github.com/geneontology/go-ontology/i id: GO:0042592 name: homeostatic process namespace: biological_process -alt_id: GO:0032844 -alt_id: GO:0032845 -alt_id: GO:0032846 def: "Any biological process involved in the maintenance of an internal steady state." [GOC:jl, ISBN:0395825172] subset: goslim_agr subset: goslim_chembl @@ -4727,7 +4892,7 @@ subset: goslim_prokaryote_ribbon synonym: "cell process" BROAD [] synonym: "cellular process" BROAD [] synonym: "cellular projection" EXACT [] -is_a: GO:0110165 ! cellular anatomical entity +is_a: GO:0110165 ! cellular anatomical structure relationship: part_of CL:0000000 ! cell [Term] @@ -4756,9 +4921,6 @@ relationship: results_in_acquisition_of_features_of CL:0000782 ! myeloid dendrit id: GO:0043170 name: macromolecule metabolic process namespace: biological_process -alt_id: GO:0034960 -alt_id: GO:0043283 -alt_id: GO:0044259 def: "The chemical reactions and pathways involving macromolecules, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass." [GOC:mah] subset: gocheck_do_not_annotate subset: goslim_pir @@ -4789,7 +4951,7 @@ subset: goslim_prokaryote subset: goslim_prokaryote_ribbon xref: NIF_Subcellular:sao1539965131 xref: Wikipedia:Organelle -is_a: GO:0110165 ! cellular anatomical entity +is_a: GO:0110165 ! cellular anatomical structure [Term] id: GO:0043227 @@ -4802,23 +4964,26 @@ xref: NIF_Subcellular:sao414196390 is_a: GO:0043226 ! organelle intersection_of: GO:0043226 ! organelle intersection_of: has_part GO:0016020 ! membrane -disjoint_from: GO:0043228 ! non-membrane-bounded organelle +disjoint_from: GO:0043228 ! membraneless organelle relationship: has_part GO:0016020 ! membrane property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28153" xsd:anyURI [Term] id: GO:0043228 -name: non-membrane-bounded organelle +name: membraneless organelle namespace: cellular_component def: "Organized structure of distinctive morphology and function, not bounded by a lipid bilayer membrane. Includes ribosomes, the cytoskeleton and chromosomes." [GOC:go_curators] subset: gocheck_do_not_annotate subset: goslim_mouse synonym: "biological condensate" RELATED [] +synonym: "membrane-less organelle" EXACT [] +synonym: "non-membrane-bounded organelle" EXACT [] synonym: "non-membrane-enclosed organelle" EXACT [] xref: NIF_Subcellular:sao1456184038 is_a: GO:0043226 ! organelle property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/21881" xsd:anyURI property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28153" xsd:anyURI +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29106" xsd:anyURI [Term] id: GO:0043229 @@ -4847,15 +5012,17 @@ intersection_of: part_of GO:0005622 ! intracellular anatomical structure [Term] id: GO:0043232 -name: intracellular non-membrane-bounded organelle +name: intracellular membraneless organelle namespace: cellular_component def: "Organized structure of distinctive morphology and function, not bounded by a lipid bilayer membrane and occurring within the cell. Includes ribosomes, the cytoskeleton and chromosomes." [GOC:go_curators] subset: goslim_pir +synonym: "intracellular non-membrane-bounded organelle" EXACT [] synonym: "intracellular non-membrane-enclosed organelle" EXACT [] -is_a: GO:0043228 ! non-membrane-bounded organelle +is_a: GO:0043228 ! membraneless organelle is_a: GO:0043229 ! intracellular organelle -intersection_of: GO:0043228 ! non-membrane-bounded organelle +intersection_of: GO:0043228 ! membraneless organelle intersection_of: part_of GO:0005622 ! intracellular anatomical structure +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29106" xsd:anyURI [Term] id: GO:0043233 @@ -4874,7 +5041,7 @@ name: contractile muscle fiber namespace: cellular_component def: "Fibers, composed of actin, myosin, and associated proteins, found in cells of smooth or striated muscle." [GOC:go_curators, ISBN:0815316194] synonym: "contractile fibre" EXACT [] -is_a: GO:0043232 ! intracellular non-membrane-bounded organelle +is_a: GO:0043232 ! intracellular membraneless organelle is_a: GO:0099512 ! supramolecular fiber relationship: part_of CL:0000187 ! muscle cell relationship: part_of GO:0005737 ! cytoplasm @@ -4886,9 +5053,6 @@ property_value: term_tracker_item "https://github.com/geneontology/go-ontology/i id: GO:0043933 name: protein-containing complex organization namespace: biological_process -alt_id: GO:0034600 -alt_id: GO:0034621 -alt_id: GO:0071822 def: "Any process in which macromolecules aggregate, disaggregate, or are modified, resulting in the formation, disassembly, or alteration of a protein complex." [GOC:mah] synonym: "cellular macromolecular complex organization" RELATED [] synonym: "cellular macromolecular complex subunit organisation" RELATED [] @@ -4904,14 +5068,12 @@ intersection_of: GO:0016043 ! cellular component organization intersection_of: results_in_organization_of GO:0032991 ! protein-containing complex relationship: results_in_organization_of GO:0032991 ! protein-containing complex property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/22580" xsd:anyURI -created_by: mah creation_date: 2010-09-08T10:01:42Z [Term] id: GO:0044085 name: cellular component biogenesis namespace: biological_process -alt_id: GO:0071843 def: "A process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of a cellular component. Includes biosynthesis of constituent macromolecules, and those macromolecular modifications that are involved in synthesis or assembly of the cellular component." [GOC:jl, GOC:mah] subset: gocheck_do_not_annotate subset: goslim_pir @@ -4928,21 +5090,8 @@ synonym: "Met-tRNA/eIF2.GTP ternary complex" NARROW [] synonym: "translation initiation (ternary) complex" EXACT [] is_a: GO:1990904 ! ribonucleoprotein complex relationship: part_of GO:0005737 ! cytoplasm -created_by: jl creation_date: 2009-10-22T02:38:55Z -[Term] -id: GO:0044237 -name: cellular metabolic process -namespace: biological_process -def: "The chemical reactions and pathways by which individual cells transform chemical substances." [GOC:go_curators] -comment: This term should not be used for direct annotation. It should be possible to make a more specific annotation to one of the children of this term. -subset: gocheck_do_not_annotate -synonym: "cellular metabolism" EXACT [] -synonym: "intermediary metabolism" RELATED [GOC:mah] -is_a: GO:0008152 ! metabolic process -is_a: GO:0009987 ! cellular process - [Term] id: GO:0044238 name: primary metabolic process @@ -4958,21 +5107,6 @@ xref: Wikipedia:Primary_metabolite is_a: GO:0008152 ! metabolic process property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/26424" xsd:anyURI -[Term] -id: GO:0044249 -name: cellular biosynthetic process -namespace: biological_process -def: "The chemical reactions and pathways resulting in the formation of substances, carried out by individual cells." [GOC:jl] -comment: This term should not be used for direct annotation. It should be possible to make a more specific annotation to one of the children of this term. -subset: gocheck_do_not_annotate -synonym: "cellular anabolism" EXACT [] -synonym: "cellular biosynthesis" EXACT [] -synonym: "cellular formation" EXACT [] -synonym: "cellular synthesis" EXACT [] -is_a: GO:0009058 ! biosynthetic process -is_a: GO:0044237 ! cellular metabolic process -property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27052" xsd:anyURI - [Term] id: GO:0044419 name: biological process involved in interspecies interaction between organisms @@ -4993,7 +5127,6 @@ property_value: term_tracker_item "https://github.com/geneontology/go-ontology/i id: GO:0045026 name: plasma membrane fusion namespace: biological_process -alt_id: GO:0006947 def: "The joining of the lipid bilayer membrane that surround a cell with that of another cell, producing a single cell." [GOC:elh, GOC:mtg_muscle] synonym: "cell fusion" BROAD [] synonym: "cell-cell fusion" BROAD [] @@ -5007,7 +5140,6 @@ relationship: results_in_fusion_of GO:0005886 ! plasma membrane id: GO:0045087 name: innate immune response namespace: biological_process -alt_id: GO:0002226 def: "Innate immune responses are defense responses mediated by germline encoded components that directly recognize components of potential pathogens." [GO_REF:0000022, GOC:add, GOC:ebc, GOC:mtg_sensu] synonym: "innate immunity" EXACT [GOC:pg] synonym: "nonspecific immune response" EXACT [] @@ -5215,7 +5347,6 @@ relationship: regulates GO:0050896 ! response to stimulus id: GO:0048598 name: embryonic morphogenesis namespace: biological_process -alt_id: GO:0048828 def: "The process in which anatomical structures are generated and organized during the embryonic phase. The embryonic phase begins with zygote formation. The end of the embryonic phase is organism-specific. For example, it would be at birth for mammals, larval hatching for insects and seed dormancy in plants." [GOC:jid, GOC:mtg_sensu] synonym: "embryonic anatomical structure morphogenesis" EXACT [GOC:dph, GOC:tb] is_a: GO:0009653 ! anatomical structure morphogenesis @@ -5336,7 +5467,6 @@ relationship: regulates GO:0006955 ! immune response id: GO:0050789 name: regulation of biological process namespace: biological_process -alt_id: GO:0050791 def: "Any process that modulates the frequency, rate or extent of a biological process. Biological processes are regulated by many means; examples include the control of gene expression, protein modification or interaction with a protein or substrate molecule." [GOC:ai, GOC:go_curators] subset: gocheck_do_not_annotate subset: goslim_candida @@ -5361,7 +5491,6 @@ relationship: regulates GO:0032502 ! developmental process id: GO:0050794 name: regulation of cellular process namespace: biological_process -alt_id: GO:0051244 def: "Any process that modulates the frequency, rate or extent of a cellular process, any of those that are carried out at the cellular level, but are not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level." [GOC:go_curators] subset: gocheck_do_not_annotate synonym: "regulation of cellular physiological process" EXACT [] @@ -5420,7 +5549,6 @@ property_value: term_tracker_item "https://github.com/geneontology/go-ontology/i id: GO:0050896 name: response to stimulus namespace: biological_process -alt_id: GO:0051869 def: "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus. The process begins with detection of the stimulus and ends with a change in state or activity or the cell or organism." [GOC:ai, GOC:bf] comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. subset: gocheck_do_not_annotate @@ -5493,7 +5621,6 @@ relationship: part_of GO:0050953 ! sensory perception of light stimulus id: GO:0051179 name: localization namespace: biological_process -alt_id: GO:1902578 def: "Any process in which a cell, a substance, or a cellular entity, such as a protein complex or organelle, is transported, tethered to or otherwise maintained in a specific location. In the case of substances, localization may also be achieved via selective degradation." [GOC:ai, GOC:dos] subset: gocheck_do_not_annotate subset: goslim_pir @@ -5507,7 +5634,6 @@ synonym: "single organism localization" RELATED [GOC:TermGenie] synonym: "single-organism localization" RELATED [] is_a: GO:0008150 ! biological_process property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27052" xsd:anyURI -created_by: jl creation_date: 2013-12-18T13:51:04Z [Term] @@ -5571,8 +5697,6 @@ is_a: GO:0050896 ! response to stimulus id: GO:0051707 name: response to other organism namespace: biological_process -alt_id: GO:0009613 -alt_id: GO:0042828 def: "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus from another living organism." [GOC:ai] is_a: GO:0043207 ! response to external biotic stimulus is_a: GO:0044419 ! biological process involved in interspecies interaction between organisms @@ -5581,7 +5705,6 @@ is_a: GO:0044419 ! biological process involved in interspecies interaction betwe id: GO:0055085 name: transmembrane transport namespace: biological_process -alt_id: GO:0090662 def: "The process in which a solute is transported across a lipid bilayer, from one side of a membrane to the other." [GOC:dph, GOC:jid] comment: Transmembrane transport is the transport of a solute across a lipid bilayer. Note that transport through the nuclear pore complex is not transmembrane because the nuclear membrane is a double membrane and is not traversed. For transport through the nuclear pore, consider instead the term 'nucleocytoplasmic transport ; GO:0006913' and its children. Note also that this term is not intended for use in annotating lateral movement within membranes. subset: goslim_chembl @@ -5597,7 +5720,6 @@ is_a: GO:0009987 ! cellular process intersection_of: GO:0006810 ! transport intersection_of: results_in_transport_across GO:0016020 ! membrane relationship: results_in_transport_across GO:0016020 ! membrane -created_by: tb creation_date: 2015-10-21T13:22:47Z [Term] @@ -5650,15 +5772,12 @@ is_a: GO:0035239 ! tube morphogenesis intersection_of: GO:0009653 ! anatomical structure morphogenesis intersection_of: results_in_morphogenesis_of UBERON:0003914 ! epithelial tube relationship: results_in_morphogenesis_of UBERON:0003914 ! epithelial tube -created_by: dph creation_date: 2009-04-28T09:33:36Z [Term] id: GO:0061024 name: membrane organization namespace: biological_process -alt_id: GO:0016044 -alt_id: GO:0044802 def: "A process which results in the assembly, arrangement of constituent parts, or disassembly of a membrane. A membrane is a double layer of lipid molecules that encloses all cells, and, in eukaryotes, many organelles; may be a single or double lipid bilayer; also includes associated proteins." [GOC:dph, GOC:tb] subset: goslim_chembl subset: goslim_drosophila @@ -5675,15 +5794,12 @@ is_a: GO:0016043 ! cellular component organization intersection_of: GO:0016043 ! cellular component organization intersection_of: results_in_organization_of GO:0016020 ! membrane relationship: results_in_organization_of GO:0016020 ! membrane -created_by: jl creation_date: 2010-02-08T02:43:11Z [Term] id: GO:0061025 name: membrane fusion namespace: biological_process -alt_id: GO:0006944 -alt_id: GO:0044801 def: "The membrane organization process that joins two lipid bilayers to form a single membrane." [GOC:dph, GOC:tb] subset: goslim_yeast synonym: "cellular membrane fusion" EXACT [] @@ -5693,7 +5809,6 @@ is_a: GO:0061024 ! membrane organization intersection_of: GO:0061024 ! membrane organization intersection_of: results_in_fusion_of GO:0016020 ! membrane relationship: results_in_fusion_of GO:0016020 ! membrane -created_by: jl creation_date: 2010-02-08T02:48:06Z [Term] @@ -5704,16 +5819,12 @@ def: "An extracellular matrix consisting mainly of proteins (especially collagen is_a: GO:0031012 ! extracellular matrix relationship: RO:0002160 NCBITaxon:33208 ! only in taxon Metazoa relationship: RO:0002162 NCBITaxon:33208 {all_only="true"} ! in taxon Metazoa -created_by: dph creation_date: 2018-04-13T12:47:21Z [Term] id: GO:0065003 name: protein-containing complex assembly namespace: biological_process -alt_id: GO:0006461 -alt_id: GO:0034622 -alt_id: GO:0043623 def: "The aggregation, arrangement and bonding together of a set of macromolecules to form a protein-containing complex." [GOC:jl] subset: goslim_chembl subset: goslim_drosophila @@ -5791,14 +5902,12 @@ intersection_of: GO:0016043 ! cellular component organization intersection_of: results_in_organization_of GO:1990904 ! ribonucleoprotein complex relationship: results_in_organization_of GO:1990904 ! ribonucleoprotein complex property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/25143" xsd:anyURI -created_by: mah creation_date: 2010-09-08T10:10:35Z [Term] id: GO:0071840 name: cellular component organization or biogenesis namespace: biological_process -alt_id: GO:0071841 def: "A process that results in the biosynthesis of constituent macromolecules, assembly, arrangement of constituent parts, or disassembly of a cellular component." [GOC:mah] comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. subset: gocheck_do_not_annotate @@ -5809,7 +5918,6 @@ synonym: "cellular component organisation or biogenesis at cellular level" EXACT synonym: "cellular component organization or biogenesis at cellular level" EXACT [] is_a: GO:0009987 ! cellular process property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27189" xsd:anyURI -created_by: mah creation_date: 2010-09-10T01:39:16Z [Term] @@ -5818,8 +5926,7 @@ name: cell periphery namespace: cellular_component def: "The broad region around and including the plasma membrane of a cell, encompassing the cell cortex (inside the cell), the plasma membrane, and any external encapsulating structures." [GOC:pdt] subset: goslim_flybase_ribbon -is_a: GO:0110165 ! cellular anatomical entity -created_by: mah +is_a: GO:0110165 ! cellular anatomical structure creation_date: 2010-10-04T01:51:47Z [Term] @@ -5831,7 +5938,6 @@ synonym: "elastic fibre" EXACT [GOC:mah] synonym: "elastin fiber" EXACT [GOC:BHF] is_a: GO:0099512 ! supramolecular fiber relationship: part_of GO:0031012 ! extracellular matrix -created_by: mah creation_date: 2010-10-11T11:44:57Z [Term] @@ -5845,7 +5951,6 @@ intersection_of: results_in_formation_of UBERON:0003914 ! epithelial tube relationship: part_of GO:0060562 ! epithelial tube morphogenesis relationship: results_in_formation_of UBERON:0003914 ! epithelial tube property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/22302" xsd:anyURI -created_by: mah creation_date: 2010-02-26T02:15:40Z [Term] @@ -5858,7 +5963,6 @@ is_a: GO:0061025 ! membrane fusion intersection_of: GO:0061025 ! membrane fusion intersection_of: results_in_fusion_of GO:0031090 ! organelle membrane relationship: results_in_fusion_of GO:0031090 ! organelle membrane -created_by: tb creation_date: 2009-12-11T11:44:58Z [Term] @@ -5871,7 +5975,6 @@ is_a: GO:1903131 ! mononuclear cell differentiation intersection_of: GO:0030154 ! cell differentiation intersection_of: results_in_acquisition_of_features_of CL:0000451 ! dendritic cell relationship: results_in_acquisition_of_features_of CL:0000451 ! dendritic cell -created_by: pr creation_date: 2011-04-01T10:08:42Z [Term] @@ -5883,14 +5986,12 @@ is_a: GO:0031982 ! vesicle is_a: GO:0043231 ! intracellular membrane-bounded organelle intersection_of: GO:0031982 ! vesicle intersection_of: part_of GO:0005622 ! intracellular anatomical structure -created_by: pr creation_date: 2016-03-29T17:39:45Z [Term] id: GO:0098542 name: defense response to other organism namespace: biological_process -alt_id: GO:0009814 def: "Reactions triggered in response to the presence of another organism that act to protect the cell or organism from damage caused by that organism." [GOC:dos] subset: goslim_generic subset: goslim_prokaryote @@ -5900,7 +6001,6 @@ synonym: "defense response, incompatible interaction" NARROW [] synonym: "resistance response to pathogen" NARROW [] is_a: GO:0051707 ! response to other organism property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/22173" xsd:anyURI -created_by: dos creation_date: 2013-11-11T12:59:11Z [Term] @@ -5915,7 +6015,6 @@ is_a: GO:0016020 ! membrane intersection_of: GO:0016020 ! membrane intersection_of: part_of GO:0005886 ! plasma membrane relationship: part_of GO:0005886 ! plasma membrane -created_by: dos creation_date: 2014-03-06T11:55:32Z [Term] @@ -5944,7 +6043,6 @@ def: "A complex of collagen trimers such as a fibril or collagen network." [GOC: synonym: "Supramolecular aggregate of collagen" EXACT [PMID:19693541] synonym: "Supramolecular collagen assembly" EXACT [PMID:21421911] is_a: GO:0099080 ! supramolecular complex -is_a: PR:000050567 ! protein-containing material entity relationship: has_part GO:0005581 ! collagen trimer relationship: part_of GO:0062023 ! collagen-containing extracellular matrix @@ -5983,7 +6081,7 @@ namespace: cellular_component def: "The part of a synapse that is part of the presynaptic cell." [GOC:dos] subset: goslim_synapse synonym: "presynaptic terminal" EXACT [] -is_a: GO:0110165 ! cellular anatomical entity +is_a: GO:0110165 ! cellular anatomical structure relationship: part_of CL:0000540 ! neuron relationship: part_of GO:0045202 ! synapse @@ -5993,7 +6091,7 @@ name: postsynapse namespace: cellular_component def: "The part of a synapse that is part of the post-synaptic cell." [GOC:dos] subset: goslim_synapse -is_a: GO:0110165 ! cellular anatomical entity +is_a: GO:0110165 ! cellular anatomical structure relationship: part_of CL:0000000 ! cell relationship: part_of GO:0045202 ! synapse @@ -6035,7 +6133,7 @@ id: GO:0099080 name: supramolecular complex namespace: cellular_component def: "A cellular component that consists of an indeterminate number of proteins or macromolecular complexes, organized into a regular, higher-order structure such as a polymer, sheet, network or a fiber." [GOC:dos] -is_a: GO:0110165 ! cellular anatomical entity +is_a: GO:0110165 ! cellular anatomical structure [Term] id: GO:0099081 @@ -6075,7 +6173,6 @@ relationship: capable_of GO:0099500 ! vesicle fusion to plasma membrane id: GO:0099512 name: supramolecular fiber namespace: cellular_component -alt_id: GO:0043205 def: "A polymer consisting of an indefinite number of protein or protein complex subunits that have polymerised to form a fiber-shaped structure." [GOC:dos] synonym: "fibril" RELATED [] is_a: GO:0099081 ! supramolecular polymer @@ -6108,16 +6205,17 @@ is_a: GO:0099536 ! synaptic signaling [Term] id: GO:0110165 -name: cellular anatomical entity +name: cellular anatomical structure namespace: cellular_component -def: "A part of a cellular organism that is either an immaterial entity or a material entity with granularity above the level of a protein complex but below that of an anatomical system. Or, a substance produced by a cellular organism with granularity above the level of a protein complex." [GOC:kmv] +def: "A part of a cellular organism consisting of a material entity with granularity above the level of a protein complex but below that of an anatomical system. Note that cellular organisms exclude viruses." [GOC:kmv] subset: gocheck_do_not_annotate subset: goslim_pir +synonym: "cellular anatomical entity" EXACT [] is_a: GO:0005575 ! cellular_component is_a: UBERON:0000061 ! anatomical structure property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/24200" xsd:anyURI property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/26424" xsd:anyURI -created_by: kmv +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28978" xsd:anyURI creation_date: 2019-08-12T18:01:37Z [Term] @@ -6130,7 +6228,6 @@ intersection_of: GO:0042995 ! cell projection intersection_of: has_part GO:0098590 ! plasma membrane region relationship: has_part GO:0098590 ! plasma membrane region property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/13193" xsd:anyURI -created_by: krc creation_date: 2017-03-21T17:26:07Z [Term] @@ -6143,7 +6240,6 @@ intersection_of: GO:0016043 ! cellular component organization intersection_of: results_in_organization_of GO:0120025 ! plasma membrane bounded cell projection relationship: results_in_organization_of GO:0120025 ! plasma membrane bounded cell projection property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/13298" xsd:anyURI -created_by: krc creation_date: 2017-04-26T16:07:02Z [Term] @@ -6156,7 +6252,6 @@ is_a: GO:0009987 ! cellular process intersection_of: GO:0009987 ! cellular process intersection_of: part_of GO:0006887 ! exocytosis relationship: part_of GO:0006887 ! exocytosis -created_by: pg creation_date: 2017-05-15T13:20:45Z [Term] @@ -6169,7 +6264,6 @@ synonym: "cell fusion" BROAD [] is_a: GO:0009987 ! cellular process relationship: has_part GO:0045026 ! plasma membrane fusion property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/15939" xsd:anyURI -created_by: pg creation_date: 2018-08-13T18:38:18Z [Term] @@ -6185,7 +6279,6 @@ intersection_of: has_target_end_location GO:0005576 ! extracellular region intersection_of: has_target_start_location GO:0005622 ! intracellular anatomical structure relationship: has_target_end_location GO:0005576 ! extracellular region relationship: has_target_start_location GO:0005622 ! intracellular anatomical structure -created_by: pg creation_date: 2019-05-22T11:20:45Z [Term] @@ -6195,7 +6288,6 @@ namespace: biological_process def: "Reactions triggered in response to the presence of a symbiont that act to protect or prevent damage to the host." [GOC:pg] is_a: GO:0098542 ! defense response to other organism property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/20261" xsd:anyURI -created_by: pg creation_date: 2020-11-11T17:19:06Z [Term] @@ -6209,7 +6301,6 @@ is_a: GO:1903706 ! regulation of hemopoiesis intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0002521 ! leukocyte differentiation relationship: regulates GO:0002521 ! leukocyte differentiation -created_by: pr creation_date: 2013-05-02T17:32:42Z [Term] @@ -6221,7 +6312,6 @@ is_a: GO:0002521 ! leukocyte differentiation intersection_of: GO:0030154 ! cell differentiation intersection_of: results_in_acquisition_of_features_of CL:0000842 ! mononuclear cell relationship: results_in_acquisition_of_features_of CL:0000842 ! mononuclear cell -created_by: cls creation_date: 2014-06-25T15:47:09Z [Term] @@ -6240,15 +6330,12 @@ is_a: GO:2000026 ! regulation of multicellular organismal development intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0030097 ! hemopoiesis relationship: regulates GO:0030097 ! hemopoiesis -created_by: pad creation_date: 2014-12-04T15:34:13Z [Term] id: GO:1990904 name: ribonucleoprotein complex namespace: cellular_component -alt_id: GO:0030529 -alt_id: GO:1990903 def: "A macromolecular complex that contains both RNA and protein molecules." [GOC:krc, GOC:vesicles] subset: goslim_pir synonym: "extracellular ribonucleoprotein complex" NARROW [] @@ -6258,7 +6345,6 @@ synonym: "RNA-protein complex" EXACT [] synonym: "RNP" EXACT [] xref: Wikipedia:Ribonucleoprotein is_a: GO:0032991 ! protein-containing complex -created_by: pr creation_date: 2015-11-19T12:26:37Z [Term] @@ -6271,7 +6357,6 @@ is_a: GO:0051239 ! regulation of multicellular organismal process intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0007275 ! multicellular organism development relationship: regulates GO:0007275 ! multicellular organism development -created_by: tb creation_date: 2010-08-05T11:25:59Z [Term] @@ -6305,7 +6390,6 @@ is_a: NCBITaxon:39107 ! Murinae id: NCBITaxon:10090 name: Mus musculus namespace: ncbi_taxonomy -alt_id: NCBITaxon:85055 synonym: "house mouse" EXACT genbank_common_name [] synonym: "mouse" EXACT OMO:0003003 [] xref: GC_ID:1 @@ -6322,7 +6406,6 @@ is_a: NCBITaxon:7776 ! Gnathostomata id: NCBITaxon:117571 name: Euteleostomi namespace: ncbi_taxonomy -alt_id: NCBITaxon:40673 synonym: "bony vertebrates" EXACT genbank_common_name [] xref: GC_ID:1 is_a: NCBITaxon:117570 ! Teleostomi @@ -6471,7 +6554,6 @@ is_a: NCBITaxon:1963758 ! Myomorpha id: NCBITaxon:39107 name: Murinae namespace: ncbi_taxonomy -alt_id: NCBITaxon:109679 xref: GC_ID:1 is_a: NCBITaxon:10066 ! Muridae @@ -6567,7 +6649,6 @@ is_a: NCBITaxon:314147 ! Glires id: PATO:0000001 name: quality namespace: quality -alt_id: PATO:0000072 def: "A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities" [PATOC:GVG] [Term] @@ -6582,7 +6663,6 @@ is_a: PATO:0001241 ! physical object quality id: PATO:0000052 name: shape namespace: quality -alt_id: PATO:0001647 def: "A morphological quality inhering in a bearer by virtue of the bearer's ratios of distances between its features (points, edges, surfaces and also holes etc)." [PATOC:GVG] comment: Shapes are invariant on size transformations. Shapes can be subdivided into 2D and 3D shapes, We can also make a distinction between shapes of complete self-connected objects, and shapes of parts of objects. subset: attribute_slim @@ -6593,7 +6673,6 @@ is_a: PATO:0000051 ! morphology id: PATO:0000141 name: structure namespace: quality -alt_id: PATO:0001452 def: "A morphology quality inhering in a bearer by virtue of the bearer's relative position, shape, arrangements and connectivity of an organism's various parts; the pattern underlying its form." [PATOC:GVG] subset: attribute_slim synonym: "conformation" BROAD [VT:1000738] @@ -6631,7 +6710,6 @@ is_a: PATO:0002318 ! superelliptic id: PATO:0001018 name: physical quality namespace: quality -alt_id: PATO:0002079 def: "A quality of a physical entity that exists through action of continuants at the physical level of organisation in relation to other entities." [PATOC:GVG] subset: attribute_slim synonym: "relational physical quality" EXACT [] @@ -6642,8 +6720,6 @@ is_a: PATO:0001241 ! physical object quality id: PATO:0001241 name: physical object quality namespace: quality -alt_id: PATO:0001237 -alt_id: PATO:0001238 def: "A quality which inheres in a continuant." [PATOC:GVG] comment: Relational qualities are qualities that hold between multiple entities. Normal (monadic) qualities such as the shape of a eyeball exist purely as a quality of that eyeball. A relational quality such as sensitivity to light is a quality of that eyeball (and connecting nervous system) as it relates to incoming light waves/particles. synonym: "monadic quality of a continuant" EXACT [] @@ -6757,7 +6833,6 @@ is_a: PATO:0001579 ! contractility id: PATO:0001873 name: cylindrical namespace: quality -alt_id: PATO:0001203 def: "A convex 3-D shape quality inhering in a bearer by virtue of the bearer's exhibiting a consistently-sized round cross section." [PATOC:MAH] subset: cell_quality subset: value_slim @@ -6963,7 +7038,6 @@ def: "A quality inhering in a cell by virtue of the cell having a high nuclear/c comment: A high nuclear/cytolasmic ratio is 70% or higher. synonym: "high N:C ratio" EXACT [] is_a: PATO:0001396 ! cellular quality -created_by: http://orcid.org/0000-0001-5208-3432 [Term] id: PATO:0070044 @@ -6971,7 +7045,6 @@ name: anatomical structure quality namespace: quality def: "A quality of continuant that exist at the anatomical level of organisation and anything under it. This includes, but is not limited to, cells , tissues, and components." [] is_a: PATO:0001241 ! physical object quality -created_by: http://orcid.org/0000-0001-7258-9596 [Term] id: PATO:0070045 @@ -6979,7 +7052,6 @@ name: anatomical histological quality namespace: quality def: "A quality inhering in an anotomical structure by virtue of its capacity to be stained by specific histological dyes." [] is_a: PATO:0070044 ! anatomical structure quality -created_by: http://orcid.org/0000-0001-7258-9596 [Term] id: PATO:0070046 @@ -6987,18 +7059,17 @@ name: neutrophillic namespace: quality def: "An affinity inhering in an anatomical structure by virtue of the bearer exhibiting a molecular interaction that stains and colors, pale-pink, with Wright-Giemsa stain." [GOC:add] is_a: PATO:0070045 ! anatomical histological quality -created_by: http://orcid.org/0000-0001-7258-9596 [Term] id: PR:000000001 name: protein namespace: protein def: "An amino acid chain that is produced de novo by ribosome-mediated translation of a genetically-encoded mRNA, and any derivatives thereof." [PRO:DAN, PRO:WCB] -comment: The definition above excludes protein complexes, which some also consider a protein. Those who wish to refer to a class representing both senses of the word are directed to CHEBI:36080. Note that the definition allows for experimentally-manipulated genes, and allows for artifically-produced derivatives that mimic those found naturally. Proteins (in the sense defined here) that descended from a common ancestor can be classified into families and superfamilies composed of products of evolutionarily-related genes. The domain architecture of a protein is described by the order of its constituent domains. Proteins with the same domains in the same order are defined as homeomorphic [PRO:WCB]. +comment: The definition above excludes protein complexes, which some also consider a protein. Those who wish to refer to a class representing both senses of the word are directed to CHEBI:36080. Note that the definition allows for experimentally-manipulated genes, and allows for artifically-produced derivatives that mimic those found naturally. Proteins (in the sense defined here) that descended from a common ancestor can be classified into families and superfamilies composed of products of evolutionarily-related genes. The domain architecture of a protein is described by the order of its constituent domains. Proteins with the same domains in the same order are defined as homeomorphic [PRO:WCB). synonym: "native protein" NARROW [IEDB:BP] synonym: "natural protein" EXACT [PRO:DAN] is_a: PR:000018263 ! amino acid chain -is_a: PR:000050567 ! protein-containing material entity +is_a: PR:000064867 ! protein-containing molecular entity relationship: output_of GO:0006412 ! translation [Term] @@ -7482,7 +7553,6 @@ namespace: protein def: "A protein with core architecture consisting of a signal sequence, followed by 7 Ig-like domains (Pfam:PF00047, Pfam:PF07679, or Pfam:PF07686), a transmembrane region, and a cytoplasmic Protein tyrosine kinase domain." [PRO:WCB] comment: Category=family. xref: PIRSF:PIRSF038502 -is_a: PR:000000001 ! protein [Term] id: PR:000002062 @@ -7740,11 +7810,11 @@ synonym: "PTPRC/iso:CD45R" EXACT PRO-short-label [PRO:DNx] is_a: PR:000001006 ! receptor-type tyrosine-protein phosphatase C [Term] -id: PR:000050567 -name: protein-containing material entity +id: PR:000064867 +name: protein-containing molecular entity namespace: protein -def: "A material entity that minimally consists of a protein." [PRO:DAN] -comment: Note: This includes single proteins and derivatives thereof (PR:000000001), protein-containing complexes (GO:0032991), and protein aggregates (PR:000050566). +def: "A molecular entity that minimally consists of a protein." [PRO:DAN] +comment: Note: This includes single proteins and derivatives thereof (PR:000000001), protein-containing complexes (GO:0032991), and protein aggregates (PR:000050565). synonym: "protein" NARROW [PRO:DAN] synonym: "protein aggregate" NARROW [PRO:DAN] synonym: "protein complex" NARROW [PRO:DAN] @@ -7875,7 +7945,6 @@ xref: UMLS:C0687028 {source="ncithesaurus:Duct"} xref: Wikipedia:Duct_(anatomy) xref: XAO:0004000 xref: ZFA:0005171 -is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0000063 ! organ subunit relationship: has_part UBERON:0034969 ! epithelial layer of duct relationship: RO:0000086 PATO:0002299 ! has quality tubular @@ -7885,7 +7954,6 @@ relationship: RO:0002570 UBERON:0000463 ! conduit for organism substance id: UBERON:0000060 name: anatomical wall namespace: uberon -alt_id: UBERON:0009915 def: "Organ component adjacent to an organ cavity and which consists of a maximal aggregate of organ component layers." [FMA:82482] subset: upper_level synonym: "organ wall" RELATED [FMA:82482] @@ -8066,7 +8134,6 @@ property_value: RO:0002175 NCBITaxon:4751 id: UBERON:0000075 name: subdivision of skeletal system namespace: uberon -alt_id: UBERON:0010322 def: "Anatomical cluster consisting of the skeletal elements and articular elements that are part of an individual subdivision of the organism." [https://orcid.org/0000-0002-6601-2165, UBERONREF:0000003] subset: non_informative synonym: "skeletal system part" RELATED [] @@ -8364,7 +8431,6 @@ property_value: seeAlso "https://github.com/obophenotype/uberon/issues/661" xsd: id: UBERON:0000307 name: blastula namespace: uberon -alt_id: UBERON:0007011 def: "Organism at the blastula stage - an early stage of embryonic development in animals. It is produced by cleavage of a fertilized ovum and consists of a spherical layer of around 128 cells surrounding a central fluid-filled cavity called the blastocoel. The blastula follows the morula and precedes the gastrula in the developmental sequence." [Wikipedia:Blastula] subset: inconsistent_with_fma synonym: "blastosphere" RELATED [Wikipedia:Blastula] @@ -8863,7 +8929,6 @@ xref: VHOG:0000387 xref: Wikipedia:Epithelium xref: XAO:0003045 xref: ZFA:0001486 -is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0000479 ! tissue intersection_of: UBERON:0000479 ! tissue intersection_of: RO:0002473 CL:0000066 ! composed primarily of epithelial cell @@ -9086,7 +9151,6 @@ property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/d/ id: UBERON:0000926 name: mesoderm namespace: uberon -alt_id: UBERON:0003263 def: "The middle germ layer of the embryo, between the endoderm and ectoderm." [Wikipedia:Mesoderm] subset: efo_slim subset: pheno_slim @@ -9334,7 +9398,6 @@ id: UBERON:0001009 name: circulatory system namespace: uberon def: "Organ system that passes nutrients (such as amino acids and electrolytes), gases, hormones, blood cells, etc. to and from cells in the body to help fight diseases and help stabilize body temperature and pH to maintain homeostasis[WP]." [Wikipedia:Circulatory_system] -subset: human_reference_atlas subset: uberon_slim synonym: "systema cardiovasculare" RELATED OMO:0003011 [Wikipedia:Circulatory_system] xref: AAO:0000959 @@ -9356,7 +9419,6 @@ property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/2/ property_value: RO:0002161 NCBITaxon:147099 {source="Wikipedia:Acoelomorpha"} property_value: RO:0002161 NCBITaxon:6073 property_value: RO:0002161 NCBITaxon:6157 -property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001015 @@ -9612,7 +9674,6 @@ property_value: RO:0002175 NCBITaxon:4751 id: UBERON:0001133 name: cardiac muscle tissue namespace: uberon -alt_id: UBERON:0007096 def: "Muscle tissue composed of cardiac muscle cells, forming the muscles of the heart[ZFA,modified]." [ZFA:0005280] subset: pheno_slim subset: uberon_slim @@ -9948,7 +10009,6 @@ relationship: part_of UBERON:0013702 ! body proper id: UBERON:0002104 name: visual system namespace: uberon -alt_id: UBERON:0007036 def: "The sensory system subserving the sense of vision." [NIFSTD:FMAID_7191] subset: pheno_slim subset: uberon_slim @@ -10125,7 +10185,6 @@ xref: NCIT:C12957 xref: UMLS:C1516995 {source="ncithesaurus:Exocrine_System"} xref: Wikipedia:Exocrine_gland xref: WikipediaCategory:Exocrine_system -is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0000467 ! anatomical system disjoint_from: UBERON:0002390 ! hematopoietic system disjoint_from: UBERON:0002405 ! immune system @@ -10235,7 +10294,6 @@ xref: NCIT:C12712 xref: SCTID:115976003 xref: UMLS:C0015282 {source="ncithesaurus:Exocrine_Gland"} xref: Wikipedia:Exocrine_gland -is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0002530 ! gland intersection_of: UBERON:0002530 ! gland intersection_of: part_of UBERON:0002330 ! exocrine system @@ -10599,6 +10657,7 @@ xref: TAO:0000279 xref: VHOG:0000559 xref: XAO:0000057 xref: ZFA:0000279 +is_a: UBERON:0000061 ! anatomical structure is_a: UBERON:0006598 ! presumptive structure intersection_of: UBERON:0005423 ! developing anatomical structure intersection_of: RO:0002387 UBERON:0002329 ! has potential to develop into somite @@ -10729,7 +10788,6 @@ property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/6/ id: UBERON:0003081 name: lateral plate mesoderm namespace: uberon -alt_id: UBERON:0006258 def: "Portion of the middle of the three primary germ layers of the embryo that resides on the periphery of the embryo, is continuous with the extra-embryonic mesoderm, splits into two layers enclosing the intra-embryonic coelom, and gives rise to body wall structures[MP]." [MP:0010117, Wikipedia:Lateral_plate_mesoderm] subset: pheno_slim subset: uberon_slim @@ -11031,7 +11089,6 @@ property_value: IAO:0000116 "EHDAA2 places this as a subtype of organism. This l id: UBERON:0004734 name: gastrula namespace: uberon -alt_id: UBERON:0007012 def: "Organism at the gastrula stage." [Wikipedia:Gastrula, Wikipedia:Trilaminar_blastocyst] subset: pheno_slim synonym: "blastocystis trilaminaris" RELATED [https://orcid.org/0000-0002-6601-2165] @@ -11354,7 +11411,6 @@ xref: NCIT:C13191 xref: SCTID:68989006 xref: UMLS:C0004799 {source="ncithesaurus:Basement_Membrane"} xref: Wikipedia:Basement_membrane -is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0005764 {source="FMA"} ! acellular membrane relationship: adjacent_to CL:0000066 ! epithelial cell relationship: has_part GO:0005587 ! collagen type IV trimer @@ -11636,7 +11692,6 @@ name: regular connective tissue namespace: uberon def: "Connective tissue, which consists of fibroblasts, the intercellular matrix of which contains a regular network of collagen and elastic fiber bundles. Examples: bone (tissue), cartilage (tissue), dense regular connective tissue." [FMA:20103] xref: FMA:20103 -is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0002384 {source="FMA"} ! connective tissue disjoint_from: UBERON:0011821 ! irregular connective tissue relationship: has_part CL:0000057 ! fibroblast @@ -11671,7 +11726,6 @@ intersection_of: RO:0002473 UBERON:0011860 ! composed primarily of collection of id: UBERON:0009142 name: entire embryonic mesenchyme namespace: uberon -alt_id: UBERON:0003313 def: "Sum total of mesenchyme in the embryo." [https://github.com/obophenotype/human-developmental-anatomy-ontology/issues/7] xref: EHDAA2:0001113 xref: EHDAA:177 @@ -11830,7 +11884,6 @@ xref: AAO:0000121 xref: NCIT:C32450 xref: UMLS:C1511770 {source="ncithesaurus:Dense_Connective_Tissue"} xref: Wikipedia:Dense_connective_tissue -is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0002384 ! connective tissue intersection_of: UBERON:0002384 ! connective tissue intersection_of: RO:0002473 UBERON:0011860 ! composed primarily of collection of collagen fibrils @@ -11845,7 +11898,6 @@ xref: FMA:63212 xref: MESH:D024022 xref: NCIT:C32339 xref: NIF_Subcellular:sao7547390221 -is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0000476 {source="ZFA"} ! acellular anatomical structure relationship: RO:0002473 GO:0005581 ! composed primarily of collagen trimer relationship: RO:0002473 GO:0098643 ! composed primarily of banded collagen fibril @@ -11880,6 +11932,7 @@ synonym: "haemocoelom" NARROW [] synonym: "schizocoelom" NARROW [] xref: EHDAA2:0004731 xref: Wikipedia:Coelom +xref: ZFA:0001438 is_a: UBERON:0000481 {source="EHDAA2"} ! multi-tissue structure relationship: RO:0002162 NCBITaxon:33213 ! in taxon Bilateria property_value: IAO:0000116 "EHDAA2 distingsuishes between the lumen, the lining, and the 'coelomic cavity', which despire it's name, is not a space - it is the aggregate of space plus lining." xsd:string @@ -12051,7 +12104,6 @@ is_a: UBERON:0000479 {source="FMA"} ! tissue id: UBERON:0016879 name: future central nervous system namespace: uberon -alt_id: UBERON:3000469 def: "Primordium that develops into the central nervous system." [http://orcid.org/0000-0002-6601-2165] synonym: "future CNS" EXACT [] synonym: "presumptive central nervous system" EXACT [] @@ -12066,7 +12118,6 @@ relationship: RO:0002387 UBERON:0001017 ! has potential to develop into central id: UBERON:0016880 name: future nervous system namespace: uberon -alt_id: UBERON:3000477 def: "Primordium that develops into the nervous system." [http://orcid.org/0000-0002-6601-2165] synonym: "presumptive nervous system" EXACT [AAO:0000477] xref: AAO:0000477 @@ -12337,7 +12388,6 @@ id: RO:0002021 name: occurs across def: "A relationship between a process and a barrier, where the process occurs in a region spanning the barrier. For cellular processes the barrier is typically a membrane. Examples include transport across a membrane and membrane depolarization." [] is_a: RO:0002479 ! has part that occurs in -created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-07-20T17:19:37Z [Typedef] @@ -13193,7 +13243,6 @@ name: causally upstream of or within, negative effect property_value: RO:0004050 RO:0002418 property_value: seeAlso "https://wiki.geneontology.org/Causally_upstream_of_or_within,_negative_effect" xsd:anyURI is_a: causally_upstream_of_or_within ! causally upstream of or within -created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-03-13T23:55:05Z [Typedef] @@ -13201,7 +13250,6 @@ id: RO:0004047 name: causally upstream of or within, positive effect property_value: seeAlso https://wiki.geneontology.org/Causally_upstream_of_or_within,_positive_effect is_a: causally_upstream_of_or_within ! causally upstream of or within -created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-03-13T23:55:19Z [Typedef] @@ -13210,7 +13258,6 @@ name: has small molecule regulator def: "a relation between a process and a continuant, in which the process is regulated by the small molecule continuant" [] is_a: has_participant ! has participant inverse_of: RO:0012004 ! is small molecule regulator of -created_by: https://orcid.org/0000-0003-1813-6857 creation_date: 2020-04-22T20:27:26Z [Typedef] @@ -13218,7 +13265,6 @@ id: RO:0012004 name: is small molecule regulator of def: "a relation between a continuant and a process, in which the continuant is a small molecule that regulates the process" [] is_a: RO:0002596 ! capable of regulating -created_by: https://orcid.org/0000-0003-1813-6857 creation_date: 2020-06-24T13:15:17Z [Typedef] @@ -13228,7 +13274,6 @@ def: "a relation between a continuant and a process, in which the continuant is property_value: seeAlso "https://wiki.geneontology.org/Is_small_molecule_activator_of" xsd:anyURI is_a: RO:0002598 ! capable of positively regulating is_a: RO:0012004 ! is small molecule regulator of -created_by: https://orcid.org/0000-0003-1813-6857 creation_date: 2020-06-24T13:15:26Z [Typedef] @@ -13238,7 +13283,6 @@ def: "A relationship between a neuron and a region, where the neuron has a funct synonym: "has synaptic input or output in" EXACT [] is_a: RO:0002130 ! has synaptic terminal in transitive_over: part_of ! part of -created_by: https://orcid.org/0000-0002-1373-1705 creation_date: 2020-07-17T09:26:52Z [Typedef] @@ -13251,9 +13295,18 @@ synonym: "has sensory terminal location" EXACT [] domain: CL:0000101 ! sensory neuron is_a: RO:0002360 ! has dendrite location transitive_over: part_of ! part of -created_by: https://orcid.org/0000-0002-1373-1705 creation_date: 2020-07-20T12:10:09Z +[Typedef] +id: RO:0015004 +name: has characterizing marker set +def: "A relation that applies between a cell type and a set of markers that can be used to uniquely identify that cell type." [] +synonym: "has marker gene combination" EXACT [] +synonym: "has marker signature set" EXACT [] +property_value: IAO:0000116 "C has_characterizing_marker_set y iff: C is a cell type and y is a collection of genes or proteins whose expression is sufficient to distinguish cell type C from most or all other cell types." xsd:string +property_value: terms:contributor https://orcid.org/0000-0001-7258-9596 +domain: CL:0000000 ! cell + [Typedef] id: RO:0015006 name: different in magnitude relative to @@ -13327,7 +13380,6 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0012003 is_a: has_participant ! has participant -created_by: https://orcid.org/0000-0003-1813-6857 creation_date: 2020-06-08T17:21:33Z [Typedef] @@ -13623,7 +13675,6 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_ontology xref: RO:0004009 is_a: has_input ! has input is_a: has_primary_input_or_output ! has primary input or output -created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-12-13T11:26:56Z [Typedef] @@ -13634,7 +13685,6 @@ def: "p 'has primary input ot output' c iff either (a) p 'has primary input' c o subset: http://purl.obolibrary.org/obo/valid_for_go_ontology xref: RO:0004007 is_a: has_participant ! has participant -created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-12-13T11:26:17Z [Typedef] @@ -13646,7 +13696,6 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_ontology xref: RO:0004008 is_a: has_output ! has output is_a: has_primary_input_or_output ! has primary input or output -created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-12-13T11:26:32Z [Typedef] @@ -13657,7 +13706,6 @@ def: "a relation between a process and a continuant, in which the process is act xref: RO:0012001 is_a: RO:0012000 ! has small molecule regulator inverse_of: RO:0012005 ! is small molecule activator of -created_by: https://orcid.org/0000-0003-1813-6857 creation_date: 2020-04-22T20:28:37Z [Typedef] @@ -13982,7 +14030,6 @@ namespace: external def: "p has anatomical participant c iff p has participant c, and c is an anatomical entity" [] xref: RO:0040036 is_a: has_participant ! has participant -created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-09-26T01:08:58Z [Typedef] @@ -14054,7 +14101,6 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0012008 is_a: results_in_organization_of ! results in organization of -created_by: https://orcid.org/0000-0003-1813-6857 creation_date: 2021-02-26T07:28:29Z [Typedef] @@ -14106,7 +14152,6 @@ name: results in organization of namespace: external def: "p results in organization of c iff p results in the assembly, arrangement of constituent parts, or disassembly of c" [] xref: RO:0002592 -is_a: has_participant ! has participant is_a: results_in_changes_to_anatomical_or_cellular_structure ! results in changes to anatomical or cellular structure [Typedef] diff --git a/subsets/general_cell_types_upper_slim.owl b/subsets/general_cell_types_upper_slim.owl index 8065f3828..bbfd7cd75 100644 --- a/subsets/general_cell_types_upper_slim.owl +++ b/subsets/general_cell_types_upper_slim.owl @@ -22,8 +22,8 @@ xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#" xmlns:ncbitaxon="http://purl.obolibrary.org/obo/ncbitaxon#"> - - 2024-09-26 + + 2025-01-08 @@ -287,13 +287,18 @@ WHERE { - 2018-03-14T00:03:24Z is negative form of + + + + + + @@ -373,6 +378,14 @@ WHERE { + + + + + + + + @@ -384,6 +397,14 @@ WHERE { + + + + + + + + @@ -1010,12 +1031,6 @@ WHERE { - - - - - - @@ -1034,6 +1049,12 @@ WHERE { + + + + + + @@ -1048,19 +1069,25 @@ WHERE { - + + description + - + + license + - + + title + @@ -1088,26 +1115,12 @@ WHERE { - - - - - - - - - - has_alternative_id - - - - @@ -1123,7 +1136,11 @@ WHERE { + An annotation property that links an ontology entity or a statement to a prefixed identifier or URI. + + database_cross_reference + has cross-reference @@ -1206,12 +1223,6 @@ WHERE { - - - - - - @@ -1681,7 +1692,6 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 A relationship between a process and a barrier, where the process occurs in a region spanning the barrier. For cellular processes the barrier is typically a membrane. Examples include transport across a membrane and membrane depolarization. - 2017-07-20T17:19:37Z occurs across @@ -3960,7 +3970,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different - p results in organization of c iff p results in the assembly, arrangement of constituent parts, or disassembly of c RO:0002592 @@ -4082,7 +4091,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different p 'has primary input ot output' c iff either (a) p 'has primary input' c or (b) p 'has primary output' c. - 2018-12-13T11:26:17Z RO:0004007 external @@ -4100,7 +4108,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different p has primary output c if (a) p has output c and (b) the goal of process is to modify, produce, or transform c. - 2018-12-13T11:26:32Z RO:0004008 external @@ -4128,7 +4135,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different p has primary input c if (a) p has input c and (b) the goal of process is to modify, consume, or transform c. - 2018-12-13T11:26:56Z RO:0004009 external @@ -4155,7 +4161,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different - 2018-03-13T23:55:05Z causally upstream of or within, negative effect https://wiki.geneontology.org/Causally_upstream_of_or_within,_negative_effect @@ -4167,7 +4172,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different - 2018-03-13T23:55:19Z causally upstream of or within, positive effect @@ -4181,7 +4185,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different a relation between a process and a continuant, in which the process is regulated by the small molecule continuant - 2020-04-22T20:27:26Z has small molecule regulator @@ -4194,7 +4197,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different a relation between a process and a continuant, in which the process is activated by the small molecule continuant - 2020-04-22T20:28:37Z RO:0012001 external @@ -4211,7 +4213,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different p acts on population of c iff c' is a collection, has members of type c, and p has participant c - 2020-06-08T17:21:33Z RO:0012003 external @@ -4231,7 +4232,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different a relation between a continuant and a process, in which the continuant is a small molecule that regulates the process - 2020-06-24T13:15:17Z is small molecule regulator of @@ -4244,7 +4244,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different a relation between a continuant and a process, in which the continuant is a small molecule that activates the process - 2020-06-24T13:15:26Z is small molecule activator of https://wiki.geneontology.org/Is_small_molecule_activator_of @@ -4256,7 +4255,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different - 2021-02-26T07:28:29Z RO:0012008 external @@ -4280,7 +4278,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different A relationship between a neuron and a region, where the neuron has a functionally relevant number of input and/or output synapses in that region. - 2020-07-17T09:26:52Z has synaptic input or output in has synaptic IO in region @@ -4298,7 +4295,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different Relation between a sensory neuron and some structure in which it receives sensory input via a sensory dendrite. - 2020-07-20T12:10:09Z has sensory dendrite location has sensory terminal in @@ -4308,6 +4304,20 @@ Each of these 3 primitives can be composed to yield a cross-product of different + + + + + A relation that applies between a cell type and a set of markers that can be used to uniquely identify that cell type. + C has_characterizing_marker_set y iff: C is a cell type and y is a collection of genes or proteins whose expression is sufficient to distinguish cell type C from most or all other cell types. + + has marker gene combination + has marker signature set + has characterizing marker set + + + + @@ -4447,7 +4457,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different p has anatomical participant c iff p has participant c, and c is an anatomical entity - 2018-09-26T01:08:58Z RO:0040036 external @@ -4791,6 +4800,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different XAO:0003012 ZFA:0009000 + + The definition of cell is intended to represent all cells, and thus a cell is defined as a material entity and not an anatomical structure, which implies that it is part of an organism (or the entirety of one). cell @@ -4822,6 +4833,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different A cell found in the embryo before the formation of all the gem layers is complete. ZFA:0009002 + + early embryonic cell (metazoa) @@ -4875,6 +4888,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different animal stem cell + + This term applies to metazoan. For plant stem cells, consider using PO:0004011 ‘initial cell’ or its parent PO:0004010 ‘meristematic cell’. stem cell @@ -5062,6 +5077,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different colony forming unit hematopoietic + + Markers differ between species, and two sets of markers have been described for mice. HSCs are reportedly CD34-positive, CD45-positive, CD48-negative, CD150-positive, CD133-positive, and CD244-negative. hematopoietic stem cell @@ -5104,6 +5121,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different A cell that is within the developmental lineage of gametes and is able to pass along its genetic material to offspring. ZFA:0009016 + + Originally this term had some plant germ line cell children. germ line cell @@ -5156,7 +5175,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different - @@ -5195,6 +5213,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different colony forming unit macrophage colony forming unit monocyte monocyte stem cell + + Morphology: mononuclear cell, diameter 12-20 _M, non-granular, N/C ratio 3/1 - 4/1; markers: CD11b (shared with many other myeloid cells); location: Adult: bone marrow; fetal: liver, Yolk Sac; role or process: hematopoiesis, monocyte development; lineage: hematopoietic, myeloid. monoblast @@ -5260,6 +5280,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different multifate stem cell multipotent cell multipotent stem cell + + multi fate stem cell @@ -5296,6 +5318,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different myeloid stem cell pluripotent stem cell (bone marrow) + + This cell type is intended to be compatible with any vertebrate common myeloid progenitor. For mammalian CMP known to be CD34-positive, please use the term 'common myeloid progenitor, CD34-positive' (CL_0001059). common myeloid progenitor @@ -5403,6 +5427,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different lymphoid stem cell lymphopoietic stem cell + + CLP are CD7-positive, CD10-positive, CD19-negative, CD34-positive, CD45RA-positive, CD79a-negative, CD127-positive, AA4.1-positive, RAG-negative, Sca-1-low, sIgM-negative, sIgD-negative, TdT-negative, Vpre-B-negative, and pre-BCR-negative. Expression of transcription factors include E2A-positive, EBF-positive, Ikaros-negative, PU.1-negative, and Pax5-negative. common lymphoid progenitor @@ -5453,6 +5479,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different MESH:D039901 ZFA:0009024 totipotential stem cell + + totipotent stem cell @@ -5480,6 +5508,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different FMA:84782 blast cell + + define using PATO mulit-potent or oligopotent? non-terminally differentiated cell @@ -5503,6 +5533,9 @@ Each of these 3 primitives can be composed to yield a cross-product of different FMA:70335 VHOG:0001529 ZFA:0009025 + + + myoblast @@ -5531,13 +5564,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - - - - - - + A connective tissue cell which secretes an extracellular matrix rich in collagen and other macromolecules. Flattened and irregular in outline with branching processes; appear fusiform or spindle-shaped. BTO:0000452 @@ -5548,6 +5575,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different ZFA:0009026 + + These cells may be vimentin-positive, fibronectin-positive, fsp1-positive, MMP-1-positive, collagen I-positive, collagen III-positive, and alpha-SMA-negative. fibroblast @@ -5592,6 +5621,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different epitheliocyte + + epithelial cell https://www.swissbiopics.org/api/image/Epithelial_cells.svg @@ -5627,6 +5658,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different ZFA:0009038 + + columnar/cuboidal epithelial cell @@ -5673,6 +5706,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different ZFA:0009044 + + blood cell @@ -5740,6 +5775,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different mature T cell + + T cell @@ -5815,7 +5852,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different - @@ -5871,13 +5907,20 @@ Each of these 3 primitives can be composed to yield a cross-product of different A specialized phagocytic cell associated with the absorption and removal of the mineralized matrix of bone tissue, which typically differentiates from monocytes. This cell has the following markers: tartrate-resistant acid phosphatase type 5-positive, PU.1-positive, c-fos-positive, nuclear factor NF-kappa-B p100 subunit-positive, tumor necrosis factor receptor superfamily member 11A-positive and macrophage colony-stimulating factor 1 receptor-positive. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Osteoclasts, derived from the monocyte/macrophage lineage, play a crucial role in bone remodeling through bone resorption. They are distinguished from other cells by their large size and their unique ability to secrete enzymes and acids that dissolve the calcium phosphate in bone. The formation of osteoclasts is influenced by two primary factors: macrophage colony-stimulating factor (M-CSF) and the ligand-activated receptor (RANKL) of nuclear factor kappa B (NF-κB). +Osteoclasts also collaborate with osteoblasts, responsible for new bone formation, to maintain bone health and adapt bone structure. Their coordinated actions allow continuous remodeling while preserving overall bone strength and integrity. Imbalances in osteoclast activity can lead to pathological conditions. For example, excessive activity may contribute to diseases like osteoporosis, periprosthetic osteolysis, bone tumors, and Paget's disease. Other the other hand, osteoclast deficiency ca result in conditions like osteopetrosis. BTO:0000968 CALOHA:TS-0721 FMA:66781 MESH:D010010 ZFA:0009047 + https://cellxgene.cziscience.com/cellguide/CL_0000092 chondroclast + + Morphology: Highly vesicular; markers: Surface: RANK, cFMS (MCSF receptor); Secreted: cathepsin K and TRAP (tartate resistant acid phosphatase); transcription factors: PU.1, cFOS, MITF, NFkB (p52); role or process: tissue remodelling: bone resorption; lineage: hematopoietic, myeloid. osteoclast @@ -5905,6 +5948,17 @@ Each of these 3 primitives can be composed to yield a cross-product of different PMID:15055519 PMID:17380158 + + + + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Osteoclasts, derived from the monocyte/macrophage lineage, play a crucial role in bone remodeling through bone resorption. They are distinguished from other cells by their large size and their unique ability to secrete enzymes and acids that dissolve the calcium phosphate in bone. The formation of osteoclasts is influenced by two primary factors: macrophage colony-stimulating factor (M-CSF) and the ligand-activated receptor (RANKL) of nuclear factor kappa B (NF-κB). +Osteoclasts also collaborate with osteoblasts, responsible for new bone formation, to maintain bone health and adapt bone structure. Their coordinated actions allow continuous remodeling while preserving overall bone strength and integrity. Imbalances in osteoclast activity can lead to pathological conditions. For example, excessive activity may contribute to diseases like osteoporosis, periprosthetic osteolysis, bone tumors, and Paget's disease. Other the other hand, osteoclast deficiency ca result in conditions like osteopetrosis. + DOI:10.3389/fmed.2017.00234 + DOI:10.37175/stemedicine.v1i4.57 + https://www.sciencedirect.com/topics/medicine-and-dentistry/osteoclast + @@ -5962,7 +6016,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different - @@ -6022,6 +6075,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different granular leukocyte polymorphonuclear leukocyte + + granulocyte @@ -6060,6 +6115,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different + + neuron associated cell @@ -6078,6 +6135,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different ZFA:0009052 motoneuron + + motor neuron @@ -6132,6 +6191,9 @@ Each of these 3 primitives can be composed to yield a cross-product of different MESH:D011984 WBbt:0005759 ZFA:0009053 + + + sensory neuron @@ -6174,7 +6236,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different A vertebrate phagocyte with a single nucleus. - This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. Mononuclear phagocytes are immune cells that form a critical part of the body's innate immune system, the body's first line of defense against infections. Mononuclear phagocytes are characterized by the presence of a single, large nucleus. The ‘Mononuclear Phagocyte System’ nomenclature was introduced to distinguish mononuclear monocytes and macrophages from other cells with multiple nuclei. However, the cells within the mononuclear phagocyte system represent a highly heterogeneous group, all of which are able to perform highly efficient phagocytosis - engulfing and digesting microbes and cellular debris to fight infections and to maintain normal tissue homeostasis. In addition to phagocytosis, mononuclear phagocytes also secrete chemical compounds to recruit other immune cells to a site of infection. These cells produce different types of signaling molecules, including cytokines, chemokines, and reactive oxygen species, triggering a cascade of responses to ensure rapid and efficient containment and neutralization of invading pathogens. These cells are also involved in antigen presentation, a process essential for stimulating an adaptive immune response. They can process and present antigens to T cells, thereby linking the innate and adaptive immune responses. @@ -6183,6 +6245,8 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf ZFA:0009064 https://cellxgene.cziscience.com/cellguide/CL_0000113 + + mononuclear phagocyte @@ -6203,7 +6267,7 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf - This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. Mononuclear phagocytes are immune cells that form a critical part of the body's innate immune system, the body's first line of defense against infections. Mononuclear phagocytes are characterized by the presence of a single, large nucleus. The ‘Mononuclear Phagocyte System’ nomenclature was introduced to distinguish mononuclear monocytes and macrophages from other cells with multiple nuclei. However, the cells within the mononuclear phagocyte system represent a highly heterogeneous group, all of which are able to perform highly efficient phagocytosis - engulfing and digesting microbes and cellular debris to fight infections and to maintain normal tissue homeostasis. In addition to phagocytosis, mononuclear phagocytes also secrete chemical compounds to recruit other immune cells to a site of infection. These cells produce different types of signaling molecules, including cytokines, chemokines, and reactive oxygen species, triggering a cascade of responses to ensure rapid and efficient containment and neutralization of invading pathogens. These cells are also involved in antigen presentation, a process essential for stimulating an adaptive immune response. They can process and present antigens to T cells, thereby linking the innate and adaptive immune responses. @@ -6227,7 +6291,7 @@ Mononuclear phagocytes play key roles in tissue repair and remodeling. After inf A non-neuronal cell of the nervous system. They not only provide physical support, but also respond to injury, regulate the ionic and chemical composition of the extracellular milieu. Guide neuronal migration during development, and exchange metabolites with neurons. - This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. Glial cells, also known as neuroglia or simply glia, are non-neuronal cells in the central and peripheral nervous systems that provide support and protection for neurons. They constitute approximately half of the total cells in the human brain and more than half in other parts of the nervous system. Glial cells perform several key functions including, but not limited to, maintaining homeostasis, forming the myelin sheath around the neuron axons, and providing support and nutrition to neurons. These different functions are performed by various glial cell types, including astrocytes, oligodendrocytes, microglia and other specialized types. Astrocytes, for example, are the most abundant glial cells and provide metabolic and nutrient support to neurons, help regulate the extracellular ion and neurotransmitter levels, and play a role in the formation and maintenance of the blood-brain barrier, contributing to the overall homeostasis and functioning of the nervous system. Additionally, astrocytes are involved in synaptic communication and participate in processes such as synaptogenesis and synaptic pruning. @@ -6244,6 +6308,8 @@ Despite their overarching function in the support and protection of neurons, gli neuroglia + + Not all glial cells develop from glioblasts, with microglia developing from the mesoderm instead. See https://github.com/obophenotype/cell-ontology/issues/1571 glial cell @@ -6257,7 +6323,7 @@ Despite their overarching function in the support and protection of neurons, gli - This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. Glial cells, also known as neuroglia or simply glia, are non-neuronal cells in the central and peripheral nervous systems that provide support and protection for neurons. They constitute approximately half of the total cells in the human brain and more than half in other parts of the nervous system. Glial cells perform several key functions including, but not limited to, maintaining homeostasis, forming the myelin sheath around the neuron axons, and providing support and nutrition to neurons. These different functions are performed by various glial cell types, including astrocytes, oligodendrocytes, microglia and other specialized types. Astrocytes, for example, are the most abundant glial cells and provide metabolic and nutrient support to neurons, help regulate the extracellular ion and neurotransmitter levels, and play a role in the formation and maintenance of the blood-brain barrier, contributing to the overall homeostasis and functioning of the nervous system. Additionally, astrocytes are involved in synaptic communication and participate in processes such as synaptogenesis and synaptic pruning. @@ -6292,6 +6358,8 @@ Despite their overarching function in the support and protection of neurons, gli Ectoderm destined to be nervous tissue. ZFA:0009080 neurectoderm cell + + neurectodermal cell @@ -6333,6 +6401,8 @@ Despite their overarching function in the support and protection of neurons, gli mesenchymal stromal cells stem cells, mesenchymal + + Many but not all mesenchymal cells derive from the mesoderm. MSCs are reportedly CD3-negative, CD4-negative, CD5-negative, CD8-negative, CD11a-negative, CD11b-negative, CD14-negative, CD19-negative, CD29-positive, CD31-negative, CD34-negative, CD38-negative, CD40-negative, CD44-positive, CD45-negative, CD49-positive, CD54-positive, CD66b-negative, CD79a-negative, CD80-negative, CD102-positive, CD106-positive, CD117-positive, CD121a-positive, CD121b-positive, CD123-positive, CD124-positive, CD133-negative, CD146-positive, CD166-positive, CD271-positive, B220-negative, Gr1-negative, MHCI-positive, MHCII-negative, SSEA4-negative, sca1-positive, Ter119-negative, and glycophorin A-negative. Cultured MSCs are capable of producing stem cell factor, IL7, IL8, IL11, TGF-beta, cofilin, galectin-1, laminin-receptor 1, cyclophilin A, and MMP-2. mesenchymal stem cell https://github.com/obophenotype/cell-ontology/issues/474 @@ -6432,6 +6502,8 @@ Despite their overarching function in the support and protection of neurons, gli fat cell + + adipocyte @@ -6476,6 +6548,8 @@ Despite their overarching function in the support and protection of neurons, gli APC + + Note change of name; nearly all somatic cells can present antigens to T cells via MHC Class I complexes leading to effector responses, but professional antigen presenting cells constitutively express MHC Class II as well as costimulatory molecules, and thus can initiate immune responses via T cells. professional antigen presenting cell @@ -6510,6 +6584,8 @@ Despite their overarching function in the support and protection of neurons, gli ZFA:0009090 chromatocyte chromatophore + + pigment cell @@ -6561,15 +6637,22 @@ Despite their overarching function in the support and protection of neurons, gli A pigment cell derived from the neural crest. Contains melanin-filled pigment granules, which gives a brown to black appearance. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Melanocytes are specialized cells prevalently found in the skin, but also present in the hair follicles, eyes, inner ear, bones, heart, and brain. Their primary function is the synthesis of melanin, a pigment responsible for coloration of skin, hair, and eyes. The presence and distribution of this pigment play a crucial role in the body's defense mechanism against harmful ultraviolet radiation. +In addition to melanin production, melanocytes also engage in a variety of other biological functions. They play a fundamental role in the immune response, owing to their ability to present antigens to T cells. Furthermore, they contribute to the maintenance of the skin's homeostasis by regulating processes such as extracellular matrix remodeling and cytokine production. A balance in melanocyte function is pivotal, as dysfunctions often result in dermatological disorders. For instance, the loss of melanocytes or reduction in their function may lead to hypopigmentation conditions such as vitiligo, whereas an abnormal increase could result in hyperpigmentation disorders or melanoma, a dangerous type of skin cancer. BTO:0000847 CALOHA:TS-0613 FMA:70545 MESH:D008544 VHOG:0001679 ZFA:0009091 + https://cellxgene.cziscience.com/cellguide/CL_0000148 melanophore + + melanocyte @@ -6579,6 +6662,19 @@ Despite their overarching function in the support and protection of neurons, gli A pigment cell derived from the neural crest. Contains melanin-filled pigment granules, which gives a brown to black appearance. SANBI:mhl + + + + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Melanocytes are specialized cells prevalently found in the skin, but also present in the hair follicles, eyes, inner ear, bones, heart, and brain. Their primary function is the synthesis of melanin, a pigment responsible for coloration of skin, hair, and eyes. The presence and distribution of this pigment play a crucial role in the body's defense mechanism against harmful ultraviolet radiation. +In addition to melanin production, melanocytes also engage in a variety of other biological functions. They play a fundamental role in the immune response, owing to their ability to present antigens to T cells. Furthermore, they contribute to the maintenance of the skin's homeostasis by regulating processes such as extracellular matrix remodeling and cytokine production. A balance in melanocyte function is pivotal, as dysfunctions often result in dermatological disorders. For instance, the loss of melanocytes or reduction in their function may lead to hypopigmentation conditions such as vitiligo, whereas an abnormal increase could result in hyperpigmentation disorders or melanoma, a dangerous type of skin cancer. + DOI:10.1002/med.21754 + DOI:10.1038/nrc.2016.37 + DOI:10.1111/j.1751-1097.2007.00226.x + DOI:10.3390/ijms21249769 + https://www.sciencedirect.com/topics/agricultural-and-biological-sciences/melanocyte + @@ -6593,6 +6689,8 @@ Despite their overarching function in the support and protection of neurons, gli pigment cell + + visual pigment cell @@ -6623,6 +6721,8 @@ Despite their overarching function in the support and protection of neurons, gli BTO:0003659 FMA:86916 + + secretory cell @@ -6661,6 +6761,8 @@ Despite their overarching function in the support and protection of neurons, gli FMA:16014 ZFA:0009092 + + exocrine cell @@ -6733,6 +6835,8 @@ Despite their overarching function in the support and protection of neurons, gli endocrinocyte + + endocrine cell @@ -6757,6 +6861,8 @@ Despite their overarching function in the support and protection of neurons, gli A cell whose primary function is to shorten. + + contractile cell @@ -6791,6 +6897,8 @@ Despite their overarching function in the support and protection of neurons, gli muscle fiber myocyte + + muscle cell https://www.swissbiopics.org/api/image/Muscle_cells.svg @@ -6838,13 +6946,21 @@ Despite their overarching function in the support and protection of neurons, gli A somatic cell located in skeletal muscle. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Skeletal muscle cells, or myocytes, are essential for the musculoskeletal system, featuring a striated appearance from tightly packed sarcomeres. These elongated, multi-nucleated cells convert ATP into mechanical energ and are key for voluntary movement and posture. They also are responsible for maintaining body temperature, storing nutrients, and stabilizing joints. +Skeletal muscle cells organize themselves tightly into bundles to form muscle fibers. Embedded within each of these cells are thousands of myofibrils, which are made up of the contractile proteins, actin (the thin filament), and myosin (the thick filament). Contraction of a skeletal muscle cell occurs when these myofibrils shorten, a process driven by the sliding of actin and myosin filaments over each other in a mechanism famously known as the sliding filament theory. +Additionally, skeletal muscle cells exhibit a high degree of plasticity, which allows for their adaptation in response to alterations in functional demands or damages. They have an innate regenerative capacity due to the presence of satellite cells—quiescent muscle stem cells that reside within the muscle fibers. Upon muscle injury, these satellite cells become activated, proliferate, and differentiate into new muscle cells, thereby contributing to the repair and growth of injured skeletal muscle. With this, skeletal muscle cells serve not only a pivotal biomechanical function but also possess a great capacity for self-healing and regeneration. BTO:0004392 CALOHA:TS-2158 FMA:9727 ZFA:0009115 + https://cellxgene.cziscience.com/cellguide/CL_0000188 skeletal muscle cell + + cell of skeletal muscle @@ -6854,6 +6970,20 @@ Despite their overarching function in the support and protection of neurons, gli A somatic cell located in skeletal muscle. GOC:tfm + + + + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Skeletal muscle cells, or myocytes, are essential for the musculoskeletal system, featuring a striated appearance from tightly packed sarcomeres. These elongated, multi-nucleated cells convert ATP into mechanical energ and are key for voluntary movement and posture. They also are responsible for maintaining body temperature, storing nutrients, and stabilizing joints. +Skeletal muscle cells organize themselves tightly into bundles to form muscle fibers. Embedded within each of these cells are thousands of myofibrils, which are made up of the contractile proteins, actin (the thin filament), and myosin (the thick filament). Contraction of a skeletal muscle cell occurs when these myofibrils shorten, a process driven by the sliding of actin and myosin filaments over each other in a mechanism famously known as the sliding filament theory. +Additionally, skeletal muscle cells exhibit a high degree of plasticity, which allows for their adaptation in response to alterations in functional demands or damages. They have an innate regenerative capacity due to the presence of satellite cells—quiescent muscle stem cells that reside within the muscle fibers. Upon muscle injury, these satellite cells become activated, proliferate, and differentiate into new muscle cells, thereby contributing to the repair and growth of injured skeletal muscle. With this, skeletal muscle cells serve not only a pivotal biomechanical function but also possess a great capacity for self-healing and regeneration. + DOI:10.1002/cphy.c160033 + DOI:10.3390/biology10101056 + https://www.nature.com/scitable/topicpage/the-sliding-filament-theory-of-muscle-contraction-14567666/ + https://www.ncbi.nlm.nih.gov/books/NBK537139 + https://www.ncbi.nlm.nih.gov/books/NBK9961/ + @@ -6876,16 +7006,24 @@ Despite their overarching function in the support and protection of neurons, gli A non-striated, elongated, spindle-shaped cell found lining the digestive tract, uterus, and blood vessels. They develop from specialized myoblasts (smooth muscle myoblast). + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Smooth muscle cells are a specialized type of muscle cells that are primarily found within the walls of hollow organs such as the intestine, stomach, bladder, uterus, and blood vessels. These cells are an essential component of the autonomic nervous system controling involuntary movements within the body. +Smooth muscle cells play a vital role in many physiological processes due to their unique functionality. They can contract and relax in a slow, sustained, and controlled manner to help modulate the size and shape of the lumens of the organs they surround. For example, in the digestive system, coordinated contraction and relaxation of smooth muscle cells propels food along the gastrointestinal tract - a process known as peristalsis. In the blood vessels, the smooth muscle cells, by contracting or relaxing, either constrict or dilate the vessels, which in turn, help regulate blood flow and pressure. +On a cellular level, smooth muscle cells possess a single, centrally located nucleus and contain an arranged network of actin and myosin filaments, which are the proteins responsible for muscle contraction. Unlike their counterparts in skeletal or cardiac muscles, these cells lack specific contact points for these filaments, hence the lack of visible striations. Furthermore, the contraction of smooth muscle cells is regulated by hormones and neurotransmitters, such as acetylcholine and norepinephrine, adding an additional layer of complex regulation to these highly specialized cells. non-striated muscle cell BTO:0004576 CALOHA:TS-2159 FMA:14072 ZFA:0009118 + https://cellxgene.cziscience.com/cellguide/CL_0000192 SMCs myocytes, smooth muscle smooth muscle fiber + + smooth muscle cell @@ -6897,6 +7035,20 @@ Despite their overarching function in the support and protection of neurons, gli PMID:9315361 http://en.wikipedia.org/wiki/Smooth_muscle_cell + + + + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Smooth muscle cells are a specialized type of muscle cells that are primarily found within the walls of hollow organs such as the intestine, stomach, bladder, uterus, and blood vessels. These cells are an essential component of the autonomic nervous system controling involuntary movements within the body. +Smooth muscle cells play a vital role in many physiological processes due to their unique functionality. They can contract and relax in a slow, sustained, and controlled manner to help modulate the size and shape of the lumens of the organs they surround. For example, in the digestive system, coordinated contraction and relaxation of smooth muscle cells propels food along the gastrointestinal tract - a process known as peristalsis. In the blood vessels, the smooth muscle cells, by contracting or relaxing, either constrict or dilate the vessels, which in turn, help regulate blood flow and pressure. +On a cellular level, smooth muscle cells possess a single, centrally located nucleus and contain an arranged network of actin and myosin filaments, which are the proteins responsible for muscle contraction. Unlike their counterparts in skeletal or cardiac muscles, these cells lack specific contact points for these filaments, hence the lack of visible striations. Furthermore, the contraction of smooth muscle cells is regulated by hormones and neurotransmitters, such as acetylcholine and norepinephrine, adding an additional layer of complex regulation to these highly specialized cells. + DOI:10.1093/ptj/81.11.1810 + https://training.seer.cancer.gov/anatomy/muscular/types.html + https://www.ncbi.nlm.nih.gov/books/NBK10854/ + https://www.ncbi.nlm.nih.gov/books/NBK526125 + https://www.ncbi.nlm.nih.gov/books/NBK556137/ + @@ -6947,6 +7099,8 @@ Despite their overarching function in the support and protection of neurons, gli FMA:86740 ZFA:0009127 + + photoreceptor cell https://www.swissbiopics.org/api/image/Photoreceptor_cell.svg @@ -6977,6 +7131,8 @@ Despite their overarching function in the support and protection of neurons, gli A cell whose function is determined by the generation or the reception of an electric signal. ZFA:0009128 + + electrically active cell @@ -7017,6 +7173,8 @@ Despite their overarching function in the support and protection of neurons, gli A cell that moves by its own activities. ZFA:0009136 + + motile cell @@ -7049,6 +7207,9 @@ Despite their overarching function in the support and protection of neurons, gli FMA:72549 ZFA:0009137 ectoderm cell + + + ectodermal cell @@ -7078,11 +7239,18 @@ Despite their overarching function in the support and protection of neurons, gli A cell of the middle germ layer of the embryo. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Mesodermal cells are pluripotent and the most abundant in the human body. They contribute to the development of several structures such as the skeletal muscles, bones, heart and blood vessels, kidneys, gonads, connective tissues, and certain layers of the skin. Hence, the mesoderm is often regarded as an active and diverse layer due to its role in forming many bodily structures. +In embryonic development, these cells are instrumental, contributing to the body's structures through a carefully coordinated sequence of morphogenetic movements. This process forms the complex multicellular architecture of tissues and organs from a simple ball of cells. Without the function of mesodermal cells, the body's integral structures and systems would cease to form correctly, leading to developmental disorders such as axial mesodermal dysplasia complex FMA:72554 ZFA:0009138 + https://cellxgene.cziscience.com/cellguide/CL_0000222 mesoblast mesoderm cell + + mesodermal cell @@ -7091,6 +7259,17 @@ Despite their overarching function in the support and protection of neurons, gli A cell of the middle germ layer of the embryo. MESH:D008648 + + + + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Mesodermal cells are pluripotent and the most abundant in the human body. They contribute to the development of several structures such as the skeletal muscles, bones, heart and blood vessels, kidneys, gonads, connective tissues, and certain layers of the skin. Hence, the mesoderm is often regarded as an active and diverse layer due to its role in forming many bodily structures. +In embryonic development, these cells are instrumental, contributing to the body's structures through a carefully coordinated sequence of morphogenetic movements. This process forms the complex multicellular architecture of tissues and organs from a simple ball of cells. Without the function of mesodermal cells, the body's integral structures and systems would cease to form correctly, leading to developmental disorders such as axial mesodermal dysplasia complex + DOI:10.1016/j.ceb.2019.07.012 + DOI:10.5535/arm.2016.40.1.162 + https://www.sciencedirect.com/topics/biochemistry-genetics-and-molecular-biology/mesoderm + @@ -7115,6 +7294,8 @@ Despite their overarching function in the support and protection of neurons, gli FMA:72555 ZFA:0009139 endoderm cell + + endodermal cell @@ -7155,6 +7336,8 @@ Despite their overarching function in the support and protection of neurons, gli A cell with a single nucleus. + + single nucleate cell @@ -7192,6 +7375,8 @@ Despite their overarching function in the support and protection of neurons, gli A cell with more than one nucleus. multinucleated cells polynuclear cells + + multinucleate cell @@ -7244,7 +7429,8 @@ Despite their overarching function in the support and protection of neurons, gli FMA:83806 MESH:D010586 ZFA:0009140 - + + phagocyte @@ -7312,6 +7498,8 @@ Despite their overarching function in the support and protection of neurons, gli + + Morphology: Diameter 30_M-80 _M, abundant cytoplasm, low N/C ratio, eccentric nucleus. Irregular shape with pseudopods, highly adhesive. Contain vacuoles and phagosomes, may contain azurophilic granules; markers: Mouse & Human: CD68, in most cases CD11b. Mouse: in most cases F4/80+; role or process: immune, antigen presentation, & tissue remodelling; lineage: hematopoietic, myeloid. macrophage @@ -7376,6 +7564,8 @@ Despite their overarching function in the support and protection of neurons, gli + + B cell @@ -7426,7 +7616,8 @@ Despite their overarching function in the support and protection of neurons, gli Any cell that in taxon some Eukaryota. MESH:D005057 - + + eukaryotic cell @@ -7443,6 +7634,8 @@ Despite their overarching function in the support and protection of neurons, gli A cell that is specialised to accumulate a particular substance(s). + + stuff accumulating cell @@ -7460,6 +7653,8 @@ Despite their overarching function in the support and protection of neurons, gli ZFA:0009162 + + extracellular matrix secreting cell @@ -7486,6 +7681,8 @@ Despite their overarching function in the support and protection of neurons, gli A cell derived from the specialized ectoderm flanking each side of the embryonic neural plate, which after the closure of the neural tube, forms masses of cells that migrate out from the dorsal aspect of the neural tube to spread throughout the body. FMA:86667 ZFA:0007086 + + migratory neural crest cell @@ -7526,7 +7723,10 @@ Despite their overarching function in the support and protection of neurons, gli Any cell that is part of some extraembryonic structure. ZFA:0009176 + + + extraembryonic cell @@ -7549,6 +7749,8 @@ Despite their overarching function in the support and protection of neurons, gli A cell of the outer layer of a blastula that gives rise to the ectoderm after gastrulation. + + epiblast cell @@ -7580,6 +7782,8 @@ Despite their overarching function in the support and protection of neurons, gli A multifate stem cell found in skeletal muscle than can differentiate into many different cell types, including muscle. Distinct cell type from satellite cell. FMA:86767 ZFA:0009179 + + Multi-potency demonstrated ex vivo. At the time of writing, it is unclear whether the endogenous population differentiates into multiple cell types in vivo. multi-potent skeletal muscle stem cell @@ -7632,6 +7836,8 @@ Despite their overarching function in the support and protection of neurons, gli BTO:0000854 EHDAA2:0004546 FMA:72395 + + animal zygote @@ -7649,6 +7855,8 @@ Despite their overarching function in the support and protection of neurons, gli A cell whose function is determined by its response to an electric signal. ZFA:0009190 + + electrically responsive cell @@ -7672,6 +7880,8 @@ Despite their overarching function in the support and protection of neurons, gli A cell that initiates an electrical signal and passes that signal to another cell. ZFA:0009193 + + electrically signaling cell @@ -7745,7 +7955,6 @@ Despite their overarching function in the support and protection of neurons, gli - @@ -7806,6 +8015,8 @@ Despite their overarching function in the support and protection of neurons, gli veiled cell + + dendritic cell @@ -7830,6 +8041,8 @@ Despite their overarching function in the support and protection of neurons, gli A cell whose primary function is to protect the organism. + + defensive cell @@ -7851,20 +8064,22 @@ Despite their overarching function in the support and protection of neurons, gli - A connective tissue cell of an organ found in the loose connective tissue. These are most often associated with the uterine mucosa and the ovary as well as the hematopoietic system and elsewhere. + A connective tissue cell of an organ found in the loose connective tissue. BTO:0002064 FMA:83624 ZFA:0009226 + + stromal cell - A connective tissue cell of an organ found in the loose connective tissue. These are most often associated with the uterine mucosa and the ovary as well as the hematopoietic system and elsewhere. + A connective tissue cell of an organ found in the loose connective tissue. GOC:tfm MESH:D017154 @@ -7909,6 +8124,8 @@ Despite their overarching function in the support and protection of neurons, gli cardiac muscle progenitor cell cardiomyocyte progenitor cell + + cardiac muscle myoblast @@ -7949,11 +8166,19 @@ Despite their overarching function in the support and protection of neurons, gli A precursor cell destined to differentiate into smooth muscle myocytes. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +A precursor to the smooth muscle cell, the smooth muscle myoblast, is integral to various body systems, including the cardiovascular, gastrointestinal, and respiratory systems. Smooth muscle myoblasts arise from the differentiation of mesenchymal stem cells, a process tightly regulated by specific genetic factors and environmental signals. Their role extends to myogenesis, particularly in the formation of muscular tissue, especially during embryonic development. +Smooth muscle myoblasts possess distinctive cellular characteristics. In contrast to skeletal muscle myoblasts, they do not fuse to create multinucleated fibers. Instead, they differentiate into individual, uninucleated smooth muscle cells. This differentiation unfolds in two distinct phases: proliferation, marked by rapid division to increase cell numbers, and differentiation, involving structural and functional transformation into mature smooth muscle cells. This intricate process is intricately mediated by various signaling molecules and transcription factors. +Functionally, smooth muscle myoblasts and the mature muscle cells they generate play pivotal roles in various physiological processes. Smooth muscle cells orchestrate involuntary muscle responses and are integral to body systems that regulate blood flow, propel food along the digestive tract, and control airflow in the respiratory tract. These diverse functions underscore the significance of smooth muscle myoblasts in the body's growth, maintenance, and overall function. FMA:84798 ZFA:0009235 + https://cellxgene.cziscience.com/cellguide/CL_0000514 myoblast, smooth muscle satellite cell + + smooth muscle myoblast @@ -7963,6 +8188,18 @@ Despite their overarching function in the support and protection of neurons, gli GOC:tfm MESH:D032390 + + + + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +A precursor to the smooth muscle cell, the smooth muscle myoblast, is integral to various body systems, including the cardiovascular, gastrointestinal, and respiratory systems. Smooth muscle myoblasts arise from the differentiation of mesenchymal stem cells, a process tightly regulated by specific genetic factors and environmental signals. Their role extends to myogenesis, particularly in the formation of muscular tissue, especially during embryonic development. +Smooth muscle myoblasts possess distinctive cellular characteristics. In contrast to skeletal muscle myoblasts, they do not fuse to create multinucleated fibers. Instead, they differentiate into individual, uninucleated smooth muscle cells. This differentiation unfolds in two distinct phases: proliferation, marked by rapid division to increase cell numbers, and differentiation, involving structural and functional transformation into mature smooth muscle cells. This intricate process is intricately mediated by various signaling molecules and transcription factors. +Functionally, smooth muscle myoblasts and the mature muscle cells they generate play pivotal roles in various physiological processes. Smooth muscle cells orchestrate involuntary muscle responses and are integral to body systems that regulate blood flow, propel food along the digestive tract, and control airflow in the respiratory tract. These diverse functions underscore the significance of smooth muscle myoblasts in the body's growth, maintenance, and overall function. + DOI:10.1074/jbc.RA118.001739 + https://www.ncbi.nlm.nih.gov/books/NBK544225/ + https://www.sciencedirect.com/topics/medicine-and-dentistry/smooth-muscle + @@ -8010,6 +8247,8 @@ Despite their overarching function in the support and protection of neurons, gli FMA:84799 ZFA:0009236 skeletal myoblast + + skeletal muscle myoblast @@ -8039,6 +8278,8 @@ Despite their overarching function in the support and protection of neurons, gli A phagocyte in vertebrates that is able to phagocytosis. + + phagocyte (sensu Vertebrata) @@ -8059,6 +8300,8 @@ Despite their overarching function in the support and protection of neurons, gli FMA:87653 ZFA:0009238 input neuron + + afferent neuron @@ -8085,6 +8328,9 @@ Despite their overarching function in the support and protection of neurons, gli A neuron which sends impulses peripherally to activate muscles or secretory cells. ZFA:0009239 output neuron + + + efferent neuron @@ -8126,6 +8372,8 @@ Despite their overarching function in the support and protection of neurons, gli nerve cell + + These cells are also reportedly CD4-negative and CD200-positive. They are also capable of producing CD40L and IFN-gamma. neuron @@ -8168,6 +8416,8 @@ Despite their overarching function in the support and protection of neurons, gli BTO:0003217 FMA:83377 ZFA:0009249 + + Derived from UBERON:0002342 neural crest. melanoblast @@ -8248,6 +8498,8 @@ Despite their overarching function in the support and protection of neurons, gli VHOG:0001535 ZFA:0009250 + + Editors note: consider adding taxon constraint to vertebrata (PMID:18025161) lymphocyte @@ -8313,9 +8565,7 @@ Despite their overarching function in the support and protection of neurons, gli - - @@ -8360,8 +8610,13 @@ Despite their overarching function in the support and protection of neurons, gli A hematopoietic progenitor cell that is committed to the granulocyte and monocyte lineages. These cells are CD123-positive, and do not express Gata1 or Gata2 but do express C/EBPa, and Pu.1. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Granulocyte monocyte progenitor cells (GMP cells), originating from hematopoietic stem cells in the bone marrow, are a critical intermediate in myeloid cell development. Positioned at a key differentiation juncture, these cells exhibit bidirectional potential, giving rise to both granulocyte and monocyte lineages. +Their primary role is to generate mature granulocytes and monocytes, essential components of the body's innate immunity and inflammatory responses. Granulocytes, such as neutrophils, eosinophils, and basophils, contribute to the first line of defense against infections by migrating to the infection site and phagocytosing pathogens. Monocytes can differentiate into macrophages or dendritic cells, playing diverse roles in immune responses. CFU-C , Colony forming unit in culture ZFA:0009251 + https://cellxgene.cziscience.com/cellguide/CL_0000557 colony forming unit granulocyte macrophage granulocyte-macrophage progenitor granulocyte/monocyte precursor @@ -8369,6 +8624,8 @@ Despite their overarching function in the support and protection of neurons, gli CFU-GM GMP + + Originally described in the dendritic cell ontology (DC_CL:0000042)(PMID:19243617). GMPs are reportedly CD16-positive, CD32-positive, CD34-positive, CD38-positive, CD45RA-positive, CD110-negative, CD117-positive, CD123-positive, and SCA1-negative. granulocyte monocyte progenitor cell @@ -8390,6 +8647,17 @@ Despite their overarching function in the support and protection of neurons, gli http://en.wikipedia.org/wiki/CFU-GM http://www.copewithcytokines.de + + + + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Granulocyte monocyte progenitor cells (GMP cells), originating from hematopoietic stem cells in the bone marrow, are a critical intermediate in myeloid cell development. Positioned at a key differentiation juncture, these cells exhibit bidirectional potential, giving rise to both granulocyte and monocyte lineages. +Their primary role is to generate mature granulocytes and monocytes, essential components of the body's innate immunity and inflammatory responses. Granulocytes, such as neutrophils, eosinophils, and basophils, contribute to the first line of defense against infections by migrating to the infection site and phagocytosing pathogens. Monocytes can differentiate into macrophages or dendritic cells, playing diverse roles in immune responses. + DOI:10.1016/j.immuni.2017.10.021 + DOI:10.1146/annurev-immunol-081022113627 + DOI:10.1186/2050-7771-2-1 + @@ -8463,7 +8731,6 @@ Despite their overarching function in the support and protection of neurons, gli - @@ -8488,6 +8755,8 @@ Despite their overarching function in the support and protection of neurons, gli FMA:83551 ZFA:0009253 + + Morphology: Mononuclear cell, diameter 14-18 _M, fine azurophilic granules; markers: CD11b (shared with many other myeloid cells); location: Adult: bone marrow; Fetal: Liver, Yolk Sac; role or process: hematopoiesis, monocyte development; lineage: hematopoietic, myeloid. promonocyte @@ -8538,7 +8807,6 @@ Despite their overarching function in the support and protection of neurons, gli - @@ -8567,6 +8835,8 @@ Despite their overarching function in the support and protection of neurons, gli ZFA:0009258 angioblast chondroplast + + These cells are reportedly CD31-positive, CD34-positive, CD144-positive, CD309-positive, and TAL1-positive. angioblastic mesenchymal cell @@ -8655,6 +8925,8 @@ Despite their overarching function in the support and protection of neurons, gli + + Morphology: Mononuclear cell, diameter, 14 to 20 _M, N/C ratio 2:1-1:1. Nucleus may appear in variety of shapes: round, kidney, lobulated, or convoluted. Fine azurophilic granules present; markers: CD11b (shared with other myeloid cells), human: CD14, mouse: F4/80-mid,GR1-low; location: Blood, but can be recruited into tissues; role or process: immune & tissue remodelling; lineage: hematopoietic, myeloid. monocyte @@ -8761,6 +9033,8 @@ Despite their overarching function in the support and protection of neurons, gli NK cell + + natural killer cell @@ -8812,6 +9086,8 @@ Despite their overarching function in the support and protection of neurons, gli A non-terminally differentiated cell that is capable of developing into a muscle cell. ZFA:0009291 + + muscle precursor cell @@ -8854,6 +9130,8 @@ Despite their overarching function in the support and protection of neurons, gli CALOHA:TS-2086 MESH:D053687 ZFA:0009307 + + somatic stem cell @@ -8908,6 +9186,8 @@ Despite their overarching function in the support and protection of neurons, gli CALOHA:TS-2157 FMA:86936 ZFA:0005784 + + striated muscle cell @@ -8984,6 +9264,8 @@ Despite their overarching function in the support and protection of neurons, gli white blood cell immune cell + + leukocyte @@ -9058,19 +9340,26 @@ Despite their overarching function in the support and protection of neurons, gli Cardiac muscle cells are striated muscle cells that are responsible for heart contraction. In mammals, the contractile fiber resembles those of skeletal muscle but are only one third as large in diameter, are richer in sarcoplasm, and contain centrally located instead of peripheral nuclei. - FMA:83808 + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Cardiac muscle cells, also known as cardiomyocytes or cardiac myocytes, are specialized cells that form the heart tissue. These cells are elongated, branched, and contain a single centrally located nucleus. Their anatomy is composed primarily of densely packed myofibrils, which are protein structures that consist of sarcomeres - the fundamental units of muscle contraction. Cardiac muscle cells are united at their ends through specialized junctions known as intercalated discs, which allow the heart to contract in a unified, powerful and rhythmic way. +Functionally, cardiac muscle cells are responsible for the heart's consistent pumping action that circulates blood throughout the body. Unlike most cells in the body, cardiac muscle cells spontaneously depolarize and generate action potentials without external stimulation. This unique trait stems from the presence of ion channels in the cells' membrane that allow a cyclic flow of ions across the membrane, which create the electrical impulses necessary for heart contraction. The spread of these electrical signals from one cardiac muscle cell to another - facilitated by the interconnected network made by the intercalated disks - results in a synchronized contraction of the heart muscle. +Unlike skeletal muscle cells which can tire and need rest, cardiac muscle cells have to work ceaselessly throughout the entire lifespan, without the opportunity for rest, to ensure continuous circulation of blood. This is made possible through the high volume of mitochondria and a constant supply of oxygen from coronary circulation. In conclusion, cardiac muscle cells, through their unique structure and vital functionality, play a pivotal role in sustaining life by providing the means for blood to reach every cell in the body. cardiocyte BTO:0001539 CALOHA:TS-0115 FMA:14067 MESH:D032383 ZFA:0009316 + https://cellxgene.cziscience.com/cellguide/CL_0000746 cardiac muscle fiber cardiac myocyte cardiomyocyte heart muscle cell + + This class encompasses the muscle cells responsible for heart* contraction in both vertebrates and arthropods. The ultrastucture of a wide range of arthropod heart cells has been examined including spiders, horseshoe crabs, crustaceans (see Sherman, 1973 and refs therein) and insects (see Lehmacher et al (2012) and refs therein). According to these refs, the cells participating in heart contraction in all cases are transversely striated. Insects hearts additionally contain ostial cells, also transversely striated muscle cells, but which do not participate in heart contraction. cardiac muscle cell @@ -9085,6 +9374,19 @@ Despite their overarching function in the support and protection of neurons, gli PMID:22426062 PMID:4711263 + + + + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Cardiac muscle cells, also known as cardiomyocytes or cardiac myocytes, are specialized cells that form the heart tissue. These cells are elongated, branched, and contain a single centrally located nucleus. Their anatomy is composed primarily of densely packed myofibrils, which are protein structures that consist of sarcomeres - the fundamental units of muscle contraction. Cardiac muscle cells are united at their ends through specialized junctions known as intercalated discs, which allow the heart to contract in a unified, powerful and rhythmic way. +Functionally, cardiac muscle cells are responsible for the heart's consistent pumping action that circulates blood throughout the body. Unlike most cells in the body, cardiac muscle cells spontaneously depolarize and generate action potentials without external stimulation. This unique trait stems from the presence of ion channels in the cells' membrane that allow a cyclic flow of ions across the membrane, which create the electrical impulses necessary for heart contraction. The spread of these electrical signals from one cardiac muscle cell to another - facilitated by the interconnected network made by the intercalated disks - results in a synchronized contraction of the heart muscle. +Unlike skeletal muscle cells which can tire and need rest, cardiac muscle cells have to work ceaselessly throughout the entire lifespan, without the opportunity for rest, to ensure continuous circulation of blood. This is made possible through the high volume of mitochondria and a constant supply of oxygen from coronary circulation. In conclusion, cardiac muscle cells, through their unique structure and vital functionality, play a pivotal role in sustaining life by providing the means for blood to reach every cell in the body. + DOI:10.1016/j.ccep.2010.10.012 + DOI:10.1038/nrcardio.2016.203 + https://www.ncbi.nlm.nih.gov/books/NBK572070 + https://www.sciencedirect.com/topics/agricultural-and-biological-sciences/cardiac-muscle + @@ -9128,6 +9430,8 @@ Despite their overarching function in the support and protection of neurons, gli MESH:D022423 ZFA:0009324 + + myeloid cell @@ -9170,6 +9474,8 @@ Despite their overarching function in the support and protection of neurons, gli A cell of the monocyte, granulocyte, or mast cell lineage. ZFA:0009326 + + myeloid leukocyte @@ -9232,6 +9538,8 @@ Despite their overarching function in the support and protection of neurons, gli CD11c+CD123- DC mDC + + These cells are CD1a-negative, CD1b-positive, CD11a-positive, CD11c-positive, CD13-positive, CD14-negative, CD20-negative, CD21-negative, CD33-positive, CD40-negative, CD50-positive, CD54-positive, CD58-positive, CD68-negative, CD80-negative, CD83-negative, CD85j-positive, CD86-positive, CD89-negative, CD95-positive, CD120a-negative, CD120b-positive, CD123-negative, CD178-negative, CD206-negative, CD207-negative, CD209-negative, and TNF-alpha-negative. Upon TLR stimulation, they are capable of producing high levels of TNF-alpha, IL-6, CXCL8 (IL-8). myeloid dendritic cell @@ -9288,7 +9596,6 @@ Despite their overarching function in the support and protection of neurons, gli - @@ -9338,6 +9645,8 @@ Despite their overarching function in the support and protection of neurons, gli pro-natural killer cell null cell preNK cell + + Most markers only described for human pro NK cells. pro-NK cell @@ -9411,7 +9720,6 @@ Despite their overarching function in the support and protection of neurons, gli - @@ -9450,6 +9758,8 @@ Despite their overarching function in the support and protection of neurons, gli progenitor B-lymphocyte pre-B cell (Philadelphia nomenclature) + + Human pro-B cells are reportedly CD10-positive, CD22-positive, CD34-positive, CD38-positive, CD45-low, CD48-positive, CD79a-positive, CD127-positive, CD184-positive, RAG-positive, TdT-positive, Vpre-B-positive, pre-BCR-negative, IgD-negative, and IgM-negative. Transcription factors expressed: Pax5-positive, EBF-positive, E2A-negative, Ikaros-negative, and PU.1-negative. pro-B cell @@ -9527,6 +9837,8 @@ Despite their overarching function in the support and protection of neurons, gli DN1 thymocyte TN1 cell + + pro-T cell @@ -9623,7 +9935,6 @@ Despite their overarching function in the support and protection of neurons, gli - @@ -9730,6 +10041,8 @@ Despite their overarching function in the support and protection of neurons, gli hemopoietic progenitor cell + + Markers differ between mouse and human. hematopoietic multipotent progenitor cell @@ -9781,6 +10094,8 @@ Despite their overarching function in the support and protection of neurons, gli FMA:70338 ZFA:0009355 + + Note that this is a class of cell types, not an identified single cell type. lymphoid lineage restricted progenitor cell @@ -9836,6 +10151,8 @@ Despite their overarching function in the support and protection of neurons, gli FMA:70339 ZFA:0009356 + + Note that this is a class of cell types, not an identified single cell type. myeloid lineage restricted progenitor cell @@ -9888,6 +10205,8 @@ Despite their overarching function in the support and protection of neurons, gli peripheral blood mononuclear cell + + mononuclear cell @@ -9923,6 +10242,9 @@ Despite their overarching function in the support and protection of neurons, gli A lymphocyte of B lineage with the commitment to express an immunoglobulin complex. + + + Types of B lineage lymphocytes include B cells and antibody secreting cells (plasmablasts and plasma cells). Lymphocytes of B cell lineage can be distinguished from those of T cell lineage by their lack of CD3e (as part of the T cell receptor complex). lymphocyte of B lineage @@ -9960,6 +10282,8 @@ Despite their overarching function in the support and protection of neurons, gli haemopoietic cell hemopoietic cell + + hematopoietic cell @@ -10010,6 +10334,8 @@ Despite their overarching function in the support and protection of neurons, gli type 1 DC + + Originally described in the dendritic cell ontology (DC_CL:0000003)(PMID:19243617) These cells are also CD20-negative, MHCII-positive. conventional dendritic cell @@ -10035,6 +10361,9 @@ Despite their overarching function in the support and protection of neurons, gli + + + Originally described in the dendritic cell ontology (DC_CL:1110000)(PMID:19243617). CD7-negative lymphoid progenitor OR granulocyte monocyte progenitor @@ -10065,8 +10394,17 @@ Despite their overarching function in the support and protection of neurons, gli A connective tissue cell found in bone. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Bone cells, also known as osteocytes, form the building blocks of the skeletal system. They represent the most common type of bone cell, making up approximately 95% of the total bone cell population in mature adult bone tissue. Osteocytes are a stellate shape with numerous long, slender dendritic processes. +The formation of bone is a complex process involving the action of osteoclasts - cells that break down and reabsorb old bone, followed by osteoblasts that rebuild the bone. Osteocytes serve as coordinators for these two types of bone cells to ensure a balance in the bone remodeling process, contributing to maintaining both bone strength and mineral homeostasis. +The primary functions of osteocytes involve the creation, maintenance, and repair of bone tissue. They ensure that bone remodeling is performed by forming a network within the bone and communicating with other cells to help them respond to mechanical strain and damage. +A remarkable aspect of osteocytes is their ability to perceive mechanical forces, translating them into biochemical signals that regulate bone remodeling and adaptation. Defects in osteocyte function, aside from other bone cells, have been associated with several bone disorders such as osteoporosis, renal osteodystrophy, and skeletal manifestations of diabetes. 2011-11-16T04:28:16Z + https://cellxgene.cziscience.com/cellguide/CL_0001035 + + bone cell @@ -10077,6 +10415,20 @@ Despite their overarching function in the support and protection of neurons, gli GOC:add GO_REF:0000034 + + + + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Bone cells, also known as osteocytes, form the building blocks of the skeletal system. They represent the most common type of bone cell, making up approximately 95% of the total bone cell population in mature adult bone tissue. Osteocytes are a stellate shape with numerous long, slender dendritic processes. +The formation of bone is a complex process involving the action of osteoclasts - cells that break down and reabsorb old bone, followed by osteoblasts that rebuild the bone. Osteocytes serve as coordinators for these two types of bone cells to ensure a balance in the bone remodeling process, contributing to maintaining both bone strength and mineral homeostasis. +The primary functions of osteocytes involve the creation, maintenance, and repair of bone tissue. They ensure that bone remodeling is performed by forming a network within the bone and communicating with other cells to help them respond to mechanical strain and damage. +A remarkable aspect of osteocytes is their ability to perceive mechanical forces, translating them into biochemical signals that regulate bone remodeling and adaptation. Defects in osteocyte function, aside from other bone cells, have been associated with several bone disorders such as osteoporosis, renal osteodystrophy, and skeletal manifestations of diabetes. + DOI:10.1007/s00795-015-0099-y + DOI:10.1007/s11914-012-0105-4 + DOI:10.1016/j.jot.2021.04.005 + DOI:10.1038/s41413-020-0099-y + @@ -10218,6 +10570,8 @@ Despite their overarching function in the support and protection of neurons, gli A hematopoietic oligopotent progenitor cell that has the ability to differentiate into limited cell types but lacks lineage cell markers and self renewal capabilities. Cell lacks hematopoeitic lineage markers. 2010-01-06T03:43:27Z + + hematopoietic oligopotent progenitor cell, lineage-negative @@ -10287,6 +10641,8 @@ Despite their overarching function in the support and protection of neurons, gli 2017-01-30T20:20:48Z + + innate lymphoid cell @@ -10327,6 +10683,8 @@ Despite their overarching function in the support and protection of neurons, gli 2017-01-30T20:42:44Z + + group 1 innate lymphoid cell @@ -10385,6 +10743,8 @@ Despite their overarching function in the support and protection of neurons, gli 2010-01-19T02:51:58Z MDP + + macrophage dendritic cell progenitor @@ -10436,6 +10796,8 @@ Despite their overarching function in the support and protection of neurons, gli 2010-01-06T03:43:20Z + + hematopoietic lineage restricted progenitor cell @@ -10480,6 +10842,8 @@ Despite their overarching function in the support and protection of neurons, gli 2010-01-06T03:43:27Z + + This cell type is intended to be compatible with any vertebrate hematopoietic oligopotent progenitor cell. For mammalian hematopoietic oligopotent progenitor cells known to be lineage-negative, please use the term 'hematopoietic oligopotent progenitor cell' (CL_0001060). hematopoietic oligopotent progenitor cell @@ -10520,6 +10884,8 @@ Despite their overarching function in the support and protection of neurons, gli 2010-06-29T03:38:22Z FMA:69074 ZFA:0009385 + + ecto-epithelial cell @@ -10566,6 +10932,8 @@ Despite their overarching function in the support and protection of neurons, gli FMA:83621 MESH:D001854 + + MH consider whether bone marrow cells are bone cells in the structural sense vs. being part of bone organ sense. bone marrow cell @@ -10610,6 +10978,8 @@ Despite their overarching function in the support and protection of neurons, gli 2010-08-30T01:27:48Z FMA:83552 + + monopoietic cell @@ -10652,6 +11022,8 @@ Despite their overarching function in the support and protection of neurons, gli 2010-09-07T03:32:33Z FMA:67513 + + nucleate cell @@ -10690,6 +11062,8 @@ Despite their overarching function in the support and protection of neurons, gli CALOHA:TS-2040 FMA:70333 + + neural cell @@ -10731,6 +11105,8 @@ Despite their overarching function in the support and protection of neurons, gli MESH:D003239 ZFA:0009392 + + connective tissue cell @@ -10755,11 +11131,19 @@ Despite their overarching function in the support and protection of neurons, gli A cell of the embryo. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Embryonic cells in metazoans, which include all multicellular animals, are biological units in their earliest developmental stages from conception until the organism is fully formed. +They are derived from a fertilized egg, which undergoes a series of cell divisions to produce a multicellular organism. During the early phases of embryonic development, these cells exhibit pluripotency, meaning they possess the potential to differentiate into a diverse array of specialized cell types that constitute different body tissues and structures. +The balance between cell proliferation and differentiation in embryonic cells is crucial for successful development. When cells continue to divide without differentiating, overgrowth may occur leading to conditions such as teratomas (tumors of embryonic cells). Conversely, if cell differentiation proceeds at the expense of cell proliferation, developmental anomalies could occur regarding size or mass of the organism or its parts. 2010-09-15T03:39:21Z CALOHA:TS-0263 FMA:82840 WBbt:0007028 ZFA:0007089 + https://cellxgene.cziscience.com/cellguide/CL_0002321 + + embryonic cell (metazoa) @@ -10768,6 +11152,18 @@ Despite their overarching function in the support and protection of neurons, gli A cell of the embryo. FMA:0618947256 + + + + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Embryonic cells in metazoans, which include all multicellular animals, are biological units in their earliest developmental stages from conception until the organism is fully formed. +They are derived from a fertilized egg, which undergoes a series of cell divisions to produce a multicellular organism. During the early phases of embryonic development, these cells exhibit pluripotency, meaning they possess the potential to differentiate into a diverse array of specialized cell types that constitute different body tissues and structures. +The balance between cell proliferation and differentiation in embryonic cells is crucial for successful development. When cells continue to divide without differentiating, overgrowth may occur leading to conditions such as teratomas (tumors of embryonic cells). Conversely, if cell differentiation proceeds at the expense of cell proliferation, developmental anomalies could occur regarding size or mass of the organism or its parts. + DOI:10.1002/iub.1404 + DOI:10.1093/molehr/gan048 + https://www.ncbi.nlm.nih.gov/books/NBK9906/ + @@ -10813,6 +11209,9 @@ Despite their overarching function in the support and protection of neurons, gli FBbt:00005812 myofiber myofibril + + + myotube @@ -10874,6 +11273,8 @@ Despite their overarching function in the support and protection of neurons, gli FMA:83808 FMA:84791 heart cell + + From Onard of the FMA: Cardiac muscle cell or cardiac myocyte is a striated muscle cell. Cardiocyte on the other hand is any cell in the heart which includes cells other than muscle cells (e.g. endothelial cell of endocardium). Unless there is a consensus among anatomists that cardiocytes refer only to muscle cells, we will treat them as a general class of cells in the heart. cardiocyte @@ -10894,6 +11295,8 @@ Despite their overarching function in the support and protection of neurons, gli 2012-06-15T02:51:27Z scleroblast + + Needs logical definition. Should be capable_of skeletal system morphogenesis? or skeletal tissue development? needs to be added to GO. NOTES:a cell type of the early embryo (see also: mesenchymal cells) that will give rise to mineralized connective tissue. Scleroblasts can differentiate into osteoblasts (bone-forming cells), chondroblasts (cartilage-forming cells), odontoblasts (dentin-forming cells), ameloblasts (enamel-forming cells). The mesenchymal cells developing into osteoblasts and chondroblasts are derived from the mesoderm. Those developing into odontoblasts are neural crest cells. Those developing into ameloblasts are derived from the ectoderm. (http://www.copewithcytokines.de/cope.cgi?key=scleroblasts) skeletogenic cell @@ -10932,6 +11335,8 @@ Despite their overarching function in the support and protection of neurons, gli 2012-06-27T08:27:35Z ZFA:0007084 + + premigratory neural crest cell @@ -10954,6 +11359,8 @@ Despite their overarching function in the support and protection of neurons, gli Any muscle cell in which the fibers are not organised into sarcomeres. + + non-striated muscle cell @@ -10971,6 +11378,8 @@ Despite their overarching function in the support and protection of neurons, gli Any hematopoietic cell that is a precursor of some other hematopoietic cell type. + + hematopoietic precursor cell @@ -11019,6 +11428,8 @@ Despite their overarching function in the support and protection of neurons, gli A transversely striated, synctial cell of skeletal muscle. It is formed when proliferating myoblasts exit the cell cycle, differentiate and fuse. MESH:D018485 + + skeletal muscle fiber @@ -11054,6 +11465,8 @@ Despite their overarching function in the support and protection of neurons, gli A muscle cell that is part of some visceral muscle. FBbt:00005070 + + visceral muscle cell @@ -11092,6 +11505,8 @@ Despite their overarching function in the support and protection of neurons, gli mesenchyme cell + + mesenchymal cell @@ -11122,6 +11537,8 @@ Despite their overarching function in the support and protection of neurons, gli Any neuron that is capable of part of some visual perception. 2017-07-09T19:12:36Z + + visual system neuron @@ -11157,6 +11574,8 @@ Despite their overarching function in the support and protection of neurons, gli Any cell in the retina, the innermost layer or coating at the back of the eyeball, which is sensitive to light and in which the optic nerve terminates. PMID:10702418 + + retinal cell @@ -11174,6 +11593,8 @@ Despite their overarching function in the support and protection of neurons, gli A zygote in a plant or an animal. MESH:D015053 + + zygote @@ -11203,6 +11624,8 @@ Despite their overarching function in the support and protection of neurons, gli Any myoblast that develops into some cardiac muscle cell. MESH:D032386 + + cardiac myoblast @@ -11220,13 +11643,15 @@ Despite their overarching function in the support and protection of neurons, gli A cell of the neural crest. Neural crest cells are multipotent. Premigratory neural crest cells are found at the neural plate boarder, some of which will undergo ectomesynchymal transition and delamination to form migratory neural crest cells. - This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. Neural crest cells are a group of transient and highly migratory cells that originate from the neuroectoderm during the early stages of embryonic development. They are multipotent cells with an exceptional degree of plasticity, capable of differentiating into various somatic cell types and therefore play a fundamental role in the formation of various organs and tissues, making them critical contributors to the developing embryo. After the initiation of neurulation (the formation of the neural tube) neural crest cells start to undergo epithelial-to-mesenchymal transition and delaminate and migrate from the dorsal neural tube to several regions throughout the embryo. They differentiate into a range of diverse cell types, such as neurons and glial cells of the peripheral nervous system, including sensory and autonomic neurons. They also contribute to the formation of adrenal glands, pigment cells in the skin (melanocytes), cardiac structures, including parts of the heart septum and major arteries, as well as bones and cartilage of the face and skull. Disorders or aberrations in the development or migration of the neural crest cells can lead to serious congenital malformations, such as neurocristopathies, including Hirschsprung disease, neuroblastoma, and neurofibromatosis. https://cellxgene.cziscience.com/cellguide/CL_0011012 + + neural crest cell @@ -11239,7 +11664,7 @@ Disorders or aberrations in the development or migration of the neural crest cel - This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. Neural crest cells are a group of transient and highly migratory cells that originate from the neuroectoderm during the early stages of embryonic development. They are multipotent cells with an exceptional degree of plasticity, capable of differentiating into various somatic cell types and therefore play a fundamental role in the formation of various organs and tissues, making them critical contributors to the developing embryo. After the initiation of neurulation (the formation of the neural tube) neural crest cells start to undergo epithelial-to-mesenchymal transition and delaminate and migrate from the dorsal neural tube to several regions throughout the embryo. They differentiate into a range of diverse cell types, such as neurons and glial cells of the peripheral nervous system, including sensory and autonomic neurons. They also contribute to the formation of adrenal glands, pigment cells in the skin (melanocytes), cardiac structures, including parts of the heart septum and major arteries, as well as bones and cartilage of the face and skull. @@ -11277,6 +11702,8 @@ Disorders or aberrations in the development or migration of the neural crest cel A precursor cell that has a tendency to differentiate into a specific type of cell. They are descendants of stem cells, only they are more constrained in their differentiation potential or capacity for self-renewal, and are often more limited in both senses. + + progenitor cell @@ -11312,6 +11739,8 @@ Disorders or aberrations in the development or migration of the neural crest cel A cell that, by division or terminal differentiation, can give rise to other cell types. + + Work is needed on GO 'cell differentiation' before it is clear whether the equivalent class definition 'native cell' that capable_of some 'cell differentiation' works. Also, may want to consider merging this with non-terminally differentiated cell. precursor cell @@ -11420,6 +11849,8 @@ Disorders or aberrations in the development or migration of the neural crest cel CALOHA:TS-2109 bone marrow hematopoietic cells bone marrow poietic cells + + bone marrow hematopoietic cell @@ -11473,6 +11904,8 @@ Disorders or aberrations in the development or migration of the neural crest cel 2024-08-15T10:38:46Z syncytium SC + + syncytial cell @@ -11560,9 +11993,6 @@ Disorders or aberrations in the development or migration of the neural crest cel The ordered and organized complex of DNA, protein, and sometimes RNA, that forms the chromosome. https://github.com/geneontology/go-ontology/issues/28301 - GO:0000789 - GO:0000790 - GO:0005717 NIF_Subcellular:sao1615953555 cytoplasmic chromatin nuclear chromatin @@ -11588,8 +12018,6 @@ Disorders or aberrations in the development or migration of the neural crest cel A dispersed and relatively uncompacted form of chromatin that is in a transcription-competent conformation. https://github.com/geneontology/go-ontology/issues/22355 - GO:0005719 - GO:0035327 NIF_Subcellular:sao445485807 Wikipedia:Euchromatin transcriptionally active chromatin @@ -11613,8 +12041,6 @@ Disorders or aberrations in the development or migration of the neural crest cel A compact and highly condensed form of chromatin that is refractory to transcription. https://github.com/geneontology/go-ontology/issues/22355 - GO:0005720 - GO:0035328 NIF_Subcellular:sao581845896 Wikipedia:Heterochromatin transcriptionally inactive chromatin @@ -11969,10 +12395,6 @@ Disorders or aberrations in the development or migration of the neural crest cel The appearance of a cytokine due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. https://github.com/geneontology/go-ontology/issues/19116 - GO:0042032 - GO:0042089 - GO:0042107 - GO:0050663 cytokine biosynthetic process cytokine metabolic process cytokine secretion @@ -12080,7 +12502,6 @@ Disorders or aberrations in the development or migration of the neural crest cel The formation of a tube from the flat layer of ectodermal cells known as the neural plate. This will give rise to the central nervous system. - GO:0001679 Wikipedia:Neurulation neural tube morphogenesis neurulation @@ -12433,8 +12854,6 @@ Disorders or aberrations in the development or migration of the neural crest cel The appearance of immunoglobulin due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. - GO:0002378 - GO:0048305 antibody production immunoglobulin biosynthetic process immunoglobulin secretion @@ -12512,8 +12931,6 @@ Disorders or aberrations in the development or migration of the neural crest cel Any process involved in the carrying out of an immune response by a leukocyte. - GO:0019723 - GO:0042087 immune cell effector process immune cell mediated immunity leucocyte immune effector process @@ -12964,7 +13381,6 @@ Disorders or aberrations in the development or migration of the neural crest cel A location, relative to cellular compartments and structures, occupied by a macromolecular machine. There are three types of cellular components described in the gene ontology: (1) the cellular anatomical entity where a gene product carries out a molecular function (e.g., plasma membrane, cytoskeleton) or membrane-enclosed compartments (e.g., mitochondrion); (2) virion components, where viral proteins act, and (3) the stable macromolecular complexes of which gene product are parts (e.g., the clathrin complex). https://github.com/geneontology/go-ontology/issues/17729 - GO:0008372 NIF_Subcellular:sao1337158144 cell or subcellular entity cellular component @@ -13034,32 +13450,32 @@ Disorders or aberrations in the development or migration of the neural crest cel - - + + A protein complex consisting of three collagen chains assembled into a left-handed triple helix. These trimers typically assemble into higher order structures. Wikipedia:Collagen cellular_component GO:0005581 collagen trimer - + - + - + PMID:12382326 - + PMID:12382326 @@ -13102,8 +13518,6 @@ Disorders or aberrations in the development or migration of the neural crest cel A collagen-containing extracellular matrix consisting of a thin layer of dense material found in various animal tissues interposed between the cells and the adjacent connective tissue. It consists of the basal lamina plus an associated layer of reticulin fibers. - GO:0005605 - GO:0008003 Wikipedia:Basement_membrane cellular_component basal lamina @@ -13430,8 +13844,6 @@ Disorders or aberrations in the development or migration of the neural crest cel The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins. - GO:0005887 - GO:0005904 juxtamembrane NIF_Subcellular:sao1663586795 Wikipedia:Cell_membrane @@ -13522,7 +13934,6 @@ Disorders or aberrations in the development or migration of the neural crest cel Any cellular metabolic process involving deoxyribonucleic acid. This is one of the two main types of nucleic acid, consisting of a long, unbranched macromolecule formed from one, or more commonly, two, strands of linked deoxyribonucleotides. - GO:0055132 DNA metabolism cellular DNA metabolism biological_process @@ -13601,9 +14012,6 @@ Disorders or aberrations in the development or migration of the neural crest cel The cellular metabolic process in which a protein is formed, using the sequence of a mature mRNA or circRNA molecule to specify the sequence of amino acids in a polypeptide chain. Translation is mediated by the ribosome, and begins with the formation of a ternary complex between aminoacylated initiator methionine tRNA, GTP, and initiation factor 2, which subsequently associates with the small subunit of the ribosome and an mRNA or circRNA. Translation ends with the release of a polypeptide chain from the ribosome. - GO:0006416 - GO:0006453 - GO:0043037 Wikipedia:Translation_(genetics) protein anabolism protein biosynthesis @@ -13636,7 +14044,7 @@ Disorders or aberrations in the development or migration of the neural crest cel - + @@ -13650,8 +14058,6 @@ Disorders or aberrations in the development or migration of the neural crest cel The process preceding formation of the peptide bond between the first two amino acids of a protein. This includes the formation of a complex of the ribosome, mRNA or circRNA, and an initiation complex that contains the first aminoacyl-tRNA. - GO:0006440 - GO:0006454 biopolymerisation biopolymerization protein synthesis initiation @@ -13681,8 +14087,6 @@ Disorders or aberrations in the development or migration of the neural crest cel The successive addition of amino acid residues to a nascent polypeptide chain during protein biosynthesis. - GO:0006442 - GO:0006455 protein synthesis elongation translation elongation biological_process @@ -13710,8 +14114,6 @@ Disorders or aberrations in the development or migration of the neural crest cel The process resulting in the release of a polypeptide chain from the ribosome, usually in response to a termination codon (UAA, UAG, or UGA in the universal genetic code). - GO:0006443 - GO:0006456 protein synthesis termination translation termination translational complex disassembly @@ -13735,11 +14137,7 @@ Disorders or aberrations in the development or migration of the neural crest cel The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter or a transporter complex, a pore or a motor protein. https://github.com/geneontology/go-ontology/issues/20292 - jl 2012-12-13T16:25:32Z - GO:0015457 - GO:0015460 - GO:0044765 biological_process single-organism transport GO:0006810 @@ -13818,8 +14216,6 @@ Disorders or aberrations in the development or migration of the neural crest cel A process of secretion by a cell that results in the release of intracellular molecules (e.g. hormones, matrix proteins) contained within a membrane-bounded vesicle. Exocytosis can occur either by full fusion, when the vesicle collapses into the plasma membrane, or by a kiss-and-run mechanism that involves the formation of a transient contact, a pore, between a granule (for example of chromaffin cells) and the plasma membrane. The latter process most of the time leads to only partial secretion of the granule content. Exocytosis begins with steps that prepare vesicles for fusion with the membrane (tethering and docking) and ends when molecules are secreted from the cell. - GO:0016194 - GO:0016195 Wikipedia:Exocytosis vesicle exocytosis biological_process @@ -13865,9 +14261,6 @@ Disorders or aberrations in the development or migration of the neural crest cel A vesicle-mediated transport process in which cells take up external materials or membrane constituents by the invagination of a part of the plasma membrane to form a new membrane-bounded vesicle. https://github.com/geneontology/go-ontology/issues/24907 https://github.com/geneontology/go-ontology/issues/25268 - GO:0016193 - GO:0016196 - GO:0098701 Wikipedia:Endocytosis endocytic import into cell vesicle endocytosis @@ -13902,10 +14295,7 @@ Disorders or aberrations in the development or migration of the neural crest cel The evagination of a membrane, resulting in formation of a vesicle. - jl 2013-12-19T15:26:17Z - GO:0006902 - GO:1902591 membrane evagination vesicle biosynthesis vesicle formation @@ -14105,9 +14495,7 @@ Disorders or aberrations in the development or migration of the neural crest cel A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of an organelle within a cell. An organelle is an organized structure of distinctive morphology and function. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton. Excludes the plasma membrane. https://github.com/geneontology/go-ontology/issues/27189 - jl 2013-12-19T15:25:51Z - GO:1902589 organelle organisation single organism organelle organization biological_process @@ -14574,7 +14962,6 @@ Disorders or aberrations in the development or migration of the neural crest cel The flow of blood through the body of an animal, enabling the transport of nutrients to the tissues and the removal of waste products. - GO:0070261 biological_process hemolymph circulation GO:0008015 @@ -14596,11 +14983,7 @@ Disorders or aberrations in the development or migration of the neural crest cel A biological process is the execution of a genetically-encoded biological module or program. It consists of all the steps required to achieve the specific biological objective of the module. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence. https://github.com/geneontology/go-ontology/issues/24968 - jl 2012-09-19T15:05:24Z - GO:0000004 - GO:0007582 - GO:0044699 Wikipedia:Biological_process biological process physiological process @@ -14630,21 +15013,15 @@ Disorders or aberrations in the development or migration of the neural crest cel - + - The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation. + A cellular process consisting of the biochemical pathways by which a living organism transforms chemical substances. This includes including anabolism (biosynthetic process) and catabolism (catabolic process). Metabolic processes includes the transformation of small molecules, as well macromolecular processes such as DNA repair and replication, protein synthesis and degradation. https://github.com/geneontology/go-ontology/issues/26424 - jl + https://github.com/geneontology/go-ontology/issues/28932 2012-10-17T15:46:40Z - GO:0044236 - GO:0044710 Wikipedia:Metabolism metabolism - metabolic process resulting in cell growth - metabolism resulting in cell growth - multicellular organism metabolic process biological_process - single-organism metabolic process GO:0008152 @@ -14659,7 +15036,7 @@ Disorders or aberrations in the development or migration of the neural crest cel - The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation. + A cellular process consisting of the biochemical pathways by which a living organism transforms chemical substances. This includes including anabolism (biosynthetic process) and catabolism (catabolic process). Metabolic processes includes the transformation of small molecules, as well macromolecular processes such as DNA repair and replication, protein synthesis and degradation. GOC:go_curators ISBN:0198547684 @@ -14670,11 +15047,9 @@ Disorders or aberrations in the development or migration of the neural crest cel - The chemical reactions and pathways resulting in the formation of substances; typically the energy-requiring part of metabolism in which simpler substances are transformed into more complex ones. - jl + A cellular process consisting of the biochemical pathways by which a living organism synthesizes chemical substances. This typically represents the energy-requiring part of metabolism in which simpler substances are transformed into more complex ones. + https://github.com/geneontology/go-ontology/issues/28932 2012-10-17T15:52:18Z - GO:0044274 - GO:0044711 formation Wikipedia:Anabolism anabolism @@ -14693,7 +15068,7 @@ Disorders or aberrations in the development or migration of the neural crest cel - The chemical reactions and pathways resulting in the formation of substances; typically the energy-requiring part of metabolism in which simpler substances are transformed into more complex ones. + A cellular process consisting of the biochemical pathways by which a living organism synthesizes chemical substances. This typically represents the energy-requiring part of metabolism in which simpler substances are transformed into more complex ones. GOC:curators ISBN:0198547684 @@ -14703,13 +15078,12 @@ Disorders or aberrations in the development or migration of the neural crest cel + - The chemical reactions and pathways resulting in the formation of a macromolecule, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass. https://github.com/geneontology/go-ontology/issues/15249 https://github.com/geneontology/go-ontology/issues/25418 https://github.com/geneontology/go-ontology/issues/27189 - GO:0043284 biopolymer biosynthetic process macromolecule anabolism macromolecule biosynthesis @@ -14983,7 +15357,6 @@ Disorders or aberrations in the development or migration of the neural crest cel The process whose specific outcome is the progression of an embryo from its formation until the end of its embryonic life stage. The end of the embryonic stage is organism-specific. For example, for mammals, the process would begin with zygote formation and end with birth. For insects, the process would begin at zygote formation and end with larval hatching. For plant zygotic embryos, this would be from zygote formation to the end of seed dormancy. For plant vegetative embryos, this would be from the initial determination of the cell or group of cells to form an embryo until the point when the embryo becomes independent of the parent plant. - GO:0009795 embryogenesis and morphogenesis Wikipedia:Embryogenesis embryogenesis @@ -15144,11 +15517,7 @@ Disorders or aberrations in the development or migration of the neural crest cel Any process that is carried out at the cellular level, but not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level. - jl 2012-12-11T16:56:55Z - GO:0008151 - GO:0044763 - GO:0050875 cell physiology cellular physiological process cell growth and/or maintenance @@ -15220,9 +15589,7 @@ Disorders or aberrations in the development or migration of the neural crest cel The infolding of a membrane. - jl 2013-12-02T13:58:34Z - GO:1902534 biological_process single-organism membrane invagination GO:0010324 @@ -15365,9 +15732,6 @@ Disorders or aberrations in the development or migration of the neural crest cel A lipid bilayer along with all the proteins and protein complexes embedded in it and attached to it. 2014-03-06T11:37:54Z - GO:0016021 - GO:0098589 - GO:0098805 Wikipedia:Biological_membrane Wikipedia:Transmembrane_protein integral component of membrane @@ -15426,8 +15790,6 @@ Disorders or aberrations in the development or migration of the neural crest cel A process that results in the assembly, arrangement of constituent parts, or disassembly of a cellular component. - GO:0044235 - GO:0071842 cell organisation cellular component organisation at cellular level cellular component organisation in other organism @@ -15542,7 +15904,6 @@ Disorders or aberrations in the development or migration of the neural crest cel A cellular transport process in which transported substances are moved in membrane-bounded vesicles; transported substances are enclosed in the vesicle lumen or located in the vesicle membrane. The process begins with a step that directs a substance to the forming vesicle, and includes vesicle budding and coating. Vesicles are then targeted to, and fuse with, an acceptor membrane. https://github.com/geneontology/go-ontology/issues/25421 - GO:0006899 vesicle transport vesicular transport nonselective vesicle transport @@ -15796,9 +16157,6 @@ Disorders or aberrations in the development or migration of the neural crest cel The chemical reactions and pathways involving a protein. Includes protein modification. https://github.com/geneontology/go-ontology/issues/23112 https://github.com/geneontology/go-ontology/issues/27189 - GO:0006411 - GO:0044267 - GO:0044268 Wikipedia:Protein_metabolism cellular protein metabolic process cellular protein metabolism @@ -15876,7 +16234,6 @@ Disorders or aberrations in the development or migration of the neural crest cel The process in which an antigen-presenting cell expresses antigen (peptide or lipid) on its cell surface in association with an MHC protein complex. - GO:0030333 Wikipedia:Antigen_presentation antigen presentation antigen processing @@ -15973,7 +16330,6 @@ Disorders or aberrations in the development or migration of the neural crest cel A cellular process that results in the breakdown of a cellular component. https://github.com/geneontology/go-ontology/issues/27189 - GO:0071845 cell structure disassembly cellular component disassembly at cellular level biological_process @@ -15998,9 +16354,7 @@ Disorders or aberrations in the development or migration of the neural crest cel A biological process that directly contributes to the process of producing new individuals by one or two organisms. The new individuals inherit some proportion of their genetic material from the parent or parents. https://github.com/geneontology/go-ontology/issues/27054 - jl 2012-09-19T15:56:06Z - GO:0044702 Wikipedia:Reproduction biological_process single organism reproductive process @@ -16091,7 +16445,6 @@ Disorders or aberrations in the development or migration of the neural crest cel The aggregation, arrangement and bonding together of a cellular component. - GO:0071844 cell structure assembly cellular component assembly at cellular level biological_process @@ -16194,10 +16547,7 @@ Disorders or aberrations in the development or migration of the neural crest cel The entirety of a process in which information is transmitted within a biological system. This process begins with an active signal and ends when a cellular response has been triggered. - jl 2010-02-16T09:30:50Z - GO:0023046 - GO:0044700 biological signaling signaling process signalling @@ -16497,7 +16847,6 @@ Disorders or aberrations in the development or migration of the neural crest cel The process in which a relatively unspecialized precursor cell acquires specialized features of a lymphocyte. A lymphocyte is a leukocyte commonly found in the blood and lymph that has the characteristics of a large nucleus, a neutral staining cytoplasm, and prominent heterochromatin. - GO:0046650 lymphocyte cell differentiation lymphocytic blood cell differentiation biological_process @@ -16690,8 +17039,6 @@ Disorders or aberrations in the development or migration of the neural crest cel The process in which a precursor cell type acquires characteristics of a more mature T-cell. A T cell is a type of lymphocyte whose definin characteristic is the expression of a T cell receptor complex. - GO:0042112 - GO:0046652 T lymphocyte differentiation T-cell differentiation T-lymphocyte differentiation @@ -16912,7 +17259,6 @@ Disorders or aberrations in the development or migration of the neural crest cel A structure lying external to one or more cells, which provides structural support, biochemical or biomechanical cues for cells or tissues. - GO:0005578 NIF_Subcellular:nlx_subcell_20090513 Wikipedia:Extracellular_matrix proteinaceous extracellular matrix @@ -17077,7 +17423,6 @@ Disorders or aberrations in the development or migration of the neural crest cel A vesicle found in the cytoplasm of a cell. - GO:0016023 NIF_Subcellular:sao180601769 cellular_component cytoplasmic membrane bounded vesicle @@ -17153,7 +17498,6 @@ Disorders or aberrations in the development or migration of the neural crest cel Any small, fluid-filled, spherical organelle enclosed by membrane. - GO:0031988 NIF_Subcellular:sao221389602 Wikipedia:Vesicle_(biology) cellular_component @@ -17184,10 +17528,7 @@ Disorders or aberrations in the development or migration of the neural crest cel - jl 2012-09-19T16:07:47Z - GO:0044707 - GO:0050874 organismal physiological process biological_process single-multicellular organism process @@ -17214,9 +17555,7 @@ Disorders or aberrations in the development or migration of the neural crest cel A biological process whose specific outcome is the progression of an integrated living unit: an anatomical structure (which may be a subcellular structure, cell, tissue, or organ), or organism over time from an initial condition to a later condition. - jl 2012-12-19T12:21:31Z - GO:0044767 development biological_process single-organism developmental process @@ -17240,8 +17579,6 @@ Disorders or aberrations in the development or migration of the neural crest cel The appearance of interferon-gamma due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. Interferon-gamma is also known as type II interferon. - GO:0042095 - GO:0072643 IFNG production interferon-gamma production type II IFN production @@ -17320,9 +17657,6 @@ Disorders or aberrations in the development or migration of the neural crest cel The disaggregation of a protein-containing macromolecular complex into its constituent components. https://github.com/geneontology/go-ontology/issues/22580 - GO:0034623 - GO:0043241 - GO:0043624 protein complex disassembly biological_process cellular macromolecule complex disassembly @@ -17344,10 +17678,14 @@ Disorders or aberrations in the development or migration of the neural crest cel - + + + + + + A stable assembly of two or more macromolecules, i.e. proteins, nucleic acids, carbohydrates or lipids, in which at least one component is a protein and the constituent parts function together. - GO:0043234 macromolecular complex macromolecule complex protein containing complex @@ -17461,7 +17799,6 @@ Disorders or aberrations in the development or migration of the neural crest cel A process in which a monoatomic ion is transported across a membrane. Monatomic ions (also called simple ions) are ions consisting of exactly one atom. - GO:0099131 ion transmembrane transport ion membrane transport transmembrane ion transport @@ -17814,9 +18151,6 @@ Disorders or aberrations in the development or migration of the neural crest cel Any biological process involved in the maintenance of an internal steady state. - GO:0032844 - GO:0032845 - GO:0032846 homeostasis activation of homeostatic process inhibition of homeostatic process @@ -17994,9 +18328,6 @@ Disorders or aberrations in the development or migration of the neural crest cel The chemical reactions and pathways involving macromolecules, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass. https://github.com/geneontology/go-ontology/issues/26424 - GO:0034960 - GO:0043283 - GO:0044259 biopolymer metabolic process macromolecule metabolism organismal macromolecule metabolism @@ -18113,14 +18444,17 @@ Disorders or aberrations in the development or migration of the neural crest cel Organized structure of distinctive morphology and function, not bounded by a lipid bilayer membrane. Includes ribosomes, the cytoskeleton and chromosomes. https://github.com/geneontology/go-ontology/issues/21881 https://github.com/geneontology/go-ontology/issues/28153 + https://github.com/geneontology/go-ontology/issues/29106 NIF_Subcellular:sao1456184038 + membrane-less organelle + non-membrane-bounded organelle non-membrane-enclosed organelle cellular_component biological condensate GO:0043228 - non-membrane-bounded organelle + membraneless organelle @@ -18218,11 +18552,13 @@ Disorders or aberrations in the development or migration of the neural crest cel Organized structure of distinctive morphology and function, not bounded by a lipid bilayer membrane and occurring within the cell. Includes ribosomes, the cytoskeleton and chromosomes. + https://github.com/geneontology/go-ontology/issues/29106 + intracellular non-membrane-bounded organelle intracellular non-membrane-enclosed organelle cellular_component GO:0043232 - intracellular non-membrane-bounded organelle + intracellular membraneless organelle @@ -18339,11 +18675,7 @@ Disorders or aberrations in the development or migration of the neural crest cel Any process in which macromolecules aggregate, disaggregate, or are modified, resulting in the formation, disassembly, or alteration of a protein complex. https://github.com/geneontology/go-ontology/issues/22580 - mah 2010-09-08T10:01:42Z - GO:0034600 - GO:0034621 - GO:0071822 protein complex subunit organisation protein complex subunit organization biological_process @@ -18378,7 +18710,6 @@ Disorders or aberrations in the development or migration of the neural crest cel A process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of a cellular component. Includes biosynthesis of constituent macromolecules, and those macromolecular modifications that are involved in synthesis or assembly of the cellular component. https://github.com/geneontology/go-ontology/issues/27194 - GO:0071843 cellular component biogenesis at cellular level biological_process GO:0044085 @@ -18407,7 +18738,6 @@ Disorders or aberrations in the development or migration of the neural crest cel A ribonucleoprotein complex that contains aminoacylated initiator methionine tRNA, GTP, and initiation factor 2 (either eIF2 in eukaryotes, or IF2 in prokaryotes). In prokaryotes, fMet-tRNA (initiator) is used rather than Met-tRNA (initiator). - jl 2009-10-22T02:38:55Z translation initiation (ternary) complex Met-tRNA/eIF2.GTP ternary complex @@ -18424,35 +18754,6 @@ Disorders or aberrations in the development or migration of the neural crest cel - - - - - - The chemical reactions and pathways by which individual cells transform chemical substances. - cellular metabolism - biological_process - intermediary metabolism - GO:0044237 - - This term should not be used for direct annotation. It should be possible to make a more specific annotation to one of the children of this term. - cellular metabolic process - - - - - The chemical reactions and pathways by which individual cells transform chemical substances. - GOC:go_curators - - - - - intermediary metabolism - GOC:mah - - - - @@ -18479,32 +18780,6 @@ Disorders or aberrations in the development or migration of the neural crest cel - - - - - - The chemical reactions and pathways resulting in the formation of substances, carried out by individual cells. - https://github.com/geneontology/go-ontology/issues/27052 - cellular anabolism - cellular biosynthesis - cellular formation - cellular synthesis - biological_process - GO:0044249 - - This term should not be used for direct annotation. It should be possible to make a more specific annotation to one of the children of this term. - cellular biosynthetic process - - - - - The chemical reactions and pathways resulting in the formation of substances, carried out by individual cells. - GOC:jl - - - - @@ -18555,7 +18830,6 @@ Disorders or aberrations in the development or migration of the neural crest cel The joining of the lipid bilayer membrane that surround a cell with that of another cell, producing a single cell. - GO:0006947 cell fusion cell-cell fusion biological_process @@ -18581,7 +18855,6 @@ Disorders or aberrations in the development or migration of the neural crest cel - GO:0002226 Wikipedia:Innate_immune_system innate immunity nonspecific immune response @@ -19201,7 +19474,6 @@ Disorders or aberrations in the development or migration of the neural crest cel The process in which anatomical structures are generated and organized during the embryonic phase. The embryonic phase begins with zygote formation. The end of the embryonic phase is organism-specific. For example, it would be at birth for mammals, larval hatching for insects and seed dormancy in plants. - GO:0048828 embryonic anatomical structure morphogenesis biological_process GO:0048598 @@ -19553,7 +19825,6 @@ Disorders or aberrations in the development or migration of the neural crest cel Any process that modulates the frequency, rate or extent of a biological process. Biological processes are regulated by many means; examples include the control of gene expression, protein modification or interaction with a protein or substrate molecule. - GO:0050791 regulation of physiological process biological_process GO:0050789 @@ -19629,7 +19900,6 @@ Disorders or aberrations in the development or migration of the neural crest cel Any process that modulates the frequency, rate or extent of a cellular process, any of those that are carried out at the cellular level, but are not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level. - GO:0051244 regulation of cellular physiological process biological_process GO:0050794 @@ -19782,7 +20052,6 @@ Disorders or aberrations in the development or migration of the neural crest cel Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus. The process begins with detection of the stimulus and ends with a change in state or activity or the cell or organism. - GO:0051869 physiological response to stimulus biological_process GO:0050896 @@ -19958,9 +20227,7 @@ Disorders or aberrations in the development or migration of the neural crest cel Any process in which a cell, a substance, or a cellular entity, such as a protein complex or organelle, is transported, tethered to or otherwise maintained in a specific location. In the case of substances, localization may also be achieved via selective degradation. https://github.com/geneontology/go-ontology/issues/27052 - jl 2013-12-18T13:51:04Z - GO:1902578 establishment and maintenance of localization establishment and maintenance of position localisation @@ -20157,8 +20424,6 @@ Disorders or aberrations in the development or migration of the neural crest cel Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus from another living organism. - GO:0009613 - GO:0042828 biological_process GO:0051707 response to other organism @@ -20195,9 +20460,7 @@ Disorders or aberrations in the development or migration of the neural crest cel The process in which a solute is transported across a lipid bilayer, from one side of a membrane to the other. - tb 2015-10-21T13:22:47Z - GO:0090662 membrane transport ATP hydrolysis coupled transmembrane transport biological_process @@ -20369,7 +20632,6 @@ Disorders or aberrations in the development or migration of the neural crest cel The process in which the anatomical structures of a tube are generated and organized from an epithelium. Epithelial tubes transport gases, liquids and cells from one site to another and form the basic structure of many organs and tissues, with tube shape and organization varying from the single-celled excretory organ in Caenorhabditis elegans to the branching trees of the mammalian kidney and insect tracheal system. - dph 2009-04-28T09:33:36Z biological_process GO:0060562 @@ -20406,10 +20668,7 @@ Disorders or aberrations in the development or migration of the neural crest cel A process which results in the assembly, arrangement of constituent parts, or disassembly of a membrane. A membrane is a double layer of lipid molecules that encloses all cells, and, in eukaryotes, many organelles; may be a single or double lipid bilayer; also includes associated proteins. - jl 2010-02-08T02:43:11Z - GO:0016044 - GO:0044802 cellular membrane organisation cellular membrane organization membrane organisation @@ -20469,10 +20728,7 @@ Disorders or aberrations in the development or migration of the neural crest cel The membrane organization process that joins two lipid bilayers to form a single membrane. - jl 2010-02-08T02:48:06Z - GO:0006944 - GO:0044801 Wikipedia:Lipid_bilayer_fusion cellular membrane fusion biological_process @@ -20508,7 +20764,6 @@ Disorders or aberrations in the development or migration of the neural crest cel An extracellular matrix consisting mainly of proteins (especially collagen) and glycosaminoglycans (mostly as proteoglycans) that provides not only essential physical scaffolding for the cellular constituents but can also initiate crucial biochemical and biomechanical cues required for tissue morphogenesis, differentiation and homeostasis. The components are secreted by cells in the vicinity and form a sheet underlying or overlying cells such as endothelial and epithelial cells. - dph 2018-04-13T12:47:21Z cellular_component GO:0062023 @@ -20549,9 +20804,6 @@ Disorders or aberrations in the development or migration of the neural crest cel The aggregation, arrangement and bonding together of a set of macromolecules to form a protein-containing complex. https://github.com/geneontology/go-ontology/issues/22580 - GO:0006461 - GO:0034622 - GO:0043623 cellular protein complex assembly biological_process cellular macromolecule complex assembly @@ -20727,7 +20979,6 @@ Disorders or aberrations in the development or migration of the neural crest cel Any process in which macromolecules aggregate, disaggregate, or are modified, resulting in the formation, disassembly, or alteration of a ribonucleoprotein complex. https://github.com/geneontology/go-ontology/issues/25143 - mah 2010-09-08T10:10:35Z RNA-protein complex subunit organization protein-RNA complex subunit organization @@ -20770,9 +21021,7 @@ Disorders or aberrations in the development or migration of the neural crest cel A process that results in the biosynthesis of constituent macromolecules, assembly, arrangement of constituent parts, or disassembly of a cellular component. https://github.com/geneontology/go-ontology/issues/27189 - mah 2010-09-10T01:39:16Z - GO:0071841 cellular component organisation or biogenesis cellular component organisation or biogenesis at cellular level cellular component organization or biogenesis at cellular level @@ -20810,7 +21059,6 @@ Disorders or aberrations in the development or migration of the neural crest cel The broad region around and including the plasma membrane of a cell, encompassing the cell cortex (inside the cell), the plasma membrane, and any external encapsulating structures. - mah 2010-10-04T01:51:47Z cellular_component GO:0071944 @@ -20837,7 +21085,6 @@ Disorders or aberrations in the development or migration of the neural crest cel An supramolecular fiber that consists of an insoluble core of polymerized tropoelastin monomers and a surrounding mantle of microfibrils. Elastic fibers provide elasticity and recoiling to tissues and organs, and maintain structural integrity against mechanical strain. - mah 2010-10-11T11:44:57Z elastic fibre elastin fiber @@ -20897,7 +21144,6 @@ Disorders or aberrations in the development or migration of the neural crest cel The developmental process pertaining to the initial formation of an epithelial tube. https://github.com/geneontology/go-ontology/issues/22302 - mah 2010-02-26T02:15:40Z biological_process GO:0072175 @@ -20935,7 +21181,6 @@ Disorders or aberrations in the development or migration of the neural crest cel The joining of two lipid bilayers to form a single organelle membrane. - tb 2009-12-11T11:44:58Z biological_process GO:0090174 @@ -20974,7 +21219,6 @@ Disorders or aberrations in the development or migration of the neural crest cel The process in which a precursor cell type acquires the specialized features of a dendritic cell. A dendritic cell is a leukocyte of dendritic lineage specialized in the uptake, processing, and transport of antigens to lymph nodes for the purpose of stimulating an immune response via T cell activation. - pr 2011-04-01T10:08:42Z biological_process GO:0097028 @@ -21008,7 +21252,6 @@ Disorders or aberrations in the development or migration of the neural crest cel Any vesicle that is part of the intracellular region. - pr 2016-03-29T17:39:45Z cellular_component GO:0097708 @@ -21029,9 +21272,7 @@ Disorders or aberrations in the development or migration of the neural crest cel Reactions triggered in response to the presence of another organism that act to protect the cell or organism from damage caused by that organism. https://github.com/geneontology/go-ontology/issues/22173 - dos 2013-11-11T12:59:11Z - GO:0009814 defence response incompatible interaction defence response to pathogen, incompatible interaction defense response, incompatible interaction @@ -21073,7 +21314,6 @@ Disorders or aberrations in the development or migration of the neural crest cel A membrane that is a (regional) part of the plasma membrane. - dos 2014-03-06T11:55:32Z region of plasma membrane cellular_component @@ -21150,7 +21390,6 @@ Disorders or aberrations in the development or migration of the neural crest cel - @@ -21619,7 +21858,6 @@ Disorders or aberrations in the development or migration of the neural crest cel A polymer consisting of an indefinite number of protein or protein complex subunits that have polymerised to form a fiber-shaped structure. - GO:0043205 cellular_component fibril GO:0099512 @@ -21707,21 +21945,22 @@ Disorders or aberrations in the development or migration of the neural crest cel - A part of a cellular organism that is either an immaterial entity or a material entity with granularity above the level of a protein complex but below that of an anatomical system. Or, a substance produced by a cellular organism with granularity above the level of a protein complex. + A part of a cellular organism consisting of a material entity with granularity above the level of a protein complex but below that of an anatomical system. Note that cellular organisms exclude viruses. https://github.com/geneontology/go-ontology/issues/24200 https://github.com/geneontology/go-ontology/issues/26424 - kmv + https://github.com/geneontology/go-ontology/issues/28978 2019-08-12T18:01:37Z + cellular anatomical entity cellular_component GO:0110165 - cellular anatomical entity + cellular anatomical structure - A part of a cellular organism that is either an immaterial entity or a material entity with granularity above the level of a protein complex but below that of an anatomical system. Or, a substance produced by a cellular organism with granularity above the level of a protein complex. + A part of a cellular organism consisting of a material entity with granularity above the level of a protein complex but below that of an anatomical system. Note that cellular organisms exclude viruses. GOC:kmv @@ -21750,7 +21989,6 @@ Disorders or aberrations in the development or migration of the neural crest cel A prolongation or process extending from a cell and that is bounded by plasma membrane, e.g. a cilium, lamellipodium, or axon. https://github.com/geneontology/go-ontology/issues/13193 - krc 2017-03-21T17:26:07Z cellular_component GO:0120025 @@ -21788,7 +22026,6 @@ Disorders or aberrations in the development or migration of the neural crest cel A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a plasma membrane bounded prolongation or process extending from a cell, e.g. a cilium or axon. https://github.com/geneontology/go-ontology/issues/13298 - krc 2017-04-26T16:07:02Z biological_process GO:0120036 @@ -21825,7 +22062,6 @@ Disorders or aberrations in the development or migration of the neural crest cel The cellular processes that contribute to exocytosis. - pg 2017-05-15T13:20:45Z biological_process GO:0140029 @@ -21853,7 +22089,6 @@ Disorders or aberrations in the development or migration of the neural crest cel A cellular process in which two or more cells combine together, their plasma membrane fusing, producing a single cell. In some cases, nuclei fuse, producing a polyploid cell, while in other cases, nuclei remain separate, producing a syncytium. https://github.com/geneontology/go-ontology/issues/15939 - pg 2018-08-13T18:38:18Z cell fusion cell cell fusion @@ -21903,7 +22138,6 @@ Disorders or aberrations in the development or migration of the neural crest cel The directed movement of some substance from a cell, into the extracellular region. This may occur via transport across the plasma membrane or via exocytosis. - pg 2019-05-22T11:20:45Z efflux biological_process @@ -21925,7 +22159,6 @@ Disorders or aberrations in the development or migration of the neural crest cel Reactions triggered in response to the presence of a symbiont that act to protect or prevent damage to the host. https://github.com/geneontology/go-ontology/issues/20261 - pg 2020-11-11T17:19:06Z biological_process GO:0140546 @@ -21962,7 +22195,6 @@ Disorders or aberrations in the development or migration of the neural crest cel Any process that modulates the frequency, rate or extent of leukocyte differentiation. - pr 2013-05-02T17:32:42Z regulation of immune cell differentiation regulation of leucocyte differentiation @@ -22014,7 +22246,6 @@ Disorders or aberrations in the development or migration of the neural crest cel The process in which a relatively unspecialized cell acquires the specialized features of a mononuclear cell. - cls 2014-06-25T15:47:09Z biological_process GO:1903131 @@ -22056,7 +22287,6 @@ Disorders or aberrations in the development or migration of the neural crest cel Any process that modulates the frequency, rate or extent of hemopoiesis. - pad 2014-12-04T15:34:13Z regulation of blood cell biosynthesis regulation of blood cell formation @@ -22109,10 +22339,7 @@ Disorders or aberrations in the development or migration of the neural crest cel A macromolecular complex that contains both RNA and protein molecules. - pr 2015-11-19T12:26:37Z - GO:0030529 - GO:1990903 Wikipedia:Ribonucleoprotein RNA-protein complex RNP @@ -22157,7 +22384,6 @@ Disorders or aberrations in the development or migration of the neural crest cel Any process that modulates the frequency, rate or extent of multicellular organismal development. - tb 2010-08-05T11:25:59Z biological_process GO:2000026 @@ -22242,7 +22468,6 @@ Disorders or aberrations in the development or migration of the neural crest cel - NCBITaxon:85055 GC_ID:1 house mouse mouse @@ -22281,7 +22506,6 @@ Disorders or aberrations in the development or migration of the neural crest cel - NCBITaxon:40673 GC_ID:1 bony vertebrates ncbi_taxonomy @@ -22648,7 +22872,6 @@ Disorders or aberrations in the development or migration of the neural crest cel - NCBITaxon:109679 GC_ID:1 ncbi_taxonomy NCBITaxon:39107 @@ -22907,7 +23130,6 @@ Disorders or aberrations in the development or migration of the neural crest cel A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities - PATO:0000072 quality PATO:0000001 quality @@ -22945,7 +23167,6 @@ Disorders or aberrations in the development or migration of the neural crest cel A morphological quality inhering in a bearer by virtue of the bearer's ratios of distances between its features (points, edges, surfaces and also holes etc). - PATO:0001647 relational shape quality quality PATO:0000052 @@ -22967,7 +23188,6 @@ Disorders or aberrations in the development or migration of the neural crest cel A morphology quality inhering in a bearer by virtue of the bearer's relative position, shape, arrangements and connectivity of an organism's various parts; the pattern underlying its form. - PATO:0001452 conformation relational structural quality quality @@ -23044,7 +23264,6 @@ Disorders or aberrations in the development or migration of the neural crest cel A quality of a physical entity that exists through action of continuants at the physical level of organisation in relation to other entities. - PATO:0002079 Wikipedia:Physical_property relational physical quality quality @@ -23066,8 +23285,6 @@ Disorders or aberrations in the development or migration of the neural crest cel A quality which inheres in a continuant. - PATO:0001237 - PATO:0001238 snap:Quality monadic quality of a continuant multiply inhering quality of a physical entity @@ -23308,7 +23525,6 @@ Disorders or aberrations in the development or migration of the neural crest cel A convex 3-D shape quality inhering in a bearer by virtue of the bearer's exhibiting a consistently-sized round cross section. - PATO:0001203 rod-like rod-shaped tubulate @@ -23735,7 +23951,6 @@ Disorders or aberrations in the development or migration of the neural crest cel A quality inhering in a cell by virtue of the cell having a high nuclear/cytoplasmic ratio. - http://orcid.org/0000-0001-5208-3432 high N:C ratio quality PATO:0040072 @@ -23757,7 +23972,6 @@ Disorders or aberrations in the development or migration of the neural crest cel A quality of continuant that exist at the anatomical level of organisation and anything under it. This includes, but is not limited to, cells , tissues, and components. - http://orcid.org/0000-0001-7258-9596 quality PATO:0070044 anatomical structure quality @@ -23770,7 +23984,6 @@ Disorders or aberrations in the development or migration of the neural crest cel A quality inhering in an anotomical structure by virtue of its capacity to be stained by specific histological dyes. - http://orcid.org/0000-0001-7258-9596 quality PATO:0070045 anatomical histological quality @@ -23783,7 +23996,6 @@ Disorders or aberrations in the development or migration of the neural crest cel An affinity inhering in an anatomical structure by virtue of the bearer exhibiting a molecular interaction that stains and colors, pale-pink, with Wright-Giemsa stain. - http://orcid.org/0000-0001-7258-9596 quality PATO:0070046 neutrophillic @@ -23801,7 +24013,7 @@ Disorders or aberrations in the development or migration of the neural crest cel - + @@ -23813,7 +24025,7 @@ Disorders or aberrations in the development or migration of the neural crest cel native protein protein PR:000000001 - The definition above excludes protein complexes, which some also consider a protein. Those who wish to refer to a class representing both senses of the word are directed to CHEBI:36080. Note that the definition allows for experimentally-manipulated genes, and allows for artifically-produced derivatives that mimic those found naturally. Proteins (in the sense defined here) that descended from a common ancestor can be classified into families and superfamilies composed of products of evolutionarily-related genes. The domain architecture of a protein is described by the order of its constituent domains. Proteins with the same domains in the same order are defined as homeomorphic [PRO:WCB]. + The definition above excludes protein complexes, which some also consider a protein. Those who wish to refer to a class representing both senses of the word are directed to CHEBI:36080. Note that the definition allows for experimentally-manipulated genes, and allows for artifically-produced derivatives that mimic those found naturally. Proteins (in the sense defined here) that descended from a common ancestor can be classified into families and superfamilies composed of products of evolutionarily-related genes. The domain architecture of a protein is described by the order of its constituent domains. Proteins with the same domains in the same order are defined as homeomorphic [PRO:WCB). protein @@ -25065,7 +25277,6 @@ Disorders or aberrations in the development or migration of the neural crest cel - A protein with core architecture consisting of a signal sequence, followed by 7 Ig-like domains (Pfam:PF00047, Pfam:PF07679, or Pfam:PF07686), a transmembrane region, and a cytoplasmic Protein tyrosine kinase domain. PIRSF:PIRSF038502 protein @@ -25826,51 +26037,51 @@ Disorders or aberrations in the development or migration of the neural crest cel - + - + - A material entity that minimally consists of a protein. + A molecular entity that minimally consists of a protein. protein protein aggregate protein complex protein-containing complex protein - PR:000050567 - Note: This includes single proteins and derivatives thereof (PR:000000001), protein-containing complexes (GO:0032991), and protein aggregates (PR:000050566). - protein-containing material entity + PR:000064867 + Note: This includes single proteins and derivatives thereof (PR:000000001), protein-containing complexes (GO:0032991), and protein aggregates (PR:000050565). + protein-containing molecular entity - + - A material entity that minimally consists of a protein. + A molecular entity that minimally consists of a protein. PRO:DAN - + protein PRO:DAN - + protein aggregate PRO:DAN - + protein complex PRO:DAN - + protein-containing complex PRO:DAN @@ -26081,8 +26292,8 @@ Disorders or aberrations in the development or migration of the neural crest cel - - + + @@ -26130,11 +26341,11 @@ Disorders or aberrations in the development or migration of the neural crest cel tendon http://upload.wikimedia.org/wikipedia/commons/3/3c/Achilles-tendon.jpg - + - + @@ -26147,13 +26358,13 @@ Disorders or aberrations in the development or migration of the neural crest cel - + OG - + AEO @@ -26190,7 +26401,6 @@ Disorders or aberrations in the development or migration of the neural crest cel - @@ -26277,7 +26487,6 @@ Disorders or aberrations in the development or migration of the neural crest cel Organ component adjacent to an organ cavity and which consists of a maximal aggregate of organ component layers. - UBERON:0009915 wall FMA:82482 galen:Wall @@ -26694,7 +26903,6 @@ Disorders or aberrations in the development or migration of the neural crest cel Anatomical cluster consisting of the skeletal elements and articular elements that are part of an individual subdivision of the organism. - UBERON:0010322 FMA:85544 NCIT:C34076 SCTID:118966000 @@ -27059,7 +27267,7 @@ Disorders or aberrations in the development or migration of the neural crest cel - + @@ -27095,14 +27303,14 @@ Disorders or aberrations in the development or migration of the neural crest cel gastrula stage - + - + BILS @@ -27437,7 +27645,6 @@ Disorders or aberrations in the development or migration of the neural crest cel Organism at the blastula stage - an early stage of embryonic development in animals. It is produced by cleavage of a fertilized ovum and consists of a spherical layer of around 128 cells surrounding a central fluid-filled cavity called the blastocoel. The blastula follows the morula and precedes the gastrula in the developmental sequence. TODO - check relationship with epiblast. Note in FMA this is not a subclass of embryo, but in uberon embryo is the whole organism from zygote onwards and thus includes the blastula - UBERON:0007011 BILA:0000059 BTO:0000128 GAID:1294 @@ -28496,7 +28703,6 @@ Disorders or aberrations in the development or migration of the neural crest cel - @@ -28510,7 +28716,7 @@ Disorders or aberrations in the development or migration of the neural crest cel - + @@ -28552,14 +28758,14 @@ Disorders or aberrations in the development or migration of the neural crest cel epithelium https://upload.wikimedia.org/wikipedia/commons/8/8f/Illu_epithelium.jpg - + - + http://palaeos.com/metazoa/porifera/homoscleromorpha.html @@ -28902,7 +29108,7 @@ Disorders or aberrations in the development or migration of the neural crest cel - + Primary germ layer that is the outer of the embryo's three germ layers and gives rise to epidermis and neural tissue. AAO:0000137 BILA:0000036 @@ -28937,14 +29143,14 @@ Disorders or aberrations in the development or migration of the neural crest cel ectoderm http://upload.wikimedia.org/wikipedia/commons/1/19/Gray32.png - + - + Bgee:AN @@ -28984,7 +29190,7 @@ Disorders or aberrations in the development or migration of the neural crest cel - + Primary germ layer that lies remote from the surface of the embryo and gives rise to internal tissues such as gut. AAO:0000139 BILA:0000038 @@ -29019,14 +29225,14 @@ Disorders or aberrations in the development or migration of the neural crest cel http://upload.wikimedia.org/wikipedia/commons/c/c0/Endoderm2.png http://upload.wikimedia.org/wikipedia/commons/d/df/Gray10.png - + - + Bgee:AN @@ -29067,10 +29273,9 @@ Disorders or aberrations in the development or migration of the neural crest cel - + The middle germ layer of the embryo, between the endoderm and ectoderm. - UBERON:0003263 AAO:0000304 BILA:0000037 BTO:0000839 @@ -29108,14 +29313,14 @@ Disorders or aberrations in the development or migration of the neural crest cel mesoderm http://upload.wikimedia.org/wikipedia/commons/e/e8/Mesoderm.png - + - + Bgee:AN @@ -29371,8 +29576,8 @@ Disorders or aberrations in the development or migration of the neural crest cel - - + + @@ -29404,24 +29609,24 @@ Disorders or aberrations in the development or migration of the neural crest cel eye - + - + - + PMID:21062451 - + PMID:21062451 @@ -29663,7 +29868,6 @@ Disorders or aberrations in the development or migration of the neural crest cel - AAO:0000959 CALOHA:TS-2103 VHOG:0001248 @@ -29671,7 +29875,6 @@ Disorders or aberrations in the development or migration of the neural crest cel uberon systema cardiovasculare UBERON:0001009 - circulatory system http://upload.wikimedia.org/wikipedia/commons/2/29/Circulatory_System_en.svg @@ -29815,7 +30018,7 @@ Disorders or aberrations in the development or migration of the neural crest cel - + @@ -29865,14 +30068,14 @@ Disorders or aberrations in the development or migration of the neural crest cel http://upload.wikimedia.org/wikipedia/commons/b/b2/TE-Nervous_system_diagram.svg http://upload.wikimedia.org/wikipedia/commons/b/ba/Nervous_system_diagram.png - + - + Bgee:AN @@ -29938,7 +30141,7 @@ Disorders or aberrations in the development or migration of the neural crest cel - + The central nervous system is the core nervous system that serves an integrating and coordinating function. In vertebrates it consists of the neural tube derivatives: the brain and spinal cord. In invertebrates it includes central ganglia plus nerve cord. @@ -29983,7 +30186,7 @@ Disorders or aberrations in the development or migration of the neural crest cel central nervous system - + @@ -29997,7 +30200,7 @@ Disorders or aberrations in the development or migration of the neural crest cel - + Bgee:AN @@ -30331,7 +30534,6 @@ Disorders or aberrations in the development or migration of the neural crest cel Muscle tissue composed of cardiac muscle cells, forming the muscles of the heart[ZFA,modified]. check relationship with myocardium. part_of in MA - but we also have a more specific class 'cardiac muscle tissue of myocardium'. Check ncit - UBERON:0007096 AAO:0010245 AEO:0000142 BILA:0000134 @@ -30717,7 +30919,7 @@ Disorders or aberrations in the development or migration of the neural crest cel - + Skeletal element that is composed of bone tissue. @@ -30759,14 +30961,14 @@ Disorders or aberrations in the development or migration of the neural crest cel bone element - + - + VSAO-modified @@ -30832,7 +31034,7 @@ Disorders or aberrations in the development or migration of the neural crest cel - + A tube extending from the mouth to the anus. @@ -30869,14 +31071,14 @@ Disorders or aberrations in the development or migration of the neural crest cel digestive tract - + - + NCBIBook:NBK10107 @@ -31233,7 +31435,6 @@ Disorders or aberrations in the development or migration of the neural crest cel The sensory system subserving the sense of vision. - UBERON:0007036 AAO:0000632 BILA:0000140 EMAPA:36003 @@ -31405,9 +31606,9 @@ Disorders or aberrations in the development or migration of the neural crest cel - - - + + + @@ -31455,15 +31656,15 @@ Disorders or aberrations in the development or migration of the neural crest cel notochord http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png - + - + - + @@ -31482,19 +31683,19 @@ Disorders or aberrations in the development or migration of the neural crest cel - + http://tolweb.org/Chordata/2499 - + ZFA - + EHDAA2 @@ -31534,8 +31735,8 @@ Disorders or aberrations in the development or migration of the neural crest cel - - + + Somites are spheres of epithelial cells that form sequentially along the anterior-posterior axis of the embryo through mesenchymal to epithelial transition of the presomitic mesoderm. mesodermal cluster @@ -31573,11 +31774,11 @@ Disorders or aberrations in the development or migration of the neural crest cel somite http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png - + - + @@ -31590,13 +31791,13 @@ Disorders or aberrations in the development or migration of the neural crest cel - + GOTAX:0000352 - + ZFA @@ -31655,7 +31856,6 @@ Disorders or aberrations in the development or migration of the neural crest cel - @@ -31722,22 +31922,22 @@ Disorders or aberrations in the development or migration of the neural crest cel - + - - + + - + A specialized region of ectoderm found between the neural ectoderm (neural plate) and non-neural ectoderm and composed of highly migratory pluripotent cells that delaminate in early embryonic development from the dorsal neural tube and give rise to an astounding variety of differentiated cell types[MP]. AAO:0010578 BTO:0001764 @@ -31770,45 +31970,45 @@ Disorders or aberrations in the development or migration of the neural crest cel http://upload.wikimedia.org/wikipedia/commons/5/5f/Gray644.png https://upload.wikimedia.org/wikipedia/commons/8/8f/Neural_Crest.png - + - + - + - + - + XAO https://github.com/obophenotype/uberon/wiki/The-neural-crest - + BTO - + PMID:11523831 - + PMID:11523831 @@ -31937,7 +32137,6 @@ Disorders or aberrations in the development or migration of the neural crest cel - @@ -32116,7 +32315,7 @@ Disorders or aberrations in the development or migration of the neural crest cel - + @@ -32172,14 +32371,14 @@ Disorders or aberrations in the development or migration of the neural crest cel bone marrow http://upload.wikimedia.org/wikipedia/commons/7/74/Gray72-en.svg - + - + FMA MA @@ -32391,7 +32590,7 @@ Disorders or aberrations in the development or migration of the neural crest cel - + @@ -32445,14 +32644,14 @@ Disorders or aberrations in the development or migration of the neural crest cel hematopoietic system - + - + FMA @@ -32849,6 +33048,7 @@ Disorders or aberrations in the development or migration of the neural crest cel + @@ -32862,7 +33062,7 @@ Disorders or aberrations in the development or migration of the neural crest cel - + Unsegmented field of paraxial mesoderm present posterior to the most recently formed somite pair, from which somites will form. AAO:0011086 EFO:0001982 @@ -32885,14 +33085,14 @@ Disorders or aberrations in the development or migration of the neural crest cel presomitic mesoderm - + - + Bgee:AN @@ -33046,9 +33246,9 @@ Disorders or aberrations in the development or migration of the neural crest cel - - - + + + A region of embryonic ectodermal cells that lie directly above the notochord. During neurulation, they change shape and produce an infolding of the neural plate (the neural fold) that then seals to form the neural tube[XAO]. The earliest recognizable dorsal ectodermal primordium of the central nervous system present near the end of gastrulation before infolding to form the neural keel; consists of a thickened pseudostratified epithelium[ZFA]. AAO:0011072 BTO:0001765 @@ -33077,34 +33277,34 @@ Disorders or aberrations in the development or migration of the neural crest cel neural plate https://upload.wikimedia.org/wikipedia/commons/8/8f/Neural_Crest.png - + - + - + - + GOTAX:0000352 - + Wikipedia - + Bgee:AN @@ -33144,7 +33344,7 @@ Disorders or aberrations in the development or migration of the neural crest cel - + The paraxial mesoderm is the mesoderm located bilaterally adjacent to the notochord and neural tube[GO]. AAO:0010568 EFO:0003515 @@ -33170,7 +33370,7 @@ Disorders or aberrations in the development or migration of the neural crest cel paraxial mesoderm http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png - + @@ -33183,7 +33383,7 @@ Disorders or aberrations in the development or migration of the neural crest cel - + Bgee:AN @@ -33230,7 +33430,7 @@ Disorders or aberrations in the development or migration of the neural crest cel - + @@ -33244,7 +33444,6 @@ Disorders or aberrations in the development or migration of the neural crest cel Portion of the middle of the three primary germ layers of the embryo that resides on the periphery of the embryo, is continuous with the extra-embryonic mesoderm, splits into two layers enclosing the intra-embryonic coelom, and gives rise to body wall structures[MP]. - UBERON:0006258 AAO:0010574 EHDAA2:0000919 EHDAA:379 @@ -33270,7 +33469,7 @@ Disorders or aberrations in the development or migration of the neural crest cel lateral plate mesoderm http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png - + @@ -33283,7 +33482,7 @@ Disorders or aberrations in the development or migration of the neural crest cel - + EHDAA2 VHOG @@ -33333,7 +33532,7 @@ Disorders or aberrations in the development or migration of the neural crest cel - + @@ -33374,7 +33573,7 @@ Disorders or aberrations in the development or migration of the neural crest cel myotome http://upload.wikimedia.org/wikipedia/commons/9/96/Gray65.png - + @@ -33387,7 +33586,7 @@ Disorders or aberrations in the development or migration of the neural crest cel - + EHDAA2-abduced @@ -33547,7 +33746,7 @@ Disorders or aberrations in the development or migration of the neural crest cel - + The part of the coelom in the embryo between the somatopleuric and splanchnopleuric mesoderm; the principal body cavities of the trunk (thoracic, abdominal, and pelvic) arise from this embryonic part of the coelom. consider merging with coelom. TODO - add spatial relationships to halves of LPM. Note the OG places XAO and ZFA coelem terms here. editor note: TODO check ZFA, which appears to be a structure present in adults EHDAA:251 @@ -33562,14 +33761,14 @@ Disorders or aberrations in the development or migration of the neural crest cel intraembryonic coelom - + - + Wikipedia @@ -33871,7 +34070,7 @@ Disorders or aberrations in the development or migration of the neural crest cel - + The bilaminar epithelium formed from the myotome and dermatome. AAO:0010572 AEO:0000214 @@ -33889,7 +34088,7 @@ Disorders or aberrations in the development or migration of the neural crest cel UBERON:0004290 dermomyotome - + @@ -33908,7 +34107,7 @@ Disorders or aberrations in the development or migration of the neural crest cel - + EHDAA2 ZFA @@ -34072,7 +34271,6 @@ Disorders or aberrations in the development or migration of the neural crest cel Organism at the gastrula stage. - UBERON:0007012 BILA:0000060 BTO:0001403 FBbt:00005317 @@ -34239,7 +34437,7 @@ Disorders or aberrations in the development or migration of the neural crest cel - + Organ consisting of skeletal tissue. Encompasses whole bones, fused bones, cartilaginious elements, teeth, dermal denticles. AAO:0011129 TAO:0001890 @@ -34253,14 +34451,14 @@ Disorders or aberrations in the development or migration of the neural crest cel skeletal element - + - + VSAO @@ -34287,7 +34485,7 @@ Disorders or aberrations in the development or migration of the neural crest cel - + @@ -34326,14 +34524,14 @@ Disorders or aberrations in the development or migration of the neural crest cel UBERON:0004770 articular system - + - + FMA @@ -34774,7 +34972,7 @@ Disorders or aberrations in the development or migration of the neural crest cel - + Mesenchyme that is part of a developing trunk. EFO:0003485 EHDAA2:0002092 @@ -34790,14 +34988,14 @@ Disorders or aberrations in the development or migration of the neural crest cel trunk mesenchyme - + - + EHDAA2 @@ -35005,7 +35203,6 @@ Disorders or aberrations in the development or migration of the neural crest cel - @@ -35107,7 +35304,7 @@ Disorders or aberrations in the development or migration of the neural crest cel - + The notochordal plate is the dorsal part of the notochordal process when the ventral portion breaks down. It is continuous laterally with the endoderm that composes the roof of the primitive foregut and is in contact dorsally with the neural tube. The folding off of the notochordal plate gives rise to the notochord. TODO - check ordering; awaiting confirmation from JB EHDAA2:0001278 @@ -35121,7 +35318,7 @@ Disorders or aberrations in the development or migration of the neural crest cel notochordal plate - + @@ -35134,7 +35331,7 @@ Disorders or aberrations in the development or migration of the neural crest cel - + EHDAA2 @@ -35162,7 +35359,7 @@ Disorders or aberrations in the development or migration of the neural crest cel - + A midline cellular cord formed from the migration of mesenchymal cells from the primitive knot. EHDAA2:0001279 EHDAA:224 @@ -35179,14 +35376,14 @@ Disorders or aberrations in the development or migration of the neural crest cel The notochordal process grows cranially until it reaches the prechordal plate, the future site of the mouth. In this area the ectoderm is attached directly to the endoderm without intervening mesoderm. This area is known as the oropharyngeal membrane, and it will break down to become the mouth. At the other end of the primitive streak the ectoderm is also fused directly to the endoderm; this is known as the cloacal membrane (proctodeum), or primordial anus. notochordal process - + - + EHDAA2 @@ -35797,7 +35994,7 @@ Disorders or aberrations in the development or migration of the neural crest cel - + @@ -35823,7 +36020,7 @@ Disorders or aberrations in the development or migration of the neural crest cel presumptive paraxial mesoderm - + @@ -35839,7 +36036,7 @@ Disorders or aberrations in the development or migration of the neural crest cel - + https://github.com/obophenotype/uberon/issues/1277 @@ -35888,7 +36085,7 @@ Disorders or aberrations in the development or migration of the neural crest cel - + Mesenchyme with little extracellular matrix. AEO:0000146 EHDAA2:0003146 @@ -35896,7 +36093,7 @@ Disorders or aberrations in the development or migration of the neural crest cel UBERON:0007524 dense mesenchyme tissue - + @@ -35909,7 +36106,7 @@ Disorders or aberrations in the development or migration of the neural crest cel - + AEO @@ -35924,7 +36121,6 @@ Disorders or aberrations in the development or migration of the neural crest cel - @@ -36068,7 +36264,7 @@ Disorders or aberrations in the development or migration of the neural crest cel - + @@ -36077,7 +36273,6 @@ Disorders or aberrations in the development or migration of the neural crest cel Sum total of mesenchyme in the embryo. consider adding new class (EMAPA:16097) for mesenchyme of embryo (some mesenchyme is extraembryonic - e.g. amnion mesoderm) - UBERON:0003313 EHDAA2:0001113 EHDAA:177 EMAPA:16097 @@ -36085,14 +36280,14 @@ Disorders or aberrations in the development or migration of the neural crest cel UBERON:0009142 entire embryonic mesenchyme - + - + EHDAA2 @@ -36114,7 +36309,7 @@ Disorders or aberrations in the development or migration of the neural crest cel - + EHDAA2:0002094 trunk and cervical paraxial mesenchyme uberon @@ -36122,14 +36317,14 @@ Disorders or aberrations in the development or migration of the neural crest cel UBERON:0009618 trunk paraxial mesoderm - + - + EHDAA2 @@ -36538,7 +36733,6 @@ Disorders or aberrations in the development or migration of the neural crest cel - @@ -36574,7 +36768,6 @@ Disorders or aberrations in the development or migration of the neural crest cel - @@ -36611,7 +36804,7 @@ Disorders or aberrations in the development or migration of the neural crest cel - + @@ -36635,7 +36828,7 @@ Disorders or aberrations in the development or migration of the neural crest cel UBERON:0011899 epimysium - + @@ -36648,7 +36841,7 @@ Disorders or aberrations in the development or migration of the neural crest cel - + FMA @@ -36694,6 +36887,7 @@ Disorders or aberrations in the development or migration of the neural crest cel EHDAA2:0004731 Wikipedia:Coelom + ZFA:0001438 enterocoelom haemocoelom schizocoelom @@ -36754,7 +36948,7 @@ Disorders or aberrations in the development or migration of the neural crest cel - + @@ -36775,7 +36969,7 @@ Disorders or aberrations in the development or migration of the neural crest cel UBERON:0012429 hematopoietic tissue - + @@ -36788,7 +36982,7 @@ Disorders or aberrations in the development or migration of the neural crest cel - + defitional @@ -37273,7 +37467,6 @@ Disorders or aberrations in the development or migration of the neural crest cel Primordium that develops into the central nervous system. - UBERON:3000469 future CNS presumptive central nervous system uberon @@ -37317,7 +37510,6 @@ Disorders or aberrations in the development or migration of the neural crest cel Primordium that develops into the nervous system. - UBERON:3000477 AAO:0000477 presumptive nervous system uberon @@ -37343,7 +37535,7 @@ Disorders or aberrations in the development or migration of the neural crest cel - + @@ -37366,7 +37558,7 @@ Disorders or aberrations in the development or migration of the neural crest cel UBERON:0016887 entire extraembryonic component - + @@ -37379,7 +37571,7 @@ Disorders or aberrations in the development or migration of the neural crest cel - + AEO @@ -37465,7 +37657,7 @@ Disorders or aberrations in the development or migration of the neural crest cel - + @@ -37482,14 +37674,14 @@ Disorders or aberrations in the development or migration of the neural crest cel skeletal musculature - + - + MA diff --git a/subsets/general_cell_types_upper_slim.tsv b/subsets/general_cell_types_upper_slim.tsv index 2bc1ed24c..0fd23a842 100644 --- a/subsets/general_cell_types_upper_slim.tsv +++ b/subsets/general_cell_types_upper_slim.tsv @@ -1,313 +1,313 @@ ?x ?label -_:B0be79aadX2D3b9dX2D4de8X2D9b61X2Dad49ee9a54c2genid1000 -_:B0be79aadX2D3b9dX2D4de8X2D9b61X2Dad49ee9a54c2genid1006 -_:B0be79aadX2D3b9dX2D4de8X2D9b61X2Dad49ee9a54c2genid1047 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+_:Be724617aX2D7808X2D41ddX2D87c4X2D66795569b4e8genid722 +_:Be724617aX2D7808X2D41ddX2D87c4X2D66795569b4e8genid73 +_:Be724617aX2D7808X2D41ddX2D87c4X2D66795569b4e8genid736 +_:Be724617aX2D7808X2D41ddX2D87c4X2D66795569b4e8genid751 +_:Be724617aX2D7808X2D41ddX2D87c4X2D66795569b4e8genid768 +_:Be724617aX2D7808X2D41ddX2D87c4X2D66795569b4e8genid789 +_:Be724617aX2D7808X2D41ddX2D87c4X2D66795569b4e8genid797 +_:Be724617aX2D7808X2D41ddX2D87c4X2D66795569b4e8genid804 +_:Be724617aX2D7808X2D41ddX2D87c4X2D66795569b4e8genid814 +_:Be724617aX2D7808X2D41ddX2D87c4X2D66795569b4e8genid827 +_:Be724617aX2D7808X2D41ddX2D87c4X2D66795569b4e8genid844 +_:Be724617aX2D7808X2D41ddX2D87c4X2D66795569b4e8genid852 +_:Be724617aX2D7808X2D41ddX2D87c4X2D66795569b4e8genid859 +_:Be724617aX2D7808X2D41ddX2D87c4X2D66795569b4e8genid869 +_:Be724617aX2D7808X2D41ddX2D87c4X2D66795569b4e8genid896 +_:Be724617aX2D7808X2D41ddX2D87c4X2D66795569b4e8genid913 +_:Be724617aX2D7808X2D41ddX2D87c4X2D66795569b4e8genid922 +_:Be724617aX2D7808X2D41ddX2D87c4X2D66795569b4e8genid972 +_:Be724617aX2D7808X2D41ddX2D87c4X2D66795569b4e8genid980 +_:Be724617aX2D7808X2D41ddX2D87c4X2D66795569b4e8genid988 "cell" "early embryonic cell (metazoa)" "stem cell" @@ -627,18 +627,16 @@ _:B0be79aadX2D3b9dX2D4de8X2D9b61X2Dad49ee9a54c2genid993 "response to external biotic stimulus" "organelle" "membrane-bounded organelle" - "non-membrane-bounded organelle" + "membraneless organelle" "intracellular organelle" "intracellular membrane-bounded organelle" - "intracellular non-membrane-bounded organelle" + "intracellular membraneless organelle" "organelle lumen" "contractile muscle fiber" "protein-containing complex organization" "cellular component biogenesis" "translation initiation ternary complex" - "cellular metabolic process" "primary metabolic process" - "cellular biosynthetic process" "biological process involved in interspecies interaction between organisms" "plasma membrane fusion" "innate immune response" @@ -729,7 +727,7 @@ _:B0be79aadX2D3b9dX2D4de8X2D9b61X2Dad49ee9a54c2genid993 "supramolecular fiber" "synaptic signaling" "trans-synaptic signaling" - "cellular anatomical entity" + "cellular anatomical structure" "plasma membrane bounded cell projection" "plasma membrane bounded cell projection organization" "exocytic process" @@ -871,7 +869,7 @@ _:B0be79aadX2D3b9dX2D4de8X2D9b61X2Dad49ee9a54c2genid993 "eukaryotic protein" "cathepsin-like protease" "receptor-type tyrosine-protein phosphatase C isoform CD45R" - "protein-containing material entity" + "protein-containing molecular entity" "processual entity" "sense organ" "tube" diff --git a/subsets/kidney_upper_slim.json b/subsets/kidney_upper_slim.json index ddee7b988..891a1d186 100644 --- a/subsets/kidney_upper_slim.json +++ b/subsets/kidney_upper_slim.json @@ -4,9 +4,9 @@ "meta" : { "basicPropertyValues" : [ { "pred" : "http://www.w3.org/2002/07/owl#versionInfo", - "val" : "2024-09-26" + "val" : "2025-01-08" } ], - "version" : "http://purl.obolibrary.org/obo/cl/releases/2024-09-26/subsets/kidney_upper_slim.owl" + "version" : "http://purl.obolibrary.org/obo/cl/releases/2025-01-08/subsets/kidney_upper_slim.owl" }, "nodes" : [ { "id" : "http://purl.obolibrary.org/obo/CL_0000000", @@ -18,7 +18,7 @@ "xrefs" : [ "CARO:mah" ] }, "comments" : [ "The definition of cell is intended to represent all cells, and thus a cell is defined as a material entity and not an anatomical structure, which implies that it is part of an organism (or the entirety of one)." ], - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/ubprop#_upper_level" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/ubprop#_upper_level" ], "xrefs" : [ { "val" : "CALOHA:TS-2035" }, { @@ -50,6 +50,7 @@ "val" : "A cell found in the embryo before the formation of all the gem layers is complete.", "xrefs" : [ "GOC:tfm" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "ZFA:0009002" } ] @@ -64,7 +65,7 @@ "xrefs" : [ "GOC:tfm", "MESH:D013234" ] }, "comments" : [ "This term applies to metazoan. For plant stem cells, consider using PO:0004011 ‘initial cell’ or its parent PO:0004010 ‘meristematic cell’." ], - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#general_cell_types_upper_slim", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#general_cell_types_upper_slim", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "animal stem cell" @@ -91,7 +92,7 @@ "xrefs" : [ "GOC:add", "GOC:dsd", "GOC:tfm", "PMID:19022770", "http://en.wikipedia.org/wiki/Hematopoietic_stem_cell" ] }, "comments" : [ "Markers differ between species, and two sets of markers have been described for mice. HSCs are reportedly CD34-positive, CD45-positive, CD48-negative, CD150-positive, CD133-positive, and CD244-negative." ], - "subsets" : [ "http://purl.obolibrary.org/obo/cl#blood_and_immune_upper_slim", "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#blood_and_immune_upper_slim", "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "blood forming stem cell" @@ -133,7 +134,7 @@ "val" : "A progenitor cell committed to the erythroid lineage.", "xrefs" : [ "GOC:add", "ISBN:0721601464" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#blood_and_immune_upper_slim", "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#blood_and_immune_upper_slim", "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003000", "pred" : "hasRelatedSynonym", @@ -171,7 +172,7 @@ "xrefs" : [ "GOC:tfm", "ISBN:0721662544" ] }, "comments" : [ "Originally this term had some plant germ line cell children." ], - "subsets" : [ "http://purl.obolibrary.org/obo/cl#general_cell_types_upper_slim", "http://purl.obolibrary.org/obo/ubprop#_upper_level" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#general_cell_types_upper_slim", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/ubprop#_upper_level" ], "xrefs" : [ { "val" : "ZFA:0009016" } ] @@ -185,6 +186,7 @@ "val" : "A stem cell that can give rise to multiple lineages of cells.", "xrefs" : [ "GOC:add" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "multi-fate stem cell" @@ -214,7 +216,7 @@ "xrefs" : [ "GOC:add", "ISBN:0878932437", "MESH:D023461" ] }, "comments" : [ "This cell type is intended to be compatible with any vertebrate common myeloid progenitor. For mammalian CMP known to be CD34-positive, please use the term 'common myeloid progenitor, CD34-positive' (CL_0001059)." ], - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "common myeloid precursor" @@ -270,7 +272,7 @@ "xrefs" : [ "GOC:add", "GOC:dsd", "GOC:tfm", "MESH:D055015", "PMID:16647566", "http://en.wikipedia.org/wiki/Megakaryocyte-erythroid_progenitor_cell" ] }, "comments" : [ "MEPs are reportedly CD19-negative, CD34-negative, CD45RA-negative, CD110-positive, CD117-positive, and SCA1-negative and reportedly express the transcription factors GATA-1 and NF-E2." ], - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "CFU-EM" @@ -310,6 +312,7 @@ "val" : "A stem cell from which all cells of the body can form.", "xrefs" : [ "GOC:add", "GOC:tfm" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "totipotential stem cell" @@ -332,7 +335,7 @@ "xrefs" : [ "SANBI:mhl" ] }, "comments" : [ "define using PATO mulit-potent or oligopotent?" ], - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "blast cell" @@ -352,6 +355,7 @@ "val" : "A cell that is commited to differentiating into a muscle cell. Embryonic myoblasts develop from the mesoderm. They undergo proliferation, migrate to their various sites, and then differentiate into the appropriate form of myocytes. Myoblasts also occur as transient populations of cells in muscles undergoing repair.", "xrefs" : [ "GOC:tfm", "MESH:D032446", "PMID:21849021" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "BTO:0000222" }, { @@ -376,7 +380,7 @@ "xrefs" : [ "ISBN:0517223651", "MESH:D005347", "http://en.wikipedia.org/wiki/Fibroblast" ] }, "comments" : [ "These cells may be vimentin-positive, fibronectin-positive, fsp1-positive, MMP-1-positive, collagen I-positive, collagen III-positive, and alpha-SMA-negative." ], - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#general_cell_types_upper_slim", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#general_cell_types_upper_slim", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "xrefs" : [ { "val" : "BTO:0000452" }, { @@ -404,7 +408,7 @@ "val" : "A cell that is usually found in a two-dimensional sheet with a free surface. The cell has a cytoskeleton that allows for tight cell to cell contact and for cell polarity where apical part is directed towards the lumen and the basal part to the basal lamina.", "xrefs" : [ "FB:ma", "GOC:tfm", "MESH:D004847" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#general_cell_types_upper_slim", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#general_cell_types_upper_slim", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "epitheliocyte" @@ -441,7 +445,7 @@ "val" : "An epithelial cell that is part of a duct.", "xrefs" : [ "https://orcid.org/0000-0001-5208-3432" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "ZFA:0009372" } ] @@ -455,7 +459,7 @@ "val" : "An endothelial cell that lines the vasculature.", "xrefs" : [ "GOC:tfm" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "xrefs" : [ { "val" : "ZFA:0009036" } ], @@ -467,7 +471,10 @@ }, { "id" : "http://purl.obolibrary.org/obo/CL_0000072", "lbl" : "non-branched duct epithelial cell", - "type" : "CLASS" + "type" : "CLASS", + "meta" : { + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ] + } }, { "id" : "http://purl.obolibrary.org/obo/CL_0000075", "lbl" : "columnar/cuboidal epithelial cell", @@ -477,7 +484,7 @@ "val" : "A columnar/cuboidal epithelial cell is a cell usually found in a two dimensional sheet with a free surface. Columnar/cuboidal epithelial cells take on the shape of a column or cube.", "xrefs" : [ "GO:0002065", "https://orcid.org/0000-0001-5208-3432" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "xrefs" : [ { "val" : "ZFA:0009038" } ], @@ -495,7 +502,7 @@ "val" : "Any epithelial cell that is part of some squamous epithelium.", "xrefs" : [ "FBC:Autogenerated" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "CALOHA:TS-1249" }, { @@ -511,7 +518,7 @@ "val" : "A cell found predominately in the blood.", "xrefs" : [ "GOC:add", "GOC:tfm" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#general_cell_types_upper_slim" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#general_cell_types_upper_slim", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "FMA:62844" }, { @@ -530,7 +537,7 @@ "xrefs" : [ "GOC:tfm", "MESH:D042783", "PMID:21275341", "http://en.wikipedia.org/wiki/Endothelial_cell", "https://sourceforge.net/tracker/?func=detail&atid=440764&aid=3364936&group_id=36855" ] }, "comments" : [ "From FMA: 9.07.2001: Endothelial cell has always been classified as a kind of epithelial cell, specifically a squamous cell but that is not true. First, endothelial cell can either be squamous or cuboidal (e.g. high-endothelial cell) and secondly, it has different embryological derivation (mesodermal) than a true epithelial cell (ectodermal and endodermal). The basis for present classification is the fact that it comprises the outermost layer or lining of anatomical structures (location-based) but a better structural basis for the differentia is the cytoskeleton of the cell. Endothelial cell has vimentin filaments while an epithelial cell has keratin filaments. [Onard]." ], - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "endotheliocyte" @@ -558,6 +565,7 @@ "val" : "Ectoderm destined to be nervous tissue.", "xrefs" : [ "GOC:tfm", "ISBN:068340007X" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "neurectoderm cell" @@ -576,7 +584,7 @@ "xrefs" : [ "FB:ma", "GOC:dsd", "PMCID:PMC2613570", "PMID:10102814", "PMID:16923606", "PMID:17986482", "PMID:19960544", "http://en.wikipedia.org/wiki/Mesenchymal_stem_cell", "http://www.copewithcytokines.de/cope.cgi?key=mesenchymal%20stem%20cells" ] }, "comments" : [ "Many but not all mesenchymal cells derive from the mesoderm. MSCs are reportedly CD3-negative, CD4-negative, CD5-negative, CD8-negative, CD11a-negative, CD11b-negative, CD14-negative, CD19-negative, CD29-positive, CD31-negative, CD34-negative, CD38-negative, CD40-negative, CD44-positive, CD45-negative, CD49-positive, CD54-positive, CD66b-negative, CD79a-negative, CD80-negative, CD102-positive, CD106-positive, CD117-positive, CD121a-positive, CD121b-positive, CD123-positive, CD124-positive, CD133-negative, CD146-positive, CD166-positive, CD271-positive, B220-negative, Gr1-negative, MHCI-positive, MHCII-negative, SSEA4-negative, sca1-positive, Ter119-negative, and glycophorin A-negative. Cultured MSCs are capable of producing stem cell factor, IL7, IL8, IL11, TGF-beta, cofilin, galectin-1, laminin-receptor 1, cyclophilin A, and MMP-2." ], - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "pred" : "hasNarrowSynonym", "val" : "bone marrow stromal cells" @@ -647,7 +655,7 @@ "val" : "A cell that specializes in controlled release of one or more substances.", "xrefs" : [ "GOC:tfm", "ISBN:0721662544" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "BTO:0003659" }, { @@ -662,7 +670,8 @@ "definition" : { "val" : "Any secretory cell that is capable of some protein secretion.", "xrefs" : [ "FBC:Autogenerated" ] - } + }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ] } }, { "id" : "http://purl.obolibrary.org/obo/CL_0000183", @@ -673,7 +682,7 @@ "val" : "A cell whose primary function is to shorten.", "xrefs" : [ "FB:ma" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ] + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ] } }, { "id" : "http://purl.obolibrary.org/obo/CL_0000187", @@ -684,7 +693,7 @@ "val" : "A mature contractile cell, commonly known as a myocyte. This cell has as part of its cytoplasm myofibrils organized in various patterns.", "xrefs" : [ "MESH:D032342" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "muscle fiber" @@ -721,7 +730,7 @@ "val" : "A non-striated, elongated, spindle-shaped cell found lining the digestive tract, uterus, and blood vessels. They develop from specialized myoblasts (smooth muscle myoblast).", "xrefs" : [ "MESH:D032389", "PMID:9315361", "http://en.wikipedia.org/wiki/Smooth_muscle_cell" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#general_cell_types_upper_slim", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#general_cell_types_upper_slim", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "synonyms" : [ { "pred" : "hasBroadSynonym", "val" : "non-striated muscle cell" @@ -745,10 +754,15 @@ "val" : "FMA:14072" }, { "val" : "ZFA:0009118" + }, { + "val" : "https://cellxgene.cziscience.com/cellguide/CL_0000192" } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" + }, { + "pred" : "http://purl.org/dc/terms/description", + "val" : "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nSmooth muscle cells are a specialized type of muscle cells that are primarily found within the walls of hollow organs such as the intestine, stomach, bladder, uterus, and blood vessels. These cells are an essential component of the autonomic nervous system controling involuntary movements within the body.\nSmooth muscle cells play a vital role in many physiological processes due to their unique functionality. They can contract and relax in a slow, sustained, and controlled manner to help modulate the size and shape of the lumens of the organs they surround. For example, in the digestive system, coordinated contraction and relaxation of smooth muscle cells propels food along the gastrointestinal tract - a process known as peristalsis. In the blood vessels, the smooth muscle cells, by contracting or relaxing, either constrict or dilate the vessels, which in turn, help regulate blood flow and pressure.\nOn a cellular level, smooth muscle cells possess a single, centrally located nucleus and contain an arranged network of actin and myosin filaments, which are the proteins responsible for muscle contraction. Unlike their counterparts in skeletal or cardiac muscles, these cells lack specific contact points for these filaments, hence the lack of visible striations. Furthermore, the contraction of smooth muscle cells is regulated by hormones and neurotransmitters, such as acetylcholine and norepinephrine, adding an additional layer of complex regulation to these highly specialized cells." } ] } }, { @@ -760,6 +774,7 @@ "val" : "A cell whose function is determined by the generation or the reception of an electric signal.", "xrefs" : [ "FB:ma" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "ZFA:0009128" } ] @@ -773,6 +788,7 @@ "val" : "A cell within an epithelial cell sheet whose main function is to act as an internal or external covering for a tissue or an organism.", "xrefs" : [ "JB:jb" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "boundary cell" @@ -790,6 +806,7 @@ "val" : "A cell whose primary function is to prevent the transport of stuff across compartments.", "xrefs" : [ "JB:jb" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "ZFA:0009132" } ] @@ -803,6 +820,7 @@ "val" : "A cell that moves by its own activities.", "xrefs" : [ "FB:ma" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "ZFA:0009136" } ] @@ -816,6 +834,7 @@ "val" : "A cell of the outer of the three germ layers of the embryo.", "xrefs" : [ "MESH:D004475" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "ectoderm cell" @@ -835,7 +854,7 @@ "val" : "A cell of the middle germ layer of the embryo.", "xrefs" : [ "MESH:D008648" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "mesoblast" @@ -847,6 +866,12 @@ "val" : "FMA:72554" }, { "val" : "ZFA:0009138" + }, { + "val" : "https://cellxgene.cziscience.com/cellguide/CL_0000222" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/description", + "val" : "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nMesodermal cells are pluripotent and the most abundant in the human body. They contribute to the development of several structures such as the skeletal muscles, bones, heart and blood vessels, kidneys, gonads, connective tissues, and certain layers of the skin. Hence, the mesoderm is often regarded as an active and diverse layer due to its role in forming many bodily structures. \nIn embryonic development, these cells are instrumental, contributing to the body's structures through a carefully coordinated sequence of morphogenetic movements. This process forms the complex multicellular architecture of tissues and organs from a simple ball of cells. Without the function of mesodermal cells, the body's integral structures and systems would cease to form correctly, leading to developmental disorders such as axial mesodermal dysplasia complex" } ] } }, { @@ -858,6 +883,7 @@ "val" : "A cell of the inner of the three germ layers of the embryo.", "xrefs" : [ "MESH:D004707" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "endoderm cell" @@ -877,7 +903,7 @@ "val" : "A red blood cell. In mammals, mature erythrocytes are biconcave disks containing hemoglobin whose function is to transport oxygen.", "xrefs" : [ "GOC:tfm", "MESH:D004912" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#blood_and_immune_upper_slim", "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#blood_and_immune_upper_slim", "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "RBC" @@ -906,7 +932,7 @@ "val" : "Any cell that in taxon some Eukaryota.", "xrefs" : [ "FBC:Autogenerated" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "MESH:D005057" } ] @@ -920,6 +946,7 @@ "val" : "Any cell that is capable of some oxygen transport.", "xrefs" : [ "FBC:Autogenerated" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "ZFA:0009164" } ] @@ -933,6 +960,7 @@ "val" : "A cell derived from the specialized ectoderm flanking each side of the embryonic neural plate, which after the closure of the neural tube, forms masses of cells that migrate out from the dorsal aspect of the neural tube to spread throughout the body.", "xrefs" : [ "doi:10.1016/j.stem.2015.02.017" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "FMA:86667" }, { @@ -948,6 +976,7 @@ "val" : "A mesenchymal cell in embryonic development found in a contracting mass and that gives rise to osteoprogenitors.", "xrefs" : [ "GOC:tfm", "PMID:5025404" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "ZFA:0009166" } ] @@ -960,7 +989,8 @@ "definition" : { "val" : "A cell of the outer layer of a blastula that gives rise to the ectoderm after gastrulation.", "xrefs" : [ "GOC:tfm", "ISBN:0618947256" ] - } + }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ] } }, { "id" : "http://purl.obolibrary.org/obo/CL_0000365", @@ -971,6 +1001,7 @@ "val" : "Diploid cell produced by the fusion of sperm cell nucleus and egg cell.", "xrefs" : [ "ISBN:0471245208" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "pred" : "hasBroadSynonym", "val" : "zygote" @@ -992,6 +1023,7 @@ "val" : "A cell whose function is determined by its response to an electric signal.", "xrefs" : [ "FB:ma" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "ZFA:0009190" } ] @@ -1005,10 +1037,33 @@ "val" : "A cell that initiates an electrical signal and passes that signal to another cell.", "xrefs" : [ "FB:ma" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "ZFA:0009193" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/CL_0000499", + "lbl" : "stromal cell", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A connective tissue cell of an organ found in the loose connective tissue.", + "xrefs" : [ "GOC:tfm", "MESH:D017154" ] + }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#general_cell_types_upper_slim", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "xrefs" : [ { + "val" : "BTO:0002064" + }, { + "val" : "FMA:83624" + }, { + "val" : "ZFA:0009226" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/RO_0002175", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/CL_0000514", "lbl" : "smooth muscle myoblast", @@ -1018,7 +1073,7 @@ "val" : "A precursor cell destined to differentiate into smooth muscle myocytes.", "xrefs" : [ "GOC:tfm", "MESH:D032390" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "myoblast, smooth muscle", @@ -1031,6 +1086,12 @@ "val" : "FMA:84798" }, { "val" : "ZFA:0009235" + }, { + "val" : "https://cellxgene.cziscience.com/cellguide/CL_0000514" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/description", + "val" : "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nA precursor to the smooth muscle cell, the smooth muscle myoblast, is integral to various body systems, including the cardiovascular, gastrointestinal, and respiratory systems. Smooth muscle myoblasts arise from the differentiation of mesenchymal stem cells, a process tightly regulated by specific genetic factors and environmental signals. Their role extends to myogenesis, particularly in the formation of muscular tissue, especially during embryonic development.\nSmooth muscle myoblasts possess distinctive cellular characteristics. In contrast to skeletal muscle myoblasts, they do not fuse to create multinucleated fibers. Instead, they differentiate into individual, uninucleated smooth muscle cells. This differentiation unfolds in two distinct phases: proliferation, marked by rapid division to increase cell numbers, and differentiation, involving structural and functional transformation into mature smooth muscle cells. This intricate process is intricately mediated by various signaling molecules and transcription factors.\nFunctionally, smooth muscle myoblasts and the mature muscle cells they generate play pivotal roles in various physiological processes. Smooth muscle cells orchestrate involuntary muscle responses and are integral to body systems that regulate blood flow, propel food along the digestive tract, and control airflow in the respiratory tract. These diverse functions underscore the significance of smooth muscle myoblasts in the body's growth, maintenance, and overall function." } ] } }, { @@ -1043,7 +1104,7 @@ "xrefs" : [ "MESH:D009474", "http://en.wikipedia.org/wiki/Neuron" ] }, "comments" : [ "These cells are also reportedly CD4-negative and CD200-positive. They are also capable of producing CD40L and IFN-gamma." ], - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#general_cell_types_upper_slim", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#general_cell_types_upper_slim", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "nerve cell" @@ -1080,7 +1141,7 @@ "val" : "An immature, nucleated erythrocyte occupying the stage of erythropoeisis that follows formation of erythroid progenitor cells. This cell is CD71-positive, has both a nucleus and a nucleolus, and lacks hematopoeitic lineage markers.", "xrefs" : [ "ISBN:0721601464", "PMID:1638021" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#blood_and_immune_upper_slim", "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#blood_and_immune_upper_slim", "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "rubriblast", @@ -1102,6 +1163,7 @@ "val" : "A nucleated immature erythrocyte, having cytoplasm generally similar to that of the earlier proerythroblast but sometimes even more basophilic, and usually regular in outline. The nucleus is still relatively large, but the chromatin strands are thicker and more deeply staining, giving a coarser appearance; the nucleoli have disappeared. This cell is CD71-positive and lacks hematopoeitic lineage markers.", "xrefs" : [ "GOC:tfm", "ISBN:0721601464" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "basophilic normoblast", @@ -1134,6 +1196,7 @@ "val" : "A nucleated, immature erythrocyte in which the nucleus occupies a relatively smaller part of the cell than in its precursor, the basophilic erythroblast. The cytoplasm is beginning to acquire hemoglobin and thus is no longer a purely basophilic, but takes on acidophilic aspects, which becomes progressively more marked as the cell matures. The chromatin of the nucleus is arranged in coarse, deeply staining clumps. This cell is CD71-positive and lacks hematopoeitic lineage markers.", "xrefs" : [ "ISBN:0721601464" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "intermediate erythroblast", @@ -1174,6 +1237,7 @@ "val" : "The final stage of the nucleated, immature erythrocyte, before nuclear loss. Typically the cytoplasm is described as acidophilic, but it still shows a faint polychromatic tint. The nucleus is small and initially may still have coarse, clumped chromatin, as in its precursor, the polychromatophilic erythroblast, but ultimately it becomes pyknotic, and appears as a deeply staining, blue-black, homogeneous structureless mass. The nucleus is often eccentric and sometimes lobulated.", "xrefs" : [ "ISBN:0721601464" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "acidophilic erythroblast", @@ -1208,7 +1272,7 @@ "xrefs" : [ "GOC:dsd", "GOC:tfm", "ISBN:0721601464" ] }, "comments" : [ "Lineage negative is described here as CD2-negative, CD3-negative, CD4-negative, CD5-negative, CD8a-negative, CD14-negative, CD19-negative, CD20-negative, CD56-negative, Ly6g-negative, and Ter119-negative." ], - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "CFU-Meg", @@ -1268,7 +1332,7 @@ "xrefs" : [ "ISBN:0721601464", "MESH:D008533", "PMID:31043076", "http://en.wikipedia.org/wiki/Megakaryocyte" ] }, "comments" : [ "Megakaryocytes are reportedly CD181-positive and CD182-positive." ], - "subsets" : [ "http://purl.obolibrary.org/obo/cl#blood_and_immune_upper_slim", "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#blood_and_immune_upper_slim", "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "megacaryocyte" @@ -1300,7 +1364,7 @@ "val" : "An immature erythrocyte that changes the protein composition of its plasma membrane by exosome formation and extrusion. The types of protein removed differ between species though removal of the transferrin receptor is apparent in mammals and birds.", "xrefs" : [ "GOC:add", "GOC:tfm", "PMID:15946868", "PMID:2037622" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#blood_and_immune_upper_slim", "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#blood_and_immune_upper_slim", "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "BTO:0001173" }, { @@ -1321,6 +1385,7 @@ "xrefs" : [ "GOC:dsd", "GOC:tfm", "PMID:12768659" ] }, "comments" : [ "These cells are reportedly CD31-positive, CD34-positive, CD144-positive, CD309-positive, and TAL1-positive." ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "angioblast" @@ -1341,7 +1406,7 @@ "val" : "The reproductive cell in multicellular organisms.", "xrefs" : [ "MESH:D005854" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "BTO:0000535" }, { @@ -1361,7 +1426,7 @@ "val" : "A cell whose primary function is to support other cell types.", "xrefs" : [ "FB:ma", "GOC:tfm" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "supportive cell" @@ -1381,7 +1446,7 @@ "val" : "A smooth muscle cell that synthesizes, stores, and secretes the enzyme renin. This cell type are located in the wall of the afferent arteriole at the entrance to the glomerulus. While having a different origin than other kidney smooth muscle cells, this cell type expresses smooth muscle actin upon maturation.", "xrefs" : [ "GOC:cvs", "GOC:tfm", "PMID:11457727" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "synonyms" : [ { "pred" : "hasBroadSynonym", "val" : "juxtaglomerular cell" @@ -1412,7 +1477,7 @@ "xrefs" : [ "GOC:tfm", "http://www.copewithcytokines.de/cope.cgi?key=mesangial%20cells" ] }, "comments" : [ "Do all of these cells really develop from some mesenchymal stem cell?" ], - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "kidney mesangial cell" @@ -1438,7 +1503,7 @@ "val" : "An endothelial cell that has small pores, or fenestrations, which allow for the efficient exchange of substances between the blood and surrounding tissues.", "xrefs" : [ "DOI:10.1007/978-3-211-99390-3_133" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "window cell" @@ -1450,7 +1515,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://purl.org/dc/terms/description", - "val" : "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional.\n\nFenestrated cells are specialized epithelial cells that are characterized by a distinctive structural feature, fenestrations or tiny pores, which allow an exchange of substances such as fluids, nutrients, and waste between blood vessels and the surrounding tissue environments. These cells are present in various types of epithelial tissues in the human body, including the intestinal tract, endocrine glands, and certain parts of the renal system. \nThere are multiple types of endothelial cell fenestrations. The most common type is found in systemic capillaries of the endocrine tissue (e.g., pancreatic islets), gastrointestinal mucosa, and renal peritubular capillaries. Here, the fenestrated cells have fenestrations in their peripheral cytoplasm with a unique thin and permeable diaphragm that provides a high degree of selectivity, blocking the passage of larger molecules while allowing the free movement of smaller ones. In contrast, other types of fenestrations, such as the discontinuous epithelium of the liver sinusoidal endothelial cells, do not have diaphragms. \nCharacteristically, fenestrated cells play a vital role in the filtering process of body systems. They are a key part of the glomeruli in the kidneys where blood is filtered under high pressure. The fenestrations present in the endothelial cells lining the capillaries of the glomerulus allow the free passage of water and small solute molecules towards the Bowman's capsule, leaving behind larger proteins and cells in the blood, thereby aiding in the filtration and waste removal process. \nIn the endocrine system, fenestrated cells in glandular capillaries allow the prompt release of hormones into the bloodstream. These cells have tightly clustered fenestrations which increase the surface area available for passive diffusion, improving the efficiency of hormone secretion. In villi of the small intestine, these cells increase absorption efficiency, permitting the exchange of water, electrolytes, and nutrients.\nOverall, fenestrated cells contribute immensely to important physiological processes of filtration, absorption, and secretion, primarily connecting our body's circulation system with the surrounding tissues and organs." + "val" : "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nFenestrated cells are specialized epithelial cells that are characterized by a distinctive structural feature, fenestrations or tiny pores, which allow an exchange of substances such as fluids, nutrients, and waste between blood vessels and the surrounding tissue environments. These cells are present in various types of epithelial tissues in the human body, including the intestinal tract, endocrine glands, and certain parts of the renal system. \nThere are multiple types of endothelial cell fenestrations. The most common type is found in systemic capillaries of the endocrine tissue (e.g., pancreatic islets), gastrointestinal mucosa, and renal peritubular capillaries. Here, the fenestrated cells have fenestrations in their peripheral cytoplasm with a unique thin and permeable diaphragm that provides a high degree of selectivity, blocking the passage of larger molecules while allowing the free movement of smaller ones. In contrast, other types of fenestrations, such as the discontinuous epithelium of the liver sinusoidal endothelial cells, do not have diaphragms. \nCharacteristically, fenestrated cells play a vital role in the filtering process of body systems. They are a key part of the glomeruli in the kidneys where blood is filtered under high pressure. The fenestrations present in the endothelial cells lining the capillaries of the glomerulus allow the free passage of water and small solute molecules towards the Bowman's capsule, leaving behind larger proteins and cells in the blood, thereby aiding in the filtration and waste removal process. \nIn the endocrine system, fenestrated cells in glandular capillaries allow the prompt release of hormones into the bloodstream. These cells have tightly clustered fenestrations which increase the surface area available for passive diffusion, improving the efficiency of hormone secretion. In villi of the small intestine, these cells increase absorption efficiency, permitting the exchange of water, electrolytes, and nutrients.\nOverall, fenestrated cells contribute immensely to important physiological processes of filtration, absorption, and secretion, primarily connecting our body's circulation system with the surrounding tissues and organs." } ] } }, { @@ -1463,7 +1528,7 @@ "xrefs" : [ "GOC:dsd", "GOC:tfm", "ISBN:0721662544", "MESH:D020286", "PMID:16807374", "PMID:17986482", "PMID:20024907" ] }, "comments" : [ "Pericytes are CD10-positive, CD13-positive, CD31-negative, CD45-negative, CD106-positive, CD117-negative, CD140-positive, CD144-negative, CD146-positive, CD271-positive, CD325-positive, NG2-positive, RGS5-positive, SMA-positive, and desmin-positive. A subpopulation is CD248-positive. They are also capable of producing angiopoietin 1, CXCL12, TGF-beta, and VEGF-A." ], - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "ARC", @@ -1505,7 +1570,7 @@ "val" : "A non-terminally differentiated cell that is capable of developing into a muscle cell.", "xrefs" : [ "GOC:add" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "ZFA:0009291" } ] @@ -1519,6 +1584,7 @@ "val" : "A stem cell that can give rise to cell types of the body other than those of the germ-line.", "xrefs" : [ "GO:0048103" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "CALOHA:TS-2086" }, { @@ -1536,7 +1602,7 @@ "val" : "A cell of the monocyte, granulocyte, mast cell, megakaryocyte, or erythroid lineage.", "xrefs" : [ "GOC:add" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "BTO:0001441" }, { @@ -1557,7 +1623,7 @@ "xrefs" : [ "GOC:add", "GOC:tfm" ] }, "comments" : [ "Note that in FMA erythropoietic cells are types of nucleated erythrocytes and thus don't include erythrocytes." ], - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "erythropoietic cell" @@ -1585,7 +1651,7 @@ "val" : "A nucleated precursor of an erythrocyte that lacks hematopoietic lineage markers.", "xrefs" : [ "GOC:add", "ISBN:0721601464", "PMID:18174176" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#blood_and_immune_upper_slim", "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#blood_and_immune_upper_slim", "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "normoblast" @@ -1612,7 +1678,7 @@ "xrefs" : [ "GOC:add", "GOC:tfm", "PMID:19022770" ] }, "comments" : [ "Markers differ between mouse and human." ], - "subsets" : [ "http://purl.obolibrary.org/obo/cl#blood_and_immune_upper_slim", "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#blood_and_immune_upper_slim", "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "MPP" @@ -1642,7 +1708,7 @@ "xrefs" : [ "GOC:add", "GOC:tfm", "PMID:19022770" ] }, "comments" : [ "Note that this is a class of cell types, not an identified single cell type." ], - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "synonyms" : [ { "pred" : "hasBroadSynonym", "val" : "myeloid progenitor cell" @@ -1670,7 +1736,7 @@ "val" : "A cell of a hematopoietic lineage.", "xrefs" : [ "GOC:add", "GO_REF:0000031" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "haematopoietic cell" @@ -1702,7 +1768,7 @@ "val" : "A hematopoietic progenitor cell that is capable of developing into only one lineage of hematopoietic cells.", "xrefs" : [ "GOC:tfm", "PMID:19022770" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#blood_and_immune_upper_slim" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#blood_and_immune_upper_slim", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "basicPropertyValues" : [ { "pred" : "http://purl.org/dc/terms/contributor", "val" : "https://orcid.org/0000-0003-1980-3228" @@ -1721,7 +1787,7 @@ "xrefs" : [ "GOC:tfm", "PMID:19022770", "https://orcid.org/0000-0001-5208-3432" ] }, "comments" : [ "This cell type is intended to be compatible with any vertebrate hematopoietic oligopotent progenitor cell. For mammalian hematopoietic oligopotent progenitor cells known to be lineage-negative, please use the term 'hematopoietic oligopotent progenitor cell' (CL_0001060)." ], - "subsets" : [ "http://purl.obolibrary.org/obo/cl#blood_and_immune_upper_slim" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#blood_and_immune_upper_slim", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "basicPropertyValues" : [ { "pred" : "http://purl.org/dc/terms/contributor", "val" : "https://orcid.org/0000-0003-1980-3228" @@ -1739,6 +1805,7 @@ "val" : "An epithelial cell derived from ectoderm.", "xrefs" : [ "FMA:69074", "GOC:tfm" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "FMA:69074" }, { @@ -1761,6 +1828,7 @@ "val" : "Epithelial cell derived from mesoderm or mesenchyme.", "xrefs" : [ "FMA:69076", "GOC:tfm" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "epithelial mesenchymal cell" @@ -1788,7 +1856,7 @@ "xrefs" : [ "GOC:dsd", "GOC:tfm", "PMID:12768659" ] }, "comments" : [ "These cells are reportedly CD31-positive, CD34-positive, CD144-positive, TAL1-positive." ], - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "vascular endothelial cell" @@ -1802,10 +1870,15 @@ "val" : "CALOHA:TS-1106" }, { "val" : "FMA:67755" + }, { + "val" : "https://cellxgene.cziscience.com/cellguide/CL_0002139" } ], "basicPropertyValues" : [ { "pred" : "http://purl.org/dc/terms/contributor", "val" : "https://orcid.org/0000-0003-1980-3228" + }, { + "pred" : "http://purl.org/dc/terms/description", + "val" : "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nEndothelial cells of the vascular tree, commonly referred to as vascular endothelial cells, line the entire circulatory system, from the heart to the smallest capillaries. These cells have a unique, flattened shape, and are tightly bound together, forming a thin layer known as the endothelium. The endothelium is responsible for maintaining the interior surface of blood vessels, and plays a critical role in ensuring the smooth flow of blood. \nVascular endothelial cells act as a semi-permeable membrane, controlling the passage of materials and the transit of white blood cells into and out of the bloodstream. These cells are also involved in blood coagulation. When a blood vessel is damaged, endothelial cells promote clotting to prevent excessive bleeding and facilitate wound healing. Other functions include regulation of blood pressure and blood volume by releasing vasodilators and vasoconstrictors to either widen or constrict blood vessels, accordingly.\nFurthermore, the endothelial cells are crucial in the formation of new blood vessels, a process known as angiogenesis. This is particularly important in wound healing and the growth of new tissues during development or after injury. In the context of diseases such as cancer, angiogenesis helps facilitate tumor growth by providing nutrients and oxygen." }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2010-08-24T02:06:40Z" @@ -1820,7 +1893,7 @@ "val" : "An endothelial cell found in capillaries.", "xrefs" : [ "GOC:tfm" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "xrefs" : [ { "val" : "BTO:0004956" }, { @@ -1848,6 +1921,7 @@ "val" : "A cell that is a specialized type of pericyte providing structural support for the capillary loops of kidney. A flat, elongated cell with extensive fine cytoplasmic processes found outside the kidney glomerulus near the macula densa and bound laterally by afferent and efferent arterioles. Being phagocytic, this cell participates in the continuous turnover of the basal lamina by removing its outer portion containing residues of filtration, while the lamina is renewed on its inner surface by the endothelial cells.", "xrefs" : [ "GOC:tfm", "ISBN:0412046911", "http:/www.copewithcytokines.de/cope.cgi?key=Lacis%20cells" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "Goormaghtigh cell" @@ -1881,7 +1955,7 @@ "xrefs" : [ "GOC:tfm", "PMID:15840009" ] }, "comments" : [ "Glomerular endothelial cells have 60-80 nm fenestrations typically lacking diaphragms in adults but present during embryonic development. Some studies found diaphragms in 2-6% of mature rat glomerular capillaries. Their presence may depend on fixation techniques, developmental stage, or dynamic cell changes. Additionally, these cells help maintain the structural integrity of glomerular capillaries through interactions with the basement membrane and podocytes." ], - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#kidney_upper_slim" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#kidney_upper_slim", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "BTO:0004632" }, { @@ -1904,6 +1978,7 @@ "val" : "A cell containing at least one nucleus.", "xrefs" : [ "GOC:tfm" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "FMA:67513" } ], @@ -1924,7 +1999,7 @@ "val" : "An epithelial cell of the distal convoluted tubule of the kidney that helps regulate systemic levels of potassium, sodium, calcium, and pH.", "xrefs" : [ "GOC:tfm", "ISBN:0517223651" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#kidney_upper_slim" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#kidney_upper_slim", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "kidney distal tubule epithelial cell" @@ -1945,7 +2020,7 @@ "xrefs" : [ "GOC:tfm", "ISBN:1-4160-2328-3" ] }, "comments" : [ "The vast majority of proximal tubule epithelial cells have a brush border, but there are rare exceptions." ], - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#kidney_upper_slim", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#kidney_upper_slim", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "kidney proximal tubule epithelial cell" @@ -1969,7 +2044,7 @@ "val" : "A cell that is part of the nervous system.", "xrefs" : [ "GOC:tfm", "ISBN:0618947256" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "CALOHA:TS-2040" }, { @@ -1992,7 +2067,7 @@ "val" : "A cell of the supporting or framework tissue of the body, arising chiefly from the embryonic mesoderm and including adipose tissue, cartilage, and bone.", "xrefs" : [ "GOC:tfm", "ISBN:0618947256" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "CALOHA:TS-2096" }, { @@ -2019,6 +2094,7 @@ "val" : "A cell of the embryo.", "xrefs" : [ "FMA:0618947256" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "CALOHA:TS-0263" }, { @@ -2027,10 +2103,15 @@ "val" : "WBbt:0007028" }, { "val" : "ZFA:0007089" + }, { + "val" : "https://cellxgene.cziscience.com/cellguide/CL_0002321" } ], "basicPropertyValues" : [ { "pred" : "http://purl.org/dc/terms/contributor", "val" : "https://orcid.org/0000-0003-1980-3228" + }, { + "pred" : "http://purl.org/dc/terms/description", + "val" : "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nEmbryonic cells in metazoans, which include all multicellular animals, are biological units in their earliest developmental stages from conception until the organism is fully formed. \nThey are derived from a fertilized egg, which undergoes a series of cell divisions to produce a multicellular organism. During the early phases of embryonic development, these cells exhibit pluripotency, meaning they possess the potential to differentiate into a diverse array of specialized cell types that constitute different body tissues and structures. \nThe balance between cell proliferation and differentiation in embryonic cells is crucial for successful development. When cells continue to divide without differentiating, overgrowth may occur leading to conditions such as teratomas (tumors of embryonic cells). Conversely, if cell differentiation proceeds at the expense of cell proliferation, developmental anomalies could occur regarding size or mass of the organism or its parts." }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2010-09-15T03:39:21Z" @@ -2046,6 +2127,7 @@ "xrefs" : [ "GOC:tfm" ] }, "comments" : [ "From Onard of the FMA: Cardiac muscle cell or cardiac myocyte is a striated muscle cell. Cardiocyte on the other hand is any cell in the heart which includes cells other than muscle cells (e.g. endothelial cell of endocardium). Unless there is a consensus among anatomists that cardiocytes refer only to muscle cells, we will treat them as a general class of cells in the heart." ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "heart cell" @@ -2076,7 +2158,7 @@ "val" : "An epithelial cell of the kidney.", "xrefs" : [ "GOC:tfm", "KUPO:SJ" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "KUPO:0001019" }, { @@ -2099,6 +2181,7 @@ "val" : "An epithelial cell of the kidney cortex.", "xrefs" : [ "GOC:tfm" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "KUPO:0001016" } ] @@ -2112,6 +2195,7 @@ "val" : "A squamous shaped endothelial cell.", "xrefs" : [ "GOC:dos" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "basicPropertyValues" : [ { "pred" : "http://purl.org/dc/terms/contributor", "val" : "https://orcid.org/0000-0003-1980-3228" @@ -2128,6 +2212,7 @@ "definition" : { "val" : "A cell that is part of a cortex of kidney." }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "basicPropertyValues" : [ { "pred" : "http://purl.org/dc/terms/contributor", "val" : "https://orcid.org/0000-0002-0956-8634" @@ -2145,7 +2230,7 @@ "val" : "A cuboidal epithelial cell of the kidney which regulates sodium and potassium balance. The activity of sodium and potassium channels on the apical membrane of the cell is regulated by aldosterone and vasopressin. In mammals this cell type is located in the renal collecting duct system.", "xrefs" : [ "CL:CVS" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "ZFA:0005322" }, { @@ -2153,7 +2238,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://purl.org/dc/terms/description", - "val" : "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional.\n\nRenal principal cells are the major cell type in the initial collecting tubule and the cortical and outer medullary collecting ducts, as well as the connecting tubule, in the nephrons of the kidneys.\nA key function of renal principal cells is the regulation of water balance in the body. These cells express aquaporin-2 (AQP2) water channels, which facilitate the reabsorption of water from the fluid within the renal tubule lumen back into the blood. The translocation of AQP2 to the cell membrane is controlled by the hormone vasopressin: In response to high vasopressin levels, AQP2 moves to the cell membrane, allowing water to pass through effectively and be reabsorbed, therefore concentrating the urine. Conversely, in low vasopressin conditions, AQP2 is removed from the membrane, reducing water reabsorption and diluting the urine. \nRenal principal cells are also involved in the regulation of sodium and potassium levels in the body. They have sodium channels (ENaC) in their luminal membranes which permit the reabsorption of sodium ions from the tubule fluid back into the blood, resulting in a net reabsorption of sodium ions into the systemic circulation. This process is controlled, in part, by the hormone aldosterone. Additionally, renal principal cells contain potassium channels that facilitate the secretion of potassium ions into the urine. The activities of these channels, in coordination with other cell types in the nephron, are critical for maintaining electrolyte balance and overall body homeostasis." + "val" : "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nRenal principal cells are the major cell type in the initial collecting tubule and the cortical and outer medullary collecting ducts, as well as the connecting tubule, in the nephrons of the kidneys.\nA key function of renal principal cells is the regulation of water balance in the body. These cells express aquaporin-2 (AQP2) water channels, which facilitate the reabsorption of water from the fluid within the renal tubule lumen back into the blood. The translocation of AQP2 to the cell membrane is controlled by the hormone vasopressin: In response to high vasopressin levels, AQP2 moves to the cell membrane, allowing water to pass through effectively and be reabsorbed, therefore concentrating the urine. Conversely, in low vasopressin conditions, AQP2 is removed from the membrane, reducing water reabsorption and diluting the urine. \nRenal principal cells are also involved in the regulation of sodium and potassium levels in the body. They have sodium channels (ENaC) in their luminal membranes which permit the reabsorption of sodium ions from the tubule fluid back into the blood, resulting in a net reabsorption of sodium ions into the systemic circulation. This process is controlled, in part, by the hormone aldosterone. Additionally, renal principal cells contain potassium channels that facilitate the secretion of potassium ions into the urine. The activities of these channels, in coordination with other cell types in the nephron, are critical for maintaining electrolyte balance and overall body homeostasis." } ] } }, { @@ -2165,6 +2250,7 @@ "val" : "Cell that is part of the neural crest region of the neuroepithelium, prior to migration. Note that not all premigratory neural crest cells may become migratory neural crest cells.", "xrefs" : [ "UBERONREF:0000002" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "ZFA:0007084" } ], @@ -2184,7 +2270,8 @@ "definition" : { "val" : "Any muscle cell in which the fibers are not organised into sarcomeres.", "xrefs" : [ "GOC:DOS" ] - } + }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ] } }, { "id" : "http://purl.obolibrary.org/obo/CL_0008001", @@ -2195,7 +2282,7 @@ "val" : "Any hematopoietic cell that is a precursor of some other hematopoietic cell type.", "xrefs" : [ "GOC:dos" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ] + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ] } }, { "id" : "http://purl.obolibrary.org/obo/CL_0008007", @@ -2206,6 +2293,7 @@ "val" : "A muscle cell that is part of some visceral muscle.", "xrefs" : [ "GOC:dos" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "FBbt:00005070" } ] @@ -2218,7 +2306,7 @@ "definition" : { "val" : "A non-polarised cell precursor cell that is part of some mesenchyme, is associated with the cell matrix but is not connected to other cells and is capable of migration." }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "mesenchyme cell" @@ -2237,7 +2325,7 @@ "val" : "Mural cells are pericytes and the vascular smooth muscle cells (vSMCs) of the microcirculation.", "xrefs" : [ "Wiki:Mural_cell&oldid=930603194" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#added_for_HCA", "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#added_for_HCA", "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "xrefs" : [ { "val" : "ZFA:0005944" } ], @@ -2260,6 +2348,7 @@ "definition" : { "val" : "A zygote in a plant or an animal." }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "MESH:D015053" } ], @@ -2277,13 +2366,13 @@ "val" : "A cell of the neural crest. Neural crest cells are multipotent. Premigratory neural crest cells are found at the neural plate boarder, some of which will undergo ectomesynchymal transition and delamination to form migratory neural crest cells.", "xrefs" : [ "https://orcid.org/0000-0001-5208-3432", "https://orcid.org/0000-0002-9900-7880" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "https://cellxgene.cziscience.com/cellguide/CL_0011012" } ], "basicPropertyValues" : [ { "pred" : "http://purl.org/dc/terms/description", - "val" : "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional.\n\nNeural crest cells are a group of transient and highly migratory cells that originate from the neuroectoderm during the early stages of embryonic development. They are multipotent cells with an exceptional degree of plasticity, capable of differentiating into various somatic cell types and therefore play a fundamental role in the formation of various organs and tissues, making them critical contributors to the developing embryo. \nAfter the initiation of neurulation (the formation of the neural tube) neural crest cells start to undergo epithelial-to-mesenchymal transition and delaminate and migrate from the dorsal neural tube to several regions throughout the embryo. They differentiate into a range of diverse cell types, such as neurons and glial cells of the peripheral nervous system, including sensory and autonomic neurons. They also contribute to the formation of adrenal glands, pigment cells in the skin (melanocytes), cardiac structures, including parts of the heart septum and major arteries, as well as bones and cartilage of the face and skull.\nDisorders or aberrations in the development or migration of the neural crest cells can lead to serious congenital malformations, such as neurocristopathies, including Hirschsprung disease, neuroblastoma, and neurofibromatosis." + "val" : "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nNeural crest cells are a group of transient and highly migratory cells that originate from the neuroectoderm during the early stages of embryonic development. They are multipotent cells with an exceptional degree of plasticity, capable of differentiating into various somatic cell types and therefore play a fundamental role in the formation of various organs and tissues, making them critical contributors to the developing embryo. \nAfter the initiation of neurulation (the formation of the neural tube) neural crest cells start to undergo epithelial-to-mesenchymal transition and delaminate and migrate from the dorsal neural tube to several regions throughout the embryo. They differentiate into a range of diverse cell types, such as neurons and glial cells of the peripheral nervous system, including sensory and autonomic neurons. They also contribute to the formation of adrenal glands, pigment cells in the skin (melanocytes), cardiac structures, including parts of the heart septum and major arteries, as well as bones and cartilage of the face and skull.\nDisorders or aberrations in the development or migration of the neural crest cells can lead to serious congenital malformations, such as neurocristopathies, including Hirschsprung disease, neuroblastoma, and neurofibromatosis." } ] } }, { @@ -2295,7 +2384,7 @@ "val" : "A precursor cell that has a tendency to differentiate into a specific type of cell. They are descendants of stem cells, only they are more constrained in their differentiation potential or capacity for self-renewal, and are often more limited in both senses.", "xrefs" : [ "ISBN:978-1-62808-994-3", "https://doi.org/10.1016/B978-0-12-409503-8.00002-0" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "basicPropertyValues" : [ { "pred" : "http://purl.org/dc/terms/contributor", "val" : "https://orcid.org/0000-0001-5208-3432" @@ -2311,7 +2400,7 @@ "xrefs" : [ "GOC:dos" ] }, "comments" : [ "Work is needed on GO 'cell differentiation' before it is clear whether the equivalent class definition 'native cell' that capable_of some 'cell differentiation' works. Also, may want to consider merging this with non-terminally differentiated cell." ], - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ] + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ] } }, { "id" : "http://purl.obolibrary.org/obo/CL_0017502", @@ -2377,9 +2466,15 @@ "val" : "An epithelial cell that is part of the nephron.", "xrefs" : [ "GOC:tfm" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "FMA:70965" + }, { + "val" : "https://cellxgene.cziscience.com/cellguide/CL_1000449" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/description", + "val" : "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nEpithelial cells of the nephron form the epithelial lining of the nephron, the functional unit of the kidney that filters the blood to produce urine. Each kidney holds approximately one million nephrons, each of which is composed of several distinct parts, including the renal corpuscle, the proximal tubule, the loop of Henle, and the distal tubule. All sections are lined with highly specialized epithelial cells adapted to perform different functions within the sections of the nephron. \nThe different epithelial cells of the nephron play crucial roles in the process of filtration, reabsorption, secretion, and excretion, essential tasks for the regulation of body fluid composition and volume. During filtration, the blood is forced through the walls of glomerular capillaries into the Bowman's capsule, where waste products, electrolytes, and water are separated from the blood cells and proteins. As the filtrate then passes through the nephron, epithelial cells of the tubular portion reabsorb useful substances such as glucose, amino acids, and electrolytes, along with most of the water back into the bloodstream. Waste products like urea and creatinine, as well as excess ions and water, remain in the tubule for elimination.\nIn addition, epithelial cells of the nephron also play a vital part in maintaining the body's acid-base balance by actively secreting hydrogen ions into the urine while reabsorbing bicarbonate from the urine back into the blood. They are also involved in the regulation of blood pressure through the renin-angiotensin-aldosterone system and contribute to erythrocyte production by releasing the hormone erythropoietin in response to low oxygen levels in the blood. Abnormalities or damage in renal epithelial cells often result in impaired kidney function, leading to various renal diseases." } ] } }, { @@ -2391,7 +2486,7 @@ "val" : "An epithelial cell that is part of the glomerular capsule.", "xrefs" : [ "GOC:tfm" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#kidney_upper_slim" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#kidney_upper_slim", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "Bowmans capsule epithelial cell" @@ -2415,7 +2510,7 @@ "val" : "An epithelial cell that is part of the collecting duct of renal tubule.", "xrefs" : [ "GOC:tfm" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#kidney_upper_slim", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#kidney_upper_slim", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "epithelial cell of renal collecting tubule", @@ -2433,7 +2528,7 @@ "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" }, { "pred" : "http://purl.org/dc/terms/description", - "val" : "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional.\n\nKidney collecting duct epithelial cells are a specialized type of cells that form an integral part of the renal system. Located in the collecting duct system of the kidneys, these cells are responsible for one of the final steps in the process of urine formation, and they are instrumental in the fine tuning of the volume and composition of urine by reabsorbing water and certain solutes back into the bloodstream.\nThese cells express specific channels and carriers that actively and passively transport ions and water. They also have channels on their membranes, such as sodium channels and potassium channels, involved in reabsorbing or secreting these electrolytes depending upon the body's needs. The function of renal collecting duct epithelial cells can be regulated by a variety of hormones, including vasopressin (antidiuretic hormone), which can modulate the ion channels and carriers and hence indirectly influence body fluid homeostasis.\nAside from their function in ion and water balance, kidney collecting duct epithelial cells also aid in maintaining the body's acid-base balance. They have specialized functionality to secret hydrogen ions into the tubular lumen, which contributes to acid excretion. Any dysfunction may have serious implications and lead to various renal or systemic diseases, exemplifying the importance of these cells in maintaining overall body homeostasis." + "val" : "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nKidney collecting duct epithelial cells are a specialized type of cells that form an integral part of the renal system. Located in the collecting duct system of the kidneys, these cells are responsible for one of the final steps in the process of urine formation, and they are instrumental in the fine tuning of the volume and composition of urine by reabsorbing water and certain solutes back into the bloodstream.\nThese cells express specific channels and carriers that actively and passively transport ions and water. They also have channels on their membranes, such as sodium channels and potassium channels, involved in reabsorbing or secreting these electrolytes depending upon the body's needs. The function of renal collecting duct epithelial cells can be regulated by a variety of hormones, including vasopressin (antidiuretic hormone), which can modulate the ion channels and carriers and hence indirectly influence body fluid homeostasis.\nAside from their function in ion and water balance, kidney collecting duct epithelial cells also aid in maintaining the body's acid-base balance. They have specialized functionality to secret hydrogen ions into the tubular lumen, which contributes to acid excretion. Any dysfunction may have serious implications and lead to various renal or systemic diseases, exemplifying the importance of these cells in maintaining overall body homeostasis." } ] } }, { @@ -2446,7 +2541,7 @@ "xrefs" : [ "GOC:tfm" ] }, "comments" : [ "This needs to be further defined as a juxtamedullary nephron. Will request the juxtamedullary nephron tubule class from UBERON." ], - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "kidney tubule epithelial cell" @@ -2465,7 +2560,7 @@ "definition" : { "val" : "A cell that is part of a kidney." }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "KUPO:0001010" }, { @@ -2480,7 +2575,7 @@ "definition" : { "val" : "A cell that is part of kidney interstitium." }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#kidney_upper_slim" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#kidney_upper_slim", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "KUPO:0001013" }, { @@ -2496,6 +2591,7 @@ "val" : "A cell that is part of a renal medulla.", "xrefs" : [ "PMID:22343825" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "KUPO:0001017" }, { @@ -2510,7 +2606,7 @@ "definition" : { "val" : "A cell that is part of a renal pelvis." }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#kidney_upper_slim" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#kidney_upper_slim", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "KUPO:0001018" } ] @@ -2523,7 +2619,7 @@ "definition" : { "val" : "A cell that is part of a nephron tubule." }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#kidney_upper_slim" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#kidney_upper_slim", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "KUPO:0001020" } ] @@ -2537,7 +2633,7 @@ "val" : "Any kidney epithelial cell that is part of some glomerular epithelium.", "xrefs" : [ "FBC:Autogenerated" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "KUPO:0001023" } ] @@ -2550,7 +2646,7 @@ "definition" : { "val" : "An epithelial cell that is part of a renal medulla collecting duct." }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#kidney_upper_slim" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#kidney_upper_slim", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "KUPO:0001060" } ] @@ -2564,7 +2660,7 @@ "val" : "Any kidney cell that is part of some papillary duct.", "xrefs" : [ "FBC:Autogenerated" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#kidney_upper_slim" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#kidney_upper_slim", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "KUPO:0001064" } ] @@ -2578,7 +2674,7 @@ "val" : "Any renal cortical epithelial cell that is part of some renal corpuscle.", "xrefs" : [ "FBC:Autogenerated" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#kidney_upper_slim" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#kidney_upper_slim", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "KUPO:0001021" } ] @@ -2592,7 +2688,7 @@ "val" : "Any kidney tubule cell that is part of some renal cortex tubule.", "xrefs" : [ "FBC:Autogenerated" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "KUPO:0001024" } ] @@ -2606,7 +2702,7 @@ "val" : "Any kidney cortical cell that is part of some juxtaglomerular apparatus.", "xrefs" : [ "FBC:Autogenerated" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#kidney_upper_slim" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#kidney_upper_slim", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "juxtaglomerulus cell", @@ -2625,7 +2721,7 @@ "val" : "A fibroblast that is part of an interstitial compartment of a kidney.", "xrefs" : [ "PMID:10559635" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "xrefs" : [ { "val" : "KUPO:0001102" } ], @@ -2643,6 +2739,7 @@ "val" : "Any kidney corpuscule cell that is part of some renal glomerulus.", "xrefs" : [ "FBC:Autogenerated" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "KUPO:0001036" } ] @@ -2656,13 +2753,18 @@ "val" : "Any nephron tubule epithelial cell that is part of some renal connecting tubule.", "xrefs" : [ "FBC:Autogenerated" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#kidney_upper_slim", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#kidney_upper_slim", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "xrefs" : [ { "val" : "KUPO:0001058" + }, { + "val" : "https://cellxgene.cziscience.com/cellguide/CL_1000768" } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" + }, { + "pred" : "http://purl.org/dc/terms/description", + "val" : "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nKidney connecting tubule epithelial cells are found in collecting duct system of the kidney, specifically in at the interconnection segment between the nephron and the collecting ducts. The epithelial cells lining the connecting tubule are crucial for the journey of filtrate before it empties into urine-collecting ducts and therefore play a critical role in maintaining the body’s fluid and electrolyte balance.\nOne of the principal functions of connecting tubule epithelial cells involves the selective reabsorption and secretion of various solutes. This reabsorption process includes critical regulatory electrolytes such as sodium ions (Na+), chloride ions (Cl-), and bicarbonate ions (HCO3-), thus playing a role in the regulation of the acid-base homeostasis. Their function also involves the secretion of potassium ions (K+) into the renal tubular fluid.\nThe connecting tubule epithelial cells are primarily intercalated cells, which can be categorized into two types according to their specific functions: type A intercalated cells, which secrete acid, and the type B intercalated cells, which secrete base (bicarbonate) and reabsorb chloride. By regulating the concentrations of these ions, as well as reabsorption of water, connecting tubule epithelial cells contribute substantively to maintaining the body's electrolyte levels, pH balance, and overall homeostasis.\nIn addition to intercalating cells, the collecting duct system also has principal cells, which are characterized by the expression of the water channel AQP2. AQP2-expressing cells have also been identified in connecting tubules, but there is some controversy whether these represent a unique cell type as there are some morphologic differences compared with principal cells." } ] } }, { @@ -2674,13 +2776,18 @@ "val" : "Any epithelial cell of distal tubule that is part of some distal convoluted tubule.", "xrefs" : [ "FBC:Autogenerated" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#kidney_upper_slim", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#kidney_upper_slim", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "xrefs" : [ { "val" : "KUPO:0001056" + }, { + "val" : "https://cellxgene.cziscience.com/cellguide/CL_1000849" } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" + }, { + "pred" : "http://purl.org/dc/terms/description", + "val" : "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nKidney distal convoluted tubule epithelial cells, often referred to simply as distal convoluted tubule (DCT) cells, constitute a significant portion of the nephron -- the functional building unit of the kidney involved in filtration and reabsorption of substances from blood. The DCT epithelial cells form lining of the distal convoluted tubule, a segment of the nephron located after the loop of Henle and before the collecting tubule. These cells are characterized by unique morphological features such as small size, low height and fewer microvilli compared to proximal convoluted tubule epithelial cells. \nThese cells perform a host of vital functions contributing to the regulation of extracellular fluid volume and electrolyte balance, blood pressure and pH. While the DCT is less prominent in water and sodium reabsorption compared to the proximal tubule and the loop of Henle, it plays a crucial role in fine-tuning the process. DCT epithelial cells are responsible for the final adjustments of sodium, potassium and calcium reabsorption, thereby affecting overall fluid and electrolyte balance, blood pressure regulation and bone health. The reabsorption process is regulated by hormones including aldosterone and parathyroid hormone.\nThe distal convoluted tubule (DCT) also plays a significant role in acid-base homeostasis by secreting protons (H+) into the tubular fluid and reabsorbing bicarbonate ions (HCO3-), thus regulating the pH of the blood. The ability of DCT cells to adjust urine concentration plays a part in maintaining the body’s pH balance and preventing conditions like acidosis or alkalosis. In summary, kidney distal convoluted tubule epithelial cells perform functions that are crucial to maintaining body's homeostasis." } ] } }, { @@ -2692,6 +2799,7 @@ "val" : "A blood vessel cell that is part of a kidney.", "xrefs" : [ "PMID:34843404" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "KUPO:0001014" } ] @@ -2705,7 +2813,7 @@ "val" : "Any kidney blood vessel cell that is part of some kidney arterial blood vessel.", "xrefs" : [ "FBC:Autogenerated" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#kidney_upper_slim" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#kidney_upper_slim", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "KUPO:0001029" } ] @@ -2718,7 +2826,7 @@ "definition" : { "val" : "An endothelial cell that is part of the capillary of the kidney." }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#kidney_upper_slim" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#kidney_upper_slim", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "KUPO:0001030" } ] @@ -2732,7 +2840,7 @@ "val" : "Any kidney blood vessel cell that is part of some renal vein.", "xrefs" : [ "FBC:Autogenerated" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#kidney_upper_slim" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#kidney_upper_slim", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "KUPO:0001031" } ] @@ -2746,7 +2854,7 @@ "val" : "Any nephron tubule epithelial cell that is part of some loop of Henle.", "xrefs" : [ "FBC:Autogenerated" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "KUPO:0001047" } ] @@ -2760,7 +2868,7 @@ "val" : "Any kidney loop of Henle epithelial cell that is part of some ascending limb of loop of Henle.", "xrefs" : [ "FBC:Autogenerated" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#kidney_upper_slim" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#kidney_upper_slim", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "KUPO:0001048" } ] @@ -2774,9 +2882,15 @@ "val" : "Any kidney loop of Henle epithelial cell that is part of some descending limb of loop of Henle.", "xrefs" : [ "FBC:Autogenerated" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#kidney_upper_slim" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#kidney_upper_slim", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "KUPO:0001053" + }, { + "val" : "https://cellxgene.cziscience.com/cellguide/CL_1001021" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/description", + "val" : "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nThe kidney loop of Henle descending limb epithelial cells are highly specialized cells that play a crucial role in maintaining the body's salt and water balance. These cells line the descending limb of the loop of Henle, which is a portion of the renal tubule located in the kidneys, an organ responsible for filtering waste products, ions and extra water from the blood and converting them into urine. However, the descending limb epithelial cells are specifically involved in the countercurrent multiplication system, a mechanism to concentrate urine that involves both active and passive transport processes. \nThese cells are notably permeable to water but relatively impermeable to solutes, a characteristic that dramatically influences the osmotic gradient in the renal medulla. As filtrate initially descends down the loop of Henle, water gets drawn out due to the increasing osmotic gradient, thereby concentrating the filtrate. Additionally, these epithelial cells are exceptionally thin walled, allowing water to freely diffuse across the membrane.\nFurthermore, the kidney loop of Henle descending limb epithelial cells are inextricably linked to the functioning of numerous diuretic drugs, which work by blocking the reabsorption of water and certain electrolytes in the kidneys, leading to increased urine production to rid the body of excess fluids." } ] } }, { @@ -2787,7 +2901,7 @@ "definition" : { "val" : "A cell that is part of a collecting duct of renal tubule." }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "xrefs" : [ { "val" : "KUPO:0001012" }, { @@ -2802,7 +2916,7 @@ "definition" : { "val" : "A pericyte cell located in the kidney interstitium." }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "xrefs" : [ { "val" : "KUPO:0001104" } ], @@ -2820,6 +2934,7 @@ "val" : "Any blood vessel endothelial cell that is part of a microvascular endothelium.", "xrefs" : [ "GOC:TermGenie" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "basicPropertyValues" : [ { "pred" : "http://purl.org/dc/terms/contributor", "val" : "http://www.wikidata.org/entity/Q35563349" @@ -2837,6 +2952,7 @@ "val" : "Any cell that is located within the interstitium between the cells most prominent in defining a given tissue. \"Interstitial cell\" is a morphological term and refers to a variety of cells with differing origins and phenotypes.", "xrefs" : [ "PMID:24987007" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "basicPropertyValues" : [ { "pred" : "http://purl.org/dc/terms/date", "val" : "2022-11-30T14:35:08Z" @@ -2851,6 +2967,7 @@ "val" : "A cell that is adjacent to a vessel. A perivascular cell plays a crucial role in maintaining vascular function and tissue homeostasis. This cell type regulates vessel integrity and flow dynamics.", "xrefs" : [ "PMID:24928499", "PMID:27889329" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#human_subset", "http://purl.obolibrary.org/obo/cl#mouse_subset" ], "basicPropertyValues" : [ { "pred" : "http://purl.org/dc/terms/contributor", "val" : "https://orcid.org/0000-0001-6677-8489" @@ -2878,9 +2995,6 @@ "val" : "Wikipedia:Mitosis" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0007067" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" } ] @@ -2930,15 +3044,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/geneontology/go-ontology/issues/28301" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0000789" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0000790" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0005717" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "cellular_component" @@ -2971,12 +3076,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/geneontology/go-ontology/issues/22355" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0005720" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0035328" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "cellular_component" @@ -3133,9 +3232,6 @@ "val" : "Wikipedia:Neurulation" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0001679" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" } ] @@ -3568,9 +3664,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/geneontology/go-ontology/issues/17729" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0008372" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "cellular_component" @@ -3684,12 +3777,6 @@ "val" : "Wikipedia:Basement_membrane" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0005605" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0008003" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "cellular_component" } ] @@ -3882,9 +3969,6 @@ "val" : "Wikipedia:Ribosome" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0033279" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "cellular_component" } ] @@ -3938,12 +4022,6 @@ "val" : "Wikipedia:Cell_membrane" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0005887" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0005904" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "cellular_component" } ] @@ -4012,15 +4090,6 @@ "val" : "Wikipedia:Translation_(genetics)" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0006416" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0006453" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0043037" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" } ] @@ -4049,12 +4118,6 @@ "val" : "translation initiation" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0006440" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0006454" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" } ] @@ -4077,12 +4140,6 @@ "val" : "translation elongation" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0006442" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0006455" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" } ] @@ -4107,12 +4164,6 @@ "val" : "translational complex disassembly" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0006443" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0006456" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" } ] @@ -4135,21 +4186,9 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/geneontology/go-ontology/issues/20292" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "jl" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2012-12-13T16:25:32Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0015457" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0015460" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0044765" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" @@ -4257,12 +4296,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002161", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_4896" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0006917" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0008632" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" @@ -4339,15 +4372,9 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/geneontology/go-ontology/issues/27189" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "jl" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2013-12-19T15:25:51Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:1902589" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" @@ -4443,21 +4470,6 @@ "val" : "Wikipedia:Signal_transduction" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0023014" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0023015" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0023016" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0023033" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0023045" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" } ] @@ -4551,9 +4563,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002161", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_4751" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0009552" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" @@ -4693,9 +4702,6 @@ "val" : "hemolymph circulation" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0070261" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" } ] @@ -4742,15 +4748,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/geneontology/go-ontology/issues/23112" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0008105" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0016249" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0034613" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" @@ -4786,21 +4783,9 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/geneontology/go-ontology/issues/24968" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "jl" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2012-09-19T15:05:24Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0000004" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0007582" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0044699" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" @@ -4812,7 +4797,7 @@ "type" : "CLASS", "meta" : { "definition" : { - "val" : "The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.", + "val" : "A cellular process consisting of the biochemical pathways by which a living organism transforms chemical substances. This includes including anabolism (biosynthetic process) and catabolism (catabolic process). Metabolic processes includes the transformation of small molecules, as well macromolecular processes such as DNA repair and replication, protein synthesis and degradation.", "xrefs" : [ "GOC:go_curators", "ISBN:0198547684" ] }, "comments" : [ "Note that metabolic processes do not include single functions or processes such as protein-protein interactions, protein-nucleic acids, nor receptor-ligand interactions." ], @@ -4820,18 +4805,6 @@ "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "metabolism" - }, { - "pred" : "hasNarrowSynonym", - "val" : "metabolic process resulting in cell growth" - }, { - "pred" : "hasNarrowSynonym", - "val" : "metabolism resulting in cell growth" - }, { - "pred" : "hasNarrowSynonym", - "val" : "multicellular organism metabolic process" - }, { - "pred" : "hasRelatedSynonym", - "val" : "single-organism metabolic process" } ], "xrefs" : [ { "val" : "Wikipedia:Metabolism" @@ -4840,17 +4813,11 @@ "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/geneontology/go-ontology/issues/26424" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "jl" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/geneontology/go-ontology/issues/28932" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2012-10-17T15:46:40Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0044236" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0044710" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" @@ -4915,7 +4882,7 @@ "type" : "CLASS", "meta" : { "definition" : { - "val" : "The chemical reactions and pathways resulting in the formation of substances; typically the energy-requiring part of metabolism in which simpler substances are transformed into more complex ones.", + "val" : "A cellular process consisting of the biochemical pathways by which a living organism synthesizes chemical substances. This typically represents the energy-requiring part of metabolism in which simpler substances are transformed into more complex ones.", "xrefs" : [ "GOC:curators", "ISBN:0198547684" ] }, "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_chembl", "http://purl.obolibrary.org/obo/go#goslim_metagenomics", "http://purl.obolibrary.org/obo/go#goslim_plant", "http://purl.obolibrary.org/obo/go#goslim_plant_ribbon" ], @@ -4942,17 +4909,11 @@ "val" : "Wikipedia:Anabolism" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "jl" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/geneontology/go-ontology/issues/28932" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2012-10-17T15:52:18Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0044274" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0044711" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" @@ -4995,9 +4956,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/geneontology/go-ontology/issues/27189" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0043284" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" @@ -5023,12 +4981,6 @@ "val" : "protein secretion resulting in cell fate commitment" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0045166" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0045731" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" } ] @@ -5108,9 +5060,6 @@ "val" : "Wikipedia:Embryogenesis" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0009795" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" } ] @@ -5212,20 +5161,8 @@ "val" : "single-organism cellular process" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "jl" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2012-12-11T16:56:55Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0008151" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0044763" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0050875" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" @@ -5294,9 +5231,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/geneontology/go-ontology/issues/24835" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0016244" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" @@ -5317,9 +5251,6 @@ "val" : "enzyme transport" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0015831" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" } ] @@ -5391,15 +5322,6 @@ "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2014-03-06T11:37:54Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0016021" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0098589" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0098805" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "cellular_component" @@ -5438,12 +5360,6 @@ "xrefs" : [ "GOC:mah" ] } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0044235" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0071842" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" } ] @@ -5596,15 +5512,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/geneontology/go-ontology/issues/27189" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0006411" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0044267" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0044268" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" @@ -5681,9 +5588,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/geneontology/go-ontology/issues/27189" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0071845" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" @@ -5709,15 +5613,9 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/geneontology/go-ontology/issues/27054" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "jl" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2012-09-19T15:56:06Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0044702" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" @@ -5756,9 +5654,6 @@ "val" : "cellular component assembly at cellular level" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0071844" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" } ] @@ -5840,17 +5735,8 @@ "val" : "single organism signaling" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "jl" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2010-02-16T09:30:50Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0023046" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0044700" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" @@ -6093,9 +5979,6 @@ "xrefs" : [ "GOC:bf" ] } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0000068" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" } ] @@ -6178,9 +6061,6 @@ "val" : "Wikipedia:Extracellular_matrix" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0005578" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "cellular_component" } ] @@ -6236,9 +6116,6 @@ "val" : "Wikipedia:Vesicle_(biology)" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0031988" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "cellular_component" } ] @@ -6333,18 +6210,9 @@ }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002161", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_4932" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "jl" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2012-09-19T16:07:47Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0044707" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0050874" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" @@ -6368,14 +6236,8 @@ "val" : "single-organism developmental process" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "jl" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2012-12-19T12:21:31Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0044767" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" @@ -6427,15 +6289,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/geneontology/go-ontology/issues/22580" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0034623" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0043241" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0043624" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" @@ -6469,9 +6322,6 @@ "val" : "protein-protein complex" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0043234" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "cellular_component" } ] @@ -6544,9 +6394,6 @@ "val" : "ATP hydrolysis coupled ion transmembrane transport" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0099131" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" } ] @@ -6620,9 +6467,6 @@ "val" : "establishment of protein localization in extracellular region" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "bf" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2010-11-09T10:25:08Z" }, { @@ -6657,9 +6501,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002161", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_4751" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "bf" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2011-12-12T10:53:24Z" @@ -6759,15 +6600,6 @@ "val" : "regulation of homeostatic process" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0032844" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0032845" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0032846" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" } ] @@ -6856,15 +6688,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/geneontology/go-ontology/issues/26424" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0034960" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0043283" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0044259" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" @@ -6917,7 +6740,7 @@ } }, { "id" : "http://purl.obolibrary.org/obo/GO_0043228", - "lbl" : "non-membrane-bounded organelle", + "lbl" : "membraneless organelle", "type" : "CLASS", "meta" : { "definition" : { @@ -6926,6 +6749,12 @@ }, "subsets" : [ "http://purl.obolibrary.org/obo/go#gocheck_do_not_annotate", "http://purl.obolibrary.org/obo/go#goslim_mouse" ], "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "membrane-less organelle" + }, { + "pred" : "hasExactSynonym", + "val" : "non-membrane-bounded organelle" + }, { "pred" : "hasExactSynonym", "val" : "non-membrane-enclosed organelle" }, { @@ -6941,6 +6770,9 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/geneontology/go-ontology/issues/28153" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/geneontology/go-ontology/issues/29106" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "cellular_component" @@ -7000,7 +6832,7 @@ } }, { "id" : "http://purl.obolibrary.org/obo/GO_0043232", - "lbl" : "intracellular non-membrane-bounded organelle", + "lbl" : "intracellular membraneless organelle", "type" : "CLASS", "meta" : { "definition" : { @@ -7009,10 +6841,16 @@ }, "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_pir" ], "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "intracellular non-membrane-bounded organelle" + }, { "pred" : "hasExactSynonym", "val" : "intracellular non-membrane-enclosed organelle" } ], "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/geneontology/go-ontology/issues/29106" + }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "cellular_component" } ] @@ -7073,21 +6911,9 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/geneontology/go-ontology/issues/22580" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "mah" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2010-09-08T10:01:42Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0034600" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0034621" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0071822" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" @@ -7124,9 +6950,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/geneontology/go-ontology/issues/27194" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0071843" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" @@ -7149,9 +6972,6 @@ "val" : "Met-tRNA/eIF2.GTP ternary complex" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "jl" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2009-10-22T02:38:55Z" }, { @@ -7159,30 +6979,6 @@ "val" : "cellular_component" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/GO_0044237", - "lbl" : "cellular metabolic process", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "The chemical reactions and pathways by which individual cells transform chemical substances.", - "xrefs" : [ "GOC:go_curators" ] - }, - "comments" : [ "This term should not be used for direct annotation. It should be possible to make a more specific annotation to one of the children of this term." ], - "subsets" : [ "http://purl.obolibrary.org/obo/go#gocheck_do_not_annotate" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "cellular metabolism" - }, { - "pred" : "hasRelatedSynonym", - "val" : "intermediary metabolism", - "xrefs" : [ "GOC:mah" ] - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "biological_process" - } ] - } }, { "id" : "http://purl.obolibrary.org/obo/GO_0044238", "lbl" : "primary metabolic process", @@ -7208,38 +7004,6 @@ "val" : "biological_process" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/GO_0044249", - "lbl" : "cellular biosynthetic process", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "The chemical reactions and pathways resulting in the formation of substances, carried out by individual cells.", - "xrefs" : [ "GOC:jl" ] - }, - "comments" : [ "This term should not be used for direct annotation. It should be possible to make a more specific annotation to one of the children of this term." ], - "subsets" : [ "http://purl.obolibrary.org/obo/go#gocheck_do_not_annotate" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "cellular anabolism" - }, { - "pred" : "hasExactSynonym", - "val" : "cellular biosynthesis" - }, { - "pred" : "hasExactSynonym", - "val" : "cellular formation" - }, { - "pred" : "hasExactSynonym", - "val" : "cellular synthesis" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", - "val" : "https://github.com/geneontology/go-ontology/issues/27052" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "biological_process" - } ] - } }, { "id" : "http://purl.obolibrary.org/obo/GO_0045184", "lbl" : "establishment of protein localization", @@ -7451,9 +7215,6 @@ "xrefs" : [ "GOC:dph", "GOC:tb" ] } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0048828" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" } ] @@ -7673,9 +7434,6 @@ "val" : "regulation of physiological process" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0050791" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" } ] @@ -7695,9 +7453,6 @@ "val" : "regulation of cellular physiological process" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0051244" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" } ] @@ -7808,9 +7563,6 @@ "val" : "physiological response to stimulus" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0051869" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" } ] @@ -7855,15 +7607,9 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/geneontology/go-ontology/issues/27052" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "jl" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2013-12-18T13:51:04Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:1902578" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" @@ -7942,15 +7688,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/geneontology/go-ontology/issues/4585" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0006323" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0007001" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0051277" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" @@ -8013,15 +7750,9 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/geneontology/go-ontology/issues/27189" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "jl" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2013-12-18T14:04:32Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:1902580" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" @@ -8062,14 +7793,8 @@ "val" : "ATP hydrolysis coupled transmembrane transport" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "tb" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2015-10-21T13:22:47Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0090662" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" @@ -8124,9 +7849,6 @@ "xrefs" : [ "GOC:dph" ] }, "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dph" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2009-04-28T09:33:36Z" }, { @@ -8144,9 +7866,6 @@ "xrefs" : [ "GOC:dph" ] }, "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dph" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2010-05-25T09:05:34Z" }, { @@ -8164,9 +7883,6 @@ "xrefs" : [ "GOC:BHF", "GOC:rph", "PMID:21123617" ] }, "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dph" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2018-04-13T12:47:21Z" }, { @@ -8212,15 +7928,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/geneontology/go-ontology/issues/22580" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0006461" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0034622" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0043623" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" @@ -8402,9 +8109,6 @@ "xrefs" : [ "GOC:mah" ] } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "mah" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2009-06-16T04:08:29Z" }, { @@ -8423,9 +8127,6 @@ }, "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_yeast" ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "mah" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2009-09-15T03:00:51Z" }, { @@ -8451,9 +8152,6 @@ "val" : "protein localization in extracellular region" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "mah" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2010-02-25T04:00:13Z" }, { @@ -8489,9 +8187,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/geneontology/go-ontology/issues/25143" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "mah" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2010-09-08T10:10:35Z" @@ -8526,15 +8221,9 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/geneontology/go-ontology/issues/27189" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "mah" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2010-09-10T01:39:16Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0071841" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" @@ -8551,9 +8240,6 @@ }, "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_flybase_ribbon" ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "mah" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2010-10-04T01:51:47Z" }, { @@ -8576,9 +8262,6 @@ "xrefs" : [ "GOC:vesicles" ] } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "mah" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2010-10-18T03:44:18Z" }, { @@ -8598,9 +8281,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/geneontology/go-ontology/issues/22302" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "mah" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2010-02-26T02:15:40Z" @@ -8628,14 +8308,8 @@ "val" : "induction of apoptosis by extracellular signals" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pr" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2011-11-23T09:30:23Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0008624" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" @@ -8658,9 +8332,6 @@ "val" : "apoptosis" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pr" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2011-11-23T09:45:24Z" }, { @@ -8678,9 +8349,6 @@ "xrefs" : [ "GOC:pr", "GOC:sart" ] }, "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pr" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2012-01-03T03:10:17Z" }, { @@ -8700,9 +8368,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/geneontology/go-ontology/issues/22368" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pr" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2012-03-05T02:03:58Z" @@ -8737,9 +8402,6 @@ "val" : "intraluminal vesicle assembly" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pr" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2016-10-03T14:35:25Z" }, { @@ -8763,9 +8425,6 @@ "val" : "region of plasma membrane" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dos" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2014-03-06T11:55:32Z" }, { @@ -8975,14 +8634,18 @@ } }, { "id" : "http://purl.obolibrary.org/obo/GO_0110165", - "lbl" : "cellular anatomical entity", + "lbl" : "cellular anatomical structure", "type" : "CLASS", "meta" : { "definition" : { - "val" : "A part of a cellular organism that is either an immaterial entity or a material entity with granularity above the level of a protein complex but below that of an anatomical system. Or, a substance produced by a cellular organism with granularity above the level of a protein complex.", + "val" : "A part of a cellular organism consisting of a material entity with granularity above the level of a protein complex but below that of an anatomical system. Note that cellular organisms exclude viruses.", "xrefs" : [ "GOC:kmv" ] }, "subsets" : [ "http://purl.obolibrary.org/obo/go#gocheck_do_not_annotate", "http://purl.obolibrary.org/obo/go#goslim_pir" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "cellular anatomical entity" + } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/geneontology/go-ontology/issues/24200" @@ -8990,8 +8653,8 @@ "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/geneontology/go-ontology/issues/26424" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "kmv" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/geneontology/go-ontology/issues/28978" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2019-08-12T18:01:37Z" @@ -9012,9 +8675,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/geneontology/go-ontology/issues/13193" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "krc" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-03-21T17:26:07Z" @@ -9040,9 +8700,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/geneontology/go-ontology/issues/13298" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "krc" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-04-24T23:56:08Z" @@ -9063,9 +8720,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/geneontology/go-ontology/issues/13298" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "krc" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-04-26T16:07:02Z" @@ -9091,9 +8745,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/geneontology/go-ontology/issues/19910" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pg" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-03-23T14:44:23Z" @@ -9118,9 +8769,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/geneontology/go-ontology/issues/14256" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pg" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-10-23T11:53:42Z" @@ -9143,9 +8791,6 @@ "val" : "efflux" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pg" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2019-05-22T11:20:45Z" }, { @@ -9164,9 +8809,6 @@ }, "subsets" : [ "http://purl.obolibrary.org/obo/go#gocheck_do_not_annotate" ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "jl" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2014-05-22T14:22:34Z" }, { @@ -9189,9 +8831,6 @@ "xrefs" : [ "GOC:vesicles" ] } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "jl" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2014-10-22T14:26:11Z" }, { @@ -9229,17 +8868,8 @@ "val" : "Wikipedia:Ribonucleoprotein" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pr" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2015-11-19T12:26:37Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0030529" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:1990903" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "cellular_component" @@ -9326,9 +8956,6 @@ "val" : "GC_ID:1" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "NCBITaxon:85055" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "ncbi_taxonomy" } ] @@ -9360,9 +8987,6 @@ "val" : "GC_ID:1" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "NCBITaxon:40673" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "ncbi_taxonomy" } ] @@ -9696,9 +9320,6 @@ "val" : "GC_ID:1" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "NCBITaxon:109679" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "ncbi_taxonomy" } ] @@ -9923,9 +9544,6 @@ "xrefs" : [ "PATOC:GVG" ] }, "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "PATO:0000072" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "quality" } ] @@ -9961,9 +9579,6 @@ "val" : "relational shape quality" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "PATO:0001647" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "quality" } ] @@ -9987,9 +9602,6 @@ "val" : "relational structural quality" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "PATO:0001452" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "quality" } ] @@ -10087,9 +9699,6 @@ "val" : "Wikipedia:Physical_property" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "PATO:0002079" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "quality" } ] @@ -10133,12 +9742,6 @@ "val" : "snap:Quality" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "PATO:0001237" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "PATO:0001238" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "quality" } ] @@ -10350,9 +9953,6 @@ "val" : "tubulate" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "PATO:0001203" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "quality" } ] @@ -10865,9 +10465,6 @@ "val" : "high N:C ratio" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "http://orcid.org/0000-0001-5208-3432" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "quality" } ] @@ -10881,9 +10478,6 @@ "val" : "A quality of continuant that exist at the anatomical level of organisation and anything under it. This includes, but is not limited to, cells , tissues, and components." }, "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "http://orcid.org/0000-0001-7258-9596" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "quality" } ] @@ -10897,9 +10491,6 @@ "val" : "A quality inhering in an anotomical structure by virtue of its capacity to be stained by specific histological dyes." }, "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "http://orcid.org/0000-0001-7258-9596" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "quality" } ] @@ -10914,9 +10505,6 @@ "xrefs" : [ "GOC:add" ] }, "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "http://orcid.org/0000-0001-7258-9596" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "quality" } ] @@ -10930,7 +10518,7 @@ "val" : "An amino acid chain that is produced de novo by ribosome-mediated translation of a genetically-encoded mRNA, and any derivatives thereof.", "xrefs" : [ "PRO:DAN", "PRO:WCB" ] }, - "comments" : [ "The definition above excludes protein complexes, which some also consider a protein. Those who wish to refer to a class representing both senses of the word are directed to CHEBI:36080. Note that the definition allows for experimentally-manipulated genes, and allows for artifically-produced derivatives that mimic those found naturally. Proteins (in the sense defined here) that descended from a common ancestor can be classified into families and superfamilies composed of products of evolutionarily-related genes. The domain architecture of a protein is described by the order of its constituent domains. Proteins with the same domains in the same order are defined as homeomorphic [PRO:WCB]." ], + "comments" : [ "The definition above excludes protein complexes, which some also consider a protein. Those who wish to refer to a class representing both senses of the word are directed to CHEBI:36080. Note that the definition allows for experimentally-manipulated genes, and allows for artifically-produced derivatives that mimic those found naturally. Proteins (in the sense defined here) that descended from a common ancestor can be classified into families and superfamilies composed of products of evolutionarily-related genes. The domain architecture of a protein is described by the order of its constituent domains. Proteins with the same domains in the same order are defined as homeomorphic [PRO:WCB)." ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "natural protein", @@ -11957,15 +11545,15 @@ } ] } }, { - "id" : "http://purl.obolibrary.org/obo/PR_000050567", - "lbl" : "protein-containing material entity", + "id" : "http://purl.obolibrary.org/obo/PR_000064867", + "lbl" : "protein-containing molecular entity", "type" : "CLASS", "meta" : { "definition" : { - "val" : "A material entity that minimally consists of a protein.", + "val" : "A molecular entity that minimally consists of a protein.", "xrefs" : [ "PRO:DAN" ] }, - "comments" : [ "Note: This includes single proteins and derivatives thereof (PR:000000001), protein-containing complexes (GO:0032991), and protein aggregates (PR:000050566)." ], + "comments" : [ "Note: This includes single proteins and derivatives thereof (PR:000000001), protein-containing complexes (GO:0032991), and protein aggregates (PR:000050565)." ], "synonyms" : [ { "pred" : "hasNarrowSynonym", "val" : "protein", @@ -12331,9 +11919,6 @@ "val" : "galen:Wall" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "UBERON:0009915" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -12803,9 +12388,6 @@ "val" : "galen:ComplexSkeletalStructure" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "UBERON:0010322" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -13932,12 +13514,6 @@ "val" : "galen:Excretion" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "UBERON:0000324" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "UBERON:0007550" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -14081,9 +13657,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "TODO - check relationship with epiblast. Note in FMA this is not a subclass of embryo, but in uberon embryo is the whole organism from zygote onwards and thus includes the blastula" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "UBERON:0007011" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -15937,9 +15510,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0002161", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_6040" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "UBERON:0003263" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -16682,7 +16252,7 @@ "val" : "Organ system that passes nutrients (such as amino acids and electrolytes), gases, hormones, blood cells, etc. to and from cells in the body to help fight diseases and help stabilize body temperature and pH to maintain homeostasis[WP].", "xrefs" : [ "Wikipedia:Circulatory_system" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#uberon_slim" ], "synonyms" : [ { "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003011", "pred" : "hasRelatedSynonym", @@ -16707,9 +16277,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002161", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_6157" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -17909,9 +17476,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "UBERON:0004210" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -18504,9 +18068,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "UBERON:0005166" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -20191,9 +19752,6 @@ "val" : "ZFA:0000151" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "UBERON:0005794" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -20572,15 +20130,10 @@ "val" : "TAO:0001438" }, { "val" : "UMLS:C0333343" - }, { - "val" : "ZFA:0001438" }, { "val" : "galen:BodyCavity" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "UBERON:0000169" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -21856,9 +21409,6 @@ "val" : "ZFA:0000121" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "UBERON:0006258" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" }, { @@ -23433,12 +22983,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "UBERON:0002449" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "UBERON:0005098" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -23909,7 +23453,7 @@ "val" : "The part of the cardiovascular system consisting of all arteries.", "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#pheno_slim" ], "xrefs" : [ { "val" : "BTO:0004690" }, { @@ -23928,9 +23472,6 @@ "val" : "VHOG:0000273" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -23944,7 +23485,6 @@ "val" : "The part of the cardiovascular system consisting of all venous vessels. In vertebrates with a double circulation, this can be divided into systemic and pulmonary portions.", "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "vein system" @@ -23969,9 +23509,6 @@ "val" : "VHOG:0000277" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -24256,9 +23793,6 @@ "val" : "Wikipedia:Trilaminar_blastocyst" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "UBERON:0007012" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -24958,9 +24492,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "UBERON:0005165" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -27119,9 +26650,6 @@ "val" : "VSAO:0000303" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "UBERON:0007824" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -27298,9 +26826,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "consider adding new class (EMAPA:16097) for mesenchyme of embryo (some mesenchyme is extraembryonic - e.g. amnion mesoderm)" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "UBERON:0003313" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -28209,6 +27734,8 @@ "val" : "EHDAA2:0004731" }, { "val" : "Wikipedia:Coelom" + }, { + "val" : "ZFA:0001438" } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", @@ -28694,9 +28221,6 @@ "val" : "presumptive central nervous system" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "UBERON:3000469" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -28719,9 +28243,6 @@ "val" : "AAO:0000477" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "UBERON:3000477" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -29058,9 +28579,6 @@ "val" : "microvessel" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "http://orcid.org/0000-0002-2825-0621" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" }, { @@ -29081,9 +28599,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "http://orcid.org/0000-0002-6095-8718" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2022-05-25T18:21:29Z" @@ -29578,9 +29093,6 @@ "val" : "A relationship between a process and a barrier, where the process occurs in a region spanning the barrier. For cellular processes the barrier is typically a membrane. Examples include transport across a membrane and membrane depolarization." }, "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "https://orcid.org/0000-0002-7073-9172" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-07-20T17:19:37Z" } ] @@ -31862,9 +31374,6 @@ "val" : "RO:0004007" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2018-12-13T11:26:17Z" }, { @@ -31890,9 +31399,6 @@ "val" : "RO:0004008" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2018-12-13T11:26:32Z" }, { @@ -31918,9 +31424,6 @@ "val" : "RO:0004009" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2018-12-13T11:26:56Z" }, { @@ -31940,9 +31443,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0004050", "val" : "http://purl.obolibrary.org/obo/RO_0002418" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2018-03-13T23:55:05Z" @@ -31958,9 +31458,6 @@ "propertyType" : "OBJECT", "meta" : { "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2018-03-13T23:55:19Z" }, { @@ -31978,9 +31475,6 @@ "val" : "a relation between a process and a continuant, in which the process is regulated by the small molecule continuant" }, "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "https://orcid.org/0000-0003-1813-6857" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2020-04-22T20:27:26Z" } ] @@ -31998,9 +31492,6 @@ "val" : "RO:0012001" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "https://orcid.org/0000-0003-1813-6857" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2020-04-22T20:28:37Z" }, { @@ -32025,9 +31516,6 @@ "val" : "RO:0012003" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "https://orcid.org/0000-0003-1813-6857" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2020-06-08T17:21:33Z" }, { @@ -32048,9 +31536,6 @@ "val" : "a relation between a continuant and a process, in which the continuant is a small molecule that regulates the process" }, "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "https://orcid.org/0000-0003-1813-6857" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2020-06-24T13:15:17Z" } ] @@ -32065,9 +31550,6 @@ "val" : "a relation between a continuant and a process, in which the continuant is a small molecule that activates the process" }, "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "https://orcid.org/0000-0003-1813-6857" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2020-06-24T13:15:26Z" }, { @@ -32086,9 +31568,6 @@ "val" : "RO:0012008" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "https://orcid.org/0000-0003-1813-6857" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2021-02-26T07:28:29Z" }, { @@ -32113,9 +31592,6 @@ "val" : "has synaptic input or output in" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "https://orcid.org/0000-0002-1373-1705" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2020-07-17T09:26:52Z" } ] @@ -32140,13 +31616,34 @@ "val" : "has sensory terminal location" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "https://orcid.org/0000-0002-1373-1705" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2020-07-20T12:10:09Z" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0015004", + "lbl" : "has characterizing marker set", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "A relation that applies between a cell type and a set of markers that can be used to uniquely identify that cell type." + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "has marker gene combination" + }, { + "pred" : "hasExactSynonym", + "val" : "has marker signature set" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "C has_characterizing_marker_set y iff: C is a cell type and y is a collection of genes or proteins whose expression is sufficient to distinguish cell type C from most or all other cell types." + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0001-7258-9596" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/RO_0015006", "lbl" : "different in magnitude relative to", @@ -32272,9 +31769,6 @@ "val" : "RO:0040036" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2018-09-26T01:08:58Z" }, { @@ -32973,13 +32467,14 @@ "propertyType" : "ANNOTATION", "meta" : { "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2018-03-14T00:03:24Z" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/STATO_0000663", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" }, { "id" : "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "type" : "PROPERTY", @@ -33032,6 +32527,10 @@ "meta" : { "comments" : [ "a subset of general classes of cell types in the cell ontology." ] } + }, { + "id" : "http://purl.obolibrary.org/obo/cl#human_subset", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" }, { "id" : "http://purl.obolibrary.org/obo/cl#kidney_upper_slim", "lbl" : "kidney_upper_slim", @@ -33044,6 +32543,10 @@ "val" : "2023-11-22T11:18:57Z" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/cl#mouse_subset", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" }, { "id" : "http://purl.obolibrary.org/obo/go#gocheck_do_not_annotate", "type" : "PROPERTY", @@ -33366,10 +32869,6 @@ "id" : "http://purl.org/dc/elements/1.1/creator", "type" : "PROPERTY", "propertyType" : "ANNOTATION" - }, { - "id" : "http://purl.org/dc/elements/1.1/date", - "type" : "PROPERTY", - "propertyType" : "ANNOTATION" }, { "id" : "http://purl.org/dc/elements/1.1/description", "type" : "PROPERTY", @@ -33382,6 +32881,10 @@ "id" : "http://purl.org/dc/elements/1.1/title", "type" : "PROPERTY", "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.org/dc/elements/1.1/type", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" }, { "id" : "http://purl.org/dc/terms/contributor", "type" : "PROPERTY", @@ -33392,14 +32895,17 @@ "propertyType" : "ANNOTATION" }, { "id" : "http://purl.org/dc/terms/description", + "lbl" : "description", "type" : "PROPERTY", "propertyType" : "ANNOTATION" }, { "id" : "http://purl.org/dc/terms/license", + "lbl" : "license", "type" : "PROPERTY", "propertyType" : "ANNOTATION" }, { "id" : "http://purl.org/dc/terms/title", + "lbl" : "title", "type" : "PROPERTY", "propertyType" : "ANNOTATION" }, { @@ -33417,19 +32923,10 @@ "lbl" : "consider", "type" : "PROPERTY", "propertyType" : "ANNOTATION" - }, { - "id" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "type" : "PROPERTY", - "propertyType" : "ANNOTATION" }, { "id" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "type" : "PROPERTY", "propertyType" : "ANNOTATION" - }, { - "id" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "lbl" : "has_alternative_id", - "type" : "PROPERTY", - "propertyType" : "ANNOTATION" }, { "id" : "http://www.geneontology.org/formats/oboInOwl#hasBroadSynonym", "lbl" : "has_broad_synonym", @@ -33449,9 +32946,21 @@ } }, { "id" : "http://www.geneontology.org/formats/oboInOwl#hasDbXref", - "lbl" : "database_cross_reference", + "lbl" : "has cross-reference", "type" : "PROPERTY", - "propertyType" : "ANNOTATION" + "propertyType" : "ANNOTATION", + "meta" : { + "definition" : { + "val" : "An annotation property that links an ontology entity or a statement to a prefixed identifier or URI." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/information-artifact-ontology/ontology-metadata/issues/123" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0002-7356-1779" + } ] + } }, { "id" : "http://www.geneontology.org/formats/oboInOwl#hasExactSynonym", "lbl" : "has_exact_synonym", @@ -33530,10 +33039,6 @@ "id" : "http://www.geneontology.org/formats/oboInOwl#is_metadata_tag", "type" : "PROPERTY", "propertyType" : "ANNOTATION" - }, { - "id" : "http://www.geneontology.org/formats/oboInOwl#note", - "type" : "PROPERTY", - "propertyType" : "ANNOTATION" }, { "id" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "lbl" : "shorthand", @@ -33759,11 +33264,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000057", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/CL_0002320" - }, { - "sub" : "http://purl.obolibrary.org/obo/CL_0000057", - "pred" : "http://purl.obolibrary.org/obo/RO_0002202", - "obj" : "http://purl.obolibrary.org/obo/CL_0000134" + "obj" : "http://purl.obolibrary.org/obo/CL_0000499" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000066", "pred" : "is_a", @@ -34054,6 +33555,14 @@ "sub" : "http://purl.obolibrary.org/obo/CL_0000404", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/CL_0000211" + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_0000499", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/CL_0002320" + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_0000499", + "pred" : "http://purl.obolibrary.org/obo/RO_0002202", + "obj" : "http://purl.obolibrary.org/obo/CL_0000134" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000514", "pred" : "is_a", @@ -34092,10 +33601,6 @@ "sub" : "http://purl.obolibrary.org/obo/CL_0000547", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/CL_0002242" - }, { - "sub" : "http://purl.obolibrary.org/obo/CL_0000547", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000547", "pred" : "http://purl.obolibrary.org/obo/BFO_0000051", @@ -34170,10 +33675,6 @@ "val" : "true" } ] } - }, { - "sub" : "http://purl.obolibrary.org/obo/CL_0000549", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000549", "pred" : "http://purl.obolibrary.org/obo/BFO_0000051", @@ -34196,10 +33697,6 @@ "val" : "true" } ] } - }, { - "sub" : "http://purl.obolibrary.org/obo/CL_0000550", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000550", "pred" : "http://purl.obolibrary.org/obo/BFO_0000051", @@ -34340,10 +33837,6 @@ "val" : "true" } ] } - }, { - "sub" : "http://purl.obolibrary.org/obo/CL_0000558", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000558", "pred" : "http://purl.obolibrary.org/obo/CL_4030046", @@ -34414,10 +33907,6 @@ "sub" : "http://purl.obolibrary.org/obo/CL_0000566", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/CL_0011026" - }, { - "sub" : "http://purl.obolibrary.org/obo/CL_0000566", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000566", "pred" : "http://purl.obolibrary.org/obo/RO_0002104", @@ -34628,10 +34117,6 @@ "sub" : "http://purl.obolibrary.org/obo/CL_0000837", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/CL_0008001" - }, { - "sub" : "http://purl.obolibrary.org/obo/CL_0000837", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000837", "pred" : "http://purl.obolibrary.org/obo/CL_4030046", @@ -34812,10 +34297,6 @@ "sub" : "http://purl.obolibrary.org/obo/CL_0002188", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/CL_0002681" - }, { - "sub" : "http://purl.obolibrary.org/obo/CL_0002188", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0002188", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", @@ -35808,8 +35289,8 @@ "obj" : "http://purl.obolibrary.org/obo/GO_0043232" }, { "sub" : "http://purl.obolibrary.org/obo/GO_0005840", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PR_000050567" + "pred" : "http://purl.obolibrary.org/obo/BFO_0000051", + "obj" : "http://purl.obolibrary.org/obo/PR_000000001" }, { "sub" : "http://purl.obolibrary.org/obo/GO_0005840", "pred" : "http://purl.obolibrary.org/obo/RO_0002216", @@ -35853,7 +35334,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/GO_0006413", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/GO_0044237" + "obj" : "http://purl.obolibrary.org/obo/GO_0008152" }, { "sub" : "http://purl.obolibrary.org/obo/GO_0006413", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", @@ -36069,7 +35550,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/GO_0008152", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/GO_0008150" + "obj" : "http://purl.obolibrary.org/obo/GO_0009987" }, { "sub" : "http://purl.obolibrary.org/obo/GO_0008217", "pred" : "is_a", @@ -36089,11 +35570,11 @@ }, { "sub" : "http://purl.obolibrary.org/obo/GO_0009059", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/GO_0043170" + "obj" : "http://purl.obolibrary.org/obo/GO_0009058" }, { "sub" : "http://purl.obolibrary.org/obo/GO_0009059", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/GO_0044249" + "obj" : "http://purl.obolibrary.org/obo/GO_0043170" }, { "sub" : "http://purl.obolibrary.org/obo/GO_0009306", "pred" : "is_a", @@ -36528,8 +36009,8 @@ "obj" : "http://purl.obolibrary.org/obo/GO_0005575" }, { "sub" : "http://purl.obolibrary.org/obo/GO_0032991", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PR_000050567" + "pred" : "http://purl.obolibrary.org/obo/BFO_0000051", + "obj" : "http://purl.obolibrary.org/obo/PR_000000001" }, { "sub" : "http://purl.obolibrary.org/obo/GO_0033036", "pred" : "is_a", @@ -36734,26 +36215,10 @@ "sub" : "http://purl.obolibrary.org/obo/GO_0044207", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", "obj" : "http://purl.obolibrary.org/obo/GO_0005737" - }, { - "sub" : "http://purl.obolibrary.org/obo/GO_0044237", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/GO_0008152" - }, { - "sub" : "http://purl.obolibrary.org/obo/GO_0044237", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/GO_0009987" }, { "sub" : "http://purl.obolibrary.org/obo/GO_0044238", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/GO_0008152" - }, { - "sub" : "http://purl.obolibrary.org/obo/GO_0044249", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/GO_0009058" - }, { - "sub" : "http://purl.obolibrary.org/obo/GO_0044249", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/GO_0044237" }, { "sub" : "http://purl.obolibrary.org/obo/GO_0045184", "pred" : "is_a", @@ -37246,10 +36711,6 @@ "sub" : "http://purl.obolibrary.org/obo/GO_0098644", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/GO_0099080" - }, { - "sub" : "http://purl.obolibrary.org/obo/GO_0098644", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/GO_0098644", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", @@ -37781,7 +37242,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/PR_000000001", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PR_000050567" + "obj" : "http://purl.obolibrary.org/obo/PR_000064867" }, { "sub" : "http://purl.obolibrary.org/obo/PR_000000001", "pred" : "http://purl.obolibrary.org/obo/RO_0002353", @@ -37862,10 +37323,6 @@ "sub" : "http://purl.obolibrary.org/obo/PR_000001945", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PR_000000001" - }, { - "sub" : "http://purl.obolibrary.org/obo/PR_000001971", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PR_000000001" }, { "sub" : "http://purl.obolibrary.org/obo/PR_000002112", "pred" : "is_a", @@ -37919,7 +37376,7 @@ "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PR_000000001" }, { - "sub" : "http://purl.obolibrary.org/obo/PR_000050567", + "sub" : "http://purl.obolibrary.org/obo/PR_000064867", "pred" : "http://purl.obolibrary.org/obo/BFO_0000051", "obj" : "http://purl.obolibrary.org/obo/PR_000000001" }, { @@ -38038,10 +37495,6 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0000057", "pred" : "http://purl.obolibrary.org/obo/uberon/core#channels_from", "obj" : "http://purl.obolibrary.org/obo/UBERON_0001255" - }, { - "sub" : "http://purl.obolibrary.org/obo/UBERON_0000058", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000058", "pred" : "is_a", @@ -38570,7 +38023,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000178", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PR_000050567" + "obj" : "http://purl.obolibrary.org/obo/UBERON_0000061" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000178", "pred" : "is_a", @@ -38791,10 +38244,6 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0000481", "pred" : "http://purl.obolibrary.org/obo/BFO_0000051", "obj" : "http://purl.obolibrary.org/obo/UBERON_0000479" - }, { - "sub" : "http://purl.obolibrary.org/obo/UBERON_0000483", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000483", "pred" : "is_a", @@ -39955,10 +39404,6 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0001915", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", "obj" : "http://purl.obolibrary.org/obo/UBERON_0001982" - }, { - "sub" : "http://purl.obolibrary.org/obo/UBERON_0001969", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0001969", "pred" : "is_a", @@ -40017,10 +39462,6 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0001980", "pred" : "http://purl.obolibrary.org/obo/RO_0002433", "obj" : "http://purl.obolibrary.org/obo/UBERON_0001637" - }, { - "sub" : "http://purl.obolibrary.org/obo/UBERON_0001981", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0001981", "pred" : "is_a", @@ -40360,10 +39801,6 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0002224", "pred" : "http://purl.obolibrary.org/obo/RO_0002572", "obj" : "http://purl.obolibrary.org/obo/UBERON_0000915" - }, { - "sub" : "http://purl.obolibrary.org/obo/UBERON_0002303", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0002303", "pred" : "is_a", @@ -40775,6 +40212,10 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0002553", "pred" : "http://purl.obolibrary.org/obo/RO_0001015", "obj" : "http://purl.obolibrary.org/obo/UBERON_0000463" + }, { + "sub" : "http://purl.obolibrary.org/obo/UBERON_0003059", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/UBERON_0000061" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0003059", "pred" : "is_a", @@ -40807,10 +40248,6 @@ "val" : "GO" } ] } - }, { - "sub" : "http://purl.obolibrary.org/obo/UBERON_0003060", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/UBERON_0012275" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0003060", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", @@ -41728,10 +41165,6 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0004341", "pred" : "http://purl.obolibrary.org/obo/RO_0002387", "obj" : "http://purl.obolibrary.org/obo/UBERON_0000926" - }, { - "sub" : "http://purl.obolibrary.org/obo/UBERON_0004535", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0004535", "pred" : "is_a", @@ -41748,10 +41181,6 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0004535", "pred" : "http://purl.obolibrary.org/obo/BFO_0000051", "obj" : "http://purl.obolibrary.org/obo/UBERON_0001981" - }, { - "sub" : "http://purl.obolibrary.org/obo/UBERON_0004537", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0004537", "pred" : "is_a", @@ -41760,10 +41189,6 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0004537", "pred" : "http://purl.obolibrary.org/obo/RO_0002473", "obj" : "http://purl.obolibrary.org/obo/UBERON_0001981" - }, { - "sub" : "http://purl.obolibrary.org/obo/UBERON_0004572", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0004572", "pred" : "is_a", @@ -41778,10 +41203,6 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0004572", "pred" : "http://purl.obolibrary.org/obo/RO_0002351", "obj" : "http://purl.obolibrary.org/obo/UBERON_0001637" - }, { - "sub" : "http://purl.obolibrary.org/obo/UBERON_0004582", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0004582", "pred" : "is_a", @@ -42494,10 +41915,6 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0005764", "pred" : "http://purl.obolibrary.org/obo/RO_0002007", "obj" : "http://purl.obolibrary.org/obo/UBERON_0000061" - }, { - "sub" : "http://purl.obolibrary.org/obo/UBERON_0005769", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0005769", "pred" : "is_a", @@ -42845,10 +42262,6 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0006914", "pred" : "http://purl.obolibrary.org/obo/BFO_0000051", "obj" : "http://purl.obolibrary.org/obo/CL_0000076" - }, { - "sub" : "http://purl.obolibrary.org/obo/UBERON_0006965", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0006965", "pred" : "is_a", @@ -43276,6 +42689,10 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0009201", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/UBERON_0006555" + }, { + "sub" : "http://purl.obolibrary.org/obo/UBERON_0009201", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/UBERON_0012275" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0009569", "pred" : "is_a", @@ -44974,10 +44391,6 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002590", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002592" - }, { - "sub" : "http://purl.obolibrary.org/obo/RO_0002592", - "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0000057" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002592", "pred" : "subPropertyOf", @@ -48089,6 +47502,9 @@ "predicateId" : "http://purl.obolibrary.org/obo/RO_0002576", "domainClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000061" ], "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000061" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0015004", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/CL_0000000" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0015006", "domainClassIds" : [ "http://purl.obolibrary.org/obo/PATO_0000001" ], diff --git a/subsets/kidney_upper_slim.obo b/subsets/kidney_upper_slim.obo index abc4ba250..13d794cca 100644 --- a/subsets/kidney_upper_slim.obo +++ b/subsets/kidney_upper_slim.obo @@ -1,5 +1,5 @@ format-version: 1.2 -data-version: cl/releases/2024-09-26/subsets/kidney_upper_slim.owl +data-version: cl/releases/2025-01-08/subsets/kidney_upper_slim.owl subsetdef: abnormal_slim "" subsetdef: added_for_HCA "" subsetdef: attribute_slim "" @@ -44,10 +44,12 @@ subsetdef: http://purl.obolibrary.org/obo/valid_for_go_gp2term "" subsetdef: http://purl.obolibrary.org/obo/valid_for_go_ontology "" subsetdef: http://purl.obolibrary.org/obo/valid_for_gocam "" subsetdef: human_reference_atlas "" +subsetdef: human_subset "" subsetdef: inconsistent_with_fma "" subsetdef: kidney_upper_slim "a subset of general classes related to specific cell types in the kidney" subsetdef: location_grouping "" subsetdef: major_organ "" +subsetdef: mouse_subset "" subsetdef: mpath_slim "" subsetdef: non_informative "" subsetdef: organ_slim "" @@ -96,7 +98,7 @@ idspace: oboInOwl http://www.geneontology.org/formats/oboInOwl# idspace: sssom https://w3id.org/sssom/ idspace: terms http://purl.org/dc/terms/ ontology: cl/subsets/kidney_upper_slim -property_value: owl:versionInfo "2024-09-26" xsd:string +property_value: owl:versionInfo "2025-01-08" xsd:string [Term] id: CL:0000000 @@ -104,6 +106,8 @@ name: cell def: "A material entity of anatomical origin (part of or deriving from an organism) that has as its parts a maximally connected cell compartment surrounded by a plasma membrane." [CARO:mah] comment: The definition of cell is intended to represent all cells, and thus a cell is defined as a material entity and not an anatomical structure, which implies that it is part of an organism (or the entirety of one). subset: cellxgene_subset +subset: human_subset +subset: mouse_subset subset: ubprop:upper_level xref: CALOHA:TS-2035 xref: FBbt:00007002 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} @@ -125,6 +129,8 @@ relationship: RO:0002162 NCBITaxon:131567 ! in taxon cellular organisms id: CL:0000007 name: early embryonic cell (metazoa) def: "A cell found in the embryo before the formation of all the gem layers is complete." [GOC:tfm] +subset: human_subset +subset: mouse_subset xref: ZFA:0009002 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0002321 ! embryonic cell (metazoa) @@ -136,6 +142,8 @@ comment: This term applies to metazoan. For plant stem cells, consider using PO: subset: cellxgene_subset subset: general_cell_types_upper_slim subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "animal stem cell" EXACT [] xref: CALOHA:TS-2086 xref: FMA:63368 @@ -156,6 +164,8 @@ comment: Markers differ between species, and two sets of markers have been descr subset: blood_and_immune_upper_slim subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "blood forming stem cell" EXACT [] synonym: "colony forming unit hematopoietic" RELATED [] synonym: "hemopoietic stem cell" EXACT [] @@ -206,6 +216,8 @@ name: erythroid progenitor cell def: "A progenitor cell committed to the erythroid lineage." [GOC:add, ISBN:0721601464] subset: blood_and_immune_upper_slim subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "BFU-E" RELATED OMO:0003000 [] synonym: "blast forming unit erythroid" RELATED [] synonym: "burst forming unit erythroid" RELATED [] @@ -224,6 +236,8 @@ name: germ line cell def: "A cell that is within the developmental lineage of gametes and is able to pass along its genetic material to offspring." [GOC:tfm, ISBN:0721662544] comment: Originally this term had some plant germ line cell children. subset: general_cell_types_upper_slim +subset: human_subset +subset: mouse_subset subset: ubprop:upper_level xref: ZFA:0009016 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000000 ! cell @@ -233,6 +247,8 @@ relationship: capable_of GO:0022414 ! reproductive process id: CL:0000048 name: multi fate stem cell def: "A stem cell that can give rise to multiple lineages of cells." [GOC:add] +subset: human_subset +subset: mouse_subset synonym: "multi-fate stem cell" EXACT [] synonym: "multifate stem cell" EXACT [] synonym: "multipotent cell" EXACT [] @@ -252,6 +268,8 @@ def: "A progenitor cell committed to myeloid lineage, including the megakaryocyt comment: This cell type is intended to be compatible with any vertebrate common myeloid progenitor. For mammalian CMP known to be CD34-positive, please use the term 'common myeloid progenitor, CD34-positive' (CL_0001059). subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "CFU-GEMM" RELATED OMO:0003000 [ISBN:0878932437] synonym: "CFU-S" RELATED OMO:0003000 [ISBN:0878932437] synonym: "CMP" RELATED OMO:0003000 [ISBN:0878932437] @@ -273,6 +291,8 @@ def: "A progenitor cell committed to the megakaryocyte and erythroid lineages." comment: MEPs are reportedly CD19-negative, CD34-negative, CD45RA-negative, CD110-positive, CD117-positive, and SCA1-negative and reportedly express the transcription factors GATA-1 and NF-E2. subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "CFU-EM" EXACT [] synonym: "CFU-MegE" EXACT [] synonym: "colony forming unit erythroid megakaryocyte" EXACT [] @@ -295,6 +315,8 @@ property_value: RO:0002175 NCBITaxon:9606 id: CL:0000052 name: totipotent stem cell def: "A stem cell from which all cells of the body can form." [GOC:add, GOC:tfm] +subset: human_subset +subset: mouse_subset synonym: "totipotential stem cell" EXACT [] xref: FMA:84790 xref: MESH:D039901 @@ -307,6 +329,8 @@ name: non-terminally differentiated cell def: "A precursor cell with a limited number of potential fates." [SANBI:mhl] comment: define using PATO mulit-potent or oligopotent? subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "blast cell" EXACT [] xref: BTO:0000125 xref: FMA:84782 @@ -316,6 +340,9 @@ is_a: CL:0011115 ! precursor cell id: CL:0000056 name: myoblast def: "A cell that is commited to differentiating into a muscle cell. Embryonic myoblasts develop from the mesoderm. They undergo proliferation, migrate to their various sites, and then differentiate into the appropriate form of myocytes. Myoblasts also occur as transient populations of cells in muscles undergoing repair." [GOC:tfm, MESH:D032446, PMID:21849021] +subset: cellxgene_subset +subset: human_subset +subset: mouse_subset xref: BTO:0000222 xref: CALOHA:TS-0650 xref: FBbt:00005083 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} @@ -332,14 +359,15 @@ comment: These cells may be vimentin-positive, fibronectin-positive, fsp1-positi subset: cellxgene_subset subset: general_cell_types_upper_slim subset: human_reference_atlas +subset: human_subset +subset: mouse_subset xref: BTO:0000452 xref: CALOHA:TS-0362 xref: FMA:63877 xref: NCIT:C12482 xref: VHOG:0001482 xref: ZFA:0009026 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} -is_a: CL:0002320 ! connective tissue cell -relationship: RO:0002202 CL:0000134 ! develops from mesenchymal stem cell +is_a: CL:0000499 ! stromal cell property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -349,6 +377,8 @@ def: "A cell that is usually found in a two-dimensional sheet with a free surfac subset: cellxgene_subset subset: general_cell_types_upper_slim subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "epitheliocyte" EXACT [] xref: BTO:0000414 xref: CALOHA:TS-2026 @@ -367,6 +397,8 @@ id: CL:0000068 name: duct epithelial cell def: "An epithelial cell that is part of a duct." [https://orcid.org/0000-0001-5208-3432] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset xref: ZFA:0009372 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000066 ! epithelial cell intersection_of: CL:0000066 ! epithelial cell @@ -379,6 +411,8 @@ name: blood vessel endothelial cell def: "An endothelial cell that lines the vasculature." [GOC:tfm] subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset xref: ZFA:0009036 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0002139 ! endothelial cell of vascular tree intersection_of: CL:0000115 ! endothelial cell @@ -389,6 +423,8 @@ property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000072 name: non-branched duct epithelial cell +subset: human_subset +subset: mouse_subset is_a: CL:0000068 ! duct epithelial cell is_a: CL:0002078 ! meso-epithelial cell @@ -398,6 +434,8 @@ name: columnar/cuboidal epithelial cell def: "A columnar/cuboidal epithelial cell is a cell usually found in a two dimensional sheet with a free surface. Columnar/cuboidal epithelial cells take on the shape of a column or cube." [GO:0002065, https://orcid.org/0000-0001-5208-3432] subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset xref: ZFA:0009038 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000066 ! epithelial cell property_value: RO:0002175 NCBITaxon:9606 @@ -407,6 +445,8 @@ id: CL:0000076 name: squamous epithelial cell def: "Any epithelial cell that is part of some squamous epithelium." [FBC:Autogenerated] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset xref: CALOHA:TS-1249 xref: ZFA:0009039 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000066 ! epithelial cell @@ -420,6 +460,8 @@ name: blood cell def: "A cell found predominately in the blood." [GOC:add, GOC:tfm] subset: cellxgene_subset subset: general_cell_types_upper_slim +subset: human_subset +subset: mouse_subset xref: FMA:62844 xref: MESH:D001773 xref: ZFA:0009044 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} @@ -435,6 +477,8 @@ def: "An endothelial cell comprises the outermost layer or lining of anatomical comment: From FMA: 9.07.2001: Endothelial cell has always been classified as a kind of epithelial cell, specifically a squamous cell but that is not true. First, endothelial cell can either be squamous or cuboidal (e.g. high-endothelial cell) and secondly, it has different embryological derivation (mesodermal) than a true epithelial cell (ectodermal and endodermal). The basis for present classification is the fact that it comprises the outermost layer or lining of anatomical structures (location-based) but a better structural basis for the differentia is the cytoskeleton of the cell. Endothelial cell has vimentin filaments while an epithelial cell has keratin filaments. [Onard]. subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "endotheliocyte" EXACT [] xref: BTO:0001176 xref: CALOHA:TS-0278 @@ -449,6 +493,8 @@ property_value: RO:0002175 NCBITaxon:9606 id: CL:0000133 name: neurectodermal cell def: "Ectoderm destined to be nervous tissue." [GOC:tfm, ISBN:068340007X] +subset: human_subset +subset: mouse_subset synonym: "neurectoderm cell" EXACT [] xref: ZFA:0009080 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000221 ! ectodermal cell @@ -459,6 +505,8 @@ name: mesenchymal stem cell def: "A connective tissue cell that normally gives rise to other cells that are organized as three-dimensional masses. In humans, this cell type is CD73-positive, CD90-positive, CD105-positive, CD45-negative, CD34-negative, and MHCII-negative. They may further differentiate into osteoblasts, adipocytes, myocytes, neurons, or chondroblasts in vitro. Originally described as residing in the bone marrow, this cell type is now known to reside in many, if not all, adult organs." [FB:ma, GOC:dsd, http://en.wikipedia.org/wiki/Mesenchymal_stem_cell, http://www.copewithcytokines.de/cope.cgi?key=mesenchymal%20stem%20cells, PMCID:PMC2613570, PMID:10102814, PMID:16923606, PMID:17986482, PMID:19960544] comment: Many but not all mesenchymal cells derive from the mesoderm. MSCs are reportedly CD3-negative, CD4-negative, CD5-negative, CD8-negative, CD11a-negative, CD11b-negative, CD14-negative, CD19-negative, CD29-positive, CD31-negative, CD34-negative, CD38-negative, CD40-negative, CD44-positive, CD45-negative, CD49-positive, CD54-positive, CD66b-negative, CD79a-negative, CD80-negative, CD102-positive, CD106-positive, CD117-positive, CD121a-positive, CD121b-positive, CD123-positive, CD124-positive, CD133-negative, CD146-positive, CD166-positive, CD271-positive, B220-negative, Gr1-negative, MHCI-positive, MHCII-negative, SSEA4-negative, sca1-positive, Ter119-negative, and glycophorin A-negative. Cultured MSCs are capable of producing stem cell factor, IL7, IL8, IL11, TGF-beta, cofilin, galectin-1, laminin-receptor 1, cyclophilin A, and MMP-2. subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "BMSC" RELATED OMO:0003000 [] synonym: "bone marrow stromal cells" NARROW [] synonym: "CFU-F" RELATED OMO:0003000 [] @@ -484,6 +532,8 @@ id: CL:0000151 name: secretory cell def: "A cell that specializes in controlled release of one or more substances." [GOC:tfm, ISBN:0721662544] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset xref: BTO:0003659 xref: FMA:86916 is_a: CL:0000000 ! cell @@ -495,6 +545,8 @@ relationship: capable_of GO:0032940 ! secretion by cell id: CL:0000154 name: protein secreting cell def: "Any secretory cell that is capable of some protein secretion." [FBC:Autogenerated] +subset: human_subset +subset: mouse_subset is_a: CL:0000151 ! secretory cell intersection_of: CL:0000151 ! secretory cell intersection_of: capable_of GO:0009306 ! protein secretion @@ -505,6 +557,8 @@ id: CL:0000183 name: contractile cell def: "A cell whose primary function is to shorten." [FB:ma] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset is_a: CL:0000000 ! cell [Term] @@ -512,6 +566,8 @@ id: CL:0000187 name: muscle cell def: "A mature contractile cell, commonly known as a myocyte. This cell has as part of its cytoplasm myofibrils organized in various patterns." [MESH:D032342] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "muscle fiber" EXACT [] synonym: "myocyte" EXACT [] xref: BTO:0000888 @@ -534,6 +590,8 @@ def: "A non-striated, elongated, spindle-shaped cell found lining the digestive subset: cellxgene_subset subset: general_cell_types_upper_slim subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "myocytes, smooth muscle" EXACT [MESH:D032389] synonym: "non-striated muscle cell" BROAD [] synonym: "SMCs" EXACT [PMID:9315361] @@ -541,16 +599,20 @@ synonym: "smooth muscle fiber" EXACT [] xref: BTO:0004576 xref: CALOHA:TS-2159 xref: FMA:14072 +xref: https://cellxgene.cziscience.com/cellguide/CL_0000192 xref: ZFA:0009118 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0008000 ! non-striated muscle cell is_a: CL:0008007 ! visceral muscle cell relationship: RO:0002202 CL:0000514 ! develops from smooth muscle myoblast property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nSmooth muscle cells are a specialized type of muscle cells that are primarily found within the walls of hollow organs such as the intestine, stomach, bladder, uterus, and blood vessels. These cells are an essential component of the autonomic nervous system controling involuntary movements within the body.\nSmooth muscle cells play a vital role in many physiological processes due to their unique functionality. They can contract and relax in a slow, sustained, and controlled manner to help modulate the size and shape of the lumens of the organs they surround. For example, in the digestive system, coordinated contraction and relaxation of smooth muscle cells propels food along the gastrointestinal tract - a process known as peristalsis. In the blood vessels, the smooth muscle cells, by contracting or relaxing, either constrict or dilate the vessels, which in turn, help regulate blood flow and pressure.\nOn a cellular level, smooth muscle cells possess a single, centrally located nucleus and contain an arranged network of actin and myosin filaments, which are the proteins responsible for muscle contraction. Unlike their counterparts in skeletal or cardiac muscles, these cells lack specific contact points for these filaments, hence the lack of visible striations. Furthermore, the contraction of smooth muscle cells is regulated by hormones and neurotransmitters, such as acetylcholine and norepinephrine, adding an additional layer of complex regulation to these highly specialized cells." xsd:string {xref="DOI:10.1093/ptj/81.11.1810", xref="https://training.seer.cancer.gov/anatomy/muscular/types.html", xref="https://www.ncbi.nlm.nih.gov/books/NBK10854/", xref="https://www.ncbi.nlm.nih.gov/books/NBK526125", xref="https://www.ncbi.nlm.nih.gov/books/NBK556137/"} [Term] id: CL:0000211 name: electrically active cell def: "A cell whose function is determined by the generation or the reception of an electric signal." [FB:ma] +subset: human_subset +subset: mouse_subset xref: ZFA:0009128 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000000 ! cell @@ -558,6 +620,8 @@ is_a: CL:0000000 ! cell id: CL:0000213 name: lining cell def: "A cell within an epithelial cell sheet whose main function is to act as an internal or external covering for a tissue or an organism." [JB:jb] +subset: human_subset +subset: mouse_subset synonym: "boundary cell" EXACT [] xref: ZFA:0009130 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000215 ! barrier cell @@ -566,6 +630,8 @@ is_a: CL:0000215 ! barrier cell id: CL:0000215 name: barrier cell def: "A cell whose primary function is to prevent the transport of stuff across compartments." [JB:jb] +subset: human_subset +subset: mouse_subset xref: ZFA:0009132 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000000 ! cell @@ -573,6 +639,8 @@ is_a: CL:0000000 ! cell id: CL:0000219 name: motile cell def: "A cell that moves by its own activities." [FB:ma] +subset: human_subset +subset: mouse_subset xref: ZFA:0009136 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000000 ! cell intersection_of: CL:0000000 ! cell @@ -583,6 +651,9 @@ relationship: capable_of GO:0048870 ! cell motility id: CL:0000221 name: ectodermal cell def: "A cell of the outer of the three germ layers of the embryo." [MESH:D004475] +subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "ectoderm cell" EXACT [] xref: FMA:72549 xref: ZFA:0009137 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} @@ -595,18 +666,24 @@ id: CL:0000222 name: mesodermal cell def: "A cell of the middle germ layer of the embryo." [MESH:D008648] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "mesoblast" EXACT [] synonym: "mesoderm cell" EXACT [] xref: FMA:72554 +xref: https://cellxgene.cziscience.com/cellguide/CL_0000222 xref: ZFA:0009138 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000255 ! eukaryotic cell is_a: CL:0002321 ! embryonic cell (metazoa) relationship: part_of UBERON:0000926 ! mesoderm +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nMesodermal cells are pluripotent and the most abundant in the human body. They contribute to the development of several structures such as the skeletal muscles, bones, heart and blood vessels, kidneys, gonads, connective tissues, and certain layers of the skin. Hence, the mesoderm is often regarded as an active and diverse layer due to its role in forming many bodily structures. \nIn embryonic development, these cells are instrumental, contributing to the body's structures through a carefully coordinated sequence of morphogenetic movements. This process forms the complex multicellular architecture of tissues and organs from a simple ball of cells. Without the function of mesodermal cells, the body's integral structures and systems would cease to form correctly, leading to developmental disorders such as axial mesodermal dysplasia complex" xsd:string {xref="DOI:10.1016/j.ceb.2019.07.012", xref="DOI:10.5535/arm.2016.40.1.162", xref="https://www.sciencedirect.com/topics/biochemistry-genetics-and-molecular-biology/mesoderm"} [Term] id: CL:0000223 name: endodermal cell def: "A cell of the inner of the three germ layers of the embryo." [MESH:D004707] +subset: human_subset +subset: mouse_subset synonym: "endoderm cell" EXACT [] xref: FMA:72555 xref: ZFA:0009139 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} @@ -621,6 +698,8 @@ def: "A red blood cell. In mammals, mature erythrocytes are biconcave disks cont subset: blood_and_immune_upper_slim subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "RBC" EXACT [] synonym: "red blood cell" EXACT [] xref: BTO:0000424 @@ -645,7 +724,8 @@ property_value: RO:0002175 NCBITaxon:9606 id: CL:0000255 name: eukaryotic cell def: "Any cell that in taxon some Eukaryota." [FBC:Autogenerated] -subset: cellxgene_subset +subset: human_subset +subset: mouse_subset xref: MESH:D005057 is_a: CL:0000000 ! cell intersection_of: CL:0000000 ! cell @@ -656,6 +736,8 @@ relationship: RO:0002162 NCBITaxon:2759 ! in taxon Eukaryota id: CL:0000329 name: oxygen accumulating cell def: "Any cell that is capable of some oxygen transport." [FBC:Autogenerated] +subset: human_subset +subset: mouse_subset xref: ZFA:0009164 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000000 ! cell intersection_of: CL:0000000 ! cell @@ -666,6 +748,8 @@ relationship: capable_of GO:0015671 ! oxygen transport id: CL:0000333 name: migratory neural crest cell def: "A cell derived from the specialized ectoderm flanking each side of the embryonic neural plate, which after the closure of the neural tube, forms masses of cells that migrate out from the dorsal aspect of the neural tube to spread throughout the body." [doi:10.1016/j.stem.2015.02.017] +subset: human_subset +subset: mouse_subset xref: FMA:86667 xref: ZFA:0007086 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000219 ! motile cell @@ -677,6 +761,8 @@ relationship: RO:0002202 CL:0007004 ! develops from premigratory neural crest ce id: CL:0000335 name: mesenchyme condensation cell def: "A mesenchymal cell in embryonic development found in a contracting mass and that gives rise to osteoprogenitors." [GOC:tfm, PMID:5025404] +subset: human_subset +subset: mouse_subset xref: ZFA:0009166 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0008019 ! mesenchymal cell @@ -684,12 +770,16 @@ is_a: CL:0008019 ! mesenchymal cell id: CL:0000352 name: epiblast cell def: "A cell of the outer layer of a blastula that gives rise to the ectoderm after gastrulation." [GOC:tfm, ISBN:0618947256] +subset: human_subset +subset: mouse_subset is_a: CL:0000052 ! totipotent stem cell [Term] id: CL:0000365 name: animal zygote def: "Diploid cell produced by the fusion of sperm cell nucleus and egg cell." [ISBN:0471245208] +subset: human_subset +subset: mouse_subset synonym: "zygote" BROAD [] xref: BTO:0000854 xref: EHDAA2:0004546 @@ -705,6 +795,8 @@ relationship: RO:0002162 NCBITaxon:33208 ! in taxon Metazoa id: CL:0000393 name: electrically responsive cell def: "A cell whose function is determined by its response to an electric signal." [FB:ma] +subset: human_subset +subset: mouse_subset xref: ZFA:0009190 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000211 ! electrically active cell @@ -712,22 +804,44 @@ is_a: CL:0000211 ! electrically active cell id: CL:0000404 name: electrically signaling cell def: "A cell that initiates an electrical signal and passes that signal to another cell." [FB:ma] +subset: human_subset +subset: mouse_subset xref: ZFA:0009193 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000211 ! electrically active cell +[Term] +id: CL:0000499 +name: stromal cell +def: "A connective tissue cell of an organ found in the loose connective tissue." [GOC:tfm, MESH:D017154] +subset: cellxgene_subset +subset: general_cell_types_upper_slim +subset: human_reference_atlas +subset: human_subset +subset: mouse_subset +xref: BTO:0002064 +xref: FMA:83624 +xref: ZFA:0009226 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +is_a: CL:0002320 ! connective tissue cell +relationship: RO:0002202 CL:0000134 ! develops from mesenchymal stem cell +property_value: RO:0002175 NCBITaxon:9606 + [Term] id: CL:0000514 name: smooth muscle myoblast def: "A precursor cell destined to differentiate into smooth muscle myocytes." [GOC:tfm, MESH:D032390] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "myoblast, smooth muscle" EXACT [MESH:D032390] synonym: "satellite cell" RELATED [] xref: FMA:84798 +xref: https://cellxgene.cziscience.com/cellguide/CL_0000514 xref: ZFA:0009235 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000056 ! myoblast intersection_of: CL:0000056 ! myoblast intersection_of: RO:0002203 CL:0000192 ! develops into smooth muscle cell relationship: RO:0002203 CL:0000192 ! develops into smooth muscle cell +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nA precursor to the smooth muscle cell, the smooth muscle myoblast, is integral to various body systems, including the cardiovascular, gastrointestinal, and respiratory systems. Smooth muscle myoblasts arise from the differentiation of mesenchymal stem cells, a process tightly regulated by specific genetic factors and environmental signals. Their role extends to myogenesis, particularly in the formation of muscular tissue, especially during embryonic development.\nSmooth muscle myoblasts possess distinctive cellular characteristics. In contrast to skeletal muscle myoblasts, they do not fuse to create multinucleated fibers. Instead, they differentiate into individual, uninucleated smooth muscle cells. This differentiation unfolds in two distinct phases: proliferation, marked by rapid division to increase cell numbers, and differentiation, involving structural and functional transformation into mature smooth muscle cells. This intricate process is intricately mediated by various signaling molecules and transcription factors.\nFunctionally, smooth muscle myoblasts and the mature muscle cells they generate play pivotal roles in various physiological processes. Smooth muscle cells orchestrate involuntary muscle responses and are integral to body systems that regulate blood flow, propel food along the digestive tract, and control airflow in the respiratory tract. These diverse functions underscore the significance of smooth muscle myoblasts in the body's growth, maintenance, and overall function." xsd:string {xref="DOI:10.1074/jbc.RA118.001739", xref="https://www.ncbi.nlm.nih.gov/books/NBK544225/", xref="https://www.sciencedirect.com/topics/medicine-and-dentistry/smooth-muscle"} [Term] id: CL:0000540 @@ -737,6 +851,8 @@ comment: These cells are also reportedly CD4-negative and CD200-positive. They a subset: cellxgene_subset subset: general_cell_types_upper_slim subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "nerve cell" EXACT [] xref: BTO:0000938 xref: CALOHA:TS-0683 @@ -758,12 +874,13 @@ name: proerythroblast def: "An immature, nucleated erythrocyte occupying the stage of erythropoeisis that follows formation of erythroid progenitor cells. This cell is CD71-positive, has both a nucleus and a nucleolus, and lacks hematopoeitic lineage markers." [ISBN:0721601464, PMID:1638021] subset: blood_and_immune_upper_slim subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "pronormoblast" RELATED [] synonym: "rubriblast" EXACT [ISBN:0721601464] xref: FMA:83518 is_a: CL:0000764 {is_inferred="true"} ! erythroid lineage cell is_a: CL:0002242 ! nucleate cell -is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000764 ! erythroid lineage cell intersection_of: bearer_of PATO:0002505 ! nucleated intersection_of: bearer_of PATO:0040072 ! high nuclear/cytoplasmic ratio @@ -802,6 +919,8 @@ relationship: RO:0002202 CL:0000038 ! develops from erythroid progenitor cell id: CL:0000549 name: basophilic erythroblast def: "A nucleated immature erythrocyte, having cytoplasm generally similar to that of the earlier proerythroblast but sometimes even more basophilic, and usually regular in outline. The nucleus is still relatively large, but the chromatin strands are thicker and more deeply staining, giving a coarser appearance; the nucleoli have disappeared. This cell is CD71-positive and lacks hematopoeitic lineage markers." [GOC:tfm, ISBN:0721601464] +subset: human_subset +subset: mouse_subset synonym: "basophilic normoblast" EXACT [ISBN:0721601464] synonym: "early erythroblast" EXACT [ISBN:0721601464] synonym: "early normoblast" EXACT [ISBN:0721601464] @@ -809,7 +928,6 @@ synonym: "prorubricyte" EXACT [ISBN:0721601464] xref: FMA:83505 xref: ZFA:0005236 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000765 {is_inferred="true"} ! erythroblast -is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000765 ! erythroblast intersection_of: has_part CL:0017503 ! basophilic cytoplasm intersection_of: has_part GO:0000792 ! heterochromatin @@ -822,6 +940,8 @@ relationship: RO:0002104 PR:000001945 ! has plasma membrane part transferrin rec id: CL:0000550 name: polychromatophilic erythroblast def: "A nucleated, immature erythrocyte in which the nucleus occupies a relatively smaller part of the cell than in its precursor, the basophilic erythroblast. The cytoplasm is beginning to acquire hemoglobin and thus is no longer a purely basophilic, but takes on acidophilic aspects, which becomes progressively more marked as the cell matures. The chromatin of the nucleus is arranged in coarse, deeply staining clumps. This cell is CD71-positive and lacks hematopoeitic lineage markers." [ISBN:0721601464] +subset: human_subset +subset: mouse_subset synonym: "intermediate erythroblast" EXACT [ISBN:0721601464] synonym: "intermediate normoblast" EXACT [ISBN:0721601464] synonym: "polychromatic erythroblast" EXACT [ISBN:0721601464] @@ -831,7 +951,6 @@ synonym: "rubricyte" EXACT [ISBN:0721601464] xref: FMA:83506 xref: ZFA:0005241 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000765 {is_inferred="true"} ! erythroblast -is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000765 ! erythroblast intersection_of: has_part CL:0017504 ! polychromatophilic cytoplasm intersection_of: has_part GO:0000792 ! heterochromatin @@ -845,6 +964,8 @@ relationship: RO:0002202 CL:0000549 ! develops from basophilic erythroblast id: CL:0000552 name: orthochromatic erythroblast def: "The final stage of the nucleated, immature erythrocyte, before nuclear loss. Typically the cytoplasm is described as acidophilic, but it still shows a faint polychromatic tint. The nucleus is small and initially may still have coarse, clumped chromatin, as in its precursor, the polychromatophilic erythroblast, but ultimately it becomes pyknotic, and appears as a deeply staining, blue-black, homogeneous structureless mass. The nucleus is often eccentric and sometimes lobulated." [ISBN:0721601464] +subset: human_subset +subset: mouse_subset synonym: "acidophilic erythroblast" EXACT [ISBN:0721601464] synonym: "eosinophilic erythroblast" EXACT [ISBN:0721601464] synonym: "late erythoblast" EXACT [] @@ -866,6 +987,8 @@ def: "The earliest cytologically identifiable precursor in the thrombocytic seri comment: Lineage negative is described here as CD2-negative, CD3-negative, CD4-negative, CD5-negative, CD8a-negative, CD14-negative, CD19-negative, CD20-negative, CD56-negative, Ly6g-negative, and Ter119-negative. subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "CFU-Meg" EXACT [PMID:11722431, PMID:12482498] synonym: "colony-forming unit-megakaryocyte" EXACT [] synonym: "Meg-CFC" EXACT [PMCID:PMC1794060] @@ -922,6 +1045,8 @@ comment: Megakaryocytes are reportedly CD181-positive and CD182-positive. subset: blood_and_immune_upper_slim subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "megacaryocyte" EXACT [] synonym: "megalocaryocyte" EXACT [] synonym: "megalokaryocyte" EXACT [] @@ -940,12 +1065,13 @@ name: reticulocyte def: "An immature erythrocyte that changes the protein composition of its plasma membrane by exosome formation and extrusion. The types of protein removed differ between species though removal of the transferrin receptor is apparent in mammals and birds." [GOC:add, GOC:tfm, PMID:15946868, PMID:2037622] subset: blood_and_immune_upper_slim subset: cellxgene_subset +subset: human_subset +subset: mouse_subset xref: BTO:0001173 xref: CALOHA:TS-0864 xref: MESH:D012156 xref: ZFA:0009252 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000764 {is_inferred="true"} ! erythroid lineage cell -is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000764 ! erythroid lineage cell intersection_of: capable_of GO:0071971 ! extracellular exosome assembly intersection_of: CL:4030046 PR:000001002 ! lacks_plasma_membrane_part CD19 molecule @@ -980,12 +1106,13 @@ id: CL:0000566 name: angioblastic mesenchymal cell def: "A mesenchymal stem cell capable of developing into blood vessel endothelium." [GOC:dsd, GOC:tfm, PMID:12768659] comment: These cells are reportedly CD31-positive, CD34-positive, CD144-positive, CD309-positive, and TAL1-positive. +subset: human_subset +subset: mouse_subset synonym: "angioblast" EXACT [] synonym: "chondroplast" EXACT [] xref: ZFA:0009258 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000134 {is_inferred="true"} ! mesenchymal stem cell is_a: CL:0011026 ! progenitor cell -is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000134 ! mesenchymal stem cell intersection_of: RO:0002104 PR:000001444 ! has plasma membrane part cadherin-5 intersection_of: RO:0002104 PR:000002112 ! has plasma membrane part vascular endothelial growth factor receptor 2 @@ -1000,6 +1127,8 @@ id: CL:0000586 name: germ cell def: "The reproductive cell in multicellular organisms." [MESH:D005854] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset xref: BTO:0000535 xref: NCIT:C12597 xref: VHOG:0001534 @@ -1012,6 +1141,8 @@ id: CL:0000630 name: supporting cell def: "A cell whose primary function is to support other cell types." [FB:ma, GOC:tfm] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "supportive cell" EXACT [] xref: BTO:0002315 xref: ZFA:0009387 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} @@ -1022,6 +1153,8 @@ id: CL:0000648 name: kidney granular cell def: "A smooth muscle cell that synthesizes, stores, and secretes the enzyme renin. This cell type are located in the wall of the afferent arteriole at the entrance to the glomerulus. While having a different origin than other kidney smooth muscle cells, this cell type expresses smooth muscle actin upon maturation." [GOC:cvs, GOC:tfm, PMID:11457727] subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "JG cell" EXACT [] synonym: "juxtaglomerular cell" BROAD [] synonym: "renin secreting cell" EXACT [] @@ -1042,6 +1175,8 @@ name: mesangial cell def: "A cell type that encapsulates the capillaries and venules in the kidney. This cell secretes mesangial matrix that provides the structural support for the capillaries." [GOC:tfm, http://www.copewithcytokines.de/cope.cgi?key=mesangial%20cells] comment: Do all of these cells really develop from some mesenchymal stem cell? subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "kidney mesangial cell" EXACT [] xref: BTO:0000853 xref: CALOHA:TS-0617 @@ -1056,6 +1191,8 @@ id: CL:0000666 name: fenestrated endothelial cell def: "An endothelial cell that has small pores, or fenestrations, which allow for the efficient exchange of substances between the blood and surrounding tissues." [DOI:10.1007/978-3-211-99390-3_133] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "window cell" EXACT [] xref: https://cellxgene.cziscience.com/cellguide/CL_0000666 xref: ZFA:0009286 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} @@ -1063,7 +1200,7 @@ is_a: CL:0000115 ! endothelial cell intersection_of: CL:0000115 ! endothelial cell intersection_of: bearer_of PATO:0002064 ! fenestrated relationship: bearer_of PATO:0002064 ! fenestrated -property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional.\n\nFenestrated cells are specialized epithelial cells that are characterized by a distinctive structural feature, fenestrations or tiny pores, which allow an exchange of substances such as fluids, nutrients, and waste between blood vessels and the surrounding tissue environments. These cells are present in various types of epithelial tissues in the human body, including the intestinal tract, endocrine glands, and certain parts of the renal system. \nThere are multiple types of endothelial cell fenestrations. The most common type is found in systemic capillaries of the endocrine tissue (e.g., pancreatic islets), gastrointestinal mucosa, and renal peritubular capillaries. Here, the fenestrated cells have fenestrations in their peripheral cytoplasm with a unique thin and permeable diaphragm that provides a high degree of selectivity, blocking the passage of larger molecules while allowing the free movement of smaller ones. In contrast, other types of fenestrations, such as the discontinuous epithelium of the liver sinusoidal endothelial cells, do not have diaphragms. \nCharacteristically, fenestrated cells play a vital role in the filtering process of body systems. They are a key part of the glomeruli in the kidneys where blood is filtered under high pressure. The fenestrations present in the endothelial cells lining the capillaries of the glomerulus allow the free passage of water and small solute molecules towards the Bowman's capsule, leaving behind larger proteins and cells in the blood, thereby aiding in the filtration and waste removal process. \nIn the endocrine system, fenestrated cells in glandular capillaries allow the prompt release of hormones into the bloodstream. These cells have tightly clustered fenestrations which increase the surface area available for passive diffusion, improving the efficiency of hormone secretion. In villi of the small intestine, these cells increase absorption efficiency, permitting the exchange of water, electrolytes, and nutrients.\nOverall, fenestrated cells contribute immensely to important physiological processes of filtration, absorption, and secretion, primarily connecting our body's circulation system with the surrounding tissues and organs." xsd:string {xref="DOI:10.1002/ar.1092200109", xref="DOI:10.1016/0306-4522(86)90162-4", xref="DOI:10.1016/j.devcel.2012.11.003", xref="DOI:10.1038/s41467-022-31571-2", xref="DOI:10.1152/ajprenal.90601.2008"} +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nFenestrated cells are specialized epithelial cells that are characterized by a distinctive structural feature, fenestrations or tiny pores, which allow an exchange of substances such as fluids, nutrients, and waste between blood vessels and the surrounding tissue environments. These cells are present in various types of epithelial tissues in the human body, including the intestinal tract, endocrine glands, and certain parts of the renal system. \nThere are multiple types of endothelial cell fenestrations. The most common type is found in systemic capillaries of the endocrine tissue (e.g., pancreatic islets), gastrointestinal mucosa, and renal peritubular capillaries. Here, the fenestrated cells have fenestrations in their peripheral cytoplasm with a unique thin and permeable diaphragm that provides a high degree of selectivity, blocking the passage of larger molecules while allowing the free movement of smaller ones. In contrast, other types of fenestrations, such as the discontinuous epithelium of the liver sinusoidal endothelial cells, do not have diaphragms. \nCharacteristically, fenestrated cells play a vital role in the filtering process of body systems. They are a key part of the glomeruli in the kidneys where blood is filtered under high pressure. The fenestrations present in the endothelial cells lining the capillaries of the glomerulus allow the free passage of water and small solute molecules towards the Bowman's capsule, leaving behind larger proteins and cells in the blood, thereby aiding in the filtration and waste removal process. \nIn the endocrine system, fenestrated cells in glandular capillaries allow the prompt release of hormones into the bloodstream. These cells have tightly clustered fenestrations which increase the surface area available for passive diffusion, improving the efficiency of hormone secretion. In villi of the small intestine, these cells increase absorption efficiency, permitting the exchange of water, electrolytes, and nutrients.\nOverall, fenestrated cells contribute immensely to important physiological processes of filtration, absorption, and secretion, primarily connecting our body's circulation system with the surrounding tissues and organs." xsd:string {xref="DOI:10.1002/ar.1092200109", xref="DOI:10.1016/0306-4522(86)90162-4", xref="DOI:10.1016/j.devcel.2012.11.003", xref="DOI:10.1038/s41467-022-31571-2", xref="DOI:10.1152/ajprenal.90601.2008"} [Term] id: CL:0000669 @@ -1072,6 +1209,8 @@ def: "An elongated, contractile cell found wrapped about precapillary arterioles comment: Pericytes are CD10-positive, CD13-positive, CD31-negative, CD45-negative, CD106-positive, CD117-negative, CD140-positive, CD144-negative, CD146-positive, CD271-positive, CD325-positive, NG2-positive, RGS5-positive, SMA-positive, and desmin-positive. A subpopulation is CD248-positive. They are also capable of producing angiopoietin 1, CXCL12, TGF-beta, and VEGF-A. subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "adventitial cell" RELATED [] synonym: "adventitial reticular cell" EXACT [] synonym: "ARC" EXACT [PMID:17986482] @@ -1092,6 +1231,8 @@ id: CL:0000680 name: muscle precursor cell def: "A non-terminally differentiated cell that is capable of developing into a muscle cell." [GOC:add] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset xref: ZFA:0009291 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000055 ! non-terminally differentiated cell is_a: CL:0000255 ! eukaryotic cell @@ -1104,6 +1245,8 @@ relationship: RO:0002203 CL:0000187 ! develops into muscle cell id: CL:0000723 name: somatic stem cell def: "A stem cell that can give rise to cell types of the body other than those of the germ-line." [GO:0048103] +subset: human_subset +subset: mouse_subset xref: CALOHA:TS-2086 xref: MESH:D053687 xref: ZFA:0009307 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} @@ -1117,6 +1260,8 @@ id: CL:0000763 name: myeloid cell def: "A cell of the monocyte, granulocyte, mast cell, megakaryocyte, or erythroid lineage." [GOC:add] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset xref: BTO:0001441 xref: CALOHA:TS-0647 xref: MESH:D022423 @@ -1134,6 +1279,8 @@ def: "A immature or mature cell in the lineage leading to and including erythroc comment: Note that in FMA erythropoietic cells are types of nucleated erythrocytes and thus don't include erythrocytes. subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "erythropoietic cell" EXACT [] xref: CALOHA:TS-0290 xref: FMA:62845 @@ -1148,6 +1295,8 @@ name: erythroblast def: "A nucleated precursor of an erythrocyte that lacks hematopoietic lineage markers." [GOC:add, ISBN:0721601464, PMID:18174176] subset: blood_and_immune_upper_slim subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "normoblast" EXACT [] xref: BTO:0001571 xref: CALOHA:TS-0289 @@ -1195,6 +1344,8 @@ comment: Markers differ between mouse and human. subset: blood_and_immune_upper_slim subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "hemopoietic progenitor cell" EXACT [] synonym: "MPP" EXACT [] xref: BTO:0000725 @@ -1202,7 +1353,6 @@ xref: CALOHA:TS-0448 xref: ZFA:0009354 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000255 ! eukaryotic cell is_a: CL:0008001 ! hematopoietic precursor cell -is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000988 ! hematopoietic cell intersection_of: bearer_of PATO:0001402 ! multipotent intersection_of: CL:4030046 PR:000001002 ! lacks_plasma_membrane_part CD19 molecule @@ -1245,6 +1395,8 @@ def: "A progenitor cell restricted to the myeloid lineage." [GOC:add, GOC:tfm, P comment: Note that this is a class of cell types, not an identified single cell type. subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "myeloid progenitor cell" BROAD [] xref: BTO:0004730 xref: CALOHA:TS-2099 @@ -1262,6 +1414,8 @@ id: CL:0000988 name: hematopoietic cell def: "A cell of a hematopoietic lineage." [GO_REF:0000031, GOC:add] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "haematopoietic cell" EXACT [] synonym: "haemopoietic cell" EXACT [] synonym: "hemopoietic cell" EXACT [] @@ -1277,6 +1431,8 @@ id: CL:0002031 name: hematopoietic lineage restricted progenitor cell def: "A hematopoietic progenitor cell that is capable of developing into only one lineage of hematopoietic cells." [GOC:tfm, PMID:19022770] subset: blood_and_immune_upper_slim +subset: human_subset +subset: mouse_subset is_a: CL:0000255 ! eukaryotic cell is_a: CL:0008001 ! hematopoietic precursor cell intersection_of: CL:0000988 ! hematopoietic cell @@ -1293,6 +1449,8 @@ name: hematopoietic oligopotent progenitor cell def: "A hematopoietic oligopotent progenitor cell that has the ability to differentiate into limited cell types but lacks lineage cell markers and self renewal capabilities." [GOC:tfm, https://orcid.org/0000-0001-5208-3432, PMID:19022770] comment: This cell type is intended to be compatible with any vertebrate hematopoietic oligopotent progenitor cell. For mammalian hematopoietic oligopotent progenitor cells known to be lineage-negative, please use the term 'hematopoietic oligopotent progenitor cell' (CL_0001060). subset: blood_and_immune_upper_slim +subset: human_subset +subset: mouse_subset is_a: CL:0000255 ! eukaryotic cell is_a: CL:0008001 ! hematopoietic precursor cell intersection_of: CL:0000988 ! hematopoietic cell @@ -1306,6 +1464,8 @@ creation_date: 2010-01-06T03:43:27Z id: CL:0002077 name: ecto-epithelial cell def: "An epithelial cell derived from ectoderm." [FMA:69074, GOC:tfm] +subset: human_subset +subset: mouse_subset xref: FMA:69074 xref: ZFA:0009385 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000066 ! epithelial cell @@ -1319,6 +1479,8 @@ creation_date: 2010-06-29T03:38:22Z id: CL:0002078 name: meso-epithelial cell def: "Epithelial cell derived from mesoderm or mesenchyme." [FMA:69076, GOC:tfm] +subset: human_subset +subset: mouse_subset synonym: "epithelial mesenchymal cell" EXACT [] xref: FMA:69076 xref: ZFA:0009388 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} @@ -1335,13 +1497,17 @@ name: endothelial cell of vascular tree def: "An endothelial cell of the vascular tree, which includes blood vessels and lymphatic vessels." [GOC:dsd, GOC:tfm, PMID:12768659] comment: These cells are reportedly CD31-positive, CD34-positive, CD144-positive, TAL1-positive. subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "cubodial endothelial cell of vascular tree" NARROW [] synonym: "vascular endothelial cell" EXACT [] xref: BTO:0001854 xref: CALOHA:TS-1106 xref: FMA:67755 +xref: https://cellxgene.cziscience.com/cellguide/CL_0002139 is_a: CL:0000115 ! endothelial cell property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nEndothelial cells of the vascular tree, commonly referred to as vascular endothelial cells, line the entire circulatory system, from the heart to the smallest capillaries. These cells have a unique, flattened shape, and are tightly bound together, forming a thin layer known as the endothelium. The endothelium is responsible for maintaining the interior surface of blood vessels, and plays a critical role in ensuring the smooth flow of blood. \nVascular endothelial cells act as a semi-permeable membrane, controlling the passage of materials and the transit of white blood cells into and out of the bloodstream. These cells are also involved in blood coagulation. When a blood vessel is damaged, endothelial cells promote clotting to prevent excessive bleeding and facilitate wound healing. Other functions include regulation of blood pressure and blood volume by releasing vasodilators and vasoconstrictors to either widen or constrict blood vessels, accordingly.\nFurthermore, the endothelial cells are crucial in the formation of new blood vessels, a process known as angiogenesis. This is particularly important in wound healing and the growth of new tissues during development or after injury. In the context of diseases such as cancer, angiogenesis helps facilitate tumor growth by providing nutrients and oxygen." xsd:string {xref="DOI:10.1038/s41569-022-00770-1", xref="DOI:10.1186/s12872-015-0124-z", xref="DOI:10.3389/fphys.2022.863265/full", xref="https://www.sciencedirect.com/topics/medicine-and-dentistry/vascular-endothelial-cell"} creation_date: 2010-08-24T02:06:40Z [Term] @@ -1350,6 +1516,8 @@ name: capillary endothelial cell def: "An endothelial cell found in capillaries." [GOC:tfm] subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset xref: BTO:0004956 xref: CALOHA:TS-0112 xref: FMA:67756 @@ -1366,6 +1534,8 @@ creation_date: 2010-08-24T10:15:00Z id: CL:0002173 name: extraglomerular mesangial cell def: "A cell that is a specialized type of pericyte providing structural support for the capillary loops of kidney. A flat, elongated cell with extensive fine cytoplasmic processes found outside the kidney glomerulus near the macula densa and bound laterally by afferent and efferent arterioles. Being phagocytic, this cell participates in the continuous turnover of the basal lamina by removing its outer portion containing residues of filtration, while the lamina is renewed on its inner surface by the endothelial cells." [GOC:tfm, http:/www.copewithcytokines.de/cope.cgi?key=Lacis%20cells, ISBN:0412046911] +subset: human_subset +subset: mouse_subset synonym: "Goormaghtigh cell" EXACT [] synonym: "lacis cell" RELATED [] synonym: "polar cushion cells" EXACT [] @@ -1386,12 +1556,13 @@ name: glomerular endothelial cell def: "An endothelial cell that is part of the glomerulus of the kidney. This cell is flattened, highly fenestrated, and plays a vital role in the formation of glomerular ultrafiltrate." [GOC:tfm, PMID:15840009] comment: Glomerular endothelial cells have 60-80 nm fenestrations typically lacking diaphragms in adults but present during embryonic development. Some studies found diaphragms in 2-6% of mature rat glomerular capillaries. Their presence may depend on fixation techniques, developmental stage, or dynamic cell changes. Additionally, these cells help maintain the structural integrity of glomerular capillaries through interactions with the basement membrane and podocytes. {xref="PMID:33123011", xref="PMID:18480313", xref="PMID:19129259"} subset: cellxgene_subset +subset: human_subset subset: kidney_upper_slim +subset: mouse_subset xref: BTO:0004632 xref: FMA:70970 is_a: CL:0000666 ! fenestrated endothelial cell is_a: CL:0002681 ! kidney cortical cell -is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000115 ! endothelial cell intersection_of: part_of UBERON:0000074 ! renal glomerulus relationship: has_part GO:0036053 ! glomerular endothelium fenestra @@ -1403,6 +1574,8 @@ creation_date: 2010-08-26T10:59:44Z id: CL:0002242 name: nucleate cell def: "A cell containing at least one nucleus." [GOC:tfm] +subset: human_subset +subset: mouse_subset xref: FMA:67513 is_a: CL:0000000 ! cell intersection_of: CL:0000000 ! cell @@ -1415,7 +1588,9 @@ creation_date: 2010-09-07T03:32:33Z id: CL:0002305 name: epithelial cell of distal tubule def: "An epithelial cell of the distal convoluted tubule of the kidney that helps regulate systemic levels of potassium, sodium, calcium, and pH." [GOC:tfm, ISBN:0517223651] +subset: human_subset subset: kidney_upper_slim +subset: mouse_subset synonym: "kidney distal tubule epithelial cell" EXACT [] xref: FMA:70981 xref: KUPO:0001055 @@ -1433,7 +1608,9 @@ def: "An epithelial cell of the proximal tubule of the kidney." [GOC:tfm, ISBN:1 comment: The vast majority of proximal tubule epithelial cells have a brush border, but there are rare exceptions. subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset subset: kidney_upper_slim +subset: mouse_subset synonym: "kidney proximal tubule epithelial cell" EXACT [] xref: FMA:70973 xref: KUPO:0001044 @@ -1450,6 +1627,8 @@ id: CL:0002319 name: neural cell def: "A cell that is part of the nervous system." [GOC:tfm, ISBN:0618947256] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset xref: CALOHA:TS-2040 xref: FMA:70333 is_a: CL:0000255 ! eukaryotic cell @@ -1464,6 +1643,8 @@ id: CL:0002320 name: connective tissue cell def: "A cell of the supporting or framework tissue of the body, arising chiefly from the embryonic mesoderm and including adipose tissue, cartilage, and bone." [GOC:tfm, ISBN:0618947256] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset xref: CALOHA:TS-2096 xref: FMA:63875 xref: MESH:D003239 @@ -1479,12 +1660,16 @@ creation_date: 2010-09-15T03:01:54Z id: CL:0002321 name: embryonic cell (metazoa) def: "A cell of the embryo." [FMA:0618947256] +subset: human_subset +subset: mouse_subset xref: CALOHA:TS-0263 xref: FMA:82840 +xref: https://cellxgene.cziscience.com/cellguide/CL_0002321 xref: WBbt:0007028 xref: ZFA:0007089 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000000 ! cell property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nEmbryonic cells in metazoans, which include all multicellular animals, are biological units in their earliest developmental stages from conception until the organism is fully formed. \nThey are derived from a fertilized egg, which undergoes a series of cell divisions to produce a multicellular organism. During the early phases of embryonic development, these cells exhibit pluripotency, meaning they possess the potential to differentiate into a diverse array of specialized cell types that constitute different body tissues and structures. \nThe balance between cell proliferation and differentiation in embryonic cells is crucial for successful development. When cells continue to divide without differentiating, overgrowth may occur leading to conditions such as teratomas (tumors of embryonic cells). Conversely, if cell differentiation proceeds at the expense of cell proliferation, developmental anomalies could occur regarding size or mass of the organism or its parts." xsd:string {xref="DOI:10.1002/iub.1404", xref="DOI:10.1093/molehr/gan048", xref="https://www.ncbi.nlm.nih.gov/books/NBK9906/"} creation_date: 2010-09-15T03:39:21Z [Term] @@ -1492,6 +1677,8 @@ id: CL:0002494 name: cardiocyte def: "A cell located in the heart, including both muscle and non muscle cells." [GOC:tfm] comment: From Onard of the FMA: Cardiac muscle cell or cardiac myocyte is a striated muscle cell. Cardiocyte on the other hand is any cell in the heart which includes cells other than muscle cells (e.g. endothelial cell of endocardium). Unless there is a consensus among anatomists that cardiocytes refer only to muscle cells, we will treat them as a general class of cells in the heart. +subset: human_subset +subset: mouse_subset synonym: "heart cell" EXACT [] xref: BTO:0001539 xref: CALOHA:TS-0115 @@ -1509,6 +1696,8 @@ id: CL:0002518 name: kidney epithelial cell def: "An epithelial cell of the kidney." [GOC:tfm, KUPO:SJ] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset xref: KUPO:0001019 xref: ZFA:0009374 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000066 ! epithelial cell @@ -1522,6 +1711,8 @@ creation_date: 2011-02-08T10:46:34Z id: CL:0002584 name: renal cortical epithelial cell def: "An epithelial cell of the kidney cortex." [GOC:tfm] +subset: human_subset +subset: mouse_subset xref: KUPO:0001016 is_a: CL:0002518 {is_inferred="true"} ! kidney epithelial cell is_a: CL:0002681 {is_inferred="true"} ! kidney cortical cell @@ -1532,6 +1723,8 @@ intersection_of: part_of UBERON:0001225 ! cortex of kidney id: CL:0002653 name: squamous endothelial cell def: "A squamous shaped endothelial cell." [GOC:dos] +subset: human_subset +subset: mouse_subset is_a: CL:0000115 ! endothelial cell property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-07-08T03:31:25Z @@ -1540,6 +1733,8 @@ creation_date: 2011-07-08T03:31:25Z id: CL:0002681 name: kidney cortical cell def: "A cell that is part of a cortex of kidney." [] +subset: human_subset +subset: mouse_subset is_a: CL:1000497 ! kidney cell intersection_of: CL:1000497 ! kidney cell intersection_of: part_of UBERON:0001225 ! cortex of kidney @@ -1552,16 +1747,20 @@ id: CL:0005009 name: renal principal cell def: "A cuboidal epithelial cell of the kidney which regulates sodium and potassium balance. The activity of sodium and potassium channels on the apical membrane of the cell is regulated by aldosterone and vasopressin. In mammals this cell type is located in the renal collecting duct system." [CL:CVS] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset xref: https://cellxgene.cziscience.com/cellguide/CL_0005009 xref: ZFA:0005322 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000075 ! columnar/cuboidal epithelial cell is_a: CL:0002518 ! kidney epithelial cell -property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional.\n\nRenal principal cells are the major cell type in the initial collecting tubule and the cortical and outer medullary collecting ducts, as well as the connecting tubule, in the nephrons of the kidneys.\nA key function of renal principal cells is the regulation of water balance in the body. These cells express aquaporin-2 (AQP2) water channels, which facilitate the reabsorption of water from the fluid within the renal tubule lumen back into the blood. The translocation of AQP2 to the cell membrane is controlled by the hormone vasopressin: In response to high vasopressin levels, AQP2 moves to the cell membrane, allowing water to pass through effectively and be reabsorbed, therefore concentrating the urine. Conversely, in low vasopressin conditions, AQP2 is removed from the membrane, reducing water reabsorption and diluting the urine. \nRenal principal cells are also involved in the regulation of sodium and potassium levels in the body. They have sodium channels (ENaC) in their luminal membranes which permit the reabsorption of sodium ions from the tubule fluid back into the blood, resulting in a net reabsorption of sodium ions into the systemic circulation. This process is controlled, in part, by the hormone aldosterone. Additionally, renal principal cells contain potassium channels that facilitate the secretion of potassium ions into the urine. The activities of these channels, in coordination with other cell types in the nephron, are critical for maintaining electrolyte balance and overall body homeostasis." xsd:string {xref="DOI:10.1016/j.krcp.2013.07.005", xref="DOI:10.2215/CJN.05760513", xref="DOI:10.2215/CJN.08580813"} +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nRenal principal cells are the major cell type in the initial collecting tubule and the cortical and outer medullary collecting ducts, as well as the connecting tubule, in the nephrons of the kidneys.\nA key function of renal principal cells is the regulation of water balance in the body. These cells express aquaporin-2 (AQP2) water channels, which facilitate the reabsorption of water from the fluid within the renal tubule lumen back into the blood. The translocation of AQP2 to the cell membrane is controlled by the hormone vasopressin: In response to high vasopressin levels, AQP2 moves to the cell membrane, allowing water to pass through effectively and be reabsorbed, therefore concentrating the urine. Conversely, in low vasopressin conditions, AQP2 is removed from the membrane, reducing water reabsorption and diluting the urine. \nRenal principal cells are also involved in the regulation of sodium and potassium levels in the body. They have sodium channels (ENaC) in their luminal membranes which permit the reabsorption of sodium ions from the tubule fluid back into the blood, resulting in a net reabsorption of sodium ions into the systemic circulation. This process is controlled, in part, by the hormone aldosterone. Additionally, renal principal cells contain potassium channels that facilitate the secretion of potassium ions into the urine. The activities of these channels, in coordination with other cell types in the nephron, are critical for maintaining electrolyte balance and overall body homeostasis." xsd:string {xref="DOI:10.1016/j.krcp.2013.07.005", xref="DOI:10.2215/CJN.05760513", xref="DOI:10.2215/CJN.08580813"} [Term] id: CL:0007004 name: premigratory neural crest cell def: "Cell that is part of the neural crest region of the neuroepithelium, prior to migration. Note that not all premigratory neural crest cells may become migratory neural crest cells." [UBERONREF:0000002] +subset: human_subset +subset: mouse_subset xref: ZFA:0007084 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0011012 ! neural crest cell relationship: part_of UBERON:0002342 ! neural crest @@ -1573,6 +1772,8 @@ creation_date: 2012-06-27T08:27:35Z id: CL:0008000 name: non-striated muscle cell def: "Any muscle cell in which the fibers are not organised into sarcomeres." [GOC:DOS] +subset: human_subset +subset: mouse_subset is_a: CL:0000187 ! muscle cell [Term] @@ -1580,12 +1781,16 @@ id: CL:0008001 name: hematopoietic precursor cell def: "Any hematopoietic cell that is a precursor of some other hematopoietic cell type." [GOC:dos] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset is_a: CL:0000988 ! hematopoietic cell [Term] id: CL:0008007 name: visceral muscle cell def: "A muscle cell that is part of some visceral muscle." [GOC:dos] +subset: human_subset +subset: mouse_subset xref: FBbt:00005070 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} is_a: CL:0000187 ! muscle cell intersection_of: CL:0000187 ! muscle cell @@ -1598,6 +1803,8 @@ name: mesenchymal cell def: "A non-polarised cell precursor cell that is part of some mesenchyme, is associated with the cell matrix but is not connected to other cells and is capable of migration." [] subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset synonym: "mesenchyme cell" EXACT [] is_a: CL:0000219 ! motile cell is_a: CL:0000255 ! eukaryotic cell @@ -1612,6 +1819,8 @@ def: "Mural cells are pericytes and the vascular smooth muscle cells (vSMCs) of subset: added_for_HCA subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset xref: ZFA:0005944 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:4033054 ! perivascular cell property_value: RO:0002175 NCBITaxon:9606 @@ -1622,6 +1831,8 @@ creation_date: 2020-02-29T17:33:55Z id: CL:0010017 name: zygote def: "A zygote in a plant or an animal." [] +subset: human_subset +subset: mouse_subset xref: MESH:D015053 is_a: CL:0000000 ! cell property_value: seeAlso https://github.com/obophenotype/cell-ontology/issues/786 @@ -1631,16 +1842,20 @@ id: CL:0011012 name: neural crest cell def: "A cell of the neural crest. Neural crest cells are multipotent. Premigratory neural crest cells are found at the neural plate boarder, some of which will undergo ectomesynchymal transition and delamination to form migratory neural crest cells." [https://orcid.org/0000-0001-5208-3432, https://orcid.org/0000-0002-9900-7880] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset xref: https://cellxgene.cziscience.com/cellguide/CL_0011012 is_a: CL:0000048 ! multi fate stem cell is_a: CL:0002321 ! embryonic cell (metazoa) -property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional.\n\nNeural crest cells are a group of transient and highly migratory cells that originate from the neuroectoderm during the early stages of embryonic development. They are multipotent cells with an exceptional degree of plasticity, capable of differentiating into various somatic cell types and therefore play a fundamental role in the formation of various organs and tissues, making them critical contributors to the developing embryo. \nAfter the initiation of neurulation (the formation of the neural tube) neural crest cells start to undergo epithelial-to-mesenchymal transition and delaminate and migrate from the dorsal neural tube to several regions throughout the embryo. They differentiate into a range of diverse cell types, such as neurons and glial cells of the peripheral nervous system, including sensory and autonomic neurons. They also contribute to the formation of adrenal glands, pigment cells in the skin (melanocytes), cardiac structures, including parts of the heart septum and major arteries, as well as bones and cartilage of the face and skull.\nDisorders or aberrations in the development or migration of the neural crest cells can lead to serious congenital malformations, such as neurocristopathies, including Hirschsprung disease, neuroblastoma, and neurofibromatosis." xsd:string {xref="DOI:10.1002/dvg.23276", xref="DOI:10.1242/dev.193193", xref="DOI:10.3389/fcell.2020.00635/full", xref="https://doi.org/10.1016/j.ydbio.2011.12.042"} +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nNeural crest cells are a group of transient and highly migratory cells that originate from the neuroectoderm during the early stages of embryonic development. They are multipotent cells with an exceptional degree of plasticity, capable of differentiating into various somatic cell types and therefore play a fundamental role in the formation of various organs and tissues, making them critical contributors to the developing embryo. \nAfter the initiation of neurulation (the formation of the neural tube) neural crest cells start to undergo epithelial-to-mesenchymal transition and delaminate and migrate from the dorsal neural tube to several regions throughout the embryo. They differentiate into a range of diverse cell types, such as neurons and glial cells of the peripheral nervous system, including sensory and autonomic neurons. They also contribute to the formation of adrenal glands, pigment cells in the skin (melanocytes), cardiac structures, including parts of the heart septum and major arteries, as well as bones and cartilage of the face and skull.\nDisorders or aberrations in the development or migration of the neural crest cells can lead to serious congenital malformations, such as neurocristopathies, including Hirschsprung disease, neuroblastoma, and neurofibromatosis." xsd:string {xref="DOI:10.1002/dvg.23276", xref="DOI:10.1242/dev.193193", xref="DOI:10.3389/fcell.2020.00635/full", xref="https://doi.org/10.1016/j.ydbio.2011.12.042"} [Term] id: CL:0011026 name: progenitor cell def: "A precursor cell that has a tendency to differentiate into a specific type of cell. They are descendants of stem cells, only they are more constrained in their differentiation potential or capacity for self-renewal, and are often more limited in both senses." [https://doi.org/10.1016/B978-0-12-409503-8.00002-0, ISBN:978-1-62808-994-3] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset is_a: CL:0000255 ! eukaryotic cell is_a: CL:0011115 ! precursor cell intersection_of: CL:0011115 ! precursor cell @@ -1654,6 +1869,8 @@ name: precursor cell def: "A cell that, by division or terminal differentiation, can give rise to other cell types." [GOC:dos] comment: Work is needed on GO 'cell differentiation' before it is clear whether the equivalent class definition 'native cell' that capable_of some 'cell differentiation' works. Also, may want to consider merging this with non-terminally differentiated cell. subset: cellxgene_subset +subset: human_subset +subset: mouse_subset is_a: CL:0000000 ! cell intersection_of: CL:0000000 ! cell intersection_of: capable_of GO:0030154 ! cell differentiation @@ -1698,18 +1915,24 @@ id: CL:1000449 name: epithelial cell of nephron def: "An epithelial cell that is part of the nephron." [GOC:tfm] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset xref: FMA:70965 +xref: https://cellxgene.cziscience.com/cellguide/CL_1000449 is_a: CL:0002518 ! kidney epithelial cell intersection_of: CL:0000066 ! epithelial cell intersection_of: part_of UBERON:0001285 ! nephron relationship: part_of UBERON:0001285 ! nephron +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nEpithelial cells of the nephron form the epithelial lining of the nephron, the functional unit of the kidney that filters the blood to produce urine. Each kidney holds approximately one million nephrons, each of which is composed of several distinct parts, including the renal corpuscle, the proximal tubule, the loop of Henle, and the distal tubule. All sections are lined with highly specialized epithelial cells adapted to perform different functions within the sections of the nephron. \nThe different epithelial cells of the nephron play crucial roles in the process of filtration, reabsorption, secretion, and excretion, essential tasks for the regulation of body fluid composition and volume. During filtration, the blood is forced through the walls of glomerular capillaries into the Bowman's capsule, where waste products, electrolytes, and water are separated from the blood cells and proteins. As the filtrate then passes through the nephron, epithelial cells of the tubular portion reabsorb useful substances such as glucose, amino acids, and electrolytes, along with most of the water back into the bloodstream. Waste products like urea and creatinine, as well as excess ions and water, remain in the tubule for elimination.\nIn addition, epithelial cells of the nephron also play a vital part in maintaining the body's acid-base balance by actively secreting hydrogen ions into the urine while reabsorbing bicarbonate from the urine back into the blood. They are also involved in the regulation of blood pressure through the renin-angiotensin-aldosterone system and contribute to erythrocyte production by releasing the hormone erythropoietin in response to low oxygen levels in the blood. Abnormalities or damage in renal epithelial cells often result in impaired kidney function, leading to various renal diseases." xsd:string {xref="DOI:10.1007/978-94-011-2354-9_6", xref="DOI:10.1007/s004670050586", xref="DOI:10.1016/B978-0-323-35775-3.00011-4", xref="DOI:10.1146/annurev-physiol-052521-121841", xref="DOI:10.1681/ASN.2012010029"} [Term] id: CL:1000450 name: epithelial cell of glomerular capsule def: "An epithelial cell that is part of the glomerular capsule." [GOC:tfm] subset: cellxgene_subset +subset: human_subset subset: kidney_upper_slim +subset: mouse_subset synonym: "Bowmans capsule epithelial cell" EXACT [] synonym: "epithelial cell of Bowman's capsule" EXACT [FMA:70966] xref: FMA:70966 @@ -1725,7 +1948,9 @@ name: kidney collecting duct epithelial cell def: "An epithelial cell that is part of the collecting duct of renal tubule." [GOC:tfm] subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset subset: kidney_upper_slim +subset: mouse_subset synonym: "epithelial cell of renal collecting tubule" EXACT [FMA:70982] xref: FMA:70982 xref: https://cellxgene.cziscience.com/cellguide/CL_1000454 @@ -1736,7 +1961,7 @@ is_a: CL:1001225 {is_inferred="true"} ! kidney collecting duct cell intersection_of: CL:0000066 ! epithelial cell intersection_of: part_of UBERON:0001232 ! collecting duct of renal tubule property_value: RO:0002175 NCBITaxon:9606 -property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional.\n\nKidney collecting duct epithelial cells are a specialized type of cells that form an integral part of the renal system. Located in the collecting duct system of the kidneys, these cells are responsible for one of the final steps in the process of urine formation, and they are instrumental in the fine tuning of the volume and composition of urine by reabsorbing water and certain solutes back into the bloodstream.\nThese cells express specific channels and carriers that actively and passively transport ions and water. They also have channels on their membranes, such as sodium channels and potassium channels, involved in reabsorbing or secreting these electrolytes depending upon the body's needs. The function of renal collecting duct epithelial cells can be regulated by a variety of hormones, including vasopressin (antidiuretic hormone), which can modulate the ion channels and carriers and hence indirectly influence body fluid homeostasis.\nAside from their function in ion and water balance, kidney collecting duct epithelial cells also aid in maintaining the body's acid-base balance. They have specialized functionality to secret hydrogen ions into the tubular lumen, which contributes to acid excretion. Any dysfunction may have serious implications and lead to various renal or systemic diseases, exemplifying the importance of these cells in maintaining overall body homeostasis." xsd:string {xref="DOI:10.1016/j.ajpath.2014.01.014", xref="DOI:10.1016/j.semnephrol.2019.04.005", xref="DOI:10.2215/CJN.05760513", xref="DOI:10.2215/CJN.08880914"} +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nKidney collecting duct epithelial cells are a specialized type of cells that form an integral part of the renal system. Located in the collecting duct system of the kidneys, these cells are responsible for one of the final steps in the process of urine formation, and they are instrumental in the fine tuning of the volume and composition of urine by reabsorbing water and certain solutes back into the bloodstream.\nThese cells express specific channels and carriers that actively and passively transport ions and water. They also have channels on their membranes, such as sodium channels and potassium channels, involved in reabsorbing or secreting these electrolytes depending upon the body's needs. The function of renal collecting duct epithelial cells can be regulated by a variety of hormones, including vasopressin (antidiuretic hormone), which can modulate the ion channels and carriers and hence indirectly influence body fluid homeostasis.\nAside from their function in ion and water balance, kidney collecting duct epithelial cells also aid in maintaining the body's acid-base balance. They have specialized functionality to secret hydrogen ions into the tubular lumen, which contributes to acid excretion. Any dysfunction may have serious implications and lead to various renal or systemic diseases, exemplifying the importance of these cells in maintaining overall body homeostasis." xsd:string {xref="DOI:10.1016/j.ajpath.2014.01.014", xref="DOI:10.1016/j.semnephrol.2019.04.005", xref="DOI:10.2215/CJN.05760513", xref="DOI:10.2215/CJN.08880914"} [Term] id: CL:1000494 @@ -1744,6 +1969,8 @@ name: nephron tubule epithelial cell def: "An epithelial cell that is part of a nephron tubule." [GOC:tfm] comment: This needs to be further defined as a juxtamedullary nephron. Will request the juxtamedullary nephron tubule class from UBERON. subset: cellxgene_subset +subset: human_subset +subset: mouse_subset synonym: "kidney tubule epithelial cell" EXACT [] xref: FMA:86785 xref: KUPO:0001022 @@ -1758,6 +1985,8 @@ id: CL:1000497 name: kidney cell def: "A cell that is part of a kidney." [] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset xref: KUPO:0001010 xref: ZFA:0009389 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000255 ! eukaryotic cell @@ -1770,7 +1999,9 @@ id: CL:1000500 name: kidney interstitial cell def: "A cell that is part of kidney interstitium." [] subset: cellxgene_subset +subset: human_subset subset: kidney_upper_slim +subset: mouse_subset xref: KUPO:0001013 xref: ZFA:0009390 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:1000497 ! kidney cell @@ -1783,6 +2014,8 @@ relationship: part_of UBERON:0005215 ! kidney interstitium id: CL:1000504 name: kidney medulla cell def: "A cell that is part of a renal medulla." [PMID:22343825] +subset: human_subset +subset: mouse_subset xref: KUPO:0001017 xref: ZFA:0009391 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:1000497 ! kidney cell @@ -1794,7 +2027,9 @@ relationship: part_of UBERON:0000362 ! renal medulla id: CL:1000505 name: kidney pelvis cell def: "A cell that is part of a renal pelvis." [] +subset: human_subset subset: kidney_upper_slim +subset: mouse_subset xref: KUPO:0001018 is_a: CL:1000497 ! kidney cell intersection_of: CL:1000497 ! kidney cell @@ -1805,7 +2040,9 @@ relationship: part_of UBERON:0001224 ! renal pelvis id: CL:1000507 name: kidney tubule cell def: "A cell that is part of a nephron tubule." [] +subset: human_subset subset: kidney_upper_slim +subset: mouse_subset xref: KUPO:0001020 is_a: CL:1000497 ! kidney cell intersection_of: CL:1000497 ! kidney cell @@ -1817,6 +2054,8 @@ id: CL:1000510 name: kidney glomerular epithelial cell def: "Any kidney epithelial cell that is part of some glomerular epithelium." [FBC:Autogenerated] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset xref: KUPO:0001023 is_a: CL:1000746 ! glomerular cell intersection_of: CL:0002518 ! kidney epithelial cell @@ -1827,7 +2066,9 @@ relationship: part_of UBERON:0004188 ! glomerular epithelium id: CL:1000546 name: kidney medulla collecting duct epithelial cell def: "An epithelial cell that is part of a renal medulla collecting duct." [] +subset: human_subset subset: kidney_upper_slim +subset: mouse_subset xref: KUPO:0001060 is_a: CL:1000454 ! kidney collecting duct epithelial cell is_a: CL:1000504 ! kidney medulla cell @@ -1839,7 +2080,9 @@ relationship: part_of UBERON:0005185 ! renal medulla collecting duct id: CL:1000550 name: kidney papillary duct principal epithelial cell def: "Any kidney cell that is part of some papillary duct." [FBC:Autogenerated] +subset: human_subset subset: kidney_upper_slim +subset: mouse_subset xref: KUPO:0001064 is_a: CL:1001225 ! kidney collecting duct cell intersection_of: CL:1000497 ! kidney cell @@ -1850,7 +2093,9 @@ relationship: part_of UBERON:0005167 ! papillary duct id: CL:1000612 name: kidney corpuscule cell def: "Any renal cortical epithelial cell that is part of some renal corpuscle." [FBC:Autogenerated] +subset: human_subset subset: kidney_upper_slim +subset: mouse_subset xref: KUPO:0001021 is_a: CL:0002584 ! renal cortical epithelial cell is_a: CL:1000449 ! epithelial cell of nephron @@ -1863,6 +2108,8 @@ id: CL:1000615 name: kidney cortex tubule cell def: "Any kidney tubule cell that is part of some renal cortex tubule." [FBC:Autogenerated] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset xref: KUPO:0001024 is_a: CL:0002584 ! renal cortical epithelial cell is_a: CL:1000449 ! epithelial cell of nephron @@ -1875,7 +2122,9 @@ relationship: part_of UBERON:0006853 ! renal cortex tubule id: CL:1000618 name: juxtaglomerular complex cell def: "Any kidney cortical cell that is part of some juxtaglomerular apparatus." [FBC:Autogenerated] +subset: human_subset subset: kidney_upper_slim +subset: mouse_subset synonym: "juxtaglomerulus cell" EXACT [GO:0072052] xref: KUPO:0001028 is_a: CL:0002681 {is_inferred="true"} ! kidney cortical cell @@ -1889,6 +2138,8 @@ name: kidney interstitial fibroblast def: "A fibroblast that is part of an interstitial compartment of a kidney." [PMID:10559635] subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset xref: KUPO:0001102 is_a: CL:0000057 ! fibroblast is_a: CL:1000500 ! kidney interstitial cell @@ -1900,6 +2151,8 @@ property_value: RO:0002175 NCBITaxon:9606 id: CL:1000746 name: glomerular cell def: "Any kidney corpuscule cell that is part of some renal glomerulus." [FBC:Autogenerated] +subset: human_subset +subset: mouse_subset xref: KUPO:0001036 is_a: CL:1000612 ! kidney corpuscule cell intersection_of: CL:1000612 ! kidney corpuscule cell @@ -1912,7 +2165,10 @@ name: kidney connecting tubule epithelial cell def: "Any nephron tubule epithelial cell that is part of some renal connecting tubule." [FBC:Autogenerated] subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset subset: kidney_upper_slim +subset: mouse_subset +xref: https://cellxgene.cziscience.com/cellguide/CL_1000768 xref: KUPO:0001058 is_a: CL:1000494 {is_inferred="true"} ! nephron tubule epithelial cell is_a: CL:1000615 ! kidney cortex tubule cell @@ -1920,6 +2176,7 @@ intersection_of: CL:1000494 ! nephron tubule epithelial cell intersection_of: part_of UBERON:0005097 ! renal connecting tubule relationship: part_of UBERON:0005097 ! renal connecting tubule property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nKidney connecting tubule epithelial cells are found in collecting duct system of the kidney, specifically in at the interconnection segment between the nephron and the collecting ducts. The epithelial cells lining the connecting tubule are crucial for the journey of filtrate before it empties into urine-collecting ducts and therefore play a critical role in maintaining the body’s fluid and electrolyte balance.\nOne of the principal functions of connecting tubule epithelial cells involves the selective reabsorption and secretion of various solutes. This reabsorption process includes critical regulatory electrolytes such as sodium ions (Na+), chloride ions (Cl-), and bicarbonate ions (HCO3-), thus playing a role in the regulation of the acid-base homeostasis. Their function also involves the secretion of potassium ions (K+) into the renal tubular fluid.\nThe connecting tubule epithelial cells are primarily intercalated cells, which can be categorized into two types according to their specific functions: type A intercalated cells, which secrete acid, and the type B intercalated cells, which secrete base (bicarbonate) and reabsorb chloride. By regulating the concentrations of these ions, as well as reabsorption of water, connecting tubule epithelial cells contribute substantively to maintaining the body's electrolyte levels, pH balance, and overall homeostasis.\nIn addition to intercalating cells, the collecting duct system also has principal cells, which are characterized by the expression of the water channel AQP2. AQP2-expressing cells have also been identified in connecting tubules, but there is some controversy whether these represent a unique cell type as there are some morphologic differences compared with principal cells." xsd:string {xref="DOI:10.1002/cphy.c110052", xref="DOI:10.1007/s00418-021-02033-5", xref="DOI:10.1097/MNH.0b013e32820ac850", xref="DOI:10.1681/ASN.2019040415", xref="DOI:10.23876/j.krcp.2017.36.4.305"} [Term] id: CL:1000849 @@ -1927,18 +2184,24 @@ name: kidney distal convoluted tubule epithelial cell def: "Any epithelial cell of distal tubule that is part of some distal convoluted tubule." [FBC:Autogenerated] subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset subset: kidney_upper_slim +subset: mouse_subset +xref: https://cellxgene.cziscience.com/cellguide/CL_1000849 xref: KUPO:0001056 is_a: CL:0002305 {is_inferred="true"} ! epithelial cell of distal tubule intersection_of: CL:0002305 ! epithelial cell of distal tubule intersection_of: part_of UBERON:0001292 ! distal convoluted tubule relationship: part_of UBERON:0001292 ! distal convoluted tubule property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nKidney distal convoluted tubule epithelial cells, often referred to simply as distal convoluted tubule (DCT) cells, constitute a significant portion of the nephron -- the functional building unit of the kidney involved in filtration and reabsorption of substances from blood. The DCT epithelial cells form lining of the distal convoluted tubule, a segment of the nephron located after the loop of Henle and before the collecting tubule. These cells are characterized by unique morphological features such as small size, low height and fewer microvilli compared to proximal convoluted tubule epithelial cells. \nThese cells perform a host of vital functions contributing to the regulation of extracellular fluid volume and electrolyte balance, blood pressure and pH. While the DCT is less prominent in water and sodium reabsorption compared to the proximal tubule and the loop of Henle, it plays a crucial role in fine-tuning the process. DCT epithelial cells are responsible for the final adjustments of sodium, potassium and calcium reabsorption, thereby affecting overall fluid and electrolyte balance, blood pressure regulation and bone health. The reabsorption process is regulated by hormones including aldosterone and parathyroid hormone.\nThe distal convoluted tubule (DCT) also plays a significant role in acid-base homeostasis by secreting protons (H+) into the tubular fluid and reabsorbing bicarbonate ions (HCO3-), thus regulating the pH of the blood. The ability of DCT cells to adjust urine concentration plays a part in maintaining the body’s pH balance and preventing conditions like acidosis or alkalosis. In summary, kidney distal convoluted tubule epithelial cells perform functions that are crucial to maintaining body's homeostasis." xsd:string {xref="DOI:10.1002/cphy.c140002", xref="DOI:10.1007/s40620-021-01032-y", xref="DOI:10.1152/physrev.2000.80.1.277", xref="DOI:10.1681/ASN.2019040415", xref="DOI:10.2215/CJN.05920613"} [Term] id: CL:1000854 name: kidney blood vessel cell def: "A blood vessel cell that is part of a kidney." [PMID:34843404] +subset: human_subset +subset: mouse_subset xref: KUPO:0001014 is_a: CL:1000504 {is_inferred="true"} ! kidney medulla cell intersection_of: CL:0000000 ! cell @@ -1950,7 +2213,9 @@ relationship: participates_in GO:0008015 ! blood circulation id: CL:1000891 name: kidney arterial blood vessel cell def: "Any kidney blood vessel cell that is part of some kidney arterial blood vessel." [FBC:Autogenerated] +subset: human_subset subset: kidney_upper_slim +subset: mouse_subset xref: KUPO:0001029 is_a: CL:1000854 {is_inferred="true"} ! kidney blood vessel cell intersection_of: CL:1000854 ! kidney blood vessel cell @@ -1962,7 +2227,9 @@ id: CL:1000892 name: kidney capillary endothelial cell def: "An endothelial cell that is part of the capillary of the kidney." [] subset: cellxgene_subset +subset: human_subset subset: kidney_upper_slim +subset: mouse_subset xref: KUPO:0001030 is_a: CL:0002144 ! capillary endothelial cell is_a: CL:1000854 ! kidney blood vessel cell @@ -1974,7 +2241,9 @@ relationship: part_of UBERON:0003527 ! kidney capillary id: CL:1000893 name: kidney venous blood vessel cell def: "Any kidney blood vessel cell that is part of some renal vein." [FBC:Autogenerated] +subset: human_subset subset: kidney_upper_slim +subset: mouse_subset xref: KUPO:0001031 is_a: CL:1000854 {is_inferred="true"} ! kidney blood vessel cell intersection_of: CL:1000854 ! kidney blood vessel cell @@ -1986,6 +2255,8 @@ id: CL:1000909 name: kidney loop of Henle epithelial cell def: "Any nephron tubule epithelial cell that is part of some loop of Henle." [FBC:Autogenerated] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset xref: KUPO:0001047 is_a: CL:1000494 {is_inferred="true"} ! nephron tubule epithelial cell intersection_of: CL:1000494 ! nephron tubule epithelial cell @@ -1997,7 +2268,9 @@ id: CL:1001016 name: kidney loop of Henle ascending limb epithelial cell def: "Any kidney loop of Henle epithelial cell that is part of some ascending limb of loop of Henle." [FBC:Autogenerated] subset: cellxgene_subset +subset: human_subset subset: kidney_upper_slim +subset: mouse_subset xref: KUPO:0001048 is_a: CL:0002305 ! epithelial cell of distal tubule is_a: CL:1000909 {is_inferred="true"} ! kidney loop of Henle epithelial cell @@ -2009,18 +2282,24 @@ relationship: part_of UBERON:0005164 ! ascending limb of loop of Henle id: CL:1001021 name: kidney loop of Henle descending limb epithelial cell def: "Any kidney loop of Henle epithelial cell that is part of some descending limb of loop of Henle." [FBC:Autogenerated] +subset: human_subset subset: kidney_upper_slim +subset: mouse_subset +xref: https://cellxgene.cziscience.com/cellguide/CL_1001021 xref: KUPO:0001053 is_a: CL:1000909 {is_inferred="true"} ! kidney loop of Henle epithelial cell intersection_of: CL:1000909 ! kidney loop of Henle epithelial cell intersection_of: part_of UBERON:0001289 ! descending limb of loop of Henle relationship: part_of UBERON:0001289 ! descending limb of loop of Henle +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.\n\nThe kidney loop of Henle descending limb epithelial cells are highly specialized cells that play a crucial role in maintaining the body's salt and water balance. These cells line the descending limb of the loop of Henle, which is a portion of the renal tubule located in the kidneys, an organ responsible for filtering waste products, ions and extra water from the blood and converting them into urine. However, the descending limb epithelial cells are specifically involved in the countercurrent multiplication system, a mechanism to concentrate urine that involves both active and passive transport processes. \nThese cells are notably permeable to water but relatively impermeable to solutes, a characteristic that dramatically influences the osmotic gradient in the renal medulla. As filtrate initially descends down the loop of Henle, water gets drawn out due to the increasing osmotic gradient, thereby concentrating the filtrate. Additionally, these epithelial cells are exceptionally thin walled, allowing water to freely diffuse across the membrane.\nFurthermore, the kidney loop of Henle descending limb epithelial cells are inextricably linked to the functioning of numerous diuretic drugs, which work by blocking the reabsorption of water and certain electrolytes in the kidneys, leading to increased urine production to rid the body of excess fluids." xsd:string {xref="DOI:10.1007/s00360-018-1164-3", xref="DOI:10.1146/annurev-physiol-021113-170350", xref="DOI:10.1152/advan.00227.2022"} [Term] id: CL:1001225 name: kidney collecting duct cell def: "A cell that is part of a collecting duct of renal tubule." [] subset: cellxgene_subset +subset: human_subset +subset: mouse_subset xref: KUPO:0001012 xref: Wikipedia:Kidney_collecting_duct_cell is_a: CL:1000497 ! kidney cell @@ -2034,6 +2313,8 @@ name: renal interstitial pericyte def: "A pericyte cell located in the kidney interstitium." [] subset: cellxgene_subset subset: human_reference_atlas +subset: human_subset +subset: mouse_subset xref: KUPO:0001104 is_a: CL:0000669 {is_inferred="true"} ! pericyte is_a: CL:1000500 ! kidney interstitial cell @@ -2045,6 +2326,9 @@ property_value: RO:0002175 NCBITaxon:9606 id: CL:2000008 name: microvascular endothelial cell def: "Any blood vessel endothelial cell that is part of a microvascular endothelium." [GOC:TermGenie] +subset: cellxgene_subset +subset: human_subset +subset: mouse_subset is_a: CL:0000071 ! blood vessel endothelial cell intersection_of: CL:0000071 ! blood vessel endothelial cell intersection_of: part_of UBERON:0008339 ! microvascular endothelium @@ -2056,6 +2340,8 @@ creation_date: 2014-06-04T15:07:42Z id: CL:4030031 name: interstitial cell def: "Any cell that is located within the interstitium between the cells most prominent in defining a given tissue. \"Interstitial cell\" is a morphological term and refers to a variety of cells with differing origins and phenotypes." [PMID:24987007] +subset: human_subset +subset: mouse_subset is_a: CL:0000255 ! eukaryotic cell intersection_of: CL:0000000 ! cell intersection_of: part_of UBERON:0005169 ! interstitial tissue @@ -2066,6 +2352,9 @@ property_value: terms:date "2022-11-30T14:35:08Z" xsd:dateTime id: CL:4033054 name: perivascular cell def: "A cell that is adjacent to a vessel. A perivascular cell plays a crucial role in maintaining vascular function and tissue homeostasis. This cell type regulates vessel integrity and flow dynamics." [PMID:24928499, PMID:27889329] +subset: cellxgene_subset +subset: human_subset +subset: mouse_subset is_a: CL:0000000 ! cell intersection_of: CL:0000000 ! cell intersection_of: adjacent_to UBERON:0002049 ! vasculature @@ -2077,7 +2366,6 @@ property_value: terms:date "2023-08-22T13:40:28Z" xsd:dateTime id: GO:0000278 name: mitotic cell cycle namespace: biological_process -alt_id: GO:0007067 def: "Progression through the phases of the mitotic cell cycle, the most common eukaryotic cell cycle, which canonically comprises four successive phases called G1, S, G2, and M and includes replication of the genome and the subsequent segregation of chromosomes into daughter cells. In some variant cell cycles nuclear replication or nuclear division may not be followed by cell division, or G1 and G2 phases may be absent." [GOC:mah, ISBN:0815316194] comment: Note that this term should not be confused with 'GO:0140014 ; mitotic nuclear division'. 'GO:0000278 ; mitotic cell cycle represents the entire mitotic cell cycle, while 'GO:0140014 ; mitotic nuclear division' specifically represents the actual nuclear division step of the mitotic cell cycle. subset: goslim_chembl @@ -2109,16 +2397,13 @@ relationship: results_in_fission_of GO:0005634 ! nucleus id: GO:0000785 name: chromatin namespace: cellular_component -alt_id: GO:0000789 -alt_id: GO:0000790 -alt_id: GO:0005717 def: "The ordered and organized complex of DNA, protein, and sometimes RNA, that forms the chromosome." [GOC:elh, PMID:20404130] comment: Chromosomes include parts that are not part of the chromatin. Examples include the kinetochore. synonym: "chromosome scaffold" RELATED [] synonym: "cytoplasmic chromatin" NARROW [] synonym: "nuclear chromatin" NARROW [] xref: NIF_Subcellular:sao1615953555 -is_a: GO:0110165 ! cellular anatomical entity +is_a: GO:0110165 ! cellular anatomical structure relationship: part_of GO:0005694 ! chromosome property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28301" xsd:anyURI @@ -2126,8 +2411,6 @@ property_value: term_tracker_item "https://github.com/geneontology/go-ontology/i id: GO:0000792 name: heterochromatin namespace: cellular_component -alt_id: GO:0005720 -alt_id: GO:0035328 def: "A compact and highly condensed form of chromatin that is refractory to transcription." [PMID:32017156] synonym: "nuclear heterochromatin" NARROW [] synonym: "transcriptionally inactive chromatin" EXACT [] @@ -2224,7 +2507,6 @@ relationship: part_of GO:0016331 ! morphogenesis of embryonic epithelium id: GO:0001841 name: neural tube formation namespace: biological_process -alt_id: GO:0001679 def: "The formation of a tube from the flat layer of ectodermal cells known as the neural plate. This will give rise to the central nervous system." [GOC:dph, ISBN:0878932437] synonym: "neural tube morphogenesis" EXACT [GOC:dph] synonym: "neurulation" EXACT [] @@ -2463,7 +2745,6 @@ relationship: part_of GO:0003091 ! renal water homeostasis id: GO:0005575 name: cellular_component namespace: cellular_component -alt_id: GO:0008372 def: "A location, relative to cellular compartments and structures, occupied by a macromolecular machine. There are three types of cellular components described in the gene ontology: (1) the cellular anatomical entity where a gene product carries out a molecular function (e.g., plasma membrane, cytoskeleton) or membrane-enclosed compartments (e.g., mitochondrion); (2) virion components, where viral proteins act, and (3) the stable macromolecular complexes of which gene product are parts (e.g., the clathrin complex)." [GOC:pdt] comment: Note that, in addition to forming the root of the cellular component ontology, this term is recommended for the annotation of gene products whose cellular component is unknown. When this term is used for annotation, it indicates that no information was available about the cellular component of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this. subset: goslim_candida @@ -2501,7 +2782,7 @@ subset: goslim_prokaryote_ribbon subset: goslim_yeast synonym: "extracellular" EXACT [] xref: Wikipedia:Extracellular -is_a: GO:0110165 ! cellular anatomical entity +is_a: GO:0110165 ! cellular anatomical structure [Term] id: GO:0005577 @@ -2538,8 +2819,6 @@ is_a: GO:0098651 ! basement membrane collagen trimer id: GO:0005604 name: basement membrane namespace: cellular_component -alt_id: GO:0005605 -alt_id: GO:0008003 def: "A collagen-containing extracellular matrix consisting of a thin layer of dense material found in various animal tissues interposed between the cells and the adjacent connective tissue. It consists of the basal lamina plus an associated layer of reticulin fibers." [ISBN:0198547684, PMID:22505934] comment: Note that this term has no relationship to 'membrane ; GO:0016020' because the basement membrane is not a lipid bilayer. synonym: "basal lamina" RELATED [] @@ -2559,7 +2838,7 @@ subset: goslim_drosophila subset: goslim_generic synonym: "intercellular space" RELATED [] xref: NIF_Subcellular:sao1425028079 -is_a: GO:0110165 ! cellular anatomical entity +is_a: GO:0110165 ! cellular anatomical structure relationship: part_of GO:0005576 ! extracellular region [Term] @@ -2577,7 +2856,7 @@ synonym: "nucleocytoplasm" RELATED [GOC:mah] synonym: "protoplasm" EXACT [] synonym: "protoplast" RELATED [GOC:mah] xref: Wikipedia:Intracellular -is_a: GO:0110165 ! cellular anatomical entity +is_a: GO:0110165 ! cellular anatomical structure relationship: part_of CL:0000000 ! cell property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/17776" xsd:anyURI @@ -2629,7 +2908,7 @@ synonym: "chromatid" RELATED [] synonym: "interphase chromosome" NARROW [] synonym: "prophase chromosome" NARROW [] xref: Wikipedia:Chromosome -is_a: GO:0043232 ! intracellular non-membrane-bounded organelle +is_a: GO:0043232 ! intracellular membraneless organelle [Term] id: GO:0005730 @@ -2645,7 +2924,7 @@ subset: goslim_plant subset: goslim_yeast xref: NIF_Subcellular:sao1820400233 xref: Wikipedia:Nucleolus -is_a: GO:0043232 ! intracellular non-membrane-bounded organelle +is_a: GO:0043232 ! intracellular membraneless organelle relationship: part_of GO:0031981 ! nuclear lumen [Term] @@ -2663,7 +2942,7 @@ subset: goslim_prokaryote subset: goslim_prokaryote_ribbon subset: goslim_yeast xref: Wikipedia:Cytoplasm -is_a: GO:0110165 ! cellular anatomical entity +is_a: GO:0110165 ! cellular anatomical structure relationship: part_of GO:0005622 ! intracellular anatomical structure property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/23023" xsd:anyURI @@ -2671,7 +2950,6 @@ property_value: term_tracker_item "https://github.com/geneontology/go-ontology/i id: GO:0005840 name: ribosome namespace: cellular_component -alt_id: GO:0033279 def: "An intracellular organelle, about 200 A in diameter, consisting of RNA and protein. It is the site of protein biosynthesis resulting from translation of messenger RNA (mRNA). It consists of two subunits, one large and one small, each containing only protein and RNA. Both the ribosome and its subunits are characterized by their sedimentation coefficients, expressed in Svedberg units (symbol: S). Hence, the prokaryotic ribosome (70S) comprises a large (50S) subunit and a small (30S) subunit, while the eukaryotic ribosome (80S) comprises a large (60S) subunit and a small (40S) subunit. Two sites on the ribosomal large subunit are involved in translation, namely the aminoacyl site (A site) and peptidyl site (P site). Ribosomes from prokaryotes, eukaryotes, mitochondria, and chloroplasts have characteristically distinct ribosomal proteins." [ISBN:0198506732] subset: goslim_candida subset: goslim_chembl @@ -2689,16 +2967,14 @@ synonym: "membrane bound ribosome" NARROW [NIF_Subcellular:sao1291545653] synonym: "ribosomal RNA" RELATED [] xref: NIF_Subcellular:sao1429207766 xref: Wikipedia:Ribosome -is_a: GO:0043232 ! intracellular non-membrane-bounded organelle -is_a: PR:000050567 ! protein-containing material entity +is_a: GO:0043232 ! intracellular membraneless organelle relationship: capable_of_part_of GO:0006412 ! translation +relationship: has_part PR:000000001 ! protein [Term] id: GO:0005886 name: plasma membrane namespace: cellular_component -alt_id: GO:0005887 -alt_id: GO:0005904 def: "The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins." [ISBN:0716731363] subset: goslim_agr subset: goslim_candida @@ -2744,9 +3020,6 @@ property_value: term_tracker_item "https://github.com/geneontology/go-ontology/i id: GO:0006412 name: translation namespace: biological_process -alt_id: GO:0006416 -alt_id: GO:0006453 -alt_id: GO:0043037 def: "The cellular metabolic process in which a protein is formed, using the sequence of a mature mRNA or circRNA molecule to specify the sequence of amino acids in a polypeptide chain. Translation is mediated by the ribosome, and begins with the formation of a ternary complex between aminoacylated initiator methionine tRNA, GTP, and initiation factor 2, which subsequently associates with the small subunit of the ribosome and an mRNA or circRNA. Translation ends with the release of a polypeptide chain from the ribosome." [GOC:go_curators] subset: goslim_candida subset: goslim_chembl @@ -2775,15 +3048,13 @@ relationship: starts_with GO:0006413 ! translational initiation id: GO:0006413 name: translational initiation namespace: biological_process -alt_id: GO:0006440 -alt_id: GO:0006454 def: "The process preceding formation of the peptide bond between the first two amino acids of a protein. This includes the formation of a complex of the ribosome, mRNA or circRNA, and an initiation complex that contains the first aminoacyl-tRNA." [ISBN:019879276X] subset: goslim_yeast synonym: "biopolymerisation" BROAD [] synonym: "biopolymerization" BROAD [] synonym: "protein synthesis initiation" BROAD [] synonym: "translation initiation" EXACT [] -is_a: GO:0044237 ! cellular metabolic process +is_a: GO:0008152 ! metabolic process relationship: part_of GO:0006412 ! translation relationship: starts_with GO:0001677 ! formation of translation initiation ternary complex @@ -2791,8 +3062,6 @@ relationship: starts_with GO:0001677 ! formation of translation initiation terna id: GO:0006414 name: translational elongation namespace: biological_process -alt_id: GO:0006442 -alt_id: GO:0006455 def: "The successive addition of amino acid residues to a nascent polypeptide chain during protein biosynthesis." [GOC:ems] subset: goslim_yeast synonym: "protein synthesis elongation" BROAD [] @@ -2804,8 +3073,6 @@ relationship: part_of GO:0006412 ! translation id: GO:0006415 name: translational termination namespace: biological_process -alt_id: GO:0006443 -alt_id: GO:0006456 def: "The process resulting in the release of a polypeptide chain from the ribosome, usually in response to a termination codon (UAA, UAG, or UGA in the universal genetic code)." [GOC:hjd, ISBN:019879276X] synonym: "protein synthesis termination" BROAD [] synonym: "translation termination" EXACT [] @@ -2817,9 +3084,6 @@ relationship: part_of GO:0006412 ! translation id: GO:0006810 name: transport namespace: biological_process -alt_id: GO:0015457 -alt_id: GO:0015460 -alt_id: GO:0044765 def: "The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter or a transporter complex, a pore or a motor protein." [GOC:dos, GOC:dph, GOC:jl, GOC:mah] comment: Note that this term should not be used for direct annotation. It should be possible to make a more specific annotation to one of the children of this term, for e.g. to transmembrane transport, to microtubule-based transport or to vesicle-mediated transport. subset: gocheck_do_not_annotate @@ -2834,7 +3098,6 @@ subset: goslim_prokaryote_ribbon synonym: "single-organism transport" RELATED [] is_a: GO:0051234 ! establishment of localization property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/20292" xsd:anyURI -created_by: jl creation_date: 2012-12-13T16:25:32Z [Term] @@ -2859,8 +3122,6 @@ is_a: GO:0042044 ! fluid transport id: GO:0006915 name: apoptotic process namespace: biological_process -alt_id: GO:0006917 -alt_id: GO:0008632 def: "A programmed cell death process which begins when a cell receives an internal (e.g. DNA damage) or external signal (e.g. an extracellular death ligand), and proceeds through a series of biochemical events (signaling pathway phase) which trigger an execution phase. The execution phase is the last step of an apoptotic process, and is typically characterized by rounding-up of the cell, retraction of pseudopodes, reduction of cellular volume (pyknosis), chromatin condensation, nuclear fragmentation (karyorrhexis), plasma membrane blebbing and fragmentation of the cell into apoptotic bodies. When the execution phase is completed, the cell has died." [GOC:cjm, GOC:dhl, GOC:ecd, GOC:go_curators, GOC:mtg_apoptosis, GOC:tb, ISBN:0198506732, PMID:18846107, PMID:21494263] synonym: "activation of apoptosis" NARROW [] synonym: "apoptosis" NARROW [] @@ -2914,7 +3175,6 @@ relationship: occurs_in UBERON:0002385 ! muscle tissue id: GO:0006996 name: organelle organization namespace: biological_process -alt_id: GO:1902589 def: "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of an organelle within a cell. An organelle is an organized structure of distinctive morphology and function. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton. Excludes the plasma membrane." [GOC:mah] comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. subset: gocheck_do_not_annotate @@ -2929,7 +3189,6 @@ intersection_of: GO:0016043 ! cellular component organization intersection_of: results_in_organization_of GO:0043226 ! organelle relationship: results_in_organization_of GO:0043226 ! organelle property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27189" xsd:anyURI -created_by: jl creation_date: 2013-12-19T15:25:51Z [Term] @@ -2973,11 +3232,6 @@ is_a: GO:0009987 ! cellular process id: GO:0007165 name: signal transduction namespace: biological_process -alt_id: GO:0023014 -alt_id: GO:0023015 -alt_id: GO:0023016 -alt_id: GO:0023033 -alt_id: GO:0023045 def: "The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell." [GOC:go_curators, GOC:mtg_signaling_feb11] comment: Note that signal transduction is defined broadly to include a ligand interacting with a receptor, downstream signaling steps and a response being triggered. A change in form of the signal in every step is not necessary. Note that in many cases the end of this process is regulation of the initiation of transcription. Note that specific transcription factors may be annotated to this term, but core/general transcription machinery such as RNA polymerase should not. subset: goslim_candida @@ -3040,7 +3294,6 @@ property_value: term_tracker_item "https://github.com/geneontology/go-ontology/i id: GO:0007276 name: gamete generation namespace: biological_process -alt_id: GO:0009552 def: "The generation and maintenance of gametes in a multicellular organism. A gamete is a haploid reproductive cell." [GOC:ems, GOC:mtg_sensu] synonym: "gametogenesis" RELATED [] is_a: GO:0048609 ! multicellular organismal reproductive process @@ -3129,7 +3382,6 @@ property_value: term_tracker_item "https://github.com/geneontology/go-ontology/i id: GO:0008015 name: blood circulation namespace: biological_process -alt_id: GO:0070261 def: "The flow of blood through the body of an animal, enabling the transport of nutrients to the tissues and the removal of waste products." [GOC:mtg_heart, ISBN:0192800825] subset: goslim_pir synonym: "hemolymph circulation" RELATED [] @@ -3139,9 +3391,6 @@ is_a: GO:0003013 ! circulatory system process id: GO:0008104 name: protein localization namespace: biological_process -alt_id: GO:0008105 -alt_id: GO:0016249 -alt_id: GO:0034613 def: "Any process in which a protein is transported to, or maintained in, a specific location." [GOC:ai] subset: goslim_drosophila synonym: "asymmetric protein localisation" RELATED [GOC:mah] @@ -3162,9 +3411,6 @@ property_value: term_tracker_item "https://github.com/geneontology/go-ontology/i id: GO:0008150 name: biological_process namespace: biological_process -alt_id: GO:0000004 -alt_id: GO:0007582 -alt_id: GO:0044699 def: "A biological process is the execution of a genetically-encoded biological module or program. It consists of all the steps required to achieve the specific biological objective of the module. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence." [GOC:pdt] comment: Note that, in addition to forming the root of the biological process ontology, this term is recommended for the annotation of gene products whose biological process is unknown. When this term is used for annotation, it indicates that no information was available about the biological process of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this. subset: goslim_candida @@ -3180,16 +3426,13 @@ synonym: "single organism process" RELATED [] synonym: "single-organism process" RELATED [] xref: Wikipedia:Biological_process property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/24968" xsd:anyURI -created_by: jl creation_date: 2012-09-19T15:05:24Z [Term] id: GO:0008152 name: metabolic process namespace: biological_process -alt_id: GO:0044236 -alt_id: GO:0044710 -def: "The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation." [GOC:go_curators, ISBN:0198547684] +def: "A cellular process consisting of the biochemical pathways by which a living organism transforms chemical substances. This includes including anabolism (biosynthetic process) and catabolism (catabolic process). Metabolic processes includes the transformation of small molecules, as well macromolecular processes such as DNA repair and replication, protein synthesis and degradation." [GOC:go_curators, ISBN:0198547684] comment: Note that metabolic processes do not include single functions or processes such as protein-protein interactions, protein-nucleic acids, nor receptor-ligand interactions. subset: gocheck_do_not_annotate subset: goslim_chembl @@ -3198,16 +3441,12 @@ subset: goslim_metagenomics subset: goslim_pir subset: goslim_plant subset: goslim_prokaryote_ribbon -synonym: "metabolic process resulting in cell growth" NARROW [] synonym: "metabolism" EXACT [] -synonym: "metabolism resulting in cell growth" NARROW [] -synonym: "multicellular organism metabolic process" NARROW [] -synonym: "single-organism metabolic process" RELATED [] xref: Wikipedia:Metabolism -is_a: GO:0008150 ! biological_process +is_a: GO:0009987 ! cellular process disjoint_from: GO:0051179 ! localization property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/26424" xsd:anyURI -created_by: jl +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28932" xsd:anyURI creation_date: 2012-10-17T15:46:40Z [Term] @@ -3238,9 +3477,7 @@ property_value: term_tracker_item "https://github.com/geneontology/go-ontology/i id: GO:0009058 name: biosynthetic process namespace: biological_process -alt_id: GO:0044274 -alt_id: GO:0044711 -def: "The chemical reactions and pathways resulting in the formation of substances; typically the energy-requiring part of metabolism in which simpler substances are transformed into more complex ones." [GOC:curators, ISBN:0198547684] +def: "A cellular process consisting of the biochemical pathways by which a living organism synthesizes chemical substances. This typically represents the energy-requiring part of metabolism in which simpler substances are transformed into more complex ones." [GOC:curators, ISBN:0198547684] subset: goslim_chembl subset: goslim_metagenomics subset: goslim_plant @@ -3253,14 +3490,13 @@ synonym: "single-organism biosynthetic process" RELATED [] synonym: "synthesis" EXACT [] xref: Wikipedia:Anabolism is_a: GO:0008152 ! metabolic process -created_by: jl +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28932" xsd:anyURI creation_date: 2012-10-17T15:52:18Z [Term] id: GO:0009059 name: macromolecule biosynthetic process namespace: biological_process -alt_id: GO:0043284 def: "The chemical reactions and pathways resulting in the formation of a macromolecule, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass." [GOC:mah] comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. subset: gocheck_do_not_annotate @@ -3270,8 +3506,8 @@ synonym: "macromolecule anabolism" EXACT [] synonym: "macromolecule biosynthesis" EXACT [] synonym: "macromolecule formation" EXACT [] synonym: "macromolecule synthesis" EXACT [] +is_a: GO:0009058 ! biosynthetic process is_a: GO:0043170 ! macromolecule metabolic process -is_a: GO:0044249 ! cellular biosynthetic process property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/15249" xsd:anyURI property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/25418" xsd:anyURI property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27189" xsd:anyURI @@ -3280,8 +3516,6 @@ property_value: term_tracker_item "https://github.com/geneontology/go-ontology/i id: GO:0009306 name: protein secretion namespace: biological_process -alt_id: GO:0045166 -alt_id: GO:0045731 def: "The controlled release of proteins from a cell." [GOC:ai] synonym: "glycoprotein secretion" NARROW [] synonym: "protein secretion during cell fate commitment" NARROW [] @@ -3325,7 +3559,6 @@ relationship: part_of GO:0048856 ! anatomical structure development id: GO:0009790 name: embryo development namespace: biological_process -alt_id: GO:0009795 def: "The process whose specific outcome is the progression of an embryo from its formation until the end of its embryonic life stage. The end of the embryonic stage is organism-specific. For example, for mammals, the process would begin with zygote formation and end with birth. For insects, the process would begin at zygote formation and end with larval hatching. For plant zygotic embryos, this would be from zygote formation to the end of seed dormancy. For plant vegetative embryos, this would be from the initial determination of the cell or group of cells to form an embryo until the point when the embryo becomes independent of the parent plant." [GOC:go_curators, GOC:isa_complete, GOC:mtg_sensu] subset: gocheck_do_not_annotate subset: goslim_chembl @@ -3382,9 +3615,6 @@ property_value: RO:0002161 NCBITaxon:4891 id: GO:0009987 name: cellular process namespace: biological_process -alt_id: GO:0008151 -alt_id: GO:0044763 -alt_id: GO:0050875 def: "Any process that is carried out at the cellular level, but not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level." [GOC:go_curators, GOC:isa_complete] comment: This term should not be used for direct annotation. It should be possible to make a more specific annotation to one of the children of this term. subset: gocheck_do_not_annotate @@ -3394,7 +3624,6 @@ synonym: "cell physiology" EXACT [] synonym: "cellular physiological process" EXACT [] synonym: "single-organism cellular process" RELATED [] is_a: GO:0008150 ! biological_process -created_by: jl creation_date: 2012-12-11T16:56:55Z [Term] @@ -3412,7 +3641,6 @@ property_value: term_tracker_item "https://github.com/geneontology/go-ontology/i id: GO:0012501 name: programmed cell death namespace: biological_process -alt_id: GO:0016244 def: "A process which begins when a cell receives an internal or external signal and activates a series of biochemical events (signaling pathway). The process ends with the death of the cell." [GOC:lr, GOC:mtg_apoptosis] comment: Note that this term should be used to annotate gene products in the organism undergoing the programmed cell death. To annotate genes in another organism whose products modulate programmed cell death in a host organism, consider the term 'modulation by symbiont of host programmed cell death ; GO:0052040'. Also, note that 'programmed cell death ; GO:0012501' should be used to refer to instances of caspase-independent cell death mechanisms, in the absence of further indications on the process taking place. At present, caspase-independent cell death is not yet represented in GO due to the lack of consensus and in-depth research on the topic. 'programmed cell death ; GO:0012501' may also be used to annotate gene products in taxa where apoptosis as defined in GO:0006915 does not occur, such as plants. You may also consider these specific children: GO:0097468 'programmed cell death in response to reactive oxygen species' (with descendants GO:0010421 'hydrogen peroxide-mediated programmed cell death' and GO:0010343 'singlet oxygen-mediated programmed cell death'), and GO:0009626 'plant-type hypersensitive response' and its children. subset: goslim_agr @@ -3442,7 +3670,6 @@ property_value: term_tracker_item "https://github.com/geneontology/go-ontology/i id: GO:0015031 name: protein transport namespace: biological_process -alt_id: GO:0015831 def: "The directed movement of proteins into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:ai] subset: goslim_chembl subset: goslim_pir @@ -3472,9 +3699,6 @@ is_a: GO:0015669 ! gas transport id: GO:0016020 name: membrane namespace: cellular_component -alt_id: GO:0016021 -alt_id: GO:0098589 -alt_id: GO:0098805 def: "A lipid bilayer along with all the proteins and protein complexes embedded in it and attached to it." [GOC:dos, GOC:mah, ISBN:0815316194] subset: goslim_candida subset: goslim_chembl @@ -3491,7 +3715,7 @@ synonym: "transmembrane" RELATED [GOC:mah] synonym: "whole membrane" NARROW [] xref: Wikipedia:Biological_membrane xref: Wikipedia:Transmembrane_protein -is_a: GO:0110165 ! cellular anatomical entity +is_a: GO:0110165 ! cellular anatomical structure disjoint_from: GO:0031012 ! extracellular matrix creation_date: 2014-03-06T11:37:54Z @@ -3499,8 +3723,6 @@ creation_date: 2014-03-06T11:37:54Z id: GO:0016043 name: cellular component organization namespace: biological_process -alt_id: GO:0044235 -alt_id: GO:0071842 def: "A process that results in the assembly, arrangement of constituent parts, or disassembly of a cellular component." [GOC:ai, GOC:jl, GOC:mah] subset: gocheck_do_not_annotate subset: goslim_agr @@ -3581,9 +3803,6 @@ relationship: part_of GO:0007154 ! cell communication id: GO:0019538 name: protein metabolic process namespace: biological_process -alt_id: GO:0006411 -alt_id: GO:0044267 -alt_id: GO:0044268 def: "The chemical reactions and pathways involving a protein. Includes protein modification." [GOC:ma] comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. subset: gocheck_do_not_annotate @@ -3646,7 +3865,6 @@ relationship: part_of GO:0007049 ! cell cycle id: GO:0022411 name: cellular component disassembly namespace: biological_process -alt_id: GO:0071845 def: "A cellular process that results in the breakdown of a cellular component." [GOC:isa_complete] comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. subset: gocheck_do_not_annotate @@ -3664,7 +3882,6 @@ property_value: term_tracker_item "https://github.com/geneontology/go-ontology/i id: GO:0022414 name: reproductive process namespace: biological_process -alt_id: GO:0044702 def: "A biological process that directly contributes to the process of producing new individuals by one or two organisms. The new individuals inherit some proportion of their genetic material from the parent or parents." [GOC:dph, GOC:isa_complete] subset: gocheck_do_not_annotate subset: goslim_agr @@ -3678,7 +3895,6 @@ synonym: "single organism reproductive process" RELATED [] xref: Wikipedia:Reproduction is_a: GO:0008150 ! biological_process property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27054" xsd:anyURI -created_by: jl creation_date: 2012-09-19T15:56:06Z [Term] @@ -3696,7 +3912,6 @@ relationship: part_of GO:0007586 ! digestion id: GO:0022607 name: cellular component assembly namespace: biological_process -alt_id: GO:0071844 def: "The aggregation, arrangement and bonding together of a cellular component." [GOC:isa_complete] subset: goslim_chembl subset: goslim_euk_cellular_processes_ribbon @@ -3738,8 +3953,6 @@ relationship: results_in_assembly_of GO:1990904 ! ribonucleoprotein complex id: GO:0023052 name: signaling namespace: biological_process -alt_id: GO:0023046 -alt_id: GO:0044700 def: "The entirety of a process in which information is transmitted within a biological system. This process begins with an active signal and ends when a cellular response has been triggered." [GOC:mtg_signal, GOC:mtg_signaling_feb11, GOC:signaling] comment: Note that a signal is any variable property or parameter that serves to convey information, and may be a physical entity such as a gene product or small molecule, a photon, or a change in state such as movement or voltage change. subset: goslim_agr @@ -3757,7 +3970,6 @@ synonym: "signalling" EXACT [] synonym: "signalling process" RELATED [GOC:mah] synonym: "single organism signaling" RELATED [] is_a: GO:0050789 ! regulation of biological process -created_by: jl creation_date: 2010-02-16T09:30:50Z [Term] @@ -3809,7 +4021,7 @@ subset: goslim_agr subset: goslim_drosophila subset: goslim_flybase_ribbon xref: Wikipedia:Cell_junction -is_a: GO:0110165 ! cellular anatomical entity +is_a: GO:0110165 ! cellular anatomical structure property_value: RO:0002161 NCBITaxon:4751 [Term] @@ -3891,7 +4103,6 @@ relationship: results_in_acquisition_of_features_of CL:0000556 ! megakaryocyte id: GO:0030261 name: chromosome condensation namespace: biological_process -alt_id: GO:0000068 def: "The progressive compaction of dispersed interphase chromatin into threadlike chromosomes prior to mitotic or meiotic nuclear division, or during apoptosis, in eukaryotic cells." [GOC:mah, ISBN:0815316194] synonym: "DNA condensation" BROAD [Wikipedia:DNA_condensation] synonym: "eukaryotic chromosome condensation" EXACT [GOC:bf] @@ -3927,7 +4138,7 @@ subset: goslim_drosophila subset: goslim_generic subset: goslim_pir subset: goslim_plant -is_a: GO:0110165 ! cellular anatomical entity +is_a: GO:0110165 ! cellular anatomical structure relationship: part_of CL:0000000 ! cell relationship: part_of GO:0071944 ! cell periphery @@ -3935,7 +4146,6 @@ relationship: part_of GO:0071944 ! cell periphery id: GO:0031012 name: extracellular matrix namespace: cellular_component -alt_id: GO:0005578 def: "A structure lying external to one or more cells, which provides structural support, biochemical or biomechanical cues for cells or tissues." [GOC:BHF, GOC:mah, GOC:rph, NIF_Subcellular:nlx_subcell_20090513, PMID:21123617, PMID:28089324] subset: goslim_chembl subset: goslim_drosophila @@ -3956,7 +4166,7 @@ id: GO:0031974 name: membrane-enclosed lumen namespace: cellular_component def: "The enclosed volume within a sealed membrane or between two sealed membranes. Encompasses the volume enclosed by the membranes of a particular organelle, e.g. endoplasmic reticulum lumen, or the space between the two lipid bilayers of a double membrane surrounding an organelle, e.g. nuclear envelope lumen." [GOC:add, GOC:mah] -is_a: GO:0110165 ! cellular anatomical entity +is_a: GO:0110165 ! cellular anatomical structure disjoint_from: GO:0045202 ! synapse [Term] @@ -3971,7 +4181,6 @@ relationship: part_of GO:0005634 ! nucleus id: GO:0031982 name: vesicle namespace: cellular_component -alt_id: GO:0031988 def: "Any small, fluid-filled, spherical organelle enclosed by membrane." [GOC:mah, GOC:pz, GOC:vesicles] subset: goslim_pir synonym: "membrane-bounded vesicle" RELATED [] @@ -4009,8 +4218,6 @@ relationship: results_in_assembly_of GO:0032059 ! bleb id: GO:0032501 name: multicellular organismal process namespace: biological_process -alt_id: GO:0044707 -alt_id: GO:0050874 def: "Any biological process, occurring at the level of a multicellular organism, pertinent to its function." [GOC:curators, GOC:dph, GOC:isa_complete, GOC:tb] comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. subset: gocheck_do_not_annotate @@ -4023,14 +4230,12 @@ property_value: RO:0002161 NCBITaxon:2157 property_value: RO:0002161 NCBITaxon:4896 property_value: RO:0002161 NCBITaxon:4932 property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27189" xsd:anyURI -created_by: jl creation_date: 2012-09-19T16:07:47Z [Term] id: GO:0032502 name: developmental process namespace: biological_process -alt_id: GO:0044767 def: "A biological process whose specific outcome is the progression of an integrated living unit: an anatomical structure (which may be a subcellular structure, cell, tissue, or organ), or organism over time from an initial condition to a later condition." [GOC:isa_complete] subset: goslim_agr subset: goslim_flybase_ribbon @@ -4038,7 +4243,6 @@ subset: goslim_pir synonym: "development" NARROW [] synonym: "single-organism developmental process" RELATED [] is_a: GO:0008150 ! biological_process -created_by: jl creation_date: 2012-12-19T12:21:31Z [Term] @@ -4055,9 +4259,6 @@ is_a: GO:0140352 ! export from cell id: GO:0032984 name: protein-containing complex disassembly namespace: biological_process -alt_id: GO:0034623 -alt_id: GO:0043241 -alt_id: GO:0043624 def: "The disaggregation of a protein-containing macromolecular complex into its constituent components." [GOC:mah] synonym: "cellular macromolecule complex disassembly" RELATED [] synonym: "cellular protein complex disassembly" RELATED [] @@ -4074,7 +4275,6 @@ property_value: term_tracker_item "https://github.com/geneontology/go-ontology/i id: GO:0032991 name: protein-containing complex namespace: cellular_component -alt_id: GO:0043234 def: "A stable assembly of two or more macromolecules, i.e. proteins, nucleic acids, carbohydrates or lipids, in which at least one component is a protein and the constituent parts function together." [GOC:dos, GOC:mah] comment: A protein complex in this context is meant as a stable set of interacting proteins which can be co-purified by an acceptable method, and where the complex has been shown to exist as an isolated, functional unit in vivo. Acceptable experimental methods include stringent protein purification followed by detection of protein interaction. The following methods should be considered non-acceptable: simple immunoprecipitation, pull-down experiments from cell extracts without further purification, colocalization and 2-hybrid screening. Interactions that should not be captured as protein complexes include: 1) enzyme/substrate, receptor/ligand or any similar transient interactions, unless these are a critical part of the complex assembly or are required e.g. for the receptor to be functional; 2) proteins associated in a pull-down/co-immunoprecipitation assay with no functional link or any evidence that this is a defined biological entity rather than a loose-affinity complex; 3) any complex where the only evidence is based on genetic interaction data; 4) partial complexes, where some subunits (e.g. transmembrane ones) cannot be expressed as recombinant proteins and are excluded from experiments (in this case, independent evidence is necessary to find out the composition of the full complex, if known). Interactions that may be captured as protein complexes include: 1) enzyme/substrate or receptor/ligand if the complex can only assemble and become functional in the presence of both classes of subunits; 2) complexes where one of the members has not been shown to be physically linked to the other(s), but is a homologue of, and has the same functionality as, a protein that has been experimentally demonstrated to form a complex with the other member(s); 3) complexes whose existence is accepted based on localization and pharmacological studies, but for which experimental evidence is not yet available for the complex as a whole. subset: goslim_agr @@ -4089,8 +4289,8 @@ synonym: "protein complex" NARROW [] synonym: "protein containing complex" EXACT [] synonym: "protein-protein complex" NARROW [] is_a: GO:0005575 ! cellular_component -is_a: PR:000050567 ! protein-containing material entity -disjoint_from: GO:0110165 ! cellular anatomical entity +disjoint_from: GO:0110165 ! cellular anatomical structure +relationship: has_part PR:000000001 ! protein [Term] id: GO:0033036 @@ -4117,7 +4317,6 @@ relationship: acts_on_population_of CL:0000232 ! erythrocyte id: GO:0034220 name: monoatomic ion transmembrane transport namespace: biological_process -alt_id: GO:0099131 def: "A process in which a monoatomic ion is transported across a membrane. Monatomic ions (also called simple ions) are ions consisting of exactly one atom." [GOC:mah] comment: Note that this term is not intended for use in annotating lateral movement within membranes. synonym: "ATP hydrolysis coupled ion transmembrane transport" NARROW [] @@ -4173,7 +4372,6 @@ is_a: GO:0045184 ! establishment of protein localization is_a: GO:0071692 ! protein localization to extracellular region intersection_of: GO:0045184 ! establishment of protein localization intersection_of: has_target_end_location GO:0005576 ! extracellular region -created_by: bf creation_date: 2010-11-09T10:25:08Z [Term] @@ -4187,7 +4385,6 @@ is_a: GO:0046930 ! pore complex property_value: RO:0002161 NCBITaxon:2 property_value: RO:0002161 NCBITaxon:2157 property_value: RO:0002161 NCBITaxon:4751 -created_by: bf creation_date: 2011-12-12T10:53:24Z [Term] @@ -4227,9 +4424,6 @@ relationship: has_part GO:0034220 ! monoatomic ion transmembrane transport id: GO:0042592 name: homeostatic process namespace: biological_process -alt_id: GO:0032844 -alt_id: GO:0032845 -alt_id: GO:0032846 def: "Any biological process involved in the maintenance of an internal steady state." [GOC:jl, ISBN:0395825172] subset: goslim_agr subset: goslim_chembl @@ -4257,7 +4451,7 @@ subset: goslim_prokaryote_ribbon synonym: "cell process" BROAD [] synonym: "cellular process" BROAD [] synonym: "cellular projection" EXACT [] -is_a: GO:0110165 ! cellular anatomical entity +is_a: GO:0110165 ! cellular anatomical structure relationship: part_of CL:0000000 ! cell [Term] @@ -4284,9 +4478,6 @@ relationship: part_of CL:0000586 ! germ cell id: GO:0043170 name: macromolecule metabolic process namespace: biological_process -alt_id: GO:0034960 -alt_id: GO:0043283 -alt_id: GO:0044259 def: "The chemical reactions and pathways involving macromolecules, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass." [GOC:mah] subset: gocheck_do_not_annotate subset: goslim_pir @@ -4309,7 +4500,7 @@ subset: goslim_prokaryote subset: goslim_prokaryote_ribbon xref: NIF_Subcellular:sao1539965131 xref: Wikipedia:Organelle -is_a: GO:0110165 ! cellular anatomical entity +is_a: GO:0110165 ! cellular anatomical structure [Term] id: GO:0043227 @@ -4322,23 +4513,26 @@ xref: NIF_Subcellular:sao414196390 is_a: GO:0043226 ! organelle intersection_of: GO:0043226 ! organelle intersection_of: has_part GO:0016020 ! membrane -disjoint_from: GO:0043228 ! non-membrane-bounded organelle +disjoint_from: GO:0043228 ! membraneless organelle relationship: has_part GO:0016020 ! membrane property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28153" xsd:anyURI [Term] id: GO:0043228 -name: non-membrane-bounded organelle +name: membraneless organelle namespace: cellular_component def: "Organized structure of distinctive morphology and function, not bounded by a lipid bilayer membrane. Includes ribosomes, the cytoskeleton and chromosomes." [GOC:go_curators] subset: gocheck_do_not_annotate subset: goslim_mouse synonym: "biological condensate" RELATED [] +synonym: "membrane-less organelle" EXACT [] +synonym: "non-membrane-bounded organelle" EXACT [] synonym: "non-membrane-enclosed organelle" EXACT [] xref: NIF_Subcellular:sao1456184038 is_a: GO:0043226 ! organelle property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/21881" xsd:anyURI property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28153" xsd:anyURI +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29106" xsd:anyURI [Term] id: GO:0043229 @@ -4379,15 +4573,17 @@ intersection_of: part_of GO:0005622 ! intracellular anatomical structure [Term] id: GO:0043232 -name: intracellular non-membrane-bounded organelle +name: intracellular membraneless organelle namespace: cellular_component def: "Organized structure of distinctive morphology and function, not bounded by a lipid bilayer membrane and occurring within the cell. Includes ribosomes, the cytoskeleton and chromosomes." [GOC:go_curators] subset: goslim_pir +synonym: "intracellular non-membrane-bounded organelle" EXACT [] synonym: "intracellular non-membrane-enclosed organelle" EXACT [] -is_a: GO:0043228 ! non-membrane-bounded organelle +is_a: GO:0043228 ! membraneless organelle is_a: GO:0043229 ! intracellular organelle -intersection_of: GO:0043228 ! non-membrane-bounded organelle +intersection_of: GO:0043228 ! membraneless organelle intersection_of: part_of GO:0005622 ! intracellular anatomical structure +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29106" xsd:anyURI [Term] id: GO:0043233 @@ -4404,9 +4600,6 @@ relationship: part_of GO:0043226 ! organelle id: GO:0043933 name: protein-containing complex organization namespace: biological_process -alt_id: GO:0034600 -alt_id: GO:0034621 -alt_id: GO:0071822 def: "Any process in which macromolecules aggregate, disaggregate, or are modified, resulting in the formation, disassembly, or alteration of a protein complex." [GOC:mah] synonym: "cellular macromolecular complex organization" RELATED [] synonym: "cellular macromolecular complex subunit organisation" RELATED [] @@ -4422,7 +4615,6 @@ intersection_of: GO:0016043 ! cellular component organization intersection_of: results_in_organization_of GO:0032991 ! protein-containing complex relationship: results_in_organization_of GO:0032991 ! protein-containing complex property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/22580" xsd:anyURI -created_by: mah creation_date: 2010-09-08T10:01:42Z [Term] @@ -4439,7 +4631,6 @@ relationship: regulates GO:0003008 ! system process id: GO:0044085 name: cellular component biogenesis namespace: biological_process -alt_id: GO:0071843 def: "A process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of a cellular component. Includes biosynthesis of constituent macromolecules, and those macromolecular modifications that are involved in synthesis or assembly of the cellular component." [GOC:jl, GOC:mah] subset: gocheck_do_not_annotate subset: goslim_pir @@ -4456,21 +4647,8 @@ synonym: "Met-tRNA/eIF2.GTP ternary complex" NARROW [] synonym: "translation initiation (ternary) complex" EXACT [] is_a: GO:1990904 ! ribonucleoprotein complex relationship: part_of GO:0005737 ! cytoplasm -created_by: jl creation_date: 2009-10-22T02:38:55Z -[Term] -id: GO:0044237 -name: cellular metabolic process -namespace: biological_process -def: "The chemical reactions and pathways by which individual cells transform chemical substances." [GOC:go_curators] -comment: This term should not be used for direct annotation. It should be possible to make a more specific annotation to one of the children of this term. -subset: gocheck_do_not_annotate -synonym: "cellular metabolism" EXACT [] -synonym: "intermediary metabolism" RELATED [GOC:mah] -is_a: GO:0008152 ! metabolic process -is_a: GO:0009987 ! cellular process - [Term] id: GO:0044238 name: primary metabolic process @@ -4486,21 +4664,6 @@ xref: Wikipedia:Primary_metabolite is_a: GO:0008152 ! metabolic process property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/26424" xsd:anyURI -[Term] -id: GO:0044249 -name: cellular biosynthetic process -namespace: biological_process -def: "The chemical reactions and pathways resulting in the formation of substances, carried out by individual cells." [GOC:jl] -comment: This term should not be used for direct annotation. It should be possible to make a more specific annotation to one of the children of this term. -subset: gocheck_do_not_annotate -synonym: "cellular anabolism" EXACT [] -synonym: "cellular biosynthesis" EXACT [] -synonym: "cellular formation" EXACT [] -synonym: "cellular synthesis" EXACT [] -is_a: GO:0009058 ! biosynthetic process -is_a: GO:0044237 ! cellular metabolic process -property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27052" xsd:anyURI - [Term] id: GO:0045184 name: establishment of protein localization @@ -4616,7 +4779,6 @@ property_value: term_tracker_item "https://github.com/geneontology/go-ontology/i id: GO:0048598 name: embryonic morphogenesis namespace: biological_process -alt_id: GO:0048828 def: "The process in which anatomical structures are generated and organized during the embryonic phase. The embryonic phase begins with zygote formation. The end of the embryonic phase is organism-specific. For example, it would be at birth for mammals, larval hatching for insects and seed dormancy in plants." [GOC:jid, GOC:mtg_sensu] synonym: "embryonic anatomical structure morphogenesis" EXACT [GOC:dph, GOC:tb] is_a: GO:0009653 ! anatomical structure morphogenesis @@ -4744,7 +4906,6 @@ property_value: term_tracker_item "https://github.com/geneontology/go-ontology/i id: GO:0050789 name: regulation of biological process namespace: biological_process -alt_id: GO:0050791 def: "Any process that modulates the frequency, rate or extent of a biological process. Biological processes are regulated by many means; examples include the control of gene expression, protein modification or interaction with a protein or substrate molecule." [GOC:ai, GOC:go_curators] subset: gocheck_do_not_annotate subset: goslim_candida @@ -4759,7 +4920,6 @@ relationship: regulates GO:0008150 ! biological_process id: GO:0050794 name: regulation of cellular process namespace: biological_process -alt_id: GO:0051244 def: "Any process that modulates the frequency, rate or extent of a cellular process, any of those that are carried out at the cellular level, but are not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level." [GOC:go_curators] subset: gocheck_do_not_annotate synonym: "regulation of cellular physiological process" EXACT [] @@ -4822,7 +4982,6 @@ property_value: term_tracker_item "https://github.com/geneontology/go-ontology/i id: GO:0050896 name: response to stimulus namespace: biological_process -alt_id: GO:0051869 def: "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus. The process begins with detection of the stimulus and ends with a change in state or activity or the cell or organism." [GOC:ai, GOC:bf] comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. subset: gocheck_do_not_annotate @@ -4839,7 +4998,6 @@ is_a: GO:0008150 ! biological_process id: GO:0051179 name: localization namespace: biological_process -alt_id: GO:1902578 def: "Any process in which a cell, a substance, or a cellular entity, such as a protein complex or organelle, is transported, tethered to or otherwise maintained in a specific location. In the case of substances, localization may also be achieved via selective degradation." [GOC:ai, GOC:dos] subset: gocheck_do_not_annotate subset: goslim_pir @@ -4853,7 +5011,6 @@ synonym: "single organism localization" RELATED [GOC:TermGenie] synonym: "single-organism localization" RELATED [] is_a: GO:0008150 ! biological_process property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27052" xsd:anyURI -created_by: jl creation_date: 2013-12-18T13:51:04Z [Term] @@ -4884,9 +5041,6 @@ relationship: regulates GO:0032501 ! multicellular organismal process id: GO:0051276 name: chromosome organization namespace: biological_process -alt_id: GO:0006323 -alt_id: GO:0007001 -alt_id: GO:0051277 def: "A process that is carried out at the cellular level that results in the assembly, arrangement of constituent parts, or disassembly of chromosomes, structures composed of a very long molecule of DNA and associated proteins that carries hereditary information. This term covers covalent modifications at the molecular level as well as spatial relationships among the major components of a chromosome." [GOC:ai, GOC:dph, GOC:jl, GOC:mah] subset: goslim_chembl subset: goslim_drosophila @@ -4920,7 +5074,6 @@ is_a: GO:0009987 ! cellular process id: GO:0051641 name: cellular localization namespace: biological_process -alt_id: GO:1902580 def: "A cellular localization process whereby a substance or cellular entity, such as a protein complex or organelle, is transported to, and/or maintained in, a specific location within a cell including the localization of substances or cellular entities to the cell membrane." [GOC:tb, GOC:vw] comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. subset: gocheck_do_not_annotate @@ -4935,7 +5088,6 @@ synonym: "single-organism cellular localization" RELATED [] is_a: GO:0009987 ! cellular process is_a: GO:0051179 ! localization property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27189" xsd:anyURI -created_by: jl creation_date: 2013-12-18T14:04:32Z [Term] @@ -4952,7 +5104,6 @@ is_a: GO:0050896 ! response to stimulus id: GO:0055085 name: transmembrane transport namespace: biological_process -alt_id: GO:0090662 def: "The process in which a solute is transported across a lipid bilayer, from one side of a membrane to the other." [GOC:dph, GOC:jid] comment: Transmembrane transport is the transport of a solute across a lipid bilayer. Note that transport through the nuclear pore complex is not transmembrane because the nuclear membrane is a double membrane and is not traversed. For transport through the nuclear pore, consider instead the term 'nucleocytoplasmic transport ; GO:0006913' and its children. Note also that this term is not intended for use in annotating lateral movement within membranes. subset: goslim_chembl @@ -4968,7 +5119,6 @@ is_a: GO:0009987 ! cellular process intersection_of: GO:0006810 ! transport intersection_of: results_in_transport_across GO:0016020 ! membrane relationship: results_in_transport_across GO:0016020 ! membrane -created_by: tb creation_date: 2015-10-21T13:22:47Z [Term] @@ -5003,7 +5153,6 @@ is_a: GO:0035239 ! tube morphogenesis intersection_of: GO:0009653 ! anatomical structure morphogenesis intersection_of: results_in_morphogenesis_of UBERON:0003914 ! epithelial tube relationship: results_in_morphogenesis_of UBERON:0003914 ! epithelial tube -created_by: dph creation_date: 2009-04-28T09:33:36Z [Term] @@ -5013,7 +5162,6 @@ namespace: biological_process def: "The process in which the anatomical structures of a branched epithelium are generated and organized." [GOC:dph] is_a: GO:0001763 ! morphogenesis of a branching structure is_a: GO:0002009 ! morphogenesis of an epithelium -created_by: dph creation_date: 2010-05-25T09:05:34Z [Term] @@ -5024,16 +5172,12 @@ def: "An extracellular matrix consisting mainly of proteins (especially collagen is_a: GO:0031012 ! extracellular matrix relationship: RO:0002160 NCBITaxon:33208 ! only in taxon Metazoa relationship: RO:0002162 NCBITaxon:33208 {all_only="true"} ! in taxon Metazoa -created_by: dph creation_date: 2018-04-13T12:47:21Z [Term] id: GO:0065003 name: protein-containing complex assembly namespace: biological_process -alt_id: GO:0006461 -alt_id: GO:0034622 -alt_id: GO:0043623 def: "The aggregation, arrangement and bonding together of a set of macromolecules to form a protein-containing complex." [GOC:jl] subset: goslim_chembl subset: goslim_drosophila @@ -5143,7 +5287,6 @@ def: "Any process in which a macromolecule is transported to, and/or maintained synonym: "cellular macromolecule localisation" EXACT [GOC:mah] is_a: GO:0033036 ! macromolecule localization is_a: GO:0051641 ! cellular localization -created_by: mah creation_date: 2009-06-16T04:08:29Z [Term] @@ -5157,7 +5300,6 @@ is_a: GO:0022607 ! cellular component assembly intersection_of: GO:0022607 ! cellular component assembly intersection_of: results_in_assembly_of GO:0043226 ! organelle relationship: results_in_assembly_of GO:0043226 ! organelle -created_by: mah creation_date: 2009-09-15T03:00:51Z [Term] @@ -5171,7 +5313,6 @@ is_a: GO:0008104 ! protein localization intersection_of: GO:0008104 ! protein localization intersection_of: has_target_end_location GO:0005576 ! extracellular region relationship: has_target_end_location GO:0005576 ! extracellular region -created_by: mah creation_date: 2010-02-25T04:00:13Z [Term] @@ -5188,14 +5329,12 @@ intersection_of: GO:0016043 ! cellular component organization intersection_of: results_in_organization_of GO:1990904 ! ribonucleoprotein complex relationship: results_in_organization_of GO:1990904 ! ribonucleoprotein complex property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/25143" xsd:anyURI -created_by: mah creation_date: 2010-09-08T10:10:35Z [Term] id: GO:0071840 name: cellular component organization or biogenesis namespace: biological_process -alt_id: GO:0071841 def: "A process that results in the biosynthesis of constituent macromolecules, assembly, arrangement of constituent parts, or disassembly of a cellular component." [GOC:mah] comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. subset: gocheck_do_not_annotate @@ -5206,7 +5345,6 @@ synonym: "cellular component organisation or biogenesis at cellular level" EXACT synonym: "cellular component organization or biogenesis at cellular level" EXACT [] is_a: GO:0009987 ! cellular process property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27189" xsd:anyURI -created_by: mah creation_date: 2010-09-10T01:39:16Z [Term] @@ -5215,8 +5353,7 @@ name: cell periphery namespace: cellular_component def: "The broad region around and including the plasma membrane of a cell, encompassing the cell cortex (inside the cell), the plasma membrane, and any external encapsulating structures." [GOC:pdt] subset: goslim_flybase_ribbon -is_a: GO:0110165 ! cellular anatomical entity -created_by: mah +is_a: GO:0110165 ! cellular anatomical structure creation_date: 2010-10-04T01:51:47Z [Term] @@ -5231,7 +5368,6 @@ intersection_of: GO:0022607 ! cellular component assembly intersection_of: results_in_assembly_of GO:0070062 ! extracellular exosome relationship: part_of GO:0097734 ! extracellular exosome biogenesis relationship: results_in_assembly_of GO:0070062 ! extracellular exosome -created_by: mah creation_date: 2010-10-18T03:44:18Z [Term] @@ -5245,21 +5381,18 @@ intersection_of: results_in_formation_of UBERON:0003914 ! epithelial tube relationship: part_of GO:0060562 ! epithelial tube morphogenesis relationship: results_in_formation_of UBERON:0003914 ! epithelial tube property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/22302" xsd:anyURI -created_by: mah creation_date: 2010-02-26T02:15:40Z [Term] id: GO:0097190 name: apoptotic signaling pathway namespace: biological_process -alt_id: GO:0008624 def: "The series of molecular signals which triggers the apoptotic death of a cell. The pathway starts with reception of a signal, and ends when the execution phase of apoptosis is triggered." [GOC:mtg_apoptosis] comment: This term can be used to annotate gene products involved in apoptotic events happening downstream of the cross-talk point between the extrinsic and intrinsic apoptotic pathways. The cross-talk starts when caspase-8 cleaves Bid and truncated Bid interacts with mitochondria. From this point on it is not possible to distinguish between extrinsic and intrinsic pathways. synonym: "apoptotic signalling pathway" EXACT [GOC:mah] synonym: "induction of apoptosis by extracellular signals" EXACT [] is_a: GO:0007165 ! signal transduction relationship: part_of GO:0006915 ! apoptotic process -created_by: pr creation_date: 2011-11-23T09:30:23Z [Term] @@ -5272,7 +5405,6 @@ synonym: "execution phase of apoptotic process" EXACT [] is_a: GO:0009987 ! cellular process relationship: has_part GO:0032060 ! bleb assembly relationship: part_of GO:0006915 ! apoptotic process -created_by: pr creation_date: 2011-11-23T09:45:24Z [Term] @@ -5281,7 +5413,6 @@ name: renal filtration namespace: biological_process def: "A renal system process in which fluid circulating through the body is filtered through a barrier system." [GOC:pr, GOC:sart] is_a: GO:0003014 ! renal system process -created_by: pr creation_date: 2012-01-03T03:10:17Z [Term] @@ -5292,7 +5423,6 @@ def: "The elimination of substances from peritubular capillaries (or surrounding is_a: GO:0003014 ! renal system process is_a: GO:0007588 ! excretion property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/22368" xsd:anyURI -created_by: pr creation_date: 2012-03-05T02:03:58Z [Term] @@ -5306,7 +5436,6 @@ synonym: "exosome production" EXACT [] synonym: "ILV assembly" RELATED [] synonym: "intraluminal vesicle assembly" RELATED [] is_a: GO:0140112 ! extracellular vesicle biogenesis -created_by: pr creation_date: 2016-10-03T14:35:25Z [Term] @@ -5321,7 +5450,6 @@ is_a: GO:0016020 ! membrane intersection_of: GO:0016020 ! membrane intersection_of: part_of GO:0005886 ! plasma membrane relationship: part_of GO:0005886 ! plasma membrane -created_by: dos creation_date: 2014-03-06T11:55:32Z [Term] @@ -5342,7 +5470,6 @@ def: "A complex of collagen trimers such as a fibril or collagen network." [GOC: synonym: "Supramolecular aggregate of collagen" EXACT [PMID:19693541] synonym: "Supramolecular collagen assembly" EXACT [PMID:21421911] is_a: GO:0099080 ! supramolecular complex -is_a: PR:000050567 ! protein-containing material entity relationship: has_part GO:0005581 ! collagen trimer relationship: part_of GO:0062023 ! collagen-containing extracellular matrix @@ -5371,7 +5498,7 @@ namespace: cellular_component def: "The part of a synapse that is part of the presynaptic cell." [GOC:dos] subset: goslim_synapse synonym: "presynaptic terminal" EXACT [] -is_a: GO:0110165 ! cellular anatomical entity +is_a: GO:0110165 ! cellular anatomical structure relationship: part_of CL:0000540 ! neuron relationship: part_of GO:0045202 ! synapse @@ -5381,7 +5508,7 @@ name: postsynapse namespace: cellular_component def: "The part of a synapse that is part of the post-synaptic cell." [GOC:dos] subset: goslim_synapse -is_a: GO:0110165 ! cellular anatomical entity +is_a: GO:0110165 ! cellular anatomical structure relationship: part_of CL:0000000 ! cell relationship: part_of GO:0045202 ! synapse @@ -5423,7 +5550,7 @@ id: GO:0099080 name: supramolecular complex namespace: cellular_component def: "A cellular component that consists of an indeterminate number of proteins or macromolecular complexes, organized into a regular, higher-order structure such as a polymer, sheet, network or a fiber." [GOC:dos] -is_a: GO:0110165 ! cellular anatomical entity +is_a: GO:0110165 ! cellular anatomical structure [Term] id: GO:0099081 @@ -5459,16 +5586,17 @@ is_a: GO:0099536 ! synaptic signaling [Term] id: GO:0110165 -name: cellular anatomical entity +name: cellular anatomical structure namespace: cellular_component -def: "A part of a cellular organism that is either an immaterial entity or a material entity with granularity above the level of a protein complex but below that of an anatomical system. Or, a substance produced by a cellular organism with granularity above the level of a protein complex." [GOC:kmv] +def: "A part of a cellular organism consisting of a material entity with granularity above the level of a protein complex but below that of an anatomical system. Note that cellular organisms exclude viruses." [GOC:kmv] subset: gocheck_do_not_annotate subset: goslim_pir +synonym: "cellular anatomical entity" EXACT [] is_a: GO:0005575 ! cellular_component is_a: UBERON:0000061 ! anatomical structure property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/24200" xsd:anyURI property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/26424" xsd:anyURI -created_by: kmv +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28978" xsd:anyURI creation_date: 2019-08-12T18:01:37Z [Term] @@ -5481,7 +5609,6 @@ intersection_of: GO:0042995 ! cell projection intersection_of: has_part GO:0098590 ! plasma membrane region relationship: has_part GO:0098590 ! plasma membrane region property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/13193" xsd:anyURI -created_by: krc creation_date: 2017-03-21T17:26:07Z [Term] @@ -5496,7 +5623,6 @@ intersection_of: GO:0022607 ! cellular component assembly intersection_of: results_in_assembly_of GO:0120025 ! plasma membrane bounded cell projection relationship: results_in_assembly_of GO:0120025 ! plasma membrane bounded cell projection property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/13298" xsd:anyURI -created_by: krc creation_date: 2017-04-24T23:56:08Z [Term] @@ -5509,7 +5635,6 @@ intersection_of: GO:0016043 ! cellular component organization intersection_of: results_in_organization_of GO:0120025 ! plasma membrane bounded cell projection relationship: results_in_organization_of GO:0120025 ! plasma membrane bounded cell projection property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/13298" xsd:anyURI -created_by: krc creation_date: 2017-04-26T16:07:02Z [Term] @@ -5525,7 +5650,6 @@ is_a: GO:1903047 ! mitotic cell cycle process intersection_of: GO:0000280 ! nuclear division intersection_of: part_of GO:0000278 ! mitotic cell cycle property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/19910" xsd:anyURI -created_by: pg creation_date: 2017-03-23T14:44:23Z [Term] @@ -5536,7 +5660,6 @@ def: "The assembly and secretion a set of components to form an extracellular ve synonym: "extracellular vesicle assembly" EXACT [] is_a: GO:0044085 ! cellular component biogenesis property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/14256" xsd:anyURI -created_by: pg creation_date: 2017-10-23T11:53:42Z [Term] @@ -5552,7 +5675,6 @@ intersection_of: has_target_end_location GO:0005576 ! extracellular region intersection_of: has_target_start_location GO:0005622 ! intracellular anatomical structure relationship: has_target_end_location GO:0005576 ! extracellular region relationship: has_target_start_location GO:0005622 ! intracellular anatomical structure -created_by: pg creation_date: 2019-05-22T11:20:45Z [Term] @@ -5565,7 +5687,6 @@ is_a: GO:0022402 ! cell cycle process intersection_of: GO:0009987 ! cellular process intersection_of: part_of GO:0000278 ! mitotic cell cycle relationship: part_of GO:0000278 ! mitotic cell cycle -created_by: jl creation_date: 2014-05-22T14:22:34Z [Term] @@ -5578,15 +5699,12 @@ is_a: GO:0031982 ! vesicle is_a: GO:0065010 ! extracellular membrane-bounded organelle intersection_of: GO:0031982 ! vesicle intersection_of: part_of GO:0005576 ! extracellular region -created_by: jl creation_date: 2014-10-22T14:26:11Z [Term] id: GO:1990904 name: ribonucleoprotein complex namespace: cellular_component -alt_id: GO:0030529 -alt_id: GO:1990903 def: "A macromolecular complex that contains both RNA and protein molecules." [GOC:krc, GOC:vesicles] subset: goslim_pir synonym: "extracellular ribonucleoprotein complex" NARROW [] @@ -5596,7 +5714,6 @@ synonym: "RNA-protein complex" EXACT [] synonym: "RNP" EXACT [] xref: Wikipedia:Ribonucleoprotein is_a: GO:0032991 ! protein-containing complex -created_by: pr creation_date: 2015-11-19T12:26:37Z [Term] @@ -5630,7 +5747,6 @@ is_a: NCBITaxon:39107 ! Murinae id: NCBITaxon:10090 name: Mus musculus namespace: ncbi_taxonomy -alt_id: NCBITaxon:85055 synonym: "house mouse" EXACT genbank_common_name [] synonym: "mouse" EXACT OMO:0003003 [] xref: GC_ID:1 @@ -5647,7 +5763,6 @@ is_a: NCBITaxon:7776 ! Gnathostomata id: NCBITaxon:117571 name: Euteleostomi namespace: ncbi_taxonomy -alt_id: NCBITaxon:40673 synonym: "bony vertebrates" EXACT genbank_common_name [] xref: GC_ID:1 is_a: NCBITaxon:117570 ! Teleostomi @@ -5796,7 +5911,6 @@ is_a: NCBITaxon:1963758 ! Myomorpha id: NCBITaxon:39107 name: Murinae namespace: ncbi_taxonomy -alt_id: NCBITaxon:109679 xref: GC_ID:1 is_a: NCBITaxon:10066 ! Muridae @@ -5892,7 +6006,6 @@ is_a: NCBITaxon:314147 ! Glires id: PATO:0000001 name: quality namespace: quality -alt_id: PATO:0000072 def: "A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities" [PATOC:GVG] [Term] @@ -5907,7 +6020,6 @@ is_a: PATO:0001241 ! physical object quality id: PATO:0000052 name: shape namespace: quality -alt_id: PATO:0001647 def: "A morphological quality inhering in a bearer by virtue of the bearer's ratios of distances between its features (points, edges, surfaces and also holes etc)." [PATOC:GVG] comment: Shapes are invariant on size transformations. Shapes can be subdivided into 2D and 3D shapes, We can also make a distinction between shapes of complete self-connected objects, and shapes of parts of objects. subset: attribute_slim @@ -5918,7 +6030,6 @@ is_a: PATO:0000051 ! morphology id: PATO:0000141 name: structure namespace: quality -alt_id: PATO:0001452 def: "A morphology quality inhering in a bearer by virtue of the bearer's relative position, shape, arrangements and connectivity of an organism's various parts; the pattern underlying its form." [PATOC:GVG] subset: attribute_slim synonym: "conformation" BROAD [VT:1000738] @@ -5968,7 +6079,6 @@ is_a: PATO:0002318 ! superelliptic id: PATO:0001018 name: physical quality namespace: quality -alt_id: PATO:0002079 def: "A quality of a physical entity that exists through action of continuants at the physical level of organisation in relation to other entities." [PATOC:GVG] subset: attribute_slim synonym: "relational physical quality" EXACT [] @@ -5979,8 +6089,6 @@ is_a: PATO:0001241 ! physical object quality id: PATO:0001241 name: physical object quality namespace: quality -alt_id: PATO:0001237 -alt_id: PATO:0001238 def: "A quality which inheres in a continuant." [PATOC:GVG] comment: Relational qualities are qualities that hold between multiple entities. Normal (monadic) qualities such as the shape of a eyeball exist purely as a quality of that eyeball. A relational quality such as sensitivity to light is a quality of that eyeball (and connecting nervous system) as it relates to incoming light waves/particles. synonym: "monadic quality of a continuant" EXACT [] @@ -6109,7 +6217,6 @@ is_a: PATO:0002005 ! concavity id: PATO:0001873 name: cylindrical namespace: quality -alt_id: PATO:0001203 def: "A convex 3-D shape quality inhering in a bearer by virtue of the bearer's exhibiting a consistently-sized round cross section." [PATOC:MAH] subset: cell_quality subset: value_slim @@ -6374,7 +6481,6 @@ def: "A quality inhering in a cell by virtue of the cell having a high nuclear/c comment: A high nuclear/cytolasmic ratio is 70% or higher. synonym: "high N:C ratio" EXACT [] is_a: PATO:0001396 ! cellular quality -created_by: http://orcid.org/0000-0001-5208-3432 [Term] id: PATO:0070044 @@ -6382,7 +6488,6 @@ name: anatomical structure quality namespace: quality def: "A quality of continuant that exist at the anatomical level of organisation and anything under it. This includes, but is not limited to, cells , tissues, and components." [] is_a: PATO:0001241 ! physical object quality -created_by: http://orcid.org/0000-0001-7258-9596 [Term] id: PATO:0070045 @@ -6390,7 +6495,6 @@ name: anatomical histological quality namespace: quality def: "A quality inhering in an anotomical structure by virtue of its capacity to be stained by specific histological dyes." [] is_a: PATO:0070044 ! anatomical structure quality -created_by: http://orcid.org/0000-0001-7258-9596 [Term] id: PATO:0070047 @@ -6398,18 +6502,17 @@ name: polychromatophilic namespace: quality def: "An affinity inhering in an anatomical structure by virtue of the bearer exhibiting a molecular interaction for both basic and acid stains under specific pH conditions." [GOC:add] is_a: PATO:0070045 ! anatomical histological quality -created_by: http://orcid.org/0000-0001-7258-9596 [Term] id: PR:000000001 name: protein namespace: protein def: "An amino acid chain that is produced de novo by ribosome-mediated translation of a genetically-encoded mRNA, and any derivatives thereof." [PRO:DAN, PRO:WCB] -comment: The definition above excludes protein complexes, which some also consider a protein. Those who wish to refer to a class representing both senses of the word are directed to CHEBI:36080. Note that the definition allows for experimentally-manipulated genes, and allows for artifically-produced derivatives that mimic those found naturally. Proteins (in the sense defined here) that descended from a common ancestor can be classified into families and superfamilies composed of products of evolutionarily-related genes. The domain architecture of a protein is described by the order of its constituent domains. Proteins with the same domains in the same order are defined as homeomorphic [PRO:WCB]. +comment: The definition above excludes protein complexes, which some also consider a protein. Those who wish to refer to a class representing both senses of the word are directed to CHEBI:36080. Note that the definition allows for experimentally-manipulated genes, and allows for artifically-produced derivatives that mimic those found naturally. Proteins (in the sense defined here) that descended from a common ancestor can be classified into families and superfamilies composed of products of evolutionarily-related genes. The domain architecture of a protein is described by the order of its constituent domains. Proteins with the same domains in the same order are defined as homeomorphic [PRO:WCB). synonym: "native protein" NARROW [IEDB:BP] synonym: "natural protein" EXACT [PRO:DAN] is_a: PR:000018263 ! amino acid chain -is_a: PR:000050567 ! protein-containing material entity +is_a: PR:000064867 ! protein-containing molecular entity relationship: output_of GO:0006412 ! translation [Term] @@ -6678,7 +6781,6 @@ namespace: protein def: "A protein with core architecture consisting of a signal sequence, followed by 7 Ig-like domains (Pfam:PF00047, Pfam:PF07679, or Pfam:PF07686), a transmembrane region, and a cytoplasmic Protein tyrosine kinase domain." [PRO:WCB] comment: Category=family. xref: PIRSF:PIRSF038502 -is_a: PR:000000001 ! protein [Term] id: PR:000002112 @@ -6820,11 +6922,11 @@ synonym: "fam:angiotensinogenase" EXACT PRO-short-label [PRO:DAN] is_a: PR:000000001 ! protein [Term] -id: PR:000050567 -name: protein-containing material entity +id: PR:000064867 +name: protein-containing molecular entity namespace: protein -def: "A material entity that minimally consists of a protein." [PRO:DAN] -comment: Note: This includes single proteins and derivatives thereof (PR:000000001), protein-containing complexes (GO:0032991), and protein aggregates (PR:000050566). +def: "A molecular entity that minimally consists of a protein." [PRO:DAN] +comment: Note: This includes single proteins and derivatives thereof (PR:000000001), protein-containing complexes (GO:0032991), and protein aggregates (PR:000050565). synonym: "protein" NARROW [PRO:DAN] synonym: "protein aggregate" NARROW [PRO:DAN] synonym: "protein complex" NARROW [PRO:DAN] @@ -7009,7 +7111,6 @@ xref: UMLS:C0687028 {source="ncithesaurus:Duct"} xref: Wikipedia:Duct_(anatomy) xref: XAO:0004000 xref: ZFA:0005171 -is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0000063 ! organ subunit relationship: has_part UBERON:0034969 ! epithelial layer of duct relationship: RO:0000086 PATO:0002299 ! has quality tubular @@ -7019,7 +7120,6 @@ relationship: RO:0002570 UBERON:0000463 ! conduit for organism substance id: UBERON:0000060 name: anatomical wall namespace: uberon -alt_id: UBERON:0009915 def: "Organ component adjacent to an organ cavity and which consists of a maximal aggregate of organ component layers." [FMA:82482] subset: upper_level synonym: "organ wall" RELATED [FMA:82482] @@ -7243,7 +7343,6 @@ creation_date: 2009-06-18T09:26:37Z id: UBERON:0000075 name: subdivision of skeletal system namespace: uberon -alt_id: UBERON:0010322 def: "Anatomical cluster consisting of the skeletal elements and articular elements that are part of an individual subdivision of the organism." [https://orcid.org/0000-0002-6601-2165, UBERONREF:0000003] subset: non_informative synonym: "skeletal system part" RELATED [] @@ -7780,8 +7879,6 @@ property_value: seeAlso "https://github.com/obophenotype/uberon/issues/661" xsd: id: UBERON:0000174 name: excreta namespace: uberon -alt_id: UBERON:0000324 -alt_id: UBERON:0007550 def: "A portion of organism substance that is the product of an excretion process that will be eliminated from the body. An excretion process is elimination by an organism of the waste products that arise as a result of metabolic activity." [GO:0007588, http://orcid.org/0000-0002-6601-2165] synonym: "excreted substance" EXACT [] synonym: "excretion" RELATED [BTO:0000491] @@ -7833,7 +7930,7 @@ xref: VHOG:0000224 xref: Wikipedia:Blood xref: XAO:0000124 xref: ZFA:0000007 -is_a: PR:000050567 ! protein-containing material entity +is_a: UBERON:0000061 ! anatomical structure is_a: UBERON:0000179 ! haemolymphatic fluid relationship: has_part CL:0000232 {source="CL:tm"} ! erythrocyte relationship: has_part UBERON:0001969 ! blood plasma @@ -7862,7 +7959,6 @@ creation_date: 2009-04-08T04:38:19Z id: UBERON:0000307 name: blastula namespace: uberon -alt_id: UBERON:0007011 def: "Organism at the blastula stage - an early stage of embryonic development in animals. It is produced by cleavage of a fertilized ovum and consists of a spherical layer of around 128 cells surrounding a central fluid-filled cavity called the blastocoel. The blastula follows the morula and precedes the gastrula in the developmental sequence." [Wikipedia:Blastula] subset: inconsistent_with_fma synonym: "blastosphere" RELATED [Wikipedia:Blastula] @@ -8415,7 +8511,6 @@ xref: VHOG:0000387 xref: Wikipedia:Epithelium xref: XAO:0003045 xref: ZFA:0001486 -is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0000479 ! tissue intersection_of: UBERON:0000479 ! tissue intersection_of: RO:0002473 CL:0000066 ! composed primarily of epithelial cell @@ -8749,7 +8844,6 @@ property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/d/ id: UBERON:0000926 name: mesoderm namespace: uberon -alt_id: UBERON:0003263 def: "The middle germ layer of the embryo, between the endoderm and ectoderm." [Wikipedia:Mesoderm] subset: efo_slim subset: pheno_slim @@ -9194,7 +9288,6 @@ id: UBERON:0001009 name: circulatory system namespace: uberon def: "Organ system that passes nutrients (such as amino acids and electrolytes), gases, hormones, blood cells, etc. to and from cells in the body to help fight diseases and help stabilize body temperature and pH to maintain homeostasis[WP]." [Wikipedia:Circulatory_system] -subset: human_reference_atlas subset: uberon_slim synonym: "systema cardiovasculare" RELATED OMO:0003011 [Wikipedia:Circulatory_system] xref: AAO:0000959 @@ -9214,7 +9307,6 @@ property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/2/ property_value: RO:0002161 NCBITaxon:147099 {source="Wikipedia:Acoelomorpha"} property_value: RO:0002161 NCBITaxon:6073 property_value: RO:0002161 NCBITaxon:6157 -property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001015 @@ -9797,7 +9889,6 @@ property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/3/ id: UBERON:0001231 name: nephron tubule namespace: uberon -alt_id: UBERON:0004210 def: "An epithelial tube that is part of the nephron, the functional part of the kidney." [GO:0072078, Wikipedia:Renal_tubule] subset: efo_slim subset: human_reference_atlas @@ -10110,7 +10201,6 @@ property_value: RO:0002175 NCBITaxon:9606 id: UBERON:0001290 name: proximal straight tubule namespace: uberon -alt_id: UBERON:0005166 def: "The proximal straight tubule is the part of the descending limb that extends from the proximal convoluted tubule to the descending thin tubule." [GO:0072020] subset: human_reference_atlas subset: uberon_slim @@ -10523,7 +10613,6 @@ xref: MIAA:0000052 xref: NCIT:C13356 xref: UMLS:C0032105 {source="ncithesaurus:Plasma"} xref: Wikipedia:Blood_plasma -is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0000179 ! haemolymphatic fluid intersection_of: UBERON:0000463 ! organism substance intersection_of: has_part GO:0005577 ! fibrinogen complex @@ -10633,7 +10722,6 @@ xref: VHOG:0001250 xref: Wikipedia:Blood_vessel xref: XAO:0001011 xref: ZFA:0005314 -is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0000055 ! vessel is_a: UBERON:0004120 ! mesoderm-derived structure relationship: capable_of_part_of GO:0008015 ! blood circulation @@ -11022,7 +11110,6 @@ property_value: terms:contributor https://orcid.org/0000-0003-2804-127X id: UBERON:0002120 name: pronephros namespace: uberon -alt_id: UBERON:0005794 def: "In mammals, the pronephros is the first of the three embryonic kidneys to be established and exists only transiently. In lower vertebrates such as fish and amphibia, the pronephros is the fully functional embryonic kidney and is indispensible for larval life[GO]." [GO:0048793, Wikipedia:Pronephros] comment: Once the more complex mesonephros forms the pronephros undergoes apoptosis in amphibians. In fishes the nephron degenerates but the organ remains and becomes a component of the immune system[Wikipedia:Pronephros]. // TODO - check developmental relationships. Note that we previously include the ZFA/XAO terms under the more specific 'pronephric kidney', but these are now merged. TODO GCI: relationship: capable_of GO:0030104 subset: efo_slim @@ -11176,7 +11263,6 @@ xref: NCIT:C32891 xref: SCTID:362219002 xref: UMLS:C0022445 {source="ncithesaurus:Juxtaglomerular_Apparatus"} xref: Wikipedia:Juxtaglomerular_apparatus -is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0000061 ! anatomical structure relationship: capable_of GO:0003093 {source="GO"} ! regulation of glomerular filtration relationship: has_part CL:0000648 ! kidney granular cell @@ -11232,7 +11318,6 @@ relationship: part_of UBERON:0002319 {source="MA"} ! mesangium id: UBERON:0002323 name: coelemic cavity lumen namespace: uberon -alt_id: UBERON:0000169 def: "The cavity within the body of all animals higher than the coelenterates and certain primitive worms, formed by the splitting of the embryonic mesoderm into two layers. In mammals it forms the peritoneal, pleural, and pericardial cavities." [BTO:0001707] comment: EDITOR_NOTE check the FMA placement here; ncit placement of body cavity here probably not correct subset: uberon_slim @@ -11258,7 +11343,6 @@ xref: RETIRED_EHDAA2:0003186 xref: SCTID:361348008 xref: TAO:0001438 xref: UMLS:C0333343 {source="ncithesaurus:Cavity"} -xref: ZFA:0001438 is_a: UBERON:0002553 ! anatomical cavity relationship: RO:0002494 UBERON:0003886 ! transformation of future coelemic cavity lumen relationship: RO:0002572 UBERON:0011997 ! luminal space of coelom @@ -11674,6 +11758,7 @@ xref: TAO:0000279 xref: VHOG:0000559 xref: XAO:0000057 xref: ZFA:0000279 +is_a: UBERON:0000061 ! anatomical structure is_a: UBERON:0006598 ! presumptive structure intersection_of: UBERON:0005423 ! developing anatomical structure intersection_of: RO:0002387 UBERON:0002329 ! has potential to develop into somite @@ -11701,7 +11786,6 @@ xref: Wikipedia:Pronephric_duct xref: XAO:0000063 xref: ZFA:0000150 is_a: UBERON:0009201 {source="GO"} ! nephric duct -is_a: UBERON:0012275 ! meso-epithelium relationship: part_of UBERON:0002120 ! pronephros relationship: RO:0002202 UBERON:0003064 {source="Wikipedia"} ! develops from intermediate mesoderm relationship: RO:0002202 UBERON:0005721 {source="XAO"} ! develops from pronephric mesoderm @@ -11894,7 +11978,6 @@ property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/6/ id: UBERON:0003081 name: lateral plate mesoderm namespace: uberon -alt_id: UBERON:0006258 def: "Portion of the middle of the three primary germ layers of the embryo that resides on the periphery of the embryo, is continuous with the extra-embryonic mesoderm, splits into two layers enclosing the intra-embryonic coelom, and gives rise to body wall structures[MP]." [MP:0010117, Wikipedia:Lateral_plate_mesoderm] subset: pheno_slim subset: uberon_slim @@ -12670,8 +12753,6 @@ property_value: IAO:0000116 "TODO" xsd:string id: UBERON:0004200 name: kidney pyramid namespace: uberon -alt_id: UBERON:0002449 -alt_id: UBERON:0005098 def: "Kidney pyramids are the conical arrangements of tubules that constitute the renal medulla in a multi-lobed mammalian kidney; they contain the loops of Henle and the medullary collecting ducts." [GO:0072056, http://anatomy.uams.edu/anatomyhtml/kidney.html] subset: human_reference_atlas subset: pheno_slim @@ -12900,7 +12981,6 @@ xref: WikipediaCategory:Cardiovascular_system xref: XAO:0000100 xref: XAO:0001010 xref: ZFA:0000010 -is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0000467 ! anatomical system intersection_of: UBERON:0000467 ! anatomical system intersection_of: has_part UBERON:0000948 ! heart @@ -12924,7 +13004,6 @@ synonym: "blood vessels" RELATED [TAO:0001079] synonym: "set of blood vessels" EXACT [] xref: TAO:0001079 xref: ZFA:0001079 -is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0002049 ! vasculature intersection_of: UBERON:0002049 ! vasculature intersection_of: RO:0002473 UBERON:0001981 ! composed primarily of blood vessel @@ -12938,7 +13017,6 @@ id: UBERON:0004572 name: arterial system namespace: uberon def: "The part of the cardiovascular system consisting of all arteries." [https://orcid.org/0000-0002-6601-2165] -subset: human_reference_atlas subset: pheno_slim xref: BTO:0004690 xref: EHDAA2:0000143 @@ -12948,17 +13026,14 @@ xref: EMAPA:16371 xref: MA:0002719 xref: SCTID:362030008 xref: VHOG:0000273 -is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0007798 {source="MA"} ! vascular system relationship: RO:0002351 UBERON:0001637 ! has member artery -property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0004582 name: venous system namespace: uberon def: "The part of the cardiovascular system consisting of all venous vessels. In vertebrates with a double circulation, this can be divided into systemic and pulmonary portions." [https://orcid.org/0000-0002-6601-2165] -subset: human_reference_atlas synonym: "vein system" EXACT [] xref: BTO:0004692 xref: EHDAA2:0002171 @@ -12969,10 +13044,8 @@ xref: NCIT:C33858 xref: SCTID:362060003 xref: UMLS:C1267406 {source="ncithesaurus:Venous_System"} xref: VHOG:0000277 -is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0007798 {source="MA"} ! vascular system relationship: RO:0002473 UBERON:0001638 ! composed primarily of vein -property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0004638 @@ -13082,7 +13155,6 @@ property_value: RO:0002175 NCBITaxon:9606 id: UBERON:0004734 name: gastrula namespace: uberon -alt_id: UBERON:0007012 def: "Organism at the gastrula stage." [Wikipedia:Gastrula, Wikipedia:Trilaminar_blastocyst] subset: pheno_slim synonym: "blastocystis trilaminaris" RELATED [https://orcid.org/0000-0002-6601-2165] @@ -13448,7 +13520,6 @@ property_value: IAO:0000116 "class added for consistency with GO - consider merg id: UBERON:0005096 name: descending thin limb namespace: uberon -alt_id: UBERON:0005165 def: "The descending thin limb is a part of the loop of Henle situated just after the proximal straight tubule (S3). It extends to the tip of the loop of Henle[GO]." [GO:0072022, Wikipedia:Descending_limb_of_loop_of_Henle] subset: human_reference_atlas subset: uberon_slim @@ -13912,7 +13983,6 @@ xref: NCIT:C13191 xref: SCTID:68989006 xref: UMLS:C0004799 {source="ncithesaurus:Basement_Membrane"} xref: Wikipedia:Basement_membrane -is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0005764 {source="FMA"} ! acellular membrane relationship: adjacent_to CL:0000066 ! epithelial cell relationship: has_part GO:0005587 ! collagen type IV trimer @@ -14310,7 +14380,6 @@ subset: efo_slim xref: EFO:0003709 xref: TAO:0005077 xref: ZFA:0005077 -is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0005423 ! developing anatomical structure relationship: has_part CL:0000115 ! endothelial cell relationship: has_part CL:0000566 ! angioblastic mesenchymal cell @@ -14627,7 +14696,6 @@ property_value: RO:0002175 NCBITaxon:9606 id: UBERON:0007823 name: appendage girdle region namespace: uberon -alt_id: UBERON:0007824 def: "An organism subdivision that encompasses the region containing the pectoral or pelvic girdle. Note that this includes both the skeletal elements and associated tissues (integument, muscle, etc)." [https://orcid.org/0000-0002-6601-2165, UBERONREF:0000003] synonym: "fin girdle" RELATED SENSU [] synonym: "fin girdle region" RELATED SENSU [] @@ -14729,7 +14797,6 @@ is_a: UBERON:0007685 ! region of nephron tubule id: UBERON:0009142 name: entire embryonic mesenchyme namespace: uberon -alt_id: UBERON:0003313 def: "Sum total of mesenchyme in the embryo." [https://github.com/obophenotype/human-developmental-anatomy-ontology/issues/7] xref: EHDAA2:0001113 xref: EHDAA:177 @@ -14761,6 +14828,7 @@ is_a: UBERON:0003914 {source="EHDAA2"} ! epithelial tube is_a: UBERON:0004819 ! kidney epithelium is_a: UBERON:0006553 ! renal duct is_a: UBERON:0006555 ! excretory tube +is_a: UBERON:0012275 ! meso-epithelium union_of: UBERON:0003060 ! pronephric duct union_of: UBERON:0003074 ! mesonephric duct @@ -15208,6 +15276,7 @@ synonym: "haemocoelom" NARROW [] synonym: "schizocoelom" NARROW [] xref: EHDAA2:0004731 xref: Wikipedia:Coelom +xref: ZFA:0001438 is_a: UBERON:0000481 {source="EHDAA2"} ! multi-tissue structure relationship: RO:0002162 NCBITaxon:33213 ! in taxon Bilateria property_value: IAO:0000116 "EHDAA2 distingsuishes between the lumen, the lining, and the 'coelomic cavity', which despire it's name, is not a space - it is the aggregate of space plus lining." xsd:string @@ -15455,7 +15524,6 @@ is_a: UBERON:0036215 ! anatomical surface region id: UBERON:0016879 name: future central nervous system namespace: uberon -alt_id: UBERON:3000469 def: "Primordium that develops into the central nervous system." [http://orcid.org/0000-0002-6601-2165] synonym: "future CNS" EXACT [] synonym: "presumptive central nervous system" EXACT [] @@ -15470,7 +15538,6 @@ relationship: RO:0002387 UBERON:0001017 ! has potential to develop into central id: UBERON:0016880 name: future nervous system namespace: uberon -alt_id: UBERON:3000477 def: "Primordium that develops into the nervous system." [http://orcid.org/0000-0002-6601-2165] synonym: "presumptive nervous system" EXACT [AAO:0000477] xref: AAO:0000477 @@ -15656,7 +15723,6 @@ synonym: "microvessel" BROAD [] is_a: UBERON:0001981 ! blood vessel is_a: UBERON:0010523 ! microcirculatory vessel property_value: seeAlso "https://github.com/obophenotype/uberon/issues/2186" xsd:string -created_by: http://orcid.org/0000-0002-2825-0621 [Term] id: UBERON:8450002 @@ -15669,7 +15735,6 @@ intersection_of: UBERON:0000467 ! anatomical system intersection_of: capable_of GO:0046903 ! secretion relationship: capable_of GO:0046903 ! secretion property_value: RO:0002175 NCBITaxon:9606 -created_by: http://orcid.org/0000-0002-6095-8718 creation_date: 2022-05-25T18:21:29Z [Term] @@ -15797,7 +15862,6 @@ id: RO:0002021 name: occurs across def: "A relationship between a process and a barrier, where the process occurs in a region spanning the barrier. For cellular processes the barrier is typically a membrane. Examples include transport across a membrane and membrane depolarization." [] is_a: RO:0002479 ! has part that occurs in -created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-07-20T17:19:37Z [Typedef] @@ -16653,7 +16717,6 @@ name: causally upstream of or within, negative effect property_value: RO:0004050 RO:0002418 property_value: seeAlso "https://wiki.geneontology.org/Causally_upstream_of_or_within,_negative_effect" xsd:anyURI is_a: causally_upstream_of_or_within ! causally upstream of or within -created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-03-13T23:55:05Z [Typedef] @@ -16661,7 +16724,6 @@ id: RO:0004047 name: causally upstream of or within, positive effect property_value: seeAlso https://wiki.geneontology.org/Causally_upstream_of_or_within,_positive_effect is_a: causally_upstream_of_or_within ! causally upstream of or within -created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-03-13T23:55:19Z [Typedef] @@ -16670,7 +16732,6 @@ name: has small molecule regulator def: "a relation between a process and a continuant, in which the process is regulated by the small molecule continuant" [] is_a: has_participant ! has participant inverse_of: RO:0012004 ! is small molecule regulator of -created_by: https://orcid.org/0000-0003-1813-6857 creation_date: 2020-04-22T20:27:26Z [Typedef] @@ -16678,7 +16739,6 @@ id: RO:0012004 name: is small molecule regulator of def: "a relation between a continuant and a process, in which the continuant is a small molecule that regulates the process" [] is_a: RO:0002596 ! capable of regulating -created_by: https://orcid.org/0000-0003-1813-6857 creation_date: 2020-06-24T13:15:17Z [Typedef] @@ -16688,7 +16748,6 @@ def: "a relation between a continuant and a process, in which the continuant is property_value: seeAlso "https://wiki.geneontology.org/Is_small_molecule_activator_of" xsd:anyURI is_a: RO:0002598 ! capable of positively regulating is_a: RO:0012004 ! is small molecule regulator of -created_by: https://orcid.org/0000-0003-1813-6857 creation_date: 2020-06-24T13:15:26Z [Typedef] @@ -16698,7 +16757,6 @@ def: "A relationship between a neuron and a region, where the neuron has a funct synonym: "has synaptic input or output in" EXACT [] is_a: RO:0002130 ! has synaptic terminal in transitive_over: part_of ! part of -created_by: https://orcid.org/0000-0002-1373-1705 creation_date: 2020-07-17T09:26:52Z [Typedef] @@ -16710,9 +16768,18 @@ synonym: "has sensory terminal in" EXACT [] synonym: "has sensory terminal location" EXACT [] is_a: RO:0002360 ! has dendrite location transitive_over: part_of ! part of -created_by: https://orcid.org/0000-0002-1373-1705 creation_date: 2020-07-20T12:10:09Z +[Typedef] +id: RO:0015004 +name: has characterizing marker set +def: "A relation that applies between a cell type and a set of markers that can be used to uniquely identify that cell type." [] +synonym: "has marker gene combination" EXACT [] +synonym: "has marker signature set" EXACT [] +property_value: IAO:0000116 "C has_characterizing_marker_set y iff: C is a cell type and y is a collection of genes or proteins whose expression is sufficient to distinguish cell type C from most or all other cell types." xsd:string +property_value: terms:contributor https://orcid.org/0000-0001-7258-9596 +domain: CL:0000000 ! cell + [Typedef] id: RO:0015006 name: different in magnitude relative to @@ -16786,7 +16853,6 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0012003 is_a: has_participant ! has participant -created_by: https://orcid.org/0000-0003-1813-6857 creation_date: 2020-06-08T17:21:33Z [Typedef] @@ -17082,7 +17148,6 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_ontology xref: RO:0004009 is_a: has_input ! has input is_a: has_primary_input_or_output ! has primary input or output -created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-12-13T11:26:56Z [Typedef] @@ -17093,7 +17158,6 @@ def: "p 'has primary input ot output' c iff either (a) p 'has primary input' c o subset: http://purl.obolibrary.org/obo/valid_for_go_ontology xref: RO:0004007 is_a: has_participant ! has participant -created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-12-13T11:26:17Z [Typedef] @@ -17105,7 +17169,6 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_ontology xref: RO:0004008 is_a: has_output ! has output is_a: has_primary_input_or_output ! has primary input or output -created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-12-13T11:26:32Z [Typedef] @@ -17116,7 +17179,6 @@ def: "a relation between a process and a continuant, in which the process is act xref: RO:0012001 is_a: RO:0012000 ! has small molecule regulator inverse_of: RO:0012005 ! is small molecule activator of -created_by: https://orcid.org/0000-0003-1813-6857 creation_date: 2020-04-22T20:28:37Z [Typedef] @@ -17441,7 +17503,6 @@ namespace: external def: "p has anatomical participant c iff p has participant c, and c is an anatomical entity" [] xref: RO:0040036 is_a: has_participant ! has participant -created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-09-26T01:08:58Z [Typedef] @@ -17513,7 +17574,6 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0012008 is_a: results_in_organization_of ! results in organization of -created_by: https://orcid.org/0000-0003-1813-6857 creation_date: 2021-02-26T07:28:29Z [Typedef] @@ -17565,7 +17625,6 @@ name: results in organization of namespace: external def: "p results in organization of c iff p results in the assembly, arrangement of constituent parts, or disassembly of c" [] xref: RO:0002592 -is_a: has_participant ! has participant is_a: results_in_changes_to_anatomical_or_cellular_structure ! results in changes to anatomical or cellular structure [Typedef] diff --git a/subsets/kidney_upper_slim.owl b/subsets/kidney_upper_slim.owl index ae3211d54..f79961ee4 100644 --- a/subsets/kidney_upper_slim.owl +++ b/subsets/kidney_upper_slim.owl @@ -22,8 +22,8 @@ xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#" xmlns:ncbitaxon="http://purl.obolibrary.org/obo/ncbitaxon#"> - - 2024-09-26 + + 2025-01-08 @@ -287,13 +287,18 @@ WHERE { - 2018-03-14T00:03:24Z is negative form of + + + + + + @@ -373,6 +378,14 @@ WHERE { + + + + + + + + @@ -384,6 +397,14 @@ WHERE { + + + + + + + + @@ -1010,12 +1031,6 @@ WHERE { - - - - - - @@ -1034,6 +1049,12 @@ WHERE { + + + + + + @@ -1048,19 +1069,25 @@ WHERE { - + + description + - + + license + - + + title + @@ -1088,26 +1115,12 @@ WHERE { - - - - - - - - - - has_alternative_id - - - - @@ -1123,7 +1136,11 @@ WHERE { + An annotation property that links an ontology entity or a statement to a prefixed identifier or URI. + + database_cross_reference + has cross-reference @@ -1206,12 +1223,6 @@ WHERE { - - - - - - @@ -1681,7 +1692,6 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 A relationship between a process and a barrier, where the process occurs in a region spanning the barrier. For cellular processes the barrier is typically a membrane. Examples include transport across a membrane and membrane depolarization. - 2017-07-20T17:19:37Z occurs across @@ -3966,7 +3976,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different - p results in organization of c iff p results in the assembly, arrangement of constituent parts, or disassembly of c RO:0002592 @@ -4088,7 +4097,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different p 'has primary input ot output' c iff either (a) p 'has primary input' c or (b) p 'has primary output' c. - 2018-12-13T11:26:17Z RO:0004007 external @@ -4106,7 +4114,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different p has primary output c if (a) p has output c and (b) the goal of process is to modify, produce, or transform c. - 2018-12-13T11:26:32Z RO:0004008 external @@ -4134,7 +4141,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different p has primary input c if (a) p has input c and (b) the goal of process is to modify, consume, or transform c. - 2018-12-13T11:26:56Z RO:0004009 external @@ -4161,7 +4167,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different - 2018-03-13T23:55:05Z causally upstream of or within, negative effect https://wiki.geneontology.org/Causally_upstream_of_or_within,_negative_effect @@ -4173,7 +4178,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different - 2018-03-13T23:55:19Z causally upstream of or within, positive effect @@ -4187,7 +4191,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different a relation between a process and a continuant, in which the process is regulated by the small molecule continuant - 2020-04-22T20:27:26Z has small molecule regulator @@ -4200,7 +4203,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different a relation between a process and a continuant, in which the process is activated by the small molecule continuant - 2020-04-22T20:28:37Z RO:0012001 external @@ -4217,7 +4219,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different p acts on population of c iff c' is a collection, has members of type c, and p has participant c - 2020-06-08T17:21:33Z RO:0012003 external @@ -4237,7 +4238,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different a relation between a continuant and a process, in which the continuant is a small molecule that regulates the process - 2020-06-24T13:15:17Z is small molecule regulator of @@ -4250,7 +4250,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different a relation between a continuant and a process, in which the continuant is a small molecule that activates the process - 2020-06-24T13:15:26Z is small molecule activator of https://wiki.geneontology.org/Is_small_molecule_activator_of @@ -4262,7 +4261,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different - 2021-02-26T07:28:29Z RO:0012008 external @@ -4286,7 +4284,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different A relationship between a neuron and a region, where the neuron has a functionally relevant number of input and/or output synapses in that region. - 2020-07-17T09:26:52Z has synaptic input or output in has synaptic IO in region @@ -4303,7 +4300,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different Relation between a sensory neuron and some structure in which it receives sensory input via a sensory dendrite. - 2020-07-20T12:10:09Z has sensory dendrite location has sensory terminal in @@ -4313,6 +4309,20 @@ Each of these 3 primitives can be composed to yield a cross-product of different + + + + + A relation that applies between a cell type and a set of markers that can be used to uniquely identify that cell type. + C has_characterizing_marker_set y iff: C is a cell type and y is a collection of genes or proteins whose expression is sufficient to distinguish cell type C from most or all other cell types. + + has marker gene combination + has marker signature set + has characterizing marker set + + + + @@ -4452,7 +4462,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different p has anatomical participant c iff p has participant c, and c is an anatomical entity - 2018-09-26T01:08:58Z RO:0040036 external @@ -4796,6 +4805,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different XAO:0003012 ZFA:0009000 + + The definition of cell is intended to represent all cells, and thus a cell is defined as a material entity and not an anatomical structure, which implies that it is part of an organism (or the entirety of one). cell @@ -4827,6 +4838,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different A cell found in the embryo before the formation of all the gem layers is complete. ZFA:0009002 + + early embryonic cell (metazoa) @@ -4880,6 +4893,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different animal stem cell + + This term applies to metazoan. For plant stem cells, consider using PO:0004011 ‘initial cell’ or its parent PO:0004010 ‘meristematic cell’. stem cell @@ -5067,6 +5082,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different colony forming unit hematopoietic + + Markers differ between species, and two sets of markers have been described for mice. HSCs are reportedly CD34-positive, CD45-positive, CD48-negative, CD150-positive, CD133-positive, and CD244-negative. hematopoietic stem cell @@ -5118,6 +5135,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different erythroid stem cell + + erythroid progenitor cell @@ -5167,6 +5186,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different A cell that is within the developmental lineage of gametes and is able to pass along its genetic material to offspring. ZFA:0009016 + + Originally this term had some plant germ line cell children. germ line cell @@ -5219,6 +5240,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different multifate stem cell multipotent cell multipotent stem cell + + multi fate stem cell @@ -5254,6 +5277,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different myeloid stem cell pluripotent stem cell (bone marrow) + + This cell type is intended to be compatible with any vertebrate common myeloid progenitor. For mammalian CMP known to be CD34-positive, please use the term 'common myeloid progenitor, CD34-positive' (CL_0001059). common myeloid progenitor @@ -5370,6 +5395,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different megakaryocyte/erythrocyte progenitor megakaryocyte/erythroid progenitor cell + + MEPs are reportedly CD19-negative, CD34-negative, CD45RA-negative, CD110-positive, CD117-positive, and SCA1-negative and reportedly express the transcription factors GATA-1 and NF-E2. megakaryocyte-erythroid progenitor cell @@ -5409,6 +5436,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different MESH:D039901 ZFA:0009024 totipotential stem cell + + totipotent stem cell @@ -5436,6 +5465,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different FMA:84782 blast cell + + define using PATO mulit-potent or oligopotent? non-terminally differentiated cell @@ -5459,6 +5490,9 @@ Each of these 3 primitives can be composed to yield a cross-product of different FMA:70335 VHOG:0001529 ZFA:0009025 + + + myoblast @@ -5487,13 +5521,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - - - - - - + A connective tissue cell which secretes an extracellular matrix rich in collagen and other macromolecules. Flattened and irregular in outline with branching processes; appear fusiform or spindle-shaped. BTO:0000452 @@ -5504,6 +5532,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different ZFA:0009026 + + These cells may be vimentin-positive, fibronectin-positive, fsp1-positive, MMP-1-positive, collagen I-positive, collagen III-positive, and alpha-SMA-negative. fibroblast @@ -5547,6 +5577,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different epitheliocyte + + epithelial cell https://www.swissbiopics.org/api/image/Epithelial_cells.svg @@ -5598,6 +5630,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different An epithelial cell that is part of a duct. ZFA:0009372 + + duct epithelial cell @@ -5640,6 +5674,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different ZFA:0009036 + + blood vessel endothelial cell @@ -5663,6 +5699,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different + + non-branched duct epithelial cell @@ -5676,6 +5714,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different ZFA:0009038 + + columnar/cuboidal epithelial cell @@ -5720,6 +5760,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different CALOHA:TS-1249 ZFA:0009039 + + squamous epithelial cell @@ -5764,6 +5806,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different ZFA:0009044 + + blood cell @@ -5807,6 +5851,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different ZFA:0009065 endotheliocyte + + From FMA: 9.07.2001: Endothelial cell has always been classified as a kind of epithelial cell, specifically a squamous cell but that is not true. First, endothelial cell can either be squamous or cuboidal (e.g. high-endothelial cell) and secondly, it has different embryological derivation (mesodermal) than a true epithelial cell (ectodermal and endodermal). The basis for present classification is the fact that it comprises the outermost layer or lining of anatomical structures (location-based) but a better structural basis for the differentia is the cytoskeleton of the cell. Endothelial cell has vimentin filaments while an epithelial cell has keratin filaments. [Onard]. endothelial cell @@ -5837,6 +5883,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different Ectoderm destined to be nervous tissue. ZFA:0009080 neurectoderm cell + + neurectodermal cell @@ -5878,6 +5926,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different mesenchymal stromal cells stem cells, mesenchymal + + Many but not all mesenchymal cells derive from the mesoderm. MSCs are reportedly CD3-negative, CD4-negative, CD5-negative, CD8-negative, CD11a-negative, CD11b-negative, CD14-negative, CD19-negative, CD29-positive, CD31-negative, CD34-negative, CD38-negative, CD40-negative, CD44-positive, CD45-negative, CD49-positive, CD54-positive, CD66b-negative, CD79a-negative, CD80-negative, CD102-positive, CD106-positive, CD117-positive, CD121a-positive, CD121b-positive, CD123-positive, CD124-positive, CD133-negative, CD146-positive, CD166-positive, CD271-positive, B220-negative, Gr1-negative, MHCI-positive, MHCII-negative, SSEA4-negative, sca1-positive, Ter119-negative, and glycophorin A-negative. Cultured MSCs are capable of producing stem cell factor, IL7, IL8, IL11, TGF-beta, cofilin, galectin-1, laminin-receptor 1, cyclophilin A, and MMP-2. mesenchymal stem cell https://github.com/obophenotype/cell-ontology/issues/474 @@ -5981,6 +6031,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different BTO:0003659 FMA:86916 + + secretory cell @@ -6015,6 +6067,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different Any secretory cell that is capable of some protein secretion. + + protein secreting cell @@ -6032,6 +6086,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different A cell whose primary function is to shorten. + + contractile cell @@ -6066,6 +6122,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different muscle fiber myocyte + + muscle cell https://www.swissbiopics.org/api/image/Muscle_cells.svg @@ -6103,16 +6161,24 @@ Each of these 3 primitives can be composed to yield a cross-product of different A non-striated, elongated, spindle-shaped cell found lining the digestive tract, uterus, and blood vessels. They develop from specialized myoblasts (smooth muscle myoblast). + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Smooth muscle cells are a specialized type of muscle cells that are primarily found within the walls of hollow organs such as the intestine, stomach, bladder, uterus, and blood vessels. These cells are an essential component of the autonomic nervous system controling involuntary movements within the body. +Smooth muscle cells play a vital role in many physiological processes due to their unique functionality. They can contract and relax in a slow, sustained, and controlled manner to help modulate the size and shape of the lumens of the organs they surround. For example, in the digestive system, coordinated contraction and relaxation of smooth muscle cells propels food along the gastrointestinal tract - a process known as peristalsis. In the blood vessels, the smooth muscle cells, by contracting or relaxing, either constrict or dilate the vessels, which in turn, help regulate blood flow and pressure. +On a cellular level, smooth muscle cells possess a single, centrally located nucleus and contain an arranged network of actin and myosin filaments, which are the proteins responsible for muscle contraction. Unlike their counterparts in skeletal or cardiac muscles, these cells lack specific contact points for these filaments, hence the lack of visible striations. Furthermore, the contraction of smooth muscle cells is regulated by hormones and neurotransmitters, such as acetylcholine and norepinephrine, adding an additional layer of complex regulation to these highly specialized cells. non-striated muscle cell BTO:0004576 CALOHA:TS-2159 FMA:14072 ZFA:0009118 + https://cellxgene.cziscience.com/cellguide/CL_0000192 SMCs myocytes, smooth muscle smooth muscle fiber + + smooth muscle cell @@ -6124,6 +6190,20 @@ Each of these 3 primitives can be composed to yield a cross-product of different PMID:9315361 http://en.wikipedia.org/wiki/Smooth_muscle_cell + + + + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Smooth muscle cells are a specialized type of muscle cells that are primarily found within the walls of hollow organs such as the intestine, stomach, bladder, uterus, and blood vessels. These cells are an essential component of the autonomic nervous system controling involuntary movements within the body. +Smooth muscle cells play a vital role in many physiological processes due to their unique functionality. They can contract and relax in a slow, sustained, and controlled manner to help modulate the size and shape of the lumens of the organs they surround. For example, in the digestive system, coordinated contraction and relaxation of smooth muscle cells propels food along the gastrointestinal tract - a process known as peristalsis. In the blood vessels, the smooth muscle cells, by contracting or relaxing, either constrict or dilate the vessels, which in turn, help regulate blood flow and pressure. +On a cellular level, smooth muscle cells possess a single, centrally located nucleus and contain an arranged network of actin and myosin filaments, which are the proteins responsible for muscle contraction. Unlike their counterparts in skeletal or cardiac muscles, these cells lack specific contact points for these filaments, hence the lack of visible striations. Furthermore, the contraction of smooth muscle cells is regulated by hormones and neurotransmitters, such as acetylcholine and norepinephrine, adding an additional layer of complex regulation to these highly specialized cells. + DOI:10.1093/ptj/81.11.1810 + https://training.seer.cancer.gov/anatomy/muscular/types.html + https://www.ncbi.nlm.nih.gov/books/NBK10854/ + https://www.ncbi.nlm.nih.gov/books/NBK526125 + https://www.ncbi.nlm.nih.gov/books/NBK556137/ + @@ -6151,6 +6231,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different A cell whose function is determined by the generation or the reception of an electric signal. ZFA:0009128 + + electrically active cell @@ -6175,6 +6257,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different A cell within an epithelial cell sheet whose main function is to act as an internal or external covering for a tissue or an organism. ZFA:0009130 boundary cell + + lining cell @@ -6198,6 +6282,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different A cell whose primary function is to prevent the transport of stuff across compartments. ZFA:0009132 + + barrier cell @@ -6238,6 +6324,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different A cell that moves by its own activities. ZFA:0009136 + + motile cell @@ -6270,6 +6358,9 @@ Each of these 3 primitives can be composed to yield a cross-product of different FMA:72549 ZFA:0009137 ectoderm cell + + + ectodermal cell @@ -6299,11 +6390,18 @@ Each of these 3 primitives can be composed to yield a cross-product of different A cell of the middle germ layer of the embryo. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Mesodermal cells are pluripotent and the most abundant in the human body. They contribute to the development of several structures such as the skeletal muscles, bones, heart and blood vessels, kidneys, gonads, connective tissues, and certain layers of the skin. Hence, the mesoderm is often regarded as an active and diverse layer due to its role in forming many bodily structures. +In embryonic development, these cells are instrumental, contributing to the body's structures through a carefully coordinated sequence of morphogenetic movements. This process forms the complex multicellular architecture of tissues and organs from a simple ball of cells. Without the function of mesodermal cells, the body's integral structures and systems would cease to form correctly, leading to developmental disorders such as axial mesodermal dysplasia complex FMA:72554 ZFA:0009138 + https://cellxgene.cziscience.com/cellguide/CL_0000222 mesoblast mesoderm cell + + mesodermal cell @@ -6312,6 +6410,17 @@ Each of these 3 primitives can be composed to yield a cross-product of different A cell of the middle germ layer of the embryo. MESH:D008648 + + + + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Mesodermal cells are pluripotent and the most abundant in the human body. They contribute to the development of several structures such as the skeletal muscles, bones, heart and blood vessels, kidneys, gonads, connective tissues, and certain layers of the skin. Hence, the mesoderm is often regarded as an active and diverse layer due to its role in forming many bodily structures. +In embryonic development, these cells are instrumental, contributing to the body's structures through a carefully coordinated sequence of morphogenetic movements. This process forms the complex multicellular architecture of tissues and organs from a simple ball of cells. Without the function of mesodermal cells, the body's integral structures and systems would cease to form correctly, leading to developmental disorders such as axial mesodermal dysplasia complex + DOI:10.1016/j.ceb.2019.07.012 + DOI:10.5535/arm.2016.40.1.162 + https://www.sciencedirect.com/topics/biochemistry-genetics-and-molecular-biology/mesoderm + @@ -6336,6 +6445,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different FMA:72555 ZFA:0009139 endoderm cell + + endodermal cell @@ -6419,6 +6530,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different red blood cell + + erythrocyte @@ -6461,7 +6574,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different Any cell that in taxon some Eukaryota. MESH:D005057 - + + eukaryotic cell @@ -6496,6 +6610,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different Any cell that is capable of some oxygen transport. ZFA:0009164 + + oxygen accumulating cell @@ -6528,6 +6644,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different A cell derived from the specialized ectoderm flanking each side of the embryonic neural plate, which after the closure of the neural tube, forms masses of cells that migrate out from the dorsal aspect of the neural tube to spread throughout the body. FMA:86667 ZFA:0007086 + + migratory neural crest cell @@ -6551,6 +6669,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different A mesenchymal cell in embryonic development found in a contracting mass and that gives rise to osteoprogenitors. ZFA:0009166 + + mesenchyme condensation cell @@ -6574,6 +6694,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different A cell of the outer layer of a blastula that gives rise to the ectoderm after gastrulation. + + epiblast cell @@ -6614,6 +6736,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different BTO:0000854 EHDAA2:0004546 FMA:72395 + + animal zygote @@ -6631,6 +6755,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different A cell whose function is determined by its response to an electric signal. ZFA:0009190 + + electrically responsive cell @@ -6654,6 +6780,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different A cell that initiates an electrical signal and passes that signal to another cell. ZFA:0009193 + + electrically signaling cell @@ -6671,6 +6799,44 @@ Each of these 3 primitives can be composed to yield a cross-product of different + + + + + + + + + + + A connective tissue cell of an organ found in the loose connective tissue. + + BTO:0002064 + FMA:83624 + ZFA:0009226 + + + + + + stromal cell + + + + + A connective tissue cell of an organ found in the loose connective tissue. + GOC:tfm + MESH:D017154 + + + + + ZFA:0009226 + + + + + @@ -6693,11 +6859,19 @@ Each of these 3 primitives can be composed to yield a cross-product of different A precursor cell destined to differentiate into smooth muscle myocytes. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +A precursor to the smooth muscle cell, the smooth muscle myoblast, is integral to various body systems, including the cardiovascular, gastrointestinal, and respiratory systems. Smooth muscle myoblasts arise from the differentiation of mesenchymal stem cells, a process tightly regulated by specific genetic factors and environmental signals. Their role extends to myogenesis, particularly in the formation of muscular tissue, especially during embryonic development. +Smooth muscle myoblasts possess distinctive cellular characteristics. In contrast to skeletal muscle myoblasts, they do not fuse to create multinucleated fibers. Instead, they differentiate into individual, uninucleated smooth muscle cells. This differentiation unfolds in two distinct phases: proliferation, marked by rapid division to increase cell numbers, and differentiation, involving structural and functional transformation into mature smooth muscle cells. This intricate process is intricately mediated by various signaling molecules and transcription factors. +Functionally, smooth muscle myoblasts and the mature muscle cells they generate play pivotal roles in various physiological processes. Smooth muscle cells orchestrate involuntary muscle responses and are integral to body systems that regulate blood flow, propel food along the digestive tract, and control airflow in the respiratory tract. These diverse functions underscore the significance of smooth muscle myoblasts in the body's growth, maintenance, and overall function. FMA:84798 ZFA:0009235 + https://cellxgene.cziscience.com/cellguide/CL_0000514 myoblast, smooth muscle satellite cell + + smooth muscle myoblast @@ -6707,6 +6881,18 @@ Each of these 3 primitives can be composed to yield a cross-product of different GOC:tfm MESH:D032390 + + + + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +A precursor to the smooth muscle cell, the smooth muscle myoblast, is integral to various body systems, including the cardiovascular, gastrointestinal, and respiratory systems. Smooth muscle myoblasts arise from the differentiation of mesenchymal stem cells, a process tightly regulated by specific genetic factors and environmental signals. Their role extends to myogenesis, particularly in the formation of muscular tissue, especially during embryonic development. +Smooth muscle myoblasts possess distinctive cellular characteristics. In contrast to skeletal muscle myoblasts, they do not fuse to create multinucleated fibers. Instead, they differentiate into individual, uninucleated smooth muscle cells. This differentiation unfolds in two distinct phases: proliferation, marked by rapid division to increase cell numbers, and differentiation, involving structural and functional transformation into mature smooth muscle cells. This intricate process is intricately mediated by various signaling molecules and transcription factors. +Functionally, smooth muscle myoblasts and the mature muscle cells they generate play pivotal roles in various physiological processes. Smooth muscle cells orchestrate involuntary muscle responses and are integral to body systems that regulate blood flow, propel food along the digestive tract, and control airflow in the respiratory tract. These diverse functions underscore the significance of smooth muscle myoblasts in the body's growth, maintenance, and overall function. + DOI:10.1074/jbc.RA118.001739 + https://www.ncbi.nlm.nih.gov/books/NBK544225/ + https://www.sciencedirect.com/topics/medicine-and-dentistry/smooth-muscle + @@ -6746,6 +6932,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different nerve cell + + These cells are also reportedly CD4-negative and CD200-positive. They are also capable of producing CD40L and IFN-gamma. neuron @@ -6849,7 +7037,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different - @@ -6952,6 +7139,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different pronormoblast + + proerythroblast @@ -6999,7 +7188,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different - @@ -7025,6 +7213,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different early erythroblast early normoblast prorubricyte + + basophilic erythroblast @@ -7096,7 +7286,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different - @@ -7130,6 +7319,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different polychromatic normoblast polychromatophilic normoblast rubricyte + + polychromatophilic erythroblast @@ -7233,6 +7424,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different late erythoblast orthochromatic normoblast pyknotic eto enrythroblast + + orthochromatic erythroblast @@ -7449,6 +7642,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different promegacaryocyte promegakaryocyte + + Lineage negative is described here as CD2-negative, CD3-negative, CD4-negative, CD5-negative, CD8a-negative, CD14-negative, CD19-negative, CD20-negative, CD56-negative, Ly6g-negative, and Ter119-negative. megakaryocyte progenitor cell @@ -7522,6 +7717,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different megalokaryocyte + + Megakaryocytes are reportedly CD181-positive and CD182-positive. megakaryocyte @@ -7607,7 +7804,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different - @@ -7699,6 +7895,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different ZFA:0009252 + + reticulocyte @@ -7749,7 +7947,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different - @@ -7778,6 +7975,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different ZFA:0009258 angioblast chondroplast + + These cells are reportedly CD31-positive, CD34-positive, CD144-positive, CD309-positive, and TAL1-positive. angioblastic mesenchymal cell @@ -7820,6 +8019,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different VHOG:0001534 WBbt:0006796 + + germ cell @@ -7846,6 +8047,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different ZFA:0009387 supportive cell + + supporting cell @@ -7898,6 +8101,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different ZFA:0005238 JG cell renin secreting cell + + kidney granular cell @@ -7936,6 +8141,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different ZFA:0009283 kidney mesangial cell + + Do all of these cells really develop from some mesenchymal stem cell? mesangial cell @@ -7977,7 +8184,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different An endothelial cell that has small pores, or fenestrations, which allow for the efficient exchange of substances between the blood and surrounding tissues. - This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. Fenestrated cells are specialized epithelial cells that are characterized by a distinctive structural feature, fenestrations or tiny pores, which allow an exchange of substances such as fluids, nutrients, and waste between blood vessels and the surrounding tissue environments. These cells are present in various types of epithelial tissues in the human body, including the intestinal tract, endocrine glands, and certain parts of the renal system. There are multiple types of endothelial cell fenestrations. The most common type is found in systemic capillaries of the endocrine tissue (e.g., pancreatic islets), gastrointestinal mucosa, and renal peritubular capillaries. Here, the fenestrated cells have fenestrations in their peripheral cytoplasm with a unique thin and permeable diaphragm that provides a high degree of selectivity, blocking the passage of larger molecules while allowing the free movement of smaller ones. In contrast, other types of fenestrations, such as the discontinuous epithelium of the liver sinusoidal endothelial cells, do not have diaphragms. @@ -7988,6 +8195,8 @@ Overall, fenestrated cells contribute immensely to important physiological proce https://cellxgene.cziscience.com/cellguide/CL_0000666 window cell + + fenestrated endothelial cell @@ -7999,7 +8208,7 @@ Overall, fenestrated cells contribute immensely to important physiological proce - This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. Fenestrated cells are specialized epithelial cells that are characterized by a distinctive structural feature, fenestrations or tiny pores, which allow an exchange of substances such as fluids, nutrients, and waste between blood vessels and the surrounding tissue environments. These cells are present in various types of epithelial tissues in the human body, including the intestinal tract, endocrine glands, and certain parts of the renal system. There are multiple types of endothelial cell fenestrations. The most common type is found in systemic capillaries of the endocrine tissue (e.g., pancreatic islets), gastrointestinal mucosa, and renal peritubular capillaries. Here, the fenestrated cells have fenestrations in their peripheral cytoplasm with a unique thin and permeable diaphragm that provides a high degree of selectivity, blocking the passage of larger molecules while allowing the free movement of smaller ones. In contrast, other types of fenestrations, such as the discontinuous epithelium of the liver sinusoidal endothelial cells, do not have diaphragms. @@ -8040,6 +8249,8 @@ Overall, fenestrated cells contribute immensely to important physiological proce pericyte of Rouget adventitial cell + + Pericytes are CD10-positive, CD13-positive, CD31-negative, CD45-negative, CD106-positive, CD117-negative, CD140-positive, CD144-negative, CD146-positive, CD271-positive, CD325-positive, NG2-positive, RGS5-positive, SMA-positive, and desmin-positive. A subpopulation is CD248-positive. They are also capable of producing angiopoietin 1, CXCL12, TGF-beta, and VEGF-A. pericyte @@ -8102,6 +8313,8 @@ Overall, fenestrated cells contribute immensely to important physiological proce A non-terminally differentiated cell that is capable of developing into a muscle cell. ZFA:0009291 + + muscle precursor cell @@ -8144,6 +8357,8 @@ Overall, fenestrated cells contribute immensely to important physiological proce CALOHA:TS-2086 MESH:D053687 ZFA:0009307 + + somatic stem cell @@ -8189,6 +8404,8 @@ Overall, fenestrated cells contribute immensely to important physiological proce MESH:D022423 ZFA:0009324 + + myeloid cell @@ -8224,6 +8441,8 @@ Overall, fenestrated cells contribute immensely to important physiological proce ZFA:0009325 erythropoietic cell + + Note that in FMA erythropoietic cells are types of nucleated erythrocytes and thus don't include erythrocytes. erythroid lineage cell @@ -8411,6 +8630,8 @@ Overall, fenestrated cells contribute immensely to important physiological proce normoblast + + erythroblast @@ -8508,7 +8729,6 @@ Overall, fenestrated cells contribute immensely to important physiological proce - @@ -8615,6 +8835,8 @@ Overall, fenestrated cells contribute immensely to important physiological proce hemopoietic progenitor cell + + Markers differ between mouse and human. hematopoietic multipotent progenitor cell @@ -8666,6 +8888,8 @@ Overall, fenestrated cells contribute immensely to important physiological proce FMA:70339 ZFA:0009356 + + Note that this is a class of cell types, not an identified single cell type. myeloid lineage restricted progenitor cell @@ -8707,6 +8931,8 @@ Overall, fenestrated cells contribute immensely to important physiological proce haemopoietic cell hemopoietic cell + + hematopoietic cell @@ -8758,6 +8984,8 @@ Overall, fenestrated cells contribute immensely to important physiological proce 2010-01-06T03:43:20Z + + hematopoietic lineage restricted progenitor cell @@ -8802,6 +9030,8 @@ Overall, fenestrated cells contribute immensely to important physiological proce 2010-01-06T03:43:27Z + + This cell type is intended to be compatible with any vertebrate hematopoietic oligopotent progenitor cell. For mammalian hematopoietic oligopotent progenitor cells known to be lineage-negative, please use the term 'hematopoietic oligopotent progenitor cell' (CL_0001060). hematopoietic oligopotent progenitor cell @@ -8842,6 +9072,8 @@ Overall, fenestrated cells contribute immensely to important physiological proce 2010-06-29T03:38:22Z FMA:69074 ZFA:0009385 + + ecto-epithelial cell @@ -8887,6 +9119,8 @@ Overall, fenestrated cells contribute immensely to important physiological proce FMA:69076 ZFA:0009388 epithelial mesenchymal cell + + meso-epithelial cell @@ -8911,13 +9145,21 @@ Overall, fenestrated cells contribute immensely to important physiological proce An endothelial cell of the vascular tree, which includes blood vessels and lymphatic vessels. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Endothelial cells of the vascular tree, commonly referred to as vascular endothelial cells, line the entire circulatory system, from the heart to the smallest capillaries. These cells have a unique, flattened shape, and are tightly bound together, forming a thin layer known as the endothelium. The endothelium is responsible for maintaining the interior surface of blood vessels, and plays a critical role in ensuring the smooth flow of blood. +Vascular endothelial cells act as a semi-permeable membrane, controlling the passage of materials and the transit of white blood cells into and out of the bloodstream. These cells are also involved in blood coagulation. When a blood vessel is damaged, endothelial cells promote clotting to prevent excessive bleeding and facilitate wound healing. Other functions include regulation of blood pressure and blood volume by releasing vasodilators and vasoconstrictors to either widen or constrict blood vessels, accordingly. +Furthermore, the endothelial cells are crucial in the formation of new blood vessels, a process known as angiogenesis. This is particularly important in wound healing and the growth of new tissues during development or after injury. In the context of diseases such as cancer, angiogenesis helps facilitate tumor growth by providing nutrients and oxygen. 2010-08-24T02:06:40Z BTO:0001854 CALOHA:TS-1106 FMA:67755 + https://cellxgene.cziscience.com/cellguide/CL_0002139 vascular endothelial cell cubodial endothelial cell of vascular tree + + These cells are reportedly CD31-positive, CD34-positive, CD144-positive, TAL1-positive. endothelial cell of vascular tree @@ -8929,6 +9171,19 @@ Overall, fenestrated cells contribute immensely to important physiological proce GOC:tfm PMID:12768659 + + + + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Endothelial cells of the vascular tree, commonly referred to as vascular endothelial cells, line the entire circulatory system, from the heart to the smallest capillaries. These cells have a unique, flattened shape, and are tightly bound together, forming a thin layer known as the endothelium. The endothelium is responsible for maintaining the interior surface of blood vessels, and plays a critical role in ensuring the smooth flow of blood. +Vascular endothelial cells act as a semi-permeable membrane, controlling the passage of materials and the transit of white blood cells into and out of the bloodstream. These cells are also involved in blood coagulation. When a blood vessel is damaged, endothelial cells promote clotting to prevent excessive bleeding and facilitate wound healing. Other functions include regulation of blood pressure and blood volume by releasing vasodilators and vasoconstrictors to either widen or constrict blood vessels, accordingly. +Furthermore, the endothelial cells are crucial in the formation of new blood vessels, a process known as angiogenesis. This is particularly important in wound healing and the growth of new tissues during development or after injury. In the context of diseases such as cancer, angiogenesis helps facilitate tumor growth by providing nutrients and oxygen. + DOI:10.1038/s41569-022-00770-1 + DOI:10.1186/s12872-015-0124-z + DOI:10.3389/fphys.2022.863265/full + https://www.sciencedirect.com/topics/medicine-and-dentistry/vascular-endothelial-cell + @@ -8962,6 +9217,8 @@ Overall, fenestrated cells contribute immensely to important physiological proce CALOHA:TS-0112 FMA:67756 + + capillary endothelial cell @@ -9005,6 +9262,8 @@ Overall, fenestrated cells contribute immensely to important physiological proce Goormaghtigh cell polar cushion cells lacis cell + + extraglomerular mesangial cell @@ -9040,7 +9299,6 @@ Overall, fenestrated cells contribute immensely to important physiological proce - @@ -9059,7 +9317,9 @@ Overall, fenestrated cells contribute immensely to important physiological proce BTO:0004632 FMA:70970 + + Glomerular endothelial cells have 60-80 nm fenestrations typically lacking diaphragms in adults but present during embryonic development. Some studies found diaphragms in 2-6% of mature rat glomerular capillaries. Their presence may depend on fixation techniques, developmental stage, or dynamic cell changes. Additionally, these cells help maintain the structural integrity of glomerular capillaries through interactions with the basement membrane and podocytes. glomerular endothelial cell @@ -9106,6 +9366,8 @@ Overall, fenestrated cells contribute immensely to important physiological proce 2010-09-07T03:32:33Z FMA:67513 + + nucleate cell @@ -9144,7 +9406,9 @@ Overall, fenestrated cells contribute immensely to important physiological proce FMA:70981 KUPO:0001055 kidney distal tubule epithelial cell + + epithelial cell of distal tubule @@ -9192,7 +9456,9 @@ Overall, fenestrated cells contribute immensely to important physiological proce KUPO:0001044 kidney proximal tubule epithelial cell + + The vast majority of proximal tubule epithelial cells have a brush border, but there are rare exceptions. epithelial cell of proximal tubule @@ -9240,6 +9506,8 @@ Overall, fenestrated cells contribute immensely to important physiological proce CALOHA:TS-2040 FMA:70333 + + neural cell @@ -9281,6 +9549,8 @@ Overall, fenestrated cells contribute immensely to important physiological proce MESH:D003239 ZFA:0009392 + + connective tissue cell @@ -9305,11 +9575,19 @@ Overall, fenestrated cells contribute immensely to important physiological proce A cell of the embryo. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Embryonic cells in metazoans, which include all multicellular animals, are biological units in their earliest developmental stages from conception until the organism is fully formed. +They are derived from a fertilized egg, which undergoes a series of cell divisions to produce a multicellular organism. During the early phases of embryonic development, these cells exhibit pluripotency, meaning they possess the potential to differentiate into a diverse array of specialized cell types that constitute different body tissues and structures. +The balance between cell proliferation and differentiation in embryonic cells is crucial for successful development. When cells continue to divide without differentiating, overgrowth may occur leading to conditions such as teratomas (tumors of embryonic cells). Conversely, if cell differentiation proceeds at the expense of cell proliferation, developmental anomalies could occur regarding size or mass of the organism or its parts. 2010-09-15T03:39:21Z CALOHA:TS-0263 FMA:82840 WBbt:0007028 ZFA:0007089 + https://cellxgene.cziscience.com/cellguide/CL_0002321 + + embryonic cell (metazoa) @@ -9318,6 +9596,18 @@ Overall, fenestrated cells contribute immensely to important physiological proce A cell of the embryo. FMA:0618947256 + + + + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Embryonic cells in metazoans, which include all multicellular animals, are biological units in their earliest developmental stages from conception until the organism is fully formed. +They are derived from a fertilized egg, which undergoes a series of cell divisions to produce a multicellular organism. During the early phases of embryonic development, these cells exhibit pluripotency, meaning they possess the potential to differentiate into a diverse array of specialized cell types that constitute different body tissues and structures. +The balance between cell proliferation and differentiation in embryonic cells is crucial for successful development. When cells continue to divide without differentiating, overgrowth may occur leading to conditions such as teratomas (tumors of embryonic cells). Conversely, if cell differentiation proceeds at the expense of cell proliferation, developmental anomalies could occur regarding size or mass of the organism or its parts. + DOI:10.1002/iub.1404 + DOI:10.1093/molehr/gan048 + https://www.ncbi.nlm.nih.gov/books/NBK9906/ + @@ -9356,6 +9646,8 @@ Overall, fenestrated cells contribute immensely to important physiological proce FMA:83808 FMA:84791 heart cell + + From Onard of the FMA: Cardiac muscle cell or cardiac myocyte is a striated muscle cell. Cardiocyte on the other hand is any cell in the heart which includes cells other than muscle cells (e.g. endothelial cell of endocardium). Unless there is a consensus among anatomists that cardiocytes refer only to muscle cells, we will treat them as a general class of cells in the heart. cardiocyte @@ -9390,6 +9682,8 @@ Overall, fenestrated cells contribute immensely to important physiological proce KUPO:0001019 ZFA:0009374 + + kidney epithelial cell @@ -9432,6 +9726,8 @@ Overall, fenestrated cells contribute immensely to important physiological proce An epithelial cell of the kidney cortex. KUPO:0001016 + + renal cortical epithelial cell @@ -9462,6 +9758,8 @@ Overall, fenestrated cells contribute immensely to important physiological proce A squamous shaped endothelial cell. 2011-07-08T03:31:25Z + + squamous endothelial cell @@ -9497,6 +9795,8 @@ Overall, fenestrated cells contribute immensely to important physiological proce A cell that is part of a cortex of kidney. 2011-10-25T03:49:41Z + + kidney cortical cell @@ -9508,7 +9808,7 @@ Overall, fenestrated cells contribute immensely to important physiological proce A cuboidal epithelial cell of the kidney which regulates sodium and potassium balance. The activity of sodium and potassium channels on the apical membrane of the cell is regulated by aldosterone and vasopressin. In mammals this cell type is located in the renal collecting duct system. - This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. Renal principal cells are the major cell type in the initial collecting tubule and the cortical and outer medullary collecting ducts, as well as the connecting tubule, in the nephrons of the kidneys. A key function of renal principal cells is the regulation of water balance in the body. These cells express aquaporin-2 (AQP2) water channels, which facilitate the reabsorption of water from the fluid within the renal tubule lumen back into the blood. The translocation of AQP2 to the cell membrane is controlled by the hormone vasopressin: In response to high vasopressin levels, AQP2 moves to the cell membrane, allowing water to pass through effectively and be reabsorbed, therefore concentrating the urine. Conversely, in low vasopressin conditions, AQP2 is removed from the membrane, reducing water reabsorption and diluting the urine. @@ -9516,6 +9816,8 @@ Renal principal cells are also involved in the regulation of sodium and potassiu ZFA:0005322 https://cellxgene.cziscience.com/cellguide/CL_0005009 + + renal principal cell @@ -9527,7 +9829,7 @@ Renal principal cells are also involved in the regulation of sodium and potassiu - This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. Renal principal cells are the major cell type in the initial collecting tubule and the cortical and outer medullary collecting ducts, as well as the connecting tubule, in the nephrons of the kidneys. A key function of renal principal cells is the regulation of water balance in the body. These cells express aquaporin-2 (AQP2) water channels, which facilitate the reabsorption of water from the fluid within the renal tubule lumen back into the blood. The translocation of AQP2 to the cell membrane is controlled by the hormone vasopressin: In response to high vasopressin levels, AQP2 moves to the cell membrane, allowing water to pass through effectively and be reabsorbed, therefore concentrating the urine. Conversely, in low vasopressin conditions, AQP2 is removed from the membrane, reducing water reabsorption and diluting the urine. @@ -9565,6 +9867,8 @@ Renal principal cells are also involved in the regulation of sodium and potassiu 2012-06-27T08:27:35Z ZFA:0007084 + + premigratory neural crest cell @@ -9587,6 +9891,8 @@ Renal principal cells are also involved in the regulation of sodium and potassiu Any muscle cell in which the fibers are not organised into sarcomeres. + + non-striated muscle cell @@ -9604,6 +9910,8 @@ Renal principal cells are also involved in the regulation of sodium and potassiu Any hematopoietic cell that is a precursor of some other hematopoietic cell type. + + hematopoietic precursor cell @@ -9638,6 +9946,8 @@ Renal principal cells are also involved in the regulation of sodium and potassiu A muscle cell that is part of some visceral muscle. FBbt:00005070 + + visceral muscle cell @@ -9676,6 +9986,8 @@ Renal principal cells are also involved in the regulation of sodium and potassiu mesenchyme cell + + mesenchymal cell @@ -9693,6 +10005,8 @@ Renal principal cells are also involved in the regulation of sodium and potassiu ZFA:0005944 + + mural cell @@ -9717,6 +10031,8 @@ Renal principal cells are also involved in the regulation of sodium and potassiu A zygote in a plant or an animal. MESH:D015053 + + zygote @@ -9729,13 +10045,15 @@ Renal principal cells are also involved in the regulation of sodium and potassiu A cell of the neural crest. Neural crest cells are multipotent. Premigratory neural crest cells are found at the neural plate boarder, some of which will undergo ectomesynchymal transition and delamination to form migratory neural crest cells. - This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. Neural crest cells are a group of transient and highly migratory cells that originate from the neuroectoderm during the early stages of embryonic development. They are multipotent cells with an exceptional degree of plasticity, capable of differentiating into various somatic cell types and therefore play a fundamental role in the formation of various organs and tissues, making them critical contributors to the developing embryo. After the initiation of neurulation (the formation of the neural tube) neural crest cells start to undergo epithelial-to-mesenchymal transition and delaminate and migrate from the dorsal neural tube to several regions throughout the embryo. They differentiate into a range of diverse cell types, such as neurons and glial cells of the peripheral nervous system, including sensory and autonomic neurons. They also contribute to the formation of adrenal glands, pigment cells in the skin (melanocytes), cardiac structures, including parts of the heart septum and major arteries, as well as bones and cartilage of the face and skull. Disorders or aberrations in the development or migration of the neural crest cells can lead to serious congenital malformations, such as neurocristopathies, including Hirschsprung disease, neuroblastoma, and neurofibromatosis. https://cellxgene.cziscience.com/cellguide/CL_0011012 + + neural crest cell @@ -9748,7 +10066,7 @@ Disorders or aberrations in the development or migration of the neural crest cel - This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. Neural crest cells are a group of transient and highly migratory cells that originate from the neuroectoderm during the early stages of embryonic development. They are multipotent cells with an exceptional degree of plasticity, capable of differentiating into various somatic cell types and therefore play a fundamental role in the formation of various organs and tissues, making them critical contributors to the developing embryo. After the initiation of neurulation (the formation of the neural tube) neural crest cells start to undergo epithelial-to-mesenchymal transition and delaminate and migrate from the dorsal neural tube to several regions throughout the embryo. They differentiate into a range of diverse cell types, such as neurons and glial cells of the peripheral nervous system, including sensory and autonomic neurons. They also contribute to the formation of adrenal glands, pigment cells in the skin (melanocytes), cardiac structures, including parts of the heart septum and major arteries, as well as bones and cartilage of the face and skull. @@ -9786,6 +10104,8 @@ Disorders or aberrations in the development or migration of the neural crest cel A precursor cell that has a tendency to differentiate into a specific type of cell. They are descendants of stem cells, only they are more constrained in their differentiation potential or capacity for self-renewal, and are often more limited in both senses. + + progenitor cell @@ -9821,6 +10141,8 @@ Disorders or aberrations in the development or migration of the neural crest cel A cell that, by division or terminal differentiation, can give rise to other cell types. + + Work is needed on GO 'cell differentiation' before it is clear whether the equivalent class definition 'native cell' that capable_of some 'cell differentiation' works. Also, may want to consider merging this with non-terminally differentiated cell. precursor cell @@ -9961,8 +10283,16 @@ Disorders or aberrations in the development or migration of the neural crest cel An epithelial cell that is part of the nephron. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Epithelial cells of the nephron form the epithelial lining of the nephron, the functional unit of the kidney that filters the blood to produce urine. Each kidney holds approximately one million nephrons, each of which is composed of several distinct parts, including the renal corpuscle, the proximal tubule, the loop of Henle, and the distal tubule. All sections are lined with highly specialized epithelial cells adapted to perform different functions within the sections of the nephron. +The different epithelial cells of the nephron play crucial roles in the process of filtration, reabsorption, secretion, and excretion, essential tasks for the regulation of body fluid composition and volume. During filtration, the blood is forced through the walls of glomerular capillaries into the Bowman's capsule, where waste products, electrolytes, and water are separated from the blood cells and proteins. As the filtrate then passes through the nephron, epithelial cells of the tubular portion reabsorb useful substances such as glucose, amino acids, and electrolytes, along with most of the water back into the bloodstream. Waste products like urea and creatinine, as well as excess ions and water, remain in the tubule for elimination. +In addition, epithelial cells of the nephron also play a vital part in maintaining the body's acid-base balance by actively secreting hydrogen ions into the urine while reabsorbing bicarbonate from the urine back into the blood. They are also involved in the regulation of blood pressure through the renin-angiotensin-aldosterone system and contribute to erythrocyte production by releasing the hormone erythropoietin in response to low oxygen levels in the blood. Abnormalities or damage in renal epithelial cells often result in impaired kidney function, leading to various renal diseases. FMA:70965 + https://cellxgene.cziscience.com/cellguide/CL_1000449 + + epithelial cell of nephron @@ -9971,6 +10301,20 @@ Disorders or aberrations in the development or migration of the neural crest cel An epithelial cell that is part of the nephron. GOC:tfm + + + + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Epithelial cells of the nephron form the epithelial lining of the nephron, the functional unit of the kidney that filters the blood to produce urine. Each kidney holds approximately one million nephrons, each of which is composed of several distinct parts, including the renal corpuscle, the proximal tubule, the loop of Henle, and the distal tubule. All sections are lined with highly specialized epithelial cells adapted to perform different functions within the sections of the nephron. +The different epithelial cells of the nephron play crucial roles in the process of filtration, reabsorption, secretion, and excretion, essential tasks for the regulation of body fluid composition and volume. During filtration, the blood is forced through the walls of glomerular capillaries into the Bowman's capsule, where waste products, electrolytes, and water are separated from the blood cells and proteins. As the filtrate then passes through the nephron, epithelial cells of the tubular portion reabsorb useful substances such as glucose, amino acids, and electrolytes, along with most of the water back into the bloodstream. Waste products like urea and creatinine, as well as excess ions and water, remain in the tubule for elimination. +In addition, epithelial cells of the nephron also play a vital part in maintaining the body's acid-base balance by actively secreting hydrogen ions into the urine while reabsorbing bicarbonate from the urine back into the blood. They are also involved in the regulation of blood pressure through the renin-angiotensin-aldosterone system and contribute to erythrocyte production by releasing the hormone erythropoietin in response to low oxygen levels in the blood. Abnormalities or damage in renal epithelial cells often result in impaired kidney function, leading to various renal diseases. + DOI:10.1007/978-94-011-2354-9_6 + DOI:10.1007/s004670050586 + DOI:10.1016/B978-0-323-35775-3.00011-4 + DOI:10.1146/annurev-physiol-052521-121841 + DOI:10.1681/ASN.2012010029 + @@ -10001,7 +10345,9 @@ Disorders or aberrations in the development or migration of the neural crest cel Bowmans capsule epithelial cell epithelial cell of Bowman's capsule + + epithelial cell of glomerular capsule @@ -10038,7 +10384,7 @@ Disorders or aberrations in the development or migration of the neural crest cel An epithelial cell that is part of the collecting duct of renal tubule. - This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. Kidney collecting duct epithelial cells are a specialized type of cells that form an integral part of the renal system. Located in the collecting duct system of the kidneys, these cells are responsible for one of the final steps in the process of urine formation, and they are instrumental in the fine tuning of the volume and composition of urine by reabsorbing water and certain solutes back into the bloodstream. These cells express specific channels and carriers that actively and passively transport ions and water. They also have channels on their membranes, such as sodium channels and potassium channels, involved in reabsorbing or secreting these electrolytes depending upon the body's needs. The function of renal collecting duct epithelial cells can be regulated by a variety of hormones, including vasopressin (antidiuretic hormone), which can modulate the ion channels and carriers and hence indirectly influence body fluid homeostasis. @@ -10048,10 +10394,18 @@ Aside from their function in ion and water balance, kidney collecting duct epith https://cellxgene.cziscience.com/cellguide/CL_1000454 epithelial cell of renal collecting tubule + + kidney collecting duct epithelial cell + + + + + true + @@ -10067,7 +10421,7 @@ Aside from their function in ion and water balance, kidney collecting duct epith - This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. Kidney collecting duct epithelial cells are a specialized type of cells that form an integral part of the renal system. Located in the collecting duct system of the kidneys, these cells are responsible for one of the final steps in the process of urine formation, and they are instrumental in the fine tuning of the volume and composition of urine by reabsorbing water and certain solutes back into the bloodstream. These cells express specific channels and carriers that actively and passively transport ions and water. They also have channels on their membranes, such as sodium channels and potassium channels, involved in reabsorbing or secreting these electrolytes depending upon the body's needs. The function of renal collecting duct epithelial cells can be regulated by a variety of hormones, including vasopressin (antidiuretic hormone), which can modulate the ion channels and carriers and hence indirectly influence body fluid homeostasis. @@ -10083,12 +10437,6 @@ Aside from their function in ion and water balance, kidney collecting duct epith epithelial cell of renal collecting tubule FMA:70982 - - - - - true - @@ -10119,6 +10467,8 @@ Aside from their function in ion and water balance, kidney collecting duct epith KUPO:0001022 kidney tubule epithelial cell + + This needs to be further defined as a juxtamedullary nephron. Will request the juxtamedullary nephron tubule class from UBERON. nephron tubule epithelial cell @@ -10156,6 +10506,8 @@ Aside from their function in ion and water balance, kidney collecting duct epith KUPO:0001010 ZFA:0009389 + + kidney cell @@ -10193,7 +10545,9 @@ Aside from their function in ion and water balance, kidney collecting duct epith KUPO:0001013 ZFA:0009390 + + kidney interstitial cell @@ -10229,6 +10583,8 @@ Aside from their function in ion and water balance, kidney collecting duct epith A cell that is part of a renal medulla. KUPO:0001017 ZFA:0009391 + + kidney medulla cell @@ -10269,7 +10625,9 @@ Aside from their function in ion and water balance, kidney collecting duct epith A cell that is part of a renal pelvis. KUPO:0001018 + + kidney pelvis cell @@ -10298,7 +10656,9 @@ Aside from their function in ion and water balance, kidney collecting duct epith A cell that is part of a nephron tubule. KUPO:0001020 + + kidney tubule cell @@ -10328,6 +10688,8 @@ Aside from their function in ion and water balance, kidney collecting duct epith Any kidney epithelial cell that is part of some glomerular epithelium. KUPO:0001023 + + kidney glomerular epithelial cell @@ -10363,7 +10725,9 @@ Aside from their function in ion and water balance, kidney collecting duct epith An epithelial cell that is part of a renal medulla collecting duct. KUPO:0001060 + + kidney medulla collecting duct epithelial cell @@ -10392,7 +10756,9 @@ Aside from their function in ion and water balance, kidney collecting duct epith Any kidney cell that is part of some papillary duct. KUPO:0001064 + + kidney papillary duct principal epithelial cell @@ -10428,7 +10794,9 @@ Aside from their function in ion and water balance, kidney collecting duct epith Any renal cortical epithelial cell that is part of some renal corpuscle. KUPO:0001021 + + kidney corpuscule cell @@ -10466,6 +10834,8 @@ Aside from their function in ion and water balance, kidney collecting duct epith Any kidney tubule cell that is part of some renal cortex tubule. KUPO:0001024 + + kidney cortex tubule cell @@ -10507,7 +10877,9 @@ Aside from their function in ion and water balance, kidney collecting duct epith Any kidney cortical cell that is part of some juxtaglomerular apparatus. KUPO:0001028 juxtaglomerulus cell + + juxtaglomerular complex cell @@ -10551,6 +10923,8 @@ Aside from their function in ion and water balance, kidney collecting duct epith KUPO:0001102 + + kidney interstitial fibroblast @@ -10586,6 +10960,8 @@ Aside from their function in ion and water balance, kidney collecting duct epith Any kidney corpuscule cell that is part of some renal glomerulus. KUPO:0001036 + + glomerular cell @@ -10621,9 +10997,18 @@ Aside from their function in ion and water balance, kidney collecting duct epith Any nephron tubule epithelial cell that is part of some renal connecting tubule. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Kidney connecting tubule epithelial cells are found in collecting duct system of the kidney, specifically in at the interconnection segment between the nephron and the collecting ducts. The epithelial cells lining the connecting tubule are crucial for the journey of filtrate before it empties into urine-collecting ducts and therefore play a critical role in maintaining the body’s fluid and electrolyte balance. +One of the principal functions of connecting tubule epithelial cells involves the selective reabsorption and secretion of various solutes. This reabsorption process includes critical regulatory electrolytes such as sodium ions (Na+), chloride ions (Cl-), and bicarbonate ions (HCO3-), thus playing a role in the regulation of the acid-base homeostasis. Their function also involves the secretion of potassium ions (K+) into the renal tubular fluid. +The connecting tubule epithelial cells are primarily intercalated cells, which can be categorized into two types according to their specific functions: type A intercalated cells, which secrete acid, and the type B intercalated cells, which secrete base (bicarbonate) and reabsorb chloride. By regulating the concentrations of these ions, as well as reabsorption of water, connecting tubule epithelial cells contribute substantively to maintaining the body's electrolyte levels, pH balance, and overall homeostasis. +In addition to intercalating cells, the collecting duct system also has principal cells, which are characterized by the expression of the water channel AQP2. AQP2-expressing cells have also been identified in connecting tubules, but there is some controversy whether these represent a unique cell type as there are some morphologic differences compared with principal cells. KUPO:0001058 + https://cellxgene.cziscience.com/cellguide/CL_1000768 + + kidney connecting tubule epithelial cell @@ -10639,6 +11024,21 @@ Aside from their function in ion and water balance, kidney collecting duct epith Any nephron tubule epithelial cell that is part of some renal connecting tubule. FBC:Autogenerated + + + + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Kidney connecting tubule epithelial cells are found in collecting duct system of the kidney, specifically in at the interconnection segment between the nephron and the collecting ducts. The epithelial cells lining the connecting tubule are crucial for the journey of filtrate before it empties into urine-collecting ducts and therefore play a critical role in maintaining the body’s fluid and electrolyte balance. +One of the principal functions of connecting tubule epithelial cells involves the selective reabsorption and secretion of various solutes. This reabsorption process includes critical regulatory electrolytes such as sodium ions (Na+), chloride ions (Cl-), and bicarbonate ions (HCO3-), thus playing a role in the regulation of the acid-base homeostasis. Their function also involves the secretion of potassium ions (K+) into the renal tubular fluid. +The connecting tubule epithelial cells are primarily intercalated cells, which can be categorized into two types according to their specific functions: type A intercalated cells, which secrete acid, and the type B intercalated cells, which secrete base (bicarbonate) and reabsorb chloride. By regulating the concentrations of these ions, as well as reabsorption of water, connecting tubule epithelial cells contribute substantively to maintaining the body's electrolyte levels, pH balance, and overall homeostasis. +In addition to intercalating cells, the collecting duct system also has principal cells, which are characterized by the expression of the water channel AQP2. AQP2-expressing cells have also been identified in connecting tubules, but there is some controversy whether these represent a unique cell type as there are some morphologic differences compared with principal cells. + DOI:10.1002/cphy.c110052 + DOI:10.1007/s00418-021-02033-5 + DOI:10.1097/MNH.0b013e32820ac850 + DOI:10.1681/ASN.2019040415 + DOI:10.23876/j.krcp.2017.36.4.305 + @@ -10665,9 +11065,17 @@ Aside from their function in ion and water balance, kidney collecting duct epith Any epithelial cell of distal tubule that is part of some distal convoluted tubule. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Kidney distal convoluted tubule epithelial cells, often referred to simply as distal convoluted tubule (DCT) cells, constitute a significant portion of the nephron -- the functional building unit of the kidney involved in filtration and reabsorption of substances from blood. The DCT epithelial cells form lining of the distal convoluted tubule, a segment of the nephron located after the loop of Henle and before the collecting tubule. These cells are characterized by unique morphological features such as small size, low height and fewer microvilli compared to proximal convoluted tubule epithelial cells. +These cells perform a host of vital functions contributing to the regulation of extracellular fluid volume and electrolyte balance, blood pressure and pH. While the DCT is less prominent in water and sodium reabsorption compared to the proximal tubule and the loop of Henle, it plays a crucial role in fine-tuning the process. DCT epithelial cells are responsible for the final adjustments of sodium, potassium and calcium reabsorption, thereby affecting overall fluid and electrolyte balance, blood pressure regulation and bone health. The reabsorption process is regulated by hormones including aldosterone and parathyroid hormone. +The distal convoluted tubule (DCT) also plays a significant role in acid-base homeostasis by secreting protons (H+) into the tubular fluid and reabsorbing bicarbonate ions (HCO3-), thus regulating the pH of the blood. The ability of DCT cells to adjust urine concentration plays a part in maintaining the body’s pH balance and preventing conditions like acidosis or alkalosis. In summary, kidney distal convoluted tubule epithelial cells perform functions that are crucial to maintaining body's homeostasis. KUPO:0001056 + https://cellxgene.cziscience.com/cellguide/CL_1000849 + + kidney distal convoluted tubule epithelial cell @@ -10683,6 +11091,20 @@ Aside from their function in ion and water balance, kidney collecting duct epith Any epithelial cell of distal tubule that is part of some distal convoluted tubule. FBC:Autogenerated + + + + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +Kidney distal convoluted tubule epithelial cells, often referred to simply as distal convoluted tubule (DCT) cells, constitute a significant portion of the nephron -- the functional building unit of the kidney involved in filtration and reabsorption of substances from blood. The DCT epithelial cells form lining of the distal convoluted tubule, a segment of the nephron located after the loop of Henle and before the collecting tubule. These cells are characterized by unique morphological features such as small size, low height and fewer microvilli compared to proximal convoluted tubule epithelial cells. +These cells perform a host of vital functions contributing to the regulation of extracellular fluid volume and electrolyte balance, blood pressure and pH. While the DCT is less prominent in water and sodium reabsorption compared to the proximal tubule and the loop of Henle, it plays a crucial role in fine-tuning the process. DCT epithelial cells are responsible for the final adjustments of sodium, potassium and calcium reabsorption, thereby affecting overall fluid and electrolyte balance, blood pressure regulation and bone health. The reabsorption process is regulated by hormones including aldosterone and parathyroid hormone. +The distal convoluted tubule (DCT) also plays a significant role in acid-base homeostasis by secreting protons (H+) into the tubular fluid and reabsorbing bicarbonate ions (HCO3-), thus regulating the pH of the blood. The ability of DCT cells to adjust urine concentration plays a part in maintaining the body’s pH balance and preventing conditions like acidosis or alkalosis. In summary, kidney distal convoluted tubule epithelial cells perform functions that are crucial to maintaining body's homeostasis. + DOI:10.1002/cphy.c140002 + DOI:10.1007/s40620-021-01032-y + DOI:10.1152/physrev.2000.80.1.277 + DOI:10.1681/ASN.2019040415 + DOI:10.2215/CJN.05920613 + @@ -10715,6 +11137,8 @@ Aside from their function in ion and water balance, kidney collecting duct epith A blood vessel cell that is part of a kidney. KUPO:0001014 + + kidney blood vessel cell @@ -10755,7 +11179,9 @@ Aside from their function in ion and water balance, kidney collecting duct epith Any kidney blood vessel cell that is part of some kidney arterial blood vessel. KUPO:0001029 + + kidney arterial blood vessel cell @@ -10798,7 +11224,9 @@ Aside from their function in ion and water balance, kidney collecting duct epith An endothelial cell that is part of the capillary of the kidney. KUPO:0001030 + + kidney capillary endothelial cell @@ -10827,7 +11255,9 @@ Aside from their function in ion and water balance, kidney collecting duct epith Any kidney blood vessel cell that is part of some renal vein. KUPO:0001031 + + kidney venous blood vessel cell @@ -10869,6 +11299,8 @@ Aside from their function in ion and water balance, kidney collecting duct epith Any nephron tubule epithelial cell that is part of some loop of Henle. KUPO:0001047 + + kidney loop of Henle epithelial cell @@ -10911,7 +11343,9 @@ Aside from their function in ion and water balance, kidney collecting duct epith Any kidney loop of Henle epithelial cell that is part of some ascending limb of loop of Henle. KUPO:0001048 + + kidney loop of Henle ascending limb epithelial cell @@ -10951,8 +11385,16 @@ Aside from their function in ion and water balance, kidney collecting duct epith Any kidney loop of Henle epithelial cell that is part of some descending limb of loop of Henle. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +The kidney loop of Henle descending limb epithelial cells are highly specialized cells that play a crucial role in maintaining the body's salt and water balance. These cells line the descending limb of the loop of Henle, which is a portion of the renal tubule located in the kidneys, an organ responsible for filtering waste products, ions and extra water from the blood and converting them into urine. However, the descending limb epithelial cells are specifically involved in the countercurrent multiplication system, a mechanism to concentrate urine that involves both active and passive transport processes. +These cells are notably permeable to water but relatively impermeable to solutes, a characteristic that dramatically influences the osmotic gradient in the renal medulla. As filtrate initially descends down the loop of Henle, water gets drawn out due to the increasing osmotic gradient, thereby concentrating the filtrate. Additionally, these epithelial cells are exceptionally thin walled, allowing water to freely diffuse across the membrane. +Furthermore, the kidney loop of Henle descending limb epithelial cells are inextricably linked to the functioning of numerous diuretic drugs, which work by blocking the reabsorption of water and certain electrolytes in the kidneys, leading to increased urine production to rid the body of excess fluids. KUPO:0001053 + https://cellxgene.cziscience.com/cellguide/CL_1001021 + + kidney loop of Henle descending limb epithelial cell @@ -10967,6 +11409,18 @@ Aside from their function in ion and water balance, kidney collecting duct epith Any kidney loop of Henle epithelial cell that is part of some descending limb of loop of Henle. FBC:Autogenerated + + + + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional. + +The kidney loop of Henle descending limb epithelial cells are highly specialized cells that play a crucial role in maintaining the body's salt and water balance. These cells line the descending limb of the loop of Henle, which is a portion of the renal tubule located in the kidneys, an organ responsible for filtering waste products, ions and extra water from the blood and converting them into urine. However, the descending limb epithelial cells are specifically involved in the countercurrent multiplication system, a mechanism to concentrate urine that involves both active and passive transport processes. +These cells are notably permeable to water but relatively impermeable to solutes, a characteristic that dramatically influences the osmotic gradient in the renal medulla. As filtrate initially descends down the loop of Henle, water gets drawn out due to the increasing osmotic gradient, thereby concentrating the filtrate. Additionally, these epithelial cells are exceptionally thin walled, allowing water to freely diffuse across the membrane. +Furthermore, the kidney loop of Henle descending limb epithelial cells are inextricably linked to the functioning of numerous diuretic drugs, which work by blocking the reabsorption of water and certain electrolytes in the kidneys, leading to increased urine production to rid the body of excess fluids. + DOI:10.1007/s00360-018-1164-3 + DOI:10.1146/annurev-physiol-021113-170350 + DOI:10.1152/advan.00227.2022 + @@ -10995,6 +11449,8 @@ Aside from their function in ion and water balance, kidney collecting duct epith KUPO:0001012 Wikipedia:Kidney_collecting_duct_cell + + kidney collecting duct cell @@ -11020,6 +11476,8 @@ Aside from their function in ion and water balance, kidney collecting duct epith KUPO:0001104 + + renal interstitial pericyte @@ -11057,6 +11515,9 @@ Aside from their function in ion and water balance, kidney collecting duct epith 2014-06-04T15:07:42Z CL:2000008 + + + microvascular endothelial cell @@ -11091,6 +11552,8 @@ Aside from their function in ion and water balance, kidney collecting duct epith Any cell that is located within the interstitium between the cells most prominent in defining a given tissue. "Interstitial cell" is a morphological term and refers to a variety of cells with differing origins and phenotypes. 2022-11-30T14:35:08Z + + interstitial cell @@ -11126,6 +11589,9 @@ Aside from their function in ion and water balance, kidney collecting duct epith A cell that is adjacent to a vessel. A perivascular cell plays a crucial role in maintaining vascular function and tissue homeostasis. This cell type regulates vessel integrity and flow dynamics. 2023-08-22T13:40:28Z + + + perivascular cell @@ -11172,7 +11638,6 @@ Aside from their function in ion and water balance, kidney collecting duct epith Progression through the phases of the mitotic cell cycle, the most common eukaryotic cell cycle, which canonically comprises four successive phases called G1, S, G2, and M and includes replication of the genome and the subsequent segregation of chromosomes into daughter cells. In some variant cell cycles nuclear replication or nuclear division may not be followed by cell division, or G1 and G2 phases may be absent. - GO:0007067 Wikipedia:Mitosis biological_process mitosis @@ -11243,9 +11708,6 @@ Aside from their function in ion and water balance, kidney collecting duct epith The ordered and organized complex of DNA, protein, and sometimes RNA, that forms the chromosome. https://github.com/geneontology/go-ontology/issues/28301 - GO:0000789 - GO:0000790 - GO:0005717 NIF_Subcellular:sao1615953555 cytoplasmic chromatin nuclear chromatin @@ -11271,8 +11733,6 @@ Aside from their function in ion and water balance, kidney collecting duct epith A compact and highly condensed form of chromatin that is refractory to transcription. https://github.com/geneontology/go-ontology/issues/22355 - GO:0005720 - GO:0035328 NIF_Subcellular:sao581845896 Wikipedia:Heterochromatin transcriptionally inactive chromatin @@ -11608,7 +12068,6 @@ Aside from their function in ion and water balance, kidney collecting duct epith The formation of a tube from the flat layer of ectodermal cells known as the neural plate. This will give rise to the central nervous system. - GO:0001679 Wikipedia:Neurulation neural tube morphogenesis neurulation @@ -12266,7 +12725,6 @@ Aside from their function in ion and water balance, kidney collecting duct epith A location, relative to cellular compartments and structures, occupied by a macromolecular machine. There are three types of cellular components described in the gene ontology: (1) the cellular anatomical entity where a gene product carries out a molecular function (e.g., plasma membrane, cytoskeleton) or membrane-enclosed compartments (e.g., mitochondrion); (2) virion components, where viral proteins act, and (3) the stable macromolecular complexes of which gene product are parts (e.g., the clathrin complex). https://github.com/geneontology/go-ontology/issues/17729 - GO:0008372 NIF_Subcellular:sao1337158144 cell or subcellular entity cellular component @@ -12364,32 +12822,32 @@ Aside from their function in ion and water balance, kidney collecting duct epith - - + + A protein complex consisting of three collagen chains assembled into a left-handed triple helix. These trimers typically assemble into higher order structures. Wikipedia:Collagen cellular_component GO:0005581 collagen trimer - + - + - + PMID:12382326 - + PMID:12382326 @@ -12432,8 +12890,6 @@ Aside from their function in ion and water balance, kidney collecting duct epith A collagen-containing extracellular matrix consisting of a thin layer of dense material found in various animal tissues interposed between the cells and the adjacent connective tissue. It consists of the basal lamina plus an associated layer of reticulin fibers. - GO:0005605 - GO:0008003 Wikipedia:Basement_membrane cellular_component basal lamina @@ -12699,7 +13155,12 @@ Aside from their function in ion and water balance, kidney collecting duct epith - + + + + + + @@ -12707,7 +13168,6 @@ Aside from their function in ion and water balance, kidney collecting duct epith An intracellular organelle, about 200 A in diameter, consisting of RNA and protein. It is the site of protein biosynthesis resulting from translation of messenger RNA (mRNA). It consists of two subunits, one large and one small, each containing only protein and RNA. Both the ribosome and its subunits are characterized by their sedimentation coefficients, expressed in Svedberg units (symbol: S). Hence, the prokaryotic ribosome (70S) comprises a large (50S) subunit and a small (30S) subunit, while the eukaryotic ribosome (80S) comprises a large (60S) subunit and a small (40S) subunit. Two sites on the ribosomal large subunit are involved in translation, namely the aminoacyl site (A site) and peptidyl site (P site). Ribosomes from prokaryotes, eukaryotes, mitochondria, and chloroplasts have characteristically distinct ribosomal proteins. - GO:0033279 NIF_Subcellular:sao1429207766 Wikipedia:Ribosome free ribosome @@ -12760,8 +13220,6 @@ Aside from their function in ion and water balance, kidney collecting duct epith The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins. - GO:0005887 - GO:0005904 juxtamembrane NIF_Subcellular:sao1663586795 Wikipedia:Cell_membrane @@ -12877,9 +13335,6 @@ Aside from their function in ion and water balance, kidney collecting duct epith The cellular metabolic process in which a protein is formed, using the sequence of a mature mRNA or circRNA molecule to specify the sequence of amino acids in a polypeptide chain. Translation is mediated by the ribosome, and begins with the formation of a ternary complex between aminoacylated initiator methionine tRNA, GTP, and initiation factor 2, which subsequently associates with the small subunit of the ribosome and an mRNA or circRNA. Translation ends with the release of a polypeptide chain from the ribosome. - GO:0006416 - GO:0006453 - GO:0043037 Wikipedia:Translation_(genetics) protein anabolism protein biosynthesis @@ -12912,7 +13367,7 @@ Aside from their function in ion and water balance, kidney collecting duct epith - + @@ -12926,8 +13381,6 @@ Aside from their function in ion and water balance, kidney collecting duct epith The process preceding formation of the peptide bond between the first two amino acids of a protein. This includes the formation of a complex of the ribosome, mRNA or circRNA, and an initiation complex that contains the first aminoacyl-tRNA. - GO:0006440 - GO:0006454 biopolymerisation biopolymerization protein synthesis initiation @@ -12957,8 +13410,6 @@ Aside from their function in ion and water balance, kidney collecting duct epith The successive addition of amino acid residues to a nascent polypeptide chain during protein biosynthesis. - GO:0006442 - GO:0006455 protein synthesis elongation translation elongation biological_process @@ -12986,8 +13437,6 @@ Aside from their function in ion and water balance, kidney collecting duct epith The process resulting in the release of a polypeptide chain from the ribosome, usually in response to a termination codon (UAA, UAG, or UGA in the universal genetic code). - GO:0006443 - GO:0006456 protein synthesis termination translation termination translational complex disassembly @@ -13011,11 +13460,7 @@ Aside from their function in ion and water balance, kidney collecting duct epith The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter or a transporter complex, a pore or a motor protein. https://github.com/geneontology/go-ontology/issues/20292 - jl 2012-12-13T16:25:32Z - GO:0015457 - GO:0015460 - GO:0044765 biological_process single-organism transport GO:0006810 @@ -13114,8 +13559,6 @@ Aside from their function in ion and water balance, kidney collecting duct epith A programmed cell death process which begins when a cell receives an internal (e.g. DNA damage) or external signal (e.g. an extracellular death ligand), and proceeds through a series of biochemical events (signaling pathway phase) which trigger an execution phase. The execution phase is the last step of an apoptotic process, and is typically characterized by rounding-up of the cell, retraction of pseudopodes, reduction of cellular volume (pyknosis), chromatin condensation, nuclear fragmentation (karyorrhexis), plasma membrane blebbing and fragmentation of the cell into apoptotic bodies. When the execution phase is completed, the cell has died. - GO:0006917 - GO:0008632 cell suicide cellular suicide Wikipedia:Apoptosis @@ -13258,9 +13701,7 @@ Aside from their function in ion and water balance, kidney collecting duct epith A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of an organelle within a cell. An organelle is an organized structure of distinctive morphology and function. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton. Excludes the plasma membrane. https://github.com/geneontology/go-ontology/issues/27189 - jl 2013-12-19T15:25:51Z - GO:1902589 organelle organisation single organism organelle organization biological_process @@ -13393,11 +13834,6 @@ Aside from their function in ion and water balance, kidney collecting duct epith The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell. - GO:0023014 - GO:0023015 - GO:0023016 - GO:0023033 - GO:0023045 Wikipedia:Signal_transduction signaling cascade signalling cascade @@ -13540,7 +13976,6 @@ Aside from their function in ion and water balance, kidney collecting duct epith - GO:0009552 biological_process gametogenesis GO:0007276 @@ -13790,7 +14225,6 @@ Aside from their function in ion and water balance, kidney collecting duct epith The flow of blood through the body of an animal, enabling the transport of nutrients to the tissues and the removal of waste products. - GO:0070261 biological_process hemolymph circulation GO:0008015 @@ -13830,9 +14264,6 @@ Aside from their function in ion and water balance, kidney collecting duct epith Any process in which a protein is transported to, or maintained in, a specific location. https://github.com/geneontology/go-ontology/issues/23112 - GO:0008105 - GO:0016249 - GO:0034613 cellular protein localisation cellular protein localization protein localisation @@ -13884,11 +14315,7 @@ Aside from their function in ion and water balance, kidney collecting duct epith A biological process is the execution of a genetically-encoded biological module or program. It consists of all the steps required to achieve the specific biological objective of the module. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence. https://github.com/geneontology/go-ontology/issues/24968 - jl 2012-09-19T15:05:24Z - GO:0000004 - GO:0007582 - GO:0044699 Wikipedia:Biological_process biological process physiological process @@ -13918,21 +14345,15 @@ Aside from their function in ion and water balance, kidney collecting duct epith - + - The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation. + A cellular process consisting of the biochemical pathways by which a living organism transforms chemical substances. This includes including anabolism (biosynthetic process) and catabolism (catabolic process). Metabolic processes includes the transformation of small molecules, as well macromolecular processes such as DNA repair and replication, protein synthesis and degradation. https://github.com/geneontology/go-ontology/issues/26424 - jl + https://github.com/geneontology/go-ontology/issues/28932 2012-10-17T15:46:40Z - GO:0044236 - GO:0044710 Wikipedia:Metabolism metabolism - metabolic process resulting in cell growth - metabolism resulting in cell growth - multicellular organism metabolic process biological_process - single-organism metabolic process GO:0008152 @@ -13947,7 +14368,7 @@ Aside from their function in ion and water balance, kidney collecting duct epith - The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation. + A cellular process consisting of the biochemical pathways by which a living organism transforms chemical substances. This includes including anabolism (biosynthetic process) and catabolism (catabolic process). Metabolic processes includes the transformation of small molecules, as well macromolecular processes such as DNA repair and replication, protein synthesis and degradation. GOC:go_curators ISBN:0198547684 @@ -14013,11 +14434,9 @@ Aside from their function in ion and water balance, kidney collecting duct epith - The chemical reactions and pathways resulting in the formation of substances; typically the energy-requiring part of metabolism in which simpler substances are transformed into more complex ones. - jl + A cellular process consisting of the biochemical pathways by which a living organism synthesizes chemical substances. This typically represents the energy-requiring part of metabolism in which simpler substances are transformed into more complex ones. + https://github.com/geneontology/go-ontology/issues/28932 2012-10-17T15:52:18Z - GO:0044274 - GO:0044711 formation Wikipedia:Anabolism anabolism @@ -14036,7 +14455,7 @@ Aside from their function in ion and water balance, kidney collecting duct epith - The chemical reactions and pathways resulting in the formation of substances; typically the energy-requiring part of metabolism in which simpler substances are transformed into more complex ones. + A cellular process consisting of the biochemical pathways by which a living organism synthesizes chemical substances. This typically represents the energy-requiring part of metabolism in which simpler substances are transformed into more complex ones. GOC:curators ISBN:0198547684 @@ -14046,13 +14465,12 @@ Aside from their function in ion and water balance, kidney collecting duct epith + - The chemical reactions and pathways resulting in the formation of a macromolecule, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass. https://github.com/geneontology/go-ontology/issues/15249 https://github.com/geneontology/go-ontology/issues/25418 https://github.com/geneontology/go-ontology/issues/27189 - GO:0043284 biopolymer biosynthetic process macromolecule anabolism macromolecule biosynthesis @@ -14098,8 +14516,6 @@ Aside from their function in ion and water balance, kidney collecting duct epith The controlled release of proteins from a cell. - GO:0045166 - GO:0045731 glycoprotein secretion protein secretion during cell fate commitment protein secretion resulting in cell fate commitment @@ -14223,7 +14639,6 @@ Aside from their function in ion and water balance, kidney collecting duct epith The process whose specific outcome is the progression of an embryo from its formation until the end of its embryonic life stage. The end of the embryonic stage is organism-specific. For example, for mammals, the process would begin with zygote formation and end with birth. For insects, the process would begin at zygote formation and end with larval hatching. For plant zygotic embryos, this would be from zygote formation to the end of seed dormancy. For plant vegetative embryos, this would be from the initial determination of the cell or group of cells to form an embryo until the point when the embryo becomes independent of the parent plant. - GO:0009795 embryogenesis and morphogenesis Wikipedia:Embryogenesis embryogenesis @@ -14364,11 +14779,7 @@ Aside from their function in ion and water balance, kidney collecting duct epith Any process that is carried out at the cellular level, but not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level. - jl 2012-12-11T16:56:55Z - GO:0008151 - GO:0044763 - GO:0050875 cell physiology cellular physiological process cell growth and/or maintenance @@ -14437,7 +14848,6 @@ Aside from their function in ion and water balance, kidney collecting duct epith A process which begins when a cell receives an internal or external signal and activates a series of biochemical events (signaling pathway). The process ends with the death of the cell. https://github.com/geneontology/go-ontology/issues/24835 - GO:0016244 regulated cell death Wikipedia:Programmed_cell_death caspase-independent cell death @@ -14487,7 +14897,6 @@ Aside from their function in ion and water balance, kidney collecting duct epith The directed movement of proteins into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. - GO:0015831 enzyme transport biological_process GO:0015031 @@ -14549,9 +14958,6 @@ Aside from their function in ion and water balance, kidney collecting duct epith A lipid bilayer along with all the proteins and protein complexes embedded in it and attached to it. 2014-03-06T11:37:54Z - GO:0016021 - GO:0098589 - GO:0098805 Wikipedia:Biological_membrane Wikipedia:Transmembrane_protein integral component of membrane @@ -14610,8 +15016,6 @@ Aside from their function in ion and water balance, kidney collecting duct epith A process that results in the assembly, arrangement of constituent parts, or disassembly of a cellular component. - GO:0044235 - GO:0071842 cell organisation cellular component organisation at cellular level cellular component organisation in other organism @@ -14855,9 +15259,6 @@ Aside from their function in ion and water balance, kidney collecting duct epith The chemical reactions and pathways involving a protein. Includes protein modification. https://github.com/geneontology/go-ontology/issues/23112 https://github.com/geneontology/go-ontology/issues/27189 - GO:0006411 - GO:0044267 - GO:0044268 Wikipedia:Protein_metabolism cellular protein metabolic process cellular protein metabolism @@ -15021,7 +15422,6 @@ Aside from their function in ion and water balance, kidney collecting duct epith A cellular process that results in the breakdown of a cellular component. https://github.com/geneontology/go-ontology/issues/27189 - GO:0071845 cell structure disassembly cellular component disassembly at cellular level biological_process @@ -15046,9 +15446,7 @@ Aside from their function in ion and water balance, kidney collecting duct epith A biological process that directly contributes to the process of producing new individuals by one or two organisms. The new individuals inherit some proportion of their genetic material from the parent or parents. https://github.com/geneontology/go-ontology/issues/27054 - jl 2012-09-19T15:56:06Z - GO:0044702 Wikipedia:Reproduction biological_process single organism reproductive process @@ -15139,7 +15537,6 @@ Aside from their function in ion and water balance, kidney collecting duct epith The aggregation, arrangement and bonding together of a cellular component. - GO:0071844 cell structure assembly cellular component assembly at cellular level biological_process @@ -15242,10 +15639,7 @@ Aside from their function in ion and water balance, kidney collecting duct epith The entirety of a process in which information is transmitted within a biological system. This process begins with an active signal and ends when a cellular response has been triggered. - jl 2010-02-16T09:30:50Z - GO:0023046 - GO:0044700 biological signaling signaling process signalling @@ -15699,7 +16093,6 @@ Aside from their function in ion and water balance, kidney collecting duct epith The progressive compaction of dispersed interphase chromatin into threadlike chromosomes prior to mitotic or meiotic nuclear division, or during apoptosis, in eukaryotic cells. - GO:0000068 DNA condensation eukaryotic chromosome condensation nuclear chromosome condensation @@ -15824,7 +16217,6 @@ Aside from their function in ion and water balance, kidney collecting duct epith A structure lying external to one or more cells, which provides structural support, biochemical or biomechanical cues for cells or tissues. - GO:0005578 NIF_Subcellular:nlx_subcell_20090513 Wikipedia:Extracellular_matrix proteinaceous extracellular matrix @@ -15903,7 +16295,6 @@ Aside from their function in ion and water balance, kidney collecting duct epith Any small, fluid-filled, spherical organelle enclosed by membrane. - GO:0031988 NIF_Subcellular:sao221389602 Wikipedia:Vesicle_(biology) cellular_component @@ -16032,10 +16423,7 @@ Aside from their function in ion and water balance, kidney collecting duct epith - jl 2012-09-19T16:07:47Z - GO:0044707 - GO:0050874 organismal physiological process biological_process single-multicellular organism process @@ -16062,9 +16450,7 @@ Aside from their function in ion and water balance, kidney collecting duct epith A biological process whose specific outcome is the progression of an integrated living unit: an anatomical structure (which may be a subcellular structure, cell, tissue, or organ), or organism over time from an initial condition to a later condition. - jl 2012-12-19T12:21:31Z - GO:0044767 development biological_process single-organism developmental process @@ -16128,9 +16514,6 @@ Aside from their function in ion and water balance, kidney collecting duct epith The disaggregation of a protein-containing macromolecular complex into its constituent components. https://github.com/geneontology/go-ontology/issues/22580 - GO:0034623 - GO:0043241 - GO:0043624 protein complex disassembly biological_process cellular macromolecule complex disassembly @@ -16152,10 +16535,14 @@ Aside from their function in ion and water balance, kidney collecting duct epith - + + + + + + A stable assembly of two or more macromolecules, i.e. proteins, nucleic acids, carbohydrates or lipids, in which at least one component is a protein and the constituent parts function together. - GO:0043234 macromolecular complex macromolecule complex protein containing complex @@ -16265,7 +16652,6 @@ Aside from their function in ion and water balance, kidney collecting duct epith A process in which a monoatomic ion is transported across a membrane. Monatomic ions (also called simple ions) are ions consisting of exactly one atom. - GO:0099131 ion transmembrane transport ion membrane transport transmembrane ion transport @@ -16448,7 +16834,6 @@ Aside from their function in ion and water balance, kidney collecting duct epith The directed movement of a protein to a specific location within the extracellular region. - bf 2010-11-09T10:25:08Z establishment of protein localisation in extracellular region establishment of protein localization in extracellular region @@ -16480,7 +16865,6 @@ Aside from their function in ion and water balance, kidney collecting duct epith - bf 2011-12-12T10:53:24Z GEnC fenestration glomerular endothelial cell fenestration @@ -16607,9 +16991,6 @@ Aside from their function in ion and water balance, kidney collecting duct epith Any biological process involved in the maintenance of an internal steady state. - GO:0032844 - GO:0032845 - GO:0032846 homeostasis activation of homeostatic process inhibition of homeostatic process @@ -16741,9 +17122,6 @@ Aside from their function in ion and water balance, kidney collecting duct epith The chemical reactions and pathways involving macromolecules, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass. https://github.com/geneontology/go-ontology/issues/26424 - GO:0034960 - GO:0043283 - GO:0044259 biopolymer metabolic process macromolecule metabolism organismal macromolecule metabolism @@ -16841,14 +17219,17 @@ Aside from their function in ion and water balance, kidney collecting duct epith Organized structure of distinctive morphology and function, not bounded by a lipid bilayer membrane. Includes ribosomes, the cytoskeleton and chromosomes. https://github.com/geneontology/go-ontology/issues/21881 https://github.com/geneontology/go-ontology/issues/28153 + https://github.com/geneontology/go-ontology/issues/29106 NIF_Subcellular:sao1456184038 + membrane-less organelle + non-membrane-bounded organelle non-membrane-enclosed organelle cellular_component biological condensate GO:0043228 - non-membrane-bounded organelle + membraneless organelle @@ -16984,11 +17365,13 @@ Aside from their function in ion and water balance, kidney collecting duct epith Organized structure of distinctive morphology and function, not bounded by a lipid bilayer membrane and occurring within the cell. Includes ribosomes, the cytoskeleton and chromosomes. + https://github.com/geneontology/go-ontology/issues/29106 + intracellular non-membrane-bounded organelle intracellular non-membrane-enclosed organelle cellular_component GO:0043232 - intracellular non-membrane-bounded organelle + intracellular membraneless organelle @@ -17059,11 +17442,7 @@ Aside from their function in ion and water balance, kidney collecting duct epith Any process in which macromolecules aggregate, disaggregate, or are modified, resulting in the formation, disassembly, or alteration of a protein complex. https://github.com/geneontology/go-ontology/issues/22580 - mah 2010-09-08T10:01:42Z - GO:0034600 - GO:0034621 - GO:0071822 protein complex subunit organisation protein complex subunit organization biological_process @@ -17133,7 +17512,6 @@ Aside from their function in ion and water balance, kidney collecting duct epith A process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of a cellular component. Includes biosynthesis of constituent macromolecules, and those macromolecular modifications that are involved in synthesis or assembly of the cellular component. https://github.com/geneontology/go-ontology/issues/27194 - GO:0071843 cellular component biogenesis at cellular level biological_process GO:0044085 @@ -17162,7 +17540,6 @@ Aside from their function in ion and water balance, kidney collecting duct epith A ribonucleoprotein complex that contains aminoacylated initiator methionine tRNA, GTP, and initiation factor 2 (either eIF2 in eukaryotes, or IF2 in prokaryotes). In prokaryotes, fMet-tRNA (initiator) is used rather than Met-tRNA (initiator). - jl 2009-10-22T02:38:55Z translation initiation (ternary) complex Met-tRNA/eIF2.GTP ternary complex @@ -17179,35 +17556,6 @@ Aside from their function in ion and water balance, kidney collecting duct epith - - - - - - The chemical reactions and pathways by which individual cells transform chemical substances. - cellular metabolism - biological_process - intermediary metabolism - GO:0044237 - - This term should not be used for direct annotation. It should be possible to make a more specific annotation to one of the children of this term. - cellular metabolic process - - - - - The chemical reactions and pathways by which individual cells transform chemical substances. - GOC:go_curators - - - - - intermediary metabolism - GOC:mah - - - - @@ -17234,32 +17582,6 @@ Aside from their function in ion and water balance, kidney collecting duct epith - - - - - - The chemical reactions and pathways resulting in the formation of substances, carried out by individual cells. - https://github.com/geneontology/go-ontology/issues/27052 - cellular anabolism - cellular biosynthesis - cellular formation - cellular synthesis - biological_process - GO:0044249 - - This term should not be used for direct annotation. It should be possible to make a more specific annotation to one of the children of this term. - cellular biosynthetic process - - - - - The chemical reactions and pathways resulting in the formation of substances, carried out by individual cells. - GOC:jl - - - - @@ -17588,7 +17910,6 @@ Aside from their function in ion and water balance, kidney collecting duct epith The process in which anatomical structures are generated and organized during the embryonic phase. The embryonic phase begins with zygote formation. The end of the embryonic phase is organism-specific. For example, it would be at birth for mammals, larval hatching for insects and seed dormancy in plants. - GO:0048828 embryonic anatomical structure morphogenesis biological_process GO:0048598 @@ -17963,7 +18284,6 @@ Aside from their function in ion and water balance, kidney collecting duct epith Any process that modulates the frequency, rate or extent of a biological process. Biological processes are regulated by many means; examples include the control of gene expression, protein modification or interaction with a protein or substrate molecule. - GO:0050791 regulation of physiological process biological_process GO:0050789 @@ -18004,7 +18324,6 @@ Aside from their function in ion and water balance, kidney collecting duct epith Any process that modulates the frequency, rate or extent of a cellular process, any of those that are carried out at the cellular level, but are not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level. - GO:0051244 regulation of cellular physiological process biological_process GO:0050794 @@ -18154,7 +18473,6 @@ Aside from their function in ion and water balance, kidney collecting duct epith Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus. The process begins with detection of the stimulus and ends with a change in state or activity or the cell or organism. - GO:0051869 physiological response to stimulus biological_process GO:0050896 @@ -18184,9 +18502,7 @@ Aside from their function in ion and water balance, kidney collecting duct epith Any process in which a cell, a substance, or a cellular entity, such as a protein complex or organelle, is transported, tethered to or otherwise maintained in a specific location. In the case of substances, localization may also be achieved via selective degradation. https://github.com/geneontology/go-ontology/issues/27052 - jl 2013-12-18T13:51:04Z - GO:1902578 establishment and maintenance of localization establishment and maintenance of position localisation @@ -18316,9 +18632,6 @@ Aside from their function in ion and water balance, kidney collecting duct epith A process that is carried out at the cellular level that results in the assembly, arrangement of constituent parts, or disassembly of chromosomes, structures composed of a very long molecule of DNA and associated proteins that carries hereditary information. This term covers covalent modifications at the molecular level as well as spatial relationships among the major components of a chromosome. https://github.com/geneontology/go-ontology/issues/22811 https://github.com/geneontology/go-ontology/issues/4585 - GO:0006323 - GO:0007001 - GO:0051277 DNA condensation chromosome organisation DNA packaging @@ -18382,9 +18695,7 @@ Aside from their function in ion and water balance, kidney collecting duct epith A cellular localization process whereby a substance or cellular entity, such as a protein complex or organelle, is transported to, and/or maintained in, a specific location within a cell including the localization of substances or cellular entities to the cell membrane. https://github.com/geneontology/go-ontology/issues/27189 - jl 2013-12-18T14:04:32Z - GO:1902580 cellular localisation establishment and maintenance of cellular localization establishment and maintenance of localization in cell or cell membrane @@ -18466,9 +18777,7 @@ Aside from their function in ion and water balance, kidney collecting duct epith The process in which a solute is transported across a lipid bilayer, from one side of a membrane to the other. - tb 2015-10-21T13:22:47Z - GO:0090662 membrane transport ATP hydrolysis coupled transmembrane transport biological_process @@ -18574,7 +18883,6 @@ Aside from their function in ion and water balance, kidney collecting duct epith The process in which the anatomical structures of a tube are generated and organized from an epithelium. Epithelial tubes transport gases, liquids and cells from one site to another and form the basic structure of many organs and tissues, with tube shape and organization varying from the single-celled excretory organ in Caenorhabditis elegans to the branching trees of the mammalian kidney and insect tracheal system. - dph 2009-04-28T09:33:36Z biological_process GO:0060562 @@ -18595,7 +18903,6 @@ Aside from their function in ion and water balance, kidney collecting duct epith The process in which the anatomical structures of a branched epithelium are generated and organized. - dph 2010-05-25T09:05:34Z biological_process GO:0061138 @@ -18627,7 +18934,6 @@ Aside from their function in ion and water balance, kidney collecting duct epith An extracellular matrix consisting mainly of proteins (especially collagen) and glycosaminoglycans (mostly as proteoglycans) that provides not only essential physical scaffolding for the cellular constituents but can also initiate crucial biochemical and biomechanical cues required for tissue morphogenesis, differentiation and homeostasis. The components are secreted by cells in the vicinity and form a sheet underlying or overlying cells such as endothelial and epithelial cells. - dph 2018-04-13T12:47:21Z cellular_component GO:0062023 @@ -18668,9 +18974,6 @@ Aside from their function in ion and water balance, kidney collecting duct epith The aggregation, arrangement and bonding together of a set of macromolecules to form a protein-containing complex. https://github.com/geneontology/go-ontology/issues/22580 - GO:0006461 - GO:0034622 - GO:0043623 cellular protein complex assembly biological_process cellular macromolecule complex assembly @@ -18960,7 +19263,6 @@ Aside from their function in ion and water balance, kidney collecting duct epith Any process in which a macromolecule is transported to, and/or maintained in, a specific location at the level of a cell. Localization at the cellular level encompasses movement within the cell, from within the cell to the cell surface, or from one location to another at the surface of a cell. - mah 2009-06-16T04:08:29Z cellular macromolecule localisation biological_process @@ -19005,7 +19307,6 @@ Aside from their function in ion and water balance, kidney collecting duct epith The aggregation, arrangement and bonding together of a set of components to form an organelle. An organelle is an organized structure of distinctive morphology and function. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton. Excludes the plasma membrane. - mah 2009-09-15T03:00:51Z biological_process GO:0070925 @@ -19043,7 +19344,6 @@ Aside from their function in ion and water balance, kidney collecting duct epith Any process in which a protein is transported from one specific location in the extracellular region to another, or maintained in a specific extracellular location. - mah 2010-02-25T04:00:13Z protein localisation in extracellular region protein localization in extracellular region @@ -19089,7 +19389,6 @@ Aside from their function in ion and water balance, kidney collecting duct epith Any process in which macromolecules aggregate, disaggregate, or are modified, resulting in the formation, disassembly, or alteration of a ribonucleoprotein complex. https://github.com/geneontology/go-ontology/issues/25143 - mah 2010-09-08T10:10:35Z RNA-protein complex subunit organization protein-RNA complex subunit organization @@ -19132,9 +19431,7 @@ Aside from their function in ion and water balance, kidney collecting duct epith A process that results in the biosynthesis of constituent macromolecules, assembly, arrangement of constituent parts, or disassembly of a cellular component. https://github.com/geneontology/go-ontology/issues/27189 - mah 2010-09-10T01:39:16Z - GO:0071841 cellular component organisation or biogenesis cellular component organisation or biogenesis at cellular level cellular component organization or biogenesis at cellular level @@ -19172,7 +19469,6 @@ Aside from their function in ion and water balance, kidney collecting duct epith The broad region around and including the plasma membrane of a cell, encompassing the cell cortex (inside the cell), the plasma membrane, and any external encapsulating structures. - mah 2010-10-04T01:51:47Z cellular_component GO:0071944 @@ -19217,7 +19513,6 @@ Aside from their function in ion and water balance, kidney collecting duct epith The aggregation, arrangement and bonding together of a set of components to form an extracellular vesicular exosome, a membrane-bounded vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Exosomes are defined by their size, which generally ranges from 30 nm to 100 nm. - mah 2010-10-18T03:44:18Z extracellular vesicular exosome assembly biological_process @@ -19271,7 +19566,6 @@ Aside from their function in ion and water balance, kidney collecting duct epith The developmental process pertaining to the initial formation of an epithelial tube. https://github.com/geneontology/go-ontology/issues/22302 - mah 2010-02-26T02:15:40Z biological_process GO:0072175 @@ -19297,9 +19591,7 @@ Aside from their function in ion and water balance, kidney collecting duct epith The series of molecular signals which triggers the apoptotic death of a cell. The pathway starts with reception of a signal, and ends when the execution phase of apoptosis is triggered. - pr 2011-11-23T09:30:23Z - GO:0008624 apoptotic signalling pathway induction of apoptosis by extracellular signals biological_process @@ -19339,7 +19631,6 @@ Aside from their function in ion and water balance, kidney collecting duct epith A stage of the apoptotic process that starts with the controlled breakdown of the cell through the action of effector caspases or other effector molecules (e.g. cathepsins, calpains etc.). Key steps of the execution phase are rounding-up of the cell, retraction of pseudopodes, reduction of cellular volume (pyknosis), chromatin condensation, nuclear fragmentation (karyorrhexis), plasma membrane blebbing and fragmentation of the cell into apoptotic bodies. When the execution phase is completed, the cell has died. - pr 2011-11-23T09:45:24Z execution phase of apoptotic process apoptosis @@ -19362,7 +19653,6 @@ Aside from their function in ion and water balance, kidney collecting duct epith A renal system process in which fluid circulating through the body is filtered through a barrier system. - pr 2012-01-03T03:10:17Z biological_process GO:0097205 @@ -19385,7 +19675,6 @@ Aside from their function in ion and water balance, kidney collecting duct epith The elimination of substances from peritubular capillaries (or surrounding hemolymph in invertebrates) into the renal tubules to be incorporated subsequently into the urine. Substances that are secreted include organic anions, ammonia, potassium and drugs. https://github.com/geneontology/go-ontology/issues/22368 - pr 2012-03-05T02:03:58Z biological_process GO:0097254 @@ -19407,7 +19696,6 @@ Aside from their function in ion and water balance, kidney collecting duct epith The assembly and secretion of an extracellular exosome, a membrane-bounded vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. - pr 2016-10-03T14:35:25Z exosome assembly or secretion exosome biogenesis @@ -19452,7 +19740,6 @@ Aside from their function in ion and water balance, kidney collecting duct epith A membrane that is a (regional) part of the plasma membrane. - dos 2014-03-06T11:55:32Z region of plasma membrane cellular_component @@ -19509,7 +19796,6 @@ Aside from their function in ion and water balance, kidney collecting duct epith - @@ -19911,21 +20197,22 @@ Aside from their function in ion and water balance, kidney collecting duct epith - A part of a cellular organism that is either an immaterial entity or a material entity with granularity above the level of a protein complex but below that of an anatomical system. Or, a substance produced by a cellular organism with granularity above the level of a protein complex. + A part of a cellular organism consisting of a material entity with granularity above the level of a protein complex but below that of an anatomical system. Note that cellular organisms exclude viruses. https://github.com/geneontology/go-ontology/issues/24200 https://github.com/geneontology/go-ontology/issues/26424 - kmv + https://github.com/geneontology/go-ontology/issues/28978 2019-08-12T18:01:37Z + cellular anatomical entity cellular_component GO:0110165 - cellular anatomical entity + cellular anatomical structure - A part of a cellular organism that is either an immaterial entity or a material entity with granularity above the level of a protein complex but below that of an anatomical system. Or, a substance produced by a cellular organism with granularity above the level of a protein complex. + A part of a cellular organism consisting of a material entity with granularity above the level of a protein complex but below that of an anatomical system. Note that cellular organisms exclude viruses. GOC:kmv @@ -19954,7 +20241,6 @@ Aside from their function in ion and water balance, kidney collecting duct epith A prolongation or process extending from a cell and that is bounded by plasma membrane, e.g. a cilium, lamellipodium, or axon. https://github.com/geneontology/go-ontology/issues/13193 - krc 2017-03-21T17:26:07Z cellular_component GO:0120025 @@ -19993,7 +20279,6 @@ Aside from their function in ion and water balance, kidney collecting duct epith Formation of a prolongation or process extending and that is bounded by plasma membrane, e.g. a cilium, lamellipodium, or axon. https://github.com/geneontology/go-ontology/issues/13298 - krc 2017-04-24T23:56:08Z eupodium biological_process @@ -20041,7 +20326,6 @@ Aside from their function in ion and water balance, kidney collecting duct epith A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a plasma membrane bounded prolongation or process extending from a cell, e.g. a cilium or axon. https://github.com/geneontology/go-ontology/issues/13298 - krc 2017-04-26T16:07:02Z biological_process GO:0120036 @@ -20074,7 +20358,6 @@ Aside from their function in ion and water balance, kidney collecting duct epith A mitotic cell cycle process comprising the steps by which the nucleus of a eukaryotic cell divides; the process involves condensation of chromosomal DNA into a highly compacted form. Canonically, mitosis produces two daughter nuclei whose chromosome complement is identical to that of the mother cell. https://github.com/geneontology/go-ontology/issues/19910 - pg 2017-03-23T14:44:23Z mitosis biological_process @@ -20098,7 +20381,6 @@ Aside from their function in ion and water balance, kidney collecting duct epith The assembly and secretion a set of components to form an extracellular vesicule, a membrane-bounded vesicle that is released into the extracellular region. Extracellular vesicles include exosomes, microvesicles and apoptotic bodies, based on the mechanism by which they are released from cells and differentiated based on their size and content. https://github.com/geneontology/go-ontology/issues/14256 - pg 2017-10-23T11:53:42Z extracellular vesicle assembly biological_process @@ -20147,7 +20429,6 @@ Aside from their function in ion and water balance, kidney collecting duct epith The directed movement of some substance from a cell, into the extracellular region. This may occur via transport across the plasma membrane or via exocytosis. - pg 2019-05-22T11:20:45Z efflux biological_process @@ -20185,7 +20466,6 @@ Aside from their function in ion and water balance, kidney collecting duct epith A process that is part of the mitotic cell cycle. - jl 2014-05-22T14:22:34Z biological_process GO:1903047 @@ -20220,7 +20500,6 @@ Aside from their function in ion and water balance, kidney collecting duct epith Any vesicle that is part of the extracellular region. - jl 2014-10-22T14:26:11Z cellular_component microparticle @@ -20250,10 +20529,7 @@ Aside from their function in ion and water balance, kidney collecting duct epith A macromolecular complex that contains both RNA and protein molecules. - pr 2015-11-19T12:26:37Z - GO:0030529 - GO:1990903 Wikipedia:Ribonucleoprotein RNA-protein complex RNP @@ -20345,7 +20621,6 @@ Aside from their function in ion and water balance, kidney collecting duct epith - NCBITaxon:85055 GC_ID:1 house mouse mouse @@ -20384,7 +20659,6 @@ Aside from their function in ion and water balance, kidney collecting duct epith - NCBITaxon:40673 GC_ID:1 bony vertebrates ncbi_taxonomy @@ -20751,7 +21025,6 @@ Aside from their function in ion and water balance, kidney collecting duct epith - NCBITaxon:109679 GC_ID:1 ncbi_taxonomy NCBITaxon:39107 @@ -21010,7 +21283,6 @@ Aside from their function in ion and water balance, kidney collecting duct epith A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities - PATO:0000072 quality PATO:0000001 quality @@ -21048,7 +21320,6 @@ Aside from their function in ion and water balance, kidney collecting duct epith A morphological quality inhering in a bearer by virtue of the bearer's ratios of distances between its features (points, edges, surfaces and also holes etc). - PATO:0001647 relational shape quality quality PATO:0000052 @@ -21070,7 +21341,6 @@ Aside from their function in ion and water balance, kidney collecting duct epith A morphology quality inhering in a bearer by virtue of the bearer's relative position, shape, arrangements and connectivity of an organism's various parts; the pattern underlying its form. - PATO:0001452 conformation relational structural quality quality @@ -21170,7 +21440,6 @@ Aside from their function in ion and water balance, kidney collecting duct epith A quality of a physical entity that exists through action of continuants at the physical level of organisation in relation to other entities. - PATO:0002079 Wikipedia:Physical_property relational physical quality quality @@ -21192,8 +21461,6 @@ Aside from their function in ion and water balance, kidney collecting duct epith A quality which inheres in a continuant. - PATO:0001237 - PATO:0001238 snap:Quality monadic quality of a continuant multiply inhering quality of a physical entity @@ -21471,7 +21738,6 @@ Aside from their function in ion and water balance, kidney collecting duct epith A convex 3-D shape quality inhering in a bearer by virtue of the bearer's exhibiting a consistently-sized round cross section. - PATO:0001203 rod-like rod-shaped tubulate @@ -22023,7 +22289,6 @@ Aside from their function in ion and water balance, kidney collecting duct epith A quality inhering in a cell by virtue of the cell having a high nuclear/cytoplasmic ratio. - http://orcid.org/0000-0001-5208-3432 high N:C ratio quality PATO:0040072 @@ -22045,7 +22310,6 @@ Aside from their function in ion and water balance, kidney collecting duct epith A quality of continuant that exist at the anatomical level of organisation and anything under it. This includes, but is not limited to, cells , tissues, and components. - http://orcid.org/0000-0001-7258-9596 quality PATO:0070044 anatomical structure quality @@ -22058,7 +22322,6 @@ Aside from their function in ion and water balance, kidney collecting duct epith A quality inhering in an anotomical structure by virtue of its capacity to be stained by specific histological dyes. - http://orcid.org/0000-0001-7258-9596 quality PATO:0070045 anatomical histological quality @@ -22071,7 +22334,6 @@ Aside from their function in ion and water balance, kidney collecting duct epith An affinity inhering in an anatomical structure by virtue of the bearer exhibiting a molecular interaction for both basic and acid stains under specific pH conditions. - http://orcid.org/0000-0001-7258-9596 quality PATO:0070047 polychromatophilic @@ -22089,7 +22351,7 @@ Aside from their function in ion and water balance, kidney collecting duct epith - + @@ -22101,7 +22363,7 @@ Aside from their function in ion and water balance, kidney collecting duct epith native protein protein PR:000000001 - The definition above excludes protein complexes, which some also consider a protein. Those who wish to refer to a class representing both senses of the word are directed to CHEBI:36080. Note that the definition allows for experimentally-manipulated genes, and allows for artifically-produced derivatives that mimic those found naturally. Proteins (in the sense defined here) that descended from a common ancestor can be classified into families and superfamilies composed of products of evolutionarily-related genes. The domain architecture of a protein is described by the order of its constituent domains. Proteins with the same domains in the same order are defined as homeomorphic [PRO:WCB]. + The definition above excludes protein complexes, which some also consider a protein. Those who wish to refer to a class representing both senses of the word are directed to CHEBI:36080. Note that the definition allows for experimentally-manipulated genes, and allows for artifically-produced derivatives that mimic those found naturally. Proteins (in the sense defined here) that descended from a common ancestor can be classified into families and superfamilies composed of products of evolutionarily-related genes. The domain architecture of a protein is described by the order of its constituent domains. Proteins with the same domains in the same order are defined as homeomorphic [PRO:WCB). protein @@ -22783,7 +23045,6 @@ Aside from their function in ion and water balance, kidney collecting duct epith - A protein with core architecture consisting of a signal sequence, followed by 7 Ig-like domains (Pfam:PF00047, Pfam:PF07679, or Pfam:PF07686), a transmembrane region, and a cytoplasmic Protein tyrosine kinase domain. PIRSF:PIRSF038502 protein @@ -23211,51 +23472,51 @@ Aside from their function in ion and water balance, kidney collecting duct epith - + - + - A material entity that minimally consists of a protein. + A molecular entity that minimally consists of a protein. protein protein aggregate protein complex protein-containing complex protein - PR:000050567 - Note: This includes single proteins and derivatives thereof (PR:000000001), protein-containing complexes (GO:0032991), and protein aggregates (PR:000050566). - protein-containing material entity + PR:000064867 + Note: This includes single proteins and derivatives thereof (PR:000000001), protein-containing complexes (GO:0032991), and protein aggregates (PR:000050565). + protein-containing molecular entity - + - A material entity that minimally consists of a protein. + A molecular entity that minimally consists of a protein. PRO:DAN - + protein PRO:DAN - + protein aggregate PRO:DAN - + protein complex PRO:DAN - + protein-containing complex PRO:DAN @@ -23458,7 +23719,7 @@ Aside from their function in ion and water balance, kidney collecting duct epith - + @@ -23512,14 +23773,14 @@ Aside from their function in ion and water balance, kidney collecting duct epith ureter https://upload.wikimedia.org/wikipedia/commons/3/30/Urinary_system.svg - + - + GO @@ -23569,7 +23830,7 @@ Aside from their function in ion and water balance, kidney collecting duct epith - + @@ -23617,14 +23878,14 @@ Aside from their function in ion and water balance, kidney collecting duct epith urethra https://upload.wikimedia.org/wikipedia/commons/c/cb/Female_anatomy.png - + - + Wikipedia @@ -23646,7 +23907,6 @@ Aside from their function in ion and water balance, kidney collecting duct epith - @@ -23733,7 +23993,6 @@ Aside from their function in ion and water balance, kidney collecting duct epith Organ component adjacent to an organ cavity and which consists of a maximal aggregate of organ component layers. - UBERON:0009915 wall FMA:82482 galen:Wall @@ -24132,7 +24391,7 @@ Aside from their function in ion and water balance, kidney collecting duct epith - + @@ -24182,14 +24441,14 @@ Aside from their function in ion and water balance, kidney collecting duct epith http://upload.wikimedia.org/wikipedia/commons/3/30/Gray1130.svg https://upload.wikimedia.org/wikipedia/commons/2/22/Renal_corpuscle.svg - + - + FMA MA @@ -24282,7 +24541,6 @@ Aside from their function in ion and water balance, kidney collecting duct epith Anatomical cluster consisting of the skeletal elements and articular elements that are part of an individual subdivision of the organism. - UBERON:0010322 FMA:85544 NCIT:C34076 SCTID:118966000 @@ -24452,14 +24710,14 @@ Aside from their function in ion and water balance, kidney collecting duct epith - + - + @@ -24491,24 +24749,24 @@ Aside from their function in ion and water balance, kidney collecting duct epith metanephros - + - + - + GO - + ISBN:9780878932504 @@ -24623,8 +24881,8 @@ Aside from their function in ion and water balance, kidney collecting duct epith - - + + An epithelial swelling on the Wolffian duct that elongates to invade the adjacent metanephric mesenchyme[MP]. BTO:0001646 EHDAA2:0002140 @@ -24648,11 +24906,11 @@ Aside from their function in ion and water balance, kidney collecting duct epith ureteric bud - + - + @@ -24665,13 +24923,13 @@ Aside from their function in ion and water balance, kidney collecting duct epith - + EHDAA2 - + ISBN:9780878932504 @@ -25052,7 +25310,7 @@ Aside from their function in ion and water balance, kidney collecting duct epith - + @@ -25088,14 +25346,14 @@ Aside from their function in ion and water balance, kidney collecting duct epith gastrula stage - + - + BILS @@ -25355,8 +25613,8 @@ Aside from their function in ion and water balance, kidney collecting duct epith - - + + @@ -25382,24 +25640,24 @@ Aside from their function in ion and water balance, kidney collecting duct epith UBERON:0000162 cloaca - + - + - + ZFA - + AAO @@ -25440,8 +25698,8 @@ Aside from their function in ion and water balance, kidney collecting duct epith - - + + @@ -25459,24 +25717,24 @@ Aside from their function in ion and water balance, kidney collecting duct epith embryonic cloaca - + - + - + EHDAA2 - + EHDAA2 @@ -25499,7 +25757,7 @@ Aside from their function in ion and water balance, kidney collecting duct epith - + @@ -25538,14 +25796,14 @@ Aside from their function in ion and water balance, kidney collecting duct epith primitive urogenital sinus http://upload.wikimedia.org/wikipedia/commons/6/6d/Gray1109.png - + - + MP-def @@ -25773,8 +26031,6 @@ Aside from their function in ion and water balance, kidney collecting duct epith A portion of organism substance that is the product of an excretion process that will be eliminated from the body. An excretion process is elimination by an organism of the waste products that arise as a result of metabolic activity. - UBERON:0000324 - UBERON:0007550 AEO:0000184 BTO:0000491 EHDAA2_RETIRED:0003184 @@ -25820,7 +26076,7 @@ Aside from their function in ion and water balance, kidney collecting duct epith - + @@ -25828,15 +26084,15 @@ Aside from their function in ion and water balance, kidney collecting duct epith - + - - + + A fluid that is composed of blood plasma and erythrocytes. AAO:0000046 @@ -25873,34 +26129,34 @@ Aside from their function in ion and water balance, kidney collecting duct epith blood - + - + - + - + CL:tm - + https://github.com/obophenotype/uberon/issues/1330 - + Bgee:AN @@ -26002,7 +26258,6 @@ Aside from their function in ion and water balance, kidney collecting duct epith Organism at the blastula stage - an early stage of embryonic development in animals. It is produced by cleavage of a fertilized ovum and consists of a spherical layer of around 128 cells surrounding a central fluid-filled cavity called the blastocoel. The blastula follows the morula and precedes the gastrula in the developmental sequence. TODO - check relationship with epiblast. Note in FMA this is not a subclass of embryo, but in uberon embryo is the whole organism from zygote onwards and thus includes the blastula - UBERON:0007011 BILA:0000059 BTO:0000128 GAID:1294 @@ -27229,7 +27484,6 @@ Aside from their function in ion and water balance, kidney collecting duct epith - @@ -27243,7 +27497,7 @@ Aside from their function in ion and water balance, kidney collecting duct epith - + @@ -27285,14 +27539,14 @@ Aside from their function in ion and water balance, kidney collecting duct epith epithelium https://upload.wikimedia.org/wikipedia/commons/8/8f/Illu_epithelium.jpg - + - + http://palaeos.com/metazoa/porifera/homoscleromorpha.html @@ -27650,7 +27904,7 @@ Aside from their function in ion and water balance, kidney collecting duct epith - + @@ -27685,14 +27939,14 @@ Aside from their function in ion and water balance, kidney collecting duct epith abdomen - + - + MA @@ -27921,7 +28175,7 @@ Aside from their function in ion and water balance, kidney collecting duct epith - + Primary germ layer that is the outer of the embryo's three germ layers and gives rise to epidermis and neural tissue. AAO:0000137 BILA:0000036 @@ -27956,14 +28210,14 @@ Aside from their function in ion and water balance, kidney collecting duct epith ectoderm http://upload.wikimedia.org/wikipedia/commons/1/19/Gray32.png - + - + Bgee:AN @@ -28003,7 +28257,7 @@ Aside from their function in ion and water balance, kidney collecting duct epith - + Primary germ layer that lies remote from the surface of the embryo and gives rise to internal tissues such as gut. AAO:0000139 BILA:0000038 @@ -28038,14 +28292,14 @@ Aside from their function in ion and water balance, kidney collecting duct epith http://upload.wikimedia.org/wikipedia/commons/c/c0/Endoderm2.png http://upload.wikimedia.org/wikipedia/commons/d/df/Gray10.png - + - + Bgee:AN @@ -28086,10 +28340,9 @@ Aside from their function in ion and water balance, kidney collecting duct epith - + The middle germ layer of the embryo, between the endoderm and ectoderm. - UBERON:0003263 AAO:0000304 BILA:0000037 BTO:0000839 @@ -28127,14 +28380,14 @@ Aside from their function in ion and water balance, kidney collecting duct epith mesoderm http://upload.wikimedia.org/wikipedia/commons/e/e8/Mesoderm.png - + - + Bgee:AN @@ -28300,7 +28553,7 @@ Aside from their function in ion and water balance, kidney collecting duct epith - + @@ -28343,7 +28596,7 @@ Aside from their function in ion and water balance, kidney collecting duct epith proctodeum https://github.com/obophenotype/uberon/issues/685 - + @@ -28356,7 +28609,7 @@ Aside from their function in ion and water balance, kidney collecting duct epith - + EHDAA2 @@ -28418,7 +28671,7 @@ Aside from their function in ion and water balance, kidney collecting duct epith - + @@ -28489,14 +28742,14 @@ Aside from their function in ion and water balance, kidney collecting duct epith https://cdn.humanatlas.io/digital-objects/ref-organ/heart-female/v1.3/assets/3d-vh-f-heart.glb https://cdn.humanatlas.io/digital-objects/ref-organ/heart-male/v1.3/assets/3d-vh-m-heart.glb - + - + MA @@ -29198,7 +29451,6 @@ Aside from their function in ion and water balance, kidney collecting duct epith - AAO:0000959 CALOHA:TS-2103 VHOG:0001248 @@ -29206,7 +29458,6 @@ Aside from their function in ion and water balance, kidney collecting duct epith uberon systema cardiovasculare UBERON:0001009 - circulatory system http://upload.wikimedia.org/wikipedia/commons/2/29/Circulatory_System_en.svg @@ -29350,7 +29601,7 @@ Aside from their function in ion and water balance, kidney collecting duct epith - + @@ -29398,14 +29649,14 @@ Aside from their function in ion and water balance, kidney collecting duct epith http://upload.wikimedia.org/wikipedia/commons/b/b2/TE-Nervous_system_diagram.svg http://upload.wikimedia.org/wikipedia/commons/b/ba/Nervous_system_diagram.png - + - + Bgee:AN @@ -29471,7 +29722,7 @@ Aside from their function in ion and water balance, kidney collecting duct epith - + The central nervous system is the core nervous system that serves an integrating and coordinating function. In vertebrates it consists of the neural tube derivatives: the brain and spinal cord. In invertebrates it includes central ganglia plus nerve cord. @@ -29516,7 +29767,7 @@ Aside from their function in ion and water balance, kidney collecting duct epith central nervous system - + @@ -29530,7 +29781,7 @@ Aside from their function in ion and water balance, kidney collecting duct epith - + Bgee:AN @@ -29727,7 +29978,7 @@ Aside from their function in ion and water balance, kidney collecting duct epith - + @@ -29761,14 +30012,14 @@ Aside from their function in ion and water balance, kidney collecting duct epith hindgut http://upload.wikimedia.org/wikipedia/commons/f/f7/Gray472.png - + - + Wikipedia @@ -30259,14 +30510,14 @@ Aside from their function in ion and water balance, kidney collecting duct epith - + - + @@ -30318,24 +30569,24 @@ Aside from their function in ion and water balance, kidney collecting duct epith renal pelvis https://upload.wikimedia.org/wikipedia/commons/c/c0/Illu_kidney2.jpg - + - + - + MA - + FMA @@ -30381,7 +30632,7 @@ Aside from their function in ion and water balance, kidney collecting duct epith - + @@ -30417,14 +30668,14 @@ Aside from their function in ion and water balance, kidney collecting duct epith https://cdn.humanatlas.io/digital-objects/ref-organ/kidney-male-right/v1.3/assets/3d-vh-m-kidney-r.glb https://upload.wikimedia.org/wikipedia/commons/6/69/Illu_kidney.jpg - + - + FMA @@ -30460,7 +30711,7 @@ Aside from their function in ion and water balance, kidney collecting duct epith - + @@ -30505,14 +30756,14 @@ Aside from their function in ion and water balance, kidney collecting duct epith renal corpuscle https://upload.wikimedia.org/wikipedia/commons/2/22/Renal_corpuscle.svg - + - + MA ZFA @@ -30586,7 +30837,7 @@ Aside from their function in ion and water balance, kidney collecting duct epith - + @@ -30628,14 +30879,14 @@ Aside from their function in ion and water balance, kidney collecting duct epith glomerular capsule http://upload.wikimedia.org/wikipedia/commons/3/30/Gray1130.svg - + - + Wikipedia @@ -30725,10 +30976,10 @@ Aside from their function in ion and water balance, kidney collecting duct epith - + - + @@ -30743,7 +30994,6 @@ Aside from their function in ion and water balance, kidney collecting duct epith An epithelial tube that is part of the nephron, the functional part of the kidney. - UBERON:0004210 renal tubule BTO:0000343 CALOHA:TS-1262 @@ -30772,7 +31022,7 @@ Aside from their function in ion and water balance, kidney collecting duct epith nephron tubule - + @@ -30781,14 +31031,14 @@ Aside from their function in ion and water balance, kidney collecting duct epith - + - + GO MA ZFA @@ -30802,7 +31052,7 @@ Aside from their function in ion and water balance, kidney collecting duct epith - + ZFA @@ -31016,7 +31266,7 @@ Aside from their function in ion and water balance, kidney collecting duct epith - + @@ -31063,7 +31313,7 @@ Aside from their function in ion and water balance, kidney collecting duct epith https://cdn.humanatlas.io/digital-objects/ref-organ/urinary-bladder-male/v1.2/assets/3d-vh-m-urinary-bladder.glb https://upload.wikimedia.org/wikipedia/commons/3/30/Urinary_system.svg - + @@ -31076,7 +31326,7 @@ Aside from their function in ion and water balance, kidney collecting duct epith - + FMA @@ -31206,7 +31456,7 @@ Aside from their function in ion and water balance, kidney collecting duct epith - + @@ -31219,7 +31469,7 @@ Aside from their function in ion and water balance, kidney collecting duct epith - + The basic functional unit of the kidney. its chief function is to regulate the concentration of water and soluble substances like sodium salts by filtering the blood, reabsorbing what is needed and excreting the rest as urine. A nephron eliminates wastes from the body, regulates blood volume and blood pressure, controls levels of electrolytes and metabolites, and regulates blood pH. Its functions are vital to life and are regulated by the endocrine system by hormones such as antidiuretic hormone, aldosterone, and parathyroid hormone.[WP]. kidney terms require review for cross-vertebrate compatibility and developmental relationships. @@ -31250,24 +31500,24 @@ Aside from their function in ion and water balance, kidney collecting duct epith nephron http://upload.wikimedia.org/wikipedia/commons/0/02/Gray1128.png - + - + - + FMA - + Bgee:AN @@ -31318,14 +31568,14 @@ Aside from their function in ion and water balance, kidney collecting duct epith - + - + @@ -31361,11 +31611,11 @@ Aside from their function in ion and water balance, kidney collecting duct epith proximal convoluted tubule http://upload.wikimedia.org/wikipedia/commons/0/02/Gray1128.png - + - + @@ -31378,13 +31628,13 @@ Aside from their function in ion and water balance, kidney collecting duct epith - + GO - + Wikipedia @@ -31516,7 +31766,7 @@ Aside from their function in ion and water balance, kidney collecting duct epith - + @@ -31543,7 +31793,7 @@ Aside from their function in ion and water balance, kidney collecting duct epith descending limb of loop of Henle http://upload.wikimedia.org/wikipedia/commons/0/02/Gray1128.png - + @@ -31556,7 +31806,7 @@ Aside from their function in ion and water balance, kidney collecting duct epith - + FMA @@ -31580,14 +31830,14 @@ Aside from their function in ion and water balance, kidney collecting duct epith - + - + @@ -31609,7 +31859,6 @@ Aside from their function in ion and water balance, kidney collecting duct epith The proximal straight tubule is the part of the descending limb that extends from the proximal convoluted tubule to the descending thin tubule. TODO - is S3 exactly coincident with PST? todo - ensure relationships work across species (loop of Henle) - UBERON:0005166 BTO:0000055 EMAPA:29661 EMAPA:29669 @@ -31632,11 +31881,11 @@ Aside from their function in ion and water balance, kidney collecting duct epith proximal straight tubule - + - + @@ -31649,13 +31898,13 @@ Aside from their function in ion and water balance, kidney collecting duct epith - + MA - + MA @@ -31697,7 +31946,7 @@ Aside from their function in ion and water balance, kidney collecting duct epith - + @@ -31733,7 +31982,7 @@ Aside from their function in ion and water balance, kidney collecting duct epith distal convoluted tubule https://upload.wikimedia.org/wikipedia/commons/2/21/Kidney_nephron.png - + @@ -31746,7 +31995,7 @@ Aside from their function in ion and water balance, kidney collecting duct epith - + EMAPA GO MA-modified-from-isa @@ -32021,7 +32270,7 @@ Aside from their function in ion and water balance, kidney collecting duct epith - + @@ -32044,14 +32293,14 @@ Aside from their function in ion and water balance, kidney collecting duct epith kidney arcuate artery https://upload.wikimedia.org/wikipedia/commons/8/87/2610_The_Kidney.jpg - + - + MA @@ -32092,7 +32341,7 @@ Aside from their function in ion and water balance, kidney collecting duct epith - + A tube extending from the mouth to the anus. @@ -32129,14 +32378,14 @@ Aside from their function in ion and water balance, kidney collecting duct epith digestive tract - + - + NCBIBook:NBK10107 @@ -32614,7 +32863,6 @@ Aside from their function in ion and water balance, kidney collecting duct epith - @@ -32842,7 +33090,6 @@ Aside from their function in ion and water balance, kidney collecting duct epith - @@ -32851,8 +33098,8 @@ Aside from their function in ion and water balance, kidney collecting duct epith - - + + @@ -32865,7 +33112,7 @@ Aside from their function in ion and water balance, kidney collecting duct epith - + @@ -32919,34 +33166,34 @@ Aside from their function in ion and water balance, kidney collecting duct epith blood vessel http://upload.wikimedia.org/wikipedia/commons/2/29/Circulatory_System_en.svg - + - + - + - + AEO - + EHDAA2 - + GO:0072360 @@ -33803,7 +34050,7 @@ Aside from their function in ion and water balance, kidney collecting duct epith - + @@ -33855,14 +34102,14 @@ Aside from their function in ion and water balance, kidney collecting duct epith kidney - + - + FMA @@ -33897,8 +34144,8 @@ Aside from their function in ion and water balance, kidney collecting duct epith - - + + @@ -33906,7 +34153,6 @@ Aside from their function in ion and water balance, kidney collecting duct epith In mammals, the pronephros is the first of the three embryonic kidneys to be established and exists only transiently. In lower vertebrates such as fish and amphibia, the pronephros is the fully functional embryonic kidney and is indispensible for larval life[GO]. - UBERON:0005794 AAO:0011089 BTO:0001541 EFO:0000927 @@ -33936,11 +34182,11 @@ Aside from their function in ion and water balance, kidney collecting duct epith Once the more complex mesonephros forms the pronephros undergoes apoptosis in amphibians. In fishes the nephron degenerates but the organ remains and becomes a component of the immune system[Wikipedia:Pronephros]. // TODO - check developmental relationships. Note that we previously include the ZFA/XAO terms under the more specific 'pronephric kidney', but these are now merged. TODO GCI: relationship: capable_of GO:0030104 pronephros - + - + @@ -33953,13 +34199,13 @@ Aside from their function in ion and water balance, kidney collecting duct epith - + OG - + ZFA @@ -34285,9 +34531,8 @@ Aside from their function in ion and water balance, kidney collecting duct epith - - + @@ -34306,7 +34551,7 @@ Aside from their function in ion and water balance, kidney collecting duct epith - + An anatomical structure which consists of juxtaglomerular cells, extraglomerular mesangial cells and the macula densa. The juxtaglomerular apparatus lies adjacent to the glomerulus and regulates kidney function by maintaining the blood flow to the kidney and the filtration rate[GO]. a microscopic structure in the kidney, which regulates the function of each nephron. The juxtaglomerular apparatus is named for its proximity to the glomerulus: it is found between the vascular pole of the renal corpuscle and the returning distal convoluted tubule of the same nephron. This location is critical to its function in regulating renal blood flow and glomerular filtration rate. The three cellular components of the apparatus are the macula densa, extraglomerular mesangial cells, and juxtaglomerular cells (also known as granular cells)[WP]. BTO:0005157 @@ -34328,24 +34573,24 @@ Aside from their function in ion and water balance, kidney collecting duct epith juxtaglomerular apparatus - + - + - + MA - + GO @@ -34469,8 +34714,8 @@ Aside from their function in ion and water balance, kidney collecting duct epith - - + + @@ -34487,24 +34732,24 @@ Aside from their function in ion and water balance, kidney collecting duct epith EDITOR_NOTE check MA part_ofs - should be spatially disjoint from renal glomerulus? extraglomerular mesangium - + - + - + MA - + MA @@ -34534,7 +34779,6 @@ Aside from their function in ion and water balance, kidney collecting duct epith The cavity within the body of all animals higher than the coelenterates and certain primitive worms, formed by the splitting of the embryonic mesoderm into two layers. In mammals it forms the peritoneal, pleural, and pericardial cavities. - UBERON:0000169 body cavity AEO:0000186 BTO:0001707 @@ -34546,7 +34790,6 @@ Aside from their function in ion and water balance, kidney collecting duct epith SCTID:361348008 TAO:0001438 UMLS:C0333343 - ZFA:0001438 galen:BodyCavity coelomic cavity coelomic cavity lumen @@ -34646,9 +34889,9 @@ Aside from their function in ion and water balance, kidney collecting duct epith - - - + + + @@ -34696,15 +34939,15 @@ Aside from their function in ion and water balance, kidney collecting duct epith notochord http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png - + - + - + @@ -34723,19 +34966,19 @@ Aside from their function in ion and water balance, kidney collecting duct epith - + http://tolweb.org/Chordata/2499 - + ZFA - + EHDAA2 @@ -34775,8 +35018,8 @@ Aside from their function in ion and water balance, kidney collecting duct epith - - + + Somites are spheres of epithelial cells that form sequentially along the anterior-posterior axis of the embryo through mesenchymal to epithelial transition of the presomitic mesoderm. mesodermal cluster @@ -34814,11 +35057,11 @@ Aside from their function in ion and water balance, kidney collecting duct epith somite http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png - + - + @@ -34831,13 +35074,13 @@ Aside from their function in ion and water balance, kidney collecting duct epith - + GOTAX:0000352 - + ZFA @@ -34897,8 +35140,8 @@ Aside from their function in ion and water balance, kidney collecting duct epith - - + + The macula densa is an area of specialized cells in the distal tubule that makes contact with the vascular pole of the glomerulus[GO]. BTO:0003940 @@ -34916,24 +35159,24 @@ Aside from their function in ion and water balance, kidney collecting duct epith macula densa - + - + - + MA - + GO @@ -34958,22 +35201,22 @@ Aside from their function in ion and water balance, kidney collecting duct epith - + - - + + - + A specialized region of ectoderm found between the neural ectoderm (neural plate) and non-neural ectoderm and composed of highly migratory pluripotent cells that delaminate in early embryonic development from the dorsal neural tube and give rise to an astounding variety of differentiated cell types[MP]. AAO:0010578 BTO:0001764 @@ -35006,45 +35249,45 @@ Aside from their function in ion and water balance, kidney collecting duct epith http://upload.wikimedia.org/wikipedia/commons/5/5f/Gray644.png https://upload.wikimedia.org/wikipedia/commons/8/8f/Neural_Crest.png - + - + - + - + - + XAO https://github.com/obophenotype/uberon/wiki/The-neural-crest - + BTO - + PMID:11523831 - + PMID:11523831 @@ -35408,7 +35651,7 @@ Aside from their function in ion and water balance, kidney collecting duct epith - + @@ -35461,14 +35704,14 @@ Aside from their function in ion and water balance, kidney collecting duct epith hematopoietic system - + - + FMA @@ -35673,6 +35916,7 @@ Aside from their function in ion and water balance, kidney collecting duct epith + @@ -35686,7 +35930,7 @@ Aside from their function in ion and water balance, kidney collecting duct epith - + Unsegmented field of paraxial mesoderm present posterior to the most recently formed somite pair, from which somites will form. AAO:0011086 EFO:0001982 @@ -35709,14 +35953,14 @@ Aside from their function in ion and water balance, kidney collecting duct epith presomitic mesoderm - + - + Bgee:AN @@ -35750,15 +35994,14 @@ Aside from their function in ion and water balance, kidney collecting duct epith - - - + + In mammals, the pronephric duct is the predecessor of the Wolffian duct[WP]. AAO:0011088 NCIT:C34279 @@ -35777,11 +36020,11 @@ Aside from their function in ion and water balance, kidney collecting duct epith The pronephric duct collects the filtrate from the pronephric tubules and opens to the exterior of the pronephric kidney[GOC:mtg_kidney_jan10, PMID:15647339, XAO:0000063, ZFA:0000150] pronephric duct - + - + @@ -35794,13 +36037,13 @@ Aside from their function in ion and water balance, kidney collecting duct epith - + Wikipedia - + XAO @@ -35906,9 +36149,9 @@ Aside from their function in ion and water balance, kidney collecting duct epith - - - + + + @@ -35947,34 +36190,34 @@ Aside from their function in ion and water balance, kidney collecting duct epith intermediate mesoderm http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png - + - + - + - + AAO - + EMAPA - + XAO @@ -36083,7 +36326,7 @@ Aside from their function in ion and water balance, kidney collecting duct epith - + Paired organ that connects the primitive kidney Wolffian body (or mesonephros) to the cloaca and serves as the anlage for certain male reproductive organs. the Wolffian duct is what remains of the pronephric duct after the atrophy of the pronephros[WP]. In Zebrafish: Duct of the adult kidney (mesonephros), present bilaterally ventral to the somites and leading to the cloacal chamber[ZFA]. Consider adding subclasses for male and female specific variants TODO - mesonephric portion of the nephric duct @@ -36112,7 +36355,7 @@ Aside from their function in ion and water balance, kidney collecting duct epith mesonephric duct http://upload.wikimedia.org/wikipedia/commons/6/6d/Gray1109.png - + @@ -36125,7 +36368,7 @@ Aside from their function in ion and water balance, kidney collecting duct epith - + EHDAA2 @@ -36179,9 +36422,9 @@ Aside from their function in ion and water balance, kidney collecting duct epith - - - + + + A region of embryonic ectodermal cells that lie directly above the notochord. During neurulation, they change shape and produce an infolding of the neural plate (the neural fold) that then seals to form the neural tube[XAO]. The earliest recognizable dorsal ectodermal primordium of the central nervous system present near the end of gastrulation before infolding to form the neural keel; consists of a thickened pseudostratified epithelium[ZFA]. AAO:0011072 BTO:0001765 @@ -36210,34 +36453,34 @@ Aside from their function in ion and water balance, kidney collecting duct epith neural plate https://upload.wikimedia.org/wikipedia/commons/8/8f/Neural_Crest.png - + - + - + - + GOTAX:0000352 - + Wikipedia - + Bgee:AN @@ -36277,7 +36520,7 @@ Aside from their function in ion and water balance, kidney collecting duct epith - + The paraxial mesoderm is the mesoderm located bilaterally adjacent to the notochord and neural tube[GO]. AAO:0010568 EFO:0003515 @@ -36303,7 +36546,7 @@ Aside from their function in ion and water balance, kidney collecting duct epith paraxial mesoderm http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png - + @@ -36316,7 +36559,7 @@ Aside from their function in ion and water balance, kidney collecting duct epith - + Bgee:AN @@ -36363,7 +36606,7 @@ Aside from their function in ion and water balance, kidney collecting duct epith - + @@ -36377,7 +36620,6 @@ Aside from their function in ion and water balance, kidney collecting duct epith Portion of the middle of the three primary germ layers of the embryo that resides on the periphery of the embryo, is continuous with the extra-embryonic mesoderm, splits into two layers enclosing the intra-embryonic coelom, and gives rise to body wall structures[MP]. - UBERON:0006258 AAO:0010574 EHDAA2:0000919 EHDAA:379 @@ -36403,7 +36645,7 @@ Aside from their function in ion and water balance, kidney collecting duct epith lateral plate mesoderm http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png - + @@ -36416,7 +36658,7 @@ Aside from their function in ion and water balance, kidney collecting duct epith - + EHDAA2 VHOG @@ -36466,15 +36708,15 @@ Aside from their function in ion and water balance, kidney collecting duct epith - - + + - + Bilateral groups of cells consisting of three rows: one row of endocardial precursors medially and two rows of myocardical precursors laterally. The two populations fuse at the midline to form the heart rudiment or cone. should probably be merged with heart rudiment. AAO:0011044 @@ -36491,15 +36733,15 @@ Aside from their function in ion and water balance, kidney collecting duct epith heart primordium - + - + - + @@ -36512,19 +36754,19 @@ Aside from their function in ion and water balance, kidney collecting duct epith - + ZFA - + ZFA - + XAO @@ -36553,8 +36795,8 @@ Aside from their function in ion and water balance, kidney collecting duct epith - - + + Ventral somitic compartment that is a precursor of the axial skeleton[XAO]. Sclerotomes eventually differentiate into the vertebrae and most of the skull. The caudal (posterior) half of one sclerotome fuses with the rostral (anterior) half of the adjacent one to form each vertebra. From their initial location within the somite, the sclerotome cells migrate medially towards the notochord. These cells meet the sclerotome cells from the other side to form the vertebral body. From this vertebral body, sclerotome cells move dorsally and surround the developing spinal cord, forming the vertebral arch[WP]. AAO:0010571 AEO:0000212 @@ -36578,11 +36820,11 @@ Aside from their function in ion and water balance, kidney collecting duct epith sclerotome http://upload.wikimedia.org/wikipedia/commons/9/96/Gray65.png - + - + @@ -36601,13 +36843,13 @@ Aside from their function in ion and water balance, kidney collecting duct epith - + VHOG:0000680 - + ZFA @@ -36852,7 +37094,7 @@ Aside from their function in ion and water balance, kidney collecting duct epith - + @@ -36878,14 +37120,14 @@ Aside from their function in ion and water balance, kidney collecting duct epith Genes: The positional specification of the metanephrogenic mesenchyme is negatively regulated by Foxc1 and Foxc2. Next the permanent kidney forming metanephrogenic mesenchyme is specified by Hox11 genes. The competence to respond to ureteric bud inducers is regulated by WT1. GDNF secretion restricted to posterior region by Robo2 and Sprouty1. The receptors for GDNF are synthesized in the nephric ducts and later in ureteric buds [ISBN:9780878932504 "Developmental Biology"] metanephric mesenchyme - + - + ISBN:9780878932504 @@ -37573,7 +37815,7 @@ Aside from their function in ion and water balance, kidney collecting duct epith - + The part of the coelom in the embryo between the somatopleuric and splanchnopleuric mesoderm; the principal body cavities of the trunk (thoracic, abdominal, and pelvic) arise from this embryonic part of the coelom. consider merging with coelom. TODO - add spatial relationships to halves of LPM. Note the OG places XAO and ZFA coelem terms here. editor note: TODO check ZFA, which appears to be a structure present in adults EHDAA:251 @@ -37588,14 +37830,14 @@ Aside from their function in ion and water balance, kidney collecting duct epith intraembryonic coelom - + - + Wikipedia @@ -38175,8 +38417,8 @@ Aside from their function in ion and water balance, kidney collecting duct epith - - + + In mammals, the proximal tubule is a nephron tubule that connects Bowman's capsule to the loop of Henle. It has a brush border epithelial morphology[GO]. TODO - ensure definition works across species. @@ -38193,24 +38435,24 @@ Aside from their function in ion and water balance, kidney collecting duct epith proximal tubule - + - + - + GO - + GO @@ -38269,7 +38511,7 @@ Aside from their function in ion and water balance, kidney collecting duct epith - + The intermediate tubule is a nephron tubule that lies between the proximal and distal tubules. TODO - check for applicability across species FMA:17718 @@ -38279,14 +38521,14 @@ Aside from their function in ion and water balance, kidney collecting duct epith UBERON:0004136 intermediate tubule - + - + FMA @@ -38362,8 +38604,8 @@ Aside from their function in ion and water balance, kidney collecting duct epith - - + + A specific region of the lateral mesoderm that will form the primary beating heart tube. In mammals the primary heart field gives rise to the left ventricle. XAO:0004185 first heart field @@ -38375,24 +38617,24 @@ Aside from their function in ion and water balance, kidney collecting duct epith UBERON:0004140 primary heart field - + - + - + GO:0003128 - + https://orcid.org/0000-0003-3308-6245 @@ -38445,7 +38687,7 @@ Aside from their function in ion and water balance, kidney collecting duct epith - + An epithelial tube that will give rise to the mature heart. AAO:0010411 EFO:0003526 @@ -38464,14 +38706,14 @@ Aside from their function in ion and water balance, kidney collecting duct epith heart tube - + - + ZFA-modified @@ -38693,8 +38935,8 @@ Aside from their function in ion and water balance, kidney collecting duct epith - - + + The comma-shaped body is the precursor structure to the S-shaped body that contributes to the morphogenesis of the nephron. EMAPA:27681 ZFA:0005588 @@ -38704,24 +38946,24 @@ Aside from their function in ion and water balance, kidney collecting duct epith comma-shaped body - + - + - + cjm - + ZFA @@ -38743,8 +38985,8 @@ Aside from their function in ion and water balance, kidney collecting duct epith - - + + The S-shaped body is the successor of the comma-shaped body that contributes to the morphogenesis of the nephron. TODO EMAPA:27756 @@ -38756,24 +38998,24 @@ Aside from their function in ion and water balance, kidney collecting duct epith S-shaped body - + - + - + cjm - + GO @@ -38815,8 +39057,6 @@ Aside from their function in ion and water balance, kidney collecting duct epith Kidney pyramids are the conical arrangements of tubules that constitute the renal medulla in a multi-lobed mammalian kidney; they contain the loops of Henle and the medullary collecting ducts. - UBERON:0002449 - UBERON:0005098 pyramid BTO:0003926 FMA:258870 @@ -39185,7 +39425,7 @@ Aside from their function in ion and water balance, kidney collecting duct epith - + @@ -39223,14 +39463,14 @@ Aside from their function in ion and water balance, kidney collecting duct epith glomerular capillary - + - + https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships @@ -39476,7 +39716,6 @@ Aside from their function in ion and water balance, kidney collecting duct epith - @@ -39573,7 +39812,6 @@ Aside from their function in ion and water balance, kidney collecting duct epith - @@ -39615,7 +39853,6 @@ Aside from their function in ion and water balance, kidney collecting duct epith - @@ -39624,7 +39861,6 @@ Aside from their function in ion and water balance, kidney collecting duct epith The part of the cardiovascular system consisting of all arteries. - BTO:0004690 EHDAA2:0000143 EHDAA:396 @@ -39635,7 +39871,6 @@ Aside from their function in ion and water balance, kidney collecting duct epith VHOG:0000273 uberon UBERON:0004572 - arterial system @@ -39657,7 +39892,6 @@ Aside from their function in ion and water balance, kidney collecting duct epith - @@ -39666,7 +39900,6 @@ Aside from their function in ion and water balance, kidney collecting duct epith The part of the cardiovascular system consisting of all venous vessels. In vertebrates with a double circulation, this can be divided into systemic and pulmonary portions. - BTO:0004692 EHDAA2:0002171 EHDAA:486 @@ -39679,7 +39912,6 @@ Aside from their function in ion and water balance, kidney collecting duct epith vein system uberon UBERON:0004582 - venous system @@ -39774,7 +40006,7 @@ Aside from their function in ion and water balance, kidney collecting duct epith - + @@ -39811,14 +40043,14 @@ Aside from their function in ion and water balance, kidney collecting duct epith renal afferent arteriole http://upload.wikimedia.org/wikipedia/commons/0/02/Gray1128.png - + - + Wikipedia @@ -40064,7 +40296,6 @@ Aside from their function in ion and water balance, kidney collecting duct epith Organism at the gastrula stage. - UBERON:0007012 BILA:0000060 BTO:0001403 FBbt:00005317 @@ -40178,7 +40409,7 @@ Aside from their function in ion and water balance, kidney collecting duct epith - + Organ consisting of skeletal tissue. Encompasses whole bones, fused bones, cartilaginious elements, teeth, dermal denticles. AAO:0011129 TAO:0001890 @@ -40192,14 +40423,14 @@ Aside from their function in ion and water balance, kidney collecting duct epith skeletal element - + - + VSAO @@ -40226,7 +40457,7 @@ Aside from their function in ion and water balance, kidney collecting duct epith - + @@ -40265,14 +40496,14 @@ Aside from their function in ion and water balance, kidney collecting duct epith UBERON:0004770 articular system - + - + FMA @@ -40570,7 +40801,7 @@ Aside from their function in ion and water balance, kidney collecting duct epith - + @@ -40591,14 +40822,14 @@ Aside from their function in ion and water balance, kidney collecting duct epith somatopleure http://upload.wikimedia.org/wikipedia/commons/2/28/Gray16.png - + - + EHDAA2 @@ -40664,9 +40895,9 @@ Aside from their function in ion and water balance, kidney collecting duct epith - - - + + + @@ -40686,34 +40917,34 @@ Aside from their function in ion and water balance, kidney collecting duct epith urogenital fold - + - + - + - + EHDAA2 - + Wikipedia - + EHDAA2 @@ -41188,7 +41419,7 @@ Aside from their function in ion and water balance, kidney collecting duct epith - + Missing definition for term UBERON:0005095. Please replace it using linked reference. class added for consistency with GO - consider merging with kidney mesenchyme. uberon @@ -41196,14 +41427,14 @@ Aside from their function in ion and water balance, kidney collecting duct epith UBERON:0005095 kidney rudiment - + - + GO @@ -41239,7 +41470,6 @@ Aside from their function in ion and water balance, kidney collecting duct epith The descending thin limb is a part of the loop of Henle situated just after the proximal straight tubule (S3). It extends to the tip of the loop of Henle[GO]. - UBERON:0005165 EMAPA:35514 FMA:17719 MA:0002625 @@ -41319,7 +41549,7 @@ Aside from their function in ion and water balance, kidney collecting duct epith - + The connecting tubule is a tubular segment of the nephron; it connects the distal convoluted tubule to the collecting duct[GO]. BTO:0004539 @@ -41337,14 +41567,14 @@ Aside from their function in ion and water balance, kidney collecting duct epith renal connecting tubule http://upload.wikimedia.org/wikipedia/commons/0/02/Gray1128.png - + - + Wikipedia @@ -42075,7 +42305,7 @@ Aside from their function in ion and water balance, kidney collecting duct epith - + Mesenchyme that is part of a developing trunk. EFO:0003485 EHDAA2:0002092 @@ -42091,14 +42321,14 @@ Aside from their function in ion and water balance, kidney collecting duct epith trunk mesenchyme - + - + EHDAA2 @@ -42215,7 +42445,7 @@ Aside from their function in ion and water balance, kidney collecting duct epith - + Multi-tissue structure that arises from the heart rudiment and will become the heart tube. EHDAA2:0001512 EHDAA:424 @@ -42233,14 +42463,14 @@ Aside from their function in ion and water balance, kidney collecting duct epith primitive heart tube - + - + ZFA @@ -42268,7 +42498,7 @@ Aside from their function in ion and water balance, kidney collecting duct epith - + @@ -42295,7 +42525,7 @@ Aside from their function in ion and water balance, kidney collecting duct epith gonad primordium - + @@ -42308,7 +42538,7 @@ Aside from their function in ion and water balance, kidney collecting duct epith - + ZFA @@ -42367,14 +42597,14 @@ Aside from their function in ion and water balance, kidney collecting duct epith - + - + A mesoderm that has the potential to develop into a pronephros. AAO:0011090 EFO:0003479 @@ -42392,24 +42622,24 @@ Aside from their function in ion and water balance, kidney collecting duct epith the intermediate mesoderm of the chick embryo acquires its ability to form kidneys through its interactions with the paraxial mesoderm [ISBN:9780878932504 "Developmental Biology", PMID:10720431 "Signals from trunk paraxial mesoderm induce pronephros formation in chick intermediate mesoderm"]. These interactions induce the expression of TFs including Lim1, Pax2 and Pax6 that cause the intermediate mesoderm to form the kidney pronephric mesoderm - + - + - + ZFA - + Bgee:AN @@ -42456,7 +42686,7 @@ Aside from their function in ion and water balance, kidney collecting duct epith - + @@ -42473,14 +42703,14 @@ Aside from their function in ion and water balance, kidney collecting duct epith glomerular tuft - + - + Wikipedia @@ -42620,7 +42850,6 @@ Aside from their function in ion and water balance, kidney collecting duct epith - @@ -42731,7 +42960,7 @@ Aside from their function in ion and water balance, kidney collecting duct epith - + @@ -42759,14 +42988,14 @@ Aside from their function in ion and water balance, kidney collecting duct epith glomerular basement membrane http://upload.wikimedia.org/wikipedia/commons/d/de/PhysiologieGlom%C3%A9rulaire.png - + - + true https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships @@ -42851,7 +43080,7 @@ Aside from their function in ion and water balance, kidney collecting duct epith - + A delimited region of dense mesenchyme within looser mesenchyme. AEO:0000148 EHDAA2_RETIRED:0003148 @@ -42861,7 +43090,7 @@ Aside from their function in ion and water balance, kidney collecting duct epith UBERON:0005856 developing mesenchymal condensation - + @@ -42880,7 +43109,7 @@ Aside from their function in ion and water balance, kidney collecting duct epith - + AEO-modified-relation @@ -42977,7 +43206,7 @@ Aside from their function in ion and water balance, kidney collecting duct epith - + @@ -43016,14 +43245,14 @@ Aside from their function in ion and water balance, kidney collecting duct epith cloacal membrane http://upload.wikimedia.org/wikipedia/commons/d/d2/Gray991.png - + - + Wikipedia @@ -43057,7 +43286,7 @@ Aside from their function in ion and water balance, kidney collecting duct epith - + The notochordal plate is the dorsal part of the notochordal process when the ventral portion breaks down. It is continuous laterally with the endoderm that composes the roof of the primitive foregut and is in contact dorsally with the neural tube. The folding off of the notochordal plate gives rise to the notochord. TODO - check ordering; awaiting confirmation from JB EHDAA2:0001278 @@ -43071,7 +43300,7 @@ Aside from their function in ion and water balance, kidney collecting duct epith notochordal plate - + @@ -43084,7 +43313,7 @@ Aside from their function in ion and water balance, kidney collecting duct epith - + EHDAA2 @@ -43112,7 +43341,7 @@ Aside from their function in ion and water balance, kidney collecting duct epith - + A midline cellular cord formed from the migration of mesenchymal cells from the primitive knot. EHDAA2:0001279 EHDAA:224 @@ -43129,14 +43358,14 @@ Aside from their function in ion and water balance, kidney collecting duct epith The notochordal process grows cranially until it reaches the prechordal plate, the future site of the mouth. In this area the ectoderm is attached directly to the endoderm without intervening mesoderm. This area is known as the oropharyngeal membrane, and it will break down to become the mouth. At the other end of the primitive streak the ectoderm is also fused directly to the endoderm; this is known as the cloacal membrane (proctodeum), or primordial anus. notochordal process - + - + EHDAA2 @@ -43680,7 +43909,7 @@ Aside from their function in ion and water balance, kidney collecting duct epith - + A region of nephron tubule that is part of a cortex of kidney. EMAPA:18976 MA:0002609 @@ -43690,14 +43919,14 @@ Aside from their function in ion and water balance, kidney collecting duct epith UBERON:0006853 renal cortex tubule - + - + MA @@ -43868,7 +44097,6 @@ Aside from their function in ion and water balance, kidney collecting duct epith - @@ -44370,7 +44598,7 @@ Aside from their function in ion and water balance, kidney collecting duct epith - + @@ -44396,7 +44624,7 @@ Aside from their function in ion and water balance, kidney collecting duct epith presumptive paraxial mesoderm - + @@ -44412,7 +44640,7 @@ Aside from their function in ion and water balance, kidney collecting duct epith - + https://github.com/obophenotype/uberon/issues/1277 @@ -44573,7 +44801,7 @@ Aside from their function in ion and water balance, kidney collecting duct epith - + Mesenchyme with little extracellular matrix. AEO:0000146 EHDAA2:0003146 @@ -44581,7 +44809,7 @@ Aside from their function in ion and water balance, kidney collecting duct epith UBERON:0007524 dense mesenchyme tissue - + @@ -44594,7 +44822,7 @@ Aside from their function in ion and water balance, kidney collecting duct epith - + AEO @@ -44808,7 +45036,7 @@ Aside from their function in ion and water balance, kidney collecting duct epith - + Anatomical system that consists of all blood and lymph vessels. consider merging with vasculature @@ -44825,14 +45053,14 @@ Aside from their function in ion and water balance, kidney collecting duct epith vascular system - + - + MA @@ -44884,7 +45112,6 @@ Aside from their function in ion and water balance, kidney collecting duct epith An organism subdivision that encompasses the region containing the pectoral or pelvic girdle. Note that this includes both the skeletal elements and associated tissues (integument, muscle, etc). - UBERON:0007824 girdle girdle region EMAPA:37854 @@ -44970,7 +45197,7 @@ Aside from their function in ion and water balance, kidney collecting duct epith - + @@ -45008,14 +45235,14 @@ Aside from their function in ion and water balance, kidney collecting duct epith pelvic girdle skeleton http://upload.wikimedia.org/wikipedia/commons/f/fe/Gray242.png - + - + PMID:21455939 @@ -45098,7 +45325,7 @@ Aside from their function in ion and water balance, kidney collecting duct epith - + The functional tissue of the kidney, consisting of the nephrons. BTO:0003604 FMA:15574 @@ -45109,7 +45336,7 @@ Aside from their function in ion and water balance, kidney collecting duct epith UBERON:0008987 renal parenchyma - + @@ -45122,7 +45349,7 @@ Aside from their function in ion and water balance, kidney collecting duct epith - + FMA @@ -45192,7 +45419,7 @@ Aside from their function in ion and water balance, kidney collecting duct epith - + @@ -45201,7 +45428,6 @@ Aside from their function in ion and water balance, kidney collecting duct epith Sum total of mesenchyme in the embryo. consider adding new class (EMAPA:16097) for mesenchyme of embryo (some mesenchyme is extraembryonic - e.g. amnion mesoderm) - UBERON:0003313 EHDAA2:0001113 EHDAA:177 EMAPA:16097 @@ -45209,14 +45435,14 @@ Aside from their function in ion and water balance, kidney collecting duct epith UBERON:0009142 entire embryonic mesenchyme - + - + EHDAA2 @@ -45268,6 +45494,7 @@ Aside from their function in ion and water balance, kidney collecting duct epith + A nephric duct is a tube that drains a primitive kidney[GO]. EMAPA:16577 Wikipedia:Wolffian_duct @@ -45335,7 +45562,7 @@ Aside from their function in ion and water balance, kidney collecting duct epith - + EHDAA2:0002094 trunk and cervical paraxial mesenchyme uberon @@ -45343,14 +45570,14 @@ Aside from their function in ion and water balance, kidney collecting duct epith UBERON:0009618 trunk paraxial mesoderm - + - + EHDAA2 @@ -45449,7 +45676,7 @@ Aside from their function in ion and water balance, kidney collecting duct epith - + EFO:0003704 TAO:0005041 ZFA:0005041 @@ -45459,14 +45686,14 @@ Aside from their function in ion and water balance, kidney collecting duct epith anterior lateral plate mesoderm - + - + ZFA @@ -45787,7 +46014,7 @@ Aside from their function in ion and water balance, kidney collecting duct epith - + @@ -45805,14 +46032,14 @@ Aside from their function in ion and water balance, kidney collecting duct epith UBERON:0010227 future cardiac atrium - + - + ZFA @@ -45955,7 +46182,7 @@ Aside from their function in ion and water balance, kidney collecting duct epith - + @@ -45969,7 +46196,7 @@ Aside from their function in ion and water balance, kidney collecting duct epith UBERON:0010377 mesenchyme from somatopleure - + @@ -45982,7 +46209,7 @@ Aside from their function in ion and water balance, kidney collecting duct epith - + EHDAA2 @@ -45998,7 +46225,7 @@ Aside from their function in ion and water balance, kidney collecting duct epith - + A vessel of the microcirculature, lying between the arterioles and venules; includes capillaries (blood and lymphatic), metarterioles and arteriovenous anastomoses. MESH:D055806 TAO:0005251 @@ -46008,14 +46235,14 @@ Aside from their function in ion and water balance, kidney collecting duct epith UBERON:0010523 microcirculatory vessel - + - + ZFA @@ -46048,7 +46275,7 @@ Aside from their function in ion and water balance, kidney collecting duct epith - + @@ -46064,7 +46291,7 @@ Aside from their function in ion and water balance, kidney collecting duct epith UBERON:0010532 primitive nephron - + @@ -46077,7 +46304,7 @@ Aside from their function in ion and water balance, kidney collecting duct epith - + EHDAA2 @@ -46093,7 +46320,7 @@ Aside from their function in ion and water balance, kidney collecting duct epith - + @@ -46104,7 +46331,7 @@ Aside from their function in ion and water balance, kidney collecting duct epith UBERON:0010536 nephron progenitor - + @@ -46117,7 +46344,7 @@ Aside from their function in ion and water balance, kidney collecting duct epith - + cjm @@ -46360,8 +46587,8 @@ Aside from their function in ion and water balance, kidney collecting duct epith - - + + Anatomical cluster consisting of the skeletal elements (i.e. bone elements, cartilage elements, cartilage condensations) that are part of an individual subdivision of the organism. Excludes joints. FMA:23879 SCTID:129140006 @@ -46373,11 +46600,11 @@ Aside from their function in ion and water balance, kidney collecting duct epith subdivision of skeleton - + - + @@ -46390,13 +46617,13 @@ Aside from their function in ion and water balance, kidney collecting duct epith - + UBERONREF:0000003 - + VSAO @@ -46457,7 +46684,7 @@ Aside from their function in ion and water balance, kidney collecting duct epith - + Subdivision of the skeletal system which consists of the postcranial axial skeleton plus associated joints. axial skeletal system FMA:302077 @@ -46467,7 +46694,7 @@ Aside from their function in ion and water balance, kidney collecting duct epith postcranial axial skeletal system http://purl.obolibrary.org/obo/uberon/docs/The-axial-skeleton - + @@ -46480,7 +46707,7 @@ Aside from their function in ion and water balance, kidney collecting duct epith - + cjm @@ -46504,7 +46731,7 @@ Aside from their function in ion and water balance, kidney collecting duct epith - + @@ -46529,14 +46756,14 @@ Aside from their function in ion and water balance, kidney collecting duct epith upper urinary tract - + - + FMA @@ -46742,6 +46969,7 @@ Aside from their function in ion and water balance, kidney collecting duct epith EHDAA2:0004731 Wikipedia:Coelom + ZFA:0001438 enterocoelom haemocoelom schizocoelom @@ -46854,7 +47082,7 @@ Aside from their function in ion and water balance, kidney collecting duct epith - + @@ -46869,14 +47097,14 @@ Aside from their function in ion and water balance, kidney collecting duct epith We presume this is distinct from AAO:0001003, an external integumentary structure - check with amphibian anatomy ontology developers. AO notes: the text def states mesenchymal swelling, EHDAA2 splits into mesenchymal and epithelial parts embryonic cloacal fold - + - + EHDAA2 @@ -46899,20 +47127,20 @@ Aside from their function in ion and water balance, kidney collecting duct epith - + EHDAA2:0004588 uberon UBERON:0012361 internal anal region - + - + EHDAA2 @@ -46922,20 +47150,20 @@ Aside from their function in ion and water balance, kidney collecting duct epith - + EHDAA2:0004589 uberon UBERON:0012469 external anal region - + - + EHDAA2 @@ -46962,7 +47190,7 @@ Aside from their function in ion and water balance, kidney collecting duct epith - + @@ -46982,14 +47210,14 @@ Aside from their function in ion and water balance, kidney collecting duct epith skeleton of pelvic complex - + - + FMA @@ -47041,7 +47269,7 @@ Aside from their function in ion and water balance, kidney collecting duct epith - + The precursor of the urethra. SCTID:361531004 Wikipedia:Urethral_groove @@ -47052,14 +47280,14 @@ Aside from their function in ion and water balance, kidney collecting duct epith UBERON:0013241 embryonic urethral groove - + - + Wikipedia @@ -47560,7 +47788,6 @@ Aside from their function in ion and water balance, kidney collecting duct epith Primordium that develops into the central nervous system. - UBERON:3000469 future CNS presumptive central nervous system uberon @@ -47604,7 +47831,6 @@ Aside from their function in ion and water balance, kidney collecting duct epith Primordium that develops into the nervous system. - UBERON:3000477 AAO:0000477 presumptive nervous system uberon @@ -47630,7 +47856,7 @@ Aside from their function in ion and water balance, kidney collecting duct epith - + @@ -47653,7 +47879,7 @@ Aside from their function in ion and water balance, kidney collecting duct epith UBERON:0016887 entire extraembryonic component - + @@ -47666,7 +47892,7 @@ Aside from their function in ion and water balance, kidney collecting duct epith - + AEO @@ -48077,7 +48303,7 @@ Aside from their function in ion and water balance, kidney collecting duct epith - + The upper tract of the renal system. The renal pelvis is the large cavity in the middle of each kidney. Urine drains from each kidney through a long tube called the ureter, into the bladder, where it is stored until it is passed from the body through the urethra. NCIT:C54419 @@ -48088,14 +48314,14 @@ Aside from their function in ion and water balance, kidney collecting duct epith renal pelvis/ureter - + - + NCIT @@ -48113,7 +48339,6 @@ Aside from their function in ion and water balance, kidney collecting duct epith Any of the smallest blood vessels where blood circulates within organ tissues. Microvessels include terminal arterioles, metarterioles, capillaries, and venules (but exclude lymphatic capillaries). Arterioles carry oxygenated blood to the capillaries, and blood flows out of the capillaries through venules into veins. - http://orcid.org/0000-0002-2825-0621 microvasculature microvessel uberon @@ -48154,7 +48379,6 @@ Aside from their function in ion and water balance, kidney collecting duct epith An anatomical system that eliminates waste products that arise as a result of metabolic activity. - http://orcid.org/0000-0002-6095-8718 2022-05-25T18:21:29Z uberon UBERON:8450002 diff --git a/subsets/kidney_upper_slim.tsv b/subsets/kidney_upper_slim.tsv index a90c4c556..79926a968 100644 --- a/subsets/kidney_upper_slim.tsv +++ b/subsets/kidney_upper_slim.tsv @@ -1,370 +1,370 @@ ?x ?label -_:B869127b4X2D9725X2D463eX2Dbe79X2D2d475f23f3cfgenid1004 -_:B869127b4X2D9725X2D463eX2Dbe79X2D2d475f23f3cfgenid1010 -_:B869127b4X2D9725X2D463eX2Dbe79X2D2d475f23f3cfgenid1016 -_:B869127b4X2D9725X2D463eX2Dbe79X2D2d475f23f3cfgenid1022 -_:B869127b4X2D9725X2D463eX2Dbe79X2D2d475f23f3cfgenid1029 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"proerythroblast" @@ -654,19 +655,17 @@ _:B869127b4X2D9725X2D463eX2Dbe79X2D2d475f23f3cfgenid995 "macromolecule metabolic process" "organelle" "membrane-bounded organelle" - "non-membrane-bounded organelle" + "membraneless organelle" "intracellular organelle" "extracellular organelle" "intracellular membrane-bounded organelle" - "intracellular non-membrane-bounded organelle" + "intracellular membraneless organelle" "organelle lumen" "protein-containing complex organization" "regulation of system process" "cellular component biogenesis" "translation initiation ternary complex" - "cellular metabolic process" "primary metabolic process" - "cellular biosynthetic process" "establishment of protein localization" "synapse" "secretion" @@ -743,7 +742,7 @@ _:B869127b4X2D9725X2D463eX2Dbe79X2D2d475f23f3cfgenid995 "supramolecular polymer" "synaptic signaling" "trans-synaptic signaling" - "cellular anatomical entity" + "cellular anatomical structure" "plasma membrane bounded cell projection" "plasma membrane bounded cell projection assembly" "plasma membrane bounded cell projection organization" @@ -869,7 +868,7 @@ _:B869127b4X2D9725X2D463eX2Dbe79X2D2d475f23f3cfgenid995 "Mus musculus protein" "eukaryotic protein" "angiotensinogenase" - "protein-containing material entity" + "protein-containing molecular entity" "processual entity" "tube" "appendage" From db33925b64ca72d8cb796855417f69231f1ed2b2 Mon Sep 17 00:00:00 2001 From: CEastwood <116108977+Caroline-99@users.noreply.github.com> Date: Wed, 8 Jan 2025 13:06:18 +0000 Subject: [PATCH 13/18] Fixes #2806 Femoral osteoblast (#2879) - Fixed typo in the label - Added references for the cell type - removed a broken link in the comment section --- src/ontology/cl-edit.owl | 7 +++---- 1 file changed, 3 insertions(+), 4 deletions(-) diff --git a/src/ontology/cl-edit.owl b/src/ontology/cl-edit.owl index 6c65df477..ecdd448ad 100644 --- a/src/ontology/cl-edit.owl +++ b/src/ontology/cl-edit.owl @@ -28850,14 +28850,13 @@ AnnotationAssertion(rdfs:label obo:CL_2000056 "Meynert cell") SubClassOf(obo:CL_2000056 obo:CL_0000598) SubClassOf(obo:CL_2000056 ObjectSomeValuesFrom(obo:RO_0002100 obo:UBERON_0001384)) -# Class: obo:CL_2000057 (femural osteoblast) +# Class: obo:CL_2000057 (femoral osteoblast) -AnnotationAssertion(Annotation(oboInOwl:hasDbXref "GOC:TermGenie") obo:IAO_0000115 obo:CL_2000057 "Any osteoblast that is part of a femur.") +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "GOC:TermGenie") Annotation(oboInOwl:hasDbXref "PMID:34565180") Annotation(oboInOwl:hasDbXref "PMID:34569806") obo:IAO_0000115 obo:CL_2000057 "Any osteoblast that is part of a femur.") AnnotationAssertion(terms:contributor obo:CL_2000057 ) AnnotationAssertion(oboInOwl:creation_date obo:CL_2000057 "2014-10-06T19:29:45Z"^^xsd:dateTime) AnnotationAssertion(oboInOwl:id obo:CL_2000057 "CL:2000057") -AnnotationAssertion(rdfs:comment obo:CL_2000057 "http://www.sciencellonline.com/site/productInformation.php?keyword=4610") -AnnotationAssertion(rdfs:label obo:CL_2000057 "femural osteoblast") +AnnotationAssertion(rdfs:label obo:CL_2000057 "femoral osteoblast") EquivalentClasses(obo:CL_2000057 ObjectIntersectionOf(obo:CL_0000062 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0000981))) # Class: obo:CL_2000058 (calvarial osteoblast) From c6a8a74bbde5e81ba98c3dc6a907340afbc57255 Mon Sep 17 00:00:00 2001 From: CEastwood <116108977+Caroline-99@users.noreply.github.com> Date: Wed, 8 Jan 2025 14:01:57 +0000 Subject: [PATCH 14/18] Fixes #2807 text and logical def- neural progenitor cell (#2881) - Fixed the textual def and added references -Added developmental logical axiom --- src/ontology/cl-edit.owl | 11 ++++++----- 1 file changed, 6 insertions(+), 5 deletions(-) diff --git a/src/ontology/cl-edit.owl b/src/ontology/cl-edit.owl index ecdd448ad..7699d525f 100644 --- a/src/ontology/cl-edit.owl +++ b/src/ontology/cl-edit.owl @@ -3386,7 +3386,7 @@ AnnotationAssertion(rdfs:label obo:IAO_0000115 "definition") AnnotationAssertion(rdfs:label obo:IAO_0000424 "expand expression to") -# Annotation Property: obo:IAO_0000700 (has ontology root term) +# Annotation Property: obo:IAO_0000700 (preferred_root) AnnotationAssertion(rdfs:label obo:IAO_0000700 "preferred_root") @@ -3472,15 +3472,15 @@ AnnotationAssertion(rdfs:label oboInOwl:consider "consider") AnnotationAssertion(rdfs:label oboInOwl:hasBroadSynonym "has_broad_synonym") -# Annotation Property: oboInOwl:hasDbXref (has cross-reference) +# Annotation Property: oboInOwl:hasDbXref (database_cross_reference) AnnotationAssertion(rdfs:label oboInOwl:hasDbXref "database_cross_reference") -# Annotation Property: oboInOwl:hasExactSynonym (has exact synonym) +# Annotation Property: oboInOwl:hasExactSynonym (has_exact_synonym) AnnotationAssertion(rdfs:label oboInOwl:hasExactSynonym "has_exact_synonym") -# Annotation Property: oboInOwl:hasNarrowSynonym (has narrow synonym) +# Annotation Property: oboInOwl:hasNarrowSynonym (has_narrow_synonym) AnnotationAssertion(rdfs:label oboInOwl:hasNarrowSynonym "has_narrow_synonym") @@ -24395,10 +24395,11 @@ SubClassOf(obo:CL_0011019 obo:CL_0000077) # Class: obo:CL_0011020 (neural progenitor cell) -AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:30574073") obo:IAO_0000115 obo:CL_0011020 "An undifferentiated cell that originates from a neural stem cell and has the capacity to generate multiple types of lineage-restricted progenitors but not to self-renew.") +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:30574073") Annotation(oboInOwl:hasDbXref "PMID:23064725") Annotation(oboInOwl:hasDbXref "PMID:37508487") obo:IAO_0000115 obo:CL_0011020 "An undifferentiated cell derived from a neural stem cell, with a limited capacity to self-renew (Dibajnia and Morshead, 2013) and the ability to generate multiple types of lineage-restricted progenitors, contributing to the formation of neurons, astrocytes, and oligodendrocytes.") AnnotationAssertion(terms:contributor obo:CL_0011020 ) AnnotationAssertion(rdfs:label obo:CL_0011020 "neural progenitor cell") SubClassOf(obo:CL_0011020 obo:CL_0000055) +SubClassOf(obo:CL_0011020 ObjectSomeValuesFrom(obo:RO_0002202 obo:CL_0000047)) # Class: obo:CL_0011021 (fibroblast of upper back skin) From 5a8888a4ed458c8a2d7dc78ea25239cda9868056 Mon Sep 17 00:00:00 2001 From: Aleix Puig <94959119+aleixpuigb@users.noreply.github.com> Date: Wed, 8 Jan 2025 14:50:54 +0000 Subject: [PATCH 15/18] Add step to clean temporary files (#2883) --- docs/cl-release.md | 1 + 1 file changed, 1 insertion(+) diff --git a/docs/cl-release.md b/docs/cl-release.md index af966ac3f..7209cfb2c 100644 --- a/docs/cl-release.md +++ b/docs/cl-release.md @@ -44,6 +44,7 @@ The release is done in two parts: 1. Ensure you are on the master branch and have locally the latest changes from master (`git pull`) 1. Ensure you have the latest ODK installed by running `docker pull obolibrary/odkfull` 1. Navigate to the cell-ontology/src/ontology directory (`cd src/ontology`) +1. Delete all temporary files (e.g., outdated plugins) by running `sh run.sh make clean` ### Refresh imports and components From 304ea5942529c4a716fc321d2a9649bde21a8d2a Mon Sep 17 00:00:00 2001 From: Aleix Puig <94959119+aleixpuigb@users.noreply.github.com> Date: Thu, 9 Jan 2025 10:08:49 +0000 Subject: [PATCH 16/18] Adresses #2791 NTR age-associated cell (#2884) Fixes #2791 NTR age-associated cell Co-authored-by: CEastwood <116108977+Caroline-99@users.noreply.github.com> --- src/ontology/cl-edit.owl | 13 ++++++++++++- 1 file changed, 12 insertions(+), 1 deletion(-) diff --git a/src/ontology/cl-edit.owl b/src/ontology/cl-edit.owl index 7699d525f..44b685703 100644 --- a/src/ontology/cl-edit.owl +++ b/src/ontology/cl-edit.owl @@ -3048,6 +3048,7 @@ Declaration(Class(obo:CL_4033090)) Declaration(Class(obo:CL_4033091)) Declaration(Class(obo:CL_4033092)) Declaration(Class(obo:CL_4033093)) +Declaration(Class(obo:CL_4033094)) Declaration(Class(obo:CL_4040000)) Declaration(Class(obo:CL_4040001)) Declaration(Class(obo:CL_4040002)) @@ -24395,7 +24396,7 @@ SubClassOf(obo:CL_0011019 obo:CL_0000077) # Class: obo:CL_0011020 (neural progenitor cell) -AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:30574073") Annotation(oboInOwl:hasDbXref "PMID:23064725") Annotation(oboInOwl:hasDbXref "PMID:37508487") obo:IAO_0000115 obo:CL_0011020 "An undifferentiated cell derived from a neural stem cell, with a limited capacity to self-renew (Dibajnia and Morshead, 2013) and the ability to generate multiple types of lineage-restricted progenitors, contributing to the formation of neurons, astrocytes, and oligodendrocytes.") +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:23064725") Annotation(oboInOwl:hasDbXref "PMID:30574073") Annotation(oboInOwl:hasDbXref "PMID:37508487") obo:IAO_0000115 obo:CL_0011020 "An undifferentiated cell derived from a neural stem cell, with a limited capacity to self-renew (Dibajnia and Morshead, 2013) and the ability to generate multiple types of lineage-restricted progenitors, contributing to the formation of neurons, astrocytes, and oligodendrocytes.") AnnotationAssertion(terms:contributor obo:CL_0011020 ) AnnotationAssertion(rdfs:label obo:CL_0011020 "neural progenitor cell") SubClassOf(obo:CL_0011020 obo:CL_0000055) @@ -32413,6 +32414,16 @@ SubClassOf(obo:CL_4033093 obo:CL_0000036) SubClassOf(obo:CL_4033093 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0000482)) SubClassOf(obo:CL_4033093 ObjectSomeValuesFrom(obo:RO_0002203 obo:CL_0000575)) +# Class: obo:CL_4033094 (age-associated B cell) + +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:30873171") Annotation(oboInOwl:hasDbXref "PMID:31986068") Annotation(oboInOwl:hasDbXref "PMID:35298565") Annotation(oboInOwl:hasDbXref "PMID:35798993") obo:IAO_0000115 obo:CL_4033094 "A transcriptionally distinct memory B cell whose presence increases with age, during infections, and in autoimmune diseases. In humans and mice, this cell type can be identified by the expression of T-bet, CD11c, CD11b, and the lack of CD21. An age-associated B cell responds to TLR stimuli, may produce autoantibodies, and participates in antiviral responses and pathogen clearance.") +AnnotationAssertion(terms:contributor obo:CL_4033094 ) +AnnotationAssertion(terms:contributor obo:CL_4033094 ) +AnnotationAssertion(terms:date obo:CL_4033094 "2025-01-08T14:44:57Z"^^xsd:dateTime) +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:35798993") Annotation(oboInOwl:hasSynonymType obo:OMO_0003000) oboInOwl:hasRelatedSynonym obo:CL_4033094 "ABC") +AnnotationAssertion(rdfs:label obo:CL_4033094 "age-associated B cell") +SubClassOf(obo:CL_4033094 obo:CL_0000787) + # Class: obo:CL_4040000 (glial restricted tripotential precursor cell) AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:10719353") obo:IAO_0000115 obo:CL_4040000 "A glial precursor cell that generates oligodendrocytes and type-1 and type-2 astrocytes. It has been shown in some mammals that this cell type may express A2B5, nestin, FGFR-1, FGFR-2, FGFR-3, PLP, and DM-20 antigens. Unlike oligodendrocyte precursor cell, it does not initially express PDGFR-alpha and can differentiate into both type-1 and type-2 astrocytes.") From 564c2377b09d5735f2938884943a8df0c512540a Mon Sep 17 00:00:00 2001 From: CEastwood <116108977+Caroline-99@users.noreply.github.com> Date: Thu, 9 Jan 2025 17:06:00 +0000 Subject: [PATCH 17/18] Fixes #2816 -surface ectodermal cell (#2885) -Added textual defs with references - Improved logical def --- src/ontology/cl-edit.owl | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/src/ontology/cl-edit.owl b/src/ontology/cl-edit.owl index 44b685703..4b5f159fc 100644 --- a/src/ontology/cl-edit.owl +++ b/src/ontology/cl-edit.owl @@ -4701,11 +4701,12 @@ SubClassOf(obo:CL_0000113 obo:CL_0000842) # Class: obo:CL_0000114 (surface ectodermal cell) +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:7892198") Annotation(oboInOwl:hasDbXref "Wikipedia:Surface_ectoderm") Annotation(oboInOwl:hasDbXref "doi:/10.1101/2024.07.02.601324") obo:IAO_0000115 obo:CL_0000114 "An ectodermal cell that is part of the external ectoderm, forming the outermost layer of the developing embryo. It is characterized by its polarized nature, with distinct apical and basal surfaces (Ferrante Jr., Reinke, & Stanley, 1995). Surface ectodermal cell gives rise to the epidermis, hair follicles, nails, sensory organs, and specialized structures like the apical ectodermal ridge crucial for limb development (Skoufa et al., 2024).") AnnotationAssertion(oboInOwl:hasDbXref obo:CL_0000114 "FMA:72552") AnnotationAssertion(oboInOwl:hasExactSynonym obo:CL_0000114 "cell of surface ectoderm") -AnnotationAssertion(oboInOwl:hasExactSynonym obo:CL_0000114 "surface ectoderm cell") +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "doi:/10.1101/2024.07.02.601324") oboInOwl:hasExactSynonym obo:CL_0000114 "surface ectoderm cell") AnnotationAssertion(rdfs:label obo:CL_0000114 "surface ectodermal cell") -SubClassOf(obo:CL_0000114 obo:CL_0000221) +EquivalentClasses(obo:CL_0000114 ObjectIntersectionOf(obo:CL_0000221 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0000076))) # Class: obo:CL_0000115 (endothelial cell) From 58677e73ac4871e99c5fc7e6139bc154b8e97a5c Mon Sep 17 00:00:00 2001 From: CEastwood <116108977+Caroline-99@users.noreply.github.com> Date: Mon, 13 Jan 2025 11:34:07 +0000 Subject: [PATCH 18/18] Fixes #2875 NTR-granzyme H-associated CD8 T cell (#2895) * Fixes #2875 NTR-granzyme H-associated CD8 T cell Added a new term * Update cl-edit.owl --- src/ontology/cl-edit.owl | 14 ++++++++++++++ src/ontology/imports/pr_terms.txt | 3 ++- 2 files changed, 16 insertions(+), 1 deletion(-) diff --git a/src/ontology/cl-edit.owl b/src/ontology/cl-edit.owl index 4b5f159fc..b60fcc0af 100644 --- a/src/ontology/cl-edit.owl +++ b/src/ontology/cl-edit.owl @@ -3145,6 +3145,7 @@ Declaration(Class(obo:CL_4052028)) Declaration(Class(obo:CL_4052029)) Declaration(Class(obo:CL_4052030)) Declaration(Class(obo:CL_4052031)) +Declaration(Class(obo:CL_4052032)) Declaration(Class(obo:CL_4052048)) Declaration(Class(obo:CL_4052049)) Declaration(Class(obo:CP_0000000)) @@ -3206,6 +3207,7 @@ Declaration(Class(obo:PR_000002030)) Declaration(Class(obo:PR_000002123)) Declaration(Class(obo:PR_000003264)) Declaration(Class(obo:PR_000003472)) +Declaration(Class(obo:PR_000003490)) Declaration(Class(obo:PR_000004691)) Declaration(Class(obo:PR_000004919)) Declaration(Class(obo:PR_000005444)) @@ -33490,6 +33492,18 @@ AnnotationAssertion(rdfs:label obo:CL_4052031 "respiratory airway secretory cell SubClassOf(obo:CL_4052031 obo:CL_1100001) SubClassOf(obo:CL_4052031 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0002051)) +# Class: obo:CL_4052032 (granzyme H-associated CD8 T cell) + +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:35389781") obo:IAO_0000115 obo:CL_4052032 "A CD8 T cell characterized by high expression of Granzyme H (GZMH). This cell exhibits a restricted TCR repertoire and elevated expression of cytotoxic, exhaustion, and type I interferon-stimulated gene signatures compared to controls.") +AnnotationAssertion(terms:contributor obo:CL_4052032 ) +AnnotationAssertion(terms:contributor obo:CL_4052032 ) +AnnotationAssertion(terms:date obo:CL_4052032 "2025-01-10T10:14:31Z"^^xsd:dateTime) +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:35389781") oboInOwl:hasExactSynonym obo:CL_4052032 "granzyme H+ CD8 T cell") +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:35389781") Annotation(oboInOwl:hasSynonymType obo:OMO_0003000) oboInOwl:hasRelatedSynonym obo:CL_4052032 "GZMH+ CD8+ T cell") +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:35389781") rdfs:comment obo:CL_4052032 "This cell type is significantly expanded in systemic lupus erythematosus (SLE) patients. Unlike other CD8 T cell populations, GZMH+ CD8 T cells can comprise up to 50% of all lymphocytes in some SLE patients.") +AnnotationAssertion(rdfs:label obo:CL_4052032 "granzyme H-associated CD8 T cell") +EquivalentClasses(obo:CL_4052032 ObjectIntersectionOf(obo:CL_0000909 ObjectSomeValuesFrom(obo:RO_0002292 obo:PR_000003490))) + # Class: obo:CL_4052048 (intercalated cell of salivary gland) AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:30855909") Annotation(oboInOwl:hasDbXref "PMID:35799078") Annotation(oboInOwl:hasDbXref "PMID:36726292") Annotation(oboInOwl:hasDbXref "PMID:37724716") obo:IAO_0000115 obo:CL_4052048 "A cuboidal epithelial cell that is part of the intercalated duct of salivary gland. This cell expresses proteins commonly associated with acinar cells and displays calcium signaling characteristics similar to secretory cells, indicating an active role in the secretory process rather than ion reabsorption.") diff --git a/src/ontology/imports/pr_terms.txt b/src/ontology/imports/pr_terms.txt index 697340509..4c403c315 100644 --- a/src/ontology/imports/pr_terms.txt +++ b/src/ontology/imports/pr_terms.txt @@ -50,4 +50,5 @@ PR:000016626 PR:000003472 PR:000012318 PR:000064867 -PR:000001440 \ No newline at end of file +PR:000001440 +PR:000003490 \ No newline at end of file